Citrus Sinensis ID: 007792

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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-------59
Protein Sequence
MSVLIVTSLGDIVVDLFVDKCPLTTKNFLKLCKIKYYNGCLFHTVQKDFTAQTGDPTGTGTGGDSVYKFLYGEQARFFGDEIRVDLKHAKTGTVAMASAGENLNASQFYMTLRDNLDYLDEKHTIFGEVAEGLETLSRINESFVDEKNRPYKNIRIKHTYILEDPFDDPAQLAELIPDASPEGKPKDEVVDEVRLEDDWVPLDEQLSAAELEQVIRSKDARSSAVVLESIGDIPDADIKPPENVLFVCKLNPVTEDEDLHTIFSRFGTVVSAEIIRDFKTGDSLNYAFIEFENRQACERAYSKMDNALIDDRRIHVDFSQSVSKLWNQFRRRDHQTGKGKGCFKCGGLDHIAKDCTGQQPAKYILRDDNRQHGGYSDSRYEMVFDGETPEKSRREKKHRGHDPDDRVERNMNRLSSDLRHRDQERRELSYRQRESDRTRENREDRRNRDGQESRNVQKQEVRDDDGRYESDHPKSSDTDRYRDWRGGGDYRKRSADSDSRAERREDGDYRKRNSDNGSHRDRRDDQDYRKKSADGDIHGDRRYDRDNRKNSGNSELRDAKKEPSYKRGRRDDDSYKRWPEDRGNRRRGE
Secondary Structure (PSIPRED)
cEEEEEEccccEEEEEEccccHHHHHHHHHHHHHccccccEEEEEEcccEEEccccccccccccccccccccccccccccccccccccccccEEEEEccccccccccEEEEEccccccccccccEEEEccccHHHHHHHHcccccccccccccccccEEEEcccccccHHHHHHccccccccccccccccccccccccccccHHHHHHHHHHHHHHHHHHccccEEEcccccccccccccccccccEEcccccccHHHHHHHccccccEEEEEEEEccccccccccHHHHcccHHHHHHHHHHHccccccccEEEEEcccHHHHHHHHHHcccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccHHHHHccccccccccHHccccccccccccccHHHHHccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccHHHHcccccccccccccccccccccccccccccccccccccccccccccccccccccccccccc
Secondary Structure Prediction (SSPRO)
cEEEEEEccEEEEEEEcccccHHHHHHHHHHHHccccccEEccEEEcccEEEEccccccccccccHHHHccccccccccHccccccccccccEEEEcccccccEcccEEEEcccccHcccccEEEEEEEEcHHHHHHHHHHHHEcccccccccEEEEEEEEEccccccccccccccccccccccccHHHHcccccccccccccccccHHHHHHHHHHHHHHHHHHHHHHHcccccccccccccEEEEEEccccccHHHHHHHHHccccEEEEEEEEEcccccccEEEEEEEccHHHHHHHHHHcccEEEcccEEEEEcHHHHHHHHHHHccccccccccccccccccccccccccccccccccEcccccccccccccccccEEEcccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccHHcccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccHcccccccccccccccccccccccc
Coil and Loop (DISEMBL)
MSVLIVTSLGDIVVDLFvdkcplttkNFLKLCKIKyyngclfhtvqkdftaqtgdptgtgtggdsVYKFLYGeqarffgdeIRVDLKHAKTGTVAMASAGENLNASQFYMTLRDNLDYLDEKHTIFGEVAEGLETLSRINESfvdeknrpyknirikhtyiledpfddpaqlaelipdaspegkpkdevvdevrleddwvpldEQLSAAELEQVIRSKDARSSAVVLesigdipdadikppenvlfvcklnpvtededlhTIFSRFGTVVSAEIIRdfktgdslnYAFIEFENRQACERAYSKMDNaliddrrihVDFSQSVSKLWNQFRrrdhqtgkgkgcfkcggldhiakdctgqqpakyilrddnrqhggysdsryemvfdgetpeksrrekkhrghdpddrveRNMNRLSSDLRHRDQERRELSYrqresdrtrenredrrnrdgqesrnvqkqevrdddgryesdhpkssdtdryrdwrgggdyrkrsadsdsraerredgdyrkrnsdngshrdrrddqdyrkksadgdihgdrrydrdnrknsgnselrdakkepsykrgrrdddsykrwpedrgnrrrge
Flexible Loop (DISEMBL)
MSVLIVTslgdivvdLFVDKCPLTTKNFLKLCKIKYYNGCLFHTVQKDFTAQTGDPTGTGTGGDSVYKFLYGEQARFFGDEIRVDLKHAKTGTVAMASAGENLNASQFYMTLRDNLDYLDEKHTIFGEVAEGLETLSRINEsfvdeknrpyknIRIKHTYILEDPFDDPAQLAElipdaspegkpkDEVVDEVRLEDDWVPLDEQLSAAELEQvirskdarssaVVLESIgdipdadikppENVLFVCKLNPVTEDEDLHTIFSRFGTVVSAEIIRDFKTGDSLNYAFIEFENRQACERAYSKMDNALIDDRRIHVDFSQSVSKLWNQFRRRDHQTGKGKGCFKCGGLDHIAKDCTgqqpakyilrddnrqhggysdsryemVFDGetpeksrrekkhrghdpddrvernmnrlssdlrhrdqerrelsyrqresdrtrenredrrnrdgqesrnvqkqevrdddgryesdhpkssdtdryrdwrgggdyrkrsadsdsraerredgdyrkrnsdngshrdrrddqdyrkksadgdihgdrrydrdnrknsgnselrdakkepsykrgrrdddsykrwpedrgnrrrge
Low Complexity Region (SEG)
MSVLIVTSLGDIVVDLFVDKCPLTTKNFLKLCKIKYYNGCLFHTVQKDFtaqtgdptgtgtggDSVYKFLYGEQARFFGDEIRVDLKHAKTGTVAMASAGENLNASQFYMTLRDNLDYLDEKHTIFGEVAEGLETLSRINESFVDEKNRPYKNIRIKHTYILEDPFDDPAQLAELIPDASPEGKPKdevvdevrleddwvPLDEQLSAAELEQVIRSKDARSSAVVLESIGDIPDADIKPPENVLFVCKLNPVTEDEDLHTIFSRFGTVVSAEIIRDFKTGDSLNYAFIEFENRQACERAYSKMDNALIDDRRIHVDFSQSVSKLWNQFRRRDHQTgkgkgcfkcggLDHIAKDCTGQQPAKYILRDDNRQHGGYSDSRYEMVFDGETPEKSRREKKHRGHDPDDRVERNMNRLSSDLRHRDQERRELSYRQresdrtrenredrrnrdGQESRNVQKQEVRDDDGRYESDHPKSSDTdryrdwrgggdyrkrsadsdsraerredGDYRKRNSDNGSHrdrrddqdyrKKSADGDIHGDRRYDRDNRKNSGNSELRDAKKEPSYKRGRRDDDSYKRWPEDRGNRRRGE
Disordered region (IsUnstruct)
**VLIVTSLGDIVVDLFVDKCPLTTKNFLKLCKIKYYNGCLFHTVQKDFTAQTGDPTGTGTGGDSVYKFLYGEQARFFGDEIRVDLKHAKTGTVAMASAGENLNASQFYMTLRDNLDYLDEKHTIFGEVAEGLETLSRINESFVDEKNRPYKNIRIKHTYILEDPFD*****************************DDWVPL*********************AVVLESIGDIPDADIKPPENVLFVCKLNPVTEDEDLHTIFSRFGTVVSAEIIRDFKTGDSLNYAFIEFENRQACERAYSKMDNALIDDRRIHVDFSQSVSKLWNQFRRRDHQTGKGKGCFKCGGLDHIAKDCTGQQPAKYILR*******************************************************************************************************************************************************************************************************************************
Disordered Region (DISOPRED)
MSVLIVTSLGDIVVDLFVDKCPLTTKNFLKLCKIKYYNGCLFHTVQKDFTAQTGDP****TGGDSVYKFLYGEQARFFGDEIRVDLKHAKTGTVAMASAGENLNASQFYMTLRDNLDYLDEKHTIFGEVAEGLETLSRINESFVDEKNRPYKNIRIKHTYILEDPFDDP**************************************************************************VLFVCKLNPVTEDEDLHTIFSRFGTVVSAEIIRDFKTGDSLNYAFIEFENRQACERAYSKMDNALIDDRRIHVDFSQSVS**************************************************************************************************************************************************************************************************************************************************************************
Disordered Region (DISEMBL)
MSVLIVTSLGDIVVDLFVDKCPLTTKNFLKLCKIKYYNGCLFHTVQKDFTAQTGDPTGTGTGGDSVYKFLYGEQARFFGDEIRVDLKHAKTGTVAMASAGENLNASQFYMTLRDNLDYLDEKHTIFGEVAEGLETLSRINESFVDEKNRPYKNIRIKHTYILEDPFDDPAQLAELIPDASPEGKPKDEVVDEVRLEDDWVPLDEQLSAAELEQVIRSKDARSSAVVLESIGDIPDADIKPPENVLFVCKLNPVTEDEDLHTIFSRFGTVVSAEIIRDFKTGDSLNYAFIEFENRQACERAYSKMDNALIDDRRIHVDFSQSVSKLWNQFRRRDHQTGKGKGCFKCGGLDHIAKDCTGQQPAKYILRDDNRQHGGYSDSRYEMVFDG******************DRVERNMNRLSSDLRHR***********************************************************YRDWRGGG********************************************ADGDIHGDRRYDRDNR*************************SYKRW***********
Disordered Region (DISPRO)
MSVLIVTSLGDIVVDLFVDKCPLTTKNFLKLCKIKYYNGCLFHTVQKDFTAQTGDPTGTGTGGDSVYKFLYGEQARFFGDEIRVDLKHAKTGTVAMASAGENLNASQFYMTLRDNLDYLDEKHTIFGEVAEGLETLSRINESFVDEKNRPYKNIRIKHTYILEDPFDDPAQLAELIP*****GK********************QLSAAELEQVIRSKDARSSAVVLESIGDIPDADIKPPENVLFVCKLNPVTEDEDLHTIFSRFGTVVSAEIIRDFKTGDSLNYAFIEFENRQACERAYSKMDNALIDDRRIHVDFSQSVSKLWNQFRR******************************************************************************************************************************************************************************************************************************************************************
Transmembrane Helix (TMHMM)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooHHHHHHHHHHHHHHHHHHHHiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
Transmembrane Helix (MEMSAT)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooohhhhhhhhhhhhhhhhhhhiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
TM Helix, Signal Peptide (MEMSAT_SVM)
iiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (Phobius)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
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Signal Peptide (SignalP NN Mode)
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Coiled Coils (COILS)
MSVLIVTSLGDIVVDLFVDKCPLTTKNFLKLCKIKYYNGCLFHTVQKDFTAQTGDPTGTGTGGDSVYKFLYGEQARFFGDEIRVDLKHAKTGTVAMASAGENLNASQFYMTLRDNLDYLDEKHTIFGEVAEGLETLSRINESFVDEKNRPYKNIRIKHTYILEDPFDDPAQLAELIPDASPEGKPKDEVVDEVRLEDDWVPLDEQLSAAELEQVIRSKDARSSAVVLESIGDIPDADIKPPENVLFVCKLNPVTEDEDLHTIFSRFGTVVSAEIIRDFKTGDSLNYAFIEFENRQACERAYSKMDNALIDDRRIHVDFSQSVSKLWNQFRRRDHQTGKGKGCFKCGGLDHIAKDCTGQQPAKYILRDDNRQHGGYSDSRYEMVFDGETPEKSRREKKHRGHDPDDRVERNMNRLSSDLRHRDQERRELSYRQRESDRTRENREDRRNRDGQESRNVQKQEVRDDDGRYESDHPKSSDTDRYRDWRGGGDYRKRSADSDSRAERREDGDYRKRNSDNGSHRDRRDDQDYRKKSADGDIHGDRRYDRDNRKNSGNSELRDAKKEPSYKRGRRDDDSYKRWPEDRGNRRRGE
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	589	2.2.26 [Sep-21-2011]
P0C1I6	446	Peptidyl-prolyl cis-trans	N/A	no	0.614	0.811	0.538	1e-107
Q4WAQ9	459	Peptidyl-prolyl cis-trans	yes	no	0.623	0.799	0.503	1e-101
Q2U256	461	Peptidyl-prolyl cis-trans	yes	no	0.731	0.934	0.458	1e-100
Q8WUA2	492	Peptidyl-prolyl cis-trans	yes	no	0.533	0.638	0.565	1e-100
Q9CXG3	492	Peptidyl-prolyl cis-trans	yes	no	0.533	0.638	0.565	1e-99
Q5ARI5	461	Peptidyl-prolyl cis-trans	yes	no	0.551	0.704	0.535	8e-95
P0CP88	504	Peptidyl-prolyl cis-trans	yes	no	0.543	0.634	0.540	7e-94
P0CP89	504	Peptidyl-prolyl cis-trans	N/A	no	0.543	0.634	0.540	7e-94
Q4IE79	485	Peptidyl-prolyl cis-trans	yes	no	0.589	0.715	0.508	3e-90
Q9UUE4	432	Peptidyl-prolyl cis-trans	yes	no	0.533	0.726	0.522	1e-89

>sp|P0C1I6|PPIL4_RHIO9 Peptidyl-prolyl cis-trans isomerase-like 4 OS=Rhizopus delemar (strain RA 99-880 / ATCC MYA-4621 / FGSC 9543 / NRRL 43880) GN=cyp13 PE=3 SV=1

 Score =  390 bits (1001), Expect = e-107,   Method: Compositional matrix adjust.
 Identities = 211/392 (53%), Positives = 272/392 (69%), Gaps = 30/392 (7%)

Query: 1   MSVLIVTSLGDIVVDLFVDKCPLTTKNFLKLCKIKYYNGCLFHTVQKDFTAQTGDPTGTG 60
           MSVLI TSLGDIV+DL+ ++CP TT NFLKLCKIKYYN   F  VQKDF AQTGDPTG G
Sbjct: 1   MSVLIETSLGDIVIDLYTEECPKTTLNFLKLCKIKYYNFAPFFNVQKDFMAQTGDPTGKG 60

Query: 61  TGGDSVYKFLYGEQARFFGDEIRVDLKHAKTGTVAMASAGE------NLNASQFYMTLRD 114
             G SVY  L G  +R+F  EI   LKH + G V+MA A +       ++ SQF++TL +
Sbjct: 61  DQGQSVYGILGG--SRYFPAEIHPTLKHVRRGMVSMAVAADASIETGGVSGSQFFITLGE 118

Query: 115 NLDYLDEKHTIFGEVAEGLETLSRINESFVDEKNRPYKNIRIKHTYILEDPFDDPAQLAE 174
           NLDYLD K+T+FGE+AEG + L +INE++ DE+ RP+++IRIKHT +L+DPF DP  L  
Sbjct: 119 NLDYLDGKYTLFGEIAEGFDVLDKINEAYCDEQGRPFRDIRIKHTVVLDDPFPDPDGL-- 176

Query: 175 LIPDASPEGKPKDEVVDEVRLEDDWVPLDEQLSAAELEQVIRSKDARSSAVVLESIGDIP 234
           +IPD SP   P  E ++ +R+ +D   L+E     ELE+ +R+++A++ A+ LE IGD+P
Sbjct: 177 VIPDESP--LPTKEQLESMRIGEDE-DLEEMGDPEELEKRVRAREAKAHALTLEMIGDLP 233

Query: 235 DADIKPPENVLFVCKLNPVTEDEDLHTIFSRFGTVVSAEIIRDFKTGDSLNYAFIEFENR 294
            A++KPPENVLFVCKLNPVT DEDL  IFSRFG + S EIIRD +TGDSL+YAF+EFEN+
Sbjct: 234 FAEVKPPENVLFVCKLNPVTRDEDLEMIFSRFGLIHSCEIIRDRQTGDSLSYAFVEFENK 293

Query: 295 QACERAYSKMDNALIDDRRIHVDFSQSVSKLWNQFRRRDHQTGKGKGCFKCGGLDHIAKD 354
           +  E AY KM + LIDDRRIHVDFSQSVSKL   +  +  +TG GK     GG D++ K 
Sbjct: 294 EDAEEAYFKMQSVLIDDRRIHVDFSQSVSKLHKDWIAK--RTGAGKESM--GGFDNLTK- 348

Query: 355 CTGQQPAKYILRDDNRQHGGYSDSR-YEMVFD 385
                      R   R+ G  +D R Y++VFD
Sbjct: 349 -----------RTRYREEGENNDKRDYDLVFD 369

PPIases accelerate the folding of proteins. It catalyzes the cis-trans isomerization of proline imidic peptide bonds in oligopeptides.
Rhizopus delemar (strain RA 99-880 / ATCC MYA-4621 / FGSC 9543 / NRRL 43880) (taxid: 246409)
EC: 5EC: .EC: 2EC: .EC: 1EC: .EC: 8

>sp|Q4WAQ9|PPIL4_ASPFU Peptidyl-prolyl cis-trans isomerase-like 4 OS=Neosartorya fumigata (strain ATCC MYA-4609 / Af293 / CBS 101355 / FGSC A1100) GN=cyp6 PE=3 SV=1

 Score =  368 bits (944), Expect = e-101,   Method: Compositional matrix adjust.
 Identities = 199/395 (50%), Positives = 258/395 (65%), Gaps = 28/395 (7%)

Query: 1   MSVLIVTSLGDIVVDLFVDKCPLTTKNFLKLCKIKYYNGCLFHTVQKDFTAQTGDPTGTG 60
           MSVL+ TSLGDIV+DL VD+ P   +NFLKLCK+KYYN    H+VQK+FT QTGDP G  
Sbjct: 1   MSVLLETSLGDIVIDLLVDESPKACENFLKLCKVKYYNFSPVHSVQKNFTFQTGDPLGPD 60

Query: 61  T----GGDSVYKFLYGEQARFFGDEIRVDLKHAKTGTVAMASAG------ENLNASQFYM 110
           +    GG S++  L G   R F  ++   LKH + GTV+MA+        E L ASQF +
Sbjct: 61  SPESDGGSSIWGLLEGPVKRTFSLKLSPKLKHTERGTVSMATVPSSHDPDERLAASQFIV 120

Query: 111 TLRDNLDYLDEKHTIFGEVAEGLETLSRINESFVDEKNRPYKNIRIKHTYILEDPFDDPA 170
           TL DNLDYLD K  IFG+V EG + L +IN +F+D++ RP K+IRI+HT IL+DP+DDP 
Sbjct: 121 TLEDNLDYLDGKAAIFGKVVEGFDVLEKINGAFIDDQGRPLKDIRIRHTVILDDPYDDPP 180

Query: 171 QLAELIPDASPEGKPKDEVVDEVRLEDDWVPLDEQLSAAELEQVIRSKDARSSAVVLESI 230
            L  ++P  SP   P    +  VR+ DD   LD+ +    +E++ R ++AR+ A+ LE +
Sbjct: 181 GL--VVPAESP--LPSKAQLATVRIADDE-ELDDNMDEEAMEKLRREREARAQALTLEMV 235

Query: 231 GDIPDADIKPPENVLFVCKLNPVTEDEDLHTIFSRFGTVVSAEIIRDFKTGDSLNYAFIE 290
           GD+P A++KPPENVLFVCKLNPVT+DEDL  IFSRFG ++S E+IRD +TGDSL YAFIE
Sbjct: 236 GDLPFAEVKPPENVLFVCKLNPVTQDEDLQLIFSRFGPILSCEVIRDKRTGDSLQYAFIE 295

Query: 291 FENRQACERAYSKMDNALIDDRRIHVDFSQSVSKLWNQFRRRDHQTGKGKGCFKCGGLDH 350
           FEN++ CE+AY KM   LIDD RIHVDFSQSVSKL   +R         +G F  GG+  
Sbjct: 296 FENQKDCEQAYFKMQGVLIDDHRIHVDFSQSVSKLSESWRNATISKRSQRGGF--GGVAE 353

Query: 351 IAKDCTGQQPAKYILRDDNRQHGGYSDSRYEMVFD 385
           + K        +Y   D+ R+   Y      MVFD
Sbjct: 354 LEKK------RQYRATDNVREQDAYG-----MVFD 377

PPIases accelerate the folding of proteins. It catalyzes the cis-trans isomerization of proline imidic peptide bonds in oligopeptides.

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

EC: 5

EC: .

EC: 2

EC: .

EC: 1

EC: .

EC: 8

>sp|Q2U256|PPIL4_ASPOR Peptidyl-prolyl cis-trans isomerase-like 4 OS=Aspergillus oryzae (strain ATCC 42149 / RIB 40) GN=cyp6 PE=3 SV=1

 Score =  367 bits (943), Expect = e-100,   Method: Compositional matrix adjust.
 Identities = 220/480 (45%), Positives = 292/480 (60%), Gaps = 49/480 (10%)

Query: 1   MSVLIVTSLGDIVVDLFVDKCPLTTKNFLKLCKIKYYNGCLFHTVQKDFTAQTGDPTGTG 60
           MSVL+ TSLGDIV+DL VD+CP   +NFLKLCK+KYYN    H+VQK+FT QTGDP G  
Sbjct: 1   MSVLLETSLGDIVIDLLVDECPKACENFLKLCKVKYYNFSPVHSVQKNFTFQTGDPLGPD 60

Query: 61  TGGDS----VYKFLYGEQARFFGDEIRVDLKHAKTGTVAMASAG------ENLNASQFYM 110
           +        ++  L G   R F  E    LKH + GTV+MA+        + + ASQF +
Sbjct: 61  SSESDGGSSIWGLLEGPPKRTFSLEPPPKLKHDERGTVSMATVPSPHDPDQRIAASQFIV 120

Query: 111 TLRDNLDYLDEKHTIFGEVAEGLETLSRINESFVDEKNRPYKNIRIKHTYILEDPFDDPA 170
           TL +NLDYLD K  IFG+V EG + L ++NE+F+D++ RP K+IRI+HT IL+DPFDDP 
Sbjct: 121 TLGENLDYLDGKAVIFGKVVEGFDVLEKVNEAFIDDRGRPLKDIRIRHTVILDDPFDDPP 180

Query: 171 QLAELIPDASPEGKPKDEVVDEVRLEDDWVPLDEQLSAAELEQVIRSKDARSSAVVLESI 230
            L  + P  SP   P    +  VR+ DD   LD+ +    +E++ R ++AR+ A+ LE +
Sbjct: 181 GL--VAPAESP--LPSKAQLATVRIADDE-ELDDNMDEESMEKLRREREARAQALTLEMV 235

Query: 231 GDIPDADIKPPENVLFVCKLNPVTEDEDLHTIFSRFGTVVSAEIIRDFKTGDSLNYAFIE 290
           GD+P A++KPPENVLFVCKLNPVT+DEDLH IFSRFGT++S E+IRD +TGDSL YAFIE
Sbjct: 236 GDLPFAEVKPPENVLFVCKLNPVTQDEDLHLIFSRFGTILSCEVIRDKRTGDSLQYAFIE 295

Query: 291 FENRQACERAYSKMDNALIDDRRIHVDFSQSVSKLWNQFRRRDHQTGKG-KGCFKCGGLD 349
           FEN++ CE+AY KM   LIDD RIHVDFSQSVSKL   +R        G +G F  GG+ 
Sbjct: 296 FENQKDCEQAYFKMQGVLIDDHRIHVDFSQSVSKLSESWRNATISKRSGQRGGF--GGVA 353

Query: 350 HIAKDCTGQQPAKYILRDDNRQHGGYSDSRYEMVFDGETPEKSRREKKHRGHDPDDRVER 409
            + K        +Y   D+ R+     ++ Y +VFD     K  +  + R +    +   
Sbjct: 354 SLEKK------RQYRASDNARE----KENDYTLVFD-----KGDKAPRRRSYSRSPQRSS 398

Query: 410 NMNRLSSDLRHRDQERRELSYRQRESDRTRENREDRRNRDGQESRNVQKQEVRDDD-GRY 468
           N +R +S    RD  R    YR+R  DR+              SR+  + E RD D GRY
Sbjct: 399 NRDRRASRSPRRDSYRD--PYRRRPGDRS-------------HSRSPARGEYRDKDRGRY 443

PPIases accelerate the folding of proteins. It catalyzes the cis-trans isomerization of proline imidic peptide bonds in oligopeptides.

Aspergillus oryzae (strain ATCC 42149 / RIB 40) (taxid: 510516)

EC: 5

EC: .

EC: 2

EC: .

EC: 1

EC: .

EC: 8

>sp|Q8WUA2|PPIL4_HUMAN Peptidyl-prolyl cis-trans isomerase-like 4 OS=Homo sapiens GN=PPIL4 PE=1 SV=1

 Score =  365 bits (938), Expect = e-100,   Method: Compositional matrix adjust.
 Identities = 186/329 (56%), Positives = 238/329 (72%), Gaps = 15/329 (4%)

Query: 1   MSVLIVTSLGDIVVDLFVDKCPLTTKNFLKLCKIKYYNGCLFHTVQKDFTAQTGDPTGTG 60
           M+VL+ T+LGD+V+DL+ ++ P    NFLKLCKIKYYN CL H VQ+DF  QTGDPTGTG
Sbjct: 1   MAVLLETTLGDVVIDLYTEERPRACLNFLKLCKIKYYNYCLIHNVQRDFIIQTGDPTGTG 60

Query: 61  TGGDSVYKFLYGEQARFFGDEIRVDLKHAKTGTVAMASAGENLNASQFYMTLRDNLDYLD 120
            GG+S++  LYG+QA FF  E    +KH K GTV+M + G + + SQF +T  +NLDYLD
Sbjct: 61  RGGESIFGQLYGDQASFFEAEKVPRIKHKKKGTVSMVNNGSDQHGSQFLITTGENLDYLD 120

Query: 121 EKHTIFGEVAEGLETLSRINESFVDEKNRPYKNIRIKHTYILEDPFDDPAQLAELIPDAS 180
             HT+FGEV EG++ + +INE+FVD+   PY++IRI HT IL+D          LIPD S
Sbjct: 121 GVHTVFGEVTEGMDIIKKINETFVDKDFVPYQDIRINHTVILDD--PFDDPPDLLIPDRS 178

Query: 181 PEGKPKDEVVDEVRLEDDWVPLDEQL------SAAELEQVIRSKDARSSAVVLESIGDIP 234
           PE  P  E +D  R     +  DE++      SA E+E++   K+A++ A++LE +GD+P
Sbjct: 179 PE--PTREQLDSGR-----IGADEEIDDFKGRSAEEVEEIKAEKEAKTQAILLEMVGDLP 231

Query: 235 DADIKPPENVLFVCKLNPVTEDEDLHTIFSRFGTVVSAEIIRDFKTGDSLNYAFIEFENR 294
           DADIKPPENVLFVCKLNPVT DEDL  IFSRFG + S E+IRD+KTG+SL YAFIEFE  
Sbjct: 232 DADIKPPENVLFVCKLNPVTTDEDLEIIFSRFGPIRSCEVIRDWKTGESLCYAFIEFEKE 291

Query: 295 QACERAYSKMDNALIDDRRIHVDFSQSVS 323
           + CE+A+ KMDN LIDDRRIHVDFSQSV+
Sbjct: 292 EDCEKAFFKMDNVLIDDRRIHVDFSQSVA 320

PPIases accelerate the folding of proteins. It catalyzes the cis-trans isomerization of proline imidic peptide bonds in oligopeptides.

Homo sapiens (taxid: 9606)

EC: 5

EC: .

EC: 2

EC: .

EC: 1

EC: .

EC: 8

>sp|Q9CXG3|PPIL4_MOUSE Peptidyl-prolyl cis-trans isomerase-like 4 OS=Mus musculus GN=Ppil4 PE=2 SV=2

 Score =  364 bits (934), Expect = 1e-99,   Method: Compositional matrix adjust.
 Identities = 186/329 (56%), Positives = 238/329 (72%), Gaps = 15/329 (4%)

Query: 1   MSVLIVTSLGDIVVDLFVDKCPLTTKNFLKLCKIKYYNGCLFHTVQKDFTAQTGDPTGTG 60
           M+VL+ T+LGD+V+DL+ ++ P    NFLKLCKIKYYN CL H VQ+DF  QTGDPTGTG
Sbjct: 1   MAVLLETTLGDVVIDLYTEERPRACLNFLKLCKIKYYNYCLIHNVQRDFIIQTGDPTGTG 60

Query: 61  TGGDSVYKFLYGEQARFFGDEIRVDLKHAKTGTVAMASAGENLNASQFYMTLRDNLDYLD 120
            GG+S++  LYG+QA FF  E    +KH K GTV+M + G + + SQF +T  +NLDYLD
Sbjct: 61  RGGESIFGQLYGDQASFFEAEKVPRIKHKKKGTVSMVNNGSDQHGSQFLITTGENLDYLD 120

Query: 121 EKHTIFGEVAEGLETLSRINESFVDEKNRPYKNIRIKHTYILEDPFDDPAQLAELIPDAS 180
             HT+FGEV EG++ + +INE+FVD+   PY++IRI HT IL+D          LIPD S
Sbjct: 121 GVHTVFGEVTEGMDIVKKINETFVDKDFVPYQDIRINHTVILDD--PFDDPPDLLIPDRS 178

Query: 181 PEGKPKDEVVDEVRLEDDWVPLDEQL------SAAELEQVIRSKDARSSAVVLESIGDIP 234
           PE  P  E +D  R     +  DE++      SA E+E++   K+A++ A++LE +GD+P
Sbjct: 179 PE--PTKEQLDSGR-----IGADEEIDDFKGRSAEEVEEIKAEKEAKTQAILLEMVGDLP 231

Query: 235 DADIKPPENVLFVCKLNPVTEDEDLHTIFSRFGTVVSAEIIRDFKTGDSLNYAFIEFENR 294
           DADIKPPENVLFVCKLNPVT DEDL  IFSRFG + S E+IRD+KTG+SL YAFIEFE  
Sbjct: 232 DADIKPPENVLFVCKLNPVTTDEDLEIIFSRFGPIRSCEVIRDWKTGESLCYAFIEFEKE 291

Query: 295 QACERAYSKMDNALIDDRRIHVDFSQSVS 323
           + CE+A+ KMDN LIDDRRIHVDFSQSV+
Sbjct: 292 EDCEKAFFKMDNVLIDDRRIHVDFSQSVA 320

PPIases accelerate the folding of proteins. It catalyzes the cis-trans isomerization of proline imidic peptide bonds in oligopeptides.

Mus musculus (taxid: 10090)

EC: 5

EC: .

EC: 2

EC: .

EC: 1

EC: .

EC: 8

>sp|Q5ARI5|PPIL4_EMENI Peptidyl-prolyl cis-trans isomerase-like 4 OS=Emericella nidulans (strain FGSC A4 / ATCC 38163 / CBS 112.46 / NRRL 194 / M139) GN=cyp6 PE=3 SV=1

 Score =  348 bits (892), Expect = 8e-95,   Method: Compositional matrix adjust.
 Identities = 182/340 (53%), Positives = 235/340 (69%), Gaps = 15/340 (4%)

Query: 1   MSVLIVTSLGDIVVDLFVDKCPLTTKNFLKLCKIKYYNGCLFHTVQKDFTAQTGDPTGT- 59
           MSVL+ TSLGDIV+DL VD+ P   +NFLKLCK+KYYN   F++VQK+F+ QTGDP G  
Sbjct: 1   MSVLLETSLGDIVIDLLVDESPKACENFLKLCKVKYYNFSPFYSVQKNFSFQTGDPIGPD 60

Query: 60  ---GTGGDSVYKFLYGEQARFFGDEIRVDLKHAKTGTVAMASAGEN------LNASQFYM 110
                GG S++  L G   +     +   LKH + GTV+MA+          L  SQF +
Sbjct: 61  SPDSNGGSSIWGLLEGPSKQAVPLALPPKLKHDEKGTVSMAAVPSPHDPDLRLVTSQFIV 120

Query: 111 TLRDNLDYLDEKHTIFGEVAEGLETLSRINESFVDEKNRPYKNIRIKHTYILEDPFDDPA 170
           TL DNLDYLD K  IFG+V EG + L ++NE+F+D++ RP K+IRI+HT IL+DPFDDP 
Sbjct: 121 TLGDNLDYLDGKAVIFGKVVEGFDVLEKVNEAFIDDRGRPLKDIRIRHTVILDDPFDDPP 180

Query: 171 QLAELIPDASPEGKPKDEVVDEVRLEDDWVPLDEQLSAAELEQVIRSKDARSSAVVLESI 230
            L E  P  SP   P    +  VR+ DD   L + +  A +E++ R ++AR+ A+ LE +
Sbjct: 181 GLVE--PPESP--LPTKAQLATVRIADDED-LGDDMDEASMEKLRREREARAQALTLEMV 235

Query: 231 GDIPDADIKPPENVLFVCKLNPVTEDEDLHTIFSRFGTVVSAEIIRDFKTGDSLNYAFIE 290
           GD+P A++KPPENVLFVCKLNPVT+DEDL  IFSRFG ++S E+IRD +TGDSL YAFIE
Sbjct: 236 GDLPFAEVKPPENVLFVCKLNPVTQDEDLELIFSRFGKILSCEVIRDKRTGDSLQYAFIE 295

Query: 291 FENRQACERAYSKMDNALIDDRRIHVDFSQSVSKLWNQFR 330
           FE+++ CE+AY KM   LIDD RIHVDFSQSVSKL   +R
Sbjct: 296 FESQKDCEQAYFKMQGVLIDDHRIHVDFSQSVSKLSESWR 335

PPIases accelerate the folding of proteins. It catalyzes the cis-trans isomerization of proline imidic peptide bonds in oligopeptides.

Emericella nidulans (strain FGSC A4 / ATCC 38163 / CBS 112.46 / NRRL 194 / M139) (taxid: 227321)

EC: 5

EC: .

EC: 2

EC: .

EC: 1

EC: .

EC: 8

>sp|P0CP88|PPIL4_CRYNJ Peptidyl-prolyl cis-trans isomerase-like 4 OS=Cryptococcus neoformans var. neoformans serotype D (strain JEC21 / ATCC MYA-565) GN=CYP6 PE=3 SV=1

 Score =  345 bits (884), Expect = 7e-94,   Method: Compositional matrix adjust.
 Identities = 180/333 (54%), Positives = 235/333 (70%), Gaps = 13/333 (3%)

Query: 1   MSVLIVTSLGDIVVDLFVDKCPLTTKNFLKLCKIKYYNGCLFHTVQKDFTAQTGDPTGTG 60
           MSV++ TSLGD+++DL VDKCP T +NF+KLCK+KYY    F  V K+F AQ+GDPT TG
Sbjct: 1   MSVMLETSLGDLIIDLEVDKCPRTCENFIKLCKLKYYALNAFFNVSKNFIAQSGDPTATG 60

Query: 61  TGGDSVYKFLYGEQA------RFFGDEIRVDLKHAKTGTVAMASAGENLNA--SQFYMTL 112
           TGG+S+  ++Y +        R+F  EI   LKH   GT++MA A  N     SQF++TL
Sbjct: 61  TGGESLASYVYSQSPSGPRPPRYFTPEILNSLKHTHKGTLSMAVAPINPPGCGSQFFITL 120

Query: 113 RDNLDYLDEKHTIFGEVAEGLETLSRINESFVDEKNRPYKNIRIKHTYILEDPFDDPAQL 172
            DN+DYLD KH +FG V EGL+TL +IN++F D++ RP +NIRI+H  ILEDPF DP   
Sbjct: 121 ADNIDYLDGKHAVFGHVIEGLDTLDKINDAFTDKEGRPLQNIRIRHVEILEDPFPDPDNF 180

Query: 173 AELIPDASPEGKPKDEVVDEVRLEDDWVPLDEQLSAAELEQVIRSKDARSSAVVLESIGD 232
              IP  SP   P D  + +VR+ D   P +  +   E E++ R  +A SSA+ LE IGD
Sbjct: 181 MP-IPQ-SPIRPPDD--LSKVRIADTEDP-NAVIPEEEAEELRRRTEAASSALTLEMIGD 235

Query: 233 IPDADIKPPENVLFVCKLNPVTEDEDLHTIFSRFGTVVSAEIIRDFKTGDSLNYAFIEFE 292
           +P A ++PPEN+LFVCKLNPVT+DEDL  IFSRFG ++S E++RD K+GDSL YAFIEF+
Sbjct: 236 LPFAAVRPPENILFVCKLNPVTQDEDLELIFSRFGKILSCEVVRDKKSGDSLQYAFIEFD 295

Query: 293 NRQACERAYSKMDNALIDDRRIHVDFSQSVSKL 325
            R+A E+AY KM N L+DDRRI VDFSQSV+K+
Sbjct: 296 EREAAEQAYFKMQNVLVDDRRIWVDFSQSVAKM 328

PPIases accelerate the folding of proteins. It catalyzes the cis-trans isomerization of proline imidic peptide bonds in oligopeptides.

Cryptococcus neoformans var. neoformans serotype D (strain JEC21 / ATCC MYA-565) (taxid: 214684)

EC: 5

EC: .

EC: 2

EC: .

EC: 1

EC: .

EC: 8

>sp|P0CP89|PPIL4_CRYNB Peptidyl-prolyl cis-trans isomerase-like 4 OS=Cryptococcus neoformans var. neoformans serotype D (strain B-3501A) GN=CYP6 PE=3 SV=1

 Score =  345 bits (884), Expect = 7e-94,   Method: Compositional matrix adjust.
 Identities = 180/333 (54%), Positives = 235/333 (70%), Gaps = 13/333 (3%)

Query: 1   MSVLIVTSLGDIVVDLFVDKCPLTTKNFLKLCKIKYYNGCLFHTVQKDFTAQTGDPTGTG 60
           MSV++ TSLGD+++DL VDKCP T +NF+KLCK+KYY    F  V K+F AQ+GDPT TG
Sbjct: 1   MSVMLETSLGDLIIDLEVDKCPRTCENFIKLCKLKYYALNAFFNVSKNFIAQSGDPTATG 60

Query: 61  TGGDSVYKFLYGEQA------RFFGDEIRVDLKHAKTGTVAMASAGENLNA--SQFYMTL 112
           TGG+S+  ++Y +        R+F  EI   LKH   GT++MA A  N     SQF++TL
Sbjct: 61  TGGESLASYVYSQSPSGPRPPRYFTPEILNSLKHTHKGTLSMAVAPINPPGCGSQFFITL 120

Query: 113 RDNLDYLDEKHTIFGEVAEGLETLSRINESFVDEKNRPYKNIRIKHTYILEDPFDDPAQL 172
            DN+DYLD KH +FG V EGL+TL +IN++F D++ RP +NIRI+H  ILEDPF DP   
Sbjct: 121 ADNIDYLDGKHAVFGHVIEGLDTLDKINDAFTDKEGRPLQNIRIRHVEILEDPFPDPDNF 180

Query: 173 AELIPDASPEGKPKDEVVDEVRLEDDWVPLDEQLSAAELEQVIRSKDARSSAVVLESIGD 232
              IP  SP   P D  + +VR+ D   P +  +   E E++ R  +A SSA+ LE IGD
Sbjct: 181 MP-IPQ-SPIRPPDD--LSKVRIADTEDP-NAVIPEEEAEELRRRTEAASSALTLEMIGD 235

Query: 233 IPDADIKPPENVLFVCKLNPVTEDEDLHTIFSRFGTVVSAEIIRDFKTGDSLNYAFIEFE 292
           +P A ++PPEN+LFVCKLNPVT+DEDL  IFSRFG ++S E++RD K+GDSL YAFIEF+
Sbjct: 236 LPFAAVRPPENILFVCKLNPVTQDEDLELIFSRFGKILSCEVVRDKKSGDSLQYAFIEFD 295

Query: 293 NRQACERAYSKMDNALIDDRRIHVDFSQSVSKL 325
            R+A E+AY KM N L+DDRRI VDFSQSV+K+
Sbjct: 296 EREAAEQAYFKMQNVLVDDRRIWVDFSQSVAKM 328

PPIases accelerate the folding of proteins. It catalyzes the cis-trans isomerization of proline imidic peptide bonds in oligopeptides.

Cryptococcus neoformans var. neoformans serotype D (strain B-3501A) (taxid: 283643)

EC: 5

EC: .

EC: 2

EC: .

EC: 1

EC: .

EC: 8

>sp|Q4IE79|PPIL4_GIBZE Peptidyl-prolyl cis-trans isomerase-like 4 OS=Gibberella zeae (strain PH-1 / ATCC MYA-4620 / FGSC 9075 / NRRL 31084) GN=CYP6 PE=3 SV=2

 Score =  333 bits (853), Expect = 3e-90,   Method: Compositional matrix adjust.
 Identities = 187/368 (50%), Positives = 243/368 (66%), Gaps = 21/368 (5%)

Query: 1   MSVLIVTSLGDIVVDLFVDKCPLTTKNFLKLCKIKYYNGCLFHTVQKDFTAQTGDPTGTG 60
           MSVL+ TS GDIV+DL VD  P   +NFLKLCK+KYYN    H+VQK+F+ QTGDP G  
Sbjct: 1   MSVLLETSAGDIVIDLLVDHAPKLCENFLKLCKVKYYNFSPVHSVQKNFSFQTGDPLGPL 60

Query: 61  T----GGDSVYKFLYGEQA-RFFGDEIRVDLKHAKTGTVAMASAGEN------LNASQFY 109
           +    GG S++  L G+ + R F       LKH + GTV+MA+A         +  SQF 
Sbjct: 61  SKDSDGGSSIWGHLSGDPSERTFPAFFHPKLKHLERGTVSMATAPLQSDPDVRVAGSQFI 120

Query: 110 MTLRDNLDYLDEKHTIFGEVAEGLETLSRINESFVDEKNRPYKNIRIKHTYILEDPFDDP 169
           +TL  + D+LD K  IFG+V EG E L +INE+ VDEK  P  +IRIKHT IL+DP+ DP
Sbjct: 121 ITLGQDTDFLDGKAAIFGKVVEGFEALDKINEAIVDEKGHPLIDIRIKHTVILDDPYADP 180

Query: 170 AQLAELIPDASPEGKPKDEVVDEVRLEDDW-VPLDEQLSAAELEQVIRSKDARSSAVVLE 228
             L E  P  SP   P D+ +  VR+ D+  +  D+ +   ELE+  R+++A++ A+ LE
Sbjct: 181 PGLRE--PSTSP--PPTDQQLKTVRIADEAALHEDDNVDEEELERRRRNREAQAQALTLE 236

Query: 229 SIGDIPDADIKPPENVLFVCKLNPVTEDEDLHTIFSRFGTVVSAEIIRDFKTGDSLNYAF 288
            +GD+P A++KPPENVLFVCKLNPVT DEDL  IF RFG ++S E+IRD KTGDSL YAF
Sbjct: 237 MMGDLPFAEVKPPENVLFVCKLNPVTGDEDLELIFGRFGKILSCEVIRDQKTGDSLQYAF 296

Query: 289 IEFENRQACERAYSKMDNALIDDRRIHVDFSQSVSKL---WNQFRRRDHQTGKGKGCFKC 345
           IE+E++ +CE AY KM   LIDDRRIHVDFSQSVSKL   W +      +T  G+G +  
Sbjct: 297 IEYEDKASCEAAYFKMQGVLIDDRRIHVDFSQSVSKLSDVWRKDTNSKRRTNAGRGGW-- 354

Query: 346 GGLDHIAK 353
           GG+D + K
Sbjct: 355 GGVDELEK 362

PPIases accelerate the folding of proteins. It catalyzes the cis-trans isomerization of proline imidic peptide bonds in oligopeptides.

Gibberella zeae (strain PH-1 / ATCC MYA-4620 / FGSC 9075 / NRRL 31084) (taxid: 229533)

EC: 5

EC: .

EC: 2

EC: .

EC: 1

EC: .

EC: 8

>sp|Q9UUE4|PPIL4_SCHPO Peptidyl-prolyl cis-trans isomerase cyp6 OS=Schizosaccharomyces pombe (strain 972 / ATCC 24843) GN=cyp6 PE=1 SV=1

 Score =  331 bits (848), Expect = 1e-89,   Method: Compositional matrix adjust.
 Identities = 175/335 (52%), Positives = 233/335 (69%), Gaps = 21/335 (6%)

Query: 1   MSVLIVTSLGDIVVDLFVDKCPLTTKNFLKLCKIKYYNGCLFHTVQKDFTAQTGDPTG-T 59
           MSVLI T++GD+V+DLFV + P T +NFLKLCK+KYYN C F+ +Q ++T QTGDP G T
Sbjct: 1   MSVLIETTVGDLVIDLFVKEAPKTCENFLKLCKLKYYNFCPFYNIQHNYTCQTGDPLGPT 60

Query: 60  GTGGDSVYKFLYGEQARFFGDEIRVDLKHAKTGTVAMASAGEN-------LNASQFYMTL 112
           G GG  V+  L  +  RFF  E    L H K G V+M++A  +       +  SQF +TL
Sbjct: 61  GDGGRCVWNVL-NKGTRFFKAEFNPSLVHNKMGLVSMSTATISSRDDKLLVCGSQFIITL 119

Query: 113 RDNLDYLDEKHTIFGEVAEGLETLSRINESFVDEKNRPYKNIRIKHTYILEDPFDDPAQL 172
            DNL+ LDE++ I+G+VAEG +TL +IN++  DE+ +PY++IRIKHT IL+DPF+DP  L
Sbjct: 120 SDNLEGLDERYPIYGQVAEGFDTLLKINDAICDEEGQPYRDIRIKHTIILDDPFEDPPDL 179

Query: 173 AELIPDASPEGKPKDEVVDEVRLEDDWVPLDEQLSAAELE---QVIRSKDARSSAVVLES 229
            E  P  SP   P  E +  VR+ ++     EQ+ +   E   Q  +  +A + AV LE 
Sbjct: 180 VE--PLRSPSPTP--EQLATVRIGEN-----EQIESETSEDKLQREKEMEAEAEAVTLEM 230

Query: 230 IGDIPDADIKPPENVLFVCKLNPVTEDEDLHTIFSRFGTVVSAEIIRDFKTGDSLNYAFI 289
           IGD+P A + PPENVLFVCKLNPVT+DEDL  IFSRFG ++S ++IRD +TGDSL YAFI
Sbjct: 231 IGDLPFAHVAPPENVLFVCKLNPVTQDEDLELIFSRFGKIISCQVIRDKETGDSLQYAFI 290

Query: 290 EFENRQACERAYSKMDNALIDDRRIHVDFSQSVSK 324
           EF+N+++ E+AY KM N LIDD RIHVDFSQSV++
Sbjct: 291 EFDNKESVEKAYFKMQNVLIDDSRIHVDFSQSVAR 325

PPIases accelerate the folding of proteins. It catalyzes the cis-trans isomerization of proline imidic peptide bonds in oligopeptides.

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

EC: 5

EC: .

EC: 2

EC: .

EC: 1

EC: .

EC: 8

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	589
296082685	633	unnamed protein product [Vitis vinifera]	0.874	0.813	0.712	0.0
359494535	627	PREDICTED: peptidyl-prolyl cis-trans iso	0.874	0.821	0.712	0.0
224083978	542	predicted protein [Populus trichocarpa]	0.860	0.935	0.667	0.0
297847776	508	hypothetical protein ARALYDRAFT_474506 [	0.672	0.779	0.796	0.0
357500333	621	Peptidyl-prolyl cis-trans isomerase-like	0.952	0.903	0.620	0.0
22330231	506	cyclophilin 59 [Arabidopsis thaliana] gi	0.670	0.780	0.787	0.0
16648909	441	Unknown protein [Arabidopsis thaliana]	0.670	0.895	0.787	0.0
255544660	587	peptidyl-prolyl cis-trans isomerase, put	0.876	0.879	0.649	0.0
356573339	640	PREDICTED: peptidyl-prolyl cis-trans iso	0.954	0.878	0.640	0.0
356556666	633	PREDICTED: peptidyl-prolyl cis-trans iso	0.957	0.890	0.638	0.0

>gi|296082685|emb|CBI21690.3| unnamed protein product [Vitis vinifera]

 Score =  758 bits (1957), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 389/546 (71%), Positives = 450/546 (82%), Gaps = 31/546 (5%)

Query: 1   MSVLIVTSLGDIVVDLFVDKCPLTTKNFLKLCKIKYYNGCLFHTVQKDFTAQTGDPTGTG 60
           MSVLIVTSLGDIVVDL+ D+CPLT+KNFLKLCKIKYYNGCLFH VQKDFTAQTGDPT TG
Sbjct: 1   MSVLIVTSLGDIVVDLYTDRCPLTSKNFLKLCKIKYYNGCLFHMVQKDFTAQTGDPTATG 60

Query: 61  TGGDSVYKFLYGEQARFFGDEIRVDLKHAKTGTVAMASAGENLNASQFYMTLRDNLDYLD 120
           TGGDS+YKFLYG+QARFF DE+ +DLKH+KTGTVAMASAGENLNASQFY TLRD+LDYLD
Sbjct: 61  TGGDSIYKFLYGDQARFFNDEVHLDLKHSKTGTVAMASAGENLNASQFYFTLRDDLDYLD 120

Query: 121 EKHTIFGEVAEGLETLSRINESFVDEKNRPYKNIRIKHTYILEDPFDDPAQLAELIPDAS 180
            KHT+FGEVAEGLETL+RINE++VD+K RPYKNIRIKHTYIL+DPF DP+QL ELIPDAS
Sbjct: 121 GKHTVFGEVAEGLETLTRINEAYVDDKGRPYKNIRIKHTYILDDPFGDPSQLTELIPDAS 180

Query: 181 PEGKPKDEVVDEVRLEDDWVPLDEQLSAAELEQVIRSKDARSSAVVLESIGDIPDADIKP 240
           PEGKPKDEV D+VRLEDDWVPLDEQL  +ELE++IRSK+A S AVVLESIGDIPDA+IKP
Sbjct: 181 PEGKPKDEVDDDVRLEDDWVPLDEQLDTSELEELIRSKEAHSRAVVLESIGDIPDAEIKP 240

Query: 241 PENVLFVCKLNPVTEDEDLHTIFSRFGTVVSAEIIRDFKTGDSLNYAFIEFENRQACERA 300
           P+NVLFVCKLNPVTEDEDLHTIFSRFGTV+SAEIIRDFKTGDSL YAFIEFE  +ACE+A
Sbjct: 241 PDNVLFVCKLNPVTEDEDLHTIFSRFGTVISAEIIRDFKTGDSLCYAFIEFETNEACEQA 300

Query: 301 YSKMDNALIDDRRIHVDFSQSVSKLWNQFRRRDHQTGKGKGCFKCGGLDHIAKDCTG--- 357
           Y KMDNALIDDRRIHVDFSQSVSKLW+Q+RRRDHQTGKG GCFKCG +DHIAKDCTG   
Sbjct: 301 YFKMDNALIDDRRIHVDFSQSVSKLWSQYRRRDHQTGKGTGCFKCGAVDHIAKDCTGSPT 360

Query: 358 --QQPAKYILRDDNRQHGGYSDSRYEMVFDGETPEKSRREKKHRGHDPDDRVER-NMNRL 414
             QQP KYIL+D+N QHGG ++SRYEMVFD +T E  +REK+ + H P+D++E+  +NR 
Sbjct: 361 KQQQPPKYILKDNNTQHGGDNNSRYEMVFDEDTSESPKREKRRQDHGPEDQIEKEKLNRR 420

Query: 415 SS-DLRHRDQERRELSYRQRESDRTRENREDRRN---RDG---QESRNVQKQEVRDDDGR 467
            S D + RD ++++   R R+SD+ +E+R  R +   RD    +E  + +K   R D+G+
Sbjct: 421 GSEDWKRRDHDKKDSDDRHRQSDKGQESRASRLSGSRRDPYHHEERIDREKHRERQDEGK 480

Query: 468 YESDHPKSSDTDRYRDWRGGGDYRKRSADSDSRAERREDGD---YRKRNSDNGSHRDRRD 524
                       R RD R   DYRKR+ADSDS  ERR+  D   +RKRN+D   H DRRD
Sbjct: 481 ------------RERDER---DYRKRNADSDSHRERRDGRDERHHRKRNADGDRHVDRRD 525

Query: 525 DQDYRK 530
             DYRK
Sbjct: 526 VGDYRK 531

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|359494535|ref|XP_002266085.2| PREDICTED: peptidyl-prolyl cis-trans isomerase-like 4-like [Vitis vinifera]

 Score =  758 bits (1956), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 389/546 (71%), Positives = 450/546 (82%), Gaps = 31/546 (5%)

Query: 1   MSVLIVTSLGDIVVDLFVDKCPLTTKNFLKLCKIKYYNGCLFHTVQKDFTAQTGDPTGTG 60
           MSVLIVTSLGDIVVDL+ D+CPLT+KNFLKLCKIKYYNGCLFH VQKDFTAQTGDPT TG
Sbjct: 1   MSVLIVTSLGDIVVDLYTDRCPLTSKNFLKLCKIKYYNGCLFHMVQKDFTAQTGDPTATG 60

Query: 61  TGGDSVYKFLYGEQARFFGDEIRVDLKHAKTGTVAMASAGENLNASQFYMTLRDNLDYLD 120
           TGGDS+YKFLYG+QARFF DE+ +DLKH+KTGTVAMASAGENLNASQFY TLRD+LDYLD
Sbjct: 61  TGGDSIYKFLYGDQARFFNDEVHLDLKHSKTGTVAMASAGENLNASQFYFTLRDDLDYLD 120

Query: 121 EKHTIFGEVAEGLETLSRINESFVDEKNRPYKNIRIKHTYILEDPFDDPAQLAELIPDAS 180
            KHT+FGEVAEGLETL+RINE++VD+K RPYKNIRIKHTYIL+DPF DP+QL ELIPDAS
Sbjct: 121 GKHTVFGEVAEGLETLTRINEAYVDDKGRPYKNIRIKHTYILDDPFGDPSQLTELIPDAS 180

Query: 181 PEGKPKDEVVDEVRLEDDWVPLDEQLSAAELEQVIRSKDARSSAVVLESIGDIPDADIKP 240
           PEGKPKDEV D+VRLEDDWVPLDEQL  +ELE++IRSK+A S AVVLESIGDIPDA+IKP
Sbjct: 181 PEGKPKDEVDDDVRLEDDWVPLDEQLDTSELEELIRSKEAHSRAVVLESIGDIPDAEIKP 240

Query: 241 PENVLFVCKLNPVTEDEDLHTIFSRFGTVVSAEIIRDFKTGDSLNYAFIEFENRQACERA 300
           P+NVLFVCKLNPVTEDEDLHTIFSRFGTV+SAEIIRDFKTGDSL YAFIEFE  +ACE+A
Sbjct: 241 PDNVLFVCKLNPVTEDEDLHTIFSRFGTVISAEIIRDFKTGDSLCYAFIEFETNEACEQA 300

Query: 301 YSKMDNALIDDRRIHVDFSQSVSKLWNQFRRRDHQTGKGKGCFKCGGLDHIAKDCTG--- 357
           Y KMDNALIDDRRIHVDFSQSVSKLW+Q+RRRDHQTGKG GCFKCG +DHIAKDCTG   
Sbjct: 301 YFKMDNALIDDRRIHVDFSQSVSKLWSQYRRRDHQTGKGTGCFKCGAVDHIAKDCTGSPT 360

Query: 358 --QQPAKYILRDDNRQHGGYSDSRYEMVFDGETPEKSRREKKHRGHDPDDRVER-NMNRL 414
             QQP KYIL+D+N QHGG ++SRYEMVFD +T E  +REK+ + H P+D++E+  +NR 
Sbjct: 361 KQQQPPKYILKDNNTQHGGDNNSRYEMVFDEDTSESPKREKRRQDHGPEDQIEKEKLNRR 420

Query: 415 SS-DLRHRDQERRELSYRQRESDRTRENREDRRN---RDG---QESRNVQKQEVRDDDGR 467
            S D + RD ++++   R R+SD+ +E+R  R +   RD    +E  + +K   R D+G+
Sbjct: 421 GSEDWKRRDHDKKDSDDRHRQSDKGQESRASRLSGSRRDPYHHEERIDREKHRERQDEGK 480

Query: 468 YESDHPKSSDTDRYRDWRGGGDYRKRSADSDSRAERREDGD---YRKRNSDNGSHRDRRD 524
                       R RD R   DYRKR+ADSDS  ERR+  D   +RKRN+D   H DRRD
Sbjct: 481 ------------RERDER---DYRKRNADSDSHRERRDGRDERHHRKRNADGDRHVDRRD 525

Query: 525 DQDYRK 530
             DYRK
Sbjct: 526 VGDYRK 531

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|224083978|ref|XP_002307193.1| predicted protein [Populus trichocarpa] gi|222856642|gb|EEE94189.1| predicted protein [Populus trichocarpa]

 Score =  722 bits (1863), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 367/550 (66%), Positives = 438/550 (79%), Gaps = 43/550 (7%)

Query: 1   MSVLIVTSLGDIVVDLFVDKCPLTTKNFLKLCKIKYYNGCLFHTVQKDFTAQTGDPTGTG 60
           MSVLIVTSLGDIVVDL+ DKCPLT KNFLKLCKIKYYNGCLFHT+QKDFTAQTGDPTGTG
Sbjct: 1   MSVLIVTSLGDIVVDLYADKCPLTCKNFLKLCKIKYYNGCLFHTIQKDFTAQTGDPTGTG 60

Query: 61  TGGDSVYKFLYGEQARFFGDEIRVDLKHAKTGTVAMASAGENLNASQFYMTLRDNLDYLD 120
            GGDSVYKFLYG+QARFFGDEI +DLKH+K GTVAMASAGENLNASQFY TLRD+LDYLD
Sbjct: 61  AGGDSVYKFLYGDQARFFGDEIHLDLKHSKMGTVAMASAGENLNASQFYFTLRDDLDYLD 120

Query: 121 EKHTIFGEVAEGLETLSRINESFVDEKNRPYKNIRIKHTYILEDPFDDPAQLAELIPDAS 180
            KHT+FGE+AEGLETL+RINE++VDEKNRP+KNIRIKH YIL+DPFDDP+QLAELIP+AS
Sbjct: 121 GKHTVFGEIAEGLETLTRINEAYVDEKNRPFKNIRIKHAYILDDPFDDPSQLAELIPEAS 180

Query: 181 PEGKPKDEVVDEVRLEDDWVPLDEQLSAAELEQVIRSKDARSSAVVLESIGDIPDADIKP 240
           PEGKPKDEV  +VRLEDDWVP+DEQL  AELE+V+R+K+A SSAVVLESIGDIP+A+ KP
Sbjct: 181 PEGKPKDEVDGDVRLEDDWVPMDEQLGTAELEEVLRAKEAHSSAVVLESIGDIPEAETKP 240

Query: 241 PENVLFVCKLNPVTEDEDLHTIFSRFGTVVSAEIIRDFKTGDSLNYAFIEFENRQACERA 300
           P+NVLFVCKLNPVTEDEDLHTIFSRFGTV+SA+IIRD+KTGDSL YAFIEFE ++ACE A
Sbjct: 241 PDNVLFVCKLNPVTEDEDLHTIFSRFGTVISADIIRDYKTGDSLCYAFIEFETKEACELA 300

Query: 301 YSKMDNALIDDRRIHVDFSQSVSKLWNQFRRRDHQTGK-GKGCFKCGGLDHIAKDCTG-- 357
           Y KMDNALIDDRRIHVDFSQSV+KLW+QFRR+D+Q GK G+GCFKCG LDH+AKDCTG  
Sbjct: 301 YFKMDNALIDDRRIHVDFSQSVAKLWSQFRRKDNQPGKAGRGCFKCGALDHMAKDCTGDP 360

Query: 358 ---QQPAKYILRDDNRQHGGYSDSRYEMVFDGETPEKSRREKKHRGHDPDDRVERNMNRL 414
               +P+KYIL+DDN Q GG ++SRYEMVFDG+TPE  R+ K+H   DPD +++R     
Sbjct: 361 ANKHRPSKYILKDDNMQRGGDNNSRYEMVFDGDTPESPRQGKRHGHRDPDYQIDR----- 415

Query: 415 SSDLRHRDQERRELSYRQRESDRTRENREDRR-------NRDGQESRNVQKQEVRDDDGR 467
                    E+++   R R+SDR R +R+D R       +R  +E  + +K   R  D  
Sbjct: 416 ---------EKKDGKERYRQSDRDRGHRQDTRYPESKGGSRYPEERLDKEKYMDRRKDRD 466

Query: 468 YESDHPKSSDTDR-YRDWRGGGDYRKRSADSDSRAERREDGDYRKRNSDNGSHRDRRDDQ 526
                 +SSD+ R Y   +   DYRKR++DS               + D+  H+  RD++
Sbjct: 467 DRDYRKRSSDSQRDYDSHKDHRDYRKRTSDS---------------HRDHDGHKGNRDER 511

Query: 527 DYRKKSADGD 536
           ++R++SA+ D
Sbjct: 512 EHRRRSAEND 521

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|297847776|ref|XP_002891769.1| hypothetical protein ARALYDRAFT_474506 [Arabidopsis lyrata subsp. lyrata] gi|297337611|gb|EFH68028.1| hypothetical protein ARALYDRAFT_474506 [Arabidopsis lyrata subsp. lyrata]

 Score =  683 bits (1762), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 318/399 (79%), Positives = 358/399 (89%), Gaps = 3/399 (0%)

Query: 1   MSVLIVTSLGDIVVDLFVDKCPLTTKNFLKLCKIKYYNGCLFHTVQKDFTAQTGDPTGTG 60
           MSVLIVTSLGDIV+DL+ +KCPLT KNFLKLCKIKYYNGCLFHTVQ DFTAQTGDPTGTG
Sbjct: 1   MSVLIVTSLGDIVIDLYPNKCPLTCKNFLKLCKIKYYNGCLFHTVQNDFTAQTGDPTGTG 60

Query: 61  TGGDSVYKFLYGEQARFFGDEIRVDLKHAKTGTVAMASAGENLNASQFYMTLRDNLDYLD 120
            GGDS+YKFLYGEQARFF DEI +DLKH+KTGTVAMAS GENLNASQFY TLRD+LDYLD
Sbjct: 61  AGGDSIYKFLYGEQARFFRDEIHLDLKHSKTGTVAMASGGENLNASQFYFTLRDDLDYLD 120

Query: 121 EKHTIFGEVAEGLETLSRINESFVDEKNRPYKNIRIKHTYILEDPFDDPAQLAELIPDAS 180
            KHT+FGE+AEG +TL+RINE++VD KNRPYKNIRIKH +ILEDPFDDP QLAE+IPDAS
Sbjct: 121 GKHTVFGEIAEGFDTLTRINEAYVDAKNRPYKNIRIKHIHILEDPFDDPPQLAEMIPDAS 180

Query: 181 PEGKPKDEVVDEVRLEDDWVPLDEQLSAAELEQVIRSKDARSSAVVLESIGDIPDADIKP 240
           PEGKPK+EV D+VRLEDDWVP+DE+L   ELE+VIR K A SSAVVLESIGDIP+A++KP
Sbjct: 181 PEGKPKEEVEDDVRLEDDWVPMDEELGVQELEEVIREKAAHSSAVVLESIGDIPEAEVKP 240

Query: 241 PENVLFVCKLNPVTEDEDLHTIFSRFGTVVSAEIIRDFKTGDSLNYAFIEFENRQACERA 300
           P+NVLFVCKLNPVTEDEDLHTIFSRFGTVVSA++IRDFKTGDSL YAFIEFEN++ACE+A
Sbjct: 241 PDNVLFVCKLNPVTEDEDLHTIFSRFGTVVSADVIRDFKTGDSLCYAFIEFENKEACEQA 300

Query: 301 YSKMDNALIDDRRIHVDFSQSVSKLWNQFRRRDHQTGKGKGCFKCGGLDHIAKDCT-GQQ 359
           Y KMDNALIDDRRIHVDFSQSVSKLW+QFR++D Q GKG GCFKCG  DHIAKDC  G Q
Sbjct: 301 YFKMDNALIDDRRIHVDFSQSVSKLWSQFRQKDSQKGKGNGCFKCGSTDHIAKDCVGGNQ 360

Query: 360 PAKYILRDDNRQHGGYSDSRYEMVFDGETPEKSRREKKH 398
           P+K+I++D NRQHGG     Y+MVF+G+ PE  +RE  H
Sbjct: 361 PSKFIVKDQNRQHGG--GEGYDMVFEGDVPEIPKREHSH 397

Source: Arabidopsis lyrata subsp. lyrata

Species: Arabidopsis lyrata

Genus: Arabidopsis

Family: Brassicaceae

Order: Brassicales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|357500333|ref|XP_003620455.1| Peptidyl-prolyl cis-trans isomerase-like protein [Medicago truncatula] gi|355495470|gb|AES76673.1| Peptidyl-prolyl cis-trans isomerase-like protein [Medicago truncatula]

 Score =  682 bits (1759), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 370/596 (62%), Positives = 443/596 (74%), Gaps = 35/596 (5%)

Query: 1   MSVLIVTSLGDIVVDLFVDKCPLTTKNFLKLCKIKYYNGCLFHTVQKDFTAQTGDPTGTG 60
           MSVL+VTSLGD+V+DL   KCPLT KNFLKLCKIKYYNGCLFHTV KDFTAQTGDPTGTG
Sbjct: 18  MSVLMVTSLGDMVIDLHTQKCPLTCKNFLKLCKIKYYNGCLFHTVLKDFTAQTGDPTGTG 77

Query: 61  TGGDSVYKFLYGEQARFFGDEIRVDLKHAKTGTVAMASAGENLNASQFYMTLRDNLDYLD 120
           T GDS+YKFLYG+QARFF DEI +DLKH+KTGTVAMASAGENLNASQFY+TLRD+LDYLD
Sbjct: 78  TAGDSIYKFLYGDQARFFNDEIHIDLKHSKTGTVAMASAGENLNASQFYITLRDDLDYLD 137

Query: 121 EKHTIFGEVAEGLETLSRINESFVDEKNRPYKNIRIKHTYILEDPFDDPAQLAELIPDAS 180
            KHT+FGEVAEG ETL+RINE++ D K RP+KNIRIKHTYILEDPFDDP QL E IP+AS
Sbjct: 138 GKHTVFGEVAEGFETLTRINEAYADGKGRPFKNIRIKHTYILEDPFDDPPQLPEFIPEAS 197

Query: 181 PEGKPKDEVVDEVRLEDDWVPLDEQLSAAELEQVIRSKDARSSAVVLESIGDIPDADIKP 240
           P+GKPKDEV DEVRLEDDWVP+DEQL+  ELE+VIRSK+A S AVVLESIGDIPDA++KP
Sbjct: 198 PDGKPKDEVDDEVRLEDDWVPMDEQLNPGELEEVIRSKEAHSRAVVLESIGDIPDAEVKP 257

Query: 241 PENVLFVCKLNPVTEDEDLHTIFSRFGTVVSAEIIRDFKTGDSLNYAFIEFENRQACERA 300
           P+NVLFVCKLNPVTEDEDLHTIFSRFGTV SAEIIRD KTGDSL YAFIEFE++ ACE+A
Sbjct: 258 PDNVLFVCKLNPVTEDEDLHTIFSRFGTVSSAEIIRDHKTGDSLCYAFIEFEDKLACEQA 317

Query: 301 YSKMDNALIDDRRIHVDFSQSVSKLWNQFRRRDHQTGKGKGCFKCGGLDHIAKDCTG--- 357
           Y KMDNALIDDRRIHVDFSQSV+KLW+Q+ R+D+   KG GCFKCG  DHIA+DCTG   
Sbjct: 318 YFKMDNALIDDRRIHVDFSQSVAKLWSQYMRKDN---KGGGCFKCGSTDHIARDCTGDGT 374

Query: 358 -QQPAKYILRDDNRQHGGYSDSRYEMVFDGETPEKSRREKKHRGHDPDDRVERNMNR--L 414
            +Q  K+I++D+N Q GG   +RYEMVFDG++ E  +RE KH+ ++  DR ++   +   
Sbjct: 375 MKQSTKFIMKDNNGQRGG-DKARYEMVFDGDSIESPKRETKHQRYERGDRYDKKGRKENF 433

Query: 415 SSDLR--HRDQERRELSYRQRESDRTRENREDRRNRDGQE--SRNVQKQEVRDDDGRY-- 468
             D R   RDQE    + R R  DR+R    +  ++ G E  +R+      + D  R+  
Sbjct: 434 KDDSRRGRRDQEMAGSNNRDRYHDRSRGLEGNGDDKAGLERGARDPDFHADKKDIERHMG 493

Query: 469 ------------ESDHPKSSDTDRYRDWRGGGDYRKRSADSDSRAERREDGDYRKRNSDN 516
                       E D  K    D+Y + R   D R+++   D+  +RR+D +YRKR  D+
Sbjct: 494 RRHRDDDYRRKDELDSRKRDLDDKYTERRASRDDRRKT--DDNHLDRRDDRNYRKRTEDS 551

Query: 517 GSHRDRRDDQDYRKKSADGDIHGDRRYDRDNRKNSGNSELRDAKKEP---SYKRGR 569
           G  +D + D   RK+S DGD +  RR D D R++      R  K+ P    YKRGR
Sbjct: 552 G-RQDVKVDSGRRKRSPDGDDYKRRRNDEDYREDVKIDSGR-RKRSPDDGDYKRGR 605

Source: Medicago truncatula

Species: Medicago truncatula

Genus: Medicago

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|22330231|ref|NP_175776.2| cyclophilin 59 [Arabidopsis thaliana] gi|45680880|gb|AAS75309.1| multidomain cyclophilin type peptidyl-prolyl cis-trans isomerase [Arabidopsis thaliana] gi|332194868|gb|AEE32989.1| cyclophilin 59 [Arabidopsis thaliana]

 Score =  675 bits (1742), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 315/400 (78%), Positives = 359/400 (89%), Gaps = 5/400 (1%)

Query: 1   MSVLIVTSLGDIVVDLFVDKCPLTTKNFLKLCKIKYYNGCLFHTVQKDFTAQTGDPTGTG 60
           MSVLIVTSLGDIV+DL  DKCPLT KNFLKLCKIKYYNGCLFHTVQKDFTAQTGDPTGTG
Sbjct: 1   MSVLIVTSLGDIVIDLHSDKCPLTCKNFLKLCKIKYYNGCLFHTVQKDFTAQTGDPTGTG 60

Query: 61  TGGDSVYKFLYGEQARFFGDEIRVDLKHAKTGTVAMASAGENLNASQFYMTLRDNLDYLD 120
            GGDS+YKFLYGEQARF+ DEI +DLKH+KTGTVAMAS GENLNASQFY TLRD+LDYLD
Sbjct: 61  AGGDSIYKFLYGEQARFYKDEIHLDLKHSKTGTVAMASGGENLNASQFYFTLRDDLDYLD 120

Query: 121 EKHTIFGEVAEGLETLSRINESFVDEKNRPYKNIRIKHTYILEDPFDDPAQLAELIPDAS 180
            KHT+FG++AEG +TL+RINE++VD KNRPYKNIRIKHT+IL+DPFDDP QLAE++PDAS
Sbjct: 121 GKHTVFGQIAEGFDTLTRINEAYVDPKNRPYKNIRIKHTHILDDPFDDPPQLAEMMPDAS 180

Query: 181 PEGKPKDEVVDEVRLEDDWVPLDEQLSAAELEQVIRSKDARSSAVVLESIGDIPDADIKP 240
           PEGKPK+EV D+VRLEDDWVP+DE+L A ELE+VIR K A SSAVVLESIGDIP+A++KP
Sbjct: 181 PEGKPKEEVKDDVRLEDDWVPMDEELGAQELEEVIREKAAHSSAVVLESIGDIPEAEVKP 240

Query: 241 PENVLFVCKLNPVTEDEDLHTIFSRFGTVVSAEIIRDFKTGDSLNYAFIEFENRQACERA 300
           P+NVLFVCKLNPVTEDEDLHTIFSRFGTVVSA++IRDFKTGDSL YAFIEFEN+++CE+A
Sbjct: 241 PDNVLFVCKLNPVTEDEDLHTIFSRFGTVVSADVIRDFKTGDSLCYAFIEFENKESCEQA 300

Query: 301 YSKMDNALIDDRRIHVDFSQSVSKLWNQFRRRDHQTGKGKGCFKCGGLDHIAKDCTGQQP 360
           Y KMDNALIDDRRIHVDFSQSVSKLW+QFR++D Q GKG GCFKCG  DHIAKDC G   
Sbjct: 301 YFKMDNALIDDRRIHVDFSQSVSKLWSQFRQKDSQKGKGNGCFKCGSTDHIAKDCVGGPS 360

Query: 361 AKYILRDDNRQHGGYSDSRYEMVFDG---ETPEKSRREKK 397
           +K+I++D NRQHGG     YEMVF+G   ETP+ +  E++
Sbjct: 361 SKFIVKDQNRQHGG--GEGYEMVFEGDVHETPKHNSHERE 398

Source: Arabidopsis thaliana

Species: Arabidopsis thaliana

Genus: Arabidopsis

Family: Brassicaceae

Order: Brassicales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|16648909|gb|AAL24306.1| Unknown protein [Arabidopsis thaliana]

 Score =  673 bits (1737), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 315/400 (78%), Positives = 359/400 (89%), Gaps = 5/400 (1%)

Query: 1   MSVLIVTSLGDIVVDLFVDKCPLTTKNFLKLCKIKYYNGCLFHTVQKDFTAQTGDPTGTG 60
           MSVLIVTSLGDIV+DL  DKCPLT KNFLKLCKIKYYNGCLFHTVQKDFTAQTGDPTGTG
Sbjct: 1   MSVLIVTSLGDIVIDLHSDKCPLTCKNFLKLCKIKYYNGCLFHTVQKDFTAQTGDPTGTG 60

Query: 61  TGGDSVYKFLYGEQARFFGDEIRVDLKHAKTGTVAMASAGENLNASQFYMTLRDNLDYLD 120
            GGDS+YKFLYGEQARF+ DEI +DLKH+KTGTVAMAS GENLNASQFY TLRD+LDYLD
Sbjct: 61  AGGDSIYKFLYGEQARFYKDEIHLDLKHSKTGTVAMASGGENLNASQFYFTLRDDLDYLD 120

Query: 121 EKHTIFGEVAEGLETLSRINESFVDEKNRPYKNIRIKHTYILEDPFDDPAQLAELIPDAS 180
            KHT+FG++AEG +TL+RINE++VD KNRPYKNIRIKHT+IL+DPFDDP QLAE++PDAS
Sbjct: 121 GKHTVFGQIAEGFDTLTRINEAYVDPKNRPYKNIRIKHTHILDDPFDDPPQLAEMMPDAS 180

Query: 181 PEGKPKDEVVDEVRLEDDWVPLDEQLSAAELEQVIRSKDARSSAVVLESIGDIPDADIKP 240
           PEGKPK+EV D+VRLEDDWVP+DE+L A ELE+VIR K A SSAVVLESIGDIP+A++KP
Sbjct: 181 PEGKPKEEVKDDVRLEDDWVPMDEELGAQELEEVIREKAAHSSAVVLESIGDIPEAEVKP 240

Query: 241 PENVLFVCKLNPVTEDEDLHTIFSRFGTVVSAEIIRDFKTGDSLNYAFIEFENRQACERA 300
           P+NVLFVCKLNPVTEDEDLHTIFSRFGTVVSA++IRDFKTGDSL YAFIEFEN+++CE+A
Sbjct: 241 PDNVLFVCKLNPVTEDEDLHTIFSRFGTVVSADVIRDFKTGDSLCYAFIEFENKESCEQA 300

Query: 301 YSKMDNALIDDRRIHVDFSQSVSKLWNQFRRRDHQTGKGKGCFKCGGLDHIAKDCTGQQP 360
           Y KMDNALIDDRRIHVDFSQSVSKLW+QFR++D Q GKG GCFKCG  DHIAKDC G   
Sbjct: 301 YFKMDNALIDDRRIHVDFSQSVSKLWSQFRQKDSQKGKGNGCFKCGSTDHIAKDCVGGPS 360

Query: 361 AKYILRDDNRQHGGYSDSRYEMVFDG---ETPEKSRREKK 397
           +K+I++D NRQHGG     YEMVF+G   ETP+ +  E++
Sbjct: 361 SKFIVKDQNRQHGG--GEGYEMVFEGDVHETPKHNSHERE 398

Source: Arabidopsis thaliana

Species: Arabidopsis thaliana

Genus: Arabidopsis

Family: Brassicaceae

Order: Brassicales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|255544660|ref|XP_002513391.1| peptidyl-prolyl cis-trans isomerase, putative [Ricinus communis] gi|223547299|gb|EEF48794.1| peptidyl-prolyl cis-trans isomerase, putative [Ricinus communis]

 Score =  671 bits (1732), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 346/533 (64%), Positives = 409/533 (76%), Gaps = 17/533 (3%)

Query: 33  KIKYYNGCLFHTVQKDFTAQTGDPTGTGTGGDSVYKFLYGEQARFFGDEIRVDLKHAKTG 92
           +IKYYNGCLFHTVQKDFTAQTGDP GTG GGDS+YKFLYG+QARFF DEI +DLKH+KTG
Sbjct: 44  EIKYYNGCLFHTVQKDFTAQTGDPAGTGAGGDSIYKFLYGDQARFFSDEIHLDLKHSKTG 103

Query: 93  TVAMASAGENLNASQFYMTLRDNLDYLDEKHTIFGEVAEGLETLSRINESFVDEKNRPYK 152
           TVAMASAGENLNASQFY TLRD LDYLD KHT+FGEVAEGLETL+RINE++VD KNRP+K
Sbjct: 104 TVAMASAGENLNASQFYFTLRDGLDYLDGKHTVFGEVAEGLETLTRINEAYVDTKNRPFK 163

Query: 153 NIRIKHTYILEDPFDDPAQLAELIPDASPEGKPKDEVVDEVRLEDDWVPLDEQLSAAELE 212
           NIRIKHTYIL+DPFDDP QL ELIPDASPEGKPK EV DEVRLEDDWVP+DEQL  AELE
Sbjct: 164 NIRIKHTYILDDPFDDPPQLTELIPDASPEGKPKQEVEDEVRLEDDWVPMDEQLGPAELE 223

Query: 213 QVIRSKDARSSAVVLESIGDIPDADIKPPENVLFVCKLNPVTEDEDLHTIFSRFGTVVSA 272
           +V+R+KDA SSAVVLESIGDIPDA++KPP+NVLFVCKLNPVTEDEDLHTIFSRFGTV+SA
Sbjct: 224 EVLRAKDAHSSAVVLESIGDIPDAEMKPPDNVLFVCKLNPVTEDEDLHTIFSRFGTVISA 283

Query: 273 EIIRDFKTGDSLNYAFIEFENRQACERAYSKMDNALIDDRRIHVDFSQSVSKLWNQFRRR 332
           EIIRDFKTGDSL YAFIEFE +++CE+AY KMDNALIDDRRIHVDFSQSV+K W ++RRR
Sbjct: 284 EIIRDFKTGDSLCYAFIEFETKESCEQAYFKMDNALIDDRRIHVDFSQSVAKQWAEYRRR 343

Query: 333 DHQTGKGKGCFKCGGLDHIAKDCTGQ------QPAKYILRDDNRQHGGYSDSRYEMVFDG 386
             Q GK +GCFKCG  DH AKDCTG       QP KY+L+DDN QHGG ++SRYEMVFDG
Sbjct: 344 GGQMGKERGCFKCGAPDHTAKDCTGGPPTKQLQPPKYVLKDDNMQHGGKNNSRYEMVFDG 403

Query: 387 ETPEKSRREKKHRGHDPDDRVERNMNRLSSDLRHRDQERRELSYRQRESDRTRENREDRR 446
           +TPE  R+EK++  HDP+   E+   R   DL+H  +E++      R+ DR R +RED R
Sbjct: 404 DTPESPRQEKRNGRHDPE--REKMHRRSLEDLKHGAEEKKYQGDGHRQRDRNRGHREDDR 461

Query: 447 NRDGQESRNVQKQEVRDDDGRYESDHP-----KSSDTDRYRDWRGGGDYRKRSADSDSRA 501
           + + + SR  +++  R  +   +         +S+D +   D R    YRKR+AD DSR 
Sbjct: 462 HHEKKPSRYPEERTDRRKERDDDRRDDRDYWNRSADVEGRGDGRENEGYRKRTADYDSRR 521

Query: 502 ERREDGDYRKRNSDNGSHRDRRDDQDYRKKSADGDIHGDRRYDRDNRKNSGNS 554
               DG   KR   +G  +D RD+  +R      D H  RR  +++R+    S
Sbjct: 522 GELRDGSNYKRRYIDGDKQDSRDESSHRNY----DGHQGRREGQEHRRRGSAS 570

Source: Ricinus communis

Species: Ricinus communis

Genus: Ricinus

Family: Euphorbiaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|356573339|ref|XP_003554819.1| PREDICTED: peptidyl-prolyl cis-trans isomerase-like 4-like [Glycine max]

 Score =  660 bits (1704), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 391/610 (64%), Positives = 465/610 (76%), Gaps = 48/610 (7%)

Query: 1   MSVLIVTSLGDIVVDLFVDKCPLTTKNFLKLCKIKYYNGCLFHTVQKDFTAQTGDPTGTG 60
           MSVLIVTSLGD+VVDL  +KCPLT KNFLKLCKIKYYNGCLFHTVQKDFTAQTGDPTGTG
Sbjct: 1   MSVLIVTSLGDLVVDLHTNKCPLTCKNFLKLCKIKYYNGCLFHTVQKDFTAQTGDPTGTG 60

Query: 61  TGGDSVYKFLYGEQARFFGDEIRVDLKHAKTGTVAMASAGENLNASQFYMTLRDNLDYLD 120
           TGGDSVYKFLYG+QARFF DEI +DLKH+KTGTVAMASAGENLNASQFY+TLRD+LDYLD
Sbjct: 61  TGGDSVYKFLYGDQARFFSDEIHIDLKHSKTGTVAMASAGENLNASQFYITLRDDLDYLD 120

Query: 121 EKHTIFGEVAEGLETLSRINESFVDEKNRPYKNIRIKHTYILEDPFDDPAQLAELIPDAS 180
            KHT+FGEVAEG ETL+RINE++VDEK RPYKNIRIKHTYILEDP++DP+QL+  IPDAS
Sbjct: 121 GKHTVFGEVAEGFETLTRINEAYVDEKGRPYKNIRIKHTYILEDPYEDPSQLSVFIPDAS 180

Query: 181 PEGKPKDEVVDEVRLEDDWVPLDEQLSAAELEQVIRSKDARSSAVVLESIGDIPDADIKP 240
           PEGKPKDEV DEVRLEDDWVP+DEQL+ AELE+VIRSK+A S AVVLESIGDIPDA+IKP
Sbjct: 181 PEGKPKDEVDDEVRLEDDWVPMDEQLNPAELEEVIRSKEAHSRAVVLESIGDIPDAEIKP 240

Query: 241 PENVLFVCKLNPVTEDEDLHTIFSRFGTVVSAEIIRDFKTGDSLNYAFIEFENRQACERA 300
           P+NVLFVCKLNPVTEDEDLHTIFSRFGTV  AEIIRD KTGDSL YAFIEFE++++CE+A
Sbjct: 241 PDNVLFVCKLNPVTEDEDLHTIFSRFGTVSMAEIIRDHKTGDSLCYAFIEFEDKRSCEQA 300

Query: 301 YSKMDNALIDDRRIHVDFSQSVSKLWNQFRRRDHQTGKGKGCFKCGGLDHIAKDCTG--- 357
           Y KMDNALIDDRRIHVDFSQSVSKLW+Q+RR+D Q GKG GCFKCG  DHIAKDCTG   
Sbjct: 301 YFKMDNALIDDRRIHVDFSQSVSKLWSQYRRKD-QKGKGGGCFKCGSTDHIAKDCTGDST 359

Query: 358 -QQP-AKYILRDDNRQHGGYSDSRYEMVFDGETPEKSRREKKHRGHDPDDRVERNMNRLS 415
            +QP AKYIL+DDN Q GG  ++RYEMVFDG+  +  RR+ KH+ HD D  VER  +R  
Sbjct: 360 MKQPQAKYILKDDNAQRGG-DNARYEMVFDGDNSQSPRRDIKHQWHDGD-LVERKDHR-- 415

Query: 416 SDLRHRDQERRELSYRQRESDRTREN--REDRRNRDGQESRNVQKQEVRDDDGRYESDHP 473
                R+Q+  + + R R  DR+R +    D + R  + +R++               H 
Sbjct: 416 ---SRREQDMVDSNNRDRYGDRSRGHGGNGDNKARSERGARDL-------------GSHA 459

Query: 474 KSSDTDRYRDWRGGGDYRK------RSADSDSRAERREDGDYRKRNSDNGSHRDRRDDQD 527
            + D DR+    G  DY++      R  D D   +R+++ D RKR+ D+G +R+RR  +D
Sbjct: 460 DTKDRDRHMGRHGDDDYKRKDECDSRKRDEDDGYKRKDEQDSRKRDEDDG-YRERRTSRD 518

Query: 528 YRKKSADGDIHGDRRYDRDNRK---NSGNSEL-------RDAKKEPSYKRGRRDDDSYKR 577
            R+       H +RR DRD RK   +SG  E+       + +  +  YK G RDD+ YK 
Sbjct: 519 DRRNMDSS--HLERRNDRDYRKRPEDSGKQEMKMDSGRRKGSPVDEDYKNG-RDDEDYKH 575

Query: 578 WPEDRGNRRR 587
             E+RG++R+
Sbjct: 576 RREERGHKRQ 585

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|356556666|ref|XP_003546644.1| PREDICTED: peptidyl-prolyl cis-trans isomerase-like 4-like [Glycine max]

 Score =  658 bits (1697), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 388/608 (63%), Positives = 462/608 (75%), Gaps = 44/608 (7%)

Query: 1   MSVLIVTSLGDIVVDLFVDKCPLTTKNFLKLCKIKYYNGCLFHTVQKDFTAQTGDPTGTG 60
           MSVLIVTSLGD+VVDL  +KCPLT KNFLKLCKIKYYNGCLFHTVQKDFTAQTGDPTGTG
Sbjct: 1   MSVLIVTSLGDLVVDLHTNKCPLTCKNFLKLCKIKYYNGCLFHTVQKDFTAQTGDPTGTG 60

Query: 61  TGGDSVYKFLYGEQARFFGDEIRVDLKHAKTGTVAMASAGENLNASQFYMTLRDNLDYLD 120
           TGGDSVYKFLYG+QARFF DEI +DLKH+KTGTV+MASAGENLNASQFY+TLRD+LDYLD
Sbjct: 61  TGGDSVYKFLYGDQARFFSDEIHIDLKHSKTGTVSMASAGENLNASQFYITLRDDLDYLD 120

Query: 121 EKHTIFGEVAEGLETLSRINESFVDEKNRPYKNIRIKHTYILEDPFDDPAQLAELIPDAS 180
            KHT+FGE+AEG ETL+RINE++VDEK RPYKNIRIKHTYILEDP+DDP+QL++ IPDAS
Sbjct: 121 GKHTVFGELAEGFETLTRINEAYVDEKGRPYKNIRIKHTYILEDPYDDPSQLSDFIPDAS 180

Query: 181 PEGKPKDEVVDEVRLEDDWVPLDEQLSAAELEQVIRSKDARSSAVVLESIGDIPDADIKP 240
           PEGKPKDEV DEVRLEDDWVP+DEQL+ AELE+VIRSK+A S AVVLESIGDIPDA+IKP
Sbjct: 181 PEGKPKDEVDDEVRLEDDWVPMDEQLNPAELEEVIRSKEAHSRAVVLESIGDIPDAEIKP 240

Query: 241 PENVLFVCKLNPVTEDEDLHTIFSRFGTVVSAEIIRDFKTGDSLNYAFIEFENRQACERA 300
           P+NVLFVCKLNPVTEDEDLHTIFSRFGTV  AEIIRD KTGDSL YAFIEFE++++CE+A
Sbjct: 241 PDNVLFVCKLNPVTEDEDLHTIFSRFGTVSMAEIIRDQKTGDSLCYAFIEFEDKRSCEQA 300

Query: 301 YSKMDNALIDDRRIHVDFSQSVSKLWNQFRRRDHQTGKGKGCFKCGGLDHIAKDCTGQ-- 358
           Y KMDNALIDDRRIHVDFSQSV+KLW+Q+RR+D Q GKG GCFKCG  DHIAKDCTG+  
Sbjct: 301 YFKMDNALIDDRRIHVDFSQSVAKLWSQYRRKD-QKGKGGGCFKCGSTDHIAKDCTGEAT 359

Query: 359 --QP-AKYILRDDNRQHGGYSDSRYEMVFDGETPEKSRREKKHRGHDPDDRVERNMNRLS 415
             QP AKYIL+DDN Q GG S +RYEMVFD +  +  R++ KH+ HD DD VER  +R  
Sbjct: 360 MKQPQAKYILKDDNVQRGGDS-ARYEMVFDEDNSQHPRQDVKHQRHDRDDPVERKDHR-- 416

Query: 416 SDLRHRDQERRELSYRQRESDRTR------ENR-------------EDRRNRDGQESRNV 456
                RDQ+  + + R R  DR+R      EN+              D+++RD    R+ 
Sbjct: 417 ---SRRDQDMIDSNNRDRYGDRSRGHGGNGENKARSERGVIDLDSNADKKDRDRHMGRHG 473

Query: 457 QKQEVRDDDGRYESDH-PKSSDTDRYRDWRGGGDYRKRSADSDSRAERREDGDYRKRNSD 515
                 DDD + + +H  +  D D    W+   D RKR  D + R    +   Y +RN+D
Sbjct: 474 ------DDDYKRKDEHDSRKRDEDYVYKWKDKRDSRKRDEDDEYRE--IQTSRYDRRNTD 525

Query: 516 NGSHRDRRDDQDYRKKSADGDIHGDRRYDRDNRKNS-GNSELRDAKKEPSYKRGRRDDDS 574
           + SH +RR+ +DYRKK  D     D + D   RK S G+ + ++ +    Y+R  +D+D 
Sbjct: 526 S-SHLERRNSRDYRKKPEDSGTQ-DMKIDSGQRKGSPGDEDYKNGRDHEDYERKMKDED- 582

Query: 575 YKRWPEDR 582
           Y+   E+R
Sbjct: 583 YRNRKEER 590

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

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	589
TAIR|locus:2024852	506	CYP59 "cyclophilin 59" [Arabid	0.797	0.928	0.623	1.8e-157
ZFIN|ZDB-GENE-030131-6251	454	ppil4 "peptidylprolyl isomeras	0.718	0.931	0.477	6.6e-102
UNIPROTKB|E1C3R0	478	PPIL4 "Uncharacterized protein	0.721	0.889	0.456	6e-97
DICTYBASE|DDB_G0292710	489	DDB_G0292710 "peptidylprolyl i	0.721	0.869	0.438	7.8e-95
UNIPROTKB|F1P661	526	PPIL4 "Uncharacterized protein	0.774	0.866	0.426	5e-92
MGI|MGI:1914668	492	Ppil4 "peptidylprolyl isomeras	0.770	0.922	0.420	1.7e-91
RGD|1311051	492	Ppil4 "peptidylprolyl isomeras	0.770	0.922	0.418	1.7e-91
UNIPROTKB|F1N6W2	492	PPIL4 "Uncharacterized protein	0.765	0.916	0.422	5.7e-91
UNIPROTKB|Q8WUA2	492	PPIL4 "Peptidyl-prolyl cis-tra	0.777	0.930	0.409	7.3e-91
WB|WBGene00000890	427	sig-7 [Caenorhabditis elegans	0.697	0.962	0.425	3.9e-89

TAIR|locus:2024852 CYP59 "cyclophilin 59" [Arabidopsis thaliana (taxid:3702)]

 Score = 1503 (534.1 bits), Expect = 1.8e-157, Sum P(2) = 1.8e-157
 Identities = 303/486 (62%), Positives = 354/486 (72%)

Query:     1 MSVLIVTSLGDIVVDLFVDKCPLTTKNFLKLCKIKYYNGCLFHTVQKDFXXXXXXXXXXX 60
             MSVLIVTSLGDIV+DL  DKCPLT KNFLKLCKIKYYNGCLFHTVQKDF           
Sbjct:     1 MSVLIVTSLGDIVIDLHSDKCPLTCKNFLKLCKIKYYNGCLFHTVQKDFTAQTGDPTGTG 60

Query:    61 XXXDSVYKFLYGEQARFFGDEIRVDLKHAKTGTVAMASAGENLNASQFYMTLRDNLDYLD 120
                DS+YKFLYGEQARF+ DEI +DLKH+KTGTVAMAS GENLNASQFY TLRD+LDYLD
Sbjct:    61 AGGDSIYKFLYGEQARFYKDEIHLDLKHSKTGTVAMASGGENLNASQFYFTLRDDLDYLD 120

Query:   121 EKHTIFGEVAEGLETLSRINESFVDEKNRPYKNIRIKHTYILEDPFDDPAQLAELIPDAS 180
              KHT+FG++AEG +TL+RINE++VD KNRPYKNIRIKHT+IL+DPFDDP QLAE++PDAS
Sbjct:   121 GKHTVFGQIAEGFDTLTRINEAYVDPKNRPYKNIRIKHTHILDDPFDDPPQLAEMMPDAS 180

Query:   181 PEGKPKXXXXXXXXXXXXXXPLDEQLSAAELEQVIRSKDARSSAVVLESIGDIPDADIKP 240
             PEGKPK              P+DE+L A ELE+VIR K A SSAVVLESIGDIP+A++KP
Sbjct:   181 PEGKPKEEVKDDVRLEDDWVPMDEELGAQELEEVIREKAAHSSAVVLESIGDIPEAEVKP 240

Query:   241 PENVLFVCKLNPVTEDEDLHTIFSRFGTVVSAEIIRDFKTGDSLNYAFIEFENRQACERA 300
             P+NVLFVCKLNPVTEDEDLHTIFSRFGTVVSA++IRDFKTGDSL YAFIEFEN+++CE+A
Sbjct:   241 PDNVLFVCKLNPVTEDEDLHTIFSRFGTVVSADVIRDFKTGDSLCYAFIEFENKESCEQA 300

Query:   301 YSKMDNALIDDRRIHVDFSQSVSKLWNQFRRRDHQTXXXXXXXXXXXLDHIAKDCTGQQP 360
             Y KMDNALIDDRRIHVDFSQSVSKLW+QFR++D Q             DHIAKDC G   
Sbjct:   301 YFKMDNALIDDRRIHVDFSQSVSKLWSQFRQKDSQKGKGNGCFKCGSTDHIAKDCVGGPS 360

Query:   361 AKYILRDDNRQHGGYSDSRYEMVFDG---ETP-----EKSRREKKHRG--HDPDDRVERN 410
             +K+I++D NRQHGG     YEMVF+G   ETP     E+ R EK  R   H   +   ++
Sbjct:   361 SKFIVKDQNRQHGG--GEGYEMVFEGDVHETPKHNSHERERSEKIQRRSPHGNGEGKRQH 418

Query:   411 MNRLSSDLRHRDQE-RRELS--YRQXXXXXXXXXXXXXXXXXGQESRNVQKQEVRD-DDG 466
              +      R  D+E  REL   +R+                  +ESR+ + +  RD DD 
Sbjct:   419 RDERDDGRRQHDREDARELERKHRERKERESREDEDRRRRRRREESRDKESRRERDEDDH 478

Query:   467 RYESDH 472
             R   D+
Sbjct:   479 RSHRDY 484

GO:0000166 "nucleotide binding" evidence=IEA

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

GO:0003755 "peptidyl-prolyl cis-trans isomerase activity" evidence=IEA;ISS

GO:0005634 "nucleus" evidence=ISM;IDA

GO:0006457 "protein folding" evidence=IEA

GO:0008270 "zinc ion binding" evidence=IEA

GO:0003723 "RNA binding" evidence=IDA

GO:0005515 "protein binding" evidence=IPI

GO:0005829 "cytosol" evidence=IDA

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

ZFIN|ZDB-GENE-030131-6251 ppil4 "peptidylprolyl isomerase (cyclophilin)-like 4" [Danio rerio (taxid:7955)]

 Score = 965 (344.8 bits), Expect = 6.6e-102, Sum P(2) = 6.6e-102
 Identities = 209/438 (47%), Positives = 278/438 (63%)

Query:     1 MSVLIVTSLGDIVVDLFVDKCPLTTKNFLKLCKIKYYNGCLFHTVQKDFXXXXXXXXXXX 60
             M+VL+ T+LGDIV+DL+ ++ P  + NFLKLCKIKYYN CL H VQ+DF           
Sbjct:     1 MAVLLETTLGDIVIDLYTEERPKASLNFLKLCKIKYYNYCLIHNVQRDFIIQTGDPTGTG 60

Query:    61 XXXDSVYKFLYGEQARFFGDEIRVDLKHAKTGTVAMASAGENLNASQFYMTLRDNLDYLD 120
                +SV+  LYG+QARFF  E    +KH K GTV+M + G + + SQF +T  +N+DYLD
Sbjct:    61 RGGESVFCKLYGDQARFFESEKMPRIKHRKKGTVSMVNNGSDQHGSQFLITTGENVDYLD 120

Query:   121 EKHTIFGEVAEGLETLSRINESFVDEKNRPYKNIRIKHTYILEDPFDDPAQLAELIPDAS 180
               HT+FGEV EG++ L++INE+FVD    P+++IRI HT IL+DPFDDPA L   +PD S
Sbjct:   121 GVHTVFGEVTEGMDVLAKINETFVDNDFIPFQDIRINHTVILDDPFDDPAGLP--VPDRS 178

Query:   181 PEGKPKXXXXXXXXXXXXXXPLDEQLSAAELEQVIRSKDARSSAVVLESIGDIPDADIKP 240
             PE   K                DE     EL+++I+ K+A++ A++LE +GD+PDADIKP
Sbjct:   179 PE-PTKQQLDSGRIGADEAINDDEGKDPEELDELIKDKEAKTQAILLEMVGDLPDADIKP 237

Query:   241 PENVLFVCKLNPVTEDEDLHTIFSRFGTVVSAEIIRDFKTGDSLNYAFIEFENRQACERA 300
             PENVLFVCKLNPVT DEDL  IFSRFG +   EIIRD+KTG+SL YAFIEFE  + CE+A
Sbjct:   238 PENVLFVCKLNPVTTDEDLEIIFSRFGLIKCCEIIRDWKTGESLCYAFIEFEKEEDCEKA 297

Query:   301 YSKMDNALIDDRRIHVDFSQSVSKLWNQFRRRDHQTXXXXXXXXXXXLDHIAK----D-C 355
             Y KMDN LIDDRRIHVDFSQSVSK+  +++ +  +            LD+ AK    D  
Sbjct:   298 YFKMDNVLIDDRRIHVDFSQSVSKI--KWKGKGGKYTKDDFKAYEKDLDNKAKLALKDKV 355

Query:   356 TGQQPAKYILRDDNRQHGGYSDSRYEMVFDGETPEKSRREKKHRGHDPDD-RVERNMNRL 414
               +Q ++Y L  D  +  G  D R +   + +    S R K  R  D D+ R E++ +R 
Sbjct:   356 KSKQDSRYELLLDEDEDDGRKDDREKR--ERKRHSDSERTKDKRSKDRDESRREKDKSRQ 413

Query:   415 SSDLRHRDQERRELSYRQ 432
              S  R RD+ER++   R+
Sbjct:   414 RS--RSRDRERQKDKQRE 429

GO:0000166 "nucleotide binding" evidence=IEA

GO:0006457 "protein folding" evidence=IEA

GO:0003676 "nucleic acid binding" evidence=IEA

GO:0003755 "peptidyl-prolyl cis-trans isomerase activity" evidence=IEA

GO:0005575 "cellular_component" evidence=ND

GO:0016853 "isomerase activity" evidence=IEA

UNIPROTKB|E1C3R0 PPIL4 "Uncharacterized protein" [Gallus gallus (taxid:9031)]

 Score = 937 (334.9 bits), Expect = 6.0e-97, Sum P(2) = 6.0e-97
 Identities = 203/445 (45%), Positives = 275/445 (61%)

Query:     1 MSVLIVTSLGDIVVDLFVDKCPLTTKNFLKLCKIKYYNGCLFHTVQKDFXXXXXXXXXXX 60
             M+VL+ T+LGD+V+DL+ ++ P    NFLKLCKIKYYN CL + VQ+DF           
Sbjct:     1 MAVLLETTLGDLVIDLYTEERPRACLNFLKLCKIKYYNYCLIYNVQRDFIIQTGDPMGTG 60

Query:    61 XXXDSVYKFLYGEQARFFGDEIRVDLKHAKTGTVAMASAGENLNASQFYMTLRDNLDYLD 120
                +S++  LYG+QARFF  E    +KH K GTV+M + G +L+ SQF +T  +NLDYLD
Sbjct:    61 RGGESIFCKLYGDQARFFEAEKVPRIKHKKKGTVSMVNNGSDLHGSQFLITTGENLDYLD 120

Query:   121 EKHTIFGEVAEGLETLSRINESFVDEKNRPYKNIRIKHTYILEDPFDDPAQLAELIPDAS 180
               HT+FGEV EG++ L  INE+FVD+   PY++IRI HT IL+DPFDDP  L   IPD S
Sbjct:   121 GVHTVFGEVTEGMDVLKTINETFVDKDFIPYQDIRINHTVILDDPFDDPPGLP--IPDRS 178

Query:   181 PEGKPKXXXXXXXXXXXXXXPLDEQLSAAELEQVIRSKDARSSAVVLESIGDIPDADIKP 240
             PE   +               +  + SA E+E+V   K+A++ A++LE +GD+PDA++KP
Sbjct:   179 PEPTKEQLDSGRIGADEEIDDMKGR-SADEIEEVQAEKEAKTRAILLEMVGDLPDAEVKP 237

Query:   241 PENVLFVCKLNPVTEDEDLHTIFSRFGTVVSAEIIRDFKTGDSLNYAFIEFENRQACERA 300
             PENVLFVCKLNPVT DEDL  IFSRFG + S E+IRD+KTG+SL YAFIEFE  + CE+A
Sbjct:   238 PENVLFVCKLNPVTTDEDLEIIFSRFGPIKSCEVIRDWKTGESLCYAFIEFEKEEDCEKA 297

Query:   301 YSKMDNALIDDRRIHVDFSQSVSKL-WN----QFRRRDHQTXXXXXXXXXXXLDHIAKDC 355
             Y KMDN LIDDRRIHVDFSQSV+K+ W     Q+ + D +               + +  
Sbjct:   298 YFKMDNVLIDDRRIHVDFSQSVAKIKWKGKGGQYTKDDFKDYEKERDKPSKFA--LKEKV 355

Query:   356 TGQQPAKY-ILRDDNRQHGGYSDS------RYEMVFDGETPEKSRREKKHRGHDPDDRVE 408
               +Q AKY ++ D+  +    S S      + +  +  E  E  +R KK++  D     E
Sbjct:   356 KPKQDAKYDLVLDEEEEESQTSQSHVAKKQKKKKHYHSEDEEDDKRTKKYKDSDRKHEGE 415

Query:   409 RNMNRLSSDL--RHRDQER-RELSY 430
             R   ++ S+   RHR + R +E SY
Sbjct:   416 RCREKMKSEKKDRHRSRSRSQERSY 440

GO:0000166 "nucleotide binding" evidence=IEA

GO:0003676 "nucleic acid binding" evidence=IEA

GO:0003755 "peptidyl-prolyl cis-trans isomerase activity" evidence=IEA

GO:0006457 "protein folding" evidence=IEA

DICTYBASE|DDB_G0292710 DDB_G0292710 "peptidylprolyl isomerase" [Dictyostelium discoideum (taxid:44689)]

 Score = 906 (324.0 bits), Expect = 7.8e-95, Sum P(2) = 7.8e-95
 Identities = 191/436 (43%), Positives = 266/436 (61%)

Query:     1 MSVLIVTSLGDIVVDLFVDKCPLTTKNFLKLCKIKYYNGCLFHTVQKDFXXXXXXXXXXX 60
             MSVLI T+LGDIV+DL  ++CP+T KNFLKLCKIKYYN CLF+ VQKDF           
Sbjct:     1 MSVLIETNLGDIVIDLNTEECPITCKNFLKLCKIKYYNFCLFYNVQKDFLVECGDPSNTG 60

Query:    61 XXXDSVYKFLYGEQARFFGDEIRVDLKHAKTGTVAMASAGENLNASQFYMTLRDNLDYLD 120
                +S+Y  LYG +A++F DEI+  L+H + GTVAMA+  ++ N S+FY+TL+ +L+ L+
Sbjct:    61 KGGESIYGLLYGNEAKYFQDEIKKSLRHNEIGTVAMANTSKDKNDSKFYITLKSDLNELN 120

Query:   121 EKHTIFGEVAEGLETLSRINESFVDEKNRPYKNIRIKHTYILEDPFDDPAQLAELIPDAS 180
             +KHTIFG V EG+E L +IN +F D  NRP +NIRI HT IL+DPF DP  L+E IP+ S
Sbjct:   121 DKHTIFGRVVEGIEVLKKINSTFSDSNNRPLQNIRILHTIILDDPFPDPNGLSEHIPNQS 180

Query:   181 PEGKPKXXXXXXXXXXXXXXPLDEQLSAAELEQVIRSKDARSSAVVLESIGDIPDADIKP 240
             P+   +                +   +  E+ ++I  KDA+S + +LE IG +P ADI+P
Sbjct:   181 PKFIKQSKTDDRFEIDEDLDKENRGKTKEEINEIIDEKDAKSRSELLEMIGVLPSADIRP 240

Query:   241 PENVLFVCKLNPVTEDEDLHTIFSRFGTVVSAEIIRDFKTGDSLNYAFIEFENRQACERA 300
             P++VLFVCKLNP+TE EDL  +FS+ GTV S E++RD  T DSL YAF+E+  ++ CE+A
Sbjct:   241 PDHVLFVCKLNPITEAEDLELVFSQCGTVKSCEVVRDKVTNDSLCYAFVEYSTKEECEKA 300

Query:   301 YSKMDNALIDDRRIHVDFSQSVSKLWNQFRRRDHQTXXXXXXXXXXXLDHIA-KDC---T 356
             Y K++N LID+RRIHVDF QSV+K+ N      +               HI  K+    +
Sbjct:   301 YLKLENILIDERRIHVDFCQSVAKVRNNQNSLKNFLTRGKGGSGRLDRKHILNKNYQQES 360

Query:   357 GQQPAKYILRDDN---RQHGGYSDSRYEMVFDGETPEKSRREKKHRGHDPDDR-VERNM- 411
             G +   Y+  DD    +Q     DSR   +    +   S  + +++  +  DR   R+  
Sbjct:   361 GTKGYNYVDDDDRNFKKQKSNEKDSRERDMKSSSSSSSSESDNRYKDRNHHDRNYNRSYD 420

Query:   412 --NRLSSDLRHRDQER 425
               NR   D R RD+ER
Sbjct:   421 RDNRNKDDERERDRER 436

GO:0006457 "protein folding" evidence=IEA

GO:0003755 "peptidyl-prolyl cis-trans isomerase activity" evidence=IEA

GO:0003676 "nucleic acid binding" evidence=IEA

GO:0000413 "protein peptidyl-prolyl isomerization" evidence=IEA

GO:0000166 "nucleotide binding" evidence=IEA

GO:0016853 "isomerase activity" evidence=IEA

UNIPROTKB|F1P661 PPIL4 "Uncharacterized protein" [Canis lupus familiaris (taxid:9615)]

 Score = 917 (327.9 bits), Expect = 5.0e-92, P = 5.0e-92
 Identities = 207/485 (42%), Positives = 283/485 (58%)

Query:     1 MSVLIVTSLGDIVVDLFVDKCPLTTKNFLKLCKIKYYNGCLFHTVQKDFXXXXXXXXXXX 60
             M+VL+ T+LGD+V+DL+ ++ P    NFLKLCKIKYYN CL H VQ+DF           
Sbjct:    35 MAVLLETTLGDVVIDLYTEERPRACLNFLKLCKIKYYNYCLIHNVQRDFIIQTGDPTGTG 94

Query:    61 XXXDSVYKFLYGEQARFFGDEIRVDLKHAKTGTVAMASAGENLNASQFYMTLRDNLDYLD 120
                +SV+  LYG+QA FF  E    +KH K GTV+M + G + + SQF +T  DNLDYLD
Sbjct:    95 RGGESVFGQLYGDQASFFEAEKVPRIKHKKKGTVSMVNNGSDQHGSQFLITTGDNLDYLD 154

Query:   121 EKHTIFGEVAEGLETLSRINESFVDEKNRPYKNIRIKHTYILEDPFDDPAQLAELIPDAS 180
               HT+FGEV EG++ + +INE+FVD+   PY++IRI HT IL+DPFDDP  L  LIPD S
Sbjct:   155 GVHTVFGEVTEGMDIIKKINETFVDKDFVPYQDIRINHTVILDDPFDDPPDL--LIPDRS 212

Query:   181 PEGKPKXXXXXXXXXXXXXXPLDEQLSAAELEQVIRSKDARSSAVVLESIGDIPDADIKP 240
             PE   +                  + SA E+E++   K+A++ A++LE +GD+PDADIKP
Sbjct:   213 PEPTREQLDSGRIGADEEIDDFKGR-SAEEVEEIKAEKEAKTQAILLEMVGDLPDADIKP 271

Query:   241 PENVLFVCKLNPVTEDEDLHTIFSRFGTVVSAEIIRDFKTGDSLNYAFIEFENRQACERA 300
             PENVLFVCKLNPVT DEDL  IFSRFG + S E+IRD+KTG+SL YAFIEFE  + CE+A
Sbjct:   272 PENVLFVCKLNPVTTDEDLEIIFSRFGPIRSCEVIRDWKTGESLCYAFIEFEKEEDCEKA 331

Query:   301 YSKMDNALIDDRRIHVDFSQSVSKL-WN----QFRRRDHQTXXXXXXXXXXXLDHIAKD- 354
             + KMDN LIDDRRIHVDFSQSV+K+ W     ++ + D +               + KD 
Sbjct:   332 FFKMDNVLIDDRRIHVDFSQSVAKVKWKGKGGKYTKSDFKEYEKEQDKSSNL---VLKDK 388

Query:   355 CTGQQPAKYILRDDNRQHGGYSDSRYEMVFDGETPEKSRREKKHRGHDPDDRVERNMNRL 414
                +Q AKY L  D +      DS+        T +K +++ +H   + +D  E  M   
Sbjct:   389 VKPKQDAKYDLILDEQAE----DSKSS---HSHTSKKHKKKTRHCSEEKED--EDYM--- 436

Query:   415 SSDLRHRDQE-RRELSYRQXXXXXXXXXXXXXXXXXGQESRNVQKQEVRDDDGRYESDHP 473
                +R+ +Q+  RE+ +                     ++R+  +   R+ DG Y + H 
Sbjct:   437 --PIRNTNQDIYREMGFGHYEEEESCWEKQKSEKRDRPQNRS--RSRSRERDGHYSNSHK 492

Query:   474 KSSDT 478
                 T
Sbjct:   493 SKYQT 497

GO:0006457 "protein folding" evidence=IEA

GO:0003755 "peptidyl-prolyl cis-trans isomerase activity" evidence=IEA

GO:0003676 "nucleic acid binding" evidence=IEA

GO:0000166 "nucleotide binding" evidence=IEA

MGI|MGI:1914668 Ppil4 "peptidylprolyl isomerase (cyclophilin)-like 4" [Mus musculus (taxid:10090)]

 Score = 912 (326.1 bits), Expect = 1.7e-91, P = 1.7e-91
 Identities = 202/480 (42%), Positives = 282/480 (58%)

Query:     1 MSVLIVTSLGDIVVDLFVDKCPLTTKNFLKLCKIKYYNGCLFHTVQKDFXXXXXXXXXXX 60
             M+VL+ T+LGD+V+DL+ ++ P    NFLKLCKIKYYN CL H VQ+DF           
Sbjct:     1 MAVLLETTLGDVVIDLYTEERPRACLNFLKLCKIKYYNYCLIHNVQRDFIIQTGDPTGTG 60

Query:    61 XXXDSVYKFLYGEQARFFGDEIRVDLKHAKTGTVAMASAGENLNASQFYMTLRDNLDYLD 120
                +S++  LYG+QA FF  E    +KH K GTV+M + G + + SQF +T  +NLDYLD
Sbjct:    61 RGGESIFGQLYGDQASFFEAEKVPRIKHKKKGTVSMVNNGSDQHGSQFLITTGENLDYLD 120

Query:   121 EKHTIFGEVAEGLETLSRINESFVDEKNRPYKNIRIKHTYILEDPFDDPAQLAELIPDAS 180
               HT+FGEV EG++ + +INE+FVD+   PY++IRI HT IL+DPFDDP  L  LIPD S
Sbjct:   121 GVHTVFGEVTEGMDIVKKINETFVDKDFVPYQDIRINHTVILDDPFDDPPDL--LIPDRS 178

Query:   181 PEGKPKXXXXXXXXXXXXXXPLDEQLSAAELEQVIRSKDARSSAVVLESIGDIPDADIKP 240
             PE   +                  + SA E+E++   K+A++ A++LE +GD+PDADIKP
Sbjct:   179 PEPTKEQLDSGRIGADEEIDDFKGR-SAEEVEEIKAEKEAKTQAILLEMVGDLPDADIKP 237

Query:   241 PENVLFVCKLNPVTEDEDLHTIFSRFGTVVSAEIIRDFKTGDSLNYAFIEFENRQACERA 300
             PENVLFVCKLNPVT DEDL  IFSRFG + S E+IRD+KTG+SL YAFIEFE  + CE+A
Sbjct:   238 PENVLFVCKLNPVTTDEDLEIIFSRFGPIRSCEVIRDWKTGESLCYAFIEFEKEEDCEKA 297

Query:   301 YSKMDNALIDDRRIHVDFSQSVSKL-WN----QFRRRDHQTXXXXXXXXXXXLDHIAKDC 355
             + KMDN LIDDRRIHVDFSQSV+K+ W     ++ + D +            +  + +  
Sbjct:   298 FFKMDNVLIDDRRIHVDFSQSVAKVKWKGKGGKYTKSDFKEYEKEQDKPANLV--LKEKV 355

Query:   356 TGQQPAKYILRDDNRQHGGYSDSRYEMVFDGETPEKSRREKKHRGHDPDDRVERNMNRLS 415
               +Q AKY L  D  + G  S S +       T +K +++ +H   + +D     +   +
Sbjct:   356 KPKQDAKYDLILD--EQGEDSKSSHS-----HTSKKHKKKTRHCSEEKEDEEYMPIKNPN 408

Query:   416 SDLRHRDQERRELSYRQXXXXXXXXXXXXXXXXXGQESRNVQKQEVRDDDGRYESDH-PK 474
              D+       RE+ +                    +++R+  +   R+ DG Y + H PK
Sbjct:   409 QDIY------REMGFGHYEEEESCWEKQKNEKRDRRQNRS--RSRSRERDGHYSNSHKPK 460

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:0003755 "peptidyl-prolyl cis-trans isomerase activity" evidence=IEA

GO:0005575 "cellular_component" evidence=ND

GO:0005634 "nucleus" evidence=IEA

GO:0006457 "protein folding" evidence=IEA

GO:0008150 "biological_process" evidence=ND

GO:0016853 "isomerase activity" evidence=IEA

RGD|1311051 Ppil4 "peptidylprolyl isomerase (cyclophilin)-like 4" [Rattus norvegicus (taxid:10116)]

 Score = 912 (326.1 bits), Expect = 1.7e-91, P = 1.7e-91
 Identities = 201/480 (41%), Positives = 284/480 (59%)

Query:     1 MSVLIVTSLGDIVVDLFVDKCPLTTKNFLKLCKIKYYNGCLFHTVQKDFXXXXXXXXXXX 60
             M+VL+ T+LGD+V+DL+ ++ P    NFLKLCKIKYYN CL H VQ+DF           
Sbjct:     1 MAVLLETTLGDVVIDLYTEERPRACLNFLKLCKIKYYNYCLIHNVQRDFIIQTGDPTGTG 60

Query:    61 XXXDSVYKFLYGEQARFFGDEIRVDLKHAKTGTVAMASAGENLNASQFYMTLRDNLDYLD 120
                +S++  LYG+QA FF  E    +KH K GTV+M + G + + SQF +T  +NLDYLD
Sbjct:    61 RGGESIFGQLYGDQASFFEAEKVPRIKHKKKGTVSMVNNGSDQHGSQFLITTGENLDYLD 120

Query:   121 EKHTIFGEVAEGLETLSRINESFVDEKNRPYKNIRIKHTYILEDPFDDPAQLAELIPDAS 180
               HT+FGEV EG++ + +INE+FVD+   PY++IRI HT IL+DPFDDP  L  LIPD S
Sbjct:   121 GVHTVFGEVTEGMDIVKKINETFVDKDFVPYQDIRINHTVILDDPFDDPPDL--LIPDRS 178

Query:   181 PEGKPKXXXXXXXXXXXXXXPLDEQLSAAELEQVIRSKDARSSAVVLESIGDIPDADIKP 240
             PE   +                  + SA E+E++   K+A++ A++LE +GD+PDADIKP
Sbjct:   179 PEPTKEQLDSGRIGADEEIDDFKGR-SAEEVEEIKAEKEAKTQAILLEMVGDLPDADIKP 237

Query:   241 PENVLFVCKLNPVTEDEDLHTIFSRFGTVVSAEIIRDFKTGDSLNYAFIEFENRQACERA 300
             PENVLFVCKLNPVT DEDL  IFSRFG + S E+IRD+KTG+SL YAFIEFE  + CE+A
Sbjct:   238 PENVLFVCKLNPVTTDEDLEIIFSRFGPIRSCEVIRDWKTGESLCYAFIEFEKEEDCEKA 297

Query:   301 YSKMDNALIDDRRIHVDFSQSVSKLWNQFRRRDHQTXXXXXXXXXXXLDHIAKDCTGQQP 360
             + KMDN LIDDRRIHVDFSQSV+K+  +++ +  +             D         +P
Sbjct:   298 FFKMDNVLIDDRRIHVDFSQSVAKV--KWKGKGGKYTKSDFKEYEKEQD---------KP 346

Query:   361 AKYILRDDNRQHGGYSDSRYEMVFDGETPEKSRREKKH--RGHDPDDR--VERNMNRLSS 416
             A  +L++  +      D++Y+++ D E  E S+    H  + H    R   E   +    
Sbjct:   347 ANLVLKEKVKPK---QDAKYDLILD-EQAEDSKSSHSHTSKKHKKKTRHCSEEKEDEDYM 402

Query:   417 DLRHRDQE-RRELSYRQXXXXXXXXXXXXXXXXXGQESRNVQKQEVRDDDGRYESDH-PK 474
              +++ +Q+  RE+ +                    +++R+  +   R+ DG Y + H PK
Sbjct:   403 PIKNPNQDIYREMGFGHYEEEESCWEKQKNEKRDRRQNRS--RSRSRERDGHYSNSHKPK 460

GO:0000166 "nucleotide binding" evidence=IEA

GO:0003676 "nucleic acid binding" evidence=IEA

GO:0003755 "peptidyl-prolyl cis-trans isomerase activity" evidence=IEA

GO:0006457 "protein folding" evidence=IEA

UNIPROTKB|F1N6W2 PPIL4 "Uncharacterized protein" [Bos taurus (taxid:9913)]

 Score = 907 (324.3 bits), Expect = 5.7e-91, P = 5.7e-91
 Identities = 202/478 (42%), Positives = 278/478 (58%)

Query:     1 MSVLIVTSLGDIVVDLFVDKCPLTTKNFLKLCKIKYYNGCLFHTVQKDFXXXXXXXXXXX 60
             M+VL+ T+LGD+V+DL+ ++ P    NFLKLCKIKYYN CL H VQ+DF           
Sbjct:     1 MAVLLETTLGDVVIDLYTEERPRACLNFLKLCKIKYYNYCLIHNVQRDFIIQTGDPTGTG 60

Query:    61 XXXDSVYKFLYGEQARFFGDEIRVDLKHAKTGTVAMASAGENLNASQFYMTLRDNLDYLD 120
                +SV+  LYG+QA FF  E    +KH K GTV+M + G + + SQF +T  +NLDYLD
Sbjct:    61 RGGESVFGQLYGDQASFFEAEKVPRIKHKKKGTVSMVNNGSDQHGSQFLITTGENLDYLD 120

Query:   121 EKHTIFGEVAEGLETLSRINESFVDEKNRPYKNIRIKHTYILEDPFDDPAQLAELIPDAS 180
               HT+FGEV EG++ + +INE+FVD+   PY++IRI HT IL+DPFDDP  L  LIPD S
Sbjct:   121 GVHTVFGEVTEGMDIIKKINETFVDKDFVPYQDIRINHTVILDDPFDDPPDL--LIPDRS 178

Query:   181 PEGKPKXXXXXXXXXXXXXXPLDEQLSAAELEQVIRSKDARSSAVVLESIGDIPDADIKP 240
             PE   +                  + SA E+E++   K+A++ A++LE +GD+PDADIKP
Sbjct:   179 PEPTREQLDSGRIGADEEIDDFKGR-SAEEVEEIKAEKEAKTQAILLEMVGDLPDADIKP 237

Query:   241 PENVLFVCKLNPVTEDEDLHTIFSRFGTVVSAEIIRDFKTGDSLNYAFIEFENRQACERA 300
             PENVLFVCKLNPVT DEDL  IFSRFG + S E+IRD+KTG+SL YAFIEFE  + CE+A
Sbjct:   238 PENVLFVCKLNPVTTDEDLEIIFSRFGPIRSCEVIRDWKTGESLCYAFIEFEKEEDCEKA 297

Query:   301 YSKMDNALIDDRRIHVDFSQSVSKL-WN----QFRRRDHQTXXXXXXXXXXXLDHIAKD- 354
             + KMDN LIDDRRIHVDFSQSV+K+ W     ++ + D +               + KD 
Sbjct:   298 FFKMDNVLIDDRRIHVDFSQSVAKVKWKGKGGKYTKSDFKEYEKEQDKPSNL---VLKDK 354

Query:   355 CTGQQPAKYILRDDNRQHGGYSDSRYEMVFDGETPEKSRREKKHRGHDPDDRVERNMNRL 414
                +Q AKY L  D +      DS+        T +K +++ +H   + +D     +   
Sbjct:   355 VKPKQDAKYELVLDEQAE----DSK---AGHSHTSKKHKKKTRHCSEEKEDEDYMPIKNT 407

Query:   415 SSDLRHRDQERRELSYRQXXXXXXXXXXXXXXXXXGQESRNVQKQEVRDDDGRYESDH 472
             + D+       RE+ +                     ++R+  +   R+ DG Y + H
Sbjct:   408 NQDIY------REMGFGHYEEEESCWEKQKSEKRDRPQNRS--RSRSRERDGHYSNSH 457

GO:0006457 "protein folding" evidence=IEA

GO:0003755 "peptidyl-prolyl cis-trans isomerase activity" evidence=IEA

GO:0003676 "nucleic acid binding" evidence=IEA

GO:0000166 "nucleotide binding" evidence=IEA

UNIPROTKB|Q8WUA2 PPIL4 "Peptidyl-prolyl cis-trans isomerase-like 4" [Homo sapiens (taxid:9606)]

 Score = 906 (324.0 bits), Expect = 7.3e-91, P = 7.3e-91
 Identities = 198/483 (40%), Positives = 281/483 (58%)

Query:     1 MSVLIVTSLGDIVVDLFVDKCPLTTKNFLKLCKIKYYNGCLFHTVQKDFXXXXXXXXXXX 60
             M+VL+ T+LGD+V+DL+ ++ P    NFLKLCKIKYYN CL H VQ+DF           
Sbjct:     1 MAVLLETTLGDVVIDLYTEERPRACLNFLKLCKIKYYNYCLIHNVQRDFIIQTGDPTGTG 60

Query:    61 XXXDSVYKFLYGEQARFFGDEIRVDLKHAKTGTVAMASAGENLNASQFYMTLRDNLDYLD 120
                +S++  LYG+QA FF  E    +KH K GTV+M + G + + SQF +T  +NLDYLD
Sbjct:    61 RGGESIFGQLYGDQASFFEAEKVPRIKHKKKGTVSMVNNGSDQHGSQFLITTGENLDYLD 120

Query:   121 EKHTIFGEVAEGLETLSRINESFVDEKNRPYKNIRIKHTYILEDPFDDPAQLAELIPDAS 180
               HT+FGEV EG++ + +INE+FVD+   PY++IRI HT IL+DPFDDP  L  LIPD S
Sbjct:   121 GVHTVFGEVTEGMDIIKKINETFVDKDFVPYQDIRINHTVILDDPFDDPPDL--LIPDRS 178

Query:   181 PEGKPKXXXXXXXXXXXXXXPLDEQLSAAELEQVIRSKDARSSAVVLESIGDIPDADIKP 240
             PE   +                  + SA E+E++   K+A++ A++LE +GD+PDADIKP
Sbjct:   179 PEPTREQLDSGRIGADEEIDDFKGR-SAEEVEEIKAEKEAKTQAILLEMVGDLPDADIKP 237

Query:   241 PENVLFVCKLNPVTEDEDLHTIFSRFGTVVSAEIIRDFKTGDSLNYAFIEFENRQACERA 300
             PENVLFVCKLNPVT DEDL  IFSRFG + S E+IRD+KTG+SL YAFIEFE  + CE+A
Sbjct:   238 PENVLFVCKLNPVTTDEDLEIIFSRFGPIRSCEVIRDWKTGESLCYAFIEFEKEEDCEKA 297

Query:   301 YSKMDNALIDDRRIHVDFSQSVSKLWNQFRRRDHQTXXXXXXXXXXXLDHIAKDCTGQQP 360
             + KMDN LIDDRRIHVDFSQSV+K+  +++ +  +             D         +P
Sbjct:   298 FFKMDNVLIDDRRIHVDFSQSVAKV--KWKGKGGKYTKSDFKEYEKEQD---------KP 346

Query:   361 AKYILRDDNRQHGGYSDSRYEMVFDGETPEK----SRREKKHRGHDPDDRVERNMNRLSS 416
                +L+D  +      D++Y+++ D +  +     S   KKH+        E+  +    
Sbjct:   347 PNLVLKDKVKPK---QDTKYDLILDEQAEDSKSSHSHTSKKHKKKTHHCSEEKE-DEDYM 402

Query:   417 DLRHRDQE-RRELSYRQXXXXXXXXXXXXXXXXXGQESRNVQKQEVRDDDGRYESDHPKS 475
              +++ +Q+  RE+ +                     ++R+  +   R+ DG Y + H   
Sbjct:   403 PIKNTNQDIYREMGFGHYEEEESCWEKQKSEKRDRTQNRS--RSRSRERDGHYSNSHKSK 460

Query:   476 SDT 478
               T
Sbjct:   461 YQT 463

GO:0000166 "nucleotide binding" evidence=IEA

GO:0003723 "RNA binding" evidence=IEA

GO:0006457 "protein folding" evidence=IEA

GO:0003755 "peptidyl-prolyl cis-trans isomerase activity" evidence=IEA

GO:0005634 "nucleus" evidence=IEA

WB|WBGene00000890 sig-7 [Caenorhabditis elegans (taxid:6239)]

 Score = 857 (306.7 bits), Expect = 3.9e-89, Sum P(2) = 3.9e-89
 Identities = 181/425 (42%), Positives = 256/425 (60%)

Query:     1 MSVLIVTSLGDIVVDLFVDKCPLTTKNFLKLCKIKYYNGCLFHTVQKDFXXXXXXXXXXX 60
             M+VLI T+LGD+++DLFV + P  + NFLKLCK KYYN   FH++++++           
Sbjct:     1 MAVLIETTLGDLIIDLFVKERPRCSLNFLKLCKKKYYNLNQFHSIERNYVAQTGDPTGTG 60

Query:    61 XXXDSVYKFLYGEQARFFGDEIRVDLKHAKTGTVAMASAGENLNASQFYMTLRDNLDYLD 120
                +SVY  +YGEQ R+F  E    ++H + G V+  + G+N+  SQF++TL +NLDYLD
Sbjct:    61 KGGESVYSDMYGEQGRYFEREDLPKMRHTRMGIVSFVNNGDNMLGSQFFITLGENLDYLD 120

Query:   121 EKHTIFGEVAEGLETLSRINESFVDEKNRPYKNIRIKHTYILEDPFDDPAQLAELIPDAS 180
             ++HTIFG+V EGLETL ++NE   D  NRP+K+IRI HT +L+DPFD+ A+++   P  S
Sbjct:   121 DQHTIFGQVTEGLETLEKLNEQLADTNNRPFKDIRISHTIVLDDPFDEDARIS--FPPRS 178

Query:   181 PEGKPKXXXXXXXXXXXXXXPLDEQLSAAELEQVIRSKDARSSAVVLESIGDIPDADIKP 240
             P    +                DE  +A E+ + ++ ++    A +LE +GD+ DAD  P
Sbjct:   179 PSPTYEMLVKTDQIALDEKEDEDEGKTAEEIAEELQQREMAEQAQILEMVGDLKDADEVP 238

Query:   241 PENVLFVCKLNPVTEDEDLHTIFSRFGTVVSAEIIRDFKTGDSLNYAFIEFENRQACERA 300
             PENVLFVCKLNPVT DEDL  IFSRFG + + EI+RD ++GDSL YAFIEF+N ++CE+A
Sbjct:   239 PENVLFVCKLNPVTTDEDLEIIFSRFGKINNCEIVRDRRSGDSLQYAFIEFDNAKSCEQA 298

Query:   301 YSKMDNALIDDRRIHVDFSQSVSKLWNQFRRRDHQTXXXXXXXXXXXLDHIAKDCTGQQP 360
             + KMDN LIDDRRIHVDFSQSVS+ + +++ +  Q               + K    + P
Sbjct:   299 FFKMDNVLIDDRRIHVDFSQSVSQNY-KYKPKSQQQEAPKRRQSPQRRPEV-KRSHQRSP 356

Query:   361 AKYILRDDNRQHGGYSDSRYEMVFDGETPEKSRREKKHRGHDPDDRVERNMNRLSSDLRH 420
             +    R  + +     D R E       P + RR   +  H   DR  R+ NR   D  H
Sbjct:   357 SPRRRRSPSPKKDKKRDYRRE-------PARRRRSSDN--HRDRDRSYRDNNRDRRD-NH 406

Query:   421 RDQER 425
             RD +R
Sbjct:   407 RDSDR 411

GO:0003676 "nucleic acid binding" evidence=IEA

GO:0003755 "peptidyl-prolyl cis-trans isomerase activity" evidence=IEA

GO:0006457 "protein folding" evidence=IEA

GO:0009792 "embryo development ending in birth or egg hatching" evidence=IMP

GO:0040007 "growth" evidence=IMP

GO:0002119 "nematode larval development" evidence=IMP

GO:0000003 "reproduction" evidence=IMP

GO:0040035 "hermaphrodite genitalia development" evidence=IMP

---

Prediction of Enzyme Commission (EC) Number

EC Number Prediction by Annotation Transfer from SWISS-PROT Entries

Original result of BLAST against SWISS-PROT

ID	Name	Annotated EC number	Identity	Query coverage	Hit coverage	RBH(Q2H)	RBH(H2Q)
Q4WAQ9	PPIL4_ASPFU	5, ., 2, ., 1, ., 8	0.5037	0.6230	0.7995	yes	no

EC Number Prediction by Ezypred Server

Original result from Ezypred Server

Fail to connect to Ezypred Server

EC Number Prediction by EFICAz Software

Prediction Level	EC number	Confidence of Prediction
3rd Layer	5.2.1	0.921
4th Layer	5.2.1.8	0.914

---

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	589
cd01921	166	cd01921, cyclophilin_RRM, cyclophilin_RRM: cycloph	1e-97
cd12235	83	cd12235, RRM_PPIL4, RNA recognition motif in pepti	1e-55
cd01928	153	cd01928, Cyclophilin_PPIL3_like, Cyclophilin_PPIL3	1e-50
pfam00160	144	pfam00160, Pro_isomerase, Cyclophilin type peptidy	3e-50
cd01923	159	cd01923, cyclophilin_RING, cyclophilin_RING: cyclo	3e-46
cd00317	146	cd00317, cyclophilin, cyclophilin: cyclophilin-typ	5e-46
cd01925	171	cd01925, cyclophilin_CeCYP16-like, cyclophilin_CeC	9e-46
cd01927	148	cd01927, cyclophilin_WD40, cyclophilin_WD40: cyclo	3e-44
COG0652	158	COG0652, PpiB, Peptidyl-prolyl cis-trans isomerase	3e-42
cd01922	146	cd01922, cyclophilin_SpCYP2_like, cyclophilin_SpCY	6e-41
cd01926	164	cd01926, cyclophilin_ABH_like, cyclophilin_ABH_lik	2e-31
PTZ00060	183	PTZ00060, PTZ00060, cyclophilin; Provisional	3e-25
PLN03149	186	PLN03149, PLN03149, peptidyl-prolyl isomerase H (c	6e-22
cd12237	93	cd12237, RRM_snRNP35, RNA recognition motif found	9e-20
smart00360	73	smart00360, RRM, RNA recognition motif	9e-20
cd01920	155	cd01920, cyclophilin_EcCYP_like, cyclophilin_EcCYP	2e-17
cd00590	72	cd00590, RRM_SF, RNA recognition motif (RRM) super	2e-17
PRK10903	190	PRK10903, PRK10903, peptidyl-prolyl cis-trans isom	2e-14
cd01924	176	cd01924, cyclophilin_TLP40_like, cyclophilin_TLP40	2e-13
pfam00076	70	pfam00076, RRM_1, RNA recognition motif	4e-13
PRK10791	164	PRK10791, PRK10791, peptidyl-prolyl cis-trans isom	5e-13
cd12236	91	cd12236, RRM_snRNP70, RNA recognition motif in U1	9e-13
cd12382	80	cd12382, RRM_RBMX_like, RNA recognition motif in h	1e-12
cd12365	73	cd12365, RRM_RNPS1, RNA recognition motif in RNA-b	6e-12
COG0724	306	COG0724, COG0724, RNA-binding proteins (RRM domain	7e-12
pfam13893	56	pfam13893, RRM_5, RNA recognition motif	1e-11
cd12378	80	cd12378, RRM1_I_PABPs, RNA recognition motif 1 in	2e-11
cd12362	73	cd12362, RRM3_CELF1-6, RNA recognition motif 3 in	5e-11
cd12392	81	cd12392, RRM2_SART3, RNA recognition motif 2 in sq	8e-11
cd12335	83	cd12335, RRM2_SF3B4, RNA recognition motif 2 in sp	8e-11
cd12384	76	cd12384, RRM_RBM24_RBM38_like, RNA recognition mot	1e-10
cd12353	75	cd12353, RRM2_TIA1_like, RNA recognition motif 2 i	1e-10
PRK12678	672	PRK12678, PRK12678, transcription termination fact	1e-10
cd12389	77	cd12389, RRM2_RAVER, RNA recognition motif 2 in ri	2e-10
cd12399	78	cd12399, RRM_HP0827_like, RNA recognition motif in	2e-10
cd12447	76	cd12447, RRM1_gar2, RNA recognition motif 1 in yea	3e-10
cd12363	78	cd12363, RRM_TRA2, RNA recognition motif in transf	3e-10
cd12343	66	cd12343, RRM1_2_CoAA_like, RNA recognition motif 1	9e-10
PRK12678	672	PRK12678, PRK12678, transcription termination fact	2e-09
cd12375	77	cd12375, RRM1_Hu_like, RNA recognition motif 1 in	2e-09
cd12312	84	cd12312, RRM_SRSF10_SRSF12, RNA recognition motif	2e-09
TIGR01628	562	TIGR01628, PABP-1234, polyadenylate binding protei	4e-09
cd12298	78	cd12298, RRM3_Prp24, RNA recognition motif 3 in fu	4e-09
cd12242	73	cd12242, RRM_SLIRP, RNA recognition motif found in	5e-09
cd12318	82	cd12318, RRM5_RBM19_like, RNA recognition motif 5	7e-09
cd12398	75	cd12398, RRM_CSTF2_RNA15_like, RNA recognition mot	9e-09
cd12347	73	cd12347, RRM_PPIE, RNA recognition motif in cyclop	1e-08
cd12619	75	cd12619, RRM2_PUB1, RNA recognition motif 2 in yea	1e-08
cd12412	80	cd12412, RRM_DAZL_BOULE, RNA recognition motif in	1e-08
cd12552	77	cd12552, RRM_Nop15p, RNA recognition motif in yeas	1e-08
cd12379	77	cd12379, RRM2_I_PABPs, RNA recognition motif 2 fou	2e-08
cd12324	88	cd12324, RRM_RBM8, RNA recognition motif in RNA-bi	2e-08
pfam14259	69	pfam14259, RRM_6, RNA recognition motif (a	2e-08
cd12650	78	cd12650, RRM1_Hu, RNA recognition motif 1 in the H	2e-08
cd12325	72	cd12325, RRM1_hnRNPA_hnRNPD_like, RNA recognition	2e-08
cd12418	75	cd12418, RRM_Aly_REF_like, RNA recognition motif i	2e-08
cd12414	76	cd12414, RRM2_RBM28_like, RNA recognition motif 2	3e-08
cd12316	74	cd12316, RRM3_RBM19_RRM2_MRD1, RNA recognition mot	3e-08
cd12449	80	cd12449, RRM_CIRBP_RBM3, RNA recognition motif in	4e-08
cd12307	74	cd12307, RRM_NIFK_like, RNA recognition motif in n	5e-08
PLN03134	144	PLN03134, PLN03134, glycine-rich RNA-binding prote	5e-08
PRK12678	672	PRK12678, PRK12678, transcription termination fact	6e-08
cd12344	81	cd12344, RRM1_SECp43_like, RNA recognition motif 1	6e-08
cd12371	77	cd12371, RRM2_PUF60, RNA recognition motif 2 in (U	7e-08
cd12229	81	cd12229, RRM_G3BP, RNA recognition motif (RRM) in	1e-07
cd12411	89	cd12411, RRM_ist3_like, RNA recognition motif in i	1e-07
cd12566	79	cd12566, RRM2_MRD1, RNA recognition motif 2 in yea	1e-07
cd12330	75	cd12330, RRM2_Hrp1p, RNA recognition motif 2 in ye	1e-07
cd12290	80	cd12290, RRM1_LARP7, RNA recognition motif 1 in La	2e-07
cd12313	84	cd12313, RRM1_RRM2_RBM5_like, RNA recognition moti	2e-07
cd12454	80	cd12454, RRM2_RIM4_like, RNA recognition motif 2 i	2e-07
cd12408	77	cd12408, RRM_eIF3G_like, RNA recognition motif in	2e-07
cd12284	73	cd12284, RRM2_RBM23_RBM39, RNA recognition motif 2	2e-07
cd12649	81	cd12649, RRM1_SXL, RNA recognition motif 1 in Dros	2e-07
cd12377	78	cd12377, RRM3_Hu, RNA recognition motif 3 in the H	2e-07
TIGR01628	562	TIGR01628, PABP-1234, polyadenylate binding protei	3e-07
cd12674	79	cd12674, RRM1_Nop4p, RNA recognition motif 1 in ye	3e-07
cd12641	89	cd12641, RRM_TRA2B, RNA recognition motif in Trans	3e-07
cd12422	85	cd12422, RRM2_PTBP1_hnRNPL_like, RNA recognition m	5e-07
cd12618	80	cd12618, RRM2_TIA1, RNA recognition motif 2 in nuc	6e-07
cd12642	79	cd12642, RRM_TRA2A, RNA recognition motif in trans	6e-07
cd12361	77	cd12361, RRM1_2_CELF1-6_like, RNA recognition moti	7e-07
cd12617	80	cd12617, RRM2_TIAR, RNA recognition motif 2 in nuc	8e-07
cd12415	82	cd12415, RRM3_RBM28_like, RNA recognition motif 3	8e-07
cd12393	78	cd12393, RRM_ZCRB1, RNA recognition motif in Zinc	9e-07
cd12613	80	cd12613, RRM2_NGR1_NAM8_like, RNA recognition moti	9e-07
cd12577	76	cd12577, RRM1_Hrp1p, RNA recognition motif 1 in ye	1e-06
cd12251	72	cd12251, RRM3_hnRNPR_like, RNA recognition motif 3	2e-06
cd12769	81	cd12769, RRM1_HuR, RNA recognition motif 1 in vert	2e-06
cd12346	72	cd12346, RRM3_NGR1_NAM8_like, RNA recognition moti	2e-06
cd12376	79	cd12376, RRM2_Hu_like, RNA recognition motif 2 in	2e-06
cd12453	86	cd12453, RRM1_RIM4_like, RNA recognition motif 1 i	2e-06
cd12654	86	cd12654, RRM3_HuB, RNA recognition motif 3 in vert	3e-06
cd12655	85	cd12655, RRM3_HuC, RNA recognition motif 3 in vert	3e-06
cd12223	84	cd12223, RRM_SR140, RNA recognition motif (RRM) in	3e-06
cd12391	72	cd12391, RRM1_SART3, RNA recognition motif 1 in sq	3e-06
TIGR01661	352	TIGR01661, ELAV_HUD_SF, ELAV/HuD family splicing f	3e-06
cd12675	83	cd12675, RRM2_Nop4p, RNA recognition motif 2 in ye	5e-06
TIGR01645	612	TIGR01645, half-pint, poly-U binding splicing fact	6e-06
cd12273	71	cd12273, RRM1_NEFsp, RNA recognition motif 1 in ve	6e-06
TIGR01659	346	TIGR01659, sex-lethal, sex-lethal family splicing	7e-06
cd12656	86	cd12656, RRM3_HuD, RNA recognition motif 3 in vert	7e-06
cd12380	80	cd12380, RRM3_I_PABPs, RNA recognition motif 3 fou	7e-06
cd12407	76	cd12407, RRM_FOX1_like, RNA recognition motif in v	7e-06
cd12421	74	cd12421, RRM1_PTBP1_hnRNPL_like, RNA recognition m	9e-06
TIGR01642	509	TIGR01642, U2AF_lg, U2 snRNP auxilliary factor, la	9e-06
cd12329	75	cd12329, RRM2_hnRNPD_like, RNA recognition motif 2	9e-06
TIGR01659	346	TIGR01659, sex-lethal, sex-lethal family splicing	1e-05
cd12395	73	cd12395, RRM2_RBM34, RNA recognition motif 2 in RN	1e-05
cd12652	79	cd12652, RRM2_Hu, RNA recognition motif 2 in the H	1e-05
cd12565	76	cd12565, RRM1_MRD1, RNA recognition motif 1 in yea	1e-05
PRK12678	672	PRK12678, PRK12678, transcription termination fact	2e-05
TIGR01642	509	TIGR01642, U2AF_lg, U2 snRNP auxilliary factor, la	2e-05
cd12340	67	cd12340, RBD_RRM1_NPL3, RNA recognition motif 1 in	2e-05
cd12345	80	cd12345, RRM2_SECp43_like, RNA recognition motif 2	2e-05
cd12352	72	cd12352, RRM1_TIA1_like, RNA recognition motif 1 i	2e-05
cd12381	79	cd12381, RRM4_I_PABPs, RNA recognition motif 4 in	2e-05
cd12328	73	cd12328, RRM2_hnRNPA_like, RNA recognition motif 2	2e-05
cd12639	79	cd12639, RRM3_CELF3_4_5_6, RNA recognition motif 2	2e-05
cd12366	81	cd12366, RRM1_RBM45, RNA recognition motif 1 in RN	2e-05
cd12640	79	cd12640, RRM3_Bruno_like, RNA recognition motif 3	2e-05
cd12417	74	cd12417, RRM_SAFB_like, RNA recognition motif in t	3e-05
cd12673	81	cd12673, RRM_BOULE, RNA recognition motif in prote	3e-05
cd12311	73	cd12311, RRM_SRSF2_SRSF8, RNA recognition motif in	3e-05
cd12310	72	cd12310, RRM3_Spen, RNA recognition motif 3 in the	3e-05
cd12446	84	cd12446, RRM_RBM25, RNA recognition motif in eukar	3e-05
cd12244	79	cd12244, RRM2_MSSP, RNA recognition motif 2 in the	3e-05
cd12579	80	cd12579, RRM2_hnRNPA0, RNA recognition motif 2 in	3e-05
PRK12678	672	PRK12678, PRK12678, transcription termination fact	4e-05
TIGR01628	562	TIGR01628, PABP-1234, polyadenylate binding protei	4e-05
cd12383	83	cd12383, RRM_RBM42, RNA recognition motif in RNA-b	4e-05
cd12243	71	cd12243, RRM1_MSSP, RNA recognition motif 1 in the	4e-05
cd12651	79	cd12651, RRM2_SXL, RNA recognition motif 2 in Dros	4e-05
cd12413	79	cd12413, RRM1_RBM28_like, RNA recognition motif 1	5e-05
cd12297	78	cd12297, RRM2_Prp24, RNA recognition motif 2 in fu	5e-05
TIGR01661	352	TIGR01661, ELAV_HUD_SF, ELAV/HuD family splicing f	6e-05
cd12638	92	cd12638, RRM3_CELF1_2, RNA recognition motif 3 in	6e-05
cd12450	77	cd12450, RRM1_NUCLs, RNA recognition motif 1 found	6e-05
TIGR01642	509	TIGR01642, U2AF_lg, U2 snRNP auxilliary factor, la	7e-05
cd12355	80	cd12355, RRM_RBM18, RNA recognition motif in eukar	7e-05
cd12614	74	cd12614, RRM1_PUB1, RNA recognition motif 1 in yea	8e-05
cd12283	73	cd12283, RRM1_RBM39_like, RNA recognition motif 1	2e-04
cd12559	84	cd12559, RRM_SRSF10, RNA recognition motif in seri	2e-04
cd12373	73	cd12373, RRM_SRSF3_like, RNA recognition motif in	2e-04
cd12560	84	cd12560, RRM_SRSF12, RNA recognition motif in seri	2e-04
cd12609	68	cd12609, RRM2_CoAA, RNA recognition motif 2 in ver	2e-04
cd12608	69	cd12608, RRM1_CoAA, RNA recognition motif 1 in ver	2e-04
cd12306	73	cd12306, RRM_II_PABPs, RNA recognition motif in ty	2e-04
cd12232	89	cd12232, RRM3_U2AF65, RNA recognition motif 3 foun	2e-04
cd12771	83	cd12771, RRM1_HuB, RNA recognition motif 1 in vert	2e-04
cd12406	78	cd12406, RRM4_NCL, RNA recognition motif 4 in vert	2e-04
cd12429	74	cd12429, RRM_DNAJC17, RNA recognition motif in the	3e-04
cd12653	84	cd12653, RRM3_HuR, RNA recognition motif 3 in vert	3e-04
cd12578	78	cd12578, RRM1_hnRNPA_like, RNA recognition motif 1	3e-04
cd12334	74	cd12334, RRM1_SF3B4, RNA recognition motif 1 in sp	4e-04
cd12567	79	cd12567, RRM3_RBM19, RNA recognition motif 3 in RN	4e-04
cd12770	83	cd12770, RRM1_HuD, RNA recognition motif 1 in vert	4e-04
cd12555	87	cd12555, RRM2_RBM15, RNA recognition motif 2 in ve	4e-04
cd12240	78	cd12240, RRM_NCBP2, RNA recognition motif found in	5e-04
cd12305	75	cd12305, RRM_NELFE, RNA recognition motif in negat	5e-04
cd12354	73	cd12354, RRM3_TIA1_like, RNA recognition motif 2 i	5e-04
cd12226	78	cd12226, RRM_NOL8, RNA recognition motif in nucleo	6e-04
cd12494	72	cd12494, RRM3_hnRNPR, RNA recognition motif 3 in v	7e-04
cd12471	75	cd12471, RRM1_MSSP2, RNA recognition motif 1 in ve	8e-04
cd12233	70	cd12233, RRM_Srp1p_AtRSp31_like, RNA recognition m	8e-04
cd12321	77	cd12321, RRM1_TDP43, RNA recognition motif 1 in TA	8e-04
cd12575	74	cd12575, RRM1_hnRNPD_like, RNA recognition motif 1	9e-04
PRK12678	672	PRK12678, PRK12678, transcription termination fact	0.001
cd12606	67	cd12606, RRM1_RBM4, RNA recognition motif 1 in ver	0.001
cd12319	84	cd12319, RRM4_MRD1, RNA recognition motif 4 in yea	0.001
cd12260	85	cd12260, RRM2_SREK1, RNA recognition motif 2 in sp	0.001
cd12327	80	cd12327, RRM2_DAZAP1, RNA recognition motif 2 in D	0.001
cd12636	81	cd12636, RRM2_Bruno_like, RNA recognition motif 2	0.001
pfam00098	18	pfam00098, zf-CCHC, Zinc knuckle	0.001
cd12239	82	cd12239, RRM2_RBM40_like, RNA recognition motif 2	0.001
cd12472	80	cd12472, RRM1_RBMS3, RNA recognition motif 1 found	0.001
TIGR01648	578	TIGR01648, hnRNP-R-Q, heterogeneous nuclear ribonu	0.001
cd12309	79	cd12309, RRM2_Spen, RNA recognition motif 2 in the	0.001
cd12470	86	cd12470, RRM1_MSSP1, RNA recognition motif 1 in ve	0.001
cd12467	78	cd12467, RRM_Srp1p_like, RNA recognition motif 1 i	0.001
cd12773	84	cd12773, RRM2_HuR, RNA recognition motif 2 in vert	0.002
cd12332	71	cd12332, RRM1_p54nrb_like, RNA recognition motif 1	0.002
cd12758	76	cd12758, RRM1_hnRPDL, RNA recognition motif 1 in h	0.002
cd12320	76	cd12320, RRM6_RBM19_RRM5_MRD1, RNA recognition mot	0.002
cd12671	75	cd12671, RRM_CSTF2_CSTF2T, RNA recognition motif i	0.002
cd12612	82	cd12612, RRM2_SECp43, RNA recognition motif 2 in t	0.002
cd12558	76	cd12558, RRM3_RBM15B, RNA recognition motif 3 in p	0.002
cd12231	77	cd12231, RRM2_U2AF65, RNA recognition motif 2 foun	0.002
cd12772	84	cd12772, RRM1_HuC, RNA recognition motif 1 in vert	0.003
cd12607	67	cd12607, RRM2_RBM4, RNA recognition motif 2 in ver	0.003
cd12326	79	cd12326, RRM1_hnRNPA0, RNA recognition motif 1 fou	0.003
cd12448	73	cd12448, RRM2_gar2, RNA recognition motif 2 in yea	0.003
cd12227	77	cd12227, RRM_SCAF4_SCAF8, RNA recognition motif in	0.004
cd12776	81	cd12776, RRM2_HuC, RNA recognition motif 2 in vert	0.004
cd12632	87	cd12632, RRM1_CELF3_4_5_6, RNA recognition motif 1	0.004

>gnl|CDD|238902 cd01921, cyclophilin_RRM, cyclophilin_RRM: cyclophilin-type peptidylprolyl cis- trans isomerase domain occuring with a C-terminal RNA recognition motif domain (RRM)

 Score =  294 bits (754), Expect = 1e-97
 Identities = 110/166 (66%), Positives = 135/166 (81%)

Query: 4   LIVTSLGDIVVDLFVDKCPLTTKNFLKLCKIKYYNGCLFHTVQKDFTAQTGDPTGTGTGG 63
           L+ T+LGD+V+DLF D+CPL   NFLKLCK+KYYN CLF+ VQKDF AQTGDPTGTG GG
Sbjct: 1   LLETTLGDLVIDLFTDECPLACLNFLKLCKLKYYNFCLFYNVQKDFIAQTGDPTGTGAGG 60

Query: 64  DSVYKFLYGEQARFFGDEIRVDLKHAKTGTVAMASAGENLNASQFYMTLRDNLDYLDEKH 123
           +S+Y  LYG QARFF  EI   LKH+K GTV+M +AG+NLN SQFY+TL +NLDYLD KH
Sbjct: 61  ESIYSQLYGRQARFFEPEILPLLKHSKKGTVSMVNAGDNLNGSQFYITLGENLDYLDGKH 120

Query: 124 TIFGEVAEGLETLSRINESFVDEKNRPYKNIRIKHTYILEDPFDDP 169
           T+FG+V EG + L +IN++ VD+  RP K+IRIKHT+IL+DPF DP
Sbjct: 121 TVFGQVVEGFDVLEKINDAIVDDDGRPLKDIRIKHTHILDDPFPDP 166

This subfamily of the cyclophilin domain family contains a number of eukaryotic cyclophilins having the RRM domain including the nuclear proteins: human hCyP-57, Arabidopsis thaliana AtCYP59, Caenorhabditis elegans CeCyP-44 and Paramecium tetrurelia Kin241. The Kin241 protein has been shown to have a role in cell morphogenesis. Length = 166

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

 Score =  182 bits (463), Expect = 1e-55
 Identities = 66/83 (79%), Positives = 70/83 (84%)

Query: 240 PPENVLFVCKLNPVTEDEDLHTIFSRFGTVVSAEIIRDFKTGDSLNYAFIEFENRQACER 299
           PPENVLFVCKLNPVT DEDL  IFSRFG + S E+IRD KTGDSL YAFIEFE ++ CE 
Sbjct: 1   PPENVLFVCKLNPVTTDEDLEIIFSRFGKIKSCEVIRDKKTGDSLQYAFIEFETKEDCEE 60

Query: 300 AYSKMDNALIDDRRIHVDFSQSV 322
           AY KMDN LIDDRRIHVDFSQSV
Sbjct: 61  AYFKMDNVLIDDRRIHVDFSQSV 83

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

>gnl|CDD|238909 cd01928, Cyclophilin_PPIL3_like, Cyclophilin_PPIL3_like

 Score =  171 bits (435), Expect = 1e-50
 Identities = 78/161 (48%), Positives = 101/161 (62%), Gaps = 8/161 (4%)

Query: 1   MSVLIVTSLGDIVVDLFVDKCPLTTKNFLKLCKIKYYNGCLFHTVQKDFTAQTGDPTGTG 60
           MSV + T+LGDI ++LF D CP   +NFL LC   YYNGC+FH   K F  QTGDPTGTG
Sbjct: 1   MSVTLHTNLGDIKIELFCDDCPKACENFLALCASGYYNGCIFHRNIKGFMVQTGDPTGTG 60

Query: 61  TGGDSVYKFLYGEQARFFGDEIRVDLKHAKTGTVAMASAGENLNASQFYMTLRDNLDYLD 120
            GG+S++        + F DE R  LKH   G V+MA+ G N N SQF++T      +LD
Sbjct: 61  KGGESIW-------GKKFEDEFRETLKHDSRGVVSMANNGPNTNGSQFFITY-AKQPHLD 112

Query: 121 EKHTIFGEVAEGLETLSRINESFVDEKNRPYKNIRIKHTYI 161
            K+T+FG+V +G ETL  + +  VD+K RP + IRIK   I
Sbjct: 113 GKYTVFGKVIDGFETLDTLEKLPVDKKYRPLEEIRIKDVTI 153

Proteins similar to Human cyclophilin-like peptidylprolyl cis- trans isomerase (PPIL3). Members of this family lack a key residue important for cyclosporin binding: the tryptophan residue corresponding to W121 in human hCyP-18a; most members have a histidine at this position. The exact function of the protein is not known. Length = 153

>gnl|CDD|215759 pfam00160, Pro_isomerase, Cyclophilin type peptidyl-prolyl cis-trans isomerase/CLD

 Score =  169 bits (431), Expect = 3e-50
 Identities = 65/157 (41%), Positives = 92/157 (58%), Gaps = 14/157 (8%)

Query: 3   VLIVTSLGDIVVDLFVDKCPLTTKNFLKLCKIKYYNGCLFHTVQKDFTAQTGDPTGTGTG 62
           + I T+LG IV++LF D+ P T +NFL LCK  +Y+G +FH V   F  Q GDPTG GTG
Sbjct: 2   LDITTNLGRIVIELFGDEAPKTVENFLSLCKKGFYDGTIFHRVIPGFMIQGGDPTGPGTG 61

Query: 63  GDSVYKFLYGEQARFFGDEIRVDLKHAKTGTVAMASAGENLNASQFYMTLRDNLDYLDEK 122
           G            R   DE    LKH + GT++MA +G N   SQF++TL D   +LD  
Sbjct: 62  GK-----------RSIPDEFVSKLKHKR-GTLSMARSGPNSAGSQFFITLGDA-PHLDGG 108

Query: 123 HTIFGEVAEGLETLSRINESFVDEKNRPYKNIRIKHT 159
           +T+FG V EG++ + +I +   D  +RP K+++I   
Sbjct: 109 YTVFGRVVEGMDVVEKIEKVETDG-DRPLKDVKITSC 144

The peptidyl-prolyl cis-trans isomerases, also known as cyclophilins, share this domain of about 109 amino acids. Cyclophilins have been found in all organisms studied so far and catalyze peptidyl-prolyl isomerisation during which the peptide bond preceding proline (the peptidyl-prolyl bond) is stabilised in the cis conformation. Mammalian cyclophilin A (CypA) is a major cellular target for the immunosuppressive drug cyclosporin A (CsA). Other roles for cyclophilins may include chaperone and cell signalling function. Length = 144

>gnl|CDD|238904 cd01923, cyclophilin_RING, cyclophilin_RING: cyclophilin-type peptidylprolyl cis- trans isomerases (cyclophilins) having a modified RING finger domain

 Score =  159 bits (405), Expect = 3e-46
 Identities = 68/164 (41%), Positives = 100/164 (60%), Gaps = 8/164 (4%)

Query: 3   VLIVTSLGDIVVDLFVDKCPLTTKNFLKLCKIKYYNGCLFHTVQKDFTAQTGDPTGTGTG 62
           V + T+ GD+ ++L  DK P   +NF+KLCK  YY+G +FH   ++F  Q GDPTGTG G
Sbjct: 2   VRLHTNKGDLNLELHCDKAPKACENFIKLCKKGYYDGTIFHRSIRNFMIQGGDPTGTGRG 61

Query: 63  GDSVYKFLYGEQARFFGDEIRVDLKHAKTGTVAMASAGENLNASQFYMTLRDNLDYLDEK 122
           G+S++        + F DE + +L H   G ++MA++G N N SQF++T R +  +LD K
Sbjct: 62  GESIW-------GKPFKDEFKPNLSHDGRGVLSMANSGPNTNGSQFFITYR-SCKHLDGK 113

Query: 123 HTIFGEVAEGLETLSRINESFVDEKNRPYKNIRIKHTYILEDPF 166
           HT+FG V  GLETL  +        +RP + I+I+ T +  DPF
Sbjct: 114 HTVFGRVVGGLETLEAMENVPDPGTDRPKEEIKIEDTSVFVDPF 157

This group includes the nuclear proteins, Human hCyP-60 and Caenorhabditis elegans MOG-6 which, compared to the archetypal cyclophilin Human cyclophilin A exhibit reduced peptidylprolyl cis- trans isomerase activity and lack a residue important for cyclophilin binding. Human hCyP-60 has been shown to physically interact with the proteinase inhibitor peptide eglin c and; C. elegans MOG-6 to physically interact with MEP-1, a nuclear zinc finger protein. MOG-6 has been shown to function in germline sex determination. Length = 159

>gnl|CDD|238194 cd00317, cyclophilin, cyclophilin: cyclophilin-type peptidylprolyl cis- trans isomerases

 Score =  158 bits (402), Expect = 5e-46
 Identities = 61/152 (40%), Positives = 85/152 (55%), Gaps = 9/152 (5%)

Query: 5   IVTSLGDIVVDLFVDKCPLTTKNFLKLCKIKYYNGCLFHTVQKDFTAQTGDPTGTGTGGD 64
           + T+ G IV++L+ D+ P T +NFL L +  +Y+G  FH V   F  Q GDPTGTG GG 
Sbjct: 2   LDTTKGRIVIELYGDEAPKTVENFLSLARGGFYDGTTFHRVIPGFMIQGGDPTGTGGGG- 60

Query: 65  SVYKFLYGEQARFFGDEIRVDLKHAKTGTVAMASAGENLNASQFYMTLRDNLDYLDEKHT 124
                        F DE      H + GT++MA+AG N N SQF++T      +LD KHT
Sbjct: 61  -------SGPGYKFPDENFPLKYHHRRGTLSMANAGPNTNGSQFFITTAPT-PHLDGKHT 112

Query: 125 IFGEVAEGLETLSRINESFVDEKNRPYKNIRI 156
           +FG+V EG++ + +I     DE  RP K + I
Sbjct: 113 VFGKVVEGMDVVDKIERGDTDENGRPIKPVTI 144

This family contains eukaryotic, bacterial and archeal proteins which exhibit a peptidylprolyl cis- trans isomerases activity (PPIase, Rotamase) and in addition bind the immunosuppressive drug cyclosporin (CsA). Immunosuppression in vertebrates is believed to be the result of the cyclophilin A-cyclosporin protein drug complex binding to and inhibiting the protein-phosphatase calcineurin. PPIase is an enzyme which accelerates protein folding by catalyzing the cis-trans isomerization of the peptide bonds preceding proline residues. Cyclophilins are a diverse family in terms of function and have been implicated in protein folding processes which depend on catalytic /chaperone-like activities. This group contains human cyclophilin 40, a co-chaperone of the hsp90 chaperone system; human cyclophilin A, a chaperone in the HIV-1 infectious process and; human cyclophilin H, a component of the U4/U6 snRNP, whose isomerization or chaperoning activities may play a role in RNA splicing. . Length = 146

>gnl|CDD|238906 cd01925, cyclophilin_CeCYP16-like, cyclophilin_CeCYP16-like: cyclophilin-type peptidylprolyl cis- trans isomerase) (PPIase) domain similar to Caenorhabditis elegans cyclophilin 16

 Score =  158 bits (402), Expect = 9e-46
 Identities = 67/168 (39%), Positives = 98/168 (58%), Gaps = 9/168 (5%)

Query: 2   SVLIVTSLGDIVVDLFVDKCPLTTKNFLKLCKIKYYNGCLFHTVQKDFTAQTGDPTGTGT 61
            V++ T+ GDI ++L+  + P   +NF++LC   YY+  +FH V   F  Q GDPTGTGT
Sbjct: 7   KVILKTTAGDIDIELWSKEAPKACRNFIQLCLEGYYDNTIFHRVVPGFIIQGGDPTGTGT 66

Query: 62  GGDSVYKFLYGEQARFFGDEIRVDLKHAKTGTVAMASAGENLNASQFYMTLRDNLDYLDE 121
           GG+S+Y          F DE    L+  + G V MA+AG++ N SQF+ TL D  D L+ 
Sbjct: 67  GGESIY-------GEPFKDEFHSRLRFNRRGLVGMANAGDDSNGSQFFFTL-DKADELNN 118

Query: 122 KHTIFGEVA-EGLETLSRINESFVDEKNRPYKNIRIKHTYILEDPFDD 168
           KHT+FG+V  + +  L ++ E   D+  RP    +I    +LE+PFDD
Sbjct: 119 KHTLFGKVTGDTIYNLLKLAEVETDKDERPVYPPKITSVEVLENPFDD 166

C. elegans CeCYP-16, compared to the archetypal cyclophilin Human cyclophilin A has, a reduced peptidylprolyl cis- trans isomerase activity, is cyclosporin insensitive and shows an altered substrate preference favoring, hydrophobic, acidic or amide amino acids. Most members of this subfamily have a glutamate residue in the active site at the position equivalent to a tryptophan (W121 in Human cyclophilin A), which has been shown to be important for cyclophilin binding. Length = 171

>gnl|CDD|238908 cd01927, cyclophilin_WD40, cyclophilin_WD40: cyclophilin-type peptidylprolyl cis- trans isomerases (cyclophilins) having a WD40 domain

 Score =  154 bits (390), Expect = 3e-44
 Identities = 65/153 (42%), Positives = 94/153 (61%), Gaps = 8/153 (5%)

Query: 4   LIVTSLGDIVVDLFVDKCPLTTKNFLKLCKIKYYNGCLFHTVQKDFTAQTGDPTGTGTGG 63
           +I T+ GDI + LF ++ P T +NF    +  YYN  +FH V K F  QTGDPTG GTGG
Sbjct: 1   IIHTTKGDIHIRLFPEEAPKTVENFTTHARNGYYNNTIFHRVIKGFMIQTGDPTGDGTGG 60

Query: 64  DSVYKFLYGEQARFFGDEIRVDLKHAKTGTVAMASAGENLNASQFYMTLRDNLDYLDEKH 123
           +S++        + F DE    LKH +  T++MA+AG N N SQF++T      +LD KH
Sbjct: 61  ESIWG-------KEFEDEFSPSLKHDRPYTLSMANAGPNTNGSQFFITT-VATPWLDNKH 112

Query: 124 TIFGEVAEGLETLSRINESFVDEKNRPYKNIRI 156
           T+FG V +G++ + RI     D+ +RPY++I+I
Sbjct: 113 TVFGRVVKGMDVVQRIENVKTDKNDRPYEDIKI 145

This group consists of several hypothetical and putative eukaryotic and bacterial proteins which have a cyclophilin domain and a WD40 domain. Function of the protein is not known. Length = 148

>gnl|CDD|223725 COG0652, PpiB, Peptidyl-prolyl cis-trans isomerase (rotamase) - cyclophilin family [Posttranslational modification, protein turnover, chaperones]

 Score =  148 bits (377), Expect = 3e-42
 Identities = 63/169 (37%), Positives = 94/169 (55%), Gaps = 18/169 (10%)

Query: 2   SVLIVTSLGDIVVDLFVDKCPLTTKNFLKLCKIKYYNGCLFHTVQKDFTAQTGDPTGT-G 60
           +V++ T+ GDI ++L+ DK P T  NFL+L K  +Y+G +FH V   F  Q GDPTG  G
Sbjct: 1   TVILETNKGDITIELYPDKAPKTVANFLQLVKEGFYDGTIFHRVIPGFMIQGGDPTGGDG 60

Query: 61  TGGDSVYKFLYGEQARFFGDEIRVDLKHA-KTGTVAMASAGE-NLNASQFYMTLRDNLDY 118
           TGG              F DE         K GT++MA AG+ N N SQF++T+ DN  +
Sbjct: 61  TGGPG----------PPFKDENFALNGDRHKRGTLSMARAGDPNSNGSQFFITVVDN-PF 109

Query: 119 LDEKHTIFGEVAEGLETLSRIN----ESFVDEKNRPYKNIRIKHTYILE 163
           LD K+T+FG+V EG++ + +I     +     ++ P   ++I    I+E
Sbjct: 110 LDGKYTVFGQVVEGMDVVDKIKNGDTDDSGYVQDVPADPVKILSVKIVE 158

Length = 158

>gnl|CDD|238903 cd01922, cyclophilin_SpCYP2_like, cyclophilin_SpCYP2_like: cyclophilin 2-like peptidylprolyl cis- trans isomerase (PPIase) domain similar to Schizosaccharomyces pombe cyp-2

 Score =  144 bits (366), Expect = 6e-41
 Identities = 66/153 (43%), Positives = 96/153 (62%), Gaps = 9/153 (5%)

Query: 4   LIVTSLGDIVVDLFVDKCPLTTKNFLKLCKIKYYNGCLFHTVQKDFTAQTGDPTGTGTGG 63
            + T++G+I ++L+ +  P T KNF +L K  YYNG +FH + KDF  Q GDPTGTG GG
Sbjct: 1   TLETTMGEITLELYWNHAPKTCKNFYELAKRGYYNGTIFHRLIKDFMIQGGDPTGTGRGG 60

Query: 64  DSVYKFLYGEQARFFGDEIRVDLKHAKTGTVAMASAGENLNASQFYMTLRDNLDYLDEKH 123
            S+    YG++   F DEI  +LKH   G ++MA+AG N N SQF++TL     +LD KH
Sbjct: 61  ASI----YGKK---FEDEIHPELKHTGAGILSMANAGPNTNGSQFFITLAP-TPWLDGKH 112

Query: 124 TIFGEVAEGLETLSRINESFVDEKNRPYKNIRI 156
           TIFG V++G++ +  + E      +RP   ++I
Sbjct: 113 TIFGRVSKGMKVIENMVEVQTQT-DRPIDEVKI 144

These proteins bind their respective SNW chromatin binding protein in autologous systems, in a CsA independent manner indicating interaction with a surface outside the PPIase active site. SNW proteins play a basic and broad range role in signaling. Length = 146

>gnl|CDD|238907 cd01926, cyclophilin_ABH_like, cyclophilin_ABH_like: Cyclophilin A, B and H-like cyclophilin-type peptidylprolyl cis- trans isomerase (PPIase) domain

 Score =  119 bits (300), Expect = 2e-31
 Identities = 64/159 (40%), Positives = 84/159 (52%), Gaps = 19/159 (11%)

Query: 7   TSLGDIVVDLFVDKCPLTTKNFLKLC--------KIKYYNGCLFHTVQKDFTAQTGDPT- 57
              G IV++LF D  P T +NF  LC        K   Y G  FH V  DF  Q GD T 
Sbjct: 12  EPAGRIVMELFADVVPKTAENFRALCTGEKGKGGKPFGYKGSTFHRVIPDFMIQGGDFTR 71

Query: 58  GTGTGGDSVYKFLYGEQARFFGDEIRVDLKHAKTGTVAMASAGENLNASQFYMTLRDNLD 117
           G GTGG S+Y    GE+   F DE    LKH   G ++MA+AG N N SQF++T      
Sbjct: 72  GNGTGGKSIY----GEK---FPDE-NFKLKHTGPGLLSMANAGPNTNGSQFFITTVKT-P 122

Query: 118 YLDEKHTIFGEVAEGLETLSRINESFVDEKNRPYKNIRI 156
           +LD KH +FG+V EG++ + +I E+      +P K + I
Sbjct: 123 WLDGKHVVFGKVVEGMDVVKKI-ENVGSGNGKPKKKVVI 160

This family represents the archetypal cystolic cyclophilin similar to human cyclophilins A, B and H. PPIase is an enzyme which accelerates protein folding by catalyzing the cis-trans isomerization of the peptide bonds preceding proline residues. These enzymes have been implicated in protein folding processes which depend on catalytic /chaperone-like activities. As cyclophilins, Human hCyP-A, human cyclophilin-B (hCyP-19), S. cerevisiae Cpr1 and C. elegans Cyp-3, are inhibited by the immunosuppressive drug cyclopsporin A (CsA). CsA binds to the PPIase active site. Cyp-3. S. cerevisiae Cpr1 interacts with the Rpd3 - Sin3 complex and in addition is a component of the Set3 complex. S. cerevisiae Cpr1 has also been shown to have a role in Zpr1p nuclear transport. Human cyclophilin H associates with the [U4/U6.U5] tri-snRNP particles of the splicesome. Length = 164

>gnl|CDD|240249 PTZ00060, PTZ00060, cyclophilin; Provisional

 Score =  102 bits (256), Expect = 3e-25
 Identities = 56/140 (40%), Positives = 75/140 (53%), Gaps = 19/140 (13%)

Query: 10  GDIVVDLFVDKCPLTTKNFLKLC---------KIKYYNGCLFHTVQKDFTAQTGDPT-GT 59
           G IV +LF D  P T +NF  LC         K  +Y G +FH +   F  Q GD T   
Sbjct: 30  GRIVFELFSDVTPKTAENFRALCIGDKVGSSGKNLHYKGSIFHRIIPQFMCQGGDITNHN 89

Query: 60  GTGGDSVYKFLYGEQARFFGDEIRVDLKHAKTGTVAMASAGENLNASQFYMTLRDNLDYL 119
           GTGG+S+Y        R F DE    LKH + G ++MA+AG N N SQF++T      +L
Sbjct: 90  GTGGESIY-------GRKFTDE-NFKLKHDQPGLLSMANAGPNTNGSQFFITTVP-CPWL 140

Query: 120 DEKHTIFGEVAEGLETLSRI 139
           D KH +FG+V EG+E +  +
Sbjct: 141 DGKHVVFGKVIEGMEVVRAM 160

Length = 183

>gnl|CDD|178694 PLN03149, PLN03149, peptidyl-prolyl isomerase H (cyclophilin H); Provisional

 Score = 93.4 bits (232), Expect = 6e-22
 Identities = 57/151 (37%), Positives = 77/151 (50%), Gaps = 19/151 (12%)

Query: 10  GDIVVDLFVDKCPLTTKNFLKLCKIKY--------YNGCLFHTVQKDFTAQTGD-PTGTG 60
           G I ++LF D  P T +NF + C  ++        Y GC FH V KDF  Q GD   G G
Sbjct: 33  GRIKMELFADIAPKTAENFRQFCTGEFRKAGLPQGYKGCQFHRVIKDFMIQGGDFLKGDG 92

Query: 61  TGGDSVYKFLYGEQARFFGDEIRVDLKHAKTGTVAMASAGENLNASQFYMTLRDNLDYLD 120
           TG  S+    YG +   F DE  +  KH   G ++MA++G N N  QF++T     D+LD
Sbjct: 93  TGCVSI----YGSK---FEDENFIA-KHTGPGLLSMANSGPNTNGCQFFITCA-KCDWLD 143

Query: 121 EKHTIFGEV-AEGLETLSRINESFVDEKNRP 150
            KH +FG V  +GL  + +I        NRP
Sbjct: 144 NKHVVFGRVLGDGLLVVRKIENVATGPNNRP 174

Length = 186

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

 Score = 83.8 bits (208), Expect = 9e-20
 Identities = 31/81 (38%), Positives = 45/81 (55%)

Query: 241 PENVLFVCKLNPVTEDEDLHTIFSRFGTVVSAEIIRDFKTGDSLNYAFIEFENRQACERA 300
           P   LFV +L+  T +E L  +FSR+G +    ++RD  TG S  YAF+E+E+ +   RA
Sbjct: 2   PYLTLFVGRLSLQTTEETLREVFSRYGDIRRLRLVRDIVTGFSKGYAFVEYEHERDALRA 61

Query: 301 YSKMDNALIDDRRIHVDFSQS 321
           Y      +ID   I VDF + 
Sbjct: 62  YRDAHKLVIDGSEIFVDFERE 82

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

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

 Score = 83.0 bits (206), Expect = 9e-20
 Identities = 29/73 (39%), Positives = 45/73 (61%)

Query: 244 VLFVCKLNPVTEDEDLHTIFSRFGTVVSAEIIRDFKTGDSLNYAFIEFENRQACERAYSK 303
            LFV  L P T +E+L  +FS+FG V S  ++RD +TG S  +AF+EFE+ +  E+A   
Sbjct: 1   TLFVGNLPPDTTEEELRELFSKFGKVESVRLVRDKETGKSKGFAFVEFESEEDAEKALEA 60

Query: 304 MDNALIDDRRIHV 316
           ++   +D R + V
Sbjct: 61  LNGKELDGRPLKV 73

Length = 73

>gnl|CDD|238901 cd01920, cyclophilin_EcCYP_like, cyclophilin_EcCYP_like: cyclophilin-type A-like peptidylprolyl cis- trans isomerase (PPIase) domain similar to the cytosolic E

 Score = 79.4 bits (196), Expect = 2e-17
 Identities = 50/138 (36%), Positives = 76/138 (55%), Gaps = 15/138 (10%)

Query: 7   TSLGDIVVDLFVDKCPLTTKNFLKLCKIKYYNGCLFHTVQKDFTAQTGDPTGTGTGGDSV 66
           TSLGDIVV+L+ DK P+T +NFL   +  +Y+  +FH V   F  Q G  T      +++
Sbjct: 4   TSLGDIVVELYDDKAPITVENFLAYVRKGFYDNTIFHRVISGFVIQGGGFTPDLAQKETL 63

Query: 67  YKFLYGEQARFFGDEIRVDLKHAKTGTVAMASAGENLNA-SQFYMTLRDN--LDYLDEK- 122
                        +E    L +   GT+AMA      +A SQF++ L+DN  LDY +E+ 
Sbjct: 64  KPIK---------NEAGNGLSN-TRGTIAMARTNAPDSATSQFFINLKDNASLDYQNEQW 113

Query: 123 -HTIFGEVAEGLETLSRI 139
            +T+FGEV EG++ + +I
Sbjct: 114 GYTVFGEVTEGMDVVDKI 131

coli cyclophilin A and Streptomyces antibioticus SanCyp18. Compared to the archetypal cyclophilin Human cyclophilin A, these have reduced affinity for cyclosporin A. E. coli cyclophilin A has a similar peptidylprolyl cis- trans isomerase activity to the human cyclophilin A. Most members of this subfamily contain a phenylalanine residue at the position equivalent to Human cyclophilin W121, where a tyrptophan has been shown to be important for cyclophilin binding. Length = 155

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

 Score = 76.6 bits (189), Expect = 2e-17
 Identities = 30/73 (41%), Positives = 45/73 (61%), Gaps = 1/73 (1%)

Query: 245 LFVCKLNPVTEDEDLHTIFSRFGTVVSAEIIRDFKTGDSLNYAFIEFENRQACERAYSKM 304
           LFV  L P T +EDL  +FS+FG + S  I+RD K G S  +AF+EFE+ +  E+A   +
Sbjct: 1   LFVGNLPPDTTEEDLRELFSKFGEIESVRIVRD-KDGKSKGFAFVEFESPEDAEKALEAL 59

Query: 305 DNALIDDRRIHVD 317
           +   +D R++ V 
Sbjct: 60  NGKELDGRKLKVS 72

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

>gnl|CDD|182824 PRK10903, PRK10903, peptidyl-prolyl cis-trans isomerase A (rotamase A); Provisional

 Score = 71.8 bits (176), Expect = 2e-14
 Identities = 50/166 (30%), Positives = 82/166 (49%), Gaps = 18/166 (10%)

Query: 3   VLIVTSLGDIVVDLFVDKCPLTTKNFLKLCKIKYYNGCLFHTVQKDFTAQTGDPTGTGTG 62
           VL+ TS G+I ++L   K P++ KNF+      +YN   FH V   F  Q G     G  
Sbjct: 31  VLLTTSAGNIELELNSQKAPVSVKNFVDYVNSGFYNNTTFHRVIPGFMIQGG-----GFT 85

Query: 63  GDSVYKFLYGEQARFFGDEIRVDLKHAKTGTVAMASAGENLNA-SQFYMTLRDN--LDY- 118
                K    +      +E    L++ + GT+AMA   +  +A SQF++ + DN  LD+ 
Sbjct: 86  EQMQQK----KPNPPIKNEADNGLRNTR-GTIAMARTADKDSATSQFFINVADNAFLDHG 140

Query: 119 -LDEKHTIFGEVAEGLETLSRINESFVDEKN-RPYKNIRIKHTYIL 162
             D  + +FG+V +G++   +I++  V   +  PY+N+  K   IL
Sbjct: 141 QRDFGYAVFGKVVKGMDVADKISQ--VPTHDVGPYQNVPSKPVVIL 184

Length = 190

>gnl|CDD|238905 cd01924, cyclophilin_TLP40_like, cyclophilin_TLP40_like: cyclophilin-type peptidylprolyl cis- trans isomerases (cyclophilins) similar ot the Spinach thylakoid lumen protein TLP40

 Score = 68.2 bits (167), Expect = 2e-13
 Identities = 47/155 (30%), Positives = 72/155 (46%), Gaps = 30/155 (19%)

Query: 12  IVVDLFVDKCPLTTKNFLKLCKIKYYNGCLFHTVQKDFTAQTGDPTGTGTGG-------- 63
           IV+D +    P+T  NF+ L +  +Y+G  FH V+  F  QTGDP G   G         
Sbjct: 11  IVLDGY--NAPVTAGNFVDLVERGFYDGMEFHRVEGGFVVQTGDPQGKNPGFPDPETGKS 68

Query: 64  ---------DSVYKFLYGEQARFFG--DEIRVDLKHAKTGTVAMASAGENLNA--SQFYM 110
                    +   + +YG+     G  DE  V   +A  G +AMA    + N+  SQF+ 
Sbjct: 69  RTIPLEIKPEGQKQPVYGKTLEEAGRYDEQPVLPFNAF-GAIAMARTEFDPNSASSQFFF 127

Query: 111 TLRDNL------DYLDEKHTIFGEVAEGLETLSRI 139
            L+DN       + LD ++ +FG V +GL+ L  +
Sbjct: 128 LLKDNELTPSRNNVLDGRYAVFGYVTDGLDILREL 162

Compared to the archetypal cyclophilin Human cyclophilin A, these proteins have similar peptidylprolyl cis- trans isomerase activity and reduced affinity for cyclosporin A. Spinach TLP40 has been shown to have a dual function as a folding catalyst and regulator of dephosphorylation. Length = 176

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

 Score = 64.2 bits (157), Expect = 4e-13
 Identities = 28/71 (39%), Positives = 42/71 (59%), Gaps = 1/71 (1%)

Query: 245 LFVCKLNPVTEDEDLHTIFSRFGTVVSAEIIRDFKTGDSLNYAFIEFENRQACERAYSKM 304
           LFV  L P T +EDL  +FS+FG + S  I+RD  TG S  +AF+EFE+ +  E+A   +
Sbjct: 1   LFVGNLPPDTTEEDLKDLFSKFGPIESIRIVRDE-TGRSKGFAFVEFEDEEDAEKALEAL 59

Query: 305 DNALIDDRRIH 315
           +   +  R + 
Sbjct: 60  NGKELGGRELR 70

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

>gnl|CDD|182734 PRK10791, PRK10791, peptidyl-prolyl cis-trans isomerase B (rotamase B); Provisional

 Score = 66.8 bits (163), Expect = 5e-13
 Identities = 46/145 (31%), Positives = 72/145 (49%), Gaps = 26/145 (17%)

Query: 7   TSLGDIVVDLFVDKCPLTTKNFLKLCKIKYYNGCLFHTVQKDFTAQTGDPTGTGTGGDSV 66
           T+ GDIV+  F DK P T KNFL  C+  +YN  +FH V   F  Q G            
Sbjct: 6   TNHGDIVIKTFDDKAPETVKNFLDYCREGFYNNTIFHRVINGFMIQGGG----------- 54

Query: 67  YKFLYGEQARFFGDEIRVD----LKHAKTGTVAMASAGENLNAS-QFYMTLRDN--LDYL 119
             F  G + +   + I+ +    LK+ + GT+AMA      +A+ QF++ + DN  L++ 
Sbjct: 55  --FEPGMKQKATKEPIKNEANNGLKNTR-GTLAMARTQAPHSATAQFFINVVDNDFLNFS 111

Query: 120 DEK-----HTIFGEVAEGLETLSRI 139
            E      + +F EV EG++ + +I
Sbjct: 112 GESLQGWGYCVFAEVVEGMDVVDKI 136

Length = 164

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

 Score = 63.8 bits (156), Expect = 9e-13
 Identities = 30/75 (40%), Positives = 40/75 (53%)

Query: 243 NVLFVCKLNPVTEDEDLHTIFSRFGTVVSAEIIRDFKTGDSLNYAFIEFENRQACERAYS 302
             LFV +LN  T +  L   F  +G +    ++RD KTG    YAFIEFE+ +  + AY 
Sbjct: 2   KTLFVARLNYDTTESKLRREFEEYGPIKRIRLVRDKKTGKPRGYAFIEFEHERDMKAAYK 61

Query: 303 KMDNALIDDRRIHVD 317
             D   ID RR+ VD
Sbjct: 62  YADGKKIDGRRVLVD 76

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

>gnl|CDD|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 = 63.4 bits (155), Expect = 1e-12
 Identities = 23/75 (30%), Positives = 44/75 (58%)

Query: 243 NVLFVCKLNPVTEDEDLHTIFSRFGTVVSAEIIRDFKTGDSLNYAFIEFENRQACERAYS 302
           N LFV  L+  T +++L  +FS+FG V    +++D +TG+S  + F+ FE+ +  + A  
Sbjct: 2   NKLFVSGLSTRTTEKELEALFSKFGRVEEVLLMKDPETGESRGFGFVTFESVEDADAAIR 61

Query: 303 KMDNALIDDRRIHVD 317
            ++   ++ R I V+
Sbjct: 62  DLNGKELEGRVIKVE 76

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

 Score = 61.0 bits (149), Expect = 6e-12
 Identities = 24/72 (33%), Positives = 36/72 (50%)

Query: 245 LFVCKLNPVTEDEDLHTIFSRFGTVVSAEIIRDFKTGDSLNYAFIEFENRQACERAYSKM 304
           L V KL      + L  IFS +GTV   ++  D +      YA++EFE+ +  E+A   M
Sbjct: 1   LHVGKLTRNVNKDHLKEIFSNYGTVKDVDLPIDREVNLPRGYAYVEFESPEDAEKAIKHM 60

Query: 305 DNALIDDRRIHV 316
           D   ID + + V
Sbjct: 61  DGGQIDGQEVTV 72

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

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

 Score = 66.5 bits (161), Expect = 7e-12
 Identities = 33/197 (16%), Positives = 69/197 (35%), Gaps = 4/197 (2%)

Query: 239 KPPENVLFVCKLNPVTEDEDLHTIFSRFGTVVSAEIIRDFKTGDSLNYAFIEFENRQACE 298
           K   N LFV  L     +EDL  +F +FG V    ++RD +TG S  +AF+EFE+ ++ E
Sbjct: 112 KEENNTLFVGNLPYDVTEEDLRELFKKFGPVKRVRLVRDRETGKSRGFAFVEFESEESAE 171

Query: 299 RAYSKMDNALIDDRRIHVDFSQSVSKLWNQFRRRDHQTGKGKGCFKCGGLDHIAKDCTGQ 358
           +A  +++   ++ R + V  +Q  S+  ++       +   K          +  + +  
Sbjct: 172 KAIEELNGKELEGRPLRVQKAQPASQPRSELSNNLDASFAKKL----SRGKALLLEKSDN 227

Query: 359 QPAKYILRDDNRQHGGYSDSRYEMVFDGETPEKSRREKKHRGHDPDDRVERNMNRLSSDL 418
                +      +           +     P     +         +   ++    +S  
Sbjct: 228 LYVGNLPLKTAEEELADLFKSRGDIVRASLPPSKDGKIPKSRSFVGNEASKDALESNSRG 287

Query: 419 RHRDQERRELSYRQRES 435
             +    R       + 
Sbjct: 288 NKKKILGRGPRKAFSQP 304

Length = 306

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

 Score = 59.4 bits (145), Expect = 1e-11
 Identities = 18/61 (29%), Positives = 32/61 (52%), Gaps = 5/61 (8%)

Query: 259 LHTIFSRFGTVVSAEIIRDFKTGDSLNYAFIEFENRQACERAYSKMDNALIDDRRIHVDF 318
           L+ +FS FG V   ++++         +AF+EF   +A E+A   ++  L   R + VD+
Sbjct: 1   LYKLFSPFGNVEKIKLLKK-----KPGFAFVEFSTEEAAEKAVQYLNGVLFGGRPLRVDY 55

Query: 319 S 319
           S
Sbjct: 56  S 56

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

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

 Score = 59.5 bits (145), Expect = 2e-11
 Identities = 27/76 (35%), Positives = 42/76 (55%)

Query: 245 LFVCKLNPVTEDEDLHTIFSRFGTVVSAEIIRDFKTGDSLNYAFIEFENRQACERAYSKM 304
           L+V  L+P   +  L+ IFS  G V+S  + RD  T  SL YA++ F+N    ERA   +
Sbjct: 2   LYVGDLHPDVTEAMLYEIFSPAGPVLSIRVCRDLITRRSLGYAYVNFQNPADAERALDTL 61

Query: 305 DNALIDDRRIHVDFSQ 320
           +  +I  + I + +SQ
Sbjct: 62  NFDVIKGKPIRIMWSQ 77

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

 Score = 58.4 bits (142), Expect = 5e-11
 Identities = 22/72 (30%), Positives = 41/72 (56%)

Query: 245 LFVCKLNPVTEDEDLHTIFSRFGTVVSAEIIRDFKTGDSLNYAFIEFENRQACERAYSKM 304
           LF+  L     D+DL+ +F+ FG V+SA++  D  TG S  + F+ ++N ++ + A   M
Sbjct: 1   LFIYHLPNEFTDQDLYQLFAPFGNVISAKVFVDKNTGQSKCFGFVSYDNPESAQAAIKAM 60

Query: 305 DNALIDDRRIHV 316
           +   +  +R+ V
Sbjct: 61  NGFQVGGKRLKV 72

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

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

 Score = 57.8 bits (140), Expect = 8e-11
 Identities = 23/77 (29%), Positives = 38/77 (49%), Gaps = 1/77 (1%)

Query: 243 NVLFVCKLNPVTEDEDLHTIFSRFGTVVSAEIIRDFKTGDSLNYAFIEFENRQACERAYS 302
           + LFV  L      E+L  +F + G V S  ++   ++G     A++E+EN  +  +A  
Sbjct: 3   HKLFVSGLPFSVTKEELEKLFKKHGVVKSVRLV-TNRSGKPKGLAYVEYENESSASQAVL 61

Query: 303 KMDNALIDDRRIHVDFS 319
           KMD   I ++ I V  S
Sbjct: 62  KMDGTEIKEKTISVAIS 78

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

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

 Score = 58.1 bits (141), Expect = 8e-11
 Identities = 24/76 (31%), Positives = 46/76 (60%), Gaps = 1/76 (1%)

Query: 245 LFVCKLNPVTEDEDLHTIFSRFGTVVSA-EIIRDFKTGDSLNYAFIEFENRQACERAYSK 303
           LF+  L+P  +++ L+  FS FG ++   +I+RD  TG+S  +AFI +++ +A + A   
Sbjct: 4   LFIGNLDPEVDEKLLYDTFSAFGVILQTPKIMRDPDTGNSKGFAFISYDSFEASDAAIEA 63

Query: 304 MDNALIDDRRIHVDFS 319
           M+   + +R I V ++
Sbjct: 64  MNGQYLCNRPITVSYA 79

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

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

 Score = 57.6 bits (140), Expect = 1e-10
 Identities = 28/72 (38%), Positives = 43/72 (59%), Gaps = 1/72 (1%)

Query: 245 LFVCKLNPVTEDEDLHTIFSRFGTVVSAEIIRDFKTGDSLNYAFIEFENRQACERAYSKM 304
           +FV  L   T D+ L   FS+FG +  A +I D +TG S  Y F+ F+++++ ERA  K 
Sbjct: 3   IFVGGLPYHTTDDSLRKYFSQFGEIEEAVVITDRQTGKSRGYGFVTFKDKESAERAC-KD 61

Query: 305 DNALIDDRRIHV 316
            N +ID R+ +V
Sbjct: 62  PNPIIDGRKANV 73

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

 Score = 57.4 bits (139), Expect = 1e-10
 Identities = 22/70 (31%), Positives = 36/70 (51%)

Query: 245 LFVCKLNPVTEDEDLHTIFSRFGTVVSAEIIRDFKTGDSLNYAFIEFENRQACERAYSKM 304
           +FV  L+P  + E L   F+ FG +  A +++D +TG S  Y F+ F  ++  E A   M
Sbjct: 2   IFVGDLSPEIDTETLRAAFAPFGEISDARVVKDMQTGKSKGYGFVSFVKKEDAENAIQSM 61

Query: 305 DNALIDDRRI 314
           +   +  R I
Sbjct: 62  NGQWLGGRAI 71

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

>gnl|CDD|237171 PRK12678, PRK12678, transcription termination factor Rho; Provisional

 Score = 64.2 bits (157), Expect = 1e-10
 Identities = 31/170 (18%), Positives = 56/170 (32%), Gaps = 14/170 (8%)

Query: 422 DQERRELSYRQRESDRTRENREDRRNRDGQESRNVQKQEVRDDDGRYESDHPKSSDTDRY 481
             E  +   R+   +  R     +    G++     + +  +     E D  +       
Sbjct: 121 APEAAQARERRERGEAARRGAARKAGEGGEQPATEARADAAERTEEEERDERRRRGDRED 180

Query: 482 RDWRGGGDYRKRSADSDSRAERREDGDYRKR--NSDNGSHRDRRDDQDYRKKSADGDIHG 539
           R        R R  +     + R+  D R++    +    RD  D +  R++    D  G
Sbjct: 181 RQAEAERGERGRREERGRDGDDRDRRDRREQGDRREERGRRDGGDRRGRRRRRDRRDARG 240

Query: 540 DRRYDRDNRKNSGNSELRDAKKEPSYKRGRRDDDSYKRWPEDRGNRRRGE 589
           D   +    ++  + E R        +RGRR  D       DR  RR G+
Sbjct: 241 DDNREDRGDRDGDDGEGRGG------RRGRRFRDR------DRRGRRGGD 278

Length = 672

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

 Score = 56.9 bits (138), Expect = 2e-10
 Identities = 21/76 (27%), Positives = 39/76 (51%)

Query: 244 VLFVCKLNPVTEDEDLHTIFSRFGTVVSAEIIRDFKTGDSLNYAFIEFENRQACERAYSK 303
           +L V  L     DE    + S FG V    ++    TG+S  Y F+E+ ++ +  +A ++
Sbjct: 1   LLCVGNLPLEFTDEQFRELVSPFGAVERCFLVYSESTGESKGYGFVEYASKASALKAKNQ 60

Query: 304 MDNALIDDRRIHVDFS 319
           +D   I  R++ VD++
Sbjct: 61  LDGKQIGGRKLQVDWA 76

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

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

 Score = 56.9 bits (138), Expect = 2e-10
 Identities = 24/72 (33%), Positives = 36/72 (50%)

Query: 245 LFVCKLNPVTEDEDLHTIFSRFGTVVSAEIIRDFKTGDSLNYAFIEFENRQACERAYSKM 304
           L+V  L     +EDL  +F +FG V SA +I D +TG S  + F+E E  +    A  K+
Sbjct: 2   LYVGNLPYNVTEEDLKDLFGQFGEVTSARVITDRETGRSRGFGFVEMETAEEANAAIEKL 61

Query: 305 DNALIDDRRIHV 316
           +      R + V
Sbjct: 62  NGTDFGGRTLTV 73

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

 Score = 56.2 bits (136), Expect = 3e-10
 Identities = 31/75 (41%), Positives = 46/75 (61%)

Query: 245 LFVCKLNPVTEDEDLHTIFSRFGTVVSAEIIRDFKTGDSLNYAFIEFENRQACERAYSKM 304
           LFV  L+   +DE L   F +FGTVV A +I D +TG S  + +++FE+ +  ++A   M
Sbjct: 2   LFVGNLSWSVDDEWLKAEFEKFGTVVGARVITDRETGRSRGFGYVDFESPEDAKKAIEAM 61

Query: 305 DNALIDDRRIHVDFS 319
           D   +D R I+VDFS
Sbjct: 62  DGKELDGRPINVDFS 76

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

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

 Score = 56.5 bits (137), Expect = 3e-10
 Identities = 27/76 (35%), Positives = 44/76 (57%)

Query: 244 VLFVCKLNPVTEDEDLHTIFSRFGTVVSAEIIRDFKTGDSLNYAFIEFENRQACERAYSK 303
            L V  L+  T + DL  +FSR+G +   +++ D KTG S  + F+ FE+ +  + A  +
Sbjct: 1   CLGVFGLSLYTTERDLREVFSRYGPIEKVQVVYDQKTGRSRGFGFVYFESVEDAKEAKER 60

Query: 304 MDNALIDDRRIHVDFS 319
           ++   ID RRI VD+S
Sbjct: 61  LNGMEIDGRRIRVDYS 76

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

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

 Score = 54.5 bits (132), Expect = 9e-10
 Identities = 20/72 (27%), Positives = 34/72 (47%), Gaps = 8/72 (11%)

Query: 245 LFVCKLNPVTEDEDLHTIFSRFGTVVSAEIIRDFKTGDSLNYAFIEFENRQACERAYSKM 304
           LFV  L   T  E+L  +F ++GTV   ++++        NY F+  E  +  E A   +
Sbjct: 2   LFVGNLPDATTSEELRALFEKYGTVTECDVVK--------NYGFVHMEEEEDAEDAIKAL 53

Query: 305 DNALIDDRRIHV 316
           +      +RI+V
Sbjct: 54  NGYEFMGKRINV 65

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

>gnl|CDD|237171 PRK12678, PRK12678, transcription termination factor Rho; Provisional

 Score = 60.3 bits (147), Expect = 2e-09
 Identities = 35/191 (18%), Positives = 53/191 (27%), Gaps = 25/191 (13%)

Query: 385 DGETPEKSRREKKHRGHDPDDRVERNMNRLSSDLRHRDQERRELSYRQRESDRTRENRED 444
             +  E+  R +  R        E      +       +   E    +R     RE+R+ 
Sbjct: 124 AAQARERRERGEAARRGAARKAGEGGEQPATEARADAAERTEEEERDERRRRGDREDRQA 183

Query: 445 RRNRDGQESRNVQKQEVRDDDGRYESDHPKSSDTDRYRDWRGGGDYRKRSADSDSRAERR 504
              R  +  R    +E   D    +    +     R               D   R  RR
Sbjct: 184 EAERGERGRR----EERGRDGDDRDRRDRREQGDRREER---------GRRDGGDRRGRR 230

Query: 505 EDGDYRKRNSDNGSHRDRRDDQDYRKKSADGDIHGDRRYDR--DNRKNSGNSELRDAKKE 562
              D R    D+        D D      DG+  G RR  R  D  +          ++E
Sbjct: 231 RRRDRRDARGDDNREDRGDRDGD------DGEGRGGRRGRRFRDRDRRGRRGGDGGNERE 284

Query: 563 PSYKRGRRDDD 573
           P      R+DD
Sbjct: 285 PE----LREDD 291

Length = 672

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

 Score = 54.3 bits (131), Expect = 2e-09
 Identities = 18/63 (28%), Positives = 37/63 (58%)

Query: 256 DEDLHTIFSRFGTVVSAEIIRDFKTGDSLNYAFIEFENRQACERAYSKMDNALIDDRRIH 315
            E+L ++F   G + S +I+RD  TG SL Y F+++ +    ++A + ++   I ++R+ 
Sbjct: 14  QEELRSLFEAIGPIESCKIVRDRITGQSLGYGFVDYVDENDAQKAINTLNGFEIRNKRLK 73

Query: 316 VDF 318
           V +
Sbjct: 74  VSY 76

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

 Score = 54.3 bits (131), Expect = 2e-09
 Identities = 22/76 (28%), Positives = 38/76 (50%)

Query: 245 LFVCKLNPVTEDEDLHTIFSRFGTVVSAEIIRDFKTGDSLNYAFIEFENRQACERAYSKM 304
           L+V  +   T  +DL  +F ++G +V   I  DF T     +A+++FE+ +  E A   +
Sbjct: 3   LYVRNVADATRPDDLRRLFGKYGPIVDVYIPLDFYTRRPRGFAYVQFEDVRDAEDALYYL 62

Query: 305 DNALIDDRRIHVDFSQ 320
           D      R I + F+Q
Sbjct: 63  DRTRFLGREIEIQFAQ 78

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

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

 Score = 59.1 bits (143), Expect = 4e-09
 Identities = 25/76 (32%), Positives = 40/76 (52%)

Query: 245 LFVCKLNPVTEDEDLHTIFSRFGTVVSAEIIRDFKTGDSLNYAFIEFENRQACERAYSKM 304
           L+V  L+P   +  L+ +F  FG V+S  + RD  T  SL Y ++ F+N    ERA   M
Sbjct: 3   LYVGDLDPDVTEAKLYDLFKPFGPVLSVRVCRDSVTRRSLGYGYVNFQNPADAERALETM 62

Query: 305 DNALIDDRRIHVDFSQ 320
           +   +  + I + +SQ
Sbjct: 63  NFKRLGGKPIRIMWSQ 78

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

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

 Score = 53.0 bits (128), Expect = 4e-09
 Identities = 22/75 (29%), Positives = 40/75 (53%), Gaps = 4/75 (5%)

Query: 245 LFVCKLNPVTEDEDLHTIFSRFGTVVSAEIIRDFKTGDS-LN--YAFIEFENRQACERAY 301
           ++V  L+   +++DL  IFS+FG V S  I +        LN  +AF+ F++  + E A 
Sbjct: 3   IYVRNLDFKLDEDDLRGIFSKFGEVESIRIPKKQDEKQGRLNNGFAFVTFKDASSAENAL 62

Query: 302 SKMDNALIDDRRIHV 316
            +++   +  R+I V
Sbjct: 63  -QLNGTELGGRKISV 76

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

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

 Score = 52.7 bits (127), Expect = 5e-09
 Identities = 23/73 (31%), Positives = 35/73 (47%), Gaps = 1/73 (1%)

Query: 244 VLFVCKLNPVTEDEDLHTIFSRFGTVVSAEIIRDFKTGDSLNYAFIEFENRQACERAYSK 303
            LFV  L      ++L   FS+FG V S  +  D +TG S  Y F+ F +R   E A  K
Sbjct: 1   KLFVGNLPWTVGSKELKEYFSQFGKVKSCNVPFDKETGLSKGYGFVSFSSRDGLENALQK 60

Query: 304 MDNALIDDRRIHV 316
               +++  ++ V
Sbjct: 61  -QKHILEGNKLQV 72

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

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

 Score = 52.6 bits (127), Expect = 7e-09
 Identities = 22/81 (27%), Positives = 39/81 (48%), Gaps = 5/81 (6%)

Query: 244 VLFVCKLNPVTEDEDLHTIFSRFGTVVSAEIIR-----DFKTGDSLNYAFIEFENRQACE 298
            LFV  LN  T +E L   F + G V S  I +           S+ Y F+EF++++A +
Sbjct: 2   TLFVKNLNFKTTEETLKKHFEKCGGVRSVTIAKKKDPKGPGKLLSMGYGFVEFKSKEAAQ 61

Query: 299 RAYSKMDNALIDDRRIHVDFS 319
           +A  ++   ++D   + +  S
Sbjct: 62  KALKRLQGTVLDGHALELKLS 82

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|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 = 51.9 bits (125), Expect = 9e-09
 Identities = 22/64 (34%), Positives = 32/64 (50%)

Query: 256 DEDLHTIFSRFGTVVSAEIIRDFKTGDSLNYAFIEFENRQACERAYSKMDNALIDDRRIH 315
           +E L  IFS  G VVS  ++ D  TG    Y F EFE+ +    A   ++    + R + 
Sbjct: 12  EEQLIEIFSEVGPVVSFRLVTDRDTGKPKGYGFCEFEDIETAASAIRNLNGYEFNGRALR 71

Query: 316 VDFS 319
           VDF+
Sbjct: 72  VDFA 75

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

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

 Score = 51.5 bits (124), Expect = 1e-08
 Identities = 21/72 (29%), Positives = 35/72 (48%)

Query: 245 LFVCKLNPVTEDEDLHTIFSRFGTVVSAEIIRDFKTGDSLNYAFIEFENRQACERAYSKM 304
           L+V  L    +++ LH  F  FG +   +I  D++T     +AF+EFE  +    A   M
Sbjct: 1   LYVGGLAEEVDEKVLHAAFIPFGDIKDIQIPLDYETQKHRGFAFVEFEEPEDAAAAIDNM 60

Query: 305 DNALIDDRRIHV 316
           + + +  R I V
Sbjct: 61  NESELFGRTIRV 72

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

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

 Score = 51.7 bits (124), Expect = 1e-08
 Identities = 23/74 (31%), Positives = 38/74 (51%)

Query: 245 LFVCKLNPVTEDEDLHTIFSRFGTVVSAEIIRDFKTGDSLNYAFIEFENRQACERAYSKM 304
           +FV  L+P   D  L   FS F +   A ++ D K+G S  Y F+ F ++Q  E A ++M
Sbjct: 2   IFVGDLSPEVTDATLFAAFSAFPSCSDARVMWDMKSGRSRGYGFVSFRSQQDAENAINEM 61

Query: 305 DNALIDDRRIHVDF 318
           +   +  R I  ++
Sbjct: 62  NGKWLGSRPIRCNW 75

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

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

 Score = 51.9 bits (125), Expect = 1e-08
 Identities = 25/75 (33%), Positives = 41/75 (54%), Gaps = 2/75 (2%)

Query: 242 ENVLFVCKLNPVTEDEDLHTIFSRFGTVVSAEIIRDFKTGDSLNYAFIEFENRQACERAY 301
            N +FV  + P T +E+L   FSRFG+V   +II D + G S  Y F+ FE ++  E+  
Sbjct: 2   PNRIFVGGIPPDTTEEELRDFFSRFGSVKDVKIITD-RAGVSKGYGFVTFETQEDAEKI- 59

Query: 302 SKMDNALIDDRRIHV 316
             M N     +++++
Sbjct: 60  LAMGNLNFRGKKLNI 74

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

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

 Score = 51.3 bits (123), Expect = 1e-08
 Identities = 24/73 (32%), Positives = 41/73 (56%)

Query: 244 VLFVCKLNPVTEDEDLHTIFSRFGTVVSAEIIRDFKTGDSLNYAFIEFENRQACERAYSK 303
           V+++  L     +++L   FS+FGTV +  + R  KTG+S +Y FI+F N +    A   
Sbjct: 1   VIYIGHLPHGFLEKELKKYFSQFGTVKNVRVARSKKTGNSKHYGFIQFLNPEVAAIAAKS 60

Query: 304 MDNALIDDRRIHV 316
           M+N L+  + + V
Sbjct: 61  MNNYLLMGKVLQV 73

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

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

 Score = 51.4 bits (124), Expect = 2e-08
 Identities = 22/72 (30%), Positives = 43/72 (59%), Gaps = 1/72 (1%)

Query: 245 LFVCKLNPVTEDEDLHTIFSRFGTVVSAEIIRDFKTGDSLNYAFIEFENRQACERAYSKM 304
           +F+  L+   +++ L+  FS FG ++S ++  D + G S  Y F+ FE  +A  RA  K+
Sbjct: 5   IFIKNLDKSIDNKALYDTFSAFGNILSCKVATD-ENGGSKGYGFVHFETEEAAVRAIEKV 63

Query: 305 DNALIDDRRIHV 316
           +  L++D+++ V
Sbjct: 64  NGMLLNDKKVFV 75

This subfamily corresponds to the RRM2 of type I poly(A)-binding proteins (PABPs), highly conserved proteins that bind to the poly(A) tail present at the 3' ends of most eukaryotic mRNAs. They have been implicated in the regulation of poly(A) tail length during the polyadenylation reaction, translation initiation, mRNA stabilization by influencing the rate of deadenylation and inhibition of mRNA decapping. The family represents type I polyadenylate-binding proteins (PABPs), including polyadenylate-binding protein 1 (PABP-1 or PABPC1), polyadenylate-binding protein 3 (PABP-3 or PABPC3), polyadenylate-binding protein 4 (PABP-4 or APP-1 or iPABP), polyadenylate-binding protein 5 (PABP-5 or PABPC5), polyadenylate-binding protein 1-like (PABP-1-like or PABPC1L), polyadenylate-binding protein 1-like 2 (PABPC1L2 or RBM32), polyadenylate-binding protein 4-like (PABP-4-like or PABPC4L), yeast polyadenylate-binding protein, cytoplasmic and nuclear (PABP or ACBP-67), and similar proteins. PABP-1 is a ubiquitously expressed multifunctional protein that may play a role in 3' end formation of mRNA, translation initiation, mRNA stabilization, protection of poly(A) from nuclease activity, mRNA deadenylation, inhibition of mRNA decapping, and mRNP maturation. Although PABP-1 is thought to be a cytoplasmic protein, it is also found in the nucleus. PABP-1 may be involved in nucleocytoplasmic trafficking and utilization of mRNP particles. PABP-1 contains four copies of RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), a less well conserved linker region, and a proline-rich C-terminal conserved domain (CTD). PABP-3 is a testis-specific poly(A)-binding protein specifically expressed in round spermatids. It is mainly found in mammalian and may play an important role in the testis-specific regulation of mRNA homeostasis. PABP-3 shows significant sequence similarity to PABP-1. However, it binds to poly(A) with a lower affinity than PABP-1. Moreover, PABP-1 possesses an A-rich sequence in its 5'-UTR and allows binding of PABP and blockage of translation of its own mRNA. In contrast, PABP-3 lacks the A-rich sequence in its 5'-UTR. PABP-4 is an inducible poly(A)-binding protein (iPABP) that is primarily localized to the cytoplasm. It shows significant sequence similarity to PABP-1 as well. The RNA binding properties of PABP-1 and PABP-4 appear to be identical. PABP-5 is encoded by PABPC5 gene within the X-specific subinterval, and expressed in fetal brain and in a range of adult tissues in mammalian, such as ovary and testis. It may play an important role in germ cell development. Unlike other PABPs, PABP-5 contains only four RRMs, but lacks both the linker region and the CTD. PABP-1-like and PABP-1-like 2 are the orthologs of PABP-1. PABP-4-like is the ortholog of PABP-5. Their cellular functions remain unclear. The family also includes the yeast PABP, a conserved poly(A) binding protein containing poly(A) tails that can be attached to the 3'-ends of mRNAs. The yeast PABP and its homologs may play important roles in the initiation of translation and in mRNA decay. Like vertebrate PABP-1, the yeast PABP contains four RRMs, a linker region, and a proline-rich CTD as well. The first two RRMs are mainly responsible for specific binding to poly(A). The proline-rich region may be involved in protein-protein interactions. . Length = 77

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

 Score = 51.4 bits (124), Expect = 2e-08
 Identities = 20/75 (26%), Positives = 41/75 (54%)

Query: 244 VLFVCKLNPVTEDEDLHTIFSRFGTVVSAEIIRDFKTGDSLNYAFIEFENRQACERAYSK 303
           ++FV  ++   ++ED+H  F+ FG + +  +  D +TG    YA IE+E ++  + A   
Sbjct: 8   IIFVTGVHEEAQEEDVHDKFAEFGEIKNLHLNLDRRTGFVKGYALIEYETKKEAQAAIEG 67

Query: 304 MDNALIDDRRIHVDF 318
           ++   +  + I VD+
Sbjct: 68  LNGKELLGQTISVDW 82

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

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

 Score = 51.0 bits (123), Expect = 2e-08
 Identities = 21/70 (30%), Positives = 36/70 (51%), Gaps = 2/70 (2%)

Query: 245 LFVCKLNPVTEDEDLHTIFSRFGTVVSAEIIRDFKTGDSLNYAFIEFENRQACERAYSKM 304
           L+V  L P   +EDL   FS +G V    ++R+        +AF+EF + +  E A  K+
Sbjct: 1   LYVRNLPPSVTEEDLREFFSPYGKVEGVRLVRNKD--RPRGFAFVEFASPEDAEAALKKL 58

Query: 305 DNALIDDRRI 314
           +  ++D R +
Sbjct: 59  NGLVLDGRTL 68

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

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

 Score = 51.3 bits (123), Expect = 2e-08
 Identities = 20/66 (30%), Positives = 40/66 (60%), Gaps = 1/66 (1%)

Query: 254 TEDEDLHTIFSRFGTVVSAEIIRDFKTGDSLNYAFIEFENRQACERAYSKMDNALIDDRR 313
           T+DE + ++FS  G + S ++IRD  TG SL Y F+ + + +  E+A + ++   + ++ 
Sbjct: 14  TQDE-IRSLFSSIGEIESCKLIRDKVTGQSLGYGFVNYVDPEDAEKAINTLNGLRLQNKT 72

Query: 314 IHVDFS 319
           I V ++
Sbjct: 73  IKVSYA 78

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

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

 Score = 50.7 bits (122), Expect = 2e-08
 Identities = 21/70 (30%), Positives = 37/70 (52%), Gaps = 1/70 (1%)

Query: 245 LFVCKLNPVTEDEDLHTIFSRFGTVVSAEIIRDFKTGDSLNYAFIEFENRQACERAYSKM 304
           LF+  L+  T +E L   FS++G VV   I++D  TG S  + F+ F +  + ++  +  
Sbjct: 1   LFIGGLSWDTTEESLREYFSKYGEVVDCVIMKDPITGRSRGFGFVTFADPSSVDKVLAA- 59

Query: 305 DNALIDDRRI 314
              ++D R I
Sbjct: 60  KPHVLDGREI 69

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

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

 Score = 50.7 bits (122), Expect = 2e-08
 Identities = 27/76 (35%), Positives = 40/76 (52%), Gaps = 3/76 (3%)

Query: 244 VLFVCKLNP-VTEDEDLHTIFSRFGTVVSAEIIRDFKTGDSLNYAFIEFENRQACERAYS 302
            L V  L+  VTE EDL  +F R G V   +I  D ++G S   A + FE R+  ERA  
Sbjct: 2   RLRVSNLHYDVTE-EDLEELFGRVGEVKKVKINYD-RSGRSEGTADVVFEKREDAERAIK 59

Query: 303 KMDNALIDDRRIHVDF 318
           + +  L+D + + V+ 
Sbjct: 60  QFNGVLLDGQPMQVEL 75

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

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

 Score = 50.7 bits (122), Expect = 3e-08
 Identities = 19/66 (28%), Positives = 32/66 (48%), Gaps = 1/66 (1%)

Query: 254 TEDEDLHTIFSRFGTVVSAEIIRDFKTGDSLNYAFIEFENRQACERAYSKMDNALIDDRR 313
             + DL  +FS FG V    I R    G    +AF++F ++   E+A   ++   I  R 
Sbjct: 11  CTEADLKKLFSPFGFVWEVTIPRKP-DGKKKGFAFVQFTSKADAEKAIKGVNGKKIKGRP 69

Query: 314 IHVDFS 319
           + VD++
Sbjct: 70  VAVDWA 75

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

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

 Score = 50.4 bits (121), Expect = 3e-08
 Identities = 23/72 (31%), Positives = 38/72 (52%)

Query: 245 LFVCKLNPVTEDEDLHTIFSRFGTVVSAEIIRDFKTGDSLNYAFIEFENRQACERAYSKM 304
           LFV  L   T +E+L  +F  FG +    +  D +T  S  +AF+ F   +   +AYS++
Sbjct: 2   LFVRNLPFTTTEEELRELFEAFGEISEVHLPLDKETKRSKGFAFVSFMFPEHAVKAYSEL 61

Query: 305 DNALIDDRRIHV 316
           D ++   R +HV
Sbjct: 62  DGSIFQGRLLHV 73

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

>gnl|CDD|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 = 50.6 bits (121), Expect = 4e-08
 Identities = 22/76 (28%), Positives = 41/76 (53%)

Query: 245 LFVCKLNPVTEDEDLHTIFSRFGTVVSAEIIRDFKTGDSLNYAFIEFENRQACERAYSKM 304
           LF+  L+  T ++ L  +FS++G +    +++D +T  S  + F+ FEN    + A   M
Sbjct: 3   LFIGGLSFDTNEQSLEQVFSKYGQISEVVVVKDRETQRSRGFGFVTFENPDDAKDAMMAM 62

Query: 305 DNALIDDRRIHVDFSQ 320
           +   +D R+I VD + 
Sbjct: 63  NGKSVDGRQIRVDQAG 78

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

 Score = 49.9 bits (120), Expect = 5e-08
 Identities = 22/60 (36%), Positives = 33/60 (55%)

Query: 257 EDLHTIFSRFGTVVSAEIIRDFKTGDSLNYAFIEFENRQACERAYSKMDNALIDDRRIHV 316
            +L   FS+FGTV    + R  KTG S  YAF+EFE+ +  +     M+N L+ +R +  
Sbjct: 14  PELRKYFSQFGTVTRLRLSRSKKTGKSKGYAFVEFESPEVAKIVAETMNNYLLFERLLKC 73

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

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

 Score = 52.0 bits (124), Expect = 5e-08
 Identities = 30/97 (30%), Positives = 47/97 (48%)

Query: 245 LFVCKLNPVTEDEDLHTIFSRFGTVVSAEIIRDFKTGDSLNYAFIEFENRQACERAYSKM 304
           LF+  L+  T+D  L   F+ FG VV A++I D +TG S  + F+ F +  A   A S+M
Sbjct: 37  LFIGGLSWGTDDASLRDAFAHFGDVVDAKVIVDRETGRSRGFGFVNFNDEGAATAAISEM 96

Query: 305 DNALIDDRRIHVDFSQSVSKLWNQFRRRDHQTGKGKG 341
           D   ++ R I V+ +         +      +G G G
Sbjct: 97  DGKELNGRHIRVNPANDRPSAPRAYGGGGGYSGGGGG 133

Length = 144

>gnl|CDD|237171 PRK12678, PRK12678, transcription termination factor Rho; Provisional

 Score = 55.3 bits (134), Expect = 6e-08
 Identities = 32/201 (15%), Positives = 54/201 (26%), Gaps = 5/201 (2%)

Query: 387 ETPEKSRREKKHRGHDPDDRVERNMNRLSSDLRHRDQERRELSYRQRESDRTRENREDRR 446
                +RR  +                 +             +  +  S        +RR
Sbjct: 72  APAAAARRAARAAAAARQAEQPAAEAAAAKAEAAPAARAAAAAAAEAASAPEAAQARERR 131

Query: 447 NRDGQESRNVQKQEVRDDDGRYESDHPKSSDTDRYRDWRGGGDYRKRSADSDSRAERRED 506
            R     R   ++     +    ++    +      + R     R    D  + AER E 
Sbjct: 132 ERGEAARRGAARKAGEGGEQP-ATEARADAAERTEEEERDERRRRGDREDRQAEAERGER 190

Query: 507 GDYRKRNSDNGSHRDRRDDQDYRKKSADGDIHGDRRYDRDNRKNSGNSELRDAKKEPSYK 566
           G   +R  D    RDRRD ++ +    +     D    R  R+     + R         
Sbjct: 191 GRREERGRDGDD-RDRRDRRE-QGDRREERGRRDGGDRRGRRRRRDRRDARGDDNREDRG 248

Query: 567 RGRRDDDSYKRWPEDRGNRRR 587
               DD   +     RG R R
Sbjct: 249 DRDGDDGEGRG--GRRGRRFR 267

Length = 672

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

 Score = 50.0 bits (120), Expect = 6e-08
 Identities = 20/55 (36%), Positives = 32/55 (58%), Gaps = 1/55 (1%)

Query: 256 DED-LHTIFSRFGTVVSAEIIRDFKTGDSLNYAFIEFENRQACERAYSKMDNALI 309
           DE  +++ F+  G V S +IIR+ +TG S  Y F+EF   +A E+A   ++   I
Sbjct: 12  DEAYIYSAFAECGEVTSVKIIRNKQTGKSAGYGFVEFATHEAAEQALQSLNGKPI 66

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

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

 Score = 49.6 bits (119), Expect = 7e-08
 Identities = 20/64 (31%), Positives = 37/64 (57%)

Query: 243 NVLFVCKLNPVTEDEDLHTIFSRFGTVVSAEIIRDFKTGDSLNYAFIEFENRQACERAYS 302
           N ++V  ++P   ++D+ ++F  FG + S  +  D +TG    Y FIE+EN Q+ + A +
Sbjct: 1   NRIYVASVHPDLSEDDIKSVFEAFGKIKSCSLAPDPETGKHKGYGFIEYENPQSAQDAIA 60

Query: 303 KMDN 306
            M+ 
Sbjct: 61  SMNL 64

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

 Score = 49.3 bits (118), Expect = 1e-07
 Identities = 19/78 (24%), Positives = 35/78 (44%)

Query: 240 PPENVLFVCKLNPVTEDEDLHTIFSRFGTVVSAEIIRDFKTGDSLNYAFIEFENRQACER 299
           P  + LFV  L     +++L   F  FG V+   I      G   N+ F+ F++ +A ++
Sbjct: 1   PDSHQLFVGNLPHDITEDELKEFFKEFGNVLEVRINSKGGGGRLPNFGFVVFDDPEAVQK 60

Query: 300 AYSKMDNALIDDRRIHVD 317
             +        D R++V+
Sbjct: 61  ILANKPIYFRGDHRLNVE 78

This subfamily corresponds to the RRM domain in the G3BP family of RNA-binding and SH3 domain-binding proteins. G3BP acts at the level of RNA metabolism in response to cell signaling, possibly as RNA transcript stabilizing factors or an RNase. Members include G3BP1, G3BP2 and similar proteins. These proteins associate directly with the SH3 domain of GTPase-activating protein (GAP), which functions as an inhibitor of Ras. They all contain an N-terminal nuclear transfer factor 2 (NTF2)-like domain, an acidic domain, a domain containing PXXP motif(s), an RNA recognition motif (RRM), and an Arg-Gly-rich region (RGG-rich region, or arginine methylation motif). Length = 81

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

 Score = 49.6 bits (119), Expect = 1e-07
 Identities = 19/60 (31%), Positives = 36/60 (60%)

Query: 258 DLHTIFSRFGTVVSAEIIRDFKTGDSLNYAFIEFENRQACERAYSKMDNALIDDRRIHVD 317
           D+  +FS++G +V   ++RD KTG S  +AF+ +E++++   A   ++   +  R I VD
Sbjct: 25  DILCVFSQYGEIVDINLVRDKKTGKSKGFAFLAYEDQRSTILAVDNLNGIKLLGRTIRVD 84

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

 Score = 48.9 bits (117), Expect = 1e-07
 Identities = 22/72 (30%), Positives = 40/72 (55%)

Query: 245 LFVCKLNPVTEDEDLHTIFSRFGTVVSAEIIRDFKTGDSLNYAFIEFENRQACERAYSKM 304
           LFV  L    +++DL  +FS+FG +    +  D K+G S  +A++ F + +   +AY ++
Sbjct: 5   LFVRNLPYSCKEDDLEKLFSKFGELSEVHVAIDKKSGKSKGFAYVLFLDPEDAVKAYKEL 64

Query: 305 DNALIDDRRIHV 316
           D  +   R IH+
Sbjct: 65  DGKVFQGRLIHI 76

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

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

 Score = 48.9 bits (117), Expect = 1e-07
 Identities = 22/58 (37%), Positives = 35/58 (60%)

Query: 245 LFVCKLNPVTEDEDLHTIFSRFGTVVSAEIIRDFKTGDSLNYAFIEFENRQACERAYS 302
           +FV  L P   +E+    FS+FG VV A++++D  TG S  + F+ F++  A ER +S
Sbjct: 2   IFVGGLPPDVTEEEFKEYFSQFGKVVDAQLMQDHDTGRSRGFGFVTFDSESAVERVFS 59

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

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

 Score = 48.5 bits (116), Expect = 2e-07
 Identities = 24/78 (30%), Positives = 38/78 (48%)

Query: 245 LFVCKLNPVTEDEDLHTIFSRFGTVVSAEIIRDFKTGDSLNYAFIEFENRQACERAYSKM 304
           ++V  L      E L  +FS++GTVV   + R   TGD   +AFIEFE  +  ++A   +
Sbjct: 2   VYVECLPKNATHEWLKAVFSKYGTVVYVSLPRYKHTGDIKGFAFIEFETPEEAQKACKHL 61

Query: 305 DNALIDDRRIHVDFSQSV 322
           +N           F ++V
Sbjct: 62  NNPPETATDKPGKFPKTV 79

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

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

 Score = 48.7 bits (117), Expect = 2e-07
 Identities = 25/84 (29%), Positives = 44/84 (52%), Gaps = 5/84 (5%)

Query: 241 PENVLFVCKLNPVTEDEDLHTIFSRFGTVVSAEI--IRDFKTGDSLNYAFIEFENRQACE 298
           P N L +  L+ +T +ED+    S   +V   ++  IRD  TG S  +AF+EF + +   
Sbjct: 1   PTNTLILRGLDLLTTEEDILQALSAIASVPIKDVRLIRDKLTGTSRGFAFVEFPSLEDAT 60

Query: 299 R---AYSKMDNALIDDRRIHVDFS 319
           +   A + +D  +ID R + V ++
Sbjct: 61  QWMDALNNLDPFVIDGRVVRVSYA 84

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

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

 Score = 48.5 bits (116), Expect = 2e-07
 Identities = 22/76 (28%), Positives = 45/76 (59%), Gaps = 2/76 (2%)

Query: 245 LFVCKLNPVTEDEDLHTIFSRFGTVVSAEIIRDFKTGDSLNYAFIEFENRQACERAYSKM 304
           +FV +L+P    E+L+  FSR G ++   +I+     ++  +AFI+FE  QA  RA    
Sbjct: 6   IFVGQLSPDVTKEELNERFSRHGKILEVNLIKRANHTNA--FAFIKFEREQAAARAVESE 63

Query: 305 DNALIDDRRIHVDFSQ 320
           +++++ ++ +HV + +
Sbjct: 64  NHSMLKNKTMHVQYKE 79

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

 Score = 48.7 bits (117), Expect = 2e-07
 Identities = 21/74 (28%), Positives = 41/74 (55%)

Query: 247 VCKLNPVTEDEDLHTIFSRFGTVVSAEIIRDFKTGDSLNYAFIEFENRQACERAYSKMDN 306
           V  L+   +++DL  +F  FG +    + +D +TG S  +AF+ F  R+  ERA  K++ 
Sbjct: 4   VTNLSEDADEDDLRELFRPFGPISRVYLAKDKETGQSRGFAFVTFHTREDAERAIEKLNG 63

Query: 307 ALIDDRRIHVDFSQ 320
              D+  + V++++
Sbjct: 64  FGYDNLILSVEWAK 77

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

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

 Score = 48.4 bits (116), Expect = 2e-07
 Identities = 19/54 (35%), Positives = 32/54 (59%), Gaps = 1/54 (1%)

Query: 252 PVTEDEDLHTIFSRFGTVVSAEIIRDFKTGDSLNYAFIEFENRQACERAYSKMD 305
            +TED DL  IF  FG +   ++ RD +TG S  Y FI+F + +  ++A  +++
Sbjct: 9   NITED-DLRGIFEPFGEIEFVQLQRDPETGRSKGYGFIQFADAEDAKKALEQLN 61

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

 Score = 48.6 bits (116), Expect = 2e-07
 Identities = 17/66 (25%), Positives = 40/66 (60%)

Query: 256 DEDLHTIFSRFGTVVSAEIIRDFKTGDSLNYAFIEFENRQACERAYSKMDNALIDDRRIH 315
           DE+  ++F   G V + +I+RD +TG S  + F+++++ +  +RA   ++   + ++RI 
Sbjct: 14  DEEFRSLFLAVGPVKNCKIVRDKRTGYSYGFGFVDYQSAEDAQRAIRTLNGLQLQNKRIK 73

Query: 316 VDFSQS 321
           V +++ 
Sbjct: 74  VAYARP 79

This subfamily corresponds to the RRM1 of SXL which governs sexual differentiation and X chromosome dosage compensation in Drosophila melanogaster. It induces female-specific alternative splicing of the transformer (tra) pre-mRNA by binding to the tra uridine-rich polypyrimidine tract at the non-sex-specific 3' splice site during the sex-determination process. SXL binds also to its own pre-mRNA and promotes female-specific alternative splicing. SXL contains an N-terminal Gly/Asn-rich domain that may be responsible for the protein-protein interaction, and tandem RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), that show high preference to bind single-stranded, uridine-rich target RNA transcripts. . Length = 81

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

 Score = 48.1 bits (115), Expect = 2e-07
 Identities = 21/74 (28%), Positives = 35/74 (47%)

Query: 245 LFVCKLNPVTEDEDLHTIFSRFGTVVSAEIIRDFKTGDSLNYAFIEFENRQACERAYSKM 304
           +FV  L P  ++  L  +FS FG V + ++IRD  T     Y F+   N +    A + +
Sbjct: 4   IFVYNLPPDADESLLWQLFSPFGAVTNVKVIRDLTTNKCKGYGFVTMTNYEEAYSAIASL 63

Query: 305 DNALIDDRRIHVDF 318
           +   +  R + V F
Sbjct: 64  NGYRLGGRVLQVSF 77

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

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

 Score = 53.3 bits (128), Expect = 3e-07
 Identities = 41/211 (19%), Positives = 86/211 (40%), Gaps = 31/211 (14%)

Query: 245 LFVCKLNPVTEDEDLHTIFSRFGTVVSAEIIRDFKTGDSLNYAFIEFENRQACERAYSKM 304
           +FV  L+   +++ L   FS+FG ++S ++  D + G S  Y F+ FE  ++ + A  K+
Sbjct: 91  IFVKNLDKSVDNKALFDTFSKFGNILSCKVATD-ENGKSRGYGFVHFEKEESAKAAIQKV 149

Query: 305 DNALIDDRRIHVDFSQSVSKLWNQFRRRDHQTGKGKGCFKCGGLDHIAKDCTGQQPAKY- 363
           +  L++D+ ++V           +  R      K    +       + +D   +  AK+ 
Sbjct: 150 NGMLLNDKEVYVGRFIK------KHEREAAPLKKFTNLYVKNLDPSVNEDKLRELFAKFG 203

Query: 364 ------ILRDDNRQHGGYSDSRYEMVFDGETPEKSRR--EKKHRGHDPDDRVERNMNRLS 415
                 +++D + +  G++   +      E  E + +  E+ +       +      +L 
Sbjct: 204 EITSAAVMKDGSGRSRGFAFVNF------EKHEDAAKAVEEMNGKKIGLAKEG---KKLY 254

Query: 416 SDLRHRDQERRELSYRQRESDRTRENREDRR 446
                R Q+R E   R+ E  R  E  +  R
Sbjct: 255 VG---RAQKRAE---REAELRRKFEELQQER 279

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

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

 Score = 47.9 bits (114), Expect = 3e-07
 Identities = 22/76 (28%), Positives = 37/76 (48%)

Query: 245 LFVCKLNPVTEDEDLHTIFSRFGTVVSAEIIRDFKTGDSLNYAFIEFENRQACERAYSKM 304
           LFV  L      EDL   FS    +  A ++ D +TG+S  Y F+ F   +  + A +K+
Sbjct: 2   LFVRNLAFSVTQEDLTDFFSDVAPIKHAVVVTDPETGESRGYGFVTFAMLEDAQEALAKL 61

Query: 305 DNALIDDRRIHVDFSQ 320
            N  +  R + +D ++
Sbjct: 62  KNKKLHGRILRLDIAE 77

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

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

 Score = 48.1 bits (114), Expect = 3e-07
 Identities = 27/79 (34%), Positives = 42/79 (53%)

Query: 241 PENVLFVCKLNPVTEDEDLHTIFSRFGTVVSAEIIRDFKTGDSLNYAFIEFENRQACERA 300
           P   L V  L+  T + DL  +FS++G +    I+ D ++  S  +AF+ FEN    + A
Sbjct: 8   PNCCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEA 67

Query: 301 YSKMDNALIDDRRIHVDFS 319
             + +   +D RRI VDFS
Sbjct: 68  KERANGMELDGRRIRVDFS 86

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

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

 Score = 47.5 bits (114), Expect = 5e-07
 Identities = 23/71 (32%), Positives = 35/71 (49%), Gaps = 8/71 (11%)

Query: 244 VLFVC---KLNPVTEDEDLHTIFSRFGTVVSAEIIRDFKTGDSLNYAFIEFENRQACERA 300
           VL V     L PVT D  LH +FS +G V   E I  F+    +  A ++F++ ++ E A
Sbjct: 1   VLLVTISNLLYPVTVDV-LHQVFSPYGAV---EKILIFEKNTGVQ-ALVQFDSVESAENA 55

Query: 301 YSKMDNALIDD 311
              ++   I D
Sbjct: 56  KKALNGRNIYD 66

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

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

 Score = 47.0 bits (111), Expect = 6e-07
 Identities = 22/75 (29%), Positives = 39/75 (52%)

Query: 245 LFVCKLNPVTEDEDLHTIFSRFGTVVSAEIIRDFKTGDSLNYAFIEFENRQACERAYSKM 304
           +FV  L+P    +D+   F+ FG +  A +++D  TG S  Y F+ F N+   E A  +M
Sbjct: 4   VFVGDLSPEITTDDIKAAFAPFGRISDARVVKDMATGKSKGYGFVSFFNKWDAENAIQQM 63

Query: 305 DNALIDDRRIHVDFS 319
               +  R+I  +++
Sbjct: 64  GGQWLGGRQIRTNWA 78

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

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

 Score = 46.9 bits (111), Expect = 6e-07
 Identities = 24/70 (34%), Positives = 38/70 (54%)

Query: 250 LNPVTEDEDLHTIFSRFGTVVSAEIIRDFKTGDSLNYAFIEFENRQACERAYSKMDNALI 309
           L+  T + DL  +FSR+G +    ++ D +TG S  +AF+ FE     + A    +   +
Sbjct: 7   LSLYTTERDLREVFSRYGPLAGVNVVYDQRTGRSRGFAFVYFERIDDSKEAMEHANGMEL 66

Query: 310 DDRRIHVDFS 319
           D RRI VD+S
Sbjct: 67  DGRRIRVDYS 76

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

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

 Score = 46.8 bits (112), Expect = 7e-07
 Identities = 22/63 (34%), Positives = 34/63 (53%), Gaps = 2/63 (3%)

Query: 245 LFVCKLNPVTEDE-DLHTIFSRFGTVVSAEIIRDFKTGDSLNYAFIEFENRQACERAYSK 303
           LFV +L P T  E D+  +F  +G +    IIRD  TG S   AF++F +R+  ++A   
Sbjct: 2   LFVGQL-PKTATEEDVRALFEEYGNIEEVTIIRDKDTGQSKGCAFVKFSSREEAQKAIEA 60

Query: 304 MDN 306
           +  
Sbjct: 61  LHG 63

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

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

 Score = 46.6 bits (110), Expect = 8e-07
 Identities = 23/75 (30%), Positives = 39/75 (52%)

Query: 245 LFVCKLNPVTEDEDLHTIFSRFGTVVSAEIIRDFKTGDSLNYAFIEFENRQACERAYSKM 304
           +FV  L+P    ED+ + F+ FG +  A +++D  TG S  Y F+ F N+   E A   M
Sbjct: 4   VFVGDLSPEITTEDIKSAFAPFGKISDARVVKDMATGKSKGYGFVSFYNKLDAENAIVHM 63

Query: 305 DNALIDDRRIHVDFS 319
               +  R+I  +++
Sbjct: 64  GGQWLGGRQIRTNWA 78

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

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

 Score = 46.8 bits (112), Expect = 8e-07
 Identities = 25/80 (31%), Positives = 40/80 (50%), Gaps = 5/80 (6%)

Query: 245 LFVCKLNPVTEDEDLHTIFSRFGTVVSAEIIRDFKTGDSLNYAFIEFENR---QACERAY 301
           +F+  L     +E+L  +FS+FG V  A I++D  TG S   AF++F+ +   Q C  A 
Sbjct: 3   VFIRNLPFDATEEELKELFSQFGEVKYARIVKDKLTGHSKGTAFVKFKTKESAQKCLEAA 62

Query: 302 SK--MDNALIDDRRIHVDFS 319
                    +D RR+ V  +
Sbjct: 63  DNAEDSGLSLDGRRLIVTLA 82

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

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

 Score = 46.5 bits (111), Expect = 9e-07
 Identities = 20/59 (33%), Positives = 32/59 (54%)

Query: 258 DLHTIFSRFGTVVSAEIIRDFKTGDSLNYAFIEFENRQACERAYSKMDNALIDDRRIHV 316
           DLH IFS++G VV   I++D +T  S   AFI F +R+   +    ++N  +  R +  
Sbjct: 17  DLHKIFSKYGKVVKVTIVKDKETRKSKGVAFILFLDREDAHKCVKALNNKELFGRTLKC 75

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

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

 Score = 46.4 bits (110), Expect = 9e-07
 Identities = 25/76 (32%), Positives = 39/76 (51%), Gaps = 1/76 (1%)

Query: 242 ENVLFVCKLNPVTEDEDLHTIF-SRFGTVVSAEIIRDFKTGDSLNYAFIEFENRQACERA 300
           E  +FV  L+P   + DL ++F SRF +  SA+I+ D  TG S  Y F+ F +    +RA
Sbjct: 1   EYSIFVGDLSPEVNESDLVSLFQSRFPSCKSAKIMTDPVTGVSRGYGFVRFSDENDQQRA 60

Query: 301 YSKMDNALIDDRRIHV 316
             +M       R + +
Sbjct: 61  LIEMQGVYCGGRPMRI 76

This subgroup corresponds to the RRM2 of NGR1 and NAM8. NGR1, also termed RNA-binding protein RBP1, is a putative glucose-repressible protein that binds both, RNA and single-stranded DNA (ssDNA), in yeast. It may function in regulating cell growth in early log phase, possibly through its participation in RNA metabolism. NGR1 contains two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), followed by a glutamine-rich stretch that may be involved in transcriptional activity. In addition, NGR1 has an asparagine-rich region near the carboxyl terminus which also harbors a methionine-rich region. The family also includes protein NAM8, which is a putative RNA-binding protein that acts as a suppressor of mitochondrial splicing deficiencies when overexpressed in yeast. It may be a non-essential component of the mitochondrial splicing machinery. Like NGR1, NAM8 contains two RRMs. . Length = 80

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

 Score = 46.0 bits (109), Expect = 1e-06
 Identities = 22/72 (30%), Positives = 36/72 (50%), Gaps = 3/72 (4%)

Query: 245 LFVCKLNPVTEDEDLHTIFSRFGTVVSAEIIRDFKTGDSLNYAFIEFENRQACERAYSK- 303
           +F+  LN  T D+ L   F +FG V    ++RD  TG S  + F+ F+  ++      K 
Sbjct: 1   MFIGGLNWETTDDSLREYFGQFGEVTDCTVMRDSATGRSRGFGFLTFKKPKSVNEVMKKE 60

Query: 304 --MDNALIDDRR 313
             +D  +ID +R
Sbjct: 61  HILDGKIIDPKR 72

This subfamily corresponds to the RRM1 of Hrp1p and similar proteins. Hrp1p or Nab4p, also termed cleavage factor IB (CFIB), is a sequence-specific trans-acting factor that is essential for mRNA 3'-end formation in yeast Saccharomyces cerevisiae. It can be UV cross-linked to RNA and specifically recognizes the (UA)6 RNA element required for both, the cleavage and poly(A) addition, steps. Moreover, Hrp1p can shuttle between the nucleus and the cytoplasm, and play an additional role in the export of mRNAs to the cytoplasm. Hrp1p also interacts with Rna15p and Rna14p, two components of CF1A. In addition, Hrp1p functions as a factor directly involved in modulating the activity of the nonsense-mediated mRNA decay (NMD) pathway. It binds specifically to a downstream sequence element (DSE)-containing RNA and interacts with Upf1p, a component of the surveillance complex, further triggering the NMD pathway. Hrp1p contains two central RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and an arginine-glycine-rich region harboring repeats of the sequence RGGF/Y. . Length = 76

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

 Score = 45.3 bits (108), Expect = 2e-06
 Identities = 23/73 (31%), Positives = 35/73 (47%), Gaps = 8/73 (10%)

Query: 244 VLFVCKLNPVTEDEDLHTIFSRFGTVVSAEIIRDFKTGDSLNYAFIEFENRQACERAYSK 303
           VL+V  L   T +E L  +FS +G V   + I+D        YAF+ FE R    +A  +
Sbjct: 3   VLYVRNLPLSTTEEQLRELFSEYGEVERVKKIKD--------YAFVHFEERDDAVKAMEE 54

Query: 304 MDNALIDDRRIHV 316
           M+   ++   I V
Sbjct: 55  MNGKELEGSPIEV 67

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

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

 Score = 45.8 bits (108), Expect = 2e-06
 Identities = 24/68 (35%), Positives = 41/68 (60%), Gaps = 1/68 (1%)

Query: 253 VTEDEDLHTIFSRFGTVVSAEIIRDFKTGDSLNYAFIEFENRQACERAYSKMDNALIDDR 312
           +T+DE L ++FS  G V SA++IRD   G SL Y F+ + N +  ERA + ++   +  +
Sbjct: 13  MTQDE-LRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVNAKDAERAINTLNGLRLQSK 71

Query: 313 RIHVDFSQ 320
            I V +++
Sbjct: 72  TIKVSYAR 79

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

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

 Score = 45.4 bits (108), Expect = 2e-06
 Identities = 20/70 (28%), Positives = 35/70 (50%), Gaps = 6/70 (8%)

Query: 245 LFVCKLNPVTEDEDLHTIFSRFGTVVSAEIIRDFKTGDSLNYAFIEFENRQACERAYSKM 304
           +FV  L+P   +++L ++F  FG +V  +I      G      F++F +R A E A  ++
Sbjct: 4   VFVGGLDPAVTEDELRSLFGPFGEIVYVKIPPGKGCG------FVQFVHRAAAEAAIQQL 57

Query: 305 DNALIDDRRI 314
              +I   RI
Sbjct: 58  QGTIIGGSRI 67

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

 Score = 45.7 bits (108), Expect = 2e-06
 Identities = 19/62 (30%), Positives = 33/62 (53%)

Query: 245 LFVCKLNPVTEDEDLHTIFSRFGTVVSAEIIRDFKTGDSLNYAFIEFENRQACERAYSKM 304
           L+V  L      ++L  +FS++G ++++ I+RD  TG S    FI F+ R   E A   +
Sbjct: 3   LYVSGLPKTMTQKELEQLFSQYGRIITSRILRDQLTGVSRGVGFIRFDKRIEAEEAIKGL 62

Query: 305 DN 306
           + 
Sbjct: 63  NG 64

This subfamily corresponds to the RRM2 of Hu proteins and SXL. The Hu proteins family represents a group of RNA-binding proteins involved in diverse biological processes. Since the Hu proteins share high homology with the Drosophila embryonic lethal abnormal vision (ELAV) protein, the Hu family is sometimes referred to as the ELAV family. Drosophila ELAV is exclusively expressed in neurons and is required for the correct differentiation and survival of neurons in flies. The neuronal members of the Hu family include Hu-antigen B (HuB or ELAV-2 or Hel-N1), Hu-antigen C (HuC or ELAV-3 or PLE21), and Hu-antigen D (HuD or ELAV-4), which play important roles in neuronal differentiation, plasticity and memory. HuB is also expressed in gonads. Hu-antigen R (HuR or ELAV-1 or HuA) is the ubiquitously expressed Hu family member. It has a variety of biological functions mostly related to the regulation of cellular response to DNA damage and other types of stress. Hu proteins perform their cytoplasmic and nuclear molecular functions by coordinately regulating functionally related mRNAs. In the cytoplasm, Hu proteins recognize and bind to AU-rich RNA elements (AREs) in the 3' untranslated regions (UTRs) of certain target mRNAs, such as GAP-43, vascular epithelial growth factor (VEGF), the glucose transporter GLUT1, eotaxin and c-fos, and stabilize those ARE-containing mRNAs. They also bind and regulate the translation of some target mRNAs, such as neurofilament M, GLUT1, and p27. In the nucleus, Hu proteins function as regulators of polyadenylation and alternative splicing. Each Hu protein contains three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). RRM1 and RRM2 may cooperate in binding to an ARE. RRM3 may help to maintain the stability of the RNA-protein complex, and might also bind to poly(A) tails or be involved in protein-protein interactions. Also included in this subfamily is the sex-lethal protein (SXL) from Drosophila melanogaster. SXL governs sexual differentiation and X chromosome dosage compensation in flies. It induces female-specific alternative splicing of the transformer (tra) pre-mRNA by binding to the tra uridine-rich polypyrimidine tract at the non-sex-specific 3' splice site during the sex-determination process. SXL binds also to its own pre-mRNA and promotes female-specific alternative splicing. SXL contains an N-terminal Gly/Asn-rich domain that may be responsible for the protein-protein interaction, and tandem RRMs that show high preference to bind single-stranded, uridine-rich target RNA transcripts. . Length = 79

>gnl|CDD|240899 cd12453, RRM1_RIM4_like, RNA recognition motif 1 in yeast meiotic activator RIM4 and similar proteins

 Score = 45.5 bits (108), Expect = 2e-06
 Identities = 23/78 (29%), Positives = 40/78 (51%), Gaps = 7/78 (8%)

Query: 241 PENVLFVCKLNPVTEDEDLHTI----FSRFGTVVSAEIIRDFKTGDSLNYAFIEFENRQA 296
           P   +FV  L     D++L       FS++GT+V  +++RD++      YAF++F N   
Sbjct: 1   PSACVFVASLPASKSDDELEAAVTEHFSKYGTLVFVKVLRDWR---QRPYAFVQFTNDDD 57

Query: 297 CERAYSKMDNALIDDRRI 314
            + A +K    ++D R I
Sbjct: 58  AKNALAKGQGTILDGRHI 75

This subfamily corresponds to the RRM1 of RIM4, also termed regulator of IME2 protein 4, a putative RNA binding protein that is expressed at elevated levels early in meiosis. It functions as a meiotic activator required for both the IME1- and IME2-dependent pathways of meiotic gene expression, as well as early events of meiosis, such as meiotic division and recombination, in Saccharomyces cerevisiae. RIM4 contains two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). The family also includes a putative RNA-binding protein termed multicopy suppressor of sporulation protein Msa1. It is a putative RNA-binding protein encoded by a novel gene, msa1, from the fission yeast Schizosaccharomyces pombe. Msa1 may be involved in the inhibition of sexual differentiation by controlling the expression of Ste11-regulated genes, possibly through the pheromone-signaling pathway. Like RIM4, Msa1 also contains two RRMs, both of which are essential for the function of Msa1. . Length = 86

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

 Score = 45.5 bits (107), Expect = 3e-06
 Identities = 21/77 (27%), Positives = 36/77 (46%)

Query: 245 LFVCKLNPVTEDEDLHTIFSRFGTVVSAEIIRDFKTGDSLNYAFIEFENRQACERAYSKM 304
           +FV  L P  ++  L  +F  FG V + ++IRDF T     + F+   N      A + +
Sbjct: 6   IFVYNLAPDADESILWQMFGPFGAVTNVKVIRDFNTNKCKGFGFVTMTNYDEAAMAIASL 65

Query: 305 DNALIDDRRIHVDFSQS 321
           +   + DR + V F  +
Sbjct: 66  NGYRLGDRVLQVSFKTN 82

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

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

 Score = 45.5 bits (107), Expect = 3e-06
 Identities = 22/77 (28%), Positives = 37/77 (48%)

Query: 245 LFVCKLNPVTEDEDLHTIFSRFGTVVSAEIIRDFKTGDSLNYAFIEFENRQACERAYSKM 304
           +FV  L+P  ++  L  +F  FG V + ++IRDF T     + F+   N      A + +
Sbjct: 4   IFVYNLSPEADESVLWQLFGPFGAVTNVKVIRDFTTNKCKGFGFVTMTNYDEAAMAIASL 63

Query: 305 DNALIDDRRIHVDFSQS 321
           +   + DR + V F  S
Sbjct: 64  NGYRLGDRVLQVSFKTS 80

This subgroup corresponds to the RRM3 of HuC, also termed ELAV-like protein 3 (ELAV-3), or paraneoplastic cerebellar degeneration-associated antigen, or paraneoplastic limbic encephalitis antigen 21 (PLE21), one of the neuronal members of the Hu family. The neuronal Hu proteins play important roles in neuronal differentiation, plasticity and memory. Like other Hu proteins, HuC contains three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). RRM1 and RRM2 may cooperate in binding to an AU-rich RNA element (ARE). The AU-rich element binding of HuC can be inhibited by flavonoids. RRM3 may help to maintain the stability of the RNA-protein complex, and might also bind to poly(A) tails or be involved in protein-protein interactions. . Length = 85

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

 Score = 45.3 bits (108), Expect = 3e-06
 Identities = 23/81 (28%), Positives = 40/81 (49%), Gaps = 3/81 (3%)

Query: 245 LFVCKLNPVTEDEDLHTIFSRFGTVVSAEII---RDFKTGDSLNYAFIEFENRQACERAY 301
           L+V  LNP   +E L   F RFG + S +I+    + +   + N  F+ F NR   ERA 
Sbjct: 4   LYVGNLNPKVTEEVLCQEFGRFGPLASVKIMWPRTEEERRRNRNCGFVAFMNRADAERAL 63

Query: 302 SKMDNALIDDRRIHVDFSQSV 322
            ++D   +    + + + ++V
Sbjct: 64  DELDGKDVMGYELKLGWGKAV 84

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

 Score = 44.6 bits (106), Expect = 3e-06
 Identities = 23/73 (31%), Positives = 43/73 (58%), Gaps = 2/73 (2%)

Query: 245 LFVCKLNPVTEDEDLHTIFSRFGTVVSAEIIRDFKTGDSLNYAFIEFENRQACERAYSKM 304
           +FV  L+    +++L  +FS+ G +    +++++K G S  YA++EFEN ++ + A  K+
Sbjct: 2   VFVSNLDYSVPEDELRKLFSKCGEITDVRLVKNYK-GKSKGYAYVEFENEESVQEAL-KL 59

Query: 305 DNALIDDRRIHVD 317
           D  LI  R + V 
Sbjct: 60  DRELIKGRPMFVS 72

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

 Score = 49.2 bits (117), Expect = 3e-06
 Identities = 22/80 (27%), Positives = 37/80 (46%)

Query: 245 LFVCKLNPVTEDEDLHTIFSRFGTVVSAEIIRDFKTGDSLNYAFIEFENRQACERAYSKM 304
           +FV  L+P T++  L  +F  FG V + +IIRD  T     Y F+   N      A   +
Sbjct: 272 IFVYNLSPDTDETVLWQLFGPFGAVQNVKIIRDLTTNQCKGYGFVSMTNYDEAAMAILSL 331

Query: 305 DNALIDDRRIHVDFSQSVSK 324
           +   + +R + V F  + + 
Sbjct: 332 NGYTLGNRVLQVSFKTNKAY 351

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

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

 Score = 44.5 bits (105), Expect = 5e-06
 Identities = 22/68 (32%), Positives = 32/68 (47%), Gaps = 3/68 (4%)

Query: 257 EDLHTIFSRFGTVVSAEIIRDFKTGDSLNYAFIEFENRQACERAYSKMDNALIDDRRIHV 316
             L  IF R+G V  A I R  + G    +AF+  + R+  E A    +   ID R + V
Sbjct: 16  VKLKKIFGRYGKVREATIPRK-RGGKLCGFAFVTMKKRKNAEIALENTNGLEIDGRPVAV 74

Query: 317 DFSQSVSK 324
           D+  +V K
Sbjct: 75  DW--AVQK 80

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

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

 Score = 48.9 bits (116), Expect = 6e-06
 Identities = 17/63 (26%), Positives = 32/63 (50%)

Query: 243 NVLFVCKLNPVTEDEDLHTIFSRFGTVVSAEIIRDFKTGDSLNYAFIEFENRQACERAYS 302
           N ++V  ++P   + D+ ++F  FG +V  ++ R         Y FIE+ N Q+   A +
Sbjct: 205 NRIYVASVHPDLSETDIKSVFEAFGEIVKCQLARAPTGRGHKGYGFIEYNNLQSQSEAIA 264

Query: 303 KMD 305
            M+
Sbjct: 265 SMN 267

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

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

 Score = 44.0 bits (104), Expect = 6e-06
 Identities = 16/73 (21%), Positives = 28/73 (38%), Gaps = 4/73 (5%)

Query: 244 VLFVCKLNPVTEDEDLHTIFSRFGTVVSAEIIRDFKTGDSLNYAFIEFENRQACERAYSK 303
            ++           D+  +F   G V    ++          +AFI FEN +A + A   
Sbjct: 1   TVYAGPFPTSFCLSDVKRLFETCGPVRKVTMLSRTVQP----HAFITFENLEAAQLAIET 56

Query: 304 MDNALIDDRRIHV 316
           ++ A +D   I V
Sbjct: 57  LNGASVDGNCIKV 69

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

>gnl|CDD|233515 TIGR01659, sex-lethal, sex-lethal family splicing factor

 Score = 48.1 bits (114), Expect = 7e-06
 Identities = 22/64 (34%), Positives = 34/64 (53%)

Query: 245 LFVCKLNPVTEDEDLHTIFSRFGTVVSAEIIRDFKTGDSLNYAFIEFENRQACERAYSKM 304
           L+V  L     D+ L TIF ++G +V   I+RD  TG     AF+ F  R+  + A S +
Sbjct: 196 LYVTNLPRTITDDQLDTIFGKYGQIVQKNILRDKLTGTPRGVAFVRFNKREEAQEAISAL 255

Query: 305 DNAL 308
           +N +
Sbjct: 256 NNVI 259

This model describes the sex-lethal family of splicing factors found in Dipteran insects. The sex-lethal phenotype, however, may be limited to the Melanogasters and closely related species. In Drosophila the protein acts as an inhibitor of splicing. This subfamily is most closely related to the ELAV/HUD subfamily of splicing factors (TIGR01661). Length = 346

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

 Score = 44.3 bits (104), Expect = 7e-06
 Identities = 21/74 (28%), Positives = 37/74 (50%)

Query: 245 LFVCKLNPVTEDEDLHTIFSRFGTVVSAEIIRDFKTGDSLNYAFIEFENRQACERAYSKM 304
           +FV  L+P +++  L  +F  FG V + ++IRDF T     + F+   N      A + +
Sbjct: 6   IFVYNLSPDSDESVLWQLFGPFGAVNNVKVIRDFNTNKCKGFGFVTMTNYDEAAMAIASL 65

Query: 305 DNALIDDRRIHVDF 318
           +   + DR + V F
Sbjct: 66  NGYRLGDRVLQVSF 79

This subgroup corresponds to the RRM3 of HuD, also termed ELAV-like protein 4 (ELAV-4), or paraneoplastic encephalomyelitis antigen HuD, one of the neuronal members of the Hu family. The neuronal Hu proteins play important roles in neuronal differentiation, plasticity and memory. HuD has been implicated in various aspects of neuronal function, such as the commitment and differentiation of neuronal precursors as well as synaptic remodeling in mature neurons. HuD also functions as an important regulator of mRNA expression in neurons by interacting with AU-rich RNA element (ARE) and stabilizing multiple transcripts. Moreover, HuD regulates the nuclear processing/stability of N-myc pre-mRNA in neuroblastoma cells. And it also regulates the neurite elongation and morphological differentiation. HuD specifically bound poly(A) RNA. Like other Hu proteins, HuD contains three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). RRM1 and RRM2 may cooperate in binding to an ARE. RRM3 may help to maintain the stability of the RNA-protein complex, and might also bind to poly(A) tails or be involved in protein-protein interactions. . Length = 86

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

 Score = 44.1 bits (105), Expect = 7e-06
 Identities = 21/74 (28%), Positives = 45/74 (60%), Gaps = 2/74 (2%)

Query: 243 NVLFVCKLNPVTEDEDLHTIFSRFGTVVSAEIIRDFKTGDSLNYAFIEFENRQACERAYS 302
           NV +V  L    +DE L  +F ++G + SA++++D   G S  + F+ FEN +A ++A  
Sbjct: 3   NV-YVKNLGEDMDDEKLKELFGKYGKITSAKVMKD-DEGKSKGFGFVNFENHEAAQKAVE 60

Query: 303 KMDNALIDDRRIHV 316
           +++   ++ ++++V
Sbjct: 61  ELNGKEVNGKKLYV 74

This subfamily corresponds to the RRM3 of type I poly(A)-binding proteins (PABPs), highly conserved proteins that bind to the poly(A) tail present at the 3' ends of most eukaryotic mRNAs. They have been implicated in the regulation of poly(A) tail length during the polyadenylation reaction, translation initiation, mRNA stabilization by influencing the rate of deadenylation and inhibition of mRNA decapping. The family represents type I polyadenylate-binding proteins (PABPs), including polyadenylate-binding protein 1 (PABP-1 or PABPC1), polyadenylate-binding protein 3 (PABP-3 or PABPC3), polyadenylate-binding protein 4 (PABP-4 or APP-1 or iPABP), polyadenylate-binding protein 5 (PABP-5 or PABPC5), polyadenylate-binding protein 1-like (PABP-1-like or PABPC1L), polyadenylate-binding protein 1-like 2 (PABPC1L2 or RBM32), polyadenylate-binding protein 4-like (PABP-4-like or PABPC4L), yeast polyadenylate-binding protein, cytoplasmic and nuclear (PABP or ACBP-67), and similar proteins. PABP-1 is an ubiquitously expressed multifunctional protein that may play a role in 3' end formation of mRNA, translation initiation, mRNA stabilization, protection of poly(A) from nuclease activity, mRNA deadenylation, inhibition of mRNA decapping, and mRNP maturation. Although PABP-1 is thought to be a cytoplasmic protein, it is also found in the nucleus. PABP-1 may be involved in nucleocytoplasmic trafficking and utilization of mRNP particles. PABP-1 contains four copies of RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), a less well conserved linker region, and a proline-rich C-terminal conserved domain (CTD). PABP-3 is a testis-specific poly(A)-binding protein specifically expressed in round spermatids. It is mainly found in mammalian and may play an important role in the testis-specific regulation of mRNA homeostasis. PABP-3 shows significant sequence similarity to PABP-1. However, it binds to poly(A) with a lower affinity than PABP-1. PABP-1 possesses an A-rich sequence in its 5'-UTR and allows binding of PABP and blockage of translation of its own mRNA. In contrast, PABP-3 lacks the A-rich sequence in its 5'-UTR. PABP-4 is an inducible poly(A)-binding protein (iPABP) that is primarily localized to the cytoplasm. It shows significant sequence similarity to PABP-1 as well. The RNA binding properties of PABP-1 and PABP-4 appear to be identical. PABP-5 is encoded by PABPC5 gene within the X-specific subinterval, and expressed in fetal brain and in a range of adult tissues in mammalian, such as ovary and testis. It may play an important role in germ cell development. Moreover, unlike other PABPs, PABP-5 contains only four RRMs, but lacks both the linker region and the CTD. PABP-1-like and PABP-1-like 2 are the orthologs of PABP-1. PABP-4-like is the ortholog of PABP-5. Their cellular functions remain unclear. The family also includes the yeast PABP, a conserved poly(A) binding protein containing poly(A) tails that can be attached to the 3'-ends of mRNAs. The yeast PABP and its homologs may play important roles in the initiation of translation and in mRNA decay. Like vertebrate PABP-1, the yeast PABP contains four RRMs, a linker region, and a proline-rich CTD as well. The first two RRMs are mainly responsible for specific binding to poly(A). The proline-rich region may be involved in protein-protein interactions. . Length = 80

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

 Score = 43.9 bits (104), Expect = 7e-06
 Identities = 20/62 (32%), Positives = 33/62 (53%), Gaps = 2/62 (3%)

Query: 256 DEDLHTIFSRFGTVVSAEIIRDFKTGDSLNYAFIEFENRQACERAYSKMDNALIDDRRIH 315
           D DL  +F +FG ++  EII  F    S  + F+ F N    +RA  K+   +++ R+I 
Sbjct: 14  DPDLRQMFGQFGPILDVEII--FNERGSKGFGFVTFANSADADRAREKLHGTVVEGRKIE 71

Query: 316 VD 317
           V+
Sbjct: 72  VN 73

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

>gnl|CDD|240867 cd12421, RRM1_PTBP1_hnRNPL_like, RNA recognition motif in polypyrimidine tract-binding protein 1 (PTB or hnRNP I), heterogeneous nuclear ribonucleoprotein L (hnRNP-L), and similar proteins

 Score = 43.7 bits (104), Expect = 9e-06
 Identities = 23/81 (28%), Positives = 38/81 (46%), Gaps = 10/81 (12%)

Query: 244 VLFVCKL-NPVTEDEDLHTIFSRFGTVVSAEIIRDFKTGDSLNYAFIEFENRQACER--A 300
           VL +  L   VTE  DL  + S FG V +  ++R        N A +E ++ ++ +    
Sbjct: 1   VLHLRNLPPDVTE-SDLIALVSPFGKVTNVLLLRGK------NQALVEMDSVESAKSMVD 53

Query: 301 YSKMDNALIDDRRIHVDFSQS 321
           Y     ALI  RR+++ +S  
Sbjct: 54  YYLTVPALIRGRRVYIQYSNH 74

This subfamily corresponds to the RRM1 of the majority of family members that include polypyrimidine tract-binding protein 1 (PTB or hnRNP I), polypyrimidine tract-binding protein 2 (PTBP2 or nPTB), regulator of differentiation 1 (Rod1), heterogeneous nuclear ribonucleoprotein L (hnRNP-L), heterogeneous nuclear ribonucleoprotein L-like (hnRNP-LL), polypyrimidine tract-binding protein homolog 3 (PTBPH3), polypyrimidine tract-binding protein homolog 1 and 2 (PTBPH1 and PTBPH2), and similar proteins. PTB is an important negative regulator of alternative splicing in mammalian cells and also functions at several other aspects of mRNA metabolism, including mRNA localization, stabilization, polyadenylation, and translation. PTBP2 is highly homologous to PTB and is perhaps specific to the vertebrates. Unlike PTB, PTBP2 is enriched in the brain and in some neural cell lines. It binds more stably to the downstream control sequence (DCS) RNA than PTB does but is a weaker repressor of splicing in vitro. PTBP2 also greatly enhances the binding of two other proteins, heterogeneous nuclear ribonucleoprotein (hnRNP) H and KH-type splicing-regulatory protein (KSRP), to the DCS RNA. The binding properties of PTBP2 and its reduced inhibitory activity on splicing imply roles in controlling the assembly of other splicing-regulatory proteins. Rod1 is a mammalian polypyrimidine tract binding protein (PTB) homolog of a regulator of differentiation in the fission yeast Schizosaccharomyces pombe, where the nrd1 gene encodes an RNA binding protein negatively regulates the onset of differentiation. ROD1 is predominantly expressed in hematopoietic cells or organs. It might play a role controlling differentiation in mammals. hnRNP-L is a higher eukaryotic specific subunit of human KMT3a (also known as HYPB or hSet2) complex required for histone H3 Lys-36 trimethylation activity. It plays both, nuclear and cytoplasmic, roles in mRNA export of intronless genes, IRES-mediated translation, mRNA stability, and splicing. hnRNP-LL protein plays a critical and unique role in the signal-induced regulation of CD45 and acts as a global regulator of alternative splicing in activated T cells. The family also includes polypyrimidine tract binding protein homolog 3 (PTBPH3) found in plant. Although its biological roles remain unclear, PTBPH3 shows significant sequence similarity to other family members, all of which contain four RNA recognition motifs (RRM), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain). Although their biological roles remain unclear, both PTBPH1 and PTBPH2 show significant sequence similarity to PTB. However, in contrast to PTB, they have three RRMs. In addition, this family also includes RNA-binding motif protein 20 (RBM20) that is an alternative splicing regulator associated with dilated cardiomyopathy (DCM) and contains only one RRM. . Length = 74

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

 Score = 48.4 bits (115), Expect = 9e-06
 Identities = 34/122 (27%), Positives = 43/122 (35%), Gaps = 13/122 (10%)

Query: 390 EKSRREKKHRGHDPDDRVERNMNRLSSDLRHRDQERRELSYRQRESDRTRENREDRRNRD 449
           E  R  +K RG D D   ER   R     R RD+ RR      RE  R R    DRR  D
Sbjct: 4   EPDREREKSRGRDRDRSSERPRRRSRDRSRFRDRHRRSRERSYREDSRPR----DRRRYD 59

Query: 450 GQESRNVQKQEVRDDDGRYESDHPKSSDTDRYRDWRGGGDYRKRSADSDSRAERREDGDY 509
            +  R++             S         R R  R    +R+R  D     + R+D   
Sbjct: 60  SRSPRSL------RYSSVRRSRDR---PRRRSRSVRSIEQHRRRLRDRSPSNQWRKDDKK 110

Query: 510 RK 511
           R 
Sbjct: 111 RS 112

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

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

 Score = 43.5 bits (103), Expect = 9e-06
 Identities = 17/56 (30%), Positives = 30/56 (53%)

Query: 245 LFVCKLNPVTEDEDLHTIFSRFGTVVSAEIIRDFKTGDSLNYAFIEFENRQACERA 300
           +FV  L+P T +E +   F +FG +V  E+  D KT     + FI F++ +  ++ 
Sbjct: 2   IFVGGLSPETTEEKIREYFGKFGNIVEIELPMDKKTNKRRGFCFITFDSEEPVKKI 57

This subfamily corresponds to the RRM2 of hnRNP D0, hnRNP A/B, hnRNP DL and similar proteins. hnRNP D0, a UUAG-specific nuclear RNA binding protein that may be involved in pre-mRNA splicing and telomere elongation. hnRNP A/B is an RNA unwinding protein with a high affinity for G- followed by U-rich regions. It has also been identified as an APOBEC1-binding protein that interacts with apolipoprotein B (apoB) mRNA transcripts around the editing site and thus plays an important role in apoB mRNA editing. hnRNP DL (or hnRNP D-like) is a dual functional protein that possesses DNA- and RNA-binding properties. It has been implicated in mRNA biogenesis at the transcriptional and post-transcriptional levels. All memembers in this family contain two putative RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a glycine- and tyrosine-rich C-terminus. . Length = 75

>gnl|CDD|233515 TIGR01659, sex-lethal, sex-lethal family splicing factor

 Score = 47.3 bits (112), Expect = 1e-05
 Identities = 19/66 (28%), Positives = 39/66 (59%)

Query: 255 EDEDLHTIFSRFGTVVSAEIIRDFKTGDSLNYAFIEFENRQACERAYSKMDNALIDDRRI 314
            D +L+ +F   G + +  I+RD+KTG S  YAF++F +    +RA   ++   + ++R+
Sbjct: 120 TDRELYALFRTIGPINTCRIMRDYKTGYSFGYAFVDFGSEADSQRAIKNLNGITVRNKRL 179

Query: 315 HVDFSQ 320
            V +++
Sbjct: 180 KVSYAR 185

This model describes the sex-lethal family of splicing factors found in Dipteran insects. The sex-lethal phenotype, however, may be limited to the Melanogasters and closely related species. In Drosophila the protein acts as an inhibitor of splicing. This subfamily is most closely related to the ELAV/HUD subfamily of splicing factors (TIGR01661). Length = 346

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

 Score = 42.9 bits (102), Expect = 1e-05
 Identities = 21/71 (29%), Positives = 35/71 (49%), Gaps = 1/71 (1%)

Query: 246 FVCKLNPVTEDEDLHTIFSRFGTVVSAEIIRDFKTGDSLNYAFIEFENRQACERAYSKMD 305
           FV  L    E+E+L   F   G V +  I+RD KTG    + ++ F+ + +   A  K++
Sbjct: 3   FVGNLPFDIEEEELRKHFEDCGDVEAVRIVRDRKTGIGKGFGYVLFKTKDSVALAL-KLN 61

Query: 306 NALIDDRRIHV 316
              +  R+I V
Sbjct: 62  GIKLKGRKIRV 72

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

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

 Score = 43.4 bits (103), Expect = 1e-05
 Identities = 19/62 (30%), Positives = 32/62 (51%)

Query: 245 LFVCKLNPVTEDEDLHTIFSRFGTVVSAEIIRDFKTGDSLNYAFIEFENRQACERAYSKM 304
           L+V  L      ++L  +FS +G ++++ I+ D  TG S    FI F+ R   ERA   +
Sbjct: 3   LYVSGLPKTMTQQELEALFSPYGRIITSRILCDNVTGLSRGVGFIRFDKRIEAERAIKAL 62

Query: 305 DN 306
           + 
Sbjct: 63  NG 64

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

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

 Score = 43.0 bits (102), Expect = 1e-05
 Identities = 18/66 (27%), Positives = 32/66 (48%), Gaps = 2/66 (3%)

Query: 253 VTEDEDLHTIFSRFGTVVSAEIIRDFKTGDSLNYAFIEFENRQACERAYSKMDNALIDDR 312
           VTED  L   F   G V   +++R  + G S  + F+ F++ +  ++A    +   ID  
Sbjct: 12  VTEDR-LREHFESKGEVTDVKVMRT-RDGKSRRFGFVGFKSEEDAQQAVKYFNKTFIDTS 69

Query: 313 RIHVDF 318
           +I V+ 
Sbjct: 70  KISVEL 75

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|237171 PRK12678, PRK12678, transcription termination factor Rho; Provisional

 Score = 47.6 bits (114), Expect = 2e-05
 Identities = 27/170 (15%), Positives = 47/170 (27%), Gaps = 3/170 (1%)

Query: 419 RHRDQERRELSYRQRESDRTRENREDRRNRDGQESRNVQKQEVRDDDGRYESDHPKSSDT 478
           R     R+        +    E     R      +      E      R E         
Sbjct: 82  RAAAAARQAEQPAAEAAAAKAEAAPAARAAAAAAAEAASAPEAAQARERRERGEAARRGA 141

Query: 479 DRYRDWRGGGDYRKRSADSDSRAERREDGDYRKRNSDNGSHRDRRDDQDYRKKSADGDIH 538
            R     GG      +    +     E+ D R+R  D    +   +  +  ++   G   
Sbjct: 142 ARKAG-EGGEQPATEARADAAERTEEEERDERRRRGDREDRQAEAERGERGRREERGR-- 198

Query: 539 GDRRYDRDNRKNSGNSELRDAKKEPSYKRGRRDDDSYKRWPEDRGNRRRG 588
                DR +R+  G+      +++   +RGRR     +    D     RG
Sbjct: 199 DGDDRDRRDRREQGDRREERGRRDGGDRRGRRRRRDRRDARGDDNREDRG 248

Length = 672

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

 Score = 47.2 bits (112), Expect = 2e-05
 Identities = 33/119 (27%), Positives = 45/119 (37%), Gaps = 5/119 (4%)

Query: 448 RDGQESRNVQKQEVRDDDGRYESDHPKSSDTDRYRDWRGGGDYRKRSADSDSRAERREDG 507
           RD +  R  +K   RD D   E    +S D  R+RD       R    DS  R  RR D 
Sbjct: 1   RDEEPDREREKSRGRDRDRSSERPRRRSRDRSRFRDRHRRSRERSYREDSRPRDRRRYD- 59

Query: 508 DYRKRNSDNGSHRDRRDDQDYRKKSADGDIHGDRRYDRDNRKNSGNSELRDAKKEPSYK 566
               R+    S R  RD    R +S         ++ R  R  S +++ R   K+ S  
Sbjct: 60  SRSPRSLRYSSVRRSRDRPRRRSRSVRSIE----QHRRRLRDRSPSNQWRKDDKKRSLW 114

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

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

 Score = 42.8 bits (101), Expect = 2e-05
 Identities = 19/72 (26%), Positives = 37/72 (51%), Gaps = 8/72 (11%)

Query: 245 LFVCKLNPVTEDEDLHTIFSRFGTVVSAEIIRDFKTGDSLNYAFIEFENRQACERAYSKM 304
           L+V    P T +  +  IFS +G V   ++I         N+AF+EFE+ ++  RA   +
Sbjct: 2   LYVRPFPPDTSESAIREIFSPYGAVKEVKMIS--------NFAFVEFESLESAIRAKDSV 53

Query: 305 DNALIDDRRIHV 316
              ++++  ++V
Sbjct: 54  HGKVLNNNPLYV 65

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

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

 Score = 43.0 bits (102), Expect = 2e-05
 Identities = 22/73 (30%), Positives = 36/73 (49%), Gaps = 1/73 (1%)

Query: 245 LFVCKLNPVTEDEDLHTIF-SRFGTVVSAEIIRDFKTGDSLNYAFIEFENRQACERAYSK 303
           +FV  L P   D  L   F +R+ +V  A+++ D  TG S  Y F+ F +    +RA ++
Sbjct: 4   IFVGDLAPDVTDYMLQETFRARYPSVRGAKVVMDPVTGRSKGYGFVRFGDEDERDRALTE 63

Query: 304 MDNALIDDRRIHV 316
           M+      R + V
Sbjct: 64  MNGVYCSSRPMRV 76

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

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

 Score = 42.7 bits (101), Expect = 2e-05
 Identities = 25/76 (32%), Positives = 43/76 (56%), Gaps = 5/76 (6%)

Query: 245 LFVCKLNP-VTEDEDLHTIFSRFGTVVSAEIIRDFKTGDSLNYAFIEFENRQACERAYSK 303
           L+V  L+  VTED  L  +FS+ G + S ++IR+    D   YAF+E+ + ++   A   
Sbjct: 1   LYVGNLDRTVTEDL-LAELFSQIGPIKSCKLIRE-HGNDP--YAFVEYYDHRSAAAALQT 56

Query: 304 MDNALIDDRRIHVDFS 319
           M+  LI  + I V+++
Sbjct: 57  MNGRLILGQEIKVNWA 72

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

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

 Score = 42.6 bits (101), Expect = 2e-05
 Identities = 24/76 (31%), Positives = 44/76 (57%), Gaps = 1/76 (1%)

Query: 245 LFVCKLNPVTEDEDLHTIFSRFGTVVSAEIIRDFKTGDSLNYAFIEFENRQACERAYSKM 304
           L+V  L+   +DE L   FS FGT+ SA+++ D K G S  + F+ F + +   +A ++M
Sbjct: 4   LYVKNLDDSIDDERLREEFSPFGTITSAKVMTDEK-GRSKGFGFVCFSSPEEATKAVTEM 62

Query: 305 DNALIDDRRIHVDFSQ 320
           +  +I  + ++V  +Q
Sbjct: 63  NGRIIGGKPLYVALAQ 78

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

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

 Score = 42.2 bits (100), Expect = 2e-05
 Identities = 20/56 (35%), Positives = 31/56 (55%)

Query: 245 LFVCKLNPVTEDEDLHTIFSRFGTVVSAEIIRDFKTGDSLNYAFIEFENRQACERA 300
           LFV  L     +EDL   FS++G V S EI+ D +TG    +AF+ F++    ++ 
Sbjct: 2   LFVGGLKEDVTEEDLREYFSQYGNVESVEIVTDKETGKKRGFAFVTFDDYDPVDKI 57

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

 Score = 42.5 bits (100), Expect = 2e-05
 Identities = 22/72 (30%), Positives = 36/72 (50%)

Query: 245 LFVCKLNPVTEDEDLHTIFSRFGTVVSAEIIRDFKTGDSLNYAFIEFENRQACERAYSKM 304
           LF+  L     D +L  +F  FG V+SA++  D  T  S  + F+ F+N  + + A   M
Sbjct: 7   LFIYHLPQEFGDAELMQMFLPFGNVISAKVFVDRATNQSKCFGFVSFDNPASAQAAIQAM 66

Query: 305 DNALIDDRRIHV 316
           +   I  +R+ V
Sbjct: 67  NGFQIGMKRLKV 78

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

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

 Score = 42.3 bits (100), Expect = 2e-05
 Identities = 24/80 (30%), Positives = 41/80 (51%), Gaps = 5/80 (6%)

Query: 240 PPENVLFVCKLNPVTEDEDLHTIFSRFGTVVSAEIIRDFKTGDSLNYAFIEFE-NRQACE 298
           PP + LF+     VTED DL   F+ FG +    +++D +T +S   A+++F     A  
Sbjct: 1   PPNSRLFIVCGKSVTED-DLREAFAPFGEIQDIWVVKDKQTKESKGVAYVKFAKASSAA- 58

Query: 299 RAYSKMDNALI--DDRRIHV 316
           RA  +M+   +  D + + V
Sbjct: 59  RAMEEMNGKCLGGDTKPLKV 78

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

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

 Score = 42.3 bits (99), Expect = 2e-05
 Identities = 24/77 (31%), Positives = 38/77 (49%), Gaps = 1/77 (1%)

Query: 241 PENV-LFVCKLNPVTEDEDLHTIFSRFGTVVSAEIIRDFKTGDSLNYAFIEFENRQACER 299
           PE   LF+  L     D DL   F  FG V+SA++  D +T  S  + F+ ++N  + + 
Sbjct: 2   PEGCNLFIYHLPQEFTDTDLAQTFLPFGNVISAKVFIDKQTNLSKCFGFVSYDNPDSAQA 61

Query: 300 AYSKMDNALIDDRRIHV 316
           A   M+   I  +R+ V
Sbjct: 62  AIQAMNGFQIGTKRLKV 78

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

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

 Score = 42.3 bits (100), Expect = 3e-05
 Identities = 17/73 (23%), Positives = 37/73 (50%)

Query: 245 LFVCKLNPVTEDEDLHTIFSRFGTVVSAEIIRDFKTGDSLNYAFIEFENRQACERAYSKM 304
           L+V  L+  T+  DL  +FS++G VV A+I+ + ++  +  + F+   + +   +    +
Sbjct: 2   LWVSGLSSTTKAADLKQLFSKYGKVVGAKIVTNARSPGARCFGFVTMASVEEAAKCIQHL 61

Query: 305 DNALIDDRRIHVD 317
               +  R I V+
Sbjct: 62  HRTELHGRVISVE 74

This subfamily corresponds to the RRM domain of the SAFB family, including scaffold attachment factor B1 (SAFB1), scaffold attachment factor B2 (SAFB2), SAFB-like transcriptional modulator (SLTM), and similar proteins, which are ubiquitously expressed. SAFB1, SAFB2 and SLTM have been implicated in many diverse cellular processes including cell growth and transformation, stress response, and apoptosis. They share high sequence similarities and all contain a scaffold attachment factor-box (SAF-box, also known as SAP domain) DNA-binding motif, an RNA recognition motif (RRM), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and a region rich in glutamine and arginine residues. SAFB1 is a nuclear protein with a distribution similar to that of SLTM, but unlike that of SAFB2, which is also found in the cytoplasm. To a large extent, SAFB1 and SLTM might share similar functions, such as the inhibition of an oestrogen reporter gene. The additional cytoplasmic localization of SAFB2 implies that it could play additional roles in the cytoplasmic compartment which are distinct from the nuclear functions shared with SAFB1 and SLTM. . Length = 74

>gnl|CDD|241117 cd12673, RRM_BOULE, RNA recognition motif in protein BOULE

 Score = 42.1 bits (99), Expect = 3e-05
 Identities = 22/82 (26%), Positives = 45/82 (54%), Gaps = 3/82 (3%)

Query: 243 NVLFVCKLNPVTEDEDLHTIFSRFGTVVSAEIIRDFKTGDSLNYAFIEFENRQACERAYS 302
           N +FV  ++  T + DL   FS++GTV   +I+ D + G S  Y F+ FE ++  ++   
Sbjct: 3   NRIFVGGIDFKTNENDLRKFFSQYGTVKEVKIVND-RAGVSKGYGFVTFETQEDAQKILQ 61

Query: 303 KMDNALIDDRRIHVDFSQSVSK 324
           + +     D+++++   Q++ K
Sbjct: 62  EANRLCFRDKKLNI--GQAIRK 81

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

 Score = 41.9 bits (99), Expect = 3e-05
 Identities = 21/64 (32%), Positives = 33/64 (51%)

Query: 254 TEDEDLHTIFSRFGTVVSAEIIRDFKTGDSLNYAFIEFENRQACERAYSKMDNALIDDRR 313
           T  +DL  +F ++G V    I RD  T +S  +AF+ F +++  E A   MD   +D R 
Sbjct: 10  TTPDDLRRVFEKYGEVGDVYIPRDRYTRESRGFAFVRFYDKRDAEDAMDAMDGKELDGRE 69

Query: 314 IHVD 317
           + V 
Sbjct: 70  LRVQ 73

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

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

 Score = 41.8 bits (99), Expect = 3e-05
 Identities = 25/77 (32%), Positives = 36/77 (46%), Gaps = 8/77 (10%)

Query: 245 LFVCKLNPVTEDEDLHTIFSRFGTVVSAEIIRDFKTGDSLNYAFIEFENRQACERAYSKM 304
           L+V  L P T   +L   F RFG       IR        NYA+IE+E+ +A + A   +
Sbjct: 1   LWVGGLGPWTSLAELEREFDRFGA------IRRIDYDPGRNYAYIEYESIEAAQAAKEAL 54

Query: 305 DNALI--DDRRIHVDFS 319
               +    RR+ VDF+
Sbjct: 55  RGFPLGGPGRRLRVDFA 71

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|240892 cd12446, RRM_RBM25, RNA recognition motif in eukaryotic RNA-binding protein 25 and similar proteins

 Score = 42.2 bits (100), Expect = 3e-05
 Identities = 18/82 (21%), Positives = 37/82 (45%)

Query: 244 VLFVCKLNPVTEDEDLHTIFSRFGTVVSAEIIRDFKTGDSLNYAFIEFENRQACERAYSK 303
            +FV  +     D+ +  +  + G V+S + ++D  TG    + F EFE+ +   RA   
Sbjct: 2   TVFVGNIPEGVSDDFIRKLLEKCGKVLSWKRVKDPSTGKLKAFGFCEFEDPEGALRALRL 61

Query: 304 MDNALIDDRRIHVDFSQSVSKL 325
           ++   +  +++ V       KL
Sbjct: 62  LNGLELGGKKLLVKVDAKTRKL 83

This subfamily corresponds to the RRM of RBM25, also termed Arg/Glu/Asp-rich protein of 120 kDa (RED120), or protein S164, or RNA-binding region-containing protein 7, an evolutionary-conserved splicing coactivator SRm160 (SR-related nuclear matrix protein of 160 kDa, )-interacting protein. RBM25 belongs to a family of RNA-binding proteins containing a well conserved RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), at the N-terminus, a RE/RD-rich (ER) central region, and a C-terminal proline-tryptophan-isoleucine (PWI) motif. It localizes to the nuclear speckles and associates with multiple splicing components, including splicing cofactors SRm160/300, U snRNAs, assembled splicing complexes, and spliced mRNAs. It may play an important role in pre-mRNA processing by coupling splicing with mRNA 3'-end formation. Additional research indicates that RBM25 is one of the RNA-binding regulators that direct the alternative splicing of apoptotic factors. It can activate proapoptotic Bcl-xS 5'ss by binding to the exonic splicing enhancer, CGGGCA, and stabilize the pre-mRNA-U1 snRNP through interaction with hLuc7A, a U1 snRNP-associated factor. . Length = 84

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

 Score = 41.9 bits (99), Expect = 3e-05
 Identities = 21/60 (35%), Positives = 30/60 (50%), Gaps = 2/60 (3%)

Query: 252 PVTEDE-DLHTIFSRFGTVVSAEIIRDFKTGDSLNYAFIEFENRQACERAYSKMDNALID 310
           P+  DE DL T+   +G V+S  I+RD   G S    F   E+R+ CE   SK +   + 
Sbjct: 9   PLHMDEQDLETMLKPYGQVISTRILRD-SKGQSRGVGFARMESREKCEDIISKFNGKYLK 67

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

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

 Score = 42.2 bits (99), Expect = 3e-05
 Identities = 21/56 (37%), Positives = 31/56 (55%)

Query: 245 LFVCKLNPVTEDEDLHTIFSRFGTVVSAEIIRDFKTGDSLNYAFIEFENRQACERA 300
           LFV  L     + DL   FS+FG V  AE+I D +TG    + F+ F+N  + ++A
Sbjct: 2   LFVGGLKGDVGEGDLTEHFSQFGPVEKAEVIADKQTGKKRGFGFVYFQNHDSADKA 57

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|237171 PRK12678, PRK12678, transcription termination factor Rho; Provisional

 Score = 46.1 bits (110), Expect = 4e-05
 Identities = 30/140 (21%), Positives = 48/140 (34%), Gaps = 6/140 (4%)

Query: 367 DDNRQHGGYSDSRYEMVFDGETPEKSRREKKHRGHDPDDRVERNMNRLSSDLRHRDQERR 426
             +       + R E    G+  ++    ++      ++R     +R   D R +   R 
Sbjct: 157 RADAAERTEEEERDERRRRGDREDRQAEAERGERGRREERGRDGDDRDRRDRREQGDRRE 216

Query: 427 ELSYRQRESDRTRENREDRRNRDGQESRNVQKQEVRDDDGRYESDHPKSSDTDRYRDWRG 486
           E   R     R R  R DRR+  G ++R  +     DD         +     R RD RG
Sbjct: 217 ERGRRDGGDRRGRRRRRDRRDARGDDNREDRGDRDGDDGEGRGGRRGRRF---RDRDRRG 273

Query: 487 GGDYRKRSADSDSRAERRED 506
               R     ++   E RED
Sbjct: 274 R---RGGDGGNEREPELRED 290

Length = 672

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

 Score = 46.3 bits (110), Expect = 4e-05
 Identities = 22/76 (28%), Positives = 41/76 (53%), Gaps = 1/76 (1%)

Query: 245 LFVCKLNPVTEDEDLHTIFSRFGTVVSAEIIRDFKTGDSLNYAFIEFENRQACERAYSKM 304
           L+V  L+    DE L  +FS  G + SA+++ D + G S  + F+ F N +   RA ++M
Sbjct: 288 LYVKNLDDTVTDEKLRELFSECGEITSAKVMLD-EKGVSRGFGFVCFSNPEEANRAVTEM 346

Query: 305 DNALIDDRRIHVDFSQ 320
              ++  + ++V  +Q
Sbjct: 347 HGRMLGGKPLYVALAQ 362

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

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

 Score = 41.8 bits (99), Expect = 4e-05
 Identities = 21/72 (29%), Positives = 37/72 (51%)

Query: 245 LFVCKLNPVTEDEDLHTIFSRFGTVVSAEIIRDFKTGDSLNYAFIEFENRQACERAYSKM 304
           +FV  L     DE L   FS++ +   A+++RD +TG S  Y F+ F +     +A  +M
Sbjct: 9   IFVGDLGNEVTDEVLARAFSKYPSFQKAKVVRDKRTGKSKGYGFVSFSDPNDYLKAMKEM 68

Query: 305 DNALIDDRRIHV 316
           +   + +R I +
Sbjct: 69  NGKYVGNRPIKL 80

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

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

 Score = 41.5 bits (98), Expect = 4e-05
 Identities = 19/56 (33%), Positives = 32/56 (57%)

Query: 245 LFVCKLNPVTEDEDLHTIFSRFGTVVSAEIIRDFKTGDSLNYAFIEFENRQACERA 300
           +++  L P T DEDL  +   FG ++S + I D KT     Y F++F++ +A  +A
Sbjct: 3   VYIRGLPPNTTDEDLEKLCQPFGKIISTKAILDKKTNKCKGYGFVDFDSPEAALKA 58

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

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

 Score = 41.8 bits (98), Expect = 4e-05
 Identities = 21/65 (32%), Positives = 35/65 (53%), Gaps = 2/65 (3%)

Query: 245 LFVCKL-NPVTEDEDLHTIFSRFGTVVSAEIIRDFKTGDSLNYAFIEFENRQACERAYSK 303
           L+V  L   +TEDE L  IF  +G +V   ++RD  TG     AF+ ++ R+  + A S 
Sbjct: 3   LYVTNLPRQLTEDE-LRKIFEAYGNIVQCNLLRDKSTGLPRGVAFVRYDKREEAQAAISS 61

Query: 304 MDNAL 308
           ++  +
Sbjct: 62  LNGTI 66

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

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

 Score = 41.4 bits (98), Expect = 5e-05
 Identities = 20/76 (26%), Positives = 35/76 (46%)

Query: 245 LFVCKLNPVTEDEDLHTIFSRFGTVVSAEIIRDFKTGDSLNYAFIEFENRQACERAYSKM 304
           LFV  L   T DE L   FS  G +    +++D  +     + ++ F   +  +RA  + 
Sbjct: 2   LFVRNLPYDTTDEQLEEFFSEVGPIKRCFVVKDKGSKKCRGFGYVTFALEEDAKRALEEK 61

Query: 305 DNALIDDRRIHVDFSQ 320
                  R+IHV+F++
Sbjct: 62  KKTKFGGRKIHVEFAK 77

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

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

 Score = 41.4 bits (98), Expect = 5e-05
 Identities = 17/82 (20%), Positives = 38/82 (46%), Gaps = 13/82 (15%)

Query: 245 LFVCKLNPVTEDEDLHTIFSRFGTVVSAEIIRDFKTGDSLNY------AFIEFENRQACE 298
           L+V    P  +  D+  +F ++G ++S   IR F    SL +       +++F + ++  
Sbjct: 3   LWVTNFPPSFDQSDIRDLFEQYGEILS---IR-FP---SLRFNKTRRFCYVQFTSPESAA 55

Query: 299 RAYSKMDNALIDDRRIHVDFSQ 320
            A + ++  L +  ++ V  S 
Sbjct: 56  AAVALLNGKLGEGYKLVVKISD 77

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

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

 Score = 45.3 bits (107), Expect = 6e-05
 Identities = 18/71 (25%), Positives = 42/71 (59%), Gaps = 1/71 (1%)

Query: 253 VTEDEDLHTIFSRFGTVVSAEIIRDFKTGDSLNYAFIEFENRQACERAYSKMDNALIDDR 312
           +T++E + ++F+  G + S +++RD  TG SL Y F+ +   +  E+A + ++   + ++
Sbjct: 15  MTQEE-IRSLFTSIGEIESCKLVRDKVTGQSLGYGFVNYVRPEDAEKAVNSLNGLRLQNK 73

Query: 313 RIHVDFSQSVS 323
            I V +++  S
Sbjct: 74  TIKVSYARPSS 84

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

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

 Score = 41.6 bits (97), Expect = 6e-05
 Identities = 26/82 (31%), Positives = 42/82 (51%), Gaps = 1/82 (1%)

Query: 241 PENV-LFVCKLNPVTEDEDLHTIFSRFGTVVSAEIIRDFKTGDSLNYAFIEFENRQACER 299
           PE   LF+  L     D+DL  +F  FG VVSA++  D +T  S  + F+ ++N  + + 
Sbjct: 5   PEGANLFIYHLPQEFGDQDLLQMFMPFGNVVSAKVFIDKQTNLSKCFGFVSYDNPVSAQA 64

Query: 300 AYSKMDNALIDDRRIHVDFSQS 321
           A   M+   I  +R+ V   +S
Sbjct: 65  AIQAMNGFQIGMKRLKVQLKRS 86

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

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

 Score = 41.1 bits (97), Expect = 6e-05
 Identities = 23/77 (29%), Positives = 33/77 (42%), Gaps = 2/77 (2%)

Query: 245 LFVCKLNPVTEDEDLHTIFSRFGTVVSAEIIRDFKTGDSLNYAFIEFENRQACERAYSKM 304
           LFV  L+   E +DL   F   G VV   I +D   G S  +  +EF   +  ++A  K 
Sbjct: 2   LFVGNLSWSAEQDDLEEFFKECGEVVDVRIAQD-DDGRSKGFGHVEFATEEGAQKALEK- 59

Query: 305 DNALIDDRRIHVDFSQS 321
               +  R I VD +  
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|233503 TIGR01642, U2AF_lg, U2 snRNP auxilliary factor, large subunit, splicing factor

 Score = 45.3 bits (107), Expect = 7e-05
 Identities = 32/119 (26%), Positives = 47/119 (39%), Gaps = 11/119 (9%)

Query: 405 DRVERNMNRLSSDLRHRDQERRELSYRQRESDRTRENREDRRNRDGQESRNVQKQEVRDD 464
           D             R RD++R     R+R  DR+R     RR+R+    R+ ++     D
Sbjct: 2   DEEPDRERE---KSRGRDRDRSSERPRRRSRDRSRFRDRHRRSRE----RSYREDSRPRD 54

Query: 465 DGRYESDHPKSSDTDRYRDWRGGGDYRKRSADSDSRAERREDGDYRKRNSDNGSHRDRR 523
             RY+S  P+S      R  R     R RS  S  +  RR     R R+  N   +D +
Sbjct: 55  RRRYDSRSPRSLRYSSVRRSRDRPRRRSRSVRSIEQHRRRL----RDRSPSNQWRKDDK 109

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

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

 Score = 41.1 bits (97), Expect = 7e-05
 Identities = 14/76 (18%), Positives = 33/76 (43%), Gaps = 3/76 (3%)

Query: 245 LFVCKLNPVTEDEDLHTIFSRFGTVVSAEII---RDFKTGDSLNYAFIEFENRQACERAY 301
           L++  L+    +  L  +FS++G +   + +        G    Y F+ FE ++  E+A 
Sbjct: 2   LWIGNLDSRLTEFHLLKLFSKYGKIKKFDFLFHKSGPLKGQPRGYCFVTFETKEEAEKAL 61

Query: 302 SKMDNALIDDRRIHVD 317
             ++      +++ V 
Sbjct: 62  KSLNGKTALGKKLVVR 77

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

 Score = 41.0 bits (96), Expect = 8e-05
 Identities = 26/76 (34%), Positives = 40/76 (52%), Gaps = 3/76 (3%)

Query: 245 LFVCKLNP-VTEDEDLHTIFSRFGTVVSAEIIRDFKTGDSLNYAFIEFENRQACERAYSK 303
           L+V  L+P VTED  L  IF   G V + +II D K    +NY F+E+      E A   
Sbjct: 1   LYVGNLDPRVTEDI-LKQIFQVGGPVQNVKIIPD-KNNKGVNYGFVEYHQSHDAEIALQT 58

Query: 304 MDNALIDDRRIHVDFS 319
           ++   I++  I V+++
Sbjct: 59  LNGRQIENNEIRVNWA 74

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

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

 Score = 39.9 bits (94), Expect = 2e-04
 Identities = 18/55 (32%), Positives = 29/55 (52%)

Query: 246 FVCKLNPVTEDEDLHTIFSRFGTVVSAEIIRDFKTGDSLNYAFIEFENRQACERA 300
           FV +L+    + DL+  FS+ G V    IIRD  +  S   A++EF + ++   A
Sbjct: 3   FVMQLSLKVRERDLYEFFSKAGKVRDVRIIRDRNSRRSKGVAYVEFYDEESVPLA 57

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

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

 Score = 40.3 bits (94), Expect = 2e-04
 Identities = 26/80 (32%), Positives = 40/80 (50%)

Query: 245 LFVCKLNPVTEDEDLHTIFSRFGTVVSAEIIRDFKTGDSLNYAFIEFENRQACERAYSKM 304
           LFV  +   T  EDL   F R+G +V   +  DF T     +A+++FE+ +  E A   +
Sbjct: 3   LFVRNIADDTRSEDLRREFGRYGPIVDVYVPLDFYTRRPRGFAYVQFEDVRDAEDALHNL 62

Query: 305 DNALIDDRRIHVDFSQSVSK 324
           D   I  R+I + F+Q   K
Sbjct: 63  DRKWICGRQIEIQFAQGDRK 82

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

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

 Score = 39.9 bits (94), Expect = 2e-04
 Identities = 21/75 (28%), Positives = 36/75 (48%), Gaps = 5/75 (6%)

Query: 245 LFVCKLNPVTEDEDLHTIFSRFGTVVSAEIIRDFKTGDSLNYAFIEFENRQACERAYSKM 304
           ++V  L P     +L   F ++G + S  + R+   G    +AF+EFE+ +  E A   +
Sbjct: 2   VYVGNLGPRATKRELEDEFEKYGPLRSVWVARN-PPG----FAFVEFEDPRDAEDAVRAL 56

Query: 305 DNALIDDRRIHVDFS 319
           D   I   R+ V+ S
Sbjct: 57  DGRRICGNRVRVELS 71

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

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

 Score = 40.0 bits (93), Expect = 2e-04
 Identities = 25/80 (31%), Positives = 40/80 (50%)

Query: 245 LFVCKLNPVTEDEDLHTIFSRFGTVVSAEIIRDFKTGDSLNYAFIEFENRQACERAYSKM 304
           LFV  +   T  EDL   F R+G +V   +  DF T     +A+I+FE+ +  E A   +
Sbjct: 3   LFVRNVADATRPEDLRREFGRYGPIVDVYVPLDFYTRRPRGFAYIQFEDVRDAEDALYNL 62

Query: 305 DNALIDDRRIHVDFSQSVSK 324
           +   +  R+I + F+Q   K
Sbjct: 63  NRKWVCGRQIEIQFAQGDRK 82

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

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

 Score = 39.5 bits (92), Expect = 2e-04
 Identities = 18/73 (24%), Positives = 34/73 (46%), Gaps = 8/73 (10%)

Query: 245 LFVCKLNPVTEDEDLHTIFSRFGTVVSAEIIRDFKTGDSLNYAFIEFENRQACERAYSKM 304
           +FV  ++     ++L  +F  FG VV  + ++D        YAF+  E  +    A   +
Sbjct: 3   IFVGNVSATCTSDELRGLFEEFGRVVECDKVKD--------YAFVHMEREEEALAAIEAL 54

Query: 305 DNALIDDRRIHVD 317
           +   +  RRI+V+
Sbjct: 55  NGKEVKGRRINVE 67

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

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

 Score = 39.4 bits (92), Expect = 2e-04
 Identities = 19/75 (25%), Positives = 37/75 (49%), Gaps = 8/75 (10%)

Query: 245 LFVCKLNPVTEDEDLHTIFSRFGTVVSAEIIRDFKTGDSLNYAFIEFENRQACERAYSKM 304
           +FV  ++  T  E+L  +F  +G V+S  ++R F        AF+      A +RA  ++
Sbjct: 3   IFVGNVDEDTSQEELRALFEAYGAVLSCAVMRQF--------AFVHLRGEAAADRAIEEL 54

Query: 305 DNALIDDRRIHVDFS 319
           +   +  R++ V+ S
Sbjct: 55  NGRELHGRKLVVEHS 69

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

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

 Score = 39.6 bits (93), Expect = 2e-04
 Identities = 21/71 (29%), Positives = 35/71 (49%), Gaps = 1/71 (1%)

Query: 246 FVCKLNPVTEDEDLHTIFSRFGTVVSAEIIRDFKTGDSLNYAFIEFENRQACERAYSKMD 305
           FV  ++  T  E+L   F   GT+    I+ D  TG    +A+IEF ++ + E A   ++
Sbjct: 3   FVGNVDYGTTPEELQEHFKSCGTINRITILCDKFTGQPKGFAYIEFLDKSSVENAL-LLN 61

Query: 306 NALIDDRRIHV 316
            +    R+I V
Sbjct: 62  ESEFRGRQIKV 72

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

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

 Score = 39.8 bits (94), Expect = 2e-04
 Identities = 17/70 (24%), Positives = 30/70 (42%), Gaps = 15/70 (21%)

Query: 246 FVCKLNPVTED------------EDLHTIFSRFGTVVSAEIIR-DFKTGDSLNY--AFIE 290
            +C LN VT +            ED+     ++G V+S  I R + +  D       F+E
Sbjct: 3   VLCLLNMVTPEELEDDEEYEEILEDVKEECGKYGKVLSVVIPRPEAEGVDVPGVGKVFVE 62

Query: 291 FENRQACERA 300
           F + +  ++A
Sbjct: 63  FADVEDAQKA 72

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

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

 Score = 39.7 bits (92), Expect = 2e-04
 Identities = 20/76 (26%), Positives = 40/76 (52%)

Query: 245 LFVCKLNPVTEDEDLHTIFSRFGTVVSAEIIRDFKTGDSLNYAFIEFENRQACERAYSKM 304
           L V  L      E+L ++F   G + S +++RD  TG SL Y F+ + + +  E+A + +
Sbjct: 7   LIVNYLPQNMTQEELKSLFGSIGEIESCKLVRDKITGQSLGYGFVNYIDPKDAEKAINTL 66

Query: 305 DNALIDDRRIHVDFSQ 320
           +   +  + I V +++
Sbjct: 67  NGLRLQTKTIKVSYAR 82

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

>gnl|CDD|240852 cd12406, RRM4_NCL, RNA recognition motif 4 in vertebrate nucleolin

 Score = 39.6 bits (92), Expect = 2e-04
 Identities = 22/76 (28%), Positives = 41/76 (53%), Gaps = 3/76 (3%)

Query: 245 LFVCKLNPVTEDEDLHTIFSRFGTVVSAEIIRDFKTGDSLNYAFIEFENRQACERAYSKM 304
           LFV  L+  T +E   T+   F   ++A I+ D  TG S  + F++F + +  + A   M
Sbjct: 3   LFVKGLSEDTTEE---TLKESFDGSIAARIVTDRDTGSSKGFGFVDFSSEEDAKAAKEAM 59

Query: 305 DNALIDDRRIHVDFSQ 320
           ++  ID  ++ +DF++
Sbjct: 60  EDGEIDGNKVTLDFAK 75

This subfamily corresponds to the RRM4 of ubiquitously expressed protein nucleolin, also termed protein C23, is a multifunctional major nucleolar phosphoprotein that has been implicated in various metabolic processes, such as ribosome biogenesis, cytokinesis, nucleogenesis, cell proliferation and growth, cytoplasmic-nucleolar transport of ribosomal components, transcriptional repression, replication, signal transduction, inducing chromatin decondensation, etc. Nucleolin exhibits intrinsic self-cleaving, DNA helicase, RNA helicase and DNA-dependent ATPase activities. It can be phosphorylated by many protein kinases, such as the major mitotic kinase Cdc2, casein kinase 2 (CK2), and protein kinase C-zeta. Nucleolin shares similar domain architecture with gar2 from Schizosaccharomyces pombe and NSR1 from Saccharomyces cerevisiae. The highly phosphorylated N-terminal domain of nucleolin is made up of highly acidic regions separated from each other by basic sequences, and contains multiple phosphorylation sites. The central domain of nucleolin contains four closely adjacent N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), which suggests that nucleolin is potentially able to interact with multiple RNA targets. The C-terminal RGG (or GAR) domain of nucleolin is rich in glycine, arginine and phenylalanine residues, and contains high levels of NG,NG-dimethylarginines. . Length = 78

>gnl|CDD|240875 cd12429, RRM_DNAJC17, RNA recognition motif in the DnaJ homolog subfamily C member 17

 Score = 39.6 bits (93), Expect = 3e-04
 Identities = 15/45 (33%), Positives = 25/45 (55%), Gaps = 5/45 (11%)

Query: 257 EDLHTIFSRFGTVVSAEIIRDFKTGDSLNYAFIEFENRQACERAY 301
           ++L  IFS++G  VS  ++   K G     A +EF +++A E A 
Sbjct: 19  DELRKIFSKYGD-VSDVVVSSKKKGS----AIVEFASKKAAEAAV 58

The CD corresponds to the RRM of some eukaryotic DnaJ homolog subfamily C member 17 and similar proteins. DnaJ/Hsp40 (heat shock protein 40) proteins are highly conserved and play crucial roles in protein translation, folding, unfolding, translocation, and degradation. They act primarily by stimulating the ATPase activity of Hsp70s, an important chaperonine family. Members in this family contains an N-terminal DnaJ domain or J-domain, which mediates the interaction with Hsp70. They also contains a RNA recognition motif (RRM), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), at the C-terminus, which may play an essential role in RNA binding. . Length = 74

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

 Score = 39.7 bits (92), Expect = 3e-04
 Identities = 20/79 (25%), Positives = 37/79 (46%)

Query: 245 LFVCKLNPVTEDEDLHTIFSRFGTVVSAEIIRDFKTGDSLNYAFIEFENRQACERAYSKM 304
           +F+  L    ++  L  +F  FG V + ++IRDF T     + F+   N +    A + +
Sbjct: 4   IFIYNLGQDADEGILWQMFGPFGAVTNVKVIRDFNTNKCKGFGFVTMTNYEEAAMAIASL 63

Query: 305 DNALIDDRRIHVDFSQSVS 323
           +   + D+ + V F  S S
Sbjct: 64  NGYRLGDKILQVSFKTSKS 82

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

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

 Score = 39.3 bits (92), Expect = 3e-04
 Identities = 18/73 (24%), Positives = 36/73 (49%), Gaps = 4/73 (5%)

Query: 245 LFVCKLNPVTEDEDLHTIFSRFGTVVSAEIIRDFKTGDSLNYAFIEFENRQACERAYS-- 302
           LF+  L+  T D+ L   FS++G +    +++D  T  S  + F+ F +    + A +  
Sbjct: 2   LFIGGLSYETTDDSLKNYFSQWGEITDCVVMKDPNTKRSRGFGFVTFASASEVDAAMNAR 61

Query: 303 --KMDNALIDDRR 313
             K+D   ++ +R
Sbjct: 62  PHKVDGREVEPKR 74

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

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

 Score = 39.1 bits (92), Expect = 4e-04
 Identities = 17/62 (27%), Positives = 30/62 (48%)

Query: 245 LFVCKLNPVTEDEDLHTIFSRFGTVVSAEIIRDFKTGDSLNYAFIEFENRQACERAYSKM 304
           ++V  L+    +E L  +F + G VV+  I +D  T     Y F+EF + +  + A   M
Sbjct: 1   VYVGNLDEKVTEELLWELFIQAGPVVNVHIPKDRVTQAHQGYGFVEFLSEEDADYAIKIM 60

Query: 305 DN 306
           + 
Sbjct: 61  NM 62

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

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

 Score = 38.9 bits (91), Expect = 4e-04
 Identities = 17/72 (23%), Positives = 36/72 (50%)

Query: 245 LFVCKLNPVTEDEDLHTIFSRFGTVVSAEIIRDFKTGDSLNYAFIEFENRQACERAYSKM 304
           LF+  L     +EDL  +FS++G +    +  D  T     +AF+ +   +   +A++++
Sbjct: 5   LFIRNLAYTCTEEDLEKLFSKYGPLSEVHLPIDKLTKKPKGFAFVTYMIPEHAVKAFAEL 64

Query: 305 DNALIDDRRIHV 316
           D  +   R +H+
Sbjct: 65  DGTVFQGRLLHL 76

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

>gnl|CDD|241214 cd12770, RRM1_HuD, RNA recognition motif 1 in vertebrate Hu-antigen D (HuD)

 Score = 39.3 bits (91), Expect = 4e-04
 Identities = 17/67 (25%), Positives = 37/67 (55%)

Query: 257 EDLHTIFSRFGTVVSAEIIRDFKTGDSLNYAFIEFENRQACERAYSKMDNALIDDRRIHV 316
           E+  ++F   G + S +++RD  TG SL Y F+ + + +  E+A + ++   +  + I V
Sbjct: 17  EEFRSLFGSIGEIESCKLVRDKITGQSLGYGFVNYIDPKDAEKAINTLNGLRLQTKTIKV 76

Query: 317 DFSQSVS 323
            +++  S
Sbjct: 77  SYARPSS 83

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

>gnl|CDD|240999 cd12555, RRM2_RBM15, RNA recognition motif 2 in vertebrate RNA binding motif protein 15 (RBM15)

 Score = 39.2 bits (91), Expect = 4e-04
 Identities = 21/78 (26%), Positives = 36/78 (46%), Gaps = 1/78 (1%)

Query: 245 LFVCKLNPVTEDEDLHTIFSRFGTVVSAEIIRDFKTGDSLNYAFIEFENRQACERAYSKM 304
           LF+  L+    + DL   F RFG +   +I R  + G +  Y F++FEN     RA   M
Sbjct: 10  LFLGNLDITVTETDLRRAFDRFGVITEVDIKRPGR-GQTSTYGFLKFENLDMAHRAKLAM 68

Query: 305 DNALIDDRRIHVDFSQSV 322
              ++    I + + ++ 
Sbjct: 69  SGKVLRRNPIKIGYGKAT 86

This subgroup corresponds to the RRM2 of RBM15, also termed one-twenty two protein 1 (OTT1), conserved in eukaryotes, a novel mRNA export factor and component of the NXF1 pathway. It binds to NXF1 and serves as receptor for the RNA export element RTE. It also possesses mRNA export activity and can facilitate the access of DEAD-box protein DBP5 to mRNA at the nuclear pore complex (NPC). RBM15 belongs to the Spen (split end) protein family, which contain three N-terminal RNA recognition motifs (RRMs), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and a C-terminal SPOC (Spen paralog and ortholog C-terminal) domain. This family also includes a RBM15-MKL1 (OTT-MAL) fusion protein that RBM15 is N-terminally fused to megakaryoblastic leukemia 1 protein (MKL1) at the C-terminus in a translocation involving chromosome 1 and 22, resulting in acute megakaryoblastic leukemia. The fusion protein could interact with the mRNA export machinery. Although it maintains the specific transactivator function of MKL1, the fusion protein cannot activate RTE-mediated mRNA expression and has lost the post-transcriptional activator function of RBM15. However, it has transdominant suppressor function contributing to its oncogenic properties. . Length = 87

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

 Score = 38.7 bits (91), Expect = 5e-04
 Identities = 24/76 (31%), Positives = 39/76 (51%), Gaps = 4/76 (5%)

Query: 245 LFVCKLNPVTEDEDLHTIFSRFGTVVSAEIIR--DFKTGDSLNYAFIEFENRQACERAYS 302
           L+V  L+  T +E ++ +FSR G +    II   D  T     + F+E+  R+  E A  
Sbjct: 1   LYVGNLSFYTTEEQIYELFSRCGDI--KRIIMGLDRFTKTPCGFCFVEYYTREDAENAVK 58

Query: 303 KMDNALIDDRRIHVDF 318
            ++   +DDR I VD+
Sbjct: 59  YLNGTKLDDRIIRVDW 74

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

>gnl|CDD|240751 cd12305, RRM_NELFE, RNA recognition motif in negative elongation factor E (NELF-E) and similar proteins

 Score = 38.8 bits (91), Expect = 5e-04
 Identities = 19/79 (24%), Positives = 37/79 (46%), Gaps = 12/79 (15%)

Query: 243 NVLFVCKLNPVTEDEDLHTIFSRFGTV--VSAEIIRDFKTGDSLNYAFIEFENRQACERA 300
           N L+V     +TE+  L   FS FG +  +S E  +        N  F+ FE  ++ +RA
Sbjct: 5   NTLYVHGYG-LTEEI-LKKAFSPFGNIINISMEKEK--------NCGFVTFEKMESADRA 54

Query: 301 YSKMDNALIDDRRIHVDFS 319
            ++++   +   ++ V  +
Sbjct: 55  IAELNGTTVQGVQLKVSLA 73

This subfamily corresponds to the RRM of NELF-E, also termed RNA-binding protein RD. NELF-E is the RNA-binding subunit of cellular negative transcription elongation factor NELF (negative elongation factor) involved in transcriptional regulation of HIV-1 by binding to the stem of the viral transactivation-response element (TAR) RNA which is synthesized by cellular RNA polymerase II at the viral long terminal repeat. NELF is a heterotetrameric protein consisting of NELF A, B, C or the splice variant D, and E. NELF-E contains an RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain). It plays a role in the control of HIV transcription by binding to TAR RNA. In addition, NELF-E is associated with the NELF-B subunit, probably via a leucine zipper motif. . Length = 75

>gnl|CDD|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 = 38.4 bits (90), Expect = 5e-04
 Identities = 18/63 (28%), Positives = 29/63 (46%), Gaps = 6/63 (9%)

Query: 250 LNPVTEDEDLHTIFSRFGTVVSAEIIRDFKTGDSLNYAFIEFENRQACERAYSKMDNALI 309
           L     +E+L   FS FG +   E +R FK      YAF+ F+  +A   A   ++   I
Sbjct: 8   LPHGLTEEELQRTFSPFGAI---EEVRVFKDK---GYAFVRFDTHEAAATAIVAVNGTSI 61

Query: 310 DDR 312
           + +
Sbjct: 62  NGQ 64

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

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

 Score = 38.3 bits (90), Expect = 6e-04
 Identities = 22/63 (34%), Positives = 31/63 (49%), Gaps = 4/63 (6%)

Query: 245 LFVCKLNPVTEDEDLHTIFSRFGTVVSAEIIRDFKTGDSLNYAFIEFENRQA----CERA 300
           LFV  L+P   + DL   FSRFGTV   EII+    G    +A+I+    +A    C+  
Sbjct: 2   LFVGGLSPSVTESDLEERFSRFGTVSDVEIIKKKDAGPDRGFAYIDLRTSEAQLKKCKST 61

Query: 301 YSK 303
            + 
Sbjct: 62  LNG 64

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|240938 cd12494, RRM3_hnRNPR, RNA recognition motif 3 in vertebrate heterogeneous nuclear ribonucleoprotein R (hnRNP R)

 Score = 38.1 bits (88), Expect = 7e-04
 Identities = 24/73 (32%), Positives = 34/73 (46%), Gaps = 8/73 (10%)

Query: 244 VLFVCKLNPVTEDEDLHTIFSRFGTVVSAEIIRDFKTGDSLNYAFIEFENRQACERAYSK 303
           VLFV  L     +E L   FS FG +   + ++D        YAF+ FE R A  RA  +
Sbjct: 3   VLFVRNLATTVTEEILEKSFSEFGKLERVKKLKD--------YAFVHFEERDAAVRAMDE 54

Query: 304 MDNALIDDRRIHV 316
           M+   I+   I +
Sbjct: 55  MNGKEIEGEEIEI 67

This subgroup corresponds to the RRM3 of hnRNP R. a ubiquitously expressed nuclear RNA-binding protein that specifically bind mRNAs with a preference for poly(U) stretches. Upon binding of RNA, hnRNP R forms oligomers, most probably dimers. hnRNP R has been implicated in mRNA processing and mRNA transport, and also acts as a regulator to modify binding to ribosomes and RNA translation. hnRNP R is predominantly located in axons of motor neurons and to a much lower degree in sensory axons. In axons of motor neurons, it also functions as a cytosolic protein and interacts with wild type of survival motor neuron (SMN) proteins directly, further providing a molecular link between SMN and the spliceosome. Moreover, hnRNP R plays an important role in neural differentiation and development, as well as in retinal development and light-elicited cellular activities. hnRNP R contains an acidic auxiliary N-terminal region, followed by two well-defined and one degenerated RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a C-terminal RGG motif; hnRNP R binds RNA through its RRM domains. . Length = 72

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

 Score = 38.2 bits (88), Expect = 8e-04
 Identities = 18/60 (30%), Positives = 34/60 (56%)

Query: 245 LFVCKLNPVTEDEDLHTIFSRFGTVVSAEIIRDFKTGDSLNYAFIEFENRQACERAYSKM 304
           L++  L+P T D+DL  +   +G +VS + I D  T     Y F++F++  A ++A + +
Sbjct: 4   LYIRGLHPGTTDQDLVKLCQPYGKIVSTKAILDKTTNKCKGYGFVDFDSPSAAQKAVTAL 63

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

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

 Score = 37.8 bits (88), Expect = 8e-04
 Identities = 22/75 (29%), Positives = 38/75 (50%), Gaps = 9/75 (12%)

Query: 245 LFVCKLNP-VTEDEDLHTIFSRFGTVVSAEIIRDFKTGDSLNYAFIEFENRQACERAYSK 303
           LFV   +P  T +ED+  +F  FG +V  +I +         +AF+EFE+ +   +A   
Sbjct: 2   LFVVGFDPGTTREEDIEKLFEPFGPLVRCDIRK--------TFAFVEFEDSEDATKALEA 53

Query: 304 MDNALIDDRRIHVDF 318
           +  + ID   + V+F
Sbjct: 54  LHGSRIDGSVLTVEF 68

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

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

 Score = 38.1 bits (89), Expect = 8e-04
 Identities = 19/63 (30%), Positives = 33/63 (52%), Gaps = 2/63 (3%)

Query: 254 TEDEDLHTIFSRFGTVVSAEIIRDFKTGDSLNYAFIEFENRQACERAYSKMDNALIDDRR 313
           T ++DL   FS FG ++  ++ +D KTG S  + F+ F + +   +  S+    +ID R 
Sbjct: 11  TTEQDLKDYFSTFGELLMVQVKKDPKTGQSKGFGFVRFADYEDQVKVLSQ--RHMIDGRW 68

Query: 314 IHV 316
             V
Sbjct: 69  CDV 71

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

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

 Score = 37.9 bits (88), Expect = 9e-04
 Identities = 25/73 (34%), Positives = 38/73 (52%), Gaps = 4/73 (5%)

Query: 245 LFVCKLNPVTEDEDLHTIFSRFGTVVSAEIIRDFKTGDSLNYAFIEFENRQACERAYS-- 302
           +FV  L+  T  +DL   FS+FG VV   I  D  TG S  + F+ F++  + E+     
Sbjct: 1   MFVGGLSWDTTKKDLKEYFSKFGEVVDCTIKIDPVTGRSRGFGFVLFKDAASVEKVLDQK 60

Query: 303 --KMDNALIDDRR 313
             K+D  +ID +R
Sbjct: 61  EHKLDGRVIDPKR 73

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

>gnl|CDD|237171 PRK12678, PRK12678, transcription termination factor Rho; Provisional

 Score = 41.0 bits (97), Expect = 0.001
 Identities = 25/89 (28%), Positives = 34/89 (38%), Gaps = 7/89 (7%)

Query: 385 DGETPEKSRREKKHRGH-DPDDRVERNMNRLSSDLRHRDQERRELSYRQ-----RESDRT 438
           D     +    ++ RG  D  DR  R   R   D R  D               R   R 
Sbjct: 204 DRRDRREQGDRREERGRRDGGDRRGRRRRRDRRDARGDDNREDRGDRDGDDGEGRGGRRG 263

Query: 439 RENRE-DRRNRDGQESRNVQKQEVRDDDG 466
           R  R+ DRR R G +  N ++ E+R+DD 
Sbjct: 264 RRFRDRDRRGRRGGDGGNEREPELREDDV 292

Length = 672

>gnl|CDD|241050 cd12606, RRM1_RBM4, RNA recognition motif 1 in vertebrate RNA-binding protein 4 (RBM4)

 Score = 37.5 bits (87), Expect = 0.001
 Identities = 17/73 (23%), Positives = 38/73 (52%), Gaps = 8/73 (10%)

Query: 245 LFVCKLNPVTEDEDLHTIFSRFGTVVSAEIIRDFKTGDSLNYAFIEFENRQACERAYSKM 304
           LFV  L P   ++++ ++F ++G V+  +II+        NY F+  +++ A + A   +
Sbjct: 3   LFVGNLPPEATEQEIRSLFEQYGKVLECDIIK--------NYGFVHMDDKTAADEAIRNL 54

Query: 305 DNALIDDRRIHVD 317
            +  +    I+V+
Sbjct: 55  HHYKLHGVAINVE 67

This subgroup corresponds to the RRM1 of RBM4, a ubiquitously expressed splicing factor that has two isoforms, RBM4A (also known as Lark homolog) and RBM4B (also known as RBM30), which are very similar in structure and sequence. RBM4 may function as a translational regulator of stress-associated mRNAs and also plays a role in micro-RNA-mediated gene regulation. RBM4 contains two N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), a CCHC-type zinc finger, and three alanine-rich regions within their C-terminal regions. The C-terminal region may be crucial for nuclear localization and protein-protein interaction. The RRMs, in combination with the C-terminal region, are responsible for the splicing function of RBM4. . Length = 67

>gnl|CDD|240765 cd12319, RRM4_MRD1, RNA recognition motif 4 in yeast multiple RNA-binding domain-containing protein 1 (MRD1) and similar proteins

 Score = 38.3 bits (89), Expect = 0.001
 Identities = 22/85 (25%), Positives = 35/85 (41%), Gaps = 13/85 (15%)

Query: 245 LFVCKLNPVTEDEDLHTIFSRFGTVVSAEIIRDFKTGD---------SLNYAFIEFENRQ 295
           LFV  LN  T ++ L   F      V A +    KT           S+ + F+ F+ ++
Sbjct: 3   LFVKNLNFSTTNQHLTDAFKHLDGFVFARV----KTKPDPKRPGQTLSMGFGFVGFKTKE 58

Query: 296 ACERAYSKMDNALIDDRRIHVDFSQ 320
             + A   MD  ++D   + V FS 
Sbjct: 59  QAQAALKAMDGFVLDGHTLVVKFSH 83

This subfamily corresponds to the RRM4 of MRD1which is encoded by a novel yeast gene MRD1 (multiple RNA-binding domain). It is well-conserved in yeast and its homologs exist in all eukaryotes. MRD1 is present in the nucleolus and the nucleoplasm. It interacts with the 35 S precursor rRNA (pre-rRNA) and U3 small nucleolar RNAs (snoRNAs). MRD1 is essential for the initial processing at the A0-A2 cleavage sites in the 35 S pre-rRNA. It contains 5 conserved RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), which may play an important structural role in organizing specific rRNA processing events. . Length = 84

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

 Score = 38.0 bits (89), Expect = 0.001
 Identities = 22/81 (27%), Positives = 38/81 (46%), Gaps = 6/81 (7%)

Query: 246 FVCKLNPVTEDEDLHTIFSRFGTVVSAEIIR-DFKTGDSLNYAFIEFENRQACERAYSKM 304
           +V  L+P T  + L   FS+ G V   + +R          YAF+EF  + +   A  K+
Sbjct: 8   YVGNLDPTTTADQLLEFFSQAGEV---KYVRMAGDETQPTRYAFVEFAEQTSVINAL-KL 63

Query: 305 DNALIDDRRIHVDFS-QSVSK 324
           + A+   R + V+ S  ++ K
Sbjct: 64  NGAMFGGRPLKVNHSNNAIVK 84

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

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

 Score = 37.7 bits (88), Expect = 0.001
 Identities = 20/60 (33%), Positives = 32/60 (53%), Gaps = 2/60 (3%)

Query: 245 LFVCKLNP-VTEDEDLHTIFSRFGTVVSAEIIRDFKTGDSLNYAFIEFENRQACERAYSK 303
           +FV  L P VTE  DL   FS+FGTV    ++ D +      + FI FE+  + ++  ++
Sbjct: 5   IFVGGLPPNVTET-DLRKYFSQFGTVTEVVVMYDHEKKRPRGFGFITFESEDSVDQVVNE 63

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|241080 cd12636, RRM2_Bruno_like, RNA recognition motif 2 in Drosophila melanogaster Bruno protein and similar proteins

 Score = 37.9 bits (88), Expect = 0.001
 Identities = 20/63 (31%), Positives = 32/63 (50%), Gaps = 1/63 (1%)

Query: 242 ENVLFVCKLNPVTEDEDLHTIFSRFGTVVSAEIIRDFKTGDSLNYAFIEFENRQACERAY 301
           E  LFV  L+    + D+  +F+ FG++    ++RD + G S   AF+ F +RQ    A 
Sbjct: 1   ERKLFVGMLSKKCNENDVRIMFAPFGSIEECTVLRD-QNGQSRGCAFVTFASRQCALNAI 59

Query: 302 SKM 304
             M
Sbjct: 60  KAM 62

This subgroup corresponds to the RRM2 of Bruno, a Drosophila RNA recognition motif (RRM)-containing protein that plays a central role in regulation of Oskar (Osk) expression. It mediates repression by binding to regulatory Bruno response elements (BREs) in the Osk mRNA 3' UTR. The full-length Bruno protein contains three RRMs, two located in the N-terminal half of the protein and the third near the C-terminus, separated by a linker region. . Length = 81

>gnl|CDD|189387 pfam00098, zf-CCHC, Zinc knuckle

 Score = 36.3 bits (85), Expect = 0.001
 Identities = 7/17 (41%), Positives = 11/17 (64%)

Query: 340 KGCFKCGGLDHIAKDCT 356
           + C+ CG   H+A+DC 
Sbjct: 1   RKCYNCGKEGHLARDCP 17

The zinc knuckle is a zinc binding motif composed of the the following CX2CX4HX4C where X can be any amino acid. The motifs are mostly from retroviral gag proteins (nucleocapsid). Prototype structure is from HIV. Also contains members involved in eukaryotic gene regulation, such as C. elegans GLH-1. Structure is an 18-residue zinc finger. Length = 18

>gnl|CDD|240685 cd12239, RRM2_RBM40_like, RNA recognition motif 2 in RNA-binding protein 40 (RBM40) and similar proteins

 Score = 37.9 bits (89), Expect = 0.001
 Identities = 19/62 (30%), Positives = 26/62 (41%), Gaps = 4/62 (6%)

Query: 243 NVLFVCKLNPVTEDEDLHTIFSRFGTVVSAE----IIRDFKTGDSLNYAFIEFENRQACE 298
             L+V  L+    +EDL  IF RF    S E     IR    G     AF+ F + +   
Sbjct: 2   KRLYVKNLSKRVTEEDLVYIFGRFVDSSSEEKNMFDIRLMTEGRMKGQAFVTFPSEEIAT 61

Query: 299 RA 300
           +A
Sbjct: 62  KA 63

This subfamily corresponds to the RRM2 of RBM40 and the RRM of RBM41. RBM40, also known as RNA-binding region-containing protein 3 (RNPC3) or U11/U12 small nuclear ribonucleoprotein 65 kDa protein (U11/U12-65K protein). It serves as a bridging factor between the U11 and U12 snRNPs. It contains two RNA recognition motifs (RRMs), also known as RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), connected by a linker that includes a proline-rich region. It binds to the U11-associated 59K protein via its RRM1 and employs the RRM2 to bind hairpin III of the U12 small nuclear RNA (snRNA). The proline-rich region might be involved in protein-protein interactions. RBM41 contains only one RRM. Its biological function remains unclear. . Length = 82

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

 Score = 37.9 bits (87), Expect = 0.001
 Identities = 18/60 (30%), Positives = 33/60 (55%)

Query: 245 LFVCKLNPVTEDEDLHTIFSRFGTVVSAEIIRDFKTGDSLNYAFIEFENRQACERAYSKM 304
           L++  L P T D+DL  +   +G +VS + I D  T     Y F++F++  A ++A + +
Sbjct: 7   LYIRGLPPGTTDQDLIKLCQPYGKIVSTKAILDKNTNQCKGYGFVDFDSPAAAQKAVASL 66

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

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

 Score = 41.1 bits (96), Expect = 0.001
 Identities = 29/110 (26%), Positives = 47/110 (42%), Gaps = 12/110 (10%)

Query: 234 PDADIKPPENVLFVCKLNPVTEDEDLHTIFSRF--GTVVSAEIIRDFKTGDSLNYAFIEF 291
            D D+     +L+V  L   T +E +   FS F  G V   + IRD        YAF+ F
Sbjct: 225 VDEDVMAKVKILYVRNLMTTTTEEIIEKSFSEFKPGKVERVKKIRD--------YAFVHF 276

Query: 292 ENRQACERAYSKMDNALIDDRRIHVDFSQSVSKLWNQFRRRDHQTGKGKG 341
           E+R+   +A  +++   ++   I V  ++ V K    + R    TG    
Sbjct: 277 EDREDAVKAMDELNGKELEGSEIEVTLAKPVDK--KSYVRYTRGTGGRGK 324

Sequences in this subfamily include the human heterogeneous nuclear ribonucleoproteins (hnRNP) R , Q and APOBEC-1 complementation factor (aka APOBEC-1 stimulating protein). These proteins contain three RNA recognition domains (rrm: pfam00076) and a somewhat variable C-terminal domain. Length = 578

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

 Score = 37.4 bits (87), Expect = 0.001
 Identities = 21/65 (32%), Positives = 29/65 (44%), Gaps = 1/65 (1%)

Query: 245 LFVCKLNPVTEDEDLHTIFSRFGTVVSAEIIRDFKTGDSLNYAFIEFENRQACERAYSKM 304
           LFV  L     +E+L   F R+G V   +I R  +   +  YAF++F N     RA   M
Sbjct: 5   LFVGNLEITITEEELRRAFERYGVVEDVDIKRPPRGQGN-AYAFVKFLNLDMAHRAKVAM 63

Query: 305 DNALI 309
               I
Sbjct: 64  SGQYI 68

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

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

 Score = 37.5 bits (86), Expect = 0.001
 Identities = 19/60 (31%), Positives = 33/60 (55%)

Query: 245 LFVCKLNPVTEDEDLHTIFSRFGTVVSAEIIRDFKTGDSLNYAFIEFENRQACERAYSKM 304
           L++  L P T D+DL  +   +G +VS + I D  T     Y F++F++  A ++A S +
Sbjct: 10  LYIRGLPPNTTDQDLVKLCQPYGKIVSTKAILDKTTNKCKGYGFVDFDSPAAAQKAVSAL 69

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

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

 Score = 37.5 bits (87), Expect = 0.001
 Identities = 21/69 (30%), Positives = 32/69 (46%), Gaps = 1/69 (1%)

Query: 245 LFVCKLNPVTEDEDLHTIFSRFGTVVSAEIIRDFKTGDSLNYAFIEFENRQACERAYSKM 304
           L+V      T   DL   F R+G +V  +I    +T  S  +AF+E+E+ +  E AY +M
Sbjct: 2   LYVTGFGAETRARDLAYEFERYGRLVRCDI-PPPRTFQSRPFAFVEYESHRDAEDAYEEM 60

Query: 305 DNALIDDRR 313
                 D  
Sbjct: 61  HGRRFPDTG 69

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

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

 Score = 37.7 bits (87), Expect = 0.002
 Identities = 19/61 (31%), Positives = 33/61 (54%)

Query: 245 LFVCKLNPVTEDEDLHTIFSRFGTVVSAEIIRDFKTGDSLNYAFIEFENRQACERAYSKM 304
           L++  L      +D+  +FSRFG ++++ ++ D  TG S   AFI F+ R   E A +  
Sbjct: 3   LYISGLPRTMTQKDVEDMFSRFGRIINSRVLVDQATGLSRGVAFIRFDKRSEAEEAITSF 62

Query: 305 D 305
           +
Sbjct: 63  N 63

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

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

 Score = 36.9 bits (86), Expect = 0.002
 Identities = 18/74 (24%), Positives = 35/74 (47%), Gaps = 6/74 (8%)

Query: 245 LFVCKLNPVTEDEDLHTIFSRFGTVVSAEIIRDFKTGDSLNYAFIEFENRQACERAYSKM 304
           LFV  L     +E+   +FS++G V    + ++        + FI  + R   E+A +++
Sbjct: 4   LFVGNLPNDITEEEFKELFSKYGEVSEVFLNKE------KGFGFIRLDTRTNAEKAKAEL 57

Query: 305 DNALIDDRRIHVDF 318
           D  +   R++ V F
Sbjct: 58  DGIMRKGRQLRVRF 71

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

>gnl|CDD|241202 cd12758, RRM1_hnRPDL, RNA recognition motif 1 in heterogeneous nuclear ribonucleoprotein D-like (hnRNP D-like or hnRNP DL) and similar proteins

 Score = 36.9 bits (85), Expect = 0.002
 Identities = 23/73 (31%), Positives = 37/73 (50%), Gaps = 4/73 (5%)

Query: 245 LFVCKLNPVTEDEDLHTIFSRFGTVVSAEIIRDFKTGDSLNYAFIEFENRQACERAYS-- 302
           +F+  L+  T  +DL    SRFG V+   I  D  TG S  + F+ F++  + ++     
Sbjct: 2   MFIGGLSWDTSKKDLTEYLSRFGEVLDCTIKTDPVTGRSRGFGFVLFKDAASVDKVLELK 61

Query: 303 --KMDNALIDDRR 313
             K+D  LID +R
Sbjct: 62  EHKLDGKLIDPKR 74

This subgroup corresponds to the RRM1 of hnRNP DL (or hnRNP D-like), also termed AU-rich element RNA-binding factor, or JKT41-binding protein (protein laAUF1 or JKTBP), which is a dual functional protein that possesses DNA- and RNA-binding properties. It has been implicated in mRNA biogenesis at the transcriptional and post-transcriptional levels. hnRNP DL binds single-stranded DNA (ssDNA) or double-stranded DNA (dsDNA) in a non-sequencespecific manner, and interacts with poly(G) and poly(A) tenaciously. It contains two putative two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a glycine- and tyrosine-rich C-terminus. . Length = 76

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

 Score = 36.8 bits (86), Expect = 0.002
 Identities = 16/63 (25%), Positives = 33/63 (52%), Gaps = 1/63 (1%)

Query: 257 EDLHTIFSRFGTVVSAEIIRDFKTGDSLNYAFIEFENRQACERAYSKMDNALIDDRRIHV 316
           ++L  +FS FG V S  + + F  G    +AF+EF  +Q  + A   + +  +  R + +
Sbjct: 15  KELRELFSPFGQVKSVRLPKKF-DGSHRGFAFVEFVTKQEAQNAMEALKSTHLYGRHLVL 73

Query: 317 DFS 319
           +++
Sbjct: 74  EYA 76

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

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

 Score = 37.1 bits (86), Expect = 0.002
 Identities = 19/64 (29%), Positives = 35/64 (54%)

Query: 256 DEDLHTIFSRFGTVVSAEIIRDFKTGDSLNYAFIEFENRQACERAYSKMDNALIDDRRIH 315
           +E L  IFS  G VVS  ++ D +TG    Y F E+++++    A   ++   ++ R++ 
Sbjct: 12  EEQLKDIFSEVGPVVSFRLVYDRETGKPKGYGFCEYKDQETALSAMRNLNGYELNGRQLR 71

Query: 316 VDFS 319
           VD +
Sbjct: 72  VDNA 75

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

>gnl|CDD|241056 cd12612, RRM2_SECp43, RNA recognition motif 2 in tRNA selenocysteine-associated protein 1 (SECp43)

 Score = 36.9 bits (86), Expect = 0.002
 Identities = 21/65 (32%), Positives = 35/65 (53%), Gaps = 2/65 (3%)

Query: 245 LFVCKLNPVTEDEDLHTIFS-RFGTVVSAEIIRDFKTGDSLNYAFIEFENRQACERAYSK 303
           LFV  L P  +D  L+  FS R+ +   A+++ D + G+S  Y F+ F +    +RA ++
Sbjct: 4   LFVGDLTPDVDDYQLYEFFSKRYPSCKGAKVVLD-QNGNSRGYGFVRFSDESEQKRALTE 62

Query: 304 MDNAL 308
           M  A 
Sbjct: 63  MQGAS 67

This subgroup corresponds to the RRM2 of SECp43, an RNA-binding protein associated specifically with eukaryotic selenocysteine tRNA [tRNA(Sec)]. It may play an adaptor role in the mechanism of selenocysteine insertion. SECp43 is located primarily in the nucleus and contains two N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a C-terminal polar/acidic region. . Length = 82

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

 Score = 36.9 bits (85), Expect = 0.002
 Identities = 26/82 (31%), Positives = 44/82 (53%), Gaps = 8/82 (9%)

Query: 241 PENVLFVCKLNPVTEDEDLHTIFSRFGTVVSAEIIRDFKTGDSLNYAFIEFENRQACERA 300
           P   L+V  L P T    L   F RFG++ +     D+  GD  ++A+I++E+  A + A
Sbjct: 1   PTTRLWVGGLGPNTSLAALAREFDRFGSIRTI----DYVKGD--SFAYIQYESLDAAQAA 54

Query: 301 YSKMDNALI--DDRRIHVDFSQ 320
            ++M    +   DRR+ VDF++
Sbjct: 55  CAQMRGFPLGGPDRRLRVDFAK 76

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|240677 cd12231, RRM2_U2AF65, RNA recognition motif 2 found in U2 large nuclear ribonucleoprotein auxiliary factor U2AF 65 kDa subunit (U2AF65) and similar proteins

 Score = 36.8 bits (86), Expect = 0.002
 Identities = 16/74 (21%), Positives = 38/74 (51%)

Query: 243 NVLFVCKLNPVTEDEDLHTIFSRFGTVVSAEIIRDFKTGDSLNYAFIEFENRQACERAYS 302
           N +F+  L     ++ +  +   FG + +  +++D  TG S  YAF E+ +    ++A +
Sbjct: 1   NKIFIGGLPNYLSEDQVKELLESFGKLKAFNLVKDSATGLSKGYAFCEYLDPSVTDQAIA 60

Query: 303 KMDNALIDDRRIHV 316
            ++   + D+++ V
Sbjct: 61  GLNGMQLGDKKLTV 74

This subfamily corresponds to the RRM2 of U2AF65 and dU2AF50. U2AF65, also termed U2AF2, is the large subunit of U2 small nuclear ribonucleoprotein (snRNP) auxiliary factor (U2AF), which has been implicated in the recruitment of U2 snRNP to pre-mRNAs and is a highly conserved heterodimer composed of large and small subunits. U2AF65 specifically recognizes the intron polypyrimidine tract upstream of the 3' splice site and promotes binding of U2 snRNP to the pre-mRNA branchpoint. U2AF65 also plays an important role in the nuclear export of mRNA. It facilitates the formation of a messenger ribonucleoprotein export complex, containing both the NXF1 receptor and the RNA substrate. Moreover, U2AF65 interacts directly and specifically with expanded CAG RNA, and serves as an adaptor to link expanded CAG RNA to NXF1 for RNA export. U2AF65 contains an N-terminal RS domain rich in arginine and serine, followed by a proline-rich segment and three C-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). The N-terminal RS domain stabilizes the interaction of U2 snRNP with the branch point (BP) by contacting the branch region, and further promotes base pair interactions between U2 snRNA and the BP. The proline-rich segment mediates protein-protein interactions with the RRM domain of the small U2AF subunit (U2AF35 or U2AF1). The RRM1 and RRM2 are sufficient for specific RNA binding, while RRM3 is responsible for protein-protein interactions. The family also includes Splicing factor U2AF 50 kDa subunit (dU2AF50), the Drosophila ortholog of U2AF65. dU2AF50 functions as an essential pre-mRNA splicing factor in flies. It associates with intronless mRNAs and plays a significant and unexpected role in the nuclear export of a large number of intronless mRNAs. Length = 77

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

 Score = 37.0 bits (85), Expect = 0.003
 Identities = 17/71 (23%), Positives = 39/71 (54%), Gaps = 1/71 (1%)

Query: 253 VTEDEDLHTIFSRFGTVVSAEIIRDFKTGDSLNYAFIEFENRQACERAYSKMDNALIDDR 312
           +T++E   ++F   G + S +++RD  TG SL Y F+ + +    ++A + ++   +  +
Sbjct: 15  MTQEE-FKSLFGSIGEIESCKLVRDKITGQSLGYGFVNYVDPNDADKAINTLNGLKLQTK 73

Query: 313 RIHVDFSQSVS 323
            I V +++  S
Sbjct: 74  TIKVSYARPSS 84

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

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

 Score = 36.2 bits (83), Expect = 0.003
 Identities = 18/72 (25%), Positives = 33/72 (45%), Gaps = 8/72 (11%)

Query: 245 LFVCKLNPVTEDEDLHTIFSRFGTVVSAEIIRDFKTGDSLNYAFIEFENRQACERAYSKM 304
           L V  ++    +++L   F  +G V+  +I++D        YAF+  E  +    A   +
Sbjct: 3   LHVGNISSSCTNQELRAKFEEYGPVIECDIVKD--------YAFVHMERAEDAVEAIRGL 54

Query: 305 DNALIDDRRIHV 316
           DN     +R+HV
Sbjct: 55  DNTEFQGKRMHV 66

This subgroup corresponds to the RRM2 of RBM4, a ubiquitously expressed splicing factor that has two isoforms, RBM4A (also known as Lark homolog) and RBM4B (also known as RBM30), which are very similar in structure and sequence. RBM4 may function as a translational regulator of stress-associated mRNAs and also plays a role in micro-RNA-mediated gene regulation. RBM4 contains two N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), a CCHC-type zinc finger, and three alanine-rich regions within their C-terminal regions. The C-terminal region may be crucial for nuclear localization and protein-protein interaction. The RRMs, in combination with the C-terminal region, are responsible for the splicing function of RBM4. . Length = 67

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

 Score = 36.3 bits (84), Expect = 0.003
 Identities = 18/67 (26%), Positives = 29/67 (43%)

Query: 242 ENVLFVCKLNPVTEDEDLHTIFSRFGTVVSAEIIRDFKTGDSLNYAFIEFENRQACERAY 301
              LFV  LN  T D  L   F+R+G +    ++ D  T  S  + FI F +    + A 
Sbjct: 2   LCKLFVGGLNLKTSDSGLRRHFTRYGKLTECVVMVDPNTKRSRGFGFITFSSADEADEAM 61

Query: 302 SKMDNAL 308
               +++
Sbjct: 62  EAQPHSI 68

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

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

 Score = 36.2 bits (84), Expect = 0.003
 Identities = 15/73 (20%), Positives = 36/73 (49%)

Query: 245 LFVCKLNPVTEDEDLHTIFSRFGTVVSAEIIRDFKTGDSLNYAFIEFENRQACERAYSKM 304
           LFV  L+   +++ ++  F  +G + S  +  D  +G    + ++EF +++A + A   +
Sbjct: 1   LFVGNLSFDADEDSIYEAFGEYGEISSVRLPTDPDSGRPKGFGYVEFSSQEAAQAALDAL 60

Query: 305 DNALIDDRRIHVD 317
               +  R + +D
Sbjct: 61  GGTDLLGRPVRLD 73

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

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

 Score = 36.2 bits (84), Expect = 0.004
 Identities = 19/73 (26%), Positives = 34/73 (46%), Gaps = 6/73 (8%)

Query: 245 LFVCKLNPVTEDEDLHTIFSRFGTVVSAEIIRDFKTGDSLNYAFIEFENRQACERAYSKM 304
           L++  L+    +EDL  +F  +G + S ++I           A++  E RQ   RA  K+
Sbjct: 5   LWIGHLSKKVTEEDLKNLFEEYGEIQSIDMI------PPRGCAYVCMETRQDAHRALQKL 58

Query: 305 DNALIDDRRIHVD 317
            N  +  ++I V 
Sbjct: 59  RNVKLAGKKIKVA 71

This subfamily corresponds to the RRM in a new class of SCAFs (SR-like CTD-associated factors), including SCAF4, SCAF8 and similar proteins. The biological role of SCAF4 remains unclear, but it shows high sequence similarity to SCAF8 (also termed CDC5L complex-associated protein 7, or RNA-binding motif protein 16, or CTD-binding SR-like protein RA8). SCAF8 is a nuclear matrix protein that interacts specifically with a highly serine-phosphorylated form of the carboxy-terminal domain (CTD) of the largest subunit of RNA polymerase II (pol II). The pol II CTD plays a role in coupling transcription and pre-mRNA processing. In addition, SCAF8 co-localizes primarily with transcription sites that are enriched in nuclear matrix fraction, which is known to contain proteins involved in pre-mRNA processing. Thus, SCAF8 may play a direct role in coupling with both, transcription and pre-mRNA processing, processes. SCAF8 and SCAF4 both contain a conserved N-terminal CTD-interacting domain (CID), an atypical RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNPs (ribonucleoprotein domain), and serine/arginine-rich motifs. Length = 77

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

 Score = 36.1 bits (83), Expect = 0.004
 Identities = 17/56 (30%), Positives = 30/56 (53%)

Query: 245 LFVCKLNPVTEDEDLHTIFSRFGTVVSAEIIRDFKTGDSLNYAFIEFENRQACERA 300
           L+V  L      +++  +FS++G ++++ I+ D  TG S    FI F+ R   E A
Sbjct: 4   LYVSGLPKTMSQKEMEQLFSQYGRIITSRILVDQVTGISRGVGFIRFDKRIEAEEA 59

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

>gnl|CDD|241076 cd12632, RRM1_CELF3_4_5_6, RNA recognition motif 1 in CUGBP Elav-like family member CELF-3, CELF-4, CELF-5, CELF-6 and similar proteins

 Score = 36.2 bits (84), Expect = 0.004
 Identities = 17/58 (29%), Positives = 32/58 (55%)

Query: 245 LFVCKLNPVTEDEDLHTIFSRFGTVVSAEIIRDFKTGDSLNYAFIEFENRQACERAYS 302
           LFV ++    E++DL  +F +FG +    +++D  TG     AF+ +  R++  +A S
Sbjct: 8   LFVGQIPRNLEEKDLRPLFEQFGKIYELTVLKDKYTGMHKGCAFLTYCARESALKAQS 65

This subfamily corresponds to the RRM1 of CELF-3, CELF-4, CELF-5, CELF-6, all of which belong to the CUGBP1 and ETR-3-like factors (CELF) or BRUNOL (Bruno-like) family of RNA-binding proteins that display dual nuclear and cytoplasmic localizations and have been implicated in the regulation of pre-mRNA splicing and in the control of mRNA translation and deadenylation. CELF-3, expressed in brain and testis only, is also known as bruno-like protein 1 (BRUNOL-1), or CAG repeat protein 4, or CUG-BP- and ETR-3-like factor 3, or embryonic lethal abnormal vision (ELAV)-type RNA-binding protein 1 (ETR-1), or expanded repeat domain protein CAG/CTG 4, or trinucleotide repeat-containing gene 4 protein (TNRC4). It plays an important role in the pathogenesis of tauopathies. CELF-3 contains three highly conserved RNA recognition motifs (RRMs), also known as RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains): two consecutive RRMs (RRM1 and RRM2) situated in the N-terminal region followed by a linker region and the third RRM (RRM3) close to the C-terminus of the protein.The effect of CELF-3 on tau splicing is mediated mainly by the RNA-binding activity of RRM2. The divergent linker region might mediate the interaction of CELF-3 with other proteins regulating its activity or involved in target recognition. CELF-4, highly expressed throughout the brain and in glandular tissues, moderately expressed in heart, skeletal muscle, and liver, is also known as bruno-like protein 4 (BRUNOL-4), or CUG-BP- and ETR-3-like factor 4. Like CELF-3, CELF-4 also contain three highly conserved RRMs. The splicing activation or repression activity of CELF-4 on some specific substrates is mediated by its RRM1/RRM2. On the other hand, both RRM1 and RRM2 of CELF-4 can activate cardiac troponin T (cTNT) exon 5 inclusion. CELF-5, expressed in brain, is also known as bruno-like protein 5 (BRUNOL-5), or CUG-BP- and ETR-3-like factor 5. Although its biological role remains unclear, CELF-5 shares same domain architecture with CELF-3. CELF-6, strongly expressed in kidney, brain, and testis, is also known as bruno-like protein 6 (BRUNOL-6), or CUG-BP- and ETR-3-like factor 6. It activates exon inclusion of a cardiac troponin T minigene in transient transfection assays in an muscle-specific splicing enhancer (MSE)-dependent manner and can activate inclusion via multiple copies of a single element, MSE2. CELF-6 also promotes skipping of exon 11 of insulin receptor, a known target of CELF activity that is expressed in kidney. In additiona to three highly conserved RRMs, CELF-6 also possesses numerous potential phosphorylation sites, a potential nuclear localization signal (NLS) at the C terminus, and an alanine-rich region within the divergent linker region. . Length = 87

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	589
KOG0415	479	consensus Predicted peptidyl prolyl cis-trans isom	100.0
KOG0881	164	consensus Cyclophilin type peptidyl-prolyl cis-tra	100.0
KOG0546	372	consensus HSP90 co-chaperone CPR7/Cyclophilin [Pos	100.0
cd01921	166	cyclophilin_RRM cyclophilin_RRM: cyclophilin-type	100.0
cd01923	159	cyclophilin_RING cyclophilin_RING: cyclophilin-typ	100.0
cd01928	153	Cyclophilin_PPIL3_like Cyclophilin_PPIL3_like. Pro	100.0
KOG0884	161	consensus Similar to cyclophilin-type peptidyl-pro	100.0
COG0652	158	PpiB Peptidyl-prolyl cis-trans isomerase (rotamase	100.0
KOG0880	217	consensus Peptidyl-prolyl cis-trans isomerase [Pos	100.0
KOG0883	518	consensus Cyclophilin type, U box-containing pepti	100.0
cd01927	148	cyclophilin_WD40 cyclophilin_WD40: cyclophilin-typ	100.0
KOG0882	558	consensus Cyclophilin-related peptidyl-prolyl cis-	100.0
cd01925	171	cyclophilin_CeCYP16-like cyclophilin_CeCYP16-like:	100.0
cd01922	146	cyclophilin_SpCYP2_like cyclophilin_SpCYP2_like: c	100.0
KOG0879	177	consensus U-snRNP-associated cyclophilin type pept	100.0
KOG0885	439	consensus Peptidyl-prolyl cis-trans isomerase [Pos	100.0
PTZ00221	249	cyclophilin; Provisional	100.0
PLN03149	186	peptidyl-prolyl isomerase H (cyclophilin H); Provi	100.0
PRK10791	164	peptidyl-prolyl cis-trans isomerase B (rotamase B)	100.0
PRK10903	190	peptidyl-prolyl cis-trans isomerase A (rotamase A)	100.0
cd01926	164	cyclophilin_ABH_like cyclophilin_ABH_like: Cycloph	100.0
PTZ00060	183	cyclophilin; Provisional	100.0
cd01920	155	cyclophilin_EcCYP_like cyclophilin_EcCYP_like: cyc	100.0
cd00317	146	cyclophilin cyclophilin: cyclophilin-type peptidyl	100.0
PF00160	155	Pro_isomerase: Cyclophilin type peptidyl-prolyl ci	100.0
KOG0111	298	consensus Cyclophilin-type peptidyl-prolyl cis-tra	100.0
cd01924	176	cyclophilin_TLP40_like cyclophilin_TLP40_like: cyc	100.0
KOG0865	167	consensus Cyclophilin type peptidyl-prolyl cis-tra	99.95
KOG0113	335	consensus U1 small nuclear ribonucleoprotein (RRM	99.86
KOG0107	195	consensus Alternative splicing factor SRp20/9G8 (R	99.79
PLN03134	144	glycine-rich RNA-binding protein 4; Provisional	99.73
KOG0126	219	consensus Predicted RNA-binding protein (RRM super	99.6
TIGR01661	352	ELAV_HUD_SF ELAV/HuD family splicing factor. These	99.57
KOG4207	256	consensus Predicted splicing factor, SR protein su	99.57
TIGR01659	346	sex-lethal sex-lethal family splicing factor. This	99.56
PF00076	70	RRM_1: RNA recognition motif. (a.k.a. RRM, RBD, or	99.55
TIGR01659	346	sex-lethal sex-lethal family splicing factor. This	99.55
TIGR01661	352	ELAV_HUD_SF ELAV/HuD family splicing factor. These	99.54
KOG0121	153	consensus Nuclear cap-binding protein complex, sub	99.53
KOG0122	270	consensus Translation initiation factor 3, subunit	99.51
KOG0109	346	consensus RNA-binding protein LARK, contains RRM a	99.51
KOG0149	247	consensus Predicted RNA-binding protein SEB4 (RRM	99.49
PF14259	70	RRM_6: RNA recognition motif (a.k.a. RRM, RBD, or	99.46
TIGR01645	612	half-pint poly-U binding splicing factor, half-pin	99.45
KOG0130	170	consensus RNA-binding protein RBM8/Tsunagi (RRM su	99.44
PLN03213	759	repressor of silencing 3; Provisional	99.42
TIGR01645	612	half-pint poly-U binding splicing factor, half-pin	99.42
PLN03120	260	nucleic acid binding protein; Provisional	99.42
TIGR01622	457	SF-CC1 splicing factor, CC1-like family. A homolog	99.4
KOG0117	506	consensus Heterogeneous nuclear ribonucleoprotein	99.38
KOG0148	321	consensus Apoptosis-promoting RNA-binding protein	99.38
TIGR01642	509	U2AF_lg U2 snRNP auxilliary factor, large subunit,	99.37
PLN03121	243	nucleic acid binding protein; Provisional	99.36
KOG0111	298	consensus Cyclophilin-type peptidyl-prolyl cis-tra	99.36
KOG0125	376	consensus Ataxin 2-binding protein (RRM superfamil	99.35
smart00362	72	RRM_2 RNA recognition motif.	99.35
TIGR01648	578	hnRNP-R-Q heterogeneous nuclear ribonucleoprotein	99.33
KOG0131	203	consensus Splicing factor 3b, subunit 4 [RNA proce	99.32
TIGR01628	562	PABP-1234 polyadenylate binding protein, human typ	99.32
TIGR01622	457	SF-CC1 splicing factor, CC1-like family. A homolog	99.31
TIGR01648	578	hnRNP-R-Q heterogeneous nuclear ribonucleoprotein	99.31
smart00360	71	RRM RNA recognition motif.	99.3
KOG0117	506	consensus Heterogeneous nuclear ribonucleoprotein	99.29
KOG0105	241	consensus Alternative splicing factor ASF/SF2 (RRM	99.29
KOG0148	321	consensus Apoptosis-promoting RNA-binding protein	99.28
KOG0145	360	consensus RNA-binding protein ELAV/HU (RRM superfa	99.27
TIGR01628	562	PABP-1234 polyadenylate binding protein, human typ	99.27
KOG0108	435	consensus mRNA cleavage and polyadenylation factor	99.26
COG0724	306	RNA-binding proteins (RRM domain) [General functio	99.26
KOG0114	124	consensus Predicted RNA-binding protein (RRM super	99.25
KOG0145	360	consensus RNA-binding protein ELAV/HU (RRM superfa	99.24
cd00590	74	RRM RRM (RNA recognition motif), also known as RBD	99.24
KOG0146	371	consensus RNA-binding protein ETR-3 (RRM superfami	99.21
TIGR01649	481	hnRNP-L_PTB hnRNP-L/PTB/hephaestus splicing factor	99.2
KOG4676	479	consensus Splicing factor, arginine/serine-rich [R	99.19
KOG0144	510	consensus RNA-binding protein CUGBP1/BRUNO (RRM su	99.17
KOG0109	346	consensus RNA-binding protein LARK, contains RRM a	99.16
TIGR01649	481	hnRNP-L_PTB hnRNP-L/PTB/hephaestus splicing factor	99.16
KOG0147	549	consensus Transcriptional coactivator CAPER (RRM s	99.15
smart00361	70	RRM_1 RNA recognition motif.	99.15
KOG0127	678	consensus Nucleolar protein fibrillarin NOP77 (RRM	99.15
KOG0124	544	consensus Polypyrimidine tract-binding protein PUF	99.14
KOG0127	678	consensus Nucleolar protein fibrillarin NOP77 (RRM	99.12
PF13893	56	RRM_5: RNA recognition motif. (a.k.a. RRM, RBD, or	99.12
KOG0131	203	consensus Splicing factor 3b, subunit 4 [RNA proce	99.11
KOG0144	510	consensus RNA-binding protein CUGBP1/BRUNO (RRM su	99.08
KOG0123	369	consensus Polyadenylate-binding protein (RRM super	98.97
KOG4676	479	consensus Splicing factor, arginine/serine-rich [R	98.95
KOG4208	214	consensus Nucleolar RNA-binding protein NIFK [Gene	98.95
KOG4212	608	consensus RNA-binding protein hnRNP-M [RNA process	98.91
KOG4661	940	consensus Hsp27-ERE-TATA-binding protein/Scaffold	98.89
KOG4206	221	consensus Spliceosomal protein snRNP-U1A/U2B [RNA	98.89
KOG0110	725	consensus RNA-binding protein (RRM superfamily) [G	98.88
KOG0110	725	consensus RNA-binding protein (RRM superfamily) [G	98.86
KOG4205	311	consensus RNA-binding protein musashi/mRNA cleavag	98.83
TIGR01642	509	U2AF_lg U2 snRNP auxilliary factor, large subunit,	98.77
KOG0132	894	consensus RNA polymerase II C-terminal domain-bind	98.76
KOG0124	544	consensus Polypyrimidine tract-binding protein PUF	98.73
KOG0123	369	consensus Polyadenylate-binding protein (RRM super	98.72
KOG1548	382	consensus Transcription elongation factor TAT-SF1	98.72
KOG0116	419	consensus RasGAP SH3 binding protein rasputin, con	98.69
KOG0153	377	consensus Predicted RNA-binding protein (RRM super	98.69
KOG4205	311	consensus RNA-binding protein musashi/mRNA cleavag	98.68
KOG0533	243	consensus RRM motif-containing protein [RNA proces	98.62
KOG4212	608	consensus RNA-binding protein hnRNP-M [RNA process	98.59
KOG4209	231	consensus Splicing factor RNPS1, SR protein superf	98.57
KOG0106	216	consensus Alternative splicing factor SRp55/B52/SR	98.56
KOG0151	877	consensus Predicted splicing regulator, contains R	98.53
KOG4454	267	consensus RNA binding protein (RRM superfamily) [G	98.51
KOG0146	371	consensus RNA-binding protein ETR-3 (RRM superfami	98.5
KOG1995	351	consensus Conserved Zn-finger protein [General fun	98.47
KOG1457	284	consensus RNA binding protein (contains RRM repeat	98.44
PF04059	97	RRM_2: RNA recognition motif 2; InterPro: IPR00720	98.32
KOG0226	290	consensus RNA-binding proteins [General function p	98.31
KOG0882	558	consensus Cyclophilin-related peptidyl-prolyl cis-	98.24
KOG0120	500	consensus Splicing factor U2AF, large subunit (RRM	98.2
KOG4660	549	consensus Protein Mei2, essential for commitment t	98.12
KOG2416	718	consensus Acinus (induces apoptotic chromatin cond	98.12
KOG4849	498	consensus mRNA cleavage factor I subunit/CPSF subu	98.08
KOG1190	492	consensus Polypyrimidine tract-binding protein [RN	97.95
KOG1457	284	consensus RNA binding protein (contains RRM repeat	97.94
KOG0147	549	consensus Transcriptional coactivator CAPER (RRM s	97.88
KOG4206	221	consensus Spliceosomal protein snRNP-U1A/U2B [RNA	97.83
PF11608	90	Limkain-b1: Limkain b1; InterPro: IPR024582 This e	97.76
KOG4211	510	consensus Splicing factor hnRNP-F and related RNA-	97.74
KOG4210	285	consensus Nuclear localization sequence binding pr	97.7
COG5175	480	MOT2 Transcriptional repressor [Transcription]	97.64
PF08777	105	RRM_3: RNA binding motif; InterPro: IPR014886 This	97.55
KOG4211	510	consensus Splicing factor hnRNP-F and related RNA-	97.47
KOG0106	216	consensus Alternative splicing factor SRp55/B52/SR	97.46
KOG3152	278	consensus TBP-binding protein, activator of basal	97.43
PF08952	146	DUF1866: Domain of unknown function (DUF1866) ; In	97.37
KOG2314	698	consensus Translation initiation factor 3, subunit	97.33
KOG1190	492	consensus Polypyrimidine tract-binding protein [RN	97.15
KOG1548	382	consensus Transcription elongation factor TAT-SF1	97.04
KOG2202	260	consensus U2 snRNP splicing factor, small subunit,	96.95
KOG0129	520	consensus Predicted RNA-binding protein (RRM super	96.92
KOG1456	494	consensus Heterogeneous nuclear ribonucleoprotein	96.9
KOG1456	494	consensus Heterogeneous nuclear ribonucleoprotein	96.89
KOG0120	500	consensus Splicing factor U2AF, large subunit (RRM	96.89
KOG1855	484	consensus Predicted RNA-binding protein [General f	96.73
KOG2193	584	consensus IGF-II mRNA-binding protein IMP, contain	96.72
KOG4307	944	consensus RNA binding protein RBM12/SWAN [General	96.67
PF14605	53	Nup35_RRM_2: Nup53/35/40-type RNA recognition moti	96.66
KOG0105	241	consensus Alternative splicing factor ASF/SF2 (RRM	96.53
PF05172	100	Nup35_RRM: Nup53/35/40-type RNA recognition motif;	96.49
KOG1365	508	consensus RNA-binding protein Fusilli, contains RR	96.37
PRK00969	508	hypothetical protein; Provisional	96.32
KOG0129	520	consensus Predicted RNA-binding protein (RRM super	96.27
TIGR03268	503	methan_mark_3 putative methanogenesis marker prote	96.19
KOG0112	975	consensus Large RNA-binding protein (RRM superfami	96.14
PRK00969	508	hypothetical protein; Provisional	96.12
TIGR03268	503	methan_mark_3 putative methanogenesis marker prote	96.11
KOG0128	881	consensus RNA-binding protein SART3 (RRM superfami	95.97
COG4070	512	Predicted peptidyl-prolyl cis-trans isomerase (rot	95.96
KOG1996	378	consensus mRNA splicing factor [RNA processing and	95.66
PF12903	147	DUF3830: Protein of unknown function (DUF3830); In	95.19
KOG2253	668	consensus U1 snRNP complex, subunit SNU71 and rela	95.13
KOG0115	275	consensus RNA-binding protein p54nrb (RRM superfam	94.93
KOG2068	327	consensus MOT2 transcription factor [Transcription	94.77
PF08675	87	RNA_bind: RNA binding domain; InterPro: IPR014789	94.72
KOG0128	881	consensus RNA-binding protein SART3 (RRM superfami	94.67
COG4070	512	Predicted peptidyl-prolyl cis-trans isomerase (rot	94.56
KOG0112	975	consensus Large RNA-binding protein (RRM superfami	94.51
PF10309	62	DUF2414: Protein of unknown function (DUF2414); In	94.1
PF15023	166	DUF4523: Protein of unknown function (DUF4523)	93.61
KOG1365	508	consensus RNA-binding protein Fusilli, contains RR	93.41
PF03467	176	Smg4_UPF3: Smg-4/UPF3 family; InterPro: IPR005120	93.33
KOG4660	549	consensus Protein Mei2, essential for commitment t	93.14
PF03880	74	DbpA: DbpA RNA binding domain ; InterPro: IPR00558	93.05
KOG4307	944	consensus RNA binding protein RBM12/SWAN [General	93.04
PF04847	184	Calcipressin: Calcipressin; InterPro: IPR006931 Ca	92.57
KOG2591	684	consensus c-Mpl binding protein, contains La domai	92.53
KOG2888	453	consensus Putative RNA binding protein [General fu	92.21
PF07576	110	BRAP2: BRCA1-associated protein 2; InterPro: IPR01	92.14
PF04126	120	Cyclophil_like: Cyclophilin-like; InterPro: IPR007	91.81
KOG4574	1007	consensus RNA-binding protein (contains RRM and Pu	90.73
KOG4285	350	consensus Mitotic phosphoprotein [Cell cycle contr	90.66
KOG4210	285	consensus Nuclear localization sequence binding pr	89.86
KOG2135	526	consensus Proteins containing the RNA recognition	89.52
KOG0804	493	consensus Cytoplasmic Zn-finger protein BRAP2 (BRC	87.42
KOG4368	757	consensus Predicted RNA binding protein, contains	86.74
KOG2318	650	consensus Uncharacterized conserved protein [Funct	82.8
KOG0151	877	consensus Predicted splicing regulator, contains R	80.33

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

Probab=100.00  E-value=7.4e-78  Score=581.61  Aligned_cols=359  Identities=67%  Similarity=1.072  Sum_probs=330.2

Q ss_pred             CEEEEEecceeEEEEecCCCChhHHHHHHHHHhcCccCCceEEEeecCcccccCCCCCCCCCCCCcccccccccccccCC
Q 007792            1 MSVLIVTSLGDIVVDLFVDKCPLTTKNFLKLCKIKYYNGCLFHTVQKDFTAQTGDPTGTGTGGDSVYKFLYGEQARFFGD   80 (589)
Q Consensus         1 ~~v~~~T~~G~i~ieL~~~~aP~~~~nF~~l~~~~~Y~g~~f~rv~~~~~iq~Gd~~~~~~~~~~~~~~~~~~~~~~~~~   80 (589)
                      |+|+|+|++|+|||.||.+.+|.||.|||+||+.+||+.|.||-|..+|++|+|||+++|.||.+||+.+++.++.+|..
T Consensus         1 MsVlieTtlGDlvIDLf~~erP~~clNFLKLCk~KYYN~clfh~vq~~f~aQTGDPtGtG~GG~si~~~lyG~q~rffea   80 (479)
T KOG0415|consen    1 MSVLIETTLGDLVIDLFVKERPRTCLNFLKLCKIKYYNFCLFHTVQRDFTAQTGDPTGTGDGGESIYGVLYGEQARFFEA   80 (479)
T ss_pred             CcEEEEeecccEEeeeecccCcHHHHHHHHHHhHhhcccceeeeccccceeecCCCCCCCCCcceeeeecccccchhhhh
Confidence            99999999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             ccccCCCCCCCceEEEeccCCCCCcceEEEEeCCCCCCCCCCcceEEEEecCHHHHHHHhhCccCCCCCcccceeecccc
Q 007792           81 EIRVDLKHAKTGTVAMASAGENLNASQFYMTLRDNLDYLDEKHTIFGEVAEGLETLSRINESFVDEKNRPYKNIRIKHTY  160 (589)
Q Consensus        81 e~~~~l~~~~~G~vs~a~~g~~~~~sqFfI~l~~~~~~ld~~~~vFG~Vv~G~~vl~~i~~~~~~~~~~p~~~i~I~~~~  160 (589)
                      |+++.|+|...|+|||+++|.+.+||||||||+.++.+||++|+|||+|++||++|.+|+.+-+++.++|+++|.|+++.
T Consensus        81 E~~p~l~Hsk~G~vsmvs~g~n~~gSQF~iTlgenLdyLDg~htvfGqV~EG~dtl~kiNea~vD~~~rPykdIRI~HTi  160 (479)
T KOG0415|consen   81 EFLPKLKHSKMGTVSMVSAGENLNGSQFFITLGENLDYLDGKHTVFGQVAEGFDTLTKINEAIVDPKNRPYKDIRIKHTI  160 (479)
T ss_pred             hhcccccccccceEEeecCCcccccceEEEEccccccccccccceeeehhhhHHHHHHHHHHhcCCCCCcccceeeeeeE
Confidence            99999999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             cccCCCCChhhhcccccCCCCCCCCCccccccccccCCCCcccccCCHHHHHHHHHhhhhhhhhhhhhccCCCCCCCCCC
Q 007792          161 ILEDPFDDPAQLAELIPDASPEGKPKDEVVDEVRLEDDWVPLDEQLSAAELEQVIRSKDARSSAVVLESIGDIPDADIKP  240 (589)
Q Consensus       161 vl~~p~~~~~~l~~~~~~~s~~~~~~~e~~~~~~l~~~~~~~~~~~~~~~~e~~~~~~~~~~~~~~~~~~~~~~~~~~~~  240 (589)
                      ||++||++|+.|.  +|..+|.+.+++.....+.++++|. .+++++++++++.+.++++++++++|+|.|++|.+..+|
T Consensus       161 iLdDPFddpp~l~--~p~rspsPt~e~l~~g~i~~de~~d-~~~g~saeel~e~~~e~ea~~~A~iLEmvGDlpdAd~~P  237 (479)
T KOG0415|consen  161 ILDDPFDDPPDLA--EPMRSPSPTPEQLVKGRIRLDEDED-DDEGLSAEELEEVLAEKEAKAQAVILEMVGDLPDADVKP  237 (479)
T ss_pred             EecCCCCCchhhc--cCCCCCCCCHHHhhccccccCcccc-cccccCHHHHHHHHHHHHHHhhHhHHHHhcCCcccccCC
Confidence            9999999999998  6777787777777666788888888 888999999999999999999999999999999999999


Q ss_pred             CCceEEEecCCCCCCHHHHHHHhccCCCeEEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHhcCCceeCCeEEEEEecc
Q 007792          241 PENVLFVCKLNPVTEDEDLHTIFSRFGTVVSAEIIRDFKTGDSLNYAFIEFENRQACERAYSKMDNALIDDRRIHVDFSQ  320 (589)
Q Consensus       241 ~~~~i~V~nL~~~~te~~L~~~F~~~G~v~~~~i~~d~~tg~~~g~aFV~f~~~~~a~~A~~~l~g~~i~gr~i~V~~a~  320 (589)
                      |.+.|||..|++.||.++|.-+|+.||+|..|.|+.|..||.+..||||+|++.++|++|+..|++..|+.+.|+|.|++
T Consensus       238 PeNVLFVCKLNPVTtDeDLeiIFSrFG~i~sceVIRD~ktgdsLqyaFiEFen~escE~AyFKMdNvLIDDrRIHVDFSQ  317 (479)
T KOG0415|consen  238 PENVLFVCKLNPVTTDEDLEIIFSRFGKIVSCEVIRDRKTGDSLQYAFIEFENKESCEQAYFKMDNVLIDDRRIHVDFSQ  317 (479)
T ss_pred             CcceEEEEecCCcccccchhhHHhhcccceeeeEEecccccchhheeeeeecchhhHHHHHhhhcceeeccceEEeehhh
Confidence            99999999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             ccccccccccCCCCCCCCCCCCccCCCCCCCCccCCCCCCcccccccCCCCCCC
Q 007792          321 SVSKLWNQFRRRDHQTGKGKGCFKCGGLDHIAKDCTGQQPAKYILRDDNRQHGG  374 (589)
Q Consensus       321 ~~~~~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~  374 (589)
                      +..+  ..|++...+.          ...+.+.+|......++.++..+.++++
T Consensus       318 SVsk--~k~r~k~~~~----------~~d~~~~d~~~~~~~k~~~kd~~~~~~~  359 (479)
T KOG0415|consen  318 SVSK--VKYRQKGSQK----------ETDHRAKDCVGGPSSKFIHKDQNRPRGR  359 (479)
T ss_pred             hhhh--hhcccccccc----------ccchhhhccccCCcccchhccCCCCCCC
Confidence            8665  2333222211          2345566666666666666665554444

>KOG0881 consensus Cyclophilin type peptidyl-prolyl cis-trans isomerase [Posttranslational modification, protein turnover, chaperones]

Probab=100.00  E-value=3e-46  Score=311.16  Aligned_cols=153  Identities=45%  Similarity=0.789  Sum_probs=148.0

Q ss_pred             EEEEEecceeEEEEecCCCChhHHHHHHHHHhcCccCCceEEEeecCcccccCCCCCCCCCCCCcccccccccccccCCc
Q 007792            2 SVLIVTSLGDIVVDLFVDKCPLTTKNFLKLCKIKYYNGCLFHTVQKDFTAQTGDPTGTGTGGDSVYKFLYGEQARFFGDE   81 (589)
Q Consensus         2 ~v~~~T~~G~i~ieL~~~~aP~~~~nF~~l~~~~~Y~g~~f~rv~~~~~iq~Gd~~~~~~~~~~~~~~~~~~~~~~~~~e   81 (589)
                      -|+|+|++|.|+||||-..||.||.||.+|++.+||+|+.||||++.||||||||+++|.+|.+||+       ..|.+|
T Consensus        11 ~V~LeTsmG~i~~ElY~kHaP~TC~NF~eLarrgYYn~v~FHRii~DFmiQGGDPTGTGRGGaSIYG-------~kF~DE   83 (164)
T KOG0881|consen   11 NVTLETSMGKITLELYWKHAPRTCQNFAELARRGYYNGVIFHRIIKDFMIQGGDPTGTGRGGASIYG-------DKFEDE   83 (164)
T ss_pred             eEEEeecccceehhhhhhcCcHHHHHHHHHHhcccccceeeeehhhhheeecCCCCCCCCCcccccc-------chhhhh
Confidence            4899999999999999999999999999999999999999999999999999999999999999998       789999


Q ss_pred             cccCCCCCCCceEEEeccCCCCCcceEEEEeCCCCCCCCCCcceEEEEecCHHHHHHHhhCccCCCCCcccceeeccccc
Q 007792           82 IRVDLKHAKTGTVAMASAGENLNASQFYMTLRDNLDYLDEKHTIFGEVAEGLETLSRINESFVDEKNRPYKNIRIKHTYI  161 (589)
Q Consensus        82 ~~~~l~~~~~G~vs~a~~g~~~~~sqFfI~l~~~~~~ld~~~~vFG~Vv~G~~vl~~i~~~~~~~~~~p~~~i~I~~~~v  161 (589)
                      ++..|+|..+|+|||||+||++|||||||||+| .+|||++|||||+|+.||+|+..|..+.++...+|..+++|..+..
T Consensus        84 i~~dLkhTGAGILsMANaGPnTNgSQFFiTLAP-t~~LDGKHTIFGRV~~Gm~vikr~G~v~Td~~DRPi~~~kIika~~  162 (164)
T KOG0881|consen   84 IHSDLKHTGAGILSMANAGPNTNGSQFFITLAP-TQWLDGKHTIFGRVCSGMEVIKRMGMVETDNSDRPIDEVKIIKAYP  162 (164)
T ss_pred             hhhhhcccchhhhhhhccCCCCCCceEEEEecC-ccccCCcceeehhhhhhHHHHHhhcceecCCCCCCccceeeEeeec
Confidence            999999999999999999999999999999999 6999999999999999999999999999999999999999988765


Q ss_pred             c
Q 007792          162 L  162 (589)
Q Consensus       162 l  162 (589)
                      .
T Consensus       163 ~  163 (164)
T KOG0881|consen  163 S  163 (164)
T ss_pred             C
Confidence            3

>KOG0546 consensus HSP90 co-chaperone CPR7/Cyclophilin [Posttranslational modification, protein turnover, chaperones]

Probab=100.00  E-value=2.9e-45  Score=361.22  Aligned_cols=157  Identities=38%  Similarity=0.599  Sum_probs=147.1

Q ss_pred             EEEEE-ecceeEEEEecCCCChhHHHHHHHHHhcC-----------ccCCceEEEeecCcccccCCCC-CCCCCCCCccc
Q 007792            2 SVLIV-TSLGDIVVDLFVDKCPLTTKNFLKLCKIK-----------YYNGCLFHTVQKDFTAQTGDPT-GTGTGGDSVYK   68 (589)
Q Consensus         2 ~v~~~-T~~G~i~ieL~~~~aP~~~~nF~~l~~~~-----------~Y~g~~f~rv~~~~~iq~Gd~~-~~~~~~~~~~~   68 (589)
                      +|.|. -++|+||||||.++||+||+||+.||++.           .|.|+.||||+++|||||||++ ++|+||.+||+
T Consensus        14 DISI~ge~~GRIvfeLf~dv~PKTaENFraLCtGE~G~~~~~gk~L~YKG~~FHRViK~FMiQgGDfs~gnGtGGeSIYG   93 (372)
T KOG0546|consen   14 DISIGGEPAGRIVFELFNDVVPKTAENFRALCTGEKGGGLTTGKPLHYKGSRFHRVIKNFMIQGGDFSEGNGTGGESIYG   93 (372)
T ss_pred             EEEeCCcccceEEEEeecccCchhHHHHHHHhccccCCCCCCCCeeeecCchhheeeecceeeccccccCCCCCcccccc
Confidence            44555 58999999999999999999999999763           4999999999999999999998 89999999998


Q ss_pred             ccccccccccCCccccCCCCCCCceEEEeccCCCCCcceEEEEeCCCCCCCCCCcceEEEEecCHHHHHHHhhCccCCCC
Q 007792           69 FLYGEQARFFGDEIRVDLKHAKTGTVAMASAGENLNASQFYMTLRDNLDYLDEKHTIFGEVAEGLETLSRINESFVDEKN  148 (589)
Q Consensus        69 ~~~~~~~~~~~~e~~~~l~~~~~G~vs~a~~g~~~~~sqFfI~l~~~~~~ld~~~~vFG~Vv~G~~vl~~i~~~~~~~~~  148 (589)
                             ..|.|| ++.|+|+++++|||||.|||+||||||||+.+ +|||||+|+|||+||.|++||..|+++.++...
T Consensus        94 -------~~FdDE-nF~lKHdrpflLSMAN~GpNTNgSQFFITT~p-~PHLdGkHVVFGqVI~G~~VVr~IEn~~~d~~s  164 (372)
T KOG0546|consen   94 -------EKFDDE-NFELKHDRPFLLSMANRGPNTNGSQFFITTVP-TPHLDGKHVVFGQVIKGKEVVREIENLETDEES  164 (372)
T ss_pred             -------cccccc-cceeccCcchhhhhhcCCCCCCCcceEEeCCC-CCCcCCceeEEeeEeechhHHHHHhccccccCC
Confidence                   789999 69999999999999999999999999999999 899999999999999999999999999999999


Q ss_pred             CcccceeecccccccCCCC
Q 007792          149 RPYKNIRIKHTYILEDPFD  167 (589)
Q Consensus       149 ~p~~~i~I~~~~vl~~p~~  167 (589)
                      +|+.+|.|.+|++|..-..
T Consensus       165 kP~~dV~I~dCGel~~~~~  183 (372)
T KOG0546|consen  165 KPLADVVISDCGELVKKSK  183 (372)
T ss_pred             CCccceEeccccccccccc
Confidence            9999999999999876533

>cd01921 cyclophilin_RRM cyclophilin_RRM: cyclophilin-type peptidylprolyl cis- trans isomerase domain occuring with a C-terminal RNA recognition motif domain (RRM)

Probab=100.00  E-value=4.3e-44  Score=333.57  Aligned_cols=166  Identities=66%  Similarity=1.137  Sum_probs=155.0

Q ss_pred             EEEecceeEEEEecCCCChhHHHHHHHHHhcCccCCceEEEeecCcccccCCCCCCCCCCCCcccccccccccccCCccc
Q 007792            4 LIVTSLGDIVVDLFVDKCPLTTKNFLKLCKIKYYNGCLFHTVQKDFTAQTGDPTGTGTGGDSVYKFLYGEQARFFGDEIR   83 (589)
Q Consensus         4 ~~~T~~G~i~ieL~~~~aP~~~~nF~~l~~~~~Y~g~~f~rv~~~~~iq~Gd~~~~~~~~~~~~~~~~~~~~~~~~~e~~   83 (589)
                      +|+|++|+|+||||.+.||+||+||++||+.+||+++.||||+++|+||||++.+++.++.++|+.........+++|+.
T Consensus         1 ll~Ts~G~i~ieL~~~~aP~t~~nF~~L~~~~~Y~g~~fhrvi~~f~iQgGd~~~~g~~~~~~~~~~~~~~~~~~~~e~~   80 (166)
T cd01921           1 LLETTLGDLVIDLFTDECPLACLNFLKLCKLKYYNFCLFYNVQKDFIAQTGDPTGTGAGGESIYSQLYGRQARFFEPEIL   80 (166)
T ss_pred             CcEeccCCEEEEEcCCCCCHHHHHHHHHHhcCCcCCCEEEEEeCCceEEECCcCCCCCCCcccccccccccCcccCcccC
Confidence            48999999999999999999999999999999999999999999999999999988888888887555555567888887


Q ss_pred             cCCCCCCCceEEEeccCCCCCcceEEEEeCCCCCCCCCCcceEEEEecCHHHHHHHhhCccCCCCCcccceeeccccccc
Q 007792           84 VDLKHAKTGTVAMASAGENLNASQFYMTLRDNLDYLDEKHTIFGEVAEGLETLSRINESFVDEKNRPYKNIRIKHTYILE  163 (589)
Q Consensus        84 ~~l~~~~~G~vs~a~~g~~~~~sqFfI~l~~~~~~ld~~~~vFG~Vv~G~~vl~~i~~~~~~~~~~p~~~i~I~~~~vl~  163 (589)
                      +.++|+.+|+||||+.++++++|||||||.+++|+||++|+|||+|++||+||++|+.++++.+++|..+|+|..|+|+.
T Consensus        81 ~~~~h~~~G~l~ma~~~~~~~~SQFfIt~~~~~~~Ldg~~tvFG~Vi~G~dvv~~I~~~~~~~~~~P~~~i~I~~~~i~~  160 (166)
T cd01921          81 PLLKHSKKGTVSMVNAGDNLNGSQFYITLGENLDYLDGKHTVFGQVVEGFDVLEKINDAIVDDDGRPLKDIRIKHTHILD  160 (166)
T ss_pred             CccccCCceEEEEeECCCCCccceEEEEcCCCCcccCCCccEEEEEEcCHHHHHHHHcCCCCCCCCCCCCeEEEEEEEEC
Confidence            88999999999999999999999999999865799999999999999999999999999999999999999999999999


Q ss_pred             CCCCCh
Q 007792          164 DPFDDP  169 (589)
Q Consensus       164 ~p~~~~  169 (589)
                      +||+++
T Consensus       161 ~pf~~~  166 (166)
T cd01921         161 DPFPDP  166 (166)
T ss_pred             CCCCCC
Confidence            999875

This subfamily of the cyclophilin domain family contains a number of eukaryotic cyclophilins having the RRM domain including the nuclear proteins: human hCyP-57, Arabidopsis thaliana AtCYP59, Caenorhabditis elegans CeCyP-44 and Paramecium tetrurelia Kin241. The Kin241 protein has been shown to have a role in cell morphogenesis.

>cd01923 cyclophilin_RING cyclophilin_RING: cyclophilin-type peptidylprolyl cis- trans isomerases (cyclophilins) having a modified RING finger domain

Probab=100.00  E-value=3.3e-43  Score=324.99  Aligned_cols=157  Identities=43%  Similarity=0.784  Sum_probs=150.2

Q ss_pred             EEEEecceeEEEEecCCCChhHHHHHHHHHhcCccCCceEEEeecCcccccCCCCCCCCCCCCcccccccccccccCCcc
Q 007792            3 VLIVTSLGDIVVDLFVDKCPLTTKNFLKLCKIKYYNGCLFHTVQKDFTAQTGDPTGTGTGGDSVYKFLYGEQARFFGDEI   82 (589)
Q Consensus         3 v~~~T~~G~i~ieL~~~~aP~~~~nF~~l~~~~~Y~g~~f~rv~~~~~iq~Gd~~~~~~~~~~~~~~~~~~~~~~~~~e~   82 (589)
                      |+|+|++|+|+|+||++.||+||+||++||+.+||+++.||||+|+|+||||++.+++.++.++|+       ..+++|+
T Consensus         2 v~~~T~~G~i~ieL~~~~aP~t~~nF~~L~~~g~Y~~~~f~rv~~~~~iq~Gd~~~~g~~~~~~~g-------~~~~~E~   74 (159)
T cd01923           2 VRLHTNKGDLNLELHCDKAPKACENFIKLCKKGYYDGTIFHRSIRNFMIQGGDPTGTGRGGESIWG-------KPFKDEF   74 (159)
T ss_pred             EEEEEccccEEEEEeCCCChHHHHHHHHHHhcCccCCcEEEEEeCCcEEEecccCCCCCCCccccC-------CccCccc
Confidence            799999999999999999999999999999999999999999999999999999988888888886       5688888


Q ss_pred             ccCCCCCCCceEEEeccCCCCCcceEEEEeCCCCCCCCCCcceEEEEecCHHHHHHHhhCccCCCCCcccceeecccccc
Q 007792           83 RVDLKHAKTGTVAMASAGENLNASQFYMTLRDNLDYLDEKHTIFGEVAEGLETLSRINESFVDEKNRPYKNIRIKHTYIL  162 (589)
Q Consensus        83 ~~~l~~~~~G~vs~a~~g~~~~~sqFfI~l~~~~~~ld~~~~vFG~Vv~G~~vl~~i~~~~~~~~~~p~~~i~I~~~~vl  162 (589)
                      ...++|+.+|+||||+.++++++|||||||.+ +|+||++|+|||+|++||+||++|+.++++.+++|+.+|.|.+|.|+
T Consensus        75 ~~~~~h~~~G~v~ma~~~~~s~~sqFfIt~~~-~~~Ld~~~~vFG~V~~G~~vl~~I~~~~~~~~~~P~~~i~I~~~~i~  153 (159)
T cd01923          75 KPNLSHDGRGVLSMANSGPNTNGSQFFITYRS-CKHLDGKHTVFGRVVGGLETLEAMENVPDPGTDRPKEEIKIEDTSVF  153 (159)
T ss_pred             ccCcCcCCCcEEEEeeCCCCCcccEEEEECCC-CcccCCCccEEEEEEcCHHHHHHHHcCCCCCCCCCCCCeEEEEeEEE
Confidence            77889999999999999999999999999998 79999999999999999999999999999989999999999999999


Q ss_pred             cCCCC
Q 007792          163 EDPFD  167 (589)
Q Consensus       163 ~~p~~  167 (589)
                      .+||+
T Consensus       154 ~dpf~  158 (159)
T cd01923         154 VDPFE  158 (159)
T ss_pred             eCCCC
Confidence            99996

This group includes the nuclear proteins, Human hCyP-60 and Caenorhabditis elegans MOG-6 which, compared to the archetypal cyclophilin Human cyclophilin A exhibit reduced peptidylprolyl cis- trans isomerase activity and lack a residue important for cyclophilin binding. Human hCyP-60 has been shown to physically interact with the proteinase inhibitor peptide eglin c and; C. elegans MOG-6 to physically interact with MEP-1, a nuclear zinc finger protein. MOG-6 has been shown to function in germline sex determination.

>cd01928 Cyclophilin_PPIL3_like Cyclophilin_PPIL3_like

Probab=100.00  E-value=4.6e-43  Score=321.65  Aligned_cols=153  Identities=51%  Similarity=0.868  Sum_probs=144.9

Q ss_pred             CEEEEEecceeEEEEecCCCChhHHHHHHHHHhcCccCCceEEEeecCcccccCCCCCCCCCCCCcccccccccccccCC
Q 007792            1 MSVLIVTSLGDIVVDLFVDKCPLTTKNFLKLCKIKYYNGCLFHTVQKDFTAQTGDPTGTGTGGDSVYKFLYGEQARFFGD   80 (589)
Q Consensus         1 ~~v~~~T~~G~i~ieL~~~~aP~~~~nF~~l~~~~~Y~g~~f~rv~~~~~iq~Gd~~~~~~~~~~~~~~~~~~~~~~~~~   80 (589)
                      |+|+|+|++|+|+||||++.||+||+||++||+.+||+|+.||||+++|+||||++.+++.++.++|+       ..|++
T Consensus         1 m~v~l~T~~G~i~ieL~~~~aP~t~~nF~~L~~~g~Y~~~~f~rv~~~f~iq~Gd~~~~g~g~~~~~~-------~~~~~   73 (153)
T cd01928           1 MSVTLHTNLGDIKIELFCDDCPKACENFLALCASGYYNGCIFHRNIKGFMVQTGDPTGTGKGGESIWG-------KKFED   73 (153)
T ss_pred             CEEEEEEccccEEEEEcCCCCcHHHHHHHHHHhcCccCCcEEEEeCCCCEEEccccCCCCCCCCccCC-------Ccccc
Confidence            99999999999999999999999999999999999999999999999999999999988888888776       56888


Q ss_pred             ccccCCCCCCCceEEEeccCCCCCcceEEEEeCCCCCCCCCCcceEEEEecCHHHHHHHhhCccCCCCCcccceeecccc
Q 007792           81 EIRVDLKHAKTGTVAMASAGENLNASQFYMTLRDNLDYLDEKHTIFGEVAEGLETLSRINESFVDEKNRPYKNIRIKHTY  160 (589)
Q Consensus        81 e~~~~l~~~~~G~vs~a~~g~~~~~sqFfI~l~~~~~~ld~~~~vFG~Vv~G~~vl~~i~~~~~~~~~~p~~~i~I~~~~  160 (589)
                      |+...++|+.+|+||||+.++++++|||||++.+ +|+||++|+|||+|++||+||++|+.+++++.++|..+|+|.+|.
T Consensus        74 e~~~~~~~~~~G~v~ma~~~~~~~~SqFfI~~~~-~~~Ld~~~tvFG~V~~G~dvl~~I~~~~~~~~~~P~~~i~I~~~~  152 (153)
T cd01928          74 EFRETLKHDSRGVVSMANNGPNTNGSQFFITYAK-QPHLDGKYTVFGKVIDGFETLDTLEKLPVDKKYRPLEEIRIKDVT  152 (153)
T ss_pred             ccccCCCcCCCcEEEEeeCCCCCcccEEEEEeCC-CcccCCCceEEEEEEeCHHHHHHHHcCCCCCCCCCcCCeEEEEeE
Confidence            8777889989999999999999999999999998 699999999999999999999999999999999999999999885


Q ss_pred             c
Q 007792          161 I  161 (589)
Q Consensus       161 v  161 (589)
                      +
T Consensus       153 ~  153 (153)
T cd01928         153 I  153 (153)
T ss_pred             C
Confidence            3

Proteins similar to Human cyclophilin-like peptidylprolyl cis- trans isomerase (PPIL3). Members of this family lack a key residue important for cyclosporin binding: the tryptophan residue corresponding to W121 in human hCyP-18a; most members have a histidine at this position. The exact function of the protein is not known.

>KOG0884 consensus Similar to cyclophilin-type peptidyl-prolyl cis-trans isomerase [Posttranslational modification, protein turnover, chaperones]

Probab=100.00  E-value=1.4e-43  Score=293.47  Aligned_cols=159  Identities=47%  Similarity=0.793  Sum_probs=154.3

Q ss_pred             CEEEEEecceeEEEEecCCCChhHHHHHHHHHhcCccCCceEEEeecCcccccCCCCCCCCCCCCcccccccccccccCC
Q 007792            1 MSVLIVTSLGDIVVDLFVDKCPLTTKNFLKLCKIKYYNGCLFHTVQKDFTAQTGDPTGTGTGGDSVYKFLYGEQARFFGD   80 (589)
Q Consensus         1 ~~v~~~T~~G~i~ieL~~~~aP~~~~nF~~l~~~~~Y~g~~f~rv~~~~~iq~Gd~~~~~~~~~~~~~~~~~~~~~~~~~   80 (589)
                      |+|+|+|..|+|.||||-+.+|+||+||+.||...||++|.||+-+++|++|+|+++.+|.||.+||+       +.|++
T Consensus         1 msvtlht~~gdikiev~~e~tpktce~~l~~~~~~~~n~~~~~~~~~~f~v~~~~~~~tgrgg~siwg-------~~fed   73 (161)
T KOG0884|consen    1 MSVTLHTDVGDIKIEVFCERTPKTCENFLALCASDYYNGCIFHRNIKGFMVQTGDPTHTGRGGNSIWG-------KKFED   73 (161)
T ss_pred             CeEEEeeccCcEEEEEEecCChhHHHHHHHHhhhhhccceeecCCCCCcEEEeCCCCCCCCCCccccC-------CcchH
Confidence            99999999999999999999999999999999999999999999999999999999999999999998       88999


Q ss_pred             ccccCCCCCCCceEEEeccCCCCCcceEEEEeCCCCCCCCCCcceEEEEecCHHHHHHHhhCccCCC-CCcccceeeccc
Q 007792           81 EIRVDLKHAKTGTVAMASAGENLNASQFYMTLRDNLDYLDEKHTIFGEVAEGLETLSRINESFVDEK-NRPYKNIRIKHT  159 (589)
Q Consensus        81 e~~~~l~~~~~G~vs~a~~g~~~~~sqFfI~l~~~~~~ld~~~~vFG~Vv~G~~vl~~i~~~~~~~~-~~p~~~i~I~~~  159 (589)
                      |+..-|+|+.+|+|+||+.||++|+||||||.+.+ ||||-+|||||+||+|+++|+.|+.++++.. -+|+..+.|.++
T Consensus        74 e~~~~lkh~~rg~vsmanngp~tn~sqffity~kq-~hldmkytvfgkvidg~etldele~l~v~~ktyrpl~~~~ik~i  152 (161)
T KOG0884|consen   74 EYSEYLKHNVRGVVSMANNGPNTNGSQFFITYGKQ-PHLDMKYTVFGKVIDGLETLDELEKLPVNEKTYRPLNDVHIKDI  152 (161)
T ss_pred             HHHHHHhhccceeEEcccCCCCCCCceEEEEecCC-CccceeEeeeeeeccchhhHHHHhhcccCccccccchheeeeee
Confidence            99999999999999999999999999999999985 9999999999999999999999999999876 799999999999


Q ss_pred             ccccCCCC
Q 007792          160 YILEDPFD  167 (589)
Q Consensus       160 ~vl~~p~~  167 (589)
                      .|..+||.
T Consensus       153 tihanp~a  160 (161)
T KOG0884|consen  153 TIHANPFA  160 (161)
T ss_pred             EEecCcCC
Confidence            99999985

>COG0652 PpiB Peptidyl-prolyl cis-trans isomerase (rotamase) - cyclophilin family [Posttranslational modification, protein turnover, chaperones]

Probab=100.00  E-value=2.1e-42  Score=312.00  Aligned_cols=149  Identities=41%  Similarity=0.689  Sum_probs=130.8

Q ss_pred             EEEEEecceeEEEEecCCCChhHHHHHHHHHhcCccCCceEEEeecCcccccCCCCCC-CCCCCCcccccccccccccCC
Q 007792            2 SVLIVTSLGDIVVDLFVDKCPLTTKNFLKLCKIKYYNGCLFHTVQKDFTAQTGDPTGT-GTGGDSVYKFLYGEQARFFGD   80 (589)
Q Consensus         2 ~v~~~T~~G~i~ieL~~~~aP~~~~nF~~l~~~~~Y~g~~f~rv~~~~~iq~Gd~~~~-~~~~~~~~~~~~~~~~~~~~~   80 (589)
                      +|+|+|++|+|+|+||++.||+||+||++||+.+||+|+.||||+++|||||||+.+. +.++++          +.|++
T Consensus         1 ~v~~~t~~G~I~ieL~~~~aP~Tv~NF~~l~~~g~Ydg~~FHRVi~~FmiQgGd~~~~~g~gg~~----------~~f~~   70 (158)
T COG0652           1 TVILETNKGDITIELYPDKAPKTVANFLQLVKEGFYDGTIFHRVIPGFMIQGGDPTGGDGTGGPG----------PPFKD   70 (158)
T ss_pred             CceeeccCCCEEEEECCCcCcHHHHHHHHHHHcCCCCCceEEEeecCceeecCCCCCCCCCCCCC----------CCCcc
Confidence            4789999999999999999999999999999999999999999999999999999976 776666          56899


Q ss_pred             ccccCCCCCC--CceEEEeccC-CCCCcceEEEEeCCCCCCCCCCcceEEEEecCHHHHHHHhhCccCCCC----Ccccc
Q 007792           81 EIRVDLKHAK--TGTVAMASAG-ENLNASQFYMTLRDNLDYLDEKHTIFGEVAEGLETLSRINESFVDEKN----RPYKN  153 (589)
Q Consensus        81 e~~~~l~~~~--~G~vs~a~~g-~~~~~sqFfI~l~~~~~~ld~~~~vFG~Vv~G~~vl~~i~~~~~~~~~----~p~~~  153 (589)
                      |+... .|..  +|+||||+.+ |++|+|||||++.+ .||||++|+|||+|++||+||++|.++.+...+    .|..+
T Consensus        71 E~~~~-~~~~~~~G~lsMA~~g~P~t~~SQFFI~~~~-~~~Ld~~ytVFG~Vv~GmdvvdkI~~~~~~~~~~~~~~~~~~  148 (158)
T COG0652          71 ENFAL-NGDRHKRGTLSMARAGDPNSNGSQFFITVVD-NPFLDGKYTVFGQVVEGMDVVDKIKNGDTDDSGYVQDVPADP  148 (158)
T ss_pred             ccccc-ccccCCcceEeEcccCCcCCccCeEEEEecC-CcccCCCCcEEEEEehhHHHHHHHHcCCccCCCcccCCCCCC
Confidence            96433 3334  8999999999 99999999999998 699999999999999999999999998887543    45567


Q ss_pred             eeecccccc
Q 007792          154 IRIKHTYIL  162 (589)
Q Consensus       154 i~I~~~~vl  162 (589)
                      ++|..+.++
T Consensus       149 ~~i~~~~~~  157 (158)
T COG0652         149 VKILSVKIV  157 (158)
T ss_pred             eEEeeeeee
Confidence            777766553

>KOG0880 consensus Peptidyl-prolyl cis-trans isomerase [Posttranslational modification, protein turnover, chaperones]

Probab=100.00  E-value=1.6e-42  Score=312.79  Aligned_cols=148  Identities=39%  Similarity=0.664  Sum_probs=140.7

Q ss_pred             ecceeEEEEecCCCChhHHHHHHHHHhc----CccCCceEEEeecCcccccCCCC-CCCCCCCCcccccccccccccCCc
Q 007792            7 TSLGDIVVDLFVDKCPLTTKNFLKLCKI----KYYNGCLFHTVQKDFTAQTGDPT-GTGTGGDSVYKFLYGEQARFFGDE   81 (589)
Q Consensus         7 T~~G~i~ieL~~~~aP~~~~nF~~l~~~----~~Y~g~~f~rv~~~~~iq~Gd~~-~~~~~~~~~~~~~~~~~~~~~~~e   81 (589)
                      -..|+|+|.||+..+|+||+||.+||..    .-|.|+.||||+|+|||||||++ ++++++.+||+       ..|++|
T Consensus        51 ~~~grIvigLfG~~vPKTV~NF~~l~~~~~~~~gY~gS~FhRVi~nfmIQGGd~t~g~gtGg~SIyG-------~~F~DE  123 (217)
T KOG0880|consen   51 EPVGRIVIGLFGKVVPKTVENFRALATSGEKGYGYKGSKFHRVIPNFMIQGGDFTKGDGTGGKSIYG-------EKFPDE  123 (217)
T ss_pred             EeccEEEEEeccccchHHHHHHHHHHccCCCCcccCCceeeeeecCceeecCccccCCCCCCeEeec-------CCCCCc
Confidence            5789999999999999999999999983    24999999999999999999999 67999999998       789999


Q ss_pred             cccCCCCCCCceEEEeccCCCCCcceEEEEeCCCCCCCCCCcceEEEEecCHHHHHHHhhCccCCCCCcccceeeccccc
Q 007792           82 IRVDLKHAKTGTVAMASAGENLNASQFYMTLRDNLDYLDEKHTIFGEVAEGLETLSRINESFVDEKNRPYKNIRIKHTYI  161 (589)
Q Consensus        82 ~~~~l~~~~~G~vs~a~~g~~~~~sqFfI~l~~~~~~ld~~~~vFG~Vv~G~~vl~~i~~~~~~~~~~p~~~i~I~~~~v  161 (589)
                       ++.|+|+.+|.|||||.||++||||||||+.. ++||||+|+|||+|++||++|.+|+.+.|+.+++|++.++|.+|+-
T Consensus       124 -Nf~LkH~rpG~lSMAn~GpDtNGsQFfItT~~-t~wLDGkhVVFGqVl~Gmdvv~~Ie~~~TD~~dkP~e~v~I~~~g~  201 (217)
T KOG0880|consen  124 -NFKLKHDRPGRLSMANAGPDTNGSQFFITTVK-TPWLDGKHVVFGQVLEGMDVVRKIENVKTDERDKPLEDVVIANCGE  201 (217)
T ss_pred             -cceeecCCCceEeeeccCCCCCCceEEEEecC-CccccCceeEEeeehhhHHHHHHHHhcccCCCCCccccEEEeecCc
Confidence             59999999999999999999999999999998 7999999999999999999999999999999999999999999997


Q ss_pred             cc
Q 007792          162 LE  163 (589)
Q Consensus       162 l~  163 (589)
                      +.
T Consensus       202 l~  203 (217)
T KOG0880|consen  202 LP  203 (217)
T ss_pred             cc
Confidence            64

>KOG0883 consensus Cyclophilin type, U box-containing peptidyl-prolyl cis-trans isomerase [Posttranslational modification, protein turnover, chaperones]

Probab=100.00  E-value=1.2e-42  Score=340.92  Aligned_cols=162  Identities=42%  Similarity=0.765  Sum_probs=156.6

Q ss_pred             EEEEEecceeEEEEecCCCChhHHHHHHHHHhcCccCCceEEEeecCcccccCCCCCCCCCCCCcccccccccccccCCc
Q 007792            2 SVLIVTSLGDIVVDLFVDKCPLTTKNFLKLCKIKYYNGCLFHTVQKDFTAQTGDPTGTGTGGDSVYKFLYGEQARFFGDE   81 (589)
Q Consensus         2 ~v~~~T~~G~i~ieL~~~~aP~~~~nF~~l~~~~~Y~g~~f~rv~~~~~iq~Gd~~~~~~~~~~~~~~~~~~~~~~~~~e   81 (589)
                      .|.|+|+.|.|.|||+.+.+|.+|+||++||+.|||+|+.|||.+.+||||||||+++|.||.+||+       ++|.||
T Consensus       279 yvrl~Tn~G~lNlELhcd~~P~aceNFI~lc~~gYYnnt~FHRsIrnFmiQGGDPTGTG~GGeSiWg-------KpFkDE  351 (518)
T KOG0883|consen  279 YVRLVTNHGPLNLELHCDYAPRACENFITLCKNGYYNNTIFHRSIRNFMIQGGDPTGTGRGGESIWG-------KPFKDE  351 (518)
T ss_pred             eEEEeccCCceeeEeecCcchHHHHHHHHHHhcccccchHHHHHHHHHeeeCCCCCCCCCCCccccC-------Cccccc
Confidence            4889999999999999999999999999999999999999999999999999999999999999998       889999


Q ss_pred             cccCCCCCCCceEEEeccCCCCCcceEEEEeCCCCCCCCCCcceEEEEecCHHHHHHHhhCccCCCCCcccceeeccccc
Q 007792           82 IRVDLKHAKTGTVAMASAGENLNASQFYMTLRDNLDYLDEKHTIFGEVAEGLETLSRINESFVDEKNRPYKNIRIKHTYI  161 (589)
Q Consensus        82 ~~~~l~~~~~G~vs~a~~g~~~~~sqFfI~l~~~~~~ld~~~~vFG~Vv~G~~vl~~i~~~~~~~~~~p~~~i~I~~~~v  161 (589)
                      +.+.|.|+.+|+|||||+|+|+|||||||++.+ |.|||.+|||||+||.|++||.+|+++++++..+|..+|+|..+.|
T Consensus       352 f~~~l~H~gRGvlSMANsGpnTNgSQFFItyrs-ckhLd~KHTIFGrvVGGldtL~amEnve~d~~DrP~e~I~i~~~~V  430 (518)
T KOG0883|consen  352 FCSNLSHDGRGVLSMANSGPNTNGSQFFITYRS-CKHLDNKHTIFGRVVGGLDTLTAMENVETDEKDRPKEEIKIEDAIV  430 (518)
T ss_pred             cCCCCCcCCcceEeeccCCCCCCCceEEEEecc-hhhccccceeeeeeeccHHHHHHHhcCCCCCCCCcccceEEeeeEE
Confidence            999999999999999999999999999999999 8999999999999999999999999999999999999999999999


Q ss_pred             ccCCCCChhh
Q 007792          162 LEDPFDDPAQ  171 (589)
Q Consensus       162 l~~p~~~~~~  171 (589)
                      +.+||.....
T Consensus       431 FVdPfeEa~~  440 (518)
T KOG0883|consen  431 FVDPFEEADK  440 (518)
T ss_pred             eeCcHHHHHH
Confidence            9999865443

>cd01927 cyclophilin_WD40 cyclophilin_WD40: cyclophilin-type peptidylprolyl cis- trans isomerases (cyclophilins) having a WD40 domain

Probab=100.00  E-value=1.6e-41  Score=310.03  Aligned_cols=148  Identities=44%  Similarity=0.772  Sum_probs=139.9

Q ss_pred             EEEecceeEEEEecCCCChhHHHHHHHHHhcCccCCceEEEeecCcccccCCCCCCCCCCCCcccccccccccccCCccc
Q 007792            4 LIVTSLGDIVVDLFVDKCPLTTKNFLKLCKIKYYNGCLFHTVQKDFTAQTGDPTGTGTGGDSVYKFLYGEQARFFGDEIR   83 (589)
Q Consensus         4 ~~~T~~G~i~ieL~~~~aP~~~~nF~~l~~~~~Y~g~~f~rv~~~~~iq~Gd~~~~~~~~~~~~~~~~~~~~~~~~~e~~   83 (589)
                      +|+|++|+|+||||.+.||+||+||++||+.+||+++.||||+|+|+||||++.+++.++.++|+       ..|++|+.
T Consensus         1 ~i~T~~G~i~ieL~~~~aP~t~~nF~~L~~~g~Y~~~~f~Rvi~~f~iq~Gd~~~~g~g~~~~~~-------~~~~~e~~   73 (148)
T cd01927           1 IIHTTKGDIHIRLFPEEAPKTVENFTTHARNGYYNNTIFHRVIKGFMIQTGDPTGDGTGGESIWG-------KEFEDEFS   73 (148)
T ss_pred             CeEeccccEEEEEeCCCCcHHHHHHHHHhhcCCcCCcEEEEEcCCcEEEecccCCCCCCCCcccC-------Cccccccc
Confidence            58999999999999999999999999999999999999999999999999999988888888886       56888987


Q ss_pred             cCCCCCCCceEEEeccCCCCCcceEEEEeCCCCCCCCCCcceEEEEecCHHHHHHHhhCccCCCCCcccceeeccc
Q 007792           84 VDLKHAKTGTVAMASAGENLNASQFYMTLRDNLDYLDEKHTIFGEVAEGLETLSRINESFVDEKNRPYKNIRIKHT  159 (589)
Q Consensus        84 ~~l~~~~~G~vs~a~~g~~~~~sqFfI~l~~~~~~ld~~~~vFG~Vv~G~~vl~~i~~~~~~~~~~p~~~i~I~~~  159 (589)
                      +.++|..+|+||||+.++++++|||||+|.+ +|+||++|+|||+|++||+||++|+.++++.+++|..+|+|.++
T Consensus        74 ~~~~h~~~G~l~ma~~~~~s~~SqFfIt~~~-~p~Ldg~~tvFG~V~~G~dvl~~I~~~~~~~~~~P~~~i~I~~~  148 (148)
T cd01927          74 PSLKHDRPYTLSMANAGPNTNGSQFFITTVA-TPWLDNKHTVFGRVVKGMDVVQRIENVKTDKNDRPYEDIKIINI  148 (148)
T ss_pred             cccCcCCCeEEEEeeCCCCCCCceEEEEcCC-CcccCCCceEEEEEEcCHHHHHHHHcCCCCCCCCCcCCeEEEeC
Confidence            7899999999999999999999999999998 69999999999999999999999999999989999999999764

This group consists of several hypothetical and putative eukaryotic and bacterial proteins which have a cyclophilin domain and a WD40 domain. Function of the protein is not known.

>KOG0882 consensus Cyclophilin-related peptidyl-prolyl cis-trans isomerase [Posttranslational modification, protein turnover, chaperones]

Probab=100.00  E-value=5.3e-42  Score=343.04  Aligned_cols=152  Identities=40%  Similarity=0.747  Sum_probs=148.4

Q ss_pred             EEEEEecceeEEEEecCCCChhHHHHHHHHHhcCccCCceEEEeecCcccccCCCCCCCCCCCCcccccccccccccCCc
Q 007792            2 SVLIVTSLGDIVVDLFVDKCPLTTKNFLKLCKIKYYNGCLFHTVQKDFTAQTGDPTGTGTGGDSVYKFLYGEQARFFGDE   81 (589)
Q Consensus         2 ~v~~~T~~G~i~ieL~~~~aP~~~~nF~~l~~~~~Y~g~~f~rv~~~~~iq~Gd~~~~~~~~~~~~~~~~~~~~~~~~~e   81 (589)
                      .++|+|++|+|.|.||+++||+||+||...|..|||+|..||||+++||||+|||.++|+||.+||+       ..|+||
T Consensus       406 ~aiihtt~gdi~~kl~p~ecpktvenf~th~rngyy~~~~fhriik~fmiqtgdp~g~gtggesiwg-------~dfede  478 (558)
T KOG0882|consen  406 AAIIHTTQGDIHIKLYPEECPKTVENFTTHSRNGYYDNHTFHRIIKGFMIQTGDPLGDGTGGESIWG-------KDFEDE  478 (558)
T ss_pred             ceEEEecccceEEEecccccchhhhhhhccccCccccCcchHHhhhhheeecCCCCCCCCCCccccc-------ccchhh
Confidence            4789999999999999999999999999999999999999999999999999999999999999998       789999


Q ss_pred             cccCCCCCCCceEEEeccCCCCCcceEEEEeCCCCCCCCCCcceEEEEecCHHHHHHHhhCccCCCCCcccceeeccccc
Q 007792           82 IRVDLKHAKTGTVAMASAGENLNASQFYMTLRDNLDYLDEKHTIFGEVAEGLETLSRINESFVDEKNRPYKNIRIKHTYI  161 (589)
Q Consensus        82 ~~~~l~~~~~G~vs~a~~g~~~~~sqFfI~l~~~~~~ld~~~~vFG~Vv~G~~vl~~i~~~~~~~~~~p~~~i~I~~~~v  161 (589)
                      +++.|+|+++.+|||||+|+|+||||||||+-+ +||||++|||||+|+.||+||+.|+++.++++++|+++|.|.++.+
T Consensus       479 fh~~lrhdrpft~smanag~ntngsqffit~~~-tpwld~khtvfgrv~~gm~vvqri~~v~t~k~drp~e~v~iinisv  557 (558)
T KOG0882|consen  479 FHPNLRHDRPFTVSMANAGPNTNGSQFFITTVP-TPWLDGKHTVFGRVTAGMDVVQRIEQVKTDKYDRPYEDVKIINISV  557 (558)
T ss_pred             cCcccccCCCceEEecccCCCCCCceEEEEecC-ccccCCcceeEEEEecchhHHhHhhhcccCcCCCCCCceeEEEEec
Confidence            999999999999999999999999999999999 7999999999999999999999999999999999999999999865

>cd01925 cyclophilin_CeCYP16-like cyclophilin_CeCYP16-like: cyclophilin-type peptidylprolyl cis- trans isomerase) (PPIase) domain similar to Caenorhabditis elegans cyclophilin 16

Probab=100.00  E-value=1e-40  Score=311.94  Aligned_cols=161  Identities=41%  Similarity=0.734  Sum_probs=151.0

Q ss_pred             EEEEEecceeEEEEecCCCChhHHHHHHHHHhcCccCCceEEEeecCcccccCCCCCCCCCCCCcccccccccccccCCc
Q 007792            2 SVLIVTSLGDIVVDLFVDKCPLTTKNFLKLCKIKYYNGCLFHTVQKDFTAQTGDPTGTGTGGDSVYKFLYGEQARFFGDE   81 (589)
Q Consensus         2 ~v~~~T~~G~i~ieL~~~~aP~~~~nF~~l~~~~~Y~g~~f~rv~~~~~iq~Gd~~~~~~~~~~~~~~~~~~~~~~~~~e   81 (589)
                      +|+|+|++|+|+|+||++.||+||+||++||+.+||+++.||||+++|+||||++.+++.++.++|+       ..|++|
T Consensus         7 ~v~i~Ts~G~i~ieL~~~~~P~t~~nF~~L~~~~~Y~~~~f~Rvi~~f~iQgGd~~~~g~g~~s~~g-------~~~~~E   79 (171)
T cd01925           7 KVILKTTAGDIDIELWSKEAPKACRNFIQLCLEGYYDNTIFHRVVPGFIIQGGDPTGTGTGGESIYG-------EPFKDE   79 (171)
T ss_pred             EEEEEEccccEEEEEeCCCChHHHHHHHHHHhcCCCCCCEEEEEcCCcEEEccccCCCCccCcccCC-------CccCcc
Confidence            6899999999999999999999999999999999999999999999999999999988888888886       568888


Q ss_pred             cccCCCCCCCceEEEeccCCCCCcceEEEEeCCCCCCCCCCcceEEEEec-CHHHHHHHhhCccCCCCCcccceeecccc
Q 007792           82 IRVDLKHAKTGTVAMASAGENLNASQFYMTLRDNLDYLDEKHTIFGEVAE-GLETLSRINESFVDEKNRPYKNIRIKHTY  160 (589)
Q Consensus        82 ~~~~l~~~~~G~vs~a~~g~~~~~sqFfI~l~~~~~~ld~~~~vFG~Vv~-G~~vl~~i~~~~~~~~~~p~~~i~I~~~~  160 (589)
                      ....++|+.+|+||||+.++++++|||||+|.+ +|+||++|+|||+|+. +|++|++|+.++++.+++|..+|.|.+|.
T Consensus        80 ~~~~~~~~~~G~l~ma~~g~~s~~sqFfIt~~~-~~~ldg~~tvFG~V~g~~~~~v~~i~~~~~~~~~~P~~~i~I~~~~  158 (171)
T cd01925          80 FHSRLRFNRRGLVGMANAGDDSNGSQFFFTLDK-ADELNNKHTLFGKVTGDTIYNLLKLAEVETDKDERPVYPPKITSVE  158 (171)
T ss_pred             cccCcCCCCCcEEEECcCCCCCcccEEEEEcCC-CcccCCCceEEEEEEECcHHHHHHHhcCCcCCCCCcCCCeEEEEEE
Confidence            877888989999999999999999999999998 7999999999999994 68999999999999999999999999999


Q ss_pred             cccCCCCChh
Q 007792          161 ILEDPFDDPA  170 (589)
Q Consensus       161 vl~~p~~~~~  170 (589)
                      ++.+||++..
T Consensus       159 i~~~pf~~~~  168 (171)
T cd01925         159 VLENPFDDIV  168 (171)
T ss_pred             EEcCCchhhc
Confidence            9999987643

C. elegans CeCYP-16, compared to the archetypal cyclophilin Human cyclophilin A has, a reduced peptidylprolyl cis- trans isomerase activity, is cyclosporin insensitive and shows an altered substrate preference favoring, hydrophobic, acidic or amide amino acids. Most members of this subfamily have a glutamate residue in the active site at the position equivalent to a tryptophan (W121 in Human cyclophilin A), which has been shown to be important for cyclophilin binding.

>cd01922 cyclophilin_SpCYP2_like cyclophilin_SpCYP2_like: cyclophilin 2-like peptidylprolyl cis- trans isomerase (PPIase) domain similar to Schizosaccharomyces pombe cyp-2

Probab=100.00  E-value=1.1e-40  Score=303.58  Aligned_cols=145  Identities=45%  Similarity=0.808  Sum_probs=136.8

Q ss_pred             EEEecceeEEEEecCCCChhHHHHHHHHHhcCccCCceEEEeecCcccccCCCCCCCCCCCCcccccccccccccCCccc
Q 007792            4 LIVTSLGDIVVDLFVDKCPLTTKNFLKLCKIKYYNGCLFHTVQKDFTAQTGDPTGTGTGGDSVYKFLYGEQARFFGDEIR   83 (589)
Q Consensus         4 ~~~T~~G~i~ieL~~~~aP~~~~nF~~l~~~~~Y~g~~f~rv~~~~~iq~Gd~~~~~~~~~~~~~~~~~~~~~~~~~e~~   83 (589)
                      +|+|++|+|+||||.+.||+||+||++||+.+||+++.||||+|+|+||||++.+++.++.++|+       ..|++|+.
T Consensus         1 ~i~T~~G~i~ieL~~~~aP~t~~nF~~L~~~g~Y~~~~f~Rvi~~f~iq~Gd~~~~g~~~~~~~~-------~~~~~e~~   73 (146)
T cd01922           1 TLETTMGEITLELYWNHAPKTCKNFYELAKRGYYNGTIFHRLIKDFMIQGGDPTGTGRGGASIYG-------KKFEDEIH   73 (146)
T ss_pred             CeEeccccEEEEEcCCCCcHHHHHHHHHHhcCCcCCcEEEEEcCCcEEEecccCCCCCCcccccC-------CCcccccc
Confidence            47899999999999999999999999999999999999999999999999999988888888776       56888877


Q ss_pred             cCCCCCCCceEEEeccCCCCCcceEEEEeCCCCCCCCCCcceEEEEecCHHHHHHHhhCccCCCCCcccceeec
Q 007792           84 VDLKHAKTGTVAMASAGENLNASQFYMTLRDNLDYLDEKHTIFGEVAEGLETLSRINESFVDEKNRPYKNIRIK  157 (589)
Q Consensus        84 ~~l~~~~~G~vs~a~~g~~~~~sqFfI~l~~~~~~ld~~~~vFG~Vv~G~~vl~~i~~~~~~~~~~p~~~i~I~  157 (589)
                      +.++|..+|+||||+.++++++|||||++.+ +|+||++|+|||+|++||+||++|++++++ +++|..+|+|.
T Consensus        74 ~~~~h~~~G~l~ma~~~~~s~~sqFfIt~~~-~p~Ld~~~tvFG~V~~G~dvl~~I~~~~~~-~~~P~~~I~I~  145 (146)
T cd01922          74 PELKHTGAGILSMANAGPNTNGSQFFITLAP-TPWLDGKHTIFGRVSKGMKVIENMVEVQTQ-TDRPIDEVKIL  145 (146)
T ss_pred             cCcCCCCCeEEEEeeCCCCCCccEEEEEcCC-CcccCCCCCEEEEEEcCHHHHHHHHhCCCC-CCCcCCCeEEe
Confidence            8899999999999999999999999999998 699999999999999999999999999998 88999999985

These proteins bind their respective SNW chromatin binding protein in autologous systems, in a CsA independent manner indicating interaction with a surface outside the PPIase active site. SNW proteins play a basic and broad range role in signaling.

>KOG0879 consensus U-snRNP-associated cyclophilin type peptidyl-prolyl cis-trans isomerase [Posttranslational modification, protein turnover, chaperones]

Probab=100.00  E-value=1e-40  Score=281.42  Aligned_cols=151  Identities=38%  Similarity=0.635  Sum_probs=142.4

Q ss_pred             EEEEE-ecceeEEEEecCCCChhHHHHHHHHHhcCc--------cCCceEEEeecCcccccCCCC-CCCCCCCCcccccc
Q 007792            2 SVLIV-TSLGDIVVDLFVDKCPLTTKNFLKLCKIKY--------YNGCLFHTVQKDFTAQTGDPT-GTGTGGDSVYKFLY   71 (589)
Q Consensus         2 ~v~~~-T~~G~i~ieL~~~~aP~~~~nF~~l~~~~~--------Y~g~~f~rv~~~~~iq~Gd~~-~~~~~~~~~~~~~~   71 (589)
                      .|.+. +++|+|.||||.+.+|+|++||.++|++.|        |.+++||||+++|||||||+. ++|++-.+||+   
T Consensus        16 dv~igg~~~GrikieLFadivPkTAENFRQFCTGE~r~~g~PiGYK~~tFHRvIkdFMiQgGDFv~gDGtG~~sIy~---   92 (177)
T KOG0879|consen   16 DVAIGGRPIGRIKIELFADIVPKTAENFRQFCTGEYRKDGVPIGYKNSTFHRVIKDFMIQGGDFVNGDGTGVASIYG---   92 (177)
T ss_pred             EEeeCCEEcceEEEEEeeccChhhHHHHHhhcccccccCCccccccccchHHHhhhheeccCceecCCCceEEEEcC---
Confidence            45555 689999999999999999999999999876        999999999999999999987 78899999998   


Q ss_pred             cccccccCCccccCCCCCCCceEEEeccCCCCCcceEEEEeCCCCCCCCCCcceEEEEecCHHHHHHHhhCccCCCCCcc
Q 007792           72 GEQARFFGDEIRVDLKHAKTGTVAMASAGENLNASQFYMTLRDNLDYLDEKHTIFGEVAEGLETLSRINESFVDEKNRPY  151 (589)
Q Consensus        72 ~~~~~~~~~e~~~~l~~~~~G~vs~a~~g~~~~~sqFfI~l~~~~~~ld~~~~vFG~Vv~G~~vl~~i~~~~~~~~~~p~  151 (589)
                          .+|++| ++.|+|+.+|+||||++|+++||+|||||... +.|||++|+|||+|++||.++.+|+++++.++++|.
T Consensus        93 ----~~F~DE-NFtlkH~~PGlLSMANsG~~tNGCQFFITcak-cdfLD~KHVVFGrvldGlli~rkIEnvp~G~NnkPK  166 (177)
T KOG0879|consen   93 ----STFPDE-NFTLKHDGPGLLSMANSGKDTNGCQFFITCAK-CDFLDGKHVVFGRVLDGLLIMRKIENVPTGPNNKPK  166 (177)
T ss_pred             ----CCCCCc-ceeeecCCCceeeccccCCCCCCceEEEEecc-cccccCceEEEeeeehhhhhhhhhhcCCCCCCCCCC
Confidence                679999 69999999999999999999999999999998 899999999999999999999999999999999999


Q ss_pred             cceeeccccc
Q 007792          152 KNIRIKHTYI  161 (589)
Q Consensus       152 ~~i~I~~~~v  161 (589)
                      .+|+|..|+.
T Consensus       167 l~v~i~qCGe  176 (177)
T KOG0879|consen  167 LPVVIVQCGE  176 (177)
T ss_pred             CcEEEeeccc
Confidence            9999999974

>KOG0885 consensus Peptidyl-prolyl cis-trans isomerase [Posttranslational modification, protein turnover, chaperones]

Probab=100.00  E-value=7.7e-40  Score=320.44  Aligned_cols=162  Identities=43%  Similarity=0.750  Sum_probs=157.1

Q ss_pred             EEEEEecceeEEEEecCCCChhHHHHHHHHHhcCccCCceEEEeecCcccccCCCCCCCCCCCCcccccccccccccCCc
Q 007792            2 SVLIVTSLGDIVVDLFVDKCPLTTKNFLKLCKIKYYNGCLFHTVQKDFTAQTGDPTGTGTGGDSVYKFLYGEQARFFGDE   81 (589)
Q Consensus         2 ~v~~~T~~G~i~ieL~~~~aP~~~~nF~~l~~~~~Y~g~~f~rv~~~~~iq~Gd~~~~~~~~~~~~~~~~~~~~~~~~~e   81 (589)
                      .|+|.|+.|+|.||||+..||++|.||++||-.|||+|+.||+++|+|++|||+|+++|+||.+||+       .+|.+|
T Consensus        14 kvil~TT~G~I~iELW~kE~P~acrnFiqKOGegyy~nt~fhrlvp~f~~Qggdp~~~gtGgesiyg-------~~fadE   86 (439)
T KOG0885|consen   14 KVILKTTKGDIDIELWAKECPKACRNFIQLCLEGYYDNTEFHRLVPGFLVQGGDPTGTGTGGESIYG-------RPFADE   86 (439)
T ss_pred             eEEEEeccCceeeeehhhhhhHHHHHHHHHHHhccccCceeeeeccchhcccCCCCCCCCCcccccc-------ccchhh
Confidence            5899999999999999999999999999999999999999999999999999999999999999998       789999


Q ss_pred             cccCCCCCCCceEEEeccCCCCCcceEEEEeCCCCCCCCCCcceEEEEec-CHHHHHHHhhCccCCCCCcccceeecccc
Q 007792           82 IRVDLKHAKTGTVAMASAGENLNASQFYMTLRDNLDYLDEKHTIFGEVAE-GLETLSRINESFVDEKNRPYKNIRIKHTY  160 (589)
Q Consensus        82 ~~~~l~~~~~G~vs~a~~g~~~~~sqFfI~l~~~~~~ld~~~~vFG~Vv~-G~~vl~~i~~~~~~~~~~p~~~i~I~~~~  160 (589)
                      +++.|.++++|+|+||+.+.+.|||||||||++ +|+|+++|||||+|+. -+..+-+|..+.++.+.+|+.+.+|..|.
T Consensus        87 ~h~Rlrf~rrGlvgmana~~~~ngsqFfftl~~-~~el~nk~tiFGKVtGdtIYn~lri~e~eida~~Rp~~p~kI~s~E  165 (439)
T KOG0885|consen   87 FHPRLRFNRRGLVGMANAGNDDNGSQFFFTLGD-TPELNNKHTIFGKVTGDTIYNMLRISEVEIDADDRPVDPPKIKSVE  165 (439)
T ss_pred             cCcceeeeccceeeecccCCCCCCceEEEEecC-ChHhcccCceeeeecchhhhhhhhhcccccccccCCCCccceeeeE
Confidence            999999999999999999999999999999999 8999999999999996 78999999999999999999999999999


Q ss_pred             cccCCCCChhh
Q 007792          161 ILEDPFDDPAQ  171 (589)
Q Consensus       161 vl~~p~~~~~~  171 (589)
                      |+.+||+++..
T Consensus       166 V~~npFdDI~p  176 (439)
T KOG0885|consen  166 VLINPFDDIKP  176 (439)
T ss_pred             eecCchhhcch
Confidence            99999999765

>PTZ00221 cyclophilin; Provisional

Probab=100.00  E-value=8.7e-38  Score=303.16  Aligned_cols=158  Identities=25%  Similarity=0.295  Sum_probs=138.9

Q ss_pred             EEEEEec-----ceeEEEEecCCCChhHHHHHHHHHhcC-----------ccCCceEEEeecC-cccccCCCCCCCCCCC
Q 007792            2 SVLIVTS-----LGDIVVDLFVDKCPLTTKNFLKLCKIK-----------YYNGCLFHTVQKD-FTAQTGDPTGTGTGGD   64 (589)
Q Consensus         2 ~v~~~T~-----~G~i~ieL~~~~aP~~~~nF~~l~~~~-----------~Y~g~~f~rv~~~-~~iq~Gd~~~~~~~~~   64 (589)
                      .|.|+|+     .|+|+|+||.+.||+||+||+.||++.           +|+++.||+|+++ |+||+|++...   +.
T Consensus        54 rVfldisig~~~~GrIvIELf~d~aP~T~eNF~~Lc~g~~g~~~~~g~k~~Y~gt~FhRVi~~~f~iqgGD~~~~---g~  130 (249)
T PTZ00221         54 RAFLDISIGDVLAGRLVFELFEDVVPETVENFRALITGSCGIDTNTGVKLDYLYTPVHHVDRNNNIIVLGELDSF---NV  130 (249)
T ss_pred             EEEEEEeeCCeecceEEEEEeCCCCcHHHHHHHHHhhcccccccccCcccccCCCEEEEEeCCCCEEEeCCCCCC---Cc
Confidence            3666665     567999999999999999999999753           3999999999986 89999998643   34


Q ss_pred             CcccccccccccccCCccccCCCCCCCceEEEeccCCCCCcceEEEEeCCCCCCCCCCcceEEEEecCHHHHHHHhhCcc
Q 007792           65 SVYKFLYGEQARFFGDEIRVDLKHAKTGTVAMASAGENLNASQFYMTLRDNLDYLDEKHTIFGEVAEGLETLSRINESFV  144 (589)
Q Consensus        65 ~~~~~~~~~~~~~~~~e~~~~l~~~~~G~vs~a~~g~~~~~sqFfI~l~~~~~~ld~~~~vFG~Vv~G~~vl~~i~~~~~  144 (589)
                      ++|+       ..|++|. +.++|+.+|+||||+.|+++|+|||||||.+ +|+||++|+|||+|++||+||++|+.+++
T Consensus       131 s~~G-------~~f~dE~-~~~~h~~~G~LsMan~GpntngSQFfITl~~-~p~LDgk~vVFGrVveGmdVv~kIe~v~~  201 (249)
T PTZ00221        131 SSTG-------TPIADEG-YRHRHTERGLLTMISEGPHTSGSVFGITLGP-SPSLDFKQVVFGKAVDDLSLLEKLESLPL  201 (249)
T ss_pred             cCCC-------CcccCcc-ccccCCCCCEEEeCcCCCCCccceEEEECCC-CCccCCCceEEEEEEeCHHHHHHHHcCCc
Confidence            4554       4688884 6789999999999999999999999999998 69999999999999999999999999999


Q ss_pred             CCCCCcccceeecccccccCCCCChhh
Q 007792          145 DEKNRPYKNIRIKHTYILEDPFDDPAQ  171 (589)
Q Consensus       145 ~~~~~p~~~i~I~~~~vl~~p~~~~~~  171 (589)
                      +..++|..+|+|.+|+++.+|-+...+
T Consensus       202 d~~grP~~~V~I~~Cgvl~~~~p~~~~  228 (249)
T PTZ00221        202 DDVGRPLLPVTVSFCGALTGEKPPGRQ  228 (249)
T ss_pred             CCCCCCCCCeEEEECeEecCCCCCccc
Confidence            889999999999999999888765554

>PLN03149 peptidyl-prolyl isomerase H (cyclophilin H); Provisional

Probab=100.00  E-value=7.5e-38  Score=295.44  Aligned_cols=147  Identities=39%  Similarity=0.642  Sum_probs=134.2

Q ss_pred             ecceeEEEEecCCCChhHHHHHHHHHhcCc--------cCCceEEEeecCcccccCCCC-CCCCCCCCcccccccccccc
Q 007792            7 TSLGDIVVDLFVDKCPLTTKNFLKLCKIKY--------YNGCLFHTVQKDFTAQTGDPT-GTGTGGDSVYKFLYGEQARF   77 (589)
Q Consensus         7 T~~G~i~ieL~~~~aP~~~~nF~~l~~~~~--------Y~g~~f~rv~~~~~iq~Gd~~-~~~~~~~~~~~~~~~~~~~~   77 (589)
                      +++|+|+|+||.+.||+||+||++||++.+        |++|.||||+++|+||||++. +++.++.++|+       ..
T Consensus        30 ~~~G~i~ieL~~~~aP~t~~NF~~Lc~g~~~~~g~~~~Y~~~~fhrVi~~f~iqgGd~~~~~g~g~~~~~g-------~~  102 (186)
T PLN03149         30 IPAGRIKMELFADIAPKTAENFRQFCTGEFRKAGLPQGYKGCQFHRVIKDFMIQGGDFLKGDGTGCVSIYG-------SK  102 (186)
T ss_pred             cccccEEEEEcCCCCcHHHHHHHHHHhhhccccCcccccCCcEEEEEcCCcEEEcCCcccCCCCCcccccC-------Cc
Confidence            367999999999999999999999998655        999999999999999999975 67788888776       45


Q ss_pred             cCCccccCCCCCCCceEEEeccCCCCCcceEEEEeCCCCCCCCCCcceEEEEe-cCHHHHHHHhhCccCCCCCcccceee
Q 007792           78 FGDEIRVDLKHAKTGTVAMASAGENLNASQFYMTLRDNLDYLDEKHTIFGEVA-EGLETLSRINESFVDEKNRPYKNIRI  156 (589)
Q Consensus        78 ~~~e~~~~l~~~~~G~vs~a~~g~~~~~sqFfI~l~~~~~~ld~~~~vFG~Vv-~G~~vl~~i~~~~~~~~~~p~~~i~I  156 (589)
                      |++|. +.++|..+|+||||+.++++++||||||+.+ +|+||++|+|||+|+ +||+||++|+.++++.+++|..+|+|
T Consensus       103 f~~e~-~~~~h~~~G~lsma~~g~~s~~sqFfIt~~~-~p~Ldg~~tVFG~Vi~eG~dvl~~I~~~~~~~~~~P~~~i~I  180 (186)
T PLN03149        103 FEDEN-FIAKHTGPGLLSMANSGPNTNGCQFFITCAK-CDWLDNKHVVFGRVLGDGLLVVRKIENVATGPNNRPKLACVI  180 (186)
T ss_pred             cCCcc-cccccCCCCEEEEeeCCCCCcccEEEEECCC-CCccCCCceEEEEEEECcHHHHHHHHcCCCCCCCCCcCCeEE
Confidence            67774 5678889999999999999999999999998 799999999999999 79999999999999999999999999


Q ss_pred             cccccc
Q 007792          157 KHTYIL  162 (589)
Q Consensus       157 ~~~~vl  162 (589)
                      .+|+++
T Consensus       181 ~~cG~~  186 (186)
T PLN03149        181 SECGEM  186 (186)
T ss_pred             EeCEeC
Confidence            999974

>PRK10791 peptidyl-prolyl cis-trans isomerase B (rotamase B); Provisional

Probab=100.00  E-value=1.1e-37  Score=288.57  Aligned_cols=149  Identities=31%  Similarity=0.504  Sum_probs=127.9

Q ss_pred             EEEEecceeEEEEecCCCChhHHHHHHHHHhcCccCCceEEEeecCcccccCCCCCCCCCCCCcccccccccccccCCcc
Q 007792            3 VLIVTSLGDIVVDLFVDKCPLTTKNFLKLCKIKYYNGCLFHTVQKDFTAQTGDPTGTGTGGDSVYKFLYGEQARFFGDEI   82 (589)
Q Consensus         3 v~~~T~~G~i~ieL~~~~aP~~~~nF~~l~~~~~Y~g~~f~rv~~~~~iq~Gd~~~~~~~~~~~~~~~~~~~~~~~~~e~   82 (589)
                      |+|+|++|+|+|+||.+.||+||+||++||+.+||+++.||||+++|+||||++... .+. ..++       ..|++|.
T Consensus         2 v~~~T~~G~i~ieL~~~~aP~t~~nF~~L~~~g~Yd~~~fhRvi~~f~iQgGd~~~~-~~~-~~~~-------~~~~~e~   72 (164)
T PRK10791          2 VTFHTNHGDIVIKTFDDKAPETVKNFLDYCREGFYNNTIFHRVINGFMIQGGGFEPG-MKQ-KATK-------EPIKNEA   72 (164)
T ss_pred             EEEEEccccEEEEEeCCCCcHHHHHHHHHHhcCCcCCcEEEEEecCcEEEeCCcCCC-CCc-CCCC-------CCcCCcc
Confidence            689999999999999999999999999999999999999999999999999986521 111 1111       3577786


Q ss_pred             ccCCCCCCCceEEEeccC-CCCCcceEEEEeCCCCCCCC-------C-CcceEEEEecCHHHHHHHhhCccCCC----CC
Q 007792           83 RVDLKHAKTGTVAMASAG-ENLNASQFYMTLRDNLDYLD-------E-KHTIFGEVAEGLETLSRINESFVDEK----NR  149 (589)
Q Consensus        83 ~~~l~~~~~G~vs~a~~g-~~~~~sqFfI~l~~~~~~ld-------~-~~~vFG~Vv~G~~vl~~i~~~~~~~~----~~  149 (589)
                      ...++| .+|+||||+.+ +++++|||||++.+ .++||       + +|+|||+|++||+||++|+.++++..    ++
T Consensus        73 ~~~~~~-~~G~lsma~~~~p~s~~SQFfI~~~~-~~~ld~~~~~~d~~~~tvFG~V~eG~dvl~~I~~~~~~~~~~~~~~  150 (164)
T PRK10791         73 NNGLKN-TRGTLAMARTQAPHSATAQFFINVVD-NDFLNFSGESLQGWGYCVFAEVVEGMDVVDKIKGVATGRSGMHQDV  150 (164)
T ss_pred             cccccC-CCcEEEECCCCCcCCccceEEEEecC-chhhcccccccCCCCccEEEEEecCHHHHHHHHcCcCCCCCccCCC
Confidence            666666 79999999875 89999999999998 47776       3 79999999999999999999999763    69


Q ss_pred             cccceeecccccc
Q 007792          150 PYKNIRIKHTYIL  162 (589)
Q Consensus       150 p~~~i~I~~~~vl  162 (589)
                      |..+|+|.+|.|.
T Consensus       151 P~~~v~I~~~~i~  163 (164)
T PRK10791        151 PKEDVIIESVTVS  163 (164)
T ss_pred             cCCCeEEEEEEEe
Confidence            9999999999775

>PRK10903 peptidyl-prolyl cis-trans isomerase A (rotamase A); Provisional

Probab=100.00  E-value=1.7e-37  Score=293.72  Aligned_cols=151  Identities=29%  Similarity=0.472  Sum_probs=130.4

Q ss_pred             CEEEEEecceeEEEEecCCCChhHHHHHHHHHhcCccCCceEEEeecCcccccCCCCCCCCCCCCcccccccccccccCC
Q 007792            1 MSVLIVTSLGDIVVDLFVDKCPLTTKNFLKLCKIKYYNGCLFHTVQKDFTAQTGDPTGTGTGGDSVYKFLYGEQARFFGD   80 (589)
Q Consensus         1 ~~v~~~T~~G~i~ieL~~~~aP~~~~nF~~l~~~~~Y~g~~f~rv~~~~~iq~Gd~~~~~~~~~~~~~~~~~~~~~~~~~   80 (589)
                      ..|+|+|++|+|+|+||.+.||+||+||++||+.+||+|+.||||+|+|+||||++.....+  ..++       ..|++
T Consensus        29 ~~v~l~T~~G~i~ieL~~~~aP~t~~NF~~L~~~g~Ydg~~FhRvi~~f~iQgG~~~~~~~~--~~~~-------~~~~~   99 (190)
T PRK10903         29 PHVLLTTSAGNIELELNSQKAPVSVKNFVDYVNSGFYNNTTFHRVIPGFMIQGGGFTEQMQQ--KKPN-------PPIKN   99 (190)
T ss_pred             cEEEEEeccccEEEEEeCCCCcHHHHHHHHHHhcCCcCCcEEEEEeCCceEEeCCcCCCCCC--CCCC-------CcccC
Confidence            36899999999999999999999999999999999999999999999999999997643221  1111       34677


Q ss_pred             ccccCCCCCCCceEEEeccC-CCCCcceEEEEeCCCCCCCCC-----CcceEEEEecCHHHHHHHhhCccCC----CCCc
Q 007792           81 EIRVDLKHAKTGTVAMASAG-ENLNASQFYMTLRDNLDYLDE-----KHTIFGEVAEGLETLSRINESFVDE----KNRP  150 (589)
Q Consensus        81 e~~~~l~~~~~G~vs~a~~g-~~~~~sqFfI~l~~~~~~ld~-----~~~vFG~Vv~G~~vl~~i~~~~~~~----~~~p  150 (589)
                      |....+.| .+|+||||+.+ +++++|||||++.+ .++||+     +|+|||+|++||+||++|+.++++.    .++|
T Consensus       100 e~~~~l~~-~~G~lama~~~~~~sn~SQFfIt~~~-~~~ld~~~~dg~ytvFG~V~eG~dvl~~I~~~~~~~~~~~~~~P  177 (190)
T PRK10903        100 EADNGLRN-TRGTIAMARTADKDSATSQFFINVAD-NAFLDHGQRDFGYAVFGKVVKGMDVADKISQVPTHDVGPYQNVP  177 (190)
T ss_pred             cccccCcC-CCcEEEeCCCCCCCCcccEEEEECcC-cccccCCccCCCccEEEEEecCHHHHHHHHcCCCCCCCCCCCcc
Confidence            76555544 78999999865 89999999999998 589984     8999999999999999999999976    4699


Q ss_pred             ccceeecccccc
Q 007792          151 YKNIRIKHTYIL  162 (589)
Q Consensus       151 ~~~i~I~~~~vl  162 (589)
                      ..+|+|.+|+|+
T Consensus       178 ~~~v~I~~~~v~  189 (190)
T PRK10903        178 SKPVVILSAKVL  189 (190)
T ss_pred             cCCeEEEEEEEe
Confidence            999999999875

>cd01926 cyclophilin_ABH_like cyclophilin_ABH_like: Cyclophilin A, B and H-like cyclophilin-type peptidylprolyl cis- trans isomerase (PPIase) domain

Probab=100.00  E-value=2.3e-37  Score=288.01  Aligned_cols=149  Identities=41%  Similarity=0.667  Sum_probs=134.5

Q ss_pred             EEEEE-ecceeEEEEecCCCChhHHHHHHHHHhc--C------ccCCceEEEeecCcccccCCCC-CCCCCCCCcccccc
Q 007792            2 SVLIV-TSLGDIVVDLFVDKCPLTTKNFLKLCKI--K------YYNGCLFHTVQKDFTAQTGDPT-GTGTGGDSVYKFLY   71 (589)
Q Consensus         2 ~v~~~-T~~G~i~ieL~~~~aP~~~~nF~~l~~~--~------~Y~g~~f~rv~~~~~iq~Gd~~-~~~~~~~~~~~~~~   71 (589)
                      .|.+. |++|+|+||||.+.||+||+||++||++  +      +|+++.||||+|+|+||||++. .++.++.++|+   
T Consensus         6 di~i~~~~~G~i~ieL~~~~aP~~~~nF~~L~~~~~g~~~~~~~Y~~~~f~Rv~~~~~iq~Gd~~~~~g~~~~~~~g---   82 (164)
T cd01926           6 DITIGGEPAGRIVMELFADVVPKTAENFRALCTGEKGKGGKPFGYKGSTFHRVIPDFMIQGGDFTRGNGTGGKSIYG---   82 (164)
T ss_pred             EEeECCeeceeEEEEEeCCCCCHHHHHHHHHhcccCCCcccccccCCCEEEEEeCCcEEEcCCccCCCCCCCCcccC---
Confidence            44443 6899999999999999999999999984  4      8999999999999999999976 66777777776   


Q ss_pred             cccccccCCccccCCCCCCCceEEEeccCCCCCcceEEEEeCCCCCCCCCCcceEEEEecCHHHHHHHhhCccCCCCCcc
Q 007792           72 GEQARFFGDEIRVDLKHAKTGTVAMASAGENLNASQFYMTLRDNLDYLDEKHTIFGEVAEGLETLSRINESFVDEKNRPY  151 (589)
Q Consensus        72 ~~~~~~~~~e~~~~l~~~~~G~vs~a~~g~~~~~sqFfI~l~~~~~~ld~~~~vFG~Vv~G~~vl~~i~~~~~~~~~~p~  151 (589)
                          ..+++| ...++|+.+|+||||+.++++++|||||+|.+ +|+||++|+|||+|++||+||++|+.++++ +++|.
T Consensus        83 ----~~~~~e-~~~~~h~~~G~lsma~~~~~~~~sqFfIt~~~-~~~Ld~~~tvFG~V~~G~dvl~~i~~~~~~-~~~P~  155 (164)
T cd01926          83 ----EKFPDE-NFKLKHTGPGLLSMANAGPNTNGSQFFITTVK-TPWLDGKHVVFGKVVEGMDVVKKIENVGSG-NGKPK  155 (164)
T ss_pred             ----CccCCC-CccccCCCccEEEeeECCCCCcccEEEEEeCC-CCccCCcccEEEEEEEcHHHHHHHHcCCCC-CCCCc
Confidence                446777 36789989999999999999999999999998 799999999999999999999999999998 89999


Q ss_pred             cceeecccc
Q 007792          152 KNIRIKHTY  160 (589)
Q Consensus       152 ~~i~I~~~~  160 (589)
                      .+|+|.+|+
T Consensus       156 ~~i~I~~cG  164 (164)
T cd01926         156 KKVVIADCG  164 (164)
T ss_pred             CCeEEEECC
Confidence            999999996

This family represents the archetypal cystolic cyclophilin similar to human cyclophilins A, B and H. PPIase is an enzyme which accelerates protein folding by catalyzing the cis-trans isomerization of the peptide bonds preceding proline residues. These enzymes have been implicated in protein folding processes which depend on catalytic /chaperone-like activities. As cyclophilins, Human hCyP-A, human cyclophilin-B (hCyP-19), S. cerevisiae Cpr1 and C. elegans Cyp-3, are inhibited by the immunosuppressive drug cyclopsporin A (CsA). CsA binds to the PPIase active site. Cyp-3. S. cerevisiae Cpr1 interacts with the Rpd3 - Sin3 complex and in addition is a component of the Set3 complex. S. cerevisiae Cpr1 has also been shown to have a role in Zpr1p nuclear transport. Human cyclophilin H associates with the [U4/U6.U5] tri-snRNP particles of the spl

>PTZ00060 cyclophilin; Provisional

Probab=100.00  E-value=4.5e-37  Score=289.94  Aligned_cols=151  Identities=39%  Similarity=0.641  Sum_probs=134.8

Q ss_pred             EEEEE-ecceeEEEEecCCCChhHHHHHHHHHh---------cCccCCceEEEeecCcccccCCCC-CCCCCCCCccccc
Q 007792            2 SVLIV-TSLGDIVVDLFVDKCPLTTKNFLKLCK---------IKYYNGCLFHTVQKDFTAQTGDPT-GTGTGGDSVYKFL   70 (589)
Q Consensus         2 ~v~~~-T~~G~i~ieL~~~~aP~~~~nF~~l~~---------~~~Y~g~~f~rv~~~~~iq~Gd~~-~~~~~~~~~~~~~   70 (589)
                      .+.+. |++|+|+||||.+.||+||+||++||+         .++|++|.||||+|+|+||||++. .++.++.++|+  
T Consensus        21 di~i~~~~~G~ivIeL~~d~aP~t~~nF~~L~~g~~~~~~g~~~~Y~~~~fhRvi~~~~iqgGd~~~~~g~~g~~~~g--   98 (183)
T PTZ00060         21 DISIDNAPAGRIVFELFSDVTPKTAENFRALCIGDKVGSSGKNLHYKGSIFHRIIPQFMCQGGDITNHNGTGGESIYG--   98 (183)
T ss_pred             EEEECCEeCceEEEEEcCCCCcHHHHHHHHHhcCCcccccCcccccCCeEEEEEcCCCeEEeCCccCCCCCCCCcccc--
Confidence            34443 678999999999999999999999997         468999999999999999999976 56777787776  


Q ss_pred             ccccccccCCccccCCCCCCCceEEEeccCCCCCcceEEEEeCCCCCCCCCCcceEEEEecCHHHHHHHhhCccCCCCCc
Q 007792           71 YGEQARFFGDEIRVDLKHAKTGTVAMASAGENLNASQFYMTLRDNLDYLDEKHTIFGEVAEGLETLSRINESFVDEKNRP  150 (589)
Q Consensus        71 ~~~~~~~~~~e~~~~l~~~~~G~vs~a~~g~~~~~sqFfI~l~~~~~~ld~~~~vFG~Vv~G~~vl~~i~~~~~~~~~~p  150 (589)
                           ..+++| ...++|..+|+|+|++.++++++|||||||.+ +|+||++|+|||+|++||+||++|+.+.+ ..+.|
T Consensus        99 -----~~~~~e-~~~~~h~~~G~lsma~~g~~~~~sqFfIt~~~-~~~Ldg~~tvFG~Vi~G~dvl~~I~~~~~-~~~~P  170 (183)
T PTZ00060         99 -----RKFTDE-NFKLKHDQPGLLSMANAGPNTNGSQFFITTVP-CPWLDGKHVVFGKVIEGMEVVRAMEKEGT-QSGYP  170 (183)
T ss_pred             -----cccCCc-cccccCCCCCEEEeccCCCCCCcceEEEEeCC-CcccCCCccEEEEEEccHHHHHHHHccCC-CCCCC
Confidence                 456777 46788988999999999999999999999998 69999999999999999999999998887 46899


Q ss_pred             ccceeecccccc
Q 007792          151 YKNIRIKHTYIL  162 (589)
Q Consensus       151 ~~~i~I~~~~vl  162 (589)
                      ..+|+|++|+++
T Consensus       171 ~~~v~I~~cg~~  182 (183)
T PTZ00060        171 KKPVVVTDCGEL  182 (183)
T ss_pred             cCCeEEEEeEEc
Confidence            999999999987

>cd01920 cyclophilin_EcCYP_like cyclophilin_EcCYP_like: cyclophilin-type A-like peptidylprolyl cis- trans isomerase (PPIase) domain similar to the cytosolic E

Probab=100.00  E-value=1.6e-36  Score=279.22  Aligned_cols=144  Identities=33%  Similarity=0.511  Sum_probs=123.1

Q ss_pred             EEEecceeEEEEecCCCChhHHHHHHHHHhcCccCCceEEEeecCcccccCCCCCCCCCCCCcccccccccccccCCccc
Q 007792            4 LIVTSLGDIVVDLFVDKCPLTTKNFLKLCKIKYYNGCLFHTVQKDFTAQTGDPTGTGTGGDSVYKFLYGEQARFFGDEIR   83 (589)
Q Consensus         4 ~~~T~~G~i~ieL~~~~aP~~~~nF~~l~~~~~Y~g~~f~rv~~~~~iq~Gd~~~~~~~~~~~~~~~~~~~~~~~~~e~~   83 (589)
                      .|+|++|+|+|+||.+.||+||+||++||+.+||+++.||||+|+||||||++.....+..  ++       ..+++|..
T Consensus         1 ~l~T~~G~i~ieL~~~~aP~t~~nF~~L~~~g~Yd~~~fhRvi~~f~iQ~Gd~~~~~~~~~--~~-------~~~~~e~~   71 (155)
T cd01920           1 EFQTSLGDIVVELYDDKAPITVENFLAYVRKGFYDNTIFHRVISGFVIQGGGFTPDLAQKE--TL-------KPIKNEAG   71 (155)
T ss_pred             CcEecceeEEEEEeCCCCcHHHHHHHHHHhcCCCCCCEEEEEeCCcEEEeCCCCCCCCccc--cC-------CcccCccc
Confidence            3789999999999999999999999999999999999999999999999999875443321  11       34667754


Q ss_pred             cCCCCCCCceEEEeccC-CCCCcceEEEEeCCCCCCCCC-----CcceEEEEecCHHHHHHHhhCccCCC----CCcccc
Q 007792           84 VDLKHAKTGTVAMASAG-ENLNASQFYMTLRDNLDYLDE-----KHTIFGEVAEGLETLSRINESFVDEK----NRPYKN  153 (589)
Q Consensus        84 ~~l~~~~~G~vs~a~~g-~~~~~sqFfI~l~~~~~~ld~-----~~~vFG~Vv~G~~vl~~i~~~~~~~~----~~p~~~  153 (589)
                      ..++ +.+|+||||+.+ +++++|||||+|.+ +|+||+     +|||||+|++||+||++|+.++++..    +.|..+
T Consensus        72 ~~~~-~~~G~v~ma~~~~~~s~~SqFfI~~~~-~~~ld~~~~~~~ytvFG~V~eG~dvl~~I~~~~~~~~~~~~~~p~~~  149 (155)
T cd01920          72 NGLS-NTRGTIAMARTNAPDSATSQFFINLKD-NASLDYQNEQWGYTVFGEVTEGMDVVDKIAGVETYSFGSYQDVPVQD  149 (155)
T ss_pred             cccc-CCceEEEECCCCCCCCccceEEEECCC-chhcCCcccCCCccEEEEEecCHHHHHHHHcCCccCCCCcCCCcCCC
Confidence            4444 589999999865 89999999999998 699995     79999999999999999999999765    588888


Q ss_pred             eeecc
Q 007792          154 IRIKH  158 (589)
Q Consensus       154 i~I~~  158 (589)
                      |+|..
T Consensus       150 v~i~~  154 (155)
T cd01920         150 VIIES  154 (155)
T ss_pred             eEEEE
Confidence            88865

coli cyclophilin A and Streptomyces antibioticus SanCyp18. Compared to the archetypal cyclophilin Human cyclophilin A, these have reduced affinity for cyclosporin A. E. coli cyclophilin A has a similar peptidylprolyl cis- trans isomerase activity to the human cyclophilin A. Most members of this subfamily contain a phenylalanine residue at the position equivalent to Human cyclophilin W121, where a tyrptophan has been shown to be important for cyclophilin binding.

>cd00317 cyclophilin cyclophilin: cyclophilin-type peptidylprolyl cis- trans isomerases

Probab=100.00  E-value=3.4e-35  Score=269.43  Aligned_cols=146  Identities=42%  Similarity=0.655  Sum_probs=132.2

Q ss_pred             EEEecceeEEEEecCCCChhHHHHHHHHHhcCccCCceEEEeecCcccccCCCCCCCCCCCCcccccccccccccCCccc
Q 007792            4 LIVTSLGDIVVDLFVDKCPLTTKNFLKLCKIKYYNGCLFHTVQKDFTAQTGDPTGTGTGGDSVYKFLYGEQARFFGDEIR   83 (589)
Q Consensus         4 ~~~T~~G~i~ieL~~~~aP~~~~nF~~l~~~~~Y~g~~f~rv~~~~~iq~Gd~~~~~~~~~~~~~~~~~~~~~~~~~e~~   83 (589)
                      +|+|++|+|+|+||++.||++|+||++||+.++|+++.||||+|+++||||++......+ +.++       ..+++|..
T Consensus         1 ~~~T~~G~i~IeL~~~~~P~~~~nF~~l~~~~~Y~~~~f~rv~~~~~iq~Gd~~~~~~~~-~~~~-------~~~~~E~~   72 (146)
T cd00317           1 TLDTTKGRIVIELYGDEAPKTVENFLSLARGGFYDGTTFHRVIPGFMIQGGDPTGTGGGG-SGPG-------YKFPDENF   72 (146)
T ss_pred             CeEeccCcEEEEEcCCCChHHHHHHHHHHhcCCcCCCEEEEEeCCCeEEECCCCCCCCCC-CcCC-------CccCCccc
Confidence            478999999999999999999999999999999999999999999999999988654432 2222       56888987


Q ss_pred             cCCCCCCCceEEEeccCCCCCcceEEEEeCCCCCCCCCCcceEEEEecCHHHHHHHhhCccCCCCCcccceeecc
Q 007792           84 VDLKHAKTGTVAMASAGENLNASQFYMTLRDNLDYLDEKHTIFGEVAEGLETLSRINESFVDEKNRPYKNIRIKH  158 (589)
Q Consensus        84 ~~l~~~~~G~vs~a~~g~~~~~sqFfI~l~~~~~~ld~~~~vFG~Vv~G~~vl~~i~~~~~~~~~~p~~~i~I~~  158 (589)
                      +.+.|..+|+|+|++.+++++++||||+|.+ +|+||++|+|||+|++||+||++|+.++++++++|..+|.|.+
T Consensus        73 ~~~~~~~~G~v~~~~~~~~~~~sqF~Itl~~-~~~ld~~~~vfG~V~~G~~vl~~I~~~~~~~~~~P~~~i~I~~  146 (146)
T cd00317          73 PLKYHHRRGTLSMANAGPNTNGSQFFITTAP-TPHLDGKHTVFGKVVEGMDVVDKIERGDTDENGRPIKPVTISD  146 (146)
T ss_pred             cCcCcCCCcEEEEeeCCCCCcccEEEEECCC-CcccCCCceEEEEEeCCHHHHHHHHcCCCCCCCcCcCceEEeC
Confidence            7776788999999999999999999999998 6999999999999999999999999999999999999999863

This family contains eukaryotic, bacterial and archeal proteins which exhibit a peptidylprolyl cis- trans isomerases activity (PPIase, Rotamase) and in addition bind the immunosuppressive drug cyclosporin (CsA). Immunosuppression in vertebrates is believed to be the result of the cyclophilin A-cyclosporin protein drug complex binding to and inhibiting the protein-phosphatase calcineurin. PPIase is an enzyme which accelerates protein folding by catalyzing the cis-trans isomerization of the peptide bonds preceding proline residues. Cyclophilins are a diverse family in terms of function and have been implicated in protein folding processes which depend on catalytic /chaperone-like activities. This group contains human cyclophilin 40, a co-chaperone of the hsp90 chaperone system; human cyclophilin A, a chaperone in the HIV-1 infectious process and; human cyclophilin H, a component of the U4/U6 snRNP

>PF00160 Pro_isomerase: Cyclophilin type peptidyl-prolyl cis-trans isomerase/CLD; InterPro: IPR002130 Cyclophilin [] is the major high-affinity binding protein in vertebrates for the immunosuppressive drug cyclosporin A (CSA), but is also found in other organisms

Probab=100.00  E-value=3.5e-34  Score=265.49  Aligned_cols=151  Identities=43%  Similarity=0.681  Sum_probs=131.2

Q ss_pred             EEEEEec-ceeEEEEecCCCChhHHHHHHHHHhcCccCCceEEEeecCcccccCCCCCCCCCCCCcccccccccccccCC
Q 007792            2 SVLIVTS-LGDIVVDLFVDKCPLTTKNFLKLCKIKYYNGCLFHTVQKDFTAQTGDPTGTGTGGDSVYKFLYGEQARFFGD   80 (589)
Q Consensus         2 ~v~~~T~-~G~i~ieL~~~~aP~~~~nF~~l~~~~~Y~g~~f~rv~~~~~iq~Gd~~~~~~~~~~~~~~~~~~~~~~~~~   80 (589)
                      .|.|+|+ +|+|+|+||++.||++|+||++||+.++|+++.||+|+|+++||+|++..++..+...+     .....+++
T Consensus         1 ~~~i~t~~~G~i~ieL~~~~aP~~~~nF~~l~~~~~y~g~~f~ri~~~~~i~~G~~~~~~~~~~~~~-----~~~~~~~~   75 (155)
T PF00160_consen    1 FVDIETSGLGRIVIELFGDEAPKTVENFLRLCTSGFYDGTKFHRIIPNFVIQGGDPTGNGGYGREDS-----TGGEPIPD   75 (155)
T ss_dssp             EEEEEETTEEEEEEEEETTTSHHHHHHHHHHHHTTSSTTEBEEEEETTTEEEESSTTTSSSSTSEEB-----TTBSCBSS
T ss_pred             CEEEEeCCccCEEEEEeCCCCcHHHHhhehhhcccccCCceeecccccceeeeeeccCCCCcccccc-----cCcccccc
Confidence            4789997 99999999999999999999999999999999999999999999999886554211101     11135888


Q ss_pred             cccc-CCCCCCCceEEEeccC--CCCCcceEEEEeCCCCCCCCCCcceEEEEecCHHHHHHHhhCccCCCCCcccceeec
Q 007792           81 EIRV-DLKHAKTGTVAMASAG--ENLNASQFYMTLRDNLDYLDEKHTIFGEVAEGLETLSRINESFVDEKNRPYKNIRIK  157 (589)
Q Consensus        81 e~~~-~l~~~~~G~vs~a~~g--~~~~~sqFfI~l~~~~~~ld~~~~vFG~Vv~G~~vl~~i~~~~~~~~~~p~~~i~I~  157 (589)
                      |..+ .+.| .+|+|+|++.+  +++++|||||+|.+ .|+||++|+|||+|++||+||++|+.++++.  +|.++|+|.
T Consensus        76 E~~~~~~~~-~~G~v~~~~~~~~~~~~~sqF~I~l~~-~~~ld~~~~vfG~V~~G~~vl~~i~~~~~~~--~p~~~v~I~  151 (155)
T PF00160_consen   76 EFNPSLLKH-RRGLVSMARSGKDPNSNGSQFFITLSD-APHLDGKYTVFGRVIEGMDVLDKIEAGPTDE--RPKQDVTIS  151 (155)
T ss_dssp             SGBTTSSSS-STTEEEEEBSSSSTTEBSSEEEEESSC-GGGGTTTSEEEEEEEEHHHHHHHHHTSBBTT--EBSSTEEEE
T ss_pred             ccccccccc-cceeeeecccccCCCCCCceEEeeccC-CCccccceeeeeEEehhHHHHHHHHCCCCCC--ccCCCeEEE
Confidence            8753 4566 89999999986  78899999999998 6999999999999999999999999998877  999999999


Q ss_pred             cccc
Q 007792          158 HTYI  161 (589)
Q Consensus       158 ~~~v  161 (589)
                      +|+|
T Consensus       152 ~cgv  155 (155)
T PF00160_consen  152 SCGV  155 (155)
T ss_dssp             EEEE
T ss_pred             EeEC
Confidence            9986

It exhibits a peptidyl-prolyl cis-trans isomerase activity (5.2.1.8 from EC) (PPIase or rotamase). PPIase is an enzyme that accelerates protein folding by catalysing the cis-trans isomerisation of proline imidic peptide bonds in oligopeptides []. It is probable that CSA mediates some of its effects via an forming a tight complex with cyclophilin that inhibits the phosphatase activity of calcineurin [], []. Cyclophilin A is a cytosolic and highly abundant protein. The protein belongs to a family of isozymes, including cyclophilins B and C, and natural killer cell cyclophilin-related protein [, , ]. Major isoforms have been found throughout the cell, including the ER, and some are even secreted. The sequences of the different forms of cyclophilin-type PPIases are well conserved. Note: FKBP's, a family of proteins that bind the immunosuppressive drug FK506, are also PPIases, but their sequence is not at all related to that of cyclophilin (see IPR001179 from INTERPRO).; GO: 0003755 peptidyl-prolyl cis-trans isomerase activity, 0006457 protein folding; PDB: 1Z81_A 1IHG_A 1IIP_A 3PMP_B 3O7T_A 2B71_A 1QNG_A 1QNH_A 2HQJ_A 2RMC_G ....

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

Probab=100.00  E-value=7.1e-35  Score=266.26  Aligned_cols=146  Identities=38%  Similarity=0.676  Sum_probs=136.3

Q ss_pred             ecceeEEEEecCCCChhHHHHHHHHHhc--Cc-cCCceEEEeecCcccccCCCC-CCCCCCCCcccccccccccccCCcc
Q 007792            7 TSLGDIVVDLFVDKCPLTTKNFLKLCKI--KY-YNGCLFHTVQKDFTAQTGDPT-GTGTGGDSVYKFLYGEQARFFGDEI   82 (589)
Q Consensus         7 T~~G~i~ieL~~~~aP~~~~nF~~l~~~--~~-Y~g~~f~rv~~~~~iq~Gd~~-~~~~~~~~~~~~~~~~~~~~~~~e~   82 (589)
                      -..|+|++.|..+..|.|++||..||.+  || |.|+.||||+|.||+||||++ ++|++|.+||+       ..|.+| 
T Consensus       148 ~~~Gri~~~lrtdv~Pmtaenfr~Lctge~gfgykgssfhriip~fmcqggdftn~ngtggksiyg-------kkfdde-  219 (298)
T KOG0111|consen  148 DRAGRIVMLLRTDVVPMTAENFRCLCTGEAGFGYKGSSFHRIIPKFMCQGGDFTNGNGTGGKSIYG-------KKFDDE-  219 (298)
T ss_pred             cccceEEEeecccCChhhhhhhhhhccccCccCccccchhhhhhhhhccCCccccCCCCCCccccc-------cccccc-
Confidence            4689999999999999999999999976  34 999999999999999999999 78999999998       788999 


Q ss_pred             ccCCCCCCCceEEEeccCCCCCcceEEEEeCCCCCCCCCCcceEEEEecCHHHHHHHhhCccCCCCCcccceeecccccc
Q 007792           83 RVDLKHAKTGTVAMASAGENLNASQFYMTLRDNLDYLDEKHTIFGEVAEGLETLSRINESFVDEKNRPYKNIRIKHTYIL  162 (589)
Q Consensus        83 ~~~l~~~~~G~vs~a~~g~~~~~sqFfI~l~~~~~~ld~~~~vFG~Vv~G~~vl~~i~~~~~~~~~~p~~~i~I~~~~vl  162 (589)
                      ++.|+|..+|+|+|||+|+|+||||||||+.. +.|||++|+|||.||+||+||.+|++..+ +.+.|...|+|..|+.+
T Consensus       220 nf~lkht~pgtlsmansgantngsqffict~k-tdwldgkhvvfghv~eg~~vvrq~e~qgs-ksgkp~qkv~i~~cge~  297 (298)
T KOG0111|consen  220 NFTLKHTMPGTLSMANSGANTNGSQFFICTEK-TDWLDGKHVVFGHVVEGMNVVRQVEQQGS-KSGKPQQKVKIVECGEI  297 (298)
T ss_pred             ceeeecCCCceeeccccCCCCCCceEEEEecc-cccccCceeEEeeecchHHHHHHHHhccC-CCCCcceEEEEEecccc
Confidence            69999999999999999999999999999988 79999999999999999999999987644 67999999999999865

>cd01924 cyclophilin_TLP40_like cyclophilin_TLP40_like: cyclophilin-type peptidylprolyl cis- trans isomerases (cyclophilins) similar ot the Spinach thylakoid lumen protein TLP40

Probab=100.00  E-value=5.8e-34  Score=266.60  Aligned_cols=134  Identities=33%  Similarity=0.500  Sum_probs=108.8

Q ss_pred             EecceeEEEEecCCCChhHHHHHHHHHhcCccCCceEEEeecCcccccCCCCCCCCCC---------------------C
Q 007792            6 VTSLGDIVVDLFVDKCPLTTKNFLKLCKIKYYNGCLFHTVQKDFTAQTGDPTGTGTGG---------------------D   64 (589)
Q Consensus         6 ~T~~G~i~ieL~~~~aP~~~~nF~~l~~~~~Y~g~~f~rv~~~~~iq~Gd~~~~~~~~---------------------~   64 (589)
                      .|++|+|+|+||++.||+||.||++||+.+||+++.||||+++||||||++..++.+.                     .
T Consensus         3 ~T~~G~i~ieL~~~~aP~t~~NF~~L~~~g~Ydg~~FhRVi~~fviQgGdp~~~~~~~~~~~~~~~~~~p~e~~~~~~~~   82 (176)
T cd01924           3 ATDNGTITIVLDGYNAPVTAGNFVDLVERGFYDGMEFHRVEGGFVVQTGDPQGKNPGFPDPETGKSRTIPLEIKPEGQKQ   82 (176)
T ss_pred             ccccceEEEEEcCCCCCHHHHHHHHHHHhCCcCCCEEEEecCCcEEEecCCCCCCCCcccccccccccccceecccCCCC
Confidence            5999999999999999999999999999999999999999999999999998654332                     1


Q ss_pred             CcccccccccccccCCccccCCCCCCCceEEEeccC--CCCCcceEEEEeCC------CCCCCCCCcceEEEEecCHHHH
Q 007792           65 SVYKFLYGEQARFFGDEIRVDLKHAKTGTVAMASAG--ENLNASQFYMTLRD------NLDYLDEKHTIFGEVAEGLETL  136 (589)
Q Consensus        65 ~~~~~~~~~~~~~~~~e~~~~l~~~~~G~vs~a~~g--~~~~~sqFfI~l~~------~~~~ld~~~~vFG~Vv~G~~vl  136 (589)
                      ++|+..+..  . ...+..+.++|+.+|+||||+.+  +++++|||||++.+      .+|+||++|+|||+|++||+||
T Consensus        83 ~~~~~~~~~--~-~~~~~~~~~~~~~~G~laMa~~~~~~ns~~SQFfI~~~~~~~~~~~~~~Ldg~ytVFG~VveG~dvl  159 (176)
T cd01924          83 PVYGKTLEE--A-GRYDEQPVLPFNAFGAIAMARTEFDPNSASSQFFFLLKDNELTPSRNNVLDGRYAVFGYVTDGLDIL  159 (176)
T ss_pred             CccCccccc--c-cccccccccccCCCCeEEEccCCCCCCCccceEEEEeccccccCCCCCccCCCceEEEEEecCHHHH
Confidence            222210000  0 00222355667789999999987  68999999999983      4799999999999999999999


Q ss_pred             HHHhhC
Q 007792          137 SRINES  142 (589)
Q Consensus       137 ~~i~~~  142 (589)
                      ++|...
T Consensus       160 ~~I~~g  165 (176)
T cd01924         160 RELKVG  165 (176)
T ss_pred             HhhcCC
Confidence            999643

Compared to the archetypal cyclophilin Human cyclophilin A, these proteins have similar peptidylprolyl cis- trans isomerase activity and reduced affinity for cyclosporin A. Spinach TLP40 has been shown to have a dual function as a folding catalyst and regulator of dephosphorylation.

>KOG0865 consensus Cyclophilin type peptidyl-prolyl cis-trans isomerase [Posttranslational modification, protein turnover, chaperones]

Probab=99.95  E-value=1.7e-28  Score=223.37  Aligned_cols=146  Identities=40%  Similarity=0.676  Sum_probs=132.9

Q ss_pred             ecceeEEEEecCCCChhHHHHHHHHHhcC---ccCCceEEE---eecCcccccCCCC-CCCCCCCCcccccccccccccC
Q 007792            7 TSLGDIVVDLFVDKCPLTTKNFLKLCKIK---YYNGCLFHT---VQKDFTAQTGDPT-GTGTGGDSVYKFLYGEQARFFG   79 (589)
Q Consensus         7 T~~G~i~ieL~~~~aP~~~~nF~~l~~~~---~Y~g~~f~r---v~~~~~iq~Gd~~-~~~~~~~~~~~~~~~~~~~~~~   79 (589)
                      +++|+++++||.+..|+|++||..||.+.   -|.+.+||+   .+++||+||||++ .+++++.+||+       ..|+
T Consensus        15 ~p~gr~~~~l~ad~~Pktaenf~al~tgekg~~yk~s~fhr~~~~~~~fm~qggDft~hngtggkSiy~-------ekF~   87 (167)
T KOG0865|consen   15 EPLGRIVFELFADKIPKTAENFRALCTGEKGFGYKGSCFHRLIPIIPGFMCQGGDFTCHNGTGGKSIYG-------EKFD   87 (167)
T ss_pred             ccccccceecccccCcchHhhhhhcccCCCccccccchhhhccccccceeeccCcccccCCccceEecc-------cccC
Confidence            78999999999999999999999999753   399999999   3447999999998 78999999986       6788


Q ss_pred             CccccCCCCCCCceEEEeccCCCCCcceEEEEeCCCCCCCCCCcceEEEEecCHHHHHHHhhCccCCCCCcccceeeccc
Q 007792           80 DEIRVDLKHAKTGTVAMASAGENLNASQFYMTLRDNLDYLDEKHTIFGEVAEGLETLSRINESFVDEKNRPYKNIRIKHT  159 (589)
Q Consensus        80 ~e~~~~l~~~~~G~vs~a~~g~~~~~sqFfI~l~~~~~~ld~~~~vFG~Vv~G~~vl~~i~~~~~~~~~~p~~~i~I~~~  159 (589)
                      +| ++.|+|..+|+|+|||.||++|+|||||++.. +.|||++|+|||+|++||+|+++|+. ....++++.++|+|.+|
T Consensus        88 De-nFilkhtgpGiLSmaNagpntngsqffictak-tewLdgkhVVfGkv~eGm~iv~a~e~-~gs~~gk~~~~i~i~dc  164 (167)
T KOG0865|consen   88 DE-NFILKHTGPGILSMANAGPNTNGSQFFICTAK-TEWLDGKHVVFGKVKEGMDIVEAMER-FGSRNGKTSKKITIADC  164 (167)
T ss_pred             Cc-CcEEecCCCCeeehhhcCCCccccEEEEEccc-cccccCceeEcCceEcccchhhhhhc-cCCcCCcccccEEEecC
Confidence            88 69999999999999999999999999999998 59999999999999999999999976 45568899999999999


Q ss_pred             ccc
Q 007792          160 YIL  162 (589)
Q Consensus       160 ~vl  162 (589)
                      +.+
T Consensus       165 g~l  167 (167)
T KOG0865|consen  165 GQL  167 (167)
T ss_pred             CcC
Confidence            864

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

Probab=99.86  E-value=2.3e-20  Score=179.17  Aligned_cols=91  Identities=36%  Similarity=0.581  Sum_probs=84.9

Q ss_pred             CCCCceEEEecCCCCCCHHHHHHHhccCCCeEEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHhcCCceeCCeEEEEEe
Q 007792          239 KPPENVLFVCKLNPVTEDEDLHTIFSRFGTVVSAEIIRDFKTGDSLNYAFIEFENRQACERAYSKMDNALIDDRRIHVDF  318 (589)
Q Consensus       239 ~~~~~~i~V~nL~~~~te~~L~~~F~~~G~v~~~~i~~d~~tg~~~g~aFV~f~~~~~a~~A~~~l~g~~i~gr~i~V~~  318 (589)
                      ..|..||||+-|+++|+|..|+..|+.||+|+.|.||.++.||+++|||||+|+++.++..|++..+|++|+|+.|.|.+
T Consensus        98 gDPy~TLFv~RLnydT~EskLrreF~~YG~IkrirlV~d~vTgkskGYAFIeye~erdm~~AYK~adG~~Idgrri~VDv  177 (335)
T KOG0113|consen   98 GDPYKTLFVARLNYDTSESKLRREFEKYGPIKRIRLVRDKVTGKSKGYAFIEYEHERDMKAAYKDADGIKIDGRRILVDV  177 (335)
T ss_pred             CCccceeeeeeccccccHHHHHHHHHhcCcceeEEEeeecccCCccceEEEEeccHHHHHHHHHhccCceecCcEEEEEe
Confidence            46889999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             ccc-cccccccc
Q 007792          319 SQS-VSKLWNQF  329 (589)
Q Consensus       319 a~~-~~~~~~~~  329 (589)
                      ... +.+.|.+.
T Consensus       178 ERgRTvkgW~PR  189 (335)
T KOG0113|consen  178 ERGRTVKGWLPR  189 (335)
T ss_pred             cccccccccccc
Confidence            875 55566443

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

Probab=99.79  E-value=2.2e-18  Score=153.68  Aligned_cols=111  Identities=25%  Similarity=0.460  Sum_probs=90.6

Q ss_pred             CCCceEEEecCCCCCCHHHHHHHhccCCCeEEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHhcCCceeCCeEEEEEec
Q 007792          240 PPENVLFVCKLNPVTEDEDLHTIFSRFGTVVSAEIIRDFKTGDSLNYAFIEFENRQACERAYSKMDNALIDDRRIHVDFS  319 (589)
Q Consensus       240 ~~~~~i~V~nL~~~~te~~L~~~F~~~G~v~~~~i~~d~~tg~~~g~aFV~f~~~~~a~~A~~~l~g~~i~gr~i~V~~a  319 (589)
                      +..+.||||||+..+++.+|+.+|..||+|..|.|..+     +.|||||+|++..+|..|+..|+|..|+|..|.|+++
T Consensus         8 ~~~~kVYVGnL~~~a~k~eLE~~F~~yG~lrsvWvArn-----PPGfAFVEFed~RDA~DAvr~LDG~~~cG~r~rVE~S   82 (195)
T KOG0107|consen    8 NGNTKVYVGNLGSRATKRELERAFSKYGPLRSVWVARN-----PPGFAFVEFEDPRDAEDAVRYLDGKDICGSRIRVELS   82 (195)
T ss_pred             CCCceEEeccCCCCcchHHHHHHHHhcCcceeEEEeec-----CCCceEEeccCcccHHHHHhhcCCccccCceEEEEee
Confidence            34689999999999999999999999999999999886     5599999999999999999999999999999999999


Q ss_pred             cccccccccccCCCCCCCCCCCCccCCCCCCCCccCCC
Q 007792          320 QSVSKLWNQFRRRDHQTGKGKGCFKCGGLDHIAKDCTG  357 (589)
Q Consensus       320 ~~~~~~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~  357 (589)
                      +............  ...+...|+.||..+++.+.|..
T Consensus        83 ~G~~r~~r~gg~~--~~~g~~~~~r~G~rg~~~r~~~~  118 (195)
T KOG0107|consen   83 TGRPRGSRRGGSR--PPRGRGFCYRCGERGHIGRNCKD  118 (195)
T ss_pred             cCCccccccCCCC--CcccccccccCCCcccccccccc
Confidence            8755422211111  11223338889988887776655

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

Probab=99.73  E-value=5.1e-17  Score=147.59  Aligned_cols=85  Identities=32%  Similarity=0.485  Sum_probs=80.3

Q ss_pred             CCCceEEEecCCCCCCHHHHHHHhccCCCeEEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHhcCCceeCCeEEEEEec
Q 007792          240 PPENVLFVCKLNPVTEDEDLHTIFSRFGTVVSAEIIRDFKTGDSLNYAFIEFENRQACERAYSKMDNALIDDRRIHVDFS  319 (589)
Q Consensus       240 ~~~~~i~V~nL~~~~te~~L~~~F~~~G~v~~~~i~~d~~tg~~~g~aFV~f~~~~~a~~A~~~l~g~~i~gr~i~V~~a  319 (589)
                      ...++|||+|||+.+|+++|+++|.+||.|..|.|+.++.|++++|||||+|.+.++|+.||+.||+..|+|+.|.|+++
T Consensus        32 ~~~~~lfVgnL~~~~te~~L~~~F~~~G~I~~v~i~~d~~tg~~kGfaFV~F~~~e~A~~Al~~lng~~i~Gr~l~V~~a  111 (144)
T PLN03134         32 LMSTKLFIGGLSWGTDDASLRDAFAHFGDVVDAKVIVDRETGRSRGFGFVNFNDEGAATAAISEMDGKELNGRHIRVNPA  111 (144)
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHhcCCCeEEEEEEecCCCCCcceEEEEEECCHHHHHHHHHHcCCCEECCEEEEEEeC
Confidence            34679999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             ccccc
Q 007792          320 QSVSK  324 (589)
Q Consensus       320 ~~~~~  324 (589)
                      .+...
T Consensus       112 ~~~~~  116 (144)
T PLN03134        112 NDRPS  116 (144)
T ss_pred             CcCCC
Confidence            86443

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

Probab=99.60  E-value=1.2e-16  Score=143.16  Aligned_cols=80  Identities=28%  Similarity=0.482  Sum_probs=77.2

Q ss_pred             CceEEEecCCCCCCHHHHHHHhccCCCeEEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHhcCCceeCCeEEEEEeccc
Q 007792          242 ENVLFVCKLNPVTEDEDLHTIFSRFGTVVSAEIIRDFKTGDSLNYAFIEFENRQACERAYSKMDNALIDDRRIHVDFSQS  321 (589)
Q Consensus       242 ~~~i~V~nL~~~~te~~L~~~F~~~G~v~~~~i~~d~~tg~~~g~aFV~f~~~~~a~~A~~~l~g~~i~gr~i~V~~a~~  321 (589)
                      ..-|||||||+.+||.+|..+|++||+|+.|.++.|+.||+++||||+.|+++.+...|+..|||+.|.|+.|+|.+...
T Consensus        35 sA~Iyiggl~~~LtEgDil~VFSqyGe~vdinLiRDk~TGKSKGFaFLcYEDQRSTILAVDN~NGiki~gRtirVDHv~~  114 (219)
T KOG0126|consen   35 SAYIYIGGLPYELTEGDILCVFSQYGEIVDINLIRDKKTGKSKGFAFLCYEDQRSTILAVDNLNGIKILGRTIRVDHVSN  114 (219)
T ss_pred             ceEEEECCCcccccCCcEEEEeeccCceEEEEEEecCCCCcccceEEEEecCccceEEEEeccCCceecceeEEeeeccc
Confidence            46899999999999999999999999999999999999999999999999999999999999999999999999998654

>TIGR01661 ELAV_HUD_SF ELAV/HuD family splicing factor

Probab=99.57  E-value=1.3e-14  Score=152.62  Aligned_cols=83  Identities=27%  Similarity=0.503  Sum_probs=78.9

Q ss_pred             CCceEEEecCCCCCCHHHHHHHhccCCCeEEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHhcCCceeCCeEEEEEecc
Q 007792          241 PENVLFVCKLNPVTEDEDLHTIFSRFGTVVSAEIIRDFKTGDSLNYAFIEFENRQACERAYSKMDNALIDDRRIHVDFSQ  320 (589)
Q Consensus       241 ~~~~i~V~nL~~~~te~~L~~~F~~~G~v~~~~i~~d~~tg~~~g~aFV~f~~~~~a~~A~~~l~g~~i~gr~i~V~~a~  320 (589)
                      ...+|||+|||+.+++++|.++|++||.|..|+|+.+..||.++|||||+|.+.++|..||..|||..|+|+.|.|.|+.
T Consensus       268 ~~~~lfV~NL~~~~~e~~L~~~F~~fG~v~~v~i~~d~~t~~skG~aFV~F~~~~~A~~Ai~~lnG~~~~gr~i~V~~~~  347 (352)
T TIGR01661       268 AGYCIFVYNLSPDTDETVLWQLFGPFGAVQNVKIIRDLTTNQCKGYGFVSMTNYDEAAMAILSLNGYTLGNRVLQVSFKT  347 (352)
T ss_pred             CCcEEEEeCCCCCCCHHHHHHHHHhCCCeEEEEEeEcCCCCCccceEEEEECCHHHHHHHHHHhCCCEECCeEEEEEEcc
Confidence            34579999999999999999999999999999999999999999999999999999999999999999999999999997


Q ss_pred             ccc
Q 007792          321 SVS  323 (589)
Q Consensus       321 ~~~  323 (589)
                      ++.
T Consensus       348 ~~~  350 (352)
T TIGR01661       348 NKA  350 (352)
T ss_pred             CCC
Confidence            653

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

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

Probab=99.57  E-value=3.6e-14  Score=129.88  Aligned_cols=81  Identities=31%  Similarity=0.470  Sum_probs=78.0

Q ss_pred             CceEEEecCCCCCCHHHHHHHhccCCCeEEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHhcCCceeCCeEEEEEeccc
Q 007792          242 ENVLFVCKLNPVTEDEDLHTIFSRFGTVVSAEIIRDFKTGDSLNYAFIEFENRQACERAYSKMDNALIDDRRIHVDFSQS  321 (589)
Q Consensus       242 ~~~i~V~nL~~~~te~~L~~~F~~~G~v~~~~i~~d~~tg~~~g~aFV~f~~~~~a~~A~~~l~g~~i~gr~i~V~~a~~  321 (589)
                      -++|-|-||.+-|+.++|..+|++||.|.+|.|+.|+.|+.++|||||-|....+|+.|+++|+|.+|+|+.|.|++|+.
T Consensus        13 m~SLkVdNLTyRTspd~LrrvFekYG~vgDVyIPrdr~Tr~sRgFaFVrf~~k~daedA~damDG~~ldgRelrVq~ary   92 (256)
T KOG4207|consen   13 MTSLKVDNLTYRTSPDDLRRVFEKYGRVGDVYIPRDRYTRQSRGFAFVRFHDKRDAEDALDAMDGAVLDGRELRVQMARY   92 (256)
T ss_pred             ceeEEecceeccCCHHHHHHHHHHhCcccceecccccccccccceeEEEeeecchHHHHHHhhcceeeccceeeehhhhc
Confidence            36899999999999999999999999999999999999999999999999999999999999999999999999999975


Q ss_pred             c
Q 007792          322 V  322 (589)
Q Consensus       322 ~  322 (589)
                      .
T Consensus        93 g   93 (256)
T KOG4207|consen   93 G   93 (256)
T ss_pred             C
Confidence            3

>TIGR01659 sex-lethal sex-lethal family splicing factor

Probab=99.56  E-value=1e-13  Score=143.80  Aligned_cols=84  Identities=29%  Similarity=0.553  Sum_probs=78.0

Q ss_pred             CCceEEEecCCCCCCHHHHHHHhccCCCeEEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHhcCCceeCC--eEEEEEe
Q 007792          241 PENVLFVCKLNPVTEDEDLHTIFSRFGTVVSAEIIRDFKTGDSLNYAFIEFENRQACERAYSKMDNALIDD--RRIHVDF  318 (589)
Q Consensus       241 ~~~~i~V~nL~~~~te~~L~~~F~~~G~v~~~~i~~d~~tg~~~g~aFV~f~~~~~a~~A~~~l~g~~i~g--r~i~V~~  318 (589)
                      ..++|||+|||+.+|+++|+++|++||.|+.|.|+.++.+++++|||||+|.+.++|++||+.||+..|.|  ++|.|.+
T Consensus       192 ~~~~lfV~nLp~~vtee~L~~~F~~fG~V~~v~i~~d~~tg~~kG~aFV~F~~~e~A~~Ai~~lng~~~~g~~~~l~V~~  271 (346)
T TIGR01659       192 KDTNLYVTNLPRTITDDQLDTIFGKYGQIVQKNILRDKLTGTPRGVAFVRFNKREEAQEAISALNNVIPEGGSQPLTVRL  271 (346)
T ss_pred             ccceeEEeCCCCcccHHHHHHHHHhcCCEEEEEEeecCCCCccceEEEEEECCHHHHHHHHHHhCCCccCCCceeEEEEE
Confidence            45789999999999999999999999999999999999999999999999999999999999999998876  7899999


Q ss_pred             cccccc
Q 007792          319 SQSVSK  324 (589)
Q Consensus       319 a~~~~~  324 (589)
                      +....+
T Consensus       272 a~~~~~  277 (346)
T TIGR01659       272 AEEHGK  277 (346)
T ss_pred             CCcccc
Confidence            986443

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

>PF00076 RRM_1: RNA recognition motif

Probab=99.55  E-value=2.3e-14  Score=113.49  Aligned_cols=70  Identities=36%  Similarity=0.726  Sum_probs=67.3

Q ss_pred             EEEecCCCCCCHHHHHHHhccCCCeEEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHhcCCceeCCeEEE
Q 007792          245 LFVCKLNPVTEDEDLHTIFSRFGTVVSAEIIRDFKTGDSLNYAFIEFENRQACERAYSKMDNALIDDRRIH  315 (589)
Q Consensus       245 i~V~nL~~~~te~~L~~~F~~~G~v~~~~i~~d~~tg~~~g~aFV~f~~~~~a~~A~~~l~g~~i~gr~i~  315 (589)
                      |||+|||+++|+++|.++|++||.|..+.++.+ .++..++||||+|.+.++|..|++.|+|..|.|+.|+
T Consensus         1 l~v~nlp~~~t~~~l~~~f~~~g~i~~~~~~~~-~~~~~~~~a~V~F~~~~~a~~a~~~l~g~~~~~~~ir   70 (70)
T PF00076_consen    1 LYVGNLPPDVTEEELRDFFSQFGKIESIKVMRN-SSGKSKGYAFVEFESEEDAEKALEELNGKKINGRKIR   70 (70)
T ss_dssp             EEEESETTTSSHHHHHHHHHTTSTEEEEEEEEE-TTSSEEEEEEEEESSHHHHHHHHHHHTTEEETTEEEE
T ss_pred             cEEcCCCCcCCHHHHHHHHHHhhhccccccccc-ccccccceEEEEEcCHHHHHHHHHHcCCCEECccCcC
Confidence            799999999999999999999999999999987 7788999999999999999999999999999999985

(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 ....

>TIGR01659 sex-lethal sex-lethal family splicing factor

Probab=99.55  E-value=2.2e-14  Score=148.74  Aligned_cols=83  Identities=27%  Similarity=0.553  Sum_probs=79.6

Q ss_pred             CCCCceEEEecCCCCCCHHHHHHHhccCCCeEEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHhcCCceeCCeEEEEEe
Q 007792          239 KPPENVLFVCKLNPVTEDEDLHTIFSRFGTVVSAEIIRDFKTGDSLNYAFIEFENRQACERAYSKMDNALIDDRRIHVDF  318 (589)
Q Consensus       239 ~~~~~~i~V~nL~~~~te~~L~~~F~~~G~v~~~~i~~d~~tg~~~g~aFV~f~~~~~a~~A~~~l~g~~i~gr~i~V~~  318 (589)
                      ....++|||+|||+++|+++|+++|..||+|+.|+|+.++.|++++|||||+|.+.++|..||+.|||..|.+++|+|.+
T Consensus       104 ~~~~~~LfVgnLp~~~te~~L~~lF~~~G~V~~v~i~~d~~tg~srGyaFVeF~~~e~A~~Ai~~LnG~~l~gr~i~V~~  183 (346)
T TIGR01659       104 NNSGTNLIVNYLPQDMTDRELYALFRTIGPINTCRIMRDYKTGYSFGYAFVDFGSEADSQRAIKNLNGITVRNKRLKVSY  183 (346)
T ss_pred             CCCCcEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEecCCCCccCcEEEEEEccHHHHHHHHHHcCCCccCCceeeeec
Confidence            44678999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             ccc
Q 007792          319 SQS  321 (589)
Q Consensus       319 a~~  321 (589)
                      +++
T Consensus       184 a~p  186 (346)
T TIGR01659       184 ARP  186 (346)
T ss_pred             ccc
Confidence            875

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=99.54  E-value=2.2e-14  Score=151.06  Aligned_cols=83  Identities=24%  Similarity=0.522  Sum_probs=79.3

Q ss_pred             CCceEEEecCCCCCCHHHHHHHhccCCCeEEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHhcCCceeCCeEEEEEecc
Q 007792          241 PENVLFVCKLNPVTEDEDLHTIFSRFGTVVSAEIIRDFKTGDSLNYAFIEFENRQACERAYSKMDNALIDDRRIHVDFSQ  320 (589)
Q Consensus       241 ~~~~i~V~nL~~~~te~~L~~~F~~~G~v~~~~i~~d~~tg~~~g~aFV~f~~~~~a~~A~~~l~g~~i~gr~i~V~~a~  320 (589)
                      +.++|||+|||+.+|+++|+++|+.||+|..|+|+.++.+|+++|||||+|.+.++|..||..|||..|.|+.|.|.+++
T Consensus         2 ~~~~l~V~nLp~~~~e~~l~~~F~~~G~i~~v~i~~d~~~g~s~g~afV~f~~~~~A~~Ai~~l~g~~l~g~~i~v~~a~   81 (352)
T TIGR01661         2 SKTNLIVNYLPQTMTQEEIRSLFTSIGEIESCKLVRDKVTGQSLGYGFVNYVRPEDAEKAVNSLNGLRLQNKTIKVSYAR   81 (352)
T ss_pred             CCcEEEEeCCCCCCCHHHHHHHHHccCCEEEEEEEEcCCCCccceEEEEEECcHHHHHHHHhhcccEEECCeeEEEEeec
Confidence            46899999999999999999999999999999999999999999999999999999999999999999999999999997


Q ss_pred             ccc
Q 007792          321 SVS  323 (589)
Q Consensus       321 ~~~  323 (589)
                      +..
T Consensus        82 ~~~   84 (352)
T TIGR01661        82 PSS   84 (352)
T ss_pred             ccc
Confidence            643

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

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

Probab=99.53  E-value=2.2e-14  Score=121.54  Aligned_cols=81  Identities=22%  Similarity=0.386  Sum_probs=77.1

Q ss_pred             CCceEEEecCCCCCCHHHHHHHhccCCCeEEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHhcCCceeCCeEEEEEecc
Q 007792          241 PENVLFVCKLNPVTEDEDLHTIFSRFGTVVSAEIIRDFKTGDSLNYAFIEFENRQACERAYSKMDNALIDDRRIHVDFSQ  320 (589)
Q Consensus       241 ~~~~i~V~nL~~~~te~~L~~~F~~~G~v~~~~i~~d~~tg~~~g~aFV~f~~~~~a~~A~~~l~g~~i~gr~i~V~~a~  320 (589)
                      ..+|||||||++.|+|++|.++|+++|+|..|-|-.|+.+..+.|||||+|.+.++|..|++.++|+.++.++|.|.|.-
T Consensus        35 ~S~tvyVgNlSfyttEEqiyELFs~cG~irriiMGLdr~kktpCGFCFVeyy~~~dA~~AlryisgtrLddr~ir~D~D~  114 (153)
T KOG0121|consen   35 KSCTVYVGNLSFYTTEEQIYELFSKCGDIRRIIMGLDRFKKTPCGFCFVEYYSRDDAEDALRYISGTRLDDRPIRIDWDA  114 (153)
T ss_pred             hcceEEEeeeeeeecHHHHHHHHHhccchheeEeccccCCcCccceEEEEEecchhHHHHHHHhccCcccccceeeeccc
Confidence            36899999999999999999999999999999999999999999999999999999999999999999999999999975


Q ss_pred             c
Q 007792          321 S  321 (589)
Q Consensus       321 ~  321 (589)
                      .
T Consensus       115 G  115 (153)
T KOG0121|consen  115 G  115 (153)
T ss_pred             c
Confidence            4

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

Probab=99.51  E-value=4.6e-14  Score=132.65  Aligned_cols=82  Identities=28%  Similarity=0.479  Sum_probs=79.3

Q ss_pred             CCceEEEecCCCCCCHHHHHHHhccCCCeEEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHhcCCceeCCeEEEEEecc
Q 007792          241 PENVLFVCKLNPVTEDEDLHTIFSRFGTVVSAEIIRDFKTGDSLNYAFIEFENRQACERAYSKMDNALIDDRRIHVDFSQ  320 (589)
Q Consensus       241 ~~~~i~V~nL~~~~te~~L~~~F~~~G~v~~~~i~~d~~tg~~~g~aFV~f~~~~~a~~A~~~l~g~~i~gr~i~V~~a~  320 (589)
                      ..++|-|.||+.++++.+|+++|.+||.|..|.|+.|+.||.++|||||.|.+.++|.+||..|||.-++.-.|.|+|++
T Consensus       188 D~~tvRvtNLsed~~E~dL~eLf~~fg~i~rvylardK~TG~~kGFAFVtF~sRddA~rAI~~LnG~gyd~LILrvEwsk  267 (270)
T KOG0122|consen  188 DEATVRVTNLSEDMREDDLEELFRPFGPITRVYLARDKETGLSKGFAFVTFESRDDAARAIADLNGYGYDNLILRVEWSK  267 (270)
T ss_pred             ccceeEEecCccccChhHHHHHhhccCccceeEEEEccccCcccceEEEEEecHHHHHHHHHHccCcccceEEEEEEecC
Confidence            45789999999999999999999999999999999999999999999999999999999999999999999999999998


Q ss_pred             cc
Q 007792          321 SV  322 (589)
Q Consensus       321 ~~  322 (589)
                      |.
T Consensus       268 P~  269 (270)
T KOG0122|consen  268 PS  269 (270)
T ss_pred             CC
Confidence            74

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

Probab=99.51  E-value=1.9e-14  Score=138.07  Aligned_cols=105  Identities=28%  Similarity=0.649  Sum_probs=93.7

Q ss_pred             CCceEEEecCCCCCCHHHHHHHhccCCCeEEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHhcCCceeCCeEEEEEecc
Q 007792          241 PENVLFVCKLNPVTEDEDLHTIFSRFGTVVSAEIIRDFKTGDSLNYAFIEFENRQACERAYSKMDNALIDDRRIHVDFSQ  320 (589)
Q Consensus       241 ~~~~i~V~nL~~~~te~~L~~~F~~~G~v~~~~i~~d~~tg~~~g~aFV~f~~~~~a~~A~~~l~g~~i~gr~i~V~~a~  320 (589)
                      +.++||||||.+.++.++|+..|.+||+|+.|.|+.+        |+||.|.-.++|..|+..|+|.+|.|++|+|+++.
T Consensus        77 ~stkl~vgNis~tctn~ElRa~fe~ygpviecdivkd--------y~fvh~d~~eda~~air~l~~~~~~gk~m~vq~st  148 (346)
T KOG0109|consen   77 ASTKLHVGNISPTCTNQELRAKFEKYGPVIECDIVKD--------YAFVHFDRAEDAVEAIRGLDNTEFQGKRMHVQLST  148 (346)
T ss_pred             CccccccCCCCccccCHHHhhhhcccCCceeeeeecc--------eeEEEEeeccchHHHHhcccccccccceeeeeeec
Confidence            5689999999999999999999999999999999874        99999999999999999999999999999999998


Q ss_pred             ccccccccccCCCCCCCCCCCCccCCCCCCCCccCCCCCC
Q 007792          321 SVSKLWNQFRRRDHQTGKGKGCFKCGGLDHIAKDCTGQQP  360 (589)
Q Consensus       321 ~~~~~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~~~  360 (589)
                      +...       ...+.+...+|++||..|||+++||....
T Consensus       149 srlr-------tapgmgDq~~cyrcGkeghwskEcP~~~~  181 (346)
T KOG0109|consen  149 SRLR-------TAPGMGDQSGCYRCGKEGHWSKECPVDRT  181 (346)
T ss_pred             cccc-------cCCCCCCHHHheeccccccccccCCccCC
Confidence            7543       22334556679999999999999998743

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

Probab=99.49  E-value=4.9e-14  Score=132.10  Aligned_cols=80  Identities=31%  Similarity=0.510  Sum_probs=74.3

Q ss_pred             CCceEEEecCCCCCCHHHHHHHhccCCCeEEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHhcCCceeCCeEEEEEecc
Q 007792          241 PENVLFVCKLNPVTEDEDLHTIFSRFGTVVSAEIIRDFKTGDSLNYAFIEFENRQACERAYSKMDNALIDDRRIHVDFSQ  320 (589)
Q Consensus       241 ~~~~i~V~nL~~~~te~~L~~~F~~~G~v~~~~i~~d~~tg~~~g~aFV~f~~~~~a~~A~~~l~g~~i~gr~i~V~~a~  320 (589)
                      ..++||||+|+|.|..+.|+.+|++||+|+++.|+.|+.||+++|||||+|.+.++|.+|++..| -.|+|++.+|++|.
T Consensus        11 ~~TKifVggL~w~T~~~~l~~yFeqfGeI~eavvitd~~t~rskGyGfVTf~d~~aa~rAc~dp~-piIdGR~aNcnlA~   89 (247)
T KOG0149|consen   11 TFTKIFVGGLAWETHKETLRRYFEQFGEIVEAVVITDKNTGRSKGYGFVTFRDAEAATRACKDPN-PIIDGRKANCNLAS   89 (247)
T ss_pred             eEEEEEEcCcccccchHHHHHHHHHhCceEEEEEEeccCCccccceeeEEeecHHHHHHHhcCCC-Ccccccccccchhh
Confidence            45799999999999999999999999999999999999999999999999999999999997544 57999999999886


Q ss_pred             c
Q 007792          321 S  321 (589)
Q Consensus       321 ~  321 (589)
                      -
T Consensus        90 l   90 (247)
T KOG0149|consen   90 L   90 (247)
T ss_pred             h
Confidence            4

>PF14259 RRM_6: RNA recognition motif (a

Probab=99.46  E-value=4.1e-13  Score=106.59  Aligned_cols=70  Identities=34%  Similarity=0.697  Sum_probs=65.1

Q ss_pred             EEEecCCCCCCHHHHHHHhccCCCeEEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHhcCCceeCCeEEE
Q 007792          245 LFVCKLNPVTEDEDLHTIFSRFGTVVSAEIIRDFKTGDSLNYAFIEFENRQACERAYSKMDNALIDDRRIH  315 (589)
Q Consensus       245 i~V~nL~~~~te~~L~~~F~~~G~v~~~~i~~d~~tg~~~g~aFV~f~~~~~a~~A~~~l~g~~i~gr~i~  315 (589)
                      |||+|||+.+++++|.++|..||.|..+.+..++. +.++|+|||+|.+.++|..|+..++|..|+|+.|.
T Consensus         1 v~i~nlp~~~~~~~l~~~f~~~g~v~~v~~~~~~~-~~~~~~a~v~f~~~~~a~~al~~~~~~~~~g~~l~   70 (70)
T PF14259_consen    1 VYISNLPPSTTEEDLRNFFSRFGPVEKVRLIKNKD-GQSRGFAFVEFSSEEDAKRALELLNGKEIDGRKLR   70 (70)
T ss_dssp             EEEESSTTT--HHHHHHHCTTSSBEEEEEEEESTT-SSEEEEEEEEESSHHHHHHHHHHHTTEEETTEEEE
T ss_pred             CEEeCCCCCCCHHHHHHHHHhcCCcceEEEEeeec-cccCCEEEEEeCCHHHHHHHHHHCCCcEECCEEcC
Confidence            79999999999999999999999999999999877 89999999999999999999999999999999884

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 ....

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

Probab=99.45  E-value=2.2e-13  Score=148.75  Aligned_cols=82  Identities=22%  Similarity=0.391  Sum_probs=78.4

Q ss_pred             CCceEEEecCCCCCCHHHHHHHhccCCCeEEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHhcCCceeCCeEEEEEecc
Q 007792          241 PENVLFVCKLNPVTEDEDLHTIFSRFGTVVSAEIIRDFKTGDSLNYAFIEFENRQACERAYSKMDNALIDDRRIHVDFSQ  320 (589)
Q Consensus       241 ~~~~i~V~nL~~~~te~~L~~~F~~~G~v~~~~i~~d~~tg~~~g~aFV~f~~~~~a~~A~~~l~g~~i~gr~i~V~~a~  320 (589)
                      ..++|||+||++.+++++|+++|+.||.|..|.|+.++.+++++|||||+|.+.++|..||..|||+.|+|+.|.|.++.
T Consensus       203 ~~~rLfVgnLp~~vteedLk~lFs~FG~I~svrl~~D~~tgksKGfGFVeFe~~e~A~kAI~amNg~elgGr~LrV~kAi  282 (612)
T TIGR01645       203 KFNRIYVASVHPDLSETDIKSVFEAFGEIVKCQLARAPTGRGHKGYGFIEYNNLQSQSEAIASMNLFDLGGQYLRVGKCV  282 (612)
T ss_pred             ccceEEeecCCCCCCHHHHHHHHhhcCCeeEEEEEecCCCCCcCCeEEEEECCHHHHHHHHHHhCCCeeCCeEEEEEecC
Confidence            35799999999999999999999999999999999999999999999999999999999999999999999999999987


Q ss_pred             cc
Q 007792          321 SV  322 (589)
Q Consensus       321 ~~  322 (589)
                      +.
T Consensus       283 ~p  284 (612)
T TIGR01645       283 TP  284 (612)
T ss_pred             CC
Confidence            53

In the case of PUF60 (GP|6176532), in complex with p54, and in the presence of U2AF, facilitates association of U2 snRNP with pre-mRNA.

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

Probab=99.44  E-value=1.6e-13  Score=117.25  Aligned_cols=81  Identities=22%  Similarity=0.420  Sum_probs=77.9

Q ss_pred             CceEEEecCCCCCCHHHHHHHhccCCCeEEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHhcCCceeCCeEEEEEeccc
Q 007792          242 ENVLFVCKLNPVTEDEDLHTIFSRFGTVVSAEIIRDFKTGDSLNYAFIEFENRQACERAYSKMDNALIDDRRIHVDFSQS  321 (589)
Q Consensus       242 ~~~i~V~nL~~~~te~~L~~~F~~~G~v~~~~i~~d~~tg~~~g~aFV~f~~~~~a~~A~~~l~g~~i~gr~i~V~~a~~  321 (589)
                      .-+|||.++...+|+++|...|..||+|+.|.+..|..||..+|||+|+|++.++|++|+..|||..|.|..|.|.|+-.
T Consensus        72 GwIi~VtgvHeEatEedi~d~F~dyGeiKNihLNLDRRtGy~KGYaLvEYet~keAq~A~~~~Ng~~ll~q~v~VDw~Fv  151 (170)
T KOG0130|consen   72 GWIIFVTGVHEEATEEDIHDKFADYGEIKNIHLNLDRRTGYVKGYALVEYETLKEAQAAIDALNGAELLGQNVSVDWCFV  151 (170)
T ss_pred             eEEEEEeccCcchhHHHHHHHHhhcccccceeeccccccccccceeeeehHhHHHHHHHHHhccchhhhCCceeEEEEEe
Confidence            46899999999999999999999999999999999999999999999999999999999999999999999999999865


Q ss_pred             c
Q 007792          322 V  322 (589)
Q Consensus       322 ~  322 (589)
                      .
T Consensus       152 ~  152 (170)
T KOG0130|consen  152 K  152 (170)
T ss_pred             c
Confidence            3

>PLN03213 repressor of silencing 3; Provisional

Probab=99.42  E-value=5.4e-13  Score=136.02  Aligned_cols=77  Identities=23%  Similarity=0.403  Sum_probs=72.0

Q ss_pred             CCceEEEecCCCCCCHHHHHHHhccCCCeEEEEEeecCCCCCcccEEEEEEcCH--HHHHHHHHhcCCceeCCeEEEEEe
Q 007792          241 PENVLFVCKLNPVTEDEDLHTIFSRFGTVVSAEIIRDFKTGDSLNYAFIEFENR--QACERAYSKMDNALIDDRRIHVDF  318 (589)
Q Consensus       241 ~~~~i~V~nL~~~~te~~L~~~F~~~G~v~~~~i~~d~~tg~~~g~aFV~f~~~--~~a~~A~~~l~g~~i~gr~i~V~~  318 (589)
                      ....||||||++.+|+++|..+|+.||.|..|.|+  +.||  +|||||+|...  .++.+||..|||..|.|+.|+|+.
T Consensus         9 ~gMRIYVGNLSydVTEDDLravFSeFGsVkdVEIp--RETG--RGFAFVEMssdddaEeeKAISaLNGAEWKGR~LKVNK   84 (759)
T PLN03213          9 GGVRLHVGGLGESVGRDDLLKIFSPMGTVDAVEFV--RTKG--RSFAYIDFSPSSTNSLTKLFSTYNGCVWKGGRLRLEK   84 (759)
T ss_pred             cceEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEe--cccC--CceEEEEecCCcHHHHHHHHHHhcCCeecCceeEEee
Confidence            45799999999999999999999999999999999  4677  89999999987  789999999999999999999999


Q ss_pred             ccc
Q 007792          319 SQS  321 (589)
Q Consensus       319 a~~  321 (589)
                      |++
T Consensus        85 AKP   87 (759)
T PLN03213         85 AKE   87 (759)
T ss_pred             ccH
Confidence            876

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

Probab=99.42  E-value=5.8e-13  Score=145.42  Aligned_cols=81  Identities=22%  Similarity=0.393  Sum_probs=77.0

Q ss_pred             CCceEEEecCCCCCCHHHHHHHhccCCCeEEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHhcCCceeCCeEEEEEecc
Q 007792          241 PENVLFVCKLNPVTEDEDLHTIFSRFGTVVSAEIIRDFKTGDSLNYAFIEFENRQACERAYSKMDNALIDDRRIHVDFSQ  320 (589)
Q Consensus       241 ~~~~i~V~nL~~~~te~~L~~~F~~~G~v~~~~i~~d~~tg~~~g~aFV~f~~~~~a~~A~~~l~g~~i~gr~i~V~~a~  320 (589)
                      ..++|||+||++.+++++|+++|.+||+|..|.|+.++.||+++|||||+|.+.++|..||..|||..|.|+.|.|.+..
T Consensus       106 ~~~rLfVGnLp~~~tEe~Lr~lF~~fG~I~sV~I~~D~~TgkskGfAFVeF~s~e~A~~Ai~~lnG~~i~GR~IkV~rp~  185 (612)
T TIGR01645       106 IMCRVYVGSISFELREDTIRRAFDPFGPIKSINMSWDPATGKHKGFAFVEYEVPEAAQLALEQMNGQMLGGRNIKVGRPS  185 (612)
T ss_pred             CCCEEEEcCCCCCCCHHHHHHHHHccCCEEEEEEeecCCCCCcCCeEEEEeCcHHHHHHHHHhcCCeEEecceeeecccc
Confidence            45799999999999999999999999999999999999999999999999999999999999999999999999998654


Q ss_pred             c
Q 007792          321 S  321 (589)
Q Consensus       321 ~  321 (589)
                      .
T Consensus       186 ~  186 (612)
T TIGR01645       186 N  186 (612)
T ss_pred             c
Confidence            3

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.

>PLN03120 nucleic acid binding protein; Provisional

Probab=99.42  E-value=7.6e-13  Score=128.63  Aligned_cols=76  Identities=18%  Similarity=0.304  Sum_probs=70.9

Q ss_pred             CceEEEecCCCCCCHHHHHHHhccCCCeEEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHhcCCceeCCeEEEEEeccc
Q 007792          242 ENVLFVCKLNPVTEDEDLHTIFSRFGTVVSAEIIRDFKTGDSLNYAFIEFENRQACERAYSKMDNALIDDRRIHVDFSQS  321 (589)
Q Consensus       242 ~~~i~V~nL~~~~te~~L~~~F~~~G~v~~~~i~~d~~tg~~~g~aFV~f~~~~~a~~A~~~l~g~~i~gr~i~V~~a~~  321 (589)
                      .++|||+|||+.+|+++|+++|+.||+|..|.|+.+..   .+|||||+|.+.++|..|| .|||..|.|+.|.|.++..
T Consensus         4 ~rtVfVgNLs~~tTE~dLrefFS~~G~I~~V~I~~d~~---~~GfAFVtF~d~eaAe~Al-lLnG~~l~gr~V~Vt~a~~   79 (260)
T PLN03120          4 VRTVKVSNVSLKATERDIKEFFSFSGDIEYVEMQSENE---RSQIAYVTFKDPQGAETAL-LLSGATIVDQSVTITPAED   79 (260)
T ss_pred             CCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEeecCC---CCCEEEEEeCcHHHHHHHH-HhcCCeeCCceEEEEeccC
Confidence            47999999999999999999999999999999998754   4699999999999999999 5999999999999999864

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

Probab=99.40  E-value=1.6e-12  Score=141.92  Aligned_cols=81  Identities=27%  Similarity=0.469  Sum_probs=77.9

Q ss_pred             CCceEEEecCCCCCCHHHHHHHhccCCCeEEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHhcCCceeCCeEEEEEecc
Q 007792          241 PENVLFVCKLNPVTEDEDLHTIFSRFGTVVSAEIIRDFKTGDSLNYAFIEFENRQACERAYSKMDNALIDDRRIHVDFSQ  320 (589)
Q Consensus       241 ~~~~i~V~nL~~~~te~~L~~~F~~~G~v~~~~i~~d~~tg~~~g~aFV~f~~~~~a~~A~~~l~g~~i~gr~i~V~~a~  320 (589)
                      ...+|||+|||+.+|+++|.++|++||.|..|.|+.+..+|+++|||||+|.+.++|..||..|||..|.|+.|.|.|+.
T Consensus       185 ~~~~l~v~nl~~~~te~~l~~~f~~~G~i~~v~~~~d~~~g~~~g~afV~f~~~e~A~~A~~~l~g~~i~g~~i~v~~a~  264 (457)
T TIGR01622       185 NFLKLYVGNLHFNITEQELRQIFEPFGDIEDVQLHRDPETGRSKGFGFIQFHDAEEAKEALEVMNGFELAGRPIKVGYAQ  264 (457)
T ss_pred             CCCEEEEcCCCCCCCHHHHHHHHHhcCCeEEEEEEEcCCCCccceEEEEEECCHHHHHHHHHhcCCcEECCEEEEEEEcc
Confidence            46899999999999999999999999999999999999999999999999999999999999999999999999999986


Q ss_pred             c
Q 007792          321 S  321 (589)
Q Consensus       321 ~  321 (589)
                      .
T Consensus       265 ~  265 (457)
T TIGR01622       265 D  265 (457)
T ss_pred             C
Confidence            4

A homologous gene from Plasmodium falciparum was identified in the course of the analysis of that genome at TIGR and was included in the model.

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

Probab=99.38  E-value=2.4e-12  Score=130.53  Aligned_cols=85  Identities=22%  Similarity=0.400  Sum_probs=78.9

Q ss_pred             CCCceEEEecCCCCCCHHHHHHHhccCCCeEEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHhcCCceeC-CeEEEEEe
Q 007792          240 PPENVLFVCKLNPVTEDEDLHTIFSRFGTVVSAEIIRDFKTGDSLNYAFIEFENRQACERAYSKMDNALID-DRRIHVDF  318 (589)
Q Consensus       240 ~~~~~i~V~nL~~~~te~~L~~~F~~~G~v~~~~i~~d~~tg~~~g~aFV~f~~~~~a~~A~~~l~g~~i~-gr~i~V~~  318 (589)
                      +..+-||||.||.++.|++|..+|++.|+|-.++|++|+.+|.++|||||+|.+.+.|+.||+.||+.+|. |+.|.|..
T Consensus        81 ~~G~EVfvGkIPrD~~EdeLvplfEkiG~I~elRLMmD~~sG~nRGYAFVtf~~Ke~Aq~Aik~lnn~Eir~GK~igvc~  160 (506)
T KOG0117|consen   81 PRGCEVFVGKIPRDVFEDELVPLFEKIGKIYELRLMMDPFSGDNRGYAFVTFCTKEEAQEAIKELNNYEIRPGKLLGVCV  160 (506)
T ss_pred             CCCceEEecCCCccccchhhHHHHHhccceeeEEEeecccCCCCcceEEEEeecHHHHHHHHHHhhCccccCCCEeEEEE
Confidence            45689999999999999999999999999999999999999999999999999999999999999999985 99999988


Q ss_pred             cccccc
Q 007792          319 SQSVSK  324 (589)
Q Consensus       319 a~~~~~  324 (589)
                      +..+..
T Consensus       161 Svan~R  166 (506)
T KOG0117|consen  161 SVANCR  166 (506)
T ss_pred             eeecce
Confidence            765443

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

Probab=99.38  E-value=7.4e-13  Score=126.12  Aligned_cols=82  Identities=32%  Similarity=0.605  Sum_probs=79.0

Q ss_pred             CceEEEecCCCCCCHHHHHHHhccCCCeEEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHhcCCceeCCeEEEEEeccc
Q 007792          242 ENVLFVCKLNPVTEDEDLHTIFSRFGTVVSAEIIRDFKTGDSLNYAFIEFENRQACERAYSKMDNALIDDRRIHVDFSQS  321 (589)
Q Consensus       242 ~~~i~V~nL~~~~te~~L~~~F~~~G~v~~~~i~~d~~tg~~~g~aFV~f~~~~~a~~A~~~l~g~~i~gr~i~V~~a~~  321 (589)
                      ...|||+.|...++-+.|++.|.+||+|.+++|++|..|+|++|||||.|...++|+.||..|||..|+++.|+-.||.-
T Consensus        62 hfhvfvgdls~eI~~e~lr~aF~pFGevS~akvirD~~T~KsKGYgFVSf~~k~dAEnAI~~MnGqWlG~R~IRTNWATR  141 (321)
T KOG0148|consen   62 HFHVFVGDLSPEIDNEKLREAFAPFGEVSDAKVIRDMNTGKSKGYGFVSFPNKEDAENAIQQMNGQWLGRRTIRTNWATR  141 (321)
T ss_pred             ceeEEehhcchhcchHHHHHHhccccccccceEeecccCCcccceeEEeccchHHHHHHHHHhCCeeeccceeecccccc
Confidence            46899999999999999999999999999999999999999999999999999999999999999999999999999976


Q ss_pred             cc
Q 007792          322 VS  323 (589)
Q Consensus       322 ~~  323 (589)
                      ++
T Consensus       142 Kp  143 (321)
T KOG0148|consen  142 KP  143 (321)
T ss_pred             Cc
Confidence            55

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

Probab=99.37  E-value=2.6e-12  Score=142.12  Aligned_cols=82  Identities=20%  Similarity=0.408  Sum_probs=78.4

Q ss_pred             CCceEEEecCCCCCCHHHHHHHhccCCCeEEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHhcCCceeCCeEEEEEecc
Q 007792          241 PENVLFVCKLNPVTEDEDLHTIFSRFGTVVSAEIIRDFKTGDSLNYAFIEFENRQACERAYSKMDNALIDDRRIHVDFSQ  320 (589)
Q Consensus       241 ~~~~i~V~nL~~~~te~~L~~~F~~~G~v~~~~i~~d~~tg~~~g~aFV~f~~~~~a~~A~~~l~g~~i~gr~i~V~~a~  320 (589)
                      ...+|||+|||+.+|+++|.++|+.||.|..+.|+.+..+|.++|||||+|.+.++|..||..|||..|.|+.|.|.++.
T Consensus       294 ~~~~l~v~nlp~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~afv~f~~~~~a~~A~~~l~g~~~~~~~l~v~~a~  373 (509)
T TIGR01642       294 SKDRIYIGNLPLYLGEDQIKELLESFGDLKAFNLIKDIATGLSKGYAFCEYKDPSVTDVAIAALNGKDTGDNKLHVQRAC  373 (509)
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEecCCCCCcCeEEEEEECCHHHHHHHHHHcCCCEECCeEEEEEECc
Confidence            46799999999999999999999999999999999999999999999999999999999999999999999999999987


Q ss_pred             cc
Q 007792          321 SV  322 (589)
Q Consensus       321 ~~  322 (589)
                      ..
T Consensus       374 ~~  375 (509)
T TIGR01642       374 VG  375 (509)
T ss_pred             cC
Confidence            53

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

>PLN03121 nucleic acid binding protein; Provisional

Probab=99.36  E-value=3.3e-12  Score=122.15  Aligned_cols=77  Identities=27%  Similarity=0.358  Sum_probs=70.6

Q ss_pred             CCCceEEEecCCCCCCHHHHHHHhccCCCeEEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHhcCCceeCCeEEEEEec
Q 007792          240 PPENVLFVCKLNPVTEDEDLHTIFSRFGTVVSAEIIRDFKTGDSLNYAFIEFENRQACERAYSKMDNALIDDRRIHVDFS  319 (589)
Q Consensus       240 ~~~~~i~V~nL~~~~te~~L~~~F~~~G~v~~~~i~~d~~tg~~~g~aFV~f~~~~~a~~A~~~l~g~~i~gr~i~V~~a  319 (589)
                      +...+|||+||++.+|+++|++||+.||+|..|.|+.+..   ..+||||+|.+.++|..|| .|+|..|.++.|.|...
T Consensus         3 ~~g~TV~V~NLS~~tTE~dLrefFS~~G~I~~V~I~~D~e---t~gfAfVtF~d~~aaetAl-lLnGa~l~d~~I~It~~   78 (243)
T PLN03121          3 PGGYTAEVTNLSPKATEKDVYDFFSHCGAIEHVEIIRSGE---YACTAYVTFKDAYALETAV-LLSGATIVDQRVCITRW   78 (243)
T ss_pred             CCceEEEEecCCCCCCHHHHHHHHHhcCCeEEEEEecCCC---cceEEEEEECCHHHHHHHH-hcCCCeeCCceEEEEeC
Confidence            3468999999999999999999999999999999998843   4589999999999999999 79999999999999876


Q ss_pred             c
Q 007792          320 Q  320 (589)
Q Consensus       320 ~  320 (589)
                      .
T Consensus        79 ~   79 (243)
T PLN03121         79 G   79 (243)
T ss_pred             c
Confidence            5

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

Probab=99.36  E-value=5.1e-13  Score=123.30  Aligned_cols=83  Identities=23%  Similarity=0.438  Sum_probs=79.7

Q ss_pred             CCceEEEecCCCCCCHHHHHHHhccCCCeEEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHhcCCceeCCeEEEEEecc
Q 007792          241 PENVLFVCKLNPVTEDEDLHTIFSRFGTVVSAEIIRDFKTGDSLNYAFIEFENRQACERAYSKMDNALIDDRRIHVDFSQ  320 (589)
Q Consensus       241 ~~~~i~V~nL~~~~te~~L~~~F~~~G~v~~~~i~~d~~tg~~~g~aFV~f~~~~~a~~A~~~l~g~~i~gr~i~V~~a~  320 (589)
                      ...+||||+|..++|+.-|...|-.||.|+.|.|+.|..+++.+|||||+|...++|.+||..||+.+|.|+.|+|.+|+
T Consensus         9 ~KrtlYVGGladeVtekvLhaAFIPFGDI~dIqiPlDyesqkHRgFgFVefe~aEDAaaAiDNMnesEL~GrtirVN~Ak   88 (298)
T KOG0111|consen    9 QKRTLYVGGLADEVTEKVLHAAFIPFGDIKDIQIPLDYESQKHRGFGFVEFEEAEDAAAAIDNMNESELFGRTIRVNLAK   88 (298)
T ss_pred             cceeEEeccchHHHHHHHHHhccccccchhhcccccchhcccccceeEEEeeccchhHHHhhcCchhhhcceeEEEeecC
Confidence            35799999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             ccc
Q 007792          321 SVS  323 (589)
Q Consensus       321 ~~~  323 (589)
                      |..
T Consensus        89 P~k   91 (298)
T KOG0111|consen   89 PEK   91 (298)
T ss_pred             Ccc
Confidence            843

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

Probab=99.35  E-value=2e-12  Score=126.29  Aligned_cols=82  Identities=27%  Similarity=0.488  Sum_probs=75.6

Q ss_pred             CCCCceEEEecCCCCCCHHHHHHHhccCCCeEEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHhcCCceeCCeEEEEEe
Q 007792          239 KPPENVLFVCKLNPVTEDEDLHTIFSRFGTVVSAEIIRDFKTGDSLNYAFIEFENRQACERAYSKMDNALIDDRRIHVDF  318 (589)
Q Consensus       239 ~~~~~~i~V~nL~~~~te~~L~~~F~~~G~v~~~~i~~d~~tg~~~g~aFV~f~~~~~a~~A~~~l~g~~i~gr~i~V~~  318 (589)
                      +...+.|||.|||+...+.||..+|.+||+|.+|.|+.+..  .+||||||+|++.++|++|-..|||..|.|++|.|..
T Consensus        93 ~~~pkRLhVSNIPFrFRdpDL~aMF~kfG~VldVEIIfNER--GSKGFGFVTmen~~dadRARa~LHgt~VEGRkIEVn~  170 (376)
T KOG0125|consen   93 KDTPKRLHVSNIPFRFRDPDLRAMFEKFGKVLDVEIIFNER--GSKGFGFVTMENPADADRARAELHGTVVEGRKIEVNN  170 (376)
T ss_pred             CCCCceeEeecCCccccCccHHHHHHhhCceeeEEEEeccC--CCCccceEEecChhhHHHHHHHhhcceeeceEEEEec
Confidence            34467999999999999999999999999999999999743  3899999999999999999999999999999999999


Q ss_pred             cccc
Q 007792          319 SQSV  322 (589)
Q Consensus       319 a~~~  322 (589)
                      |...
T Consensus       171 ATar  174 (376)
T KOG0125|consen  171 ATAR  174 (376)
T ss_pred             cchh
Confidence            8763

>smart00362 RRM_2 RNA recognition motif

Probab=99.35  E-value=5.4e-12  Score=99.37  Aligned_cols=72  Identities=36%  Similarity=0.679  Sum_probs=67.5

Q ss_pred             eEEEecCCCCCCHHHHHHHhccCCCeEEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHhcCCceeCCeEEEEE
Q 007792          244 VLFVCKLNPVTEDEDLHTIFSRFGTVVSAEIIRDFKTGDSLNYAFIEFENRQACERAYSKMDNALIDDRRIHVD  317 (589)
Q Consensus       244 ~i~V~nL~~~~te~~L~~~F~~~G~v~~~~i~~d~~tg~~~g~aFV~f~~~~~a~~A~~~l~g~~i~gr~i~V~  317 (589)
                      +|||+|||..+++++|..+|.+||+|..+.++.++  +.++|+|||+|.+.++|..|+..|+|..|.|+.|.|+
T Consensus         1 ~v~i~~l~~~~~~~~l~~~~~~~g~v~~~~~~~~~--~~~~~~~~v~f~~~~~a~~a~~~~~~~~~~~~~i~v~   72 (72)
T smart00362        1 TLFVGNLPPDVTEEDLKELFSKFGPIESVKIPKDT--GKSKGFAFVEFESEEDAEKAIEALNGTKLGGRPLRVE   72 (72)
T ss_pred             CEEEcCCCCcCCHHHHHHHHHhcCCEEEEEEecCC--CCCCceEEEEeCCHHHHHHHHHHhCCcEECCEEEeeC
Confidence            58999999999999999999999999999998875  6788999999999999999999999999999999874

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

Probab=99.33  E-value=4.3e-12  Score=138.48  Aligned_cols=76  Identities=30%  Similarity=0.563  Sum_probs=70.3

Q ss_pred             CCceEEEecCCCCCCHHHHHHHhccC--CCeEEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHhcCCceeCCeEEEEEe
Q 007792          241 PENVLFVCKLNPVTEDEDLHTIFSRF--GTVVSAEIIRDFKTGDSLNYAFIEFENRQACERAYSKMDNALIDDRRIHVDF  318 (589)
Q Consensus       241 ~~~~i~V~nL~~~~te~~L~~~F~~~--G~v~~~~i~~d~~tg~~~g~aFV~f~~~~~a~~A~~~l~g~~i~gr~i~V~~  318 (589)
                      ..++|||+||++.+|+++|+++|++|  |.|..|.++.        +||||+|.+.++|.+||+.|||.+|.|+.|.|.|
T Consensus       232 ~~k~LfVgNL~~~~tee~L~~~F~~f~~G~I~rV~~~r--------gfAFVeF~s~e~A~kAi~~lnG~~i~Gr~I~V~~  303 (578)
T TIGR01648       232 KVKILYVRNLMTTTTEEIIEKSFSEFKPGKVERVKKIR--------DYAFVHFEDREDAVKAMDELNGKELEGSEIEVTL  303 (578)
T ss_pred             cccEEEEeCCCCCCCHHHHHHHHHhcCCCceEEEEeec--------CeEEEEeCCHHHHHHHHHHhCCCEECCEEEEEEE
Confidence            45789999999999999999999999  9999998754        6999999999999999999999999999999999


Q ss_pred             cccccc
Q 007792          319 SQSVSK  324 (589)
Q Consensus       319 a~~~~~  324 (589)
                      |++...
T Consensus       304 Akp~~~  309 (578)
T TIGR01648       304 AKPVDK  309 (578)
T ss_pred             ccCCCc
Confidence            987543

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.

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

Probab=99.32  E-value=1.5e-12  Score=117.33  Aligned_cols=80  Identities=25%  Similarity=0.371  Sum_probs=77.3

Q ss_pred             CCceEEEecCCCCCCHHHHHHHhccCCCeEEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHhcCCceeCCeEEEEEecc
Q 007792          241 PENVLFVCKLNPVTEDEDLHTIFSRFGTVVSAEIIRDFKTGDSLNYAFIEFENRQACERAYSKMDNALIDDRRIHVDFSQ  320 (589)
Q Consensus       241 ~~~~i~V~nL~~~~te~~L~~~F~~~G~v~~~~i~~d~~tg~~~g~aFV~f~~~~~a~~A~~~l~g~~i~gr~i~V~~a~  320 (589)
                      ...|||||||+..++++.|.++|-+.|+|+.+.|+.++.+.+..|||||+|.++++|+-||+.||...+-|++|+|..+.
T Consensus         8 qd~tiyvgnld~kvs~~~l~EL~iqagpVv~i~iPkDrv~~~~qGygF~Ef~~eedadYAikiln~VkLYgrpIrv~kas   87 (203)
T KOG0131|consen    8 QDATLYVGNLDEKVSEELLYELFIQAGPVVNLHIPKDRVTQKHQGYGFAEFRTEEDADYAIKILNMVKLYGRPIRVNKAS   87 (203)
T ss_pred             CCceEEEecCCHHHHHHHHHHHHHhcCceeeeecchhhhcccccceeEEEEechhhhHHHHHHHHHHHhcCceeEEEecc
Confidence            35799999999999999999999999999999999999999999999999999999999999999999999999999886

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

Probab=99.32  E-value=4.7e-12  Score=141.66  Aligned_cols=79  Identities=32%  Similarity=0.547  Sum_probs=76.1

Q ss_pred             ceEEEecCCCCCCHHHHHHHhccCCCeEEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHhcCCceeCCeEEEEEeccc
Q 007792          243 NVLFVCKLNPVTEDEDLHTIFSRFGTVVSAEIIRDFKTGDSLNYAFIEFENRQACERAYSKMDNALIDDRRIHVDFSQS  321 (589)
Q Consensus       243 ~~i~V~nL~~~~te~~L~~~F~~~G~v~~~~i~~d~~tg~~~g~aFV~f~~~~~a~~A~~~l~g~~i~gr~i~V~~a~~  321 (589)
                      .+|||+|||+++|+++|.++|++||+|..|.|+.+..|++++|||||+|.+.++|..||..||+..|.|+.|.|.|+..
T Consensus         1 ~sl~VgnLp~~vte~~L~~~F~~~G~v~~v~v~~d~~t~~s~G~afV~F~~~~~A~~Al~~ln~~~i~gk~i~i~~s~~   79 (562)
T TIGR01628         1 ASLYVGDLDPDVTEAKLYDLFKPFGPVLSVRVCRDSVTRRSLGYGYVNFQNPADAERALETMNFKRLGGKPIRIMWSQR   79 (562)
T ss_pred             CeEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEecCCCCCcceEEEEEECCHHHHHHHHHHhCCCEECCeeEEeecccc
Confidence            3799999999999999999999999999999999999999999999999999999999999999999999999999864

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=99.31  E-value=7.4e-12  Score=136.58  Aligned_cols=81  Identities=26%  Similarity=0.396  Sum_probs=76.6

Q ss_pred             CCCceEEEecCCCCCCHHHHHHHhccCCCeEEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHhcCCceeCCeEEEEEec
Q 007792          240 PPENVLFVCKLNPVTEDEDLHTIFSRFGTVVSAEIIRDFKTGDSLNYAFIEFENRQACERAYSKMDNALIDDRRIHVDFS  319 (589)
Q Consensus       240 ~~~~~i~V~nL~~~~te~~L~~~F~~~G~v~~~~i~~d~~tg~~~g~aFV~f~~~~~a~~A~~~l~g~~i~gr~i~V~~a  319 (589)
                      .+..+|||+|||+.+++++|+++|++||.|..|.|+.++.+++++|||||+|.+.++|.+|| .|+|..|.|++|.|.++
T Consensus        87 ~~~~~l~V~nlp~~~~~~~l~~~F~~~G~v~~v~i~~d~~~~~skg~afVeF~~~e~A~~Al-~l~g~~~~g~~i~v~~~  165 (457)
T TIGR01622        87 RDDRTVFVLQLALKARERDLYEFFSKVGKVRDVQCIKDRNSRRSKGVAYVEFYDVESVIKAL-ALTGQMLLGRPIIVQSS  165 (457)
T ss_pred             cCCcEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEeecCCCCCcceEEEEEECCHHHHHHHH-HhCCCEECCeeeEEeec
Confidence            35689999999999999999999999999999999999999999999999999999999999 58999999999999987


Q ss_pred             cc
Q 007792          320 QS  321 (589)
Q Consensus       320 ~~  321 (589)
                      ..
T Consensus       166 ~~  167 (457)
T TIGR01622       166 QA  167 (457)
T ss_pred             ch
Confidence            54

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.

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

Probab=99.31  E-value=5.3e-12  Score=137.81  Aligned_cols=80  Identities=23%  Similarity=0.369  Sum_probs=74.2

Q ss_pred             CCceEEEecCCCCCCHHHHHHHhccCCCeEEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHhcCCceeC-CeEEEEEec
Q 007792          241 PENVLFVCKLNPVTEDEDLHTIFSRFGTVVSAEIIRDFKTGDSLNYAFIEFENRQACERAYSKMDNALID-DRRIHVDFS  319 (589)
Q Consensus       241 ~~~~i~V~nL~~~~te~~L~~~F~~~G~v~~~~i~~d~~tg~~~g~aFV~f~~~~~a~~A~~~l~g~~i~-gr~i~V~~a  319 (589)
                      ..++|||+|||+++++++|.++|++||.|..|+|+.| .+|+++|||||+|.+.++|+.||+.||+..|. |+.|.|.++
T Consensus        57 ~~~~lFVgnLp~~~tEd~L~~~F~~~G~I~~vrl~~D-~sG~sRGfaFV~F~~~e~A~~Ai~~lng~~i~~Gr~l~V~~S  135 (578)
T TIGR01648        57 RGCEVFVGKIPRDLYEDELVPLFEKAGPIYELRLMMD-FSGQNRGYAFVTFCGKEEAKEAVKLLNNYEIRPGRLLGVCIS  135 (578)
T ss_pred             CCCEEEeCCCCCCCCHHHHHHHHHhhCCEEEEEEEEC-CCCCccceEEEEeCCHHHHHHHHHHcCCCeecCCcccccccc
Confidence            3589999999999999999999999999999999999 88999999999999999999999999999885 888888766


Q ss_pred             cc
Q 007792          320 QS  321 (589)
Q Consensus       320 ~~  321 (589)
                      ..
T Consensus       136 ~~  137 (578)
T TIGR01648       136 VD  137 (578)
T ss_pred             cc
Confidence            43

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.

>smart00360 RRM RNA recognition motif

Probab=99.30  E-value=1e-11  Score=97.37  Aligned_cols=71  Identities=35%  Similarity=0.670  Sum_probs=67.3

Q ss_pred             EecCCCCCCHHHHHHHhccCCCeEEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHhcCCceeCCeEEEEE
Q 007792          247 VCKLNPVTEDEDLHTIFSRFGTVVSAEIIRDFKTGDSLNYAFIEFENRQACERAYSKMDNALIDDRRIHVD  317 (589)
Q Consensus       247 V~nL~~~~te~~L~~~F~~~G~v~~~~i~~d~~tg~~~g~aFV~f~~~~~a~~A~~~l~g~~i~gr~i~V~  317 (589)
                      |+|||..+++++|..+|.+||.|..+.+..++.++.++|||||+|.+.++|..|+..|++..|.|+.|.|.
T Consensus         1 i~~l~~~~~~~~l~~~f~~~g~v~~~~i~~~~~~~~~~~~a~v~f~~~~~a~~a~~~~~~~~~~~~~~~v~   71 (71)
T smart00360        1 VGNLPPDVTEEELRELFSKFGKIESVRLVRDKDTGKSKGFAFVEFESEEDAEKALEALNGKELDGRPLKVK   71 (71)
T ss_pred             CCCCCcccCHHHHHHHHHhhCCEeEEEEEeCCCCCCCCceEEEEeCCHHHHHHHHHHcCCCeeCCcEEEeC
Confidence            57999999999999999999999999999988788999999999999999999999999999999999874

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

Probab=99.29  E-value=5.6e-12  Score=127.84  Aligned_cols=75  Identities=32%  Similarity=0.551  Sum_probs=70.7

Q ss_pred             CceEEEecCCCCCCHHHHHHHhccCCCeEEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHhcCCceeCCeEEEEEeccc
Q 007792          242 ENVLFVCKLNPVTEDEDLHTIFSRFGTVVSAEIIRDFKTGDSLNYAFIEFENRQACERAYSKMDNALIDDRRIHVDFSQS  321 (589)
Q Consensus       242 ~~~i~V~nL~~~~te~~L~~~F~~~G~v~~~~i~~d~~tg~~~g~aFV~f~~~~~a~~A~~~l~g~~i~gr~i~V~~a~~  321 (589)
                      -+.|||.||+.+||++.|+++|++||.|..|+.+.|        ||||.|.+.++|.+|++.|||++|+|..|.|.+|+|
T Consensus       259 VKvLYVRNL~~~tTeE~lk~~F~~~G~veRVkk~rD--------YaFVHf~eR~davkAm~~~ngkeldG~~iEvtLAKP  330 (506)
T KOG0117|consen  259 VKVLYVRNLMESTTEETLKKLFNEFGKVERVKKPRD--------YAFVHFAEREDAVKAMKETNGKELDGSPIEVTLAKP  330 (506)
T ss_pred             eeeeeeeccchhhhHHHHHHHHHhccceEEeecccc--------eeEEeecchHHHHHHHHHhcCceecCceEEEEecCC
Confidence            479999999999999999999999999999988765        999999999999999999999999999999999998


Q ss_pred             ccc
Q 007792          322 VSK  324 (589)
Q Consensus       322 ~~~  324 (589)
                      ..+
T Consensus       331 ~~k  333 (506)
T KOG0117|consen  331 VDK  333 (506)
T ss_pred             hhh
Confidence            544

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

Probab=99.29  E-value=1.2e-11  Score=111.44  Aligned_cols=79  Identities=22%  Similarity=0.400  Sum_probs=71.5

Q ss_pred             CCceEEEecCCCCCCHHHHHHHhccCCCeEEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHhcCCceeCCeEEEEEecc
Q 007792          241 PENVLFVCKLNPVTEDEDLHTIFSRFGTVVSAEIIRDFKTGDSLNYAFIEFENRQACERAYSKMDNALIDDRRIHVDFSQ  320 (589)
Q Consensus       241 ~~~~i~V~nL~~~~te~~L~~~F~~~G~v~~~~i~~d~~tg~~~g~aFV~f~~~~~a~~A~~~l~g~~i~gr~i~V~~a~  320 (589)
                      ....|||||||.++.+.+|+.+|-+||.|..|.|...   ..+.+||||+|++..+|+.||..-+|..++|..|.|+|+.
T Consensus         5 ~~~~iyvGNLP~diRekeieDlFyKyg~i~~ieLK~r---~g~ppfafVeFEd~RDAeDAiygRdGYdydg~rLRVEfpr   81 (241)
T KOG0105|consen    5 NSRRIYVGNLPGDIREKEIEDLFYKYGRIREIELKNR---PGPPPFAFVEFEDPRDAEDAIYGRDGYDYDGCRLRVEFPR   81 (241)
T ss_pred             ccceEEecCCCcchhhccHHHHHhhhcceEEEEeccC---CCCCCeeEEEecCccchhhhhhcccccccCcceEEEEecc
Confidence            4579999999999999999999999999999988543   2356899999999999999999999999999999999998


Q ss_pred             cc
Q 007792          321 SV  322 (589)
Q Consensus       321 ~~  322 (589)
                      ..
T Consensus        82 gg   83 (241)
T KOG0105|consen   82 GG   83 (241)
T ss_pred             CC
Confidence            64

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

Probab=99.28  E-value=1.4e-11  Score=117.61  Aligned_cols=77  Identities=22%  Similarity=0.507  Sum_probs=72.8

Q ss_pred             CCCCceEEEecCCCCCCHHHHHHHhccCCCeEEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHhcCCceeCCeEEEEEe
Q 007792          239 KPPENVLFVCKLNPVTEDEDLHTIFSRFGTVVSAEIIRDFKTGDSLNYAFIEFENRQACERAYSKMDNALIDDRRIHVDF  318 (589)
Q Consensus       239 ~~~~~~i~V~nL~~~~te~~L~~~F~~~G~v~~~~i~~d~~tg~~~g~aFV~f~~~~~a~~A~~~l~g~~i~gr~i~V~~  318 (589)
                      .+.+++||||||+..+|++.|++.|+.||.|.+|+|.++      +|||||.|++.|+|..||..|||.+|.|..++|.|
T Consensus       161 sp~NtsVY~G~I~~~lte~~mr~~Fs~fG~I~EVRvFk~------qGYaFVrF~tkEaAahAIv~mNntei~G~~VkCsW  234 (321)
T KOG0148|consen  161 SPDNTSVYVGNIASGLTEDLMRQTFSPFGPIQEVRVFKD------QGYAFVRFETKEAAAHAIVQMNNTEIGGQLVRCSW  234 (321)
T ss_pred             CCCCceEEeCCcCccccHHHHHHhcccCCcceEEEEecc------cceEEEEecchhhHHHHHHHhcCceeCceEEEEec
Confidence            556899999999999999999999999999999999886      48999999999999999999999999999999999


Q ss_pred             ccc
Q 007792          319 SQS  321 (589)
Q Consensus       319 a~~  321 (589)
                      -+.
T Consensus       235 GKe  237 (321)
T KOG0148|consen  235 GKE  237 (321)
T ss_pred             ccc
Confidence            875

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

Probab=99.27  E-value=1.4e-11  Score=116.55  Aligned_cols=86  Identities=23%  Similarity=0.490  Sum_probs=80.9

Q ss_pred             CCCCCceEEEecCCCCCCHHHHHHHhccCCCeEEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHhcCCceeCCeEEEEE
Q 007792          238 IKPPENVLFVCKLNPVTEDEDLHTIFSRFGTVVSAEIIRDFKTGDSLNYAFIEFENRQACERAYSKMDNALIDDRRIHVD  317 (589)
Q Consensus       238 ~~~~~~~i~V~nL~~~~te~~L~~~F~~~G~v~~~~i~~d~~tg~~~g~aFV~f~~~~~a~~A~~~l~g~~i~gr~i~V~  317 (589)
                      .....+.|.|--||.++|+++|+.+|...|+|.+|+++.|+.+|++.||+||.|-.+++|++||..|||..+..+.|+|.
T Consensus        37 t~~skTNLIvNYLPQ~MTqdE~rSLF~SiGeiEScKLvRDKitGqSLGYGFVNYv~p~DAe~AintlNGLrLQ~KTIKVS  116 (360)
T KOG0145|consen   37 TDESKTNLIVNYLPQNMTQDELRSLFGSIGEIESCKLVRDKITGQSLGYGFVNYVRPKDAEKAINTLNGLRLQNKTIKVS  116 (360)
T ss_pred             cCcccceeeeeecccccCHHHHHHHhhcccceeeeeeeeccccccccccceeeecChHHHHHHHhhhcceeeccceEEEE
Confidence            34456789999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             eccccc
Q 007792          318 FSQSVS  323 (589)
Q Consensus       318 ~a~~~~  323 (589)
                      ||+|..
T Consensus       117 yARPSs  122 (360)
T KOG0145|consen  117 YARPSS  122 (360)
T ss_pred             eccCCh
Confidence            999843

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

Probab=99.27  E-value=1.5e-11  Score=137.67  Aligned_cols=83  Identities=27%  Similarity=0.479  Sum_probs=78.2

Q ss_pred             CCCceEEEecCCCCCCHHHHHHHhccCCCeEEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHhcCCceeCCeEEEEEec
Q 007792          240 PPENVLFVCKLNPVTEDEDLHTIFSRFGTVVSAEIIRDFKTGDSLNYAFIEFENRQACERAYSKMDNALIDDRRIHVDFS  319 (589)
Q Consensus       240 ~~~~~i~V~nL~~~~te~~L~~~F~~~G~v~~~~i~~d~~tg~~~g~aFV~f~~~~~a~~A~~~l~g~~i~gr~i~V~~a  319 (589)
                      ....+|||+||++.+|+++|+++|++||.|..|+|+.+ .+|.++|||||+|.+.++|.+|+..|||..|+|++|.|.+|
T Consensus       283 ~~~~~l~V~nl~~~~~~~~L~~~F~~~G~i~~~~i~~d-~~g~~~g~gfV~f~~~~~A~~A~~~~~g~~~~gk~l~V~~a  361 (562)
T TIGR01628       283 AQGVNLYVKNLDDTVTDEKLRELFSECGEITSAKVMLD-EKGVSRGFGFVCFSNPEEANRAVTEMHGRMLGGKPLYVALA  361 (562)
T ss_pred             cCCCEEEEeCCCCccCHHHHHHHHHhcCCeEEEEEEEC-CCCCcCCeEEEEeCCHHHHHHHHHHhcCCeeCCceeEEEec
Confidence            35678999999999999999999999999999999998 78999999999999999999999999999999999999999


Q ss_pred             cccc
Q 007792          320 QSVS  323 (589)
Q Consensus       320 ~~~~  323 (589)
                      ..+.
T Consensus       362 ~~k~  365 (562)
T TIGR01628       362 QRKE  365 (562)
T ss_pred             cCcH
Confidence            8643

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

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

Probab=99.26  E-value=1e-11  Score=130.66  Aligned_cols=81  Identities=27%  Similarity=0.517  Sum_probs=78.5

Q ss_pred             ceEEEecCCCCCCHHHHHHHhccCCCeEEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHhcCCceeCCeEEEEEecccc
Q 007792          243 NVLFVCKLNPVTEDEDLHTIFSRFGTVVSAEIIRDFKTGDSLNYAFIEFENRQACERAYSKMDNALIDDRRIHVDFSQSV  322 (589)
Q Consensus       243 ~~i~V~nL~~~~te~~L~~~F~~~G~v~~~~i~~d~~tg~~~g~aFV~f~~~~~a~~A~~~l~g~~i~gr~i~V~~a~~~  322 (589)
                      ..|||||||+++++++|..+|+..|.|..++++.|+.||+++|||||+|.+.+.|..|+..|||.++.|++|+|.|+...
T Consensus        19 ~~v~vgnip~~~se~~l~~~~~~~g~v~s~~~v~D~~tG~~~G~~f~~~~~~~~~~~a~~~lNg~~~~gr~l~v~~~~~~   98 (435)
T KOG0108|consen   19 SSVFVGNIPYEGSEEQLLSIFSGVGPVLSFRLVYDRETGKPKGFGFCEFTDEETAERAIRNLNGAEFNGRKLRVNYASNR   98 (435)
T ss_pred             cceEecCCCCcccHHHHHHHHhccCccceeeecccccCCCcCceeeEecCchhhHHHHHHhcCCcccCCceEEeeccccc
Confidence            89999999999999999999999999999999999999999999999999999999999999999999999999998763


Q ss_pred             c
Q 007792          323 S  323 (589)
Q Consensus       323 ~  323 (589)
                      .
T Consensus        99 ~   99 (435)
T KOG0108|consen   99 K   99 (435)
T ss_pred             c
Confidence            3

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

Probab=99.26  E-value=2e-11  Score=122.67  Aligned_cols=80  Identities=34%  Similarity=0.617  Sum_probs=77.3

Q ss_pred             CceEEEecCCCCCCHHHHHHHhccCCCeEEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHhcCCceeCCeEEEEEeccc
Q 007792          242 ENVLFVCKLNPVTEDEDLHTIFSRFGTVVSAEIIRDFKTGDSLNYAFIEFENRQACERAYSKMDNALIDDRRIHVDFSQS  321 (589)
Q Consensus       242 ~~~i~V~nL~~~~te~~L~~~F~~~G~v~~~~i~~d~~tg~~~g~aFV~f~~~~~a~~A~~~l~g~~i~gr~i~V~~a~~  321 (589)
                      ..+|||+|||+.+|+++|..+|.+||.|..+.|+.++.++.++|||||+|.+.++|..|+..|+|..|.|+.|.|.++.+
T Consensus       115 ~~~l~v~nL~~~~~~~~l~~~F~~~g~~~~~~~~~d~~~~~~~g~~~v~f~~~~~~~~a~~~~~~~~~~~~~~~v~~~~~  194 (306)
T COG0724         115 NNTLFVGNLPYDVTEEDLRELFKKFGPVKRVRLVRDRETGKSRGFAFVEFESEESAEKAIEELNGKELEGRPLRVQKAQP  194 (306)
T ss_pred             CceEEEeCCCCCCCHHHHHHHHHhcCceeEEEeeeccccCccCceEEEEecCHHHHHHHHHHcCCCeECCceeEeecccc
Confidence            68999999999999999999999999999999999999999999999999999999999999999999999999999753

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

Probab=99.25  E-value=4.6e-11  Score=97.79  Aligned_cols=78  Identities=19%  Similarity=0.354  Sum_probs=72.4

Q ss_pred             CCceEEEecCCCCCCHHHHHHHhccCCCeEEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHhcCCceeCCeEEEEEecc
Q 007792          241 PENVLFVCKLNPVTEDEDLHTIFSRFGTVVSAEIIRDFKTGDSLNYAFIEFENRQACERAYSKMDNALIDDRRIHVDFSQ  320 (589)
Q Consensus       241 ~~~~i~V~nL~~~~te~~L~~~F~~~G~v~~~~i~~d~~tg~~~g~aFV~f~~~~~a~~A~~~l~g~~i~gr~i~V~~a~  320 (589)
                      -+..|||.|||+.+|.+++.++|++||.|.+|+|-..+.   .+|-|||.|++..+|..|+..|+|..++++.|.|-+-+
T Consensus        17 vnriLyirNLp~~ITseemydlFGkyg~IrQIRiG~~k~---TrGTAFVVYedi~dAk~A~dhlsg~n~~~ryl~vlyyq   93 (124)
T KOG0114|consen   17 VNRILYIRNLPFKITSEEMYDLFGKYGTIRQIRIGNTKE---TRGTAFVVYEDIFDAKKACDHLSGYNVDNRYLVVLYYQ   93 (124)
T ss_pred             hheeEEEecCCccccHHHHHHHhhcccceEEEEecCccC---cCceEEEEehHhhhHHHHHHHhcccccCCceEEEEecC
Confidence            357899999999999999999999999999999977655   46999999999999999999999999999999999987


Q ss_pred             c
Q 007792          321 S  321 (589)
Q Consensus       321 ~  321 (589)
                      +
T Consensus        94 ~   94 (124)
T KOG0114|consen   94 P   94 (124)
T ss_pred             H
Confidence            6

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

Probab=99.24  E-value=2.1e-10  Score=108.67  Aligned_cols=82  Identities=26%  Similarity=0.507  Sum_probs=78.3

Q ss_pred             CCceEEEecCCCCCCHHHHHHHhccCCCeEEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHhcCCceeCCeEEEEEecc
Q 007792          241 PENVLFVCKLNPVTEDEDLHTIFSRFGTVVSAEIIRDFKTGDSLNYAFIEFENRQACERAYSKMDNALIDDRRIHVDFSQ  320 (589)
Q Consensus       241 ~~~~i~V~nL~~~~te~~L~~~F~~~G~v~~~~i~~d~~tg~~~g~aFV~f~~~~~a~~A~~~l~g~~i~gr~i~V~~a~  320 (589)
                      ....|||-||.+++.|.-|.++|++||.|..|+|+.|..|.+.+|||||.+.+.++|..||..|||..++++.|.|.|..
T Consensus       277 ~g~ciFvYNLspd~de~~LWQlFgpFGAv~nVKvirD~ttnkCKGfgFVtMtNYdEAamAi~sLNGy~lg~rvLQVsFKt  356 (360)
T KOG0145|consen  277 GGWCIFVYNLSPDADESILWQLFGPFGAVTNVKVIRDFTTNKCKGFGFVTMTNYDEAAMAIASLNGYRLGDRVLQVSFKT  356 (360)
T ss_pred             CeeEEEEEecCCCchHhHHHHHhCcccceeeEEEEecCCcccccceeEEEecchHHHHHHHHHhcCccccceEEEEEEec
Confidence            46799999999999999999999999999999999999999999999999999999999999999999999999999976


Q ss_pred             cc
Q 007792          321 SV  322 (589)
Q Consensus       321 ~~  322 (589)
                      .+
T Consensus       357 nk  358 (360)
T KOG0145|consen  357 NK  358 (360)
T ss_pred             CC
Confidence            53

>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=99.24  E-value=6.3e-11  Score=93.71  Aligned_cols=74  Identities=39%  Similarity=0.705  Sum_probs=68.7

Q ss_pred             eEEEecCCCCCCHHHHHHHhccCCCeEEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHhcCCceeCCeEEEEEe
Q 007792          244 VLFVCKLNPVTEDEDLHTIFSRFGTVVSAEIIRDFKTGDSLNYAFIEFENRQACERAYSKMDNALIDDRRIHVDF  318 (589)
Q Consensus       244 ~i~V~nL~~~~te~~L~~~F~~~G~v~~~~i~~d~~tg~~~g~aFV~f~~~~~a~~A~~~l~g~~i~gr~i~V~~  318 (589)
                      +|||+|||+.+++++|..+|..||.|..+.+..+..+ .+.|+|||+|.+.++|..|+..|++..+.|+.|.|.+
T Consensus         1 ~i~i~~l~~~~~~~~i~~~~~~~g~i~~~~~~~~~~~-~~~~~~~v~f~s~~~a~~a~~~~~~~~~~~~~~~v~~   74 (74)
T cd00590           1 TLFVGNLPPDVTEEDLRELFSKFGKVESVRIVRDKDT-KSKGFAFVEFEDEEDAEKALEALNGKELGGRPLRVEF   74 (74)
T ss_pred             CEEEeCCCCccCHHHHHHHHHhcCCEEEEEEeeCCCC-CcceEEEEEECCHHHHHHHHHHhCCCeECCeEEEEeC
Confidence            5899999999999999999999999999999987554 6789999999999999999999999999999999864

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).

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

Probab=99.21  E-value=1.2e-11  Score=117.38  Aligned_cols=86  Identities=27%  Similarity=0.434  Sum_probs=81.7

Q ss_pred             CCCCCceEEEecCCCCCCHHHHHHHhccCCCeEEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHhcCCceeCCeEEEEE
Q 007792          238 IKPPENVLFVCKLNPVTEDEDLHTIFSRFGTVVSAEIIRDFKTGDSLNYAFIEFENRQACERAYSKMDNALIDDRRIHVD  317 (589)
Q Consensus       238 ~~~~~~~i~V~nL~~~~te~~L~~~F~~~G~v~~~~i~~d~~tg~~~g~aFV~f~~~~~a~~A~~~l~g~~i~gr~i~V~  317 (589)
                      ..|.+++|||-.||.+..+.+|.++|..||.|++.+|..|..|+.++||+||.|.+..+|+.||..|||+.|+-++|+|+
T Consensus       281 eGPeGCNlFIYHLPQEFgDaEliQmF~PFGhivSaKVFvDRATNQSKCFGFVSfDNp~SaQaAIqAMNGFQIGMKRLKVQ  360 (371)
T KOG0146|consen  281 EGPEGCNLFIYHLPQEFGDAELIQMFLPFGHIVSAKVFVDRATNQSKCFGFVSFDNPASAQAAIQAMNGFQIGMKRLKVQ  360 (371)
T ss_pred             cCCCcceEEEEeCchhhccHHHHHHhccccceeeeeeeehhccccccceeeEecCCchhHHHHHHHhcchhhhhhhhhhh
Confidence            35678999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             eccccc
Q 007792          318 FSQSVS  323 (589)
Q Consensus       318 ~a~~~~  323 (589)
                      +.+++.
T Consensus       361 LKRPkd  366 (371)
T KOG0146|consen  361 LKRPKD  366 (371)
T ss_pred             hcCccc
Confidence            987743

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

Probab=99.20  E-value=6e-11  Score=129.77  Aligned_cols=79  Identities=19%  Similarity=0.320  Sum_probs=73.0

Q ss_pred             CCCCceEEEecCCC-CCCHHHHHHHhccCCCeEEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHhcCCceeCCeEEEEE
Q 007792          239 KPPENVLFVCKLNP-VTEDEDLHTIFSRFGTVVSAEIIRDFKTGDSLNYAFIEFENRQACERAYSKMDNALIDDRRIHVD  317 (589)
Q Consensus       239 ~~~~~~i~V~nL~~-~~te~~L~~~F~~~G~v~~~~i~~d~~tg~~~g~aFV~f~~~~~a~~A~~~l~g~~i~gr~i~V~  317 (589)
                      .++.++|||+||++ .+|+++|.++|+.||.|..|+|+.+     .+|||||+|.+.++|..||..|||..|.|+.|.|.
T Consensus       272 ~~~~~~l~v~nL~~~~vt~~~L~~lF~~yG~V~~vki~~~-----~~g~afV~f~~~~~A~~Ai~~lng~~l~g~~l~v~  346 (481)
T TIGR01649       272 GGPGSVLMVSGLHQEKVNCDRLFNLFCVYGNVERVKFMKN-----KKETALIEMADPYQAQLALTHLNGVKLFGKPLRVC  346 (481)
T ss_pred             CCCCCEEEEeCCCCCCCCHHHHHHHHHhcCCeEEEEEEeC-----CCCEEEEEECCHHHHHHHHHHhCCCEECCceEEEE
Confidence            45778999999998 6999999999999999999999886     35899999999999999999999999999999999


Q ss_pred             ecccc
Q 007792          318 FSQSV  322 (589)
Q Consensus       318 ~a~~~  322 (589)
                      +++..
T Consensus       347 ~s~~~  351 (481)
T TIGR01649       347 PSKQQ  351 (481)
T ss_pred             Ecccc
Confidence            98753

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).

>KOG4676 consensus Splicing factor, arginine/serine-rich [RNA processing and modification]

Probab=99.19  E-value=3e-13  Score=134.55  Aligned_cols=64  Identities=14%  Similarity=0.032  Sum_probs=53.9

Q ss_pred             CceEEEecCCCCCCHHHHHHHhccCCCeEEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHhcCCceeC
Q 007792          242 ENVLFVCKLNPVTEDEDLHTIFSRFGTVVSAEIIRDFKTGDSLNYAFIEFENRQACERAYSKMDNALID  310 (589)
Q Consensus       242 ~~~i~V~nL~~~~te~~L~~~F~~~G~v~~~~i~~d~~tg~~~g~aFV~f~~~~~a~~A~~~l~g~~i~  310 (589)
                      ..+|+|++|+..+...++.++|..+|+|.+..+..    +...-+|-|+|....+...|+. ++|.++.
T Consensus       151 rRt~~v~sl~~~~~l~e~~e~f~r~Gev~ya~~as----k~~s~~c~~sf~~qts~~halr-~~gre~k  214 (479)
T KOG4676|consen  151 RRTREVQSLISAAILPESGESFERKGEVSYAHTAS----KSRSSSCSHSFRKQTSSKHALR-SHGRERK  214 (479)
T ss_pred             Hhhhhhhcchhhhcchhhhhhhhhcchhhhhhhhc----cCCCcchhhhHhhhhhHHHHHH-hcchhhh
Confidence            46899999999999999999999999999887754    3344678899999999999995 6777766

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

Probab=99.17  E-value=2.7e-11  Score=122.34  Aligned_cols=82  Identities=27%  Similarity=0.495  Sum_probs=74.4

Q ss_pred             CCceEEEecCCCCCCHHHHHHHhccCCCeEEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHhcCCc-eeC--CeEEEEE
Q 007792          241 PENVLFVCKLNPVTEDEDLHTIFSRFGTVVSAEIIRDFKTGDSLNYAFIEFENRQACERAYSKMDNA-LID--DRRIHVD  317 (589)
Q Consensus       241 ~~~~i~V~nL~~~~te~~L~~~F~~~G~v~~~~i~~d~~tg~~~g~aFV~f~~~~~a~~A~~~l~g~-~i~--gr~i~V~  317 (589)
                      ...+||||-|+..+||.+|+++|++||.|++|.|+.+ ..+.++|||||.|.+.+.|..||+.|||. .+.  ..+|.|.
T Consensus       123 ~e~KLFvg~lsK~~te~evr~iFs~fG~Ied~~ilrd-~~~~sRGcaFV~fstke~A~~Aika~ng~~tmeGcs~PLVVk  201 (510)
T KOG0144|consen  123 EERKLFVGMLSKQCTENEVREIFSRFGHIEDCYILRD-PDGLSRGCAFVKFSTKEMAVAAIKALNGTQTMEGCSQPLVVK  201 (510)
T ss_pred             cchhhhhhhccccccHHHHHHHHHhhCccchhhheec-ccccccceeEEEEehHHHHHHHHHhhccceeeccCCCceEEE
Confidence            3679999999999999999999999999999999998 45889999999999999999999999995 454  4789999


Q ss_pred             eccccc
Q 007792          318 FSQSVS  323 (589)
Q Consensus       318 ~a~~~~  323 (589)
                      ||.+..
T Consensus       202 FADtqk  207 (510)
T KOG0144|consen  202 FADTQK  207 (510)
T ss_pred             ecccCC
Confidence            998744

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

Probab=99.16  E-value=5.8e-11  Score=114.43  Aligned_cols=74  Identities=27%  Similarity=0.559  Sum_probs=70.1

Q ss_pred             ceEEEecCCCCCCHHHHHHHhccCCCeEEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHhcCCceeCCeEEEEEecccc
Q 007792          243 NVLFVCKLNPVTEDEDLHTIFSRFGTVVSAEIIRDFKTGDSLNYAFIEFENRQACERAYSKMDNALIDDRRIHVDFSQSV  322 (589)
Q Consensus       243 ~~i~V~nL~~~~te~~L~~~F~~~G~v~~~~i~~d~~tg~~~g~aFV~f~~~~~a~~A~~~l~g~~i~gr~i~V~~a~~~  322 (589)
                      .+|||||||.++++.+|+.+|++||+|.+|.|+++        ||||..++...|..||..|||.+|+|..|+|+-++++
T Consensus         3 ~KLFIGNLp~~~~~~elr~lFe~ygkVlECDIvKN--------YgFVHiEdktaaedairNLhgYtLhg~nInVeaSksK   74 (346)
T KOG0109|consen    3 VKLFIGNLPREATEQELRSLFEQYGKVLECDIVKN--------YGFVHIEDKTAAEDAIRNLHGYTLHGVNINVEASKSK   74 (346)
T ss_pred             cchhccCCCcccchHHHHHHHHhhCceEeeeeecc--------cceEEeecccccHHHHhhcccceecceEEEEEecccc
Confidence            47999999999999999999999999999999885        9999999999999999999999999999999999876


Q ss_pred             cc
Q 007792          323 SK  324 (589)
Q Consensus       323 ~~  324 (589)
                      .+
T Consensus        75 sk   76 (346)
T KOG0109|consen   75 SK   76 (346)
T ss_pred             CC
Confidence            44

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

Probab=99.16  E-value=1e-10  Score=127.94  Aligned_cols=75  Identities=21%  Similarity=0.304  Sum_probs=69.1

Q ss_pred             CCceEEEecCCCCCCHHHHHHHhccCCCeEEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHh--cCCceeCCeEEEEEe
Q 007792          241 PENVLFVCKLNPVTEDEDLHTIFSRFGTVVSAEIIRDFKTGDSLNYAFIEFENRQACERAYSK--MDNALIDDRRIHVDF  318 (589)
Q Consensus       241 ~~~~i~V~nL~~~~te~~L~~~F~~~G~v~~~~i~~d~~tg~~~g~aFV~f~~~~~a~~A~~~--l~g~~i~gr~i~V~~  318 (589)
                      |..+|||+|||+.+++++|.++|++||.|..|.|+.      .++||||+|.+.++|..||..  +++..|.|++|.|+|
T Consensus         1 ps~vv~V~nLp~~~te~~L~~~f~~fG~V~~v~i~~------~k~~afVef~~~e~A~~Ai~~~~~~~~~l~g~~l~v~~   74 (481)
T TIGR01649         1 PSPVVHVRNLPQDVVEADLVEALIPFGPVSYVMMLP------GKRQALVEFEDEESAKACVNFATSVPIYIRGQPAFFNY   74 (481)
T ss_pred             CccEEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEEC------CCCEEEEEeCchHHHHHHHHHhhcCCceEcCeEEEEEe
Confidence            468999999999999999999999999999999986      348999999999999999986  478999999999999


Q ss_pred             ccc
Q 007792          319 SQS  321 (589)
Q Consensus       319 a~~  321 (589)
                      +..
T Consensus        75 s~~   77 (481)
T TIGR01649        75 STS   77 (481)
T ss_pred             cCC
Confidence            975

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).

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

Probab=99.15  E-value=5.4e-11  Score=124.10  Aligned_cols=79  Identities=25%  Similarity=0.463  Sum_probs=75.3

Q ss_pred             ceEEEecCCCCCCHHHHHHHhccCCCeEEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHhcCCceeCCeEEEEEeccc
Q 007792          243 NVLFVCKLNPVTEDEDLHTIFSRFGTVVSAEIIRDFKTGDSLNYAFIEFENRQACERAYSKMDNALIDDRRIHVDFSQS  321 (589)
Q Consensus       243 ~~i~V~nL~~~~te~~L~~~F~~~G~v~~~~i~~d~~tg~~~g~aFV~f~~~~~a~~A~~~l~g~~i~gr~i~V~~a~~  321 (589)
                      ..||||||.+++++.+|..+|+.||.|..|.+..+..||.++|||||+|.+.++|..|+..|||++|.|+.|+|.+-..
T Consensus       279 ~rl~vgnLHfNite~~lr~ifepfg~Ie~v~l~~d~~tG~skgfGfi~f~~~~~ar~a~e~lngfelAGr~ikV~~v~~  357 (549)
T KOG0147|consen  279 RRLYVGNLHFNITEDMLRGIFEPFGKIENVQLTKDSETGRSKGFGFITFVNKEDARKALEQLNGFELAGRLIKVSVVTE  357 (549)
T ss_pred             hhhhhcccccCchHHHHhhhccCcccceeeeeccccccccccCcceEEEecHHHHHHHHHHhccceecCceEEEEEeee
Confidence            3499999999999999999999999999999999988999999999999999999999999999999999999987654

>smart00361 RRM_1 RNA recognition motif

Probab=99.15  E-value=1.4e-10  Score=92.08  Aligned_cols=61  Identities=28%  Similarity=0.425  Sum_probs=55.6

Q ss_pred             HHHHHHHhc----cCCCeEEEE-EeecCCC--CCcccEEEEEEcCHHHHHHHHHhcCCceeCCeEEEE
Q 007792          256 DEDLHTIFS----RFGTVVSAE-IIRDFKT--GDSLNYAFIEFENRQACERAYSKMDNALIDDRRIHV  316 (589)
Q Consensus       256 e~~L~~~F~----~~G~v~~~~-i~~d~~t--g~~~g~aFV~f~~~~~a~~A~~~l~g~~i~gr~i~V  316 (589)
                      +++|.++|.    +||.|..|. |+.++.+  +.++|||||+|.+.++|..|+..|||..|.|+.|.+
T Consensus         2 ~~~l~~~~~~~~~~fG~v~~v~~v~~~~~~~~~~~rG~~fV~f~~~~dA~~A~~~l~g~~~~gr~l~~   69 (70)
T smart00361        2 DEDFEREFSEEEEYFGEVGKINKIYIDNVGYENHKRGNVYITFERSEDAARAIVDLNGRYFDGRTVKA   69 (70)
T ss_pred             chhHHHHHHHHHHhcCCeeEEEEEEeCCCCCCCCCcEEEEEEECCHHHHHHHHHHhCCCEECCEEEEe
Confidence            578888888    999999995 7777666  899999999999999999999999999999999986

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

Probab=99.15  E-value=1.1e-10  Score=120.94  Aligned_cols=81  Identities=32%  Similarity=0.495  Sum_probs=75.6

Q ss_pred             CCceEEEecCCCCCCHHHHHHHhccCCCeEEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHhc-----CC-ceeCCeEE
Q 007792          241 PENVLFVCKLNPVTEDEDLHTIFSRFGTVVSAEIIRDFKTGDSLNYAFIEFENRQACERAYSKM-----DN-ALIDDRRI  314 (589)
Q Consensus       241 ~~~~i~V~nL~~~~te~~L~~~F~~~G~v~~~~i~~d~~tg~~~g~aFV~f~~~~~a~~A~~~l-----~g-~~i~gr~i  314 (589)
                      -..+|||.|||+++|++.|.+.|++||+|.++.|+.++.|+.++|.|||.|.++..|+.||.+.     .| ..|+|+.|
T Consensus       291 ~~~tVFvRNL~fD~tEEel~~~fskFG~v~ya~iV~~k~T~~skGtAFv~Fkt~~~~~~ci~~Aspa~e~g~~ll~GR~L  370 (678)
T KOG0127|consen  291 EGKTVFVRNLPFDTTEEELKEHFSKFGEVKYAIIVKDKDTGHSKGTAFVKFKTQIAAQNCIEAASPASEDGSVLLDGRLL  370 (678)
T ss_pred             ccceEEEecCCccccHHHHHHHHHhhccceeEEEEeccCCCCcccceEEEeccHHHHHHHHHhcCccCCCceEEEeccEE
Confidence            3579999999999999999999999999999999999999999999999999999999999876     24 78999999


Q ss_pred             EEEeccc
Q 007792          315 HVDFSQS  321 (589)
Q Consensus       315 ~V~~a~~  321 (589)
                      .|..|-+
T Consensus       371 kv~~Av~  377 (678)
T KOG0127|consen  371 KVTLAVT  377 (678)
T ss_pred             eeeeccc
Confidence            9998865

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

Probab=99.14  E-value=3.2e-11  Score=119.07  Aligned_cols=77  Identities=23%  Similarity=0.428  Sum_probs=74.7

Q ss_pred             ceEEEecCCCCCCHHHHHHHhccCCCeEEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHhcCCceeCCeEEEEEec
Q 007792          243 NVLFVCKLNPVTEDEDLHTIFSRFGTVVSAEIIRDFKTGDSLNYAFIEFENRQACERAYSKMDNALIDDRRIHVDFS  319 (589)
Q Consensus       243 ~~i~V~nL~~~~te~~L~~~F~~~G~v~~~~i~~d~~tg~~~g~aFV~f~~~~~a~~A~~~l~g~~i~gr~i~V~~a  319 (589)
                      +.||||.|.+++.|+.|+..|..||+|++|.+.+|+.|++.+|||||+|+-.+.|+.|++.|||..++|+.|+|...
T Consensus       114 cRvYVGSIsfEl~EDtiR~AF~PFGPIKSInMSWDp~T~kHKgFAFVEYEvPEaAqLAlEqMNg~mlGGRNiKVgrP  190 (544)
T KOG0124|consen  114 CRVYVGSISFELREDTIRRAFDPFGPIKSINMSWDPATGKHKGFAFVEYEVPEAAQLALEQMNGQMLGGRNIKVGRP  190 (544)
T ss_pred             HheeeeeeEEEechHHHHhhccCCCCcceeecccccccccccceEEEEEeCcHHHHHHHHHhccccccCccccccCC
Confidence            68999999999999999999999999999999999999999999999999999999999999999999999999753

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

Probab=99.12  E-value=1.9e-10  Score=119.39  Aligned_cols=82  Identities=29%  Similarity=0.495  Sum_probs=75.2

Q ss_pred             CCceEEEecCCCCCCHHHHHHHhccCCCeEEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHhcCCceeCCeEEEEEecc
Q 007792          241 PENVLFVCKLNPVTEDEDLHTIFSRFGTVVSAEIIRDFKTGDSLNYAFIEFENRQACERAYSKMDNALIDDRRIHVDFSQ  320 (589)
Q Consensus       241 ~~~~i~V~nL~~~~te~~L~~~F~~~G~v~~~~i~~d~~tg~~~g~aFV~f~~~~~a~~A~~~l~g~~i~gr~i~V~~a~  320 (589)
                      +.-.|.|.||||.+...+|+.+|+.||.|..|.|+..+ .|+.+|||||.|....+|..||+.|||.+|+|++|-|.||-
T Consensus       116 ~k~rLIIRNLPf~~k~~dLk~vFs~~G~V~Ei~IP~k~-dgklcGFaFV~fk~~~dA~~Al~~~N~~~i~gR~VAVDWAV  194 (678)
T KOG0127|consen  116 PKWRLIIRNLPFKCKKPDLKNVFSNFGKVVEIVIPRKK-DGKLCGFAFVQFKEKKDAEKALEFFNGNKIDGRPVAVDWAV  194 (678)
T ss_pred             ccceEEeecCCcccCcHHHHHHHhhcceEEEEEcccCC-CCCccceEEEEEeeHHHHHHHHHhccCceecCceeEEeeec
Confidence            35689999999999999999999999999999999764 46667999999999999999999999999999999999998


Q ss_pred             ccc
Q 007792          321 SVS  323 (589)
Q Consensus       321 ~~~  323 (589)
                      ++.
T Consensus       195 ~Kd  197 (678)
T KOG0127|consen  195 DKD  197 (678)
T ss_pred             ccc
Confidence            754

>PF13893 RRM_5: RNA recognition motif

Probab=99.12  E-value=3e-10  Score=85.90  Aligned_cols=56  Identities=25%  Similarity=0.572  Sum_probs=50.9

Q ss_pred             HHHHhccCCCeEEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHhcCCceeCCeEEEEEec
Q 007792          259 LHTIFSRFGTVVSAEIIRDFKTGDSLNYAFIEFENRQACERAYSKMDNALIDDRRIHVDFS  319 (589)
Q Consensus       259 L~~~F~~~G~v~~~~i~~d~~tg~~~g~aFV~f~~~~~a~~A~~~l~g~~i~gr~i~V~~a  319 (589)
                      |.++|++||+|..+.+....     .++|||+|.+.++|..|+..|||..|.|++|+|+||
T Consensus         1 L~~~f~~fG~V~~i~~~~~~-----~~~a~V~f~~~~~A~~a~~~l~~~~~~g~~l~V~~a   56 (56)
T PF13893_consen    1 LYKLFSKFGEVKKIKIFKKK-----RGFAFVEFASVEDAQKAIEQLNGRQFNGRPLKVSYA   56 (56)
T ss_dssp             HHHHHTTTS-EEEEEEETTS-----TTEEEEEESSHHHHHHHHHHHTTSEETTEEEEEEEE
T ss_pred             ChHHhCCcccEEEEEEEeCC-----CCEEEEEECCHHHHHHHHHHhCCCEECCcEEEEEEC
Confidence            67899999999999997653     589999999999999999999999999999999986

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

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

Probab=99.11  E-value=1.3e-10  Score=105.03  Aligned_cols=83  Identities=29%  Similarity=0.510  Sum_probs=76.9

Q ss_pred             CCCCceEEEecCCCCCCHHHHHHHhccCCCeEE-EEEeecCCCCCcccEEEEEEcCHHHHHHHHHhcCCceeCCeEEEEE
Q 007792          239 KPPENVLFVCKLNPVTEDEDLHTIFSRFGTVVS-AEIIRDFKTGDSLNYAFIEFENRQACERAYSKMDNALIDDRRIHVD  317 (589)
Q Consensus       239 ~~~~~~i~V~nL~~~~te~~L~~~F~~~G~v~~-~~i~~d~~tg~~~g~aFV~f~~~~~a~~A~~~l~g~~i~gr~i~V~  317 (589)
                      -..+..|||+||.+.+++..|..+|+.||.|.. -.|+.+..||.++|||||.|.+.+.+.+|+..|||..++.++|.|.
T Consensus        93 l~vganlfvgNLd~~vDe~~L~dtFsafG~l~~~P~i~rd~~tg~~~~~g~i~~~sfeasd~ai~s~ngq~l~nr~itv~  172 (203)
T KOG0131|consen   93 LDVGANLFVGNLDPEVDEKLLYDTFSAFGVLISPPKIMRDPDTGNPKGFGFINYASFEASDAAIGSMNGQYLCNRPITVS  172 (203)
T ss_pred             ccccccccccccCcchhHHHHHHHHHhccccccCCcccccccCCCCCCCeEEechhHHHHHHHHHHhccchhcCCceEEE
Confidence            344589999999999999999999999999875 4788999999999999999999999999999999999999999999


Q ss_pred             eccc
Q 007792          318 FSQS  321 (589)
Q Consensus       318 ~a~~  321 (589)
                      ++..
T Consensus       173 ya~k  176 (203)
T KOG0131|consen  173 YAFK  176 (203)
T ss_pred             EEEe
Confidence            9975

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

Probab=99.08  E-value=1.7e-10  Score=116.72  Aligned_cols=81  Identities=22%  Similarity=0.500  Sum_probs=74.4

Q ss_pred             CceEEEecCCCCCCHHHHHHHhccCCCeEEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHhcCCc-eeCC--eEEEEEe
Q 007792          242 ENVLFVCKLNPVTEDEDLHTIFSRFGTVVSAEIIRDFKTGDSLNYAFIEFENRQACERAYSKMDNA-LIDD--RRIHVDF  318 (589)
Q Consensus       242 ~~~i~V~nL~~~~te~~L~~~F~~~G~v~~~~i~~d~~tg~~~g~aFV~f~~~~~a~~A~~~l~g~-~i~g--r~i~V~~  318 (589)
                      ..++|||.||..++|.+|+++|++||.|.+|.|++|+.|+.++|||||.|.+.++|.+|+.+|++. .|-|  .+|.|.+
T Consensus        34 ~vKlfVgqIprt~sE~dlr~lFe~yg~V~einl~kDk~t~~s~gcCFv~~~trk~a~~a~~Alhn~ktlpG~~~pvqvk~  113 (510)
T KOG0144|consen   34 AVKLFVGQIPRTASEKDLRELFEKYGNVYEINLIKDKSTGQSKGCCFVKYYTRKEADEAINALHNQKTLPGMHHPVQVKY  113 (510)
T ss_pred             hhhheeccCCccccHHHHHHHHHHhCceeEEEeecccccCcccceEEEEeccHHHHHHHHHHhhcccccCCCCcceeecc
Confidence            468999999999999999999999999999999999999999999999999999999999999884 4555  7888988


Q ss_pred             cccc
Q 007792          319 SQSV  322 (589)
Q Consensus       319 a~~~  322 (589)
                      |...
T Consensus       114 Ad~E  117 (510)
T KOG0144|consen  114 ADGE  117 (510)
T ss_pred             cchh
Confidence            8763

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

Probab=98.97  E-value=9.8e-10  Score=114.83  Aligned_cols=114  Identities=21%  Similarity=0.456  Sum_probs=87.1

Q ss_pred             cccCCCCcccccCCHHHHHHHHHhhhh---hhhhhhhhccCCCCCCCCCCCCceEEEecCCCCCCHHHHHHHhccCCCeE
Q 007792          194 RLEDDWVPLDEQLSAAELEQVIRSKDA---RSSAVVLESIGDIPDADIKPPENVLFVCKLNPVTEDEDLHTIFSRFGTVV  270 (589)
Q Consensus       194 ~l~~~~~~~~~~~~~~~~e~~~~~~~~---~~~~~~~~~~~~~~~~~~~~~~~~i~V~nL~~~~te~~L~~~F~~~G~v~  270 (589)
                      .|.++++++.   ++...+.++.+...   +.....+....        .....|||.||++.++...|..+|+.||.|+
T Consensus        36 slgy~yvnf~---~~~da~~A~~~~n~~~~~~~~~rim~s~--------rd~~~~~i~nl~~~~~~~~~~d~f~~~g~il  104 (369)
T KOG0123|consen   36 SLGYAYVNFQ---QPADAERALDTMNFDVLKGKPIRIMWSQ--------RDPSLVFIKNLDESIDNKSLYDTFSEFGNIL  104 (369)
T ss_pred             ccceEEEecC---CHHHHHHHHHHcCCcccCCcEEEeehhc--------cCCceeeecCCCcccCcHHHHHHHHhhcCee
Confidence            3566666655   45555655555444   22222111111        1122399999999999999999999999999


Q ss_pred             EEEEeecCCCCCcccEEEEEEcCHHHHHHHHHhcCCceeCCeEEEEEeccc
Q 007792          271 SAEIIRDFKTGDSLNYAFIEFENRQACERAYSKMDNALIDDRRIHVDFSQS  321 (589)
Q Consensus       271 ~~~i~~d~~tg~~~g~aFV~f~~~~~a~~A~~~l~g~~i~gr~i~V~~a~~  321 (589)
                      +|+++.+.. | ++|| ||+|+++++|..||..|||..+.|+.|-|.....
T Consensus       105 S~kv~~~~~-g-~kg~-FV~f~~e~~a~~ai~~~ng~ll~~kki~vg~~~~  152 (369)
T KOG0123|consen  105 SCKVATDEN-G-SKGY-FVQFESEESAKKAIEKLNGMLLNGKKIYVGLFER  152 (369)
T ss_pred             EEEEEEcCC-C-ceee-EEEeCCHHHHHHHHHHhcCcccCCCeeEEeeccc
Confidence            999999854 4 9999 9999999999999999999999999999988765

>KOG4676 consensus Splicing factor, arginine/serine-rich [RNA processing and modification]

Probab=98.95  E-value=1.4e-09  Score=108.78  Aligned_cols=82  Identities=15%  Similarity=0.308  Sum_probs=63.0

Q ss_pred             ceEEEecCCCCCCHHHHHHHhccCCCeEEEEEeecCC---CCCcccEEEEEEcCHHHHHHHHHhcCCceeCCeEEEEEec
Q 007792          243 NVLFVCKLNPVTEDEDLHTIFSRFGTVVSAEIIRDFK---TGDSLNYAFIEFENRQACERAYSKMDNALIDDRRIHVDFS  319 (589)
Q Consensus       243 ~~i~V~nL~~~~te~~L~~~F~~~G~v~~~~i~~d~~---tg~~~g~aFV~f~~~~~a~~A~~~l~g~~i~gr~i~V~~a  319 (589)
                      ..|.|.||.+.+|.++++.+|+..|+|..+.|+.+..   .....-.|||.|.+...+..|-.+.|-+.|+--.|+|-+.
T Consensus         8 ~vIqvanispsat~dqm~tlFg~lGkI~elrlyp~~~d~~~pv~sRtcyVkf~d~~sv~vaQhLtntvfvdraliv~p~~   87 (479)
T KOG4676|consen    8 GVIQVANISPSATKDQMQTLFGNLGKIPELRLYPNVDDSKIPVISRTCYVKFLDSQSVTVAQHLTNTVFVDRALIVRPYG   87 (479)
T ss_pred             ceeeecccCchhhHHHHHHHHhhccccccccccCCCCCccCcceeeeEEEeccCCcceeHHhhhccceeeeeeEEEEecC
Confidence            3899999999999999999999999999999876422   2334568999999999999998654545555555566665


Q ss_pred             ccccc
Q 007792          320 QSVSK  324 (589)
Q Consensus       320 ~~~~~  324 (589)
                      .....
T Consensus        88 ~~~~p   92 (479)
T KOG4676|consen   88 DEVIP   92 (479)
T ss_pred             CCCCc
Confidence            54433

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

Probab=98.95  E-value=2e-09  Score=99.62  Aligned_cols=82  Identities=27%  Similarity=0.431  Sum_probs=76.6

Q ss_pred             CCceEEEecCCCCCCHHHHHHHhccC-CCeEEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHhcCCceeCCeEEEEEec
Q 007792          241 PENVLFVCKLNPVTEDEDLHTIFSRF-GTVVSAEIIRDFKTGDSLNYAFIEFENRQACERAYSKMDNALIDDRRIHVDFS  319 (589)
Q Consensus       241 ~~~~i~V~nL~~~~te~~L~~~F~~~-G~v~~~~i~~d~~tg~~~g~aFV~f~~~~~a~~A~~~l~g~~i~gr~i~V~~a  319 (589)
                      ....+||..||..+.+.+|..+|.+| |.|..+.+.+++.||.++|||||+|++.+.|.-|.+.||+..|.|+.|.|.+-
T Consensus        48 ~~g~~~~~~~p~g~~e~~~~~~~~q~~g~v~r~rlsRnkrTGNSKgYAFVEFEs~eVA~IaAETMNNYLl~e~lL~c~vm  127 (214)
T KOG4208|consen   48 IEGVVYVDHIPHGFFETEILNYFRQFGGTVTRFRLSRNKRTGNSKGYAFVEFESEEVAKIAAETMNNYLLMEHLLECHVM  127 (214)
T ss_pred             CccceeecccccchhHHHHhhhhhhcCCeeEEEEeecccccCCcCceEEEEeccHHHHHHHHHHhhhhhhhhheeeeEEe
Confidence            45789999999999999999999998 78888899899999999999999999999999999999999999999999997


Q ss_pred             ccc
Q 007792          320 QSV  322 (589)
Q Consensus       320 ~~~  322 (589)
                      .+.
T Consensus       128 ppe  130 (214)
T KOG4208|consen  128 PPE  130 (214)
T ss_pred             Cch
Confidence            664

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

Probab=98.91  E-value=3.8e-09  Score=106.95  Aligned_cols=79  Identities=19%  Similarity=0.381  Sum_probs=73.5

Q ss_pred             CceEEEecCCCCCCHHHHHHHhc-cCCCeEEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHhcCCceeCCeEEEEEecc
Q 007792          242 ENVLFVCKLNPVTEDEDLHTIFS-RFGTVVSAEIIRDFKTGDSLNYAFIEFENRQACERAYSKMDNALIDDRRIHVDFSQ  320 (589)
Q Consensus       242 ~~~i~V~nL~~~~te~~L~~~F~-~~G~v~~~~i~~d~~tg~~~g~aFV~f~~~~~a~~A~~~l~g~~i~gr~i~V~~a~  320 (589)
                      ...+||.|||+++.|++|+.+|. +.|+|.+|.+..| .+||++|+|.|+|++++.+++|++.||...+.|++|.|+-..
T Consensus        44 ~R~vfItNIpyd~rWqdLKdLvrekvGev~yveLl~D-~~GK~rGcavVEFk~~E~~qKa~E~lnk~~~~GR~l~vKEd~  122 (608)
T KOG4212|consen   44 DRSVFITNIPYDYRWQDLKDLVREKVGEVEYVELLFD-ESGKARGCAVVEFKDPENVQKALEKLNKYEVNGRELVVKEDH  122 (608)
T ss_pred             cceEEEecCcchhhhHhHHHHHHHhcCceEeeeeecc-cCCCcCCceEEEeeCHHHHHHHHHHhhhccccCceEEEeccC
Confidence            45699999999999999999996 7899999999999 679999999999999999999999999999999999998654


Q ss_pred             c
Q 007792          321 S  321 (589)
Q Consensus       321 ~  321 (589)
                      .
T Consensus       123 d  123 (608)
T KOG4212|consen  123 D  123 (608)
T ss_pred             c
Confidence            3

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

Probab=98.89  E-value=3.9e-09  Score=109.74  Aligned_cols=82  Identities=21%  Similarity=0.440  Sum_probs=77.2

Q ss_pred             CceEEEecCCCCCCHHHHHHHhccCCCeEEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHhcCCceeCCeEEEEEeccc
Q 007792          242 ENVLFVCKLNPVTEDEDLHTIFSRFGTVVSAEIIRDFKTGDSLNYAFIEFENRQACERAYSKMDNALIDDRRIHVDFSQS  321 (589)
Q Consensus       242 ~~~i~V~nL~~~~te~~L~~~F~~~G~v~~~~i~~d~~tg~~~g~aFV~f~~~~~a~~A~~~l~g~~i~gr~i~V~~a~~  321 (589)
                      ..+|||.+|+..|...+|+.+|++||+|+-++||.+..+...+||+||++.+..+|.+||..|+-++|+|+.|.|+-++.
T Consensus       405 gRNlWVSGLSstTRAtDLKnlFSKyGKVvGAKVVTNaRsPGaRCYGfVTMSts~eAtkCI~hLHrTELHGrmISVEkaKN  484 (940)
T KOG4661|consen  405 GRNLWVSGLSSTTRATDLKNLFSKYGKVVGAKVVTNARSPGARCYGFVTMSTSAEATKCIEHLHRTELHGRMISVEKAKN  484 (940)
T ss_pred             ccceeeeccccchhhhHHHHHHHHhcceeceeeeecCCCCCcceeEEEEecchHHHHHHHHHhhhhhhcceeeeeeeccc
Confidence            35899999999999999999999999999999999988888899999999999999999999999999999999999876


Q ss_pred             cc
Q 007792          322 VS  323 (589)
Q Consensus       322 ~~  323 (589)
                      .+
T Consensus       485 Ep  486 (940)
T KOG4661|consen  485 EP  486 (940)
T ss_pred             Cc
Confidence            43

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

Probab=98.89  E-value=5.1e-09  Score=98.53  Aligned_cols=81  Identities=22%  Similarity=0.455  Sum_probs=73.1

Q ss_pred             CCceEEEecCCCCCCHHHHHH----HhccCCCeEEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHhcCCceeCCeEEEE
Q 007792          241 PENVLFVCKLNPVTEDEDLHT----IFSRFGTVVSAEIIRDFKTGDSLNYAFIEFENRQACERAYSKMDNALIDDRRIHV  316 (589)
Q Consensus       241 ~~~~i~V~nL~~~~te~~L~~----~F~~~G~v~~~~i~~d~~tg~~~g~aFV~f~~~~~a~~A~~~l~g~~i~gr~i~V  316 (589)
                      |+.||||-||+..+..++|+.    +|++||.|..|...   .|.+.+|-|||.|.+.+.|-.|+..|+|+.+-|+.+.|
T Consensus         8 pn~TlYInnLnekI~~~elkrsL~~LFsqfG~ildI~a~---kt~KmRGQA~VvFk~~~~As~A~r~l~gfpFygK~mri   84 (221)
T KOG4206|consen    8 PNGTLYINNLNEKIKKDELKRSLYLLFSQFGKILDISAF---KTPKMRGQAFVVFKETEAASAALRALQGFPFYGKPMRI   84 (221)
T ss_pred             CCceEeehhccccccHHHHHHHHHHHHHhhCCeEEEEec---CCCCccCceEEEecChhHHHHHHHHhcCCcccCchhhe
Confidence            344999999999999998887    99999999988775   36789999999999999999999999999999999999


Q ss_pred             Eecccccc
Q 007792          317 DFSQSVSK  324 (589)
Q Consensus       317 ~~a~~~~~  324 (589)
                      +||+....
T Consensus        85 qyA~s~sd   92 (221)
T KOG4206|consen   85 QYAKSDSD   92 (221)
T ss_pred             ecccCccc
Confidence            99987544

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

Probab=98.88  E-value=1.3e-09  Score=116.86  Aligned_cols=131  Identities=13%  Similarity=0.284  Sum_probs=97.4

Q ss_pred             ccccCCCCcccccCCHHHHHHHHHhhhhhhhhhhhhccC-----CC-CCCCCCCCCceEEEecCCCCCCHHHHHHHhccC
Q 007792          193 VRLEDDWVPLDEQLSAAELEQVIRSKDARSSAVVLESIG-----DI-PDADIKPPENVLFVCKLNPVTEDEDLHTIFSRF  266 (589)
Q Consensus       193 ~~l~~~~~~~~~~~~~~~~e~~~~~~~~~~~~~~~~~~~-----~~-~~~~~~~~~~~i~V~nL~~~~te~~L~~~F~~~  266 (589)
                      +.+++.+|++....++..+.++++..........+..--     .. .....+...+.|+|.|||+.++-.+|+++|..|
T Consensus       558 lSmGfgFVEF~~~e~A~~a~k~lqgtvldGH~l~lk~S~~k~~~~~gK~~~~kk~~tKIlVRNipFeAt~rEVr~LF~aF  637 (725)
T KOG0110|consen  558 LSMGFGFVEFAKPESAQAALKALQGTVLDGHKLELKISENKPASTVGKKKSKKKKGTKILVRNIPFEATKREVRKLFTAF  637 (725)
T ss_pred             cccceeEEEecCHHHHHHHHHHhcCceecCceEEEEeccCccccccccccccccccceeeeeccchHHHHHHHHHHHhcc
Confidence            456778888776555555555555333322222111111     00 111223346799999999999999999999999


Q ss_pred             CCeEEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHhcCCceeCCeEEEEEeccccc
Q 007792          267 GTVVSAEIIRDFKTGDSLNYAFIEFENRQACERAYSKMDNALIDDRRIHVDFSQSVS  323 (589)
Q Consensus       267 G~v~~~~i~~d~~tg~~~g~aFV~f~~~~~a~~A~~~l~g~~i~gr~i~V~~a~~~~  323 (589)
                      |.|..|.|+.-...+.++|||||+|-+..+|..|+.+|..+-|.|+.|.++||+.-.
T Consensus       638 GqlksvRlPKK~~k~a~rGF~Fv~f~t~~ea~nA~~al~STHlyGRrLVLEwA~~d~  694 (725)
T KOG0110|consen  638 GQLKSVRLPKKIGKGAHRGFGFVDFLTPREAKNAFDALGSTHLYGRRLVLEWAKSDN  694 (725)
T ss_pred             cceeeeccchhhcchhhccceeeeccCcHHHHHHHHhhcccceechhhheehhccch
Confidence            999999998765566679999999999999999999999999999999999998633

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

Probab=98.86  E-value=4e-09  Score=113.25  Aligned_cols=78  Identities=31%  Similarity=0.494  Sum_probs=70.5

Q ss_pred             ceEEEecCCCCCCHHHHHHHhccCCCeEEEEEeecCCC---CCcccEEEEEEcCHHHHHHHHHhcCCceeCCeEEEEEec
Q 007792          243 NVLFVCKLNPVTEDEDLHTIFSRFGTVVSAEIIRDFKT---GDSLNYAFIEFENRQACERAYSKMDNALIDDRRIHVDFS  319 (589)
Q Consensus       243 ~~i~V~nL~~~~te~~L~~~F~~~G~v~~~~i~~d~~t---g~~~g~aFV~f~~~~~a~~A~~~l~g~~i~gr~i~V~~a  319 (589)
                      ++|||.||++.+|.+.|...|...|.|..+.|...+..   -.+.|||||+|.+.++|+.|++.|+|+.|+|+.|.|.++
T Consensus       516 t~lfvkNlnf~Tt~e~l~~~F~k~G~VlS~~I~kkkd~~~k~lSmGfgFVEF~~~e~A~~a~k~lqgtvldGH~l~lk~S  595 (725)
T KOG0110|consen  516 TKLFVKNLNFDTTLEDLEDLFSKQGTVLSIEISKKKDPANKYLSMGFGFVEFAKPESAQAALKALQGTVLDGHKLELKIS  595 (725)
T ss_pred             hhhhhhcCCcccchhHHHHHHHhcCeEEEEEEeccccccccccccceeEEEecCHHHHHHHHHHhcCceecCceEEEEec
Confidence            34999999999999999999999999999988765432   235699999999999999999999999999999999999


Q ss_pred             c
Q 007792          320 Q  320 (589)
Q Consensus       320 ~  320 (589)
                      .
T Consensus       596 ~  596 (725)
T KOG0110|consen  596 E  596 (725)
T ss_pred             c
Confidence            8

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

Probab=98.83  E-value=3.3e-09  Score=107.17  Aligned_cols=117  Identities=17%  Similarity=0.334  Sum_probs=94.0

Q ss_pred             HHHHHHHHHhhhhhhhhhhhhccCCCCCCCCCC-----CCceEEEecCCCCCCHHHHHHHhccCCCeEEEEEeecCCCCC
Q 007792          208 AAELEQVIRSKDARSSAVVLESIGDIPDADIKP-----PENVLFVCKLNPVTEDEDLHTIFSRFGTVVSAEIIRDFKTGD  282 (589)
Q Consensus       208 ~~~~e~~~~~~~~~~~~~~~~~~~~~~~~~~~~-----~~~~i~V~nL~~~~te~~L~~~F~~~G~v~~~~i~~d~~tg~  282 (589)
                      ++.+..++....++..+..++.+.+++......     ...+||||+||..+++.+|+++|.+||.|..+.++.|..+..
T Consensus        58 ~~~v~~vl~~~~h~~dgr~ve~k~av~r~~~~~~~~~~~tkkiFvGG~~~~~~e~~~r~yfe~~g~v~~~~~~~d~~~~~  137 (311)
T KOG4205|consen   58 PEGVDAVLNARTHKLDGRSVEPKRAVSREDQTKVGRHLRTKKIFVGGLPPDTTEEDFKDYFEQFGKVADVVIMYDKTTSR  137 (311)
T ss_pred             CcchheeecccccccCCccccceeccCcccccccccccceeEEEecCcCCCCchHHHhhhhhccceeEeeEEeecccccc
Confidence            334445555555555555566555555544333     345999999999999999999999999999999999999999


Q ss_pred             cccEEEEEEcCHHHHHHHHHhcCCceeCCeEEEEEeccccccc
Q 007792          283 SLNYAFIEFENRQACERAYSKMDNALIDDRRIHVDFSQSVSKL  325 (589)
Q Consensus       283 ~~g~aFV~f~~~~~a~~A~~~l~g~~i~gr~i~V~~a~~~~~~  325 (589)
                      ++||+||.|.+.+++..++ ...-+.|+|+.+.|..|.++...
T Consensus       138 ~rgFgfv~~~~e~sVdkv~-~~~f~~~~gk~vevkrA~pk~~~  179 (311)
T KOG4205|consen  138 PRGFGFVTFDSEDSVDKVT-LQKFHDFNGKKVEVKRAIPKEVM  179 (311)
T ss_pred             cccceeeEeccccccceec-ccceeeecCceeeEeeccchhhc
Confidence            9999999999999999998 46788999999999999885543

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

Probab=98.77  E-value=2e-08  Score=111.14  Aligned_cols=82  Identities=23%  Similarity=0.389  Sum_probs=69.2

Q ss_pred             CCCceEEEecCCCC----------CCHHHHHHHhccCCCeEEEEEeecC---CCCCcccEEEEEEcCHHHHHHHHHhcCC
Q 007792          240 PPENVLFVCKLNPV----------TEDEDLHTIFSRFGTVVSAEIIRDF---KTGDSLNYAFIEFENRQACERAYSKMDN  306 (589)
Q Consensus       240 ~~~~~i~V~nL~~~----------~te~~L~~~F~~~G~v~~~~i~~d~---~tg~~~g~aFV~f~~~~~a~~A~~~l~g  306 (589)
                      .+..+|+|.||...          ...++|+++|++||.|+.|.|+.+.   .++...|||||+|.+.++|+.||..|||
T Consensus       407 ~~s~v~~l~N~~~~~~l~~d~~~~~~~edl~~~f~~~G~v~~v~i~~~~~~~~~~~~~G~~fV~F~~~e~A~~A~~~lnG  486 (509)
T TIGR01642       407 KPTKVVQLTNLVTGDDLMDDEEYEEIYEDVKTEFSKYGPLINIVIPRPNGDRNSTPGVGKVFLEYADVRSAEKAMEGMNG  486 (509)
T ss_pred             CCceEEEeccCCchhHhcCcchHHHHHHHHHHHHHhcCCeeEEEeeccCcCCCcCCCcceEEEEECCHHHHHHHHHHcCC
Confidence            35678999999642          1236789999999999999998652   3456789999999999999999999999


Q ss_pred             ceeCCeEEEEEeccc
Q 007792          307 ALIDDRRIHVDFSQS  321 (589)
Q Consensus       307 ~~i~gr~i~V~~a~~  321 (589)
                      .+|+|+.|.|.|...
T Consensus       487 r~~~gr~v~~~~~~~  501 (509)
T TIGR01642       487 RKFNDRVVVAAFYGE  501 (509)
T ss_pred             CEECCeEEEEEEeCH
Confidence            999999999999754

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

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

Probab=98.76  E-value=1.3e-08  Score=109.87  Aligned_cols=77  Identities=26%  Similarity=0.453  Sum_probs=71.8

Q ss_pred             CCceEEEecCCCCCCHHHHHHHhccCCCeEEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHhcCCceeCCeEEEEEecc
Q 007792          241 PENVLFVCKLNPVTEDEDLHTIFSRFGTVVSAEIIRDFKTGDSLNYAFIEFENRQACERAYSKMDNALIDDRRIHVDFSQ  320 (589)
Q Consensus       241 ~~~~i~V~nL~~~~te~~L~~~F~~~G~v~~~~i~~d~~tg~~~g~aFV~f~~~~~a~~A~~~l~g~~i~gr~i~V~~a~  320 (589)
                      ..+|||||+|+.++++.+|..+|+.||+|.+|.++.      ++|||||.+....+|.+|+.+|+...|.++.|+|.||.
T Consensus       420 ~SrTLwvG~i~k~v~e~dL~~~feefGeiqSi~li~------~R~cAfI~M~~RqdA~kalqkl~n~kv~~k~Iki~Wa~  493 (894)
T KOG0132|consen  420 CSRTLWVGGIPKNVTEQDLANLFEEFGEIQSIILIP------PRGCAFIKMVRRQDAEKALQKLSNVKVADKTIKIAWAV  493 (894)
T ss_pred             eeeeeeeccccchhhHHHHHHHHHhcccceeEeecc------CCceeEEEEeehhHHHHHHHHHhcccccceeeEEeeec
Confidence            457999999999999999999999999999999876      56899999999999999999999999999999999997


Q ss_pred             ccc
Q 007792          321 SVS  323 (589)
Q Consensus       321 ~~~  323 (589)
                      .+.
T Consensus       494 g~G  496 (894)
T KOG0132|consen  494 GKG  496 (894)
T ss_pred             cCC
Confidence            643

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

Probab=98.73  E-value=2e-08  Score=99.61  Aligned_cols=80  Identities=23%  Similarity=0.411  Sum_probs=75.9

Q ss_pred             CceEEEecCCCCCCHHHHHHHhccCCCeEEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHhcCCceeCCeEEEEEeccc
Q 007792          242 ENVLFVCKLNPVTEDEDLHTIFSRFGTVVSAEIIRDFKTGDSLNYAFIEFENRQACERAYSKMDNALIDDRRIHVDFSQS  321 (589)
Q Consensus       242 ~~~i~V~nL~~~~te~~L~~~F~~~G~v~~~~i~~d~~tg~~~g~aFV~f~~~~~a~~A~~~l~g~~i~gr~i~V~~a~~  321 (589)
                      .+.|||..+.+++++++|+.+|+-||+|+.|.+...+.++..+||+||+|.+..+...||..||-+.++|.-|+|--+-.
T Consensus       210 fnRiYVaSvHpDLSe~DiKSVFEAFG~I~~C~LAr~pt~~~HkGyGfiEy~n~qs~~eAiasMNlFDLGGQyLRVGk~vT  289 (544)
T KOG0124|consen  210 FNRIYVASVHPDLSETDIKSVFEAFGEIVKCQLARAPTGRGHKGYGFIEYNNLQSQSEAIASMNLFDLGGQYLRVGKCVT  289 (544)
T ss_pred             hheEEeeecCCCccHHHHHHHHHhhcceeeEEeeccCCCCCccceeeEEeccccchHHHhhhcchhhcccceEecccccC
Confidence            57999999999999999999999999999999999999999999999999999999999999999999999999976543

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

Probab=98.72  E-value=2.4e-08  Score=104.43  Aligned_cols=75  Identities=32%  Similarity=0.503  Sum_probs=70.7

Q ss_pred             ceEEEecCCCCCCHHHHHHHhccCCCeEEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHhcCCceeCCeEEEEEecccc
Q 007792          243 NVLFVCKLNPVTEDEDLHTIFSRFGTVVSAEIIRDFKTGDSLNYAFIEFENRQACERAYSKMDNALIDDRRIHVDFSQSV  322 (589)
Q Consensus       243 ~~i~V~nL~~~~te~~L~~~F~~~G~v~~~~i~~d~~tg~~~g~aFV~f~~~~~a~~A~~~l~g~~i~gr~i~V~~a~~~  322 (589)
                      ..||||   +.+|+..|.++|+.+|+|.+++|+.+. |  +.|||||.|.+..+|.+||..||...|.|++|.|.|+...
T Consensus         2 ~sl~vg---~~v~e~~l~~~f~~~~~v~s~rvc~d~-t--slgy~yvnf~~~~da~~A~~~~n~~~~~~~~~rim~s~rd   75 (369)
T KOG0123|consen    2 ASLYVG---PDVTEAMLFDKFSPAGPVLSIRVCRDA-T--SLGYAYVNFQQPADAERALDTMNFDVLKGKPIRIMWSQRD   75 (369)
T ss_pred             CceecC---CcCChHHHHHHhcccCCceeEEEeecC-C--ccceEEEecCCHHHHHHHHHHcCCcccCCcEEEeehhccC
Confidence            468999   999999999999999999999999997 6  9999999999999999999999999999999999999754


Q ss_pred             c
Q 007792          323 S  323 (589)
Q Consensus       323 ~  323 (589)
                      +
T Consensus        76 ~   76 (369)
T KOG0123|consen   76 P   76 (369)
T ss_pred             C
Confidence            3

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

Probab=98.72  E-value=7.3e-08  Score=95.53  Aligned_cols=79  Identities=16%  Similarity=0.310  Sum_probs=72.8

Q ss_pred             CceEEEecCCCCCCHHHHHHHhccCCCeEE--------EEEeecCCCCCcccEEEEEEcCHHHHHHHHHhcCCceeCCeE
Q 007792          242 ENVLFVCKLNPVTEDEDLHTIFSRFGTVVS--------AEIIRDFKTGDSLNYAFIEFENRQACERAYSKMDNALIDDRR  313 (589)
Q Consensus       242 ~~~i~V~nL~~~~te~~L~~~F~~~G~v~~--------~~i~~d~~tg~~~g~aFV~f~~~~~a~~A~~~l~g~~i~gr~  313 (589)
                      ++.|||.|||.++|.+++.++|++||.|..        |+|..+.. |+.+|-|+|.|.-.+++..||+.|++..|.|+.
T Consensus       134 Nt~VYVsgLP~DiT~dE~~~~~sKcGiI~~d~~t~epk~KlYrd~~-G~lKGDaLc~y~K~ESVeLA~~ilDe~~~rg~~  212 (382)
T KOG1548|consen  134 NTSVYVSGLPLDITVDEFAEVMSKCGIIMRDPQTGEPKVKLYRDNQ-GKLKGDALCCYIKRESVELAIKILDEDELRGKK  212 (382)
T ss_pred             CceEEecCCCCcccHHHHHHHHHhcceEeccCCCCCeeEEEEecCC-CCccCceEEEeecccHHHHHHHHhCcccccCcE
Confidence            456999999999999999999999998863        78888844 999999999999999999999999999999999


Q ss_pred             EEEEeccc
Q 007792          314 IHVDFSQS  321 (589)
Q Consensus       314 i~V~~a~~  321 (589)
                      |+|+.|+-
T Consensus       213 ~rVerAkf  220 (382)
T KOG1548|consen  213 LRVERAKF  220 (382)
T ss_pred             EEEehhhh
Confidence            99999874

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

Probab=98.69  E-value=6.4e-08  Score=101.56  Aligned_cols=80  Identities=25%  Similarity=0.391  Sum_probs=69.1

Q ss_pred             ceEEEecCCCCCCHHHHHHHhccCCCeEEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHhcCCceeCCeEEEEEecccc
Q 007792          243 NVLFVCKLNPVTEDEDLHTIFSRFGTVVSAEIIRDFKTGDSLNYAFIEFENRQACERAYSKMDNALIDDRRIHVDFSQSV  322 (589)
Q Consensus       243 ~~i~V~nL~~~~te~~L~~~F~~~G~v~~~~i~~d~~tg~~~g~aFV~f~~~~~a~~A~~~l~g~~i~gr~i~V~~a~~~  322 (589)
                      .+|||.|||++++..+|+++|.+||.|+...|..-...+++.|||||+|.+..+++.||++ +-..|++++|.|+-.++.
T Consensus       289 ~~i~V~nlP~da~~~~l~~~Fk~FG~Ik~~~I~vr~~~~~~~~fgFV~f~~~~~~~~~i~A-sp~~ig~~kl~Veek~~~  367 (419)
T KOG0116|consen  289 LGIFVKNLPPDATPAELEEVFKQFGPIKEGGIQVRSPGGKNPCFGFVEFENAAAVQNAIEA-SPLEIGGRKLNVEEKRPG  367 (419)
T ss_pred             cceEeecCCCCCCHHHHHHHHhhcccccccceEEeccCCCcCceEEEEEeecchhhhhhhc-CccccCCeeEEEEecccc
Confidence            4699999999999999999999999999887765433455559999999999999999965 688899999999987764


Q ss_pred             c
Q 007792          323 S  323 (589)
Q Consensus       323 ~  323 (589)
                      .
T Consensus       368 ~  368 (419)
T KOG0116|consen  368 F  368 (419)
T ss_pred             c
Confidence            3

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

Probab=98.69  E-value=4.1e-08  Score=97.38  Aligned_cols=74  Identities=24%  Similarity=0.480  Sum_probs=66.6

Q ss_pred             CceEEEecCCCCCCHHHHHHHhccCCCeEEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHhc-CCceeCCeEEEEEecc
Q 007792          242 ENVLFVCKLNPVTEDEDLHTIFSRFGTVVSAEIIRDFKTGDSLNYAFIEFENRQACERAYSKM-DNALIDDRRIHVDFSQ  320 (589)
Q Consensus       242 ~~~i~V~nL~~~~te~~L~~~F~~~G~v~~~~i~~d~~tg~~~g~aFV~f~~~~~a~~A~~~l-~g~~i~gr~i~V~~a~  320 (589)
                      -++|||++|...+++.+|...|.+||+|..+.++..      +++|||+|.+.++|+.|...+ |...|+|.+|.|.|+.
T Consensus       228 I~tLyIg~l~d~v~e~dIrdhFyqyGeirsi~~~~~------~~CAFv~ftTR~aAE~Aae~~~n~lvI~G~Rl~i~Wg~  301 (377)
T KOG0153|consen  228 IKTLYIGGLNDEVLEQDIRDHFYQYGEIRSIRILPR------KGCAFVTFTTREAAEKAAEKSFNKLVINGFRLKIKWGR  301 (377)
T ss_pred             eeEEEecccccchhHHHHHHHHhhcCCeeeEEeecc------cccceeeehhhHHHHHHHHhhcceeeecceEEEEEeCC
Confidence            369999999999999999999999999999999774      369999999999999888654 6677899999999998


Q ss_pred             c
Q 007792          321 S  321 (589)
Q Consensus       321 ~  321 (589)
                      +
T Consensus       302 ~  302 (377)
T KOG0153|consen  302 P  302 (377)
T ss_pred             C
Confidence            7

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

Probab=98.68  E-value=1.5e-08  Score=102.50  Aligned_cols=81  Identities=26%  Similarity=0.423  Sum_probs=74.1

Q ss_pred             CCceEEEecCCCCCCHHHHHHHhccCCCeEEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHhcCCceeCCeEEEEEecc
Q 007792          241 PENVLFVCKLNPVTEDEDLHTIFSRFGTVVSAEIIRDFKTGDSLNYAFIEFENRQACERAYSKMDNALIDDRRIHVDFSQ  320 (589)
Q Consensus       241 ~~~~i~V~nL~~~~te~~L~~~F~~~G~v~~~~i~~d~~tg~~~g~aFV~f~~~~~a~~A~~~l~g~~i~gr~i~V~~a~  320 (589)
                      ...+||||+|+|.++++.|...|.+||+|.+|.++.++.++.++||+||+|.+.+.+.++|. ..-..|+|+.|.+.-|.
T Consensus         5 ~~~KlfiGgisw~ttee~Lr~yf~~~Gev~d~~vm~d~~t~rsrgFgfv~f~~~~~v~~vl~-~~~h~~dgr~ve~k~av   83 (311)
T KOG4205|consen    5 ESGKLFIGGLSWETTEESLREYFSQFGEVTDCVVMRDPSTGRSRGFGFVTFATPEGVDAVLN-ARTHKLDGRSVEPKRAV   83 (311)
T ss_pred             CCcceeecCcCccccHHHHHHHhcccCceeeEEEeccCCCCCcccccceecCCCcchheeec-ccccccCCccccceecc
Confidence            46899999999999999999999999999999999999999999999999999999998884 45678999999998887


Q ss_pred             cc
Q 007792          321 SV  322 (589)
Q Consensus       321 ~~  322 (589)
                      +.
T Consensus        84 ~r   85 (311)
T KOG4205|consen   84 SR   85 (311)
T ss_pred             Cc
Confidence            63

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

Probab=98.62  E-value=1e-07  Score=92.73  Aligned_cols=82  Identities=27%  Similarity=0.426  Sum_probs=75.0

Q ss_pred             CCCCceEEEecCCCCCCHHHHHHHhccCCCeEEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHhcCCceeCCeEEEEEe
Q 007792          239 KPPENVLFVCKLNPVTEDEDLHTIFSRFGTVVSAEIIRDFKTGDSLNYAFIEFENRQACERAYSKMDNALIDDRRIHVDF  318 (589)
Q Consensus       239 ~~~~~~i~V~nL~~~~te~~L~~~F~~~G~v~~~~i~~d~~tg~~~g~aFV~f~~~~~a~~A~~~l~g~~i~gr~i~V~~  318 (589)
                      ....+.|+|.|||+.|++++|+++|..||.++.+.|.++ .+|.+.|.|-|.|...++|..|++.|||+.++|+.|.+..
T Consensus        80 ~~~~~~v~v~NL~~~V~~~Dl~eLF~~~~~~~r~~vhy~-~~G~s~Gta~v~~~r~~DA~~avk~~~gv~ldG~~mk~~~  158 (243)
T KOG0533|consen   80 ETRSTKVNVSNLPYGVIDADLKELFAEFGELKRVAVHYD-RAGRSLGTADVSFNRRDDAERAVKKYNGVALDGRPMKIEI  158 (243)
T ss_pred             CCCcceeeeecCCcCcchHHHHHHHHHhccceEEeeccC-CCCCCCccceeeecchHhHHHHHHHhcCcccCCceeeeEE
Confidence            334589999999999999999999999999988888887 5689999999999999999999999999999999999988


Q ss_pred             ccc
Q 007792          319 SQS  321 (589)
Q Consensus       319 a~~  321 (589)
                      ..+
T Consensus       159 i~~  161 (243)
T KOG0533|consen  159 ISS  161 (243)
T ss_pred             ecC
Confidence            765

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

Probab=98.59  E-value=8.2e-08  Score=97.46  Aligned_cols=76  Identities=24%  Similarity=0.329  Sum_probs=68.9

Q ss_pred             CCCCceEEEecCCCCCCHHHHHHHhccCCCeEEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHhcCCceeCCeEEEEEe
Q 007792          239 KPPENVLFVCKLNPVTEDEDLHTIFSRFGTVVSAEIIRDFKTGDSLNYAFIEFENRQACERAYSKMDNALIDDRRIHVDF  318 (589)
Q Consensus       239 ~~~~~~i~V~nL~~~~te~~L~~~F~~~G~v~~~~i~~d~~tg~~~g~aFV~f~~~~~a~~A~~~l~g~~i~gr~i~V~~  318 (589)
                      ....++|||.|||+++||+.|+.-|..||.|.++.|+.   .|+++|  .|.|.+.++|+.|+..|+|..+.|+.|.|.+
T Consensus       533 arKa~qIiirNlP~dfTWqmlrDKfre~G~v~yadime---~GkskG--VVrF~s~edAEra~a~Mngs~l~Gr~I~V~y  607 (608)
T KOG4212|consen  533 ARKACQIIIRNLPFDFTWQMLRDKFREIGHVLYADIME---NGKSKG--VVRFFSPEDAERACALMNGSRLDGRNIKVTY  607 (608)
T ss_pred             cccccEEEEecCCccccHHHHHHHHHhccceehhhhhc---cCCccc--eEEecCHHHHHHHHHHhccCcccCceeeeee
Confidence            34567999999999999999999999999999999954   477777  8999999999999999999999999999987


Q ss_pred             c
Q 007792          319 S  319 (589)
Q Consensus       319 a  319 (589)
                      .
T Consensus       608 ~  608 (608)
T KOG4212|consen  608 F  608 (608)
T ss_pred             C
Confidence            3

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

Probab=98.57  E-value=1.2e-07  Score=92.53  Aligned_cols=83  Identities=18%  Similarity=0.326  Sum_probs=77.4

Q ss_pred             CCCCceEEEecCCCCCCHHHHHHHhccCCCeEEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHhcCCceeCCeEEEEEe
Q 007792          239 KPPENVLFVCKLNPVTEDEDLHTIFSRFGTVVSAEIIRDFKTGDSLNYAFIEFENRQACERAYSKMDNALIDDRRIHVDF  318 (589)
Q Consensus       239 ~~~~~~i~V~nL~~~~te~~L~~~F~~~G~v~~~~i~~d~~tg~~~g~aFV~f~~~~~a~~A~~~l~g~~i~gr~i~V~~  318 (589)
                      ......+||+|+.+.+|.++|...|..||.|..+.|+.++.+|.++|||||+|.+.+.++.||. |+|..|.|..|.|.+
T Consensus        98 ~~d~~sv~v~nvd~~~t~~~~e~hf~~Cg~i~~~ti~~d~~~~~~k~~~yvef~~~~~~~~ay~-l~gs~i~~~~i~vt~  176 (231)
T KOG4209|consen   98 EVDAPSVWVGNVDFLVTLTKIELHFESCGGINRVTVPKDKFRGHPKGFAYVEFSSYELVEEAYK-LDGSEIPGPAIEVTL  176 (231)
T ss_pred             ccCCceEEEeccccccccchhhheeeccCCccceeeeccccCCCcceeEEEecccHhhhHHHhh-cCCcccccccceeee
Confidence            3456899999999999999999999999999999999999999999999999999999999997 999999999999998


Q ss_pred             cccc
Q 007792          319 SQSV  322 (589)
Q Consensus       319 a~~~  322 (589)
                      ....
T Consensus       177 ~r~~  180 (231)
T KOG4209|consen  177 KRTN  180 (231)
T ss_pred             eeee
Confidence            7654

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

Probab=98.56  E-value=4.7e-08  Score=92.99  Aligned_cols=72  Identities=18%  Similarity=0.455  Sum_probs=66.6

Q ss_pred             ceEEEecCCCCCCHHHHHHHhccCCCeEEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHhcCCceeCCeEEEEEecccc
Q 007792          243 NVLFVCKLNPVTEDEDLHTIFSRFGTVVSAEIIRDFKTGDSLNYAFIEFENRQACERAYSKMDNALIDDRRIHVDFSQSV  322 (589)
Q Consensus       243 ~~i~V~nL~~~~te~~L~~~F~~~G~v~~~~i~~d~~tg~~~g~aFV~f~~~~~a~~A~~~l~g~~i~gr~i~V~~a~~~  322 (589)
                      ..||||+||+.+.+.+|+.||..||.|..|.+..        ||+||+|.+..+|..|+..||+..|+|-.+.|+++...
T Consensus         2 ~rv~vg~~~~~~~~~d~E~~f~~yg~~~d~~mk~--------gf~fv~fed~rda~Dav~~l~~~~l~~e~~vve~~r~~   73 (216)
T KOG0106|consen    2 PRVYIGRLPYRARERDVERFFKGYGKIPDADMKN--------GFGFVEFEDPRDADDAVHDLDGKELCGERLVVEHARGK   73 (216)
T ss_pred             CceeecccCCccchhHHHHHHhhccccccceeec--------ccceeccCchhhhhcccchhcCceecceeeeeeccccc
Confidence            3689999999999999999999999999988854        79999999999999999999999999999999998753

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

Probab=98.53  E-value=1.4e-07  Score=101.21  Aligned_cols=83  Identities=25%  Similarity=0.493  Sum_probs=74.1

Q ss_pred             CCCCceEEEecCCCCCCHHHHHHHhccCCCeEEEEEeecCC---CCCcccEEEEEEcCHHHHHHHHHhcCCceeCCeEEE
Q 007792          239 KPPENVLFVCKLNPVTEDEDLHTIFSRFGTVVSAEIIRDFK---TGDSLNYAFIEFENRQACERAYSKMDNALIDDRRIH  315 (589)
Q Consensus       239 ~~~~~~i~V~nL~~~~te~~L~~~F~~~G~v~~~~i~~d~~---tg~~~g~aFV~f~~~~~a~~A~~~l~g~~i~gr~i~  315 (589)
                      .|..++|||+||++.++++.|...|+.||+|..|+|+....   ......||||.|.+..+|++|++.|+|..|.+..|+
T Consensus       171 DP~TTNlyv~Nlnpsv~E~~ll~tfGrfgPlasvKimwpRtEeEk~r~r~cgfvafmnR~D~era~k~lqg~iv~~~e~K  250 (877)
T KOG0151|consen  171 DPQTTNLYVGNLNPSVDENFLLRTFGRFGPLASVKIMWPRTEEEKRRERNCGFVAFMNRADAERALKELQGIIVMEYEMK  250 (877)
T ss_pred             CCcccceeeecCCccccHHHHHHHhcccCcccceeeecccchhhhccccccceeeehhhhhHHHHHHHhcceeeeeeeee
Confidence            45668999999999999999999999999999999997642   233567999999999999999999999999999999


Q ss_pred             EEeccc
Q 007792          316 VDFSQS  321 (589)
Q Consensus       316 V~~a~~  321 (589)
                      +-|+++
T Consensus       251 ~gWgk~  256 (877)
T KOG0151|consen  251 LGWGKA  256 (877)
T ss_pred             eccccc
Confidence            999864

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

Probab=98.51  E-value=4e-08  Score=91.45  Aligned_cols=80  Identities=15%  Similarity=0.204  Sum_probs=71.9

Q ss_pred             CCCceEEEecCCCCCCHHHHHHHhccCCCeEEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHhcCCceeCCeEEEEEec
Q 007792          240 PPENVLFVCKLNPVTEDEDLHTIFSRFGTVVSAEIIRDFKTGDSLNYAFIEFENRQACERAYSKMDNALIDDRRIHVDFS  319 (589)
Q Consensus       240 ~~~~~i~V~nL~~~~te~~L~~~F~~~G~v~~~~i~~d~~tg~~~g~aFV~f~~~~~a~~A~~~l~g~~i~gr~i~V~~a  319 (589)
                      +...||||+||...++|+-|.++|-+.|+|..|.|..++. ++.+ ||||.|.++-++.-|++.|||..+-+..|.|.+-
T Consensus         7 e~drtl~v~n~~~~v~eelL~ElfiqaGPV~kv~ip~~~d-~~~k-Fa~v~f~~E~sv~~a~~L~ng~~l~~~e~q~~~r   84 (267)
T KOG4454|consen    7 EMDRTLLVQNMYSGVSEELLSELFIQAGPVYKVGIPSGQD-QEQK-FAYVFFPNENSVQLAGQLENGDDLEEDEEQRTLR   84 (267)
T ss_pred             chhhHHHHHhhhhhhhHHHHHHHhhccCceEEEeCCCCcc-CCCc-eeeeecccccchhhhhhhcccchhccchhhcccc
Confidence            3468999999999999999999999999999999987744 5556 9999999999999999999999999999999876


Q ss_pred             cc
Q 007792          320 QS  321 (589)
Q Consensus       320 ~~  321 (589)
                      ..
T Consensus        85 ~G   86 (267)
T KOG4454|consen   85 CG   86 (267)
T ss_pred             cC
Confidence            54

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

Probab=98.50  E-value=2.2e-07  Score=88.88  Aligned_cols=81  Identities=22%  Similarity=0.482  Sum_probs=72.2

Q ss_pred             CCceEEEecCCCCCCHHHHHHHhccCCCeEEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHhcCCc-eeCC--eEEEEE
Q 007792          241 PENVLFVCKLNPVTEDEDLHTIFSRFGTVVSAEIIRDFKTGDSLNYAFIEFENRQACERAYSKMDNA-LIDD--RRIHVD  317 (589)
Q Consensus       241 ~~~~i~V~nL~~~~te~~L~~~F~~~G~v~~~~i~~d~~tg~~~g~aFV~f~~~~~a~~A~~~l~g~-~i~g--r~i~V~  317 (589)
                      ...+||||-|...-.|++++.+|..||.|.+|.+... ..|.++|+|||.|.+.-+|+.||..|+|. .+-|  ..|.|+
T Consensus        18 ~drklfvgml~kqq~e~dvrrlf~pfG~~~e~tvlrg-~dg~sKGCAFVKf~s~~eAqaAI~aLHgSqTmpGASSSLVVK   96 (371)
T KOG0146|consen   18 DDRKLFVGMLNKQQSEDDVRRLFQPFGNIEECTVLRG-PDGNSKGCAFVKFSSHAEAQAAINALHGSQTMPGASSSLVVK   96 (371)
T ss_pred             cchhhhhhhhcccccHHHHHHHhcccCCcceeEEecC-CCCCCCCceEEEeccchHHHHHHHHhcccccCCCCccceEEE
Confidence            4579999999999999999999999999999999887 45889999999999999999999999995 3444  679999


Q ss_pred             ecccc
Q 007792          318 FSQSV  322 (589)
Q Consensus       318 ~a~~~  322 (589)
                      |+...
T Consensus        97 ~ADTd  101 (371)
T KOG0146|consen   97 FADTD  101 (371)
T ss_pred             eccch
Confidence            98763

>KOG1995 consensus Conserved Zn-finger protein [General function prediction only]

Probab=98.47  E-value=5.4e-06  Score=83.29  Aligned_cols=85  Identities=19%  Similarity=0.244  Sum_probs=77.5

Q ss_pred             CCCCceEEEecCCCCCCHHHHHHHhccCCCeE--------EEEEeecCCCCCcccEEEEEEcCHHHHHHHHHhcCCceeC
Q 007792          239 KPPENVLFVCKLNPVTEDEDLHTIFSRFGTVV--------SAEIIRDFKTGDSLNYAFIEFENRQACERAYSKMDNALID  310 (589)
Q Consensus       239 ~~~~~~i~V~nL~~~~te~~L~~~F~~~G~v~--------~~~i~~d~~tg~~~g~aFV~f~~~~~a~~A~~~l~g~~i~  310 (589)
                      .....+|||.+||..+++.+|..+|.+||.|.        .|.|.++++|+.++|-|.|.|.+...|++||..+++..++
T Consensus        63 ~s~~~ti~v~g~~d~~~~~~~~~~f~qcg~ikrnK~t~kPki~~y~dkeT~~~KGeatvS~~D~~~akaai~~~agkdf~  142 (351)
T KOG1995|consen   63 KSDNETIFVWGCPDSVCENDNADFFLQCGVIKRNKRTGKPKIKIYTDKETGAPKGEATVSYEDPPAAKAAIEWFAGKDFC  142 (351)
T ss_pred             ccccccceeeccCccchHHHHHHHHhhcceeccCCCCCCcchhccccccccCcCCceeeeecChhhhhhhhhhhcccccc
Confidence            44567999999999999999999999999885        3678889999999999999999999999999999999999


Q ss_pred             CeEEEEEeccccc
Q 007792          311 DRRIHVDFSQSVS  323 (589)
Q Consensus       311 gr~i~V~~a~~~~  323 (589)
                      |.+|+|.+|....
T Consensus       143 gn~ikvs~a~~r~  155 (351)
T KOG1995|consen  143 GNTIKVSLAERRT  155 (351)
T ss_pred             CCCchhhhhhhcc
Confidence            9999999987544

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

Probab=98.44  E-value=1.2e-06  Score=81.82  Aligned_cols=84  Identities=19%  Similarity=0.257  Sum_probs=68.8

Q ss_pred             CceEEEecCCCCCCHHHHHHHhccCCCeEEEEEeec-CCCCCcccEEEEEEcCHHHHHHHHHhcCCceeC---CeEEEEE
Q 007792          242 ENVLFVCKLNPVTEDEDLHTIFSRFGTVVSAEIIRD-FKTGDSLNYAFIEFENRQACERAYSKMDNALID---DRRIHVD  317 (589)
Q Consensus       242 ~~~i~V~nL~~~~te~~L~~~F~~~G~v~~~~i~~d-~~tg~~~g~aFV~f~~~~~a~~A~~~l~g~~i~---gr~i~V~  317 (589)
                      -.||||.+||.++..-+|..+|-.|--...+.|... +.....+-+|||+|.+..+|.+|+.+|||..|+   +..|+|+
T Consensus        34 VRTLFVSGLP~DvKpREiynLFR~f~GYEgslLK~Tsk~~~~~~pvaFatF~s~q~A~aamnaLNGvrFDpE~~stLhiE  113 (284)
T KOG1457|consen   34 VRTLFVSGLPNDVKPREIYNLFRRFHGYEGSLLKYTSKGDQVCKPVAFATFTSHQFALAAMNALNGVRFDPETGSTLHIE  113 (284)
T ss_pred             cceeeeccCCcccCHHHHHHHhccCCCccceeeeeccCCCccccceEEEEecchHHHHHHHHHhcCeeeccccCceeEee
Confidence            479999999999999999999998866665555432 221223479999999999999999999999986   8999999


Q ss_pred             eccccccc
Q 007792          318 FSQSVSKL  325 (589)
Q Consensus       318 ~a~~~~~~  325 (589)
                      +|++..+.
T Consensus       114 lAKSNtK~  121 (284)
T KOG1457|consen  114 LAKSNTKR  121 (284)
T ss_pred             ehhcCccc
Confidence            99875543

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

Probab=98.32  E-value=3.1e-06  Score=70.80  Aligned_cols=79  Identities=20%  Similarity=0.293  Sum_probs=70.3

Q ss_pred             ceEEEecCCCCCCHHHHHHHhcc--CCCeEEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHhcCCceeC----CeEEEE
Q 007792          243 NVLFVCKLNPVTEDEDLHTIFSR--FGTVVSAEIIRDFKTGDSLNYAFIEFENRQACERAYSKMDNALID----DRRIHV  316 (589)
Q Consensus       243 ~~i~V~nL~~~~te~~L~~~F~~--~G~v~~~~i~~d~~tg~~~g~aFV~f~~~~~a~~A~~~l~g~~i~----gr~i~V  316 (589)
                      +||-|.|||-..|.++|.+++..  .|..-.+.++.|..++-+.|||||.|.+.+.|....+.++|..+.    .+.+.|
T Consensus         2 TTvMirNIPn~~t~~~L~~~l~~~~~g~yDF~YLPiDf~~~~N~GYAFVNf~~~~~~~~F~~~f~g~~w~~~~s~Kvc~i   81 (97)
T PF04059_consen    2 TTVMIRNIPNKYTQEMLIQILDEHFKGKYDFFYLPIDFKNKCNLGYAFVNFTSPQAAIRFYKAFNGKKWPNFNSKKVCEI   81 (97)
T ss_pred             eeEEEecCCCCCCHHHHHHHHHHhccCcceEEEeeeeccCCCceEEEEEEcCCHHHHHHHHHHHcCCccccCCCCcEEEE
Confidence            68999999999999999998874  366777899999999999999999999999999999999998875    577888


Q ss_pred             Eeccc
Q 007792          317 DFSQS  321 (589)
Q Consensus       317 ~~a~~  321 (589)
                      .+|+-
T Consensus        82 ~yAri   86 (97)
T PF04059_consen   82 SYARI   86 (97)
T ss_pred             ehhHh
Confidence            88864

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

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

Probab=98.31  E-value=5.5e-07  Score=85.87  Aligned_cols=82  Identities=27%  Similarity=0.444  Sum_probs=75.7

Q ss_pred             CCCCCceEEEecCCCCCCHHHHHHHhccCCCeEEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHhcCCceeCCeEEEEE
Q 007792          238 IKPPENVLFVCKLNPVTEDEDLHTIFSRFGTVVSAEIIRDFKTGDSLNYAFIEFENRQACERAYSKMDNALIDDRRIHVD  317 (589)
Q Consensus       238 ~~~~~~~i~V~nL~~~~te~~L~~~F~~~G~v~~~~i~~d~~tg~~~g~aFV~f~~~~~a~~A~~~l~g~~i~gr~i~V~  317 (589)
                      .+.....||.|.|.-+++.+.|-..|.+|-.....+++.++.||+++||+||.|.+..++..|+..|+|..++.++|++.
T Consensus       186 w~~~DfRIfcgdlgNevnd~vl~raf~Kfpsf~~akviRdkRTgKSkgygfVSf~~pad~~rAmrem~gkyVgsrpiklR  265 (290)
T KOG0226|consen  186 WDEDDFRIFCGDLGNEVNDDVLARAFKKFPSFQKAKVIRDKRTGKSKGYGFVSFRDPADYVRAMREMNGKYVGSRPIKLR  265 (290)
T ss_pred             CccccceeecccccccccHHHHHHHHHhccchhhccccccccccccccceeeeecCHHHHHHHHHhhcccccccchhHhh
Confidence            34456799999999999999999999999888889999999999999999999999999999999999999999999876


Q ss_pred             ec
Q 007792          318 FS  319 (589)
Q Consensus       318 ~a  319 (589)
                      -+
T Consensus       266 kS  267 (290)
T KOG0226|consen  266 KS  267 (290)
T ss_pred             hh
Confidence            44

>KOG0882 consensus Cyclophilin-related peptidyl-prolyl cis-trans isomerase [Posttranslational modification, protein turnover, chaperones]

Probab=98.24  E-value=8.9e-07  Score=90.80  Aligned_cols=157  Identities=22%  Similarity=0.242  Sum_probs=126.7

Q ss_pred             EEEEecce----eEEEEecCCCChhHHHHHHHHHhcCccCCceEEEeecCcccccCCCCCCCC-CCCCcccccccccccc
Q 007792            3 VLIVTSLG----DIVVDLFVDKCPLTTKNFLKLCKIKYYNGCLFHTVQKDFTAQTGDPTGTGT-GGDSVYKFLYGEQARF   77 (589)
Q Consensus         3 v~~~T~~G----~i~ieL~~~~aP~~~~nF~~l~~~~~Y~g~~f~rv~~~~~iq~Gd~~~~~~-~~~~~~~~~~~~~~~~   77 (589)
                      +.+.|..|    -|.|+|+..-+|..++-|..+|...++++..|.+|...+++|.|+...... +|. |-.|....+..+
T Consensus       101 a~wv~skGd~~s~IAVs~~~sg~i~VvD~~~d~~q~~~fkklH~sPV~~i~y~qa~Ds~vSiD~~gm-VEyWs~e~~~qf  179 (558)
T KOG0882|consen  101 AEWVTSKGDKISLIAVSLFKSGKIFVVDGFGDFCQDGYFKKLHFSPVKKIRYNQAGDSAVSIDISGM-VEYWSAEGPFQF  179 (558)
T ss_pred             eEEecCCCCeeeeEEeecccCCCcEEECCcCCcCccceecccccCceEEEEeeccccceeeccccce-eEeecCCCcccC
Confidence            67789999    899999999999999999999999999999999999999999998663221 111 111111111122


Q ss_pred             cCCccccCCCCCCCceEEEeccCCCCCcceEEEEeCCCCCCCCCCcceEEEEecCHHHHHHHhhCccCCCCCcccceeec
Q 007792           78 FGDEIRVDLKHAKTGTVAMASAGENLNASQFYMTLRDNLDYLDEKHTIFGEVAEGLETLSRINESFVDEKNRPYKNIRIK  157 (589)
Q Consensus        78 ~~~e~~~~l~~~~~G~vs~a~~g~~~~~sqFfI~l~~~~~~ld~~~~vFG~Vv~G~~vl~~i~~~~~~~~~~p~~~i~I~  157 (589)
                      ...+++..++| ..-++.+...-....+.+|+|...+ .+.|+.+..|||.|+.|-.+++.|....++....|..++.|.
T Consensus       180 Pr~~l~~~~K~-eTdLy~f~K~Kt~pts~Efsp~g~q-istl~~DrkVR~F~~KtGklvqeiDE~~t~~~~q~ks~y~l~  257 (558)
T KOG0882|consen  180 PRTNLNFELKH-ETDLYGFPKAKTEPTSFEFSPDGAQ-ISTLNPDRKVRGFVFKTGKLVQEIDEVLTDAQYQPKSPYGLM  257 (558)
T ss_pred             ccccccccccc-cchhhcccccccCccceEEccccCc-ccccCcccEEEEEEeccchhhhhhhccchhhhhccccccccc
Confidence            33456788898 5688888887767778899998887 899999999999999999999999999999888999899998


Q ss_pred             ccccc
Q 007792          158 HTYIL  162 (589)
Q Consensus       158 ~~~vl  162 (589)
                      ++.+.
T Consensus       258 ~Velg  262 (558)
T KOG0882|consen  258 HVELG  262 (558)
T ss_pred             eeehh
Confidence            88764

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

Probab=98.20  E-value=1.1e-06  Score=93.50  Aligned_cols=82  Identities=20%  Similarity=0.400  Sum_probs=78.1

Q ss_pred             CCceEEEecCCCCCCHHHHHHHhccCCCeEEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHhcCCceeCCeEEEEEecc
Q 007792          241 PENVLFVCKLNPVTEDEDLHTIFSRFGTVVSAEIIRDFKTGDSLNYAFIEFENRQACERAYSKMDNALIDDRRIHVDFSQ  320 (589)
Q Consensus       241 ~~~~i~V~nL~~~~te~~L~~~F~~~G~v~~~~i~~d~~tg~~~g~aFV~f~~~~~a~~A~~~l~g~~i~gr~i~V~~a~  320 (589)
                      ....|||++||..+++.++.+++..||.+....++.+..+|.++||||.+|.+..-+..|+..|||..+++++|.|+.|.
T Consensus       288 ~~~ki~v~~lp~~l~~~q~~Ell~~fg~lk~f~lv~d~~~g~skg~af~ey~dpsvtd~A~agLnGm~lgd~~lvvq~A~  367 (500)
T KOG0120|consen  288 SPNKIFVGGLPLYLTEDQVKELLDSFGPLKAFRLVKDSATGNSKGFAFCEYCDPSVTDQAIAGLNGMQLGDKKLVVQRAI  367 (500)
T ss_pred             ccchhhhccCcCccCHHHHHHHHHhcccchhheeecccccccccceeeeeeeCCcchhhhhcccchhhhcCceeEeehhh
Confidence            45799999999999999999999999999999999999999999999999999999999999999999999999999987


Q ss_pred             cc
Q 007792          321 SV  322 (589)
Q Consensus       321 ~~  322 (589)
                      ..
T Consensus       368 ~g  369 (500)
T KOG0120|consen  368 VG  369 (500)
T ss_pred             cc
Confidence            63

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

Probab=98.12  E-value=1.5e-06  Score=91.60  Aligned_cols=70  Identities=23%  Similarity=0.401  Sum_probs=64.4

Q ss_pred             CCceEEEecCCCCCCHHHHHHHhccCCCeEEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHhcCCceeCCeEEE
Q 007792          241 PENVLFVCKLNPVTEDEDLHTIFSRFGTVVSAEIIRDFKTGDSLNYAFIEFENRQACERAYSKMDNALIDDRRIH  315 (589)
Q Consensus       241 ~~~~i~V~nL~~~~te~~L~~~F~~~G~v~~~~i~~d~~tg~~~g~aFV~f~~~~~a~~A~~~l~g~~i~gr~i~  315 (589)
                      +..+|+|-|||..|++++|..+|+.||+|..|+.-..     ..|.+||+|-+..+|+.|+++|++..|.|+.|+
T Consensus        74 ~~~~L~v~nl~~~Vsn~~L~~~f~~yGeir~ir~t~~-----~~~~~~v~FyDvR~A~~Alk~l~~~~~~~~~~k  143 (549)
T KOG4660|consen   74 NQGTLVVFNLPRSVSNDTLLRIFGAYGEIREIRETPN-----KRGIVFVEFYDVRDAERALKALNRREIAGKRIK  143 (549)
T ss_pred             ccceEEEEecCCcCCHHHHHHHHHhhcchhhhhcccc-----cCceEEEEEeehHhHHHHHHHHHHHHhhhhhhc
Confidence            5679999999999999999999999999999766443     558999999999999999999999999999998

>KOG2416 consensus Acinus (induces apoptotic chromatin condensation) [Chromatin structure and dynamics]

Probab=98.12  E-value=5.2e-06  Score=87.77  Aligned_cols=83  Identities=17%  Similarity=0.259  Sum_probs=68.3

Q ss_pred             CCCCCCCCCCceEEEecCCCCCCHHHHHHHhc-cCCCeEEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHhcCCcee--
Q 007792          233 IPDADIKPPENVLFVCKLNPVTEDEDLHTIFS-RFGTVVSAEIIRDFKTGDSLNYAFIEFENRQACERAYSKMDNALI--  309 (589)
Q Consensus       233 ~~~~~~~~~~~~i~V~nL~~~~te~~L~~~F~-~~G~v~~~~i~~d~~tg~~~g~aFV~f~~~~~a~~A~~~l~g~~i--  309 (589)
                      ++...-+++.+.|||.||-.-+|..+|+.+++ .+|.|..+  ++|+    .+..|||.|.+.++|.+.+.+|||..|  
T Consensus       435 vpSPsR~~~SnvlhI~nLvRPFTlgQLkelL~rtgg~Vee~--WmDk----IKShCyV~yss~eEA~atr~AlhnV~WP~  508 (718)
T KOG2416|consen  435 VPSPSRKEPSNVLHIDNLVRPFTLGQLKELLGRTGGNVEEF--WMDK----IKSHCYVSYSSVEEAAATREALHNVQWPP  508 (718)
T ss_pred             CCCCCCCCccceEeeecccccchHHHHHHHHhhccCchHHH--HHHH----hhcceeEecccHHHHHHHHHHHhccccCC
Confidence            34444566789999999999999999999999 56666666  3342    567999999999999999999999877  


Q ss_pred             -CCeEEEEEeccc
Q 007792          310 -DDRRIHVDFSQS  321 (589)
Q Consensus       310 -~gr~i~V~~a~~  321 (589)
                       +++.|.|.|...
T Consensus       509 sNPK~L~adf~~~  521 (718)
T KOG2416|consen  509 SNPKHLIADFVRA  521 (718)
T ss_pred             CCCceeEeeecch
Confidence             578999999864

>KOG4849 consensus mRNA cleavage factor I subunit/CPSF subunit [RNA processing and modification]

Probab=98.08  E-value=2.6e-06  Score=84.34  Aligned_cols=81  Identities=17%  Similarity=0.202  Sum_probs=70.9

Q ss_pred             CCCCCceEEEecCCCCCCHHHHHHHhccCC--CeEEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHhcCCceeCCeEEE
Q 007792          238 IKPPENVLFVCKLNPVTEDEDLHTIFSRFG--TVVSAEIIRDFKTGDSLNYAFIEFENRQACERAYSKMDNALIDDRRIH  315 (589)
Q Consensus       238 ~~~~~~~i~V~nL~~~~te~~L~~~F~~~G--~v~~~~i~~d~~tg~~~g~aFV~f~~~~~a~~A~~~l~g~~i~gr~i~  315 (589)
                      .......+|||||-|++|+++|.+.+...|  .+.++++..+..+|+++|||+|...+..++.+.++.|...+|+|..-.
T Consensus        76 ~~Grk~~~YvGNL~W~TTD~DL~~A~~S~G~~~~~dmKFFENR~NGQSKG~AL~~~~SdAa~Kq~MeiLP~k~iHGQ~P~  155 (498)
T KOG4849|consen   76 SEGRKYCCYVGNLLWYTTDADLLKALQSTGLAQFADMKFFENRTNGQSKGYALLVLNSDAAVKQTMEILPTKTIHGQSPT  155 (498)
T ss_pred             ccCceEEEEecceeEEeccHHHHHHHHhhhHHHHhhhhhhhcccCCcccceEEEEecchHHHHHHHHhcccceecCCCCe
Confidence            344567999999999999999999998777  466788888999999999999999999999999999999999997766


Q ss_pred             EEe
Q 007792          316 VDF  318 (589)
Q Consensus       316 V~~  318 (589)
                      |--
T Consensus       156 V~~  158 (498)
T KOG4849|consen  156 VLS  158 (498)
T ss_pred             eec
Confidence            643

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

Probab=97.95  E-value=2.8e-05  Score=78.96  Aligned_cols=76  Identities=24%  Similarity=0.420  Sum_probs=69.5

Q ss_pred             CceEEEecCCC-CCCHHHHHHHhccCCCeEEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHhcCCceeCCeEEEEEecc
Q 007792          242 ENVLFVCKLNP-VTEDEDLHTIFSRFGTVVSAEIIRDFKTGDSLNYAFIEFENRQACERAYSKMDNALIDDRRIHVDFSQ  320 (589)
Q Consensus       242 ~~~i~V~nL~~-~~te~~L~~~F~~~G~v~~~~i~~d~~tg~~~g~aFV~f~~~~~a~~A~~~l~g~~i~gr~i~V~~a~  320 (589)
                      +..|.|.||.. .+|.+-|..+|+-||.|..|+|..++.     -.|+|.|.+...|+.|+..|+|..|.|++|+|.+++
T Consensus       297 n~vllvsnln~~~VT~d~LftlFgvYGdVqRVkil~nkk-----d~ALIQmsd~~qAqLA~~hL~g~~l~gk~lrvt~SK  371 (492)
T KOG1190|consen  297 NVVLLVSNLNEEAVTPDVLFTLFGVYGDVQRVKILYNKK-----DNALIQMSDGQQAQLAMEHLEGHKLYGKKLRVTLSK  371 (492)
T ss_pred             ceEEEEecCchhccchhHHHHHHhhhcceEEEEeeecCC-----cceeeeecchhHHHHHHHHhhcceecCceEEEeecc
Confidence            57899999966 489999999999999999999998754     589999999999999999999999999999999998


Q ss_pred             cc
Q 007792          321 SV  322 (589)
Q Consensus       321 ~~  322 (589)
                      -.
T Consensus       372 H~  373 (492)
T KOG1190|consen  372 HT  373 (492)
T ss_pred             Cc
Confidence            63

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

Probab=97.94  E-value=7e-06  Score=76.88  Aligned_cols=65  Identities=22%  Similarity=0.448  Sum_probs=55.3

Q ss_pred             CCceEEEecCCCCCCHHHHHHHhccCCCeEEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHhcCCcee
Q 007792          241 PENVLFVCKLNPVTEDEDLHTIFSRFGTVVSAEIIRDFKTGDSLNYAFIEFENRQACERAYSKMDNALI  309 (589)
Q Consensus       241 ~~~~i~V~nL~~~~te~~L~~~F~~~G~v~~~~i~~d~~tg~~~g~aFV~f~~~~~a~~A~~~l~g~~i  309 (589)
                      ...||||.||.+++||++|+.+|+.|--..-++|-.  .  ...+.|||+|++.+.|..|+..|+|..|
T Consensus       209 acstlfianl~~~~~ed~l~~~~~~~~gf~~l~~~~--~--~g~~vaf~~~~~~~~at~am~~lqg~~~  273 (284)
T KOG1457|consen  209 ACSTLFIANLGPNCTEDELKQLLSRYPGFHILKIRA--R--GGMPVAFADFEEIEQATDAMNHLQGNLL  273 (284)
T ss_pred             hhhhHhhhccCCCCCHHHHHHHHHhCCCceEEEEec--C--CCcceEeecHHHHHHHHHHHHHhhccee
Confidence            457999999999999999999999997766666633  1  2347999999999999999999999776

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

Probab=97.88  E-value=5.7e-06  Score=87.14  Aligned_cols=79  Identities=24%  Similarity=0.338  Sum_probs=74.4

Q ss_pred             CceEEEecCCCCCCHHHHHHHhccCCCeEEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHhcCCceeCCeEEEEEeccc
Q 007792          242 ENVLFVCKLNPVTEDEDLHTIFSRFGTVVSAEIIRDFKTGDSLNYAFIEFENRQACERAYSKMDNALIDDRRIHVDFSQS  321 (589)
Q Consensus       242 ~~~i~V~nL~~~~te~~L~~~F~~~G~v~~~~i~~d~~tg~~~g~aFV~f~~~~~a~~A~~~l~g~~i~gr~i~V~~a~~  321 (589)
                      ..+||+-.|+..+++-+|.+||+.+|+|..|.|+.|..++.++|.|||+|.+.+++..|| .|.|..+.|-+|.|+....
T Consensus       179 ~Rtvf~~qla~r~~pRdL~efFs~~gkVrdVriI~Dr~s~rskgi~Yvef~D~~sVp~ai-aLsGqrllg~pv~vq~sEa  257 (549)
T KOG0147|consen  179 QRTVFCMQLARRNPPRDLEEFFSIVGKVRDVRIIGDRNSRRSKGIAYVEFCDEQSVPLAI-ALSGQRLLGVPVIVQLSEA  257 (549)
T ss_pred             HHHHHHHHHhhcCCchhHHHHHHhhcCcceeEeeccccchhhcceeEEEEecccchhhHh-hhcCCcccCceeEecccHH
Confidence            468888889989999999999999999999999999999999999999999999999999 8999999999999998765

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

Probab=97.83  E-value=5.3e-05  Score=71.78  Aligned_cols=79  Identities=23%  Similarity=0.451  Sum_probs=70.3

Q ss_pred             CCCCCCceEEEecCCCCCCHHHHHHHhccCCCeEEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHhcCCceeC-CeEEE
Q 007792          237 DIKPPENVLFVCKLNPVTEDEDLHTIFSRFGTVVSAEIIRDFKTGDSLNYAFIEFENRQACERAYSKMDNALID-DRRIH  315 (589)
Q Consensus       237 ~~~~~~~~i~V~nL~~~~te~~L~~~F~~~G~v~~~~i~~d~~tg~~~g~aFV~f~~~~~a~~A~~~l~g~~i~-gr~i~  315 (589)
                      ...+|..++|+.|||..++.+.|..+|.+|.-...+.++...     .+.|||+|.+...|..|...|+|..|- ...|.
T Consensus       141 ~~~ppn~ilf~~niP~es~~e~l~~lf~qf~g~keir~i~~~-----~~iAfve~~~d~~a~~a~~~lq~~~it~~~~m~  215 (221)
T KOG4206|consen  141 QMAPPNNILFLTNIPSESESEMLSDLFEQFPGFKEIRLIPPR-----SGIAFVEFLSDRQASAAQQALQGFKITKKNTMQ  215 (221)
T ss_pred             cCCCCceEEEEecCCcchhHHHHHHHHhhCcccceeEeccCC-----CceeEEecchhhhhHHHhhhhccceeccCceEE
Confidence            346788999999999999999999999999999999998753     389999999999999999999999886 88888


Q ss_pred             EEecc
Q 007792          316 VDFSQ  320 (589)
Q Consensus       316 V~~a~  320 (589)
                      |.++.
T Consensus       216 i~~a~  220 (221)
T KOG4206|consen  216 ITFAK  220 (221)
T ss_pred             ecccC
Confidence            88774

>PF11608 Limkain-b1: Limkain b1; InterPro: IPR024582 This entry represents a conserved domain found in limkain b1, which is a novel human autoantigen, localised to a subset of ABCD3 and PXF marked peroxisomes

Probab=97.76  E-value=7.8e-05  Score=59.51  Aligned_cols=69  Identities=26%  Similarity=0.412  Sum_probs=48.1

Q ss_pred             ceEEEecCCCCCCHHH----HHHHhccCC-CeEEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHhcCCceeCCeEEEEE
Q 007792          243 NVLFVCKLNPVTEDED----LHTIFSRFG-TVVSAEIIRDFKTGDSLNYAFIEFENRQACERAYSKMDNALIDDRRIHVD  317 (589)
Q Consensus       243 ~~i~V~nL~~~~te~~----L~~~F~~~G-~v~~~~i~~d~~tg~~~g~aFV~f~~~~~a~~A~~~l~g~~i~gr~i~V~  317 (589)
                      +.|||.|||.+.....    |.+++..|| .|..|.          .+-|+|.|.+++.|..|.+.|+|..+-|.+|.|.
T Consensus         3 s~L~V~NLP~~~d~~~I~~RL~qLsdNCGGkVl~v~----------~~tAilrF~~~~~A~RA~KRmegEdVfG~kI~v~   72 (90)
T PF11608_consen    3 SLLYVSNLPTNKDPSSIKNRLRQLSDNCGGKVLSVS----------GGTAILRFPNQEFAERAQKRMEGEDVFGNKISVS   72 (90)
T ss_dssp             EEEEEES--TTS-HHHHHHHHHHHHHTTT--EEE------------TT-EEEEESSHHHHHHHHHHHTT--SSSS--EEE
T ss_pred             cEEEEecCCCCCCHHHHHHHHHHHhhccCCEEEEEe----------CCEEEEEeCCHHHHHHHHHhhcccccccceEEEE
Confidence            5799999999988765    456677776 565541          2689999999999999999999999999999999


Q ss_pred             eccc
Q 007792          318 FSQS  321 (589)
Q Consensus       318 ~a~~  321 (589)
                      |...
T Consensus        73 ~~~~   76 (90)
T PF11608_consen   73 FSPK   76 (90)
T ss_dssp             SS--
T ss_pred             EcCC
Confidence            9743

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

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

Probab=97.74  E-value=9.3e-05  Score=77.24  Aligned_cols=81  Identities=22%  Similarity=0.336  Sum_probs=68.6

Q ss_pred             CceEEEecCCCCCCHHHHHHHhccCCCeEEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHhcCCceeCCeEEEEEeccc
Q 007792          242 ENVLFVCKLNPVTEDEDLHTIFSRFGTVVSAEIIRDFKTGDSLNYAFIEFENRQACERAYSKMDNALIDDRRIHVDFSQS  321 (589)
Q Consensus       242 ~~~i~V~nL~~~~te~~L~~~F~~~G~v~~~~i~~d~~tg~~~g~aFV~f~~~~~a~~A~~~l~g~~i~gr~i~V~~a~~  321 (589)
                      ...|-+.+|||++|+++|..||+.|+ |..+.+.+  .+|++.|-|||+|.++++++.||+ .+-..+..+-|.|--+.+
T Consensus        10 ~~~vr~rGLPwsat~~ei~~Ff~~~~-I~~~~~~r--~~Gr~sGeA~Ve~~seedv~~Alk-kdR~~mg~RYIEVf~~~~   85 (510)
T KOG4211|consen   10 AFEVRLRGLPWSATEKEILDFFSNCG-IENLEIPR--RNGRPSGEAYVEFTSEEDVEKALK-KDRESMGHRYIEVFTAGG   85 (510)
T ss_pred             ceEEEecCCCccccHHHHHHHHhcCc-eeEEEEec--cCCCcCcceEEEeechHHHHHHHH-hhHHHhCCceEEEEccCC
Confidence            45677889999999999999999995 77765554  679999999999999999999995 587888889999988876


Q ss_pred             ccccc
Q 007792          322 VSKLW  326 (589)
Q Consensus       322 ~~~~~  326 (589)
                      ....|
T Consensus        86 ~e~d~   90 (510)
T KOG4211|consen   86 AEADW   90 (510)
T ss_pred             ccccc
Confidence            55544

>KOG4210 consensus Nuclear localization sequence binding protein [Transcription]

Probab=97.70  E-value=4.1e-05  Score=77.46  Aligned_cols=83  Identities=23%  Similarity=0.416  Sum_probs=75.1

Q ss_pred             CCceEE-EecCCCCCCHHHHHHHhccCCCeEEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHhcCCceeCCeEEEEEec
Q 007792          241 PENVLF-VCKLNPVTEDEDLHTIFSRFGTVVSAEIIRDFKTGDSLNYAFIEFENRQACERAYSKMDNALIDDRRIHVDFS  319 (589)
Q Consensus       241 ~~~~i~-V~nL~~~~te~~L~~~F~~~G~v~~~~i~~d~~tg~~~g~aFV~f~~~~~a~~A~~~l~g~~i~gr~i~V~~a  319 (589)
                      +..++| |++|+..+++++|...|..+|.|..+.+..+..++.++|||||.|.....+..|+.. +...|.+.++.|...
T Consensus       183 ~s~~~~~~~~~~f~~~~d~~~~~~~~~~~i~~~r~~~~~~s~~~kg~a~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~~~  261 (285)
T KOG4210|consen  183 PSDTIFFVGELDFSLTRDDLKEHFVSSGEITSVRLPTDEESGDSKGFAYVDFSAGNSKKLALND-QTRSIGGRPLRLEED  261 (285)
T ss_pred             ccccceeecccccccchHHHhhhccCcCcceeeccCCCCCccchhhhhhhhhhhchhHHHHhhc-ccCcccCcccccccC
Confidence            344555 999999999999999999999999999999999999999999999999999999976 788999999999998


Q ss_pred             ccccc
Q 007792          320 QSVSK  324 (589)
Q Consensus       320 ~~~~~  324 (589)
                      .+...
T Consensus       262 ~~~~~  266 (285)
T KOG4210|consen  262 EPRPK  266 (285)
T ss_pred             CCCcc
Confidence            87544

>COG5175 MOT2 Transcriptional repressor [Transcription]

Probab=97.64  E-value=0.00029  Score=69.89  Aligned_cols=80  Identities=19%  Similarity=0.518  Sum_probs=61.6

Q ss_pred             CceEEEecCCCCCCHHH----H--HHHhccCCCeEEEEEeecCCC-CCcccE--EEEEEcCHHHHHHHHHhcCCceeCCe
Q 007792          242 ENVLFVCKLNPVTEDED----L--HTIFSRFGTVVSAEIIRDFKT-GDSLNY--AFIEFENRQACERAYSKMDNALIDDR  312 (589)
Q Consensus       242 ~~~i~V~nL~~~~te~~----L--~~~F~~~G~v~~~~i~~d~~t-g~~~g~--aFV~f~~~~~a~~A~~~l~g~~i~gr  312 (589)
                      .+-+||-+||+.+..++    |  .++|++||.|..|.|-.-..+ ....+.  .||+|.+.++|..||...+|..++|+
T Consensus       114 KNLvYVigi~pkva~Ee~~~vLk~~eyFGQyGkI~KIvvNkkt~s~nst~~h~gvYITy~~kedAarcIa~vDgs~~DGr  193 (480)
T COG5175         114 KNLVYVIGIPPKVADEEVAPVLKRHEYFGQYGKIKKIVVNKKTSSLNSTASHAGVYITYSTKEDAARCIAEVDGSLLDGR  193 (480)
T ss_pred             cceeEEecCCCCCCcccccccccchhhhhhccceeEEEecccccccccccccceEEEEecchHHHHHHHHHhccccccCc
Confidence            46789999999877665    2  479999999988766432111 111222  49999999999999999999999999


Q ss_pred             EEEEEeccc
Q 007792          313 RIHVDFSQS  321 (589)
Q Consensus       313 ~i~V~~a~~  321 (589)
                      .|+..|...
T Consensus       194 ~lkatYGTT  202 (480)
T COG5175         194 VLKATYGTT  202 (480)
T ss_pred             eEeeecCch
Confidence            999988653

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

Probab=97.55  E-value=0.00015  Score=61.97  Aligned_cols=70  Identities=23%  Similarity=0.430  Sum_probs=45.2

Q ss_pred             ceEEEecCCCCCCHHHHHHHhccCCCeEEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHhcCC-----ceeCCeEEEEE
Q 007792          243 NVLFVCKLNPVTEDEDLHTIFSRFGTVVSAEIIRDFKTGDSLNYAFIEFENRQACERAYSKMDN-----ALIDDRRIHVD  317 (589)
Q Consensus       243 ~~i~V~nL~~~~te~~L~~~F~~~G~v~~~~i~~d~~tg~~~g~aFV~f~~~~~a~~A~~~l~g-----~~i~gr~i~V~  317 (589)
                      ..|+|.+++..++.++|+.+|++||.|.+|.+....      .-|||-|.+.+.|+.|+..+.-     ..|.+..+.+.
T Consensus         2 ~il~~~g~~~~~~re~iK~~f~~~g~V~yVD~~~G~------~~g~VRf~~~~~A~~a~~~~~~~~~~~~~i~~~~~~~~   75 (105)
T PF08777_consen    2 CILKFSGLGEPTSREDIKEAFSQFGEVAYVDFSRGD------TEGYVRFKTPEAAQKALEKLKEANDGKLKIKGKEVTLE   75 (105)
T ss_dssp             -EEEEEE--SS--HHHHHHHT-SS--EEEEE--TT-------SEEEEEESS---HHHHHHHHHHTTTS-B-TTSSSEEEE
T ss_pred             eEEEEecCCCCcCHHHHHHHHHhcCCcceEEecCCC------CEEEEEECCcchHHHHHHHHHhccCCceEEcCceEEEE
Confidence            578999999999999999999999999999886532      4899999999999999986643     46677776666


Q ss_pred             e
Q 007792          318 F  318 (589)
Q Consensus       318 ~  318 (589)
                      +
T Consensus        76 v   76 (105)
T PF08777_consen   76 V   76 (105)
T ss_dssp             -
T ss_pred             E
Confidence            5

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

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

Probab=97.47  E-value=0.00044  Score=72.29  Aligned_cols=78  Identities=24%  Similarity=0.289  Sum_probs=63.6

Q ss_pred             CCceEEEecCCCCCCHHHHHHHhccCCCeEE-EEEeecCCCCCcccEEEEEEcCHHHHHHHHHhcCCceeCCeEEEEEec
Q 007792          241 PENVLFVCKLNPVTEDEDLHTIFSRFGTVVS-AEIIRDFKTGDSLNYAFIEFENRQACERAYSKMDNALIDDRRIHVDFS  319 (589)
Q Consensus       241 ~~~~i~V~nL~~~~te~~L~~~F~~~G~v~~-~~i~~d~~tg~~~g~aFV~f~~~~~a~~A~~~l~g~~i~gr~i~V~~a  319 (589)
                      +..+|-+.+||+.||+++|.+||+..-.|.. +.++.+ ..+.+.|-|||.|++++.|+.||. -|...|+-+-|.|--|
T Consensus       102 ~d~vVRLRGLPfscte~dI~~FFaGL~Iv~~gi~l~~d-~rgR~tGEAfVqF~sqe~ae~Al~-rhre~iGhRYIEvF~S  179 (510)
T KOG4211|consen  102 NDGVVRLRGLPFSCTEEDIVEFFAGLEIVPDGILLPMD-QRGRPTGEAFVQFESQESAEIALG-RHRENIGHRYIEVFRS  179 (510)
T ss_pred             CCceEEecCCCccCcHHHHHHHhcCCcccccceeeecc-CCCCcccceEEEecCHHHHHHHHH-HHHHhhccceEEeehh
Confidence            4568889999999999999999997755544 455565 446788999999999999999995 4777888888888765


Q ss_pred             c
Q 007792          320 Q  320 (589)
Q Consensus       320 ~  320 (589)
                      .
T Consensus       180 s  180 (510)
T KOG4211|consen  180 S  180 (510)
T ss_pred             H
Confidence            4

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

Probab=97.46  E-value=7e-05  Score=71.55  Aligned_cols=67  Identities=31%  Similarity=0.465  Sum_probs=60.3

Q ss_pred             CceEEEecCCCCCCHHHHHHHhccCCCeEEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHhcCCceeCCeEEEE
Q 007792          242 ENVLFVCKLNPVTEDEDLHTIFSRFGTVVSAEIIRDFKTGDSLNYAFIEFENRQACERAYSKMDNALIDDRRIHV  316 (589)
Q Consensus       242 ~~~i~V~nL~~~~te~~L~~~F~~~G~v~~~~i~~d~~tg~~~g~aFV~f~~~~~a~~A~~~l~g~~i~gr~i~V  316 (589)
                      .+.|+|-||+..+.+++|...|.++|++....+        ..++|||+|+.+++|..||..|+|..+.|+.|.|
T Consensus        99 ~~r~~~~~~~~r~~~qdl~d~~~~~g~~~~~~~--------~~~~~~v~Fs~~~da~ra~~~l~~~~~~~~~l~~  165 (216)
T KOG0106|consen   99 HFRLIVRNLSLRVSWQDLKDHFRPAGEVTYVDA--------RRNFAFVEFSEQEDAKRALEKLDGKKLNGRRISV  165 (216)
T ss_pred             cceeeeccchhhhhHHHHhhhhcccCCCchhhh--------hccccceeehhhhhhhhcchhccchhhcCceeee
Confidence            467889999999999999999999999854443        3479999999999999999999999999999999

>KOG3152 consensus TBP-binding protein, activator of basal transcription (contains rrm motif) [Transcription]

Probab=97.43  E-value=7.4e-05  Score=71.72  Aligned_cols=73  Identities=18%  Similarity=0.402  Sum_probs=62.7

Q ss_pred             CCceEEEecCCCCCCHHHHHHHhccCCCeEEEEEeecCCC--------CCccc----EEEEEEcCHHHHHHHHHhcCCce
Q 007792          241 PENVLFVCKLNPVTEDEDLHTIFSRFGTVVSAEIIRDFKT--------GDSLN----YAFIEFENRQACERAYSKMDNAL  308 (589)
Q Consensus       241 ~~~~i~V~nL~~~~te~~L~~~F~~~G~v~~~~i~~d~~t--------g~~~g----~aFV~f~~~~~a~~A~~~l~g~~  308 (589)
                      ..-.|||++||+.+...-|+++|++||.|-.|.|.....+        |.+..    -|+|+|.+...|..+...|||..
T Consensus        73 k~GVvylS~IPp~m~~~rlReil~~yGeVGRvylqpE~~s~~~~r~~~~~n~~~~y~EGWvEF~~KrvAK~iAe~Lnn~~  152 (278)
T KOG3152|consen   73 KTGVVYLSNIPPYMDPVRLREILSQYGEVGRVYLQPEDDSKRAARKRKGGNYKKLYSEGWVEFISKRVAKRIAELLNNTP  152 (278)
T ss_pred             cceEEEeccCCCccCHHHHHHHHHhccccceEEecchhhHHHHHHhhcCCCccccchhHHHHHHHHHHHHHHHHHhCCCc
Confidence            3569999999999999999999999999999988765443        33322    47899999999999999999999


Q ss_pred             eCCeE
Q 007792          309 IDDRR  313 (589)
Q Consensus       309 i~gr~  313 (589)
                      |+|+.
T Consensus       153 Iggkk  157 (278)
T KOG3152|consen  153 IGGKK  157 (278)
T ss_pred             cCCCC
Confidence            99976

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

Probab=97.37  E-value=0.00083  Score=60.00  Aligned_cols=76  Identities=21%  Similarity=0.471  Sum_probs=54.8

Q ss_pred             CCCCCCceEEEecCCC------CCCH---HHHHHHhccCCCeEEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHhcCCc
Q 007792          237 DIKPPENVLFVCKLNP------VTED---EDLHTIFSRFGTVVSAEIIRDFKTGDSLNYAFIEFENRQACERAYSKMDNA  307 (589)
Q Consensus       237 ~~~~~~~~i~V~nL~~------~~te---~~L~~~F~~~G~v~~~~i~~d~~tg~~~g~aFV~f~~~~~a~~A~~~l~g~  307 (589)
                      ...||..||.|.=+.+      ...+   .+|.+.|..||.|.-++++.+        .-+|+|.+-++|.+|+ .|+|.
T Consensus        22 ~~GPpDaTVvVsv~~~~~~e~~~Fdd~l~~~ll~~~~~~GevvLvRfv~~--------~mwVTF~dg~sALaal-s~dg~   92 (146)
T PF08952_consen   22 SQGPPDATVVVSVDSPSEDEDSSFDDNLMDELLQKFAQYGEVVLVRFVGD--------TMWVTFRDGQSALAAL-SLDGI   92 (146)
T ss_dssp             ----TT-EEEEEECS-SCCCCHS--HHHHHHHHHHHHCCS-ECEEEEETT--------CEEEEESSCHHHHHHH-HGCCS
T ss_pred             hcCCCCceEEEEecCCCccccCcCCHHHHHHHHHHHHhCCceEEEEEeCC--------eEEEEECccHHHHHHH-ccCCc
Confidence            3467778888876661      2222   367788999999998888763        6799999999999999 68999


Q ss_pred             eeCCeEEEEEeccc
Q 007792          308 LIDDRRIHVDFSQS  321 (589)
Q Consensus       308 ~i~gr~i~V~~a~~  321 (589)
                      +|+|+.|+|....+
T Consensus        93 ~v~g~~l~i~LKtp  106 (146)
T PF08952_consen   93 QVNGRTLKIRLKTP  106 (146)
T ss_dssp             EETTEEEEEEE---
T ss_pred             EECCEEEEEEeCCc
Confidence            99999999999765

; PDB: 1UFW_A 2DNR_A.

>KOG2314 consensus Translation initiation factor 3, subunit b (eIF-3b) [Translation, ribosomal structure and biogenesis]

Probab=97.33  E-value=0.00041  Score=73.40  Aligned_cols=77  Identities=21%  Similarity=0.350  Sum_probs=63.5

Q ss_pred             CceEEEecCCCCCCH------HHHHHHhccCCCeEEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHhcCCceeC-CeEE
Q 007792          242 ENVLFVCKLNPVTED------EDLHTIFSRFGTVVSAEIIRDFKTGDSLNYAFIEFENRQACERAYSKMDNALID-DRRI  314 (589)
Q Consensus       242 ~~~i~V~nL~~~~te------~~L~~~F~~~G~v~~~~i~~d~~tg~~~g~aFV~f~~~~~a~~A~~~l~g~~i~-gr~i  314 (589)
                      .+.|+|.|+|..-..      .-|..+|+++|+|+.+.++.+..+| .+||.|++|.+..+|+.|++.|||..|+ .+++
T Consensus        58 D~vVvv~g~PvV~~~rl~klk~vl~kvfsk~gk~vn~~~P~~e~gg-tkG~lf~E~~~~~~A~~aVK~l~G~~ldknHtf  136 (698)
T KOG2314|consen   58 DSVVVVDGAPVVGPARLEKLKKVLTKVFSKAGKIVNMYYPIDEEGG-TKGYLFVEYASMRDAKKAVKSLNGKRLDKNHTF  136 (698)
T ss_pred             ceEEEECCCcccChhHHHHHHHHHHHHHHhhccccceeeccCccCC-eeeEEEEEecChhhHHHHHHhcccceecccceE
Confidence            478999999875332      3456889999999999999886655 9999999999999999999999998875 6777


Q ss_pred             EEEec
Q 007792          315 HVDFS  319 (589)
Q Consensus       315 ~V~~a  319 (589)
                      .|..-
T Consensus       137 ~v~~f  141 (698)
T KOG2314|consen  137 FVRLF  141 (698)
T ss_pred             Eeehh
Confidence            77643

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

Probab=97.15  E-value=0.0009  Score=68.32  Aligned_cols=79  Identities=24%  Similarity=0.393  Sum_probs=65.9

Q ss_pred             CCCCceEEEecCCCCCCHHHHHHHhccCCCeEEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHhcCCceeCCe-EEEEE
Q 007792          239 KPPENVLFVCKLNPVTEDEDLHTIFSRFGTVVSAEIIRDFKTGDSLNYAFIEFENRQACERAYSKMDNALIDDR-RIHVD  317 (589)
Q Consensus       239 ~~~~~~i~V~nL~~~~te~~L~~~F~~~G~v~~~~i~~d~~tg~~~g~aFV~f~~~~~a~~A~~~l~g~~i~gr-~i~V~  317 (589)
                      -||..+|++.|+|+.++|++|+..|..-|-.+......    ++.+-+|++.+++.++|..|+..|+...+++. .|+|.
T Consensus       411 ~PpsatlHlsnip~svsee~lk~~f~~~g~~vkafkff----~kd~kmal~q~~sveeA~~ali~~hnh~lgen~hlRvS  486 (492)
T KOG1190|consen  411 FPPSATLHLSNIPPSVSEEDLKNLFQEPGGQVKAFKFF----QKDRKMALPQLESVEEAIQALIDLHNHYLGENHHLRVS  486 (492)
T ss_pred             CCchhheeeccCCcccchhHHHHhhhcCCceEEeeeec----CCCcceeecccCChhHhhhhccccccccCCCCceEEEE
Confidence            36778999999999999999999999888765443322    23446999999999999999999999888754 89999


Q ss_pred             eccc
Q 007792          318 FSQS  321 (589)
Q Consensus       318 ~a~~  321 (589)
                      |+++
T Consensus       487 FSks  490 (492)
T KOG1190|consen  487 FSKS  490 (492)
T ss_pred             eecc
Confidence            9875

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

Probab=97.04  E-value=0.0045  Score=62.21  Aligned_cols=79  Identities=15%  Similarity=0.288  Sum_probs=63.3

Q ss_pred             CCCCceEEEecCCC----CCC-------HHHHHHHhccCCCeEEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHhcCCc
Q 007792          239 KPPENVLFVCKLNP----VTE-------DEDLHTIFSRFGTVVSAEIIRDFKTGDSLNYAFIEFENRQACERAYSKMDNA  307 (589)
Q Consensus       239 ~~~~~~i~V~nL~~----~~t-------e~~L~~~F~~~G~v~~~~i~~d~~tg~~~g~aFV~f~~~~~a~~A~~~l~g~  307 (589)
                      .....+|.|.||-.    ..+       .++|.+-..+||.|..|.|.-.    .+.|.+-|.|.+.++|..||+.|+|.
T Consensus       262 ~r~~~tVi~kn~Ftp~~~~~~~~l~~dlkedl~eec~K~G~v~~vvv~d~----hPdGvvtV~f~n~eeA~~ciq~m~GR  337 (382)
T KOG1548|consen  262 ARADRTVILKNMFTPEDFEKNPDLLNDLKEDLTEECEKFGQVRKVVVYDR----HPDGVVTVSFRNNEEADQCIQTMDGR  337 (382)
T ss_pred             ccCCcEEEeeecCCHHHhccCHHHHHHHHHHHHHHHHHhCCcceEEEecc----CCCceeEEEeCChHHHHHHHHHhcCe
Confidence            34567899999832    233       2456667889999999987532    36699999999999999999999999


Q ss_pred             eeCCeEEEEEeccc
Q 007792          308 LIDDRRIHVDFSQS  321 (589)
Q Consensus       308 ~i~gr~i~V~~a~~  321 (589)
                      .|+|+.|...+...
T Consensus       338 ~fdgRql~A~i~DG  351 (382)
T KOG1548|consen  338 WFDGRQLTASIWDG  351 (382)
T ss_pred             eecceEEEEEEeCC
Confidence            99999999887654

>KOG2202 consensus U2 snRNP splicing factor, small subunit, and related proteins [RNA processing and modification]

Probab=96.95  E-value=0.00031  Score=67.81  Aligned_cols=64  Identities=19%  Similarity=0.429  Sum_probs=54.1

Q ss_pred             HHHHHHhc-cCCCeEEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHhcCCceeCCeEEEEEeccc
Q 007792          257 EDLHTIFS-RFGTVVSAEIIRDFKTGDSLNYAFIEFENRQACERAYSKMDNALIDDRRIHVDFSQS  321 (589)
Q Consensus       257 ~~L~~~F~-~~G~v~~~~i~~d~~tg~~~g~aFV~f~~~~~a~~A~~~l~g~~i~gr~i~V~~a~~  321 (589)
                      ++|...|+ +||+|..+.|..+ ..-...|.+||.|...++|++|+..||+-.|.|++|..+++.-
T Consensus        83 Ed~f~E~~~kygEiee~~Vc~N-l~~hl~GNVYV~f~~Ee~ae~a~~~lnnRw~~G~pi~ae~~pv  147 (260)
T KOG2202|consen   83 EDVFTELEDKYGEIEELNVCDN-LGDHLVGNVYVKFRSEEDAEAALEDLNNRWYNGRPIHAELSPV  147 (260)
T ss_pred             HHHHHHHHHHhhhhhhhhhhcc-cchhhhhhhhhhcccHHHHHHHHHHHcCccccCCcceeeecCc
Confidence            45555566 9999999987665 3344679999999999999999999999999999999999854

>KOG0129 consensus Predicted RNA-binding protein (RRM superfamily) [Translation, ribosomal structure and biogenesis]

Probab=96.92  E-value=0.0018  Score=68.42  Aligned_cols=62  Identities=31%  Similarity=0.326  Sum_probs=58.7

Q ss_pred             CCceEEEecCCCCCCHHHHHHHhc-cCCCeEEEEEeecCCCCCcccEEEEEEcCHHHHHHHHH
Q 007792          241 PENVLFVCKLNPVTEDEDLHTIFS-RFGTVVSAEIIRDFKTGDSLNYAFIEFENRQACERAYS  302 (589)
Q Consensus       241 ~~~~i~V~nL~~~~te~~L~~~F~-~~G~v~~~~i~~d~~tg~~~g~aFV~f~~~~~a~~A~~  302 (589)
                      |..|||||+||--++.++|..+|. -||.|..+.|-.|++-+-++|-|-|+|.+..+-.+||.
T Consensus       369 prrTVFVGgvprpl~A~eLA~imd~lyGgV~yaGIDtD~k~KYPkGaGRVtFsnqqsYi~AIs  431 (520)
T KOG0129|consen  369 PRRTVFVGGLPRPLTAEELAMIMEDLFGGVLYVGIDTDPKLKYPKGAGRVTFSNQQAYIKAIS  431 (520)
T ss_pred             ccceEEecCCCCcchHHHHHHHHHHhcCceEEEEeccCcccCCCCCcceeeecccHHHHHHHh
Confidence            678999999999999999999999 89999999999998888899999999999999999996

>KOG1456 consensus Heterogeneous nuclear ribonucleoprotein L (contains RRM repeats) [RNA processing and modification]

Probab=96.90  E-value=0.0054  Score=62.05  Aligned_cols=79  Identities=22%  Similarity=0.339  Sum_probs=70.6

Q ss_pred             CCCCceEEEecCCCC-CCHHHHHHHhccCCCeEEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHhcCCceeCCeEEEEE
Q 007792          239 KPPENVLFVCKLNPV-TEDEDLHTIFSRFGTVVSAEIIRDFKTGDSLNYAFIEFENRQACERAYSKMDNALIDDRRIHVD  317 (589)
Q Consensus       239 ~~~~~~i~V~nL~~~-~te~~L~~~F~~~G~v~~~~i~~d~~tg~~~g~aFV~f~~~~~a~~A~~~l~g~~i~gr~i~V~  317 (589)
                      ..+...+.|-+|... ++-+.|..+|-.||.|..|++++.+.     |-|.|++.+..+.+.|+..||+..+-|.+|.|.
T Consensus       284 ~~~g~VmMVyGLdh~k~N~drlFNl~ClYGNV~rvkFmkTk~-----gtamVemgd~~aver~v~hLnn~~lfG~kl~v~  358 (494)
T KOG1456|consen  284 GAPGCVMMVYGLDHGKMNCDRLFNLFCLYGNVERVKFMKTKP-----GTAMVEMGDAYAVERAVTHLNNIPLFGGKLNVC  358 (494)
T ss_pred             CCCCcEEEEEeccccccchhhhhhhhhhcCceeeEEEeeccc-----ceeEEEcCcHHHHHHHHHHhccCccccceEEEe
Confidence            556789999999775 67788999999999999999998643     799999999999999999999999999999999


Q ss_pred             ecccc
Q 007792          318 FSQSV  322 (589)
Q Consensus       318 ~a~~~  322 (589)
                      +++..
T Consensus       359 ~SkQ~  363 (494)
T KOG1456|consen  359 VSKQN  363 (494)
T ss_pred             ecccc
Confidence            99863

>KOG1456 consensus Heterogeneous nuclear ribonucleoprotein L (contains RRM repeats) [RNA processing and modification]

Probab=96.89  E-value=0.0051  Score=62.24  Aligned_cols=80  Identities=23%  Similarity=0.358  Sum_probs=65.6

Q ss_pred             CCCCceEEEecC--CCCCCHHHHHHHhccCCCeEEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHhcCCcee--CCeEE
Q 007792          239 KPPENVLFVCKL--NPVTEDEDLHTIFSRFGTVVSAEIIRDFKTGDSLNYAFIEFENRQACERAYSKMDNALI--DDRRI  314 (589)
Q Consensus       239 ~~~~~~i~V~nL--~~~~te~~L~~~F~~~G~v~~~~i~~d~~tg~~~g~aFV~f~~~~~a~~A~~~l~g~~i--~gr~i  314 (589)
                      ..+++.|.+.=|  -+.+|.+-|.++....|+|..|.|...  +|   -.|.|+|++.+.|++|...|||..|  +-.+|
T Consensus       117 ~~pN~VLl~TIlNp~YpItvDVly~Icnp~GkVlRIvIfkk--ng---VQAmVEFdsv~~AqrAk~alNGADIYsGCCTL  191 (494)
T KOG1456|consen  117 ATPNKVLLFTILNPQYPITVDVLYTICNPQGKVLRIVIFKK--NG---VQAMVEFDSVEVAQRAKAALNGADIYSGCCTL  191 (494)
T ss_pred             CCCCeEEEEEeecCccccchhhhhhhcCCCCceEEEEEEec--cc---eeeEEeechhHHHHHHHhhcccccccccceeE
Confidence            446677776655  456899999999999999999988763  33   4799999999999999999999876  34789


Q ss_pred             EEEeccccc
Q 007792          315 HVDFSQSVS  323 (589)
Q Consensus       315 ~V~~a~~~~  323 (589)
                      +|+||+|..
T Consensus       192 KIeyAkP~r  200 (494)
T KOG1456|consen  192 KIEYAKPTR  200 (494)
T ss_pred             EEEecCcce
Confidence            999999843

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

Probab=96.89  E-value=0.0026  Score=68.28  Aligned_cols=64  Identities=25%  Similarity=0.458  Sum_probs=53.4

Q ss_pred             HHHHHHhccCCCeEEEEEeecC---CCCCcccEEEEEEcCHHHHHHHHHhcCCceeCCeEEEEEecc
Q 007792          257 EDLHTIFSRFGTVVSAEIIRDF---KTGDSLNYAFIEFENRQACERAYSKMDNALIDDRRIHVDFSQ  320 (589)
Q Consensus       257 ~~L~~~F~~~G~v~~~~i~~d~---~tg~~~g~aFV~f~~~~~a~~A~~~l~g~~i~gr~i~V~~a~  320 (589)
                      ++|+..+++||.|..|.|..+.   ...-..|..||+|.+.++|+.|+++|+|.+|.|+.|...|..
T Consensus       424 Edvr~ec~k~g~v~~v~ipr~~~~~~~~~G~GkVFVefas~ed~qrA~~~L~GrKF~nRtVvtsYyd  490 (500)
T KOG0120|consen  424 EDVRTECAKFGAVRSVEIPRPYPDENPVPGTGKVFVEFADTEDSQRAMEELTGRKFANRTVVASYYD  490 (500)
T ss_pred             HHHHHHhcccCceeEEecCCCCCCCCcCCCcccEEEEecChHHHHHHHHHccCceeCCcEEEEEecC
Confidence            3455567799999999998762   223356889999999999999999999999999999998864

>KOG1855 consensus Predicted RNA-binding protein [General function prediction only]

Probab=96.73  E-value=0.0018  Score=66.65  Aligned_cols=67  Identities=22%  Similarity=0.331  Sum_probs=56.9

Q ss_pred             CCCceEEEecCCCCCCHHHHHHHhccCCCeEEEEEeec---CCC--CCc--------ccEEEEEEcCHHHHHHHHHhcCC
Q 007792          240 PPENVLFVCKLNPVTEDEDLHTIFSRFGTVVSAEIIRD---FKT--GDS--------LNYAFIEFENRQACERAYSKMDN  306 (589)
Q Consensus       240 ~~~~~i~V~nL~~~~te~~L~~~F~~~G~v~~~~i~~d---~~t--g~~--------~g~aFV~f~~~~~a~~A~~~l~g  306 (589)
                      .+..+|.+.|||.+-.-+.|.+||+.||.|+.|+|+..   +..  +.+        +-+|||+|...+.|.+|.+.|+.
T Consensus       229 l~srtivaenLP~Dh~~enl~kiFg~~G~IksIRIckPgaip~d~r~~~~~~~~~~tk~~AlvEye~~~~A~KA~e~~~~  308 (484)
T KOG1855|consen  229 LPSRTIVAENLPLDHSYENLSKIFGTVGSIKSIRICKPGAIPEDVRGFPKKYFELQTKECALVEYEEVEAARKARELLNP  308 (484)
T ss_pred             cccceEEEecCCcchHHHHHHHHhhcccceeeeeecCCCCCCcccccCCccchhhhhhhhhhhhhhhhHHHHHHHHhhch
Confidence            57889999999999888999999999999999999876   222  222        35799999999999999988765

>KOG2193 consensus IGF-II mRNA-binding protein IMP, contains RRM and KH domains [RNA processing and modification; General function prediction only]

Probab=96.72  E-value=0.0012  Score=67.63  Aligned_cols=75  Identities=21%  Similarity=0.384  Sum_probs=59.6

Q ss_pred             ceEEEecCCCCCCHHHHHHHhccCCCeEEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHhcCCc-eeCCeEEEEEeccc
Q 007792          243 NVLFVCKLNPVTEDEDLHTIFSRFGTVVSAEIIRDFKTGDSLNYAFIEFENRQACERAYSKMDNA-LIDDRRIHVDFSQS  321 (589)
Q Consensus       243 ~~i~V~nL~~~~te~~L~~~F~~~G~v~~~~i~~d~~tg~~~g~aFV~f~~~~~a~~A~~~l~g~-~i~gr~i~V~~a~~  321 (589)
                      +.+||+||.+.++..+|..+|...-....-.++.      ..|||||.+.+...|.+|++.|+|. ++.|+++.|.++-+
T Consensus         2 nklyignL~p~~~psdl~svfg~ak~~~~g~fl~------k~gyafvd~pdq~wa~kaie~~sgk~elqGkr~e~~~sv~   75 (584)
T KOG2193|consen    2 NKLYIGNLSPQVTPSDLESVFGDAKIPGSGQFLV------KSGYAFVDCPDQQWANKAIETLSGKVELQGKRQEVEHSVP   75 (584)
T ss_pred             CcccccccCCCCChHHHHHHhccccCCCCcceee------ecceeeccCCchhhhhhhHHhhchhhhhcCceeeccchhh
Confidence            4789999999999999999998542111222222      1289999999999999999999994 68999999999876


Q ss_pred             cc
Q 007792          322 VS  323 (589)
Q Consensus       322 ~~  323 (589)
                      +.
T Consensus        76 kk   77 (584)
T KOG2193|consen   76 KK   77 (584)
T ss_pred             HH
Confidence            43

>KOG4307 consensus RNA binding protein RBM12/SWAN [General function prediction only]

Probab=96.67  E-value=0.0051  Score=66.82  Aligned_cols=75  Identities=21%  Similarity=0.302  Sum_probs=65.0

Q ss_pred             ceEEEecCCCCCCHHHHHHHhccCCCeE-EEEEeecCCCCCcccEEEEEEcCHHHHHHHHHhcCCceeCCeEEEEEe
Q 007792          243 NVLFVCKLNPVTEDEDLHTIFSRFGTVV-SAEIIRDFKTGDSLNYAFIEFENRQACERAYSKMDNALIDDRRIHVDF  318 (589)
Q Consensus       243 ~~i~V~nL~~~~te~~L~~~F~~~G~v~-~~~i~~d~~tg~~~g~aFV~f~~~~~a~~A~~~l~g~~i~gr~i~V~~  318 (589)
                      +.|-+-|+|+.++-++|.+||..|-.+- +|.+-.+ ..|+..|-|.|.|++.++|..|...|++..|..+.|.|.+
T Consensus       868 ~V~~~~n~Pf~v~l~dI~~FF~dY~~~p~sI~~r~n-d~G~pTGe~mvAfes~~eAr~A~~dl~~~~i~nr~V~l~i  943 (944)
T KOG4307|consen  868 RVLSCNNFPFDVTLEDIVEFFNDYEPDPNSIRIRRN-DDGVPTGECMVAFESQEEARRASMDLDGQKIRNRVVSLRI  943 (944)
T ss_pred             eEEEecCCCccccHHHHHHHhcccccCCCceeEeec-CCCCcccceeEeecCHHHHHhhhhccccCcccceeEEEEe
Confidence            4788899999999999999999996554 4444444 6789999999999999999999999999999999998864

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

Probab=96.66  E-value=0.0043  Score=46.00  Aligned_cols=52  Identities=21%  Similarity=0.470  Sum_probs=42.1

Q ss_pred             ceEEEecCCCCCCHHHHHHHhccCCCeEEEEEeecCCCCCcccEEEEEEcCHHHHHHHH
Q 007792          243 NVLFVCKLNPVTEDEDLHTIFSRFGTVVSAEIIRDFKTGDSLNYAFIEFENRQACERAY  301 (589)
Q Consensus       243 ~~i~V~nL~~~~te~~L~~~F~~~G~v~~~~i~~d~~tg~~~g~aFV~f~~~~~a~~A~  301 (589)
                      +.|-|.+.++...+ .|...|.+||+|..+.+..      ...+.||.|.+..+|+.||
T Consensus         2 ~wI~V~Gf~~~~~~-~vl~~F~~fGeI~~~~~~~------~~~~~~l~y~~~~~ae~Al   53 (53)
T PF14605_consen    2 TWISVSGFPPDLAE-EVLEHFASFGEIVDIYVPE------STNWMYLKYKSRKDAEKAL   53 (53)
T ss_pred             cEEEEEeECchHHH-HHHHHHHhcCCEEEEEcCC------CCcEEEEEECCHHHHHhhC
Confidence            56788899887764 4556888999999988852      2359999999999999985

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

Probab=96.53  E-value=0.0071  Score=55.51  Aligned_cols=71  Identities=21%  Similarity=0.302  Sum_probs=60.8

Q ss_pred             CCceEEEecCCCCCCHHHHHHHhccCCCeEEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHhcCCceeC--CeEEEEEe
Q 007792          241 PENVLFVCKLNPVTEDEDLHTIFSRFGTVVSAEIIRDFKTGDSLNYAFIEFENRQACERAYSKMDNALID--DRRIHVDF  318 (589)
Q Consensus       241 ~~~~i~V~nL~~~~te~~L~~~F~~~G~v~~~~i~~d~~tg~~~g~aFV~f~~~~~a~~A~~~l~g~~i~--gr~i~V~~  318 (589)
                      ....|.|.+||+..++++|+...-+.|.|....+..|       |++.|+|...++++-||..|....+.  |-...+.+
T Consensus       114 Se~RVvVsGLp~SgSWQDLKDHmReaGdvCfadv~rD-------g~GvV~~~r~eDMkYAvr~ld~~~~~seGe~~yirv  186 (241)
T KOG0105|consen  114 SEYRVVVSGLPPSGSWQDLKDHMREAGDVCFADVQRD-------GVGVVEYLRKEDMKYAVRKLDDQKFRSEGETAYIRV  186 (241)
T ss_pred             cceeEEEecCCCCCchHHHHHHHHhhCCeeeeeeecc-------cceeeeeeehhhHHHHHHhhccccccCcCcEeeEEe
Confidence            3468999999999999999999999999999999887       79999999999999999999886654  44444333

>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=96.49  E-value=0.016  Score=48.88  Aligned_cols=78  Identities=19%  Similarity=0.308  Sum_probs=51.9

Q ss_pred             CceEEEecCCCCCCHHHHHHHhccCCCeEEEEEe-ecC------CCCCcccEEEEEEcCHHHHHHHHHhcCCceeCCe-E
Q 007792          242 ENVLFVCKLNPVTEDEDLHTIFSRFGTVVSAEII-RDF------KTGDSLNYAFIEFENRQACERAYSKMDNALIDDR-R  313 (589)
Q Consensus       242 ~~~i~V~nL~~~~te~~L~~~F~~~G~v~~~~i~-~d~------~tg~~~g~aFV~f~~~~~a~~A~~~l~g~~i~gr-~  313 (589)
                      .+.|.|-+.|+..+ ..|...|++||.|.+..-+ .+.      ..........|.|.+..+|.+|| ..||..|.|. .
T Consensus         6 ~~wVtVFGfp~~~~-~~Vl~~F~~~G~Ile~~~~~~~~~~~~~~~~~~~~NWi~I~Y~~~~~A~rAL-~~NG~i~~g~~m   83 (100)
T PF05172_consen    6 ETWVTVFGFPPSAS-NQVLRHFSSFGTILEHFEVLRSSSGINPYPIPSGGNWIHITYDNPLSAQRAL-QKNGTIFSGSLM   83 (100)
T ss_dssp             CCEEEEE---GGGH-HHHHHHHHCCS-EECEEGGG----------E-CCTTEEEEEESSHHHHHHHH-TTTTEEETTCEE
T ss_pred             CeEEEEEccCHHHH-HHHHHHHHhcceEEEeecccccccccccccCCCCCCEEEEECCCHHHHHHHH-HhCCeEEcCcEE
Confidence            45688889998854 7788999999999876400 000      00112358999999999999999 4699999885 5


Q ss_pred             EEEEeccc
Q 007792          314 IHVDFSQS  321 (589)
Q Consensus       314 i~V~~a~~  321 (589)
                      +-|.++++
T Consensus        84 vGV~~~~~   91 (100)
T PF05172_consen   84 VGVKPCDP   91 (100)
T ss_dssp             EEEEE-HH
T ss_pred             EEEEEcHH
Confidence            56777754

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.

>KOG1365 consensus RNA-binding protein Fusilli, contains RRM domain [RNA processing and modification; General function prediction only]

Probab=96.37  E-value=0.0069  Score=61.49  Aligned_cols=78  Identities=21%  Similarity=0.256  Sum_probs=66.3

Q ss_pred             CceEEEecCCCCCCHHHHHHHhccCCC-eEE--EEEeecCCCCCcccEEEEEEcCHHHHHHHHHhcCCceeCCeEEEEEe
Q 007792          242 ENVLFVCKLNPVTEDEDLHTIFSRFGT-VVS--AEIIRDFKTGDSLNYAFIEFENRQACERAYSKMDNALIDDRRIHVDF  318 (589)
Q Consensus       242 ~~~i~V~nL~~~~te~~L~~~F~~~G~-v~~--~~i~~d~~tg~~~g~aFV~f~~~~~a~~A~~~l~g~~i~gr~i~V~~  318 (589)
                      ..+|-+.+||+.++.++|..||..|.. |..  |.|+.+ ..|.+.|-|||+|.+.+.|.+|....+.+....+-|.|--
T Consensus       280 kdcvRLRGLPy~AtvEdIL~FlgdFa~~i~f~gVHmv~N-~qGrPSGeAFIqm~nae~a~aaaqk~hk~~mk~RYiEvfp  358 (508)
T KOG1365|consen  280 KDCVRLRGLPYEATVEDILDFLGDFATDIRFQGVHMVLN-GQGRPSGEAFIQMRNAERARAAAQKCHKKLMKSRYIEVFP  358 (508)
T ss_pred             CCeeEecCCChhhhHHHHHHHHHHHhhhcccceeEEEEc-CCCCcChhhhhhhhhhHHHHHHHHHHHHhhcccceEEEee
Confidence            468999999999999999999998864 333  777777 4588999999999999999999988888777789898876


Q ss_pred             cc
Q 007792          319 SQ  320 (589)
Q Consensus       319 a~  320 (589)
                      +.
T Consensus       359 ~S  360 (508)
T KOG1365|consen  359 CS  360 (508)
T ss_pred             cc
Confidence            54

>PRK00969 hypothetical protein; Provisional

Probab=96.32  E-value=0.024  Score=60.42  Aligned_cols=116  Identities=16%  Similarity=0.229  Sum_probs=77.4

Q ss_pred             EEEEEecceeEEEEecCCCChhHHHHHHHHHhcCccCCceEEEeecCcccccCCCCCCCCCCCCcccccccccccccCCc
Q 007792            2 SVLIVTSLGDIVVDLFVDKCPLTTKNFLKLCKIKYYNGCLFHTVQKDFTAQTGDPTGTGTGGDSVYKFLYGEQARFFGDE   81 (589)
Q Consensus         2 ~v~~~T~~G~i~ieL~~~~aP~~~~nF~~l~~~~~Y~g~~f~rv~~~~~iq~Gd~~~~~~~~~~~~~~~~~~~~~~~~~e   81 (589)
                      ...|.|+.|.|+|+|.  ....++.-|+..++.  |.|..++...+.- +.+|-+..+                  |+..
T Consensus        52 ~y~IkTtkG~i~Iel~--~~~~~~~~w~e~yk~--~e~~~i~W~s~~~-vAfGp~~s~------------------l~p~  108 (508)
T PRK00969         52 KYRIKTTKGEIVIELT--EENESVDFWLENYKE--FEGKSLRWTSRSA-VAFGPFESD------------------LEPS  108 (508)
T ss_pred             eEEEEccCceEEEEEc--cCcchhhHHHHhHHh--hcCCceEeccccc-eeEcccccC------------------cccc
Confidence            4578999999999999  566777888877765  6788887766544 333322110                  1101


Q ss_pred             cccCCCCCCCceEEEeccCCCCCcceEEEEeCCCCCCCCC-CcceEEEEecCHHHHHHHhhC
Q 007792           82 IRVDLKHAKTGTVAMASAGENLNASQFYMTLRDNLDYLDE-KHTIFGEVAEGLETLSRINES  142 (589)
Q Consensus        82 ~~~~l~~~~~G~vs~a~~g~~~~~sqFfI~l~~~~~~ld~-~~~vFG~Vv~G~~vl~~i~~~  142 (589)
                        ..-....++-|.|.-+|-+...+.+.|+..+++....- .--|||+||.|..+|+.+...
T Consensus       109 --~~~~~y~r~DV~lg~~G~dp~~thLIfsk~~h~a~YG~p~~gv~grVi~Gk~vl~~L~~~  168 (508)
T PRK00969        109 --REEYEYERWDVVLSLSGFDPSETHLIFSKRDHSADYGAPNDGVIGRVVGGKRVLDRLTDG  168 (508)
T ss_pred             --cCcceeecccEEEEccCCCCCCceEEEEecchhhhhCCCCCCceEEEccchhhHhhccCC
Confidence              01111257888898888877788888887764222111 127999999999999999654

>KOG0129 consensus Predicted RNA-binding protein (RRM superfamily) [Translation, ribosomal structure and biogenesis]

Probab=96.27  E-value=0.012  Score=62.43  Aligned_cols=61  Identities=20%  Similarity=0.341  Sum_probs=46.3

Q ss_pred             CceEEEecCCCCCCHHHHHHHhccCCCeEEEEEee--cC-CCCCccc---EEEEEEcCHHHHHHHHHh
Q 007792          242 ENVLFVCKLNPVTEDEDLHTIFSRFGTVVSAEIIR--DF-KTGDSLN---YAFIEFENRQACERAYSK  303 (589)
Q Consensus       242 ~~~i~V~nL~~~~te~~L~~~F~~~G~v~~~~i~~--d~-~tg~~~g---~aFV~f~~~~~a~~A~~~  303 (589)
                      ...||||+||+.++|+.|...|..||.+. |.+..  .. .--.++|   |+|+.|+++.++..-|.+
T Consensus       259 S~KVFvGGlp~dise~~i~~~F~~FGs~~-VdWP~k~~~~~~~ppkGs~~YvflvFe~E~sV~~Ll~a  325 (520)
T KOG0129|consen  259 SRKVFVGGLPWDITEAQINASFGQFGSVK-VDWPGKANSRGRAPPKGSYGYVFLVFEDERSVQSLLSA  325 (520)
T ss_pred             ccceeecCCCccccHHHHHhhcccccceE-eecCCCccccccCCCCCcccEEEEEecchHHHHHHHHH
Confidence            46999999999999999999999999865 33331  11 1112456   999999999888776654

>TIGR03268 methan_mark_3 putative methanogenesis marker protein 3

Probab=96.19  E-value=0.035  Score=59.00  Aligned_cols=116  Identities=14%  Similarity=0.197  Sum_probs=78.2

Q ss_pred             EEEEEecceeEEEEecCCCChhHHHHHHHHHhcCccCCceEEEeecCcccccCCCCCCCCCCCCcccccccccccccCCc
Q 007792            2 SVLIVTSLGDIVVDLFVDKCPLTTKNFLKLCKIKYYNGCLFHTVQKDFTAQTGDPTGTGTGGDSVYKFLYGEQARFFGDE   81 (589)
Q Consensus         2 ~v~~~T~~G~i~ieL~~~~aP~~~~nF~~l~~~~~Y~g~~f~rv~~~~~iq~Gd~~~~~~~~~~~~~~~~~~~~~~~~~e   81 (589)
                      ...|.|+.|.|+|+|-.  ...+++-|++.++.  |-|..++...+.- +.+|-+..+                  |+..
T Consensus        48 ~y~IkTtkG~i~iel~~--~~~~~~~w~e~y~~--~e~~~i~W~s~~~-vAfGp~~sd------------------l~p~  104 (503)
T TIGR03268        48 EYLIKTTKGEVVIELTP--NTEAGKFWSEIYKE--LEGKQIRWTTPQE-VAFGPFPSD------------------LEPS  104 (503)
T ss_pred             eEEEEccCceEEEEecC--CchHHHHHHHHHHh--hcCCceeecchhh-eeeCcccCC------------------cccc
Confidence            45789999999999993  67778888877765  6777777665543 333322110                  1100


Q ss_pred             cccCCCCCCCceEEEeccCCCCCcceEEEEeCCCCCCCC--CCcceEEEEecCHHHHHHHhhC
Q 007792           82 IRVDLKHAKTGTVAMASAGENLNASQFYMTLRDNLDYLD--EKHTIFGEVAEGLETLSRINES  142 (589)
Q Consensus        82 ~~~~l~~~~~G~vs~a~~g~~~~~sqFfI~l~~~~~~ld--~~~~vFG~Vv~G~~vl~~i~~~  142 (589)
                        ..-....++-|.+.-+|-+...+.+.|+..+++....  ...-|||+||.|..||++|...
T Consensus       105 --~~~~~y~r~DV~lg~~G~d~~~thLIfsk~~h~~~YG~p~~~gvigrvi~Gk~vl~~L~~~  165 (503)
T TIGR03268       105 --REPSEYERWDVILSLSGFDPDETHIIFSKKRHAAEYGVPDENGIIARVVGGKRVIDRLSDG  165 (503)
T ss_pred             --CCcceeecccEEEEccCCCCCCceEEEEecchhhhhCCCCCCCEEEEEccchhhHhhccCC
Confidence              0111135788899888888888888888877532221  1467999999999999999654

A single member of this protein family is found in each of the first ten complete genome sequences of archaeal methanogens, and nowhere else. This protein family was detected by the method of partial phylogenetic profiling (see Haft, et al., 2006). The functions of proteins in this family are unknown, but their role is likely one essential to methanogenesis.

>KOG0112 consensus Large RNA-binding protein (RRM superfamily) [General function prediction only]

Probab=96.14  E-value=0.0052  Score=68.79  Aligned_cols=79  Identities=27%  Similarity=0.424  Sum_probs=68.6

Q ss_pred             CCCceEEEecCCCCCCHHHHHHHhccCCCeEEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHhcCCceeCC--eEEEEE
Q 007792          240 PPENVLFVCKLNPVTEDEDLHTIFSRFGTVVSAEIIRDFKTGDSLNYAFIEFENRQACERAYSKMDNALIDD--RRIHVD  317 (589)
Q Consensus       240 ~~~~~i~V~nL~~~~te~~L~~~F~~~G~v~~~~i~~d~~tg~~~g~aFV~f~~~~~a~~A~~~l~g~~i~g--r~i~V~  317 (589)
                      .+.+.+||++|..++....|..+|..||.|..|.+-.      .--||+|.|++...|+.|+..|-|+.|+|  +.|.|.
T Consensus       453 t~ttr~~sgglg~w~p~~~l~r~fd~fGpir~Idy~h------gq~yayi~yes~~~aq~a~~~~rgap~G~P~~r~rvd  526 (975)
T KOG0112|consen  453 TPTTRLQSGGLGPWSPVSRLNREFDRFGPIRIIDYRH------GQPYAYIQYESPPAAQAATHDMRGAPLGGPPRRLRVD  526 (975)
T ss_pred             ccceeeccCCCCCCChHHHHHHHhhccCcceeeeccc------CCcceeeecccCccchhhHHHHhcCcCCCCCcccccc
Confidence            3567899999999999999999999999999877633      22599999999999999999999999986  779999


Q ss_pred             ecccccc
Q 007792          318 FSQSVSK  324 (589)
Q Consensus       318 ~a~~~~~  324 (589)
                      |+.....
T Consensus       527 la~~~~~  533 (975)
T KOG0112|consen  527 LASPPGA  533 (975)
T ss_pred             cccCCCC
Confidence            9986433

>PRK00969 hypothetical protein; Provisional

Probab=96.12  E-value=0.016  Score=61.69  Aligned_cols=96  Identities=24%  Similarity=0.340  Sum_probs=62.2

Q ss_pred             EEEEecCCCChhHHHHHHHHHhcCccC----CceEEEeecCcccccCCCCCCCCCCCCcccccccccccccCCccccCCC
Q 007792           12 IVVDLFVDKCPLTTKNFLKLCKIKYYN----GCLFHTVQKDFTAQTGDPTGTGTGGDSVYKFLYGEQARFFGDEIRVDLK   87 (589)
Q Consensus        12 i~ieL~~~~aP~~~~nF~~l~~~~~Y~----g~~f~rv~~~~~iq~Gd~~~~~~~~~~~~~~~~~~~~~~~~~e~~~~l~   87 (589)
                      +.|+|.+ .||.+|++|+.+.+.|.+.    -.+|-.   ...+||                      ..+|.|.   +.
T Consensus       206 ~eve~~~-~~p~s~EH~la~~~~G~f~Vd~~tstfI~---d~~L~g----------------------~~~p~En---~~  256 (508)
T PRK00969        206 VEVELDP-GAPKSVEHFLALLEDGTFEVDFETSTFIA---DDRLQG----------------------LKIPEEN---FE  256 (508)
T ss_pred             EEEEEcC-CCCchHHHHHHHHhCCeEEEeeeecceEe---eccccC----------------------ccCCccc---cC
Confidence            5677775 5999999999999987532    122211   111111                      2344442   22


Q ss_pred             CCCCceEEEeccCCCCCcceEEEEeCCCCCCCCCCcceEEEEecCHHHHHHHh
Q 007792           88 HAKTGTVAMASAGENLNASQFYMTLRDNLDYLDEKHTIFGEVAEGLETLSRIN  140 (589)
Q Consensus        88 ~~~~G~vs~a~~g~~~~~sqFfI~l~~~~~~ld~~~~vFG~Vv~G~~vl~~i~  140 (589)
                      .-..|+|.+-+.|.+  ..-.||...+-.+.  -.|+|+|+|+.||++++--.
T Consensus       257 ~R~~GtVTVRt~G~g--~G~vYIyredr~ss--~sHtvVG~V~~GiELi~~a~  305 (508)
T PRK00969        257 PRRRGTVTVRTAGVG--VGKVYIYREDRPSS--LSHTVVGRVTHGIELIDFAK  305 (508)
T ss_pred             ccccceEEEEeeccC--ceeEEEECCCCCCC--ccceeEEEEecceeeeeccc
Confidence            235799999998754  34688888763333  45999999999999986543

>TIGR03268 methan_mark_3 putative methanogenesis marker protein 3

Probab=96.11  E-value=0.033  Score=59.23  Aligned_cols=115  Identities=18%  Similarity=0.227  Sum_probs=64.0

Q ss_pred             ceeEEEEecCCCChhHHHHHHHHHhcCcc--CCceEEEeecCcccccCCCCCCCCCCCCcccccccccccccCCccccCC
Q 007792            9 LGDIVVDLFVDKCPLTTKNFLKLCKIKYY--NGCLFHTVQKDFTAQTGDPTGTGTGGDSVYKFLYGEQARFFGDEIRVDL   86 (589)
Q Consensus         9 ~G~i~ieL~~~~aP~~~~nF~~l~~~~~Y--~g~~f~rv~~~~~iq~Gd~~~~~~~~~~~~~~~~~~~~~~~~~e~~~~l   86 (589)
                      ---|.|+||.+.||.||..|..+.-....  --+.+|-..++.++.-|++.         +.       +.+-.|..+.-
T Consensus       374 ~~vi~IeLydd~AP~s~~yFRk~tGL~~~~VG~L~v~F~~~d~~mFk~~~~---------~~-------k~LiPEN~P~~  437 (503)
T TIGR03268       374 DKVIEIELYDDNAPRSVWYFRKFTGLKTKPVGRLPVHFAFKEMIMFKGNKE---------LA-------KGLIPENTPED  437 (503)
T ss_pred             HhEEEEEEcccCCchHHHHHHHhcCCcccccceeEEEEEeCCeeEeccCch---------hc-------cccCCCCCCCC
Confidence            34579999999999999999998754321  22355555555444422221         10       11222222222


Q ss_pred             CCCCCceEEEeccCCCCCcceEEEEeC------CCCCCCCCCcceEEEEecCHHHHHHHhhC
Q 007792           87 KHAKTGTVAMASAGENLNASQFYMTLR------DNLDYLDEKHTIFGEVAEGLETLSRINES  142 (589)
Q Consensus        87 ~~~~~G~vs~a~~g~~~~~sqFfI~l~------~~~~~ld~~~~vFG~Vv~G~~vl~~i~~~  142 (589)
                      + ..+|.|+|.|...-. -...-|-|.      |....|++.+. +|+|+++++.|.+|...
T Consensus       438 ~-V~ag~IgvTN~a~k~-~G~IGVRl~d~defGPTGE~F~gTNI-iG~Vv~~~e~Lk~~KeG  496 (503)
T TIGR03268       438 K-VEAGVIGVTNQACKH-VGMIGVRLEDSDEFGPTGEPFSGTNI-IGRVVEGMERLKGLKEG  496 (503)
T ss_pred             c-cccceEeeechhhhc-CceEEEEccCCcccCCCCCCccCcce-EEEecCChhHhcccccC
Confidence            2 246888876642110 011222232      22344666554 59999999999888653

A single member of this protein family is found in each of the first ten complete genome sequences of archaeal methanogens, and nowhere else. This protein family was detected by the method of partial phylogenetic profiling (see Haft, et al., 2006). The functions of proteins in this family are unknown, but their role is likely one essential to methanogenesis.

>KOG0128 consensus RNA-binding protein SART3 (RRM superfamily) [RNA processing and modification]

Probab=95.97  E-value=0.0048  Score=68.77  Aligned_cols=80  Identities=16%  Similarity=0.203  Sum_probs=73.1

Q ss_pred             CceEEEecCCCCCCHHHHHHHhccCCCeEEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHhcCCceeCCeEEEEEeccc
Q 007792          242 ENVLFVCKLNPVTEDEDLHTIFSRFGTVVSAEIIRDFKTGDSLNYAFIEFENRQACERAYSKMDNALIDDRRIHVDFSQS  321 (589)
Q Consensus       242 ~~~i~V~nL~~~~te~~L~~~F~~~G~v~~~~i~~d~~tg~~~g~aFV~f~~~~~a~~A~~~l~g~~i~gr~i~V~~a~~  321 (589)
                      ...|||.|+|+..|.+.|+.+|..+|.++.+.++.. ..|+++|.|||.|.++.+|..++..+....+.-..+.|.+++|
T Consensus       736 K~~v~i~g~pf~gt~e~~k~l~~~~gn~~~~~~vt~-r~gkpkg~a~v~y~~ea~~s~~~~s~d~~~~rE~~~~v~vsnp  814 (881)
T KOG0128|consen  736 KISVAISGPPFQGTKEELKSLASKTGNVTSLRLVTV-RAGKPKGKARVDYNTEADASRKVASVDVAGKRENNGEVQVSNP  814 (881)
T ss_pred             hhhhheeCCCCCCchHHHHhhccccCCccccchhhh-hccccccceeccCCCcchhhhhcccchhhhhhhcCccccccCC
Confidence            458999999999999999999999999999998877 4699999999999999999999988888888888999999887


Q ss_pred             c
Q 007792          322 V  322 (589)
Q Consensus       322 ~  322 (589)
                      .
T Consensus       815 ~  815 (881)
T KOG0128|consen  815 E  815 (881)
T ss_pred             c
Confidence            3

>COG4070 Predicted peptidyl-prolyl cis-trans isomerase (rotamase), cyclophilin family [Posttranslational modification, protein turnover, chaperones]

Probab=95.96  E-value=0.013  Score=59.76  Aligned_cols=97  Identities=23%  Similarity=0.364  Sum_probs=63.6

Q ss_pred             eEEEEecCCCChhHHHHHHHHHhcCc----cCCceEEEeecCcccccCCCCCCCCCCCCcccccccccccccCCccccCC
Q 007792           11 DIVVDLFVDKCPLTTKNFLKLCKIKY----YNGCLFHTVQKDFTAQTGDPTGTGTGGDSVYKFLYGEQARFFGDEIRVDL   86 (589)
Q Consensus        11 ~i~ieL~~~~aP~~~~nF~~l~~~~~----Y~g~~f~rv~~~~~iq~Gd~~~~~~~~~~~~~~~~~~~~~~~~~e~~~~l   86 (589)
                      .+.|+|-++ +|.+|++|++|.+.|.    |.-.+|--..+   +|                      ...++.| ++.+
T Consensus       204 y~eve~s~n-sP~saEH~lalmedG~lri~~~tntfis~~~---lq----------------------~~~~~~e-n~d~  256 (512)
T COG4070         204 YFEVELSRN-SPKSAEHFLALMEDGTLRIDVTTNTFISDDT---LQ----------------------EEKVPEE-NFDL  256 (512)
T ss_pred             EEEEEeCCC-CchhHHHHHHHhhcceEEEEEeccceeeccc---cc----------------------cccCChh-hhhh
Confidence            357788764 9999999999998764    22222211111   11                      1334545 3444


Q ss_pred             CCCCCceEEEeccCCCCCcceEEEEeCCCCCCCCCCcceEEEEecCHHHHHHHh
Q 007792           87 KHAKTGTVAMASAGENLNASQFYMTLRDNLDYLDEKHTIFGEVAEGLETLSRIN  140 (589)
Q Consensus        87 ~~~~~G~vs~a~~g~~~~~sqFfI~l~~~~~~ld~~~~vFG~Vv~G~~vl~~i~  140 (589)
                      .  .+|.|.+-|.|-+  ...-||.-.+-.+.|  .|+|.|+|++||++|+--.
T Consensus       257 R--erG~iTvRn~Gvg--eGrvYIyRedR~ss~--sHnvVGrV~eGiELid~a~  304 (512)
T COG4070         257 R--ERGAITVRNVGVG--EGRVYIYREDRPSSL--SHNVVGRVIEGIELIDLAE  304 (512)
T ss_pred             h--hcceEEEEeeecc--cceEEEEecCCCCcc--ccceeeeeecceEEEEecc
Confidence            4  4799999987743  346788776644444  4899999999999887543

>KOG1996 consensus mRNA splicing factor [RNA processing and modification]

Probab=95.66  E-value=0.031  Score=54.95  Aligned_cols=64  Identities=16%  Similarity=0.255  Sum_probs=51.5

Q ss_pred             HHHHHHhccCCCeEEEEEeecCCCCCc-ccEEEEEEcCHHHHHHHHHhcCCceeCCeEEEEEecc
Q 007792          257 EDLHTIFSRFGTVVSAEIIRDFKTGDS-LNYAFIEFENRQACERAYSKMDNALIDDRRIHVDFSQ  320 (589)
Q Consensus       257 ~~L~~~F~~~G~v~~~~i~~d~~tg~~-~g~aFV~f~~~~~a~~A~~~l~g~~i~gr~i~V~~a~  320 (589)
                      .++.+.+.+||.|..|-|...+.-..- ---.||+|+..++|.+|+-.|||..|+|+.+...|.+
T Consensus       301 de~keEceKyg~V~~viifeip~~p~deavRiFveF~r~e~aiKA~VdlnGRyFGGr~v~A~Fyn  365 (378)
T KOG1996|consen  301 DETKEECEKYGKVGNVIIFEIPSQPEDEAVRIFVEFERVESAIKAVVDLNGRYFGGRVVSACFYN  365 (378)
T ss_pred             HHHHHHHHhhcceeeEEEEecCCCccchhheeeeeeccHHHHHHHHHhcCCceecceeeeheecc
Confidence            567788899999999877665321111 2358999999999999999999999999999988765

>PF12903 DUF3830: Protein of unknown function (DUF3830); InterPro: IPR024532 This is a family of bacterial and archaeal proteins

Probab=95.19  E-value=0.099  Score=47.05  Aligned_cols=42  Identities=19%  Similarity=0.196  Sum_probs=27.6

Q ss_pred             EEEecceeEEEEecCCCChhHHHHHHHHHhcCccCCceEEEeecC
Q 007792            4 LIVTSLGDIVVDLFVDKCPLTTKNFLKLCKIKYYNGCLFHTVQKD   48 (589)
Q Consensus         4 ~~~T~~G~i~ieL~~~~aP~~~~nF~~l~~~~~Y~g~~f~rv~~~   48 (589)
                      .|...--.++.+|+.+.||.||+.|.++.   =|.+..+|-...+
T Consensus         2 ~~~~~g~~~~A~l~~d~AP~Tcaa~~~~L---P~~~~~~HarwSG   43 (147)
T PF12903_consen    2 TLTKRGVSFTARLLDDKAPKTCAAFWEAL---PLKGKVIHARWSG   43 (147)
T ss_dssp             EETTTTEEEEEEE-TTTSHHHHHHHHHH-----EEEE-EE-SSSS
T ss_pred             eEecCCeEEEEEEcccCChHHHHHHHHhC---CCCCcEEEEEEEC
Confidence            34445557899999999999999999988   3555555554444

The structure of one of family members, A0JVT3 from SWISSPROT, has been characterised and shown to contain a cyclophilin-like fold.; PDB: 3KOP_B.

>KOG2253 consensus U1 snRNP complex, subunit SNU71 and related PWI-motif proteins [RNA processing and modification]

Probab=95.13  E-value=0.011  Score=64.21  Aligned_cols=75  Identities=23%  Similarity=0.334  Sum_probs=66.8

Q ss_pred             CCCCCCceEEEecCCCCCCHHHHHHHhccCCCeEEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHhcCCceeCCeEEEE
Q 007792          237 DIKPPENVLFVCKLNPVTEDEDLHTIFSRFGTVVSAEIIRDFKTGDSLNYAFIEFENRQACERAYSKMDNALIDDRRIHV  316 (589)
Q Consensus       237 ~~~~~~~~i~V~nL~~~~te~~L~~~F~~~G~v~~~~i~~d~~tg~~~g~aFV~f~~~~~a~~A~~~l~g~~i~gr~i~V  316 (589)
                      ...+|..+|||+||...+..+-+..++..||-|..+..+.         |||+.|....-+..|+..|+-..++|..|.+
T Consensus        35 ~~~~~~~~vfv~~~~~~~s~~~~~~il~~~g~v~s~kr~~---------fgf~~f~~~~~~~ra~r~~t~~~~~~~kl~~  105 (668)
T KOG2253|consen   35 QPLPPRDTVFVGNISYLVSQEFWKSILAKSGFVPSWKRDK---------FGFCEFLKHIGDLRASRLLTELNIDDQKLIE  105 (668)
T ss_pred             cCCCCCceeEecchhhhhhHHHHHHHHhhCCcchhhhhhh---------hcccchhhHHHHHHHHHHhcccCCCcchhhc
Confidence            3456788999999999999999999999999998876644         9999999999999999999999999999988


Q ss_pred             Eecc
Q 007792          317 DFSQ  320 (589)
Q Consensus       317 ~~a~  320 (589)
                      ....
T Consensus       106 ~~d~  109 (668)
T KOG2253|consen  106 NVDE  109 (668)
T ss_pred             cchh
Confidence            8753

>KOG0115 consensus RNA-binding protein p54nrb (RRM superfamily) [RNA processing and modification]

Probab=94.93  E-value=0.029  Score=54.40  Aligned_cols=76  Identities=21%  Similarity=0.329  Sum_probs=63.0

Q ss_pred             ceEEEecCCCCCCHHHHHHHhccCCCeEEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHhcCC----ceeCCeEEEEEe
Q 007792          243 NVLFVCKLNPVTEDEDLHTIFSRFGTVVSAEIIRDFKTGDSLNYAFIEFENRQACERAYSKMDN----ALIDDRRIHVDF  318 (589)
Q Consensus       243 ~~i~V~nL~~~~te~~L~~~F~~~G~v~~~~i~~d~~tg~~~g~aFV~f~~~~~a~~A~~~l~g----~~i~gr~i~V~~  318 (589)
                      ..|||.||+..+..+.|...|..||+|....++.| ..+++.+-++|+|...-.|..|+..++-    ..+.+.+.-|..
T Consensus        32 a~l~V~nl~~~~sndll~~~f~~fg~~e~av~~vD-~r~k~t~eg~v~~~~k~~a~~a~rr~~~~g~~~~~~~~p~~VeP  110 (275)
T KOG0115|consen   32 AELYVVNLMQGASNDLLEQAFRRFGPIERAVAKVD-DRGKPTREGIVEFAKKPNARKAARRCREGGFGGTTGGRPVGVEP  110 (275)
T ss_pred             ceEEEEecchhhhhHHHHHhhhhcCccchheeeec-ccccccccchhhhhcchhHHHHHHHhccCccccCCCCCccCCCh
Confidence            79999999999999999999999999998777776 5578889999999999999999987732    234566666654


Q ss_pred             c
Q 007792          319 S  319 (589)
Q Consensus       319 a  319 (589)
                      .
T Consensus       111 ~  111 (275)
T KOG0115|consen  111 M  111 (275)
T ss_pred             h
Confidence            4

>KOG2068 consensus MOT2 transcription factor [Transcription]

Probab=94.77  E-value=0.015  Score=58.57  Aligned_cols=80  Identities=18%  Similarity=0.352  Sum_probs=62.1

Q ss_pred             CceEEEecCCCCCCHHHHH---HHhccCCCeEEEEEeecCC--CC-CcccEEEEEEcCHHHHHHHHHhcCCceeCCeEEE
Q 007792          242 ENVLFVCKLNPVTEDEDLH---TIFSRFGTVVSAEIIRDFK--TG-DSLNYAFIEFENRQACERAYSKMDNALIDDRRIH  315 (589)
Q Consensus       242 ~~~i~V~nL~~~~te~~L~---~~F~~~G~v~~~~i~~d~~--tg-~~~g~aFV~f~~~~~a~~A~~~l~g~~i~gr~i~  315 (589)
                      .+-+||-+|+..+..+.+.   +.|.+||.|..|.+..+..  .+ ...+-++|+|...++|..||...+|+.++|+.|+
T Consensus        77 knlvyvvgl~~~~ade~~l~~~eyfgqygki~ki~~~~~~S~~s~~~~~~s~yITy~~~eda~rci~~v~g~~~dg~~lk  156 (327)
T KOG2068|consen   77 KNLVYVVGLPLDLADESVLERTEYFGQYGKINKIVKNKDPSSSSSSGGTCSVYITYEEEEDADRCIDDVDGFVDDGRALK  156 (327)
T ss_pred             hhhhhhhCCCccccchhhhhCcccccccccceEEeecCCcccccCCCCCCcccccccchHhhhhHHHHhhhHHhhhhhhH
Confidence            3678999998886655543   6899999999888776542  11 1223489999999999999999999999999988


Q ss_pred             EEeccc
Q 007792          316 VDFSQS  321 (589)
Q Consensus       316 V~~a~~  321 (589)
                      ..+...
T Consensus       157 a~~gtt  162 (327)
T KOG2068|consen  157 ASLGTT  162 (327)
T ss_pred             HhhCCC
Confidence            777654

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

Probab=94.72  E-value=0.14  Score=41.14  Aligned_cols=54  Identities=22%  Similarity=0.436  Sum_probs=41.5

Q ss_pred             ceEEEecCCCCCCHHHHHHHhccCCCeEEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHhcC
Q 007792          243 NVLFVCKLNPVTEDEDLHTIFSRFGTVVSAEIIRDFKTGDSLNYAFIEFENRQACERAYSKMD  305 (589)
Q Consensus       243 ~~i~V~nL~~~~te~~L~~~F~~~G~v~~~~i~~d~~tg~~~g~aFV~f~~~~~a~~A~~~l~  305 (589)
                      ...||+ +|..+...+|.++|+.||.|. |.++.+       .-|||.....+.|..|+..+.
T Consensus        10 HVFhlt-FPkeWK~~DI~qlFspfG~I~-VsWi~d-------TSAfV~l~~r~~~~~v~~~~~   63 (87)
T PF08675_consen   10 HVFHLT-FPKEWKTSDIYQLFSPFGQIY-VSWIND-------TSAFVALHNRDQAKVVMNTLK   63 (87)
T ss_dssp             CEEEEE---TT--HHHHHHHCCCCCCEE-EEEECT-------TEEEEEECCCHHHHHHHHHHT
T ss_pred             eEEEEe-CchHhhhhhHHHHhccCCcEE-EEEEcC-------CcEEEEeecHHHHHHHHHHhc
Confidence            455565 999999999999999999864 666665       479999999999999998775

; GO: 0003723 RNA binding, 0004535 poly(A)-specific ribonuclease activity, 0046872 metal ion binding, 0006402 mRNA catabolic process, 0005634 nucleus, 0005737 cytoplasm; PDB: 3CTR_A 2ROK_A 3D45_B 1WHV_A.

>KOG0128 consensus RNA-binding protein SART3 (RRM superfamily) [RNA processing and modification]

Probab=94.67  E-value=0.0025  Score=70.88  Aligned_cols=67  Identities=25%  Similarity=0.340  Sum_probs=58.6

Q ss_pred             ceEEEecCCCCCCHHHHHHHhccCCCeEEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHhcCCcee
Q 007792          243 NVLFVCKLNPVTEDEDLHTIFSRFGTVVSAEIIRDFKTGDSLNYAFIEFENRQACERAYSKMDNALI  309 (589)
Q Consensus       243 ~~i~V~nL~~~~te~~L~~~F~~~G~v~~~~i~~d~~tg~~~g~aFV~f~~~~~a~~A~~~l~g~~i  309 (589)
                      .++||.||++.+.+.+|...|..+|.|..++|.....++..+|+|||+|...+.+.+||....+..+
T Consensus       668 ~~~fvsnl~~~~~~~dl~~~~~~~~~~e~vqi~~h~n~~~~rG~~Y~~F~~~~~~~aaV~f~d~~~~  734 (881)
T KOG0128|consen  668 IKIFVSNLSPKMSEEDLSERFSPSGTIEVVQIVIHKNEKRFRGKAYVEFLKPEHAGAAVAFRDSCFF  734 (881)
T ss_pred             HHHHHhhcchhhcCchhhhhcCccchhhhHHHHHHhhccccccceeeEeecCCchhhhhhhhhhhhh
Confidence            4899999999999999999999999998888876677899999999999999999999965444433

>COG4070 Predicted peptidyl-prolyl cis-trans isomerase (rotamase), cyclophilin family [Posttranslational modification, protein turnover, chaperones]

Probab=94.56  E-value=0.11  Score=53.30  Aligned_cols=24  Identities=21%  Similarity=0.387  Sum_probs=21.3

Q ss_pred             eEEEEecCCCChhHHHHHHHHHhc
Q 007792           11 DIVVDLFVDKCPLTTKNFLKLCKI   34 (589)
Q Consensus        11 ~i~ieL~~~~aP~~~~nF~~l~~~   34 (589)
                      -|.||||.+.||.+|..|..+...
T Consensus       377 iieIELyed~APrSv~yFRr~t~l  400 (512)
T COG4070         377 IIEIELYEDRAPRSVWYFRRSTGL  400 (512)
T ss_pred             EEEEEecCCCCchhhHHHHhhccc
Confidence            379999999999999999988753

>KOG0112 consensus Large RNA-binding protein (RRM superfamily) [General function prediction only]

Probab=94.51  E-value=0.012  Score=65.90  Aligned_cols=83  Identities=19%  Similarity=0.276  Sum_probs=68.5

Q ss_pred             CCCCCCceEEEecCCCCCCHHHHHHHhccCCCeEEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHhcCCceeCCeEEEE
Q 007792          237 DIKPPENVLFVCKLNPVTEDEDLHTIFSRFGTVVSAEIIRDFKTGDSLNYAFIEFENRQACERAYSKMDNALIDDRRIHV  316 (589)
Q Consensus       237 ~~~~~~~~i~V~nL~~~~te~~L~~~F~~~G~v~~~~i~~d~~tg~~~g~aFV~f~~~~~a~~A~~~l~g~~i~gr~i~V  316 (589)
                      +....+.+||+|||+..+++.+|+..|..+|.|..|.|-..+. +.-..||||.|.+...+..|+..|.+..|.--.+.+
T Consensus       367 DD~~atrTLf~Gnl~~kl~eseiR~af~e~gkve~VDiKtP~~-~~esa~~f~~~~n~dmtp~ak~e~s~~~I~~g~~r~  445 (975)
T KOG0112|consen  367 DDFRATRTLFLGNLDSKLTESEIRPAFDESGKVEEVDIKTPHI-KTESAYAFVSLLNTDMTPSAKFEESGPLIGNGTHRI  445 (975)
T ss_pred             cchhhhhhhhhcCcccchhhhhhhhhhhhhccccccccccCCC-CcccchhhhhhhccccCcccchhhcCCccccCcccc
Confidence            3344567999999999999999999999999999998866532 334579999999999999999999998887656666


Q ss_pred             Eecc
Q 007792          317 DFSQ  320 (589)
Q Consensus       317 ~~a~  320 (589)
                      -+.+
T Consensus       446 glG~  449 (975)
T KOG0112|consen  446 GLGQ  449 (975)
T ss_pred             cccc
Confidence            6654

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

Probab=94.10  E-value=0.26  Score=37.59  Aligned_cols=55  Identities=16%  Similarity=0.317  Sum_probs=44.6

Q ss_pred             CceEEEecCCCCCCHHHHHHHhccC---CCeEEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHhc
Q 007792          242 ENVLFVCKLNPVTEDEDLHTIFSRF---GTVVSAEIIRDFKTGDSLNYAFIEFENRQACERAYSKM  304 (589)
Q Consensus       242 ~~~i~V~nL~~~~te~~L~~~F~~~---G~v~~~~i~~d~~tg~~~g~aFV~f~~~~~a~~A~~~l  304 (589)
                      ...|+|.++.. ++.++|+.+|..|   .....|.++-|.       -|-|.|.+...|.+||.+|
T Consensus         5 peavhirGvd~-lsT~dI~~y~~~y~~~~~~~~IEWIdDt-------ScNvvf~d~~~A~~AL~~L   62 (62)
T PF10309_consen    5 PEAVHIRGVDE-LSTDDIKAYFSEYFDEEGPFRIEWIDDT-------SCNVVFKDEETAARALVAL   62 (62)
T ss_pred             eceEEEEcCCC-CCHHHHHHHHHHhcccCCCceEEEecCC-------cEEEEECCHHHHHHHHHcC
Confidence            46899999854 6778999999988   235678888873       5789999999999999765

>PF15023 DUF4523: Protein of unknown function (DUF4523)

Probab=93.61  E-value=0.26  Score=43.71  Aligned_cols=74  Identities=18%  Similarity=0.245  Sum_probs=56.6

Q ss_pred             CCCCceEEEecCCCCCC----HHHHHHHhccCCCeEEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHhcCCceeCCeEE
Q 007792          239 KPPENVLFVCKLNPVTE----DEDLHTIFSRFGTVVSAEIIRDFKTGDSLNYAFIEFENRQACERAYSKMDNALIDDRRI  314 (589)
Q Consensus       239 ~~~~~~i~V~nL~~~~t----e~~L~~~F~~~G~v~~~~i~~d~~tg~~~g~aFV~f~~~~~a~~A~~~l~g~~i~gr~i  314 (589)
                      .||-.||.|.=|..++.    -..|...++.||+|.+|.++.       +.-|.|.|.+..+|-.|+.+++. ...|..+
T Consensus        83 epPMsTIVVRWlkknm~~~edl~sV~~~Ls~fGpI~SVT~cG-------rqsavVvF~d~~SAC~Av~Af~s-~~pgtm~  154 (166)
T PF15023_consen   83 EPPMSTIVVRWLKKNMQPTEDLKSVIQRLSVFGPIQSVTLCG-------RQSAVVVFKDITSACKAVSAFQS-RAPGTMF  154 (166)
T ss_pred             CCCceeEEeehhhhcCChHHHHHHHHHHHHhcCCcceeeecC-------CceEEEEehhhHHHHHHHHhhcC-CCCCceE
Confidence            55667888876655543    234556678999999998754       24799999999999999998876 5678888


Q ss_pred             EEEecc
Q 007792          315 HVDFSQ  320 (589)
Q Consensus       315 ~V~~a~  320 (589)
                      .+.|-+
T Consensus       155 qCsWqq  160 (166)
T PF15023_consen  155 QCSWQQ  160 (166)
T ss_pred             Eeeccc
Confidence            888764

>KOG1365 consensus RNA-binding protein Fusilli, contains RRM domain [RNA processing and modification; General function prediction only]

Probab=93.41  E-value=0.32  Score=49.79  Aligned_cols=73  Identities=18%  Similarity=0.191  Sum_probs=54.1

Q ss_pred             CceEEEecCCCCCCHHHHHHHhccC----CCeEEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHhcCCceeCCeEEEE
Q 007792          242 ENVLFVCKLNPVTEDEDLHTIFSRF----GTVVSAEIIRDFKTGDSLNYAFIEFENRQACERAYSKMDNALIDDRRIHV  316 (589)
Q Consensus       242 ~~~i~V~nL~~~~te~~L~~~F~~~----G~v~~~~i~~d~~tg~~~g~aFV~f~~~~~a~~A~~~l~g~~i~gr~i~V  316 (589)
                      .-.|-+.+||+++|+.++.+||..-    |-+..|-++.. ..|+..|-|||.|..+++|+.||.. |-..|+-+-|.|
T Consensus       161 qvivRmRGLPfdat~~dVv~FF~~~cpv~~g~egvLFV~r-pdgrpTGdAFvlfa~ee~aq~aL~k-hrq~iGqRYIEl  237 (508)
T KOG1365|consen  161 QVIVRMRGLPFDATALDVVEFFGPPCPVTGGTEGVLFVTR-PDGRPTGDAFVLFACEEDAQFALRK-HRQNIGQRYIEL  237 (508)
T ss_pred             ceEEEecCCCCCcchHHHHHhcCCCCcccCCccceEEEEC-CCCCcccceEEEecCHHHHHHHHHH-HHHHHhHHHHHH
Confidence            4567778999999999999999732    23345555553 4688899999999999999999964 444455444544

>PF03467 Smg4_UPF3: Smg-4/UPF3 family; InterPro: IPR005120 Nonsense-mediated mRNA decay (NMD) is a surveillance mechanism by which eukaryotic cells detect and degrade transcripts containing premature termination codons

Probab=93.33  E-value=0.25  Score=46.54  Aligned_cols=81  Identities=16%  Similarity=0.183  Sum_probs=51.6

Q ss_pred             CCceEEEecCCCCCCHHHHHHHhcc-CCCe---EEEEEeecCCC--CCcccEEEEEEcCHHHHHHHHHhcCCceeCC---
Q 007792          241 PENVLFVCKLNPVTEDEDLHTIFSR-FGTV---VSAEIIRDFKT--GDSLNYAFIEFENRQACERAYSKMDNALIDD---  311 (589)
Q Consensus       241 ~~~~i~V~nL~~~~te~~L~~~F~~-~G~v---~~~~i~~d~~t--g~~~g~aFV~f~~~~~a~~A~~~l~g~~i~g---  311 (589)
                      ....|.|.+||+.+|++++.+.+.. ++.-   ..+.......+  .....-|||.|.+.+++...+..++|..|.+   
T Consensus         6 ~~~KvVIR~LPP~LteeeF~~~i~~~l~~~~~w~y~~g~~~~~~~~~~~~SRaYi~F~~~~~~~~F~~~~~g~~F~D~kg   85 (176)
T PF03467_consen    6 EGTKVVIRRLPPNLTEEEFWEQISPWLPDEWDWYYFQGKYGKKSFKPPTYSRAYINFKNPEDLLEFRDRFDGHVFVDSKG   85 (176)
T ss_dssp             ---EEEEEEE-TTS-HHHHCCCCSS--SSE---EEEEEEES-SSSTTS--EEEEEEESSCHHHHHHHHHCTTEEEE-TTS
T ss_pred             cCceEEEeCCCCCCCHHHHHHHhhhhcccccceEEEecCCCCccCCCCcceEEEEEeCCHHHHHHHHHhcCCcEEECCCC
Confidence            3568999999999999998887776 6655   33332222221  1124679999999999999999999977643   


Q ss_pred             --eEEEEEeccc
Q 007792          312 --RRIHVDFSQS  321 (589)
Q Consensus       312 --r~i~V~~a~~  321 (589)
                        ....|++|--
T Consensus        86 ~~~~~~VE~Apy   97 (176)
T PF03467_consen   86 NEYPAVVEFAPY   97 (176)
T ss_dssp             -EEEEEEEE-SS
T ss_pred             CCcceeEEEcch
Confidence              4456777654

Three 'up-frameshift' proteins, UPF1, UPF2 and UPF3, are essential for this process in organisms ranging from yeast, human to plants []. Exon junction complexes (EJCs) are deposited ~24 nucleotides upstream of exon-exon junctions after splicing. Translation causes displacement of the EJCs, however, premature translation termination upstream of one or more EJCs triggers the recruitment of UPF1, UPF2 and UPF3 and activates the NMD pathway [, ]. This family contains UPF3. The crystal structure of the complex between human UPF2 and UPF3b, which are, respectively, a MIF4G (middle portion of eIF4G) domain and an RNP domain (ribonucleoprotein-type RNA-binding domain) has been determined to 1.95A. The protein-protein interface is mediated by highly conserved charged residues in UPF2 and UPF3b and involves the beta-sheet surface of the UPF3b ribonucleoprotein (RNP) domain, which is generally used by these domains to bind nucleic acids. In UPF3b the RNP domain does not bind RNA, whereas the UPF2 construct and the complex do. It is clear that some RNP domains have evolved for specific protein-protein interactions rather than as nucleic acid binding modules [].; PDB: 1UW4_A 2L08_A.

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

Probab=93.14  E-value=0.15  Score=54.78  Aligned_cols=86  Identities=19%  Similarity=0.232  Sum_probs=67.9

Q ss_pred             CCceEEEecCCCCCCHHHHHHHhc-cCCCeEEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHhcCCceeC----CeEEE
Q 007792          241 PENVLFVCKLNPVTEDEDLHTIFS-RFGTVVSAEIIRDFKTGDSLNYAFIEFENRQACERAYSKMDNALID----DRRIH  315 (589)
Q Consensus       241 ~~~~i~V~nL~~~~te~~L~~~F~-~~G~v~~~~i~~d~~tg~~~g~aFV~f~~~~~a~~A~~~l~g~~i~----gr~i~  315 (589)
                      +.+++-|.|++-..|-..|...-. ..|.--.+.++.|-.+....|||||.|.+.+++..+.+++||+.+.    .+.+.
T Consensus       387 ~rtt~~iknipNK~T~~ml~~~d~~~~gtYDFlYLPiDF~nkcNvGYAFINm~sp~ai~~F~kAFnGk~W~~FnS~Kia~  466 (549)
T KOG4660|consen  387 PRTTLMIKNIPNKYTSKMLLAADEKNKGTYDFLYLPIDFKNKCNVGYAFINMTSPEAIIRFYKAFNGKKWEKFNSEKIAS  466 (549)
T ss_pred             chhhhHhhccCchhhHHhhhhhhccccCccceEEeccccccccccceeEEeecCHHHHHHHHHHHcCCchhhhcceeeee
Confidence            457888889988877777665543 3566667888888778888999999999999999999999997653    57778


Q ss_pred             EEecccccccc
Q 007792          316 VDFSQSVSKLW  326 (589)
Q Consensus       316 V~~a~~~~~~~  326 (589)
                      |.||.-..+.|
T Consensus       467 itYArIQGk~~  477 (549)
T KOG4660|consen  467 ITYARIQGKEA  477 (549)
T ss_pred             eehhhhhchHH
Confidence            88887655543

>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=93.05  E-value=0.31  Score=38.76  Aligned_cols=66  Identities=15%  Similarity=0.359  Sum_probs=39.3

Q ss_pred             eEEEecC--CCCCCHHHHHHHhccCC-----CeEEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHhcCCceeCCeEEEE
Q 007792          244 VLFVCKL--NPVTEDEDLHTIFSRFG-----TVVSAEIIRDFKTGDSLNYAFIEFENRQACERAYSKMDNALIDDRRIHV  316 (589)
Q Consensus       244 ~i~V~nL--~~~~te~~L~~~F~~~G-----~v~~~~i~~d~~tg~~~g~aFV~f~~~~~a~~A~~~l~g~~i~gr~i~V  316 (589)
                      ++|| |+  -..++..+|..+|...+     .|-.+.|..        .|+||+... +.|..++..|++..+.|++|.|
T Consensus         2 rl~i-n~Gr~dg~~~~~iv~~i~~~~gi~~~~IG~I~I~~--------~~S~vev~~-~~a~~v~~~l~~~~~~gk~v~v   71 (74)
T PF03880_consen    2 RLFI-NVGRKDGLTPRDIVGAICNEAGIPGRDIGRIDIFD--------NFSFVEVPE-EVAEKVLEALNGKKIKGKKVRV   71 (74)
T ss_dssp             EEEE-S-SGGGT--HHHHHHHHHTCTTB-GGGEEEEEE-S--------S-EEEEE-T-T-HHHHHHHHTT--SSS----E
T ss_pred             EEEE-EcccccCCCHHHHHHHHHhccCCCHHhEEEEEEee--------eEEEEEECH-HHHHHHHHHhcCCCCCCeeEEE
Confidence            3455 33  34578889998887664     345677754        499999974 5889999999999999999999


Q ss_pred             Eec
Q 007792          317 DFS  319 (589)
Q Consensus       317 ~~a  319 (589)
                      +.|
T Consensus        72 e~A   74 (74)
T PF03880_consen   72 ERA   74 (74)
T ss_dssp             EE-
T ss_pred             EEC
Confidence            875

; PDB: 2G0C_A 3MOJ_B.

>KOG4307 consensus RNA binding protein RBM12/SWAN [General function prediction only]

Probab=93.04  E-value=0.068  Score=58.46  Aligned_cols=79  Identities=24%  Similarity=0.116  Sum_probs=65.1

Q ss_pred             CCceEEEecCCCCCCHHHHHHHhccCCCeEE-EEEeecCCCCCcccEEEEEEcCHHHHHHHHHhcCCceeCCeEEEEEec
Q 007792          241 PENVLFVCKLNPVTEDEDLHTIFSRFGTVVS-AEIIRDFKTGDSLNYAFIEFENRQACERAYSKMDNALIDDRRIHVDFS  319 (589)
Q Consensus       241 ~~~~i~V~nL~~~~te~~L~~~F~~~G~v~~-~~i~~d~~tg~~~g~aFV~f~~~~~a~~A~~~l~g~~i~gr~i~V~~a  319 (589)
                      ....|||..||..+++..+..+|...-.|++ |.|... -+++..+-|||+|...+++..|+..-+.+.++-+.|.|.-.
T Consensus       433 ag~~lyv~~lP~~t~~~~~v~~f~~~~~Ved~I~lt~~-P~~~~~~~afv~F~~~~a~~~a~~~~~k~y~G~r~irv~si  511 (944)
T KOG4307|consen  433 AGGALYVFQLPVMTPIVPPVNKFMGAAAVEDFIELTRL-PTDLLRPAAFVAFIHPTAPLTASSVKTKFYPGHRIIRVDSI  511 (944)
T ss_pred             ccceEEeccCCccccccchhhhhhhhhhhhheeEeccC-CcccccchhhheeccccccchhhhcccccccCceEEEeech
Confidence            3569999999999999999999998877776 655544 46778899999999999999998766667777888888754


Q ss_pred             c
Q 007792          320 Q  320 (589)
Q Consensus       320 ~  320 (589)
                      .
T Consensus       512 ~  512 (944)
T KOG4307|consen  512 A  512 (944)
T ss_pred             h
Confidence            3

>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=92.57  E-value=0.35  Score=45.73  Aligned_cols=63  Identities=21%  Similarity=0.373  Sum_probs=46.8

Q ss_pred             CHHHHHHHhccCCCeEEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHhcC--CceeCCeEEEEEeccccc
Q 007792          255 EDEDLHTIFSRFGTVVSAEIIRDFKTGDSLNYAFIEFENRQACERAYSKMD--NALIDDRRIHVDFSQSVS  323 (589)
Q Consensus       255 te~~L~~~F~~~G~v~~~~i~~d~~tg~~~g~aFV~f~~~~~a~~A~~~l~--g~~i~gr~i~V~~a~~~~  323 (589)
                      ....|+.+|..|+.+..+.+..      +-+-..|.|.+.+.|..|...|+  +..|.|..|+|.|+....
T Consensus         8 ~~~~l~~l~~~~~~~~~~~~L~------sFrRi~v~f~~~~~A~~~r~~l~~~~~~~~g~~l~~yf~~~~~   72 (184)
T PF04847_consen    8 NLAELEELFSTYDPPVQFSPLK------SFRRIRVVFESPESAQRARQLLHWDGTSFNGKRLRVYFGQPTP   72 (184)
T ss_dssp             -HHHHHHHHHTT-SS-EEEEET------TTTEEEEE-SSTTHHHHHHHTST--TSEETTEE-EEE----SS
T ss_pred             hHHHHHHHHHhcCCceEEEEcC------CCCEEEEEeCCHHHHHHHHHHhcccccccCCCceEEEEccccc
Confidence            3478999999999998877665      34678999999999999999999  999999999999996543

Calcipressin 1 is a phosphoprotein that increases its capacity to inhibit calcineurin when phosphorylated at the FLISPP motif, and this phosphorylation also controls the half-life of calcipressin 1 by accelerating its degradation []. Calcineurin is a calcium-responsive enzyme that dephosphorylates the nuclear factor of activated T cells (NFAT). In so doing it promotes its nuclear translocation and uniquely links calcium signalling to transcriptional regulation []. Calcipressins are a family of proteins derived from three genes. Calcipressin 1 is also known as modulatory calcineurin-interacting protein 1 (MCIP1), Adapt78 and Down syndrome critical region 1 (DSCR1). Calcipressin 2 is variously known as MCIP2, ZAKI-4 and DSCR1-like 1. Calcipressin 3 is also called MCIP3 and DSCR1-like 2 []. DSCR1 (Adapt78) is associated with successful adaptation to oxidative stress and calcium stress as well as with diseases like Alzheimer's and Down syndrome. The DSCR1 (Adapt78) isoform 1 protein, calcipressin 1, inhibits calcineurin and protects against acute calcium-mediated stress damage, including transient oxidative stress []. Calcipressin 1 is encoded by DSCR1, a gene on human chromosome 21. Calcipressin 1 isoform 1 has an N-terminal coding region, which generates a new polypeptide of 252 amino acids. Endogenous calcipressin 1 exists as a complex together with the calcineurin A and B heterodimer []. ; GO: 0019722 calcium-mediated signaling; PDB: 1WEY_A.

>KOG2591 consensus c-Mpl binding protein, contains La domain [Signal transduction mechanisms]

Probab=92.53  E-value=0.23  Score=53.20  Aligned_cols=71  Identities=17%  Similarity=0.329  Sum_probs=58.7

Q ss_pred             CCceEEEecCCCCCCHHHHHHHhc--cCCCeEEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHhcCC--ceeCCeEEEE
Q 007792          241 PENVLFVCKLNPVTEDEDLHTIFS--RFGTVVSAEIIRDFKTGDSLNYAFIEFENRQACERAYSKMDN--ALIDDRRIHV  316 (589)
Q Consensus       241 ~~~~i~V~nL~~~~te~~L~~~F~--~~G~v~~~~i~~d~~tg~~~g~aFV~f~~~~~a~~A~~~l~g--~~i~gr~i~V  316 (589)
                      ..++|.|.-||..+-.++|+.+|.  .|-+++.|.+..+       .-=||+|++..+|+.|++.|..  ++|-|++|..
T Consensus       174 kRcIvilREIpettp~e~Vk~lf~~encPk~iscefa~N-------~nWyITfesd~DAQqAykylreevk~fqgKpImA  246 (684)
T KOG2591|consen  174 KRCIVILREIPETTPIEVVKALFKGENCPKVISCEFAHN-------DNWYITFESDTDAQQAYKYLREEVKTFQGKPIMA  246 (684)
T ss_pred             ceeEEEEeecCCCChHHHHHHHhccCCCCCceeeeeeec-------CceEEEeecchhHHHHHHHHHHHHHhhcCcchhh
Confidence            457888999999999999999997  5888999998775       2468999999999999988764  5677877765


Q ss_pred             Ee
Q 007792          317 DF  318 (589)
Q Consensus       317 ~~  318 (589)
                      .+
T Consensus       247 RI  248 (684)
T KOG2591|consen  247 RI  248 (684)
T ss_pred             hh
Confidence            44

>KOG2888 consensus Putative RNA binding protein [General function prediction only]

Probab=92.21  E-value=0.093  Score=52.48  Aligned_cols=14  Identities=14%  Similarity=0.344  Sum_probs=8.8

Q ss_pred             CCCHHHHHHHhccC
Q 007792          253 VTEDEDLHTIFSRF  266 (589)
Q Consensus       253 ~~te~~L~~~F~~~  266 (589)
                      .....+|...|+.|
T Consensus       168 tqpp~dLw~WyEpy  181 (453)
T KOG2888|consen  168 TQPPADLWDWYEPY  181 (453)
T ss_pred             cCChhHHHHHhhhh
Confidence            34456677777766

>PF07576 BRAP2: BRCA1-associated protein 2; InterPro: IPR011422 These proteins include BRCA1-associated protein 2 (BRAP2), which binds nuclear localisation signals (NLSs) in vitro and in yeast two-hybrid screening []

Probab=92.14  E-value=1.5  Score=37.84  Aligned_cols=76  Identities=17%  Similarity=0.249  Sum_probs=53.7

Q ss_pred             CceEEEecCCCCCCHHHHHHHhccCC-CeEEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHhcCCceeCC---eEEEEE
Q 007792          242 ENVLFVCKLNPVTEDEDLHTIFSRFG-TVVSAEIIRDFKTGDSLNYAFIEFENRQACERAYSKMDNALIDD---RRIHVD  317 (589)
Q Consensus       242 ~~~i~V~nL~~~~te~~L~~~F~~~G-~v~~~~i~~d~~tg~~~g~aFV~f~~~~~a~~A~~~l~g~~i~g---r~i~V~  317 (589)
                      ...+.+...|+.++-++|..+.+.+- .|..++|+.+..  .++-.+++.|.++..|......+||+.+..   ..++|-
T Consensus        13 ~~~~~l~vp~~~~~~d~l~~f~~~~~~~i~~~riird~~--pnrymVLikF~~~~~Ad~Fy~~fNGk~FnslEpE~Chvv   90 (110)
T PF07576_consen   13 STLCCLAVPPYMTPSDFLLFFGAPFREDIEHIRIIRDGT--PNRYMVLIKFRDQESADEFYEEFNGKPFNSLEPETCHVV   90 (110)
T ss_pred             ceEEEEEeCcccccHHHHHHhhhcccccEEEEEEeeCCC--CceEEEEEEECCHHHHHHHHHHhCCCccCCCCCceeEEE
Confidence            34455555666666677766666554 466888988633  256789999999999999999999987753   445544


Q ss_pred             ec
Q 007792          318 FS  319 (589)
Q Consensus       318 ~a  319 (589)
                      |-
T Consensus        91 fV   92 (110)
T PF07576_consen   91 FV   92 (110)
T ss_pred             EE
Confidence            43

These proteins share a region of sequence similarity at their N terminus. They also have IPR001607 from INTERPRO at the C terminus.

>PF04126 Cyclophil_like: Cyclophilin-like; InterPro: IPR007256 Proteins of this family have no known function

Probab=91.81  E-value=0.85  Score=40.02  Aligned_cols=101  Identities=15%  Similarity=0.158  Sum_probs=58.1

Q ss_pred             CEEEEEecceeEEEEecCCCChhHHHHHHHHHh----cCccCCceEEEeecCcccccCCCCCCCCCCCCccccccccccc
Q 007792            1 MSVLIVTSLGDIVVDLFVDKCPLTTKNFLKLCK----IKYYNGCLFHTVQKDFTAQTGDPTGTGTGGDSVYKFLYGEQAR   76 (589)
Q Consensus         1 ~~v~~~T~~G~i~ieL~~~~aP~~~~nF~~l~~----~~~Y~g~~f~rv~~~~~iq~Gd~~~~~~~~~~~~~~~~~~~~~   76 (589)
                      |.|.|......|.++|+..   .|+..|++++=    -..|.+ -+|--.|-                            
T Consensus         1 mkI~i~i~~~~~~a~L~d~---~ta~~~~~~LPlt~~~~~~g~-E~y~~~p~----------------------------   48 (120)
T PF04126_consen    1 MKIKITIGGQEIEAELNDS---PTARAFAAQLPLTVTMNDWGN-EKYFSLPL----------------------------   48 (120)
T ss_dssp             EEEEEEETTEEEEEEEETT---HHHHHHHHC-SEEEEEEECTT-EEEEE-S-----------------------------
T ss_pred             CeEEEEECCEEEEEEECCC---HHHHHHHHhCCeEEEHHHCCc-eEEEeCCC----------------------------
Confidence            7899999999999999976   88999988772    122422 22211121                            


Q ss_pred             ccC-CccccCCCCCCCceEEEeccCCCCCcceEEEEeCCCCC-------CCCCCcceEEEEecCHHHHHHHhh
Q 007792           77 FFG-DEIRVDLKHAKTGTVAMASAGENLNASQFYMTLRDNLD-------YLDEKHTIFGEVAEGLETLSRINE  141 (589)
Q Consensus        77 ~~~-~e~~~~l~~~~~G~vs~a~~g~~~~~sqFfI~l~~~~~-------~ld~~~~vFG~Vv~G~~vl~~i~~  141 (589)
                      .++ ++ ... .-...|-|++...+.+     |.|-+.+ .|       .+-...++||+|+.|++.|.+|..
T Consensus        49 ~l~~~~-~~~-~~~~~GDi~Yw~pg~~-----l~ifyg~-~p~S~~~~~~~~~~v~~lG~i~~~~~~l~~~~~  113 (120)
T PF04126_consen   49 KLPTEE-NPR-SSVEAGDIAYWPPGGA-----LAIFYGD-TPISEGGEIRPASPVNVLGRIVSDLENLKEVKG  113 (120)
T ss_dssp             ----SS-SEE-SSB-TTEEEEECCCTE-----EEEESS---TT--TTSB--SSSEEEEEEEEC-GGGGGG--T
T ss_pred             CCCccc-Ccc-ccccCceEEEeCCCCE-----EEEEecC-cccccccccccCCcceEEEEECCCHHHHhhCCC
Confidence            011 11 011 1125688888765433     6666655 22       455678899999999998888853

; PDB: 2KA0_A 1ZX8_C 2NNZ_A.

>KOG4574 consensus RNA-binding protein (contains RRM and Pumilio-like repeats) [General function prediction only]

Probab=90.73  E-value=0.15  Score=57.17  Aligned_cols=78  Identities=21%  Similarity=0.297  Sum_probs=66.4

Q ss_pred             CCCceEEEecCCCCCCHHHHHHHhccCCCeEEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHhcCCcee--CCeEEEEE
Q 007792          240 PPENVLFVCKLNPVTEDEDLHTIFSRFGTVVSAEIIRDFKTGDSLNYAFIEFENRQACERAYSKMDNALI--DDRRIHVD  317 (589)
Q Consensus       240 ~~~~~i~V~nL~~~~te~~L~~~F~~~G~v~~~~i~~d~~tg~~~g~aFV~f~~~~~a~~A~~~l~g~~i--~gr~i~V~  317 (589)
                      |-..+.++-|++..++-..|..+|..||.|..++...+-      ..|.|+|.+.+.|..|+.+|+|+++  -|-+.+|.
T Consensus       296 plqp~~~~~nn~v~~tSssL~~l~s~yg~v~s~wtlr~~------N~alvs~~s~~sai~a~dAl~gkevs~~g~Ps~V~  369 (1007)
T KOG4574|consen  296 PLQPKQSLENNAVNLTSSSLATLCSDYGSVASAWTLRDL------NMALVSFSSVESAILALDALQGKEVSVTGAPSRVS  369 (1007)
T ss_pred             cCcchhhhhcccccchHHHHHHHHHhhcchhhheecccc------cchhhhhHHHHHHHHhhhhhcCCcccccCCceeEE
Confidence            334567777888888999999999999999999887753      4899999999999999999999865  58889999


Q ss_pred             eccccc
Q 007792          318 FSQSVS  323 (589)
Q Consensus       318 ~a~~~~  323 (589)
                      +|+...
T Consensus       370 ~ak~~~  375 (1007)
T KOG4574|consen  370 FAKTLP  375 (1007)
T ss_pred             eccccc
Confidence            998643

>KOG4285 consensus Mitotic phosphoprotein [Cell cycle control, cell division, chromosome partitioning]

Probab=90.66  E-value=0.72  Score=45.96  Aligned_cols=70  Identities=23%  Similarity=0.296  Sum_probs=51.7

Q ss_pred             ceEEEecCCCCCCHHHHHHHhccCCCeEEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHhcCCceeCCeE-EEEEecc
Q 007792          243 NVLFVCKLNPVTEDEDLHTIFSRFGTVVSAEIIRDFKTGDSLNYAFIEFENRQACERAYSKMDNALIDDRR-IHVDFSQ  320 (589)
Q Consensus       243 ~~i~V~nL~~~~te~~L~~~F~~~G~v~~~~i~~d~~tg~~~g~aFV~f~~~~~a~~A~~~l~g~~i~gr~-i~V~~a~  320 (589)
                      .=|-|-++|+..+ ..|..+|.+||.|+......      .-.+-+|.|.+..+|++|| ..||..|+|-. |-|.-+.
T Consensus       198 ~WVTVfGFppg~~-s~vL~~F~~cG~Vvkhv~~~------ngNwMhirYssr~~A~KAL-skng~ii~g~vmiGVkpCt  268 (350)
T KOG4285|consen  198 TWVTVFGFPPGQV-SIVLNLFSRCGEVVKHVTPS------NGNWMHIRYSSRTHAQKAL-SKNGTIIDGDVMIGVKPCT  268 (350)
T ss_pred             ceEEEeccCccch-hHHHHHHHhhCeeeeeecCC------CCceEEEEecchhHHHHhh-hhcCeeeccceEEeeeecC
Confidence            4555667877655 56778999999997654431      2258999999999999999 46999998854 4455433

>KOG4210 consensus Nuclear localization sequence binding protein [Transcription]

Probab=89.86  E-value=0.2  Score=50.86  Aligned_cols=81  Identities=16%  Similarity=0.140  Sum_probs=67.9

Q ss_pred             CCceEEEecCCCCCCHHHHHHHhccCCCeEEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHhcCCceeCCeEEEEEecc
Q 007792          241 PENVLFVCKLNPVTEDEDLHTIFSRFGTVVSAEIIRDFKTGDSLNYAFIEFENRQACERAYSKMDNALIDDRRIHVDFSQ  320 (589)
Q Consensus       241 ~~~~i~V~nL~~~~te~~L~~~F~~~G~v~~~~i~~d~~tg~~~g~aFV~f~~~~~a~~A~~~l~g~~i~gr~i~V~~a~  320 (589)
                      ...++|++++.+.+.+.++..+|..+|.+..+.+........++|+++|.|...+.+..||.......+.+..+...+.+
T Consensus        87 ~~~~~f~g~~s~~~e~~~~~~~~~~~g~~~~~~~S~~~~~~~sk~~~s~~f~~ks~~~~~l~~s~~~~~~~~~~~~dl~~  166 (285)
T KOG4210|consen   87 SSSTFFVGELSENIEESEDDNFSSEAGLRVDARSSSLEDSLSSKGGLSVHFAGKSQFFAALEESGSKVLDGNKGEKDLNT  166 (285)
T ss_pred             ccccccccccccchhhccccccchhhcCcccchhhhhccccccccceeeccccHHHHHHHHHhhhccccccccccCcccc
Confidence            46799999999999999899999999988888777766778899999999999999999996544457777777776665


Q ss_pred             c
Q 007792          321 S  321 (589)
Q Consensus       321 ~  321 (589)
                      .
T Consensus       167 ~  167 (285)
T KOG4210|consen  167 R  167 (285)
T ss_pred             c
Confidence            4

>KOG2135 consensus Proteins containing the RNA recognition motif [General function prediction only]

Probab=89.52  E-value=0.22  Score=52.37  Aligned_cols=71  Identities=21%  Similarity=0.276  Sum_probs=56.8

Q ss_pred             eEEEecCCCCC-CHHHHHHHhccCCCeEEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHhcCCceeCCeEEEEEeccc
Q 007792          244 VLFVCKLNPVT-EDEDLHTIFSRFGTVVSAEIIRDFKTGDSLNYAFIEFENRQACERAYSKMDNALIDDRRIHVDFSQS  321 (589)
Q Consensus       244 ~i~V~nL~~~~-te~~L~~~F~~~G~v~~~~i~~d~~tg~~~g~aFV~f~~~~~a~~A~~~l~g~~i~gr~i~V~~a~~  321 (589)
                      .|-+.-.++.. |-.+|...|.+||+|..|.|-..      .-.|.|+|.+..+|-.|. ..++..|+++.|+|-|-++
T Consensus       374 ~l~lek~~~glnt~a~ln~hfA~fG~i~n~qv~~~------~~~a~vTF~t~aeag~a~-~s~~avlnnr~iKl~whnp  445 (526)
T KOG2135|consen  374 PLALEKSPFGLNTIADLNPHFAQFGEIENIQVDYS------SLHAVVTFKTRAEAGEAY-ASHGAVLNNRFIKLFWHNP  445 (526)
T ss_pred             hhhhhccCCCCchHhhhhhhhhhcCccccccccCc------hhhheeeeeccccccchh-ccccceecCceeEEEEecC
Confidence            33344444443 45789999999999999988553      247999999999997787 5799999999999999887

>KOG0804 consensus Cytoplasmic Zn-finger protein BRAP2 (BRCA1 associated protein) [General function prediction only]

Probab=87.42  E-value=1.8  Score=45.64  Aligned_cols=69  Identities=14%  Similarity=0.311  Sum_probs=58.2

Q ss_pred             CCceEEEecCCCCCCHHHHHHHhccC-CCeEEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHhcCCceeCC
Q 007792          241 PENVLFVCKLNPVTEDEDLHTIFSRF-GTVVSAEIIRDFKTGDSLNYAFIEFENRQACERAYSKMDNALIDD  311 (589)
Q Consensus       241 ~~~~i~V~nL~~~~te~~L~~~F~~~-G~v~~~~i~~d~~tg~~~g~aFV~f~~~~~a~~A~~~l~g~~i~g  311 (589)
                      +.+.|+|=.+|..+|--+|..|+..| -.|..++|+++...  .+-.++|.|.+..+|...+..+||..|..
T Consensus        73 ~~~mLcilaVP~~mt~~Dll~F~~~~~~~I~~irivRd~~p--nrymvLIkFr~q~da~~Fy~efNGk~Fn~  142 (493)
T KOG0804|consen   73 SSTMLCILAVPAYMTSHDLLRFCASFIKQISDIRIVRDGMP--NRYMVLIKFRDQADADTFYEEFNGKQFNS  142 (493)
T ss_pred             CCcEEEEEeccccccHHHHHHHHHHHhhhhheeEEeecCCC--ceEEEEEEeccchhHHHHHHHcCCCcCCC
Confidence            37899999999999999999998866 46779999996432  34468899999999999999999998764

>KOG4368 consensus Predicted RNA binding protein, contains SWAP, RPR and G-patch domains [General function prediction only]

Probab=86.74  E-value=0.82  Score=49.36  Aligned_cols=10  Identities=10%  Similarity=0.640  Sum_probs=4.7

Q ss_pred             CccCCceEEE
Q 007792           35 KYYNGCLFHT   44 (589)
Q Consensus        35 ~~Y~g~~f~r   44 (589)
                      +||+.+.|..
T Consensus       220 ~yf~ds~~~q  229 (757)
T KOG4368|consen  220 GYFDDSIIQQ  229 (757)
T ss_pred             CchhHHHHHH
Confidence            4455554443

>KOG2318 consensus Uncharacterized conserved protein [Function unknown]

Probab=82.80  E-value=5.2  Score=43.59  Aligned_cols=80  Identities=20%  Similarity=0.383  Sum_probs=61.1

Q ss_pred             CCCCceEEEecCCCC-CCHHHHHHHhccC----CCeEEEEEeecCC----------CCC---------------------
Q 007792          239 KPPENVLFVCKLNPV-TEDEDLHTIFSRF----GTVVSAEIIRDFK----------TGD---------------------  282 (589)
Q Consensus       239 ~~~~~~i~V~nL~~~-~te~~L~~~F~~~----G~v~~~~i~~d~~----------tg~---------------------  282 (589)
                      ..+.+.|-|.||.|. +...+|..+|..|    |.|.+|.|+....          .|.                     
T Consensus       171 ~~~T~RLAVvNMDWd~v~AkDL~v~~nSFlP~gGsilSV~IYpSeFGkeRM~eEeV~GP~~el~~~~e~~~~s~sD~ee~  250 (650)
T KOG2318|consen  171 GEETKRLAVVNMDWDRVKAKDLFVLFNSFLPKGGSILSVKIYPSEFGKERMKEEEVHGPPKELFKPVEEYKESESDDEEE  250 (650)
T ss_pred             ccccceeeEeccccccccHHHHHHHHHhhcCCCCceeEEEechhhhhHHHhhhhcccCChhhhccccccCcccccchhhh
Confidence            446789999999997 7889999999866    6899998765311          122                     


Q ss_pred             ---------------c-ccEEEEEEcCHHHHHHHHHhcCCceeCC--eEEEEEe
Q 007792          283 ---------------S-LNYAFIEFENRQACERAYSKMDNALIDD--RRIHVDF  318 (589)
Q Consensus       283 ---------------~-~g~aFV~f~~~~~a~~A~~~l~g~~i~g--r~i~V~~  318 (589)
                                     . .-||.|+|.+...|...+..++|++|..  ..|-+.|
T Consensus       251 ~~~~~~kLR~Yq~~rLkYYyAVvecDsi~tA~~vYe~CDG~EfEsS~~~~DLRF  304 (650)
T KOG2318|consen  251 EDVDREKLRQYQLNRLKYYYAVVECDSIETAKAVYEECDGIEFESSANKLDLRF  304 (650)
T ss_pred             hhHHHHHHHHHHhhhheeEEEEEEecCchHHHHHHHhcCcceeccccceeeeee
Confidence                           0 1289999999999999999999999875  4444444

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

Probab=80.33  E-value=1.4  Score=48.76  Aligned_cols=16  Identities=25%  Similarity=0.152  Sum_probs=10.1

Q ss_pred             CCChhHHHHHHHHHhc
Q 007792           19 DKCPLTTKNFLKLCKI   34 (589)
Q Consensus        19 ~~aP~~~~nF~~l~~~   34 (589)
                      +..|...++||-..-+
T Consensus       181 Nlnpsv~E~~ll~tfG  196 (877)
T KOG0151|consen  181 NLNPSVDENFLLRTFG  196 (877)
T ss_pred             cCCccccHHHHHHHhc
Confidence            5566677777765544

---

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

ID	Length	Definition	E-value
Query	589
1xyh_A	161	Crystal Structure Of Recombinant Human Cyclophilin		5e-24
2oju_A	167	X-Ray Structure Of Complex Of Human Cyclophilin J W		7e-24
2k7n_A	203	Solution Structure Of The Ppil1 Bound To A Fragment		9e-23
1zkc_A	197	Crystal Structure Of The Cyclophiln_ring Domain Of		2e-22
2x7k_A	166	The Crystal Structure Of Ppil1 In Complex With Cycl		3e-22
1xwn_A	174	Solution Structure Of Cyclophilin Like 1(Ppil1) And		3e-22
2a2n_A	176	Crystal Structure Of The Peptidylprolyl Isomerase D		4e-20
2hq6_A	185	Structure Of The Cyclophilin_cecyp16-like Domain Of		1e-19
2poe_A	185	Crystal Structure Of Cryptosporidium Parvum Cycloph		2e-18
2b71_A	196	Plasmodium Yoelii Cyclophilin-Like Protein Length =		2e-17
2fu0_A	160	Plasmodium Falciparum Cyclophilin Pfe0505w Putative		2e-17
3bkp_A	232	Crystal Structure Of The Toxoplasma Gondii Cyclophi		4e-15
2haq_A	172	Crystal Structure Of Cyclophilin A From Leishmania		5e-15
3bt8_A	172	Crystal Structure Of Mutant Cyclophilin (R147a) Fro		7e-15
3k2c_A	193	Crystal Structure Of Peptidyl-Prolyl Cis-Trans Isom		1e-14
2wfj_A	179	Atomic Resolution Crystal Structure Of The Ppiase D		1e-14
2gw2_A	198	Crystal Structure Of The Peptidyl-Prolyl Isomerase		3e-14
2he9_A	192	Structure Of The Peptidylprolyl Isomerase Domain Of		5e-14
2bit_X	165	Crystal Structure Of Human Cyclophilin D At 1.7 A R		1e-13
3r49_A	166	Human Cyclophilin D Complexed With Quinolin-8-Amine		1e-13
3qyu_A	164	Crystal Structure Of Human Cyclophilin D At 1.54 A		1e-13
2z6w_A	165	Crystal Structure Of Human Cyclophilin D In Complex		1e-13
2rmc_A	182	Crystal Structure Of Murine Cyclophilin C Complexed		3e-13
3bo7_A	201	Crystal Structure Of Toxoplasma Gondii Peptidyl-Pro		3e-13
2wfi_A	179	Atomic Resolution Crystal Structure Of The Ppiase D		4e-13
2esl_A	190	Human Cyclophilin C In Complex With Cyclosporin A L		7e-13
4fru_A	185	Crystal Structure Of Horse Wild-Type Cyclophilin B		7e-13
1ihg_A	370	Bovine Cyclophilin 40, Monoclinic Form Length = 370		9e-13
4frv_A	185	Crystal Structure Of Mutated Cyclophilin B That Cau		9e-13
1cyn_A	178	Cyclophilin B Complexed With [d-(Cholinylester)ser8		9e-13
3ich_A	188	Crystal Structure Of Cyclophilin B At 1.2 A Resolut		2e-12
4i9y_A	167	Structure Of The C-terminal Domain Of Nup358 Length		4e-12
3pmp_A	164	Crystal Structure Of Cyclophilin A From Moniliophth		4e-12
3o7t_A	164	Crystal Structure Of Cyclophilin A From Moniliophth		6e-12
2cfe_A	162	The 1.5 A Crystal Structure Of The Malassezia Sympo		8e-12
1h0p_A	182	Cyclophilin_5 From C. Elegans Length = 182		8e-12
1c5f_A	177	Crystal Structure Of The Cyclophilin-Like Domain Fr		1e-11
1xo7_A	166	Crystal Structure Of Cyclophilin From Trypanosoma C		2e-11
1qoi_A	177	U4U6 SNRNP-Specific Cyclophilin Snucyp-20 Length =		2e-11
2r99_A	173	Crystal Structure Of Cyclophilin Abh-Like Domain Of		2e-11
1zmf_A	165	C Domain Of Human Cyclophilin-33(Hcyp33) Length = 1		2e-11
3k0r_A	165	Cryogenic Structure Of Cypa Mutant Arg55lys Length		2e-11
2xgy_B	173	Complex Of Rabbit Endogenous Lentivirus (Relik)caps		2e-11
2wlw_A	165	Structure Of The N-Terminal Capsid Domain Of Hiv-2		3e-11
1m9e_A	164	X-Ray Crystal Structure Of Cyclophilin AHIV-1 Ca N-		3e-11
2rma_A	165	Crystal Structures Of Cyclophilin A Complexed With		3e-11
3rdd_A	184	Human Cyclophilin A Complexed With An Inhibitor Len		4e-11
1bck_A	165	Human Cyclophilin A Complexed With 2-Thr Cyclospori		4e-11
5cyh_A	164	Cyclophilin A Complexed With Dipeptide Gly-Pro Leng		4e-11
4dgd_A	165	Trimcyp Cyclophilin Domain From Macaca Mulatta: H70		4e-11
3k0o_A	165	Room Temperature Structure Of Cypa Mutant Ser99thr		4e-11
2alf_A	164	Crystal Structure Of Human Cypa Mutant K131a Length		9e-11
2x83_B	163	Evolutionary Basis Of Hiv Restriction By The Antire		1e-10
1qng_A	170	Plasmodium Falciparum Cyclophilin Complexed With Cy		1e-10
2plu_A	186	Crystal Structure Of Cryptosporidium Parvum Cycloph		1e-10
2x2c_K	165	Acetyl-Cypa:cyclosporine Complex Length = 165		1e-10
1dyw_A	173	Biochemical And Structural Characterization Of A Di		1e-10
2x2a_A	165	Free Acetyl-Cypa Trigonal Form Length = 165		2e-10
1qnh_A	170	Plasmodium Falciparum Cyclophilin (Double Mutant) C		3e-10
2x25_B	169	Free Acetyl-Cypa Orthorhombic Form Length = 169		4e-10
2c3b_A	172	The Crystal Structure Of Aspergillus Fumigatus Cycl		7e-10
3uch_A	174	Crystal Structure Of A Hypotherical Peptidyl-Prolyl		1e-09
1aws_A	164	Secypa Complexed With Hagpia (Pseudo-Symmetric Mono		2e-09
1ist_A	162	Crystal Structure Of Yeast Cyclophilin A, Cpr1 Leng		2e-09
1w74_A	191	X-Ray Structure Of Peptidyl-Prolyl Cis-Trans Isomer		3e-09
2ck1_A	172	The Structure Of Oxidised Cyclophilin A From S. Man		4e-09
2hqj_A	183	Cyclophilin From Leishmania Major Length = 183		5e-09
1z81_A	229	Crystal Structure Of Cyclophilin From Plasmodium Yo		4e-08
2k8g_A	95	Solution Structure Of Rrm2 Domain Of Pabp1 Length =		4e-07
4f02_A	213	Crystal Structure Of The Pabp-Binding Site Of Eif4g		5e-07
1cvj_A	190	X-Ray Crystal Structure Of The Poly(A)-Binding Prot		6e-07
2kxn_B	129	Nmr Structure Of Human Tra2beta1 Rrm In Complex Wit		1e-06
2nul_A	164	Peptidylprolyl Isomerase From E. Coli Length = 164		1e-06
2rra_A	99	Solution Structure Of Rna Binding Domain In Human T		2e-06
1lop_A	164	Cyclophilin A Complexed With Succinyl-Ala-Pro-Ala-P		2e-06
4f25_A	115	Crystal Structure Of The Second Rrm Domain Of Human		3e-06
2rrb_A	96	Refinement Of Rna Binding Domain In Human Tra2 Beta		3e-06
3pgw_S	437	Crystal Structure Of Human U1 Snrnp Length = 437		7e-06
2dh7_A	105	Solution Structure Of The Second Rna Binding Domain		7e-06
1b7f_A	168	Sxl-Lethal ProteinRNA COMPLEX Length = 168		9e-06
1x5s_A	102	Solution Structure Of Rrm Domain In A18 Hnrnp Lengt		1e-05
2dgo_A	115	Solution Structure Of The Rna Binding Domain In Cyt		1e-05
1sxl_A	97	Resonance Assignments And Solution Structure Of The		1e-05
1j2a_A	166	Structure Of E. Coli Cyclophilin B K163t Mutant Len		1e-05
3sxl_A	184	Sex-Lethal Rna Recognition Domains 1 And 2 From Dro		2e-05
3t1u_A	163	Crystal Structure Of The Complex Of Cyclophilin-a E		2e-05
1clh_A	166	Three-Dimensional Solution Structure Of Escherichia		2e-05
2qfj_A	216	Crystal Structure Of First Two Rrm Domains Of Fir B		3e-05
2sxl_A	88	Sex-Lethal Rbd1, Nmr, Minimized Average Structure L		3e-05
1x5t_A	96	Solution Structure Of The Second Rrm Domain In Spli		4e-05
3cw1_K	216	Crystal Structure Of Human Spliceosomal U1 Snrnp Le		5e-05
2lea_A	135	Solution Structure Of Human Srsf2 (Sc35) Rrm Length		5e-05
4ed5_A	177	Crystal Structure Of The Two N-Terminal Rrm Domains		6e-05
4egl_A	177	Crystal Structure Of Two Tandem Rna Recognition Mot		6e-05
2cqd_A	116	Solution Structure Of The Rna Recognition Motif In		7e-05
2cpz_A	115	Solution Structure Of Rna Binding Domain 3 In Cug T		7e-05
1u6f_A	139	Nmr Solution Structure Of Tcubp1, A Single Rbd-Unit		9e-05
4fxv_A	99	Crystal Structure Of An Elav-Like Protein 1 (Elavl1		1e-04
2cqc_A	95	Solution Structure Of The Rna Recognition Motif In		1e-04
3hi9_A	84	The X-Ray Crystal Structure Of The First Rna Recogn		2e-04
2kxf_A	199	Solution Structure Of The First Two Rrm Domains Of		2e-04
2err_A	109	Nmr Structure Of The Rna Binding Domain Of Human Fo		4e-04
2cq3_A	103	Solution Structure Of Rna Binding Domain In Rna Bin		4e-04
2fc8_A	102	Solution Structure Of The Rrm_1 Domain Of Ncl Prote		4e-04
2khc_A	118	Bruno Rrm3+ Length = 118		5e-04
2cjk_A	167	Structure Of The Rna Binding Domain Of Hrp1 In Comp		7e-04
3md3_A	166	Crystal Structure Of The First Two Rrm Domains Of Y		8e-04

>pdb|1XYH|A Chain A, Crystal Structure Of Recombinant Human Cyclophilin J Length = 161

Iteration: 1
 Score =  109 bits (272), Expect = 5e-24,   Method: Composition-based stats.
 Identities = 64/167 (38%), Positives = 92/167 (55%), Gaps = 9/167 (5%)
Query: 1   MSVLIVTSLGDIVVDLFVDKCPLTTKNFLKLCKIKYYNGCLFHTVQKDFXXXXXXXXXXX 60
           MSV + T +GDI +++F ++ P T +NFL LC   YYNGC+FH   K F           
Sbjct: 1   MSVTLHTDVGDIKIEVFCERTPKTCENFLALCASNYYNGCIFHRNIKGFMVQTGDPTGTG 60
Query: 61  XXXDSVYKFLYGEQARFFGDEIRVDLKHAKTGTVAMASAGENLNASQFYMTLRDNLDYLD 120
              +S++        + F DE    LKH   G V+MA+ G N N SQF++T      +LD
Sbjct: 61  RGGNSIW-------GKKFEDEYSEYLKHNVRGVVSMANNGPNTNGSQFFITYGKQ-PHLD 112
Query: 121 EKHTIFGEVAEGLETLSRINESFVDEKN-RPYKNIRIKHTYILEDPF 166
            K+T+FG+V +GLETL  + +  V+EK  RP  ++ IK   I  +PF
Sbjct: 113 MKYTVFGKVIDGLETLDELEKLPVNEKTYRPLNDVHIKDITIHANPF 159

>pdb|2OJU|A Chain A, X-Ray Structure Of Complex Of Human Cyclophilin J With Cyclosporin A Length = 167

Iteration: 1
 Score =  108 bits (270), Expect = 7e-24,   Method: Composition-based stats.
 Identities = 64/167 (38%), Positives = 92/167 (55%), Gaps = 9/167 (5%)
Query: 1   MSVLIVTSLGDIVVDLFVDKCPLTTKNFLKLCKIKYYNGCLFHTVQKDFXXXXXXXXXXX 60
           MSV + T +GDI +++F ++ P T +NFL LC   YYNGC+FH   K F           
Sbjct: 7   MSVTLHTDVGDIKIEVFCERTPKTCENFLALCASNYYNGCIFHRNIKGFMVQTGDPTGTG 66
Query: 61  XXXDSVYKFLYGEQARFFGDEIRVDLKHAKTGTVAMASAGENLNASQFYMTLRDNLDYLD 120
              +S++        + F DE    LKH   G V+MA+ G N N SQF++T      +LD
Sbjct: 67  RGGNSIW-------GKKFEDEYSEYLKHNVRGVVSMANNGPNTNGSQFFITYGKQ-PHLD 118
Query: 121 EKHTIFGEVAEGLETLSRINESFVDEKN-RPYKNIRIKHTYILEDPF 166
            K+T+FG+V +GLETL  + +  V+EK  RP  ++ IK   I  +PF
Sbjct: 119 MKYTVFGKVIDGLETLDELEKLPVNEKTYRPLNDVHIKDITIHANPF 165

>pdb|2K7N|A Chain A, Solution Structure Of The Ppil1 Bound To A Fragment Of Skip Length = 203

Iteration: 1
 Score =  105 bits (261), Expect = 9e-23,   Method: Compositional matrix adjust.
 Identities = 59/159 (37%), Positives = 88/159 (55%), Gaps = 8/159 (5%)
Query: 2   SVLIVTSLGDIVVDLFVDKCPLTTKNFLKLCKIKYYNGCLFHTVQKDFXXXXXXXXXXXX 61
           +V + TS+G IV++L+    P T KNF +L +  YYNG  FH + KDF            
Sbjct: 13  NVYLETSMGIIVLELYWKHAPKTCKNFAELARRGYYNGTKFHRIIKDFMIQGGDPTGTGR 72
Query: 62  XXDSVYKFLYGEQARFFGDEIRVDLKHAKTGTVAMASAGENLNASQFYMTLRDNLDYLDE 121
              S+    YG+Q   F DE+  DLK    G +AMA+AG + N SQF++TL     +LD 
Sbjct: 73  GGASI----YGKQ---FEDELHPDLKFTGAGILAMANAGPDTNGSQFFVTLAPT-QWLDG 124
Query: 122 KHTIFGEVAEGLETLSRINESFVDEKNRPYKNIRIKHTY 160
           KHTIFG V +G+  ++R+     + ++RP  +++I   Y
Sbjct: 125 KHTIFGRVCQGIGMVNRVGMVETNSQDRPVDDVKIIKAY 163

>pdb|1ZKC|A Chain A, Crystal Structure Of The Cyclophiln_ring Domain Of Human Peptidylprolyl Isomerase (Cyclophilin)-Like 2 Isoform B Length = 197

Iteration: 1
 Score =  104 bits (259), Expect = 2e-22,   Method: Compositional matrix adjust.
 Identities = 62/174 (35%), Positives = 96/174 (55%), Gaps = 10/174 (5%)
Query: 3   VLIVTSLGDIVVDLFVDKCPLTTKNFLKLCKIKYYNGCLFHTVQKDFXXXXXXXXXXXXX 62
           V + T+ GD+ ++L  D  P T +NF++LCK  YY+G +FH   ++F             
Sbjct: 22  VRLHTNKGDLNLELHCDLTPKTCENFIRLCKKHYYDGTIFHRSIRNFVIQGGDPTGTGTG 81
Query: 63  XDSVYKFLYGEQARFFGDEIRVDLKHAKTGTVAMASAGENLNASQFYMTLRDNLDYLDEK 122
            +S +        + F DE R +L H   G ++MA++G N N SQF++T R +  YLD+K
Sbjct: 82  GESYW-------GKPFKDEFRPNLSHTGRGILSMANSGPNSNRSQFFITFR-SCAYLDKK 133
Query: 123 HTIFGEVAEGLETLSRINESFVDEKN-RPYKNIRIKHTYILEDPFDDP-AQLAE 174
           HTIFG V  G + L+ +     D K  RP + IRI  T +  DP+++  AQ+A+
Sbjct: 134 HTIFGRVVGGFDVLTAMENVESDPKTDRPKEEIRIDATTVFVDPYEEADAQIAQ 187

>pdb|2X7K|A Chain A, The Crystal Structure Of Ppil1 In Complex With Cyclosporine A Suggests A Binding Mode For Skip Length = 166

Iteration: 1
 Score =  103 bits (256), Expect = 3e-22,   Method: Composition-based stats.
 Identities = 59/159 (37%), Positives = 88/159 (55%), Gaps = 8/159 (5%)
Query: 2   SVLIVTSLGDIVVDLFVDKCPLTTKNFLKLCKIKYYNGCLFHTVQKDFXXXXXXXXXXXX 61
           +V + TS+G IV++L+    P T KNF +L +  YYNG  FH + KDF            
Sbjct: 13  NVYLETSMGIIVLELYWKHAPKTCKNFAELARRGYYNGTKFHRIIKDFMIQGGDPTGTGR 72
Query: 62  XXDSVYKFLYGEQARFFGDEIRVDLKHAKTGTVAMASAGENLNASQFYMTLRDNLDYLDE 121
              S+    YG+Q   F DE+  DLK    G +AMA+AG + N SQF++TL     +LD 
Sbjct: 73  GGASI----YGKQ---FEDELHPDLKFTGAGILAMANAGPDTNGSQFFVTLAPT-QWLDG 124
Query: 122 KHTIFGEVAEGLETLSRINESFVDEKNRPYKNIRIKHTY 160
           KHTIFG V +G+  ++R+     + ++RP  +++I   Y
Sbjct: 125 KHTIFGRVCQGIGMVNRVGMVETNSQDRPVDDVKIIKAY 163

>pdb|1XWN|A Chain A, Solution Structure Of Cyclophilin Like 1(Ppil1) And Insights Into Its Interaction With Skip Length = 174

Iteration: 1
 Score =  103 bits (256), Expect = 3e-22,   Method: Composition-based stats.
 Identities = 59/159 (37%), Positives = 88/159 (55%), Gaps = 8/159 (5%)
Query: 2   SVLIVTSLGDIVVDLFVDKCPLTTKNFLKLCKIKYYNGCLFHTVQKDFXXXXXXXXXXXX 61
           +V + TS+G IV++L+    P T KNF +L +  YYNG  FH + KDF            
Sbjct: 13  NVYLETSMGIIVLELYWKHAPKTCKNFAELARRGYYNGTKFHRIIKDFMIQGGDPTGTGR 72
Query: 62  XXDSVYKFLYGEQARFFGDEIRVDLKHAKTGTVAMASAGENLNASQFYMTLRDNLDYLDE 121
              S+    YG+Q   F DE+  DLK    G +AMA+AG + N SQF++TL     +LD 
Sbjct: 73  GGASI----YGKQ---FEDELHPDLKFTGAGILAMANAGPDTNGSQFFVTLAPT-QWLDG 124
Query: 122 KHTIFGEVAEGLETLSRINESFVDEKNRPYKNIRIKHTY 160
           KHTIFG V +G+  ++R+     + ++RP  +++I   Y
Sbjct: 125 KHTIFGRVCQGIGMVNRVGMVETNSQDRPVDDVKIIKAY 163

>pdb|2A2N|A Chain A, Crystal Structure Of The Peptidylprolyl Isomerase Domain Of Human Ppwd1 Length = 176

Iteration: 1
 Score = 96.3 bits (238), Expect = 4e-20,   Method: Composition-based stats.
 Identities = 58/156 (37%), Positives = 87/156 (55%), Gaps = 9/156 (5%)
Query: 2   SVLIVTSLGDIVVDLFVDKCPLTTKNFLKLCKIKYYNGCLFHTVQKDFXXXXXXXXXXXX 61
           S +I TS+GDI   LF  +CP T +NF    +  YYNG  FH + K F            
Sbjct: 23  SAIIHTSMGDIHTKLFPVECPKTVENFCVHSRNGYYNGHTFHRIIKGFMIQTGDPTGTGM 82
Query: 62  XXDSVYKFLYGEQARFFGDEIRVDLKHAKTGTVAMASAGENLNASQFYMTLRDNLDYLDE 121
             +S++    GE    F DE    L+H +  T++MA+AG N N SQF++T+     +LD 
Sbjct: 83  GGESIWG---GE----FEDEFHSTLRHDRPYTLSMANAGSNTNGSQFFITVVPT-PWLDN 134
Query: 122 KHTIFGEVAEGLETLSRINESFVDEK-NRPYKNIRI 156
           KHT+FG V +G+E + RI+   V+ K ++PY+++ I
Sbjct: 135 KHTVFGRVTKGMEVVQRISNVKVNPKTDKPYEDVSI 170

>pdb|2HQ6|A Chain A, Structure Of The Cyclophilin_cecyp16-like Domain Of The Serologically Defined Colon Cancer Antigen 10 From Homo Sapiens Length = 185

Iteration: 1
 Score = 94.7 bits (234), Expect = 1e-19,   Method: Compositional matrix adjust.
 Identities = 58/167 (34%), Positives = 89/167 (53%), Gaps = 9/167 (5%)
Query: 3   VLIVTSLGDIVVDLFVDKCPLTTKNFLKLCKIKYYNGCLFHTVQKDFXXXXXXXXXXXXX 62
           VL+ T+ GDI ++L+  + P   +NF++LC   YY+  +FH V   F             
Sbjct: 27  VLLKTTAGDIDIELWSKEAPKACRNFIQLCLEAYYDNTIFHRVVPGFIVQGGDPTGTGSG 86
Query: 63  XDSVYKFLYGEQARFFGDEIRVDLKHAKTGTVAMASAGENLNASQFYMTLRDNLDYLDEK 122
            +S+Y          F DE    L+  + G VAMA+AG + N SQF+ TL    D L+ K
Sbjct: 87  GESIY-------GAPFKDEFHSRLRFNRRGLVAMANAGSHDNGSQFFFTL-GRADELNNK 138
Query: 123 HTIFGEV-AEGLETLSRINESFVDEKNRPYKNIRIKHTYILEDPFDD 168
           HTIFG+V  + +  + R++E  +D+  RP+   +IK   +L +PFDD
Sbjct: 139 HTIFGKVTGDTVYNMLRLSEVDIDDDERPHNPHKIKSCEVLFNPFDD 185

>pdb|2POE|A Chain A, Crystal Structure Of Cryptosporidium Parvum Cyclophilin Type Peptidyl-Prolyl Cis-Trans Isomerase Cgd2_1660 Length = 185

Iteration: 1
 Score = 90.9 bits (224), Expect = 2e-18,   Method: Composition-based stats.
 Identities = 57/170 (33%), Positives = 86/170 (50%), Gaps = 12/170 (7%)
Query: 3   VLIVTSLGDIVVDLFVDKCPLTTKNFLKLCKIKYYNGCLFHTVQKDFXXXXXXXXXXXXX 62
           V I+T+ GD+  +LF  +CP   KNFL L    YY   +FH   K F             
Sbjct: 19  VRIITNYGDLKFELFCSQCPKACKNFLALSASGYYKNTIFHKNIKGFIIQGGDPTGTGKG 78
Query: 63  XDSVYKFLYGEQARFFGDEIRVDLKHAKTGTVAMASAGE----NLNASQFYMTLRDNLDY 118
            +S+Y        R+F DEI  +LK+ + G ++MAS G     N N SQF++T   +L  
Sbjct: 79  GESIY-------GRYFDDEIYPELKYDRRGILSMASKGASKKPNTNGSQFFITY-SSLPQ 130
Query: 119 LDEKHTIFGEVAEGLETLSRINESFVDEKNRPYKNIRIKHTYILEDPFDD 168
           L+ ++ IFG++ +G ETL+ +     D+ ++P   I IK   I  +P  D
Sbjct: 131 LNGEYVIFGKLIDGFETLNTLENCPSDKSHKPIDEIIIKDIVIHSNPIAD 180

>pdb|2B71|A Chain A, Plasmodium Yoelii Cyclophilin-Like Protein Length = 196

Iteration: 1
 Score = 87.4 bits (215), Expect = 2e-17,   Method: Composition-based stats.
 Identities = 53/157 (33%), Positives = 82/157 (52%), Gaps = 8/157 (5%)
Query: 3   VLIVTSLGDIVVDLFVDKCPLTTKNFLKLCKIKYYNGCLFHTVQKDFXXXXXXXXXXXXX 62
           + I T+LGD  V+L+    P T  NF  LC++ +Y+  +FH V  +F             
Sbjct: 41  ITIYTNLGDFEVELYWYHSPKTCLNFYTLCEMGFYDNTIFHRVIPNFVIQGGDPTGTGKG 100
Query: 63  XDSVYKFLYGEQARFFGDEIRVDLKHAKTGTVAMASAGENLNASQFYMTLRDNLDYLDEK 122
             S+Y    GE   +F DEI  +LKH   G ++M++ G N N+SQF++TL   L +LD K
Sbjct: 101 GKSIY----GE---YFEDEINKELKHTGAGILSMSNNGPNTNSSQFFITLAP-LPHLDGK 152
Query: 123 HTIFGEVAEGLETLSRINESFVDEKNRPYKNIRIKHT 159
           HTIF  V++ +  +  I        N+P  +++I  T
Sbjct: 153 HTIFARVSKNMTCIENIASVQTTATNKPIFDLKILRT 189

>pdb|2FU0|A Chain A, Plasmodium Falciparum Cyclophilin Pfe0505w Putative Cyclosporin- Binding Domain Length = 160

Iteration: 1
 Score = 87.4 bits (215), Expect = 2e-17,   Method: Composition-based stats.
 Identities = 53/155 (34%), Positives = 83/155 (53%), Gaps = 8/155 (5%)
Query: 2   SVLIVTSLGDIVVDLFVDKCPLTTKNFLKLCKIKYYNGCLFHTVQKDFXXXXXXXXXXXX 61
           S +I T++GDI + LF  +C  T +NF       YYN C+FH V K F            
Sbjct: 7   SAIIYTTMGDIHISLFYKECKKTVQNFSVHSINGYYNNCIFHRVIKHFMVQTGDPSGDGT 66
Query: 62  XXDSVYKFLYGEQARFFGDEIRVDLKHAKTGTVAMASAGENLNASQFYMTLRDNLDYLDE 121
             +S++    G +   F DE    L H+K   V+MA+ G N N SQF++T      +LD 
Sbjct: 67  GGESIW----GNE---FEDEFFDHLNHSKPFMVSMANCGPNTNGSQFFITTVP-CPWLDF 118
Query: 122 KHTIFGEVAEGLETLSRINESFVDEKNRPYKNIRI 156
           KHT+FG+V +G + +  I +   D++++P ++I+I
Sbjct: 119 KHTVFGKVTQGSKIVLDIEKVRTDKRDKPLEDIKI 153

>pdb|3BKP|A Chain A, Crystal Structure Of The Toxoplasma Gondii Cyclophilin, 49.m03261 Length = 232

Iteration: 1
 Score = 79.7 bits (195), Expect = 4e-15,   Method: Compositional matrix adjust.
 Identities = 60/198 (30%), Positives = 93/198 (46%), Gaps = 25/198 (12%)
Query: 3   VLIVTSLGDIVVDLFVDKCPLTTKNFLKLCKIKYYNGCLFHTVQKDFXXXXX-XXXXXXX 61
           V++ TSLGD+ V+L+  +CPL  +NF++LC   YY   +FH V KDF             
Sbjct: 24  VVLHTSLGDLDVELWARECPLACRNFVQLCLEGYYVNTIFHRVVKDFIVQGGDPTGTGRG 83
Query: 62  XXDSVYKFLYGEQARFFGDEIRVDLKHAKTGTVAMASAGEN--------------LNASQ 107
             D+ +        + F  E    LK    G V +A+ G +               N +Q
Sbjct: 84  GADTTF------DGKPFDVETHPRLKFRYRGLVGVANLGRSSKDAENDERGRSLGTNGNQ 137
Query: 108 FYMTLRDNLDYLDEKHTIFGEV-AEGLETLSRINESFVDEKNRPYKNIRIKHTYILEDPF 166
           F++TL    D L+  +T+FG+V    L  L + N+  V +++RP     IK   +L +PF
Sbjct: 138 FFITL-ARADVLNNAYTLFGKVTGHTLYNLMKFNDLEVGKEDRPMTPPFIKSVDVLWNPF 196
Query: 167 DDPAQLAELIPDASPEGK 184
           +D   +   +PDA P  K
Sbjct: 197 ED--LVPRRLPDAPPAQK 212

>pdb|2HAQ|A Chain A, Crystal Structure Of Cyclophilin A From Leishmania Donovani Length = 172

Iteration: 1
 Score = 79.3 bits (194), Expect = 5e-15,   Method: Composition-based stats.
 Identities = 51/151 (33%), Positives = 83/151 (54%), Gaps = 12/151 (7%)
Query: 9   LGDIVVDLFVDKCPLTTKNFLKLCKIKY---YNGCLFHTVQKDFXXXXXXXXXXXXXXDS 65
           LG I + LF    PLTT+NF +LC  ++   Y   +FH V ++F                
Sbjct: 25  LGRITIGLFGKDAPLTTENFRQLCTGEHGFGYKDSIFHRVIQNFMIQGGDFTNFDGTGG- 83
Query: 66  VYKFLYGEQARFFGDEIRVDLKHAKTGTVAMASAGENLNASQFYMTLRDNLDYLDEKHTI 125
             K +YGE+   F DE  +++KH   G ++MA+AG N N SQF++T      +LD +H +
Sbjct: 84  --KSIYGEK---FADE-NLNVKHF-VGALSMANAGPNTNGSQFFITTAPT-PWLDGRHVV 135
Query: 126 FGEVAEGLETLSRINESFVDEKNRPYKNIRI 156
           FG+V +G++ + RI ++  +  +RP K ++I
Sbjct: 136 FGKVLDGMDVVLRIEKTKTNSHDRPVKPVKI 166

>pdb|3BT8|A Chain A, Crystal Structure Of Mutant Cyclophilin (R147a) From Leishmania Donovani Length = 172

Iteration: 1
 Score = 79.0 bits (193), Expect = 7e-15,   Method: Composition-based stats.
 Identities = 51/151 (33%), Positives = 82/151 (54%), Gaps = 12/151 (7%)
Query: 9   LGDIVVDLFVDKCPLTTKNFLKLCKIKY---YNGCLFHTVQKDFXXXXXXXXXXXXXXDS 65
           LG I + LF    PLTT+NF +LC  ++   Y   +FH V ++F                
Sbjct: 25  LGRITIGLFGKDAPLTTENFRQLCTGEHGFGYKDSIFHRVIQNFMIQGGDFTNFDGTGG- 83
Query: 66  VYKFLYGEQARFFGDEIRVDLKHAKTGTVAMASAGENLNASQFYMTLRDNLDYLDEKHTI 125
             K +YGE+   F DE  +++KH   G ++MA+AG N N SQF++T      +LD  H +
Sbjct: 84  --KSIYGEK---FADE-NLNVKHF-VGALSMANAGPNTNGSQFFITTAPT-PWLDGAHVV 135
Query: 126 FGEVAEGLETLSRINESFVDEKNRPYKNIRI 156
           FG+V +G++ + RI ++  +  +RP K ++I
Sbjct: 136 FGKVLDGMDVVLRIEKTKTNSHDRPVKPVKI 166

>pdb|3K2C|A Chain A, Crystal Structure Of Peptidyl-Prolyl Cis-Trans Isomerase From Encephalitozoon Cuniculi At 1.9 A Resolution Length = 193

Iteration: 1
 Score = 77.8 bits (190), Expect = 1e-14,   Method: Composition-based stats.
 Identities = 56/153 (36%), Positives = 79/153 (51%), Gaps = 12/153 (7%)
Query: 8   SLGDIVVDLFVDKCPLTTKNFLKLC---KIKYYNGCLFHTVQKDFXXXXXXXXXXXXXXD 64
           SLG IV+ L  D  P T KNF  LC   K + Y G  FH +   F               
Sbjct: 40  SLGRIVMKLEDDIVPKTAKNFRTLCERPKGEGYKGSTFHRIIPGFMVQGGDYTAHNGTGG 99
Query: 65  SVYKFLYGEQARFFGDEIRVDLKHAKTGTVAMASAGENLNASQFYMTLRDNLDYLDEKHT 124
              + +YGE+   F DE   +LKH K G ++MA+ G + N SQF++TL     +LDEKH 
Sbjct: 100 ---RSIYGEK---FPDE-NFELKHTKEGILSMANCGAHTNGSQFFITL-GKTQWLDEKHV 151
Query: 125 IFGEVAEGLETLSRINESFVDEKNRPYKNIRIK 157
           +FGEV EG++ + +I + +  E  +  K  RI+
Sbjct: 152 VFGEVVEGMDVVHKIAK-YGSESGQVKKGYRIE 183

>pdb|2WFJ|A Chain A, Atomic Resolution Crystal Structure Of The Ppiase Domain Of Human Cyclophilin G In Complex With Cyclosporin A Length = 179

Iteration: 1
 Score = 77.8 bits (190), Expect = 1e-14,   Method: Composition-based stats.
 Identities = 52/159 (32%), Positives = 75/159 (47%), Gaps = 21/159 (13%)
Query: 10  GDIVVDLFVDKCPLTTKNFLKLC-----------KIKYYNGCLFHTVQKDFXXXXXX-XX 57
           G +V +LF D CP T +NF  LC           K  +Y  CLFH V KDF         
Sbjct: 24  GRVVFELFSDVCPKTCENFRCLCTGEKGTGKSTQKPLHYKSCLFHRVVKDFMVQGGDFSE 83
Query: 58  XXXXXXDSVYKFLYGEQARFFGDEIRVDLKHAKTGTVAMASAGENLNASQFYMTLRDNLD 117
                 +S+Y         FF DE    +KH K   ++MA+ G++ N SQF++T +    
Sbjct: 84  GNGRGGESIY-------GGFFEDE-SFAVKHNKEFLLSMANRGKDTNGSQFFITTKPT-P 134
Query: 118 YLDEKHTIFGEVAEGLETLSRINESFVDEKNRPYKNIRI 156
           +LD  H +FG+V  G E +  I     D  ++P+  +RI
Sbjct: 135 HLDGHHVVFGQVISGQEVVREIENQKTDAASKPFAEVRI 173

>pdb|2GW2|A Chain A, Crystal Structure Of The Peptidyl-Prolyl Isomerase Domain Of Human Cyclophilin G Length = 198

Iteration: 1
 Score = 77.0 bits (188), Expect = 3e-14,   Method: Compositional matrix adjust.
 Identities = 51/159 (32%), Positives = 74/159 (46%), Gaps = 21/159 (13%)
Query: 10  GDIVVDLFVDKCPLTTKNFLKLC-----------KIKYYNGCLFHTVQKDFXXXXX-XXX 57
           G +V +LF D CP T +NF  LC           K  +Y  CLFH V KDF         
Sbjct: 41  GRVVFELFSDVCPKTCENFRCLCTGEKGTGKSTQKPLHYKSCLFHRVVKDFMVQGGDFSE 100
Query: 58  XXXXXXDSVYKFLYGEQARFFGDEIRVDLKHAKTGTVAMASAGENLNASQFYMTLRDNLD 117
                 +S+Y         FF DE    +KH     ++MA+ G++ N SQF++T +    
Sbjct: 101 GNGRGGESIY-------GGFFEDE-SFAVKHNAAFLLSMANRGKDTNGSQFFITTKPT-P 151
Query: 118 YLDEKHTIFGEVAEGLETLSRINESFVDEKNRPYKNIRI 156
           +LD  H +FG+V  G E +  I     D  ++P+  +RI
Sbjct: 152 HLDGHHVVFGQVISGQEVVREIENQKTDAASKPFAEVRI 190

>pdb|2HE9|A Chain A, Structure Of The Peptidylprolyl Isomerase Domain Of The Human Nk-Tumour Recognition Protein Length = 192

Iteration: 1
 Score = 75.9 bits (185), Expect = 5e-14,   Method: Composition-based stats.
 Identities = 52/160 (32%), Positives = 76/160 (47%), Gaps = 21/160 (13%)
Query: 9   LGDIVVDLFVDKCPLTTKNFLKLC-----------KIKYYNGCLFHTVQKDFXXXXXX-X 56
           +G I+  LF D CP T KNFL LC           K   Y G  FH V K+F        
Sbjct: 33  VGRIMFQLFSDICPKTCKNFLCLCSGEKGLGKTTGKKLCYKGSTFHRVVKNFMIQGGDFS 92
Query: 57  XXXXXXXDSVYKFLYGEQARFFGDEIRVDLKHAKTGTVAMASAGENLNASQFYMTLRDNL 116
                  +S+Y         +F DE  + LKH +   ++MA+ G++ N SQF++T +   
Sbjct: 93  EGNGKGGESIY-------GGYFKDENFI-LKHDRAFLLSMANRGKHTNGSQFFITTKP-A 143
Query: 117 DYLDEKHTIFGEVAEGLETLSRINESFVDEKNRPYKNIRI 156
            +LD  H +FG V  G E + +I     D  +RPY ++R+
Sbjct: 144 PHLDGVHVVFGLVISGFEVIEQIENLKTDAASRPYADVRV 183

>pdb|2BIT|X Chain X, Crystal Structure Of Human Cyclophilin D At 1.7 A Resolution Length = 165

Iteration: 1
 Score = 75.1 bits (183), Expect = 1e-13,   Method: Composition-based stats.
 Identities = 56/152 (36%), Positives = 76/152 (50%), Gaps = 14/152 (9%)
Query: 9   LGDIVVDLFVDKCPLTTKNFLKLC---KIKYYNGCLFHTVQKDFXXXXXXXXXXXXXXDS 65
           LG +V++L  D  P T +NF  LC   K   Y G  FH V   F                
Sbjct: 17  LGRVVLELKADVVPKTAENFRALCTGEKGFGYKGSTFHRVIPSFMCQAGDFTNHNGTGG- 75
Query: 66  VYKFLYGEQARFFGDEIRVDLKHAKTGTVAMASAGENLNASQFYM-TLRDNLDYLDEKHT 124
             K +YG +   F DE    LKH   G ++MA+AG N N SQF++ T++   D+LD KH 
Sbjct: 76  --KSIYGSR---FPDE-NFTLKHVGPGVLSMANAGPNTNGSQFFICTIKT--DWLDGKHV 127
Query: 125 IFGEVAEGLETLSRINESFVDEKNRPYKNIRI 156
           +FG V EG++ + +I ESF  +  R  K I I
Sbjct: 128 VFGHVIEGMDVVKKI-ESFGSKSGRTSKKIVI 158

>pdb|3R49|A Chain A, Human Cyclophilin D Complexed With Quinolin-8-Amine Length = 166

Iteration: 1
 Score = 75.1 bits (183), Expect = 1e-13,   Method: Composition-based stats.
 Identities = 56/152 (36%), Positives = 76/152 (50%), Gaps = 14/152 (9%)
Query: 9   LGDIVVDLFVDKCPLTTKNFLKLC---KIKYYNGCLFHTVQKDFXXXXXXXXXXXXXXDS 65
           LG +V++L  D  P T +NF  LC   K   Y G  FH V   F                
Sbjct: 18  LGRVVLELKADVVPKTAENFRALCTGEKGFGYKGSTFHRVIPSFMCQAGDFTNHNGTGG- 76
Query: 66  VYKFLYGEQARFFGDEIRVDLKHAKTGTVAMASAGENLNASQFYM-TLRDNLDYLDEKHT 124
             K +YG +   F DE    LKH   G ++MA+AG N N SQF++ T++   D+LD KH 
Sbjct: 77  --KSIYGSR---FPDE-NFTLKHVGPGVLSMANAGPNTNGSQFFICTIKT--DWLDGKHV 128
Query: 125 IFGEVAEGLETLSRINESFVDEKNRPYKNIRI 156
           +FG V EG++ + +I ESF  +  R  K I I
Sbjct: 129 VFGHVIEGMDVVKKI-ESFGSKSGRTSKKIVI 159

>pdb|3QYU|A Chain A, Crystal Structure Of Human Cyclophilin D At 1.54 A Resolution At Room Temperature Length = 164

Iteration: 1
 Score = 75.1 bits (183), Expect = 1e-13,   Method: Composition-based stats.
 Identities = 56/152 (36%), Positives = 76/152 (50%), Gaps = 14/152 (9%)
Query: 9   LGDIVVDLFVDKCPLTTKNFLKLC---KIKYYNGCLFHTVQKDFXXXXXXXXXXXXXXDS 65
           LG +V++L  D  P T +NF  LC   K   Y G  FH V   F                
Sbjct: 16  LGRVVLELKADVVPKTAENFRALCTGEKGFGYKGSTFHRVIPSFMCQAGDFTNHNGTGG- 74
Query: 66  VYKFLYGEQARFFGDEIRVDLKHAKTGTVAMASAGENLNASQFYM-TLRDNLDYLDEKHT 124
             K +YG +   F DE    LKH   G ++MA+AG N N SQF++ T++   D+LD KH 
Sbjct: 75  --KSIYGSR---FPDE-NFTLKHVGPGVLSMANAGPNTNGSQFFICTIKT--DWLDGKHV 126
Query: 125 IFGEVAEGLETLSRINESFVDEKNRPYKNIRI 156
           +FG V EG++ + +I ESF  +  R  K I I
Sbjct: 127 VFGHVIEGMDVVKKI-ESFGSKSGRTSKKIVI 157

>pdb|2Z6W|A Chain A, Crystal Structure Of Human Cyclophilin D In Complex With Cyclosporin A Length = 165

Iteration: 1
 Score = 75.1 bits (183), Expect = 1e-13,   Method: Composition-based stats.
 Identities = 56/152 (36%), Positives = 76/152 (50%), Gaps = 14/152 (9%)
Query: 9   LGDIVVDLFVDKCPLTTKNFLKLC---KIKYYNGCLFHTVQKDFXXXXXXXXXXXXXXDS 65
           LG +V++L  D  P T +NF  LC   K   Y G  FH V   F                
Sbjct: 17  LGRVVLELKADVVPKTAENFRALCTGEKGFGYKGSTFHRVIPSFMCQAGDFTNHNGTGG- 75
Query: 66  VYKFLYGEQARFFGDEIRVDLKHAKTGTVAMASAGENLNASQFYM-TLRDNLDYLDEKHT 124
             K +YG +   F DE    LKH   G ++MA+AG N N SQF++ T++   D+LD KH 
Sbjct: 76  --KSIYGSR---FPDE-NFTLKHVGPGVLSMANAGPNTNGSQFFICTIKT--DWLDGKHV 127
Query: 125 IFGEVAEGLETLSRINESFVDEKNRPYKNIRI 156
           +FG V EG++ + +I ESF  +  R  K I I
Sbjct: 128 VFGHVIEGMDVVKKI-ESFGSKSGRTSKKIVI 158

>pdb|2RMC|A Chain A, Crystal Structure Of Murine Cyclophilin C Complexed With Immunosuppressive Drug Cyclosporin A Length = 182

Iteration: 1
 Score = 73.6 bits (179), Expect = 3e-13,   Method: Composition-based stats.
 Identities = 56/168 (33%), Positives = 80/168 (47%), Gaps = 19/168 (11%)
Query: 9   LGDIVVDLFVDKCPLTTKNFLKLC---KIKYYNGCLFHTVQKDFXXXXXXXXXXXXXXDS 65
           +G IV+ LF +  P T +NF+ L    K   Y G +FH V KDF                
Sbjct: 21  VGRIVIGLFGNVVPKTVENFVALATGEKGYGYKGSIFHRVIKDFMIQGGDFTARDGTGGM 80
Query: 66  VYKFLYGEQARFFGDEIRVDLKHAKTGTVAMASAGENLNASQFYMTLRDNLDYLDEKHTI 125
               +YGE    F DE    LKH   G V+MA+AG + N SQF++TL     +LD KH +
Sbjct: 81  S---IYGET---FPDE-NFKLKHYGIGWVSMANAGPDTNGSQFFITLTKP-TWLDGKHVV 132
Query: 126 FGEVAEGLETLSRINESFVDEKNRPYKN--------IRIKHTYILEDP 165
           FG+V +G+  +  I     D  +RP  +        I +K  +++E P
Sbjct: 133 FGKVLDGMTVVHSIELQATDGHDRPLTDCTIVNSGKIDVKTPFVVEVP 180

>pdb|3BO7|A Chain A, Crystal Structure Of Toxoplasma Gondii Peptidyl-Prolyl Cis-Trans Isomerase, 541.M00136 Length = 201

Iteration: 1
 Score = 73.6 bits (179), Expect = 3e-13,   Method: Compositional matrix adjust.
 Identities = 50/172 (29%), Positives = 89/172 (51%), Gaps = 12/172 (6%)
Query: 5   IVTSLGDIVVDLFVDKCPLTTKNFLKLCKIKYYNGCLFHTVQKDFXXXX--------XXX 56
           IVT+ G + ++L  D  P    +FL+LC +KY++  +FH   ++F               
Sbjct: 11  IVTTQGSLNIELHADMAPRACDSFLRLCAVKYFDDTIFHRCIRNFMIQGGRAELRQPSKK 70
Query: 57  XXXXXXXDSVYKFLYGEQARFFGDEIRVDLKHAKTGTVAMASAGENLNASQFYMTLRDNL 116
                   S+  F  G     F DE    L H   G ++MA+ G++ N S+F++T + + 
Sbjct: 71  KEVQQSPRSISGFPGGAP---FEDEFDNRLVHQGIGVLSMANDGKHSNLSEFFITFK-SC 126
Query: 117 DYLDEKHTIFGEVAEGLETLSRINESFVDEKNRPYKNIRIKHTYILEDPFDD 168
           ++L+ KHTIFG V  GL+ L +  +   D+K++P K  +++   + ++PF+D
Sbjct: 127 EHLNNKHTIFGRVVGGLDVLRQWEKLETDKKDKPLKPPKVEEIIVFKNPFED 178

>pdb|2WFI|A Chain A, Atomic Resolution Crystal Structure Of The Ppiase Domain Of Human Cyclophilin G Length = 179

Iteration: 1
 Score = 73.2 bits (178), Expect = 4e-13,   Method: Composition-based stats.
 Identities = 51/159 (32%), Positives = 74/159 (46%), Gaps = 21/159 (13%)
Query: 10  GDIVVDLFVDKCPLTTKNFLKLC-----------KIKYYNGCLFHTVQKDFXXXXXX-XX 57
           G +V +LF D CP T +NF  LC           K  +Y   LFH V KDF         
Sbjct: 24  GRVVFELFSDVCPKTCENFRCLCTGEKGTGKSTQKPLHYKSXLFHRVVKDFMVQGGDFSE 83
Query: 58  XXXXXXDSVYKFLYGEQARFFGDEIRVDLKHAKTGTVAMASAGENLNASQFYMTLRDNLD 117
                 +S+Y         FF DE    +KH K   ++MA+ G++ N SQF++T +    
Sbjct: 84  GNGRGGESIY-------GGFFEDE-SFAVKHNKEFLLSMANRGKDTNGSQFFITTKPT-P 134
Query: 118 YLDEKHTIFGEVAEGLETLSRINESFVDEKNRPYKNIRI 156
           +LD  H +FG+V  G E +  I     D  ++P+  +RI
Sbjct: 135 HLDGHHVVFGQVISGQEVVREIENQKTDAASKPFAEVRI 173

>pdb|2ESL|A Chain A, Human Cyclophilin C In Complex With Cyclosporin A Length = 190

Iteration: 1
 Score = 72.4 bits (176), Expect = 7e-13,   Method: Composition-based stats.
 Identities = 54/151 (35%), Positives = 71/151 (47%), Gaps = 11/151 (7%)
Query: 9   LGDIVVDLFVDKCPLTTKNFLKLC---KIKYYNGCLFHTVQKDFXXXXXXXXXXXXXXDS 65
           +G IV+ LF    P T +NF+ L    K   Y G  FH V KDF                
Sbjct: 29  VGRIVIGLFGKVVPKTVENFVALATGEKGYGYKGSKFHRVIKDFMIQGGDITTGDGTGGV 88
Query: 66  VYKFLYGEQARFFGDEIRVDLKHAKTGTVAMASAGENLNASQFYMTLRDNLDYLDEKHTI 125
               +YGE    F DE    LKH   G V+MA+AG + N SQF++TL     +LD KH +
Sbjct: 89  S---IYGET---FPDE-NFKLKHYGIGWVSMANAGPDTNGSQFFITLTKP-TWLDGKHVV 140
Query: 126 FGEVAEGLETLSRINESFVDEKNRPYKNIRI 156
           FG+V +G+  +  I     D  +RP  N  I
Sbjct: 141 FGKVIDGMTVVHSIELQATDGHDRPLTNCSI 171

>pdb|4FRU|A Chain A, Crystal Structure Of Horse Wild-Type Cyclophilin B Length = 185

Iteration: 1
 Score = 72.4 bits (176), Expect = 7e-13,   Method: Composition-based stats.
 Identities = 52/151 (34%), Positives = 77/151 (50%), Gaps = 11/151 (7%)
Query: 9   LGDIVVDLFVDKCPLTTKNFLKLC---KIKYYNGCLFHTVQKDFXXXXXXXXXXXXXXDS 65
           +G +V+ LF    P T  NF+ L    K   Y    FH V KDF                
Sbjct: 26  IGRVVIGLFGKTVPKTVDNFVALATGEKGFGYKDSKFHRVIKDFMIQGGDFTRGDGTGG- 84
Query: 66  VYKFLYGEQARFFGDEIRVDLKHAKTGTVAMASAGENLNASQFYMTLRDNLDYLDEKHTI 125
             K +YGE+   F DE    LKH   G V+MA+AG++ N SQF++T      +LD KH +
Sbjct: 85  --KSIYGER---FPDE-NFKLKHYGPGWVSMANAGKDTNGSQFFITTVKTA-WLDGKHVV 137
Query: 126 FGEVAEGLETLSRINESFVDEKNRPYKNIRI 156
           FG+V EG+E + ++  +  D +++P K++ I
Sbjct: 138 FGKVLEGMEVVRKVETTKTDGRDKPLKDVTI 168

>pdb|1IHG|A Chain A, Bovine Cyclophilin 40, Monoclinic Form Length = 370

Iteration: 1
 Score = 72.0 bits (175), Expect = 9e-13,   Method: Compositional matrix adjust.
 Identities = 52/159 (32%), Positives = 77/159 (48%), Gaps = 20/159 (12%)
Query: 9   LGDIVVDLFVDKCPLTTKNFLKLC-----------KIKYYNGCLFHTVQKDFXXXXXXXX 57
           +G IV++LF D  P T +NF  LC           K  ++ GC FH + K F        
Sbjct: 29  VGRIVLELFADIVPKTAENFRALCTGEKGIGPTTGKPLHFKGCPFHRIIKKFMIQGGDFS 88
Query: 58  XXXXXXDSVYKFLYGEQARFFGDEIRVDLKHAKTGTVAMASAGENLNASQFYMTLRDNLD 117
                       +YGE+   F DE     KH K G ++MA+AG N N SQF++T      
Sbjct: 89  NQNGTGGES---IYGEK---FEDE-NFHYKHDKEGLLSMANAGSNTNGSQFFITTVPT-P 140
Query: 118 YLDEKHTIFGEVAEGLETLSRINESFVDEKNRPYKNIRI 156
           +LD KH +FG+V +G+  +++I E+   +  +P K   I
Sbjct: 141 HLDGKHVVFGQVIKGM-GVAKILENVEVKGEKPAKLCVI 178

>pdb|4FRV|A Chain A, Crystal Structure Of Mutated Cyclophilin B That Causes Hyperelastosis Cutis In The American Quarter Horse Length = 185

Iteration: 1
 Score = 72.0 bits (175), Expect = 9e-13,   Method: Composition-based stats.
 Identities = 52/151 (34%), Positives = 77/151 (50%), Gaps = 11/151 (7%)
Query: 9   LGDIVVDLFVDKCPLTTKNFLKLC---KIKYYNGCLFHTVQKDFXXXXXXXXXXXXXXDS 65
           +G +V+ LF    P T  NF+ L    K   Y    FH V KDF                
Sbjct: 26  IGRVVIGLFGKTVPKTVDNFVALATGEKGFGYKDSKFHRVIKDFMIQGGDFTRGDGTGG- 84
Query: 66  VYKFLYGEQARFFGDEIRVDLKHAKTGTVAMASAGENLNASQFYMTLRDNLDYLDEKHTI 125
             K +YGE+   F DE    LKH   G V+MA+AG++ N SQF++T      +LD KH +
Sbjct: 85  --KSIYGER---FPDE-NFKLKHYGPGWVSMANAGKDTNGSQFFITTVKTA-WLDGKHVV 137
Query: 126 FGEVAEGLETLSRINESFVDEKNRPYKNIRI 156
           FG+V EG+E + ++  +  D +++P K++ I
Sbjct: 138 FGKVLEGMEVVRKVETTKTDGRDKPLKDVTI 168

>pdb|1CYN|A Chain A, Cyclophilin B Complexed With [d-(Cholinylester)ser8]-Cyclosporin Length = 178

Iteration: 1
 Score = 72.0 bits (175), Expect = 9e-13,   Method: Composition-based stats.
 Identities = 51/151 (33%), Positives = 76/151 (50%), Gaps = 11/151 (7%)
Query: 9   LGDIVVDLFVDKCPLTTKNFLKLC---KIKYYNGCLFHTVQKDFXXXXXXXXXXXXXXDS 65
           +G ++  LF    P T  NF+ L    K   Y    FH V KDF                
Sbjct: 19  VGRVIFGLFGKTVPKTVDNFVALATGEKGFGYKNSKFHRVIKDFMIQGGDFTRGDGTGG- 77
Query: 66  VYKFLYGEQARFFGDEIRVDLKHAKTGTVAMASAGENLNASQFYMTLRDNLDYLDEKHTI 125
             K +YGE+   F DE    LKH   G V+MA+AG++ N SQF++T      +LD KH +
Sbjct: 78  --KSIYGER---FPDE-NFKLKHYGPGWVSMANAGKDTNGSQFFITTVKTA-WLDGKHVV 130
Query: 126 FGEVAEGLETLSRINESFVDEKNRPYKNIRI 156
           FG+V EG+E + ++  +  D +++P K++ I
Sbjct: 131 FGKVLEGMEVVRKVESTKTDSRDKPLKDVII 161

>pdb|3ICH|A Chain A, Crystal Structure Of Cyclophilin B At 1.2 A Resolution Length = 188

Iteration: 1
 Score = 71.2 bits (173), Expect = 2e-12,   Method: Composition-based stats.
 Identities = 51/151 (33%), Positives = 76/151 (50%), Gaps = 11/151 (7%)
Query: 9   LGDIVVDLFVDKCPLTTKNFLKLC---KIKYYNGCLFHTVQKDFXXXXXXXXXXXXXXDS 65
           +G ++  LF    P T  NF+ L    K   Y    FH V KDF                
Sbjct: 29  VGRVIFGLFGKTVPKTVDNFVALATGEKGFGYKNSKFHRVIKDFMIQGGDFTRGDGTGG- 87
Query: 66  VYKFLYGEQARFFGDEIRVDLKHAKTGTVAMASAGENLNASQFYMTLRDNLDYLDEKHTI 125
             K +YGE+   F DE    LKH   G V+MA+AG++ N SQF++T      +LD KH +
Sbjct: 88  --KSIYGER---FPDE-NFKLKHYGPGWVSMANAGKDTNGSQFFITTVKTA-WLDGKHVV 140
Query: 126 FGEVAEGLETLSRINESFVDEKNRPYKNIRI 156
           FG+V EG+E + ++  +  D +++P K++ I
Sbjct: 141 FGKVLEGMEVVRKVESTKTDSRDKPLKDVII 171

>pdb|4I9Y|A Chain A, Structure Of The C-terminal Domain Of Nup358 Length = 167

Iteration: 1
 Score = 69.7 bits (169), Expect = 4e-12,   Method: Composition-based stats.
 Identities = 52/151 (34%), Positives = 78/151 (51%), Gaps = 12/151 (7%)
Query: 9   LGDIVVDLFVDKCPLTTKNFLKLC---KIKYYNGCLFHTVQKDFXXXXXXXXXXXXXXDS 65
           LG I ++LF +  P T +NF  LC   K   +   +FH V  DF                
Sbjct: 20  LGRITMELFSNIVPRTAENFRALCTGEKGFGFKNSIFHRVIPDFVCQGGDITKHDGTGG- 78
Query: 66  VYKFLYGEQARFFGDEIRVDLKHAKTGTVAMASAGENLNASQFYMTLRDNLDYLDEKHTI 125
             + +YG++   F DE   D+KH   G ++MA+ G+N N SQF +TL+   ++LD KH +
Sbjct: 79  --QSIYGDK---FEDE-NFDVKHTGPGLLSMANQGQNTNNSQFVITLK-KAEHLDFKHVV 131
Query: 126 FGEVAEGLETLSRINESFVDEKNRPYKNIRI 156
           FG V +G++T+ +I ESF   K    + I I
Sbjct: 132 FGFVKDGMDTVKKI-ESFGSPKGSVCRRITI 161

>pdb|3PMP|A Chain A, Crystal Structure Of Cyclophilin A From Moniliophthora Perniciosa In Complex With Cyclosporin A Length = 164

Iteration: 1
 Score = 69.7 bits (169), Expect = 4e-12,   Method: Composition-based stats.
 Identities = 47/133 (35%), Positives = 67/133 (50%), Gaps = 11/133 (8%)
Query: 10  GDIVVDLFVDKCPLTTKNFLKLCKIKY---YNGCLFHTVQKDFXXXXXXXXXXXXXXDSV 66
           G IV  L+ +  P T KNF +L   ++   Y   +FH V   F                 
Sbjct: 17  GRIVFKLYDEAVPKTAKNFRELATGQHGFGYKDSIFHRVIPQFMLQGGDFTRHNGTGG-- 74
Query: 67  YKFLYGEQARFFGDEIRVDLKHAKTGTVAMASAGENLNASQFYMTLRDNLDYLDEKHTIF 126
            K +YGE+   F DE    +KH K G ++MA+AG N N SQF++T      +LD KH +F
Sbjct: 75  -KSIYGEK---FADE-NFQVKHTKPGLLSMANAGANTNGSQFFITTVPT-SWLDGKHVVF 128
Query: 127 GEVAEGLETLSRI 139
           GEV EGL+ + ++
Sbjct: 129 GEVIEGLDIVRKV 141

>pdb|3O7T|A Chain A, Crystal Structure Of Cyclophilin A From Moniliophthora Perniciosa Length = 164

Iteration: 1
 Score = 69.3 bits (168), Expect = 6e-12,   Method: Composition-based stats.
 Identities = 47/133 (35%), Positives = 67/133 (50%), Gaps = 11/133 (8%)
Query: 10  GDIVVDLFVDKCPLTTKNFLKLCKIKY---YNGCLFHTVQKDFXXXXXXXXXXXXXXDSV 66
           G IV  L+ +  P T KNF +L   ++   Y   +FH V   F                 
Sbjct: 18  GRIVFKLYDEAVPKTAKNFRELATGQHGFGYKDSIFHRVIPQFMLQGGDFTRHNGTGG-- 75
Query: 67  YKFLYGEQARFFGDEIRVDLKHAKTGTVAMASAGENLNASQFYMTLRDNLDYLDEKHTIF 126
            K +YGE+   F DE    +KH K G ++MA+AG N N SQF++T      +LD KH +F
Sbjct: 76  -KSIYGEK---FADE-NFQVKHTKPGLLSMANAGANTNGSQFFITTVPT-SWLDGKHVVF 129
Query: 127 GEVAEGLETLSRI 139
           GEV EGL+ + ++
Sbjct: 130 GEVIEGLDIVRKV 142

>pdb|2CFE|A Chain A, The 1.5 A Crystal Structure Of The Malassezia Sympodialis Mala S 6 Allergen, A Member Of The Cyclophilin Pan- Allergen Family Length = 162

Iteration: 1
 Score = 68.9 bits (167), Expect = 8e-12,   Method: Composition-based stats.
 Identities = 55/151 (36%), Positives = 69/151 (45%), Gaps = 12/151 (7%)
Query: 9   LGDIVVDLFVDKCPLTTKNFLKLC---KIKYYNGCLFHTVQKDFXXXXXXXXXXXXXXDS 65
           LG I   LF D  P T  NF  LC   K   Y G  FH V  DF                
Sbjct: 15  LGTIKFKLFDDVVPKTAANFRALCTGEKGFGYAGSHFHRVIPDFMLQGGDFTAGNGTGG- 73
Query: 66  VYKFLYGEQARFFGDEIRVDLKHAKTGTVAMASAGENLNASQFYMTLRDNLDYLDEKHTI 125
             K +YG +   F DE    LKH K G ++MA+AG N N SQF++T      +LD KH +
Sbjct: 74  --KSIYGAK---FADE-NFQLKHNKPGLLSMANAGPNTNGSQFFITTVVT-SWLDGKHVV 126
Query: 126 FGEVAEGLETLSRINESFVDEKNRPYKNIRI 156
           FGEV +G+  +  I E+      +P   I I
Sbjct: 127 FGEVIDGMNVVKAI-EAEGSGSGKPRSRIEI 156

>pdb|1H0P|A Chain A, Cyclophilin_5 From C. Elegans Length = 182

Iteration: 1
 Score = 68.9 bits (167), Expect = 8e-12,   Method: Composition-based stats.
 Identities = 48/151 (31%), Positives = 77/151 (50%), Gaps = 11/151 (7%)
Query: 9   LGDIVVDLFVDKCPLTTKNFLKLCKI---KYYNGCLFHTVQKDFXXXXXXXXXXXXXXDS 65
           +G IV+ LF    P T  NF++L K    + Y G  FH V  DF                
Sbjct: 20  IGRIVIGLFGKTVPKTATNFIELAKKPKGEGYPGSKFHRVIADFMIQGGDFTRGDGTGG- 78
Query: 66  VYKFLYGEQARFFGDEIRVDLKHAKTGTVAMASAGENLNASQFYMTLRDNLDYLDEKHTI 125
             + +YGE+   F DE    LKH   G ++MA+AG + N SQF++T      +LD +H +
Sbjct: 79  --RSIYGEK---FADE-NFKLKHYGAGWLSMANAGADTNGSQFFITTVKT-PWLDGRHVV 131
Query: 126 FGEVAEGLETLSRINESFVDEKNRPYKNIRI 156
           FG++ EG++ + +I ++     +RP +++ I
Sbjct: 132 FGKILEGMDVVRKIEQTEKLPGDRPKQDVII 162

>pdb|1C5F|A Chain A, Crystal Structure Of The Cyclophilin-Like Domain From Brugia Malayi Complexed With Cyclosporin A Length = 177

Iteration: 1
 Score = 68.6 bits (166), Expect = 1e-11,   Method: Composition-based stats.
 Identities = 51/159 (32%), Positives = 74/159 (46%), Gaps = 21/159 (13%)
Query: 10  GDIVVDLFVDKCPLTTKNFLKLC-----------KIKYYNGCLFHTVQKDFXXXXXX-XX 57
           G IV++L+ D  P T  NFL LC           K  +Y G  FH V K+F         
Sbjct: 21  GRIVMELYNDIAPRTCNNFLMLCTGMAGTGKISGKPLHYKGSTFHRVIKNFMIQGGDFTK 80
Query: 58  XXXXXXDSVYKFLYGEQARFFGDEIRVDLKHAKTGTVAMASAGENLNASQFYMTLRDNLD 117
                 +S+Y          F DE  V +KH +   V+MA+ G N N SQF++T      
Sbjct: 81  GDGTGGESIY-------GGMFDDEEFV-MKHDEPFVVSMANKGPNTNGSQFFITTTP-AP 131
Query: 118 YLDEKHTIFGEVAEGLETLSRINESFVDEKNRPYKNIRI 156
           +L+  H +FG+V  G E +++I     + KNRP  ++ I
Sbjct: 132 HLNNIHVVFGKVVSGQEVVTKIEYLKTNSKNRPLADVVI 170

>pdb|1XO7|A Chain A, Crystal Structure Of Cyclophilin From Trypanosoma Cruzi Length = 166

Iteration: 1
 Score = 67.8 bits (164), Expect = 2e-11,   Method: Composition-based stats.
 Identities = 47/157 (29%), Positives = 80/157 (50%), Gaps = 12/157 (7%)
Query: 9   LGDIVVDLFVDKCPLTTKNFLKLCKIKY---YNGCLFHTVQKDFXXXXXXXXXXXXXXDS 65
           +G +V+ LF +  P T +NF +L   +    Y G +FH V ++F                
Sbjct: 19  VGRVVIGLFGNDVPKTVENFKQLASGENGFGYKGSIFHRVIRNFMIQGGDFTNFDGTGG- 77
Query: 66  VYKFLYGEQARFFGDEIRVDLKHAKTGTVAMASAGENLNASQFYMTLRDNLDYLDEKHTI 125
             K +YG   RF  D+  + +KH   G V+MA+AG N N SQF++T      +LD +H +
Sbjct: 78  --KSIYG--TRF--DDENLKIKHF-VGAVSMANAGPNSNGSQFFVTTAPT-PWLDGRHVV 129
Query: 126 FGEVAEGLETLSRINESFVDEKNRPYKNIRIKHTYIL 162
           FG+V EG++ + ++  +     ++P K ++I    +L
Sbjct: 130 FGKVVEGMDVVKKVENTKTGLNDKPKKAVKINDCGVL 166

>pdb|1QOI|A Chain A, U4U6 SNRNP-Specific Cyclophilin Snucyp-20 Length = 177

Iteration: 1
 Score = 67.8 bits (164), Expect = 2e-11,   Method: Composition-based stats.
 Identities = 45/151 (29%), Positives = 72/151 (47%), Gaps = 18/151 (11%)
Query: 9   LGDIVVDLFVDKCPLTTKNFLKLCKIKY--------YNGCLFHTVQKDFXXXXXX-XXXX 59
           +G + ++LF D  P T +NF + C  ++        Y G  FH V KDF           
Sbjct: 24  VGRMKIELFADVVPKTAENFRQFCTGEFRKDGVPIGYKGSTFHRVIKDFMIQGGDFVNGD 83
Query: 60  XXXXDSVYKFLYGEQARFFGDEIRVDLKHAKTGTVAMASAGENLNASQFYMTLRDNLDYL 119
                S+Y+   G     F DE    L+H+  G ++MA++G + N  QF++T     D+L
Sbjct: 84  GTGVASIYR---GP----FADE-NFKLRHSAPGLLSMANSGPSTNGCQFFITC-SKCDWL 134
Query: 120 DEKHTIFGEVAEGLETLSRINESFVDEKNRP 150
           D KH +FG++ +GL  + +I        N+P
Sbjct: 135 DGKHVVFGKIIDGLLVMRKIENVPTGPNNKP 165

>pdb|2R99|A Chain A, Crystal Structure Of Cyclophilin Abh-Like Domain Of Human Peptidylprolyl Isomerase E Isoform 1 Length = 173

Iteration: 1
 Score = 67.4 bits (163), Expect = 2e-11,   Method: Composition-based stats.
 Identities = 51/150 (34%), Positives = 76/150 (50%), Gaps = 12/150 (8%)
Query: 10  GDIVVDLFVDKCPLTTKNFLKLCKIKY---YNGCLFHTVQKDFXXXXXXXXXXXXXXDSV 66
           G I + L  D  P+T +NF  LC  +    + G  FH +   F                 
Sbjct: 26  GRIQMLLRSDVVPMTAENFRCLCTHEKGFGFKGSSFHRIIPQFMCQGGDFTNHNGTGG-- 83
Query: 67  YKFLYGEQARFFGDEIRVDLKHAKTGTVAMASAGENLNASQFYMTLRDNLDYLDEKHTIF 126
            K +YG++   F DE  + LKH   G ++MA++G N N SQF++T  D  D+LD KH +F
Sbjct: 84  -KSIYGKK---FDDENFI-LKHTGPGLLSMANSGPNTNGSQFFLTC-DKTDWLDGKHVVF 137
Query: 127 GEVAEGLETLSRINESFVDEKNRPYKNIRI 156
           GEV EGL+ L +I E+   +  +P + + I
Sbjct: 138 GEVTEGLDVLRQI-EAQGSKDGKPKQKVII 166

>pdb|1ZMF|A Chain A, C Domain Of Human Cyclophilin-33(Hcyp33) Length = 165

Iteration: 1
 Score = 67.4 bits (163), Expect = 2e-11,   Method: Composition-based stats.
 Identities = 51/150 (34%), Positives = 76/150 (50%), Gaps = 12/150 (8%)
Query: 10  GDIVVDLFVDKCPLTTKNFLKLCKIKY---YNGCLFHTVQKDFXXXXXXXXXXXXXXDSV 66
           G I + L  D  P+T +NF  LC  +    + G  FH +   F                 
Sbjct: 18  GRIQMLLRSDVVPMTAENFRCLCTHEKGFGFKGSSFHRIIPQFMCQGGDFTNHNGTGG-- 75
Query: 67  YKFLYGEQARFFGDEIRVDLKHAKTGTVAMASAGENLNASQFYMTLRDNLDYLDEKHTIF 126
            K +YG++   F DE  + LKH   G ++MA++G N N SQF++T  D  D+LD KH +F
Sbjct: 76  -KSIYGKK---FDDENFI-LKHTGPGLLSMANSGPNTNGSQFFLTC-DKTDWLDGKHVVF 129
Query: 127 GEVAEGLETLSRINESFVDEKNRPYKNIRI 156
           GEV EGL+ L +I E+   +  +P + + I
Sbjct: 130 GEVTEGLDVLRQI-EAQGSKDGKPKQKVII 158

>pdb|3K0R|A Chain A, Cryogenic Structure Of Cypa Mutant Arg55lys Length = 165

Iteration: 1
 Score = 67.4 bits (163), Expect = 2e-11,   Method: Composition-based stats.
 Identities = 53/158 (33%), Positives = 73/158 (46%), Gaps = 12/158 (7%)
Query: 9   LGDIVVDLFVDKCPLTTKNFLKLC---KIKYYNGCLFHTVQKDFXXXXXXXXXXXXXXDS 65
           LG +  +LF DK P T +NF  L    K   Y G  FH +   F                
Sbjct: 17  LGRVSFELFADKVPKTAENFRALSTGEKGFGYKGSCFHKIIPGFMCQGGDFTRHNGTGG- 75
Query: 66  VYKFLYGEQARFFGDEIRVDLKHAKTGTVAMASAGENLNASQFYMTLRDNLDYLDEKHTI 125
             K +YGE+   F DE  + LKH   G ++MA+AG N N SQF++      ++LD KH +
Sbjct: 76  --KSIYGEK---FEDENFI-LKHTGPGILSMANAGPNTNGSQFFICTAKT-EWLDGKHVV 128
Query: 126 FGEVAEGLETLSRINESFVDEKNRPYKNIRIKHTYILE 163
           FG+V EG+  +  + E F     +  K I I     LE
Sbjct: 129 FGKVKEGMNIVEAM-ERFGSRNGKTSKKITIADCGQLE 165

>pdb|2XGY|B Chain B, Complex Of Rabbit Endogenous Lentivirus (Relik)capsid With Cyclophilin A Length = 173

Iteration: 1
 Score = 67.4 bits (163), Expect = 2e-11,   Method: Composition-based stats.
 Identities = 53/158 (33%), Positives = 73/158 (46%), Gaps = 12/158 (7%)
Query: 9   LGDIVVDLFVDKCPLTTKNFLKLC---KIKYYNGCLFHTVQKDFXXXXXXXXXXXXXXDS 65
           LG +  +LF DK P T +NF  L    K   Y G  FH +   F                
Sbjct: 25  LGRVSFELFADKVPKTAENFRALSTGEKGFGYKGSCFHRIIPGFMCQGGDFTRHNGTGG- 83
Query: 66  VYKFLYGEQARFFGDEIRVDLKHAKTGTVAMASAGENLNASQFYMTLRDNLDYLDEKHTI 125
             K +YGE+   F DE  + LKH   G ++MA+AG N N SQF++      ++LD KH +
Sbjct: 84  --KSIYGEK---FEDENFI-LKHTGPGILSMANAGPNTNGSQFFICTAKT-EWLDGKHVV 136
Query: 126 FGEVAEGLETLSRINESFVDEKNRPYKNIRIKHTYILE 163
           FG+V EG+  +  + E F     +  K I I     LE
Sbjct: 137 FGKVKEGMNIVEAM-ERFGSRNGKTSKKITIADCGQLE 173

>pdb|2WLW|A Chain A, Structure Of The N-Terminal Capsid Domain Of Hiv-2 Length = 165

Iteration: 1
 Score = 67.0 bits (162), Expect = 3e-11,   Method: Composition-based stats.
 Identities = 53/158 (33%), Positives = 73/158 (46%), Gaps = 12/158 (7%)
Query: 9   LGDIVVDLFVDKCPLTTKNFLKLC---KIKYYNGCLFHTVQKDFXXXXXXXXXXXXXXDS 65
           LG +  +LF DK P T +NF  L    K   Y G  FH +   F                
Sbjct: 17  LGRVSFELFADKVPKTAENFRALSTGEKGFGYKGSCFHRIIPGFMCQGGNFTHHNGTGG- 75
Query: 66  VYKFLYGEQARFFGDEIRVDLKHAKTGTVAMASAGENLNASQFYMTLRDNLDYLDEKHTI 125
             K +YGE+   F DE  + LKH   G ++MA+AG N N SQF++      ++LD KH +
Sbjct: 76  --KSIYGEK---FEDENFI-LKHTGPGILSMANAGPNTNGSQFFICTAKT-EWLDGKHVV 128
Query: 126 FGEVAEGLETLSRINESFVDEKNRPYKNIRIKHTYILE 163
           FG+V EG+  +  + E F     +  K I I     LE
Sbjct: 129 FGKVKEGMNIVEAM-ERFGSRNGKTSKKITIADCGQLE 165

>pdb|1M9E|A Chain A, X-Ray Crystal Structure Of Cyclophilin AHIV-1 Ca N- Terminal Domain (1-146) M-Type H87a Complex. Length = 164

Iteration: 1
 Score = 67.0 bits (162), Expect = 3e-11,   Method: Composition-based stats.
 Identities = 51/151 (33%), Positives = 71/151 (47%), Gaps = 12/151 (7%)
Query: 9   LGDIVVDLFVDKCPLTTKNFLKLC---KIKYYNGCLFHTVQKDFXXXXXXXXXXXXXXDS 65
           LG +  +LF DK P T +NF  L    K   Y G  FH +   F                
Sbjct: 17  LGRVSFELFADKVPKTAENFRALSTGEKGFGYKGSCFHRIIPGFMCQGGDFTRHNGTGG- 75
Query: 66  VYKFLYGEQARFFGDEIRVDLKHAKTGTVAMASAGENLNASQFYMTLRDNLDYLDEKHTI 125
             K +YGE+   F DE  + LKH   G ++MA+AG N N SQF++      ++LD KH +
Sbjct: 76  --KSIYGEK---FEDENFI-LKHTGPGILSMANAGPNTNGSQFFICTAKT-EWLDGKHVV 128
Query: 126 FGEVAEGLETLSRINESFVDEKNRPYKNIRI 156
           FG+V EG+  +  + E F     +  K I I
Sbjct: 129 FGKVKEGMNIVEAM-ERFGSRNGKTSKKITI 158

>pdb|2RMA|A Chain A, Crystal Structures Of Cyclophilin A Complexed With Cyclosporin A And N-Methyl-4-[(E)-2-Butenyl]-4,4-Dimethylthreonine Cyclosporin A Length = 165

Iteration: 1
 Score = 66.6 bits (161), Expect = 3e-11,   Method: Composition-based stats.
 Identities = 53/158 (33%), Positives = 73/158 (46%), Gaps = 12/158 (7%)
Query: 9   LGDIVVDLFVDKCPLTTKNFLKLC---KIKYYNGCLFHTVQKDFXXXXXXXXXXXXXXDS 65
           LG +  +LF DK P T +NF  L    K   Y G  FH +   F                
Sbjct: 17  LGRVSFELFADKVPKTAENFRALSTGEKGFGYKGSCFHRIIPGFMCQGGDFTRHNGTGG- 75
Query: 66  VYKFLYGEQARFFGDEIRVDLKHAKTGTVAMASAGENLNASQFYMTLRDNLDYLDEKHTI 125
             K +YGE+   F DE  + LKH   G ++MA+AG N N SQF++      ++LD KH +
Sbjct: 76  --KSIYGEK---FEDENFI-LKHTGPGILSMANAGPNTNGSQFFICTAKT-EWLDGKHVV 128
Query: 126 FGEVAEGLETLSRINESFVDEKNRPYKNIRIKHTYILE 163
           FG+V EG+  +  + E F     +  K I I     LE
Sbjct: 129 FGKVKEGMNIVEAM-ERFGSRNGKTSKKITIADCGQLE 165

>pdb|3RDD|A Chain A, Human Cyclophilin A Complexed With An Inhibitor Length = 184

Iteration: 1
 Score = 66.6 bits (161), Expect = 4e-11,   Method: Composition-based stats.
 Identities = 53/158 (33%), Positives = 73/158 (46%), Gaps = 12/158 (7%)
Query: 9   LGDIVVDLFVDKCPLTTKNFLKLC---KIKYYNGCLFHTVQKDFXXXXXXXXXXXXXXDS 65
           LG +  +LF DK P T +NF  L    K   Y G  FH +   F                
Sbjct: 36  LGRVSFELFADKVPKTAENFRALSTGEKGFGYKGSCFHRIIPGFMCQGGDFTRHNGTGG- 94
Query: 66  VYKFLYGEQARFFGDEIRVDLKHAKTGTVAMASAGENLNASQFYMTLRDNLDYLDEKHTI 125
             K +YGE+   F DE  + LKH   G ++MA+AG N N SQF++      ++LD KH +
Sbjct: 95  --KSIYGEK---FEDENFI-LKHTGPGILSMANAGPNTNGSQFFICTAKT-EWLDGKHVV 147
Query: 126 FGEVAEGLETLSRINESFVDEKNRPYKNIRIKHTYILE 163
           FG+V EG+  +  + E F     +  K I I     LE
Sbjct: 148 FGKVKEGMNIVEAM-ERFGSRNGKTSKKITIADCGQLE 184

>pdb|1BCK|A Chain A, Human Cyclophilin A Complexed With 2-Thr Cyclosporin Length = 165

Iteration: 1
 Score = 66.6 bits (161), Expect = 4e-11,   Method: Composition-based stats.
 Identities = 53/158 (33%), Positives = 73/158 (46%), Gaps = 12/158 (7%)
Query: 9   LGDIVVDLFVDKCPLTTKNFLKLC---KIKYYNGCLFHTVQKDFXXXXXXXXXXXXXXDS 65
           LG +  +LF DK P T +NF  L    K   Y G  FH +   F                
Sbjct: 17  LGRVSFELFADKVPKTAENFRALSTGEKGFGYKGSCFHRIIPGFMCQGGDFTRHNGTGG- 75
Query: 66  VYKFLYGEQARFFGDEIRVDLKHAKTGTVAMASAGENLNASQFYMTLRDNLDYLDEKHTI 125
             K +YGE+   F DE  + LKH   G ++MA+AG N N SQF++      ++LD KH +
Sbjct: 76  --KSIYGEK---FEDENFI-LKHTGPGILSMANAGPNTNGSQFFICTAKT-EWLDGKHVV 128
Query: 126 FGEVAEGLETLSRINESFVDEKNRPYKNIRIKHTYILE 163
           FG+V EG+  +  + E F     +  K I I     LE
Sbjct: 129 FGKVKEGMNIVEAM-ERFGSRNGKTSKKITIADCGQLE 165

>pdb|5CYH|A Chain A, Cyclophilin A Complexed With Dipeptide Gly-Pro Length = 164

Iteration: 1
 Score = 66.6 bits (161), Expect = 4e-11,   Method: Composition-based stats.
 Identities = 53/158 (33%), Positives = 73/158 (46%), Gaps = 12/158 (7%)
Query: 9   LGDIVVDLFVDKCPLTTKNFLKLC---KIKYYNGCLFHTVQKDFXXXXXXXXXXXXXXDS 65
           LG +  +LF DK P T +NF  L    K   Y G  FH +   F                
Sbjct: 16  LGRVSFELFADKVPKTAENFRALSTGEKGFGYKGSCFHRIIPGFMCQGGDFTRHNGTGG- 74
Query: 66  VYKFLYGEQARFFGDEIRVDLKHAKTGTVAMASAGENLNASQFYMTLRDNLDYLDEKHTI 125
             K +YGE+   F DE  + LKH   G ++MA+AG N N SQF++      ++LD KH +
Sbjct: 75  --KSIYGEK---FEDENFI-LKHTGPGILSMANAGPNTNGSQFFICTAKT-EWLDGKHVV 127
Query: 126 FGEVAEGLETLSRINESFVDEKNRPYKNIRIKHTYILE 163
           FG+V EG+  +  + E F     +  K I I     LE
Sbjct: 128 FGKVKEGMNIVEAM-ERFGSRNGKTSKKITIADCGQLE 164

>pdb|4DGD|A Chain A, Trimcyp Cyclophilin Domain From Macaca Mulatta: H70c Mutant Length = 165

Iteration: 1
 Score = 66.6 bits (161), Expect = 4e-11,   Method: Composition-based stats.
 Identities = 53/158 (33%), Positives = 73/158 (46%), Gaps = 12/158 (7%)
Query: 9   LGDIVVDLFVDKCPLTTKNFLKLC---KIKYYNGCLFHTVQKDFXXXXXXXXXXXXXXDS 65
           LG +  +LF DK P T +NF  L    K   Y G  FH +   F                
Sbjct: 17  LGRVSFELFADKVPKTAENFRALSTGEKGFGYKGSCFHRIIPGFMCQGGNFTHCNGTGG- 75
Query: 66  VYKFLYGEQARFFGDEIRVDLKHAKTGTVAMASAGENLNASQFYMTLRDNLDYLDEKHTI 125
             K +YGE+   F DE  + LKH   G ++MA+AG N N SQF++      ++LD KH +
Sbjct: 76  --KSIYGEK---FEDENFI-LKHTGPGILSMANAGPNTNGSQFFICTAKT-EWLDGKHVV 128
Query: 126 FGEVAEGLETLSRINESFVDEKNRPYKNIRIKHTYILE 163
           FG+V EG+  +  + E F     +  K I I     LE
Sbjct: 129 FGKVKEGMNIVEAM-ERFGSRNGKTSKKITIADCGQLE 165

>pdb|3K0O|A Chain A, Room Temperature Structure Of Cypa Mutant Ser99thr Length = 165

Iteration: 1
 Score = 66.6 bits (161), Expect = 4e-11,   Method: Composition-based stats.
 Identities = 53/158 (33%), Positives = 72/158 (45%), Gaps = 12/158 (7%)
Query: 9   LGDIVVDLFVDKCPLTTKNFLKLC---KIKYYNGCLFHTVQKDFXXXXXXXXXXXXXXDS 65
           LG +  +LF DK P T +NF  L    K   Y G  FH +   F                
Sbjct: 17  LGRVSFELFADKVPKTAENFRALSTGEKGFGYKGSCFHRIIPGFMCQGGDFTRHNGTGG- 75
Query: 66  VYKFLYGEQARFFGDEIRVDLKHAKTGTVAMASAGENLNASQFYMTLRDNLDYLDEKHTI 125
             K +YGE+   F DE  + LKH   G + MA+AG N N SQF++      ++LD KH +
Sbjct: 76  --KSIYGEK---FEDENFI-LKHTGPGILTMANAGPNTNGSQFFICTAKT-EWLDGKHVV 128
Query: 126 FGEVAEGLETLSRINESFVDEKNRPYKNIRIKHTYILE 163
           FG+V EG+  +  + E F     +  K I I     LE
Sbjct: 129 FGKVKEGMNIVEAM-ERFGSRNGKTSKKITIADCGQLE 165

>pdb|2ALF|A Chain A, Crystal Structure Of Human Cypa Mutant K131a Length = 164

Iteration: 1
 Score = 65.5 bits (158), Expect = 9e-11,   Method: Composition-based stats.
 Identities = 53/158 (33%), Positives = 71/158 (44%), Gaps = 12/158 (7%)
Query: 9   LGDIVVDLFVDKCPLTTKNFLKLC---KIKYYNGCLFHTVQKDFXXXXXXXXXXXXXXDS 65
           LG +  +LF DK P T +NF  L    K   Y G  FH +   F                
Sbjct: 16  LGRVSFELFADKVPKTAENFRALSTGEKGFGYKGSCFHRIIPGFMCQGGDFTRHNGTGG- 74
Query: 66  VYKFLYGEQARFFGDEIRVDLKHAKTGTVAMASAGENLNASQFYMTLRDNLDYLDEKHTI 125
             K +YGE+   F DE  + LKH   G ++MA+AG N N SQF++       +LD KH +
Sbjct: 75  --KSIYGEK---FEDENFI-LKHTGPGILSMANAGPNTNGSQFFICTAKT-KWLDGKHVV 127
Query: 126 FGEVAEGLETLSRINESFVDEKNRPYKNIRIKHTYILE 163
           FG V EG+  +  + E F     +  K I I     LE
Sbjct: 128 FGAVKEGMNIVEAM-ERFGSRNGKTSKKITIADCGQLE 164

>pdb|2X83|B Chain B, Evolutionary Basis Of Hiv Restriction By The Antiretroviral Trimcyp Length = 163

Iteration: 1
 Score = 65.1 bits (157), Expect = 1e-10,   Method: Composition-based stats.
 Identities = 50/151 (33%), Positives = 71/151 (47%), Gaps = 12/151 (7%)
Query: 9   LGDIVVDLFVDKCPLTTKNFLKLC---KIKYYNGCLFHTVQKDFXXXXXXXXXXXXXXDS 65
           LG +  +LF DK P T +NF  L    K   Y G  FH +   F                
Sbjct: 16  LGRVSFELFADKVPKTAENFRALSTGEKGFGYKGSCFHRIIPGFMCQGGDFTHHNGTGG- 74
Query: 66  VYKFLYGEQARFFGDEIRVDLKHAKTGTVAMASAGENLNASQFYMTLRDNLDYLDEKHTI 125
             K +YGE+   F DE  + LKH   G ++MA+AG N N SQF++      ++LD KH +
Sbjct: 75  --KSIYGEK---FEDENFI-LKHTGPGILSMANAGPNTNGSQFFICTAKT-EWLDGKHVV 127
Query: 126 FGEVAEGLETLSRINESFVDEKNRPYKNIRI 156
           FG+V EG+  +  + + F     +  K I I
Sbjct: 128 FGKVKEGMNIVEAM-KRFGSRNGKTSKKITI 157

>pdb|1QNG|A Chain A, Plasmodium Falciparum Cyclophilin Complexed With Cyclosporin A Length = 170

Iteration: 1
 Score = 65.1 bits (157), Expect = 1e-10,   Method: Composition-based stats.
 Identities = 45/145 (31%), Positives = 71/145 (48%), Gaps = 19/145 (13%)
Query: 7   TSLGDIVVDLFVDKCPLTTKNFLKLC---------KIKYYNGCLFHTVQKDFX-XXXXXX 56
           ++ G I+ +LF D  P T +NF  LC         K  +Y   +FH +   F        
Sbjct: 15  SNAGRIIFELFSDITPRTCENFRALCTGEKIGSRGKNLHYKNSIFHRIIPQFMCQGGDIT 74
Query: 57  XXXXXXXDSVYKFLYGEQARFFGDEIRVDLKHAKTGTVAMASAGENLNASQFYMTLRDNL 116
                  +S+Y        R F DE   ++KH + G ++MA+AG N N+SQF++TL    
Sbjct: 75  NGNGSGGESIY-------GRSFTDE-NFNMKHDQPGLLSMANAGPNTNSSQFFITLVP-C 125
Query: 117 DYLDEKHTIFGEVAEGLETLSRINE 141
            +LD KH +FG+V EG+  +  + +
Sbjct: 126 PWLDGKHVVFGKVIEGMNVVREMEK 150

>pdb|2PLU|A Chain A, Crystal Structure Of Cryptosporidium Parvum Cyclophilin Type Peptidyl-Prolyl Cis-Trans Isomerase Cgd2_4120 Length = 186

Iteration: 1
 Score = 65.1 bits (157), Expect = 1e-10,   Method: Composition-based stats.
 Identities = 51/160 (31%), Positives = 73/160 (45%), Gaps = 19/160 (11%)
Query: 7   TSLGDIVVDLFVDKCPLTTKNFLKLC----------KIKYYNGCLFHTVQKDFXXXXXXX 56
           T  G I ++LF DK P+T +NF  LC          K   Y G  FH +   F       
Sbjct: 31  TPAGRITMELFADKVPITAENFRALCTGEKGMGQSGKPLCYTGSFFHRIIPQFMIQGGDF 90
Query: 57  XXXXXXXDSVYKFLYGEQARFFGDEIRVDLKHAKTGTVAMASAGENLNASQFYMTLRDNL 116
                      + +YG +   F DE  V   H     ++MA+AG N N SQF++T     
Sbjct: 91  TRGDGTGG---ESIYGSK---FRDENFV-YTHDAPFLLSMANAGPNTNGSQFFITTVP-C 142
Query: 117 DYLDEKHTIFGEVAEGLETLSRINESFVDEKNRPYKNIRI 156
            +LD KH +FG+V EG+E +  I E    +  +P K++ I
Sbjct: 143 PWLDGKHVVFGKVLEGMEVVKSI-EKCGSQNGKPTKSVCI 181

>pdb|2X2C|K Chain K, Acetyl-Cypa:cyclosporine Complex Length = 165

Iteration: 1
 Score = 65.1 bits (157), Expect = 1e-10,   Method: Composition-based stats.
 Identities = 52/158 (32%), Positives = 72/158 (45%), Gaps = 12/158 (7%)
Query: 9   LGDIVVDLFVDKCPLTTKNFLKLC---KIKYYNGCLFHTVQKDFXXXXXXXXXXXXXXDS 65
           LG +  +LF DK P T +NF  L    K   Y G  FH +   F                
Sbjct: 17  LGRVSFELFADKVPKTAENFRALSTGEKGFGYKGSCFHRIIPGFMCQGGDFTRHNGTGG- 75
Query: 66  VYKFLYGEQARFFGDEIRVDLKHAKTGTVAMASAGENLNASQFYMTLRDNLDYLDEKHTI 125
             K +YGE+   F DE  + LKH   G ++MA+AG N N SQF++      ++LD  H +
Sbjct: 76  --KSIYGEK---FEDENFI-LKHTGPGILSMANAGPNTNGSQFFICTAKT-EWLDGXHVV 128
Query: 126 FGEVAEGLETLSRINESFVDEKNRPYKNIRIKHTYILE 163
           FG+V EG+  +  + E F     +  K I I     LE
Sbjct: 129 FGKVKEGMNIVEAM-ERFGSRNGKTSKKITIADCGQLE 165

>pdb|1DYW|A Chain A, Biochemical And Structural Characterization Of A Divergent Loop Cyclophilin From Caenorhabditis Elegans Length = 173

Iteration: 1
 Score = 64.7 bits (156), Expect = 1e-10,   Method: Composition-based stats.
 Identities = 49/157 (31%), Positives = 73/157 (46%), Gaps = 19/157 (12%)
Query: 10  GDIVVDLFVDKCPLTTKNFLKLC----------KIKYYNGCLFHTVQKDFXXXXXXXXXX 59
           G IV++L+ D  P T  NF  LC          K  ++ G  FH +  +F          
Sbjct: 18  GRIVMELYDDVVPKTAGNFRALCTGENGIGKSGKPLHFKGSKFHRIIPNFMIQGGDFTRG 77
Query: 60  XXXXDSVYKFLYGEQARFFGDEIRVDLKHAKTGTVAMASAGENLNASQFYMTLRDNLDYL 119
                   + +YGE+   F DE     KH   G ++MA+AG N N SQF++      ++L
Sbjct: 78  NGTGG---ESIYGEK---FPDE-NFKEKHTGPGVLSMANAGPNTNGSQFFLCTVKT-EWL 129
Query: 120 DEKHTIFGEVAEGLETLSRINESFVDEKNRPYKNIRI 156
           D KH +FG V EGL+ +  + ES   +  +P K+  I
Sbjct: 130 DGKHVVFGRVVEGLDVVKAV-ESNGSQSGKPVKDCMI 165

>pdb|2X2A|A Chain A, Free Acetyl-Cypa Trigonal Form Length = 165

Iteration: 1
 Score = 63.9 bits (154), Expect = 2e-10,   Method: Composition-based stats.
 Identities = 52/158 (32%), Positives = 71/158 (44%), Gaps = 12/158 (7%)
Query: 9   LGDIVVDLFVDKCPLTTKNFLKLC---KIKYYNGCLFHTVQKDFXXXXXXXXXXXXXXDS 65
           LG +  +LF DK P T +NF  L    K   Y G  FH +   F                
Sbjct: 17  LGRVSFELFADKVPKTAENFRALSTGEKGFGYKGSCFHRIIPGFMCQGGDFTRHNGTGG- 75
Query: 66  VYKFLYGEQARFFGDEIRVDLKHAKTGTVAMASAGENLNASQFYMTLRDNLDYLDEKHTI 125
             K +YGE+   F DE  + LKH   G ++MA+AG N N SQF++       +LD  H +
Sbjct: 76  --KSIYGEK---FEDENFI-LKHTGPGILSMANAGPNTNGSQFFICTAKT-KWLDGXHVV 128
Query: 126 FGEVAEGLETLSRINESFVDEKNRPYKNIRIKHTYILE 163
           FG+V EG+  +  + E F     +  K I I     LE
Sbjct: 129 FGKVKEGMNIVEAM-ERFGSRNGKTSKKITIADCGQLE 165

>pdb|1QNH|A Chain A, Plasmodium Falciparum Cyclophilin (Double Mutant) Complexed With Cyclosporin A Length = 170

Iteration: 1
 Score = 63.5 bits (153), Expect = 3e-10,   Method: Composition-based stats.
 Identities = 45/145 (31%), Positives = 70/145 (48%), Gaps = 19/145 (13%)
Query: 7   TSLGDIVVDLFVDKCPLTTKNFLKLC---------KIKYYNGCLFHTVQKDFX-XXXXXX 56
           ++ G I+ +LF D  P T +NF  LC         K  +Y   +FH +   F        
Sbjct: 15  SNAGRIIFELFSDITPRTCENFRALCTGEKIGSRGKNLHYKNSIFHRIIPQFMCQGGDIT 74
Query: 57  XXXXXXXDSVYKFLYGEQARFFGDEIRVDLKHAKTGTVAMASAGENLNASQFYMTLRDNL 116
                  +S+Y        R F DE   ++KH + G ++MA+AG N N+SQF +TL    
Sbjct: 75  NGNGSGGESIY-------GRSFTDE-NFNMKHDQPGLLSMANAGPNTNSSQFLITLVP-C 125
Query: 117 DYLDEKHTIFGEVAEGLETLSRINE 141
            +LD KH +FG+V EG+  +  + +
Sbjct: 126 PWLDGKHVVFGKVIEGMNVVREMEK 150

>pdb|2X25|B Chain B, Free Acetyl-Cypa Orthorhombic Form Length = 169

Iteration: 1
 Score = 63.2 bits (152), Expect = 4e-10,   Method: Composition-based stats.
 Identities = 52/158 (32%), Positives = 71/158 (44%), Gaps = 12/158 (7%)
Query: 9   LGDIVVDLFVDKCPLTTKNFLKLC---KIKYYNGCLFHTVQKDFXXXXXXXXXXXXXXDS 65
           LG +  +LF DK P T +NF  L    K   Y G  FH +   F                
Sbjct: 21  LGRVSFELFADKVPKTAENFRALSTGEKGFGYKGSCFHRIIPGFMCQGGDFTRHNGTGG- 79
Query: 66  VYKFLYGEQARFFGDEIRVDLKHAKTGTVAMASAGENLNASQFYMTLRDNLDYLDEKHTI 125
             K +YGE+   F DE  + LKH   G ++MA+AG N N SQF++       +LD  H +
Sbjct: 80  --KSIYGEK---FEDENFI-LKHTGPGILSMANAGPNTNGSQFFICTAKT-KWLDGXHVV 132
Query: 126 FGEVAEGLETLSRINESFVDEKNRPYKNIRIKHTYILE 163
           FG+V EG+  +  + E F     +  K I I     LE
Sbjct: 133 FGKVKEGMNIVEAM-ERFGSRNGKTSKKITIADCGQLE 169

>pdb|2C3B|A Chain A, The Crystal Structure Of Aspergillus Fumigatus Cyclophilin Reveals 3d Domain Swapping Of A Central Element Length = 172

Iteration: 1
 Score = 62.4 bits (150), Expect = 7e-10,   Method: Composition-based stats.
 Identities = 46/128 (35%), Positives = 64/128 (50%), Gaps = 11/128 (8%)
Query: 7   TSLGDIVVDLFVDKCPLTTKNFLKLCKI---KYYNGCLFHTVQKDFXXXXXXXXXXXXXX 63
           T +G IV +LF    P T KNF +LCK    + Y    FH +  +F              
Sbjct: 19  TKVGRIVFNLFDKDVPKTAKNFRELCKRPAGEGYRESTFHRIIPNFMIQGGDFTRGNGTG 78
Query: 64  DSVYKFLYGEQARFFGDEIRVDLKHAKTGTVAMASAGENLNASQFYMTLRDNLDYLDEKH 123
               + +YG++   F DE     KH K G ++MA+AG N N SQF++T      +LD KH
Sbjct: 79  G---RSIYGDK---FADE-NFSRKHDKKGILSMANAGPNTNGSQFFITTAVT-SWLDGKH 130
Query: 124 TIFGEVAE 131
            +FGEVA+
Sbjct: 131 VVFGEVAD 138

>pdb|3UCH|A Chain A, Crystal Structure Of A Hypotherical Peptidyl-Prolyl Cis-Trans Isomerase E (Ppie) From Homo Sapiens At 2.50 A Resolution Length = 174

Iteration: 1
 Score = 61.6 bits (148), Expect = 1e-09,   Method: Composition-based stats.
 Identities = 48/133 (36%), Positives = 66/133 (49%), Gaps = 11/133 (8%)
Query: 10  GDIVVDLFVDKCPLTTKNFLKLCKIKY---YNGCLFHTVQKDFXXXXXXXXXXXXXXDSV 66
           G I   L  D  P T +NF  LC  +    + G  FH +   F                 
Sbjct: 27  GRIQXLLRSDVVPXTAENFRCLCTHEKGFGFKGSSFHRIIPQFXCQGGDFTNHNGTGG-- 84
Query: 67  YKFLYGEQARFFGDEIRVDLKHAKTGTVAMASAGENLNASQFYMTLRDNLDYLDEKHTIF 126
            K +YG++   F DE  + LKH   G ++ A++G N N SQF++T  D  D+LD KH +F
Sbjct: 85  -KSIYGKK---FDDENFI-LKHTGPGLLSXANSGPNTNGSQFFLTC-DKTDWLDGKHVVF 138
Query: 127 GEVAEGLETLSRI 139
           GEV EGL+ L +I
Sbjct: 139 GEVTEGLDVLRQI 151

>pdb|1AWS|A Chain A, Secypa Complexed With Hagpia (Pseudo-Symmetric Monomer) Length = 164

Iteration: 1
 Score = 61.2 bits (147), Expect = 2e-09,   Method: Composition-based stats.
 Identities = 53/158 (33%), Positives = 71/158 (44%), Gaps = 12/158 (7%)
Query: 9   LGDIVVDLFVDKCPLTTKNFLKLC---KIKYYNGCLFHTVQKDFXXXXXXXXXXXXXXDS 65
           LG +  +LF DK P T +NF  L    K   Y G  FH +   F                
Sbjct: 16  LGRVSFELFADKVPKTAENFRALSTGEKGFGYKGSCFHRIIPGFXCQGGDFTRHNGTGG- 74
Query: 66  VYKFLYGEQARFFGDEIRVDLKHAKTGTVAMASAGENLNASQFYMTLRDNLDYLDEKHTI 125
             K +YGE+   F DE  + LKH   G ++ A+AG N N SQF++      ++LD KH +
Sbjct: 75  --KSIYGEK---FEDENFI-LKHTGPGILSXANAGPNTNGSQFFICTAKT-EWLDGKHVV 127
Query: 126 FGEVAEGLETLSRINESFVDEKNRPYKNIRIKHTYILE 163
           FG+V EG   +    E F     +  K I I     LE
Sbjct: 128 FGKVKEG-XNIVEAXERFGSRNGKTSKKITIADCGQLE 164

>pdb|1IST|A Chain A, Crystal Structure Of Yeast Cyclophilin A, Cpr1 Length = 162

Iteration: 1
 Score = 60.5 bits (145), Expect = 2e-09,   Method: Composition-based stats.
 Identities = 45/134 (33%), Positives = 64/134 (47%), Gaps = 11/134 (8%)
Query: 9   LGDIVVDLFVDKCPLTTKNFLKLC---KIKYYNGCLFHTVQKDFXXXXXXXXXXXXXXDS 65
           +G +V  L+ D  P T +NF  LC   K   Y G  FH V  DF                
Sbjct: 15  IGRVVFKLYNDIVPKTAENFRALCTGEKGFGYAGSPFHRVIPDFMLQGGDFTAGNGTGG- 73
Query: 66  VYKFLYGEQARFFGDEIRVDLKHAKTGTVAMASAGENLNASQFYMTLRDNLDYLDEKHTI 125
             K +YG +   F DE      H + G ++MA+AG N N SQF++T      +LD KH +
Sbjct: 74  --KSIYGGK---FPDE-NFKKHHDRPGLLSMANAGPNTNGSQFFITTVP-CPWLDGKHVV 126
Query: 126 FGEVAEGLETLSRI 139
           FGEV +G + + ++
Sbjct: 127 FGEVVDGYDIVKKV 140

>pdb|1W74|A Chain A, X-Ray Structure Of Peptidyl-Prolyl Cis-Trans Isomerase A, Ppia, Rv0009, From Mycobacterium Tuberculosis. Length = 191

Iteration: 1
 Score = 60.1 bits (144), Expect = 3e-09,   Method: Composition-based stats.
 Identities = 50/172 (29%), Positives = 76/172 (44%), Gaps = 28/172 (16%)
Query: 7   TSLGDIVVDLFVDKCPLTTKNFLKLCKIK---------------YYNGCLFHTVQKDFXX 51
           T+ GDI + LF +  P T  NF+ L +                 +Y+G +FH V + F  
Sbjct: 30  TNRGDIKIALFGNHAPKTVANFVGLAQGTKDYSTQNASGGPSGPFYDGAVFHRVIQGFMI 89
Query: 52  XXXXXXXXXXXXDSVYKFLYGEQARFFGDEIRVDLKHAKTGTVAMASAGENLNASQFYMT 111
                          YKF          DE   +L+  K   +AMA+AG   N SQF++T
Sbjct: 90  QGGDPTGTGRGGPG-YKF---------ADEFHPELQFDKPYLLAMANAGPGTNGSQFFIT 139
Query: 112 LRDNLDYLDEKHTIFGEV--AEGLETLSRINESFVDEKNRPYKNIRIKHTYI 161
           +     +L+ +HTIFGEV  AE    +  I+++  D  +RP   + I+   I
Sbjct: 140 V-GKTPHLNRRHTIFGEVIDAESQRVVEAISKTATDGNDRPTDPVVIESITI 190

>pdb|2CK1|A Chain A, The Structure Of Oxidised Cyclophilin A From S. Mansoni Length = 172

Iteration: 1
 Score = 60.1 bits (144), Expect = 4e-09,   Method: Composition-based stats.
 Identities = 44/133 (33%), Positives = 63/133 (47%), Gaps = 11/133 (8%)
Query: 10  GDIVVDLFVDKCPLTTKNFLKLCKIKY---YNGCLFHTVQKDFXXXXXXXXXXXXXXDSV 66
           G IV++L  D  P T +NF  LC  +    Y+ C FH V   F                 
Sbjct: 25  GRIVMELRSDIVPRTAENFRALCTGERGFGYHNCCFHRVIPQFMCQGGDFVKGDGTGG-- 82
Query: 67  YKFLYGEQARFFGDEIRVDLKHAKTGTVAMASAGENLNASQFYMTLRDNLDYLDEKHTIF 126
            K +YG   R F DE    L+H   G ++MA++G N N SQF++      D+LD KH +F
Sbjct: 83  -KSIYG---RKFDDE-NFQLRHEGFGVLSMANSGPNTNGSQFFIC-TTKCDWLDGKHVVF 136
Query: 127 GEVAEGLETLSRI 139
           G V +G   + ++
Sbjct: 137 GRVVDGQNVVKKM 149

>pdb|2HQJ|A Chain A, Cyclophilin From Leishmania Major Length = 183

Iteration: 1
 Score = 59.7 bits (143), Expect = 5e-09,   Method: Composition-based stats.
 Identities = 42/141 (29%), Positives = 67/141 (47%), Gaps = 17/141 (12%)
Query: 10  GDIVVDLFVDKCPLTTKNFLKLC----------KIKYYNGCLFHTVQKDFXXXXXX-XXX 58
           G IV++L+ D  P T +NF  LC          K  +Y   +FH V  +F          
Sbjct: 22  GRIVMELYADTVPKTAENFRALCTGEKGKGRSGKPLHYKSSVFHRVIPNFMIQGGDFTRG 81
Query: 59  XXXXXDSVYKFLYGEQARFFGDEIRVDLKHAKTGTVAMASAGENLNASQFYMTLRDNLDY 118
                +S+Y   + +++ F G   R    H   G ++MA+AG N N SQF++       +
Sbjct: 82  NGTGGESIYGTTFRDES-FSGKAGR----HTGLGCLSMANAGPNTNGSQFFICTAAT-PW 135
Query: 119 LDEKHTIFGEVAEGLETLSRI 139
           LD KH +FG V +GL+ + ++
Sbjct: 136 LDGKHVVFGRVIDGLDVVKKV 156

>pdb|1Z81|A Chain A, Crystal Structure Of Cyclophilin From Plasmodium Yoelii Length = 229

Iteration: 1
 Score = 56.6 bits (135), Expect = 4e-08,   Method: Compositional matrix adjust.
 Identities = 40/131 (30%), Positives = 64/131 (48%), Gaps = 16/131 (12%)
Query: 9   LGDIVVDLFVDKCPLTTKNFLKLCKIKY--------YNGCLFHTVQKDFXXXXXXXXXXX 60
           LG    +LF +  P T++NF + C  +Y        Y   +FH V K+F           
Sbjct: 73  LGKFKFELFQNIVPKTSENFRQFCTGEYKVNNLPVGYKNTIFHRVIKEFMIQGGDFINHN 132
Query: 61  XXXDSVYKFLYGEQARFFGDEIRVDLKHAKTGTVAMASAGENLNASQFYMTLRDNLDYLD 120
                    +YGE+   F DE   D+KH K G ++MA++G N N  QF++T +   ++LD
Sbjct: 133 GSGSLS---IYGEK---FDDE-NFDIKHDKEGLLSMANSGPNTNGCQFFITTKK-CEWLD 184
Query: 121 EKHTIFGEVAE 131
            K+ +FG + +
Sbjct: 185 GKNVVFGRIID 195

>pdb|2K8G|A Chain A, Solution Structure Of Rrm2 Domain Of Pabp1 Length = 95

Iteration: 1
 Score = 53.1 bits (126), Expect = 4e-07,   Method: Compositional matrix adjust.
 Identities = 24/72 (33%), Positives = 44/72 (61%), Gaps = 2/72 (2%)
Query: 245 LFVCKLNPVTEDEDLHTIFSRFGTVVSAEIIRDFKTGDSLNYAFIEFENRQACERAYSKM 304
           +F+  L+   +++ L+  FS FG ++S +++ D     S  Y F+ FE ++A ERA  KM
Sbjct: 14  IFIKNLDKSIDNKALYDTFSAFGNILSCKVVCD--ENGSKGYGFVHFETQEAAERAIEKM 71
Query: 305 DNALIDDRRIHV 316
           +  L++DR++ V
Sbjct: 72  NGMLLNDRKVFV 83

>pdb|4F02|A Chain A, Crystal Structure Of The Pabp-Binding Site Of Eif4g In Complex With Rrm1-2 Of Pabp And Poly(A) Length = 213

Iteration: 1
 Score = 46.6 bits (109), Expect = 3e-05,   Method: Compositional matrix adjust.
 Identities = 25/80 (31%), Positives = 41/80 (51%)
Query: 241 PENVLFVCKLNPVTEDEDLHTIFSRFGTVVSAEIIRDFKTGDSLNYAFIEFENRQACERA 300
           P   L+V  L+P   +  L+  FS  G ++S  + RD  T  SL YA++ F+     ERA
Sbjct: 14  PMASLYVGDLHPDVTEAMLYEKFSPAGPILSIRVCRDMITRRSLGYAYVNFQQPADAERA 73
Query: 301 YSKMDNALIDDRRIHVDFSQ 320
              M+  +I  + + + +SQ
Sbjct: 74  LDTMNFDVIKGKPVRIMWSQ 93

>pdb|1CVJ|A Chain A, X-Ray Crystal Structure Of The Poly(A)-Binding Protein In Complex With Polyadenylate Rna Length = 190

Iteration: 1
 Score = 46.2 bits (108), Expect = 5e-05,   Method: Compositional matrix adjust.
 Identities = 25/80 (31%), Positives = 41/80 (51%)
Query: 241 PENVLFVCKLNPVTEDEDLHTIFSRFGTVVSAEIIRDFKTGDSLNYAFIEFENRQACERA 300
           P   L+V  L+P   +  L+  FS  G ++S  + RD  T  SL YA++ F+     ERA
Sbjct: 9   PMASLYVGDLHPDVTEAMLYEKFSPAGPILSIRVCRDMITRRSLGYAYVNFQQPADAERA 68
Query: 301 YSKMDNALIDDRRIHVDFSQ 320
              M+  +I  + + + +SQ
Sbjct: 69  LDTMNFDVIKGKPVRIMWSQ 88

>pdb|2KXN|B Chain B, Nmr Structure Of Human Tra2beta1 Rrm In Complex With Aagaac Rna Length = 129

Iteration: 1
 Score = 51.6 bits (122), Expect = 1e-06,   Method: Compositional matrix adjust.
 Identities = 27/79 (34%), Positives = 42/79 (53%)
Query: 241 PENVLFVCKLNPVTEDEDLHTIFSRFGTVVSAEIIRDFKTGDSLNYAFIEFENRQACERA 300
           P   L V  L+  T + DL  +FS++G +    I+ D ++  S  +AF+ FEN    + A
Sbjct: 45  PNCCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEA 104
Query: 301 YSKMDNALIDDRRIHVDFS 319
             + +   +D RRI VDFS
Sbjct: 105 KERANGMELDGRRIRVDFS 123

>pdb|2NUL|A Chain A, Peptidylprolyl Isomerase From E. Coli Length = 164

Iteration: 1
 Score = 51.2 bits (121), Expect = 1e-06,   Method: Composition-based stats.
 Identities = 43/145 (29%), Positives = 70/145 (48%), Gaps = 26/145 (17%)
Query: 7   TSLGDIVVDLFVDKCPLTTKNFLKLCKIKYYNGCLFHTVQKDFXXXXXXXXXXXXXXDSV 66
           T+ GDIV+  F DK P T KNFL  C+  +YN  +FH V   F                 
Sbjct: 6   TNHGDIVIKTFDDKAPETVKNFLDYCREGFYNNTIFHRVINGFMIQGG------------ 53
Query: 67  YKFLYGEQARFFGDEIRVD----LKHAKTGTVAMASAGENLNAS-QFYMTLRDN--LDYL 119
             F  G + +   + I+ +    LK+ + GT+AMA      +A+ QF++ + DN  L++ 
Sbjct: 54  -GFEPGMKQKATKEPIKNEANNGLKNTR-GTLAMARTQAPHSATAQFFINVVDNDFLNFS 111
Query: 120 DEK-----HTIFGEVAEGLETLSRI 139
            E      + +F EV +G++ + +I
Sbjct: 112 GESLQGWGYCVFAEVVDGMDVVDKI 136

>pdb|2RRA|A Chain A, Solution Structure Of Rna Binding Domain In Human Tra2 Beta Protein In Complex With Rna (Gaagaa) Length = 99

Iteration: 1
 Score = 50.8 bits (120), Expect = 2e-06,   Method: Compositional matrix adjust.
 Identities = 27/79 (34%), Positives = 42/79 (53%)
Query: 241 PENVLFVCKLNPVTEDEDLHTIFSRFGTVVSAEIIRDFKTGDSLNYAFIEFENRQACERA 300
           P   L V  L+  T + DL  +FS++G +    I+ D ++  S  +AF+ FEN    + A
Sbjct: 14  PNCCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEA 73
Query: 301 YSKMDNALIDDRRIHVDFS 319
             + +   +D RRI VDFS
Sbjct: 74  KERANGMELDGRRIRVDFS 92

>pdb|1LOP|A Chain A, Cyclophilin A Complexed With Succinyl-Ala-Pro-Ala-P-Nitroanilide Length = 164

Iteration: 1
 Score = 50.8 bits (120), Expect = 2e-06,   Method: Composition-based stats.
 Identities = 43/145 (29%), Positives = 70/145 (48%), Gaps = 26/145 (17%)
Query: 7   TSLGDIVVDLFVDKCPLTTKNFLKLCKIKYYNGCLFHTVQKDFXXXXXXXXXXXXXXDSV 66
           T+ GDIV+  F DK P T KNFL  C+  +YN  +FH V   F                 
Sbjct: 6   TNHGDIVIKTFDDKAPETVKNFLDYCREGFYNNTIFHRVINGFMIQGG------------ 53
Query: 67  YKFLYGEQARFFGDEIRVD----LKHAKTGTVAMASAGENLNAS-QFYMTLRDN--LDYL 119
             F  G + +   + I+ +    LK+ + GT+AMA      +A+ QF++ + DN  L++ 
Sbjct: 54  -GFEPGMKQKATKEPIKNEANNGLKNTR-GTLAMARTQAPHSATAQFFINVVDNDFLNFS 111
Query: 120 DEK-----HTIFGEVAEGLETLSRI 139
            E      + +F EV +G++ + +I
Sbjct: 112 GESLQGWGYCVFAEVVDGMDEVDKI 136

>pdb|4F25|A Chain A, Crystal Structure Of The Second Rrm Domain Of Human Pabpc1 At Ph 6.0 Length = 115

Iteration: 1
 Score = 50.4 bits (119), Expect = 3e-06,   Method: Composition-based stats.
 Identities = 24/72 (33%), Positives = 44/72 (61%), Gaps = 2/72 (2%)
Query: 245 LFVCKLNPVTEDEDLHTIFSRFGTVVSAEIIRDFKTGDSLNYAFIEFENRQACERAYSKM 304
           +F+  L+   +++ L+  FS FG ++S +++ D     S  Y F+ FE ++A ERA  KM
Sbjct: 8   IFIKNLDKSIDNKALYDTFSAFGNILSCKVVCD--ENGSKGYGFVHFETQEAAERAIEKM 65
Query: 305 DNALIDDRRIHV 316
           +  L++DR++ V
Sbjct: 66  NGMLLNDRKVFV 77

>pdb|2RRB|A Chain A, Refinement Of Rna Binding Domain In Human Tra2 Beta Protein Length = 96

Iteration: 1
 Score = 50.4 bits (119), Expect = 3e-06,   Method: Compositional matrix adjust.
 Identities = 27/79 (34%), Positives = 42/79 (53%)
Query: 241 PENVLFVCKLNPVTEDEDLHTIFSRFGTVVSAEIIRDFKTGDSLNYAFIEFENRQACERA 300
           P   L V  L+  T + DL  +FS++G +    I+ D ++  S  +AF+ FEN    + A
Sbjct: 11  PNCCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEA 70
Query: 301 YSKMDNALIDDRRIHVDFS 319
             + +   +D RRI VDFS
Sbjct: 71  KERANGMELDGRRIRVDFS 89

>pdb|3PGW|S Chain S, Crystal Structure Of Human U1 Snrnp Length = 437

Iteration: 1
 Score = 49.3 bits (116), Expect = 7e-06,   Method: Compositional matrix adjust.
 Identities = 26/84 (30%), Positives = 40/84 (47%), Gaps = 1/84 (1%)
Query: 244 VLFVCKLNPVTEDEDLHTIFSRFGTVVSAEIIRDFKTGDSLNYAFIEFENRQACERAYSK 303
            LFV ++N  T +  L   F  +G +    ++   ++G    YAFIE+E+ +    AY  
Sbjct: 104 TLFVARVNYDTTESKLRREFEVYGPIKRIHMVYSKRSGKPRGYAFIEYEHERDMHSAYKH 163
Query: 304 MDNALIDDRRIHVDFSQS-VSKLW 326
            D   ID RR+ VD  +    K W
Sbjct: 164 ADGKKIDGRRVLVDVERGRTVKGW 187

>pdb|2DH7|A Chain A, Solution Structure Of The Second Rna Binding Domain In Nucleolysin Tiar Length = 105

Iteration: 1
 Score = 48.9 bits (115), Expect = 7e-06,   Method: Composition-based stats.
 Identities = 23/75 (30%), Positives = 39/75 (52%)
Query: 245 LFVCKLNPVTEDEDLHTIFSRFGTVVSAEIIRDFKTGDSLNYAFIEFENRQACERAYSKM 304
           +FV  L+P    ED+ + F+ FG +  A +++D  TG S  Y F+ F N+   E A   M
Sbjct: 18  VFVGDLSPEITTEDIKSAFAPFGKISDARVVKDMATGKSKGYGFVSFYNKLDAENAIVHM 77
Query: 305 DNALIDDRRIHVDFS 319
               +  R+I  +++
Sbjct: 78  GGQWLGGRQIRTNWA 92

>pdb|1B7F|A Chain A, Sxl-Lethal ProteinRNA COMPLEX Length = 168

Iteration: 1
 Score = 48.5 bits (114), Expect = 9e-06,   Method: Compositional matrix adjust.
 Identities = 19/65 (29%), Positives = 39/65 (60%)
Query: 256 DEDLHTIFSRFGTVVSAEIIRDFKTGDSLNYAFIEFENRQACERAYSKMDNALIDDRRIH 315
           D +L+ +F   G + +  I+RD+KTG S  YAF++F +    +RA   ++   + ++R+ 
Sbjct: 17  DRELYALFRAIGPINTCRIMRDYKTGYSYGYAFVDFTSEMDSQRAIKVLNGITVRNKRLK 76
Query: 316 VDFSQ 320
           V +++
Sbjct: 77  VSYAR 81

>pdb|1X5S|A Chain A, Solution Structure Of Rrm Domain In A18 Hnrnp Length = 102

Iteration: 1
 Score = 48.5 bits (114), Expect = 1e-05,   Method: Compositional matrix adjust.
 Identities = 24/76 (31%), Positives = 41/76 (53%)
Query: 242 ENVLFVCKLNPVTEDEDLHTIFSRFGTVVSAEIIRDFKTGDSLNYAFIEFENRQACERAY 301
           E  LFV  L+  T ++ L  +FS++G +    +++D +T  S  + F+ FEN    + A 
Sbjct: 12  EGKLFVGGLSFDTNEQSLEQVFSKYGQISEVVVVKDRETQRSRGFGFVTFENIDDAKDAM 71
Query: 302 SKMDNALIDDRRIHVD 317
             M+   +D R+I VD
Sbjct: 72  MAMNGKSVDGRQIRVD 87

>pdb|2DGO|A Chain A, Solution Structure Of The Rna Binding Domain In Cytotoxic Granule-Associated Rna Binding Protein 1 Length = 115

Iteration: 1
 Score = 48.5 bits (114), Expect = 1e-05,   Method: Composition-based stats.
 Identities = 23/75 (30%), Positives = 39/75 (52%)
Query: 245 LFVCKLNPVTEDEDLHTIFSRFGTVVSAEIIRDFKTGDSLNYAFIEFENRQACERAYSKM 304
           +FV  L+P    ED+   F+ FG +  A +++D  TG S  Y F+ F N+   E A  +M
Sbjct: 18  VFVGDLSPEITTEDIKAAFAPFGRISDARVVKDMATGKSKGYGFVSFFNKWDAENAIQQM 77
Query: 305 DNALIDDRRIHVDFS 319
               +  R+I  +++
Sbjct: 78  GGQWLGGRQIRTNWA 92

>pdb|1SXL|A Chain A, Resonance Assignments And Solution Structure Of The Second Rna-Binding Domain Of Sex-Lethal Determined By Multidimensional Heteronuclear Magnetic Resonance Spectroscopy Length = 97

Iteration: 1
 Score = 48.1 bits (113), Expect = 1e-05,   Method: Compositional matrix adjust.
 Identities = 21/64 (32%), Positives = 35/64 (54%)
Query: 245 LFVCKLNPVTEDEDLHTIFSRFGTVVSAEIIRDFKTGDSLNYAFIEFENRQACERAYSKM 304
           L+V  L     D+ L TIF ++G++V   I+RD  TG     AF+ +  R+  + A S +
Sbjct: 16  LYVTNLPRTITDDQLDTIFGKYGSIVQKNILRDKLTGRPRGVAFVRYNKREEAQEAISAL 75
Query: 305 DNAL 308
           +N +
Sbjct: 76  NNVI 79

>pdb|1J2A|A Chain A, Structure Of E. Coli Cyclophilin B K163t Mutant Length = 166

Iteration: 1
 Score = 48.1 bits (113), Expect = 1e-05,   Method: Composition-based stats.
 Identities = 44/165 (26%), Positives = 78/165 (47%), Gaps = 16/165 (9%)
Query: 3   VLIVTSLGDIVVDLFVDKCPLTTKNFLKLCKIKYYNGCLFHTVQKDFXXXXXXXXXXXXX 62
           VL+ TS G+I ++L   K P++ +NF+      +YN   FH V   F             
Sbjct: 7   VLLTTSAGNIELELDKQKAPVSVQNFVDYVNSGFYNNTTFHRVIPGFMIQGGGFTEQMQQ 66
Query: 63  XDSVYKFLYGEQARFFGDEIRVDLKHAKTGTVAMA-SAGENLNASQFYMTLRDN--LDY- 118
                     +      +E    L++ + GT+AMA +A ++   SQF++ + DN  LD+ 
Sbjct: 67  K---------KPNPPIKNEADNGLRNTR-GTIAMARTADKDSATSQFFINVADNAFLDHG 116
Query: 119 -LDEKHTIFGEVAEGLETLSRINESFVDEKNRPYKNIRIKHTYIL 162
             D  + +FG+V +G++   +I++    +   PY+N+  K   IL
Sbjct: 117 QRDFGYAVFGKVVKGMDVADKISQVPTHDVG-PYQNVPSKPVVIL 160

>pdb|3SXL|A Chain A, Sex-Lethal Rna Recognition Domains 1 And 2 From Drosophila Melanogaster Length = 184

Iteration: 1
 Score = 48.1 bits (113), Expect = 2e-05,   Method: Compositional matrix adjust.
 Identities = 22/76 (28%), Positives = 41/76 (53%)
Query: 245 LFVCKLNPVTEDEDLHTIFSRFGTVVSAEIIRDFKTGDSLNYAFIEFENRQACERAYSKM 304
           L V  L     D +L+ +F   G + +  I RD+KTG S  YAF++F +    +RA   +
Sbjct: 17  LIVNYLPQDXTDRELYALFRAIGPINTCRIXRDYKTGYSFGYAFVDFTSEXDSQRAIKVL 76
Query: 305 DNALIDDRRIHVDFSQ 320
           +   + ++R+ V +++
Sbjct: 77  NGITVRNKRLKVSYAR 92

>pdb|3T1U|A Chain A, Crystal Structure Of The Complex Of Cyclophilin-a Enzyme From Azotobacter Vinelandii With Sucafpfpna Peptide Length = 163

Iteration: 1
 Score = 47.8 bits (112), Expect = 2e-05,   Method: Composition-based stats.
 Identities = 43/150 (28%), Positives = 68/150 (45%), Gaps = 26/150 (17%)
Query: 2   SVLIVTSLGDIVVDLFVDKCPLTTKNFLKLCKIKYYNGCLFHTVQKDFXXXXXXXXXXXX 61
           S+ + T+ G I + LF DK P T  NF +  K  +Y+G +FH V   F            
Sbjct: 1   SIKLQTNHGTITLKLFADKAPETAANFEQYVKDGHYDGTIFHRVIDGFMIQGG------- 53
Query: 62  XXDSVYKFLYGEQARFFGDEIRVDLKHA---KTGTVAMASAGENLNAS-QFYMTLRDNLD 117
                  F  G + +     I+ +  +    K  T+AMA   +  +AS QF++ ++DN  
Sbjct: 54  ------GFEPGMKQKSTRAPIKNEANNGLSNKKYTIAMARTPDPHSASAQFFINVKDNA- 106
Query: 118 YLDEK--------HTIFGEVAEGLETLSRI 139
           +LD          + +FGEV EG + + RI
Sbjct: 107 FLDHTAPTAHGWGYAVFGEVVEGTDVVDRI 136

>pdb|1CLH|A Chain A, Three-Dimensional Solution Structure Of Escherichia Coli Periplasmic Cyclophilin Length = 166

Iteration: 1
 Score = 47.8 bits (112), Expect = 2e-05,   Method: Composition-based stats.
 Identities = 44/165 (26%), Positives = 78/165 (47%), Gaps = 16/165 (9%)
Query: 3   VLIVTSLGDIVVDLFVDKCPLTTKNFLKLCKIKYYNGCLFHTVQKDFXXXXXXXXXXXXX 62
           VL+ TS G+I ++L   K P++ +NF+      +YN   FH V   F             
Sbjct: 7   VLLTTSAGNIELELDKQKAPVSVQNFVDYVNSGFYNNTTFHRVIPGFMIQGGGFTEQMQQ 66
Query: 63  XDSVYKFLYGEQARFFGDEIRVDLKHAKTGTVAMA-SAGENLNASQFYMTLRDN--LDY- 118
                     +      +E    L++ + GT+AMA +A ++   SQF++ + DN  LD+ 
Sbjct: 67  K---------KPNPPIKNEADNGLRNTR-GTIAMARTADKDSATSQFFINVADNAFLDHG 116
Query: 119 -LDEKHTIFGEVAEGLETLSRINESFVDEKNRPYKNIRIKHTYIL 162
             D  + +FG+V +G++   +I++    +   PY+N+  K   IL
Sbjct: 117 QRDFGYAVFGKVVKGMDVADKISQVPTHDVG-PYQNVPSKPVVIL 160

>pdb|2QFJ|A Chain A, Crystal Structure Of First Two Rrm Domains Of Fir Bound To Ssdna From A Portion Of Fuse Length = 216

Iteration: 1
 Score = 47.0 bits (110), Expect = 3e-05,   Method: Compositional matrix adjust.
 Identities = 22/63 (34%), Positives = 36/63 (57%)
Query: 243 NVLFVCKLNPVTEDEDLHTIFSRFGTVVSAEIIRDFKTGDSLNYAFIEFENRQACERAYS 302
           N ++V  ++    D+D+ ++F  FG + SA + RD  TG    Y FIE+E  Q+ + A S
Sbjct: 126 NRIYVASVHQDLSDDDIKSVFEAFGKIKSATLARDPTTGKHKGYGFIEYEKAQSSQDAVS 185
Query: 303 KMD 305
            M+
Sbjct: 186 SMN 188

>pdb|2SXL|A Chain A, Sex-Lethal Rbd1, Nmr, Minimized Average Structure Length = 88

Iteration: 1
 Score = 47.0 bits (110), Expect = 3e-05,   Method: Composition-based stats.
 Identities = 19/65 (29%), Positives = 39/65 (60%)
Query: 256 DEDLHTIFSRFGTVVSAEIIRDFKTGDSLNYAFIEFENRQACERAYSKMDNALIDDRRIH 315
           D +L+ +F   G + +  I+RD+KTG S  YAF++F +    +RA   ++   + ++R+ 
Sbjct: 17  DRELYALFRAIGPINTCRIMRDYKTGYSYGYAFVDFTSEMDSQRAIKVLNGITVRNKRLK 76
Query: 316 VDFSQ 320
           V +++
Sbjct: 77  VSYAR 81

>pdb|1X5T|A Chain A, Solution Structure Of The Second Rrm Domain In Splicing Factor 3b Length = 96

Iteration: 1
 Score = 46.6 bits (109), Expect = 4e-05,   Method: Composition-based stats.
 Identities = 25/76 (32%), Positives = 45/76 (59%), Gaps = 1/76 (1%)
Query: 245 LFVCKLNPVTEDEDLHTIFSRFGTVV-SAEIIRDFKTGDSLNYAFIEFENRQACERAYSK 303
           +F+  L+P  +++ L+  FS FG ++ + +I+RD  TG+S  YAFI F +  A + A   
Sbjct: 8   IFIGNLDPEIDEKLLYDTFSAFGVILQTPKIMRDPDTGNSKGYAFINFASFDASDAAIEA 67
Query: 304 MDNALIDDRRIHVDFS 319
           M+   + +R I V ++
Sbjct: 68  MNGQYLCNRPITVSYA 83

>pdb|3CW1|K Chain K, Crystal Structure Of Human Spliceosomal U1 Snrnp Length = 216

Iteration: 1
 Score = 46.2 bits (108), Expect = 5e-05,   Method: Compositional matrix adjust.
 Identities = 26/84 (30%), Positives = 40/84 (47%), Gaps = 1/84 (1%)
Query: 244 VLFVCKLNPVTEDEDLHTIFSRFGTVVSAEIIRDFKTGDSLNYAFIEFENRQACERAYSK 303
            LFV ++N  T +  L   F  +G +    ++   ++G    YAFIE+E+ +    AY  
Sbjct: 104 TLFVARVNYDTTESKLRREFEVYGPIKRIHMVYSKRSGKPRGYAFIEYEHERDMHSAYKH 163
Query: 304 MDNALIDDRRIHVDFSQS-VSKLW 326
            D   ID RR+ VD  +    K W
Sbjct: 164 ADGKKIDGRRVLVDVERGRTVKGW 187

>pdb|2LEA|A Chain A, Solution Structure Of Human Srsf2 (Sc35) Rrm Length = 135

Iteration: 1
 Score = 46.2 bits (108), Expect = 5e-05,   Method: Compositional matrix adjust.
 Identities = 27/87 (31%), Positives = 44/87 (50%), Gaps = 5/87 (5%)
Query: 239 KPPENV-----LFVCKLNPVTEDEDLHTIFSRFGTVVSAEIIRDFKTGDSLNYAFIEFEN 293
           +PP +V     L V  L   T  + L  +F ++G V    I RD  T +S  +AF+ F +
Sbjct: 39  RPPPDVEGMTSLKVDNLTYRTSPDTLRRVFEKYGRVGDVYIPRDRYTKESRGFAFVRFHD 98
Query: 294 RQACERAYSKMDNALIDDRRIHVDFSQ 320
           ++  E A   MD A++D R + V  ++
Sbjct: 99  KRDAEDAMDAMDGAVLDGRELRVQMAR 125

>pdb|4ED5|A Chain A, Crystal Structure Of The Two N-Terminal Rrm Domains Of Hur Complexed With Rna Length = 177

Iteration: 1
 Score = 45.8 bits (107), Expect = 6e-05,   Method: Compositional matrix adjust.
 Identities = 24/73 (32%), Positives = 43/73 (58%), Gaps = 1/73 (1%)
Query: 253 VTEDEDLHTIFSRFGTVVSAEIIRDFKTGDSLNYAFIEFENRQACERAYSKMDNALIDDR 312
           +T+DE L ++FS  G V SA++IRD   G SL Y F+ +   +  ERA + ++   +  +
Sbjct: 14  MTQDE-LRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVTAKDAERAINTLNGLRLQSK 72
Query: 313 RIHVDFSQSVSKL 325
            I V +++  S++
Sbjct: 73  TIKVSYARPSSEV 85

>pdb|4EGL|A Chain A, Crystal Structure Of Two Tandem Rna Recognition Motifs Of Human Antigen R Length = 177

Iteration: 1
 Score = 45.8 bits (107), Expect = 6e-05,   Method: Compositional matrix adjust.
 Identities = 24/73 (32%), Positives = 43/73 (58%), Gaps = 1/73 (1%)
Query: 253 VTEDEDLHTIFSRFGTVVSAEIIRDFKTGDSLNYAFIEFENRQACERAYSKMDNALIDDR 312
           +T+DE L ++FS  G V SA++IRD   G SL Y F+ +   +  ERA + ++   +  +
Sbjct: 14  MTQDE-LRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVTAKDAERAINTLNGLRLQSK 72
Query: 313 RIHVDFSQSVSKL 325
            I V +++  S++
Sbjct: 73  TIKVSYARPSSEV 85

>pdb|2CQD|A Chain A, Solution Structure Of The Rna Recognition Motif In Rna- Binding Region Containing Protein 1 Length = 116

Iteration: 1
 Score = 45.8 bits (107), Expect = 7e-05,   Method: Composition-based stats.
 Identities = 28/75 (37%), Positives = 39/75 (52%), Gaps = 1/75 (1%)
Query: 245 LFVCKLNPVTEDEDLHTIFSRFGTVVSAEIIRDFKTGDSLNYAFIEFENRQACERAYSKM 304
           +FV  L   T D  L   F  FG +  A +I D +TG S  Y F+   +R A ERA  K 
Sbjct: 20  IFVGGLPYHTTDASLRKYFEGFGDIEEAVVITDRQTGKSRGYGFVTMADRAAAERA-CKD 78
Query: 305 DNALIDDRRIHVDFS 319
            N +ID R+ +V+ +
Sbjct: 79  PNPIIDGRKANVNLA 93

>pdb|2CPZ|A Chain A, Solution Structure Of Rna Binding Domain 3 In Cug Triplet Repeat Rna-Binding Protein 1 Length = 115

Iteration: 1
 Score = 45.8 bits (107), Expect = 7e-05,   Method: Composition-based stats.
 Identities = 30/100 (30%), Positives = 48/100 (48%)
Query: 222 SSAVVLESIGDIPDADIKPPENVLFVCKLNPVTEDEDLHTIFSRFGTVVSAEIIRDFKTG 281
           SS +  +SIG        P    LF+  L     D+DL  +F  FG VVSA++  D +T 
Sbjct: 5   SSGLTQQSIGAAGSQKEGPEGANLFIYHLPQEFGDQDLLQMFMPFGNVVSAKVFIDKQTN 64
Query: 282 DSLNYAFIEFENRQACERAYSKMDNALIDDRRIHVDFSQS 321
            S  + F+ ++N  + + A   M+   I  +R+ V   +S
Sbjct: 65  LSKCFGFVSYDNPVSAQAAIQSMNGFQIGMKRLKVQLKRS 104

>pdb|1U6F|A Chain A, Nmr Solution Structure Of Tcubp1, A Single Rbd-Unit From Trypanosoma Cruzi Length = 139

Iteration: 1
 Score = 45.4 bits (106), Expect = 9e-05,   Method: Composition-based stats.
 Identities = 27/92 (29%), Positives = 50/92 (54%), Gaps = 3/92 (3%)
Query: 233 IPDADIKPPENVLFVCKLN--PVTEDE-DLHTIFSRFGTVVSAEIIRDFKTGDSLNYAFI 289
           IP   + P  +VL    +N  P T DE  L  +F R+G + S +I+ D +T  S  Y F+
Sbjct: 30  IPPTQMNPEPDVLRNLMVNYIPTTVDEVQLRQLFERYGPIESVKIVCDRETRQSRGYGFV 89
Query: 290 EFENRQACERAYSKMDNALIDDRRIHVDFSQS 321
           +F++  + ++A + ++   I ++R+ V  + S
Sbjct: 90  KFQSGSSAQQAIAGLNGFNILNKRLKVALAAS 121

>pdb|4FXV|A Chain A, Crystal Structure Of An Elav-Like Protein 1 (Elavl1) From Homo Sapiens At 1.90 A Resolution Length = 99

Iteration: 1
 Score = 45.4 bits (106), Expect = 1e-04,   Method: Compositional matrix adjust.
 Identities = 23/67 (34%), Positives = 39/67 (58%), Gaps = 1/67 (1%)
Query: 254 TEDEDLHTIFSRFGTVVSAEIIRDFKTGDSLNYAFIEFENRQACERAYSKMDNALIDDRR 313
           T+DE L ++FS  G V SA++IRD   G SL Y F+ +   +  ERA + ++   +  + 
Sbjct: 32  TQDE-LRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVTAKDAERAINTLNGLRLQSKT 90
Query: 314 IHVDFSQ 320
           I V +++
Sbjct: 91  IKVSYAR 97

>pdb|2CQC|A Chain A, Solution Structure Of The Rna Recognition Motif In ArginineSERINE-Rich Splicing Factor 10 Length = 95

Iteration: 1
 Score = 45.1 bits (105), Expect = 1e-04,   Method: Compositional matrix adjust.
 Identities = 24/76 (31%), Positives = 39/76 (51%)
Query: 241 PENVLFVCKLNPVTEDEDLHTIFSRFGTVVSAEIIRDFKTGDSLNYAFIEFENRQACERA 300
           P   L V  L+  T + DL  +FS++G +    I+ D ++  S  +AF+ FEN    + A
Sbjct: 14  PNCCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEA 73
Query: 301 YSKMDNALIDDRRIHV 316
             + +   +D RRI V
Sbjct: 74  KERANGMELDGRRIRV 89

>pdb|3HI9|A Chain A, The X-Ray Crystal Structure Of The First Rna Recognition Motif (Rrm1) Of The Au-Rich Element (Are) Binding Protein Hur At 2.0 Angstrom Resolution Length = 84

Iteration: 1
 Score = 44.3 bits (103), Expect = 2e-04,   Method: Composition-based stats.
 Identities = 23/68 (33%), Positives = 40/68 (58%), Gaps = 1/68 (1%)
Query: 253 VTEDEDLHTIFSRFGTVVSAEIIRDFKTGDSLNYAFIEFENRQACERAYSKMDNALIDDR 312
           +T+DE L ++FS  G V SA++IRD   G SL Y F+ +   +  ERA + ++   +  +
Sbjct: 16  MTQDE-LRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVTAKDAERAINTLNGLRLQSK 74
Query: 313 RIHVDFSQ 320
            I V +++
Sbjct: 75  TIKVSYAR 82

>pdb|2KXF|A Chain A, Solution Structure Of The First Two Rrm Domains Of Fbp-Interacting Repressor (Fir) Length = 199

Iteration: 1
 Score = 44.3 bits (103), Expect = 2e-04,   Method: Compositional matrix adjust.
 Identities = 21/63 (33%), Positives = 35/63 (55%)
Query: 243 NVLFVCKLNPVTEDEDLHTIFSRFGTVVSAEIIRDFKTGDSLNYAFIEFENRQACERAYS 302
           N ++V  ++    D+D+ ++F  FG + S  + RD  TG    Y FIE+E  Q+ + A S
Sbjct: 111 NRIYVASVHQDLSDDDIKSVFEAFGKIKSCTLARDPTTGKHKGYGFIEYEKAQSSQDAVS 170
Query: 303 KMD 305
            M+
Sbjct: 171 SMN 173

>pdb|2ERR|A Chain A, Nmr Structure Of The Rna Binding Domain Of Human Fox-1 In Complex With Ugcaugu Length = 109

Iteration: 1
 Score = 43.1 bits (100), Expect = 4e-04,   Method: Compositional matrix adjust.
 Identities = 21/62 (33%), Positives = 34/62 (54%), Gaps = 2/62 (3%)
Query: 256 DEDLHTIFSRFGTVVSAEIIRDFKTGDSLNYAFIEFENRQACERAYSKMDNALIDDRRIH 315
           D DL  +F +FG ++  EII  F    S  + F+ FEN    +RA  K+   +++ R+I 
Sbjct: 43  DPDLRQMFGQFGKILDVEII--FNERGSKGFGFVTFENSADADRAREKLHGTVVEGRKIE 100
Query: 316 VD 317
           V+
Sbjct: 101 VN 102

>pdb|2CQ3|A Chain A, Solution Structure Of Rna Binding Domain In Rna Binding Motif Protein 9 Length = 103

Iteration: 1
 Score = 43.1 bits (100), Expect = 4e-04,   Method: Compositional matrix adjust.
 Identities = 21/62 (33%), Positives = 34/62 (54%), Gaps = 2/62 (3%)
Query: 256 DEDLHTIFSRFGTVVSAEIIRDFKTGDSLNYAFIEFENRQACERAYSKMDNALIDDRRIH 315
           D DL  +F +FG ++  EII  F    S  + F+ FEN    +RA  K+   +++ R+I 
Sbjct: 29  DPDLRQMFGQFGKILDVEII--FNERGSKGFGFVTFENSADADRAREKLHGTVVEGRKIE 86
Query: 316 VD 317
           V+
Sbjct: 87  VN 88

>pdb|2FC8|A Chain A, Solution Structure Of The Rrm_1 Domain Of Ncl Protein Length = 102

Iteration: 1
 Score = 43.1 bits (100), Expect = 4e-04,   Method: Compositional matrix adjust.
 Identities = 23/80 (28%), Positives = 41/80 (51%), Gaps = 3/80 (3%)
Query: 241 PENVLFVCKLNPVTEDEDLHTIFSRFGTVVSAEIIRDFKTGDSLNYAFIEFENRQACERA 300
           P   LFV  L   +ED    T+   F   V A I+ D +TG S  + F++F + +  + A
Sbjct: 14  PSKTLFVKGL---SEDTTEETLKESFDGSVRARIVTDRETGSSKGFGFVDFNSEEDAKAA 70
Query: 301 YSKMDNALIDDRRIHVDFSQ 320
              M++  ID  ++ +D+++
Sbjct: 71  KEAMEDGEIDGNKVTLDWAK 90

>pdb|2KHC|A Chain A, Bruno Rrm3+ Length = 118

Iteration: 1
 Score = 42.7 bits (99), Expect = 5e-04,   Method: Composition-based stats.
 Identities = 25/84 (29%), Positives = 42/84 (50%), Gaps = 1/84 (1%)
Query: 238 IKPPENV-LFVCKLNPVTEDEDLHTIFSRFGTVVSAEIIRDFKTGDSLNYAFIEFENRQA 296
           I+ PE   LF+  L     D DL + F  FG V+SA++  D +T  S  + F+ F+N  +
Sbjct: 35  IEGPEGCNLFIYHLPQEFTDTDLASTFLPFGNVISAKVFIDKQTSLSKCFGFVSFDNPDS 94
Query: 297 CERAYSKMDNALIDDRRIHVDFSQ 320
            + A   M+   +  +R+ V   +
Sbjct: 95  AQVAIKAMNGFQVGTKRLKVQLKK 118

>pdb|2CJK|A Chain A, Structure Of The Rna Binding Domain Of Hrp1 In Complex With Rna Length = 167

Iteration: 1
 Score = 42.4 bits (98), Expect = 7e-04,   Method: Compositional matrix adjust.
 Identities = 21/74 (28%), Positives = 40/74 (54%), Gaps = 5/74 (6%)
Query: 245 LFVCKLNPVTEDEDLHTIFSRFGTVVSAEIIRDFKTGDSLNYAFIEFENRQACERAYSKM 304
           +FV  + P    ++    FS++GT++ A+++ D  TG S  + F+ +++  A +R     
Sbjct: 90  IFVGGIGPDVRPKEFEEFFSQWGTIIDAQLMLDKDTGQSRGFGFVTYDSADAVDRV---C 146
Query: 305 DNALID--DRRIHV 316
            N  ID  DR+I +
Sbjct: 147 QNKFIDFKDRKIEI 160

>pdb|3MD3|A Chain A, Crystal Structure Of The First Two Rrm Domains Of Yeast Poly Binding Protein (Pub1) Length = 166

Iteration: 1
 Score = 42.4 bits (98), Expect = 8e-04,   Method: Composition-based stats.
 Identities = 21/75 (28%), Positives = 38/75 (50%)
Query: 245 LFVCKLNPVTEDEDLHTIFSRFGTVVSAEIIRDFKTGDSLNYAFIEFENRQACERAYSKM 304
           LFV  LN   +DE L   F  F + +S  ++ D +TG S  Y F+ F ++   + A   M
Sbjct: 90  LFVGDLNVNVDDETLRNAFKDFPSYLSGHVMWDMQTGSSRGYGFVSFTSQDDAQNAMDSM 149
Query: 305 DNALIDDRRIHVDFS 319
               ++ R + ++++
Sbjct: 150 QGQDLNGRPLRINWA 164

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Length	Definition	E-value
Query	589
3bkp_A	232	Cyclophilin; malaria, isomerase, structural GENO s	4e-80
3bo7_A	201	Peptidyl-prolyl CIS-trans isomerase cyclophilin-T;	4e-79
2ok3_A	161	Peptidyl-prolyl CIS-trans isomerase-like 3; beta-b	5e-79
2hq6_A	185	Serologically defined colon cancer antigen 10; pro	1e-78
2poe_A	185	Cyclophilin-like protein, putative; cryptosporidiu	2e-78
1zkc_A	197	Peptidyl-prolyl CIS-trans isomerase like 2; CIS-tr	7e-76
2x7k_A	166	Peptidyl-prolyl CIS-trans isomerase-like 1; isomer	2e-62
2b71_A	196	Cyclophilin-like protein; structural genomics, str	2e-62
2fu0_A	160	Cyclophilin, putative; PFE0505W, cyclosporin-bindi	2e-61
2k7n_A	203	Peptidyl-prolyl CIS-trans isomerase-like 1; beta b	3e-61
2a2n_A	176	Peptidylprolyl isomerase domain and WD repeat CON;	5e-59
1w74_A	191	Peptidyl-prolyl CIS-trans isomerase A; cyclophilin	4e-51
1lop_A	164	Cyclophilin A; rotamase, isomerase-isomerase inhib	2e-39
3s6m_A	167	Peptidyl-prolyl CIS-trans isomerase; seattle struc	3e-38
1v9t_A	166	Cyclophilin B; beta barrel, isomerase-isomerase in	1e-37
2wfi_A	179	Peptidyl-prolyl CIS-trans isomerase G; phosphoprot	1e-35
1a58_A	177	Cyclophilin; isomerase, ppiase; 1.95A {Brugia mala	2e-35
2he9_A	192	NK-tumor recognition protein; cyclosporin, isomera	7e-35
1mzw_A	177	Cyclophilin H, U-snRNP-ASSOCIATED cyclophilin; cyc	3e-34
2igv_A	173	Peptidyl-prolyl CIS-trans isomerase 3; rotamase; 1	1e-33
2poy_A	186	Peptidyl-prolyl CIS-trans isomerase; isomerase-imm	3e-33
2r99_A	173	Peptidyl-prolyl CIS-trans isomerase E; CIS-trans i	3e-33
2cmt_A	172	Peptidyl-prolyl CIS-trans isomerase E; rotamase ac	4e-33
2z6w_A	165	Peptidyl-prolyl CIS-trans isomerase; isomerase-imm	6e-33
3pmp_A	164	Cyclophilin A; peptidyl prolyl isomerase, isomeras	9e-33
1qng_A	170	Peptidyl-prolyl CIS-trans isomerase; isomerase-imm	9e-33
3rdd_A	184	Peptidyl-prolyl CIS-trans isomerase A; beta barrel	1e-32
3ich_A	188	Peptidyl-prolyl CIS-trans isomerase B; beta sandwi	6e-32
1ihg_A	370	Cyclophilin 40; ppiase immunophilin tetratricopept	6e-32
2haq_A	172	Cyclophilin; rotamase, proline, isomerase, CIS-tra	2e-31
3k2c_A	193	Peptidyl-prolyl CIS-trans isomerase; ssgcid, NIH,	4e-31
2ose_A	234	Probable peptidyl-prolyl CIS-trans isomerase; cycl	3e-30
1z81_A	229	Cyclophilin; structural genomics, structural genom	3e-30
2c3b_A	172	Ppiase, cyclophilin; isomerase, 3D domain swapping	1e-29
1why_A	97	Hypothetical protein riken cDNA 1810017N16; RNA re	1e-27
3pgw_S	437	U1-70K; protein-RNA complex, U1 snRNA, SM fold, SM	2e-27
3rfy_A	369	Peptidyl-prolyl CIS-trans isomerase CYP38, chloro;	4e-26
3s8s_A	110	Histone-lysine N-methyltransferase SETD1A; chromat	3e-22
1b7f_A	168	Protein (SXL-lethal protein), RNA (5'-R(P*GP*UP*UP	1e-19
1b7f_A	168	Protein (SXL-lethal protein), RNA (5'-R(P*GP*UP*UP	3e-16
2cpx_A	115	Hypothetical protein FLJ11016; RRM domain, structu	1e-19
1fxl_A	167	Paraneoplastic encephalomyelitis antigen HUD; prot	1e-18
1fxl_A	167	Paraneoplastic encephalomyelitis antigen HUD; prot	5e-16
2lkz_A	95	RNA-binding protein 5; RRM; NMR {Homo sapiens} Len	1e-18
2cqc_A	95	Arginine/serine-rich splicing factor 10; RNA recog	2e-18
2khc_A	118	Testis-specific RNP-type RNA binding protein; RRM,	4e-18
2cpf_A	98	RNA binding motif protein 19; RNA recognition moti	1e-17
2cpz_A	115	CUG triplet repeat RNA-binding protein 1; RRM doma	1e-17
3bs9_A	87	Nucleolysin TIA-1 isoform P40; RNA recognition mot	1e-17
3smz_A	284	Protein raver-1, ribonucleoprotein PTB-binding 1;	2e-17
3smz_A	284	Protein raver-1, ribonucleoprotein PTB-binding 1;	2e-13
3smz_A	284	Protein raver-1, ribonucleoprotein PTB-binding 1;	3e-11
3r27_A	100	HnRNP L, heterogeneous nuclear ribonucleoprotein L	2e-17
1x4e_A	85	RNA binding motif, single-stranded interacting pro	2e-17
2qfj_A	216	FBP-interacting repressor; protein-DNA complex; HE	2e-17
2qfj_A	216	FBP-interacting repressor; protein-DNA complex; HE	3e-15
2kxn_B	129	Transformer-2 protein homolog beta; SR protein, RR	2e-17
2cq0_A	103	Eukaryotic translation initiation factor 3 subunit	3e-17
4f02_A	213	Polyadenylate-binding protein 1; mRNA, eukaryotic	6e-17
4f02_A	213	Polyadenylate-binding protein 1; mRNA, eukaryotic	7e-16
3md3_A	166	Nuclear and cytoplasmic polyadenylated RNA-bindin	6e-17
3md3_A	166	Nuclear and cytoplasmic polyadenylated RNA-bindin	8e-17
3md1_A	83	Nuclear and cytoplasmic polyadenylated RNA-bindin	1e-16
1x5t_A	96	Splicing factor 3B subunit 4; structure genomics,	1e-16
2e5h_A	94	Zinc finger CCHC-type and RNA-binding motif- conta	1e-16
4f25_A	115	Polyadenylate-binding protein 1; RRM fold, transla	2e-16
1x5s_A	102	Cold-inducible RNA-binding protein; structure geno	2e-16
1x5o_A	114	RNA binding motif, single-stranded interacting pro	3e-16
2dgo_A	115	Cytotoxic granule-associated RNA binding protein 1	3e-16
2do4_A	100	Squamous cell carcinoma antigen recognized by T- c	3e-16
1u6f_A	139	Tcubp1, RNA-binding protein UBP1; trypanosome, mRN	4e-16
1whw_A	99	Hypothetical protein riken cDNA 1200009A02; RNA re	5e-16
2x1f_A	96	MRNA 3'-END-processing protein RNA15; transcriptio	6e-16
2dnm_A	103	SRP46 splicing factor; RRM domain, RBD, structural	7e-16
1p27_B	106	RNA-binding protein 8A; nuclear protein, mRNA spli	1e-15
4a8x_A	88	RNA-binding protein with serine-rich domain 1; tra	1e-15
2fy1_A	116	RNA-binding motif protein, Y chromosome, family 1	2e-15
2yh0_A	198	Splicing factor U2AF 65 kDa subunit; PRE-mRNA spli	2e-15
2yh0_A	198	Splicing factor U2AF 65 kDa subunit; PRE-mRNA spli	9e-10
2cqi_A	103	Nucleolysin TIAR; RNA recognition motif, RRM, RNA	2e-15
2ku7_A	140	MLL1 PHD3-CYP33 RRM chimeric protein; transcriptio	2e-15
2cpd_A	99	Apobec-1 stimulating protein; RNA recognition moti	3e-15
1h2v_Z	156	20 kDa nuclear CAP binding protein; CAP-binding-co	3e-15
3mdf_A	85	Peptidyl-prolyl CIS-trans isomerase E; RRM domain,	3e-15
1wex_A	104	Hypothetical protein (riken cDNA 2810036L13); stru	3e-15
3pgw_A	282	U1-A; protein-RNA complex, U1 snRNA, SM fold, SM c	3e-15
3pgw_A	282	U1-A; protein-RNA complex, U1 snRNA, SM fold, SM c	7e-07
2g4b_A	172	Splicing factor U2AF 65 kDa subunit; protein-RNA c	3e-15
2g4b_A	172	Splicing factor U2AF 65 kDa subunit; protein-RNA c	5e-10
2lea_A	135	Serine/arginine-rich splicing factor 2; SR protein	3e-15
2dgp_A	106	Bruno-like 4, RNA binding protein; RRM domain, str	4e-15
2dgu_A	103	Heterogeneous nuclear ribonucleoprotein Q; RRM dom	6e-15
2dnz_A	95	Probable RNA-binding protein 23; RNA recognition m	6e-15
2dnh_A	105	Bruno-like 5, RNA binding protein; RRM domain, RBD	8e-15
1x5u_A	105	Splicing factor 3B subunit 4 (spliceosome associat	8e-15
3ulh_A	107	THO complex subunit 4; nuclear protein, RNA bindin	8e-15
2kn4_A	158	Immunoglobulin G-binding protein G, splicing FACT	9e-15
1oo0_B	110	CG8781-PA, drosophila Y14; RNA recognition motif,	1e-14
2d9p_A	103	Polyadenylate-binding protein 3; RRM domain, struc	1e-14
3ex7_B	126	RNA-binding protein 8A; protein-RNA complex, mRNA	1e-14
2div_A	99	TRNA selenocysteine associated protein; structural	1e-14
2kt5_A	124	RNA and export factor-binding protein 2; chaperone	2e-14
2ywk_A	95	Putative RNA-binding protein 11; RRM-domain, struc	2e-14
2cpj_A	99	Non-POU domain-containing octamer-binding protein;	2e-14
2cqb_A	102	Peptidyl-prolyl CIS-trans isomerase E; RNA recogni	2e-14
1fje_B	175	Nucleolin RBD12, protein C23; RNP, RRM, RNA bindin	2e-14
1fje_B	175	Nucleolin RBD12, protein C23; RNP, RRM, RNA bindin	1e-10
2cq3_A	103	RNA-binding protein 9; RRM domain, structural geno	5e-14
3nmr_A	175	Cugbp ELAV-like family member 1; RRM, PRE-mRNA spl	5e-14
3nmr_A	175	Cugbp ELAV-like family member 1; RRM, PRE-mRNA spl	4e-12
1x5p_A	97	Negative elongation factor E; structure genomics,	7e-14
2dgv_A	92	HnRNP M, heterogeneous nuclear ribonucleoprotein M	7e-14
1x4g_A	109	Nucleolysin TIAR; structural genomics, RRM domain,	1e-13
1nu4_A	97	U1A RNA binding domain; RNA recognition motif, U1	2e-13
2la4_A	101	Nuclear and cytoplasmic polyadenylated RNA-bindin	2e-13
3sde_A	261	Paraspeckle component 1; RRM, anti parallel right	2e-13
3sde_A	261	Paraspeckle component 1; RRM, anti parallel right	2e-11
1p1t_A	104	Cleavage stimulation factor, 64 kDa subunit; RNA r	2e-13
2do0_A	114	HnRNP M, heterogeneous nuclear ribonucleoprotein M	2e-13
2adc_A	229	Polypyrimidine tract-binding protein 1; RBD, RRM,	2e-13
2adc_A	229	Polypyrimidine tract-binding protein 1; RBD, RRM,	1e-11
2f3j_A	177	RNA and export factor binding protein 2; RRM domai	2e-13
2dgt_A	92	RNA-binding protein 30; RRM domain, structural gen	2e-13
2dnp_A	90	RNA-binding protein 14; RRM domain, RBD, structura	3e-13
1rk8_A	165	CG8781-PA, CG8781-PA protein; mRNA processing, RRM	3e-13
1sjq_A	105	Polypyrimidine tract-binding protein 1; babbab mot	3e-13
2jrs_A	108	RNA-binding protein 39; RNA binding motif of RBM39	4e-13
2bz2_A	121	Negative elongation factor E; NELF E, RNA recognit	4e-13
2cph_A	107	RNA binding motif protein 19; RNA recognition moti	5e-13
2err_A	109	Ataxin-2-binding protein 1; protein-RNA complex, R	5e-13
2cq1_A	101	PTB-like protein L; RRM domain, structural genomic	5e-13
2a3j_A	127	U1 small nuclear ribonucleoprotein A; computationa	5e-13
2e44_A	96	Insulin-like growth factor 2 mRNA binding protein	6e-13
2fc8_A	102	NCL protein; structure genomics, RRM_1 domain, str	6e-13
1qm9_A	198	Polypyrimidine tract-binding protein; ribonucleopr	7e-13
1qm9_A	198	Polypyrimidine tract-binding protein; ribonucleopr	7e-11
2fc9_A	101	NCL protein; structure genomics, RRM_1 domain, str	1e-12
2ghp_A	292	U4/U6 snRNA-associated splicing factor PRP24; RNA	1e-12
2ghp_A	292	U4/U6 snRNA-associated splicing factor PRP24; RNA	3e-12
2ghp_A	292	U4/U6 snRNA-associated splicing factor PRP24; RNA	2e-11
3tyt_A	205	Heterogeneous nuclear ribonucleoprotein L; ferredo	1e-12
3tyt_A	205	Heterogeneous nuclear ribonucleoprotein L; ferredo	8e-11
1fjc_A	96	Nucleolin RBD2, protein C23; RNP, RRM, RNA binding	2e-12
2xs2_A	102	Deleted in azoospermia-like; RNA binding protein-R	2e-12
3ucg_A	89	Polyadenylate-binding protein 2; ferredoxin-like,	2e-12
1x4h_A	111	RNA-binding protein 28; structural genomics, RRM d	2e-12
3egn_A	143	RNA-binding protein 40; RNA recognition motif (RRM	2e-12
2ad9_A	119	Polypyrimidine tract-binding protein 1; RBD, RRM,	2e-12
2jvo_A	108	Nucleolar protein 3; nucleus, phosphorylation, rib	3e-12
2jwn_A	124	Embryonic polyadenylate-binding protein 2-B; epabp	4e-12
2kvi_A	96	Nuclear polyadenylated RNA-binding protein 3; RNA-	5e-12
2cqd_A	116	RNA-binding region containing protein 1; RNA recog	7e-12
3lqv_A	115	PRE-mRNA branch site protein P14; cysless mutant,	7e-12
2dgs_A	99	DAZ-associated protein 1; RRM domain, structural g	8e-12
3q2s_C	229	Cleavage and polyadenylation specificity factor S;	8e-12
3n9u_C	156	Cleavage and polyadenylation specificity factor S;	9e-12
1wf1_A	110	RNA-binding protein RALY; structural genomics, RRM	9e-12
2dnq_A	90	RNA-binding protein 4B; RRM domain,RBD, structural	1e-11
2la6_A	99	RNA-binding protein FUS; structural genomics, nort	2e-11
2dis_A	109	Unnamed protein product; structural genomics, RRM	2e-11
2cq4_A	114	RNA binding motif protein 23; RRM domain, structur	2e-11
1iqt_A	75	AUF1, heterogeneous nuclear ribonucleoprotein D0;	2e-11
3p5t_L	90	Cleavage and polyadenylation specificity factor S;	2e-11
2cjk_A	167	Nuclear polyadenylated RNA-binding protein 4; HRP1	3e-11
2cjk_A	167	Nuclear polyadenylated RNA-binding protein 4; HRP1	2e-09
2mss_A	75	Protein (musashi1); RNA-binding domain, RNA bindin	3e-11
2xnq_A	97	Nuclear polyadenylated RNA-binding protein 3; tran	3e-11
2cqg_A	103	TDP-43, TAR DNA-binding protein-43; RNA recognitio	4e-11
2ki2_A	90	SS-DNA binding protein 12RNP2; HP0827, RRM, SS-DNA	4e-11
2ytc_A	85	PRE-mRNA-splicing factor RBM22; RRM domain, RBD, s	5e-11
1fj7_A	101	Nucleolin RBD1, protein C23; RNP, RRM, RNA binding	5e-11
2cqp_A	98	RNA-binding protein 12; RNA recognition motif, RRM	6e-11
2ek1_A	95	RNA-binding protein 12; RNA recognition motif, dim	1e-10
2cpi_A	111	CCR4-NOT transcription complex subunit 4; RNA reco	1e-10
1l3k_A	196	Heterogeneous nuclear ribonucleoprotein A1; nuclea	1e-10
1l3k_A	196	Heterogeneous nuclear ribonucleoprotein A1; nuclea	2e-09
2lcw_A	116	RNA-binding protein FUS; RRM, nucleic acid binding	3e-10
2i2y_A	150	Fusion protein consists of immunoglobin G- binding	5e-10
2hvz_A	101	Splicing factor, arginine/serine-rich 7; RRM, RNA	5e-10
3ns6_A	100	Eukaryotic translation initiation factor 3 subuni;	7e-10
1uaw_A	77	Mouse-musashi-1; RNP-type structure, RNA binding p	8e-10
3s7r_A	87	Heterogeneous nuclear ribonucleoprotein A/B; ferre	9e-10
2cqh_A	93	IGF-II mRNA-binding protein 2 isoform A; RNA recog	2e-09
1sjr_A	164	Polypyrimidine tract-binding protein 1; extended b	2e-09
2rs2_A	109	Musashi-1, RNA-binding protein musashi homolog 1;	3e-09
1wf0_A	88	TDP-43, TAR DNA-binding protein-43; structural gen	4e-09
2dhg_A	104	TRNA selenocysteine associated protein (SECP43); R	4e-09
1x4a_A	109	Splicing factor, arginine/serine-rich 1 (splicing	4e-09
2krb_A	81	Eukaryotic translation initiation factor 3 subunit	4e-09
2cpe_A	113	RNA-binding protein EWS; RNA recognition motif, RR	5e-09
2dh8_A	105	DAZ-associated protein 1; RRM domain, structural g	6e-09
2e5g_A	94	U6 snRNA-specific terminal uridylyltransferase 1;	7e-09
1x4b_A	116	Heterogeneous nuclear ribonucleoproteins A2/B1; st	8e-09
2dng_A	103	Eukaryotic translation initiation factor 4H; RRM d	1e-08
1whx_A	111	Hypothetical protein riken cDNA 1200009A02; RNA re	2e-08
3zzy_A	130	Polypyrimidine tract-binding protein 1; protein bi	2e-08
2nlw_A	105	Eukaryotic translation initiation factor 3 subunit	2e-08
1wi8_A	104	EIF-4B, eukaryotic translation initiation factor 4	3e-08
3d2w_A	89	TAR DNA-binding protein 43; DP-43 proteinopathy, T	3e-08
2cq2_A	114	Hypothetical protein LOC91801; RRM domain, structu	4e-08
1wg1_A	88	KIAA1579 protein, homolog EXC-7; RBD, structural g	4e-08
1x4f_A	112	Matrin 3; structural genomics, RRM domain, NPPSFA,	6e-08
2j76_E	100	EIF-4B, EIF4B, eukaryotic translation initiation f	9e-08
1wg5_A	104	Heterogeneous nuclear ribonucleoprotein H; structu	5e-07
2cpy_A	114	RNA-binding protein 12; RRM domain, structural gen	6e-07
2hgm_A	126	HNRPF protein, heterogeneous nuclear ribonucleopro	8e-07
1x4c_A	108	Splicing factor, arginine/serine-rich 1; structura	2e-06
1s79_A	103	Lupus LA protein; RRM, alpha/beta, RNA binding pro	2e-06
1x4d_A	102	Matrin 3; structural genomics, RRM domain, NPPSFA,	4e-06
1wel_A	124	RNA-binding protein 12; structural genomics, NPPSF	4e-06
2hzc_A	87	Splicing factor U2AF 65 kDa subunit; RNA splicing,	5e-06
2e5j_A	97	Methenyltetrahydrofolate synthetase domain contain	6e-06
2jvr_A	111	Nucleolar protein 3; RNA recognition motif, nucleu	1e-05
2dnn_A	109	RNA-binding protein 12; RRM domain, RBD, structura	1e-05
1wez_A	102	HnRNP H', FTP-3, heterogeneous nuclear ribonucleop	2e-05
2e5i_A	124	Heterogeneous nuclear ribonucleoprotein L-like; RR	2e-05
2voo_A	193	Lupus LA protein; RNA-binding protein, RNA recogni	2e-05
2dnl_A	114	Cytoplasmic polyadenylation element binding protei	3e-05
2dgx_A	96	KIAA0430 protein; RRM domain, structural genomics,	6e-05
3beg_B	115	Splicing factor, arginine/serine-rich 1; kinase, S	8e-05
1vt4_I	1221	APAF-1 related killer DARK; drosophila apoptosome,	1e-04
1vt4_I	1221	APAF-1 related killer DARK; drosophila apoptosome,	1e-04
2cqf_A	63	RNA-binding protein LIN-28; CCHC zinc-finger, stru	2e-04
1wey_A	104	Calcipressin 1; structural genomics, RRM domain, r	3e-04
2dgw_A	91	Probable RNA-binding protein 19; RRM domain, struc	4e-04
3u1l_A	240	PRE-mRNA-splicing factor CWC2; CSMP, zinc finger;	5e-04

>3bkp_A Cyclophilin; malaria, isomerase, structural GENO structural genomics consortium, SGC; 1.80A {Toxoplasma gondii} Length = 232

 Score =  250 bits (641), Expect = 4e-80
 Identities = 69/214 (32%), Positives = 102/214 (47%), Gaps = 23/214 (10%)

Query: 1   MSVLIVTSLGDIVVDLFVDKCPLTTKNFLKLCKIKYYNGCLFHTVQKDFTAQTGDPTGTG 60
             V++ TSLGD+ V+L+  +CPL  +NF++LC   YY   +FH V KDF  Q GDPTGTG
Sbjct: 22  GKVVLHTSLGDLDVELWARECPLACRNFVQLCLEGYYVNTIFHRVVKDFIVQGGDPTGTG 81

Query: 61  TGGDSVYKFLYGEQARFFGDEIRVDLKHAKTGTVAMASAGENL--------------NAS 106
            GG            + F  E    LK    G V +A+ G +               N +
Sbjct: 82  RGGAD-----TTFDGKPFDVETHPRLKFRYRGLVGVANLGRSSKDAENDERGRSLGTNGN 136

Query: 107 QFYMTLRDNLDYLDEKHTIFGEVA-EGLETLSRINESFVDEKNRPYKNIRIKHTYILEDP 165
           QF++TL    D L+  +T+FG+V    L  L + N+  V +++RP     IK   +L +P
Sbjct: 137 QFFITL-ARADVLNNAYTLFGKVTGHTLYNLMKFNDLEVGKEDRPMTPPFIKSVDVLWNP 195

Query: 166 FDDPAQLAELIPDASPEGKPKDEVVDEVRLEDDW 199
           F+D   +   +PDA P  K + +           
Sbjct: 196 FEDL--VPRRLPDAPPAQKDERKRARAAGGRTTE 227

>3bo7_A Peptidyl-prolyl CIS-trans isomerase cyclophilin-T; isomerase-immunosuppressant complex, immunosuppressant, cyclophilin, structural G structural genomics consortium, SGC; HET: BMT; 2.35A {Toxoplasma gondii} Length = 201

 Score =  247 bits (632), Expect = 4e-79
 Identities = 56/200 (28%), Positives = 103/200 (51%), Gaps = 13/200 (6%)

Query: 3   VLIVTSLGDIVVDLFVDKCPLTTKNFLKLCKIKYYNGCLFHTVQKDFTAQTG-----DPT 57
           + IVT+ G + ++L  D  P    +FL+LC +KY++  +FH   ++F  Q G      P+
Sbjct: 9   LRIVTTQGSLNIELHADMAPRACDSFLRLCAVKYFDDTIFHRCIRNFMIQGGRAELRQPS 68

Query: 58  GTGTGGDSVYKFLYGEQARFFGDEIRVDLKHAKTGTVAMASAGENLNASQFYMTLRDNLD 117
                  S            F DE    L H   G ++MA+ G++ N S+F++T +   +
Sbjct: 69  KKKEVQQSPRSISGFPGGAPFEDEFDNRLVHQGIGVLSMANDGKHSNLSEFFITFKS-CE 127

Query: 118 YLDEKHTIFGEVAEGLETLSRINESFVDEKNRPYKNIRIKHTYILEDPFDDPAQLAELIP 177
           +L+ KHTIFG V  GL+ L +  +   D+K++P K  +++   + ++PF+D  +  E   
Sbjct: 128 HLNNKHTIFGRVVGGLDVLRQWEKLETDKKDKPLKPPKVEEIIVFKNPFEDARKEME--- 184

Query: 178 DASPEGKPKDEVVDEVRLED 197
               + K ++E  ++ +LE+
Sbjct: 185 ----DEKREEEEKEKKKLEN 200

>2ok3_A Peptidyl-prolyl CIS-trans isomerase-like 3; beta-barrel, helix, disulfide bridge; 2.00A {Homo sapiens} SCOP: b.62.1.1 PDB: 1xyh_A 2oju_A* Length = 161

 Score =  245 bits (627), Expect = 5e-79
 Identities = 75/167 (44%), Positives = 103/167 (61%), Gaps = 9/167 (5%)

Query: 1   MSVLIVTSLGDIVVDLFVDKCPLTTKNFLKLCKIKYYNGCLFHTVQKDFTAQTGDPTGTG 60
           MSV + T +GDI +++F ++ P T +NFL LC   YYNGC+FH   K F  QTGDPTGTG
Sbjct: 1   MSVTLHTDVGDIKIEVFCERTPKTCENFLALCASNYYNGCIFHRNIKGFMVQTGDPTGTG 60

Query: 61  TGGDSVYKFLYGEQARFFGDEIRVDLKHAKTGTVAMASAGENLNASQFYMTLRDNLDYLD 120
            GG+S++        + F DE    LKH   G V+MA+ G N N SQF++T      +LD
Sbjct: 61  RGGNSIW-------GKKFEDEYSEYLKHNVRGVVSMANNGPNTNGSQFFITYGKQ-PHLD 112

Query: 121 EKHTIFGEVAEGLETLSRINESFVDEKN-RPYKNIRIKHTYILEDPF 166
            K+T+FG+V +GLETL  + +  V+EK  RP  ++ IK   I  +PF
Sbjct: 113 MKYTVFGKVIDGLETLDELEKLPVNEKTYRPLNDVHIKDITIHANPF 159

>2hq6_A Serologically defined colon cancer antigen 10; protein folding, peptidyl-prolyl CIS-trans isomerase, struct genomics; 1.75A {Homo sapiens} Length = 185

 Score =  245 bits (627), Expect = 1e-78
 Identities = 68/169 (40%), Positives = 100/169 (59%), Gaps = 9/169 (5%)

Query: 1   MSVLIVTSLGDIVVDLFVDKCPLTTKNFLKLCKIKYYNGCLFHTVQKDFTAQTGDPTGTG 60
             VL+ T+ GDI ++L+  + P   +NF++LC   YY+  +FH V   F  Q GDPTGTG
Sbjct: 25  GKVLLKTTAGDIDIELWSKEAPKACRNFIQLCLEAYYDNTIFHRVVPGFIVQGGDPTGTG 84

Query: 61  TGGDSVYKFLYGEQARFFGDEIRVDLKHAKTGTVAMASAGENLNASQFYMTLRDNLDYLD 120
           +GG+S+Y          F DE    L+  + G VAMA+AG + N SQF+ TL    D L+
Sbjct: 85  SGGESIY-------GAPFKDEFHSRLRFNRRGLVAMANAGSHDNGSQFFFTL-GRADELN 136

Query: 121 EKHTIFGEVA-EGLETLSRINESFVDEKNRPYKNIRIKHTYILEDPFDD 168
            KHTIFG+V  + +  + R++E  +D+  RP+   +IK   +L +PFDD
Sbjct: 137 NKHTIFGKVTGDTVYNMLRLSEVDIDDDERPHNPHKIKSCEVLFNPFDD 185

>2poe_A Cyclophilin-like protein, putative; cryptosporidium parvum cyclophilin isomerase, structural genomics; 2.01A {Cryptosporidium parvum iowa II} PDB: 2qer_A Length = 185

 Score =  244 bits (626), Expect = 2e-78
 Identities = 68/175 (38%), Positives = 96/175 (54%), Gaps = 12/175 (6%)

Query: 2   SVLIVTSLGDIVVDLFVDKCPLTTKNFLKLCKIKYYNGCLFHTVQKDFTAQTGDPTGTGT 61
            V I+T+ GD+  +LF  +CP   KNFL L    YY   +FH   K F  Q GDPTGTG 
Sbjct: 18  GVRIITNYGDLKFELFCSQCPKACKNFLALSASGYYKNTIFHKNIKGFIIQGGDPTGTGK 77

Query: 62  GGDSVYKFLYGEQARFFGDEIRVDLKHAKTGTVAMASAGE----NLNASQFYMTLRDNLD 117
           GG+S+Y        R+F DEI  +LK+ + G ++MAS G     N N SQF++T    L 
Sbjct: 78  GGESIY-------GRYFDDEIYPELKYDRRGILSMASKGASKKPNTNGSQFFITYSS-LP 129

Query: 118 YLDEKHTIFGEVAEGLETLSRINESFVDEKNRPYKNIRIKHTYILEDPFDDPAQL 172
            L+ ++ IFG++ +G ETL+ +     D+ ++P   I IK   I  +P  D   L
Sbjct: 130 QLNGEYVIFGKLIDGFETLNTLENCPSDKSHKPIDEIIIKDIVIHSNPIADQEIL 184

>1zkc_A Peptidyl-prolyl CIS-trans isomerase like 2; CIS-trans isomerization, peptidylprolyl isomerase, protein- folding, structural genomics consortium; 1.65A {Homo sapiens} SCOP: b.62.1.1 Length = 197

 Score =  238 bits (610), Expect = 7e-76
 Identities = 72/184 (39%), Positives = 107/184 (58%), Gaps = 11/184 (5%)

Query: 3   VLIVTSLGDIVVDLFVDKCPLTTKNFLKLCKIKYYNGCLFHTVQKDFTAQTGDPTGTGTG 62
           V + T+ GD+ ++L  D  P T +NF++LCK  YY+G +FH   ++F  Q GDPTGTGTG
Sbjct: 22  VRLHTNKGDLNLELHCDLTPKTCENFIRLCKKHYYDGTIFHRSIRNFVIQGGDPTGTGTG 81

Query: 63  GDSVYKFLYGEQARFFGDEIRVDLKHAKTGTVAMASAGENLNASQFYMTLRDNLDYLDEK 122
           G+S +        + F DE R +L H   G ++MA++G N N SQF++T R    YLD+K
Sbjct: 82  GESYW-------GKPFKDEFRPNLSHTGRGILSMANSGPNSNRSQFFITFRS-CAYLDKK 133

Query: 123 HTIFGEVAEGLETLSRINESFVDEKN-RPYKNIRIKHTYILEDPFDDPAQLAELIPDASP 181
           HTIFG V  G + L+ +     D K  RP + IRI  T +  DP+++    A++  +   
Sbjct: 134 HTIFGRVVGGFDVLTAMENVESDPKTDRPKEEIRIDATTVFVDPYEEAD--AQIAQERKT 191

Query: 182 EGKP 185
           + K 
Sbjct: 192 QLKV 195

>2x7k_A Peptidyl-prolyl CIS-trans isomerase-like 1; isomerase-immunosuppressant complex, immunosuppressant; HET: MLE MVA BMT ABA SAR; 1.15A {Homo sapiens} PDB: 1xwn_A Length = 166

 Score =  202 bits (516), Expect = 2e-62
 Identities = 69/161 (42%), Positives = 98/161 (60%), Gaps = 8/161 (4%)

Query: 1   MSVLIVTSLGDIVVDLFVDKCPLTTKNFLKLCKIKYYNGCLFHTVQKDFTAQTGDPTGTG 60
            +V + TS+G IV++L+    P T KNF +L +  YYNG  FH + KDF  Q GDPTGTG
Sbjct: 12  PNVYLETSMGIIVLELYWKHAPKTCKNFAELARRGYYNGTKFHRIIKDFMIQGGDPTGTG 71

Query: 61  TGGDSVYKFLYGEQARFFGDEIRVDLKHAKTGTVAMASAGENLNASQFYMTLRDNLDYLD 120
            GG S+    YG+Q   F DE+  DLK    G +AMA+AG + N SQF++TL     +LD
Sbjct: 72  RGGASI----YGKQ---FEDELHPDLKFTGAGILAMANAGPDTNGSQFFVTLAPT-QWLD 123

Query: 121 EKHTIFGEVAEGLETLSRINESFVDEKNRPYKNIRIKHTYI 161
            KHTIFG V +G+  ++R+     + ++RP  +++I   Y 
Sbjct: 124 GKHTIFGRVCQGIGMVNRVGMVETNSQDRPVDDVKIIKAYP 164

>2b71_A Cyclophilin-like protein; structural genomics, structural genomics consortium, SGC, isomerase; 2.50A {Plasmodium yoelii} SCOP: b.62.1.1 Length = 196

 Score =  203 bits (519), Expect = 2e-62
 Identities = 63/163 (38%), Positives = 92/163 (56%), Gaps = 8/163 (4%)

Query: 2   SVLIVTSLGDIVVDLFVDKCPLTTKNFLKLCKIKYYNGCLFHTVQKDFTAQTGDPTGTGT 61
            + I T+LGD  V+L+    P T  NF  LC++ +Y+  +FH V  +F  Q GDPTGTG 
Sbjct: 40  YITIYTNLGDFEVELYWYHSPKTCLNFYTLCEMGFYDNTIFHRVIPNFVIQGGDPTGTGK 99

Query: 62  GGDSVYKFLYGEQARFFGDEIRVDLKHAKTGTVAMASAGENLNASQFYMTLRDNLDYLDE 121
           GG S+    YGE    F DEI  +LKH   G ++M++ G N N+SQF++TL   L +LD 
Sbjct: 100 GGKSI----YGEY---FEDEINKELKHTGAGILSMSNNGPNTNSSQFFITLAP-LPHLDG 151

Query: 122 KHTIFGEVAEGLETLSRINESFVDEKNRPYKNIRIKHTYILED 164
           KHTIF  V++ +  +  I        N+P  +++I  T    +
Sbjct: 152 KHTIFARVSKNMTCIENIASVQTTATNKPIFDLKILRTSTAVN 194

>2fu0_A Cyclophilin, putative; PFE0505W, cyclosporin-binding domain, structura genomics, structural genomics consortium, SGC, unknown FUNC; 1.80A {Plasmodium falciparum} SCOP: b.62.1.1 Length = 160

 Score =  199 bits (508), Expect = 2e-61
 Identities = 64/160 (40%), Positives = 96/160 (60%), Gaps = 8/160 (5%)

Query: 2   SVLIVTSLGDIVVDLFVDKCPLTTKNFLKLCKIKYYNGCLFHTVQKDFTAQTGDPTGTGT 61
           S +I T++GDI + LF  +C  T +NF       YYN C+FH V K F  QTGDP+G GT
Sbjct: 7   SAIIYTTMGDIHISLFYKECKKTVQNFSVHSINGYYNNCIFHRVIKHFMVQTGDPSGDGT 66

Query: 62  GGDSVYKFLYGEQARFFGDEIRVDLKHAKTGTVAMASAGENLNASQFYMTLRDNLDYLDE 121
           GG+S+    +G +   F DE    L H+K   V+MA+ G N N SQF++T      +LD 
Sbjct: 67  GGESI----WGNE---FEDEFFDHLNHSKPFMVSMANCGPNTNGSQFFITTVP-CPWLDF 118

Query: 122 KHTIFGEVAEGLETLSRINESFVDEKNRPYKNIRIKHTYI 161
           KHT+FG+V +G + +  I +   D++++P ++I+I +  I
Sbjct: 119 KHTVFGKVTQGSKIVLDIEKVRTDKRDKPLEDIKILNIKI 158

>2k7n_A Peptidyl-prolyl CIS-trans isomerase-like 1; beta barrel, disorder-order transition, HOOK-like, mRNA processing, mRNA splicing, rotamase; NMR {Homo sapiens} Length = 203

 Score =  200 bits (511), Expect = 3e-61
 Identities = 72/196 (36%), Positives = 103/196 (52%), Gaps = 17/196 (8%)

Query: 1   MSVLIVTSLGDIVVDLFVDKCPLTTKNFLKLCKIKYYNGCLFHTVQKDFTAQTGDPTGTG 60
            +V + TS+G IV++L+    P T KNF +L +  YYNG  FH + KDF  Q GDPTGTG
Sbjct: 12  PNVYLETSMGIIVLELYWKHAPKTCKNFAELARRGYYNGTKFHRIIKDFMIQGGDPTGTG 71

Query: 61  TGGDSVYKFLYGEQARFFGDEIRVDLKHAKTGTVAMASAGENLNASQFYMTLRDNLDYLD 120
            GG S+    YG+Q   F DE+  DLK    G +AMA+AG + N SQF++TL     +LD
Sbjct: 72  RGGASI----YGKQ---FEDELHPDLKFTGAGILAMANAGPDTNGSQFFVTLAPT-QWLD 123

Query: 121 EKHTIFGEVAEGLETLSRINESFVDEKNRPYKNIRIKHTYILE---------DPFDDPAQ 171
            KHTIFG V +G+  ++R+     + ++RP  +++I   Y                  + 
Sbjct: 124 GKHTIFGRVCQGIGMVNRVGMVETNSQDRPVDDVKIIKAYPSGGGGSGGGSGGGSGGGSG 183

Query: 172 LAELIPDASPEGKPKD 187
                P+      P D
Sbjct: 184 DGGAFPEIHVAQYPLD 199

>2a2n_A Peptidylprolyl isomerase domain and WD repeat CON; CIS-trans isomerization, protein-folding, peptidylprolyl ISO structural genomics; 1.65A {Homo sapiens} SCOP: b.62.1.1 Length = 176

 Score =  193 bits (493), Expect = 5e-59
 Identities = 68/161 (42%), Positives = 99/161 (61%), Gaps = 9/161 (5%)

Query: 2   SVLIVTSLGDIVVDLFVDKCPLTTKNFLKLCKIKYYNGCLFHTVQKDFTAQTGDPTGTGT 61
           S +I TS+GDI   LF  +CP T +NF    +  YYNG  FH + K F  QTGDPTGTG 
Sbjct: 23  SAIIHTSMGDIHTKLFPVECPKTVENFCVHSRNGYYNGHTFHRIIKGFMIQTGDPTGTGM 82

Query: 62  GGDSVYKFLYGEQARFFGDEIRVDLKHAKTGTVAMASAGENLNASQFYMTLRDNLDYLDE 121
           GG+S+    +G +   F DE    L+H +  T++MA+AG N N SQF++T+     +LD 
Sbjct: 83  GGESI----WGGE---FEDEFHSTLRHDRPYTLSMANAGSNTNGSQFFITVVPT-PWLDN 134

Query: 122 KHTIFGEVAEGLETLSRINESFVDEKN-RPYKNIRIKHTYI 161
           KHT+FG V +G+E + RI+   V+ K  +PY+++ I +  +
Sbjct: 135 KHTVFGRVTKGMEVVQRISNVKVNPKTDKPYEDVSIINITV 175

>1w74_A Peptidyl-prolyl CIS-trans isomerase A; cyclophilin, ppiase, RV0009, rotamase, structural proteomics in europe, spine; 2.6A {Mycobacterium tuberculosis} SCOP: b.62.1.1 Length = 191

 Score =  173 bits (440), Expect = 4e-51
 Identities = 60/178 (33%), Positives = 88/178 (49%), Gaps = 28/178 (15%)

Query: 1   MSVLIVTSLGDIVVDLFVDKCPLTTKNFLKLCK---------------IKYYNGCLFHTV 45
            +  + T+ GDI + LF +  P T  NF+ L +                 +Y+G +FH V
Sbjct: 24  ATATLHTNRGDIKIALFGNHAPKTVANFVGLAQGTKDYSTQNASGGPSGPFYDGAVFHRV 83

Query: 46  QKDFTAQTGDPTGTGTGGDSVYKFLYGEQARFFGDEIRVDLKHAKTGTVAMASAGENLNA 105
            + F  Q GDPTGTG GG   YK         F DE   +L+  K   +AMA+AG   N 
Sbjct: 84  IQGFMIQGGDPTGTGRGGPG-YK---------FADEFHPELQFDKPYLLAMANAGPGTNG 133

Query: 106 SQFYMTLRDNLDYLDEKHTIFGEV--AEGLETLSRINESFVDEKNRPYKNIRIKHTYI 161
           SQF++T+     +L+ +HTIFGEV  AE    +  I+++  D  +RP   + I+   I
Sbjct: 134 SQFFITVGKT-PHLNRRHTIFGEVIDAESQRVVEAISKTATDGNDRPTDPVVIESITI 190

>1lop_A Cyclophilin A; rotamase, isomerase-isomerase inhibitor complex; HET: NIT; 1.80A {Escherichia coli} SCOP: b.62.1.1 PDB: 2nul_A 2rs4_A Length = 164

 Score =  140 bits (356), Expect = 2e-39
 Identities = 45/173 (26%), Positives = 75/173 (43%), Gaps = 22/173 (12%)

Query: 3   VLIVTSLGDIVVDLFVDKCPLTTKNFLKLCKIKYYNGCLFHTVQKDFTAQTGDPTGTGTG 62
           V   T+ GDIV+  F DK P T KNFL  C+  +YN  +FH V   F  Q G        
Sbjct: 2   VTFHTNHGDIVIKTFDDKAPETVKNFLDYCREGFYNNTIFHRVINGFMIQGGGFEPGMKQ 61

Query: 63  GDSVYKFLYGEQARFFGDEIRVDLKHAKTGTVAMA-SAGENLNASQFYMTLRDN--LDY- 118
             +              +E    LK+   GT+AMA +   +   +QF++ + DN  L++ 
Sbjct: 62  KATKE---------PIKNEANNGLKN-TRGTLAMARTQAPHSATAQFFINVVDNDFLNFS 111

Query: 119 ----LDEKHTIFGEVAEGLETLSRINESFVDEK----NRPYKNIRIKHTYILE 163
                   + +F EV +G++ + +I            + P +++ I+   + E
Sbjct: 112 GESLQGWGYCVFAEVVDGMDEVDKIKGVATGRSGMHQDVPKEDVIIESVTVSE 164

>3s6m_A Peptidyl-prolyl CIS-trans isomerase; seattle structural genomics center for infectious disease; 1.65A {Burkholderia pseudomallei} PDB: 3t1u_A* Length = 167

 Score =  137 bits (348), Expect = 3e-38
 Identities = 42/173 (24%), Positives = 75/173 (43%), Gaps = 24/173 (13%)

Query: 3   VLIVTSLGDIVVDLFVDKCPLTTKNFLKLCKIKYYNGCLFHTVQKDFTAQTGDPTGTGTG 62
           V + T+ G I ++L   K P T +NFL   K  +Y+G +FH V   F  Q G        
Sbjct: 6   VELHTNHGVIKLELDEAKAPKTVENFLNYVKKGHYDGTIFHRVINGFMIQGGGFEPGLKQ 65

Query: 63  GDSVYKFLYGEQARFFGDEIRVDLKHAKTGTVAMA-SAGENLNASQFYMTLRDNLDYLDE 121
             +              +E    LK+  T T+AMA +   +   +QF++ + DN ++L+ 
Sbjct: 66  KPTDA---------PIANEANNGLKN-DTYTIAMARTNDPHSATAQFFINVNDN-EFLNH 114

Query: 122 K--------HTIFGEVAEGLETLSRINESFVDEK----NRPYKNIRIKHTYIL 162
                    + +FG+V EG + + +I       K    + P  ++ I+   ++
Sbjct: 115 SSPTPQGWGYAVFGKVVEGQDIVDKIKAVKTGSKGFHQDVPNDDVVIEKAVVV 167

>1v9t_A Cyclophilin B; beta barrel, isomerase-isomerase inhibitor complex; HET: NIT; 1.70A {Escherichia coli} SCOP: b.62.1.1 PDB: 1j2a_A* 1vai_A* 1clh_A Length = 166

 Score =  135 bits (343), Expect = 1e-37
 Identities = 46/169 (27%), Positives = 78/169 (46%), Gaps = 19/169 (11%)

Query: 3   VLIVTSLGDIVVDLFVDKCPLTTKNFLKLCKIKYYNGCLFHTVQKDFTAQTGDPTGTGTG 62
           VL+ TS G+I ++L   K P++ +NF+      +YN   FH V   F  Q G  T     
Sbjct: 7   VLLTTSAGNIELELDKQKAPVSVQNFVDYVNSGFYNNTTFHRVIPGFMIQGGGFTEQMQQ 66

Query: 63  GDSVYKFLYGEQARFFGDEIRVDLKHAKTGTVAMA-SAGENLNASQFYMTLRDN--LDY- 118
                            +E    L++   GT+AMA +A ++   SQF++ + DN  LD+ 
Sbjct: 67  KKPNP---------PIKNEADNGLRN-TRGTIAMARTADKDSATSQFFINVADNAFLDHG 116

Query: 119 -LDEKHTIFGEVAEGLETLSRINESFVDEK----NRPYKNIRIKHTYIL 162
             D  + +FG+V +G++   +I++    +     N P K + I    +L
Sbjct: 117 QRDFGYAVFGKVVKGMDVADKISQVPTHDVGPYQNVPSKPVVILSATVL 165

>2wfi_A Peptidyl-prolyl CIS-trans isomerase G; phosphoprotein, PRE-mRNA splicing, alternative splicing, nucleus, rotamase, cyclosporin; HET: OCS; 0.75A {Homo sapiens} PDB: 2wfj_A* 2gw2_A Length = 179

 Score =  130 bits (330), Expect = 1e-35
 Identities = 59/160 (36%), Positives = 83/160 (51%), Gaps = 21/160 (13%)

Query: 9   LGDIVVDLFVDKCPLTTKNFLKLC-----------KIKYYNGCLFHTVQKDFTAQTGDPT 57
            G +V +LF D CP T +NF  LC           K  +Y  CLFH V KDF  Q GD +
Sbjct: 23  AGRVVFELFSDVCPKTCENFRCLCTGEKGTGKSTQKPLHYKSCLFHRVVKDFMVQGGDFS 82

Query: 58  -GTGTGGDSVYKFLYGEQARFFGDEIRVDLKHAKTGTVAMASAGENLNASQFYMTLRDNL 116
            G G GG+S+Y    G     F DE    +KH K   ++MA+ G++ N SQF++T +   
Sbjct: 83  EGNGRGGESIY----GGF---FEDE-SFAVKHNKEFLLSMANRGKDTNGSQFFITTKPT- 133

Query: 117 DYLDEKHTIFGEVAEGLETLSRINESFVDEKNRPYKNIRI 156
            +LD  H +FG+V  G E +  I     D  ++P+  +RI
Sbjct: 134 PHLDGHHVVFGQVISGQEVVREIENQKTDAASKPFAEVRI 173

>1a58_A Cyclophilin; isomerase, ppiase; 1.95A {Brugia malayi} SCOP: b.62.1.1 PDB: 1a33_A 1c5f_A* Length = 177

 Score =  129 bits (328), Expect = 2e-35
 Identities = 60/160 (37%), Positives = 83/160 (51%), Gaps = 21/160 (13%)

Query: 9   LGDIVVDLFVDKCPLTTKNFLKLC-----------KIKYYNGCLFHTVQKDFTAQTGDPT 57
            G IV++L+ D  P T  NFL LC           K  +Y G  FH V K+F  Q GD T
Sbjct: 20  AGRIVMELYNDIAPRTCNNFLMLCTGMAGTGKISGKPLHYKGSTFHRVIKNFMIQGGDFT 79

Query: 58  -GTGTGGDSVYKFLYGEQARFFGDEIRVDLKHAKTGTVAMASAGENLNASQFYMTLRDNL 116
            G GTGG+S+Y    G     F DE    +KH +   V+MA+ G N N SQF++T     
Sbjct: 80  KGDGTGGESIY----GGM---FDDE-EFVMKHDEPFVVSMANKGPNTNGSQFFITTTPA- 130

Query: 117 DYLDEKHTIFGEVAEGLETLSRINESFVDEKNRPYKNIRI 156
            +L+  H +FG+V  G E +++I     + KNRP  ++ I
Sbjct: 131 PHLNNIHVVFGKVVSGQEVVTKIEYLKTNSKNRPLADVVI 170

>2he9_A NK-tumor recognition protein; cyclosporin, isomerase, membrane, repeat, rotamase, peptidylprolyl isomerase, structural genomics; 2.00A {Homo sapiens} Length = 192

 Score =  129 bits (326), Expect = 7e-35
 Identities = 60/160 (37%), Positives = 83/160 (51%), Gaps = 21/160 (13%)

Query: 9   LGDIVVDLFVDKCPLTTKNFLKLC-----------KIKYYNGCLFHTVQKDFTAQTGDPT 57
           +G I+  LF D CP T KNFL LC           K   Y G  FH V K+F  Q GD +
Sbjct: 33  VGRIMFQLFSDICPKTCKNFLCLCSGEKGLGKTTGKKLCYKGSTFHRVVKNFMIQGGDFS 92

Query: 58  -GTGTGGDSVYKFLYGEQARFFGDEIRVDLKHAKTGTVAMASAGENLNASQFYMTLRDNL 116
            G G GG+S+Y    G     F DE    LKH +   ++MA+ G++ N SQF++T +   
Sbjct: 93  EGNGKGGESIY----GGY---FKDE-NFILKHDRAFLLSMANRGKHTNGSQFFITTKPA- 143

Query: 117 DYLDEKHTIFGEVAEGLETLSRINESFVDEKNRPYKNIRI 156
            +LD  H +FG V  G E + +I     D  +RPY ++R+
Sbjct: 144 PHLDGVHVVFGLVISGFEVIEQIENLKTDAASRPYADVRV 183

>1mzw_A Cyclophilin H, U-snRNP-ASSOCIATED cyclophilin; cyclophilin, peptidyl-prolyl-CIS/trans isomerase, spliceosome, U4/U6-60K protein, WD protein; 2.00A {Homo sapiens} SCOP: b.62.1.1 PDB: 1qoi_A Length = 177

 Score =  126 bits (320), Expect = 3e-34
 Identities = 52/157 (33%), Positives = 77/157 (49%), Gaps = 18/157 (11%)

Query: 9   LGDIVVDLFVDKCPLTTKNFLKLC--------KIKYYNGCLFHTVQKDFTAQTGDPT-GT 59
           +G + ++LF D  P T +NF + C            Y G  FH V KDF  Q GD   G 
Sbjct: 24  VGRMKIELFADVVPKTAENFRQFCTGEFRKDGVPIGYKGSTFHRVIKDFMIQGGDFVNGD 83

Query: 60  GTGGDSVYKFLYGEQARFFGDEIRVDLKHAKTGTVAMASAGENLNASQFYMTLRDNLDYL 119
           GTG  S+Y          F DE    L+H+  G ++MA++G + N  QF++T     D+L
Sbjct: 84  GTGVASIY----RGP---FADE-NFKLRHSAPGLLSMANSGPSTNGCQFFITCSKC-DWL 134

Query: 120 DEKHTIFGEVAEGLETLSRINESFVDEKNRPYKNIRI 156
           D KH +FG++ +GL  + +I        N+P   + I
Sbjct: 135 DGKHVVFGKIIDGLLVMRKIENVPTGPNNKPKLPVVI 171

>2igv_A Peptidyl-prolyl CIS-trans isomerase 3; rotamase; 1.67A {Caenorhabditis elegans} SCOP: b.62.1.1 PDB: 1e3b_A 1e8k_A 1dyw_A 2igw_A 2hqj_A Length = 173

 Score =  125 bits (316), Expect = 1e-33
 Identities = 59/159 (37%), Positives = 83/159 (52%), Gaps = 21/159 (13%)

Query: 9   LGDIVVDLFVDKCPLTTKNFLKLC----------KIKYYNGCLFHTVQKDFTAQTGDPT- 57
            G IV++L+ D  P T  NF  LC          K  ++ G  FH +  +F  Q GD T 
Sbjct: 17  SGRIVMELYDDVVPKTAGNFRALCTGENGIGKSGKPLHFKGSKFHRIIPNFMIQGGDFTR 76

Query: 58  GTGTGGDSVYKFLYGEQARFFGDEIRVDLKHAKTGTVAMASAGENLNASQFYMTLRDNLD 117
           G GTGG+S+Y    GE+   F DE     KH   G ++MA+AG N N SQF++      +
Sbjct: 77  GNGTGGESIY----GEK---FPDE-NFKEKHTGPGVLSMANAGPNTNGSQFFLCTVKT-E 127

Query: 118 YLDEKHTIFGEVAEGLETLSRINESFVDEKNRPYKNIRI 156
           +LD KH +FG V EGL+ +  + ES   +  +P K+  I
Sbjct: 128 WLDGKHVVFGRVVEGLDVVKAV-ESNGSQSGKPVKDCMI 165

>2poy_A Peptidyl-prolyl CIS-trans isomerase; isomerase-immunosuppressant complex, immunosuppressant, cyclophilin, isomerase, S genomics, structural genomics consortium; HET: BMT; 1.80A {Cryptosporidium parvum iowa II} PDB: 2plu_A* Length = 186

 Score =  124 bits (314), Expect = 3e-33
 Identities = 59/159 (37%), Positives = 81/159 (50%), Gaps = 21/159 (13%)

Query: 9   LGDIVVDLFVDKCPLTTKNFLKLC----------KIKYYNGCLFHTVQKDFTAQTGDPT- 57
            G I ++LF DK P+T +NF  LC          K   Y G  FH +   F  Q GD T 
Sbjct: 33  AGRITMELFADKVPITAENFRALCTGEKGMGQSGKPLCYTGSFFHRIIPQFMIQGGDFTR 92

Query: 58  GTGTGGDSVYKFLYGEQARFFGDEIRVDLKHAKTGTVAMASAGENLNASQFYMTLRDNLD 117
           G GTGG+S+Y    G +   F DE      H     ++MA+AG N N SQF++T      
Sbjct: 93  GDGTGGESIY----GSK---FRDE-NFVYTHDAPFLLSMANAGPNTNGSQFFITTVPC-P 143

Query: 118 YLDEKHTIFGEVAEGLETLSRINESFVDEKNRPYKNIRI 156
           +LD KH +FG+V EG+E +  I E    +  +P K++ I
Sbjct: 144 WLDGKHVVFGKVLEGMEVVKSI-EKCGSQNGKPTKSVCI 181

>2r99_A Peptidyl-prolyl CIS-trans isomerase E; CIS-trans isomerization, structural genomics consortium, SGC, alternative splicing, mRNA processing; 1.61A {Homo sapiens} SCOP: b.62.1.1 PDB: 3uch_A 1zmf_A Length = 173

 Score =  123 bits (312), Expect = 3e-33
 Identities = 59/152 (38%), Positives = 82/152 (53%), Gaps = 14/152 (9%)

Query: 9   LGDIVVDLFVDKCPLTTKNFLKLC---KIKYYNGCLFHTVQKDFTAQTGDPT-GTGTGGD 64
            G I + L  D  P+T +NF  LC   K   + G  FH +   F  Q GD T   GTGG 
Sbjct: 25  AGRIQMLLRSDVVPMTAENFRCLCTHEKGFGFKGSSFHRIIPQFMCQGGDFTNHNGTGGK 84

Query: 65  SVYKFLYGEQARFFGDEIRVDLKHAKTGTVAMASAGENLNASQFYMTLRDNLDYLDEKHT 124
           S+Y    G++   F DE    LKH   G ++MA++G N N SQF++T     D+LD KH 
Sbjct: 85  SIY----GKK---FDDE-NFILKHTGPGLLSMANSGPNTNGSQFFLTCDKT-DWLDGKHV 135

Query: 125 IFGEVAEGLETLSRINESFVDEKNRPYKNIRI 156
           +FGEV EGL+ L +I E+   +  +P + + I
Sbjct: 136 VFGEVTEGLDVLRQI-EAQGSKDGKPKQKVII 166

>2cmt_A Peptidyl-prolyl CIS-trans isomerase E; rotamase activity, rotamase, RNA-binding, cyclosporin, cyclophilin, beta-barrel; 1.50A {Schistosoma mansoni} PDB: 2ck1_A Length = 172

 Score =  123 bits (311), Expect = 4e-33
 Identities = 54/152 (35%), Positives = 78/152 (51%), Gaps = 14/152 (9%)

Query: 9   LGDIVVDLFVDKCPLTTKNFLKLC---KIKYYNGCLFHTVQKDFTAQTGDPT-GTGTGGD 64
            G IV++L  D  P T +NF  LC   +   Y+ C FH V   F  Q GD   G GTGG 
Sbjct: 24  AGRIVMELRSDIVPRTAENFRALCTGERGFGYHNCCFHRVIPQFMCQGGDFVKGDGTGGK 83

Query: 65  SVYKFLYGEQARFFGDEIRVDLKHAKTGTVAMASAGENLNASQFYMTLRDNLDYLDEKHT 124
           S+Y    G +   F DE    L+H   G ++MA++G N N SQF++      D+LD KH 
Sbjct: 84  SIY----GRK---FDDE-NFQLRHEGFGVLSMANSGPNTNGSQFFICTTKC-DWLDGKHV 134

Query: 125 IFGEVAEGLETLSRINESFVDEKNRPYKNIRI 156
           +FG V +G   + ++ ES   +  +  + + I
Sbjct: 135 VFGRVVDGQNVVKKM-ESVGSKSGKVKEPVII 165

>2z6w_A Peptidyl-prolyl CIS-trans isomerase; isomerase-immunosuppressant complex, immunosuppressant, cyclophilin D; HET: BMT MLE CIT; 0.96A {Homo sapiens} SCOP: b.62.1.1 PDB: 3rcg_A* 3r49_A* 3r54_A 3r56_A* 3r57_A* 3r59_A* 3rcf_A* 3r4g_A* 3rci_X* 3rck_X* 3rcl_A* 3rd9_X* 3rda_X* 3rdb_A* 3rdc_A* 2bit_X 2biu_X 3qyu_A 3k0m_A 1ak4_A* ... Length = 165

 Score =  122 bits (310), Expect = 6e-33
 Identities = 63/152 (41%), Positives = 81/152 (53%), Gaps = 14/152 (9%)

Query: 9   LGDIVVDLFVDKCPLTTKNFLKLC---KIKYYNGCLFHTVQKDFTAQTGDPT-GTGTGGD 64
           LG +V++L  D  P T +NF  LC   K   Y G  FH V   F  Q GD T   GTGG 
Sbjct: 17  LGRVVLELKADVVPKTAENFRALCTGEKGFGYKGSTFHRVIPSFMCQAGDFTNHNGTGGK 76

Query: 65  SVYKFLYGEQARFFGDEIRVDLKHAKTGTVAMASAGENLNASQFYMTLRDNLDYLDEKHT 124
           S+Y    G +   F DE    LKH   G ++MA+AG N N SQF++      D+LD KH 
Sbjct: 77  SIY----GSR---FPDE-NFTLKHVGPGVLSMANAGPNTNGSQFFICTIKT-DWLDGKHV 127

Query: 125 IFGEVAEGLETLSRINESFVDEKNRPYKNIRI 156
           +FG V EG++ + +I ESF  +  R  K I I
Sbjct: 128 VFGHVIEGMDVVKKI-ESFGSKSGRTSKKIVI 158

>3pmp_A Cyclophilin A; peptidyl prolyl isomerase, isomerase-immunosuppressant compl; HET: BMT; 1.47A {Moniliophthora perniciosa} PDB: 3o7t_A Length = 164

 Score =  122 bits (309), Expect = 9e-33
 Identities = 58/152 (38%), Positives = 78/152 (51%), Gaps = 14/152 (9%)

Query: 9   LGDIVVDLFVDKCPLTTKNFLKLC---KIKYYNGCLFHTVQKDFTAQTGDPT-GTGTGGD 64
            G IV  L+ +  P T KNF +L        Y   +FH V   F  Q GD T   GTGG 
Sbjct: 16  EGRIVFKLYDEAVPKTAKNFRELATGQHGFGYKDSIFHRVIPQFMLQGGDFTRHNGTGGK 75

Query: 65  SVYKFLYGEQARFFGDEIRVDLKHAKTGTVAMASAGENLNASQFYMTLRDNLDYLDEKHT 124
           S+Y    GE+   F DE    +KH K G ++MA+AG N N SQF++T      +LD KH 
Sbjct: 76  SIY----GEK---FADE-NFQVKHTKPGLLSMANAGANTNGSQFFITTVPT-SWLDGKHV 126

Query: 125 IFGEVAEGLETLSRINESFVDEKNRPYKNIRI 156
           +FGEV EGL+ + ++ E       +    I+I
Sbjct: 127 VFGEVIEGLDIVRKV-EGKGSASGKTNATIKI 157

>1qng_A Peptidyl-prolyl CIS-trans isomerase; isomerase-immunosuppressant complex, cyclophilin-cyclosporin complex, immunosuppressant, cyclophilin; HET: BMT; 2.1A {Plasmodium falciparum} SCOP: b.62.1.1 PDB: 1qnh_A* Length = 170

 Score =  122 bits (309), Expect = 9e-33
 Identities = 56/159 (35%), Positives = 84/159 (52%), Gaps = 20/159 (12%)

Query: 8   SLGDIVVDLFVDKCPLTTKNFLKLC---KIKY------YNGCLFHTVQKDFTAQTGDPT- 57
           + G I+ +LF D  P T +NF  LC   KI        Y   +FH +   F  Q GD T 
Sbjct: 16  NAGRIIFELFSDITPRTCENFRALCTGEKIGSRGKNLHYKNSIFHRIIPQFMCQGGDITN 75

Query: 58  GTGTGGDSVYKFLYGEQARFFGDEIRVDLKHAKTGTVAMASAGENLNASQFYMTLRDNLD 117
           G G+GG+S+Y    G     F DE   ++KH + G ++MA+AG N N+SQF++TL     
Sbjct: 76  GNGSGGESIY----GRS---FTDE-NFNMKHDQPGLLSMANAGPNTNSSQFFITLVPC-P 126

Query: 118 YLDEKHTIFGEVAEGLETLSRINESFVDEKNRPYKNIRI 156
           +LD KH +FG+V EG+  +  + E    +     +++ I
Sbjct: 127 WLDGKHVVFGKVIEGMNVVREM-EKEGAKSGYVKRSVVI 164

>3rdd_A Peptidyl-prolyl CIS-trans isomerase A; beta barrel, cytosolic, inhibito isomerase-isomerase inhibitor complex; HET: EA4; 2.14A {Homo sapiens} Length = 184

 Score =  122 bits (309), Expect = 1e-32
 Identities = 59/152 (38%), Positives = 78/152 (51%), Gaps = 14/152 (9%)

Query: 9   LGDIVVDLFVDKCPLTTKNFLKLC---KIKYYNGCLFHTVQKDFTAQTGDPT-GTGTGGD 64
           LG +  +LF DK P T +NF  L    K   Y G  FH +   F  Q GD T   GTGG 
Sbjct: 36  LGRVSFELFADKVPKTAENFRALSTGEKGFGYKGSCFHRIIPGFMCQGGDFTRHNGTGGK 95

Query: 65  SVYKFLYGEQARFFGDEIRVDLKHAKTGTVAMASAGENLNASQFYMTLRDNLDYLDEKHT 124
           S+Y    GE+   F DE    LKH   G ++MA+AG N N SQF++      ++LD KH 
Sbjct: 96  SIY----GEK---FEDE-NFILKHTGPGILSMANAGPNTNGSQFFICTAKT-EWLDGKHV 146

Query: 125 IFGEVAEGLETLSRINESFVDEKNRPYKNIRI 156
           +FG+V EG+  +  + E F     +  K I I
Sbjct: 147 VFGKVKEGMNIVEAM-ERFGSRNGKTSKKITI 177

>3ich_A Peptidyl-prolyl CIS-trans isomerase B; beta sandwich, cyclosporin, endoplasmic reticulum, glycoprot isomerase, rotamase; 1.20A {Homo sapiens} PDB: 3ici_A* 1cyn_A* 2esl_A* 2rmc_A* 1h0p_A 1xo7_A 1xq7_A* Length = 188

 Score =  121 bits (305), Expect = 6e-32
 Identities = 60/152 (39%), Positives = 85/152 (55%), Gaps = 13/152 (8%)

Query: 9   LGDIVVDLFVDKCPLTTKNFLKLC---KIKYYNGCLFHTVQKDFTAQTGDPT-GTGTGGD 64
           +G ++  LF    P T  NF+ L    K   Y    FH V KDF  Q GD T G GTGG 
Sbjct: 29  VGRVIFGLFGKTVPKTVDNFVALATGEKGFGYKNSKFHRVIKDFMIQGGDFTRGDGTGGK 88

Query: 65  SVYKFLYGEQARFFGDEIRVDLKHAKTGTVAMASAGENLNASQFYMTLRDNLDYLDEKHT 124
           S+Y    GE+   F DE    LKH   G V+MA+AG++ N SQF++T      +LD KH 
Sbjct: 89  SIY----GER---FPDE-NFKLKHYGPGWVSMANAGKDTNGSQFFITTVKT-AWLDGKHV 139

Query: 125 IFGEVAEGLETLSRINESFVDEKNRPYKNIRI 156
           +FG+V EG+E + ++  +  D +++P K++ I
Sbjct: 140 VFGKVLEGMEVVRKVESTKTDSRDKPLKDVII 171

>1ihg_A Cyclophilin 40; ppiase immunophilin tetratricopeptide, isomerase; 1.80A {Bos taurus} SCOP: a.118.8.1 b.62.1.1 PDB: 1iip_A Length = 370

 Score =  125 bits (317), Expect = 6e-32
 Identities = 64/196 (32%), Positives = 96/196 (48%), Gaps = 22/196 (11%)

Query: 9   LGDIVVDLFVDKCPLTTKNFLKLC-----------KIKYYNGCLFHTVQKDFTAQTGDPT 57
           +G IV++LF D  P T +NF  LC           K  ++ GC FH + K F  Q GD +
Sbjct: 29  VGRIVLELFADIVPKTAENFRALCTGEKGIGPTTGKPLHFKGCPFHRIIKKFMIQGGDFS 88

Query: 58  -GTGTGGDSVYKFLYGEQARFFGDEIRVDLKHAKTGTVAMASAGENLNASQFYMTLRDNL 116
              GTGG+S+Y    GE+   F DE     KH K G ++MA+AG N N SQF++T     
Sbjct: 89  NQNGTGGESIY----GEK---FEDE-NFHYKHDKEGLLSMANAGSNTNGSQFFITTVPT- 139

Query: 117 DYLDEKHTIFGEVAEGLETLSRINESFVDEKNRPYKNIRIKHTYILEDPFDDPAQLAELI 176
            +LD KH +FG+V +G+     + E+   +  +P K   I     L++  D      +  
Sbjct: 140 PHLDGKHVVFGQVIKGMGVAKIL-ENVEVKGEKPAKLCVIAECGELKEGDDWGIFPKDGS 198

Query: 177 PDASPEGKPKDEVVDE 192
            D+ P+     +V  +
Sbjct: 199 GDSHPDFPEDADVDLK 214

>2haq_A Cyclophilin; rotamase, proline, isomerase, CIS-trans, protozoa, KAla-AZAR.; 1.97A {Leishmania donovani} PDB: 3eov_A* 3bt8_A Length = 172

 Score =  118 bits (299), Expect = 2e-31
 Identities = 59/152 (38%), Positives = 89/152 (58%), Gaps = 14/152 (9%)

Query: 9   LGDIVVDLFVDKCPLTTKNFLKLC---KIKYYNGCLFHTVQKDFTAQTGDPT-GTGTGGD 64
           LG I + LF    PLTT+NF +LC       Y   +FH V ++F  Q GD T   GTGG 
Sbjct: 25  LGRITIGLFGKDAPLTTENFRQLCTGEHGFGYKDSIFHRVIQNFMIQGGDFTNFDGTGGK 84

Query: 65  SVYKFLYGEQARFFGDEIRVDLKHAKTGTVAMASAGENLNASQFYMTLRDNLDYLDEKHT 124
           S+Y    GE+   F DE  +++KH   G ++MA+AG N N SQF++T      +LD +H 
Sbjct: 85  SIY----GEK---FADE-NLNVKHFV-GALSMANAGPNTNGSQFFITTAPT-PWLDGRHV 134

Query: 125 IFGEVAEGLETLSRINESFVDEKNRPYKNIRI 156
           +FG+V +G++ + RI ++  +  +RP K ++I
Sbjct: 135 VFGKVLDGMDVVLRIEKTKTNSHDRPVKPVKI 166

>3k2c_A Peptidyl-prolyl CIS-trans isomerase; ssgcid, NIH, niaid, SBRI, UW, decode, cytoplasm, rotamase, structural genomics; HET: PG5; 1.95A {Encephalitozoon cuniculi} Length = 193

 Score =  118 bits (299), Expect = 4e-31
 Identities = 64/153 (41%), Positives = 85/153 (55%), Gaps = 14/153 (9%)

Query: 9   LGDIVVDLFVDKCPLTTKNFLKLC---KIKYYNGCLFHTVQKDFTAQTGDPT-GTGTGGD 64
           LG IV+ L  D  P T KNF  LC   K + Y G  FH +   F  Q GD T   GTGG 
Sbjct: 41  LGRIVMKLEDDIVPKTAKNFRTLCERPKGEGYKGSTFHRIIPGFMVQGGDYTAHNGTGGR 100

Query: 65  SVYKFLYGEQARFFGDEIRVDLKHAKTGTVAMASAGENLNASQFYMTLRDNLDYLDEKHT 124
           S+Y    GE+   F DE   +LKH K G ++MA+ G + N SQF++TL     +LDEKH 
Sbjct: 101 SIY----GEK---FPDE-NFELKHTKEGILSMANCGAHTNGSQFFITLGKT-QWLDEKHV 151

Query: 125 IFGEVAEGLETLSRINESFVDEKNRPYKNIRIK 157
           +FGEV EG++ + +I   +  E  +  K  RI+
Sbjct: 152 VFGEVVEGMDVVHKI-AKYGSESGQVKKGYRIE 183

>2ose_A Probable peptidyl-prolyl CIS-trans isomerase; cyclophilin; 2.04A {Mimivirus} Length = 234

 Score =  117 bits (295), Expect = 3e-30
 Identities = 41/180 (22%), Positives = 64/180 (35%), Gaps = 39/180 (21%)

Query: 9   LGDIVVDLFVDKCPLTTKNFLKLC--------------------KIKYYNGCLFHTVQKD 48
           +G + + LF D  P   +NF++L                       + Y GC FH V  +
Sbjct: 28  IGRLQIKLFRDAFPAGVENFVQLTNGKTYRVNSNGTGKYKYNRHINRTYEGCKFHNVLHN 87

Query: 49  FTAQTGDPT-GTGTGGDSVYKFLYGEQARFFGDEIRVD--LKHAKTGTVAMAS----AGE 101
               +GD     G+   +VY     ++       +  D    H   G +++      +G 
Sbjct: 88  NYIVSGDIYNSNGSSAGTVY----CDE---PIPPVFGDYFYPHESKGLLSLVPYTDESGN 140

Query: 102 NLNASQFYMTLRDNL-----DYLDEKHTIFGEVAEGLETLSRINESFVDEKNRPYKNIRI 156
               S F +TL D       D LD    + G+V  GL+ L +IN        R Y    I
Sbjct: 141 RYYDSTFMITLDDIRPSNVLDELDRDQVVIGQVYGGLDVLDKINSMIKPYAGRKYPTFSI 200

>1z81_A Cyclophilin; structural genomics, structural genomics consortium, SGC, isomerase; 2.80A {Plasmodium yoelii yoelii} SCOP: b.62.1.1 Length = 229

 Score =  117 bits (295), Expect = 3e-30
 Identities = 51/161 (31%), Positives = 79/161 (49%), Gaps = 23/161 (14%)

Query: 9   LGDIVVDLFVDKCPLTTKNFLKLC--------KIKYYNGCLFHTVQKDFTAQTGDPT-GT 59
           LG    +LF +  P T++NF + C            Y   +FH V K+F  Q GD     
Sbjct: 73  LGKFKFELFQNIVPKTSENFRQFCTGEYKVNNLPVGYKNTIFHRVIKEFMIQGGDFINHN 132

Query: 60  GTGGDSVYKFLYGEQARFFGDEIRVDLKHAKTGTVAMASAGENLNASQFYMTLRDNLDYL 119
           G+G  S+Y    GE+   F DE   D+KH K G ++MA++G N N  QF++T +   ++L
Sbjct: 133 GSGSLSIY----GEK---FDDE-NFDIKHDKEGLLSMANSGPNTNGCQFFITTKKC-EWL 183

Query: 120 DEKHTIFGEV--AEGLETLSRINESF--VDEKNRPYKNIRI 156
           D K+ +FG +   + L  L +I E+        +P   I +
Sbjct: 184 DGKNVVFGRIIDNDSLLLLKKI-ENVSVTPYIYKPKIPINV 223

>2c3b_A Ppiase, cyclophilin; isomerase, 3D domain swapping, misfolding, Asp F 11, allergen, rotamase; 1.85A {Aspergillus fumigatus} SCOP: b.62.1.1 Length = 172

 Score =  114 bits (287), Expect = 1e-29
 Identities = 57/157 (36%), Positives = 77/157 (49%), Gaps = 18/157 (11%)

Query: 8   SLGDIVVDLFVDKCPLTTKNFLKLC---KIKYYNGCLFHTVQKDFTAQTGDPT-GTGTGG 63
            +G IV +LF    P T KNF +LC     + Y    FH +  +F  Q GD T G GTGG
Sbjct: 20  KVGRIVFNLFDKDVPKTAKNFRELCKRPAGEGYRESTFHRIIPNFMIQGGDFTRGNGTGG 79

Query: 64  DSVYKFLYGEQARFFGDEIRVDLKHAKTGTVAMASAGENLNASQFYMTLRDNLDYLDEKH 123
            S+Y    G++   F DE     KH K G ++MA+AG N N SQF++T      +LD KH
Sbjct: 80  RSIY----GDK---FADE-NFSRKHDKKGILSMANAGPNTNGSQFFITTAVT-SWLDGKH 130

Query: 124 TIFGEV--AEGLETLSRINESF--VDEKNRPYKNIRI 156
            +FGEV   +    +  I E+        R     +I
Sbjct: 131 VVFGEVADEKSYSVVKEI-EALGSSSGSVRSNTRPKI 166

>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 =  105 bits (265), Expect = 1e-27
 Identities = 25/84 (29%), Positives = 44/84 (52%), Gaps = 8/84 (9%)

Query: 240 PPENVLFVCKLNPVTEDEDLHTIFSRFGTVVSAEIIRDFKTGDSLNYAFIEFENRQACER 299
            P   L+V  L P T    L   F RFG++ + + ++        ++A+I++E+  A + 
Sbjct: 15  NPTTRLWVGGLGPNTSLAALAREFDRFGSIRTIDHVKGD------SFAYIQYESLDAAQA 68

Query: 300 AYSKMDNALID--DRRIHVDFSQS 321
           A +KM    +   DRR+ VDF++S
Sbjct: 69  ACAKMRGFPLGGPDRRLRVDFAKS 92

>3pgw_S U1-70K; protein-RNA complex, U1 snRNA, SM fold, SM core, RRM, splici SNRNPS, splicing factors; HET: DNA; 4.40A {Homo sapiens} PDB: 3cw1_K 2l5i_A 2l5j_A* Length = 437

 Score =  114 bits (286), Expect = 2e-27
 Identities = 61/401 (15%), Positives = 114/401 (28%), Gaps = 5/401 (1%)

Query: 165 PFDDPAQLAELIPDASPEGKPKDEVVDEVRLEDDWVPLDEQLSAAELEQVIRSKDARSSA 224
           P+  P +        +         + E     D  P     +  E  +  R +      
Sbjct: 20  PYLPPLEKLPHEKHHNQPYCGIAPYIREFEDPRDAPPPTRAETREERMERKRREKIERRQ 79

Query: 225 VVLESIGDIPDADIKP-----PENVLFVCKLNPVTEDEDLHTIFSRFGTVVSAEIIRDFK 279
             +E+   + D    P         LFV ++N  T +  L   F  +G +    ++   +
Sbjct: 80  QEVETELKMWDPHNDPNAQGDAFKTLFVARVNYDTTESKLRREFEVYGPIKRIHMVYSKR 139

Query: 280 TGDSLNYAFIEFENRQACERAYSKMDNALIDDRRIHVDFSQSVSKLWNQFRRRDHQTGKG 339
           +G    YAFIE+E+ +    AY   D   ID RR+ VD  +  +    + RR     G  
Sbjct: 140 SGKPRGYAFIEYEHERDMHSAYKHADGKKIDGRRVLVDVERGRTVKGWRPRRLGGGLGGT 199

Query: 340 KGCFKCGGLDHIAKDCTGQQPAKYILRDDNRQHGGYSDSRYEMVFDGETPEKSRREKKHR 399
           +       + H  +D T +   +        +       R       E  ++  R +   
Sbjct: 200 RRGGADVNIRHSGRDDTSRYDERPGPSPLPHRDRDRDRERERRERSRERDKERERRRSRS 259

Query: 400 GHDPDDRVERNMNRLSSDLRHRDQERRELSYRQRESDRTRENREDRRNRDGQESRNVQKQ 459
                    R+             + R+   R   S        +R+        ++ + 
Sbjct: 260 RDRRRRSRSRDKEERRRSRERSKDKDRDRKRRSSRSRERARRERERKEELRGGGGDMAEP 319

Query: 460 EVRDDDGRYESDHPKSSDTDRYRDWRGGGDYRKRSADSDSRAERREDGDYRKRNSDNGSH 519
               D    +    +            G D  +    S      R     R R+ D    
Sbjct: 320 SEAGDAPPDDGPPGELGPDGPDGPEEKGRDRDRERRRSHRSERERRRDRDRDRDRDREHK 379

Query: 520 RDRRDDQDYRKKSADGDIHGDRRYDRDNRKNSGNSELRDAK 560
           R  R  +  R ++  G    D   +     +       +  
Sbjct: 380 RGERGSERGRDEARGGGGGQDNGLEGLGNDSRDMYMESEGG 420

>3rfy_A Peptidyl-prolyl CIS-trans isomerase CYP38, chloro; cyclophilin, peptidyl prolyl isomerase, ppiase, TLP,; 2.39A {Arabidopsis thaliana} Length = 369

 Score =  109 bits (273), Expect = 4e-26
 Identities = 34/163 (20%), Positives = 58/163 (35%), Gaps = 27/163 (16%)

Query: 5   IVTSLGDIVVDLFVDKCPLTTKNFLKLCKIKYYNGCLFHTVQKDFTAQTGDPTGTGTGGD 64
                    + L     P+T  NF+ L +  +Y+G         F  QTGDP G   G  
Sbjct: 183 PNIEDCVFRIVLDGYNAPVTAGNFVDLVERHFYDGMEIQRS-DGFVVQTGDPEGPAEGFI 241

Query: 65  S-----------------VYKFLYGEQARFFGD-EIRVDLKHAKTGTVAMASAGENLNA- 105
                                  YG      G  + +V +     GT+AMA      ++ 
Sbjct: 242 DPSTEKTRTVPLEIMVTGEKTPFYGSTLEELGLYKAQVVIPFNAFGTMAMAREEFENDSG 301

Query: 106 -SQFYMTLRDN------LDYLDEKHTIFGEVAEGLETLSRINE 141
            SQ +  L+++       + LD ++ +FG V +  + L+ +  
Sbjct: 302 SSQVFWLLKESELTPSNSNILDGRYAVFGYVTDNEDFLADLKV 344

>3s8s_A Histone-lysine N-methyltransferase SETD1A; chromatin modification, transcription regulation, structural genomics, structural genomics consortium; 1.30A {Homo sapiens} Length = 110

 Score = 90.9 bits (226), Expect = 3e-22
 Identities = 14/92 (15%), Positives = 30/92 (32%)

Query: 240 PPENVLFVCKLNPVTEDEDLHTIFSRFGTVVSAEIIRDFKTGDSLNYAFIEFENRQACER 299
            P   +   +LN    +  L  +  ++G V   EI+   +T   L  A + F + +  + 
Sbjct: 4   IPLKEVTFARLNDNVRETFLKDMCRKYGEVEEVEILLHPRTRKHLGLARVLFTSTRGAKE 63

Query: 300 AYSKMDNALIDDRRIHVDFSQSVSKLWNQFRR 331
               +    +    IH        +    +  
Sbjct: 64  TVKNLHLTSVMGNIIHAQLDIKGQQRMKYYEL 95

>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 = 85.3 bits (212), Expect = 1e-19
 Identities = 29/128 (22%), Positives = 53/128 (41%), Gaps = 30/128 (23%)

Query: 245 LFVCKLNPVTEDEDLHTIFSRFGTVVSAEIIRDFKTGDSLNYAFIEFENRQACERAYSKM 304
           L V  L     D +L+ +F   G + +  I+RD+KTG S  YAF++F +    +RA   +
Sbjct: 6   LIVNYLPQDMTDRELYALFRAIGPINTCRIMRDYKTGYSYGYAFVDFTSEMDSQRAIKVL 65

Query: 305 DNALIDDRRIHVDFSQSVSK--------------------LWNQFRR----------RDH 334
           +   + ++R+ V +++   +                    L   F +          RD 
Sbjct: 66  NGITVRNKRLKVSYARPGGESIKDTNLYVTNLPRTITDDQLDTIFGKYGSIVQKNILRDK 125

Query: 335 QTGKGKGC 342
            TG+ +G 
Sbjct: 126 LTGRPRGV 133

>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 = 75.7 bits (187), Expect = 3e-16
 Identities = 22/82 (26%), Positives = 40/82 (48%), Gaps = 2/82 (2%)

Query: 239 KPPENVLFVCKLNPVTEDEDLHTIFSRFGTVVSAEIIRDFKTGDSLNYAFIEFENRQACE 298
              +  L+V  L     D+ L TIF ++G++V   I+RD  TG     AF+ +  R+  +
Sbjct: 86  SIKDTNLYVTNLPRTITDDQLDTIFGKYGSIVQKNILRDKLTGRPRGVAFVRYNKREEAQ 145

Query: 299 RAYSKMDNALID--DRRIHVDF 318
            A S ++N + +   + + V  
Sbjct: 146 EAISALNNVIPEGGSQPLSVRL 167

>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 = 83.5 bits (207), Expect = 1e-19
 Identities = 25/122 (20%), Positives = 50/122 (40%), Gaps = 9/122 (7%)

Query: 220 ARSSAVVLESIGDIPDADIKPPENVLFVCKLNPVTEDEDLHTIFSRFGTVVSAEIIRDFK 279
           + SS   +  I      +   P  VL++  L+P   + DL ++F+RF       I     
Sbjct: 3   SGSSGEEIRKIPMFSSYNPGEPNKVLYLKNLSPRVTERDLVSLFARFQEKKGPPIQFRMM 62

Query: 280 TGDSLNYAFIEFENRQACERAYSKMDNALIDDRRIHVDFSQSVSKLWNQFRRRDHQTGKG 339
           TG     AFI F N++   +A   ++   +  + + ++F ++         ++   +G  
Sbjct: 63  TGRMRGQAFITFPNKEIAWQALHLVNGYKLYGKILVIEFGKN---------KKQRSSGPS 113

Query: 340 KG 341
            G
Sbjct: 114 SG 115

>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 = 82.6 bits (205), Expect = 1e-18
 Identities = 19/76 (25%), Positives = 39/76 (51%)

Query: 245 LFVCKLNPVTEDEDLHTIFSRFGTVVSAEIIRDFKTGDSLNYAFIEFENRQACERAYSKM 304
           L V  L      E+  ++F   G + S +++RD  TG SL Y F+ + + +  E+A + +
Sbjct: 5   LIVNYLPQNMTQEEFRSLFGSIGEIESCKLVRDKITGQSLGYGFVNYIDPKDAEKAINTL 64

Query: 305 DNALIDDRRIHVDFSQ 320
           +   +  + I V +++
Sbjct: 65  NGLRLQTKTIKVSYAR 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 = 74.9 bits (185), Expect = 5e-16
 Identities = 21/76 (27%), Positives = 35/76 (46%), Gaps = 2/76 (2%)

Query: 245 LFVCKLNPVTEDEDLHTIFSRFGTVVSAEIIRDFKTGDSLNYAFIEFENRQACERAYSKM 304
           L+V  L      ++L  +FS++G ++++ I+ D  TG S    FI F+ R   E A   +
Sbjct: 91  LYVSGLPKTMTQKELEQLFSQYGRIITSRILVDQVTGVSRGVGFIRFDKRIEAEEAIKGL 150

Query: 305 DNALID--DRRIHVDF 318
           +          I V F
Sbjct: 151 NGQKPSGATEPITVKF 166

>2lkz_A RNA-binding protein 5; RRM; NMR {Homo sapiens} Length = 95

 Score = 80.1 bits (198), Expect = 1e-18
 Identities = 18/98 (18%), Positives = 42/98 (42%), Gaps = 10/98 (10%)

Query: 230 IGDIPDADIKPPENVLFVCKLNPVTEDEDLHTIFSRFGT--VVSAEIIRDFKTGDSLNYA 287
           +G           + + +  + P T  + + T  S + +  V +  +I+D +T  +  +A
Sbjct: 1   MGHHHH----HHMDTIILRNIAPHTVVDSIMTALSPYASLAVNNIRLIKDKQTQQNRGFA 56

Query: 288 FIEFENRQACERAYSKMDNA----LIDDRRIHVDFSQS 321
           F++  +     +    + +      ID + I VDF++S
Sbjct: 57  FVQLSSAMDASQLLQILQSLHPPLKIDGKTIGVDFAKS 94

>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 = 79.6 bits (197), Expect = 2e-18
 Identities = 27/93 (29%), Positives = 43/93 (46%)

Query: 229 SIGDIPDADIKPPENVLFVCKLNPVTEDEDLHTIFSRFGTVVSAEIIRDFKTGDSLNYAF 288
           S G   +     P   L V  L+  T + DL  +FS++G +    I+ D ++  S  +AF
Sbjct: 2   SSGSSGNRANPDPNCCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAF 61

Query: 289 IEFENRQACERAYSKMDNALIDDRRIHVDFSQS 321
           + FEN    + A  + +   +D RRI V    S
Sbjct: 62  VYFENVDDAKEAKERANGMELDGRRIRVSGPSS 94

>2khc_A Testis-specific RNP-type RNA binding protein; RRM, RNA recognition motif, bruno; NMR {Drosophila melanogaster} Length = 118

 Score = 79.7 bits (197), Expect = 4e-18
 Identities = 23/82 (28%), Positives = 39/82 (47%)

Query: 239 KPPENVLFVCKLNPVTEDEDLHTIFSRFGTVVSAEIIRDFKTGDSLNYAFIEFENRQACE 298
            P    LF+  L     D DL + F  FG V+SA++  D +T  S  + F+ F+N  + +
Sbjct: 37  GPEGCNLFIYHLPQEFTDTDLASTFLPFGNVISAKVFIDKQTSLSKCFGFVSFDNPDSAQ 96

Query: 299 RAYSKMDNALIDDRRIHVDFSQ 320
            A   M+   +  +R+ V   +
Sbjct: 97  VAIKAMNGFQVGTKRLKVQLKK 118

>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 = 77.7 bits (192), Expect = 1e-17
 Identities = 22/105 (20%), Positives = 44/105 (41%), Gaps = 12/105 (11%)

Query: 240 PPENVLFVCKLNPVTEDEDLHTIFSRFGTVVSAEIIRDFKTGD---SLNYAFIEFENRQA 296
              + LF+  LN  T +E L  +FS+ G + S  I +         S+ + F+E++  + 
Sbjct: 3   SGSSGLFIKNLNFSTTEETLKGVFSKVGAIKSCTISKKKNKAGVLLSMGFGFVEYKKPEQ 62

Query: 297 CERAYSKMDNALIDDRRIHVDFSQSVSKLWNQFRRRDHQTGKGKG 341
            ++A  ++    +D  ++ V  S+         R     +G   G
Sbjct: 63  AQKALKQLQGHTVDGHKLEVRISE---------RATKPASGPSSG 98

>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 = 77.7 bits (192), Expect = 1e-17
 Identities = 29/99 (29%), Positives = 47/99 (47%)

Query: 222 SSAVVLESIGDIPDADIKPPENVLFVCKLNPVTEDEDLHTIFSRFGTVVSAEIIRDFKTG 281
           SS +  +SIG        P    LF+  L     D+DL  +F  FG VVSA++  D +T 
Sbjct: 5   SSGLTQQSIGAAGSQKEGPEGANLFIYHLPQEFGDQDLLQMFMPFGNVVSAKVFIDKQTN 64

Query: 282 DSLNYAFIEFENRQACERAYSKMDNALIDDRRIHVDFSQ 320
            S  + F+ ++N  + + A   M+   I  +R+ V   +
Sbjct: 65  LSKCFGFVSYDNPVSAQAAIQSMNGFQIGMKRLKVQLKR 103

>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 = 76.8 bits (190), Expect = 1e-17
 Identities = 21/76 (27%), Positives = 37/76 (48%)

Query: 245 LFVCKLNPVTEDEDLHTIFSRFGTVVSAEIIRDFKTGDSLNYAFIEFENRQACERAYSKM 304
           +FV  L+P      +   F+ FG +  A +++D  TG S  Y F+ F N+   E A  +M
Sbjct: 9   VFVGDLSPEITTAAIAAAFAPFGRISDARVVKDMATGKSKGYGFVSFFNKWDAENAIQQM 68

Query: 305 DNALIDDRRIHVDFSQ 320
               +  R+I  +++ 
Sbjct: 69  GGQWLGGRQIRTNWAT 84

>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 = 82.3 bits (204), Expect = 2e-17
 Identities = 18/82 (21%), Positives = 37/82 (45%)

Query: 240 PPENVLFVCKLNPVTEDEDLHTIFSRFGTVVSAEIIRDFKTGDSLNYAFIEFENRQACER 299
           P + +L V  L P    +    +   FG++    ++   +TG S  Y F E+  + +  R
Sbjct: 93  PTDALLCVANLPPSLTQQQFEELVRPFGSLERCFLVYSERTGQSKGYGFAEYMKKDSAAR 152

Query: 300 AYSKMDNALIDDRRIHVDFSQS 321
           A S +    +  R ++V ++ +
Sbjct: 153 AKSDLLGKPLGPRTLYVHWTDA 174

>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 = 70.0 bits (172), Expect = 2e-13
 Identities = 15/88 (17%), Positives = 29/88 (32%), Gaps = 2/88 (2%)

Query: 234 PDADIKPPENVLFVCKLNP-VTEDEDLHTIFSRFGTVVSAEIIRDFKTGDSLNYAFIEFE 292
                      L V +L P   + + L    S   +    ++    + G    +A +E+E
Sbjct: 176 QLTPALLHSRCLCVDRLPPGFNDVDALCRALSAVHSPTFCQLACG-QDGQLKGFAVLEYE 234

Query: 293 NRQACERAYSKMDNALIDDRRIHVDFSQ 320
             +  E A  + D   +    + V F  
Sbjct: 235 TAEMAEEAQQQADGLSLGGSHLRVSFCA 262

>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 = 63.5 bits (155), Expect = 3e-11
 Identities = 16/121 (13%), Positives = 39/121 (32%), Gaps = 31/121 (25%)

Query: 245 LFVCKLNPVTEDEDLHTIFSRFGTVVSAEIIRDFKTGDSLNYAFIEFENRQACERAYSKM 304
           + +  L     ++++H + S +        ++          AF+   N +  E A +  
Sbjct: 25  ILIRGLPGDVTNQEVHDLLSDYE-------LKYCFVDKYKGTAFVTLLNGEQAEAAINAF 77

Query: 305 DNALIDDRRIHV------------DFSQSVS--KLWNQFRR----------RDHQTGKGK 340
             + + +R + V            +   S++  +     R              +TG+ K
Sbjct: 78  HQSRLRERELSVQLQPTDALLCVANLPPSLTQQQFEELVRPFGSLERCFLVYSERTGQSK 137

Query: 341 G 341
           G
Sbjct: 138 G 138

>3r27_A HnRNP L, heterogeneous nuclear ribonucleoprotein L; RBD fold, protein binding, nucleus; 2.04A {Homo sapiens} Length = 100

 Score = 77.1 bits (190), Expect = 2e-17
 Identities = 18/92 (19%), Positives = 31/92 (33%), Gaps = 8/92 (8%)

Query: 232 DIPDADIKPPENVLFVCKLNPVTEDEDLHTIFSRFGTVVSAEIIRDFKTGDSLNYAFIEF 291
           +  D    P   V+ +  L     + DL      FG +    ++           A +EF
Sbjct: 11  NYDDPHKTPASPVVHIRGLIDGVVEADLVEALQEFGPISYVVVMPKK------RQALVEF 64

Query: 292 ENRQACERA--YSKMDNALIDDRRIHVDFSQS 321
           E+      A  Y+  +   I      V++S S
Sbjct: 65  EDVLGACNAVNYAADNQIYIAGHPAFVNYSTS 96

>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 = 76.4 bits (189), Expect = 2e-17
 Identities = 19/77 (24%), Positives = 37/77 (48%)

Query: 245 LFVCKLNPVTEDEDLHTIFSRFGTVVSAEIIRDFKTGDSLNYAFIEFENRQACERAYSKM 304
           L++  L P T D+DL  +   +G +VS + I D  T     Y F++F++  A ++A + +
Sbjct: 8   LYIRGLQPGTTDQDLVKLCQPYGKIVSTKAILDKTTNKCKGYGFVDFDSPSAAQKAVTAL 67

Query: 305 DNALIDDRRIHVDFSQS 321
             + +  +        S
Sbjct: 68  KASGVQAQMAKQSGPSS 84

>2qfj_A FBP-interacting repressor; protein-DNA complex; HET: DNA; 2.10A {Homo sapiens} PDB: 3uwt_A 2kxf_A 2kxh_A Length = 216

 Score = 80.4 bits (199), Expect = 2e-17
 Identities = 17/105 (16%), Positives = 44/105 (41%), Gaps = 1/105 (0%)

Query: 245 LFVCKLNPVTEDEDLHTIFSRFGTVVSAEIIRDFKTGDSLNYAFIEFENRQACERAYSKM 304
           ++V  +     ++ +   F+ FG + S ++  D  T     +AF+E+E  +A + A  +M
Sbjct: 31  VYVGSIYYELGEDTIRQAFAPFGPIKSIDMSWDSVTMKHKGFAFVEYEVPEAAQLALEQM 90

Query: 305 DNALIDDRRIHVDFSQSVSKLWNQFRRRDHQTGKGKGCFKCGGLD 349
           ++ ++  R I V    ++ +      +   +       +    + 
Sbjct: 91  NSVMLGGRNIKVGRPSNIGQAQPIIDQLAEEARAFNRIY-VASVH 134

>2qfj_A FBP-interacting repressor; protein-DNA complex; HET: DNA; 2.10A {Homo sapiens} PDB: 3uwt_A 2kxf_A 2kxh_A Length = 216

 Score = 73.9 bits (182), Expect = 3e-15
 Identities = 24/93 (25%), Positives = 45/93 (48%), Gaps = 1/93 (1%)

Query: 228 ESIGDIPDADIKPPENVLFVCKLNPVTEDEDLHTIFSRFGTVVSAEIIRDFKTGDSLNYA 287
           + I D    + +    + +V  ++    D+D+ ++F  FG + SA + RD  TG    Y 
Sbjct: 112 QPIIDQLAEEARAFNRI-YVASVHQDLSDDDIKSVFEAFGKIKSATLARDPTTGKHKGYG 170

Query: 288 FIEFENRQACERAYSKMDNALIDDRRIHVDFSQ 320
           FIE+E  Q+ + A S M+   +  + + V  + 
Sbjct: 171 FIEYEKAQSSQDAVSSMNLFDLGGQYLRVGKAV 203

>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 = 77.8 bits (192), Expect = 2e-17
 Identities = 27/105 (25%), Positives = 45/105 (42%)

Query: 216 RSKDARSSAVVLESIGDIPDADIKPPENVLFVCKLNPVTEDEDLHTIFSRFGTVVSAEII 275
                     +      + +     P   L V  L+  T + DL  +FS++G +    I+
Sbjct: 20  HMASMTGGQQMGRGSRHVGNRANPDPNCCLGVFGLSLYTTERDLREVFSKYGPIADVSIV 79

Query: 276 RDFKTGDSLNYAFIEFENRQACERAYSKMDNALIDDRRIHVDFSQ 320
            D ++  S  +AF+ FEN    + A  + +   +D RRI VDFS 
Sbjct: 80  YDQQSRRSRGFAFVYFENVDDAKEAKERANGMELDGRRIRVDFSI 124

>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 = 76.5 bits (189), Expect = 3e-17
 Identities = 21/81 (25%), Positives = 39/81 (48%)

Query: 240 PPENVLFVCKLNPVTEDEDLHTIFSRFGTVVSAEIIRDFKTGDSLNYAFIEFENRQACER 299
                + V  L+  T + DL  +F  FG++    + +D  TG S  +AFI F  R+   R
Sbjct: 13  DDNATIRVTNLSEDTRETDLQELFRPFGSISRIYLAKDKTTGQSKGFAFISFHRREDAAR 72

Query: 300 AYSKMDNALIDDRRIHVDFSQ 320
           A + +     D   ++V++++
Sbjct: 73  AIAGVSGFGYDHLILNVEWAK 93

>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 = 78.9 bits (195), Expect = 6e-17
 Identities = 27/88 (30%), Positives = 43/88 (48%), Gaps = 1/88 (1%)

Query: 234 PDADIKPPENVLFVCKLNPVTEDEDLHTIFSRFGTVVSAEIIRDFKTGDSLNYAFIEFEN 293
           P A    P   L+V  L+P   +  L+  FS  G ++S  + RD  T  SL YA++ F+ 
Sbjct: 8   PSAP-SYPMASLYVGDLHPDVTEAMLYEKFSPAGPILSIRVCRDMITRRSLGYAYVNFQQ 66

Query: 294 RQACERAYSKMDNALIDDRRIHVDFSQS 321
               ERA   M+  +I  + + + +SQ 
Sbjct: 67  PADAERALDTMNFDVIKGKPVRIMWSQR 94

>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 = 75.8 bits (187), Expect = 7e-16
 Identities = 25/77 (32%), Positives = 46/77 (59%), Gaps = 2/77 (2%)

Query: 245 LFVCKLNPVTEDEDLHTIFSRFGTVVSAEIIRDFKTGDSLNYAFIEFENRQACERAYSKM 304
           +F+  L+   +++ L+  FS FG ++S +++ D     S  Y F+ FE ++A ERA  KM
Sbjct: 106 IFIKNLDKSIDNKALYDTFSAFGNILSCKVVCD--ENGSKGYGFVHFETQEAAERAIEKM 163

Query: 305 DNALIDDRRIHVDFSQS 321
           +  L++DR++ V   +S
Sbjct: 164 NGMLLNDRKVFVGRFKS 180

>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 = 77.6 bits (192), Expect = 6e-17
 Identities = 16/77 (20%), Positives = 37/77 (48%), Gaps = 1/77 (1%)

Query: 245 LFVCKLNPVTEDEDLHTIFSRFGTVVSAEIIRDFKTGDSLNYAFIEFENRQACERAYSKM 304
           L+V  L+    ++ L   F   G + + +I+ D K   ++NYAF+E+        A   +
Sbjct: 3   LYVGNLDKAITEDILKQYFQVGGPIANIKIMID-KNNKNVNYAFVEYHQSHDANIALQTL 61

Query: 305 DNALIDDRRIHVDFSQS 321
           +   I++  + ++++  
Sbjct: 62  NGKQIENNIVKINWAFQ 78

>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 = 77.2 bits (191), Expect = 8e-17
 Identities = 21/82 (25%), Positives = 38/82 (46%)

Query: 239 KPPENVLFVCKLNPVTEDEDLHTIFSRFGTVVSAEIIRDFKTGDSLNYAFIEFENRQACE 298
                 LFV  LN   +DE L   F  F + +S  ++ D +TG S  Y F+ F ++   +
Sbjct: 84  SDDTFNLFVGDLNVNVDDETLRNAFKDFPSYLSGHVMWDMQTGSSRGYGFVSFTSQDDAQ 143

Query: 299 RAYSKMDNALIDDRRIHVDFSQ 320
            A   M    ++ R + ++++ 
Sbjct: 144 NAMDSMQGQDLNGRPLRINWAA 165

>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 = 74.1 bits (183), Expect = 1e-16
 Identities = 21/76 (27%), Positives = 38/76 (50%)

Query: 245 LFVCKLNPVTEDEDLHTIFSRFGTVVSAEIIRDFKTGDSLNYAFIEFENRQACERAYSKM 304
           LFV  LN   +DE L   F  F + +S  ++ D +TG S  Y F+ F ++   + A   M
Sbjct: 4   LFVGDLNVNVDDETLRNAFKDFPSYLSGHVMWDMQTGSSRGYGFVSFTSQDDAQNAMDSM 63

Query: 305 DNALIDDRRIHVDFSQ 320
               ++ R + ++++ 
Sbjct: 64  QGQDLNGRPLRINWAA 79

>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 = 74.5 bits (184), Expect = 1e-16
 Identities = 27/98 (27%), Positives = 49/98 (50%), Gaps = 10/98 (10%)

Query: 245 LFVCKLNPVTEDEDLHTIFSRFGTVVS-AEIIRDFKTGDSLNYAFIEFENRQACERAYSK 303
           +F+  L+P  +++ L+  FS FG ++   +I+RD  TG+S  YAFI F +  A + A   
Sbjct: 8   IFIGNLDPEIDEKLLYDTFSAFGVILQTPKIMRDPDTGNSKGYAFINFASFDASDAAIEA 67

Query: 304 MDNALIDDRRIHVDFSQSVSKLWNQFRRRDHQTGKGKG 341
           M+   + +R I V ++          ++    +G   G
Sbjct: 68  MNGQYLCNRPITVSYAF---------KKDSKGSGPSSG 96

>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 = 74.2 bits (183), Expect = 1e-16
 Identities = 22/84 (26%), Positives = 41/84 (48%)

Query: 236 ADIKPPENVLFVCKLNPVTEDEDLHTIFSRFGTVVSAEIIRDFKTGDSLNYAFIEFENRQ 295
             + P ++ ++V  L     + DL+ IFS++G VV   I++D  T  S   AFI F ++ 
Sbjct: 10  GGLAPSKSTVYVSNLPFSLTNNDLYRIFSKYGKVVKVTIMKDKDTRKSKGVAFILFLDKD 69

Query: 296 ACERAYSKMDNALIDDRRIHVDFS 319
           + +     ++N  +  R I    +
Sbjct: 70  SAQNCTRAINNKQLFGRVIKASIA 93

>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 = 75.0 bits (185), Expect = 2e-16
 Identities = 25/77 (32%), Positives = 46/77 (59%), Gaps = 2/77 (2%)

Query: 245 LFVCKLNPVTEDEDLHTIFSRFGTVVSAEIIRDFKTGDSLNYAFIEFENRQACERAYSKM 304
           +F+  L+   +++ L+  FS FG ++S +++ D     S  Y F+ FE ++A ERA  KM
Sbjct: 8   IFIKNLDKSIDNKALYDTFSAFGNILSCKVVCD--ENGSKGYGFVHFETQEAAERAIEKM 65

Query: 305 DNALIDDRRIHVDFSQS 321
           +  L++DR++ V   +S
Sbjct: 66  NGMLLNDRKVFVGRFKS 82

>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 = 73.8 bits (182), Expect = 2e-16
 Identities = 28/111 (25%), Positives = 51/111 (45%), Gaps = 9/111 (8%)

Query: 231 GDIPDADIKPPENVLFVCKLNPVTEDEDLHTIFSRFGTVVSAEIIRDFKTGDSLNYAFIE 290
           G    + +   E  LFV  L+  T ++ L  +FS++G +    +++D +T  S  + F+ 
Sbjct: 1   GSSGSSGMASDEGKLFVGGLSFDTNEQSLEQVFSKYGQISEVVVVKDRETQRSRGFGFVT 60

Query: 291 FENRQACERAYSKMDNALIDDRRIHVDFSQSVSKLWNQFRRRDHQTGKGKG 341
           FEN    + A   M+   +D R+I VD +             D+++G   G
Sbjct: 61  FENIDDAKDAMMAMNGKSVDGRQIRVDQAGK---------SSDNRSGPSSG 102

>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 = 73.8 bits (182), Expect = 3e-16
 Identities = 17/76 (22%), Positives = 32/76 (42%), Gaps = 1/76 (1%)

Query: 245 LFVCKLNPVTEDEDLHTIFSRFGTVVSAEIIRDFKTGDSLNYAFIEFENRQACERAYSKM 304
           L++  L    ++++L  +   FG V+S  I+RD  +G S    F   E+ + CE      
Sbjct: 28  LYISNLPLSMDEQELENMLKPFGQVISTRILRD-SSGTSRGVGFARMESTEKCEAVIGHF 86

Query: 305 DNALIDDRRIHVDFSQ 320
           +   I         ++
Sbjct: 87  NGKFIKTPPGVSAPTE 102

>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 = 73.9 bits (182), Expect = 3e-16
 Identities = 26/98 (26%), Positives = 45/98 (45%), Gaps = 1/98 (1%)

Query: 245 LFVCKLNPVTEDEDLHTIFSRFGTVVSAEIIRDFKTGDSLNYAFIEFENRQACERAYSKM 304
           +FV  L+P    ED+   F+ FG +  A +++D  TG S  Y F+ F N+   E A  +M
Sbjct: 18  VFVGDLSPEITTEDIKAAFAPFGRISDARVVKDMATGKSKGYGFVSFFNKWDAENAIQQM 77

Query: 305 DNALIDDRRIHVDFSQS-VSKLWNQFRRRDHQTGKGKG 341
               +  R+I  +++        + +     Q+G   G
Sbjct: 78  GGQWLGGRQIRTNWATRKPPAPKSTYESNTKQSGPSSG 115

>2do4_A Squamous cell carcinoma antigen recognized by T- cells 3; RRM domaim, RDB, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 100

 Score = 73.5 bits (181), Expect = 3e-16
 Identities = 23/82 (28%), Positives = 36/82 (43%), Gaps = 1/82 (1%)

Query: 240 PPENVLFVCKLNPVTEDEDLHTIFSRFGTVVSAEIIRDFKTGDSLNYAFIEFENRQACER 299
             ++ LF+  L      E+L  I    GTV    ++ + + G     A++E+EN     +
Sbjct: 15  LEKHKLFISGLPFSCTKEELEEICKAHGTVKDLRLVTN-RAGKPKGLAYVEYENESQASQ 73

Query: 300 AYSKMDNALIDDRRIHVDFSQS 321
           A  KMD   I +  I V  S S
Sbjct: 74  AVMKMDGMTIKENIIKVAISNS 95

>1u6f_A Tcubp1, RNA-binding protein UBP1; trypanosome, mRNA-binding protein, GU-rich RNA, structure; NMR {Trypanosoma cruzi} SCOP: d.58.7.1 Length = 139

 Score = 74.4 bits (183), Expect = 4e-16
 Identities = 19/77 (24%), Positives = 42/77 (54%)

Query: 245 LFVCKLNPVTEDEDLHTIFSRFGTVVSAEIIRDFKTGDSLNYAFIEFENRQACERAYSKM 304
           L V  +    ++  L  +F R+G + S +I+ D +T  S  Y F++F++  + ++A + +
Sbjct: 45  LMVNYIPTTVDEVQLRQLFERYGPIESVKIVCDRETRQSRGYGFVKFQSGSSAQQAIAGL 104

Query: 305 DNALIDDRRIHVDFSQS 321
           +   I ++R+ V  + S
Sbjct: 105 NGFNILNKRLKVALAAS 121

>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 = 73.0 bits (180), Expect = 5e-16
 Identities = 22/82 (26%), Positives = 37/82 (45%)

Query: 239 KPPENVLFVCKLNPVTEDEDLHTIFSRFGTVVSAEIIRDFKTGDSLNYAFIEFENRQACE 298
                 LFV  L+  + +EDL  +FS +G +       D  T     +AF+ F   +   
Sbjct: 5   SSGSGRLFVRNLSYTSSEEDLEKLFSAYGPLSELHYPIDSLTKKPKGFAFVTFMFPEHAV 64

Query: 299 RAYSKMDNALIDDRRIHVDFSQ 320
           +AY+++D  +   R +HV  S 
Sbjct: 65  KAYAEVDGQVFQGRMLHVLPST 86

>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 = 72.7 bits (179), Expect = 6e-16
 Identities = 19/80 (23%), Positives = 40/80 (50%)

Query: 241 PENVLFVCKLNPVTEDEDLHTIFSRFGTVVSAEIIRDFKTGDSLNYAFIEFENRQACERA 300
           P  V+++  +     +E +  + S  G V++ +++ D +TG S  YAFIEF + ++   A
Sbjct: 1   PSRVVYLGSIPYDQTEEQILDLCSNVGPVINLKMMFDPQTGRSKGYAFIEFRDLESSASA 60

Query: 301 YSKMDNALIDDRRIHVDFSQ 320
              ++   +  R +   +S 
Sbjct: 61  VRNLNGYQLGSRFLKCGYSS 80

>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 = 72.6 bits (179), Expect = 7e-16
 Identities = 22/80 (27%), Positives = 37/80 (46%)

Query: 241 PENVLFVCKLNPVTEDEDLHTIFSRFGTVVSAEIIRDFKTGDSLNYAFIEFENRQACERA 300
               L V  L   T  + L  +F ++G V    I R+  T     +AF+ F +R+  + A
Sbjct: 12  GMITLKVDNLTYRTSPDSLRRVFEKYGRVGDVYIPREPHTKAPRGFAFVRFHDRRDAQDA 71

Query: 301 YSKMDNALIDDRRIHVDFSQ 320
            + MD A +D R + V  ++
Sbjct: 72  EAAMDGAELDGRELRVQVAR 91

>1p27_B RNA-binding protein 8A; nuclear protein, mRNA splicing; 2.00A {Homo sapiens} SCOP: d.58.7.1 Length = 106

 Score = 72.3 bits (178), Expect = 1e-15
 Identities = 22/94 (23%), Positives = 43/94 (45%)

Query: 227 LESIGDIPDADIKPPENVLFVCKLNPVTEDEDLHTIFSRFGTVVSAEIIRDFKTGDSLNY 286
           +E  GD P         +LFV  ++    +ED+H  F+ +G + +  +  D +TG    Y
Sbjct: 8   VEQDGDEPGPQRSVEGWILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGY 67

Query: 287 AFIEFENRQACERAYSKMDNALIDDRRIHVDFSQ 320
             +E+E  +  + A   ++   +  + I VD+  
Sbjct: 68  TLVEYETYKEAQAAMEGLNGQDLMGQPISVDWCF 101

>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 = 71.4 bits (176), Expect = 1e-15
 Identities = 19/82 (23%), Positives = 33/82 (40%), Gaps = 1/82 (1%)

Query: 240 PPENVLFVCKLNPVTEDEDLHTIFSRFGTVVSAEIIRD-FKTGDSLNYAFIEFENRQACE 298
                + + +L      + +  IFS +G +   ++  +      S  YA++EFEN    E
Sbjct: 2   MKPTKVHIGRLTRNVTKDHIMEIFSTYGKIKMIDMPVERMHPHLSKGYAYVEFENPDEAE 61

Query: 299 RAYSKMDNALIDDRRIHVDFSQ 320
           +A   MD   ID + I      
Sbjct: 62  KALKHMDGGQIDGQEITATAVL 83

>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 = 71.6 bits (176), Expect = 2e-15
 Identities = 22/82 (26%), Positives = 39/82 (47%), Gaps = 1/82 (1%)

Query: 239 KPPENVLFVCKLNPVTEDEDLHTIFSRFGTVVSAEIIRDFKTGDSLNYAFIEFENRQACE 298
                 LF+  LN  T ++ L  +F + G +    +I+D +T  S  +AFI FEN    +
Sbjct: 4   ADHPGKLFIGGLNRETNEKMLKAVFGKHGPISEVLLIKD-RTSKSRGFAFITFENPADAK 62

Query: 299 RAYSKMDNALIDDRRIHVDFSQ 320
            A   M+   +  + I V+ ++
Sbjct: 63  NAAKDMNGKSLHGKAIKVEQAK 84

>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 = 73.9 bits (182), Expect = 2e-15
 Identities = 18/105 (17%), Positives = 44/105 (41%)

Query: 216 RSKDARSSAVVLESIGDIPDADIKPPENVLFVCKLNPVTEDEDLHTIFSRFGTVVSAEII 275
                  S      +  +    +    + LF+  L     D+ +  + + FG + +  ++
Sbjct: 88  YQPLPGMSENPSVYVPGVVSTVVPDSAHKLFIGGLPNYLNDDQVKELLTSFGPLKAFNLV 147

Query: 276 RDFKTGDSLNYAFIEFENRQACERAYSKMDNALIDDRRIHVDFSQ 320
           +D  TG S  YAF E+ +    ++A + ++   + D+++ V  + 
Sbjct: 148 KDSATGLSKGYAFCEYVDINVTDQAIAGLNGMQLGDKKLLVQRAS 192

>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 = 57.7 bits (140), Expect = 9e-10
 Identities = 11/81 (13%), Positives = 27/81 (33%), Gaps = 6/81 (7%)

Query: 245 LFVCKLNPVTEDEDLHTIFSRFGTVVS-----AEIIRDFKTGDSLNYAFIEFENRQACER 299
           L+V  +     +E +   F+    +          +   +     N+AF+EF +     +
Sbjct: 7   LYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLEFRSVDETTQ 66

Query: 300 AYSKMDNALIDDRRIHVDFSQ 320
           A    D  +   + + +    
Sbjct: 67  AM-AFDGIIFQGQSLKIRRPH 86

>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 = 71.1 bits (175), Expect = 2e-15
 Identities = 17/77 (22%), Positives = 37/77 (48%), Gaps = 2/77 (2%)

Query: 245 LFVCKLNPVTEDEDLHTIFSRFGTVVSAEIIRDFKTGDSLNYAFIEFENRQACERAYSKM 304
           L+V  L+    +  +  +FS+ G   S ++I +  + D   Y F+EF   +    A + M
Sbjct: 18  LYVGNLSRDVTEVLILQLFSQIGPCKSCKMITEHTSNDP--YCFVEFYEHRDAAAALAAM 75

Query: 305 DNALIDDRRIHVDFSQS 321
           +   I  + + V+++ +
Sbjct: 76  NGRKILGKEVKVNWATT 92

>2ku7_A MLL1 PHD3-CYP33 RRM chimeric protein; transcriptional regulation, RRM domain, transcr; NMR {Homo sapiens} Length = 140

 Score = 72.5 bits (178), Expect = 2e-15
 Identities = 26/103 (25%), Positives = 43/103 (41%)

Query: 217 SKDARSSAVVLESIGDIPDADIKPPENVLFVCKLNPVTEDEDLHTIFSRFGTVVSAEIIR 276
             +     V   S G          + VL+V  L    +D+ LH  F  FG +   +I  
Sbjct: 38  CVNCTERHVDGGSGGSGGSGGSATTKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPL 97

Query: 277 DFKTGDSLNYAFIEFENRQACERAYSKMDNALIDDRRIHVDFS 319
           D++T     +AF+EFE  +    A   M+ + +  R I V+ +
Sbjct: 98  DYETEKHRGFAFVEFELAEDAAAAIDNMNESELFGRTIRVNLA 140

>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 = 70.8 bits (174), Expect = 3e-15
 Identities = 22/96 (22%), Positives = 38/96 (39%), Gaps = 6/96 (6%)

Query: 229 SIGDIPDADIKPPENVLFVCKLNPVTEDEDLHTIFSRFGTVVSAEIIRDFKTGDSLNYAF 288
           S G   D D      +L+V  L   T +E +   F+         + +        +YAF
Sbjct: 2   SSGSSGDEDTMSSVKILYVRNLMLSTSEEMIEKEFNNIKPGAVERVKK------IRDYAF 55

Query: 289 IEFENRQACERAYSKMDNALIDDRRIHVDFSQSVSK 324
           + F NR+    A   ++  ++D   I V  ++ V K
Sbjct: 56  VHFSNREDAVEAMKALNGKVLDGSPIEVTLAKPVDK 91

>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 = 72.5 bits (178), Expect = 3e-15
 Identities = 22/102 (21%), Positives = 43/102 (42%), Gaps = 8/102 (7%)

Query: 240 PPENVLFVCKLNPVTEDEDLHTIFSRFGTVVSAEIIRDFKTGDSLNYAFIEFENRQACER 299
                L+V  L+  T +E ++ +FS+ G +    +  D     +  + F+E+ +R   E 
Sbjct: 37  KKSCTLYVGNLSFYTTEEQIYELFSKSGDIKKIIMGLDKMKKTACGFCFVEYYSRADAEN 96

Query: 300 AYSKMDNALIDDRRIHVDFSQSVSKLWNQFRRRDHQTGKGKG 341
           A   ++   +DDR I  D+            +   Q G+G+ 
Sbjct: 97  AMRYINGTRLDDRIIRTDWDAG--------FKEGRQYGRGRS 130

>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 = 69.9 bits (172), Expect = 3e-15
 Identities = 23/81 (28%), Positives = 40/81 (49%)

Query: 240 PPENVLFVCKLNPVTEDEDLHTIFSRFGTVVSAEIIRDFKTGDSLNYAFIEFENRQACER 299
             + VL+V  L    +D+ LH  F  FG +   +I  D++T     +AF+EFE  +    
Sbjct: 5   TTKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAA 64

Query: 300 AYSKMDNALIDDRRIHVDFSQ 320
           A   M+ + +  R I V+ ++
Sbjct: 65  AIDNMNESELFGRTIRVNLAK 85

>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 = 70.6 bits (173), Expect = 3e-15
 Identities = 16/90 (17%), Positives = 31/90 (34%), Gaps = 8/90 (8%)

Query: 234 PDADIKPPENVLFVCKLNPVTEDEDLHTIFSRFGTVVSAEIIRDFKTGDSLNYAFIEFEN 293
                     V+ V  L     + DL     +FGT+    ++           A +EFEN
Sbjct: 7   GSHHKVSVSPVVHVRGLCESVVEADLVEALEKFGTICYVMMMPFK------RQALVEFEN 60

Query: 294 RQACERA--YSKMDNALIDDRRIHVDFSQS 321
             + +    ++      I  ++   ++S S
Sbjct: 61  IDSAKECVTFAADVPVYIAGQQAFFNYSTS 90

>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 = 75.3 bits (184), Expect = 3e-15
 Identities = 29/164 (17%), Positives = 61/164 (37%), Gaps = 12/164 (7%)

Query: 234 PDADIKPPENVLFVCKLNP-VTEDE---DLHTIFSRFGTVVSAEIIRDFKTGDSLNYAFI 289
              +   P + +++  LN  + +DE    L+ IFS+FG ++    I   ++      AF+
Sbjct: 2   AVPET-RPNHTIYINNLNEKIKKDELKKSLYAIFSQFGQILD---ILVSRSLKMRGQAFV 57

Query: 290 EFENRQACERAYSKMDNALIDDRRIHVDFSQS----VSKLWNQFRRRDHQTGKGKGCFKC 345
            F+   +   A   M      D+ + + ++++    ++K+   F  RD +  K K   + 
Sbjct: 58  IFKEVSSATNALRSMQGFPFYDKPMRIQYAKTDSDIIAKMKGTFVERDRKREKRKPKSQE 117

Query: 346 GGLDHIAKDCTGQQPAKYILRDDNRQHGGYSDSRYEMVFDGETP 389
                 A    G  P    ++         + +   M      P
Sbjct: 118 TPATKKAVQGGGATPVVGAVQGPVPGMPPMTQAPRIMHHMPGQP 161

>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 = 50.3 bits (119), Expect = 7e-07
 Identities = 16/82 (19%), Positives = 34/82 (41%), Gaps = 6/82 (7%)

Query: 240 PPENVLFVCKLNPVTEDEDLHTIFSRFGTVVSAEIIRDFKTGDSLNYAFIEFENRQACER 299
           PP ++LF+  L   T +  L  +F++F       ++           AF+EF+N      
Sbjct: 205 PPNHILFLTNLPEETNELMLSMLFNQFPGFKEVRLVPGRHD-----IAFVEFDNEVQAGA 259

Query: 300 AYSKMDNA-LIDDRRIHVDFSQ 320
           A   +    +  +  + + F++
Sbjct: 260 ARDALQGFKITQNNAMKISFAK 281

>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 = 72.6 bits (179), Expect = 3e-15
 Identities = 17/73 (23%), Positives = 38/73 (52%)

Query: 245 LFVCKLNPVTEDEDLHTIFSRFGTVVSAEIIRDFKTGDSLNYAFIEFENRQACERAYSKM 304
           LF+  L     D+ +  + + FG + +  +++D  TG S  YAF E+ +    ++A + +
Sbjct: 97  LFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIAGL 156

Query: 305 DNALIDDRRIHVD 317
           +   + D+++ V 
Sbjct: 157 NGMQLGDKKLLVQ 169

>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 = 58.0 bits (141), Expect = 5e-10
 Identities = 11/81 (13%), Positives = 27/81 (33%), Gaps = 6/81 (7%)

Query: 245 LFVCKLNPVTEDEDLHTIFSRFGTVVS-----AEIIRDFKTGDSLNYAFIEFENRQACER 299
           L+V  +     +E +   F+    +          +   +     N+AF+EF +     +
Sbjct: 7   LYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLEFRSVDETTQ 66

Query: 300 AYSKMDNALIDDRRIHVDFSQ 320
           A    D  +   + + +    
Sbjct: 67  AM-AFDGIIFQGQSLKIRRPH 86

>2lea_A Serine/arginine-rich splicing factor 2; SR protein, RNA binding protein; NMR {Homo sapiens} PDB: 2leb_A 2lec_A Length = 135

 Score = 71.7 bits (176), Expect = 3e-15
 Identities = 24/81 (29%), Positives = 39/81 (48%)

Query: 240 PPENVLFVCKLNPVTEDEDLHTIFSRFGTVVSAEIIRDFKTGDSLNYAFIEFENRQACER 299
                L V  L   T  + L  +F ++G V    I RD  T +S  +AF+ F +++  E 
Sbjct: 45  EGMTSLKVDNLTYRTSPDTLRRVFEKYGRVGDVYIPRDRYTKESRGFAFVRFHDKRDAED 104

Query: 300 AYSKMDNALIDDRRIHVDFSQ 320
           A   MD A++D R + V  ++
Sbjct: 105 AMDAMDGAVLDGRELRVQMAR 125

>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 = 70.4 bits (173), Expect = 4e-15
 Identities = 20/90 (22%), Positives = 43/90 (47%), Gaps = 4/90 (4%)

Query: 236 ADIKPPENV-LFVCKLNPVTEDEDLHTIFSRFGTVVSAEIIRDFKTGDSLNYAFIEFENR 294
           + +K  + + LF+ ++    +++DL  +F  FG +    +++D  TG     AF+ +  R
Sbjct: 6   SGMKDHDAIKLFIGQIPRNLDEKDLKPLFEEFGKIYELTVLKDRFTGMHKGCAFLTYCER 65

Query: 295 QACERAYSKMDNALI---DDRRIHVDFSQS 321
           ++  +A S +         +R I V  + S
Sbjct: 66  ESALKAQSALHEQKTLPGMNRPIQVKPADS 95

>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 = 70.0 bits (172), Expect = 6e-15
 Identities = 24/105 (22%), Positives = 44/105 (41%), Gaps = 9/105 (8%)

Query: 235 DADIKPPENVLFVCKLNPVTEDEDLHTIFSRFGTVVSAEIIRDFKTGDSLNYAFIEFENR 294
            +       VLFV  L     +E L   FS+FG +   + ++D+        AFI F+ R
Sbjct: 4   GSSGMAKVKVLFVRNLANTVTEEILEKAFSQFGKLERVKKLKDY--------AFIHFDER 55

Query: 295 QACERAYSKMDNALIDDRRIHVDFSQSVSKLWNQFRRRDHQTGKG 339
               +A  +M+   ++   I + F++   +   + R+   Q   G
Sbjct: 56  DGAVKAMEEMNGKDLEGENIEIVFAKPPDQKRKE-RKAQRQAASG 99

>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 = 69.5 bits (171), Expect = 6e-15
 Identities = 20/81 (24%), Positives = 37/81 (45%)

Query: 240 PPENVLFVCKLNPVTEDEDLHTIFSRFGTVVSAEIIRDFKTGDSLNYAFIEFENRQACER 299
              + L+V  L+    ++ L  IF  FG + +  +++D  TG S  Y FI F + +   R
Sbjct: 3   SGSSGLYVGSLHFNITEDMLRGIFEPFGKIDNIVLMKDSDTGRSKGYGFITFSDSECARR 62

Query: 300 AYSKMDNALIDDRRIHVDFSQ 320
           A  +++   +  R + V    
Sbjct: 63  ALEQLNGFELAGRPMRVGHVT 83

>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 = 69.6 bits (171), Expect = 8e-15
 Identities = 21/96 (21%), Positives = 37/96 (38%), Gaps = 4/96 (4%)

Query: 229 SIGDIPDADIKPPENVLFVCKLNPVTEDEDLHTIFSRFGTVVSAEIIRDFKTGDSLNYAF 288
           S G          +  LFV  LN    +ED+  +F  FG +    ++R    G S   AF
Sbjct: 2   SSGSSGSESRGGRDRKLFVGMLNKQQSEEDVLRLFQPFGVIDECTVLRG-PDGSSKGCAF 60

Query: 289 IEFENRQACERAYSKMDNALIDD---RRIHVDFSQS 321
           ++F +    + A   +  +         + V F+ +
Sbjct: 61  VKFSSHTEAQAAIHALHGSQTMPGASSSLVVKFADT 96

>1x5u_A Splicing factor 3B subunit 4 (spliceosome associated protein 49) (SAP 49) (SF3B50)...; structure genomics,RRM domain,splicing factor 3B; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 105

 Score = 69.6 bits (171), Expect = 8e-15
 Identities = 21/92 (22%), Positives = 40/92 (43%)

Query: 229 SIGDIPDADIKPPENVLFVCKLNPVTEDEDLHTIFSRFGTVVSAEIIRDFKTGDSLNYAF 288
           S G       +  +  ++V  L+    +  L  +F + G VV+  + +D  TG    Y F
Sbjct: 2   SSGSSGPISERNQDATVYVGGLDEKVSEPLLWELFLQAGPVVNTHMPKDRVTGQHQGYGF 61

Query: 289 IEFENRQACERAYSKMDNALIDDRRIHVDFSQ 320
           +EF + +  + A   MD   +  + I V+ + 
Sbjct: 62  VEFLSEEDADYAIKIMDMIKLYGKPIRVNKAS 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 = 69.6 bits (171), Expect = 8e-15
 Identities = 23/106 (21%), Positives = 40/106 (37%), Gaps = 1/106 (0%)

Query: 216 RSKDARSSAVVLESIGDIPDADIKPPENVLFVCKLNPVTEDEDLHTIFSRFGTVVSAEII 275
           R K                          L V  L+    D D+  +F+ FGT+  A + 
Sbjct: 3   RPKQLPDKWQHDLFDSGFGGGAGVETGGKLLVSNLDFGVSDADIQELFAEFGTLKKAAVH 62

Query: 276 RDFKTGDSLNYAFIEFENRQACERAYSKMDNALIDDRRIHVDFSQS 321
            D ++G SL  A + FE +    +A  + +   +D R +++    S
Sbjct: 63  YD-RSGRSLGTADVHFERKADALKAMKQYNGVPLDGRPMNIQLVTS 107

>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 = 71.0 bits (174), Expect = 9e-15
 Identities = 28/105 (26%), Positives = 44/105 (41%)

Query: 216 RSKDARSSAVVLESIGDIPDADIKPPENVLFVCKLNPVTEDEDLHTIFSRFGTVVSAEII 275
              DA  +  V E                L V  L   T  + L  +F ++G V    I 
Sbjct: 44  TYDDATKTFTVTEGSHHHHHHMDVEGMTSLKVDNLTYRTSPDTLRRVFEKYGRVGDVYIP 103

Query: 276 RDFKTGDSLNYAFIEFENRQACERAYSKMDNALIDDRRIHVDFSQ 320
           RD  T +S  +AF+ F +++  E A   MD A++D R + V  ++
Sbjct: 104 RDRYTKESRGFAFVRFHDKRDAEDAMDAMDGAVLDGRELRVQMAR 148

>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 = 69.2 bits (170), Expect = 1e-14
 Identities = 20/87 (22%), Positives = 40/87 (45%)

Query: 234 PDADIKPPENVLFVCKLNPVTEDEDLHTIFSRFGTVVSAEIIRDFKTGDSLNYAFIEFEN 293
           P         +LFV  ++   +++++   F  +G + +  +  D +TG S  YA +E+E 
Sbjct: 18  PGPQRSVEGWILFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYET 77

Query: 294 RQACERAYSKMDNALIDDRRIHVDFSQ 320
            +    A   ++ A I  + I VD+  
Sbjct: 78  HKQALAAKEALNGAEIMGQTIQVDWCF 104

>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 = 68.8 bits (169), Expect = 1e-14
 Identities = 21/76 (27%), Positives = 43/76 (56%), Gaps = 2/76 (2%)

Query: 245 LFVCKLNPVTEDEDLHTIFSRFGTVVSAEIIRDFKTGDSLNYAFIEFENRQACERAYSKM 304
           L+V  L+   +DE L   FS FGT+ SA+++ +   G S  + F+ F + +   +A ++M
Sbjct: 18  LYVKNLDDGIDDERLRKAFSPFGTITSAKVMME--GGRSKGFGFVCFSSPEEATKAVTEM 75

Query: 305 DNALIDDRRIHVDFSQ 320
           +  ++  + ++V  +Q
Sbjct: 76  NGRIVATKPLYVALAQ 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 = 69.7 bits (171), Expect = 1e-14
 Identities = 23/100 (23%), Positives = 44/100 (44%)

Query: 221 RSSAVVLESIGDIPDADIKPPENVLFVCKLNPVTEDEDLHTIFSRFGTVVSAEIIRDFKT 280
           R     +E  GD P         +LFV  ++    +ED+H  F+ +G + +  +  D +T
Sbjct: 1   REDYDSVEQDGDEPGPQRSVEGWILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRT 60

Query: 281 GDSLNYAFIEFENRQACERAYSKMDNALIDDRRIHVDFSQ 320
           G    Y  +E+E  +  + A   ++   +  + I VD+  
Sbjct: 61  GYLKGYTLVEYETYKEAQAAMEGLNGQDLMGQPISVDWCF 100

>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 = 68.9 bits (169), Expect = 1e-14
 Identities = 20/80 (25%), Positives = 35/80 (43%), Gaps = 1/80 (1%)

Query: 240 PPENVLFVCKLNPVTEDEDLHTIFSRFG-TVVSAEIIRDFKTGDSLNYAFIEFENRQACE 298
                L++  L P  ++  +   F+  G TV+S +IIR+  TG    Y F+EF +    E
Sbjct: 7   GMAASLWMGDLEPYMDENFISRAFATMGETVMSVKIIRNRLTGIPAGYCFVEFADLATAE 66

Query: 299 RAYSKMDNALIDDRRIHVDF 318
           +   K++   +        F
Sbjct: 67  KCLHKINGKPLPGATPAKRF 86

>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 = 69.3 bits (170), Expect = 2e-14
 Identities = 22/83 (26%), Positives = 36/83 (43%), Gaps = 1/83 (1%)

Query: 239 KPPENVLFVCKLNPVTEDEDLHTIFSRFGTVVSAEIIRDFKTGDSLNYAFIEFENRQACE 298
                 L V  L+    D D+  +F+ FGT+  A +  D ++G SL  A + FE R    
Sbjct: 32  VETGAKLLVSNLDFGVSDADIQELFAEFGTLKKAAVDYD-RSGRSLGTADVHFERRADAL 90

Query: 299 RAYSKMDNALIDDRRIHVDFSQS 321
           +A  +     +D R + +    S
Sbjct: 91  KAMKQYKGVPLDGRPMDIQLVAS 113

>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 = 68.4 bits (168), Expect = 2e-14
 Identities = 17/83 (20%), Positives = 39/83 (46%), Gaps = 1/83 (1%)

Query: 239 KPPENVLFVCKLNPVTEDEDLHTIFSRFGTVVSAEIIRDFKTGDSLNYAFIEFENRQACE 298
           +  +  +FV  L     +E L+ +F + G +    I +D + G   ++ F+ F++ ++  
Sbjct: 13  EEADRTVFVGNLEARVREEILYELFLQAGPLTKVTICKD-REGKPKSFGFVCFKHPESVS 71

Query: 299 RAYSKMDNALIDDRRIHVDFSQS 321
            A + ++   +  R I+V    S
Sbjct: 72  YAIALLNGIRLYGRPINVSGPSS 94

>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 = 68.4 bits (168), Expect = 2e-14
 Identities = 21/83 (25%), Positives = 37/83 (44%), Gaps = 6/83 (7%)

Query: 239 KPPENVLFVCKLNPVTEDEDLHTIFSRFGTVVSAEIIRDFKTGDSLNYAFIEFENRQACE 298
               + LFV  L P   +E++  +F ++G      I +D K      + FI  E R   E
Sbjct: 12  FTQRSRLFVGNLPPDITEEEMRKLFEKYGKAGEVFIHKD-K-----GFGFIRLETRTLAE 65

Query: 299 RAYSKMDNALIDDRRIHVDFSQS 321
            A  ++DN  +  +++ V F+  
Sbjct: 66  IAKVELDNMPLRGKQLRVRFACH 88

>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 = 68.4 bits (168), Expect = 2e-14
 Identities = 23/85 (27%), Positives = 42/85 (49%)

Query: 236 ADIKPPENVLFVCKLNPVTEDEDLHTIFSRFGTVVSAEIIRDFKTGDSLNYAFIEFENRQ 295
           + +   + VL+V  L    +D+ LH  F  FG +   +I  D++T     +AF+EFE  +
Sbjct: 6   SGMATTKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAE 65

Query: 296 ACERAYSKMDNALIDDRRIHVDFSQ 320
               A   M+ + +  R I V+ ++
Sbjct: 66  DAAAAIDNMNESELFGRTIRVNLAK 90

>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 = 70.3 bits (173), Expect = 2e-14
 Identities = 14/83 (16%), Positives = 33/83 (39%), Gaps = 2/83 (2%)

Query: 239 KPPENVLFVCKLNPVTEDEDLHTIFSRFGTVVSAEIIRDFKTGDSLNYAFIEFENRQACE 298
                 LF+  LNP     +L    S         ++   +TG +  + +++FE+ +  E
Sbjct: 10  STTPFNLFIGNLNPNKSVAELKVAISELFAKNDLAVVDV-RTGTNRKFGYVDFESAEDLE 68

Query: 299 RAYSKMDNALIDDRRIHVDFSQS 321
           +A  ++    +    I ++  + 
Sbjct: 69  KAL-ELTGLKVFGNEIKLEKPKG 90

>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 = 59.5 bits (145), Expect = 1e-10
 Identities = 17/87 (19%), Positives = 34/87 (39%), Gaps = 6/87 (6%)

Query: 234 PDADIKPPENVLFVCKLNPVTEDEDLHTIFSRFGTVVSAEIIRDFKTGDSLNYAFIEFEN 293
               ++     L    L+    +++L  +F         EI    + G S   A+IEF++
Sbjct: 92  DSKKVRAART-LLAKNLSFNITEDELKEVFEDAL-----EIRLVSQDGKSKGIAYIEFKS 145

Query: 294 RQACERAYSKMDNALIDDRRIHVDFSQ 320
               E+   +   A ID R + + ++ 
Sbjct: 146 EADAEKNLEEKQGAEIDGRSVSLYYTG 172

>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 = 67.3 bits (165), Expect = 5e-14
 Identities = 28/113 (24%), Positives = 49/113 (43%), Gaps = 11/113 (9%)

Query: 229 SIGDIPDADIKPPENVLFVCKLNPVTEDEDLHTIFSRFGTVVSAEIIRDFKTGDSLNYAF 288
           S G   +++ K     L V  +     D DL  +F +FG ++  EII +     S  + F
Sbjct: 2   SSGSSGNSESKSTPKRLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFN--ERGSKGFGF 59

Query: 289 IEFENRQACERAYSKMDNALIDDRRIHVDFSQSVSKLWNQFRRRDHQTGKGKG 341
           + FEN    +RA  K+   +++ R+I V+ + +         R    +G   G
Sbjct: 60  VTFENSADADRAREKLHGTVVEGRKIEVNNATA---------RVMTNSGPSSG 103

>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 = 69.6 bits (171), Expect = 5e-14
 Identities = 17/74 (22%), Positives = 32/74 (43%), Gaps = 2/74 (2%)

Query: 245 LFVCKLNPVTEDEDLHTIFSRFGTVVSAEIIRDFKTGD--SLNYAFIEFENRQACERAYS 302
           +FV ++     ++DL  +F ++G V    ++RD       S    F+ F  R+A   A +
Sbjct: 6   MFVGQVPRTWSEKDLRELFEQYGAVYEINVLRDRSQNPPQSKGCCFVTFYTRKAALEAQN 65

Query: 303 KMDNALIDDRRIHV 316
            + N  +     H 
Sbjct: 66  ALHNMKVLPGMHHP 79

>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 = 63.8 bits (156), Expect = 4e-12
 Identities = 18/65 (27%), Positives = 28/65 (43%), Gaps = 1/65 (1%)

Query: 245 LFVCKLNPVTEDEDLHTIFSRFGTVVSAEIIRDFKTGDSLNYAFIEFENRQACERAYSKM 304
           LF+  ++    + D+  +FS FG +    I+R    G S   AF+ F  R   + A   M
Sbjct: 98  LFIGMISKKCTENDIRVMFSSFGQIEECRILRG-PDGLSRGCAFVTFTTRAMAQTAIKAM 156

Query: 305 DNALI 309
             A  
Sbjct: 157 HQAQT 161

>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 = 66.5 bits (163), Expect = 7e-14
 Identities = 19/113 (16%), Positives = 47/113 (41%), Gaps = 17/113 (15%)

Query: 229 SIGDIPDADIKPPENVLFVCKLNPVTEDEDLHTIFSRFGTVVSAEIIRDFKTGDSLNYAF 288
           S G   +       N L+V   + +T    L   FS FG ++   +    +     N AF
Sbjct: 2   SSGSSGERRAPRKGNTLYVYGED-MTP-TLLRGAFSPFGNIIDLSMDPP-R-----NCAF 53

Query: 289 IEFENRQACERAYSKMDNALIDDRRIHVDFSQSVSKLWNQFRRRDHQTGKGKG 341
           + +E  ++ ++A ++++   ++  ++ V+ ++         ++    +G   G
Sbjct: 54  VTYEKMESADQAVAELNGTQVESVQLKVNIAR---------KQPMLDSGPSSG 97

>2dgv_A HnRNP M, heterogeneous nuclear ribonucleoprotein M; RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} PDB: 2dh9_A Length = 92

 Score = 66.4 bits (163), Expect = 7e-14
 Identities = 21/86 (24%), Positives = 35/86 (40%), Gaps = 2/86 (2%)

Query: 239 KPPENVLFVCKLNPVTEDEDLHTIFSRFGTVVSAEIIRDFKTGDSLNYAFIEFENRQACE 298
                 +FV  L      + L   F+  G V+ A+I  +   G S     ++FE+ +  E
Sbjct: 5   SSGACQIFVRNLPFDFTWKMLKDKFNECGHVLYADIKME--NGKSKGCGVVKFESPEVAE 62

Query: 299 RAYSKMDNALIDDRRIHVDFSQSVSK 324
           RA   M+   +  R I V   ++ S 
Sbjct: 63  RACRMMNGMKLSGREIDVRIDRNASG 88

>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 = 66.6 bits (163), Expect = 1e-13
 Identities = 11/82 (13%), Positives = 30/82 (36%), Gaps = 6/82 (7%)

Query: 240 PPENVLFVCKLNPVTEDEDLHTIFSRFGTVVSAEIIRDFKTGDSLNYAFIEFENRQACER 299
           P    ++   +     D+ +   FS FG ++   +  +        Y+F+ F   ++   
Sbjct: 23  PKNCTVYCGGIASGLTDQLMRQTFSPFGQIMEIRVFPE------KGYSFVRFSTHESAAH 76

Query: 300 AYSKMDNALIDDRRIHVDFSQS 321
           A   ++   I+   +   + + 
Sbjct: 77  AIVSVNGTTIEGHVVKCYWGKE 98

>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 = 65.7 bits (161), Expect = 2e-13
 Identities = 21/89 (23%), Positives = 41/89 (46%), Gaps = 7/89 (7%)

Query: 240 PPENVLFVCKLNP-VTEDE---DLHTIFSRFGTVVSAEIIRDFKTGDSLNYAFIEFENRQ 295
            P + +++  LN  + +DE    LH IFSRFG ++    I   ++      AF+ F+   
Sbjct: 6   RPNHTIYINNLNEKIKKDELKKSLHAIFSRFGQILD---ILVSRSLKMRGQAFVIFKEVS 62

Query: 296 ACERAYSKMDNALIDDRRIHVDFSQSVSK 324
           +   A   M      D+ + + ++++ S 
Sbjct: 63  SATNALRSMQGFPFYDKPMRIQYAKTDSD 91

>2la4_A Nuclear and cytoplasmic polyadenylated RNA-bindin PUB1; RRM, RNA recognition, stress granules, nucleus, RNA-binding, transcription; NMR {Saccharomyces cerevisiae} Length = 101

 Score = 65.8 bits (161), Expect = 2e-13
 Identities = 12/83 (14%), Positives = 29/83 (34%), Gaps = 7/83 (8%)

Query: 240 PPENV-LFVCKLNPVTEDEDLHTIFSRFGTVVSAEIIRDFKTGDSLNYAFIEFENRQACE 298
           PP     ++  +     + DL  +F  FG ++  +   + K        FI+++  +   
Sbjct: 24  PPRVTTAYIGNIPHFATEADLIPLFQNFGFILDFKHYPE-K-----GCCFIKYDTHEQAA 77

Query: 299 RAYSKMDNALIDDRRIHVDFSQS 321
                + N     R +   + + 
Sbjct: 78  VCIVALANFPFQGRNLRTGWGKE 100

>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 = 70.1 bits (172), Expect = 2e-13
 Identities = 23/92 (25%), Positives = 37/92 (40%), Gaps = 6/92 (6%)

Query: 234 PDADIKPPENVLFVCKLNPVTEDEDLHTIFSRFGTVVSAEIIRDFKTGDSLNYAFIEFEN 293
           P          LFV  L     +ED   +F R+G      I RD        + FI  E+
Sbjct: 14  PGEKTYTQRCRLFVGNLPTDITEEDFKRLFERYGEPSEVFINRD------RGFGFIRLES 67

Query: 294 RQACERAYSKMDNALIDDRRIHVDFSQSVSKL 325
           R   E A +++D  ++  R + + F+   + L
Sbjct: 68  RTLAEIAKAELDGTILKSRPLRIRFATHGAAL 99

>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 = 2e-11
 Identities = 19/69 (27%), Positives = 30/69 (43%), Gaps = 1/69 (1%)

Query: 245 LFVCKLNPVTEDEDLHTIFSRFGTVVSAEIIRDFKTGDSLNYAFIEFENRQACERAYSKM 304
           L V  L+PV  +E L   FS+FG V  A ++ D   G +    F+EF  +    +A  + 
Sbjct: 99  LTVKNLSPVVSNELLEQAFSQFGPVEKAVVVVD-DRGRATGKGFVEFAAKPPARKALERC 157

Query: 305 DNALIDDRR 313
            +       
Sbjct: 158 GDGAFLLTT 166

>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 = 65.7 bits (161), Expect = 2e-13
 Identities = 23/87 (26%), Positives = 39/87 (44%)

Query: 235 DADIKPPENVLFVCKLNPVTEDEDLHTIFSRFGTVVSAEIIRDFKTGDSLNYAFIEFENR 294
           D  +      +FV  +     +E L  IFS  G VVS  ++ D +TG    Y F E++++
Sbjct: 1   DPAVDRSLRSVFVGNIPYEATEEQLKDIFSEVGPVVSFRLVYDRETGKPKGYGFCEYQDQ 60

Query: 295 QACERAYSKMDNALIDDRRIHVDFSQS 321
           +    A   ++      R + VD + S
Sbjct: 61  ETALSAMRNLNGREFSGRALRVDNAAS 87

>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 = 66.2 bits (162), Expect = 2e-13
 Identities = 26/92 (28%), Positives = 39/92 (42%), Gaps = 1/92 (1%)

Query: 229 SIGDIPDADIKPPENVLFVCKLNPVTEDEDLHTIFSRFGTVVSAEIIRDFKTGDSLNYAF 288
           S G           + +FV  L+     + L  +FS  G VV A+I+ D K G S     
Sbjct: 2   SSGSSGALQAGRLGSTVFVANLDYKVGWKKLKEVFSMAGVVVRADILED-KDGKSRGIGT 60

Query: 289 IEFENRQACERAYSKMDNALIDDRRIHVDFSQ 320
           + FE      +A S  +  L+ DR +HV   +
Sbjct: 61  VTFEQSIEAVQAISMFNGQLLFDRPMHVKMDE 92

>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 = 69.3 bits (169), Expect = 2e-13
 Identities = 17/84 (20%), Positives = 34/84 (40%), Gaps = 6/84 (7%)

Query: 239 KPPENVLFVCKLNP-VTEDEDLHTIFSRFGTVVSAEIIRDFKTGDSLNYAFIEFENRQAC 297
               +VL V  LNP     + L  +F  +G V   +I+ + K       A ++  +    
Sbjct: 31  GAGNSVLLVSNLNPERVTPQSLFILFGVYGDVQRVKILFNKKE-----NALVQMADGNQA 85

Query: 298 ERAYSKMDNALIDDRRIHVDFSQS 321
           + A S ++   +  + I +  S+ 
Sbjct: 86  QLAMSHLNGHKLHGKPIRITLSKH 109

>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 = 63.9 bits (155), Expect = 1e-11
 Identities = 22/87 (25%), Positives = 36/87 (41%), Gaps = 5/87 (5%)

Query: 236 ADIKPPENVLFVCKLNPVTEDEDLHTIFSRFGTVVSAEIIRDFKTGDSLNYAFIEFENRQ 295
            +I PP   L +  + P   +EDL  +FS  G VV                A I+  + +
Sbjct: 145 QNIFPPSATLHLSNIPPSVSEEDLKVLFSSNGGVVKGFKFFQKDRK----MALIQMGSVE 200

Query: 296 ACERAYSKMDNA-LIDDRRIHVDFSQS 321
              +A   + N  L ++  + V FS+S
Sbjct: 201 EAVQALIDLHNHDLGENHHLRVSFSKS 227

>2f3j_A RNA and export factor binding protein 2; RRM domain, RBD domain., transport protein; NMR {Mus musculus} Length = 177

 Score = 67.6 bits (165), Expect = 2e-13
 Identities = 22/83 (26%), Positives = 36/83 (43%), Gaps = 1/83 (1%)

Query: 239 KPPENVLFVCKLNPVTEDEDLHTIFSRFGTVVSAEIIRDFKTGDSLNYAFIEFENRQACE 298
                 L V  L+    D D+  +F+ FGT+  A +  D ++G SL  A + FE R    
Sbjct: 85  VETGAKLLVSNLDFGVSDADIQELFAEFGTLKKAAVDYD-RSGRSLGTADVHFERRADAL 143

Query: 299 RAYSKMDNALIDDRRIHVDFSQS 321
           +A  +     +D R + +    S
Sbjct: 144 KAMKQYKGVPLDGRPMDIQLVAS 166

>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 = 64.9 bits (159), Expect = 2e-13
 Identities = 20/77 (25%), Positives = 36/77 (46%), Gaps = 8/77 (10%)

Query: 245 LFVCKLNPVTEDEDLHTIFSRFGTVVSAEIIRDFKTGDSLNYAFIEFENRQACERAYSKM 304
           L V  ++P   +++L   F  +G V+  +I++D+        AF+  E  +    A   +
Sbjct: 13  LHVGNISPTCTNQELRAKFEEYGPVIECDIVKDY--------AFVHMERAEDAVEAIRGL 64

Query: 305 DNALIDDRRIHVDFSQS 321
           DN     +R+HV  S S
Sbjct: 65  DNTEFQGKRMHVQLSTS 81

>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 = 64.9 bits (159), Expect = 3e-13
 Identities = 17/80 (21%), Positives = 40/80 (50%), Gaps = 8/80 (10%)

Query: 245 LFVCKLNPVTEDEDLHTIFSRFGTVVSAEIIRDFKTGDSLNYAFIEFENRQACERAYSKM 304
           +FV  ++     ++L ++F R G V+  ++++D+        AF+  E     + A +++
Sbjct: 12  IFVGNVSAACTSQELRSLFERRGRVIECDVVKDY--------AFVHMEKEADAKAAIAQL 63

Query: 305 DNALIDDRRIHVDFSQSVSK 324
           +   +  +RI+V+ S    K
Sbjct: 64  NGKEVKGKRINVELSTKGQK 83

>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 = 66.8 bits (163), Expect = 3e-13
 Identities = 20/88 (22%), Positives = 40/88 (45%)

Query: 234 PDADIKPPENVLFVCKLNPVTEDEDLHTIFSRFGTVVSAEIIRDFKTGDSLNYAFIEFEN 293
           P         +LFV  ++   +++++   F  +G + +  +  D +TG S  YA +E+E 
Sbjct: 64  PGPQRSVEGWILFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYET 123

Query: 294 RQACERAYSKMDNALIDDRRIHVDFSQS 321
            +    A   ++ A I  + I VD+   
Sbjct: 124 HKQALAAKEALNGAEIMGQTIQVDWCFV 151

>1sjq_A Polypyrimidine tract-binding protein 1; babbab motif, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 105

 Score = 64.9 bits (158), Expect = 3e-13
 Identities = 17/84 (20%), Positives = 34/84 (40%), Gaps = 8/84 (9%)

Query: 240 PPENVLFVCKLNPVTEDEDLHTIFSRFGTVVSAEIIRDFKTGDSLNYAFIEFENRQACER 299
            P  V+ + KL     + ++ ++   FG V +  +++        N AFIE    +A   
Sbjct: 14  VPSRVIHIRKLPIDVTEGEVISLGLPFGKVTNLLMLKGK------NQAFIEMNTEEAANT 67

Query: 300 A--YSKMDNALIDDRRIHVDFSQS 321
              Y      ++  + I++ FS  
Sbjct: 68  MVNYYTSVTPVLRGQPIYIQFSNH 91

>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 = 65.0 bits (159), Expect = 4e-13
 Identities = 20/76 (26%), Positives = 38/76 (50%)

Query: 245 LFVCKLNPVTEDEDLHTIFSRFGTVVSAEIIRDFKTGDSLNYAFIEFENRQACERAYSKM 304
           L+V  L+    ++ L  IF  FG + S +++ D +TG S  Y FI F + +  ++A  ++
Sbjct: 29  LYVGSLHFNITEDMLRGIFEPFGRIESIQLMMDSETGRSKGYGFITFSDSECAKKALEQL 88

Query: 305 DNALIDDRRIHVDFSQ 320
           +   +  R + V    
Sbjct: 89  NGFELAGRPMKVGHVT 104

>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 = 64.6 bits (158), Expect = 5e-13
 Identities = 18/105 (17%), Positives = 46/105 (43%), Gaps = 11/105 (10%)

Query: 239 KPPENVLFVCKLNPVTEDEDLHTIFSRFGTVVSAEIIRDF-KTGDSLNYAFIEFENRQAC 297
           K   + + V  +       ++  +FS FG + +  + +    TG    + F++F  +Q  
Sbjct: 12  KQTTSKILVRNIPFQANQREIRELFSTFGELKTVRLPKKMTGTGAHRGFGFVDFITKQDA 71

Query: 298 ERAYSKMDNAL-IDDRRIHVDFSQSVSKLWNQFRRRDHQTGKGKG 341
           ++A++ + ++  +  RR+ ++++ S             Q+G   G
Sbjct: 72  KKAFNALCHSTHLYGRRLVLEWADS---------EVTVQSGPSSG 107

>2err_A Ataxin-2-binding protein 1; protein-RNA complex, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 109

 Score = 64.6 bits (158), Expect = 5e-13
 Identities = 24/90 (26%), Positives = 42/90 (46%), Gaps = 2/90 (2%)

Query: 231 GDIPDADIKPPENVLFVCKLNPVTEDEDLHTIFSRFGTVVSAEIIRDFKTGDSLNYAFIE 290
           G   + + K     L V  +     D DL  +F +FG ++  EII +     S  + F+ 
Sbjct: 18  GSHMNTENKSQPKRLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFN--ERGSKGFGFVT 75

Query: 291 FENRQACERAYSKMDNALIDDRRIHVDFSQ 320
           FEN    +RA  K+   +++ R+I V+ + 
Sbjct: 76  FENSADADRAREKLHGTVVEGRKIEVNNAT 105

>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 = 64.5 bits (157), Expect = 5e-13
 Identities = 19/95 (20%), Positives = 36/95 (37%), Gaps = 8/95 (8%)

Query: 229 SIGDIPDADIKPPENVLFVCKLNPVTEDEDLHTIFSRFGTVVSAEIIRDFKTGDSLNYAF 288
           S G   D     P  VL + KL     + ++  +   FG V +  +++        N AF
Sbjct: 2   SSGSSGDKMDGAPSRVLHIRKLPGEVTETEVIALGLPFGKVTNILMLKGK------NQAF 55

Query: 289 IEFENRQACERA--YSKMDNALIDDRRIHVDFSQS 321
           +E    +A      Y       + ++ I++ +S  
Sbjct: 56  LELATEEAAITMVNYYSAVTPHLRNQPIYIQYSNH 90

>2a3j_A U1 small nuclear ribonucleoprotein A; computationally designed protein, RRM, U1A, RNA binding protein; NMR {Homo sapiens} Length = 127

 Score = 64.9 bits (158), Expect = 5e-13
 Identities = 17/112 (15%), Positives = 42/112 (37%), Gaps = 7/112 (6%)

Query: 217 SKDARSSAVVLESIGDIPDADIKPPENVLFVCKLNP-VTEDE---DLHTIFSRFGTVVSA 272
           +  A+     ++S           P  V+ +  +NP V +++    L+ + S  G ++  
Sbjct: 4   TAAAKFERQHMDSPDLGSTPPHTEPSQVVLITNINPEVPKEKLQALLYALASSQGDILD- 62

Query: 273 EIIRDFKTGDSLNYAFIEFENRQACERAYSKMDNALIDDRRIHVDFSQSVSK 324
             I    + D+   A+I F  +++ +               + + FS++   
Sbjct: 63  --IVVDLSDDNSGKAYIVFATQESAQAFVEAFQGYPFQGNPLVITFSETPQS 112

>2e44_A Insulin-like growth factor 2 mRNA binding protein 3; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 96

 Score = 64.0 bits (156), Expect = 6e-13
 Identities = 13/90 (14%), Positives = 34/90 (37%), Gaps = 3/90 (3%)

Query: 229 SIGDIPDADIKPPENVLFVCKLNPVTEDEDLHTIFSRFGTVVSAEIIRDFKTGDSLNYAF 288
           S G       +     L +  + P  + E L ++  ++G V S E +             
Sbjct: 2   SSGSSGSVPKRQRIRKLQIRNIPPHLQWEVLDSLLVQYGVVESCEQVNTDSET---AVVN 58

Query: 289 IEFENRQACERAYSKMDNALIDDRRIHVDF 318
           + + ++    +A  K++   +++  + V +
Sbjct: 59  VTYSSKDQARQALDKLNGFQLENFTLKVAY 88

>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 = 64.2 bits (157), Expect = 6e-13
 Identities = 23/81 (28%), Positives = 41/81 (50%), Gaps = 3/81 (3%)

Query: 240 PPENVLFVCKLNPVTEDEDLHTIFSRFGTVVSAEIIRDFKTGDSLNYAFIEFENRQACER 299
            P   LFV  L+  T +E L   F      V A I+ D +TG S  + F++F + +  + 
Sbjct: 13  QPSKTLFVKGLSEDTTEETLKESF---DGSVRARIVTDRETGSSKGFGFVDFNSEEDAKA 69

Query: 300 AYSKMDNALIDDRRIHVDFSQ 320
           A   M++  ID  ++ +D+++
Sbjct: 70  AKEAMEDGEIDGNKVTLDWAK 90

>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 = 66.8 bits (163), Expect = 7e-13
 Identities = 17/77 (22%), Positives = 32/77 (41%), Gaps = 6/77 (7%)

Query: 244 VLFVCKLNP-VTEDEDLHTIFSRFGTVVSAEIIRDFKTGDSLNYAFIEFENRQACERAYS 302
           VL V  LNP     + L  +F  +G V   +I+ + K       A ++  +    + A S
Sbjct: 5   VLLVSNLNPERVTPQSLFILFGVYGDVQRVKILFNKKE-----NALVQMADGNQAQLAMS 59

Query: 303 KMDNALIDDRRIHVDFS 319
            ++   +  + I +  S
Sbjct: 60  HLNGHKLHGKPIRITLS 76

>1qm9_A Polypyrimidine tract-binding protein; ribonucleoprotein, RNP, RNA, spicing, translation; NMR {Homo sapiens} SCOP: d.58.7.1 d.58.7.1 Length = 198

 Score = 61.1 bits (148), Expect = 7e-11
 Identities = 22/87 (25%), Positives = 36/87 (41%), Gaps = 5/87 (5%)

Query: 236 ADIKPPENVLFVCKLNPVTEDEDLHTIFSRFGTVVSAEIIRDFKTGDSLNYAFIEFENRQ 295
            +I PP   L +  + P   +EDL  +FS  G VV                A I+  + +
Sbjct: 114 QNIFPPSATLHLSNIPPSVSEEDLKVLFSSNGGVVKGFKFFQKDRK----MALIQMGSVE 169

Query: 296 ACERAYSKMDNA-LIDDRRIHVDFSQS 321
              +A   + N  L ++  + V FS+S
Sbjct: 170 EAVQALIDLHNHDLGENHHLRVSFSKS 196

>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 = 63.5 bits (155), Expect = 1e-12
 Identities = 17/81 (20%), Positives = 33/81 (40%), Gaps = 4/81 (4%)

Query: 240 PPENVLFVCKLNPVTEDEDLHTIFSRFGTVVSAEIIRDFKTGDSLNYAFIEFENRQACER 299
                L +  L+    +E L  +F +   +     +   + G S  YAFIEF + +  + 
Sbjct: 13  GESKTLVLSNLSYSATEETLQEVFEKATFIK----VPQNQNGKSKGYAFIEFASFEDAKE 68

Query: 300 AYSKMDNALIDDRRIHVDFSQ 320
           A +  +   I+ R I ++   
Sbjct: 69  ALNSCNKREIEGRAIRLELQG 89

>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 = 67.7 bits (166), Expect = 1e-12
 Identities = 20/85 (23%), Positives = 38/85 (44%), Gaps = 3/85 (3%)

Query: 239 KPPENVLFVCKLNP-VTEDEDLHTIFSRFGTVVSAEIIRDFK-TGDSLNYAFIEFENRQA 296
                 + +  L+  + ++  L   F  FG++    I    K    +   AF+ FEN+ +
Sbjct: 207 TLEGREIMIRNLSTELLDENLLRESFEGFGSIEKINIPAGQKEHSFNNCCAFMVFENKDS 266

Query: 297 CERAYSKMDNALIDDRRIHVDFSQS 321
            ERA  +M+ +L+ +R I V  +  
Sbjct: 267 AERAL-QMNRSLLGNREISVSLADK 290

>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 = 66.5 bits (163), Expect = 3e-12
 Identities = 10/80 (12%), Positives = 29/80 (36%)

Query: 245 LFVCKLNPVTEDEDLHTIFSRFGTVVSAEIIRDFKTGDSLNYAFIEFENRQACERAYSKM 304
           L++    P     ++  +      V  +  +   +   S  +A+I+  +++       K+
Sbjct: 120 LWMTNFPPSYTQRNIRDLLQDINVVALSIRLPSLRFNTSRRFAYIDVTSKEDARYCVEKL 179

Query: 305 DNALIDDRRIHVDFSQSVSK 324
           +   I+   +    S  + K
Sbjct: 180 NGLKIEGYTLVTKVSNPLEK 199

>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 = 64.2 bits (157), Expect = 2e-11
 Identities = 18/102 (17%), Positives = 34/102 (33%), Gaps = 4/102 (3%)

Query: 216 RSKDARSSAVVLESIGDIPDADIKPPENV-LFVCKLNPVTEDEDLHTIFSRFGTVVSAEI 274
           R  D  S A    +     +A  +  E   + V  L        ++  F   G ++  ++
Sbjct: 14  RPLDEGSPAAAGLTSKKANEALTRNRELTTVLVKNLPKSYNQNKVYKYFKHCGPIIHVDV 73

Query: 275 IRDFKTGDSLNYAFIEFENRQACERAYSKMDNALIDDRRIHV 316
                   +  +A IEF        A +K  + ++    I V
Sbjct: 74  ADS--LKKNFRFARIEFARYDGALAAITKT-HKVVGQNEIIV 112

>3tyt_A Heterogeneous nuclear ribonucleoprotein L; ferredoxin-like, structural genomics, joint center for struc genomics, JCSG; 1.60A {Mus musculus} PDB: 3s01_A 3to8_A Length = 205

 Score = 66.3 bits (161), Expect = 1e-12
 Identities = 16/81 (19%), Positives = 35/81 (43%), Gaps = 6/81 (7%)

Query: 240 PPENVLFVCKLNPVTEDED-LHTIFSRFGTVVSAEIIRDFKTGDSLNYAFIEFENRQACE 298
               VL V  L+    + D +  +F  +G V   + ++          A +E  +  A +
Sbjct: 2   ADSPVLMVYGLDQSKMNCDRVFNVFCLYGNVEKVKFMKSKP-----GAAMVEMADGYAVD 56

Query: 299 RAYSKMDNALIDDRRIHVDFS 319
           RA + ++N  +  ++++V  S
Sbjct: 57  RAITHLNNNFMFGQKMNVCVS 77

>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 = 60.9 bits (147), Expect = 8e-11
 Identities = 9/87 (10%), Positives = 28/87 (32%)

Query: 237 DIKPPENVLFVCKLNPVTEDEDLHTIFSRFGTVVSAEIIRDFKTGDSLNYAFIEFENRQA 296
            I+ P NVL          +E+   I    G      +       +  +   +E++++  
Sbjct: 118 RIQHPSNVLHFFNAPLEVTEENFFEICDELGVKRPTSVKVFSGKSERSSSGLLEWDSKSD 177

Query: 297 CERAYSKMDNALIDDRRIHVDFSQSVS 323
                  +++  + +      ++  + 
Sbjct: 178 ALETLGFLNHYQMKNPNGPYPYTLKLC 204

>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 = 62.7 bits (153), Expect = 2e-12
 Identities = 18/94 (19%), Positives = 35/94 (37%), Gaps = 5/94 (5%)

Query: 228 ESIGDIPDADIKPPENVLFVCKLNPVTEDEDLHTIFSRFGTVVSAEIIRDFKTGDSLNYA 287
             + D   +        L    L+    +++L  +F         EI    + G S   A
Sbjct: 2   HMLEDPCTSKKVRAARTLLAKNLSFNITEDELKEVFEDAL-----EIRLVSQDGKSKGIA 56

Query: 288 FIEFENRQACERAYSKMDNALIDDRRIHVDFSQS 321
           +IEF++    E+   +   A ID R + + ++  
Sbjct: 57  YIEFKSEADAEKNLEEKQGAEIDGRSVSLYYTGE 90

>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 = 62.6 bits (153), Expect = 2e-12
 Identities = 21/84 (25%), Positives = 43/84 (51%), Gaps = 5/84 (5%)

Query: 233 IPDADIKPPENVLFVCKLNPVTEDEDLHTIFSRFGTVVSAEIIRDFKTGDSLNYAFIEFE 292
           +P+  I P  N +FV  ++   ++ ++ + F+R+G+V   +II D +TG S  Y F+ F 
Sbjct: 2   LPEGKIMP--NTVFVGGIDVRMDETEIRSFFARYGSVKEVKIITD-RTGVSKGYGFVSFY 58

Query: 293 NRQACERAYSKMDNALIDDRRIHV 316
           N    ++      N     +++ +
Sbjct: 59  NDVDVQKIVESQIN--FHGKKLKL 80

>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 = 62.1 bits (152), Expect = 2e-12
 Identities = 18/73 (24%), Positives = 36/73 (49%), Gaps = 1/73 (1%)

Query: 245 LFVCKLNPVTEDEDLHTIFSRFGTVVSAEIIRDFKTGDSLNYAFIEFENRQACERAYSKM 304
           ++V  ++     E+L   F   G+V    I+ D  +G    +A+IEF ++++   +   +
Sbjct: 9   IYVGNVDYGATAEELEAHFHGCGSVNRVTILCDKFSGHPKGFAYIEFSDKESVRTS-LAL 67

Query: 305 DNALIDDRRIHVD 317
           D +L   R+I V 
Sbjct: 68  DESLFRGRQIKVI 80

>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 = 63.1 bits (154), Expect = 2e-12
 Identities = 17/83 (20%), Positives = 38/83 (45%), Gaps = 6/83 (7%)

Query: 245 LFVCKLNPVTEDEDLHTIFSRFGTVVSAEIIRDFKTGDSLNYAFIEFENRQACERAYSKM 304
           +F+  L+  +E+E L  +  +FG +    ++    T  S   AF +F  ++A ++  +  
Sbjct: 18  VFIRNLSFDSEEEALGEVLQQFGDLKYVRVVLHPDTEHSKGCAFAQFMTQEAAQKCLAAA 77

Query: 305 DNAL------IDDRRIHVDFSQS 321
                     +D R++ VD + +
Sbjct: 78  SLEAEGGGLKLDGRQLKVDLAVT 100

>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 = 63.7 bits (155), Expect = 2e-12
 Identities = 24/111 (21%), Positives = 42/111 (37%), Gaps = 15/111 (13%)

Query: 240 PPENVLFVCKLNPVTEDEDLHTIFSRFGTVVSAEI-----IRDFKTGDSLNYAFIEFENR 294
            P   ++V  L    +++DL  IF R+    S        IR  K G     AFI   N 
Sbjct: 43  EPNCRIYVKNLAKHVQEKDLKYIFGRYVDFSSETQRIMFDIRLMKEGRMKGQAFIGLPNE 102

Query: 295 QACERAYSKMDNALIDDRRIHVDFSQSVSKLWNQFRRRDHQTGKGKGCFKC 345
           +A  +A  + +  ++  + + V F++              +    +G  KC
Sbjct: 103 KAAAKALKEANGYVLFGKPMVVQFAR----------SARPKQDPKEGKRKC 143

>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 = 63.0 bits (153), Expect = 2e-12
 Identities = 17/84 (20%), Positives = 34/84 (40%), Gaps = 8/84 (9%)

Query: 240 PPENVLFVCKLNPVTEDEDLHTIFSRFGTVVSAEIIRDFKTGDSLNYAFIEFENRQACER 299
            P  V+ + KL     + ++ ++   FG V +  +++        N AFIE    +A   
Sbjct: 29  VPSRVIHIRKLPIDVTEGEVISLGLPFGKVTNLLMLKGK------NQAFIEMNTEEAANT 82

Query: 300 A--YSKMDNALIDDRRIHVDFSQS 321
              Y      ++  + I++ FS  
Sbjct: 83  MVNYYTSVTPVLRGQPIYIQFSNH 106

>2jvo_A Nucleolar protein 3; nucleus, phosphorylation, ribonucleoprotein, ribosome biogenesis, RNA-binding, rRNA processing; NMR {Saccharomyces cerevisiae} PDB: 2osq_A Length = 108

 Score = 62.3 bits (152), Expect = 3e-12
 Identities = 18/85 (21%), Positives = 38/85 (44%), Gaps = 8/85 (9%)

Query: 237 DIKPPENVLFVCKLNPVTEDEDLHTIFSRFGTVVSAEIIRDFKTGDSLNYAFIEFENRQA 296
           + +     LFV       ++ +L+ IF  FG +   +I+  F        AF+EFE  ++
Sbjct: 26  EGELSNTRLFVRPFPLDVQESELNEIFGPFGPMKEVKILNGF--------AFVEFEEAES 77

Query: 297 CERAYSKMDNALIDDRRIHVDFSQS 321
             +A  ++      ++ + V +S+ 
Sbjct: 78  AAKAIEEVHGKSFANQPLEVVYSKL 102

>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 = 62.4 bits (152), Expect = 4e-12
 Identities = 25/109 (22%), Positives = 43/109 (39%), Gaps = 1/109 (0%)

Query: 209 AELEQVIRSKDARSSAVVLESIGDIPDADIKPPENVLFVCKLNPVTEDEDLHTIFSRFGT 268
           A   Q   SK    +           +   +  +  ++V  ++  +  +DL   FS  G+
Sbjct: 3   APCMQTTHSKMTAGAYTEGPPQPLSAEEKKEIDKRSVYVGNVDYGSTAQDLEAHFSSCGS 62

Query: 269 VVSAEIIRDFKTGDSLNYAFIEFENRQACERAYSKMDNALIDDRRIHVD 317
           +    I+ D  +G    YA+IEF  R + + A   MD  +   R I V 
Sbjct: 63  INRITILCDKFSGHPKGYAYIEFAERNSVDAA-VAMDETVFRGRTIKVL 110

>2kvi_A Nuclear polyadenylated RNA-binding protein 3; RNA-binding motif, RRM, transcription termination, NUC phosphoprotein; NMR {Saccharomyces cerevisiae} Length = 96

 Score = 61.5 bits (150), Expect = 5e-12
 Identities = 25/96 (26%), Positives = 43/96 (44%), Gaps = 11/96 (11%)

Query: 240 PPENVLFVCKLNP-VTEDEDLHTIFSRFGTVVSAEIIRDFKTGDSLNYAFIEFENRQACE 298
           PP++ LF+  L       EDL  IFS +G ++   I           + FI+F+N Q+  
Sbjct: 8   PPKSRLFIGNLPLKNVSKEDLFRIFSPYGHIMQINIKN--------AFGFIQFDNPQSVR 59

Query: 299 RAYSKMDNALIDDRRIHVDFSQSVSKLWNQFRRRDH 334
            A       +   +++ ++ S S ++   QF   DH
Sbjct: 60  DAIECESQEMNFGKKLILEVSSSNAR--PQFDHGDH 93

>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 = 61.5 bits (150), Expect = 7e-12
 Identities = 32/97 (32%), Positives = 45/97 (46%), Gaps = 7/97 (7%)

Query: 245 LFVCKLNPVTEDEDLHTIFSRFGTVVSAEIIRDFKTGDSLNYAFIEFENRQACERAYSKM 304
           +FV  L   T D  L   F  FG +  A +I D +TG S  Y F+   +R A ERA    
Sbjct: 20  IFVGGLPYHTTDASLRKYFEGFGDIEEAVVITDRQTGKSRGYGFVTMADRAAAERACKDP 79

Query: 305 DNALIDDRRIHVDFSQSVSKLWNQFRRRDHQTGKGKG 341
            N +ID R+ +V+ +   +      + R  QTG   G
Sbjct: 80  -NPIIDGRKANVNLAYLGA------KPRSLQTGFAIG 109

>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 = 61.6 bits (150), Expect = 7e-12
 Identities = 17/84 (20%), Positives = 39/84 (46%), Gaps = 5/84 (5%)

Query: 240 PPE--NVLFVCKLNPVTEDEDLHTIFSRFGTVVSAEIIRDFKTGDSLNYAFIEFENRQAC 297
           PPE   +L++  L      E+++ IF ++G +     IR   T ++   A++ +E+    
Sbjct: 4   PPEVNRILYIRNLPYKITAEEMYDIFGKYGPIRQ---IRVGNTPETRGTAYVVYEDIFDA 60

Query: 298 ERAYSKMDNALIDDRRIHVDFSQS 321
           + A   +    + +R + V +  +
Sbjct: 61  KNAVDHLSGFNVSNRYLVVLYYNA 84

>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 = 60.7 bits (148), Expect = 8e-12
 Identities = 18/77 (23%), Positives = 35/77 (45%), Gaps = 1/77 (1%)

Query: 245 LFVCKLNPVTEDEDLHTIFSRFGTVVSAEIIRDFKTGDSLNYAFIEFENRQACERAYSKM 304
           +FV  +     + +L   F +FG V    +I D +      + FI FE+ Q+ ++A   M
Sbjct: 13  IFVGGIPHNCGETELREYFKKFGVVTEVVMIYDAEKQRPRGFGFITFEDEQSVDQA-VNM 71

Query: 305 DNALIDDRRIHVDFSQS 321
               I  +++ V  ++ 
Sbjct: 72  HFHDIMGKKVEVKRAEP 88

>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 = 64.4 bits (156), Expect = 8e-12
 Identities = 23/154 (14%), Positives = 49/154 (31%), Gaps = 5/154 (3%)

Query: 191 DEVRLEDDWV-PLDEQLSAAELEQVIRSKDARSSAVVLESIGDIPDADIKPPENVLFVCK 249
           D++ L DD + P      A E    + +        V +                L++  
Sbjct: 16  DQIDLYDDVISPSANNGDAPEDRDYMDTLPPTVGDDVGKGAAPNVVYTYTGKRIALYIGN 75

Query: 250 LNPVTEDEDLHTIFSRFGT--VVSAEIIRDFKTGDSLNYAFIEFENRQACERAYSKMDNA 307
           L   T DEDL       G   ++  +   +   G S  +A +   +  + ++    +   
Sbjct: 76  LTWWTTDEDLTEAVHSLGVNDILEIKFFENRANGQSKGFALVGVGSEASSKKLMDLLPKR 135

Query: 308 LIDDRRIHVDFSQSVSKLWNQFRRRDHQTGKGKG 341
            +  +   V       +  +QF  +  +T +   
Sbjct: 136 ELHGQNPVVTPVN--KQFLSQFEMQSRKTTQSGQ 167

>3n9u_C Cleavage and polyadenylation specificity factor S; protein-protein complex, coexpression, heterotetramer, mRNA maturation, mRNA cleavage; 1.92A {Homo sapiens} Length = 156

 Score = 62.6 bits (152), Expect = 9e-12
 Identities = 14/101 (13%), Positives = 38/101 (37%), Gaps = 4/101 (3%)

Query: 234 PDADIKPPENVLFVCKLNPVTEDEDLHTIFSRFGT--VVSAEIIRDFKTGDSLNYAFIEF 291
             + ++     ++V   +  T D+ L  +    G   VV  +   +   G S  YA +  
Sbjct: 47  TYSGLRNRRAAVYVGSFSWWTTDQQLIQVIRSIGVYDVVELKFAENRANGQSKGYAEVVV 106

Query: 292 ENRQACERAYSKMDNALIDDRRIHVDFSQSVSKLWNQFRRR 332
            +  +  +    +   +++  ++ V  +   +   +QF  +
Sbjct: 107 ASENSVHKLLELLPGKVLNGEKVDVRPATRQNL--SQFEAQ 145

>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 = 60.9 bits (148), Expect = 9e-12
 Identities = 21/126 (16%), Positives = 51/126 (40%), Gaps = 18/126 (14%)

Query: 217 SKDARSSAVVLESIGDIPDADIKPPENVLFVCKLNP-VTEDEDLHTIFSRFGTVVSAEII 275
           S  +   ++ L++       D K   + +F+  LN  + +  D+ TIFS++G V    + 
Sbjct: 2   SSGSSGMSLKLQASNVTNKNDPKSINSRVFIGNLNTALVKKSDVETIFSKYGRVAGCSVH 61

Query: 276 RDFKTGDSLNYAFIEFENRQACERAYSKMDNALIDDRRIHVDFSQSVSKLWNQFRRRDHQ 335
           +         YAF+++ N +    A    +  ++  + + ++ +            +  +
Sbjct: 62  K--------GYAFVQYSNERHARAAVLGENGRVLAGQTLDINMAGE---------PKPDR 104

Query: 336 TGKGKG 341
           +G   G
Sbjct: 105 SGPSSG 110

>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 = 59.9 bits (146), Expect = 1e-11
 Identities = 18/97 (18%), Positives = 44/97 (45%), Gaps = 17/97 (17%)

Query: 245 LFVCKLNPVTEDEDLHTIFSRFGTVVSAEIIRDFKTGDSLNYAFIEFENRQACERAYSKM 304
           LF+  L     ++++ ++F ++G V+  +II+++         F+  E++ A E A   +
Sbjct: 11  LFIGNLPREATEQEIRSLFEQYGKVLECDIIKNY--------GFVHIEDKTAAEDAIRNL 62

Query: 305 DNALIDDRRIHVDFSQSVSKLWNQFRRRDHQTGKGKG 341
            +  +    I+V+ S++         +    +G   G
Sbjct: 63  HHYKLHGVNINVEASKN---------KSKASSGPSSG 90

>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 = 59.6 bits (145), Expect = 2e-11
 Identities = 18/97 (18%), Positives = 32/97 (32%), Gaps = 8/97 (8%)

Query: 230 IGDIPDADIKPPENVLFVCKLNPVTEDEDLHTIFSRFGTVVSAE--------IIRDFKTG 281
           +G           N +FV  L      E +   F + G + + +        +  D +TG
Sbjct: 1   MGHHHHHHSHSDNNTIFVQGLGENVTIESVADYFKQIGIIKTNKKTGQPMINLYTDRETG 60

Query: 282 DSLNYAFIEFENRQACERAYSKMDNALIDDRRIHVDF 318
                A + F++  + + A    D        I V F
Sbjct: 61  KLKGEATVSFDDPPSAKAAIDWFDGKEFSGNPIKVSF 97

>2dis_A Unnamed protein product; structural genomics, RRM domain, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 109

 Score = 60.2 bits (146), Expect = 2e-11
 Identities = 15/80 (18%), Positives = 36/80 (45%), Gaps = 4/80 (5%)

Query: 245 LFVCKLNPVTEDEDLHTIFSRFGTVVSAEII--RDFKTGDSLNYAFIEFENRQACERAYS 302
           LF+  +  + + E++    ++    V   I+         +  +AF+E+E+ +A   A  
Sbjct: 11  LFIGGIPKMKKREEILEEIAKVTEGVLDVIVYASAADKMKNRGFAFVEYESHRAAAMARR 70

Query: 303 KMDNA--LIDDRRIHVDFSQ 320
           K+      +   +I VD+++
Sbjct: 71  KLMPGRIQLWGHQIAVDWAE 90

>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 = 60.0 bits (146), Expect = 2e-11
 Identities = 21/77 (27%), Positives = 30/77 (38%), Gaps = 1/77 (1%)

Query: 245 LFVCKLNPVTEDEDLHTIFSRFGTVVSAEIIRDFKTGDSLNYAFIEFENRQACERAYSKM 304
           +F  +L       DL   FS  G V    II D  +  S   A++EF   Q+   A   +
Sbjct: 28  VFCMQLAARIRPRDLEDFFSAVGKVRDVRIISDRNSRRSKGIAYVEFCEIQSVPLAI-GL 86

Query: 305 DNALIDDRRIHVDFSQS 321
               +    I V  SQ+
Sbjct: 87  TGQRLLGVPIIVQASQA 103

>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 = 58.7 bits (143), Expect = 2e-11
 Identities = 18/73 (24%), Positives = 32/73 (43%), Gaps = 1/73 (1%)

Query: 245 LFVCKLNPVTEDEDLHTIFSRFGTVVSAEIIRDFKTGDSLNYAFIEFENRQACERAYSKM 304
           +FV  L+P T +E +   F  FG V S E+  D KT     + FI F+  +  ++   + 
Sbjct: 2   IFVGGLSPDTPEEKIREYFGGFGEVESIELPMDNKTNKRRGFCFITFKEEEPVKKI-MEK 60

Query: 305 DNALIDDRRIHVD 317
               +   +  + 
Sbjct: 61  KYHNVGLSKCEIK 73

>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 = 59.1 bits (144), Expect = 2e-11
 Identities = 13/79 (16%), Positives = 28/79 (35%), Gaps = 2/79 (2%)

Query: 245 LFVCKLNPVTEDEDLHTIFSRFGT--VVSAEIIRDFKTGDSLNYAFIEFENRQACERAYS 302
           L++  L   T DEDL       G   ++  +   +   G S  +A +   +  + ++   
Sbjct: 4   LYIGNLTWWTTDEDLTEAVHSLGVNDILEIKFFENRANGQSKGFALVGVGSEASSKKLMD 63

Query: 303 KMDNALIDDRRIHVDFSQS 321
            +    +  +   V  S  
Sbjct: 64  LLPKRELHGQNPVVTPSNK 82

>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 = 61.4 bits (150), Expect = 3e-11
 Identities = 20/89 (22%), Positives = 43/89 (48%), Gaps = 2/89 (2%)

Query: 233 IPDADIKPPENVLFVCKLNPVTEDEDLHTIFSRFGTVVSAEIIRDFKTGDSLNYAFIEFE 292
           IP  +      + FV  + P    ++    FS++GT++ A+++ D  TG S  + F+ ++
Sbjct: 79  IPRDEQDKTGKI-FVGGIGPDVRPKEFEEFFSQWGTIIDAQLMLDKDTGQSRGFGFVTYD 137

Query: 293 NRQACERAYSKMDNALIDDRRIHVDFSQS 321
           +  A +R   +       DR+I +  ++ 
Sbjct: 138 SADAVDRVC-QNKFIDFKDRKIEIKRAEP 165

>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 = 56.0 bits (136), Expect = 2e-09
 Identities = 23/94 (24%), Positives = 42/94 (44%), Gaps = 10/94 (10%)

Query: 245 LFVCKLNPVTEDEDLHTIFSRFGTVVSAEIIRDFKTGDSLNYAFIEFENRQACERAYSKM 304
           +F+  LN  T +++L   F ++GTV   +I++D  TG S  + F+ FE   + +      
Sbjct: 6   MFIGGLNWDTTEDNLREYFGKYGTVTDLKIMKDPATGRSRGFGFLSFEKPSSVDEVVKTQ 65

Query: 305 DNALIDDRRIHVDFSQSVSKLWNQFRRRDHQTGK 338
              ++D + I    +          R    +TGK
Sbjct: 66  --HILDGKVIDPKRAIP--------RDEQDKTGK 89

>2mss_A Protein (musashi1); RNA-binding domain, RNA binding protein; NMR {Mus musculus} SCOP: d.58.7.1 PDB: 2mst_A Length = 75

 Score = 58.6 bits (143), Expect = 3e-11
 Identities = 18/73 (24%), Positives = 34/73 (46%), Gaps = 1/73 (1%)

Query: 245 LFVCKLNPVTEDEDLHTIFSRFGTVVSAEIIRDFKTGDSLNYAFIEFENRQACERAYSKM 304
           +FV  L+  T  ED+   F +FG V  A ++ D  T     + F+ FE+    E+   ++
Sbjct: 2   IFVGGLSVNTTVEDVKHYFEQFGKVDDAMLMFDKTTNRHRGFGFVTFESEDIVEKV-CEI 60

Query: 305 DNALIDDRRIHVD 317
               I+++ +   
Sbjct: 61  HFHEINNKMVECK 73

>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 = 58.9 bits (143), Expect = 3e-11
 Identities = 20/88 (22%), Positives = 40/88 (45%), Gaps = 11/88 (12%)

Query: 239 KPPENVLFVCKLNP--VTEDEDLHTIFSRFGTVVSAEIIRDFKTGDSLNYAFIEFENRQA 296
              ++ LF+  L    V++ EDL  IFS +G ++   I           + FI+F+N Q+
Sbjct: 19  SHMKSRLFIGNLPLKNVSK-EDLFRIFSPYGHIMQINIKN--------AFGFIQFDNPQS 69

Query: 297 CERAYSKMDNALIDDRRIHVDFSQSVSK 324
              A       +   +++ ++ S S ++
Sbjct: 70  VRDAIEXESQEMNFGKKLILEVSSSNAR 97

>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 = 58.8 bits (143), Expect = 4e-11
 Identities = 25/97 (25%), Positives = 39/97 (40%), Gaps = 11/97 (11%)

Query: 245 LFVCKLNPVTEDEDLHTIFSRFGTVVSAEIIRDFKTGDSLNYAFIEFENRQACERAYSKM 304
           L V  L   T ++DL   FS FG V+  ++ +D KTG S  + F+ F   +   +  S+ 
Sbjct: 18  LIVLGLPWKTTEQDLKEYFSTFGEVLMVQVKKDLKTGHSKGFGFVRFTEYETQVKVMSQR 77

Query: 305 DNALIDDRRIHVDFSQSVSKLWNQFRRRDHQTGKGKG 341
               ID R        S         ++   +G   G
Sbjct: 78  HM--IDGRWCDCKLPNS---------KQSQDSGPSSG 103

>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 = 58.3 bits (142), Expect = 4e-11
 Identities = 20/76 (26%), Positives = 35/76 (46%), Gaps = 1/76 (1%)

Query: 245 LFVCKLNPVTEDEDLHTIFSRFGTVVSAEIIRDFKTGDSLNYAFIEFENRQACERAYSKM 304
           ++V  L      E +  +FS+FG V + ++I D +T     + F+E +       A +K+
Sbjct: 4   IYVGNLVYSATSEQVKELFSQFGKVFNVKLIYDRETKKPKGFGFVEMQEESV-SEAIAKL 62

Query: 305 DNALIDDRRIHVDFSQ 320
           DN     R I V  + 
Sbjct: 63  DNTDFMGRTIRVTEAN 78

>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 = 58.1 bits (141), Expect = 5e-11
 Identities = 22/75 (29%), Positives = 37/75 (49%), Gaps = 7/75 (9%)

Query: 245 LFVCKLNPVTEDEDLHTIFSRFGTVVSAEIIRDFKTGDSLNYAFIEFENRQACERAYSKM 304
           L+V  L     + DL   F +FG + +  +++          AFI+F  RQA E A  K 
Sbjct: 15  LYVGGLGDTITETDLRNHFYQFGEIRTITVVQRQ------QCAFIQFATRQAAEVAAEKS 68

Query: 305 DN-ALIDDRRIHVDF 318
            N  +++ RR++V +
Sbjct: 69  FNKLIVNGRRLNVKW 83

>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 = 58.4 bits (142), Expect = 5e-11
 Identities = 15/82 (18%), Positives = 33/82 (40%), Gaps = 2/82 (2%)

Query: 240 PPENVLFVCKLNPVTEDEDLHTIFSRFGTVVSAEIIRDFKTGDSLNYAFIEFENRQACER 299
                LF+  LNP     +L    S          + D +TG +  + +++FE+ +  E+
Sbjct: 15  TTPFNLFIGNLNPNKSVAELKVAISELFAKNDL-AVVDVRTGTNRKFGYVDFESAEDLEK 73

Query: 300 AYSKMDNALIDDRRIHVDFSQS 321
           A  ++    +    I ++  + 
Sbjct: 74  AL-ELTGLKVFGNEIKLEKPKG 94

>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 = 58.1 bits (141), Expect = 6e-11
 Identities = 12/81 (14%), Positives = 32/81 (39%)

Query: 239 KPPENVLFVCKLNPVTEDEDLHTIFSRFGTVVSAEIIRDFKTGDSLNYAFIEFENRQACE 298
           KP   ++ V  +      +++   F  +  +  +  ++  + G     A + FE+R    
Sbjct: 12  KPGPTIIKVQNMPFTVSIDEILDFFYGYQVIPGSVCLKYNEKGMPTGEAMVAFESRDEAT 71

Query: 299 RAYSKMDNALIDDRRIHVDFS 319
            A   +++  I  R++ +   
Sbjct: 72  AAVIDLNDRPIGSRKVKLVLG 92

>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 = 57.7 bits (140), Expect = 1e-10
 Identities = 14/83 (16%), Positives = 33/83 (39%)

Query: 239 KPPENVLFVCKLNPVTEDEDLHTIFSRFGTVVSAEIIRDFKTGDSLNYAFIEFENRQACE 298
           KP   V+ V  +      +++   F  +  +  +  ++  + G     A + FE+R    
Sbjct: 12  KPGPTVIKVQNMPFTVSIDEILDFFYGYQVIPGSVCLKYNEKGMPTGEAMVAFESRDEAT 71

Query: 299 RAYSKMDNALIDDRRIHVDFSQS 321
            A   +++  I  R++ +    S
Sbjct: 72  AAVIDLNDRPIGSRKVKLSGPSS 94

>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 = 57.9 bits (140), Expect = 1e-10
 Identities = 16/83 (19%), Positives = 32/83 (38%), Gaps = 6/83 (7%)

Query: 243 NVLFVCKLNPVTEDEDL---HTIFSRFGTVVSAEIIRDFKTGDSLN---YAFIEFENRQA 296
           N++FV  L+    D ++      F +FG +    I        S      A++ +   + 
Sbjct: 16  NLVFVVGLSQRLADPEVLKRPEYFGKFGKIHKVVINNSTSYAGSQGPSASAYVTYIRSED 75

Query: 297 CERAYSKMDNALIDDRRIHVDFS 319
             RA   ++N ++D R +     
Sbjct: 76  ALRAIQCVNNVVVDGRTLKASLG 98

>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 = 60.0 bits (146), Expect = 1e-10
 Identities = 16/77 (20%), Positives = 34/77 (44%), Gaps = 1/77 (1%)

Query: 245 LFVCKLNPVTEDEDLHTIFSRFGTVVSAEIIRDFKTGDSLNYAFIEFENRQACERAYSKM 304
           +FV  +   TE+  L   F ++G +   EI+ D  +G    +AF+ F++  + ++     
Sbjct: 107 IFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIV-IQ 165

Query: 305 DNALIDDRRIHVDFSQS 321
               ++     V  + S
Sbjct: 166 KYHTVNGHNCEVRKALS 182

>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 = 56.9 bits (138), Expect = 2e-09
 Identities = 19/77 (24%), Positives = 35/77 (45%), Gaps = 1/77 (1%)

Query: 245 LFVCKLNPVTEDEDLHTIFSRFGTVVSAEIIRDFKTGDSLNYAFIEFENRQACERAYSKM 304
           LF+  L+  T DE L + F ++GT+    ++RD  T  S  + F+ +   +  + A    
Sbjct: 16  LFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAM-NA 74

Query: 305 DNALIDDRRIHVDFSQS 321
               +D R +    + S
Sbjct: 75  RPHKVDGRVVEPKRAVS 91

>2lcw_A RNA-binding protein FUS; RRM, nucleic acid binding protein; NMR {Homo sapiens} Length = 116

 Score = 57.0 bits (138), Expect = 3e-10
 Identities = 17/90 (18%), Positives = 31/90 (34%), Gaps = 8/90 (8%)

Query: 239 KPPENVLFVCKLNPVTEDEDLHTIFSRFGTVVSAE--------IIRDFKTGDSLNYAFIE 290
               N +FV  L      E +   F + G + + +        +  D +TG     A + 
Sbjct: 4   NSDNNTIFVQGLGENVTIESVADYFKQIGIIKTNKKTGQPMINLYTDRETGKLKGEATVS 63

Query: 291 FENRQACERAYSKMDNALIDDRRIHVDFSQ 320
           F++  + + A    D        I V F+ 
Sbjct: 64  FDDPPSAKAAIDWFDGKEFSGNPIKVSFAT 93

>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 = 57.2 bits (138), Expect = 5e-10
 Identities = 24/141 (17%), Positives = 47/141 (33%), Gaps = 5/141 (3%)

Query: 180 SPEGKPKDEVVDEVRLEDDWVPLDEQLSAAELEQVIRSKDARSSAVVLESIGDIPDADIK 239
           + +G+   E VD    E  +                 +    +              D  
Sbjct: 11  TLKGETTTEAVDAATAEKVFKQYANDNGVDGEWTYDDATKTFTVTEGSHHHHHHMHRDSC 70

Query: 240 PPENVLFVCKLNPVTEDEDLHTIFSRFGTVVSAEIIRDFKTGDSLNYAFIEFENRQACER 299
           P +  ++V  L       +L   F  +G + S  + R+        +AF+EFE+ +    
Sbjct: 71  PLDCKVYVGNLGNNGNKTELERAFGYYGPLRSVWVARN-----PPGFAFVEFEDPRDAAD 125

Query: 300 AYSKMDNALIDDRRIHVDFSQ 320
           A  ++D   +   R+ V+ S 
Sbjct: 126 AVRELDGRTLCGCRVRVELSN 146

>2hvz_A Splicing factor, arginine/serine-rich 7; RRM, RNA binding protein; NMR {Homo sapiens} Length = 101

 Score = 55.8 bits (135), Expect = 5e-10
 Identities = 20/77 (25%), Positives = 35/77 (45%), Gaps = 5/77 (6%)

Query: 245 LFVCKLNPVTEDEDLHTIFSRFGTVVSAEIIRDFKTGDSLNYAFIEFENRQACERAYSKM 304
           ++V  L       +L   FS +G + +  I R+        +AF+EFE+ +  E A   +
Sbjct: 3   VYVGNLGTGAGKGELERAFSYYGPLRTVWIARNPP-----GFAFVEFEDPRDAEDAVRGL 57

Query: 305 DNALIDDRRIHVDFSQS 321
           D  +I   R+ V+ S  
Sbjct: 58  DGKVICGSRVRVELSTG 74

>3ns6_A Eukaryotic translation initiation factor 3 subuni; 1.25A {Saccharomyces cerevisiae} PDB: 3ns5_A Length = 100

 Score = 55.1 bits (133), Expect = 7e-10
 Identities = 14/79 (17%), Positives = 30/79 (37%), Gaps = 6/79 (7%)

Query: 242 ENVLFVCKLNPVTED------EDLHTIFSRFGTVVSAEIIRDFKTGDSLNYAFIEFENRQ 295
           +  + V     +         + L ++FS+ G VV+ E   D  TG +  + F+E  +  
Sbjct: 6   DQYIVVNGAPVIPSAKVPVLKKALTSLFSKAGKVVNMEFPIDEATGKTKGFLFVECGSMN 65

Query: 296 ACERAYSKMDNALIDDRRI 314
             ++         +D +  
Sbjct: 66  DAKKIIKSFHGKRLDLKHR 84

>1uaw_A Mouse-musashi-1; RNP-type structure, RNA binding protein; NMR {Mus musculus} SCOP: d.58.7.1 Length = 77

 Score = 54.4 bits (132), Expect = 8e-10
 Identities = 17/73 (23%), Positives = 31/73 (42%), Gaps = 1/73 (1%)

Query: 245 LFVCKLNPVTEDEDLHTIFSRFGTVVSAEIIRDFKTGDSLNYAFIEFENRQACERAYSKM 304
           +F+  L+  T  E L   F +FG V    ++RD  T  S  + F+ F ++   ++     
Sbjct: 3   MFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQAGVDKV-LAQ 61

Query: 305 DNALIDDRRIHVD 317
               +D + I   
Sbjct: 62  SRHELDSKTIDPK 74

>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 = 54.5 bits (132), Expect = 9e-10
 Identities = 23/73 (31%), Positives = 37/73 (50%), Gaps = 1/73 (1%)

Query: 245 LFVCKLNPVTEDEDLHTIFSRFGTVVSAEIIRDFKTGDSLNYAFIEFENRQACERAYSKM 304
           +FV  L+  T  +DL   F++FG VV   I  D  TG S  + FI F++  + E+   + 
Sbjct: 14  MFVGGLSWDTSKKDLKDYFTKFGEVVDCTIKMDPNTGRSRGFGFILFKDAASVEKVLDQK 73

Query: 305 DNALIDDRRIHVD 317
           ++  +D R I   
Sbjct: 74  EH-RLDGRVIDPK 85

>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 = 54.2 bits (131), Expect = 2e-09
 Identities = 16/80 (20%), Positives = 36/80 (45%), Gaps = 7/80 (8%)

Query: 243 NVLFVCKLNPVTEDEDLHTIFSRFGTVVSAEIIRDFKTGDSLNYAFIEFENRQACERAYS 302
           N L++  L+P    +DL  +F      ++ +++          YAF+++ ++    RA  
Sbjct: 9   NKLYIGNLSPAVTADDLRQLFGDRKLPLAGQVLL------KSGYAFVDYPDQNWAIRAIE 62

Query: 303 KMD-NALIDDRRIHVDFSQS 321
            +     +  + + VD+S S
Sbjct: 63  TLSGKVELHGKIMEVDYSVS 82

>1sjr_A Polypyrimidine tract-binding protein 1; extended babbab motif, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1 PDB: 2adb_A Length = 164

 Score = 55.9 bits (134), Expect = 2e-09
 Identities = 32/136 (23%), Positives = 56/136 (41%), Gaps = 12/136 (8%)

Query: 205 QLSAAELEQVIRSKDARSSAVVLESIGDIPDADIKPPENVLFVCKLN---PVTEDEDLHT 261
             SA    Q + S  + + A+   +        +     VL +   N   PVT D  LH 
Sbjct: 7   HGSAQAALQAVNSVQSGNLALAASAAAVDAGMAMAGQSPVLRIIVENLFYPVTLDV-LHQ 65

Query: 262 IFSRFGTVVSAEIIRDFKTGDSLNYAFIEFENRQACERAYSKMDNALIDDRR--IHVDFS 319
           IFS+FGTV+                A +++ +  + + A   +D   I +    + +DFS
Sbjct: 66  IFSKFGTVLKIITFTKNNQF----QALLQYADPVSAQHAKLSLDGQNIYNACCTLRIDFS 121

Query: 320 Q--SVSKLWNQFRRRD 333
           +  S++  +N  + RD
Sbjct: 122 KLTSLNVKYNNDKSRD 137

>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 = 53.8 bits (130), Expect = 3e-09
 Identities = 17/73 (23%), Positives = 31/73 (42%), Gaps = 1/73 (1%)

Query: 245 LFVCKLNPVTEDEDLHTIFSRFGTVVSAEIIRDFKTGDSLNYAFIEFENRQACERAYSKM 304
           +F+  L+  T  E L   F +FG V    ++RD  T  S  + F+ F ++   ++     
Sbjct: 28  MFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQAGVDKV-LAQ 86

Query: 305 DNALIDDRRIHVD 317
               +D + I   
Sbjct: 87  SRHELDSKTIDPK 99

>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 = 53.0 bits (128), Expect = 4e-09
 Identities = 15/73 (20%), Positives = 34/73 (46%), Gaps = 7/73 (9%)

Query: 245 LFVCKLNPVTEDEDLHTIFSRFGTVVSAEIIRDFKTGDSLNYAFIEFENRQACERAYSKM 304
           +FV +      +++L   FS++G V+   I + F+      +AF+ F + Q  +      
Sbjct: 8   VFVGRCTGDMTEDELREFFSQYGDVMDVFIPKPFR-----AFAFVTFADDQIAQSLC--G 60

Query: 305 DNALIDDRRIHVD 317
           ++ +I    +H+ 
Sbjct: 61  EDLIIKGISVHIS 73

>2dhg_A TRNA selenocysteine associated protein (SECP43); RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 104

 Score = 53.4 bits (129), Expect = 4e-09
 Identities = 23/103 (22%), Positives = 45/103 (43%), Gaps = 8/103 (7%)

Query: 241 PENVLFVCKLNPVTEDEDLHTIFS-RFGTVVSAEIIRDFKTGDSLNYAFIEFENRQACER 299
           PE  LFV  L P  +D  L+  F   + +    +++ D +TG S  Y F++F +    +R
Sbjct: 8   PEYSLFVGDLTPDVDDGMLYEFFVKVYPSCRGGKVVLD-QTGVSKGYGFVKFTDELEQKR 66

Query: 300 AYSKMDNA-LIDDRRIHVDFSQSVSKLWNQFRRRDHQTGKGKG 341
           A ++   A  +  + + +  +          R +  ++G   G
Sbjct: 67  ALTECQGAVGLGSKPVRLSVAI-----PKASRVKPVESGPSSG 104

>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 = 53.5 bits (129), Expect = 4e-09
 Identities = 19/82 (23%), Positives = 37/82 (45%), Gaps = 3/82 (3%)

Query: 240 PPENVLFVCKLNPVTEDEDLHTIFSRFGTVVSAEIIRDFKTGDSLNYAFIEFENRQACER 299
             +  ++V  L P    +D+  +F ++G +   ++           +AF+EFE+ +  E 
Sbjct: 20  NNDCRIYVGNLPPDIRTKDIEDVFYKYGAIRDIDLKNR---RGGPPFAFVEFEDPRDAED 76

Query: 300 AYSKMDNALIDDRRIHVDFSQS 321
           A    D    D  R+ V+F +S
Sbjct: 77  AVYGRDGYDYDGYRLRVEFPRS 98

>2krb_A Eukaryotic translation initiation factor 3 subunit B; EIF3, eukaryotic initiation factor, EIF3B, EIF3J; NMR {Homo sapiens} Length = 81

 Score = 52.4 bits (126), Expect = 4e-09
 Identities = 17/79 (21%), Positives = 32/79 (40%), Gaps = 8/79 (10%)

Query: 242 ENVLFVCKLNPVTED------EDLHTIFSRFGTVVSAEIIRDFKTGDSLNYAFIEFENRQ 295
           ++V+ V  +  V  D        +H IFS+FG + +     +   G +  Y F+E+ +  
Sbjct: 1   DSVIVVDNVPQVGPDRLEKLKNVIHKIFSKFGKITNDFYPEE--DGKTKGYIFLEYASPA 58

Query: 296 ACERAYSKMDNALIDDRRI 314
               A    D   +D +  
Sbjct: 59  HAVDAVKNADGYKLDKQHT 77

>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 = 53.6 bits (129), Expect = 5e-09
 Identities = 21/100 (21%), Positives = 35/100 (35%), Gaps = 8/100 (8%)

Query: 229 SIGDIPDADIKPPENVLFVCKLNPVTEDEDLHTIFSRFGTV--------VSAEIIRDFKT 280
           S G   D D     + ++V  LN     +DL   F + G V            I  D +T
Sbjct: 2   SSGSSGDPDEDSDNSAIYVQGLNDSVTLDDLADFFKQCGVVKMNKRTGQPMIHIYLDKET 61

Query: 281 GDSLNYAFIEFENRQACERAYSKMDNALIDDRRIHVDFSQ 320
           G     A + +E+    + A    D       ++ V  ++
Sbjct: 62  GKPKGDATVSYEDPPTAKAAVEWFDGKDFQGSKLKVSLAR 101

>2dh8_A DAZ-associated protein 1; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Length = 105

 Score = 53.0 bits (128), Expect = 6e-09
 Identities = 24/97 (24%), Positives = 37/97 (38%), Gaps = 10/97 (10%)

Query: 245 LFVCKLNPVTEDEDLHTIFSRFGTVVSAEIIRDFKTGDSLNYAFIEFENRQACERAYSKM 304
           LFV  L+  T  E L + FS++G VV   I++D  T  S  + F++F++           
Sbjct: 19  LFVGGLDWSTTQETLRSYFSQYGEVVDCVIMKDKTTNQSRGFGFVKFKDPNCVGTV-LAS 77

Query: 305 DNALIDDRRIHVDFSQSVSKLWNQFRRRDHQTGKGKG 341
               +D R I                R    +G   G
Sbjct: 78  RPHTLDGRNIDPKPCTP---------RGMQPSGPSSG 105

>2e5g_A U6 snRNA-specific terminal uridylyltransferase 1; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 94

 Score = 52.3 bits (126), Expect = 7e-09
 Identities = 15/72 (20%), Positives = 24/72 (33%), Gaps = 6/72 (8%)

Query: 245 LFVCKLNPVTEDEDLHTIFSRFGTVVSAEIIRDFKTGDSLNYAFIEFENRQACERAYSKM 304
           +FV       +   L   F  FG V S  + +D        +A +E  +  A E      
Sbjct: 11  VFVSGFPRGVDSAQLSEYFLAFGPVASVVMDKDKGV-----FAIVEMGDVGAREAVL-SQ 64

Query: 305 DNALIDDRRIHV 316
               +   R+ V
Sbjct: 65  SQHSLGGHRLRV 76

>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 = 52.7 bits (127), Expect = 8e-09
 Identities = 19/97 (19%), Positives = 38/97 (39%), Gaps = 10/97 (10%)

Query: 245 LFVCKLNPVTEDEDLHTIFSRFGTVVSAEIIRDFKTGDSLNYAFIEFENRQACERAYSKM 304
           LF+  L+  T +E L   + ++G +    ++RD  +  S  + F+ F +    + A    
Sbjct: 30  LFIGGLSFETTEESLRNYYEQWGKLTDCVVMRDPASKRSRGFGFVTFSSMAEVDAA-MAA 88

Query: 305 DNALIDDRRIHVDFSQSVSKLWNQFRRRDHQTGKGKG 341
               ID R +    + +         R +  +G   G
Sbjct: 89  RPHSIDGRVVEPKRAVA---------REESGSGPSSG 116

>2dng_A Eukaryotic translation initiation factor 4H; RRM domain, RBD, structural genomics, NPPSFA; NMR {Mus musculus} Length = 103

 Score = 51.9 bits (125), Expect = 1e-08
 Identities = 22/90 (24%), Positives = 39/90 (43%), Gaps = 6/90 (6%)

Query: 231 GDIPDADIKPPENVLFVCKLNPVTEDEDLHTIFSRFGTVVSAEIIRDFKTGDSLNYAFIE 290
            ++P      P    +V  L   T   D+  IF     + S  ++RD  T     + ++E
Sbjct: 8   KELPT----EPPYTAYVGNLPFNTVQGDIDAIFKDLS-IRSVRLVRDKDTDKFKGFCYVE 62

Query: 291 FENRQACERAYSKMDNALIDDRRIHVDFSQ 320
           F+   + + A    D AL+ DR + VD ++
Sbjct: 63  FDEVDSLKEA-LTYDGALLGDRSLRVDIAE 91

>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 = 51.7 bits (124), Expect = 2e-08
 Identities = 12/76 (15%), Positives = 29/76 (38%), Gaps = 6/76 (7%)

Query: 243 NVLFVCKLNPVTEDEDLHTIFSRFGTVVSAEIIRDFKTGDSLNYAFIEFENRQACERAYS 302
            V+    L   T   ++   FSRFG++    +       +    A +EF       +A+ 
Sbjct: 11  TVILAKNLPAGTLAAEIQETFSRFGSLGRVLL------PEGGITAIVEFLEPLEARKAFR 64

Query: 303 KMDNALIDDRRIHVDF 318
            +  +      +++++
Sbjct: 65  HLAYSKFHHVPLYLEW 80

>3zzy_A Polypyrimidine tract-binding protein 1; protein binding, peptide binding, RNA recognition motif; 1.40A {Homo sapiens} PDB: 3zzz_A Length = 130

 Score = 52.3 bits (125), Expect = 2e-08
 Identities = 23/86 (26%), Positives = 37/86 (43%), Gaps = 10/86 (11%)

Query: 240 PPENVLFVCKLN---PVTEDEDLHTIFSRFGTVVSAEIIRDFKTGDSLNYAFIEFENRQA 296
               VL +   N   PVT D  LH IFS+FGTV+                A +++ +  +
Sbjct: 24  GQSPVLRIIVENLFYPVTLDV-LHQIFSKFGTVLKIITFTKNNQF----QALLQYADPVS 78

Query: 297 CERAYSKMDNALIDDR--RIHVDFSQ 320
            + A   +D   I +    + +DFS+
Sbjct: 79  AQHAKLSLDGQNIYNACCTLRIDFSK 104

>2nlw_A Eukaryotic translation initiation factor 3 subunit 9; eukaryotic initiation factor 3 complex, RNA recognition motif; NMR {Homo sapiens} Length = 105

 Score = 51.3 bits (123), Expect = 2e-08
 Identities = 19/90 (21%), Positives = 35/90 (38%), Gaps = 9/90 (10%)

Query: 242 ENVLFVCKLNPVTED------EDLHTIFSRFGTVVSAEIIRDFKTGDSLNYAFIEFENRQ 295
           ++V+ V  +  V  D        +H IFS+FG + +     +   G +  Y F+E+ +  
Sbjct: 15  DSVIVVDNVPQVGPDRLEKLKNVIHKIFSKFGKITNDFYPEE--DGKTKGYIFLEYASPA 72

Query: 296 ACERAYSKMDNALIDDR-RIHVDFSQSVSK 324
               A    D   +D +    V+      K
Sbjct: 73  HAVDAVKNADGYKLDKQHTFRVNLFTDFDK 102

>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 = 51.1 bits (123), Expect = 3e-08
 Identities = 16/84 (19%), Positives = 34/84 (40%), Gaps = 3/84 (3%)

Query: 239 KPPENVLFVCKLNPVTEDEDLHTIFSRFGTVVSAEIIRDFKTGDSLN-YAFIEFENRQAC 297
           K P    F+  L     +E +   F     + +  + R+    + L  + + EFE+  + 
Sbjct: 12  KSPPYTAFLGNLPYDVTEESIKEFFRGLN-ISAVRLPREPSNPERLKGFGYAEFEDLDSL 70

Query: 298 ERAYSKMDNALIDDRRIHVDFSQS 321
             A   ++   + ++RI VD +  
Sbjct: 71  LSAL-SLNEESLGNKRIRVDVADQ 93

>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 = 50.3 bits (121), Expect = 3e-08
 Identities = 15/73 (20%), Positives = 32/73 (43%), Gaps = 7/73 (9%)

Query: 245 LFVCKLNPVTEDEDLHTIFSRFGTVVSAEIIRDFKTGDSLNYAFIEFENRQACERAYSKM 304
           +FV +       E+L   F ++G VV   I + F+      +AF+ F + +  +      
Sbjct: 14  VFVGRCTEDMTAEELQQFFCQYGEVVDVFIPKPFR-----AFAFVTFADDKVAQSLC--G 66

Query: 305 DNALIDDRRIHVD 317
           ++ +I    +H+ 
Sbjct: 67  EDLIIKGISVHIS 79

>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 = 50.7 bits (121), Expect = 4e-08
 Identities = 12/81 (14%), Positives = 25/81 (30%), Gaps = 9/81 (11%)

Query: 241 PENVLFVC--KLNPVTEDEDLHTIFSRFGTVVSAEIIRDFKTGDSLNYAFIEFENRQACE 298
               L V    L        L  +  + G       +       +  Y+F  +   +  +
Sbjct: 24  ATQSLVVANGGLGNGVSRNQLLPVLEKCGL------VDALLMPPNKPYSFARYRTTEESK 77

Query: 299 RAYSKMDN-ALIDDRRIHVDF 318
           RAY  ++   ++DD    +  
Sbjct: 78  RAYVTLNGKEVVDDLGQKITL 98

>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 = 50.1 bits (120), Expect = 4e-08
 Identities = 9/81 (11%), Positives = 26/81 (32%), Gaps = 7/81 (8%)

Query: 245 LFVCKLNPVTEDEDLHTIFSRFGTVVSAEIIRDFKTGDSLNYAFIEFENRQACERAYSKM 304
           + V  L   +  +++H +   +        ++      +   AF+   N +  + A    
Sbjct: 8   ILVKNLPQDSNCQEVHDLLKDYD-------LKYCYVDRNKRTAFVTLLNGEQAQNAIQMF 60

Query: 305 DNALIDDRRIHVDFSQSVSKL 325
                  + + V    + + L
Sbjct: 61  HQYSFRGKDLIVQLQPTDALL 81

>1x4f_A Matrin 3; structural genomics, RRM domain, NPPSFA, national project on protein structural and functional analyses; NMR {Mus musculus} SCOP: d.58.7.1 Length = 112

 Score = 50.3 bits (120), Expect = 6e-08
 Identities = 17/89 (19%), Positives = 32/89 (35%), Gaps = 9/89 (10%)

Query: 240 PPENVLFVCKL-NPVTEDEDLHTIFSRFGTVVSAEIIRDFKTGDSLNYAFIEFENRQACE 298
               V+ +  L +    D  +  +   +G + +  ++R        + AFIE E R+   
Sbjct: 23  ELGRVIHLSNLPHSGYSDSAVLKLAEPYGKIKNYILMR------MKSQAFIEMETREDAM 76

Query: 299 RA--YSKMDNALIDDRRIHVDFSQSVSKL 325
               +          R + VD S+   KL
Sbjct: 77  AMVDHCLKKALWFQGRCVKVDLSEKYKKL 105

>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 = 9e-08
 Identities = 17/84 (20%), Positives = 34/84 (40%), Gaps = 3/84 (3%)

Query: 239 KPPENVLFVCKLNPVTEDEDLHTIFSRFGTVVSAEIIRDFKTGDSLN-YAFIEFENRQAC 297
           K P    F+  L     +E +   F     + +  + R+    + L  + + EFE+  + 
Sbjct: 16  KSPPYTAFLGNLPYDVTEESIKEFFRGLN-ISAVRLPREPSNPERLKGFGYAEFEDLDSL 74

Query: 298 ERAYSKMDNALIDDRRIHVDFSQS 321
             A   ++   + +RRI VD +  
Sbjct: 75  LSAL-SLNEESLGNRRIRVDVADQ 97

>1wg5_A Heterogeneous nuclear ribonucleoprotein H; structural genomics, RRM domain, riken structural genomics/proteomics initiative, RSGI; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 104

 Score = 47.4 bits (113), Expect = 5e-07
 Identities = 18/89 (20%), Positives = 34/89 (38%), Gaps = 1/89 (1%)

Query: 231 GDIPDADIKPPENVLFVCKLNPVTEDEDLHTIFSRFGTVVSAEIIRDFKTGDSLNYAFIE 290
           G   ++     +  + +  L      E++   FS    V +   +     G S   AF++
Sbjct: 4   GSSGNSPDTANDGFVRLRGLPFGCSKEEIVQFFSGLEIVPNGMTLPVDFQGRSTGEAFVQ 63

Query: 291 FENRQACERAYSKMDNALIDDRRIHVDFS 319
           F +++  E+A  K     I  R I +  S
Sbjct: 64  FASQEIAEKALKK-HKERIGHRYIEIFKS 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 = 47.4 bits (113), Expect = 6e-07
 Identities = 12/107 (11%), Positives = 30/107 (28%), Gaps = 1/107 (0%)

Query: 229 SIGDIPDADIKPPENVLFVCKLNPVTEDEDLHTIFSRFGTVVSAEIIRDFKTGDSLNYAF 288
           S G   + D+   +    +  +       D+           +A  +     G  L  A 
Sbjct: 2   SSGSSGEGDVNSAKVCAHITNIPFSITKMDVLQFLEGIPVDENAVHVLVDNNGQGLGQAL 61

Query: 289 IEFENRQACERAYSKMDNALIDDRRIHVDFSQSVSKLWNQFRRRDHQ 335
           ++F+N     ++  ++    ++ R   V           +       
Sbjct: 62  VQFKNEDDARKSE-RLHRKKLNGREAFVHVVTLEDMREIEKNPPAQG 107

>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 = 47.6 bits (113), Expect = 8e-07
 Identities = 18/92 (19%), Positives = 35/92 (38%), Gaps = 1/92 (1%)

Query: 228 ESIGDIPDADIKPPENVLFVCKLNPVTEDEDLHTIFSRFGTVVSAEIIRDFKTGDSLNYA 287
           + +G   ++     +  + +  L      E++   FS    V +   +     G     A
Sbjct: 28  QQMGRGSNSADSANDGFVRLRGLPFGCTKEEIVQFFSGLEIVPNGITLPVDPEGKITGEA 87

Query: 288 FIEFENRQACERAYSKMDNALIDDRRIHVDFS 319
           F++F +++  E+A  K     I  R I V  S
Sbjct: 88  FVQFASQELAEKALGK-HKERIGHRYIEVFKS 118

>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 = 45.6 bits (108), Expect = 2e-06
 Identities = 18/80 (22%), Positives = 28/80 (35%), Gaps = 7/80 (8%)

Query: 239 KPPENVLFVCKLNPVTEDEDLHTIFSRFGTVVSAEIIRDFKTGDSLNYAFIEFENRQACE 298
           +  EN + V  L P    +DL       G V  A++ RD           +EF  ++   
Sbjct: 12  RRSENRVVVSGLPPSGSWQDLKDHMREAGDVCYADVYRD-------GTGVVEFVRKEDMT 64

Query: 299 RAYSKMDNALIDDRRIHVDF 318
            A  K+DN           +
Sbjct: 65  YAVRKLDNTKFRSHEGETAY 84

>1s79_A Lupus LA protein; RRM, alpha/beta, RNA binding protein, translation; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 103

 Score = 45.5 bits (108), Expect = 2e-06
 Identities = 6/75 (8%), Positives = 26/75 (34%), Gaps = 2/75 (2%)

Query: 242 ENVLFVCKLNPVTEDEDLHTIFSRFGTVVSAEIIRDFKTGDSLNYAFIEFENRQACERAY 301
              +++         +D+       G V++ ++ R           F+ F++ ++ ++  
Sbjct: 11  NRSVYIKGFPTDATLDDIKEWLEDKGQVLNIQMRRT-LHKAFKGSIFVVFDSIESAKKF- 68

Query: 302 SKMDNALIDDRRIHV 316
            +       +  + +
Sbjct: 69  VETPGQKYKETDLLI 83

>1x4d_A Matrin 3; structural genomics, RRM domain, NPPSFA, national project on protein structural and functional analyses; NMR {Mus musculus} SCOP: d.58.7.1 Length = 102

 Score = 44.5 bits (105), Expect = 4e-06
 Identities = 16/90 (17%), Positives = 30/90 (33%), Gaps = 9/90 (10%)

Query: 239 KPPENVLFVCKL-NPVTEDEDLHTIFSRFGTVVSAEIIRDFKTGDSLNYAFIEFENRQAC 297
                V+ +            L  +   FG +       +    + +N AFIE    +  
Sbjct: 12  VETRRVVHIMDFQRGKNLRYQLLQLVEPFGVIS------NHLILNKINEAFIEMATTEDA 65

Query: 298 ERA--YSKMDNALIDDRRIHVDFSQSVSKL 325
           + A  Y     AL+  + + V  SQ   ++
Sbjct: 66  QAAVDYYTTTPALVFGKPVRVHLSQKYKRI 95

>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 = 45.2 bits (107), Expect = 4e-06
 Identities = 16/104 (15%), Positives = 35/104 (33%), Gaps = 3/104 (2%)

Query: 234 PDADIKPPENVLFVCKLNPVTEDEDLHTIFSRFGTVVSAEIIRDFKTGDSLNYAFIEFEN 293
                      +++  L    E++ +   F +   V  +  I     G +    F+EF N
Sbjct: 17  RSRSPHEAGFCVYLKGLPFEAENKHVIDFFKKLDIVEDSIYIAYGPNGKATGEGFVEFRN 76

Query: 294 RQACERAYSKMDNALIDDRRIHVDFS--QSVSKLWNQFRRRDHQ 335
               + A  +     + +R I V     + + +  +  R+R   
Sbjct: 77  EADYKAALCR-HKQYMGNRFIQVHPITKKGMLEKIDMIRKRLQS 119

>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 = 44.0 bits (104), Expect = 5e-06
 Identities = 12/77 (15%), Positives = 28/77 (36%), Gaps = 6/77 (7%)

Query: 245 LFVCKLNPVTEDEDLHTIFSRFG-----TVVSAEIIRDFKTGDSLNYAFIEFENRQACER 299
           L+V  +     +E +   F+        T      +   +     N+AF+EF +     +
Sbjct: 9   LYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLEFRSVDETTQ 68

Query: 300 AYSKMDNALIDDRRIHV 316
           A +  D  +   + + +
Sbjct: 69  AMA-FDGIIFQGQSLKI 84

>2e5j_A Methenyltetrahydrofolate synthetase domain containing; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 97

 Score = 44.1 bits (104), Expect = 6e-06
 Identities = 14/88 (15%), Positives = 30/88 (34%), Gaps = 5/88 (5%)

Query: 234 PDADIKPPENVLFVCKLNPVTEDEDLHTIFSRFGTVVSAEIIRDFKTGDSLNYAFIEFEN 293
           P  +  P    ++V  L       DL       G+V      +  +       AF+ + +
Sbjct: 11  PPGEGAPLAADVYVGNLPRDARVSDLKRALRELGSVPLRLTWQGPRR-----RAFLHYPD 65

Query: 294 RQACERAYSKMDNALIDDRRIHVDFSQS 321
             A ++A S +    +    + V  ++ 
Sbjct: 66  SAAAQQAVSCLQGLRLGTDTLRVALARQ 93

>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 = 1e-05
 Identities = 11/77 (14%), Positives = 21/77 (27%), Gaps = 3/77 (3%)

Query: 240 PPENVLFVCKLNPVTEDEDLHTIFSRFGTVVSAEIIRDFKTGDSLNYAFIEFENRQACER 299
                + +  L      +DL  +                 T D      +EF + +    
Sbjct: 26  AKRYRITMKNLPEGCSWQDLKDLARENSLET---TFSSVNTRDFDGTGALEFPSEEILVE 82

Query: 300 AYSKMDNALIDDRRIHV 316
           A  +++N       I V
Sbjct: 83  ALERLNNIEFRGSVITV 99

>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 = 43.6 bits (103), Expect = 1e-05
 Identities = 13/81 (16%), Positives = 31/81 (38%), Gaps = 3/81 (3%)

Query: 239 KPPENVLFVCKLNPVTEDEDLHTIFSRFGTVVSAEIIRDFKTGDSLNYAFIEFENRQACE 298
            P +  + V  +     + D+   F     V +  +++D   G +     ++F + Q   
Sbjct: 13  NPDDLYVSVHGMPFSAMENDVRDFFHGLR-VDAVHLLKD-HVGRNNGNGLVKFLSPQDTF 70

Query: 299 RAYSKMDNALIDDRRIHVDFS 319
            A  + +  L+  R + V  +
Sbjct: 71  EALKR-NRMLMIQRYVEVSPA 90

>1wez_A HnRNP H', FTP-3, heterogeneous nuclear ribonucleoprotein H'; structural genomics, RRM domain, riken structural genomics/proteomics initiative, RSGI; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 102

 Score = 42.8 bits (101), Expect = 2e-05
 Identities = 16/91 (17%), Positives = 31/91 (34%), Gaps = 3/91 (3%)

Query: 229 SIGDIPDADIKPPENVLFVCKLNPVTEDEDLHTIFSRFGTVVSAEIIRDFKTGDSLNYAF 288
           S G    +      + + +  L     + D++  FS     +   I      G     A 
Sbjct: 2   SSGSSGSSFQSTTGHCVHMRGLPYRATENDIYNFFSPLN-PMRVHIEIG-PDGRVTGEAD 59

Query: 289 IEFENRQACERAYSKMDNALIDDRRIHVDFS 319
           +EF   +    A +K D A +  R + +  +
Sbjct: 60  VEFATHEDAVAAMAK-DKANMQHRYVELFLN 89

>2e5i_A Heterogeneous nuclear ribonucleoprotein L-like; RRM domain, RBD, structural genomics, NPPSFA; NMR {Mus musculus} Length = 124

 Score = 43.5 bits (102), Expect = 2e-05
 Identities = 16/85 (18%), Positives = 36/85 (42%), Gaps = 9/85 (10%)

Query: 240 PPENVLFVCKLNPV--TEDEDLHTIFSRFGTVVSAEIIRDFKTGDSLNYAFIEFENRQAC 297
               VL +   NP+     + L+T+ +  G V    I +          A +EFE+    
Sbjct: 21  GGNKVLLLSIQNPLYPITVDVLYTVCNPVGKVQRIVIFKRNGI-----QAMVEFESVLCA 75

Query: 298 ERAYSKMDNALIDDR--RIHVDFSQ 320
           ++A + ++ A I      + +++++
Sbjct: 76  QKAKAALNGADIYAGCCTLKIEYAR 100

>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 = 44.4 bits (104), Expect = 2e-05
 Identities = 12/125 (9%), Positives = 39/125 (31%), Gaps = 2/125 (1%)

Query: 196 EDDWVPLDEQLSAAELEQVIRSKDARSSAVVLESIGDIPDADIKPPENVLFVCKLNPVTE 255
           + + +      S AEL ++   K     +          +         +++        
Sbjct: 63  DFNVIVEALSKSKAELMEISEDKTKIRRSPSKPLPEVTDEYKNDVKNRSVYIKGFPTDAT 122

Query: 256 DEDLHTIFSRFGTVVSAEIIRDFKTGDSLNYAFIEFENRQACERAYSKMDNALIDDRRIH 315
            +D+       G V++ ++ R           F+ F++ ++ ++   +       +  + 
Sbjct: 123 LDDIKEWLEDKGQVLNIQMRRT-LHKAFKGSIFVVFDSIESAKKFV-ETPGQKYKETDLL 180

Query: 316 VDFSQ 320
           + F  
Sbjct: 181 ILFKD 185

>2dnl_A Cytoplasmic polyadenylation element binding protein 3; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 114

 Score = 42.7 bits (100), Expect = 3e-05
 Identities = 13/61 (21%), Positives = 25/61 (40%), Gaps = 2/61 (3%)

Query: 245 LFVCKLNPVTEDEDLHTIFSRFGTVVSAEIIRDFK--TGDSLNYAFIEFENRQACERAYS 302
           +FV  L P  +++++   F RFG +V     +           YAF+ F+   + +    
Sbjct: 11  VFVGGLPPDIDEDEITASFRRFGPLVVDWPHKAESKSYFPPKGYAFLLFQEESSVQALID 70

Query: 303 K 303
            
Sbjct: 71  A 71

>2dgx_A KIAA0430 protein; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 96

 Score = 41.1 bits (96), Expect = 6e-05
 Identities = 17/68 (25%), Positives = 27/68 (39%), Gaps = 3/68 (4%)

Query: 257 EDLHTIFSRFGTVVSAEIIRDFKTGDSLNYAFIEFENRQACERAYSKMDNALIDDRRIHV 316
           + L   F+R G V S E+       D    A ++ EN Q    A + +    I  ++I V
Sbjct: 28  QLLQEAFARHGKVKSVELSPH---TDYQLKAVVQMENLQDAIGAVNSLHRYKIGSKKILV 84

Query: 317 DFSQSVSK 324
             +   S 
Sbjct: 85  SLATGASG 92

>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 = 41.3 bits (97), Expect = 8e-05
 Identities = 18/80 (22%), Positives = 28/80 (35%), Gaps = 7/80 (8%)

Query: 239 KPPENVLFVCKLNPVTEDEDLHTIFSRFGTVVSAEIIRDFKTGDSLNYAFIEFENRQACE 298
           +  EN + V  L P    +DL       G V  A++ RD           +EF  ++   
Sbjct: 13  RRSENRVVVSGLPPSGSWQDLKDHMREAGDVCYADVYRD-------GTGVVEFVRKEDMT 65

Query: 299 RAYSKMDNALIDDRRIHVDF 318
            A  K+DN           +
Sbjct: 66  YAVRKLDNTKFRSHEGETAY 85

>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 = 44.1 bits (103), Expect = 1e-04
 Identities = 79/559 (14%), Positives = 168/559 (30%), Gaps = 158/559 (28%)

Query: 80  DEIRVDLKHAKTGTV----AMASAGENLNASQFYMT-LRDNLDYLDEKHTIFGEVAEGLE 134
           D I +  K A +GT+     + S  E +   +F    LR N  +L         +     
Sbjct: 52  DHI-IMSKDAVSGTLRLFWTLLSKQEEM-VQKFVEEVLRINYKFLMSP------IKTEQR 103

Query: 135 TLSRINESFVDEKNRPYKNIRI--KHTYILEDPF---------DDPAQ------------ 171
             S +   ++++++R Y + ++  K+      P+           PA+            
Sbjct: 104 QPSMMTRMYIEQRDRLYNDNQVFAKYNVSRLQPYLKLRQALLELRPAKNVLIDGVLGSGK 163

Query: 172 --LA-ELIPDASPEGKPKDEV----------VDEV---------RLEDDWVPLDEQLSA- 208
             +A ++      + K   ++           + V         +++ +W    +  S  
Sbjct: 164 TWVALDVCLSYKVQCKMDFKIFWLNLKNCNSPETVLEMLQKLLYQIDPNWTSRSDHSSNI 223

Query: 209 --------AELEQVIRSKDARSSAVVLESIGD--IPDA-DIKPPENVLFVCKLNPVTEDE 257
                   AEL ++++SK   +  +VL ++ +    +A ++         CK+   T  +
Sbjct: 224 KLRIHSIQAELRRLLKSKPYENCLLVLLNVQNAKAWNAFNLS--------CKILLTTRFK 275

Query: 258 DLHTIFSRFGT--VVSAEIIRDFKTGDSL----NYAFIEFEN--RQACE---RAYSKMDN 306
            +    S   T  +            +       Y     ++  R+      R  S +  
Sbjct: 276 QVTDFLSAATTTHISLDHHSMTLTPDEVKSLLLKYLDCRPQDLPREVLTTNPRRLS-IIA 334

Query: 307 ALIDDRRIHVDFSQSVSKLWNQFRRRDHQTGKGKGCFKCGGLDHIAKDCTGQQPAKYILR 366
             I D              W+ ++  +              L  I +             
Sbjct: 335 ESIRDGLAT----------WDNWKHVNCDK-----------LTTIIESSLNVLEP----- 368

Query: 367 DDNRQHGGYSDSRYEM--VF--DGETPEK--SR--REKKHRGHDPDDRVERNMNRLSSDL 418
            + R+        ++   VF      P    S    +      D    V + +++ S   
Sbjct: 369 AEYRKM-------FDRLSVFPPSAHIPTILLSLIWFDVIKS--DVMVVVNK-LHKYSLVE 418

Query: 419 RHRDQERRELSYRQRESDRTRENREDRRNRDGQESRNVQKQEVRDDDGRYESDHPKSSDT 478
           +   +    +     E     EN E   +R   +  N+ K         ++SD       
Sbjct: 419 KQPKESTISIPSIYLELKVKLEN-EYALHRSIVDHYNIPK--------TFDSDDLIPPYL 469

Query: 479 DRYRDWRGGGDYRKRSADSDSRAE--RREDGDYR----K-RNSD-----NGSHRDRRDD- 525
           D+Y     G  +  ++ +   R    R    D+R    K R+       +GS  +     
Sbjct: 470 DQYFYSHIG--HHLKNIEHPERMTLFRMVFLDFRFLEQKIRHDSTAWNASGSILNTLQQL 527

Query: 526 QDYRKKSADGDIHGDRRYD 544
           + Y+    D D   +R  +
Sbjct: 528 KFYKPYICDNDPKYERLVN 546

>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 = 44.1 bits (103), Expect = 1e-04
 Identities = 67/494 (13%), Positives = 141/494 (28%), Gaps = 149/494 (30%)

Query: 58  GTGTGGDSVYKFLYGEQAR------FFGDEIR-VDLKHAKTGTVAMASAGENLNASQFYM 110
           G    G +    +  +             +I  ++LK+  +    +    E L   +   
Sbjct: 157 GVLGSGKTW---VALDVCLSYKVQCKMDFKIFWLNLKNCNSPETVL----EMLQ--KLLY 207

Query: 111 TLRDNL-DYLDEKHTIFGEVAEGLETLSRINESFVDEKNRPYKNIRIKHTYILED----- 164
            +  N     D    I   +      L R+       K++PY+N  +    +L +     
Sbjct: 208 QIDPNWTSRSDHSSNIKLRIHSIQAELRRL------LKSKPYENCLL----VLLNVQNAK 257

Query: 165 ---PFDDPAQLAELI--PDASPEGKPKDEVVDEVRLEDDWVPLDEQLSAAELEQVIRSKD 219
               F+   ++  L+                  + L+   + L      + L + +    
Sbjct: 258 AWNAFNLSCKI--LLTTRFKQVTDFLSAATTTHISLDHHSMTLTPDEVKSLLLKYL---- 311

Query: 220 ARSSAVVLESIGDIPDADIKPPENVLFVCKLNPVTEDEDLHTIFSRFGTVVSAEIIRDFK 279
                       D    D+ P E    V   NP        +I         AE IRD  
Sbjct: 312 ------------DCRPQDL-PRE----VLTTNPR-----RLSII--------AESIRDGL 341

Query: 280 -TGDSLNYAFIEFEN-RQACERAYSKMDNALIDDRRIHVDFS----------QSVSKLWN 327
            T D  N+  +  +      E + + ++ A  + R++    S            +S +W 
Sbjct: 342 ATWD--NWKHVNCDKLTTIIESSLNVLEPA--EYRKMFDRLSVFPPSAHIPTILLSLIWF 397

Query: 328 QFRRRDHQTGKGKGCFKCGGLDHIAKDCTGQQPAKYIL--RDDNRQ----HGGYSDSRYE 381
              + D              +  +          KY L  +            Y + + +
Sbjct: 398 DVIKSD--------------VMVVVNKL-----HKYSLVEKQPKESTISIPSIYLELKVK 438

Query: 382 MVFDGETPEKSRR--EK--KHRGHDPDDRVERNM-----NRLSSDLRHRDQERRELSYRQ 432
           +          R   +     +  D DD +   +     + +   L++ +   R   +R 
Sbjct: 439 LE---NEYALHRSIVDHYNIPKTFDSDDLIPPYLDQYFYSHIGHHLKNIEHPERMTLFRM 495

Query: 433 RESDRTRENREDRRNRDGQESRNVQKQEVRDDDGRYESDHPKSSDTDRYRDWRGGGDYRK 492
              D                 R ++ Q++R D     + +   S  +  +  +    Y+ 
Sbjct: 496 VFLD----------------FRFLE-QKIRHDS---TAWNASGSILNTLQQLK---FYKP 532

Query: 493 RSADSDSRAERRED 506
              D+D + ER  +
Sbjct: 533 YICDNDPKYERLVN 546

>2cqf_A RNA-binding protein LIN-28; CCHC zinc-finger, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Length = 63

 Score = 38.8 bits (90), Expect = 2e-04
 Identities = 14/30 (46%), Positives = 16/30 (53%), Gaps = 1/30 (3%)

Query: 334 HQTGKGKGCFKCGGLDHIAKDCT-GQQPAK 362
                G  C+ CGGLDH AK+C    QP K
Sbjct: 2   SSGSSGDRCYNCGGLDHHAKECKLPPQPKK 31

>1wey_A Calcipressin 1; structural genomics, RRM domain, riken structural genomics/proteomics initiative, RSGI, RNA binding protein; NMR {Mus musculus} SCOP: d.58.7.1 Length = 104

 Score = 39.2 bits (91), Expect = 3e-04
 Identities = 13/89 (14%), Positives = 30/89 (33%), Gaps = 11/89 (12%)

Query: 240 PPENVLFVCKLNP-VTEDEDLHT----IFSRFGTVVSAEIIRDFKTGDSLNYAFIEFENR 294
              + L  C  N  V  + +       +F  +    + +  + FK         I F N 
Sbjct: 3   SGSSGLIACVANDDVFSESETRAKFESLFRTYDKDTTFQYFKSFKR------VRINFSNP 56

Query: 295 QACERAYSKMDNALIDDRRIHVDFSQSVS 323
            +   A  ++       + + + F+Q++ 
Sbjct: 57  LSAADARLRLHKTEFLGKEMKLYFAQTLH 85

>2dgw_A Probable RNA-binding protein 19; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Length = 91

 Score = 38.8 bits (91), Expect = 4e-04
 Identities = 13/81 (16%), Positives = 33/81 (40%), Gaps = 3/81 (3%)

Query: 241 PENVLFVCKLNPVTEDEDLHTIFSRFGTVVSAEIIRDFKTGDSLNYAFIEFENRQACERA 300
             + + +        ++++    +     V+  I+R+   G+   Y F++F N +  ++A
Sbjct: 9   TCHTVKLRGAPFNVTEKNVMEFLAPLK-PVAIRIVRN-AHGNKTGYIFVDFSNEEEVKQA 66

Query: 301 YSKMDNALIDDRRIHVDFSQS 321
               +   +  R I V   +S
Sbjct: 67  LKC-NREYMGGRYIEVFREKS 86

>3u1l_A PRE-mRNA-splicing factor CWC2; CSMP, zinc finger; 1.64A {Saccharomyces cerevisiae} PDB: 3u1m_A 3tp2_A Length = 240

 Score = 40.9 bits (95), Expect = 5e-04
 Identities = 14/72 (19%), Positives = 25/72 (34%), Gaps = 6/72 (8%)

Query: 250 LNPVTEDEDLHTIFSRFGTVVSAEIIRDFKTGDSLNYAFIEFENRQACERAYSKMDNALI 309
           L P   +  +  +FSR G +     +       S N  F++F+ +   E A   M N  +
Sbjct: 151 LKPAQIESRIRFVFSRLGDIDRIRYVE------SKNCGFVKFKYQANAEFAKEAMSNQTL 204

Query: 310 DDRRIHVDFSQS 321
                     + 
Sbjct: 205 LLPSDKEWDDRR 216

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	589
2ok3_A	161	Peptidyl-prolyl CIS-trans isomerase-like 3; beta-b	100.0
2poe_A	185	Cyclophilin-like protein, putative; cryptosporidiu	100.0
1zkc_A	197	Peptidyl-prolyl CIS-trans isomerase like 2; CIS-tr	100.0
3bo7_A	201	Peptidyl-prolyl CIS-trans isomerase cyclophilin-T;	100.0
2b71_A	196	Cyclophilin-like protein; structural genomics, str	100.0
2fu0_A	160	Cyclophilin, putative; PFE0505W, cyclosporin-bindi	100.0
2x7k_A	166	Peptidyl-prolyl CIS-trans isomerase-like 1; isomer	100.0
2k7n_A	203	Peptidyl-prolyl CIS-trans isomerase-like 1; beta b	100.0
2a2n_A	176	Peptidylprolyl isomerase domain and WD repeat CON;	100.0
3bkp_A	232	Cyclophilin; malaria, isomerase, structural GENO s	100.0
2hq6_A	185	Serologically defined colon cancer antigen 10; pro	100.0
1w74_A	191	Peptidyl-prolyl CIS-trans isomerase A; cyclophilin	100.0
3ich_A	188	Peptidyl-prolyl CIS-trans isomerase B; beta sandwi	100.0
2wfi_A	179	Peptidyl-prolyl CIS-trans isomerase G; phosphoprot	100.0
1a58_A	177	Cyclophilin; isomerase, ppiase; 1.95A {Brugia mala	100.0
2haq_A	172	Cyclophilin; rotamase, proline, isomerase, CIS-tra	100.0
2he9_A	192	NK-tumor recognition protein; cyclosporin, isomera	100.0
1mzw_A	177	Cyclophilin H, U-snRNP-ASSOCIATED cyclophilin; cyc	100.0
3pmp_A	164	Cyclophilin A; peptidyl prolyl isomerase, isomeras	100.0
2cmt_A	172	Peptidyl-prolyl CIS-trans isomerase E; rotamase ac	100.0
2z6w_A	165	Peptidyl-prolyl CIS-trans isomerase; isomerase-imm	100.0
1qng_A	170	Peptidyl-prolyl CIS-trans isomerase; isomerase-imm	100.0
2igv_A	173	Peptidyl-prolyl CIS-trans isomerase 3; rotamase; 1	100.0
2r99_A	173	Peptidyl-prolyl CIS-trans isomerase E; CIS-trans i	100.0
3s6m_A	167	Peptidyl-prolyl CIS-trans isomerase; seattle struc	100.0
1lop_A	164	Cyclophilin A; rotamase, isomerase-isomerase inhib	100.0
2ose_A	234	Probable peptidyl-prolyl CIS-trans isomerase; cycl	100.0
2poy_A	186	Peptidyl-prolyl CIS-trans isomerase; isomerase-imm	100.0
2c3b_A	172	Ppiase, cyclophilin; isomerase, 3D domain swapping	100.0
1v9t_A	166	Cyclophilin B; beta barrel, isomerase-isomerase in	100.0
3rdd_A	184	Peptidyl-prolyl CIS-trans isomerase A; beta barrel	100.0
1z81_A	229	Cyclophilin; structural genomics, structural genom	100.0
4fru_A	185	Cyclophilin B, peptidyl-prolyl CIS-trans isomerase	100.0
3k2c_A	193	Peptidyl-prolyl CIS-trans isomerase; ssgcid, NIH,	100.0
1ihg_A	370	Cyclophilin 40; ppiase immunophilin tetratricopept	100.0
3rfy_A	369	Peptidyl-prolyl CIS-trans isomerase CYP38, chloro;	100.0
3pgw_S	437	U1-70K; protein-RNA complex, U1 snRNA, SM fold, SM	99.95
4fxv_A	99	ELAV-like protein 1; RNA recognition motif, putati	99.82
3s8s_A	110	Histone-lysine N-methyltransferase SETD1A; chromat	99.79
2lxi_A	91	RNA-binding protein 10; NMR {Homo sapiens}	99.78
2lkz_A	95	RNA-binding protein 5; RRM; NMR {Homo sapiens}	99.76
3bs9_A	87	Nucleolysin TIA-1 isoform P40; RNA recognition mot	99.76
3md1_A	83	Nuclear and cytoplasmic polyadenylated RNA-bindin	99.75
2cq0_A	103	Eukaryotic translation initiation factor 3 subunit	99.75
2cqc_A	95	Arginine/serine-rich splicing factor 10; RNA recog	99.75
3mdf_A	85	Peptidyl-prolyl CIS-trans isomerase E; RRM domain,	99.75
2x1f_A	96	MRNA 3'-END-processing protein RNA15; transcriptio	99.75
2dnz_A	95	Probable RNA-binding protein 23; RNA recognition m	99.74
1x5u_A	105	Splicing factor 3B subunit 4 (spliceosome associat	99.74
2e5h_A	94	Zinc finger CCHC-type and RNA-binding motif- conta	99.74
2dgs_A	99	DAZ-associated protein 1; RRM domain, structural g	99.74
1whw_A	99	Hypothetical protein riken cDNA 1200009A02; RNA re	99.74
2cqb_A	102	Peptidyl-prolyl CIS-trans isomerase E; RNA recogni	99.74
2dgo_A	115	Cytotoxic granule-associated RNA binding protein 1	99.74
2dnm_A	103	SRP46 splicing factor; RRM domain, RBD, structural	99.74
2la6_A	99	RNA-binding protein FUS; structural genomics, nort	99.74
2do4_A	100	Squamous cell carcinoma antigen recognized by T- c	99.73
1x5t_A	96	Splicing factor 3B subunit 4; structure genomics,	99.73
3ex7_B	126	RNA-binding protein 8A; protein-RNA complex, mRNA	99.73
2cpz_A	115	CUG triplet repeat RNA-binding protein 1; RRM doma	99.73
1p27_B	106	RNA-binding protein 8A; nuclear protein, mRNA spli	99.73
1x4h_A	111	RNA-binding protein 28; structural genomics, RRM d	99.73
3p5t_L	90	Cleavage and polyadenylation specificity factor S;	99.73
2cqd_A	116	RNA-binding region containing protein 1; RNA recog	99.73
2cpf_A	98	RNA binding motif protein 19; RNA recognition moti	99.73
2dng_A	103	Eukaryotic translation initiation factor 4H; RRM d	99.73
1x5s_A	102	Cold-inducible RNA-binding protein; structure geno	99.73
2jrs_A	108	RNA-binding protein 39; RNA binding motif of RBM39	99.72
1oo0_B	110	CG8781-PA, drosophila Y14; RNA recognition motif,	99.72
3ns6_A	100	Eukaryotic translation initiation factor 3 subuni;	99.72
2fy1_A	116	RNA-binding motif protein, Y chromosome, family 1	99.72
1wi8_A	104	EIF-4B, eukaryotic translation initiation factor 4	99.72
2cph_A	107	RNA binding motif protein 19; RNA recognition moti	99.72
2d9p_A	103	Polyadenylate-binding protein 3; RRM domain, struc	99.72
2cpe_A	113	RNA-binding protein EWS; RNA recognition motif, RR	99.72
3ulh_A	107	THO complex subunit 4; nuclear protein, RNA bindin	99.72
4f25_A	115	Polyadenylate-binding protein 1; RRM fold, transla	99.72
2dnh_A	105	Bruno-like 5, RNA binding protein; RRM domain, RBD	99.72
3s7r_A	87	Heterogeneous nuclear ribonucleoprotein A/B; ferre	99.72
2div_A	99	TRNA selenocysteine associated protein; structural	99.72
2dhg_A	104	TRNA selenocysteine associated protein (SECP43); R	99.72
1u6f_A	139	Tcubp1, RNA-binding protein UBP1; trypanosome, mRN	99.71
3ucg_A	89	Polyadenylate-binding protein 2; ferredoxin-like,	99.71
2kxn_B	129	Transformer-2 protein homolog beta; SR protein, RR	99.71
4a8x_A	88	RNA-binding protein with serine-rich domain 1; tra	99.71
1h2v_Z	156	20 kDa nuclear CAP binding protein; CAP-binding-co	99.71
2cqi_A	103	Nucleolysin TIAR; RNA recognition motif, RRM, RNA	99.71
2cq3_A	103	RNA-binding protein 9; RRM domain, structural geno	99.71
3r27_A	100	HnRNP L, heterogeneous nuclear ribonucleoprotein L	99.71
2khc_A	118	Testis-specific RNP-type RNA binding protein; RRM,	99.71
2cqp_A	98	RNA-binding protein 12; RNA recognition motif, RRM	99.71
2ywk_A	95	Putative RNA-binding protein 11; RRM-domain, struc	99.71
2dgp_A	106	Bruno-like 4, RNA binding protein; RRM domain, str	99.71
3n9u_C	156	Cleavage and polyadenylation specificity factor S;	99.7
2ek1_A	95	RNA-binding protein 12; RNA recognition motif, dim	99.7
2do0_A	114	HnRNP M, heterogeneous nuclear ribonucleoprotein M	99.7
1rk8_A	165	CG8781-PA, CG8781-PA protein; mRNA processing, RRM	99.7
1s79_A	103	Lupus LA protein; RRM, alpha/beta, RNA binding pro	99.7
1sjq_A	105	Polypyrimidine tract-binding protein 1; babbab mot	99.7
2dgx_A	96	KIAA0430 protein; RRM domain, structural genomics,	99.7
2kn4_A	158	Immunoglobulin G-binding protein G, splicing FACT	99.7
2dh8_A	105	DAZ-associated protein 1; RRM domain, structural g	99.7
2wbr_A	89	GW182, gawky, LD47780P; DNA-binding protein, RRM,	99.7
2dis_A	109	Unnamed protein product; structural genomics, RRM	99.69
2rs2_A	109	Musashi-1, RNA-binding protein musashi homolog 1;	99.69
1p1t_A	104	Cleavage stimulation factor, 64 kDa subunit; RNA r	99.69
2cq4_A	114	RNA binding motif protein 23; RRM domain, structur	99.69
1x4e_A	85	RNA binding motif, single-stranded interacting pro	99.69
2cqg_A	103	TDP-43, TAR DNA-binding protein-43; RNA recognitio	99.69
2dgw_A	91	Probable RNA-binding protein 19; RRM domain, struc	99.69
2cpi_A	111	CCR4-NOT transcription complex subunit 4; RNA reco	99.68
2dgv_A	92	HnRNP M, heterogeneous nuclear ribonucleoprotein M	99.68
1x4a_A	109	Splicing factor, arginine/serine-rich 1 (splicing	99.68
2mss_A	75	Protein (musashi1); RNA-binding domain, RNA bindin	99.68
2j76_E	100	EIF-4B, EIF4B, eukaryotic translation initiation f	99.68
2nlw_A	105	Eukaryotic translation initiation factor 3 subunit	99.68
1x4c_A	108	Splicing factor, arginine/serine-rich 1; structura	99.68
2a3j_A	127	U1 small nuclear ribonucleoprotein A; computationa	99.68
1x4b_A	116	Heterogeneous nuclear ribonucleoproteins A2/B1; st	99.68
2cq1_A	101	PTB-like protein L; RRM domain, structural genomic	99.68
1x4d_A	102	Matrin 3; structural genomics, RRM domain, NPPSFA,	99.67
2cpy_A	114	RNA-binding protein 12; RRM domain, structural gen	99.67
2fc9_A	101	NCL protein; structure genomics, RRM_1 domain, str	99.67
2kt5_A	124	RNA and export factor-binding protein 2; chaperone	99.67
2jwn_A	124	Embryonic polyadenylate-binding protein 2-B; epabp	99.67
2ku7_A	140	MLL1 PHD3-CYP33 RRM chimeric protein; transcriptio	99.67
2ki2_A	90	SS-DNA binding protein 12RNP2; HP0827, RRM, SS-DNA	99.67
2m2b_A	131	RNA-binding protein 10; T-cell, JCSG, MPP, PSI-bio	99.67
2ad9_A	119	Polypyrimidine tract-binding protein 1; RBD, RRM,	99.67
1uaw_A	77	Mouse-musashi-1; RNP-type structure, RNA binding p	99.66
1wez_A	102	HnRNP H', FTP-3, heterogeneous nuclear ribonucleop	99.66
2err_A	109	Ataxin-2-binding protein 1; protein-RNA complex, R	99.66
2dgu_A	103	Heterogeneous nuclear ribonucleoprotein Q; RRM dom	99.66
1x5o_A	114	RNA binding motif, single-stranded interacting pro	99.66
1wg5_A	104	Heterogeneous nuclear ribonucleoprotein H; structu	99.66
3q2s_C	229	Cleavage and polyadenylation specificity factor S;	99.65
2ytc_A	85	PRE-mRNA-splicing factor RBM22; RRM domain, RBD, s	99.65
2jvr_A	111	Nucleolar protein 3; RNA recognition motif, nucleu	99.65
2cpd_A	99	Apobec-1 stimulating protein; RNA recognition moti	99.65
2fc8_A	102	NCL protein; structure genomics, RRM_1 domain, str	99.65
2lea_A	135	Serine/arginine-rich splicing factor 2; SR protein	99.65
1wex_A	104	Hypothetical protein (riken cDNA 2810036L13); stru	99.65
2db1_A	118	Heterogeneous nuclear ribonucleoprotein F; RRM dom	99.65
2cpj_A	99	Non-POU domain-containing octamer-binding protein;	99.65
1fj7_A	101	Nucleolin RBD1, protein C23; RNP, RRM, RNA binding	99.65
2dnq_A	90	RNA-binding protein 4B; RRM domain,RBD, structural	99.65
2dgt_A	92	RNA-binding protein 30; RRM domain, structural gen	99.64
2krb_A	81	Eukaryotic translation initiation factor 3 subunit	99.64
2cpx_A	115	Hypothetical protein FLJ11016; RRM domain, structu	99.64
1why_A	97	Hypothetical protein riken cDNA 1810017N16; RNA re	99.64
1wel_A	124	RNA-binding protein 12; structural genomics, NPPSF	99.64
1nu4_A	97	U1A RNA binding domain; RNA recognition motif, U1	99.64
2hgl_A	136	HNRPF protein, heterogeneous nuclear ribonucleopro	99.64
1x4g_A	109	Nucleolysin TIAR; structural genomics, RRM domain,	99.64
2xnq_A	97	Nuclear polyadenylated RNA-binding protein 3; tran	99.63
2e5j_A	97	Methenyltetrahydrofolate synthetase domain contain	99.63
1fjc_A	96	Nucleolin RBD2, protein C23; RNP, RRM, RNA binding	99.63
2jvo_A	108	Nucleolar protein 3; nucleus, phosphorylation, rib	99.63
2dnp_A	90	RNA-binding protein 14; RRM domain, RBD, structura	99.63
2lcw_A	116	RNA-binding protein FUS; RRM, nucleic acid binding	99.43
1iqt_A	75	AUF1, heterogeneous nuclear ribonucleoprotein D0;	99.63
3lqv_A	115	PRE-mRNA branch site protein P14; cysless mutant,	99.63
2j8a_A	136	Histone-lysine N-methyltransferase, H3 lysine-4 sp	99.63
2f3j_A	177	RNA and export factor binding protein 2; RRM domai	99.63
3md3_A	166	Nuclear and cytoplasmic polyadenylated RNA-bindin	99.63
4f02_A	213	Polyadenylate-binding protein 1; mRNA, eukaryotic	99.62
1x4f_A	112	Matrin 3; structural genomics, RRM domain, NPPSFA,	99.62
2la4_A	101	Nuclear and cytoplasmic polyadenylated RNA-bindin	99.62
2dnn_A	109	RNA-binding protein 12; RRM domain, RBD, structura	99.62
2kvi_A	96	Nuclear polyadenylated RNA-binding protein 3; RNA-	99.61
3egn_A	143	RNA-binding protein 40; RNA recognition motif (RRM	99.61
2lmi_A	107	GRSF-1, G-rich sequence factor 1; G-rich RNA seque	99.61
2hvz_A	101	Splicing factor, arginine/serine-rich 7; RRM, RNA	99.61
2xs2_A	102	Deleted in azoospermia-like; RNA binding protein-R	99.61
1wf1_A	110	RNA-binding protein RALY; structural genomics, RRM	99.6
2hgn_A	139	Heterogeneous nuclear ribonucleoprotein F; RNA rec	99.59
2g4b_A	172	Splicing factor U2AF 65 kDa subunit; protein-RNA c	99.59
2cqh_A	93	IGF-II mRNA-binding protein 2 isoform A; RNA recog	99.59
1x5p_A	97	Negative elongation factor E; structure genomics,	99.59
2e5g_A	94	U6 snRNA-specific terminal uridylyltransferase 1;	99.59
2diu_A	96	KIAA0430 protein; structural genomics, RRM domain,	99.59
1whx_A	111	Hypothetical protein riken cDNA 1200009A02; RNA re	99.59
2e44_A	96	Insulin-like growth factor 2 mRNA binding protein	99.58
2dha_A	123	FLJ20171 protein; RRM domain, structural genomics,	99.58
1fxl_A	167	Paraneoplastic encephalomyelitis antigen HUD; prot	99.58
2i2y_A	150	Fusion protein consists of immunoglobin G- binding	99.58
3beg_B	115	Splicing factor, arginine/serine-rich 1; kinase, S	99.58
1wg1_A	88	KIAA1579 protein, homolog EXC-7; RBD, structural g	99.58
2hgm_A	126	HNRPF protein, heterogeneous nuclear ribonucleopro	99.57
3d2w_A	89	TAR DNA-binding protein 43; DP-43 proteinopathy, T	99.57
1b7f_A	168	Protein (SXL-lethal protein), RNA (5'-R(P*GP*UP*UP	99.57
2cq2_A	114	Hypothetical protein LOC91801; RRM domain, structu	99.57
1l3k_A	196	Heterogeneous nuclear ribonucleoprotein A1; nuclea	99.57
3zzy_A	130	Polypyrimidine tract-binding protein 1; protein bi	99.56
1b7f_A	168	Protein (SXL-lethal protein), RNA (5'-R(P*GP*UP*UP	99.55
2e5i_A	124	Heterogeneous nuclear ribonucleoprotein L-like; RR	99.55
2yh0_A	198	Splicing factor U2AF 65 kDa subunit; PRE-mRNA spli	99.54
2qfj_A	216	FBP-interacting repressor; protein-DNA complex; HE	99.54
4f02_A	213	Polyadenylate-binding protein 1; mRNA, eukaryotic	99.54
2pe8_A	105	Splicing factor 45; RRM, protein binding; 2.00A {H	99.54
1l3k_A	196	Heterogeneous nuclear ribonucleoprotein A1; nuclea	99.54
2dnl_A	114	Cytoplasmic polyadenylation element binding protei	99.53
1sjr_A	164	Polypyrimidine tract-binding protein 1; extended b	99.53
2cjk_A	167	Nuclear polyadenylated RNA-binding protein 4; HRP1	99.53
3nmr_A	175	Cugbp ELAV-like family member 1; RRM, PRE-mRNA spl	99.53
1fxl_A	167	Paraneoplastic encephalomyelitis antigen HUD; prot	99.53
2bz2_A	121	Negative elongation factor E; NELF E, RNA recognit	99.52
3tyt_A	205	Heterogeneous nuclear ribonucleoprotein L; ferredo	99.52
1fje_B	175	Nucleolin RBD12, protein C23; RNP, RRM, RNA bindin	99.51
2hzc_A	87	Splicing factor U2AF 65 kDa subunit; RNA splicing,	99.5
1wf0_A	88	TDP-43, TAR DNA-binding protein-43; structural gen	99.5
3md3_A	166	Nuclear and cytoplasmic polyadenylated RNA-bindin	99.49
2qfj_A	216	FBP-interacting repressor; protein-DNA complex; HE	99.48
2ghp_A	292	U4/U6 snRNA-associated splicing factor PRP24; RNA	99.48
2voo_A	193	Lupus LA protein; RNA-binding protein, RNA recogni	99.47
3smz_A	284	Protein raver-1, ribonucleoprotein PTB-binding 1;	99.46
2cjk_A	167	Nuclear polyadenylated RNA-binding protein 4; HRP1	99.46
3nmr_A	175	Cugbp ELAV-like family member 1; RRM, PRE-mRNA spl	99.45
3u1l_A	240	PRE-mRNA-splicing factor CWC2; CSMP, zinc finger;	99.44
3smz_A	284	Protein raver-1, ribonucleoprotein PTB-binding 1;	99.43
3pgw_A	282	U1-A; protein-RNA complex, U1 snRNA, SM fold, SM c	99.43
2dit_A	112	HIV TAT specific factor 1 variant; structural geno	99.42
2adc_A	229	Polypyrimidine tract-binding protein 1; RBD, RRM,	99.41
3v4m_A	105	Splicing factor U2AF 65 kDa subunit; canonical RNA	99.39
3pgw_A	282	U1-A; protein-RNA complex, U1 snRNA, SM fold, SM c	99.38
3tyt_A	205	Heterogeneous nuclear ribonucleoprotein L; ferredo	99.38
2adc_A	229	Polypyrimidine tract-binding protein 1; RBD, RRM,	99.37
1qm9_A	198	Polypyrimidine tract-binding protein; ribonucleopr	99.37
1fje_B	175	Nucleolin RBD12, protein C23; RNP, RRM, RNA bindin	99.37
1jmt_A	104	Splicing factor U2AF 35 kDa subunit; RRM, RNA spli	99.37
3ue2_A	118	Poly(U)-binding-splicing factor PUF60; RNA recogni	99.36
3sde_A	261	Paraspeckle component 1; RRM, anti parallel right	99.34
1qm9_A	198	Polypyrimidine tract-binding protein; ribonucleopr	99.33
3sde_A	261	Paraspeckle component 1; RRM, anti parallel right	99.31
2ghp_A	292	U4/U6 snRNA-associated splicing factor PRP24; RNA	99.29
2g4b_A	172	Splicing factor U2AF 65 kDa subunit; protein-RNA c	99.27
2yh0_A	198	Splicing factor U2AF 65 kDa subunit; PRE-mRNA spli	99.26
2d9o_A	100	DNAJ (HSP40) homolog, subfamily C, member 17; RRM	99.25
3tht_A	345	Alkylated DNA repair protein ALKB homolog 8; struc	99.23
3s6e_A	114	RNA-binding protein 39; ferredoxin-like, structura	99.17
2dnr_A	91	Synaptojanin-1; RRM domain, RBD, structural genomi	99.16
1owx_A	121	Lupus LA protein, SS-B, LA; RRM, transcription; NM	99.07
1ufw_A	95	Synaptojanin 2; RNP domain, structural genomics, r	98.96
3dxb_A	222	Thioredoxin N-terminally fused to PUF60(UHM); spli	98.66
3pgw_S	437	U1-70K; protein-RNA complex, U1 snRNA, SM fold, SM	98.44
2l9w_A	117	U4/U6 snRNA-associated-splicing factor PRP24; RRM,	98.09
1wey_A	104	Calcipressin 1; structural genomics, RRM domain, r	97.6
1uw4_A	91	UPF3X; nonsense mediated mRNA decay protein, RNA-b	96.96
1whv_A	100	Poly(A)-specific ribonuclease; RNA recognition mot	96.91
3ctr_A	101	Poly(A)-specific ribonuclease PARN; protein-RNA-co	96.71
2dhx_A	104	Poly (ADP-ribose) polymerase family, member 10 var	96.5
1wwh_A	119	Nucleoporin 35, nucleoporin; structural genomics,	96.17
2l08_A	97	Regulator of nonsense transcripts 3A; NESG, nonsen	95.72
2nnz_A	153	Hypothetical protein; beta-barrel, structural geno	95.68
3kop_A	188	Uncharacterized protein; protein with A cyclophili	95.33
3p3d_A	132	Nucleoporin 53; structural genomics, PSI-2, protei	95.03
1zx8_A	136	Hypothetical protein TM1367; structural genomics,	93.89
3pq1_A	464	Poly(A) RNA polymerase; nucleotidyl transferase, R	93.69
2kn4_A	158	Immunoglobulin G-binding protein G, splicing FACT	93.63
2i2y_A	150	Fusion protein consists of immunoglobin G- binding	93.08
3ts2_A	148	Protein LIN-28 homolog A; microrna biogenesis, pro	92.04

>2ok3_A Peptidyl-prolyl CIS-trans isomerase-like 3; beta-barrel, helix, disulfide bridge; 2.00A {Homo sapiens} SCOP: b.62.1.1 PDB: 1xyh_A 2oju_A*

Probab=100.00  E-value=7.3e-48  Score=354.49  Aligned_cols=160  Identities=47%  Similarity=0.803  Sum_probs=153.6

Q ss_pred             CEEEEEecceeEEEEecCCCChhHHHHHHHHHhcCccCCceEEEeecCcccccCCCCCCCCCCCCcccccccccccccCC
Q 007792            1 MSVLIVTSLGDIVVDLFVDKCPLTTKNFLKLCKIKYYNGCLFHTVQKDFTAQTGDPTGTGTGGDSVYKFLYGEQARFFGD   80 (589)
Q Consensus         1 ~~v~~~T~~G~i~ieL~~~~aP~~~~nF~~l~~~~~Y~g~~f~rv~~~~~iq~Gd~~~~~~~~~~~~~~~~~~~~~~~~~   80 (589)
                      |+|+|+|++|+|+|+||++.||+||+||++||+.+||+|+.||||+|+||||||++.+++.++.++|+       ..|++
T Consensus         1 m~v~~~T~~G~i~ieL~~~~aP~t~~NF~~L~~~g~Y~g~~fhRvi~~f~iQgGd~~~~g~gg~si~g-------~~~~d   73 (161)
T 2ok3_A            1 MSVTLHTDVGDIKIEVFCERTPKTCENFLALCASNYYNGCIFHRNIKGFMVQTGDPTGTGRGGNSIWG-------KKFED   73 (161)
T ss_dssp             CEEEEEETTEEEEEEECTTTCHHHHHHHHHHHHTTTTTTCBCCEEETTTEEEECCTTSSSSCCCCTTS-------SCBCC
T ss_pred             CEEEEEeCCccEEEEEcCCCCcHHHHHHHHHhhhcccCCCEEEEEECCCEEecCCCCCCCCCCCcccC-------Ccccc
Confidence            99999999999999999999999999999999999999999999999999999999999999999987       57899


Q ss_pred             ccccCCCCCCCceEEEeccCCCCCcceEEEEeCCCCCCCCCCcceEEEEecCHHHHHHHhhCccCCC-CCcccceeeccc
Q 007792           81 EIRVDLKHAKTGTVAMASAGENLNASQFYMTLRDNLDYLDEKHTIFGEVAEGLETLSRINESFVDEK-NRPYKNIRIKHT  159 (589)
Q Consensus        81 e~~~~l~~~~~G~vs~a~~g~~~~~sqFfI~l~~~~~~ld~~~~vFG~Vv~G~~vl~~i~~~~~~~~-~~p~~~i~I~~~  159 (589)
                      |..+.|+|+.+|+||||+.++++++|||||++.+ +||||++|+|||+|++||+||++|++++++.. ++|..+|+|.+|
T Consensus        74 E~~~~l~h~~~G~lsma~~gp~s~~SQFfI~~~~-~~~Ldg~~tvFG~Vv~G~dvv~~I~~~~~~~~~~~P~~~v~I~~~  152 (161)
T 2ok3_A           74 EYSEYLKHNVRGVVSMANNGPNTNGSQFFITYGK-QPHLDMKYTVFGKVIDGLETLDELEKLPVNEKTYRPLNDVHIKDI  152 (161)
T ss_dssp             CCCTTCCSCSTTEEEECCSSTTCBCSCEEEESSC-CGGGTTTSCEEEEEEECHHHHHHHHTCCBCTTTCCBSSCCBEEEE
T ss_pred             ccCcCcCcCCCeEEEEecCCCCCcceEEEEEcCC-CCccCCCEeEEEEEeCCHHHHHHHHhCCccCCCCCcCCCeEEEEE
Confidence            9878899999999999999999999999999998 69999999999999999999999999999887 999999999999


Q ss_pred             ccccCCCCC
Q 007792          160 YILEDPFDD  168 (589)
Q Consensus       160 ~vl~~p~~~  168 (589)
                      .++.+||++
T Consensus       153 ~i~~~Pf~d  161 (161)
T 2ok3_A          153 TIHANPFAQ  161 (161)
T ss_dssp             EEECCSCC-
T ss_pred             EEecCCCCC
Confidence            999999974

>2poe_A Cyclophilin-like protein, putative; cryptosporidium parvum cyclophilin isomerase, structural genomics; 2.01A {Cryptosporidium parvum iowa II} PDB: 2qer_A

Probab=100.00  E-value=3.3e-47  Score=356.68  Aligned_cols=162  Identities=41%  Similarity=0.735  Sum_probs=151.9

Q ss_pred             CEEEEEecceeEEEEecCCCChhHHHHHHHHHhcCccCCceEEEeecCcccccCCCCCCCCCCCCcccccccccccccCC
Q 007792            1 MSVLIVTSLGDIVVDLFVDKCPLTTKNFLKLCKIKYYNGCLFHTVQKDFTAQTGDPTGTGTGGDSVYKFLYGEQARFFGD   80 (589)
Q Consensus         1 ~~v~~~T~~G~i~ieL~~~~aP~~~~nF~~l~~~~~Y~g~~f~rv~~~~~iq~Gd~~~~~~~~~~~~~~~~~~~~~~~~~   80 (589)
                      |.|+|+|++|+|+|+||++.||+||+||++||+.+||+|+.||||+|+||||||++.+++.++.++|+       ..|++
T Consensus        17 ~~v~i~t~~G~i~ieL~~~~aP~t~~NF~~L~~~g~Y~g~~FhRvi~~f~iQgGd~~~~g~gg~si~g-------~~~~d   89 (185)
T 2poe_A           17 QGVRIITNYGDLKFELFCSQCPKACKNFLALSASGYYKNTIFHKNIKGFIIQGGDPTGTGKGGESIYG-------RYFDD   89 (185)
T ss_dssp             CEEEEEETTEEEEEEECTTTCHHHHHHHHHHHHTTTTTTEEEEEECTTSEEEEEETTSSSSCCCBTTB-------SCBCC
T ss_pred             eEEEEEecCccEEEEEeCCCCcHHHHHHHHHhccCCCCCCEEEEEECCCEEEcCCCCCCCCCCCccCC-------Ccccc
Confidence            78999999999999999999999999999999999999999999999999999999999999999987       67899


Q ss_pred             ccccCCCCCCCceEEEeccC----CCCCcceEEEEeCCCCCCCCCCcceEEEEecCHHHHHHHhhCccCCCCCcccceee
Q 007792           81 EIRVDLKHAKTGTVAMASAG----ENLNASQFYMTLRDNLDYLDEKHTIFGEVAEGLETLSRINESFVDEKNRPYKNIRI  156 (589)
Q Consensus        81 e~~~~l~~~~~G~vs~a~~g----~~~~~sqFfI~l~~~~~~ld~~~~vFG~Vv~G~~vl~~i~~~~~~~~~~p~~~i~I  156 (589)
                      |+.+.|+|+.+|+||||+.+    +++++||||||+.+ +||||++|+|||+|++||+||++|+.++++.+++|.++|+|
T Consensus        90 E~~~~l~h~~~G~lsmA~~g~~~~p~s~gSQFFIt~~~-~~~LDg~~tVFG~Vv~Gmdvv~~I~~~~t~~~~~P~~~v~I  168 (185)
T 2poe_A           90 EIYPELKYDRRGILSMASKGASKKPNTNGSQFFITYSS-LPQLNGEYVIFGKLIDGFETLNTLENCPSDKSHKPIDEIII  168 (185)
T ss_dssp             CCCTTSCCCSTTEEEECCSCC-CCCSCBCSCEEEESSC-CGGGTTTSCEEEEEEECHHHHHHHHHSCBCTTSCBSSCCEE
T ss_pred             cccCCCccCCCeEEEEecCCCCCCCCCccceEEEECCC-CCccCCCeeEEEEEeCCHHHHHHHHhCCcCCCCCcCCCeEE
Confidence            98889999999999999999    99999999999998 69999999999999999999999999999988999999999


Q ss_pred             cccccccCCCCChh
Q 007792          157 KHTYILEDPFDDPA  170 (589)
Q Consensus       157 ~~~~vl~~p~~~~~  170 (589)
                      .+|+++.+||+++.
T Consensus       169 ~~~~i~~dPf~d~~  182 (185)
T 2poe_A          169 KDIVIHSNPIADQE  182 (185)
T ss_dssp             EEEEEECCC-----
T ss_pred             EEEEEECCCCCCcc
Confidence            99999999998874

>1zkc_A Peptidyl-prolyl CIS-trans isomerase like 2; CIS-trans isomerization, peptidylprolyl isomerase, protein- folding, structural genomics consortium; 1.65A {Homo sapiens} SCOP: b.62.1.1

Probab=100.00  E-value=1.3e-46  Score=354.36  Aligned_cols=162  Identities=43%  Similarity=0.792  Sum_probs=155.3

Q ss_pred             EEEEEecceeEEEEecCCCChhHHHHHHHHHhcCccCCceEEEeecCcccccCCCCCCCCCCCCcccccccccccccCCc
Q 007792            2 SVLIVTSLGDIVVDLFVDKCPLTTKNFLKLCKIKYYNGCLFHTVQKDFTAQTGDPTGTGTGGDSVYKFLYGEQARFFGDE   81 (589)
Q Consensus         2 ~v~~~T~~G~i~ieL~~~~aP~~~~nF~~l~~~~~Y~g~~f~rv~~~~~iq~Gd~~~~~~~~~~~~~~~~~~~~~~~~~e   81 (589)
                      .|+|+|++|+|+|+||++.||+||+||++||+.+||+|+.||||+|+||||||++.+++.++.++|+       ..|++|
T Consensus        21 ~v~l~T~~G~I~ieL~~~~aP~tv~NF~~L~~~g~Ydg~~FhRVi~~f~iQgGd~~~~g~Gg~si~g-------~~f~dE   93 (197)
T 1zkc_A           21 YVRLHTNKGDLNLELHCDLTPKTCENFIRLCKKHYYDGTIFHRSIRNFVIQGGDPTGTGTGGESYWG-------KPFKDE   93 (197)
T ss_dssp             EEEEEETTEEEEEEECTTTSHHHHHHHHHHHHTTTTTTEEEEEEETTTEEEECCTTSSSSCCCBTTB-------SCBCCC
T ss_pred             EEEEEeCCccEEEEEcCCCCcHHHHHHHHHHhcCCCCCCEEEEEeCCCEEEcCCCCCCCCCCCccCC-------Cccccc
Confidence            6899999999999999999999999999999999999999999999999999999999999999987       678999


Q ss_pred             cccCCCCCCCceEEEeccCCCCCcceEEEEeCCCCCCCCCCcceEEEEecCHHHHHHHhhCccCCC-CCcccceeecccc
Q 007792           82 IRVDLKHAKTGTVAMASAGENLNASQFYMTLRDNLDYLDEKHTIFGEVAEGLETLSRINESFVDEK-NRPYKNIRIKHTY  160 (589)
Q Consensus        82 ~~~~l~~~~~G~vs~a~~g~~~~~sqFfI~l~~~~~~ld~~~~vFG~Vv~G~~vl~~i~~~~~~~~-~~p~~~i~I~~~~  160 (589)
                      +.+.|+|+.+|+||||+.++++++||||||+.+ +|+||++|+|||+|++||+||++|+.++++.+ ++|..+|+|.+|+
T Consensus        94 ~~~~l~h~~~G~lsMAn~gp~sngSQFFIt~~~-~~~LDg~~tVFG~Vv~Gmdvv~~I~~~~t~~~~~~P~~~i~I~~~~  172 (197)
T 1zkc_A           94 FRPNLSHTGRGILSMANSGPNSNRSQFFITFRS-CAYLDKKHTIFGRVVGGFDVLTAMENVESDPKTDRPKEEIRIDATT  172 (197)
T ss_dssp             CCTTCCSCSTTEEEECCSSTTCBCSCEEEESSC-CGGGTTTSCEEEEEEECHHHHHHHHHSCBCTTTCCBSSCCEEEEEE
T ss_pred             cCcCcCCCCceEEEEecCCCCCcccEEEEEcCC-CCccCCCccEEEEEEcCHHHHHHHHcCCCCCCCCCcCCCeEEEEEE
Confidence            888999999999999999999999999999998 69999999999999999999999999999987 9999999999999


Q ss_pred             cccCCCCChhh
Q 007792          161 ILEDPFDDPAQ  171 (589)
Q Consensus       161 vl~~p~~~~~~  171 (589)
                      ++.+||+++..
T Consensus       173 v~~dPf~d~~~  183 (197)
T 1zkc_A          173 VFVDPYEEADA  183 (197)
T ss_dssp             EEECTTHHHHH
T ss_pred             EEcCCcccHHH
Confidence            99999987765

>3bo7_A Peptidyl-prolyl CIS-trans isomerase cyclophilin-T; isomerase-immunosuppressant complex, immunosuppressant, cyclophilin, structural G structural genomics consortium, SGC; HET: BMT; 2.35A {Toxoplasma gondii}

Probab=100.00  E-value=1.5e-46  Score=357.68  Aligned_cols=169  Identities=30%  Similarity=0.567  Sum_probs=149.9

Q ss_pred             EEEEEecceeEEEEecCCCChhHHHHHHHHHhcCccCCceEEEeecCcccccC-----CCCCCCCCCCCccccccccccc
Q 007792            2 SVLIVTSLGDIVVDLFVDKCPLTTKNFLKLCKIKYYNGCLFHTVQKDFTAQTG-----DPTGTGTGGDSVYKFLYGEQAR   76 (589)
Q Consensus         2 ~v~~~T~~G~i~ieL~~~~aP~~~~nF~~l~~~~~Y~g~~f~rv~~~~~iq~G-----d~~~~~~~~~~~~~~~~~~~~~   76 (589)
                      .|+|+|++|+|+|+||++.||+||+||++||+.+||+|+.||||+++||||||     |+++++.++.++|..+....+.
T Consensus         8 ~v~l~T~~G~i~ieL~~~~aP~t~~NF~~L~~~g~Ydg~~FhRvi~~f~iQgG~~~~~Dp~~~g~gg~si~~~~~~~~g~   87 (201)
T 3bo7_A            8 YLRIVTTQGSLNIELHADMAPRACDSFLRLCAVKYFDDTIFHRCIRNFMIQGGRAELRQPSKKKEVQQSPRSISGFPGGA   87 (201)
T ss_dssp             EEEEEETTEEEEEEECTTTCHHHHHHHHHHHHTTTTTTCBEEEEETTTEEEECCGGGCCC-------CCSSCCCSSTTCC
T ss_pred             EEEEEeCCCCEEEEEcCCCCcHHHHHHHHHHhcCccCCCEEEEeeCCCEEEcCcccccCCCCCCCCCccccccccccCCC
Confidence            69999999999999999999999999999999999999999999999999999     9999999999999655555567


Q ss_pred             ccCCccccCCCCCCCceEEEeccCCCCCcceEEEEeCCCCCCCCCCcceEEEEecCHHHHHHHhhCccCCCCCcccceee
Q 007792           77 FFGDEIRVDLKHAKTGTVAMASAGENLNASQFYMTLRDNLDYLDEKHTIFGEVAEGLETLSRINESFVDEKNRPYKNIRI  156 (589)
Q Consensus        77 ~~~~e~~~~l~~~~~G~vs~a~~g~~~~~sqFfI~l~~~~~~ld~~~~vFG~Vv~G~~vl~~i~~~~~~~~~~p~~~i~I  156 (589)
                      .|++|+.+.|+|+.+|+||||+.++++++|||||||.+ +||||++|+|||+|++||+||++|+.++++.+++|..+|.|
T Consensus        88 ~f~dE~~~~l~h~~~G~lsmA~~gp~s~gSQFFIt~~~-~~~LDg~~tVFG~Vv~Gmdvv~~I~~~~t~~~~~P~~~i~I  166 (201)
T 3bo7_A           88 PFEDEFDNRLVHQGIGVLSMANDGKHSNLSEFFITFKS-CEHLNNKHTIFGRVVGGLDVLRQWEKLETDKKDKPLKPPKV  166 (201)
T ss_dssp             CBCCCCCTTCCCCSTTEEEECCSSTTCBSSCEEEESSC-CGGGTTTSCEEEEEEECHHHHHHHTTCCBCTTSCBSSCCBE
T ss_pred             cccCcccCCCCcCCCcEEEEeeCCCCCcccEEEEECCC-CcccCCCceEEEEEecCHHHHHHHHhCCcCCCCCcCCCeEE
Confidence            89999889999999999999999999999999999998 69999999999999999999999999999999999999999


Q ss_pred             cccccccCCCCChhh
Q 007792          157 KHTYILEDPFDDPAQ  171 (589)
Q Consensus       157 ~~~~vl~~p~~~~~~  171 (589)
                      .+|+++.+||+++..
T Consensus       167 ~~~~v~~dPf~d~~~  181 (201)
T 3bo7_A          167 EEIIVFKNPFEDARK  181 (201)
T ss_dssp             EEEEEEECCC-----
T ss_pred             EEEEEEcCCccCHHH
Confidence            999999999998765

>2b71_A Cyclophilin-like protein; structural genomics, structural genomics consortium, SGC, isomerase; 2.50A {Plasmodium yoelii} SCOP: b.62.1.1

Probab=100.00  E-value=5.5e-46  Score=350.29  Aligned_cols=157  Identities=39%  Similarity=0.685  Sum_probs=148.1

Q ss_pred             CEEEEEecceeEEEEecCCCChhHHHHHHHHHhcCccCCceEEEeecCcccccCCCCCCCCCCCCcccccccccccccCC
Q 007792            1 MSVLIVTSLGDIVVDLFVDKCPLTTKNFLKLCKIKYYNGCLFHTVQKDFTAQTGDPTGTGTGGDSVYKFLYGEQARFFGD   80 (589)
Q Consensus         1 ~~v~~~T~~G~i~ieL~~~~aP~~~~nF~~l~~~~~Y~g~~f~rv~~~~~iq~Gd~~~~~~~~~~~~~~~~~~~~~~~~~   80 (589)
                      |.|+|+|++|+|+|+||++.||+||+||++||+.+||+|+.||||+|+||||||++.+++.++.++|+       ..|++
T Consensus        39 ~~V~l~T~~G~I~ieL~~~~aP~tv~NF~~L~~~g~Y~g~~FhRVi~~f~iQgGd~~~~g~gg~si~g-------~~~~d  111 (196)
T 2b71_A           39 GYITIYTNLGDFEVELYWYHSPKTCLNFYTLCEMGFYDNTIFHRVIPNFVIQGGDPTGTGKGGKSIYG-------EYFED  111 (196)
T ss_dssp             CEEEEEETTEEEEEEECTTTSHHHHHHHHHHHHTTTTTTEEEEEEETTTEEEEEETTSSSSCCCBTTB-------SCBCC
T ss_pred             cEEEEEeCCCCEEEEEeCCCCcHHHHHHHHHhhcCCcCCCEEEEEeCCcEEEcCCCCCCCCCCCccCC-------Ccccc
Confidence            68999999999999999999999999999999999999999999999999999999999999999987       67899


Q ss_pred             ccccCCCCCCCceEEEeccCCCCCcceEEEEeCCCCCCCCCCcceEEEEecCHHHHHHHhhCccCCCCCcccceeecccc
Q 007792           81 EIRVDLKHAKTGTVAMASAGENLNASQFYMTLRDNLDYLDEKHTIFGEVAEGLETLSRINESFVDEKNRPYKNIRIKHTY  160 (589)
Q Consensus        81 e~~~~l~~~~~G~vs~a~~g~~~~~sqFfI~l~~~~~~ld~~~~vFG~Vv~G~~vl~~i~~~~~~~~~~p~~~i~I~~~~  160 (589)
                      |+.+.|+|+.+|+||||+.++++++||||||+.+ +||||++|+|||+|++||+||++|+.++++.+++|..+|+|.+|.
T Consensus       112 E~~~~l~h~~~G~lsMAn~gpns~gSQFFIt~~~-~~~LDg~~tVFG~Vv~Gmdvv~~I~~~~t~~~~~P~~~i~I~~~~  190 (196)
T 2b71_A          112 EINKELKHTGAGILSMSNNGPNTNSSQFFITLAP-LPHLDGKHTIFARVSKNMTCIENIASVQTTATNKPIFDLKILRTS  190 (196)
T ss_dssp             CCCTTCCCCSTTEEEECCSSTTCBSSCEEEESSC-CGGGTTTSCEEEEEEECHHHHHHHHTSCBCTTCCBSSCCEEEEEE
T ss_pred             cccCCcCcCCCeEEEEccCCCCCcccEEEEECCC-CCccCCCEeEEEEEecCHHHHHHHHhCCcCCCCCCCCCeEEEEEE
Confidence            9888999999999999999999999999999998 699999999999999999999999999999999999999999999


Q ss_pred             cccCC
Q 007792          161 ILEDP  165 (589)
Q Consensus       161 vl~~p  165 (589)
                      |+.+|
T Consensus       191 i~~dP  195 (196)
T 2b71_A          191 TAVNA  195 (196)
T ss_dssp             C----
T ss_pred             EecCC
Confidence            99876

>2fu0_A Cyclophilin, putative; PFE0505W, cyclosporin-binding domain, structura genomics, structural genomics consortium, SGC, unknown FUNC; 1.80A {Plasmodium falciparum} SCOP: b.62.1.1

Probab=100.00  E-value=8.8e-46  Score=339.58  Aligned_cols=154  Identities=41%  Similarity=0.688  Sum_probs=147.7

Q ss_pred             CEEEEEecceeEEEEecCCCChhHHHHHHHHHhcCccCCceEEEeecCcccccCCCCCCCCCCCCcccccccccccccCC
Q 007792            1 MSVLIVTSLGDIVVDLFVDKCPLTTKNFLKLCKIKYYNGCLFHTVQKDFTAQTGDPTGTGTGGDSVYKFLYGEQARFFGD   80 (589)
Q Consensus         1 ~~v~~~T~~G~i~ieL~~~~aP~~~~nF~~l~~~~~Y~g~~f~rv~~~~~iq~Gd~~~~~~~~~~~~~~~~~~~~~~~~~   80 (589)
                      +.|+|+|++|+|+|+||++.||+||+||++||+.+||+|+.||||+|+||||||++.+++++++++|+       ..|++
T Consensus         6 ~~v~~~T~~G~i~ieL~~~~aP~t~~NF~~L~~~g~Y~g~~fhRvi~~f~iQgGd~~~~g~gg~si~g-------~~~~d   78 (160)
T 2fu0_A            6 KSAIIYTTMGDIHISLFYKECKKTVQNFSVHSINGYYNNCIFHRVIKHFMVQTGDPSGDGTGGESIWG-------NEFED   78 (160)
T ss_dssp             CEEEEEETTEEEEEEECTTTCHHHHHHHHHHHHTTTTTTCBCCEEETTTEEEECCTTSSSSCCCCTTS-------SCBCC
T ss_pred             CEEEEEecCccEEEEEeCCCChHHHHHHHHHhccCccCCCEEEEEECCCEEEeCCcCCCCCCCCcccC-------CCccc
Confidence            57999999999999999999999999999999999999999999999999999999999999999987       67899


Q ss_pred             ccccCCCCCCCceEEEeccCCCCCcceEEEEeCCCCCCCCCCcceEEEEecCHHHHHHHhhCccCCCCCcccceeecccc
Q 007792           81 EIRVDLKHAKTGTVAMASAGENLNASQFYMTLRDNLDYLDEKHTIFGEVAEGLETLSRINESFVDEKNRPYKNIRIKHTY  160 (589)
Q Consensus        81 e~~~~l~~~~~G~vs~a~~g~~~~~sqFfI~l~~~~~~ld~~~~vFG~Vv~G~~vl~~i~~~~~~~~~~p~~~i~I~~~~  160 (589)
                      |+.+.|+|+.+|+||||+.++++++|||||++.+ +||||++|+|||+|++||+||++|+.++++.+++|.++|+|.+|.
T Consensus        79 E~~~~l~h~~~G~lsmA~~gp~s~~SQFfI~~~~-~~~Ldg~~tvFG~Vv~G~dvv~~I~~~~t~~~~~P~~~v~I~~~~  157 (160)
T 2fu0_A           79 EFFDHLNHSKPFMVSMANCGPNTNGSQFFITTVP-CPWLDFKHTVFGKVTQGSKIVLDIEKVRTDKRDKPLEDIKILNIK  157 (160)
T ss_dssp             CCBTTBCSSSSSEEEECCSSTTCBCSCEEEESSC-CGGGTTTSCEEEEEEECHHHHHHHHTSCBCTTSCBSSCCBEEEEE
T ss_pred             cccCCcccCCceEEEEecCCCCCcccEEEEECCC-CCccCCCcEEEEEEEcCHHHHHHHHhCCcCCCCCcCCCeEEEEEE
Confidence            9877899999999999999999999999999998 699999999999999999999999999999899999999999998


Q ss_pred             cc
Q 007792          161 IL  162 (589)
Q Consensus       161 vl  162 (589)
                      ++
T Consensus       158 v~  159 (160)
T 2fu0_A          158 IN  159 (160)
T ss_dssp             EC
T ss_pred             Ee
Confidence            75

>2x7k_A Peptidyl-prolyl CIS-trans isomerase-like 1; isomerase-immunosuppressant complex, immunosuppressant; HET: MLE MVA BMT ABA SAR; 1.15A {Homo sapiens} PDB: 1xwn_A

Probab=100.00  E-value=1.3e-45  Score=340.56  Aligned_cols=154  Identities=44%  Similarity=0.751  Sum_probs=148.1

Q ss_pred             CEEEEEecceeEEEEecCCCChhHHHHHHHHHhcCccCCceEEEeecCcccccCCCCCCCCCCCCcccccccccccccCC
Q 007792            1 MSVLIVTSLGDIVVDLFVDKCPLTTKNFLKLCKIKYYNGCLFHTVQKDFTAQTGDPTGTGTGGDSVYKFLYGEQARFFGD   80 (589)
Q Consensus         1 ~~v~~~T~~G~i~ieL~~~~aP~~~~nF~~l~~~~~Y~g~~f~rv~~~~~iq~Gd~~~~~~~~~~~~~~~~~~~~~~~~~   80 (589)
                      |.|+|+|++|+|+|+||++.||+||+||++||+.+||+|+.||||+|+||||||++.+++.++.++|+       ..|++
T Consensus        12 ~~v~l~t~~G~i~ieL~~~~aP~t~~NF~~L~~~g~Y~g~~fhRvi~~f~iQgGd~~~~g~gg~si~g-------~~~~d   84 (166)
T 2x7k_A           12 PNVYLETSMGIIVLELYWKHAPKTCKNFAELARRGYYNGTKFHRIIKDFMIQGGDPTGTGRGGASIYG-------KQFED   84 (166)
T ss_dssp             SEEEEEETTEEEEEEECTTTCHHHHHHHHHHHHHTTTTTEECCEEETTTEEEECCTTSSSSCCCCTTS-------SCBCC
T ss_pred             CEEEEEeCCCcEEEEEccCCCCHHHHHHHHHHhcCCCCCCEEEEEECCCEEEcCCCCCCCCCCCccCC-------Ccccc
Confidence            68999999999999999999999999999999999999999999999999999999999999999987       67899


Q ss_pred             ccccCCCCCCCceEEEeccCCCCCcceEEEEeCCCCCCCCCCcceEEEEecCHHHHHHHhhCccCCCCCcccceeecccc
Q 007792           81 EIRVDLKHAKTGTVAMASAGENLNASQFYMTLRDNLDYLDEKHTIFGEVAEGLETLSRINESFVDEKNRPYKNIRIKHTY  160 (589)
Q Consensus        81 e~~~~l~~~~~G~vs~a~~g~~~~~sqFfI~l~~~~~~ld~~~~vFG~Vv~G~~vl~~i~~~~~~~~~~p~~~i~I~~~~  160 (589)
                      |+.+.|+|..+|+||||+.++++++|||||++.+ +||||++|+|||+|++||+||++|+.++++..++|.++|+|.+|.
T Consensus        85 E~~~~l~h~~~G~lsmAn~gp~s~gSQFfI~~~~-~~~Ldg~~tvFG~Vv~G~dvv~~I~~~~t~~~~~P~~~i~I~~~~  163 (166)
T 2x7k_A           85 ELHPDLKFTGAGILAMANAGPDTNGSQFFVTLAP-TQWLDGKHTIFGRVCQGIGMVNRVGMVETNSQDRPVDDVKIIKAY  163 (166)
T ss_dssp             CCCTTSCCCSTTEEEECBSSTTCBCSCEEEESSC-CGGGTTTSCEEEEEEECHHHHHHHTTSCBCTTSCBSSCCEEEEEE
T ss_pred             ccccccCCCCCeEEEEeeCCCCCccceEEEECCC-CCccCCCeeEEEEEEcCHHHHHHHHcCCcCCCCCcCCCeEEEEEE
Confidence            9878999988999999999999999999999998 699999999999999999999999999999889999999999998


Q ss_pred             cc
Q 007792          161 IL  162 (589)
Q Consensus       161 vl  162 (589)
                      |+
T Consensus       164 i~  165 (166)
T 2x7k_A          164 PS  165 (166)
T ss_dssp             EC
T ss_pred             Ee
Confidence            85

>2k7n_A Peptidyl-prolyl CIS-trans isomerase-like 1; beta barrel, disorder-order transition, HOOK-like, mRNA processing, mRNA splicing, rotamase; NMR {Homo sapiens}

Probab=100.00  E-value=3.9e-45  Score=345.47  Aligned_cols=163  Identities=41%  Similarity=0.694  Sum_probs=154.7

Q ss_pred             CEEEEEecceeEEEEecCCCChhHHHHHHHHHhcCccCCceEEEeecCcccccCCCCCCCCCCCCcccccccccccccCC
Q 007792            1 MSVLIVTSLGDIVVDLFVDKCPLTTKNFLKLCKIKYYNGCLFHTVQKDFTAQTGDPTGTGTGGDSVYKFLYGEQARFFGD   80 (589)
Q Consensus         1 ~~v~~~T~~G~i~ieL~~~~aP~~~~nF~~l~~~~~Y~g~~f~rv~~~~~iq~Gd~~~~~~~~~~~~~~~~~~~~~~~~~   80 (589)
                      |.|+|+|++|+|+|+||++.||+||+||++||+.+||+|+.||||+|+||||||++.+++.++.++|+       ..|++
T Consensus        12 ~~V~l~T~~G~I~ieL~~d~aP~tv~NF~~L~~~g~Ydg~~FhRVi~~F~iQgGd~~~~g~gg~si~g-------~~f~d   84 (203)
T 2k7n_A           12 PNVYLETSMGIIVLELYWKHAPKTCKNFAELARRGYYNGTKFHRIIKDFMIQGGDPTGTGRGGASIYG-------KQFED   84 (203)
T ss_dssp             SEEEEEESSCEEEEEECTTTCTTHHHHHHHHHHHTCGGGCEEEEEETTTEEEEECSSSSSSCCCTTSC-------SCBCC
T ss_pred             CEEEEEeCCCcEEEEEccCCCcHHHHHHHHHHhcCccCCCEEEEEeCCcEEEcCCCCCCCCCCCccCC-------Ccccc
Confidence            68999999999999999999999999999999999999999999999999999999999999999887       67899


Q ss_pred             ccccCCCCCCCceEEEeccCCCCCcceEEEEeCCCCCCCCCCcceEEEEecCHHHHHHHhhCccCCCCCcccceeecccc
Q 007792           81 EIRVDLKHAKTGTVAMASAGENLNASQFYMTLRDNLDYLDEKHTIFGEVAEGLETLSRINESFVDEKNRPYKNIRIKHTY  160 (589)
Q Consensus        81 e~~~~l~~~~~G~vs~a~~g~~~~~sqFfI~l~~~~~~ld~~~~vFG~Vv~G~~vl~~i~~~~~~~~~~p~~~i~I~~~~  160 (589)
                      |+.+.|+|..+|+||||+.++++++|||||+|.+ +||||++|+|||+|++||+||++|+.++++..++|.++|+|.+|.
T Consensus        85 E~~~~l~h~~~G~lsMAn~gpnsngSQFFIt~~~-~~~LDg~~tVFG~VveGmdvv~kI~~~~t~~~~~P~~~V~I~~~~  163 (203)
T 2k7n_A           85 ELHPDLKFTGAGILAMANAGPDTNGSQFFVTLAP-TQWLDGKHTIFGRVCQGIGMVNRVGMVETNSQDRPVDDVKIIKAY  163 (203)
T ss_dssp             CCCCSSCCCSSCEEEEEESSTTCEEEEEEEESSC-CCSSTTTSCEEEEEESCHHHHHHHHSCCEEETTEECCCCBEEEEE
T ss_pred             cccccccCCCCeEEEEeeCCCCCcccEEEEEcCC-CCccCCCeeEEEEEEcCHHHHHHHHcCCcCCCCCcCCCeEEEEEE
Confidence            9878999988999999999999999999999998 699999999999999999999999999999889999999999999


Q ss_pred             cccCCCCChhh
Q 007792          161 ILEDPFDDPAQ  171 (589)
Q Consensus       161 vl~~p~~~~~~  171 (589)
                      ++..+..+...
T Consensus       164 v~~~~~s~~g~  174 (203)
T 2k7n_A          164 PSGGGGSGGGS  174 (203)
T ss_dssp             ECCCCCCCCCT
T ss_pred             EEecCCCCCCC
Confidence            99887766554

>2a2n_A Peptidylprolyl isomerase domain and WD repeat CON; CIS-trans isomerization, protein-folding, peptidylprolyl ISO structural genomics; 1.65A {Homo sapiens} SCOP: b.62.1.1

Probab=100.00  E-value=1.4e-44  Score=336.20  Aligned_cols=153  Identities=43%  Similarity=0.754  Sum_probs=146.0

Q ss_pred             CEEEEEecceeEEEEecCCCChhHHHHHHHHHhcCccCCceEEEeecCcccccCCCCCCCCCCCCcccccccccccccCC
Q 007792            1 MSVLIVTSLGDIVVDLFVDKCPLTTKNFLKLCKIKYYNGCLFHTVQKDFTAQTGDPTGTGTGGDSVYKFLYGEQARFFGD   80 (589)
Q Consensus         1 ~~v~~~T~~G~i~ieL~~~~aP~~~~nF~~l~~~~~Y~g~~f~rv~~~~~iq~Gd~~~~~~~~~~~~~~~~~~~~~~~~~   80 (589)
                      +.|+|+|++|+|+|+||++.||+||+||++||+.+||+|+.||||+|+||||||++.++++++.++|+       ..|++
T Consensus        22 ~~v~~~t~~G~i~ieL~~~~aP~t~~NF~~L~~~g~Y~g~~FhRvi~~f~iQgGd~~~~g~gg~si~g-------~~~~d   94 (176)
T 2a2n_A           22 DSAIIHTSMGDIHTKLFPVECPKTVENFCVHSRNGYYNGHTFHRIIKGFMIQTGDPTGTGMGGESIWG-------GEFED   94 (176)
T ss_dssp             SEEEEEETTEEEEEEECTTTCHHHHHHHHHHHHTTTTTTCBCCEEETTTEEEECCTTSSSSCCCCTTS-------SCBCC
T ss_pred             CEEEEEecCccEEEEEeCCCChHHHHHHHHHhhcCccCCCEEEEEECCcEEEccCCCCCCCCCCcccC-------Ccccc
Confidence            47999999999999999999999999999999999999999999999999999999999999999987       67899


Q ss_pred             ccccCCCCCCCceEEEeccCCCCCcceEEEEeCCCCCCCCCCcceEEEEecCHHHHHHHhhCccC-CCCCcccceeeccc
Q 007792           81 EIRVDLKHAKTGTVAMASAGENLNASQFYMTLRDNLDYLDEKHTIFGEVAEGLETLSRINESFVD-EKNRPYKNIRIKHT  159 (589)
Q Consensus        81 e~~~~l~~~~~G~vs~a~~g~~~~~sqFfI~l~~~~~~ld~~~~vFG~Vv~G~~vl~~i~~~~~~-~~~~p~~~i~I~~~  159 (589)
                      |+.+.|+|+.+|+||||+.++++++|||||++.+ +||||++|+|||+|++||+||++|+.++++ .+++|..+|+|.+|
T Consensus        95 E~~~~l~h~~~G~lsmA~~gp~s~gSQFFIt~~~-~~~LDg~~tVFG~Vv~Gmdvv~~I~~~~t~~~~~~P~~~v~I~~v  173 (176)
T 2a2n_A           95 EFHSTLRHDRPYTLSMANAGSNTNGSQFFITVVP-TPWLDNKHTVFGRVTKGMEVVQRISNVKVNPKTDKPYEDVSIINI  173 (176)
T ss_dssp             CCCTTCCSCSSSEEEECCSSTTCBCSCEEEESSC-CGGGTTTSCEEEEEEECHHHHHHHHTSCBCTTTCCBSSCCBEEEE
T ss_pred             ccccccccCCceEEEEEeCCCCCcccEEEEECCC-CCccCCCeeEEEEEeCCHHHHHHHHcCCccCCCCccCCCeEEEEE
Confidence            9877899999999999999999999999999998 699999999999999999999999999998 68999999999998


Q ss_pred             cc
Q 007792          160 YI  161 (589)
Q Consensus       160 ~v  161 (589)
                      .|
T Consensus       174 ~v  175 (176)
T 2a2n_A          174 TV  175 (176)
T ss_dssp             EE
T ss_pred             EE
Confidence            76

>3bkp_A Cyclophilin; malaria, isomerase, structural GENO structural genomics consortium, SGC; 1.80A {Toxoplasma gondii}

Probab=100.00  E-value=9.6e-45  Score=350.77  Aligned_cols=164  Identities=39%  Similarity=0.653  Sum_probs=150.3

Q ss_pred             CEEEEEecceeEEEEecCCCChhHHHHHHHHHhcCccCCceEEEeecCcccccCCCCCCCCCCCCcccccccccccccCC
Q 007792            1 MSVLIVTSLGDIVVDLFVDKCPLTTKNFLKLCKIKYYNGCLFHTVQKDFTAQTGDPTGTGTGGDSVYKFLYGEQARFFGD   80 (589)
Q Consensus         1 ~~v~~~T~~G~i~ieL~~~~aP~~~~nF~~l~~~~~Y~g~~f~rv~~~~~iq~Gd~~~~~~~~~~~~~~~~~~~~~~~~~   80 (589)
                      +.|+|+|++|+|+|+||++.||+||+||++||+.+||+|+.||||+++||||||+++++++++.++|.     .+..|++
T Consensus        22 ~~V~l~T~~G~I~ieL~~d~aP~tv~NF~~L~~~g~Ydgt~FhRVi~~FmiQgGdp~~~G~Gg~si~~-----~g~~f~d   96 (232)
T 3bkp_A           22 GKVVLHTSLGDLDVELWARECPLACRNFVQLCLEGYYVNTIFHRVVKDFIVQGGDPTGTGRGGADTTF-----DGKPFDV   96 (232)
T ss_dssp             CEEEEEETTEEEEEEEBTTTCHHHHHHHHHHHHHTTTTTCBEEEEETTTEEEECCTTSSSSCCCCCTT-----TTCCBCC
T ss_pred             CEEEEEECCCcEEEEEcCCCCcHHHHHHHHHhhcCccCCCEEEEEeCCCEEEcCCCCCCCCCCCcccc-----CCCccCC
Confidence            46999999999999999999999999999999999999999999999999999999999999999882     1267899


Q ss_pred             ccccCCCCCCCceEEEeccCC--------------CCCcceEEEEeCCCCCCCCCCcceEEEEecCHH--HHHHHhhCcc
Q 007792           81 EIRVDLKHAKTGTVAMASAGE--------------NLNASQFYMTLRDNLDYLDEKHTIFGEVAEGLE--TLSRINESFV  144 (589)
Q Consensus        81 e~~~~l~~~~~G~vs~a~~g~--------------~~~~sqFfI~l~~~~~~ld~~~~vFG~Vv~G~~--vl~~i~~~~~  144 (589)
                      |+.+.|+|+.+|+||||+.++              ++++|||||||.+ +||||++|+|||+|+ ||+  +|++|+.+++
T Consensus        97 E~~~~l~h~~~G~lsMA~~g~~~~~~~n~e~g~~~~sngSQFFIt~~~-~p~LDg~~tVFG~Vv-g~~v~~v~kI~~~~t  174 (232)
T 3bkp_A           97 ETHPRLKFRYRGLVGVANLGRSSKDAENDERGRSLGTNGNQFFITLAR-ADVLNNAYTLFGKVT-GHTLYNLMKFNDLEV  174 (232)
T ss_dssp             CCCTTCCCCSTTEEEECCCC----------------CBCSCEEEESSC-CGGGTTTSCEEEEEC-GGGHHHHHHHTTSCB
T ss_pred             ccccCcCcCCCeEEEEeccCCcccccccccccccCCCcCCEEEEECCC-CcccCCCccEEEEEE-eCchHHHHHHHcCCc
Confidence            987889999999999999987              5999999999998 699999999999999 664  4899999999


Q ss_pred             CCCCCcccceeecccccccCCCCChhh
Q 007792          145 DEKNRPYKNIRIKHTYILEDPFDDPAQ  171 (589)
Q Consensus       145 ~~~~~p~~~i~I~~~~vl~~p~~~~~~  171 (589)
                      +.+++|+.+|+|.+|+++.+||++...
T Consensus       175 ~~~~~P~~~i~I~~~~vl~dPf~d~~~  201 (232)
T 3bkp_A          175 GKEDRPMTPPFIKSVDVLWNPFEDLVP  201 (232)
T ss_dssp             CGGGCBSSCCBEEEEEEEECCCTTCCC
T ss_pred             CCCCCcCCCeEEEEEEEEcCChhhhhh
Confidence            999999999999999999999987664

>2hq6_A Serologically defined colon cancer antigen 10; protein folding, peptidyl-prolyl CIS-trans isomerase, struct genomics; 1.75A {Homo sapiens}

Probab=100.00  E-value=2.9e-44  Score=336.28  Aligned_cols=158  Identities=44%  Similarity=0.762  Sum_probs=148.9

Q ss_pred             EEEEEecceeEEEEecCCCChhHHHHHHHHHhcCccCCceEEEeecCcccccCCCCCCCCCCCCcccccccccccccCCc
Q 007792            2 SVLIVTSLGDIVVDLFVDKCPLTTKNFLKLCKIKYYNGCLFHTVQKDFTAQTGDPTGTGTGGDSVYKFLYGEQARFFGDE   81 (589)
Q Consensus         2 ~v~~~T~~G~i~ieL~~~~aP~~~~nF~~l~~~~~Y~g~~f~rv~~~~~iq~Gd~~~~~~~~~~~~~~~~~~~~~~~~~e   81 (589)
                      .|+|+|++|+|+|+||++.||+||+||++||+.+||+|+.||||+|+||||||++.+++.++.++|+       ..|++|
T Consensus        26 ~V~l~T~~G~I~ieL~~~~aP~tv~NF~~L~~~g~Y~g~~FhRvi~~f~iQgGd~~~~g~gg~si~g-------~~~~dE   98 (185)
T 2hq6_A           26 KVLLKTTAGDIDIELWSKEAPKACRNFIQLCLEAYYDNTIFHRVVPGFIVQGGDPTGTGSGGESIYG-------APFKDE   98 (185)
T ss_dssp             EEEEEETTEEEEEEEBTTTCHHHHHHHHHHHHTTTTTTEECCEEETTTEEEECCTTSSSSCCCCTTS-------SCBCCC
T ss_pred             EEEEEeCCccEEEEEeCCCCcHHHHHHHHHhhcCccCCCEEEEEECCCEEEcCCCCCCCCCCCcccC-------Cccccc
Confidence            6999999999999999999999999999999999999999999999999999999999999999987       578999


Q ss_pred             cccCCCCCCCceEEEeccCCCCCcceEEEEeCCCCCCCCCCcceEEEEecCHHH--HHHHhhCccCCCCCcccceeeccc
Q 007792           82 IRVDLKHAKTGTVAMASAGENLNASQFYMTLRDNLDYLDEKHTIFGEVAEGLET--LSRINESFVDEKNRPYKNIRIKHT  159 (589)
Q Consensus        82 ~~~~l~~~~~G~vs~a~~g~~~~~sqFfI~l~~~~~~ld~~~~vFG~Vv~G~~v--l~~i~~~~~~~~~~p~~~i~I~~~  159 (589)
                      +.+.|+|+.+|+||||+.++++++|||||++.+ +|+||++|+|||+|+ ||+|  +++|+.++++.+++|..+|+|.+|
T Consensus        99 ~~~~l~h~~~G~lsMA~~g~~s~gSQFFIt~~~-~~~LDg~~tVFG~V~-G~~v~~~~~i~~~~~~~~~~P~~~v~I~~~  176 (185)
T 2hq6_A           99 FHSRLRFNRRGLVAMANAGSHDNGSQFFFTLGR-ADELNNKHTIFGKVT-GDTVYNMLRLSEVDIDDDERPHNPHKIKSC  176 (185)
T ss_dssp             CBTTBCSCSSSEEEECCSSTTCBCSCEEEESSC-CGGGTTTSCEEEEEC-GGGHHHHHHTTCSCBCTTSCBSSCCEEEEE
T ss_pred             cccCcccCCCeEEEEccCCCCCccceEEEECCC-CCccCCCceEEEEEE-eCeeehhhHHhhCCcCCCCCCCCCeEEEEE
Confidence            877899999999999999999999999999998 699999999999999 7766  478999999999999999999999


Q ss_pred             ccccCCCCC
Q 007792          160 YILEDPFDD  168 (589)
Q Consensus       160 ~vl~~p~~~  168 (589)
                      +++.+||++
T Consensus       177 ~v~~~Pf~d  185 (185)
T 2hq6_A          177 EVLFNPFDD  185 (185)
T ss_dssp             EEEECTTC-
T ss_pred             EEeCCCCCC
Confidence            999999975

>1w74_A Peptidyl-prolyl CIS-trans isomerase A; cyclophilin, ppiase, RV0009, rotamase, structural proteomics in europe, spine; 2.6A {Mycobacterium tuberculosis} SCOP: b.62.1.1

Probab=100.00  E-value=1.1e-43  Score=333.61  Aligned_cols=151  Identities=37%  Similarity=0.607  Sum_probs=141.3

Q ss_pred             CEEEEEecceeEEEEecCCCChhHHHHHHHHH---------------hcCccCCceEEEeecCcccccCCCCCCCCCCCC
Q 007792            1 MSVLIVTSLGDIVVDLFVDKCPLTTKNFLKLC---------------KIKYYNGCLFHTVQKDFTAQTGDPTGTGTGGDS   65 (589)
Q Consensus         1 ~~v~~~T~~G~i~ieL~~~~aP~~~~nF~~l~---------------~~~~Y~g~~f~rv~~~~~iq~Gd~~~~~~~~~~   65 (589)
                      +.|+|+|++|+|+|+||++.||+||+||++||               +.+||+|+.||||+|+|||||||+.+++++++ 
T Consensus        24 ~~v~l~t~~G~I~ieL~~~~aP~tv~NF~~L~tG~~~~~~~~~g~~~~~~~Y~g~~FhRVi~~fmiQgGd~~g~G~gg~-  102 (191)
T 1w74_A           24 ATATLHTNRGDIKIALFGNHAPKTVANFVGLAQGTKDYSTQNASGGPSGPFYDGAVFHRVIQGFMIQGGDPTGTGRGGP-  102 (191)
T ss_dssp             EEEEEEETTEEEEEEECTTTSHHHHHHHHHHHHTCSCCSSCCTTBSSSSCSSTTEEEEEEETTTEEEECCTTSSSSCCS-
T ss_pred             eEEEEEecceeEEEEEcCCCChHHHHHHHHHhcCCcccccccccccccCCccCCCEEEEEeCCCEEecCCCCCCCCCCC-
Confidence            47999999999999999999999999999999               45799999999999999999999988777663 


Q ss_pred             cccccccccccccCCccccCCCCCCCceEEEeccCCCCCcceEEEEeCCCCCCCCCCcceEEEEec--CHHHHHHHhhCc
Q 007792           66 VYKFLYGEQARFFGDEIRVDLKHAKTGTVAMASAGENLNASQFYMTLRDNLDYLDEKHTIFGEVAE--GLETLSRINESF  143 (589)
Q Consensus        66 ~~~~~~~~~~~~~~~e~~~~l~~~~~G~vs~a~~g~~~~~sqFfI~l~~~~~~ld~~~~vFG~Vv~--G~~vl~~i~~~~  143 (589)
                        +       ..|++|+.+.|+|+.+|+||||+.++++|+||||||+.+ +||||++|+|||+|++  ||+||++|+.++
T Consensus       103 --g-------~~f~dE~~~~l~h~~~G~lsMAn~gpntngSQFFIt~~~-~~~LDg~~tVFG~Vv~~~Gmdvv~~I~~~~  172 (191)
T 1w74_A          103 --G-------YKFADEFHPELQFDKPYLLAMANAGPGTNGSQFFITVGK-TPHLNRRHTIFGEVIDAESQRVVEAISKTA  172 (191)
T ss_dssp             --S-------CCBCCCCCTTCCSCSSSEEEECCSSTTCBSSCEEEESSC-CGGGTTTSCEEEEECSHHHHHHHHHHHTSC
T ss_pred             --C-------CccccccccCCCcCCCcEEEEeeCCCCCccceEEEEcCC-CcccCCCeeEEEEEEECCCHHHHHHHHcCC
Confidence              2       568999888999999999999999999999999999998 6999999999999999  999999999999


Q ss_pred             cCCCCCcccceeecccccc
Q 007792          144 VDEKNRPYKNIRIKHTYIL  162 (589)
Q Consensus       144 ~~~~~~p~~~i~I~~~~vl  162 (589)
                      ++..++|..+|+|.+|+|+
T Consensus       173 t~~~~~P~~~v~I~~~~i~  191 (191)
T 1w74_A          173 TDGNDRPTDPVVIESITIS  191 (191)
T ss_dssp             BCTTSCBSSCCEEEEEEEC
T ss_pred             cCCCCCcCCCeEEEEEEEC
Confidence            9999999999999999874

>3ich_A Peptidyl-prolyl CIS-trans isomerase B; beta sandwich, cyclosporin, endoplasmic reticulum, glycoprot isomerase, rotamase; 1.20A {Homo sapiens} PDB: 3ici_A* 1cyn_A* 2esl_A* 2rmc_A* 1h0p_A 1xo7_A 1xq7_A*

Probab=100.00  E-value=6.4e-44  Score=335.24  Aligned_cols=155  Identities=38%  Similarity=0.677  Sum_probs=145.2

Q ss_pred             ecceeEEEEecCCCChhHHHHHHHHHh--cCc-cCCceEEEeecCcccccCC-CCCCCCCCCCcccccccccccccCCcc
Q 007792            7 TSLGDIVVDLFVDKCPLTTKNFLKLCK--IKY-YNGCLFHTVQKDFTAQTGD-PTGTGTGGDSVYKFLYGEQARFFGDEI   82 (589)
Q Consensus         7 T~~G~i~ieL~~~~aP~~~~nF~~l~~--~~~-Y~g~~f~rv~~~~~iq~Gd-~~~~~~~~~~~~~~~~~~~~~~~~~e~   82 (589)
                      |++|+|+|+||++.||+||+||++||+  .+| |+|+.||||+++||||||+ +.++++++.+||+       ..|++| 
T Consensus        27 t~~G~i~ieL~~~~aP~t~~NF~~L~~g~~g~~Y~g~~FhRvi~~f~iQgGd~~~~~g~gg~si~g-------~~f~dE-   98 (188)
T 3ich_A           27 EDVGRVIFGLFGKTVPKTVDNFVALATGEKGFGYKNSKFHRVIKDFMIQGGDFTRGDGTGGKSIYG-------ERFPDE-   98 (188)
T ss_dssp             EEEEEEEEEECTTTCHHHHHHHHHHHHTTTSCSSTTCBCCEEETTTEEEECCTTTSSSSCCCBTTB-------SCBCCC-
T ss_pred             EeceeEEEEEcCCCCcHHHHHHHHHhcccCCccccCCEEEEEECCCEEEcCCccCCCCCCCccccC-------Cccccc-
Confidence            899999999999999999999999995  678 9999999999999999999 5688899999987       578899 


Q ss_pred             ccCCCCCCCceEEEeccCCCCCcceEEEEeCCCCCCCCCCcceEEEEecCHHHHHHHhhCccCCCCCcccceeecccccc
Q 007792           83 RVDLKHAKTGTVAMASAGENLNASQFYMTLRDNLDYLDEKHTIFGEVAEGLETLSRINESFVDEKNRPYKNIRIKHTYIL  162 (589)
Q Consensus        83 ~~~l~~~~~G~vs~a~~g~~~~~sqFfI~l~~~~~~ld~~~~vFG~Vv~G~~vl~~i~~~~~~~~~~p~~~i~I~~~~vl  162 (589)
                      .+.|+|+.+|+||||+.++++|+||||||+.+ +||||++|+|||+|++||+||++|+.++++..++|..+|+|.+|+++
T Consensus        99 ~~~l~h~~~G~lsmAn~gp~tngSQFfIt~~~-~~~LDg~~tVFG~Vv~G~dvv~~I~~~~~~~~~~P~~~v~I~~~~~l  177 (188)
T 3ich_A           99 NFKLKHYGPGWVSMANAGKDTNGSQFFITTVK-TAWLDGKHVVFGKVLEGMEVVRKVESTKTDSRDKPLKDVIIADCGKI  177 (188)
T ss_dssp             CCCSCCCSTTEEEECCSSTTCBCSCEEEESSC-CGGGTTTSCEEEEEEECHHHHHHHHTSCBCTTSCBSSCEEEEEEEEE
T ss_pred             ccCcccCCCeEEEEccCCCCCcccEEEEECCC-CcccCCCeeEEEEEeCCHHHHHHHHhCCcCCCCeECCCEEEEEeEEE
Confidence            68899999999999999999999999999998 69999999999999999999999999999988999999999999988


Q ss_pred             --cCCCCChh
Q 007792          163 --EDPFDDPA  170 (589)
Q Consensus       163 --~~p~~~~~  170 (589)
                        ++||+++.
T Consensus       178 ~~~~Pf~~~~  187 (188)
T 3ich_A          178 EVEKPFAIAK  187 (188)
T ss_dssp             EEEEEEECCC
T ss_pred             ecCCCCCCCC
Confidence              67887654

>2wfi_A Peptidyl-prolyl CIS-trans isomerase G; phosphoprotein, PRE-mRNA splicing, alternative splicing, nucleus, rotamase, cyclosporin; HET: OCS; 0.75A {Homo sapiens} PDB: 2wfj_A* 2gw2_A

Probab=100.00  E-value=5.7e-43  Score=326.88  Aligned_cols=148  Identities=40%  Similarity=0.697  Sum_probs=139.2

Q ss_pred             EecceeEEEEecCCCChhHHHHHHHHHh-----------cCccCCceEEEeecCcccccCCCC-CCCCCCCCcccccccc
Q 007792            6 VTSLGDIVVDLFVDKCPLTTKNFLKLCK-----------IKYYNGCLFHTVQKDFTAQTGDPT-GTGTGGDSVYKFLYGE   73 (589)
Q Consensus         6 ~T~~G~i~ieL~~~~aP~~~~nF~~l~~-----------~~~Y~g~~f~rv~~~~~iq~Gd~~-~~~~~~~~~~~~~~~~   73 (589)
                      .|++|+|+|+||++.||+||+||++||+           .+||+|+.||||+|+|||||||++ ++++++.++|+     
T Consensus        20 ~t~~G~i~ieL~~~~aP~t~~NF~~L~~g~~g~~~~~~~~~~Y~g~~FhRvi~~f~iQgGd~~~~~g~gg~si~g-----   94 (179)
T 2wfi_A           20 NQPAGRVVFELFSDVCPKTCENFRCLCTGEKGTGKSTQKPLHYKSCLFHRVVKDFMVQGGDFSEGNGRGGESIYG-----   94 (179)
T ss_dssp             TEEEEEEEEEECTTTCHHHHHHHHHHHHCTTCBCTTTCSBSCCTTCBEEEEETTTEEEECCTTTSSSSCCCCTTS-----
T ss_pred             CccceEEEEEEcCCCCChHHHHHHHHhcCCcCcccccccCCeECCCEEEEEECCCEEEcccccCCCCCCCCcccC-----
Confidence            3899999999999999999999999996           568999999999999999999986 78889999987     


Q ss_pred             cccccCCccccCCCCCCCceEEEeccCCCCCcceEEEEeCCCCCCCCCCcceEEEEecCHHHHHHHhhCccCCCCCcccc
Q 007792           74 QARFFGDEIRVDLKHAKTGTVAMASAGENLNASQFYMTLRDNLDYLDEKHTIFGEVAEGLETLSRINESFVDEKNRPYKN  153 (589)
Q Consensus        74 ~~~~~~~e~~~~l~~~~~G~vs~a~~g~~~~~sqFfI~l~~~~~~ld~~~~vFG~Vv~G~~vl~~i~~~~~~~~~~p~~~  153 (589)
                        ..|++|. +.++|+.+|+||||+.++++|+||||||+.+ +||||++|+|||+|++||+||++|+.++++..++|..+
T Consensus        95 --~~f~dE~-~~~~h~~~G~lsMAn~gp~tngSQFfIt~~~-~~~LDg~~tVFG~Vv~G~dvv~~I~~~~t~~~~~P~~~  170 (179)
T 2wfi_A           95 --GFFEDES-FAVKHNKEFLLSMANRGKDTNGSQFFITTKP-TPHLDGHHVVFGQVISGQEVVREIENQKTDAASKPFAE  170 (179)
T ss_dssp             --SCBCCCC-CCSCCCSTTEEEECCSSTTCBCSCEEEESSC-CGGGTTTSCEEEEEEECHHHHHHHHTCCBCTTSCBSSC
T ss_pred             --Ccccccc-cCcCcCCCeEEEEEeCCCCCcceEEEEEcCC-CcccCCCeeEEEEEeCCHHHHHHHHcCCCCCCCCCCCC
Confidence              5688884 6899999999999999999999999999998 69999999999999999999999999999999999999


Q ss_pred             eeecccccc
Q 007792          154 IRIKHTYIL  162 (589)
Q Consensus       154 i~I~~~~vl  162 (589)
                      |+|.+|++|
T Consensus       171 v~I~~~G~l  179 (179)
T 2wfi_A          171 VRILSCGEL  179 (179)
T ss_dssp             EEEEEEEEC
T ss_pred             eEEEeCeeC
Confidence            999999875

>1a58_A Cyclophilin; isomerase, ppiase; 1.95A {Brugia malayi} SCOP: b.62.1.1 PDB: 1a33_A 1c5f_A*

Probab=100.00  E-value=8.3e-43  Score=325.56  Aligned_cols=147  Identities=40%  Similarity=0.627  Sum_probs=138.7

Q ss_pred             ecceeEEEEecCCCChhHHHHHHHHHhc--------C---ccCCceEEEeecCcccccCCCC-CCCCCCCCccccccccc
Q 007792            7 TSLGDIVVDLFVDKCPLTTKNFLKLCKI--------K---YYNGCLFHTVQKDFTAQTGDPT-GTGTGGDSVYKFLYGEQ   74 (589)
Q Consensus         7 T~~G~i~ieL~~~~aP~~~~nF~~l~~~--------~---~Y~g~~f~rv~~~~~iq~Gd~~-~~~~~~~~~~~~~~~~~   74 (589)
                      |++|+|+|+||++.||+||+||++||++        +   ||+|+.||||+|+|||||||++ ++++++.++|+      
T Consensus        18 ~~~G~i~ieL~~~~aP~t~~NF~~L~~~~~g~~~~~g~~~~Y~g~~FhRvi~~f~iQgGd~~~~~g~gg~si~g------   91 (177)
T 1a58_A           18 NLAGRIVMELYNDIAPRTCNNFLMLCTGMAGTGKISGKPLHYKGSTFHRVIKNFMIQGGDFTKGDGTGGESIYG------   91 (177)
T ss_dssp             EEEEEEEEEECTTTCHHHHHHHHHHHHCTTCBCTTTCSBCCCTTCBEEEEETTTEEEECCCSSSSSSCCCCTTS------
T ss_pred             EeceeEEEEEcCCCCchHHHHHHHHhcCCcCcccccCCcceeCCCEEEEEECCCEEEeCCccCCCCCCCCcccC------
Confidence            7899999999999999999999999985        3   8999999999999999999987 78899999987      


Q ss_pred             ccccCCccccCCCCCCCceEEEeccCCCCCcceEEEEeCCCCCCCCCCcceEEEEecCHHHHHHHhhCccCCCCCcccce
Q 007792           75 ARFFGDEIRVDLKHAKTGTVAMASAGENLNASQFYMTLRDNLDYLDEKHTIFGEVAEGLETLSRINESFVDEKNRPYKNI  154 (589)
Q Consensus        75 ~~~~~~e~~~~l~~~~~G~vs~a~~g~~~~~sqFfI~l~~~~~~ld~~~~vFG~Vv~G~~vl~~i~~~~~~~~~~p~~~i  154 (589)
                       ..|++|. +.++|+.+|+||||+.++++|+||||||+.+ +||||++|+|||+|++||+||++|+.++++..++|..+|
T Consensus        92 -~~f~dE~-~~~~h~~~G~lsmAn~gp~tngSQFfIt~~~-~~~LDg~~~VFG~Vv~G~dvv~~I~~~~~~~~~~P~~~v  168 (177)
T 1a58_A           92 -GMFDDEE-FVMKHDEPFVVSMANKGPNTNGSQFFITTTP-APHLNNIHVVFGKVVSGQEVVTKIEYLKTNSKNRPLADV  168 (177)
T ss_dssp             -SCBCCCC-CCSCCCSSSEEEECCSSTTCBCSCEEEESSC-CGGGTTTSCEEEEEEECHHHHHHHHTSCBCTTSCBSSCE
T ss_pred             -CcccCcc-cCcccCCCeEEEEeeCCCCCceeEEEEECCC-CCccCCCEEEEEEEEcCHHHHHHHHhCCCCCCCcCCCCe
Confidence             5688884 6889999999999999999999999999998 699999999999999999999999999999999999999


Q ss_pred             eecccccc
Q 007792          155 RIKHTYIL  162 (589)
Q Consensus       155 ~I~~~~vl  162 (589)
                      +|.+|++|
T Consensus       169 ~I~~~G~l  176 (177)
T 1a58_A          169 VILNCGEL  176 (177)
T ss_dssp             EEEEEEEE
T ss_pred             EEEEeEEE
Confidence            99999986

>2haq_A Cyclophilin; rotamase, proline, isomerase, CIS-trans, protozoa, KAla-AZAR.; 1.97A {Leishmania donovani} PDB: 3eov_A* 3bt8_A

Probab=100.00  E-value=5.1e-43  Score=324.02  Aligned_cols=151  Identities=39%  Similarity=0.721  Sum_probs=140.7

Q ss_pred             EEEE-EecceeEEEEecCCCChhHHHHHHHHH--hcCc-cCCceEEEeecCcccccCC-CCCCCCCCCCccccccccccc
Q 007792            2 SVLI-VTSLGDIVVDLFVDKCPLTTKNFLKLC--KIKY-YNGCLFHTVQKDFTAQTGD-PTGTGTGGDSVYKFLYGEQAR   76 (589)
Q Consensus         2 ~v~~-~T~~G~i~ieL~~~~aP~~~~nF~~l~--~~~~-Y~g~~f~rv~~~~~iq~Gd-~~~~~~~~~~~~~~~~~~~~~   76 (589)
                      .|.+ .|++|+|+|+||++.||+||+||++||  +.+| |+|+.||||+|+||||||+ +.++++++.++|+       .
T Consensus        17 di~i~~t~~G~i~ieL~~~~aP~t~~NF~~L~~g~~g~~Y~g~~FhRvi~~f~iQgGd~~~~~g~gg~si~g-------~   89 (172)
T 2haq_A           17 DVMIDSEPLGRITIGLFGKDAPLTTENFRQLCTGEHGFGYKDSIFHRVIQNFMIQGGDFTNFDGTGGKSIYG-------E   89 (172)
T ss_dssp             EEEETTEEEEEEEEEECTTTCHHHHHHHHHHHHTTTSCCSTTCBCCEEETTTEEEECCTTTSSSSCCCCSSS-------S
T ss_pred             EEEECCEecceEEEEEeCCCCcHHHHHHHHHhccCCCcccCCCEEEEEECCCEEecCCccCCCCCCCccccC-------C
Confidence            4544 499999999999999999999999999  6789 9999999999999999999 5678889999887       5


Q ss_pred             ccCCccccCCCCCCCceEEEeccCCCCCcceEEEEeCCCCCCCCCCcceEEEEecCHHHHHHHhhCccCCCCCcccceee
Q 007792           77 FFGDEIRVDLKHAKTGTVAMASAGENLNASQFYMTLRDNLDYLDEKHTIFGEVAEGLETLSRINESFVDEKNRPYKNIRI  156 (589)
Q Consensus        77 ~~~~e~~~~l~~~~~G~vs~a~~g~~~~~sqFfI~l~~~~~~ld~~~~vFG~Vv~G~~vl~~i~~~~~~~~~~p~~~i~I  156 (589)
                      .|++| .+.|+|. +|+||||+.++++|+||||||+.+ +|+||++|+|||+|++||+||++|++++++..++|.++|+|
T Consensus        90 ~f~dE-~~~l~h~-~G~lsmAn~gp~tngSQFfIt~~~-~~~LDg~~~vFG~Vv~G~dvv~~I~~~~t~~~~~P~~~v~I  166 (172)
T 2haq_A           90 KFADE-NLNVKHF-VGALSMANAGPNTNGSQFFITTAP-TPWLDGRHVVFGKVLDGMDVVLRIEKTKTNSHDRPVKPVKI  166 (172)
T ss_dssp             CBCCC-CCCSCCC-TTEEEECCSSTTCBCSCEEEESSC-CGGGTTTSCEEEEEEECHHHHHHHHTSCBCGGGCBSSCEEE
T ss_pred             cccCc-CCCcccC-ceEEEEccCCCCCcccEEEEECCC-CCccCCCEeEEEEEeCCHHHHHHHHhCCcCCCCcCCCCeEE
Confidence            68899 6889998 999999999999999999999998 69999999999999999999999999999988899999999


Q ss_pred             cccccc
Q 007792          157 KHTYIL  162 (589)
Q Consensus       157 ~~~~vl  162 (589)
                      .+|++|
T Consensus       167 ~~~g~l  172 (172)
T 2haq_A          167 VASGEL  172 (172)
T ss_dssp             EEEEEC
T ss_pred             EEeEEC
Confidence            999875

>2he9_A NK-tumor recognition protein; cyclosporin, isomerase, membrane, repeat, rotamase, peptidylprolyl isomerase, structural genomics; 2.00A {Homo sapiens}

Probab=100.00  E-value=1.1e-42  Score=327.65  Aligned_cols=153  Identities=39%  Similarity=0.685  Sum_probs=142.1

Q ss_pred             EEEE-EecceeEEEEecCCCChhHHHHHHHHHh-----------cCccCCceEEEeecCcccccCCCC-CCCCCCCCccc
Q 007792            2 SVLI-VTSLGDIVVDLFVDKCPLTTKNFLKLCK-----------IKYYNGCLFHTVQKDFTAQTGDPT-GTGTGGDSVYK   68 (589)
Q Consensus         2 ~v~~-~T~~G~i~ieL~~~~aP~~~~nF~~l~~-----------~~~Y~g~~f~rv~~~~~iq~Gd~~-~~~~~~~~~~~   68 (589)
                      .|.+ .|++|+|+||||++.||+||+||++||+           .+||+|+.||||+|+|||||||++ ++++++.+||+
T Consensus        25 di~i~~t~~G~I~ieL~~~~aP~t~~NF~~L~~g~~g~~~~~~k~~~Y~g~~FhRVi~~fmiQgGd~~~~~G~gg~siyg  104 (192)
T 2he9_A           25 DIEINREPVGRIMFQLFSDICPKTCKNFLCLCSGEKGLGKTTGKKLCYKGSTFHRVVKNFMIQGGDFSEGNGKGGESIYG  104 (192)
T ss_dssp             EEEETTEEEEEEEEEECTTTCHHHHHHHHHHHHCTTCBCTTTCSBSCCTTCBEEEEETTTEEEECCTTTSSSSCCCCTTS
T ss_pred             EEEECCEecceEEEEEcCCCCchHHHHHHHHhcCCCCcccccccCCeECCCEEEEEECCCEEEcCcccCCCCCCCCcccC
Confidence            3433 5899999999999999999999999996           468999999999999999999986 78899999987


Q ss_pred             ccccccccccCCccccCCCCCCCceEEEeccCCCCCcceEEEEeCCCCCCCCCCcceEEEEecCHHHHHHHhhCccCCCC
Q 007792           69 FLYGEQARFFGDEIRVDLKHAKTGTVAMASAGENLNASQFYMTLRDNLDYLDEKHTIFGEVAEGLETLSRINESFVDEKN  148 (589)
Q Consensus        69 ~~~~~~~~~~~~e~~~~l~~~~~G~vs~a~~g~~~~~sqFfI~l~~~~~~ld~~~~vFG~Vv~G~~vl~~i~~~~~~~~~  148 (589)
                             ..|++|. +.|+|+.+|+||||+.++++|+||||||+.+ +||||++|+|||+|++||+||++|+.++++.++
T Consensus       105 -------~~f~dE~-~~l~h~~~G~lsMAn~gp~tngSQFFIt~~~-~~~LDg~~tVFG~Vv~Gmdvv~~I~~~~t~~~~  175 (192)
T 2he9_A          105 -------GYFKDEN-FILKHDRAFLLSMANRGKHTNGSQFFITTKP-APHLDGVHVVFGLVISGFEVIEQIENLKTDAAS  175 (192)
T ss_dssp             -------SCBCCCC-CCSCCCSTTEEEECCSSTTCBCSCEEEESSC-CGGGTTTSCEEEEEEECHHHHHHHHTSCBCTTS
T ss_pred             -------CcccCcc-ccCCCCCCeEEEEEeCCCCCcceEEEEEcCC-CcccCCCccEEEEEEeCHHHHHHHHcCCcCCCC
Confidence                   5688884 7899999999999999999999999999998 699999999999999999999999999999999


Q ss_pred             Ccccceeeccccccc
Q 007792          149 RPYKNIRIKHTYILE  163 (589)
Q Consensus       149 ~p~~~i~I~~~~vl~  163 (589)
                      +|..+|+|.+|+++.
T Consensus       176 ~P~~~v~I~~~g~l~  190 (192)
T 2he9_A          176 RPYADVRVIDCGVLA  190 (192)
T ss_dssp             CBSSCEEEEEEEECC
T ss_pred             CCcCCeEEEEeEEEc
Confidence            999999999999974

>1mzw_A Cyclophilin H, U-snRNP-ASSOCIATED cyclophilin; cyclophilin, peptidyl-prolyl-CIS/trans isomerase, spliceosome, U4/U6-60K protein, WD protein; 2.00A {Homo sapiens} SCOP: b.62.1.1 PDB: 1qoi_A

Probab=100.00  E-value=1e-42  Score=324.54  Aligned_cols=147  Identities=35%  Similarity=0.659  Sum_probs=139.3

Q ss_pred             ecceeEEEEecCCCChhHHHHHHHHHhcCc--------cCCceEEEeecCcccccCCCC-CCCCCCCCcccccccccccc
Q 007792            7 TSLGDIVVDLFVDKCPLTTKNFLKLCKIKY--------YNGCLFHTVQKDFTAQTGDPT-GTGTGGDSVYKFLYGEQARF   77 (589)
Q Consensus         7 T~~G~i~ieL~~~~aP~~~~nF~~l~~~~~--------Y~g~~f~rv~~~~~iq~Gd~~-~~~~~~~~~~~~~~~~~~~~   77 (589)
                      |++|+|+||||++.||+||+||++||++++        |+|+.||||+|+|||||||+. ++++++.++|+       ..
T Consensus        22 t~~G~i~ieL~~~~aP~t~~NF~~L~~~~~g~~g~~~~Y~g~~FhRvi~~f~iQgGd~~~~~G~gg~si~g-------~~   94 (177)
T 1mzw_A           22 QEVGRMKIELFADVVPKTAENFRQFCTGEFRKDGVPIGYKGSTFHRVIKDFMIQGGDFVNGDGTGVASIYR-------GP   94 (177)
T ss_dssp             EEEEEEEEEECTTTCHHHHHHHHHHHHTCCEETTEECSSTTCBCCEEETTTEEEECCTTTSSSCCCCCTTS-------SC
T ss_pred             eeceeEEEEEcCCCCcHHHHHHHHHHhcccCCcCccceECCCEEEEEECCCEEEcCCcccCCCCCCCccCC-------Cc
Confidence            679999999999999999999999999998        999999999999999999986 78889999887       56


Q ss_pred             cCCccccCCCCCCCceEEEeccCCCCCcceEEEEeCCCCCCCCCCcceEEEEecCHHHHHHHhhCccCCCCCcccceeec
Q 007792           78 FGDEIRVDLKHAKTGTVAMASAGENLNASQFYMTLRDNLDYLDEKHTIFGEVAEGLETLSRINESFVDEKNRPYKNIRIK  157 (589)
Q Consensus        78 ~~~e~~~~l~~~~~G~vs~a~~g~~~~~sqFfI~l~~~~~~ld~~~~vFG~Vv~G~~vl~~i~~~~~~~~~~p~~~i~I~  157 (589)
                      |++|. +.|+|+.+|+||||+.++++++||||||+.+ +||||++|+|||+|++||+||++|++++++.+++|.++|+|.
T Consensus        95 f~dE~-~~l~h~~~G~lsmAn~gp~tngSQFfIt~~~-~~~LDg~~~VFG~Vv~G~dvv~~I~~~~t~~~~~P~~~v~I~  172 (177)
T 1mzw_A           95 FADEN-FKLRHSAPGLLSMANSGPSTNGCQFFITCSK-CDWLDGKHVVFGKIIDGLLVMRKIENVPTGPNNKPKLPVVIS  172 (177)
T ss_dssp             BCCCC-CCSCCCSTTEEEECCSSTTCBCSCEEEESSC-CGGGTTTSCEEEEEEECHHHHHHHHTSCBCGGGCBSSCEEEE
T ss_pred             ccCcc-cccccCCCCEEEEccCCCCCcceEEEEECCC-CCccCCCeeEEEEEeCCHHHHHHHHhCCcCCCCCCCCCEEEE
Confidence            88884 7899999999999999999999999999998 699999999999999999999999999999899999999999


Q ss_pred             ccccc
Q 007792          158 HTYIL  162 (589)
Q Consensus       158 ~~~vl  162 (589)
                      +|++|
T Consensus       173 ~cG~l  177 (177)
T 1mzw_A          173 QCGEM  177 (177)
T ss_dssp             EEEEC
T ss_pred             eceeC
Confidence            99975

>3pmp_A Cyclophilin A; peptidyl prolyl isomerase, isomerase-immunosuppressant compl; HET: BMT; 1.47A {Moniliophthora perniciosa} SCOP: b.62.1.1 PDB: 3o7t_A

Probab=100.00  E-value=1.3e-42  Score=320.69  Aligned_cols=153  Identities=36%  Similarity=0.613  Sum_probs=142.3

Q ss_pred             CEEEEE-ecceeEEEEecCCCChhHHHHHHHHHh--cCc-cCCceEEEeecCcccccCC-CCCCCCCCCCcccccccccc
Q 007792            1 MSVLIV-TSLGDIVVDLFVDKCPLTTKNFLKLCK--IKY-YNGCLFHTVQKDFTAQTGD-PTGTGTGGDSVYKFLYGEQA   75 (589)
Q Consensus         1 ~~v~~~-T~~G~i~ieL~~~~aP~~~~nF~~l~~--~~~-Y~g~~f~rv~~~~~iq~Gd-~~~~~~~~~~~~~~~~~~~~   75 (589)
                      |+|.+. |++|+|+||||++.||+||+||++||+  .+| |+|+.||||+|+||||||| +.+++.++.++|+       
T Consensus         7 ~di~i~~t~~G~i~ieL~~~~aP~t~~nF~~L~~g~~g~~Y~g~~fhRvi~~f~iQgGd~~~~~g~gg~si~g-------   79 (164)
T 3pmp_A            7 FNISINDKPEGRIVFKLYDEAVPKTAKNFRELATGQHGFGYKDSIFHRVIPQFMLQGGDFTRHNGTGGKSIYG-------   79 (164)
T ss_dssp             EEEEETTEEEEEEEEEECTTTCHHHHHHHHHHHHTTTSCSSTTCBEEEEETTTEEEECCTTTSSSSCCCBTTB-------
T ss_pred             EEEEECCEEeeEEEEEEeCCCCcHHHHHHHHHhcccCCCcccCCEEEEEECCCeEEeCCCCCCCCCCCcccCC-------
Confidence            567777 999999999999999999999999999  778 9999999999999999999 5688899999987       


Q ss_pred             cccCCccccCCCCCCCceEEEeccCCCCCcceEEEEeCCCCCCCCCCcceEEEEecCHHHHHHHhhCccCCCCCccccee
Q 007792           76 RFFGDEIRVDLKHAKTGTVAMASAGENLNASQFYMTLRDNLDYLDEKHTIFGEVAEGLETLSRINESFVDEKNRPYKNIR  155 (589)
Q Consensus        76 ~~~~~e~~~~l~~~~~G~vs~a~~g~~~~~sqFfI~l~~~~~~ld~~~~vFG~Vv~G~~vl~~i~~~~~~~~~~p~~~i~  155 (589)
                      ..|++| .+.++|+.+|+||||+.++++++|||||++.+ +||||++|+|||+|++||+||++|++++++ +++|..+|+
T Consensus        80 ~~~~dE-~~~l~h~~~G~lsma~~g~~t~~SQFfIt~~~-~~~Ld~~~~vFG~Vv~G~~vv~~I~~~~~~-~~~P~~~v~  156 (164)
T 3pmp_A           80 EKFADE-NFQVKHTKPGLLSMANAGANTNGSQFFITTVP-TSWLDGKHVVFGEVIEGLDIVRKVEGKGSA-SGKTNATIK  156 (164)
T ss_dssp             SCBCCC-CCCSCCCSTTEEEECBSSTTCBCSCEEEESSC-CGGGTTTSCEEEEEEECHHHHHHHHTTCCT-TCCCSSCEE
T ss_pred             cccccc-ccccCcCCCcEEEEeeCCCCCcccEEEEECCC-ChhhCCCccEEEEEeCCHHHHHHHHhCCCC-CCCcccCEE
Confidence            668888 68899999999999999999999999999998 699999999999999999999999999886 689999999


Q ss_pred             eccccccc
Q 007792          156 IKHTYILE  163 (589)
Q Consensus       156 I~~~~vl~  163 (589)
                      |.+|++|+
T Consensus       157 I~~cg~l~  164 (164)
T 3pmp_A          157 ITDCGTVA  164 (164)
T ss_dssp             EEEEEEC-
T ss_pred             EEeCeEEC
Confidence            99999873

>2cmt_A Peptidyl-prolyl CIS-trans isomerase E; rotamase activity, rotamase, RNA-binding, cyclosporin, cyclophilin, beta-barrel; 1.50A {Schistosoma mansoni} PDB: 2ck1_A

Probab=100.00  E-value=2.8e-42  Score=319.85  Aligned_cols=146  Identities=36%  Similarity=0.625  Sum_probs=136.9

Q ss_pred             ecceeEEEEecCCCChhHHHHHHHHHhc--Cc-cCCceEEEeecCcccccCCCC-CCCCCCCCcccccccccccccCCcc
Q 007792            7 TSLGDIVVDLFVDKCPLTTKNFLKLCKI--KY-YNGCLFHTVQKDFTAQTGDPT-GTGTGGDSVYKFLYGEQARFFGDEI   82 (589)
Q Consensus         7 T~~G~i~ieL~~~~aP~~~~nF~~l~~~--~~-Y~g~~f~rv~~~~~iq~Gd~~-~~~~~~~~~~~~~~~~~~~~~~~e~   82 (589)
                      |++|+|+|+||++.||+||+||++||++  +| |+|+.||||+|+||||||++. ++++++.++|+       ..|++|.
T Consensus        22 t~~G~i~ieL~~~~aP~t~~NF~~L~~~~~g~~Y~g~~FhRvi~~f~iQgGd~~~~~G~gg~si~g-------~~f~dE~   94 (172)
T 2cmt_A           22 GDAGRIVMELRSDIVPRTAENFRALCTGERGFGYHNCCFHRVIPQFMCQGGDFVKGDGTGGKSIYG-------RKFDDEN   94 (172)
T ss_dssp             EEEEEEEEEECTTTCHHHHHHHHHHHHTTTSCSSTTCBEEEEETTTEEEECCTTTSSSSCCCBTTB-------SCBCCCC
T ss_pred             eecceEEEEEcCCCCCHHHHHHHHHhccCCCceECCCEEEEEECCCEEEcCCccCCCCCCCCccCC-------Ccccccc
Confidence            8999999999999999999999999985  78 999999999999999999987 68889999887       5688884


Q ss_pred             ccCCCCCCCceEEEeccCCCCCcceEEEEeCCCCCCCCCCcceEEEEecCHHHHHHHhhCccCCCCCcccceeecccccc
Q 007792           83 RVDLKHAKTGTVAMASAGENLNASQFYMTLRDNLDYLDEKHTIFGEVAEGLETLSRINESFVDEKNRPYKNIRIKHTYIL  162 (589)
Q Consensus        83 ~~~l~~~~~G~vs~a~~g~~~~~sqFfI~l~~~~~~ld~~~~vFG~Vv~G~~vl~~i~~~~~~~~~~p~~~i~I~~~~vl  162 (589)
                       +.|+|+.+|+||||+.++++++|||||++.+ +||||++|+|||+|++||+||++|+++++. +++|.++|+|.+|++|
T Consensus        95 -~~l~h~~~G~lsmA~~gp~t~gSQFfIt~~~-~~~LDg~~tvFG~Vv~G~dvv~~I~~~~~~-~~~P~~~v~I~~~g~l  171 (172)
T 2cmt_A           95 -FQLRHEGFGVLSMANSGPNTNGSQFFICTTK-CDWLDGKHVVFGRVVDGQNVVKKMESVGSK-SGKVKEPVIISRCGEL  171 (172)
T ss_dssp             -CCSCCCSTTEEEECCSSTTCBCSCEEEESSC-CGGGTTTSCEEEEEEECHHHHHHGGGGCCT-TCCCSSCEEEEEEEEE
T ss_pred             -cCcccCCceEEEEeeCCCCCcccEEEEECCC-CCccCCCeeEEEEEEcCHHHHHHHHhCCCC-CCCCCCCEEEEEeEeE
Confidence             6899999999999999999999999999998 699999999999999999999999998884 6899999999999987

>2z6w_A Peptidyl-prolyl CIS-trans isomerase; isomerase-immunosuppressant complex, immunosuppressant, cyclophilin D; HET: BMT MLE CIT; 0.96A {Homo sapiens} SCOP: b.62.1.1 PDB: 3rcg_A* 3r49_A* 3r54_A 3r56_A* 3r57_A* 3r59_A* 3rcf_A* 3r4g_A* 3rci_X* 3rck_X* 3rcl_A* 3rd9_X* 3rda_X* 3rdb_A* 3rdc_A* 2bit_X 2biu_X 3qyu_A 3k0m_A 1ak4_A* ...

Probab=100.00  E-value=3.4e-42  Score=317.68  Aligned_cols=146  Identities=40%  Similarity=0.658  Sum_probs=137.2

Q ss_pred             ecceeEEEEecCCCChhHHHHHHHHHh--cCc-cCCceEEEeecCcccccCCCC-CCCCCCCCcccccccccccccCCcc
Q 007792            7 TSLGDIVVDLFVDKCPLTTKNFLKLCK--IKY-YNGCLFHTVQKDFTAQTGDPT-GTGTGGDSVYKFLYGEQARFFGDEI   82 (589)
Q Consensus         7 T~~G~i~ieL~~~~aP~~~~nF~~l~~--~~~-Y~g~~f~rv~~~~~iq~Gd~~-~~~~~~~~~~~~~~~~~~~~~~~e~   82 (589)
                      |++|+|+|+||++.||+||+||++||+  .+| |+|+.||||+|+||||||+++ ++++++.++|+       ..|++| 
T Consensus        15 t~~G~i~ieL~~~~aP~t~~NF~~L~~g~~g~~Y~g~~fhRvi~~f~iQgGd~~~~~g~gg~si~g-------~~f~dE-   86 (165)
T 2z6w_A           15 KPLGRVVLELKADVVPKTAENFRALCTGEKGFGYKGSTFHRVIPSFMCQAGDFTNHNGTGGKSIYG-------SRFPDE-   86 (165)
T ss_dssp             EEEEEEEEEECTTTCHHHHHHHHHHHHTTTSCCSTTCBEEEEETTTEEEECCTTTSSSSCCCBTTB-------SCBCCC-
T ss_pred             EeeeEEEEEEeCCCCcHHHHHHHHHhccCCCccCcCCEEEEEECCCEEEeCCccCCCCCCCCcccC-------CcccCc-
Confidence            589999999999999999999999999  889 999999999999999999986 67888889887       568888 


Q ss_pred             ccCCCCCCCceEEEeccCCCCCcceEEEEeCCCCCCCCCCcceEEEEecCHHHHHHHhhCccCCCCCcccceeecccccc
Q 007792           83 RVDLKHAKTGTVAMASAGENLNASQFYMTLRDNLDYLDEKHTIFGEVAEGLETLSRINESFVDEKNRPYKNIRIKHTYIL  162 (589)
Q Consensus        83 ~~~l~~~~~G~vs~a~~g~~~~~sqFfI~l~~~~~~ld~~~~vFG~Vv~G~~vl~~i~~~~~~~~~~p~~~i~I~~~~vl  162 (589)
                      .+.|+|+.+|+||||+.++++++|||||++.+ +||||++|+|||+|++||+||++|+.+++ .+++|.++|+|.+|+++
T Consensus        87 ~~~l~h~~~G~lsmA~~gp~s~~SQFfI~~~~-~~~Ldg~~~vFG~Vv~G~dvv~~I~~~~~-~~~~P~~~v~I~~~g~l  164 (165)
T 2z6w_A           87 NFTLKHVGPGVLSMANAGPNTNGSQFFICTIK-TDWLDGKHVVFGHVIEGMDVVKKIESFGS-KSGRTSKKIVITDCGQL  164 (165)
T ss_dssp             CCCSCCCSTTEEEECCSSTTCBCSCEEEESSC-CGGGTTTSCEEEEEEECHHHHHHHHHTCC-TTSCCSSCEEEEEEEEC
T ss_pred             ccccccCCCCEEEEeeCCCCCcccEEEEEcCC-CcccCCCeeEEEEEEcCHHHHHHHHhCCC-CCCCCCCcEEEEEeEEE
Confidence            58899998999999999999999999999998 69999999999999999999999999885 67899999999999987

>1qng_A Peptidyl-prolyl CIS-trans isomerase; isomerase-immunosuppressant complex, cyclophilin-cyclosporin complex, immunosuppressant, cyclophilin; HET: BMT; 2.1A {Plasmodium falciparum} SCOP: b.62.1.1 PDB: 1qnh_A*

Probab=100.00  E-value=4.1e-42  Score=318.77  Aligned_cols=150  Identities=38%  Similarity=0.657  Sum_probs=138.9

Q ss_pred             EEEEec-----ceeEEEEecCCCChhHHHHHHHHHhc-Cc--------cCCceEEEeecCcccccCCCC-CCCCCCCCcc
Q 007792            3 VLIVTS-----LGDIVVDLFVDKCPLTTKNFLKLCKI-KY--------YNGCLFHTVQKDFTAQTGDPT-GTGTGGDSVY   67 (589)
Q Consensus         3 v~~~T~-----~G~i~ieL~~~~aP~~~~nF~~l~~~-~~--------Y~g~~f~rv~~~~~iq~Gd~~-~~~~~~~~~~   67 (589)
                      |.|+++     +|+|+|+||++.||+||+||++||++ +|        |+|+.||||+|+|||||||+. ++++++.++|
T Consensus         6 v~~di~i~~~~~G~i~ieL~~~~aP~t~~NF~~L~~~~g~g~~~~~~~Y~g~~FhRvi~~f~iQgGd~~~~~g~gg~si~   85 (170)
T 1qng_A            6 VFFDISIDNSNAGRIIFELFSDITPRTCENFRALCTGEKIGSRGKNLHYKNSIFHRIIPQFMCQGGDITNGNGSGGESIY   85 (170)
T ss_dssp             EEEEEEESSSEEEEEEEEECTTTCHHHHHHHHHHHHTCEECTTSSEECCTTCBCCEEETTTEEEECCTTTSSSSCCCBTT
T ss_pred             EEEEEeECCEeceeEEEEEcCCCCCHHHHHHHHHhccCCcCccCccceECCCEEEEEECCCEEEcCCccCCCCCCCcccc
Confidence            555554     99999999999999999999999984 88        999999999999999999986 7888999998


Q ss_pred             cccccccccccCCccccCCCCCCCceEEEeccCCCCCcceEEEEeCCCCCCCCCCcceEEEEecCHHHHHHHhhCccCCC
Q 007792           68 KFLYGEQARFFGDEIRVDLKHAKTGTVAMASAGENLNASQFYMTLRDNLDYLDEKHTIFGEVAEGLETLSRINESFVDEK  147 (589)
Q Consensus        68 ~~~~~~~~~~~~~e~~~~l~~~~~G~vs~a~~g~~~~~sqFfI~l~~~~~~ld~~~~vFG~Vv~G~~vl~~i~~~~~~~~  147 (589)
                      +       ..|++| .+.|+|+.+|+||||+.++++|+||||||+.+ +||||++|+|||+|++||+||++|+.+++ .+
T Consensus        86 g-------~~f~dE-~~~l~h~~~G~lsmAn~gp~tngSQFfIt~~~-~~~Ldg~~~vFG~Vv~G~dvv~~I~~~~t-~~  155 (170)
T 1qng_A           86 G-------RSFTDE-NFNMKHDQPGLLSMANAGPNTNSSQFFITLVP-CPWLDGKHVVFGKVIEGMNVVREMEKEGA-KS  155 (170)
T ss_dssp             B-------SCBCCC-CCCSCCCSTTEEEECCSSTTCBCSCEEEESSC-CGGGTTTSCEEEEEEECHHHHHHHHTTCC-TT
T ss_pred             C-------Cccccc-ccccccCCCCEEEEeecCCCCcccEEEEECCC-CcccCCCeeEEEEEECCHHHHHHHHhCCC-CC
Confidence            7       568888 47899999999999999999999999999998 69999999999999999999999999999 67


Q ss_pred             CCcccceeecccccc
Q 007792          148 NRPYKNIRIKHTYIL  162 (589)
Q Consensus       148 ~~p~~~i~I~~~~vl  162 (589)
                      ++|..+|+|.+|++|
T Consensus       156 ~~P~~~v~I~~cG~l  170 (170)
T 1qng_A          156 GYVKRSVVITDCGEL  170 (170)
T ss_dssp             CCCSSCEEEEEEEEC
T ss_pred             CCCCCCeEEEeceeC
Confidence            899999999999875

>2igv_A Peptidyl-prolyl CIS-trans isomerase 3; rotamase; 1.67A {Caenorhabditis elegans} SCOP: b.62.1.1 PDB: 1e3b_A 1e8k_A 1dyw_A 2igw_A 2hqj_A

Probab=100.00  E-value=5.6e-42  Score=318.77  Aligned_cols=147  Identities=37%  Similarity=0.630  Sum_probs=136.7

Q ss_pred             ecceeEEEEecCCCChhHHHHHHHHHhc--C--------ccCCceEEEeecCcccccCCCC-CCCCCCCCcccccccccc
Q 007792            7 TSLGDIVVDLFVDKCPLTTKNFLKLCKI--K--------YYNGCLFHTVQKDFTAQTGDPT-GTGTGGDSVYKFLYGEQA   75 (589)
Q Consensus         7 T~~G~i~ieL~~~~aP~~~~nF~~l~~~--~--------~Y~g~~f~rv~~~~~iq~Gd~~-~~~~~~~~~~~~~~~~~~   75 (589)
                      |++|+|+|+||++.||+||+||++||++  +        ||+|+.||||+|+|||||||+. ++++++.++|+       
T Consensus        15 ~~~G~i~ieL~~~~aP~t~~NF~~L~~~~~g~g~~~~~~~Y~g~~FhRvi~~f~iQgGd~~~~~G~gg~siyg-------   87 (173)
T 2igv_A           15 KASGRIVMELYDDVVPKTAGNFRALCTGENGIGKSGKPLHFKGSKFHRIIPNFMIQGGDFTRGNGTGGESIYG-------   87 (173)
T ss_dssp             EEEEEEEEEECTTTCHHHHHHHHHHHHTTTCBCTTSSBSCCTTCBCCEEETTTEEEECCTTTSSSSCCCBTTB-------
T ss_pred             EecceEEEEEeCCCCcHHHHHHHHHhcCCCCCCccCccceECCCEEEEEECCCEEEcCCCCCCCCCCCCccCC-------
Confidence            4599999999999999999999999987  5        7999999999999999999987 78889999887       


Q ss_pred             cccCCccccCCCCCCCceEEEeccCCCCCcceEEEEeCCCCCCCCCCcceEEEEecCHHHHHHHhhCccCCCCCccccee
Q 007792           76 RFFGDEIRVDLKHAKTGTVAMASAGENLNASQFYMTLRDNLDYLDEKHTIFGEVAEGLETLSRINESFVDEKNRPYKNIR  155 (589)
Q Consensus        76 ~~~~~e~~~~l~~~~~G~vs~a~~g~~~~~sqFfI~l~~~~~~ld~~~~vFG~Vv~G~~vl~~i~~~~~~~~~~p~~~i~  155 (589)
                      ..|++|. +.|+|+.+|+||||+.++++|+||||||+.+ +||||++|+|||+|++||+||++|+.+++ .+++|..+|+
T Consensus        88 ~~f~dE~-~~l~h~~~G~lsmAn~gp~tngSQFfIt~~~-~~~LDg~~~vFG~Vv~G~dvv~~I~~~~t-~~~~P~~~v~  164 (173)
T 2igv_A           88 EKFPDEN-FKEKHTGPGVLSMANAGPNTNGSQFFLCTVK-TEWLDGKHVVFGRVVEGLDVVKAVESNGS-QSGKPVKDCM  164 (173)
T ss_dssp             SCBCCCC-CCSCCCSTTEEEECCSSTTCBSSCEEEESSC-CGGGTTTSCEEEEEEECHHHHHHHHTTCC-TTSCCSSCEE
T ss_pred             CcccCcc-cccCCCCCeEEEEeeCCCCCcceEEEEEcCC-ccccCCCeeEEEEEecCHHHHHHHHhCCC-CCCCCCCCEE
Confidence            5688884 7899999999999999999999999999998 69999999999999999999999999888 4689999999


Q ss_pred             eccccccc
Q 007792          156 IKHTYILE  163 (589)
Q Consensus       156 I~~~~vl~  163 (589)
                      |.+|++++
T Consensus       165 I~~~g~l~  172 (173)
T 2igv_A          165 IADCGQLK  172 (173)
T ss_dssp             EEEEEEEC
T ss_pred             EEEeEEEc
Confidence            99999974

>2r99_A Peptidyl-prolyl CIS-trans isomerase E; CIS-trans isomerization, structural genomics consortium, SGC, alternative splicing, mRNA processing; 1.61A {Homo sapiens} SCOP: b.62.1.1 PDB: 3uch_A 1zmf_A

Probab=100.00  E-value=9.4e-42  Score=316.91  Aligned_cols=147  Identities=38%  Similarity=0.627  Sum_probs=136.8

Q ss_pred             ecceeEEEEecCCCChhHHHHHHHHHh--cCc-cCCceEEEeecCcccccCCCC-CCCCCCCCcccccccccccccCCcc
Q 007792            7 TSLGDIVVDLFVDKCPLTTKNFLKLCK--IKY-YNGCLFHTVQKDFTAQTGDPT-GTGTGGDSVYKFLYGEQARFFGDEI   82 (589)
Q Consensus         7 T~~G~i~ieL~~~~aP~~~~nF~~l~~--~~~-Y~g~~f~rv~~~~~iq~Gd~~-~~~~~~~~~~~~~~~~~~~~~~~e~   82 (589)
                      |++|+|+|+||++.||+||+||++||+  .+| |+|+.||||+|+||||||+++ ++++++.++|+       ..|++| 
T Consensus        23 t~~G~i~ieL~~~~aP~t~~NF~~L~~g~~g~~Y~g~~FhRvi~~f~iQgGd~~~~~g~gg~si~g-------~~f~dE-   94 (173)
T 2r99_A           23 KPAGRIQMLLRSDVVPMTAENFRCLCTHEKGFGFKGSSFHRIIPQFMCQGGDFTNHNGTGGKSIYG-------KKFDDE-   94 (173)
T ss_dssp             EEEEEEEEEECTTTCHHHHHHHHHHHHTTTSCCSTTCBEEEEETTTEEEECCTTTSSSSCCCBTTB-------SCBCCC-
T ss_pred             ccceeEEEEECCCCCcHHHHHHHHHhcccCCceecCCEEEEeeCCCEEEeCCcCCCCCCCCCccCC-------CcccCc-
Confidence            899999999999999999999999995  577 999999999999999999987 68888999887       568888 


Q ss_pred             ccCCCCCCCceEEEeccCCCCCcceEEEEeCCCCCCCCCCcceEEEEecCHHHHHHHhhCccCCCCCcccceeecccccc
Q 007792           83 RVDLKHAKTGTVAMASAGENLNASQFYMTLRDNLDYLDEKHTIFGEVAEGLETLSRINESFVDEKNRPYKNIRIKHTYIL  162 (589)
Q Consensus        83 ~~~l~~~~~G~vs~a~~g~~~~~sqFfI~l~~~~~~ld~~~~vFG~Vv~G~~vl~~i~~~~~~~~~~p~~~i~I~~~~vl  162 (589)
                      .+.|+|+.+|+||||+.++++++||||||+.+ +||||++|+|||+|++||+||++|+.+++. +++|.++|+|.+|++|
T Consensus        95 ~~~l~h~~~G~lsmA~~gp~t~gSQFfIt~~~-~~~LDg~~tVFG~Vv~G~dvv~~I~~~~~~-~~~P~~~v~I~~cG~l  172 (173)
T 2r99_A           95 NFILKHTGPGLLSMANSGPNTNGSQFFLTCDK-TDWLDGKHVVFGEVTEGLDVLRQIEAQGSK-DGKPKQKVIIADCGEY  172 (173)
T ss_dssp             CCCSCCCSSSEEEECCSSTTCBCSCEEEESSC-CGGGTTTSCEEEEEEECHHHHHHHHTTCCT-TCCCSSCEEEEEEEEC
T ss_pred             ccCcccCCCcEEEEccCCCCCcccEEEEECCC-CCccCCCeeEEEEEEcCHHHHHHHHhCCCC-CCCCCCCeEEEEeeeE
Confidence            47899999999999999999999999999998 699999999999999999999999998875 5899999999999987


Q ss_pred             c
Q 007792          163 E  163 (589)
Q Consensus       163 ~  163 (589)
                      .
T Consensus       173 ~  173 (173)
T 2r99_A          173 V  173 (173)
T ss_dssp             C
T ss_pred             C
Confidence            3

>3s6m_A Peptidyl-prolyl CIS-trans isomerase; seattle structural genomics center for infectious disease; 1.65A {Burkholderia pseudomallei} SCOP: b.62.1.1 PDB: 3t1u_A*

Probab=100.00  E-value=3.2e-42  Score=319.69  Aligned_cols=151  Identities=26%  Similarity=0.406  Sum_probs=137.0

Q ss_pred             CEEEEEecceeEEEEecCCCChhHHHHHHHHHhcCccCCceEEEeecCcccccCCCCCCCCCCCCcccccccccccccCC
Q 007792            1 MSVLIVTSLGDIVVDLFVDKCPLTTKNFLKLCKIKYYNGCLFHTVQKDFTAQTGDPTGTGTGGDSVYKFLYGEQARFFGD   80 (589)
Q Consensus         1 ~~v~~~T~~G~i~ieL~~~~aP~~~~nF~~l~~~~~Y~g~~f~rv~~~~~iq~Gd~~~~~~~~~~~~~~~~~~~~~~~~~   80 (589)
                      |.|+|+|++|+|+|+||++.||+||+||++||+.+||+|+.||||+++||||||+++.....  .+++       ..|++
T Consensus         4 ~~v~l~T~~G~i~ieL~~~~aP~t~~NF~~L~~~g~Y~g~~FhRvi~~f~iQgGd~~~~~~~--~~~~-------~~~~~   74 (167)
T 3s6m_A            4 SMVELHTNHGVIKLELDEAKAPKTVENFLNYVKKGHYDGTIFHRVINGFMIQGGGFEPGLKQ--KPTD-------APIAN   74 (167)
T ss_dssp             CEEEEEETTEEEEEEECTTTCHHHHHHHHHHHHHTTTTTEECCEEETTTEEEESSEETTTEE--CCCC-------CCBCC
T ss_pred             cEEEEEeCCceEEEEEeCCCCcHHHHHHHHHhhhcccCCCEeEEecCCcEEEeccccCCCCC--CCCC-------CccCC
Confidence            79999999999999999999999999999999999999999999999999999998754321  2222       46888


Q ss_pred             ccccCCCCCCCceEEEec-cCCCCCcceEEEEeCCCCCCCCCC--------cceEEEEecCHHHHHHHhhCccCC----C
Q 007792           81 EIRVDLKHAKTGTVAMAS-AGENLNASQFYMTLRDNLDYLDEK--------HTIFGEVAEGLETLSRINESFVDE----K  147 (589)
Q Consensus        81 e~~~~l~~~~~G~vs~a~-~g~~~~~sqFfI~l~~~~~~ld~~--------~~vFG~Vv~G~~vl~~i~~~~~~~----~  147 (589)
                      |..+.|+| .+|+||||+ .++++++|||||++.+ ++|||++        |+|||+|++||+||++|++++++.    +
T Consensus        75 E~~~~l~~-~~G~lsmA~~~~p~t~gSQFfI~~~~-~~~Ld~~~~~~~~~~~~VFG~Vv~G~dvv~~I~~~~t~~~~~~~  152 (167)
T 3s6m_A           75 EANNGLKN-DTYTIAMARTNDPHSATAQFFINVND-NEFLNHSSPTPQGWGYAVFGKVVEGQDIVDKIKAVKTGSKGFHQ  152 (167)
T ss_dssp             CGGGCCCC-CTTEEEECCCSSTTCBCSCEEEESSC-CGGGSCCSSSTTTCCCCEEEEEEECHHHHHHHTTSCBBC---CB
T ss_pred             cccccccC-CccEEEEecCCCCCCccceEEEEcCC-chhcCCcccccCCCCceEEEEEEcCHHHHHHHHcCCcCCCcccC
Confidence            88778887 799999999 6899999999999998 6999998        999999999999999999999987    6


Q ss_pred             CCcccceeecccccc
Q 007792          148 NRPYKNIRIKHTYIL  162 (589)
Q Consensus       148 ~~p~~~i~I~~~~vl  162 (589)
                      ++|+.+|+|.+|.||
T Consensus       153 ~~P~~~v~I~~~~il  167 (167)
T 3s6m_A          153 DVPNDDVVIEKAVVV  167 (167)
T ss_dssp             TCBSSCCEEEEEEEC
T ss_pred             CCcCCCeEEEEEEEC
Confidence            899999999999875

>1lop_A Cyclophilin A; rotamase, isomerase-isomerase inhibitor complex; HET: NIT; 1.80A {Escherichia coli} SCOP: b.62.1.1 PDB: 2nul_A 2rs4_A

Probab=100.00  E-value=4.5e-42  Score=317.19  Aligned_cols=150  Identities=31%  Similarity=0.504  Sum_probs=135.4

Q ss_pred             EEEEecceeEEEEecCCCChhHHHHHHHHHhcCccCCceEEEeecCcccccCCCCCCCCCCCCcccccccccccccCCcc
Q 007792            3 VLIVTSLGDIVVDLFVDKCPLTTKNFLKLCKIKYYNGCLFHTVQKDFTAQTGDPTGTGTGGDSVYKFLYGEQARFFGDEI   82 (589)
Q Consensus         3 v~~~T~~G~i~ieL~~~~aP~~~~nF~~l~~~~~Y~g~~f~rv~~~~~iq~Gd~~~~~~~~~~~~~~~~~~~~~~~~~e~   82 (589)
                      |+|+|++|+|+|+||++.||+||+||++||+.+||+|+.||||+|+||||||+++..  .+.++|+       ..|++|.
T Consensus         2 v~l~T~~G~i~ieL~~~~aP~t~~NF~~L~~~g~Y~g~~FhRvi~~f~iQgGd~~~~--~g~~~~g-------~~~~dE~   72 (164)
T 1lop_A            2 VTFHTNHGDIVIKTFDDKAPETVKNFLDYCREGFYNNTIFHRVINGFMIQGGGFEPG--MKQKATK-------EPIKNEA   72 (164)
T ss_dssp             EEEEETTEEEEEEECTTTSHHHHHHHHHHHHTTTTTTEECCEEETTTEEEESSEETT--TEECCCC-------CCBCCCC
T ss_pred             EEEEeCCCCEEEEEeCCCCcHHHHHHHHHHhcCCCCCCEEEEEeCCceEecCCcccC--CCcCCCC-------Ccccccc
Confidence            899999999999999999999999999999999999999999999999999998732  1334444       5789998


Q ss_pred             ccCCCCCCCceEEEec-cCCCCCcceEEEEeCCCCCCCCCC--------cceEEEEecCHHHHHHHhhCccCC----CCC
Q 007792           83 RVDLKHAKTGTVAMAS-AGENLNASQFYMTLRDNLDYLDEK--------HTIFGEVAEGLETLSRINESFVDE----KNR  149 (589)
Q Consensus        83 ~~~l~~~~~G~vs~a~-~g~~~~~sqFfI~l~~~~~~ld~~--------~~vFG~Vv~G~~vl~~i~~~~~~~----~~~  149 (589)
                      .+.|+| .+|+||||+ .++++++|||||++.+ +||||++        |+|||+|++||+||++|+.++++.    .++
T Consensus        73 ~~~l~~-~~G~lsmA~~~~p~s~gSQFfI~~~~-~~~Ld~~~~~~~~~~~tvFG~Vv~G~dvv~~I~~~~t~~~~~~~~~  150 (164)
T 1lop_A           73 NNGLKN-TRGTLAMARTQAPHSATAQFFINVVD-NDFLNFSGESLQGWGYCVFAEVVDGMDEVDKIKGVATGRSGMHQDV  150 (164)
T ss_dssp             CSSCCC-CTTEEEECCCSSTTCBCSCEEEESSC-CGGGSCCSSSTTTSCCCEEEEEEECHHHHHHHHTSCEEEETTEEEE
T ss_pred             cccccc-CccEEEEeecCCCCCccceEEEEcCC-ccccCCccccccCCceEEEEEEecCHHHHHHHHhCCcCCccccCCC
Confidence            777888 699999997 5899999999999998 6999998        999999999999999999999975    479


Q ss_pred             cccceeeccccccc
Q 007792          150 PYKNIRIKHTYILE  163 (589)
Q Consensus       150 p~~~i~I~~~~vl~  163 (589)
                      |..+|+|.+|.+++
T Consensus       151 P~~~v~I~~~~v~~  164 (164)
T 1lop_A          151 PKEDVIIESVTVSE  164 (164)
T ss_dssp             ESSCCEEEEEEECC
T ss_pred             cCCCeEEEEEEEeC
Confidence            99999999999863

>2ose_A Probable peptidyl-prolyl CIS-trans isomerase; cyclophilin; 2.04A {Mimivirus}

Probab=100.00  E-value=2.1e-42  Score=335.25  Aligned_cols=166  Identities=27%  Similarity=0.448  Sum_probs=140.9

Q ss_pred             CEEEEE-ecceeEEEEecCCCChhHHHHHHHHHhc-----------------C--c-cCCceEEEeecCcccccCC-CCC
Q 007792            1 MSVLIV-TSLGDIVVDLFVDKCPLTTKNFLKLCKI-----------------K--Y-YNGCLFHTVQKDFTAQTGD-PTG   58 (589)
Q Consensus         1 ~~v~~~-T~~G~i~ieL~~~~aP~~~~nF~~l~~~-----------------~--~-Y~g~~f~rv~~~~~iq~Gd-~~~   58 (589)
                      |.|.|. |++|+|+|+||++.||+||+||++||++                 +  | |+|+.||||+++||||||| +.+
T Consensus        19 ~di~i~~t~~G~I~ieL~~d~aP~tv~NF~~L~~g~~~~~~p~~~~~~~~~~G~~~~Y~gt~FHRVi~~FmiQgGd~~~g   98 (234)
T 2ose_A           19 MDIVLNNEIIGRLQIKLFRDAFPAGVENFVQLTNGKTYRVNSNGTGKYKYNRHINRTYEGCKFHNVLHNNYIVSGDIYNS   98 (234)
T ss_dssp             EEEEETTEEEEEEEEEECGGGCHHHHHHHHHHHHTCCCC---------------CCCSTTCBCCEEETTTEEEECCCC--
T ss_pred             EEEEECCcccceEEEEEcCCCCcHHHHHHHHHhcCCccccccccccccccccCCceEECCcEEEEEECCCEEEcCCccCC
Confidence            345555 9999999999999999999999999984                 3  7 9999999999999999999 568


Q ss_pred             CCCCCCCcccccccccccccCCccccCCCCCCCceEEEec----cCCCCCcceEEEEeCCC-----CCCCCCCcceEEEE
Q 007792           59 TGTGGDSVYKFLYGEQARFFGDEIRVDLKHAKTGTVAMAS----AGENLNASQFYMTLRDN-----LDYLDEKHTIFGEV  129 (589)
Q Consensus        59 ~~~~~~~~~~~~~~~~~~~~~~e~~~~l~~~~~G~vs~a~----~g~~~~~sqFfI~l~~~-----~~~ld~~~~vFG~V  129 (589)
                      +|+++.+||+...  ....|+   .+.|+|+.+|+||||+    .++++++||||||+.+.     +||||++|+|||+|
T Consensus        99 ~G~Gg~siyg~~~--~p~~f~---~~~l~h~~~G~lsMAn~~~~~gpntngSQFFIt~~~~~~~~g~p~LDg~~tVFG~V  173 (234)
T 2ose_A           99 NGSSAGTVYCDEP--IPPVFG---DYFYPHESKGLLSLVPYTDESGNRYYDSTFMITLDDIRPSNVLDELDRDQVVIGQV  173 (234)
T ss_dssp             --CCCCCTTTTCC--BCCCCC---SCCCCSCSTTEEEECCEECTTSCEEBCSCEEEESSCCCTTSSGGGSCTTSEEEEEE
T ss_pred             CCCCCccccCCcc--Cccccc---CcCccCCCCCEEEEecccccCCCCCccceEEEEecCccccCCCcccCCCeeEEEEE
Confidence            8999999987320  001133   3579999999999999    99999999999999973     59999999999999


Q ss_pred             ecCHHHHHHHhhCccCCCCCcccceeecccccccCCCCChhh
Q 007792          130 AEGLETLSRINESFVDEKNRPYKNIRIKHTYILEDPFDDPAQ  171 (589)
Q Consensus       130 v~G~~vl~~i~~~~~~~~~~p~~~i~I~~~~vl~~p~~~~~~  171 (589)
                      |+||+||++|+.++++..++|..+|+|.+|+++.+|+++++.
T Consensus       174 v~GmdVv~~I~~~~t~~~~~P~~~V~I~~~~~l~~p~~~~~k  215 (234)
T 2ose_A          174 YGGLDVLDKINSMIKPYAGRKYPTFSIGKCGAYLDSSQAQRK  215 (234)
T ss_dssp             EECHHHHHHHHHHTCCCTTCCCCCEEEEEEEECCCHHHHCC-
T ss_pred             eCCHHHHHHHHhCCcCCCCCccCCEEEEEEEEecCCcccccc
Confidence            999999999999999988999999999999999888766554

>2poy_A Peptidyl-prolyl CIS-trans isomerase; isomerase-immunosuppressant complex, immunosuppressant, cyclophilin, isomerase, S genomics, structural genomics consortium; HET: BMT; 1.80A {Cryptosporidium parvum iowa II} PDB: 2plu_A*

Probab=100.00  E-value=2.1e-41  Score=317.19  Aligned_cols=145  Identities=39%  Similarity=0.663  Sum_probs=134.5

Q ss_pred             ecceeEEEEecCCCChhHHHHHHHHHh--cCc--------cCCceEEEeecCcccccCCCC-CCCCCCCCcccccccccc
Q 007792            7 TSLGDIVVDLFVDKCPLTTKNFLKLCK--IKY--------YNGCLFHTVQKDFTAQTGDPT-GTGTGGDSVYKFLYGEQA   75 (589)
Q Consensus         7 T~~G~i~ieL~~~~aP~~~~nF~~l~~--~~~--------Y~g~~f~rv~~~~~iq~Gd~~-~~~~~~~~~~~~~~~~~~   75 (589)
                      |++|+|+|+||++.||+||+||++||+  .+|        |+|+.||||+|+|||||||+. ++++++.++|+       
T Consensus        31 t~~G~I~ieL~~~~aP~t~~NF~~L~~g~~g~~~~~~~~~Y~g~~FhRVi~~f~iQgGd~~~~~G~gg~si~g-------  103 (186)
T 2poy_A           31 TPAGRITMELFADKVPITAENFRALCTGEKGMGQSGKPLCYTGSFFHRIIPQFMIQGGDFTRGDGTGGESIYG-------  103 (186)
T ss_dssp             EEEEEEEEEECTTTCHHHHHHHHHHHHTTTCBCTTSSBSCCTTCBCCEEETTTEEEECCTTTSSSSCCCCTTC-------
T ss_pred             EecccEEEEEeCCCCcHHHHHHHHHhcccCCccccCccceECCCEEEEEeCCCEEEeCCCCCCCCCCCCccCC-------
Confidence            459999999999999999999999996  478        999999999999999999986 78889999987       


Q ss_pred             cccCCccccCCCCCCCceEEEeccCCCCCcceEEEEeCCCCCCCCCCcceEEEEecCHHHHHHHhhCccCCCCCccccee
Q 007792           76 RFFGDEIRVDLKHAKTGTVAMASAGENLNASQFYMTLRDNLDYLDEKHTIFGEVAEGLETLSRINESFVDEKNRPYKNIR  155 (589)
Q Consensus        76 ~~~~~e~~~~l~~~~~G~vs~a~~g~~~~~sqFfI~l~~~~~~ld~~~~vFG~Vv~G~~vl~~i~~~~~~~~~~p~~~i~  155 (589)
                      ..|++|. +.|+|+.+|+||||+.++++|+||||||+.+ +||||++|+|||+|++||+||++|+.+++ .+++|..+|+
T Consensus       104 ~~f~dE~-~~l~h~~~G~lsMAn~gpntngSQFFIt~~~-~~~LDg~~tVFG~Vv~Gmdvv~~I~~~~t-~~~~P~~~v~  180 (186)
T 2poy_A          104 SKFRDEN-FVYTHDAPFLLSMANAGPNTNGSQFFITTVP-CPWLDGKHVVFGKVLEGMEVVKSIEKCGS-QNGKPTKSVC  180 (186)
T ss_dssp             -CBCCCC-CCSCCCSTTEEEECCSSTTCBCSCEEEESSC-CGGGTTTSCEEEEEEECHHHHHHHHHTCC-TTSCCSSCEE
T ss_pred             CcccCcc-cccccCCCcEEEEeeCCCCCcccEEEEECCC-CcccCCCeeEEEEEecCHHHHHHHHhCCC-CCCCCCCCEE
Confidence            5688884 7899999999999999999999999999998 69999999999999999999999999988 5789999999


Q ss_pred             eccccc
Q 007792          156 IKHTYI  161 (589)
Q Consensus       156 I~~~~v  161 (589)
                      |.+|++
T Consensus       181 I~~cG~  186 (186)
T 2poy_A          181 ITASGV  186 (186)
T ss_dssp             EEEEEC
T ss_pred             EEeCCC
Confidence            999974

>2c3b_A Ppiase, cyclophilin; isomerase, 3D domain swapping, misfolding, Asp F 11, allergen, rotamase; 1.85A {Aspergillus fumigatus} SCOP: b.62.1.1

Probab=100.00  E-value=2.4e-42  Score=320.55  Aligned_cols=147  Identities=39%  Similarity=0.618  Sum_probs=111.7

Q ss_pred             ecceeEEEEecCCCChhHHHHHHHHHh--cCc-cCCceEEEeecCcccccCC-CCCCCCCCCCcccccccccccccCCcc
Q 007792            7 TSLGDIVVDLFVDKCPLTTKNFLKLCK--IKY-YNGCLFHTVQKDFTAQTGD-PTGTGTGGDSVYKFLYGEQARFFGDEI   82 (589)
Q Consensus         7 T~~G~i~ieL~~~~aP~~~~nF~~l~~--~~~-Y~g~~f~rv~~~~~iq~Gd-~~~~~~~~~~~~~~~~~~~~~~~~~e~   82 (589)
                      |++|+|+|+||++.||+||+||++||+  .++ |+|+.||||+|+||||||+ +.++++++.++|+       ..|++| 
T Consensus        19 T~~G~i~ieL~~~~aP~t~~NF~~L~~g~~g~~Y~g~~fhRvi~~f~iQgGd~~~~~g~gg~si~g-------~~f~dE-   90 (172)
T 2c3b_A           19 TKVGRIVFNLFDKDVPKTAKNFRELCKRPAGEGYRESTFHRIIPNFMIQGGDFTRGNGTGGRSIYG-------DKFADE-   90 (172)
T ss_dssp             CEEEEEEEEECTTTSHHHHHHHHHHHHSCTTTSSTTCBCCEEETTTEEEECC----------------------------
T ss_pred             cccccEEEEEcCCCCcHHHHHHHHHhccCCCcccCCCEEEEEeCCCEEEeCCcCCCCCCCCcccCC-------CcccCc-
Confidence            889999999999999999999999999  668 9999999999999999999 6788899999887       568888 


Q ss_pred             ccCCCCCCCceEEEeccCCCCCcceEEEEeCCCCCCCCCCcceEEEEec--CHHHHHHHhhCccCCCC-Ccccceeeccc
Q 007792           83 RVDLKHAKTGTVAMASAGENLNASQFYMTLRDNLDYLDEKHTIFGEVAE--GLETLSRINESFVDEKN-RPYKNIRIKHT  159 (589)
Q Consensus        83 ~~~l~~~~~G~vs~a~~g~~~~~sqFfI~l~~~~~~ld~~~~vFG~Vv~--G~~vl~~i~~~~~~~~~-~p~~~i~I~~~  159 (589)
                      .+.++|+.+|+||||+.++++++||||||+.+ +||||++|+|||+|++  ||+||++|++++++... +|.++|+|.+|
T Consensus        91 ~~~~~h~~~G~lsmA~~gp~t~gSQFfIt~~~-~~~LDg~~tvFG~Vv~~~G~dvv~~I~~~~t~~~~~~P~~~v~I~~c  169 (172)
T 2c3b_A           91 NFSRKHDKKGILSMANAGPNTNGSQFFITTAV-TSWLDGKHVVFGEVADEKSYSVVKEIEALGSSSGSVRSNTRPKIVNC  169 (172)
T ss_dssp             --CHHHHHTCEEEEC---------CEEEECSC-CTTCCSCCEEEEEECSHHHHHHHHHHHTTCCTTSCCCSSSCCEEEEE
T ss_pred             ccccccCCCeEEEEeeCCCCCcccEEEEECCC-CCccCCCeeEEEEEEecCCHHHHHHHHhCCCCCCCccCCCCeEEEeC
Confidence            67889989999999999999999999999998 6999999999999999  99999999999998765 99999999999


Q ss_pred             ccc
Q 007792          160 YIL  162 (589)
Q Consensus       160 ~vl  162 (589)
                      ++|
T Consensus       170 G~l  172 (172)
T 2c3b_A          170 GEL  172 (172)
T ss_dssp             EEC
T ss_pred             eeC
Confidence            875

>1v9t_A Cyclophilin B; beta barrel, isomerase-isomerase inhibitor complex; HET: NIT; 1.70A {Escherichia coli} SCOP: b.62.1.1 PDB: 1j2a_A* 1vai_A* 1clh_A

Probab=100.00  E-value=1.9e-41  Score=313.59  Aligned_cols=151  Identities=28%  Similarity=0.463  Sum_probs=135.0

Q ss_pred             CEEEEEecceeEEEEecCCCChhHHHHHHHHHhcCccCCceEEEeecCcccccCCCCCCCCCCCCcccccccccccccCC
Q 007792            1 MSVLIVTSLGDIVVDLFVDKCPLTTKNFLKLCKIKYYNGCLFHTVQKDFTAQTGDPTGTGTGGDSVYKFLYGEQARFFGD   80 (589)
Q Consensus         1 ~~v~~~T~~G~i~ieL~~~~aP~~~~nF~~l~~~~~Y~g~~f~rv~~~~~iq~Gd~~~~~~~~~~~~~~~~~~~~~~~~~   80 (589)
                      ..|+|+|++|+|+|+||++.||+||+||++||+.+||+|+.||||+|+||||||+++..+.+  ..++       ..|++
T Consensus         5 ~~v~~~t~~G~i~ieL~~~~aP~t~~NF~~L~~~g~Y~g~~FhRvi~~f~iQgGd~~~~~~~--~~~g-------~~~~d   75 (166)
T 1v9t_A            5 PHVLLTTSAGNIELELDKQKAPVSVQNFVDYVNSGFYNNTTFHRVIPGFMIQGGGFTEQMQQ--KKPN-------PPIKN   75 (166)
T ss_dssp             CEEEEEETTEEEEEEECTTTCHHHHHHHHHHHHTTTTTTCBEEEEETTTEEEESSBCTTCCB--CCCC-------CCBCC
T ss_pred             eEEEEEeCCccEEEEEcCCCCcHHHHHHHHHhccCCCCCCEEEEEECCcEEEcCCcCcCCCC--CCCC-------Ccccc
Confidence            46999999999999999999999999999999999999999999999999999998865422  1222       45888


Q ss_pred             ccccCCCCCCCceEEEecc-CCCCCcceEEEEeCCCCCCCCCC-----cceEEEEecCHHHHHHHhhCccCC----CCCc
Q 007792           81 EIRVDLKHAKTGTVAMASA-GENLNASQFYMTLRDNLDYLDEK-----HTIFGEVAEGLETLSRINESFVDE----KNRP  150 (589)
Q Consensus        81 e~~~~l~~~~~G~vs~a~~-g~~~~~sqFfI~l~~~~~~ld~~-----~~vFG~Vv~G~~vl~~i~~~~~~~----~~~p  150 (589)
                      |....|+| .+|+||||+. ++++++||||||+.+ +||||++     |+|||+|++||+||++|+.++++.    .++|
T Consensus        76 E~~~~l~~-~~G~lsmA~~~~p~t~gSQFfI~~~~-~~~Ld~~~~~~~~tvFG~Vv~G~dvv~~I~~~~~~~~~~~~~~P  153 (166)
T 1v9t_A           76 EADNGLRN-TRGTIAMARTADKDSATSQFFINVAD-NAFLDHGQRDFGYAVFGKVVKGMDVADKISQVPTHDVGPYQNVP  153 (166)
T ss_dssp             CGGGSCCC-CTTEEEECCCSSTTCBCSCEEEESSC-CGGGSCCSSCCCCCEEEEEEECHHHHHHHHTSCEEEETTEEEEE
T ss_pred             cccccccC-CceEEEEeecCCCCCccceEEEEeCC-ccccCCccCcCCeeEEEEEecCHHHHHHHHhCCCCCCCccCCCc
Confidence            97666766 6899999996 699999999999998 6999998     999999999999999999999976    4789


Q ss_pred             ccceeecccccc
Q 007792          151 YKNIRIKHTYIL  162 (589)
Q Consensus       151 ~~~i~I~~~~vl  162 (589)
                      ..+|+|.+|.++
T Consensus       154 ~~~v~I~~~~v~  165 (166)
T 1v9t_A          154 SKPVVILSATVL  165 (166)
T ss_dssp             SSCCBEEEEEEC
T ss_pred             CCCeEEEEEEEe
Confidence            999999999986

>3rdd_A Peptidyl-prolyl CIS-trans isomerase A; beta barrel, cytosolic, inhibito isomerase-isomerase inhibitor complex; HET: EA4; 2.14A {Homo sapiens}

Probab=100.00  E-value=3.9e-41  Score=315.56  Aligned_cols=152  Identities=38%  Similarity=0.604  Sum_probs=138.9

Q ss_pred             EEEEEec-----ceeEEEEecCCCChhHHHHHHHHHhcCc---cCCceEEEeecCcccccCCCC-CCCCCCCCccccccc
Q 007792            2 SVLIVTS-----LGDIVVDLFVDKCPLTTKNFLKLCKIKY---YNGCLFHTVQKDFTAQTGDPT-GTGTGGDSVYKFLYG   72 (589)
Q Consensus         2 ~v~~~T~-----~G~i~ieL~~~~aP~~~~nF~~l~~~~~---Y~g~~f~rv~~~~~iq~Gd~~-~~~~~~~~~~~~~~~   72 (589)
                      .|.|+|+     +|+|+|+||++.||+||+||++||++++   |+|+.||||+|+|||||||+. +++.++.++|+    
T Consensus        24 ~v~~di~i~~~~~G~I~ieL~~~~aP~t~~NF~~L~~~~~g~~Y~g~~FhRvi~~f~iQgGd~~~~~g~gg~si~g----   99 (184)
T 3rdd_A           24 TVFFDIAVDGEPLGRVSFELFADKVPKTAENFRALSTGEKGFGYKGSCFHRIIPGFMCQGGDFTRHNGTGGKSIYG----   99 (184)
T ss_dssp             EEEEEEEETTEEEEEEEEEECTTTSHHHHHHHHHHHHTTTSCSSTTCBCCEEETTTEEEECCTTTSSSSCCCBTTB----
T ss_pred             EEEEEEeECCEeeeEEEEEEeCCCCcHHHHHHHHHhccCcCcccCCCEEEEccCCcEEEeCCCCCCCCCCCcccCC----
Confidence            3677766     9999999999999999999999997755   999999999999999999954 78889999887    


Q ss_pred             ccccccCCccccCCCCCCCceEEEeccCCCCCcceEEEEeCCCCCCCCCCcceEEEEecCHHHHHHHhhCccCCCCCccc
Q 007792           73 EQARFFGDEIRVDLKHAKTGTVAMASAGENLNASQFYMTLRDNLDYLDEKHTIFGEVAEGLETLSRINESFVDEKNRPYK  152 (589)
Q Consensus        73 ~~~~~~~~e~~~~l~~~~~G~vs~a~~g~~~~~sqFfI~l~~~~~~ld~~~~vFG~Vv~G~~vl~~i~~~~~~~~~~p~~  152 (589)
                         ..|++| .+.++|+.+|+||||+.++++++|||||++.+ +|+||++|+|||+|++||+||++|+++++ .+++|..
T Consensus       100 ---~~~~de-~~~l~h~~~G~lsmA~~gp~s~gSQFfIt~~~-~~~LDg~~tVFG~Vv~G~dvv~~I~~~~~-~~g~P~~  173 (184)
T 3rdd_A          100 ---EKFEDE-NFILKHTGPGILSMANAGPNTNGSQFFICTAK-TEWLDGKHVVFGKVKEGMNIVEAMERFGS-RNGKTSK  173 (184)
T ss_dssp             ---SCBCCC-CCCSCCCSTTEEEECCSSTTCBSSCEEEESSC-CGGGTTTSCEEEEEEECHHHHHHHHTTCC-TTSCCSS
T ss_pred             ---CcccCc-ccccccCCCcEEEEEeCCCCCcccEEEEEeCC-chhhCCCceEEEEEecCHHHHHHHHhcCC-CCCCCcC
Confidence               567888 47899999999999999999999999999998 69999999999999999999999999886 4789999


Q ss_pred             ceeeccccccc
Q 007792          153 NIRIKHTYILE  163 (589)
Q Consensus       153 ~i~I~~~~vl~  163 (589)
                      +|+|.+|++|+
T Consensus       174 ~v~I~~cG~l~  184 (184)
T 3rdd_A          174 KITIADCGQLE  184 (184)
T ss_dssp             CEEEEEEEECC
T ss_pred             CeEEEeCeEEC
Confidence            99999999974

>1z81_A Cyclophilin; structural genomics, structural genomics consortium, SGC, isomerase; 2.80A {Plasmodium yoelii yoelii} SCOP: b.62.1.1

Probab=100.00  E-value=2.9e-41  Score=324.50  Aligned_cols=147  Identities=34%  Similarity=0.580  Sum_probs=138.3

Q ss_pred             ecceeEEEEecCCCChhHHHHHHHHHhcC--------ccCCceEEEeecCcccccCCCC-CCCCCCCCcccccccccccc
Q 007792            7 TSLGDIVVDLFVDKCPLTTKNFLKLCKIK--------YYNGCLFHTVQKDFTAQTGDPT-GTGTGGDSVYKFLYGEQARF   77 (589)
Q Consensus         7 T~~G~i~ieL~~~~aP~~~~nF~~l~~~~--------~Y~g~~f~rv~~~~~iq~Gd~~-~~~~~~~~~~~~~~~~~~~~   77 (589)
                      |++|+|+||||++.||+||+||++||+++        +|+|+.||||+|+|||||||++ ++++++.+||+       ..
T Consensus        71 t~~G~I~ieL~~d~aP~tv~NF~~L~~~~~g~~g~~~~Y~gt~FHRVi~~FmiQgGD~~~g~G~Gg~siyg-------~~  143 (229)
T 1z81_A           71 NFLGKFKFELFQNIVPKTSENFRQFCTGEYKVNNLPVGYKNTIFHRVIKEFMIQGGDFINHNGSGSLSIYG-------EK  143 (229)
T ss_dssp             EEEEEEEEEECTTTCHHHHHHHHHHHHTCCBSSSSBCSSTTEECCEEETTTEEEECCTTTSSSCCCCBTTB-------SC
T ss_pred             eecccEEEEEcCCCCCHHHHHHHHHhhCCCCCcCCCceECCCEEEEEeCCCEEEcCCCcCCCCCCCCccCC-------Cc
Confidence            45999999999999999999999999987        7999999999999999999986 78899999987       56


Q ss_pred             cCCccccCCCCCCCceEEEeccCCCCCcceEEEEeCCCCCCCCCCcceEEEEe--cCHHHHHHHhhCccCCC-CCcccce
Q 007792           78 FGDEIRVDLKHAKTGTVAMASAGENLNASQFYMTLRDNLDYLDEKHTIFGEVA--EGLETLSRINESFVDEK-NRPYKNI  154 (589)
Q Consensus        78 ~~~e~~~~l~~~~~G~vs~a~~g~~~~~sqFfI~l~~~~~~ld~~~~vFG~Vv--~G~~vl~~i~~~~~~~~-~~p~~~i  154 (589)
                      |++| .+.|+|+.+|+||||+.++++++||||||+.+ +||||++|+|||+|+  +||+||++|+.++++.. ++|.++|
T Consensus       144 f~dE-~~~l~h~~~G~LsMAn~gpntngSQFFIt~~~-~~~LDg~~tVFG~Vv~~eGmdVv~~I~~~~t~~~~~~P~~~V  221 (229)
T 1z81_A          144 FDDE-NFDIKHDKEGLLSMANSGPNTNGCQFFITTKK-CEWLDGKNVVFGRIIDNDSLLLLKKIENVSVTPYIYKPKIPI  221 (229)
T ss_dssp             CCCC-CCCSCCCSTTEEEECCSSSSCCCSCEEEESSC-CGGGBTTBCEEEEECSHHHHHHHHHHHHSCBCTTTCCBSSCE
T ss_pred             cccc-ccccccCCCcEEEeccCCCCCcccEEEEECCC-CcccCCCeeEEEEEEecCcHHHHHHHHhCCCCCCCCCCCCCe
Confidence            8888 47899999999999999999999999999998 799999999999999  99999999999999887 9999999


Q ss_pred             eecccccc
Q 007792          155 RIKHTYIL  162 (589)
Q Consensus       155 ~I~~~~vl  162 (589)
                      +|.+|++|
T Consensus       222 ~I~~cG~l  229 (229)
T 1z81_A          222 NVVECGEL  229 (229)
T ss_dssp             EEEEEEEC
T ss_pred             EEEeCeeC
Confidence            99999975

>4fru_A Cyclophilin B, peptidyl-prolyl CIS-trans isomerase; cyclophilin-type ppiase, peptidyl-prolyl CIS-trans isomerase chaperone, foldase; HET: ME2 PEG; 1.10A {Equus caballus} PDB: 4frv_A* 3ich_A 3ici_A* 1cyn_A* 2esl_A* 2rmc_A* 1h0p_A 1xo7_A 1xq7_A*

Probab=100.00  E-value=6e-41  Score=315.54  Aligned_cols=148  Identities=40%  Similarity=0.667  Sum_probs=139.0

Q ss_pred             ecceeEEEEecCCCChhHHHHHHHHHhc--C-ccCCceEEEeecCcccccCCCC-CCCCCCCCcccccccccccccCCcc
Q 007792            7 TSLGDIVVDLFVDKCPLTTKNFLKLCKI--K-YYNGCLFHTVQKDFTAQTGDPT-GTGTGGDSVYKFLYGEQARFFGDEI   82 (589)
Q Consensus         7 T~~G~i~ieL~~~~aP~~~~nF~~l~~~--~-~Y~g~~f~rv~~~~~iq~Gd~~-~~~~~~~~~~~~~~~~~~~~~~~e~   82 (589)
                      |++|+|+|+||++.||+||+||++||++  + +|+|+.||||+|+||||||++. ++++++.++|+       ..|++| 
T Consensus        24 ~~~G~i~ieL~~~~aP~t~~NF~~L~~~~~g~~Y~g~~FhRvi~~f~iQgGd~~~~~g~gg~si~g-------~~f~de-   95 (185)
T 4fru_A           24 EDIGRVVIGLFGKTVPKTVDNFVALATGEKGFGYKDSKFHRVIKDFMIQGGDFTRGDGTGGKSIYG-------ERFPDE-   95 (185)
T ss_dssp             EEEEEEEEEECTTTSHHHHHHHHHHHHTTTSCCSTTCBCCEEETTTEEEECCTTTSSSSCCCBTTB-------SCBCCC-
T ss_pred             EecceEEEEEeCCCCcHHHHHHHHHHhcCCCCeEcCCEEEEeeCCCeEEECCCCCCCCCCCccccC-------CccCcc-
Confidence            5699999999999999999999999976  5 7999999999999999999987 78889999887       568888 


Q ss_pred             ccCCCCCCCceEEEeccCCCCCcceEEEEeCCCCCCCCCCcceEEEEecCHHHHHHHhhCccCCCCCcccceeecccccc
Q 007792           83 RVDLKHAKTGTVAMASAGENLNASQFYMTLRDNLDYLDEKHTIFGEVAEGLETLSRINESFVDEKNRPYKNIRIKHTYIL  162 (589)
Q Consensus        83 ~~~l~~~~~G~vs~a~~g~~~~~sqFfI~l~~~~~~ld~~~~vFG~Vv~G~~vl~~i~~~~~~~~~~p~~~i~I~~~~vl  162 (589)
                      .+.++|+.+|+||||+.++++++|||||++.+ +||||++|+|||+|++||+||++|+.++++.+++|..+|+|.+|+++
T Consensus        96 ~~~~~h~~~G~lsma~~gp~t~~SQFfI~~~~-~~~Ld~~~~vFG~Vv~G~dvv~~I~~~~t~~~~~P~~~v~I~~~g~l  174 (185)
T 4fru_A           96 NFKLKHYGPGWVSMANAGKDTNGSQFFITTVK-TAWLDGKHVVFGKVLEGMEVVRKVETTKTDGRDKPLKDVTIADCGKI  174 (185)
T ss_dssp             CCCSCCCSTTEEEECCSSTTCBCSCEEEESSC-CGGGTTTSCEEEEEEECHHHHHHHHTSCBCTTSCBSSCEEEEEEEEE
T ss_pred             ccccCcCCCeEEEEeeCCCCCcceEEEEEeCC-CcccCCCccEEEEEeCCHHHHHHHHhCCCCCCCcCCCCEEEEEceEE
Confidence            47899999999999999999999999999998 69999999999999999999999999999999999999999999987


Q ss_pred             c
Q 007792          163 E  163 (589)
Q Consensus       163 ~  163 (589)
                      .
T Consensus       175 ~  175 (185)
T 4fru_A          175 E  175 (185)
T ss_dssp             E
T ss_pred             e
Confidence            3

>3k2c_A Peptidyl-prolyl CIS-trans isomerase; ssgcid, NIH, niaid, SBRI, UW, decode, cytoplasm, rotamase, structural genomics; HET: PG5; 1.95A {Encephalitozoon cuniculi}

Probab=100.00  E-value=1e-40  Score=314.79  Aligned_cols=147  Identities=41%  Similarity=0.664  Sum_probs=137.2

Q ss_pred             ecceeEEEEecCCCChhHHHHHHHHHh--cCc-cCCceEEEeecCcccccCCC-CCCCCCCCCcccccccccccccCCcc
Q 007792            7 TSLGDIVVDLFVDKCPLTTKNFLKLCK--IKY-YNGCLFHTVQKDFTAQTGDP-TGTGTGGDSVYKFLYGEQARFFGDEI   82 (589)
Q Consensus         7 T~~G~i~ieL~~~~aP~~~~nF~~l~~--~~~-Y~g~~f~rv~~~~~iq~Gd~-~~~~~~~~~~~~~~~~~~~~~~~~e~   82 (589)
                      |++|+|+|+||++.||+||+||++||+  .++ |+|+.||||+|+|||||||+ .+++.++.++|+       ..|++| 
T Consensus        39 t~~G~I~ieL~~~~aP~tv~NF~~L~~g~~g~~Y~g~~FhRvi~~f~iQgGd~~~~~g~gg~si~g-------~~f~dE-  110 (193)
T 3k2c_A           39 ESLGRIVMKLEDDIVPKTAKNFRTLCERPKGEGYKGSTFHRIIPGFMVQGGDYTAHNGTGGRSIYG-------EKFPDE-  110 (193)
T ss_dssp             EEEEEEEEEECTTTSHHHHHHHHHHHHSCTTSSSTTCBEEEEETTTEEEECCTTTSSSSCCCCTTS-------SCBCCC-
T ss_pred             EEeeEEEEEEcCCCChHHHHHHHHHhccccCCcccCCEEEEEeCCCEEEeCCCCCCCCcCCcccCC-------Cccccc-
Confidence            889999999999999999999999998  567 99999999999999999994 578889999887       568888 


Q ss_pred             ccCCCCCCCceEEEeccCCCCCcceEEEEeCCCCCCCCCCcceEEEEecCHHHHHHHhhCccCCCCCcc--cceeecccc
Q 007792           83 RVDLKHAKTGTVAMASAGENLNASQFYMTLRDNLDYLDEKHTIFGEVAEGLETLSRINESFVDEKNRPY--KNIRIKHTY  160 (589)
Q Consensus        83 ~~~l~~~~~G~vs~a~~g~~~~~sqFfI~l~~~~~~ld~~~~vFG~Vv~G~~vl~~i~~~~~~~~~~p~--~~i~I~~~~  160 (589)
                      .+.++|+.+|+||||+.++++++|||||+|.+ +|+||++|+|||+|++||+||++|++++++ .++|.  .+|+|.+|+
T Consensus       111 ~~~l~h~~~G~lsmAn~gp~t~gSQFFIt~~~-~~~LDg~~tVFG~Vv~Gmdvv~~I~~~~t~-~g~P~~~~~v~I~~cG  188 (193)
T 3k2c_A          111 NFELKHTKEGILSMANCGAHTNGSQFFITLGK-TQWLDEKHVVFGEVVEGMDVVHKIAKYGSE-SGQVKKGYRIEIRDCG  188 (193)
T ss_dssp             CCCSCCCSTTEEEECCSSTTCBCSCEEEESSC-CGGGTTTSCEEEEEEECHHHHHHHHTTCCT-TCCCCTTCCEEEEEEE
T ss_pred             ccccccCCCcEEEEEeCCCCCCccEEEEECCC-CcccCCCccEEEEEeCCHHHHHHHHhcCCC-CCcCccCccEEEEEce
Confidence            68899999999999999999999999999998 699999999999999999999999999887 67999  999999999


Q ss_pred             ccc
Q 007792          161 ILE  163 (589)
Q Consensus       161 vl~  163 (589)
                      +|.
T Consensus       189 ~l~  191 (193)
T 3k2c_A          189 VLG  191 (193)
T ss_dssp             ECC
T ss_pred             EeC
Confidence            985

>1ihg_A Cyclophilin 40; ppiase immunophilin tetratricopeptide, isomerase; 1.80A {Bos taurus} SCOP: a.118.8.1 b.62.1.1 PDB: 1iip_A

Probab=100.00  E-value=1.1e-37  Score=328.62  Aligned_cols=154  Identities=38%  Similarity=0.601  Sum_probs=143.6

Q ss_pred             EEEEec-----ceeEEEEecCCCChhHHHHHHHHHhc--------C---ccCCceEEEeecCcccccCCCC-CCCCCCCC
Q 007792            3 VLIVTS-----LGDIVVDLFVDKCPLTTKNFLKLCKI--------K---YYNGCLFHTVQKDFTAQTGDPT-GTGTGGDS   65 (589)
Q Consensus         3 v~~~T~-----~G~i~ieL~~~~aP~~~~nF~~l~~~--------~---~Y~g~~f~rv~~~~~iq~Gd~~-~~~~~~~~   65 (589)
                      |.|+|+     +|+|+|+||++.||+||+||+.||++        |   ||+||.||||+|+|||||||++ ++|+++.+
T Consensus        18 v~~~~~~~~~~~G~i~~~l~~~~~P~t~~nf~~l~~~~~~~~~~~g~~~~y~~~~fhrv~~~f~~q~Gd~~~~~g~g~~~   97 (370)
T 1ihg_A           18 VFFDVDIGGERVGRIVLELFADIVPKTAENFRALCTGEKGIGPTTGKPLHFKGCPFHRIIKKFMIQGGDFSNQNGTGGES   97 (370)
T ss_dssp             EEEEEEETTEEEEEEEEEECTTTCHHHHHHHHHHHHCTTCBCTTTSSBSCCTTCBEEEEETTTEEEECCTTTSSSSCCCB
T ss_pred             EEEEEEECCEecccEEEEEcCCCCchHHHHHHHHcCCCcCcCccCCCcceeCCcEeEEEECCcEEECCCCCCCCCCCCCC
Confidence            677776     89999999999999999999999997        6   7999999999999999999998 88999999


Q ss_pred             cccccccccccccCCccccCCCCCCCceEEEeccCCCCCcceEEEEeCCCCCCCCCCcceEEEEecCHHHHHHHhhCccC
Q 007792           66 VYKFLYGEQARFFGDEIRVDLKHAKTGTVAMASAGENLNASQFYMTLRDNLDYLDEKHTIFGEVAEGLETLSRINESFVD  145 (589)
Q Consensus        66 ~~~~~~~~~~~~~~~e~~~~l~~~~~G~vs~a~~g~~~~~sqFfI~l~~~~~~ld~~~~vFG~Vv~G~~vl~~i~~~~~~  145 (589)
                      ||+       ..|++| .+.++|+.+|+||||+.|+++|+||||||+.+ +||||++|||||+|++||+||++|..++++
T Consensus        98 ~~~-------~~~~~e-~~~~~~~~~g~l~ma~~~~~~~~sqffi~~~~-~~~ld~~~~vfG~v~~g~~v~~~i~~~~~~  168 (370)
T 1ihg_A           98 IYG-------EKFEDE-NFHYKHDKEGLLSMANAGSNTNGSQFFITTVP-TPHLDGKHVVFGQVIKGMGVAKILENVEVK  168 (370)
T ss_dssp             TTB-------SCBCCC-CCCBCCCSTTEEEECCSSTTCBCSCEEEESSC-CGGGTTTSCEEEEEEECHHHHHHHHTSCEE
T ss_pred             CCC-------CCcCCC-cCCcCCCCCeEEEEeeCCCCCCCceEEEeCCC-CcccCCCceEEEEEecCHHHHHHHHcCCCC
Confidence            997       678899 46899999999999999999999999999998 699999999999999999999999999988


Q ss_pred             CCCCcccceeecccccccCCC
Q 007792          146 EKNRPYKNIRIKHTYILEDPF  166 (589)
Q Consensus       146 ~~~~p~~~i~I~~~~vl~~p~  166 (589)
                      . ++|..+|+|..|+++..+.
T Consensus       169 ~-~~P~~~v~I~~~g~l~~~~  188 (370)
T 1ihg_A          169 G-EKPAKLCVIAECGELKEGD  188 (370)
T ss_dssp             T-TEESSCEEEEEEEEECTTC
T ss_pred             C-CccceeEEEEEEEEeccCc
Confidence            7 8999999999999986543

>3rfy_A Peptidyl-prolyl CIS-trans isomerase CYP38, chloro; cyclophilin, peptidyl prolyl isomerase, ppiase, TLP,; 2.39A {Arabidopsis thaliana}

Probab=100.00  E-value=5e-35  Score=298.43  Aligned_cols=133  Identities=26%  Similarity=0.395  Sum_probs=114.0

Q ss_pred             EEEEEec--------ceeEEEEecCCCChhHHHHHHHHHhcCccCCceEEEeecCcccccCCCCCCCCCC----------
Q 007792            2 SVLIVTS--------LGDIVVDLFVDKCPLTTKNFLKLCKIKYYNGCLFHTVQKDFTAQTGDPTGTGTGG----------   63 (589)
Q Consensus         2 ~v~~~T~--------~G~i~ieL~~~~aP~~~~nF~~l~~~~~Y~g~~f~rv~~~~~iq~Gd~~~~~~~~----------   63 (589)
                      +|.|.|+        +|+|+|+||++.||+||+||++||+.+||+|+.|||| ++|||||||++++++++          
T Consensus       172 ~V~m~t~~~~~~~~~~G~I~IeL~~d~AP~Tv~NFl~L~~~GfYdGt~FHRV-~gFmIQgGDp~g~G~G~~~~~~g~~~~  250 (369)
T 3rfy_A          172 SVDMKVKIKDNPNIEDCVFRIVLDGYNAPVTAGNFVDLVERHFYDGMEIQRS-DGFVVQTGDPEGPAEGFIDPSTEKTRT  250 (369)
T ss_dssp             EEEEEEECCSCSSCSEEEEEEEEETTTCHHHHHHHHHHHHTTTTTTEECEEE-EEEEECCCCCCCCCSCCCSCCCCCCCS
T ss_pred             EEEEEEeccCCCcccceEEEEEEeCCCCcHHHHHHHHHhhcCCcCCCeeeee-CCeeEecCCCCCCCCCccCcccCcCcc
Confidence            5778886        9999999999999999999999999999999999999 99999999999877662          


Q ss_pred             -----------CCcccccccccccccCCc----cccCCCCCCCceEEEecc--CCCCCcceEEEEeCC------CCCCCC
Q 007792           64 -----------DSVYKFLYGEQARFFGDE----IRVDLKHAKTGTVAMASA--GENLNASQFYMTLRD------NLDYLD  120 (589)
Q Consensus        64 -----------~~~~~~~~~~~~~~~~~e----~~~~l~~~~~G~vs~a~~--g~~~~~sqFfI~l~~------~~~~ld  120 (589)
                                 .++|+       ..|++|    ..+.|+|+.+|+||||+.  ++++++||||||+.+      .++|||
T Consensus       251 iP~E~~~~G~g~piyg-------~~fedegf~~~~~~L~h~~~G~LsMAns~~gPnSngSQFFItl~d~~L~~~~~~~LD  323 (369)
T 3rfy_A          251 VPLEIMVTGEKTPFYG-------STLEELGLYKAQVVIPFNAFGTMAMAREEFENDSGSSQVFWLLKESELTPSNSNILD  323 (369)
T ss_dssp             SSSSSCSSSSCCSCCC-------SSTGGGTEEEEEEEECCCCCCCCCCSSCCCCCCCSSCCCCCCCEEEEECSCCCSSSC
T ss_pred             cCccccccCCCCCcCC-------CccccccccccccccccCCCceEEEeecCCCCCCccceEEEEecccccCCCCCcccC
Confidence                       22222       223343    135788889999999998  899999999999942      379999


Q ss_pred             CCcceEEEEecCHHHHHHHhhC
Q 007792          121 EKHTIFGEVAEGLETLSRINES  142 (589)
Q Consensus       121 ~~~~vFG~Vv~G~~vl~~i~~~  142 (589)
                      ++|+|||+|++||+||++|+..
T Consensus       324 gkytVFG~VveGmdVVdkI~~G  345 (369)
T 3rfy_A          324 GRYAVFGYVTDNEDFLADLKVG  345 (369)
T ss_dssp             SCEEEEEEEEESTTGGGGCCTT
T ss_pred             CCeeEEEEEecCHHHHHHHhCC
Confidence            9999999999999999999764

>3pgw_S U1-70K; protein-RNA complex, U1 snRNA, SM fold, SM core, RRM, splici SNRNPS, splicing factors; HET: DNA; 4.40A {Homo sapiens} PDB: 3cw1_K 2l5i_A 2l5j_A*

Probab=99.95  E-value=7.2e-27  Score=249.73  Aligned_cols=85  Identities=28%  Similarity=0.497  Sum_probs=80.6

Q ss_pred             CCCCceEEEecCCCCCCHHHHHHHhccCCCeEEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHhcCCceeCCeEEEEEe
Q 007792          239 KPPENVLFVCKLNPVTEDEDLHTIFSRFGTVVSAEIIRDFKTGDSLNYAFIEFENRQACERAYSKMDNALIDDRRIHVDF  318 (589)
Q Consensus       239 ~~~~~~i~V~nL~~~~te~~L~~~F~~~G~v~~~~i~~d~~tg~~~g~aFV~f~~~~~a~~A~~~l~g~~i~gr~i~V~~  318 (589)
                      ..+.++|||+|||+.||+++|..+|++||.|+.|.|+.++.||+++|||||+|.+.++|.+||..|||+.|+|+.|.|.|
T Consensus        99 ~~~~~~lfV~nL~~~~te~~L~~~F~~~G~I~~v~i~~d~~tg~~kG~aFV~F~~~e~A~~Ai~~lng~~i~gr~i~V~~  178 (437)
T 3pgw_S           99 GDAFKTLFVARVNYDTTESKLRREFEVYGPIKRIHMVYSKRSGKPRGYAFIEYEHERDMHSAYKHADGKKIDGRRVLVDV  178 (437)
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHHcCCeeEEEeeccCCCCCccceEEEeeccHHHHHHHHHHcCCCEECCEEEEEEE
Confidence            34568999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             ccccc
Q 007792          319 SQSVS  323 (589)
Q Consensus       319 a~~~~  323 (589)
                      +.+..
T Consensus       179 a~~~~  183 (437)
T 3pgw_S          179 ERGRT  183 (437)
T ss_pred             eCCCC
Confidence            98743

>4fxv_A ELAV-like protein 1; RNA recognition motif, putative RNA-binding domain, transcri structural genomics, joint center for structural genomics; 1.90A {Homo sapiens}

Probab=99.82  E-value=6.2e-20  Score=155.32  Aligned_cols=81  Identities=28%  Similarity=0.522  Sum_probs=78.6

Q ss_pred             CCceEEEecCCCCCCHHHHHHHhccCCCeEEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHhcCCceeCCeEEEEEecc
Q 007792          241 PENVLFVCKLNPVTEDEDLHTIFSRFGTVVSAEIIRDFKTGDSLNYAFIEFENRQACERAYSKMDNALIDDRRIHVDFSQ  320 (589)
Q Consensus       241 ~~~~i~V~nL~~~~te~~L~~~F~~~G~v~~~~i~~d~~tg~~~g~aFV~f~~~~~a~~A~~~l~g~~i~gr~i~V~~a~  320 (589)
                      ..++|||+|||+++|+++|.++|++||+|..|.|+.++.+|.++|||||+|.+.++|..||+.|||..|.|++|.|+||+
T Consensus        18 ~gt~lfV~nLp~~~te~~L~~~F~~~G~I~~v~i~~d~~tg~~kG~afV~f~~~~~A~~Ai~~lng~~~~gr~l~V~~Ak   97 (99)
T 4fxv_A           18 QGTNLIVNYLPQNMTQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVTAKDAERAINTLNGLRLQSKTIKVSYAR   97 (99)
T ss_dssp             CCSEEEEESCCTTCCHHHHHHHHHTTSCEEEEEEEECSSSCCEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEECC
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEeEeeecCCCCcccccEEEEECCHHHHHHHHHHhCCCEECCEEEEEEEee
Confidence            46899999999999999999999999999999999999999999999999999999999999999999999999999997


Q ss_pred             c
Q 007792          321 S  321 (589)
Q Consensus       321 ~  321 (589)
                      |
T Consensus        98 P   98 (99)
T 4fxv_A           98 P   98 (99)
T ss_dssp             B
T ss_pred             C
Confidence            6

>3s8s_A Histone-lysine N-methyltransferase SETD1A; chromatin modification, transcription regulation, structural genomics, structural genomics consortium; 1.30A {Homo sapiens}

Probab=99.79  E-value=5.2e-19  Score=152.61  Aligned_cols=84  Identities=17%  Similarity=0.246  Sum_probs=80.5

Q ss_pred             CCCCceEEEecCCCCCCHHHHHHHhccCCCeEEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHhcCCceeCCeEEEEEe
Q 007792          239 KPPENVLFVCKLNPVTEDEDLHTIFSRFGTVVSAEIIRDFKTGDSLNYAFIEFENRQACERAYSKMDNALIDDRRIHVDF  318 (589)
Q Consensus       239 ~~~~~~i~V~nL~~~~te~~L~~~F~~~G~v~~~~i~~d~~tg~~~g~aFV~f~~~~~a~~A~~~l~g~~i~gr~i~V~~  318 (589)
                      .+|.++|||+|||+.+|+++|.++|++||.|..|.|+.++.||+++|||||+|.+.++|.+||+.|||..|.|+.|.|.+
T Consensus         3 ~~p~~~lfV~nL~~~~te~~L~~~F~~~G~i~~v~i~~d~~tg~~rG~aFV~f~~~~~A~~Ai~~lng~~~~gr~i~V~~   82 (110)
T 3s8s_A            3 QIPLKEVTFARLNDNVRETFLKDMCRKYGEVEEVEILLHPRTRKHLGLARVLFTSTRGAKETVKNLHLTSVMGNIIHAQL   82 (110)
T ss_dssp             CSCCCEEEEESCCTTCCHHHHHHHHTTTSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEE
T ss_pred             CCCCcEEEEECCCCCCCHHHHHHHHHhcCCeeEEEEEECCCCCceeeEEEEEECCHHHHHHHHHHhCCCEECCeEEEEEE
Confidence            45778999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             cccc
Q 007792          319 SQSV  322 (589)
Q Consensus       319 a~~~  322 (589)
                      |...
T Consensus        83 a~~~   86 (110)
T 3s8s_A           83 DIKG   86 (110)
T ss_dssp             CSTT
T ss_pred             CCCC
Confidence            9753

>2lxi_A RNA-binding protein 10; NMR {Homo sapiens}

Probab=99.78  E-value=1.5e-19  Score=150.59  Aligned_cols=84  Identities=19%  Similarity=0.385  Sum_probs=77.9

Q ss_pred             CceEEEecCCCCCCHHHHHHHhccCC-CeEEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHhc-CCceeCCeEEEEEec
Q 007792          242 ENVLFVCKLNPVTEDEDLHTIFSRFG-TVVSAEIIRDFKTGDSLNYAFIEFENRQACERAYSKM-DNALIDDRRIHVDFS  319 (589)
Q Consensus       242 ~~~i~V~nL~~~~te~~L~~~F~~~G-~v~~~~i~~d~~tg~~~g~aFV~f~~~~~a~~A~~~l-~g~~i~gr~i~V~~a  319 (589)
                      .++|||+|||+.+|+++|.++|++|| +|..|.|+.++.||.++|||||+|.+.++|.+||+.| ++..|+|++|.|++|
T Consensus         1 S~~i~v~nLp~~~te~~l~~~F~~~G~~v~~v~i~~d~~t~~~rg~aFV~F~~~~~A~~Ai~~~~~~~~~~gr~i~V~~a   80 (91)
T 2lxi_A            1 SNIVMLRMLPQAATEDDIRGQLQSHGVQAREVRLMRNKSSGQSRGFAFVEFSHLQDATRWMEANQHSLNILGQKVSMHYS   80 (91)
T ss_dssp             CCEEEEETCCSSCCHHHHHHHHHHHTCCCSBCCSSSCSSSCCCSSEEEEECSSHHHHHHHHHTTTTEEEETTEEEEEECC
T ss_pred             CCEEEEeCCCCCCCHHHHHHHHHHhCCEeEEEEEEecCCCCCcCceEEEEecCHHHHHHHHHhcCCCeEECCEEEEEEEc
Confidence            36899999999999999999999999 8999999999999999999999999999999999887 457899999999999


Q ss_pred             cccccc
Q 007792          320 QSVSKL  325 (589)
Q Consensus       320 ~~~~~~  325 (589)
                      .++.+.
T Consensus        81 ~~~~~~   86 (91)
T 2lxi_A           81 DPKPKI   86 (91)
T ss_dssp             CSCCCC
T ss_pred             CCCCCC
Confidence            886554

>2lkz_A RNA-binding protein 5; RRM; NMR {Homo sapiens}

Probab=99.76  E-value=6.8e-19  Score=147.46  Aligned_cols=81  Identities=21%  Similarity=0.397  Sum_probs=75.8

Q ss_pred             CCceEEEecCCCCCCHHHHHHHhccCCC--eEEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHhcCCc----eeCCeEE
Q 007792          241 PENVLFVCKLNPVTEDEDLHTIFSRFGT--VVSAEIIRDFKTGDSLNYAFIEFENRQACERAYSKMDNA----LIDDRRI  314 (589)
Q Consensus       241 ~~~~i~V~nL~~~~te~~L~~~F~~~G~--v~~~~i~~d~~tg~~~g~aFV~f~~~~~a~~A~~~l~g~----~i~gr~i  314 (589)
                      .=+||||+|||+.+|+++|.++|++||.  |..|.|+.|+.||+++|||||+|.+.++|..||+.|||.    .|+|++|
T Consensus         8 ~m~tlfV~nL~~~~tee~L~~~F~~~G~i~v~~v~i~~d~~tg~srG~aFV~f~~~~~A~~Ai~~lng~~~~~~i~Gr~i   87 (95)
T 2lkz_A            8 HMDTIILRNIAPHTVVDSIMTALSPYASLAVNNIRLIKDKQTQQNRGFAFVQLSSAMDASQLLQILQSLHPPLKIDGKTI   87 (95)
T ss_dssp             CCCEEEEESCCTTCCHHHHHHHSTTTCCCCGGGEECCCCSSSSSCSSEEEEECSSSHHHHHHHHHHHSSSSCEEETTEEE
T ss_pred             ccCEEEEeCCCCcCCHHHHHHHHHhhCCccEEEEEEEecCCCCCCceEeEEEECCHHHHHHHHHHhcCCCCCceECCEEE
Confidence            3479999999999999999999999995  668999999999999999999999999999999999996    5999999


Q ss_pred             EEEeccc
Q 007792          315 HVDFSQS  321 (589)
Q Consensus       315 ~V~~a~~  321 (589)
                      .|+||++
T Consensus        88 ~V~~Aks   94 (95)
T 2lkz_A           88 GVDFAKS   94 (95)
T ss_dssp             EEEECCC
T ss_pred             EEEEccC
Confidence            9999975

>3bs9_A Nucleolysin TIA-1 isoform P40; RNA recognition motif, RRM, RNA binding domain, RBD, RNA splicing, apoptosis, phosphoprotein, RNA-binding; 1.95A {Homo sapiens}

Probab=99.76  E-value=3.3e-18  Score=140.87  Aligned_cols=83  Identities=25%  Similarity=0.494  Sum_probs=77.4

Q ss_pred             CCCceEEEecCCCCCCHHHHHHHhccCCCeEEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHhcCCceeCCeEEEEEec
Q 007792          240 PPENVLFVCKLNPVTEDEDLHTIFSRFGTVVSAEIIRDFKTGDSLNYAFIEFENRQACERAYSKMDNALIDDRRIHVDFS  319 (589)
Q Consensus       240 ~~~~~i~V~nL~~~~te~~L~~~F~~~G~v~~~~i~~d~~tg~~~g~aFV~f~~~~~a~~A~~~l~g~~i~gr~i~V~~a  319 (589)
                      ++..+|||+|||+.+++++|+++|++||.|..|.|+.++.++.++|||||+|.+.++|..|+..|||..|.|+.|.|.+|
T Consensus         4 ~~~~~l~v~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~~a   83 (87)
T 3bs9_A            4 GSHFHVFVGDLSPEITTAAIAAAFAPFGRISDARVVKDMATGKSKGYGFVSFFNKWDAENAIQQMGGQWLGGRQIRTNWA   83 (87)
T ss_dssp             --CEEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEEE
T ss_pred             CCceEEEEeCCCCCCCHHHHHHHHHhcCCEeEEEEEecCCCCccceEEEEEECCHHHHHHHHHHcCCCEECCeEEEEEec
Confidence            35689999999999999999999999999999999999889999999999999999999999999999999999999999


Q ss_pred             ccc
Q 007792          320 QSV  322 (589)
Q Consensus       320 ~~~  322 (589)
                      +++
T Consensus        84 ~~k   86 (87)
T 3bs9_A           84 TRK   86 (87)
T ss_dssp             C--
T ss_pred             CCC
Confidence            864

>3md1_A Nuclear and cytoplasmic polyadenylated RNA-bindin PUB1; RRM, RBD, RNP, poly(U) binding, nucleus, RNA-binding, binding protein; 1.60A {Saccharomyces cerevisiae} SCOP: d.58.7.0

Probab=99.75  E-value=5.5e-18  Score=138.19  Aligned_cols=80  Identities=26%  Similarity=0.522  Sum_probs=77.6

Q ss_pred             ceEEEecCCCCCCHHHHHHHhccCCCeEEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHhcCCceeCCeEEEEEecccc
Q 007792          243 NVLFVCKLNPVTEDEDLHTIFSRFGTVVSAEIIRDFKTGDSLNYAFIEFENRQACERAYSKMDNALIDDRRIHVDFSQSV  322 (589)
Q Consensus       243 ~~i~V~nL~~~~te~~L~~~F~~~G~v~~~~i~~d~~tg~~~g~aFV~f~~~~~a~~A~~~l~g~~i~gr~i~V~~a~~~  322 (589)
                      .+|||+|||+.+++++|.++|++||.|..+.|+.++.+|.++|||||+|.+.++|..|+..|||..|.|+.|.|.++.++
T Consensus         2 ~~l~V~nlp~~~t~~~l~~~f~~~G~i~~~~i~~~~~~~~~~g~afV~f~~~~~a~~a~~~l~g~~~~g~~l~v~~a~~~   81 (83)
T 3md1_A            2 FNLFVGDLNVNVDDETLRNAFKDFPSYLSGHVMWDMQTGSSRGYGFVSFTSQDDAQNAMDSMQGQDLNGRPLRINWAAKL   81 (83)
T ss_dssp             EEEEEECCCTTCCHHHHHHHHTTSTTEEEEEEEECTTTCCEEEEEEEEESCHHHHHHHHHHHTTCEETTEECEEEECCCC
T ss_pred             eEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEEcCCCCCccceEEEEECCHHHHHHHHHHhcCCeeCCcEEEEEecCcC
Confidence            68999999999999999999999999999999999999999999999999999999999999999999999999999874

>2cq0_A Eukaryotic translation initiation factor 3 subunit 4; RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.75  E-value=6.8e-18  Score=143.78  Aligned_cols=86  Identities=24%  Similarity=0.418  Sum_probs=81.5

Q ss_pred             CCCCCceEEEecCCCCCCHHHHHHHhccCCCeEEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHhcCCceeCCeEEEEE
Q 007792          238 IKPPENVLFVCKLNPVTEDEDLHTIFSRFGTVVSAEIIRDFKTGDSLNYAFIEFENRQACERAYSKMDNALIDDRRIHVD  317 (589)
Q Consensus       238 ~~~~~~~i~V~nL~~~~te~~L~~~F~~~G~v~~~~i~~d~~tg~~~g~aFV~f~~~~~a~~A~~~l~g~~i~gr~i~V~  317 (589)
                      ...+.++|||+|||+.+|+++|.++|++||.|..|.|+.++.++.++|||||+|.+.++|..||..|||..|.|+.|.|.
T Consensus        11 ~~~~~~~l~V~nlp~~~t~~~l~~~f~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~   90 (103)
T 2cq0_A           11 RADDNATIRVTNLSEDTRETDLQELFRPFGSISRIYLAKDKTTGQSKGFAFISFHRREDAARAIAGVSGFGYDHLILNVE   90 (103)
T ss_dssp             CCSSSEEEEEESCCTTCCHHHHHTTSTTTCCEEEEEEEECSSSCSEEEEEEEEESSHHHHHHHHHHTTTCEETTEECEEE
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHhCCCeEEEEEeecCCCCceeeEEEEEECCHHHHHHHHHHcCCCeeCCcEEEEE
Confidence            35567999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             eccccc
Q 007792          318 FSQSVS  323 (589)
Q Consensus       318 ~a~~~~  323 (589)
                      ++++..
T Consensus        91 ~a~~~~   96 (103)
T 2cq0_A           91 WAKPST   96 (103)
T ss_dssp             ESSCCC
T ss_pred             ECCCCC
Confidence            998744

>2cqc_A Arginine/serine-rich splicing factor 10; RNA recognition motif, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.75  E-value=8e-18  Score=140.97  Aligned_cols=85  Identities=29%  Similarity=0.447  Sum_probs=80.5

Q ss_pred             CCCCCCceEEEecCCCCCCHHHHHHHhccCCCeEEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHhcCCceeCCeEEEE
Q 007792          237 DIKPPENVLFVCKLNPVTEDEDLHTIFSRFGTVVSAEIIRDFKTGDSLNYAFIEFENRQACERAYSKMDNALIDDRRIHV  316 (589)
Q Consensus       237 ~~~~~~~~i~V~nL~~~~te~~L~~~F~~~G~v~~~~i~~d~~tg~~~g~aFV~f~~~~~a~~A~~~l~g~~i~gr~i~V  316 (589)
                      ...++.++|||+|||+.+++++|.++|++||.|..|.|+.++.++.++|||||+|.+.++|..||..|||..|.|+.|.|
T Consensus        10 ~~~~~~~~l~v~nlp~~~t~~~l~~~f~~~G~v~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v   89 (95)
T 2cqc_A           10 ANPDPNCCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKERANGMELDGRRIRV   89 (95)
T ss_dssp             CSCCGGGCEEEESCCSSCCHHHHHHHHHTTSCEEEEEEEECSSSSSEEEEEEEEESSHHHHHHHHHHHTTEEETTEEEEE
T ss_pred             CCCCCCCEEEEECCCCCCCHHHHHHHHHhcCCeeEEEEEEcCCCCCcccEEEEEECCHHHHHHHHHHhCCCEECCEEEEE
Confidence            34567789999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             Eeccc
Q 007792          317 DFSQS  321 (589)
Q Consensus       317 ~~a~~  321 (589)
                      .+|++
T Consensus        90 ~~a~~   94 (95)
T 2cqc_A           90 SGPSS   94 (95)
T ss_dssp             ECCSC
T ss_pred             EecCC
Confidence            99874

>3mdf_A Peptidyl-prolyl CIS-trans isomerase E; RRM domain, PHD finger, CYP33, MLL, RNA binding protein, ISO mRNA processing, mRNA splicing, nucleus; 1.85A {Homo sapiens} SCOP: d.58.7.1 PDB: 2kyx_A 3lpy_A*

Probab=99.75  E-value=4.9e-18  Score=139.14  Aligned_cols=82  Identities=28%  Similarity=0.487  Sum_probs=78.6

Q ss_pred             CCCCceEEEecCCCCCCHHHHHHHhccCCCeEEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHhcCCceeCCeEEEEEe
Q 007792          239 KPPENVLFVCKLNPVTEDEDLHTIFSRFGTVVSAEIIRDFKTGDSLNYAFIEFENRQACERAYSKMDNALIDDRRIHVDF  318 (589)
Q Consensus       239 ~~~~~~i~V~nL~~~~te~~L~~~F~~~G~v~~~~i~~d~~tg~~~g~aFV~f~~~~~a~~A~~~l~g~~i~gr~i~V~~  318 (589)
                      .++.++|||+|||+.+++++|.++|++||.|..|.|+.++.++.++|||||+|.+.++|..|+..|||..|.|+.|.|++
T Consensus         4 ~~~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~   83 (85)
T 3mdf_A            4 ATTKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNMNESELFGRTIRVNL   83 (85)
T ss_dssp             CCCSSEEEEECCCTTCCHHHHHHHHGGGSCEEEEECCEETTTTEECSEEEEEESSHHHHHHHHHHHTTCEETTEECEEEE
T ss_pred             CCCCCEEEEECCCCCCCHHHHHHHHhccCCEEEEEEEECCCCCccccEEEEEECCHHHHHHHHHHhCCCEECCcEEEEEE
Confidence            45679999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             cc
Q 007792          319 SQ  320 (589)
Q Consensus       319 a~  320 (589)
                      |+
T Consensus        84 ak   85 (85)
T 3mdf_A           84 AK   85 (85)
T ss_dssp             CC
T ss_pred             cC
Confidence            84

>2x1f_A MRNA 3'-END-processing protein RNA15; transcription-RNA complex, mRNA processing; 1.60A {Saccharomyces cerevisiae} PDB: 2x1b_A 2x1a_A 2km8_B

Probab=99.75  E-value=6.5e-18  Score=141.99  Aligned_cols=85  Identities=22%  Similarity=0.412  Sum_probs=80.7

Q ss_pred             CCceEEEecCCCCCCHHHHHHHhccCCCeEEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHhcCCceeCCeEEEEEecc
Q 007792          241 PENVLFVCKLNPVTEDEDLHTIFSRFGTVVSAEIIRDFKTGDSLNYAFIEFENRQACERAYSKMDNALIDDRRIHVDFSQ  320 (589)
Q Consensus       241 ~~~~i~V~nL~~~~te~~L~~~F~~~G~v~~~~i~~d~~tg~~~g~aFV~f~~~~~a~~A~~~l~g~~i~gr~i~V~~a~  320 (589)
                      |.++|||+|||+.+++++|.++|++||.|..|.|+.++.+|.++|||||+|.+.++|..|+..|||..|+|+.|.|.+|.
T Consensus         1 P~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~~a~   80 (96)
T 2x1f_A            1 PSRVVYLGSIPYDQTEEQILDLCSNVGPVINLKMMFDPQTGRSKGYAFIEFRDLESSASAVRNLNGYQLGSRFLKCGYSS   80 (96)
T ss_dssp             CCSEEEEESCCTTCCHHHHHHHHHTTSCEEEEECCBCTTTCCBCSEEEEEESSHHHHHHHHHHHTTCEETTEECEEEECS
T ss_pred             CCcEEEEECCCCCCCHHHHHHHHHhcCCEEEEEEEeCCCCCccceEEEEEECCHHHHHHHHHHhCCCeECCeEEEEEEcC
Confidence            46899999999999999999999999999999999999999999999999999999999999999999999999999998


Q ss_pred             ccccc
Q 007792          321 SVSKL  325 (589)
Q Consensus       321 ~~~~~  325 (589)
                      +....
T Consensus        81 ~~~~~   85 (96)
T 2x1f_A           81 NSDIS   85 (96)
T ss_dssp             CSSGG
T ss_pred             CCCCC
Confidence            75543

>2dnz_A Probable RNA-binding protein 23; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.74  E-value=7e-18  Score=141.35  Aligned_cols=84  Identities=24%  Similarity=0.407  Sum_probs=80.2

Q ss_pred             CCCceEEEecCCCCCCHHHHHHHhccCCCeEEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHhcCCceeCCeEEEEEec
Q 007792          240 PPENVLFVCKLNPVTEDEDLHTIFSRFGTVVSAEIIRDFKTGDSLNYAFIEFENRQACERAYSKMDNALIDDRRIHVDFS  319 (589)
Q Consensus       240 ~~~~~i~V~nL~~~~te~~L~~~F~~~G~v~~~~i~~d~~tg~~~g~aFV~f~~~~~a~~A~~~l~g~~i~gr~i~V~~a  319 (589)
                      ++.++|||+|||+.+|+++|.++|++||.|..|.|+.++.+++++|||||+|.+.++|..||..|||..|.|+.|.|.++
T Consensus         3 ~~~~~l~v~nlp~~~t~~~l~~~f~~~G~v~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V~~a   82 (95)
T 2dnz_A            3 SGSSGLYVGSLHFNITEDMLRGIFEPFGKIDNIVLMKDSDTGRSKGYGFITFSDSECARRALEQLNGFELAGRPMRVGHV   82 (95)
T ss_dssp             SCCCEEEEESCCTTCCHHHHHHHHTTTSCEEEEEEECCSSSCCCCSEEEEEESCHHHHHHHHHHHTTCCSSSSCCEEEES
T ss_pred             CCCcEEEEeCCCCCCCHHHHHHHHHhcCCEeEEEEeecCCCCceeeEEEEEECCHHHHHHHHHHhCCCeeCCcEEEEEEc
Confidence            46789999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             cccc
Q 007792          320 QSVS  323 (589)
Q Consensus       320 ~~~~  323 (589)
                      .+..
T Consensus        83 ~~~~   86 (95)
T 2dnz_A           83 TERL   86 (95)
T ss_dssp             SCCC
T ss_pred             cccc
Confidence            8744

>1x5u_A Splicing factor 3B subunit 4 (spliceosome associated protein 49) (SAP 49) (SF3B50)...; structure genomics,RRM domain,splicing factor 3B; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.74  E-value=8e-18  Score=143.82  Aligned_cols=88  Identities=23%  Similarity=0.361  Sum_probs=82.3

Q ss_pred             CCCCCCceEEEecCCCCCCHHHHHHHhccCCCeEEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHhcCCceeCCeEEEE
Q 007792          237 DIKPPENVLFVCKLNPVTEDEDLHTIFSRFGTVVSAEIIRDFKTGDSLNYAFIEFENRQACERAYSKMDNALIDDRRIHV  316 (589)
Q Consensus       237 ~~~~~~~~i~V~nL~~~~te~~L~~~F~~~G~v~~~~i~~d~~tg~~~g~aFV~f~~~~~a~~A~~~l~g~~i~gr~i~V  316 (589)
                      ....+.++|||+|||+.+|+++|.++|++||.|..|.|+.++.++.++|||||+|.+.++|..||..|||..|.|+.|.|
T Consensus        10 ~~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v   89 (105)
T 1x5u_A           10 SERNQDATVYVGGLDEKVSEPLLWELFLQAGPVVNTHMPKDRVTGQHQGYGFVEFLSEEDADYAIKIMDMIKLYGKPIRV   89 (105)
T ss_dssp             CCCCTTTEEEEECCCTTCCHHHHHHHHHTTSCEEEEECCBCSSSCSBCSCEEEEESSHHHHHHHHHHSSSCBCSSCBCEE
T ss_pred             ccCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEecCCCCcCCcEEEEEECCHHHHHHHHHHhCCCeECCeEEEE
Confidence            34557789999999999999999999999999999999999889999999999999999999999999999999999999


Q ss_pred             Eecccccc
Q 007792          317 DFSQSVSK  324 (589)
Q Consensus       317 ~~a~~~~~  324 (589)
                      .++.+...
T Consensus        90 ~~a~~~~~   97 (105)
T 1x5u_A           90 NKASAHNK   97 (105)
T ss_dssp             EETTTTSC
T ss_pred             EECCCCCc
Confidence            99987543

>2e5h_A Zinc finger CCHC-type and RNA-binding motif- containing protein 1; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.74  E-value=1.2e-17  Score=139.73  Aligned_cols=83  Identities=27%  Similarity=0.452  Sum_probs=79.2

Q ss_pred             CCCCCceEEEecCCCCCCHHHHHHHhccCCCeEEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHhcCCceeCCeEEEEE
Q 007792          238 IKPPENVLFVCKLNPVTEDEDLHTIFSRFGTVVSAEIIRDFKTGDSLNYAFIEFENRQACERAYSKMDNALIDDRRIHVD  317 (589)
Q Consensus       238 ~~~~~~~i~V~nL~~~~te~~L~~~F~~~G~v~~~~i~~d~~tg~~~g~aFV~f~~~~~a~~A~~~l~g~~i~gr~i~V~  317 (589)
                      ..++.++|||+|||+.+++++|.++|++||+|..|.|+.++.++.++|||||+|.+.++|..|++.|||..|.|+.|.|.
T Consensus        12 ~~~~~~~l~V~nlp~~~t~~~l~~~f~~~G~v~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~   91 (94)
T 2e5h_A           12 LAPSKSTVYVSNLPFSLTNNDLYRIFSKYGKVVKVTIMKDKDTRKSKGVAFILFLDKDSAQNCTRAINNKQLFGRVIKAS   91 (94)
T ss_dssp             CCCCTTSEEEESCCTTSCHHHHHHHTTTTSCEEEEEECCCSSSCCCTTCEEEEESCHHHHHHHHHHTTTEEETTEEEEEE
T ss_pred             CCCCCCEEEEECCCCCCCHHHHHHHHHhcCCeEEEEEEeCCCCCCcccEEEEEECCHHHHHHHHHHcCCCeeCCcEEEEE
Confidence            35567899999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             ecc
Q 007792          318 FSQ  320 (589)
Q Consensus       318 ~a~  320 (589)
                      ||+
T Consensus        92 ~ak   94 (94)
T 2e5h_A           92 IAI   94 (94)
T ss_dssp             ECC
T ss_pred             ecC
Confidence            985

>2dgs_A DAZ-associated protein 1; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.74  E-value=1.1e-17  Score=141.45  Aligned_cols=84  Identities=23%  Similarity=0.388  Sum_probs=79.7

Q ss_pred             CCCCceEEEecCCCCCCHHHHHHHhccCCCeEEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHhcCCceeCCeEEEEEe
Q 007792          239 KPPENVLFVCKLNPVTEDEDLHTIFSRFGTVVSAEIIRDFKTGDSLNYAFIEFENRQACERAYSKMDNALIDDRRIHVDF  318 (589)
Q Consensus       239 ~~~~~~i~V~nL~~~~te~~L~~~F~~~G~v~~~~i~~d~~tg~~~g~aFV~f~~~~~a~~A~~~l~g~~i~gr~i~V~~  318 (589)
                      ..+.++|||+|||+.+|+++|+++|++||.|..|.|+.++.++.++|||||+|.+.++|..||. ||+..|.|+.|.|.+
T Consensus         7 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~-~~~~~~~g~~l~V~~   85 (99)
T 2dgs_A            7 GSKSNKIFVGGIPHNCGETELREYFKKFGVVTEVVMIYDAEKQRPRGFGFITFEDEQSVDQAVN-MHFHDIMGKKVEVKR   85 (99)
T ss_dssp             CSSCCEEEEESCCSSCCHHHHHHHHSSSSCEEEEEECCCTTTCSCCSEEEEEESSHHHHHHHHH-HCCCBSSSCBCEEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEeCCCCCCCCceEEEEECCHHHHHHHHH-hCCCEECCeEEEEEE
Confidence            4567899999999999999999999999999999999999999999999999999999999998 999999999999999


Q ss_pred             ccccc
Q 007792          319 SQSVS  323 (589)
Q Consensus       319 a~~~~  323 (589)
                      +.+..
T Consensus        86 a~~~~   90 (99)
T 2dgs_A           86 AEPRD   90 (99)
T ss_dssp             CCCCC
T ss_pred             CCCCc
Confidence            98744

>1whw_A Hypothetical protein riken cDNA 1200009A02; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, structural genomics; NMR {Mus musculus} SCOP: d.58.7.1

Probab=99.74  E-value=1.3e-17  Score=140.86  Aligned_cols=85  Identities=26%  Similarity=0.383  Sum_probs=80.6

Q ss_pred             CCCCceEEEecCCCCCCHHHHHHHhccCCCeEEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHhcCCceeCCeEEEEEe
Q 007792          239 KPPENVLFVCKLNPVTEDEDLHTIFSRFGTVVSAEIIRDFKTGDSLNYAFIEFENRQACERAYSKMDNALIDDRRIHVDF  318 (589)
Q Consensus       239 ~~~~~~i~V~nL~~~~te~~L~~~F~~~G~v~~~~i~~d~~tg~~~g~aFV~f~~~~~a~~A~~~l~g~~i~gr~i~V~~  318 (589)
                      ..+.++|||+|||+.+|+++|.++|++||+|..|.|+.++.++.++|||||+|.+.++|..||..|||..|.|+.|.|.+
T Consensus         5 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V~~   84 (99)
T 1whw_A            5 SSGSGRLFVRNLSYTSSEEDLEKLFSAYGPLSELHYPIDSLTKKPKGFAFVTFMFPEHAVKAYAEVDGQVFQGRMLHVLP   84 (99)
T ss_dssp             CCSCEEEEEECCCTTCCHHHHHHHHHTTSCEEEEECCCCTTTCCCCSEEEEEESSHHHHHHHHHHTTTEESSSCEEEEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEeEEEEEecCCCCCcCeEEEEEECCHHHHHHHHHHhCCCEECCcEEEEEE
Confidence            34678999999999999999999999999999999999988999999999999999999999999999999999999999


Q ss_pred             ccccc
Q 007792          319 SQSVS  323 (589)
Q Consensus       319 a~~~~  323 (589)
                      +.+..
T Consensus        85 a~~~~   89 (99)
T 1whw_A           85 STIKK   89 (99)
T ss_dssp             CCCCS
T ss_pred             cCCCc
Confidence            98754

>2cqb_A Peptidyl-prolyl CIS-trans isomerase E; RNA recognition motif, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.74  E-value=7.1e-18  Score=143.33  Aligned_cols=86  Identities=27%  Similarity=0.481  Sum_probs=81.4

Q ss_pred             CCCCCceEEEecCCCCCCHHHHHHHhccCCCeEEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHhcCCceeCCeEEEEE
Q 007792          238 IKPPENVLFVCKLNPVTEDEDLHTIFSRFGTVVSAEIIRDFKTGDSLNYAFIEFENRQACERAYSKMDNALIDDRRIHVD  317 (589)
Q Consensus       238 ~~~~~~~i~V~nL~~~~te~~L~~~F~~~G~v~~~~i~~d~~tg~~~g~aFV~f~~~~~a~~A~~~l~g~~i~gr~i~V~  317 (589)
                      ...+.++|||+|||+.+|+++|.++|++||.|..|.|+.++.++.++|||||+|.+.++|..||+.|||..|.|+.|.|.
T Consensus         8 ~~~~~~~l~V~nLp~~~t~~~l~~~f~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~V~   87 (102)
T 2cqb_A            8 MATTKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNMNESELFGRTIRVN   87 (102)
T ss_dssp             SCCCCSCEEEESCCSSCCHHHHHHHHTTTSCCCCEECCCCSSSCCCSSEEEECCSSHHHHHHHHHHHTTEEETTEEEEEE
T ss_pred             cCCCCCEEEEeCCCCCCCHHHHHHHhhccCCEEEEEEEecCCCCCcceEEEEEECCHHHHHHHHHHhCCCEECCcEEEEE
Confidence            34577999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             eccccc
Q 007792          318 FSQSVS  323 (589)
Q Consensus       318 ~a~~~~  323 (589)
                      ++.+..
T Consensus        88 ~a~~~~   93 (102)
T 2cqb_A           88 LAKPMR   93 (102)
T ss_dssp             ECCCCC
T ss_pred             eCCCCC
Confidence            998744

>2dgo_A Cytotoxic granule-associated RNA binding protein 1; RRM domain, structural genomics, NPPSFA; NMR {Mus musculus} PDB: 2rne_A 2dh7_A

Probab=99.74  E-value=3.1e-17  Score=142.60  Aligned_cols=86  Identities=27%  Similarity=0.518  Sum_probs=81.3

Q ss_pred             CCCCceEEEecCCCCCCHHHHHHHhccCCCeEEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHhcCCceeCCeEEEEEe
Q 007792          239 KPPENVLFVCKLNPVTEDEDLHTIFSRFGTVVSAEIIRDFKTGDSLNYAFIEFENRQACERAYSKMDNALIDDRRIHVDF  318 (589)
Q Consensus       239 ~~~~~~i~V~nL~~~~te~~L~~~F~~~G~v~~~~i~~d~~tg~~~g~aFV~f~~~~~a~~A~~~l~g~~i~gr~i~V~~  318 (589)
                      ..+.++|||+|||+.+|+++|+++|++||.|..|.|+.++.++.++|||||+|.+.++|+.||..|||..|.|+.|.|.+
T Consensus        12 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V~~   91 (115)
T 2dgo_A           12 TSNHFHVFVGDLSPEITTEDIKAAFAPFGRISDARVVKDMATGKSKGYGFVSFFNKWDAENAIQQMGGQWLGGRQIRTNW   91 (115)
T ss_dssp             STTCEEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHTTTCEETTEECEEEE
T ss_pred             CCCCcEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEEcCCCCCcceEEEEEECCHHHHHHHHHHhCCCEECCEEEEEEE
Confidence            45678999999999999999999999999999999999988999999999999999999999999999999999999999


Q ss_pred             cccccc
Q 007792          319 SQSVSK  324 (589)
Q Consensus       319 a~~~~~  324 (589)
                      +.+...
T Consensus        92 a~~~~~   97 (115)
T 2dgo_A           92 ATRKPP   97 (115)
T ss_dssp             SSCCCC
T ss_pred             ccCCCC
Confidence            987543

>2dnm_A SRP46 splicing factor; RRM domain, RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.74  E-value=7e-18  Score=143.69  Aligned_cols=85  Identities=26%  Similarity=0.363  Sum_probs=80.5

Q ss_pred             CCCCceEEEecCCCCCCHHHHHHHhccCCCeEEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHhcCCceeCCeEEEEEe
Q 007792          239 KPPENVLFVCKLNPVTEDEDLHTIFSRFGTVVSAEIIRDFKTGDSLNYAFIEFENRQACERAYSKMDNALIDDRRIHVDF  318 (589)
Q Consensus       239 ~~~~~~i~V~nL~~~~te~~L~~~F~~~G~v~~~~i~~d~~tg~~~g~aFV~f~~~~~a~~A~~~l~g~~i~gr~i~V~~  318 (589)
                      ..+.++|||+|||+.+|+++|.++|++||.|..|.|+.++.++.++|||||+|.+.++|..||..|||..|.|+.|.|.+
T Consensus        10 ~~~~~~l~V~nLp~~~t~~~l~~~f~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~V~~   89 (103)
T 2dnm_A           10 VDGMITLKVDNLTYRTSPDSLRRVFEKYGRVGDVYIPREPHTKAPRGFAFVRFHDRRDAQDAEAAMDGAELDGRELRVQV   89 (103)
T ss_dssp             CSCCCEEEEESCCTTCCHHHHHHHHTTTSCEEEEECCBCSSSCSBCSCEEEEESSSSHHHHHHHHHSSCCBTTBCCEEEE
T ss_pred             CCCCeEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEeCCCCCCCCeEEEEEECCHHHHHHHHHHcCCCEECCcEEEEEE
Confidence            44678999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             ccccc
Q 007792          319 SQSVS  323 (589)
Q Consensus       319 a~~~~  323 (589)
                      |++..
T Consensus        90 a~~~~   94 (103)
T 2dnm_A           90 ARYGR   94 (103)
T ss_dssp             CSSCC
T ss_pred             CCcCC
Confidence            98743

>2la6_A RNA-binding protein FUS; structural genomics, northeast structural genomics consortiu PSI-biology, protein structure initiative, RNA recognition; NMR {Homo sapiens}

Probab=99.74  E-value=8.6e-18  Score=142.08  Aligned_cols=85  Identities=20%  Similarity=0.305  Sum_probs=80.2

Q ss_pred             CCCCCCCceEEEecCCCCCCHHHHHHHhccCCCeEE--------EEEeecCCCCCcccEEEEEEcCHHHHHHHHHhcCCc
Q 007792          236 ADIKPPENVLFVCKLNPVTEDEDLHTIFSRFGTVVS--------AEIIRDFKTGDSLNYAFIEFENRQACERAYSKMDNA  307 (589)
Q Consensus       236 ~~~~~~~~~i~V~nL~~~~te~~L~~~F~~~G~v~~--------~~i~~d~~tg~~~g~aFV~f~~~~~a~~A~~~l~g~  307 (589)
                      ....++.++|||+|||+.+|+++|+++|++||.|..        |.|+.++.+|.++|||||+|.+.++|..||+.|||.
T Consensus         7 ~~~~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~~~~~~~~~v~i~~~~~~g~~~G~afV~f~~~~~a~~Ai~~l~g~   86 (99)
T 2la6_A            7 HHSHSDNNTIFVQGLGENVTIESVADYFKQIGIIKTNKKTGQPMINLYTDRETGKLKGEATVSFDDPPSAKAAIDWFDGK   86 (99)
T ss_dssp             CCSCCCCSEEEEECCCSSCCHHHHHHHHTTTSCBCEETTTTEESEEEEECTTTCSEEEEEEEEBSSHHHHHHHHHHHTTC
T ss_pred             CCCCCCCCEEEEeCCCCCCCHHHHHHHHHHhCCEeeccccccccEEEEecCCCCCeeeEEEEEECCHHHHHHHHHHhCCC
Confidence            344667899999999999999999999999999999        999999999999999999999999999999999999


Q ss_pred             eeCCeEEEEEecc
Q 007792          308 LIDDRRIHVDFSQ  320 (589)
Q Consensus       308 ~i~gr~i~V~~a~  320 (589)
                      .|.|+.|.|++|+
T Consensus        87 ~~~g~~l~V~~A~   99 (99)
T 2la6_A           87 EFSGNPIKVSFAT   99 (99)
T ss_dssp             BSSSSBCEEEECC
T ss_pred             EeCCcEEEEEecC
Confidence            9999999999984

>2do4_A Squamous cell carcinoma antigen recognized by T- cells 3; RRM domaim, RDB, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.73  E-value=1.9e-17  Score=140.12  Aligned_cols=84  Identities=27%  Similarity=0.398  Sum_probs=79.6

Q ss_pred             CCCCceEEEecCCCCCCHHHHHHHhccCCCeEEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHhcCCceeCCeEEEEEe
Q 007792          239 KPPENVLFVCKLNPVTEDEDLHTIFSRFGTVVSAEIIRDFKTGDSLNYAFIEFENRQACERAYSKMDNALIDDRRIHVDF  318 (589)
Q Consensus       239 ~~~~~~i~V~nL~~~~te~~L~~~F~~~G~v~~~~i~~d~~tg~~~g~aFV~f~~~~~a~~A~~~l~g~~i~gr~i~V~~  318 (589)
                      ..+.++|||+|||+.+|+++|.++|++||.|..|.|+.++ +|+++|||||+|.+.++|..||..|||..|.|+.|.|.+
T Consensus        14 ~~~~~~l~v~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~-~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~   92 (100)
T 2do4_A           14 SLEKHKLFISGLPFSCTKEELEEICKAHGTVKDLRLVTNR-AGKPKGLAYVEYENESQASQAVMKMDGMTIKENIIKVAI   92 (100)
T ss_dssp             CCCCSCEEEESCCTTCCHHHHHHHHTTTSCEEEEEEEECT-TSCEEEEEEEEESSHHHHHHHHHHHTTEESSSCEEEEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhCCCeEEEEEEECC-CCCEEeEEEEEECCHHHHHHHHHHhCCCEECCEEEEEEE
Confidence            4567899999999999999999999999999999999997 899999999999999999999999999999999999999


Q ss_pred             ccccc
Q 007792          319 SQSVS  323 (589)
Q Consensus       319 a~~~~  323 (589)
                      +++..
T Consensus        93 a~~~~   97 (100)
T 2do4_A           93 SNSGP   97 (100)
T ss_dssp             CCCCS
T ss_pred             CCCCC
Confidence            98744

>1x5t_A Splicing factor 3B subunit 4; structure genomics, RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.73  E-value=7.3e-18  Score=141.54  Aligned_cols=84  Identities=30%  Similarity=0.529  Sum_probs=80.0

Q ss_pred             CCCceEEEecCCCCCCHHHHHHHhccCCCeEEE-EEeecCCCCCcccEEEEEEcCHHHHHHHHHhcCCceeCCeEEEEEe
Q 007792          240 PPENVLFVCKLNPVTEDEDLHTIFSRFGTVVSA-EIIRDFKTGDSLNYAFIEFENRQACERAYSKMDNALIDDRRIHVDF  318 (589)
Q Consensus       240 ~~~~~i~V~nL~~~~te~~L~~~F~~~G~v~~~-~i~~d~~tg~~~g~aFV~f~~~~~a~~A~~~l~g~~i~gr~i~V~~  318 (589)
                      .+.++|||+|||+.+|+++|.++|++||.|..| .|+.++.++.++|||||+|.+.++|..||..|||..|.|+.|.|.+
T Consensus         3 ~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~~~~i~~~~~~g~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~~   82 (96)
T 1x5t_A            3 SGSSGIFIGNLDPEIDEKLLYDTFSAFGVILQTPKIMRDPDTGNSKGYAFINFASFDASDAAIEAMNGQYLCNRPITVSY   82 (96)
T ss_dssp             SCCCEEEEECCCTTCCHHHHHHHHHTTSCBSSCCEECCCTTTCSCCSEEEEEBSSHHHHHHHHHTTTTCEETTEECEEEE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEEEcCCCCCcCeEEEEEECCHHHHHHHHHHcCCCEECCEEEEEEE
Confidence            467899999999999999999999999999999 9999989999999999999999999999999999999999999999


Q ss_pred             ccccc
Q 007792          319 SQSVS  323 (589)
Q Consensus       319 a~~~~  323 (589)
                      +.+..
T Consensus        83 a~~~~   87 (96)
T 1x5t_A           83 AFKKD   87 (96)
T ss_dssp             SCCCC
T ss_pred             ecccC
Confidence            98744

>3ex7_B RNA-binding protein 8A; protein-RNA complex, mRNA processing, mRNA splicing, mRNA transport, nonsense-mediated mRNA decay, nucleus; HET: ADP; 2.30A {Homo sapiens} PDB: 2j0q_D*

Probab=99.73  E-value=5.7e-18  Score=149.81  Aligned_cols=89  Identities=20%  Similarity=0.353  Sum_probs=82.4

Q ss_pred             CCCCCCCceEEEecCCCCCCHHHHHHHhccCCCeEEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHhcCCceeCCeEEE
Q 007792          236 ADIKPPENVLFVCKLNPVTEDEDLHTIFSRFGTVVSAEIIRDFKTGDSLNYAFIEFENRQACERAYSKMDNALIDDRRIH  315 (589)
Q Consensus       236 ~~~~~~~~~i~V~nL~~~~te~~L~~~F~~~G~v~~~~i~~d~~tg~~~g~aFV~f~~~~~a~~A~~~l~g~~i~gr~i~  315 (589)
                      .....+.++|||+|||+.+|+++|.++|++||.|..|.|+.++.++.++|||||+|.+.++|..||..|||..|.|+.|.
T Consensus        16 ~~~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~   95 (126)
T 3ex7_B           16 PQRSVEGWILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEGLNGQDLMGQPIS   95 (126)
T ss_dssp             BCCCSSSEEEEEESCCTTCCHHHHHHHHHTTSCEEEEECCBCTTTSSBCSCEEEEESSHHHHHHHHHHHTTCBSSSSBCE
T ss_pred             CCCCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEecCCCCccceEEEEEECCHHHHHHHHHHhCCCeeCCeEEE
Confidence            33455678999999999999999999999999999999999988999999999999999999999999999999999999


Q ss_pred             EEecccccc
Q 007792          316 VDFSQSVSK  324 (589)
Q Consensus       316 V~~a~~~~~  324 (589)
                      |++|.+...
T Consensus        96 v~~a~~~~~  104 (126)
T 3ex7_B           96 VDWCFVRGP  104 (126)
T ss_dssp             EEESEESSS
T ss_pred             EEEecCCCC
Confidence            999987543

>2cpz_A CUG triplet repeat RNA-binding protein 1; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1 PDB: 2rq4_A 2rqc_A

Probab=99.73  E-value=9.4e-18  Score=145.93  Aligned_cols=86  Identities=29%  Similarity=0.447  Sum_probs=81.2

Q ss_pred             CCCCCceEEEecCCCCCCHHHHHHHhccCCCeEEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHhcCCceeCCeEEEEE
Q 007792          238 IKPPENVLFVCKLNPVTEDEDLHTIFSRFGTVVSAEIIRDFKTGDSLNYAFIEFENRQACERAYSKMDNALIDDRRIHVD  317 (589)
Q Consensus       238 ~~~~~~~i~V~nL~~~~te~~L~~~F~~~G~v~~~~i~~d~~tg~~~g~aFV~f~~~~~a~~A~~~l~g~~i~gr~i~V~  317 (589)
                      ..++.++|||+|||+.+++++|+++|++||.|..|.|+.++.++.++|||||+|.+.++|..||..|||..|.|+.|.|.
T Consensus        21 ~~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V~  100 (115)
T 2cpz_A           21 EGPEGANLFIYHLPQEFGDQDLLQMFMPFGNVVSAKVFIDKQTNLSKCFGFVSYDNPVSAQAAIQSMNGFQIGMKRLKVQ  100 (115)
T ss_dssp             CCSTTCCEEEESCCSSCCHHHHHHHHGGGSCCSEEEEEECSSSCSEEEEEEEECSSHHHHHHHHHHHTTCEETTEECEEE
T ss_pred             CCCCCcEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEECCCCCCcCccEEEEECCHHHHHHHHHHcCCCEECCEEEEEE
Confidence            34567899999999999999999999999999999999999899999999999999999999999999999999999999


Q ss_pred             eccccc
Q 007792          318 FSQSVS  323 (589)
Q Consensus       318 ~a~~~~  323 (589)
                      ++++..
T Consensus       101 ~a~~~~  106 (115)
T 2cpz_A          101 LKRSKN  106 (115)
T ss_dssp             CCCCSC
T ss_pred             EcCCCC
Confidence            998754

>1p27_B RNA-binding protein 8A; nuclear protein, mRNA splicing; 2.00A {Homo sapiens} SCOP: d.58.7.1

Probab=99.73  E-value=8.5e-18  Score=143.92  Aligned_cols=85  Identities=21%  Similarity=0.376  Sum_probs=80.5

Q ss_pred             CCCCceEEEecCCCCCCHHHHHHHhccCCCeEEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHhcCCceeCCeEEEEEe
Q 007792          239 KPPENVLFVCKLNPVTEDEDLHTIFSRFGTVVSAEIIRDFKTGDSLNYAFIEFENRQACERAYSKMDNALIDDRRIHVDF  318 (589)
Q Consensus       239 ~~~~~~i~V~nL~~~~te~~L~~~F~~~G~v~~~~i~~d~~tg~~~g~aFV~f~~~~~a~~A~~~l~g~~i~gr~i~V~~  318 (589)
                      ..+.++|||+|||+.+|+++|.++|++||.|..|.|+.++.+|.++|||||+|.+.++|..||..|||..|.|+.|.|.+
T Consensus        20 ~~~~~~l~V~nlp~~~t~~~l~~~f~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V~~   99 (106)
T 1p27_B           20 SVEGWILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEGLNGQDLMGQPISVDW   99 (106)
T ss_dssp             BTTBEEEEEECCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTSSEEEEEEEEESCHHHHHHHHHHHTTCBSSSSBCEEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHhccCCeEEEEEEecCCCCceeeEEEEEECCHHHHHHHHHHhcCCEECCcEEEEEe
Confidence            44568999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             ccccc
Q 007792          319 SQSVS  323 (589)
Q Consensus       319 a~~~~  323 (589)
                      |.+..
T Consensus       100 a~~~~  104 (106)
T 1p27_B          100 CFVRG  104 (106)
T ss_dssp             SEESS
T ss_pred             ecCCC
Confidence            98743

>1x4h_A RNA-binding protein 28; structural genomics, RRM domain, NPPSFA, national project on protein structural and functional analyses; NMR {Mus musculus} SCOP: d.58.7.1

Probab=99.73  E-value=1.8e-17  Score=143.02  Aligned_cols=86  Identities=20%  Similarity=0.350  Sum_probs=81.3

Q ss_pred             CCCCCceEEEecCCCCCCHHHHHHHhccCCCeEEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHhcC------CceeCC
Q 007792          238 IKPPENVLFVCKLNPVTEDEDLHTIFSRFGTVVSAEIIRDFKTGDSLNYAFIEFENRQACERAYSKMD------NALIDD  311 (589)
Q Consensus       238 ~~~~~~~i~V~nL~~~~te~~L~~~F~~~G~v~~~~i~~d~~tg~~~g~aFV~f~~~~~a~~A~~~l~------g~~i~g  311 (589)
                      ...+.++|||+|||+.+|+++|.++|.+||.|..|.|+.++.++.++|||||+|.+.++|..||..||      |..|.|
T Consensus        11 ~~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~A~~~~~~~~~~~~~~~~g   90 (111)
T 1x4h_A           11 DVTEGKTVFIRNLSFDSEEEALGEVLQQFGDLKYVRVVLHPDTEHSKGCAFAQFMTQEAAQKCLAAASLEAEGGGLKLDG   90 (111)
T ss_dssp             CCCCCCCEEEESCCTTCCHHHHHHHHHTTSCEEEEECCBCSSSCCBCSEEEEEESSHHHHHHHHHHHCTTTTTCCEESSS
T ss_pred             cCCCCCEEEEECCCCCCCHHHHHHHHHhcCCeEEEEEEecCCCCCCccEEEEEECCHHHHHHHHHHhccccccCCcEEcC
Confidence            35567899999999999999999999999999999999999999999999999999999999999999      999999


Q ss_pred             eEEEEEeccccc
Q 007792          312 RRIHVDFSQSVS  323 (589)
Q Consensus       312 r~i~V~~a~~~~  323 (589)
                      +.|.|.++.+..
T Consensus        91 ~~l~v~~a~~~~  102 (111)
T 1x4h_A           91 RQLKVDLAVTRD  102 (111)
T ss_dssp             CEEEEECCCCCC
T ss_pred             EEEEEEECCCCc
Confidence            999999998743

>3p5t_L Cleavage and polyadenylation specificity factor S; RRM domain, poly(A) site recognition, RNA, nuclear, RNA BIND protein; 2.70A {Homo sapiens} PDB: 3p6y_C

Probab=99.73  E-value=1.8e-18  Score=143.67  Aligned_cols=81  Identities=16%  Similarity=0.272  Sum_probs=73.1

Q ss_pred             ceEEEecCCCCCCHHHHHHHhccCC--CeEEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHhcCCceeCCeEEEEEecc
Q 007792          243 NVLFVCKLNPVTEDEDLHTIFSRFG--TVVSAEIIRDFKTGDSLNYAFIEFENRQACERAYSKMDNALIDDRRIHVDFSQ  320 (589)
Q Consensus       243 ~~i~V~nL~~~~te~~L~~~F~~~G--~v~~~~i~~d~~tg~~~g~aFV~f~~~~~a~~A~~~l~g~~i~gr~i~V~~a~  320 (589)
                      .+|||+|||+.+|+++|+++|++||  .|..|.|+.++.+|+++|||||+|.+.++|.+||+.|||..|+|+.|.|.++.
T Consensus         2 ~~l~V~nL~~~~t~~~l~~~F~~~G~~~v~~v~i~~~~~~g~~kG~afV~f~~~~~a~~Ai~~l~g~~~~gr~i~V~~~~   81 (90)
T 3p5t_L            2 IALYIGNLTWWTTDEDLTEAVHSLGVNDILEIKFFENRANGQSKGFALVGVGSEASSKKLMDLLPKRELHGQNPVVTPSN   81 (90)
T ss_dssp             --CEEESCCTTCCHHHHHHHHHTTTCCCCCCEEEEECTTTCCEEEEEEECC-CHHHHHHHHHHGGGSCSSSCCCEECCC-
T ss_pred             eEEEEeCCCCCCCHHHHHHHHHHhCCCceEEEEEEecCCCCccCcEEEEEECCHHHHHHHHHHcCCCeeCCEEEEEEECC
Confidence            5899999999999999999999999  99999999999999999999999999999999999999999999999999998


Q ss_pred             ccc
Q 007792          321 SVS  323 (589)
Q Consensus       321 ~~~  323 (589)
                      +..
T Consensus        82 ~~~   84 (90)
T 3p5t_L           82 KLE   84 (90)
T ss_dssp             ---
T ss_pred             CCc
Confidence            754

>2cqd_A RNA-binding region containing protein 1; RNA recognition motif, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.73  E-value=3.8e-17  Score=142.31  Aligned_cols=84  Identities=31%  Similarity=0.457  Sum_probs=79.5

Q ss_pred             CCCCCceEEEecCCCCCCHHHHHHHhccCCCeEEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHhcCCceeCCeEEEEE
Q 007792          238 IKPPENVLFVCKLNPVTEDEDLHTIFSRFGTVVSAEIIRDFKTGDSLNYAFIEFENRQACERAYSKMDNALIDDRRIHVD  317 (589)
Q Consensus       238 ~~~~~~~i~V~nL~~~~te~~L~~~F~~~G~v~~~~i~~d~~tg~~~g~aFV~f~~~~~a~~A~~~l~g~~i~gr~i~V~  317 (589)
                      ...+.++|||+|||+.+|+++|+++|++||.|..|.|+.++.+++++|||||+|.+.++|++||..|++ .|.|+.|.|.
T Consensus        13 ~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~Ai~~~~~-~~~g~~l~V~   91 (116)
T 2cqd_A           13 KDTTFTKIFVGGLPYHTTDASLRKYFEGFGDIEEAVVITDRQTGKSRGYGFVTMADRAAAERACKDPNP-IIDGRKANVN   91 (116)
T ss_dssp             CSCSSSEEEEECCCSSCCHHHHHHHHHTTSCEEEEEESCCSSSCCCCSEEEEEESSHHHHHHHHTCSSC-EETTEECEEE
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHhCCCeeEEEEEEcCCCCccceEEEEEECCHHHHHHHHHhCCC-cCCCEEEEEE
Confidence            355678999999999999999999999999999999999999999999999999999999999999998 8999999999


Q ss_pred             ecccc
Q 007792          318 FSQSV  322 (589)
Q Consensus       318 ~a~~~  322 (589)
                      ++.+.
T Consensus        92 ~a~~~   96 (116)
T 2cqd_A           92 LAYLG   96 (116)
T ss_dssp             ESTTT
T ss_pred             EcccC
Confidence            99764

>2cpf_A RNA binding motif protein 19; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Mus musculus} SCOP: d.58.7.1

Probab=99.73  E-value=1.4e-17  Score=140.39  Aligned_cols=84  Identities=23%  Similarity=0.445  Sum_probs=78.8

Q ss_pred             CCCceEEEecCCCCCCHHHHHHHhccCCCeEEEEEeecCC---CCCcccEEEEEEcCHHHHHHHHHhcCCceeCCeEEEE
Q 007792          240 PPENVLFVCKLNPVTEDEDLHTIFSRFGTVVSAEIIRDFK---TGDSLNYAFIEFENRQACERAYSKMDNALIDDRRIHV  316 (589)
Q Consensus       240 ~~~~~i~V~nL~~~~te~~L~~~F~~~G~v~~~~i~~d~~---tg~~~g~aFV~f~~~~~a~~A~~~l~g~~i~gr~i~V  316 (589)
                      ++.++|||+|||+.+|+++|.++|++||.|..|.|+.++.   |+.++|||||+|.+.++|..||..|||..|.|+.|.|
T Consensus         3 ~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~gt~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V   82 (98)
T 2cpf_A            3 SGSSGLFIKNLNFSTTEETLKGVFSKVGAIKSCTISKKKNKAGVLLSMGFGFVEYKKPEQAQKALKQLQGHTVDGHKLEV   82 (98)
T ss_dssp             CCCCCEEEESCCTTCCHHHHHHHHHTTSCEEEEEEEEEECTTCCEEEEEEEEEEESSHHHHHHHHHHSTTCEETTEECEE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEecCCCCCCcCcccEEEEEECCHHHHHHHHHHhCCCeeCCeEEEE
Confidence            4678999999999999999999999999999999998876   6689999999999999999999999999999999999


Q ss_pred             Eeccccc
Q 007792          317 DFSQSVS  323 (589)
Q Consensus       317 ~~a~~~~  323 (589)
                      .++.+..
T Consensus        83 ~~a~~~~   89 (98)
T 2cpf_A           83 RISERAT   89 (98)
T ss_dssp             ECSSCSS
T ss_pred             EEccCCC
Confidence            9998744

>2dng_A Eukaryotic translation initiation factor 4H; RRM domain, RBD, structural genomics, NPPSFA; NMR {Mus musculus}

Probab=99.73  E-value=3.2e-17  Score=139.63  Aligned_cols=83  Identities=25%  Similarity=0.457  Sum_probs=78.4

Q ss_pred             CCCCceEEEecCCCCCCHHHHHHHhccCCCeEEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHhcCCceeCCeEEEEEe
Q 007792          239 KPPENVLFVCKLNPVTEDEDLHTIFSRFGTVVSAEIIRDFKTGDSLNYAFIEFENRQACERAYSKMDNALIDDRRIHVDF  318 (589)
Q Consensus       239 ~~~~~~i~V~nL~~~~te~~L~~~F~~~G~v~~~~i~~d~~tg~~~g~aFV~f~~~~~a~~A~~~l~g~~i~gr~i~V~~  318 (589)
                      ..+.++|||+|||+.+|+++|.++|++|| |..|.|+.++.+++++|||||+|.+.++|..|| .|||..|.|+.|.|.+
T Consensus        12 ~~~~~~l~V~nLp~~~t~~~l~~~F~~~g-i~~v~i~~~~~~g~~~g~afV~f~~~~~a~~A~-~l~g~~~~g~~l~V~~   89 (103)
T 2dng_A           12 TEPPYTAYVGNLPFNTVQGDIDAIFKDLS-IRSVRLVRDKDTDKFKGFCYVEFDEVDSLKEAL-TYDGALLGDRSLRVDI   89 (103)
T ss_dssp             SSSCEEEEEESCCTTCCHHHHHHHTTTSC-EEEEEEEECSSSCSEEEEEEEEESSHHHHHHHG-GGTTCEETTEECEEEE
T ss_pred             CCCCeEEEEeCCCCCCCHHHHHHHHHhCC-ceEEEEeecCCCCccceEEEEEECCHHHHHHHH-hhCCCeECCeEEEEEE
Confidence            45678999999999999999999999997 999999999999999999999999999999999 8999999999999999


Q ss_pred             ccccc
Q 007792          319 SQSVS  323 (589)
Q Consensus       319 a~~~~  323 (589)
                      +.+..
T Consensus        90 a~~~~   94 (103)
T 2dng_A           90 AEGRK   94 (103)
T ss_dssp             CCCCC
T ss_pred             ecCCC
Confidence            98743

>1x5s_A Cold-inducible RNA-binding protein; structure genomics, RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.73  E-value=1.1e-17  Score=142.10  Aligned_cols=86  Identities=29%  Similarity=0.492  Sum_probs=81.2

Q ss_pred             CCCCCceEEEecCCCCCCHHHHHHHhccCCCeEEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHhcCCceeCCeEEEEE
Q 007792          238 IKPPENVLFVCKLNPVTEDEDLHTIFSRFGTVVSAEIIRDFKTGDSLNYAFIEFENRQACERAYSKMDNALIDDRRIHVD  317 (589)
Q Consensus       238 ~~~~~~~i~V~nL~~~~te~~L~~~F~~~G~v~~~~i~~d~~tg~~~g~aFV~f~~~~~a~~A~~~l~g~~i~gr~i~V~  317 (589)
                      ...+.++|||+|||+.+|+++|.++|++||.|..|.|+.++.++.++|||||+|.+.++|..||+.|||..|.|+.|.|.
T Consensus         8 ~~~~~~~l~v~nLp~~~t~~~l~~~f~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~   87 (102)
T 1x5s_A            8 MASDEGKLFVGGLSFDTNEQSLEQVFSKYGQISEVVVVKDRETQRSRGFGFVTFENIDDAKDAMMAMNGKSVDGRQIRVD   87 (102)
T ss_dssp             CCCCCSEEEEESCCTTCCHHHHHHHHHHHSCCCEEEECCCSSSCSCCSEEEEECSSHHHHHHHHHHHTTCCTTSCCCEEE
T ss_pred             CCCCCCEEEEECCCCCCCHHHHHHHHHhcCCeEEEEEEeCCCCCCcccEEEEEECCHHHHHHHHHHhCCCEECCeEEEEE
Confidence            34567899999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             eccccc
Q 007792          318 FSQSVS  323 (589)
Q Consensus       318 ~a~~~~  323 (589)
                      ++++..
T Consensus        88 ~a~~~~   93 (102)
T 1x5s_A           88 QAGKSS   93 (102)
T ss_dssp             EEECCC
T ss_pred             ECCCCC
Confidence            998744

>2jrs_A RNA-binding protein 39; RNA binding motif of RBM39_human (caper), RRM2 domain, solution structure, structural genomics, PSI-2; NMR {Homo sapiens}

Probab=99.72  E-value=1.4e-17  Score=143.25  Aligned_cols=85  Identities=24%  Similarity=0.386  Sum_probs=80.6

Q ss_pred             CCCCCceEEEecCCCCCCHHHHHHHhccCCCeEEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHhcCCceeCCeEEEEE
Q 007792          238 IKPPENVLFVCKLNPVTEDEDLHTIFSRFGTVVSAEIIRDFKTGDSLNYAFIEFENRQACERAYSKMDNALIDDRRIHVD  317 (589)
Q Consensus       238 ~~~~~~~i~V~nL~~~~te~~L~~~F~~~G~v~~~~i~~d~~tg~~~g~aFV~f~~~~~a~~A~~~l~g~~i~gr~i~V~  317 (589)
                      ..++.++|||+|||+.+|+++|.++|++||.|..|.|+.++.+|.++|||||+|.+.++|..||..|||..|.|+.|.|.
T Consensus        22 ~~~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~F~~~~~A~~Ai~~l~g~~i~g~~l~V~  101 (108)
T 2jrs_A           22 GSAGPMRLYVGSLHFNITEDMLRGIFEPFGRIESIQLMMDSETGRSKGYGFITFSDSECAKKALEQLNGFELAGRPMKVG  101 (108)
T ss_dssp             SCSSCEEEEEECCCSSCCHHHHHHHHTTTSCEEEEEEEEETTTTEEEEEEEEEESCHHHHHHHHHHHTTCCSSSSCCEEE
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEEcCCCCccceEEEEEECCHHHHHHHHHHcCCCEECCEEEEEE
Confidence            35567899999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             ecccc
Q 007792          318 FSQSV  322 (589)
Q Consensus       318 ~a~~~  322 (589)
                      +++++
T Consensus       102 ~a~~k  106 (108)
T 2jrs_A          102 HVTER  106 (108)
T ss_dssp             CSCSS
T ss_pred             EcccC
Confidence            99764

>1oo0_B CG8781-PA, drosophila Y14; RNA recognition motif, splicing, protein complex, EXON junct complex, signaling protein; 1.85A {Drosophila melanogaster} SCOP: d.58.7.1 PDB: 2hyi_B* 2j0s_D* 2xb2_D*

Probab=99.72  E-value=1.6e-17  Score=143.27  Aligned_cols=85  Identities=22%  Similarity=0.387  Sum_probs=80.5

Q ss_pred             CCCCceEEEecCCCCCCHHHHHHHhccCCCeEEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHhcCCceeCCeEEEEEe
Q 007792          239 KPPENVLFVCKLNPVTEDEDLHTIFSRFGTVVSAEIIRDFKTGDSLNYAFIEFENRQACERAYSKMDNALIDDRRIHVDF  318 (589)
Q Consensus       239 ~~~~~~i~V~nL~~~~te~~L~~~F~~~G~v~~~~i~~d~~tg~~~g~aFV~f~~~~~a~~A~~~l~g~~i~gr~i~V~~  318 (589)
                      ..+.++|||+|||+.+|+++|.++|++||.|..|.|+.++.+|.++|||||+|.+.++|..||..|||..|.|+.|.|.+
T Consensus        23 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~~  102 (110)
T 1oo0_B           23 SVEGWILFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYETHKQALAAKEALNGAEIMGQTIQVDW  102 (110)
T ss_dssp             BTTBEEEEEESCCTTCCHHHHHHHHGGGSCEEEEECCBCTTTSSBCSEEEEEESSHHHHHHHHHHHTTCEETTEECEEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEecCCCCCcceEEEEEECCHHHHHHHHHHcCCCEECCcEEEEEE
Confidence            45678999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             ccccc
Q 007792          319 SQSVS  323 (589)
Q Consensus       319 a~~~~  323 (589)
                      +.+..
T Consensus       103 a~~~~  107 (110)
T 1oo0_B          103 CFVKG  107 (110)
T ss_dssp             SEESS
T ss_pred             cccCC
Confidence            98643

>3ns6_A Eukaryotic translation initiation factor 3 subuni; 1.25A {Saccharomyces cerevisiae} PDB: 3ns5_A

Probab=99.72  E-value=3.1e-18  Score=145.16  Aligned_cols=83  Identities=19%  Similarity=0.286  Sum_probs=79.2

Q ss_pred             CCceEEEecCCC------CCCHHHHHHHhccCCCeEEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHhcCCceeCC-eE
Q 007792          241 PENVLFVCKLNP------VTEDEDLHTIFSRFGTVVSAEIIRDFKTGDSLNYAFIEFENRQACERAYSKMDNALIDD-RR  313 (589)
Q Consensus       241 ~~~~i~V~nL~~------~~te~~L~~~F~~~G~v~~~~i~~d~~tg~~~g~aFV~f~~~~~a~~A~~~l~g~~i~g-r~  313 (589)
                      ..++|||+|||+      .+++++|.++|++||.|..|.|+.++.||+++|||||+|.+.++|.+||+.|||..|.| +.
T Consensus         5 ~~~~vfV~nLp~v~~~~~~~~~~~L~~~F~~~G~i~~v~i~~d~~tg~~kG~afV~f~~~~~A~~Ai~~lng~~~~g~r~   84 (100)
T 3ns6_A            5 SDQYIVVNGAPVIPSAKVPVLKKALTSLFSKAGKVVNMEFPIDEATGKTKGFLFVECGSMNDAKKIIKSFHGKRLDLKHR   84 (100)
T ss_dssp             GGGEEEEESCCCCBGGGHHHHHHHHHHHHHTTSCEEEEECCEETTTTEECSEEEEEESSHHHHHHHHHHHTTCBSSSSCB
T ss_pred             cCcEEEEeCCCcCChHHHHHHHHHHHHHHHhcCCEeEEEEEEcCCCCccceEEEEEECCHHHHHHHHHHhCCcccCCCeE
Confidence            468999999999      99999999999999999999999999999999999999999999999999999999999 99


Q ss_pred             EEEEeccccc
Q 007792          314 IHVDFSQSVS  323 (589)
Q Consensus       314 i~V~~a~~~~  323 (589)
                      |.|.+|.+..
T Consensus        85 l~V~~a~~~~   94 (100)
T 3ns6_A           85 LFLYTMKDVE   94 (100)
T ss_dssp             CEEEESHHHH
T ss_pred             EEEEECchhh
Confidence            9999998643

>2fy1_A RNA-binding motif protein, Y chromosome, family 1 member A1; RNA binding protein, structure, protein-RNA complex, RNA stem-loop, structural protein/RNA complex; NMR {Homo sapiens}

Probab=99.72  E-value=2.1e-17  Score=144.01  Aligned_cols=83  Identities=28%  Similarity=0.448  Sum_probs=78.7

Q ss_pred             CCCceEEEecCCCCCCHHHHHHHhccCCCeEEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHhcCCceeCCeEEEEEec
Q 007792          240 PPENVLFVCKLNPVTEDEDLHTIFSRFGTVVSAEIIRDFKTGDSLNYAFIEFENRQACERAYSKMDNALIDDRRIHVDFS  319 (589)
Q Consensus       240 ~~~~~i~V~nL~~~~te~~L~~~F~~~G~v~~~~i~~d~~tg~~~g~aFV~f~~~~~a~~A~~~l~g~~i~gr~i~V~~a  319 (589)
                      .+.++|||+|||+.+|+++|.++|++||.|..|.|+.+. +|+++|||||+|.+.++|+.||..|||..|.|+.|.|.++
T Consensus         5 ~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~-~g~~~g~afV~F~~~~~A~~Ai~~l~g~~~~g~~l~V~~a   83 (116)
T 2fy1_A            5 DHPGKLFIGGLNRETNEKMLKAVFGKHGPISEVLLIKDR-TSKSRGFAFITFENPADAKNAAKDMNGKSLHGKAIKVEQA   83 (116)
T ss_dssp             CSCCEEEEECCTTTCCHHHHHHHHHTSSCCSEEEEECST-TTTCCCEEEEECSSHHHHHHHHHHCSSCBCSSSBCEEEEC
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEECC-CCCcccEEEEEECCHHHHHHHHHHhCCCEECCEEEEEEEC
Confidence            356899999999999999999999999999999999997 8999999999999999999999999999999999999999


Q ss_pred             cccc
Q 007792          320 QSVS  323 (589)
Q Consensus       320 ~~~~  323 (589)
                      ++..
T Consensus        84 ~~~~   87 (116)
T 2fy1_A           84 KKPS   87 (116)
T ss_dssp             CCSS
T ss_pred             CCCC
Confidence            8744

>1wi8_A EIF-4B, eukaryotic translation initiation factor 4B; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, structural genomics; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.72  E-value=3e-17  Score=139.99  Aligned_cols=83  Identities=18%  Similarity=0.366  Sum_probs=78.4

Q ss_pred             CCCCceEEEecCCCCCCHHHHHHHhccCCCeEEEEEeecCCC-CCcccEEEEEEcCHHHHHHHHHhcCCceeCCeEEEEE
Q 007792          239 KPPENVLFVCKLNPVTEDEDLHTIFSRFGTVVSAEIIRDFKT-GDSLNYAFIEFENRQACERAYSKMDNALIDDRRIHVD  317 (589)
Q Consensus       239 ~~~~~~i~V~nL~~~~te~~L~~~F~~~G~v~~~~i~~d~~t-g~~~g~aFV~f~~~~~a~~A~~~l~g~~i~gr~i~V~  317 (589)
                      ..+.++|||+|||+.+|+++|+++|++|| |..|.|+.++.+ |.++|||||+|.+.++|..|| .|||..|.|+.|.|.
T Consensus        12 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~G-i~~v~i~~~~~~~g~~~g~afV~f~~~~~a~~A~-~l~g~~~~g~~l~V~   89 (104)
T 1wi8_A           12 KSPPYTAFLGNLPYDVTEESIKEFFRGLN-ISAVRLPREPSNPERLKGFGYAEFEDLDSLLSAL-SLNEESLGNKRIRVD   89 (104)
T ss_dssp             SSSCEEEEEESCCSSCCHHHHHHHTTTSC-EEEEECCBCSSCTTSBCSCEEEEESSHHHHHHHH-GGGTCEETTEECEEE
T ss_pred             CCCCCEEEEeCCCCcCCHHHHHHHHHHCC-ceEEEEecCCCCCCCcCeEEEEEECCHHHHHHHH-hcCCCEeCCcEEEEE
Confidence            45678999999999999999999999999 999999999887 999999999999999999999 999999999999999


Q ss_pred             eccccc
Q 007792          318 FSQSVS  323 (589)
Q Consensus       318 ~a~~~~  323 (589)
                      ++.+..
T Consensus        90 ~a~~~~   95 (104)
T 1wi8_A           90 VADQAQ   95 (104)
T ss_dssp             ECCCCC
T ss_pred             EccCCC
Confidence            998744

>2cph_A RNA binding motif protein 19; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Mus musculus} SCOP: d.58.7.1

Probab=99.72  E-value=2.3e-17  Score=141.35  Aligned_cols=86  Identities=17%  Similarity=0.427  Sum_probs=80.8

Q ss_pred             CCCCCceEEEecCCCCCCHHHHHHHhccCCCeEEEEEeec-CCCCCcccEEEEEEcCHHHHHHHHHhc-CCceeCCeEEE
Q 007792          238 IKPPENVLFVCKLNPVTEDEDLHTIFSRFGTVVSAEIIRD-FKTGDSLNYAFIEFENRQACERAYSKM-DNALIDDRRIH  315 (589)
Q Consensus       238 ~~~~~~~i~V~nL~~~~te~~L~~~F~~~G~v~~~~i~~d-~~tg~~~g~aFV~f~~~~~a~~A~~~l-~g~~i~gr~i~  315 (589)
                      ..++.++|||+|||+.+|+++|+++|++||.|..|.|+.+ +.++.++|||||+|.+.++|..||..| ||..|.|+.|.
T Consensus        11 ~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~~~~~~~g~~l~   90 (107)
T 2cph_A           11 KKQTTSKILVRNIPFQANQREIRELFSTFGELKTVRLPKKMTGTGAHRGFGFVDFITKQDAKKAFNALCHSTHLYGRRLV   90 (107)
T ss_dssp             CSSCCCCEEEESCCTTCCHHHHHHHHHTTSCEEEEECCCCCSSSCSSCSEEEEEESSHHHHHHHHHHHHTCCBSSSCBCE
T ss_pred             cCCCCCEEEEeCCCCcCCHHHHHHHHHccCCeEEEEEecCCCCCCCcCceEEEEECCHHHHHHHHHHhccCCeECCCEEE
Confidence            3556789999999999999999999999999999999998 789999999999999999999999999 99999999999


Q ss_pred             EEeccccc
Q 007792          316 VDFSQSVS  323 (589)
Q Consensus       316 V~~a~~~~  323 (589)
                      |.++.+..
T Consensus        91 v~~a~~~~   98 (107)
T 2cph_A           91 LEWADSEV   98 (107)
T ss_dssp             EEECCCCC
T ss_pred             EEeCCCCC
Confidence            99998744

>2d9p_A Polyadenylate-binding protein 3; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.72  E-value=3e-17  Score=139.74  Aligned_cols=83  Identities=25%  Similarity=0.465  Sum_probs=78.6

Q ss_pred             CCCCceEEEecCCCCCCHHHHHHHhccCCCeEEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHhcCCceeCCeEEEEEe
Q 007792          239 KPPENVLFVCKLNPVTEDEDLHTIFSRFGTVVSAEIIRDFKTGDSLNYAFIEFENRQACERAYSKMDNALIDDRRIHVDF  318 (589)
Q Consensus       239 ~~~~~~i~V~nL~~~~te~~L~~~F~~~G~v~~~~i~~d~~tg~~~g~aFV~f~~~~~a~~A~~~l~g~~i~gr~i~V~~  318 (589)
                      ..+.++|||+|||+.+|+++|.++|++||.|..|.|+.+  ++.++|||||+|.+.++|..||..|||..|.|+.|.|.+
T Consensus        12 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~--~g~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~V~~   89 (103)
T 2d9p_A           12 RYQVVNLYVKNLDDGIDDERLRKAFSPFGTITSAKVMME--GGRSKGFGFVCFSSPEEATKAVTEMNGRIVATKPLYVAL   89 (103)
T ss_dssp             CSSCCCEEEECCCTTCCHHHHHHTTTTTSCEEEEEEEEC--SSSEEEEEEEEESSHHHHHHHHHHHTTCBSSSSBCEEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEcC--CCCcCEEEEEEECCHHHHHHHHHHhCCCEeCCcEEEEEE
Confidence            456789999999999999999999999999999999997  889999999999999999999999999999999999999


Q ss_pred             ccccc
Q 007792          319 SQSVS  323 (589)
Q Consensus       319 a~~~~  323 (589)
                      +.+..
T Consensus        90 a~~~~   94 (103)
T 2d9p_A           90 AQRKE   94 (103)
T ss_dssp             CSSCC
T ss_pred             ecccc
Confidence            98754

>2cpe_A RNA-binding protein EWS; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.72  E-value=2.3e-17  Score=143.01  Aligned_cols=87  Identities=20%  Similarity=0.286  Sum_probs=81.2

Q ss_pred             CCCCCceEEEecCCCCCCHHHHHHHhccCCCeE--------EEEEeecCCCCCcccEEEEEEcCHHHHHHHHHhcCCcee
Q 007792          238 IKPPENVLFVCKLNPVTEDEDLHTIFSRFGTVV--------SAEIIRDFKTGDSLNYAFIEFENRQACERAYSKMDNALI  309 (589)
Q Consensus       238 ~~~~~~~i~V~nL~~~~te~~L~~~F~~~G~v~--------~~~i~~d~~tg~~~g~aFV~f~~~~~a~~A~~~l~g~~i  309 (589)
                      ...+.++|||+|||+.+|+++|+++|++||.|.        .|.|+.++.++.++|||||+|.+.++|..||..|||..|
T Consensus        11 ~~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~~~~~~~~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~   90 (113)
T 2cpe_A           11 EDSDNSAIYVQGLNDSVTLDDLADFFKQCGVVKMNKRTGQPMIHIYLDKETGKPKGDATVSYEDPPTAKAAVEWFDGKDF   90 (113)
T ss_dssp             CCCCCCEEEEECCCTTCCHHHHHHHHTTTSCBCBCSSSCCBSEECCBCTTTCSBCSEEEEEBSSHHHHHHHHHHHTTCEE
T ss_pred             cCCCCCEEEEcCCCCCCCHHHHHHHHHhcCCEeEccccCccCEEEEEeCCCCCeeeEEEEEECCHHHHHHHHHHcCCCcc
Confidence            355678999999999999999999999999999        699999999999999999999999999999999999999


Q ss_pred             CCeEEEEEecccccc
Q 007792          310 DDRRIHVDFSQSVSK  324 (589)
Q Consensus       310 ~gr~i~V~~a~~~~~  324 (589)
                      .|+.|.|.++++...
T Consensus        91 ~g~~l~V~~a~~~~~  105 (113)
T 2cpe_A           91 QGSKLKVSLARKKPP  105 (113)
T ss_dssp             TTEECEEECSSCCCC
T ss_pred             CCCEEEEEECCCCCC
Confidence            999999999987543

>3ulh_A THO complex subunit 4; nuclear protein, RNA binding, structural genomi center for structural genomics, JCSG, protein structure INI PSI-biology; 2.54A {Homo sapiens} PDB: 1no8_A

Probab=99.72  E-value=3e-17  Score=140.77  Aligned_cols=81  Identities=25%  Similarity=0.416  Sum_probs=77.5

Q ss_pred             CCCCceEEEecCCCCCCHHHHHHHhccCCCeEEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHhcCCceeCCeEEEEEe
Q 007792          239 KPPENVLFVCKLNPVTEDEDLHTIFSRFGTVVSAEIIRDFKTGDSLNYAFIEFENRQACERAYSKMDNALIDDRRIHVDF  318 (589)
Q Consensus       239 ~~~~~~i~V~nL~~~~te~~L~~~F~~~G~v~~~~i~~d~~tg~~~g~aFV~f~~~~~a~~A~~~l~g~~i~gr~i~V~~  318 (589)
                      ..+.++|||+|||+.+|+++|.++|++||.|..|.|+.++ +|+++|||||+|.+.++|..||..|||..|.|+.|.|++
T Consensus        26 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~-~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V~~  104 (107)
T 3ulh_A           26 VETGGKLLVSNLDFGVSDADIQELFAEFGTLKKAAVHYDR-SGRSLGTADVHFERKADALKAMKQYNGVPLDGRPMNIQL  104 (107)
T ss_dssp             CCCSEEEEEESCCTTCCHHHHHHHHHTTSCEEEEEEEECT-TSCEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEECC-CCCcceEEEEEECCHHHHHHHHHHhCCCEeCCcEEEEEE
Confidence            3567899999999999999999999999999999999997 999999999999999999999999999999999999999


Q ss_pred             cc
Q 007792          319 SQ  320 (589)
Q Consensus       319 a~  320 (589)
                      |.
T Consensus       105 a~  106 (107)
T 3ulh_A          105 VT  106 (107)
T ss_dssp             EC
T ss_pred             eC
Confidence            85

>4f25_A Polyadenylate-binding protein 1; RRM fold, translation initiation, RNA-binding, EIF4G-binding translation; 1.90A {Homo sapiens} PDB: 4f26_A 2k8g_A

Probab=99.72  E-value=2e-17  Score=143.96  Aligned_cols=80  Identities=31%  Similarity=0.570  Sum_probs=74.7

Q ss_pred             CceEEEecCCCCCCHHHHHHHhccCCCeEEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHhcCCceeCCeEEEEEeccc
Q 007792          242 ENVLFVCKLNPVTEDEDLHTIFSRFGTVVSAEIIRDFKTGDSLNYAFIEFENRQACERAYSKMDNALIDDRRIHVDFSQS  321 (589)
Q Consensus       242 ~~~i~V~nL~~~~te~~L~~~F~~~G~v~~~~i~~d~~tg~~~g~aFV~f~~~~~a~~A~~~l~g~~i~gr~i~V~~a~~  321 (589)
                      .++|||+|||+.+|+++|+++|++||.|..|.|+.+.  +.++|||||+|.+.++|+.||+.|||..|+|+.|.|.++.+
T Consensus         5 ~~~lfV~nLp~~~te~~L~~~F~~~G~v~~v~i~~d~--~~~kg~afV~f~~~~~A~~Ai~~l~~~~~~g~~i~V~~a~~   82 (115)
T 4f25_A            5 SGNIFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDE--NGSKGYGFVHFETQEAAERAIEKMNGMLLNDRKVFVGRFKS   82 (115)
T ss_dssp             CCEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEEET--TEEEEEEEEEESCHHHHHHHHHHHTTCEETTEECEEEESSC
T ss_pred             CCEEEECCCCCCCCHHHHHHHHhccCCEEEEEEeecC--CCCCceEEEEECCHHHHHHHHHHcCCCEECCEEEEEEECCC
Confidence            5789999999999999999999999999999999985  44899999999999999999999999999999999999976


Q ss_pred             cc
Q 007792          322 VS  323 (589)
Q Consensus       322 ~~  323 (589)
                      ..
T Consensus        83 ~~   84 (115)
T 4f25_A           83 RK   84 (115)
T ss_dssp             CC
T ss_pred             cc
Confidence            43

>2dnh_A Bruno-like 5, RNA binding protein; RRM domain, RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} PDB: 2dnk_A 2dno_A

Probab=99.72  E-value=3.4e-17  Score=139.91  Aligned_cols=84  Identities=23%  Similarity=0.393  Sum_probs=79.1

Q ss_pred             CCCCceEEEecCCCCCCHHHHHHHhccCCCeEEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHhcCCceeCC---eEEE
Q 007792          239 KPPENVLFVCKLNPVTEDEDLHTIFSRFGTVVSAEIIRDFKTGDSLNYAFIEFENRQACERAYSKMDNALIDD---RRIH  315 (589)
Q Consensus       239 ~~~~~~i~V~nL~~~~te~~L~~~F~~~G~v~~~~i~~d~~tg~~~g~aFV~f~~~~~a~~A~~~l~g~~i~g---r~i~  315 (589)
                      .++.++|||+|||+.+++++|.++|++||.|..|.|+.++ +|.++|||||+|.+.++|..||..|||..|.|   +.|.
T Consensus        12 ~~~~~~l~v~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~-~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~gg~~~~l~   90 (105)
T 2dnh_A           12 GGRDRKLFVGMLNKQQSEEDVLRLFQPFGVIDECTVLRGP-DGSSKGCAFVKFSSHTEAQAAIHALHGSQTMPGASSSLV   90 (105)
T ss_dssp             CCCCCEEEEESCCTTCCHHHHHHHHTTTSCEEEEEEEECS-SSCEEEEEEEEESSHHHHHHHHHHHSSCCCCTTCSSCCE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEECC-CCCcCcEEEEEeCCHHHHHHHHHHHcCCccCCCCCccEE
Confidence            4567999999999999999999999999999999999987 79999999999999999999999999999998   9999


Q ss_pred             EEeccccc
Q 007792          316 VDFSQSVS  323 (589)
Q Consensus       316 V~~a~~~~  323 (589)
                      |.+|.+..
T Consensus        91 V~~a~~~~   98 (105)
T 2dnh_A           91 VKFADTDK   98 (105)
T ss_dssp             EEESCSSC
T ss_pred             EEECccCc
Confidence            99998744

>3s7r_A Heterogeneous nuclear ribonucleoprotein A/B; ferredoxin-like, structural genomics, joint center for struc genomics, JCSG; 2.15A {Homo sapiens} PDB: 1hd0_A 1hd1_A

Probab=99.72  E-value=4.4e-17  Score=134.13  Aligned_cols=80  Identities=29%  Similarity=0.427  Sum_probs=75.6

Q ss_pred             CCCCceEEEecCCCCCCHHHHHHHhccCCCeEEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHhcCCceeCCeEEEEEe
Q 007792          239 KPPENVLFVCKLNPVTEDEDLHTIFSRFGTVVSAEIIRDFKTGDSLNYAFIEFENRQACERAYSKMDNALIDDRRIHVDF  318 (589)
Q Consensus       239 ~~~~~~i~V~nL~~~~te~~L~~~F~~~G~v~~~~i~~d~~tg~~~g~aFV~f~~~~~a~~A~~~l~g~~i~gr~i~V~~  318 (589)
                      ..+.++|||+|||+.+|+++|.++|++||.|..|.|+.++.+|.++|||||+|.+.++|..||+ +++..|+|+.|.|++
T Consensus         8 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~a~~A~~-~~~~~~~g~~i~v~~   86 (87)
T 3s7r_A            8 EEDAGKMFVGGLSWDTSKKDLKDYFTKFGEVVDCTIKMDPNTGRSRGFGFILFKDAASVEKVLD-QKEHRLDGRVIDPKK   86 (87)
T ss_dssp             CSCTTEEEEECCCTTCCHHHHHHHHTTTSCEEEEEEEECTTTCCEEEEEEEEESSTHHHHHHHH-SSCEEETTEEEEEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhCCCEEEEEEeecCCCCccccEEEEEECCHHHHHHHHH-hCCCEECCEEEEEEe
Confidence            4567899999999999999999999999999999999999999999999999999999999995 588899999999998


Q ss_pred             c
Q 007792          319 S  319 (589)
Q Consensus       319 a  319 (589)
                      |
T Consensus        87 A   87 (87)
T 3s7r_A           87 A   87 (87)
T ss_dssp             C
T ss_pred             C
Confidence            6

>2div_A TRNA selenocysteine associated protein; structural genomics, RRM domain, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.72  E-value=1.7e-17  Score=140.19  Aligned_cols=84  Identities=21%  Similarity=0.424  Sum_probs=79.9

Q ss_pred             CCCCceEEEecCCCCCCHHHHHHHhccCCCeE-EEEEeecCCCCCcccEEEEEEcCHHHHHHHHHhcCCceeCCeE----
Q 007792          239 KPPENVLFVCKLNPVTEDEDLHTIFSRFGTVV-SAEIIRDFKTGDSLNYAFIEFENRQACERAYSKMDNALIDDRR----  313 (589)
Q Consensus       239 ~~~~~~i~V~nL~~~~te~~L~~~F~~~G~v~-~~~i~~d~~tg~~~g~aFV~f~~~~~a~~A~~~l~g~~i~gr~----  313 (589)
                      ..+.++|||+|||+.+++++|.++|++||.|. .|.|+.++.++.++|||||+|.+.++|+.||..|||..|.|+.    
T Consensus         6 ~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~~v~i~~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~~~~~   85 (99)
T 2div_A            6 SGMAASLWMGDLEPYMDENFISRAFATMGETVMSVKIIRNRLTGIPAGYCFVEFADLATAEKCLHKINGKPLPGATPAKR   85 (99)
T ss_dssp             CSSSSEEEECSCCTTCCHHHHHHHHHHTTCCCCEEEEEECSSSCCEEEEEEEECSCHHHHHHHHHTTTTSEESSCSSCEE
T ss_pred             CCCccEEEEeCCCCCCCHHHHHHHHHHhCCcceEEEEeecCCCCCcCCEEEEEeCCHHHHHHHHHHHcCCccCCCCccee
Confidence            44678999999999999999999999999999 9999999999999999999999999999999999999999999    


Q ss_pred             EEEEecccc
Q 007792          314 IHVDFSQSV  322 (589)
Q Consensus       314 i~V~~a~~~  322 (589)
                      |.|.||++.
T Consensus        86 l~v~~a~~~   94 (99)
T 2div_A           86 FKLNYATYS   94 (99)
T ss_dssp             CCEEETTCC
T ss_pred             EEEeecCCC
Confidence            999999863

>2dhg_A TRNA selenocysteine associated protein (SECP43); RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.72  E-value=2.2e-17  Score=140.75  Aligned_cols=85  Identities=24%  Similarity=0.446  Sum_probs=79.7

Q ss_pred             CCCCceEEEecCCCCCCHHHHHHHhcc-CCCeEEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHhcCCce-eCCeEEEE
Q 007792          239 KPPENVLFVCKLNPVTEDEDLHTIFSR-FGTVVSAEIIRDFKTGDSLNYAFIEFENRQACERAYSKMDNAL-IDDRRIHV  316 (589)
Q Consensus       239 ~~~~~~i~V~nL~~~~te~~L~~~F~~-~G~v~~~~i~~d~~tg~~~g~aFV~f~~~~~a~~A~~~l~g~~-i~gr~i~V  316 (589)
                      ..+.++|||+|||+.+|+++|.++|++ ||.|..|.|+.++ +|.++|||||+|.+.++|..||..|||.. |.|+.|.|
T Consensus         6 ~~~~~~l~V~nLp~~~t~~~l~~~F~~~~G~v~~v~i~~~~-~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~~g~~l~v   84 (104)
T 2dhg_A            6 SGPEYSLFVGDLTPDVDDGMLYEFFVKVYPSCRGGKVVLDQ-TGVSKGYGFVKFTDELEQKRALTECQGAVGLGSKPVRL   84 (104)
T ss_dssp             SSCCCCEEEECCCTTCCHHHHHHHHHHHCTTEEEEEEEECT-TCCEEEEEEEEESCHHHHHHHHHHTTTCCSSSSSCCCC
T ss_pred             CCCCcEEEEeCCCCCCCHHHHHHHHHHhCCCeEEEEEEECC-CCCccceEEEEECCHHHHHHHHHHccCCcccCCEeEEE
Confidence            446789999999999999999999999 9999999999998 99999999999999999999999999999 99999999


Q ss_pred             Eecccccc
Q 007792          317 DFSQSVSK  324 (589)
Q Consensus       317 ~~a~~~~~  324 (589)
                      .++.+...
T Consensus        85 ~~a~~~~~   92 (104)
T 2dhg_A           85 SVAIPKAS   92 (104)
T ss_dssp             CBCCCCCS
T ss_pred             EEccCCCc
Confidence            99976443

>1u6f_A Tcubp1, RNA-binding protein UBP1; trypanosome, mRNA-binding protein, GU-rich RNA, structure; NMR {Trypanosoma cruzi} SCOP: d.58.7.1

Probab=99.71  E-value=4.3e-17  Score=146.69  Aligned_cols=85  Identities=22%  Similarity=0.404  Sum_probs=80.6

Q ss_pred             CCCCceEEEecCCCCCCHHHHHHHhccCCCeEEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHhcCCceeCCeEEEEEe
Q 007792          239 KPPENVLFVCKLNPVTEDEDLHTIFSRFGTVVSAEIIRDFKTGDSLNYAFIEFENRQACERAYSKMDNALIDDRRIHVDF  318 (589)
Q Consensus       239 ~~~~~~i~V~nL~~~~te~~L~~~F~~~G~v~~~~i~~d~~tg~~~g~aFV~f~~~~~a~~A~~~l~g~~i~gr~i~V~~  318 (589)
                      ..+.++|||+|||+.+|+++|.++|+.||.|..|.|+.++.+++++|||||+|.+.++|..||..|||..|.|+.|.|.+
T Consensus        39 ~~~~~~l~V~nLp~~~~~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~  118 (139)
T 1u6f_A           39 PDVLRNLMVNYIPTTVDEVQLRQLFERYGPIESVKIVCDRETRQSRGYGFVKFQSGSSAQQAIAGLNGFNILNKRLKVAL  118 (139)
T ss_dssp             TTTTSEEEEESCSTTCCHHHHHHHHHHHSCEEEEEEEEETTTTEEEEEEEEEESSHHHHHHHHHHTTTEECSSCEEEEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEEcCCCCCcceEEEEEECCHHHHHHHHHHhCCCEECCeEEEEEE
Confidence            34568999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             ccccc
Q 007792          319 SQSVS  323 (589)
Q Consensus       319 a~~~~  323 (589)
                      |.+..
T Consensus       119 a~~~~  123 (139)
T 1u6f_A          119 AASGH  123 (139)
T ss_dssp             SSCCC
T ss_pred             CCCCC
Confidence            98754

>3ucg_A Polyadenylate-binding protein 2; ferredoxin-like, structural genomics, joint center for struc genomics, JCSG, protein structure initiative; HET: PGE; 1.95A {Homo sapiens} PDB: 3b4d_A 3b4m_A

Probab=99.71  E-value=3.6e-17  Score=135.20  Aligned_cols=80  Identities=23%  Similarity=0.410  Sum_probs=77.1

Q ss_pred             CceEEEecCCCCCCHHHHHHHhccCCCeEEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHhcCCceeCCeEEEEEeccc
Q 007792          242 ENVLFVCKLNPVTEDEDLHTIFSRFGTVVSAEIIRDFKTGDSLNYAFIEFENRQACERAYSKMDNALIDDRRIHVDFSQS  321 (589)
Q Consensus       242 ~~~i~V~nL~~~~te~~L~~~F~~~G~v~~~~i~~d~~tg~~~g~aFV~f~~~~~a~~A~~~l~g~~i~gr~i~V~~a~~  321 (589)
                      .++|||+|||+.+|+++|.++|++||.|..|.|+.++.++.++|||||+|.+.++|..|+ .|||..|.|+.|.|.++++
T Consensus         6 ~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~a~-~~~g~~~~g~~l~V~~a~~   84 (89)
T 3ucg_A            6 ARSIYVGNVDYGATAEELEAHFHGCGSVNRVTILCDKFSGHPKGFAYIEFSDKESVRTSL-ALDESLFRGRQIKVIPKRT   84 (89)
T ss_dssp             HTEEEEESCCTTCCHHHHHHHHGGGCCEEEEEEEESCSSSSCCEEEEEEESSTHHHHHHG-GGTTCEETTEECEEEETTT
T ss_pred             CCEEEEeCCCCCCCHHHHHHHHHhCCCEEEEEEEecCCCCCcceEEEEEECCHHHHHHHH-hcCCCEECCcEEEEEEccC
Confidence            479999999999999999999999999999999999889999999999999999999999 9999999999999999986


Q ss_pred             c
Q 007792          322 V  322 (589)
Q Consensus       322 ~  322 (589)
                      .
T Consensus        85 ~   85 (89)
T 3ucg_A           85 N   85 (89)
T ss_dssp             T
T ss_pred             C
Confidence            4

>2kxn_B Transformer-2 protein homolog beta; SR protein, RRM, splicing factor, RNA protein complex, SMN, binding protein-RNA complex; NMR {Homo sapiens} PDB: 2rra_A 2rrb_A

Probab=99.71  E-value=1.7e-17  Score=147.29  Aligned_cols=87  Identities=31%  Similarity=0.489  Sum_probs=81.8

Q ss_pred             CCCCCCceEEEecCCCCCCHHHHHHHhccCCCeEEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHhcCCceeCCeEEEE
Q 007792          237 DIKPPENVLFVCKLNPVTEDEDLHTIFSRFGTVVSAEIIRDFKTGDSLNYAFIEFENRQACERAYSKMDNALIDDRRIHV  316 (589)
Q Consensus       237 ~~~~~~~~i~V~nL~~~~te~~L~~~F~~~G~v~~~~i~~d~~tg~~~g~aFV~f~~~~~a~~A~~~l~g~~i~gr~i~V  316 (589)
                      ...++.++|||+|||+.+|+++|+++|++||+|..|.|+.++.++.++|||||+|.+.++|+.||..|||..|.|+.|.|
T Consensus        41 ~~~~~~~~l~V~nLp~~~te~~L~~~F~~~G~I~~v~i~~d~~tg~~~G~afV~F~~~~~A~~Ai~~lng~~i~g~~l~V  120 (129)
T 2kxn_B           41 ANPDPNCCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKERANGMELDGRRIRV  120 (129)
T ss_dssp             SCCCCSSCBCEETCTTSCCHHHHHHHHTTTSCEEEEEEECCSSSSCCCCEEEEEESCHHHHHHHHHHHTTCCSSSSCCEE
T ss_pred             CCCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEecCCCCccceEEEEEECCHHHHHHHHHHhCCCEECCEEEEE
Confidence            34567889999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             Eeccccc
Q 007792          317 DFSQSVS  323 (589)
Q Consensus       317 ~~a~~~~  323 (589)
                      .++.++.
T Consensus       121 ~~a~~~~  127 (129)
T 2kxn_B          121 DFSITKR  127 (129)
T ss_dssp             SCCSSSS
T ss_pred             EEecCCC
Confidence            9998743

>4a8x_A RNA-binding protein with serine-rich domain 1; transcription, splicing, RNA processing, nonsense mediated D NMD, HDAC, histone deacetylation; 1.90A {Homo sapiens}

Probab=99.71  E-value=2.2e-17  Score=136.08  Aligned_cols=82  Identities=23%  Similarity=0.386  Sum_probs=77.3

Q ss_pred             CCceEEEecCCCCCCHHHHHHHhccCCCeEEEEEeecCCCCC-cccEEEEEEcCHHHHHHHHHhcCCceeCCeEEEEEec
Q 007792          241 PENVLFVCKLNPVTEDEDLHTIFSRFGTVVSAEIIRDFKTGD-SLNYAFIEFENRQACERAYSKMDNALIDDRRIHVDFS  319 (589)
Q Consensus       241 ~~~~i~V~nL~~~~te~~L~~~F~~~G~v~~~~i~~d~~tg~-~~g~aFV~f~~~~~a~~A~~~l~g~~i~gr~i~V~~a  319 (589)
                      ..++|||+|||+.+|+++|.++|++||.|..|.|+.+..++. ++|||||+|.+.++|..|+..|||..|+|+.|.|.++
T Consensus         3 ~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~~~i~~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a   82 (88)
T 4a8x_A            3 KPTKVHIGRLTRNVTKDHIMEIFSTYGKIKMIDMPVERMHPHLSKGYAYVEFENPDEAEKALKHMDGGQIDGQEITATAV   82 (88)
T ss_dssp             CCCEEEEECCCTTCCHHHHHHHHHTTSCEEEEECCEETTEEEEECSEEEEEESSHHHHHHHHHHHTTCEETTEECEEEEE
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhCCCEEEEEEEeCCCCCCCCCcEEEEEEecHHHHHHHHHHcCCCeECCeEEEEEEC
Confidence            458999999999999999999999999999999999887766 8999999999999999999999999999999999999


Q ss_pred             ccc
Q 007792          320 QSV  322 (589)
Q Consensus       320 ~~~  322 (589)
                      .+.
T Consensus        83 ~~~   85 (88)
T 4a8x_A           83 LAP   85 (88)
T ss_dssp             CCC
T ss_pred             CCC
Confidence            764

>1h2v_Z 20 kDa nuclear CAP binding protein; CAP-binding-complex, RNP domain, MIF4G domain, RNA maturation, RNA export, nuclear protein, RNA-binding; 2.0A {Homo sapiens} SCOP: d.58.7.1 PDB: 1h2u_X* 1h2t_Z 1n52_B* 1n54_B 3fex_B 3fey_B 1h6k_X

Probab=99.71  E-value=4.7e-17  Score=149.54  Aligned_cols=85  Identities=22%  Similarity=0.357  Sum_probs=80.7

Q ss_pred             CCCCceEEEecCCCCCCHHHHHHHhccCCCeEEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHhcCCceeCCeEEEEEe
Q 007792          239 KPPENVLFVCKLNPVTEDEDLHTIFSRFGTVVSAEIIRDFKTGDSLNYAFIEFENRQACERAYSKMDNALIDDRRIHVDF  318 (589)
Q Consensus       239 ~~~~~~i~V~nL~~~~te~~L~~~F~~~G~v~~~~i~~d~~tg~~~g~aFV~f~~~~~a~~A~~~l~g~~i~gr~i~V~~  318 (589)
                      ..+.++|||+|||+.+|+++|.++|++||+|..|.|+.++.++.++|||||+|.+.++|.+||..|||..|.|+.|.|+|
T Consensus        36 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~~  115 (156)
T 1h2v_Z           36 LKKSCTLYVGNLSFYTTEEQIYELFSKSGDIKKIIMGLDKMKKTACGFCFVEYYSRADAENAMRYINGTRLDDRIIRTDW  115 (156)
T ss_dssp             TTTCCEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHTTTSEETTEECEEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEecCCCCccceEEEEEECCHHHHHHHHHHhCCCEECCeEEEEEE
Confidence            34678999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             ccccc
Q 007792          319 SQSVS  323 (589)
Q Consensus       319 a~~~~  323 (589)
                      |.+..
T Consensus       116 a~~~~  120 (156)
T 1h2v_Z          116 DAGFK  120 (156)
T ss_dssp             ESCCC
T ss_pred             CCCCC
Confidence            98744

>2cqi_A Nucleolysin TIAR; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, ST genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.71  E-value=8e-17  Score=137.09  Aligned_cols=84  Identities=20%  Similarity=0.358  Sum_probs=77.3

Q ss_pred             CCCCCceEEEecCCCCCCHHHHHHHhccCCCeEEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHhcCCceeCCeEEEEE
Q 007792          238 IKPPENVLFVCKLNPVTEDEDLHTIFSRFGTVVSAEIIRDFKTGDSLNYAFIEFENRQACERAYSKMDNALIDDRRIHVD  317 (589)
Q Consensus       238 ~~~~~~~i~V~nL~~~~te~~L~~~F~~~G~v~~~~i~~d~~tg~~~g~aFV~f~~~~~a~~A~~~l~g~~i~gr~i~V~  317 (589)
                      ...+.++|||+|||+.+|+++|.++|++||.|..|.|+.++.+  ++|||||+|.+.++|..||..|||..|.|+.|.|.
T Consensus        11 ~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~--~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V~   88 (103)
T 2cqi_A           11 DDGQPRTLYVGNLSRDVTEVLILQLFSQIGPCKSCKMITEHTS--NDPYCFVEFYEHRDAAAALAAMNGRKILGKEVKVN   88 (103)
T ss_dssp             CSCCCCEEEEESCCTTCCHHHHHHHHHHHSCEEEEEEECCCCS--SCCEEEEEESSHHHHHHHHHHHTTEEETTEEEEEE
T ss_pred             CCCCCCEEEEeCCCccCCHHHHHHHHHhcCCEeEEEEEecCCC--CCCEEEEEECCHHHHHHHHHHhCCCCcCCCeEEEE
Confidence            3456799999999999999999999999999999999998544  68999999999999999999999999999999999


Q ss_pred             eccccc
Q 007792          318 FSQSVS  323 (589)
Q Consensus       318 ~a~~~~  323 (589)
                      ++.+..
T Consensus        89 ~a~~~~   94 (103)
T 2cqi_A           89 WATTPS   94 (103)
T ss_dssp             ECCCTT
T ss_pred             ECCCCc
Confidence            998744

>2cq3_A RNA-binding protein 9; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.71  E-value=1e-16  Score=136.44  Aligned_cols=85  Identities=27%  Similarity=0.495  Sum_probs=78.1

Q ss_pred             CCCCCCceEEEecCCCCCCHHHHHHHhccCCCeEEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHhcCCceeCCeEEEE
Q 007792          237 DIKPPENVLFVCKLNPVTEDEDLHTIFSRFGTVVSAEIIRDFKTGDSLNYAFIEFENRQACERAYSKMDNALIDDRRIHV  316 (589)
Q Consensus       237 ~~~~~~~~i~V~nL~~~~te~~L~~~F~~~G~v~~~~i~~d~~tg~~~g~aFV~f~~~~~a~~A~~~l~g~~i~gr~i~V  316 (589)
                      ....+.++|||+|||+.+|+++|+++|++||.|..|.|+.++.  .++|||||+|.+.++|..||..|||..|.|+.|.|
T Consensus        10 ~~~~~~~~l~V~nlp~~~t~~~l~~~f~~~G~v~~v~i~~~~~--~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v   87 (103)
T 2cq3_A           10 ESKSTPKRLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNER--GSKGFGFVTFENSADADRAREKLHGTVVEGRKIEV   87 (103)
T ss_dssp             CCSCCCCEEEEESCCTTCCHHHHHHHGGGTSCEEEEEEECCTT--TTCCEEEEEESCHHHHHHHHHHHTTCEETTEECEE
T ss_pred             CCCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEecCC--CCcEEEEEEECCHHHHHHHHHHhCCCEECCEEEEE
Confidence            3456779999999999999999999999999999999998754  38899999999999999999999999999999999


Q ss_pred             Eeccccc
Q 007792          317 DFSQSVS  323 (589)
Q Consensus       317 ~~a~~~~  323 (589)
                      .++.+..
T Consensus        88 ~~a~~~~   94 (103)
T 2cq3_A           88 NNATARV   94 (103)
T ss_dssp             EECCSSC
T ss_pred             EEcccCC
Confidence            9998754

>3r27_A HnRNP L, heterogeneous nuclear ribonucleoprotein L; RBD fold, protein binding, nucleus; 2.04A {Homo sapiens}

Probab=99.71  E-value=3.1e-17  Score=137.64  Aligned_cols=84  Identities=20%  Similarity=0.272  Sum_probs=72.9

Q ss_pred             CCCCCCCCCCceEEEecCCCCCCHHHHHHHhccCCCeEEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHhcCCce--eC
Q 007792          233 IPDADIKPPENVLFVCKLNPVTEDEDLHTIFSRFGTVVSAEIIRDFKTGDSLNYAFIEFENRQACERAYSKMDNAL--ID  310 (589)
Q Consensus       233 ~~~~~~~~~~~~i~V~nL~~~~te~~L~~~F~~~G~v~~~~i~~d~~tg~~~g~aFV~f~~~~~a~~A~~~l~g~~--i~  310 (589)
                      +.+....+|..+|||+|||+.+|+++|.++|++||.|..|.|+.      .+|||||+|.+.++|..|+..|++..  |.
T Consensus        12 ~~~~~~~~ps~~l~V~NLp~~~te~~L~~lF~~fG~V~~v~i~~------~kg~AFVef~~~~~A~~Av~~ln~~~~~i~   85 (100)
T 3r27_A           12 YDDPHKTPASPVVHIRGLIDGVVEADLVEALQEFGPISYVVVMP------KKRQALVEFEDVLGACNAVNYAADNQIYIA   85 (100)
T ss_dssp             -----CCCCCSEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEET------TTTEEEEEESSHHHHHHHHHHHHHSCEEET
T ss_pred             ccccccCCCCcEEEEeCCCCCCCHHHHHHHHhccCCEEEEEEEc------CCCEEEEEECCHHHHHHHHHHhcCCCceeC
Confidence            34455677889999999999999999999999999999999975      46899999999999999999999864  88


Q ss_pred             CeEEEEEecccc
Q 007792          311 DRRIHVDFSQSV  322 (589)
Q Consensus       311 gr~i~V~~a~~~  322 (589)
                      |++|.|+||+++
T Consensus        86 Gr~i~V~~S~~k   97 (100)
T 3r27_A           86 GHPAFVNYSTSQ   97 (100)
T ss_dssp             TEEEEEEECSCS
T ss_pred             CcEEEEEecccc
Confidence            999999999863

>2khc_A Testis-specific RNP-type RNA binding protein; RRM, RNA recognition motif, bruno; NMR {Drosophila melanogaster}

Probab=99.71  E-value=3.7e-17  Score=142.84  Aligned_cols=82  Identities=28%  Similarity=0.475  Sum_probs=78.0

Q ss_pred             CCCCceEEEecCCCCCCHHHHHHHhccCCCeEEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHhcCCceeCCeEEEEEe
Q 007792          239 KPPENVLFVCKLNPVTEDEDLHTIFSRFGTVVSAEIIRDFKTGDSLNYAFIEFENRQACERAYSKMDNALIDDRRIHVDF  318 (589)
Q Consensus       239 ~~~~~~i~V~nL~~~~te~~L~~~F~~~G~v~~~~i~~d~~tg~~~g~aFV~f~~~~~a~~A~~~l~g~~i~gr~i~V~~  318 (589)
                      .++.++|||+|||+.+++++|+++|++||.|..|.|+.++.+|+++|||||+|.+.++|..||+.|||..|+|+.|.|++
T Consensus        37 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~~~i~~~~~~g~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~V~~  116 (118)
T 2khc_A           37 GPEGCNLFIYHLPQEFTDTDLASTFLPFGNVISAKVFIDKQTSLSKCFGFVSFDNPDSAQVAIKAMNGFQVGTKRLKVQL  116 (118)
T ss_dssp             CCCSEEEEEECSCTTCCHHHHHHHTTTSCEEEEEEECCCSSSSCCCCEEEEEEESSHHHHHHHHHCCCCEETTEECCEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEeCCCCCCcCcEEEEEECCHHHHHHHHHHcCCCEECCEEEEEEe
Confidence            45678999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             cc
Q 007792          319 SQ  320 (589)
Q Consensus       319 a~  320 (589)
                      ++
T Consensus       117 ak  118 (118)
T 2khc_A          117 KK  118 (118)
T ss_dssp             C-
T ss_pred             cC
Confidence            74

>2cqp_A RNA-binding protein 12; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, structural genomics, NPPSFA; NMR {Mus musculus} SCOP: d.58.7.1

Probab=99.71  E-value=2.5e-17  Score=138.82  Aligned_cols=83  Identities=14%  Similarity=0.285  Sum_probs=78.7

Q ss_pred             CCCCceEEEecCCCCCCHHHHHHHhccCCCeEEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHhcCCceeCCeEEEEEe
Q 007792          239 KPPENVLFVCKLNPVTEDEDLHTIFSRFGTVVSAEIIRDFKTGDSLNYAFIEFENRQACERAYSKMDNALIDDRRIHVDF  318 (589)
Q Consensus       239 ~~~~~~i~V~nL~~~~te~~L~~~F~~~G~v~~~~i~~d~~tg~~~g~aFV~f~~~~~a~~A~~~l~g~~i~gr~i~V~~  318 (589)
                      .+..++|||+|||+.+++++|+++|.+||.|..+.++.++.+|.++|||||+|.+.++|+.||..|||..|.|+.|.|++
T Consensus        12 ~~~~~~l~v~nLp~~~t~~~l~~~F~~~G~v~~~~~~~~~~~g~~~g~afV~f~~~~~a~~Ai~~l~g~~~~g~~l~V~~   91 (98)
T 2cqp_A           12 KPGPTIIKVQNMPFTVSIDEILDFFYGYQVIPGSVCLKYNEKGMPTGEAMVAFESRDEATAAVIDLNDRPIGSRKVKLVL   91 (98)
T ss_dssp             CCSSEEEEEESCCTTCCHHHHHHHTTTSCCCTTTCEEEECSSSCEEEEEEEEESCHHHHHHHHHHTTTCEETTEECEEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHHcCCccceEEEEECCCCCeeeEEEEEECCHHHHHHHHHHhCCCeeCCeEEEEEE
Confidence            45678999999999999999999999999999888888889999999999999999999999999999999999999999


Q ss_pred             ccc
Q 007792          319 SQS  321 (589)
Q Consensus       319 a~~  321 (589)
                      +..
T Consensus        92 a~~   94 (98)
T 2cqp_A           92 GSG   94 (98)
T ss_dssp             SSC
T ss_pred             cCC
Confidence            875

>2ywk_A Putative RNA-binding protein 11; RRM-domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; 1.54A {Homo sapiens}

Probab=99.71  E-value=3.8e-17  Score=136.87  Aligned_cols=82  Identities=21%  Similarity=0.363  Sum_probs=77.4

Q ss_pred             CCCCceEEEecCCCCCCHHHHHHHhccCCCeEEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHhcCCceeCCeEEEEEe
Q 007792          239 KPPENVLFVCKLNPVTEDEDLHTIFSRFGTVVSAEIIRDFKTGDSLNYAFIEFENRQACERAYSKMDNALIDDRRIHVDF  318 (589)
Q Consensus       239 ~~~~~~i~V~nL~~~~te~~L~~~F~~~G~v~~~~i~~d~~tg~~~g~aFV~f~~~~~a~~A~~~l~g~~i~gr~i~V~~  318 (589)
                      .++.++|||+|||+.+++++|+++|++||+|..|.|+.++. +.++|||||+|.+.++|..||..|||..|.|+.|.|.+
T Consensus        13 ~~~~~~l~v~nlp~~~~~~~l~~~F~~~G~i~~v~i~~~~~-g~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V~~   91 (95)
T 2ywk_A           13 EEADRTVFVGNLEARVREEILYELFLQAGPLTKVTICKDRE-GKPKSFGFVCFKHPESVSYAIALLNGIRLYGRPINVSG   91 (95)
T ss_dssp             TTGGGEEEEECCCTTCCHHHHHHHHGGGSCEEEEEEEECTT-SCEEEEEEEEESSTHHHHHHHHHHTTCEETTEECEEEC
T ss_pred             CCCCCEEEEECCCCCCCHHHHHHHHHhcCCEEEEEEEECCC-CCCceEEEEEECCHHHHHHHHHHhCCCEECCCEEEEEE
Confidence            44678999999999999999999999999999999999875 89999999999999999999999999999999999999


Q ss_pred             ccc
Q 007792          319 SQS  321 (589)
Q Consensus       319 a~~  321 (589)
                      ++.
T Consensus        92 a~~   94 (95)
T 2ywk_A           92 PSS   94 (95)
T ss_dssp             CCC
T ss_pred             cCC
Confidence            864

>2dgp_A Bruno-like 4, RNA binding protein; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} PDB: 2dgq_A

Probab=99.71  E-value=2.5e-17  Score=140.92  Aligned_cols=85  Identities=24%  Similarity=0.379  Sum_probs=80.2

Q ss_pred             CCCCceEEEecCCCCCCHHHHHHHhccCCCeEEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHhcCCcee---CCeEEE
Q 007792          239 KPPENVLFVCKLNPVTEDEDLHTIFSRFGTVVSAEIIRDFKTGDSLNYAFIEFENRQACERAYSKMDNALI---DDRRIH  315 (589)
Q Consensus       239 ~~~~~~i~V~nL~~~~te~~L~~~F~~~G~v~~~~i~~d~~tg~~~g~aFV~f~~~~~a~~A~~~l~g~~i---~gr~i~  315 (589)
                      .++.++|||+|||+.+|+++|+++|++||.|..|.|+.++.+++++|||||+|.+.++|..||..|||..+   .|+.|.
T Consensus        10 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~A~~~l~g~~~~~~~g~~l~   89 (106)
T 2dgp_A           10 DHDAIKLFIGQIPRNLDEKDLKPLFEEFGKIYELTVLKDRFTGMHKGCAFLTYCERESALKAQSALHEQKTLPGMNRPIQ   89 (106)
T ss_dssp             CTTCEEEEEESCCTTCCHHHHHHHHHHHSCCCEEECCCCSSSCSCCSEEEEEESSHHHHHHHHHHHTTTCCCTTCSSCCE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEecCCCCCcceEEEEEECCHHHHHHHHHHhcCCcccCCCCceEE
Confidence            45678999999999999999999999999999999999999999999999999999999999999999988   899999


Q ss_pred             EEeccccc
Q 007792          316 VDFSQSVS  323 (589)
Q Consensus       316 V~~a~~~~  323 (589)
                      |.++.+..
T Consensus        90 v~~a~~~~   97 (106)
T 2dgp_A           90 VKPADSES   97 (106)
T ss_dssp             EEECCCCS
T ss_pred             EEECCccc
Confidence            99998743

>3n9u_C Cleavage and polyadenylation specificity factor S; protein-protein complex, coexpression, heterotetramer, mRNA maturation, mRNA cleavage; 1.92A {Homo sapiens}

Probab=99.70  E-value=3.6e-17  Score=150.11  Aligned_cols=82  Identities=15%  Similarity=0.268  Sum_probs=77.9

Q ss_pred             CCceEEEecCCCCCCHHHHHHHhccCC--CeEEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHhcCCceeCCeEEEEEe
Q 007792          241 PENVLFVCKLNPVTEDEDLHTIFSRFG--TVVSAEIIRDFKTGDSLNYAFIEFENRQACERAYSKMDNALIDDRRIHVDF  318 (589)
Q Consensus       241 ~~~~i~V~nL~~~~te~~L~~~F~~~G--~v~~~~i~~d~~tg~~~g~aFV~f~~~~~a~~A~~~l~g~~i~gr~i~V~~  318 (589)
                      ..++|||+|||+++|+++|.++|++||  .|..|.|+.++.+|+++|||||+|.+.++|..||..|||..|+|+.|.|.+
T Consensus        54 ~~~~lfVgnLp~~~te~~L~~~F~~~G~i~v~~v~i~~d~~tg~skGfaFV~f~~~~~A~~Ai~~lng~~~~Gr~l~V~~  133 (156)
T 3n9u_C           54 RRAAVYVGSFSWWTTDQQLIQVIRSIGVYDVVELKFAENRANGQSKGYAEVVVASENSVHKLLELLPGKVLNGEKVDVRP  133 (156)
T ss_dssp             --CEEEEECCCTTCCHHHHHHHHHHTTCCCEEEEEEEECTTTCCEEEEEEEEESCHHHHHHHHHHSTTCEETTEECEEEE
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHHHCCccEEEEEEEecCCCCccceEEEEEECCHHHHHHHHHHcCCCEECCeEeEEEE
Confidence            468999999999999999999999999  999999999999999999999999999999999999999999999999999


Q ss_pred             cccc
Q 007792          319 SQSV  322 (589)
Q Consensus       319 a~~~  322 (589)
                      |.+.
T Consensus       134 a~~~  137 (156)
T 3n9u_C          134 ATRQ  137 (156)
T ss_dssp             CCHH
T ss_pred             cCCC
Confidence            9763

>2ek1_A RNA-binding protein 12; RNA recognition motif, dimer, structural genomics, NPPSFA, national project on protein structural and functional analyses; 2.00A {Homo sapiens} PDB: 2ek6_A

Probab=99.70  E-value=1.3e-17  Score=139.69  Aligned_cols=83  Identities=17%  Similarity=0.278  Sum_probs=76.5

Q ss_pred             CCCCceEEEecCCCCCCHHHHHHHhccCCCeEEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHhcCCceeCCeEEEEEe
Q 007792          239 KPPENVLFVCKLNPVTEDEDLHTIFSRFGTVVSAEIIRDFKTGDSLNYAFIEFENRQACERAYSKMDNALIDDRRIHVDF  318 (589)
Q Consensus       239 ~~~~~~i~V~nL~~~~te~~L~~~F~~~G~v~~~~i~~d~~tg~~~g~aFV~f~~~~~a~~A~~~l~g~~i~gr~i~V~~  318 (589)
                      .++.++|||+|||+.+|+++|+++|.+||.|..+.++.++.++.++|||||+|.+.++|.+||..|||..|.|+.|.|++
T Consensus        12 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~~~~~~~~~~g~~~g~afV~f~~~~~a~~Ai~~l~g~~~~gr~l~v~~   91 (95)
T 2ek1_A           12 KPGPTVIKVQNMPFTVSIDEILDFFYGYQVIPGSVCLKYNEKGMPTGEAMVAFESRDEATAAVIDLNDRPIGSRKVKLSG   91 (95)
T ss_dssp             ---CEEEEEECCCTTCCHHHHHHHTTTSCBCTTCCEEEECTTSCEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEC
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCccceEEEEeCCCCCEeeEEEEEECCHHHHHHHHHHhCCCeECCcEEEEEe
Confidence            44568999999999999999999999999999999999989999999999999999999999999999999999999999


Q ss_pred             ccc
Q 007792          319 SQS  321 (589)
Q Consensus       319 a~~  321 (589)
                      +.+
T Consensus        92 a~s   94 (95)
T 2ek1_A           92 PSS   94 (95)
T ss_dssp             CC-
T ss_pred             ccC
Confidence            864

>2do0_A HnRNP M, heterogeneous nuclear ribonucleoprotein M; RNA recognition motif, RRM, RNA binding domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.70  E-value=1.7e-16  Score=137.70  Aligned_cols=83  Identities=28%  Similarity=0.390  Sum_probs=78.3

Q ss_pred             CCCCceEEEecCCCCCCHHHHHHHhccCCCeEEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHhcCCceeCCeEEEEEe
Q 007792          239 KPPENVLFVCKLNPVTEDEDLHTIFSRFGTVVSAEIIRDFKTGDSLNYAFIEFENRQACERAYSKMDNALIDDRRIHVDF  318 (589)
Q Consensus       239 ~~~~~~i~V~nL~~~~te~~L~~~F~~~G~v~~~~i~~d~~tg~~~g~aFV~f~~~~~a~~A~~~l~g~~i~gr~i~V~~  318 (589)
                      ..+.++|||+|||+.+|+++|+++|.+||.|..|.|+.++ +++++|||||+|.+.++|..||..|||..|.|+.|.|.+
T Consensus        12 ~~~~~~l~V~nlp~~~~~~~l~~~f~~~G~i~~~~i~~~~-~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~   90 (114)
T 2do0_A           12 GRLGSTVFVANLDYKVGWKKLKEVFSMAGVVVRADILEDK-DGKSRGIGTVTFEQSIEAVQAISMFNGQLLFDRPMHVKM   90 (114)
T ss_dssp             CCCCSCEEEESCCTTCCHHHHHHHHTTTSCEEEEEEEECT-TCSEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEECC-CCCeeeEEEEEECCHHHHHHHHHHhCCCEeCCCEEEEEE
Confidence            4567899999999999999999999999999999999986 599999999999999999999999999999999999999


Q ss_pred             cccc
Q 007792          319 SQSV  322 (589)
Q Consensus       319 a~~~  322 (589)
                      +...
T Consensus        91 a~~~   94 (114)
T 2do0_A           91 DERA   94 (114)
T ss_dssp             CSCC
T ss_pred             cccC
Confidence            9753

>1rk8_A CG8781-PA, CG8781-PA protein; mRNA processing, RRM, RBD, NMD, oskar mRNA localization, translation; 1.90A {Drosophila melanogaster} SCOP: d.58.7.1 PDB: 1hl6_A 2x1g_A

Probab=99.70  E-value=4.8e-17  Score=150.93  Aligned_cols=86  Identities=22%  Similarity=0.380  Sum_probs=80.1

Q ss_pred             CCCCceEEEecCCCCCCHHHHHHHhccCCCeEEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHhcCCceeCCeEEEEEe
Q 007792          239 KPPENVLFVCKLNPVTEDEDLHTIFSRFGTVVSAEIIRDFKTGDSLNYAFIEFENRQACERAYSKMDNALIDDRRIHVDF  318 (589)
Q Consensus       239 ~~~~~~i~V~nL~~~~te~~L~~~F~~~G~v~~~~i~~d~~tg~~~g~aFV~f~~~~~a~~A~~~l~g~~i~gr~i~V~~  318 (589)
                      ..+.++|||+|||+.+|+++|..+|++||.|..|.|+.++.+|.++|||||+|.+.++|..||..|||..|.|+.|.|.|
T Consensus        69 ~~~~~~l~V~nLp~~~t~~~L~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~~  148 (165)
T 1rk8_A           69 SVEGWILFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYETHKQALAAKEALNGAEIMGQTIQVDW  148 (165)
T ss_dssp             CC-CEEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTSSEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHhhcCCCEEEEEEEecCCCCcEeeEEEEEECCHHHHHHHHHHhCCCEECCEEEEEEE
Confidence            45678999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             cccccc
Q 007792          319 SQSVSK  324 (589)
Q Consensus       319 a~~~~~  324 (589)
                      +.+...
T Consensus       149 a~~~~~  154 (165)
T 1rk8_A          149 CFVKGP  154 (165)
T ss_dssp             SEECC-
T ss_pred             ecCCCC
Confidence            987543

>1s79_A Lupus LA protein; RRM, alpha/beta, RNA binding protein, translation; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.70  E-value=2.4e-17  Score=140.32  Aligned_cols=80  Identities=9%  Similarity=0.195  Sum_probs=75.9

Q ss_pred             CCCceEEEecCCCCCCHHHHHHHhccCCCeEEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHhcCCceeCCeEEEEEec
Q 007792          240 PPENVLFVCKLNPVTEDEDLHTIFSRFGTVVSAEIIRDFKTGDSLNYAFIEFENRQACERAYSKMDNALIDDRRIHVDFS  319 (589)
Q Consensus       240 ~~~~~i~V~nL~~~~te~~L~~~F~~~G~v~~~~i~~d~~tg~~~g~aFV~f~~~~~a~~A~~~l~g~~i~gr~i~V~~a  319 (589)
                      .+..+|||+|||+.+|+++|.++|++||+|..|.|+.++. |.++|||||+|.+.++|..||. ++|..|+|+.|.|.++
T Consensus         9 ~~~~~lfV~~Lp~~~te~~L~~~F~~~G~v~~v~i~~d~~-g~~rG~aFV~F~~~e~a~~Ai~-~~~~~~~gr~l~V~~~   86 (103)
T 1s79_A            9 VKNRSVYIKGFPTDATLDDIKEWLEDKGQVLNIQMRRTLH-KAFKGSIFVVFDSIESAKKFVE-TPGQKYKETDLLILFK   86 (103)
T ss_dssp             SGGGCEEEECCCTTCCHHHHHHHHHTSSCEEEEEEECCCT-TSCCCEEEEEESSHHHHHHHHT-SSCCCCTTTTCEEEEH
T ss_pred             CCCCEEEEECCCCCCCHHHHHHHHhhcCCEEEEEEEECCC-CCCccEEEEEECCHHHHHHHHH-cCCCEECCEEEEEEEc
Confidence            3568999999999999999999999999999999999977 9999999999999999999997 8999999999999998


Q ss_pred             cc
Q 007792          320 QS  321 (589)
Q Consensus       320 ~~  321 (589)
                      ..
T Consensus        87 ~~   88 (103)
T 1s79_A           87 DD   88 (103)
T ss_dssp             HH
T ss_pred             hH
Confidence            75

>1sjq_A Polypyrimidine tract-binding protein 1; babbab motif, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.70  E-value=2.6e-17  Score=139.46  Aligned_cols=80  Identities=20%  Similarity=0.317  Sum_probs=73.0

Q ss_pred             CCCCCceEEEecCCCCCCHHHHHHHhccCCCeEEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHhcC--CceeCCeEEE
Q 007792          238 IKPPENVLFVCKLNPVTEDEDLHTIFSRFGTVVSAEIIRDFKTGDSLNYAFIEFENRQACERAYSKMD--NALIDDRRIH  315 (589)
Q Consensus       238 ~~~~~~~i~V~nL~~~~te~~L~~~F~~~G~v~~~~i~~d~~tg~~~g~aFV~f~~~~~a~~A~~~l~--g~~i~gr~i~  315 (589)
                      .+++.++|||+|||+.+|+++|+++|++||.|..|.|+.+      +|||||+|.+.++|..||+.|+  +..|.|++|.
T Consensus        12 ~~~~~~~LfV~nLp~~vte~dL~~lF~~fG~V~~v~i~~~------kGfaFVeF~~~~~A~~Ai~~l~~~~~~l~Gr~l~   85 (105)
T 1sjq_A           12 SGVPSRVIHIRKLPIDVTEGEVISLGLPFGKVTNLLMLKG------KNQAFIEMNTEEAANTMVNYYTSVTPVLRGQPIY   85 (105)
T ss_dssp             CCCCCCEEEECSCCTTSCHHHHHHHHHHHCCEEEEEEETT------TTEEEEEESSHHHHHHHHHHHTTSCCEETTEECC
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEcC------CCEEEEEECCHHHHHHHHHHhccCCceECCEEEE
Confidence            4567899999999999999999999999999999999874      5999999999999999999886  4789999999


Q ss_pred             EEeccccc
Q 007792          316 VDFSQSVS  323 (589)
Q Consensus       316 V~~a~~~~  323 (589)
                      |.+|++..
T Consensus        86 V~~A~~~~   93 (105)
T 1sjq_A           86 IQFSNHKE   93 (105)
T ss_dssp             BCCCSSSS
T ss_pred             EEEcCCCC
Confidence            99998743

>2dgx_A KIAA0430 protein; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.70  E-value=7.1e-17  Score=135.64  Aligned_cols=80  Identities=21%  Similarity=0.248  Sum_probs=75.0

Q ss_pred             CCceEEEecCCCCCCHHHHH----HHhccCCCeEEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHhcCCceeCCeEEEE
Q 007792          241 PENVLFVCKLNPVTEDEDLH----TIFSRFGTVVSAEIIRDFKTGDSLNYAFIEFENRQACERAYSKMDNALIDDRRIHV  316 (589)
Q Consensus       241 ~~~~i~V~nL~~~~te~~L~----~~F~~~G~v~~~~i~~d~~tg~~~g~aFV~f~~~~~a~~A~~~l~g~~i~gr~i~V  316 (589)
                      ..++|||+|||+.+++++|+    ++|++||.|..|.|+.++.+   +|||||+|.+.++|..||..|||..|+|+.|.|
T Consensus         8 ~~~~l~V~nL~~~~~~~~l~~~l~~~F~~~G~v~~v~i~~~~~~---rg~afV~f~~~~~A~~Ai~~l~g~~~~gr~l~V   84 (96)
T 2dgx_A            8 NGADVQVSNIDYRLSRKELQQLLQEAFARHGKVKSVELSPHTDY---QLKAVVQMENLQDAIGAVNSLHRYKIGSKKILV   84 (96)
T ss_dssp             SCEEEEEESCCTTSCHHHHHHHHHHHHHHHSCEEEEEECSCCST---TCCEEEEESSHHHHHHHHHHHTTEEETTEEEEE
T ss_pred             CCCEEEEECCCCCCCHHHHHHHHHHhccccCcEEEEEEEeCCCC---CeEEEEEECCHHHHHHHHHHhCCCEECCeEEEE
Confidence            46899999999999999999    99999999999999988765   789999999999999999999999999999999


Q ss_pred             Eeccccc
Q 007792          317 DFSQSVS  323 (589)
Q Consensus       317 ~~a~~~~  323 (589)
                      .+|++..
T Consensus        85 ~~a~~~~   91 (96)
T 2dgx_A           85 SLATGAS   91 (96)
T ss_dssp             EECCCSS
T ss_pred             EEcCCCC
Confidence            9998743

>2kn4_A Immunoglobulin G-binding protein G, splicing FACT arginine/serine-rich 2, S35, splicing factor SC35,; RRM domain, cell WALL; NMR {Streptococcus SP}

Probab=99.70  E-value=9.9e-17  Score=147.60  Aligned_cols=85  Identities=28%  Similarity=0.420  Sum_probs=80.7

Q ss_pred             CCCCceEEEecCCCCCCHHHHHHHhccCCCeEEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHhcCCceeCCeEEEEEe
Q 007792          239 KPPENVLFVCKLNPVTEDEDLHTIFSRFGTVVSAEIIRDFKTGDSLNYAFIEFENRQACERAYSKMDNALIDDRRIHVDF  318 (589)
Q Consensus       239 ~~~~~~i~V~nL~~~~te~~L~~~F~~~G~v~~~~i~~d~~tg~~~g~aFV~f~~~~~a~~A~~~l~g~~i~gr~i~V~~  318 (589)
                      ..+..+|||+|||+.+|+++|.++|++||.|..|.|+.++.+|.++|||||+|.+.++|..||..|||..|.|+.|.|.+
T Consensus        67 ~~~~~~l~v~nl~~~~~~~~l~~~F~~~G~v~~~~i~~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~  146 (158)
T 2kn4_A           67 VEGMTSLKVDNLTYRTSPDTLRRVFEKYGRVGDVYIPRDRYTKESRGFAFVRFHDKRDAEDAMDAMDGAVLDGRELRVQM  146 (158)
T ss_dssp             CCBCCEEEEESCCTTCCHHHHHHHHHHHSCEEEEECCCCSSCTTSCCEEEEEESBHHHHHHHHHHSTTEESSSSEEEEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEeecCCCCccceEEEEEECCHHHHHHHHHHhCCCEECCeEEEEEE
Confidence            45678999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             ccccc
Q 007792          319 SQSVS  323 (589)
Q Consensus       319 a~~~~  323 (589)
                      |.+..
T Consensus       147 a~~~~  151 (158)
T 2kn4_A          147 ARYGR  151 (158)
T ss_dssp             ECCSS
T ss_pred             CCCCC
Confidence            98743

>2dh8_A DAZ-associated protein 1; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.70  E-value=5.1e-17  Score=138.84  Aligned_cols=84  Identities=25%  Similarity=0.385  Sum_probs=79.7

Q ss_pred             CCCCceEEEecCCCCCCHHHHHHHhccCCCeEEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHhcCCceeCCeEEEEEe
Q 007792          239 KPPENVLFVCKLNPVTEDEDLHTIFSRFGTVVSAEIIRDFKTGDSLNYAFIEFENRQACERAYSKMDNALIDDRRIHVDF  318 (589)
Q Consensus       239 ~~~~~~i~V~nL~~~~te~~L~~~F~~~G~v~~~~i~~d~~tg~~~g~aFV~f~~~~~a~~A~~~l~g~~i~gr~i~V~~  318 (589)
                      .++.++|||+|||+.+|+++|+++|++||+|..|.|+.++.++.++|||||+|.+.++|..||.. ++..|.|+.|.|.+
T Consensus        13 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~v~~v~i~~~~~~g~~~g~afV~f~~~~~a~~a~~~-~~~~~~g~~l~V~~   91 (105)
T 2dh8_A           13 ADEIGKLFVGGLDWSTTQETLRSYFSQYGEVVDCVIMKDKTTNQSRGFGFVKFKDPNCVGTVLAS-RPHTLDGRNIDPKP   91 (105)
T ss_dssp             SSSSSEECCBSCCTTCCHHHHHHHHHTTSCEEEEEEEECSSSCCEEEEEEEEESSTTHHHHHHHH-CSEEETTEEEBCCC
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEeeCCCCCCcceEEEEEECCHHHHHHHHHh-CCCeECCEEEEEEE
Confidence            45678999999999999999999999999999999999999999999999999999999999988 99999999999999


Q ss_pred             ccccc
Q 007792          319 SQSVS  323 (589)
Q Consensus       319 a~~~~  323 (589)
                      +.+..
T Consensus        92 a~~~~   96 (105)
T 2dh8_A           92 CTPRG   96 (105)
T ss_dssp             SCCSS
T ss_pred             ccCCC
Confidence            98754

>2wbr_A GW182, gawky, LD47780P; DNA-binding protein, RRM, RBD, TNRC6A, mirnas, P-bodies, argonaute, mRNA decay; NMR {Drosophila melanogaster}

Probab=99.70  E-value=5.6e-17  Score=131.34  Aligned_cols=75  Identities=16%  Similarity=0.254  Sum_probs=70.8

Q ss_pred             CCCceEEEecCCCCCCHHHHHHHhccCCCeEEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHhcCCceeCCeEEEEEec
Q 007792          240 PPENVLFVCKLNPVTEDEDLHTIFSRFGTVVSAEIIRDFKTGDSLNYAFIEFENRQACERAYSKMDNALIDDRRIHVDFS  319 (589)
Q Consensus       240 ~~~~~i~V~nL~~~~te~~L~~~F~~~G~v~~~~i~~d~~tg~~~g~aFV~f~~~~~a~~A~~~l~g~~i~gr~i~V~~a  319 (589)
                      ....-|||+||++.+|+++|+++|.+||+|..+.|+.      ++|||||+|.+.++|..|++.|||..|.|++|.|++|
T Consensus         5 ~~~~wL~VgNL~~~~te~~L~~lF~q~G~V~~~~l~~------~kGfaFVey~~~~eA~~Ai~~Ln~~~l~gr~I~V~~A   78 (89)
T 2wbr_A            5 WGSSWLLLKNLTAQIDGPTLRTLCMQHGPLVSFHPYL------NQGIALCKYTTREEANKAQMALNNCVLANTTIFAESP   78 (89)
T ss_dssp             CCCCEEEEECCCTTCCCHHHHHHHHHHSCEEEEEEET------TTTEEEEEESSHHHHHHHHHHHTTEEETTEEEEEECC
T ss_pred             CccceEEEeCCCccCCHHHHHHHHHhhCCEEEEEEcC------CCcEEEEEECCHHHHHHHHHHhcCCEECCcEEEEEEC
Confidence            3467899999999999999999999999999999965      6799999999999999999999999999999999999


Q ss_pred             c
Q 007792          320 Q  320 (589)
Q Consensus       320 ~  320 (589)
                      .
T Consensus        79 ~   79 (89)
T 2wbr_A           79 S   79 (89)
T ss_dssp             C
T ss_pred             C
Confidence            4

>2dis_A Unnamed protein product; structural genomics, RRM domain, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.69  E-value=6.3e-17  Score=139.20  Aligned_cols=85  Identities=16%  Similarity=0.270  Sum_probs=78.7

Q ss_pred             CCCceEEEecCCCCCCHHHHHHHhccCCC-eEEEEEe-ecCCCCCcccEEEEEEcCHHHHHHHHHhcC--CceeCCeEEE
Q 007792          240 PPENVLFVCKLNPVTEDEDLHTIFSRFGT-VVSAEII-RDFKTGDSLNYAFIEFENRQACERAYSKMD--NALIDDRRIH  315 (589)
Q Consensus       240 ~~~~~i~V~nL~~~~te~~L~~~F~~~G~-v~~~~i~-~d~~tg~~~g~aFV~f~~~~~a~~A~~~l~--g~~i~gr~i~  315 (589)
                      .+.++|||+|||+.+|+++|.++|.+||. |..|.|+ .++.+|.++|||||+|.+.++|..||..|+  +..|.|+.|.
T Consensus         6 ~~~~~l~V~nLp~~~t~~~l~~~f~~~G~~v~~v~i~~~~~~~g~~~g~afV~f~~~~~A~~A~~~l~~g~~~~~g~~l~   85 (109)
T 2dis_A            6 SGNCRLFIGGIPKMKKREEILEEIAKVTEGVLDVIVYASAADKMKNRGFAFVEYESHRAAAMARRKLMPGRIQLWGHQIA   85 (109)
T ss_dssp             CCSEEEEEECCCTTSCHHHHHHHHHHHSTTEEEEECCSSSCTTTTTCCEEEEEESSHHHHHHHHTTTTTCCSCBTTBCCE
T ss_pred             cCCCEEEEeCCCCcCCHHHHHHHHHHhcCCceEEEEEccCCCCCCcCcEEEEEecCHHHHHHHHHHhhCCCceecCCeEE
Confidence            45789999999999999999999999998 9999998 788889999999999999999999999996  5899999999


Q ss_pred             EEecccccc
Q 007792          316 VDFSQSVSK  324 (589)
Q Consensus       316 V~~a~~~~~  324 (589)
                      |.+|.+...
T Consensus        86 V~~a~~~~~   94 (109)
T 2dis_A           86 VDWAEPEID   94 (109)
T ss_dssp             EEESCSSCS
T ss_pred             EEEcCCCCC
Confidence            999987543

>2rs2_A Musashi-1, RNA-binding protein musashi homolog 1; protein-RNA complex, RRM, RBD, RNA binding protein- complex; NMR {Mus musculus}

Probab=99.69  E-value=9.2e-17  Score=138.29  Aligned_cols=85  Identities=20%  Similarity=0.346  Sum_probs=76.1

Q ss_pred             CCCCCceEEEecCCCCCCHHHHHHHhccCCCeEEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHhcCCceeCCeEEEEE
Q 007792          238 IKPPENVLFVCKLNPVTEDEDLHTIFSRFGTVVSAEIIRDFKTGDSLNYAFIEFENRQACERAYSKMDNALIDDRRIHVD  317 (589)
Q Consensus       238 ~~~~~~~i~V~nL~~~~te~~L~~~F~~~G~v~~~~i~~d~~tg~~~g~aFV~f~~~~~a~~A~~~l~g~~i~gr~i~V~  317 (589)
                      ...+.++|||+|||+.+|+++|.++|++||.|..|.|+.++.+|.++|||||+|.+.++|..||..+ +..|+|+.|.|.
T Consensus        21 ~~~~~~~lfV~nLp~~~te~~L~~~F~~~G~i~~v~i~~~~~tg~~kg~afV~f~~~~~A~~Ai~~~-~~~l~g~~l~V~   99 (109)
T 2rs2_A           21 MGSSGCKMFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQAGVDKVLAQS-RHELDSKTIDPK   99 (109)
T ss_dssp             -----CCEEEESCCTTCCHHHHHHHHTTTSCEEEEEECCCTTTCCCTTCEEEEESSHHHHHHHHHSS-CEEETTEEEEEE
T ss_pred             cCCCCCEEEEeCCCCCCCHHHHHHHHHccCCeEEEEEEECCCCCCcCcEEEEEECCHHHHHHHHHHC-CCcCCCEEEEEE
Confidence            3456789999999999999999999999999999999999999999999999999999999999876 599999999999


Q ss_pred             eccccc
Q 007792          318 FSQSVS  323 (589)
Q Consensus       318 ~a~~~~  323 (589)
                      ++.+..
T Consensus       100 ~a~~~~  105 (109)
T 2rs2_A          100 VAFPRR  105 (109)
T ss_dssp             ECCCCC
T ss_pred             EccCCC
Confidence            998643

>1p1t_A Cleavage stimulation factor, 64 kDa subunit; RNA recognition motif, C-terminal helix, N-terminal helix, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.69  E-value=1.6e-17  Score=141.54  Aligned_cols=84  Identities=26%  Similarity=0.433  Sum_probs=79.8

Q ss_pred             CCceEEEecCCCCCCHHHHHHHhccCCCeEEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHhcCCceeCCeEEEEEecc
Q 007792          241 PENVLFVCKLNPVTEDEDLHTIFSRFGTVVSAEIIRDFKTGDSLNYAFIEFENRQACERAYSKMDNALIDDRRIHVDFSQ  320 (589)
Q Consensus       241 ~~~~i~V~nL~~~~te~~L~~~F~~~G~v~~~~i~~d~~tg~~~g~aFV~f~~~~~a~~A~~~l~g~~i~gr~i~V~~a~  320 (589)
                      +.++|||+|||+.+++++|.++|++||.|..|.|+.++.+|.++|||||+|.+.++|..|++.|||..|.|+.|.|.++.
T Consensus         7 ~~~~l~V~nlp~~~~~~~l~~~f~~~G~i~~~~i~~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a~   86 (104)
T 1p1t_A            7 SLRSVFVGNIPYEATEEQLKDIFSEVGPVVSFRLVYDRETGKPKGYGFCEYQDQETALSAMRNLNGREFSGRALRVDNAA   86 (104)
T ss_dssp             HHSCEEEESCCTTSCHHHHHHHHHTTSCCSEEEEEEETTTTEEEEEEEEECSCHHHHHHHHHHSSSBSCSSSCBEEEETT
T ss_pred             CccEEEEeCCCCcCCHHHHHHHHHhcCCeeEEEEEeCCCCCccceEEEEEECCHHHHHHHHHHhCCCeeCCcEEEEEeCC
Confidence            45899999999999999999999999999999999999899999999999999999999999999999999999999998


Q ss_pred             cccc
Q 007792          321 SVSK  324 (589)
Q Consensus       321 ~~~~  324 (589)
                      +...
T Consensus        87 ~~~~   90 (104)
T 1p1t_A           87 SEKN   90 (104)
T ss_dssp             CTTH
T ss_pred             Cccc
Confidence            7543

>2cq4_A RNA binding motif protein 23; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.69  E-value=4.6e-17  Score=141.31  Aligned_cols=81  Identities=26%  Similarity=0.299  Sum_probs=77.6

Q ss_pred             CceEEEecCCCCCCHHHHHHHhccCCCeEEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHhcCCceeCCeEEEEEeccc
Q 007792          242 ENVLFVCKLNPVTEDEDLHTIFSRFGTVVSAEIIRDFKTGDSLNYAFIEFENRQACERAYSKMDNALIDDRRIHVDFSQS  321 (589)
Q Consensus       242 ~~~i~V~nL~~~~te~~L~~~F~~~G~v~~~~i~~d~~tg~~~g~aFV~f~~~~~a~~A~~~l~g~~i~gr~i~V~~a~~  321 (589)
                      .++|||+|||+.+++++|+++|++||.|..|.|+.++.++.++|||||+|.+.++|..|| .|||..|.|+.|.|.++.+
T Consensus        25 ~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~a~~A~-~l~g~~~~g~~l~V~~a~~  103 (114)
T 2cq4_A           25 ARTVFCMQLAARIRPRDLEDFFSAVGKVRDVRIISDRNSRRSKGIAYVEFCEIQSVPLAI-GLTGQRLLGVPIIVQASQA  103 (114)
T ss_dssp             HTEEEEESCCTTCCHHHHHHHHTTTSCEEEEEECCSCCSSSCCCCEEEEESCGGGHHHHH-HHTTEEETTEEEEEEEHHH
T ss_pred             CCEEEEeCCCCCCCHHHHHHHHHhCCCEeEEEEEecCCCCccCcEEEEEeCcHHHHHHHH-HcCCCEeCCeEEEEEecCC
Confidence            479999999999999999999999999999999999999999999999999999999999 9999999999999999987


Q ss_pred             cc
Q 007792          322 VS  323 (589)
Q Consensus       322 ~~  323 (589)
                      ..
T Consensus       104 ~~  105 (114)
T 2cq4_A          104 EK  105 (114)
T ss_dssp             HH
T ss_pred             Cc
Confidence            43

>1x4e_A RNA binding motif, single-stranded interacting protein 2; structural genomics, RRM domain, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.69  E-value=1.1e-17  Score=137.05  Aligned_cols=81  Identities=22%  Similarity=0.397  Sum_probs=76.9

Q ss_pred             CCCceEEEecCCCCCCHHHHHHHhccCCCeEEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHhcCCceeCCeEEEEEec
Q 007792          240 PPENVLFVCKLNPVTEDEDLHTIFSRFGTVVSAEIIRDFKTGDSLNYAFIEFENRQACERAYSKMDNALIDDRRIHVDFS  319 (589)
Q Consensus       240 ~~~~~i~V~nL~~~~te~~L~~~F~~~G~v~~~~i~~d~~tg~~~g~aFV~f~~~~~a~~A~~~l~g~~i~gr~i~V~~a  319 (589)
                      .+.++|||+|||+.+++++|.++|++||.|..|.|+.++.++.++|||||+|.+.++|..|+..|||..|.|+.|+|.++
T Consensus         3 ~~~~~l~v~nlp~~~t~~~l~~~f~~~G~i~~~~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~~~~~~~   82 (85)
T 1x4e_A            3 SGSSGLYIRGLQPGTTDQDLVKLCQPYGKIVSTKAILDKTTNKCKGYGFVDFDSPSAAQKAVTALKASGVQAQMAKQSGP   82 (85)
T ss_dssp             CCCCEEEEESCCTTCCHHHHHTTSTTTSCEEEEEEECCSSSCSCCSEEEEEESCHHHHHHHHHHHHHHTCCEESCCSSCC
T ss_pred             CCCcEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEecCCCCCcCcEEEEEECCHHHHHHHHHHhcCCeEeeEEEeecCC
Confidence            46789999999999999999999999999999999999999999999999999999999999999999999999988776


Q ss_pred             c
Q 007792          320 Q  320 (589)
Q Consensus       320 ~  320 (589)
                      .
T Consensus        83 ~   83 (85)
T 1x4e_A           83 S   83 (85)
T ss_dssp             C
T ss_pred             C
Confidence            4

>2cqg_A TDP-43, TAR DNA-binding protein-43; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.69  E-value=2.4e-16  Score=134.07  Aligned_cols=83  Identities=28%  Similarity=0.436  Sum_probs=77.6

Q ss_pred             CCCCceEEEecCCCCCCHHHHHHHhccCCCeEEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHhcCCceeCCeEEEEEe
Q 007792          239 KPPENVLFVCKLNPVTEDEDLHTIFSRFGTVVSAEIIRDFKTGDSLNYAFIEFENRQACERAYSKMDNALIDDRRIHVDF  318 (589)
Q Consensus       239 ~~~~~~i~V~nL~~~~te~~L~~~F~~~G~v~~~~i~~d~~tg~~~g~aFV~f~~~~~a~~A~~~l~g~~i~gr~i~V~~  318 (589)
                      ..+.++|||+|||+.+++++|+++|++||.|..|.|+.++.+|.++|||||+|.+.++|..||.  ++..|+|+.|.|.+
T Consensus        12 ~~~~~~l~v~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~a~~A~~--~~~~~~g~~l~v~~   89 (103)
T 2cqg_A           12 VQKTSDLIVLGLPWKTTEQDLKEYFSTFGEVLMVQVKKDLKTGHSKGFGFVRFTEYETQVKVMS--QRHMIDGRWCDCKL   89 (103)
T ss_dssp             CCCCCCEEEESCCSSCCHHHHHHHHGGGSCEEEEEEEECSSSCSEEEEEEEEESSHHHHHHHHH--SCEEETTEEEEEEC
T ss_pred             cCCCCEEEEEcCCCcCCHHHHHHHHHhcCCeEEEEEEecCCCCCccceEEEEECCHHHHHHHHH--cCCeeCCeEEEEEe
Confidence            4467899999999999999999999999999999999999999999999999999999999997  57899999999999


Q ss_pred             ccccc
Q 007792          319 SQSVS  323 (589)
Q Consensus       319 a~~~~  323 (589)
                      +.+..
T Consensus        90 a~~~~   94 (103)
T 2cqg_A           90 PNSKQ   94 (103)
T ss_dssp             CCTTC
T ss_pred             cCCCC
Confidence            98754

>2dgw_A Probable RNA-binding protein 19; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.69  E-value=1.7e-16  Score=131.85  Aligned_cols=82  Identities=16%  Similarity=0.278  Sum_probs=77.0

Q ss_pred             CCCCceEEEecCCCCCCHHHHHHHhccCCCeEEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHhcCCceeCCeEEEEEe
Q 007792          239 KPPENVLFVCKLNPVTEDEDLHTIFSRFGTVVSAEIIRDFKTGDSLNYAFIEFENRQACERAYSKMDNALIDDRRIHVDF  318 (589)
Q Consensus       239 ~~~~~~i~V~nL~~~~te~~L~~~F~~~G~v~~~~i~~d~~tg~~~g~aFV~f~~~~~a~~A~~~l~g~~i~gr~i~V~~  318 (589)
                      .....+|||+|||+.+|+++|+++|++| .|..|.|+.+ .+|+++|||||+|.+.++|..||. |||..|+|+.|.|.+
T Consensus         7 ~~~~~~l~v~nLp~~~t~~~l~~~F~~~-~i~~v~i~~~-~~g~~~g~afV~f~~~~~a~~A~~-~~g~~~~gr~i~v~~   83 (91)
T 2dgw_A            7 GTTCHTVKLRGAPFNVTEKNVMEFLAPL-KPVAIRIVRN-AHGNKTGYIFVDFSNEEEVKQALK-CNREYMGGRYIEVFR   83 (91)
T ss_dssp             CCCCCEEEEECCCSSCCHHHHHHHHTTS-CCSEEEEEEC-TTSCEEEEEEEECSSHHHHHHHHH-SCSEEETTEEEEEEE
T ss_pred             CCCccEEEEECCCCCCCHHHHHHHHhhC-CceEEEEEEC-CCCCCceEEEEEECCHHHHHHHHH-hCCceeCCcEEEEEE
Confidence            3457899999999999999999999999 9999999999 889999999999999999999999 999999999999999


Q ss_pred             ccccc
Q 007792          319 SQSVS  323 (589)
Q Consensus       319 a~~~~  323 (589)
                      +++.+
T Consensus        84 a~~~~   88 (91)
T 2dgw_A           84 EKSGP   88 (91)
T ss_dssp             ESSCC
T ss_pred             CCcCC
Confidence            98753

>2cpi_A CCR4-NOT transcription complex subunit 4; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Mus musculus} SCOP: d.58.7.1

Probab=99.68  E-value=6.4e-17  Score=139.75  Aligned_cols=84  Identities=18%  Similarity=0.332  Sum_probs=77.1

Q ss_pred             CCCceEEEecCCCCCCHHHHH---HHhccCCCeEEEEEeecCCCC---CcccEEEEEEcCHHHHHHHHHhcCCceeCCeE
Q 007792          240 PPENVLFVCKLNPVTEDEDLH---TIFSRFGTVVSAEIIRDFKTG---DSLNYAFIEFENRQACERAYSKMDNALIDDRR  313 (589)
Q Consensus       240 ~~~~~i~V~nL~~~~te~~L~---~~F~~~G~v~~~~i~~d~~tg---~~~g~aFV~f~~~~~a~~A~~~l~g~~i~gr~  313 (589)
                      .+.++|||+|||+.+++++|.   ++|++||+|..|.|+.+..++   .++|||||+|.+.++|+.||+.|||..|+|+.
T Consensus        13 ~~~~~l~V~nLp~~~~~~~l~~~~~~F~~~G~i~~v~i~~~~~~~~~~~~~G~afV~f~~~~~A~~Ai~~lng~~~~gr~   92 (111)
T 2cpi_A           13 VQKNLVFVVGLSQRLADPEVLKRPEYFGKFGKIHKVVINNSTSYAGSQGPSASAYVTYIRSEDALRAIQCVNNVVVDGRT   92 (111)
T ss_dssp             CCSSCEEEEEECTTTCCHHHHHSTTTTTTTSCEEEEEEECCSSCCSSSCCCEEEEEEESSHHHHHHHHHHHTTEEETTEE
T ss_pred             cCCCEEEEECCCCCCCHHHHHHHHHHhhccCCEEEEEEecCCCcCccCCCCeEEEEEECcHHHHHHHHHHhCCCEECCEE
Confidence            356899999999999999999   999999999999999887654   45699999999999999999999999999999


Q ss_pred             EEEEeccccc
Q 007792          314 IHVDFSQSVS  323 (589)
Q Consensus       314 i~V~~a~~~~  323 (589)
                      |.|.+|.++.
T Consensus        93 l~V~~a~~k~  102 (111)
T 2cpi_A           93 LKASLGTTKY  102 (111)
T ss_dssp             EEEESCCCCS
T ss_pred             EEEEeccccc
Confidence            9999998754

>2dgv_A HnRNP M, heterogeneous nuclear ribonucleoprotein M; RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} PDB: 2dh9_A

Probab=99.68  E-value=9e-17  Score=133.71  Aligned_cols=83  Identities=25%  Similarity=0.326  Sum_probs=77.4

Q ss_pred             CCCCceEEEecCCCCCCHHHHHHHhccCCCeEEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHhcCCceeCCeEEEEEe
Q 007792          239 KPPENVLFVCKLNPVTEDEDLHTIFSRFGTVVSAEIIRDFKTGDSLNYAFIEFENRQACERAYSKMDNALIDDRRIHVDF  318 (589)
Q Consensus       239 ~~~~~~i~V~nL~~~~te~~L~~~F~~~G~v~~~~i~~d~~tg~~~g~aFV~f~~~~~a~~A~~~l~g~~i~gr~i~V~~  318 (589)
                      .++.++|||+|||+.+++++|+++|++||.|..|.|+.  .++.++|||||+|.+.++|..||..|||..|.|+.|.|.+
T Consensus         5 ~~~~~~l~V~nlp~~~t~~~l~~~f~~~G~v~~~~i~~--~~g~~~g~afV~f~~~~~a~~a~~~l~g~~~~g~~l~v~~   82 (92)
T 2dgv_A            5 SSGACQIFVRNLPFDFTWKMLKDKFNECGHVLYADIKM--ENGKSKGCGVVKFESPEVAERACRMMNGMKLSGREIDVRI   82 (92)
T ss_dssp             SSSCCEEEECSCCTTCCHHHHHHHHHTTSCEEEEEEEE--SSSCEEEEEEEEESSHHHHHHHHHHHTTCCBTTBCCCCEE
T ss_pred             CCCCcEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEc--cCCCcceEEEEEECCHHHHHHHHHHhCCCEECCcEEEEEE
Confidence            34678999999999999999999999999999999987  4788999999999999999999999999999999999999


Q ss_pred             ccccc
Q 007792          319 SQSVS  323 (589)
Q Consensus       319 a~~~~  323 (589)
                      +++..
T Consensus        83 a~~~~   87 (92)
T 2dgv_A           83 DRNAS   87 (92)
T ss_dssp             CSCCS
T ss_pred             cCCCC
Confidence            98743

>1x4a_A Splicing factor, arginine/serine-rich 1 (splicing factor 2, alternate splicing factor)...; structure genomics, SURP domain, splicing factor SF2; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.68  E-value=2.5e-16  Score=135.52  Aligned_cols=82  Identities=23%  Similarity=0.425  Sum_probs=75.4

Q ss_pred             CCCCceEEEecCCCCCCHHHHHHHhccCCCeEEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHhcCCceeCCeEEEEEe
Q 007792          239 KPPENVLFVCKLNPVTEDEDLHTIFSRFGTVVSAEIIRDFKTGDSLNYAFIEFENRQACERAYSKMDNALIDDRRIHVDF  318 (589)
Q Consensus       239 ~~~~~~i~V~nL~~~~te~~L~~~F~~~G~v~~~~i~~d~~tg~~~g~aFV~f~~~~~a~~A~~~l~g~~i~gr~i~V~~  318 (589)
                      ..+.++|||+|||+.+|+++|+++|++||.|..|.|+.+   +.++|||||+|.+.++|..||+.||+..|.|+.|.|.+
T Consensus        19 ~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~~~i~~~---~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~V~~   95 (109)
T 1x4a_A           19 GNNDCRIYVGNLPPDIRTKDIEDVFYKYGAIRDIDLKNR---RGGPPFAFVEFEDPRDAEDAVYGRDGYDYDGYRLRVEF   95 (109)
T ss_dssp             CCCSSEEEEESCCTTCCHHHHHHHHGGGSCEEEEEECCS---SSSSCCEEEEESCHHHHHHHHHHHTTCEETTEECEEEC
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEEC---CCCCcEEEEEECCHHHHHHHHHHcCCCEECCeEEEEEE
Confidence            456789999999999999999999999999999999654   55889999999999999999999999999999999999


Q ss_pred             ccccc
Q 007792          319 SQSVS  323 (589)
Q Consensus       319 a~~~~  323 (589)
                      +++..
T Consensus        96 a~~~~  100 (109)
T 1x4a_A           96 PRSGR  100 (109)
T ss_dssp             CCCCC
T ss_pred             cccCC
Confidence            98743

>2mss_A Protein (musashi1); RNA-binding domain, RNA binding protein; NMR {Mus musculus} SCOP: d.58.7.1 PDB: 2mst_A

Probab=99.68  E-value=2.8e-17  Score=131.27  Aligned_cols=75  Identities=24%  Similarity=0.391  Sum_probs=72.3

Q ss_pred             eEEEecCCCCCCHHHHHHHhccCCCeEEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHhcCCceeCCeEEEEEec
Q 007792          244 VLFVCKLNPVTEDEDLHTIFSRFGTVVSAEIIRDFKTGDSLNYAFIEFENRQACERAYSKMDNALIDDRRIHVDFS  319 (589)
Q Consensus       244 ~i~V~nL~~~~te~~L~~~F~~~G~v~~~~i~~d~~tg~~~g~aFV~f~~~~~a~~A~~~l~g~~i~gr~i~V~~a  319 (589)
                      +|||+|||+.+|+++|.++|++||+|..|.|+.++.+|.++|||||+|.+.++|++|++ |||..|+|+.|.|++|
T Consensus         1 ~l~v~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~a~~-~~~~~~~g~~l~v~~A   75 (75)
T 2mss_A            1 KIFVGGLSVNTTVEDVKHYFEQFGKVDDAMLMFDKTTNRHRGFGFVTFESEDIVEKVCE-IHFHEINNKMVECKKA   75 (75)
T ss_dssp             CEEEECCCSSCCHHHHHHHHHTTSCCSEECCCBCSSSTTSCBEEEEECSCHHHHHHHHS-SSCCCSSSCCCEEECC
T ss_pred             CEEEecCCCCCCHHHHHHHHHhcCCEEEEEEEecCCCCCcCcEEEEEECCHHHHHHHHH-CCCCEECCEEEEEEeC
Confidence            58999999999999999999999999999999998899999999999999999999996 9999999999999875

>2j76_E EIF-4B, EIF4B, eukaryotic translation initiation factor 4B; protein biosynthesis, RNA recognition motif, RNA binding domain, RRM, RBD, RNP; NMR {Homo sapiens}

Probab=99.68  E-value=2.6e-17  Score=139.39  Aligned_cols=83  Identities=19%  Similarity=0.364  Sum_probs=75.1

Q ss_pred             CCCCCceEEEecCCCCCCHHHHHHHhccCCCeEEEEEeecC-CCCCcccEEEEEEcCHHHHHHHHHhcCCceeCCeEEEE
Q 007792          238 IKPPENVLFVCKLNPVTEDEDLHTIFSRFGTVVSAEIIRDF-KTGDSLNYAFIEFENRQACERAYSKMDNALIDDRRIHV  316 (589)
Q Consensus       238 ~~~~~~~i~V~nL~~~~te~~L~~~F~~~G~v~~~~i~~d~-~tg~~~g~aFV~f~~~~~a~~A~~~l~g~~i~gr~i~V  316 (589)
                      ...+.++|||+|||+.+++++|.++|++|| |..|.|+.++ .+|+++|||||+|.+.++|..|| .|||..|+|+.|.|
T Consensus        15 ~~~~~~~l~V~nLp~~~t~~~l~~~F~~~G-i~~v~i~~~~~~~g~~~g~afV~f~~~~~a~~Ai-~l~g~~~~g~~l~V   92 (100)
T 2j76_E           15 PKSPPYTAFLGNLPYDVTEESIKEFFRGLN-ISAVRLPREPSNPERLKGFGYAEFEDLDSLLSAL-SLNEESLGNRRIRV   92 (100)
T ss_dssp             -----CEEEESCCSSCCSSSHHHHHSCSSC-EEEEECSCCTTTTCCCCSCEEEEECCHHHHHHHH-HTTTCCBTTBCCCC
T ss_pred             CCCCCcEEEEeCCCCCCCHHHHHHHHHhcC-CeEEEEEecCCcCCccCeEEEEEECCHHHHHHHH-hcCCCEECCeEEEE
Confidence            345678999999999999999999999999 9999999998 68999999999999999999999 89999999999999


Q ss_pred             Eecccc
Q 007792          317 DFSQSV  322 (589)
Q Consensus       317 ~~a~~~  322 (589)
                      .++++.
T Consensus        93 ~~a~~~   98 (100)
T 2j76_E           93 DVADQA   98 (100)
T ss_dssp             EECCCS
T ss_pred             EeccCC
Confidence            999864

>2nlw_A Eukaryotic translation initiation factor 3 subunit 9; eukaryotic initiation factor 3 complex, RNA recognition motif; NMR {Homo sapiens}

Probab=99.68  E-value=9.3e-17  Score=137.28  Aligned_cols=82  Identities=21%  Similarity=0.353  Sum_probs=75.6

Q ss_pred             CCCCceEEEecCCCCC------CHHHHHHHhccCCCeEEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHhcCCceeCCe
Q 007792          239 KPPENVLFVCKLNPVT------EDEDLHTIFSRFGTVVSAEIIRDFKTGDSLNYAFIEFENRQACERAYSKMDNALIDDR  312 (589)
Q Consensus       239 ~~~~~~i~V~nL~~~~------te~~L~~~F~~~G~v~~~~i~~d~~tg~~~g~aFV~f~~~~~a~~A~~~l~g~~i~gr  312 (589)
                      ....++|||+|||+.+      |+++|..+|++||.|..|.|+  ..+|+++|||||+|.+.++|..||..|||..|.|+
T Consensus        12 ~~~~~~l~V~nLp~~~~~~~~~t~~~l~~~F~~~G~v~~v~i~--~~~g~~~G~afV~f~~~~~A~~Ai~~l~g~~~~g~   89 (105)
T 2nlw_A           12 DGIDSVIVVDNVPQVGPDRLEKLKNVIHKIFSKFGKITNDFYP--EEDGKTKGYIFLEYASPAHAVDAVKNADGYKLDKQ   89 (105)
T ss_dssp             CSCCSEEEEESCCCCCTTTTTHHHHHHHHHHGGGSCEEEEECC--CBTTBSCCEEEEEECSSSHHHHHHHHCSSEECSTT
T ss_pred             CCCCCEEEEeCCCcchhhhhHHHHHHHHHHHhcCCCEEEEEee--CCCCCeeeEEEEEECCHHHHHHHHHHhCCcccCCC
Confidence            3346899999999999      789999999999999999988  47899999999999999999999999999999998


Q ss_pred             -EEEEEecccc
Q 007792          313 -RIHVDFSQSV  322 (589)
Q Consensus       313 -~i~V~~a~~~  322 (589)
                       +|.|.++...
T Consensus        90 ~~l~V~~a~~~  100 (105)
T 2nlw_A           90 HTFRVNLFTDF  100 (105)
T ss_dssp             CEEEEECSCCC
T ss_pred             ceEEEEEcchH
Confidence             9999999753

>1x4c_A Splicing factor, arginine/serine-rich 1; structural genomics, RRM domain, NPPSFA, national project on protein structural and functional analyses; NMR {Mus musculus} SCOP: d.58.7.1

Probab=99.68  E-value=2.8e-16  Score=134.98  Aligned_cols=78  Identities=27%  Similarity=0.342  Sum_probs=72.8

Q ss_pred             CCCceEEEecCCCCCCHHHHHHHhccCCCeEEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHhcCCceeCC-----eEE
Q 007792          240 PPENVLFVCKLNPVTEDEDLHTIFSRFGTVVSAEIIRDFKTGDSLNYAFIEFENRQACERAYSKMDNALIDD-----RRI  314 (589)
Q Consensus       240 ~~~~~i~V~nL~~~~te~~L~~~F~~~G~v~~~~i~~d~~tg~~~g~aFV~f~~~~~a~~A~~~l~g~~i~g-----r~i  314 (589)
                      .+.++|||+|||+.+|+++|+++|.+||.|..|.|+.+       |||||+|.+.++|+.||+.|||..|.|     +.|
T Consensus        13 ~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~~~i~~~-------g~afV~f~~~~~a~~Ai~~l~g~~~~g~~~~~~~i   85 (108)
T 1x4c_A           13 RSENRVVVSGLPPSGSWQDLKDHMREAGDVCYADVYRD-------GTGVVEFVRKEDMTYAVRKLDNTKFRSHEGETAYI   85 (108)
T ss_dssp             SCCCEEEEESCCSSCCHHHHHHHHGGGSCEEEEEEETT-------TEEEEEESSHHHHHHHHHHSSSEEEECTTSCEEEE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCEeEEEEecC-------CEEEEEECCHHHHHHHHHHHCcCCccCCcCcceEE
Confidence            35689999999999999999999999999999999876       899999999999999999999999999     999


Q ss_pred             EEEecccccc
Q 007792          315 HVDFSQSVSK  324 (589)
Q Consensus       315 ~V~~a~~~~~  324 (589)
                      .|++|.+...
T Consensus        86 ~V~~a~~~~~   95 (108)
T 1x4c_A           86 RVKVDGPRSP   95 (108)
T ss_dssp             EEEESSCCSC
T ss_pred             EEEeCCCCCC
Confidence            9999987443

>2a3j_A U1 small nuclear ribonucleoprotein A; computationally designed protein, RRM, U1A, RNA binding protein; NMR {Homo sapiens}

Probab=99.68  E-value=9.8e-17  Score=141.67  Aligned_cols=83  Identities=17%  Similarity=0.341  Sum_probs=74.7

Q ss_pred             CCCCceEEEecCCCCCCHHHHH----HHhccCCCeEEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHhcCCceeCCeEE
Q 007792          239 KPPENVLFVCKLNPVTEDEDLH----TIFSRFGTVVSAEIIRDFKTGDSLNYAFIEFENRQACERAYSKMDNALIDDRRI  314 (589)
Q Consensus       239 ~~~~~~i~V~nL~~~~te~~L~----~~F~~~G~v~~~~i~~d~~tg~~~g~aFV~f~~~~~a~~A~~~l~g~~i~gr~i  314 (589)
                      .+|.++|||+|||+.+++++|+    ++|++||.|..|.+..   +++++|||||+|.+.++|..||..|||..|.|++|
T Consensus        26 ~~p~~~LfV~nL~~~~~e~~L~~~L~~~F~~~G~I~~v~i~~---~~~~rG~aFV~F~~~~~A~~Ai~~lng~~l~gr~l  102 (127)
T 2a3j_A           26 TEPSQVVLITNINPEVPKEKLQALLYALASSQGDILDIVVDL---SDDNSGKAYIVFATQESAQAFVEAFQGYPFQGNPL  102 (127)
T ss_dssp             CSCCSEEEEESCCTTSCHHHHHHHHHHHHHHHSCEEEEEECC---CCSSCCCEEEEESSHHHHHHHHHHSTTCCCTTSCC
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHHHhccCCCeEEEEecc---CCCcCCEEEEEECCHHHHHHHHHHHCCCEeCCCEE
Confidence            4567899999999999999876    6999999999988753   67899999999999999999999999999999999


Q ss_pred             EEEecccccc
Q 007792          315 HVDFSQSVSK  324 (589)
Q Consensus       315 ~V~~a~~~~~  324 (589)
                      .|.||++...
T Consensus       103 ~V~~a~~~~~  112 (127)
T 2a3j_A          103 VITFSETPQS  112 (127)
T ss_dssp             EEEECCCCCH
T ss_pred             EEEEccCcch
Confidence            9999987443

>1x4b_A Heterogeneous nuclear ribonucleoproteins A2/B1; structure genomics, RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.68  E-value=1.4e-16  Score=138.70  Aligned_cols=82  Identities=20%  Similarity=0.325  Sum_probs=77.8

Q ss_pred             CCceEEEecCCCCCCHHHHHHHhccCCCeEEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHhcCCceeCCeEEEEEecc
Q 007792          241 PENVLFVCKLNPVTEDEDLHTIFSRFGTVVSAEIIRDFKTGDSLNYAFIEFENRQACERAYSKMDNALIDDRRIHVDFSQ  320 (589)
Q Consensus       241 ~~~~i~V~nL~~~~te~~L~~~F~~~G~v~~~~i~~d~~tg~~~g~aFV~f~~~~~a~~A~~~l~g~~i~gr~i~V~~a~  320 (589)
                      +.++|||+|||+.+|+++|+++|.+||.|..|.|+.++.++.++|||||+|.+.++|..||.. ++..|.|+.|.|.++.
T Consensus        26 ~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~a~~Ai~~-~~~~~~g~~l~V~~a~  104 (116)
T 1x4b_A           26 QFRKLFIGGLSFETTEESLRNYYEQWGKLTDCVVMRDPASKRSRGFGFVTFSSMAEVDAAMAA-RPHSIDGRVVEPKRAV  104 (116)
T ss_dssp             HHTEEEEECCTTCCCHHHHHHHHTSSCCCSEEEEECCTTTSSCCSEEEEECSSHHHHHHHHTS-CSEEETTEEEEEECCS
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEECCCCCCcCceEEEEeCCHHHHHHHHHh-CCcEECCEEEEEEECC
Confidence            347999999999999999999999999999999999999999999999999999999999987 9999999999999998


Q ss_pred             ccc
Q 007792          321 SVS  323 (589)
Q Consensus       321 ~~~  323 (589)
                      +..
T Consensus       105 ~~~  107 (116)
T 1x4b_A          105 ARE  107 (116)
T ss_dssp             SCC
T ss_pred             CCc
Confidence            754

>2cq1_A PTB-like protein L; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.68  E-value=3.6e-16  Score=132.31  Aligned_cols=80  Identities=19%  Similarity=0.283  Sum_probs=72.4

Q ss_pred             CCCCCceEEEecCCCCCCHHHHHHHhccCCCeEEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHhc--CCceeCCeEEE
Q 007792          238 IKPPENVLFVCKLNPVTEDEDLHTIFSRFGTVVSAEIIRDFKTGDSLNYAFIEFENRQACERAYSKM--DNALIDDRRIH  315 (589)
Q Consensus       238 ~~~~~~~i~V~nL~~~~te~~L~~~F~~~G~v~~~~i~~d~~tg~~~g~aFV~f~~~~~a~~A~~~l--~g~~i~gr~i~  315 (589)
                      ..+|.++|||+|||+.+|+++|.++|++||.|..|.|+.+      +|||||+|.+.++|..|+..|  ++..|.|++|.
T Consensus        11 ~~~p~~~l~V~nLp~~~te~~L~~~F~~fG~v~~v~i~~~------kg~aFVef~~~~~A~~Ai~~l~~~~~~~~Gr~l~   84 (101)
T 2cq1_A           11 DGAPSRVLHIRKLPGEVTETEVIALGLPFGKVTNILMLKG------KNQAFLELATEEAAITMVNYYSAVTPHLRNQPIY   84 (101)
T ss_dssp             CSSCCSEEEEESCCTTCCHHHHHHTTTTTSCEEEEEEETT------TTEEEEEESSHHHHHHHHHHHHHSCCEETTEECE
T ss_pred             cCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEECC------CCEEEEEECCHHHHHHHHHHhccCCceECCcEEE
Confidence            3567899999999999999999999999999999988764      699999999999999999977  57889999999


Q ss_pred             EEeccccc
Q 007792          316 VDFSQSVS  323 (589)
Q Consensus       316 V~~a~~~~  323 (589)
                      |.||++..
T Consensus        85 V~~a~~~~   92 (101)
T 2cq1_A           85 IQYSNHKE   92 (101)
T ss_dssp             EEECSCSS
T ss_pred             EEEcCccc
Confidence            99998644

>1x4d_A Matrin 3; structural genomics, RRM domain, NPPSFA, national project on protein structural and functional analyses; NMR {Mus musculus} SCOP: d.58.7.1

Probab=99.67  E-value=1.1e-16  Score=135.52  Aligned_cols=80  Identities=20%  Similarity=0.318  Sum_probs=72.3

Q ss_pred             CCCCceEEEecCCC-CCCHHHHHHHhccCCCeEEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHhcCC--ceeCCeEEE
Q 007792          239 KPPENVLFVCKLNP-VTEDEDLHTIFSRFGTVVSAEIIRDFKTGDSLNYAFIEFENRQACERAYSKMDN--ALIDDRRIH  315 (589)
Q Consensus       239 ~~~~~~i~V~nL~~-~~te~~L~~~F~~~G~v~~~~i~~d~~tg~~~g~aFV~f~~~~~a~~A~~~l~g--~~i~gr~i~  315 (589)
                      ..|..+|||+|||+ .+|+++|.++|++||.|..|.|+.+      +|||||+|.+.++|..||+.||+  ..|.|++|.
T Consensus        12 ~~p~~~l~V~nLp~~~~te~dL~~lF~~fG~V~~v~i~~~------kg~aFVef~~~~~A~~Ai~~l~~~~~~~~Gr~l~   85 (102)
T 1x4d_A           12 VETRRVVHIMDFQRGKNLRYQLLQLVEPFGVISNHLILNK------INEAFIEMATTEDAQAAVDYYTTTPALVFGKPVR   85 (102)
T ss_dssp             CCCCCEEEEESCCCSSSHHHHHHTTTGGGSCEEEEEECSS------SSCEEEEESSHHHHHHHHHHHHHSCCEETTEECE
T ss_pred             CCCCCEEEEeCCCCCcCCHHHHHHHHHhcCCEEEEEEEcC------CCEEEEEECCHHHHHHHHHHHcCCCceECCcEEE
Confidence            44788999999999 9999999999999999999999864      48999999999999999999886  469999999


Q ss_pred             EEecccccc
Q 007792          316 VDFSQSVSK  324 (589)
Q Consensus       316 V~~a~~~~~  324 (589)
                      |++|+....
T Consensus        86 V~~a~~~~~   94 (102)
T 1x4d_A           86 VHLSQKYKR   94 (102)
T ss_dssp             EEEECCCTT
T ss_pred             EEECCCCCC
Confidence            999986443

>2cpy_A RNA-binding protein 12; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.67  E-value=1.1e-16  Score=138.87  Aligned_cols=84  Identities=11%  Similarity=0.195  Sum_probs=77.9

Q ss_pred             CCCCCceEEEecCCCCCCHHHHHHHhccCCCe-EEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHhcCCceeCCeEEEE
Q 007792          238 IKPPENVLFVCKLNPVTEDEDLHTIFSRFGTV-VSAEIIRDFKTGDSLNYAFIEFENRQACERAYSKMDNALIDDRRIHV  316 (589)
Q Consensus       238 ~~~~~~~i~V~nL~~~~te~~L~~~F~~~G~v-~~~~i~~d~~tg~~~g~aFV~f~~~~~a~~A~~~l~g~~i~gr~i~V  316 (589)
                      ...+..+|||+|||+.+|+++|+++|++||.| ..|.|+.++ +|+++|||||+|.+.++|..||.. |+..|+|+.|.|
T Consensus        11 ~~~~~~~l~V~nLp~~~t~~~l~~~F~~~g~v~~~v~i~~d~-~g~~~G~afV~F~~~~~a~~Al~~-~~~~~~gr~i~v   88 (114)
T 2cpy_A           11 VNSAKVCAHITNIPFSITKMDVLQFLEGIPVDENAVHVLVDN-NGQGLGQALVQFKNEDDARKSERL-HRKKLNGREAFV   88 (114)
T ss_dssp             CCSCCCEEEEESCCTTSCHHHHHHHTTTSCCCSTTEEECCCT-TSSCSSCEEEECSSHHHHHHHGGG-CSEEETTEEEEE
T ss_pred             CCCCccEEEEeCcCCcCCHHHHHHHHHhCCCcCCeEEEEECC-CCCcceEEEEEECCHHHHHHHHHh-CCCccCCeEEEE
Confidence            34567899999999999999999999999999 889999997 899999999999999999999976 999999999999


Q ss_pred             Eeccccc
Q 007792          317 DFSQSVS  323 (589)
Q Consensus       317 ~~a~~~~  323 (589)
                      .++.+..
T Consensus        89 ~~a~~~~   95 (114)
T 2cpy_A           89 HVVTLED   95 (114)
T ss_dssp             EEECHHH
T ss_pred             EECCHHH
Confidence            9998643

>2fc9_A NCL protein; structure genomics, RRM_1 domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.67  E-value=3.3e-16  Score=132.71  Aligned_cols=82  Identities=21%  Similarity=0.397  Sum_probs=74.8

Q ss_pred             CCCCCceEEEecCCCCCCHHHHHHHhccCCCeEEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHhcCCceeCCeEEEEE
Q 007792          238 IKPPENVLFVCKLNPVTEDEDLHTIFSRFGTVVSAEIIRDFKTGDSLNYAFIEFENRQACERAYSKMDNALIDDRRIHVD  317 (589)
Q Consensus       238 ~~~~~~~i~V~nL~~~~te~~L~~~F~~~G~v~~~~i~~d~~tg~~~g~aFV~f~~~~~a~~A~~~l~g~~i~gr~i~V~  317 (589)
                      ...+.++|||+|||+.+|+++|+++|++||.|   .|+.+ .+++++|||||+|.+.++|+.||..|||..|.|+.|.|.
T Consensus        11 ~~~~~~~l~V~nLp~~~t~~~l~~~F~~~g~v---~~~~~-~~g~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~   86 (101)
T 2fc9_A           11 WSGESKTLVLSNLSYSATEETLQEVFEKATFI---KVPQN-QNGKSKGYAFIEFASFEDAKEALNSCNKREIEGRAIRLE   86 (101)
T ss_dssp             CSCCCSEEEEESCCTTCCHHHHHHHCSSCSEE---ECCBC-SSSCBCSEEEEECSSHHHHHHHHHHTSSEEETTEEEEEE
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHhCCEE---EEEEC-CCCCEeeEEEEEECCHHHHHHHHHHhCCCEeCCeEEEEE
Confidence            45578999999999999999999999999987   56665 688999999999999999999999999999999999999


Q ss_pred             eccccc
Q 007792          318 FSQSVS  323 (589)
Q Consensus       318 ~a~~~~  323 (589)
                      ++.+..
T Consensus        87 ~a~~~~   92 (101)
T 2fc9_A           87 LQGPRG   92 (101)
T ss_dssp             ECSSCC
T ss_pred             EcCCCC
Confidence            998743

>2kt5_A RNA and export factor-binding protein 2; chaperone, mRNA processing, mRNA splicing, transport, nucleus, RNA-binding, spliceosome, transport; NMR {Mus musculus}

Probab=99.67  E-value=2.1e-16  Score=139.35  Aligned_cols=84  Identities=26%  Similarity=0.385  Sum_probs=79.2

Q ss_pred             CCCCceEEEecCCCCCCHHHHHHHhccCCCeEEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHhcCCceeCCeEEEEEe
Q 007792          239 KPPENVLFVCKLNPVTEDEDLHTIFSRFGTVVSAEIIRDFKTGDSLNYAFIEFENRQACERAYSKMDNALIDDRRIHVDF  318 (589)
Q Consensus       239 ~~~~~~i~V~nL~~~~te~~L~~~F~~~G~v~~~~i~~d~~tg~~~g~aFV~f~~~~~a~~A~~~l~g~~i~gr~i~V~~  318 (589)
                      ..+.++|||+|||+.+++++|+++|++||.|..|.|+.+. +|.++|||||+|.+.++|..|+..|||..|.|+.|.|.+
T Consensus        32 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~v~~v~i~~~~-~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~~  110 (124)
T 2kt5_A           32 VETGAKLLVSNLDFGVSDADIQELFAEFGTLKKAAVDYDR-SGRSLGTADVHFERRADALKAMKQYKGVPLDGRPMDIQL  110 (124)
T ss_dssp             CSSCEEEEEESCCSSCCHHHHHHHHHTTSCCSEEEEECCS-SSSCCSEEEEEESSHHHHHHHHHHHTTEESSSCEEEEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEECC-CCCEeeEEEEEECCHHHHHHHHHHcCCCEECCcEEEEEE
Confidence            4467899999999999999999999999999999999997 899999999999999999999999999999999999999


Q ss_pred             ccccc
Q 007792          319 SQSVS  323 (589)
Q Consensus       319 a~~~~  323 (589)
                      |.+..
T Consensus       111 a~~~~  115 (124)
T 2kt5_A          111 VASQI  115 (124)
T ss_dssp             ECCTT
T ss_pred             eCCCC
Confidence            98643

>2jwn_A Embryonic polyadenylate-binding protein 2-B; epabp2, poly(A) binding, structural genomics, protein structure initiative, PSI-2; NMR {Xenopus laevis}

Probab=99.67  E-value=2.4e-16  Score=138.92  Aligned_cols=81  Identities=26%  Similarity=0.417  Sum_probs=77.3

Q ss_pred             CceEEEecCCCCCCHHHHHHHhccCCCeEEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHhcCCceeCCeEEEEEeccc
Q 007792          242 ENVLFVCKLNPVTEDEDLHTIFSRFGTVVSAEIIRDFKTGDSLNYAFIEFENRQACERAYSKMDNALIDDRRIHVDFSQS  321 (589)
Q Consensus       242 ~~~i~V~nL~~~~te~~L~~~F~~~G~v~~~~i~~d~~tg~~~g~aFV~f~~~~~a~~A~~~l~g~~i~gr~i~V~~a~~  321 (589)
                      .++|||+|||+.+|+++|.++|++||.|..|.|+.++.+|.++|||||+|.+.++|..|| .|||..|+|+.|.|.++++
T Consensus        36 ~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~-~l~g~~~~g~~l~V~~a~~  114 (124)
T 2jwn_A           36 KRSVYVGNVDYGSTAQDLEAHFSSCGSINRITILCDKFSGHPKGYAYIEFAERNSVDAAV-AMDETVFRGRTIKVLPKRT  114 (124)
T ss_dssp             HTEEEEEEECTTCCHHHHHHHHHTTSCEEEEEEEEECTTSSCEEEEEEEESSHHHHHHHH-TTTTCEETTEECEEEESSC
T ss_pred             CCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEecCCCCCcccEEEEEECCHHHHHHHH-hcCCCeECCeEEEEEECCC
Confidence            479999999999999999999999999999999999999999999999999999999999 8999999999999999986


Q ss_pred             cc
Q 007792          322 VS  323 (589)
Q Consensus       322 ~~  323 (589)
                      ..
T Consensus       115 ~~  116 (124)
T 2jwn_A          115 NM  116 (124)
T ss_dssp             CC
T ss_pred             CC
Confidence            43

>2ku7_A MLL1 PHD3-CYP33 RRM chimeric protein; transcriptional regulation, RRM domain, transcr; NMR {Homo sapiens}

Probab=99.67  E-value=2.7e-16  Score=141.49  Aligned_cols=82  Identities=28%  Similarity=0.474  Sum_probs=77.6

Q ss_pred             CCCCCceEEEecCCCCCCHHHHHHHhccCCCeEEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHhcCCceeCCeEEEEE
Q 007792          238 IKPPENVLFVCKLNPVTEDEDLHTIFSRFGTVVSAEIIRDFKTGDSLNYAFIEFENRQACERAYSKMDNALIDDRRIHVD  317 (589)
Q Consensus       238 ~~~~~~~i~V~nL~~~~te~~L~~~F~~~G~v~~~~i~~d~~tg~~~g~aFV~f~~~~~a~~A~~~l~g~~i~gr~i~V~  317 (589)
                      ..++.++|||+|||+.+|+++|+++|++||+|..|.|+.++.++.++|||||+|.+.++|..||..|||..|.|+.|.|.
T Consensus        59 ~~~~~~~l~v~nlp~~~~~~~l~~~f~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~  138 (140)
T 2ku7_A           59 SATTKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNMNESELFGRTIRVN  138 (140)
T ss_dssp             SCSSCCEEEEECCCTTCCHHHHHHHHGGGSCEEEEECCCCTTTCCCCSEEEEEESCHHHHHHHHHHSTEEEETTEEEEEE
T ss_pred             CCCCCcEEEEEeCCCCCCHHHHHHHHHhcCCEEEEEEeecCCCCCcCcEEEEEECCHHHHHHHHHHhCCCEECCEEEEEE
Confidence            34567899999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             ec
Q 007792          318 FS  319 (589)
Q Consensus       318 ~a  319 (589)
                      +|
T Consensus       139 ~A  140 (140)
T 2ku7_A          139 LA  140 (140)
T ss_dssp             C-
T ss_pred             eC
Confidence            86

>2ki2_A SS-DNA binding protein 12RNP2; HP0827, RRM, SS-DNA binding proteins, RNA binding protein/SS-DNA binding protein complex; NMR {Helicobacter pylori}

Probab=99.67  E-value=2.4e-17  Score=136.62  Aligned_cols=81  Identities=25%  Similarity=0.416  Sum_probs=74.3

Q ss_pred             ceEEEecCCCCCCHHHHHHHhccCCCeEEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHhcCCceeCCeEEEEEecccc
Q 007792          243 NVLFVCKLNPVTEDEDLHTIFSRFGTVVSAEIIRDFKTGDSLNYAFIEFENRQACERAYSKMDNALIDDRRIHVDFSQSV  322 (589)
Q Consensus       243 ~~i~V~nL~~~~te~~L~~~F~~~G~v~~~~i~~d~~tg~~~g~aFV~f~~~~~a~~A~~~l~g~~i~gr~i~V~~a~~~  322 (589)
                      ++|||+|||+.+++++|.++|++||+|..|.|+.++.+|.++|||||+|.+.+ |..|+..|||..|.|+.|.|.+|.+.
T Consensus         2 ~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~-a~~a~~~l~g~~~~g~~l~V~~a~~~   80 (90)
T 2ki2_A            2 RNIYVGNLVYSATSEQVKELFSQFGKVFNVKLIYDRETKKPKGFGFVEMQEES-VSEAIAKLDNTDFMGRTIRVTEANPK   80 (90)
T ss_dssp             EEEEEEEECTTSSHHHHTTTHHHHTCCSEEEECCCSSSCCCCEEEEEEECTTH-HHHHHHTSCSSCCSSSSCSEEEC---
T ss_pred             cEEEECCCCCCCCHHHHHHHHHhcCCEEEEEEEEcCCCCCcceEEEEEECCHH-HHHHHHHhCCCEECCeEEEEEEcCCC
Confidence            58999999999999999999999999999999999999999999999999999 99999999999999999999999874


Q ss_pred             cc
Q 007792          323 SK  324 (589)
Q Consensus       323 ~~  324 (589)
                      ..
T Consensus        81 ~~   82 (90)
T 2ki2_A           81 KS   82 (90)
T ss_dssp             --
T ss_pred             CC
Confidence            43

>2m2b_A RNA-binding protein 10; T-cell, JCSG, MPP, PSI-biology; NMR {Homo sapiens}

Probab=99.67  E-value=3.2e-17  Score=146.10  Aligned_cols=84  Identities=18%  Similarity=0.376  Sum_probs=79.0

Q ss_pred             CCCCceEEEecCCCCCCHHHHHHHhccCCCeEE--EEEeecCCCCCcccEEEEEEcCHHHHHHHHHhcCCc----eeCCe
Q 007792          239 KPPENVLFVCKLNPVTEDEDLHTIFSRFGTVVS--AEIIRDFKTGDSLNYAFIEFENRQACERAYSKMDNA----LIDDR  312 (589)
Q Consensus       239 ~~~~~~i~V~nL~~~~te~~L~~~F~~~G~v~~--~~i~~d~~tg~~~g~aFV~f~~~~~a~~A~~~l~g~----~i~gr  312 (589)
                      ..+.++|||+|||+.+|+++|+++|++||.|..  |.|+.++.||+++|||||+|.+. +|..||..|||.    .|+|+
T Consensus        20 ~~~~~~lfV~nL~~~~te~~L~~~F~~~G~v~~~~v~i~~d~~tg~~rG~aFV~f~~~-~a~~Ai~~l~g~~~~~~~~gr   98 (131)
T 2m2b_A           20 ENANDTIILRNLNPHSTMDSILGALAPYAVLSSSNVRVIKDKQTQLNRGFAFIQLSTI-EAAQLLQILQALHPPLTIDGK   98 (131)
T ss_dssp             SCCCCEEEECSCCTTCCSHHHHHHHGGGCCCCTTTEECCBCSSSSSBCSCEEEECCHH-HHHHHHHHHTTCCCSCCGGGC
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHHhCCcceeeEEEEEcCCCCCcceEEEEEECCH-HHHHHHHHhcCCCCCccCCCE
Confidence            456789999999999999999999999999976  99999999999999999999999 999999999999    99999


Q ss_pred             EEEEEeccccc
Q 007792          313 RIHVDFSQSVS  323 (589)
Q Consensus       313 ~i~V~~a~~~~  323 (589)
                      .|.|.++.+..
T Consensus        99 ~l~V~~a~~~~  109 (131)
T 2m2b_A           99 TINVEFAKGSK  109 (131)
T ss_dssp             CCCCEECCCSC
T ss_pred             EEEEEECCCCC
Confidence            99999998743

>2ad9_A Polypyrimidine tract-binding protein 1; RBD, RRM, protein-RNA complex, RNA binding protein/RNA complex; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.67  E-value=1.5e-16  Score=138.28  Aligned_cols=81  Identities=20%  Similarity=0.321  Sum_probs=73.6

Q ss_pred             CCCCCCceEEEecCCCCCCHHHHHHHhccCCCeEEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHhcCC--ceeCCeEE
Q 007792          237 DIKPPENVLFVCKLNPVTEDEDLHTIFSRFGTVVSAEIIRDFKTGDSLNYAFIEFENRQACERAYSKMDN--ALIDDRRI  314 (589)
Q Consensus       237 ~~~~~~~~i~V~nL~~~~te~~L~~~F~~~G~v~~~~i~~d~~tg~~~g~aFV~f~~~~~a~~A~~~l~g--~~i~gr~i  314 (589)
                      ...+|.++|||+|||+.+|+++|+++|++||.|..|.|+.+      +|||||+|.+.++|.+|++.|++  ..|.|++|
T Consensus        26 ~~~~ps~~LfVgNLp~~vte~dL~~lF~~fG~V~~v~i~~~------kG~AFVeF~~~e~A~~Ai~~l~~~~~~l~Gr~l   99 (119)
T 2ad9_A           26 SAGVPSRVIHIRKLPIDVTEGEVISLGLPFGKVTNLLMLKG------KNQAFIEMNTEEAANTMVNYYTSVTPVLRGQPI   99 (119)
T ss_dssp             SCSSCCSEEEEESCCTTCCHHHHHHHHTTTSCCCEEEEEGG------GTEEEEECSCHHHHHHHHHHHHHHCCCBTTBCC
T ss_pred             ccCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEeCC------CCEEEEEECCHHHHHHHHHHhccCCceECCeEE
Confidence            34567899999999999999999999999999999999874      69999999999999999998874  68999999


Q ss_pred             EEEeccccc
Q 007792          315 HVDFSQSVS  323 (589)
Q Consensus       315 ~V~~a~~~~  323 (589)
                      .|.+|++..
T Consensus       100 ~V~~a~~k~  108 (119)
T 2ad9_A          100 YIQFSNHKE  108 (119)
T ss_dssp             EEEECSSSS
T ss_pred             EEEEccCCC
Confidence            999998744

>1uaw_A Mouse-musashi-1; RNP-type structure, RNA binding protein; NMR {Mus musculus} SCOP: d.58.7.1

Probab=99.66  E-value=5.6e-17  Score=130.17  Aligned_cols=76  Identities=22%  Similarity=0.397  Sum_probs=73.4

Q ss_pred             ceEEEecCCCCCCHHHHHHHhccCCCeEEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHhcCCceeCCeEEEEEec
Q 007792          243 NVLFVCKLNPVTEDEDLHTIFSRFGTVVSAEIIRDFKTGDSLNYAFIEFENRQACERAYSKMDNALIDDRRIHVDFS  319 (589)
Q Consensus       243 ~~i~V~nL~~~~te~~L~~~F~~~G~v~~~~i~~d~~tg~~~g~aFV~f~~~~~a~~A~~~l~g~~i~gr~i~V~~a  319 (589)
                      ++|||+|||+.+++++|.++|++||+|..|.|+.++.+|.++|||||+|.+.++|..|+..|+ ..|+|+.|.|++|
T Consensus         1 ~~l~v~nlp~~~t~~~l~~~F~~~G~v~~v~i~~~~~~~~~~g~afV~f~~~~~a~~a~~~~~-~~~~g~~l~v~~a   76 (77)
T 1uaw_A            1 CKMFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQAGVDKVLAQSR-HELDSKTIDPKVA   76 (77)
T ss_dssp             CCEEEESCCSSCCSHHHHHHHTTTSCCCCEEEECCCCSSSCSSEEEECCCCTTHHHHHHHTTT-CCCSSCCCEEEEC
T ss_pred             CEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEecCCCCCCcCceEEEEEcCHHHHHHHHHhCC-CccCCEEEEEEec
Confidence            479999999999999999999999999999999999999999999999999999999999999 9999999999987

>1wez_A HnRNP H', FTP-3, heterogeneous nuclear ribonucleoprotein H'; structural genomics, RRM domain, riken structural genomics/proteomics initiative, RSGI; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.66  E-value=2.2e-16  Score=134.19  Aligned_cols=81  Identities=16%  Similarity=0.203  Sum_probs=74.8

Q ss_pred             CCCCceEEEecCCCCCCHHHHHHHhccCCCeEEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHhcCCceeCCeEEEEEe
Q 007792          239 KPPENVLFVCKLNPVTEDEDLHTIFSRFGTVVSAEIIRDFKTGDSLNYAFIEFENRQACERAYSKMDNALIDDRRIHVDF  318 (589)
Q Consensus       239 ~~~~~~i~V~nL~~~~te~~L~~~F~~~G~v~~~~i~~d~~tg~~~g~aFV~f~~~~~a~~A~~~l~g~~i~gr~i~V~~  318 (589)
                      ..+..+|||+|||+.+|+++|+++|++||.| .|.|+.++ +|+++|||||+|.+.++|++|| .||+..|+|+.|.|.+
T Consensus        12 ~~~~~~l~V~nLp~~~te~~l~~~F~~~G~~-~v~i~~d~-~g~~~G~afV~F~~~~~a~~Al-~~~~~~~~gr~i~V~~   88 (102)
T 1wez_A           12 STTGHCVHMRGLPYRATENDIYNFFSPLNPM-RVHIEIGP-DGRVTGEADVEFATHEDAVAAM-AKDKANMQHRYVELFL   88 (102)
T ss_dssp             CSSSCEEEEESCCTTCCHHHHHHSSCSCCCS-EEEEEESS-SSCEEEEEEEECSSSHHHHHHH-TTSSCCSSSSCCEEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHHcCce-EEEEEECC-CCCEeeEEEEEECCHHHHHHHH-HhCCCeECCcEEEEEE
Confidence            4567899999999999999999999999954 99999997 8999999999999999999999 5799999999999999


Q ss_pred             cccc
Q 007792          319 SQSV  322 (589)
Q Consensus       319 a~~~  322 (589)
                      +.+.
T Consensus        89 ~~~~   92 (102)
T 1wez_A           89 NSTA   92 (102)
T ss_dssp             ECCC
T ss_pred             CCCC
Confidence            8763

>2err_A Ataxin-2-binding protein 1; protein-RNA complex, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.66  E-value=2.2e-16  Score=135.93  Aligned_cols=84  Identities=27%  Similarity=0.485  Sum_probs=77.1

Q ss_pred             CCCCCCceEEEecCCCCCCHHHHHHHhccCCCeEEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHhcCCceeCCeEEEE
Q 007792          237 DIKPPENVLFVCKLNPVTEDEDLHTIFSRFGTVVSAEIIRDFKTGDSLNYAFIEFENRQACERAYSKMDNALIDDRRIHV  316 (589)
Q Consensus       237 ~~~~~~~~i~V~nL~~~~te~~L~~~F~~~G~v~~~~i~~d~~tg~~~g~aFV~f~~~~~a~~A~~~l~g~~i~gr~i~V  316 (589)
                      ....+.++|||+|||+.+|+++|+++|++||.|..|.|+.++  +.++|||||+|.+.++|..|+..|||..|+|+.|.|
T Consensus        24 ~~~~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~--~~~kg~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V  101 (109)
T 2err_A           24 ENKSQPKRLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNE--RGSKGFGFVTFENSADADRAREKLHGTVVEGRKIEV  101 (109)
T ss_dssp             SCTTCCCEEEEESCCTTCCHHHHHHHGGGTCCCSCEEECCBT--TBCTTEEEEECCCSHHHHHHHHHHTTCEETTEECEE
T ss_pred             cCCCCCCEEEEECCCCcCCHHHHHHHHHhcCCEEEEEEEECC--CCCceEEEEEECCHHHHHHHHHHcCCCEECCEEEEE
Confidence            335567899999999999999999999999999999999874  348999999999999999999999999999999999


Q ss_pred             Eecccc
Q 007792          317 DFSQSV  322 (589)
Q Consensus       317 ~~a~~~  322 (589)
                      .+++++
T Consensus       102 ~~a~~~  107 (109)
T 2err_A          102 NNATAR  107 (109)
T ss_dssp             EECCCS
T ss_pred             EECCCC
Confidence            999864

>2dgu_A Heterogeneous nuclear ribonucleoprotein Q; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} PDB: 2dk2_A

Probab=99.66  E-value=7e-16  Score=131.28  Aligned_cols=78  Identities=27%  Similarity=0.494  Sum_probs=72.0

Q ss_pred             CCCCceEEEecCCCCCCHHHHHHHhccCCCeEEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHhcCCceeCCeEEEEEe
Q 007792          239 KPPENVLFVCKLNPVTEDEDLHTIFSRFGTVVSAEIIRDFKTGDSLNYAFIEFENRQACERAYSKMDNALIDDRRIHVDF  318 (589)
Q Consensus       239 ~~~~~~i~V~nL~~~~te~~L~~~F~~~G~v~~~~i~~d~~tg~~~g~aFV~f~~~~~a~~A~~~l~g~~i~gr~i~V~~  318 (589)
                      ..+.++|||+|||+.+|+++|+++|++||.|..|.|+        ++||||+|.+.++|..||..|||..|.|+.|.|.+
T Consensus         8 ~~~~~~l~V~nl~~~~t~~~l~~~F~~~G~i~~v~~~--------~~~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~   79 (103)
T 2dgu_A            8 MAKVKVLFVRNLANTVTEEILEKAFSQFGKLERVKKL--------KDYAFIHFDERDGAVKAMEEMNGKDLEGENIEIVF   79 (103)
T ss_dssp             CCCCCCEEEECCCTTCCHHHHHHHHHHHSCEEEEEEC--------SSCEEEEESSHHHHHHHHHHHTTEEETTEEEEEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEE--------CCEEEEEeCCHHHHHHHHHHHCCCccCCCEEEEEE
Confidence            3467899999999999999999999999999999986        36999999999999999999999999999999999


Q ss_pred             cccccc
Q 007792          319 SQSVSK  324 (589)
Q Consensus       319 a~~~~~  324 (589)
                      +.+...
T Consensus        80 a~~~~~   85 (103)
T 2dgu_A           80 AKPPDQ   85 (103)
T ss_dssp             CCCCCC
T ss_pred             cCCCcc
Confidence            987544

>1x5o_A RNA binding motif, single-stranded interacting protein 1; structure genomics, RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.66  E-value=4.2e-16  Score=135.20  Aligned_cols=82  Identities=23%  Similarity=0.492  Sum_probs=76.9

Q ss_pred             CCCCceEEEecCCCCCCHHHHHHHhccCCCeEEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHhcCCcee--------C
Q 007792          239 KPPENVLFVCKLNPVTEDEDLHTIFSRFGTVVSAEIIRDFKTGDSLNYAFIEFENRQACERAYSKMDNALI--------D  310 (589)
Q Consensus       239 ~~~~~~i~V~nL~~~~te~~L~~~F~~~G~v~~~~i~~d~~tg~~~g~aFV~f~~~~~a~~A~~~l~g~~i--------~  310 (589)
                      ..+.++|||+|||+.+|+++|..+|.+||.|..|.|+.++ ++.++|||||+|.+.++|..||..|||..|        .
T Consensus        22 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~~~i~~~~-~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~~~~~~~~~  100 (114)
T 1x5o_A           22 EQDPTNLYISNLPLSMDEQELENMLKPFGQVISTRILRDS-SGTSRGVGFARMESTEKCEAVIGHFNGKFIKTPPGVSAP  100 (114)
T ss_dssp             CCCTTEEEEESCCTTCCHHHHHHTTTTTSCEEEEEEEECS-SSCEEEEEEEEESCHHHHHHHHHHHBTCCCCCCTTSCCC
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEECC-CCCcceEEEEEECCHHHHHHHHHHhCCCEEcCCccccCC
Confidence            3467899999999999999999999999999999999997 899999999999999999999999999999        5


Q ss_pred             CeEEEEEeccc
Q 007792          311 DRRIHVDFSQS  321 (589)
Q Consensus       311 gr~i~V~~a~~  321 (589)
                      +++|.|.||.+
T Consensus       101 ~~~l~v~~a~p  111 (114)
T 1x5o_A          101 TEPLLCKFSGP  111 (114)
T ss_dssp             SSCBEEEECCC
T ss_pred             CCceeEEccCC
Confidence            78899999975

>1wg5_A Heterogeneous nuclear ribonucleoprotein H; structural genomics, RRM domain, riken structural genomics/proteomics initiative, RSGI; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.66  E-value=3.7e-16  Score=133.29  Aligned_cols=82  Identities=22%  Similarity=0.264  Sum_probs=75.8

Q ss_pred             CCCCceEEEecCCCCCCHHHHHHHhccCCCeEE-EEEeecCCCCCcccEEEEEEcCHHHHHHHHHhcCCceeCCeEEEEE
Q 007792          239 KPPENVLFVCKLNPVTEDEDLHTIFSRFGTVVS-AEIIRDFKTGDSLNYAFIEFENRQACERAYSKMDNALIDDRRIHVD  317 (589)
Q Consensus       239 ~~~~~~i~V~nL~~~~te~~L~~~F~~~G~v~~-~~i~~d~~tg~~~g~aFV~f~~~~~a~~A~~~l~g~~i~gr~i~V~  317 (589)
                      ..+..+|||+|||+.+|+++|+++|.+||.|.. |.|+.+ .+|+++|||||+|.+.++|..||.. |+..|+|+.|.|.
T Consensus        12 ~~~~~~l~V~nLp~~~te~~l~~~F~~~G~v~~~v~i~~~-~~g~~~G~afV~F~~~~~a~~A~~~-~~~~~~gr~i~v~   89 (104)
T 1wg5_A           12 TANDGFVRLRGLPFGCSKEEIVQFFSGLEIVPNGMTLPVD-FQGRSTGEAFVQFASQEIAEKALKK-HKERIGHRYIEIF   89 (104)
T ss_dssp             CSCCCEEEEESCCTTCCHHHHHHHTTTCCEEEEEEECCBC-SSSCBCSEEEEEESSHHHHHHHHTT-TTCCSSSSCCEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCcceeEEEEEC-CCCCcceEEEEEECCHHHHHHHHHh-CcchhCCcEEEEE
Confidence            345789999999999999999999999999997 888888 8899999999999999999999986 9999999999999


Q ss_pred             ecccc
Q 007792          318 FSQSV  322 (589)
Q Consensus       318 ~a~~~  322 (589)
                      ++.+.
T Consensus        90 ~~~~~   94 (104)
T 1wg5_A           90 KSSRA   94 (104)
T ss_dssp             EECTT
T ss_pred             ECCHH
Confidence            98753

>3q2s_C Cleavage and polyadenylation specificity factor S; CFIM, CFIM25, CFIM68, CPSF5, CPSF6, CPSF, 3' END processing, processing, cleavage factor; 2.90A {Homo sapiens} PDB: 3q2t_C

Probab=99.65  E-value=1.5e-16  Score=155.39  Aligned_cols=82  Identities=15%  Similarity=0.240  Sum_probs=77.7

Q ss_pred             CCceEEEecCCCCCCHHHHHHHhccCC--CeEEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHhcCCceeCCeEEEEEe
Q 007792          241 PENVLFVCKLNPVTEDEDLHTIFSRFG--TVVSAEIIRDFKTGDSLNYAFIEFENRQACERAYSKMDNALIDDRRIHVDF  318 (589)
Q Consensus       241 ~~~~i~V~nL~~~~te~~L~~~F~~~G--~v~~~~i~~d~~tg~~~g~aFV~f~~~~~a~~A~~~l~g~~i~gr~i~V~~  318 (589)
                      ..++|||+||++.+|+++|+++|++||  .|+.|.|+.++.||+++|||||+|.+.++|.+||+.|||..|.|+.|.|.+
T Consensus        67 ~~~~lfVgnL~~~~te~~L~~~F~~~G~~~v~~v~i~~d~~tg~skGfaFV~f~~~~~a~~Ai~~lng~~~~Gr~l~V~~  146 (229)
T 3q2s_C           67 KRIALYIGNLTWWTTDEDLTEAVHSLGVNDILEIKFFENRANGQSKGFALVGVGSEASSKKLMDLLPKRELHGQNPVVTP  146 (229)
T ss_dssp             --CEEEEESCCTTCCHHHHHHHHHTTTCCCEEEEEEEECTTTCCEEEEEEEEESCTTHHHHHHTTSTTSCBTTBCCEEEE
T ss_pred             CccEEEEeCCCCCCCHHHHHHHHHHHCCcceEEEEEEecCCCCccceEEEEEECCHHHHHHHHHHcCCCeECCEEeEEEE
Confidence            467999999999999999999999999  999999999999999999999999999999999999999999999999999


Q ss_pred             cccc
Q 007792          319 SQSV  322 (589)
Q Consensus       319 a~~~  322 (589)
                      |++.
T Consensus       147 a~~~  150 (229)
T 3q2s_C          147 VNKQ  150 (229)
T ss_dssp             CCHH
T ss_pred             CCCC
Confidence            9763

>2ytc_A PRE-mRNA-splicing factor RBM22; RRM domain, RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.65  E-value=6.3e-16  Score=126.54  Aligned_cols=76  Identities=28%  Similarity=0.517  Sum_probs=71.1

Q ss_pred             CCCCceEEEecCCCCCCHHHHHHHhccCCCeEEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHhc-CCceeCCeEEEEE
Q 007792          239 KPPENVLFVCKLNPVTEDEDLHTIFSRFGTVVSAEIIRDFKTGDSLNYAFIEFENRQACERAYSKM-DNALIDDRRIHVD  317 (589)
Q Consensus       239 ~~~~~~i~V~nL~~~~te~~L~~~F~~~G~v~~~~i~~d~~tg~~~g~aFV~f~~~~~a~~A~~~l-~g~~i~gr~i~V~  317 (589)
                      .++.++|||+|||+.+|+++|.++|++||.|..|.|+.      ++|||||+|.+.++|..|+..| +|..|.|+.|.|+
T Consensus         9 ~~~~~~l~V~~l~~~~t~~~l~~~f~~~G~i~~~~~~~------~kg~afV~f~~~~~A~~a~~~l~~~~~~~g~~l~v~   82 (85)
T 2ytc_A            9 DKTITTLYVGGLGDTITETDLRNHFYQFGEIRTITVVQ------RQQCAFIQFATRQAAEVAAEKSFNKLIVNGRRLNVK   82 (85)
T ss_dssp             CSSCCCEEEECCTTTSCHHHHHHHHHTTSCEEEEEEEG------GGTEEEEEESSHHHHHHHHHTTTTTCEETTEECCEE
T ss_pred             CCCccEEEEcCCCCCCCHHHHHHHHHhCCCEeEEEEEC------CCCEEEEEECCHHHHHHHHHHhcCCeeECCCEEEEE
Confidence            45678999999999999999999999999999999986      4699999999999999999988 9999999999999


Q ss_pred             ecc
Q 007792          318 FSQ  320 (589)
Q Consensus       318 ~a~  320 (589)
                      ||+
T Consensus        83 ~ak   85 (85)
T 2ytc_A           83 WGR   85 (85)
T ss_dssp             ECC
T ss_pred             ecC
Confidence            984

>2jvr_A Nucleolar protein 3; RNA recognition motif, nucleus, phosphorylation, ribonucleoprotein, ribosome biogenesis, RNA-binding; NMR {Saccharomyces cerevisiae} PDB: 2osr_A

Probab=99.65  E-value=2.7e-16  Score=135.41  Aligned_cols=80  Identities=13%  Similarity=0.084  Sum_probs=72.3

Q ss_pred             CCCCceEEEecCCCCCCHHHHHHHhccCC-CeEEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHhcCCceeCCeEEEEE
Q 007792          239 KPPENVLFVCKLNPVTEDEDLHTIFSRFG-TVVSAEIIRDFKTGDSLNYAFIEFENRQACERAYSKMDNALIDDRRIHVD  317 (589)
Q Consensus       239 ~~~~~~i~V~nL~~~~te~~L~~~F~~~G-~v~~~~i~~d~~tg~~~g~aFV~f~~~~~a~~A~~~l~g~~i~gr~i~V~  317 (589)
                      .+...+|||+|||+.+|+++|+++|++|| .|..+.|+.    ..++|||||+|.+.++|+.||+.|||..|.|+.|.|.
T Consensus        25 p~~~~~l~VgnLp~~~te~dL~~~F~~~G~~v~~v~i~~----~~~rGfaFV~F~~~e~A~~Ai~~lng~~l~Gr~i~V~  100 (111)
T 2jvr_A           25 PAKRYRITMKNLPEGCSWQDLKDLARENSLETTFSSVNT----RDFDGTGALEFPSEEILVEALERLNNIEFRGSVITVE  100 (111)
T ss_dssp             CCCCEEEEEECSSCCCCHHHHHHHHHHHTCCCSEEECSS----CSSSCCEEEEESSHHHHHHHHHHTTTEEETTEEEEEE
T ss_pred             CCCCCEEEEECCCCCCCHHHHHHHHHHhCCeeEEEEEEc----CCCCCEEEEEECCHHHHHHHHHHcCCCEECCeEEEEE
Confidence            33568999999999999999999999999 899998854    2478999999999999999999999999999999999


Q ss_pred             ecccc
Q 007792          318 FSQSV  322 (589)
Q Consensus       318 ~a~~~  322 (589)
                      ++...
T Consensus       101 ~a~~~  105 (111)
T 2jvr_A          101 RDDNP  105 (111)
T ss_dssp             ESCC-
T ss_pred             ECCCC
Confidence            99753

>2cpd_A Apobec-1 stimulating protein; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.65  E-value=1.2e-15  Score=128.77  Aligned_cols=82  Identities=27%  Similarity=0.466  Sum_probs=73.7

Q ss_pred             CCCCCCCCCceEEEecCCCCCCHHHHHHHhccC--CCeEEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHhcCCceeCC
Q 007792          234 PDADIKPPENVLFVCKLNPVTEDEDLHTIFSRF--GTVVSAEIIRDFKTGDSLNYAFIEFENRQACERAYSKMDNALIDD  311 (589)
Q Consensus       234 ~~~~~~~~~~~i~V~nL~~~~te~~L~~~F~~~--G~v~~~~i~~d~~tg~~~g~aFV~f~~~~~a~~A~~~l~g~~i~g  311 (589)
                      +.....++.++|||+|||+.+|+++|+.+|++|  |.|..|.++        +|||||+|.+.++|..||..|||..|.|
T Consensus         7 ~~~~~~~~~~~l~V~nLp~~~t~~~l~~~F~~~g~g~v~~~~~~--------~g~afV~f~~~~~A~~A~~~l~g~~~~g   78 (99)
T 2cpd_A            7 GDEDTMSSVKILYVRNLMLSTSEEMIEKEFNNIKPGAVERVKKI--------RDYAFVHFSNREDAVEAMKALNGKVLDG   78 (99)
T ss_dssp             CCCSCSSCCCEEEEESCCTTCCHHHHHHHHHTTSTTCEEEEEEC--------SSEEEEEESSHHHHHHHHHHHSSEEETT
T ss_pred             ccccccCCcCEEEEeCCCCCCCHHHHHHHHHhcCCcceEEEEEe--------CCeEEEEeCCHHHHHHHHHHhCCCEeCC
Confidence            334445677999999999999999999999999  999998874        4799999999999999999999999999


Q ss_pred             eEEEEEeccccc
Q 007792          312 RRIHVDFSQSVS  323 (589)
Q Consensus       312 r~i~V~~a~~~~  323 (589)
                      +.|.|.++++..
T Consensus        79 ~~l~v~~a~~~~   90 (99)
T 2cpd_A           79 SPIEVTLAKPVD   90 (99)
T ss_dssp             EEEEEECCCCCC
T ss_pred             cEEEEEECCCCC
Confidence            999999998754

>2fc8_A NCL protein; structure genomics, RRM_1 domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.65  E-value=6.1e-16  Score=131.28  Aligned_cols=82  Identities=27%  Similarity=0.481  Sum_probs=75.7

Q ss_pred             CCCCceEEEecCCCCCCHHHHHHHhccCCCeEEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHhcCCceeCCeEEEEEe
Q 007792          239 KPPENVLFVCKLNPVTEDEDLHTIFSRFGTVVSAEIIRDFKTGDSLNYAFIEFENRQACERAYSKMDNALIDDRRIHVDF  318 (589)
Q Consensus       239 ~~~~~~i~V~nL~~~~te~~L~~~F~~~G~v~~~~i~~d~~tg~~~g~aFV~f~~~~~a~~A~~~l~g~~i~gr~i~V~~  318 (589)
                      ..+.++|||+|||+.+|+++|+++|+.|+   .|.++.++.++.++|||||+|.+.++|..||..|||..|.|+.|.|.+
T Consensus        12 ~~~~~~l~V~nLp~~~t~~~l~~~F~~~~---~~~~~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~V~~   88 (102)
T 2fc8_A           12 SQPSKTLFVKGLSEDTTEETLKESFDGSV---RARIVTDRETGSSKGFGFVDFNSEEDAKAAKEAMEDGEIDGNKVTLDW   88 (102)
T ss_dssp             SCCCSSEEEECCCTTCCHHHHHHTSTTCS---EEEEEECSSSCSEEEEEEEECSSHHHHHHHHHHHTTCEETTEECEEEE
T ss_pred             CCCCCEEEEeCCCCccCHHHHHHHhcCCe---EEEEEecCCCCCcCcEEEEEECCHHHHHHHHHHhCCCeECCeEEEEEE
Confidence            45678999999999999999999999874   677888888999999999999999999999999999999999999999


Q ss_pred             ccccc
Q 007792          319 SQSVS  323 (589)
Q Consensus       319 a~~~~  323 (589)
                      +++..
T Consensus        89 a~~~~   93 (102)
T 2fc8_A           89 AKPKG   93 (102)
T ss_dssp             CCCCC
T ss_pred             ecCCC
Confidence            98744

>2lea_A Serine/arginine-rich splicing factor 2; SR protein, RNA binding protein; NMR {Homo sapiens} PDB: 2leb_A 2lec_A

Probab=99.65  E-value=7.8e-17  Score=144.30  Aligned_cols=85  Identities=28%  Similarity=0.420  Sum_probs=80.0

Q ss_pred             CCCCceEEEecCCCCCCHHHHHHHhccCCCeEEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHhcCCceeCCeEEEEEe
Q 007792          239 KPPENVLFVCKLNPVTEDEDLHTIFSRFGTVVSAEIIRDFKTGDSLNYAFIEFENRQACERAYSKMDNALIDDRRIHVDF  318 (589)
Q Consensus       239 ~~~~~~i~V~nL~~~~te~~L~~~F~~~G~v~~~~i~~d~~tg~~~g~aFV~f~~~~~a~~A~~~l~g~~i~gr~i~V~~  318 (589)
                      ..+.++|||+|||+.+|+++|.++|++||.|..|.|+.++.+++++|||||+|.+.++|+.||..|||..|.|+.|.|.+
T Consensus        44 ~~~~~~l~V~nLp~~~te~~L~~~F~~~G~i~~v~i~~~~~~g~~~G~afV~F~~~~~A~~Ai~~l~g~~i~g~~l~V~~  123 (135)
T 2lea_A           44 VEGMTSLKVDNLTYRTSPDTLRRVFEKYGRVGDVYIPRDRYTKESRGFAFVRFHDKRDAEDAMDAMDGAVLDGRELRVQM  123 (135)
T ss_dssp             GGGCCCEEEECCCSSCHHHHHHHHHGGGSCCSEEECCCCSSSSSCCSCCEEECSCHHHHHHHHTTTTTCCSSSSCCEEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEecCCCCccceEEEEEECCHHHHHHHHHHcCCCEECCEEEEEEE
Confidence            34567999999999999999999999999999999999988999999999999999999999999999999999999999


Q ss_pred             ccccc
Q 007792          319 SQSVS  323 (589)
Q Consensus       319 a~~~~  323 (589)
                      +++..
T Consensus       124 a~~~~  128 (135)
T 2lea_A          124 ARYGR  128 (135)
T ss_dssp             CCCCC
T ss_pred             CCCCC
Confidence            98743

>1wex_A Hypothetical protein (riken cDNA 2810036L13); structural genomics, RRM domain, riken structural genomics/proteomics initiative, RSGI; NMR {Mus musculus} SCOP: d.58.7.1

Probab=99.65  E-value=3.8e-16  Score=133.00  Aligned_cols=81  Identities=20%  Similarity=0.270  Sum_probs=72.3

Q ss_pred             CCCCCCceEEEecCCCCCCHHHHHHHhccCCCeEEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHhcCC--ceeCCeEE
Q 007792          237 DIKPPENVLFVCKLNPVTEDEDLHTIFSRFGTVVSAEIIRDFKTGDSLNYAFIEFENRQACERAYSKMDN--ALIDDRRI  314 (589)
Q Consensus       237 ~~~~~~~~i~V~nL~~~~te~~L~~~F~~~G~v~~~~i~~d~~tg~~~g~aFV~f~~~~~a~~A~~~l~g--~~i~gr~i  314 (589)
                      ...+|..+|||+|||+.+++++|+++|++||.|..|.|+.+      +|||||+|.+.++|..|++.|++  ..|.|++|
T Consensus        10 ~~~~p~~~l~V~nLp~~~te~~L~~~F~~fG~V~~v~i~~~------kg~aFVef~~~~~A~~Ai~~l~~~~~~i~Gr~l   83 (104)
T 1wex_A           10 HKVSVSPVVHVRGLCESVVEADLVEALEKFGTICYVMMMPF------KRQALVEFENIDSAKECVTFAADVPVYIAGQQA   83 (104)
T ss_dssp             CCCCCCSEEEEESCCSSCCHHHHHHHHTTTSCEEEEEEETT------TTEEEEEESSHHHHHHHHHHHHHSCCBSSSSBC
T ss_pred             CcCCCCCEEEEeCCCCCCCHHHHHHHHHhCCCEEEEEEECC------CCEEEEEECCHHHHHHHHHHhccCCceECCEEE
Confidence            34567899999999999999999999999999999998763      68999999999999999998875  45999999


Q ss_pred             EEEeccccc
Q 007792          315 HVDFSQSVS  323 (589)
Q Consensus       315 ~V~~a~~~~  323 (589)
                      .|+|+++..
T Consensus        84 ~V~~a~~~~   92 (104)
T 1wex_A           84 FFNYSTSKR   92 (104)
T ss_dssp             EEEECSSSS
T ss_pred             EEEEccCcc
Confidence            999998643

>2db1_A Heterogeneous nuclear ribonucleoprotein F; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Mus musculus}

Probab=99.65  E-value=2.3e-16  Score=137.83  Aligned_cols=82  Identities=22%  Similarity=0.193  Sum_probs=76.5

Q ss_pred             CCCceEEEecCCCCCCHHHHHHHhccCCC---eEEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHhcCCceeCCeEEEE
Q 007792          240 PPENVLFVCKLNPVTEDEDLHTIFSRFGT---VVSAEIIRDFKTGDSLNYAFIEFENRQACERAYSKMDNALIDDRRIHV  316 (589)
Q Consensus       240 ~~~~~i~V~nL~~~~te~~L~~~F~~~G~---v~~~~i~~d~~tg~~~g~aFV~f~~~~~a~~A~~~l~g~~i~gr~i~V  316 (589)
                      ...++|||+|||+++|+++|+++|+.||.   |..|.|+.++. |+++|||||+|.+.++|.+||+ |||..|+|+.|.|
T Consensus        15 ~~~~~l~V~nLp~~~te~~l~~~F~~~G~~~~v~~v~i~~~~~-g~~~G~afV~F~~~~~a~~Al~-~~g~~~~gr~i~V   92 (118)
T 2db1_A           15 GEGYVVKLRGLPWSCSIEDVQNFLSDCTIHDGVAGVHFIYTRE-GRQSGEAFVELESEDDVKLALK-KDRESMGHRYIEV   92 (118)
T ss_dssp             CCCCEEEEESCCTTCCHHHHHHHTTTSCBTTGGGGEEEEECSS-SCEEEEEEEEBSSHHHHHHHGG-GTTEEETTEEEEE
T ss_pred             CCCcEEEEeCCCCCCCHHHHHHHHHHcCCccCceeEEEEECCC-CCCCeEEEEEECCHHHHHHHHh-cCCCeECCeEEEE
Confidence            35689999999999999999999999999   89999999976 9999999999999999999998 9999999999999


Q ss_pred             Eeccccc
Q 007792          317 DFSQSVS  323 (589)
Q Consensus       317 ~~a~~~~  323 (589)
                      .++....
T Consensus        93 ~~a~~~~   99 (118)
T 2db1_A           93 FKSHRTE   99 (118)
T ss_dssp             EEECHHH
T ss_pred             EECCHHH
Confidence            9997644

>2cpj_A Non-POU domain-containing octamer-binding protein; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Mus musculus} SCOP: d.58.7.1

Probab=99.65  E-value=4.7e-16  Score=131.33  Aligned_cols=83  Identities=25%  Similarity=0.458  Sum_probs=75.3

Q ss_pred             CCCCCCceEEEecCCCCCCHHHHHHHhccCCCeEEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHhcCCceeCCeEEEE
Q 007792          237 DIKPPENVLFVCKLNPVTEDEDLHTIFSRFGTVVSAEIIRDFKTGDSLNYAFIEFENRQACERAYSKMDNALIDDRRIHV  316 (589)
Q Consensus       237 ~~~~~~~~i~V~nL~~~~te~~L~~~F~~~G~v~~~~i~~d~~tg~~~g~aFV~f~~~~~a~~A~~~l~g~~i~gr~i~V  316 (589)
                      ...++.++|||+|||+.+|+++|+++|++||.|..|.|+.+      +|||||+|.+.++|..|+..|||..|.|+.|.|
T Consensus        10 ~~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~~~~~------kg~afV~f~~~~~a~~a~~~l~g~~~~g~~l~v   83 (99)
T 2cpj_A           10 KTFTQRSRLFVGNLPPDITEEEMRKLFEKYGKAGEVFIHKD------KGFGFIRLETRTLAEIAKVELDNMPLRGKQLRV   83 (99)
T ss_dssp             CCCCCTTEEEEESCCTTCCHHHHHHHTSTTCCCSEEEEETT------TTEEEEECSSSHHHHHHHHHHTTCCBTTBCCEE
T ss_pred             CcCCCCCEEEEeCCCCCCCHHHHHHHHhhcCCeEEEEEecC------CCEEEEEECCHHHHHHHHHHhCCCEeCCceEEE
Confidence            34556789999999999999999999999999999999753      689999999999999999999999999999999


Q ss_pred             Eeccccccc
Q 007792          317 DFSQSVSKL  325 (589)
Q Consensus       317 ~~a~~~~~~  325 (589)
                      .++.+....
T Consensus        84 ~~a~~~~~~   92 (99)
T 2cpj_A           84 RFACHSASL   92 (99)
T ss_dssp             EESSCCSCC
T ss_pred             EEcCCCCCC
Confidence            999875543

>1fj7_A Nucleolin RBD1, protein C23; RNP, RRM, RNA binding domain, nucleolus, structural protein; NMR {Mesocricetus auratus} SCOP: d.58.7.1

Probab=99.65  E-value=3.8e-17  Score=138.55  Aligned_cols=83  Identities=18%  Similarity=0.314  Sum_probs=76.1

Q ss_pred             CCCCceEEEecCCCCCCHHHHHHHhccCCCeEEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHhcCCceeCCeEEEEEe
Q 007792          239 KPPENVLFVCKLNPVTEDEDLHTIFSRFGTVVSAEIIRDFKTGDSLNYAFIEFENRQACERAYSKMDNALIDDRRIHVDF  318 (589)
Q Consensus       239 ~~~~~~i~V~nL~~~~te~~L~~~F~~~G~v~~~~i~~d~~tg~~~g~aFV~f~~~~~a~~A~~~l~g~~i~gr~i~V~~  318 (589)
                      ..+..+|||+|||+.+|+++|+++|++||.|.. .++.+..+|.++|||||+|.+.++|..||+ |||..|.|+.|.|.+
T Consensus        14 ~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~-~~~~~~~~g~~~g~afV~f~~~~~a~~A~~-l~g~~~~g~~l~V~~   91 (101)
T 1fj7_A           14 STTPFNLFIGNLNPNKSVAELKVAISELFAKND-LAVVDVRTGTNRKFGYVDFESAEDLEKALE-LTGLKVFGNEIKLEK   91 (101)
T ss_dssp             CSCSEEEEEECCCTTSCHHHHHHHHHHHHHHHT-CCCCEEEEETTTTEEEEEESSHHHHHHHHH-GGGCCBTTBCCEEEC
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHHhCCcce-EEEecCCCCCcCcEEEEEECCHHHHHHHHh-cCCcEECCcEEEEEE
Confidence            446789999999999999999999999999888 667777789999999999999999999998 999999999999999


Q ss_pred             ccccc
Q 007792          319 SQSVS  323 (589)
Q Consensus       319 a~~~~  323 (589)
                      +++..
T Consensus        92 a~~~~   96 (101)
T 1fj7_A           92 PKGRD   96 (101)
T ss_dssp             CSCCC
T ss_pred             cCCCC
Confidence            98743

>2dnq_A RNA-binding protein 4B; RRM domain,RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.65  E-value=6.3e-16  Score=128.09  Aligned_cols=78  Identities=26%  Similarity=0.497  Sum_probs=72.4

Q ss_pred             CCCCceEEEecCCCCCCHHHHHHHhccCCCeEEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHhcCCceeCCeEEEEEe
Q 007792          239 KPPENVLFVCKLNPVTEDEDLHTIFSRFGTVVSAEIIRDFKTGDSLNYAFIEFENRQACERAYSKMDNALIDDRRIHVDF  318 (589)
Q Consensus       239 ~~~~~~i~V~nL~~~~te~~L~~~F~~~G~v~~~~i~~d~~tg~~~g~aFV~f~~~~~a~~A~~~l~g~~i~gr~i~V~~  318 (589)
                      .++.++|||+|||+.+|+++|.++|++||.|..|.|+        +|||||+|.+.++|..|+..|||..|.|+.|.|.+
T Consensus         5 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~~~--------~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~~   76 (90)
T 2dnq_A            5 SSGMVKLFIGNLPREATEQEIRSLFEQYGKVLECDII--------KNYGFVHIEDKTAAEDAIRNLHHYKLHGVNINVEA   76 (90)
T ss_dssp             SSCCEEEEEESCCSSCCHHHHHHHHHTSSCEEEEEEE--------TTEEEEEESSHHHHHHHHHHHTTCBCSSCBCEEEC
T ss_pred             CCCCeEEEEeCCCCCCCHHHHHHHHHhCCCEEEEEEE--------CCEEEEEECCHHHHHHHHHHhcCCccCCcEEEEEE
Confidence            3467899999999999999999999999999999997        48999999999999999999999999999999999


Q ss_pred             cccccc
Q 007792          319 SQSVSK  324 (589)
Q Consensus       319 a~~~~~  324 (589)
                      +.+...
T Consensus        77 a~~~~~   82 (90)
T 2dnq_A           77 SKNKSK   82 (90)
T ss_dssp             SSCCCC
T ss_pred             CCCCCC
Confidence            987543

>2dgt_A RNA-binding protein 30; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.64  E-value=9.9e-16  Score=127.45  Aligned_cols=78  Identities=26%  Similarity=0.548  Sum_probs=72.2

Q ss_pred             CCCCceEEEecCCCCCCHHHHHHHhccCCCeEEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHhcCCceeCCeEEEEEe
Q 007792          239 KPPENVLFVCKLNPVTEDEDLHTIFSRFGTVVSAEIIRDFKTGDSLNYAFIEFENRQACERAYSKMDNALIDDRRIHVDF  318 (589)
Q Consensus       239 ~~~~~~i~V~nL~~~~te~~L~~~F~~~G~v~~~~i~~d~~tg~~~g~aFV~f~~~~~a~~A~~~l~g~~i~gr~i~V~~  318 (589)
                      ..+.++|||+|||+.+|+++|+++|++||.|..|.|+.        +||||+|.+.++|..|+..|||..|.|+.|.|.+
T Consensus         7 ~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~v~~~~--------~~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V~~   78 (92)
T 2dgt_A            7 GKASTKLHVGNISPTCTNQELRAKFEEYGPVIECDIVK--------DYAFVHMERAEDAVEAIRGLDNTEFQGKRMHVQL   78 (92)
T ss_dssp             CCSSEEEEEESCCSSCCHHHHHHHHHTTSCCCEEEECS--------SEEEEEESCHHHHHHHHHHHTTEEETTEEEEEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEC--------CEEEEEECCHHHHHHHHHHhCCCeeCCcEEEEEE
Confidence            45678999999999999999999999999999999964        5999999999999999999999999999999999


Q ss_pred             cccccc
Q 007792          319 SQSVSK  324 (589)
Q Consensus       319 a~~~~~  324 (589)
                      +++...
T Consensus        79 a~~~~~   84 (92)
T 2dgt_A           79 STSRLR   84 (92)
T ss_dssp             SSCCCS
T ss_pred             ccCCCC
Confidence            987543

>2krb_A Eukaryotic translation initiation factor 3 subunit B; EIF3, eukaryotic initiation factor, EIF3B, EIF3J; NMR {Homo sapiens}

Probab=99.64  E-value=1.2e-16  Score=129.71  Aligned_cols=72  Identities=24%  Similarity=0.397  Sum_probs=67.8

Q ss_pred             ceEEEecCCCCC------CHHHHHHHhccCCCeEEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHhcCCceeCCe-EEE
Q 007792          243 NVLFVCKLNPVT------EDEDLHTIFSRFGTVVSAEIIRDFKTGDSLNYAFIEFENRQACERAYSKMDNALIDDR-RIH  315 (589)
Q Consensus       243 ~~i~V~nL~~~~------te~~L~~~F~~~G~v~~~~i~~d~~tg~~~g~aFV~f~~~~~a~~A~~~l~g~~i~gr-~i~  315 (589)
                      ++|||+|||+.+      |+++|.++|++||+|..|.|+  +.+|+++|||||+|.+.++|..|+..|||..|+|+ +|.
T Consensus         2 ~~l~V~nLp~~~~~~~~~t~~~l~~~F~~~G~i~~v~i~--~~~g~~~g~afV~f~~~~~A~~Ai~~lng~~~~g~~~l~   79 (81)
T 2krb_A            2 SVIVVDNVPQVGPDRLEKLKNVIHKIFSKFGKITNDFYP--EEDGKTKGYIFLEYASPAHAVDAVKNADGYKLDKQHTFR   79 (81)
T ss_dssp             CEEEEESCCCCCTTTHHHHHHHHHHHHHTTCCEEEEECC--CBTTBCCCEEEEEESSHHHHHHHHTTSSSCCCSSSSCCC
T ss_pred             CEEEEeCCCCCcHHHHHHHHHHHHHHHhhcCCeEEEEec--CCCCcEeEEEEEEECCHHHHHHHHHHhcCcccCCceeEE
Confidence            689999999999      789999999999999999987  46889999999999999999999999999999999 887


Q ss_pred             E
Q 007792          316 V  316 (589)
Q Consensus       316 V  316 (589)
                      |
T Consensus        80 V   80 (81)
T 2krb_A           80 V   80 (81)
T ss_dssp             C
T ss_pred             e
Confidence            6

>2cpx_A Hypothetical protein FLJ11016; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.64  E-value=8.6e-17  Score=139.76  Aligned_cols=85  Identities=24%  Similarity=0.404  Sum_probs=73.5

Q ss_pred             CCCCceEEEecCCCCCCHHHHHHHhccCCCeEEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHhcCCceeCCeEEEEEe
Q 007792          239 KPPENVLFVCKLNPVTEDEDLHTIFSRFGTVVSAEIIRDFKTGDSLNYAFIEFENRQACERAYSKMDNALIDDRRIHVDF  318 (589)
Q Consensus       239 ~~~~~~i~V~nL~~~~te~~L~~~F~~~G~v~~~~i~~d~~tg~~~g~aFV~f~~~~~a~~A~~~l~g~~i~gr~i~V~~  318 (589)
                      .++.++|||+|||+.+|+++|.++|++||.|..+.+..+..+++++|||||+|.+.++|..||..|||..|.|+.|.|.+
T Consensus        22 ~~~~~~l~V~nLp~~~t~~~l~~~f~~~G~v~~~~~~~~~~~g~~~g~afV~f~~~~~a~~Ai~~l~g~~~~g~~l~v~~  101 (115)
T 2cpx_A           22 GEPNKVLYLKNLSPRVTERDLVSLFARFQEKKGPPIQFRMMTGRMRGQAFITFPNKEIAWQALHLVNGYKLYGKILVIEF  101 (115)
T ss_dssp             CSCCSEEEEECCCTTCCHHHHHHHTHHHHHSSSSCCEEEEECSSSCSEEEEECSSHHHHHHHHHHSTTCBCSSCBCEEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHHhCCccceEEEEEcCCCccceEEEEEECCHHHHHHHHHHhCCCEeCCcEEEEEE
Confidence            45678999999999999999999999999984332222223788999999999999999999999999999999999999


Q ss_pred             ccccc
Q 007792          319 SQSVS  323 (589)
Q Consensus       319 a~~~~  323 (589)
                      |.+..
T Consensus       102 a~~~~  106 (115)
T 2cpx_A          102 GKNKK  106 (115)
T ss_dssp             CCCCS
T ss_pred             ccCCC
Confidence            98744

>1why_A Hypothetical protein riken cDNA 1810017N16; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, structural genomics; NMR {Mus musculus} SCOP: d.58.7.1

Probab=99.64  E-value=4.8e-16  Score=130.72  Aligned_cols=79  Identities=32%  Similarity=0.539  Sum_probs=73.1

Q ss_pred             CCCCceEEEecCCCCCCHHHHHHHhccCCCeEEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHhcCCceeC--CeEEEE
Q 007792          239 KPPENVLFVCKLNPVTEDEDLHTIFSRFGTVVSAEIIRDFKTGDSLNYAFIEFENRQACERAYSKMDNALID--DRRIHV  316 (589)
Q Consensus       239 ~~~~~~i~V~nL~~~~te~~L~~~F~~~G~v~~~~i~~d~~tg~~~g~aFV~f~~~~~a~~A~~~l~g~~i~--gr~i~V  316 (589)
                      .++.++|||+|||+.+|+++|.++|++||.|..|.|+.+      +|||||+|.+.++|+.|+..|||..|.  |+.|.|
T Consensus        14 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~v~~v~~~~~------~g~afV~f~~~~~A~~A~~~l~g~~~~~~g~~l~V   87 (97)
T 1why_A           14 ANPTTRLWVGGLGPNTSLAALAREFDRFGSIRTIDHVKG------DSFAYIQYESLDAAQAACAKMRGFPLGGPDRRLRV   87 (97)
T ss_dssp             CCCCSCEEEECCCSSCCHHHHHHHHHTTSCEEEEEECSS------SCCEEEEESSHHHHHHHHHHHTTCBCSSSSCBCEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEeCC------CCEEEEEECCHHHHHHHHHHHCCCEeCCCCcEEEE
Confidence            456789999999999999999999999999999998753      689999999999999999999999999  999999


Q ss_pred             Eeccccc
Q 007792          317 DFSQSVS  323 (589)
Q Consensus       317 ~~a~~~~  323 (589)
                      .++++..
T Consensus        88 ~~a~~~~   94 (97)
T 1why_A           88 DFAKSGP   94 (97)
T ss_dssp             EECCCCC
T ss_pred             EECCCCC
Confidence            9998743

>1wel_A RNA-binding protein 12; structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.64  E-value=1.2e-16  Score=140.97  Aligned_cols=82  Identities=17%  Similarity=0.217  Sum_probs=76.1

Q ss_pred             CCCceEEEecCCCCCCHHHHHHHhccCCCeEEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHhcCCceeCCeEEEEEec
Q 007792          240 PPENVLFVCKLNPVTEDEDLHTIFSRFGTVVSAEIIRDFKTGDSLNYAFIEFENRQACERAYSKMDNALIDDRRIHVDFS  319 (589)
Q Consensus       240 ~~~~~i~V~nL~~~~te~~L~~~F~~~G~v~~~~i~~d~~tg~~~g~aFV~f~~~~~a~~A~~~l~g~~i~gr~i~V~~a  319 (589)
                      .+..+|||+|||+.+|+++|.++|..||.|..+.++.+..+|+++|||||+|.+.++|..||. |||..|+|+.|.|.++
T Consensus        23 ~~~~~l~V~nLp~~~te~~l~~~F~~~G~v~~~~~~~~~~~g~~~G~afV~F~~~~~a~~Al~-~~g~~~~gr~i~V~~a  101 (124)
T 1wel_A           23 EAGFCVYLKGLPFEAENKHVIDFFKKLDIVEDSIYIAYGPNGKATGEGFVEFRNEADYKAALC-RHKQYMGNRFIQVHPI  101 (124)
T ss_dssp             CCCCEEEEECCCTTCCHHHHHHHSCSSCBCTTTCEEEECTTSSEEEEEEEEBSSSHHHHHHHT-SCSBCSTTSCBEEEEE
T ss_pred             CCCcEEEEeCCCCCCCHHHHHHHHHhcCCccceEEEEECCCCCCCeEEEEEECCHHHHHHHHH-hCCCeECCcEEEEEEC
Confidence            356899999999999999999999999999887777777899999999999999999999998 9999999999999999


Q ss_pred             ccc
Q 007792          320 QSV  322 (589)
Q Consensus       320 ~~~  322 (589)
                      .+.
T Consensus       102 ~~~  104 (124)
T 1wel_A          102 TKK  104 (124)
T ss_dssp             CHH
T ss_pred             CHH
Confidence            763

>1nu4_A U1A RNA binding domain; RNA recognition motif, U1 small nuclear ribonucleoprotein, R binding domain, RNA binding protein; HET: MLA; 1.80A {Homo sapiens} SCOP: d.58.7.1 PDB: 1drz_A* 1urn_A 3hhn_B* 3egz_A* 1zzn_A* 1u6b_A* 3cun_A* 3cul_A* 3g8s_A* 3g8t_A* 3g96_A* 3g9c_A* 3irw_P* 3mum_P* 3mur_P* 3mut_P* 3muv_P* 3mxh_P* 3p49_B 3r1h_A* ...

Probab=99.64  E-value=2.4e-16  Score=132.47  Aligned_cols=82  Identities=22%  Similarity=0.451  Sum_probs=75.3

Q ss_pred             CCCCceEEEecCCCCCCHHHHH----HHhccCCCeEEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHhcCCceeCCeEE
Q 007792          239 KPPENVLFVCKLNPVTEDEDLH----TIFSRFGTVVSAEIIRDFKTGDSLNYAFIEFENRQACERAYSKMDNALIDDRRI  314 (589)
Q Consensus       239 ~~~~~~i~V~nL~~~~te~~L~----~~F~~~G~v~~~~i~~d~~tg~~~g~aFV~f~~~~~a~~A~~~l~g~~i~gr~i  314 (589)
                      .++.++|||+|||+.+++++|.    ++|++||.|..|.|+.   +|.++|||||+|.+.++|..|+..|||..|.|+.|
T Consensus         5 ~~~~~~l~V~nLp~~~~~~~l~~~l~~~f~~~G~i~~v~i~~---~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l   81 (97)
T 1nu4_A            5 TRPNHTIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSR---SLKMRGQAFVIFKEVSSATNALRSMQGFPFYDKPM   81 (97)
T ss_dssp             -CCCSEEEEESCCTTSCHHHHHHHHHHHHGGGSCEEEEECCH---HHHHTTCEEEEESSHHHHHHHHHHHTTCEETTEEC
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHHHHHhCCCEEEEEEEc---CCCcCcEEEEEeCCHHHHHHHHHHhCCCEECCcEE
Confidence            4577999999999999999999    9999999999998873   56788999999999999999999999999999999


Q ss_pred             EEEeccccc
Q 007792          315 HVDFSQSVS  323 (589)
Q Consensus       315 ~V~~a~~~~  323 (589)
                      .|.++.+..
T Consensus        82 ~v~~a~~~~   90 (97)
T 1nu4_A           82 RIQYAKTDS   90 (97)
T ss_dssp             EEEECSSCC
T ss_pred             EEEEccCCC
Confidence            999998754

>2hgl_A HNRPF protein, heterogeneous nuclear ribonucleoprotein F; RNA recognition motif, G-tract, G-quadruplex, alternative, splicing, RNA binding protein; NMR {Homo sapiens} PDB: 2kfy_A

Probab=99.64  E-value=2.5e-16  Score=140.70  Aligned_cols=82  Identities=20%  Similarity=0.160  Sum_probs=76.6

Q ss_pred             CCCceEEEecCCCCCCHHHHHHHhccCCC---eEEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHhcCCceeCCeEEEE
Q 007792          240 PPENVLFVCKLNPVTEDEDLHTIFSRFGT---VVSAEIIRDFKTGDSLNYAFIEFENRQACERAYSKMDNALIDDRRIHV  316 (589)
Q Consensus       240 ~~~~~i~V~nL~~~~te~~L~~~F~~~G~---v~~~~i~~d~~tg~~~g~aFV~f~~~~~a~~A~~~l~g~~i~gr~i~V  316 (589)
                      ...++|||+|||+++|+++|+++|++||.   |..|.|+.++. |+++|||||+|.+.++|.+||+ |||..|+|+.|.|
T Consensus        42 ~~~~~lfVgnLp~~~te~dL~~~F~~~G~v~~v~~v~i~~d~~-g~srG~aFV~F~~~e~a~~Al~-~~g~~l~gr~i~V  119 (136)
T 2hgl_A           42 GEGFVVKLRGLPWSCSVEDVQNFLSDCTIHDGAAGVHFIYTRE-GRQSGEAFVELGSEDDVKMALK-KDRESMGHRYIEV  119 (136)
T ss_dssp             CTTCEEEEESCCTTCCHHHHHHHTTTCCCSSSSTTEEEEECSS-SCEEEEEEEECSSHHHHHHHHT-TTEEESSSSEEEE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHHhCCcCceeEEEEEECCC-CCCCeEEEEEECCHHHHHHHHh-cCCCEECCEEEEE
Confidence            45689999999999999999999999999   88999999977 9999999999999999999998 9999999999999


Q ss_pred             Eeccccc
Q 007792          317 DFSQSVS  323 (589)
Q Consensus       317 ~~a~~~~  323 (589)
                      .++.+..
T Consensus       120 ~~a~~~e  126 (136)
T 2hgl_A          120 FKSHRTE  126 (136)
T ss_dssp             EECCHHH
T ss_pred             EECChHH
Confidence            9987643

>1x4g_A Nucleolysin TIAR; structural genomics, RRM domain, TIA-1 related protein, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.64  E-value=7.8e-16  Score=132.39  Aligned_cols=79  Identities=14%  Similarity=0.388  Sum_probs=73.6

Q ss_pred             CCCceEEEecCCCCCCHHHHHHHhccCCCeEEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHhcCCceeCCeEEEEEec
Q 007792          240 PPENVLFVCKLNPVTEDEDLHTIFSRFGTVVSAEIIRDFKTGDSLNYAFIEFENRQACERAYSKMDNALIDDRRIHVDFS  319 (589)
Q Consensus       240 ~~~~~i~V~nL~~~~te~~L~~~F~~~G~v~~~~i~~d~~tg~~~g~aFV~f~~~~~a~~A~~~l~g~~i~gr~i~V~~a  319 (589)
                      ++.++|||+|||+.+|+++|..+|++||.|..|.|+.+      +|||||+|.+.++|..||..|||..|.|+.|.|.|+
T Consensus        23 ~~~~~l~V~nl~~~~t~~~l~~~F~~~G~i~~v~i~~~------~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a   96 (109)
T 1x4g_A           23 PKNCTVYCGGIASGLTDQLMRQTFSPFGQIMEIRVFPE------KGYSFVRFSTHESAAHAIVSVNGTTIEGHVVKCYWG   96 (109)
T ss_dssp             SSCCEEEEECCSSCCCHHHHHHHHHHHSCEEEEEEETT------TTEEEEEESSHHHHHHHHHHHTTCEETTEECEEECC
T ss_pred             CCCcEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEeCC------CCEEEEEECCHHHHHHHHHHcCCCEECCcEEEEEec
Confidence            35689999999999999999999999999999999875      689999999999999999999999999999999999


Q ss_pred             ccccc
Q 007792          320 QSVSK  324 (589)
Q Consensus       320 ~~~~~  324 (589)
                      ++...
T Consensus        97 ~~~~~  101 (109)
T 1x4g_A           97 KESPD  101 (109)
T ss_dssp             CCCCS
T ss_pred             CCCCC
Confidence            87543

>2xnq_A Nuclear polyadenylated RNA-binding protein 3; transcription termination, RNA processi recognition, RRM; HET: CAF; 1.30A {Saccharomyces cerevisiae} PDB: 2xnr_A 2l41_A

Probab=99.63  E-value=1.1e-15  Score=128.55  Aligned_cols=77  Identities=25%  Similarity=0.380  Sum_probs=71.3

Q ss_pred             CCCCCceEEEecCCC-CCCHHHHHHHhccCCCeEEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHhcCCceeCCeEEEE
Q 007792          238 IKPPENVLFVCKLNP-VTEDEDLHTIFSRFGTVVSAEIIRDFKTGDSLNYAFIEFENRQACERAYSKMDNALIDDRRIHV  316 (589)
Q Consensus       238 ~~~~~~~i~V~nL~~-~~te~~L~~~F~~~G~v~~~~i~~d~~tg~~~g~aFV~f~~~~~a~~A~~~l~g~~i~gr~i~V  316 (589)
                      ..++.++|||+|||+ .+++++|..+|++||.|..|.|.        +|||||+|.+.++|..|+..|||..|.|+.|.|
T Consensus        18 ~~~~~~~l~V~nLp~~~~t~~~L~~~F~~~G~v~~v~i~--------~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V   89 (97)
T 2xnq_A           18 GSHMKSRLFIGNLPLKNVSKEDLFRIFSPYGHIMQINIK--------NAFGFIQFDNPQSVRDAIEXESQEMNFGKKLIL   89 (97)
T ss_dssp             -CCTTCEEEEESCCSSCCCHHHHHHHHGGGSCEEEEEEC--------SSEEEEEESSHHHHHHHHHHHTTSEETTEECEE
T ss_pred             CCCCCCEEEEeCCCcccCCHHHHHHHHHhcCCEEEEEEe--------CCEEEEEECCHHHHHHHHHHcCCCEECCEEEEE
Confidence            355789999999998 99999999999999999999983        589999999999999999999999999999999


Q ss_pred             Eecccc
Q 007792          317 DFSQSV  322 (589)
Q Consensus       317 ~~a~~~  322 (589)
                      +++++.
T Consensus        90 ~~a~~~   95 (97)
T 2xnq_A           90 EVSSSN   95 (97)
T ss_dssp             EECCCC
T ss_pred             EecCCC
Confidence            999764

>2e5j_A Methenyltetrahydrofolate synthetase domain containing; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.63  E-value=5e-16  Score=130.65  Aligned_cols=81  Identities=16%  Similarity=0.257  Sum_probs=72.9

Q ss_pred             CCCCCceEEEecCCCCCCHHHHHHHhccCCCeEEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHhcCCceeCCeEEEEE
Q 007792          238 IKPPENVLFVCKLNPVTEDEDLHTIFSRFGTVVSAEIIRDFKTGDSLNYAFIEFENRQACERAYSKMDNALIDDRRIHVD  317 (589)
Q Consensus       238 ~~~~~~~i~V~nL~~~~te~~L~~~F~~~G~v~~~~i~~d~~tg~~~g~aFV~f~~~~~a~~A~~~l~g~~i~gr~i~V~  317 (589)
                      ..+..++|||+|||+.+|+++|+.+|++||.|. +.++.+    .++|||||+|.+.++|..||..|||..|.|+.|.|.
T Consensus        15 ~~~~~~~l~V~nL~~~~t~~~l~~~F~~~G~v~-~~~~~~----~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V~   89 (97)
T 2e5j_A           15 GAPLAADVYVGNLPRDARVSDLKRALRELGSVP-LRLTWQ----GPRRRAFLHYPDSAAAQQAVSCLQGLRLGTDTLRVA   89 (97)
T ss_dssp             SSCCCCEEEEECCCTTCCHHHHHHHHHHTTCCC-SEEEEE----TTTTEEEEECSSHHHHHHHHHHHTTCCSSSSCCEEE
T ss_pred             CCCCCCEEEEeCCCCcCcHHHHHHHHHhcCCEE-EEEEcC----CCCcEEEEEECCHHHHHHHHHHhCCCEECCcEEEEE
Confidence            345578999999999999999999999999997 666653    578999999999999999999999999999999999


Q ss_pred             eccccc
Q 007792          318 FSQSVS  323 (589)
Q Consensus       318 ~a~~~~  323 (589)
                      ++++..
T Consensus        90 ~a~~~~   95 (97)
T 2e5j_A           90 LARQQR   95 (97)
T ss_dssp             ECCCCC
T ss_pred             EcCCCC
Confidence            998743

>1fjc_A Nucleolin RBD2, protein C23; RNP, RRM, RNA binding domain, nucleolus, structural protein; NMR {Mesocricetus auratus} SCOP: d.58.7.1

Probab=99.63  E-value=4.5e-16  Score=130.57  Aligned_cols=80  Identities=19%  Similarity=0.302  Sum_probs=72.8

Q ss_pred             CCCCceEEEecCCCCCCHHHHHHHhccCCCeEEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHhcCCceeCCeEEEEEe
Q 007792          239 KPPENVLFVCKLNPVTEDEDLHTIFSRFGTVVSAEIIRDFKTGDSLNYAFIEFENRQACERAYSKMDNALIDDRRIHVDF  318 (589)
Q Consensus       239 ~~~~~~i~V~nL~~~~te~~L~~~F~~~G~v~~~~i~~d~~tg~~~g~aFV~f~~~~~a~~A~~~l~g~~i~gr~i~V~~  318 (589)
                      ..+.++|||+|||+.+|+++|.++|++||.|..+     ..++.++|||||+|.+.++|..||..|||..|.|+.|.|.+
T Consensus        13 ~~~~~~l~V~nL~~~~t~~~l~~~F~~~g~v~~~-----~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~   87 (96)
T 1fjc_A           13 VRAARTLLAKNLSFNITEDELKEVFEDALEIRLV-----SQDGKSKGIAYIEFKSEADAEKNLEEKQGAEIDGRSVSLYY   87 (96)
T ss_dssp             TTGGGEEEEESCCSSCCHHHHHHHHCSEEEECCE-----EETTEEEEEEEEEESSHHHHHHHHHHTTEEEETTEEEEEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHhhCCcEEEe-----CCCCCcceEEEEEECCHHHHHHHHHHhCCCEECCeEEEEEE
Confidence            4467899999999999999999999999988765     35688999999999999999999999999999999999999


Q ss_pred             ccccc
Q 007792          319 SQSVS  323 (589)
Q Consensus       319 a~~~~  323 (589)
                      +.+..
T Consensus        88 a~~~~   92 (96)
T 1fjc_A           88 TGEKG   92 (96)
T ss_dssp             CSSSC
T ss_pred             cCCCC
Confidence            98743

>2jvo_A Nucleolar protein 3; nucleus, phosphorylation, ribonucleoprotein, ribosome biogenesis, RNA-binding, rRNA processing; NMR {Saccharomyces cerevisiae} PDB: 2osq_A

Probab=99.63  E-value=6e-16  Score=132.91  Aligned_cols=78  Identities=23%  Similarity=0.454  Sum_probs=72.5

Q ss_pred             CCCCceEEEecCCCCCCHHHHHHHhccCCCeEEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHhcCCceeCCeEEEEEe
Q 007792          239 KPPENVLFVCKLNPVTEDEDLHTIFSRFGTVVSAEIIRDFKTGDSLNYAFIEFENRQACERAYSKMDNALIDDRRIHVDF  318 (589)
Q Consensus       239 ~~~~~~i~V~nL~~~~te~~L~~~F~~~G~v~~~~i~~d~~tg~~~g~aFV~f~~~~~a~~A~~~l~g~~i~gr~i~V~~  318 (589)
                      ..+.++|||+|||+.+|+++|.++|++||.|..|.|+        +|||||+|.+.++|..|+..|||..|+|+.|.|.+
T Consensus        28 ~~~~~~l~V~nLp~~~t~~~L~~~F~~~G~i~~v~i~--------kg~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~~   99 (108)
T 2jvo_A           28 ELSNTRLFVRPFPLDVQESELNEIFGPFGPMKEVKIL--------NGFAFVEFEEAESAAKAIEEVHGKSFANQPLEVVY   99 (108)
T ss_dssp             CCSCSEEEECSSCTTCCHHHHHHHHTTTSCCCEEEEE--------TTEEEEECSSHHHHHHHHHHHTTCEETTEECEEES
T ss_pred             CCCCCEEEEECCCCCCCHHHHHHHHHhcCCEEEEEEE--------CCEEEEEECCHHHHHHHHHHcCCCEECCeEEEEEE
Confidence            4567899999999999999999999999999999997        58999999999999999999999999999999999


Q ss_pred             cccccc
Q 007792          319 SQSVSK  324 (589)
Q Consensus       319 a~~~~~  324 (589)
                      +++...
T Consensus       100 a~~~~~  105 (108)
T 2jvo_A          100 SKLPAK  105 (108)
T ss_dssp             CSCCC-
T ss_pred             ecCCCC
Confidence            987554

>2dnp_A RNA-binding protein 14; RRM domain, RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.63  E-value=1.1e-15  Score=126.59  Aligned_cols=77  Identities=21%  Similarity=0.496  Sum_probs=71.7

Q ss_pred             CCCCceEEEecCCCCCCHHHHHHHhccCCCeEEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHhcCCceeCCeEEEEEe
Q 007792          239 KPPENVLFVCKLNPVTEDEDLHTIFSRFGTVVSAEIIRDFKTGDSLNYAFIEFENRQACERAYSKMDNALIDDRRIHVDF  318 (589)
Q Consensus       239 ~~~~~~i~V~nL~~~~te~~L~~~F~~~G~v~~~~i~~d~~tg~~~g~aFV~f~~~~~a~~A~~~l~g~~i~gr~i~V~~  318 (589)
                      .++.++|||+|||+.+|+++|..+|++||.|..|.|+.        +||||+|.+.++|..||..|||..|.|+.|.|.+
T Consensus         6 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~v~~~~~~~--------~~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~   77 (90)
T 2dnp_A            6 SGNTWKIFVGNVSAACTSQELRSLFERRGRVIECDVVK--------DYAFVHMEKEADAKAAIAQLNGKEVKGKRINVEL   77 (90)
T ss_dssp             SCCSCCEEEESCCTTCCHHHHHHHHHHHSCEEEEEECS--------SCEEEEESCHHHHHHHHHHHTTCEETTEECEEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHcCCCEEEEEEEC--------CEEEEEECCHHHHHHHHHHhCCCEECCcEEEEEE
Confidence            45678999999999999999999999999999999974        5999999999999999999999999999999999


Q ss_pred             ccccc
Q 007792          319 SQSVS  323 (589)
Q Consensus       319 a~~~~  323 (589)
                      +++..
T Consensus        78 a~~~~   82 (90)
T 2dnp_A           78 STKGQ   82 (90)
T ss_dssp             SCCCC
T ss_pred             CCCCC
Confidence            98743

>2lcw_A RNA-binding protein FUS; RRM, nucleic acid binding protein; NMR {Homo sapiens}

Probab=99.43  E-value=2.2e-17  Score=143.82  Aligned_cols=85  Identities=20%  Similarity=0.310  Sum_probs=80.1

Q ss_pred             CCCCceEEEecCCCCCCHHHHHHHhccCCCeEE--------EEEeecCCCCCcccEEEEEEcCHHHHHHHHHhcCCceeC
Q 007792          239 KPPENVLFVCKLNPVTEDEDLHTIFSRFGTVVS--------AEIIRDFKTGDSLNYAFIEFENRQACERAYSKMDNALID  310 (589)
Q Consensus       239 ~~~~~~i~V~nL~~~~te~~L~~~F~~~G~v~~--------~~i~~d~~tg~~~g~aFV~f~~~~~a~~A~~~l~g~~i~  310 (589)
                      ..+.++|||+|||+.+++++|+++|++||.|..        |.|+.++.++.++|||||+|.+.++|..||..|||..|.
T Consensus         4 ~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~~~~~~~~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~   83 (116)
T 2lcw_A            4 NSDNNTIFVQGLGENVTIESVADYFKQIGIIKTNKKTGQPMINLYTDRETGKLKGEATVSFDDPPSAKAAIDWFDGKEFS   83 (116)
Confidence            346789999999999999999999999999998        899999899999999999999999999999999999999


Q ss_pred             CeEEEEEeccccc
Q 007792          311 DRRIHVDFSQSVS  323 (589)
Q Consensus       311 gr~i~V~~a~~~~  323 (589)
                      |+.|.|.++.+..
T Consensus        84 g~~l~V~~a~~~~   96 (116)
T 2lcw_A           84 GNPIKVSFATRRA   96 (116)
Confidence            9999999998754

>1iqt_A AUF1, heterogeneous nuclear ribonucleoprotein D0; RNA-binding protein, hnRNP, telomere, DNA-binding protein, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1 PDB: 1wtb_A 1x0f_A

Probab=99.63  E-value=1.2e-16  Score=127.46  Aligned_cols=75  Identities=24%  Similarity=0.407  Sum_probs=71.7

Q ss_pred             eEEEecCCCCCCHHHHHHHhccCCCeEEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHhcCCceeCCeEEEEEec
Q 007792          244 VLFVCKLNPVTEDEDLHTIFSRFGTVVSAEIIRDFKTGDSLNYAFIEFENRQACERAYSKMDNALIDDRRIHVDFS  319 (589)
Q Consensus       244 ~i~V~nL~~~~te~~L~~~F~~~G~v~~~~i~~d~~tg~~~g~aFV~f~~~~~a~~A~~~l~g~~i~gr~i~V~~a  319 (589)
                      +|||+|||+.+|+++|.++|++||+|..|.|+.++.+|.++|||||+|.+.++|..|+. +++..|.|+.|.|.+|
T Consensus         1 ~l~v~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~Ai~-~~~~~~~g~~l~v~~a   75 (75)
T 1iqt_A            1 KIFVGGLSPDTPEEKIREYFGGFGEVESIELPMDNKTNKRRGFCFITFKEEEPVKKIME-KKYHNVGLSKCEIKVA   75 (75)
T ss_dssp             CEEESCCCSSCCHHHHHHHHHHHSCCSEECCCCSCCCSSSCCCEEEECSSSHHHHHHHT-TSSCCBTTBCCCEEEC
T ss_pred             CEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEecCCCCCcCCEEEEEECCHHHHHHHHH-hCCCeECCEEEEEEEC
Confidence            69999999999999999999999999999999999999999999999999999999997 5899999999999875

>3lqv_A PRE-mRNA branch site protein P14; cysless mutant, PRE-mRNA splicing, adenine, mRNA processing, nucleus, phosphoprotein, RNA-binding; HET: ADE; 2.38A {Homo sapiens} SCOP: d.58.7.1 PDB: 2f9d_A 2f9j_A 2fho_B

Probab=99.63  E-value=8e-16  Score=133.62  Aligned_cols=81  Identities=14%  Similarity=0.289  Sum_probs=74.9

Q ss_pred             CCCCceEEEecCCCCCCHHHHHHHhccCCCeEEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHhcCCceeCCeEEEEEe
Q 007792          239 KPPENVLFVCKLNPVTEDEDLHTIFSRFGTVVSAEIIRDFKTGDSLNYAFIEFENRQACERAYSKMDNALIDDRRIHVDF  318 (589)
Q Consensus       239 ~~~~~~i~V~nL~~~~te~~L~~~F~~~G~v~~~~i~~d~~tg~~~g~aFV~f~~~~~a~~A~~~l~g~~i~gr~i~V~~  318 (589)
                      .++.++|||+|||+.+|+++|..+|++||.|..|.|+.+   +.++|||||+|.+.++|..|+..|||..|+|+.|.|.+
T Consensus         5 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~v~~v~i~~~---~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~~   81 (115)
T 3lqv_A            5 PEVNRILYIRNLPYKITAEEMYDIFGKYGPIRQIRVGNT---PETRGTAYVVYEDIFDAKNAVDHLSGFNVSNRYLVVLY   81 (115)
T ss_dssp             TTCCSEEEEESCCTTCCHHHHHHHHHTTSCEEEEEEECS---TTTTTCEEEEESSHHHHHHHHHHHTTCBSSSCBCEEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEeeC---CCCCcEEEEEECCHHHHHHHHHHcCCCEECCeEEEEEE
Confidence            346789999999999999999999999999999999875   45689999999999999999999999999999999999


Q ss_pred             cccc
Q 007792          319 SQSV  322 (589)
Q Consensus       319 a~~~  322 (589)
                      +.+.
T Consensus        82 a~~~   85 (115)
T 3lqv_A           82 YNAN   85 (115)
T ss_dssp             CCHH
T ss_pred             ecCC
Confidence            9863

>2j8a_A Histone-lysine N-methyltransferase, H3 lysine-4 specific; histone methyltransferase, RRM fold, telomere, nuclear protein; 3.0A {Saccharomyces cerevisiae}

Probab=99.63  E-value=7.4e-16  Score=133.08  Aligned_cols=80  Identities=14%  Similarity=0.212  Sum_probs=72.9

Q ss_pred             CceEEEecC----CCCCCHHHHHHHhccCCCeEEEEEeecCCCCCcccEEEEEEcC----HHH----HHHHHH--hcCCc
Q 007792          242 ENVLFVCKL----NPVTEDEDLHTIFSRFGTVVSAEIIRDFKTGDSLNYAFIEFEN----RQA----CERAYS--KMDNA  307 (589)
Q Consensus       242 ~~~i~V~nL----~~~~te~~L~~~F~~~G~v~~~~i~~d~~tg~~~g~aFV~f~~----~~~----a~~A~~--~l~g~  307 (589)
                      .+.|||+||    |+.|++.+|+.+|++||+|..|.++.|+.||.++|||||+|.+    ..+    |..|+.  .|||.
T Consensus         2 p~kI~VgnL~~~~~~~tte~~Lk~~Fs~fGeV~~~~li~Dp~Tg~slGfgfVef~d~~g~~d~a~kAA~kAi~~~~lng~   81 (136)
T 2j8a_A            2 SCEIVVYPAQDSTTTNIQDISIKNYFKKYGEISHFEAFNDPNSALPLHVYLIKYASSDGKINDAAKAAFSAVRKHESSGC   81 (136)
T ss_dssp             CCEEEEEESSSSCCCCCCHHHHHHHHHTTSCCSEEEEEECTTTCCEEEEEEEECC------CCHHHHHHHHHHHTTTTCE
T ss_pred             CcEEEEeCCCCCCCCCCCHHHHHHHHHhcCCeEEEEEEecCCCCceeeEEEEEECCCCCCcchHHHHHHHHHHHhhhcCC
Confidence            378999999    9999999999999999999999999999999999999999996    333    888988  78999


Q ss_pred             eeCCeEEEEEeccc
Q 007792          308 LIDDRRIHVDFSQS  321 (589)
Q Consensus       308 ~i~gr~i~V~~a~~  321 (589)
                      .|+|++|+|.+...
T Consensus        82 ~I~Gr~irV~ln~~   95 (136)
T 2j8a_A           82 FIMGFKFEVILNKH   95 (136)
T ss_dssp             EETTEEEEEEECCT
T ss_pred             eecCcEEEEEECcc
Confidence            99999999998764

>2f3j_A RNA and export factor binding protein 2; RRM domain, RBD domain., transport protein; NMR {Mus musculus}

Probab=99.63  E-value=7.3e-16  Score=144.46  Aligned_cols=84  Identities=26%  Similarity=0.385  Sum_probs=79.3

Q ss_pred             CCCCceEEEecCCCCCCHHHHHHHhccCCCeEEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHhcCCceeCCeEEEEEe
Q 007792          239 KPPENVLFVCKLNPVTEDEDLHTIFSRFGTVVSAEIIRDFKTGDSLNYAFIEFENRQACERAYSKMDNALIDDRRIHVDF  318 (589)
Q Consensus       239 ~~~~~~i~V~nL~~~~te~~L~~~F~~~G~v~~~~i~~d~~tg~~~g~aFV~f~~~~~a~~A~~~l~g~~i~gr~i~V~~  318 (589)
                      ..+.++|||+|||+.+++++|+++|++||.|..|.|+.+. ++.++|||||+|.+.++|..||..|||..|.|+.|.|+|
T Consensus        85 ~~~~~~l~V~nLp~~~te~~L~~~F~~~G~I~~v~i~~d~-~g~~kG~afV~F~~~~~A~~Ai~~lng~~l~Gr~l~V~~  163 (177)
T 2f3j_A           85 VETGAKLLVSNLDFGVSDADIQELFAEFGTLKKAAVDYDR-SGRSLGTADVHFERRADALKAMKQYKGVPLDGRPMDIQL  163 (177)
T ss_dssp             CTTCEEEEEECCCSCCCHHHHHHHHHHTSCCSEEEECCCT-TSSCSCCEEEEESCHHHHHHHHHHSTTCBCSSSBCEEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEECC-CCCEeeEEEEEeCCHHHHHHHHHHhCCCEECCEEEEEEE
Confidence            4567899999999999999999999999999999999997 899999999999999999999999999999999999999


Q ss_pred             ccccc
Q 007792          319 SQSVS  323 (589)
Q Consensus       319 a~~~~  323 (589)
                      |....
T Consensus       164 a~~~~  168 (177)
T 2f3j_A          164 VASQI  168 (177)
T ss_dssp             ESSGG
T ss_pred             ecCCC
Confidence            98643

>3md3_A Nuclear and cytoplasmic polyadenylated RNA-bindin PUB1; RRM, RNP, RBD, poly(U) binding, tandem, acetylation, cytopla nucleus; 2.70A {Saccharomyces cerevisiae}

Probab=99.63  E-value=9.7e-16  Score=141.23  Aligned_cols=83  Identities=25%  Similarity=0.483  Sum_probs=79.3

Q ss_pred             CCCCCceEEEecCCCCCCHHHHHHHhccCCCeEEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHhcCCceeCCeEEEEE
Q 007792          238 IKPPENVLFVCKLNPVTEDEDLHTIFSRFGTVVSAEIIRDFKTGDSLNYAFIEFENRQACERAYSKMDNALIDDRRIHVD  317 (589)
Q Consensus       238 ~~~~~~~i~V~nL~~~~te~~L~~~F~~~G~v~~~~i~~d~~tg~~~g~aFV~f~~~~~a~~A~~~l~g~~i~gr~i~V~  317 (589)
                      ...+..+|||+|||+.+|+++|.++|++||.|..+.|+.++.+|.++|||||+|.+.++|..|+..|||..|+|+.|.|.
T Consensus        83 ~~~~~~~l~v~nl~~~~t~~~l~~~f~~~G~i~~~~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~i~v~  162 (166)
T 3md3_A           83 SSDDTFNLFVGDLNVNVDDETLRNAFKDFPSYLSGHVMWDMQTGSSRGYGFVSFTSQDDAQNAMDSMQGQDLNGRPLRIN  162 (166)
T ss_dssp             CCTTCEEEEEESCCTTCCHHHHHHHHTTSTTEEEEEEEECTTTCCEEEEEEEEESCHHHHHHHHHHHTTCEETTEECEEE
T ss_pred             CCCCCceEEECCCCCCCCHHHHHHHHhccCCeeEEEEEecCCCCCcceEEEEEeCCHHHHHHHHHHhCCCccCCcEEEEE
Confidence            35567899999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             ecc
Q 007792          318 FSQ  320 (589)
Q Consensus       318 ~a~  320 (589)
                      ||+
T Consensus       163 ~a~  165 (166)
T 3md3_A          163 WAA  165 (166)
T ss_dssp             ESC
T ss_pred             ecC
Confidence            986

>4f02_A Polyadenylate-binding protein 1; mRNA, eukaryotic initiation factors PAIP1 and PAIP2, translation-RNA complex; 2.00A {Homo sapiens} PDB: 1cvj_A*

Probab=99.62  E-value=1.1e-15  Score=147.76  Aligned_cols=85  Identities=29%  Similarity=0.470  Sum_probs=78.8

Q ss_pred             CCCCceEEEecCCCCCCHHHHHHHhccCCCeEEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHhcCCceeCCeEEEEEe
Q 007792          239 KPPENVLFVCKLNPVTEDEDLHTIFSRFGTVVSAEIIRDFKTGDSLNYAFIEFENRQACERAYSKMDNALIDDRRIHVDF  318 (589)
Q Consensus       239 ~~~~~~i~V~nL~~~~te~~L~~~F~~~G~v~~~~i~~d~~tg~~~g~aFV~f~~~~~a~~A~~~l~g~~i~gr~i~V~~  318 (589)
                      ..|.++|||+|||+++|+++|.++|++||+|..|.|+.++.|++++|||||+|.+.++|..||..||+..+.|+.|.|.+
T Consensus        12 ~~p~~tlfVgnLp~~~te~~L~~~F~~~G~I~~v~i~~d~~tg~~~G~afV~F~~~~~A~~Ai~~~~~~~~~g~~i~~~~   91 (213)
T 4f02_A           12 SYPMASLYVGDLHPDVTEAMLYEKFSPAGPILSIRVCRDMITRRSLGYAYVNFQQPADAERALDTMNFDVIKGKPVRIMW   91 (213)
T ss_dssp             ---CCEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEE
T ss_pred             CCCCcEEEEeCCCCCCCHHHHHHHHHhhCCEEEEEEecccCCCCccccccceeCCHHHHHHHHHHhhhhhcCCccccccc
Confidence            34678999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             ccccc
Q 007792          319 SQSVS  323 (589)
Q Consensus       319 a~~~~  323 (589)
                      +....
T Consensus        92 ~~~~~   96 (213)
T 4f02_A           92 SQRDP   96 (213)
T ss_dssp             CCCCT
T ss_pred             ccccc
Confidence            87533

>1x4f_A Matrin 3; structural genomics, RRM domain, NPPSFA, national project on protein structural and functional analyses; NMR {Mus musculus} SCOP: d.58.7.1

Probab=99.62  E-value=4.7e-16  Score=133.59  Aligned_cols=79  Identities=19%  Similarity=0.279  Sum_probs=71.3

Q ss_pred             CCCCceEEEecCCCC-CCHHHHHHHhccCCCeEEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHhcC--CceeCCeEEE
Q 007792          239 KPPENVLFVCKLNPV-TEDEDLHTIFSRFGTVVSAEIIRDFKTGDSLNYAFIEFENRQACERAYSKMD--NALIDDRRIH  315 (589)
Q Consensus       239 ~~~~~~i~V~nL~~~-~te~~L~~~F~~~G~v~~~~i~~d~~tg~~~g~aFV~f~~~~~a~~A~~~l~--g~~i~gr~i~  315 (589)
                      .+|.++|||+|||+. +|+++|.++|++||.|..|.|+.      ++|||||+|.+.++|..||+.|+  +..|.|++|.
T Consensus        22 ~~p~~~l~V~NLp~~~~te~~L~~lF~~fG~V~~v~i~~------~kg~aFVef~~~~~A~~Ai~~l~~~~~~l~Gr~l~   95 (112)
T 1x4f_A           22 QELGRVIHLSNLPHSGYSDSAVLKLAEPYGKIKNYILMR------MKSQAFIEMETREDAMAMVDHCLKKALWFQGRCVK   95 (112)
T ss_dssp             SCCCCEEEEESCCCSSCCSHHHHTTTTTTSCCSEEEEET------TTTEEEEECSSHHHHHHHHHHHHHSCCCSSSSCCE
T ss_pred             CCCCCEEEEeCCCCccCCHHHHHHHHHhcCCEEEEEEec------CCCEEEEEECCHHHHHHHHHHhccCCceECCEEEE
Confidence            456889999999998 99999999999999999999974      46999999999999999999886  4669999999


Q ss_pred             EEeccccc
Q 007792          316 VDFSQSVS  323 (589)
Q Consensus       316 V~~a~~~~  323 (589)
                      |.+|+...
T Consensus        96 V~~a~~~~  103 (112)
T 1x4f_A           96 VDLSEKYK  103 (112)
T ss_dssp             EEEECSCS
T ss_pred             EEECcccc
Confidence            99998644

>2la4_A Nuclear and cytoplasmic polyadenylated RNA-bindin PUB1; RRM, RNA recognition, stress granules, nucleus, RNA-binding, transcription; NMR {Saccharomyces cerevisiae}

Probab=99.62  E-value=7.2e-16  Score=130.64  Aligned_cols=75  Identities=12%  Similarity=0.323  Sum_probs=70.8

Q ss_pred             CCceEEEecCCCCCCHHHHHHHhccCCCeEEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHhcCCceeCCeEEEEEecc
Q 007792          241 PENVLFVCKLNPVTEDEDLHTIFSRFGTVVSAEIIRDFKTGDSLNYAFIEFENRQACERAYSKMDNALIDDRRIHVDFSQ  320 (589)
Q Consensus       241 ~~~~i~V~nL~~~~te~~L~~~F~~~G~v~~~~i~~d~~tg~~~g~aFV~f~~~~~a~~A~~~l~g~~i~gr~i~V~~a~  320 (589)
                      ..++|||+|||+.+++++|..+|++||.|..|.|+.      ++|||||+|.+.++|..|+..|||..|+|+.|.|.|++
T Consensus        26 ~~~~l~V~nlp~~~~~~~l~~~f~~~G~i~~~~~~~------~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~~a~   99 (101)
T 2la4_A           26 RVTTAYIGNIPHFATEADLIPLFQNFGFILDFKHYP------EKGCCFIKYDTHEQAAVCIVALANFPFQGRNLRTGWGK   99 (101)
T ss_dssp             SCCEEEEESCCTTCCHHHHHHHHHTTSCCSEEEEET------TTTEEEEECSSHHHHHHHHHHHTTCEETTEECCCCBCC
T ss_pred             CCCEEEEcCCCcccCHHHHHHHHHhCCCEEEEEEec------CCCEEEEEECCHHHHHHHHHHhCCCeECCeEEEEEecc
Confidence            468999999999999999999999999999999973      57999999999999999999999999999999999987


Q ss_pred             c
Q 007792          321 S  321 (589)
Q Consensus       321 ~  321 (589)
                      +
T Consensus       100 ~  100 (101)
T 2la4_A          100 E  100 (101)
T ss_dssp             C
T ss_pred             C
Confidence            5

>2dnn_A RNA-binding protein 12; RRM domain, RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.62  E-value=1.3e-15  Score=130.83  Aligned_cols=77  Identities=17%  Similarity=0.247  Sum_probs=72.6

Q ss_pred             CceEEEecCCCCCCHHHHHHHhccCCCeEEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHhcCCceeCCeEEEEEeccc
Q 007792          242 ENVLFVCKLNPVTEDEDLHTIFSRFGTVVSAEIIRDFKTGDSLNYAFIEFENRQACERAYSKMDNALIDDRRIHVDFSQS  321 (589)
Q Consensus       242 ~~~i~V~nL~~~~te~~L~~~F~~~G~v~~~~i~~d~~tg~~~g~aFV~f~~~~~a~~A~~~l~g~~i~gr~i~V~~a~~  321 (589)
                      ..+|||+|||+.+|+++|+++|++| .|..|.|+.++. |+++|||||+|.+.++|++|| .||+..|+|+.|.|..+.+
T Consensus        16 ~~~v~V~nLp~~~te~dl~~~F~~~-~v~~v~i~~d~~-g~~~G~afV~F~~~~~a~~Al-~~~~~~~~gr~i~V~~a~~   92 (109)
T 2dnn_A           16 DLYVSVHGMPFSAMENDVRDFFHGL-RVDAVHLLKDHV-GRNNGNGLVKFLSPQDTFEAL-KRNRMLMIQRYVEVSPATE   92 (109)
T ss_dssp             HHEEEEECCCSSCCHHHHHHHTTTS-CCCEEEECCCTT-CCCCSEEEEECSSHHHHHHHH-HTTTEEETTEEEEEEECCH
T ss_pred             CCEEEEeCCCCCCCHHHHHHHhccC-CeeEEEEEECCC-CCCCeEEEEEECCHHHHHHHH-hcCCCeECCeEEEEEECCc
Confidence            4699999999999999999999999 899999999965 999999999999999999999 6999999999999998865

>2kvi_A Nuclear polyadenylated RNA-binding protein 3; RNA-binding motif, RRM, transcription termination, NUC phosphoprotein; NMR {Saccharomyces cerevisiae}

Probab=99.61  E-value=7.7e-16  Score=129.26  Aligned_cols=77  Identities=27%  Similarity=0.466  Sum_probs=70.7

Q ss_pred             CCCCceEEEecCCC-CCCHHHHHHHhccCCCeEEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHhcCCceeCCeEEEEE
Q 007792          239 KPPENVLFVCKLNP-VTEDEDLHTIFSRFGTVVSAEIIRDFKTGDSLNYAFIEFENRQACERAYSKMDNALIDDRRIHVD  317 (589)
Q Consensus       239 ~~~~~~i~V~nL~~-~~te~~L~~~F~~~G~v~~~~i~~d~~tg~~~g~aFV~f~~~~~a~~A~~~l~g~~i~gr~i~V~  317 (589)
                      .++.++|||+|||+ .+|+++|..+|++||.|..|.|.        +|||||+|.+.++|..||..|||..|.|+.|.|.
T Consensus         7 ~~~~~~l~V~nlp~~~~t~~~l~~~F~~~G~v~~v~i~--------~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~V~   78 (96)
T 2kvi_A            7 IPPKSRLFIGNLPLKNVSKEDLFRIFSPYGHIMQINIK--------NAFGFIQFDNPQSVRDAIECESQEMNFGKKLILE   78 (96)
T ss_dssp             --CCEEEEEESSTTSCCCHHHHHHHHTTTCCCCEEEEE--------TTEEEEEESCHHHHHHHHHHHTCSSCBTTTBCEE
T ss_pred             CCCCCEEEEeCCCcccCCHHHHHHHHHhcCCEEEEEEe--------CCEEEEEECCHHHHHHHHHHcCCCeeCCcEEEEE
Confidence            45678999999999 99999999999999999999984        5899999999999999999999999999999999


Q ss_pred             eccccc
Q 007792          318 FSQSVS  323 (589)
Q Consensus       318 ~a~~~~  323 (589)
                      ++++..
T Consensus        79 ~a~~~~   84 (96)
T 2kvi_A           79 VSSSNA   84 (96)
T ss_dssp             EEECCC
T ss_pred             EcCcCC
Confidence            998644

>3egn_A RNA-binding protein 40; RNA recognition motif (RRM), RNP motif, U11/U12-65K protein, DI-snRNP, U1A protein, U2B protein; 2.50A {Homo sapiens}

Probab=99.61  E-value=5.4e-16  Score=140.25  Aligned_cols=85  Identities=27%  Similarity=0.424  Sum_probs=73.7

Q ss_pred             CCCCceEEEecCCCCCCHHHHHHHhccCCCeEEEE--E---eecCCCCCcccEEEEEEcCHHHHHHHHHhcCCceeCCeE
Q 007792          239 KPPENVLFVCKLNPVTEDEDLHTIFSRFGTVVSAE--I---IRDFKTGDSLNYAFIEFENRQACERAYSKMDNALIDDRR  313 (589)
Q Consensus       239 ~~~~~~i~V~nL~~~~te~~L~~~F~~~G~v~~~~--i---~~d~~tg~~~g~aFV~f~~~~~a~~A~~~l~g~~i~gr~  313 (589)
                      ..+.++|||+|||+.+|+++|..+|++||.|..+.  +   +....+|.++|||||+|.+.++|..||..|||..|.|+.
T Consensus        42 ~~~~~~l~V~nLp~~~te~~L~~~F~~~G~i~~~~~~~~~di~~~~~g~~~g~afV~f~~~~~A~~Ai~~lng~~~~g~~  121 (143)
T 3egn_A           42 GEPNCRIYVKNLAKHVQEKDLKYIFGRYVDFSSETQRIMFDIRLMKEGRMKGQAFIGLPNEKAAAKALKEANGYVLFGKP  121 (143)
T ss_dssp             CSCCSEEEEEEECTTCCHHHHHHHHGGGCCTTCHHHHHHCEEEEEEETTTEEEEEEECSSHHHHHHHHHHHTTBEETTEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHHhCCcccccccceeeEEeccCCCcccEEEEEeCCHHHHHHHHHHhCCCEeCCcE
Confidence            45779999999999999999999999999987641  1   111246889999999999999999999999999999999


Q ss_pred             EEEEeccccc
Q 007792          314 IHVDFSQSVS  323 (589)
Q Consensus       314 i~V~~a~~~~  323 (589)
                      |.|.+|++..
T Consensus       122 l~V~~a~~~~  131 (143)
T 3egn_A          122 MVVQFARSAR  131 (143)
T ss_dssp             CEEEECCCSC
T ss_pred             EEEEECCCCC
Confidence            9999998643

>2lmi_A GRSF-1, G-rich sequence factor 1; G-rich RNA sequence binding factor, RNA binding domain, STRU genomics, joint center for structural genomics, JCSG; NMR {Homo sapiens}

Probab=99.61  E-value=3.1e-16  Score=134.50  Aligned_cols=83  Identities=17%  Similarity=0.124  Sum_probs=76.8

Q ss_pred             CCCCceEEEecCCCCCCHHHHHHHhccCCC---eEEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHhcCCceeCCeEEE
Q 007792          239 KPPENVLFVCKLNPVTEDEDLHTIFSRFGT---VVSAEIIRDFKTGDSLNYAFIEFENRQACERAYSKMDNALIDDRRIH  315 (589)
Q Consensus       239 ~~~~~~i~V~nL~~~~te~~L~~~F~~~G~---v~~~~i~~d~~tg~~~g~aFV~f~~~~~a~~A~~~l~g~~i~gr~i~  315 (589)
                      .....+|||+|||+.+|+++|+++|+.||.   |..|.|+.++. |+++|||||+|.+.++|..||. ||+..|+|+.|.
T Consensus         8 ~~~~~~l~V~nLp~~~te~~l~~~F~~~g~~~~v~~v~i~~~~~-g~~~G~afV~F~~~~~a~~Al~-~~~~~~~gr~i~   85 (107)
T 2lmi_A            8 VDDVFLIRAQGLPWSCTMEDVLNFFSDCRIRNGENGIHFLLNRD-GKRRGDALIEMESEQDVQKALE-KHRMYMGQRYVE   85 (107)
T ss_dssp             CSSCCEEEEECCCSSCCSHHHHHHTTTSCBTTTTTTEECCCCTT-STTCSEEEEEBSSHHHHHHHHT-TTTCCSSSSCCC
T ss_pred             CCCccEEEEeCCCCCCCHHHHHHHHHhcCCcCCcceEEEEECCC-CCEeeEEEEEECCHHHHHHHHH-hCcceeCCeEEE
Confidence            345689999999999999999999999998   89999999977 9999999999999999999998 999999999999


Q ss_pred             EEeccccc
Q 007792          316 VDFSQSVS  323 (589)
Q Consensus       316 V~~a~~~~  323 (589)
                      |.++.+..
T Consensus        86 V~~a~~~~   93 (107)
T 2lmi_A           86 VYEINNED   93 (107)
T ss_dssp             CEECCHHH
T ss_pred             EEECCHHH
Confidence            99997643

>2hvz_A Splicing factor, arginine/serine-rich 7; RRM, RNA binding protein; NMR {Homo sapiens}

Probab=99.61  E-value=6.5e-16  Score=130.89  Aligned_cols=76  Identities=26%  Similarity=0.466  Sum_probs=72.0

Q ss_pred             ceEEEecCCCCCCHHHHHHHhccCCCeEEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHhcCCceeCCeEEEEEecccc
Q 007792          243 NVLFVCKLNPVTEDEDLHTIFSRFGTVVSAEIIRDFKTGDSLNYAFIEFENRQACERAYSKMDNALIDDRRIHVDFSQSV  322 (589)
Q Consensus       243 ~~i~V~nL~~~~te~~L~~~F~~~G~v~~~~i~~d~~tg~~~g~aFV~f~~~~~a~~A~~~l~g~~i~gr~i~V~~a~~~  322 (589)
                      ++|||+|||+.+|+++|.++|++||+|..|.|+.+     ++|||||+|.+.++|..|+..|||..|.|+.|.|.++++.
T Consensus         1 ~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~-----~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V~~a~~~   75 (101)
T 2hvz_A            1 MKVYVGNLGTGAGKGELERAFSYYGPLRTVWIARN-----PPGFAFVEFEDPRDAEDAVRGLDGKVICGSRVRVELSTGM   75 (101)
T ss_dssp             CEEEEECCCSSCSHHHHHHHHHHHCCCSEEEEESS-----SSSEEEEECSSHHHHHHHHHHHHHSCSSSCCCEEEESSSC
T ss_pred             CEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEeeC-----CCCEEEEEECCHHHHHHHHHHHCCCeECCcEEEEEEccCC
Confidence            48999999999999999999999999999999886     6799999999999999999999999999999999999875


Q ss_pred             c
Q 007792          323 S  323 (589)
Q Consensus       323 ~  323 (589)
                      .
T Consensus        76 ~   76 (101)
T 2hvz_A           76 P   76 (101)
T ss_dssp             C
T ss_pred             C
Confidence            4

>2xs2_A Deleted in azoospermia-like; RNA binding protein-RNA complex; 1.35A {Mus musculus} PDB: 2xs7_A 2xs5_A 2xsf_A

Probab=99.61  E-value=9.1e-16  Score=130.24  Aligned_cols=81  Identities=21%  Similarity=0.403  Sum_probs=76.1

Q ss_pred             CCCceEEEecCCCCCCHHHHHHHhccCCCeEEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHhcCCceeCCeEEEEEec
Q 007792          240 PPENVLFVCKLNPVTEDEDLHTIFSRFGTVVSAEIIRDFKTGDSLNYAFIEFENRQACERAYSKMDNALIDDRRIHVDFS  319 (589)
Q Consensus       240 ~~~~~i~V~nL~~~~te~~L~~~F~~~G~v~~~~i~~d~~tg~~~g~aFV~f~~~~~a~~A~~~l~g~~i~gr~i~V~~a  319 (589)
                      .+.++|||+|||+.+++++|..+|++||.|..|.|+.++ +|.++|||||+|.+.++|..||.  ++..|+|+.|.|.++
T Consensus         7 ~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~-~g~~~g~afV~f~~~~~a~~Ai~--~~~~~~g~~l~v~~a   83 (102)
T 2xs2_A            7 IMPNTVFVGGIDVRMDETEIRSFFARYGSVKEVKIITDR-TGVSKGYGFVSFYNDVDVQKIVE--SQINFHGKKLKLGPA   83 (102)
T ss_dssp             EEEEEEEEECCCTTCCHHHHHHHHGGGSCEEEEEEEECT-TSCEEEEEEEEESSCCCHHHHTT--CCCEETTEECEEEEE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhCCCeEEEEEEECC-CCCccceEEEEECCHHHHHHHHh--CCCeECCEEEEEEEC
Confidence            356899999999999999999999999999999999997 99999999999999999999997  999999999999999


Q ss_pred             cccc
Q 007792          320 QSVS  323 (589)
Q Consensus       320 ~~~~  323 (589)
                      .++.
T Consensus        84 ~~~~   87 (102)
T 2xs2_A           84 IRKQ   87 (102)
T ss_dssp             EECC
T ss_pred             CcCc
Confidence            7644

>1wf1_A RNA-binding protein RALY; structural genomics, RRM domain, riken structural genomics/proteomics initiative, RSGI; NMR {Homo sapiens} SCOP: d.58.7.1 PDB: 1wf2_A

Probab=99.60  E-value=2.1e-15  Score=129.88  Aligned_cols=75  Identities=21%  Similarity=0.493  Sum_probs=70.3

Q ss_pred             CCCCceEEEecCCCC-CCHHHHHHHhccCCCeEEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHhcCCceeCCeEEEEE
Q 007792          239 KPPENVLFVCKLNPV-TEDEDLHTIFSRFGTVVSAEIIRDFKTGDSLNYAFIEFENRQACERAYSKMDNALIDDRRIHVD  317 (589)
Q Consensus       239 ~~~~~~i~V~nL~~~-~te~~L~~~F~~~G~v~~~~i~~d~~tg~~~g~aFV~f~~~~~a~~A~~~l~g~~i~gr~i~V~  317 (589)
                      .++.++|||+|||+. +|+++|+++|++||.|..|.|        ++|||||+|.+.++|..||..|||..|+|+.|.|.
T Consensus        24 ~~~~~~l~V~nl~~~~~t~~~l~~~F~~~G~v~~v~i--------~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~V~   95 (110)
T 1wf1_A           24 KSINSRVFIGNLNTALVKKSDVETIFSKYGRVAGCSV--------HKGYAFVQYSNERHARAAVLGENGRVLAGQTLDIN   95 (110)
T ss_dssp             TTCSSEEEECSCCCSSCCHHHHHHHHGGGSCCSEEEE--------ETTEEEEECSSSHHHHHHHHHHTTCEETTEECCEE
T ss_pred             CCCCcEEEEeCCCcccCCHHHHHHHHHhCCCeEEEEE--------eCCEEEEEECCHHHHHHHHHHcCCCEECCeEEEEE
Confidence            345689999999999 999999999999999999998        46899999999999999999999999999999999


Q ss_pred             eccc
Q 007792          318 FSQS  321 (589)
Q Consensus       318 ~a~~  321 (589)
                      ++.+
T Consensus        96 ~a~~   99 (110)
T 1wf1_A           96 MAGE   99 (110)
T ss_dssp             ESCC
T ss_pred             ECCC
Confidence            9975

>2hgn_A Heterogeneous nuclear ribonucleoprotein F; RNA recognition motif, G-tract, G-quadruplex, alternative splicing, RNA binding protein; NMR {Homo sapiens} PDB: 2kg1_A

Probab=99.59  E-value=2.9e-16  Score=140.71  Aligned_cols=82  Identities=18%  Similarity=0.209  Sum_probs=74.6

Q ss_pred             CCCCceEEEecCCCCCCHHHHHHHhccCCCeEEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHhcCCceeCCeEEEEEe
Q 007792          239 KPPENVLFVCKLNPVTEDEDLHTIFSRFGTVVSAEIIRDFKTGDSLNYAFIEFENRQACERAYSKMDNALIDDRRIHVDF  318 (589)
Q Consensus       239 ~~~~~~i~V~nL~~~~te~~L~~~F~~~G~v~~~~i~~d~~tg~~~g~aFV~f~~~~~a~~A~~~l~g~~i~gr~i~V~~  318 (589)
                      .....+|||+|||+++|+++|+++|++|| |+.|.|+.++. |+++|||||+|.+.++|++|| .||+..|.|+.|.|.+
T Consensus        43 ~~~~~~lfV~nLp~~~te~dL~~~F~~~G-i~~v~i~~d~~-g~srGfaFV~F~~~e~A~~Al-~~~g~~l~gR~i~V~~  119 (139)
T 2hgn_A           43 STTGHCVHMRGLPYKATENDIYNFFSPLN-PVRVHIEIGPD-GRVTGEADVEFATHEEAVAAM-SKDRANMQHRYIELFL  119 (139)
T ss_dssp             --CCCCEECCSCCTTCCHHHHHHHHCSCC-CSEEECCCSSS-SCSSCCCEEECSHHHHHHHHT-TCCSCSSSSCCCCCEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcC-CeEEEEEECCC-CCCceEEEEEeCCHHHHHHHH-hhCCCEECCEEEEEEE
Confidence            34568999999999999999999999999 67999999976 999999999999999999999 7899999999999999


Q ss_pred             ccccc
Q 007792          319 SQSVS  323 (589)
Q Consensus       319 a~~~~  323 (589)
                      +.+..
T Consensus       120 a~~~~  124 (139)
T 2hgn_A          120 NSTTG  124 (139)
T ss_dssp             CCCSC
T ss_pred             CCCCC
Confidence            87643

>2g4b_A Splicing factor U2AF 65 kDa subunit; protein-RNA complex, RNA splicing factor, RNA recognition motif, RNA binding protein/RNA complex; 2.50A {Homo sapiens} PDB: 2u2f_A

Probab=99.59  E-value=4.8e-15  Score=137.67  Aligned_cols=82  Identities=22%  Similarity=0.445  Sum_probs=78.0

Q ss_pred             CCCCceEEEecCCCCCCHHHHHHHhccCCCeEEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHhcCCceeCCeEEEEEe
Q 007792          239 KPPENVLFVCKLNPVTEDEDLHTIFSRFGTVVSAEIIRDFKTGDSLNYAFIEFENRQACERAYSKMDNALIDDRRIHVDF  318 (589)
Q Consensus       239 ~~~~~~i~V~nL~~~~te~~L~~~F~~~G~v~~~~i~~d~~tg~~~g~aFV~f~~~~~a~~A~~~l~g~~i~gr~i~V~~  318 (589)
                      ..+..+|||+|||+.+|+++|.++|++||.|..+.|+.++.+|.++|||||+|.+.++|.+|+..|||..|+|+.|.|.+
T Consensus        91 ~~~~~~l~v~nlp~~~t~~~l~~~f~~~G~v~~v~i~~~~~~g~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~V~~  170 (172)
T 2g4b_A           91 LPGAHKLFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIAGLNGMQLGDKKLLVQR  170 (172)
T ss_dssp             CTTTTCEEEECCCTTCCHHHHHHHHHTTSCEEEEEEEECTTTCSEEEEEEEEESSTTHHHHHHHHHTTCEETTEECEEEE
T ss_pred             CCCCCEEEEEcCCCcCCHHHHHHHHHhcCCceEEEEEecCCCCCcceEEEEEeCCHHHHHHHHHHcCCCEECCeEEEEEe
Confidence            34568999999999999999999999999999999999988999999999999999999999999999999999999999


Q ss_pred             cc
Q 007792          319 SQ  320 (589)
Q Consensus       319 a~  320 (589)
                      |.
T Consensus       171 As  172 (172)
T 2g4b_A          171 AS  172 (172)
T ss_dssp             CC
T ss_pred             CC
Confidence            73

>2cqh_A IGF-II mRNA-binding protein 2 isoform A; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.59  E-value=1.7e-15  Score=126.29  Aligned_cols=78  Identities=21%  Similarity=0.418  Sum_probs=69.5

Q ss_pred             CCCCceEEEecCCCCCCHHHHHHHhccCCC-eEEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHhcCC-ceeCCeEEEE
Q 007792          239 KPPENVLFVCKLNPVTEDEDLHTIFSRFGT-VVSAEIIRDFKTGDSLNYAFIEFENRQACERAYSKMDN-ALIDDRRIHV  316 (589)
Q Consensus       239 ~~~~~~i~V~nL~~~~te~~L~~~F~~~G~-v~~~~i~~d~~tg~~~g~aFV~f~~~~~a~~A~~~l~g-~~i~gr~i~V  316 (589)
                      ..+.++|||+|||+.+|+++|+++|++||. |..+.+.       ++|||||+|.+.++|..||..||| ..|+|+.|.|
T Consensus         5 ~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~vv~~~~~~-------~~g~afV~f~~~~~A~~A~~~l~g~~~~~g~~l~v   77 (93)
T 2cqh_A            5 SSGMNKLYIGNLSPAVTADDLRQLFGDRKLPLAGQVLL-------KSGYAFVDYPDQNWAIRAIETLSGKVELHGKIMEV   77 (93)
T ss_dssp             CCCCCCEEEECCCTTCCHHHHHHHHHHTTCCCSSCEEE-------ETTEEEECCSCHHHHHHHHHHHTTTCEETTEECEE
T ss_pred             CCCCcEEEEeCCCCCCCHHHHHHHHHHcCCceEEEEEc-------CCCEEEEEECCHHHHHHHHHHccCCeeECCEEEEE
Confidence            345689999999999999999999999999 5555552       469999999999999999999999 9999999999


Q ss_pred             Eeccccc
Q 007792          317 DFSQSVS  323 (589)
Q Consensus       317 ~~a~~~~  323 (589)
                      .++.+..
T Consensus        78 ~~a~~~~   84 (93)
T 2cqh_A           78 DYSVSKK   84 (93)
T ss_dssp             EECCCCC
T ss_pred             EEccCcc
Confidence            9998743

>1x5p_A Negative elongation factor E; structure genomics, RRM domain, PARP14, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.59  E-value=1.2e-14  Score=122.06  Aligned_cols=78  Identities=18%  Similarity=0.357  Sum_probs=71.1

Q ss_pred             CCCCCceEEEecCCCCCCHHHHHHHhccCCCeEEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHhcCCceeCCeEEEEE
Q 007792          238 IKPPENVLFVCKLNPVTEDEDLHTIFSRFGTVVSAEIIRDFKTGDSLNYAFIEFENRQACERAYSKMDNALIDDRRIHVD  317 (589)
Q Consensus       238 ~~~~~~~i~V~nL~~~~te~~L~~~F~~~G~v~~~~i~~d~~tg~~~g~aFV~f~~~~~a~~A~~~l~g~~i~gr~i~V~  317 (589)
                      ...+.++|||+||  .+|+++|+++|++||.|..|.|.      .++|||||+|.+.++|..||..|||..|.|+.|.|.
T Consensus        11 ~~~~~~~l~V~n~--~~t~~~l~~~F~~~G~i~~v~i~------~~~g~afV~f~~~~~a~~Ai~~l~g~~~~g~~l~v~   82 (97)
T 1x5p_A           11 APRKGNTLYVYGE--DMTPTLLRGAFSPFGNIIDLSMD------PPRNCAFVTYEKMESADQAVAELNGTQVESVQLKVN   82 (97)
T ss_dssp             CCCCCSEEEEECS--SCCHHHHHHHHTTTSCEEEEEEE------TTTTEEEEEESSHHHHHHHHHHTTTEEETTEEEEEE
T ss_pred             CCCCCCEEEEcCC--CCCHHHHHHHHhhCCCEEEEEec------CCCCEEEEEECCHHHHHHHHHHhCCCeECCeEEEEE
Confidence            3456789999996  89999999999999999999984      367999999999999999999999999999999999


Q ss_pred             eccccc
Q 007792          318 FSQSVS  323 (589)
Q Consensus       318 ~a~~~~  323 (589)
                      ++.+..
T Consensus        83 ~a~~~~   88 (97)
T 1x5p_A           83 IARKQP   88 (97)
T ss_dssp             CCSSCC
T ss_pred             ECCCCC
Confidence            998744

>2e5g_A U6 snRNA-specific terminal uridylyltransferase 1; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.59  E-value=5e-15  Score=123.69  Aligned_cols=76  Identities=22%  Similarity=0.309  Sum_probs=69.2

Q ss_pred             CCceEEEecCCCCCCHHHHHHHhccCCCeEEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHhcCCceeCCeEEEEEecc
Q 007792          241 PENVLFVCKLNPVTEDEDLHTIFSRFGTVVSAEIIRDFKTGDSLNYAFIEFENRQACERAYSKMDNALIDDRRIHVDFSQ  320 (589)
Q Consensus       241 ~~~~i~V~nL~~~~te~~L~~~F~~~G~v~~~~i~~d~~tg~~~g~aFV~f~~~~~a~~A~~~l~g~~i~gr~i~V~~a~  320 (589)
                      ...+|||+|||+.+|+++|..+|++||.|..|  +.++.++.   ||||+|.+.++|..||. |||..|+|+.|.|.++.
T Consensus         7 ~~~~l~V~nl~~~~t~~~l~~~F~~~G~v~~v--~~~~~~g~---~afV~f~~~~~a~~ai~-l~g~~~~g~~l~V~~a~   80 (94)
T 2e5g_A            7 GLRSVFVSGFPRGVDSAQLSEYFLAFGPVASV--VMDKDKGV---FAIVEMGDVGAREAVLS-QSQHSLGGHRLRVRPRE   80 (94)
T ss_dssp             TCCEEEEECCCTTCCHHHHHHHGGGTSCEEEE--EECSSSCC---EEEEEESSHHHHHHHHT-CSCCEETTEECCCBCSC
T ss_pred             CCCEEEEECCCCCCCHHHHHHHHHhcCCeEEE--EEcCCCCc---EEEEEECCHHHHHHHHh-cCCeEECCEEEEEEECC
Confidence            45799999999999999999999999999987  56666665   99999999999999998 99999999999999887


Q ss_pred             cc
Q 007792          321 SV  322 (589)
Q Consensus       321 ~~  322 (589)
                      +.
T Consensus        81 ~~   82 (94)
T 2e5g_A           81 QK   82 (94)
T ss_dssp             CS
T ss_pred             cC
Confidence            53

>2diu_A KIAA0430 protein; structural genomics, RRM domain, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.59  E-value=2.4e-15  Score=122.84  Aligned_cols=73  Identities=29%  Similarity=0.417  Sum_probs=65.4

Q ss_pred             CCce-EEEecCCCCCCHHH----HHHHhccC-CCeEEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHhcCCceeCCeEE
Q 007792          241 PENV-LFVCKLNPVTEDED----LHTIFSRF-GTVVSAEIIRDFKTGDSLNYAFIEFENRQACERAYSKMDNALIDDRRI  314 (589)
Q Consensus       241 ~~~~-i~V~nL~~~~te~~----L~~~F~~~-G~v~~~~i~~d~~tg~~~g~aFV~f~~~~~a~~A~~~l~g~~i~gr~i  314 (589)
                      |..| |||+|||+.+++++    |.++|++| |+|..|       |+   |||||.|.+.++|..|++.|||..|.|++|
T Consensus         7 p~~T~lYV~NL~~~~~~~~lk~~L~~lF~~yGG~Vl~V-------tg---G~AfV~F~~~esA~~A~~~l~G~~l~gr~i   76 (96)
T 2diu_A            7 GCHTLLYVYNLPANKDGKSVSNRLRRLSDNCGGKVLSI-------TG---CSAILRFINQDSAERAQKRMENEDVFGNRI   76 (96)
T ss_dssp             CSSEEEEEESCCTTSCHHHHHHHHHHHHHTTTCCEEEC-------CT---TCEEEEESSHHHHHHHHHHHTTCCSSSSCC
T ss_pred             CcceEEEEeCCCCcCCHHHHHHHHHHHHHHcCCeeEEE-------ec---CEEEEEECCHHHHHHHHHHhcCCccCCceE
Confidence            4444 99999999999988    55899999 599887       33   999999999999999999999999999999


Q ss_pred             EEEeccccc
Q 007792          315 HVDFSQSVS  323 (589)
Q Consensus       315 ~V~~a~~~~  323 (589)
                      +|+||+...
T Consensus        77 ~v~~A~~~s   85 (96)
T 2diu_A           77 IVSFTPKNR   85 (96)
T ss_dssp             EEESSCCSC
T ss_pred             EEEecCCCc
Confidence            999998744

>1whx_A Hypothetical protein riken cDNA 1200009A02; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, structural genomics; NMR {Mus musculus} SCOP: d.58.7.1

Probab=99.59  E-value=1.7e-15  Score=130.71  Aligned_cols=75  Identities=16%  Similarity=0.275  Sum_probs=70.4

Q ss_pred             CCceEEEecCCCCCCHHHHHHHhccCCCeEEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHhcCCceeCCeEEEEEecc
Q 007792          241 PENVLFVCKLNPVTEDEDLHTIFSRFGTVVSAEIIRDFKTGDSLNYAFIEFENRQACERAYSKMDNALIDDRRIHVDFSQ  320 (589)
Q Consensus       241 ~~~~i~V~nL~~~~te~~L~~~F~~~G~v~~~~i~~d~~tg~~~g~aFV~f~~~~~a~~A~~~l~g~~i~gr~i~V~~a~  320 (589)
                      ..++|||+|||+.+|+++|+++|++||.|..|.|+.      ++|||||+|.+.++|..||..|||..|.|+.|.|+||.
T Consensus         9 ~~~~l~V~nLp~~~te~~L~~~F~~~G~i~~v~i~~------~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~~a~   82 (111)
T 1whx_A            9 SKTVILAKNLPAGTLAAEIQETFSRFGSLGRVLLPE------GGITAIVEFLEPLEARKAFRHLAYSKFHHVPLYLEWAP   82 (111)
T ss_dssp             EEEEEEEESCCTTCCHHHHHHHHHTTSCEEEEECCS------SSSCEEEEESCHHHHHHHHHHHTTCBSSSSBCEEEEEE
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEeC------CCCEEEEEeCCHHHHHHHHHHhCCCEECCeEEEEEECC
Confidence            457999999999999999999999999999998864      56899999999999999999999999999999999997


Q ss_pred             c
Q 007792          321 S  321 (589)
Q Consensus       321 ~  321 (589)
                      .
T Consensus        83 ~   83 (111)
T 1whx_A           83 I   83 (111)
T ss_dssp             T
T ss_pred             C
Confidence            5

>2e44_A Insulin-like growth factor 2 mRNA binding protein 3; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.58  E-value=2.8e-15  Score=125.66  Aligned_cols=79  Identities=15%  Similarity=0.286  Sum_probs=72.3

Q ss_pred             CCCceEEEecCCCCCCHHHHHHHhccCCCeEEE-EEeecCCCCCcccEEEEEEcCHHHHHHHHHhcCCceeCCeEEEEEe
Q 007792          240 PPENVLFVCKLNPVTEDEDLHTIFSRFGTVVSA-EIIRDFKTGDSLNYAFIEFENRQACERAYSKMDNALIDDRRIHVDF  318 (589)
Q Consensus       240 ~~~~~i~V~nL~~~~te~~L~~~F~~~G~v~~~-~i~~d~~tg~~~g~aFV~f~~~~~a~~A~~~l~g~~i~gr~i~V~~  318 (589)
                      ...++|||+|||+.+|+++|..+|++||.|..| .|+.++.++    .|||+|.+.++|..||..|||..|.|+.|.|.+
T Consensus        13 ~~~~~l~V~nlp~~~t~~~l~~~F~~~G~v~~~~~i~~~~~~~----~afV~f~~~~~a~~Ai~~l~g~~~~g~~l~V~~   88 (96)
T 2e44_A           13 QRIRKLQIRNIPPHLQWEVLDSLLVQYGVVESCEQVNTDSETA----VVNVTYSSKDQARQALDKLNGFQLENFTLKVAY   88 (96)
T ss_dssp             CSCCCEEEEEECSSSCHHHHHHHHHHHSCEEEEEEECCSSSSE----EEEEEESSHHHHHHHHHHHTTCBCSSCBCEEEE
T ss_pred             CCCCEEEEEcCCCCCCHHHHHHHHHhcCCeEEEEEeecCCCCC----EEEEEECCHHHHHHHHHHhCCCEECCcEEEEEE
Confidence            356899999999999999999999999999999 588876553    499999999999999999999999999999999


Q ss_pred             cccc
Q 007792          319 SQSV  322 (589)
Q Consensus       319 a~~~  322 (589)
                      +.+.
T Consensus        89 a~~~   92 (96)
T 2e44_A           89 IPDE   92 (96)
T ss_dssp             CCCC
T ss_pred             cCcc
Confidence            9874

>2dha_A FLJ20171 protein; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.58  E-value=1.4e-15  Score=133.47  Aligned_cols=80  Identities=16%  Similarity=0.210  Sum_probs=73.5

Q ss_pred             CCceEEEecCCCCCCHHHHHHHhccCCCe----EEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHhcCCceeCCeEEEE
Q 007792          241 PENVLFVCKLNPVTEDEDLHTIFSRFGTV----VSAEIIRDFKTGDSLNYAFIEFENRQACERAYSKMDNALIDDRRIHV  316 (589)
Q Consensus       241 ~~~~i~V~nL~~~~te~~L~~~F~~~G~v----~~~~i~~d~~tg~~~g~aFV~f~~~~~a~~A~~~l~g~~i~gr~i~V  316 (589)
                      ...+|||+|||+.+|+++|+++|++||.|    ..|.|+.+ .+|+++|||||+|.+.++|++||+. |+..|+|+.|.|
T Consensus        22 ~~~~v~V~nLp~~~te~dl~~~F~~~g~v~g~v~~v~i~~d-~~gr~~G~aFV~F~~~~~A~~Al~~-~~~~l~gR~i~V   99 (123)
T 2dha_A           22 NQVIVRMRGLPFTATAEEVVAFFGQHCPITGGKEGILFVTY-PDGRPTGDAFVLFACEEYAQNALRK-HKDLLGKRYIEL   99 (123)
T ss_dssp             SCCEEEECSCCTTCCHHHHHHHHHTTSCCTTGGGGEEEEEC-TTSCEEEEEEECCSSHHHHHHHHTT-TTEESSSCEECC
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhhCCccCCcceEEEEEC-CCCCEeeEEEEEECCHHHHHHHHHh-CCCeeCCeEEEE
Confidence            46899999999999999999999999986    68999998 5899999999999999999999975 999999999999


Q ss_pred             Eecccc
Q 007792          317 DFSQSV  322 (589)
Q Consensus       317 ~~a~~~  322 (589)
                      ..+.+.
T Consensus       100 ~~a~~~  105 (123)
T 2dha_A          100 FRSTAA  105 (123)
T ss_dssp             EEECHH
T ss_pred             EECCHH
Confidence            998753

>1fxl_A Paraneoplastic encephalomyelitis antigen HUD; protein-RNA complex, AU-rich element, transcription/RNA complex; 1.80A {Homo sapiens} SCOP: d.58.7.1 d.58.7.1 PDB: 1g2e_A 1fnx_H 1d8z_A 1d9a_A 3hi9_A

Probab=99.58  E-value=7.1e-15  Score=135.50  Aligned_cols=82  Identities=24%  Similarity=0.505  Sum_probs=78.5

Q ss_pred             CceEEEecCCCCCCHHHHHHHhccCCCeEEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHhcCCceeCCeEEEEEeccc
Q 007792          242 ENVLFVCKLNPVTEDEDLHTIFSRFGTVVSAEIIRDFKTGDSLNYAFIEFENRQACERAYSKMDNALIDDRRIHVDFSQS  321 (589)
Q Consensus       242 ~~~i~V~nL~~~~te~~L~~~F~~~G~v~~~~i~~d~~tg~~~g~aFV~f~~~~~a~~A~~~l~g~~i~gr~i~V~~a~~  321 (589)
                      .++|||+|||+.+|+++|.++|++||.|..+.|+.++.+|.++|||||+|.+.++|..|+..|||..|.|+.|.|.++.+
T Consensus         2 ~~~l~v~nlp~~~~~~~l~~~f~~~G~i~~v~~~~~~~~~~~~g~afV~f~~~~~A~~a~~~l~~~~~~g~~l~v~~~~~   81 (167)
T 1fxl_A            2 KTNLIVNYLPQNMTQEEFRSLFGSIGEIESCKLVRDKITGQSLGYGFVNYIDPKDAEKAINTLNGLRLQTKTIKVSYARP   81 (167)
T ss_dssp             CSEEEEESCCTTCCHHHHHHHHHTTSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEECCC
T ss_pred             cceEEEcCCCCCCCHHHHHHHHHhcCCeEEEEEEeCCCCCcceeEEEEEECCHHHHHHHHHHcCCCccCCceEEEEecCC
Confidence            58999999999999999999999999999999999988999999999999999999999999999999999999999986


Q ss_pred             cc
Q 007792          322 VS  323 (589)
Q Consensus       322 ~~  323 (589)
                      ..
T Consensus        82 ~~   83 (167)
T 1fxl_A           82 SS   83 (167)
T ss_dssp             CC
T ss_pred             Cc
Confidence            43

>2i2y_A Fusion protein consists of immunoglobin G- binding protein G and splicing factor,...; protein-RNA complex RRM alpha-beta sandwich BETA1-alpha1- BETA2-BETA3-alpha2-BETA4; NMR {Streptococcus SP} PDB: 2i38_A

Probab=99.58  E-value=3.2e-15  Score=136.27  Aligned_cols=79  Identities=23%  Similarity=0.421  Sum_probs=74.2

Q ss_pred             CCCCceEEEecCCCCCCHHHHHHHhccCCCeEEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHhcCCceeCCeEEEEEe
Q 007792          239 KPPENVLFVCKLNPVTEDEDLHTIFSRFGTVVSAEIIRDFKTGDSLNYAFIEFENRQACERAYSKMDNALIDDRRIHVDF  318 (589)
Q Consensus       239 ~~~~~~i~V~nL~~~~te~~L~~~F~~~G~v~~~~i~~d~~tg~~~g~aFV~f~~~~~a~~A~~~l~g~~i~gr~i~V~~  318 (589)
                      ..+.++|||+|||+.+|+++|.++|++||.|..|.|+.+     ++|||||+|.+.++|..||..|||..|.|++|.|.+
T Consensus        70 ~~~~~~l~V~nl~~~~t~~~l~~~F~~~G~i~~v~i~~~-----~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~  144 (150)
T 2i2y_A           70 CPLDCKVYVGNLGNNGNKTELERAFGYYGPLRSVWVARN-----PPGFAFVEFEDPRDAADAVRELDGRTLCGCRVRVEL  144 (150)
T ss_dssp             STTSCEEEEESCCSCCSCHHHHHHHHHHSCEEEEEECSS-----SCSEEEEEESSHHHHHHHHHHHSSSCSSSSCCEEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhhCCEEEEEEeeC-----CCcEEEEEECCHHHHHHHHHHcCCCEECCeEEEEEE
Confidence            456789999999999999999999999999999999876     579999999999999999999999999999999999


Q ss_pred             cccc
Q 007792          319 SQSV  322 (589)
Q Consensus       319 a~~~  322 (589)
                      +.+.
T Consensus       145 a~~~  148 (150)
T 2i2y_A          145 SNGE  148 (150)
T ss_dssp             CCCC
T ss_pred             cCCC
Confidence            9864

>3beg_B Splicing factor, arginine/serine-rich 1; kinase, SR protein kinase, SR protein, PRE-mRNA splicing, at binding, chromosome partition; HET: SEP ANP; 2.90A {Homo sapiens} SCOP: d.58.7.1 PDB: 2o3d_A 1wg4_A

Probab=99.58  E-value=2.6e-15  Score=130.50  Aligned_cols=74  Identities=27%  Similarity=0.381  Sum_probs=66.7

Q ss_pred             CCceEEEecCCCCCCHHHHHHHhccCCCeEEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHhcCCceeCCeE-----EE
Q 007792          241 PENVLFVCKLNPVTEDEDLHTIFSRFGTVVSAEIIRDFKTGDSLNYAFIEFENRQACERAYSKMDNALIDDRR-----IH  315 (589)
Q Consensus       241 ~~~~i~V~nL~~~~te~~L~~~F~~~G~v~~~~i~~d~~tg~~~g~aFV~f~~~~~a~~A~~~l~g~~i~gr~-----i~  315 (589)
                      ..++|||+|||+.+|+++|+++|++||+|..|.|+.+       |||||+|.+.++|+.||+.|||..|+|+.     |.
T Consensus        15 ~~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~~~i~~~-------g~afV~f~~~~~a~~Ai~~l~g~~~~gr~~~~~~i~   87 (115)
T 3beg_B           15 SENRVVVSGLPPSGSWQDLKDHMREAGDVCYADVYRD-------GTGVVEFVRKEDMTYAVRKLDNTKFRSHEGETAYIR   87 (115)
T ss_dssp             --CCEEEEECCSSCCTTHHHHHHGGGSCEEEEEECTT-------SEEEEEESSHHHHHHHHHHHTTCBCCCTTSCCCBCE
T ss_pred             CCcEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEecC-------CEEEEEECCHHHHHHHHHHhCCCEECCcEeeeEEEE
Confidence            3589999999999999999999999999999999765       89999999999999999999999999998     67


Q ss_pred             EEeccc
Q 007792          316 VDFSQS  321 (589)
Q Consensus       316 V~~a~~  321 (589)
                      |..+.+
T Consensus        88 v~~~~~   93 (115)
T 3beg_B           88 VKVDGP   93 (115)
T ss_dssp             EEECC-
T ss_pred             eccCCC
Confidence            776655

>1wg1_A KIAA1579 protein, homolog EXC-7; RBD, structural genomics, riken structural genomics/proteomics initiative, RSGI, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1 PDB: 1wi6_A

Probab=99.58  E-value=4.6e-15  Score=122.33  Aligned_cols=75  Identities=11%  Similarity=0.187  Sum_probs=70.0

Q ss_pred             CCceEEEecCCCCCCHHHHHHHhccCCCeEEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHhcCCceeCCeEEEEEecc
Q 007792          241 PENVLFVCKLNPVTEDEDLHTIFSRFGTVVSAEIIRDFKTGDSLNYAFIEFENRQACERAYSKMDNALIDDRRIHVDFSQ  320 (589)
Q Consensus       241 ~~~~i~V~nL~~~~te~~L~~~F~~~G~v~~~~i~~d~~tg~~~g~aFV~f~~~~~a~~A~~~l~g~~i~gr~i~V~~a~  320 (589)
                      ..++|||+|||+.+++++|+++|++| .|..+.|.      +++|||||+|.+.++|..|+..|||..|.|++|.|+++.
T Consensus         4 ~~~~l~V~nLp~~~t~~~l~~~F~~~-~v~~~~i~------~~~g~afV~f~~~~~a~~Ai~~l~g~~~~g~~l~V~~a~   76 (88)
T 1wg1_A            4 GSSGILVKNLPQDSNCQEVHDLLKDY-DLKYCYVD------RNKRTAFVTLLNGEQAQNAIQMFHQYSFRGKDLIVQLQP   76 (88)
T ss_dssp             CCCCEEEESCCSSCCHHHHHHHTCSS-CCCCEEEE------GGGTEEEECCSCHHHHHHHHHHHTTEEETTEEEEEEECC
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHhhC-CeEEEEEe------CCCcEEEEEECCHHHHHHHHHHhCCCeECCcEEEEEEcC
Confidence            46899999999999999999999999 99999884      478999999999999999999999999999999999996


Q ss_pred             cc
Q 007792          321 SV  322 (589)
Q Consensus       321 ~~  322 (589)
                      ..
T Consensus        77 ~~   78 (88)
T 1wg1_A           77 TD   78 (88)
T ss_dssp             CC
T ss_pred             CC
Confidence            53

>2hgm_A HNRPF protein, heterogeneous nuclear ribonucleoprotein F; RNA recognition motif, G-tract, G-quadruplex, alternative splicing, RNA binding protein; NMR {Homo sapiens} PDB: 2kg0_A

Probab=99.57  E-value=2.5e-15  Score=132.10  Aligned_cols=79  Identities=22%  Similarity=0.268  Sum_probs=72.3

Q ss_pred             CCCceEEEecCCCCCCHHHHHHHhccCCCeE--EEEEeecCCCCCcccEEEEEEcCHHHHHHHHHhcCCceeCCeEEEEE
Q 007792          240 PPENVLFVCKLNPVTEDEDLHTIFSRFGTVV--SAEIIRDFKTGDSLNYAFIEFENRQACERAYSKMDNALIDDRRIHVD  317 (589)
Q Consensus       240 ~~~~~i~V~nL~~~~te~~L~~~F~~~G~v~--~~~i~~d~~tg~~~g~aFV~f~~~~~a~~A~~~l~g~~i~gr~i~V~  317 (589)
                      .+..+|||+|||+.+|+++|+++|++| .|+  .|.|+.++. |+++|||||+|.+.++|.+||+ +++..|+|+.|.|.
T Consensus        40 ~~~~~lfVgnLp~~~te~dL~~~F~~~-~i~~~~v~i~~d~~-GrsrGfaFV~F~~~e~A~~Al~-~~~~~l~gR~I~V~  116 (126)
T 2hgm_A           40 ANDGFVRLRGLPFGCTKEEIVQFFSGL-EIVPNGITLPVDPE-GKITGEAFVQFASQELAEKALG-KHKERIGHRYIEVF  116 (126)
T ss_dssp             SSCCEEEEECCCTTCCHHHHHHHTTTS-CEEEEEEECCCCSS-SSSCSEEEEEESSTTHHHHHHT-TTTCCBTTBCCCCE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHhcC-CceeeEEEEEECCC-CCCceEEEEEECCHHHHHHHHH-HCCCEECCEEEEEE
Confidence            456899999999999999999999999 577  899999977 9999999999999999999997 57899999999999


Q ss_pred             eccc
Q 007792          318 FSQS  321 (589)
Q Consensus       318 ~a~~  321 (589)
                      .+.+
T Consensus       117 ~a~~  120 (126)
T 2hgm_A          117 KSSQ  120 (126)
T ss_dssp             EECH
T ss_pred             ECCH
Confidence            8864

>3d2w_A TAR DNA-binding protein 43; DP-43 proteinopathy, TDP-43 inclusions, RNA recognition MOTI U, ALS, RRM; HET: DNA; 1.65A {Mus musculus}

Probab=99.57  E-value=4.8e-15  Score=122.56  Aligned_cols=77  Identities=18%  Similarity=0.357  Sum_probs=63.1

Q ss_pred             CCCCCceEEEecCCCCCCHHHHHHHhccCCCeEEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHhcCCc--eeCCeEEE
Q 007792          238 IKPPENVLFVCKLNPVTEDEDLHTIFSRFGTVVSAEIIRDFKTGDSLNYAFIEFENRQACERAYSKMDNA--LIDDRRIH  315 (589)
Q Consensus       238 ~~~~~~~i~V~nL~~~~te~~L~~~F~~~G~v~~~~i~~d~~tg~~~g~aFV~f~~~~~a~~A~~~l~g~--~i~gr~i~  315 (589)
                      ..++.++|||+|||+++|+++|+++|++||.|..|.|+.+     ++|||||+|.+.++|.+    |+|.  .+.|+.|.
T Consensus         7 ~~~~~~~l~V~~Lp~~~te~~L~~~F~~~G~i~~v~i~~~-----srGfaFV~F~~~~~A~~----~~~~~~~~~g~~v~   77 (89)
T 3d2w_A            7 HHHHGSKVFVGRCTEDMTAEELQQFFCQYGEVVDVFIPKP-----FRAFAFVTFADDKVAQS----LCGEDLIIKGISVH   77 (89)
T ss_dssp             ----CCEEEEESCCTTCCHHHHHHHHTTTSCEEEEECCSS-----CCSEEEEEESCHHHHHH----HTTCEEEETTEEEE
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHhccCCEEEEEEeeC-----CCCEEEEEECCHHHHHH----HcCCCcccCCEEEE
Confidence            3567899999999999999999999999999999999874     78999999999999984    3444  45699999


Q ss_pred             EEeccccc
Q 007792          316 VDFSQSVS  323 (589)
Q Consensus       316 V~~a~~~~  323 (589)
                      |.+|.++.
T Consensus        78 v~~a~~k~   85 (89)
T 3d2w_A           78 ISNAEPKH   85 (89)
T ss_dssp             EEECC---
T ss_pred             EEEcCCCC
Confidence            99998643

>1b7f_A Protein (SXL-lethal protein), RNA (5'-R(P*GP*UP*UP*GP*UP*UP*UP*UP*UP*UP*UP*U)-3; splicing regulation, RNP domain, RNA complex; 2.60A {Drosophila melanogaster} SCOP: d.58.7.1 d.58.7.1 PDB: 3sxl_A* 1sxl_A 2sxl_A

Probab=99.57  E-value=5.7e-15  Score=136.53  Aligned_cols=83  Identities=27%  Similarity=0.528  Sum_probs=79.1

Q ss_pred             CCceEEEecCCCCCCHHHHHHHhccCCCeEEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHhcCCceeCCeEEEEEecc
Q 007792          241 PENVLFVCKLNPVTEDEDLHTIFSRFGTVVSAEIIRDFKTGDSLNYAFIEFENRQACERAYSKMDNALIDDRRIHVDFSQ  320 (589)
Q Consensus       241 ~~~~i~V~nL~~~~te~~L~~~F~~~G~v~~~~i~~d~~tg~~~g~aFV~f~~~~~a~~A~~~l~g~~i~gr~i~V~~a~  320 (589)
                      +.++|||+|||+.+|+++|.++|++||+|..|.|+.++.+|.++|||||+|.+.++|..|+..|+|..|.|+.|.|.++.
T Consensus         2 ~~~~l~v~nlp~~~~~~~l~~~f~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~a~~~l~~~~~~g~~l~v~~~~   81 (168)
T 1b7f_A            2 SNTNLIVNYLPQDMTDRELYALFRAIGPINTCRIMRDYKTGYSYGYAFVDFTSEMDSQRAIKVLNGITVRNKRLKVSYAR   81 (168)
T ss_dssp             CCSEEEEECCCTTCCHHHHHHHHHTTSCEEEEECCEETTTTEECSEEEEEESSHHHHHHHHHHHTTCEETTEECEEEECC
T ss_pred             CccEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEEeCCCCccceEEEEEECCHHHHHHHHHhcCCCEeCCcEEEEEecC
Confidence            56899999999999999999999999999999999999999999999999999999999999999999999999999998


Q ss_pred             ccc
Q 007792          321 SVS  323 (589)
Q Consensus       321 ~~~  323 (589)
                      +..
T Consensus        82 ~~~   84 (168)
T 1b7f_A           82 PGG   84 (168)
T ss_dssp             CCS
T ss_pred             CCc
Confidence            643

>2cq2_A Hypothetical protein LOC91801; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.57  E-value=3e-15  Score=128.65  Aligned_cols=78  Identities=17%  Similarity=0.303  Sum_probs=70.4

Q ss_pred             CCCCceEEE--ecCCCCCCHHHHHHHhccCCCeEEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHhcCCcee-----CC
Q 007792          239 KPPENVLFV--CKLNPVTEDEDLHTIFSRFGTVVSAEIIRDFKTGDSLNYAFIEFENRQACERAYSKMDNALI-----DD  311 (589)
Q Consensus       239 ~~~~~~i~V--~nL~~~~te~~L~~~F~~~G~v~~~~i~~d~~tg~~~g~aFV~f~~~~~a~~A~~~l~g~~i-----~g  311 (589)
                      ..|..+|||  |||++.+|+++|+++|++||.|..|.|+.      .+|||||+|.+.++|.+|++.|||..|     .|
T Consensus        22 ~~pt~~L~V~Ng~L~~~~te~~L~~~F~~fG~v~~v~i~~------~rgfaFV~f~~~~~A~~Ai~~lnG~~~~~~lg~g   95 (114)
T 2cq2_A           22 SYATQSLVVANGGLGNGVSRNQLLPVLEKCGLVDALLMPP------NKPYSFARYRTTEESKRAYVTLNGKEVVDDLGQK   95 (114)
T ss_dssp             SSCCSEEEEETCTGGGTCCHHHHHHHHHHHSCEEEEECCT------TCSCEEEEESSHHHHHHHHHHTTTCEEECTTSCE
T ss_pred             CCCCCEEEEECCCCCCCCCHHHHHHHHHhcCCeEEEEEeC------CCCEEEEEECCHHHHHHHHHHhCCCEEccccCCC
Confidence            346789999  77999999999999999999999988764      368999999999999999999999998     78


Q ss_pred             eEEEEEecccc
Q 007792          312 RRIHVDFSQSV  322 (589)
Q Consensus       312 r~i~V~~a~~~  322 (589)
                      ++|.|.|+...
T Consensus        96 ~~l~v~~a~~~  106 (114)
T 2cq2_A           96 ITLYLNFVEKV  106 (114)
T ss_dssp             EECEEEEESCC
T ss_pred             cEEEEEecccC
Confidence            99999999753

>1l3k_A Heterogeneous nuclear ribonucleoprotein A1; nuclear protein hnRNP A1, RNA-recognition motif, RNA- binding, UP1, RNA binding protein; 1.10A {Homo sapiens} SCOP: d.58.7.1 d.58.7.1 PDB: 1u1k_A* 1u1l_A* 1u1m_A* 1u1n_A* 1u1o_A 1u1p_A* 1u1q_A 1u1r_A* 1pgz_A* 1ha1_A 1po6_A* 2up1_A* 1up1_A

Probab=99.57  E-value=1e-14  Score=138.49  Aligned_cols=84  Identities=19%  Similarity=0.378  Sum_probs=75.9

Q ss_pred             CCCceEEEecCCCCCCHHHHHHHhccCCCeEEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHhcCCceeCCeEEEEEec
Q 007792          240 PPENVLFVCKLNPVTEDEDLHTIFSRFGTVVSAEIIRDFKTGDSLNYAFIEFENRQACERAYSKMDNALIDDRRIHVDFS  319 (589)
Q Consensus       240 ~~~~~i~V~nL~~~~te~~L~~~F~~~G~v~~~~i~~d~~tg~~~g~aFV~f~~~~~a~~A~~~l~g~~i~gr~i~V~~a  319 (589)
                      .+..+|||+|||+.+|+++|.++|++||.|..|.|+.+..+|.++|||||+|.+.++|.+||.. +|..|+|+.|.|.+|
T Consensus       102 ~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~F~~~~~A~~A~~~-~~~~~~G~~i~v~~a  180 (196)
T 1l3k_A          102 LTVKKIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIVIQ-KYHTVNGHNCEVRKA  180 (196)
T ss_dssp             -CCSEEEEECCTTTCCHHHHHHHHTTTSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHC-SCCEETTEECEEEEC
T ss_pred             CCcceEEEeCCCCCCCHHHHHHHHhcCCCeEEEEEeecCCCCCccceEEEEECCHHHHHHHHHh-CCcEECCEEEEEEec
Confidence            3568999999999999999999999999999999999988999999999999999999999975 899999999999999


Q ss_pred             ccccc
Q 007792          320 QSVSK  324 (589)
Q Consensus       320 ~~~~~  324 (589)
                      .++..
T Consensus       181 ~~k~~  185 (196)
T 1l3k_A          181 LSKQE  185 (196)
T ss_dssp             C----
T ss_pred             CChhH
Confidence            87544

>3zzy_A Polypyrimidine tract-binding protein 1; protein binding, peptide binding, RNA recognition motif; 1.40A {Homo sapiens} PDB: 3zzz_A

Probab=99.56  E-value=1.2e-14  Score=127.78  Aligned_cols=75  Identities=24%  Similarity=0.363  Sum_probs=69.0

Q ss_pred             ceEEEecCCCCCCHHHHHHHhccCCCeEEEEEeecCCCCCcccE-EEEEEcCHHHHHHHHHhcCCceeCC--eEEEEEec
Q 007792          243 NVLFVCKLNPVTEDEDLHTIFSRFGTVVSAEIIRDFKTGDSLNY-AFIEFENRQACERAYSKMDNALIDD--RRIHVDFS  319 (589)
Q Consensus       243 ~~i~V~nL~~~~te~~L~~~F~~~G~v~~~~i~~d~~tg~~~g~-aFV~f~~~~~a~~A~~~l~g~~i~g--r~i~V~~a  319 (589)
                      -.|||+||++.+|+++|.++|++||.|..|.|+..     .+|| |||+|.+.++|..|++.|||..|.|  +.|+|+||
T Consensus        29 L~I~V~NL~~~vte~~L~~lFs~yG~V~~V~i~~~-----~~gfqAFVef~~~~~A~~Ai~~LnG~~i~g~~~~LrI~~a  103 (130)
T 3zzy_A           29 LRIIVENLFYPVTLDVLHQIFSKFGTVLKIITFTK-----NNQFQALLQYADPVSAQHAKLSLDGQNIYNACCTLRIDFS  103 (130)
T ss_dssp             EEEEEESCCSCCCHHHHHHHHTTSSCEEEEEEEEE-----TTEEEEEEEESCHHHHHHHHHHHTTCEEETTEEEEEEEEC
T ss_pred             EEEEECCCCCCCCHHHHHHHHhCcCCEEEEEEEcC-----CCCcEEEEEECCHHHHHHHHHHcCCCeecCCCcEEEEEec
Confidence            46789999999999999999999999999988764     3578 9999999999999999999999988  99999999


Q ss_pred             ccc
Q 007792          320 QSV  322 (589)
Q Consensus       320 ~~~  322 (589)
                      ++.
T Consensus       104 k~~  106 (130)
T 3zzy_A          104 KLT  106 (130)
T ss_dssp             SCS
T ss_pred             CCC
Confidence            874

>1b7f_A Protein (SXL-lethal protein), RNA (5'-R(P*GP*UP*UP*GP*UP*UP*UP*UP*UP*UP*UP*U)-3; splicing regulation, RNP domain, RNA complex; 2.60A {Drosophila melanogaster} SCOP: d.58.7.1 d.58.7.1 PDB: 3sxl_A* 1sxl_A 2sxl_A

Probab=99.55  E-value=2e-14  Score=132.78  Aligned_cols=81  Identities=27%  Similarity=0.546  Sum_probs=77.0

Q ss_pred             CCCCceEEEecCCCCCCHHHHHHHhccCCCeEEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHhcCCceeCC--eEEEE
Q 007792          239 KPPENVLFVCKLNPVTEDEDLHTIFSRFGTVVSAEIIRDFKTGDSLNYAFIEFENRQACERAYSKMDNALIDD--RRIHV  316 (589)
Q Consensus       239 ~~~~~~i~V~nL~~~~te~~L~~~F~~~G~v~~~~i~~d~~tg~~~g~aFV~f~~~~~a~~A~~~l~g~~i~g--r~i~V  316 (589)
                      ..+..+|||+|||+.+++++|.++|++||.|..+.|+.+..+|.++|||||+|.+.++|..|+..|||..|.|  ++|.|
T Consensus        86 ~~~~~~l~v~nl~~~~t~~~l~~~f~~~G~i~~~~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~~~l~V  165 (168)
T 1b7f_A           86 SIKDTNLYVTNLPRTITDDQLDTIFGKYGSIVQKNILRDKLTGRPRGVAFVRYNKREEAQEAISALNNVIPEGGSQPLSV  165 (168)
T ss_dssp             TTTTCEEEEESCCTTCCHHHHHHHHTSSSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCCCTTCSSCCEE
T ss_pred             cCCCCCEEEeCCCCCCCHHHHHHhhhcCCcEEEEEEEEcCCCCCcceEEEEEECCHHHHHHHHHHhcCCEecCCCeEEEE
Confidence            4567899999999999999999999999999999999998899999999999999999999999999999988  99999


Q ss_pred             Eec
Q 007792          317 DFS  319 (589)
Q Consensus       317 ~~a  319 (589)
                      .||
T Consensus       166 ~~A  168 (168)
T 1b7f_A          166 RLA  168 (168)
T ss_dssp             EEC
T ss_pred             EeC
Confidence            986

>2e5i_A Heterogeneous nuclear ribonucleoprotein L-like; RRM domain, RBD, structural genomics, NPPSFA; NMR {Mus musculus}

Probab=99.55  E-value=3.2e-14  Score=124.56  Aligned_cols=77  Identities=18%  Similarity=0.226  Sum_probs=68.4

Q ss_pred             CCCce--EEEecCCCCCCHHHHHHHhccCCCeEEEEEeecCCCCCcccE-EEEEEcCHHHHHHHHHhcCCceeCC--eEE
Q 007792          240 PPENV--LFVCKLNPVTEDEDLHTIFSRFGTVVSAEIIRDFKTGDSLNY-AFIEFENRQACERAYSKMDNALIDD--RRI  314 (589)
Q Consensus       240 ~~~~~--i~V~nL~~~~te~~L~~~F~~~G~v~~~~i~~d~~tg~~~g~-aFV~f~~~~~a~~A~~~l~g~~i~g--r~i  314 (589)
                      +|..+  |||+||++.+|+++|.++|++||.|..|.|+..      .|| |||+|.+.++|..|++.|||..|.|  +.|
T Consensus        21 ~ps~vl~l~V~NL~~~vt~~~L~~~Fs~yG~V~~v~i~~~------~Gf~aFVef~~~~~A~~A~~~LnG~~i~g~~~~l   94 (124)
T 2e5i_A           21 GGNKVLLLSIQNPLYPITVDVLYTVCNPVGKVQRIVIFKR------NGIQAMVEFESVLCAQKAKAALNGADIYAGCCTL   94 (124)
T ss_dssp             CCCSEEEEEEESCCSCCCHHHHHHHHTTTSCEEEEEEEES------SSEEEEEEESSHHHHHHHHHHHTTCCCBTTBSEE
T ss_pred             CCCcEEEEEEcCcCCCCCHHHHHHHHHhcCCEEEEEEEeC------CCCEEEEEECCHHHHHHHHHHhCCCEecCCCeEE
Confidence            44554  679999999999999999999999999998652      286 9999999999999999999999987  699


Q ss_pred             EEEecccc
Q 007792          315 HVDFSQSV  322 (589)
Q Consensus       315 ~V~~a~~~  322 (589)
                      .|++|++.
T Consensus        95 ~V~~Ak~~  102 (124)
T 2e5i_A           95 KIEYARPT  102 (124)
T ss_dssp             EEECCSCS
T ss_pred             EEEEecCC
Confidence            99999874

>2yh0_A Splicing factor U2AF 65 kDa subunit; PRE-mRNA splicing, transcription, RNA binding protein, mRNA processing; NMR {Homo sapiens} PDB: 2yh1_A

Probab=99.54  E-value=2.2e-14  Score=136.42  Aligned_cols=85  Identities=20%  Similarity=0.398  Sum_probs=80.6

Q ss_pred             CCCCceEEEecCCCCCCHHHHHHHhccCCCeEEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHhcCCceeCCeEEEEEe
Q 007792          239 KPPENVLFVCKLNPVTEDEDLHTIFSRFGTVVSAEIIRDFKTGDSLNYAFIEFENRQACERAYSKMDNALIDDRRIHVDF  318 (589)
Q Consensus       239 ~~~~~~i~V~nL~~~~te~~L~~~F~~~G~v~~~~i~~d~~tg~~~g~aFV~f~~~~~a~~A~~~l~g~~i~gr~i~V~~  318 (589)
                      ..+.++|||+|||+.+++++|.++|++||.|..|.|+.++.+|.++|||||+|.+.++|..|+..|||..|+|+.|.|.+
T Consensus       111 ~~~~~~l~v~nl~~~~~~~~l~~~f~~~G~v~~~~~~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~  190 (198)
T 2yh0_A          111 PDSAHKLFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIAGLNGMQLGDKKLLVQR  190 (198)
T ss_dssp             SCCCCEEEEECCCTTCCHHHHHHHHHTBSCEEEEEEEECTTTCSEEEEEEEEESSSSHHHHHHHHHTTCEETTEECEEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHHcCCccEEEEeecCCCCCcceEEEEEECCHHHHHHHHHHcCCCEECCEEEEEEE
Confidence            35678999999999999999999999999999999999988999999999999999999999999999999999999999


Q ss_pred             ccccc
Q 007792          319 SQSVS  323 (589)
Q Consensus       319 a~~~~  323 (589)
                      +.+..
T Consensus       191 a~~~~  195 (198)
T 2yh0_A          191 ASVGA  195 (198)
T ss_dssp             SCCCC
T ss_pred             CCCCC
Confidence            98743

>2qfj_A FBP-interacting repressor; protein-DNA complex; HET: DNA; 2.10A {Homo sapiens} PDB: 3uwt_A 2kxf_A 2kxh_A

Probab=99.54  E-value=1.7e-14  Score=139.19  Aligned_cols=83  Identities=28%  Similarity=0.461  Sum_probs=79.5

Q ss_pred             CCceEEEecCCCCCCHHHHHHHhccCCCeEEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHhcCCceeCCeEEEEEecc
Q 007792          241 PENVLFVCKLNPVTEDEDLHTIFSRFGTVVSAEIIRDFKTGDSLNYAFIEFENRQACERAYSKMDNALIDDRRIHVDFSQ  320 (589)
Q Consensus       241 ~~~~i~V~nL~~~~te~~L~~~F~~~G~v~~~~i~~d~~tg~~~g~aFV~f~~~~~a~~A~~~l~g~~i~gr~i~V~~a~  320 (589)
                      +.++|||+|||+.+|+++|.++|++||.|..|.|+.++.+|.++|||||+|.+.++|..|+..|||..|+|+.|.|.++.
T Consensus       124 ~~~~l~v~nlp~~~t~~~l~~~f~~~G~v~~v~i~~~~~~g~~~g~afV~F~~~~~A~~A~~~l~g~~~~g~~i~V~~a~  203 (216)
T 2qfj_A          124 AFNRIYVASVHQDLSDDDIKSVFEAFGKIKSATLARDPTTGKHKGYGFIEYEKAQSSQDAVSSMNLFDLGGQYLRVGKAV  203 (216)
T ss_dssp             TSCEEEEECCCTTCCHHHHHHHHTTSSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCBCSSSBCEEEECS
T ss_pred             CCcEEEEeCCCCcCCHHHHHHHHhccCCeeEEEEEecCCCCCcCceEEEEecCHHHHHHHHHHccCCEeCCcEEEEEEec
Confidence            46899999999999999999999999999999999999999999999999999999999999999999999999999998


Q ss_pred             ccc
Q 007792          321 SVS  323 (589)
Q Consensus       321 ~~~  323 (589)
                      +.+
T Consensus       204 ~~~  206 (216)
T 2qfj_A          204 TPP  206 (216)
T ss_dssp             SCS
T ss_pred             CCC
Confidence            754

>4f02_A Polyadenylate-binding protein 1; mRNA, eukaryotic initiation factors PAIP1 and PAIP2, translation-RNA complex; 2.00A {Homo sapiens} PDB: 1cvj_A*

Probab=99.54  E-value=2.4e-15  Score=145.49  Aligned_cols=81  Identities=31%  Similarity=0.548  Sum_probs=75.2

Q ss_pred             CCceEEEecCCCCCCHHHHHHHhccCCCeEEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHhcCCceeCCeEEEEEecc
Q 007792          241 PENVLFVCKLNPVTEDEDLHTIFSRFGTVVSAEIIRDFKTGDSLNYAFIEFENRQACERAYSKMDNALIDDRRIHVDFSQ  320 (589)
Q Consensus       241 ~~~~i~V~nL~~~~te~~L~~~F~~~G~v~~~~i~~d~~tg~~~g~aFV~f~~~~~a~~A~~~l~g~~i~gr~i~V~~a~  320 (589)
                      ...+|||+|||+.+|+++|.++|++||.|..|.|+.+.  +.++|||||+|.+.++|..||+.|||..|+|+.|.|.+|.
T Consensus       102 ~~~~l~v~nl~~~~t~~~l~~~F~~~G~i~~~~i~~d~--~~~~g~~fV~f~~~~~a~~Ai~~lng~~~~g~~i~V~~a~  179 (213)
T 4f02_A          102 GVGNIFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDE--NGSKGYGFVHFETQEAAERAIEKMNGMLLNDRKVFVGRFK  179 (213)
T ss_dssp             CTTEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEEET--TEEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEECC
T ss_pred             ccccceECCcccccHHHHHHHHHhhcCCeEEEEeeccC--CCCceEEEEEeCCHHHHHHHHHHhCCCEECCEEEEEEEcC
Confidence            45789999999999999999999999999999999874  4479999999999999999999999999999999999998


Q ss_pred             ccc
Q 007792          321 SVS  323 (589)
Q Consensus       321 ~~~  323 (589)
                      ++.
T Consensus       180 ~~~  182 (213)
T 4f02_A          180 SRK  182 (213)
T ss_dssp             CHH
T ss_pred             CCc
Confidence            743

>2pe8_A Splicing factor 45; RRM, protein binding; 2.00A {Homo sapiens} PDB: 2peh_A

Probab=99.54  E-value=2.6e-14  Score=121.75  Aligned_cols=83  Identities=17%  Similarity=0.237  Sum_probs=74.0

Q ss_pred             CCCCceEEEecCCC-----CCCHHHHHHHhccCCCeEEEEEeecCCC-CCcccEEEEEEcCHHHHHHHHHhcCCceeCCe
Q 007792          239 KPPENVLFVCKLNP-----VTEDEDLHTIFSRFGTVVSAEIIRDFKT-GDSLNYAFIEFENRQACERAYSKMDNALIDDR  312 (589)
Q Consensus       239 ~~~~~~i~V~nL~~-----~~te~~L~~~F~~~G~v~~~~i~~d~~t-g~~~g~aFV~f~~~~~a~~A~~~l~g~~i~gr  312 (589)
                      ..|..+|+|.||..     +.++++|+++|++||.|..|.|+.++.+ +.++|||||+|.+.++|.+|+..|||..|+|+
T Consensus         5 ~~~s~~l~l~Nm~~~~~l~dd~~~dl~~~f~~~G~V~~v~i~~~~~~~~~~~G~~FV~f~~~~~A~~Ai~~lnG~~~~Gr   84 (105)
T 2pe8_A            5 KCPTKVVLLRNMVGAGEVDEDLEVETKEECEKYGKVGKCVIFEIPGAPDDEAVRIFLEFERVESAIKAVVDLNGRYFGGR   84 (105)
T ss_dssp             GSCCSEEEEESSSCSCCC---CHHHHHHHGGGGSCEEEEEEEECSSCCTTTSEEEEEEESSHHHHHHHHHHHTTCEETTE
T ss_pred             CCCCCEEEEEcCCChHHhhHHHHHHHHHHHHhcCCEEEEEEecCCCCCCCCcEEEEEEECCHHHHHHHHHHHCCCEECCc
Confidence            34678999999963     2378999999999999999999998654 68899999999999999999999999999999


Q ss_pred             EEEEEeccc
Q 007792          313 RIHVDFSQS  321 (589)
Q Consensus       313 ~i~V~~a~~  321 (589)
                      .|.|.++.+
T Consensus        85 ~i~v~~a~~   93 (105)
T 2pe8_A           85 VVKACFYNL   93 (105)
T ss_dssp             ECEEEECCH
T ss_pred             EEEEEEcCH
Confidence            999999975

>1l3k_A Heterogeneous nuclear ribonucleoprotein A1; nuclear protein hnRNP A1, RNA-recognition motif, RNA- binding, UP1, RNA binding protein; 1.10A {Homo sapiens} SCOP: d.58.7.1 d.58.7.1 PDB: 1u1k_A* 1u1l_A* 1u1m_A* 1u1n_A* 1u1o_A 1u1p_A* 1u1q_A 1u1r_A* 1pgz_A* 1ha1_A 1po6_A* 2up1_A* 1up1_A

Probab=99.54  E-value=2.2e-14  Score=136.10  Aligned_cols=83  Identities=23%  Similarity=0.349  Sum_probs=77.5

Q ss_pred             CCCCceEEEecCCCCCCHHHHHHHhccCCCeEEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHhcCCceeCCeEEEEEe
Q 007792          239 KPPENVLFVCKLNPVTEDEDLHTIFSRFGTVVSAEIIRDFKTGDSLNYAFIEFENRQACERAYSKMDNALIDDRRIHVDF  318 (589)
Q Consensus       239 ~~~~~~i~V~nL~~~~te~~L~~~F~~~G~v~~~~i~~d~~tg~~~g~aFV~f~~~~~a~~A~~~l~g~~i~gr~i~V~~  318 (589)
                      ..+.++|||+|||+.+|+++|.++|++||.|..|.|+.++.+|.++|||||+|.+.++|..||.. ++..|.|+.|.|.+
T Consensus        10 ~~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~A~~~-~~~~~~g~~l~v~~   88 (196)
T 1l3k_A           10 PEQLRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMNA-RPHKVDGRVVEPKR   88 (196)
T ss_dssp             CGGGGEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHT-CSCEETTEECEEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhCCCEEEEEEEEcCCCCCccceEEEEeCCHHHHHHHHhc-CCCEECCEEeeeec
Confidence            44678999999999999999999999999999999999999999999999999999999999965 99999999999999


Q ss_pred             cccc
Q 007792          319 SQSV  322 (589)
Q Consensus       319 a~~~  322 (589)
                      +.+.
T Consensus        89 ~~~~   92 (196)
T 1l3k_A           89 AVSR   92 (196)
T ss_dssp             CCC-
T ss_pred             ccCc
Confidence            8764

>2dnl_A Cytoplasmic polyadenylation element binding protein 3; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.53  E-value=1.1e-14  Score=126.29  Aligned_cols=79  Identities=19%  Similarity=0.284  Sum_probs=70.8

Q ss_pred             CCCceEEEecCCCCCCHHHHHHHhccCCCeEEEEEeecCCC---CCcccEEEEEEcCHHHHHHHHHhcCCceeCCeEEEE
Q 007792          240 PPENVLFVCKLNPVTEDEDLHTIFSRFGTVVSAEIIRDFKT---GDSLNYAFIEFENRQACERAYSKMDNALIDDRRIHV  316 (589)
Q Consensus       240 ~~~~~i~V~nL~~~~te~~L~~~F~~~G~v~~~~i~~d~~t---g~~~g~aFV~f~~~~~a~~A~~~l~g~~i~gr~i~V  316 (589)
                      ...++|||+|||+.+|+++|+++|++||+|. +.++.+..+   |+++|||||+|.+.++|+.||+.|+  .++|+.|.|
T Consensus         6 ~~~~~lfVgnLp~~~te~~L~~~F~~~G~i~-~~~~~~~~~~~~g~~~G~aFV~f~~~~~a~~Ai~~~~--~~~G~~~~~   82 (114)
T 2dnl_A            6 SGSRKVFVGGLPPDIDEDEITASFRRFGPLV-VDWPHKAESKSYFPPKGYAFLLFQEESSVQALIDACL--EEDGKLYLC   82 (114)
T ss_dssp             SCCCCEEEECCCTTCCHHHHHHHTTTTCCCC-EECTTSSSSCCCSCTTSEEEECCSSHHHHHHHHHHSE--EETTEEEEE
T ss_pred             CCCCEEEEcCCCCCCCHHHHHHHHHhcCCEE-EEEeecCCCCCCCCcccEEEEEECCHHHHHHHHHhhh--hcCCcEEEe
Confidence            3568999999999999999999999999999 888888777   7999999999999999999999985  488888888


Q ss_pred             Eeccc
Q 007792          317 DFSQS  321 (589)
Q Consensus       317 ~~a~~  321 (589)
                      ..+.+
T Consensus        83 ~~~~~   87 (114)
T 2dnl_A           83 VSSPT   87 (114)
T ss_dssp             ECCSS
T ss_pred             ccCCC
Confidence            76654

>1sjr_A Polypyrimidine tract-binding protein 1; extended babbab motif, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1 PDB: 2adb_A

Probab=99.53  E-value=1.7e-14  Score=131.60  Aligned_cols=76  Identities=24%  Similarity=0.328  Sum_probs=69.5

Q ss_pred             ceEEEecCCCCCCHHHHHHHhccCCCeEEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHhcCCceeCC--eEEEEEecc
Q 007792          243 NVLFVCKLNPVTEDEDLHTIFSRFGTVVSAEIIRDFKTGDSLNYAFIEFENRQACERAYSKMDNALIDD--RRIHVDFSQ  320 (589)
Q Consensus       243 ~~i~V~nL~~~~te~~L~~~F~~~G~v~~~~i~~d~~tg~~~g~aFV~f~~~~~a~~A~~~l~g~~i~g--r~i~V~~a~  320 (589)
                      .+|||+||++.+|+++|.++|++||.|..|.|+..    .++|||||+|.+.++|..|++.|||..|.|  +.|+|+||+
T Consensus        47 l~l~VgNL~~~vted~L~~~Fs~fG~V~~V~i~~k----~~rgfAFVeF~d~~~A~~Ai~~LnG~~i~g~g~~L~V~~Ak  122 (164)
T 1sjr_A           47 LRIIVENLFYPVTLDVLHQIFSKFGTVLKIITFTK----NNQFQALLQYADPVSAQHAKLSLDGQNIYNACCTLRIDFSK  122 (164)
T ss_dssp             EEEEECSCCSCCCHHHHHHHHHHHSCEEEEEEEES----SSCEEEEEEESCHHHHHHHHHHSTTBCSSSSCSCEEEEECS
T ss_pred             EEEEEeCcCCCCCHHHHHHHHHhcCCEEEEEEEeC----CCCCEEEEEECCHHHHHHHHHHhCCCEecCCCcEEEEEEec
Confidence            46899999999999999999999999999998653    256899999999999999999999999965  999999998


Q ss_pred             cc
Q 007792          321 SV  322 (589)
Q Consensus       321 ~~  322 (589)
                      +.
T Consensus       123 ~~  124 (164)
T 1sjr_A          123 LT  124 (164)
T ss_dssp             SS
T ss_pred             CC
Confidence            74

>2cjk_A Nuclear polyadenylated RNA-binding protein 4; HRP1, RNA-binding, RNA processing, mRNA processing, nonsense-mediated mRNA decay, cleavage; NMR {Saccharomyces cerevisiae} PDB: 2km8_C

Probab=99.53  E-value=7.8e-15  Score=135.55  Aligned_cols=80  Identities=23%  Similarity=0.490  Sum_probs=76.6

Q ss_pred             CceEEEecCCCCCCHHHHHHHhccCCCeEEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHhcCCceeCCeEEEEEeccc
Q 007792          242 ENVLFVCKLNPVTEDEDLHTIFSRFGTVVSAEIIRDFKTGDSLNYAFIEFENRQACERAYSKMDNALIDDRRIHVDFSQS  321 (589)
Q Consensus       242 ~~~i~V~nL~~~~te~~L~~~F~~~G~v~~~~i~~d~~tg~~~g~aFV~f~~~~~a~~A~~~l~g~~i~gr~i~V~~a~~  321 (589)
                      ..+|||+|||+.+|+++|.++|++||.|..+.|+.++.+|.++|||||+|.+.++|.+|++ |+|..|.|+.|.|.+|.+
T Consensus        87 ~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~~~i~~~~~~g~~~g~afV~f~~~~~a~~A~~-~~~~~~~g~~i~V~~a~p  165 (167)
T 2cjk_A           87 TGKIFVGGIGPDVRPKEFEEFFSQWGTIIDAQLMLDKDTGQSRGFGFVTYDSADAVDRVCQ-NKFIDFKDRKIEIKRAEP  165 (167)
T ss_dssp             CEEEEEEEECTTCCHHHHHHHHHTTSCCSEEECCCSSSSSTTSEEEEEEESSHHHHHHHHH-CSEECSSSSCEEEEECCC
T ss_pred             CCeEEECCCCCCCCHHHHHHHHHhCccEEEEEEEEcCCCCccceEEEEEECCHHHHHHHHh-CCCEEeCCeEEEEeecCC
Confidence            5699999999999999999999999999999999998899999999999999999999997 899999999999999986


Q ss_pred             c
Q 007792          322 V  322 (589)
Q Consensus       322 ~  322 (589)
                      +
T Consensus       166 k  166 (167)
T 2cjk_A          166 R  166 (167)
T ss_dssp             C
T ss_pred             C
Confidence            4

>3nmr_A Cugbp ELAV-like family member 1; RRM, PRE-mRNA splicing, RNA binding protein-RNA complex; 1.85A {Homo sapiens} PDB: 3nna_A 3nnc_A 2dhs_A 3nnh_A

Probab=99.53  E-value=9.7e-15  Score=135.79  Aligned_cols=81  Identities=25%  Similarity=0.420  Sum_probs=74.4

Q ss_pred             CCCCceEEEecCCCCCCHHHHHHHhccCCCeEEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHhcCCceeC---CeEEE
Q 007792          239 KPPENVLFVCKLNPVTEDEDLHTIFSRFGTVVSAEIIRDFKTGDSLNYAFIEFENRQACERAYSKMDNALID---DRRIH  315 (589)
Q Consensus       239 ~~~~~~i~V~nL~~~~te~~L~~~F~~~G~v~~~~i~~d~~tg~~~g~aFV~f~~~~~a~~A~~~l~g~~i~---gr~i~  315 (589)
                      ..+..+|||+|||+.+|+++|.++|++||.|..+.|+.+. +|.++|||||+|.+.++|..|+..|||..+.   |++|.
T Consensus        92 ~~~~~~l~v~nl~~~~t~~~l~~~F~~~G~i~~v~~~~~~-~g~~~g~afV~f~~~~~A~~A~~~l~g~~~~~g~~~~l~  170 (175)
T 3nmr_A           92 AVEDRKLFIGMISKKCTENDIRVMFSSFGQIEECRILRGP-DGLSRGCAFVTFTTRAMAQTAIKAMHQAQTMEGCSSPMV  170 (175)
T ss_dssp             CGGGSEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECT-TSCEEEEEEEEESSHHHHHHHHHHHTTSCCCTTCSSCCE
T ss_pred             cCCCCeEEEcCCCCcCCHHHHHHHHHhCCCEEEEEEEECC-CCCEEEEEEEEECCHHHHHHHHHHhcCCcccCCCCCCeE
Confidence            3467899999999999999999999999999999999985 5899999999999999999999999998776   49999


Q ss_pred             EEecc
Q 007792          316 VDFSQ  320 (589)
Q Consensus       316 V~~a~  320 (589)
                      |.||.
T Consensus       171 V~~ad  175 (175)
T 3nmr_A          171 VKFAD  175 (175)
T ss_dssp             EEECC
T ss_pred             EEecC
Confidence            99973

>1fxl_A Paraneoplastic encephalomyelitis antigen HUD; protein-RNA complex, AU-rich element, transcription/RNA complex; 1.80A {Homo sapiens} SCOP: d.58.7.1 d.58.7.1 PDB: 1g2e_A 1fnx_H 1d8z_A 1d9a_A 3hi9_A

Probab=99.53  E-value=3e-14  Score=131.31  Aligned_cols=81  Identities=26%  Similarity=0.456  Sum_probs=75.6

Q ss_pred             CCCCceEEEecCCCCCCHHHHHHHhccCCCeEEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHhcCCceeCCeE--EEE
Q 007792          239 KPPENVLFVCKLNPVTEDEDLHTIFSRFGTVVSAEIIRDFKTGDSLNYAFIEFENRQACERAYSKMDNALIDDRR--IHV  316 (589)
Q Consensus       239 ~~~~~~i~V~nL~~~~te~~L~~~F~~~G~v~~~~i~~d~~tg~~~g~aFV~f~~~~~a~~A~~~l~g~~i~gr~--i~V  316 (589)
                      ..+..+|||+|||+.+++++|.++|++||.|..+.|+.+..+|.++|||||+|.+.++|..|+..|||..|.|+.  |.|
T Consensus        85 ~~~~~~l~v~nl~~~~t~~~l~~~f~~~G~i~~~~i~~~~~~g~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~~~i~v  164 (167)
T 1fxl_A           85 SIRDANLYVSGLPKTMTQKELEQLFSQYGRIITSRILVDQVTGVSRGVGFIRFDKRIEAEEAIKGLNGQKPSGATEPITV  164 (167)
T ss_dssp             GGTTCEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCCCTTCSSCCEE
T ss_pred             cCCCCcEEECCCCCcCCHHHHHHHHHhcCCEeEEEEEecCCCCCccceEEEEeCCHHHHHHHHHHhcCCccCCCccceEE
Confidence            345689999999999999999999999999999999999889999999999999999999999999999999965  888


Q ss_pred             Eec
Q 007792          317 DFS  319 (589)
Q Consensus       317 ~~a  319 (589)
                      .||
T Consensus       165 ~~A  167 (167)
T 1fxl_A          165 KFA  167 (167)
T ss_dssp             EEC
T ss_pred             EeC
Confidence            875

>3tyt_A Heterogeneous nuclear ribonucleoprotein L; ferredoxin-like, structural genomics, joint center for struc genomics, JCSG; 1.60A {Mus musculus} PDB: 3s01_A 3to8_A

Probab=99.52  E-value=3.3e-14  Score=136.53  Aligned_cols=78  Identities=19%  Similarity=0.370  Sum_probs=72.7

Q ss_pred             CCCceEEEecCC-CCCCHHHHHHHhccCCCeEEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHhcCCceeCCeEEEEEe
Q 007792          240 PPENVLFVCKLN-PVTEDEDLHTIFSRFGTVVSAEIIRDFKTGDSLNYAFIEFENRQACERAYSKMDNALIDDRRIHVDF  318 (589)
Q Consensus       240 ~~~~~i~V~nL~-~~~te~~L~~~F~~~G~v~~~~i~~d~~tg~~~g~aFV~f~~~~~a~~A~~~l~g~~i~gr~i~V~~  318 (589)
                      ++.++|||+||| +.+|+++|..+|++||.|..|+|+.+     .+|||||+|.+.++|..||+.|||..|.|+.|.|.+
T Consensus         2 ~~~~~l~V~nL~~~~~~~~~L~~~F~~~G~v~~v~i~~~-----~~g~afV~f~~~~~A~~Ai~~lng~~~~g~~l~v~~   76 (205)
T 3tyt_A            2 ADSPVLMVYGLDQSKMNCDRVFNVFCLYGNVEKVKFMKS-----KPGAAMVEMADGYAVDRAITHLNNNFMFGQKMNVCV   76 (205)
T ss_dssp             CCCSEEEEECCCTTTCCHHHHHHHHTTTSCEEEEEECTT-----STTCEEEEESSHHHHHHHHHHHTTCEETTEECEEEE
T ss_pred             CCCCEEEEeCCCcccCCHHHHHHHHHhcCCeEEEEEecC-----CCCEEEEEECCHHHHHHHHHHhCCCEECCceEEEEE
Confidence            467899999999 89999999999999999999999875     469999999999999999999999999999999999


Q ss_pred             cccc
Q 007792          319 SQSV  322 (589)
Q Consensus       319 a~~~  322 (589)
                      ++..
T Consensus        77 s~~~   80 (205)
T 3tyt_A           77 SKQP   80 (205)
T ss_dssp             CSCS
T ss_pred             ccCC
Confidence            9753

>1fje_B Nucleolin RBD12, protein C23; RNP, RRM, RNA binding domain, RNA-protein complex, nucleolus, structural protein/RNA complex; NMR {Mesocricetus auratus} SCOP: d.58.7.1 d.58.7.1 PDB: 1rkj_A 2krr_A

Probab=99.51  E-value=6.5e-14  Score=130.52  Aligned_cols=112  Identities=18%  Similarity=0.236  Sum_probs=84.9

Q ss_pred             CCHHHHHHHHHhhhhhhhhhhhhccCCCC-CCCCCCCCceEEEecCCCCCCHHHHHHHhccCCCeEEEEEeecCCCCCcc
Q 007792          206 LSAAELEQVIRSKDARSSAVVLESIGDIP-DADIKPPENVLFVCKLNPVTEDEDLHTIFSRFGTVVSAEIIRDFKTGDSL  284 (589)
Q Consensus       206 ~~~~~~e~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~i~V~nL~~~~te~~L~~~F~~~G~v~~~~i~~d~~tg~~~  284 (589)
                      .+++.+++++.-......+..+...-..+ ......+..+|||+|||+.+|+++|.++|++||.|..+     ..++.++
T Consensus        62 ~~~~~a~~A~~l~g~~~~g~~l~v~~~~~~~~~~~~~~~~l~v~nlp~~~t~~~l~~~F~~~g~v~~~-----~~~~~~~  136 (175)
T 1fje_B           62 ESAEDLEKALELTGLKVFGNEIKLEKPKGRDSKKVRAARTLLAKNLSFNITEDELKEVFEDALEIRLV-----SQDGKSK  136 (175)
T ss_dssp             SSHHHHHHHHHGGGEEETTEEEEEECCCCSSCSTTGGGGEEEEESCCSSCCHHHHHHHCTTCSEEEEE-----CSSSSCC
T ss_pred             CCHHHHHHHHhcCCCEeCCeEEEEecCCCccccccccCCEEEEeCCCCCCCHHHHHHHHHhcCeEEEe-----cCCCCCc
Confidence            35666666663211222233332222111 12234467899999999999999999999999988765     4678899


Q ss_pred             cEEEEEEcCHHHHHHHHHhcCCceeCCeEEEEEecccc
Q 007792          285 NYAFIEFENRQACERAYSKMDNALIDDRRIHVDFSQSV  322 (589)
Q Consensus       285 g~aFV~f~~~~~a~~A~~~l~g~~i~gr~i~V~~a~~~  322 (589)
                      |||||+|.+.++|..|+..|||..|.|+.|.|.||.++
T Consensus       137 g~afV~f~~~~~A~~A~~~l~g~~~~g~~i~v~~a~~k  174 (175)
T 1fje_B          137 GIAYIEFKSEADAEKNLEEKQGAEIDGRSVSLYYTGEK  174 (175)
T ss_dssp             SEEEEECSSHHHHHHHHHHHTEEEETTEEEEEEECSSC
T ss_pred             eEEEEEECCHHHHHHHHHHhCCCEECCeEEEEEecCCC
Confidence            99999999999999999999999999999999999864

>2hzc_A Splicing factor U2AF 65 kDa subunit; RNA splicing, RRM, RNA recognition, alternative conformation binding protein; HET: P6G; 1.47A {Homo sapiens} PDB: 1u2f_A

Probab=99.50  E-value=3.8e-14  Score=116.28  Aligned_cols=71  Identities=21%  Similarity=0.410  Sum_probs=66.3

Q ss_pred             CCceEEEecCCCCCCHHHHHHHhccC----C-------CeEEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHhcCCcee
Q 007792          241 PENVLFVCKLNPVTEDEDLHTIFSRF----G-------TVVSAEIIRDFKTGDSLNYAFIEFENRQACERAYSKMDNALI  309 (589)
Q Consensus       241 ~~~~i~V~nL~~~~te~~L~~~F~~~----G-------~v~~~~i~~d~~tg~~~g~aFV~f~~~~~a~~A~~~l~g~~i  309 (589)
                      +..+|||+|||+.+|+++|+++|++|    |       .|..+.++.+      +|||||+|.+.++|..|+ .|||..|
T Consensus         5 ~~~~l~V~nLp~~~t~~~l~~~F~~~~~~~g~~~~~~~~v~~~~~~~~------kg~afV~f~~~~~a~~A~-~l~g~~~   77 (87)
T 2hzc_A            5 SARRLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQD------KNFAFLEFRSVDETTQAM-AFDGIIF   77 (87)
T ss_dssp             GGGEEEEESCCTTCCHHHHHHHHHHHHHHTTCCSSSSCSEEEEEECSS------SSEEEEEESSHHHHHHHG-GGTTCEE
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHHHhhhcccccCCCCcceEEEecCC------CcEEEEEcCCHHHHHHHH-hcCCCEE
Confidence            56899999999999999999999999    8       9999998754      699999999999999999 9999999


Q ss_pred             CCeEEEEEe
Q 007792          310 DDRRIHVDF  318 (589)
Q Consensus       310 ~gr~i~V~~  318 (589)
                      .|+.|.|+.
T Consensus        78 ~g~~l~V~r   86 (87)
T 2hzc_A           78 QGQSLKIRR   86 (87)
T ss_dssp             TTEECEEEC
T ss_pred             CCeEEEEeC
Confidence            999999974

>1wf0_A TDP-43, TAR DNA-binding protein-43; structural genomics, RRM domain, riken structural genomics/proteomics initiative RSGI, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.50  E-value=2.4e-14  Score=117.90  Aligned_cols=76  Identities=18%  Similarity=0.383  Sum_probs=66.1

Q ss_pred             CCceEEEecCCCCCCHHHHHHHhccCCCeEEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHhcCCceeCCeEEEEEecc
Q 007792          241 PENVLFVCKLNPVTEDEDLHTIFSRFGTVVSAEIIRDFKTGDSLNYAFIEFENRQACERAYSKMDNALIDDRRIHVDFSQ  320 (589)
Q Consensus       241 ~~~~i~V~nL~~~~te~~L~~~F~~~G~v~~~~i~~d~~tg~~~g~aFV~f~~~~~a~~A~~~l~g~~i~gr~i~V~~a~  320 (589)
                      +.++|||+|||+.+|+++|+++|++||.|..|.|+.+     ++|||||+|.+.++|++|+.  ....+.|+.|.|.++.
T Consensus         4 ~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~-----~~g~afV~f~~~~~a~~~~~--~~~~~~g~~l~v~~a~   76 (88)
T 1wf0_A            4 GSSGVFVGRCTGDMTEDELREFFSQYGDVMDVFIPKP-----FRAFAFVTFADDQIAQSLCG--EDLIIKGISVHISNAE   76 (88)
T ss_dssp             CCCEEEEESCCSSSCHHHHHHHSTTTSCCCEEECCSS-----CCSCCEEECSCHHHHHHTTT--CEEEETTEEEEEECCC
T ss_pred             CCcEEEEeCCCCCCCHHHHHHHHHHcCCeeEEEEecC-----CCCEEEEEECCHHHHHHHhc--CCceeCCEEEEEEecC
Confidence            5689999999999999999999999999999999865     67999999999999976542  2456699999999998


Q ss_pred             ccc
Q 007792          321 SVS  323 (589)
Q Consensus       321 ~~~  323 (589)
                      +..
T Consensus        77 ~~~   79 (88)
T 1wf0_A           77 PKH   79 (88)
T ss_dssp             CCC
T ss_pred             CCC
Confidence            744

>3md3_A Nuclear and cytoplasmic polyadenylated RNA-bindin PUB1; RRM, RNP, RBD, poly(U) binding, tandem, acetylation, cytopla nucleus; 2.70A {Saccharomyces cerevisiae}

Probab=99.49  E-value=7e-14  Score=128.66  Aligned_cols=79  Identities=20%  Similarity=0.436  Sum_probs=73.8

Q ss_pred             ceEEEecCCCCCCHHHHHHHhccCCCeEEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHhcCCceeCCeEEEEEecccc
Q 007792          243 NVLFVCKLNPVTEDEDLHTIFSRFGTVVSAEIIRDFKTGDSLNYAFIEFENRQACERAYSKMDNALIDDRRIHVDFSQSV  322 (589)
Q Consensus       243 ~~i~V~nL~~~~te~~L~~~F~~~G~v~~~~i~~d~~tg~~~g~aFV~f~~~~~a~~A~~~l~g~~i~gr~i~V~~a~~~  322 (589)
                      .+|||+|||+.+|+++|.++|++||+|..|.|+.++ +++++|||||+|.+.++|..|+..|||..|.|+.|.|.++.+.
T Consensus         1 R~l~V~nlp~~~t~~~l~~~f~~~G~i~~v~i~~~~-~~~~~g~afV~f~~~~~a~~A~~~l~~~~~~g~~i~v~~~~~~   79 (166)
T 3md3_A            1 RVLYVGNLDKAITEDILKQYFQVGGPIANIKIMIDK-NNKNVNYAFVEYHQSHDANIALQTLNGKQIENNIVKINWAFQS   79 (166)
T ss_dssp             CEEEEEEEETTCCHHHHHHHHGGGSCEEEEEEECCC-C-CCEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEECCCC
T ss_pred             CEEEECCCCCcCCHHHHHHHHHhcCCeEEEEEEECC-CCCCCCEEEEEeCCHHHHHHHHHHcCCCccCCCeeEEEEcCCC
Confidence            489999999999999999999999999999999985 4779999999999999999999999999999999999999764

>2qfj_A FBP-interacting repressor; protein-DNA complex; HET: DNA; 2.10A {Homo sapiens} PDB: 3uwt_A 2kxf_A 2kxh_A

Probab=99.48  E-value=6.4e-14  Score=135.06  Aligned_cols=81  Identities=21%  Similarity=0.387  Sum_probs=74.5

Q ss_pred             CceEEEecCCCCCCHHHHHHHhccCCCeEEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHhcCCceeCCeEEEEEeccc
Q 007792          242 ENVLFVCKLNPVTEDEDLHTIFSRFGTVVSAEIIRDFKTGDSLNYAFIEFENRQACERAYSKMDNALIDDRRIHVDFSQS  321 (589)
Q Consensus       242 ~~~i~V~nL~~~~te~~L~~~F~~~G~v~~~~i~~d~~tg~~~g~aFV~f~~~~~a~~A~~~l~g~~i~gr~i~V~~a~~  321 (589)
                      .++|||+|||+.+|+++|.++|++||.|..|.|+.++.+|.++|||||+|.+.++|..||..|||..|.|+.|.|.++..
T Consensus        28 ~~~l~V~nLp~~~t~~~l~~~f~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~A~~~l~~~~~~g~~l~v~~~~~  107 (216)
T 2qfj_A           28 MSRVYVGSIYYELGEDTIRQAFAPFGPIKSIDMSWDSVTMKHKGFAFVEYEVPEAAQLALEQMNSVMLGGRNIKVGRPSN  107 (216)
T ss_dssp             HTEEEEECCCTTCCHHHHHHHHGGGSCEEEEEECCC-CC-CCCSEEEEEESSHHHHHHHHHHHSSCCCC-CCCEEECCSC
T ss_pred             CCEEEEECCCCCCCHHHHHHHHHhCCCEEEEEEeecCCCCccCceEEEEeCCHHHHHHHHHHccCCeeCCeeEEEecCCC
Confidence            47999999999999999999999999999999999988999999999999999999999999999999999999998765


Q ss_pred             c
Q 007792          322 V  322 (589)
Q Consensus       322 ~  322 (589)
                      .
T Consensus       108 ~  108 (216)
T 2qfj_A          108 I  108 (216)
T ss_dssp             C
T ss_pred             c
Confidence            4

>2ghp_A U4/U6 snRNA-associated splicing factor PRP24; RNA chaperone, RNA binding domain, RNA recognition motif, SP factor, snRNP, spliceosome; 2.70A {Saccharomyces cerevisiae} SCOP: d.58.7.1 d.58.7.1 d.58.7.1 PDB: 2go9_A 2kh9_A

Probab=99.48  E-value=5.3e-14  Score=142.53  Aligned_cols=83  Identities=24%  Similarity=0.392  Sum_probs=76.6

Q ss_pred             CCCCceEEEecCCCC-CCHHHHHHHhccCCCeEEEEEeecCC-CCCcccEEEEEEcCHHHHHHHHHhcCCceeCCeEEEE
Q 007792          239 KPPENVLFVCKLNPV-TEDEDLHTIFSRFGTVVSAEIIRDFK-TGDSLNYAFIEFENRQACERAYSKMDNALIDDRRIHV  316 (589)
Q Consensus       239 ~~~~~~i~V~nL~~~-~te~~L~~~F~~~G~v~~~~i~~d~~-tg~~~g~aFV~f~~~~~a~~A~~~l~g~~i~gr~i~V  316 (589)
                      ..+..+|||+|||+. +|+++|.++|++||.|..|.|+.+.. ||.++|||||+|.+.++|..|+ .|||..|.|+.|.|
T Consensus       207 ~~~~~~l~v~nlp~~~~t~~~l~~~F~~~G~v~~v~i~~~~~~tg~~~g~afV~F~~~~~A~~A~-~l~g~~~~g~~i~V  285 (292)
T 2ghp_A          207 TLEGREIMIRNLSTELLDENLLRESFEGFGSIEKINIPAGQKEHSFNNCCAFMVFENKDSAERAL-QMNRSLLGNREISV  285 (292)
T ss_dssp             CCTTTEEEEEEECTTTCCHHHHHHHHGGGSCEEEEECCSCCC---CCCEEEEEEESSHHHHHHHG-GGTTEEETTEEEEE
T ss_pred             CCCCceEEEECCCcccCCHHHHHHHHhccCCeeEEEEEecCCcCCCCceEEEEEeCCHHHHHHHH-HhcCCEECCcEEEE
Confidence            456789999999999 99999999999999999999999876 6999999999999999999999 99999999999999


Q ss_pred             Eecccc
Q 007792          317 DFSQSV  322 (589)
Q Consensus       317 ~~a~~~  322 (589)
                      .||.++
T Consensus       286 ~~a~~k  291 (292)
T 2ghp_A          286 SLADKK  291 (292)
T ss_dssp             EECCCC
T ss_pred             EEecCC
Confidence            999874

>2voo_A Lupus LA protein; RNA-binding protein, RNA recognition motif, systemic lupus erythematosus, phosphoprotein, RNA maturation; 1.8A {Homo sapiens} SCOP: a.4.5.46 d.58.7.1 PDB: 2von_A 2vod_A 2vop_A 1zh5_A 1yty_A 1s7a_A

Probab=99.47  E-value=1.6e-13  Score=130.28  Aligned_cols=78  Identities=9%  Similarity=0.201  Sum_probs=72.0

Q ss_pred             CceEEEecCCCCCCHHHHHHHhccCCCeEEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHhcCCceeCCeEEEEEeccc
Q 007792          242 ENVLFVCKLNPVTEDEDLHTIFSRFGTVVSAEIIRDFKTGDSLNYAFIEFENRQACERAYSKMDNALIDDRRIHVDFSQS  321 (589)
Q Consensus       242 ~~~i~V~nL~~~~te~~L~~~F~~~G~v~~~~i~~d~~tg~~~g~aFV~f~~~~~a~~A~~~l~g~~i~gr~i~V~~a~~  321 (589)
                      .++|||+|||+.+|+++|.++|++||+|..|.|+.+. +|.++|||||+|.+.++|..||..++ ..|+|+.|.|.+++.
T Consensus       109 ~~~l~V~nLp~~~t~~~L~~~F~~~G~v~~v~i~~~~-~~~~kG~aFVeF~~~e~A~~A~~~~~-~~~~Gr~l~V~~~~~  186 (193)
T 2voo_A          109 NRSVYIKGFPTDATLDDIKEWLEDKGQVLNIQMRRTL-HKAFKGSIFVVFDSIESAKKFVETPG-QKYKETDLLILFKDD  186 (193)
T ss_dssp             HTEEEEECCCTTCCHHHHHHHHTTSCCEEEEEEEECT-TCCEEEEEEEEESSHHHHHHHHHCTT-CEETTEECEEEETTT
T ss_pred             cCEEEecCCCCcCCHHHHHHHHhcCCCEEEEEEEECC-CCCcccEEEEEECCHHHHHHHHHhCC-CeECCEEEEEEEhHH
Confidence            4799999999999999999999999999999999985 58899999999999999999997654 599999999999865

>3smz_A Protein raver-1, ribonucleoprotein PTB-binding 1; RNA binding, RNA recognition motif, vincu alpha-actinin, nucleus, RNA binding protein; 1.99A {Homo sapiens} PDB: 3vf0_B* 3h2u_B 3h2v_E

Probab=99.46  E-value=7.5e-14  Score=140.82  Aligned_cols=85  Identities=18%  Similarity=0.232  Sum_probs=78.8

Q ss_pred             CCCCceEEEecCCCCC-CHHHHHHHhccCCCeEEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHhcCCceeCCeEEEEE
Q 007792          239 KPPENVLFVCKLNPVT-EDEDLHTIFSRFGTVVSAEIIRDFKTGDSLNYAFIEFENRQACERAYSKMDNALIDDRRIHVD  317 (589)
Q Consensus       239 ~~~~~~i~V~nL~~~~-te~~L~~~F~~~G~v~~~~i~~d~~tg~~~g~aFV~f~~~~~a~~A~~~l~g~~i~gr~i~V~  317 (589)
                      ..+.++|||+|||+.+ |+++|.++|+.||.|..|.|+.+. +|.++|||||+|.+.++|..|+..|||..|.|+.|.|.
T Consensus       181 ~~~~~~l~v~nlp~~~~~~~~l~~~f~~~G~i~~v~i~~~~-~g~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~  259 (284)
T 3smz_A          181 LLHSRCLCVDRLPPGFNDVDALCRALSAVHSPTFCQLACGQ-DGQLKGFAVLEYETAEMAEEAQQQADGLSLGGSHLRVS  259 (284)
T ss_dssp             TTSCSEEEEECCCTTCCCHHHHHHHTCSSSCCSEEEEEECS-SCCEEEEEEEECSSHHHHHHHHHHHTTCEETTEECEEE
T ss_pred             cCCccEEEEecCCcccCCHHHHHHHhhCCCCeEEEEEEECC-CCCcccEEEEEeCCHHHHHHHHHHhCCCccCCeEEEEE
Confidence            4567899999999995 999999999999999999999985 79999999999999999999999999999999999999


Q ss_pred             ecccccc
Q 007792          318 FSQSVSK  324 (589)
Q Consensus       318 ~a~~~~~  324 (589)
                      |+.+...
T Consensus       260 ~a~~~~~  266 (284)
T 3smz_A          260 FCAPGPP  266 (284)
T ss_dssp             ECCSSSC
T ss_pred             EecCCCc
Confidence            9987543

>2cjk_A Nuclear polyadenylated RNA-binding protein 4; HRP1, RNA-binding, RNA processing, mRNA processing, nonsense-mediated mRNA decay, cleavage; NMR {Saccharomyces cerevisiae} PDB: 2km8_C

Probab=99.46  E-value=9.7e-14  Score=128.12  Aligned_cols=80  Identities=24%  Similarity=0.439  Sum_probs=74.6

Q ss_pred             CCceEEEecCCCCCCHHHHHHHhccCCCeEEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHhcCCceeCCeEEEEEecc
Q 007792          241 PENVLFVCKLNPVTEDEDLHTIFSRFGTVVSAEIIRDFKTGDSLNYAFIEFENRQACERAYSKMDNALIDDRRIHVDFSQ  320 (589)
Q Consensus       241 ~~~~i~V~nL~~~~te~~L~~~F~~~G~v~~~~i~~d~~tg~~~g~aFV~f~~~~~a~~A~~~l~g~~i~gr~i~V~~a~  320 (589)
                      +.++|||+|||+.+|+++|.++|++||.|..|.|+.++.+|.++|||||+|.+.++|..|+..  +..|.|+.|.|.++.
T Consensus         2 ~~~~l~v~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~a~~A~~~--~~~~~g~~i~v~~~~   79 (167)
T 2cjk_A            2 ESCKMFIGGLNWDTTEDNLREYFGKYGTVTDLKIMKDPATGRSRGFGFLSFEKPSSVDEVVKT--QHILDGKVIDPKRAI   79 (167)
T ss_dssp             GGGEEEECSCCTTCCHHHHHHHHTTTCCEEEEECCCCTTTSSCCSCEEEEESSTHHHHHHHHS--CCEETTEECCCEECC
T ss_pred             CCcEEEEeCCCCCCCHHHHHHHHHhCCCEEEEEEEECCCCCCccceEEEEEccHHHHHHHHhc--ccccCCeEccccccc
Confidence            468999999999999999999999999999999999999999999999999999999999974  678999999999987


Q ss_pred             cc
Q 007792          321 SV  322 (589)
Q Consensus       321 ~~  322 (589)
                      +.
T Consensus        80 ~~   81 (167)
T 2cjk_A           80 PR   81 (167)
T ss_dssp             CH
T ss_pred             ch
Confidence            53

>3nmr_A Cugbp ELAV-like family member 1; RRM, PRE-mRNA splicing, RNA binding protein-RNA complex; 1.85A {Homo sapiens} PDB: 3nna_A 3nnc_A 2dhs_A 3nnh_A

Probab=99.45  E-value=1.5e-13  Score=127.68  Aligned_cols=82  Identities=22%  Similarity=0.366  Sum_probs=75.1

Q ss_pred             CCceEEEecCCCCCCHHHHHHHhccCCCeEEEEEeecCCCC--CcccEEEEEEcCHHHHHHHHHhcCCceeC---CeEEE
Q 007792          241 PENVLFVCKLNPVTEDEDLHTIFSRFGTVVSAEIIRDFKTG--DSLNYAFIEFENRQACERAYSKMDNALID---DRRIH  315 (589)
Q Consensus       241 ~~~~i~V~nL~~~~te~~L~~~F~~~G~v~~~~i~~d~~tg--~~~g~aFV~f~~~~~a~~A~~~l~g~~i~---gr~i~  315 (589)
                      ..++|||+|||+.+|+++|.++|++||+|..|.|+.++.++  .++|||||+|.+.++|..|++.|||..+.   ++.|.
T Consensus         2 ~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~~~~~~~~~~~~~~   81 (175)
T 3nmr_A            2 DAIKMFVGQVPRTWSEKDLRELFEQYGAVYEINVLRDRSQNPPQSKGCCFVTFYTRKAALEAQNALHNMKVLPGMHHPIQ   81 (175)
T ss_dssp             CCEEEEEESCCTTCCHHHHHHHHHTTSCEEEEEEEEECSSSSCEEEEEEEEEESSHHHHHHHHHHHTTTCCCTTCSSCCE
T ss_pred             CceEEEEeCCCCCCCHHHHHHHHHhCCCEEEEEEEecCCCCCCCcceEEEEEECCHHHHHHHHHHhcCcEEccCCccceE
Confidence            35799999999999999999999999999999999998887  89999999999999999999999998776   68888


Q ss_pred             EEecccc
Q 007792          316 VDFSQSV  322 (589)
Q Consensus       316 V~~a~~~  322 (589)
                      |.++.+.
T Consensus        82 ~~~~~~~   88 (175)
T 3nmr_A           82 MKPADSE   88 (175)
T ss_dssp             EEECGGG
T ss_pred             Ecccccc
Confidence            8887653

>3u1l_A PRE-mRNA-splicing factor CWC2; CSMP, zinc finger; 1.64A {Saccharomyces cerevisiae} PDB: 3u1m_A 3tp2_A

Probab=99.44  E-value=1.1e-13  Score=134.66  Aligned_cols=79  Identities=19%  Similarity=0.370  Sum_probs=71.1

Q ss_pred             CCCCceEEEecCCCCC---------CHHHHHHHhccCCCeEEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHhcCCcee
Q 007792          239 KPPENVLFVCKLNPVT---------EDEDLHTIFSRFGTVVSAEIIRDFKTGDSLNYAFIEFENRQACERAYSKMDNALI  309 (589)
Q Consensus       239 ~~~~~~i~V~nL~~~~---------te~~L~~~F~~~G~v~~~~i~~d~~tg~~~g~aFV~f~~~~~a~~A~~~l~g~~i  309 (589)
                      ....++||||||+..+         ++++|..+|++||+|..|.|+.      ++|||||+|.+.++|+.|++.|+|..|
T Consensus       131 ~~~~rtLfVgnL~~~~~~~~~~~~~tEe~L~~~F~~fG~I~~v~v~~------~kG~AFV~F~~~~~Ae~A~~am~g~~l  204 (240)
T 3u1l_A          131 RKKNKTLYVGGIDGALNSKHLKPAQIESRIRFVFSRLGDIDRIRYVE------SKNCGFVKFKYQANAEFAKEAMSNQTL  204 (240)
T ss_dssp             CCCCCEEEEECTTGGGTTCCCCHHHHHHHHHHHHHTTSCEEEEEEEG------GGTEEEEEESSHHHHHHHHHHHTTCCC
T ss_pred             ccCCceeecCCCChhhhcccccccCcHHHHHHHHHccCCEEEEEEEC------CCCEEEEEeCCHHHHHHHHHHhCCCEE
Confidence            3457899999999998         7999999999999999999986      479999999999999999999999999


Q ss_pred             ------------CCeEEEEEeccccc
Q 007792          310 ------------DDRRIHVDFSQSVS  323 (589)
Q Consensus       310 ------------~gr~i~V~~a~~~~  323 (589)
                                  .|+.|.|.||+..+
T Consensus       205 ~~~~~~e~~~~~~gr~L~V~wA~~~p  230 (240)
T 3u1l_A          205 LLPSDKEWDDRREGTGLLVKWANEDP  230 (240)
T ss_dssp             CCTTSTTGGGGGGSCCCEEEECC---
T ss_pred             eccccccccccCCCCEEEEEEccCCC
Confidence                        89999999998644

>3smz_A Protein raver-1, ribonucleoprotein PTB-binding 1; RNA binding, RNA recognition motif, vincu alpha-actinin, nucleus, RNA binding protein; 1.99A {Homo sapiens} PDB: 3vf0_B* 3h2u_B 3h2v_E

Probab=99.43  E-value=2.2e-13  Score=137.44  Aligned_cols=85  Identities=21%  Similarity=0.429  Sum_probs=80.3

Q ss_pred             CCCCceEEEecCCCCCCHHHHHHHhccCCCeEEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHhcCCceeCCeEEEEEe
Q 007792          239 KPPENVLFVCKLNPVTEDEDLHTIFSRFGTVVSAEIIRDFKTGDSLNYAFIEFENRQACERAYSKMDNALIDDRRIHVDF  318 (589)
Q Consensus       239 ~~~~~~i~V~nL~~~~te~~L~~~F~~~G~v~~~~i~~d~~tg~~~g~aFV~f~~~~~a~~A~~~l~g~~i~gr~i~V~~  318 (589)
                      .++..+|||+|||+.+|+++|.++|++||.|..+.|+.+..+|.++|||||+|.+.++|..|+..|+|..|.|+.|.|.+
T Consensus        92 ~~~~~~l~v~nlp~~~t~~~l~~~f~~~G~i~~~~i~~~~~~g~~~g~afV~f~~~~~a~~A~~~l~~~~~~g~~i~v~~  171 (284)
T 3smz_A           92 QPTDALLCVANLPPSLTQQQFEELVRPFGSLERCFLVYSERTGQSKGYGFAEYMKKDSAARAKSDLLGKPLGPRTLYVHW  171 (284)
T ss_dssp             CCCSCEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEE
T ss_pred             cCCCCEEEEcCCCCcCCHHHHHHHHHhcCCeeEEEEEeeCCCCccceEEEEEECCHHHHHHHHHHhCCCEeCCcEEEEEE
Confidence            34668999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             ccccc
Q 007792          319 SQSVS  323 (589)
Q Consensus       319 a~~~~  323 (589)
                      +.+..
T Consensus       172 a~~~~  176 (284)
T 3smz_A          172 TDAGQ  176 (284)
T ss_dssp             CCGGG
T ss_pred             CCCCC
Confidence            98643

>3pgw_A U1-A; protein-RNA complex, U1 snRNA, SM fold, SM core, RRM, splici SNRNPS, splicing factors; HET: DNA; 4.40A {Homo sapiens} PDB: 1fht_A 2u1a_A 2aym_A 2b0g_A

Probab=99.43  E-value=4e-13  Score=135.36  Aligned_cols=82  Identities=21%  Similarity=0.438  Sum_probs=75.5

Q ss_pred             CCCCceEEEecCCCCCCHHHHH----HHhccCCCeEEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHhcCCceeCCeEE
Q 007792          239 KPPENVLFVCKLNPVTEDEDLH----TIFSRFGTVVSAEIIRDFKTGDSLNYAFIEFENRQACERAYSKMDNALIDDRRI  314 (589)
Q Consensus       239 ~~~~~~i~V~nL~~~~te~~L~----~~F~~~G~v~~~~i~~d~~tg~~~g~aFV~f~~~~~a~~A~~~l~g~~i~gr~i  314 (589)
                      ..+.++|||+|||+.+|+++|+    ++|++||.|..|.|+.   +++++|||||+|.+.++|..||..|||..|.|+.|
T Consensus         6 ~~~~~~l~V~nlp~~~~~~~l~~~L~~~F~~~G~i~~v~~~~---~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l   82 (282)
T 3pgw_A            6 TRPNHTIYINNLNEKIKKDELKKSLYAIFSQFGQILDILVSR---SLKMRGQAFVIFKEVSSATNALRSMQGFPFYDKPM   82 (282)
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHHHHhccCCeEEEEEcC---CCCcceEEEEEECCHHHHHHHHHHhcCCeeCCcEE
Confidence            4568999999999999999966    8999999999999875   68899999999999999999999999999999999


Q ss_pred             EEEeccccc
Q 007792          315 HVDFSQSVS  323 (589)
Q Consensus       315 ~V~~a~~~~  323 (589)
                      .|.++....
T Consensus        83 ~v~~a~~~~   91 (282)
T 3pgw_A           83 RIQYAKTDS   91 (282)
T ss_pred             EEEEeccCc
Confidence            999997644

>2dit_A HIV TAT specific factor 1 variant; structural genomics, RRM_1 domain, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.42  E-value=8.9e-13  Score=113.77  Aligned_cols=82  Identities=17%  Similarity=0.233  Sum_probs=70.4

Q ss_pred             CCCCCceEEEecCCCCCC-----------HHHHHHHhccCCCeEEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHhcCC
Q 007792          238 IKPPENVLFVCKLNPVTE-----------DEDLHTIFSRFGTVVSAEIIRDFKTGDSLNYAFIEFENRQACERAYSKMDN  306 (589)
Q Consensus       238 ~~~~~~~i~V~nL~~~~t-----------e~~L~~~F~~~G~v~~~~i~~d~~tg~~~g~aFV~f~~~~~a~~A~~~l~g  306 (589)
                      .+.+..+|+|.||.....           +++|+++|++||.|..|.| .++   .++|||||+|.+.++|..|+..|||
T Consensus        11 ~~~~s~~l~l~Nl~~~~~~~~~~~~~~~~e~~l~~~f~~~G~v~~v~i-~~~---~~~G~afV~f~~~~~A~~Ai~~lng   86 (112)
T 2dit_A           11 RMRHERVVIIKNMFHPMDFEDDPLVLNEIREDLRVECSKFGQIRKLLL-FDR---HPDGVASVSFRDPEEADYCIQTLDG   86 (112)
T ss_dssp             CCCSCCEEEEESSCCTTHHHHCSHHHHHHHHHHHHHGGGTSCCSEEEE-ETT---CTTCEEEEECSCHHHHHHHHHHSTT
T ss_pred             CCCCceEEEEEcCCCHHHhccCHHHHHHHHHHHHHHHHccCCEeEEEE-ecC---CCCEEEEEEECCHHHHHHHHHHcCC
Confidence            345688999999954432           5899999999999999965 543   3789999999999999999999999


Q ss_pred             ceeCCeEEEEEeccccc
Q 007792          307 ALIDDRRIHVDFSQSVS  323 (589)
Q Consensus       307 ~~i~gr~i~V~~a~~~~  323 (589)
                      ..|+|++|.|.++.+..
T Consensus        87 ~~~~gr~l~v~~a~~~~  103 (112)
T 2dit_A           87 RWFGGRQITAQAWDGTT  103 (112)
T ss_dssp             CEETTEECEEEECCSCC
T ss_pred             CEECCcEEEEEEeCCCC
Confidence            99999999999997743

>2adc_A Polypyrimidine tract-binding protein 1; RBD, RRM, protein-RNA complex, RNA binding protein/RNA complex; NMR {Homo sapiens} SCOP: d.58.7.1 d.58.7.1 PDB: 2evz_A

Probab=99.41  E-value=3e-13  Score=132.13  Aligned_cols=80  Identities=20%  Similarity=0.376  Sum_probs=74.4

Q ss_pred             CCCCCceEEEecCCC-CCCHHHHHHHhccCCCeEEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHhcCCceeCCeEEEE
Q 007792          238 IKPPENVLFVCKLNP-VTEDEDLHTIFSRFGTVVSAEIIRDFKTGDSLNYAFIEFENRQACERAYSKMDNALIDDRRIHV  316 (589)
Q Consensus       238 ~~~~~~~i~V~nL~~-~~te~~L~~~F~~~G~v~~~~i~~d~~tg~~~g~aFV~f~~~~~a~~A~~~l~g~~i~gr~i~V  316 (589)
                      ..++.++|||+|||+ .+++++|.++|++||.|..|.|+.++     +|||||+|.+.++|..||+.|||..|.|+.|.|
T Consensus        30 ~~~~~~~l~V~nLp~~~~te~~L~~~F~~~G~i~~v~i~~~~-----~g~afV~F~~~~~A~~Ai~~l~g~~~~g~~l~v  104 (229)
T 2adc_A           30 AGAGNSVLLVSNLNPERVTPQSLFILFGVYGDVQRVKILFNK-----KENALVQMADGNQAQLAMSHLNGHKLHGKPIRI  104 (229)
T ss_dssp             GCCCCSEEEEESCCTTTCCHHHHHHHHHHHTCEEEEEECCTT-----SCCEEEEESCHHHHHHHHHHHTTCBCSSSBCEE
T ss_pred             CCCCCCEEEEeCCCcccCCHHHHHHHHHhCCCeEEEEEEECC-----CCEEEEEECCHHHHHHHHHHhCCCeECCeEEEE
Confidence            355778999999999 99999999999999999999998874     689999999999999999999999999999999


Q ss_pred             Eecccc
Q 007792          317 DFSQSV  322 (589)
Q Consensus       317 ~~a~~~  322 (589)
                      .++.+.
T Consensus       105 ~~a~~~  110 (229)
T 2adc_A          105 TLSKHQ  110 (229)
T ss_dssp             ECCSCC
T ss_pred             EEecCc
Confidence            999764

>3v4m_A Splicing factor U2AF 65 kDa subunit; canonical RNA binding protein, RNA splicing, structural GENO joint center for structural genomics, JCSG; HET: MSE; 1.80A {Mus musculus} PDB: 1o0p_A 1opi_A

Probab=99.39  E-value=7.5e-13  Score=112.73  Aligned_cols=82  Identities=22%  Similarity=0.337  Sum_probs=71.8

Q ss_pred             CCCceEEEecC--CCCCC--------HHHHHHHhccCCCeEEEEEeecCCC--CCcccEEEEEEcCHHHHHHHHHhcCCc
Q 007792          240 PPENVLFVCKL--NPVTE--------DEDLHTIFSRFGTVVSAEIIRDFKT--GDSLNYAFIEFENRQACERAYSKMDNA  307 (589)
Q Consensus       240 ~~~~~i~V~nL--~~~~t--------e~~L~~~F~~~G~v~~~~i~~d~~t--g~~~g~aFV~f~~~~~a~~A~~~l~g~  307 (589)
                      .|..+|.|.|+  |..+.        +++|+++|++||+|..|.|+.+..+  +.++|||||+|.+.++|.+|++.|||.
T Consensus         3 ~ps~vl~L~Nm~~~~~l~~d~~~~~~~~dl~~~f~k~G~V~~v~i~~~~~~~~~~~~G~~fV~f~~~~~A~~Ai~~lnG~   82 (105)
T 3v4m_A            3 HPTEVLCLMNMVLPEELLDDEEYEEIVEDVRDECSKYGLVKSIEIPRPVDGVEVPGCGKIFVEFTSVFDCQKAMQGLTGR   82 (105)
T ss_dssp             SCCSEEEEESSCCGGGSSSHHHHHHHHHHHHHHHHTTSCEEEEECCCCBTTBCCTTTTEEEEEESSHHHHHHHHHHHTTC
T ss_pred             CCCeEEEEECCCCHHHccChHHHHHHHHHHHHHHHccCCEEEEEEeccCCCCCcCCcEEEEEEECCHHHHHHHHHHhCCC
Confidence            46789999998  33343        3689999999999999999988755  467999999999999999999999999


Q ss_pred             eeCCeEEEEEeccc
Q 007792          308 LIDDRRIHVDFSQS  321 (589)
Q Consensus       308 ~i~gr~i~V~~a~~  321 (589)
                      .|+|++|.|.++..
T Consensus        83 ~f~GR~i~v~~~~~   96 (105)
T 3v4m_A           83 KFANRVVVTKYCDP   96 (105)
T ss_dssp             EETTEECEEEEECH
T ss_pred             EeCCCEEEEEEeCH
Confidence            99999999999865

>3pgw_A U1-A; protein-RNA complex, U1 snRNA, SM fold, SM core, RRM, splici SNRNPS, splicing factors; HET: DNA; 4.40A {Homo sapiens} PDB: 1fht_A 2u1a_A 2aym_A 2b0g_A

Probab=99.38  E-value=1.3e-12  Score=131.62  Aligned_cols=78  Identities=22%  Similarity=0.441  Sum_probs=72.5

Q ss_pred             CCCCCceEEEecCCCCCCHHHHHHHhccCCCeEEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHhcCCceeC-CeEEEE
Q 007792          238 IKPPENVLFVCKLNPVTEDEDLHTIFSRFGTVVSAEIIRDFKTGDSLNYAFIEFENRQACERAYSKMDNALID-DRRIHV  316 (589)
Q Consensus       238 ~~~~~~~i~V~nL~~~~te~~L~~~F~~~G~v~~~~i~~d~~tg~~~g~aFV~f~~~~~a~~A~~~l~g~~i~-gr~i~V  316 (589)
                      ..++.++|||+|||+.+|+++|.++|++||.|..|.|+.++     +|||||+|.+.++|..||..|||..|. |+.|.|
T Consensus       203 ~~~~~~~l~v~nl~~~~~~~~l~~~F~~~G~i~~v~~~~~~-----~g~afV~f~~~~~A~~A~~~l~g~~~~~g~~l~v  277 (282)
T 3pgw_A          203 ENPPNHILFLTNLPEETNELMLSMLFNQFPGFKEVRLVPGR-----HDIAFVEFDNEVQAGAARDALQGFKITQNNAMKI  277 (282)
T ss_pred             CCCCCCEEEEeCCCCcCCHHHHHHHHHhcCCeEEEEEecCC-----CcEEEEEeCCHHHHHHHHHHcCCcEeCCCCEEEE
Confidence            35567899999999999999999999999999999998653     589999999999999999999999999 999999


Q ss_pred             Eecc
Q 007792          317 DFSQ  320 (589)
Q Consensus       317 ~~a~  320 (589)
                      .||+
T Consensus       278 ~~ak  281 (282)
T 3pgw_A          278 SFAK  281 (282)
T ss_pred             EEec
Confidence            9986

>3tyt_A Heterogeneous nuclear ribonucleoprotein L; ferredoxin-like, structural genomics, joint center for struc genomics, JCSG; 1.60A {Mus musculus} PDB: 3s01_A 3to8_A

Probab=99.38  E-value=4.7e-13  Score=128.40  Aligned_cols=79  Identities=11%  Similarity=0.263  Sum_probs=70.9

Q ss_pred             CCCCceEEEecCCCCCCHHHHHHHhccCCCe--EEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHhcCCceeCCe----
Q 007792          239 KPPENVLFVCKLNPVTEDEDLHTIFSRFGTV--VSAEIIRDFKTGDSLNYAFIEFENRQACERAYSKMDNALIDDR----  312 (589)
Q Consensus       239 ~~~~~~i~V~nL~~~~te~~L~~~F~~~G~v--~~~~i~~d~~tg~~~g~aFV~f~~~~~a~~A~~~l~g~~i~gr----  312 (589)
                      .+|..+|||+|||+.+|+++|+++|++||.|  ..+.|+.+.  +..+|||||+|.+.++|..||..|||..|.|.    
T Consensus       120 ~~p~~~l~v~NLp~~~t~~~L~~~F~~~G~v~~~~v~~~~~~--~~~~g~gfV~f~~~~~A~~Ai~~lng~~~~g~~~~~  197 (205)
T 3tyt_A          120 QHPSNVLHFFNAPLEVTEENFFEICDELGVKRPTSVKVFSGK--SERSSSGLLEWDSKSDALETLGFLNHYQMKNPNGPY  197 (205)
T ss_dssp             CCCCSEEEEEEECTTCCHHHHHHHHHHHTCCCCSEEEECSCC--SSSSEEEEEECSSHHHHHHHHHHHTTCEECCSSSSS
T ss_pred             CCCcceEEEeCCCCCCCHHHHHHHHHhcCCcceEEEEEEcCC--CCCceEEEEEeCCHHHHHHHHHHhCCCCccCCCCCc
Confidence            4567899999999999999999999999999  899988764  55679999999999999999999999999986    


Q ss_pred             EEEEEec
Q 007792          313 RIHVDFS  319 (589)
Q Consensus       313 ~i~V~~a  319 (589)
                      ++.|++|
T Consensus       198 p~~vk~~  204 (205)
T 3tyt_A          198 PYTLKLC  204 (205)
T ss_dssp             CEECEEE
T ss_pred             ceEEEec
Confidence            6777775

>2adc_A Polypyrimidine tract-binding protein 1; RBD, RRM, protein-RNA complex, RNA binding protein/RNA complex; NMR {Homo sapiens} SCOP: d.58.7.1 d.58.7.1 PDB: 2evz_A

Probab=99.37  E-value=9.5e-13  Score=128.57  Aligned_cols=79  Identities=24%  Similarity=0.437  Sum_probs=72.7

Q ss_pred             CCCCceEEEecCCCCCCHHHHHHHhccCC-CeEEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHhcCCceeC-CeEEEE
Q 007792          239 KPPENVLFVCKLNPVTEDEDLHTIFSRFG-TVVSAEIIRDFKTGDSLNYAFIEFENRQACERAYSKMDNALID-DRRIHV  316 (589)
Q Consensus       239 ~~~~~~i~V~nL~~~~te~~L~~~F~~~G-~v~~~~i~~d~~tg~~~g~aFV~f~~~~~a~~A~~~l~g~~i~-gr~i~V  316 (589)
                      .++.++|||+|||+.+++++|.++|++|| .|..|.|+..     .+|||||+|.+.++|..|+..|||..|. |+.|.|
T Consensus       148 ~~~~~~l~V~nlp~~~t~~~l~~~f~~~G~~i~~v~i~~~-----~~g~afV~f~~~~~A~~Ai~~l~g~~~~~g~~l~v  222 (229)
T 2adc_A          148 FPPSATLHLSNIPPSVSEEDLKVLFSSNGGVVKGFKFFQK-----DRKMALIQMGSVEEAVQALIDLHNHDLGENHHLRV  222 (229)
T ss_dssp             CCSCSEEEEECCCTTCCHHHHHHHHHTTSCCEEEEEECSS-----STTCEEEEESSHHHHHHHHHHHTTCBSSSSCBCEE
T ss_pred             CCCCCEEEEeCCCccCCHHHHHHHHHHcCCCeeEEEEEEC-----CCcEEEEEECCHHHHHHHHHHHCCCccCCCCeEEE
Confidence            45678999999999999999999999999 9999999653     4689999999999999999999999999 999999


Q ss_pred             Eecccc
Q 007792          317 DFSQSV  322 (589)
Q Consensus       317 ~~a~~~  322 (589)
                      .|+++.
T Consensus       223 ~~a~~~  228 (229)
T 2adc_A          223 SFSKST  228 (229)
T ss_dssp             EECSSC
T ss_pred             EEecCC
Confidence            999863

>1qm9_A Polypyrimidine tract-binding protein; ribonucleoprotein, RNP, RNA, spicing, translation; NMR {Homo sapiens} SCOP: d.58.7.1 d.58.7.1

Probab=99.37  E-value=5.2e-13  Score=127.11  Aligned_cols=79  Identities=24%  Similarity=0.437  Sum_probs=73.0

Q ss_pred             CCCCceEEEecCCCCCCHHHHHHHhccCC-CeEEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHhcCCceeC-CeEEEE
Q 007792          239 KPPENVLFVCKLNPVTEDEDLHTIFSRFG-TVVSAEIIRDFKTGDSLNYAFIEFENRQACERAYSKMDNALID-DRRIHV  316 (589)
Q Consensus       239 ~~~~~~i~V~nL~~~~te~~L~~~F~~~G-~v~~~~i~~d~~tg~~~g~aFV~f~~~~~a~~A~~~l~g~~i~-gr~i~V  316 (589)
                      .++.++|||+|||+.+++++|.++|++|| .|..|.|+.+     .+|||||+|.+.++|..|+..|||..|. |+.|.|
T Consensus       117 ~~~~~~l~v~nl~~~~~~~~l~~~f~~~G~~v~~v~i~~~-----~~g~afV~f~~~~~A~~A~~~l~g~~~~~g~~l~v  191 (198)
T 1qm9_A          117 FPPSATLHLSNIPPSVSEEDLKVLFSSNGGVVKGFKFFQK-----DRKMALIQMGSVEEAVQALIDLHNHDLGENHHLRV  191 (198)
T ss_dssp             CCCCCEEEECCCCTTCCHHHHHHHHHHTTSCCCEEEESST-----TSSCEEEECSSHHHHHHHHHHHTSSCCSSCCSCCE
T ss_pred             CCCccEEEEeCCCCCCCHHHHHHHHHHcCCCceEEEEEeC-----CCcEEEEEeCCHHHHHHHHHHhcCCccCCCCeEEE
Confidence            45688999999999999999999999999 9999999764     3689999999999999999999999999 999999


Q ss_pred             Eecccc
Q 007792          317 DFSQSV  322 (589)
Q Consensus       317 ~~a~~~  322 (589)
                      .|+++.
T Consensus       192 ~~a~~~  197 (198)
T 1qm9_A          192 SFSKST  197 (198)
T ss_dssp             EEECCC
T ss_pred             Eeeccc
Confidence            999863

>1fje_B Nucleolin RBD12, protein C23; RNP, RRM, RNA binding domain, RNA-protein complex, nucleolus, structural protein/RNA complex; NMR {Mesocricetus auratus} SCOP: d.58.7.1 d.58.7.1 PDB: 1rkj_A 2krr_A

Probab=99.37  E-value=2.1e-13  Score=127.06  Aligned_cols=82  Identities=18%  Similarity=0.320  Sum_probs=72.6

Q ss_pred             CCCCceEEEecCCCCCCHHHHHHHhccCCCeEEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHhcCCceeCCeEEEEEe
Q 007792          239 KPPENVLFVCKLNPVTEDEDLHTIFSRFGTVVSAEIIRDFKTGDSLNYAFIEFENRQACERAYSKMDNALIDDRRIHVDF  318 (589)
Q Consensus       239 ~~~~~~i~V~nL~~~~te~~L~~~F~~~G~v~~~~i~~d~~tg~~~g~aFV~f~~~~~a~~A~~~l~g~~i~gr~i~V~~  318 (589)
                      ..+.++|||+|||+.+|+++|+++|..||.|.. .++.+..+|.++|||||+|.+.++|..|| .|||..|.|+.|.|.+
T Consensus        10 ~~~~~~l~V~nLp~~~t~~~l~~~f~~~g~~~~-~~~~~~~~~~~~g~afV~f~~~~~a~~A~-~l~g~~~~g~~l~v~~   87 (175)
T 1fje_B           10 STTPFNLFIGNLNPNKSVAELKVAISELFAKND-LAVVDVRTGTNRKFGYVDFESAEDLEKAL-ELTGLKVFGNEIKLEK   87 (175)
T ss_dssp             CSSSEEEEEECCCTTSCHHHHHHHHHHHHHHHT-CCCCEEEEETTTTEEEEEESSHHHHHHHH-HGGGEEETTEEEEEEC
T ss_pred             CCCCcEEEEeCCCCCCCHHHHHHHHHHhCCcce-EEEEECCCCccccEEEEEECCHHHHHHHH-hcCCCEeCCeEEEEec
Confidence            456789999999999999999999999998766 33445567889999999999999999999 5999999999999999


Q ss_pred             cccc
Q 007792          319 SQSV  322 (589)
Q Consensus       319 a~~~  322 (589)
                      +.+.
T Consensus        88 ~~~~   91 (175)
T 1fje_B           88 PKGR   91 (175)
T ss_dssp             CCCS
T ss_pred             CCCc
Confidence            9764

>1jmt_A Splicing factor U2AF 35 kDa subunit; RRM, RNA splicing, proline, PPII helix, peptide recognition, RNA binding protein; 2.20A {Homo sapiens} SCOP: d.58.7.3

Probab=99.37  E-value=2.7e-13  Score=115.37  Aligned_cols=73  Identities=15%  Similarity=0.389  Sum_probs=65.2

Q ss_pred             EEecCCCCCCHHHHHHHh------------ccCCCeEEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHhcCCceeCCeE
Q 007792          246 FVCKLNPVTEDEDLHTIF------------SRFGTVVSAEIIRDFKTGDSLNYAFIEFENRQACERAYSKMDNALIDDRR  313 (589)
Q Consensus       246 ~V~nL~~~~te~~L~~~F------------~~~G~v~~~~i~~d~~tg~~~g~aFV~f~~~~~a~~A~~~l~g~~i~gr~  313 (589)
                      .+.||++.+++++|.++|            ++||+|..|.|+.+. ++.++|||||+|.+.++|.+|+..|||..|+|++
T Consensus        19 ~~~~l~~~~~~~~l~~~f~~~~edl~~~f~~~~G~V~~v~i~~~~-~~~~~G~~fV~f~~~~~A~~A~~~lng~~~~Gr~   97 (104)
T 1jmt_A           19 SADGLRSAVSDVEMQEHYDEFFEEVFTEMEEKYGEVEEMNVCDNL-GDHLVGNVYVKFRREEDAEKAVIDLNNRWFNGQP   97 (104)
T ss_dssp             --CHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTCCEEEEEECCSS-SSSSEEEEEEEESCHHHHHHHHHHHTTCEETTEE
T ss_pred             ccCCcccccCHHHHHHHHHHHHHHHHHHhhccCCceEEEEEEeCC-CCCccEEEEEEECCHHHHHHHHHHHCCCEECCEE
Confidence            367888888888877666            999999999999875 4789999999999999999999999999999999


Q ss_pred             EEEEec
Q 007792          314 IHVDFS  319 (589)
Q Consensus       314 i~V~~a  319 (589)
                      |.|.|+
T Consensus        98 i~v~~s  103 (104)
T 1jmt_A           98 IHAELS  103 (104)
T ss_dssp             CCEEEC
T ss_pred             EEEEEc
Confidence            999986

>3ue2_A Poly(U)-binding-splicing factor PUF60; RNA recognition motif, RRM, RNA binding domain, ST genomics, joint center for structural genomics, JCSG; HET: MSE; 1.23A {Homo sapiens} SCOP: d.58.7.0 PDB: 3us5_A 2dny_A

Probab=99.36  E-value=1.1e-12  Score=113.91  Aligned_cols=81  Identities=12%  Similarity=0.252  Sum_probs=71.6

Q ss_pred             CCceEEEecCCC--CC---CHHHHHHHhccCCCeEEEEEeecCC----CCCcccEEEEEEcCHHHHHHHHHhcCCceeCC
Q 007792          241 PENVLFVCKLNP--VT---EDEDLHTIFSRFGTVVSAEIIRDFK----TGDSLNYAFIEFENRQACERAYSKMDNALIDD  311 (589)
Q Consensus       241 ~~~~i~V~nL~~--~~---te~~L~~~F~~~G~v~~~~i~~d~~----tg~~~g~aFV~f~~~~~a~~A~~~l~g~~i~g  311 (589)
                      |..+|+|.||-.  ++   .+++|++.|++||+|..|.|+.+..    ++.++|||||+|.+.++|.+|+..|||..|+|
T Consensus        19 ps~vl~L~Nm~~~~el~ddleedl~eef~k~G~V~~v~I~~~~~~~~~~~~~~G~~FV~F~~~e~A~~Ai~~LnGr~f~G   98 (118)
T 3ue2_A           19 ESTVMVLRNMVDPKDIDDDLEGEVTEECGKFGAVNRVIIYQEKQGEEEDAEIIVKIFVEFSIASETHKAIQALNGRWFAG   98 (118)
T ss_dssp             SCCEEEEESCSCGGGCCTTHHHHHHHHHTTTSCEEEEEEEEEEESSSTTCEEEEEEEEEESSHHHHHHHHHHHTTCEETT
T ss_pred             CCCEEEEECCCCHHHHHHHHHHHHHHHHhccCCEeEEEEeecCCCcccCCcceEEEEEEECCHHHHHHHHHHHCCCEECC
Confidence            678999999932  22   3689999999999999999998864    46788999999999999999999999999999


Q ss_pred             eEEEEEeccc
Q 007792          312 RRIHVDFSQS  321 (589)
Q Consensus       312 r~i~V~~a~~  321 (589)
                      +.|.|.++..
T Consensus        99 R~i~v~~~~~  108 (118)
T 3ue2_A           99 RKVVAEVYDQ  108 (118)
T ss_dssp             EECEEEEECH
T ss_pred             cEEEEEEcCh
Confidence            9999999864

>3sde_A Paraspeckle component 1; RRM, anti parallel right handed coiled-coil, NOPS, DBHS, RNA protein, RNA binding; 1.90A {Homo sapiens} PDB: 3sde_B

Probab=99.34  E-value=1.9e-12  Score=128.99  Aligned_cols=80  Identities=25%  Similarity=0.446  Sum_probs=72.9

Q ss_pred             CCCCceEEEecCCCCCCHHHHHHHhccCCCeEEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHhcCCceeCCeEEEEEe
Q 007792          239 KPPENVLFVCKLNPVTEDEDLHTIFSRFGTVVSAEIIRDFKTGDSLNYAFIEFENRQACERAYSKMDNALIDDRRIHVDF  318 (589)
Q Consensus       239 ~~~~~~i~V~nL~~~~te~~L~~~F~~~G~v~~~~i~~d~~tg~~~g~aFV~f~~~~~a~~A~~~l~g~~i~gr~i~V~~  318 (589)
                      ..+.++|||+|||+.+|+++|..+|++||.|..|.|..      ++|||||+|.+.++|..|+..|||..|.|+.|.|.+
T Consensus        19 ~~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~------~kg~afV~f~~~~~A~~A~~~l~g~~i~g~~l~v~~   92 (261)
T 3sde_A           19 YTQRCRLFVGNLPTDITEEDFKRLFERYGEPSEVFINR------DRGFGFIRLESRTLAEIAKAELDGTILKSRPLRIRF   92 (261)
T ss_dssp             SCGGGEEEEESCCTTCCHHHHHHHTGGGCCCSEEEEET------TTTEEEEECSSHHHHHHHHHHHTTCEETTEECEEEE
T ss_pred             CCCCCEEEEECCCCCCCHHHHHHHHHhcCCEEEEEEeC------CCcEEEEEECCHHHHHHHHHHcCCcEECCceeEeee
Confidence            34567999999999999999999999999999999965      469999999999999999999999999999999999


Q ss_pred             cccccc
Q 007792          319 SQSVSK  324 (589)
Q Consensus       319 a~~~~~  324 (589)
                      +.+...
T Consensus        93 a~~~~~   98 (261)
T 3sde_A           93 ATHGAA   98 (261)
T ss_dssp             CCCSSE
T ss_pred             cccCCc
Confidence            986443

>1qm9_A Polypyrimidine tract-binding protein; ribonucleoprotein, RNP, RNA, spicing, translation; NMR {Homo sapiens} SCOP: d.58.7.1 d.58.7.1

Probab=99.33  E-value=9.2e-13  Score=125.37  Aligned_cols=76  Identities=21%  Similarity=0.410  Sum_probs=71.6

Q ss_pred             CceEEEecCCC-CCCHHHHHHHhccCCCeEEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHhcCCceeCCeEEEEEecc
Q 007792          242 ENVLFVCKLNP-VTEDEDLHTIFSRFGTVVSAEIIRDFKTGDSLNYAFIEFENRQACERAYSKMDNALIDDRRIHVDFSQ  320 (589)
Q Consensus       242 ~~~i~V~nL~~-~~te~~L~~~F~~~G~v~~~~i~~d~~tg~~~g~aFV~f~~~~~a~~A~~~l~g~~i~gr~i~V~~a~  320 (589)
                      .++|||+|||+ .+++++|.++|++||.|..|.|+.++     +|||||+|.+.++|..|+..|||..|.|+.|.|.++.
T Consensus         3 ~~~l~v~nlp~~~~~~~~l~~~F~~~G~i~~v~i~~~~-----~g~afV~f~~~~~a~~A~~~l~~~~~~g~~l~v~~a~   77 (198)
T 1qm9_A            3 NSVLLVSNLNPERVTPQSLFILFGVYGDVQRVKILFNK-----KENALVQMADGNQAQLAMSHLNGHKLHGKPIRITLSK   77 (198)
T ss_dssp             CCEEEEECCCSSSCCHHHHHHHHHTTCCCSEEECSTTC-----SSCCEEECTTTHHHHHHHHHHTTCCCSSCCCEEEECC
T ss_pred             CcEEEEeCCCcccCCHHHHHHHHHhcCCEEEEEEEeCC-----CCEEEEEECCHHHHHHHHHHhCCCeecCeEEEEEEec
Confidence            57999999999 99999999999999999999998864     6899999999999999999999999999999999998


Q ss_pred             cc
Q 007792          321 SV  322 (589)
Q Consensus       321 ~~  322 (589)
                      +.
T Consensus        78 ~~   79 (198)
T 1qm9_A           78 HQ   79 (198)
T ss_dssp             CC
T ss_pred             CC
Confidence            64

>3sde_A Paraspeckle component 1; RRM, anti parallel right handed coiled-coil, NOPS, DBHS, RNA protein, RNA binding; 1.90A {Homo sapiens} PDB: 3sde_B

Probab=99.31  E-value=4.1e-12  Score=126.57  Aligned_cols=81  Identities=27%  Similarity=0.433  Sum_probs=74.4

Q ss_pred             CCceEEEecCCCCCCHHHHHHHhccCCCeEEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHhcC-CceeC---CeEEEE
Q 007792          241 PENVLFVCKLNPVTEDEDLHTIFSRFGTVVSAEIIRDFKTGDSLNYAFIEFENRQACERAYSKMD-NALID---DRRIHV  316 (589)
Q Consensus       241 ~~~~i~V~nL~~~~te~~L~~~F~~~G~v~~~~i~~d~~tg~~~g~aFV~f~~~~~a~~A~~~l~-g~~i~---gr~i~V  316 (589)
                      +..+|||+|||+.+|+++|..+|+.||.|..|.|+.+ .+|.++|||||+|.+.++|..||..|| |..+.   |++|.|
T Consensus        95 ~~~~l~v~nl~~~~t~~~l~~~F~~~G~i~~v~i~~~-~~g~~~g~afV~f~~~~~A~~A~~~l~~~~~~~~~~~r~i~v  173 (261)
T 3sde_A           95 HGAALTVKNLSPVVSNELLEQAFSQFGPVEKAVVVVD-DRGRATGKGFVEFAAKPPARKALERCGDGAFLLTTTPRPVIV  173 (261)
T ss_dssp             CSSEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEEE-TTSCEEEEEEEEESSHHHHHHHHHHHHHSCEESSSSCCBCEE
T ss_pred             cCCcccccCCCCCCCHHHHHHHHHhcCCeEEEEeeeC-CCCCcCcEEEEEeCCHHHHHHHHHHhcCCeEEecCCCceEEE
Confidence            5689999999999999999999999999999999999 689999999999999999999999995 55555   999999


Q ss_pred             Eecccc
Q 007792          317 DFSQSV  322 (589)
Q Consensus       317 ~~a~~~  322 (589)
                      .++.+.
T Consensus       174 ~~~~~~  179 (261)
T 3sde_A          174 EPMEQF  179 (261)
T ss_dssp             EECCCE
T ss_pred             eecccc
Confidence            999763

>2ghp_A U4/U6 snRNA-associated splicing factor PRP24; RNA chaperone, RNA binding domain, RNA recognition motif, SP factor, snRNP, spliceosome; 2.70A {Saccharomyces cerevisiae} SCOP: d.58.7.1 d.58.7.1 d.58.7.1 PDB: 2go9_A 2kh9_A

Probab=99.29  E-value=4e-12  Score=128.67  Aligned_cols=82  Identities=12%  Similarity=0.261  Sum_probs=71.2

Q ss_pred             CCceEEEecCCCCCCHHHHHHHhccCC-CeEEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHhcCCceeCCeEEEEEec
Q 007792          241 PENVLFVCKLNPVTEDEDLHTIFSRFG-TVVSAEIIRDFKTGDSLNYAFIEFENRQACERAYSKMDNALIDDRRIHVDFS  319 (589)
Q Consensus       241 ~~~~i~V~nL~~~~te~~L~~~F~~~G-~v~~~~i~~d~~tg~~~g~aFV~f~~~~~a~~A~~~l~g~~i~gr~i~V~~a  319 (589)
                      +..+|||+|||+.+|+++|.++|.+|| .|..|.|+.+.. |.++|||||+|.+.++|..|+..|||..|.|+.|.|.++
T Consensus       116 ~~~~l~v~nlp~~~t~~~l~~~f~~~G~~i~~v~i~~~~~-~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a  194 (292)
T 2ghp_A          116 TECTLWMTNFPPSYTQRNIRDLLQDINVVALSIRLPSLRF-NTSRRFAYIDVTSKEDARYCVEKLNGLKIEGYTLVTKVS  194 (292)
T ss_dssp             CSCEEEEECCCTTCCHHHHHHHHHHTTCCCCEEECC--------CCEEEEECSSHHHHHHHHHHHTTCEETTEECEEEEC
T ss_pred             CCCEEEEECCCCCCCHHHHHHHHHHhCCCeEEEEEEeCCC-CCcceEEEEEECCHHHHHHHHHHhCCCEeCCcEEEEEEC
Confidence            478999999999999999999999999 999999998865 788999999999999999999999999999999999999


Q ss_pred             cccc
Q 007792          320 QSVS  323 (589)
Q Consensus       320 ~~~~  323 (589)
                      .+..
T Consensus       195 ~~~~  198 (292)
T 2ghp_A          195 NPLE  198 (292)
T ss_dssp             CCC-
T ss_pred             CCCc
Confidence            8644

>2g4b_A Splicing factor U2AF 65 kDa subunit; protein-RNA complex, RNA splicing factor, RNA recognition motif, RNA binding protein/RNA complex; 2.50A {Homo sapiens} PDB: 2u2f_A

Probab=99.27  E-value=8.2e-12  Score=115.64  Aligned_cols=75  Identities=19%  Similarity=0.374  Sum_probs=67.6

Q ss_pred             CCceEEEecCCCCCCHHHHHHHhccC----C-------CeEEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHhcCCcee
Q 007792          241 PENVLFVCKLNPVTEDEDLHTIFSRF----G-------TVVSAEIIRDFKTGDSLNYAFIEFENRQACERAYSKMDNALI  309 (589)
Q Consensus       241 ~~~~i~V~nL~~~~te~~L~~~F~~~----G-------~v~~~~i~~d~~tg~~~g~aFV~f~~~~~a~~A~~~l~g~~i  309 (589)
                      +.++|||+|||+.+|+++|.++|++|    |       .|..+.+..      ++|||||+|.+.++|..|+ .|||..|
T Consensus         3 ~~~~l~V~nLp~~~t~~~l~~~F~~~g~~~g~~~~~~~~v~~~~~~~------~~g~afV~f~~~~~A~~A~-~~~~~~~   75 (172)
T 2g4b_A            3 SARRLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQ------DKNFAFLEFRSVDETTQAM-AFDGIIF   75 (172)
T ss_dssp             GGGEEEEESCCTTCCHHHHHHHHHHHHHHTTCCSSSSCSEEEEEEET------TTTEEEEEESSHHHHHHHG-GGTTCEE
T ss_pred             cccEEEEcCCCcccCHHHHHHHHHHHhhhcccccCCCCceeeeEecC------CCCEEEEEeCCHHHHHHHH-HhCCcEe
Confidence            46899999999999999999999999    6       777777754      5799999999999999999 8999999


Q ss_pred             CCeEEEEEecccc
Q 007792          310 DDRRIHVDFSQSV  322 (589)
Q Consensus       310 ~gr~i~V~~a~~~  322 (589)
                      .|+.|.|.++...
T Consensus        76 ~g~~i~v~~~~~~   88 (172)
T 2g4b_A           76 QGQSLKIRRPHDY   88 (172)
T ss_dssp             TTEECEEECCSSC
T ss_pred             cCceeeecCCccc
Confidence            9999999997653

>2yh0_A Splicing factor U2AF 65 kDa subunit; PRE-mRNA splicing, transcription, RNA binding protein, mRNA processing; NMR {Homo sapiens} PDB: 2yh1_A

Probab=99.26  E-value=1.1e-11  Score=117.69  Aligned_cols=75  Identities=19%  Similarity=0.359  Sum_probs=66.6

Q ss_pred             CCceEEEecCCCCCCHHHHHHHhccC----C-------CeEEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHhcCCcee
Q 007792          241 PENVLFVCKLNPVTEDEDLHTIFSRF----G-------TVVSAEIIRDFKTGDSLNYAFIEFENRQACERAYSKMDNALI  309 (589)
Q Consensus       241 ~~~~i~V~nL~~~~te~~L~~~F~~~----G-------~v~~~~i~~d~~tg~~~g~aFV~f~~~~~a~~A~~~l~g~~i  309 (589)
                      ..++|||+|||+.+|+++|.++|++|    |       .|..+.+.      .++|||||+|.+.++|..|| .|||..|
T Consensus         3 ~~~~l~V~nLp~~~te~~l~~~F~~~g~i~g~~~~~~~~v~~~~~~------~~~g~afV~F~~~~~A~~Al-~l~g~~~   75 (198)
T 2yh0_A            3 MARRLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQIN------QDKNFAFLEFRSVDETTQAM-AFDGIIF   75 (198)
T ss_dssp             -CCEEEEESCCTTCCHHHHHHHHHHHHHHHTCCSSSSCSEEEEEEE------TTTTEEEEEESCSHHHHHHG-GGTTEEE
T ss_pred             ceeEEEEcCCCCCCCHHHHHHHHHHHHhhcccccCCCCceEEeEec------CCCCEEEEEeCCHHHHHHHH-HhcCCEE
Confidence            36899999999999999999999999    5       66666653      46799999999999999999 8999999


Q ss_pred             CCeEEEEEecccc
Q 007792          310 DDRRIHVDFSQSV  322 (589)
Q Consensus       310 ~gr~i~V~~a~~~  322 (589)
                      .|+.|.|.++...
T Consensus        76 ~g~~i~v~~~~~~   88 (198)
T 2yh0_A           76 QGQSLKIRRPHDY   88 (198)
T ss_dssp             TTEEEEEECCCCC
T ss_pred             cCceEEEeCCCCC
Confidence            9999999998764

>2d9o_A DNAJ (HSP40) homolog, subfamily C, member 17; RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.25  E-value=4.6e-11  Score=100.45  Aligned_cols=65  Identities=15%  Similarity=0.247  Sum_probs=58.0

Q ss_pred             CCCCHHHHHHHhccCCCeEEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHhcCCceeCCeEEEEEeccccc
Q 007792          252 PVTEDEDLHTIFSRFGTVVSAEIIRDFKTGDSLNYAFIEFENRQACERAYSKMDNALIDDRRIHVDFSQSVS  323 (589)
Q Consensus       252 ~~~te~~L~~~F~~~G~v~~~~i~~d~~tg~~~g~aFV~f~~~~~a~~A~~~l~g~~i~gr~i~V~~a~~~~  323 (589)
                      ..+++++|+++|++||.|..|.|+     ++++|||||+|.+.++|..||..+++  +.|++|.|.|+.+..
T Consensus        27 ~~~te~~L~~~F~~~G~V~~v~i~-----~~~rGfaFVeF~~~~~A~~Ai~~~~~--~~g~~l~V~~a~~~~   91 (100)
T 2d9o_A           27 GGYSKDVLLRLLQKYGEVLNLVLS-----SKKPGTAVVEFATVKAAELAVQNEVG--LVDNPLKISWLEGQP   91 (100)
T ss_dssp             CSCCHHHHHHHHHTTSCEEEEEEE-----SSSSSEEEEEESCHHHHHHHHHTCCB--CSSSBCEEECSSCCC
T ss_pred             CCCCHHHHHHHHHhcCCEEEEEEc-----cCCCCEEEEEECCHHHHHHHHHhcCC--CCCCeEEEEEccCCC
Confidence            468999999999999999999997     35789999999999999999988665  679999999998654

>3tht_A Alkylated DNA repair protein ALKB homolog 8; structural genomics, PSI-biology, northeast structural genom consortium, NESG; HET: AKG; 3.01A {Homo sapiens} PDB: 3thp_A*

Probab=99.23  E-value=2e-11  Score=125.14  Aligned_cols=77  Identities=16%  Similarity=0.310  Sum_probs=66.7

Q ss_pred             CCCCceEEEec--CCCCCCHHHHHHHhccCCCeEEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHhcCCceeC---Ce-
Q 007792          239 KPPENVLFVCK--LNPVTEDEDLHTIFSRFGTVVSAEIIRDFKTGDSLNYAFIEFENRQACERAYSKMDNALID---DR-  312 (589)
Q Consensus       239 ~~~~~~i~V~n--L~~~~te~~L~~~F~~~G~v~~~~i~~d~~tg~~~g~aFV~f~~~~~a~~A~~~l~g~~i~---gr-  312 (589)
                      .+|..+|||||  |++.+|+++|+++|++||+|..|.|+.      ++|||||+|.+.++|++||+.|||..+.   |+ 
T Consensus        15 ~~ps~~l~VgN~gl~~~~te~~L~~~F~~~G~V~~v~~~~------~kgfaFV~f~~~~~A~~Ai~~lnG~~~~~~~g~~   88 (345)
T 3tht_A           15 SYATQSLVVANGGLGNGVSRNQLLPVLEKCGLVDALLMPP------NKPYSFARYRTTEESKRAYVTLNGKEVVDDLGQK   88 (345)
T ss_dssp             SSCCSEEEEETCSGGGTCCHHHHHHHHHTTSCEEEEECCT------TCSEEEEEESSHHHHHHHHHHTTTCEEECTTSCE
T ss_pred             CCCCCEEEEEcCCCCCCCCHHHHHHHHHhcCCeEEEEEeC------CCCEEEEEECCHHHHHHHHHHhCCCccccccCCc
Confidence            56789999999  588999999999999999999887743      4699999999999999999999999883   45 


Q ss_pred             -EEEEEeccc
Q 007792          313 -RIHVDFSQS  321 (589)
Q Consensus       313 -~i~V~~a~~  321 (589)
                       .|.|.|+..
T Consensus        89 ~~ly~~~~~~   98 (345)
T 3tht_A           89 ITLYLNFVEK   98 (345)
T ss_dssp             EECEEEECSS
T ss_pred             eEEEEEEeec
Confidence             577777753

>3s6e_A RNA-binding protein 39; ferredoxin-like, structural genomics, joint center for struc genomics, JCSG, protein structure initiative, PSI-biology; HET: MSE CIT; 0.95A {Mus musculus} PDB: 2lq5_A

Probab=99.17  E-value=7.8e-11  Score=101.51  Aligned_cols=78  Identities=8%  Similarity=0.132  Sum_probs=66.4

Q ss_pred             CCCceEEEecCCCCCC----------HHHHHHHhccCCCeEEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHhcCCcee
Q 007792          240 PPENVLFVCKLNPVTE----------DEDLHTIFSRFGTVVSAEIIRDFKTGDSLNYAFIEFENRQACERAYSKMDNALI  309 (589)
Q Consensus       240 ~~~~~i~V~nL~~~~t----------e~~L~~~F~~~G~v~~~~i~~d~~tg~~~g~aFV~f~~~~~a~~A~~~l~g~~i  309 (589)
                      .|..+|.|.|+-....          +++|++.|++||.|..|.|+.+.    ++|||||+|.+.++|.+|++.|||..|
T Consensus         5 ~ps~vv~L~Nm~~~~e~~d~~~~~el~edl~~~f~kfG~V~~v~i~~~~----~~G~~fV~f~~~e~A~~Ai~~lnG~~f   80 (114)
T 3s6e_A            5 LATQCFQLSNMFNPQTEEEVGWDTEIKDDVIEECNKHGGVIHIYVDKNS----AQGNVYVKCPSIAAAIAAVNALHGRWF   80 (114)
T ss_dssp             CCCSEEEEESSCCTTTCCSTTHHHHHHHHHHHHHTTTTCCSEEEECTTC----TTCCEEEECSSHHHHHHHHHHHTTCEE
T ss_pred             CCCcEEEEECCCChHHccChhHHHHHHHHHHHHHhccCCEEEEEEecCC----CcEEEEEEECCHHHHHHHHHHhCCCEE
Confidence            3567899999833221          35789999999999999987652    589999999999999999999999999


Q ss_pred             CCeEEEEEeccc
Q 007792          310 DDRRIHVDFSQS  321 (589)
Q Consensus       310 ~gr~i~V~~a~~  321 (589)
                      +|+.|.|.++..
T Consensus        81 ~GR~i~v~~~~~   92 (114)
T 3s6e_A           81 AGKMITAAYVPL   92 (114)
T ss_dssp             TTEECEEEEECH
T ss_pred             CCEEEEEEEEcH
Confidence            999999999864

>2dnr_A Synaptojanin-1; RRM domain, RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.16  E-value=1.2e-10  Score=94.17  Aligned_cols=75  Identities=16%  Similarity=0.284  Sum_probs=65.7

Q ss_pred             CCCCCceEEEecCC----CCCCH----HHHHHHhccCCCeEEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHhcCCcee
Q 007792          238 IKPPENVLFVCKLN----PVTED----EDLHTIFSRFGTVVSAEIIRDFKTGDSLNYAFIEFENRQACERAYSKMDNALI  309 (589)
Q Consensus       238 ~~~~~~~i~V~nL~----~~~te----~~L~~~F~~~G~v~~~~i~~d~~tg~~~g~aFV~f~~~~~a~~A~~~l~g~~i  309 (589)
                      ..||..||+|.-++    .++-.    .+|.+.|.+||.|..++|+.+        .+||+|.+.++|.+||. |||..|
T Consensus         3 ~GPpd~tv~V~~~~~~~~~~~fd~~l~~~L~~~F~~~G~Vi~vr~~~d--------~~fVtF~d~~sAlaAi~-mnG~~v   73 (91)
T 2dnr_A            3 SGSSGGTVLVSIKSSLPENNFFDDALIDELLQQFASFGEVILIRFVED--------KMWVTFLEGSSALNVLS-LNGKEL   73 (91)
T ss_dssp             CCCSSCEEEEEEECSSTTTCSCCHHHHHHHHHHHHTTCCEEEEEECSS--------SEEEEESSHHHHHHGGG-GTTCEE
T ss_pred             CCCCCCeEEEEeccCccccccCCHHHHHHHHHHHHhCCCeEEEEEecC--------CEEEEECChHHHHHHHh-cCCeEe
Confidence            46788999998877    23433    678899999999999999886        38999999999999997 999999


Q ss_pred             CCeEEEEEeccc
Q 007792          310 DDRRIHVDFSQS  321 (589)
Q Consensus       310 ~gr~i~V~~a~~  321 (589)
                      +|+.|+|+++.+
T Consensus        74 ~Gr~LkV~lkt~   85 (91)
T 2dnr_A           74 LNRTITIALKSP   85 (91)
T ss_dssp             TTEEEEEEECCC
T ss_pred             CCeEEEEEeCCC
Confidence            999999999876

>1owx_A Lupus LA protein, SS-B, LA; RRM, transcription; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.07  E-value=3.3e-10  Score=97.81  Aligned_cols=77  Identities=18%  Similarity=0.217  Sum_probs=69.1

Q ss_pred             CCCCceEEEecCCCC-CCHHHHHHHhccCCCeEEEEEeecCCCCCcccEEEEEEcC-HHHHHHHHHhcC--CceeCCeEE
Q 007792          239 KPPENVLFVCKLNPV-TEDEDLHTIFSRFGTVVSAEIIRDFKTGDSLNYAFIEFEN-RQACERAYSKMD--NALIDDRRI  314 (589)
Q Consensus       239 ~~~~~~i~V~nL~~~-~te~~L~~~F~~~G~v~~~~i~~d~~tg~~~g~aFV~f~~-~~~a~~A~~~l~--g~~i~gr~i  314 (589)
                      -+++..|||+||++. ++.++|+++|++||+|.+|.|+.+..      .|||.|.+ ..+|..|+..||  +..|+|..+
T Consensus        15 ~~~G~il~v~~l~~~~~sredLke~F~~~G~V~~Vd~~~g~~------tgfVrf~~~~~~A~~av~~ln~~~~~i~g~~~   88 (121)
T 1owx_A           15 EKIGCLLKFSGDLDDQTCREDLHILFSNHGEIKWIDFVRGAK------EGIILFKEKAKEALGKAKDANNGNLQLRNKEV   88 (121)
T ss_dssp             CCCCCEEEEEESCCSSCCHHHHHHHTCSSCCEEEEECCTTCS------EEEEEESSCHHHHHHHHHHTTTSCBCTTSSSE
T ss_pred             ccCCeEEEEecCCCCcCCHHHHHHHHHhcCCEEEEEEecCCC------EEEEEECCChHHHHHHHHHhhcCCcEEeCcEE
Confidence            456899999999999 99999999999999999999988754      59999999 899999999995  789999999


Q ss_pred             EEEeccc
Q 007792          315 HVDFSQS  321 (589)
Q Consensus       315 ~V~~a~~  321 (589)
                      .|++...
T Consensus        89 ~~evL~G   95 (121)
T 1owx_A           89 TWEVLEG   95 (121)
T ss_dssp             EEEECCH
T ss_pred             EEEECCC
Confidence            9987653

>1ufw_A Synaptojanin 2; RNP domain, structural genomics, riken structural genomics/proteomics initiative, RSGI, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=98.96  E-value=1.1e-09  Score=89.03  Aligned_cols=77  Identities=16%  Similarity=0.267  Sum_probs=65.7

Q ss_pred             CCCCCCCceEEEecCCCC-----CCH----HHHHHHhccCCCeEEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHhcCC
Q 007792          236 ADIKPPENVLFVCKLNPV-----TED----EDLHTIFSRFGTVVSAEIIRDFKTGDSLNYAFIEFENRQACERAYSKMDN  306 (589)
Q Consensus       236 ~~~~~~~~~i~V~nL~~~-----~te----~~L~~~F~~~G~v~~~~i~~d~~tg~~~g~aFV~f~~~~~a~~A~~~l~g  306 (589)
                      ....||..||+|.-++..     +-.    .+|.+.|.+||.|..++|+.++        +||+|.+.++|.+||. |||
T Consensus         9 ~~~GPpD~Tv~V~~~~~~~~~~~~fd~~l~~~L~~~F~~~G~Vilvr~v~d~--------~fVtF~d~~sAl~AI~-ldG   79 (95)
T 1ufw_A            9 SFQGPLDATVVVNLQSPTLEEKNEFPEDLRTELMQTLGSYGTIVLVRINQGQ--------MLVTFADSHSALSVLD-VDG   79 (95)
T ss_dssp             CCCCCTTCEEEEEESSCCHHHHHSCCHHHHHHHHHHHHHHSCCSEEEEETTE--------EEEECSCSHHHHHHHH-GGG
T ss_pred             eecCCCCCeEEEEecCCcccccccCCHHHHHHHHHHHHHCCCEEEEEEecCc--------EEEEEcChHHHHHHHh-cCC
Confidence            345788999999988743     322    5688999999999999999873        9999999999999997 999


Q ss_pred             ceeCCeEEEEEeccc
Q 007792          307 ALIDDRRIHVDFSQS  321 (589)
Q Consensus       307 ~~i~gr~i~V~~a~~  321 (589)
                      ..|+|+.|+|.+..+
T Consensus        80 ~~v~Gr~L~V~~k~~   94 (95)
T 1ufw_A           80 MKVKGRAVKISGPSS   94 (95)
T ss_dssp             SEETTEEEEEECCCC
T ss_pred             eeeCCeEEEEeccCC
Confidence            999999999998643

>3dxb_A Thioredoxin N-terminally fused to PUF60(UHM); splicing, FBP interacting repressor, RRM, electron TRAN redox-active center, transport; 2.20A {Escherichia coli O157}

Probab=98.66  E-value=3.5e-08  Score=95.44  Aligned_cols=67  Identities=13%  Similarity=0.286  Sum_probs=60.7

Q ss_pred             CHHHHHHHhccCCCeEEEEEeecC----CCCCcccEEEEEEcCHHHHHHHHHhcCCceeCCeEEEEEeccc
Q 007792          255 EDEDLHTIFSRFGTVVSAEIIRDF----KTGDSLNYAFIEFENRQACERAYSKMDNALIDDRRIHVDFSQS  321 (589)
Q Consensus       255 te~~L~~~F~~~G~v~~~~i~~d~----~tg~~~g~aFV~f~~~~~a~~A~~~l~g~~i~gr~i~V~~a~~  321 (589)
                      .+++|.+.|++||.|..+.|+.+.    .++.++||+||+|.+.++|.+|+..|||..|+|+.|.|.++..
T Consensus       142 ~~~dl~~e~~~~G~v~~~~v~~~~~~~~~~~~~~G~~fv~f~~~~~a~~a~~~l~gr~~~gr~i~~~~~~~  212 (222)
T 3dxb_A          142 LEGEVTEECGKFGAVNRVIIYQEKQGEEEDAEIIVKIFVEFSIASETHKAIQALNGRWFAGRKVVAEVYDQ  212 (222)
T ss_dssp             HHHHHHHHHTTTSCEEEEEEEEEECCSSTTCCEEEEEEEEESSHHHHHHHHHHHTTCBSSSSBCEEEECCH
T ss_pred             HHHHHHHHHHccCCeEEEEEecCCCCcccCcCceeEEEEEECCHHHHHHHHHHhcCceECCeEEEEEEcCH
Confidence            467899999999999999998554    4558999999999999999999999999999999999999864

>3pgw_S U1-70K; protein-RNA complex, U1 snRNA, SM fold, SM core, RRM, splici SNRNPS, splicing factors; HET: DNA; 4.40A {Homo sapiens} PDB: 3cw1_K 2l5i_A 2l5j_A*

Probab=98.44  E-value=1.7e-07  Score=99.74  Aligned_cols=14  Identities=14%  Similarity=0.190  Sum_probs=7.7

Q ss_pred             HHHHhccCCCeEEE
Q 007792          259 LHTIFSRFGTVVSA  272 (589)
Q Consensus       259 L~~~F~~~G~v~~~  272 (589)
                      |..+|.++|+|..|
T Consensus         9 L~~lF~p~pPl~~~   22 (437)
T 3pgw_S            9 LLALFAPRDPIPYL   22 (437)
T ss_pred             HHHhcCCCCCCcCC
Confidence            44555555555554

>2l9w_A U4/U6 snRNA-associated-splicing factor PRP24; RRM, U6 snRNP, RNA binding protein; NMR {Saccharomyces cerevisiae}

Probab=98.09  E-value=1.2e-05  Score=66.64  Aligned_cols=73  Identities=12%  Similarity=0.179  Sum_probs=66.5

Q ss_pred             CCceEEEecCCCCCCHHHHHHHhccC-----CCeEEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHhcCCceeCCeEEE
Q 007792          241 PENVLFVCKLNPVTEDEDLHTIFSRF-----GTVVSAEIIRDFKTGDSLNYAFIEFENRQACERAYSKMDNALIDDRRIH  315 (589)
Q Consensus       241 ~~~~i~V~nL~~~~te~~L~~~F~~~-----G~v~~~~i~~d~~tg~~~g~aFV~f~~~~~a~~A~~~l~g~~i~gr~i~  315 (589)
                      ...+|-|-|||..++...|..++..+     |.|+.+.++.+.      +-|+|+|.+...|-+|.-+|+|.+|.|++|+
T Consensus        20 ~~rtiaL~~ipDtvndarIr~lve~~~~i~~g~i~KI~L~pDH------~GAivef~d~~~AgKasLaL~G~ef~gr~Lr   93 (117)
T 2l9w_A           20 LETLICLFPLSDKVSPSLICQFLQEEIHINEKDIRKILLVSDF------NGAIIIFRDSKFAAKMLMILNGSQFQGKVIR   93 (117)
T ss_dssp             TTSCEEEECCCTTCCHHHHHHHHHHHTCCCTTTCSEEEEETTT------TEEEEECSCHHHHHHHHHHHSSEEETTEEEE
T ss_pred             CCcEEEEecCCCCCCHHHHHHHHhhhhccCccceeEEEEecCC------CceEEEEccchhhHHHHhhcCCeeecCeEEE
Confidence            35788889999999999999999999     999999998874      5799999999999999999999999999999


Q ss_pred             EEec
Q 007792          316 VDFS  319 (589)
Q Consensus       316 V~~a  319 (589)
                      |.-.
T Consensus        94 ~gTv   97 (117)
T 2l9w_A           94 SGTI   97 (117)
T ss_dssp             EECH
T ss_pred             ecCH
Confidence            8743

>1wey_A Calcipressin 1; structural genomics, RRM domain, riken structural genomics/proteomics initiative, RSGI, RNA binding protein; NMR {Mus musculus} SCOP: d.58.7.1

Probab=97.60  E-value=0.00011  Score=60.66  Aligned_cols=75  Identities=13%  Similarity=0.300  Sum_probs=63.7

Q ss_pred             CceEEEecCCCCC-CH----HHHHHHhccCCCeEEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHhcCCceeCCeEEEE
Q 007792          242 ENVLFVCKLNPVT-ED----EDLHTIFSRFGTVVSAEIIRDFKTGDSLNYAFIEFENRQACERAYSKMDNALIDDRRIHV  316 (589)
Q Consensus       242 ~~~i~V~nL~~~~-te----~~L~~~F~~~G~v~~~~i~~d~~tg~~~g~aFV~f~~~~~a~~A~~~l~g~~i~gr~i~V  316 (589)
                      .++|+|.||+..+ ..    +.++.+|..|+++........      -.-..|.|.+.++|.+|-..|++..|+|+.|+|
T Consensus         5 pntLiitnl~~~vF~~~~lk~~~e~Lf~~~~~~~tF~~lkS------FRRirv~F~~~~~A~~AR~~Lh~~~f~g~~~r~   78 (104)
T 1wey_A            5 SSGLIACVANDDVFSESETRAKFESLFRTYDKDTTFQYFKS------FKRVRINFSNPLSAADARLRLHKTEFLGKEMKL   78 (104)
T ss_dssp             CCEEEEECCCGGGGSTTTHHHHHHHHHHTTCSSCEEEEETT------TTEEEEECSSTTHHHHHHHTSTTSEETTEECEE
T ss_pred             CceEEEecCCHHHcCCHHHHHHHHHHHHhhCcCcceeecCc------ceEEEEEeCChHHHHHHHHHhccceecCceeEE
Confidence            4789999998865 32    567899999999988777653      346789999999999999999999999999999


Q ss_pred             Eecccc
Q 007792          317 DFSQSV  322 (589)
Q Consensus       317 ~~a~~~  322 (589)
                      -++++.
T Consensus        79 YFgq~~   84 (104)
T 1wey_A           79 YFAQTL   84 (104)
T ss_dssp             ECCCCS
T ss_pred             EecCCC
Confidence            999853

>1uw4_A UPF3X; nonsense mediated mRNA decay protein, RNA-binding protein, N domain, MIF4G domain; 1.95A {Homo sapiens} SCOP: d.58.7.4

Probab=96.96  E-value=0.0056  Score=49.62  Aligned_cols=68  Identities=15%  Similarity=0.157  Sum_probs=57.7

Q ss_pred             ceEEEecCCCCCCHHHHHHHhccCCCeEEEEEeecCCCCC--cccEEEEEEcCHHHHHHHHHhcCCceeC
Q 007792          243 NVLFVCKLNPVTEDEDLHTIFSRFGTVVSAEIIRDFKTGD--SLNYAFIEFENRQACERAYSKMDNALID  310 (589)
Q Consensus       243 ~~i~V~nL~~~~te~~L~~~F~~~G~v~~~~i~~d~~tg~--~~g~aFV~f~~~~~a~~A~~~l~g~~i~  310 (589)
                      ++|.|.+||+.+|++++.+.++.+..+....++..+.+.+  ..+-|||.|.+.+++....+.++|..+-
T Consensus         2 ~KvVIRrLPP~LteeeF~~~l~~~~~~d~~~fv~G~~s~~~~~~SRaYi~f~~~e~v~~f~~~~~g~~F~   71 (91)
T 1uw4_A            2 SKVVIRRLPPTLTKEQLQEHLQPMPEHDYFEFFSNDTSLYPHMYARAYINFKNQEDIILFRDRFDGYVFL   71 (91)
T ss_dssp             CEEEEEEECTTCCHHHHHHHHCSCCCEEEEEEEESCCSSTTCCCEEEEEEESSSHHHHHHHHHHTTCEEE
T ss_pred             cEEEEeCCCCCCCHHHHHHHhcCcccceEEEEeCCccCCCCCcceEEEEEeCCHHHHHHHHHHhCCcEEE
Confidence            5789999999999999999999998887777776554433  3467999999999999999999998774

>1whv_A Poly(A)-specific ribonuclease; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, PARN, structural genomics; NMR {Mus musculus} SCOP: d.58.7.1 PDB: 2rok_A*

Probab=96.91  E-value=0.0027  Score=51.53  Aligned_cols=54  Identities=26%  Similarity=0.404  Sum_probs=45.6

Q ss_pred             ceEEEecCCCCCCHHHHHHHhccCCCeEEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHhcC
Q 007792          243 NVLFVCKLNPVTEDEDLHTIFSRFGTVVSAEIIRDFKTGDSLNYAFIEFENRQACERAYSKMD  305 (589)
Q Consensus       243 ~~i~V~nL~~~~te~~L~~~F~~~G~v~~~~i~~d~~tg~~~g~aFV~f~~~~~a~~A~~~l~  305 (589)
                      ..++| ++|.++...+|.++|+.||. ..|.++-|       .-|||.|.+.+.|..|+..+.
T Consensus        17 HVf~l-~FP~ewKt~DI~~lFs~fgg-v~I~WidD-------TsAlvvf~~~~~a~~al~~i~   70 (100)
T 1whv_A           17 HVLHV-TFPKEWKTSDLYQLFSAFGN-IQISWIDD-------TSAFVSLSQPEQVQIAVNTSK   70 (100)
T ss_dssp             SEEEE-ECCTTCCHHHHHHHHTTTCS-CCCEEEET-------TEEEEECSCHHHHHHHHHHHH
T ss_pred             eEEEE-eCChhhhhHHHHHHhhccCC-EEEEEEcC-------CeEEEEecCHHHHHHHHHhcc
Confidence            45555 99999999999999999994 45777776       489999999999999998663

>3ctr_A Poly(A)-specific ribonuclease PARN; protein-RNA-complex, M7G-CAP, M7GTP, RNA recognition motif, RRM, cytoplasm, exonuclease, hydrolase, magnesium; HET: MGP; 2.10A {Homo sapiens}

Probab=96.71  E-value=0.0027  Score=51.71  Aligned_cols=54  Identities=26%  Similarity=0.385  Sum_probs=46.3

Q ss_pred             ceEEEecCCCCCCHHHHHHHhccCCCeEEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHhcC
Q 007792          243 NVLFVCKLNPVTEDEDLHTIFSRFGTVVSAEIIRDFKTGDSLNYAFIEFENRQACERAYSKMD  305 (589)
Q Consensus       243 ~~i~V~nL~~~~te~~L~~~F~~~G~v~~~~i~~d~~tg~~~g~aFV~f~~~~~a~~A~~~l~  305 (589)
                      ..++| ++|.++...+|.++|+.|| -..|.++-|       .-|||.|.+.+.|..|+..+.
T Consensus         7 HV~~l-~FP~ewKt~Di~~lFs~fg-gv~I~WidD-------TsAlvvf~~~~~a~~al~~i~   60 (101)
T 3ctr_A            7 HVLHV-TFPKEWKTSDLYQLFSAFG-NIQISWIDD-------TSAFVSLSQPEQVKIAVNTSK   60 (101)
T ss_dssp             EEEEE-ECCTTCCHHHHHHHTTTSE-EEEEEEEET-------TEEEEEEEEECHHHHHHHHHT
T ss_pred             eEEEE-eCChhhhhHHHHHHHhccC-CEEEEEEcC-------CeEEEEecCHHHHHHHHHhcc
Confidence            45666 9999999999999999999 456777776       489999999999999998664

>2dhx_A Poly (ADP-ribose) polymerase family, member 10 variant; RRM domain, RNA- binding, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=96.50  E-value=0.017  Score=47.37  Aligned_cols=72  Identities=18%  Similarity=0.204  Sum_probs=58.9

Q ss_pred             CCceEEEecCCCCCCHHHHHHHhcc-----CCCeEEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHhcCCceeCCeEEE
Q 007792          241 PENVLFVCKLNPVTEDEDLHTIFSR-----FGTVVSAEIIRDFKTGDSLNYAFIEFENRQACERAYSKMDNALIDDRRIH  315 (589)
Q Consensus       241 ~~~~i~V~nL~~~~te~~L~~~F~~-----~G~v~~~~i~~d~~tg~~~g~aFV~f~~~~~a~~A~~~l~g~~i~gr~i~  315 (589)
                      -..+|.|.|||+.+.++.|.-+|+.     -|+|..+....        +-|+|+|.+...|+..|+. ....|.|..|.
T Consensus         7 ~~~~I~V~~lPp~~~~e~L~LYFEn~rrsGGG~V~~v~~~~--------~~AvItF~d~~va~rVL~k-~~H~L~~~~Ls   77 (104)
T 2dhx_A            7 GGVAVEVRGLPPAVPDELLTLYFENRRRSGGGPVLSWQRLG--------CGGVLTFREPADAERVLAQ-ADHELHGAQLS   77 (104)
T ss_dssp             CCCEEEEESCCTTSCHHHHHHHHHCTTTTCCCCEEEEEEET--------TEEEEEESSHHHHHHHHTC-SCCBSSSSBCE
T ss_pred             CccEEEEECCCCCCChhHheEEEeCCCcCCCceeeEEEEcC--------CcEEEEEcChHHHHHHhcC-CcceecCeEEE
Confidence            3579999999999999999999986     26888887643        5799999999999999853 35678888899


Q ss_pred             EEeccc
Q 007792          316 VDFSQS  321 (589)
Q Consensus       316 V~~a~~  321 (589)
                      |....+
T Consensus        78 V~P~~~   83 (104)
T 2dhx_A           78 LRPAPP   83 (104)
T ss_dssp             EEECCC
T ss_pred             EEcCCC
Confidence            876544

>1wwh_A Nucleoporin 35, nucleoporin; structural genomics, MPPN, riken structural genomics/proteomics initiative, RSGI, protein transport; 2.70A {Mus musculus} SCOP: d.58.7.1

Probab=96.17  E-value=0.018  Score=48.81  Aligned_cols=72  Identities=13%  Similarity=0.248  Sum_probs=57.8

Q ss_pred             CCceEEEecCCCCCCHHHHHHHhccCCCeEEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHhcCCceeCC-eEEEEEec
Q 007792          241 PENVLFVCKLNPVTEDEDLHTIFSRFGTVVSAEIIRDFKTGDSLNYAFIEFENRQACERAYSKMDNALIDD-RRIHVDFS  319 (589)
Q Consensus       241 ~~~~i~V~nL~~~~te~~L~~~F~~~G~v~~~~i~~d~~tg~~~g~aFV~f~~~~~a~~A~~~l~g~~i~g-r~i~V~~a  319 (589)
                      ..+-|.|-+.|+.. -..|...|++||.|.......      ...+-.|.|.+..+|++|| ..||..|+| -.|-|...
T Consensus        23 ~~~wVtVFGFp~~~-~~~VL~~F~~~G~Iv~~~~~~------~~NWihI~Y~s~~~A~rAL-~kNG~ii~g~~mIGV~p~   94 (119)
T 1wwh_A           23 DDTWVTVFGFPQAS-ASYILLQFAQYGNILKHVMSN------TGNWMHIRYQSKLQARKAL-SKDGRIFGESIMIGVKPC   94 (119)
T ss_dssp             GGGEEEEECCCGGG-HHHHHHHHHTTSCEEEEEECS------SSSEEEEEESSHHHHHHHH-TTTTCEETTTEECEEEEC
T ss_pred             CCCEEEEECCCHHH-HHHHHHHHHhhCcEEEeccCC------CCCeEEEEeCCHHHHHHHH-HhCCeEecCCEEEEEEEC
Confidence            35788899999886 467888999999999877621      2369999999999999999 569999985 66777765


Q ss_pred             c
Q 007792          320 Q  320 (589)
Q Consensus       320 ~  320 (589)
                      .
T Consensus        95 ~   95 (119)
T 1wwh_A           95 I   95 (119)
T ss_dssp             C
T ss_pred             C
Confidence            3

>2l08_A Regulator of nonsense transcripts 3A; NESG, nonsense regulator, structural genomics, PSI-2, protei structure initiative; NMR {Homo sapiens}

Probab=95.72  E-value=0.025  Score=46.10  Aligned_cols=78  Identities=17%  Similarity=0.165  Sum_probs=56.6

Q ss_pred             CceEEEecCCCCCCHHHHHHHhccCCCeEEEEEeecCCCCC--cccEEEEEEcCHHHHHHHHHhcCCceeCC-----eEE
Q 007792          242 ENVLFVCKLNPVTEDEDLHTIFSRFGTVVSAEIIRDFKTGD--SLNYAFIEFENRQACERAYSKMDNALIDD-----RRI  314 (589)
Q Consensus       242 ~~~i~V~nL~~~~te~~L~~~F~~~G~v~~~~i~~d~~tg~--~~g~aFV~f~~~~~a~~A~~~l~g~~i~g-----r~i  314 (589)
                      .-+|.|..||+.+|++++.+.++.+-++.....+..+.+.+  ...-|||.|.+.+++....+.++|..+-+     -+.
T Consensus         9 ~~KvVIRrLPP~Ltee~F~~~l~~~~~~d~~~fv~G~~s~~~~~~SRAYI~F~~~edv~~F~~~f~g~~F~D~kg~~~~a   88 (97)
T 2l08_A            9 SHMVVIRRLPPGLTKEQLEEQLRPLPAHDYFEFFAADLSLYPHLYSRAYINFRNPDDILLFRDRFDGYIFLDSKGLEYPA   88 (97)
T ss_dssp             CCCEEEECCCSCSCHHHHTTTTSCCSSEEECCCCCCCSSSCCSCCCCCEEEESCHHHHHHHHHHSTTEEEECTTCCEEEE
T ss_pred             ceeEEEeCCCCCCCHHHHHHHhCCcCccceEEEeCCccCCCCCcceEEEEEeCCHHHHHHHHHHcCCcEEEeCCCCEeee
Confidence            35789999999999999888887765554433333332222  23579999999999999999999987743     334


Q ss_pred             EEEec
Q 007792          315 HVDFS  319 (589)
Q Consensus       315 ~V~~a  319 (589)
                      .|++|
T Consensus        89 ~VE~A   93 (97)
T 2l08_A           89 VVEFA   93 (97)
T ss_dssp             EEEEC
T ss_pred             EEEec
Confidence            56665

>2nnz_A Hypothetical protein; beta-barrel, structural genomics, ontario centre for structu proteomics, OCSP, unknown function; NMR {Archaeoglobus fulgidus}

Probab=95.68  E-value=0.017  Score=51.56  Aligned_cols=103  Identities=15%  Similarity=0.199  Sum_probs=63.0

Q ss_pred             CEEEEEecceeEEEEecCCCChhHHHHHHHHHh----cCccCCceEEEeecCcccccCCCCCCCCCCCCccccccccccc
Q 007792            1 MSVLIVTSLGDIVVDLFVDKCPLTTKNFLKLCK----IKYYNGCLFHTVQKDFTAQTGDPTGTGTGGDSVYKFLYGEQAR   76 (589)
Q Consensus         1 ~~v~~~T~~G~i~ieL~~~~aP~~~~nF~~l~~----~~~Y~g~~f~rv~~~~~iq~Gd~~~~~~~~~~~~~~~~~~~~~   76 (589)
                      |.|.|.-.-..|+++|+.+.||+||..|+++.=    ...|.+ -++-..|-.                           
T Consensus        30 ~~I~i~~~~~~~~a~L~D~~aP~Ta~~f~~~LPl~~~~~~~g~-E~y~~lp~~---------------------------   81 (153)
T 2nnz_A           30 MRLRIRFESAECEVELYEEWAPETVRAIADALPIKSTANRWGD-EIYFTTQVA---------------------------   81 (153)
T ss_dssp             CCEEEEETTEEEEECCCTTSCHHHHHHHHHTCSEEEEEEEETT-EEEECCSCC---------------------------
T ss_pred             eEEEEEECCEEEEEEEcCCCCHHHHHHHHHhCCcEEEHHhhCC-cEEEECCCC---------------------------
Confidence            667888888899999999999999999999872    112322 222111211                           


Q ss_pred             ccCC-ccccCCCCCCCceEEEeccCCCCCcceEEEEeCCCCCCCCC------CcceEEEEecCHHHHHHHh
Q 007792           77 FFGD-EIRVDLKHAKTGTVAMASAGENLNASQFYMTLRDNLDYLDE------KHTIFGEVAEGLETLSRIN  140 (589)
Q Consensus        77 ~~~~-e~~~~l~~~~~G~vs~a~~g~~~~~sqFfI~l~~~~~~ld~------~~~vFG~Vv~G~~vl~~i~  140 (589)
                       ++. | +.. ....+|-|++...+.     .|.|-..+ .|...+      .-.+||+|++|++.|..+.
T Consensus        82 -l~~~e-n~~-~~~~~GDI~Yy~pg~-----~LaIFYg~-~p~s~~e~~~as~~~~lG~I~~gle~L~~~~  143 (153)
T 2nnz_A           82 -VEKEE-NSK-DVVELGDVAYWIPGK-----AICLFFGK-TPISDDKIRPASAVNVIGRIVNSMEGLKGVA  143 (153)
T ss_dssp             -CCCSS-CCB-CCCCTTEEEEETTTT-----EEEEESSC-CTTCTTSCCCCSSEEEEEECCSCCCCGGGCC
T ss_pred             -CCCCC-CCc-ccCCCCeEEEeCCCC-----EEEEEECC-ccccccccccccccEEEEEEccCHHHHhhCC
Confidence             111 1 011 112568888776543     26666665 332221      2578999999988776663

>3kop_A Uncharacterized protein; protein with A cyclophilin-like fold, structural genomics, J center for structural genomics, JCSG; 1.90A {Arthrobacter SP}

Probab=95.33  E-value=0.12  Score=46.42  Aligned_cols=42  Identities=19%  Similarity=0.126  Sum_probs=28.6

Q ss_pred             ccee-EEEEecCCCChhHHHHHHHHHh--cC----ccCCceEEEeecCc
Q 007792            8 SLGD-IVVDLFVDKCPLTTKNFLKLCK--IK----YYNGCLFHTVQKDF   49 (589)
Q Consensus         8 ~~G~-i~ieL~~~~aP~~~~nF~~l~~--~~----~Y~g~~f~rv~~~~   49 (589)
                      ..|- ++.+|..+.||+||+.|+++.=  +.    -|-|-.++-.+|.|
T Consensus        30 ~~g~~~~A~Lldd~APkTcaA~~~~LP~~~~viHarwSGeeVy~~lp~f   78 (188)
T 3kop_A           30 KRGVTCKALLLDDVAPRTSKAVWDALPQSSQVFHGKYARNEIYNLVPAF   78 (188)
T ss_dssp             TTTEEEEEEECTTTSHHHHHHHHHHCCEEEECEECSSSSSEEEEEEECC
T ss_pred             cCCeEEEEEEccccChHHHHHHHHhCCCCcceEEEEEecceEEEECCcc
Confidence            3344 7899999999999999999772  11    15555555444443

>3p3d_A Nucleoporin 53; structural genomics, PSI-2, protein structure initiative, NE structural genomix research consortium, nysgxrc; 2.35A {Pichia guilliermondii}

Probab=95.03  E-value=0.019  Score=49.35  Aligned_cols=78  Identities=18%  Similarity=0.268  Sum_probs=56.0

Q ss_pred             CceEEEecCCCCCCHHHHHHHhccCCCeEE-EEEee------------cCCCC-CcccEEEEEEcCHHHHHHHHHhcCCc
Q 007792          242 ENVLFVCKLNPVTEDEDLHTIFSRFGTVVS-AEIIR------------DFKTG-DSLNYAFIEFENRQACERAYSKMDNA  307 (589)
Q Consensus       242 ~~~i~V~nL~~~~te~~L~~~F~~~G~v~~-~~i~~------------d~~tg-~~~g~aFV~f~~~~~a~~A~~~l~g~  307 (589)
                      ...|.|-+.|+..+ ..+...|++||.|.. +.+..            .+... ....+..|+|.+..+|.+|| ..||.
T Consensus         7 e~~VtVFGFp~~~~-~~VI~~Fs~~G~IlE~~~~~~~~~~~~~~~~~~k~yP~f~g~NWikItYds~~~A~rAL-~~NG~   84 (132)
T 3p3d_A            7 ELAILVFGYPETMA-NQVIAYFQEFGTILEDFEVLRKPQAMTVGLQDRQFVPIFSGNSWTKITYDNPASAVDAL-LENGA   84 (132)
T ss_dssp             -CEEEEECCCGGGH-HHHHHHHGGGSCBCSCCGGGCCC-----------CCCCCEETTEEEEEBSSHHHHHHHH-TTTTC
T ss_pred             ceEEEEEecCHHHH-HHHHHHHHhhceEeeeccccccccccccccccccccCccCCCcEEEEEcCCHHHHHHHH-HhCCe
Confidence            46777888877765 567789999999875 21110            00000 02467899999999999999 57999


Q ss_pred             eeCCeEEEEEeccc
Q 007792          308 LIDDRRIHVDFSQS  321 (589)
Q Consensus       308 ~i~gr~i~V~~a~~  321 (589)
                      .|+|..|=|....+
T Consensus        85 ii~G~mIGV~Py~~   98 (132)
T 3p3d_A           85 VFNGVLLGVIPYTK   98 (132)
T ss_dssp             EETTEECEEEECCH
T ss_pred             EeCcEEEEEEECCH
Confidence            99999888887754

>1zx8_A Hypothetical protein TM1367; structural genomics, joint center for structural genomics, J protein structure initiative, PSI; HET: 1PE; 1.90A {Thermotoga maritima} SCOP: b.62.1.3 PDB: 2ka0_A

Probab=93.89  E-value=0.2  Score=43.59  Aligned_cols=102  Identities=20%  Similarity=0.204  Sum_probs=63.4

Q ss_pred             CEEEEEecceeEEEEecCCCChhHHHHHHHHHh----cCccCCceEEEeecCcccccCCCCCCCCCCCCccccccccccc
Q 007792            1 MSVLIVTSLGDIVVDLFVDKCPLTTKNFLKLCK----IKYYNGCLFHTVQKDFTAQTGDPTGTGTGGDSVYKFLYGEQAR   76 (589)
Q Consensus         1 ~~v~~~T~~G~i~ieL~~~~aP~~~~nF~~l~~----~~~Y~g~~f~rv~~~~~iq~Gd~~~~~~~~~~~~~~~~~~~~~   76 (589)
                      |-|.+......|+++|+.  .|.|+..|+++.=    ...|. .-+|-..|.. +..                       
T Consensus        13 ~~~~~~~~~~~v~a~L~D--np~Ta~~~~~~LPl~~~~~~~g-~E~y~~~p~~-l~~-----------------------   65 (136)
T 1zx8_A           13 MRVELLFESGKCVIDLNE--EYEVVKLLKEKIPFESVVNTWG-EEIYFSTPVN-VQK-----------------------   65 (136)
T ss_dssp             EEEEEECSSCEEEEEEET--TSHHHHHHHHHCSEEEECEESS-SEEEEECSCC-CCC-----------------------
T ss_pred             eEEEEeeCCcEEEEEEcC--CHHHHHHHHHHCCcEEEHHHhC-CcEEEECCcc-CCC-----------------------
Confidence            678888888999999984  4889999999872    22353 4444333422 100                       


Q ss_pred             ccCCccccCCCCCCCceEEEeccCCCCCcceEEEEeCCCCCCCCC------CcceEEEEecCHHHHHHHh
Q 007792           77 FFGDEIRVDLKHAKTGTVAMASAGENLNASQFYMTLRDNLDYLDE------KHTIFGEVAEGLETLSRIN  140 (589)
Q Consensus        77 ~~~~e~~~~l~~~~~G~vs~a~~g~~~~~sqFfI~l~~~~~~ld~------~~~vFG~Vv~G~~vl~~i~  140 (589)
                         .| ..... ...|-|++...+.     .|.|-+.+ .|...+      .-++||+|++|++.|..+.
T Consensus        66 ---~e-~~~~~-~~~GDIaYw~pgg-----~LaIFyg~-~p~s~~e~~~a~~v~~lGrI~~~l~~l~~v~  124 (136)
T 1zx8_A           66 ---ME-NPREV-VEIGDVGYWPPGK-----ALCLFFGK-TPMSDDKIQPASAVNVIGKIVEGLEDLKKIK  124 (136)
T ss_dssp             ---CS-SEESS-BCTTEEEEEGGGT-----EEEEESSC-CTTCSSSBCCSSCEEEEEEEEECGGGGGGCC
T ss_pred             ---CC-CCCcc-CCCCcEEEeCCCC-----EEEEEeCC-CccccCccccCcCcEEEEEEccCHHHHhhCC
Confidence               01 01111 2568888776543     36676666 343332      3678999999988776663

>3pq1_A Poly(A) RNA polymerase; nucleotidyl transferase, RNP-type RNA binding domain, poly(A polymerase, mitochondria, transferase; 3.10A {Homo sapiens}

Probab=93.69  E-value=0.032  Score=58.91  Aligned_cols=56  Identities=14%  Similarity=0.272  Sum_probs=42.4

Q ss_pred             CceEEEecCCCCCCHHHHHHHhccCCCeEEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHh
Q 007792          242 ENVLFVCKLNPVTEDEDLHTIFSRFGTVVSAEIIRDFKTGDSLNYAFIEFENRQACERAYSK  303 (589)
Q Consensus       242 ~~~i~V~nL~~~~te~~L~~~F~~~G~v~~~~i~~d~~tg~~~g~aFV~f~~~~~a~~A~~~  303 (589)
                      ..+|||. +|..+++.+|.++|++||+|..+.+..++     .-||.|+|.+.+++..++..
T Consensus        53 ~rsv~v~-~~~~~~~~~l~~y~~~~g~i~~~~~~~~~-----g~~~~vef~~~~~~~~~~~~  108 (464)
T 3pq1_A           53 QRTVLIH-CPEKISENKFLKYLSQFGPINNHFFYESF-----GLYAVVEFCQKESIGSLQNG  108 (464)
T ss_dssp             HTEEEEE-ECCC---CHHHHHHGGGSCCCCEEEECSS-----SEEEEEECC---CCHHHHSS
T ss_pred             cceEEEE-cCCCCCHHHHHHHHHhcCCcceEEEEccC-----CeEEEEEeCCHHHHHHHHhc
Confidence            3799997 79999999999999999999998887642     26999999999999987743

>2kn4_A Immunoglobulin G-binding protein G, splicing FACT arginine/serine-rich 2, S35, splicing factor SC35,; RRM domain, cell WALL; NMR {Streptococcus SP}

Probab=93.63  E-value=0.065  Score=47.84  Aligned_cols=36  Identities=14%  Similarity=0.098  Sum_probs=29.7

Q ss_pred             EEEEeecCCCCCcccEEEEEEcCHHHHHHHHHhcCCce
Q 007792          271 SAEIIRDFKTGDSLNYAFIEFENRQACERAYSKMDNAL  308 (589)
Q Consensus       271 ~~~i~~d~~tg~~~g~aFV~f~~~~~a~~A~~~l~g~~  308 (589)
                      ++.|+.+..  +++|||||+|.+.++|++|+..+++..
T Consensus         2 ~~kl~ln~~--~~~G~~fV~f~~~~~A~~al~~~~~~~   37 (158)
T 2kn4_A            2 QYKLILNGK--TLKGETTTEAVDAATAEKVFKQYANDN   37 (158)
T ss_dssp             EEEEEEECS--SCEEEEEEECSSHHHHHHHHHHHHHHH
T ss_pred             cEEEEecCc--cccchhHHHHHHHHhHHHHHHhhcccC
Confidence            466777644  589999999999999999998887643

>2i2y_A Fusion protein consists of immunoglobin G- binding protein G and splicing factor,...; protein-RNA complex RRM alpha-beta sandwich BETA1-alpha1- BETA2-BETA3-alpha2-BETA4; NMR {Streptococcus SP} PDB: 2i38_A

Probab=93.08  E-value=0.027  Score=50.05  Aligned_cols=42  Identities=10%  Similarity=0.082  Sum_probs=38.0

Q ss_pred             CCCcccEEEEEEcCHHHHHHHHHhc-CCceeCCeEEEEEecccc
Q 007792          280 TGDSLNYAFIEFENRQACERAYSKM-DNALIDDRRIHVDFSQSV  322 (589)
Q Consensus       280 tg~~~g~aFV~f~~~~~a~~A~~~l-~g~~i~gr~i~V~~a~~~  322 (589)
                      ..+.+|+++|+|.+.++|++|++.| ||..|+| .|.|.++...
T Consensus         9 g~~l~G~~~ve~~~~~~A~~a~~~~~ng~~~~G-~~~~~~a~~~   51 (150)
T 2i2y_A            9 GKTLKGETTTEAVDAATAEKVFKQYANDNGVDG-EWTYDDATKT   51 (150)
T ss_dssp             CSSSCEEEEEECSSHHHHTTTHHHHHHHHTCCC-EEEEETTTTE
T ss_pred             cccccccceeeecCHHHHHHHHHHHhcCCCCCC-ceecccccCc
Confidence            4567899999999999999999999 9999999 9999988753

>3ts2_A Protein LIN-28 homolog A; microrna biogenesis, protein-RNA complex, PRE-element, CCHC knuckle; HET: GMP; 2.01A {Mus musculus} PDB: 3trz_A* 3ts0_A*

Probab=92.04  E-value=0.031  Score=49.72  Aligned_cols=93  Identities=20%  Similarity=0.415  Sum_probs=47.9

Q ss_pred             HHHHHHhccCCCeEEEEEeecCCCCCcccEEEEEEcC--------HHHH---HHHHHhcCCc--eeCCeEEEEEeccccc
Q 007792          257 EDLHTIFSRFGTVVSAEIIRDFKTGDSLNYAFIEFEN--------RQAC---ERAYSKMDNA--LIDDRRIHVDFSQSVS  323 (589)
Q Consensus       257 ~~L~~~F~~~G~v~~~~i~~d~~tg~~~g~aFV~f~~--------~~~a---~~A~~~l~g~--~i~gr~i~V~~a~~~~  323 (589)
                      +++.++|...|.|+....        .+||+||+-.+        .+++   ..||. ..|+  .-.|..|...+.....
T Consensus         2 ~~~~~l~~~~G~Vkwfn~--------~kGfGFI~~~~~~g~p~~~g~DvFvH~s~i~-~~g~~~l~eG~~V~f~~~~g~k   72 (148)
T 3ts2_A            2 ADEPQLLHGAGICKWFNV--------RMGFGFLSMTARAGVALDPPVDVFVHQSKLH-MEGFRSLKEGEAVEFTFKKSAK   72 (148)
T ss_dssp             ----CCEEEEEEEEEEET--------TTTEEEEEEEEETTEEEEEEEEEEEEGGGBC-SSSSCCCCTTCEEEEEEEEETT
T ss_pred             CcccccccceeEEEEEEC--------CCCeeEEeeCccccccCCCCccEEEEhHHhc-ccCCccCCCCCEEEEEEEEccc
Confidence            455567777777654432        45899998752        1121   12221 2332  2356676666654321


Q ss_pred             cc---------cccccCCCCCCCCCCCCccCCCCCCCCccCCCC
Q 007792          324 KL---------WNQFRRRDHQTGKGKGCFKCGGLDHIAKDCTGQ  358 (589)
Q Consensus       324 ~~---------~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~  358 (589)
                      ..         ................||+|+..+|++.+|+..
T Consensus        73 G~~A~~V~~pgg~pv~GS~rrp~~~~~C~~Cg~~GH~a~~C~~~  116 (148)
T 3ts2_A           73 GLESIRVTGPGGVFCIGSERRPKGGDRCYNCGGLDHHAKECKLP  116 (148)
T ss_dssp             EEEEEEEESGGGCCCCCCTTSCCCSCCCTTTCCSSCCGGGCCSC
T ss_pred             cchhhcccccCCccccccccccCCCCcccEeCCccchhhhCCCC
Confidence            11         001111112223345699999999999999863

---

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	589
d1zkca1	178	b.62.1.1 (A:280-457) Peptidyl-prolyl cis-trans iso	6e-42
d2ok3a1	159	b.62.1.1 (A:1-159) Cyclophilin-like protein PPIL3B	7e-40
d1xwna1	166	b.62.1.1 (A:1-166) Peptidyl-prolyl cis-trans isome	6e-39
d2fu0a1	155	b.62.1.1 (A:5-159) Putative cyclophilin PFE0505w {	4e-30
d2b71a1	169	b.62.1.1 (A:23-191) Cyclophilin-like protein PY006	6e-30
d2cfea1	162	b.62.1.1 (A:1-162) Cyclophilin-like allergen Mal s	6e-30
d1w74a_	171	b.62.1.1 (A:) Peptidyl-prolyl cis-trans isomerase	8e-29
d2a2na1	164	b.62.1.1 (A:483-646) Peptidylprolyl isomerase doma	3e-28
d1h0pa_	182	b.62.1.1 (A:) Cyclophilin (eukaryotic) {Caenorhabd	2e-27
d1a33a_	174	b.62.1.1 (A:) Cyclophilin (eukaryotic) {Nematode (	8e-27
d1lopa_	164	b.62.1.1 (A:) Peptidyl-prolyl cis-trans isomerase	3e-26
d1xo7a_	166	b.62.1.1 (A:) Cyclophilin (eukaryotic) {Trypanosom	6e-26
d1qnga_	170	b.62.1.1 (A:) Cyclophilin (eukaryotic) {Plasmodium	9e-26
d2rmca_	182	b.62.1.1 (A:) Cyclophilin (eukaryotic) {Mouse (Mus	6e-25
d2igva1	172	b.62.1.1 (A:1-172) Cyclophilin (eukaryotic) {Caeno	7e-25
d1ihga2	195	b.62.1.1 (A:2-196) Cyclophilin 40 isomerase domain	5e-24
d2z6wa1	164	b.62.1.1 (A:2-165) Mitochondrial peptidyl-prolyl c	9e-23
d2c3ba1	171	b.62.1.1 (A:1-171) Cyclophilin (eukaryotic) {Asper	2e-22
d2r99a1	161	b.62.1.1 (A:139-299) Mitochondrial peptidyl-prolyl	5e-22
d1v9ta_	166	b.62.1.1 (A:) Peptidyl-prolyl cis-trans isomerase	5e-21
d1qoia_	173	b.62.1.1 (A:) Cyclophilin (eukaryotic) {Human (Hom	2e-20
d1z81a1	186	b.62.1.1 (A:25-210) Cyclophilin (eukaryotic) {Plas	1e-19
d1cvja1	80	d.58.7.1 (A:11-90) Poly(A)-binding protein {Human	5e-17
d2cpha1	94	d.58.7.1 (A:454-547) Probable RNA-binding protein	7e-15
d1no8a_	78	d.58.7.1 (A:) Nuclear factor Aly {Mouse (Mus muscu	2e-14
d1b7fa1	82	d.58.7.1 (A:123-204) Sex-lethal protein {Drosophil	2e-14
d1wf2a_	98	d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprot	2e-14
d1b7fa2	85	d.58.7.1 (A:205-289) Sex-lethal protein {Drosophil	3e-14
d2cqca1	83	d.58.7.1 (A:109-191) Arginine/serine-rich splicing	9e-14
d2cpfa1	85	d.58.7.1 (A:362-446) Probable RNA-binding protein	1e-13
d1x5ua1	93	d.58.7.1 (A:7-99) Splicing factor 3B subunit 4 {Hu	2e-13
d2cqba1	89	d.58.7.1 (A:1-89) Peptidyl-prolyl cis-trans isomer	4e-13
d1fxla1	82	d.58.7.1 (A:37-118) Hu antigen D (Hud) {Human (Hom	8e-13
d2f9da1	114	d.58.7.1 (A:12-125) Pre-mRNA branch site protein p	9e-13
d1h2vz_	93	d.58.7.1 (Z:) CBP20, 20KDa nuclear cap-binding pro	1e-12
d2cqpa1	86	d.58.7.1 (A:917-1002) RNA-binding protein 12 {Mous	2e-12
d1uawa_	77	d.58.7.1 (A:) Musashi-1 {Mouse (Mus musculus) [Tax	6e-12
d1fxla2	85	d.58.7.1 (A:119-203) Hu antigen D (Hud) {Human (Ho	6e-12
d2cpda1	86	d.58.7.1 (A:223-308) APOBEC1 stimulating protein {	9e-12
d2cpza1	102	d.58.7.1 (A:383-484) CUG triplet repeat RNA-bindin	1e-11
d2u2fa_	85	d.58.7.1 (A:) Splicing factor U2AF 65 KDa subunit	1e-11
d1x4ga1	96	d.58.7.1 (A:8-103) Nucleolysin TIAR {Human (Homo s	2e-11
d1x5ta1	83	d.58.7.1 (A:8-90) Splicing factor 3B subunit 4 {Hu	3e-11
d2cq0a1	90	d.58.7.1 (A:231-320) Eukaryotic translation initia	4e-11
d1nu4a_	91	d.58.7.1 (A:) Splicesomal U1A protein {Human (Homo	4e-11
d1l3ka1	84	d.58.7.1 (A:8-91) Nuclear ribonucleoprotein A1 (RN	5e-11
d1rk8a_	88	d.58.7.1 (A:) RNA-binding protein 8 {Fruit fly (Dr	7e-11
d1cvja2	89	d.58.7.1 (A:91-179) Poly(A)-binding protein {Human	8e-11
d2cpja1	86	d.58.7.1 (A:65-150) Non-POU domain-containing octa	8e-11
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:) 8e-11
d2cq3a1	93	d.58.7.1 (A:110-202) RNA-binding protein 9 {Human	1e-10
d2cqga1	90	d.58.7.1 (A:96-185) TAR DNA-binding protein 43, TD	1e-10
d1weya_	104	d.58.7.1 (A:) Calcipressin-1 {Mouse (Mus musculus)	2e-10
d2cpea1	101	d.58.7.1 (A:353-453) RNA-binding protein EWS {Huma	2e-10
d2cpxa1	102	d.58.7.1 (A:291-392) RNA-binding protein 41, RBM41	3e-10
d1x0fa1	75	d.58.7.1 (A:183-257) Nuclear ribonucleoprotein D0	3e-10
d2ghpa1	81	d.58.7.1 (A:116-196) U4/U6 snRNA-associated-splici	4e-10
d1hd0a_	75	d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprot	5e-10
d2msta_	75	d.58.7.1 (A:) Neural RNA-binding protein Musashi-1	5e-10
d1whwa_	99	d.58.7.1 (A:) Probable RNA-binding protein 19, Rbm	6e-10
d2adca2	88	d.58.7.1 (A:444-531) Polypyrimidine tract-binding	7e-10
d2cq4a1	101	d.58.7.1 (A:132-232) RNA binding protein 23 {Human	8e-10
d2cqia1	90	d.58.7.1 (A:1-90) Nucleolysin TIAR {Human (Homo sa	9e-10
d1x4aa1	95	d.58.7.1 (A:9-103) Splicing factor, arginine/serin	1e-09
d1fjca_	96	d.58.7.1 (A:) Nucleolin {Golden hamster (Mesocrice	3e-09
d1u6fa1	139	d.58.7.1 (A:1-139) RNA-binding protein UBP1 {Trypa	3e-09
d2dita1	99	d.58.7.1 (A:8-106) HIV Tat-specific factor 1 {Huma	6e-09
d2cqda1	103	d.58.7.1 (A:1-103) RNA-binding region containing p	8e-09
d1l3ka2	79	d.58.7.1 (A:103-181) Nuclear ribonucleoprotein A1	9e-09
d2bz2a1	79	d.58.7.1 (A:35-113) Negative elongation factor E,	1e-08
d1x4ba1	103	d.58.7.1 (A:8-110) Heterogeneous nuclear ribonucle	1e-08
d2cqha1	80	d.58.7.1 (A:2-81) IGF-II mRNA-binding protein 2 is	1e-08
d2disa1	96	d.58.7.1 (A:8-103) Hypothetical protein FLJ20273 {	2e-08
d1wi8a_	104	d.58.7.1 (A:) Eukaryotic translation initiation fa	2e-08
d1whya_	97	d.58.7.1 (A:) Putative RNA-binding protein 15B, Rb	4e-08
d1u1qa_	183	d.58.7.1 (A:) Nuclear ribonucleoprotein A1 (RNP A1	5e-08
d1x5sa1	90	d.58.7.1 (A:8-97) Cold-inducible RNA-binding prote	5e-08
d1u2fa_	90	d.58.7.1 (A:) Splicing factor U2AF 65 KDa subunit	6e-08
d1wg1a_	88	d.58.7.1 (A:) Probable RNA-binding protein KIAA157	8e-08
d1wf0a_	88	d.58.7.1 (A:) TAR DNA-binding protein 43, TDP-43 {	1e-07
d1x4da1	89	d.58.7.1 (A:8-96) Matrin 3 {Mouse (Mus musculus) [	1e-07
d2adba1	108	d.58.7.1 (A:177-284) Polypyrimidine tract-binding	2e-07
d2cpia1	89	d.58.7.1 (A:101-189) E3 ubiquitin protein ligase C	3e-07
d2adca1	109	d.58.7.1 (A:335-443) Polypyrimidine tract-binding	3e-07
d1wexa_	104	d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprot	4e-07
d1p1ta_	104	d.58.7.1 (A:) Cleavage stimulation factor, 64 kda	9e-07
d2b0ga1	83	d.58.7.1 (A:1-83) Splicesomal U1A protein {Drosoph	1e-06
d1x4ea1	72	d.58.7.1 (A:8-79) RNA-binding motif, single-strand	1e-06
d2ghpa3	86	d.58.7.1 (A:206-291) U4/U6 snRNA-associated-splici	2e-06
d2cq2a1	101	d.58.7.1 (A:25-125) Alkylation repair AlkB homolog	2e-06
d1x4ha1	98	d.58.7.1 (A:8-105) RNA-binding protein 28 {Mouse (	2e-06
d1wi6a1	75	d.58.7.1 (A:69-143) Ribonucleoprotein PTB-binding	5e-06
d1o0pa_	104	d.58.7.1 (A:) Splicing factor U2AF 65 KDa subunit	6e-06
d2cq1a1	88	d.58.7.1 (A:51-138) Polypyrimidine tract-binding p	9e-05
d1wg4a_	98	d.58.7.1 (A:) Splicing factor, arginine/serine-ric	1e-04
d1x5oa1	101	d.58.7.1 (A:8-108) RNA-binding motif, single-stran	2e-04
d1zh5a2	85	d.58.7.1 (A:105-189) Lupus LA protein {Human (Homo	7e-04
d1weza_	102	d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprot	0.001
d1whxa_	111	d.58.7.1 (A:) Probable RNA-binding protein 19, Rbm	0.002
d2exfa1	42	g.40.1.1 (A:12-53) HIV nucleocapsid {Human immunod	0.003

>d1zkca1 b.62.1.1 (A:280-457) Peptidyl-prolyl cis-trans isomerase-like 2, Cyclophilin-60, PPI domain {Human (Homo sapiens) [TaxId: 9606]} Length = 178

class: All beta proteins
fold: Cyclophilin-like
superfamily: Cyclophilin-like
family: Cyclophilin (peptidylprolyl isomerase)
domain: Peptidyl-prolyl cis-trans isomerase-like 2, Cyclophilin-60, PPI domain
species: Human (Homo sapiens) [TaxId: 9606]

 Score =  147 bits (371), Expect = 6e-42
 Identities = 73/174 (41%), Positives = 106/174 (60%), Gaps = 10/174 (5%)

Query: 3   VLIVTSLGDIVVDLFVDKCPLTTKNFLKLCKIKYYNGCLFHTVQKDFTAQTGDPTGTGTG 62
           V + T+ GD+ ++L  D  P T +NF++LCK  YY+G +FH   ++F  Q GDPTGTGTG
Sbjct: 3   VRLHTNKGDLNLELHCDLTPKTCENFIRLCKKHYYDGTIFHRSIRNFVIQGGDPTGTGTG 62

Query: 63  GDSVYKFLYGEQARFFGDEIRVDLKHAKTGTVAMASAGENLNASQFYMTLRDNLDYLDEK 122
           G+S +        + F DE R +L H   G ++MA++G N N SQF++T R    YLD+K
Sbjct: 63  GESYWG-------KPFKDEFRPNLSHTGRGILSMANSGPNSNRSQFFITFRSC-AYLDKK 114

Query: 123 HTIFGEVAEGLETLSRINESFVDEKN-RPYKNIRIKHTYILEDPFDDP-AQLAE 174
           HTIFG V  G + L+ +     D K  RP + IRI  T +  DP+++  AQ+A+
Sbjct: 115 HTIFGRVVGGFDVLTAMENVESDPKTDRPKEEIRIDATTVFVDPYEEADAQIAQ 168

>d2ok3a1 b.62.1.1 (A:1-159) Cyclophilin-like protein PPIL3B {Human (Homo sapiens) [TaxId: 9606]} Length = 159

class: All beta proteins
fold: Cyclophilin-like
superfamily: Cyclophilin-like
family: Cyclophilin (peptidylprolyl isomerase)
domain: Cyclophilin-like protein PPIL3B
species: Human (Homo sapiens) [TaxId: 9606]

 Score =  140 bits (354), Expect = 7e-40
 Identities = 75/167 (44%), Positives = 102/167 (61%), Gaps = 9/167 (5%)

Query: 1   MSVLIVTSLGDIVVDLFVDKCPLTTKNFLKLCKIKYYNGCLFHTVQKDFTAQTGDPTGTG 60
           MSV + T +GDI +++F ++ P T +NFL LC   YYNGC+FH   K F  QTGDPTGTG
Sbjct: 1   MSVTLHTDVGDIKIEVFCERTPKTCENFLALCASNYYNGCIFHRNIKGFMVQTGDPTGTG 60

Query: 61  TGGDSVYKFLYGEQARFFGDEIRVDLKHAKTGTVAMASAGENLNASQFYMTLRDNLDYLD 120
            GG+S++          F DE    LKH   G V+MA+ G N N SQF++T      +LD
Sbjct: 61  RGGNSIWGK-------KFEDEYSEYLKHNVRGVVSMANNGPNTNGSQFFITYGKQ-PHLD 112

Query: 121 EKHTIFGEVAEGLETLSRINESFVDEKN-RPYKNIRIKHTYILEDPF 166
            K+T+FG+V +GLETL  + +  V+EK  RP  ++ IK   I  +PF
Sbjct: 113 MKYTVFGKVIDGLETLDELEKLPVNEKTYRPLNDVHIKDITIHANPF 159

>d1xwna1 b.62.1.1 (A:1-166) Peptidyl-prolyl cis-trans isomerase-like 1, PPIL1 {Human (Homo sapiens) [TaxId: 9606]} Length = 166

class: All beta proteins
fold: Cyclophilin-like
superfamily: Cyclophilin-like
family: Cyclophilin (peptidylprolyl isomerase)
domain: Peptidyl-prolyl cis-trans isomerase-like 1, PPIL1
species: Human (Homo sapiens) [TaxId: 9606]

 Score =  138 bits (348), Expect = 6e-39
 Identities = 67/158 (42%), Positives = 95/158 (60%), Gaps = 8/158 (5%)

Query: 3   VLIVTSLGDIVVDLFVDKCPLTTKNFLKLCKIKYYNGCLFHTVQKDFTAQTGDPTGTGTG 62
           V + TS+G IV++L+    P T KNF +L +  YYNG  FH + KDF  Q GDPTGTG G
Sbjct: 14  VYLETSMGIIVLELYWKHAPKTCKNFAELARRGYYNGTKFHRIIKDFMIQGGDPTGTGRG 73

Query: 63  GDSVYKFLYGEQARFFGDEIRVDLKHAKTGTVAMASAGENLNASQFYMTLRDNLDYLDEK 122
           G S+Y        + F DE+  DLK    G +AMA+AG + N SQF++TL     +LD K
Sbjct: 74  GASIYG-------KQFEDELHPDLKFTGAGILAMANAGPDTNGSQFFVTLAPT-QWLDGK 125

Query: 123 HTIFGEVAEGLETLSRINESFVDEKNRPYKNIRIKHTY 160
           HTIFG V +G+  ++R+     + ++RP  +++I   Y
Sbjct: 126 HTIFGRVCQGIGMVNRVGMVETNSQDRPVDDVKIIKAY 163

>d2fu0a1 b.62.1.1 (A:5-159) Putative cyclophilin PFE0505w {Plasmodium falciparum [TaxId: 5833]} Length = 155

class: All beta proteins
fold: Cyclophilin-like
superfamily: Cyclophilin-like
family: Cyclophilin (peptidylprolyl isomerase)
domain: Putative cyclophilin PFE0505w
species: Plasmodium falciparum [TaxId: 5833]

 Score =  113 bits (283), Expect = 4e-30
 Identities = 63/160 (39%), Positives = 94/160 (58%), Gaps = 8/160 (5%)

Query: 2   SVLIVTSLGDIVVDLFVDKCPLTTKNFLKLCKIKYYNGCLFHTVQKDFTAQTGDPTGTGT 61
           S +I T++GDI + LF  +C  T +NF       YYN C+FH V K F  QTGDP+G GT
Sbjct: 3   SAIIYTTMGDIHISLFYKECKKTVQNFSVHSINGYYNNCIFHRVIKHFMVQTGDPSGDGT 62

Query: 62  GGDSVYKFLYGEQARFFGDEIRVDLKHAKTGTVAMASAGENLNASQFYMTLRDNLDYLDE 121
           GG+S++          F DE    L H+K   V+MA+ G N N SQF++T      +LD 
Sbjct: 63  GGESIWG-------NEFEDEFFDHLNHSKPFMVSMANCGPNTNGSQFFITTVPC-PWLDF 114

Query: 122 KHTIFGEVAEGLETLSRINESFVDEKNRPYKNIRIKHTYI 161
           KHT+FG+V +G + +  I +   D++++P ++I+I +  I
Sbjct: 115 KHTVFGKVTQGSKIVLDIEKVRTDKRDKPLEDIKILNIKI 154

>d2b71a1 b.62.1.1 (A:23-191) Cyclophilin-like protein PY00693 {Plasmodium yoelii [TaxId: 5861]} Length = 169

class: All beta proteins
fold: Cyclophilin-like
superfamily: Cyclophilin-like
family: Cyclophilin (peptidylprolyl isomerase)
domain: Cyclophilin-like protein PY00693
species: Plasmodium yoelii [TaxId: 5861]

 Score =  113 bits (284), Expect = 6e-30
 Identities = 60/157 (38%), Positives = 89/157 (56%), Gaps = 8/157 (5%)

Query: 3   VLIVTSLGDIVVDLFVDKCPLTTKNFLKLCKIKYYNGCLFHTVQKDFTAQTGDPTGTGTG 62
           + I T+LGD  V+L+    P T  NF  LC++ +Y+  +FH V  +F  Q GDPTGTG G
Sbjct: 19  ITIYTNLGDFEVELYWYHSPKTCLNFYTLCEMGFYDNTIFHRVIPNFVIQGGDPTGTGKG 78

Query: 63  GDSVYKFLYGEQARFFGDEIRVDLKHAKTGTVAMASAGENLNASQFYMTLRDNLDYLDEK 122
           G S+Y         +F DEI  +LKH   G ++M++ G N N+SQF++TL     +LD K
Sbjct: 79  GKSIYG-------EYFEDEINKELKHTGAGILSMSNNGPNTNSSQFFITLAPL-PHLDGK 130

Query: 123 HTIFGEVAEGLETLSRINESFVDEKNRPYKNIRIKHT 159
           HTIF  V++ +  +  I        N+P  +++I  T
Sbjct: 131 HTIFARVSKNMTCIENIASVQTTATNKPIFDLKILRT 167

>d2cfea1 b.62.1.1 (A:1-162) Cyclophilin-like allergen Mal s 6 {Malassezia sympodialis [TaxId: 76777]} Length = 162

class: All beta proteins
fold: Cyclophilin-like
superfamily: Cyclophilin-like
family: Cyclophilin (peptidylprolyl isomerase)
domain: Cyclophilin-like allergen Mal s 6
species: Malassezia sympodialis [TaxId: 76777]

 Score =  113 bits (283), Expect = 6e-30
 Identities = 63/155 (40%), Positives = 76/155 (49%), Gaps = 14/155 (9%)

Query: 7   TSLGDIVVDLFVDKCPLTTKNFLKLC---KIKYYNGCLFHTVQKDFTAQTGDPT-GTGTG 62
             LG I   LF D  P T  NF  LC   K   Y G  FH V  DF  Q GD T G GTG
Sbjct: 13  APLGTIKFKLFDDVVPKTAANFRALCTGEKGFGYAGSHFHRVIPDFMLQGGDFTAGNGTG 72

Query: 63  GDSVYKFLYGEQARFFGDEIRVDLKHAKTGTVAMASAGENLNASQFYMTLRDNLDYLDEK 122
           G S+Y          F DE    LKH K G ++MA+AG N N SQF++T      +LD K
Sbjct: 73  GKSIYG-------AKFADE-NFQLKHNKPGLLSMANAGPNTNGSQFFITTVVT-SWLDGK 123

Query: 123 HTIFGEVAEGLETLSRINESFVDEKNRPYKNIRIK 157
           H +FGEV +G+  +  I E+      +P   I I 
Sbjct: 124 HVVFGEVIDGMNVVKAI-EAEGSGSGKPRSRIEIA 157

>d1w74a_ b.62.1.1 (A:) Peptidyl-prolyl cis-trans isomerase A, PpiA {Mycobacterium tuberculosis [TaxId: 1773]} Length = 171

class: All beta proteins
fold: Cyclophilin-like
superfamily: Cyclophilin-like
family: Cyclophilin (peptidylprolyl isomerase)
domain: Peptidyl-prolyl cis-trans isomerase A, PpiA
species: Mycobacterium tuberculosis [TaxId: 1773]

 Score =  110 bits (276), Expect = 8e-29
 Identities = 58/178 (32%), Positives = 86/178 (48%), Gaps = 28/178 (15%)

Query: 1   MSVLIVTSLGDIVVDLFVDKCPLTTKNFLKLCKIK---------------YYNGCLFHTV 45
            +  + T+ GDI + LF +  P T  NF+ L +                 +Y+G +FH V
Sbjct: 4   ATATLHTNRGDIKIALFGNHAPKTVANFVGLAQGTKDYSTQNASGGPSGPFYDGAVFHRV 63

Query: 46  QKDFTAQTGDPTGTGTGGDSVYKFLYGEQARFFGDEIRVDLKHAKTGTVAMASAGENLNA 105
            + F  Q GDPTGTG GG              F DE   +L+  K   +AMA+AG   N 
Sbjct: 64  IQGFMIQGGDPTGTGRGG----------PGYKFADEFHPELQFDKPYLLAMANAGPGTNG 113

Query: 106 SQFYMTLRDNLDYLDEKHTIFGEV--AEGLETLSRINESFVDEKNRPYKNIRIKHTYI 161
           SQF++T+     +L+ +HTIFGEV  AE    +  I+++  D  +RP   + I+   I
Sbjct: 114 SQFFITVGKT-PHLNRRHTIFGEVIDAESQRVVEAISKTATDGNDRPTDPVVIESITI 170

>d2a2na1 b.62.1.1 (A:483-646) Peptidylprolyl isomerase domain and WD repeat-containing protein 1, PPWD1, C-terminal domain {Human (Homo sapiens) [TaxId: 9606]} Length = 164

class: All beta proteins
fold: Cyclophilin-like
superfamily: Cyclophilin-like
family: Cyclophilin (peptidylprolyl isomerase)
domain: Peptidylprolyl isomerase domain and WD repeat-containing protein 1, PPWD1, C-terminal domain
species: Human (Homo sapiens) [TaxId: 9606]

 Score =  108 bits (271), Expect = 3e-28
 Identities = 67/161 (41%), Positives = 97/161 (60%), Gaps = 9/161 (5%)

Query: 2   SVLIVTSLGDIVVDLFVDKCPLTTKNFLKLCKIKYYNGCLFHTVQKDFTAQTGDPTGTGT 61
           S +I TS+GDI   LF  +CP T +NF    +  YYNG  FH + K F  QTGDPTGTG 
Sbjct: 11  SAIIHTSMGDIHTKLFPVECPKTVENFCVHSRNGYYNGHTFHRIIKGFMIQTGDPTGTGM 70

Query: 62  GGDSVYKFLYGEQARFFGDEIRVDLKHAKTGTVAMASAGENLNASQFYMTLRDNLDYLDE 121
           GG+S++          F DE    L+H +  T++MA+AG N N SQF++T+     +LD 
Sbjct: 71  GGESIWGG-------EFEDEFHSTLRHDRPYTLSMANAGSNTNGSQFFITVVPT-PWLDN 122

Query: 122 KHTIFGEVAEGLETLSRINESFVDEKN-RPYKNIRIKHTYI 161
           KHT+FG V +G+E + RI+   V+ K  +PY+++ I +  +
Sbjct: 123 KHTVFGRVTKGMEVVQRISNVKVNPKTDKPYEDVSIINITV 163

>d1h0pa_ b.62.1.1 (A:) Cyclophilin (eukaryotic) {Caenorhabditis elegans, isoform 5 [TaxId: 6239]} Length = 182

class: All beta proteins
fold: Cyclophilin-like
superfamily: Cyclophilin-like
family: Cyclophilin (peptidylprolyl isomerase)
domain: Cyclophilin (eukaryotic)
species: Caenorhabditis elegans, isoform 5 [TaxId: 6239]

 Score =  107 bits (267), Expect = 2e-27
 Identities = 55/171 (32%), Positives = 88/171 (51%), Gaps = 15/171 (8%)

Query: 7   TSLGDIVVDLFVDKCPLTTKNFLKLCKI---KYYNGCLFHTVQKDFTAQTGDPT-GTGTG 62
             +G IV+ LF    P T  NF++L K    + Y G  FH V  DF  Q GD T G GTG
Sbjct: 18  KPIGRIVIGLFGKTVPKTATNFIELAKKPKGEGYPGSKFHRVIADFMIQGGDFTRGDGTG 77

Query: 63  GDSVYKFLYGEQARFFGDEIRVDLKHAKTGTVAMASAGENLNASQFYMTLRDNLDYLDEK 122
           G S+Y   +         +    LKH   G ++MA+AG + N SQF++T      +LD +
Sbjct: 78  GRSIYGEKF--------ADENFKLKHYGAGWLSMANAGADTNGSQFFITTVKT-PWLDGR 128

Query: 123 HTIFGEVAEGLETLSRINESFVDEKNRPYKNIRIKHT--YILEDPFDDPAQ 171
           H +FG++ EG++ + +I ++     +RP +++ I  +    ++ PF    +
Sbjct: 129 HVVFGKILEGMDVVRKIEQTEKLPGDRPKQDVIIAASGHIAVDTPFSVERE 179

>d1a33a_ b.62.1.1 (A:) Cyclophilin (eukaryotic) {Nematode (Brugia malayi) [TaxId: 6279]} Length = 174

class: All beta proteins
fold: Cyclophilin-like
superfamily: Cyclophilin-like
family: Cyclophilin (peptidylprolyl isomerase)
domain: Cyclophilin (eukaryotic)
species: Nematode (Brugia malayi) [TaxId: 6279]

 Score =  104 bits (261), Expect = 8e-27
 Identities = 57/162 (35%), Positives = 81/162 (50%), Gaps = 21/162 (12%)

Query: 7   TSLGDIVVDLFVDKCPLTTKNFLKLC-----------KIKYYNGCLFHTVQKDFTAQTGD 55
              G IV++L+ D  P T  NFL LC           K  +Y G  FH V K+F  Q GD
Sbjct: 15  NLAGRIVMELYNDIAPRTCNNFLMLCTGMAGTGKISGKPLHYKGSTFHRVIKNFMIQGGD 74

Query: 56  PT-GTGTGGDSVYKFLYGEQARFFGDEIRVDLKHAKTGTVAMASAGENLNASQFYMTLRD 114
            T G GTGG+S+Y            D+    +KH +   V+MA+ G N N SQF++T   
Sbjct: 75  FTKGDGTGGESIYG--------GMFDDEEFVMKHDEPFVVSMANKGPNTNGSQFFITTTP 126

Query: 115 NLDYLDEKHTIFGEVAEGLETLSRINESFVDEKNRPYKNIRI 156
              +L+  H +FG+V  G E +++I     + KNRP  ++ I
Sbjct: 127 A-PHLNNIHVVFGKVVSGQEVVTKIEYLKTNSKNRPLADVVI 167

>d1lopa_ b.62.1.1 (A:) Peptidyl-prolyl cis-trans isomerase A, PpiA {Escherichia coli [TaxId: 562]} Length = 164

class: All beta proteins
fold: Cyclophilin-like
superfamily: Cyclophilin-like
family: Cyclophilin (peptidylprolyl isomerase)
domain: Peptidyl-prolyl cis-trans isomerase A, PpiA
species: Escherichia coli [TaxId: 562]

 Score =  103 bits (256), Expect = 3e-26
 Identities = 39/172 (22%), Positives = 68/172 (39%), Gaps = 20/172 (11%)

Query: 3   VLIVTSLGDIVVDLFVDKCPLTTKNFLKLCKIKYYNGCLFHTVQKDFTAQTGDPTGTGTG 62
           V   T+ GDIV+  F DK P T KNFL  C+  +YN  +FH V   F  Q G        
Sbjct: 2   VTFHTNHGDIVIKTFDDKAPETVKNFLDYCREGFYNNTIFHRVINGFMIQGGGFEPGMKQ 61

Query: 63  GDSVYKFLYGEQARFFGDEIRVDLKHAKTGTVAMASAGENLNASQFYMTLRDNLDY---- 118
             +              +E    LK+ +       +   +   +QF++ + DN       
Sbjct: 62  KATKEPIK---------NEANNGLKNTRGTLAMARTQAPHSATAQFFINVVDNDFLNFSG 112

Query: 119 ---LDEKHTIFGEVAEGLETLSRINESFVDE----KNRPYKNIRIKHTYILE 163
                  + +F EV +G++ + +I           ++ P +++ I+   + E
Sbjct: 113 ESLQGWGYCVFAEVVDGMDEVDKIKGVATGRSGMHQDVPKEDVIIESVTVSE 164

>d1xo7a_ b.62.1.1 (A:) Cyclophilin (eukaryotic) {Trypanosoma cruzi [TaxId: 5693]} Length = 166

class: All beta proteins
fold: Cyclophilin-like
superfamily: Cyclophilin-like
family: Cyclophilin (peptidylprolyl isomerase)
domain: Cyclophilin (eukaryotic)
species: Trypanosoma cruzi [TaxId: 5693]

 Score =  102 bits (254), Expect = 6e-26
 Identities = 48/154 (31%), Positives = 79/154 (51%), Gaps = 14/154 (9%)

Query: 7   TSLGDIVVDLFVDKCPLTTKNFLKLC---KIKYYNGCLFHTVQKDFTAQTGDPT-GTGTG 62
             +G +V+ LF +  P T +NF +L        Y G +FH V ++F  Q GD T   GTG
Sbjct: 17  EPVGRVVIGLFGNDVPKTVENFKQLASGENGFGYKGSIFHRVIRNFMIQGGDFTNFDGTG 76

Query: 63  GDSVYKFLYGEQARFFGDEIRVDLKHAKTGTVAMASAGENLNASQFYMTLRDNLDYLDEK 122
           G S+Y   + ++                 G V+MA+AG N N SQF++T      +LD +
Sbjct: 77  GKSIYGTRFDDENLKI---------KHFVGAVSMANAGPNSNGSQFFVTTAPT-PWLDGR 126

Query: 123 HTIFGEVAEGLETLSRINESFVDEKNRPYKNIRI 156
           H +FG+V EG++ + ++  +     ++P K ++I
Sbjct: 127 HVVFGKVVEGMDVVKKVENTKTGLNDKPKKAVKI 160

>d1qnga_ b.62.1.1 (A:) Cyclophilin (eukaryotic) {Plasmodium falciparum [TaxId: 5833]} Length = 170

class: All beta proteins
fold: Cyclophilin-like
superfamily: Cyclophilin-like
family: Cyclophilin (peptidylprolyl isomerase)
domain: Cyclophilin (eukaryotic)
species: Plasmodium falciparum [TaxId: 5833]

 Score =  101 bits (253), Expect = 9e-26
 Identities = 50/160 (31%), Positives = 82/160 (51%), Gaps = 20/160 (12%)

Query: 7   TSLGDIVVDLFVDKCPLTTKNFLKLC---------KIKYYNGCLFHTVQKDFTAQTGDP- 56
           ++ G I+ +LF D  P T +NF  LC         K  +Y   +FH +   F  Q GD  
Sbjct: 15  SNAGRIIFELFSDITPRTCENFRALCTGEKIGSRGKNLHYKNSIFHRIIPQFMCQGGDIT 74

Query: 57  TGTGTGGDSVYKFLYGEQARFFGDEIRVDLKHAKTGTVAMASAGENLNASQFYMTLRDNL 116
            G G+GG+S+Y   +         +   ++KH + G ++MA+AG N N+SQF++TL    
Sbjct: 75  NGNGSGGESIYGRSF--------TDENFNMKHDQPGLLSMANAGPNTNSSQFFITLVPC- 125

Query: 117 DYLDEKHTIFGEVAEGLETLSRINESFVDEKNRPYKNIRI 156
            +LD KH +FG+V EG+  +  + E    +     +++ I
Sbjct: 126 PWLDGKHVVFGKVIEGMNVVREM-EKEGAKSGYVKRSVVI 164

>d2rmca_ b.62.1.1 (A:) Cyclophilin (eukaryotic) {Mouse (Mus musculus), variant C [TaxId: 10090]} Length = 182

class: All beta proteins
fold: Cyclophilin-like
superfamily: Cyclophilin-like
family: Cyclophilin (peptidylprolyl isomerase)
domain: Cyclophilin (eukaryotic)
species: Mouse (Mus musculus), variant C [TaxId: 10090]

 Score =   99 bits (248), Expect = 6e-25
 Identities = 58/168 (34%), Positives = 85/168 (50%), Gaps = 15/168 (8%)

Query: 7   TSLGDIVVDLFVDKCPLTTKNFLKLCKIK---YYNGCLFHTVQKDFTAQTGDPT-GTGTG 62
             +G IV+ LF +  P T +NF+ L   +    Y G +FH V KDF  Q GD T   GTG
Sbjct: 19  KDVGRIVIGLFGNVVPKTVENFVALATGEKGYGYKGSIFHRVIKDFMIQGGDFTARDGTG 78

Query: 63  GDSVYKFLYGEQARFFGDEIRVDLKHAKTGTVAMASAGENLNASQFYMTLRDNLDYLDEK 122
           G S+Y   +         +    LKH   G V+MA+AG + N SQF++TL     +LD K
Sbjct: 79  GMSIYGETF--------PDENFKLKHYGIGWVSMANAGPDTNGSQFFITLTKP-TWLDGK 129

Query: 123 HTIFGEVAEGLETLSRINESFVDEKNRPYKNIRIKHTYILE--DPFDD 168
           H +FG+V +G+  +  I     D  +RP  +  I ++  ++   PF  
Sbjct: 130 HVVFGKVLDGMTVVHSIELQATDGHDRPLTDCTIVNSGKIDVKTPFVV 177

>d2igva1 b.62.1.1 (A:1-172) Cyclophilin (eukaryotic) {Caenorhabditis elegans, isoform 3 [TaxId: 6239]} Length = 172

class: All beta proteins
fold: Cyclophilin-like
superfamily: Cyclophilin-like
family: Cyclophilin (peptidylprolyl isomerase)
domain: Cyclophilin (eukaryotic)
species: Caenorhabditis elegans, isoform 3 [TaxId: 6239]

 Score = 99.5 bits (247), Expect = 7e-25
 Identities = 56/161 (34%), Positives = 80/161 (49%), Gaps = 21/161 (13%)

Query: 7   TSLGDIVVDLFVDKCPLTTKNFLKLC----------KIKYYNGCLFHTVQKDFTAQTGD- 55
            + G IV++L+ D  P T  NF  LC          K  ++ G  FH +  +F  Q GD 
Sbjct: 15  KASGRIVMELYDDVVPKTAGNFRALCTGENGIGKSGKPLHFKGSKFHRIIPNFMIQGGDF 74

Query: 56  PTGTGTGGDSVYKFLYGEQARFFGDEIRVDLKHAKTGTVAMASAGENLNASQFYMTLRDN 115
             G GTGG+S+Y          F DE     KH   G ++MA+AG N N SQF++     
Sbjct: 75  TRGNGTGGESIYG-------EKFPDENF-KEKHTGPGVLSMANAGPNTNGSQFFLCTVKT 126

Query: 116 LDYLDEKHTIFGEVAEGLETLSRINESFVDEKNRPYKNIRI 156
            ++LD KH +FG V EGL+ +  + ES   +  +P K+  I
Sbjct: 127 -EWLDGKHVVFGRVVEGLDVVKAV-ESNGSQSGKPVKDCMI 165

>d1ihga2 b.62.1.1 (A:2-196) Cyclophilin 40 isomerase domain {Cow (Bos taurus) [TaxId: 9913]} Length = 195

class: All beta proteins
fold: Cyclophilin-like
superfamily: Cyclophilin-like
family: Cyclophilin (peptidylprolyl isomerase)
domain: Cyclophilin 40 isomerase domain
species: Cow (Bos taurus) [TaxId: 9913]

 Score = 97.6 bits (242), Expect = 5e-24
 Identities = 56/175 (32%), Positives = 84/175 (48%), Gaps = 22/175 (12%)

Query: 7   TSLGDIVVDLFVDKCPLTTKNFLKLC-----------KIKYYNGCLFHTVQKDFTAQTGD 55
             +G IV++LF D  P T +NF  LC           K  ++ GC FH + K F  Q GD
Sbjct: 26  ERVGRIVLELFADIVPKTAENFRALCTGEKGIGPTTGKPLHFKGCPFHRIIKKFMIQGGD 85

Query: 56  -PTGTGTGGDSVYKFLYGEQARFFGDEIRVDLKHAKTGTVAMASAGENLNASQFYMTLRD 114
                GTGG+S+Y   + ++            KH K G ++MA+AG N N SQF++T   
Sbjct: 86  FSNQNGTGGESIYGEKFEDENF--------HYKHDKEGLLSMANAGSNTNGSQFFITTVP 137

Query: 115 NLDYLDEKHTIFGEVAEGLETLSRINESFVDEKNRPYKNIRIKHTYILEDPFDDP 169
              +LD KH +FG+V +G+     + E+   +  +P K   I     L++  D  
Sbjct: 138 T-PHLDGKHVVFGQVIKGMGVAKIL-ENVEVKGEKPAKLCVIAECGELKEGDDWG 190

>d2z6wa1 b.62.1.1 (A:2-165) Mitochondrial peptidyl-prolyl cis-trans isomerase, cyclophilin F {Human (Homo sapiens) [TaxId: 9606]} Length = 164

class: All beta proteins
fold: Cyclophilin-like
superfamily: Cyclophilin-like
family: Cyclophilin (peptidylprolyl isomerase)
domain: Mitochondrial peptidyl-prolyl cis-trans isomerase, cyclophilin F
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 93.0 bits (230), Expect = 9e-23
 Identities = 57/153 (37%), Positives = 76/153 (49%), Gaps = 12/153 (7%)

Query: 7   TSLGDIVVDLFVDKCPLTTKNFLKLC---KIKYYNGCLFHTVQKDFTAQTGDPTGTGTGG 63
             LG +V++L  D  P T +NF  LC   K   Y G  FH V   F  Q GD T     G
Sbjct: 14  KPLGRVVLELKADVVPKTAENFRALCTGEKGFGYKGSTFHRVIPSFMCQAGDFTNHNGTG 73

Query: 64  DSVYKFLYGEQARFFGDEIRVDLKHAKTGTVAMASAGENLNASQFYMTLRDNLDYLDEKH 123
               K +YG +      +    LKH   G ++MA+AG N N SQF++      D+LD KH
Sbjct: 74  G---KSIYGSRF----PDENFTLKHVGPGVLSMANAGPNTNGSQFFICTIKT-DWLDGKH 125

Query: 124 TIFGEVAEGLETLSRINESFVDEKNRPYKNIRI 156
            +FG V EG++ + +I ESF  +  R  K I I
Sbjct: 126 VVFGHVIEGMDVVKKI-ESFGSKSGRTSKKIVI 157

>d2c3ba1 b.62.1.1 (A:1-171) Cyclophilin (eukaryotic) {Aspergillus fumigatus [TaxId: 5085]} Length = 171

class: All beta proteins
fold: Cyclophilin-like
superfamily: Cyclophilin-like
family: Cyclophilin (peptidylprolyl isomerase)
domain: Cyclophilin (eukaryotic)
species: Aspergillus fumigatus [TaxId: 5085]

 Score = 92.6 bits (229), Expect = 2e-22
 Identities = 54/157 (34%), Positives = 73/157 (46%), Gaps = 16/157 (10%)

Query: 7   TSLGDIVVDLFVDKCPLTTKNFLKLCKIK---YYNGCLFHTVQKDFTAQTGDP-TGTGTG 62
           T +G IV +LF    P T KNF +LCK      Y    FH +  +F  Q GD   G GTG
Sbjct: 18  TKVGRIVFNLFDKDVPKTAKNFRELCKRPAGEGYRESTFHRIIPNFMIQGGDFTRGNGTG 77

Query: 63  GDSVYKFLYGEQARFFGDEIRVDLKHAKTGTVAMASAGENLNASQFYMTLRDNLDYLDEK 122
           G S+Y   +         +     KH K G ++MA+AG N N SQF++T      +LD K
Sbjct: 78  GRSIYGDKF--------ADENFSRKHDKKGILSMANAGPNTNGSQFFITTAVT-SWLDGK 128

Query: 123 HTIFGEVAE--GLETLSRINESFVDEKN-RPYKNIRI 156
           H +FGEVA+      +  I        + R     +I
Sbjct: 129 HVVFGEVADEKSYSVVKEIEALGSSSGSVRSNTRPKI 165

>d2r99a1 b.62.1.1 (A:139-299) Mitochondrial peptidyl-prolyl cis-trans isomerase, cyclophilin F {Human (Homo sapiens) [TaxId: 9606]} Length = 161

class: All beta proteins
fold: Cyclophilin-like
superfamily: Cyclophilin-like
family: Cyclophilin (peptidylprolyl isomerase)
domain: Mitochondrial peptidyl-prolyl cis-trans isomerase, cyclophilin F
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 91.1 bits (225), Expect = 5e-22
 Identities = 56/154 (36%), Positives = 79/154 (51%), Gaps = 14/154 (9%)

Query: 7   TSLGDIVVDLFVDKCPLTTKNFLKLC---KIKYYNGCLFHTVQKDFTAQTGDPT-GTGTG 62
              G I + L  D  P+T +NF  LC   K   + G  FH +   F  Q GD T   GTG
Sbjct: 13  KPAGRIQMLLRSDVVPMTAENFRCLCTHEKGFGFKGSSFHRIIPQFMCQGGDFTNHNGTG 72

Query: 63  GDSVYKFLYGEQARFFGDEIRVDLKHAKTGTVAMASAGENLNASQFYMTLRDNLDYLDEK 122
           G S+Y   +        D+    LKH   G ++MA++G N N SQF++T     D+LD K
Sbjct: 73  GKSIYGKKF--------DDENFILKHTGPGLLSMANSGPNTNGSQFFLTCDKT-DWLDGK 123

Query: 123 HTIFGEVAEGLETLSRINESFVDEKNRPYKNIRI 156
           H +FGEV EGL+ L +I E+   +  +P + + I
Sbjct: 124 HVVFGEVTEGLDVLRQI-EAQGSKDGKPKQKVII 156

>d1v9ta_ b.62.1.1 (A:) Peptidyl-prolyl cis-trans isomerase A, PpiA {Escherichia coli [TaxId: 562]} Length = 166

class: All beta proteins
fold: Cyclophilin-like
superfamily: Cyclophilin-like
family: Cyclophilin (peptidylprolyl isomerase)
domain: Peptidyl-prolyl cis-trans isomerase A, PpiA
species: Escherichia coli [TaxId: 562]

 Score = 88.1 bits (217), Expect = 5e-21
 Identities = 38/168 (22%), Positives = 70/168 (41%), Gaps = 17/168 (10%)

Query: 3   VLIVTSLGDIVVDLFVDKCPLTTKNFLKLCKIKYYNGCLFHTVQKDFTAQTGDPTGTGTG 62
           VL+ TS G+I ++L   K P++ +NF+      +YN   FH V   F  Q G  T     
Sbjct: 7   VLLTTSAGNIELELDKQKAPVSVQNFVDYVNSGFYNNTTFHRVIPGFMIQGGGFTEQMQQ 66

Query: 63  GDSVYKFLYGEQARFFGDEIRVDLKHAKTGTVAMASAGENLNASQFYMTLRD----NLDY 118
                            +E    L++ +       +A ++   SQF++ + D    +   
Sbjct: 67  KKPNPP---------IKNEADNGLRNTRGTIAMARTADKDSATSQFFINVADNAFLDHGQ 117

Query: 119 LDEKHTIFGEVAEGLETLSRINESFVDEK----NRPYKNIRIKHTYIL 162
            D  + +FG+V +G++   +I++    +     N P K + I    +L
Sbjct: 118 RDFGYAVFGKVVKGMDVADKISQVPTHDVGPYQNVPSKPVVILSATVL 165

>d1qoia_ b.62.1.1 (A:) Cyclophilin (eukaryotic) {Human (Homo sapiens), U4/U6 snRNP-specific cyclophilin snucyp-20 [TaxId: 9606]} Length = 173

class: All beta proteins
fold: Cyclophilin-like
superfamily: Cyclophilin-like
family: Cyclophilin (peptidylprolyl isomerase)
domain: Cyclophilin (eukaryotic)
species: Human (Homo sapiens), U4/U6 snRNP-specific cyclophilin snucyp-20 [TaxId: 9606]

 Score = 86.5 bits (213), Expect = 2e-20
 Identities = 47/158 (29%), Positives = 71/158 (44%), Gaps = 16/158 (10%)

Query: 7   TSLGDIVVDLFVDKCPLTTKNFLKLC--------KIKYYNGCLFHTVQKDFTAQTGDPTG 58
             +G + ++LF D  P T +NF + C            Y G  FH V KDF  Q GD   
Sbjct: 18  QEVGRMKIELFADVVPKTAENFRQFCTGEFRKDGVPIGYKGSTFHRVIKDFMIQGGDFV- 76

Query: 59  TGTGGDSVYKFLYGEQARFFGDEIRVDLKHAKTGTVAMASAGENLNASQFYMTLRDNLDY 118
              G  +    +Y      F DE       A  G ++MA++G + N  QF++T     D+
Sbjct: 77  --NGDGTGVASIYRG---PFADENFKLRHSAP-GLLSMANSGPSTNGCQFFITCSKC-DW 129

Query: 119 LDEKHTIFGEVAEGLETLSRINESFVDEKNRPYKNIRI 156
           LD KH +FG++ +GL  + +I        N+P   + I
Sbjct: 130 LDGKHVVFGKIIDGLLVMRKIENVPTGPNNKPKLPVVI 167

>d1z81a1 b.62.1.1 (A:25-210) Cyclophilin (eukaryotic) {Plasmodium yoelii [TaxId: 5861]} Length = 186

class: All beta proteins
fold: Cyclophilin-like
superfamily: Cyclophilin-like
family: Cyclophilin (peptidylprolyl isomerase)
domain: Cyclophilin (eukaryotic)
species: Plasmodium yoelii [TaxId: 5861]

 Score = 84.5 bits (208), Expect = 1e-19
 Identities = 44/161 (27%), Positives = 69/161 (42%), Gaps = 19/161 (11%)

Query: 7   TSLGDIVVDLFVDKCPLTTKNFLKLCKIKY--------YNGCLFHTVQKDFTAQTGDPTG 58
             LG    +LF +  P T++NF + C  +Y        Y   +FH V K+F  Q GD   
Sbjct: 28  NFLGKFKFELFQNIVPKTSENFRQFCTGEYKVNNLPVGYKNTIFHRVIKEFMIQGGDFIN 87

Query: 59  TGTGGDSVYKFLYGEQARFFGDEIRVDLKHAKTGTVAMASAGENLNASQFYMTLRDNLDY 118
                                D+   D+KH K G ++MA++G N N  QF++T     ++
Sbjct: 88  HNG-------SGSLSIYGEKFDDENFDIKHDKEGLLSMANSGPNTNGCQFFITT-KKCEW 139

Query: 119 LDEKHTIFGEVAEG--LETLSRINESFVDEKN-RPYKNIRI 156
           LD K+ +FG + +   L  L +I    V     +P   I +
Sbjct: 140 LDGKNVVFGRIIDNDSLLLLKKIENVSVTPYIYKPKIPINV 180

>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 = 73.8 bits (181), Expect = 5e-17
 Identities = 24/76 (31%), Positives = 40/76 (52%)

Query: 245 LFVCKLNPVTEDEDLHTIFSRFGTVVSAEIIRDFKTGDSLNYAFIEFENRQACERAYSKM 304
           L+V  L+P   +  L+  FS  G ++S  + RD  T  SL YA++ F+     ERA   M
Sbjct: 3   LYVGDLHPDVTEAMLYEKFSPAGPILSIRVCRDMITRRSLGYAYVNFQQPADAERALDTM 62

Query: 305 DNALIDDRRIHVDFSQ 320
           +  +I  + + + +SQ
Sbjct: 63  NFDVIKGKPVRIMWSQ 78

>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 = 68.0 bits (166), Expect = 7e-15
 Identities = 15/85 (17%), Positives = 41/85 (48%), Gaps = 2/85 (2%)

Query: 239 KPPENVLFVCKLNPVTEDEDLHTIFSRFGTVVSAEIIRDFK-TGDSLNYAFIEFENRQAC 297
           K   + + V  +       ++  +FS FG + +  + +    TG    + F++F  +Q  
Sbjct: 5   KQTTSKILVRNIPFQANQREIRELFSTFGELKTVRLPKKMTGTGAHRGFGFVDFITKQDA 64

Query: 298 ERAYSKMDN-ALIDDRRIHVDFSQS 321
           ++A++ + +   +  RR+ ++++ S
Sbjct: 65  KKAFNALCHSTHLYGRRLVLEWADS 89

>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 = 66.5 bits (162), Expect = 2e-14
 Identities = 21/77 (27%), Positives = 37/77 (48%), Gaps = 1/77 (1%)

Query: 245 LFVCKLNPVTEDEDLHTIFSRFGTVVSAEIIRDFKTGDSLNYAFIEFENRQACERAYSKM 304
           L V  L+    D D+  +F+ FGT+  A +  D  +G SL  A + FE +    +A  + 
Sbjct: 3   LLVSNLDFGVSDADIQELFAEFGTLKKAAVHYDR-SGRSLGTADVHFERKADALKAMKQY 61

Query: 305 DNALIDDRRIHVDFSQS 321
           +   +D R +++    S
Sbjct: 62  NGVPLDGRPMNIQLVTS 78

>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 = 66.6 bits (162), Expect = 2e-14
 Identities = 22/76 (28%), Positives = 42/76 (55%)

Query: 245 LFVCKLNPVTEDEDLHTIFSRFGTVVSAEIIRDFKTGDSLNYAFIEFENRQACERAYSKM 304
           L V  L     D +L+ +F   G + +  I+RD+KTG S  YAF++F +    +RA   +
Sbjct: 5   LIVNYLPQDMTDRELYALFRAIGPINTCRIMRDYKTGYSYGYAFVDFTSEMDSQRAIKVL 64

Query: 305 DNALIDDRRIHVDFSQ 320
           +   + ++R+ V +++
Sbjct: 65  NGITVRNKRLKVSYAR 80

>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 = 67.2 bits (164), Expect = 2e-14
 Identities = 21/114 (18%), Positives = 48/114 (42%), Gaps = 18/114 (15%)

Query: 229 SIGDIPDADIKPPENVLFVCKLNP-VTEDEDLHTIFSRFGTVVSAEIIRDFKTGDSLNYA 287
           S G     D +   + +F+  LN  V +  D+  IFS++G +V   + +         +A
Sbjct: 2   SSGSSGKTDPRSMNSRVFIGNLNTLVVKKSDVEAIFSKYGKIVGCSVHK--------GFA 53

Query: 288 FIEFENRQACERAYSKMDNALIDDRRIHVDFSQSVSKLWNQFRRRDHQTGKGKG 341
           F+++ N +    A +  D  +I  + + ++ +            + +++G   G
Sbjct: 54  FVQYVNERNARAAVAGEDGRMIAGQVLDINLAA---------EPKVNRSGPSSG 98

>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 = 66.1 bits (161), Expect = 3e-14
 Identities = 22/76 (28%), Positives = 39/76 (51%), Gaps = 2/76 (2%)

Query: 245 LFVCKLNPVTEDEDLHTIFSRFGTVVSAEIIRDFKTGDSLNYAFIEFENRQACERAYSKM 304
           L+V  L     D+ L TIF ++G++V   I+RD  TG     AF+ +  R+  + A S +
Sbjct: 9   LYVTNLPRTITDDQLDTIFGKYGSIVQKNILRDKLTGRPRGVAFVRYNKREEAQEAISAL 68

Query: 305 DNALID--DRRIHVDF 318
           +N + +   + + V  
Sbjct: 69  NNVIPEGGSQPLSVRL 84

>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 = 64.7 bits (157), Expect = 9e-14
 Identities = 24/77 (31%), Positives = 39/77 (50%)

Query: 240 PPENVLFVCKLNPVTEDEDLHTIFSRFGTVVSAEIIRDFKTGDSLNYAFIEFENRQACER 299
            P   L V  L+  T + DL  +FS++G +    I+ D ++  S  +AF+ FEN    + 
Sbjct: 7   DPNCCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKE 66

Query: 300 AYSKMDNALIDDRRIHV 316
           A  + +   +D RRI V
Sbjct: 67  AKERANGMELDGRRIRV 83

>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 = 64.7 bits (157), Expect = 1e-13
 Identities = 20/83 (24%), Positives = 40/83 (48%), Gaps = 3/83 (3%)

Query: 245 LFVCKLNPVTEDEDLHTIFSRFGTVVSAEII---RDFKTGDSLNYAFIEFENRQACERAY 301
           LF+  LN  T +E L  +FS+ G + S  I           S+ + F+E++  +  ++A 
Sbjct: 1   LFIKNLNFSTTEETLKGVFSKVGAIKSCTISKKKNKAGVLLSMGFGFVEYKKPEQAQKAL 60

Query: 302 SKMDNALIDDRRIHVDFSQSVSK 324
            ++    +D  ++ V  S+  +K
Sbjct: 61  KQLQGHTVDGHKLEVRISERATK 83

>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 = 64.3 bits (156), Expect = 2e-13
 Identities = 21/91 (23%), Positives = 44/91 (48%), Gaps = 1/91 (1%)

Query: 234 PDADIKPPENVLFVCKLNPVTEDEDLHTIFSRFGTVVSAEIIRDFKTGDSLNYAFIEFEN 293
           P ++ +  +  ++V  L+    +  L  +F + G VV+  + +D  TG    Y F+EF +
Sbjct: 2   PISE-RNQDATVYVGGLDEKVSEPLLWELFLQAGPVVNTHMPKDRVTGQHQGYGFVEFLS 60

Query: 294 RQACERAYSKMDNALIDDRRIHVDFSQSVSK 324
            +  + A   MD   +  + I V+ + + +K
Sbjct: 61  EEDADYAIKIMDMIKLYGKPIRVNKASAHNK 91

>d2cqba1 d.58.7.1 (A:1-89) Peptidyl-prolyl cis-trans isomerase E, N-terminal domain {Human (Homo sapiens) [TaxId: 9606]} Length = 89

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Peptidyl-prolyl cis-trans isomerase E, N-terminal domain
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 63.1 bits (153), Expect = 4e-13
 Identities = 23/83 (27%), Positives = 41/83 (49%)

Query: 238 IKPPENVLFVCKLNPVTEDEDLHTIFSRFGTVVSAEIIRDFKTGDSLNYAFIEFENRQAC 297
           +   + VL+V  L    +D+ LH  F  FG +   +I  D++T     +AF+EFE  +  
Sbjct: 1   MATTKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDA 60

Query: 298 ERAYSKMDNALIDDRRIHVDFSQ 320
             A   M+ + +  R I V+ ++
Sbjct: 61  AAAIDNMNESELFGRTIRVNLAK 83

>d1fxla1 d.58.7.1 (A:37-118) Hu antigen D (Hud) {Human (Homo sapiens) [TaxId: 9606]} Length = 82

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Hu antigen D (Hud)
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 62.0 bits (150), Expect = 8e-13
 Identities = 19/76 (25%), Positives = 39/76 (51%)

Query: 245 LFVCKLNPVTEDEDLHTIFSRFGTVVSAEIIRDFKTGDSLNYAFIEFENRQACERAYSKM 304
           L V  L      E+  ++F   G + S +++RD  TG SL Y F+ + + +  E+A + +
Sbjct: 5   LIVNYLPQNMTQEEFRSLFGSIGEIESCKLVRDKITGQSLGYGFVNYIDPKDAEKAINTL 64

Query: 305 DNALIDDRRIHVDFSQ 320
           +   +  + I V +++
Sbjct: 65  NGLRLQTKTIKVSYAR 80

>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 = 62.7 bits (152), Expect = 9e-13
 Identities = 17/98 (17%), Positives = 42/98 (42%), Gaps = 5/98 (5%)

Query: 240 PPE--NVLFVCKLNPVTEDEDLHTIFSRFGTVVSAEIIRDFKTGDSLNYAFIEFENRQAC 297
           PPE   +L++  L      E+++ IF ++G +     IR   T ++   A++ +E+    
Sbjct: 3   PPEVNRILYIRNLPYKITAEEMYDIFGKYGPIRQ---IRVGNTPETRGTAYVVYEDIFDA 59

Query: 298 ERAYSKMDNALIDDRRIHVDFSQSVSKLWNQFRRRDHQ 335
           + A   +    + +R + V +  +         ++  +
Sbjct: 60  KNACDHLSGFNVCNRYLVVLYYNANRAFQKMDTKKKEE 97

>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 = 61.9 bits (150), Expect = 1e-12
 Identities = 19/80 (23%), Positives = 38/80 (47%)

Query: 245 LFVCKLNPVTEDEDLHTIFSRFGTVVSAEIIRDFKTGDSLNYAFIEFENRQACERAYSKM 304
           L+V  L+  T +E ++ +FS+ G +    +  D     +  + F+E+ +R   E A   +
Sbjct: 10  LYVGNLSFYTTEEQIYELFSKSGDIKKIIMGLDKMKKTACGFCFVEYYSRADAENAMRYI 69

Query: 305 DNALIDDRRIHVDFSQSVSK 324
           +   +DDR I  D+     +
Sbjct: 70  NGTRLDDRIIRTDWDAGFKE 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 = 61.2 bits (148), Expect = 2e-12
 Identities = 12/80 (15%), Positives = 32/80 (40%)

Query: 239 KPPENVLFVCKLNPVTEDEDLHTIFSRFGTVVSAEIIRDFKTGDSLNYAFIEFENRQACE 298
           KP   ++ V  +      +++   F  +  +  +  ++  + G     A + FE+R    
Sbjct: 6   KPGPTIIKVQNMPFTVSIDEILDFFYGYQVIPGSVCLKYNEKGMPTGEAMVAFESRDEAT 65

Query: 299 RAYSKMDNALIDDRRIHVDF 318
            A   +++  I  R++ +  
Sbjct: 66  AAVIDLNDRPIGSRKVKLVL 85

>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 = 59.2 bits (143), Expect = 6e-12
 Identities = 17/74 (22%), Positives = 31/74 (41%), Gaps = 1/74 (1%)

Query: 245 LFVCKLNPVTEDEDLHTIFSRFGTVVSAEIIRDFKTGDSLNYAFIEFENRQACERAYSKM 304
           +F+  L+  T  E L   F +FG V    ++RD  T  S  + F+ F ++   ++     
Sbjct: 3   MFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQAGVDKVL-AQ 61

Query: 305 DNALIDDRRIHVDF 318
               +D + I    
Sbjct: 62  SRHELDSKTIDPKV 75

>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 = 59.7 bits (144), Expect = 6e-12
 Identities = 21/77 (27%), Positives = 36/77 (46%), Gaps = 2/77 (2%)

Query: 245 LFVCKLNPVTEDEDLHTIFSRFGTVVSAEIIRDFKTGDSLNYAFIEFENRQACERAYSKM 304
           L+V  L      ++L  +FS++G ++++ I+ D  TG S    FI F+ R   E A   +
Sbjct: 9   LYVSGLPKTMTQKELEQLFSQYGRIITSRILVDQVTGVSRGVGFIRFDKRIEAEEAIKGL 68

Query: 305 DNALID--DRRIHVDFS 319
           +          I V F+
Sbjct: 69  NGQKPSGATEPITVKFA 85

>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 = 58.9 bits (142), Expect = 9e-12
 Identities = 20/90 (22%), Positives = 36/90 (40%), Gaps = 6/90 (6%)

Query: 235 DADIKPPENVLFVCKLNPVTEDEDLHTIFSRFGTVVSAEIIRDFKTGDSLNYAFIEFENR 294
           D D      +L+V  L   T +E +   F+        +     +     +YAF+ F NR
Sbjct: 1   DEDTMSSVKILYVRNLMLSTSEEMIEKEFNNI------KPGAVERVKKIRDYAFVHFSNR 54

Query: 295 QACERAYSKMDNALIDDRRIHVDFSQSVSK 324
           +    A   ++  ++D   I V  ++ V K
Sbjct: 55  EDAVEAMKALNGKVLDGSPIEVTLAKPVDK 84

>d2cpza1 d.58.7.1 (A:383-484) CUG triplet repeat RNA-binding protein 1 {Human (Homo sapiens) [TaxId: 9606]} Length = 102

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: CUG triplet repeat RNA-binding protein 1
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 59.3 bits (143), Expect = 1e-11
 Identities = 28/94 (29%), Positives = 45/94 (47%)

Query: 228 ESIGDIPDADIKPPENVLFVCKLNPVTEDEDLHTIFSRFGTVVSAEIIRDFKTGDSLNYA 287
           +SIG        P    LF+  L     D+DL  +F  FG VVSA++  D +T  S  + 
Sbjct: 4   QSIGAAGSQKEGPEGANLFIYHLPQEFGDQDLLQMFMPFGNVVSAKVFIDKQTNLSKCFG 63

Query: 288 FIEFENRQACERAYSKMDNALIDDRRIHVDFSQS 321
           F+ ++N  + + A   M+   I  +R+ V   +S
Sbjct: 64  FVSYDNPVSAQAAIQSMNGFQIGMKRLKVQLKRS 97

>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 = 58.9 bits (142), Expect = 1e-11
 Identities = 18/80 (22%), Positives = 41/80 (51%)

Query: 245 LFVCKLNPVTEDEDLHTIFSRFGTVVSAEIIRDFKTGDSLNYAFIEFENRQACERAYSKM 304
           LF+  L     D+ +  + + FG + +  +++D  TG S  YAF E+ +    ++A + +
Sbjct: 4   LFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIAGL 63

Query: 305 DNALIDDRRIHVDFSQSVSK 324
           +   + D+++ V  +   +K
Sbjct: 64  NGMQLGDKKLLVQRASVGAK 83

>d1x4ga1 d.58.7.1 (A:8-103) Nucleolysin TIAR {Human (Homo sapiens) [TaxId: 9606]} Length = 96

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nucleolysin TIAR
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 58.4 bits (141), Expect = 2e-11
 Identities = 11/82 (13%), Positives = 30/82 (36%), Gaps = 6/82 (7%)

Query: 240 PPENVLFVCKLNPVTEDEDLHTIFSRFGTVVSAEIIRDFKTGDSLNYAFIEFENRQACER 299
           P    ++   +     D+ +   FS FG ++   +  +        Y+F+ F   ++   
Sbjct: 16  PKNCTVYCGGIASGLTDQLMRQTFSPFGQIMEIRVFPEK------GYSFVRFSTHESAAH 69

Query: 300 AYSKMDNALIDDRRIHVDFSQS 321
           A   ++   I+   +   + + 
Sbjct: 70  AIVSVNGTTIEGHVVKCYWGKE 91

>d1x5ta1 d.58.7.1 (A:8-90) Splicing factor 3B subunit 4 {Human (Homo sapiens) [TaxId: 9606]} Length = 83

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicing factor 3B subunit 4
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 57.4 bits (138), Expect = 3e-11
 Identities = 25/78 (32%), Positives = 42/78 (53%), Gaps = 1/78 (1%)

Query: 245 LFVCKLNPVTEDEDLHTIFSRFGTVVSAEII-RDFKTGDSLNYAFIEFENRQACERAYSK 303
           +F+  L+P  +++ L+  FS FG ++    I RD  TG+S  YAFI F +  A + A   
Sbjct: 1   IFIGNLDPEIDEKLLYDTFSAFGVILQTPKIMRDPDTGNSKGYAFINFASFDASDAAIEA 60

Query: 304 MDNALIDDRRIHVDFSQS 321
           M+   + +R I V ++  
Sbjct: 61  MNGQYLCNRPITVSYAFK 78

>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 = 57.4 bits (138), Expect = 4e-11
 Identities = 21/82 (25%), Positives = 39/82 (47%)

Query: 239 KPPENVLFVCKLNPVTEDEDLHTIFSRFGTVVSAEIIRDFKTGDSLNYAFIEFENRQACE 298
                 + V  L+  T + DL  +F  FG++    + +D  TG S  +AFI F  R+   
Sbjct: 5   ADDNATIRVTNLSEDTRETDLQELFRPFGSISRIYLAKDKTTGQSKGFAFISFHRREDAA 64

Query: 299 RAYSKMDNALIDDRRIHVDFSQ 320
           RA + +     D   ++V++++
Sbjct: 65  RAIAGVSGFGYDHLILNVEWAK 86

>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 = 57.4 bits (138), Expect = 4e-11
 Identities = 14/85 (16%), Positives = 35/85 (41%), Gaps = 1/85 (1%)

Query: 241 PENVLFVCKLNP-VTEDEDLHTIFSRFGTVVSAEIIRDFKTGDSLNYAFIEFENRQACER 299
           P + +++  LN  + +DE   ++ + F        I   ++      AF+ F+   +   
Sbjct: 2   PNHTIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSRSLKMRGQAFVIFKEVSSATN 61

Query: 300 AYSKMDNALIDDRRIHVDFSQSVSK 324
           A   M      D+ + + ++++ S 
Sbjct: 62  ALRSMQGFPFYDKPMRIQYAKTDSD 86

>d1l3ka1 d.58.7.1 (A:8-91) Nuclear ribonucleoprotein A1 (RNP A1, UP1) {Human (Homo sapiens) [TaxId: 9606]} Length = 84

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nuclear ribonucleoprotein A1 (RNP A1, UP1)
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 57.0 bits (137), Expect = 5e-11
 Identities = 22/85 (25%), Positives = 39/85 (45%), Gaps = 3/85 (3%)

Query: 239 KPPENV--LFVCKLNPVTEDEDLHTIFSRFGTVVSAEIIRDFKTGDSLNYAFIEFENRQA 296
           K PE +  LF+  L+  T DE L + F ++GT+    ++RD  T  S  + F+ +   + 
Sbjct: 1   KEPEQLRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEE 60

Query: 297 CERAYSKMDNALIDDRRIHVDFSQS 321
            + A        +D R +    + S
Sbjct: 61  VDAAM-NARPHKVDGRVVEPKRAVS 84

>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 = 56.7 bits (136), Expect = 7e-11
 Identities = 19/79 (24%), Positives = 39/79 (49%)

Query: 243 NVLFVCKLNPVTEDEDLHTIFSRFGTVVSAEIIRDFKTGDSLNYAFIEFENRQACERAYS 302
            +LFV  ++   +++++   F  +G + +  +  D +TG S  YA +E+E  +    A  
Sbjct: 8   WILFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYETHKQALAAKE 67

Query: 303 KMDNALIDDRRIHVDFSQS 321
            ++ A I  + I VD+   
Sbjct: 68  ALNGAEIMGQTIQVDWCFV 86

>d1cvja2 d.58.7.1 (A:91-179) Poly(A)-binding protein {Human (Homo sapiens) [TaxId: 9606]} Length = 89

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Poly(A)-binding protein
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 56.6 bits (136), Expect = 8e-11
 Identities = 26/83 (31%), Positives = 47/83 (56%), Gaps = 2/83 (2%)

Query: 239 KPPENVLFVCKLNPVTEDEDLHTIFSRFGTVVSAEIIRDFKTGDSLNYAFIEFENRQACE 298
           K     +F+  L+   +++ L+  FS FG ++S +++ D     S  Y F+ FE ++A E
Sbjct: 5   KSGVGNIFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDENG--SKGYGFVHFETQEAAE 62

Query: 299 RAYSKMDNALIDDRRIHVDFSQS 321
           RA  KM+  L++DR++ V   +S
Sbjct: 63  RAIEKMNGMLLNDRKVFVGRFKS 85

>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 = 56.5 bits (136), Expect = 8e-11
 Identities = 21/84 (25%), Positives = 38/84 (45%), Gaps = 6/84 (7%)

Query: 242 ENVLFVCKLNPVTEDEDLHTIFSRFGTVVSAEIIRDFKTGDSLNYAFIEFENRQACERAY 301
            + LFV  L P   +E++  +F ++G      I +D        + FI  E R   E A 
Sbjct: 8   RSRLFVGNLPPDITEEEMRKLFEKYGKAGEVFIHKDK------GFGFIRLETRTLAEIAK 61

Query: 302 SKMDNALIDDRRIHVDFSQSVSKL 325
            ++DN  +  +++ V F+   + L
Sbjct: 62  VELDNMPLRGKQLRVRFACHSASL 85

>d1jmta_ d.58.7.3 (A:) U2AF35 (35 KDa subunit) {Human (Homo sapiens) [TaxId: 9606]} Length = 104

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Splicing factor U2AF subunits
domain: U2AF35 (35 KDa subunit)
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 57.0 bits (137), Expect = 8e-11
 Identities = 10/65 (15%), Positives = 27/65 (41%), Gaps = 1/65 (1%)

Query: 255 EDEDLHTIFSRFGTVVSAEIIRDFKTGDSLNYAFIEFENRQACERAYSKMDNALIDDRRI 314
            +E    +  ++G V    +  +      +   +++F   +  E+A   ++N   + + I
Sbjct: 40  FEEVFTEMEEKYGEVEEMNVCDN-LGDHLVGNVYVKFRREEDAEKAVIDLNNRWFNGQPI 98

Query: 315 HVDFS 319
           H + S
Sbjct: 99  HAELS 103

>d2cq3a1 d.58.7.1 (A:110-202) RNA-binding protein 9 {Human (Homo sapiens) [TaxId: 9606]} Length = 93

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding protein 9
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 56.2 bits (135), Expect = 1e-10
 Identities = 23/87 (26%), Positives = 43/87 (49%), Gaps = 2/87 (2%)

Query: 235 DADIKPPENVLFVCKLNPVTEDEDLHTIFSRFGTVVSAEIIRDFKTGDSLNYAFIEFENR 294
           +++ K     L V  +     D DL  +F +FG ++  EII +     S  + F+ FEN 
Sbjct: 4   NSESKSTPKRLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFN--ERGSKGFGFVTFENS 61

Query: 295 QACERAYSKMDNALIDDRRIHVDFSQS 321
              +RA  K+   +++ R+I V+ + +
Sbjct: 62  ADADRAREKLHGTVVEGRKIEVNNATA 88

>d2cqga1 d.58.7.1 (A:96-185) TAR DNA-binding protein 43, TDP-43 {Human (Homo sapiens) [TaxId: 9606]} Length = 90

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: TAR DNA-binding protein 43, TDP-43
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 56.1 bits (135), Expect = 1e-10
 Identities = 23/77 (29%), Positives = 35/77 (45%), Gaps = 2/77 (2%)

Query: 245 LFVCKLNPVTEDEDLHTIFSRFGTVVSAEIIRDFKTGDSLNYAFIEFENRQACERAYSKM 304
           L V  L   T ++DL   FS FG V+  ++ +D KTG S  + F+ F   +   +  S+ 
Sbjct: 11  LIVLGLPWKTTEQDLKEYFSTFGEVLMVQVKKDLKTGHSKGFGFVRFTEYETQVKVMSQR 70

Query: 305 DNALIDDRRIHVDFSQS 321
              +ID R        S
Sbjct: 71  H--MIDGRWCDCKLPNS 85

>d1weya_ d.58.7.1 (A:) Calcipressin-1 {Mouse (Mus musculus) [TaxId: 10090]} Length = 104

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Calcipressin-1
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 56.3 bits (135), Expect = 2e-10
 Identities = 11/90 (12%), Positives = 27/90 (30%), Gaps = 11/90 (12%)

Query: 240 PPENVLFVCKLNP-----VTEDEDLHTIFSRFGTVVSAEIIRDFKTGDSLNYAFIEFENR 294
              + L  C  N              ++F  +    + +  + F          I F N 
Sbjct: 3   SGSSGLIACVANDDVFSESETRAKFESLFRTYDKDTTFQYFKSF------KRVRINFSNP 56

Query: 295 QACERAYSKMDNALIDDRRIHVDFSQSVSK 324
            +   A  ++       + + + F+Q++  
Sbjct: 57  LSAADARLRLHKTEFLGKEMKLYFAQTLHI 86

>d2cpea1 d.58.7.1 (A:353-453) RNA-binding protein EWS {Human (Homo sapiens) [TaxId: 9606]} Length = 101

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding protein EWS
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 55.6 bits (133), Expect = 2e-10
 Identities = 18/95 (18%), Positives = 33/95 (34%), Gaps = 8/95 (8%)

Query: 235 DADIKPPENVLFVCKLNPVTEDEDLHTIFSRFGTVVSAEII--------RDFKTGDSLNY 286
           D D     + ++V  LN     +DL   F + G V   +           D +TG     
Sbjct: 1   DPDEDSDNSAIYVQGLNDSVTLDDLADFFKQCGVVKMNKRTGQPMIHIYLDKETGKPKGD 60

Query: 287 AFIEFENRQACERAYSKMDNALIDDRRIHVDFSQS 321
           A + +E+    + A    D       ++ V  ++ 
Sbjct: 61  ATVSYEDPPTAKAAVEWFDGKDFQGSKLKVSLARK 95

>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 = 55.6 bits (133), Expect = 3e-10
 Identities = 24/97 (24%), Positives = 44/97 (45%), Gaps = 3/97 (3%)

Query: 228 ESIGDIP---DADIKPPENVLFVCKLNPVTEDEDLHTIFSRFGTVVSAEIIRDFKTGDSL 284
           E I  IP     +   P  VL++  L+P   + DL ++F+RF       I     TG   
Sbjct: 1   EEIRKIPMFSSYNPGEPNKVLYLKNLSPRVTERDLVSLFARFQEKKGPPIQFRMMTGRMR 60

Query: 285 NYAFIEFENRQACERAYSKMDNALIDDRRIHVDFSQS 321
             AFI F N++   +A   ++   +  + + ++F ++
Sbjct: 61  GQAFITFPNKEIAWQALHLVNGYKLYGKILVIEFGKN 97

>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 = 54.2 bits (130), Expect = 3e-10
 Identities = 18/72 (25%), Positives = 32/72 (44%), Gaps = 1/72 (1%)

Query: 245 LFVCKLNPVTEDEDLHTIFSRFGTVVSAEIIRDFKTGDSLNYAFIEFENRQACERAYSKM 304
           +FV  L+P T +E +   F  FG V S E+  D KT     + FI F+  +  ++   + 
Sbjct: 2   IFVGGLSPDTPEEKIREYFGGFGEVESIELPMDNKTNKRRGFCFITFKEEEPVKKIM-EK 60

Query: 305 DNALIDDRRIHV 316
               +   +  +
Sbjct: 61  KYHNVGLSKCEI 72

>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 = 54.4 bits (130), Expect = 4e-10
 Identities = 10/79 (12%), Positives = 28/79 (35%)

Query: 242 ENVLFVCKLNPVTEDEDLHTIFSRFGTVVSAEIIRDFKTGDSLNYAFIEFENRQACERAY 301
           E  L++    P     ++  +      V  +  +   +   S  +A+I+  +++      
Sbjct: 1   ECTLWMTNFPPSYTQRNIRDLLQDINVVALSIRLPSLRFNTSRRFAYIDVTSKEDARYCV 60

Query: 302 SKMDNALIDDRRIHVDFSQ 320
            K++   I+   +    S 
Sbjct: 61  EKLNGLKIEGYTLVTKVSN 79

>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 = 53.8 bits (129), Expect = 5e-10
 Identities = 18/72 (25%), Positives = 34/72 (47%), Gaps = 1/72 (1%)

Query: 245 LFVCKLNPVTEDEDLHTIFSRFGTVVSAEIIRDFKTGDSLNYAFIEFENRQACERAYSKM 304
           +F+  L+  T  +DL   FS+FG VV   +  D  TG S  + F+ F+  ++ ++     
Sbjct: 2   MFIGGLSWDTTKKDLKDYFSKFGEVVDCTLKLDPITGRSRGFGFVLFKESESVDKVM-DQ 60

Query: 305 DNALIDDRRIHV 316
               ++ + I  
Sbjct: 61  KEHKLNGKVIDP 72

>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 = 53.6 bits (128), Expect = 5e-10
 Identities = 18/74 (24%), Positives = 34/74 (45%), Gaps = 1/74 (1%)

Query: 245 LFVCKLNPVTEDEDLHTIFSRFGTVVSAEIIRDFKTGDSLNYAFIEFENRQACERAYSKM 304
           +FV  L+  T  ED+   F +FG V  A ++ D  T     + F+ FE+    E+   ++
Sbjct: 2   IFVGGLSVNTTVEDVKHYFEQFGKVDDAMLMFDKTTNRHRGFGFVTFESEDIVEKVC-EI 60

Query: 305 DNALIDDRRIHVDF 318
               I+++ +    
Sbjct: 61  HFHEINNKMVECKK 74

>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 = 54.3 bits (130), Expect = 6e-10
 Identities = 25/102 (24%), Positives = 43/102 (42%), Gaps = 8/102 (7%)

Query: 240 PPENVLFVCKLNPVTEDEDLHTIFSRFGTVVSAEIIRDFKTGDSLNYAFIEFENRQACER 299
                LFV  L+  + +EDL  +FS +G +       D  T     +AF+ F   +   +
Sbjct: 6   SGSGRLFVRNLSYTSSEEDLEKLFSAYGPLSELHYPIDSLTKKPKGFAFVTFMFPEHAVK 65

Query: 300 AYSKMDNALIDDRRIHVDFSQSVSKLWNQFRRRDHQTGKGKG 341
           AY+++D  +   R +HV  S          ++   Q+G   G
Sbjct: 66  AYAEVDGQVFQGRMLHVLPSTI--------KKEASQSGPSSG 99

>d2adca2 d.58.7.1 (A:444-531) Polypyrimidine tract-binding protein {Human (Homo sapiens) [TaxId: 9606]} Length = 88

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Polypyrimidine tract-binding protein
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 54.0 bits (129), Expect = 7e-10
 Identities = 21/86 (24%), Positives = 35/86 (40%), Gaps = 5/86 (5%)

Query: 237 DIKPPENVLFVCKLNPVTEDEDLHTIFSRFGTVVSAEIIRDFKTGDSLNYAFIEFENRQA 296
           +I PP   L +  + P   +EDL  +FS  G VV                A I+  + + 
Sbjct: 5   NIFPPSATLHLSNIPPSVSEEDLKVLFSSNGGVVKGFKFFQKDR----KMALIQMGSVEE 60

Query: 297 CERAYSKMDNALIDD-RRIHVDFSQS 321
             +A   + N  + +   + V FS+S
Sbjct: 61  AVQALIDLHNHDLGENHHLRVSFSKS 86

>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 = 53.9 bits (129), Expect = 8e-10
 Identities = 23/91 (25%), Positives = 34/91 (37%), Gaps = 4/91 (4%)

Query: 234 PDADIKPPE---NVLFVCKLNPVTEDEDLHTIFSRFGTVVSAEIIRDFKTGDSLNYAFIE 290
           P  ++ P E     +F  +L       DL   FS  G V    II D  +  S   A++E
Sbjct: 7   PVDNLSPEERDARTVFCMQLAARIRPRDLEDFFSAVGKVRDVRIISDRNSRRSKGIAYVE 66

Query: 291 FENRQACERAYSKMDNALIDDRRIHVDFSQS 321
           F   Q+       +    +    I V  SQ+
Sbjct: 67  FCEIQSVPL-AIGLTGQRLLGVPIIVQASQA 96

>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 = 53.5 bits (128), Expect = 9e-10
 Identities = 16/82 (19%), Positives = 36/82 (43%), Gaps = 2/82 (2%)

Query: 240 PPENVLFVCKLNPVTEDEDLHTIFSRFGTVVSAEIIRDFKTGDSLNYAFIEFENRQACER 299
                L+V  L+    +  +  +FS+ G   S ++I +     +  Y F+EF   +    
Sbjct: 6   GQPRTLYVGNLSRDVTEVLILQLFSQIGPCKSCKMITE--HTSNDPYCFVEFYEHRDAAA 63

Query: 300 AYSKMDNALIDDRRIHVDFSQS 321
           A + M+   I  + + V+++ +
Sbjct: 64  ALAAMNGRKILGKEVKVNWATT 85

>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 = 53.5 bits (128), Expect = 1e-09
 Identities = 19/82 (23%), Positives = 37/82 (45%), Gaps = 3/82 (3%)

Query: 240 PPENVLFVCKLNPVTEDEDLHTIFSRFGTVVSAEIIRDFKTGDSLNYAFIEFENRQACER 299
             +  ++V  L P    +D+  +F ++G +   ++           +AF+EFE+ +  E 
Sbjct: 12  NNDCRIYVGNLPPDIRTKDIEDVFYKYGAIRDIDLKNRRGGP---PFAFVEFEDPRDAED 68

Query: 300 AYSKMDNALIDDRRIHVDFSQS 321
           A    D    D  R+ V+F +S
Sbjct: 69  AVYGRDGYDYDGYRLRVEFPRS 90

>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 = 52.4 bits (125), Expect = 3e-09
 Identities = 17/92 (18%), Positives = 34/92 (36%), Gaps = 5/92 (5%)

Query: 230 IGDIPDADIKPPENVLFVCKLNPVTEDEDLHTIFSRFGTVVSAEIIRDFKTGDSLNYAFI 289
           + D   +        L    L+    +++L  +F          I    + G S   A+I
Sbjct: 4   LEDPCTSKKVRAARTLLAKNLSFNITEDELKEVFEDALE-----IRLVSQDGKSKGIAYI 58

Query: 290 EFENRQACERAYSKMDNALIDDRRIHVDFSQS 321
           EF++    E+   +   A ID R + + ++  
Sbjct: 59  EFKSEADAEKNLEEKQGAEIDGRSVSLYYTGE 90

>d1u6fa1 d.58.7.1 (A:1-139) RNA-binding protein UBP1 {Trypanosoma cruzi [TaxId: 5693]} Length = 139

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding protein UBP1
species: Trypanosoma cruzi [TaxId: 5693]

 Score = 53.4 bits (127), Expect = 3e-09
 Identities = 24/112 (21%), Positives = 54/112 (48%), Gaps = 3/112 (2%)

Query: 216 RSKDARSSAVVLESIGDIPDADIKPPENV---LFVCKLNPVTEDEDLHTIFSRFGTVVSA 272
             + A+   +  +    IP   + P  +V   L V  +    ++  L  +F R+G + S 
Sbjct: 13  YGQTAQLQQLQQQQQQHIPPTQMNPEPDVLRNLMVNYIPTTVDEVQLRQLFERYGPIESV 72

Query: 273 EIIRDFKTGDSLNYAFIEFENRQACERAYSKMDNALIDDRRIHVDFSQSVSK 324
           +I+ D +T  S  Y F++F++  + ++A + ++   I ++R+ V  + S  +
Sbjct: 73  KIVCDRETRQSRGYGFVKFQSGSSAQQAIAGLNGFNILNKRLKVALAASGHQ 124

>d2dita1 d.58.7.1 (A:8-106) HIV Tat-specific factor 1 {Human (Homo sapiens) [TaxId: 9606]} Length = 99

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: HIV Tat-specific factor 1
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 51.5 bits (123), Expect = 6e-09
 Identities = 12/68 (17%), Positives = 22/68 (32%), Gaps = 4/68 (5%)

Query: 257 EDLHTIFSRFGTVVSAEIIRDFKTGDSLNYAFIEFENRQACERAYSKMDNALIDDRRIHV 316
           EDL    S+FG +    +      G     A + F + +  +     +D      R+I  
Sbjct: 34  EDLRVECSKFGQIRKLLLFDRHPDG----VASVSFRDPEEADYCIQTLDGRWFGGRQITA 89

Query: 317 DFSQSVSK 324
                 + 
Sbjct: 90  QAWDGTTD 97

>d2cqda1 d.58.7.1 (A:1-103) RNA-binding region containing protein 1 {Human (Homo sapiens) [TaxId: 9606]} Length = 103

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding region containing protein 1
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 51.3 bits (122), Expect = 8e-09
 Identities = 32/97 (32%), Positives = 45/97 (46%), Gaps = 7/97 (7%)

Query: 245 LFVCKLNPVTEDEDLHTIFSRFGTVVSAEIIRDFKTGDSLNYAFIEFENRQACERAYSKM 304
           +FV  L   T D  L   F  FG +  A +I D +TG S  Y F+   +R A ERA    
Sbjct: 13  IFVGGLPYHTTDASLRKYFEGFGDIEEAVVITDRQTGKSRGYGFVTMADRAAAERACKDP 72

Query: 305 DNALIDDRRIHVDFSQSVSKLWNQFRRRDHQTGKGKG 341
            N +ID R+ +V+ +   +      + R  QTG   G
Sbjct: 73  -NPIIDGRKANVNLAYLGA------KPRSLQTGFAIG 102

>d1l3ka2 d.58.7.1 (A:103-181) Nuclear ribonucleoprotein A1 (RNP A1, UP1) {Human (Homo sapiens) [TaxId: 9606]} Length = 79

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nuclear ribonucleoprotein A1 (RNP A1, UP1)
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 50.5 bits (120), Expect = 9e-09
 Identities = 15/75 (20%), Positives = 33/75 (44%), Gaps = 1/75 (1%)

Query: 245 LFVCKLNPVTEDEDLHTIFSRFGTVVSAEIIRDFKTGDSLNYAFIEFENRQACERAYSKM 304
           +FV  +   TE+  L   F ++G +   EI+ D  +G    +AF+ F++  + ++     
Sbjct: 5   IFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIV-IQ 63

Query: 305 DNALIDDRRIHVDFS 319
               ++     V  +
Sbjct: 64  KYHTVNGHNCEVRKA 78

>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 = 50.0 bits (119), Expect = 1e-08
 Identities = 17/78 (21%), Positives = 36/78 (46%), Gaps = 8/78 (10%)

Query: 243 NVLFVCKLNPVTEDEDLHTIFSRFGTVVSAEIIRDFKTGDSLNYAFIEFENRQACERAYS 302
           N L+V     +T    L   FS FG       I D       N AF+ +E  ++ ++A +
Sbjct: 6   NTLYVYGE-DMTP-TLLRGAFSPFGN------IIDLSMDPPRNCAFVTYEKMESADQAVA 57

Query: 303 KMDNALIDDRRIHVDFSQ 320
           +++   ++  ++ V+ ++
Sbjct: 58  ELNGTQVESVQLKVNIAR 75

>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 = 50.8 bits (121), Expect = 1e-08
 Identities = 16/77 (20%), Positives = 33/77 (42%), Gaps = 1/77 (1%)

Query: 245 LFVCKLNPVTEDEDLHTIFSRFGTVVSAEIIRDFKTGDSLNYAFIEFENRQACERAYSKM 304
           LF+  L+  T +E L   + ++G +    ++RD  +  S  + F+ F +    + A    
Sbjct: 23  LFIGGLSFETTEESLRNYYEQWGKLTDCVVMRDPASKRSRGFGFVTFSSMAEVDAAM-AA 81

Query: 305 DNALIDDRRIHVDFSQS 321
               ID R +    + +
Sbjct: 82  RPHSIDGRVVEPKRAVA 98

>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 = 49.7 bits (118), Expect = 1e-08
 Identities = 16/80 (20%), Positives = 34/80 (42%), Gaps = 7/80 (8%)

Query: 243 NVLFVCKLNPVTEDEDLHTIFSRFGTVVSAEIIRDFKTGDSLNYAFIEFENRQACERAYS 302
           N L++  L+P    +DL  +F      +        +      YAF+++ ++    RA  
Sbjct: 2   NKLYIGNLSPAVTADDLRQLFGDRKLPL------AGQVLLKSGYAFVDYPDQNWAIRAIE 55

Query: 303 KMDNAL-IDDRRIHVDFSQS 321
            +   + +  + + VD+S S
Sbjct: 56  TLSGKVELHGKIMEVDYSVS 75

>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 = 49.7 bits (118), Expect = 2e-08
 Identities = 14/80 (17%), Positives = 34/80 (42%), Gaps = 4/80 (5%)

Query: 245 LFVCKLNPVTEDEDLHTIFSRFGTVVSA--EIIRDFKTGDSLNYAFIEFENRQACERAYS 302
           LF+  +  + + E++    ++    V              +  +AF+E+E+ +A   A  
Sbjct: 4   LFIGGIPKMKKREEILEEIAKVTEGVLDVIVYASAADKMKNRGFAFVEYESHRAAAMARR 63

Query: 303 KMDNA--LIDDRRIHVDFSQ 320
           K+      +   +I VD+++
Sbjct: 64  KLMPGRIQLWGHQIAVDWAE 83

>d1wi8a_ d.58.7.1 (A:) Eukaryotic translation initiation factor 4B {Human (Homo sapiens) [TaxId: 9606]} Length = 104

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Eukaryotic translation initiation factor 4B
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 49.7 bits (118), Expect = 2e-08
 Identities = 13/81 (16%), Positives = 26/81 (32%), Gaps = 1/81 (1%)

Query: 241 PENVLFVCKLNPVTEDEDLHTIFSRFGTVVSAEIIRDFKTGDSLNYAFIEFENRQACERA 300
           P    F+  L     +E +   F                      + + EFE+  +   A
Sbjct: 14  PPYTAFLGNLPYDVTEESIKEFFRGLNISAVRLPREPSNPERLKGFGYAEFEDLDSLLSA 73

Query: 301 YSKMDNALIDDRRIHVDFSQS 321
              ++   + ++RI VD +  
Sbjct: 74  L-SLNEESLGNKRIRVDVADQ 93

>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 = 48.9 bits (116), Expect = 4e-08
 Identities = 25/84 (29%), Positives = 44/84 (52%), Gaps = 8/84 (9%)

Query: 240 PPENVLFVCKLNPVTEDEDLHTIFSRFGTVVSAEIIRDFKTGDSLNYAFIEFENRQACER 299
            P   L+V  L P T    L   F RFG++ + + ++        ++A+I++E+  A + 
Sbjct: 15  NPTTRLWVGGLGPNTSLAALAREFDRFGSIRTIDHVKGD------SFAYIQYESLDAAQA 68

Query: 300 AYSKMDNALID--DRRIHVDFSQS 321
           A +KM    +   DRR+ VDF++S
Sbjct: 69  ACAKMRGFPLGGPDRRLRVDFAKS 92

>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 = 51.2 bits (121), Expect = 5e-08
 Identities = 29/170 (17%), Positives = 56/170 (32%), Gaps = 6/170 (3%)

Query: 239 KPPENV--LFVCKLNPVTEDEDLHTIFSRFGTVVSAEIIRDFKTGDSLNYAFIEFENRQA 296
           K PE +  LF+  L+  T DE L + F ++GT+    ++RD  T  S  + F+ +   + 
Sbjct: 1   KEPEQLRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEE 60

Query: 297 CERAYSKMDNALIDDRRIHVDFSQSVSKLWNQFRRRDHQTGKGKGCFKCGGLDHIAKDCT 356
            + A        +D R +    + S             +     G  +     H+     
Sbjct: 61  VDAAM-NARPHKVDGRVVEPKRAVSREDSQRPGAHLTVKKIFVGGIKEDTEEHHLRDYFE 119

Query: 357 GQQPAKYILRDDNRQHGGYSDSRYEMVFDGETPEKSRREKKHRGHDPDDR 406
                + I    +R  G     R       +  +   +    + H  +  
Sbjct: 120 QYGKIEVIEIMTDRGSGKK---RGFAFVTFDDHDSVDKIVIQKYHTVNGH 166

>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 = 48.6 bits (115), Expect = 5e-08
 Identities = 25/83 (30%), Positives = 43/83 (51%)

Query: 242 ENVLFVCKLNPVTEDEDLHTIFSRFGTVVSAEIIRDFKTGDSLNYAFIEFENRQACERAY 301
           E  LFV  L+  T ++ L  +FS++G +    +++D +T  S  + F+ FEN    + A 
Sbjct: 5   EGKLFVGGLSFDTNEQSLEQVFSKYGQISEVVVVKDRETQRSRGFGFVTFENIDDAKDAM 64

Query: 302 SKMDNALIDDRRIHVDFSQSVSK 324
             M+   +D R+I VD +   S 
Sbjct: 65  MAMNGKSVDGRQIRVDQAGKSSD 87

>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 = 48.2 bits (114), Expect = 6e-08
 Identities = 11/77 (14%), Positives = 27/77 (35%), Gaps = 6/77 (7%)

Query: 245 LFVCKLNPVTEDEDLHTIFSRFGTVVSAEI-----IRDFKTGDSLNYAFIEFENRQACER 299
           L+V  +     +E +   F+    +          +   +     N+AF+EF +     +
Sbjct: 4   LYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLEFRSVDETTQ 63

Query: 300 AYSKMDNALIDDRRIHV 316
           A    D  +   + + +
Sbjct: 64  AM-AFDGIIFQGQSLKI 79

>d1wg1a_ d.58.7.1 (A:) Probable RNA-binding protein KIAA1579 {Human (Homo sapiens) [TaxId: 9606]} Length = 88

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Probable RNA-binding protein KIAA1579
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 48.2 bits (114), Expect = 8e-08
 Identities = 9/81 (11%), Positives = 26/81 (32%), Gaps = 7/81 (8%)

Query: 245 LFVCKLNPVTEDEDLHTIFSRFGTVVSAEIIRDFKTGDSLNYAFIEFENRQACERAYSKM 304
           + V  L   +  +++H +   +        ++      +   AF+   N +  + A    
Sbjct: 8   ILVKNLPQDSNCQEVHDLLKDYD-------LKYCYVDRNKRTAFVTLLNGEQAQNAIQMF 60

Query: 305 DNALIDDRRIHVDFSQSVSKL 325
                  + + V    + + L
Sbjct: 61  HQYSFRGKDLIVQLQPTDALL 81

>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 = 47.7 bits (113), Expect = 1e-07
 Identities = 17/97 (17%), Positives = 41/97 (42%), Gaps = 16/97 (16%)

Query: 245 LFVCKLNPVTEDEDLHTIFSRFGTVVSAEIIRDFKTGDSLNYAFIEFENRQACERAYSKM 304
           +FV +      +++L   FS++G V+   I + F+      +AF+ F + Q  +      
Sbjct: 8   VFVGRCTGDMTEDELREFFSQYGDVMDVFIPKPFR-----AFAFVTFADDQIAQSL--CG 60

Query: 305 DNALIDDRRIHVDFSQSVSKLWNQFRRRDHQTGKGKG 341
           ++ +I    +H+  ++          + +  +G   G
Sbjct: 61  EDLIIKGISVHISNAEP---------KHNSNSGPSSG 88

>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 = 47.4 bits (112), Expect = 1e-07
 Identities = 17/88 (19%), Positives = 30/88 (34%), Gaps = 9/88 (10%)

Query: 241 PENVLFVCKLNP-VTEDEDLHTIFSRFGTVVSAEIIRDFKTGDSLNYAFIEFENRQACER 299
              V+ +            L  +   FG + +  I+         N AFIE    +  + 
Sbjct: 7   TRRVVHIMDFQRGKNLRYQLLQLVEPFGVISNHLILNKI------NEAFIEMATTEDAQA 60

Query: 300 A--YSKMDNALIDDRRIHVDFSQSVSKL 325
           A  Y     AL+  + + V  SQ   ++
Sbjct: 61  AVDYYTTTPALVFGKPVRVHLSQKYKRI 88

>d2adba1 d.58.7.1 (A:177-284) Polypyrimidine tract-binding protein {Human (Homo sapiens) [TaxId: 9606]} Length = 108

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Polypyrimidine tract-binding protein
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 47.7 bits (113), Expect = 2e-07
 Identities = 18/89 (20%), Positives = 31/89 (34%), Gaps = 4/89 (4%)

Query: 245 LFVCKLNPVTEDEDLHTIFSRFGTVVSAEIIRDFKTGDSLNYAFIEFENRQACERAYSKM 304
           + V  L      + LH IFS+FGTV+                A +++ +  + + A   +
Sbjct: 10  IIVENLFYPVTLDVLHQIFSKFGTVLKIITFTKNNQF----QALLQYADPVSAQHAKLSL 65

Query: 305 DNALIDDRRIHVDFSQSVSKLWNQFRRRD 333
           D   I +    +    S     N     D
Sbjct: 66  DGQNIYNACCTLRIDFSKLTSLNVKYNND 94

>d2cpia1 d.58.7.1 (A:101-189) E3 ubiquitin protein ligase CNOT4 {Mouse (Mus musculus) [TaxId: 10090]} Length = 89

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: E3 ubiquitin protein ligase CNOT4
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 46.7 bits (110), Expect = 3e-07
 Identities = 15/80 (18%), Positives = 31/80 (38%), Gaps = 6/80 (7%)

Query: 243 NVLFVCKLNPVTEDEDLHTIF---SRFGTVVSAEIIRDFKTGDSLN---YAFIEFENRQA 296
           N++FV  L+    D ++        +FG +    I        S      A++ +   + 
Sbjct: 9   NLVFVVGLSQRLADPEVLKRPEYFGKFGKIHKVVINNSTSYAGSQGPSASAYVTYIRSED 68

Query: 297 CERAYSKMDNALIDDRRIHV 316
             RA   ++N ++D R +  
Sbjct: 69  ALRAIQCVNNVVVDGRTLKA 88

>d2adca1 d.58.7.1 (A:335-443) Polypyrimidine tract-binding protein {Human (Homo sapiens) [TaxId: 9606]} Length = 109

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Polypyrimidine tract-binding protein
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 47.1 bits (111), Expect = 3e-07
 Identities = 17/80 (21%), Positives = 34/80 (42%), Gaps = 6/80 (7%)

Query: 243 NVLFVCKLNP-VTEDEDLHTIFSRFGTVVSAEIIRDFKTGDSLNYAFIEFENRQACERAY 301
           +VL V  LNP     + L  +F  +G V   +I+ + K       A ++  +    + A 
Sbjct: 3   SVLLVSNLNPERVTPQSLFILFGVYGDVQRVKILFNKK-----ENALVQMADGNQAQLAM 57

Query: 302 SKMDNALIDDRRIHVDFSQS 321
           S ++   +  + I +  S+ 
Sbjct: 58  SHLNGHKLHGKPIRITLSKH 77

>d1wexa_ d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprotein L-like {Mouse (Mus musculus) [TaxId: 10090]} Length = 104

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Heterogeneous nuclear ribonucleoprotein L-like
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 46.3 bits (109), Expect = 4e-07
 Identities = 19/109 (17%), Positives = 36/109 (33%), Gaps = 14/109 (12%)

Query: 235 DADIKPPENVLFVCKLNPVTEDEDLHTIFSRFGTVVSAEIIRDFKTGDSLNYAFIEFENR 294
                    V+ V  L     + DL     +FGT+    ++           A +EFEN 
Sbjct: 8   SHHKVSVSPVVHVRGLCESVVEADLVEALEKFGTICYVMMMPFK------RQALVEFENI 61

Query: 295 QACERAYSKMDN--ALIDDRRIHVDFSQSVSKLWNQFRRRDHQTGKGKG 341
            + +   +   +    I  ++   ++S S      +   R   +G   G
Sbjct: 62  DSAKECVTFAADVPVYIAGQQAFFNYSTS------KRITRPGNSGPSSG 104

>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 = 45.5 bits (107), Expect = 9e-07
 Identities = 22/77 (28%), Positives = 37/77 (48%)

Query: 245 LFVCKLNPVTEDEDLHTIFSRFGTVVSAEIIRDFKTGDSLNYAFIEFENRQACERAYSKM 304
           +FV  +     +E L  IFS  G VVS  ++ D +TG    Y F E+++++    A   +
Sbjct: 11  VFVGNIPYEATEEQLKDIFSEVGPVVSFRLVYDRETGKPKGYGFCEYQDQETALSAMRNL 70

Query: 305 DNALIDDRRIHVDFSQS 321
           +      R + VD + S
Sbjct: 71  NGREFSGRALRVDNAAS 87

>d2b0ga1 d.58.7.1 (A:1-83) Splicesomal U1A protein {Drosophila melanogaster [TaxId: 7227]} Length = 83

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicesomal U1A protein
species: Drosophila melanogaster [TaxId: 7227]

 Score = 44.5 bits (104), Expect = 1e-06
 Identities = 16/82 (19%), Positives = 32/82 (39%), Gaps = 6/82 (7%)

Query: 240 PPENVLFVCKLNPVTEDEDLHTIFSRFGTVVSAEIIRDFKTGDSLNYAFIEFENRQACER 299
           PP  +LF+  L   T +  L  +F++F       ++ +       + AF+EF        
Sbjct: 6   PPNQILFLTNLPEETNEMMLSMLFNQFPGFKEVRLVPNRH-----DIAFVEFTTELQSNA 60

Query: 300 AYSKMDNALIDD-RRIHVDFSQ 320
           A   +    I     + + F++
Sbjct: 61  AKEALQGFKITPTHAMKITFAK 82

>d1x4ea1 d.58.7.1 (A:8-79) RNA-binding motif, single-stranded-interacting protein 2, RBMS2 {Human (Homo sapiens) [TaxId: 9606]} Length = 72

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding motif, single-stranded-interacting protein 2, RBMS2
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 44.0 bits (103), Expect = 1e-06
 Identities = 18/70 (25%), Positives = 36/70 (51%)

Query: 245 LFVCKLNPVTEDEDLHTIFSRFGTVVSAEIIRDFKTGDSLNYAFIEFENRQACERAYSKM 304
           L++  L P T D+DL  +   +G +VS + I D  T     Y F++F++  A ++A + +
Sbjct: 1   LYIRGLQPGTTDQDLVKLCQPYGKIVSTKAILDKTTNKCKGYGFVDFDSPSAAQKAVTAL 60

Query: 305 DNALIDDRRI 314
             + +  +  
Sbjct: 61  KASGVQAQMA 70

>d2ghpa3 d.58.7.1 (A:206-291) U4/U6 snRNA-associated-splicing factor PRP24 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]} Length = 86

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: U4/U6 snRNA-associated-splicing factor PRP24
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

 Score = 44.0 bits (103), Expect = 2e-06
 Identities = 20/78 (25%), Positives = 38/78 (48%), Gaps = 3/78 (3%)

Query: 245 LFVCKLNP-VTEDEDLHTIFSRFGTVVSAEIIRDFK-TGDSLNYAFIEFENRQACERAYS 302
           + +  L+  + ++  L   F  FG++    I    K    +   AF+ FEN+ + ERA  
Sbjct: 7   IMIRNLSTELLDENLLRESFEGFGSIEKINIPAGQKEHSFNNCCAFMVFENKDSAERAL- 65

Query: 303 KMDNALIDDRRIHVDFSQ 320
           +M+ +L+ +R I V  + 
Sbjct: 66  QMNRSLLGNREISVSLAD 83

>d2cq2a1 d.58.7.1 (A:25-125) Alkylation repair AlkB homolog 8, ALKBH8 {Human (Homo sapiens) [TaxId: 9606]} Length = 101

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Alkylation repair AlkB homolog 8, ALKBH8
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 44.3 bits (104), Expect = 2e-06
 Identities = 13/85 (15%), Positives = 28/85 (32%), Gaps = 9/85 (10%)

Query: 240 PPENVLFVCK--LNPVTEDEDLHTIFSRFGTVVSAEIIRDFKTGDSLNYAFIEFENRQAC 297
                L V    L        L  +  + G V +  +  +        Y+F  +   +  
Sbjct: 16  YATQSLVVANGGLGNGVSRNQLLPVLEKCGLVDALLMPPNK------PYSFARYRTTEES 69

Query: 298 ERAYSKMDNA-LIDDRRIHVDFSQS 321
           +RAY  ++   ++DD    +    +
Sbjct: 70  KRAYVTLNGKEVVDDLGQKITLYLN 94

>d1x4ha1 d.58.7.1 (A:8-105) RNA-binding protein 28 {Mouse (Mus musculus) [TaxId: 10090]} Length = 98

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding protein 28
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 44.0 bits (103), Expect = 2e-06
 Identities = 17/83 (20%), Positives = 38/83 (45%), Gaps = 6/83 (7%)

Query: 245 LFVCKLNPVTEDEDLHTIFSRFGTVVSAEIIRDFKTGDSLNYAFIEFENRQACERAYSKM 304
           +F+  L+  +E+E L  +  +FG +    ++    T  S   AF +F  ++A ++  +  
Sbjct: 11  VFIRNLSFDSEEEALGEVLQQFGDLKYVRVVLHPDTEHSKGCAFAQFMTQEAAQKCLAAA 70

Query: 305 DNAL------IDDRRIHVDFSQS 321
                     +D R++ VD + +
Sbjct: 71  SLEAEGGGLKLDGRQLKVDLAVT 93

>d1wi6a1 d.58.7.1 (A:69-143) Ribonucleoprotein PTB-binding 1, Raver-1 {Mouse (Mus musculus) [TaxId: 10090]} Length = 75

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Ribonucleoprotein PTB-binding 1, Raver-1
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 42.2 bits (98), Expect = 5e-06
 Identities = 11/81 (13%), Positives = 30/81 (37%), Gaps = 7/81 (8%)

Query: 245 LFVCKLNPVTEDEDLHTIFSRFGTVVSAEIIRDFKTGDSLNYAFIEFENRQACERAYSKM 304
           + +  L     ++++H + S +        ++          AF+   N +  E A +  
Sbjct: 1   ILIRGLPGDVTNQEVHDLLSDY-------ELKYCFVDKYKGTAFVTLLNGEQAEAAINTF 53

Query: 305 DNALIDDRRIHVDFSQSVSKL 325
             + + +R + V    + + L
Sbjct: 54  HQSRLRERELSVQLQPTDALL 74

>d1o0pa_ d.58.7.1 (A:) Splicing factor U2AF 65 KDa subunit {Human (Homo sapiens) [TaxId: 9606]} Length = 104

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicing factor U2AF 65 KDa subunit
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 43.0 bits (101), Expect = 6e-06
 Identities = 18/79 (22%), Positives = 32/79 (40%), Gaps = 7/79 (8%)

Query: 257 EDLHTIFSRFGTVVSAEIIRDFKTGDSLN--YAFIEFENRQACERAYSKMDNALIDDRRI 314
           ED+    S++G V S EI R     +       F+EF +   C++A   +      +R +
Sbjct: 29  EDVRDECSKYGLVKSIEIPRPVDGVEVPGCGKIFVEFTSVFDCQKAMQGLTGRKFANRVV 88

Query: 315 HVDFSQSVSKLWNQFRRRD 333
              +        + + RRD
Sbjct: 89  VTKYCDP-----DSYHRRD 102

>d2cq1a1 d.58.7.1 (A:51-138) Polypyrimidine tract-binding protein 2, PTBP2 {Human (Homo sapiens) [TaxId: 9606]} Length = 88

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Polypyrimidine tract-binding protein 2, PTBP2
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 39.1 bits (90), Expect = 9e-05
 Identities = 13/84 (15%), Positives = 29/84 (34%), Gaps = 8/84 (9%)

Query: 240 PPENVLFVCKLNPVTEDEDLHTIFSRFGTVVSAEIIRDFKTGDSLNYAFIEFENRQACER 299
            P  VL + KL     + ++  +   F        + +       N AF+E    +A   
Sbjct: 6   APSRVLHIRKLPGEVTETEVIALGLPF------GKVTNILMLKGKNQAFLELATEEAAIT 59

Query: 300 AYSKM--DNALIDDRRIHVDFSQS 321
             +        + ++ I++ +S  
Sbjct: 60  MVNYYSAVTPHLRNQPIYIQYSNH 83

>d1wg4a_ d.58.7.1 (A:) Splicing factor, arginine/serine-rich 9 (SFRS9) {Mouse (Mus musculus) [TaxId: 10090]} Length = 98

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicing factor, arginine/serine-rich 9 (SFRS9)
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 39.4 bits (91), Expect = 1e-04
 Identities = 14/82 (17%), Positives = 29/82 (35%), Gaps = 7/82 (8%)

Query: 239 KPPENVLFVCKLNPVTEDEDLHTIFSRFGTVVSAEIIRDFKTGDSLNYAFIEFENRQACE 298
           +  +  + V  L P    +DL       G V  A++ +D           +E+  ++  E
Sbjct: 12  RRSDFRVLVSGLPPSGSWQDLKDHMREAGDVCYADVQKDG-------MGMVEYLRKEDME 64

Query: 299 RAYSKMDNALIDDRRIHVDFSQ 320
            A  K+D+           + +
Sbjct: 65  YALRKLDDTKFRSHEGETSYIR 86

>d1x5oa1 d.58.7.1 (A:8-108) RNA-binding motif, single-stranded-interacting protein 1, RBMS1 {Human (Homo sapiens) [TaxId: 9606]} Length = 101

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding motif, single-stranded-interacting protein 1, RBMS1
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 38.6 bits (89), Expect = 2e-04
 Identities = 13/76 (17%), Positives = 27/76 (35%), Gaps = 1/76 (1%)

Query: 245 LFVCKLNPVTEDEDLHTIFSRFGTVVSAEIIRDFKTGDSLNYAFIEFENRQACERAYSKM 304
           L++  L    ++++L  +   F   V +  I    +G S    F   E+ + CE      
Sbjct: 21  LYISNLPLSMDEQELENMLKPF-GQVISTRILRDSSGTSRGVGFARMESTEKCEAVIGHF 79

Query: 305 DNALIDDRRIHVDFSQ 320
           +   I         ++
Sbjct: 80  NGKFIKTPPGVSAPTE 95

>d1zh5a2 d.58.7.1 (A:105-189) Lupus LA protein {Human (Homo sapiens) [TaxId: 9606]} Length = 85

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Lupus LA protein
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 36.6 bits (84), Expect = 7e-04
 Identities = 7/78 (8%), Positives = 26/78 (33%), Gaps = 2/78 (2%)

Query: 242 ENVLFVCKLNPVTEDEDLHTIFSRFGTVVSAEIIRDFKTGDSLNYAFIEFENRQACERAY 301
              +++         +D+       G V++   +R           F+ F++ ++ ++  
Sbjct: 6   NRSVYIKGFPTDATLDDIKEWLEDKGQVLN-IQMRRTLHKAFKGSIFVVFDSIESAKKFV 64

Query: 302 SKMDNALIDDRRIHVDFS 319
            +       +  + + F 
Sbjct: 65  -ETPGQKYKETDLLILFK 81

>d1weza_ d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprotein H' {Human (Homo sapiens) [TaxId: 9606]} Length = 102

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Heterogeneous nuclear ribonucleoprotein H'
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 36.6 bits (84), Expect = 0.001
 Identities = 15/93 (16%), Positives = 30/93 (32%), Gaps = 3/93 (3%)

Query: 229 SIGDIPDADIKPPENVLFVCKLNPVTEDEDLHTIFSRFGTVVSAEIIRDFKTGDSLNYAF 288
           S G    +      + + +  L     + D++  FS    +     I     G     A 
Sbjct: 2   SSGSSGSSFQSTTGHCVHMRGLPYRATENDIYNFFSPLNPMRVHIEIGPD--GRVTGEAD 59

Query: 289 IEFENRQACERAYSKMDNALIDDRRIHVDFSQS 321
           +EF   +    A    D A +  R + +  + +
Sbjct: 60  VEFATHEDAVAAM-AKDKANMQHRYVELFLNST 91

>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 = 36.1 bits (82), Expect = 0.002
 Identities = 12/83 (14%), Positives = 30/83 (36%), Gaps = 6/83 (7%)

Query: 239 KPPENVLFVCKLNPVTEDEDLHTIFSRFGTVVSAEIIRDFKTGDSLNYAFIEFENRQACE 298
              + V+    L   T   ++   FSRFG++            +    A +EF       
Sbjct: 7   GRSKTVILAKNLPAGTLAAEIQETFSRFGSLGR------VLLPEGGITAIVEFLEPLEAR 60

Query: 299 RAYSKMDNALIDDRRIHVDFSQS 321
           +A+  +  +      ++++++  
Sbjct: 61  KAFRHLAYSKFHHVPLYLEWAPI 83

>d2exfa1 g.40.1.1 (A:12-53) HIV nucleocapsid {Human immunodeficiency virus type 1, different isolates [TaxId: 11676]} Length = 42

class: Small proteins
fold: Retrovirus zinc finger-like domains
superfamily: Retrovirus zinc finger-like domains
family: Retrovirus zinc finger-like domains
domain: HIV nucleocapsid
species: Human immunodeficiency virus type 1, different isolates [TaxId: 11676]

 Score = 33.7 bits (77), Expect = 0.003
 Identities = 13/30 (43%), Positives = 18/30 (60%)

Query: 330 RRRDHQTGKGKGCFKCGGLDHIAKDCTGQQ 359
             R+ +  + KGC+KCG   H  KDCT +Q
Sbjct: 13  TARNCRAPRKKGCWKCGKEGHQMKDCTERQ 42

Homologous Domains Detected by HHsearch

Original result of HHsearch against SCOP70(version1.75) database

ID	Length	Definition	Probability
Query	589
d2ok3a1	159	Cyclophilin-like protein PPIL3B {Human (Homo sapie	100.0
d1zkca1	178	Peptidyl-prolyl cis-trans isomerase-like 2, Cyclop	100.0
d2fu0a1	155	Putative cyclophilin PFE0505w {Plasmodium falcipar	100.0
d1xwna1	166	Peptidyl-prolyl cis-trans isomerase-like 1, PPIL1	100.0
d2b71a1	169	Cyclophilin-like protein PY00693 {Plasmodium yoeli	100.0
d1w74a_	171	Peptidyl-prolyl cis-trans isomerase A, PpiA {Mycob	100.0
d2a2na1	164	Peptidylprolyl isomerase domain and WD repeat-cont	100.0
d1h0pa_	182	Cyclophilin (eukaryotic) {Caenorhabditis elegans,	100.0
d1v9ta_	166	Peptidyl-prolyl cis-trans isomerase A, PpiA {Esche	100.0
d1xo7a_	166	Cyclophilin (eukaryotic) {Trypanosoma cruzi [TaxId	100.0
d2z6wa1	164	Mitochondrial peptidyl-prolyl cis-trans isomerase,	100.0
d2igva1	172	Cyclophilin (eukaryotic) {Caenorhabditis elegans,	100.0
d2rmca_	182	Cyclophilin (eukaryotic) {Mouse (Mus musculus), va	100.0
d1lopa_	164	Peptidyl-prolyl cis-trans isomerase A, PpiA {Esche	100.0
d2r99a1	161	Mitochondrial peptidyl-prolyl cis-trans isomerase,	100.0
d2cfea1	162	Cyclophilin-like allergen Mal s 6 {Malassezia symp	100.0
d1qnga_	170	Cyclophilin (eukaryotic) {Plasmodium falciparum [T	100.0
d1qoia_	173	Cyclophilin (eukaryotic) {Human (Homo sapiens), U4	100.0
d1a33a_	174	Cyclophilin (eukaryotic) {Nematode (Brugia malayi)	100.0
d1ihga2	195	Cyclophilin 40 isomerase domain {Cow (Bos taurus)	100.0
d1z81a1	186	Cyclophilin (eukaryotic) {Plasmodium yoelii [TaxId	100.0
d2c3ba1	171	Cyclophilin (eukaryotic) {Aspergillus fumigatus [T	100.0
d1b7fa1	82	Sex-lethal protein {Drosophila melanogaster [TaxId	99.81
d1x5ua1	93	Splicing factor 3B subunit 4 {Human (Homo sapiens)	99.8
d2cq0a1	90	Eukaryotic translation initiation factor 3 subunit	99.8
d1cvja1	80	Poly(A)-binding protein {Human (Homo sapiens) [Tax	99.8
d1fxla1	82	Hu antigen D (Hud) {Human (Homo sapiens) [TaxId: 9	99.8
d2cpza1	102	CUG triplet repeat RNA-binding protein 1 {Human (H	99.8
d1rk8a_	88	RNA-binding protein 8 {Fruit fly (Drosophila melan	99.8
d1h2vz_	93	CBP20, 20KDa nuclear cap-binding protein {Human (H	99.8
d2cqba1	89	Peptidyl-prolyl cis-trans isomerase E, N-terminal	99.79
d2cqca1	83	Arginine/serine-rich splicing factor 10 {Human (Ho	99.79
d2u2fa_	85	Splicing factor U2AF 65 KDa subunit {Human (Homo s	99.79
d1whwa_	99	Probable RNA-binding protein 19, Rbm19 {Mouse (Mus	99.78
d1u6fa1	139	RNA-binding protein UBP1 {Trypanosoma cruzi [TaxId	99.77
d1b7fa2	85	Sex-lethal protein {Drosophila melanogaster [TaxId	99.77
d1fxla2	85	Hu antigen D (Hud) {Human (Homo sapiens) [TaxId: 9	99.77
d2ghpa1	81	U4/U6 snRNA-associated-splicing factor PRP24 {Bake	99.76
d2cqga1	90	TAR DNA-binding protein 43, TDP-43 {Human (Homo sa	99.76
d2cpha1	94	Probable RNA-binding protein 19, Rbm19 {Mouse (Mus	99.76
d1l3ka1	84	Nuclear ribonucleoprotein A1 (RNP A1, UP1) {Human	99.76
d1no8a_	78	Nuclear factor Aly {Mouse (Mus musculus) [TaxId: 1	99.76
d2cqda1	103	RNA-binding region containing protein 1 {Human (Ho	99.76
d2cq4a1	101	RNA binding protein 23 {Human (Homo sapiens) [TaxI	99.76
d2cqia1	90	Nucleolysin TIAR {Human (Homo sapiens) [TaxId: 960	99.75
d2cpfa1	85	Probable RNA-binding protein 19, Rbm19 {Mouse (Mus	99.75
d1x5ta1	83	Splicing factor 3B subunit 4 {Human (Homo sapiens)	99.75
d1uawa_	77	Musashi-1 {Mouse (Mus musculus) [TaxId: 10090]}	99.75
d2cq3a1	93	RNA-binding protein 9 {Human (Homo sapiens) [TaxId	99.75
d1x4ba1	103	Heterogeneous nuclear ribonucleoproteins A2/B1 {Hu	99.74
d1x5sa1	90	Cold-inducible RNA-binding protein {Human (Homo sa	99.74
d1p1ta_	104	Cleavage stimulation factor, 64 kda subunit {Human	99.74
d1hd0a_	75	Heterogeneous nuclear ribonucleoprotein d0 {Human	99.74
d1cvja2	89	Poly(A)-binding protein {Human (Homo sapiens) [Tax	99.74
d1l3ka2	79	Nuclear ribonucleoprotein A1 (RNP A1, UP1) {Human	99.74
d2cpea1	101	RNA-binding protein EWS {Human (Homo sapiens) [Tax	99.73
d1x0fa1	75	Nuclear ribonucleoprotein D0 (AUF1) {Human (Homo s	99.73
d2ghpa3	86	U4/U6 snRNA-associated-splicing factor PRP24 {Bake	99.73
d1x4ha1	98	RNA-binding protein 28 {Mouse (Mus musculus) [TaxI	99.72
d2f9da1	114	Pre-mRNA branch site protein p14 {Human (Homo sapi	99.71
d2msta_	75	Neural RNA-binding protein Musashi-1 {Mouse (Mus m	99.71
d2cpxa1	102	RNA-binding protein 41, RBM41 {Human (Homo sapiens	99.71
d1x4aa1	95	Splicing factor, arginine/serine-rich 1, SFRS1 {Hu	99.71
d2b0ga1	83	Splicesomal U1A protein {Drosophila melanogaster [	99.71
d1x4ga1	96	Nucleolysin TIAR {Human (Homo sapiens) [TaxId: 960	99.7
d1zh5a2	85	Lupus LA protein {Human (Homo sapiens) [TaxId: 960	99.69
d1fjeb1	91	Nucleolin {Golden hamster (Mesocricetus auratus) [	99.69
d2cpda1	86	APOBEC1 stimulating protein {Human (Homo sapiens)	99.69
d1wi8a_	104	Eukaryotic translation initiation factor 4B {Human	99.68
d1x5oa1	101	RNA-binding motif, single-stranded-interacting pro	99.68
d2cpia1	89	E3 ubiquitin protein ligase CNOT4 {Mouse (Mus musc	99.68
d2adca2	88	Polypyrimidine tract-binding protein {Human (Homo	99.68
d1fjca_	96	Nucleolin {Golden hamster (Mesocricetus auratus) [	99.68
d2cqpa1	86	RNA-binding protein 12 {Mouse (Mus musculus) [TaxI	99.68
d1wf2a_	98	Heterogeneous nuclear ribonucleoproteins C1/C2 {Hu	99.67
d1x4ea1	72	RNA-binding motif, single-stranded-interacting pro	99.67
d2cqha1	80	IGF-II mRNA-binding protein 2 isoform A {Human (Ho	99.67
d2cpja1	86	Non-POU domain-containing octamer-binding protein,	99.66
d2ghpa2	75	U4/U6 snRNA-associated-splicing factor PRP24 {Bake	99.66
d1nu4a_	91	Splicesomal U1A protein {Human (Homo sapiens) [Tax	99.66
d2bz2a1	79	Negative elongation factor E, NELF-E {Human (Homo	99.65
d2disa1	96	Hypothetical protein FLJ20273 {Human (Homo sapiens	99.65
d3begb1	87	Splicing factor, arginine/serine-rich 1, SFRS1 {Hu	99.64
d2cpya1	103	RNA-binding protein 12 {Human (Homo sapiens) [TaxI	99.64
d1whxa_	111	Probable RNA-binding protein 19, Rbm19 {Mouse (Mus	99.64
d1wf0a_	88	TAR DNA-binding protein 43, TDP-43 {Human (Homo sa	99.64
d2adca1	109	Polypyrimidine tract-binding protein {Human (Homo	99.64
d1wg1a_	88	Probable RNA-binding protein KIAA1579 {Human (Homo	99.64
d1weza_	102	Heterogeneous nuclear ribonucleoprotein H' {Human	99.64
d1wg5a_	104	Heterogeneous nuclear ribonucleoprotein H' {Human	99.63
d1whya_	97	Putative RNA-binding protein 15B, Rbm15b {Mouse (M	99.62
d2cq1a1	88	Polypyrimidine tract-binding protein 2, PTBP2 {Hum	99.62
d1wi6a1	75	Ribonucleoprotein PTB-binding 1, Raver-1 {Mouse (M	99.62
d1wg4a_	98	Splicing factor, arginine/serine-rich 9 (SFRS9) {M	99.61
d1wexa_	104	Heterogeneous nuclear ribonucleoprotein L-like {Mo	99.59
d2adba1	108	Polypyrimidine tract-binding protein {Human (Homo	99.58
d1wela1	112	RNA-binding protein 12 {Human (Homo sapiens) [TaxI	99.56
d1x4da1	89	Matrin 3 {Mouse (Mus musculus) [TaxId: 10090]}	99.55
d1x4fa1	99	Matrin 3 {Mouse (Mus musculus) [TaxId: 10090]}	99.55
d1u1qa_	183	Nuclear ribonucleoprotein A1 (RNP A1, UP1) {Human	99.52
d1weya_	104	Calcipressin-1 {Mouse (Mus musculus) [TaxId: 10090	99.52
d1u2fa_	90	Splicing factor U2AF 65 KDa subunit {Human (Homo s	99.48
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	99.44
d2cq2a1	101	Alkylation repair AlkB homolog 8, ALKBH8 {Human (H	99.38
d1owxa_	113	Lupus LA protein {Human (Homo sapiens) [TaxId: 960	99.35
d1u1qa_	183	Nuclear ribonucleoprotein A1 (RNP A1, UP1) {Human	99.3
d2dita1	99	HIV Tat-specific factor 1 {Human (Homo sapiens) [T	99.28
d1wwha1	81	Nucleoporin 35 {Mouse (Mus musculus) [TaxId: 10090	99.25
d1o0pa_	104	Splicing factor U2AF 65 KDa subunit {Human (Homo s	99.23
d1ufwa_	95	Synaptojanin 2 {Human (Homo sapiens) [TaxId: 9606]	97.82
d2dgxa1	73	Limkain-b1, LKAP {Human (Homo sapiens) [TaxId: 960	97.08
d1uw4a_	91	RNA processing protein UPF3x, RRM domain {Human (H	97.06
d1whva_	100	Poly(A)-specific ribonuclease PARN {Mouse (Mus mus	94.19
d1zx8a1	124	Hypothetical protein TM1367 {Thermotoga maritima [	93.99

>d2ok3a1 b.62.1.1 (A:1-159) Cyclophilin-like protein PPIL3B {Human (Homo sapiens) [TaxId: 9606]}

class: All beta proteins
fold: Cyclophilin-like
superfamily: Cyclophilin-like
family: Cyclophilin (peptidylprolyl isomerase)
domain: Cyclophilin-like protein PPIL3B
species: Human (Homo sapiens) [TaxId: 9606]

Probab=100.00  E-value=3.8e-43  Score=322.58  Aligned_cols=158  Identities=47%  Similarity=0.805  Sum_probs=147.6

Q ss_pred             CEEEEEecceeEEEEecCCCChhHHHHHHHHHhcCccCCceEEEeecCcccccCCCCCCCCCCCCcccccccccccccCC
Q 007792            1 MSVLIVTSLGDIVVDLFVDKCPLTTKNFLKLCKIKYYNGCLFHTVQKDFTAQTGDPTGTGTGGDSVYKFLYGEQARFFGD   80 (589)
Q Consensus         1 ~~v~~~T~~G~i~ieL~~~~aP~~~~nF~~l~~~~~Y~g~~f~rv~~~~~iq~Gd~~~~~~~~~~~~~~~~~~~~~~~~~   80 (589)
                      |+|+|+|++|+|+|+||++.||+||+||++||+++||+|+.||||+++|+||+|++.....++...++       ..++.
T Consensus         1 msV~~~T~~G~i~ieL~~~~aP~tv~nF~~L~~~g~Y~~~~f~rv~~~~~iq~Gd~~~~~~~~~~~~~-------~~~~~   73 (159)
T d2ok3a1           1 MSVTLHTDVGDIKIEVFCERTPKTCENFLALCASNYYNGCIFHRNIKGFMVQTGDPTGTGRGGNSIWG-------KKFED   73 (159)
T ss_dssp             CEEEEEETTEEEEEEECTTTCHHHHHHHHHHHHTTTTTTCBCCEEETTTEEEECCTTSSSSCCCCTTS-------SCBCC
T ss_pred             CEEEEEeCCeEEEEEEcCCCChHHHHHHHHHHhhhcccceeEecccCCeEEEeCCccccCCCCcccCC-------Ccccc
Confidence            99999999999999999999999999999999999999999999999999999999877766666554       56777


Q ss_pred             ccccCCCCCCCceEEEeccCCCCCcceEEEEeCCCCCCCCCCcceEEEEecCHHHHHHHhhCccCC-CCCcccceeeccc
Q 007792           81 EIRVDLKHAKTGTVAMASAGENLNASQFYMTLRDNLDYLDEKHTIFGEVAEGLETLSRINESFVDE-KNRPYKNIRIKHT  159 (589)
Q Consensus        81 e~~~~l~~~~~G~vs~a~~g~~~~~sqFfI~l~~~~~~ld~~~~vFG~Vv~G~~vl~~i~~~~~~~-~~~p~~~i~I~~~  159 (589)
                      |....++|+.+|+||||+.++++++|||||++.+ .|+||++|+|||+|++||+||++|++++++. +++|..+|+|.+|
T Consensus        74 e~~~~~~~~~~G~lsma~~~~~s~~sqFfIt~~~-~p~ld~~~tvFG~V~~G~~vl~~I~~~~~~~~~~~P~~~i~I~~v  152 (159)
T d2ok3a1          74 EYSEYLKHNVRGVVSMANNGPNTNGSQFFITYGK-QPHLDMKYTVFGKVIDGLETLDELEKLPVNEKTYRPLNDVHIKDI  152 (159)
T ss_dssp             CCCTTCCSCSTTEEEECCSSTTCBCSCEEEESSC-CGGGTTTSCEEEEEEECHHHHHHHHTCCBCTTTCCBSSCCBEEEE
T ss_pred             ccccCCCCCCCeEEEEeeCCCCCcCcceEeeecc-CcccccceEEEEecccchHHHHHHHcCcCCCCCCCcCCCcEEEEE
Confidence            8778899999999999999999999999999998 6999999999999999999999999999976 5789999999999


Q ss_pred             ccccCCC
Q 007792          160 YILEDPF  166 (589)
Q Consensus       160 ~vl~~p~  166 (589)
                      +|+.+||
T Consensus       153 ~i~~~Pf  159 (159)
T d2ok3a1         153 TIHANPF  159 (159)
T ss_dssp             EEECCSC
T ss_pred             EEEeCCC
Confidence            9999997

>d1zkca1 b.62.1.1 (A:280-457) Peptidyl-prolyl cis-trans isomerase-like 2, Cyclophilin-60, PPI domain {Human (Homo sapiens) [TaxId: 9606]}

class: All beta proteins
fold: Cyclophilin-like
superfamily: Cyclophilin-like
family: Cyclophilin (peptidylprolyl isomerase)
domain: Peptidyl-prolyl cis-trans isomerase-like 2, Cyclophilin-60, PPI domain
species: Human (Homo sapiens) [TaxId: 9606]

Probab=100.00  E-value=3e-41  Score=315.37  Aligned_cols=162  Identities=43%  Similarity=0.789  Sum_probs=151.6

Q ss_pred             EEEEEecceeEEEEecCCCChhHHHHHHHHHhcCccCCceEEEeecCcccccCCCCCCCCCCCCcccccccccccccCCc
Q 007792            2 SVLIVTSLGDIVVDLFVDKCPLTTKNFLKLCKIKYYNGCLFHTVQKDFTAQTGDPTGTGTGGDSVYKFLYGEQARFFGDE   81 (589)
Q Consensus         2 ~v~~~T~~G~i~ieL~~~~aP~~~~nF~~l~~~~~Y~g~~f~rv~~~~~iq~Gd~~~~~~~~~~~~~~~~~~~~~~~~~e   81 (589)
                      .|.|+|++|+|+|+||++.||+||+||++||+.++|+|+.||||+++++||+|++..++.++.+.++       ..+++|
T Consensus         2 ~v~l~T~~G~i~IeL~~~~aP~tv~nF~~L~~~~~Y~g~~f~rv~~~~~iq~Gd~~~~~~~~~~~~~-------~~~~~E   74 (178)
T d1zkca1           2 YVRLHTNKGDLNLELHCDLTPKTCENFIRLCKKHYYDGTIFHRSIRNFVIQGGDPTGTGTGGESYWG-------KPFKDE   74 (178)
T ss_dssp             EEEEEETTEEEEEEECTTTSHHHHHHHHHHHHTTTTTTEEEEEEETTTEEEECCTTSSSSCCCBTTB-------SCBCCC
T ss_pred             EEEEEeCCEEEEEEEcCCCChHHHHHHHHHHhcCCcCceEeeeccceeEEecCCccCCCCCCcccCC-------CCcCCc
Confidence            4899999999999999999999999999999999999999999999999999999888888777665       678889


Q ss_pred             cccCCCCCCCceEEEeccCCCCCcceEEEEeCCCCCCCCCCcceEEEEecCHHHHHHHhhCccC-CCCCcccceeecccc
Q 007792           82 IRVDLKHAKTGTVAMASAGENLNASQFYMTLRDNLDYLDEKHTIFGEVAEGLETLSRINESFVD-EKNRPYKNIRIKHTY  160 (589)
Q Consensus        82 ~~~~l~~~~~G~vs~a~~g~~~~~sqFfI~l~~~~~~ld~~~~vFG~Vv~G~~vl~~i~~~~~~-~~~~p~~~i~I~~~~  160 (589)
                      ..+.|+|..+|+|||++.++++++|||||+|.+ +|+||++|+|||+|++||+||++|++++++ .+++|.++|+|.+|.
T Consensus        75 ~~~~l~~~~~G~lsma~~~~~s~~sqF~It~~~-~~~ld~~~~vFG~Vv~G~dvl~~I~~~~t~~~~~~P~~~v~I~~~~  153 (178)
T d1zkca1          75 FRPNLSHTGRGILSMANSGPNSNRSQFFITFRS-CAYLDKKHTIFGRVVGGFDVLTAMENVESDPKTDRPKEEIRIDATT  153 (178)
T ss_dssp             CCTTCCSCSTTEEEECCSSTTCBCSCEEEESSC-CGGGTTTSCEEEEEEECHHHHHHHHHSCBCTTTCCBSSCCEEEEEE
T ss_pred             cccccCCCCCeEEEEeecCCCCccceeeccccC-CcccCCcceEEEEeeCcHHHHHHHHcCCCCCCCCccCCCeEEEEEE
Confidence            888899999999999999999999999999998 699999999999999999999999999997 468999999999999


Q ss_pred             cccCCCCChhh
Q 007792          161 ILEDPFDDPAQ  171 (589)
Q Consensus       161 vl~~p~~~~~~  171 (589)
                      |+.+||+++..
T Consensus       154 Il~~pf~~~~~  164 (178)
T d1zkca1         154 VFVDPYEEADA  164 (178)
T ss_dssp             EEECTTHHHHH
T ss_pred             EEcCCcchhhH
Confidence            99999987654

>d2fu0a1 b.62.1.1 (A:5-159) Putative cyclophilin PFE0505w {Plasmodium falciparum [TaxId: 5833]}

class: All beta proteins
fold: Cyclophilin-like
superfamily: Cyclophilin-like
family: Cyclophilin (peptidylprolyl isomerase)
domain: Putative cyclophilin PFE0505w
species: Plasmodium falciparum [TaxId: 5833]

Probab=100.00  E-value=1.5e-40  Score=304.12  Aligned_cols=152  Identities=41%  Similarity=0.707  Sum_probs=144.1

Q ss_pred             EEEEEecceeEEEEecCCCChhHHHHHHHHHhcCccCCceEEEeecCcccccCCCCCCCCCCCCcccccccccccccCCc
Q 007792            2 SVLIVTSLGDIVVDLFVDKCPLTTKNFLKLCKIKYYNGCLFHTVQKDFTAQTGDPTGTGTGGDSVYKFLYGEQARFFGDE   81 (589)
Q Consensus         2 ~v~~~T~~G~i~ieL~~~~aP~~~~nF~~l~~~~~Y~g~~f~rv~~~~~iq~Gd~~~~~~~~~~~~~~~~~~~~~~~~~e   81 (589)
                      +|+|+|++|+|+|+||++.||+||+||++||+.+||+|+.||||+++++||+|++.+.+.++.++++       ..++++
T Consensus         3 ~~~i~T~~G~i~ieL~~~~aP~tv~nF~~l~~~g~Y~g~~f~rv~~~~~iq~Gd~~~~~~~~~~~~~-------~~~~~~   75 (155)
T d2fu0a1           3 SAIIYTTMGDIHISLFYKECKKTVQNFSVHSINGYYNNCIFHRVIKHFMVQTGDPSGDGTGGESIWG-------NEFEDE   75 (155)
T ss_dssp             EEEEEETTEEEEEEECTTTCHHHHHHHHHHHHTTTTTTCBCCEEETTTEEEECCTTSSSSCCCCTTS-------SCBCCC
T ss_pred             eEEEEEcccEEEEEEcCCCChHHHHHHhhHhhCCccccceeeeeeecceeeccCCCCCCcCCcccCC-------Cccccc
Confidence            6899999999999999999999999999999999999999999999999999999988877777665       568888


Q ss_pred             cccCCCCCCCceEEEeccCCCCCcceEEEEeCCCCCCCCCCcceEEEEecCHHHHHHHhhCccCCCCCcccceeeccccc
Q 007792           82 IRVDLKHAKTGTVAMASAGENLNASQFYMTLRDNLDYLDEKHTIFGEVAEGLETLSRINESFVDEKNRPYKNIRIKHTYI  161 (589)
Q Consensus        82 ~~~~l~~~~~G~vs~a~~g~~~~~sqFfI~l~~~~~~ld~~~~vFG~Vv~G~~vl~~i~~~~~~~~~~p~~~i~I~~~~v  161 (589)
                      ....+.|...|+|+|++.++++++|||||++.+ .|+||++|+|||+|++||+||++|++++++.+++|+.+|+|.+|.|
T Consensus        76 ~~~~~~~~~~~~~~~~~~~~~s~~sqFfI~~~~-~~~ld~~~tvFG~Vi~G~~vv~~I~~~~t~~~~~P~~~i~I~~v~i  154 (155)
T d2fu0a1          76 FFDHLNHSKPFMVSMANCGPNTNGSQFFITTVP-CPWLDFKHTVFGKVTQGSKIVLDIEKVRTDKRDKPLEDIKILNIKI  154 (155)
T ss_dssp             CBTTBCSSSSSEEEECCSSTTCBCSCEEEESSC-CGGGTTTSCEEEEEEECHHHHHHHHTSCBCTTSCBSSCCBEEEEEE
T ss_pred             cccccccCCccEEEecccCCCCCCccceecccC-ccccccceEEEEEEeccHHHHHHHHhCCCCCCCCcCCCcEEEEEEE
Confidence            888899999999999999999999999999998 6999999999999999999999999999999999999999999875

>d1xwna1 b.62.1.1 (A:1-166) Peptidyl-prolyl cis-trans isomerase-like 1, PPIL1 {Human (Homo sapiens) [TaxId: 9606]}

class: All beta proteins
fold: Cyclophilin-like
superfamily: Cyclophilin-like
family: Cyclophilin (peptidylprolyl isomerase)
domain: Peptidyl-prolyl cis-trans isomerase-like 1, PPIL1
species: Human (Homo sapiens) [TaxId: 9606]

Probab=100.00  E-value=1.1e-39  Score=301.49  Aligned_cols=152  Identities=44%  Similarity=0.771  Sum_probs=143.0

Q ss_pred             CEEEEEecceeEEEEecCCCChhHHHHHHHHHhcCccCCceEEEeecCcccccCCCCCCCCCCCCcccccccccccccCC
Q 007792            1 MSVLIVTSLGDIVVDLFVDKCPLTTKNFLKLCKIKYYNGCLFHTVQKDFTAQTGDPTGTGTGGDSVYKFLYGEQARFFGD   80 (589)
Q Consensus         1 ~~v~~~T~~G~i~ieL~~~~aP~~~~nF~~l~~~~~Y~g~~f~rv~~~~~iq~Gd~~~~~~~~~~~~~~~~~~~~~~~~~   80 (589)
                      +.|+|+|++|+|+||||++.||+||+||++||+.+||+|+.||||+++|+||+|++.+++.++.++++       ..++.
T Consensus        12 p~v~~~T~~G~i~ieL~~~~aP~tv~nF~~L~~~g~Y~g~~f~rv~~~~~iq~Gd~~~~~~~~~~~~~-------~~~~~   84 (166)
T d1xwna1          12 PNVYLETSMGIIVLELYWKHAPKTCKNFAELARRGYYNGTKFHRIIKDFMIQGGDPTGTGRGGASIYG-------KQFED   84 (166)
T ss_dssp             CEEEEEESSCEEEEEECTTTCHHHHHHHHHHHHHTSSTTCCEEEEETTTEEEECCSTTTTSSCCCSSC-------SCCCC
T ss_pred             CEEEEEECceeEEEEEcCCCChHHHHHHHHHHhcCCcCceeeeEEcccEEEEeCCCCCCCCCCccCCC-------Ccccc
Confidence            47999999999999999999999999999999999999999999999999999999988877777665       56888


Q ss_pred             ccccCCCCCCCceEEEeccCCCCCcceEEEEeCCCCCCCCCCcceEEEEecCHHHHHHHhhCccCCCCCcccceeecccc
Q 007792           81 EIRVDLKHAKTGTVAMASAGENLNASQFYMTLRDNLDYLDEKHTIFGEVAEGLETLSRINESFVDEKNRPYKNIRIKHTY  160 (589)
Q Consensus        81 e~~~~l~~~~~G~vs~a~~g~~~~~sqFfI~l~~~~~~ld~~~~vFG~Vv~G~~vl~~i~~~~~~~~~~p~~~i~I~~~~  160 (589)
                      |.++.+.|+.+|+|+|++.++++++|||||+|.+ .++||++|+|||+|++||+||++|+.++++.+++|..+|+|.+..
T Consensus        85 e~~~~~~~~~~G~lsm~~~~~~s~~sqFfI~~~~-~~~ld~~~tvFG~Vi~G~dvl~~I~~~~t~~~~~P~~~I~I~~a~  163 (166)
T d1xwna1          85 ELHPDLKFTGAGILAMANAGPDTNGSQFFVTLAP-TQWLDGKHTIFGRVCQGIGMVNRVGMVETNSQDRPVDDVKIIKAY  163 (166)
T ss_dssp             CCCTTCCSCSSSEEEEEEEETTEEEEEEEEECSC-CSTTTTTSEEEEECSSCHHHHHHHHHSCBCSSSCBSSCCCEEEEE
T ss_pred             ccCCCCCCCCCeEEEecccCCCCCCcceEEeecC-hhhccccceEEEEEechHHHHHHHHhCCCCCCCCCCCCeEEEEee
Confidence            8888899999999999999999999999999998 699999999999999999999999999999999999999998764

>d2b71a1 b.62.1.1 (A:23-191) Cyclophilin-like protein PY00693 {Plasmodium yoelii [TaxId: 5861]}

class: All beta proteins
fold: Cyclophilin-like
superfamily: Cyclophilin-like
family: Cyclophilin (peptidylprolyl isomerase)
domain: Cyclophilin-like protein PY00693
species: Plasmodium yoelii [TaxId: 5861]

Probab=100.00  E-value=2.3e-39  Score=300.06  Aligned_cols=151  Identities=40%  Similarity=0.722  Sum_probs=141.4

Q ss_pred             EEEEEecceeEEEEecCCCChhHHHHHHHHHhcCccCCceEEEeecCcccccCCCCCCCCCCCCcccccccccccccCCc
Q 007792            2 SVLIVTSLGDIVVDLFVDKCPLTTKNFLKLCKIKYYNGCLFHTVQKDFTAQTGDPTGTGTGGDSVYKFLYGEQARFFGDE   81 (589)
Q Consensus         2 ~v~~~T~~G~i~ieL~~~~aP~~~~nF~~l~~~~~Y~g~~f~rv~~~~~iq~Gd~~~~~~~~~~~~~~~~~~~~~~~~~e   81 (589)
                      .|+|+|++|+|+|+||++.||+||+||++||+.+||+|+.||||++++++|||++.+...++.+++.       ..++.|
T Consensus        18 ~V~l~T~~G~i~IeL~~d~aP~tv~nF~~L~~~g~Y~~~~f~rv~~~~~iq~g~~~~~~~~~~~~~~-------~~~~~e   90 (169)
T d2b71a1          18 YITIYTNLGDFEVELYWYHSPKTCLNFYTLCEMGFYDNTIFHRVIPNFVIQGGDPTGTGKGGKSIYG-------EYFEDE   90 (169)
T ss_dssp             EEEEEETTEEEEEEECTTTSHHHHHHHHHHHHTTTTTTEEEEEEETTTEEEEEETTSSSSCCCBTTB-------SCBCCC
T ss_pred             EEEEEeCceeEEEEEeCCCCcHHHHHHHHHhhCCccceeeeccccceeeEeccccccccCCCccccc-------cccccc
Confidence            5899999999999999999999999999999999999999999999999999999877766666554       567888


Q ss_pred             cccCCCCCCCceEEEeccCCCCCcceEEEEeCCCCCCCCCCcceEEEEecCHHHHHHHhhCccCCCCCcccceeecccc
Q 007792           82 IRVDLKHAKTGTVAMASAGENLNASQFYMTLRDNLDYLDEKHTIFGEVAEGLETLSRINESFVDEKNRPYKNIRIKHTY  160 (589)
Q Consensus        82 ~~~~l~~~~~G~vs~a~~g~~~~~sqFfI~l~~~~~~ld~~~~vFG~Vv~G~~vl~~i~~~~~~~~~~p~~~i~I~~~~  160 (589)
                      ....|+|..+|+|+|++.++++++|||||++.+ .|+||++|+|||+|++||+||++|++++++++++|..+|.|.+|.
T Consensus        91 ~~~~l~h~~~g~ls~~~~~p~s~~sqFfIt~~~-~~~ld~~~tvFG~Vv~G~dvl~~I~~~~~~~~~~P~~~i~I~~~~  168 (169)
T d2b71a1          91 INKELKHTGAGILSMSNNGPNTNSSQFFITLAP-LPHLDGKHTIFARVSKNMTCIENIASVQTTATNKPIFDLKILRTS  168 (169)
T ss_dssp             CCTTCCCCSTTEEEECCSSTTCBSSCEEEESSC-CGGGTTTSCEEEEEEECHHHHHHHHTSCBCTTCCBSSCCEEEEEE
T ss_pred             cccccCCCCcEEEEhhhCCCCCCCCEEEEecCC-cchhhhhcceeeEEeccHHHHHHHHhCCCCCCCCCCCCeEEEEcc
Confidence            888899999999999999999999999999998 699999999999999999999999999999999999999998874

>d1w74a_ b.62.1.1 (A:) Peptidyl-prolyl cis-trans isomerase A, PpiA {Mycobacterium tuberculosis [TaxId: 1773]}

class: All beta proteins
fold: Cyclophilin-like
superfamily: Cyclophilin-like
family: Cyclophilin (peptidylprolyl isomerase)
domain: Peptidyl-prolyl cis-trans isomerase A, PpiA
species: Mycobacterium tuberculosis [TaxId: 1773]

Probab=100.00  E-value=5.6e-38  Score=291.85  Aligned_cols=149  Identities=38%  Similarity=0.631  Sum_probs=137.3

Q ss_pred             EEEEEecceeEEEEecCCCChhHHHHHHHHHhcC---------------ccCCceEEEeecCcccccCCCCCCCCCCCCc
Q 007792            2 SVLIVTSLGDIVVDLFVDKCPLTTKNFLKLCKIK---------------YYNGCLFHTVQKDFTAQTGDPTGTGTGGDSV   66 (589)
Q Consensus         2 ~v~~~T~~G~i~ieL~~~~aP~~~~nF~~l~~~~---------------~Y~g~~f~rv~~~~~iq~Gd~~~~~~~~~~~   66 (589)
                      +|+|+|++|+|+||||++.||+||+||++||+++               ||+++.||++++++++|||++...+.++.. 
T Consensus         5 ~~ti~T~~G~I~ieL~~d~aP~tv~nF~~L~~~~~~~~~~~~~~~~~~~~Y~g~~~~rv~~~~~iq~g~~~~~~~~~~~-   83 (171)
T d1w74a_           5 TATLHTNRGDIKIALFGNHAPKTVANFVGLAQGTKDYSTQNASGGPSGPFYDGAVFHRVIQGFMIQGGDPTGTGRGGPG-   83 (171)
T ss_dssp             EEEEEETTEEEEEEECTTTSHHHHHHHHHHHHTCSCCSSCCTTBSSSSCSSTTEEEEEEETTTEEEECCTTSSSSCCSS-
T ss_pred             EEEEEECCEEEEEEEcCCCChHHHHHHHHHHhcCCccccccccccccCceECCeecccccCCceeEcccccCCCCCCcc-
Confidence            7999999999999999999999999999999877               799999999999999999998876655443 


Q ss_pred             ccccccccccccCCccccCCCCCCCceEEEeccCCCCCcceEEEEeCCCCCCCCCCcceEEEEe--cCHHHHHHHhhCcc
Q 007792           67 YKFLYGEQARFFGDEIRVDLKHAKTGTVAMASAGENLNASQFYMTLRDNLDYLDEKHTIFGEVA--EGLETLSRINESFV  144 (589)
Q Consensus        67 ~~~~~~~~~~~~~~e~~~~l~~~~~G~vs~a~~g~~~~~sqFfI~l~~~~~~ld~~~~vFG~Vv--~G~~vl~~i~~~~~  144 (589)
                               ..++.|..+.++|+.+|+|+|++.++++++|||||+|.+ .|+||++|+|||+||  +||+||++|+++++
T Consensus        84 ---------~~~~~e~~~~~~~~~~g~v~~~~~~~~s~~sqFfIt~~~-~p~ld~~~tVFG~Vv~geGmdvl~~I~~~~~  153 (171)
T d1w74a_          84 ---------YKFADEFHPELQFDKPYLLAMANAGPGTNGSQFFITVGK-TPHLNRRHTIFGEVIDAESQRVVEAISKTAT  153 (171)
T ss_dssp             ---------CCBCCCCCTTCCSCSSSEEEECCSSTTCBSSCEEEESSC-CGGGTTTSCEEEEECSHHHHHHHHHHHTSCB
T ss_pred             ---------cccccccCCCcCCCCCEEEEEEecCCCCCCcceEeeccC-CCccccccEEEEEEeccccHHHHHHHHcCCc
Confidence                     236677778899999999999999999999999999998 699999999999999  49999999999999


Q ss_pred             CCCCCcccceeeccccc
Q 007792          145 DEKNRPYKNIRIKHTYI  161 (589)
Q Consensus       145 ~~~~~p~~~i~I~~~~v  161 (589)
                      +.+++|..+|+|.+|.|
T Consensus       154 ~~~~~P~~~i~I~~v~i  170 (171)
T d1w74a_         154 DGNDRPTDPVVIESITI  170 (171)
T ss_dssp             CTTSCBSSCCEEEEEEE
T ss_pred             CCCCccCCCcEEEEEEE
Confidence            99999999999999876

>d2a2na1 b.62.1.1 (A:483-646) Peptidylprolyl isomerase domain and WD repeat-containing protein 1, PPWD1, C-terminal domain {Human (Homo sapiens) [TaxId: 9606]}

class: All beta proteins
fold: Cyclophilin-like
superfamily: Cyclophilin-like
family: Cyclophilin (peptidylprolyl isomerase)
domain: Peptidylprolyl isomerase domain and WD repeat-containing protein 1, PPWD1, C-terminal domain
species: Human (Homo sapiens) [TaxId: 9606]

Probab=100.00  E-value=7.5e-38  Score=289.06  Aligned_cols=153  Identities=43%  Similarity=0.750  Sum_probs=138.5

Q ss_pred             CEEEEEecceeEEEEecCCCChhHHHHHHHHHhcCccCCceEEEeecCcccccCCCCCCCCCCCCcccccccccccccCC
Q 007792            1 MSVLIVTSLGDIVVDLFVDKCPLTTKNFLKLCKIKYYNGCLFHTVQKDFTAQTGDPTGTGTGGDSVYKFLYGEQARFFGD   80 (589)
Q Consensus         1 ~~v~~~T~~G~i~ieL~~~~aP~~~~nF~~l~~~~~Y~g~~f~rv~~~~~iq~Gd~~~~~~~~~~~~~~~~~~~~~~~~~   80 (589)
                      ++|+|+|++|+|+|+||.+.||+||+||++||+.++|+|+.|||++++|++|+|++.+...++.....       ..+..
T Consensus        10 ~~a~~~T~~G~i~ieL~~~~aP~tv~nF~~l~~~g~Y~g~~f~rv~~~~~iq~G~~~~~~~~~~~~~~-------~~~~~   82 (164)
T d2a2na1          10 DSAIIHTSMGDIHTKLFPVECPKTVENFCVHSRNGYYNGHTFHRIIKGFMIQTGDPTGTGMGGESIWG-------GEFED   82 (164)
T ss_dssp             SEEEEEETTEEEEEEECTTTCHHHHHHHHHHHHTTTTTTCBCCEEETTTEEEECCTTSSSSCCCCTTS-------SCBCC
T ss_pred             CEEEEEeceeEEEEEEcCCCChHHHHHHHHHHhCCCcccceeeEEeeeeeEeecccccccCCCceeee-------ccccc
Confidence            47999999999999999999999999999999999999999999999999999998765544443222       44667


Q ss_pred             ccccCCCCCCCceEEEeccCCCCCcceEEEEeCCCCCCCCCCcceEEEEecCHHHHHHHhhCccCC-CCCcccceeeccc
Q 007792           81 EIRVDLKHAKTGTVAMASAGENLNASQFYMTLRDNLDYLDEKHTIFGEVAEGLETLSRINESFVDE-KNRPYKNIRIKHT  159 (589)
Q Consensus        81 e~~~~l~~~~~G~vs~a~~g~~~~~sqFfI~l~~~~~~ld~~~~vFG~Vv~G~~vl~~i~~~~~~~-~~~p~~~i~I~~~  159 (589)
                      +....++|+..|+|+|++.++++++|||||+|.+ .|+||++|+|||+|++||+||++|++++++. +++|+++|.|.+|
T Consensus        83 ~~~~~~~~~~~~~l~~~~~~~~s~~sqFfI~~~~-~~~ld~~~tVFG~V~~G~dvv~~I~~~~~~~~~~~P~~~V~I~~v  161 (164)
T d2a2na1          83 EFHSTLRHDRPYTLSMANAGSNTNGSQFFITVVP-TPWLDNKHTVFGRVTKGMEVVQRISNVKVNPKTDKPYEDVSIINI  161 (164)
T ss_dssp             CCCTTCCSCSSSEEEECCSSTTCBCSCEEEESSC-CGGGTTTSCEEEEEEECHHHHHHHHTSCBCTTTCCBSSCCBEEEE
T ss_pred             ccccccccCccceeehhhcCCCCCcccceecccC-ccccccceeEEEEecChHHHHHHHHcCCcCCCCCCcCCCcEEEEE
Confidence            7778899999999999999999999999999998 6999999999999999999999999999985 5899999999999


Q ss_pred             cc
Q 007792          160 YI  161 (589)
Q Consensus       160 ~v  161 (589)
                      .|
T Consensus       162 ~i  163 (164)
T d2a2na1         162 TV  163 (164)
T ss_dssp             EE
T ss_pred             EE
Confidence            76

>d1h0pa_ b.62.1.1 (A:) Cyclophilin (eukaryotic) {Caenorhabditis elegans, isoform 5 [TaxId: 6239]}

class: All beta proteins
fold: Cyclophilin-like
superfamily: Cyclophilin-like
family: Cyclophilin (peptidylprolyl isomerase)
domain: Cyclophilin (eukaryotic)
species: Caenorhabditis elegans, isoform 5 [TaxId: 6239]

Probab=100.00  E-value=2.2e-37  Score=290.43  Aligned_cols=161  Identities=37%  Similarity=0.618  Sum_probs=139.6

Q ss_pred             EEEE-EecceeEEEEecCCCChhHHHHHHHHHhcC---ccCCceEEEeecCcccccCCCC-CCCCCCCCccccccccccc
Q 007792            2 SVLI-VTSLGDIVVDLFVDKCPLTTKNFLKLCKIK---YYNGCLFHTVQKDFTAQTGDPT-GTGTGGDSVYKFLYGEQAR   76 (589)
Q Consensus         2 ~v~~-~T~~G~i~ieL~~~~aP~~~~nF~~l~~~~---~Y~g~~f~rv~~~~~iq~Gd~~-~~~~~~~~~~~~~~~~~~~   76 (589)
                      .|.+ .|++|+|+||||.+.||+||+||++||+.+   +|+++.||||+++|+||+|++. +++.++.++++       .
T Consensus        12 di~i~~~~~G~i~IeL~~d~aP~tv~nF~~l~~~g~~~~y~g~~f~rv~~~~~iq~G~~~~~~~~g~~~~~~-------~   84 (182)
T d1h0pa_          12 DMEIGGKPIGRIVIGLFGKTVPKTATNFIELAKKPKGEGYPGSKFHRVIADFMIQGGDFTRGDGTGGRSIYG-------E   84 (182)
T ss_dssp             EEEETTEEEEEEEEEECTTTSHHHHHHHHHHHHSCTTTSSTTCBCCEEETTTEEEECCTTTSSSSCCCBTTB-------S
T ss_pred             EEEECCEECeEEEEEECCCCChHHHHHHHHHHHhcccCCcCCceEEEEEecceEEcCCCCCCCCCCCCCCCC-------C
Confidence            4444 388999999999999999999999999765   8999999999999999999977 45666666554       3


Q ss_pred             ccCCccccCCCCCCCceEEEeccCCCCCcceEEEEeCCCCCCCCCCcceEEEEecCHHHHHHHhhCccCCCCCcccceee
Q 007792           77 FFGDEIRVDLKHAKTGTVAMASAGENLNASQFYMTLRDNLDYLDEKHTIFGEVAEGLETLSRINESFVDEKNRPYKNIRI  156 (589)
Q Consensus        77 ~~~~e~~~~l~~~~~G~vs~a~~g~~~~~sqFfI~l~~~~~~ld~~~~vFG~Vv~G~~vl~~i~~~~~~~~~~p~~~i~I  156 (589)
                      .+.++ .+.+.|..+|+|+||+.++++++|||||+|.+ .|+||++|+|||+|++||+||++|++++++.+++|.++|+|
T Consensus        85 ~~~~~-~~~~~~~~~G~~~~a~~g~~s~~sqFfIt~~~-~~~ldg~ytvFG~Vi~G~dvl~~I~~~~~~~~~~P~~~v~I  162 (182)
T d1h0pa_          85 KFADE-NFKLKHYGAGWLSMANAGADTNGSQFFITTVK-TPWLDGRHVVFGKILEGMDVVRKIEQTEKLPGDRPKQDVII  162 (182)
T ss_dssp             CBCCC-CCCSCCCSTTEEEECCSSTTCBCSCEEEESSC-CGGGTTTSCEEEEEEECHHHHHHHHTSCEETTTEESSCEEE
T ss_pred             ccCcc-cccccccCCceeeecccCCCCcCccccccccc-cccccccceeEEEEeehHHHHHHHHhcCCCCCCCCCCCEEE
Confidence            45555 35667778999999999999999999999998 69999999999999999999999999999999999999999


Q ss_pred             ccccccc--CCCCChhh
Q 007792          157 KHTYILE--DPFDDPAQ  171 (589)
Q Consensus       157 ~~~~vl~--~p~~~~~~  171 (589)
                      .+|+++.  +||+.+++
T Consensus       163 ~~cG~l~~~~p~~~~~~  179 (182)
T d1h0pa_         163 AASGHIAVDTPFSVERE  179 (182)
T ss_dssp             EEEEEEEEEEEEECCSS
T ss_pred             EECCeEeCCCCCccccc
Confidence            9998764  56665544

>d1v9ta_ b.62.1.1 (A:) Peptidyl-prolyl cis-trans isomerase A, PpiA {Escherichia coli [TaxId: 562]}

class: All beta proteins
fold: Cyclophilin-like
superfamily: Cyclophilin-like
family: Cyclophilin (peptidylprolyl isomerase)
domain: Peptidyl-prolyl cis-trans isomerase A, PpiA
species: Escherichia coli [TaxId: 562]

Probab=100.00  E-value=5.6e-37  Score=283.38  Aligned_cols=150  Identities=29%  Similarity=0.461  Sum_probs=131.2

Q ss_pred             EEEEEecceeEEEEecCCCChhHHHHHHHHHhcCccCCceEEEeecCcccccCCCCCCCCCCCCcccccccccccccCCc
Q 007792            2 SVLIVTSLGDIVVDLFVDKCPLTTKNFLKLCKIKYYNGCLFHTVQKDFTAQTGDPTGTGTGGDSVYKFLYGEQARFFGDE   81 (589)
Q Consensus         2 ~v~~~T~~G~i~ieL~~~~aP~~~~nF~~l~~~~~Y~g~~f~rv~~~~~iq~Gd~~~~~~~~~~~~~~~~~~~~~~~~~e   81 (589)
                      .|+|+|++|+|+|+||++.||+||+||++||+.+||+|+.||||+++|++|+|++......+.  +       ...+++|
T Consensus         6 ~V~l~T~~G~i~ieL~~~~aP~tv~nF~~L~~~~~Y~g~~fhRv~~~~~iq~G~~~~~~~~~~--~-------~~~~~~e   76 (166)
T d1v9ta_           6 HVLLTTSAGNIELELDKQKAPVSVQNFVDYVNSGFYNNTTFHRVIPGFMIQGGGFTEQMQQKK--P-------NPPIKNE   76 (166)
T ss_dssp             EEEEEETTEEEEEEECTTTCHHHHHHHHHHHHTTTTTTCBEEEEETTTEEEESSBCTTCCBCC--C-------CCCBCCC
T ss_pred             EEEEEECCeeEEEEEeCCCChHHHHHHHHHhhCCccccceeeEEEEEeecccCCcCCcccccC--C-------CCCcccc
Confidence            589999999999999999999999999999999999999999999999999998764332221  1       2457888


Q ss_pred             cccCCCCCCCceEEEec-cCCCCCcceEEEEeCCCCCCCCC-----CcceEEEEecCHHHHHHHhhCccCCCC----Ccc
Q 007792           82 IRVDLKHAKTGTVAMAS-AGENLNASQFYMTLRDNLDYLDE-----KHTIFGEVAEGLETLSRINESFVDEKN----RPY  151 (589)
Q Consensus        82 ~~~~l~~~~~G~vs~a~-~g~~~~~sqFfI~l~~~~~~ld~-----~~~vFG~Vv~G~~vl~~i~~~~~~~~~----~p~  151 (589)
                      ....++| .+|+|+|++ .++++++|||||++.+ .|+||+     +|||||+|++||+||++|+.++++..+    +|+
T Consensus        77 ~~~~~~~-~rg~v~~~~~~~~~s~~sqFfI~~~~-~~~ld~~~~~~~~tvfG~VveG~dvl~~I~~~~~~~~~~~~~~P~  154 (166)
T d1v9ta_          77 ADNGLRN-TRGTIAMARTADKDSATSQFFINVAD-NAFLDHGQRDFGYAVFGKVVKGMDVADKISQVPTHDVGPYQNVPS  154 (166)
T ss_dssp             GGGSCCC-CTTEEEECCCSSTTCBCSCEEEESSC-CGGGSCCSSCCCCCEEEEEEECHHHHHHHHTSCEEEETTEEEEES
T ss_pred             ccccccc-cCCEEEEEeeecCCCcccccccccCC-ccccccccccCCEEEeeEEeccHHHHHHHHhCcccCCCCCCCccC
Confidence            7777877 679999988 5679999999999998 588876     489999999999999999999987643    899


Q ss_pred             cceeecccccc
Q 007792          152 KNIRIKHTYIL  162 (589)
Q Consensus       152 ~~i~I~~~~vl  162 (589)
                      ++|+|.+|+|+
T Consensus       155 ~~v~I~~~~vl  165 (166)
T d1v9ta_         155 KPVVILSATVL  165 (166)
T ss_dssp             SCCBEEEEEEC
T ss_pred             CCeEEEEEEEc
Confidence            99999999986

>d1xo7a_ b.62.1.1 (A:) Cyclophilin (eukaryotic) {Trypanosoma cruzi [TaxId: 5693]}

class: All beta proteins
fold: Cyclophilin-like
superfamily: Cyclophilin-like
family: Cyclophilin (peptidylprolyl isomerase)
domain: Cyclophilin (eukaryotic)
species: Trypanosoma cruzi [TaxId: 5693]

Probab=100.00  E-value=1e-36  Score=281.57  Aligned_cols=146  Identities=36%  Similarity=0.617  Sum_probs=129.4

Q ss_pred             ecceeEEEEecCCCChhHHHHHHHHHhcCc---cCCceEEEeecCcccccCCCC-CCCCCCCCcccccccccccccCCcc
Q 007792            7 TSLGDIVVDLFVDKCPLTTKNFLKLCKIKY---YNGCLFHTVQKDFTAQTGDPT-GTGTGGDSVYKFLYGEQARFFGDEI   82 (589)
Q Consensus         7 T~~G~i~ieL~~~~aP~~~~nF~~l~~~~~---Y~g~~f~rv~~~~~iq~Gd~~-~~~~~~~~~~~~~~~~~~~~~~~e~   82 (589)
                      |++|+|+||||.+.||+||+||++||+.++   |+|+.|||+++++++|+|++. .++.++...++       ..++.+.
T Consensus        17 ~~~G~i~ieL~~~~aP~t~~nF~~l~~~~~~~~Y~g~~f~rv~~~~~iq~G~~~~~~~~~~~~~~~-------~~~~~~~   89 (166)
T d1xo7a_          17 EPVGRVVIGLFGNDVPKTVENFKQLASGENGFGYKGSIFHRVIRNFMIQGGDFTNFDGTGGKSIYG-------TRFDDEN   89 (166)
T ss_dssp             EEEEEEEEEECTTTCHHHHHHHHHHHHTTTSCCSTTCBEEEEETTTEEEECCTTTSSSSCCCBTTB-------SCBCCCC
T ss_pred             EECcEEEEEECCCCChHHHHHHHHhhcccccccccCcEEEEEcCCCEEEeCCCCCCCCCCCCCCCC-------ccccccc
Confidence            789999999999999999999999999988   999999999999999999877 34555555443       3344442


Q ss_pred             ccCCCCCCCceEEEeccCCCCCcceEEEEeCCCCCCCCCCcceEEEEecCHHHHHHHhhCccCCCCCcccceeecccccc
Q 007792           83 RVDLKHAKTGTVAMASAGENLNASQFYMTLRDNLDYLDEKHTIFGEVAEGLETLSRINESFVDEKNRPYKNIRIKHTYIL  162 (589)
Q Consensus        83 ~~~l~~~~~G~vs~a~~g~~~~~sqFfI~l~~~~~~ld~~~~vFG~Vv~G~~vl~~i~~~~~~~~~~p~~~i~I~~~~vl  162 (589)
                        ...|..+|+|+||+.++++++|||||+|.+ +|+||++|+|||+|++||+||++|++++++.+++|..+|.|.+|++|
T Consensus        90 --~~~~~~~G~l~~a~~g~~s~~sqFfIt~~~-~~~ld~~~~vfG~Vi~G~~vl~~I~~~~~~~~~~P~~~i~I~~cgvl  166 (166)
T d1xo7a_          90 --LKIKHFVGAVSMANAGPNSNGSQFFVTTAP-TPWLDGRHVVFGKVVEGMDVVKKVENTKTGLNDKPKKAVKINDCGVL  166 (166)
T ss_dssp             --CCSCCCTTEEEECCSSTTCBCSCEEEESSC-CGGGTTTSCEEEEEEECHHHHHHHHTSCBCGGGCBSSCEEEEEEEEC
T ss_pred             --ccccccccceeecccCCCCCCCeeEEccCC-ccccCccceeeeEEeeHHHHHHHHHcCCCCCCCCCCCCEEEEeeEeC
Confidence              334457899999999999999999999998 69999999999999999999999999999999999999999999986

>d2z6wa1 b.62.1.1 (A:2-165) Mitochondrial peptidyl-prolyl cis-trans isomerase, cyclophilin F {Human (Homo sapiens) [TaxId: 9606]}

class: All beta proteins
fold: Cyclophilin-like
superfamily: Cyclophilin-like
family: Cyclophilin (peptidylprolyl isomerase)
domain: Mitochondrial peptidyl-prolyl cis-trans isomerase, cyclophilin F
species: Human (Homo sapiens) [TaxId: 9606]

Probab=100.00  E-value=1.5e-36  Score=279.90  Aligned_cols=146  Identities=40%  Similarity=0.639  Sum_probs=129.0

Q ss_pred             ecceeEEEEecCCCChhHHHHHHHHHhcC---ccCCceEEEeecCcccccCCCCC-CCCCCCCcccccccccccccCCcc
Q 007792            7 TSLGDIVVDLFVDKCPLTTKNFLKLCKIK---YYNGCLFHTVQKDFTAQTGDPTG-TGTGGDSVYKFLYGEQARFFGDEI   82 (589)
Q Consensus         7 T~~G~i~ieL~~~~aP~~~~nF~~l~~~~---~Y~g~~f~rv~~~~~iq~Gd~~~-~~~~~~~~~~~~~~~~~~~~~~e~   82 (589)
                      +++|+|+|+||++.||+||+||++||..+   +|+|+.||||++++++|+|++.. .+.++..+++       ..++++ 
T Consensus        14 ~~~G~i~ieL~~~~aP~tv~nF~~l~~~~~~~~Y~g~~f~rv~~~~~iq~g~~~~~~~~~~~~~~~-------~~~~~~-   85 (164)
T d2z6wa1          14 KPLGRVVLELKADVVPKTAENFRALCTGEKGFGYKGSTFHRVIPSFMCQAGDFTNHNGTGGKSIYG-------SRFPDE-   85 (164)
T ss_dssp             EEEEEEEEEECTTTCHHHHHHHHHHHHTTTSCCSTTCBEEEEETTTEEEECCTTTSSSSCCCBTTB-------SCBCCC-
T ss_pred             EeceEEEEEECCCcCcHHHHHHHHHHhcCCCcccCCcEEEEecccceEecCCccCCCCCCCccccC-------CcCCcc-
Confidence            45899999999999999999999999766   79999999999999999999874 4555555554       345555 


Q ss_pred             ccCCCCCCCceEEEeccCCCCCcceEEEEeCCCCCCCCCCcceEEEEecCHHHHHHHhhCccCCCCCcccceeecccccc
Q 007792           83 RVDLKHAKTGTVAMASAGENLNASQFYMTLRDNLDYLDEKHTIFGEVAEGLETLSRINESFVDEKNRPYKNIRIKHTYIL  162 (589)
Q Consensus        83 ~~~l~~~~~G~vs~a~~g~~~~~sqFfI~l~~~~~~ld~~~~vFG~Vv~G~~vl~~i~~~~~~~~~~p~~~i~I~~~~vl  162 (589)
                      .+.+.|+.+|+||||+.++++++|||||++.+ +|+||++|+|||+|++||+||++|+++++. +++|.++|+|.+|+.|
T Consensus        86 ~~~~~~~~~G~lsma~~~~~s~~sqFfi~~~~-~~~ldg~ytVFG~Vv~G~dvl~~I~~~~~~-~~~P~~~i~I~~cG~l  163 (164)
T d2z6wa1          86 NFTLKHVGPGVLSMANAGPNTNGSQFFICTIK-TDWLDGKHVVFGHVIEGMDVVKKIESFGSK-SGRTSKKIVITDCGQL  163 (164)
T ss_dssp             CCCSCCCSTTEEEECCSSTTCBCSCEEEESSC-CGGGTTTSCEEEEEEECHHHHHHHHHTCCT-TSCCSSCEEEEEEEEC
T ss_pred             ccccccCCccEEEEecCCCCCCCcceeccccC-CCcccccceEEEEecccHHHHHHHHhCCCC-CCCCCCCEEEEeCeec
Confidence            45677778999999999999999999999998 699999999999999999999999998865 6899999999999987

>d2igva1 b.62.1.1 (A:1-172) Cyclophilin (eukaryotic) {Caenorhabditis elegans, isoform 3 [TaxId: 6239]}

class: All beta proteins
fold: Cyclophilin-like
superfamily: Cyclophilin-like
family: Cyclophilin (peptidylprolyl isomerase)
domain: Cyclophilin (eukaryotic)
species: Caenorhabditis elegans, isoform 3 [TaxId: 6239]

Probab=100.00  E-value=1e-36  Score=283.21  Aligned_cols=152  Identities=37%  Similarity=0.614  Sum_probs=133.1

Q ss_pred             EEEEE-ecceeEEEEecCCCChhHHHHHHHHHhc----------CccCCceEEEeecCcccccCCCC-CCCCCCCCcccc
Q 007792            2 SVLIV-TSLGDIVVDLFVDKCPLTTKNFLKLCKI----------KYYNGCLFHTVQKDFTAQTGDPT-GTGTGGDSVYKF   69 (589)
Q Consensus         2 ~v~~~-T~~G~i~ieL~~~~aP~~~~nF~~l~~~----------~~Y~g~~f~rv~~~~~iq~Gd~~-~~~~~~~~~~~~   69 (589)
                      .|.|. |++|+|+|+||.+.||+||+||++||++          ++|++|.||||+++++||+|++. ++++++..+++ 
T Consensus         9 Di~i~~~~~G~i~ieL~~~~aP~tv~nF~~L~~~~~~~~~~~k~~~y~~~~f~rv~~~~~i~~G~~~~~~~~~~~~~~~-   87 (172)
T d2igva1           9 DITIGGKASGRIVMELYDDVVPKTAGNFRALCTGENGIGKSGKPLHFKGSKFHRIIPNFMIQGGDFTRGNGTGGESIYG-   87 (172)
T ss_dssp             EEEETTEEEEEEEEEECTTTCHHHHHHHHHHHHTTTCBCTTSSBSCCTTCBCCEEETTTEEEECCTTTSSSSCCCBTTB-
T ss_pred             EEEECCEeccEEEEEEcCCCCcHHHHHHHHHHhccccccccCcccccCCcceeEEEecceEEcCCccCCCCCCCcccCC-
Confidence            44443 7799999999999999999999999964          58999999999999999999876 45666666554 


Q ss_pred             cccccccccCCccccCCCCCCCceEEEeccCCCCCcceEEEEeCCCCCCCCCCcceEEEEecCHHHHHHHhhCccCCCCC
Q 007792           70 LYGEQARFFGDEIRVDLKHAKTGTVAMASAGENLNASQFYMTLRDNLDYLDEKHTIFGEVAEGLETLSRINESFVDEKNR  149 (589)
Q Consensus        70 ~~~~~~~~~~~e~~~~l~~~~~G~vs~a~~g~~~~~sqFfI~l~~~~~~ld~~~~vFG~Vv~G~~vl~~i~~~~~~~~~~  149 (589)
                            ..+++|. ..+.|..+|+||||+.++++++|||||+|.+ +|+||++|+|||+||+||+||++|+.+++ .+++
T Consensus        88 ------~~~~~e~-~~~~~~~~G~lsma~~~~~~~~sqFfIt~~~-~~~ld~~~~vFG~Vv~Gmdvl~~I~~~~~-~~g~  158 (172)
T d2igva1          88 ------EKFPDEN-FKEKHTGPGVLSMANAGPNTNGSQFFLCTVK-TEWLDGKHVVFGRVVEGLDVVKAVESNGS-QSGK  158 (172)
T ss_dssp             ------SCBCCCC-CCSCCCSTTEEEECCSSTTCBSSCEEEESSC-CGGGTTTSCEEEEEEECHHHHHHHHTTCC-TTSC
T ss_pred             ------CccCccc-cccccCCCcEEEEeecCCCCcCceeEeeecC-CcccCCceeEEEEEeccHHHHHHHHcCCC-CCCC
Confidence                  5677884 5667778999999999999999999999998 79999999999999999999999988764 5789


Q ss_pred             cccceeeccccccc
Q 007792          150 PYKNIRIKHTYILE  163 (589)
Q Consensus       150 p~~~i~I~~~~vl~  163 (589)
                      |+++|.|.+|++|+
T Consensus       159 P~~~i~I~~cG~l~  172 (172)
T d2igva1         159 PVKDCMIADCGQLK  172 (172)
T ss_dssp             CSSCEEEEEEEEEC
T ss_pred             CCCCeEEEeccccC
Confidence            99999999999874

>d2rmca_ b.62.1.1 (A:) Cyclophilin (eukaryotic) {Mouse (Mus musculus), variant C [TaxId: 10090]}

class: All beta proteins
fold: Cyclophilin-like
superfamily: Cyclophilin-like
family: Cyclophilin (peptidylprolyl isomerase)
domain: Cyclophilin (eukaryotic)
species: Mouse (Mus musculus), variant C [TaxId: 10090]

Probab=100.00  E-value=1.5e-36  Score=284.50  Aligned_cols=148  Identities=40%  Similarity=0.653  Sum_probs=132.9

Q ss_pred             ecceeEEEEecCCCChhHHHHHHHHHhcC---ccCCceEEEeecCcccccCCCCC-CCCCCCCcccccccccccccCCcc
Q 007792            7 TSLGDIVVDLFVDKCPLTTKNFLKLCKIK---YYNGCLFHTVQKDFTAQTGDPTG-TGTGGDSVYKFLYGEQARFFGDEI   82 (589)
Q Consensus         7 T~~G~i~ieL~~~~aP~~~~nF~~l~~~~---~Y~g~~f~rv~~~~~iq~Gd~~~-~~~~~~~~~~~~~~~~~~~~~~e~   82 (589)
                      |++|+|+|+||.+.||+||+||++||+++   +|+++.||||++++++|+|++.. .+.++.++++       ..++++ 
T Consensus        19 ~~~G~ivieL~~d~aP~tv~nF~~l~~~~k~~~Y~g~~f~rv~~~~~iq~G~~~~~~~~~~~~~~~-------~~~~~~-   90 (182)
T d2rmca_          19 KDVGRIVIGLFGNVVPKTVENFVALATGEKGYGYKGSIFHRVIKDFMIQGGDFTARDGTGGMSIYG-------ETFPDE-   90 (182)
T ss_dssp             EEEEEEEEEECTTTSHHHHHHHHHHHHTTTSCSSTTCBEEEEETTTEEEECCCSSSSSSCCCBTTB-------SCBCCC-
T ss_pred             EECcEEEEEEcCCCCcHHHHHHHHhhhcCCCccccCceeeeeecCceEEcCCCCCCCCCCCCCCcC-------Cccccc-
Confidence            88999999999999999999999999665   79999999999999999999873 4455555554       445666 


Q ss_pred             ccCCCCCCCceEEEeccCCCCCcceEEEEeCCCCCCCCCCcceEEEEecCHHHHHHHhhCccCCCCCcccceeecccccc
Q 007792           83 RVDLKHAKTGTVAMASAGENLNASQFYMTLRDNLDYLDEKHTIFGEVAEGLETLSRINESFVDEKNRPYKNIRIKHTYIL  162 (589)
Q Consensus        83 ~~~l~~~~~G~vs~a~~g~~~~~sqFfI~l~~~~~~ld~~~~vFG~Vv~G~~vl~~i~~~~~~~~~~p~~~i~I~~~~vl  162 (589)
                      .+.+.|..+|+||||+.++++++|||||+|.+ +++||++|+|||+|++||+||++|+.++++.+++|.++|.|.+|++|
T Consensus        91 ~~~~~~~~~G~lsma~~~~~s~~sqFfI~~~~-~~~ld~~~~vFG~Vi~G~dvl~~I~~~~~~~~~~P~~~v~I~~~g~l  169 (182)
T d2rmca_          91 NFKLKHYGIGWVSMANAGPDTNGSQFFITLTK-PTWLDGKHVVFGKVLDGMTVVHSIELQATDGHDRPLTDCTIVNSGKI  169 (182)
T ss_dssp             CCCSCCCSTTEEEECCSSTTCBCSCEEEESSC-CGGGTTTSCEEEEEEECHHHHHHHHTSCBCTTSCBSSCEEEEEEEEE
T ss_pred             ccccccCCCccEehhhcCCCccCccccccccC-CchhcccceEEEEEechHHHHHHHHhCCcCCCCcCCCCeEEEEeeEE
Confidence            45667778999999999999999999999998 69999999999999999999999999999999999999999999998


Q ss_pred             c
Q 007792          163 E  163 (589)
Q Consensus       163 ~  163 (589)
                      +
T Consensus       170 ~  170 (182)
T d2rmca_         170 D  170 (182)
T ss_dssp             E
T ss_pred             e
Confidence            5

>d1lopa_ b.62.1.1 (A:) Peptidyl-prolyl cis-trans isomerase A, PpiA {Escherichia coli [TaxId: 562]}

class: All beta proteins
fold: Cyclophilin-like
superfamily: Cyclophilin-like
family: Cyclophilin (peptidylprolyl isomerase)
domain: Peptidyl-prolyl cis-trans isomerase A, PpiA
species: Escherichia coli [TaxId: 562]

Probab=100.00  E-value=7.6e-37  Score=281.93  Aligned_cols=151  Identities=29%  Similarity=0.450  Sum_probs=131.5

Q ss_pred             EEEEecceeEEEEecCCCChhHHHHHHHHHhcCccCCceEEEeecCcccccCCCCCCCCCCCCcccccccccccccCCcc
Q 007792            3 VLIVTSLGDIVVDLFVDKCPLTTKNFLKLCKIKYYNGCLFHTVQKDFTAQTGDPTGTGTGGDSVYKFLYGEQARFFGDEI   82 (589)
Q Consensus         3 v~~~T~~G~i~ieL~~~~aP~~~~nF~~l~~~~~Y~g~~f~rv~~~~~iq~Gd~~~~~~~~~~~~~~~~~~~~~~~~~e~   82 (589)
                      |+|+|++|+|+|+||.+.||+||+||++||+.+||+|+.||||+++|++|+|++......+.  +       ...+++|.
T Consensus         2 V~l~T~~G~i~ieL~~~~aP~t~~nF~~l~~~g~Y~g~~fhrv~~~~~iq~G~~~~~~~~~~--~-------~~~~~~e~   72 (164)
T d1lopa_           2 VTFHTNHGDIVIKTFDDKAPETVKNFLDYCREGFYNNTIFHRVINGFMIQGGGFEPGMKQKA--T-------KEPIKNEA   72 (164)
T ss_dssp             EEEEETTEEEEEEECTTTSHHHHHHHHHHHHTTTTTTEECCEEETTTEEEESSEETTTEECC--C-------CCCBCCCC
T ss_pred             EEEEeCCeEEEEEEcCCCCHHHHHHHHHHHHccCcCCceeeEEcCCceeeeeccccCCcCCc--c-------CCCccccc
Confidence            89999999999999999999999999999999999999999999999999998764322211  1       24578887


Q ss_pred             ccCCCCCCCceEEEecc-CCCCCcceEEEEeCCC-------CCCCCCCcceEEEEecCHHHHHHHhhCccCCCC----Cc
Q 007792           83 RVDLKHAKTGTVAMASA-GENLNASQFYMTLRDN-------LDYLDEKHTIFGEVAEGLETLSRINESFVDEKN----RP  150 (589)
Q Consensus        83 ~~~l~~~~~G~vs~a~~-g~~~~~sqFfI~l~~~-------~~~ld~~~~vFG~Vv~G~~vl~~i~~~~~~~~~----~p  150 (589)
                      ...++| .+|+|+|++. ++++++|||||++.+.       .|+||++|+|||+|++||+||++|++++++..+    +|
T Consensus        73 ~~~~~h-~~g~l~~~~~~~~~~~~sqFfi~~~~~~~~~~~~~~~~~~~ytvFG~Vv~G~dvl~~I~~~~t~~~~~~~~~P  151 (164)
T d1lopa_          73 NNGLKN-TRGTLAMARTQAPHSATAQFFINVVDNDFLNFSGESLQGWGYCVFAEVVDGMDEVDKIKGVATGRSGMHQDVP  151 (164)
T ss_dssp             CSSCCC-CTTEEEECCCSSTTCBCSCEEEESSCCGGGSCCSSSTTTSCCCEEEEEEECHHHHHHHHTSCEEEETTEEEEE
T ss_pred             cccccc-eeeEEEEeccCCCCCccceeeeeccccccccccCCCcCCCceeecCEEeccHHHHHHHHhCCcCCCCCcCCCc
Confidence            778888 5799999964 6899999999999763       488999999999999999999999999997665    89


Q ss_pred             ccceeeccccccc
Q 007792          151 YKNIRIKHTYILE  163 (589)
Q Consensus       151 ~~~i~I~~~~vl~  163 (589)
                      +++|+|.++.|++
T Consensus       152 ~~~v~I~~v~I~e  164 (164)
T d1lopa_         152 KEDVIIESVTVSE  164 (164)
T ss_dssp             SSCCEEEEEEECC
T ss_pred             CCCeEEEEEEEeC
Confidence            9999999998863

>d2r99a1 b.62.1.1 (A:139-299) Mitochondrial peptidyl-prolyl cis-trans isomerase, cyclophilin F {Human (Homo sapiens) [TaxId: 9606]}

class: All beta proteins
fold: Cyclophilin-like
superfamily: Cyclophilin-like
family: Cyclophilin (peptidylprolyl isomerase)
domain: Mitochondrial peptidyl-prolyl cis-trans isomerase, cyclophilin F
species: Human (Homo sapiens) [TaxId: 9606]

Probab=100.00  E-value=1.9e-36  Score=277.94  Aligned_cols=150  Identities=39%  Similarity=0.620  Sum_probs=129.0

Q ss_pred             CEEEEE-ecceeEEEEecCCCChhHHHHHHHHHh---cCccCCceEEEeecCcccccCCCCCC-CCCCCCcccccccccc
Q 007792            1 MSVLIV-TSLGDIVVDLFVDKCPLTTKNFLKLCK---IKYYNGCLFHTVQKDFTAQTGDPTGT-GTGGDSVYKFLYGEQA   75 (589)
Q Consensus         1 ~~v~~~-T~~G~i~ieL~~~~aP~~~~nF~~l~~---~~~Y~g~~f~rv~~~~~iq~Gd~~~~-~~~~~~~~~~~~~~~~   75 (589)
                      |.|.|. |++|+|+|+||.+.||+||+||++||.   .++|+++.||||+|+|+||+|++... +.++.++++       
T Consensus         6 ~di~i~~~~~G~i~ieL~~~~aP~tv~nF~~L~~~~~~~~Y~g~~f~Rv~~~~~iq~G~~~~~~~~~~~~~~~-------   78 (161)
T d2r99a1           6 MDIKIGNKPAGRIQMLLRSDVVPMTAENFRCLCTHEKGFGFKGSSFHRIIPQFMCQGGDFTNHNGTGGKSIYG-------   78 (161)
T ss_dssp             EEEEETTEEEEEEEEEECTTTCHHHHHHHHHHHHTTTSCCSTTCBEEEEETTTEEEECCTTTSSSSCCCBTTB-------
T ss_pred             EEEEECCEeceEEEEEEcCCCCcHHHHHHHHhhhhccccccCCcEEEEEEEeeeEEeeeccCCCCCCCccccC-------
Confidence            445543 678999999999999999999999995   46899999999999999999998853 444455443       


Q ss_pred             cccCCccccCCCCCCCceEEEeccCCCCCcceEEEEeCCCCCCCCCCcceEEEEecCHHHHHHHhhCccCCCCCccccee
Q 007792           76 RFFGDEIRVDLKHAKTGTVAMASAGENLNASQFYMTLRDNLDYLDEKHTIFGEVAEGLETLSRINESFVDEKNRPYKNIR  155 (589)
Q Consensus        76 ~~~~~e~~~~l~~~~~G~vs~a~~g~~~~~sqFfI~l~~~~~~ld~~~~vFG~Vv~G~~vl~~i~~~~~~~~~~p~~~i~  155 (589)
                      ..++++ .+.++|..+|+|+|++.++++++|||||+|.+ +|+||++|+|||+|++||+||++|+.. ++.+++|+++|+
T Consensus        79 ~~~~~~-~~~~~~~~~G~ls~~~~~~~s~~sqFfI~~~~-~~~Ldg~~tvFG~Vv~G~dvl~~I~~~-~~~~~~P~~~i~  155 (161)
T d2r99a1          79 KKFDDE-NFILKHTGPGLLSMANSGPNTNGSQFFLTCDK-TDWLDGKHVVFGEVTEGLDVLRQIEAQ-GSKDGKPKQKVI  155 (161)
T ss_dssp             SCBCCC-CCCSCCCSSSEEEECCSSTTCBCSCEEEESSC-CGGGTTTSCEEEEEEECHHHHHHHHTT-CCTTCCCSSCEE
T ss_pred             cccccc-ccccccccceeeeecccCCCCcCcceEeccCC-ccccCCcceEEEEEeehHHHHHHHHcc-CCCCCcCCCCEE
Confidence            233334 57788889999999999999999999999998 799999999999999999999999765 456899999999


Q ss_pred             ecccc
Q 007792          156 IKHTY  160 (589)
Q Consensus       156 I~~~~  160 (589)
                      |++|+
T Consensus       156 I~~CG  160 (161)
T d2r99a1         156 IADCG  160 (161)
T ss_dssp             EEEEE
T ss_pred             EEeCC
Confidence            99997

>d2cfea1 b.62.1.1 (A:1-162) Cyclophilin-like allergen Mal s 6 {Malassezia sympodialis [TaxId: 76777]}

class: All beta proteins
fold: Cyclophilin-like
superfamily: Cyclophilin-like
family: Cyclophilin (peptidylprolyl isomerase)
domain: Cyclophilin-like allergen Mal s 6
species: Malassezia sympodialis [TaxId: 76777]

Probab=100.00  E-value=1.5e-36  Score=279.16  Aligned_cols=145  Identities=41%  Similarity=0.661  Sum_probs=128.8

Q ss_pred             ecceeEEEEecCCCChhHHHHHHHHHhcCc---cCCceEEEeecCcccccCCCCC-CCCCCCCcccccccccccccCCcc
Q 007792            7 TSLGDIVVDLFVDKCPLTTKNFLKLCKIKY---YNGCLFHTVQKDFTAQTGDPTG-TGTGGDSVYKFLYGEQARFFGDEI   82 (589)
Q Consensus         7 T~~G~i~ieL~~~~aP~~~~nF~~l~~~~~---Y~g~~f~rv~~~~~iq~Gd~~~-~~~~~~~~~~~~~~~~~~~~~~e~   82 (589)
                      |++|+|+|+||+++||+||+||++||+.++   |+++.||||+++++||+|++.. ++.++.+++.       ..+++| 
T Consensus        13 ~~~G~i~ieL~~~~aP~tv~nF~~L~~~~~~~~Y~g~~f~rv~~~~~iq~G~~~~~~~~~~~~~~~-------~~~~~e-   84 (162)
T d2cfea1          13 APLGTIKFKLFDDVVPKTAANFRALCTGEKGFGYAGSHFHRVIPDFMLQGGDFTAGNGTGGKSIYG-------AKFADE-   84 (162)
T ss_dssp             EEEEEEEEEECTTTCHHHHHHHHHHHHTTTSCCSTTCBCCEEETTTEEEECCTTTSSSSCCCBTTB-------SCBCCC-
T ss_pred             EEeeEEEEEEcCCCChHHHHHHHHHHhhccCCccCCCEEEEEEecceEecCCCCCCCCCCCcccCC-------Cccccc-
Confidence            568999999999999999999999999996   9999999999999999999873 4444555443       346666 


Q ss_pred             ccCCCCCCCceEEEeccCCCCCcceEEEEeCCCCCCCCCCcceEEEEecCHHHHHHHhhCccCCCCCcccceeeccccc
Q 007792           83 RVDLKHAKTGTVAMASAGENLNASQFYMTLRDNLDYLDEKHTIFGEVAEGLETLSRINESFVDEKNRPYKNIRIKHTYI  161 (589)
Q Consensus        83 ~~~l~~~~~G~vs~a~~g~~~~~sqFfI~l~~~~~~ld~~~~vFG~Vv~G~~vl~~i~~~~~~~~~~p~~~i~I~~~~v  161 (589)
                      .+.++|+.+|+|||++.++++++|||||++.+ +|+||++|+|||+|++||+||++|+.. .+.+++|.++|+|.+|+|
T Consensus        85 ~~~~~h~~~G~vsm~~~~~~s~~sqF~I~~~~-~~~ld~~~~vFG~Vi~G~dvl~~I~~~-~~~~~~P~~~i~I~~cgv  161 (162)
T d2cfea1          85 NFQLKHNKPGLLSMANAGPNTNGSQFFITTVV-TSWLDGKHVVFGEVIDGMNVVKAIEAE-GSGSGKPRSRIEIAKCGV  161 (162)
T ss_dssp             CCCSCCCSTTEEEECCSSTTCBSSCEEEESSC-CGGGTTTSCEEEEEEECHHHHHHHHTT-CCTTSCCSSCEEEEEEEE
T ss_pred             cCCCCCCCceEEEEeecCCCCCCcceEEeecC-CccccccceEEEEEEehHHHHHHHhcC-CCCCCCCCCCeEEEeeEc
Confidence            47789999999999999999999999999998 699999999999999999999999764 456899999999999987

>d1qnga_ b.62.1.1 (A:) Cyclophilin (eukaryotic) {Plasmodium falciparum [TaxId: 5833]}

class: All beta proteins
fold: Cyclophilin-like
superfamily: Cyclophilin-like
family: Cyclophilin (peptidylprolyl isomerase)
domain: Cyclophilin (eukaryotic)
species: Plasmodium falciparum [TaxId: 5833]

Probab=100.00  E-value=1.2e-36  Score=282.33  Aligned_cols=152  Identities=36%  Similarity=0.622  Sum_probs=131.9

Q ss_pred             CEEEEE-ecceeEEEEecCCCChhHHHHHHHHHhc---------CccCCceEEEeecCcccccCCCCC-CCCCCCCcccc
Q 007792            1 MSVLIV-TSLGDIVVDLFVDKCPLTTKNFLKLCKI---------KYYNGCLFHTVQKDFTAQTGDPTG-TGTGGDSVYKF   69 (589)
Q Consensus         1 ~~v~~~-T~~G~i~ieL~~~~aP~~~~nF~~l~~~---------~~Y~g~~f~rv~~~~~iq~Gd~~~-~~~~~~~~~~~   69 (589)
                      |+|.|. |++|+|+|+||++.||+||+||++||++         ++|+++.||||+++++||+|++.. ++.++..+++ 
T Consensus         8 ~Di~i~~t~~G~ivIeL~~~~aP~tv~nF~~l~~~~~~~~~~~~~~y~g~~~~rv~~~~~iq~g~~~~~~~~~~~~~~~-   86 (170)
T d1qnga_           8 FDISIDNSNAGRIIFELFSDITPRTCENFRALCTGEKIGSRGKNLHYKNSIFHRIIPQFMCQGGDITNGNGSGGESIYG-   86 (170)
T ss_dssp             EEEEESSSEEEEEEEEECTTTCHHHHHHHHHHHHTCEECTTSSEECCTTCBCCEEETTTEEEECCTTTSSSSCCCBTTB-
T ss_pred             EEEEECCEEccEEEEEECCCCChHHHHHHHhhhccccccccCccCccCcccceEEEeCceEEecCccCCCCCCCcccCC-
Confidence            456665 8999999999999999999999999974         579999999999999999999763 3444444443 


Q ss_pred             cccccccccCCccccCCCCCCCceEEEeccCCCCCcceEEEEeCCCCCCCCCCcceEEEEecCHHHHHHHhhCccCCCCC
Q 007792           70 LYGEQARFFGDEIRVDLKHAKTGTVAMASAGENLNASQFYMTLRDNLDYLDEKHTIFGEVAEGLETLSRINESFVDEKNR  149 (589)
Q Consensus        70 ~~~~~~~~~~~e~~~~l~~~~~G~vs~a~~g~~~~~sqFfI~l~~~~~~ld~~~~vFG~Vv~G~~vl~~i~~~~~~~~~~  149 (589)
                            ..++++ .+.++|+.+|+||||+.++++++|||||+|.+ +|+||++|+|||+|++||+||++|+.++++ ++.
T Consensus        87 ------~~~~~~-~~~~~~~~~G~lsma~~~~~s~~sqFfIt~~~-~~~Ld~~~~vFG~Vv~Gmdvl~~I~~~~~~-~g~  157 (170)
T d1qnga_          87 ------RSFTDE-NFNMKHDQPGLLSMANAGPNTNSSQFFITLVP-CPWLDGKHVVFGKVIEGMNVVREMEKEGAK-SGY  157 (170)
T ss_dssp             ------SCBCCC-CCCSCCCSTTEEEECCSSTTCBCSCEEEESSC-CGGGTTTSCEEEEEEECHHHHHHHHTTCCT-TCC
T ss_pred             ------Cccccc-cccccCCCCeEEEEeecCCCCccccceeccCC-cccccccccEEeEEeccHHHHHHHHhcCCC-CcC
Confidence                  345555 46778889999999999999999999999998 699999999999999999999999987764 578


Q ss_pred             cccceeecccccc
Q 007792          150 PYKNIRIKHTYIL  162 (589)
Q Consensus       150 p~~~i~I~~~~vl  162 (589)
                      |.++|+|++|+.|
T Consensus       158 P~~~i~I~~CG~l  170 (170)
T d1qnga_         158 VKRSVVITDCGEL  170 (170)
T ss_dssp             CSSCEEEEEEEEC
T ss_pred             CccCEEEEeeEcC
Confidence            9999999999875

>d1qoia_ b.62.1.1 (A:) Cyclophilin (eukaryotic) {Human (Homo sapiens), U4/U6 snRNP-specific cyclophilin snucyp-20 [TaxId: 9606]}

class: All beta proteins
fold: Cyclophilin-like
superfamily: Cyclophilin-like
family: Cyclophilin (peptidylprolyl isomerase)
domain: Cyclophilin (eukaryotic)
species: Human (Homo sapiens), U4/U6 snRNP-specific cyclophilin snucyp-20 [TaxId: 9606]

Probab=100.00  E-value=2.2e-36  Score=281.60  Aligned_cols=147  Identities=35%  Similarity=0.642  Sum_probs=128.0

Q ss_pred             ecceeEEEEecCCCChhHHHHHHHHHhcCc--------cCCceEEEeecCcccccCCCCCC-CCCCCCcccccccccccc
Q 007792            7 TSLGDIVVDLFVDKCPLTTKNFLKLCKIKY--------YNGCLFHTVQKDFTAQTGDPTGT-GTGGDSVYKFLYGEQARF   77 (589)
Q Consensus         7 T~~G~i~ieL~~~~aP~~~~nF~~l~~~~~--------Y~g~~f~rv~~~~~iq~Gd~~~~-~~~~~~~~~~~~~~~~~~   77 (589)
                      |++|+|+|+||++.||+||+||++||+.+|        |+++.||||++++++|+|++... +......+.       ..
T Consensus        18 ~~~G~i~ieL~~~~aP~tv~nF~~L~~~~~~~~~~~~~y~~~~f~rv~~~~~~q~G~~~~~~~~~~~~~~~-------~~   90 (173)
T d1qoia_          18 QEVGRMKIELFADVVPKTAENFRQFCTGEFRKDGVPIGYKGSTFHRVIKDFMIQGGDFVNGDGTGVASIYR-------GP   90 (173)
T ss_dssp             EEEEEEEEEECTTTCHHHHHHHHHHHHSCCEETTEECSSTTCBCCEEETTTEEEECCTTTSSSCCCCCTTS-------SC
T ss_pred             EeCeEEEEEEcCCCCcHHHHHHHHhhcccccccCCCCCcCCcccceeccceeeccCCcccCCcceeecccC-------Cc
Confidence            568999999999999999999999999998        99999999999999999998732 222222222       33


Q ss_pred             cCCccccCCCCCCCceEEEeccCCCCCcceEEEEeCCCCCCCCCCcceEEEEecCHHHHHHHhhCccCCCCCcccceeec
Q 007792           78 FGDEIRVDLKHAKTGTVAMASAGENLNASQFYMTLRDNLDYLDEKHTIFGEVAEGLETLSRINESFVDEKNRPYKNIRIK  157 (589)
Q Consensus        78 ~~~e~~~~l~~~~~G~vs~a~~g~~~~~sqFfI~l~~~~~~ld~~~~vFG~Vv~G~~vl~~i~~~~~~~~~~p~~~i~I~  157 (589)
                      +.++. +.+.|..+|+|+||+.++++++|||||+|.+ .|+||++|||||+|++||+||++|++++++++++|+++|+|.
T Consensus        91 ~~~~~-~~~~~~~~G~l~ma~~~~~s~~sqFfI~~~~-~~~ldg~~tvFG~Vi~G~dvl~~I~~~~t~~~~~P~~~i~I~  168 (173)
T d1qoia_          91 FADEN-FKLRHSAPGLLSMANSGPSTNGCQFFITCSK-CDWLDGKHVVFGKIIDGLLVMRKIENVPTGPNNKPKLPVVIS  168 (173)
T ss_dssp             BCCCC-CCSCCCSTTEEEECCSSTTCBCSCEEEESSC-CGGGTTTSCEEEEEEECHHHHHHHHTSCBCGGGCBSSCEEEE
T ss_pred             ccccc-cccccCCCcEEEeeecCCCCCCceeeeeccC-CccCCcceeEEEEEechHHHHHHHHhCCcCCCCcCCCCEEEE
Confidence            55553 4556668999999999999999999999998 699999999999999999999999999999999999999999


Q ss_pred             ccccc
Q 007792          158 HTYIL  162 (589)
Q Consensus       158 ~~~vl  162 (589)
                      +|+.|
T Consensus       169 ~cGel  173 (173)
T d1qoia_         169 QCGEM  173 (173)
T ss_dssp             EEEEC
T ss_pred             cccCC
Confidence            99864

>d1a33a_ b.62.1.1 (A:) Cyclophilin (eukaryotic) {Nematode (Brugia malayi) [TaxId: 6279]}

class: All beta proteins
fold: Cyclophilin-like
superfamily: Cyclophilin-like
family: Cyclophilin (peptidylprolyl isomerase)
domain: Cyclophilin (eukaryotic)
species: Nematode (Brugia malayi) [TaxId: 6279]

Probab=100.00  E-value=4e-36  Score=280.04  Aligned_cols=147  Identities=39%  Similarity=0.586  Sum_probs=130.8

Q ss_pred             ecceeEEEEecCCCChhHHHHHHHHHhc-----------CccCCceEEEeecCcccccCCCC-CCCCCCCCccccccccc
Q 007792            7 TSLGDIVVDLFVDKCPLTTKNFLKLCKI-----------KYYNGCLFHTVQKDFTAQTGDPT-GTGTGGDSVYKFLYGEQ   74 (589)
Q Consensus         7 T~~G~i~ieL~~~~aP~~~~nF~~l~~~-----------~~Y~g~~f~rv~~~~~iq~Gd~~-~~~~~~~~~~~~~~~~~   74 (589)
                      +++|+|+|+||++.||+||+||++||++           ++|+++.||||++++++|+|++. +.+.++.+++.      
T Consensus        15 ~~~G~I~ieL~~d~aP~tv~nF~~l~~~~~~~~~~~~k~~~Y~~~~f~Rv~~~~~iq~g~~~~~~~~~~~~~~~------   88 (174)
T d1a33a_          15 NLAGRIVMELYNDIAPRTCNNFLMLCTGMAGTGKISGKPLHYKGSTFHRVIKNFMIQGGDFTKGDGTGGESIYG------   88 (174)
T ss_dssp             EEEEEEEEEECTTTCHHHHHHHHHHHHCTTCBCTTTCSBCCCTTCBEEEEETTTEEEECCTTTSSSSCCCCTTS------
T ss_pred             EeceEEEEEECCCCChHHHHHHHHHHhcccCCCcccCccceeCCceeeEEEeCCEEeeCCCCCCCCCCCCCccC------
Confidence            3479999999999999999999999965           58999999999999999999987 34455555443      


Q ss_pred             ccccCCccccCCCCCCCceEEEeccCCCCCcceEEEEeCCCCCCCCCCcceEEEEecCHHHHHHHhhCccCCCCCcccce
Q 007792           75 ARFFGDEIRVDLKHAKTGTVAMASAGENLNASQFYMTLRDNLDYLDEKHTIFGEVAEGLETLSRINESFVDEKNRPYKNI  154 (589)
Q Consensus        75 ~~~~~~e~~~~l~~~~~G~vs~a~~g~~~~~sqFfI~l~~~~~~ld~~~~vFG~Vv~G~~vl~~i~~~~~~~~~~p~~~i  154 (589)
                        ....+....++|+.+|+|+|++.++++++|||||+|.+ +|+||++|+|||+|++||+||++|++++++.+++|.++|
T Consensus        89 --~~~~~~~~~~~~~~~g~l~~~~~~~~s~~sqFfI~~~~-~p~ld~~~~vFG~VveG~dvl~~I~~~~t~~~~~P~~~i  165 (174)
T d1a33a_          89 --GMFDDEEFVMKHDEPFVVSMANKGPNTNGSQFFITTTP-APHLNNIHVVFGKVVSGQEVVTKIEYLKTNSKNRPLADV  165 (174)
T ss_dssp             --SCBCCCCSCSCCCSTTEEEECCSSTTCBCSCEEEESSC-CGGGTTTSCEEEEEEECHHHHHHHHTSCBCTTSCBSSCE
T ss_pred             --ccccccccccccCcceeeeeeccCCCCCCcccccccCC-cccccccceeEEEEechHHHHHHHHhCCcCCCCCCCCCE
Confidence              23344467888999999999999999999999999998 799999999999999999999999999999999999999


Q ss_pred             eecccccc
Q 007792          155 RIKHTYIL  162 (589)
Q Consensus       155 ~I~~~~vl  162 (589)
                      +|.+|+.|
T Consensus       166 ~I~~cGel  173 (174)
T d1a33a_         166 VILNCGEL  173 (174)
T ss_dssp             EEEEEEEC
T ss_pred             EEEeeEEE
Confidence            99999876

>d1ihga2 b.62.1.1 (A:2-196) Cyclophilin 40 isomerase domain {Cow (Bos taurus) [TaxId: 9913]}

class: All beta proteins
fold: Cyclophilin-like
superfamily: Cyclophilin-like
family: Cyclophilin (peptidylprolyl isomerase)
domain: Cyclophilin 40 isomerase domain
species: Cow (Bos taurus) [TaxId: 9913]

Probab=100.00  E-value=1.7e-35  Score=280.21  Aligned_cols=151  Identities=38%  Similarity=0.621  Sum_probs=132.0

Q ss_pred             ecceeEEEEecCCCChhHHHHHHHHHhcC-----------ccCCceEEEeecCcccccCCCCC-CCCCCCCccccccccc
Q 007792            7 TSLGDIVVDLFVDKCPLTTKNFLKLCKIK-----------YYNGCLFHTVQKDFTAQTGDPTG-TGTGGDSVYKFLYGEQ   74 (589)
Q Consensus         7 T~~G~i~ieL~~~~aP~~~~nF~~l~~~~-----------~Y~g~~f~rv~~~~~iq~Gd~~~-~~~~~~~~~~~~~~~~   74 (589)
                      +++|+|+|+||.+.||+||+||++||+.+           +|+|+.||||++++++|+|++.. .+.++...++      
T Consensus        26 ~~~G~I~IeL~~d~aP~tv~nF~~L~~~~~~~~~~~~~~~~y~g~~f~rv~~~~~i~~G~~~~~~~~~~~~~~~------   99 (195)
T d1ihga2          26 ERVGRIVLELFADIVPKTAENFRALCTGEKGIGPTTGKPLHFKGCPFHRIIKKFMIQGGDFSNQNGTGGESIYG------   99 (195)
T ss_dssp             EEEEEEEEEECTTTCHHHHHHHHHHHHCTTCBCTTTSSBSCCTTCBEEEEETTTEEEECCTTTSSSSCCCBTTB------
T ss_pred             EeeeEEEEEECCCCChHHHHHHHHHhccccccccccCCccccCCceeeEEEcCceeecCCccCCCCCCCccCCC------
Confidence            56899999999999999999999999854           69999999999999999999764 3444444443      


Q ss_pred             ccccCCccccCCCCCCCceEEEeccCCCCCcceEEEEeCCCCCCCCCCcceEEEEecCHHHHHHHhhCccCCCCCcccce
Q 007792           75 ARFFGDEIRVDLKHAKTGTVAMASAGENLNASQFYMTLRDNLDYLDEKHTIFGEVAEGLETLSRINESFVDEKNRPYKNI  154 (589)
Q Consensus        75 ~~~~~~e~~~~l~~~~~G~vs~a~~g~~~~~sqFfI~l~~~~~~ld~~~~vFG~Vv~G~~vl~~i~~~~~~~~~~p~~~i  154 (589)
                       ..+++| ...+.|+.+|+|+|++.++++++|||||+|.+ +|+||++|+|||+|++||+||++|+++++. +++|.++|
T Consensus       100 -~~~~~~-~~~~~h~~~G~lsm~~~~~~s~~SqFfItl~~-~~~LDg~ytVFG~Vv~Gmdvl~~I~~~~t~-~~~P~~~i  175 (195)
T d1ihga2         100 -EKFEDE-NFHYKHDKEGLLSMANAGSNTNGSQFFITTVP-TPHLDGKHVVFGQVIKGMGVAKILENVEVK-GEKPAKLC  175 (195)
T ss_dssp             -SCBCCC-CCCBCCCSTTEEEECCSSTTCBCSCEEEESSC-CGGGTTTSCEEEEEEECHHHHHHHHTSCEE-TTEESSCE
T ss_pred             -Cccccc-ccCcccCcceEEeeeecCCCCCCceeEeeccC-CcccCCcceEEEEEecCHHHHHHHHcCCCC-CCCcCCCe
Confidence             446666 45678889999999999999999999999998 699999999999999999999999998875 78999999


Q ss_pred             eecccccccCCCC
Q 007792          155 RIKHTYILEDPFD  167 (589)
Q Consensus       155 ~I~~~~vl~~p~~  167 (589)
                      +|.+|++|..-.+
T Consensus       176 ~I~~cG~l~~~~~  188 (195)
T d1ihga2         176 VIAECGELKEGDD  188 (195)
T ss_dssp             EEEEEEEECTTCC
T ss_pred             EEEECcccCCCCc
Confidence            9999999976544

>d1z81a1 b.62.1.1 (A:25-210) Cyclophilin (eukaryotic) {Plasmodium yoelii [TaxId: 5861]}

class: All beta proteins
fold: Cyclophilin-like
superfamily: Cyclophilin-like
family: Cyclophilin (peptidylprolyl isomerase)
domain: Cyclophilin (eukaryotic)
species: Plasmodium yoelii [TaxId: 5861]

Probab=100.00  E-value=3.7e-35  Score=275.94  Aligned_cols=147  Identities=35%  Similarity=0.611  Sum_probs=129.2

Q ss_pred             ecceeEEEEecCCCChhHHHHHHHHHhcCc--------cCCceEEEeecCcccccCCCCC-CCCCCCCcccccccccccc
Q 007792            7 TSLGDIVVDLFVDKCPLTTKNFLKLCKIKY--------YNGCLFHTVQKDFTAQTGDPTG-TGTGGDSVYKFLYGEQARF   77 (589)
Q Consensus         7 T~~G~i~ieL~~~~aP~~~~nF~~l~~~~~--------Y~g~~f~rv~~~~~iq~Gd~~~-~~~~~~~~~~~~~~~~~~~   77 (589)
                      +++|+|+|+||++.||+||+||++||++++        |+|+.||++++++++|+|++.. .+.....+++       ..
T Consensus        28 ~~~G~I~ieL~~d~aP~tv~nF~~L~~~~~~~~~~~~~Y~g~~f~rv~~~~~i~~G~~~~~~~~~~~~~~~-------~~  100 (186)
T d1z81a1          28 NFLGKFKFELFQNIVPKTSENFRQFCTGEYKVNNLPVGYKNTIFHRVIKEFMIQGGDFINHNGSGSLSIYG-------EK  100 (186)
T ss_dssp             EEEEEEEEEECTTTCHHHHHHHHHHHHTCCBSSSSBCSSTTEECCEEETTTEEEECCTTTSSSCCCCBTTB-------SC
T ss_pred             EeceEEEEEEcCCCChHHHHHHHHHHhcccccCCcccccCCCeeeeeecceeeecCCccccCCcccccccC-------Cc
Confidence            457999999999999999999999999998        9999999999999999999763 3333333333       34


Q ss_pred             cCCccccCCCCCCCceEEEeccCCCCCcceEEEEeCCCCCCCCCCcceEEEEecC--HHHHHHHhhCccCC-CCCcccce
Q 007792           78 FGDEIRVDLKHAKTGTVAMASAGENLNASQFYMTLRDNLDYLDEKHTIFGEVAEG--LETLSRINESFVDE-KNRPYKNI  154 (589)
Q Consensus        78 ~~~e~~~~l~~~~~G~vs~a~~g~~~~~sqFfI~l~~~~~~ld~~~~vFG~Vv~G--~~vl~~i~~~~~~~-~~~p~~~i  154 (589)
                      ++++ ...++|+.+|+|+|++.++++++|||||+|.+ +|+||++|+|||+||+|  |+||++|+.++++. .++|..+|
T Consensus       101 ~~~~-~~~~~~~~~G~~~~~~~g~~~~~sqFfIt~~~-~p~Ldg~~tVFG~Vv~G~~mdvv~kI~~~~~~~~~~~P~~~i  178 (186)
T d1z81a1         101 FDDE-NFDIKHDKEGLLSMANSGPNTNGCQFFITTKK-CEWLDGKNVVFGRIIDNDSLLLLKKIENVSVTPYIYKPKIPI  178 (186)
T ss_dssp             CCCC-CCCSCCCSTTEEEECCSSSSCCCSCEEEESSC-CGGGBTTBCEEEEECSHHHHHHHHHHHHSCBCTTTCCBSSCE
T ss_pred             cccc-ccccccCCCccchhhhcCCCccccceeeeccc-ccccCCCccEEEEEEeCccHHHHHHHhccCCCCCCCccCCCE
Confidence            5555 46778889999999999999999999999998 79999999999999998  99999999999975 68999999


Q ss_pred             eecccccc
Q 007792          155 RIKHTYIL  162 (589)
Q Consensus       155 ~I~~~~vl  162 (589)
                      +|.+|+.|
T Consensus       179 ~I~~CGel  186 (186)
T d1z81a1         179 NVVECGEL  186 (186)
T ss_dssp             EEEEEEEC
T ss_pred             EEEeCCcC
Confidence            99999874

>d2c3ba1 b.62.1.1 (A:1-171) Cyclophilin (eukaryotic) {Aspergillus fumigatus [TaxId: 5085]}

class: All beta proteins
fold: Cyclophilin-like
superfamily: Cyclophilin-like
family: Cyclophilin (peptidylprolyl isomerase)
domain: Cyclophilin (eukaryotic)
species: Aspergillus fumigatus [TaxId: 5085]

Probab=100.00  E-value=1.2e-35  Score=275.40  Aligned_cols=149  Identities=40%  Similarity=0.592  Sum_probs=110.2

Q ss_pred             EEecceeEEEEecCCCChhHHHHHHHHHhcCc---cCCceEEEeecCcccccCCCC-CCCCCCCCcccccccccccccCC
Q 007792            5 IVTSLGDIVVDLFVDKCPLTTKNFLKLCKIKY---YNGCLFHTVQKDFTAQTGDPT-GTGTGGDSVYKFLYGEQARFFGD   80 (589)
Q Consensus         5 ~~T~~G~i~ieL~~~~aP~~~~nF~~l~~~~~---Y~g~~f~rv~~~~~iq~Gd~~-~~~~~~~~~~~~~~~~~~~~~~~   80 (589)
                      .+|++|+|+|+||.+.||+||+||++||+.++   |+++.||||++++++|+|++. +++.++..+++       ..+.+
T Consensus        16 ~~T~~G~i~IeL~~~~aP~tv~nF~~l~~~~~~~~y~~~~f~ri~~~~~iq~G~~~~~~~~~~~~~~~-------~~~~~   88 (171)
T d2c3ba1          16 AETKVGRIVFNLFDKDVPKTAKNFRELCKRPAGEGYRESTFHRIIPNFMIQGGDFTRGNGTGGRSIYG-------DKFAD   88 (171)
T ss_dssp             SCCEEEEEEEEECTTTSHHHHHHHHHHHHSCTTTSSTTCBCCEEETTTEEEECC--------------------------
T ss_pred             ccceeeEEEEEEcCCCChHHHHHHHHHhhhcccccccCceeeEEEEEEeeEcCCccCCCCCCCCcCCC-------Ccccc
Confidence            45899999999999999999999999999887   999999999999999999976 33444444333       22333


Q ss_pred             ccccCCCCCCCceEEEeccCCCCCcceEEEEeCCCCCCCCCCcceEEEEec--CHHHHHHHhhCccCCC-CCcccceeec
Q 007792           81 EIRVDLKHAKTGTVAMASAGENLNASQFYMTLRDNLDYLDEKHTIFGEVAE--GLETLSRINESFVDEK-NRPYKNIRIK  157 (589)
Q Consensus        81 e~~~~l~~~~~G~vs~a~~g~~~~~sqFfI~l~~~~~~ld~~~~vFG~Vv~--G~~vl~~i~~~~~~~~-~~p~~~i~I~  157 (589)
                      + ...++|+.+|+||||+.++++++|||||+|.+ +|+||++|||||+|++  ||+||++|+++++... ..|..+|+|.
T Consensus        89 ~-~~~~~~~~~G~lsma~~~~~s~~sqFfI~~~~-~~~ldg~~tvFG~Vie~~G~dvl~~I~~~~t~~g~~~p~~~v~I~  166 (171)
T d2c3ba1          89 E-NFSRKHDKKGILSMANAGPNTNGSQFFITTAV-TSWLDGKHVVFGEVADEKSYSVVKEIEALGSSSGSVRSNTRPKIV  166 (171)
T ss_dssp             ----CHHHHHTCEEEEC---------CEEEECSC-CTTCCSCCEEEEEECSHHHHHHHHHHHTTCCTTSCCCSSSCCEEE
T ss_pred             c-cccccCCCCceEEeeecCCCCCCcceeeccCC-ccccCCCceEEEEEEeccCHHHHHHHHcCCCCCCCcCCCCCEEEE
Confidence            3 46677888999999999999999999999998 6999999999999994  9999999999998774 4688899999


Q ss_pred             ccccc
Q 007792          158 HTYIL  162 (589)
Q Consensus       158 ~~~vl  162 (589)
                      +|+.|
T Consensus       167 ~cGel  171 (171)
T d2c3ba1         167 NCGEL  171 (171)
T ss_dssp             EEEEC
T ss_pred             eCccC
Confidence            99864

>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=99.81  E-value=3.5e-20  Score=149.23  Aligned_cols=80  Identities=28%  Similarity=0.559  Sum_probs=77.6

Q ss_pred             CceEEEecCCCCCCHHHHHHHhccCCCeEEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHhcCCceeCCeEEEEEeccc
Q 007792          242 ENVLFVCKLNPVTEDEDLHTIFSRFGTVVSAEIIRDFKTGDSLNYAFIEFENRQACERAYSKMDNALIDDRRIHVDFSQS  321 (589)
Q Consensus       242 ~~~i~V~nL~~~~te~~L~~~F~~~G~v~~~~i~~d~~tg~~~g~aFV~f~~~~~a~~A~~~l~g~~i~gr~i~V~~a~~  321 (589)
                      .++|||+|||+.+|+++|.++|++||+|..|.|+.++.+|.++|||||+|.+.++|+.||+.|||..|.|+.|.|+||+|
T Consensus         2 ~t~l~V~nLp~~~t~~~l~~~F~~~G~v~~~~i~~~~~~g~~~g~afV~f~~~~~A~~ai~~lng~~~~g~~l~v~~a~p   81 (82)
T d1b7fa1           2 NTNLIVNYLPQDMTDRELYALFRAIGPINTCRIMRDYKTGYSYGYAFVDFTSEMDSQRAIKVLNGITVRNKRLKVSYARP   81 (82)
T ss_dssp             CSEEEEECCCTTCCHHHHHHHHHTTSCEEEEECCEETTTTEECSEEEEEESSHHHHHHHHHHHTTCEETTEECEEEECCC
T ss_pred             CCEEEEeCCCCCCCHHHHHHHHHHhCCcceeeeeeecccCCccccceEEECCHHHHHHHHHHhCCCEECCEEEEEEEcCC
Confidence            47899999999999999999999999999999999999999999999999999999999999999999999999999976

>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=99.80  E-value=6.7e-20  Score=151.15  Aligned_cols=85  Identities=22%  Similarity=0.370  Sum_probs=80.5

Q ss_pred             CCCCceEEEecCCCCCCHHHHHHHhccCCCeEEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHhcCCceeCCeEEEEEe
Q 007792          239 KPPENVLFVCKLNPVTEDEDLHTIFSRFGTVVSAEIIRDFKTGDSLNYAFIEFENRQACERAYSKMDNALIDDRRIHVDF  318 (589)
Q Consensus       239 ~~~~~~i~V~nL~~~~te~~L~~~F~~~G~v~~~~i~~d~~tg~~~g~aFV~f~~~~~a~~A~~~l~g~~i~gr~i~V~~  318 (589)
                      .++.++|||+|||+.+|+++|+++|++||.|..|.|+.++.||.++|||||+|.+.++|+.||+.|||..|+|+.|+|.+
T Consensus         6 ~~~~~tlfV~nLp~~~t~~~l~~~F~~~G~v~~v~~~~d~~tg~~kg~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~~   85 (93)
T d1x5ua1           6 RNQDATVYVGGLDEKVSEPLLWELFLQAGPVVNTHMPKDRVTGQHQGYGFVEFLSEEDADYAIKIMDMIKLYGKPIRVNK   85 (93)
T ss_dssp             CCTTTEEEEECCCTTCCHHHHHHHHHTTSCEEEEECCBCSSSCSBCSCEEEEESSHHHHHHHHHHSSSCBCSSCBCEEEE
T ss_pred             CCCCCEEEEeCCCCcCCHHHHHHHHHHhCCccccceeecccccccccceEEEECCHHHHHHHHHHcCCCEECCEEEEEEE
Confidence            34567999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             ccccc
Q 007792          319 SQSVS  323 (589)
Q Consensus       319 a~~~~  323 (589)
                      |++..
T Consensus        86 A~~~~   90 (93)
T d1x5ua1          86 ASAHN   90 (93)
T ss_dssp             TTTTS
T ss_pred             cCCCC
Confidence            98754

>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=99.80  E-value=1.1e-19  Score=148.97  Aligned_cols=83  Identities=25%  Similarity=0.438  Sum_probs=79.5

Q ss_pred             CCCceEEEecCCCCCCHHHHHHHhccCCCeEEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHhcCCceeCCeEEEEEec
Q 007792          240 PPENVLFVCKLNPVTEDEDLHTIFSRFGTVVSAEIIRDFKTGDSLNYAFIEFENRQACERAYSKMDNALIDDRRIHVDFS  319 (589)
Q Consensus       240 ~~~~~i~V~nL~~~~te~~L~~~F~~~G~v~~~~i~~d~~tg~~~g~aFV~f~~~~~a~~A~~~l~g~~i~gr~i~V~~a  319 (589)
                      .+.++|||+|||+.+|+++|.++|++||+|..|.|+.++.+|.++|||||+|.+.++|..||+.|||..|+|+.|.|+||
T Consensus         6 ~~~~~i~V~nLp~~~t~~~l~~~f~~~G~v~~v~i~~d~~t~~~rg~afV~f~~~~~A~~Ai~~l~g~~~~g~~i~v~~a   85 (90)
T d2cq0a1           6 DDNATIRVTNLSEDTRETDLQELFRPFGSISRIYLAKDKTTGQSKGFAFISFHRREDAARAIAGVSGFGYDHLILNVEWA   85 (90)
T ss_dssp             SSSEEEEEESCCTTCCHHHHHTTSTTTCCEEEEEEEECSSSCSEEEEEEEEESSHHHHHHHHHHTTTCEETTEECEEEES
T ss_pred             CCCCEEEEECCCCCCCHHHHHHHHHHhcccccccccccccccccccceeEEECCHHHHHHHHHHhCCCEECCEEEEEEee
Confidence            35689999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             ccc
Q 007792          320 QSV  322 (589)
Q Consensus       320 ~~~  322 (589)
                      +|.
T Consensus        86 kp~   88 (90)
T d2cq0a1          86 KPS   88 (90)
T ss_dssp             SCC
T ss_pred             eCC
Confidence            874

>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=99.80  E-value=1e-19  Score=145.62  Aligned_cols=77  Identities=31%  Similarity=0.520  Sum_probs=75.5

Q ss_pred             eEEEecCCCCCCHHHHHHHhccCCCeEEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHhcCCceeCCeEEEEEecc
Q 007792          244 VLFVCKLNPVTEDEDLHTIFSRFGTVVSAEIIRDFKTGDSLNYAFIEFENRQACERAYSKMDNALIDDRRIHVDFSQ  320 (589)
Q Consensus       244 ~i~V~nL~~~~te~~L~~~F~~~G~v~~~~i~~d~~tg~~~g~aFV~f~~~~~a~~A~~~l~g~~i~gr~i~V~~a~  320 (589)
                      +|||+|||+.+|+++|.++|++||+|..|.|+.++.||+++|||||+|.+.++|..|++.|||..|.|++|+|.||+
T Consensus         2 slfV~nL~~~~te~~l~~~F~~~G~i~~v~i~~d~~tg~~~g~aFV~f~~~~~a~~ai~~l~g~~~~gr~i~v~~a~   78 (80)
T d1cvja1           2 SLYVGDLHPDVTEAMLYEKFSPAGPILSIRVCRDMITRRSLGYAYVNFQQPADAERALDTMNFDVIKGKPVRIMWSQ   78 (80)
T ss_dssp             EEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHTTSTTCEETTEECEEEECC
T ss_pred             EEEEeCCCCcCCHHHHHHHHHHhCCEeEEEEEecccccCCCCceEEEECCHHHHHHHHHHcCCCEECCEEEEEEEeC
Confidence            69999999999999999999999999999999999999999999999999999999999999999999999999985

>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=99.80  E-value=1.2e-19  Score=146.00  Aligned_cols=80  Identities=24%  Similarity=0.513  Sum_probs=77.4

Q ss_pred             CceEEEecCCCCCCHHHHHHHhccCCCeEEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHhcCCceeCCeEEEEEeccc
Q 007792          242 ENVLFVCKLNPVTEDEDLHTIFSRFGTVVSAEIIRDFKTGDSLNYAFIEFENRQACERAYSKMDNALIDDRRIHVDFSQS  321 (589)
Q Consensus       242 ~~~i~V~nL~~~~te~~L~~~F~~~G~v~~~~i~~d~~tg~~~g~aFV~f~~~~~a~~A~~~l~g~~i~gr~i~V~~a~~  321 (589)
                      .++|||+|||+++++++|.++|++||+|..|.|+.+..+|.++|||||+|.+.++|+.|++.|||..|.|++|.|.||+|
T Consensus         2 ~t~l~V~nLp~~~te~~l~~~f~~~G~v~~v~i~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~g~~~~g~~l~v~~AkP   81 (82)
T d1fxla1           2 KTNLIVNYLPQNMTQEEFRSLFGSIGEIESCKLVRDKITGQSLGYGFVNYIDPKDAEKAINTLNGLRLQTKTIKVSYARP   81 (82)
T ss_dssp             CSEEEEESCCTTCCHHHHHHHHHTTSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEECCC
T ss_pred             CCEEEEECCCCCCCHHHHHHHHHHhCCcccccceeeccCCCceeeEEEEECCHHHHHHHHHHhCCCEECCEEEEEEEeeC
Confidence            36899999999999999999999999999999999999999999999999999999999999999999999999999976

>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=99.80  E-value=8.5e-20  Score=153.24  Aligned_cols=88  Identities=28%  Similarity=0.438  Sum_probs=82.5

Q ss_pred             CCCCCCCceEEEecCCCCCCHHHHHHHhccCCCeEEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHhcCCceeCCeEEE
Q 007792          236 ADIKPPENVLFVCKLNPVTEDEDLHTIFSRFGTVVSAEIIRDFKTGDSLNYAFIEFENRQACERAYSKMDNALIDDRRIH  315 (589)
Q Consensus       236 ~~~~~~~~~i~V~nL~~~~te~~L~~~F~~~G~v~~~~i~~d~~tg~~~g~aFV~f~~~~~a~~A~~~l~g~~i~gr~i~  315 (589)
                      ....|+.++|||+|||+++|+++|.++|++||.|..+.++.++.+|.++|||||+|.+.++|..||..|||..|.|+.|.
T Consensus        12 ~~~~p~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~~~~~~~~~~g~~kG~afV~f~~~~~A~~Ai~~lng~~~~g~~i~   91 (102)
T d2cpza1          12 QKEGPEGANLFIYHLPQEFGDQDLLQMFMPFGNVVSAKVFIDKQTNLSKCFGFVSYDNPVSAQAAIQSMNGFQIGMKRLK   91 (102)
T ss_dssp             CCCCSTTCCEEEESCCSSCCHHHHHHHHGGGSCCSEEEEEECSSSCSEEEEEEEECSSHHHHHHHHHHHTTCEETTEECE
T ss_pred             CCCCCCCCEEEEeCCCCCCCHHHHHHHHHhhccccccceeeecccCCCccceEEEeCCHHHHHHHHHHhCCCEECCEEEE
Confidence            34456778999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             EEeccccc
Q 007792          316 VDFSQSVS  323 (589)
Q Consensus       316 V~~a~~~~  323 (589)
                      |+||.++.
T Consensus        92 V~~a~~k~   99 (102)
T d2cpza1          92 VQLKRSKN   99 (102)
T ss_dssp             EECCCCSC
T ss_pred             EEEeCCCC
Confidence            99998753

>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=99.80  E-value=1.3e-19  Score=147.72  Aligned_cols=82  Identities=23%  Similarity=0.406  Sum_probs=78.4

Q ss_pred             CCceEEEecCCCCCCHHHHHHHhccCCCeEEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHhcCCceeCCeEEEEEecc
Q 007792          241 PENVLFVCKLNPVTEDEDLHTIFSRFGTVVSAEIIRDFKTGDSLNYAFIEFENRQACERAYSKMDNALIDDRRIHVDFSQ  320 (589)
Q Consensus       241 ~~~~i~V~nL~~~~te~~L~~~F~~~G~v~~~~i~~d~~tg~~~g~aFV~f~~~~~a~~A~~~l~g~~i~gr~i~V~~a~  320 (589)
                      ...+|||+|||+.+|+++|.++|++||+|..|.|+.++.+|+++|||||+|.+.++|+.|+..|||..|.|+.|.|+||.
T Consensus         6 ~~~~l~V~nL~~~~t~~~l~~~F~~~G~i~~v~i~~d~~tg~~~g~afV~f~~~~~A~~A~~~lng~~l~g~~l~V~~a~   85 (88)
T d1rk8a_           6 EGWILFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYETHKQALAAKEALNGAEIMGQTIQVDWCF   85 (88)
T ss_dssp             -CEEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTSSEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEESE
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHHcCCcccccccccccccccccceeEEECCHHHHHHHHHHcCCCEECCEEEEEEEec
Confidence            46799999999999999999999999999999999999999999999999999999999999999999999999999997


Q ss_pred             cc
Q 007792          321 SV  322 (589)
Q Consensus       321 ~~  322 (589)
                      ++
T Consensus        86 ~k   87 (88)
T d1rk8a_          86 VK   87 (88)
T ss_dssp             EC
T ss_pred             CC
Confidence            64

>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=99.80  E-value=2.1e-19  Score=148.12  Aligned_cols=82  Identities=23%  Similarity=0.378  Sum_probs=78.8

Q ss_pred             CCCceEEEecCCCCCCHHHHHHHhccCCCeEEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHhcCCceeCCeEEEEEec
Q 007792          240 PPENVLFVCKLNPVTEDEDLHTIFSRFGTVVSAEIIRDFKTGDSLNYAFIEFENRQACERAYSKMDNALIDDRRIHVDFS  319 (589)
Q Consensus       240 ~~~~~i~V~nL~~~~te~~L~~~F~~~G~v~~~~i~~d~~tg~~~g~aFV~f~~~~~a~~A~~~l~g~~i~gr~i~V~~a  319 (589)
                      .+.++|||+|||+++|+++|.++|++||+|..|.|+.++.+|.++|||||+|.+.++|..||+.|||..|+|++|.|+||
T Consensus         5 ~~s~tlfV~nlp~~~te~~l~~~F~~~G~i~~v~i~~~~~~~~~kg~afV~f~~~~~A~~Ai~~l~g~~~~gr~i~V~~a   84 (93)
T d1h2vz_           5 KKSCTLYVGNLSFYTTEEQIYELFSKSGDIKKIIMGLDKMKKTACGFCFVEYYSRADAENAMRYINGTRLDDRIIRTDWD   84 (93)
T ss_dssp             TTCCEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHTTTSEETTEECEEEEE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHHHCCcceeccccccccccccceEEEEECCHHHHHHHHHHhCCCEECCEEEEEEEc
Confidence            35689999999999999999999999999999999999999999999999999999999999999999999999999998


Q ss_pred             cc
Q 007792          320 QS  321 (589)
Q Consensus       320 ~~  321 (589)
                      .+
T Consensus        85 ~~   86 (93)
T d1h2vz_          85 AG   86 (93)
T ss_dssp             SC
T ss_pred             CC
Confidence            65

>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=99.79  E-value=7.2e-20  Score=149.74  Aligned_cols=82  Identities=28%  Similarity=0.496  Sum_probs=78.9

Q ss_pred             CCceEEEecCCCCCCHHHHHHHhccCCCeEEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHhcCCceeCCeEEEEEecc
Q 007792          241 PENVLFVCKLNPVTEDEDLHTIFSRFGTVVSAEIIRDFKTGDSLNYAFIEFENRQACERAYSKMDNALIDDRRIHVDFSQ  320 (589)
Q Consensus       241 ~~~~i~V~nL~~~~te~~L~~~F~~~G~v~~~~i~~d~~tg~~~g~aFV~f~~~~~a~~A~~~l~g~~i~gr~i~V~~a~  320 (589)
                      ...+|||+|||+++|+++|.++|++||+|..|.|+.++.+|.++|||||+|.+.++|..||..|||..|+|+.|.|++|+
T Consensus         4 ~~~tlfV~nLp~~~te~~l~~~F~~~G~i~~v~i~~d~~~~~~kg~afV~f~~~~~A~~ai~~l~~~~i~g~~l~v~~a~   83 (89)
T d2cqba1           4 TKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNMNESELFGRTIRVNLAK   83 (89)
T ss_dssp             CCSCEEEESCCSSCCHHHHHHHHTTTSCCCCEECCCCSSSCCCSSEEEECCSSHHHHHHHHHHHTTEEETTEEEEEEECC
T ss_pred             CCcEEEEeCCCCcCCHHHHHHHHhhCCeEEecccccccccccccceeEEEECCHHHHHHHHHHcCCCEECCEEEEEEEeC
Confidence            45799999999999999999999999999999999999999999999999999999999999999999999999999998


Q ss_pred             cc
Q 007792          321 SV  322 (589)
Q Consensus       321 ~~  322 (589)
                      +.
T Consensus        84 p~   85 (89)
T d2cqba1          84 PM   85 (89)
T ss_dssp             CC
T ss_pred             CC
Confidence            64

>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=99.79  E-value=2.1e-19  Score=144.95  Aligned_cols=78  Identities=31%  Similarity=0.509  Sum_probs=75.0

Q ss_pred             CCCCceEEEecCCCCCCHHHHHHHhccCCCeEEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHhcCCceeCCeEEEE
Q 007792          239 KPPENVLFVCKLNPVTEDEDLHTIFSRFGTVVSAEIIRDFKTGDSLNYAFIEFENRQACERAYSKMDNALIDDRRIHV  316 (589)
Q Consensus       239 ~~~~~~i~V~nL~~~~te~~L~~~F~~~G~v~~~~i~~d~~tg~~~g~aFV~f~~~~~a~~A~~~l~g~~i~gr~i~V  316 (589)
                      ++|.++|||+|||+.+|+++|+++|++||.|..|.|+.++.+|+++|||||+|.+.++|..||..|||..|+|++|+|
T Consensus         6 p~~~~~l~V~nL~~~~te~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~gr~i~V   83 (83)
T d2cqca1           6 PDPNCCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKERANGMELDGRRIRV   83 (83)
T ss_dssp             CCGGGCEEEESCCSSCCHHHHHHHHHTTSCEEEEEEEECSSSSSEEEEEEEEESSHHHHHHHHHHHTTEEETTEEEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHHhCCCccccccccccccccccceEEEECCHHHHHHHHHHcCCCEECCEEeEC
Confidence            456789999999999999999999999999999999999999999999999999999999999999999999999987

>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=99.79  E-value=1.2e-19  Score=147.00  Aligned_cols=81  Identities=21%  Similarity=0.422  Sum_probs=78.0

Q ss_pred             ceEEEecCCCCCCHHHHHHHhccCCCeEEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHhcCCceeCCeEEEEEecccc
Q 007792          243 NVLFVCKLNPVTEDEDLHTIFSRFGTVVSAEIIRDFKTGDSLNYAFIEFENRQACERAYSKMDNALIDDRRIHVDFSQSV  322 (589)
Q Consensus       243 ~~i~V~nL~~~~te~~L~~~F~~~G~v~~~~i~~d~~tg~~~g~aFV~f~~~~~a~~A~~~l~g~~i~gr~i~V~~a~~~  322 (589)
                      ..|||+|||+.+|+++|.++|++||+|..|.|+.++.||.++|||||+|.+.++|..|+..|||..|.|++|.|++|.+.
T Consensus         2 ~rlfV~nlp~~~te~~l~~~F~~~G~v~~v~i~~d~~tg~~rg~aFV~f~~~~~A~~a~~~l~~~~l~g~~l~V~~A~~~   81 (85)
T d2u2fa_           2 HKLFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIAGLNGMQLGDKKLLVQRASVG   81 (85)
T ss_dssp             CCEEEETCCSSCCSHHHHHHHTSSSCEEEEEEECCCSSSCCCCEEEEEESSSHHHHHHHHTSSSCCCSSSCCEEEECCCC
T ss_pred             CEEEEECCCCCCCHHHHHHHHHhcCccceEEeeccccccccceeEEEEECCHHHHHHHHHHhCCCEECCEEEEEEECCCC
Confidence            57999999999999999999999999999999999999999999999999999999999999999999999999999864


Q ss_pred             c
Q 007792          323 S  323 (589)
Q Consensus       323 ~  323 (589)
                      .
T Consensus        82 ~   82 (85)
T d2u2fa_          82 A   82 (85)
T ss_dssp             C
T ss_pred             C
Confidence            3

>d1whwa_ d.58.7.1 (A:) Probable RNA-binding protein 19, Rbm19 {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Probable RNA-binding protein 19, Rbm19
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.78  E-value=3.7e-19  Score=148.52  Aligned_cols=83  Identities=27%  Similarity=0.390  Sum_probs=79.1

Q ss_pred             CCceEEEecCCCCCCHHHHHHHhccCCCeEEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHhcCCceeCCeEEEEEecc
Q 007792          241 PENVLFVCKLNPVTEDEDLHTIFSRFGTVVSAEIIRDFKTGDSLNYAFIEFENRQACERAYSKMDNALIDDRRIHVDFSQ  320 (589)
Q Consensus       241 ~~~~i~V~nL~~~~te~~L~~~F~~~G~v~~~~i~~d~~tg~~~g~aFV~f~~~~~a~~A~~~l~g~~i~gr~i~V~~a~  320 (589)
                      ..++|||+|||+.+|+++|+++|.+||+|..|.|+.++.|+.++|||||+|.+.++|..||+.|||..|+|+.|+|.+|.
T Consensus         7 ~~~~lfV~nL~~~~t~~~l~~~F~~~g~v~~v~i~~d~~tg~~~g~afV~f~~~~~a~~A~~~l~g~~~~gr~i~V~~a~   86 (99)
T d1whwa_           7 GSGRLFVRNLSYTSSEEDLEKLFSAYGPLSELHYPIDSLTKKPKGFAFVTFMFPEHAVKAYAEVDGQVFQGRMLHVLPST   86 (99)
T ss_dssp             SCEEEEEECCCTTCCHHHHHHHHHTTSCEEEEECCCCTTTCCCCSEEEEEESSHHHHHHHHHHTTTEESSSCEEEEEECC
T ss_pred             CCCEEEEECCCCcCCHHHHHHHHHhcCCceeeeecccccccccCcceEEEECCHHHHHHHHHHcCCCEECCEEEEEEECC
Confidence            45789999999999999999999999999999999999999999999999999999999999999999999999999998


Q ss_pred             ccc
Q 007792          321 SVS  323 (589)
Q Consensus       321 ~~~  323 (589)
                      +..
T Consensus        87 ~~~   89 (99)
T d1whwa_          87 IKK   89 (99)
T ss_dssp             CCS
T ss_pred             CCC
Confidence            743

>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=99.77  E-value=9.1e-19  Score=155.65  Aligned_cols=83  Identities=23%  Similarity=0.418  Sum_probs=79.0

Q ss_pred             CCceEEEecCCCCCCHHHHHHHhccCCCeEEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHhcCCceeCCeEEEEEecc
Q 007792          241 PENVLFVCKLNPVTEDEDLHTIFSRFGTVVSAEIIRDFKTGDSLNYAFIEFENRQACERAYSKMDNALIDDRRIHVDFSQ  320 (589)
Q Consensus       241 ~~~~i~V~nL~~~~te~~L~~~F~~~G~v~~~~i~~d~~tg~~~g~aFV~f~~~~~a~~A~~~l~g~~i~gr~i~V~~a~  320 (589)
                      ..++|||+|||+++|+++|.++|++||.|..|.|+.++.||+++|||||+|.+.++|..||+.|||..|+|+.|.|.+|.
T Consensus        41 ~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~d~~t~~~rg~afV~f~~~~~A~~Ai~~lng~~~~gr~l~V~~a~  120 (139)
T d1u6fa1          41 VLRNLMVNYIPTTVDEVQLRQLFERYGPIESVKIVCDRETRQSRGYGFVKFQSGSSAQQAIAGLNGFNILNKRLKVALAA  120 (139)
T ss_dssp             TTSEEEEESCSTTCCHHHHHHHHHHHSCEEEEEEEEETTTTEEEEEEEEEESSHHHHHHHHHHTTTEECSSCEEEEEESS
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhhccccccccccccccccccceeeEEECCHHHHHHHHHHhCCCEECCEEEEEEEcC
Confidence            34689999999999999999999999999999999999999999999999999999999999999999999999999997


Q ss_pred             ccc
Q 007792          321 SVS  323 (589)
Q Consensus       321 ~~~  323 (589)
                      +..
T Consensus       121 ~~~  123 (139)
T d1u6fa1         121 SGH  123 (139)
T ss_dssp             CCC
T ss_pred             CCC
Confidence            643

>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=99.77  E-value=6.5e-19  Score=142.66  Aligned_cols=79  Identities=28%  Similarity=0.570  Sum_probs=75.5

Q ss_pred             CCceEEEecCCCCCCHHHHHHHhccCCCeEEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHhcCCceeCC--eEEEEEe
Q 007792          241 PENVLFVCKLNPVTEDEDLHTIFSRFGTVVSAEIIRDFKTGDSLNYAFIEFENRQACERAYSKMDNALIDD--RRIHVDF  318 (589)
Q Consensus       241 ~~~~i~V~nL~~~~te~~L~~~F~~~G~v~~~~i~~d~~tg~~~g~aFV~f~~~~~a~~A~~~l~g~~i~g--r~i~V~~  318 (589)
                      ..++|||+|||+.+++++|.++|++||+|..++|+.++.+|+++|||||+|.+.++|..||+.|||..+.|  ++|.|+|
T Consensus         5 ~~t~lfV~nlp~~~te~~l~~~F~~~G~i~~~~~~~d~~~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~~~l~V~~   84 (85)
T d1b7fa2           5 KDTNLYVTNLPRTITDDQLDTIFGKYGSIVQKNILRDKLTGRPRGVAFVRYNKREEAQEAISALNNVIPEGGSQPLSVRL   84 (85)
T ss_dssp             TTCEEEEESCCTTCCHHHHHHHHTSSSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCCCTTCSSCCEEEE
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhhCCEeeeeeecccccccCceeEEEEECCHHHHHHHHHHHCCCEeCCCCeEEEEEE
Confidence            45789999999999999999999999999999999999999999999999999999999999999999976  8899998


Q ss_pred             c
Q 007792          319 S  319 (589)
Q Consensus       319 a  319 (589)
                      |
T Consensus        85 A   85 (85)
T d1b7fa2          85 A   85 (85)
T ss_dssp             C
T ss_pred             C
Confidence            6

>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=99.77  E-value=5.7e-19  Score=142.96  Aligned_cols=78  Identities=27%  Similarity=0.489  Sum_probs=74.4

Q ss_pred             CceEEEecCCCCCCHHHHHHHhccCCCeEEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHhcCCceeCC--eEEEEEec
Q 007792          242 ENVLFVCKLNPVTEDEDLHTIFSRFGTVVSAEIIRDFKTGDSLNYAFIEFENRQACERAYSKMDNALIDD--RRIHVDFS  319 (589)
Q Consensus       242 ~~~i~V~nL~~~~te~~L~~~F~~~G~v~~~~i~~d~~tg~~~g~aFV~f~~~~~a~~A~~~l~g~~i~g--r~i~V~~a  319 (589)
                      .++|||+|||+.+|+++|+++|++||+|..+.|+.++.+|.++|||||+|.+.++|..|++.|||..|.|  ++|.|.||
T Consensus         6 ~~~lfV~nLp~~~te~~L~~~F~~~G~v~~v~i~~d~~~g~~kg~afV~f~~~~~a~~Ai~~lng~~~~G~~~~i~V~~A   85 (85)
T d1fxla2           6 DANLYVSGLPKTMTQKELEQLFSQYGRIITSRILVDQVTGVSRGVGFIRFDKRIEAEEAIKGLNGQKPSGATEPITVKFA   85 (85)
T ss_dssp             TCEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCCCTTCSSCCEEEEC
T ss_pred             CCEEEEeCCCCCCCHHHHHHHHHHhCCccccccccccccccCCCeeEEEEcCHHHHHHHHHHhCCCEeCCCCEEEEEEeC
Confidence            5789999999999999999999999999999999999999999999999999999999999999999998  55999886

>d2ghpa1 d.58.7.1 (A:116-196) U4/U6 snRNA-associated-splicing factor PRP24 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: U4/U6 snRNA-associated-splicing factor PRP24
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=99.76  E-value=3.9e-19  Score=142.67  Aligned_cols=79  Identities=11%  Similarity=0.285  Sum_probs=70.0

Q ss_pred             ceEEEecCCCCCCHHHHHHHhccCCCeEEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHhcCCceeCCeEEEEEeccc
Q 007792          243 NVLFVCKLNPVTEDEDLHTIFSRFGTVVSAEIIRDFKTGDSLNYAFIEFENRQACERAYSKMDNALIDDRRIHVDFSQS  321 (589)
Q Consensus       243 ~~i~V~nL~~~~te~~L~~~F~~~G~v~~~~i~~d~~tg~~~g~aFV~f~~~~~a~~A~~~l~g~~i~gr~i~V~~a~~  321 (589)
                      ++|||+|||+++|+++|.++|++||.|..+.++.+..+|+++|||||+|.+.++|..|++.|||..|.|++|.|++|+|
T Consensus         2 ~tl~v~nLp~~~t~~~l~~~f~~~G~v~~~~~~~~~~~~~~~g~afV~f~~~e~A~~Ai~~l~g~~~~g~~i~V~~a~P   80 (81)
T d2ghpa1           2 CTLWMTNFPPSYTQRNIRDLLQDINVVALSIRLPSLRFNTSRRFAYIDVTSKEDARYCVEKLNGLKIEGYTLVTKVSNP   80 (81)
T ss_dssp             CEEEEECCCTTCCHHHHHHHHHHTTCCCCEEECC-------CCEEEEECSSHHHHHHHHHHHTTCEETTEECEEEECCC
T ss_pred             cEEEEECCCCcCCHHHHHHHHHHhCcEEeeeeecccccccccceeEEEECCHHHHHHHHHHhCCCEECCEEEEEEEccC
Confidence            6999999999999999999999999999998888888999999999999999999999999999999999999999987

>d2cqga1 d.58.7.1 (A:96-185) TAR DNA-binding protein 43, TDP-43 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: TAR DNA-binding protein 43, TDP-43
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.76  E-value=1.1e-18  Score=142.53  Aligned_cols=80  Identities=29%  Similarity=0.453  Sum_probs=75.0

Q ss_pred             CCceEEEecCCCCCCHHHHHHHhccCCCeEEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHhcCCceeCCeEEEEEecc
Q 007792          241 PENVLFVCKLNPVTEDEDLHTIFSRFGTVVSAEIIRDFKTGDSLNYAFIEFENRQACERAYSKMDNALIDDRRIHVDFSQ  320 (589)
Q Consensus       241 ~~~~i~V~nL~~~~te~~L~~~F~~~G~v~~~~i~~d~~tg~~~g~aFV~f~~~~~a~~A~~~l~g~~i~gr~i~V~~a~  320 (589)
                      ..++|||+|||+++|+++|+++|++||+|..|.|+.++.||.++|||||+|.+.++|..||+.+  ..|+|+.|.|.+|.
T Consensus         7 ~~~~lfV~nLp~~~te~~l~~~F~~~G~i~~v~i~~d~~tg~srG~aFV~f~~~~~a~~al~~~--~~l~Gr~i~v~~a~   84 (90)
T d2cqga1           7 KTSDLIVLGLPWKTTEQDLKEYFSTFGEVLMVQVKKDLKTGHSKGFGFVRFTEYETQVKVMSQR--HMIDGRWCDCKLPN   84 (90)
T ss_dssp             CCCCEEEESCCSSCCHHHHHHHHGGGSCEEEEEEEECSSSCSEEEEEEEEESSHHHHHHHHHSC--EEETTEEEEEECCC
T ss_pred             CCCeEEEECCCCCCCHHHHHHHHHhhcccceeeeccCCCCcccCCEEEEEECCHHHHHHHHhcC--CccCCEEeEEEeCC
Confidence            4679999999999999999999999999999999999999999999999999999999999854  48999999999998


Q ss_pred             cc
Q 007792          321 SV  322 (589)
Q Consensus       321 ~~  322 (589)
                      ++
T Consensus        85 ~k   86 (90)
T d2cqga1          85 SK   86 (90)
T ss_dssp             TT
T ss_pred             CC
Confidence            74

>d2cpha1 d.58.7.1 (A:454-547) Probable RNA-binding protein 19, Rbm19 {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Probable RNA-binding protein 19, Rbm19
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.76  E-value=6.9e-19  Score=145.29  Aligned_cols=84  Identities=17%  Similarity=0.447  Sum_probs=77.8

Q ss_pred             CCCceEEEecCCCCCCHHHHHHHhccCCCeEEEEEeecC-CCCCcccEEEEEEcCHHHHHHHHHhc-CCceeCCeEEEEE
Q 007792          240 PPENVLFVCKLNPVTEDEDLHTIFSRFGTVVSAEIIRDF-KTGDSLNYAFIEFENRQACERAYSKM-DNALIDDRRIHVD  317 (589)
Q Consensus       240 ~~~~~i~V~nL~~~~te~~L~~~F~~~G~v~~~~i~~d~-~tg~~~g~aFV~f~~~~~a~~A~~~l-~g~~i~gr~i~V~  317 (589)
                      .+.++|||+|||+.+++++|..+|++||.|..|.|+.+. .+|.++|||||+|.+.++|..||..| ||..|.|++|.|+
T Consensus         6 ~~~~~l~V~nLp~~~~e~~l~~~F~~~G~i~~v~i~~~~~~~g~~rg~afV~f~~~~~A~~Ai~~l~~~~~~~Gr~l~V~   85 (94)
T d2cpha1           6 QTTSKILVRNIPFQANQREIRELFSTFGELKTVRLPKKMTGTGAHRGFGFVDFITKQDAKKAFNALCHSTHLYGRRLVLE   85 (94)
T ss_dssp             SCCCCEEEESCCTTCCHHHHHHHHHTTSCEEEEECCCCCSSSCSSCSEEEEEESSHHHHHHHHHHHHTCCBSSSCBCEEE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHHhCCceEEEEEeccccCCCcccEEEEEECCHHHHHHHHHHccCCcEECCEEEEEE
Confidence            356899999999999999999999999999999998875 48999999999999999999999998 8999999999999


Q ss_pred             eccccc
Q 007792          318 FSQSVS  323 (589)
Q Consensus       318 ~a~~~~  323 (589)
                      ||.+..
T Consensus        86 ~A~~~~   91 (94)
T d2cpha1          86 WADSEV   91 (94)
T ss_dssp             ECCCCC
T ss_pred             EcCCCC
Confidence            998643

>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=99.76  E-value=1.4e-18  Score=140.24  Aligned_cols=78  Identities=23%  Similarity=0.375  Sum_probs=74.6

Q ss_pred             CceEEEecCCCCCCHHHHHHHhccCCCeEEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHhcCCceeCCeEEEEEecc
Q 007792          242 ENVLFVCKLNPVTEDEDLHTIFSRFGTVVSAEIIRDFKTGDSLNYAFIEFENRQACERAYSKMDNALIDDRRIHVDFSQ  320 (589)
Q Consensus       242 ~~~i~V~nL~~~~te~~L~~~F~~~G~v~~~~i~~d~~tg~~~g~aFV~f~~~~~a~~A~~~l~g~~i~gr~i~V~~a~  320 (589)
                      ..+|||+|||+++|+++|.++|++||+|..+.|+.++.||+++|||||+|.+.++|.+||+ +++..|+|+.|.|..|.
T Consensus         6 ~~~lfV~nlp~~~te~~l~~~F~~~G~i~~v~i~~d~~tg~~kG~afV~f~~~~~a~~ai~-~~~~~i~Gr~i~V~~A~   83 (84)
T d1l3ka1           6 LRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMN-ARPHKVDGRVVEPKRAV   83 (84)
T ss_dssp             GGEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHH-TCSCEETTEECEEEECC
T ss_pred             CcEEEEECCCCCCCHHHHHHHHHhhccccceeecccccCCCcccEEEEEEcCHHHHHHHHH-hCCCEECCEEEEEEeee
Confidence            4689999999999999999999999999999999999999999999999999999999996 69999999999999875

>d1no8a_ d.58.7.1 (A:) Nuclear factor Aly {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nuclear factor Aly
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.76  E-value=9.4e-19  Score=139.21  Aligned_cols=77  Identities=27%  Similarity=0.458  Sum_probs=73.6

Q ss_pred             eEEEecCCCCCCHHHHHHHhccCCCeEEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHhcCCceeCCeEEEEEeccc
Q 007792          244 VLFVCKLNPVTEDEDLHTIFSRFGTVVSAEIIRDFKTGDSLNYAFIEFENRQACERAYSKMDNALIDDRRIHVDFSQS  321 (589)
Q Consensus       244 ~i~V~nL~~~~te~~L~~~F~~~G~v~~~~i~~d~~tg~~~g~aFV~f~~~~~a~~A~~~l~g~~i~gr~i~V~~a~~  321 (589)
                      .|||+|||+.+++++|.++|++||+|..|.|+.++ +|+++|||||+|.+.++|+.|++.|||..|+|++|.|++|.+
T Consensus         2 rl~V~nLp~~~~~~~l~~~F~~~G~v~~~~i~~~~-~g~~~g~afV~f~~~~~A~~Ai~~l~g~~l~g~~l~V~~a~S   78 (78)
T d1no8a_           2 KLLVSNLDFGVSDADIQELFAEFGTLKKAAVHYDR-SGRSLGTADVHFERKADALKAMKQYNGVPLDGRPMNIQLVTS   78 (78)
T ss_dssp             EEEEESCCTTCCHHHHHHHHHHHSCEEEEEESCSS-CCCSCCEEEEEESCHHHHHHHHHHHTTCEETTEECEEEEECC
T ss_pred             EEEEECCCCCCCHHHHHHHHHHhCCCeEEEEEEee-ccccceeEEEEECCHHHHHHHHHHhCCCEECCEEEEEEEeeC
Confidence            59999999999999999999999999999999885 799999999999999999999999999999999999999863

>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=99.76  E-value=2.5e-18  Score=144.42  Aligned_cols=81  Identities=32%  Similarity=0.480  Sum_probs=76.3

Q ss_pred             CCceEEEecCCCCCCHHHHHHHhccCCCeEEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHhcCCceeCCeEEEEEecc
Q 007792          241 PENVLFVCKLNPVTEDEDLHTIFSRFGTVVSAEIIRDFKTGDSLNYAFIEFENRQACERAYSKMDNALIDDRRIHVDFSQ  320 (589)
Q Consensus       241 ~~~~i~V~nL~~~~te~~L~~~F~~~G~v~~~~i~~d~~tg~~~g~aFV~f~~~~~a~~A~~~l~g~~i~gr~i~V~~a~  320 (589)
                      ..++|||+|||+.+|+++|.++|++||+|..|.|+.++.||.++|||||+|.+.++|+.||+.+|+ .|.|+.|.|++|.
T Consensus         9 ~~~~lfV~nLp~~~te~~l~~~F~~~G~i~~v~i~~d~~tg~~kg~afV~f~~~~~A~~Ai~~~~~-~l~Gr~l~V~~a~   87 (103)
T d2cqda1           9 TFTKIFVGGLPYHTTDASLRKYFEGFGDIEEAVVITDRQTGKSRGYGFVTMADRAAAERACKDPNP-IIDGRKANVNLAY   87 (103)
T ss_dssp             SSSEEEEECCCSSCCHHHHHHHHHTTSCEEEEEESCCSSSCCCCSEEEEEESSHHHHHHHHTCSSC-EETTEECEEEEST
T ss_pred             CCcEEEEeCCCCcCcHHHHHHHHhhcccccceeccccccccccCCeEEEEECCHHHHHHHHHHCCC-cCCCEEEEEEEcC
Confidence            456899999999999999999999999999999999999999999999999999999999998876 7999999999997


Q ss_pred             cc
Q 007792          321 SV  322 (589)
Q Consensus       321 ~~  322 (589)
                      ..
T Consensus        88 ~~   89 (103)
T d2cqda1          88 LG   89 (103)
T ss_dssp             TT
T ss_pred             CC
Confidence            63

>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=99.76  E-value=9.5e-19  Score=146.21  Aligned_cols=80  Identities=26%  Similarity=0.303  Sum_probs=76.2

Q ss_pred             CceEEEecCCCCCCHHHHHHHhccCCCeEEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHhcCCceeCCeEEEEEeccc
Q 007792          242 ENVLFVCKLNPVTEDEDLHTIFSRFGTVVSAEIIRDFKTGDSLNYAFIEFENRQACERAYSKMDNALIDDRRIHVDFSQS  321 (589)
Q Consensus       242 ~~~i~V~nL~~~~te~~L~~~F~~~G~v~~~~i~~d~~tg~~~g~aFV~f~~~~~a~~A~~~l~g~~i~gr~i~V~~a~~  321 (589)
                      ..+|||+|||+.+|+++|.++|+.||+|..|.|+.++.+|+++|||||+|.+.++|.+|| .|||..|+|+.|.|.+|.+
T Consensus        18 ~~tifV~nL~~~~te~~l~~~F~~~G~V~~v~i~~d~~tg~~kG~afV~F~~~e~a~~A~-~l~g~~~~G~~l~V~~a~~   96 (101)
T d2cq4a1          18 ARTVFCMQLAARIRPRDLEDFFSAVGKVRDVRIISDRNSRRSKGIAYVEFCEIQSVPLAI-GLTGQRLLGVPIIVQASQA   96 (101)
T ss_dssp             HTEEEEESCCTTCCHHHHHHHHTTTSCEEEEEECCSCCSSSCCCCEEEEESCGGGHHHHH-HHTTEEETTEEEEEEEHHH
T ss_pred             CCEEEEECCCCCCCHHHHHHHHcCCCeEEEEEeeecCCCccccceEEEEECCHHHHHHHH-HHCCCEECCEEEEEEECCC
Confidence            368999999999999999999999999999999999999999999999999999999999 5999999999999999875


Q ss_pred             c
Q 007792          322 V  322 (589)
Q Consensus       322 ~  322 (589)
                      .
T Consensus        97 ~   97 (101)
T d2cq4a1          97 E   97 (101)
T ss_dssp             H
T ss_pred             C
Confidence            3

>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=99.75  E-value=2.3e-18  Score=140.98  Aligned_cols=81  Identities=20%  Similarity=0.374  Sum_probs=75.3

Q ss_pred             CCCceEEEecCCCCCCHHHHHHHhccCCCeEEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHhcCCceeCCeEEEEEec
Q 007792          240 PPENVLFVCKLNPVTEDEDLHTIFSRFGTVVSAEIIRDFKTGDSLNYAFIEFENRQACERAYSKMDNALIDDRRIHVDFS  319 (589)
Q Consensus       240 ~~~~~i~V~nL~~~~te~~L~~~F~~~G~v~~~~i~~d~~tg~~~g~aFV~f~~~~~a~~A~~~l~g~~i~gr~i~V~~a  319 (589)
                      .+.++|||+|||+.+|+++|.++|++||+|..|.|+.+..++  +|||||+|.+.++|..|+..|||..|.|+.|+|.||
T Consensus         6 ~~~~tl~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~d~~~~--~~~afV~f~~~~~A~~A~~~l~~~~~~g~~i~v~~a   83 (90)
T d2cqia1           6 GQPRTLYVGNLSRDVTEVLILQLFSQIGPCKSCKMITEHTSN--DPYCFVEFYEHRDAAAALAAMNGRKILGKEVKVNWA   83 (90)
T ss_dssp             CCCCEEEEESCCTTCCHHHHHHHHHHHSCEEEEEEECCCCSS--CCEEEEEESSHHHHHHHHHHHTTEEETTEEEEEEEC
T ss_pred             CCCCEEEEECCCCCCCHHHHHHHHHhcCCceeeeeecccCcc--ceeeEEEECCHHHHHHHHHHcCCCEECCEEEEEEEc
Confidence            456799999999999999999999999999999999986654  789999999999999999999999999999999999


Q ss_pred             ccc
Q 007792          320 QSV  322 (589)
Q Consensus       320 ~~~  322 (589)
                      ++.
T Consensus        84 ~~~   86 (90)
T d2cqia1          84 TTP   86 (90)
T ss_dssp             CCT
T ss_pred             CCC
Confidence            864

>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=99.75  E-value=1.2e-18  Score=141.03  Aligned_cols=77  Identities=25%  Similarity=0.514  Sum_probs=72.7

Q ss_pred             EEEecCCCCCCHHHHHHHhccCCCeEEEEEeecCCCC---CcccEEEEEEcCHHHHHHHHHhcCCceeCCeEEEEEeccc
Q 007792          245 LFVCKLNPVTEDEDLHTIFSRFGTVVSAEIIRDFKTG---DSLNYAFIEFENRQACERAYSKMDNALIDDRRIHVDFSQS  321 (589)
Q Consensus       245 i~V~nL~~~~te~~L~~~F~~~G~v~~~~i~~d~~tg---~~~g~aFV~f~~~~~a~~A~~~l~g~~i~gr~i~V~~a~~  321 (589)
                      |||+|||+++|+++|.++|++||+|..|.|+.++.++   .++|||||+|.+.++|..|++.|||..|+|+.|.|++|.+
T Consensus         1 LfV~nLp~~~t~~~l~~~F~~~G~v~~v~i~~~~~~~~~~~~kG~afV~f~~~~~A~~A~~~~~~~~~~g~~i~V~~a~~   80 (85)
T d2cpfa1           1 LFIKNLNFSTTEETLKGVFSKVGAIKSCTISKKKNKAGVLLSMGFGFVEYKKPEQAQKALKQLQGHTVDGHKLEVRISER   80 (85)
T ss_dssp             EEEESCCTTCCHHHHHHHHHTTSCEEEEEEEEEECTTCCEEEEEEEEEEESSHHHHHHHHHHSTTCEETTEECEEECSSC
T ss_pred             CEEcCCCCCCCHHHHHHHHHHhCCccccceecccccccccccceEEEEEECCHHHHHHHHHHhCCCEECCEEEEEEECCC
Confidence            8999999999999999999999999999999887665   4689999999999999999999999999999999999865

>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=99.75  E-value=8.7e-19  Score=141.25  Aligned_cols=78  Identities=32%  Similarity=0.582  Sum_probs=74.0

Q ss_pred             EEEecCCCCCCHHHHHHHhccCCCeEEE-EEeecCCCCCcccEEEEEEcCHHHHHHHHHhcCCceeCCeEEEEEecccc
Q 007792          245 LFVCKLNPVTEDEDLHTIFSRFGTVVSA-EIIRDFKTGDSLNYAFIEFENRQACERAYSKMDNALIDDRRIHVDFSQSV  322 (589)
Q Consensus       245 i~V~nL~~~~te~~L~~~F~~~G~v~~~-~i~~d~~tg~~~g~aFV~f~~~~~a~~A~~~l~g~~i~gr~i~V~~a~~~  322 (589)
                      |||+|||+++|+++|.++|++||.|..+ .|+.++.+|+++|||||+|.+.++|..||+.|||..|.|++|.|.+|.++
T Consensus         1 lfV~nLp~~~te~~l~~~F~~~G~i~~~~~i~~~~~~g~~~g~afV~f~~~~~a~~Ai~~~~g~~~~gr~l~v~~a~~k   79 (83)
T d1x5ta1           1 IFIGNLDPEIDEKLLYDTFSAFGVILQTPKIMRDPDTGNSKGYAFINFASFDASDAAIEAMNGQYLCNRPITVSYAFKK   79 (83)
T ss_dssp             EEEECCCTTCCHHHHHHHHHTTSCBSSCCEECCCTTTCSCCSEEEEEBSSHHHHHHHHHTTTTCEETTEECEEEESCCC
T ss_pred             CEEcCCCCcCcHHHHHHHHHHhCceeeeEEEEeeccccccCceEEEEECCHHHHHHHHHhCCCcEECCEEEEEEEecCC
Confidence            8999999999999999999999999764 78889999999999999999999999999999999999999999999864

>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=99.75  E-value=3.7e-19  Score=141.08  Aligned_cols=76  Identities=22%  Similarity=0.397  Sum_probs=73.1

Q ss_pred             ceEEEecCCCCCCHHHHHHHhccCCCeEEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHhcCCceeCCeEEEEEec
Q 007792          243 NVLFVCKLNPVTEDEDLHTIFSRFGTVVSAEIIRDFKTGDSLNYAFIEFENRQACERAYSKMDNALIDDRRIHVDFS  319 (589)
Q Consensus       243 ~~i~V~nL~~~~te~~L~~~F~~~G~v~~~~i~~d~~tg~~~g~aFV~f~~~~~a~~A~~~l~g~~i~gr~i~V~~a  319 (589)
                      ++|||+|||+++|+++|.++|++||+|..+.|+.++.||+++|||||+|.+.++|.+||. +|+..|+|+.|.|++|
T Consensus         1 cklfV~nLp~~~te~~l~~~F~~~G~i~~v~i~~d~~tg~~kG~aFV~f~~~~~a~~al~-~~~~~i~Gr~i~V~~A   76 (77)
T d1uawa_           1 CKMFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQAGVDKVLA-QSRHELDSKTIDPKVA   76 (77)
T ss_dssp             CCEEEESCCSSCCSHHHHHHHTTTSCCCCEEEECCCCSSSCSSEEEECCCCTTHHHHHHH-TTTCCCSSCCCEEEEC
T ss_pred             CEEEEeCCCCcCCHHHHHHHHHHhCCcceeeeecccCCCCccceEEEEECCHHHHHHHHH-cCCCEECCeEEEEEEC
Confidence            479999999999999999999999999999999999999999999999999999999996 7999999999999986

>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=99.75  E-value=4.6e-18  Score=139.99  Aligned_cols=83  Identities=28%  Similarity=0.504  Sum_probs=76.3

Q ss_pred             CCCCceEEEecCCCCCCHHHHHHHhccCCCeEEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHhcCCceeCCeEEEEEe
Q 007792          239 KPPENVLFVCKLNPVTEDEDLHTIFSRFGTVVSAEIIRDFKTGDSLNYAFIEFENRQACERAYSKMDNALIDDRRIHVDF  318 (589)
Q Consensus       239 ~~~~~~i~V~nL~~~~te~~L~~~F~~~G~v~~~~i~~d~~tg~~~g~aFV~f~~~~~a~~A~~~l~g~~i~gr~i~V~~  318 (589)
                      ....++|||+|||+.+|+++|.++|++||+|..|.|+.++.  .++|||||+|.+.++|..||..|||..|+|+.|.|++
T Consensus         8 ~~~~~~l~v~nLp~~~t~~~L~~~F~~~G~v~~v~~~~~~~--~~kg~afV~f~~~~~a~~Ai~~l~~~~~~g~~l~V~~   85 (93)
T d2cq3a1           8 KSTPKRLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNER--GSKGFGFVTFENSADADRAREKLHGTVVEGRKIEVNN   85 (93)
T ss_dssp             SCCCCEEEEESCCTTCCHHHHHHHGGGTSCEEEEEEECCTT--TTCCEEEEEESCHHHHHHHHHHHTTCEETTEECEEEE
T ss_pred             CCCCCEEEEECCCCCCCHHHHHHHHhhcceeeecccccccc--CCcceeEEEECCHHHHHHHHHHcCCCEECCEEEEEEe
Confidence            34567899999999999999999999999999999998754  3789999999999999999999999999999999999


Q ss_pred             ccccc
Q 007792          319 SQSVS  323 (589)
Q Consensus       319 a~~~~  323 (589)
                      |+++.
T Consensus        86 A~~r~   90 (93)
T d2cq3a1          86 ATARV   90 (93)
T ss_dssp             CCSSC
T ss_pred             cCcCC
Confidence            98754

>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=99.74  E-value=2.2e-18  Score=144.44  Aligned_cols=79  Identities=20%  Similarity=0.347  Sum_probs=75.7

Q ss_pred             ceEEEecCCCCCCHHHHHHHhccCCCeEEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHhcCCceeCCeEEEEEecccc
Q 007792          243 NVLFVCKLNPVTEDEDLHTIFSRFGTVVSAEIIRDFKTGDSLNYAFIEFENRQACERAYSKMDNALIDDRRIHVDFSQSV  322 (589)
Q Consensus       243 ~~i~V~nL~~~~te~~L~~~F~~~G~v~~~~i~~d~~tg~~~g~aFV~f~~~~~a~~A~~~l~g~~i~gr~i~V~~a~~~  322 (589)
                      ++|||+|||+++|+++|+++|++||.|..+.|+.++.++.++|||||+|.+.++|.+|| .++|..|.|+.|.|.+|.++
T Consensus        21 ~~lfVgnLp~~~te~~L~~~F~~~G~i~~~~i~~d~~~~~~kg~aFV~f~~~~~a~~al-~~~~~~l~G~~i~V~~a~~k   99 (103)
T d1x4ba1          21 RKLFIGGLSFETTEESLRNYYEQWGKLTDCVVMRDPASKRSRGFGFVTFSSMAEVDAAM-AARPHSIDGRVVEPKRAVAR   99 (103)
T ss_dssp             TEEEEECCTTCCCHHHHHHHHTSSCCCSEEEEECCTTTSSCCSEEEEECSSHHHHHHHH-TSCSEEETTEEEEEECCSSC
T ss_pred             CEEEEeCCCCcCCHHHHHHHHHhhCcccceeecccccCCCccCeEEEEECCHHHHHHHH-HhCCCeECCEEEEEEECccc
Confidence            68999999999999999999999999999999999999999999999999999999999 57999999999999999864

>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=99.74  E-value=1.2e-18  Score=142.68  Aligned_cols=82  Identities=30%  Similarity=0.509  Sum_probs=78.2

Q ss_pred             CceEEEecCCCCCCHHHHHHHhccCCCeEEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHhcCCceeCCeEEEEEeccc
Q 007792          242 ENVLFVCKLNPVTEDEDLHTIFSRFGTVVSAEIIRDFKTGDSLNYAFIEFENRQACERAYSKMDNALIDDRRIHVDFSQS  321 (589)
Q Consensus       242 ~~~i~V~nL~~~~te~~L~~~F~~~G~v~~~~i~~d~~tg~~~g~aFV~f~~~~~a~~A~~~l~g~~i~gr~i~V~~a~~  321 (589)
                      ..+|||+|||+++|+++|.++|++||.|..+.++.+..+|.++|||||+|.+.++|+.||..|||..|+|+.|.|++|.+
T Consensus         5 ~~kifV~nLp~~~t~~~l~~~F~~~G~i~~~~~~~~~~~~~~~g~afV~f~~~~~a~~Ai~~l~~~~~~g~~l~V~~a~~   84 (90)
T d1x5sa1           5 EGKLFVGGLSFDTNEQSLEQVFSKYGQISEVVVVKDRETQRSRGFGFVTFENIDDAKDAMMAMNGKSVDGRQIRVDQAGK   84 (90)
T ss_dssp             CSEEEEESCCTTCCHHHHHHHHHHHSCCCEEEECCCSSSCSCCSEEEEECSSHHHHHHHHHHHTTCCTTSCCCEEEEEEC
T ss_pred             CCEEEEECCCCcCCHHHHHHhhhccccccceeeccccccccccceEEEEECCHHHHHHHHHHcCCCEECCEEEEEEEcCC
Confidence            46899999999999999999999999999999999999999999999999999999999999999999999999999976


Q ss_pred             cc
Q 007792          322 VS  323 (589)
Q Consensus       322 ~~  323 (589)
                      ..
T Consensus        85 ~~   86 (90)
T d1x5sa1          85 SS   86 (90)
T ss_dssp             CC
T ss_pred             CC
Confidence            43

>d1p1ta_ d.58.7.1 (A:) Cleavage stimulation factor, 64 kda subunit {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Cleavage stimulation factor, 64 kda subunit
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.74  E-value=1.1e-18  Score=146.98  Aligned_cols=82  Identities=27%  Similarity=0.438  Sum_probs=78.3

Q ss_pred             CceEEEecCCCCCCHHHHHHHhccCCCeEEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHhcCCceeCCeEEEEEeccc
Q 007792          242 ENVLFVCKLNPVTEDEDLHTIFSRFGTVVSAEIIRDFKTGDSLNYAFIEFENRQACERAYSKMDNALIDDRRIHVDFSQS  321 (589)
Q Consensus       242 ~~~i~V~nL~~~~te~~L~~~F~~~G~v~~~~i~~d~~tg~~~g~aFV~f~~~~~a~~A~~~l~g~~i~gr~i~V~~a~~  321 (589)
                      ..+|||+|||+++|+++|.++|++||+|..|.|+.++.||+++|||||+|.+.++|..||+.|||..|.|+.|.|++|.+
T Consensus         8 ~rtl~V~nLp~~~te~~l~~~f~~~G~i~~v~i~~~~~tg~~~g~afV~f~~~~~a~~ai~~l~~~~~~g~~i~V~~a~~   87 (104)
T d1p1ta_           8 LRSVFVGNIPYEATEEQLKDIFSEVGPVVSFRLVYDRETGKPKGYGFCEYQDQETALSAMRNLNGREFSGRALRVDNAAS   87 (104)
T ss_dssp             HSCEEEESCCTTSCHHHHHHHHHTTSCCSEEEEEEETTTTEEEEEEEEECSCHHHHHHHHHHSSSBSCSSSCBEEEETTC
T ss_pred             CCEEEEECCCCcCCHHHHHHhhhccccccccccccccceeccCCceEEEECCHHHHHHHHHHcCCCEECCEEEEEEECCC
Confidence            46899999999999999999999999999999999999999999999999999999999999999999999999999976


Q ss_pred             cc
Q 007792          322 VS  323 (589)
Q Consensus       322 ~~  323 (589)
                      ..
T Consensus        88 ~~   89 (104)
T d1p1ta_          88 EK   89 (104)
T ss_dssp             TT
T ss_pred             CC
Confidence            43

>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=99.74  E-value=1.4e-18  Score=137.14  Aligned_cols=75  Identities=24%  Similarity=0.410  Sum_probs=71.3

Q ss_pred             eEEEecCCCCCCHHHHHHHhccCCCeEEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHhcCCceeCCeEEEEEec
Q 007792          244 VLFVCKLNPVTEDEDLHTIFSRFGTVVSAEIIRDFKTGDSLNYAFIEFENRQACERAYSKMDNALIDDRRIHVDFS  319 (589)
Q Consensus       244 ~i~V~nL~~~~te~~L~~~F~~~G~v~~~~i~~d~~tg~~~g~aFV~f~~~~~a~~A~~~l~g~~i~gr~i~V~~a  319 (589)
                      .|||+|||+++|+++|.++|++||+|..|.|+.++.|++++|||||+|.+.++|+.||+ +++..|+|+.|.|..|
T Consensus         1 klfV~nl~~~~te~~l~~~F~~~G~i~~~~i~~d~~t~~~kg~afV~f~~~~~a~~Al~-~~~~~l~Gr~i~V~rA   75 (75)
T d1hd0a_           1 KMFIGGLSWDTTKKDLKDYFSKFGEVVDCTLKLDPITGRSRGFGFVLFKESESVDKVMD-QKEHKLNGKVIDPKRA   75 (75)
T ss_dssp             CEEEECCCTTCCHHHHHHHHHTTSCEEEEECCCBTTTTBCCSEEEEEESSHHHHHHHHH-TCCCCBTTBCCEECCC
T ss_pred             CEEEeCCCCcCCHHHHHHHHHhhccccccccccCCCCCCcCceEEEEECCHHHHHHHHh-cCCCEECCCEEEeeEC
Confidence            48999999999999999999999999999999999999999999999999999999996 7999999999998654

>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=99.74  E-value=2.8e-18  Score=140.10  Aligned_cols=79  Identities=32%  Similarity=0.569  Sum_probs=73.9

Q ss_pred             CceEEEecCCCCCCHHHHHHHhccCCCeEEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHhcCCceeCCeEEEEEeccc
Q 007792          242 ENVLFVCKLNPVTEDEDLHTIFSRFGTVVSAEIIRDFKTGDSLNYAFIEFENRQACERAYSKMDNALIDDRRIHVDFSQS  321 (589)
Q Consensus       242 ~~~i~V~nL~~~~te~~L~~~F~~~G~v~~~~i~~d~~tg~~~g~aFV~f~~~~~a~~A~~~l~g~~i~gr~i~V~~a~~  321 (589)
                      ..+|||+|||+++|+++|+++|++||.|..+.|+.+..  .++|||||+|.+.++|+.||+.|||..|+|+.|.|.+|++
T Consensus         8 ~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~~~i~~~~~--~~kg~afV~f~~~~~A~~Ai~~l~g~~~~g~~i~V~~a~~   85 (89)
T d1cvja2           8 VGNIFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDEN--GSKGYGFVHFETQEAAERAIEKMNGMLLNDRKVFVGRFKS   85 (89)
T ss_dssp             TTEEEEESCCSSCCHHHHHHHHHTTSCEEEEEECCBTT--BCCSCEEEEESCHHHHHHHTTSSSEEEETTEEEEEEECCC
T ss_pred             CCEEEEeCCCCCCCHHHHHHHHHhcCCceEEEEEeecC--CCcceeEEEECCHHHHHHHHHHcCCCEECCEEEEEEECCC
Confidence            46899999999999999999999999999999998854  3789999999999999999999999999999999999986


Q ss_pred             c
Q 007792          322 V  322 (589)
Q Consensus       322 ~  322 (589)
                      +
T Consensus        86 ~   86 (89)
T d1cvja2          86 R   86 (89)
T ss_dssp             T
T ss_pred             C
Confidence            4

>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=99.74  E-value=5.5e-18  Score=135.11  Aligned_cols=76  Identities=20%  Similarity=0.422  Sum_probs=73.1

Q ss_pred             ceEEEecCCCCCCHHHHHHHhccCCCeEEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHhcCCceeCCeEEEEEec
Q 007792          243 NVLFVCKLNPVTEDEDLHTIFSRFGTVVSAEIIRDFKTGDSLNYAFIEFENRQACERAYSKMDNALIDDRRIHVDFS  319 (589)
Q Consensus       243 ~~i~V~nL~~~~te~~L~~~F~~~G~v~~~~i~~d~~tg~~~g~aFV~f~~~~~a~~A~~~l~g~~i~gr~i~V~~a  319 (589)
                      .+|||+|||+++|+++|+++|++||.|..+.++.++.+++++|||||+|.+.++|.+|+ .|||..|+|+.|.|+.|
T Consensus         3 r~lfV~nLp~~~te~~l~~~F~~~G~i~~~~~~~~~~~~~~~g~afV~f~~~e~~~~al-~~~~~~l~Gr~i~V~~A   78 (79)
T d1l3ka2           3 KKIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIV-IQKYHTVNGHNCEVRKA   78 (79)
T ss_dssp             SEEEEECCTTTCCHHHHHHHHTTTSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHH-HCSCCEETTEECEEEEC
T ss_pred             CEEEECCCCCcCCHHHHHHHHHHhccccccccccCCCCcccccEEEEEEcCHHHHHHHH-HhCCCEECCEEEEEEEC
Confidence            68999999999999999999999999999999999999999999999999999999999 58999999999999876

>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=99.73  E-value=3.4e-18  Score=143.16  Aligned_cols=85  Identities=20%  Similarity=0.306  Sum_probs=78.0

Q ss_pred             CCCCceEEEecCCCCCCHHHHHHHhccCCCeE--------EEEEeecCCCCCcccEEEEEEcCHHHHHHHHHhcCCceeC
Q 007792          239 KPPENVLFVCKLNPVTEDEDLHTIFSRFGTVV--------SAEIIRDFKTGDSLNYAFIEFENRQACERAYSKMDNALID  310 (589)
Q Consensus       239 ~~~~~~i~V~nL~~~~te~~L~~~F~~~G~v~--------~~~i~~d~~tg~~~g~aFV~f~~~~~a~~A~~~l~g~~i~  310 (589)
                      .+..++|||+|||+.+|+++|.++|.+||+|.        .+.+..++.+|+++|||||+|.+.++|..||+.|||..|.
T Consensus         5 ~~~~~~i~V~nLp~~~te~~l~~~F~~~G~i~~~~~~~~~~~~~~~d~~~~~~~g~afV~f~~~~~a~~Ai~~l~g~~~~   84 (101)
T d2cpea1           5 DSDNSAIYVQGLNDSVTLDDLADFFKQCGVVKMNKRTGQPMIHIYLDKETGKPKGDATVSYEDPPTAKAAVEWFDGKDFQ   84 (101)
T ss_dssp             CCCCCEEEEECCCTTCCHHHHHHHHTTTSCBCBCSSSCCBSEECCBCTTTCSBCSEEEEEBSSHHHHHHHHHHHTTCEET
T ss_pred             CCCCCEEEEECCCCcCCHHHHHHHHHHCceEEEeeecccceeEEeeccccccccceeeEEecCHHHHHHHHHHhCCCEEC
Confidence            45678999999999999999999999999874        4677788889999999999999999999999999999999


Q ss_pred             CeEEEEEeccccc
Q 007792          311 DRRIHVDFSQSVS  323 (589)
Q Consensus       311 gr~i~V~~a~~~~  323 (589)
                      |+.|.|++|+++.
T Consensus        85 gr~i~V~~a~~~~   97 (101)
T d2cpea1          85 GSKLKVSLARKKP   97 (101)
T ss_dssp             TEECEEECSSCCC
T ss_pred             CEEEEEEEcCCCC
Confidence            9999999998754

>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=99.73  E-value=1.3e-18  Score=137.03  Aligned_cols=75  Identities=24%  Similarity=0.407  Sum_probs=71.2

Q ss_pred             eEEEecCCCCCCHHHHHHHhccCCCeEEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHhcCCceeCCeEEEEEec
Q 007792          244 VLFVCKLNPVTEDEDLHTIFSRFGTVVSAEIIRDFKTGDSLNYAFIEFENRQACERAYSKMDNALIDDRRIHVDFS  319 (589)
Q Consensus       244 ~i~V~nL~~~~te~~L~~~F~~~G~v~~~~i~~d~~tg~~~g~aFV~f~~~~~a~~A~~~l~g~~i~gr~i~V~~a  319 (589)
                      .|||||||+++|+++|+++|++||+|..|.|+.++.|++++|||||+|.+.++|++||+ +++..|+|+.|.|..|
T Consensus         1 klfVgnLp~~~te~~l~~~F~~~G~I~~v~i~~d~~t~~~rG~~FV~f~~~~~a~~al~-~~~~~i~g~~i~vk~A   75 (75)
T d1x0fa1           1 KIFVGGLSPDTPEEKIREYFGGFGEVESIELPMDNKTNKRRGFCFITFKEEEPVKKIME-KKYHNVGLSKCEIKVA   75 (75)
T ss_dssp             EEEEESCCSSCCHHHHHHHHHHHSCEEEEECCCCTTTCCTTCCEEEEESSSHHHHHHTT-CSSCCBTTBCCEEECC
T ss_pred             CEEEcCCCCCCCHHHHHHHHHHhCCcccccccccccccccccEEEEEECCHHHHHHHHh-hCCCEECCEEeEEEEC
Confidence            59999999999999999999999999999999999999999999999999999999995 5778899999999875

>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=99.73  E-value=3.1e-18  Score=138.85  Aligned_cols=80  Identities=24%  Similarity=0.378  Sum_probs=70.6

Q ss_pred             CceEEEecCCCCCC-HHHHHHHhccCCCeEEEEEeec-CCCCCcccEEEEEEcCHHHHHHHHHhcCCceeCCeEEEEEec
Q 007792          242 ENVLFVCKLNPVTE-DEDLHTIFSRFGTVVSAEIIRD-FKTGDSLNYAFIEFENRQACERAYSKMDNALIDDRRIHVDFS  319 (589)
Q Consensus       242 ~~~i~V~nL~~~~t-e~~L~~~F~~~G~v~~~~i~~d-~~tg~~~g~aFV~f~~~~~a~~A~~~l~g~~i~gr~i~V~~a  319 (589)
                      ..+|||+|||+++| ++.|.++|++||.|..|.|+.+ ..+++++|||||+|.+.++|..||+ |||..|+|+.|.|++|
T Consensus         4 ~~~l~V~nLp~~~t~ed~l~~~F~~~G~i~~v~i~~~~~~~~~~kg~afV~f~~~~~a~~Al~-~n~~~~~gr~l~V~~a   82 (86)
T d2ghpa3           4 GREIMIRNLSTELLDENLLRESFEGFGSIEKINIPAGQKEHSFNNCCAFMVFENKDSAERALQ-MNRSLLGNREISVSLA   82 (86)
T ss_dssp             TTEEEEEEECTTTCCHHHHHHHHGGGSCEEEEECCSCCC---CCCEEEEEEESSHHHHHHHGG-GTTEEETTEEEEEEEC
T ss_pred             CCEEEEECCCCCcccHHHHHHHHHhhhhccceeeecccCCccccceeeeEEECCHHHHHHHHh-cCCCEECCEEEEEEEc
Confidence            57999999999976 5669999999999999998764 5789999999999999999999995 9999999999999999


Q ss_pred             ccc
Q 007792          320 QSV  322 (589)
Q Consensus       320 ~~~  322 (589)
                      +++
T Consensus        83 ~~k   85 (86)
T d2ghpa3          83 DKK   85 (86)
T ss_dssp             CCC
T ss_pred             CCC
Confidence            864

>d1x4ha1 d.58.7.1 (A:8-105) RNA-binding protein 28 {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding protein 28
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.72  E-value=9.9e-18  Score=139.45  Aligned_cols=82  Identities=21%  Similarity=0.387  Sum_probs=77.1

Q ss_pred             CCceEEEecCCCCCCHHHHHHHhccCCCeEEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHhcC------CceeCCeEE
Q 007792          241 PENVLFVCKLNPVTEDEDLHTIFSRFGTVVSAEIIRDFKTGDSLNYAFIEFENRQACERAYSKMD------NALIDDRRI  314 (589)
Q Consensus       241 ~~~~i~V~nL~~~~te~~L~~~F~~~G~v~~~~i~~d~~tg~~~g~aFV~f~~~~~a~~A~~~l~------g~~i~gr~i  314 (589)
                      ..++|||+|||+++|+++|+++|++||+|..+.++.+..++.++|||||+|.+.++|..||+.||      |..|.|+.|
T Consensus         7 ~~~tlfV~nLp~~~te~~l~~~f~~~G~v~~~~~~~~~~~~~~~g~afV~F~~~~~a~~ai~~l~~~~~~~g~~~~gr~l   86 (98)
T d1x4ha1           7 EGKTVFIRNLSFDSEEEALGEVLQQFGDLKYVRVVLHPDTEHSKGCAFAQFMTQEAAQKCLAAASLEAEGGGLKLDGRQL   86 (98)
T ss_dssp             CCCCEEEESCCTTCCHHHHHHHHHTTSCEEEEECCBCSSSCCBCSEEEEEESSHHHHHHHHHHHCTTTTTCCEESSSCEE
T ss_pred             CCCEEEEcCCCCcCCHHHHHHHHhccccceeeeeccccccccccceEEEEEcCHHHHHHHHHHcccccccCCcEECCEEE
Confidence            46799999999999999999999999999999999999999999999999999999999999876      678999999


Q ss_pred             EEEecccc
Q 007792          315 HVDFSQSV  322 (589)
Q Consensus       315 ~V~~a~~~  322 (589)
                      .|.+|.++
T Consensus        87 ~v~~a~~k   94 (98)
T d1x4ha1          87 KVDLAVTR   94 (98)
T ss_dssp             EEECCCCC
T ss_pred             EEEECCCC
Confidence            99999874

>d2f9da1 d.58.7.1 (A:12-125) Pre-mRNA branch site protein p14 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Pre-mRNA branch site protein p14
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.71  E-value=1.3e-17  Score=142.76  Aligned_cols=78  Identities=14%  Similarity=0.301  Sum_probs=72.9

Q ss_pred             CCceEEEecCCCCCCHHHHHHHhccCCCeEEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHhcCCceeCCeEEEEEecc
Q 007792          241 PENVLFVCKLNPVTEDEDLHTIFSRFGTVVSAEIIRDFKTGDSLNYAFIEFENRQACERAYSKMDNALIDDRRIHVDFSQ  320 (589)
Q Consensus       241 ~~~~i~V~nL~~~~te~~L~~~F~~~G~v~~~~i~~d~~tg~~~g~aFV~f~~~~~a~~A~~~l~g~~i~gr~i~V~~a~  320 (589)
                      .+.+|||+|||+.+|+++|.++|++||.|..|.|+.+   +.++|||||+|.+.++|..||+.|||..|.|+.|.|.++.
T Consensus         6 ~~r~l~V~nLp~~~te~~l~~~F~~~G~v~~i~~~~~---~~~kG~afV~f~~~~~A~~Ai~~l~g~~~~gr~l~V~~a~   82 (114)
T d2f9da1           6 VNRILYIRNLPYKITAEEMYDIFGKYGPIRQIRVGNT---PETRGTAYVVYEDIFDAKNACDHLSGFNVCNRYLVVLYYN   82 (114)
T ss_dssp             CCSEEEEESCCTTCCHHHHHHHHHTTSCEEEEEEECS---TTTTTEEEEEESSHHHHHHHHHHHTTCEETTEECEEEECC
T ss_pred             CCCEEEEECCCCCCCHHHHHHHHhhcCCeEeeccccc---CCcCCeEEEEECCHHHHHHHHHHhCCCEECCEEEEEEEcC
Confidence            4679999999999999999999999999999999764   5678999999999999999999999999999999999987


Q ss_pred             c
Q 007792          321 S  321 (589)
Q Consensus       321 ~  321 (589)
                      +
T Consensus        83 ~   83 (114)
T d2f9da1          83 A   83 (114)
T ss_dssp             H
T ss_pred             C
Confidence            5

>d2msta_ d.58.7.1 (A:) Neural RNA-binding protein Musashi-1 {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Neural RNA-binding protein Musashi-1
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.71  E-value=5e-18  Score=133.93  Aligned_cols=75  Identities=24%  Similarity=0.391  Sum_probs=72.2

Q ss_pred             eEEEecCCCCCCHHHHHHHhccCCCeEEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHhcCCceeCCeEEEEEec
Q 007792          244 VLFVCKLNPVTEDEDLHTIFSRFGTVVSAEIIRDFKTGDSLNYAFIEFENRQACERAYSKMDNALIDDRRIHVDFS  319 (589)
Q Consensus       244 ~i~V~nL~~~~te~~L~~~F~~~G~v~~~~i~~d~~tg~~~g~aFV~f~~~~~a~~A~~~l~g~~i~gr~i~V~~a  319 (589)
                      .|||+|||+++|+++|.++|++||.|..+.++.++.++.++|||||+|.+.++|.+|++ |||..|+|++|.|++|
T Consensus         1 rlfV~nLp~~~te~~l~~~F~~~G~i~~~~~~~~~~~~~~~~~afV~F~~~~~a~~al~-~~~~~l~gr~i~V~~A   75 (75)
T d2msta_           1 KIFVGGLSVNTTVEDVKHYFEQFGKVDDAMLMFDKTTNRHRGFGFVTFESEDIVEKVCE-IHFHEINNKMVECKKA   75 (75)
T ss_dssp             CEEEECCCSSCCHHHHHHHHHTTSCCSEECCBCCTTCTTSCCEEEEECSCHHHHHHHHH-CSSCCBTTBCCEEEEC
T ss_pred             CEEEeCCCCCCCHHHHHHHHHHhCCcceeeeeeeccccccCceeEEEECCHHHHHHHHh-cCCCEECCeEEEEEEC
Confidence            48999999999999999999999999999999999999999999999999999999995 9999999999999876

>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=99.71  E-value=2.1e-18  Score=144.77  Aligned_cols=84  Identities=24%  Similarity=0.409  Sum_probs=79.6

Q ss_pred             CCCCceEEEecCCCCCCHHHHHHHhccCCCeEEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHhcCCceeCCeEEEEEe
Q 007792          239 KPPENVLFVCKLNPVTEDEDLHTIFSRFGTVVSAEIIRDFKTGDSLNYAFIEFENRQACERAYSKMDNALIDDRRIHVDF  318 (589)
Q Consensus       239 ~~~~~~i~V~nL~~~~te~~L~~~F~~~G~v~~~~i~~d~~tg~~~g~aFV~f~~~~~a~~A~~~l~g~~i~gr~i~V~~  318 (589)
                      ..|.++|||+|||..+++++|.++|++||.|..+.++.+..+|+++|||||+|.+.++|..||+.|||..|.|++|.|+|
T Consensus        15 ~~ps~tl~V~nLp~~~t~~~l~~~f~~~G~v~~~~~~~~~~~g~~~g~~fV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~~   94 (102)
T d2cpxa1          15 GEPNKVLYLKNLSPRVTERDLVSLFARFQEKKGPPIQFRMMTGRMRGQAFITFPNKEIAWQALHLVNGYKLYGKILVIEF   94 (102)
T ss_dssp             CSCCSEEEEECCCTTCCHHHHHHHTHHHHHSSSSCCEEEEECSSSCSEEEEECSSHHHHHHHHHHSTTCBCSSCBCEEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHhhccceeeEEeecccccccccccceEEeccHHHHHHHHHHhCCCEECCEEEEEEe
Confidence            45778999999999999999999999999999999988888999999999999999999999999999999999999999


Q ss_pred             cccc
Q 007792          319 SQSV  322 (589)
Q Consensus       319 a~~~  322 (589)
                      |+++
T Consensus        95 ak~k   98 (102)
T d2cpxa1          95 GKNK   98 (102)
T ss_dssp             CCCC
T ss_pred             CCCc
Confidence            9874

>d1x4aa1 d.58.7.1 (A:9-103) Splicing factor, arginine/serine-rich 1, SFRS1 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicing factor, arginine/serine-rich 1, SFRS1
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.71  E-value=2.9e-17  Score=135.70  Aligned_cols=80  Identities=24%  Similarity=0.450  Sum_probs=73.2

Q ss_pred             CCCCceEEEecCCCCCCHHHHHHHhccCCCeEEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHhcCCceeCCeEEEEEe
Q 007792          239 KPPENVLFVCKLNPVTEDEDLHTIFSRFGTVVSAEIIRDFKTGDSLNYAFIEFENRQACERAYSKMDNALIDDRRIHVDF  318 (589)
Q Consensus       239 ~~~~~~i~V~nL~~~~te~~L~~~F~~~G~v~~~~i~~d~~tg~~~g~aFV~f~~~~~a~~A~~~l~g~~i~gr~i~V~~  318 (589)
                      ..+.++|||+|||+.+|+++|+++|++||.|..+.+..+   +.++|||||+|.+.++|+.||+.|||..|.|++|+|+|
T Consensus        11 ~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~~~~~~~---~~~~g~afV~f~~~e~a~~Ai~~l~g~~~~g~~l~V~~   87 (95)
T d1x4aa1          11 GNNDCRIYVGNLPPDIRTKDIEDVFYKYGAIRDIDLKNR---RGGPPFAFVEFEDPRDAEDAVYGRDGYDYDGYRLRVEF   87 (95)
T ss_dssp             CCCSSEEEEESCCTTCCHHHHHHHHGGGSCEEEEEECCS---SSSSCCEEEEESCHHHHHHHHHHHTTCEETTEECEEEC
T ss_pred             CCCCCEEEEECCCCCCCHHHHHHHHhcCCceEEEEeccc---ccccceEEEEECCHHHHHHHHHHhCCCEECCEEEEEEe
Confidence            445679999999999999999999999999999887654   45789999999999999999999999999999999999


Q ss_pred             ccc
Q 007792          319 SQS  321 (589)
Q Consensus       319 a~~  321 (589)
                      |++
T Consensus        88 a~~   90 (95)
T d1x4aa1          88 PRS   90 (95)
T ss_dssp             CCC
T ss_pred             ccC
Confidence            976

>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=99.71  E-value=1.7e-17  Score=133.57  Aligned_cols=78  Identities=21%  Similarity=0.430  Sum_probs=71.8

Q ss_pred             CCCCCceEEEecCCCCCCHHHHHHHhccCCCeEEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHhcCCcee-CCeEEEE
Q 007792          238 IKPPENVLFVCKLNPVTEDEDLHTIFSRFGTVVSAEIIRDFKTGDSLNYAFIEFENRQACERAYSKMDNALI-DDRRIHV  316 (589)
Q Consensus       238 ~~~~~~~i~V~nL~~~~te~~L~~~F~~~G~v~~~~i~~d~~tg~~~g~aFV~f~~~~~a~~A~~~l~g~~i-~gr~i~V  316 (589)
                      ..||.++|||+|||+.+|+++|..+|++||.|..|.|+.+     .+|||||+|.+.++|..|+..|||..| +|+.|.|
T Consensus         4 ~~pP~~tl~V~nLp~~~t~~~l~~~f~~~G~i~~v~~~~~-----~~g~afV~f~~~~~A~~A~~~l~g~~~~~~~~i~v   78 (83)
T d2b0ga1           4 EQPPNQILFLTNLPEETNEMMLSMLFNQFPGFKEVRLVPN-----RHDIAFVEFTTELQSNAAKEALQGFKITPTHAMKI   78 (83)
T ss_dssp             CCSCCSEEEEESCCTTCCHHHHHHHHTTSTTEEEEEECTT-----TCSCEEEEESSHHHHHHHHHHHTTCBSSTTCBCEE
T ss_pred             CCCCCCEEEEECCCCCCCHHHHHhhhccCccEEEeeeecc-----cceeEEEecCCHHHHHHHHHHhCCcEeCCCcEEEE
Confidence            4678899999999999999999999999999999999764     358999999999999999999999888 5799999


Q ss_pred             Eecc
Q 007792          317 DFSQ  320 (589)
Q Consensus       317 ~~a~  320 (589)
                      .||+
T Consensus        79 ~~ak   82 (83)
T d2b0ga1          79 TFAK   82 (83)
T ss_dssp             EECC
T ss_pred             EEec
Confidence            9986

>d1x4ga1 d.58.7.1 (A:8-103) Nucleolysin TIAR {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nucleolysin TIAR
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.70  E-value=2.1e-17  Score=136.63  Aligned_cols=78  Identities=14%  Similarity=0.391  Sum_probs=72.5

Q ss_pred             CCCceEEEecCCCCCCHHHHHHHhccCCCeEEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHhcCCceeCCeEEEEEec
Q 007792          240 PPENVLFVCKLNPVTEDEDLHTIFSRFGTVVSAEIIRDFKTGDSLNYAFIEFENRQACERAYSKMDNALIDDRRIHVDFS  319 (589)
Q Consensus       240 ~~~~~i~V~nL~~~~te~~L~~~F~~~G~v~~~~i~~d~~tg~~~g~aFV~f~~~~~a~~A~~~l~g~~i~gr~i~V~~a  319 (589)
                      ++.++|||+|||..+++++|.++|++||+|..|.|+.+      +|||||+|.+.++|..||..|||..|.|+.|+|.|+
T Consensus        16 ~~~~~l~v~nL~~~~te~~L~~~F~~fG~i~~v~i~~~------kg~afV~f~~~~~A~~Ai~~l~~~~i~g~~l~v~~a   89 (96)
T d1x4ga1          16 PKNCTVYCGGIASGLTDQLMRQTFSPFGQIMEIRVFPE------KGYSFVRFSTHESAAHAIVSVNGTTIEGHVVKCYWG   89 (96)
T ss_dssp             SSCCEEEEECCSSCCCHHHHHHHHHHHSCEEEEEEETT------TTEEEEEESSHHHHHHHHHHHTTCEETTEECEEECC
T ss_pred             CCCCEEEEcCCCCCCCHHHHHHHHHHhCCceEEEEEec------ceEEEEEECCHHHHHHHHHHhCCCEECCEEEEEEEc
Confidence            34579999999999999999999999999999999875      589999999999999999999999999999999999


Q ss_pred             cccc
Q 007792          320 QSVS  323 (589)
Q Consensus       320 ~~~~  323 (589)
                      ++.+
T Consensus        90 k~~p   93 (96)
T d1x4ga1          90 KESP   93 (96)
T ss_dssp             CCCC
T ss_pred             CCCC
Confidence            8644

>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=99.69  E-value=6e-17  Score=130.75  Aligned_cols=77  Identities=9%  Similarity=0.189  Sum_probs=72.4

Q ss_pred             CceEEEecCCCCCCHHHHHHHhccCCCeEEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHhcCCceeCCeEEEEEecc
Q 007792          242 ENVLFVCKLNPVTEDEDLHTIFSRFGTVVSAEIIRDFKTGDSLNYAFIEFENRQACERAYSKMDNALIDDRRIHVDFSQ  320 (589)
Q Consensus       242 ~~~i~V~nL~~~~te~~L~~~F~~~G~v~~~~i~~d~~tg~~~g~aFV~f~~~~~a~~A~~~l~g~~i~gr~i~V~~a~  320 (589)
                      ..+|||+|||+++|+++|.++|+.||+|..|.|+.+ .+|.++|||||+|.+.++|.+||+ ++|..|.|+.|.|.++.
T Consensus         6 ~rtvfV~nlp~~~te~~l~~~F~~~G~v~~v~l~~~-~~~~~kG~afV~f~~~e~a~~al~-~~~~~~~g~~l~v~~~~   82 (85)
T d1zh5a2           6 NRSVYIKGFPTDATLDDIKEWLEDKGQVLNIQMRRT-LHKAFKGSIFVVFDSIESAKKFVE-TPGQKYKETDLLILFKD   82 (85)
T ss_dssp             TTEEEEECCCTTCCHHHHHHHHTTSCCEEEEEEEEC-TTCCEEEEEEEEESCHHHHHHHHT-CCCCEETTEECEEEEGG
T ss_pred             cCEEEEECCCCCCCHHHHHHHHHHhcccccceeeee-ccCCcceEEEEEEcCHHHHHHHHH-HCCCEECCEEEEEEEcC
Confidence            479999999999999999999999999999999887 478999999999999999999994 79999999999999864

>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=99.69  E-value=4.4e-18  Score=139.38  Aligned_cols=80  Identities=18%  Similarity=0.329  Sum_probs=73.8

Q ss_pred             CCCceEEEecCCCCCCHHHHHHHhccCCCeEEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHhcCCceeCCeEEEEEec
Q 007792          240 PPENVLFVCKLNPVTEDEDLHTIFSRFGTVVSAEIIRDFKTGDSLNYAFIEFENRQACERAYSKMDNALIDDRRIHVDFS  319 (589)
Q Consensus       240 ~~~~~i~V~nL~~~~te~~L~~~F~~~G~v~~~~i~~d~~tg~~~g~aFV~f~~~~~a~~A~~~l~g~~i~gr~i~V~~a  319 (589)
                      ....+|||+|||+.+|+++|+.+|++||.|..+.|+.+ .+|+++|||||+|.+.++|+.||+ |||..|+|+.|.|.+|
T Consensus        11 ~~~~~ifV~nL~~~~te~~l~~~F~~~G~i~~~~v~~~-~~g~~kg~afv~F~~~e~a~~Al~-~~g~~~~g~~i~V~~a   88 (91)
T d1fjeb1          11 TTPFNLFIGNLNPNKSVAELKVAISELFAKNDLAVVDV-RTGTNRKFGYVDFESAEDLEKALE-LTGLKVFGNEIKLEKP   88 (91)
T ss_dssp             SSSEEEEEECCCTTSCHHHHHHHHHHHHHHHTCCCCEE-EEETTTTEEEEEESSHHHHHHHHH-GGGEEETTEEEEEECC
T ss_pred             CCCcEEEEeCccCcchHHHHHHHHhcCCcEEEeeeeec-CCCCccEEeEEeeCCHHHHHHHHh-cCCcEECCEEEEEEec
Confidence            34579999999999999999999999999998888654 689999999999999999999995 9999999999999999


Q ss_pred             cc
Q 007792          320 QS  321 (589)
Q Consensus       320 ~~  321 (589)
                      ++
T Consensus        89 k~   90 (91)
T d1fjeb1          89 KG   90 (91)
T ss_dssp             CC
T ss_pred             CC
Confidence            75

>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=99.69  E-value=6.3e-17  Score=131.07  Aligned_cols=77  Identities=22%  Similarity=0.406  Sum_probs=70.6

Q ss_pred             CCceEEEecCCCCCCHHHHHHHhccCCCeEEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHhcCCceeCCeEEEEEecc
Q 007792          241 PENVLFVCKLNPVTEDEDLHTIFSRFGTVVSAEIIRDFKTGDSLNYAFIEFENRQACERAYSKMDNALIDDRRIHVDFSQ  320 (589)
Q Consensus       241 ~~~~i~V~nL~~~~te~~L~~~F~~~G~v~~~~i~~d~~tg~~~g~aFV~f~~~~~a~~A~~~l~g~~i~gr~i~V~~a~  320 (589)
                      ..++|||+|||+++|+++|.++|++||.|..+.+..      ++|||||+|.+.++|..||..|||..|.|+.|.|.||+
T Consensus         7 ~~k~l~V~nLp~~~te~~l~~~F~~~g~i~~~~~~~------~rg~afV~f~~~~~A~~Ai~~l~~~~i~g~~i~V~~ak   80 (86)
T d2cpda1           7 SVKILYVRNLMLSTSEEMIEKEFNNIKPGAVERVKK------IRDYAFVHFSNREDAVEAMKALNGKVLDGSPIEVTLAK   80 (86)
T ss_dssp             CCCEEEEESCCTTCCHHHHHHHHHTTSTTCEEEEEE------CSSEEEEEESSHHHHHHHHHHHSSEEETTEEEEEECCC
T ss_pred             CCCEEEEcCCCCCCCHHHHHHhhcccceeeeEEEcc------ccEEEEEEeCCHHHHHHHHHHcCCCEECCEEEEEEecc
Confidence            457999999999999999999999999988777744      56899999999999999999999999999999999998


Q ss_pred             ccc
Q 007792          321 SVS  323 (589)
Q Consensus       321 ~~~  323 (589)
                      |..
T Consensus        81 P~~   83 (86)
T d2cpda1          81 PVD   83 (86)
T ss_dssp             CCC
T ss_pred             CCC
Confidence            754

>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=99.68  E-value=8.3e-17  Score=135.30  Aligned_cols=81  Identities=17%  Similarity=0.362  Sum_probs=72.6

Q ss_pred             CCceEEEecCCCCCCHHHHHHHhccCCCeEEEEEeecC-CCCCcccEEEEEEcCHHHHHHHHHhcCCceeCCeEEEEEec
Q 007792          241 PENVLFVCKLNPVTEDEDLHTIFSRFGTVVSAEIIRDF-KTGDSLNYAFIEFENRQACERAYSKMDNALIDDRRIHVDFS  319 (589)
Q Consensus       241 ~~~~i~V~nL~~~~te~~L~~~F~~~G~v~~~~i~~d~-~tg~~~g~aFV~f~~~~~a~~A~~~l~g~~i~gr~i~V~~a  319 (589)
                      |.++|||+|||+.+|+++|+++|++|| |+.+.++.+. .++.++|||||+|.+.++|++|+ .||+..|.|+.|.|.+|
T Consensus        14 p~~~v~V~nLp~~~te~~l~~~f~~~g-~~~~~~~~~~~~~g~~~g~afV~f~~~e~a~~~~-~~~~~~~~gr~l~V~~a   91 (104)
T d1wi8a_          14 PPYTAFLGNLPYDVTEESIKEFFRGLN-ISAVRLPREPSNPERLKGFGYAEFEDLDSLLSAL-SLNEESLGNKRIRVDVA   91 (104)
T ss_dssp             SCEEEEEESCCSSCCHHHHHHHTTTSC-EEEEECCBCSSCTTSBCSCEEEEESSHHHHHHHH-GGGTCEETTEECEEEEC
T ss_pred             CCCEEEEeCCCCcCCHHHHHHHHHHhc-cccceeeeeeccCCCcceeeeEEECCHHHHHHHH-HcCCCEECCEEEEEEEC
Confidence            568999999999999999999999999 7777777655 57889999999999999998777 69999999999999999


Q ss_pred             cccc
Q 007792          320 QSVS  323 (589)
Q Consensus       320 ~~~~  323 (589)
                      .+..
T Consensus        92 ~~~~   95 (104)
T d1wi8a_          92 DQAQ   95 (104)
T ss_dssp             CCCC
T ss_pred             CCCC
Confidence            8643

>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=99.68  E-value=1.6e-17  Score=138.92  Aligned_cols=80  Identities=21%  Similarity=0.436  Sum_probs=75.1

Q ss_pred             CCceEEEecCCCCCCHHHHHHHhccCCCeEEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHhcCCceeCCeEEEEEecc
Q 007792          241 PENVLFVCKLNPVTEDEDLHTIFSRFGTVVSAEIIRDFKTGDSLNYAFIEFENRQACERAYSKMDNALIDDRRIHVDFSQ  320 (589)
Q Consensus       241 ~~~~i~V~nL~~~~te~~L~~~F~~~G~v~~~~i~~d~~tg~~~g~aFV~f~~~~~a~~A~~~l~g~~i~gr~i~V~~a~  320 (589)
                      ..++|||+|||+++|+++|.++|++||.|..+.++.+ .++.++|||||+|.+.++|.+||+.|||..|.|++|.|.++.
T Consensus        17 ~~~~lfV~nLp~~~te~~L~~~F~~~G~i~~~~~~~~-~~~~~~g~afV~f~~~~~A~~Ai~~lng~~i~gr~~~v~~~~   95 (101)
T d1x5oa1          17 DPTNLYISNLPLSMDEQELENMLKPFGQVISTRILRD-SSGTSRGVGFARMESTEKCEAVIGHFNGKFIKTPPGVSAPTE   95 (101)
T ss_dssp             CTTEEEEESCCTTCCHHHHHHTTTTTSCEEEEEEEEC-SSSCEEEEEEEEESCHHHHHHHHHHHBTCCCCCCTTSCCCSS
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHhhcccccceeeecc-cccccccceeEEeCCHHHHHHHHHHhCCCEECCcCCccCCCC
Confidence            4579999999999999999999999999999999887 578999999999999999999999999999999999998877


Q ss_pred             c
Q 007792          321 S  321 (589)
Q Consensus       321 ~  321 (589)
                      |
T Consensus        96 P   96 (101)
T d1x5oa1          96 P   96 (101)
T ss_dssp             C
T ss_pred             C
Confidence            6

>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=99.68  E-value=3e-17  Score=133.76  Aligned_cols=76  Identities=21%  Similarity=0.385  Sum_probs=69.9

Q ss_pred             CceEEEecCCCCCCHHHH---HHHhccCCCeEEEEEeecCCCCCc---ccEEEEEEcCHHHHHHHHHhcCCceeCCeEEE
Q 007792          242 ENVLFVCKLNPVTEDEDL---HTIFSRFGTVVSAEIIRDFKTGDS---LNYAFIEFENRQACERAYSKMDNALIDDRRIH  315 (589)
Q Consensus       242 ~~~i~V~nL~~~~te~~L---~~~F~~~G~v~~~~i~~d~~tg~~---~g~aFV~f~~~~~a~~A~~~l~g~~i~gr~i~  315 (589)
                      .++|||+|||+.+++++|   .++|++||+|..|.|+.++.++.+   .|||||+|.+.++|..||+.|||..|+|+.|+
T Consensus         8 ~n~vyV~nLp~~~t~~~l~~~~e~F~~~G~I~~v~i~~~~~~~~~~~~~g~aFV~f~~~~~A~~Ai~~lng~~~~gr~lk   87 (89)
T d2cpia1           8 KNLVFVVGLSQRLADPEVLKRPEYFGKFGKIHKVVINNSTSYAGSQGPSASAYVTYIRSEDALRAIQCVNNVVVDGRTLK   87 (89)
T ss_dssp             SSCEEEEEECTTTCCHHHHHSTTTTTTTSCEEEEEEECCSSCCSSSCCCEEEEEEESSHHHHHHHHHHHTTEEETTEEEE
T ss_pred             cCEEEEECCCCccCHHHHHHHHHHhcccCCceEEEEeeccCcCCCCCcceEEEEecccchhHHHHHHHhCCCEECCEEEE
Confidence            468999999999999999   678999999999999998876654   48999999999999999999999999999999


Q ss_pred             EE
Q 007792          316 VD  317 (589)
Q Consensus       316 V~  317 (589)
                      |.
T Consensus        88 vS   89 (89)
T d2cpia1          88 AS   89 (89)
T ss_dssp             EE
T ss_pred             EC
Confidence            84

>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=99.68  E-value=5.9e-17  Score=131.85  Aligned_cols=79  Identities=25%  Similarity=0.425  Sum_probs=71.7

Q ss_pred             CCCCceEEEecCCCCCCHHHHHHHhccCCCeEEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHhcCCcee-CCeEEEEE
Q 007792          239 KPPENVLFVCKLNPVTEDEDLHTIFSRFGTVVSAEIIRDFKTGDSLNYAFIEFENRQACERAYSKMDNALI-DDRRIHVD  317 (589)
Q Consensus       239 ~~~~~~i~V~nL~~~~te~~L~~~F~~~G~v~~~~i~~d~~tg~~~g~aFV~f~~~~~a~~A~~~l~g~~i-~gr~i~V~  317 (589)
                      .||.++|||+|||+.+|+++|.++|++||.|..+.+...    +.+|||||+|.+.++|..|+..|||..| +|+.|+|.
T Consensus         7 ~pPs~tL~V~NLp~~~te~~l~~~F~~~G~v~~~~~~~~----~~~~~afV~f~~~~~A~~A~~~l~~~~i~~g~~l~v~   82 (88)
T d2adca2           7 FPPSATLHLSNIPPSVSEEDLKVLFSSNGGVVKGFKFFQ----KDRKMALIQMGSVEEAVQALIDLHNHDLGENHHLRVS   82 (88)
T ss_dssp             CCSCSEEEEECCCTTCCHHHHHHHHHTTSCCEEEEEECS----SSTTCEEEEESSHHHHHHHHHHHTTCBSSSSCBCEEE
T ss_pred             CCCCCEEEEECCCCCCCHHHHHHHhhccCCEEEEEEeee----cccceeEEEECCHHHHHHHHHhccCCEecCCCEEEEE
Confidence            467899999999999999999999999999988877553    4578999999999999999999999988 58999999


Q ss_pred             eccc
Q 007792          318 FSQS  321 (589)
Q Consensus       318 ~a~~  321 (589)
                      ||++
T Consensus        83 ~sk~   86 (88)
T d2adca2          83 FSKS   86 (88)
T ss_dssp             ECSS
T ss_pred             eCCC
Confidence            9976

>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=99.68  E-value=5.2e-17  Score=134.41  Aligned_cols=80  Identities=19%  Similarity=0.314  Sum_probs=72.2

Q ss_pred             CCCCceEEEecCCCCCCHHHHHHHhccCCCeEEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHhcCCceeCCeEEEEEe
Q 007792          239 KPPENVLFVCKLNPVTEDEDLHTIFSRFGTVVSAEIIRDFKTGDSLNYAFIEFENRQACERAYSKMDNALIDDRRIHVDF  318 (589)
Q Consensus       239 ~~~~~~i~V~nL~~~~te~~L~~~F~~~G~v~~~~i~~d~~tg~~~g~aFV~f~~~~~a~~A~~~l~g~~i~gr~i~V~~  318 (589)
                      ..+.++|||+|||+++|+++|.++|++||.|..+.     .++.++|||||+|.+.++|..|+..|||..|+|++|.|.|
T Consensus        13 ~~~~~~l~V~nL~~~~te~~l~~~F~~~g~v~~~~-----~~~~~~~~afV~f~~~~~A~~A~~~l~~~~~~gr~i~V~~   87 (96)
T d1fjca_          13 VRAARTLLAKNLSFNITEDELKEVFEDALEIRLVS-----QDGKSKGIAYIEFKSEADAEKNLEEKQGAEIDGRSVSLYY   87 (96)
T ss_dssp             TTGGGEEEEESCCSSCCHHHHHHHHCSEEEECCEE-----ETTEEEEEEEEEESSHHHHHHHHHHTTEEEETTEEEEEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcccceeee-----ecCccccEEEEEeCCHHHHHHHHHHcCCCEECCEEEEEEE
Confidence            44568999999999999999999999999886554     3577899999999999999999999999999999999999


Q ss_pred             ccccc
Q 007792          319 SQSVS  323 (589)
Q Consensus       319 a~~~~  323 (589)
                      +.++.
T Consensus        88 a~~k~   92 (96)
T d1fjca_          88 TGEKG   92 (96)
T ss_dssp             CSSSC
T ss_pred             eCCCC
Confidence            98743

>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=99.68  E-value=3.8e-17  Score=132.38  Aligned_cols=81  Identities=15%  Similarity=0.290  Sum_probs=72.6

Q ss_pred             CCCCceEEEecCCCCCCHHHHHHHhccCCCeEEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHhcCCceeCCeEEEEEe
Q 007792          239 KPPENVLFVCKLNPVTEDEDLHTIFSRFGTVVSAEIIRDFKTGDSLNYAFIEFENRQACERAYSKMDNALIDDRRIHVDF  318 (589)
Q Consensus       239 ~~~~~~i~V~nL~~~~te~~L~~~F~~~G~v~~~~i~~d~~tg~~~g~aFV~f~~~~~a~~A~~~l~g~~i~gr~i~V~~  318 (589)
                      +|..++|||+|||+.+++++|.++|..||.|....++....+|.++|||||+|.+.++|..||..|||..|.|++|.|.+
T Consensus         6 ~p~~~~l~v~nLp~~~~~~di~~~F~~~~~~~~~~~~~~~~~g~~~G~afV~f~~~e~a~~Ai~~l~~~~l~gr~i~v~l   85 (86)
T d2cqpa1           6 KPGPTIIKVQNMPFTVSIDEILDFFYGYQVIPGSVCLKYNEKGMPTGEAMVAFESRDEATAAVIDLNDRPIGSRKVKLVL   85 (86)
T ss_dssp             CCSSEEEEEESCCTTCCHHHHHHHTTTSCCCTTTCEEEECSSSCEEEEEEEEESCHHHHHHHHHHTTTCEETTEECEEEE
T ss_pred             CCCCCEEEEECCCCCCCHHHHHHHHhhcccceeEEEEEeCCCCCcceEEEEEEcCcHHHHHHHHHcCCCEECCEEEEEEE
Confidence            45667899999999999999999999999987643444447899999999999999999999999999999999999987


Q ss_pred             c
Q 007792          319 S  319 (589)
Q Consensus       319 a  319 (589)
                      +
T Consensus        86 ~   86 (86)
T d2cqpa1          86 G   86 (86)
T ss_dssp             S
T ss_pred             C
Confidence            5

>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=99.67  E-value=1.2e-16  Score=132.58  Aligned_cols=75  Identities=21%  Similarity=0.515  Sum_probs=68.4

Q ss_pred             CCCCceEEEecCC-CCCCHHHHHHHhccCCCeEEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHhcCCceeCCeEEEEE
Q 007792          239 KPPENVLFVCKLN-PVTEDEDLHTIFSRFGTVVSAEIIRDFKTGDSLNYAFIEFENRQACERAYSKMDNALIDDRRIHVD  317 (589)
Q Consensus       239 ~~~~~~i~V~nL~-~~~te~~L~~~F~~~G~v~~~~i~~d~~tg~~~g~aFV~f~~~~~a~~A~~~l~g~~i~gr~i~V~  317 (589)
                      ....++|||+||| ..+++++|+.+|++||+|..|.|        ++|||||+|.+.++|..||+.|||..|.|++|.|+
T Consensus        12 ~~~~~~lfV~nL~~~~~~~~~L~~~F~~~G~i~~~~i--------~rg~aFV~f~~~~~A~~Ai~~lng~~~~g~~l~V~   83 (98)
T d1wf2a_          12 RSMNSRVFIGNLNTLVVKKSDVEAIFSKYGKIVGCSV--------HKGFAFVQYVNERNARAAVAGEDGRMIAGQVLDIN   83 (98)
T ss_dssp             SSCCCCEEEEEECTTTCCHHHHHHSSTTSSCEEEEEE--------ETEEEEEEESSHHHHHHHHHTTTTCEETTEECEEE
T ss_pred             CCCCcEEEEeCCCcccCCHHHHHHHHhhcCCEEEEEE--------eCCeEEEEECCHHHHHHHHHHcCCCEECCEEEEEE
Confidence            3445789999997 57889999999999999999998        35899999999999999999999999999999999


Q ss_pred             eccc
Q 007792          318 FSQS  321 (589)
Q Consensus       318 ~a~~  321 (589)
                      ||.+
T Consensus        84 ~a~~   87 (98)
T d1wf2a_          84 LAAE   87 (98)
T ss_dssp             ETTS
T ss_pred             ECCC
Confidence            9975

>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=99.67  E-value=1.7e-17  Score=129.65  Aligned_cols=71  Identities=25%  Similarity=0.494  Sum_probs=68.6

Q ss_pred             EEEecCCCCCCHHHHHHHhccCCCeEEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHhcCCceeCCeEEE
Q 007792          245 LFVCKLNPVTEDEDLHTIFSRFGTVVSAEIIRDFKTGDSLNYAFIEFENRQACERAYSKMDNALIDDRRIH  315 (589)
Q Consensus       245 i~V~nL~~~~te~~L~~~F~~~G~v~~~~i~~d~~tg~~~g~aFV~f~~~~~a~~A~~~l~g~~i~gr~i~  315 (589)
                      |||+|||+.+|+++|.++|++||.|..+.++.++.++.++|||||+|.+.++|+.|++.|||..|.|+.|+
T Consensus         1 lyV~nLp~~~te~~l~~~F~~~G~v~~~~~~~~~~~~~~~g~afV~f~~~~~A~~Ai~~lng~~~~Gr~~k   71 (72)
T d1x4ea1           1 LYIRGLQPGTTDQDLVKLCQPYGKIVSTKAILDKTTNKCKGYGFVDFDSPSAAQKAVTALKASGVQAQMAK   71 (72)
T ss_dssp             EEEESCCTTCCHHHHHTTSTTTSCEEEEEEECCSSSCSCCSEEEEEESCHHHHHHHHHHHHHHTCCEESCC
T ss_pred             CEEeCCCCcCCHHHHHHHHhhhccccccccccccccccccceeEEEECCHHHHHHHHHHhCCCEECCEECc
Confidence            89999999999999999999999999999999999999999999999999999999999999999998763

>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=99.67  E-value=2.9e-17  Score=131.06  Aligned_cols=75  Identities=21%  Similarity=0.452  Sum_probs=68.3

Q ss_pred             ceEEEecCCCCCCHHHHHHHhccCCCeEEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHhcCCc-eeCCeEEEEEeccc
Q 007792          243 NVLFVCKLNPVTEDEDLHTIFSRFGTVVSAEIIRDFKTGDSLNYAFIEFENRQACERAYSKMDNA-LIDDRRIHVDFSQS  321 (589)
Q Consensus       243 ~~i~V~nL~~~~te~~L~~~F~~~G~v~~~~i~~d~~tg~~~g~aFV~f~~~~~a~~A~~~l~g~-~i~gr~i~V~~a~~  321 (589)
                      ++|||+|||+++|+++|.++|++||.|..+.++.      ++|||||+|.+.++|..|++.|||. .|+|++|.|+||.+
T Consensus         2 n~l~V~nLp~~~te~~L~~~F~~~G~i~~~~~~~------~rg~aFV~f~~~~~A~~Ai~~lng~~~~~G~~i~V~~a~~   75 (80)
T d2cqha1           2 NKLYIGNLSPAVTADDLRQLFGDRKLPLAGQVLL------KSGYAFVDYPDQNWAIRAIETLSGKVELHGKIMEVDYSVS   75 (80)
T ss_dssp             CCEEEECCCTTCCHHHHHHHHHHTTCCCSSCEEE------ETTEEEECCSCHHHHHHHHHHHTTTCEETTEECEEEECCC
T ss_pred             CEEEEECCCCCCCHHHHHHHHHHhCcEEEeEEec------ccceEEEEECCHHHHHHHHHHhCCCeEECCEEEEEEEcCC
Confidence            4799999999999999999999999998777665      4689999999999999999999995 69999999999987


Q ss_pred             cc
Q 007792          322 VS  323 (589)
Q Consensus       322 ~~  323 (589)
                      +.
T Consensus        76 k~   77 (80)
T d2cqha1          76 KK   77 (80)
T ss_dssp             CC
T ss_pred             cC
Confidence            43

>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=99.66  E-value=9.7e-17  Score=129.82  Aligned_cols=76  Identities=26%  Similarity=0.498  Sum_probs=71.1

Q ss_pred             CceEEEecCCCCCCHHHHHHHhccCCCeEEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHhcCCceeCCeEEEEEeccc
Q 007792          242 ENVLFVCKLNPVTEDEDLHTIFSRFGTVVSAEIIRDFKTGDSLNYAFIEFENRQACERAYSKMDNALIDDRRIHVDFSQS  321 (589)
Q Consensus       242 ~~~i~V~nL~~~~te~~L~~~F~~~G~v~~~~i~~d~~tg~~~g~aFV~f~~~~~a~~A~~~l~g~~i~gr~i~V~~a~~  321 (589)
                      .++|||+|||+++++++|.++|++||+|..|.++.+      +|||||+|.+.++|..|+..|||..|.|+.|.|+||.+
T Consensus         8 ~~~l~V~nLp~~~~~~~l~~~F~~~G~i~~i~~~~~------k~~afV~f~~~~~A~~A~~~l~g~~i~g~~l~V~~A~~   81 (86)
T d2cpja1           8 RSRLFVGNLPPDITEEEMRKLFEKYGKAGEVFIHKD------KGFGFIRLETRTLAEIAKVELDNMPLRGKQLRVRFACH   81 (86)
T ss_dssp             TTEEEEESCCTTCCHHHHHHHTSTTCCCSEEEEETT------TTEEEEECSSSHHHHHHHHHHTTCCBTTBCCEEEESSC
T ss_pred             CCEEEEECCCCCCCHHHHHHHHHHhCCceEeeeecc------cceEEEEECCHHHHHHHHHHhCCCEECCEEEEEEECCC
Confidence            468999999999999999999999999999999764      58999999999999999999999999999999999986


Q ss_pred             cc
Q 007792          322 VS  323 (589)
Q Consensus       322 ~~  323 (589)
                      ..
T Consensus        82 ~~   83 (86)
T d2cpja1          82 SA   83 (86)
T ss_dssp             CS
T ss_pred             cC
Confidence            43

>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=99.66  E-value=1.9e-16  Score=124.52  Aligned_cols=74  Identities=16%  Similarity=0.308  Sum_probs=68.4

Q ss_pred             ceEEEecCCCCCCHHHHHHHhccCCCeEEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHhcCCceeCCeEEEEEec
Q 007792          243 NVLFVCKLNPVTEDEDLHTIFSRFGTVVSAEIIRDFKTGDSLNYAFIEFENRQACERAYSKMDNALIDDRRIHVDFS  319 (589)
Q Consensus       243 ~~i~V~nL~~~~te~~L~~~F~~~G~v~~~~i~~d~~tg~~~g~aFV~f~~~~~a~~A~~~l~g~~i~gr~i~V~~a  319 (589)
                      ++|||+|||+.+++++|+++|+.||+|..|.|+.++.+  ..+||||+|.+.++|.+|| .||+..|+|+.|.|..+
T Consensus         1 Ttv~V~nlp~~~t~~~l~~~F~~~G~I~~v~~~~~~~~--~~~~afV~F~~~~~a~~Al-~~~~~~i~g~~i~V~~~   74 (75)
T d2ghpa2           1 TTVLVKNLPKSYNQNKVYKYFKHCGPIIHVDVADSLKK--NFRFARIEFARYDGALAAI-TKTHKVVGQNEIIVSHL   74 (75)
T ss_dssp             CEEEEEEECTTCCHHHHHHHHGGGSCEEEEEEEECTTS--SSEEEEEEESSHHHHHHHH-TTTTCEETTEECEEEEC
T ss_pred             CEEEEECCCCCCCHHHHHHHHhcCCceEEEEEEeeccc--cceEEEEEEcchHHhHHHH-HhcCcEECCEEEEEEEC
Confidence            58999999999999999999999999999999988654  4579999999999999999 58999999999999875

>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=99.66  E-value=6.4e-17  Score=132.48  Aligned_cols=80  Identities=23%  Similarity=0.463  Sum_probs=72.2

Q ss_pred             CCceEEEecCCCCCCHHHHHH----HhccCCCeEEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHhcCCceeCCeEEEE
Q 007792          241 PENVLFVCKLNPVTEDEDLHT----IFSRFGTVVSAEIIRDFKTGDSLNYAFIEFENRQACERAYSKMDNALIDDRRIHV  316 (589)
Q Consensus       241 ~~~~i~V~nL~~~~te~~L~~----~F~~~G~v~~~~i~~d~~tg~~~g~aFV~f~~~~~a~~A~~~l~g~~i~gr~i~V  316 (589)
                      |.++|||+|||+.+++++|++    +|++||+|..|.+..   +++++|||||+|.+.++|..|+..|||..|.|+.|.|
T Consensus         2 P~~tl~V~nLp~~~t~~dl~~~l~~~f~~~G~i~~i~~~~---~~~~~g~afV~F~~~~~A~~A~~~~~~~~~~g~~l~v   78 (91)
T d1nu4a_           2 PNHTIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSR---SLKMRGQAFVIFKEVSSATNALRSMQGFPFYDKPMRI   78 (91)
T ss_dssp             CCSEEEEESCCTTSCHHHHHHHHHHHHGGGSCEEEEECCH---HHHHTTCEEEEESSHHHHHHHHHHHTTCEETTEECEE
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHHHhcccccccceEEee---eccCCCceEEEECCHHHHHHHHHHhCCCEECCEEEEE
Confidence            578999999999999998864    689999999988754   4668899999999999999999999999999999999


Q ss_pred             Eeccccc
Q 007792          317 DFSQSVS  323 (589)
Q Consensus       317 ~~a~~~~  323 (589)
                      .||++..
T Consensus        79 ~~ak~~~   85 (91)
T d1nu4a_          79 QYAKTDS   85 (91)
T ss_dssp             EECSSCC
T ss_pred             EEeCCCc
Confidence            9998643

>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=99.65  E-value=9.2e-17  Score=127.82  Aligned_cols=76  Identities=18%  Similarity=0.394  Sum_probs=69.4

Q ss_pred             CCCceEEEecCCCCCCHHHHHHHhccCCCeEEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHhcCCceeCCeEEEEEec
Q 007792          240 PPENVLFVCKLNPVTEDEDLHTIFSRFGTVVSAEIIRDFKTGDSLNYAFIEFENRQACERAYSKMDNALIDDRRIHVDFS  319 (589)
Q Consensus       240 ~~~~~i~V~nL~~~~te~~L~~~F~~~G~v~~~~i~~d~~tg~~~g~aFV~f~~~~~a~~A~~~l~g~~i~gr~i~V~~a  319 (589)
                      ..+++|||+||+  +|+++|.++|++||.|..|.+..      .+|||||+|.+.++|..|+..|||..|+|++|+|.||
T Consensus         3 ~~~~ti~V~~~~--~te~~L~~~F~~~G~I~~v~~~~------~~~~afV~f~~~~~A~~Ai~~lng~~~~g~~l~V~~a   74 (79)
T d2bz2a1           3 RKGNTLYVYGED--MTPTLLRGAFSPFGNIIDLSMDP------PRNCAFVTYEKMESADQAVAELNGTQVESVQLKVNIA   74 (79)
T ss_dssp             CCCCEEEEECSS--CCHHHHHHHHSTTCCCSCEEEET------TTTEEEEECSSHHHHHHHHHHHTTCBCSSCBCEEEEC
T ss_pred             CCCCEEEEECCC--CCHHHHHHHHhccCccceeeecc------CCCEEEEEEcccHHHHHHHHHhCCCEECCEEEEEEEe
Confidence            356899999996  89999999999999999999865      4589999999999999999999999999999999999


Q ss_pred             cccc
Q 007792          320 QSVS  323 (589)
Q Consensus       320 ~~~~  323 (589)
                      ++.+
T Consensus        75 ~~~P   78 (79)
T d2bz2a1          75 RKQP   78 (79)
T ss_dssp             CSSC
T ss_pred             cCCC
Confidence            8643

>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=99.65  E-value=1.7e-16  Score=131.29  Aligned_cols=81  Identities=17%  Similarity=0.279  Sum_probs=73.1

Q ss_pred             ceEEEecCCCCCCHHHHHHHhccCCC-eEEEEEeecC-CCCCcccEEEEEEcCHHHHHHHHHhcCC--ceeCCeEEEEEe
Q 007792          243 NVLFVCKLNPVTEDEDLHTIFSRFGT-VVSAEIIRDF-KTGDSLNYAFIEFENRQACERAYSKMDN--ALIDDRRIHVDF  318 (589)
Q Consensus       243 ~~i~V~nL~~~~te~~L~~~F~~~G~-v~~~~i~~d~-~tg~~~g~aFV~f~~~~~a~~A~~~l~g--~~i~gr~i~V~~  318 (589)
                      +.|||+|||..+|+++|.++|++||+ |..+.|+.+. .+|.++|||||+|.+.++|..|++.|++  ..+.|+.|.|+|
T Consensus         2 ~rLyV~nLp~~~te~~l~~~f~~~g~~i~~v~~~~~~~~~~~~rg~aFV~F~~~~~A~~Ai~~l~~~~~~~~g~~i~V~~   81 (96)
T d2disa1           2 CRLFIGGIPKMKKREEILEEIAKVTEGVLDVIVYASAADKMKNRGFAFVEYESHRAAAMARRKLMPGRIQLWGHQIAVDW   81 (96)
T ss_dssp             EEEEEECCCTTSCHHHHHHHHHHHSTTEEEEECCSSSCTTTTTCCEEEEEESSHHHHHHHHTTTTTCCSCBTTBCCEEEE
T ss_pred             CEEEEcCCCCcCCHHHHHHHHHHhCCcceEEEEeeeccccccCCCeEEEEEcCHHHHHHHHHHHcCCCeEECCEEEEEEE
Confidence            57999999999999999999999996 8899998875 4688999999999999999999999964  566899999999


Q ss_pred             ccccc
Q 007792          319 SQSVS  323 (589)
Q Consensus       319 a~~~~  323 (589)
                      |.+..
T Consensus        82 A~p~~   86 (96)
T d2disa1          82 AEPEI   86 (96)
T ss_dssp             SCSSC
T ss_pred             cCCCC
Confidence            98744

>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=99.64  E-value=4.5e-17  Score=132.17  Aligned_cols=73  Identities=23%  Similarity=0.319  Sum_probs=68.1

Q ss_pred             ceEEEecCCCCCCHHHHHHHhccCCCeEEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHhcCCceeCCeEEEEEecccc
Q 007792          243 NVLFVCKLNPVTEDEDLHTIFSRFGTVVSAEIIRDFKTGDSLNYAFIEFENRQACERAYSKMDNALIDDRRIHVDFSQSV  322 (589)
Q Consensus       243 ~~i~V~nL~~~~te~~L~~~F~~~G~v~~~~i~~d~~tg~~~g~aFV~f~~~~~a~~A~~~l~g~~i~gr~i~V~~a~~~  322 (589)
                      ++|||+|||+.+|+++|.++|++||+|..+.|+.+       |||||+|.+.++|+.||..|||..|.|+.|.|.++++.
T Consensus         1 nrvfV~nlp~~~~~~~l~~~F~~~G~v~~~~i~~~-------g~afV~f~~~~~a~~Ai~~l~g~~~~g~~i~v~~~~~~   73 (87)
T d3begb1           1 NRVVVSGLPPSGSWQDLKDHMREAGDVCYADVYRD-------GTGVVEFVRKEDMTYAVRKLDNTKFRSHEGETAYIRVK   73 (87)
T ss_dssp             CCEEEEECCSSCCTTHHHHHHGGGSCEEEEEECTT-------SEEEEEESSHHHHHHHHHHHTTCBCCCTTSCCCBCEEE
T ss_pred             CeEEEECCCCcCCHHHHHHHHhhhccccccccccc-------ceeeEEeCCHHHHHHHHHHhCCCEECCcEeEEeEEecC
Confidence            46999999999999999999999999999998654       89999999999999999999999999999999987653

>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=99.64  E-value=1.1e-16  Score=134.25  Aligned_cols=82  Identities=11%  Similarity=0.159  Sum_probs=73.1

Q ss_pred             CCCCceEEEecCCCCCCHHHHHHHhccCCCeEEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHhcCCceeCCeEEEEEe
Q 007792          239 KPPENVLFVCKLNPVTEDEDLHTIFSRFGTVVSAEIIRDFKTGDSLNYAFIEFENRQACERAYSKMDNALIDDRRIHVDF  318 (589)
Q Consensus       239 ~~~~~~i~V~nL~~~~te~~L~~~F~~~G~v~~~~i~~d~~tg~~~g~aFV~f~~~~~a~~A~~~l~g~~i~gr~i~V~~  318 (589)
                      .....+|||+|||+++|+++|.++|..||.|..+.++....+|+++|||||+|.+.++|+.||. |||..|+|+.|.|.+
T Consensus         5 ~~~~~~v~v~nLp~~~t~~~l~~~F~~~g~i~~~~~~~~~~~g~~~G~afV~F~s~~~a~~Al~-~n~~~i~gr~i~V~~   83 (103)
T d2cpya1           5 NSAKVCAHITNIPFSITKMDVLQFLEGIPVDENAVHVLVDNNGQGLGQALVQFKNEDDARKSER-LHRKKLNGREAFVHV   83 (103)
T ss_dssp             CSCCCEEEEESCCTTSCHHHHHHHTTTSCCCSTTEEECCCTTSSCSSCEEEECSSHHHHHHHGG-GCSEEETTEEEEEEE
T ss_pred             CCCceEEEEeCCCCCCCHHHHhhhhcccceEEEEEEEEeCCCCCcCccEEEEECCHHHHHHHHh-cCCCeECCcEEEEEE
Confidence            3345789999999999999999999999998875555555789999999999999999999995 899999999999999


Q ss_pred             ccc
Q 007792          319 SQS  321 (589)
Q Consensus       319 a~~  321 (589)
                      +..
T Consensus        84 ~~~   86 (103)
T d2cpya1          84 VTL   86 (103)
T ss_dssp             ECH
T ss_pred             CCH
Confidence            865

>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=99.64  E-value=1.1e-16  Score=136.21  Aligned_cols=75  Identities=16%  Similarity=0.275  Sum_probs=69.7

Q ss_pred             CCceEEEecCCCCCCHHHHHHHhccCCCeEEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHhcCCceeCCeEEEEEecc
Q 007792          241 PENVLFVCKLNPVTEDEDLHTIFSRFGTVVSAEIIRDFKTGDSLNYAFIEFENRQACERAYSKMDNALIDDRRIHVDFSQ  320 (589)
Q Consensus       241 ~~~~i~V~nL~~~~te~~L~~~F~~~G~v~~~~i~~d~~tg~~~g~aFV~f~~~~~a~~A~~~l~g~~i~gr~i~V~~a~  320 (589)
                      ..++|||+|||+.+++++|.++|++||+|..|.|..      .+|||||+|.+.++|..||+.|||..|.|++|.|+|+.
T Consensus         9 ~~~~l~V~nLp~~~t~~~L~~~F~~fG~I~~v~l~~------~kg~afV~f~~~~~A~~A~~~lng~~~~gr~l~v~~a~   82 (111)
T d1whxa_           9 SKTVILAKNLPAGTLAAEIQETFSRFGSLGRVLLPE------GGITAIVEFLEPLEARKAFRHLAYSKFHHVPLYLEWAP   82 (111)
T ss_dssp             EEEEEEEESCCTTCCHHHHHHHHHTTSCEEEEECCS------SSSCEEEEESCHHHHHHHHHHHTTCBSSSSBCEEEEEE
T ss_pred             CCCEEEEECCCCCCCHHHHHhhhhccCCccEEEeec------cCceEEEEEcCHHHHHHHHHHHcCCccCCCeEEEEECC
Confidence            457999999999999999999999999999998843      56999999999999999999999999999999999986


Q ss_pred             c
Q 007792          321 S  321 (589)
Q Consensus       321 ~  321 (589)
                      .
T Consensus        83 ~   83 (111)
T d1whxa_          83 I   83 (111)
T ss_dssp             T
T ss_pred             C
Confidence            5

>d1wf0a_ d.58.7.1 (A:) TAR DNA-binding protein 43, TDP-43 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: TAR DNA-binding protein 43, TDP-43
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.64  E-value=1.1e-16  Score=130.04  Aligned_cols=76  Identities=18%  Similarity=0.383  Sum_probs=68.6

Q ss_pred             CCceEEEecCCCCCCHHHHHHHhccCCCeEEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHhcCCceeCCeEEEEEecc
Q 007792          241 PENVLFVCKLNPVTEDEDLHTIFSRFGTVVSAEIIRDFKTGDSLNYAFIEFENRQACERAYSKMDNALIDDRRIHVDFSQ  320 (589)
Q Consensus       241 ~~~~i~V~nL~~~~te~~L~~~F~~~G~v~~~~i~~d~~tg~~~g~aFV~f~~~~~a~~A~~~l~g~~i~gr~i~V~~a~  320 (589)
                      +.++|||+|||+.+|+++|+++|++||.|..|.++.     .++|||||+|.+.++|+.||.  ++..|+|++|.|.+|.
T Consensus         4 ~s~~lfV~nLp~~~te~~L~~~F~~~G~v~~v~~~~-----~~~gfafV~f~~~~~a~~a~~--~~~~i~g~~l~v~~a~   76 (88)
T d1wf0a_           4 GSSGVFVGRCTGDMTEDELREFFSQYGDVMDVFIPK-----PFRAFAFVTFADDQIAQSLCG--EDLIIKGISVHISNAE   76 (88)
T ss_dssp             CCCEEEEESCCSSSCHHHHHHHSTTTSCCCEEECCS-----SCCSCCEEECSCHHHHHHTTT--CEEEETTEEEEEECCC
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHHcCCceEEEEee-----ccCceEEEEECCHHHHHHHHh--CCCEECCEEeEEEeCC
Confidence            568999999999999999999999999999987754     367999999999999999984  8889999999999997


Q ss_pred             ccc
Q 007792          321 SVS  323 (589)
Q Consensus       321 ~~~  323 (589)
                      ++.
T Consensus        77 ~k~   79 (88)
T d1wf0a_          77 PKH   79 (88)
T ss_dssp             CCC
T ss_pred             CCC
Confidence            643

>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=99.64  E-value=1.6e-16  Score=134.74  Aligned_cols=75  Identities=21%  Similarity=0.422  Sum_probs=69.8

Q ss_pred             CceEEEecCCC-CCCHHHHHHHhccCCCeEEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHhcCCceeCCeEEEEEecc
Q 007792          242 ENVLFVCKLNP-VTEDEDLHTIFSRFGTVVSAEIIRDFKTGDSLNYAFIEFENRQACERAYSKMDNALIDDRRIHVDFSQ  320 (589)
Q Consensus       242 ~~~i~V~nL~~-~~te~~L~~~F~~~G~v~~~~i~~d~~tg~~~g~aFV~f~~~~~a~~A~~~l~g~~i~gr~i~V~~a~  320 (589)
                      .++|||+|||+ .+|+++|.++|++||+|..|.|+.++     +|||||+|.+.++|.+||+.|||..|.|+.|.|.|++
T Consensus         2 ~~~l~V~nL~p~~~te~~L~~~F~~fG~I~~v~i~~~~-----kg~afV~f~~~~~A~~ai~~lng~~l~g~~l~v~~s~   76 (109)
T d2adca1           2 NSVLLVSNLNPERVTPQSLFILFGVYGDVQRVKILFNK-----KENALVQMADGNQAQLAMSHLNGHKLHGKPIRITLSK   76 (109)
T ss_dssp             CSEEEEESCCTTTCCHHHHHHHHHHHTCEEEEEECCTT-----SCCEEEEESCHHHHHHHHHHHTTCBCSSSBCEEECCS
T ss_pred             CCEEEEeCCCcccCCHHHHHHHHhhccccceEEEEecc-----cceEEEEECCHHHHHHHHHHhCCCEECCEEEEEEECC
Confidence            47999999965 59999999999999999999998863     6899999999999999999999999999999999987


Q ss_pred             c
Q 007792          321 S  321 (589)
Q Consensus       321 ~  321 (589)
                      .
T Consensus        77 ~   77 (109)
T d2adca1          77 H   77 (109)
T ss_dssp             C
T ss_pred             C
Confidence            5

>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=99.64  E-value=2.9e-16  Score=127.57  Aligned_cols=76  Identities=11%  Similarity=0.207  Sum_probs=66.6

Q ss_pred             CCceEEEecCCCCCCHHHHHHHhccCCCeEEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHhcCCceeCCeEEEEEecc
Q 007792          241 PENVLFVCKLNPVTEDEDLHTIFSRFGTVVSAEIIRDFKTGDSLNYAFIEFENRQACERAYSKMDNALIDDRRIHVDFSQ  320 (589)
Q Consensus       241 ~~~~i~V~nL~~~~te~~L~~~F~~~G~v~~~~i~~d~~tg~~~g~aFV~f~~~~~a~~A~~~l~g~~i~gr~i~V~~a~  320 (589)
                      ..++|||+|||+.+++++|+++|.+|| +..+.+      +..+|||||+|.+.++|++||..|||..|.|++|.|++++
T Consensus         4 ~s~~i~V~nLp~~~t~~~l~~lF~~~G-~~~~~~------~~~kg~afV~f~~~~~A~~Ai~~ln~~~~~G~~l~V~~a~   76 (88)
T d1wg1a_           4 GSSGILVKNLPQDSNCQEVHDLLKDYD-LKYCYV------DRNKRTAFVTLLNGEQAQNAIQMFHQYSFRGKDLIVQLQP   76 (88)
T ss_dssp             CCCCEEEESCCSSCCHHHHHHHTCSSC-CCCEEE------EGGGTEEEECCSCHHHHHHHHHHHTTEEETTEEEEEEECC
T ss_pred             CCCEEEEeCCCCccChHHHHHHHHhcC-ceeeee------eccCCceEEEECCHHHHHHHHHHhCCCEECCEEEEEEEcC
Confidence            357899999999999999999999999 333333      3367999999999999999999999999999999999997


Q ss_pred             ccc
Q 007792          321 SVS  323 (589)
Q Consensus       321 ~~~  323 (589)
                      +..
T Consensus        77 ~~~   79 (88)
T d1wg1a_          77 TDA   79 (88)
T ss_dssp             CCC
T ss_pred             CCC
Confidence            643

>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=99.64  E-value=2.7e-16  Score=131.49  Aligned_cols=82  Identities=16%  Similarity=0.212  Sum_probs=73.1

Q ss_pred             CCCCCceEEEecCCCCCCHHHHHHHhccCCCeEEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHhcCCceeCCeEEEEE
Q 007792          238 IKPPENVLFVCKLNPVTEDEDLHTIFSRFGTVVSAEIIRDFKTGDSLNYAFIEFENRQACERAYSKMDNALIDDRRIHVD  317 (589)
Q Consensus       238 ~~~~~~~i~V~nL~~~~te~~L~~~F~~~G~v~~~~i~~d~~tg~~~g~aFV~f~~~~~a~~A~~~l~g~~i~gr~i~V~  317 (589)
                      ..+...+|||+|||+++|+++|+++|..||. ..|.++.+ .++.++|||||+|.+.++|++||+ ||+..|+|+.|.|.
T Consensus        11 ~~~~~~~v~v~nLp~~~te~dl~~~F~~~~~-~~v~~~~~-~~g~~~G~afVeF~~~~~a~~Al~-~~~~~i~gR~I~V~   87 (102)
T d1weza_          11 QSTTGHCVHMRGLPYRATENDIYNFFSPLNP-MRVHIEIG-PDGRVTGEADVEFATHEDAVAAMA-KDKANMQHRYVELF   87 (102)
T ss_dssp             CCSSSCEEEEESCCTTCCHHHHHHSSCSCCC-SEEEEEES-SSSCEEEEEEEECSSSHHHHHHHT-TSSCCSSSSCCEEE
T ss_pred             cCCCCCEEEEeCCCCcCCHHHHHHHHhccCc-ceeeeEEe-cCCcceEEEEEEECCHHHHHHHHH-cCCCEECCEEEEEE
Confidence            3456689999999999999999999999984 57778777 458899999999999999999995 89999999999999


Q ss_pred             ecccc
Q 007792          318 FSQSV  322 (589)
Q Consensus       318 ~a~~~  322 (589)
                      ++.+.
T Consensus        88 ~s~~~   92 (102)
T d1weza_          88 LNSTA   92 (102)
T ss_dssp             EECCC
T ss_pred             EcCCC
Confidence            98764

>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=99.63  E-value=6.7e-16  Score=129.59  Aligned_cols=82  Identities=20%  Similarity=0.205  Sum_probs=74.9

Q ss_pred             CCCceEEEecCCCCCCHHHHHHHhccCCCeEEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHhcCCceeCCeEEEEEec
Q 007792          240 PPENVLFVCKLNPVTEDEDLHTIFSRFGTVVSAEIIRDFKTGDSLNYAFIEFENRQACERAYSKMDNALIDDRRIHVDFS  319 (589)
Q Consensus       240 ~~~~~i~V~nL~~~~te~~L~~~F~~~G~v~~~~i~~d~~tg~~~g~aFV~f~~~~~a~~A~~~l~g~~i~gr~i~V~~a  319 (589)
                      ....+|||+|||+++|+++|+++|..||.|..+.++.+..+++++|||||+|.+.++|++|++ ||+..|+|+.|.|.++
T Consensus        13 ~~~~~v~v~nLP~~~te~dI~~~F~~~g~v~~~v~~~~~~~~~~kG~afV~F~~~e~a~~a~~-~~~~~i~gR~i~V~~~   91 (104)
T d1wg5a_          13 ANDGFVRLRGLPFGCSKEEIVQFFSGLEIVPNGMTLPVDFQGRSTGEAFVQFASQEIAEKALK-KHKERIGHRYIEIFKS   91 (104)
T ss_dssp             SCCCEEEEESCCTTCCHHHHHHHTTTCCEEEEEEECCBCSSSCBCSEEEEEESSHHHHHHHHT-TTTCCSSSSCCEEEEE
T ss_pred             CCCcEEEEeCCCCCCCHHHHHHHHHhcCCceEEEEEEeCCCCCcceEEEEEeCCHHHHHHHHh-hCCCEEcceEEEEEEC
Confidence            345689999999999999999999999999887777777889999999999999999999995 8999999999999999


Q ss_pred             ccc
Q 007792          320 QSV  322 (589)
Q Consensus       320 ~~~  322 (589)
                      ++.
T Consensus        92 ~~~   94 (104)
T d1wg5a_          92 SRA   94 (104)
T ss_dssp             CTT
T ss_pred             CHH
Confidence            764

>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=99.62  E-value=4.2e-16  Score=129.07  Aligned_cols=78  Identities=31%  Similarity=0.524  Sum_probs=71.4

Q ss_pred             CCCCceEEEecCCCCCCHHHHHHHhccCCCeEEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHhcCCceeCC--eEEEE
Q 007792          239 KPPENVLFVCKLNPVTEDEDLHTIFSRFGTVVSAEIIRDFKTGDSLNYAFIEFENRQACERAYSKMDNALIDD--RRIHV  316 (589)
Q Consensus       239 ~~~~~~i~V~nL~~~~te~~L~~~F~~~G~v~~~~i~~d~~tg~~~g~aFV~f~~~~~a~~A~~~l~g~~i~g--r~i~V  316 (589)
                      .+|.++|||+|||+++++++|+++|++||+|..|.++.+      ++||||+|.+.++|..|++.|||..|.|  ++|.|
T Consensus        14 ~~Ps~tl~V~nLp~~~t~~~l~~~f~~~G~i~~~~~~~~------~~~afV~f~~~~~A~~A~~~l~~~~i~g~~~~l~v   87 (97)
T d1whya_          14 ANPTTRLWVGGLGPNTSLAALAREFDRFGSIRTIDHVKG------DSFAYIQYESLDAAQAACAKMRGFPLGGPDRRLRV   87 (97)
T ss_dssp             CCCCSCEEEECCCSSCCHHHHHHHHHTTSCEEEEEECSS------SCCEEEEESSHHHHHHHHHHHTTCBCSSSSCBCEE
T ss_pred             CCCCCEEEEcCCCCCCCHHHHHHHHHhhcccceEeeecc------ccEEEeccCCHHHHHHHHHHhCCCEeCCCceEEEE
Confidence            457799999999999999999999999999999999764      5799999999999999999999999986  58999


Q ss_pred             Eecccc
Q 007792          317 DFSQSV  322 (589)
Q Consensus       317 ~~a~~~  322 (589)
                      +||++.
T Consensus        88 ~~ak~~   93 (97)
T d1whya_          88 DFAKSG   93 (97)
T ss_dssp             EECCCC
T ss_pred             EeCCCC
Confidence            999864

>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=99.62  E-value=1e-15  Score=124.28  Aligned_cols=78  Identities=19%  Similarity=0.306  Sum_probs=71.0

Q ss_pred             CCCCceEEEecCCCCCCHHHHHHHhccCCCeEEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHhc--CCceeCCeEEEE
Q 007792          239 KPPENVLFVCKLNPVTEDEDLHTIFSRFGTVVSAEIIRDFKTGDSLNYAFIEFENRQACERAYSKM--DNALIDDRRIHV  316 (589)
Q Consensus       239 ~~~~~~i~V~nL~~~~te~~L~~~F~~~G~v~~~~i~~d~~tg~~~g~aFV~f~~~~~a~~A~~~l--~g~~i~gr~i~V  316 (589)
                      .+|..+|||+|||+.+++++|.++|++||.|..+.++.+      ++||||+|.+.++|..|++.|  ++..|.|++|.|
T Consensus         5 ~~Ps~~l~V~nLp~~~t~~~L~~~f~~~G~i~~v~~~~~------~~~afV~f~~~e~A~~a~~~~~~~~~~~~g~~l~v   78 (88)
T d2cq1a1           5 GAPSRVLHIRKLPGEVTETEVIALGLPFGKVTNILMLKG------KNQAFLELATEEAAITMVNYYSAVTPHLRNQPIYI   78 (88)
T ss_dssp             SSCCSEEEEESCCTTCCHHHHHHTTTTTSCEEEEEEETT------TTEEEEEESSHHHHHHHHHHHHHSCCEETTEECEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHhccccccccccccc------ceEEEEEeCCHHHHHHHHHHHccCCCccCCCEEEE
Confidence            568899999999999999999999999999999998764      489999999999999999865  678999999999


Q ss_pred             Eecccc
Q 007792          317 DFSQSV  322 (589)
Q Consensus       317 ~~a~~~  322 (589)
                      .|++.+
T Consensus        79 ~~sk~~   84 (88)
T d2cq1a1          79 QYSNHK   84 (88)
T ss_dssp             EECSCS
T ss_pred             EECCCC
Confidence            999753

>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=99.62  E-value=9.4e-16  Score=120.47  Aligned_cols=70  Identities=14%  Similarity=0.315  Sum_probs=63.9

Q ss_pred             EEEecCCCCCCHHHHHHHhccCCCeEEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHhcCCceeCCeEEEEEeccc
Q 007792          245 LFVCKLNPVTEDEDLHTIFSRFGTVVSAEIIRDFKTGDSLNYAFIEFENRQACERAYSKMDNALIDDRRIHVDFSQS  321 (589)
Q Consensus       245 i~V~nL~~~~te~~L~~~F~~~G~v~~~~i~~d~~tg~~~g~aFV~f~~~~~a~~A~~~l~g~~i~gr~i~V~~a~~  321 (589)
                      |||+|||+++++++|+++|++|| +..+.+      ++++|||||+|.+.++|.+|+..|||..|.|++|.|++++.
T Consensus         1 i~V~nLp~~~t~~~l~~~F~~~g-~~~~~~------~~~~g~afv~f~~~~~A~~Ai~~ln~~~~~g~~l~V~~a~~   70 (75)
T d1wi6a1           1 ILIRGLPGDVTNQEVHDLLSDYE-LKYCFV------DKYKGTAFVTLLNGEQAEAAINTFHQSRLRERELSVQLQPT   70 (75)
T ss_dssp             EEEECCCTTCCHHHHHHHTTTSC-EEEEEE------ETTTTEEEEEESSHHHHHHHHHHHTTEESSSCEEEEEECCS
T ss_pred             CEEeCCCCcCCHHHHHHHHhccc-ccceee------cccceeEEEEECCHHHHHHHHHHhCCccCCCCEEEEEEeCC
Confidence            79999999999999999999999 555554      34679999999999999999999999999999999999975

>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=99.61  E-value=8e-16  Score=127.48  Aligned_cols=75  Identities=17%  Similarity=0.271  Sum_probs=69.9

Q ss_pred             CCceEEEecCCCCCCHHHHHHHhccCCCeEEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHhcCCceeCCeEEEEEecc
Q 007792          241 PENVLFVCKLNPVTEDEDLHTIFSRFGTVVSAEIIRDFKTGDSLNYAFIEFENRQACERAYSKMDNALIDDRRIHVDFSQ  320 (589)
Q Consensus       241 ~~~~i~V~nL~~~~te~~L~~~F~~~G~v~~~~i~~d~~tg~~~g~aFV~f~~~~~a~~A~~~l~g~~i~gr~i~V~~a~  320 (589)
                      ...+|||+|||+.+++++|.++|++||+|+.+.|..       +|||||+|.+.++|+.||+.|||..|.|+.|.|.+++
T Consensus        14 ~~~~i~V~Nlp~~~~~~~L~~~F~~~G~v~~~~i~~-------~g~afV~f~~~~~a~~Ai~~lng~~~~g~~i~v~~~~   86 (98)
T d1wg4a_          14 SDFRVLVSGLPPSGSWQDLKDHMREAGDVCYADVQK-------DGMGMVEYLRKEDMEYALRKLDDTKFRSHEGETSYIR   86 (98)
T ss_dssp             CSCEEEEECCCSSCCHHHHHHHHTTSSCEEEEEEET-------TTEEEEEESSHHHHHHHHHHHSSEEEECTTSCEEEEE
T ss_pred             CCCEEEEECCCCCCCHHHHHHHHHhhcccccccccc-------cceEEEEECCHHHHHHHHHHhCCCEeCCeEEEEEEEe
Confidence            457899999999999999999999999999999864       3899999999999999999999999999999999987


Q ss_pred             cc
Q 007792          321 SV  322 (589)
Q Consensus       321 ~~  322 (589)
                      ..
T Consensus        87 ~~   88 (98)
T d1wg4a_          87 VY   88 (98)
T ss_dssp             EE
T ss_pred             cC
Confidence            63

>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=99.59  E-value=4.9e-15  Score=124.19  Aligned_cols=79  Identities=20%  Similarity=0.259  Sum_probs=71.1

Q ss_pred             CCCCCceEEEecCCCCCCHHHHHHHhccCCCeEEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHhc--CCceeCCeEEE
Q 007792          238 IKPPENVLFVCKLNPVTEDEDLHTIFSRFGTVVSAEIIRDFKTGDSLNYAFIEFENRQACERAYSKM--DNALIDDRRIH  315 (589)
Q Consensus       238 ~~~~~~~i~V~nL~~~~te~~L~~~F~~~G~v~~~~i~~d~~tg~~~g~aFV~f~~~~~a~~A~~~l--~g~~i~gr~i~  315 (589)
                      ..+|..+|||+|||+.+|+++|.++|++||.|..+.|..      .+|||||+|.+.++|+.||..|  ++..+.|++|.
T Consensus        11 ~~~ps~~l~v~nlp~~~te~~l~~~F~~fG~I~~~~~~~------~k~~AfV~f~~~e~A~~ai~~~~~~~~~~~g~~l~   84 (104)
T d1wexa_          11 KVSVSPVVHVRGLCESVVEADLVEALEKFGTICYVMMMP------FKRQALVEFENIDSAKECVTFAADVPVYIAGQQAF   84 (104)
T ss_dssp             CCCCCSEEEEESCCSSCCHHHHHHHHTTTSCEEEEEEET------TTTEEEEEESSHHHHHHHHHHHHHSCCBSSSSBCE
T ss_pred             cCCCCCEEEEeCCCCCCCHHHHHHhhhhcccceEEEEEe------cceeEEEEeCCHHHHHHHHHHHcCCCcEEeeEEEE
Confidence            356788999999999999999999999999999999875      4589999999999999999977  56788999999


Q ss_pred             EEecccc
Q 007792          316 VDFSQSV  322 (589)
Q Consensus       316 V~~a~~~  322 (589)
                      |.|++..
T Consensus        85 v~~s~~~   91 (104)
T d1wexa_          85 FNYSTSK   91 (104)
T ss_dssp             EEECSSS
T ss_pred             EEEcCCC
Confidence            9999763

>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=99.58  E-value=8.3e-16  Score=129.93  Aligned_cols=78  Identities=24%  Similarity=0.309  Sum_probs=71.1

Q ss_pred             CCceEEEecCCCCCCHHHHHHHhccCCCeEEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHhcCCcee--CCeEEEEEe
Q 007792          241 PENVLFVCKLNPVTEDEDLHTIFSRFGTVVSAEIIRDFKTGDSLNYAFIEFENRQACERAYSKMDNALI--DDRRIHVDF  318 (589)
Q Consensus       241 ~~~~i~V~nL~~~~te~~L~~~F~~~G~v~~~~i~~d~~tg~~~g~aFV~f~~~~~a~~A~~~l~g~~i--~gr~i~V~~  318 (589)
                      +...|||+|||+.+|+++|.++|++||.|..|.|+.++    .+|||||+|.+.++|+.||..|||..|  .|..|.|.+
T Consensus         6 ~~~~v~V~NL~~~vte~~L~~~F~~~G~i~~~~i~~~~----~~g~aFV~f~~~e~A~~Ai~~ln~~~l~~~~~~l~v~~   81 (108)
T d2adba1           6 PVLRIIVENLFYPVTLDVLHQIFSKFGTVLKIITFTKN----NQFQALLQYADPVSAQHAKLSLDGQNIYNACCTLRIDF   81 (108)
T ss_dssp             CEEEEESCSCCSTTHHHHHHHHHTTTSCEEEEEEEEET----TEEEEEEEESCHHHHHHHHHHHHSCCSSTTCCCCEEEE
T ss_pred             CeEEEEEeCcCCCCCHHHHHHHHccCCcEEEEEEEeeC----CCCeEEEEECCHHHHHHHHHHHCCCEeccCCcEEEEEe
Confidence            56789999999999999999999999999999998763    579999999999999999999999988  578999999


Q ss_pred             cccc
Q 007792          319 SQSV  322 (589)
Q Consensus       319 a~~~  322 (589)
                      +++.
T Consensus        82 s~~~   85 (108)
T d2adba1          82 SKLT   85 (108)
T ss_dssp             CSSC
T ss_pred             cCCc
Confidence            8763

>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=99.56  E-value=1.2e-15  Score=129.76  Aligned_cols=80  Identities=18%  Similarity=0.231  Sum_probs=73.0

Q ss_pred             CCceEEEecCCCCCCHHHHHHHhccCCCeEEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHhcCCceeCCeEEEEEecc
Q 007792          241 PENVLFVCKLNPVTEDEDLHTIFSRFGTVVSAEIIRDFKTGDSLNYAFIEFENRQACERAYSKMDNALIDDRRIHVDFSQ  320 (589)
Q Consensus       241 ~~~~i~V~nL~~~~te~~L~~~F~~~G~v~~~~i~~d~~tg~~~g~aFV~f~~~~~a~~A~~~l~g~~i~gr~i~V~~a~  320 (589)
                      +.++|||+|||+.+|+++|.++|+.||.|..+.++.+..+|.++|||||+|.+.++|++|+. |||..|+|+.|.|..+.
T Consensus        17 ~~~~i~v~nLp~~~t~~di~~~F~~~g~~~~~~~~~~~~~g~~~G~afVeF~~~e~a~~al~-~~~~~i~gR~i~V~~~~   95 (112)
T d1wela1          17 AGFCVYLKGLPFEAENKHVIDFFKKLDIVEDSIYIAYGPNGKATGEGFVEFRNEADYKAALC-RHKQYMGNRFIQVHPIT   95 (112)
T ss_dssp             CCCEEEEECCCTTCCHHHHHHHSCSSCBCTTTCEEEECTTSSEEEEEEEEBSSSHHHHHHHT-SCSBCSTTSCBEEEEEC
T ss_pred             CCeEEEEecCCCcCcHHHHhhHHhhccccccceeeecCcccceeeEEEEEECCHHHHHHHHH-cCCCcCCCEEEEEEEcC
Confidence            46799999999999999999999999999876666666889999999999999999999995 99999999999999886


Q ss_pred             c
Q 007792          321 S  321 (589)
Q Consensus       321 ~  321 (589)
                      +
T Consensus        96 ~   96 (112)
T d1wela1          96 K   96 (112)
T ss_dssp             H
T ss_pred             h
Confidence            5

>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=99.55  E-value=6.9e-15  Score=119.42  Aligned_cols=79  Identities=20%  Similarity=0.298  Sum_probs=70.5

Q ss_pred             CCCCceEEEecCCCC-CCHHHHHHHhccCCCeEEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHhc--CCceeCCeEEE
Q 007792          239 KPPENVLFVCKLNPV-TEDEDLHTIFSRFGTVVSAEIIRDFKTGDSLNYAFIEFENRQACERAYSKM--DNALIDDRRIH  315 (589)
Q Consensus       239 ~~~~~~i~V~nL~~~-~te~~L~~~F~~~G~v~~~~i~~d~~tg~~~g~aFV~f~~~~~a~~A~~~l--~g~~i~gr~i~  315 (589)
                      ..+..+|||+|||.. +|+++|.++|++||.|..|.|+.+      ++||||+|.+.++|..|++.|  ++..|.|++|.
T Consensus         5 ~~~sr~v~v~nl~~~~~t~~eL~~lF~~fG~I~~i~i~~~------k~~afV~f~~~~~A~~A~~~l~~~~~~~~gr~l~   78 (89)
T d1x4da1           5 VETRRVVHIMDFQRGKNLRYQLLQLVEPFGVISNHLILNK------INEAFIEMATTEDAQAAVDYYTTTPALVFGKPVR   78 (89)
T ss_dssp             CCCCCEEEEESCCCSSSHHHHHHTTTGGGSCEEEEEECSS------SSCEEEEESSHHHHHHHHHHHHHSCCEETTEECE
T ss_pred             CCCCcEEEEECCCCCcCCHHHHHHHHHhhCCeEEEEeecc------ceEEEEEEcchhhHHHHHHHHhhCCCccCCceEE
Confidence            456789999999986 889999999999999999999764      369999999999999999966  68899999999


Q ss_pred             EEeccccc
Q 007792          316 VDFSQSVS  323 (589)
Q Consensus       316 V~~a~~~~  323 (589)
                      |.||++..
T Consensus        79 V~~s~~~~   86 (89)
T d1x4da1          79 VHLSQKYK   86 (89)
T ss_dssp             EEEECCCT
T ss_pred             EEECCCcc
Confidence            99998643

>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=99.55  E-value=3.9e-15  Score=123.52  Aligned_cols=79  Identities=19%  Similarity=0.278  Sum_probs=70.4

Q ss_pred             CCCCceEEEecCCCC-CCHHHHHHHhccCCCeEEEEEeecCCCCCcccEEEEEEcCHHHHHHHHH--hcCCceeCCeEEE
Q 007792          239 KPPENVLFVCKLNPV-TEDEDLHTIFSRFGTVVSAEIIRDFKTGDSLNYAFIEFENRQACERAYS--KMDNALIDDRRIH  315 (589)
Q Consensus       239 ~~~~~~i~V~nL~~~-~te~~L~~~F~~~G~v~~~~i~~d~~tg~~~g~aFV~f~~~~~a~~A~~--~l~g~~i~gr~i~  315 (589)
                      ..+.++|||+|||.. +|+++|.++|++||.|..+.|+.+      +|||||+|.+.++|..|++  .+++..|+|+.|.
T Consensus        15 ~~~~~~l~v~nLp~~~~te~~l~~~F~~fG~V~~v~~~~~------k~~afV~f~~~~~A~~Ai~~~~~~~~~~~gr~l~   88 (99)
T d1x4fa1          15 QELGRVIHLSNLPHSGYSDSAVLKLAEPYGKIKNYILMRM------KSQAFIEMETREDAMAMVDHCLKKALWFQGRCVK   88 (99)
T ss_dssp             SCCCCEEEEESCCCSSCCSHHHHTTTTTTSCCSEEEEETT------TTEEEEECSSHHHHHHHHHHHHHSCCCSSSSCCE
T ss_pred             CCCCCEEEEeCCcCCccCHHHHHhhhccccceeEEEEeec------CCcEEEEecchHHHHHHHHHHhcCCceECCEEEE
Confidence            345689999999985 899999999999999999999764      5899999999999999997  5789999999999


Q ss_pred             EEeccccc
Q 007792          316 VDFSQSVS  323 (589)
Q Consensus       316 V~~a~~~~  323 (589)
                      |.||+...
T Consensus        89 V~~s~~~~   96 (99)
T d1x4fa1          89 VDLSEKYK   96 (99)
T ss_dssp             EEEECSCS
T ss_pred             EEEcCCcc
Confidence            99997644

>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=99.52  E-value=2.7e-14  Score=132.17  Aligned_cols=83  Identities=19%  Similarity=0.369  Sum_probs=77.7

Q ss_pred             CCCCceEEEecCCCCCCHHHHHHHhccCCCeEEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHhcCCceeCCeEEEEEe
Q 007792          239 KPPENVLFVCKLNPVTEDEDLHTIFSRFGTVVSAEIIRDFKTGDSLNYAFIEFENRQACERAYSKMDNALIDDRRIHVDF  318 (589)
Q Consensus       239 ~~~~~~i~V~nL~~~~te~~L~~~F~~~G~v~~~~i~~d~~tg~~~g~aFV~f~~~~~a~~A~~~l~g~~i~gr~i~V~~  318 (589)
                      ..+..+|||+|||+.+|+++|.++|+.||.|..+.|+.+..+|.++|||||+|.+.++|.+||. +++..|.|+.|.|.+
T Consensus        94 ~~~~~~i~V~~lp~~~te~~L~~~f~~~G~v~~~~i~~~~~~~~~~g~~fV~f~~~e~A~~Al~-~~~~~~~G~~i~V~~  172 (183)
T d1u1qa_          94 HLTVKKIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIVI-QKYHTVNGHNCEVRK  172 (183)
T ss_dssp             TCCCSEEEEECCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESCHHHHHHHHT-SSCEEETTEEEEEEE
T ss_pred             ccccceeEEccCCCcCCHHHHhhhhccCCceeeeeeecccccCccceeEEEEECCHHHHHHHHH-hCCCeECCEEEEEEe
Confidence            3456799999999999999999999999999999999999999999999999999999999996 799999999999999


Q ss_pred             cccc
Q 007792          319 SQSV  322 (589)
Q Consensus       319 a~~~  322 (589)
                      |.++
T Consensus       173 A~~k  176 (183)
T d1u1qa_         173 ALSK  176 (183)
T ss_dssp             CCCH
T ss_pred             cCCc
Confidence            9764

>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=99.52  E-value=8.4e-15  Score=122.42  Aligned_cols=79  Identities=14%  Similarity=0.278  Sum_probs=69.8

Q ss_pred             CCCceEEEecCCCCC-CH----HHHHHHhccCCCeEEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHhcCCceeCCeEE
Q 007792          240 PPENVLFVCKLNPVT-ED----EDLHTIFSRFGTVVSAEIIRDFKTGDSLNYAFIEFENRQACERAYSKMDNALIDDRRI  314 (589)
Q Consensus       240 ~~~~~i~V~nL~~~~-te----~~L~~~F~~~G~v~~~~i~~d~~tg~~~g~aFV~f~~~~~a~~A~~~l~g~~i~gr~i  314 (589)
                      ...++|||+||+..+ ++    ++|+.+|++||.|+.+.++.      +++||||+|.+.++|..|+..|||..|.|+.|
T Consensus         3 ~~~~~L~v~nl~~~v~~~d~~k~~l~~lF~~~G~i~~~~~~k------~~~~afV~f~~~~~A~~Ai~~lng~~~~g~~l   76 (104)
T d1weya_           3 SGSSGLIACVANDDVFSESETRAKFESLFRTYDKDTTFQYFK------SFKRVRINFSNPLSAADARLRLHKTEFLGKEM   76 (104)
T ss_dssp             SCCCEEEEECCCGGGGSTTTHHHHHHHHHHTTCSSCEEEEET------TTTEEEEECSSTTHHHHHHHTSTTSEETTEEC
T ss_pred             CCCceEEEEeCCchhcCcHHHHHHHHHHhcccccceEEEEec------CCCEEEEEECCHHHHHHHHHHhcccccCCCEe
Confidence            356899999999986 33    56999999999999999974      56899999999999999999999999999999


Q ss_pred             EEEecccccc
Q 007792          315 HVDFSQSVSK  324 (589)
Q Consensus       315 ~V~~a~~~~~  324 (589)
                      +|.||++...
T Consensus        77 ~v~~a~~~~~   86 (104)
T d1weya_          77 KLYFAQTLHI   86 (104)
T ss_dssp             EEECCCCSSC
T ss_pred             EEeecccCCC
Confidence            9999986443

>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=99.48  E-value=5.3e-16  Score=126.63  Aligned_cols=77  Identities=14%  Similarity=0.251  Sum_probs=67.8

Q ss_pred             ceEEEecCCCCCCHHHHHHHhccCCCeEEEEEe-----ecCCCCCcccEEEEEEcCHHHHHHHHHhcCCceeCCeEEEEE
Q 007792          243 NVLFVCKLNPVTEDEDLHTIFSRFGTVVSAEII-----RDFKTGDSLNYAFIEFENRQACERAYSKMDNALIDDRRIHVD  317 (589)
Q Consensus       243 ~~i~V~nL~~~~te~~L~~~F~~~G~v~~~~i~-----~d~~tg~~~g~aFV~f~~~~~a~~A~~~l~g~~i~gr~i~V~  317 (589)
                      ..|||+|||+.+|+++|.++|++||.|..+.++     .+..+++++|||||+|.+.++|+.|+ .|||..|.|+.|+|.
T Consensus         2 RrlyVgNLp~~~te~~l~~~F~~~g~~~~~~~~~~~~~~~~~~~~~kg~afV~f~~~e~a~~a~-~l~g~~~~Gr~l~V~   80 (90)
T d1u2fa_           2 RRLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLEFRSVDETTQAM-AFDGIIFQGQSLKIR   80 (90)
T ss_dssp             CEEEECSCCTTCCTTHHHHHHHHHHTTTTSCCSSSCSEEECCEETTTTEEEEEESSCTTTTTGG-GGSSCCSSSSCCCCB
T ss_pred             CEEEEcCCCCccchHHHHHHHHhhCcEEEEEEeccceeeecccCCCceEEEEEeCCHHHHHHHH-hhCCcEECCEEEEEC
Confidence            579999999999999999999999988766543     34567889999999999999999999 599999999999997


Q ss_pred             ecc
Q 007792          318 FSQ  320 (589)
Q Consensus       318 ~a~  320 (589)
                      .++
T Consensus        81 r~k   83 (90)
T d1u2fa_          81 RPH   83 (90)
T ss_dssp             CTT
T ss_pred             CCC
Confidence            544

>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=99.44  E-value=4.9e-15  Score=123.89  Aligned_cols=76  Identities=13%  Similarity=0.258  Sum_probs=70.6

Q ss_pred             ceEEEecCCCCCCHHHHHHHhccCCCeEEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHhcCCceeCCeEEEEEec
Q 007792          243 NVLFVCKLNPVTEDEDLHTIFSRFGTVVSAEIIRDFKTGDSLNYAFIEFENRQACERAYSKMDNALIDDRRIHVDFS  319 (589)
Q Consensus       243 ~~i~V~nL~~~~te~~L~~~F~~~G~v~~~~i~~d~~tg~~~g~aFV~f~~~~~a~~A~~~l~g~~i~gr~i~V~~a  319 (589)
                      +.++|.+++..+++++|.++|++||+|..|.|+.+ .+|+++|||||+|.+.++|.+|+..|||..|+|++|.|+|+
T Consensus        28 ~~~~v~~~~~~~~ed~l~e~f~k~G~I~~v~I~~~-~~~~~~G~~fV~f~~~~~A~~Ai~~lng~~~~gr~i~v~~s  103 (104)
T d1jmta_          28 SDVEMQEHYDEFFEEVFTEMEEKYGEVEEMNVCDN-LGDHLVGNVYVKFRREEDAEKAVIDLNNRWFNGQPIHAELS  103 (104)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHTCCEEEEEECCS-SSSSSEEEEEEEESCHHHHHHHHHHHTTCEETTEECCEEEC
T ss_pred             chHHhhhhhhhhhHHHHHHHhccCCCEEEEEeecC-CCCCEeeEEEEEEechhHHHHHHHHHCCCEECCEEEEEEEC
Confidence            35777888888999999999999999999999876 68999999999999999999999999999999999999986

>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=99.38  E-value=3.7e-13  Score=111.69  Aligned_cols=65  Identities=17%  Similarity=0.318  Sum_probs=58.7

Q ss_pred             CCCCceEEEec--CCCCCCHHHHHHHhccCCCeEEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHhcCCcee
Q 007792          239 KPPENVLFVCK--LNPVTEDEDLHTIFSRFGTVVSAEIIRDFKTGDSLNYAFIEFENRQACERAYSKMDNALI  309 (589)
Q Consensus       239 ~~~~~~i~V~n--L~~~~te~~L~~~F~~~G~v~~~~i~~d~~tg~~~g~aFV~f~~~~~a~~A~~~l~g~~i  309 (589)
                      ..|..+|||+|  ||+.+|+++|+.+|++||.|..|.++.+      ++||||+|.+.++|..|+..|||..|
T Consensus        15 ~~pt~~l~V~ng~L~~~vte~~L~~~F~~~G~i~~i~~~~~------k~~aFV~f~~~e~A~~A~~~lng~~i   81 (101)
T d2cq2a1          15 SYATQSLVVANGGLGNGVSRNQLLPVLEKCGLVDALLMPPN------KPYSFARYRTTEESKRAYVTLNGKEV   81 (101)
T ss_dssp             SSCCSEEEEETCTGGGTCCHHHHHHHHHHHSCEEEEECCTT------CSCEEEEESSHHHHHHHHHHTTTCEE
T ss_pred             CCCCceEEEECCCCCCCCCHHHHHHHHHhhCcccEEeeccC------ccEEEEEECCHHHHHHHHHHhCCCCC
Confidence            34678899965  9999999999999999999999988764      47999999999999999999999877

>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=99.35  E-value=5.4e-13  Score=113.14  Aligned_cols=75  Identities=21%  Similarity=0.278  Sum_probs=65.4

Q ss_pred             CCceEEEecCCCCCCHHHHHHHhccCCCeEEEEEeecCCCCCcccEEEEEEcCH-HHHHHHHHhcCCceeCCeEEEEEec
Q 007792          241 PENVLFVCKLNPVTEDEDLHTIFSRFGTVVSAEIIRDFKTGDSLNYAFIEFENR-QACERAYSKMDNALIDDRRIHVDFS  319 (589)
Q Consensus       241 ~~~~i~V~nL~~~~te~~L~~~F~~~G~v~~~~i~~d~~tg~~~g~aFV~f~~~-~~a~~A~~~l~g~~i~gr~i~V~~a  319 (589)
                      -.-.+||||||+.+|+++|+.+|++||+|..|.|+.+      +|||||.|.+. ++|..|+..||+..|.++.+.|.++
T Consensus        10 g~~~~fvgnL~~~~tee~Lk~~F~~fG~V~~v~i~~~------kg~gfV~F~~~~~~A~~a~~~~~~~~l~~~~~~v~~~   83 (113)
T d1owxa_          10 GCLLKFSGDLDDQTCREDLHILFSNHGEIKWIDFVRG------AKEGIILFKEKAKEALGKAKDANNGNLQLRNKEVTWE   83 (113)
T ss_dssp             CCEEEEEESCCSSCCHHHHHHHTCSSCCEEEEECCTT------CSEEEEEESSCHHHHHHHHHHTTTSCBCTTSSSEEEE
T ss_pred             CCeEEEECCCCCCCCHHHHHHHHHhcCChheEEEecC------CceEEEEecCcHHHHHHHHHHhcCCceecCceEEEEe
Confidence            3456799999999999999999999999999999753      58999999985 7899999999999888877777776


Q ss_pred             cc
Q 007792          320 QS  321 (589)
Q Consensus       320 ~~  321 (589)
                      ..
T Consensus        84 ~~   85 (113)
T d1owxa_          84 VL   85 (113)
T ss_dssp             EC
T ss_pred             ec
Confidence            54

>d1u1qa_ d.58.7.1 (A:) Nuclear ribonucleoprotein A1 (RNP A1, UP1) {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nuclear ribonucleoprotein A1 (RNP A1, UP1)
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.30  E-value=4.7e-12  Score=116.71  Aligned_cols=78  Identities=24%  Similarity=0.396  Sum_probs=72.2

Q ss_pred             ceEEEecCCCCCCHHHHHHHhccCCCeEEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHhcCCceeCCeEEEEEeccc
Q 007792          243 NVLFVCKLNPVTEDEDLHTIFSRFGTVVSAEIIRDFKTGDSLNYAFIEFENRQACERAYSKMDNALIDDRRIHVDFSQS  321 (589)
Q Consensus       243 ~~i~V~nL~~~~te~~L~~~F~~~G~v~~~~i~~d~~tg~~~g~aFV~f~~~~~a~~A~~~l~g~~i~gr~i~V~~a~~  321 (589)
                      .+|||+|||+.+|+++|.++|++||.|..+.|+.+..++.++|||||+|.+.++|.+|+. +++..+.++.+.+....+
T Consensus         7 r~lfV~nLp~~~te~~L~~~F~~~G~v~~~~~~~~~~~~~~~g~afv~f~~~~~a~~a~~-~~~~~~~~~~~~~~~~~~   84 (183)
T d1u1qa_           7 RKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMN-ARPHKVDGRVVEPKRAVS   84 (183)
T ss_dssp             HEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHH-TCSCEETTEECEEEECCC
T ss_pred             CEEEEECCCCCCCHHHHHHHHHHcCCEEEEEeeecccCCCccCceecccCCHHHHHHHHH-hcCCcccccchhhhhhhh
Confidence            699999999999999999999999999999999999999999999999999999999996 567778888888887654

>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=99.28  E-value=4.1e-12  Score=104.82  Aligned_cols=80  Identities=16%  Similarity=0.234  Sum_probs=68.4

Q ss_pred             CCCceEEEecC--CCCC---------CHHHHHHHhccCCCeEEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHhcCCce
Q 007792          240 PPENVLFVCKL--NPVT---------EDEDLHTIFSRFGTVVSAEIIRDFKTGDSLNYAFIEFENRQACERAYSKMDNAL  308 (589)
Q Consensus       240 ~~~~~i~V~nL--~~~~---------te~~L~~~F~~~G~v~~~~i~~d~~tg~~~g~aFV~f~~~~~a~~A~~~l~g~~  308 (589)
                      ....+|+|.||  |.++         ..++|.+.|++||.|..|.++.+    .++|||||+|.+.++|..|+..|||..
T Consensus         6 ~~~r~v~l~nmf~~~~~~~~~~~~~~i~edv~~~~~~~G~V~~v~~~~~----~~~G~~fV~f~~~e~A~~A~~~lng~~   81 (99)
T d2dita1           6 RHERVVIIKNMFHPMDFEDDPLVLNEIREDLRVECSKFGQIRKLLLFDR----HPDGVASVSFRDPEEADYCIQTLDGRW   81 (99)
T ss_dssp             CSCCEEEEESSCCTTHHHHCSHHHHHHHHHHHHHGGGTSCCSEEEEETT----CTTCEEEEECSCHHHHHHHHHHSTTCE
T ss_pred             CCccEEEEccCCCHHHhhcchHHHHHHHHHHHHHhcCcccEEEEeccCC----CCccEEEEEECCHHHHHHHHHHhCCcE
Confidence            45689999999  5432         13678899999999999988664    367999999999999999999999999


Q ss_pred             eCCeEEEEEeccccc
Q 007792          309 IDDRRIHVDFSQSVS  323 (589)
Q Consensus       309 i~gr~i~V~~a~~~~  323 (589)
                      |+|++|.|+++.++.
T Consensus        82 ~~gr~i~v~~~~g~~   96 (99)
T d2dita1          82 FGGRQITAQAWDGTT   96 (99)
T ss_dssp             ETTEECEEEECCSCC
T ss_pred             ECCEEEEEEEeCCcC
Confidence            999999999987643

>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=99.25  E-value=5.2e-12  Score=99.89  Aligned_cols=73  Identities=15%  Similarity=0.259  Sum_probs=61.8

Q ss_pred             CceEEEecCCCCCCHHHHHHHhccCCCeEEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHhcCCceeCCeE-EEEEecc
Q 007792          242 ENVLFVCKLNPVTEDEDLHTIFSRFGTVVSAEIIRDFKTGDSLNYAFIEFENRQACERAYSKMDNALIDDRR-IHVDFSQ  320 (589)
Q Consensus       242 ~~~i~V~nL~~~~te~~L~~~F~~~G~v~~~~i~~d~~tg~~~g~aFV~f~~~~~a~~A~~~l~g~~i~gr~-i~V~~a~  320 (589)
                      .+.|||++||++++++.| .+|++||+|.++.+..      .+|||||+|.+.++|++||+ |||..|+|+. |.|..+.
T Consensus         4 ~~wV~V~G~p~~~~~~il-~~F~~~G~I~~~~~~~------~~~~~fV~f~~~~~A~~Al~-~nG~~~~g~~~vgV~~~~   75 (81)
T d1wwha1           4 DTWVTVFGFPQASASYIL-LQFAQYGNILKHVMSN------TGNWMHIRYQSKLQARKALS-KDGRIFGESIMIGVKPCI   75 (81)
T ss_dssp             GGEEEEECCCGGGHHHHH-HHHHTTSCEEEEEECS------SSSEEEEEESSHHHHHHHHT-TTTCEETTTEECEEEECC
T ss_pred             ccEEEEECCChHHHHHHH-HHHHhhhhhheEEecC------CCCEEEEEEcccHHHHHHHh-cCCCeECCcEEEEEEeCC
Confidence            467999999999987655 5799999999998743      46899999999999999995 9999999985 5688775


Q ss_pred             cc
Q 007792          321 SV  322 (589)
Q Consensus       321 ~~  322 (589)
                      .+
T Consensus        76 ~k   77 (81)
T d1wwha1          76 DK   77 (81)
T ss_dssp             CH
T ss_pred             Ch
Confidence            43

>d1o0pa_ d.58.7.1 (A:) Splicing factor U2AF 65 KDa subunit {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicing factor U2AF 65 KDa subunit
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.23  E-value=3.4e-12  Score=106.44  Aligned_cols=82  Identities=22%  Similarity=0.337  Sum_probs=70.0

Q ss_pred             CCCceEEEecC--CCCCC--------HHHHHHHhccCCCeEEEEEeecCCC--CCcccEEEEEEcCHHHHHHHHHhcCCc
Q 007792          240 PPENVLFVCKL--NPVTE--------DEDLHTIFSRFGTVVSAEIIRDFKT--GDSLNYAFIEFENRQACERAYSKMDNA  307 (589)
Q Consensus       240 ~~~~~i~V~nL--~~~~t--------e~~L~~~F~~~G~v~~~~i~~d~~t--g~~~g~aFV~f~~~~~a~~A~~~l~g~  307 (589)
                      +|..+|.|.||  +..+.        .++|++.|++||.|..|.|+.+..+  ....|++||+|.+.++|..|+..|||.
T Consensus         2 ~Ps~vl~l~N~~~~~~l~~~~~~~~i~edi~~e~~k~G~v~~v~I~~~~~~~~~~~~g~vfV~f~~~e~A~~A~~~l~Gr   81 (104)
T d1o0pa_           2 HPTEVLCLMNMVLPEELLDDEEYEEIVEDVRDECSKYGLVKSIEIPRPVDGVEVPGCGKIFVEFTSVFDCQKAMQGLTGR   81 (104)
T ss_dssp             CCCSEEEEESSCCTTTTTSHHHHHHHHHHHHHHHTTTSCEEEEECCCCTTSSSCTTCCEEEEEESCHHHHHHHHHHHSSC
T ss_pred             CCCcEEEEeCCCCHHHcCCchhHHHHHHHHHHHhcccCceEEEEEeecCCCCccCCceEEEEEECCHHHHHHHHHHHCCC
Confidence            57889999999  44432        3578999999999999999876544  334689999999999999999999999


Q ss_pred             eeCCeEEEEEeccc
Q 007792          308 LIDDRRIHVDFSQS  321 (589)
Q Consensus       308 ~i~gr~i~V~~a~~  321 (589)
                      .|+|+.|.|.++..
T Consensus        82 ~f~gR~v~v~f~~~   95 (104)
T d1o0pa_          82 KFANRVVVTKYCDP   95 (104)
T ss_dssp             CSSSSCCEEEEECH
T ss_pred             EECCeEEEEEEcCH
Confidence            99999999999864

>d1ufwa_ d.58.7.1 (A:) Synaptojanin 2 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Synaptojanin 2
species: Human (Homo sapiens) [TaxId: 9606]

Probab=97.82  E-value=2.1e-05  Score=60.54  Aligned_cols=75  Identities=16%  Similarity=0.307  Sum_probs=61.5

Q ss_pred             CCCCCCceEEEecCCCCCCH---------HHHHHHhccCCCeEEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHhcCCc
Q 007792          237 DIKPPENVLFVCKLNPVTED---------EDLHTIFSRFGTVVSAEIIRDFKTGDSLNYAFIEFENRQACERAYSKMDNA  307 (589)
Q Consensus       237 ~~~~~~~~i~V~nL~~~~te---------~~L~~~F~~~G~v~~~~i~~d~~tg~~~g~aFV~f~~~~~a~~A~~~l~g~  307 (589)
                      ...||..||.|.=+.+...+         .+|.+.|..||+|.-++++.+        -.+|+|.+-++|.+|+ .|+|.
T Consensus        10 ~qGPpDgTIvV~i~~~s~e~~~~FDe~l~~~Llq~l~~~GeViLvRFv~d--------~mwVTF~dG~SAL~al-~l~g~   80 (95)
T d1ufwa_          10 FQGPLDATVVVNLQSPTLEEKNEFPEDLRTELMQTLGSYGTIVLVRINQG--------QMLVTFADSHSALSVL-DVDGM   80 (95)
T ss_dssp             CCCCTTCEEEEEESSCCHHHHHSCCHHHHHHHHHHHHHHSCCSEEEEETT--------EEEEECSCSHHHHHHH-HGGGS
T ss_pred             ccCCCCcEEEEEeccCCccccccCCHHHHHHHHHHHhhCCeEEEEEEeCC--------eEEEEECCcHHHHHHh-ccCCe
Confidence            34677888988655544333         467888999999999999875        7899999999999999 58999


Q ss_pred             eeCCeEEEEEecc
Q 007792          308 LIDDRRIHVDFSQ  320 (589)
Q Consensus       308 ~i~gr~i~V~~a~  320 (589)
                      +++|+.|+|....
T Consensus        81 ~v~G~~l~It~~~   93 (95)
T d1ufwa_          81 KVKGRAVKISGPS   93 (95)
T ss_dssp             EETTEEEEEECCC
T ss_pred             EEcceEEEEecCC
Confidence            9999999998643

>d2dgxa1 d.58.7.1 (A:563-635) Limkain-b1, LKAP {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Limkain-b1, LKAP
species: Human (Homo sapiens) [TaxId: 9606]

Probab=97.08  E-value=0.0011  Score=48.38  Aligned_cols=62  Identities=24%  Similarity=0.275  Sum_probs=52.4

Q ss_pred             HHHHHHhccCCCeEEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHhcCCceeCCeEEEEEeccc
Q 007792          257 EDLHTIFSRFGTVVSAEIIRDFKTGDSLNYAFIEFENRQACERAYSKMDNALIDDRRIHVDFSQS  321 (589)
Q Consensus       257 ~~L~~~F~~~G~v~~~~i~~d~~tg~~~g~aFV~f~~~~~a~~A~~~l~g~~i~gr~i~V~~a~~  321 (589)
                      +.|...|.++|+|..+.|.... .|  .-.|-|...+..+|..|+..|+-..|++++|.|.++..
T Consensus        11 q~L~~~f~~h~~V~sv~l~~~~-dg--~~~A~V~v~~~q~A~~~v~~LhR~KiG~KRI~Vs~~~~   72 (73)
T d2dgxa1          11 QLLQEAFARHGKVKSVELSPHT-DY--QLKAVVQMENLQDAIGAVNSLHRYKIGSKKILVSLATG   72 (73)
T ss_dssp             HHHHHHHHHHSCEEEEEECSCC-ST--TCCEEEEESSHHHHHHHHHHHTTEEETTEEEEEEECCC
T ss_pred             HHHHHHHHhheeEEEEEEEecc-CC--cEEEEEEcCCHHHHHHHHHHHHHHhcCCeEEEEEEecC
Confidence            4466788999999999886642 22  24799999999999999999999999999999999853

>d1uw4a_ d.58.7.4 (A:) RNA processing protein UPF3x, RRM domain {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Smg-4/UPF3
domain: RNA processing protein UPF3x, RRM domain
species: Human (Homo sapiens) [TaxId: 9606]

Probab=97.06  E-value=0.002  Score=50.18  Aligned_cols=78  Identities=17%  Similarity=0.201  Sum_probs=63.6

Q ss_pred             ceEEEecCCCCCCHHHHHHHhccCCCeEEEEEeecCCCCCc--ccEEEEEEcCHHHHHHHHHhcCCceeCC-----eEEE
Q 007792          243 NVLFVCKLNPVTEDEDLHTIFSRFGTVVSAEIIRDFKTGDS--LNYAFIEFENRQACERAYSKMDNALIDD-----RRIH  315 (589)
Q Consensus       243 ~~i~V~nL~~~~te~~L~~~F~~~G~v~~~~i~~d~~tg~~--~g~aFV~f~~~~~a~~A~~~l~g~~i~g-----r~i~  315 (589)
                      ++|.|..||+.+|++++.+.++..|++.....+..+.+.+.  ..-|||.|.+.+++....+.++|..+.+     .+-.
T Consensus         2 tKvVvRrLPP~Lte~~F~~~l~~~~~~d~~~f~~Gk~s~~~~~~SRAYi~F~~~~~v~~F~~~f~g~~F~D~~g~~~~a~   81 (91)
T d1uw4a_           2 SKVVIRRLPPTLTKEQLQEHLQPMPEHDYFEFFSNDTSLYPHMYARAYINFKNQEDIILFRDRFDGYVFLDNKGQEYPAI   81 (91)
T ss_dssp             CEEEEEEECTTCCHHHHHHHHCSCCCEEEEEEEESCCSSTTCCCEEEEEEESSSHHHHHHHHHHTTCEEECTTCCEEECE
T ss_pred             ceEEEecCCCCCCHHHHHHHhCCcCceEEEEEeCCCcCCCCCcceEEEEEeCCHHHHHHHHHHcCCcEEEcCCCCEeeeE
Confidence            57899999999999999999999999988888776555443  3679999999999999999999988743     2345


Q ss_pred             EEecc
Q 007792          316 VDFSQ  320 (589)
Q Consensus       316 V~~a~  320 (589)
                      |++|-
T Consensus        82 VE~AP   86 (91)
T d1uw4a_          82 VEFAP   86 (91)
T ss_dssp             EEECS
T ss_pred             EEEcC
Confidence            56653

>d1whva_ d.58.7.1 (A:) Poly(A)-specific ribonuclease PARN {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Poly(A)-specific ribonuclease PARN
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=94.19  E-value=0.096  Score=40.46  Aligned_cols=60  Identities=20%  Similarity=0.365  Sum_probs=49.4

Q ss_pred             CCCCCceEEEecCCCCCCHHHHHHHhccCCCeEEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHhcC
Q 007792          238 IKPPENVLFVCKLNPVTEDEDLHTIFSRFGTVVSAEIIRDFKTGDSLNYAFIEFENRQACERAYSKMD  305 (589)
Q Consensus       238 ~~~~~~~i~V~nL~~~~te~~L~~~F~~~G~v~~~~i~~d~~tg~~~g~aFV~f~~~~~a~~A~~~l~  305 (589)
                      ..|+...||.-..|..+...+|.++|+.||.|. |.++-+       --|||...+.++|..++..+.
T Consensus        11 ~~p~RdHVf~~tFP~~Wk~~dI~~lFSpfG~V~-VswIdd-------TSa~V~L~~~e~~~~v~~~~~   70 (100)
T d1whva_          11 LQPKRDHVLHVTFPKEWKTSDLYQLFSAFGNIQ-ISWIDD-------TSAFVSLSQPEQVQIAVNTSK   70 (100)
T ss_dssp             CCCCCCSEEEEECCTTCCHHHHHHHHTTTCSCC-CEEEET-------TEEEEECSCHHHHHHHHHHHH
T ss_pred             CCCCcceeEEEeCCcccchhHHHHHhcCCCceE-EEEecC-------ceEEEEecCHHHHHHHHHHhc
Confidence            355677899999999999999999999999875 455544       279999999999999987544

>d1zx8a1 b.62.1.3 (A:1-124) Hypothetical protein TM1367 {Thermotoga maritima [TaxId: 2336]}

class: All beta proteins
fold: Cyclophilin-like
superfamily: Cyclophilin-like
family: TM1367-like
domain: Hypothetical protein TM1367
species: Thermotoga maritima [TaxId: 2336]

Probab=93.99  E-value=0.091  Score=42.95  Aligned_cols=102  Identities=18%  Similarity=0.172  Sum_probs=63.6

Q ss_pred             CEEEEEecceeEEEEecCCCChhHHHHHHHHHh----cCccCCceEEEeecCcccccCCCCCCCCCCCCccccccccccc
Q 007792            1 MSVLIVTSLGDIVVDLFVDKCPLTTKNFLKLCK----IKYYNGCLFHTVQKDFTAQTGDPTGTGTGGDSVYKFLYGEQAR   76 (589)
Q Consensus         1 ~~v~~~T~~G~i~ieL~~~~aP~~~~nF~~l~~----~~~Y~g~~f~rv~~~~~iq~Gd~~~~~~~~~~~~~~~~~~~~~   76 (589)
                      |.+.|...-+.++|+|..  .|.|+..|++++=    ...| |.-+|--.|-                            
T Consensus         1 mki~l~f~~~~~~~~l~~--s~~ta~~i~~~LPl~~~~~~w-G~Eiyf~~p~----------------------------   49 (124)
T d1zx8a1           1 MRVELLFESGKCVIDLNE--EYEVVKLLKEKIPFESVVNTW-GEEIYFSTPV----------------------------   49 (124)
T ss_dssp             EEEEEECSSCEEEEEEET--TSHHHHHHHHHCSEEEECEES-SSEEEEECSC----------------------------
T ss_pred             CeEEEEeCCeEEEEEeCC--CHHHHHHHHHhCCeEEEHHHc-cceEEEeCCc----------------------------
Confidence            789999999999999993  7889999998862    2234 2322211110                            


Q ss_pred             ccCCccccCCCCCCCceEEEeccCCCCCcceEEEEeCCCCCCC------CCCcceEEEEecCHHHHHHHh
Q 007792           77 FFGDEIRVDLKHAKTGTVAMASAGENLNASQFYMTLRDNLDYL------DEKHTIFGEVAEGLETLSRIN  140 (589)
Q Consensus        77 ~~~~e~~~~l~~~~~G~vs~a~~g~~~~~sqFfI~l~~~~~~l------d~~~~vFG~Vv~G~~vl~~i~  140 (589)
                      .++.|-.+.-. ...|-|++...+.+     |.|-+++ .|+=      -....+||+|+.+++.|..|.
T Consensus        50 ~l~~e~~~~~~-~~~GDiaYw~pg~~-----iaifyg~-tp~S~~~irlas~~n~iGki~~~~~~l~~i~  112 (124)
T d1zx8a1          50 NVQKMENPREV-VEIGDVGYWPPGKA-----LCLFFGK-TPMSDDKIQPASAVNVIGKIVEGLEDLKKIK  112 (124)
T ss_dssp             CCCCCSSEESS-BCTTEEEEEGGGTE-----EEEESSC-CTTCSSSBCCSSCEEEEEEEEECGGGGGGCC
T ss_pred             CCCcccCcccc-cccccEEEECCCCE-----EEEEECC-ccCCCCcccccCcceEeEEecCCHHHHhcCC
Confidence            01111111111 24688888776544     7776765 3443      234678999999988777663