Psyllid ID: psy11929

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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---
Protein Sequence
MDGNGDGKIDEDTLITMRCLFHSSVNVNEISCLIGPGGCIVRRLRKESGAKISITDGACPDRIVTVSGSVDNSSTSSVETGYPGHTLWVTSVDNVCTAYNFMCRSLEDYHINRNRMENCSPQPLQLKLVIPATHCGSLIGKGGCKIKDIRDLSGANVQVASDMLPMSTERIVTVHGNPDTISQAIYQICLVLIECTLQVVKGAVIPYEPKTMNAGPVILSGGQAYTLHGEYAVPVQEVAGKKQPHPLAGLAVLGIEGIGSTSLTPAALAALSGSRVKSGGKDTGDDFVETEIVLTDDIAGCVIGKAGSRLLEIRQISGAQINIHTGTESHKKMFHIQGCQEAVSLAQYLINMCIELQKNNTTNTSDNPEPADLDAAISAFMTASVNSSLIEKPTPHPGSMVTLGGLSELLANIAASNVKSTVQTTGAYRRDVE
Secondary Structure (PSIPRED)
ccccccccccccccEEEEEEEEEccccccEEEEEccccHHHHHHHHHHccEEEEccccccccEEEEEcccccccccccccccccccccccccHHHHHHHHHHHHHccccccccccccccccccEEEEEEEEcccccEEEccccccHHHHHHHcccEEEEcccccccccccEEEEEccHHHHHHHHHHHHHHHHHccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccHHHHHHcccccccccccccccccEEEEEEEccccccEEEEcccccHHHHHHHcccEEEEcccccccEEEEEEEEcHHHHHHHHHHHHHHHHHHHcccccccccccccccccccccccccccccccccccccccccccccccccccHHHHHHcccccccccccccccccc
Secondary Structure Prediction (SSPRO)
cccccccccccccEEEEEEEEEEEEccccEEEEEcccccEHHHHHHHcccEEEEcccccccEEEEEEccHHHHHHHHHHHHHHHHHcccccccHHHHHHHHHHHccHHHccccccccccccccEEEEEEEcccccEEEEccccccHHHHHHHcccEEEEccccccccccEEEEEEccHHHHHHHHHHHHHHHccccccccccccccccccccccccEEcccccccccccccccccHHHccccccccccccccccccccccccccccccHHccccccccccccccccccEEEEEEccccEEEEEcccccHHHHHHHHcccEEEEccccccccEEEEEEccHHHHHHHHHHHHHHHHHcccccccccccccccccccccccccccccccccccccccccccEEccccHHHHHHHcccHccccccccccccccccc
Coil and Loop (DISEMBL)
mdgngdgkidedtLITMRCLFHssvnvneiscligpggciVRRLRkesgakisitdgacpdrivtvsgsvdnsstssvetgypghtLWVTSVDNVCTAYNFMCRSLEDYHinrnrmencspqplqlklvipathcgsligkggckikdirdlsganvqvasdmlpmstERIVtvhgnpdtiSQAIYQICLVLIECTLQVVkgavipyepktmnagpvilsggqaytlhgeyavpvqevagkkqphplaglavlgiegigstsltPAALAALSgsrvksggkdtgddfveteivltddiagcvigKAGSRLLEIRQISGaqinihtgteshKKMFHIQGCQEAVSLAQYLINMCIELqknnttntsdnpepadLDAAISAFMTASVnssliekptphpgsmvtlGGLSELLANIAAsnvkstvqttgayrrdve
Flexible Loop (DISEMBL)
mdgngdgkidedtLITMRCLFHSSVNVNEISCLIGPGGCIVRRLRKESGakisitdgacpdrivtvsgsvdnsstssvetgypghtLWVTSVDNVCTAYNFMCRSLEDYHINRNRMENCSPQPLQLKLVIPATHCGSLIGKGGCKIKDIRDLSGANVQVASDMLPMSTERIVTVHGNPDTISQAIYQICLVLIECTLQVVKGAVIPYEPKTMNAGPVILSGGQAYTLHGEYAVPVQEVAGKKQPHPLAGLAVLGIEGIGSTSLTPAALAALSgsrvksggkdtGDDFVETEivltddiagCVIGKAGSRLLEIRQISGAQINIHTGTESHKKMFHIQGCQEAVSLAQYLINMCIELQKNNTTNTSDNPEPADLDAAISAFMTASVNSSLIEKPTPHPGSMVTLGGLSELLANIAasnvkstvqttgayrrdve
Low Complexity Region (SEG)
MDGNGDGKIDEDTLITMRCLFHSSVNVNEISCLIGPGGCIVRRLRKESGAKISITDGACPDRIvtvsgsvdnsstssvetGYPGHTLWVTSVDNVCTAYNFMCRSLEDYHINRNRMENCSPQPLQLKLVIPATHCGSLIGKGGCKIKDIRDLSGANVQVASDMLPMSTERIVTVHGNPDTISQAIYQICLVLIECTLQVVKGAVIPYEPKTMNAGPVILSGGQAYTLHGEYAVPVQEVAGKKQPHPLAGLAVLGIEGIgstsltpaalaalsgsRVKSGGKDTGDDFVETEIVLTDDIAGCVIGKAGSRLLEIRQISGAQINIHTGTESHKKMFHIQGCQEAVSLAQYLINMCIELQKNNTTNTSDNPEPADLDAAISAFMTASVNSSLIEKPTPHPGSMVTLGGLSELLANIAASNVKSTVQTTGAYRRDVE
Disordered region (IsUnstruct)
***********DTLITMRCLFHSSVNVNEISCLIGPGGCIVRRLRKESGAKISITDGACPDRIVT****************YPGHTLWVTSVDNVCTAYNFMCRSLEDYHINRNRMENCSPQPLQLKLVIPATHCGSLIGKGGCKIKDIRDLSGANVQVASDMLPMSTERIVTVHGNPDTISQAIYQICLVLIECTLQVVKGAVIPYEPKTMNAGPVILSGGQAYTLHGEYAVPVQEVAGKKQPHPLAGLAVLGIEGIGSTSL***********************FVETEIVLTDDIAGCVIGKAGSRLLEIRQISGAQINIHTGTESHKKMFHIQGCQEAVSLAQYLINMCIELQ********************************************TLGGLSELLANIAA******************
Disordered Region (DISOPRED)
****************MRCLFHSSVNVNEISCLIGPGGCIVRRLRKESGAKISITDGACPDRIVTVSGSVDNSSTSSVETGYPGHTLWVTSVDNVCTAYNFM**********************QLKLVIPATHCGSLIGKGGCKIKD*RDL*GA*VQVASDMLPMSTERIVTVHGNPDTISQAIYQICLVLIECT*******************PVILSGGQ************************AGLAVLGIEGIGSTSLTPAALAALSGSRVK*******DDFVETEIVLTDDIAGCVIGKAGSRLLEIRQISGAQ*********HKKMFHIQGCQEAVSLAQYLINM***********************************************MVTLGGLSELLA**********************
Disordered Region (DISEMBL)
MDGNGDGKIDEDTLITMRCLFHSSVNVNEISCLIGPGGCIVRRLRKESGAKISITDGACPDRIVTVSGSV*********TGYPGHTLWVTSVDNVCTAYNFMCRSLEDYHINRNRMENCSPQPLQLKLVIPATHCGSLIGKGGCKIKDIRDLSGANVQVASDMLPMSTERIVTVHGNPDTISQAIYQICLVLIECTLQVVKGAVIPYEPKTMNAGPVILSGGQAYTLHGEYAVPVQEVAGKKQPHPLAGLAVLGIEGIGSTSLTPAALAAL**********DTGDDFVETEIVLTDDIAGCVIGKAGSRLLEIRQISGAQINIHTGTESHKKMFHIQGCQEAVSLAQYLINMCIELQKNNTTNTSDNPEPADLDAAISAFMTASVNSSLIEKPTPHPGSMVTLGGLSELLANIAASNVKSTVQTTGAYRRDVE
Disordered Region (DISPRO)
**********EDTLITMRCLFHSSVNVNEISCLIGPGGCIVRRLRKESGAKISITDGACPDRIVTVSGSVDNSSTSSVETGYPGHTLWVTSVDNVCTAYNFMCRSLEDYHINRN***NCSPQPLQLKLVIPATHCGSLIGKGGCKIKDIRDLSGANVQVASDMLPMSTERIVTVHGNPDTISQAIYQICLVLIECTLQVVKGAVIPYEPKTMNAGPVILSGGQAYTLHGEYAVPVQEVAGKKQPHPLAGLAVLGIEGIGSTSLTPAALAALSGS********TGDDFVETEIVLTDDIAGCVIGKAGSRLLEIRQISGAQINIHTGTESHKKMFHIQGCQEAVSLAQYLINMCIELQ*****************AAISAFMTASVNSSLIEKPTPHPGSMVTLGGLSELLANIAASNVKST************
Transmembrane Helix (TMHMM)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (MEMSAT)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhhhhhoooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (MEMSAT_SVM)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooohhhhhhhhhhhhhhhhiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
TM Helix, Signal Peptide (Phobius)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
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Signal Peptide (SignalP NN Mode)
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Coiled Coils (COILS)
MDGNGDGKIDEDTLITMRCLFHSSVNVNEISCLIGPGGCIVRRLRKESGAKISITDGACPDRIVTVSGSVDNSSTSSVETGYPGHTLWVTSVDNVCTAYNFMCRSLEDYHINRNRMENCSPQPLQLKLVIPATHCGSLIGKGGCKIKDIRDLSGANVQVASDMLPMSTERIVTVHGNPDTISQAIYQICLVLIECTLQVVKGAVIPYEPKTMNAGPVILSGGQAYTLHGEYAVPVQEVAGKKQPHPLAGLAVLGIEGIGSTSLTPAALAALSGSRVKSGGKDTGDDFVETEIVLTDDIAGCVIGKAGSRLLEIRQISGAQINIHTGTESHKKMFHIQGCQEAVSLAQYLINMCIELQKNNTTNTSDNPEPADLDAAISAFMTASVNSSLIEKPTPHPGSMVTLGGLSELLANIAASNVKSTVQTTGAYRRDVE
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	433	2.2.26 [Sep-21-2011]
P57722	371	Poly(rC)-binding protein	yes	N/A	0.725	0.846	0.393	2e-59
P57721	371	Poly(rC)-binding protein	yes	N/A	0.718	0.838	0.394	2e-59
P57723	403	Poly(rC)-binding protein	no	N/A	0.752	0.808	0.368	2e-53
Q0VCU0	403	Poly(rC)-binding protein	no	N/A	0.752	0.808	0.365	1e-52
P57724	403	Poly(rC)-binding protein	no	N/A	0.720	0.774	0.368	4e-52
Q15366	365	Poly(rC)-binding protein	no	N/A	0.690	0.819	0.350	3e-50
Q61990	362	Poly(rC)-binding protein	no	N/A	0.688	0.823	0.347	4e-50
O19048	356	Poly(rC)-binding protein	no	N/A	0.704	0.856	0.350	4e-48
P60335	356	Poly(rC)-binding protein	no	N/A	0.704	0.856	0.350	4e-48
Q15365	356	Poly(rC)-binding protein	no	N/A	0.704	0.856	0.350	4e-48

>sp|P57722|PCBP3_MOUSE Poly(rC)-binding protein 3 OS=Mus musculus GN=Pcbp3 PE=2 SV=3

 Score =  230 bits (586), Expect = 2e-59,   Method: Compositional matrix adjust.
 Identities = 143/363 (39%), Positives = 201/363 (55%), Gaps = 49/363 (13%)

Query: 3   GNGDGKIDEDTL---ITMRCLFHSSVNVNEISCLIGPGGCIVRRLRKESGAKISITDGAC 59
           G  + K+ E  L   +T+R L H      E+  +IG  G  V+++R+ESGA+I+I++G C
Sbjct: 31  GKMESKVSEGGLNVTLTIRLLMHG----KEVGSIIGKKGETVKKMREESGARINISEGNC 86

Query: 60  PDRIVTVSGSVDNSSTSSVETGYPGHTLWVTSVDNVCTAYNFMCRSLEDYHINRNRMENC 119
           P+RIVT++G  D                       +  A+  +    E+  IN   M N 
Sbjct: 87  PERIVTITGPTDA----------------------IFKAFAMIAYKFEEDIINS--MSNS 122

Query: 120 ---SPQPLQLKLVIPATHCGSLIGKGGCKIKDIRDLSGANVQVASDMLPMSTERIVTVHG 176
              S  P+ L+LV+PA+ CGSLIGKGG KIK+IR+ +GA VQVA DMLP STER VT+ G
Sbjct: 123 PATSKPPVTLRLVVPASQCGSLIGKGGSKIKEIRESTGAQVQVAGDMLPNSTERAVTISG 182

Query: 177 NPDTISQAIYQICLVLIECTLQVVKGAVIPYEPKTMNAGPVILSGGQAYTLHGEYAVP-- 234
            PD I Q + QIC+V++E      KGA IPY PK  +  PVI +GGQAYT+ G+YA+P  
Sbjct: 183 TPDAIIQCVKQICVVMLESP---PKGATIPYRPKPAST-PVIFAGGQAYTIQGQYAIPHP 238

Query: 235 -----VQEVAGKKQPHPLAGLAVLGIEGIGSTSLTPAALAALSGSRVKSGGKDTGDDFVE 289
                + ++A ++ P P  G       G      +      L G   +S G D       
Sbjct: 239 DQLTKLHQLAMQQTPFPPLGQTNPAFPGEKLPLHSSEEAQNLMG---QSSGLDASPPAST 295

Query: 290 TEIVLTDDIAGCVIGKAGSRLLEIRQISGAQINIHTGTE-SHKKMFHIQGCQEAVSLAQY 348
            E+ + +D+ GC+IG+ G+++ EIRQ+SGAQI I   TE S ++   I G    +SLAQY
Sbjct: 296 HELTIPNDLIGCIIGRQGTKINEIRQMSGAQIKIANATEGSSERQITITGTPANISLAQY 355

Query: 349 LIN 351
           LIN
Sbjct: 356 LIN 358

Single-stranded nucleic acid binding protein that binds preferentially to oligo dC.
Mus musculus (taxid: 10090)

>sp|P57721|PCBP3_HUMAN Poly(rC)-binding protein 3 OS=Homo sapiens GN=PCBP3 PE=2 SV=2

 Score =  229 bits (585), Expect = 2e-59,   Method: Compositional matrix adjust.
 Identities = 142/360 (39%), Positives = 200/360 (55%), Gaps = 49/360 (13%)

Query: 6   DGKIDEDTL---ITMRCLFHSSVNVNEISCLIGPGGCIVRRLRKESGAKISITDGACPDR 62
           + K+ E  L   +T+R L H      E+  +IG  G  V+++R+ESGA+I+I++G CP+R
Sbjct: 34  ESKVSEGGLNVTLTIRLLMHG----KEVGSIIGKKGETVKKMREESGARINISEGNCPER 89

Query: 63  IVTVSGSVDNSSTSSVETGYPGHTLWVTSVDNVCTAYNFMCRSLEDYHINRNRMENC--- 119
           IVT++G  D                       +  A+  +    E+  IN   M N    
Sbjct: 90  IVTITGPTDA----------------------IFKAFAMIAYKFEEDIINS--MSNSPAT 125

Query: 120 SPQPLQLKLVIPATHCGSLIGKGGCKIKDIRDLSGANVQVASDMLPMSTERIVTVHGNPD 179
           S  P+ L+LV+PA+ CGSLIGKGG KIK+IR+ +GA VQVA DMLP STER VT+ G PD
Sbjct: 126 SKPPVTLRLVVPASQCGSLIGKGGSKIKEIRESTGAQVQVAGDMLPNSTERAVTISGTPD 185

Query: 180 TISQAIYQICLVLIECTLQVVKGAVIPYEPKTMNAGPVILSGGQAYTLHGEYAVP----- 234
            I Q + QIC+V++E      KGA IPY PK  +  PVI +GGQAYT+ G+YA+P     
Sbjct: 186 AIIQCVKQICVVMLESP---PKGATIPYRPKPAST-PVIFAGGQAYTIQGQYAIPHPDQL 241

Query: 235 --VQEVAGKKQPHPLAGLAVLGIEGIGSTSLTPAALAALSGSRVKSGGKDTGDDFVETEI 292
             + ++A ++ P P  G       G      +      L G   +S G D        E+
Sbjct: 242 TKLHQLAMQQTPFPPLGQTNPAFPGEKLPLHSSEEAQNLMG---QSSGLDASPPASTHEL 298

Query: 293 VLTDDIAGCVIGKAGSRLLEIRQISGAQINIHTGTE-SHKKMFHIQGCQEAVSLAQYLIN 351
            + +D+ GC+IG+ G+++ EIRQ+SGAQI I   TE S ++   I G    +SLAQYLIN
Sbjct: 299 TIPNDLIGCIIGRQGTKINEIRQMSGAQIKIANATEGSSERQITITGTPANISLAQYLIN 358

Single-stranded nucleic acid binding protein that binds preferentially to oligo dC.

Homo sapiens (taxid: 9606)

>sp|P57723|PCBP4_HUMAN Poly(rC)-binding protein 4 OS=Homo sapiens GN=PCBP4 PE=2 SV=1

 Score =  210 bits (534), Expect = 2e-53,   Method: Compositional matrix adjust.
 Identities = 145/394 (36%), Positives = 209/394 (53%), Gaps = 68/394 (17%)

Query: 1   MDGNGDGKIDEDTL---ITMRCLFHSSVNVNEISCLIGPGGCIVRRLRKESGAKISITDG 57
           M G+  G  +E  L   +T+R L H      E+  +IG  G  V+R+R++S A+I+I++G
Sbjct: 1   MSGSDGGLEEEPELSITLTLRMLMHG----KEVGSIIGKKGETVKRIREQSSARITISEG 56

Query: 58  ACPDRIVTVSGSVDNSSTSSVETGYPGHTLWVTSVDNVCTAYNFMCRSLEDYHINRNRME 117
           +CP+RI T++GS                           TA  F   S+  + ++ +   
Sbjct: 57  SCPERITTITGS---------------------------TAAVFHAVSMIAFKLDEDLCA 89

Query: 118 ------NCSPQPLQLKLVIPATHCGSLIGKGGCKIKDIRDLSGANVQVASDMLPMSTERI 171
                 N S  P+ L+LVIPA+ CGSLIGK G KIK+IR+ +GA VQVA D+LP STER 
Sbjct: 90  APANGGNVSRPPVTLRLVIPASQCGSLIGKAGTKIKEIRETTGAQVQVAGDLLPNSTERA 149

Query: 172 VTVHGNPDTISQAIYQICLVLIECTLQVVKGAVIPYEPKTMNAGPVILSGGQAYTLHGEY 231
           VTV G PD I   + QIC V++E      KGA IPY P +++ G V+LS  Q +++ G+Y
Sbjct: 150 VTVSGVPDAIILCVRQICAVILESP---PKGATIPYHP-SLSLGTVLLSANQGFSVQGQY 205

Query: 232 -AVPVQEVAGKKQPHPLAGLAVLGIEGIGSTSLTPAALAALSGSRVKSGGKDTGDDFVET 290
            AV   EV   +Q   L+  AV       + S+ P              G D G      
Sbjct: 206 GAVTPAEVTKLQQ---LSSHAV----PFATPSVVP--------------GLDPGTQTSSQ 244

Query: 291 EIVLTDDIAGCVIGKAGSRLLEIRQISGAQINIHTGTE-SHKKMFHIQGCQEAVSLAQYL 349
           E ++ +D+ GCVIG+ GS++ EIRQ+SGA I I    E + ++   I G   +++LAQYL
Sbjct: 245 EFLVPNDLIGCVIGRQGSKISEIRQMSGAHIKIGNQAEGAGERHVTITGSPVSIALAQYL 304

Query: 350 INMCIELQKNNTTNTSDNPEPADLDAAISAFMTA 383
           I  C+E  K+ +  T  +  PADL A  S  +TA
Sbjct: 305 ITACLETAKSTSGGTPSS-APADLPAPFSPPLTA 337

Single-stranded nucleic acid binding protein that binds preferentially to oligo dC.

Homo sapiens (taxid: 9606)

>sp|Q0VCU0|PCBP4_BOVIN Poly(rC)-binding protein 4 OS=Bos taurus GN=PCBP4 PE=2 SV=1

 Score =  207 bits (527), Expect = 1e-52,   Method: Compositional matrix adjust.
 Identities = 144/394 (36%), Positives = 207/394 (52%), Gaps = 68/394 (17%)

Query: 1   MDGNGDGKIDEDTL---ITMRCLFHSSVNVNEISCLIGPGGCIVRRLRKESGAKISITDG 57
           M G+  G  +E  L   +T+R L H      E+  +IG  G  V+R+R++S A+I+I++G
Sbjct: 1   MSGSDAGLEEEPELSITLTLRMLMHG----KEVGSIIGKKGETVKRIREQSSARITISEG 56

Query: 58  ACPDRIVTVSGSVDNSSTSSVETGYPGHTLWVTSVDNVCTAYNFMCRSLEDYHINRNRME 117
           +CP+RI T++GS                           TA  F   S+  + ++ +   
Sbjct: 57  SCPERITTITGS---------------------------TAAVFHAVSMIAFKLDEDLCA 89

Query: 118 ------NCSPQPLQLKLVIPATHCGSLIGKGGCKIKDIRDLSGANVQVASDMLPMSTERI 171
                 N S  P+ L+LVIPA+ CGSLIGK G KIK+IR+ +GA VQVA D+LP STER 
Sbjct: 90  APANGGNVSRPPVTLRLVIPASQCGSLIGKAGTKIKEIRETTGAQVQVAGDLLPNSTERA 149

Query: 172 VTVHGNPDTISQAIYQICLVLIECTLQVVKGAVIPYEPKTMNAGPVILSGGQAYTLHGEY 231
           VTV G PD I   + QIC V++E      KGA IPY P +++ G V+LS  Q +++ G+Y
Sbjct: 150 VTVSGVPDAIILCVRQICAVILESP---PKGATIPYHP-SLSLGTVLLSTNQGFSVQGQY 205

Query: 232 A-VPVQEVAGKKQPHPLAGLAVLGIEGIGSTSLTPAALAALSGSRVKSGGKDTGDDFVET 290
             V   EV   +Q   L+G AV       S S+ P              G D        
Sbjct: 206 GTVTPAEVTKLQQ---LSGHAV----PFASPSMVP--------------GLDPSTQTSSQ 244

Query: 291 EIVLTDDIAGCVIGKAGSRLLEIRQISGAQINIHTGTE-SHKKMFHIQGCQEAVSLAQYL 349
           E ++ +D+ GCVIG+ GS++ EIRQ+SGA I I    E + ++   I G   +++LAQYL
Sbjct: 245 EFLVPNDLIGCVIGRQGSKISEIRQMSGAHIKIGNQAEGAGERHVTITGSPVSIALAQYL 304

Query: 350 INMCIELQKNNTTNTSDNPEPADLDAAISAFMTA 383
           I  C+E  K+ +  T  +  P DL A  S  +TA
Sbjct: 305 ITACLETAKSTSGGTPGS-APTDLPAPFSPPLTA 337

Single-stranded nucleic acid binding protein that binds preferentially to oligo dC.

Bos taurus (taxid: 9913)

>sp|P57724|PCBP4_MOUSE Poly(rC)-binding protein 4 OS=Mus musculus GN=Pcbp4 PE=2 SV=1

 Score =  206 bits (523), Expect = 4e-52,   Method: Compositional matrix adjust.
 Identities = 139/377 (36%), Positives = 201/377 (53%), Gaps = 65/377 (17%)

Query: 15  ITMRCLFHSSVNVNEISCLIGPGGCIVRRLRKESGAKISITDGACPDRIVTVSGSVDNSS 74
           +T+R L H      E+  +IG  G  V+R+R++S A+I+I++G+CP+RI T++GS     
Sbjct: 18  LTLRMLMHG----KEVGSIIGKKGETVKRIREQSSARITISEGSCPERITTITGS----- 68

Query: 75  TSSVETGYPGHTLWVTSVDNVCTAYNFMCRSLEDYHINRNRME------NCSPQPLQLKL 128
                                 TA  F   S+  + ++ +         + S  P+ L+L
Sbjct: 69  ----------------------TAAVFHAVSMIAFKLDEDLCAAPANGGSVSRPPVTLRL 106

Query: 129 VIPATHCGSLIGKGGCKIKDIRDLSGANVQVASDMLPMSTERIVTVHGNPDTISQAIYQI 188
           VIPA+ CGSLIGK G KIK+IR+ +GA VQVA D+LP STER VTV G PD I   + QI
Sbjct: 107 VIPASQCGSLIGKAGTKIKEIRETTGAQVQVAGDLLPNSTERAVTVSGVPDAIILCVRQI 166

Query: 189 CLVLIECTLQVVKGAVIPYEPKTMNAGPVILSGGQAYTLHGEY-AVPVQEVAGKKQPHPL 247
           C V++E      KGA IPY P +++ G V+LS  Q +++ G+Y AV   EV   +Q   L
Sbjct: 167 CAVILESP---PKGATIPYHP-SLSLGTVLLSANQGFSVQGQYGAVTPAEVTKLQQ---L 219

Query: 248 AGLAVLGIEGIGSTSLTPAALAALSGSRVKSGGKDTGDDFVETEIVLTDDIAGCVIGKAG 307
           +G AV       S S+ P              G D        E ++ +D+ GCVIG+ G
Sbjct: 220 SGHAV----PFASPSVVP--------------GMDPSTQTSSQEFLVPNDLIGCVIGRQG 261

Query: 308 SRLLEIRQISGAQINIHTGTE-SHKKMFHIQGCQEAVSLAQYLINMCIELQKNNTTNTSD 366
           S++ EIRQ+SGA I I    E + ++   I G   +++LAQYLI  C+E  K+ +  T  
Sbjct: 262 SKISEIRQMSGAHIKIGNQAEGAGERHVTITGSPVSIALAQYLITACLETAKSTSGGTPG 321

Query: 367 NPEPADLDAAISAFMTA 383
           +  PADL    S  +TA
Sbjct: 322 S-APADLPTPFSPPLTA 337

Single-stranded nucleic acid binding protein that binds preferentially to oligo dC.

Mus musculus (taxid: 10090)

>sp|Q15366|PCBP2_HUMAN Poly(rC)-binding protein 2 OS=Homo sapiens GN=PCBP2 PE=1 SV=1

 Score =  199 bits (507), Expect = 3e-50,   Method: Compositional matrix adjust.
 Identities = 133/379 (35%), Positives = 196/379 (51%), Gaps = 80/379 (21%)

Query: 15  ITMRCLFHSSVNVNEISCLIGPGGCIVRRLRKESGAKISITDGACPDRIVTVSGSVDNSS 74
           +T+R L H      E+  +IG  G  V+++R+ESGA+I+I++G CP+RI+T++G      
Sbjct: 14  LTIRLLMHG----KEVGSIIGKKGESVKKMREESGARINISEGNCPERIITLAG------ 63

Query: 75  TSSVETGYPGHTLWVTSVDNVCTAYNFMCRSL-EDYHINRNRMENCSPQPLQLKLVIPAT 133
                             + +  A+  +   L ED   +       S  P+ L+LV+PA+
Sbjct: 64  ----------------PTNAIFKAFAMIIDKLEEDISSSMTNSTAASRPPVTLRLVVPAS 107

Query: 134 HCGSLIGKGGCKIKDIRDLSGANVQVASDMLPMSTERIVTVHGNPDTISQAIYQICLVLI 193
            CGSLIGKGGCKIK+IR+ +GA VQVA DMLP STER +T+ G P +I + + QIC+V++
Sbjct: 108 QCGSLIGKGGCKIKEIRESTGAQVQVAGDMLPNSTERAITIAGIPQSIIECVKQICVVML 167

Query: 194 ECTLQV-VKGAVIPYEPKTMNAGPVILSGGQ----------------------------- 223
           E   Q   KG  IPY PK  ++ PVI +GGQ                             
Sbjct: 168 ETLSQSPPKGVTIPYRPKP-SSSPVIFAGGQDRYSTGSDSASFPHTTPSMCLNPDLEGPP 226

Query: 224 --AYTLHGEYAVP------VQEVAGKKQPHPLAGLAVLGIEGIGSTSLTPAALAALSGSR 275
             AYT+ G+YA+P      + ++A ++   P+      G  GI S+S             
Sbjct: 227 LEAYTIQGQYAIPQPDLTKLHQLAMQQSHFPMTH-GNTGFSGIESSS-----------PE 274

Query: 276 VKS-GGKDTGDDFVETEIVLTDDIAGCVIGKAGSRLLEIRQISGAQINIHTGTE-SHKKM 333
           VK   G D        E+ + +D+ GC+IG+ G+++ EIRQ+SGAQI I    E S  + 
Sbjct: 275 VKGYWGLDASAQTTSHELTIPNDLIGCIIGRQGAKINEIRQMSGAQIKIANPVEGSTDRQ 334

Query: 334 FHIQGCQEAVSLAQYLINM 352
             I G   ++SLAQYLIN+
Sbjct: 335 VTITGSAASISLAQYLINV 353

Single-stranded nucleic acid binding protein that binds preferentially to oligo dC. Major cellular poly(rC)-binding protein. Binds also poly(rU). Negatively regulates cellular antiviral responses mediated by MAVS signaling. It acts as an adapter between MAVS and the E3 ubiquitin ligase ITCH, therefore triggering MAVS ubiquitinationa and degradation.

Homo sapiens (taxid: 9606)

>sp|Q61990|PCBP2_MOUSE Poly(rC)-binding protein 2 OS=Mus musculus GN=Pcbp2 PE=1 SV=1

 Score =  199 bits (506), Expect = 4e-50,   Method: Compositional matrix adjust.
 Identities = 131/377 (34%), Positives = 194/377 (51%), Gaps = 79/377 (20%)

Query: 15  ITMRCLFHSSVNVNEISCLIGPGGCIVRRLRKESGAKISITDGACPDRIVTVSGSVDNSS 74
           +T+R L H      E+  +IG  G  V+++R+ESGA+I+I++G CP+RI+T++G      
Sbjct: 14  LTIRLLMHG----KEVGSIIGKKGESVKKMREESGARINISEGNCPERIITLAG------ 63

Query: 75  TSSVETGYPGHTLWVTSVDNVCTAYNFMCRSL-EDYHINRNRMENCSPQPLQLKLVIPAT 133
                             + +  A+  +   L ED   +       S  P+ L+LV+PA+
Sbjct: 64  ----------------PTNAIFKAFAMIIDKLEEDISSSMTNSTAASRPPVTLRLVVPAS 107

Query: 134 HCGSLIGKGGCKIKDIRDLSGANVQVASDMLPMSTERIVTVHGNPDTISQAIYQICLVLI 193
            CGSLIGKGGCKIK+IR+ +GA VQVA DMLP STER +T+ G P +I + + QIC+V++
Sbjct: 108 QCGSLIGKGGCKIKEIRESTGAQVQVAGDMLPNSTERAITIAGIPQSIIECVKQICVVML 167

Query: 194 ECTLQVVKGAVIPYEPKTMNAGPVILSGGQ------------------------------ 223
           E      KG  IPY PK  ++ PVI +GGQ                              
Sbjct: 168 ESP---PKGVTIPYRPKP-SSSPVIFAGGQDRYSTGSDSASFPHTTPSMCLNPDLEGPPL 223

Query: 224 -AYTLHGEYAVP------VQEVAGKKQPHPLAGLAVLGIEGIGSTSLTPAALAALSGSRV 276
            AYT+ G+YA+P      + ++A ++   P+      G  GI S+S       A      
Sbjct: 224 EAYTIQGQYAIPQPDLTKLHQLAMQQSHFPMTH-GNTGFSGIESSSPEVKGYWA------ 276

Query: 277 KSGGKDTGDDFVETEIVLTDDIAGCVIGKAGSRLLEIRQISGAQINIHTGTE-SHKKMFH 335
              G D        E+ + +D+ GC+IG+ G+++ EIRQ+SGAQI I    E S  +   
Sbjct: 277 ---GLDASAQTTSHELTIPNDLIGCIIGRQGAKINEIRQMSGAQIKIANPVEGSTDRQVT 333

Query: 336 IQGCQEAVSLAQYLINM 352
           I G   ++SLAQYLIN+
Sbjct: 334 ITGSAASISLAQYLINV 350

Single-stranded nucleic acid binding protein that binds preferentially to oligo dC. Major cellular poly(rC)-binding protein. Binds also poly(rU). Negatively regulates cellular antiviral responses mediated by MAVS signaling. It acts as an adapter between MAVS and the E3 ubiquitin ligase ITCH, therefore triggering MAVS ubiquitinationa and degradation.

Mus musculus (taxid: 10090)

>sp|O19048|PCBP1_RABIT Poly(rC)-binding protein 1 OS=Oryctolagus cuniculus GN=PCBP1 PE=2 SV=1

 Score =  192 bits (488), Expect = 4e-48,   Method: Compositional matrix adjust.
 Identities = 132/377 (35%), Positives = 200/377 (53%), Gaps = 72/377 (19%)

Query: 15  ITMRCLFHSSVNVNEISCLIGPGGCIVRRLRKESGAKISITDGACPDRIVTVSGSVDNSS 74
           +T+R L H      E+  +IG  G  V+R+R+ESGA+I+I++G CP+RI+T++G  +   
Sbjct: 14  LTIRLLMHG----KEVGSIIGKKGESVKRIREESGARINISEGNCPERIITLTGPTNA-- 67

Query: 75  TSSVETGYPGHTLWVTSVDNVCTAYNFMCRSLE-DYHINRNRMENCSPQPLQLKLVIPAT 133
                               +  A+  +   LE D + +       S  P+ L+LV+PAT
Sbjct: 68  --------------------IFKAFAMIIDKLEEDINSSMTNSTAASRPPVTLRLVVPAT 107

Query: 134 HCGSLIGKGGCKIKDIRDLSGANVQVASDMLPMSTERIVTVHGNPDTISQAIYQICLVLI 193
            CGSLIGKGGCKIK+IR+ +GA VQVA DMLP STER +T+ G P ++++ + QICLV++
Sbjct: 108 QCGSLIGKGGCKIKEIRESTGAQVQVAGDMLPNSTERAITIAGVPQSVTECVKQICLVML 167

Query: 194 ECTLQVVKGAV--IPYEPKTMNAGPVILSGGQ----------------------AYTLHG 229
           E   Q  +G V  IPY+P   ++ PVI +GGQ                      AY++ G
Sbjct: 168 ETLSQSPQGRVMTIPYQPMPASS-PVICAGGQDRCSDAAGYPHATHDLEGPPLDAYSIQG 226

Query: 230 EYAVPVQEVA-----GKKQPHPLAGLAVLGIEGIGSTSLTPAALAALSGSRVKSGGKDTG 284
           ++ +   ++A      ++Q H        G  GI S+S             VK G   + 
Sbjct: 227 QHTISPLDLAKLNQVARQQSHFAMMHGGTGFAGIDSSS-----------PEVK-GYWASL 274

Query: 285 DDFVET--EIVLTDDIAGCVIGKAGSRLLEIRQISGAQINIHTGTE-SHKKMFHIQGCQE 341
           D   +T  E+ + +++ GC+IG+ G+ + EIRQ+SGAQI I    E S  +   I G   
Sbjct: 275 DASTQTTHELTIPNNLIGCIIGRQGANINEIRQMSGAQIKIANPVEGSSGRQVTITGSAA 334

Query: 342 AVSLAQYLINMCIELQK 358
           ++SLAQYLIN  +  +K
Sbjct: 335 SISLAQYLINARLSSEK 351

Single-stranded nucleic acid binding protein that binds preferentially to oligo dC.

Oryctolagus cuniculus (taxid: 9986)

>sp|P60335|PCBP1_MOUSE Poly(rC)-binding protein 1 OS=Mus musculus GN=Pcbp1 PE=1 SV=1

 Score =  192 bits (488), Expect = 4e-48,   Method: Compositional matrix adjust.
 Identities = 132/377 (35%), Positives = 200/377 (53%), Gaps = 72/377 (19%)

Query: 15  ITMRCLFHSSVNVNEISCLIGPGGCIVRRLRKESGAKISITDGACPDRIVTVSGSVDNSS 74
           +T+R L H      E+  +IG  G  V+R+R+ESGA+I+I++G CP+RI+T++G  +   
Sbjct: 14  LTIRLLMHG----KEVGSIIGKKGESVKRIREESGARINISEGNCPERIITLTGPTNA-- 67

Query: 75  TSSVETGYPGHTLWVTSVDNVCTAYNFMCRSLE-DYHINRNRMENCSPQPLQLKLVIPAT 133
                               +  A+  +   LE D + +       S  P+ L+LV+PAT
Sbjct: 68  --------------------IFKAFAMIIDKLEEDINSSMTNSTAASRPPVTLRLVVPAT 107

Query: 134 HCGSLIGKGGCKIKDIRDLSGANVQVASDMLPMSTERIVTVHGNPDTISQAIYQICLVLI 193
            CGSLIGKGGCKIK+IR+ +GA VQVA DMLP STER +T+ G P ++++ + QICLV++
Sbjct: 108 QCGSLIGKGGCKIKEIRESTGAQVQVAGDMLPNSTERAITIAGVPQSVTECVKQICLVML 167

Query: 194 ECTLQVVKGAV--IPYEPKTMNAGPVILSGGQ----------------------AYTLHG 229
           E   Q  +G V  IPY+P   ++ PVI +GGQ                      AY++ G
Sbjct: 168 ETLSQSPQGRVMTIPYQPMPASS-PVICAGGQDRCSDAAGYPHATHDLEGPPLDAYSIQG 226

Query: 230 EYAVPVQEVA-----GKKQPHPLAGLAVLGIEGIGSTSLTPAALAALSGSRVKSGGKDTG 284
           ++ +   ++A      ++Q H        G  GI S+S             VK G   + 
Sbjct: 227 QHTISPLDLAKLNQVARQQSHFAMMHGGTGFAGIDSSS-----------PEVK-GYWASL 274

Query: 285 DDFVET--EIVLTDDIAGCVIGKAGSRLLEIRQISGAQINIHTGTE-SHKKMFHIQGCQE 341
           D   +T  E+ + +++ GC+IG+ G+ + EIRQ+SGAQI I    E S  +   I G   
Sbjct: 275 DASTQTTHELTIPNNLIGCIIGRQGANINEIRQMSGAQIKIANPVEGSSGRQVTITGSAA 334

Query: 342 AVSLAQYLINMCIELQK 358
           ++SLAQYLIN  +  +K
Sbjct: 335 SISLAQYLINARLSSEK 351

Single-stranded nucleic acid binding protein that binds preferentially to oligo dC.

Mus musculus (taxid: 10090)

>sp|Q15365|PCBP1_HUMAN Poly(rC)-binding protein 1 OS=Homo sapiens GN=PCBP1 PE=1 SV=2

 Score =  192 bits (488), Expect = 4e-48,   Method: Compositional matrix adjust.
 Identities = 132/377 (35%), Positives = 200/377 (53%), Gaps = 72/377 (19%)

Query: 15  ITMRCLFHSSVNVNEISCLIGPGGCIVRRLRKESGAKISITDGACPDRIVTVSGSVDNSS 74
           +T+R L H      E+  +IG  G  V+R+R+ESGA+I+I++G CP+RI+T++G  +   
Sbjct: 14  LTIRLLMHG----KEVGSIIGKKGESVKRIREESGARINISEGNCPERIITLTGPTNA-- 67

Query: 75  TSSVETGYPGHTLWVTSVDNVCTAYNFMCRSLE-DYHINRNRMENCSPQPLQLKLVIPAT 133
                               +  A+  +   LE D + +       S  P+ L+LV+PAT
Sbjct: 68  --------------------IFKAFAMIIDKLEEDINSSMTNSTAASRPPVTLRLVVPAT 107

Query: 134 HCGSLIGKGGCKIKDIRDLSGANVQVASDMLPMSTERIVTVHGNPDTISQAIYQICLVLI 193
            CGSLIGKGGCKIK+IR+ +GA VQVA DMLP STER +T+ G P ++++ + QICLV++
Sbjct: 108 QCGSLIGKGGCKIKEIRESTGAQVQVAGDMLPNSTERAITIAGVPQSVTECVKQICLVML 167

Query: 194 ECTLQVVKGAV--IPYEPKTMNAGPVILSGGQ----------------------AYTLHG 229
           E   Q  +G V  IPY+P   ++ PVI +GGQ                      AY++ G
Sbjct: 168 ETLSQSPQGRVMTIPYQPMPASS-PVICAGGQDRCSDAAGYPHATHDLEGPPLDAYSIQG 226

Query: 230 EYAVPVQEVA-----GKKQPHPLAGLAVLGIEGIGSTSLTPAALAALSGSRVKSGGKDTG 284
           ++ +   ++A      ++Q H        G  GI S+S             VK G   + 
Sbjct: 227 QHTISPLDLAKLNQVARQQSHFAMMHGGTGFAGIDSSS-----------PEVK-GYWASL 274

Query: 285 DDFVET--EIVLTDDIAGCVIGKAGSRLLEIRQISGAQINIHTGTE-SHKKMFHIQGCQE 341
           D   +T  E+ + +++ GC+IG+ G+ + EIRQ+SGAQI I    E S  +   I G   
Sbjct: 275 DASTQTTHELTIPNNLIGCIIGRQGANINEIRQMSGAQIKIANPVEGSSGRQVTITGSAA 334

Query: 342 AVSLAQYLINMCIELQK 358
           ++SLAQYLIN  +  +K
Sbjct: 335 SISLAQYLINARLSSEK 351

Single-stranded nucleic acid binding protein that binds preferentially to oligo dC.

Homo sapiens (taxid: 9606)

Close Homologs in the Non-Redundant Database Detected by BLAST

Original result of BLAST against Nonredundant Database

GI	Length	Definition	Q cover	H cover	Identity	E-value
Query	433
116007842	539	mushroom-body expressed, isoform D [Dros	0.739	0.593	0.408	7e-65
195377361	589	GJ11921 [Drosophila virilis] gi|19415461	0.736	0.541	0.407	2e-64
189234912	446	PREDICTED: similar to AGAP004942-PA [Tri	0.914	0.887	0.386	1e-63
328720738	436	PREDICTED: poly(rC)-binding protein 3-li	0.859	0.853	0.348	5e-63
328778258	466	PREDICTED: poly(rC)-binding protein 3-li	0.743	0.690	0.427	3e-62
307199010	469	Poly(rC)-binding protein 3 [Harpegnathos	0.759	0.701	0.435	4e-62
350405177	466	PREDICTED: poly(rC)-binding protein 3-li	0.743	0.690	0.424	7e-62
340726176	466	PREDICTED: poly(rC)-binding protein 3-li	0.741	0.688	0.426	7e-62
345486914	476	PREDICTED: poly(rC)-binding protein 3-li	0.780	0.710	0.432	1e-61
45553235	364	mushroom-body expressed, isoform C [Dros	0.732	0.870	0.401	1e-61

>gi|116007842|ref|NP_001036619.1| mushroom-body expressed, isoform D [Drosophila melanogaster] gi|113194920|gb|ABI31266.1| mushroom-body expressed, isoform D [Drosophila melanogaster]

 Score =  254 bits (649), Expect = 7e-65,   Method: Compositional matrix adjust.
 Identities = 146/357 (40%), Positives = 207/357 (57%), Gaps = 37/357 (10%)

Query: 10  DEDTLITMRCLFHSSVNVNEISCLIGPGGCIVRRLRKESGAKISITDGACPDRIVTVSGS 69
           D    +T+R +        E+  +IG  G IV R R+ESGAKI+I+DG+CP+RIVTVSG+
Sbjct: 19  DPSVTLTIRLIMQGK----EVGSIIGKKGEIVNRFREESGAKINISDGSCPERIVTVSGT 74

Query: 70  VDNSSTSSVETGYPGHTLWVTSVDNVCTAYNFMCRSLEDYHINRNRMENCSPQPLQLKLV 129
            +                       + +A+  + +  E++    N +       + ++L+
Sbjct: 75  TNA----------------------IFSAFTLITKKFEEWCSQFNDVGKVGKTQIPIRLI 112

Query: 130 IPATHCGSLIGKGGCKIKDIRDLSGANVQVASDMLPMSTERIVTVHGNPDTISQAIYQIC 189
           +PA+ CGSLIGK G KIK+IR  +G ++QVAS+MLP STER VT+ G+ + I+Q IYQIC
Sbjct: 113 VPASQCGSLIGKSGSKIKEIRQTTGCSIQVASEMLPNSTERAVTLSGSAEQITQCIYQIC 172

Query: 190 LVLIECTLQVVKGAVIPYEPKTMNAGPVILSGGQAYTLHGEYAVPVQEVAGKKQPHPLAG 249
           LV++E      +GA IPY PK    GPVIL+ GQA+T+ G YAVP QEVA  K P     
Sbjct: 173 LVMLESP---PRGATIPYRPKPQVTGPVILANGQAFTIQGNYAVPTQEVA--KNPLASLA 227

Query: 250 LAVLGIEGIGSTSLT--PAALAALSGSRVKSGGKDTGDDFVETEIVLTDDIAGCVIGKAG 307
              L      ST      AALAAL+GS++++          + E+ +++D+ GC+IGK G
Sbjct: 228 ALGLAGMNPASTGGINHTAALAALAGSQLRTANPANRAQQQQHEMTVSNDLIGCIIGKGG 287

Query: 308 SRLLEIRQISGAQINIHTGTESH----KKMFHIQGCQEAVSLAQYLINMCIELQKNN 360
           +++ EIRQISGA I I    E       +   I G  ++V+LAQYLINM +ELQK N
Sbjct: 288 TKIAEIRQISGAMIRISNCEEREGGNTDRTITISGNPDSVALAQYLINMSVELQKAN 344

Source: Drosophila melanogaster

Species: Drosophila melanogaster

Genus: Drosophila

Family: Drosophilidae

Order: Diptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|195377361|ref|XP_002047459.1| GJ11921 [Drosophila virilis] gi|194154617|gb|EDW69801.1| GJ11921 [Drosophila virilis]

 Score =  253 bits (645), Expect = 2e-64,   Method: Compositional matrix adjust.
 Identities = 145/356 (40%), Positives = 208/356 (58%), Gaps = 37/356 (10%)

Query: 10  DEDTLITMRCLFHSSVNVNEISCLIGPGGCIVRRLRKESGAKISITDGACPDRIVTVSGS 69
           D    +T+R +        E+  +IG  G IV R R+ESGAKI+I+DG+CP+RIVTVSG+
Sbjct: 19  DPSVTLTIRLIMQG----KEVGSIIGKKGEIVNRFREESGAKINISDGSCPERIVTVSGT 74

Query: 70  VDNSSTSSVETGYPGHTLWVTSVDNVCTAYNFMCRSLEDYHINRNRMENCSPQPLQLKLV 129
            +                       + +A+  + +  E++    N +       + ++L+
Sbjct: 75  TNA----------------------IFSAFTLITKKFEEWCSQFNDVGKVGKTQIPIRLI 112

Query: 130 IPATHCGSLIGKGGCKIKDIRDLSGANVQVASDMLPMSTERIVTVHGNPDTISQAIYQIC 189
           +PA+ CGSLIGK G KIK+IR  +G ++QVAS+MLP STER VT+ G+ + I+Q IYQIC
Sbjct: 113 VPASQCGSLIGKSGSKIKEIRQTTGCSIQVASEMLPNSTERAVTLSGSAEQITQCIYQIC 172

Query: 190 LVLIECTLQVVKGAVIPYEPKTMNAGPVILSGGQAYTLHGEYAVPVQEVAGKKQPHPLAG 249
           LV++E      +GA IPY PK    GPVIL+ GQA+T+ G YAVP QEVA  K P     
Sbjct: 173 LVMLESP---PRGATIPYRPKPQVTGPVILANGQAFTIQGNYAVPTQEVA--KNPLASLA 227

Query: 250 LAVLGIEGIGST-SLTPAALAALSGSRVKSGGKDTGDDFVETEIVLTDDIAGCVIGKAGS 308
              L      ST  +   ALAAL+GS++++   +      + E+ +++D+ GC+IGK G+
Sbjct: 228 ALGLAGMTPASTGGINHTALAALAGSQLRTANANRAQQ-QQHEMTVSNDLIGCIIGKGGT 286

Query: 309 RLLEIRQISGAQINIHTGTESH----KKMFHIQGCQEAVSLAQYLINMCIELQKNN 360
           ++ EIRQISGA I I    E       +   I G  ++V+LAQYLINM +ELQK N
Sbjct: 287 KIAEIRQISGAMIRISNCEEREGGNTDRTITISGNPDSVALAQYLINMSVELQKAN 342

Source: Drosophila virilis

Species: Drosophila virilis

Genus: Drosophila

Family: Drosophilidae

Order: Diptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|189234912|ref|XP_969611.2| PREDICTED: similar to AGAP004942-PA [Tribolium castaneum]

 Score =  250 bits (638), Expect = 1e-63,   Method: Compositional matrix adjust.
 Identities = 172/445 (38%), Positives = 250/445 (56%), Gaps = 49/445 (11%)

Query: 1   MDGNGDGKIDEDT--LITMRCLFHSSVNVNEISCLIGPGGCIVRRLRKESGAKISITDGA 58
           MD +    I++D+   +T+R +        E+  +IG  G IV+R R+ESGAKI+I+DG+
Sbjct: 1   MDMDNKNMINDDSNVTLTIRLIMQGK----EVGSIIGKKGEIVKRFREESGAKINISDGS 56

Query: 59  CPDRIVTVSGSVDNSSTSSVETGYPGHTLWVTSVDNVCTAYNFMCRSLEDYHINRNRMEN 118
           CP+RIVTV+GS +                       +  A+  +C+  E++    +    
Sbjct: 57  CPERIVTVTGSTNA----------------------IFKAFTLICKKFEEFQDINSGGSG 94

Query: 119 CSPQPLQLKLVIPATHCGSLIGKGGCKIKDIRDLSGANVQVASDMLPMSTERIVTVHGNP 178
               P+ L+L++PA+ CGSLIGKGG KIK+IR+++GA++QVAS+MLP STER VT+ G  
Sbjct: 95  VPRPPITLRLIVPASQCGSLIGKGGSKIKEIREVTGASIQVASEMLPNSTERAVTISGTG 154

Query: 179 DTISQAIYQICLVLIECTLQVVKGAVIPYEPKTMNAGPVILSGGQAYTLHGEYAVPVQ-- 236
           + I+Q IY IC V++E      KGA IPY PK    GPVIL+GGQAYT+ G YAVP    
Sbjct: 155 EAITQCIYHICTVMLESP---PKGATIPYRPKPQVGGPVILAGGQAYTIQGNYAVPAHTD 211

Query: 237 -EVAGKKQPHPLAGLAVLGIEGIGSTSLTPAALAALSGSRVK-SGGKDTGDDFVET-EIV 293
               GK     LA L + G+    +  L PAALAAL+GS+++ S  ++  +   +T E+ 
Sbjct: 212 MSALGKSPLAGLAALGLGGLAPTNTGGLNPAALAALAGSQLRTSNSRNQQNSNQQTHEMT 271

Query: 294 LTDDIAGCVIGKAGSRLLEIRQISGAQINIHTGTESHK----KMFHIQGCQEAVSLAQYL 349
           + +++ GC+IGK G+++ EIRQISGA I I    +       +   I G  +AV+LAQYL
Sbjct: 272 VPNELIGCIIGKGGTKIAEIRQISGAMIRISNCDDRESGVTDRTITISGNPDAVALAQYL 331

Query: 350 INMCIELQKNN--TTNTSDNPEPADLDAAISAFMTASVNSSLIEKPTPHPGSMVTLGGLS 407
           INM +ELQK N    N+      +    A S   +A   + L+ K    PG++  L  LS
Sbjct: 332 INMSVELQKANLEAQNSPSTGGSSQSSTAASPLASAIPLAQLLAK----PGALNALTSLS 387

Query: 408 ELLANIAASNVKS---TVQTTGAYR 429
            L         ++    VQTTG +R
Sbjct: 388 ALGGLTELLGGQAGAPPVQTTGVHR 412

Source: Tribolium castaneum

Species: Tribolium castaneum

Genus: Tribolium

Family: Tenebrionidae

Order: Coleoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|328720738|ref|XP_001949210.2| PREDICTED: poly(rC)-binding protein 3-like [Acyrthosiphon pisum]

 Score =  248 bits (633), Expect = 5e-63,   Method: Compositional matrix adjust.
 Identities = 153/439 (34%), Positives = 245/439 (55%), Gaps = 67/439 (15%)

Query: 12  DTLITMRCLFHSSVNVNEISCLIGPGGCIVRRLRKESGAKISITDGACPDRIVTVSGSVD 71
           D  +T+R LFH      E+  +IG GG  V+ +R +SGA++ I+DG+ P+RIVT++G+ +
Sbjct: 18  DVNLTIRILFHG----REVGNVIGKGGETVKNIRDQSGARVLISDGSTPERIVTITGTTN 73

Query: 72  NSSTSSVETGYPGHTLWVTSVDNVCTAYNFMCRSLEDYHINRNRMENCSPQPLQLKLVIP 131
                                  +C A   +   +E++   +N   N    PL  KL++P
Sbjct: 74  A----------------------ICKATELIGLKVEEFFERQNGDWNGPKAPLTFKLIVP 111

Query: 132 ATHCGSLIGKGGCKIKDIRDLSGANVQVASDMLPMSTERIVTVHGNPDTISQAIYQICLV 191
           A+ CG +IGKGGCKIK+IR+ SGA +QVASDMLP STER+V++ G   TISQ +YQ+C V
Sbjct: 112 ASQCGFIIGKGGCKIKEIRESSGAAIQVASDMLPNSTERLVSITGTTGTISQCVYQVCNV 171

Query: 192 LIECTLQVVKGAVIPYEPKTMNAGPVILSGGQAYTLHGEYAVPVQEVAGKKQPHPLAGLA 251
           L++      + A IPY+P++  +G    + G  +              G+++ +PLA LA
Sbjct: 172 LLDSP---PRSATIPYDPRSKTSGFASSAVGNDF--------------GRQRTNPLASLA 214

Query: 252 VLGIEGIGSTSLTPAALAALSGSRVKSGGKDTGDDFVE---------TEIV---LTDDIA 299
            LG+    +  + PAALAAL+GS++++G +   +   E         TE +   + +D+ 
Sbjct: 215 ALGLGTASTGGINPAALAALAGSQLRTGNRQNRNGSGEHKNQNSNSNTETISMTVPNDLI 274

Query: 300 GCVIGKAGSRLLEIRQISGAQINIHTGTESHK------KMFHIQGCQEAVSLAQYLINMC 353
           GCVIG+ GS++ EIRQISGA ++I  G  +H+      +   I G ++++S+A+YLI M 
Sbjct: 275 GCVIGRRGSKIAEIRQISGALVHIAKGEGTHENGENEDRHITITGNKDSISVAKYLIEMS 334

Query: 354 IELQKNNTTNTSDNPEPADLDAAISAFMTASVN-SSLIEKPTP--HPGSMVTLGGLSELL 410
           +ELQK    N      P  L    ++ +++++  + L  KP       S+  LGGL++LL
Sbjct: 335 VELQK---ANLEGQTHPLVLTMVAASPLSSAIPLAQLFAKPGAINALSSLSALGGLTDLL 391

Query: 411 ANIAASNVKSTVQTTGAYR 429
             ++ +N    +QTTG +R
Sbjct: 392 GALSGANQSPPIQTTGVHR 410

Source: Acyrthosiphon pisum

Species: Acyrthosiphon pisum

Genus: Acyrthosiphon

Family: Aphididae

Order: Hemiptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|328778258|ref|XP_391921.3| PREDICTED: poly(rC)-binding protein 3-like [Apis mellifera]

 Score =  245 bits (626), Expect = 3e-62,   Method: Compositional matrix adjust.
 Identities = 156/365 (42%), Positives = 222/365 (60%), Gaps = 43/365 (11%)

Query: 10  DEDTLITMRCLFHSSVNVNEISCLIGPGGCIVRRLRKESGAKISITDGACPDRIVTVSGS 69
           D    +T+R +        E+  +IG  G IV+R R+ESGAKI+I+DG+CP+RIVTV+G 
Sbjct: 13  DPSVTLTIRLIMQG----KEVGSIIGKKGEIVKRFREESGAKINISDGSCPERIVTVTGP 68

Query: 70  VDNSSTSSVETGYPGHTLWVTSVDNVCTAYNFMCRSLEDYHINRNRMENCS--PQP-LQL 126
            ++                      +  A+  +C+  E++    + ++     P+P + L
Sbjct: 69  TNS----------------------IFKAFTLICKKFEEWCSQFHDIQGSGGVPRPPITL 106

Query: 127 KLVIPATHCGSLIGKGGCKIKDIRDLSGANVQVASDMLPMSTERIVTVHGNPDTISQAIY 186
           +L++PA+ CGSLIGKGG KIK+IR+++GA++QVASDMLP STER VT+ G  + I+Q IY
Sbjct: 107 RLIVPASQCGSLIGKGGSKIKEIREVTGASIQVASDMLPNSTERAVTISGTSEAITQCIY 166

Query: 187 QICLVLIECTLQVVKGAVIPYEPKTMNAGPVILSGGQAYTLHGEYAVPVQEVAGKKQPHP 246
            IC V++E      KGA IPY PK    GPVIL+GGQAYT+ G YAVP     GK   +P
Sbjct: 167 HICCVMLESP---PKGATIPYRPKPQVGGPVILAGGQAYTIQGNYAVPAHSDMGKLGSNP 223

Query: 247 LAGLAVLGIEGIGSTS----LTPAALAALSGSRVKSGGKDTGDDFVET---EIVLTDDIA 299
           LAGLA LG+ G+ + +    L PAALAAL+GS++++   +           E+ + +++ 
Sbjct: 224 LAGLAALGLGGLATPANTGGLNPAALAALAGSQLRTSNTNRQQPAANNQTHEMTVPNELI 283

Query: 300 GCVIGKAGSRLLEIRQISGAQINIHTGTESH----KKMFHIQGCQEAVSLAQYLINMCIE 355
           GC+IGK G+++ EIRQISGA I I    E       +   I G  +AVSLAQYLI+M +E
Sbjct: 284 GCIIGKGGTKIAEIRQISGAMIRISNCEEREGGATDRTITITGNPDAVSLAQYLISMSVE 343

Query: 356 LQKNN 360
           LQK N
Sbjct: 344 LQKAN 348

Source: Apis mellifera

Species: Apis mellifera

Genus: Apis

Family: Apidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|307199010|gb|EFN79734.1| Poly(rC)-binding protein 3 [Harpegnathos saltator]

 Score =  244 bits (624), Expect = 4e-62,   Method: Compositional matrix adjust.
 Identities = 158/363 (43%), Positives = 218/363 (60%), Gaps = 34/363 (9%)

Query: 10  DEDTLITMRCLFHSSVNVNEISCLIGPGGCIVRRLRKESGAKISITDGACPDRIVTVSGS 69
           D    +T+R +        E+  +IG  G IV+R R+ESGAKI+I+DG+CP+RIVTV+G 
Sbjct: 10  DPSVTLTIRLIMQG----KEVGSIIGKKGEIVKRFREESGAKINISDGSCPERIVTVTGP 65

Query: 70  VDNSSTSSVETGYPGHTLWVTSVDNVCTAYNFMCRSLEDYHINRNRMEN-CSPQPLQLKL 128
                T+S+   +   TL       +C  +   C    D            S  P+ L+L
Sbjct: 66  -----TNSI---FKAFTL-------ICKKFEEWCSQFHDIQGGGAGGGGGVSRPPITLRL 110

Query: 129 VIPATHCGSLIGKGGCKIKDIRDLSGANVQVASDMLPMSTERIVTVHGNPDTISQAIYQI 188
           ++PA+ CGSLIGKGG KIK+IR+++GA++QVAS+MLP STER VT+ G  + I+Q IY I
Sbjct: 111 IVPASQCGSLIGKGGSKIKEIREVTGASIQVASEMLPNSTERAVTISGTSEAITQCIYHI 170

Query: 189 CLVLIECTLQVVKGAVIPYEPKTMNAGPVILSGGQAYTLHGEYAVPVQEVAGKKQPHPLA 248
           C V++E      KGA IPY PK    GPVIL+GGQAYT+ G YAVP     GK   +PLA
Sbjct: 171 CCVMLESP---PKGATIPYRPKPQVGGPVILAGGQAYTIQGNYAVPAHSDMGKLGSNPLA 227

Query: 249 GLAVLGIEGIGSTS----LTPAALAALSGSRVKSGGKDTGDDFVET---EIVLTDDIAGC 301
            LA LG+ G+ + +    L PAALAAL+GS++++   +           E+ + +++ GC
Sbjct: 228 SLAALGLGGLATPANTGGLNPAALAALAGSQLRTSNTNRQQPAANNQTHEMTVPNELIGC 287

Query: 302 VIGKAGSRLLEIRQISGAQINIHTGTESH----KKMFHIQGCQEAVSLAQYLINMCIELQ 357
           +IGK G+++ EIRQISGA I I    E       +   I G  +AV+LAQYLINM +ELQ
Sbjct: 288 IIGKGGTKIAEIRQISGAMIRISNCEEREGGATDRTITITGNPDAVALAQYLINMSVELQ 347

Query: 358 KNN 360
           K N
Sbjct: 348 KAN 350

Source: Harpegnathos saltator

Species: Harpegnathos saltator

Genus: Harpegnathos

Family: Formicidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|350405177|ref|XP_003487350.1| PREDICTED: poly(rC)-binding protein 3-like [Bombus impatiens]

 Score =  244 bits (623), Expect = 7e-62,   Method: Compositional matrix adjust.
 Identities = 155/365 (42%), Positives = 222/365 (60%), Gaps = 43/365 (11%)

Query: 10  DEDTLITMRCLFHSSVNVNEISCLIGPGGCIVRRLRKESGAKISITDGACPDRIVTVSGS 69
           D    +T+R +        E+  +IG  G IV+R R+ESGAKI+I+DG+CP+RIVTV+G 
Sbjct: 13  DPSVTLTIRLIMQG----KEVGSIIGKKGEIVKRFREESGAKINISDGSCPERIVTVTGP 68

Query: 70  VDNSSTSSVETGYPGHTLWVTSVDNVCTAYNFMCRSLEDYHINRNRMENCS--PQP-LQL 126
            ++                      +  A+  +C+  E++    + ++     P+P + L
Sbjct: 69  TNS----------------------IFKAFTLICKKFEEWCSQFHDIQGSGGVPRPPITL 106

Query: 127 KLVIPATHCGSLIGKGGCKIKDIRDLSGANVQVASDMLPMSTERIVTVHGNPDTISQAIY 186
           +L++PA+ CGSLIGKGG KIK+IR+++GA++QVASDMLP STER VT+ G  + I+Q IY
Sbjct: 107 RLIVPASQCGSLIGKGGSKIKEIREVTGASIQVASDMLPNSTERAVTISGTSEAITQCIY 166

Query: 187 QICLVLIECTLQVVKGAVIPYEPKTMNAGPVILSGGQAYTLHGEYAVPVQEVAGKKQPHP 246
            IC V++E      KGA IPY PK    GPVIL+GGQAYT+ G YAVP     GK   +P
Sbjct: 167 HICCVMLESP---PKGATIPYRPKPQVGGPVILAGGQAYTIQGNYAVPAHSDMGKLGSNP 223

Query: 247 LAGLAVLGIEGIGSTS----LTPAALAALSGSRVKSGGKDTGDDFVET---EIVLTDDIA 299
           LAGLA LG+ G+ + +    L PAALAAL+GS++++   +           E+ + +++ 
Sbjct: 224 LAGLAALGLGGLATPANTGGLNPAALAALAGSQLRTSNTNRQQPAANNQTHEMTVPNELI 283

Query: 300 GCVIGKAGSRLLEIRQISGAQINIHTGTESH----KKMFHIQGCQEAVSLAQYLINMCIE 355
           GC+IGK G+++ EIRQISGA I I    E       +   I G  +AV+LAQYLI+M +E
Sbjct: 284 GCIIGKGGTKIAEIRQISGAMIRISNCEEREGGATDRTITITGNPDAVALAQYLISMSVE 343

Query: 356 LQKNN 360
           LQK N
Sbjct: 344 LQKAN 348

Source: Bombus impatiens

Species: Bombus impatiens

Genus: Bombus

Family: Apidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|340726176|ref|XP_003401437.1| PREDICTED: poly(rC)-binding protein 3-like [Bombus terrestris]

 Score =  244 bits (623), Expect = 7e-62,   Method: Compositional matrix adjust.
 Identities = 156/366 (42%), Positives = 225/366 (61%), Gaps = 45/366 (12%)

Query: 10  DEDTLITMRCLFHSSVNVNEISCLIGPGGCIVRRLRKESGAKISITDGACPDRIVTVSGS 69
           D    +T+R +        E+  +IG  G IV+R R+ESGAKI+I+DG+CP+RIVTV+G 
Sbjct: 13  DPSVTLTIRLIMQG----KEVGSIIGKKGEIVKRFREESGAKINISDGSCPERIVTVTGP 68

Query: 70  VDNSSTSSVETGYPGHTLWVTSVDNVCTAYNFMCRSLEDYHINRNRMENCS--PQP-LQL 126
            ++                      +  A+  +C+  E++    + ++     P+P + L
Sbjct: 69  TNS----------------------IFKAFTLICKKFEEWCSQFHDIQGSGGVPRPPITL 106

Query: 127 KLVIPATHCGSLIGKGGCKIKDIRDLSGANVQVASDMLPMSTERIVTVHGNPDTISQAIY 186
           +L++PA+ CGSLIGKGG KIK+IR+++GA++QVASDMLP STER VT+ G  + I+Q IY
Sbjct: 107 RLIVPASQCGSLIGKGGSKIKEIREVTGASIQVASDMLPNSTERAVTISGTSEAITQCIY 166

Query: 187 QICLVLIECTLQVVKGAVIPYEPKTMNAGPVILSGGQAYTLHGEYAVPVQEVAGKKQPHP 246
            IC V++E      KGA IPY PK    GPVIL+GGQAYT+ G YAVP     GK   +P
Sbjct: 167 HICCVMLESP---PKGATIPYRPKPQVGGPVILAGGQAYTIQGNYAVPAHSDMGKLGSNP 223

Query: 247 LAGLAVLGIEGIGSTS----LTPAALAALSGSRVKSGGKD----TGDDFVETEIVLTDDI 298
           LAGLA LG+ G+ + +    L PAALAAL+GS++++   +     G++    E+ + +++
Sbjct: 224 LAGLAALGLGGLATPANTGGLNPAALAALAGSQLRTSNTNRQQPAGNNQTH-EMTVPNEL 282

Query: 299 AGCVIGKAGSRLLEIRQISGAQINIHTGTESH----KKMFHIQGCQEAVSLAQYLINMCI 354
            GC+IGK G+++ EIRQISGA I I    E       +   I G  +AV+LAQYLI+M +
Sbjct: 283 IGCIIGKGGTKIAEIRQISGAMIRISNCEEREGGATDRTITITGNPDAVALAQYLISMSV 342

Query: 355 ELQKNN 360
           ELQK N
Sbjct: 343 ELQKAN 348

Source: Bombus terrestris

Species: Bombus terrestris

Genus: Bombus

Family: Apidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|345486914|ref|XP_001607400.2| PREDICTED: poly(rC)-binding protein 3-like [Nasonia vitripennis]

 Score =  243 bits (621), Expect = 1e-61,   Method: Compositional matrix adjust.
 Identities = 162/375 (43%), Positives = 227/375 (60%), Gaps = 37/375 (9%)

Query: 1   MDGNGDGKIDEDTLITM--RCLFHSSVNVNEISCLIGPGGCIVRRLRKESGAKISITDGA 58
           MDGN    +++D  +T+  R +        E+  +IG  G IV+R R+ESGAKI+I+DG+
Sbjct: 4   MDGNNKPVLNDDPSVTLTIRLIMQG----KEVGSIIGKKGEIVKRFREESGAKINISDGS 59

Query: 59  CPDRIVTVSGSVDNSSTSSVETGYPGHTLWVTSVDNVCTAYNFMCRSLEDYHINRNRMEN 118
           CP+RIVTV+G      T+S+   +   TL       +C  +   C    D     N    
Sbjct: 60  CPERIVTVTGP-----TNSI---FKAFTL-------ICKKFEEWCSQFHDIQGGGNAGGG 104

Query: 119 CS-PQP-LQLKLVIPATHCGSLIGKGGCKIKDIRDLSGANVQVASDMLPMSTERIVTVHG 176
              P+P + L+L++PA+ CGSLIGKGG KIK+IR+++GA++QVAS+MLP STER VT+ G
Sbjct: 105 GGVPRPPITLRLIVPASQCGSLIGKGGSKIKEIREVTGASIQVASEMLPNSTERAVTISG 164

Query: 177 NPDTISQAIYQICLVLIECTLQVVKGAVIPYEPKTMNAGPVILSGGQAYTLHGEYAVPVQ 236
             + I+Q IY IC V++E      KGA IPY PK    GPVIL+GGQA+T+ G YAVP  
Sbjct: 165 TSEAITQCIYHICCVMLESP---PKGATIPYRPKPQVGGPVILAGGQAFTIQGNYAVPAH 221

Query: 237 EVAGKKQPHPLAGLAVLGIEGIGSTS----LTPAALAALSGSRVKSGGKDTGDDFVET-- 290
              GK    PLAGLA LG+ G+ + +    L PAALAAL+GS++++   +          
Sbjct: 222 SDMGKLGSSPLAGLAALGLGGLAAPANTGGLNPAALAALAGSQLRTNNANRQQPAANNQT 281

Query: 291 -EIVLTDDIAGCVIGKAGSRLLEIRQISGAQINIHTGTESH----KKMFHIQGCQEAVSL 345
            E+ + +++ GC+IGK G+++ EIRQISGA I I    E       +   I G  ++V+L
Sbjct: 282 HEMTVPNELIGCIIGKGGTKIAEIRQISGAMIRISNCEEREGGPTDRTITITGNPDSVAL 341

Query: 346 AQYLINMCIELQKNN 360
           AQYLINM +ELQK N
Sbjct: 342 AQYLINMSVELQKAN 356

Source: Nasonia vitripennis

Species: Nasonia vitripennis

Genus: Nasonia

Family: Pteromalidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|45553235|ref|NP_996145.1| mushroom-body expressed, isoform C [Drosophila melanogaster] gi|194876029|ref|XP_001973701.1| GG16232 [Drosophila erecta] gi|195496648|ref|XP_002095782.1| GE22592 [Drosophila yakuba] gi|16648354|gb|AAL25442.1| LD32520p [Drosophila melanogaster] gi|45446078|gb|AAS65095.1| mushroom-body expressed, isoform C [Drosophila melanogaster] gi|190655484|gb|EDV52727.1| GG16232 [Drosophila erecta] gi|194181883|gb|EDW95494.1| GE22592 [Drosophila yakuba] gi|220951950|gb|ACL88518.1| mub-PC [synthetic construct]

 Score =  243 bits (620), Expect = 1e-61,   Method: Compositional matrix adjust.
 Identities = 142/354 (40%), Positives = 204/354 (57%), Gaps = 37/354 (10%)

Query: 10  DEDTLITMRCLFHSSVNVNEISCLIGPGGCIVRRLRKESGAKISITDGACPDRIVTVSGS 69
           D    +T+R +        E+  +IG  G IV R R+ESGAKI+I+DG+CP+RIVTVSG+
Sbjct: 19  DPSVTLTIRLIMQG----KEVGSIIGKKGEIVNRFREESGAKINISDGSCPERIVTVSGT 74

Query: 70  VDNSSTSSVETGYPGHTLWVTSVDNVCTAYNFMCRSLEDYHINRNRMENCSPQPLQLKLV 129
            +                       + +A+  + +  E++    N +       + ++L+
Sbjct: 75  TNA----------------------IFSAFTLITKKFEEWCSQFNDVGKVGKTQIPIRLI 112

Query: 130 IPATHCGSLIGKGGCKIKDIRDLSGANVQVASDMLPMSTERIVTVHGNPDTISQAIYQIC 189
           +PA+ CGSLIGK G KIK+IR  +G ++QVAS+MLP STER VT+ G+ + I+Q IYQIC
Sbjct: 113 VPASQCGSLIGKSGSKIKEIRQTTGCSIQVASEMLPNSTERAVTLSGSAEQITQCIYQIC 172

Query: 190 LVLIECTLQVVKGAVIPYEPKTMNAGPVILSGGQAYTLHGEYAVPVQEVAGKKQPHPLAG 249
           LV++E      +GA IPY PK    GPVIL+ GQA+T+ G YAVP QEVA  K P     
Sbjct: 173 LVMLESP---PRGATIPYRPKPQVTGPVILANGQAFTIQGNYAVPTQEVA--KNPLASLA 227

Query: 250 LAVLGIEGIGSTSLT--PAALAALSGSRVKSGGKDTGDDFVETEIVLTDDIAGCVIGKAG 307
              L      ST      AALAAL+GS++++          + E+ +++D+ GC+IGK G
Sbjct: 228 ALGLAGMNPASTGGINHTAALAALAGSQLRTANPANRAQQQQHEMTVSNDLIGCIIGKGG 287

Query: 308 SRLLEIRQISGAQINIHTGTESH----KKMFHIQGCQEAVSLAQYLINMCIELQ 357
           +++ EIRQISGA I I    E       +   I G  ++V+LAQYLINM I ++
Sbjct: 288 TKIAEIRQISGAMIRISNCEEREGGNTDRTITISGNPDSVALAQYLINMRISME 341

Source: Drosophila melanogaster

Species: Drosophila melanogaster

Genus: Drosophila

Family: Drosophilidae

Order: Diptera

Class: Insecta

Phylum: Arthropoda

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	433
UNIPROTKB|F1NPL2	319	PCBP3 "Uncharacterized protein	0.341	0.463	0.474	3.1e-57
RGD|1307430	319	Pcbp3 "poly(rC) binding protei	0.341	0.463	0.487	1.7e-56
UNIPROTKB|B4DXP5	322	PCBP2 "Poly(rC)-binding protei	0.293	0.394	0.527	1.5e-55
MGI|MGI:1890470	371	Pcbp3 "poly(rC) binding protei	0.605	0.706	0.405	3.3e-55
UNIPROTKB|D4A1P3	371	Pcbp3 "Protein Pcbp3" [Rattus	0.605	0.706	0.405	3.3e-55
UNIPROTKB|G3V0E8	318	PCBP2 "Poly(RC) binding protei	0.286	0.389	0.523	4.9e-55
UNIPROTKB|E2QUE1	371	PCBP3 "Uncharacterized protein	0.605	0.706	0.405	6.9e-55
UNIPROTKB|P57721	371	PCBP3 "Poly(rC)-binding protei	0.605	0.706	0.405	6.9e-55
UNIPROTKB|P57723	403	PCBP4 "Poly(rC)-binding protei	0.281	0.302	0.519	1e-54
UNIPROTKB|E2RCH9	370	PCBP3 "Uncharacterized protein	0.602	0.705	0.401	1.4e-54

UNIPROTKB|F1NPL2 PCBP3 "Uncharacterized protein" [Gallus gallus (taxid:9031)]

 Score = 353 (129.3 bits), Expect = 3.1e-57, Sum P(3) = 3.1e-57
 Identities = 73/154 (47%), Positives = 100/154 (64%)

Query:    83 PGHTLWVTS-VDNVCTAYNFMCRSLE-DYHINRNRMENCSPQPLQLKLVIPATHCGSLIG 140
             P   + +T   D +  A++ +    E D + +       S  P+ L+LV+PA+ CGSLIG
Sbjct:    55 PERIVTITGPTDAIFKAFSMIALKFEEDINASMTNSTVTSKPPVTLRLVVPASQCGSLIG 114

Query:   141 KGGCKIKDIRDLSGANVQVASDMLPMSTERIVTVHGNPDTISQAIYQICLVLIECTLQVV 200
             KGG KIK+IR+ +GA VQVA DMLP STER VT+ G PD I Q + QIC+V++E      
Sbjct:   115 KGGSKIKEIRESTGAQVQVAGDMLPNSTERAVTISGTPDAIIQCVKQICVVMLESP---P 171

Query:   201 KGAVIPYEPKTMNAGPVILSGGQAYTLHGEYAVP 234
             KGA IPY PK  +A P+I +GGQA+T+ G+YA+P
Sbjct:   172 KGATIPYRPKPASA-PIIFAGGQAFTIQGQYAIP 204

GO:0003723 "RNA binding" evidence=IEA

RGD|1307430 Pcbp3 "poly(rC) binding protein 3" [Rattus norvegicus (taxid:10116)]

 Score = 353 (129.3 bits), Expect = 1.7e-56, Sum P(3) = 1.7e-56
 Identities = 75/154 (48%), Positives = 99/154 (64%)

Query:    83 PGHTLWVTS-VDNVCTAYNFMCRSLEDYHINR-NRMENCSPQPLQLKLVIPATHCGSLIG 140
             P   + +T   D +  A+  +    E+  IN  +     S  P+ L+LV+PA+ CGSLIG
Sbjct:    55 PERIVTITGPTDAIFKAFAMIAYKFEEDIINSMSNSPATSKPPVTLRLVVPASQCGSLIG 114

Query:   141 KGGCKIKDIRDLSGANVQVASDMLPMSTERIVTVHGNPDTISQAIYQICLVLIECTLQVV 200
             KGG KIK+IR+ +GA VQVA DMLP STER VT+ G PD I Q + QIC+V++E      
Sbjct:   115 KGGSKIKEIRESTGAQVQVAGDMLPNSTERAVTISGTPDAIIQCVKQICVVMLESP---P 171

Query:   201 KGAVIPYEPKTMNAGPVILSGGQAYTLHGEYAVP 234
             KGA IPY PK  +  PVI +GGQAYT+ G+YA+P
Sbjct:   172 KGATIPYRPKPAST-PVIFAGGQAYTIQGQYAIP 204

GO:0003723 "RNA binding" evidence=IEA

GO:0005634 "nucleus" evidence=IEA;ISO

GO:0005739 "mitochondrion" evidence=IEA;ISO

GO:0005829 "cytosol" evidence=IEA;ISO

GO:0043231 "intracellular membrane-bounded organelle" evidence=ISO

GO:0005730 "nucleolus" evidence=ISO

UNIPROTKB|B4DXP5 PCBP2 "Poly(rC)-binding protein 2" [Homo sapiens (taxid:9606)]

 Score = 348 (127.6 bits), Expect = 1.5e-55, Sum P(3) = 1.5e-55
 Identities = 68/129 (52%), Positives = 90/129 (69%)

Query:   107 EDYHINRNRMENCSPQPLQLKLVIPATHCGSLIGKGGCKIKDIRDLSGANVQVASDMLPM 166
             ED   +       S  P+ L+LV+PA+ CGSLIGKGGCKIK+IR+ +GA VQVA DMLP 
Sbjct:    81 EDISSSMTNSTAASRPPVTLRLVVPASQCGSLIGKGGCKIKEIRESTGAQVQVAGDMLPN 140

Query:   167 STERIVTVHGNPDTISQAIYQICLVLIECTLQVV-KGAVIPYEPKTMNAGPVILSGGQAY 225
             STER +T+ G P +I + + QIC+V++E   Q   KG  IPY PK  ++ PVI +GGQAY
Sbjct:   141 STERAITIAGIPQSIIECVKQICVVMLETLSQSPPKGVTIPYRPKP-SSSPVIFAGGQAY 199

Query:   226 TLHGEYAVP 234
             T+ G+YA+P
Sbjct:   200 TIQGQYAIP 208

GO:0003723 "RNA binding" evidence=IEA

MGI|MGI:1890470 Pcbp3 "poly(rC) binding protein 3" [Mus musculus (taxid:10090)]

 Score = 475 (172.3 bits), Expect = 3.3e-55, Sum P(2) = 3.3e-55
 Identities = 113/279 (40%), Positives = 156/279 (55%)

Query:    83 PGHTLWVTS-VDNVCTAYNFMCRSLEDYHINR-NRMENCSPQPLQLKLVIPATHCGSLIG 140
             P   + +T   D +  A+  +    E+  IN  +     S  P+ L+LV+PA+ CGSLIG
Sbjct:    87 PERIVTITGPTDAIFKAFAMIAYKFEEDIINSMSNSPATSKPPVTLRLVVPASQCGSLIG 146

Query:   141 KGGCKIKDIRDLSGANVQVASDMLPMSTERIVTVHGNPDTISQAIYQICLVLIECTLQVV 200
             KGG KIK+IR+ +GA VQVA DMLP STER VT+ G PD I Q + QIC+V++E      
Sbjct:   147 KGGSKIKEIRESTGAQVQVAGDMLPNSTERAVTISGTPDAIIQCVKQICVVMLESP---P 203

Query:   201 KGAVIPYEPKTMNAGPVILSGGQAYTLHGEYAVP-------VQEVAGKKQPHPLAGLAVL 253
             KGA IPY PK  +  PVI +GGQAYT+ G+YA+P       + ++A ++ P P  G    
Sbjct:   204 KGATIPYRPKPAST-PVIFAGGQAYTIQGQYAIPHPDQLTKLHQLAMQQTPFPPLGQTNP 262

Query:   254 GIEGIXXXXXXXXXXXXXXXXRVKSGGKDTGDDFVETEIVLTDDIAGCVIGKAGSRLLEI 313
                G                   +S G D        E+ + +D+ GC+IG+ G+++ EI
Sbjct:   263 AFPGEKLPLHSSEEAQNLMG---QSSGLDASPPASTHELTIPNDLIGCIIGRQGTKINEI 319

Query:   314 RQISGAQINIHTGTE-SHKKMFHIQGCQEAVSLAQYLIN 351
             RQ+SGAQI I   TE S ++   I G    +SLAQYLIN
Sbjct:   320 RQMSGAQIKIANATEGSSERQITITGTPANISLAQYLIN 358

GO:0003677 "DNA binding" evidence=IEA

GO:0003723 "RNA binding" evidence=IEA

GO:0005634 "nucleus" evidence=ISO

GO:0005737 "cytoplasm" evidence=IEA

GO:0005829 "cytosol" evidence=ISO

GO:0030529 "ribonucleoprotein complex" evidence=IEA

UNIPROTKB|D4A1P3 Pcbp3 "Protein Pcbp3" [Rattus norvegicus (taxid:10116)]

 Score = 475 (172.3 bits), Expect = 3.3e-55, Sum P(2) = 3.3e-55
 Identities = 113/279 (40%), Positives = 156/279 (55%)

Query:    83 PGHTLWVTS-VDNVCTAYNFMCRSLEDYHINR-NRMENCSPQPLQLKLVIPATHCGSLIG 140
             P   + +T   D +  A+  +    E+  IN  +     S  P+ L+LV+PA+ CGSLIG
Sbjct:    87 PERIVTITGPTDAIFKAFAMIAYKFEEDIINSMSNSPATSKPPVTLRLVVPASQCGSLIG 146

Query:   141 KGGCKIKDIRDLSGANVQVASDMLPMSTERIVTVHGNPDTISQAIYQICLVLIECTLQVV 200
             KGG KIK+IR+ +GA VQVA DMLP STER VT+ G PD I Q + QIC+V++E      
Sbjct:   147 KGGSKIKEIRESTGAQVQVAGDMLPNSTERAVTISGTPDAIIQCVKQICVVMLESP---P 203

Query:   201 KGAVIPYEPKTMNAGPVILSGGQAYTLHGEYAVP-------VQEVAGKKQPHPLAGLAVL 253
             KGA IPY PK  +  PVI +GGQAYT+ G+YA+P       + ++A ++ P P  G    
Sbjct:   204 KGATIPYRPKPAST-PVIFAGGQAYTIQGQYAIPHPDQLTKLHQLAMQQTPFPPLGQTNP 262

Query:   254 GIEGIXXXXXXXXXXXXXXXXRVKSGGKDTGDDFVETEIVLTDDIAGCVIGKAGSRLLEI 313
                G                   +S G D        E+ + +D+ GC+IG+ G+++ EI
Sbjct:   263 AFPGEKLPLHSSEEAQNLMG---QSSGLDASPPASTHELTIPNDLIGCIIGRQGTKINEI 319

Query:   314 RQISGAQINIHTGTE-SHKKMFHIQGCQEAVSLAQYLIN 351
             RQ+SGAQI I   TE S ++   I G    +SLAQYLIN
Sbjct:   320 RQMSGAQIKIANATEGSSERQITITGTPANISLAQYLIN 358

GO:0003723 "RNA binding" evidence=IEA

GO:0005634 "nucleus" evidence=IEA

GO:0005739 "mitochondrion" evidence=IEA

GO:0005829 "cytosol" evidence=IEA

UNIPROTKB|G3V0E8 PCBP2 "Poly(RC) binding protein 2, isoform CRA_f" [Homo sapiens (taxid:9606)]

 Score = 343 (125.8 bits), Expect = 4.9e-55, Sum P(3) = 4.9e-55
 Identities = 67/128 (52%), Positives = 89/128 (69%)

Query:   107 EDYHINRNRMENCSPQPLQLKLVIPATHCGSLIGKGGCKIKDIRDLSGANVQVASDMLPM 166
             ED   +       S  P+ L+LV+PA+ CGSLIGKGGCKIK+IR+ +GA VQVA DMLP 
Sbjct:    81 EDISSSMTNSTAASRPPVTLRLVVPASQCGSLIGKGGCKIKEIRESTGAQVQVAGDMLPN 140

Query:   167 STERIVTVHGNPDTISQAIYQICLVLIECTLQVVKGAVIPYEPKTMNAGPVILSGGQAYT 226
             STER +T+ G P +I + + QIC+V++E      KG  IPY PK  ++ PVI +GGQAYT
Sbjct:   141 STERAITIAGIPQSIIECVKQICVVMLESP---PKGVTIPYRPKP-SSSPVIFAGGQAYT 196

Query:   227 LHGEYAVP 234
             + G+YA+P
Sbjct:   197 IQGQYAIP 204

GO:0003723 "RNA binding" evidence=IEA

UNIPROTKB|E2QUE1 PCBP3 "Uncharacterized protein" [Canis lupus familiaris (taxid:9615)]

 Score = 475 (172.3 bits), Expect = 6.9e-55, Sum P(2) = 6.9e-55
 Identities = 113/279 (40%), Positives = 156/279 (55%)

Query:    83 PGHTLWVTS-VDNVCTAYNFMCRSLEDYHINR-NRMENCSPQPLQLKLVIPATHCGSLIG 140
             P   + +T   D +  A+  +    E+  IN  +     S  P+ L+LV+PA+ CGSLIG
Sbjct:    87 PERIVTITGPTDAIFKAFAMIAYKFEEDIINSMSNSPATSKPPVTLRLVVPASQCGSLIG 146

Query:   141 KGGCKIKDIRDLSGANVQVASDMLPMSTERIVTVHGNPDTISQAIYQICLVLIECTLQVV 200
             KGG KIK+IR+ +GA VQVA DMLP STER VT+ G PD I Q + QIC+V++E      
Sbjct:   147 KGGSKIKEIRESTGAQVQVAGDMLPNSTERAVTISGTPDAIIQCVKQICVVMLESP---P 203

Query:   201 KGAVIPYEPKTMNAGPVILSGGQAYTLHGEYAVP-------VQEVAGKKQPHPLAGLAVL 253
             KGA IPY PK  +  PVI +GGQAYT+ G+YA+P       + ++A ++ P P  G    
Sbjct:   204 KGATIPYRPKPAST-PVIFAGGQAYTIQGQYAIPHPDQLTKLHQLAMQQTPFPPLGQTNP 262

Query:   254 GIEGIXXXXXXXXXXXXXXXXRVKSGGKDTGDDFVETEIVLTDDIAGCVIGKAGSRLLEI 313
                G                   +S G D        E+ + +D+ GC+IG+ G+++ EI
Sbjct:   263 AFPGEKLPLHSSEEAQNLMG---QSSGLDASPPASTHELTIPNDLIGCIIGRQGTKINEI 319

Query:   314 RQISGAQINIHTGTE-SHKKMFHIQGCQEAVSLAQYLIN 351
             RQ+SGAQI I   TE S ++   I G    +SLAQYLIN
Sbjct:   320 RQMSGAQIKIANATEGSSERQITITGTPANISLAQYLIN 358

GO:0003723 "RNA binding" evidence=IEA

UNIPROTKB|P57721 PCBP3 "Poly(rC)-binding protein 3" [Homo sapiens (taxid:9606)]

 Score = 475 (172.3 bits), Expect = 6.9e-55, Sum P(2) = 6.9e-55
 Identities = 113/279 (40%), Positives = 156/279 (55%)

Query:    83 PGHTLWVTS-VDNVCTAYNFMCRSLEDYHINR-NRMENCSPQPLQLKLVIPATHCGSLIG 140
             P   + +T   D +  A+  +    E+  IN  +     S  P+ L+LV+PA+ CGSLIG
Sbjct:    87 PERIVTITGPTDAIFKAFAMIAYKFEEDIINSMSNSPATSKPPVTLRLVVPASQCGSLIG 146

Query:   141 KGGCKIKDIRDLSGANVQVASDMLPMSTERIVTVHGNPDTISQAIYQICLVLIECTLQVV 200
             KGG KIK+IR+ +GA VQVA DMLP STER VT+ G PD I Q + QIC+V++E      
Sbjct:   147 KGGSKIKEIRESTGAQVQVAGDMLPNSTERAVTISGTPDAIIQCVKQICVVMLESP---P 203

Query:   201 KGAVIPYEPKTMNAGPVILSGGQAYTLHGEYAVP-------VQEVAGKKQPHPLAGLAVL 253
             KGA IPY PK  +  PVI +GGQAYT+ G+YA+P       + ++A ++ P P  G    
Sbjct:   204 KGATIPYRPKPAST-PVIFAGGQAYTIQGQYAIPHPDQLTKLHQLAMQQTPFPPLGQTNP 262

Query:   254 GIEGIXXXXXXXXXXXXXXXXRVKSGGKDTGDDFVETEIVLTDDIAGCVIGKAGSRLLEI 313
                G                   +S G D        E+ + +D+ GC+IG+ G+++ EI
Sbjct:   263 AFPGEKLPLHSSEEAQNLMG---QSSGLDASPPASTHELTIPNDLIGCIIGRQGTKINEI 319

Query:   314 RQISGAQINIHTGTE-SHKKMFHIQGCQEAVSLAQYLIN 351
             RQ+SGAQI I   TE S ++   I G    +SLAQYLIN
Sbjct:   320 RQMSGAQIKIANATEGSSERQITITGTPANISLAQYLIN 358

GO:0003677 "DNA binding" evidence=IEA

GO:0030529 "ribonucleoprotein complex" evidence=IEA

GO:0003723 "RNA binding" evidence=NAS

GO:0016071 "mRNA metabolic process" evidence=NAS

GO:0005829 "cytosol" evidence=IDA

GO:0005634 "nucleus" evidence=IDA

GO:0005730 "nucleolus" evidence=IDA

GO:0005739 "mitochondrion" evidence=IDA

GO:0043231 "intracellular membrane-bounded organelle" evidence=IDA

UNIPROTKB|P57723 PCBP4 "Poly(rC)-binding protein 4" [Homo sapiens (taxid:9606)]

 Score = 301 (111.0 bits), Expect = 1.0e-54, Sum P(3) = 1.0e-54
 Identities = 66/127 (51%), Positives = 85/127 (66%)

Query:   118 NCSPQPLQLKLVIPATHCGSLIGKGGCKIKDIRDLSGANVQVASDMLPMSTERIVTVHGN 177
             N S  P+ L+LVIPA+ CGSLIGK G KIK+IR+ +GA VQVA D+LP STER VTV G 
Sbjct:    96 NVSRPPVTLRLVIPASQCGSLIGKAGTKIKEIRETTGAQVQVAGDLLPNSTERAVTVSGV 155

Query:   178 PDTISQAIYQICLVLIECTLQVVKGAVIPYEPKTMNAGPVILSGGQAYTLHGEY-AVPVQ 236
             PD I   + QIC V++E      KGA IPY P +++ G V+LS  Q +++ G+Y AV   
Sbjct:   156 PDAIILCVRQICAVILESP---PKGATIPYHP-SLSLGTVLLSANQGFSVQGQYGAVTPA 211

Query:   237 EVAGKKQ 243
             EV   +Q
Sbjct:   212 EVTKLQQ 218

GO:0003677 "DNA binding" evidence=IEA

GO:0030529 "ribonucleoprotein complex" evidence=IEA

GO:0005737 "cytoplasm" evidence=IEA

GO:0003723 "RNA binding" evidence=NAS

UNIPROTKB|E2RCH9 PCBP3 "Uncharacterized protein" [Canis lupus familiaris (taxid:9615)]

 Score = 472 (171.2 bits), Expect = 1.4e-54, Sum P(2) = 1.4e-54
 Identities = 112/279 (40%), Positives = 154/279 (55%)

Query:    83 PGHTLWVTS-VDNVCTAYNFMCRSLEDYHINR-NRMENCSPQPLQLKLVIPATHCGSLIG 140
             P   + +T   D +  A+  +    E+  IN  +     S  P+ L+LV+PA+ CGSLIG
Sbjct:    87 PERIVTITGPTDAIFKAFAMIAYKFEEDIINSMSNSPATSKPPVTLRLVVPASQCGSLIG 146

Query:   141 KGGCKIKDIRDLSGANVQVASDMLPMSTERIVTVHGNPDTISQAIYQICLVLIECTLQVV 200
             KGG KIK+IR+ +GA VQVA DMLP STER VT+ G PD I Q + QIC+V++E      
Sbjct:   147 KGGSKIKEIRESTGAQVQVAGDMLPNSTERAVTISGTPDAIIQCVKQICVVMLESP---P 203

Query:   201 KGAVIPYEPKTMNAGPVILSGGQAYTLHGEYAVP-------VQEVAGKKQPHPLAGLAVL 253
             KGA IPY PK  +  PVI +GGQAYT+ G+YA+P       + ++A ++ P P  G    
Sbjct:   204 KGATIPYRPKPAST-PVIFAGGQAYTIQGQYAIPHPDQLTKLHQLAMQQTPFPPLGQTNP 262

Query:   254 GIEGIXXXXXXXXXXXXXXXXRVKSGGKDTGDDFVETEIVLTDDIAGCVIGKAGSRLLEI 313
                G                      G D        E+ + +D+ GC+IG+ G+++ EI
Sbjct:   263 AFPGTYPAALSDLLSSHLGTL----SGLDASPPASTHELTIPNDLIGCIIGRQGTKINEI 318

Query:   314 RQISGAQINIHTGTE-SHKKMFHIQGCQEAVSLAQYLIN 351
             RQ+SGAQI I   TE S ++   I G    +SLAQYLIN
Sbjct:   319 RQMSGAQIKIANATEGSSERQITITGTPANISLAQYLIN 357

GO:0003723 "RNA binding" evidence=IEA

---

Prediction of Enzyme Commission (EC) Number

EC Number Prediction by Annotation Transfer from SWISS-PROT Entries

Original result of BLAST against SWISS-PROT

ID	Name	Annotated EC number	Identity	Query coverage	Hit coverage	RBH(Q2H)	RBH(H2Q)
P57722	PCBP3_MOUSE	No assigned EC number	0.3939	0.7251	0.8463	yes	N/A
P57721	PCBP3_HUMAN	No assigned EC number	0.3944	0.7182	0.8382	yes	N/A

EC Number Prediction by EFICAz Software

No EC number assignment, probably not an enzyme!

---

Conserved Domains and Related Protein Families

Conserved Domains Detected by RPS-BLAST

Original result of RPS-BLAST against CDD database

ID	Length	Definition	E-value
Query	433
cd02396	65	cd02396, PCBP_like_KH, K homology RNA-binding doma	5e-21
cd00105	64	cd00105, KH-I, K homology RNA-binding domain, type	2e-13
cd02396	65	cd02396, PCBP_like_KH, K homology RNA-binding doma	1e-11
smart00322	68	smart00322, KH, K homology RNA-binding domain	1e-10
pfam00013	59	pfam00013, KH_1, KH domain	1e-10
cd00105	64	cd00105, KH-I, K homology RNA-binding domain, type	1e-08
pfam13014	42	pfam13014, KH_3, KH domain	2e-08
smart00322	68	smart00322, KH, K homology RNA-binding domain	4e-08
pfam00013	59	pfam00013, KH_1, KH domain	2e-07
pfam00013	59	pfam00013, KH_1, KH domain	2e-07
smart00322	68	smart00322, KH, K homology RNA-binding domain	7e-07
cd00105	64	cd00105, KH-I, K homology RNA-binding domain, type	1e-06
pfam13014	42	pfam13014, KH_3, KH domain	1e-06
cd02394	62	cd02394, vigilin_like_KH, K homology RNA-binding d	6e-05
cd02394	62	cd02394, vigilin_like_KH, K homology RNA-binding d	3e-04
pfam13014	42	pfam13014, KH_3, KH domain	0.001
cd02393	61	cd02393, PNPase_KH, Polynucleotide phosphorylase (	0.001
cd02396	65	cd02396, PCBP_like_KH, K homology RNA-binding doma	0.002
cd02395	120	cd02395, SF1_like-KH, Splicing factor 1 (SF1) K ho	0.002
COG1185	692	COG1185, Pnp, Polyribonucleotide nucleotidyltransf	0.003
TIGR03591	684	TIGR03591, polynuc_phos, polyribonucleotide nucleo	0.003

>gnl|CDD|239089 cd02396, PCBP_like_KH, K homology RNA-binding domain, PCBP_like

 Score = 86.0 bits (214), Expect = 5e-21
 Identities = 29/65 (44%), Positives = 47/65 (72%)

Query: 125 QLKLVIPATHCGSLIGKGGCKIKDIRDLSGANVQVASDMLPMSTERIVTVHGNPDTISQA 184
            L+L++P++  GS+IGKGG  IK+IR+ +GA ++V+  +LP STER+VT+ G P  + +A
Sbjct: 1   TLRLLVPSSQAGSIIGKGGSTIKEIREETGAKIRVSKSVLPGSTERVVTISGKPSAVQKA 60

Query: 185 IYQIC 189
           +  I 
Sbjct: 61  LLLIL 65

Members of this group possess KH domains in a tandem arrangement. Most members, similar to the poly(C) binding proteins (PCBPs) and Nova, containing three KH domains, with the first and second domains, which are represented here, in tandem arrangement, followed by a large spacer region, with the third domain near the C-terminal end of the protein. The poly(C) binding proteins (PCBPs) can be divided into two groups, hnRNPs K/J and the alphaCPs, which share a triple KH domain configuration and poly(C) binding specificity. They play roles in mRNA stabilization, translational activation, and translational silencing. Nova-1 and Nova-2 are nuclear RNA-binding proteins that regulate splicing. This group also contains plant proteins that seem to have two tandem repeat arrrangements, like Hen4, a protein that plays a role in AGAMOUS (AG) pre-mRNA processing and important step in plant development. In general, KH binds single-stranded RNA or DNA. It is found in a wide variety of proteins including ribosomal proteins, transcription factors and post-transcriptional modifiers of mRNA. Length = 65

>gnl|CDD|238053 cd00105, KH-I, K homology RNA-binding domain, type I

 Score = 64.5 bits (158), Expect = 2e-13
 Identities = 23/64 (35%), Positives = 40/64 (62%), Gaps = 1/64 (1%)

Query: 126 LKLVIPATHCGSLIGKGGCKIKDIRDLSGANVQVASDMLPMSTERIVTVHGNPDTISQAI 185
            ++++P++  G +IGKGG  IK+IR+ +GA +++       S ERIVT+ G P+ + +A 
Sbjct: 2   ERVLVPSSLVGRIIGKGGSTIKEIREETGAKIKIPDSG-SGSEERIVTITGTPEAVEKAK 60

Query: 186 YQIC 189
             I 
Sbjct: 61  ELIL 64

KH binds single-stranded RNA or DNA. It is found in a wide variety of proteins including ribosomal proteins, transcription factors and post-transcriptional modifiers of mRNA. There are two different KH domains that belong to different protein folds, but they share a single KH motif. The KH motif is folded into a beta alpha alpha beta unit. In addition to the core, type II KH domains (e.g. ribosomal protein S3) include N-terminal extension and type I KH domains (e.g. hnRNP K) contain C-terminal extension. Length = 64

>gnl|CDD|239089 cd02396, PCBP_like_KH, K homology RNA-binding domain, PCBP_like

 Score = 59.4 bits (145), Expect = 1e-11
 Identities = 20/60 (33%), Positives = 33/60 (55%), Gaps = 7/60 (11%)

Query: 16 TMRCLFHSSVNVNEISCLIGPGGCIVRRLRKESGAKISITDG---ACPDRIVTVSGSVDN 72
          T+R L  SS    +   +IG GG  ++ +R+E+GAKI ++        +R+VT+SG    
Sbjct: 1  TLRLLVPSS----QAGSIIGKGGSTIKEIREETGAKIRVSKSVLPGSTERVVTISGKPSA 56

Members of this group possess KH domains in a tandem arrangement. Most members, similar to the poly(C) binding proteins (PCBPs) and Nova, containing three KH domains, with the first and second domains, which are represented here, in tandem arrangement, followed by a large spacer region, with the third domain near the C-terminal end of the protein. The poly(C) binding proteins (PCBPs) can be divided into two groups, hnRNPs K/J and the alphaCPs, which share a triple KH domain configuration and poly(C) binding specificity. They play roles in mRNA stabilization, translational activation, and translational silencing. Nova-1 and Nova-2 are nuclear RNA-binding proteins that regulate splicing. This group also contains plant proteins that seem to have two tandem repeat arrrangements, like Hen4, a protein that plays a role in AGAMOUS (AG) pre-mRNA processing and important step in plant development. In general, KH binds single-stranded RNA or DNA. It is found in a wide variety of proteins including ribosomal proteins, transcription factors and post-transcriptional modifiers of mRNA. Length = 65

>gnl|CDD|197652 smart00322, KH, K homology RNA-binding domain

 Score = 56.9 bits (138), Expect = 1e-10
 Identities = 23/66 (34%), Positives = 38/66 (57%), Gaps = 3/66 (4%)

Query: 123 PLQLKLVIPATHCGSLIGKGGCKIKDIRDLSGANVQVASDMLPMSTERIVTVHGNPDTIS 182
           P+ ++++IPA   G +IGKGG  IK I + +G  + +     P S ER+V + G P+ + 
Sbjct: 2   PVTIEVLIPADKVGLIIGKGGSTIKKIEEETGVKIDI---PGPGSEERVVEITGPPENVE 58

Query: 183 QAIYQI 188
           +A   I
Sbjct: 59  KAAELI 64

Length = 68

>gnl|CDD|215657 pfam00013, KH_1, KH domain

 Score = 56.4 bits (137), Expect = 1e-10
 Identities = 20/63 (31%), Positives = 35/63 (55%), Gaps = 5/63 (7%)

Query: 126 LKLVIPATHCGSLIGKGGCKIKDIRDLSGANVQVASDMLPMSTERIVTVHGNPDTISQAI 185
            +++IP    G +IGKGG  IK+IR+ +G  +++  D      +  VT+ G P+ + +A 
Sbjct: 2   ERILIPPDKVGRIIGKGGSNIKEIREETGVKIRIPDD-----RDDTVTISGTPEQVEKAK 56

Query: 186 YQI 188
             I
Sbjct: 57  ELI 59

KH motifs bind RNA in vitro. Autoantibodies to Nova, a KH domain protein, cause paraneoplastic opsoclonus ataxia. Length = 59

>gnl|CDD|238053 cd00105, KH-I, K homology RNA-binding domain, type I

 Score = 51.0 bits (123), Expect = 1e-08
 Identities = 18/50 (36%), Positives = 31/50 (62%), Gaps = 2/50 (4%)

Query: 25 VNVNEISCLIGPGGCIVRRLRKESGAKISITD--GACPDRIVTVSGSVDN 72
          V  + +  +IG GG  ++ +R+E+GAKI I D      +RIVT++G+ + 
Sbjct: 6  VPSSLVGRIIGKGGSTIKEIREETGAKIKIPDSGSGSEERIVTITGTPEA 55

KH binds single-stranded RNA or DNA. It is found in a wide variety of proteins including ribosomal proteins, transcription factors and post-transcriptional modifiers of mRNA. There are two different KH domains that belong to different protein folds, but they share a single KH motif. The KH motif is folded into a beta alpha alpha beta unit. In addition to the core, type II KH domains (e.g. ribosomal protein S3) include N-terminal extension and type I KH domains (e.g. hnRNP K) contain C-terminal extension. Length = 64

>gnl|CDD|221895 pfam13014, KH_3, KH domain

 Score = 49.9 bits (120), Expect = 2e-08
 Identities = 21/43 (48%), Positives = 29/43 (67%), Gaps = 1/43 (2%)

Query: 134 HCGSLIGKGGCKIKDIRDLSGANVQVASDMLPMSTERIVTVHG 176
             G++IGKGG  IK+IR+ +GA +Q+     P S ERIVT+ G
Sbjct: 1   LVGAIIGKGGETIKEIREETGAKIQI-PKPEPGSGERIVTITG 42

KH motifs bind RNA in vitro. This RNA-binding domain is required for the efficient anchoring of ASH1-mRNA to the distal tip of the daughter cell. ASH1 is a specific repressor of transcription that localizes asymmetrically to the daughter cell nucleus. RNA localisation is a widespread mechanism for achieving localised protein synthesis. Length = 42

>gnl|CDD|197652 smart00322, KH, K homology RNA-binding domain

 Score = 49.6 bits (119), Expect = 4e-08
 Identities = 13/48 (27%), Positives = 29/48 (60%)

Query: 25 VNVNEISCLIGPGGCIVRRLRKESGAKISITDGACPDRIVTVSGSVDN 72
          +  +++  +IG GG  ++++ +E+G KI I      +R+V ++G  +N
Sbjct: 9  IPADKVGLIIGKGGSTIKKIEEETGVKIDIPGPGSEERVVEITGPPEN 56

Length = 68

>gnl|CDD|215657 pfam00013, KH_1, KH domain

 Score = 47.6 bits (114), Expect = 2e-07
 Identities = 21/62 (33%), Positives = 30/62 (48%), Gaps = 3/62 (4%)

Query: 289 ETEIVLTDDIAGCVIGKAGSRLLEIRQISGAQINIHTGTESHKKMFHIQGCQEAVSLAQY 348
              I++  D  G +IGK GS + EIR+ +G +I I    +       I G  E V  A+ 
Sbjct: 1   TERILIPPDKVGRIIGKGGSNIKEIREETGVKIRIP---DDRDDTVTISGTPEQVEKAKE 57

Query: 349 LI 350
           LI
Sbjct: 58  LI 59

KH motifs bind RNA in vitro. Autoantibodies to Nova, a KH domain protein, cause paraneoplastic opsoclonus ataxia. Length = 59

>gnl|CDD|215657 pfam00013, KH_1, KH domain

 Score = 47.6 bits (114), Expect = 2e-07
 Identities = 16/49 (32%), Positives = 29/49 (59%), Gaps = 2/49 (4%)

Query: 24 SVNVNEISCLIGPGGCIVRRLRKESGAKISITDGACPDRIVTVSGSVDN 72
           +  +++  +IG GG  ++ +R+E+G KI I D    D  VT+SG+ + 
Sbjct: 5  LIPPDKVGRIIGKGGSNIKEIREETGVKIRIPDD--RDDTVTISGTPEQ 51

KH motifs bind RNA in vitro. Autoantibodies to Nova, a KH domain protein, cause paraneoplastic opsoclonus ataxia. Length = 59

>gnl|CDD|197652 smart00322, KH, K homology RNA-binding domain

 Score = 46.1 bits (110), Expect = 7e-07
 Identities = 21/69 (30%), Positives = 33/69 (47%), Gaps = 1/69 (1%)

Query: 286 DFVETEIVLTDDIAGCVIGKAGSRLLEIRQISGAQINIHTGTESHKKMFHIQGCQEAVSL 345
           D V  E+++  D  G +IGK GS + +I + +G +I+I       +    I G  E V  
Sbjct: 1   DPVTIEVLIPADKVGLIIGKGGSTIKKIEEETGVKIDIPGPGSEERV-VEITGPPENVEK 59

Query: 346 AQYLINMCI 354
           A  LI   +
Sbjct: 60  AAELILEIL 68

Length = 68

>gnl|CDD|238053 cd00105, KH-I, K homology RNA-binding domain, type I

 Score = 45.2 bits (108), Expect = 1e-06
 Identities = 23/63 (36%), Positives = 37/63 (58%), Gaps = 1/63 (1%)

Query: 289 ETEIVLTDDIAGCVIGKAGSRLLEIRQISGAQINIHT-GTESHKKMFHIQGCQEAVSLAQ 347
              +++   + G +IGK GS + EIR+ +GA+I I   G+ S +++  I G  EAV  A+
Sbjct: 1   TERVLVPSSLVGRIIGKGGSTIKEIREETGAKIKIPDSGSGSEERIVTITGTPEAVEKAK 60

Query: 348 YLI 350
            LI
Sbjct: 61  ELI 63

KH binds single-stranded RNA or DNA. It is found in a wide variety of proteins including ribosomal proteins, transcription factors and post-transcriptional modifiers of mRNA. There are two different KH domains that belong to different protein folds, but they share a single KH motif. The KH motif is folded into a beta alpha alpha beta unit. In addition to the core, type II KH domains (e.g. ribosomal protein S3) include N-terminal extension and type I KH domains (e.g. hnRNP K) contain C-terminal extension. Length = 64

>gnl|CDD|221895 pfam13014, KH_3, KH domain

 Score = 44.5 bits (106), Expect = 1e-06
 Identities = 16/41 (39%), Positives = 27/41 (65%), Gaps = 2/41 (4%)

Query: 30 ISCLIGPGGCIVRRLRKESGAKISI--TDGACPDRIVTVSG 68
          +  +IG GG  ++ +R+E+GAKI I   +    +RIVT++G
Sbjct: 2  VGAIIGKGGETIKEIREETGAKIQIPKPEPGSGERIVTITG 42

KH motifs bind RNA in vitro. This RNA-binding domain is required for the efficient anchoring of ASH1-mRNA to the distal tip of the daughter cell. ASH1 is a specific repressor of transcription that localizes asymmetrically to the daughter cell nucleus. RNA localisation is a widespread mechanism for achieving localised protein synthesis. Length = 42

>gnl|CDD|239087 cd02394, vigilin_like_KH, K homology RNA-binding domain_vigilin_like

 Score = 40.2 bits (95), Expect = 6e-05
 Identities = 15/64 (23%), Positives = 29/64 (45%), Gaps = 3/64 (4%)

Query: 126 LKLVIPATHCGSLIGKGGCKIKDIRDLSGANVQVASDMLPMSTERIVTVHGNPDTISQAI 185
            ++ IP      +IGK G  I+ I + +G  ++      P S    +T+ G  + + +A 
Sbjct: 2   EEVEIPKKLHRFIIGKKGSNIRKIMEETGVKIRFPD---PGSKSDTITITGPKENVEKAK 58

Query: 186 YQIC 189
            +I 
Sbjct: 59  EEIL 62

The vigilin family is a large and extended family of multiple KH-domain proteins, including vigilin, also called high density lipoprotein binding protien (HBP), fungal Scp160 and bicaudal-C. Yeast Scp160p has been shown to bind RNA and to associate with both soluble and membrane-bound polyribosomes as a mRNP component. Bicaudal-C is a RNA-binding molecule believed to function in embryonic development at the post-transcriptional level. In general, KH binds single-stranded RNA or DNA. It is found in a wide variety of proteins including ribosomal proteins, transcription factors and post-transcriptional modifiers of mRNA. Length = 62

>gnl|CDD|239087 cd02394, vigilin_like_KH, K homology RNA-binding domain_vigilin_like

 Score = 38.6 bits (91), Expect = 3e-04
 Identities = 12/40 (30%), Positives = 22/40 (55%)

Query: 33 LIGPGGCIVRRLRKESGAKISITDGACPDRIVTVSGSVDN 72
          +IG  G  +R++ +E+G KI   D       +T++G  +N
Sbjct: 14 IIGKKGSNIRKIMEETGVKIRFPDPGSKSDTITITGPKEN 53

The vigilin family is a large and extended family of multiple KH-domain proteins, including vigilin, also called high density lipoprotein binding protien (HBP), fungal Scp160 and bicaudal-C. Yeast Scp160p has been shown to bind RNA and to associate with both soluble and membrane-bound polyribosomes as a mRNP component. Bicaudal-C is a RNA-binding molecule believed to function in embryonic development at the post-transcriptional level. In general, KH binds single-stranded RNA or DNA. It is found in a wide variety of proteins including ribosomal proteins, transcription factors and post-transcriptional modifiers of mRNA. Length = 62

>gnl|CDD|221895 pfam13014, KH_3, KH domain

 Score = 36.4 bits (85), Expect = 0.001
 Identities = 15/41 (36%), Positives = 23/41 (56%), Gaps = 1/41 (2%)

Query: 299 AGCVIGKAGSRLLEIRQISGAQINIH-TGTESHKKMFHIQG 338
            G +IGK G  + EIR+ +GA+I I      S +++  I G
Sbjct: 2   VGAIIGKGGETIKEIREETGAKIQIPKPEPGSGERIVTITG 42

KH motifs bind RNA in vitro. This RNA-binding domain is required for the efficient anchoring of ASH1-mRNA to the distal tip of the daughter cell. ASH1 is a specific repressor of transcription that localizes asymmetrically to the daughter cell nucleus. RNA localisation is a widespread mechanism for achieving localised protein synthesis. Length = 42

>gnl|CDD|239086 cd02393, PNPase_KH, Polynucleotide phosphorylase (PNPase) K homology RNA-binding domain (KH)

 Score = 36.7 bits (86), Expect = 0.001
 Identities = 15/45 (33%), Positives = 27/45 (60%), Gaps = 4/45 (8%)

Query: 25 VNVNEISCLIGPGGCIVRRLRKESGAKISITDGACPDRIVTVSGS 69
          +  ++I  +IGPGG  ++++ +E+G KI I D    D  V ++ S
Sbjct: 8  IPPDKIRDVIGPGGKTIKKIIEETGVKIDIED----DGTVYIAAS 48

PNPase is a polyribonucleotide nucleotidyl transferase that degrades mRNA in prokaryotes and plant chloroplasts. The C-terminal region of PNPase contains domains homologous to those in other RNA binding proteins: a KH domain and an S1 domain. KH domains bind single-stranded RNA and are found in a wide variety of proteins including ribosomal proteins, transcription factors and post-transcriptional modifiers of mRNA. Length = 61

>gnl|CDD|239089 cd02396, PCBP_like_KH, K homology RNA-binding domain, PCBP_like

 Score = 35.9 bits (84), Expect = 0.002
 Identities = 13/25 (52%), Positives = 19/25 (76%)

Query: 299 AGCVIGKAGSRLLEIRQISGAQINI 323
           AG +IGK GS + EIR+ +GA+I +
Sbjct: 11  AGSIIGKGGSTIKEIREETGAKIRV 35

Members of this group possess KH domains in a tandem arrangement. Most members, similar to the poly(C) binding proteins (PCBPs) and Nova, containing three KH domains, with the first and second domains, which are represented here, in tandem arrangement, followed by a large spacer region, with the third domain near the C-terminal end of the protein. The poly(C) binding proteins (PCBPs) can be divided into two groups, hnRNPs K/J and the alphaCPs, which share a triple KH domain configuration and poly(C) binding specificity. They play roles in mRNA stabilization, translational activation, and translational silencing. Nova-1 and Nova-2 are nuclear RNA-binding proteins that regulate splicing. This group also contains plant proteins that seem to have two tandem repeat arrrangements, like Hen4, a protein that plays a role in AGAMOUS (AG) pre-mRNA processing and important step in plant development. In general, KH binds single-stranded RNA or DNA. It is found in a wide variety of proteins including ribosomal proteins, transcription factors and post-transcriptional modifiers of mRNA. Length = 65

>gnl|CDD|239088 cd02395, SF1_like-KH, Splicing factor 1 (SF1) K homology RNA-binding domain (KH)

 Score = 37.6 bits (88), Expect = 0.002
 Identities = 13/27 (48%), Positives = 20/27 (74%)

Query: 28 NEISCLIGPGGCIVRRLRKESGAKISI 54
          N +  ++GP G  +++L KE+GAKISI
Sbjct: 15 NFVGLILGPRGNTLKQLEKETGAKISI 41

Splicing factor 1 (SF1) specifically recognizes the intron branch point sequence (BPS) UACUAAC in the pre-mRNA transcripts during spliceosome assembly. We show that the KH-QUA2 region of SF1 defines an enlarged KH (hnRNP K) fold which is necessary and sufficient for BPS binding. KH binds single-stranded RNA or DNA. It is found in a wide variety of proteins including ribosomal proteins, transcription factors and post-transcriptional modifiers of mRNA. Length = 120

>gnl|CDD|224106 COG1185, Pnp, Polyribonucleotide nucleotidyltransferase (polynucleotide phosphorylase) [Translation, ribosomal structure and biogenesis]

 Score = 39.9 bits (94), Expect = 0.003
 Identities = 16/49 (32%), Positives = 28/49 (57%), Gaps = 4/49 (8%)

Query: 25  VNVNEISCLIGPGGCIVRRLRKESGAKISITDGACPDRIVTVSGSVDNS 73
           ++ ++I  +IGPGG  ++ + +E+G KI I D    D  V ++ S   S
Sbjct: 558 IDPDKIRDVIGPGGKTIKAITEETGVKIDIED----DGTVKIAASDGES 602

Length = 692

>gnl|CDD|234271 TIGR03591, polynuc_phos, polyribonucleotide nucleotidyltransferase

 Score = 39.4 bits (93), Expect = 0.003
 Identities = 18/45 (40%), Positives = 29/45 (64%), Gaps = 4/45 (8%)

Query: 25  VNVNEISCLIGPGGCIVRRLRKESGAKISITDGACPDRIVTVSGS 69
           +N ++I  +IGPGG ++R + +E+GAKI I D    D  V ++ S
Sbjct: 557 INPDKIRDVIGPGGKVIREITEETGAKIDIED----DGTVKIAAS 597

Members of this protein family are polyribonucleotide nucleotidyltransferase, also called polynucleotide phosphorylase. Some members have been shown also to have additional functions as guanosine pentaphosphate synthetase and as poly(A) polymerase (see model TIGR02696 for an exception clade, within this family) [Transcription, Degradation of RNA]. Length = 684

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	433
KOG2193|consensus	584		100.0
KOG2192|consensus	390		100.0
KOG1676|consensus	600		100.0
KOG2190|consensus	485		100.0
KOG1676|consensus	600		100.0
KOG2193|consensus	584		99.97
KOG2191|consensus	402		99.97
KOG2191|consensus	402		99.93
KOG2190|consensus	485		99.93
KOG2192|consensus	390		99.76
TIGR03665	172	arCOG04150 arCOG04150 universal archaeal KH domain	99.67
PRK13763	180	putative RNA-processing protein; Provisional	99.64
TIGR03665	172	arCOG04150 arCOG04150 universal archaeal KH domain	99.64
PRK13763	180	putative RNA-processing protein; Provisional	99.6
cd02396	65	PCBP_like_KH K homology RNA-binding domain, PCBP_l	99.47
KOG2279|consensus	608		99.43
cd02396	65	PCBP_like_KH K homology RNA-binding domain, PCBP_l	99.41
cd02394	62	vigilin_like_KH K homology RNA-binding domain_vigi	99.33
PF00013	60	KH_1: KH domain syndrome, contains KH motifs.; Int	99.31
cd00105	64	KH-I K homology RNA-binding domain, type I. KH bin	99.25
PF00013	60	KH_1: KH domain syndrome, contains KH motifs.; Int	99.24
cd02393	61	PNPase_KH Polynucleotide phosphorylase (PNPase) K	99.22
cd02394	62	vigilin_like_KH K homology RNA-binding domain_vigi	99.21
cd02393	61	PNPase_KH Polynucleotide phosphorylase (PNPase) K	99.1
cd00105	64	KH-I K homology RNA-binding domain, type I. KH bin	99.06
PF13014	43	KH_3: KH domain	99.01
smart00322	69	KH K homology RNA-binding domain.	98.95
PF13014	43	KH_3: KH domain	98.94
KOG2208|consensus	753		98.89
smart00322	69	KH K homology RNA-binding domain.	98.85
KOG2208|consensus	753		98.84
COG1094	194	Predicted RNA-binding protein (contains KH domains	98.81
KOG2279|consensus	608		98.69
COG1094	194	Predicted RNA-binding protein (contains KH domains	98.5
cd02395	120	SF1_like-KH Splicing factor 1 (SF1) K homology RNA	98.39
cd02395	120	SF1_like-KH Splicing factor 1 (SF1) K homology RNA	98.33
KOG2113|consensus	394		98.26
KOG2113|consensus	394		98.12
PRK08406	140	transcription elongation factor NusA-like protein;	98.06
PRK08406	140	transcription elongation factor NusA-like protein;	98.05
TIGR02696	719	pppGpp_PNP guanosine pentaphosphate synthetase I/p	97.96
TIGR02696	719	pppGpp_PNP guanosine pentaphosphate synthetase I/p	97.79
TIGR01952	141	nusA_arch NusA family KH domain protein, archaeal.	97.59
TIGR03591	684	polynuc_phos polyribonucleotide nucleotidyltransfe	97.5
TIGR03591	684	polynuc_phos polyribonucleotide nucleotidyltransfe	97.49
KOG0119|consensus	554		97.46
KOG0336|consensus	629		97.46
KOG1588|consensus	259		97.39
TIGR01952	141	nusA_arch NusA family KH domain protein, archaeal.	97.29
KOG0119|consensus	554		97.16
KOG2814|consensus	345		97.11
COG0195	190	NusA Transcription elongation factor [Transcriptio	97.09
PLN00207	891	polyribonucleotide nucleotidyltransferase; Provisi	97.06
PLN00207	891	polyribonucleotide nucleotidyltransferase; Provisi	97.01
COG1185	692	Pnp Polyribonucleotide nucleotidyltransferase (pol	96.9
COG1185	692	Pnp Polyribonucleotide nucleotidyltransferase (pol	96.85
KOG2814|consensus	345		96.83
cd02134	61	NusA_KH NusA_K homology RNA-binding domain (KH). N	96.76
KOG0336|consensus	629		96.7
cd02134	61	NusA_KH NusA_K homology RNA-binding domain (KH). N	96.69
PF14611	210	SLS: Mitochondrial inner-membrane-bound regulator	96.5
PRK00106	535	hypothetical protein; Provisional	96.27
PRK00468	75	hypothetical protein; Provisional	96.25
TIGR03319	514	YmdA_YtgF conserved hypothetical protein YmdA/YtgF	96.22
PRK11824	693	polynucleotide phosphorylase/polyadenylase; Provis	96.15
COG0195	190	NusA Transcription elongation factor [Transcriptio	96.13
TIGR03319	514	YmdA_YtgF conserved hypothetical protein YmdA/YtgF	96.1
PRK12704	520	phosphodiesterase; Provisional	96.06
PRK12328	374	nusA transcription elongation factor NusA; Provisi	96.06
PRK11824	693	polynucleotide phosphorylase/polyadenylase; Provis	96.02
TIGR01953	341	NusA transcription termination factor NusA. This m	96.02
PRK00106	535	hypothetical protein; Provisional	95.99
PRK12327	362	nusA transcription elongation factor NusA; Provisi	95.95
PRK12704	520	phosphodiesterase; Provisional	95.94
KOG1588|consensus	259		95.92
PRK02821	77	hypothetical protein; Provisional	95.84
PRK04163	235	exosome complex RNA-binding protein Rrp4; Provisio	95.8
PRK12329	449	nusA transcription elongation factor NusA; Provisi	95.79
COG1837	76	Predicted RNA-binding protein (contains KH domain)	95.79
PRK12328	374	nusA transcription elongation factor NusA; Provisi	95.68
PF14611	210	SLS: Mitochondrial inner-membrane-bound regulator	95.63
PRK09202	470	nusA transcription elongation factor NusA; Validat	95.54
COG5176	269	MSL5 Splicing factor (branch point binding protein	95.39
TIGR01953	341	NusA transcription termination factor NusA. This m	95.38
PRK01064	78	hypothetical protein; Provisional	95.33
PRK02821	77	hypothetical protein; Provisional	95.3
PRK12327	362	nusA transcription elongation factor NusA; Provisi	95.26
PRK00468	75	hypothetical protein; Provisional	95.25
PRK09202	470	nusA transcription elongation factor NusA; Validat	95.11
COG1837	76	Predicted RNA-binding protein (contains KH domain)	94.99
PRK04163	235	exosome complex RNA-binding protein Rrp4; Provisio	94.97
PRK12329	449	nusA transcription elongation factor NusA; Provisi	94.61
COG5176	269	MSL5 Splicing factor (branch point binding protein	94.53
KOG4369|consensus	2131		94.21
PRK12705	508	hypothetical protein; Provisional	94.04
PRK01064	78	hypothetical protein; Provisional	94.01
KOG1067|consensus	760		93.6
PRK12705	508	hypothetical protein; Provisional	93.39
KOG4369|consensus	2131		92.0
PF13083	73	KH_4: KH domain; PDB: 3GKU_B.	91.97
cd02409	68	KH-II KH-II (K homology RNA-binding domain, type I	91.49
PF13184	69	KH_5: NusA-like KH domain; PDB: 1HH2_P 1L2F_A 2ATW	90.95
PF13184	69	KH_5: NusA-like KH domain; PDB: 1HH2_P 1L2F_A 2ATW	90.27
KOG1067|consensus	760		89.92
KOG3273|consensus	252		89.36
PF13083	73	KH_4: KH domain; PDB: 3GKU_B.	89.33
cd02409	68	KH-II KH-II (K homology RNA-binding domain, type I	89.3
PF07650	78	KH_2: KH domain syndrome, contains KH motifs.; Int	88.25
COG1855	604	ATPase (PilT family) [General function prediction	87.38
cd02414	77	jag_KH jag_K homology RNA-binding domain. The KH d	87.25
KOG3273|consensus	252		86.88
COG1097	239	RRP4 RNA-binding protein Rrp4 and related proteins	86.5
cd02413	81	40S_S3_KH K homology RNA-binding (KH) domain of th	85.87
cd02410	145	archeal_CPSF_KH The archaeal cleavage and polyaden	85.44
COG5166	657	Uncharacterized conserved protein [Function unknow	84.54
cd02410	145	archeal_CPSF_KH The archaeal cleavage and polyaden	84.04
PRK13764	602	ATPase; Provisional	83.84
cd02414	77	jag_KH jag_K homology RNA-binding domain. The KH d	83.36
PF07650	78	KH_2: KH domain syndrome, contains KH motifs.; Int	82.6
COG1855	604	ATPase (PilT family) [General function prediction	82.45
COG1097	239	RRP4 RNA-binding protein Rrp4 and related proteins	81.57
PRK06418	166	transcription elongation factor NusA-like protein;	80.83
KOG2874|consensus	356		80.79

>KOG2193|consensus

Probab=100.00  E-value=5.1e-53  Score=404.28  Aligned_cols=329  Identities=20%  Similarity=0.309  Sum_probs=257.6

Q ss_pred             CceEEEEEEeccCCcccccceeeecCchHHHHHHHHhCCeEEEeC---CCCCcceEEEecccCCCCCCccccCCCCCccc
Q psy11929         12 DTLITMRCLFHSSVNVNEISCLIGPGGCIVRRLRKESGAKISITD---GACPDRIVTVSGSVDNSSTSSVETGYPGHTLW   88 (433)
Q Consensus        12 ~~~~~~rilvp~~~~~~~vg~IIGk~G~~Ik~I~~~tga~I~v~~---~~~~eRvv~I~G~~~~~~~~~v~~~~~~~~~~   88 (433)
                      ..++++|+|||.    .+||.||||.|.|||.|...|.|+|+|..   .|..||+|+|.|+++                 
T Consensus       196 ~~D~PlR~lVpt----qyvgaIIGkeG~TIknItkqTqsriD~hrken~Gaaek~itvh~tpE-----------------  254 (584)
T KOG2193|consen  196 LKDWPLRLLVPT----QYVGAIIGKEGATIKNITKQTQSRIDVHRKENAGAAEKIITVHSTPE-----------------  254 (584)
T ss_pred             ccCcceeeeecc----ceeEEEecCCCccccCcchhhhheeeeeecccCCcccCceEEecCcc-----------------
Confidence            357999999999    99999999999999999999999999986   378999999999999                 


Q ss_pred             cchHHHHHHHHHHHHhhhhhhcccccCCCCCCCCCeEEEEEeccCcccceecCCchhHHHHHHhhCceEEecc--CCCCC
Q psy11929         89 VTSVDNVCTAYNFMCRSLEDYHINRNRMENCSPQPLQLKLVIPATHCGSLIGKGGCKIKDIRDLSGANVQVAS--DMLPM  166 (433)
Q Consensus        89 ~~a~~~v~~A~~~I~~~~~~~~~~~~~~~~~~~~~~~~~l~ip~~~vg~iIGk~G~~Ik~I~~~sga~I~i~~--~~~~~  166 (433)
                           ...+|+++|++++......     +.-...+.++++.++.+||+||||.|++||+|+.+||++|.|++  +....
T Consensus       255 -----g~s~Ac~~ILeimqkEA~~-----~k~~~e~pLk~lAHN~lvGRLIGKeGrnlKkIeq~TgTkITis~lqels~y  324 (584)
T KOG2193|consen  255 -----GTSKACKMILEIMQKEAVD-----DKVAEEIPLKILAHNNLVGRLIGKEGRNLKKIEQDTGTKITISKLQELSLY  324 (584)
T ss_pred             -----chHHHHHHHHHHHHHhhhc-----cchhhhcchhhhhhcchhhhhhhhccccHHHHHhhcCCceeeeehhhhccc
Confidence                 8999999999998764321     12246788999999999999999999999999999999999986  43335


Q ss_pred             CCccEEEEEccHHHHHHHHHHHHHHHHhhccccCCCcccccCCCCCCCCCccccCCcccccCCCCCCCcccccCCCCCCC
Q psy11929        167 STERIVTVHGNPDTISQAIYQICLVLIECTLQVVKGAVIPYEPKTMNAGPVILSGGQAYTLHGEYAVPVQEVAGKKQPHP  246 (433)
Q Consensus       167 ~~er~v~I~G~~~~v~~A~~~I~~~l~e~~~~~~~~~~~~~~p~~~~~~p~~~~g~~~~~~~g~~~~P~~~~~~~~~~~p  246 (433)
                      ..||+|++.|+.++|.+|..+|+.+|++|++++...  ..++.+..   |.+..  ..+   |.+  |.           
T Consensus       325 npERTItVkGsiEac~~AE~eImkKlre~yEnDl~a--~s~q~~l~---P~l~~--~~l---~~f--~s-----------  381 (584)
T KOG2193|consen  325 NPERTITVKGSIEACVQAEAEIMKKLRECYENDLAA--MSLQCHLP---PGLNL--PAL---GLF--PS-----------  381 (584)
T ss_pred             CccceEEecccHHHHHHHHHHHHHHHHHHHhhhHHH--hhccCCCC---cccCc--ccc---CCC--Cc-----------
Confidence            679999999999999999999999999999866432  11111100   00000  000   000  00           


Q ss_pred             CccccccCcCCCCCCCC---CccccccccCCCcccCCCCCCCCceEEEEEeCcccccccccCCCchHHHHHhHhCCeEEE
Q psy11929        247 LAGLAVLGIEGIGSTSL---TPAALAALSGSRVKSGGKDTGDDFVETEIVLTDDIAGCVIGKAGSRLLEIRQISGAQINI  323 (433)
Q Consensus       247 ~~~~~~~~~~~~~~p~~---~~~~~~~~~~~~~~~~~~~~~~~~~t~~i~VP~~~vG~IIGkgG~~Ik~I~~~sGA~I~I  323 (433)
                           ..++.+++||-.   ..++|+          ......+...++|+||...||+||||+|.+||+|.+++||+|+|
T Consensus       382 -----sS~~~~Ph~~Ps~v~~a~p~~----------~~hq~pe~e~V~~fiP~~~vGAiIGkkG~hIKql~RfagASiKI  446 (584)
T KOG2193|consen  382 -----SSAVSPPHFPPSPVTFASPYP----------LFHQNPEQEQVRMFIPAQAVGAIIGKKGQHIKQLSRFAGASIKI  446 (584)
T ss_pred             -----ccccCCCCCCCCccccCCCch----------hhhcCcchhheeeeccHHHHHHHHhhcchhHHHHHHhccceeee
Confidence                 001111111100   000111          01123367788999999999999999999999999999999999


Q ss_pred             ccCCC--CCceEEEEEeCHHHHHHHHHHHHHHHHhccccCCCCCCCCCccccccccccchhccccccccccCCCCCccee
Q psy11929        324 HTGTE--SHKKMFHIQGCQEAVSLAQYLINMCIELQKNNTTNTSDNPEPADLDAAISAFMTASVNSSLIEKPTPHPGSMV  401 (433)
Q Consensus       324 ~~~~~--~~er~V~IsGt~e~v~~A~~lI~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~vP~~~~G~ii  401 (433)
                      .+++.  ..+|+|+|+|.+++..+|+..|+.+|.++..-.  .   .+.++++.             ++.||++.+||||
T Consensus       447 appE~pdvseRMViItGppeaqfKAQgrifgKikEenf~~--P---keevklet-------------hirVPs~~aGRvI  508 (584)
T KOG2193|consen  447 APPEIPDVSERMVIITGPPEAQFKAQGRIFGKIKEENFFL--P---KEEVKLET-------------HIRVPSSAAGRVI  508 (584)
T ss_pred             cCCCCCCcceeEEEecCChHHHHhhhhhhhhhhhhhccCC--c---hhhheeee-------------eeeccchhhhhhh
Confidence            98876  889999999999999999999999999874322  2   24566664             4669999999999


Q ss_pred             cccc--HHHHHHhhhccccccceeecccc
Q psy11929        402 TLGG--LSELLANIAASNVKSTVQTTGAY  428 (433)
Q Consensus       402 GkgG--~~e~~~~~~~~~~~~~~~~~~~~  428 (433)
                      ||||  ++|| ||||+|+|++|++-|+-.
T Consensus       509 GKGGktVnEL-Qnlt~AeV~vPrdqtpdE  536 (584)
T KOG2193|consen  509 GKGGKTVNEL-QNLTSAEVVVPRDQTPDE  536 (584)
T ss_pred             ccccccHHHH-hccccceEEccccCCCCc
Confidence            9999  7999 999999999999987643

>KOG2192|consensus

Probab=100.00  E-value=1.4e-42  Score=315.47  Aligned_cols=307  Identities=27%  Similarity=0.498  Sum_probs=235.4

Q ss_pred             CceEEEEEEeccCCcccccceeeecCchHHHHHHHHhCCeEEEeCCCCCcceEEEecccCCCCCCccccCCCCCccccch
Q psy11929         12 DTLITMRCLFHSSVNVNEISCLIGPGGCIVRRLRKESGAKISITDGACPDRIVTVSGSVDNSSTSSVETGYPGHTLWVTS   91 (433)
Q Consensus        12 ~~~~~~rilvp~~~~~~~vg~IIGk~G~~Ik~I~~~tga~I~v~~~~~~eRvv~I~G~~~~~~~~~v~~~~~~~~~~~~a   91 (433)
                      ...+.+|||+.+    +.+|+||||+|++||.|+.+++|+|+|++.+.++|+++|+...+                    
T Consensus        45 ~~r~e~ril~~s----k~agavigkgg~nik~lr~d~na~v~vpds~~peri~tisad~~--------------------  100 (390)
T KOG2192|consen   45 RSRVELRILLQS----KNAGAVIGKGGKNIKALRTDYNASVSVPDSSGPERILTISADIE--------------------  100 (390)
T ss_pred             hcceeEEEEEec----ccccceeccccccHHHHhhhccceeeccCCCCCceeEEEeccHH--------------------
Confidence            356999999999    99999999999999999999999999999999999999999999                    


Q ss_pred             HHHHHHHHHHHHhhhhhhcccccCCCCCCCCCeEEEEEeccCcccceecCCchhHHHHHHhhCceEEeccCCCCCCCccE
Q psy11929         92 VDNVCTAYNFMCRSLEDYHINRNRMENCSPQPLQLKLVIPATHCGSLIGKGGCKIKDIRDLSGANVQVASDMLPMSTERI  171 (433)
Q Consensus        92 ~~~v~~A~~~I~~~~~~~~~~~~~~~~~~~~~~~~~l~ip~~~vg~iIGk~G~~Ik~I~~~sga~I~i~~~~~~~~~er~  171 (433)
                        .+...++.|+..|++...        ...++.++|||+.+++|.|||++|++||+|++++.|+.+|..+++|++++|+
T Consensus       101 --ti~~ilk~iip~lee~f~--------~~~pce~rllihqs~ag~iigrngskikelrekcsarlkift~c~p~stdrv  170 (390)
T KOG2192|consen  101 --TIGEILKKIIPTLEEGFQ--------LPSPCELRLLIHQSLAGGIIGRNGSKIKELREKCSARLKIFTECCPHSTDRV  170 (390)
T ss_pred             --HHHHHHHHHhhhhhhCCC--------CCCchhhhhhhhhhhccceecccchhHHHHHHhhhhhhhhhhccCCCCcceE
Confidence              889988888888776321        2567899999999999999999999999999999999999999999999999


Q ss_pred             EEEEccHHHHHHHHHHHHHHHHhhccccCCCcccccCCCCCCC------CCccccCCcccccCCCCCCCcccccCCCCCC
Q psy11929        172 VTVHGNPDTISQAIYQICLVLIECTLQVVKGAVIPYEPKTMNA------GPVILSGGQAYTLHGEYAVPVQEVAGKKQPH  245 (433)
Q Consensus       172 v~I~G~~~~v~~A~~~I~~~l~e~~~~~~~~~~~~~~p~~~~~------~p~~~~g~~~~~~~g~~~~P~~~~~~~~~~~  245 (433)
                      |.|.|.+.+|..+++.|++.|.|   .|.|+.+.||.|.+++.      ++++|.+..+.+  |  +.|.... .+.+++
T Consensus       171 ~l~~g~~k~v~~~i~~il~~i~e---~pikgsa~py~p~fyd~t~dyggf~M~f~d~pg~p--g--papqrgg-qgpp~~  242 (390)
T KOG2192|consen  171 VLIGGKPKRVVECIKIILDLISE---SPIKGSAQPYDPNFYDETYDYGGFTMMFDDRPGRP--G--PAPQRGG-QGPPPP  242 (390)
T ss_pred             EEecCCcchHHHHHHHHHHHhhc---CCcCCcCCcCCccccCcccccCCceeecCCCCCCC--C--CCCCCCC-CCCCCC
Confidence            99999999999999999999999   99999999999988763      333443322111  0  0010000 000000


Q ss_pred             C---CccccccCcCCCC-CCCC-------CccccccccCCCcc---------------c---C-CCCCCCCceEEEEEeC
Q psy11929        246 P---LAGLAVLGIEGIG-STSL-------TPAALAALSGSRVK---------------S---G-GKDTGDDFVETEIVLT  295 (433)
Q Consensus       246 p---~~~~~~~~~~~~~-~p~~-------~~~~~~~~~~~~~~---------------~---~-~~~~~~~~~t~~i~VP  295 (433)
                      +   ++.....+..+.. +.+.       .+.++..|+.+.|.               .   + -.+......|.++.||
T Consensus       243 ~~sdlmay~r~GrpG~rydg~vdFs~detw~saidtw~~SewqmaYePQgGs~ydysyAG~~GsYGdlGGPitTaQvtip  322 (390)
T KOG2192|consen  243 RGSDLMAYDRRGRPGDRYDGMVDFSADETWPSAIDTWSPSEWQMAYEPQGGSGYDYSYAGGYGSYGDLGGPITTAQVTIP  322 (390)
T ss_pred             CccccceeccCCCCCccccccccccccccCCCcCCCcCccccccccCCCCCCCCCccccccccccCCCCCceeeeeEecc
Confidence            0   1111111100000 0000       01111112111110               0   0 1123456788999999


Q ss_pred             cccccccccCCCchHHHHHhHhCCeEEEccCCC-CCceEEEEEeCHHHHHHHHHHHHHHHHhcccc
Q psy11929        296 DDIAGCVIGKAGSRLLEIRQISGAQINIHTGTE-SHKKMFHIQGCQEAVSLAQYLINMCIELQKNN  360 (433)
Q Consensus       296 ~~~vG~IIGkgG~~Ik~I~~~sGA~I~I~~~~~-~~er~V~IsGt~e~v~~A~~lI~~~i~~~~~~  360 (433)
                      .++-|.||||+|++|++|++++||+|+|+++.+ +.+|+++|+||.+|++.||+|+++++.+-+++
T Consensus       323 ~dlggsiigkggqri~~ir~esGA~IkidepleGsedrIitItGTqdQIqnAQYLlQn~Vkq~rer  388 (390)
T KOG2192|consen  323 KDLGGSIIGKGGQRIKQIRHESGASIKIDEPLEGSEDRIITITGTQDQIQNAQYLLQNSVKQYRER  388 (390)
T ss_pred             cccCcceecccchhhhhhhhccCceEEecCcCCCCCceEEEEeccHHHHhhHHHHHHHHHHhhhcc
Confidence            999999999999999999999999999999888 99999999999999999999999999865443

>KOG1676|consensus

Probab=100.00  E-value=7.6e-40  Score=328.38  Aligned_cols=297  Identities=23%  Similarity=0.368  Sum_probs=237.7

Q ss_pred             CceEEEEEEeccCCcccccceeeecCchHHHHHHHHhCCeEEEeCC--CCCcceEEEecccCCCCCCccccCCCCCcccc
Q psy11929         12 DTLITMRCLFHSSVNVNEISCLIGPGGCIVRRLRKESGAKISITDG--ACPDRIVTVSGSVDNSSTSSVETGYPGHTLWV   89 (433)
Q Consensus        12 ~~~~~~rilvp~~~~~~~vg~IIGk~G~~Ik~I~~~tga~I~v~~~--~~~eRvv~I~G~~~~~~~~~v~~~~~~~~~~~   89 (433)
                      +..++.+.-||.    ..||.||||+|+.|..|..++||+|++...  +..+|-|.+.|.++                  
T Consensus        51 ~~~~~~~~~VPd----~~VglvIGrgG~qI~~iqq~SgCrvq~~~~~s~~~~r~~~~~G~pe------------------  108 (600)
T KOG1676|consen   51 DTVQTERYKVPD----EAVGLVIGRGGSQIQAIQQKSGCRVQIAADPSGIGYRSVDLTGSPE------------------  108 (600)
T ss_pred             ccccccccCCCc----hhceeEeeccHHHhhhhhhhcCCccccCCCCCCcccccccccCCcc------------------
Confidence            356788899999    999999999999999999999999998653  67899999999999                  


Q ss_pred             chHHHHHHHHHHHHhhhhhhc--ccccCCCCCCCCCeEEEEEeccCcccceecCCchhHHHHHHhhCceEEeccCCC-CC
Q psy11929         90 TSVDNVCTAYNFMCRSLEDYH--INRNRMENCSPQPLQLKLVIPATHCGSLIGKGGCKIKDIRDLSGANVQVASDML-PM  166 (433)
Q Consensus        90 ~a~~~v~~A~~~I~~~~~~~~--~~~~~~~~~~~~~~~~~l~ip~~~vg~iIGk~G~~Ik~I~~~sga~I~i~~~~~-~~  166 (433)
                          .+..|+.||.+++....  ..+.  .......++.+++||++.+|.||||+|++||.|++.+||++.+..|.. ..
T Consensus       109 ----~v~~aK~li~evv~r~~~~~~~~--~~q~~~~ttqeI~IPa~k~GlIIGKgGETikqlqe~sg~k~i~iqd~~~~~  182 (600)
T KOG1676|consen  109 ----NVEVAKQLIGEVVSRGRPPGGFP--DNQGSVETTQEILIPANKCGLIIGKGGETIKQLQEQSGVKMILVQDGSIAT  182 (600)
T ss_pred             ----cHHHHHHhhhhhhhccCCCCCcc--ccCCccceeeeeccCccceeeEeccCccHHHHHHhhcCCceEEEecCCcCC
Confidence                99999999998876642  1111  112245688999999999999999999999999999999998887543 33


Q ss_pred             CCccEEEEEccHHHHHHHHHHHHHHHHhhccccCCCcccccCCCCCCCCCccccCCcccccCCCCCCCcccccCCCCCCC
Q psy11929        167 STERIVTVHGNPDTISQAIYQICLVLIECTLQVVKGAVIPYEPKTMNAGPVILSGGQAYTLHGEYAVPVQEVAGKKQPHP  246 (433)
Q Consensus       167 ~~er~v~I~G~~~~v~~A~~~I~~~l~e~~~~~~~~~~~~~~p~~~~~~p~~~~g~~~~~~~g~~~~P~~~~~~~~~~~p  246 (433)
                      ..++.+.|+|+++.|+.|+.+|.++|++......                         +..+.+               
T Consensus       183 ~~~KplritGdp~~ve~a~~lV~dil~e~~~~~~-------------------------g~~~~~---------------  222 (600)
T KOG1676|consen  183 GADKPLRITGDPDKVEQAKQLVADILREEDDEVP-------------------------GSGGHA---------------  222 (600)
T ss_pred             CCCCceeecCCHHHHHHHHHHHHHHHHhcccCCC-------------------------cccccc---------------
Confidence            4889999999999999999999999997321000                         000000               


Q ss_pred             CccccccCcCCCCCCCCCccccccccCCCcccCCCCCCCCceEEEEEeCcccccccccCCCchHHHHHhHhCCeEEEccC
Q psy11929        247 LAGLAVLGIEGIGSTSLTPAALAALSGSRVKSGGKDTGDDFVETEIVLTDDIAGCVIGKAGSRLLEIRQISGAQINIHTG  326 (433)
Q Consensus       247 ~~~~~~~~~~~~~~p~~~~~~~~~~~~~~~~~~~~~~~~~~~t~~i~VP~~~vG~IIGkgG~~Ik~I~~~sGA~I~I~~~  326 (433)
                                                       +.. .....+.+|.||...||.||||+|++||.|+.+|||+|+|.++
T Consensus       223 ---------------------------------g~~-~g~~~~~~V~VPr~~VG~IIGkgGE~IKklq~etG~KIQfkpD  268 (600)
T KOG1676|consen  223 ---------------------------------GVR-GGGSATREVKVPRSKVGIIIGKGGEMIKKLQNETGAKIQFKPD  268 (600)
T ss_pred             ---------------------------------CcC-ccccceeEEeccccceeeEEecCchHHHHHhhccCceeEeecC
Confidence                                             000 0123378999999999999999999999999999999999988


Q ss_pred             CC--CCceEEEEEeCHHHHHHHHHHHHHHHHhccccCCCCCCCCCccccccccccchhccccccccccCCCCCcceeccc
Q psy11929        327 TE--SHKKMFHIQGCQEAVSLAQYLINMCIELQKNNTTNTSDNPEPADLDAAISAFMTASVNSSLIEKPTPHPGSMVTLG  404 (433)
Q Consensus       327 ~~--~~er~V~IsGt~e~v~~A~~lI~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~vP~~~~G~iiGkg  404 (433)
                      .+  +.||.+.|.|+.++|+.|..||.++|+...+...+..+.-.+.-.            ..++++||+++||.|||||
T Consensus       269 d~p~speR~~~IiG~~d~ie~Aa~lI~eii~~~~~~~~~~~~~G~P~~~------------~~fy~~VPa~KcGLvIGrG  336 (600)
T KOG1676|consen  269 DDPSSPERPAQIIGTVDQIEHAAELINEIIAEAEAGAGGGMGGGAPGLV------------AQFYMKVPADKCGLVIGRG  336 (600)
T ss_pred             CCCCCccceeeeecCHHHHHHHHHHHHHHHHHHhccCCCCcCCCCccce------------eeEEEeccccccccccCCC
Confidence            87  899999999999999999999999999876654332211111110            1367999999999999999


Q ss_pred             c--HHHHHHhhhcccccccee
Q psy11929        405 G--LSELLANIAASNVKSTVQ  423 (433)
Q Consensus       405 G--~~e~~~~~~~~~~~~~~~  423 (433)
                      |  ++.| ..-++|.+-.+++
T Consensus       337 GEtIK~i-n~qSGA~~el~r~  356 (600)
T KOG1676|consen  337 GETIKQI-NQQSGARCELSRQ  356 (600)
T ss_pred             ccchhhh-cccCCccccccCC
Confidence            9  7877 6678886666666

>KOG2190|consensus

Probab=100.00  E-value=6.6e-39  Score=326.63  Aligned_cols=321  Identities=30%  Similarity=0.498  Sum_probs=242.9

Q ss_pred             CCceEEEEEEeccCCcccccceeeecCchHHHHHHHHhCCeEEEeC--CCCCcceEEEecccCCCCCCccccCCCCCccc
Q psy11929         11 EDTLITMRCLFHSSVNVNEISCLIGPGGCIVRRLRKESGAKISITD--GACPDRIVTVSGSVDNSSTSSVETGYPGHTLW   88 (433)
Q Consensus        11 ~~~~~~~rilvp~~~~~~~vg~IIGk~G~~Ik~I~~~tga~I~v~~--~~~~eRvv~I~G~~~~~~~~~v~~~~~~~~~~   88 (433)
                      .+.+.++|||||.    +.+|.||||+|.+||+||.+|.++|+|.+  +++.+|+++|+|...             +..+
T Consensus        39 p~~t~~~RlL~~~----kevG~IIGk~G~~vkkir~~t~s~i~i~~~~~~c~eRIiti~g~~~-------------~~~~  101 (485)
T KOG2190|consen   39 PDETLTYRLLCHV----KEVGSIIGKKGDIVKKIRKETESKIRVNESLPGCPERIITITGNRV-------------ELNL  101 (485)
T ss_pred             CCCcceEEEEecc----ccceeEEccCcHHHHHHhhcccccceeecCCCCCCcceEEEecccc-------------cccC
Confidence            3445569999999    99999999999999999999999999977  489999999999733             1267


Q ss_pred             cchHHHHHHHHHHHHhhhhhhccccc-CCCCCCCCCeEEEEEeccCcccceecCCchhHHHHHHhhCceEEeccCCCCCC
Q psy11929         89 VTSVDNVCTAYNFMCRSLEDYHINRN-RMENCSPQPLQLKLVIPATHCGSLIGKGGCKIKDIRDLSGANVQVASDMLPMS  167 (433)
Q Consensus        89 ~~a~~~v~~A~~~I~~~~~~~~~~~~-~~~~~~~~~~~~~l~ip~~~vg~iIGk~G~~Ik~I~~~sga~I~i~~~~~~~~  167 (433)
                      +++++++++|+.+|...+++...... ...+....+++++|+||.+++|+||||+|+.||+|+++|||+|++.++.+|.+
T Consensus       102 ~~~~~al~ka~~~iv~~~~~d~~~~~d~~~~~~~~~v~~RLlVp~sq~GslIGK~G~~Ik~Ire~TgA~I~v~~~~lP~s  181 (485)
T KOG2190|consen  102 SPATDALFKAFDMIVFKLEEDDEAAEDNGEDASGPEVTCRLLVPSSQVGSLIGKGGSLIKEIREETGAKIRVSSDMLPNS  181 (485)
T ss_pred             CchHHHHHHHHHHHhhcccccccccccCCccccCCceEEEEEechhheeeeeccCcHHHHHHHHhcCceEEecCCCCCcc
Confidence            88999999999999998764322221 11122233689999999999999999999999999999999999999999999


Q ss_pred             CccEEEEEccHHHHHHHHHHHHHHHHhhc--cccCCCcccccCCCCCCCCCccccCCcccccCCCCCCCcccccCCCCCC
Q psy11929        168 TERIVTVHGNPDTISQAIYQICLVLIECT--LQVVKGAVIPYEPKTMNAGPVILSGGQAYTLHGEYAVPVQEVAGKKQPH  245 (433)
Q Consensus       168 ~er~v~I~G~~~~v~~A~~~I~~~l~e~~--~~~~~~~~~~~~p~~~~~~p~~~~g~~~~~~~g~~~~P~~~~~~~~~~~  245 (433)
                      ++|.|+|.|.+++|.+|+..|..+|+++.  ..+.+..+++|.|......+.+...++...                   
T Consensus       182 ter~V~IsG~~~av~~al~~Is~~L~~~~~~~~~~~~st~~y~P~~~~~~~~~~s~~~~~~-------------------  242 (485)
T KOG2190|consen  182 TERAVTISGEPDAVKKALVQISSRLLENPPRSPPPLVSTIPYRPSASQGGPVLPSTAQTSP-------------------  242 (485)
T ss_pred             cceeEEEcCchHHHHHHHHHHHHHHHhcCCcCCCCCCCcccCCCcccccCccccccccCCc-------------------
Confidence            99999999999999999999999999942  133355667777622221121111111000                   


Q ss_pred             CCccccccCcCCCCCCCCCccccccccCCCcccCCCCCCCCceEEEEEeCcccccccccCCCchHHHHHhHhCCeEEEcc
Q psy11929        246 PLAGLAVLGIEGIGSTSLTPAALAALSGSRVKSGGKDTGDDFVETEIVLTDDIAGCVIGKAGSRLLEIRQISGAQINIHT  325 (433)
Q Consensus       246 p~~~~~~~~~~~~~~p~~~~~~~~~~~~~~~~~~~~~~~~~~~t~~i~VP~~~vG~IIGkgG~~Ik~I~~~sGA~I~I~~  325 (433)
                                           .+.+        .+......+...++.+|...++.|||++|..|+.|+.++|+.|.+..
T Consensus       243 ---------------------~~~~--------~~~~~~~~e~~~~~~~p~~~~~~v~g~~~~~i~~l~~~~~~~i~v~~  293 (485)
T KOG2190|consen  243 ---------------------DAHP--------FGGIVPEEELVFKLICPSDKVGSVIGKGGLVIRALRNETGASISVGD  293 (485)
T ss_pred             ---------------------cccc--------ccccccchhhhhhhcCchhhceeeecCCCccchhhhhhcCCceEecc
Confidence                                 0000        01112345677889999999999999999999999999999999999


Q ss_pred             CCCCCceEEEEEeCH--H----HHHHHHHHHHHHHHhccccCCCCCCCCCccccccccccchhccccccccccCCCCCcc
Q psy11929        326 GTESHKKMFHIQGCQ--E----AVSLAQYLINMCIELQKNNTTNTSDNPEPADLDAAISAFMTASVNSSLIEKPTPHPGS  399 (433)
Q Consensus       326 ~~~~~er~V~IsGt~--e----~v~~A~~lI~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~vP~~~~G~  399 (433)
                      +. .+ |.|+++...  +    ..+.|..+++..+.+.....           ....         .++.|.||++.+||
T Consensus       294 ~~-~~-~~i~~s~~e~~~~~~s~a~~a~~~~~~~~~~~~~~~-----------~~~~---------v~~~l~vps~~igc  351 (485)
T KOG2190|consen  294 SR-TD-RIVTISARENPEDRYSMAQEALLLVQPRISENAGDD-----------LTQT---------VTQRLLVPSDLIGC  351 (485)
T ss_pred             cc-Cc-ceeeeccccCcccccccchhhhhhcccccccccccc-----------ccce---------eeeeeccCccccce
Confidence            87 33 899998875  3    34667777777665432100           0111         23668899999999


Q ss_pred             eecccc--HHHHHHhhhccccc
Q psy11929        400 MVTLGG--LSELLANIAASNVK  419 (433)
Q Consensus       400 iiGkgG--~~e~~~~~~~~~~~  419 (433)
                      +|||+|  ++|||| .|+|.+.
T Consensus       352 iiGk~G~~iseir~-~tgA~I~  372 (485)
T KOG2190|consen  352 IIGKGGAKISEIRQ-RTGASIS  372 (485)
T ss_pred             eecccccchHHHHH-hcCCceE
Confidence            999999  799955 5777544

>KOG1676|consensus

Probab=100.00  E-value=3.1e-35  Score=295.24  Aligned_cols=248  Identities=26%  Similarity=0.380  Sum_probs=206.1

Q ss_pred             CceEEEEEEeccCCcccccceeeecCchHHHHHHHHhCCeEEEeCCC----CCcceEEEecccCCCCCCccccCCCCCcc
Q psy11929         12 DTLITMRCLFHSSVNVNEISCLIGPGGCIVRRLRKESGAKISITDGA----CPDRIVTVSGSVDNSSTSSVETGYPGHTL   87 (433)
Q Consensus        12 ~~~~~~rilvp~~~~~~~vg~IIGk~G~~Ik~I~~~tga~I~v~~~~----~~eRvv~I~G~~~~~~~~~v~~~~~~~~~   87 (433)
                      ...++..|+||.    +++|.||||+|++||+|++++||++.+-.++    ...+-+.|+|.++                
T Consensus       136 ~~~ttqeI~IPa----~k~GlIIGKgGETikqlqe~sg~k~i~iqd~~~~~~~~KplritGdp~----------------  195 (600)
T KOG1676|consen  136 SVETTQEILIPA----NKCGLIIGKGGETIKQLQEQSGVKMILVQDGSIATGADKPLRITGDPD----------------  195 (600)
T ss_pred             ccceeeeeccCc----cceeeEeccCccHHHHHHhhcCCceEEEecCCcCCCCCCceeecCCHH----------------
Confidence            567899999999    9999999999999999999999999987653    2678999999999                


Q ss_pred             ccchHHHHHHHHHHHHhhhhhhcccccCC----CCCCCCCeEEEEEeccCcccceecCCchhHHHHHHhhCceEEeccCC
Q psy11929         88 WVTSVDNVCTAYNFMCRSLEDYHINRNRM----ENCSPQPLQLKLVIPATHCGSLIGKGGCKIKDIRDLSGANVQVASDM  163 (433)
Q Consensus        88 ~~~a~~~v~~A~~~I~~~~~~~~~~~~~~----~~~~~~~~~~~l~ip~~~vg~iIGk~G~~Ik~I~~~sga~I~i~~~~  163 (433)
                            .|..|..++.++|.+...+....    ........++++.||...||.||||+|++||+|+.+||++|+|.+|.
T Consensus       196 ------~ve~a~~lV~dil~e~~~~~~g~~~~~g~~~g~~~~~~V~VPr~~VG~IIGkgGE~IKklq~etG~KIQfkpDd  269 (600)
T KOG1676|consen  196 ------KVEQAKQLVADILREEDDEVPGSGGHAGVRGGGSATREVKVPRSKVGIIIGKGGEMIKKLQNETGAKIQFKPDD  269 (600)
T ss_pred             ------HHHHHHHHHHHHHHhcccCCCccccccCcCccccceeEEeccccceeeEEecCchHHHHHhhccCceeEeecCC
Confidence                  99999999999998633221111    11223344899999999999999999999999999999999999988


Q ss_pred             CCCCCccEEEEEccHHHHHHHHHHHHHHHHhhccccCCCcccccCCCCCCCCCccccCCcccccCCCCCCCcccccCCCC
Q psy11929        164 LPMSTERIVTVHGNPDTISQAIYQICLVLIECTLQVVKGAVIPYEPKTMNAGPVILSGGQAYTLHGEYAVPVQEVAGKKQ  243 (433)
Q Consensus       164 ~~~~~er~v~I~G~~~~v~~A~~~I~~~l~e~~~~~~~~~~~~~~p~~~~~~p~~~~g~~~~~~~g~~~~P~~~~~~~~~  243 (433)
                      .|.+.||.+.|.|+.+.|+.|.++|.++|.+..+..                     ++   +                 
T Consensus       270 ~p~speR~~~IiG~~d~ie~Aa~lI~eii~~~~~~~---------------------~~---~-----------------  308 (600)
T KOG1676|consen  270 DPSSPERPAQIIGTVDQIEHAAELINEIIAEAEAGA---------------------GG---G-----------------  308 (600)
T ss_pred             CCCCccceeeeecCHHHHHHHHHHHHHHHHHHhccC---------------------CC---C-----------------
Confidence            888999999999999999999999999999832100                     00   0                 


Q ss_pred             CCCCccccccCcCCCCCCCCCccccccccCCCcccCCCCCCCCceEEEEEeCcccccccccCCCchHHHHHhHhCCeEEE
Q psy11929        244 PHPLAGLAVLGIEGIGSTSLTPAALAALSGSRVKSGGKDTGDDFVETEIVLTDDIAGCVIGKAGSRLLEIRQISGAQINI  323 (433)
Q Consensus       244 ~~p~~~~~~~~~~~~~~p~~~~~~~~~~~~~~~~~~~~~~~~~~~t~~i~VP~~~vG~IIGkgG~~Ik~I~~~sGA~I~I  323 (433)
                               ++.                        +. +. ....++|.||.+++|.||||+|++||+|.++|||++.+
T Consensus       309 ---------~~~------------------------G~-P~-~~~~fy~~VPa~KcGLvIGrGGEtIK~in~qSGA~~el  353 (600)
T KOG1676|consen  309 ---------MGG------------------------GA-PG-LVAQFYMKVPADKCGLVIGRGGETIKQINQQSGARCEL  353 (600)
T ss_pred             ---------cCC------------------------CC-cc-ceeeEEEeccccccccccCCCccchhhhcccCCccccc
Confidence                     000                        00 00 11278999999999999999999999999999999999


Q ss_pred             ccCCC---CCceEEEEEeCHHHHHHHHHHHHHHHHhccccC
Q psy11929        324 HTGTE---SHKKMFHIQGCQEAVSLAQYLINMCIELQKNNT  361 (433)
Q Consensus       324 ~~~~~---~~er~V~IsGt~e~v~~A~~lI~~~i~~~~~~~  361 (433)
                      .+..+   ..|++|+|+|++.+|+.|+.||..++..-..+.
T Consensus       354 ~r~~p~~~~~ektf~IrG~~~QIdhAk~LIr~kvg~~~~n~  394 (600)
T KOG1676|consen  354 SRQPPNGNPKEKTFVIRGDKRQIDHAKQLIRDKVGDIAPNT  394 (600)
T ss_pred             cCCCCCCCccceEEEEecCcccchHHHHHHHHHhcccCCCC
Confidence            98733   889999999999999999999999998754333

>KOG2193|consensus

Probab=99.97  E-value=3.6e-31  Score=254.32  Aligned_cols=244  Identities=27%  Similarity=0.410  Sum_probs=206.6

Q ss_pred             CCCCCceEEEEEEeccCCcccccceeeecCchHHHHHHHHhCCeEEEeCC-----CCCcceEEEecccCCCCCCccccCC
Q psy11929          8 KIDEDTLITMRCLFHSSVNVNEISCLIGPGGCIVRRLRKESGAKISITDG-----ACPDRIVTVSGSVDNSSTSSVETGY   82 (433)
Q Consensus         8 ~~~~~~~~~~rilvp~~~~~~~vg~IIGk~G~~Ik~I~~~tga~I~v~~~-----~~~eRvv~I~G~~~~~~~~~v~~~~   82 (433)
                      +|+...++++|||.++    ..+|++|||.|.+||+|+++||++|.|+.-     -.+||.|+|.|+.+           
T Consensus       273 ~~k~~~e~pLk~lAHN----~lvGRLIGKeGrnlKkIeq~TgTkITis~lqels~ynpERTItVkGsiE-----------  337 (584)
T KOG2193|consen  273 DDKVAEEIPLKILAHN----NLVGRLIGKEGRNLKKIEQDTGTKITISKLQELSLYNPERTITVKGSIE-----------  337 (584)
T ss_pred             ccchhhhcchhhhhhc----chhhhhhhhccccHHHHHhhcCCceeeeehhhhcccCccceEEecccHH-----------
Confidence            4566789999999999    999999999999999999999999999872     36899999999999           


Q ss_pred             CCCccccchHHHHHHHHHHHHhhhhhhccc--------------c--------cCCC---------------------CC
Q psy11929         83 PGHTLWVTSVDNVCTAYNFMCRSLEDYHIN--------------R--------NRME---------------------NC  119 (433)
Q Consensus        83 ~~~~~~~~a~~~v~~A~~~I~~~~~~~~~~--------------~--------~~~~---------------------~~  119 (433)
                                 +|.+|..+|+.++.+..++              +        ....                     ..
T Consensus       338 -----------ac~~AE~eImkKlre~yEnDl~a~s~q~~l~P~l~~~~l~~f~ssS~~~~Ph~~Ps~v~~a~p~~~~hq  406 (584)
T KOG2193|consen  338 -----------ACVQAEAEIMKKLRECYENDLAAMSLQCHLPPGLNLPALGLFPSSSAVSPPHFPPSPVTFASPYPLFHQ  406 (584)
T ss_pred             -----------HHHHHHHHHHHHHHHHHhhhHHHhhccCCCCcccCccccCCCCcccccCCCCCCCCccccCCCchhhhc
Confidence                       9999999999988762110              0        0000                     00


Q ss_pred             CCCCeEEEEEeccCcccceecCCchhHHHHHHhhCceEEeccCCCCCCCccEEEEEccHHHHHHHHHHHHHHHHhhcccc
Q psy11929        120 SPQPLQLKLVIPATHCGSLIGKGGCKIKDIRDLSGANVQVASDMLPMSTERIVTVHGNPDTISQAIYQICLVLIECTLQV  199 (433)
Q Consensus       120 ~~~~~~~~l~ip~~~vg~iIGk~G~~Ik~I~~~sga~I~i~~~~~~~~~er~v~I~G~~~~v~~A~~~I~~~l~e~~~~~  199 (433)
                      ......++|.||...+|.||||+|.+||.|.+.+||.|+|.+...|+..+|.|+|+|++++..+|...|..+|.|...  
T Consensus       407 ~pe~e~V~~fiP~~~vGAiIGkkG~hIKql~RfagASiKIappE~pdvseRMViItGppeaqfKAQgrifgKikEenf--  484 (584)
T KOG2193|consen  407 NPEQEQVRMFIPAQAVGAIIGKKGQHIKQLSRFAGASIKIAPPEIPDVSERMVIITGPPEAQFKAQGRIFGKIKEENF--  484 (584)
T ss_pred             CcchhheeeeccHHHHHHHHhhcchhHHHHHHhccceeeecCCCCCCcceeEEEecCChHHHHhhhhhhhhhhhhhcc--
Confidence            123456899999999999999999999999999999999998778889999999999999999999999999998210  


Q ss_pred             CCCcccccCCCCCCCCCccccCCcccccCCCCCCCcccccCCCCCCCCccccccCcCCCCCCCCCccccccccCCCcccC
Q psy11929        200 VKGAVIPYEPKTMNAGPVILSGGQAYTLHGEYAVPVQEVAGKKQPHPLAGLAVLGIEGIGSTSLTPAALAALSGSRVKSG  279 (433)
Q Consensus       200 ~~~~~~~~~p~~~~~~p~~~~g~~~~~~~g~~~~P~~~~~~~~~~~p~~~~~~~~~~~~~~p~~~~~~~~~~~~~~~~~~  279 (433)
                             +.                         |.                                            
T Consensus       485 -------~~-------------------------Pk--------------------------------------------  488 (584)
T KOG2193|consen  485 -------FL-------------------------PK--------------------------------------------  488 (584)
T ss_pred             -------CC-------------------------ch--------------------------------------------
Confidence                   11                         10                                            


Q ss_pred             CCCCCCCceEEEEEeCcccccccccCCCchHHHHHhHhCCeEEEccCCC---CCceEEEEEeCHHHHHHHHHHHHHHHHh
Q psy11929        280 GKDTGDDFVETEIVLTDDIAGCVIGKAGSRLLEIRQISGAQINIHTGTE---SHKKMFHIQGCQEAVSLAQYLINMCIEL  356 (433)
Q Consensus       280 ~~~~~~~~~t~~i~VP~~~vG~IIGkgG~~Ik~I~~~sGA~I~I~~~~~---~~er~V~IsGt~e~v~~A~~lI~~~i~~  356 (433)
                          ........+.||...+|+||||||.++++|++.|+|.|.|+++..   .+.-+|.|.|..-+.+.|++.|.+++.+
T Consensus       489 ----eevklethirVPs~~aGRvIGKGGktVnELQnlt~AeV~vPrdqtpdEnd~vivriiGhfyatq~aQrki~~iv~q  564 (584)
T KOG2193|consen  489 ----EEVKLETHIRVPSSAAGRVIGKGGKTVNELQNLTSAEVVVPRDQTPDENDQVIVRIIGHFYATQNAQRKIAHIVNQ  564 (584)
T ss_pred             ----hhheeeeeeeccchhhhhhhccccccHHHHhccccceEEccccCCCCccceeeeeeechhhcchHHHHHHHHHHHH
Confidence                123556789999999999999999999999999999999998776   6667889999999999999999999987


Q ss_pred             ccc
Q psy11929        357 QKN  359 (433)
Q Consensus       357 ~~~  359 (433)
                      -+.
T Consensus       565 vkq  567 (584)
T KOG2193|consen  565 VKQ  567 (584)
T ss_pred             HHH
Confidence            643

>KOG2191|consensus

Probab=99.97  E-value=6.5e-29  Score=232.60  Aligned_cols=268  Identities=23%  Similarity=0.343  Sum_probs=204.8

Q ss_pred             CceEEEEEEeccCCcccccceeeecCchHHHHHHHHhCCeEEEeCC-----CCCcceEEEecccCCCCCCccccCCCCCc
Q psy11929         12 DTLITMRCLFHSSVNVNEISCLIGPGGCIVRRLRKESGAKISITDG-----ACPDRIVTVSGSVDNSSTSSVETGYPGHT   86 (433)
Q Consensus        12 ~~~~~~rilvp~~~~~~~vg~IIGk~G~~Ik~I~~~tga~I~v~~~-----~~~eRvv~I~G~~~~~~~~~v~~~~~~~~   86 (433)
                      +..+.+|+|||+    ..+|.||||+|++|.+|+++|||+|++++.     ++.||||.|+|+.+               
T Consensus        36 ~~~y~ikvLips----~AaGsIIGKGG~ti~~lqk~tgariklSks~dfyPGTTeRvcli~Gt~e---------------   96 (402)
T KOG2191|consen   36 DGQYFLKVLIPS----YAAGSIIGKGGQTIVQLQKETGARIKLSKSKDFYPGTTERVCLIQGTVE---------------   96 (402)
T ss_pred             CCceEEEEEeec----ccccceeccchHHHHHHHhccCcEEEeccccccCCCccceEEEEeccHH---------------
Confidence            344999999999    999999999999999999999999999983     89999999999999               


Q ss_pred             cccchHHHHHHHHHHHHhhhhhhcccccCC-C----CCCCCCeEEEEEeccCcccceecCCchhHHHHHHhhCceEEecc
Q psy11929         87 LWVTSVDNVCTAYNFMCRSLEDYHINRNRM-E----NCSPQPLQLKLVIPATHCGSLIGKGGCKIKDIRDLSGANVQVAS  161 (433)
Q Consensus        87 ~~~~a~~~v~~A~~~I~~~~~~~~~~~~~~-~----~~~~~~~~~~l~ip~~~vg~iIGk~G~~Ik~I~~~sga~I~i~~  161 (433)
                             ++..++++|.+++++........ +    ...+....+++++|++.+|.||||+|.+||.|++++||.|+|++
T Consensus        97 -------ai~av~efI~dKire~p~~~~k~v~~~~pqt~~r~kqikivvPNstag~iigkggAtiK~~~Eqsga~iqisP  169 (402)
T KOG2191|consen   97 -------ALNAVHEFIADKIREKPQAVAKPVDILQPQTPDRIKQIKIVVPNSTAGMIIGKGGATIKAIQEQSGAWIQISP  169 (402)
T ss_pred             -------HHHHHHHHHHHHHHHhHHhhcCCccccCCCCccccceeEEeccCCcccceecCCcchHHHHHHhhCcceEecc
Confidence                   99999999999999865443321 1    11223345899999999999999999999999999999999984


Q ss_pred             --CCCCCCCccEEEEEccHHHHHHHHHHHHHHHHhhccccCCCcccccCCCCCCCCCccccCCcccccCCCCCCCccccc
Q psy11929        162 --DMLPMSTERIVTVHGNPDTISQAIYQICLVLIECTLQVVKGAVIPYEPKTMNAGPVILSGGQAYTLHGEYAVPVQEVA  239 (433)
Q Consensus       162 --~~~~~~~er~v~I~G~~~~v~~A~~~I~~~l~e~~~~~~~~~~~~~~p~~~~~~p~~~~g~~~~~~~g~~~~P~~~~~  239 (433)
                        +....-.+|+|++.|++++..+|..+|+++|.+   +|..+..+. .+.....+|+..+                   
T Consensus       170 qkpt~~sLqervvt~sge~e~~~~A~~~IL~Ki~e---Dpqs~scln-~sya~vsGpvaNs-------------------  226 (402)
T KOG2191|consen  170 QKPTGISLQERVVTVSGEPEQNMKAVSLILQKIQE---DPQSGSCLN-ISYANVSGPVANS-------------------  226 (402)
T ss_pred             cCCCCccceeEEEEecCCHHHHHHHHHHHHHHhhc---CCcccceec-cchhcccCccccc-------------------
Confidence              223345899999999999999999999999999   665443222 0000000000000                   


Q ss_pred             CCCCCCCCccccccCcCCCCCCCCCccccccccCCCcccCCCCCCCCceEEEEEeCcccccccccCCCchHHHHHhHhCC
Q psy11929        240 GKKQPHPLAGLAVLGIEGIGSTSLTPAALAALSGSRVKSGGKDTGDDFVETEIVLTDDIAGCVIGKAGSRLLEIRQISGA  319 (433)
Q Consensus       240 ~~~~~~p~~~~~~~~~~~~~~p~~~~~~~~~~~~~~~~~~~~~~~~~~~t~~i~VP~~~vG~IIGkgG~~Ik~I~~~sGA  319 (433)
                                 .     |    .+.+-.+           ..+...........++...+|..-|.+|.++-.|-..+|+
T Consensus       227 -----------n-----P----tGspya~-----------~~~~~~astas~~sva~~~iG~a~gaG~~~~a~l~~~~G~  275 (402)
T KOG2191|consen  227 -----------N-----P----TGSPYAY-----------QAHVLPASTASTISVAAGLIGGANGAGGAFGAALSGFTGA  275 (402)
T ss_pred             -----------C-----C----CCCCCCC-----------CCccccccchhhccccccccccccccccccceeeeccccc
Confidence                       0     0    0000000           1112223344567789999999999999999999999999


Q ss_pred             eEEEccCCC----CCceEEEEEeCHHHHHHHHHHHHHHHHhcccc
Q psy11929        320 QINIHTGTE----SHKKMFHIQGCQEAVSLAQYLINMCIELQKNN  360 (433)
Q Consensus       320 ~I~I~~~~~----~~er~V~IsGt~e~v~~A~~lI~~~i~~~~~~  360 (433)
                      .+.+++..+    ...+ .-+.|.+-++..|..+|..++.....+
T Consensus       276 l~~itq~l~~m~g~gy~-~n~~g~~ls~~aa~g~L~~~~~~a~t~  319 (402)
T KOG2191|consen  276 LIAITQALNTMAGYGYN-TNILGLGLSILAAEGVLAAKVASANTA  319 (402)
T ss_pred             ceeeccccccccccccc-ccccchhhhhhhhhhHHHHhhcccCcc
Confidence            999998766    4444 888999999999999999888776443

>KOG2191|consensus

Probab=99.93  E-value=1.7e-24  Score=203.02  Aligned_cols=212  Identities=26%  Similarity=0.364  Sum_probs=158.3

Q ss_pred             CCCeEEEEEeccCcccceecCCchhHHHHHHhhCceEEecc--CCCCCCCccEEEEEccHHHHHHHHHHHHHHHHhhccc
Q psy11929        121 PQPLQLKLVIPATHCGSLIGKGGCKIKDIRDLSGANVQVAS--DMLPMSTERIVTVHGNPDTISQAIYQICLVLIECTLQ  198 (433)
Q Consensus       121 ~~~~~~~l~ip~~~vg~iIGk~G~~Ik~I~~~sga~I~i~~--~~~~~~~er~v~I~G~~~~v~~A~~~I~~~l~e~~~~  198 (433)
                      .....+++|||+..+|.||||+|++|.+++++|||+|++++  |.+|+.+||++-|+|+.+++......|.++|++.   
T Consensus        36 ~~~y~ikvLips~AaGsIIGKGG~ti~~lqk~tgariklSks~dfyPGTTeRvcli~Gt~eai~av~efI~dKire~---  112 (402)
T KOG2191|consen   36 DGQYFLKVLIPSYAAGSIIGKGGQTIVQLQKETGARIKLSKSKDFYPGTTERVCLIQGTVEALNAVHEFIADKIREK---  112 (402)
T ss_pred             CCceEEEEEeecccccceeccchHHHHHHHhccCcEEEeccccccCCCccceEEEEeccHHHHHHHHHHHHHHHHHh---
Confidence            34489999999999999999999999999999999999985  8899999999999999999999999999999992   


Q ss_pred             cCCCcccccCCCCCCCCCccccCCcccccCCCCCCCcccccCCCCCCCCccccccCcCCCCCCCCCccccccccCCCccc
Q psy11929        199 VVKGAVIPYEPKTMNAGPVILSGGQAYTLHGEYAVPVQEVAGKKQPHPLAGLAVLGIEGIGSTSLTPAALAALSGSRVKS  278 (433)
Q Consensus       199 ~~~~~~~~~~p~~~~~~p~~~~g~~~~~~~g~~~~P~~~~~~~~~~~p~~~~~~~~~~~~~~p~~~~~~~~~~~~~~~~~  278 (433)
                      +...          . .|+            + .+.++                                          
T Consensus       113 p~~~----------~-k~v------------~-~~~pq------------------------------------------  126 (402)
T KOG2191|consen  113 PQAV----------A-KPV------------D-ILQPQ------------------------------------------  126 (402)
T ss_pred             HHhh----------c-CCc------------c-ccCCC------------------------------------------
Confidence            2100          0 000            0 00000                                          


Q ss_pred             CCCCCCCCceEEEEEeCcccccccccCCCchHHHHHhHhCCeEEEccCCC----CCceEEEEEeCHHHHHHHHHHHHHHH
Q psy11929        279 GGKDTGDDFVETEIVLTDDIAGCVIGKAGSRLLEIRQISGAQINIHTGTE----SHKKMFHIQGCQEAVSLAQYLINMCI  354 (433)
Q Consensus       279 ~~~~~~~~~~t~~i~VP~~~vG~IIGkgG~~Ik~I~~~sGA~I~I~~~~~----~~er~V~IsGt~e~v~~A~~lI~~~i  354 (433)
                          ........++.||+.-+|.||||+|.+||.|++++||.|+|.+..+    -.+|+|+++|++|+..+|..||.++|
T Consensus       127 ----t~~r~kqikivvPNstag~iigkggAtiK~~~Eqsga~iqisPqkpt~~sLqervvt~sge~e~~~~A~~~IL~Ki  202 (402)
T KOG2191|consen  127 ----TPDRIKQIKIVVPNSTAGMIIGKGGATIKAIQEQSGAWIQISPQKPTGISLQERVVTVSGEPEQNMKAVSLILQKI  202 (402)
T ss_pred             ----CccccceeEEeccCCcccceecCCcchHHHHHHhhCcceEecccCCCCccceeEEEEecCCHHHHHHHHHHHHHHh
Confidence                0012334799999999999999999999999999999999995443    67999999999999999999999999


Q ss_pred             HhccccCCC---CC----C---CCCccccccccccchhccccccccccCCCCCcceecccc
Q psy11929        355 ELQKNNTTN---TS----D---NPEPADLDAAISAFMTASVNSSLIEKPTPHPGSMVTLGG  405 (433)
Q Consensus       355 ~~~~~~~~~---~~----~---~~~~~~~~~~~~~~~~~~~~~~~~~vP~~~~G~iiGkgG  405 (433)
                      .+.......   .|    +   ++.|..-.-.+..-.....++.+.+||+..+|-.-|.||
T Consensus       203 ~eDpqs~scln~sya~vsGpvaNsnPtGspya~~~~~~~astas~~sva~~~iG~a~gaG~  263 (402)
T KOG2191|consen  203 QEDPQSGSCLNISYANVSGPVANSNPTGSPYAYQAHVLPASTASTISVAAGLIGGANGAGG  263 (402)
T ss_pred             hcCCcccceeccchhcccCcccccCCCCCCCCCCCccccccchhhcccccccccccccccc
Confidence            887542211   00    0   000110000011100111146778899999999888887

>KOG2190|consensus

Probab=99.93  E-value=8.5e-25  Score=223.36  Aligned_cols=237  Identities=33%  Similarity=0.520  Sum_probs=180.1

Q ss_pred             eEEEEEEeccCCcccccceeeecCchHHHHHHHHhCCeEEEeCC---CCCcceEEEecccCCCCCCccccCCCCCccccc
Q psy11929         14 LITMRCLFHSSVNVNEISCLIGPGGCIVRRLRKESGAKISITDG---ACPDRIVTVSGSVDNSSTSSVETGYPGHTLWVT   90 (433)
Q Consensus        14 ~~~~rilvp~~~~~~~vg~IIGk~G~~Ik~I~~~tga~I~v~~~---~~~eRvv~I~G~~~~~~~~~v~~~~~~~~~~~~   90 (433)
                      .+++|||||.    +++|+||||+|+.||+|+++|||+|+|..+   .+.+|.|+|.|.++                   
T Consensus       137 ~v~~RLlVp~----sq~GslIGK~G~~Ik~Ire~TgA~I~v~~~~lP~ster~V~IsG~~~-------------------  193 (485)
T KOG2190|consen  137 EVTCRLLVPS----SQVGSLIGKGGSLIKEIREETGAKIRVSSDMLPNSTERAVTISGEPD-------------------  193 (485)
T ss_pred             ceEEEEEech----hheeeeeccCcHHHHHHHHhcCceEEecCCCCCcccceeEEEcCchH-------------------
Confidence            6999999999    999999999999999999999999999874   78999999999999                   


Q ss_pred             hHHHHHHHHHHHHhhhhhhc----cccc-----CC-----------C------------CCCCCCeEEEEEeccCcccce
Q psy11929         91 SVDNVCTAYNFMCRSLEDYH----INRN-----RM-----------E------------NCSPQPLQLKLVIPATHCGSL  138 (433)
Q Consensus        91 a~~~v~~A~~~I~~~~~~~~----~~~~-----~~-----------~------------~~~~~~~~~~l~ip~~~vg~i  138 (433)
                         ++.+|...|...|.+..    ....     .+           .            .........+++.|...++.+
T Consensus       194 ---av~~al~~Is~~L~~~~~~~~~~~~st~~y~P~~~~~~~~~~s~~~~~~~~~~~~~~~~~~e~~~~~~~p~~~~~~v  270 (485)
T KOG2190|consen  194 ---AVKKALVQISSRLLENPPRSPPPLVSTIPYRPSASQGGPVLPSTAQTSPDAHPFGGIVPEEELVFKLICPSDKVGSV  270 (485)
T ss_pred             ---HHHHHHHHHHHHHHhcCCcCCCCCCCcccCCCcccccCccccccccCCcccccccccccchhhhhhhcCchhhceee
Confidence               99999999988877632    1000     00           0            011223446788999999999


Q ss_pred             ecCCchhHHHHHHhhCceEEeccCCCCCCCccEEEEEccH--HHH-HHHHHHHHHHHHhhccccCCCcccccCCCCCCCC
Q psy11929        139 IGKGGCKIKDIRDLSGANVQVASDMLPMSTERIVTVHGNP--DTI-SQAIYQICLVLIECTLQVVKGAVIPYEPKTMNAG  215 (433)
Q Consensus       139 IGk~G~~Ik~I~~~sga~I~i~~~~~~~~~er~v~I~G~~--~~v-~~A~~~I~~~l~e~~~~~~~~~~~~~~p~~~~~~  215 (433)
                      +|++|..|+.|+.++++.|.+....    ++++++++...  +.. ..|...+......                     
T Consensus       271 ~g~~~~~i~~l~~~~~~~i~v~~~~----~~~~i~~s~~e~~~~~~s~a~~a~~~~~~~---------------------  325 (485)
T KOG2190|consen  271 IGKGGLVIRALRNETGASISVGDSR----TDRIVTISARENPEDRYSMAQEALLLVQPR---------------------  325 (485)
T ss_pred             ecCCCccchhhhhhcCCceEecccc----CcceeeeccccCcccccccchhhhhhcccc---------------------
Confidence            9999999999999999999997421    12666666521  000 0000000000000                     


Q ss_pred             CccccCCcccccCCCCCCCcccccCCCCCCCCccccccCcCCCCCCCCCccccccccCCCcccCCCCCCCCceEEEEEeC
Q psy11929        216 PVILSGGQAYTLHGEYAVPVQEVAGKKQPHPLAGLAVLGIEGIGSTSLTPAALAALSGSRVKSGGKDTGDDFVETEIVLT  295 (433)
Q Consensus       216 p~~~~g~~~~~~~g~~~~P~~~~~~~~~~~p~~~~~~~~~~~~~~p~~~~~~~~~~~~~~~~~~~~~~~~~~~t~~i~VP  295 (433)
                                                                          ....       ...+. ...++.++.||
T Consensus       326 ----------------------------------------------------~~~~-------~~~~~-~~~v~~~l~vp  345 (485)
T KOG2190|consen  326 ----------------------------------------------------ISEN-------AGDDL-TQTVTQRLLVP  345 (485)
T ss_pred             ----------------------------------------------------cccc-------ccccc-cceeeeeeccC
Confidence                                                                0000       01111 35788999999


Q ss_pred             cccccccccCCCchHHHHHhHhCCeEEEccCCC---CCceEEEEEeCHHHHHHHHHHHHHHHHhccccC
Q psy11929        296 DDIAGCVIGKAGSRLLEIRQISGAQINIHTGTE---SHKKMFHIQGCQEAVSLAQYLINMCIELQKNNT  361 (433)
Q Consensus       296 ~~~vG~IIGkgG~~Ik~I~~~sGA~I~I~~~~~---~~er~V~IsGt~e~v~~A~~lI~~~i~~~~~~~  361 (433)
                      .+++||||||+|.+|.+||+.|||.|+|.+...   ..++.++|+|...+...|++++..++...+...
T Consensus       346 s~~igciiGk~G~~iseir~~tgA~I~I~~~~~~~~~~e~~~~I~~~~~~~~~~~~~~~~~~~~~~~~~  414 (485)
T KOG2190|consen  346 SDLIGCIIGKGGAKISEIRQRTGASISILNKEEVSGVREALVQITGMLREDLLAQYLIRARLSAPKSSM  414 (485)
T ss_pred             ccccceeecccccchHHHHHhcCCceEEccccccCCcceeEEEecchhHHHHhhhhhcccccccCccCC
Confidence            999999999999999999999999999998875   789999999999999999999999998876644

>KOG2192|consensus

Probab=99.76  E-value=3.6e-18  Score=156.32  Aligned_cols=158  Identities=27%  Similarity=0.407  Sum_probs=131.2

Q ss_pred             CCCceEEEEEEeccCCcccccceeeecCchHHHHHHHHhCCeEEEeC---CCCCcceEEEecccCCCCCCccccCCCCCc
Q psy11929         10 DEDTLITMRCLFHSSVNVNEISCLIGPGGCIVRRLRKESGAKISITD---GACPDRIVTVSGSVDNSSTSSVETGYPGHT   86 (433)
Q Consensus        10 ~~~~~~~~rilvp~~~~~~~vg~IIGk~G~~Ik~I~~~tga~I~v~~---~~~~eRvv~I~G~~~~~~~~~v~~~~~~~~   86 (433)
                      .+.....+||||+.    +.+|.|||++|+.||.||+++.|+++|-.   +++.+|+|.|.|.+.               
T Consensus       118 ~~~~pce~rllihq----s~ag~iigrngskikelrekcsarlkift~c~p~stdrv~l~~g~~k---------------  178 (390)
T KOG2192|consen  118 QLPSPCELRLLIHQ----SLAGGIIGRNGSKIKELREKCSARLKIFTECCPHSTDRVVLIGGKPK---------------  178 (390)
T ss_pred             CCCCchhhhhhhhh----hhccceecccchhHHHHHHhhhhhhhhhhccCCCCcceEEEecCCcc---------------
Confidence            34556789999999    99999999999999999999999999976   478999999999999               


Q ss_pred             cccchHHHHHHHHHHHHhhhhhhc---------cccc--------------C------C---------------------
Q psy11929         87 LWVTSVDNVCTAYNFMCRSLEDYH---------INRN--------------R------M---------------------  116 (433)
Q Consensus        87 ~~~~a~~~v~~A~~~I~~~~~~~~---------~~~~--------------~------~---------------------  116 (433)
                             .|..+++.|++.+.+..         .+|-              +      .                     
T Consensus       179 -------~v~~~i~~il~~i~e~pikgsa~py~p~fyd~t~dyggf~M~f~d~pg~pgpapqrggqgpp~~~~sdlmay~  251 (390)
T KOG2192|consen  179 -------RVVECIKIILDLISESPIKGSAQPYDPNFYDETYDYGGFTMMFDDRPGRPGPAPQRGGQGPPPPRGSDLMAYD  251 (390)
T ss_pred             -------hHHHHHHHHHHHhhcCCcCCcCCcCCccccCcccccCCceeecCCCCCCCCCCCCCCCCCCCCCCccccceec
Confidence                   77777777776665410         0000              0      0                     


Q ss_pred             --------------------------------------------------------CCCCCCCeEEEEEeccCcccceec
Q psy11929        117 --------------------------------------------------------ENCSPQPLQLKLVIPATHCGSLIG  140 (433)
Q Consensus       117 --------------------------------------------------------~~~~~~~~~~~l~ip~~~vg~iIG  140 (433)
                                                                              .+......+..+.||..+-|.|||
T Consensus       252 r~GrpG~rydg~vdFs~detw~saidtw~~SewqmaYePQgGs~ydysyAG~~GsYGdlGGPitTaQvtip~dlggsiig  331 (390)
T KOG2192|consen  252 RRGRPGDRYDGMVDFSADETWPSAIDTWSPSEWQMAYEPQGGSGYDYSYAGGYGSYGDLGGPITTAQVTIPKDLGGSIIG  331 (390)
T ss_pred             cCCCCCccccccccccccccCCCcCCCcCccccccccCCCCCCCCCccccccccccCCCCCceeeeeEecccccCcceec
Confidence                                                                    012344578899999999999999


Q ss_pred             CCchhHHHHHHhhCceEEeccCCCCCCCccEEEEEccHHHHHHHHHHHHHHHHh
Q psy11929        141 KGGCKIKDIRDLSGANVQVASDMLPMSTERIVTVHGNPDTISQAIYQICLVLIE  194 (433)
Q Consensus       141 k~G~~Ik~I~~~sga~I~i~~~~~~~~~er~v~I~G~~~~v~~A~~~I~~~l~e  194 (433)
                      |+|+.|++|+.++||.|++.. .+.++.||+++|+|+.+++..|..++...++.
T Consensus       332 kggqri~~ir~esGA~Ikide-pleGsedrIitItGTqdQIqnAQYLlQn~Vkq  384 (390)
T KOG2192|consen  332 KGGQRIKQIRHESGASIKIDE-PLEGSEDRIITITGTQDQIQNAQYLLQNSVKQ  384 (390)
T ss_pred             ccchhhhhhhhccCceEEecC-cCCCCCceEEEEeccHHHHhhHHHHHHHHHHh
Confidence            999999999999999999973 56789999999999999999999999888875

>TIGR03665 arCOG04150 arCOG04150 universal archaeal KH domain protein

Probab=99.67  E-value=3.3e-16  Score=140.72  Aligned_cols=136  Identities=20%  Similarity=0.312  Sum_probs=104.6

Q ss_pred             EeccCCcccccceeeecCchHHHHHHHHhCCeEEEeCCCCCcceEEE---ecccCCCCCCccccCCCCCccccchHHHHH
Q psy11929         20 LFHSSVNVNEISCLIGPGGCIVRRLRKESGAKISITDGACPDRIVTV---SGSVDNSSTSSVETGYPGHTLWVTSVDNVC   96 (433)
Q Consensus        20 lvp~~~~~~~vg~IIGk~G~~Ik~I~~~tga~I~v~~~~~~eRvv~I---~G~~~~~~~~~v~~~~~~~~~~~~a~~~v~   96 (433)
                      .||.    +.+|.|||++|++||.|+++|||+|++.+.   +..|.|   .+.++                      ++.
T Consensus         3 ~Ip~----~kig~vIG~gG~~Ik~I~~~tgv~I~Id~~---~g~V~I~~~t~d~~----------------------~i~   53 (172)
T TIGR03665         3 KIPK----DRIGVLIGKGGETKKEIEERTGVKLDIDSE---TGEVKIEEEDEDPL----------------------AVM   53 (172)
T ss_pred             cCCH----HHhhhHhCCchhHHHHHHHHhCcEEEEEcC---CceEEEecCCCCHH----------------------HHH
Confidence            4566    999999999999999999999999999973   356888   44444                      999


Q ss_pred             HHHHHHHhhhhhhcccccCCCCCCCCCeEEE-EEecc---------CcccceecCCchhHHHHHHhhCceEEeccCCCCC
Q psy11929         97 TAYNFMCRSLEDYHINRNRMENCSPQPLQLK-LVIPA---------THCGSLIGKGGCKIKDIRDLSGANVQVASDMLPM  166 (433)
Q Consensus        97 ~A~~~I~~~~~~~~~~~~~~~~~~~~~~~~~-l~ip~---------~~vg~iIGk~G~~Ik~I~~~sga~I~i~~~~~~~  166 (433)
                      +|.++|..+...+....  ........+..+ +.|+.         ..+|+|||++|++++.|++.|||+|.+.      
T Consensus        54 kA~~~I~~i~~gf~~e~--A~~l~gd~y~~~Vi~I~~~~~~~~~~~~~~griIG~~G~t~~~ie~~t~~~i~i~------  125 (172)
T TIGR03665        54 KAREVVKAIGRGFSPEK--ALKLLDDDYMLEVIDLKEYGKSPNALRRIKGRIIGEGGKTRRIIEELTGVSISVY------  125 (172)
T ss_pred             HHHHHHHHHHcCCCHHH--HHHhcCCcceEEEEEhhhccCCHHHHHHHHhhhcCCCcHHHHHHHHHHCCeEEEc------
Confidence            99999988665422110  000001222222 23433         3689999999999999999999999996      


Q ss_pred             CCccEEEEEccHHHHHHHHHHHHHHHHh
Q psy11929        167 STERIVTVHGNPDTISQAIYQICLVLIE  194 (433)
Q Consensus       167 ~~er~v~I~G~~~~v~~A~~~I~~~l~e  194 (433)
                        ++.|.|.|++++++.|..+|.+++.+
T Consensus       126 --~~~v~i~G~~~~~~~A~~~i~~li~~  151 (172)
T TIGR03665       126 --GKTVGIIGDPEQVQIAREAIEMLIEG  151 (172)
T ss_pred             --CCEEEEECCHHHHHHHHHHHHHHHcC
Confidence              36899999999999999999999965

This family of proteins is universal among the 41 archaeal genomes analyzed in and is not observed outside of the archaea. The proteins contain a single KH domain (pfam00013) which is likely to confer the ability to bind RNA.

>PRK13763 putative RNA-processing protein; Provisional

Probab=99.64  E-value=1.8e-15  Score=136.87  Aligned_cols=141  Identities=18%  Similarity=0.286  Sum_probs=108.2

Q ss_pred             EEEEEEeccCCcccccceeeecCchHHHHHHHHhCCeEEEeCCCCCcceEEEe----cccCCCCCCccccCCCCCccccc
Q psy11929         15 ITMRCLFHSSVNVNEISCLIGPGGCIVRRLRKESGAKISITDGACPDRIVTVS----GSVDNSSTSSVETGYPGHTLWVT   90 (433)
Q Consensus        15 ~~~rilvp~~~~~~~vg~IIGk~G~~Ik~I~~~tga~I~v~~~~~~eRvv~I~----G~~~~~~~~~v~~~~~~~~~~~~   90 (433)
                      +...+.||.    +.+|.|||++|++||.|+++|||+|++.+.   +..|.|.    +.++                   
T Consensus         3 ~~~~i~IP~----~kig~iIG~gGk~Ik~I~e~tg~~I~i~~~---~g~V~I~~~~~~d~~-------------------   56 (180)
T PRK13763          3 MMEYVKIPK----DRIGVLIGKKGETKKEIEERTGVKLEIDSE---TGEVIIEPTDGEDPL-------------------   56 (180)
T ss_pred             ceEEEEcCH----HHhhhHhccchhHHHHHHHHHCcEEEEECC---CCeEEEEeCCCCCHH-------------------
Confidence            567788898    999999999999999999999999999973   3567785    4555                   


Q ss_pred             hHHHHHHHHHHHHhhhhhhcccccCCCCCCCCCeEEEE-Eec---------cCcccceecCCchhHHHHHHhhCceEEec
Q psy11929         91 SVDNVCTAYNFMCRSLEDYHINRNRMENCSPQPLQLKL-VIP---------ATHCGSLIGKGGCKIKDIRDLSGANVQVA  160 (433)
Q Consensus        91 a~~~v~~A~~~I~~~~~~~~~~~~~~~~~~~~~~~~~l-~ip---------~~~vg~iIGk~G~~Ik~I~~~sga~I~i~  160 (433)
                         ++.+|.++|..+...+.....  .......+..++ .+.         ...+|+|||++|++++.|++.|||+|.|.
T Consensus        57 ---~i~kA~~~I~ai~~gf~~e~A--~~l~gd~y~~~Vi~i~~~~~~~~~~~r~~griIG~~G~~~k~ie~~t~~~i~i~  131 (180)
T PRK13763         57 ---AVLKARDIVKAIGRGFSPEKA--LRLLDDDYVLEVIDLSDYGDSPNALRRIKGRIIGEGGKTRRIIEELTGVDISVY  131 (180)
T ss_pred             ---HHHHHHHHHHHHhcCCCHHHH--HHHhCCCceEEEEEhhhccCChhHHHHHhhheeCCCcHHHHHHHHHHCcEEEEc
Confidence               899999999887664211100  000011222222 111         13689999999999999999999999997


Q ss_pred             cCCCCCCCccEEEEEccHHHHHHHHHHHHHHHHh
Q psy11929        161 SDMLPMSTERIVTVHGNPDTISQAIYQICLVLIE  194 (433)
Q Consensus       161 ~~~~~~~~er~v~I~G~~~~v~~A~~~I~~~l~e  194 (433)
                      .        +.|.|.|++++++.|...|..+++.
T Consensus       132 ~--------~~v~i~G~~~~~~~A~~~I~~li~g  157 (180)
T PRK13763        132 G--------KTVAIIGDPEQVEIAREAIEMLIEG  157 (180)
T ss_pred             C--------CEEEEEeCHHHHHHHHHHHHHHHcC
Confidence            3        4599999999999999999999865

>TIGR03665 arCOG04150 arCOG04150 universal archaeal KH domain protein

Probab=99.64  E-value=1.3e-15  Score=136.94  Aligned_cols=138  Identities=28%  Similarity=0.389  Sum_probs=106.6

Q ss_pred             EEeccCcccceecCCchhHHHHHHhhCceEEeccCCCCCCCccEEEE---EccHHHHHHHHHHHHHHHHhhccccCCCcc
Q psy11929        128 LVIPATHCGSLIGKGGCKIKDIRDLSGANVQVASDMLPMSTERIVTV---HGNPDTISQAIYQICLVLIECTLQVVKGAV  204 (433)
Q Consensus       128 l~ip~~~vg~iIGk~G~~Ik~I~~~sga~I~i~~~~~~~~~er~v~I---~G~~~~v~~A~~~I~~~l~e~~~~~~~~~~  204 (433)
                      +.||.+.+|.|||++|++|+.|+++||++|.+..+      +..|.|   +++++++.+|..+|..+.+.   ..+..  
T Consensus         2 i~Ip~~kig~vIG~gG~~Ik~I~~~tgv~I~Id~~------~g~V~I~~~t~d~~~i~kA~~~I~~i~~g---f~~e~--   70 (172)
T TIGR03665         2 VKIPKDRIGVLIGKGGETKKEIEERTGVKLDIDSE------TGEVKIEEEDEDPLAVMKAREVVKAIGRG---FSPEK--   70 (172)
T ss_pred             ccCCHHHhhhHhCCchhHHHHHHHHhCcEEEEEcC------CceEEEecCCCCHHHHHHHHHHHHHHHcC---CCHHH--
Confidence            56899999999999999999999999999999853      357888   78999999999999987764   11100  


Q ss_pred             cccCCCCCCCCCccccCCcccccCCCCCCCcccccCCCCCCCCccccccCcCCCCCCCCCccccccccCCCcccCCCCCC
Q psy11929        205 IPYEPKTMNAGPVILSGGQAYTLHGEYAVPVQEVAGKKQPHPLAGLAVLGIEGIGSTSLTPAALAALSGSRVKSGGKDTG  284 (433)
Q Consensus       205 ~~~~p~~~~~~p~~~~g~~~~~~~g~~~~P~~~~~~~~~~~p~~~~~~~~~~~~~~p~~~~~~~~~~~~~~~~~~~~~~~  284 (433)
                                         ++...+.                                                      
T Consensus        71 -------------------A~~l~gd------------------------------------------------------   77 (172)
T TIGR03665        71 -------------------ALKLLDD------------------------------------------------------   77 (172)
T ss_pred             -------------------HHHhcCC------------------------------------------------------
Confidence                               0000000                                                      


Q ss_pred             CCceEEEEEeC---------cccccccccCCCchHHHHHhHhCCeEEEccCCCCCceEEEEEeCHHHHHHHHHHHHHHHH
Q psy11929        285 DDFVETEIVLT---------DDIAGCVIGKAGSRLLEIRQISGAQINIHTGTESHKKMFHIQGCQEAVSLAQYLINMCIE  355 (433)
Q Consensus       285 ~~~~t~~i~VP---------~~~vG~IIGkgG~~Ik~I~~~sGA~I~I~~~~~~~er~V~IsGt~e~v~~A~~lI~~~i~  355 (433)
                       ...-.-+.|+         ...+|+|||++|++++.|+..|||+|.|++      ..|.|+|++++++.|+.+|.++++
T Consensus        78 -~y~~~Vi~I~~~~~~~~~~~~~~griIG~~G~t~~~ie~~t~~~i~i~~------~~v~i~G~~~~~~~A~~~i~~li~  150 (172)
T TIGR03665        78 -DYMLEVIDLKEYGKSPNALRRIKGRIIGEGGKTRRIIEELTGVSISVYG------KTVGIIGDPEQVQIAREAIEMLIE  150 (172)
T ss_pred             -cceEEEEEhhhccCCHHHHHHHHhhhcCCCcHHHHHHHHHHCCeEEEcC------CEEEEECCHHHHHHHHHHHHHHHc
Confidence             0000001111         137899999999999999999999999986      569999999999999999999995


Q ss_pred             h
Q psy11929        356 L  356 (433)
Q Consensus       356 ~  356 (433)
                      .
T Consensus       151 ~  151 (172)
T TIGR03665       151 G  151 (172)
T ss_pred             C
Confidence            4

This family of proteins is universal among the 41 archaeal genomes analyzed in and is not observed outside of the archaea. The proteins contain a single KH domain (pfam00013) which is likely to confer the ability to bind RNA.

>PRK13763 putative RNA-processing protein; Provisional

Probab=99.60  E-value=1.1e-14  Score=131.71  Aligned_cols=151  Identities=25%  Similarity=0.295  Sum_probs=109.4

Q ss_pred             eEEEEEeccCcccceecCCchhHHHHHHhhCceEEeccCCCCCCCccEEEEE----ccHHHHHHHHHHHHHHHHhhcccc
Q psy11929        124 LQLKLVIPATHCGSLIGKGGCKIKDIRDLSGANVQVASDMLPMSTERIVTVH----GNPDTISQAIYQICLVLIECTLQV  199 (433)
Q Consensus       124 ~~~~l~ip~~~vg~iIGk~G~~Ik~I~~~sga~I~i~~~~~~~~~er~v~I~----G~~~~v~~A~~~I~~~l~e~~~~~  199 (433)
                      ....+.||.+.+|.|||++|++|+.|+++||++|.+..+      +..|.|.    ++++++.+|+.+|..+++.   +.
T Consensus         3 ~~~~i~IP~~kig~iIG~gGk~Ik~I~e~tg~~I~i~~~------~g~V~I~~~~~~d~~~i~kA~~~I~ai~~g---f~   73 (180)
T PRK13763          3 MMEYVKIPKDRIGVLIGKKGETKKEIEERTGVKLEIDSE------TGEVIIEPTDGEDPLAVLKARDIVKAIGRG---FS   73 (180)
T ss_pred             ceEEEEcCHHHhhhHhccchhHHHHHHHHHCcEEEEECC------CCeEEEEeCCCCCHHHHHHHHHHHHHHhcC---CC
Confidence            456889999999999999999999999999999999853      3678885    8999999999999998774   11


Q ss_pred             CCCcccccCCCCCCCCCccccCCcccccCCCCCCCcccccCCCCCCCCccccccCcCCCCCCCCCccccccccCCCcccC
Q psy11929        200 VKGAVIPYEPKTMNAGPVILSGGQAYTLHGEYAVPVQEVAGKKQPHPLAGLAVLGIEGIGSTSLTPAALAALSGSRVKSG  279 (433)
Q Consensus       200 ~~~~~~~~~p~~~~~~p~~~~g~~~~~~~g~~~~P~~~~~~~~~~~p~~~~~~~~~~~~~~p~~~~~~~~~~~~~~~~~~  279 (433)
                      +..+                     +...+....-.           +..+...+                         
T Consensus        74 ~e~A---------------------~~l~gd~y~~~-----------Vi~i~~~~-------------------------   96 (180)
T PRK13763         74 PEKA---------------------LRLLDDDYVLE-----------VIDLSDYG-------------------------   96 (180)
T ss_pred             HHHH---------------------HHHhCCCceEE-----------EEEhhhcc-------------------------
Confidence            1000                     00000000000           00000000                         


Q ss_pred             CCCCCCCceEEEEEeCcccccccccCCCchHHHHHhHhCCeEEEccCCCCCceEEEEEeCHHHHHHHHHHHHHHHHh
Q psy11929        280 GKDTGDDFVETEIVLTDDIAGCVIGKAGSRLLEIRQISGAQINIHTGTESHKKMFHIQGCQEAVSLAQYLINMCIEL  356 (433)
Q Consensus       280 ~~~~~~~~~t~~i~VP~~~vG~IIGkgG~~Ik~I~~~sGA~I~I~~~~~~~er~V~IsGt~e~v~~A~~lI~~~i~~  356 (433)
                      .   .      . ......+|+|||++|++++.|+..|||+|.|.+.      .|.|.|++++++.|+..|..+++.
T Consensus        97 ~---~------~-~~~~r~~griIG~~G~~~k~ie~~t~~~i~i~~~------~v~i~G~~~~~~~A~~~I~~li~g  157 (180)
T PRK13763         97 D---S------P-NALRRIKGRIIGEGGKTRRIIEELTGVDISVYGK------TVAIIGDPEQVEIAREAIEMLIEG  157 (180)
T ss_pred             C---C------h-hHHHHHhhheeCCCcHHHHHHHHHHCcEEEEcCC------EEEEEeCHHHHHHHHHHHHHHHcC
Confidence            0   0      0 0112379999999999999999999999999863      499999999999999999998854

>cd02396 PCBP_like_KH K homology RNA-binding domain, PCBP_like

Probab=99.47  E-value=1.1e-13  Score=104.20  Aligned_cols=63  Identities=33%  Similarity=0.496  Sum_probs=58.9

Q ss_pred             EEEEEeCcccccccccCCCchHHHHHhHhCCeEEEccCCC--CCceEEEEEeCHHHHHHHHHHHH
Q psy11929        289 ETEIVLTDDIAGCVIGKAGSRLLEIRQISGAQINIHTGTE--SHKKMFHIQGCQEAVSLAQYLIN  351 (433)
Q Consensus       289 t~~i~VP~~~vG~IIGkgG~~Ik~I~~~sGA~I~I~~~~~--~~er~V~IsGt~e~v~~A~~lI~  351 (433)
                      +.+|.||..++|+|||++|.+|++|+++|||+|++.+...  ..+|.|+|+|+++++++|+.+|+
T Consensus         1 ~~r~~ip~~~vg~iIG~~G~~i~~i~~~tga~I~i~~~~~~~~~~r~v~I~G~~~~v~~A~~~I~   65 (65)
T cd02396           1 TLRLLVPSSQAGSIIGKGGSTIKEIREETGAKIRVSKSVLPGSTERVVTISGKPSAVQKALLLIL   65 (65)
T ss_pred             CEEEEECHHHcCeeECCCcHHHHHHHHHHCCEEEEcCCCCCCCCceEEEEEeCHHHHHHHHHhhC
Confidence            3689999999999999999999999999999999998775  78999999999999999999873

Members of this group possess KH domains in a tandem arrangement. Most members, similar to the poly(C) binding proteins (PCBPs) and Nova, containing three KH domains, with the first and second domains, which are represented here, in tandem arrangement, followed by a large spacer region, with the third domain near the C-terminal end of the protein. The poly(C) binding proteins (PCBPs) can be divided into two groups, hnRNPs K/J and the alphaCPs, which share a triple KH domain configuration and poly(C) binding specificity. They play roles in mRNA stabilization, translational activation, and translational silencing. Nova-1 and Nova-2 are nuclear RNA-binding proteins that regulate splicing. This group also contains plant proteins that seem to have two tandem repeat arrrangements, like Hen4, a protein that plays a role in AGAMOUS (AG) pre-mRNA processing and important step in plant development. In general, KH binds single-stran

>KOG2279|consensus

Probab=99.43  E-value=9.8e-13  Score=131.93  Aligned_cols=291  Identities=20%  Similarity=0.284  Sum_probs=186.5

Q ss_pred             ceEEEEEEeccCCcccccceeeecCchHHHHHHHHhCCeEEEeCCC-CCcceEEEecccCCCCCCccccCCCCCccccch
Q psy11929         13 TLITMRCLFHSSVNVNEISCLIGPGGCIVRRLRKESGAKISITDGA-CPDRIVTVSGSVDNSSTSSVETGYPGHTLWVTS   91 (433)
Q Consensus        13 ~~~~~rilvp~~~~~~~vg~IIGk~G~~Ik~I~~~tga~I~v~~~~-~~eRvv~I~G~~~~~~~~~v~~~~~~~~~~~~a   91 (433)
                      .++.+.++++.    ..|-++|||+|++||.|+..|++||.+.+.. .++++.++.|.+.                    
T Consensus        66 k~v~~e~Vv~~----e~vkli~gr~gsnik~l~~~t~aKi~L~~ed~g~e~~~~~~~~p~--------------------  121 (608)
T KOG2279|consen   66 KDIEIEMVVPQ----EAVKLIIGRQGSNIKQLRKQTGAKIDLDTEDVGDERVLLISGFPV--------------------  121 (608)
T ss_pred             hheeeeEeecc----cceeeeeccccCCcchhhcccccceecCcccCCcccchhhccCCC--------------------
Confidence            56888999999    9999999999999999999999999998864 4566666666777                    


Q ss_pred             HHHHHHHHHHHHhhhhhhcccccCCCCCCCCCeEEEEEeccCcccceecCCchhHHHHHHhhCceEEeccCCCCCCCccE
Q psy11929         92 VDNVCTAYNFMCRSLEDYHINRNRMENCSPQPLQLKLVIPATHCGSLIGKGGCKIKDIRDLSGANVQVASDMLPMSTERI  171 (433)
Q Consensus        92 ~~~v~~A~~~I~~~~~~~~~~~~~~~~~~~~~~~~~l~ip~~~vg~iIGk~G~~Ik~I~~~sga~I~i~~~~~~~~~er~  171 (433)
                        ++..|...++.++.+            ..++...+-+|...+++|+|++|++++.|+.-++++|.+..+ .-..-.+.
T Consensus       122 --~v~~a~a~~~~~~~~------------~~pvk~~lsvpqr~~~~i~grgget~~si~~ss~aki~~d~n-gr~g~~~~  186 (608)
T KOG2279|consen  122 --QVCKAKAAIHQILTE------------NTPVSEQLSVPQRSVGRIIGRGGETIRSICKSSGAKITCDKN-GRLGLSRL  186 (608)
T ss_pred             --CCChHHHHHHHHHhc------------CCcccccccchhhhcccccccchhhhcchhcccccccccccc-cccccccc
Confidence              677777787777655            467788899999999999999999999999999999999864 22345678


Q ss_pred             EEEEccHHHHHHHHHHHHHHHHhhccccCCC--cccccCCCCCCCCCccccCCcccccCCCCCCCcccccCCCCCCCCcc
Q psy11929        172 VTVHGNPDTISQAIYQICLVLIECTLQVVKG--AVIPYEPKTMNAGPVILSGGQAYTLHGEYAVPVQEVAGKKQPHPLAG  249 (433)
Q Consensus       172 v~I~G~~~~v~~A~~~I~~~l~e~~~~~~~~--~~~~~~p~~~~~~p~~~~g~~~~~~~g~~~~P~~~~~~~~~~~p~~~  249 (433)
                      ..|.|....+..|..++.+.+.+..+.-.+.  ....-.|...   |....+...+. ++....|+.......+..|-.+
T Consensus       187 ~~i~~qqk~~~~a~~~~~~~~~edeelv~~~~e~~q~rvprk~---p~n~~~~~m~~-~~~s~~~h~~~~t~~s~spg~~  262 (608)
T KOG2279|consen  187 IKISGQQKEVAAAKHLILEKVSEDEELVKRIAESAQTRVPRKQ---PINVRREDMTE-PGGAGEPHLWKNTSSSMSPGAP  262 (608)
T ss_pred             eecccccchHHHHHhhhhccccchhHHhhhchhhcccCCCCCC---Cccccchhhcc-cccCCccccCccchhccCCCCC
Confidence            8888888888899999988877643211100  0000011110   00000000010 0000011110000000000000


Q ss_pred             ccccCcCCCCCCCCCccccccccCCCccc---CCCCCCCCceEEEEEeCcccccccccCCCchHHHHHhHhCCeEEEccC
Q psy11929        250 LAVLGIEGIGSTSLTPAALAALSGSRVKS---GGKDTGDDFVETEIVLTDDIAGCVIGKAGSRLLEIRQISGAQINIHTG  326 (433)
Q Consensus       250 ~~~~~~~~~~~p~~~~~~~~~~~~~~~~~---~~~~~~~~~~t~~i~VP~~~vG~IIGkgG~~Ik~I~~~sGA~I~I~~~  326 (433)
                      ...  +.+  -+|    ...---+.++..   +...........+|.+|...+|.+||+.|..++.+...|++.+.|.-.
T Consensus       263 ~~~--~eg--~dm----~v~vsk~~s~~~~~d~s~~k~~~l~i~e~e~p~~lsg~lig~~gey~s~yssasn~~~hi~t~  334 (608)
T KOG2279|consen  263 LVT--KEG--GDM----AVVVSKEGSWEKPSDDSFQKSEALAIPEMEMPEILSGDLIGHAGEYLSVYSSASNHPNHIWTQ  334 (608)
T ss_pred             Ccc--cCC--Ccc----eeEEecccccCCccccccccccccccceeecCcccccchhhhhhhhhhhhhhccCccceEEec
Confidence            000  000  000    000000000100   001112334567999999999999999999999999999999888765


Q ss_pred             CC----CCceEEEEEeCHHHHHHHHHHHHHHH
Q psy11929        327 TE----SHKKMFHIQGCQEAVSLAQYLINMCI  354 (433)
Q Consensus       327 ~~----~~er~V~IsGt~e~v~~A~~lI~~~i  354 (433)
                      .-    -.-.++.+.|+..-+..+..++...+
T Consensus       335 pyt~~v~~~qic~~egkqh~~n~vl~ml~~~~  366 (608)
T KOG2279|consen  335 PYTSRVLQLQICVNEGKQHYENSVLEMLTVHV  366 (608)
T ss_pred             cccchhhhhhhheecchhHHHHHHHhhhhccC
Confidence            43    22367889999999999999997433

>cd02396 PCBP_like_KH K homology RNA-binding domain, PCBP_like

Probab=99.41  E-value=6.9e-13  Score=99.82  Aligned_cols=64  Identities=45%  Similarity=0.879  Sum_probs=59.6

Q ss_pred             EEEEEeccCcccceecCCchhHHHHHHhhCceEEeccCCCCCCCccEEEEEccHHHHHHHHHHH
Q psy11929        125 QLKLVIPATHCGSLIGKGGCKIKDIRDLSGANVQVASDMLPMSTERIVTVHGNPDTISQAIYQI  188 (433)
Q Consensus       125 ~~~l~ip~~~vg~iIGk~G~~Ik~I~~~sga~I~i~~~~~~~~~er~v~I~G~~~~v~~A~~~I  188 (433)
                      +++|+||.+.+|+|||++|++|++|+++|||+|.+.++..+...+|+|+|.|+++++.+|+.+|
T Consensus         1 ~~r~~ip~~~vg~iIG~~G~~i~~i~~~tga~I~i~~~~~~~~~~r~v~I~G~~~~v~~A~~~I   64 (65)
T cd02396           1 TLRLLVPSSQAGSIIGKGGSTIKEIREETGAKIRVSKSVLPGSTERVVTISGKPSAVQKALLLI   64 (65)
T ss_pred             CEEEEECHHHcCeeECCCcHHHHHHHHHHCCEEEEcCCCCCCCCceEEEEEeCHHHHHHHHHhh
Confidence            3689999999999999999999999999999999997655678899999999999999999887

Members of this group possess KH domains in a tandem arrangement. Most members, similar to the poly(C) binding proteins (PCBPs) and Nova, containing three KH domains, with the first and second domains, which are represented here, in tandem arrangement, followed by a large spacer region, with the third domain near the C-terminal end of the protein. The poly(C) binding proteins (PCBPs) can be divided into two groups, hnRNPs K/J and the alphaCPs, which share a triple KH domain configuration and poly(C) binding specificity. They play roles in mRNA stabilization, translational activation, and translational silencing. Nova-1 and Nova-2 are nuclear RNA-binding proteins that regulate splicing. This group also contains plant proteins that seem to have two tandem repeat arrrangements, like Hen4, a protein that plays a role in AGAMOUS (AG) pre-mRNA processing and important step in plant development. In general, KH binds single-stran

>cd02394 vigilin_like_KH K homology RNA-binding domain_vigilin_like

Probab=99.33  E-value=2.8e-12  Score=95.51  Aligned_cols=60  Identities=27%  Similarity=0.381  Sum_probs=56.7

Q ss_pred             EEEEeCcccccccccCCCchHHHHHhHhCCeEEEccCCCCCceEEEEEeCHHHHHHHHHHH
Q psy11929        290 TEIVLTDDIAGCVIGKAGSRLLEIRQISGAQINIHTGTESHKKMFHIQGCQEAVSLAQYLI  350 (433)
Q Consensus       290 ~~i~VP~~~vG~IIGkgG~~Ik~I~~~sGA~I~I~~~~~~~er~V~IsGt~e~v~~A~~lI  350 (433)
                      .++.||.+++|+|||++|++|++|+++|||+|.|++.. ..++.|+|+|+++++..|+.+|
T Consensus         2 ~~i~Vp~~~~~~iIG~~G~~i~~i~~~~g~~I~i~~~~-~~~~~v~I~G~~~~v~~A~~~i   61 (62)
T cd02394           2 EEVEIPKKLHRFIIGKKGSNIRKIMEETGVKIRFPDPG-SKSDTITITGPKENVEKAKEEI   61 (62)
T ss_pred             eEEEeCHHHhhhccCCCCCcHHHHHHHhCCEEEcCCCC-CCCCEEEEEcCHHHHHHHHHHh
Confidence            57899999999999999999999999999999999977 6789999999999999999887

The vigilin family is a large and extended family of multiple KH-domain proteins, including vigilin, also called high density lipoprotein binding protien (HBP), fungal Scp160 and bicaudal-C. Yeast Scp160p has been shown to bind RNA and to associate with both soluble and membrane-bound polyribosomes as a mRNP component. Bicaudal-C is a RNA-binding molecule believed to function in embryonic development at the post-transcriptional level. In general, KH binds single-stranded RNA or DNA. It is found in a wide variety of proteins including ribosomal proteins, transcription factors and post-transcriptional modifiers of mRNA.

>PF00013 KH_1: KH domain syndrome, contains KH motifs

Probab=99.31  E-value=2.5e-12  Score=95.18  Aligned_cols=60  Identities=30%  Similarity=0.534  Sum_probs=55.4

Q ss_pred             EEEEEeCcccccccccCCCchHHHHHhHhCCeEEEccCCCCCceEEEEEeCHHHHHHHHHHH
Q psy11929        289 ETEIVLTDDIAGCVIGKAGSRLLEIRQISGAQINIHTGTESHKKMFHIQGCQEAVSLAQYLI  350 (433)
Q Consensus       289 t~~i~VP~~~vG~IIGkgG~~Ik~I~~~sGA~I~I~~~~~~~er~V~IsGt~e~v~~A~~lI  350 (433)
                      |.+|.||.+++|+|||++|++|++|++.|||+|+|++. + .+..|+|+|+++++++|+.+|
T Consensus         1 T~~i~vp~~~~~~iIG~~G~~i~~I~~~t~~~I~i~~~-~-~~~~v~I~G~~~~v~~A~~~I   60 (60)
T PF00013_consen    1 TERIEVPSSLVGRIIGKKGSNIKEIEEETGVKIQIPDD-D-ERDIVTISGSPEQVEKAKKMI   60 (60)
T ss_dssp             EEEEEEEHHHHHHHHTGGGHHHHHHHHHHTSEEEEEST-T-EEEEEEEEESHHHHHHHHHHH
T ss_pred             CEEEEECHHHcCEEECCCCCcHHHhhhhcCeEEEEcCC-C-CcEEEEEEeCHHHHHHHHhhC
Confidence            57899999999999999999999999999999999887 2 456999999999999999886

; InterPro: IPR018111 The K homology (KH) domain was first identified in the human heterogeneous nuclear ribonucleoprotein (hnRNP) K. It is a domain of around 70 amino acids that is present in a wide variety of quite diverse nucleic acid-binding proteins []. It has been shown to bind RNA [, ]. Like many other RNA-binding motifs, KH motifs are found in one or multiple copies (14 copies in chicken vigilin) and, at least for hnRNP K (three copies) and FMR-1 (two copies), each motif is necessary for in vitro RNA binding activity, suggesting that they may function cooperatively or, in the case of single KH motif proteins (for example, Mer1p), independently []. According to structural [, , ] analysis the KH domain can be separated in two groups. The first group or type-1 contain a beta-alpha-alpha-beta-beta-alpha structure, whereas in the type-2 the two last beta-sheet are located in the N-terminal part of the domain (alpha-beta-beta-alpha-alpha-beta). Sequence similarity between these two folds are limited to a short region (VIGXXGXXI) in the RNA binding motif. This motif is located between helice 1 and 2 in type-1 and between helice 2 and 3 in type-2. Proteins known to contain a type-1 KH domain include bacterial polyribonucleotide nucleotidyltransferases (2.7.7.8 from EC); vertebrate fragile X mental retardation protein 1 (FMR1); eukaryotic heterogeneous nuclear ribonucleoprotein K (hnRNP K), one of at least 20 major proteins that are part of hnRNP particles in mammalian cells; mammalian poly(rC) binding proteins; Artemia salina glycine-rich protein GRP33; yeast PAB1-binding protein 2 (PBP2); vertebrate vigilin; and human high-density lipoprotein binding protein (HDL-binding protein). More information about these proteins can be found at Protein of the Month: RNA Exosomes [].; GO: 0003723 RNA binding; PDB: 1TUA_A 2Z0S_A 1WE8_A 4AM3_B 4AIM_A 4AID_A 2HH3_A 2JVZ_A 1J4W_A 2HH2_A ....

>cd00105 KH-I K homology RNA-binding domain, type I

Probab=99.25  E-value=2e-11  Score=91.26  Aligned_cols=61  Identities=36%  Similarity=0.591  Sum_probs=57.4

Q ss_pred             EEEEeCcccccccccCCCchHHHHHhHhCCeEEEccCCC-CCceEEEEEeCHHHHHHHHHHH
Q psy11929        290 TEIVLTDDIAGCVIGKAGSRLLEIRQISGAQINIHTGTE-SHKKMFHIQGCQEAVSLAQYLI  350 (433)
Q Consensus       290 ~~i~VP~~~vG~IIGkgG~~Ik~I~~~sGA~I~I~~~~~-~~er~V~IsGt~e~v~~A~~lI  350 (433)
                      .+|.||..++|+|||++|++|++|++.|||+|.|++... ..++.|+|+|+.+++..|+.+|
T Consensus         2 ~~i~ip~~~~~~vIG~~G~~i~~I~~~s~~~I~i~~~~~~~~~~~v~i~G~~~~v~~a~~~i   63 (64)
T cd00105           2 ERVLVPSSLVGRIIGKGGSTIKEIREETGAKIKIPDSGSGSEERIVTITGTPEAVEKAKELI   63 (64)
T ss_pred             EEEEEchhhcceeECCCCHHHHHHHHHHCCEEEEcCCCCCCCceEEEEEcCHHHHHHHHHHh
Confidence            589999999999999999999999999999999998765 6789999999999999999887

KH binds single-stranded RNA or DNA. It is found in a wide variety of proteins including ribosomal proteins, transcription factors and post-transcriptional modifiers of mRNA. There are two different KH domains that belong to different protein folds, but they share a single KH motif. The KH motif is folded into a beta alpha alpha beta unit. In addition to the core, type II KH domains (e.g. ribosomal protein S3) include N-terminal extension and type I KH domains (e.g. hnRNP K) contain C-terminal extension.

>PF00013 KH_1: KH domain syndrome, contains KH motifs

Probab=99.24  E-value=7.9e-12  Score=92.45  Aligned_cols=60  Identities=33%  Similarity=0.479  Sum_probs=55.2

Q ss_pred             EEEEEeccCCcccccceeeecCchHHHHHHHHhCCeEEEeCCCCCcceEEEecccCCCCCCccccCCCCCccccchHHHH
Q psy11929         16 TMRCLFHSSVNVNEISCLIGPGGCIVRRLRKESGAKISITDGACPDRIVTVSGSVDNSSTSSVETGYPGHTLWVTSVDNV   95 (433)
Q Consensus        16 ~~rilvp~~~~~~~vg~IIGk~G~~Ik~I~~~tga~I~v~~~~~~eRvv~I~G~~~~~~~~~v~~~~~~~~~~~~a~~~v   95 (433)
                      |++|+||.    +++|+|||++|++|++|+++|||+|+|++.+ .+..|+|+|+++                      ++
T Consensus         1 T~~i~vp~----~~~~~iIG~~G~~i~~I~~~t~~~I~i~~~~-~~~~v~I~G~~~----------------------~v   53 (60)
T PF00013_consen    1 TERIEVPS----SLVGRIIGKKGSNIKEIEEETGVKIQIPDDD-ERDIVTISGSPE----------------------QV   53 (60)
T ss_dssp             EEEEEEEH----HHHHHHHTGGGHHHHHHHHHHTSEEEEESTT-EEEEEEEEESHH----------------------HH
T ss_pred             CEEEEECH----HHcCEEECCCCCcHHHhhhhcCeEEEEcCCC-CcEEEEEEeCHH----------------------HH
Confidence            68999999    9999999999999999999999999999874 455999999888                      99


Q ss_pred             HHHHHHH
Q psy11929         96 CTAYNFM  102 (433)
Q Consensus        96 ~~A~~~I  102 (433)
                      .+|+++|
T Consensus        54 ~~A~~~I   60 (60)
T PF00013_consen   54 EKAKKMI   60 (60)
T ss_dssp             HHHHHHH
T ss_pred             HHHHhhC
Confidence            9999876

; InterPro: IPR018111 The K homology (KH) domain was first identified in the human heterogeneous nuclear ribonucleoprotein (hnRNP) K. It is a domain of around 70 amino acids that is present in a wide variety of quite diverse nucleic acid-binding proteins []. It has been shown to bind RNA [, ]. Like many other RNA-binding motifs, KH motifs are found in one or multiple copies (14 copies in chicken vigilin) and, at least for hnRNP K (three copies) and FMR-1 (two copies), each motif is necessary for in vitro RNA binding activity, suggesting that they may function cooperatively or, in the case of single KH motif proteins (for example, Mer1p), independently []. According to structural [, , ] analysis the KH domain can be separated in two groups. The first group or type-1 contain a beta-alpha-alpha-beta-beta-alpha structure, whereas in the type-2 the two last beta-sheet are located in the N-terminal part of the domain (alpha-beta-beta-alpha-alpha-beta). Sequence similarity between these two folds are limited to a short region (VIGXXGXXI) in the RNA binding motif. This motif is located between helice 1 and 2 in type-1 and between helice 2 and 3 in type-2. Proteins known to contain a type-1 KH domain include bacterial polyribonucleotide nucleotidyltransferases (2.7.7.8 from EC); vertebrate fragile X mental retardation protein 1 (FMR1); eukaryotic heterogeneous nuclear ribonucleoprotein K (hnRNP K), one of at least 20 major proteins that are part of hnRNP particles in mammalian cells; mammalian poly(rC) binding proteins; Artemia salina glycine-rich protein GRP33; yeast PAB1-binding protein 2 (PBP2); vertebrate vigilin; and human high-density lipoprotein binding protein (HDL-binding protein). More information about these proteins can be found at Protein of the Month: RNA Exosomes [].; GO: 0003723 RNA binding; PDB: 1TUA_A 2Z0S_A 1WE8_A 4AM3_B 4AIM_A 4AID_A 2HH3_A 2JVZ_A 1J4W_A 2HH2_A ....

>cd02393 PNPase_KH Polynucleotide phosphorylase (PNPase) K homology RNA-binding domain (KH)

Probab=99.22  E-value=3.5e-11  Score=89.15  Aligned_cols=58  Identities=24%  Similarity=0.328  Sum_probs=53.4

Q ss_pred             EEEEEeCcccccccccCCCchHHHHHhHhCCeEEEccCCCCCceEEEEEeC-HHHHHHHHHHHH
Q psy11929        289 ETEIVLTDDIAGCVIGKAGSRLLEIRQISGAQINIHTGTESHKKMFHIQGC-QEAVSLAQYLIN  351 (433)
Q Consensus       289 t~~i~VP~~~vG~IIGkgG~~Ik~I~~~sGA~I~I~~~~~~~er~V~IsGt-~e~v~~A~~lI~  351 (433)
                      +..+.||.+++|+||||+|++|++|+++|||+|.|++.     +.|.|+|+ +++++.|+.+|.
T Consensus         3 ~~~i~Ip~~~ig~iIGkgG~~ik~I~~~tg~~I~i~~~-----g~v~I~G~~~~~v~~A~~~I~   61 (61)
T cd02393           3 IETMKIPPDKIRDVIGPGGKTIKKIIEETGVKIDIEDD-----GTVYIAASDKEAAEKAKKMIE   61 (61)
T ss_pred             EEEEEeChhheeeeECCCchHHHHHHHHHCCEEEeCCC-----CEEEEEeCCHHHHHHHHHHhC
Confidence            56899999999999999999999999999999999872     67999999 999999998873

PNPase is a polyribonucleotide nucleotidyl transferase that degrades mRNA in prokaryotes and plant chloroplasts. The C-terminal region of PNPase contains domains homologous to those in other RNA binding proteins: a KH domain and an S1 domain. KH domains bind single-stranded RNA and are found in a wide variety of proteins including ribosomal proteins, transcription factors and post-transcriptional modifiers of mRNA.

>cd02394 vigilin_like_KH K homology RNA-binding domain_vigilin_like

Probab=99.21  E-value=1.7e-11  Score=91.36  Aligned_cols=61  Identities=23%  Similarity=0.341  Sum_probs=56.7

Q ss_pred             EEEEeccCCcccccceeeecCchHHHHHHHHhCCeEEEeCCCCCcceEEEecccCCCCCCccccCCCCCccccchHHHHH
Q psy11929         17 MRCLFHSSVNVNEISCLIGPGGCIVRRLRKESGAKISITDGACPDRIVTVSGSVDNSSTSSVETGYPGHTLWVTSVDNVC   96 (433)
Q Consensus        17 ~rilvp~~~~~~~vg~IIGk~G~~Ik~I~~~tga~I~v~~~~~~eRvv~I~G~~~~~~~~~v~~~~~~~~~~~~a~~~v~   96 (433)
                      .+|.||.    .++++|||++|++|++|+++|||+|.|++...+++.|+|+|+.+                      ++.
T Consensus         2 ~~i~Vp~----~~~~~iIG~~G~~i~~i~~~~g~~I~i~~~~~~~~~v~I~G~~~----------------------~v~   55 (62)
T cd02394           2 EEVEIPK----KLHRFIIGKKGSNIRKIMEETGVKIRFPDPGSKSDTITITGPKE----------------------NVE   55 (62)
T ss_pred             eEEEeCH----HHhhhccCCCCCcHHHHHHHhCCEEEcCCCCCCCCEEEEEcCHH----------------------HHH
Confidence            5788999    99999999999999999999999999999778899999999999                      999


Q ss_pred             HHHHHHH
Q psy11929         97 TAYNFMC  103 (433)
Q Consensus        97 ~A~~~I~  103 (433)
                      .|..+|.
T Consensus        56 ~A~~~i~   62 (62)
T cd02394          56 KAKEEIL   62 (62)
T ss_pred             HHHHHhC
Confidence            9988863

The vigilin family is a large and extended family of multiple KH-domain proteins, including vigilin, also called high density lipoprotein binding protien (HBP), fungal Scp160 and bicaudal-C. Yeast Scp160p has been shown to bind RNA and to associate with both soluble and membrane-bound polyribosomes as a mRNP component. Bicaudal-C is a RNA-binding molecule believed to function in embryonic development at the post-transcriptional level. In general, KH binds single-stranded RNA or DNA. It is found in a wide variety of proteins including ribosomal proteins, transcription factors and post-transcriptional modifiers of mRNA.

>cd02393 PNPase_KH Polynucleotide phosphorylase (PNPase) K homology RNA-binding domain (KH)

Probab=99.10  E-value=3.5e-10  Score=83.85  Aligned_cols=58  Identities=22%  Similarity=0.371  Sum_probs=53.0

Q ss_pred             eEEEEEeccCcccceecCCchhHHHHHHhhCceEEeccCCCCCCCccEEEEEcc-HHHHHHHHHHH
Q psy11929        124 LQLKLVIPATHCGSLIGKGGCKIKDIRDLSGANVQVASDMLPMSTERIVTVHGN-PDTISQAIYQI  188 (433)
Q Consensus       124 ~~~~l~ip~~~vg~iIGk~G~~Ik~I~~~sga~I~i~~~~~~~~~er~v~I~G~-~~~v~~A~~~I  188 (433)
                      ....+.||.+++|+|||++|++|++|+++|||+|.+++       ++.|.|+|+ .++++.|+.+|
T Consensus         2 ~~~~i~Ip~~~ig~iIGkgG~~ik~I~~~tg~~I~i~~-------~g~v~I~G~~~~~v~~A~~~I   60 (61)
T cd02393           2 RIETMKIPPDKIRDVIGPGGKTIKKIIEETGVKIDIED-------DGTVYIAASDKEAAEKAKKMI   60 (61)
T ss_pred             eEEEEEeChhheeeeECCCchHHHHHHHHHCCEEEeCC-------CCEEEEEeCCHHHHHHHHHHh
Confidence            45678999999999999999999999999999999975       468999998 99999999886

PNPase is a polyribonucleotide nucleotidyl transferase that degrades mRNA in prokaryotes and plant chloroplasts. The C-terminal region of PNPase contains domains homologous to those in other RNA binding proteins: a KH domain and an S1 domain. KH domains bind single-stranded RNA and are found in a wide variety of proteins including ribosomal proteins, transcription factors and post-transcriptional modifiers of mRNA.

>cd00105 KH-I K homology RNA-binding domain, type I

Probab=99.06  E-value=6.7e-10  Score=82.93  Aligned_cols=62  Identities=37%  Similarity=0.696  Sum_probs=55.9

Q ss_pred             EEEEeccCcccceecCCchhHHHHHHhhCceEEeccCCCCCCCccEEEEEccHHHHHHHHHHH
Q psy11929        126 LKLVIPATHCGSLIGKGGCKIKDIRDLSGANVQVASDMLPMSTERIVTVHGNPDTISQAIYQI  188 (433)
Q Consensus       126 ~~l~ip~~~vg~iIGk~G~~Ik~I~~~sga~I~i~~~~~~~~~er~v~I~G~~~~v~~A~~~I  188 (433)
                      .++.||..++++|||++|++|++|+++|||+|.|+... ....++.|.|.|+.+++..|+.+|
T Consensus         2 ~~i~ip~~~~~~vIG~~G~~i~~I~~~s~~~I~i~~~~-~~~~~~~v~i~G~~~~v~~a~~~i   63 (64)
T cd00105           2 ERVLVPSSLVGRIIGKGGSTIKEIREETGAKIKIPDSG-SGSEERIVTITGTPEAVEKAKELI   63 (64)
T ss_pred             EEEEEchhhcceeECCCCHHHHHHHHHHCCEEEEcCCC-CCCCceEEEEEcCHHHHHHHHHHh
Confidence            58999999999999999999999999999999998632 246789999999999999998876

KH binds single-stranded RNA or DNA. It is found in a wide variety of proteins including ribosomal proteins, transcription factors and post-transcriptional modifiers of mRNA. There are two different KH domains that belong to different protein folds, but they share a single KH motif. The KH motif is folded into a beta alpha alpha beta unit. In addition to the core, type II KH domains (e.g. ribosomal protein S3) include N-terminal extension and type I KH domains (e.g. hnRNP K) contain C-terminal extension.

>PF13014 KH_3: KH domain

Probab=99.01  E-value=4.9e-10  Score=76.96  Aligned_cols=40  Identities=38%  Similarity=0.737  Sum_probs=37.6

Q ss_pred             ccceeeecCchHHHHHHHHhCCeEEEeC---CCCCcceEEEec
Q psy11929         29 EISCLIGPGGCIVRRLRKESGAKISITD---GACPDRIVTVSG   68 (433)
Q Consensus        29 ~vg~IIGk~G~~Ik~I~~~tga~I~v~~---~~~~eRvv~I~G   68 (433)
                      ++|+||||+|++|++|+++|||+|+|++   ++..+|+|+|+|
T Consensus         1 ~vg~iIG~~G~~I~~I~~~tg~~I~i~~~~~~~~~~~~v~I~G   43 (43)
T PF13014_consen    1 FVGRIIGKGGSTIKEIREETGAKIQIPPENEPGSNERVVTITG   43 (43)
T ss_pred             CcCeEECCCChHHHHHHHHhCcEEEECCccCCCCCceEEEEEC
Confidence            5899999999999999999999999999   578999999987

>smart00322 KH K homology RNA-binding domain

Probab=98.95  E-value=4.2e-09  Score=78.96  Aligned_cols=67  Identities=31%  Similarity=0.457  Sum_probs=60.8

Q ss_pred             ceEEEEEeCcccccccccCCCchHHHHHhHhCCeEEEccCCCCCceEEEEEeCHHHHHHHHHHHHHHH
Q psy11929        287 FVETEIVLTDDIAGCVIGKAGSRLLEIRQISGAQINIHTGTESHKKMFHIQGCQEAVSLAQYLINMCI  354 (433)
Q Consensus       287 ~~t~~i~VP~~~vG~IIGkgG~~Ik~I~~~sGA~I~I~~~~~~~er~V~IsGt~e~v~~A~~lI~~~i  354 (433)
                      ..+.++.||..++|.+||++|.+|++|++.||++|.+.... .....|.|.|+++++..|..+|.+.+
T Consensus         2 ~~~~~i~i~~~~~~~liG~~G~~i~~i~~~~~~~i~~~~~~-~~~~~v~i~g~~~~v~~a~~~i~~~~   68 (69)
T smart00322        2 PVTIEVLIPADKVGLIIGKGGSTIKKIEEETGVKIDIPEDG-SEERVVEITGPPENVEKAAELILEIL   68 (69)
T ss_pred             ceEEEEEEcchhcceeECCCchHHHHHHHHHCCEEEECCCC-CCccEEEEEcCHHHHHHHHHHHHHHh
Confidence            35679999999999999999999999999999999998765 36688999999999999999998776

>PF13014 KH_3: KH domain

Probab=98.94  E-value=1.6e-09  Score=74.43  Aligned_cols=43  Identities=47%  Similarity=0.828  Sum_probs=40.3

Q ss_pred             cccceecCCchhHHHHHHhhCceEEeccCCCCCCCccEEEEEc
Q psy11929        134 HCGSLIGKGGCKIKDIRDLSGANVQVASDMLPMSTERIVTVHG  176 (433)
Q Consensus       134 ~vg~iIGk~G~~Ik~I~~~sga~I~i~~~~~~~~~er~v~I~G  176 (433)
                      ++|+|||++|++|++|+++|||+|.|+++..+...++.|+|+|
T Consensus         1 ~vg~iIG~~G~~I~~I~~~tg~~I~i~~~~~~~~~~~~v~I~G   43 (43)
T PF13014_consen    1 FVGRIIGKGGSTIKEIREETGAKIQIPPENEPGSNERVVTITG   43 (43)
T ss_pred             CcCeEECCCChHHHHHHHHhCcEEEECCccCCCCCceEEEEEC
Confidence            5899999999999999999999999998777888999999998

>KOG2208|consensus

Probab=98.89  E-value=6.2e-09  Score=113.03  Aligned_cols=247  Identities=17%  Similarity=0.172  Sum_probs=180.0

Q ss_pred             eEEEEEEeccCCcccccceeeecCchHHHHHHHHhCCeEEEeCCCCCcceEEEecccCCCCCCccccCCCCCccccchHH
Q psy11929         14 LITMRCLFHSSVNVNEISCLIGPGGCIVRRLRKESGAKISITDGACPDRIVTVSGSVDNSSTSSVETGYPGHTLWVTSVD   93 (433)
Q Consensus        14 ~~~~rilvp~~~~~~~vg~IIGk~G~~Ik~I~~~tga~I~v~~~~~~eRvv~I~G~~~~~~~~~v~~~~~~~~~~~~a~~   93 (433)
                      .+..++.+..    ..++++||++|.+++.+++++.+.|+++..+.......|.|......-               +.-
T Consensus       200 ~~~~k~~v~~----~~~~~~~g~g~~~~~~~~d~~~~~i~ip~sn~~~~~~~i~~~~~~~~~---------------~~~  260 (753)
T KOG2208|consen  200 SVFEKMNVGI----TLHSHIIGRGGSNISIIMDETKVHIHIPDSNKSSPSNKIDGRLNSSSS---------------INV  260 (753)
T ss_pred             eEEEEeeccc----cchhhhccccccccccccccceeEEEcccccccchhhhhcccccccee---------------hhh
Confidence            3778888888    999999999999999999999999999986544444555554441100               000


Q ss_pred             HHHHHHHHHHhhhhhhcccccCCCCCCCCCeEEEEEeccCcccceecCCchhHHHHHHhhCceEEeccCCCCCCCccEEE
Q psy11929         94 NVCTAYNFMCRSLEDYHINRNRMENCSPQPLQLKLVIPATHCGSLIGKGGCKIKDIRDLSGANVQVASDMLPMSTERIVT  173 (433)
Q Consensus        94 ~v~~A~~~I~~~~~~~~~~~~~~~~~~~~~~~~~l~ip~~~vg~iIGk~G~~Ik~I~~~sga~I~i~~~~~~~~~er~v~  173 (433)
                      .+..+..++                  ..+..+.+.++..+.-.++|..|..+..++...--...+.++  +.+.+..+.
T Consensus       261 ~i~~~~~~l------------------e~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~~~--~~s~~~~~~  320 (753)
T KOG2208|consen  261 EIQEALTRL------------------ESEFDYDEIIYRRLPRFIRGIPGEEINQLRDYMPEVDSIFQN--YPSKDDSIV  320 (753)
T ss_pred             hhHHHHHHh------------------cChhhhhhhhhccccccccccccchhhHHHhhcchhhhhhcc--ccccceeEe
Confidence            233333222                  234455667788888899999999999998876544333322  235566788


Q ss_pred             EEccHHHHHHHHHHHHHHHHhhccccCCCcccccCCCCCCCCCccccCCcccccCCCCCCCcccccCCCCCCCCcccccc
Q psy11929        174 VHGNPDTISQAIYQICLVLIECTLQVVKGAVIPYEPKTMNAGPVILSGGQAYTLHGEYAVPVQEVAGKKQPHPLAGLAVL  253 (433)
Q Consensus       174 I~G~~~~v~~A~~~I~~~l~e~~~~~~~~~~~~~~p~~~~~~p~~~~g~~~~~~~g~~~~P~~~~~~~~~~~p~~~~~~~  253 (433)
                      +.|....+..+......++....                                                         
T Consensus       321 ~~~~~~~~~~~~~~~~~~~~~~~---------------------------------------------------------  343 (753)
T KOG2208|consen  321 LSGFEVGAVLAKRDKTLLLKNSE---------------------------------------------------------  343 (753)
T ss_pred             ecccccchhhhhhHHHHHHHHhh---------------------------------------------------------
Confidence            88887777666555554444310                                                         


Q ss_pred             CcCCCCCCCCCccccccccCCCcccCCCCCCCCceEEEEEeCcccccccccCCCchHHHHHhHhCCeEEEccCCCCCceE
Q psy11929        254 GIEGIGSTSLTPAALAALSGSRVKSGGKDTGDDFVETEIVLTDDIAGCVIGKAGSRLLEIRQISGAQINIHTGTESHKKM  333 (433)
Q Consensus       254 ~~~~~~~p~~~~~~~~~~~~~~~~~~~~~~~~~~~t~~i~VP~~~vG~IIGkgG~~Ik~I~~~sGA~I~I~~~~~~~er~  333 (433)
                                                     .+.....+.+-++.+..++||+|.+|.+|++++.+.|.+.... +++..
T Consensus       344 -------------------------------~nn~~i~~~i~~~~~~~v~GK~~~ni~ki~e~~~~~i~~~~~~-~~~~~  391 (753)
T KOG2208|consen  344 -------------------------------ENNENIKREIFPEELKFVIGKKGANIEKIREESQVKIDLPKQG-SNNKK  391 (753)
T ss_pred             -------------------------------ccceeeEEeecHHhhhhhcCCCCccHHHHHHhhhhceeccccc-CCCCC
Confidence                                           0123457788889999999999999999999999999999955 67889


Q ss_pred             EEEEeCHHHHHHHHHHHHHHHHhccccCCCCCCCCCccccccccccchhccccccccccCCCCCcceecccc--HHHHHH
Q psy11929        334 FHIQGCQEAVSLAQYLINMCIELQKNNTTNTSDNPEPADLDAAISAFMTASVNSSLIEKPTPHPGSMVTLGG--LSELLA  411 (433)
Q Consensus       334 V~IsGt~e~v~~A~~lI~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~vP~~~~G~iiGkgG--~~e~~~  411 (433)
                      ++++|....+++|...++..+.+....-                        ..-++.+|+....+++|.||  ++++..
T Consensus       392 v~~~~~~~~~~ka~~~v~~~~~ei~n~~------------------------~~~~~~iP~k~~~~iig~~g~~i~~I~~  447 (753)
T KOG2208|consen  392 VVITGVSANDEKAVEDVEKIIAEILNSI------------------------VKEEVQIPTKSHKRIIGTKGALINYIMG  447 (753)
T ss_pred             eEEeccccchhHHHHHHHHHHHhhhccc------------------------ccceeecCccchhhhhccccccHHHHHh
Confidence            9999999999999999988887754310                        01235699999999999999  677754


Q ss_pred             h
Q psy11929        412 N  412 (433)
Q Consensus       412 ~  412 (433)
                      .
T Consensus       448 k  448 (753)
T KOG2208|consen  448 K  448 (753)
T ss_pred             h
Confidence            4

>smart00322 KH K homology RNA-binding domain

Probab=98.85  E-value=1.2e-08  Score=76.57  Aligned_cols=67  Identities=27%  Similarity=0.592  Sum_probs=60.6

Q ss_pred             eEEEEEEeccCCcccccceeeecCchHHHHHHHHhCCeEEEeCCCCCcceEEEecccCCCCCCccccCCCCCccccchHH
Q psy11929         14 LITMRCLFHSSVNVNEISCLIGPGGCIVRRLRKESGAKISITDGACPDRIVTVSGSVDNSSTSSVETGYPGHTLWVTSVD   93 (433)
Q Consensus        14 ~~~~rilvp~~~~~~~vg~IIGk~G~~Ik~I~~~tga~I~v~~~~~~eRvv~I~G~~~~~~~~~v~~~~~~~~~~~~a~~   93 (433)
                      .++.++.||.    .++|.+||++|.+|++|+++|||+|.+.......+++.|.|..+                      
T Consensus         2 ~~~~~i~i~~----~~~~~liG~~G~~i~~i~~~~~~~i~~~~~~~~~~~v~i~g~~~----------------------   55 (69)
T smart00322        2 PVTIEVLIPA----DKVGLIIGKGGSTIKKIEEETGVKIDIPEDGSEERVVEITGPPE----------------------   55 (69)
T ss_pred             ceEEEEEEcc----hhcceeECCCchHHHHHHHHHCCEEEECCCCCCccEEEEEcCHH----------------------
Confidence            4678999999    99999999999999999999999999988665789999999988                      


Q ss_pred             HHHHHHHHHHhhh
Q psy11929         94 NVCTAYNFMCRSL  106 (433)
Q Consensus        94 ~v~~A~~~I~~~~  106 (433)
                      ++..|..+|.+.+
T Consensus        56 ~v~~a~~~i~~~~   68 (69)
T smart00322       56 NVEKAAELILEIL   68 (69)
T ss_pred             HHHHHHHHHHHHh
Confidence            9999999987754

>KOG2208|consensus

Probab=98.84  E-value=8.7e-09  Score=111.89  Aligned_cols=216  Identities=19%  Similarity=0.259  Sum_probs=164.3

Q ss_pred             EEEEEEeccCCcccccceeeecCchHHHHHHHHhCCeEEEeCCCCCcceEEEecccCCCCCCccccCCCCCccccchHHH
Q psy11929         15 ITMRCLFHSSVNVNEISCLIGPGGCIVRRLRKESGAKISITDGACPDRIVTVSGSVDNSSTSSVETGYPGHTLWVTSVDN   94 (433)
Q Consensus        15 ~~~rilvp~~~~~~~vg~IIGk~G~~Ik~I~~~tga~I~v~~~~~~eRvv~I~G~~~~~~~~~v~~~~~~~~~~~~a~~~   94 (433)
                      +...+-+..    ..+..|+||+|.+|.+|++++.|+|.++..+..+..+.++|...                      +
T Consensus       347 ~~i~~~i~~----~~~~~v~GK~~~ni~ki~e~~~~~i~~~~~~~~~~~v~~~~~~~----------------------~  400 (753)
T KOG2208|consen  347 ENIKREIFP----EELKFVIGKKGANIEKIREESQVKIDLPKQGSNNKKVVITGVSA----------------------N  400 (753)
T ss_pred             eeeEEeecH----HhhhhhcCCCCccHHHHHHhhhhceecccccCCCCCeEEecccc----------------------c
Confidence            555666666    88999999999999999999999999999888999999999999                      8


Q ss_pred             HHHHHHHHHhhhhhhcccccCCCCCCCCCeEEEEEeccCcccceecCCchhHHHHHHhhC-ceEEeccCCCCCCCccEEE
Q psy11929         95 VCTAYNFMCRSLEDYHINRNRMENCSPQPLQLKLVIPATHCGSLIGKGGCKIKDIRDLSG-ANVQVASDMLPMSTERIVT  173 (433)
Q Consensus        95 v~~A~~~I~~~~~~~~~~~~~~~~~~~~~~~~~l~ip~~~vg~iIGk~G~~Ik~I~~~sg-a~I~i~~~~~~~~~er~v~  173 (433)
                      +.+|.+.+.....++..          ......+.+|...+.++||.+|..|.+|..+++ ..|.+..+   .+....++
T Consensus       401 ~~ka~~~v~~~~~ei~n----------~~~~~~~~iP~k~~~~iig~~g~~i~~I~~k~~~v~i~f~~~---~~~~~~~~  467 (753)
T KOG2208|consen  401 DEKAVEDVEKIIAEILN----------SIVKEEVQIPTKSHKRIIGTKGALINYIMGKHGGVHIKFQNN---NNSSDMVT  467 (753)
T ss_pred             hhHHHHHHHHHHHhhhc----------ccccceeecCccchhhhhccccccHHHHHhhcCcEEEecCCC---Ccccccce
Confidence            88999998888777532          145667899999999999999999999999999 66766642   34455678


Q ss_pred             EEccHHHHHHHHHHHHHHHHhhccccCCCcccccCCCCCCCCCccccCCcccccCCCCCCCcccccCCCCCCCCcccccc
Q psy11929        174 VHGNPDTISQAIYQICLVLIECTLQVVKGAVIPYEPKTMNAGPVILSGGQAYTLHGEYAVPVQEVAGKKQPHPLAGLAVL  253 (433)
Q Consensus       174 I~G~~~~v~~A~~~I~~~l~e~~~~~~~~~~~~~~p~~~~~~p~~~~g~~~~~~~g~~~~P~~~~~~~~~~~p~~~~~~~  253 (433)
                      +.|....+..+..+...+.....+ ..                                                     
T Consensus       468 ~~~~~~dv~~~~~~~~~~~~~a~~-~~-----------------------------------------------------  493 (753)
T KOG2208|consen  468 IRGISKDVEKSVSLLKALKADAKN-LK-----------------------------------------------------  493 (753)
T ss_pred             EeccccccchhHHHHHhhhhhhhc-ch-----------------------------------------------------
Confidence            888888887776666555443110 00                                                     


Q ss_pred             CcCCCCCCCCCccccccccCCCcccCCCCCCCCceEEEEEeCcccccccccCCCchHHHHHhHhCCeEEEccCCCCCceE
Q psy11929        254 GIEGIGSTSLTPAALAALSGSRVKSGGKDTGDDFVETEIVLTDDIAGCVIGKAGSRLLEIRQISGAQINIHTGTESHKKM  333 (433)
Q Consensus       254 ~~~~~~~p~~~~~~~~~~~~~~~~~~~~~~~~~~~t~~i~VP~~~vG~IIGkgG~~Ik~I~~~sGA~I~I~~~~~~~er~  333 (433)
                                                    .....+.+...|..+.+..+|+.|..+    +..+....++...+.++..
T Consensus       494 ------------------------------~~~~~~~d~~~~~~~~~~~~g~~~~i~----d~~~~~~i~~~~~~~~~~~  539 (753)
T KOG2208|consen  494 ------------------------------FRDVVTKDKLLPVKYIGKEIGKNGTIR----DSLGDKSIFPPNEDEDHEK  539 (753)
T ss_pred             ------------------------------hhhhhhccccchHHhhcccccCceeee----ccCCceeecccccccccce
Confidence                                          001122345567777777777776654    4555555666554456789


Q ss_pred             EEEEeCHHHHHHHHHHHHHHHHhc
Q psy11929        334 FHIQGCQEAVSLAQYLINMCIELQ  357 (433)
Q Consensus       334 V~IsGt~e~v~~A~~lI~~~i~~~  357 (433)
                      ++|.|..+.+..|+..+...+...
T Consensus       540 i~i~gk~~~v~~a~~~L~~~~~~~  563 (753)
T KOG2208|consen  540 ITIEGKLELVLEAPAELKALIEAL  563 (753)
T ss_pred             eeecccccchhhhHHHHHhcchhh
Confidence            999999999999999888877654

>COG1094 Predicted RNA-binding protein (contains KH domains) [General function prediction only]

Probab=98.81  E-value=2.4e-08  Score=89.33  Aligned_cols=148  Identities=16%  Similarity=0.223  Sum_probs=107.2

Q ss_pred             ceEEEEEEeccCCcccccceeeecCchHHHHHHHHhCCeEEEeCCCCCcceEEEecccCCCCCCccccCCCCCccccchH
Q psy11929         13 TLITMRCLFHSSVNVNEISCLIGPGGCIVRRLRKESGAKISITDGACPDRIVTVSGSVDNSSTSSVETGYPGHTLWVTSV   92 (433)
Q Consensus        13 ~~~~~rilvp~~~~~~~vg~IIGk~G~~Ik~I~~~tga~I~v~~~~~~eRvv~I~G~~~~~~~~~v~~~~~~~~~~~~a~   92 (433)
                      ......+.||.    ..++.+||+.|++.+.|.+.++++|.+..   .+..|.|..+..-.      ++           
T Consensus         6 ~~~~~~v~iPk----~R~~~lig~~g~v~k~ie~~~~~~~~iD~---~~~~V~i~~~~~t~------Dp-----------   61 (194)
T COG1094           6 EKSSEAVKIPK----DRIGVLIGKWGEVKKAIEEKTGVKLRIDS---KTGSVTIRTTRKTE------DP-----------   61 (194)
T ss_pred             ccceeeeecCc----hhheeeecccccchHHHHhhcCeEEEEEC---CCCeEEEEecCCCC------Ch-----------
Confidence            34566789999    99999999999999999999999999987   55678887773200      00           


Q ss_pred             HHHHHHHHHHHhhhhhhcccccCCCCCCCCCeEEE-EE----ec------cCcccceecCCchhHHHHHHhhCceEEecc
Q psy11929         93 DNVCTAYNFMCRSLEDYHINRNRMENCSPQPLQLK-LV----IP------ATHCGSLIGKGGCKIKDIRDLSGANVQVAS  161 (433)
Q Consensus        93 ~~v~~A~~~I~~~~~~~~~~~~~~~~~~~~~~~~~-l~----ip------~~~vg~iIGk~G~~Ik~I~~~sga~I~i~~  161 (433)
                      ..+.+|.+.|..+-..+.....  -....+...+. +.    +-      ....|+|||++|.+-+-|++-|+|.|.+. 
T Consensus        62 ~~~~ka~d~VkAIgrGF~pe~A--~~LL~d~~~levIdi~~~~~~~~~~l~R~kgRIIG~~GkTr~~IE~lt~~~I~V~-  138 (194)
T COG1094          62 LALLKARDVVKAIGRGFPPEKA--LKLLEDDYYLEVIDLKDVVTLSGDHLRRIKGRIIGREGKTRRAIEELTGVYISVY-  138 (194)
T ss_pred             HHHHHHHHHHHHHhcCCCHHHH--HHHhcCCcEEEEEEHHHhccCchhhhhHhhceeeCCCchHHHHHHHHhCCeEEEe-
Confidence            0677777777665443321100  00001111221 11    11      12459999999999999999999999997 


Q ss_pred             CCCCCCCccEEEEEccHHHHHHHHHHHHHHHHh
Q psy11929        162 DMLPMSTERIVTVHGNPDTISQAIYQICLVLIE  194 (433)
Q Consensus       162 ~~~~~~~er~v~I~G~~~~v~~A~~~I~~~l~e  194 (433)
                             ...|.|.|.++++..|...|..++..
T Consensus       139 -------g~tVaiiG~~~~v~iAr~AVemli~G  164 (194)
T COG1094         139 -------GKTVAIIGGFEQVEIAREAVEMLING  164 (194)
T ss_pred             -------CcEEEEecChhhhHHHHHHHHHHHcC
Confidence                   46899999999999999999999976

>KOG2279|consensus

Probab=98.69  E-value=1.3e-08  Score=102.83  Aligned_cols=146  Identities=24%  Similarity=0.439  Sum_probs=123.3

Q ss_pred             CCCCeEEEEEeccCcccceecCCchhHHHHHHhhCceEEeccCCCCCCCccEEEEEccHHHHHHHHHHHHHHHHhhcccc
Q psy11929        120 SPQPLQLKLVIPATHCGSLIGKGGCKIKDIRDLSGANVQVASDMLPMSTERIVTVHGNPDTISQAIYQICLVLIECTLQV  199 (433)
Q Consensus       120 ~~~~~~~~l~ip~~~vg~iIGk~G~~Ik~I~~~sga~I~i~~~~~~~~~er~v~I~G~~~~v~~A~~~I~~~l~e~~~~~  199 (433)
                      ....+.+++.++...+-+++|+.|++|+.|+..++++|.+..+..  ..++...+.|-+.++..|...++.++.+   +.
T Consensus        64 ~~k~v~~e~Vv~~e~vkli~gr~gsnik~l~~~t~aKi~L~~ed~--g~e~~~~~~~~p~~v~~a~a~~~~~~~~---~~  138 (608)
T KOG2279|consen   64 PQKDIEIEMVVPQEAVKLIIGRQGSNIKQLRKQTGAKIDLDTEDV--GDERVLLISGFPVQVCKAKAAIHQILTE---NT  138 (608)
T ss_pred             chhheeeeEeecccceeeeeccccCCcchhhcccccceecCcccC--CcccchhhccCCCCCChHHHHHHHHHhc---CC
Confidence            356788999999999999999999999999999999999986532  2455666677899999999999998876   11


Q ss_pred             CCCcccccCCCCCCCCCccccCCcccccCCCCCCCcccccCCCCCCCCccccccCcCCCCCCCCCccccccccCCCcccC
Q psy11929        200 VKGAVIPYEPKTMNAGPVILSGGQAYTLHGEYAVPVQEVAGKKQPHPLAGLAVLGIEGIGSTSLTPAALAALSGSRVKSG  279 (433)
Q Consensus       200 ~~~~~~~~~p~~~~~~p~~~~g~~~~~~~g~~~~P~~~~~~~~~~~p~~~~~~~~~~~~~~p~~~~~~~~~~~~~~~~~~  279 (433)
                                                                                                      
T Consensus       139 --------------------------------------------------------------------------------  138 (608)
T KOG2279|consen  139 --------------------------------------------------------------------------------  138 (608)
T ss_pred             --------------------------------------------------------------------------------
Confidence                                                                                            


Q ss_pred             CCCCCCCceEEEEEeCcccccccccCCCchHHHHHhHhCCeEEEccCCC-CCceEEEEEeCHHHHHHHHHHHHHHHHhc
Q psy11929        280 GKDTGDDFVETEIVLTDDIAGCVIGKAGSRLLEIRQISGAQINIHTGTE-SHKKMFHIQGCQEAVSLAQYLINMCIELQ  357 (433)
Q Consensus       280 ~~~~~~~~~t~~i~VP~~~vG~IIGkgG~~Ik~I~~~sGA~I~I~~~~~-~~er~V~IsGt~e~v~~A~~lI~~~i~~~  357 (433)
                             .+..++.+|...+++|+|++|.++..|+..++|+|.+..... .-.+.+.|.|...-+..|+.++.+++++.
T Consensus       139 -------pvk~~lsvpqr~~~~i~grgget~~si~~ss~aki~~d~ngr~g~~~~~~i~~qqk~~~~a~~~~~~~~~ed  210 (608)
T KOG2279|consen  139 -------PVSEQLSVPQRSVGRIIGRGGETIRSICKSSGAKITCDKNGRLGLSRLIKISGQQKEVAAAKHLILEKVSED  210 (608)
T ss_pred             -------cccccccchhhhcccccccchhhhcchhcccccccccccccccccccceecccccchHHHHHhhhhccccch
Confidence                   223355678899999999999999999999999999998866 66788889999888889999998888664

>COG1094 Predicted RNA-binding protein (contains KH domains) [General function prediction only]

Probab=98.50  E-value=6.1e-07  Score=80.47  Aligned_cols=148  Identities=24%  Similarity=0.302  Sum_probs=106.2

Q ss_pred             CeEEEEEeccCcccceecCCchhHHHHHHhhCceEEeccCCCCCCCccEEEEEc-----cHHHHHHHHHHHHHHHHhhcc
Q psy11929        123 PLQLKLVIPATHCGSLIGKGGCKIKDIRDLSGANVQVASDMLPMSTERIVTVHG-----NPDTISQAIYQICLVLIECTL  197 (433)
Q Consensus       123 ~~~~~l~ip~~~vg~iIGk~G~~Ik~I~~~sga~I~i~~~~~~~~~er~v~I~G-----~~~~v~~A~~~I~~~l~e~~~  197 (433)
                      .....+.||...++.+||+.|+.-+.|.+.+++++.+..+      +..|.|..     +|-.+.+|...|..+=+.   
T Consensus         7 ~~~~~v~iPk~R~~~lig~~g~v~k~ie~~~~~~~~iD~~------~~~V~i~~~~~t~Dp~~~~ka~d~VkAIgrG---   77 (194)
T COG1094           7 KSSEAVKIPKDRIGVLIGKWGEVKKAIEEKTGVKLRIDSK------TGSVTIRTTRKTEDPLALLKARDVVKAIGRG---   77 (194)
T ss_pred             cceeeeecCchhheeeecccccchHHHHhhcCeEEEEECC------CCeEEEEecCCCCChHHHHHHHHHHHHHhcC---
Confidence            3455689999999999999999999999999999999743      45666643     578889998888776554   


Q ss_pred             ccCCCcccccCCCCCCCCCccccCCcccccCCCCCCCcccccCCCCCCCCccccccCcCCCCCCCCCccccccccCCCcc
Q psy11929        198 QVVKGAVIPYEPKTMNAGPVILSGGQAYTLHGEYAVPVQEVAGKKQPHPLAGLAVLGIEGIGSTSLTPAALAALSGSRVK  277 (433)
Q Consensus       198 ~~~~~~~~~~~p~~~~~~p~~~~g~~~~~~~g~~~~P~~~~~~~~~~~p~~~~~~~~~~~~~~p~~~~~~~~~~~~~~~~  277 (433)
                      +++..+-.            +......+-                    .-.                  +         
T Consensus        78 F~pe~A~~------------LL~d~~~le--------------------vId------------------i---------   98 (194)
T COG1094          78 FPPEKALK------------LLEDDYYLE--------------------VID------------------L---------   98 (194)
T ss_pred             CCHHHHHH------------HhcCCcEEE--------------------EEE------------------H---------
Confidence            22111000            000000000                    000                  0         


Q ss_pred             cCCCCCCCCceEEEEEe-----CcccccccccCCCchHHHHHhHhCCeEEEccCCCCCceEEEEEeCHHHHHHHHHHHHH
Q psy11929        278 SGGKDTGDDFVETEIVL-----TDDIAGCVIGKAGSRLLEIRQISGAQINIHTGTESHKKMFHIQGCQEAVSLAQYLINM  352 (433)
Q Consensus       278 ~~~~~~~~~~~t~~i~V-----P~~~vG~IIGkgG~~Ik~I~~~sGA~I~I~~~~~~~er~V~IsGt~e~v~~A~~lI~~  352 (433)
                                  ..+.-     =....|+|||++|.+-+.|+..|||.|-|....      |-|-|.+++++.|+..|..
T Consensus        99 ------------~~~~~~~~~~l~R~kgRIIG~~GkTr~~IE~lt~~~I~V~g~t------VaiiG~~~~v~iAr~AVem  160 (194)
T COG1094          99 ------------KDVVTLSGDHLRRIKGRIIGREGKTRRAIEELTGVYISVYGKT------VAIIGGFEQVEIAREAVEM  160 (194)
T ss_pred             ------------HHhccCchhhhhHhhceeeCCCchHHHHHHHHhCCeEEEeCcE------EEEecChhhhHHHHHHHHH
Confidence                        00000     112569999999999999999999999999865      9999999999999999999


Q ss_pred             HHHh
Q psy11929        353 CIEL  356 (433)
Q Consensus       353 ~i~~  356 (433)
                      +++.
T Consensus       161 li~G  164 (194)
T COG1094         161 LING  164 (194)
T ss_pred             HHcC
Confidence            9975

>cd02395 SF1_like-KH Splicing factor 1 (SF1) K homology RNA-binding domain (KH)

Probab=98.39  E-value=8.4e-07  Score=74.72  Aligned_cols=64  Identities=25%  Similarity=0.353  Sum_probs=48.5

Q ss_pred             ccccceeeecCchHHHHHHHHhCCeEEEeCCCCC-------------------cceEEEecccCCCCCCccccCCCCCcc
Q psy11929         27 VNEISCLIGPGGCIVRRLRKESGAKISITDGACP-------------------DRIVTVSGSVDNSSTSSVETGYPGHTL   87 (433)
Q Consensus        27 ~~~vg~IIGk~G~~Ik~I~~~tga~I~v~~~~~~-------------------eRvv~I~G~~~~~~~~~v~~~~~~~~~   87 (433)
                      ++++|.|||++|.+||+|+++|||+|.|...++.                   .-.|.|++..                 
T Consensus        14 ~N~IG~IIGPgG~tiK~i~~eTg~kI~Irg~gs~~~~~~~~~~~~~~~~~~~eplhV~I~a~~-----------------   76 (120)
T cd02395          14 YNFVGLILGPRGNTLKQLEKETGAKISIRGKGSMKDGKKEEELRGPKYAHLNEPLHVLITAET-----------------   76 (120)
T ss_pred             CCeeEEEECCCChHHHHHHHHHCCEEEEecCcccccccccccccCcccccCCCCcEEEEEeCC-----------------
Confidence            5889999999999999999999999999875311                   1234444443                 


Q ss_pred             ccchHHHHHHHHHHHHhhhhhh
Q psy11929         88 WVTSVDNVCTAYNFMCRSLEDY  109 (433)
Q Consensus        88 ~~~a~~~v~~A~~~I~~~~~~~  109 (433)
                        ++.+++.+|..+|..++...
T Consensus        77 --~~~e~~~~A~~~I~~ll~~~   96 (120)
T cd02395          77 --PPEEALAKAVEAIEELLKPA   96 (120)
T ss_pred             --cHHHHHHHHHHHHHHHhccC
Confidence              12458999999998887653

Splicing factor 1 (SF1) specifically recognizes the intron branch point sequence (BPS) UACUAAC in the pre-mRNA transcripts during spliceosome assembly. We show that the KH-QUA2 region of SF1 defines an enlarged KH (hnRNP K) fold which is necessary and sufficient for BPS binding. KH binds single-stranded RNA or DNA. It is found in a wide variety of proteins including ribosomal proteins, transcription factors and post-transcriptional modifiers of mRNA.

>cd02395 SF1_like-KH Splicing factor 1 (SF1) K homology RNA-binding domain (KH)

Probab=98.33  E-value=1.5e-06  Score=73.22  Aligned_cols=60  Identities=22%  Similarity=0.306  Sum_probs=51.4

Q ss_pred             ccccccccCCCchHHHHHhHhCCeEEEccCCC------------------CCceEEEEEeCH---HHHHHHHHHHHHHHH
Q psy11929        297 DIAGCVIGKAGSRLLEIRQISGAQINIHTGTE------------------SHKKMFHIQGCQ---EAVSLAQYLINMCIE  355 (433)
Q Consensus       297 ~~vG~IIGkgG~~Ik~I~~~sGA~I~I~~~~~------------------~~er~V~IsGt~---e~v~~A~~lI~~~i~  355 (433)
                      +++|.|||.+|++||+|+++|||+|.|.....                  .++-.|.|++..   +++++|..+|..++.
T Consensus        15 N~IG~IIGPgG~tiK~i~~eTg~kI~Irg~gs~~~~~~~~~~~~~~~~~~~eplhV~I~a~~~~~e~~~~A~~~I~~ll~   94 (120)
T cd02395          15 NFVGLILGPRGNTLKQLEKETGAKISIRGKGSMKDGKKEEELRGPKYAHLNEPLHVLITAETPPEEALAKAVEAIEELLK   94 (120)
T ss_pred             CeeEEEECCCChHHHHHHHHHCCEEEEecCcccccccccccccCcccccCCCCcEEEEEeCCcHHHHHHHHHHHHHHHhc
Confidence            57899999999999999999999999997632                  233678899964   899999999999987


Q ss_pred             h
Q psy11929        356 L  356 (433)
Q Consensus       356 ~  356 (433)
                      .
T Consensus        95 ~   95 (120)
T cd02395          95 P   95 (120)
T ss_pred             c
Confidence            4

Splicing factor 1 (SF1) specifically recognizes the intron branch point sequence (BPS) UACUAAC in the pre-mRNA transcripts during spliceosome assembly. We show that the KH-QUA2 region of SF1 defines an enlarged KH (hnRNP K) fold which is necessary and sufficient for BPS binding. KH binds single-stranded RNA or DNA. It is found in a wide variety of proteins including ribosomal proteins, transcription factors and post-transcriptional modifiers of mRNA.

>KOG2113|consensus

Probab=98.26  E-value=1.4e-06  Score=82.57  Aligned_cols=149  Identities=21%  Similarity=0.358  Sum_probs=110.1

Q ss_pred             CCeEEEEEeccCcccceecCCchhHHHHHHhhCceEEeccCCCCCCCccEEEEEccHHHHHHHHHHHHHHHHhhccccCC
Q psy11929        122 QPLQLKLVIPATHCGSLIGKGGCKIKDIRDLSGANVQVASDMLPMSTERIVTVHGNPDTISQAIYQICLVLIECTLQVVK  201 (433)
Q Consensus       122 ~~~~~~l~ip~~~vg~iIGk~G~~Ik~I~~~sga~I~i~~~~~~~~~er~v~I~G~~~~v~~A~~~I~~~l~e~~~~~~~  201 (433)
                      ..++..+.+|..+++.++|++|.+||.|+.+|...|.-+..    ..+.++.++|..+.|+.|+..|...-+.   ..  
T Consensus        24 ~nvt~sv~vps~~v~~ivg~qg~kikalr~KTqtyi~tPsr----~eePiF~vTg~~edv~~aRrei~saaeH---~~--   94 (394)
T KOG2113|consen   24 QNVTESVEVPSEHVAEIVGRQGCKIKALRAKTQTYIKTPSR----GEEPIFPVTGRHEDVRRARREIPSAAEH---FG--   94 (394)
T ss_pred             CccceeeecCcccceeecccCccccchhhhhhcceeccCCC----CCCCcceeccCchhHHHHhhcCccccce---ee--
Confidence            67888899999999999999999999999999999998742    2457899999999999998876543221   00  


Q ss_pred             CcccccCCCCCCCCCccccCCcccccCCCCCCCcccccCCCCCCCCccccccCcCCCCCCCCCccccccccCCCcccCCC
Q psy11929        202 GAVIPYEPKTMNAGPVILSGGQAYTLHGEYAVPVQEVAGKKQPHPLAGLAVLGIEGIGSTSLTPAALAALSGSRVKSGGK  281 (433)
Q Consensus       202 ~~~~~~~p~~~~~~p~~~~g~~~~~~~g~~~~P~~~~~~~~~~~p~~~~~~~~~~~~~~p~~~~~~~~~~~~~~~~~~~~  281 (433)
                        -+.|.+...        |                                     ..+     .+             
T Consensus        95 --l~~~s~s~S--------g-------------------------------------g~~-----~~-------------  109 (394)
T KOG2113|consen   95 --LIRASRSFS--------G-------------------------------------GTN-----GA-------------  109 (394)
T ss_pred             --eeeeccccc--------C-------------------------------------CCc-----cc-------------
Confidence              000100000        0                                     000     00             


Q ss_pred             CCCCCceEEEEEeCcccccccccCCCchHHHHHhHhCCeEEEccCCCCCceEEEEEeCHHH-HHHHH
Q psy11929        282 DTGDDFVETEIVLTDDIAGCVIGKAGSRLLEIRQISGAQINIHTGTESHKKMFHIQGCQEA-VSLAQ  347 (433)
Q Consensus       282 ~~~~~~~t~~i~VP~~~vG~IIGkgG~~Ik~I~~~sGA~I~I~~~~~~~er~V~IsGt~e~-v~~A~  347 (433)
                       ....+.+.+..+|-..+|.|.|.+|.+|+.|++.+...|.-.-+.  .+.++.++|.+.. +++|.
T Consensus       110 -s~s~qt~sy~svP~rvvglvv~~~~~ti~~iqq~tnt~I~T~v~~--~~~Vf~Vtg~~~nC~kra~  173 (394)
T KOG2113|consen  110 -SASGQTTSYVSVPLRVVGLVVGPKGATIKRIQQFTNTYIATPVRC--GEPVFCVTGAPKNCVKRAR  173 (394)
T ss_pred             -cccCCCceeeeccceeeeeccccccCccchheecccceEeeeccC--CCceEEEecCCcchhhhcc
Confidence             012355678889999999999999999999999999999877665  6778888998876 55555

>KOG2113|consensus

Probab=98.12  E-value=5e-06  Score=78.79  Aligned_cols=151  Identities=18%  Similarity=0.284  Sum_probs=115.0

Q ss_pred             CCCceEEEEEEeccCCcccccceeeecCchHHHHHHHHhCCeEEEeCCCCCcceEEEecccCCCCCCccccCCCCCcccc
Q psy11929         10 DEDTLITMRCLFHSSVNVNEISCLIGPGGCIVRRLRKESGAKISITDGACPDRIVTVSGSVDNSSTSSVETGYPGHTLWV   89 (433)
Q Consensus        10 ~~~~~~~~rilvp~~~~~~~vg~IIGk~G~~Ik~I~~~tga~I~v~~~~~~eRvv~I~G~~~~~~~~~v~~~~~~~~~~~   89 (433)
                      +-...++..+-+|.    .+++.|.|++|.+||.|+.+|...|.-+..+ .+-+..++|..+                  
T Consensus        21 ~~p~nvt~sv~vps----~~v~~ivg~qg~kikalr~KTqtyi~tPsr~-eePiF~vTg~~e------------------   77 (394)
T KOG2113|consen   21 SIGQNVTESVEVPS----EHVAEIVGRQGCKIKALRAKTQTYIKTPSRG-EEPIFPVTGRHE------------------   77 (394)
T ss_pred             CCCCccceeeecCc----ccceeecccCccccchhhhhhcceeccCCCC-CCCcceeccCch------------------
Confidence            34467888889998    9999999999999999999999999887655 347889999999                  


Q ss_pred             chHHHHHHHHHHHHhhhhhhc-----ccccCCC--CCCCCCeEEEEEeccCcccceecCCchhHHHHHHhhCceEEeccC
Q psy11929         90 TSVDNVCTAYNFMCRSLEDYH-----INRNRME--NCSPQPLQLKLVIPATHCGSLIGKGGCKIKDIRDLSGANVQVASD  162 (433)
Q Consensus        90 ~a~~~v~~A~~~I~~~~~~~~-----~~~~~~~--~~~~~~~~~~l~ip~~~vg~iIGk~G~~Ik~I~~~sga~I~i~~~  162 (433)
                          .|.+|++.|....+.+.     ..+.+..  .......+...-+|-..+|.+.|..|.+|+.|++.++..|.-.- 
T Consensus        78 ----dv~~aRrei~saaeH~~l~~~s~s~Sgg~~~~s~s~qt~sy~svP~rvvglvv~~~~~ti~~iqq~tnt~I~T~v-  152 (394)
T KOG2113|consen   78 ----DVRRARREIPSAAEHFGLIRASRSFSGGTNGASASGQTTSYVSVPLRVVGLVVGPKGATIKRIQQFTNTYIATPV-  152 (394)
T ss_pred             ----hHHHHhhcCccccceeeeeeecccccCCCccccccCCCceeeeccceeeeeccccccCccchheecccceEeeec-
Confidence                89999988876433321     1111111  11234455667889999999999999999999999999887753 


Q ss_pred             CCCCCCccEEEEEccHHH-HHHHH-HHHHHH
Q psy11929        163 MLPMSTERIVTVHGNPDT-ISQAI-YQICLV  191 (433)
Q Consensus       163 ~~~~~~er~v~I~G~~~~-v~~A~-~~I~~~  191 (433)
                         .+.+.++.++|.+.+ +++|. +.|...
T Consensus       153 ---~~~~~Vf~Vtg~~~nC~kra~s~eie~t  180 (394)
T KOG2113|consen  153 ---RCGEPVFCVTGAPKNCVKRARSCEIEQT  180 (394)
T ss_pred             ---cCCCceEEEecCCcchhhhccccchhhh
Confidence               345778999998888 56665 555543

>PRK08406 transcription elongation factor NusA-like protein; Validated

Probab=98.06  E-value=9.2e-06  Score=70.43  Aligned_cols=104  Identities=18%  Similarity=0.272  Sum_probs=71.1

Q ss_pred             EEEEEEeccCCcccccceeeecCchHHHHHHHHhCCeEEEeCCCCCcceEEEecccCCCCCCccccCCCCCccccchHHH
Q psy11929         15 ITMRCLFHSSVNVNEISCLIGPGGCIVRRLRKESGAKISITDGACPDRIVTVSGSVDNSSTSSVETGYPGHTLWVTSVDN   94 (433)
Q Consensus        15 ~~~rilvp~~~~~~~vg~IIGk~G~~Ik~I~~~tga~I~v~~~~~~eRvv~I~G~~~~~~~~~v~~~~~~~~~~~~a~~~   94 (433)
                      =.+.++|+.    ..+|..||++|++|+.|++..|-+|.|-.-.            +                       
T Consensus        32 ~~vi~vV~~----~~vG~~IG~~G~rI~~i~e~lgekIdVve~s------------~-----------------------   72 (140)
T PRK08406         32 DRIIFVVKE----GDMGLAIGKGGENVKRLEEKLGKDIELVEYS------------D-----------------------   72 (140)
T ss_pred             CEEEEEEeC----CCccccCCcCchHHHHHHHHhCCceEEEEcC------------C-----------------------
Confidence            356788888    9999999999999999999999888876410            1                       


Q ss_pred             HHHHHHHHHhhhhhhcccccCCCCCCCCCeEEEEEeccCcccceecCCchhHHHHHHhhCceEEec
Q psy11929         95 VCTAYNFMCRSLEDYHINRNRMENCSPQPLQLKLVIPATHCGSLIGKGGCKIKDIRDLSGANVQVA  160 (433)
Q Consensus        95 v~~A~~~I~~~~~~~~~~~~~~~~~~~~~~~~~l~ip~~~vg~iIGk~G~~Ik~I~~~sga~I~i~  160 (433)
                        .+..+|...+......--. -........+.+.|+....|.+|||+|.+++.++.-++-.+.+.
T Consensus        73 --d~~~fI~n~l~Pa~V~~v~-I~~~~~~~~~~V~V~~~d~g~aIGK~G~ni~la~~L~~~~~di~  135 (140)
T PRK08406         73 --DPEEFIKNIFAPAAVRSVT-IKKKNGDKVAYVEVAPEDKGIAIGKNGKNIERAKDLAKRHFDID  135 (140)
T ss_pred             --CHHHHHHHHcCCCEEEEEE-EEecCCcEEEEEEECccccchhhCCCCHHHHHHHHHhCCccCCe
Confidence              1122222222211000000 00012235667789999999999999999999999998877663

>PRK08406 transcription elongation factor NusA-like protein; Validated

Probab=98.05  E-value=1.6e-05  Score=69.00  Aligned_cols=38  Identities=24%  Similarity=0.489  Sum_probs=34.3

Q ss_pred             eEEEEEeccCcccceecCCchhHHHHHHhhCceEEecc
Q psy11929        124 LQLKLVIPATHCGSLIGKGGCKIKDIRDLSGANVQVAS  161 (433)
Q Consensus       124 ~~~~l~ip~~~vg~iIGk~G~~Ik~I~~~sga~I~i~~  161 (433)
                      -.+.++|+...+|..||++|++|+.|++..|-+|.+-.
T Consensus        32 ~~vi~vV~~~~vG~~IG~~G~rI~~i~e~lgekIdVve   69 (140)
T PRK08406         32 DRIIFVVKEGDMGLAIGKGGENVKRLEEKLGKDIELVE   69 (140)
T ss_pred             CEEEEEEeCCCccccCCcCchHHHHHHHHhCCceEEEE
Confidence            46778999999999999999999999999999988863

>TIGR02696 pppGpp_PNP guanosine pentaphosphate synthetase I/polynucleotide phosphorylase

Probab=97.96  E-value=4.1e-05  Score=82.13  Aligned_cols=98  Identities=17%  Similarity=0.210  Sum_probs=77.1

Q ss_pred             ccchHHHHHHHHHHHHhhhhhhcccccCCCCCCCCCeEEEEEeccCcccceecCCchhHHHHHHhhCceEEeccCCCCCC
Q psy11929         88 WVTSVDNVCTAYNFMCRSLEDYHINRNRMENCSPQPLQLKLVIPATHCGSLIGKGGCKIKDIRDLSGANVQVASDMLPMS  167 (433)
Q Consensus        88 ~~~a~~~v~~A~~~I~~~~~~~~~~~~~~~~~~~~~~~~~l~ip~~~vg~iIGk~G~~Ik~I~~~sga~I~i~~~~~~~~  167 (433)
                      +..|++.+.+++..|.+.+++.-...  .......+....+.||.+++|.|||+||.+||.|+++||++|.+..      
T Consensus       544 l~~aL~~A~~g~~~Il~~m~~al~~p--~~~s~~aP~~~~~~I~~~ki~~vIG~gGk~I~~i~~~tg~~Idi~d------  615 (719)
T TIGR02696       544 LASALKQARDARLAILDVMAEAIDTP--DEMSPYAPRIITVKIPVDKIGEVIGPKGKMINQIQDETGAEISIED------  615 (719)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHhCc--cccccCCCeeEEEEeChHHhhheeCCCcHhHHHHHHHHCCEEEEec------
Confidence            44466777777778877776632222  1223345677889999999999999999999999999999999974      


Q ss_pred             CccEEEEEc-cHHHHHHHHHHHHHHHHh
Q psy11929        168 TERIVTVHG-NPDTISQAIYQICLVLIE  194 (433)
Q Consensus       168 ~er~v~I~G-~~~~v~~A~~~I~~~l~e  194 (433)
                       +..|.|.+ +.+.+++|+.+|..++..
T Consensus       616 -~G~V~I~a~d~~~~~~A~~~I~~i~~~  642 (719)
T TIGR02696       616 -DGTVYIGAADGPSAEAARAMINAIANP  642 (719)
T ss_pred             -CcEEEEEeCCHHHHHHHHHHHHHhhCc
Confidence             57788888 788999999999988873

Sohlberg, et al. present characterization of two proteins from Streptomyces coelicolor. The protein in this family was shown to have poly(A) polymerase activity and may be responsible for polyadenylating RNA in this species. Reference 2 showed that a nearly identical plasmid-encoded protein from Streptomyces antibioticus is a bifunctional enzyme that acts also as a guanosine pentaphosphate synthetase.

>TIGR02696 pppGpp_PNP guanosine pentaphosphate synthetase I/polynucleotide phosphorylase

Probab=97.79  E-value=0.00012  Score=78.56  Aligned_cols=64  Identities=23%  Similarity=0.280  Sum_probs=57.4

Q ss_pred             eEEEEEeCcccccccccCCCchHHHHHhHhCCeEEEccCCCCCceEEEEEeC-HHHHHHHHHHHHHHHHh
Q psy11929        288 VETEIVLTDDIAGCVIGKAGSRLLEIRQISGAQINIHTGTESHKKMFHIQGC-QEAVSLAQYLINMCIEL  356 (433)
Q Consensus       288 ~t~~i~VP~~~vG~IIGkgG~~Ik~I~~~sGA~I~I~~~~~~~er~V~IsGt-~e~v~~A~~lI~~~i~~  356 (433)
                      ...++.||.+++|.|||.||.+||.|+++|||+|.|.++     ..|.|.+. .++.++|+.+|...+..
T Consensus       578 ~~~~~~I~~~ki~~vIG~gGk~I~~i~~~tg~~Idi~d~-----G~V~I~a~d~~~~~~A~~~I~~i~~~  642 (719)
T TIGR02696       578 RIITVKIPVDKIGEVIGPKGKMINQIQDETGAEISIEDD-----GTVYIGAADGPSAEAARAMINAIANP  642 (719)
T ss_pred             eeEEEEeChHHhhheeCCCcHhHHHHHHHHCCEEEEecC-----cEEEEEeCCHHHHHHHHHHHHHhhCc
Confidence            356899999999999999999999999999999999984     57888885 68999999999998874

Sohlberg, et al. present characterization of two proteins from Streptomyces coelicolor. The protein in this family was shown to have poly(A) polymerase activity and may be responsible for polyadenylating RNA in this species. Reference 2 showed that a nearly identical plasmid-encoded protein from Streptomyces antibioticus is a bifunctional enzyme that acts also as a guanosine pentaphosphate synthetase.

>TIGR01952 nusA_arch NusA family KH domain protein, archaeal

Probab=97.59  E-value=0.00039  Score=60.18  Aligned_cols=103  Identities=20%  Similarity=0.311  Sum_probs=68.7

Q ss_pred             EEEEEeccCCcccccceeeecCchHHHHHHHHhCCeEEEeCCCCCcceEEEecccCCCCCCccccCCCCCccccchHHHH
Q psy11929         16 TMRCLFHSSVNVNEISCLIGPGGCIVRRLRKESGAKISITDGACPDRIVTVSGSVDNSSTSSVETGYPGHTLWVTSVDNV   95 (433)
Q Consensus        16 ~~rilvp~~~~~~~vg~IIGk~G~~Ik~I~~~tga~I~v~~~~~~eRvv~I~G~~~~~~~~~v~~~~~~~~~~~~a~~~v   95 (433)
                      .+-+++..    ..+|..||++|++|+.|++..|=+|.|-.=.            +                      ..
T Consensus        34 riifvV~~----g~vG~~IG~~G~rIk~i~el~gekIdVVeys------------~----------------------D~   75 (141)
T TIGR01952        34 RVVFVVKE----GEMGAAIGKGGENVKRLEELIGKSIELIEYS------------E----------------------NL   75 (141)
T ss_pred             EEEEEEcC----CCccccCCCCchHHHHHHHhcCCeeEEEEcC------------C----------------------CH
Confidence            56677777    8999999999999999998889888876411            0                      00


Q ss_pred             HHHHHHHHhhhhhhcccccCCCCCCCCCeEEEEEeccCcccceecCCchhHHHHHHhhCceEEec
Q psy11929         96 CTAYNFMCRSLEDYHINRNRMENCSPQPLQLKLVIPATHCGSLIGKGGCKIKDIRDLSGANVQVA  160 (433)
Q Consensus        96 ~~A~~~I~~~~~~~~~~~~~~~~~~~~~~~~~l~ip~~~vg~iIGk~G~~Ik~I~~~sga~I~i~  160 (433)
                      .   .+|...+....-..- .....+....+.+.||.+..+..|||+|.+++...+-++-++.+.
T Consensus        76 ~---~fI~N~l~PA~V~~V-~i~~~~~~~~a~V~V~~~d~~~AIGk~G~Ni~la~~l~~~~~dI~  136 (141)
T TIGR01952        76 E---EFVANKLAPAEVKNV-TVSEFNGKKVAYVEVHPRDKGIAIGKGGKNIERAKELAKRHHDID  136 (141)
T ss_pred             H---HHHHHcCCCceEEEE-EEEcCCCCEEEEEEEChhhhhhhhCCCchhHHHHHHHhcCccCCe
Confidence            1   111111111000000 000012345677889999999999999999999999998877664

This model represents a family of archaeal proteins found in a single copy per genome. It contains two KH domains (pfam00013) and is most closely related to the central region bacterial NusA, a transcription termination factor named for its iteraction with phage lambda protein N in E. coli. The proteins required for antitermination by N include NusA, NusB, nusE (ribosomal protein S10), and nusG. This system, on the whole, appears not to be present in the Archaea.

>TIGR03591 polynuc_phos polyribonucleotide nucleotidyltransferase

Probab=97.50  E-value=0.00034  Score=76.08  Aligned_cols=97  Identities=16%  Similarity=0.234  Sum_probs=70.1

Q ss_pred             chHHHHHHHHHHHHhhhhhhcccccCCCCCCCCCeEEEEEeccCcccceecCCchhHHHHHHhhCceEEeccCCCCCCCc
Q psy11929         90 TSVDNVCTAYNFMCRSLEDYHINRNRMENCSPQPLQLKLVIPATHCGSLIGKGGCKIKDIRDLSGANVQVASDMLPMSTE  169 (433)
Q Consensus        90 ~a~~~v~~A~~~I~~~~~~~~~~~~~~~~~~~~~~~~~l~ip~~~vg~iIGk~G~~Ik~I~~~sga~I~i~~~~~~~~~e  169 (433)
                      .|++...+++..|.+.+++.-.... .......+....+.||.+.++.|||++|++||+|+++|||+|.|..       +
T Consensus       518 ~al~~a~~~~~~I~~~m~~~l~~~~-~~~~~~~p~~~~~~I~~~kI~~vIG~gGk~Ik~I~~~tg~~I~i~d-------d  589 (684)
T TIGR03591       518 QALEQAKEGRLHILGEMNKVISEPR-AELSPYAPRIETIKINPDKIRDVIGPGGKVIREITEETGAKIDIED-------D  589 (684)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHhhhh-ccccccCCeEEEEecCHHHHHhhcCCCcHHHHHHHHHHCCEEEEec-------C
Confidence            3445555666666665555221110 1122345667788999999999999999999999999999999974       4


Q ss_pred             cEEEEEc-cHHHHHHHHHHHHHHHHh
Q psy11929        170 RIVTVHG-NPDTISQAIYQICLVLIE  194 (433)
Q Consensus       170 r~v~I~G-~~~~v~~A~~~I~~~l~e  194 (433)
                      ..|.|.+ +.+.+.+|...|..+..+
T Consensus       590 G~V~i~~~~~~~~~~a~~~I~~~~~~  615 (684)
T TIGR03591       590 GTVKIAASDGEAAEAAIKMIEGITAE  615 (684)
T ss_pred             eEEEEEECcHHHHHHHHHHHHhhhcc
Confidence            5677766 678889999998887653

Members of this protein family are polyribonucleotide nucleotidyltransferase, also called polynucleotide phosphorylase. Some members have been shown also to have additional functions as guanosine pentaphosphate synthetase and as poly(A) polymerase (see model TIGR02696 for an exception clade, within this family).

>TIGR03591 polynuc_phos polyribonucleotide nucleotidyltransferase

Probab=97.49  E-value=0.00041  Score=75.45  Aligned_cols=64  Identities=27%  Similarity=0.270  Sum_probs=55.2

Q ss_pred             eEEEEEeCcccccccccCCCchHHHHHhHhCCeEEEccCCCCCceEEEEEeC-HHHHHHHHHHHHHHHHh
Q psy11929        288 VETEIVLTDDIAGCVIGKAGSRLLEIRQISGAQINIHTGTESHKKMFHIQGC-QEAVSLAQYLINMCIEL  356 (433)
Q Consensus       288 ~t~~i~VP~~~vG~IIGkgG~~Ik~I~~~sGA~I~I~~~~~~~er~V~IsGt-~e~v~~A~~lI~~~i~~  356 (433)
                      ...++.||.+++|.|||+||++||.|+++|||+|.|.++     -.|.|.+. .+.+++|..+|..+...
T Consensus       551 ~~~~~~I~~~kI~~vIG~gGk~Ik~I~~~tg~~I~i~dd-----G~V~i~~~~~~~~~~a~~~I~~~~~~  615 (684)
T TIGR03591       551 RIETIKINPDKIRDVIGPGGKVIREITEETGAKIDIEDD-----GTVKIAASDGEAAEAAIKMIEGITAE  615 (684)
T ss_pred             eEEEEecCHHHHHhhcCCCcHHHHHHHHHHCCEEEEecC-----eEEEEEECcHHHHHHHHHHHHhhhcc
Confidence            356899999999999999999999999999999999875     45667664 68899999999888653

Members of this protein family are polyribonucleotide nucleotidyltransferase, also called polynucleotide phosphorylase. Some members have been shown also to have additional functions as guanosine pentaphosphate synthetase and as poly(A) polymerase (see model TIGR02696 for an exception clade, within this family).

>KOG0119|consensus

Probab=97.46  E-value=0.00094  Score=67.48  Aligned_cols=73  Identities=23%  Similarity=0.362  Sum_probs=56.3

Q ss_pred             CeEEEEEecc------CcccceecCCchhHHHHHHhhCceEEecc-----CC---------CCCCCc-cEEEEEc-cHHH
Q psy11929        123 PLQLKLVIPA------THCGSLIGKGGCKIKDIRDLSGANVQVAS-----DM---------LPMSTE-RIVTVHG-NPDT  180 (433)
Q Consensus       123 ~~~~~l~ip~------~~vg~iIGk~G~~Ik~I~~~sga~I~i~~-----~~---------~~~~~e-r~v~I~G-~~~~  180 (433)
                      ..+-++.||-      +++|+|||..|.|.|+|+++|||+|.|-.     +.         .+...| =-+.|++ +.+.
T Consensus       137 ~~~~Kv~IPvke~Pd~NFvGLiiGPRG~TqK~lE~etgAKI~IRGkgSvkEgk~~~~d~~~~~~~~epLH~~Isadt~ek  216 (554)
T KOG0119|consen  137 KLHDKVYIPVKEFPDINFVGLIIGPRGNTQKRLERETGAKIAIRGKGSVKEGKGRSDDLSYIPKENEPLHCLISADTQEK  216 (554)
T ss_pred             ccccceecchhhcCCcceeEEEecCCccHHHHHHHHhCCeEEEeccccccccccCCcccccccccccceeEEEecchHHH
Confidence            6677888883      58999999999999999999999999963     11         112222 3456777 5678


Q ss_pred             HHHHHHHHHHHHHhh
Q psy11929        181 ISQAIYQICLVLIEC  195 (433)
Q Consensus       181 v~~A~~~I~~~l~e~  195 (433)
                      |++|++.|..+|.+.
T Consensus       217 i~~Ai~vienli~~a  231 (554)
T KOG0119|consen  217 IKKAIAVIENLIQSA  231 (554)
T ss_pred             HHHHHHHHHHHHHhh
Confidence            899999999998863

>KOG0336|consensus

Probab=97.46  E-value=0.00016  Score=71.58  Aligned_cols=72  Identities=19%  Similarity=0.245  Sum_probs=61.3

Q ss_pred             CCCceEEEEEeCcccccccccCCCchHHHHHhHhCCeEEEccCCCCCceEEEEEeCHHHHHHHHHHHHHHHHhc
Q psy11929        284 GDDFVETEIVLTDDIAGCVIGKAGSRLLEIRQISGAQINIHTGTESHKKMFHIQGCQEAVSLAQYLINMCIELQ  357 (433)
Q Consensus       284 ~~~~~t~~i~VP~~~vG~IIGkgG~~Ik~I~~~sGA~I~I~~~~~~~er~V~IsGt~e~v~~A~~lI~~~i~~~  357 (433)
                      +..+...-+.|-.++||.|||++|++|++||..|+++|+|.+.+  -+..|+|-|...--.+|+..|...+..+
T Consensus        43 g~~e~plcf~iks~mvg~vigrggskik~iq~~tnt~iqii~~~--~e~kv~ifg~~~m~~kaka~id~~~~k~  114 (629)
T KOG0336|consen   43 GGGEFPLCFSIKSEMVGKVIGRGGSKIKRIQNDTNTRIQIIKCD--LEVKVTIFGINHMRKKAKASIDRGQDKD  114 (629)
T ss_pred             CCCCCchhhhhhhhhhheeeccCcchhhhhhcccceeEEEeccC--ceeEEEEechHHHHHHHHhhHhhhhhhh
Confidence            34566778889999999999999999999999999999999876  6788999999988888888776665443

>KOG1588|consensus

Probab=97.39  E-value=0.00029  Score=66.13  Aligned_cols=50  Identities=26%  Similarity=0.422  Sum_probs=41.6

Q ss_pred             CCCCceEEEEEEeccC--CcccccceeeecCchHHHHHHHHhCCeEEEeCCC
Q psy11929          9 IDEDTLITMRCLFHSS--VNVNEISCLIGPGGCIVRRLRKESGAKISITDGA   58 (433)
Q Consensus         9 ~~~~~~~~~rilvp~~--~~~~~vg~IIGk~G~~Ik~I~~~tga~I~v~~~~   58 (433)
                      ......++.|++||.+  ...++||.|+|++|.++|+|+++|||+|.|-..+
T Consensus        86 ~~~~vk~~~Kv~vPv~~yP~fNFVGRILGPrGnSlkrLe~eTgCki~IrGrg  137 (259)
T KOG1588|consen   86 SGKPVKLTEKVLVPVKEYPKFNFVGRILGPRGNSLKRLEEETGCKIMIRGRG  137 (259)
T ss_pred             cCCceeEEEEEEeccCCCCCCccccccccCCcchHHHHHHHHCCeEEEecCC
Confidence            3455678899999874  3456899999999999999999999999987643

>TIGR01952 nusA_arch NusA family KH domain protein, archaeal

Probab=97.29  E-value=0.00081  Score=58.24  Aligned_cols=39  Identities=15%  Similarity=0.234  Sum_probs=34.2

Q ss_pred             ceEEEEEeCcccccccccCCCchHHHHHhHhCCeEEEcc
Q psy11929        287 FVETEIVLTDDIAGCVIGKAGSRLLEIRQISGAQINIHT  325 (433)
Q Consensus       287 ~~t~~i~VP~~~vG~IIGkgG~~Ik~I~~~sGA~I~I~~  325 (433)
                      .....+.||.+..+..|||+|+||+...+.+|-++.|.+
T Consensus        99 ~~~a~V~V~~~d~~~AIGk~G~Ni~la~~l~~~~~dI~~  137 (141)
T TIGR01952        99 KKVAYVEVHPRDKGIAIGKGGKNIERAKELAKRHHDIDD  137 (141)
T ss_pred             CEEEEEEEChhhhhhhhCCCchhHHHHHHHhcCccCCeE
Confidence            356788999999999999999999999999998887653

This model represents a family of archaeal proteins found in a single copy per genome. It contains two KH domains (pfam00013) and is most closely related to the central region bacterial NusA, a transcription termination factor named for its iteraction with phage lambda protein N in E. coli. The proteins required for antitermination by N include NusA, NusB, nusE (ribosomal protein S10), and nusG. This system, on the whole, appears not to be present in the Archaea.

>KOG0119|consensus

Probab=97.16  E-value=0.00077  Score=68.07  Aligned_cols=87  Identities=21%  Similarity=0.322  Sum_probs=53.9

Q ss_pred             eEEEEEEeccC--CcccccceeeecCchHHHHHHHHhCCeEEEeCCCC-CcceEEEecccCCCCCCccccCCCCCcccc-
Q psy11929         14 LITMRCLFHSS--VNVNEISCLIGPGGCIVRRLRKESGAKISITDGAC-PDRIVTVSGSVDNSSTSSVETGYPGHTLWV-   89 (433)
Q Consensus        14 ~~~~rilvp~~--~~~~~vg~IIGk~G~~Ik~I~~~tga~I~v~~~~~-~eRvv~I~G~~~~~~~~~v~~~~~~~~~~~-   89 (433)
                      .++-|+.||.+  =.+++||+|||.+|.|.|+|++||||||.|-..++ .|..    |..+.-.    .....++..+| 
T Consensus       137 ~~~~Kv~IPvke~Pd~NFvGLiiGPRG~TqK~lE~etgAKI~IRGkgSvkEgk----~~~~d~~----~~~~~~epLH~~  208 (554)
T KOG0119|consen  137 KLHDKVYIPVKEFPDINFVGLIIGPRGNTQKRLERETGAKIAIRGKGSVKEGK----GRSDDLS----YIPKENEPLHCL  208 (554)
T ss_pred             ccccceecchhhcCCcceeEEEecCCccHHHHHHHHhCCeEEEeccccccccc----cCCcccc----cccccccceeEE
Confidence            55667777641  12368999999999999999999999999976421 2211    1111000    00011112222 


Q ss_pred             ---chHHHHHHHHHHHHhhhhh
Q psy11929         90 ---TSVDNVCTAYNFMCRSLED  108 (433)
Q Consensus        90 ---~a~~~v~~A~~~I~~~~~~  108 (433)
                         ..+|.|.+|++.|..++.+
T Consensus       209 Isadt~eki~~Ai~vienli~~  230 (554)
T KOG0119|consen  209 ISADTQEKIKKAIAVIENLIQS  230 (554)
T ss_pred             EecchHHHHHHHHHHHHHHHHh
Confidence               2467899999998888775

>KOG2814|consensus

Probab=97.11  E-value=0.00033  Score=67.60  Aligned_cols=71  Identities=20%  Similarity=0.253  Sum_probs=59.2

Q ss_pred             ceEEEEEEeccCCcccccceeeecCchHHHHHHHHhCCeEEEeCCCCCcceEEEec-ccCCCCCCccccCCCCCccccch
Q psy11929         13 TLITMRCLFHSSVNVNEISCLIGPGGCIVRRLRKESGAKISITDGACPDRIVTVSG-SVDNSSTSSVETGYPGHTLWVTS   91 (433)
Q Consensus        13 ~~~~~rilvp~~~~~~~vg~IIGk~G~~Ik~I~~~tga~I~v~~~~~~eRvv~I~G-~~~~~~~~~v~~~~~~~~~~~~a   91 (433)
                      .+...-++++.    ...|.|||++|.|-++|++||+++|.++.++...-.|+|.| ..+                    
T Consensus        55 ~~~~~si~v~s----~~~~~lig~~g~trkkle~Etq~~i~lp~p~~n~~~i~i~~~~~~--------------------  110 (345)
T KOG2814|consen   55 KDFSSSILVRS----SFIGWLIGKQGKTRKKLEEETQTNIFLPRPNTNKEEIKIIGISRN--------------------  110 (345)
T ss_pred             ccchhhhhhhH----HHhhhhhcccchHHHHHHHhhccceEccCCCCCcceEEEeehhHH--------------------
Confidence            35777888998    99999999999999999999999999999875554555554 445                    


Q ss_pred             HHHHHHHHHHHHhhhhhh
Q psy11929         92 VDNVCTAYNFMCRSLEDY  109 (433)
Q Consensus        92 ~~~v~~A~~~I~~~~~~~  109 (433)
                        +|.+|.++|.-.+.+.
T Consensus       111 --~V~~a~~Ri~~~ids~  126 (345)
T KOG2814|consen  111 --CVIQALERIAKLIDSD  126 (345)
T ss_pred             --HHHHHHHHHHHHHHhh
Confidence              8999999998887764

>COG0195 NusA Transcription elongation factor [Transcription]

Probab=97.09  E-value=0.0018  Score=58.92  Aligned_cols=96  Identities=22%  Similarity=0.346  Sum_probs=64.9

Q ss_pred             ccccceeeecCchHHHHHHHHhCCeEEEeCCCCCcceEEEecccCCCCCCccccCCCCCccccchHHHHHHHHHHHHhhh
Q psy11929         27 VNEISCLIGPGGCIVRRLRKESGAKISITDGACPDRIVTVSGSVDNSSTSSVETGYPGHTLWVTSVDNVCTAYNFMCRSL  106 (433)
Q Consensus        27 ~~~vg~IIGk~G~~Ik~I~~~tga~I~v~~~~~~eRvv~I~G~~~~~~~~~v~~~~~~~~~~~~a~~~v~~A~~~I~~~~  106 (433)
                      ...+|..||++|++|+.|.++.|=+|.|-.-+           ++                      -..-+..++. -.
T Consensus        84 ~d~vG~~iG~~G~rvk~i~~eLgekIdVVe~s-----------~d----------------------~~~fI~nal~-Pa  129 (190)
T COG0195          84 IDPVGACIGKRGSRVKAVSEELGEKIDVVEWS-----------ED----------------------PAEFIKNALA-PA  129 (190)
T ss_pred             cCchhhhccCCChHHHHHHHHhCCceEEEEeC-----------CC----------------------HHHHHHHhcC-cc
Confidence            48899999999999999999999777775411           11                      1111111111 00


Q ss_pred             hhhcccccCCCCCCCCCeEEEEEeccCcccceecCCchhHHHHHHhhCceEEecc
Q psy11929        107 EDYHINRNRMENCSPQPLQLKLVIPATHCGSLIGKGGCKIKDIRDLSGANVQVAS  161 (433)
Q Consensus       107 ~~~~~~~~~~~~~~~~~~~~~l~ip~~~vg~iIGk~G~~Ik~I~~~sga~I~i~~  161 (433)
                      +-..-...    ..+.. ...+.||.+..+..|||+|.+++-+.+-||-++.|..
T Consensus       130 ~v~~V~~~----~~d~~-~~~v~V~~~~~~~aIGk~G~Nvrla~~Ltg~~i~I~~  179 (190)
T COG0195         130 EVLSVNIK----EDDGH-VAIVVVPPDQLSLAIGKGGQNVRLASQLTGWEIDIET  179 (190)
T ss_pred             eEeEEEEE----eCCCc-EEEEEECHHHHhhccCcccHHHHHHHHHhCCEEEEEe
Confidence            00000000    00112 7788999999999999999999999999999998864

>PLN00207 polyribonucleotide nucleotidyltransferase; Provisional

Probab=97.06  E-value=0.0013  Score=72.54  Aligned_cols=99  Identities=12%  Similarity=0.187  Sum_probs=73.8

Q ss_pred             ccchHHHHHHHHHHHHhhhhhhcccccCCCCCCCCCeEEEEEeccCcccceecCCchhHHHHHHhhCce-EEeccCCCCC
Q psy11929         88 WVTSVDNVCTAYNFMCRSLEDYHINRNRMENCSPQPLQLKLVIPATHCGSLIGKGGCKIKDIRDLSGAN-VQVASDMLPM  166 (433)
Q Consensus        88 ~~~a~~~v~~A~~~I~~~~~~~~~~~~~~~~~~~~~~~~~l~ip~~~vg~iIGk~G~~Ik~I~~~sga~-I~i~~~~~~~  166 (433)
                      +..|++.+.+++..|++.+++.-... ........+....+.||.++++.|||.||.+||.|.++||++ |.+..     
T Consensus       650 l~eAL~~A~~g~~~Il~~M~~~i~~p-r~~~s~~aP~i~~~~i~~~ki~~vIG~GGktIk~I~eetg~~~Idi~d-----  723 (891)
T PLN00207        650 MERALLQAKDGRKHILAEMSKCSPPP-SKRLSKYAPLIHIMKVKPEKVNMIIGSGGKKVKSIIEETGVEAIDTQD-----  723 (891)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHhhh-hhhhcccCCeeEEEEcCHHHHHHHhcCCchhHHHHHHHHCCCccCcCC-----
Confidence            33455666666677776666532111 111223456778899999999999999999999999999999 88864     


Q ss_pred             CCccEEEEEc-cHHHHHHHHHHHHHHHHh
Q psy11929        167 STERIVTVHG-NPDTISQAIYQICLVLIE  194 (433)
Q Consensus       167 ~~er~v~I~G-~~~~v~~A~~~I~~~l~e  194 (433)
                        +-.|.|.+ +.+.+++|+.+|..++.+
T Consensus       724 --dg~V~I~a~d~~~i~~A~~~I~~l~~~  750 (891)
T PLN00207        724 --DGTVKITAKDLSSLEKSKAIISSLTMV  750 (891)
T ss_pred             --CeeEEEEeCCHHHHHHHHHHHHHHhcC
Confidence              45788877 788999999999888764

>PLN00207 polyribonucleotide nucleotidyltransferase; Provisional

Probab=97.01  E-value=0.0018  Score=71.32  Aligned_cols=64  Identities=13%  Similarity=0.231  Sum_probs=56.1

Q ss_pred             eEEEEEeCcccccccccCCCchHHHHHhHhCCe-EEEccCCCCCceEEEEEeC-HHHHHHHHHHHHHHHHh
Q psy11929        288 VETEIVLTDDIAGCVIGKAGSRLLEIRQISGAQ-INIHTGTESHKKMFHIQGC-QEAVSLAQYLINMCIEL  356 (433)
Q Consensus       288 ~t~~i~VP~~~vG~IIGkgG~~Ik~I~~~sGA~-I~I~~~~~~~er~V~IsGt-~e~v~~A~~lI~~~i~~  356 (433)
                      ....|.||.+++|.|||.||.+||.|.++||+. |.|.+.     -.|.|.+. .+.+++|+.+|.+.+..
T Consensus       685 ~i~~~~i~~~ki~~vIG~GGktIk~I~eetg~~~Idi~dd-----g~V~I~a~d~~~i~~A~~~I~~l~~~  750 (891)
T PLN00207        685 LIHIMKVKPEKVNMIIGSGGKKVKSIIEETGVEAIDTQDD-----GTVKITAKDLSSLEKSKAIISSLTMV  750 (891)
T ss_pred             eeEEEEcCHHHHHHHhcCCchhHHHHHHHHCCCccCcCCC-----eeEEEEeCCHHHHHHHHHHHHHHhcC
Confidence            356899999999999999999999999999999 988875     46777775 78999999999988863

>COG1185 Pnp Polyribonucleotide nucleotidyltransferase (polynucleotide phosphorylase) [Translation, ribosomal structure and biogenesis]

Probab=96.90  E-value=0.0035  Score=66.30  Aligned_cols=64  Identities=22%  Similarity=0.252  Sum_probs=57.1

Q ss_pred             EEEEEeCcccccccccCCCchHHHHHhHhCCeEEEccCCCCCceEEEEEeCH-HHHHHHHHHHHHHHHhc
Q psy11929        289 ETEIVLTDDIAGCVIGKAGSRLLEIRQISGAQINIHTGTESHKKMFHIQGCQ-EAVSLAQYLINMCIELQ  357 (433)
Q Consensus       289 t~~i~VP~~~vG~IIGkgG~~Ik~I~~~sGA~I~I~~~~~~~er~V~IsGt~-e~v~~A~~lI~~~i~~~  357 (433)
                      ..++.|+.+.++.+||++|.+|++|..+|||+|.|.++.     .|.|.++. +.+.+|+.+|.++.++.
T Consensus       553 i~t~~i~~dKI~dvIG~gGk~I~~I~eetg~~IdieddG-----tv~i~~s~~~~~~~ak~~I~~i~~e~  617 (692)
T COG1185         553 IETIKIDPDKIRDVIGPGGKTIKAITEETGVKIDIEDDG-----TVKIAASDGESAKKAKERIEAITREV  617 (692)
T ss_pred             eEEEccCHHHHhhccCCcccchhhhhhhhCcEEEecCCC-----cEEEEecchHHHHHHHHHHHHHHhhc
Confidence            468899999999999999999999999999999999544     68888886 78999999999999664

>COG1185 Pnp Polyribonucleotide nucleotidyltransferase (polynucleotide phosphorylase) [Translation, ribosomal structure and biogenesis]

Probab=96.85  E-value=0.0028  Score=67.10  Aligned_cols=99  Identities=17%  Similarity=0.220  Sum_probs=73.7

Q ss_pred             ccchHHHHHHHHHHHHhhhhhhcccccCCCCCCCCCeEEEEEeccCcccceecCCchhHHHHHHhhCceEEeccCCCCCC
Q psy11929         88 WVTSVDNVCTAYNFMCRSLEDYHINRNRMENCSPQPLQLKLVIPATHCGSLIGKGGCKIKDIRDLSGANVQVASDMLPMS  167 (433)
Q Consensus        88 ~~~a~~~v~~A~~~I~~~~~~~~~~~~~~~~~~~~~~~~~l~ip~~~vg~iIGk~G~~Ik~I~~~sga~I~i~~~~~~~~  167 (433)
                      +..|..+...|.-.|+..+.+.-... ........+....+-|+...+.-+||++|.+|++|.++||++|.+..      
T Consensus       517 m~~AL~QAk~aRlhIL~~M~~ai~~p-r~els~~aPri~t~~i~~dKI~dvIG~gGk~I~~I~eetg~~Idied------  589 (692)
T COG1185         517 MKKALEQAKGARLHILIVMNEAISEP-RKELSPYAPRIETIKIDPDKIRDVIGPGGKTIKAITEETGVKIDIED------  589 (692)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHhhh-hhhhhccCCceEEEccCHHHHhhccCCcccchhhhhhhhCcEEEecC------
Confidence            44455666667667776665522111 01122244556778899999999999999999999999999999973      


Q ss_pred             CccEEEEEccH-HHHHHHHHHHHHHHHh
Q psy11929        168 TERIVTVHGNP-DTISQAIYQICLVLIE  194 (433)
Q Consensus       168 ~er~v~I~G~~-~~v~~A~~~I~~~l~e  194 (433)
                       +..|.|.++. +.+.+|+..|..+.++
T Consensus       590 -dGtv~i~~s~~~~~~~ak~~I~~i~~e  616 (692)
T COG1185         590 -DGTVKIAASDGESAKKAKERIEAITRE  616 (692)
T ss_pred             -CCcEEEEecchHHHHHHHHHHHHHHhh
Confidence             5678888854 7889999999999987

>KOG2814|consensus

Probab=96.83  E-value=0.0018  Score=62.56  Aligned_cols=74  Identities=16%  Similarity=0.201  Sum_probs=63.8

Q ss_pred             CceEEEEEeCcccccccccCCCchHHHHHhHhCCeEEEccCCCCCceEEEEEeCHHHHHHHHHHHHHHHHhccc
Q psy11929        286 DFVETEIVLTDDIAGCVIGKAGSRLLEIRQISGAQINIHTGTESHKKMFHIQGCQEAVSLAQYLINMCIELQKN  359 (433)
Q Consensus       286 ~~~t~~i~VP~~~vG~IIGkgG~~Ik~I~~~sGA~I~I~~~~~~~er~V~IsGt~e~v~~A~~lI~~~i~~~~~  359 (433)
                      ......+.++..+.|.|||++|.+-+.|+.+|+++|.++.+.+..+.++.+-+..++|.+|...|.-.|...+.
T Consensus        55 ~~~~~si~v~s~~~~~lig~~g~trkkle~Etq~~i~lp~p~~n~~~i~i~~~~~~~V~~a~~Ri~~~ids~r~  128 (345)
T KOG2814|consen   55 KDFSSSILVRSSFIGWLIGKQGKTRKKLEEETQTNIFLPRPNTNKEEIKIIGISRNCVIQALERIAKLIDSDRK  128 (345)
T ss_pred             ccchhhhhhhHHHhhhhhcccchHHHHHHHhhccceEccCCCCCcceEEEeehhHHHHHHHHHHHHHHHHhhhh
Confidence            35667889999999999999999999999999999999998855555555566689999999999999988763

>cd02134 NusA_KH NusA_K homology RNA-binding domain (KH)

Probab=96.76  E-value=0.0023  Score=47.18  Aligned_cols=37  Identities=32%  Similarity=0.395  Sum_probs=34.3

Q ss_pred             eEEEEEEeccCCcccccceeeecCchHHHHHHHHhCCeEEE
Q psy11929         14 LITMRCLFHSSVNVNEISCLIGPGGCIVRRLRKESGAKISI   54 (433)
Q Consensus        14 ~~~~rilvp~~~~~~~vg~IIGk~G~~Ik~I~~~tga~I~v   54 (433)
                      ...+++.|+.    ...|..|||+|.+|+.+++.+|-+|.|
T Consensus        24 ~~~~~v~V~~----~~~~~aIGk~G~nI~~~~~l~~~~I~v   60 (61)
T cd02134          24 EKRARVVVPD----DQLGLAIGKGGQNVRLASKLLGEKIDI   60 (61)
T ss_pred             CcEEEEEECc----ccceeeECCCCHHHHHHHHHHCCCeEE
Confidence            3688999999    999999999999999999999998876

NusA is an essential multifunctional transcription elongation factor that is universally conserved among prokaryotes and archaea. NusA anti-termination function plays an important role in the expression of ribosomal rrn operons. During transcription of many other genes, NusA-induced RNAP pausing provides a mechanism for synchronizing transcription and translation . The N-terminal RNAP-binding domain (NTD) is connected through a flexible hinge helix to three globular domains, S1, KH1 and KH2. The KH motif is a beta-alpha-alpha-beta-beta unit that folds into an alpha-beta structure with a three stranded beta-sheet interupted by two contiguous helices.

>KOG0336|consensus

Probab=96.70  E-value=0.002  Score=64.03  Aligned_cols=73  Identities=25%  Similarity=0.276  Sum_probs=59.8

Q ss_pred             CCCCCCeEEEEEeccCcccceecCCchhHHHHHHhhCceEEeccCCCCCCCccEEEEEccHHHHHHHHHHHHHHHHh
Q psy11929        118 NCSPQPLQLKLVIPATHCGSLIGKGGCKIKDIRDLSGANVQVASDMLPMSTERIVTVHGNPDTISQAIYQICLVLIE  194 (433)
Q Consensus       118 ~~~~~~~~~~l~ip~~~vg~iIGk~G~~Ik~I~~~sga~I~i~~~~~~~~~er~v~I~G~~~~v~~A~~~I~~~l~e  194 (433)
                      ..+.....+.|-|-++++|.+||++|++|+.||..|+++|++.+.    ..+-.|+|.|...--.+|+..|......
T Consensus        41 aag~~e~plcf~iks~mvg~vigrggskik~iq~~tnt~iqii~~----~~e~kv~ifg~~~m~~kaka~id~~~~k  113 (629)
T KOG0336|consen   41 AAGGGEFPLCFSIKSEMVGKVIGRGGSKIKRIQNDTNTRIQIIKC----DLEVKVTIFGINHMRKKAKASIDRGQDK  113 (629)
T ss_pred             ccCCCCCchhhhhhhhhhheeeccCcchhhhhhcccceeEEEecc----CceeEEEEechHHHHHHHHhhHhhhhhh
Confidence            345667788899999999999999999999999999999999863    2367899999887777777766655443

>cd02134 NusA_KH NusA_K homology RNA-binding domain (KH)

Probab=96.69  E-value=0.0023  Score=47.24  Aligned_cols=37  Identities=30%  Similarity=0.482  Sum_probs=34.4

Q ss_pred             ceEEEEEeCcccccccccCCCchHHHHHhHhCCeEEE
Q psy11929        287 FVETEIVLTDDIAGCVIGKAGSRLLEIRQISGAQINI  323 (433)
Q Consensus       287 ~~t~~i~VP~~~vG~IIGkgG~~Ik~I~~~sGA~I~I  323 (433)
                      .....+.||.+..|..|||+|.+|+.+++.+|-+|.|
T Consensus        24 ~~~~~v~V~~~~~~~aIGk~G~nI~~~~~l~~~~I~v   60 (61)
T cd02134          24 EKRARVVVPDDQLGLAIGKGGQNVRLASKLLGEKIDI   60 (61)
T ss_pred             CcEEEEEECcccceeeECCCCHHHHHHHHHHCCCeEE
Confidence            3678999999999999999999999999999988876

NusA is an essential multifunctional transcription elongation factor that is universally conserved among prokaryotes and archaea. NusA anti-termination function plays an important role in the expression of ribosomal rrn operons. During transcription of many other genes, NusA-induced RNAP pausing provides a mechanism for synchronizing transcription and translation . The N-terminal RNAP-binding domain (NTD) is connected through a flexible hinge helix to three globular domains, S1, KH1 and KH2. The KH motif is a beta-alpha-alpha-beta-beta unit that folds into an alpha-beta structure with a three stranded beta-sheet interupted by two contiguous helices.

>PF14611 SLS: Mitochondrial inner-membrane-bound regulator

Probab=96.50  E-value=0.079  Score=49.16  Aligned_cols=64  Identities=17%  Similarity=0.251  Sum_probs=55.6

Q ss_pred             EEEEEeccCcccceecCCchhHHHHHHhhCceEEeccCCCCCCCccEEEEEccHHHHHHHHHHHHHHHHh
Q psy11929        125 QLKLVIPATHCGSLIGKGGCKIKDIRDLSGANVQVASDMLPMSTERIVTVHGNPDTISQAIYQICLVLIE  194 (433)
Q Consensus       125 ~~~l~ip~~~vg~iIGk~G~~Ik~I~~~sga~I~i~~~~~~~~~er~v~I~G~~~~v~~A~~~I~~~l~e  194 (433)
                      .+.+.++....-.|...+|..++.|....||+|.+..+      +..+.|+|+...+..+...|.+.+..
T Consensus        27 ~l~v~l~~~~~~LLl~~~~~~L~~l~~~~~~~I~~~~~------~~~i~I~g~k~~~~~i~~~i~~~l~~   90 (210)
T PF14611_consen   27 DLDVWLQPDEFFLLLTGNGRILENLAARNGAKIEVSRS------ENRIRITGTKSTAEYIEASINEILSN   90 (210)
T ss_pred             eeEEEecchheeeeecCCchHHHHHHHhcCceEEEecC------CcEEEEEccHHHHHHHHHHHHHHHhh
Confidence            44556668888999999999999998889999999754      56899999999999999999998876

>PRK00106 hypothetical protein; Provisional

Probab=96.27  E-value=0.02  Score=60.19  Aligned_cols=66  Identities=21%  Similarity=0.399  Sum_probs=48.9

Q ss_pred             CeEEEEEecc-CcccceecCCchhHHHHHHhhCceEEeccCCCCCCCccEEEEEc-cHHHHHHHHHHHHHHHHh
Q psy11929        123 PLQLKLVIPA-THCGSLIGKGGCKIKDIRDLSGANVQVASDMLPMSTERIVTVHG-NPDTISQAIYQICLVLIE  194 (433)
Q Consensus       123 ~~~~~l~ip~-~~vg~iIGk~G~~Ik~I~~~sga~I~i~~~~~~~~~er~v~I~G-~~~~v~~A~~~I~~~l~e  194 (433)
                      ..+-.+.+|+ ++-|+|||+.|.+|+-++..||+.+.|..      +...|+|+| +|-.-+-|...+..++.+
T Consensus       224 ~tvs~v~lp~demkGriIGreGrNir~~E~~tGvdliidd------tp~~v~lS~fdpvRReiAr~~le~Li~d  291 (535)
T PRK00106        224 QTITTVHLPDDNMKGRIIGREGRNIRTLESLTGIDVIIDD------TPEVVVLSGFDPIRREIARMTLESLIKD  291 (535)
T ss_pred             heeeeEEcCChHhhcceeCCCcchHHHHHHHhCceEEEcC------CCCeEEEeCCChHHHHHHHHHHHHHHHc
Confidence            3444567887 78899999999999999999999999974      245677888 665555555555554443

>PRK00468 hypothetical protein; Provisional

Probab=96.25  E-value=0.0053  Score=47.20  Aligned_cols=33  Identities=15%  Similarity=0.327  Sum_probs=29.4

Q ss_pred             CceEEEEEEeccCCcccccceeeecCchHHHHHHHHh
Q psy11929         12 DTLITMRCLFHSSVNVNEISCLIGPGGCIVRRLRKES   48 (433)
Q Consensus        12 ~~~~~~rilvp~~~~~~~vg~IIGk~G~~Ik~I~~~t   48 (433)
                      +..+.+++-|..    ..+|.||||+|.+|+.||.--
T Consensus        27 ~~~~~~~l~v~~----~D~GrVIGk~Gr~i~AIRtvv   59 (75)
T PRK00468         27 EQSVILELKVAP----EDMGKVIGKQGRIAKAIRTVV   59 (75)
T ss_pred             CCeEEEEEEECh----hhCcceecCCChhHHHHHHHH
Confidence            345889999999    999999999999999999753

>TIGR03319 YmdA_YtgF conserved hypothetical protein YmdA/YtgF

Probab=96.22  E-value=0.02  Score=60.28  Aligned_cols=65  Identities=20%  Similarity=0.352  Sum_probs=47.8

Q ss_pred             CeEEEEEecc-CcccceecCCchhHHHHHHhhCceEEeccCCCCCCCccEEEEEc-cHHHHHHHHHHHHHHHH
Q psy11929        123 PLQLKLVIPA-THCGSLIGKGGCKIKDIRDLSGANVQVASDMLPMSTERIVTVHG-NPDTISQAIYQICLVLI  193 (433)
Q Consensus       123 ~~~~~l~ip~-~~vg~iIGk~G~~Ik~I~~~sga~I~i~~~~~~~~~er~v~I~G-~~~~v~~A~~~I~~~l~  193 (433)
                      ..+-.+.+|+ ++-|+|||+.|.+|+-++..||+.+.|..      +...|+|+| +|-.-+-|...+..++.
T Consensus       203 ~~~~~v~lp~d~~kgriigreGrnir~~e~~tgvd~iidd------tp~~v~ls~fdp~rreia~~~l~~li~  269 (514)
T TIGR03319       203 TTVSVVNLPNDEMKGRIIGREGRNIRALETLTGVDLIIDD------TPEAVILSGFDPVRREIARMALEKLIQ  269 (514)
T ss_pred             heeeeEEcCChhhhccccCCCcchHHHHHHHhCceEEEcC------CCCeEEecCCchHHHHHHHHHHHHHHH
Confidence            3344567887 78899999999999999999999999974      245677888 56444455555544443

>PRK11824 polynucleotide phosphorylase/polyadenylase; Provisional

Probab=96.15  E-value=0.0087  Score=65.42  Aligned_cols=97  Identities=18%  Similarity=0.273  Sum_probs=68.8

Q ss_pred             chHHHHHHHHHHHHhhhhhhcccccCCCCCCCCCeEEEEEeccCcccceecCCchhHHHHHHhhCceEEeccCCCCCCCc
Q psy11929         90 TSVDNVCTAYNFMCRSLEDYHINRNRMENCSPQPLQLKLVIPATHCGSLIGKGGCKIKDIRDLSGANVQVASDMLPMSTE  169 (433)
Q Consensus        90 ~a~~~v~~A~~~I~~~~~~~~~~~~~~~~~~~~~~~~~l~ip~~~vg~iIGk~G~~Ik~I~~~sga~I~i~~~~~~~~~e  169 (433)
                      .|++...+++..|.+.+.+.-... ........+....+.||.+.++.+||.||.+||+|.++||++|.+..       +
T Consensus       521 ~al~~a~~g~~~I~~~M~~aI~~~-r~~~~~~ap~~~~~~I~~~kI~~vIG~gg~~ik~I~~~~~~~idi~d-------~  592 (693)
T PRK11824        521 EALEQAKEGRLHILGKMNEAISEP-RAELSPYAPRIETIKIPPDKIRDVIGPGGKTIREITEETGAKIDIED-------D  592 (693)
T ss_pred             HHHHHHHHHHHHHHHHHHHHhcCC-hhhhcccCchheeecCCHHHHHHHhcCCchhHHHHHHHHCCccccCC-------C
Confidence            345556666667776665532111 01111233455567789999999999999999999999999888753       4


Q ss_pred             cEEEEEc-cHHHHHHHHHHHHHHHHh
Q psy11929        170 RIVTVHG-NPDTISQAIYQICLVLIE  194 (433)
Q Consensus       170 r~v~I~G-~~~~v~~A~~~I~~~l~e  194 (433)
                      -.|.|.+ +.+.+.+|...|..+..+
T Consensus       593 G~v~i~~~~~~~~~~a~~~I~~~~~~  618 (693)
T PRK11824        593 GTVKIAATDGEAAEAAKERIEGITAE  618 (693)
T ss_pred             ceEEEEcccHHHHHHHHHHHHHhccc
Confidence            5688887 778899999999887754

>COG0195 NusA Transcription elongation factor [Transcription]

Probab=96.13  E-value=0.022  Score=51.93  Aligned_cols=39  Identities=28%  Similarity=0.371  Sum_probs=36.0

Q ss_pred             EEEEEeCcccccccccCCCchHHHHHhHhCCeEEEccCC
Q psy11929        289 ETEIVLTDDIAGCVIGKAGSRLLEIRQISGAQINIHTGT  327 (433)
Q Consensus       289 t~~i~VP~~~vG~IIGkgG~~Ik~I~~~sGA~I~I~~~~  327 (433)
                      ...+.||.+..+..|||+|.|++-+.+.||-+|.|....
T Consensus       143 ~~~v~V~~~~~~~aIGk~G~Nvrla~~Ltg~~i~I~~~~  181 (190)
T COG0195         143 VAIVVVPPDQLSLAIGKGGQNVRLASQLTGWEIDIETIS  181 (190)
T ss_pred             EEEEEECHHHHhhccCcccHHHHHHHHHhCCEEEEEehh
Confidence            678899999999999999999999999999999987643

>TIGR03319 YmdA_YtgF conserved hypothetical protein YmdA/YtgF

Probab=96.10  E-value=0.016  Score=61.18  Aligned_cols=66  Identities=17%  Similarity=0.371  Sum_probs=50.1

Q ss_pred             CceEEEEEeCcc-cccccccCCCchHHHHHhHhCCeEEEccCCCCCceEEEEEeC-HHHHHHHHHHHHHHHH
Q psy11929        286 DFVETEIVLTDD-IAGCVIGKAGSRLLEIRQISGAQINIHTGTESHKKMFHIQGC-QEAVSLAQYLINMCIE  355 (433)
Q Consensus       286 ~~~t~~i~VP~~-~vG~IIGkgG~~Ik~I~~~sGA~I~I~~~~~~~er~V~IsGt-~e~v~~A~~lI~~~i~  355 (433)
                      ...+..+.+|++ +-|+||||.|.||+-+...||++|.|++.+    ..|+|||- |---+.|+.-|...|.
T Consensus       202 e~~~~~v~lp~d~~kgriigreGrnir~~e~~tgvd~iiddtp----~~v~ls~fdp~rreia~~~l~~li~  269 (514)
T TIGR03319       202 ETTVSVVNLPNDEMKGRIIGREGRNIRALETLTGVDLIIDDTP----EAVILSGFDPVRREIARMALEKLIQ  269 (514)
T ss_pred             hheeeeEEcCChhhhccccCCCcchHHHHHHHhCceEEEcCCC----CeEEecCCchHHHHHHHHHHHHHHH
Confidence            455667889995 559999999999999999999999999876    67888883 5333445544444443

>PRK12704 phosphodiesterase; Provisional

Probab=96.06  E-value=0.026  Score=59.65  Aligned_cols=64  Identities=20%  Similarity=0.368  Sum_probs=48.2

Q ss_pred             EEEEEecc-CcccceecCCchhHHHHHHhhCceEEeccCCCCCCCccEEEEEc-cHHHHHHHHHHHHHHHHh
Q psy11929        125 QLKLVIPA-THCGSLIGKGGCKIKDIRDLSGANVQVASDMLPMSTERIVTVHG-NPDTISQAIYQICLVLIE  194 (433)
Q Consensus       125 ~~~l~ip~-~~vg~iIGk~G~~Ik~I~~~sga~I~i~~~~~~~~~er~v~I~G-~~~~v~~A~~~I~~~l~e  194 (433)
                      +-.+.+|+ ++-|+|||+.|.+|+-++..||+.|.|..      +...|.|+| ++-.-+.|...+..++.+
T Consensus       211 ~~~v~lp~d~mkgriigreGrnir~~e~~tgvd~iidd------tp~~v~ls~~~~~rre~a~~~l~~l~~d  276 (520)
T PRK12704        211 VSVVNLPNDEMKGRIIGREGRNIRALETLTGVDLIIDD------TPEAVILSGFDPIRREIARLALEKLVQD  276 (520)
T ss_pred             eeeeecCCchhhcceeCCCcchHHHHHHHhCCeEEEcC------CCCeEEEecCChhhHHHHHHHHHHHHhc
Confidence            34466887 78899999999999999999999999974      245778888 555545565555555544

>PRK12328 nusA transcription elongation factor NusA; Provisional

Probab=96.06  E-value=0.02  Score=57.28  Aligned_cols=96  Identities=20%  Similarity=0.299  Sum_probs=64.8

Q ss_pred             cccccceeeecCchHHHHHHHHh-CCeEEEeCCCCCcceEEEecccCCCCCCccccCCCCCccccchHHHHHHHHHHHHh
Q psy11929         26 NVNEISCLIGPGGCIVRRLRKES-GAKISITDGACPDRIVTVSGSVDNSSTSSVETGYPGHTLWVTSVDNVCTAYNFMCR  104 (433)
Q Consensus        26 ~~~~vg~IIGk~G~~Ik~I~~~t-ga~I~v~~~~~~eRvv~I~G~~~~~~~~~v~~~~~~~~~~~~a~~~v~~A~~~I~~  104 (433)
                      .++-+|+.||++|.+|+.|.++- |=+|.|-.=+           .+                       .   ..+|..
T Consensus       249 ~iDPvGacIG~~G~rI~~I~~eL~gEkIDvI~~s-----------~D-----------------------~---~~fI~N  291 (374)
T PRK12328        249 NIDPIGATVGVKGVRINAVSKELNGENIDCIEYS-----------NV-----------------------P---EIFIAR  291 (374)
T ss_pred             CCChHHhhcCCCcchHHHHHHHhCCCeEEEEEcC-----------CC-----------------------H---HHHHHH
Confidence            35779999999999999999998 7788875411           01                       0   011111


Q ss_pred             hhhhhcccccCCCCCCCCCeEEEEEeccCcccceecCCchhHHHHHHhhCceEEecc
Q psy11929        105 SLEDYHINRNRMENCSPQPLQLKLVIPATHCGSLIGKGGCKIKDIRDLSGANVQVAS  161 (433)
Q Consensus       105 ~~~~~~~~~~~~~~~~~~~~~~~l~ip~~~vg~iIGk~G~~Ik~I~~~sga~I~i~~  161 (433)
                      .|.-....  .-. .........+.||..+.+..|||+|.+++-..+-||.+|.|..
T Consensus       292 al~Pa~V~--~V~-i~~~~~~~~V~V~~~qlslAIGk~GqNvrLA~~LtGwkIDI~s  345 (374)
T PRK12328        292 ALAPAIIS--SVK-IEEEEKKAIVTLLSDQKSKAIGKNGINIRLASMLTGYEIELNE  345 (374)
T ss_pred             hCCCceee--EEE-EcCCCcEEEEEEChHHhhhhhcCCChhHHHHHHHhCCEEEEEE
Confidence            11110000  000 0012246788999999999999999999999999999999964

>PRK11824 polynucleotide phosphorylase/polyadenylase; Provisional

Probab=96.02  E-value=0.014  Score=63.75  Aligned_cols=63  Identities=27%  Similarity=0.277  Sum_probs=53.5

Q ss_pred             EEEEEeCcccccccccCCCchHHHHHhHhCCeEEEccCCCCCceEEEEEeC-HHHHHHHHHHHHHHHHh
Q psy11929        289 ETEIVLTDDIAGCVIGKAGSRLLEIRQISGAQINIHTGTESHKKMFHIQGC-QEAVSLAQYLINMCIEL  356 (433)
Q Consensus       289 t~~i~VP~~~vG~IIGkgG~~Ik~I~~~sGA~I~I~~~~~~~er~V~IsGt-~e~v~~A~~lI~~~i~~  356 (433)
                      ...+.||.+.++.+||.||.+|++|.++||+.|.+.++     -.|.|.+. .+.+++|+.+|......
T Consensus       555 ~~~~~I~~~kI~~vIG~gg~~ik~I~~~~~~~idi~d~-----G~v~i~~~~~~~~~~a~~~I~~~~~~  618 (693)
T PRK11824        555 IETIKIPPDKIRDVIGPGGKTIREITEETGAKIDIEDD-----GTVKIAATDGEAAEAAKERIEGITAE  618 (693)
T ss_pred             heeecCCHHHHHHHhcCCchhHHHHHHHHCCccccCCC-----ceEEEEcccHHHHHHHHHHHHHhccc
Confidence            34677799999999999999999999999998888654     46778775 68899999999888753

>TIGR01953 NusA transcription termination factor NusA

Probab=96.02  E-value=0.029  Score=55.90  Aligned_cols=96  Identities=25%  Similarity=0.456  Sum_probs=64.5

Q ss_pred             ccccceeeecCchHHHHHHHHh-CCeEEEeCCCCCcceEEEecccCCCCCCccccCCCCCccccchHHHHHHHHHHHHhh
Q psy11929         27 VNEISCLIGPGGCIVRRLRKES-GAKISITDGACPDRIVTVSGSVDNSSTSSVETGYPGHTLWVTSVDNVCTAYNFMCRS  105 (433)
Q Consensus        27 ~~~vg~IIGk~G~~Ik~I~~~t-ga~I~v~~~~~~eRvv~I~G~~~~~~~~~v~~~~~~~~~~~~a~~~v~~A~~~I~~~  105 (433)
                      ++-+|+.||++|++|+.|.++- |=+|.|-.=+.           +                       ..   .+|...
T Consensus       242 iDpvga~vG~~G~ri~~i~~el~ge~Idiv~~s~-----------d-----------------------~~---~fi~na  284 (341)
T TIGR01953       242 IDPVGACVGPKGSRIQAISKELNGEKIDIIEYSD-----------D-----------------------PA---EFIANA  284 (341)
T ss_pred             CCcceeeECCCCchHHHHHHHhCCCeEEEEEcCC-----------C-----------------------HH---HHHHHh
Confidence            5679999999999999999998 78888754110           0                       00   011111


Q ss_pred             hhhhcccccCCCCCCCCCeEEEEEeccCcccceecCCchhHHHHHHhhCceEEecc
Q psy11929        106 LEDYHINRNRMENCSPQPLQLKLVIPATHCGSLIGKGGCKIKDIRDLSGANVQVAS  161 (433)
Q Consensus       106 ~~~~~~~~~~~~~~~~~~~~~~l~ip~~~vg~iIGk~G~~Ik~I~~~sga~I~i~~  161 (433)
                      +.-....  .-.-.......+.+.||..+.+..|||+|.+++-...-||.+|.|..
T Consensus       285 l~Pa~v~--~v~i~~~~~~~~~v~V~~~~~~~aIGk~G~Nv~la~~l~g~~IdI~s  338 (341)
T TIGR01953       285 LSPAKVI--SVEVLDEDKHSAEVVVPDDQLSLAIGKGGQNVRLASKLTGWNIDVKT  338 (341)
T ss_pred             cCCceEE--EEEEEcCCCcEEEEEEChHHcchhhcCCChhHHHHHHHhCCEEEEEe
Confidence            1100000  00000012246788999999999999999999999999999999864

This model describes NusA, or N utilization substance protein A, a bacterial transcription termination factor. It binds to RNA polymerase alpha subunit and promotes termination at certain RNA hairpin structures. It is named for the interaction in E. coli of phage lambda antitermination protein N with the N-utilization substance, consisting of NusA, NusB, NusE (ribosomal protein S10), and nusG. This model represents a region of NusA shared in all bacterial forms, and including an S1 (pfam00575) and a KH (pfam00013) RNA binding domains. Proteobacterial forms have an additional C-terminal region, not included in this model, with two repeats of 50-residue domain rich in acidic amino acids.

>PRK00106 hypothetical protein; Provisional

Probab=95.99  E-value=0.019  Score=60.40  Aligned_cols=66  Identities=20%  Similarity=0.384  Sum_probs=50.1

Q ss_pred             CceEEEEEeCcc-cccccccCCCchHHHHHhHhCCeEEEccCCCCCceEEEEEe-CHHHHHHHHHHHHHHHH
Q psy11929        286 DFVETEIVLTDD-IAGCVIGKAGSRLLEIRQISGAQINIHTGTESHKKMFHIQG-CQEAVSLAQYLINMCIE  355 (433)
Q Consensus       286 ~~~t~~i~VP~~-~vG~IIGkgG~~Ik~I~~~sGA~I~I~~~~~~~er~V~IsG-t~e~v~~A~~lI~~~i~  355 (433)
                      ...+..+.+|++ +-|+||||-|.||+-+...||++|.|++.+    ..|+||| .|---+.|+..+...|.
T Consensus       223 e~tvs~v~lp~demkGriIGreGrNir~~E~~tGvdliiddtp----~~v~lS~fdpvRReiAr~~le~Li~  290 (535)
T PRK00106        223 EQTITTVHLPDDNMKGRIIGREGRNIRTLESLTGIDVIIDDTP----EVVVLSGFDPIRREIARMTLESLIK  290 (535)
T ss_pred             hheeeeEEcCChHhhcceeCCCcchHHHHHHHhCceEEEcCCC----CeEEEeCCChHHHHHHHHHHHHHHH
Confidence            456678889994 559999999999999999999999999976    6788888 35333444444444443

>PRK12327 nusA transcription elongation factor NusA; Provisional

Probab=95.95  E-value=0.032  Score=56.06  Aligned_cols=96  Identities=25%  Similarity=0.358  Sum_probs=65.0

Q ss_pred             ccccceeeecCchHHHHHHHHh-CCeEEEeCCCCCcceEEEecccCCCCCCccccCCCCCccccchHHHHHHHHHHHHhh
Q psy11929         27 VNEISCLIGPGGCIVRRLRKES-GAKISITDGACPDRIVTVSGSVDNSSTSSVETGYPGHTLWVTSVDNVCTAYNFMCRS  105 (433)
Q Consensus        27 ~~~vg~IIGk~G~~Ik~I~~~t-ga~I~v~~~~~~eRvv~I~G~~~~~~~~~v~~~~~~~~~~~~a~~~v~~A~~~I~~~  105 (433)
                      ++-+|+.||++|.+|+.|.++. |=+|.|-.=+.           +                       .   ..+|...
T Consensus       244 iDpvGa~iG~~G~rI~~i~~el~gekIdiv~~s~-----------d-----------------------~---~~fi~na  286 (362)
T PRK12327        244 VDAKGACVGPKGQRVQNIVSELKGEKIDIIDWSE-----------D-----------------------P---AEFVANA  286 (362)
T ss_pred             CCchheeECCCChhHHHHHHHhCCCeEEEEEcCC-----------C-----------------------H---HHHHHHh
Confidence            5679999999999999999998 78888754110           0                       0   0111111


Q ss_pred             hhhhcccccCCCCCCCCCeEEEEEeccCcccceecCCchhHHHHHHhhCceEEecc
Q psy11929        106 LEDYHINRNRMENCSPQPLQLKLVIPATHCGSLIGKGGCKIKDIRDLSGANVQVAS  161 (433)
Q Consensus       106 ~~~~~~~~~~~~~~~~~~~~~~l~ip~~~vg~iIGk~G~~Ik~I~~~sga~I~i~~  161 (433)
                      |.-....  .-.........+.+.||..+.+..|||+|.+++-...-||.+|.|..
T Consensus       287 l~Pa~v~--~v~i~~~~~~~~~v~V~~~~~~~AIGk~G~Nv~la~~L~~~~idi~s  340 (362)
T PRK12327        287 LSPAKVV--SVEVDDEEEKAARVVVPDYQLSLAIGKEGQNARLAARLTGWKIDIKS  340 (362)
T ss_pred             CCCceEE--EEEEEcCCCcEEEEEEChhhcchhhcCCChhHHHHHHHHCCeeeEEE
Confidence            1110000  00000012346788999999999999999999999999999999875

>PRK12704 phosphodiesterase; Provisional

Probab=95.94  E-value=0.019  Score=60.56  Aligned_cols=67  Identities=15%  Similarity=0.339  Sum_probs=52.2

Q ss_pred             CceEEEEEeCcc-cccccccCCCchHHHHHhHhCCeEEEccCCCCCceEEEEEeC-HHHHHHHHHHHHHHHHh
Q psy11929        286 DFVETEIVLTDD-IAGCVIGKAGSRLLEIRQISGAQINIHTGTESHKKMFHIQGC-QEAVSLAQYLINMCIEL  356 (433)
Q Consensus       286 ~~~t~~i~VP~~-~vG~IIGkgG~~Ik~I~~~sGA~I~I~~~~~~~er~V~IsGt-~e~v~~A~~lI~~~i~~  356 (433)
                      ...+..+.+|++ +-|+||||.|.||+-+...||++|.|++.+    ..|+|||. |---+.|+..+...+..
T Consensus       208 e~~~~~v~lp~d~mkgriigreGrnir~~e~~tgvd~iiddtp----~~v~ls~~~~~rre~a~~~l~~l~~d  276 (520)
T PRK12704        208 ETTVSVVNLPNDEMKGRIIGREGRNIRALETLTGVDLIIDDTP----EAVILSGFDPIRREIARLALEKLVQD  276 (520)
T ss_pred             hhceeeeecCCchhhcceeCCCcchHHHHHHHhCCeEEEcCCC----CeEEEecCChhhHHHHHHHHHHHHhc
Confidence            455667889985 559999999999999999999999999976    67889984 54444566666555543

>KOG1588|consensus

Probab=95.92  E-value=0.0092  Score=56.23  Aligned_cols=41  Identities=17%  Similarity=0.359  Sum_probs=36.6

Q ss_pred             CceEEEEEeCcc------cccccccCCCchHHHHHhHhCCeEEEccC
Q psy11929        286 DFVETEIVLTDD------IAGCVIGKAGSRLLEIRQISGAQINIHTG  326 (433)
Q Consensus       286 ~~~t~~i~VP~~------~vG~IIGkgG~~Ik~I~~~sGA~I~I~~~  326 (433)
                      ...+.+|+||..      +||+|+|.+|.++|+|+++|||+|-|-..
T Consensus        90 vk~~~Kv~vPv~~yP~fNFVGRILGPrGnSlkrLe~eTgCki~IrGr  136 (259)
T KOG1588|consen   90 VKLTEKVLVPVKEYPKFNFVGRILGPRGNSLKRLEEETGCKIMIRGR  136 (259)
T ss_pred             eeEEEEEEeccCCCCCCccccccccCCcchHHHHHHHHCCeEEEecC
Confidence            467788899875      89999999999999999999999999754

>PRK02821 hypothetical protein; Provisional

Probab=95.84  E-value=0.0094  Score=46.00  Aligned_cols=33  Identities=24%  Similarity=0.364  Sum_probs=28.9

Q ss_pred             ceEEEEEEeccCCcccccceeeecCchHHHHHHHHhC
Q psy11929         13 TLITMRCLFHSSVNVNEISCLIGPGGCIVRRLRKESG   49 (433)
Q Consensus        13 ~~~~~rilvp~~~~~~~vg~IIGk~G~~Ik~I~~~tg   49 (433)
                      ..+.+.+.|..    ..+|.||||+|.+|+.||.--.
T Consensus        29 ~~~~i~l~v~~----~D~GrVIGk~Gr~i~AIRtlv~   61 (77)
T PRK02821         29 RGRTLEVRVHP----DDLGKVIGRGGRTATALRTVVA   61 (77)
T ss_pred             CcEEEEEEECh----hhCcceeCCCCchHHHHHHHHH
Confidence            34778899998    9999999999999999998754

>PRK04163 exosome complex RNA-binding protein Rrp4; Provisional

Probab=95.80  E-value=0.025  Score=53.60  Aligned_cols=62  Identities=23%  Similarity=0.216  Sum_probs=53.1

Q ss_pred             EEEEeCcccccccccCCCchHHHHHhHhCCeEEEccCCCCCceEEEEEeC-HHHHHHHHHHHHHHHHh
Q psy11929        290 TEIVLTDDIAGCVIGKAGSRLLEIRQISGAQINIHTGTESHKKMFHIQGC-QEAVSLAQYLINMCIEL  356 (433)
Q Consensus       290 ~~i~VP~~~vG~IIGkgG~~Ik~I~~~sGA~I~I~~~~~~~er~V~IsGt-~e~v~~A~~lI~~~i~~  356 (433)
                      +.+.||..+++.+||++|.+|+.|.+.+++.|.|....     .|-|+++ .+.+.+|..+|+..-++
T Consensus       147 ~~~~V~~~~i~~lig~~g~~i~~l~~~~~~~I~ig~NG-----~VwI~~~~~~~~~~a~~~I~~~e~~  209 (235)
T PRK04163        147 TIVEIKPVKVPRVIGKKGSMINMLKEETGCDIIVGQNG-----RIWIKGPDEEDEEIAIEAIKKIERE  209 (235)
T ss_pred             EEEEECHHHHHhhcCCCChhHhhhhhhhCcEEEEcCCc-----EEEEeeCCHHHHHHHHHHHHHHHhh
Confidence            57889999999999999999999999999999998754     6788777 45888898888766544

>PRK12329 nusA transcription elongation factor NusA; Provisional

Probab=95.79  E-value=0.028  Score=57.16  Aligned_cols=96  Identities=20%  Similarity=0.403  Sum_probs=64.0

Q ss_pred             ccccceeeecCchHHHHHHHHh-CCeEEEeCCCCCcceEEEecccCCCCCCccccCCCCCccccchHHHHHHHHHHHHhh
Q psy11929         27 VNEISCLIGPGGCIVRRLRKES-GAKISITDGACPDRIVTVSGSVDNSSTSSVETGYPGHTLWVTSVDNVCTAYNFMCRS  105 (433)
Q Consensus        27 ~~~vg~IIGk~G~~Ik~I~~~t-ga~I~v~~~~~~eRvv~I~G~~~~~~~~~v~~~~~~~~~~~~a~~~v~~A~~~I~~~  105 (433)
                      ++-+|+.||++|.+|+.|.++. |=+|.|-.=+           .+                       .   ..+|...
T Consensus       276 VDPvGacVG~kG~RI~~I~~eL~gEkIDVI~ys-----------~D-----------------------p---~~fI~Na  318 (449)
T PRK12329        276 VDPVGACIGARGSRIQAVVNELRGEKIDVIRWS-----------PD-----------------------P---ATYIANA  318 (449)
T ss_pred             CChhhccCCCCcchHHHHHHHhCCCeEEEEEcC-----------CC-----------------------H---HHHHHHh
Confidence            5679999999999999999998 7888875411           01                       0   0111111


Q ss_pred             hhhhcccccCCCCCCCCCeEEEEEeccCcccceecCCchhHHHHHHhhCceEEecc
Q psy11929        106 LEDYHINRNRMENCSPQPLQLKLVIPATHCGSLIGKGGCKIKDIRDLSGANVQVAS  161 (433)
Q Consensus       106 ~~~~~~~~~~~~~~~~~~~~~~l~ip~~~vg~iIGk~G~~Ik~I~~~sga~I~i~~  161 (433)
                      |.-.....-.-.+  .....+.+.||..+.+..|||+|.+++-...-||.+|.|..
T Consensus       319 LsPA~V~~V~i~~--~~~k~a~V~V~~~qlslAIGK~GqNvrLAs~Ltg~~idI~s  372 (449)
T PRK12329        319 LSPARVDEVRLVD--PEGRHAHVLVPPDQLSLAIGKEGQNVRLAARLTGWKIDIKD  372 (449)
T ss_pred             cCCceeeEEEEEc--CCCcEEEEEEChHhcchhhcCCChhHHHHHHHHCCEecccc
Confidence            1100000000000  11235688999999999999999999999999999999864

>COG1837 Predicted RNA-binding protein (contains KH domain) [General function prediction only]

Probab=95.79  E-value=0.011  Score=45.26  Aligned_cols=32  Identities=16%  Similarity=0.346  Sum_probs=29.5

Q ss_pred             CceEEEEEEeccCCcccccceeeecCchHHHHHHHH
Q psy11929         12 DTLITMRCLFHSSVNVNEISCLIGPGGCIVRRLRKE   47 (433)
Q Consensus        12 ~~~~~~rilvp~~~~~~~vg~IIGk~G~~Ik~I~~~   47 (433)
                      +..+.+++-+..    ..+|.||||+|.+|+.||.-
T Consensus        27 ~~~~~~~l~v~~----~D~GkvIGk~GRti~AIRTl   58 (76)
T COG1837          27 EKTVTIELRVAP----EDMGKVIGKQGRTIQAIRTL   58 (76)
T ss_pred             CCeEEEEEEECc----ccccceecCCChhHHHHHHH
Confidence            567889999999    99999999999999999975

>PRK12328 nusA transcription elongation factor NusA; Provisional

Probab=95.68  E-value=0.031  Score=55.88  Aligned_cols=41  Identities=20%  Similarity=0.262  Sum_probs=37.4

Q ss_pred             eEEEEEeCcccccccccCCCchHHHHHhHhCCeEEEccCCC
Q psy11929        288 VETEIVLTDDIAGCVIGKAGSRLLEIRQISGAQINIHTGTE  328 (433)
Q Consensus       288 ~t~~i~VP~~~vG~IIGkgG~~Ik~I~~~sGA~I~I~~~~~  328 (433)
                      ....+.||.+..+..|||+|+|++-.++.||.+|.|..-.+
T Consensus       308 ~~~~V~V~~~qlslAIGk~GqNvrLA~~LtGwkIDI~s~~~  348 (374)
T PRK12328        308 KKAIVTLLSDQKSKAIGKNGINIRLASMLTGYEIELNEIGS  348 (374)
T ss_pred             cEEEEEEChHHhhhhhcCCChhHHHHHHHhCCEEEEEECCC
Confidence            46789999999999999999999999999999999986553

>PF14611 SLS: Mitochondrial inner-membrane-bound regulator

Probab=95.63  E-value=0.28  Score=45.44  Aligned_cols=121  Identities=14%  Similarity=0.162  Sum_probs=86.9

Q ss_pred             cccceeeecCchHHHHHHHHhCCeEEEeCCCCCcceEEEecccCCCCCCccccCCCCCccccchHHHHHHHHHHHHhhhh
Q psy11929         28 NEISCLIGPGGCIVRRLRKESGAKISITDGACPDRIVTVSGSVDNSSTSSVETGYPGHTLWVTSVDNVCTAYNFMCRSLE  107 (433)
Q Consensus        28 ~~vg~IIGk~G~~Ik~I~~~tga~I~v~~~~~~eRvv~I~G~~~~~~~~~v~~~~~~~~~~~~a~~~v~~A~~~I~~~~~  107 (433)
                      ...-.+...+|..++.|-...||+|.+..   .+..|.|+|+..                      .+..+...|.+.+.
T Consensus        35 ~~~~LLl~~~~~~L~~l~~~~~~~I~~~~---~~~~i~I~g~k~----------------------~~~~i~~~i~~~l~   89 (210)
T PF14611_consen   35 DEFFLLLTGNGRILENLAARNGAKIEVSR---SENRIRITGTKS----------------------TAEYIEASINEILS   89 (210)
T ss_pred             hheeeeecCCchHHHHHHHhcCceEEEec---CCcEEEEEccHH----------------------HHHHHHHHHHHHHh
Confidence            78889999999999999888899999987   566899999999                      77777777777664


Q ss_pred             hhcccccCCCCCCCCCeEEEEEeccCccccee----cCCchhHHHHHHhhCceEEeccCCCCCCCccEEEEE-----ccH
Q psy11929        108 DYHINRNRMENCSPQPLQLKLVIPATHCGSLI----GKGGCKIKDIRDLSGANVQVASDMLPMSTERIVTVH-----GNP  178 (433)
Q Consensus       108 ~~~~~~~~~~~~~~~~~~~~l~ip~~~vg~iI----Gk~G~~Ik~I~~~sga~I~i~~~~~~~~~er~v~I~-----G~~  178 (433)
                      .              ..+..+.++.-.--.-.    -.....++.|++.|++.|....+      +..+.|.     -..
T Consensus        90 ~--------------i~~~~i~l~~~~~~~~~~~~~~~~~~~l~~i~~~t~~~ie~~~~------~~~~~i~~~~~~~~~  149 (210)
T PF14611_consen   90 N--------------IRTEEIDLSPIISKHSEKKNSQFTPDLLEEIQKLTNVYIEKNPD------GNKLKISWLASPENE  149 (210)
T ss_pred             h--------------cEEEEEecchhhhhhcccccccccHHHHHHHHHHHcEEEEECCC------CCeEEEEEEeecccc
Confidence            4              33444444422111111    12356799999999999998753      2234444     456


Q ss_pred             HHHHHHHHHHHHHHH
Q psy11929        179 DTISQAIYQICLVLI  193 (433)
Q Consensus       179 ~~v~~A~~~I~~~l~  193 (433)
                      ..+..|+.++...+.
T Consensus       150 ~~~~~a~RlL~~a~~  164 (210)
T PF14611_consen  150 KRADRAKRLLLWALD  164 (210)
T ss_pred             chHHHHHHHHHHhcc
Confidence            788888888877764

>PRK09202 nusA transcription elongation factor NusA; Validated

Probab=95.54  E-value=0.035  Score=57.69  Aligned_cols=95  Identities=19%  Similarity=0.348  Sum_probs=64.3

Q ss_pred             ccccceeeecCchHHHHHHHHh-CCeEEEeCCCCCcceEEEecccCCCCCCccccCCCCCccccchHHHHHHHHHHHHhh
Q psy11929         27 VNEISCLIGPGGCIVRRLRKES-GAKISITDGACPDRIVTVSGSVDNSSTSSVETGYPGHTLWVTSVDNVCTAYNFMCRS  105 (433)
Q Consensus        27 ~~~vg~IIGk~G~~Ik~I~~~t-ga~I~v~~~~~~eRvv~I~G~~~~~~~~~v~~~~~~~~~~~~a~~~v~~A~~~I~~~  105 (433)
                      ++-+|+.||++|++|+.|.++- |=+|.|-.=+           .+                       .   ..+|...
T Consensus       244 iDpvga~vG~~G~ri~~i~~el~ge~Idiv~~s-----------~d-----------------------~---~~fi~na  286 (470)
T PRK09202        244 IDPVGACVGMRGSRIQAISNELGGEKIDIILWS-----------DD-----------------------P---AQFIINA  286 (470)
T ss_pred             CChhHccCCCCCchHHHHHHHhCCCeEEEEEcC-----------CC-----------------------H---HHHHHHh
Confidence            4668999999999999999998 7888875411           01                       0   0111111


Q ss_pred             hhhhcccccCCCCCCCCCeEEEEEeccCcccceecCCchhHHHHHHhhCceEEecc
Q psy11929        106 LEDYHINRNRMENCSPQPLQLKLVIPATHCGSLIGKGGCKIKDIRDLSGANVQVAS  161 (433)
Q Consensus       106 ~~~~~~~~~~~~~~~~~~~~~~l~ip~~~vg~iIGk~G~~Ik~I~~~sga~I~i~~  161 (433)
                      +.......  - ......-.+.+.||..+.+..|||+|.+++-..+-||.+|.|..
T Consensus       287 l~pa~v~~--v-~~~~~~~~~~v~V~~~~~~~AIGk~G~Nvrla~~l~g~~idi~~  339 (470)
T PRK09202        287 LSPAEVSS--V-VVDEDEHSADVVVPDDQLSLAIGKNGQNVRLASKLTGWKIDIMT  339 (470)
T ss_pred             CCCCEEEE--E-EEeCCCCEEEEEECcchHHHhhCCCCeeHHHHHHHHCCeEEEEE
Confidence            11100000  0 00011237789999999999999999999999999999999864

>COG5176 MSL5 Splicing factor (branch point binding protein) [RNA processing and modification]

Probab=95.39  E-value=0.022  Score=51.48  Aligned_cols=46  Identities=26%  Similarity=0.375  Sum_probs=36.2

Q ss_pred             ceEEEEEEeccC--CcccccceeeecCchHHHHHHHHhCCeEEEeCCC
Q psy11929         13 TLITMRCLFHSS--VNVNEISCLIGPGGCIVRRLRKESGAKISITDGA   58 (433)
Q Consensus        13 ~~~~~rilvp~~--~~~~~vg~IIGk~G~~Ik~I~~~tga~I~v~~~~   58 (433)
                      ..++-++.||..  -.+++||.|||+.|.|+|+|+..|+|+|-|-..+
T Consensus       146 sk~q~KiYIPV~eyPe~NFVGLliGPRG~Tlk~le~~s~akIaIRG~g  193 (269)
T COG5176         146 SKYQNKIYIPVQEYPESNFVGLLIGPRGSTLKQLERISRAKIAIRGSG  193 (269)
T ss_pred             ccccceEEeehhhCcccceeEEEecCCcchHHHHHHHhCCeEEEeccc
Confidence            445566776631  1237899999999999999999999999998754

>TIGR01953 NusA transcription termination factor NusA

Probab=95.38  E-value=0.06  Score=53.71  Aligned_cols=39  Identities=28%  Similarity=0.466  Sum_probs=36.3

Q ss_pred             eEEEEEeCcccccccccCCCchHHHHHhHhCCeEEEccC
Q psy11929        288 VETEIVLTDDIAGCVIGKAGSRLLEIRQISGAQINIHTG  326 (433)
Q Consensus       288 ~t~~i~VP~~~vG~IIGkgG~~Ik~I~~~sGA~I~I~~~  326 (433)
                      ....+.||.+..+..|||+|.|++-.++.||.+|.|...
T Consensus       301 ~~~~v~V~~~~~~~aIGk~G~Nv~la~~l~g~~IdI~s~  339 (341)
T TIGR01953       301 HSAEVVVPDDQLSLAIGKGGQNVRLASKLTGWNIDVKTE  339 (341)
T ss_pred             cEEEEEEChHHcchhhcCCChhHHHHHHHhCCEEEEEeC
Confidence            468999999999999999999999999999999998754

This model describes NusA, or N utilization substance protein A, a bacterial transcription termination factor. It binds to RNA polymerase alpha subunit and promotes termination at certain RNA hairpin structures. It is named for the interaction in E. coli of phage lambda antitermination protein N with the N-utilization substance, consisting of NusA, NusB, NusE (ribosomal protein S10), and nusG. This model represents a region of NusA shared in all bacterial forms, and including an S1 (pfam00575) and a KH (pfam00013) RNA binding domains. Proteobacterial forms have an additional C-terminal region, not included in this model, with two repeats of 50-residue domain rich in acidic amino acids.

>PRK01064 hypothetical protein; Provisional

Probab=95.33  E-value=0.022  Score=44.10  Aligned_cols=33  Identities=18%  Similarity=0.261  Sum_probs=29.6

Q ss_pred             CceEEEEEEeccCCcccccceeeecCchHHHHHHHHh
Q psy11929         12 DTLITMRCLFHSSVNVNEISCLIGPGGCIVRRLRKES   48 (433)
Q Consensus        12 ~~~~~~rilvp~~~~~~~vg~IIGk~G~~Ik~I~~~t   48 (433)
                      +..+.+++.|..    ...|.+|||+|.+|+.||.-.
T Consensus        27 ~~~~~~~l~v~~----~D~g~vIGk~G~~i~air~l~   59 (78)
T PRK01064         27 THTIIYELTVAK----PDIGKIIGKEGRTIKAIRTLL   59 (78)
T ss_pred             CCEEEEEEEECc----ccceEEECCCCccHHHHHHHH
Confidence            456889999999    999999999999999999853

>PRK02821 hypothetical protein; Provisional

Probab=95.30  E-value=0.026  Score=43.61  Aligned_cols=33  Identities=21%  Similarity=0.437  Sum_probs=28.7

Q ss_pred             CCCeEEEEEeccCcccceecCCchhHHHHHHhh
Q psy11929        121 PQPLQLKLVIPATHCGSLIGKGGCKIKDIRDLS  153 (433)
Q Consensus       121 ~~~~~~~l~ip~~~vg~iIGk~G~~Ik~I~~~s  153 (433)
                      .....+++.+..+-+|+||||+|.+|+.|+.--
T Consensus        28 ~~~~~i~l~v~~~D~GrVIGk~Gr~i~AIRtlv   60 (77)
T PRK02821         28 RRGRTLEVRVHPDDLGKVIGRGGRTATALRTVV   60 (77)
T ss_pred             CCcEEEEEEEChhhCcceeCCCCchHHHHHHHH
Confidence            345778999999999999999999999998754

>PRK12327 nusA transcription elongation factor NusA; Provisional

Probab=95.26  E-value=0.061  Score=54.05  Aligned_cols=41  Identities=22%  Similarity=0.312  Sum_probs=37.3

Q ss_pred             ceEEEEEeCcccccccccCCCchHHHHHhHhCCeEEEccCC
Q psy11929        287 FVETEIVLTDDIAGCVIGKAGSRLLEIRQISGAQINIHTGT  327 (433)
Q Consensus       287 ~~t~~i~VP~~~vG~IIGkgG~~Ik~I~~~sGA~I~I~~~~  327 (433)
                      .....+.||.+..+..|||+|.|++-..+.||.+|.|....
T Consensus       302 ~~~~~v~V~~~~~~~AIGk~G~Nv~la~~L~~~~idi~s~~  342 (362)
T PRK12327        302 EKAARVVVPDYQLSLAIGKEGQNARLAARLTGWKIDIKSES  342 (362)
T ss_pred             CcEEEEEEChhhcchhhcCCChhHHHHHHHHCCeeeEEEHH
Confidence            34689999999999999999999999999999999998754

>PRK00468 hypothetical protein; Provisional

Probab=95.25  E-value=0.027  Score=43.31  Aligned_cols=32  Identities=34%  Similarity=0.514  Sum_probs=28.6

Q ss_pred             CCCeEEEEEeccCcccceecCCchhHHHHHHh
Q psy11929        121 PQPLQLKLVIPATHCGSLIGKGGCKIKDIRDL  152 (433)
Q Consensus       121 ~~~~~~~l~ip~~~vg~iIGk~G~~Ik~I~~~  152 (433)
                      ...+.+++.+..+-+|+||||+|.+|+.|+.-
T Consensus        27 ~~~~~~~l~v~~~D~GrVIGk~Gr~i~AIRtv   58 (75)
T PRK00468         27 EQSVILELKVAPEDMGKVIGKQGRIAKAIRTV   58 (75)
T ss_pred             CCeEEEEEEEChhhCcceecCCChhHHHHHHH
Confidence            45588899999999999999999999999864

>PRK09202 nusA transcription elongation factor NusA; Validated

Probab=95.11  E-value=0.06  Score=55.99  Aligned_cols=40  Identities=28%  Similarity=0.438  Sum_probs=36.9

Q ss_pred             eEEEEEeCcccccccccCCCchHHHHHhHhCCeEEEccCC
Q psy11929        288 VETEIVLTDDIAGCVIGKAGSRLLEIRQISGAQINIHTGT  327 (433)
Q Consensus       288 ~t~~i~VP~~~vG~IIGkgG~~Ik~I~~~sGA~I~I~~~~  327 (433)
                      ....+.||.+..+.-|||+|+|++..++.||.+|.|-...
T Consensus       302 ~~~~v~V~~~~~~~AIGk~G~Nvrla~~l~g~~idi~~~~  341 (470)
T PRK09202        302 HSADVVVPDDQLSLAIGKNGQNVRLASKLTGWKIDIMTEE  341 (470)
T ss_pred             CEEEEEECcchHHHhhCCCCeeHHHHHHHHCCeEEEEEhh
Confidence            4789999999999999999999999999999999997644

>COG1837 Predicted RNA-binding protein (contains KH domain) [General function prediction only]

Probab=94.99  E-value=0.033  Score=42.73  Aligned_cols=32  Identities=31%  Similarity=0.581  Sum_probs=29.2

Q ss_pred             CCCeEEEEEeccCcccceecCCchhHHHHHHh
Q psy11929        121 PQPLQLKLVIPATHCGSLIGKGGCKIKDIRDL  152 (433)
Q Consensus       121 ~~~~~~~l~ip~~~vg~iIGk~G~~Ik~I~~~  152 (433)
                      .....+++.+...-+|++|||+|.+|+.|+.-
T Consensus        27 ~~~~~~~l~v~~~D~GkvIGk~GRti~AIRTl   58 (76)
T COG1837          27 EKTVTIELRVAPEDMGKVIGKQGRTIQAIRTL   58 (76)
T ss_pred             CCeEEEEEEECcccccceecCCChhHHHHHHH
Confidence            56788999999999999999999999999864

>PRK04163 exosome complex RNA-binding protein Rrp4; Provisional

Probab=94.97  E-value=0.059  Score=51.05  Aligned_cols=62  Identities=21%  Similarity=0.290  Sum_probs=52.5

Q ss_pred             EEEEeccCcccceecCCchhHHHHHHhhCceEEeccCCCCCCCccEEEEEc-cHHHHHHHHHHHHHHHHh
Q psy11929        126 LKLVIPATHCGSLIGKGGCKIKDIRDLSGANVQVASDMLPMSTERIVTVHG-NPDTISQAIYQICLVLIE  194 (433)
Q Consensus       126 ~~l~ip~~~vg~iIGk~G~~Ik~I~~~sga~I~i~~~~~~~~~er~v~I~G-~~~~v~~A~~~I~~~l~e  194 (433)
                      +.+.||..+++++||++|.+|+.|.++++++|.+-.       +-.|.|.+ +.+++.+|..+|..+-++
T Consensus       147 ~~~~V~~~~i~~lig~~g~~i~~l~~~~~~~I~ig~-------NG~VwI~~~~~~~~~~a~~~I~~~e~~  209 (235)
T PRK04163        147 TIVEIKPVKVPRVIGKKGSMINMLKEETGCDIIVGQ-------NGRIWIKGPDEEDEEIAIEAIKKIERE  209 (235)
T ss_pred             EEEEECHHHHHhhcCCCChhHhhhhhhhCcEEEEcC-------CcEEEEeeCCHHHHHHHHHHHHHHHhh
Confidence            557899999999999999999999999999999964       35677777 556888888888877666

>PRK12329 nusA transcription elongation factor NusA; Provisional

Probab=94.61  E-value=0.094  Score=53.47  Aligned_cols=40  Identities=20%  Similarity=0.372  Sum_probs=36.6

Q ss_pred             eEEEEEeCcccccccccCCCchHHHHHhHhCCeEEEccCC
Q psy11929        288 VETEIVLTDDIAGCVIGKAGSRLLEIRQISGAQINIHTGT  327 (433)
Q Consensus       288 ~t~~i~VP~~~vG~IIGkgG~~Ik~I~~~sGA~I~I~~~~  327 (433)
                      ....+.||.+..+.-|||+|.|++-..+.||.+|.|....
T Consensus       335 k~a~V~V~~~qlslAIGK~GqNvrLAs~Ltg~~idI~s~~  374 (449)
T PRK12329        335 RHAHVLVPPDQLSLAIGKEGQNVRLAARLTGWKIDIKDSA  374 (449)
T ss_pred             cEEEEEEChHhcchhhcCCChhHHHHHHHHCCEeccccHH
Confidence            4578999999999999999999999999999999998654

>COG5176 MSL5 Splicing factor (branch point binding protein) [RNA processing and modification]

Probab=94.53  E-value=0.042  Score=49.79  Aligned_cols=40  Identities=30%  Similarity=0.507  Sum_probs=33.4

Q ss_pred             eEEEEEeC------cccccccccCCCchHHHHHhHhCCeEEEccCC
Q psy11929        288 VETEIVLT------DDIAGCVIGKAGSRLLEIRQISGAQINIHTGT  327 (433)
Q Consensus       288 ~t~~i~VP------~~~vG~IIGkgG~~Ik~I~~~sGA~I~I~~~~  327 (433)
                      .+-+++||      .++||.+||..|++.++|++.|+|+|-|-...
T Consensus       148 ~q~KiYIPV~eyPe~NFVGLliGPRG~Tlk~le~~s~akIaIRG~g  193 (269)
T COG5176         148 YQNKIYIPVQEYPESNFVGLLIGPRGSTLKQLERISRAKIAIRGSG  193 (269)
T ss_pred             ccceEEeehhhCcccceeEEEecCCcchHHHHHHHhCCeEEEeccc
Confidence            34456665      46899999999999999999999999997654

>KOG4369|consensus

Probab=94.21  E-value=0.017  Score=63.93  Aligned_cols=70  Identities=19%  Similarity=0.061  Sum_probs=60.5

Q ss_pred             ceEEEEEeCcccccccccCCCchHHHHHhHhCCeEEEccCCC--CCceEEEEEeCHHHHHHHHHHHHHHHHh
Q psy11929        287 FVETEIVLTDDIAGCVIGKAGSRLLEIRQISGAQINIHTGTE--SHKKMFHIQGCQEAVSLAQYLINMCIEL  356 (433)
Q Consensus       287 ~~t~~i~VP~~~vG~IIGkgG~~Ik~I~~~sGA~I~I~~~~~--~~er~V~IsGt~e~v~~A~~lI~~~i~~  356 (433)
                      ....++.+|-....+|||++|++|+.++.-|||.|+|.+-..  ..||.+.+.|.++.+..|..+|.-.|-.
T Consensus      1339 ~~~~k~~~P~~a~SRVig~ggsnVna~r~~tga~ielekmq~~Nqaers~~~kg~p~~~r~a~~~I~~~i~D 1410 (2131)
T KOG4369|consen 1339 ANQGKGDGPLYASSRVIGDGGSNVNAARLGTGALIELEKMQPDNQAERSKAPKGRPPSQRVATSPIGLPIID 1410 (2131)
T ss_pred             ccccccccchhhhhhhhccCcchhhhHhhccceEEehhhcCCccchhhhcccCCCChhhhhhhccccceeec
Confidence            344577899999999999999999999999999999998443  7899999999999999999888665543

>PRK12705 hypothetical protein; Provisional

Probab=94.04  E-value=0.12  Score=54.06  Aligned_cols=37  Identities=24%  Similarity=0.508  Sum_probs=32.0

Q ss_pred             EEEEEecc-CcccceecCCchhHHHHHHhhCceEEecc
Q psy11929        125 QLKLVIPA-THCGSLIGKGGCKIKDIRDLSGANVQVAS  161 (433)
Q Consensus       125 ~~~l~ip~-~~vg~iIGk~G~~Ik~I~~~sga~I~i~~  161 (433)
                      .-.+.+|+ ++-|+|||+.|.+|+.++..||+.+.|..
T Consensus       199 vs~v~lp~demkGriIGreGrNir~~E~~tGvdliidd  236 (508)
T PRK12705        199 VSVVPIPSDAMKGRIIGREGRNIRAFEGLTGVDLIIDD  236 (508)
T ss_pred             eeeeecCChHhhccccCccchhHHHHHHhhCCceEecC
Confidence            33456776 67899999999999999999999999974

>PRK01064 hypothetical protein; Provisional

Probab=94.01  E-value=0.081  Score=40.98  Aligned_cols=32  Identities=34%  Similarity=0.589  Sum_probs=28.8

Q ss_pred             CCCeEEEEEeccCcccceecCCchhHHHHHHh
Q psy11929        121 PQPLQLKLVIPATHCGSLIGKGGCKIKDIRDL  152 (433)
Q Consensus       121 ~~~~~~~l~ip~~~vg~iIGk~G~~Ik~I~~~  152 (433)
                      ...+.+++.+..+-.|++|||+|.+|+.|+.-
T Consensus        27 ~~~~~~~l~v~~~D~g~vIGk~G~~i~air~l   58 (78)
T PRK01064         27 THTIIYELTVAKPDIGKIIGKEGRTIKAIRTL   58 (78)
T ss_pred             CCEEEEEEEECcccceEEECCCCccHHHHHHH
Confidence            56688999999999999999999999999864

>KOG1067|consensus

Probab=93.60  E-value=0.14  Score=53.12  Aligned_cols=95  Identities=20%  Similarity=0.194  Sum_probs=68.2

Q ss_pred             hHHHHHHHHHHHHhhhhhhcccccCCCCCCCCCeEEEEEeccCcccceecCCchhHHHHHHhhCceEEeccCCCCCCCcc
Q psy11929         91 SVDNVCTAYNFMCRSLEDYHINRNRMENCSPQPLQLKLVIPATHCGSLIGKGGCKIKDIRDLSGANVQVASDMLPMSTER  170 (433)
Q Consensus        91 a~~~v~~A~~~I~~~~~~~~~~~~~~~~~~~~~~~~~l~ip~~~vg~iIGk~G~~Ik~I~~~sga~I~i~~~~~~~~~er  170 (433)
                      |..+...|...|++.+++.-. .+........++...+-++++....+||.+|...|+|+.+||+.-.+.        +.
T Consensus       565 al~~a~~ar~~Il~~m~k~i~-~Pr~~~~~y~P~~~tlkv~~sk~~~lIGp~G~~~kki~~EtGai~~vD--------e~  635 (760)
T KOG1067|consen  565 ALQKAREARLQILDIMEKNIN-SPRGSDKEYSPVLETLKVSPSKRATLIGPGGVLKKKIEVETGAISQVD--------EG  635 (760)
T ss_pred             HHHhhhHHHHHHHHHHHhhcC-CcccCccccCceeeEEeecchhhheeecCccceeeeEeeeccceeeec--------Cc
Confidence            334444555566666554221 111223345677888999999999999999999999999999555553        56


Q ss_pred             EEEEEc-cHHHHHHHHHHHHHHHHh
Q psy11929        171 IVTVHG-NPDTISQAIYQICLVLIE  194 (433)
Q Consensus       171 ~v~I~G-~~~~v~~A~~~I~~~l~e  194 (433)
                      .++|.. ++.+.++|++.|..++..
T Consensus       636 t~~i~A~~~~am~~Ak~~I~~i~~~  660 (760)
T KOG1067|consen  636 TFSIFAPTQAAMEEAKEFIDGIIKD  660 (760)
T ss_pred             eEEEEecCHHHHHHHHHHHHHHhcC
Confidence            777776 678889999999988765

>PRK12705 hypothetical protein; Provisional

Probab=93.39  E-value=0.11  Score=54.48  Aligned_cols=65  Identities=15%  Similarity=0.315  Sum_probs=47.0

Q ss_pred             CceEEEEEeCcccc-cccccCCCchHHHHHhHhCCeEEEccCCCCCceEEEEEeC-HHHHHHHHHHHHHHH
Q psy11929        286 DFVETEIVLTDDIA-GCVIGKAGSRLLEIRQISGAQINIHTGTESHKKMFHIQGC-QEAVSLAQYLINMCI  354 (433)
Q Consensus       286 ~~~t~~i~VP~~~v-G~IIGkgG~~Ik~I~~~sGA~I~I~~~~~~~er~V~IsGt-~e~v~~A~~lI~~~i  354 (433)
                      ...+..+.+|++-+ |+||||-|.||+.+...||+.|.|++..    ..|+|++- |.--+.|...+...|
T Consensus       196 e~tvs~v~lp~demkGriIGreGrNir~~E~~tGvdliiddtp----~~V~ls~fdp~rreia~~~l~~Li  262 (508)
T PRK12705        196 DLSVSVVPIPSDAMKGRIIGREGRNIRAFEGLTGVDLIIDDTP----EAVVISSFNPIRREIARLTLEKLL  262 (508)
T ss_pred             hheeeeeecCChHhhccccCccchhHHHHHHhhCCceEecCCc----cchhhcccCccchHHHHHHHHHHH
Confidence            45566778888655 9999999999999999999999999876    45666654 333333444444443

>KOG4369|consensus

Probab=92.00  E-value=0.064  Score=59.64  Aligned_cols=52  Identities=23%  Similarity=0.180  Sum_probs=45.7

Q ss_pred             EEEEEeccCCcccccceeeecCchHHHHHHHHhCCeEEEeC---CCCCcceEEEecccC
Q psy11929         16 TMRCLFHSSVNVNEISCLIGPGGCIVRRLRKESGAKISITD---GACPDRIVTVSGSVD   71 (433)
Q Consensus        16 ~~rilvp~~~~~~~vg~IIGk~G~~Ik~I~~~tga~I~v~~---~~~~eRvv~I~G~~~   71 (433)
                      .-+.-+|.    ...++|||++|.+|..+|.-||+.|.+.+   .+..||.+.+.|.++
T Consensus      1341 ~~k~~~P~----~a~SRVig~ggsnVna~r~~tga~ielekmq~~Nqaers~~~kg~p~ 1395 (2131)
T KOG4369|consen 1341 QGKGDGPL----YASSRVIGDGGSNVNAARLGTGALIELEKMQPDNQAERSKAPKGRPP 1395 (2131)
T ss_pred             ccccccch----hhhhhhhccCcchhhhHhhccceEEehhhcCCccchhhhcccCCCCh
Confidence            34556666    89999999999999999999999999977   356899999999999

>PF13083 KH_4: KH domain; PDB: 3GKU_B

Probab=91.97  E-value=0.068  Score=40.76  Aligned_cols=33  Identities=21%  Similarity=0.147  Sum_probs=27.2

Q ss_pred             eEEEEEEeccCCcccccceeeecCchHHHHHHHHhCC
Q psy11929         14 LITMRCLFHSSVNVNEISCLIGPGGCIVRRLRKESGA   50 (433)
Q Consensus        14 ~~~~rilvp~~~~~~~vg~IIGk~G~~Ik~I~~~tga   50 (433)
                      ...+.+-|..    ...|.||||+|.+++.||.-.+.
T Consensus        28 ~~~i~v~i~~----ed~g~lIGk~G~tl~ALq~l~~~   60 (73)
T PF13083_consen   28 GDTIVVNIDG----EDAGRLIGKHGKTLNALQYLVNA   60 (73)
T ss_dssp             TTEEEEEEES----CCCHHHCTTHHHHHHHHHHHHHH
T ss_pred             ceEEEEEECC----CccceEECCCCeeHHHHHHHHHH
Confidence            4466777788    99999999999999999976543

>cd02409 KH-II KH-II (K homology RNA-binding domain, type II)

Probab=91.49  E-value=0.32  Score=35.75  Aligned_cols=34  Identities=21%  Similarity=0.243  Sum_probs=27.2

Q ss_pred             EEEEEEeccCCcccccceeeecCchHHHHHHHHhCCeE
Q psy11929         15 ITMRCLFHSSVNVNEISCLIGPGGCIVRRLRKESGAKI   52 (433)
Q Consensus        15 ~~~rilvp~~~~~~~vg~IIGk~G~~Ik~I~~~tga~I   52 (433)
                      ....+.+..    ...|.+||++|.+|+.|+..++-.+
T Consensus        25 ~~~~i~~~~----~~~g~lIGk~G~~l~~l~~l~~~~~   58 (68)
T cd02409          25 IEIIIVVAR----GQPGLVIGKKGQNIRALQKLLQKLL   58 (68)
T ss_pred             EEEEEEECC----CCCceEECCCCccHHHHHHHHHHHc
Confidence            455566655    5689999999999999999998544

KH binds single-stranded RNA or DNA. It is found in a wide variety of proteins including ribosomal proteins (e.g. ribosomal protein S3), transcription factors (e.g. NusA_K), and post-transcriptional modifiers of mRNA (e.g. hnRNP K). There are two different KH domains that belong to different protein folds, but they share a single KH motif. The KH motif is a beta-alpha-alpha-beta-beta unit that folds into an alpha-beta structure with a three stranded beta-sheet interupted by two contiguous helices. In addition to their KH core domain, KH-II proteins have an N-terminal alpha helical extension while KH-I proteins have a C-terminal alpha helical extension.

>PF13184 KH_5: NusA-like KH domain; PDB: 1HH2_P 1L2F_A 2ATW_A 1K0R_B 2ASB_A

Probab=90.95  E-value=0.25  Score=37.30  Aligned_cols=38  Identities=29%  Similarity=0.464  Sum_probs=29.3

Q ss_pred             EEEEEeCccc-----ccccccCCCchHHHHHhHh-CCeEEEccC
Q psy11929        289 ETEIVLTDDI-----AGCVIGKAGSRLLEIRQIS-GAQINIHTG  326 (433)
Q Consensus       289 t~~i~VP~~~-----vG~IIGkgG~~Ik~I~~~s-GA~I~I~~~  326 (433)
                      ...+.|-...     +|..||++|++|+.|.++. |-+|.|-.-
T Consensus         4 r~kvaV~~~~~~~d~vG~~iG~~G~rik~i~~~L~gekIdvV~~   47 (69)
T PF13184_consen    4 RTKVAVKSGDPNIDPVGACIGKKGSRIKAISEELNGEKIDVVEY   47 (69)
T ss_dssp             EEEEEEEESSTTS-HHHHHH-CCCCCHHHHHHHTTT-EEEEEE-
T ss_pred             eEEEEEEcCCCCcCcceecCccccHHHHHHHHHhCCCeEEEEEc
Confidence            3466666666     9999999999999999999 888887653

>PF13184 KH_5: NusA-like KH domain; PDB: 1HH2_P 1L2F_A 2ATW_A 1K0R_B 2ASB_A

Probab=90.27  E-value=0.2  Score=37.81  Aligned_cols=27  Identities=26%  Similarity=0.572  Sum_probs=23.3

Q ss_pred             cceeeecCchHHHHHHHHh-CCeEEEeC
Q psy11929         30 ISCLIGPGGCIVRRLRKES-GAKISITD   56 (433)
Q Consensus        30 vg~IIGk~G~~Ik~I~~~t-ga~I~v~~   56 (433)
                      +|..||++|..||.|.++. |-+|+|-.
T Consensus        19 vG~~iG~~G~rik~i~~~L~gekIdvV~   46 (69)
T PF13184_consen   19 VGACIGKKGSRIKAISEELNGEKIDVVE   46 (69)
T ss_dssp             HHHHH-CCCCCHHHHHHHTTT-EEEEEE
T ss_pred             ceecCccccHHHHHHHHHhCCCeEEEEE
Confidence            9999999999999999999 89988864

>KOG1067|consensus

Probab=89.92  E-value=0.89  Score=47.43  Aligned_cols=64  Identities=22%  Similarity=0.213  Sum_probs=53.6

Q ss_pred             eEEEEEeCcccccccccCCCchHHHHHhHhCCeEEEccCCCCCceEEEEEeC-HHHHHHHHHHHHHHHHhc
Q psy11929        288 VETEIVLTDDIAGCVIGKAGSRLLEIRQISGAQINIHTGTESHKKMFHIQGC-QEAVSLAQYLINMCIELQ  357 (433)
Q Consensus       288 ~t~~i~VP~~~vG~IIGkgG~~Ik~I~~~sGA~I~I~~~~~~~er~V~IsGt-~e~v~~A~~lI~~~i~~~  357 (433)
                      ...++.|+.+....+||.+|.+.|.|..+|||.-.+++      -.+.|-.. +.+.++|+.+|..++...
T Consensus       597 ~~~tlkv~~sk~~~lIGp~G~~~kki~~EtGai~~vDe------~t~~i~A~~~~am~~Ak~~I~~i~~~~  661 (760)
T KOG1067|consen  597 VLETLKVSPSKRATLIGPGGVLKKKIEVETGAISQVDE------GTFSIFAPTQAAMEEAKEFIDGIIKDD  661 (760)
T ss_pred             eeeEEeecchhhheeecCccceeeeEeeeccceeeecC------ceEEEEecCHHHHHHHHHHHHHHhcCc
Confidence            45688999999999999999999999999996666655      34777665 678999999999988664

>KOG3273|consensus

Probab=89.36  E-value=0.25  Score=44.61  Aligned_cols=55  Identities=20%  Similarity=0.388  Sum_probs=49.9

Q ss_pred             cCcccceecCCchhHHHHHHhhCceEEeccCCCCCCCccEEEEEccHHHHHHHHHHHHHHHHh
Q psy11929        132 ATHCGSLIGKGGCKIKDIRDLSGANVQVASDMLPMSTERIVTVHGNPDTISQAIYQICLVLIE  194 (433)
Q Consensus       132 ~~~vg~iIGk~G~~Ik~I~~~sga~I~i~~~~~~~~~er~v~I~G~~~~v~~A~~~I~~~l~e  194 (433)
                      ...+|+|.||+|.+--.|++.|.++|.+.        +..|.|-|..++++-|...|+.++..
T Consensus       177 sRAIGRiaGk~GkTkfaIEn~trtrIVla--------d~kIHiLG~~~niriAR~avcsLIlG  231 (252)
T KOG3273|consen  177 SRAIGRIAGKGGKTKFAIENVTRTRIVLA--------DSKIHILGAFQNIRIARDAVCSLILG  231 (252)
T ss_pred             HHHHHHhhcCCCcceeeeeccceeEEEec--------CceEEEeecchhhHHHHHhhHhhhcc
Confidence            55789999999999889999999999996        45799999999999999999999887

>PF13083 KH_4: KH domain; PDB: 3GKU_B

Probab=89.33  E-value=0.24  Score=37.71  Aligned_cols=34  Identities=24%  Similarity=0.345  Sum_probs=28.6

Q ss_pred             CCCeEEEEEeccCcccceecCCchhHHHHHHhhC
Q psy11929        121 PQPLQLKLVIPATHCGSLIGKGGCKIKDIRDLSG  154 (433)
Q Consensus       121 ~~~~~~~l~ip~~~vg~iIGk~G~~Ik~I~~~sg  154 (433)
                      .....+.+.+..+..|+||||+|.+++.||--.+
T Consensus        26 ~~~~~i~v~i~~ed~g~lIGk~G~tl~ALq~l~~   59 (73)
T PF13083_consen   26 EDGDTIVVNIDGEDAGRLIGKHGKTLNALQYLVN   59 (73)
T ss_dssp             TTTTEEEEEEESCCCHHHCTTHHHHHHHHHHHHH
T ss_pred             CCceEEEEEECCCccceEECCCCeeHHHHHHHHH
Confidence            4556778888999999999999999999986543

>cd02409 KH-II KH-II (K homology RNA-binding domain, type II)

Probab=89.30  E-value=0.6  Score=34.24  Aligned_cols=35  Identities=26%  Similarity=0.421  Sum_probs=28.4

Q ss_pred             ceEEEEEeCcccccccccCCCchHHHHHhHhCCeE
Q psy11929        287 FVETEIVLTDDIAGCVIGKAGSRLLEIRQISGAQI  321 (433)
Q Consensus       287 ~~t~~i~VP~~~vG~IIGkgG~~Ik~I~~~sGA~I  321 (433)
                      .....+.+.....|.+||++|.+|+.|+..++-.+
T Consensus        24 ~~~~~i~~~~~~~g~lIGk~G~~l~~l~~l~~~~~   58 (68)
T cd02409          24 RIEIIIVVARGQPGLVIGKKGQNIRALQKLLQKLL   58 (68)
T ss_pred             cEEEEEEECCCCCceEECCCCccHHHHHHHHHHHc
Confidence            35556677766789999999999999999988554

KH binds single-stranded RNA or DNA. It is found in a wide variety of proteins including ribosomal proteins (e.g. ribosomal protein S3), transcription factors (e.g. NusA_K), and post-transcriptional modifiers of mRNA (e.g. hnRNP K). There are two different KH domains that belong to different protein folds, but they share a single KH motif. The KH motif is a beta-alpha-alpha-beta-beta unit that folds into an alpha-beta structure with a three stranded beta-sheet interupted by two contiguous helices. In addition to their KH core domain, KH-II proteins have an N-terminal alpha helical extension while KH-I proteins have a C-terminal alpha helical extension.

>PF07650 KH_2: KH domain syndrome, contains KH motifs

Probab=88.25  E-value=0.26  Score=37.95  Aligned_cols=34  Identities=15%  Similarity=0.383  Sum_probs=28.4

Q ss_pred             EEEEEeccCCcccccceeeecCchHHHHHHHHhCCeEE
Q psy11929         16 TMRCLFHSSVNVNEISCLIGPGGCIVRRLRKESGAKIS   53 (433)
Q Consensus        16 ~~rilvp~~~~~~~vg~IIGk~G~~Ik~I~~~tga~I~   53 (433)
                      ...+.+..    .+.|.|||++|++|++|+++.+-.+.
T Consensus        26 ~~~i~i~~----~~~~ivIGk~G~~ik~i~~~~~k~l~   59 (78)
T PF07650_consen   26 QIIIVIKA----SQPGIVIGKKGSNIKKIREELRKELE   59 (78)
T ss_dssp             EEEEEEEE----SSHHHHHTGGGHHHHHHHHHHHHHHH
T ss_pred             eEEEEEeC----CCccHhHHhhhHHHHHHHHHHHHHHh
Confidence            45677788    99999999999999999988765553

; InterPro: IPR004044 The K homology (KH) domain was first identified in the human heterogeneous nuclear ribonucleoprotein (hnRNP) K. It is a domain of around 70 amino acids that is present in a wide variety of quite diverse nucleic acid-binding proteins []. It has been shown to bind RNA [, ]. Like many other RNA-binding motifs, KH motifs are found in one or multiple copies (14 copies in chicken vigilin) and, at least for hnRNP K (three copies) and FMR-1 (two copies), each motif is necessary for in vitro RNA binding activity, suggesting that they may function cooperatively or, in the case of single KH motif proteins (for example, Mer1p), independently []. According to structural [, , ] analysis the KH domain can be separated in two groups. The first group or type-1 contain a beta-alpha-alpha-beta-beta-alpha structure, whereas in the type-2 the two last beta-sheet are located in the N-terminal part of the domain (alpha-beta-beta-alpha-alpha-beta). Sequence similarity between these two folds are limited to a short region (VIGXXGXXI) in the RNA binding motif. This motif is located between helice 1 and 2 in type-1 and between helice 2 and 3 in type-2. Proteins known to contain a type-2 KH domain include eukaryotic and prokaryotic S3 family of ribosomal proteins, and the prokaryotic GTP-binding protein, era.; GO: 0003723 RNA binding; PDB: 2XR1_B 3OAR_C 3OFX_C 1VS7_C 3I1O_C 2WWL_C 3R8O_C 2QAL_C 3J00_C 3J0V_F ....

>COG1855 ATPase (PilT family) [General function prediction only]

Probab=87.38  E-value=0.47  Score=48.51  Aligned_cols=41  Identities=27%  Similarity=0.391  Sum_probs=37.3

Q ss_pred             eEEEEEeCcccccccccCCCchHHHHHhHhCCeEEEccCCC
Q psy11929        288 VETEIVLTDDIAGCVIGKAGSRLLEIRQISGAQINIHTGTE  328 (433)
Q Consensus       288 ~t~~i~VP~~~vG~IIGkgG~~Ik~I~~~sGA~I~I~~~~~  328 (433)
                      ....+.||..+++.+|||+|.+|++|.+..|-+|.|.....
T Consensus       486 ~~avv~vpe~~i~~vigk~g~~i~~ie~klgi~I~v~~~e~  526 (604)
T COG1855         486 GRAVVKVPEKYIPKVIGKGGKRIKEIEKKLGIKIDVKPLEE  526 (604)
T ss_pred             CeEEEEeCHHHhhHHhhcccchHHHHHHHhCCceEEEEccc
Confidence            34678999999999999999999999999999999988764

>cd02414 jag_KH jag_K homology RNA-binding domain

Probab=87.25  E-value=0.62  Score=35.89  Aligned_cols=33  Identities=18%  Similarity=0.284  Sum_probs=26.0

Q ss_pred             EEEEeccCCcccccceeeecCchHHHHHHHHhCCeEE
Q psy11929         17 MRCLFHSSVNVNEISCLIGPGGCIVRRLRKESGAKIS   53 (433)
Q Consensus        17 ~rilvp~~~~~~~vg~IIGk~G~~Ik~I~~~tga~I~   53 (433)
                      +.+-+..    ...|.+|||+|+++..||--++.-++
T Consensus        26 i~i~i~~----~~~g~LIGk~G~tL~AlQ~L~~~~~~   58 (77)
T cd02414          26 VEVNISG----DDIGLLIGKRGKTLDALQYLANLVLN   58 (77)
T ss_pred             EEEEEec----CCCCeEECCCCccHHHHHHHHHHHHh
Confidence            4455566    88899999999999999987664443

The KH domain is found in proteins homologous to the Bacillus subtilis protein Jag, which is associated with SpoIIIJ and is necessary for the third stage of sporulation. The KH motif is a beta-alpha-alpha-beta-beta unit that folds into an alpha-beta structure with a three stranded beta-sheet interupted by two contiguous helices. In general, KH binds single-stranded RNA or DNA. It is found in a wide variety of proteins including ribosomal proteins, transcription factors and post-transcriptional modifiers of mRNA.

>KOG3273|consensus

Probab=86.88  E-value=0.42  Score=43.22  Aligned_cols=53  Identities=21%  Similarity=0.360  Sum_probs=48.5

Q ss_pred             ccccccccCCCchHHHHHhHhCCeEEEccCCCCCceEEEEEeCHHHHHHHHHHHHHHHH
Q psy11929        297 DIAGCVIGKAGSRLLEIRQISGAQINIHTGTESHKKMFHIQGCQEAVSLAQYLINMCIE  355 (433)
Q Consensus       297 ~~vG~IIGkgG~~Ik~I~~~sGA~I~I~~~~~~~er~V~IsGt~e~v~~A~~lI~~~i~  355 (433)
                      ..+|+|+||+|.+--.|...|.++|-+.+..      |-|-|+.+++..|+..|...|-
T Consensus       178 RAIGRiaGk~GkTkfaIEn~trtrIVlad~k------IHiLG~~~niriAR~avcsLIl  230 (252)
T KOG3273|consen  178 RAIGRIAGKGGKTKFAIENVTRTRIVLADSK------IHILGAFQNIRIARDAVCSLIL  230 (252)
T ss_pred             HHHHHhhcCCCcceeeeeccceeEEEecCce------EEEeecchhhHHHHHhhHhhhc
Confidence            4789999999999999999999999998854      9999999999999999988774

>COG1097 RRP4 RNA-binding protein Rrp4 and related proteins (contain S1 domain and KH domain) [Translation, ribosomal structure and biogenesis]

Probab=86.50  E-value=1.6  Score=40.93  Aligned_cols=45  Identities=18%  Similarity=0.410  Sum_probs=38.8

Q ss_pred             EEeccCCcccccceeeecCchHHHHHHHHhCCeEEEeCCCCCcceEEEecccC
Q psy11929         19 CLFHSSVNVNEISCLIGPGGCIVRRLRKESGAKISITDGACPDRIVTVSGSVD   71 (433)
Q Consensus        19 ilvp~~~~~~~vg~IIGk~G~~Ik~I~~~tga~I~v~~~~~~eRvv~I~G~~~   71 (433)
                      +.+|.    ..|.++|||+|+.++.|.++|+|+|-|..+|    .|-|.+..+
T Consensus       150 v~i~p----~kVpRvig~~~sm~~~l~~~~~~~I~VG~NG----~IWV~~~~~  194 (239)
T COG1097         150 VKIPP----SKVPRVIGKKGSMLNMLKEKTGCEIIVGQNG----RIWVDGENE  194 (239)
T ss_pred             EEEch----hhcceEecCCCcHHHHhhhhcCeEEEEecCC----EEEecCCCc
Confidence            56777    9999999999999999999999999998765    367777766

>cd02413 40S_S3_KH K homology RNA-binding (KH) domain of the eukaryotic 40S small ribosomal subunit protein S3

Probab=85.87  E-value=0.89  Score=35.48  Aligned_cols=36  Identities=11%  Similarity=0.251  Sum_probs=29.6

Q ss_pred             EEEEEeccCCcccccceeeecCchHHHHHHHHhCCeEEEe
Q psy11929         16 TMRCLFHSSVNVNEISCLIGPGGCIVRRLRKESGAKISIT   55 (433)
Q Consensus        16 ~~rilvp~~~~~~~vg~IIGk~G~~Ik~I~~~tga~I~v~   55 (433)
                      .+++.+..    ..-|.|||++|+.|++|+++-.-...+.
T Consensus        31 ~i~I~I~t----arPg~vIG~~G~~i~~L~~~L~k~~~~~   66 (81)
T cd02413          31 RTEIIIRA----TRTQNVLGEKGRRIRELTSLVQKRFNFP   66 (81)
T ss_pred             eEEEEEEe----CCCceEECCCchhHHHHHHHHHHHhCCC
Confidence            36777777    8899999999999999999876655553

S3 is part of the head region of the 40S ribosomal subunit and is believed to interact with mRNA as it threads its way from the latch into the channel. The KH motif is a beta-alpha-alpha-beta-beta unit that folds into an alpha-beta structure with a three stranded beta-sheet interupted by two contiguous helices. In general, KH binds single-stranded RNA or DNA. It is found in a wide variety of proteins including ribosomal proteins, transcription factors and post-transcriptional modifiers of mRNA.

>cd02410 archeal_CPSF_KH The archaeal cleavage and polyadenylation specificity factor (CPSF) contains an N-terminal K homology RNA-binding domain (KH)

Probab=85.44  E-value=4  Score=35.39  Aligned_cols=94  Identities=20%  Similarity=0.241  Sum_probs=61.1

Q ss_pred             eeecCchHHHHHHHHhCCeEEEeCCCCCcceEEEecccCCCCCCccccCCCCCccccchHHHHHHHHHHHHhhhhhhccc
Q psy11929         33 LIGPGGCIVRRLRKESGAKISITDGACPDRIVTVSGSVDNSSTSSVETGYPGHTLWVTSVDNVCTAYNFMCRSLEDYHIN  112 (433)
Q Consensus        33 IIGk~G~~Ik~I~~~tga~I~v~~~~~~eRvv~I~G~~~~~~~~~v~~~~~~~~~~~~a~~~v~~A~~~I~~~~~~~~~~  112 (433)
                      .+=.+|+.|+.|-++-.-+|.|-.+            +..                   ...=.+|.+.|.+.+-+... 
T Consensus        20 ~~~~~~dli~~lAk~lrKRIvvR~d------------ps~-------------------l~~~e~A~~~I~~ivP~ea~-   67 (145)
T cd02410          20 LFAEDGDLVKDLAKDLRKRIVIRPD------------PSV-------------------LKPPEEAIKIILEIVPEEAG-   67 (145)
T ss_pred             HHhcccHHHHHHHHHHhceEEEcCC------------hhh-------------------cCCHHHHHHHHHHhCCCccC-
Confidence            4445688999999998888877542            110                   00124677777776633100 


Q ss_pred             ccCCCCCCCCCeEEEEEeccCcccceecCCchhHHHHHHhhCceEEecc
Q psy11929        113 RNRMENCSPQPLQLKLVIPATHCGSLIGKGGCKIKDIRDLSGANVQVAS  161 (433)
Q Consensus       113 ~~~~~~~~~~~~~~~l~ip~~~vg~iIGk~G~~Ik~I~~~sga~I~i~~  161 (433)
                      .   .+-.=+..+-++.|-...-|.+||++|.++++|..+||-.-.+..
T Consensus        68 i---~di~Fd~~tGEV~IeaeKPG~ViGk~g~~~reI~~~tgW~p~vvR  113 (145)
T cd02410          68 I---TDIYFDDDTGEVIIEAEKPGLVIGKGGSTLREITRETGWAPKVVR  113 (145)
T ss_pred             c---eeeEecCCCcEEEEEEcCCeEEEecCchhHHHHHHHhCCeeEEEe
Confidence            0   000011224466777888899999999999999999998877764

The archeal CPSFs are predicted to be metal-dependent RNases belonging to the beta-CASP family, a subgroup enzymes within the metallo-beta-lactamase fold. The KH motif is a beta-alpha-alpha-beta-beta unit that folds into an alpha-beta structure with a three stranded beta-sheet interupted by two contiguous helices. In general, KH domains are known to bind single-stranded RNA or DNA and are found in a wide variety of proteins including ribosomal proteins, transcription factors and post-transcriptional modifiers of mRNA.

>COG5166 Uncharacterized conserved protein [Function unknown]

Probab=84.54  E-value=1.4  Score=45.55  Aligned_cols=125  Identities=14%  Similarity=0.084  Sum_probs=82.5

Q ss_pred             eeeecCchHHHHHHHHhCCeEEEeCC-CCCcceE-EEecccCCCCCCccccCCCCCccccchHHHHHHHHHHHHhhhhhh
Q psy11929         32 CLIGPGGCIVRRLRKESGAKISITDG-ACPDRIV-TVSGSVDNSSTSSVETGYPGHTLWVTSVDNVCTAYNFMCRSLEDY  109 (433)
Q Consensus        32 ~IIGk~G~~Ik~I~~~tga~I~v~~~-~~~eRvv-~I~G~~~~~~~~~v~~~~~~~~~~~~a~~~v~~A~~~I~~~~~~~  109 (433)
                      .|-||+--.+.+|++...|.+.+.=. ..+.++. .+.|...                      +-.++++.+.   .+ 
T Consensus       393 Fl~gkkngK~TrIm~~v~c~~~~~i~~~~gs~~~~~~~g~~~----------------------~F~k~~~~~~---~E-  446 (657)
T COG5166         393 FLRGKKNGKATRIMKGVSCSELSSIVSSTGSIVETNGIGEKM----------------------SFSKKLSIPP---TE-  446 (657)
T ss_pred             HhccccCcchhhhhhhcccceeeEEEecCCcEEEEeccCcch----------------------hhHHHhcCCc---cc-
Confidence            56777666699999999888544321 1122332 2344444                      4444444332   22 


Q ss_pred             cccccCCCCCCCCCeEEEEEeccCcccceecCCchhHHHHHHhhCceEEecc-CCCCCCCccE-EEEEcc---HHHHHHH
Q psy11929        110 HINRNRMENCSPQPLQLKLVIPATHCGSLIGKGGCKIKDIRDLSGANVQVAS-DMLPMSTERI-VTVHGN---PDTISQA  184 (433)
Q Consensus       110 ~~~~~~~~~~~~~~~~~~l~ip~~~vg~iIGk~G~~Ik~I~~~sga~I~i~~-~~~~~~~er~-v~I~G~---~~~v~~A  184 (433)
                                  -+..+.+.||...+-.|||.||..|++++.+-++.|++.. -.++.+..+- |.|.-+   .+++.-+
T Consensus       447 ------------Fpae~~f~i~e~~h~~IIgtgG~~iQ~~m~kh~v~i~f~n~~~~~qs~~~dNV~I~~PrKn~~ni~~~  514 (657)
T COG5166         447 ------------FPAEIAFIIMESGHEMIIGTGGIEIQENMVKHAVDIAFKNFYKFGQSQWHDNVLIEAPRKNQDNISGK  514 (657)
T ss_pred             ------------CchheEEEeecccceeeeccCchhhHHhhhhhhhhhhhhhhhhcchhhhhcceEEECCccCccchhcc
Confidence                        2445678999999999999999999999999999999874 2334444443 666654   4566667


Q ss_pred             HHHHHHHHHh
Q psy11929        185 IYQICLVLIE  194 (433)
Q Consensus       185 ~~~I~~~l~e  194 (433)
                      +.-+++++.+
T Consensus       515 KNd~~~~V~~  524 (657)
T COG5166         515 KNDKLDKVKQ  524 (657)
T ss_pred             cccHHHHHhh
Confidence            7777777775

>cd02410 archeal_CPSF_KH The archaeal cleavage and polyadenylation specificity factor (CPSF) contains an N-terminal K homology RNA-binding domain (KH)

Probab=84.04  E-value=5  Score=34.78  Aligned_cols=39  Identities=31%  Similarity=0.460  Sum_probs=33.8

Q ss_pred             EEEEEeCcccccccccCCCchHHHHHhHhCCeEEEccCC
Q psy11929        289 ETEIVLTDDIAGCVIGKAGSRLLEIRQISGAQINIHTGT  327 (433)
Q Consensus       289 t~~i~VP~~~vG~IIGkgG~~Ik~I~~~sGA~I~I~~~~  327 (433)
                      +-++.|-.+.-|.+||++|.++++|...||-.-+|-...
T Consensus        77 tGEV~IeaeKPG~ViGk~g~~~reI~~~tgW~p~vvRtp  115 (145)
T cd02410          77 TGEVIIEAEKPGLVIGKGGSTLREITRETGWAPKVVRTP  115 (145)
T ss_pred             CcEEEEEEcCCeEEEecCchhHHHHHHHhCCeeEEEecC
Confidence            347888889999999999999999999999887776554

The archeal CPSFs are predicted to be metal-dependent RNases belonging to the beta-CASP family, a subgroup enzymes within the metallo-beta-lactamase fold. The KH motif is a beta-alpha-alpha-beta-beta unit that folds into an alpha-beta structure with a three stranded beta-sheet interupted by two contiguous helices. In general, KH domains are known to bind single-stranded RNA or DNA and are found in a wide variety of proteins including ribosomal proteins, transcription factors and post-transcriptional modifiers of mRNA.

>PRK13764 ATPase; Provisional

Probab=83.84  E-value=0.94  Score=48.68  Aligned_cols=42  Identities=24%  Similarity=0.318  Sum_probs=38.0

Q ss_pred             ceEEEEEeCcccccccccCCCchHHHHHhHhCCeEEEccCCC
Q psy11929        287 FVETEIVLTDDIAGCVIGKAGSRLLEIRQISGAQINIHTGTE  328 (433)
Q Consensus       287 ~~t~~i~VP~~~vG~IIGkgG~~Ik~I~~~sGA~I~I~~~~~  328 (433)
                      .....+.||..+++.+|||+|.+|++|.+..|.+|.|....+
T Consensus       480 ~~~~~v~~~~~~~~~~~~k~~~~~~~~~~~~~~~i~v~~~~~  521 (602)
T PRK13764        480 DNKAVVYVPEKDIPKVIGKGGKRIKKIEKKLGIDIDVRPLDE  521 (602)
T ss_pred             CCeEEEEEChhhhhHHhccCcchHHHHHHHhCCceEEEEccc
Confidence            455688999999999999999999999999999999987664

>cd02414 jag_KH jag_K homology RNA-binding domain

Probab=83.36  E-value=1.2  Score=34.24  Aligned_cols=35  Identities=26%  Similarity=0.414  Sum_probs=28.6

Q ss_pred             eEEEEEeCcccccccccCCCchHHHHHhHhCCeEE
Q psy11929        288 VETEIVLTDDIAGCVIGKAGSRLLEIRQISGAQIN  322 (433)
Q Consensus       288 ~t~~i~VP~~~vG~IIGkgG~~Ik~I~~~sGA~I~  322 (433)
                      ....+.+..+..|.+|||+|++++.||-.+...+.
T Consensus        24 ~~i~i~i~~~~~g~LIGk~G~tL~AlQ~L~~~~~~   58 (77)
T cd02414          24 DTVEVNISGDDIGLLIGKRGKTLDALQYLANLVLN   58 (77)
T ss_pred             CEEEEEEecCCCCeEECCCCccHHHHHHHHHHHHh
Confidence            34667777888999999999999999988765544

The KH domain is found in proteins homologous to the Bacillus subtilis protein Jag, which is associated with SpoIIIJ and is necessary for the third stage of sporulation. The KH motif is a beta-alpha-alpha-beta-beta unit that folds into an alpha-beta structure with a three stranded beta-sheet interupted by two contiguous helices. In general, KH binds single-stranded RNA or DNA. It is found in a wide variety of proteins including ribosomal proteins, transcription factors and post-transcriptional modifiers of mRNA.

>PF07650 KH_2: KH domain syndrome, contains KH motifs

Probab=82.60  E-value=0.89  Score=34.93  Aligned_cols=34  Identities=38%  Similarity=0.523  Sum_probs=28.6

Q ss_pred             eEEEEEeccCcccceecCCchhHHHHHHhhCceE
Q psy11929        124 LQLKLVIPATHCGSLIGKGGCKIKDIRDLSGANV  157 (433)
Q Consensus       124 ~~~~l~ip~~~vg~iIGk~G~~Ik~I~~~sga~I  157 (433)
                      ..+.+.+...+-|.+||++|++|++|.+...-.+
T Consensus        25 ~~~~i~i~~~~~~ivIGk~G~~ik~i~~~~~k~l   58 (78)
T PF07650_consen   25 DQIIIVIKASQPGIVIGKKGSNIKKIREELRKEL   58 (78)
T ss_dssp             SEEEEEEEESSHHHHHTGGGHHHHHHHHHHHHHH
T ss_pred             CeEEEEEeCCCccHhHHhhhHHHHHHHHHHHHHH
Confidence            4567889999999999999999999987765444

; InterPro: IPR004044 The K homology (KH) domain was first identified in the human heterogeneous nuclear ribonucleoprotein (hnRNP) K. It is a domain of around 70 amino acids that is present in a wide variety of quite diverse nucleic acid-binding proteins []. It has been shown to bind RNA [, ]. Like many other RNA-binding motifs, KH motifs are found in one or multiple copies (14 copies in chicken vigilin) and, at least for hnRNP K (three copies) and FMR-1 (two copies), each motif is necessary for in vitro RNA binding activity, suggesting that they may function cooperatively or, in the case of single KH motif proteins (for example, Mer1p), independently []. According to structural [, , ] analysis the KH domain can be separated in two groups. The first group or type-1 contain a beta-alpha-alpha-beta-beta-alpha structure, whereas in the type-2 the two last beta-sheet are located in the N-terminal part of the domain (alpha-beta-beta-alpha-alpha-beta). Sequence similarity between these two folds are limited to a short region (VIGXXGXXI) in the RNA binding motif. This motif is located between helice 1 and 2 in type-1 and between helice 2 and 3 in type-2. Proteins known to contain a type-2 KH domain include eukaryotic and prokaryotic S3 family of ribosomal proteins, and the prokaryotic GTP-binding protein, era.; GO: 0003723 RNA binding; PDB: 2XR1_B 3OAR_C 3OFX_C 1VS7_C 3I1O_C 2WWL_C 3R8O_C 2QAL_C 3J00_C 3J0V_F ....

>COG1855 ATPase (PilT family) [General function prediction only]

Probab=82.45  E-value=0.89  Score=46.58  Aligned_cols=38  Identities=24%  Similarity=0.326  Sum_probs=34.6

Q ss_pred             EEEEEeccCCcccccceeeecCchHHHHHHHHhCCeEEEeCC
Q psy11929         16 TMRCLFHSSVNVNEISCLIGPGGCIVRRLRKESGAKISITDG   57 (433)
Q Consensus        16 ~~rilvp~~~~~~~vg~IIGk~G~~Ik~I~~~tga~I~v~~~   57 (433)
                      ...+.+|.    .+++.+|||+|.+|++|++..|-+|.|...
T Consensus       487 ~avv~vpe----~~i~~vigk~g~~i~~ie~klgi~I~v~~~  524 (604)
T COG1855         487 RAVVKVPE----KYIPKVIGKGGKRIKEIEKKLGIKIDVKPL  524 (604)
T ss_pred             eEEEEeCH----HHhhHHhhcccchHHHHHHHhCCceEEEEc
Confidence            36678888    999999999999999999999999999764

>COG1097 RRP4 RNA-binding protein Rrp4 and related proteins (contain S1 domain and KH domain) [Translation, ribosomal structure and biogenesis]

Probab=81.57  E-value=3.3  Score=38.94  Aligned_cols=57  Identities=23%  Similarity=0.376  Sum_probs=42.1

Q ss_pred             EEEEeccCcccceecCCchhHHHHHHhhCceEEeccCCCCCCCccEEEEEccHHH-HHHHHHHHH
Q psy11929        126 LKLVIPATHCGSLIGKGGCKIKDIRDLSGANVQVASDMLPMSTERIVTVHGNPDT-ISQAIYQIC  189 (433)
Q Consensus       126 ~~l~ip~~~vg~iIGk~G~~Ik~I~~~sga~I~i~~~~~~~~~er~v~I~G~~~~-v~~A~~~I~  189 (433)
                      .-+.|+...+-++||++|+.++-+.++++|+|.+-.+       -.|=|.+..+. ...|...|.
T Consensus       148 ~iv~i~p~kVpRvig~~~sm~~~l~~~~~~~I~VG~N-------G~IWV~~~~~~~e~~~~~aI~  205 (239)
T COG1097         148 QIVKIPPSKVPRVIGKKGSMLNMLKEKTGCEIIVGQN-------GRIWVDGENESLEELAIEAIR  205 (239)
T ss_pred             EEEEEchhhcceEecCCCcHHHHhhhhcCeEEEEecC-------CEEEecCCCcchHHHHHHHHH
Confidence            3468999999999999999999999999999999753       34555555442 333444443

>PRK06418 transcription elongation factor NusA-like protein; Validated

Probab=80.83  E-value=2.1  Score=38.18  Aligned_cols=35  Identities=29%  Similarity=0.480  Sum_probs=29.8

Q ss_pred             EEEEeccCCcccccceeeecCchHHHHHHHHhCCeEEEeC
Q psy11929         17 MRCLFHSSVNVNEISCLIGPGGCIVRRLRKESGAKISITD   56 (433)
Q Consensus        17 ~rilvp~~~~~~~vg~IIGk~G~~Ik~I~~~tga~I~v~~   56 (433)
                      +-++|-.    .. |.-|||+|++|+++++..|-+|.+-+
T Consensus        63 vIfvV~~----gd-g~aIGk~G~~ik~l~~~lgk~VevVE   97 (166)
T PRK06418         63 VILLVTS----GP-RIPIGKGGKIAKALSRKLGKKVRVVE   97 (166)
T ss_pred             EEEEEeC----CC-cccccccchHHHHHHHHhCCcEEEEE
Confidence            3455655    66 99999999999999999999999865

>KOG2874|consensus

Probab=80.79  E-value=3.1  Score=39.76  Aligned_cols=51  Identities=18%  Similarity=0.298  Sum_probs=45.8

Q ss_pred             cccccCCCchHHHHHhHhCCeEEEccCCCCCceEEEEEeCHHHHHHHHHHHHHHHHh
Q psy11929        300 GCVIGKAGSRLLEIRQISGAQINIHTGTESHKKMFHIQGCQEAVSLAQYLINMCIEL  356 (433)
Q Consensus       300 G~IIGkgG~~Ik~I~~~sGA~I~I~~~~~~~er~V~IsGt~e~v~~A~~lI~~~i~~  356 (433)
                      -++||.+|++++.|+-.|.|-|-|....      |.+.|....+..+...+.+++..
T Consensus       161 qRLiGpng~TLKAlelLT~CYilVqG~T------VsaiGpfkGlkevr~IV~DcM~N  211 (356)
T KOG2874|consen  161 QRLIGPNGSTLKALELLTNCYILVQGNT------VSAIGPFKGLKEVRKIVEDCMKN  211 (356)
T ss_pred             HHhcCCCchhHHHHHHHhhcEEEeeCcE------EEeecCcchHHHHHHHHHHHHhc
Confidence            5789999999999999999999999855      99999999999998888887764

---

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

ID	Length	Definition	E-value
Query	433
2jzx_A	160	Pcbp2 Kh1-Kh2 Domains Length = 160		2e-29
2p2r_A	76	Crystal Structure Of The Third Kh Domain Of Human P		1e-08
1wvn_A	82	Crsytal Structure Of Domain 3 Of Human Alpha Polyc		5e-08
2anr_A	178	Crystal Structure (Ii) Of Nova-1 Kh1KH2 DOMAIN TAND		1e-07
2anr_A	178	Crystal Structure (Ii) Of Nova-1 Kh1KH2 DOMAIN TAND		5e-04
2ann_A	178	Crystal Structure (I) Of Nova-1 Kh1KH2 DOMAIN TANDE		1e-07
2ann_A	178	Crystal Structure (I) Of Nova-1 Kh1KH2 DOMAIN TANDE		5e-04
1j5k_A	89	Complex Of The Kh3 Domain Of Hnrnp K With A Single_		1e-06
1zzi_A	82	Crystal Structure Analysis Of The Third Kh Domain O		4e-06
1zzi_A	82	Crystal Structure Analysis Of The Third Kh Domain O		6e-06
1khm_A	89	C-Terminal Kh Domain Of Hnrnp K (Kh3) Length = 89		5e-06
1ztg_A	74	Human Alpha Polyc Binding Protein Kh1 Length = 74		1e-05
3vke_A	76	Contribution Of The First K-Homology Domain Of Poly		1e-04
2axy_A	73	Crystal Structure Of Kh1 Domain Of Human Poly(C)-Bi		2e-04
1dtj_A	76	Crystal Structure Of Nova-2 Kh3 K-Homology Rna-Bind		6e-04
1ec6_A	87	Crystal Structure Of Nova-2 Kh3 K-Homology Rna-Bind		8e-04

>pdb|2JZX|A Chain A, Pcbp2 Kh1-Kh2 Domains Length = 160

Iteration: 1
 Score =  126 bits (317), Expect = 2e-29,   Method: Compositional matrix adjust.
 Identities = 71/185 (38%), Positives = 107/185 (57%), Gaps = 27/185 (14%)
Query: 11  EDTLITMRCLFHSSVNVNEISCLIGPGGCIVRRLRKESGAKISITDGACPDRIXXXXXXX 70
           ++  +T+R L H      E+  +IG  G  V+++R+ESGA+I+I++G CP+RI       
Sbjct: 1   KNVTLTIRLLMHG----KEVGSIIGKKGESVKKMREESGARINISEGNCPERIITL---- 52
Query: 71  XXXXXXXXXXGYPGHTLWVTSVDNVCTAYNFMCRSLE-DYHINRNRMENCSPQPLQLKLV 129
                       P + ++         A+  +   LE D   +       S  P+ L+LV
Sbjct: 53  ----------AGPTNAIF--------KAFAMIIDKLEEDISSSMTNSTAASRPPVTLRLV 94
Query: 130 IPATHCGSLIGKGGCKIKDIRDLSGANVQVASDMLPMSTERIVTVHGNPDTISQAIYQIC 189
           +PA+ CGSLIGKGGCKIK+IR+ +GA VQVA DMLP STER +T+ G P +I + + QIC
Sbjct: 95  VPASQCGSLIGKGGCKIKEIRESTGAQVQVAGDMLPNSTERAITIAGIPQSIIECVKQIC 154
Query: 190 LVLIE 194
           +V++E
Sbjct: 155 VVMLE 159

>pdb|2P2R|A Chain A, Crystal Structure Of The Third Kh Domain Of Human Poly(C)- Binding Protein-2 In Complex With C-Rich Strand Of Human Telomeric Dna Length = 76

Iteration: 1
 Score = 57.4 bits (137), Expect = 1e-08,   Method: Compositional matrix adjust.
 Identities = 29/63 (46%), Positives = 42/63 (66%), Gaps = 1/63 (1%)
Query: 291 EIVLTDDIAGCVIGKAGSRLLEIRQISGAQINIHTGTE-SHKKMFHIQGCQEAVSLAQYL 349
           E+ + +D+ GC+IG+ G+++ EIRQ SGAQI I    E S  +   I G   ++SLAQYL
Sbjct: 8   ELTIPNDLIGCIIGRQGAKINEIRQXSGAQIKIANPVEGSTDRQVTITGSAASISLAQYL 67
Query: 350 INM 352
           IN+
Sbjct: 68  INV 70

>pdb|1WVN|A Chain A, Crsytal Structure Of Domain 3 Of Human Alpha Polyc Binding Protein Length = 82

Iteration: 1
 Score = 55.8 bits (133), Expect = 5e-08,   Method: Compositional matrix adjust.
 Identities = 29/69 (42%), Positives = 44/69 (63%), Gaps = 1/69 (1%)
Query: 291 EIVLTDDIAGCVIGKAGSRLLEIRQISGAQINIHTGTE-SHKKMFHIQGCQEAVSLAQYL 349
           E+ + +++ GC+IG+ G+ + EIRQ+SGAQI I    E S  +   I G   ++SLAQYL
Sbjct: 9   ELTIPNNLIGCIIGRQGANINEIRQMSGAQIKIANPVEGSSGRQVTITGSAASISLAQYL 68
Query: 350 INMCIELQK 358
           IN  +  +K
Sbjct: 69  INARLSSEK 77

>pdb|2ANR|A Chain A, Crystal Structure (Ii) Of Nova-1 Kh1KH2 DOMAIN TANDEM WITH 25NT RNA Hairpin Length = 178

Iteration: 1
 Score = 54.7 bits (130), Expect = 1e-07,   Method: Compositional matrix adjust.
 Identities = 46/169 (27%), Positives = 75/169 (44%), Gaps = 36/169 (21%)
Query: 32  CLIGPGGCIVRRLRKESGAKISITDGACPDRIXXXXXXXXXXXXXXXXXGYPGHTLWVTS 91
            +IG GG  + +L+KE+GA I ++                          YPG T  V  
Sbjct: 19  SIIGKGGQTIVQLQKETGATIKLSK---------------------SKDFYPGTTERVCL 57
Query: 92  VDNVCTAYN----FMCRSLEDYHINRNRMENCS---PQPL-------QLKLVIPATHCGS 137
           +     A N    F+   + +   N  + E  S   PQ         Q+K+++P +  G 
Sbjct: 58  IQGTIEALNAVHGFIAEKIREXPQNVAKTEPVSILQPQTTVNPDRANQVKIIVPNSTAGL 117
Query: 138 LIGKGGCKIKDIRDLSGANVQVASDMLPMSTE-RIVTVHGNPDTISQAI 185
           +IGKGG  +K I + SGA VQ++     ++ + R+VTV G P+   +A+
Sbjct: 118 IIGKGGATVKAIXEQSGAWVQLSQKPDGINLQNRVVTVSGEPEQNRKAV 166

>pdb|2ANR|A Chain A, Crystal Structure (Ii) Of Nova-1 Kh1KH2 DOMAIN TANDEM WITH 25NT RNA Hairpin Length = 178

Iteration: 1
 Score = 42.4 bits (98), Expect = 5e-04,   Method: Compositional matrix adjust.
 Identities = 20/53 (37%), Positives = 34/53 (64%), Gaps = 2/53 (3%)
Query: 126 LKLVIPATHCGSLIGKGGCKIKDIRDLSGANVQV--ASDMLPMSTERIVTVHG 176
           LK++IP+   GS+IGKGG  I  ++  +GA +++  + D  P +TER+  + G
Sbjct: 8   LKVLIPSYAAGSIIGKGGQTIVQLQKETGATIKLSKSKDFYPGTTERVCLIQG 60

>pdb|2ANN|A Chain A, Crystal Structure (I) Of Nova-1 Kh1KH2 DOMAIN TANDEM WITH 25 NT RNA Hairpin Length = 178

Iteration: 1
 Score = 54.3 bits (129), Expect = 1e-07,   Method: Compositional matrix adjust.
 Identities = 46/169 (27%), Positives = 75/169 (44%), Gaps = 36/169 (21%)
Query: 32  CLIGPGGCIVRRLRKESGAKISITDGACPDRIXXXXXXXXXXXXXXXXXGYPGHTLWVTS 91
            +IG GG  + +L+KE+GA I ++                          YPG T  V  
Sbjct: 19  SIIGKGGQTIVQLQKETGATIKLSKSK---------------------DFYPGTTERVCL 57
Query: 92  VDNVCTAYN----FMCRSLEDYHINRNRMENCS---PQPL-------QLKLVIPATHCGS 137
           +     A N    F+   + +   N  + E  S   PQ         Q+K+++P +  G 
Sbjct: 58  IQGTIEALNAVHGFIAEKIREMPQNVAKTEPVSILQPQTTVNPDRANQVKIIVPNSTAGL 117
Query: 138 LIGKGGCKIKDIRDLSGANVQVASDMLPMSTE-RIVTVHGNPDTISQAI 185
           +IGKGG  +K I + SGA VQ++     ++ + R+VTV G P+   +A+
Sbjct: 118 IIGKGGATVKAIMEQSGAWVQLSQKPDGINLQNRVVTVSGEPEQNRKAV 166

>pdb|2ANN|A Chain A, Crystal Structure (I) Of Nova-1 Kh1KH2 DOMAIN TANDEM WITH 25 NT RNA Hairpin Length = 178

Iteration: 1
 Score = 42.4 bits (98), Expect = 5e-04,   Method: Compositional matrix adjust.
 Identities = 20/53 (37%), Positives = 34/53 (64%), Gaps = 2/53 (3%)
Query: 126 LKLVIPATHCGSLIGKGGCKIKDIRDLSGANVQV--ASDMLPMSTERIVTVHG 176
           LK++IP+   GS+IGKGG  I  ++  +GA +++  + D  P +TER+  + G
Sbjct: 8   LKVLIPSYAAGSIIGKGGQTIVQLQKETGATIKLSKSKDFYPGTTERVCLIQG 60

>pdb|1J5K|A Chain A, Complex Of The Kh3 Domain Of Hnrnp K With A Single_stranded 10mer Dna Oligonucleotide Length = 89

Iteration: 1
 Score = 51.2 bits (121), Expect = 1e-06,   Method: Compositional matrix adjust.
 Identities = 27/75 (36%), Positives = 42/75 (56%), Gaps = 1/75 (1%)
Query: 282 DTGDDFVETEIVLTDDIAGCVIGKAGSRLLEIRQISGAQINIHTGTE-SHKKMFHIQGCQ 340
           D G   + T++ +  D+AG +IGK G R+ +IR  SGA I I    E S  ++  I G Q
Sbjct: 8   DLGGPIITTQVTIPKDLAGSIIGKGGQRIKQIRHESGASIKIDEPLEGSEDRIITITGTQ 67
Query: 341 EAVSLAQYLINMCIE 355
           + +  AQYL+   ++
Sbjct: 68  DQIQNAQYLLQNSVK 82

>pdb|1ZZI|A Chain A, Crystal Structure Analysis Of The Third Kh Domain Of Hnrnp K In Complex With Ssdna Length = 82

Iteration: 1
 Score = 49.3 bits (116), Expect = 4e-06,   Method: Compositional matrix adjust.
 Identities = 26/60 (43%), Positives = 38/60 (63%), Gaps = 1/60 (1%)
Query: 127 KLVIPATHCGSLIGKGGCKIKDIRDLSGANVQVASDMLPMSTERIVTVHGNPDTISQAIY 186
           ++ IP    GS+IGKGG +IK IR  SGA++++  + L  S +RI+T+ G  D I  A Y
Sbjct: 10  QVTIPKDLAGSIIGKGGQRIKQIRHESGASIKI-DEPLEGSEDRIITITGTQDQIQNAQY 68

>pdb|1ZZI|A Chain A, Crystal Structure Analysis Of The Third Kh Domain Of Hnrnp K In Complex With Ssdna Length = 82

Iteration: 1
 Score = 48.9 bits (115), Expect = 6e-06,   Method: Compositional matrix adjust.
 Identities = 25/69 (36%), Positives = 40/69 (57%), Gaps = 1/69 (1%)
Query: 288 VETEIVLTDDIAGCVIGKAGSRLLEIRQISGAQINIHTGTE-SHKKMFHIQGCQEAVSLA 346
           + T++ +  D+AG +IGK G R+ +IR  SGA I I    E S  ++  I G Q+ +  A
Sbjct: 7   ITTQVTIPKDLAGSIIGKGGQRIKQIRHESGASIKIDEPLEGSEDRIITITGTQDQIQNA 66
Query: 347 QYLINMCIE 355
           QYL+   ++
Sbjct: 67  QYLLQNSVK 75

>pdb|1KHM|A Chain A, C-Terminal Kh Domain Of Hnrnp K (Kh3) Length = 89

Iteration: 1
 Score = 48.9 bits (115), Expect = 5e-06,   Method: Compositional matrix adjust.
 Identities = 26/75 (34%), Positives = 41/75 (54%), Gaps = 1/75 (1%)
Query: 282 DTGDDFVETEIVLTDDIAGCVIGKAGSRLLEIRQISGAQINIHTGTE-SHKKMFHIQGCQ 340
           D G   + T++ +  D+A  +IGK G R+ +IR  SGA I I    E S  ++  I G Q
Sbjct: 8   DLGGPIITTQVTIPKDLARSIIGKGGQRIKQIRHESGASIKIDEPLEGSEDRIITITGTQ 67
Query: 341 EAVSLAQYLINMCIE 355
           + +  AQYL+   ++
Sbjct: 68  DQIQNAQYLLQNSVK 82

>pdb|1ZTG|A Chain A, Human Alpha Polyc Binding Protein Kh1 Length = 74

Iteration: 1
 Score = 48.1 bits (113), Expect = 1e-05,   Method: Compositional matrix adjust.
 Identities = 22/50 (44%), Positives = 35/50 (70%), Gaps = 4/50 (8%)
Query: 14 LITMRCLFHSSVNVNEISCLIGPGGCIVRRLRKESGAKISITDGACPDRI 63
          ++T+R L H      E+  +IG  G  V+R+R+ESGA+I+I++G CP+RI
Sbjct: 2  ILTIRLLMHGK----EVGSIIGKKGESVKRIREESGARINISEGNCPERI 47

>pdb|3VKE|A Chain A, Contribution Of The First K-Homology Domain Of Poly(C)-Binding Protein 1 To Its Affinity And Specificity For C-Rich Oligonucleotides Length = 76

Iteration: 1
 Score = 44.3 bits (103), Expect = 1e-04,   Method: Composition-based stats.
 Identities = 21/50 (42%), Positives = 34/50 (68%), Gaps = 4/50 (8%)
Query: 14 LITMRCLFHSSVNVNEISCLIGPGGCIVRRLRKESGAKISITDGACPDRI 63
          ++T+R L H      E+  +IG  G  V+R+R+ESGA+I+I++G  P+RI
Sbjct: 2  MLTIRLLMHG----KEVGSIIGKKGESVKRIREESGARINISEGNSPERI 47

>pdb|2AXY|A Chain A, Crystal Structure Of Kh1 Domain Of Human Poly(C)-Binding Protein-2 With C-Rich Strand Of Human Telomeric Dna Length = 73

Iteration: 1
 Score = 43.5 bits (101), Expect = 2e-04,   Method: Composition-based stats.
 Identities = 21/53 (39%), Positives = 35/53 (66%), Gaps = 4/53 (7%)
Query: 11 EDTLITMRCLFHSSVNVNEISCLIGPGGCIVRRLRKESGAKISITDGACPDRI 63
          ++  +T+R L H      E+  +IG  G  V++ R+ESGA+I+I++G CP+RI
Sbjct: 1  KNVTLTIRLLXHG----KEVGSIIGKKGESVKKXREESGARINISEGNCPERI 49

>pdb|1DTJ|A Chain A, Crystal Structure Of Nova-2 Kh3 K-Homology Rna-Binding Domain Length = 76

Iteration: 1
 Score = 42.0 bits (97), Expect = 6e-04,   Method: Composition-based stats.
 Identities = 20/65 (30%), Positives = 39/65 (60%), Gaps = 2/65 (3%)
Query: 126 LKLVIPATHCGSLIGKGGCKIKDIRDLSGANVQVAS--DMLPMSTERIVTVHGNPDTISQ 183
           +++ +P    G+++GKGG  + + ++L+GA +Q++   + LP +  R VT+ G+P     
Sbjct: 5   VEMAVPENLVGAILGKGGKTLVEYQELTGARIQISKKGEFLPGTRNRRVTITGSPAATQA 64
Query: 184 AIYQI 188
           A Y I
Sbjct: 65  AQYLI 69

>pdb|1EC6|A Chain A, Crystal Structure Of Nova-2 Kh3 K-Homology Rna-Binding Domain Bound To 20-Mer Rna Hairpin Length = 87

Iteration: 1
 Score = 41.6 bits (96), Expect = 8e-04,   Method: Composition-based stats.
 Identities = 20/65 (30%), Positives = 39/65 (60%), Gaps = 2/65 (3%)
Query: 126 LKLVIPATHCGSLIGKGGCKIKDIRDLSGANVQVAS--DMLPMSTERIVTVHGNPDTISQ 183
           +++ +P    G+++GKGG  + + ++L+GA +Q++   + LP +  R VT+ G+P     
Sbjct: 5   VEIAVPENLVGAILGKGGKTLVEYQELTGARIQISKKGEFLPGTRNRRVTITGSPAATQA 64
Query: 184 AIYQI 188
           A Y I
Sbjct: 65  AQYLI 69

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Length	Definition	E-value
Query	433
2jzx_A	160	Poly(RC)-binding protein 2; PCBP2, KH domains, RNA	6e-41
2jzx_A	160	Poly(RC)-binding protein 2; PCBP2, KH domains, RNA	3e-14
2jzx_A	160	Poly(RC)-binding protein 2; PCBP2, KH domains, RNA	2e-09
2jzx_A	160	Poly(RC)-binding protein 2; PCBP2, KH domains, RNA	1e-06
2anr_A	178	Neuro-oncological ventral antigen 1; protein-RNA c	2e-34
2anr_A	178	Neuro-oncological ventral antigen 1; protein-RNA c	4e-16
2anr_A	178	Neuro-oncological ventral antigen 1; protein-RNA c	9e-11
2anr_A	178	Neuro-oncological ventral antigen 1; protein-RNA c	2e-06
3krm_A	163	Insulin-like growth factor 2 mRNA-binding protein	2e-33
3krm_A	163	Insulin-like growth factor 2 mRNA-binding protein	3e-16
3krm_A	163	Insulin-like growth factor 2 mRNA-binding protein	7e-10
3krm_A	163	Insulin-like growth factor 2 mRNA-binding protein	7e-06
2jvz_A	164	KH type-splicing, FAR upstream element-binding pro	1e-30
2jvz_A	164	KH type-splicing, FAR upstream element-binding pro	3e-14
2jvz_A	164	KH type-splicing, FAR upstream element-binding pro	3e-09
2jvz_A	164	KH type-splicing, FAR upstream element-binding pro	8e-06
1j4w_A	174	FUSE binding protein; single-stranded DNA binding	2e-30
1j4w_A	174	FUSE binding protein; single-stranded DNA binding	2e-16
1j4w_A	174	FUSE binding protein; single-stranded DNA binding	5e-10
1j4w_A	174	FUSE binding protein; single-stranded DNA binding	3e-06
1dtj_A	76	RNA-binding neurooncological ventral antigen 2; KH	3e-18
1dtj_A	76	RNA-binding neurooncological ventral antigen 2; KH	3e-14
1dtj_A	76	RNA-binding neurooncological ventral antigen 2; KH	9e-07
1ec6_A	87	RNA-binding protein NOVA-2; KH domain, alpha-beta	4e-18
1ec6_A	87	RNA-binding protein NOVA-2; KH domain, alpha-beta	1e-14
1ec6_A	87	RNA-binding protein NOVA-2; KH domain, alpha-beta	6e-07
1zzk_A	82	Heterogeneous nuclear ribonucleoprotein K; KH domi	1e-17
1zzk_A	82	Heterogeneous nuclear ribonucleoprotein K; KH domi	4e-14
1zzk_A	82	Heterogeneous nuclear ribonucleoprotein K; KH domi	1e-07
2p2r_A	76	Poly(RC)-binding protein 2; protein-DNA complex, R	3e-17
2p2r_A	76	Poly(RC)-binding protein 2; protein-DNA complex, R	5e-14
2p2r_A	76	Poly(RC)-binding protein 2; protein-DNA complex, R	4e-07
2opv_A	85	KHSRP protein; KH domain, RNA binding protein, KSR	3e-17
2opv_A	85	KHSRP protein; KH domain, RNA binding protein, KSR	7e-12
2opv_A	85	KHSRP protein; KH domain, RNA binding protein, KSR	1e-06
1x4m_A	94	FAR upstream element binding protein 1; KH domain,	3e-17
1x4m_A	94	FAR upstream element binding protein 1; KH domain,	6e-12
1x4m_A	94	FAR upstream element binding protein 1; KH domain,	6e-06
1j5k_A	89	Heterogeneous nuclear ribonucleoprotein K; single-	5e-17
1j5k_A	89	Heterogeneous nuclear ribonucleoprotein K; single-	7e-15
1j5k_A	89	Heterogeneous nuclear ribonucleoprotein K; single-	1e-07
1wvn_A	82	Poly(RC)-binding protein 1; KH domain, RNA binding	5e-17
1wvn_A	82	Poly(RC)-binding protein 1; KH domain, RNA binding	1e-14
1wvn_A	82	Poly(RC)-binding protein 1; KH domain, RNA binding	2e-07
2axy_A	73	Poly(RC)-binding protein 2; protein-DNA complex, D	6e-17
2axy_A	73	Poly(RC)-binding protein 2; protein-DNA complex, D	2e-15
2axy_A	73	Poly(RC)-binding protein 2; protein-DNA complex, D	2e-08
2hh3_A	106	KH-type splicing regulatory protein; KH-RNA bindin	8e-17
2hh3_A	106	KH-type splicing regulatory protein; KH-RNA bindin	1e-10
2hh3_A	106	KH-type splicing regulatory protein; KH-RNA bindin	7e-07
2hh2_A	107	KH-type splicing regulatory protein; KH-RNA bindin	1e-16
2hh2_A	107	KH-type splicing regulatory protein; KH-RNA bindin	5e-12
2hh2_A	107	KH-type splicing regulatory protein; KH-RNA bindin	4e-05
1we8_A	104	Tudor and KH domain containing protein; structural	3e-15
1we8_A	104	Tudor and KH domain containing protein; structural	6e-12
1we8_A	104	Tudor and KH domain containing protein; structural	2e-06
1x4n_A	92	FAR upstream element binding protein 1; KH domain,	1e-14
1x4n_A	92	FAR upstream element binding protein 1; KH domain,	2e-14
1x4n_A	92	FAR upstream element binding protein 1; KH domain,	3e-07
2cte_A	94	Vigilin; K homology type I domain, RNA-binding, ce	4e-10
2cte_A	94	Vigilin; K homology type I domain, RNA-binding, ce	4e-07
2cte_A	94	Vigilin; K homology type I domain, RNA-binding, ce	2e-05
2ctl_A	97	Vigilin; K homology type I domain, RNA-binding, ce	2e-09
2ctl_A	97	Vigilin; K homology type I domain, RNA-binding, ce	4e-05
2dgr_A	83	Ring finger and KH domain-containing protein 1; st	2e-09
2dgr_A	83	Ring finger and KH domain-containing protein 1; st	1e-06
2ctk_A	104	Vigilin; K homology type I domain, RNA-binding, ce	8e-09
2ctk_A	104	Vigilin; K homology type I domain, RNA-binding, ce	7e-05
1vig_A	71	Vigilin; RNA-binding protein, ribonucleoprotein; N	4e-08
1vig_A	71	Vigilin; RNA-binding protein, ribonucleoprotein; N	2e-05
2e3u_A	219	PH-DIM2P, hypothetical protein PH1566; PRE-ribosom	5e-08
2qnd_A	144	FMR1 protein; KH domain, eukaryotic KH domains, ta	2e-07
2qnd_A	144	FMR1 protein; KH domain, eukaryotic KH domains, ta	2e-04
1vt4_I	1221	APAF-1 related killer DARK; drosophila apoptosome,	2e-07
1vt4_I	1221	APAF-1 related killer DARK; drosophila apoptosome,	3e-06
2ctm_A	95	Vigilin; K homology type I domain, RNA-binding, ce	4e-07
2ctm_A	95	Vigilin; K homology type I domain, RNA-binding, ce	1e-04
1tua_A	191	Hypothetical protein APE0754; structural genomics,	2e-06
2ctj_A	95	Vigilin; K homology type I domain, RNA-binding, ce	5e-05
3n89_A	376	Defective in GERM LINE development protein 3, ISO;	7e-05
3u1k_A	630	Polyribonucleotide nucleotidyltransferase 1, MITO;	9e-04

>2jzx_A Poly(RC)-binding protein 2; PCBP2, KH domains, RNA binding, DNA-binding, nucleus, phosph ribonucleoprotein, RNA-binding, RNA binding protein; NMR {Homo sapiens} Length = 160

 Score =  142 bits (359), Expect = 6e-41
 Identities = 71/185 (38%), Positives = 110/185 (59%), Gaps = 27/185 (14%)

Query: 11  EDTLITMRCLFHSSVNVNEISCLIGPGGCIVRRLRKESGAKISITDGACPDRIVTVSGSV 70
           ++  +T+R L H      E+  +IG  G  V+++R+ESGA+I+I++G CP+RI+T++G  
Sbjct: 1   KNVTLTIRLLMHGK----EVGSIIGKKGESVKKMREESGARINISEGNCPERIITLAGPT 56

Query: 71  DNSSTSSVETGYPGHTLWVTSVDNVCTAYNFMCRSLEDYHINR-NRMENCSPQPLQLKLV 129
           +                       +  A+  +   LE+   +        S  P+ L+LV
Sbjct: 57  NA----------------------IFKAFAMIIDKLEEDISSSMTNSTAASRPPVTLRLV 94

Query: 130 IPATHCGSLIGKGGCKIKDIRDLSGANVQVASDMLPMSTERIVTVHGNPDTISQAIYQIC 189
           +PA+ CGSLIGKGGCKIK+IR+ +GA VQVA DMLP STER +T+ G P +I + + QIC
Sbjct: 95  VPASQCGSLIGKGGCKIKEIRESTGAQVQVAGDMLPNSTERAITIAGIPQSIIECVKQIC 154

Query: 190 LVLIE 194
           +V++E
Sbjct: 155 VVMLE 159

>2jzx_A Poly(RC)-binding protein 2; PCBP2, KH domains, RNA binding, DNA-binding, nucleus, phosph ribonucleoprotein, RNA-binding, RNA binding protein; NMR {Homo sapiens} Length = 160

 Score = 69.0 bits (169), Expect = 3e-14
 Identities = 23/75 (30%), Positives = 38/75 (50%), Gaps = 3/75 (4%)

Query: 121 PQPLQLKLVIPATHCGSLIGKGGCKIKDIRDLSGANVQVASDMLPMSTERIVTVHGNPDT 180
              L ++L++     GS+IGK G  +K +R+ SGA + ++        ERI+T+ G  + 
Sbjct: 2   NVTLTIRLLMHGKEVGSIIGKKGESVKKMREESGARINISE---GNCPERIITLAGPTNA 58

Query: 181 ISQAIYQICLVLIEC 195
           I +A   I   L E 
Sbjct: 59  IFKAFAMIIDKLEED 73

>2jzx_A Poly(RC)-binding protein 2; PCBP2, KH domains, RNA binding, DNA-binding, nucleus, phosph ribonucleoprotein, RNA-binding, RNA binding protein; NMR {Homo sapiens} Length = 160

 Score = 55.2 bits (133), Expect = 2e-09
 Identities = 17/79 (21%), Positives = 34/79 (43%), Gaps = 2/79 (2%)

Query: 278 SGGKDTGDDFVETEIVLTDDIAGCVIGKAGSRLLEIRQISGAQINI--HTGTESHKKMFH 335
           +         V   +V+     G +IGK G ++ EIR+ +GAQ+ +       S ++   
Sbjct: 79  TNSTAASRPPVTLRLVVPASQCGSLIGKGGCKIKEIRESTGAQVQVAGDMLPNSTERAIT 138

Query: 336 IQGCQEAVSLAQYLINMCI 354
           I G  +++      I + +
Sbjct: 139 IAGIPQSIIECVKQICVVM 157

>2jzx_A Poly(RC)-binding protein 2; PCBP2, KH domains, RNA binding, DNA-binding, nucleus, phosph ribonucleoprotein, RNA-binding, RNA binding protein; NMR {Homo sapiens} Length = 160

 Score = 47.1 bits (112), Expect = 1e-06
 Identities = 25/105 (23%), Positives = 48/105 (45%), Gaps = 3/105 (2%)

Query: 288 VETEIVLTDDIAGCVIGKAGSRLLEIRQISGAQINIHTGTESHKKMFHIQGCQEAVSLAQ 347
           +   +++     G +IGK G  + ++R+ SGA+INI  G    +++  + G   A+  A 
Sbjct: 5   LTIRLLMHGKEVGSIIGKKGESVKKMREESGARINISEG-NCPERIITLAGPTNAIFKAF 63

Query: 348 YLINMCIELQKNNTTNTSDNPEPADLDAAISAFMTASVNSSLIEK 392
            +I   +E   +++   S       +   +   + AS   SLI K
Sbjct: 64  AMIIDKLEEDISSSMTNSTAASRPPVTLRL--VVPASQCGSLIGK 106

>2anr_A Neuro-oncological ventral antigen 1; protein-RNA complex, KH domain, hairpin, RNA-binding protein complex; HET: 5BU; 1.94A {Homo sapiens} PDB: 2ann_A* Length = 178

 Score =  125 bits (316), Expect = 2e-34
 Identities = 43/196 (21%), Positives = 79/196 (40%), Gaps = 42/196 (21%)

Query: 15  ITMRCLFHSSVNVNEISCLIGPGGCIVRRLRKESGAKISITDGA-----CPDRIVTVSGS 69
             ++ L  S         +IG GG  + +L+KE+GA I ++          +R+  + G+
Sbjct: 6   YFLKVLIPSY----AAGSIIGKGGQTIVQLQKETGATIKLSKSKDFYPGTTERVCLIQGT 61

Query: 70  VDNSSTSSVETGYPGHTLWVTSVDNVCTAYNFMCRSLEDYHINRNRMENCSPQP------ 123
           ++                       +   + F+   + +   N  + E  S         
Sbjct: 62  IEA----------------------LNAVHGFIAEKIREMPQNVAKTEPVSILQPQTTVN 99

Query: 124 ----LQLKLVIPATHCGSLIGKGGCKIKDIRDLSGANVQVASD-MLPMSTERIVTVHGNP 178
                Q+K+++P +  G +IGKGG  +K I + SGA VQ++          R+VTV G P
Sbjct: 100 PDRANQVKIIVPNSTAGLIIGKGGATVKAIMEQSGAWVQLSQKPDGINLQNRVVTVSGEP 159

Query: 179 DTISQAIYQICLVLIE 194
           +   +A+  I   + E
Sbjct: 160 EQNRKAVELIIQKIQE 175

>2anr_A Neuro-oncological ventral antigen 1; protein-RNA complex, KH domain, hairpin, RNA-binding protein complex; HET: 5BU; 1.94A {Homo sapiens} PDB: 2ann_A* Length = 178

 Score = 74.9 bits (184), Expect = 4e-16
 Identities = 25/98 (25%), Positives = 44/98 (44%), Gaps = 2/98 (2%)

Query: 121 PQPLQLKLVIPATHCGSLIGKGGCKIKDIRDLSGANVQV--ASDMLPMSTERIVTVHGNP 178
                LK++IP+   GS+IGKGG  I  ++  +GA +++  + D  P +TER+  + G  
Sbjct: 3   GSQYFLKVLIPSYAAGSIIGKGGQTIVQLQKETGATIKLSKSKDFYPGTTERVCLIQGTI 62

Query: 179 DTISQAIYQICLVLIECTLQVVKGAVIPYEPKTMNAGP 216
           + ++     I   + E    V K   +          P
Sbjct: 63  EALNAVHGFIAEKIREMPQNVAKTEPVSILQPQTTVNP 100

>2anr_A Neuro-oncological ventral antigen 1; protein-RNA complex, KH domain, hairpin, RNA-binding protein complex; HET: 5BU; 1.94A {Homo sapiens} PDB: 2ann_A* Length = 178

 Score = 59.5 bits (144), Expect = 9e-11
 Identities = 20/87 (22%), Positives = 37/87 (42%), Gaps = 3/87 (3%)

Query: 272 SGSRVKSGGKDTGDDFVETEIVLTDDIAGCVIGKAGSRLLEIRQISGAQINI---HTGTE 328
             S ++       D   + +I++ +  AG +IGK G+ +  I + SGA + +     G  
Sbjct: 88  PVSILQPQTTVNPDRANQVKIIVPNSTAGLIIGKGGATVKAIMEQSGAWVQLSQKPDGIN 147

Query: 329 SHKKMFHIQGCQEAVSLAQYLINMCIE 355
              ++  + G  E    A  LI   I+
Sbjct: 148 LQNRVVTVSGEPEQNRKAVELIIQKIQ 174

>2anr_A Neuro-oncological ventral antigen 1; protein-RNA complex, KH domain, hairpin, RNA-binding protein complex; HET: 5BU; 1.94A {Homo sapiens} PDB: 2ann_A* Length = 178

 Score = 47.2 bits (112), Expect = 2e-06
 Identities = 18/93 (19%), Positives = 38/93 (40%), Gaps = 4/93 (4%)

Query: 288 VETEIVLTDDIAGCVIGKAGSRLLEIRQISGAQINIHTGTE----SHKKMFHIQGCQEAV 343
              ++++    AG +IGK G  ++++++ +GA I +    +    + +++  IQG  EA+
Sbjct: 6   YFLKVLIPSYAAGSIIGKGGQTIVQLQKETGATIKLSKSKDFYPGTTERVCLIQGTIEAL 65

Query: 344 SLAQYLINMCIELQKNNTTNTSDNPEPADLDAA 376
           +     I   I     N   T            
Sbjct: 66  NAVHGFIAEKIREMPQNVAKTEPVSILQPQTTV 98

>3krm_A Insulin-like growth factor 2 mRNA-binding protein 1; KH domain, cell projection, cytoplasm, nucleus, phosphoprotein, translation regulation; 2.75A {Homo sapiens} Length = 163

 Score =  122 bits (308), Expect = 2e-33
 Identities = 35/185 (18%), Positives = 69/185 (37%), Gaps = 34/185 (18%)

Query: 15  ITMRCLFHSSVNVNEISCLIGPGGCIVRRLRKESGAKISITDGACP---DRIVTVSGSVD 71
             ++      +    +  +IG  G  +++L + + A I I     P    R+V ++G  +
Sbjct: 3   EMVQVF----IPAQAVGAIIGKKGQHIKQLSRFASASIKIAPPETPDSKVRMVIITGPPE 58

Query: 72  NSSTSSVETGYPGHTLWVTSVDNVCTAYNFMCRSLEDYHINRNRMENCSPQPLQLKLVIP 131
                                     A   +   L++     N         L+  + +P
Sbjct: 59  A----------------------QFKAQGRIYGKLKE----ENFFGPKEEVKLETHIRVP 92

Query: 132 ATHCGSLIGKGGCKIKDIRDLSGANVQVASDMLPMST-ERIVTVHGNPDTISQAIYQICL 190
           A+  G +IGKGG  + ++++L+ A V V  D  P    + IV + G+      A  +I  
Sbjct: 93  ASAAGRVIGKGGKTVNELQNLTAAEVVVPRDQTPDENDQVIVKIIGHFYASQMAQRKIRD 152

Query: 191 VLIEC 195
           +L + 
Sbjct: 153 ILAQV 157

>3krm_A Insulin-like growth factor 2 mRNA-binding protein 1; KH domain, cell projection, cytoplasm, nucleus, phosphoprotein, translation regulation; 2.75A {Homo sapiens} Length = 163

 Score = 75.2 bits (185), Expect = 3e-16
 Identities = 22/73 (30%), Positives = 39/73 (53%)

Query: 122 QPLQLKLVIPATHCGSLIGKGGCKIKDIRDLSGANVQVASDMLPMSTERIVTVHGNPDTI 181
           +   +++ IPA   G++IGK G  IK +   + A++++A    P S  R+V + G P+  
Sbjct: 1   EQEMVQVFIPAQAVGAIIGKKGQHIKQLSRFASASIKIAPPETPDSKVRMVIITGPPEAQ 60

Query: 182 SQAIYQICLVLIE 194
            +A  +I   L E
Sbjct: 61  FKAQGRIYGKLKE 73

>3krm_A Insulin-like growth factor 2 mRNA-binding protein 1; KH domain, cell projection, cytoplasm, nucleus, phosphoprotein, translation regulation; 2.75A {Homo sapiens} Length = 163

 Score = 56.7 bits (137), Expect = 7e-10
 Identities = 20/86 (23%), Positives = 38/86 (44%), Gaps = 3/86 (3%)

Query: 277 KSGGKDTGDDFVETEIVLTDDIAGCVIGKAGSRLLEIRQISGAQINIHTGT---ESHKKM 333
           ++      +  +ET I +    AG VIGK G  + E++ ++ A++ +       E+ + +
Sbjct: 74  ENFFGPKEEVKLETHIRVPASAAGRVIGKGGKTVNELQNLTAAEVVVPRDQTPDENDQVI 133

Query: 334 FHIQGCQEAVSLAQYLINMCIELQKN 359
             I G   A  +AQ  I   +   K 
Sbjct: 134 VKIIGHFYASQMAQRKIRDILAQVKQ 159

>3krm_A Insulin-like growth factor 2 mRNA-binding protein 1; KH domain, cell projection, cytoplasm, nucleus, phosphoprotein, translation regulation; 2.75A {Homo sapiens} Length = 163

 Score = 45.1 bits (107), Expect = 7e-06
 Identities = 17/82 (20%), Positives = 31/82 (37%), Gaps = 2/82 (2%)

Query: 288 VETEIVLTDDIAGCVIGKAGSRLLEIRQISGAQINIH--TGTESHKKMFHIQGCQEAVSL 345
              ++ +     G +IGK G  + ++ + + A I I      +S  +M  I G  EA   
Sbjct: 3   EMVQVFIPAQAVGAIIGKKGQHIKQLSRFASASIKIAPPETPDSKVRMVIITGPPEAQFK 62

Query: 346 AQYLINMCIELQKNNTTNTSDN 367
           AQ  I   ++ +          
Sbjct: 63  AQGRIYGKLKEENFFGPKEEVK 84

>2jvz_A KH type-splicing, FAR upstream element-binding protein 2; RNA binding protein, KH domain, KSRP, posttranscriptional regulation, mRNA decay; NMR {Homo sapiens} Length = 164

 Score =  114 bits (288), Expect = 1e-30
 Identities = 31/170 (18%), Positives = 58/170 (34%), Gaps = 29/170 (17%)

Query: 25  VNVNEISCLIGPGGCIVRRLRKESGAKISIT----DGACPDRIVTVSGSVDNSSTSSVET 80
           +   +   +IG GG  +++L++ +G K+ +          D+ + + G            
Sbjct: 8   IPAGKAGLVIGKGGETIKQLQERAGVKMILIQDGSQNTNVDKPLRIIGDPYK-------- 59

Query: 81  GYPGHTLWVTSVDNVCTAYNFMCRSLEDYHINRNRMEN--CSPQPLQLKLVIPATHCGSL 138
                         V  A   +   L +         N   S     + + +P    G +
Sbjct: 60  --------------VQQACEMVMDILRERDQGGFGDRNEYGSRIGGGIDVPVPRHSVGVV 105

Query: 139 IGKGGCKIKDIRDLSGANVQVASDMLPMSTERIVTVHGNPDTISQAIYQI 188
           IG+ G  IK I++ +G  +Q          E+I  + G PD    A   I
Sbjct: 106 IGRSGEMIKKIQNDAGVRIQF-KQDDGTGPEKIAHIMGPPDRCEHAARII 154

>2jvz_A KH type-splicing, FAR upstream element-binding protein 2; RNA binding protein, KH domain, KSRP, posttranscriptional regulation, mRNA decay; NMR {Homo sapiens} Length = 164

 Score = 69.0 bits (169), Expect = 3e-14
 Identities = 18/68 (26%), Positives = 37/68 (54%), Gaps = 1/68 (1%)

Query: 126 LKLVIPATHCGSLIGKGGCKIKDIRDLSGANVQVASDM-LPMSTERIVTVHGNPDTISQA 184
            +++IPA   G +IGKGG  IK +++ +G  + +  D     + ++ + + G+P  + QA
Sbjct: 4   QEIMIPAGKAGLVIGKGGETIKQLQERAGVKMILIQDGSQNTNVDKPLRIIGDPYKVQQA 63

Query: 185 IYQICLVL 192
              +  +L
Sbjct: 64  CEMVMDIL 71

>2jvz_A KH type-splicing, FAR upstream element-binding protein 2; RNA binding protein, KH domain, KSRP, posttranscriptional regulation, mRNA decay; NMR {Homo sapiens} Length = 164

 Score = 55.2 bits (133), Expect = 3e-09
 Identities = 16/90 (17%), Positives = 33/90 (36%), Gaps = 1/90 (1%)

Query: 267 ALAALSGSRVKSGGKDTGDDFVETEIVLTDDIAGCVIGKAGSRLLEIRQISGAQINIH-T 325
            L            +         ++ +     G VIG++G  + +I+  +G +I     
Sbjct: 70  ILRERDQGGFGDRNEYGSRIGGGIDVPVPRHSVGVVIGRSGEMIKKIQNDAGVRIQFKQD 129

Query: 326 GTESHKKMFHIQGCQEAVSLAQYLINMCIE 355
                +K+ HI G  +    A  +IN  ++
Sbjct: 130 DGTGPEKIAHIMGPPDRCEHAARIINDLLQ 159

>2jvz_A KH type-splicing, FAR upstream element-binding protein 2; RNA binding protein, KH domain, KSRP, posttranscriptional regulation, mRNA decay; NMR {Homo sapiens} Length = 164

 Score = 44.8 bits (106), Expect = 8e-06
 Identities = 15/85 (17%), Positives = 32/85 (37%), Gaps = 3/85 (3%)

Query: 291 EIVLTDDIAGCVIGKAGSRLLEIRQISGAQINIHTGTE---SHKKMFHIQGCQEAVSLAQ 347
           EI++    AG VIGK G  + ++++ +G ++ +        +  K   I G    V  A 
Sbjct: 5   EIMIPAGKAGLVIGKGGETIKQLQERAGVKMILIQDGSQNTNVDKPLRIIGDPYKVQQAC 64

Query: 348 YLINMCIELQKNNTTNTSDNPEPAD 372
            ++   +  +        +      
Sbjct: 65  EMVMDILRERDQGGFGDRNEYGSRI 89

>1j4w_A FUSE binding protein; single-stranded DNA binding protein; HET: DNA; NMR {Homo sapiens} SCOP: d.51.1.1 d.51.1.1 Length = 174

 Score =  114 bits (287), Expect = 2e-30
 Identities = 35/179 (19%), Positives = 66/179 (36%), Gaps = 18/179 (10%)

Query: 16  TMRCLFHSSVNVNEISCLIGPGGCIVRRLRKESGAKISIT--DGACPDRIVTVSGSVDNS 73
            +            +  +IG  G ++++++ ++G +I     DG  P+RI  ++G  D +
Sbjct: 4   MIDVPIPRF----AVGIVIGRNGEMIKKIQNDAGVRIQFKPDDGTTPERIAQITGPPDRA 59

Query: 74  STSSVETGYPGHTLWVTSVDNVCTAYNFMCRSLEDYHINRNRMENCSPQP--LQLKLVIP 131
                        +    + +V                      N  P     +   ++P
Sbjct: 60  Q--------HAAEIITDLLRSVQAGNPGGPGPGGRGRGRGQGNWNMGPPGGLQEFNFIVP 111

Query: 132 ATHCGSLIGKGGCKIKDIRDLSGANVQVASDMLPMS--TERIVTVHGNPDTISQAIYQI 188
               G +IGKGG  IK I   SGA +++  +  P +    ++ T+ G P  I  A   I
Sbjct: 112 TGKTGLIIGKGGETIKSISQQSGARIELQRNPPPNADPNMKLFTIRGTPQQIDYARQLI 170

>1j4w_A FUSE binding protein; single-stranded DNA binding protein; HET: DNA; NMR {Homo sapiens} SCOP: d.51.1.1 d.51.1.1 Length = 174

 Score = 76.1 bits (187), Expect = 2e-16
 Identities = 23/92 (25%), Positives = 35/92 (38%), Gaps = 1/92 (1%)

Query: 125 QLKLVIPATHCGSLIGKGGCKIKDIRDLSGANVQVASDMLPMSTERIVTVHGNPDTISQA 184
            + + IP    G +IG+ G  IK I++ +G  +Q   D    + ERI  + G PD    A
Sbjct: 4   MIDVPIPRFAVGIVIGRNGEMIKKIQNDAGVRIQFKPDD-GTTPERIAQITGPPDRAQHA 62

Query: 185 IYQICLVLIECTLQVVKGAVIPYEPKTMNAGP 216
              I  +L         G       +    G 
Sbjct: 63  AEIITDLLRSVQAGNPGGPGPGGRGRGRGQGN 94

>1j4w_A FUSE binding protein; single-stranded DNA binding protein; HET: DNA; NMR {Homo sapiens} SCOP: d.51.1.1 d.51.1.1 Length = 174

 Score = 57.6 bits (139), Expect = 5e-10
 Identities = 21/87 (24%), Positives = 35/87 (40%), Gaps = 4/87 (4%)

Query: 272 SGSRVKSGGKDTGDDFVETEIVLTDDIAGCVIGKAGSRLLEIRQISGAQINIHT----GT 327
            G    +          E   ++     G +IGK G  +  I Q SGA+I +        
Sbjct: 88  RGRGQGNWNMGPPGGLQEFNFIVPTGKTGLIIGKGGETIKSISQQSGARIELQRNPPPNA 147

Query: 328 ESHKKMFHIQGCQEAVSLAQYLINMCI 354
           + + K+F I+G  + +  A+ LI   I
Sbjct: 148 DPNMKLFTIRGTPQQIDYARQLIEEKI 174

>1j4w_A FUSE binding protein; single-stranded DNA binding protein; HET: DNA; NMR {Homo sapiens} SCOP: d.51.1.1 d.51.1.1 Length = 174

 Score = 46.0 bits (109), Expect = 3e-06
 Identities = 23/141 (16%), Positives = 45/141 (31%), Gaps = 13/141 (9%)

Query: 291 EIVLTDDIAGCVIGKAGSRLLEIRQISGAQINIHTGTE-SHKKMFHIQGCQEAVSLAQYL 349
           ++ +     G VIG+ G  + +I+  +G +I        + +++  I G  +    A  +
Sbjct: 6   DVPIPRFAVGIVIGRNGEMIKKIQNDAGVRIQFKPDDGTTPERIAQITGPPDRAQHAAEI 65

Query: 350 INMCIE--LQKNNTTNTSDNPEPADLDAAISAFMTASVNSSLIEKPTPHPGSMVTLGGLS 407
           I   +      N                  +      +       PT   G ++  GG  
Sbjct: 66  ITDLLRSVQAGNPGGPGPGGRGRGRGQGNWNMGPPGGLQEFNFIVPTGKTGLIIGKGG-- 123

Query: 408 ELLANIAASNVKSTVQTTGAY 428
                     +KS  Q +GA 
Sbjct: 124 --------ETIKSISQQSGAR 136

>1dtj_A RNA-binding neurooncological ventral antigen 2; KH domain, alpha-beta fold RNA-binding motif, immune system; 2.00A {Homo sapiens} SCOP: d.51.1.1 PDB: 1dt4_A Length = 76

 Score = 78.1 bits (193), Expect = 3e-18
 Identities = 20/66 (30%), Positives = 39/66 (59%), Gaps = 2/66 (3%)

Query: 125 QLKLVIPATHCGSLIGKGGCKIKDIRDLSGANVQVA--SDMLPMSTERIVTVHGNPDTIS 182
            +++ +P    G+++GKGG  + + ++L+GA +Q++   + LP +  R VT+ G+P    
Sbjct: 4   LVEMAVPENLVGAILGKGGKTLVEYQELTGARIQISKKGEFLPGTRNRRVTITGSPAATQ 63

Query: 183 QAIYQI 188
            A Y I
Sbjct: 64  AAQYLI 69

>1dtj_A RNA-binding neurooncological ventral antigen 2; KH domain, alpha-beta fold RNA-binding motif, immune system; 2.00A {Homo sapiens} SCOP: d.51.1.1 PDB: 1dt4_A Length = 76

 Score = 66.5 bits (163), Expect = 3e-14
 Identities = 20/70 (28%), Positives = 37/70 (52%), Gaps = 4/70 (5%)

Query: 290 TEIVLTDDIAGCVIGKAGSRLLEIRQISGAQINIHTGTE----SHKKMFHIQGCQEAVSL 345
            E+ + +++ G ++GK G  L+E ++++GA+I I    E    +  +   I G   A   
Sbjct: 5   VEMAVPENLVGAILGKGGKTLVEYQELTGARIQISKKGEFLPGTRNRRVTITGSPAATQA 64

Query: 346 AQYLINMCIE 355
           AQYLI+  + 
Sbjct: 65  AQYLISQRVT 74

>1dtj_A RNA-binding neurooncological ventral antigen 2; KH domain, alpha-beta fold RNA-binding motif, immune system; 2.00A {Homo sapiens} SCOP: d.51.1.1 PDB: 1dt4_A Length = 76

 Score = 45.3 bits (108), Expect = 9e-07
 Identities = 12/48 (25%), Positives = 24/48 (50%), Gaps = 5/48 (10%)

Query: 30 ISCLIGPGGCIVRRLRKESGAKISITDGA-----CPDRIVTVSGSVDN 72
          +  ++G GG  +   ++ +GA+I I+          +R VT++GS   
Sbjct: 14 VGAILGKGGKTLVEYQELTGARIQISKKGEFLPGTRNRRVTITGSPAA 61

>1ec6_A RNA-binding protein NOVA-2; KH domain, alpha-beta fold, RNA-binding motif, protein/RNA structure, RNA binding protein/RNA complex; 2.40A {Homo sapiens} SCOP: d.51.1.1 Length = 87

 Score = 77.8 bits (192), Expect = 4e-18
 Identities = 20/66 (30%), Positives = 39/66 (59%), Gaps = 2/66 (3%)

Query: 125 QLKLVIPATHCGSLIGKGGCKIKDIRDLSGANVQVA--SDMLPMSTERIVTVHGNPDTIS 182
            +++ +P    G+++GKGG  + + ++L+GA +Q++   + LP +  R VT+ G+P    
Sbjct: 4   LVEIAVPENLVGAILGKGGKTLVEYQELTGARIQISKKGEFLPGTRNRRVTITGSPAATQ 63

Query: 183 QAIYQI 188
            A Y I
Sbjct: 64  AAQYLI 69

>1ec6_A RNA-binding protein NOVA-2; KH domain, alpha-beta fold, RNA-binding motif, protein/RNA structure, RNA binding protein/RNA complex; 2.40A {Homo sapiens} SCOP: d.51.1.1 Length = 87

 Score = 67.7 bits (166), Expect = 1e-14
 Identities = 21/75 (28%), Positives = 39/75 (52%), Gaps = 4/75 (5%)

Query: 290 TEIVLTDDIAGCVIGKAGSRLLEIRQISGAQINIHTGTE----SHKKMFHIQGCQEAVSL 345
            EI + +++ G ++GK G  L+E ++++GA+I I    E    +  +   I G   A   
Sbjct: 5   VEIAVPENLVGAILGKGGKTLVEYQELTGARIQISKKGEFLPGTRNRRVTITGSPAATQA 64

Query: 346 AQYLINMCIELQKNN 360
           AQYLI+  +  ++  
Sbjct: 65  AQYLISQRVTYEQGV 79

>1ec6_A RNA-binding protein NOVA-2; KH domain, alpha-beta fold, RNA-binding motif, protein/RNA structure, RNA binding protein/RNA complex; 2.40A {Homo sapiens} SCOP: d.51.1.1 Length = 87

 Score = 46.2 bits (110), Expect = 6e-07
 Identities = 12/48 (25%), Positives = 24/48 (50%), Gaps = 5/48 (10%)

Query: 30 ISCLIGPGGCIVRRLRKESGAKISITDGA-----CPDRIVTVSGSVDN 72
          +  ++G GG  +   ++ +GA+I I+          +R VT++GS   
Sbjct: 14 VGAILGKGGKTLVEYQELTGARIQISKKGEFLPGTRNRRVTITGSPAA 61

>1zzk_A Heterogeneous nuclear ribonucleoprotein K; KH domian, alpha-beta fold, DNA binding protein; 0.95A {Homo sapiens} SCOP: d.51.1.1 PDB: 1zzj_A 1zzi_A Length = 82

 Score = 76.2 bits (188), Expect = 1e-17
 Identities = 26/75 (34%), Positives = 42/75 (56%), Gaps = 1/75 (1%)

Query: 120 SPQPLQLKLVIPATHCGSLIGKGGCKIKDIRDLSGANVQVASDMLPMSTERIVTVHGNPD 179
               +  ++ IP    GS+IGKGG +IK IR  SGA++++  + L  S +RI+T+ G  D
Sbjct: 3   MGPIITTQVTIPKDLAGSIIGKGGQRIKQIRHESGASIKI-DEPLEGSEDRIITITGTQD 61

Query: 180 TISQAIYQICLVLIE 194
            I  A Y +   + +
Sbjct: 62  QIQNAQYLLQNSVKQ 76

>1zzk_A Heterogeneous nuclear ribonucleoprotein K; KH domian, alpha-beta fold, DNA binding protein; 0.95A {Homo sapiens} SCOP: d.51.1.1 PDB: 1zzj_A 1zzi_A Length = 82

 Score = 66.2 bits (162), Expect = 4e-14
 Identities = 24/69 (34%), Positives = 39/69 (56%), Gaps = 1/69 (1%)

Query: 288 VETEIVLTDDIAGCVIGKAGSRLLEIRQISGAQINIH-TGTESHKKMFHIQGCQEAVSLA 346
           + T++ +  D+AG +IGK G R+ +IR  SGA I I      S  ++  I G Q+ +  A
Sbjct: 7   ITTQVTIPKDLAGSIIGKGGQRIKQIRHESGASIKIDEPLEGSEDRIITITGTQDQIQNA 66

Query: 347 QYLINMCIE 355
           QYL+   ++
Sbjct: 67  QYLLQNSVK 75

>1zzk_A Heterogeneous nuclear ribonucleoprotein K; KH domian, alpha-beta fold, DNA binding protein; 0.95A {Homo sapiens} SCOP: d.51.1.1 PDB: 1zzj_A 1zzi_A Length = 82

 Score = 47.7 bits (114), Expect = 1e-07
 Identities = 17/51 (33%), Positives = 30/51 (58%), Gaps = 2/51 (3%)

Query: 24 SVNVNEISCLIGPGGCIVRRLRKESGAKISITD--GACPDRIVTVSGSVDN 72
          ++  +    +IG GG  ++++R ESGA I I +      DRI+T++G+ D 
Sbjct: 12 TIPKDLAGSIIGKGGQRIKQIRHESGASIKIDEPLEGSEDRIITITGTQDQ 62

>2p2r_A Poly(RC)-binding protein 2; protein-DNA complex, RNA and DNA binding protein/DNA complex; 1.60A {Homo sapiens} Length = 76

 Score = 75.4 bits (186), Expect = 3e-17
 Identities = 27/68 (39%), Positives = 41/68 (60%), Gaps = 1/68 (1%)

Query: 121 PQPLQLKLVIPATHCGSLIGKGGCKIKDIRDLSGANVQVASDMLPMSTERIVTVHGNPDT 180
            Q    +L IP    G +IG+ G KI +IR +SGA +++A+  +  ST+R VT+ G+  +
Sbjct: 2   AQTTSHELTIPNDLIGCIIGRQGAKINEIRQMSGAQIKIANP-VEGSTDRQVTITGSAAS 60

Query: 181 ISQAIYQI 188
           IS A Y I
Sbjct: 61  ISLAQYLI 68

>2p2r_A Poly(RC)-binding protein 2; protein-DNA complex, RNA and DNA binding protein/DNA complex; 1.60A {Homo sapiens} Length = 76

 Score = 65.8 bits (161), Expect = 5e-14
 Identities = 29/69 (42%), Positives = 44/69 (63%), Gaps = 1/69 (1%)

Query: 288 VETEIVLTDDIAGCVIGKAGSRLLEIRQISGAQINIHTGTE-SHKKMFHIQGCQEAVSLA 346
              E+ + +D+ GC+IG+ G+++ EIRQ+SGAQI I    E S  +   I G   ++SLA
Sbjct: 5   TSHELTIPNDLIGCIIGRQGAKINEIRQMSGAQIKIANPVEGSTDRQVTITGSAASISLA 64

Query: 347 QYLINMCIE 355
           QYLIN+ + 
Sbjct: 65  QYLINVRLS 73

>2p2r_A Poly(RC)-binding protein 2; protein-DNA complex, RNA and DNA binding protein/DNA complex; 1.60A {Homo sapiens} Length = 76

 Score = 46.5 bits (111), Expect = 4e-07
 Identities = 17/45 (37%), Positives = 26/45 (57%), Gaps = 2/45 (4%)

Query: 30 ISCLIGPGGCIVRRLRKESGAKISITD--GACPDRIVTVSGSVDN 72
          I C+IG  G  +  +R+ SGA+I I +      DR VT++GS  +
Sbjct: 16 IGCIIGRQGAKINEIRQMSGAQIKIANPVEGSTDRQVTITGSAAS 60

>2opv_A KHSRP protein; KH domain, RNA binding protein, KSRP; NMR {Homo sapiens} Length = 85

 Score = 75.1 bits (185), Expect = 3e-17
 Identities = 20/78 (25%), Positives = 39/78 (50%), Gaps = 1/78 (1%)

Query: 118 NCSPQPLQLKLVIPATHCGSLIGKGGCKIKDIRDLSGANVQVASDM-LPMSTERIVTVHG 176
           N        +++IPA   G +IGKGG  IK +++ +G  + +  D     + ++ + + G
Sbjct: 8   NGGQNGTVQEIMIPAGKAGLVIGKGGETIKQLQERAGVKMILIQDGSQNTNVDKPLRIIG 67

Query: 177 NPDTISQAIYQICLVLIE 194
           +P  + QA   +  +L E
Sbjct: 68  DPYKVQQACEMVMDILRE 85

>2opv_A KHSRP protein; KH domain, RNA binding protein, KSRP; NMR {Homo sapiens} Length = 85

 Score = 60.1 bits (146), Expect = 7e-12
 Identities = 16/80 (20%), Positives = 34/80 (42%), Gaps = 3/80 (3%)

Query: 279 GGKDTGDDFVETEIVLTDDIAGCVIGKAGSRLLEIRQISGAQINI---HTGTESHKKMFH 335
              + G +    EI++    AG VIGK G  + ++++ +G ++ +    +   +  K   
Sbjct: 5   DNANGGQNGTVQEIMIPAGKAGLVIGKGGETIKQLQERAGVKMILIQDGSQNTNVDKPLR 64

Query: 336 IQGCQEAVSLAQYLINMCIE 355
           I G    V  A  ++   + 
Sbjct: 65  IIGDPYKVQQACEMVMDILR 84

>2opv_A KHSRP protein; KH domain, RNA binding protein, KSRP; NMR {Homo sapiens} Length = 85

 Score = 45.4 bits (108), Expect = 1e-06
 Identities = 9/53 (16%), Positives = 24/53 (45%), Gaps = 4/53 (7%)

Query: 24 SVNVNEISCLIGPGGCIVRRLRKESGAKISI----TDGACPDRIVTVSGSVDN 72
           +   +   +IG GG  +++L++ +G K+ +    +     D+ + + G    
Sbjct: 19 MIPAGKAGLVIGKGGETIKQLQERAGVKMILIQDGSQNTNVDKPLRIIGDPYK 71

>1x4m_A FAR upstream element binding protein 1; KH domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Mus musculus} SCOP: d.51.1.1 Length = 94

 Score = 75.5 bits (186), Expect = 3e-17
 Identities = 18/81 (22%), Positives = 39/81 (48%), Gaps = 1/81 (1%)

Query: 115 RMENCSPQPLQLKLVIPATHCGSLIGKGGCKIKDIRDLSGANVQVASD-MLPMSTERIVT 173
                 P     +++IPA+  G +IGKGG  IK +++ +G  + +  D       ++ + 
Sbjct: 6   SGHGDGPGNAVQEIMIPASKAGLVIGKGGETIKQLQERAGVKMVMIQDGPQNTGADKPLR 65

Query: 174 VHGNPDTISQAIYQICLVLIE 194
           + G+P  + QA   +  ++ +
Sbjct: 66  ITGDPYKVQQAKEMVLELIRD 86

>1x4m_A FAR upstream element binding protein 1; KH domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Mus musculus} SCOP: d.51.1.1 Length = 94

 Score = 60.5 bits (147), Expect = 6e-12
 Identities = 20/87 (22%), Positives = 35/87 (40%), Gaps = 3/87 (3%)

Query: 278 SGGKDTGDDFVETEIVLTDDIAGCVIGKAGSRLLEIRQISGAQINI---HTGTESHKKMF 334
           S G   G      EI++    AG VIGK G  + ++++ +G ++ +           K  
Sbjct: 5   SSGHGDGPGNAVQEIMIPASKAGLVIGKGGETIKQLQERAGVKMVMIQDGPQNTGADKPL 64

Query: 335 HIQGCQEAVSLAQYLINMCIELQKNNT 361
            I G    V  A+ ++   I  Q +  
Sbjct: 65  RITGDPYKVQQAKEMVLELIRDQGSGP 91

>1x4m_A FAR upstream element binding protein 1; KH domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Mus musculus} SCOP: d.51.1.1 Length = 94

 Score = 43.6 bits (103), Expect = 6e-06
 Identities = 9/49 (18%), Positives = 24/49 (48%), Gaps = 4/49 (8%)

Query: 28 NEISCLIGPGGCIVRRLRKESGAKISI----TDGACPDRIVTVSGSVDN 72
          ++   +IG GG  +++L++ +G K+ +          D+ + ++G    
Sbjct: 24 SKAGLVIGKGGETIKQLQERAGVKMVMIQDGPQNTGADKPLRITGDPYK 72

>1j5k_A Heterogeneous nuclear ribonucleoprotein K; single-stranded DNA binding protein, transcription factor, hnRNP K, CT element, C-MYC oncogene; NMR {Homo sapiens} SCOP: d.51.1.1 PDB: 1khm_A Length = 89

 Score = 75.1 bits (185), Expect = 5e-17
 Identities = 26/75 (34%), Positives = 42/75 (56%), Gaps = 1/75 (1%)

Query: 120 SPQPLQLKLVIPATHCGSLIGKGGCKIKDIRDLSGANVQVASDMLPMSTERIVTVHGNPD 179
               +  ++ IP    GS+IGKGG +IK IR  SGA++++  + L  S +RI+T+ G  D
Sbjct: 10  GGPIITTQVTIPKDLAGSIIGKGGQRIKQIRHESGASIKI-DEPLEGSEDRIITITGTQD 68

Query: 180 TISQAIYQICLVLIE 194
            I  A Y +   + +
Sbjct: 69  QIQNAQYLLQNSVKQ 83

>1j5k_A Heterogeneous nuclear ribonucleoprotein K; single-stranded DNA binding protein, transcription factor, hnRNP K, CT element, C-MYC oncogene; NMR {Homo sapiens} SCOP: d.51.1.1 PDB: 1khm_A Length = 89

 Score = 68.9 bits (169), Expect = 7e-15
 Identities = 27/79 (34%), Positives = 42/79 (53%), Gaps = 1/79 (1%)

Query: 278 SGGKDTGDDFVETEIVLTDDIAGCVIGKAGSRLLEIRQISGAQINIHTGTE-SHKKMFHI 336
               D G   + T++ +  D+AG +IGK G R+ +IR  SGA I I    E S  ++  I
Sbjct: 4   MSYGDLGGPIITTQVTIPKDLAGSIIGKGGQRIKQIRHESGASIKIDEPLEGSEDRIITI 63

Query: 337 QGCQEAVSLAQYLINMCIE 355
            G Q+ +  AQYL+   ++
Sbjct: 64  TGTQDQIQNAQYLLQNSVK 82

>1j5k_A Heterogeneous nuclear ribonucleoprotein K; single-stranded DNA binding protein, transcription factor, hnRNP K, CT element, C-MYC oncogene; NMR {Homo sapiens} SCOP: d.51.1.1 PDB: 1khm_A Length = 89

 Score = 48.1 bits (115), Expect = 1e-07
 Identities = 17/45 (37%), Positives = 27/45 (60%), Gaps = 2/45 (4%)

Query: 30 ISCLIGPGGCIVRRLRKESGAKISITD--GACPDRIVTVSGSVDN 72
             +IG GG  ++++R ESGA I I +      DRI+T++G+ D 
Sbjct: 25 AGSIIGKGGQRIKQIRHESGASIKIDEPLEGSEDRIITITGTQDQ 69

>1wvn_A Poly(RC)-binding protein 1; KH domain, RNA binding domain, RNA binding protein; 2.10A {Homo sapiens} SCOP: d.51.1.1 Length = 82

 Score = 74.6 bits (184), Expect = 5e-17
 Identities = 24/68 (35%), Positives = 38/68 (55%), Gaps = 1/68 (1%)

Query: 121 PQPLQLKLVIPATHCGSLIGKGGCKIKDIRDLSGANVQVASDMLPMSTERIVTVHGNPDT 180
                 +L IP    G +IG+ G  I +IR +SGA +++A+ +   S+ R VT+ G+  +
Sbjct: 3   GSQTTHELTIPNNLIGCIIGRQGANINEIRQMSGAQIKIANPV-EGSSGRQVTITGSAAS 61

Query: 181 ISQAIYQI 188
           IS A Y I
Sbjct: 62  ISLAQYLI 69

>1wvn_A Poly(RC)-binding protein 1; KH domain, RNA binding domain, RNA binding protein; 2.10A {Homo sapiens} SCOP: d.51.1.1 Length = 82

 Score = 67.7 bits (166), Expect = 1e-14
 Identities = 28/74 (37%), Positives = 43/74 (58%), Gaps = 1/74 (1%)

Query: 288 VETEIVLTDDIAGCVIGKAGSRLLEIRQISGAQINIH-TGTESHKKMFHIQGCQEAVSLA 346
              E+ + +++ GC+IG+ G+ + EIRQ+SGAQI I      S  +   I G   ++SLA
Sbjct: 6   TTHELTIPNNLIGCIIGRQGANINEIRQMSGAQIKIANPVEGSSGRQVTITGSAASISLA 65

Query: 347 QYLINMCIELQKNN 360
           QYLIN  +  +K  
Sbjct: 66  QYLINARLSSEKGM 79

>1wvn_A Poly(RC)-binding protein 1; KH domain, RNA binding domain, RNA binding protein; 2.10A {Homo sapiens} SCOP: d.51.1.1 Length = 82

 Score = 47.3 bits (113), Expect = 2e-07
 Identities = 16/45 (35%), Positives = 25/45 (55%), Gaps = 2/45 (4%)

Query: 30 ISCLIGPGGCIVRRLRKESGAKISITD--GACPDRIVTVSGSVDN 72
          I C+IG  G  +  +R+ SGA+I I +       R VT++GS  +
Sbjct: 17 IGCIIGRQGANINEIRQMSGAQIKIANPVEGSSGRQVTITGSAAS 61

>2axy_A Poly(RC)-binding protein 2; protein-DNA complex, DNA binding protein-DNA complex; 1.70A {Homo sapiens} SCOP: d.51.1.1 PDB: 2pqu_A 2py9_A 1ztg_A 3vke_A* Length = 73

 Score = 74.2 bits (183), Expect = 6e-17
 Identities = 24/73 (32%), Positives = 39/73 (53%), Gaps = 3/73 (4%)

Query: 122 QPLQLKLVIPATHCGSLIGKGGCKIKDIRDLSGANVQVASDMLPMSTERIVTVHGNPDTI 181
             L ++L++     GS+IGK G  +K +R+ SGA + ++    P   ERI+T+ G  + I
Sbjct: 3   VTLTIRLLMHGKEVGSIIGKKGESVKKMREESGARINISEGNCP---ERIITLAGPTNAI 59

Query: 182 SQAIYQICLVLIE 194
            +A   I   L E
Sbjct: 60  FKAFAMIIDKLEE 72

>2axy_A Poly(RC)-binding protein 2; protein-DNA complex, DNA binding protein-DNA complex; 1.70A {Homo sapiens} SCOP: d.51.1.1 PDB: 2pqu_A 2py9_A 1ztg_A 3vke_A* Length = 73

 Score = 70.0 bits (172), Expect = 2e-15
 Identities = 23/62 (37%), Positives = 42/62 (67%), Gaps = 4/62 (6%)

Query: 11 EDTLITMRCLFHSSVNVNEISCLIGPGGCIVRRLRKESGAKISITDGACPDRIVTVSGSV 70
          ++  +T+R L H      E+  +IG  G  V+++R+ESGA+I+I++G CP+RI+T++G  
Sbjct: 1  KNVTLTIRLLMHGK----EVGSIIGKKGESVKKMREESGARINISEGNCPERIITLAGPT 56

Query: 71 DN 72
          + 
Sbjct: 57 NA 58

>2axy_A Poly(RC)-binding protein 2; protein-DNA complex, DNA binding protein-DNA complex; 1.70A {Homo sapiens} SCOP: d.51.1.1 PDB: 2pqu_A 2py9_A 1ztg_A 3vke_A* Length = 73

 Score = 49.6 bits (119), Expect = 2e-08
 Identities = 18/71 (25%), Positives = 36/71 (50%), Gaps = 1/71 (1%)

Query: 285 DDFVETEIVLTDDIAGCVIGKAGSRLLEIRQISGAQINIHTGTESHKKMFHIQGCQEAVS 344
           +  +   +++     G +IGK G  + ++R+ SGA+INI  G    +++  + G   A+ 
Sbjct: 2   NVTLTIRLLMHGKEVGSIIGKKGESVKKMREESGARINISEGN-CPERIITLAGPTNAIF 60

Query: 345 LAQYLINMCIE 355
            A  +I   +E
Sbjct: 61  KAFAMIIDKLE 71

>2hh3_A KH-type splicing regulatory protein; KH-RNA binding domain, RNA binding protein; NMR {Homo sapiens} Length = 106

 Score = 74.8 bits (184), Expect = 8e-17
 Identities = 22/97 (22%), Positives = 34/97 (35%), Gaps = 1/97 (1%)

Query: 120 SPQPLQLKLVIPATHCGSLIGKGGCKIKDIRDLSGANVQVASDMLPMSTERIVTVHGNPD 179
           S     + + +P    G +IG+ G  IK I++ +G  +Q   D      E+I  + G PD
Sbjct: 7   SRIGGGIDVPVPRHSVGVVIGRSGEMIKKIQNDAGVRIQFKQDD-GTGPEKIAHIMGPPD 65

Query: 180 TISQAIYQICLVLIECTLQVVKGAVIPYEPKTMNAGP 216
               A   I  +L             P  P       
Sbjct: 66  RCEHAARIINDLLQSLRSGPPGPPGGPGMPPGGRGRG 102

>2hh3_A KH-type splicing regulatory protein; KH-RNA binding domain, RNA binding protein; NMR {Homo sapiens} Length = 106

 Score = 57.5 bits (139), Expect = 1e-10
 Identities = 19/92 (20%), Positives = 37/92 (40%), Gaps = 2/92 (2%)

Query: 279 GGKDTGDDFVET-EIVLTDDIAGCVIGKAGSRLLEIRQISGAQINIHTGTE-SHKKMFHI 336
           G   TG       ++ +     G VIG++G  + +I+  +G +I          +K+ HI
Sbjct: 1   GAMATGSRIGGGIDVPVPRHSVGVVIGRSGEMIKKIQNDAGVRIQFKQDDGTGPEKIAHI 60

Query: 337 QGCQEAVSLAQYLINMCIELQKNNTTNTSDNP 368
            G  +    A  +IN  ++  ++        P
Sbjct: 61  MGPPDRCEHAARIINDLLQSLRSGPPGPPGGP 92

>2hh3_A KH-type splicing regulatory protein; KH-RNA binding domain, RNA binding protein; NMR {Homo sapiens} Length = 106

 Score = 46.7 bits (111), Expect = 7e-07
 Identities = 12/51 (23%), Positives = 27/51 (52%), Gaps = 2/51 (3%)

Query: 24 SVNVNEISCLIGPGGCIVRRLRKESGAKISIT--DGACPDRIVTVSGSVDN 72
           V  + +  +IG  G ++++++ ++G +I     DG  P++I  + G  D 
Sbjct: 16 PVPRHSVGVVIGRSGEMIKKIQNDAGVRIQFKQDDGTGPEKIAHIMGPPDR 66

>2hh2_A KH-type splicing regulatory protein; KH-RNA binding domain, RNA binding protein; NMR {Homo sapiens} Length = 107

 Score = 74.5 bits (183), Expect = 1e-16
 Identities = 26/109 (23%), Positives = 44/109 (40%), Gaps = 11/109 (10%)

Query: 120 SPQPLQ-LKLVIPATHCGSLIGKGGCKIKDIRDLSGANVQVASDMLPMS--TERIVTVHG 176
           +  P   +   IP   CG +IG+GG  +K I   +GA V+++  + P      ++  + G
Sbjct: 2   AMAPGGEMTFSIPTHKCGLVIGRGGENVKAINQQTGAFVEISRQLPPNGDPNFKLFIIRG 61

Query: 177 NPDTISQAIYQICLVLIECTLQVVKGAVIPYEPKTMNAGPVILSGGQAY 225
           +P  I  A   I         + ++G + P  P     GP    G    
Sbjct: 62  SPQQIDHAKQLIE--------EKIEGPLCPVGPGPGGPGPAGPMGPFNP 102

>2hh2_A KH-type splicing regulatory protein; KH-RNA binding domain, RNA binding protein; NMR {Homo sapiens} Length = 107

 Score = 61.4 bits (149), Expect = 5e-12
 Identities = 23/87 (26%), Positives = 34/87 (39%), Gaps = 4/87 (4%)

Query: 289 ETEIVLTDDIAGCVIGKAGSRLLEIRQISGAQINIHTGTESHK----KMFHIQGCQEAVS 344
           E    +     G VIG+ G  +  I Q +GA + I      +     K+F I+G  + + 
Sbjct: 8   EMTFSIPTHKCGLVIGRGGENVKAINQQTGAFVEISRQLPPNGDPNFKLFIIRGSPQQID 67

Query: 345 LAQYLINMCIELQKNNTTNTSDNPEPA 371
            A+ LI   IE            P PA
Sbjct: 68  HAKQLIEEKIEGPLCPVGPGPGGPGPA 94

>2hh2_A KH-type splicing regulatory protein; KH-RNA binding domain, RNA binding protein; NMR {Homo sapiens} Length = 107

 Score = 41.8 bits (98), Expect = 4e-05
 Identities = 12/54 (22%), Positives = 26/54 (48%), Gaps = 5/54 (9%)

Query: 24 SVNVNEISCLIGPGGCIVRRLRKESGAKISITDGACP-----DRIVTVSGSVDN 72
          S+  ++   +IG GG  V+ + +++GA + I+    P      ++  + GS   
Sbjct: 12 SIPTHKCGLVIGRGGENVKAINQQTGAFVEISRQLPPNGDPNFKLFIIRGSPQQ 65

>1we8_A Tudor and KH domain containing protein; structural genomics, riken structural genomics/proteomics initiative, RSGI, RNA binding protein; NMR {Mus musculus} SCOP: d.51.1.1 Length = 104

 Score = 70.6 bits (173), Expect = 3e-15
 Identities = 18/74 (24%), Positives = 34/74 (45%), Gaps = 1/74 (1%)

Query: 122 QPLQLKLVIPATHCGSLIGKGGCKIKDIRDLSGANVQVASD-MLPMSTERIVTVHGNPDT 180
            P+  +L +P    G +IG+GG  I+ I   SGA +    +    +   R++ + G    
Sbjct: 13  TPVFEQLSVPQRSVGRIIGRGGETIRSICKASGAKITCDKESEGTLLLSRLIKISGTQKE 72

Query: 181 ISQAIYQICLVLIE 194
           ++ A + I   + E
Sbjct: 73  VAAAKHLILEKVSE 86

>1we8_A Tudor and KH domain containing protein; structural genomics, riken structural genomics/proteomics initiative, RSGI, RNA binding protein; NMR {Mus musculus} SCOP: d.51.1.1 Length = 104

 Score = 61.0 bits (148), Expect = 6e-12
 Identities = 22/81 (27%), Positives = 38/81 (46%), Gaps = 3/81 (3%)

Query: 278 SGGKDTGDDFVETEIVLTDDIAGCVIGKAGSRLLEIRQISGAQINI---HTGTESHKKMF 334
           S G  T +  V  ++ +     G +IG+ G  +  I + SGA+I       GT    ++ 
Sbjct: 5   SSGILTENTPVFEQLSVPQRSVGRIIGRGGETIRSICKASGAKITCDKESEGTLLLSRLI 64

Query: 335 HIQGCQEAVSLAQYLINMCIE 355
            I G Q+ V+ A++LI   + 
Sbjct: 65  KISGTQKEVAAAKHLILEKVS 85

>1we8_A Tudor and KH domain containing protein; structural genomics, riken structural genomics/proteomics initiative, RSGI, RNA binding protein; NMR {Mus musculus} SCOP: d.51.1.1 Length = 104

 Score = 45.6 bits (108), Expect = 2e-06
 Identities = 16/53 (30%), Positives = 25/53 (47%), Gaps = 4/53 (7%)

Query: 24 SVNVNEISCLIGPGGCIVRRLRKESGAKISITD----GACPDRIVTVSGSVDN 72
          SV    +  +IG GG  +R + K SGAKI+            R++ +SG+   
Sbjct: 20 SVPQRSVGRIIGRGGETIRSICKASGAKITCDKESEGTLLLSRLIKISGTQKE 72

>1x4n_A FAR upstream element binding protein 1; KH domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Mus musculus} SCOP: d.51.1.1 PDB: 2opu_A Length = 92

 Score = 67.8 bits (166), Expect = 1e-14
 Identities = 18/69 (26%), Positives = 32/69 (46%), Gaps = 1/69 (1%)

Query: 120 SPQPLQLKLVIPATHCGSLIGKGGCKIKDIRDLSGANVQVASDMLPMSTERIVTVHGNPD 179
               +  +  +P    G +IG+GG +I  I+  SG  +Q+A D      ER   + G P+
Sbjct: 11  QRSVMTEEYKVPDGMVGFIIGRGGEQISRIQQESGCKIQIAPDS-GGLPERSCMLTGTPE 69

Query: 180 TISQAIYQI 188
           ++  A   +
Sbjct: 70  SVQSAKRLL 78

>1x4n_A FAR upstream element binding protein 1; KH domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Mus musculus} SCOP: d.51.1.1 PDB: 2opu_A Length = 92

 Score = 67.8 bits (166), Expect = 2e-14
 Identities = 20/84 (23%), Positives = 40/84 (47%), Gaps = 1/84 (1%)

Query: 278 SGGKDTGDDFVETEIVLTDDIAGCVIGKAGSRLLEIRQISGAQINIHTGTE-SHKKMFHI 336
           S G       +  E  + D + G +IG+ G ++  I+Q SG +I I   +    ++   +
Sbjct: 5   SSGHQQQRSVMTEEYKVPDGMVGFIIGRGGEQISRIQQESGCKIQIAPDSGGLPERSCML 64

Query: 337 QGCQEAVSLAQYLINMCIELQKNN 360
            G  E+V  A+ L++  +E  ++ 
Sbjct: 65  TGTPESVQSAKRLLDQIVEKGRSG 88

>1x4n_A FAR upstream element binding protein 1; KH domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Mus musculus} SCOP: d.51.1.1 PDB: 2opu_A Length = 92

 Score = 47.0 bits (112), Expect = 3e-07
 Identities = 15/45 (33%), Positives = 27/45 (60%), Gaps = 2/45 (4%)

Query: 30 ISCLIGPGGCIVRRLRKESGAKISITD--GACPDRIVTVSGSVDN 72
          +  +IG GG  + R+++ESG KI I    G  P+R   ++G+ ++
Sbjct: 26 VGFIIGRGGEQISRIQQESGCKIQIAPDSGGLPERSCMLTGTPES 70

>2cte_A Vigilin; K homology type I domain, RNA-binding, cell sterol metabolism, beta-alpha-alpha-beta-BETA-alpha structure, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.51.1.1 Length = 94

 Score = 55.5 bits (134), Expect = 4e-10
 Identities = 14/63 (22%), Positives = 29/63 (46%), Gaps = 3/63 (4%)

Query: 126 LKLVIPATHCGSLIGKGGCKIKDIRDLSGANVQVASDMLPMSTERIVTVHGNPDTISQAI 185
             + IP  H   +IGK G K++D+   +   +Q+     P      + + G  + I +A 
Sbjct: 19  ATVAIPKEHHRFVIGKNGEKLQDLELKTATKIQIPR---PDDPSNQIKITGTKEGIEKAR 75

Query: 186 YQI 188
           +++
Sbjct: 76  HEV 78

>2cte_A Vigilin; K homology type I domain, RNA-binding, cell sterol metabolism, beta-alpha-alpha-beta-BETA-alpha structure, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.51.1.1 Length = 94

 Score = 47.0 bits (112), Expect = 4e-07
 Identities = 9/49 (18%), Positives = 21/49 (42%)

Query: 24 SVNVNEISCLIGPGGCIVRRLRKESGAKISITDGACPDRIVTVSGSVDN 72
          ++       +IG  G  ++ L  ++  KI I     P   + ++G+ + 
Sbjct: 22 AIPKEHHRFVIGKNGEKLQDLELKTATKIQIPRPDDPSNQIKITGTKEG 70

>2cte_A Vigilin; K homology type I domain, RNA-binding, cell sterol metabolism, beta-alpha-alpha-beta-BETA-alpha structure, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.51.1.1 Length = 94

 Score = 42.0 bits (99), Expect = 2e-05
 Identities = 14/78 (17%), Positives = 31/78 (39%), Gaps = 1/78 (1%)

Query: 288 VETEIVLTDDIAGCVIGKAGSRLLEIRQISGAQINIHTGTESHKKMFHIQGCQEAVSLAQ 347
               + +  +    VIGK G +L ++   +  +I I    +       I G +E +  A+
Sbjct: 17  ASATVAIPKEHHRFVIGKNGEKLQDLELKTATKIQIP-RPDDPSNQIKITGTKEGIEKAR 75

Query: 348 YLINMCIELQKNNTTNTS 365
           + + +    Q   +  +S
Sbjct: 76  HEVLLISAEQDKRSGPSS 93

>2ctl_A Vigilin; K homology type I domain, RNA-binding, cell sterol metabolism, beta-alpha-alpha-beta-BETA-alpha structure, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.51.1.1 Length = 97

 Score = 53.7 bits (129), Expect = 2e-09
 Identities = 13/64 (20%), Positives = 23/64 (35%)

Query: 125 QLKLVIPATHCGSLIGKGGCKIKDIRDLSGANVQVASDMLPMSTERIVTVHGNPDTISQA 184
           +L + +   +   +IG+ G  I  IR     N+Q          +  +T+ G       A
Sbjct: 18  KLSVTVDPKYHPKIIGRKGAVITQIRLEHDVNIQFPDKDDGNQPQDQITITGYEKNTEAA 77

Query: 185 IYQI 188
              I
Sbjct: 78  RDAI 81

>2ctl_A Vigilin; K homology type I domain, RNA-binding, cell sterol metabolism, beta-alpha-alpha-beta-BETA-alpha structure, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.51.1.1 Length = 97

 Score = 41.3 bits (97), Expect = 4e-05
 Identities = 13/52 (25%), Positives = 23/52 (44%), Gaps = 3/52 (5%)

Query: 24 SVNVNEISCLIGPGGCIVRRLRKESGAKISI---TDGACPDRIVTVSGSVDN 72
          +V+      +IG  G ++ ++R E    I      DG  P   +T++G   N
Sbjct: 22 TVDPKYHPKIIGRKGAVITQIRLEHDVNIQFPDKDDGNQPQDQITITGYEKN 73

>2dgr_A Ring finger and KH domain-containing protein 1; structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Length = 83

 Score = 53.0 bits (127), Expect = 2e-09
 Identities = 14/70 (20%), Positives = 28/70 (40%), Gaps = 4/70 (5%)

Query: 119 CSPQPLQLKLVIPATHCGSLIGKGGCKIKDIRDLSGANVQVASDMLPMSTERIVTVHGNP 178
            S     +++ +P    G ++G  G  IK I+  +   +           E +  V G P
Sbjct: 5   SSGGQTTIQVRVPYRVVGLVVGPKGATIKRIQQRTHTYIVTPGR----DKEPVFAVTGMP 60

Query: 179 DTISQAIYQI 188
           + + +A  +I
Sbjct: 61  ENVDRAREEI 70

>2dgr_A Ring finger and KH domain-containing protein 1; structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Length = 83

 Score = 44.9 bits (106), Expect = 1e-06
 Identities = 16/84 (19%), Positives = 33/84 (39%), Gaps = 2/84 (2%)

Query: 279 GGKDTGDDFVETEIVLTDDIAGCVIGKAGSRLLEIRQISGAQINIHTGTESHKKMFHIQG 338
           G   +       ++ +   + G V+G  G+ +  I+Q +   I         + +F + G
Sbjct: 1   GSSGSSGGQTTIQVRVPYRVVGLVVGPKGATIKRIQQRTHTYIVTP--GRDKEPVFAVTG 58

Query: 339 CQEAVSLAQYLINMCIELQKNNTT 362
             E V  A+  I   I L+   ++
Sbjct: 59  MPENVDRAREEIEAHITLRSGPSS 82

>2ctk_A Vigilin; K homology type I domain, RNA-binding, cell sterol metabolism, beta-alpha-alpha-beta-BETA-alpha structure, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.51.1.1 Length = 104

 Score = 52.1 bits (125), Expect = 8e-09
 Identities = 13/66 (19%), Positives = 29/66 (43%), Gaps = 3/66 (4%)

Query: 123 PLQLKLVIPATHCGSLIGKGGCKIKDIRDLSGANVQVASDMLPMSTERIVTVHGNPDTIS 182
           P+ +++ +P      +IG+ G  I+ + D    N+ V +   P     I+ + G    + 
Sbjct: 16  PVTIEVEVPFDLHRYVIGQKGSGIRKMMDEFEVNIHVPA---PELQSDIIAITGLAANLD 72

Query: 183 QAIYQI 188
           +A   +
Sbjct: 73  RAKAGL 78

>2ctk_A Vigilin; K homology type I domain, RNA-binding, cell sterol metabolism, beta-alpha-alpha-beta-BETA-alpha structure, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.51.1.1 Length = 104

 Score = 40.9 bits (96), Expect = 7e-05
 Identities = 10/49 (20%), Positives = 19/49 (38%)

Query: 24 SVNVNEISCLIGPGGCIVRRLRKESGAKISITDGACPDRIVTVSGSVDN 72
           V  +    +IG  G  +R++  E    I +        I+ ++G   N
Sbjct: 22 EVPFDLHRYVIGQKGSGIRKMMDEFEVNIHVPAPELQSDIIAITGLAAN 70

>1vig_A Vigilin; RNA-binding protein, ribonucleoprotein; NMR {Homo sapiens} SCOP: d.51.1.1 PDB: 1vih_A Length = 71

 Score = 49.3 bits (118), Expect = 4e-08
 Identities = 15/63 (23%), Positives = 29/63 (46%), Gaps = 3/63 (4%)

Query: 126 LKLVIPATHCGSLIGKGGCKIKDIRDLSGANVQVASDMLPMSTERIVTVHGNPDTISQAI 185
           +++ I       LIGK G  I  I+D    +V++  D        ++ + G+P  + QA 
Sbjct: 7   VEINIDHKFHRHLIGKSGANINRIKDQYKVSVRIPPD---SEKSNLIRIEGDPQGVQQAK 63

Query: 186 YQI 188
            ++
Sbjct: 64  REL 66

>1vig_A Vigilin; RNA-binding protein, ribonucleoprotein; NMR {Homo sapiens} SCOP: d.51.1.1 PDB: 1vih_A Length = 71

 Score = 41.6 bits (98), Expect = 2e-05
 Identities = 8/64 (12%), Positives = 22/64 (34%), Gaps = 6/64 (9%)

Query: 9  IDEDTLITMRCLFHSSVNVNEISCLIGPGGCIVRRLRKESGAKISITDGACPDRIVTVSG 68
          I+    + +       ++      LIG  G  + R++ +    + I   +    ++ + G
Sbjct: 1  INRMDYVEIN------IDHKFHRHLIGKSGANINRIKDQYKVSVRIPPDSEKSNLIRIEG 54

Query: 69 SVDN 72
              
Sbjct: 55 DPQG 58

>2e3u_A PH-DIM2P, hypothetical protein PH1566; PRE-ribosomal RNA processing factor, RNA binding protein; 2.30A {Pyrococcus horikoshii} PDB: 3aev_B Length = 219

 Score = 52.4 bits (125), Expect = 5e-08
 Identities = 30/160 (18%), Positives = 52/160 (32%), Gaps = 18/160 (11%)

Query: 33  LIGPGGCIVRRLRKESGAKISITDGACPDRIVTVSGSVDNSSTSSVETGYPGHTLWVTSV 92
           LIG  G   + + K +  KI+I         V ++ + +     +V              
Sbjct: 48  LIGKKGQTKKEIEKRTKTKITIDS---ETGEVWITSTKETEDPLAVWKARDIVLAIGRGF 104

Query: 93  DNVCTAYNFMCRSLEDYHINRNRMENCSPQPLQLKLVIPATHCGSLIGKGGCKIKDIRDL 152
                      R L +         N +   +  +        G +IG+ G   + I ++
Sbjct: 105 S-----PERAFRLLNEGEYLEII--NLTDIIIGNEKNALPRVRGRIIGRKGRTRQIIEEM 157

Query: 153 SGANVQVASDMLPMSTERIVTVHGNPDTISQAIYQICLVL 192
           SGA+V V          + V + GNP  I  A   I  + 
Sbjct: 158 SGASVSVY--------GKTVAIIGNPIQIEIAKTAIEKLA 189

>2qnd_A FMR1 protein; KH domain, eukaryotic KH domains, tandem KH domains, type I domains, fragIle X mental retardation protein, RNA BI protein; 1.90A {Homo sapiens} PDB: 2fmr_A Length = 144

 Score = 49.2 bits (117), Expect = 2e-07
 Identities = 31/175 (17%), Positives = 54/175 (30%), Gaps = 54/175 (30%)

Query: 33  LIGPGGCIVRRLRKESGA-KISITDGACPDRIVTVSGSVDNSSTSSVETGYPGHTLWVTS 91
            IG  G  +++ RK  G   I + +  C   I          + S +E            
Sbjct: 18  AIGTHGANIQQARKVPGVTAIDLDEDTCTFHIYGEDQDAVKKARSFLE------------ 65

Query: 92  VDNVCTAYNFMCRSLEDYHINRNRMENCSPQPLQLKLVIPATHCGSLIGKGGCKIKDIRD 151
                                            +  + +P    G +IGK G  I++I D
Sbjct: 66  -------------------------------FAEDVIQVPRNLVGKVIGKNGKLIQEIVD 94

Query: 152 LSGAN-VQVASDMLPMSTERI----VTVHGNPDTISQAIYQICLVLIECTLQVVK 201
            SG   V++ ++      +          G  D+I+ A      VL++  L  +K
Sbjct: 95  KSGVVRVRIEAENEKNVPQEEGMVPFVFVGTKDSIANA-----TVLLDYHLNYLK 144

>2qnd_A FMR1 protein; KH domain, eukaryotic KH domains, tandem KH domains, type I domains, fragIle X mental retardation protein, RNA BI protein; 1.90A {Homo sapiens} PDB: 2fmr_A Length = 144

 Score = 40.8 bits (95), Expect = 2e-04
 Identities = 19/77 (24%), Positives = 35/77 (45%), Gaps = 7/77 (9%)

Query: 286 DFVETEIVLTDDIAGCVIGKAGSRLLEIRQISGA-QINI------HTGTESHKKMFHIQG 338
           +F E  I +  ++ G VIGK G  + EI   SG  ++ I      +   E     F   G
Sbjct: 65  EFAEDVIQVPRNLVGKVIGKNGKLIQEIVDKSGVVRVRIEAENEKNVPQEEGMVPFVFVG 124

Query: 339 CQEAVSLAQYLINMCIE 355
            +++++ A  L++  + 
Sbjct: 125 TKDSIANATVLLDYHLN 141

>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 = 52.2 bits (124), Expect = 2e-07
 Identities = 46/336 (13%), Positives = 96/336 (28%), Gaps = 112/336 (33%)

Query: 149 IRDLSGANVQVASDMLP--MSTERIVTVHGNPDTISQAIYQICLVLIECTLQVVKGAV-- 204
           + +    +VQ   DM    +S E I  +  + D +S    ++   L+    ++V+  V  
Sbjct: 30  VDNFDCKDVQ---DMPKSILSKEEIDHIIMSKDAVSG-TLRLFWTLLSKQEEMVQKFVEE 85

Query: 205 ------------IPYEPKTMNAGP------------VILSGGQAYTLHGEYAVP------ 234
                       I  E +     P             + +  Q +    +Y V       
Sbjct: 86  VLRINYKFLMSPIKTEQR----QPSMMTRMYIEQRDRLYNDNQVFA---KYNVSRLQPYL 138

Query: 235 -VQEVAGKKQPHPLAGLAVLGIEGIGSTSLTPAALAALSGSRVKS-----------GGKD 282
            +++   + +P     + + G+ G G T +   AL      +V+               +
Sbjct: 139 KLRQALLELRPAK--NVLIDGVLGSGKTWV---ALDVCLSYKVQCKMDFKIFWLNLKNCN 193

Query: 283 TGDDFVETEIVLTDDIAGCV-IGKAGSRLLEIRQISGAQINIHTGTESHKKMFHIQGCQE 341
           + +  +E    L         I    +   +    S  ++ IH+     +++   +  + 
Sbjct: 194 SPETVLEMLQKL------LYQIDPNWTSRSD--HSSNIKLRIHSIQAELRRLLKSKPYEN 245

Query: 342 AVSLAQYLI--NMCIELQKNNTTNTSDNPEPADLDAAISAF-------MT---ASVNSSL 389
                  L+  N+              N +      A +AF       +T     V   L
Sbjct: 246 C-----LLVLLNVQ-------------NAK------AWNAFNLSCKILLTTRFKQVTDFL 281

Query: 390 IEKPTPHPGSMVTLGGLSE-----LLANIAASNVKS 420
               T H         L+      LL        + 
Sbjct: 282 SAATTTHISLDHHSMTLTPDEVKSLLLKYLDCRPQD 317

>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 = 48.7 bits (115), Expect = 3e-06
 Identities = 44/301 (14%), Positives = 77/301 (25%), Gaps = 90/301 (29%)

Query: 1   MDGN------GDGKIDEDTLITMRCLFHSSVNVNEISCLIGPGGCIVRRLRKESGAKISI 54
           MD         +    E  L  ++ L +           I P                S 
Sbjct: 180 MDFKIFWLNLKNCNSPETVLEMLQKLLY----------QIDPNWT-------------SR 216

Query: 55  TDGACPDRIVTVSGSVDNSSTSSVETGYPGHTLWVTSVDNVCT-----AYNFMCRSL--- 106
           +D +   ++   S              Y  + L V  + NV       A+N  C+ L   
Sbjct: 217 SDHSSNIKLRIHSIQ-AELRRLLKSKPYE-NCLLV--LLNVQNAKAWNAFNLSCKILLTT 272

Query: 107 ------------EDYHINRNRME----------------NCSPQ--PLQLKLVIPATHCG 136
                          HI+ +                   +C PQ  P ++    P     
Sbjct: 273 RFKQVTDFLSAATTTHISLDHHSMTLTPDEVKSLLLKYLDCRPQDLPREVLTTNPRRL-- 330

Query: 137 SLIGKGGCKIKDIRDLSGANVQVASDMLPMSTERIVTVHGNPDTISQAIYQICLVL---- 192
           S+I +    I+D          V  D L    E  + V   P    + ++    V     
Sbjct: 331 SIIAE---SIRDGLATWDNWKHVNCDKLTTIIESSLNVL-EPAEY-RKMFDRLSVFPPSA 385

Query: 193 -I-ECTLQVVKGAVIPYEPKTMNAGPVILS------GGQAYTLHGEYAVPVQEVAGKKQP 244
            I    L ++   VI  +   +       S           ++   Y     ++  +   
Sbjct: 386 HIPTILLSLIWFDVIKSDVMVVVNKLHKYSLVEKQPKESTISIPSIYLELKVKLENEYAL 445

Query: 245 H 245
           H
Sbjct: 446 H 446

>2ctm_A Vigilin; K homology type I domain, RNA-binding, cell sterol metabolism, beta-alpha-alpha-beta-BETA-alpha structure, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.51.1.1 Length = 95

 Score = 46.7 bits (111), Expect = 4e-07
 Identities = 14/63 (22%), Positives = 24/63 (38%), Gaps = 2/63 (3%)

Query: 126 LKLVIPATHCGSLIGKGGCKIKDIRDLSGANVQVASDMLPMSTERIVTVHGNPDTISQAI 185
             + +       +IG  G  I+ I D    +++             VTV G P+ + +AI
Sbjct: 19  EDVPLDHRVHARIIGARGKAIRKIMDEFKVDIRFPQSG--APDPNCVTVTGLPENVEEAI 76

Query: 186 YQI 188
             I
Sbjct: 77  DHI 79

>2ctm_A Vigilin; K homology type I domain, RNA-binding, cell sterol metabolism, beta-alpha-alpha-beta-BETA-alpha structure, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.51.1.1 Length = 95

 Score = 40.1 bits (94), Expect = 1e-04
 Identities = 13/50 (26%), Positives = 22/50 (44%), Gaps = 1/50 (2%)

Query: 24 SVNVNEISCLIGPGGCIVRRLRKESGAKISITD-GACPDRIVTVSGSVDN 72
           ++    + +IG  G  +R++  E    I     GA     VTV+G  +N
Sbjct: 22 PLDHRVHARIIGARGKAIRKIMDEFKVDIRFPQSGAPDPNCVTVTGLPEN 71

>1tua_A Hypothetical protein APE0754; structural genomics, protein structure initiative, MCSG, four layers alpha-beta sandwich, PSI; 1.50A {Aeropyrum pernix} SCOP: d.51.1.1 d.51.1.1 Length = 191

 Score = 47.3 bits (112), Expect = 2e-06
 Identities = 25/166 (15%), Positives = 53/166 (31%), Gaps = 31/166 (18%)

Query: 33  LIGPGGCIVRRLRKESGAKISITDGACPDRIVTVSGSVDNSSTSSVETGYPGHTLWVTSV 92
           +IGP G +   + + +G  I++                 ++  S V        +   ++
Sbjct: 18  VIGPRGEVKAEIMRRTGTVITV-----------------DTENSMVIVEPEAEGIPPVNL 60

Query: 93  DNVCTAYNFMCRSLEDYHINRNRMENCSPQPLQLKLVI------PATHCGSLIGKGGCKI 146
                    +          R   E+     + LK V+           G +IG+GG   
Sbjct: 61  MKAAEVVKAISLGFPPEKAFRLLEEDQILVVVDLKQVVGDSQNHLKRIKGRIIGEGGRAR 120

Query: 147 KDIRDLSGANVQVASDMLPMSTERIVTVHGNPDTISQAIYQICLVL 192
           + I +++   + V         E  V + G+ +    A   I ++ 
Sbjct: 121 RTIEEMTDTYINVG--------EYEVAIIGDYERAMAAKQAIEMLA 158

>2ctj_A Vigilin; K homology type I domain, RNA-binding, cell sterol metabolism, beta-alpha-alpha-beta-BETA-alpha structure, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.51.1.1 Length = 95

 Score = 40.9 bits (96), Expect = 5e-05
 Identities = 16/64 (25%), Positives = 27/64 (42%), Gaps = 4/64 (6%)

Query: 126 LKLVIPATHCGSLIGKGGCKIKDIRD-LSGANVQVASDMLPMSTERIVTVHGNPDTISQA 184
           +++ IPA    SLIG  G  I+ I +   G ++         S    V + G    + +A
Sbjct: 19  VEVSIPAKLHNSLIGTKGRLIRSIMEECGGVHIHFPV---EGSGSDTVVIRGPSSDVEKA 75

Query: 185 IYQI 188
             Q+
Sbjct: 76  KKQL 79

>3n89_A Defective in GERM LINE development protein 3, ISO; KH domains, RNA binding, cell cycle; 2.79A {Caenorhabditis elegans} Length = 376

 Score = 43.8 bits (102), Expect = 7e-05
 Identities = 35/305 (11%), Positives = 85/305 (27%), Gaps = 35/305 (11%)

Query: 126 LKLVIPATHCGSLIGKGGCK--IKDIRDLSGANVQV----ASDMLPMSTERIVTVHGNPD 179
           L +   + +   +    G    +  I   +   +Q+         P    + VT+ G   
Sbjct: 32  LNMEFESQYYSLMTSDNGDHENVASIMAETNTLIQLPDRSVGGTTPDPFAQQVTITGYFG 91

Query: 180 TISQA---IYQICLVLIECTLQVVKGAVIPYEPKTMNAGPVILSGGQAYTLHGEYAVPVQ 236
            + +A   + + C   +   L  +K  +   +        V  +  Q   +         
Sbjct: 92  DVDRARMLMRRNCHFTVFMALSKMKMPLHELQA------HVRQNPIQNVEMS-------- 137

Query: 237 EVAGKKQPHPLAGLAVLGIEGIGSTSLTPAALAALSG-SRVKSGGKDTGDDFVETEIVLT 295
                       G+    +            + A    + +        ++       L+
Sbjct: 138 ----FVDAPEKNGIVTTYLRITAREKNQHELIEAAKRLNEILFRESPAPENNFTLHFTLS 193

Query: 296 DDIAGCVIGKAGSRLL--EIRQISGAQI-----NIHTGTESHKKMFHIQGCQEAVSLAQY 348
                 V+G + +  L   I + +   I     N    T  +     + G  + V  A+ 
Sbjct: 194 TYYVDQVLGSSSTAQLMPVIERETTTIISYPCYNNRNETRGNIYEIKVVGNIDNVLKARR 253

Query: 349 LINMCIELQKNNTTNTSDNPEPADLDAAISAFMTASVNSSLIEKPTPHPGSMVTLGGLSE 408
            I   + +        +D  EP+ +       +       L   P+ +  + +  G +  
Sbjct: 254 YIMDLLPISMCFNIKNTDMAEPSRVSDRNIHMIIDESGIILKMTPSVYEPADLLSGEVPL 313

Query: 409 LLANI 413
             A++
Sbjct: 314 NCASL 318

>3u1k_A Polyribonucleotide nucleotidyltransferase 1, MITO; RNAse PH, KH domain, exoribonuclease; HET: CIT; 2.13A {Homo sapiens} Length = 630

 Score = 40.6 bits (96), Expect = 9e-04
 Identities = 12/45 (26%), Positives = 24/45 (53%), Gaps = 4/45 (8%)

Query: 25  VNVNEISCLIGPGGCIVRRLRKESGAKISITDGACPDRIVTVSGS 69
           V +++ +  +GPGG  +++L+ E+G  IS  D    +   +V   
Sbjct: 573 VPLSKRAKFVGPGGYNLKKLQAETGVTISQVD----EETFSVFAP 613

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	433
2jzx_A	160	Poly(RC)-binding protein 2; PCBP2, KH domains, RNA	99.95
3krm_A	163	Insulin-like growth factor 2 mRNA-binding protein	99.94
3krm_A	163	Insulin-like growth factor 2 mRNA-binding protein	99.94
2anr_A	178	Neuro-oncological ventral antigen 1; protein-RNA c	99.94
2anr_A	178	Neuro-oncological ventral antigen 1; protein-RNA c	99.94
2jvz_A	164	KH type-splicing, FAR upstream element-binding pro	99.93
1j4w_A	174	FUSE binding protein; single-stranded DNA binding	99.93
2jzx_A	160	Poly(RC)-binding protein 2; PCBP2, KH domains, RNA	99.93
2jvz_A	164	KH type-splicing, FAR upstream element-binding pro	99.93
1j4w_A	174	FUSE binding protein; single-stranded DNA binding	99.92
3n89_A	376	Defective in GERM LINE development protein 3, ISO;	99.92
2qnd_A	144	FMR1 protein; KH domain, eukaryotic KH domains, ta	99.78
2qnd_A	144	FMR1 protein; KH domain, eukaryotic KH domains, ta	99.77
2e3u_A	219	PH-DIM2P, hypothetical protein PH1566; PRE-ribosom	99.71
2e3u_A	219	PH-DIM2P, hypothetical protein PH1566; PRE-ribosom	99.67
1zzk_A	82	Heterogeneous nuclear ribonucleoprotein K; KH domi	99.62
2p2r_A	76	Poly(RC)-binding protein 2; protein-DNA complex, R	99.61
1wvn_A	82	Poly(RC)-binding protein 1; KH domain, RNA binding	99.6
1tua_A	191	Hypothetical protein APE0754; structural genomics,	99.6
2axy_A	73	Poly(RC)-binding protein 2; protein-DNA complex, D	99.58
1dtj_A	76	RNA-binding neurooncological ventral antigen 2; KH	99.58
2axy_A	73	Poly(RC)-binding protein 2; protein-DNA complex, D	99.58
1j5k_A	89	Heterogeneous nuclear ribonucleoprotein K; single-	99.57
1x4n_A	92	FAR upstream element binding protein 1; KH domain,	99.56
1tua_A	191	Hypothetical protein APE0754; structural genomics,	99.56
2dgr_A	83	Ring finger and KH domain-containing protein 1; st	99.56
3n89_A	376	Defective in GERM LINE development protein 3, ISO;	99.55
2hh3_A	106	KH-type splicing regulatory protein; KH-RNA bindin	99.53
1ec6_A	87	RNA-binding protein NOVA-2; KH domain, alpha-beta	99.52
2opv_A	85	KHSRP protein; KH domain, RNA binding protein, KSR	99.51
2hh2_A	107	KH-type splicing regulatory protein; KH-RNA bindin	99.51
1x4m_A	94	FAR upstream element binding protein 1; KH domain,	99.51
1zzk_A	82	Heterogeneous nuclear ribonucleoprotein K; KH domi	99.47
2p2r_A	76	Poly(RC)-binding protein 2; protein-DNA complex, R	99.46
1wvn_A	82	Poly(RC)-binding protein 1; KH domain, RNA binding	99.46
2cte_A	94	Vigilin; K homology type I domain, RNA-binding, ce	99.46
1we8_A	104	Tudor and KH domain containing protein; structural	99.46
1dtj_A	76	RNA-binding neurooncological ventral antigen 2; KH	99.45
1j5k_A	89	Heterogeneous nuclear ribonucleoprotein K; single-	99.45
2ctl_A	97	Vigilin; K homology type I domain, RNA-binding, ce	99.45
2opv_A	85	KHSRP protein; KH domain, RNA binding protein, KSR	99.44
1vig_A	71	Vigilin; RNA-binding protein, ribonucleoprotein; N	99.43
2ctm_A	95	Vigilin; K homology type I domain, RNA-binding, ce	99.43
2hh2_A	107	KH-type splicing regulatory protein; KH-RNA bindin	99.42
1x4n_A	92	FAR upstream element binding protein 1; KH domain,	99.42
1ec6_A	87	RNA-binding protein NOVA-2; KH domain, alpha-beta	99.41
1x4m_A	94	FAR upstream element binding protein 1; KH domain,	99.41
1vig_A	71	Vigilin; RNA-binding protein, ribonucleoprotein; N	99.38
2dgr_A	83	Ring finger and KH domain-containing protein 1; st	99.36
2hh3_A	106	KH-type splicing regulatory protein; KH-RNA bindin	99.35
1we8_A	104	Tudor and KH domain containing protein; structural	99.35
2cte_A	94	Vigilin; K homology type I domain, RNA-binding, ce	99.33
2ctk_A	104	Vigilin; K homology type I domain, RNA-binding, ce	99.32
2ctl_A	97	Vigilin; K homology type I domain, RNA-binding, ce	99.32
2ctj_A	95	Vigilin; K homology type I domain, RNA-binding, ce	99.29
2ctm_A	95	Vigilin; K homology type I domain, RNA-binding, ce	99.27
2ctf_A	102	Vigilin; K homology type I domain, RNA-binding, ce	99.21
2ctk_A	104	Vigilin; K homology type I domain, RNA-binding, ce	99.21
2ctf_A	102	Vigilin; K homology type I domain, RNA-binding, ce	99.18
2ctj_A	95	Vigilin; K homology type I domain, RNA-binding, ce	99.13
2cpq_A	91	FragIle X mental retardation syndrome related prot	98.96
2cpq_A	91	FragIle X mental retardation syndrome related prot	98.68
2yqr_A	119	KIAA0907 protein; structure genomics, KH domain, s	98.63
2yqr_A	119	KIAA0907 protein; structure genomics, KH domain, s	98.63
1k1g_A	131	SF1-BO isoform; splicing, branch point sequence, p	98.58
1k1g_A	131	SF1-BO isoform; splicing, branch point sequence, p	98.58
2bl5_A	140	MGC83862 protein, quaking protein; STAR proteins,	98.3
2bl5_A	140	MGC83862 protein, quaking protein; STAR proteins,	98.09
3v69_A	140	Protein filia; RNA-binding, embryogenesis, KH doma	98.08
3u1k_A	630	Polyribonucleotide nucleotidyltransferase 1, MITO;	97.95
3u1k_A	630	Polyribonucleotide nucleotidyltransferase 1, MITO;	97.87
2cxc_A	144	NUSA; transcription termination, RNA binding prote	97.64
3v69_A	140	Protein filia; RNA-binding, embryogenesis, KH doma	97.49
2cxc_A	144	NUSA; transcription termination, RNA binding prote	97.29
4aid_A	726	Polyribonucleotide nucleotidyltransferase; transfe	97.22
4aid_A	726	Polyribonucleotide nucleotidyltransferase; transfe	97.13
1k0r_A	366	NUSA; two component arrangement, S1 domain, two K-	95.79
2asb_A	251	Transcription elongation protein NUSA; protein-RNA	95.6
2asb_A	251	Transcription elongation protein NUSA; protein-RNA	95.34
1k0r_A	366	NUSA; two component arrangement, S1 domain, two K-	95.31
3cdi_A	723	Polynucleotide phosphorylase; mRNA turnover, RNAse	94.71
1e3p_A	757	Guanosine pentaphosphate synthetase; polyribonucle	94.17
1e3p_A	757	Guanosine pentaphosphate synthetase; polyribonucle	93.9
3cdi_A	723	Polynucleotide phosphorylase; mRNA turnover, RNAse	93.88
1hh2_P	344	NUSA, N utilization substance protein A; transcrip	93.82
1hh2_P	344	NUSA, N utilization substance protein A; transcrip	93.49

>2jzx_A Poly(RC)-binding protein 2; PCBP2, KH domains, RNA binding, DNA-binding, nucleus, phosph ribonucleoprotein, RNA-binding, RNA binding protein; NMR {Homo sapiens}

Probab=99.95  E-value=4.1e-28  Score=215.17  Aligned_cols=157  Identities=45%  Similarity=0.853  Sum_probs=139.2

Q ss_pred             CceEEEEEEeccCCcccccceeeecCchHHHHHHHHhCCeEEEeCCCCCcceEEEecccCCCCCCccccCCCCCccccch
Q psy11929         12 DTLITMRCLFHSSVNVNEISCLIGPGGCIVRRLRKESGAKISITDGACPDRIVTVSGSVDNSSTSSVETGYPGHTLWVTS   91 (433)
Q Consensus        12 ~~~~~~rilvp~~~~~~~vg~IIGk~G~~Ik~I~~~tga~I~v~~~~~~eRvv~I~G~~~~~~~~~v~~~~~~~~~~~~a   91 (433)
                      +.+++++|+||.    +++|.||||+|++||+|+++|||+|+|++.++++|+|+|+|+.+                    
T Consensus         2 ~~~~~~~~~vp~----~~~g~iIGkgG~~Ik~i~~~tg~~I~i~~~~~~~r~v~I~G~~~--------------------   57 (160)
T 2jzx_A            2 NVTLTIRLLMHG----KEVGSIIGKKGESVKKMREESGARINISEGNCPERIITLAGPTN--------------------   57 (160)
T ss_dssp             CCEEEEEEEEEH----HHHHHHHCGGGHHHHHHHHHHCSEEEEECCTTTEEEEEEEEEHH--------------------
T ss_pred             CccEEEEEEEch----hheeeeECCCcHHHHHHHHHHCCEEEEcCCCCCceEEEEEeCHH--------------------
Confidence            467899999999    99999999999999999999999999999888999999999988                    


Q ss_pred             HHHHHHHHHHHHhhhhhhc-ccccCCCCCCCCCeEEEEEeccCcccceecCCchhHHHHHHhhCceEEeccCCCCCCCcc
Q psy11929         92 VDNVCTAYNFMCRSLEDYH-INRNRMENCSPQPLQLKLVIPATHCGSLIGKGGCKIKDIRDLSGANVQVASDMLPMSTER  170 (433)
Q Consensus        92 ~~~v~~A~~~I~~~~~~~~-~~~~~~~~~~~~~~~~~l~ip~~~vg~iIGk~G~~Ik~I~~~sga~I~i~~~~~~~~~er  170 (433)
                        ++.+|+.+|.+.+.+.. ..+.+.........+++++||.+++|+||||+|++|++|+++|||+|.+.++..|.+.++
T Consensus        58 --~v~~A~~~I~~~i~e~~~~~~~~~~~~~~~~~~~~i~vp~~~~g~iIGkgG~~Ik~i~~~tga~I~i~~~~~~~~~~~  135 (160)
T 2jzx_A           58 --AIFKAFAMIIDKLEEDISSSMTNSTAASRPPVTLRLVVPASQCGSLIGKGGCKIKEIRESTGAQVQVAGDMLPNSTER  135 (160)
T ss_dssp             --HHHHHHHHHHHHHHHHHTSCCCSSSCCCCCSEEEEEEEEHHHHHHHHCGGGHHHHHHHHHHSSEECCCCCCSTTCCEE
T ss_pred             --HHHHHHHHHHHHHHhhccccCCCCccCCCCCEEEEEEEChhheeeEECCCCHHHHHHHHHhCCeEEECCCCCCCCCce
Confidence              99999999998876632 111111112345689999999999999999999999999999999999998777888999


Q ss_pred             EEEEEccHHHHHHHHHHHHHHHHh
Q psy11929        171 IVTVHGNPDTISQAIYQICLVLIE  194 (433)
Q Consensus       171 ~v~I~G~~~~v~~A~~~I~~~l~e  194 (433)
                      .|+|+|+++++.+|+.+|.+++.|
T Consensus       136 ~v~I~G~~~~v~~A~~~I~~~i~e  159 (160)
T 2jzx_A          136 AITIAGIPQSIIECVKQICVVMLE  159 (160)
T ss_dssp             EEEEEECHHHHHHHHHHHHHHHHH
T ss_pred             EEEEEcCHHHHHHHHHHHHHHHhc
Confidence            999999999999999999999876

>3krm_A Insulin-like growth factor 2 mRNA-binding protein 1; KH domain, cell projection, cytoplasm, nucleus, phosphoprotein, translation regulation; 2.75A {Homo sapiens}

Probab=99.94  E-value=2e-26  Score=204.98  Aligned_cols=155  Identities=27%  Similarity=0.384  Sum_probs=134.3

Q ss_pred             CeEEEEEeccCcccceecCCchhHHHHHHhhCceEEeccCCCCCCCccEEEEEccHHHHHHHHHHHHHHHHhhccccCCC
Q psy11929        123 PLQLKLVIPATHCGSLIGKGGCKIKDIRDLSGANVQVASDMLPMSTERIVTVHGNPDTISQAIYQICLVLIECTLQVVKG  202 (433)
Q Consensus       123 ~~~~~l~ip~~~vg~iIGk~G~~Ik~I~~~sga~I~i~~~~~~~~~er~v~I~G~~~~v~~A~~~I~~~l~e~~~~~~~~  202 (433)
                      +.+++|+||..++|.||||+|++|++|+++|||+|.|+++..+++.+|.|+|+|+++++.+|+.+|.+++.+.   ..  
T Consensus         2 ~~~~~~~ip~~~~g~iIGk~G~~Ik~i~~~tg~~I~i~~~~~~~~~~r~v~I~G~~e~v~~A~~~I~~~~~e~---~~--   76 (163)
T 3krm_A            2 QEMVQVFIPAQAVGAIIGKKGQHIKQLSRFASASIKIAPPETPDSKVRMVIITGPPEAQFKAQGRIYGKLKEE---NF--   76 (163)
T ss_dssp             CEEEEEEEEGGGHHHHHCGGGHHHHHHHHHHTCEEEECCCSSTTCSEEEEEEEECHHHHHHHHHHHHHHHHHT---TS--
T ss_pred             ceEEEEEechhhcceeECCCcHHHHHHHHHHCCeEEEcCCCCCCCCceEEEEEcCHHHHHHHHHHHHHHHhcc---cc--
Confidence            4578999999999999999999999999999999999987678899999999999999999999999999871   00  


Q ss_pred             cccccCCCCCCCCCccccCCcccccCCCCCCCcccccCCCCCCCCccccccCcCCCCCCCCCccccccccCCCcccCCCC
Q psy11929        203 AVIPYEPKTMNAGPVILSGGQAYTLHGEYAVPVQEVAGKKQPHPLAGLAVLGIEGIGSTSLTPAALAALSGSRVKSGGKD  282 (433)
Q Consensus       203 ~~~~~~p~~~~~~p~~~~g~~~~~~~g~~~~P~~~~~~~~~~~p~~~~~~~~~~~~~~p~~~~~~~~~~~~~~~~~~~~~  282 (433)
                          +.|                                                                         
T Consensus        77 ----~~~-------------------------------------------------------------------------   79 (163)
T 3krm_A           77 ----FGP-------------------------------------------------------------------------   79 (163)
T ss_dssp             ----SCS-------------------------------------------------------------------------
T ss_pred             ----ccc-------------------------------------------------------------------------
Confidence                000                                                                         


Q ss_pred             CCCCceEEEEEeCcccccccccCCCchHHHHHhHhCCeEEEccCCC---CCceEEEEEeCHHHHHHHHHHHHHHHHhccc
Q psy11929        283 TGDDFVETEIVLTDDIAGCVIGKAGSRLLEIRQISGAQINIHTGTE---SHKKMFHIQGCQEAVSLAQYLINMCIELQKN  359 (433)
Q Consensus       283 ~~~~~~t~~i~VP~~~vG~IIGkgG~~Ik~I~~~sGA~I~I~~~~~---~~er~V~IsGt~e~v~~A~~lI~~~i~~~~~  359 (433)
                      ......+.+|.||..++|+||||+|++|++|++.|||+|+|++...   .+++.|+|+|++++|++|+.+|.+++++.+.
T Consensus        80 ~~~~~~~~~i~vp~~~~g~iIGkgG~~I~~i~~~tga~I~i~~~~~~~~~~~~~v~I~G~~~~v~~A~~~I~~~i~~~~~  159 (163)
T 3krm_A           80 KEEVKLETHIRVPASAAGRVIGKGGKTVNELQNLTAAEVVVPRDQTPDENDQVIVKIIGHFYASQMAQRKIRDILAQVKQ  159 (163)
T ss_dssp             SCCCCEEEEEEEETTTHHHHHCGGGHHHHHHHHHHCCEEECCTTCCCCTTSEEEEEEEECHHHHHHHHHHHHHHHHHHTC
T ss_pred             ccCCceEEEEEcChhheeeEEcCCChHHHHHHHHhCCeEEECCCCCCCCCCceEEEEEeCHHHHHHHHHHHHHHHHHHHH
Confidence            0012456799999999999999999999999999999999987653   4455899999999999999999999987543

>3krm_A Insulin-like growth factor 2 mRNA-binding protein 1; KH domain, cell projection, cytoplasm, nucleus, phosphoprotein, translation regulation; 2.75A {Homo sapiens}

Probab=99.94  E-value=1.8e-26  Score=205.23  Aligned_cols=151  Identities=22%  Similarity=0.351  Sum_probs=132.8

Q ss_pred             eEEEEEEeccCCcccccceeeecCchHHHHHHHHhCCeEEEeCC---CCCcceEEEecccCCCCCCccccCCCCCccccc
Q psy11929         14 LITMRCLFHSSVNVNEISCLIGPGGCIVRRLRKESGAKISITDG---ACPDRIVTVSGSVDNSSTSSVETGYPGHTLWVT   90 (433)
Q Consensus        14 ~~~~rilvp~~~~~~~vg~IIGk~G~~Ik~I~~~tga~I~v~~~---~~~eRvv~I~G~~~~~~~~~v~~~~~~~~~~~~   90 (433)
                      +-+++|+||.    +++|.||||+|++||+|+++|||+|+|++.   ++.+|+|+|+|+++                   
T Consensus         2 ~~~~~~~ip~----~~~g~iIGk~G~~Ik~i~~~tg~~I~i~~~~~~~~~~r~v~I~G~~e-------------------   58 (163)
T 3krm_A            2 QEMVQVFIPA----QAVGAIIGKKGQHIKQLSRFASASIKIAPPETPDSKVRMVIITGPPE-------------------   58 (163)
T ss_dssp             CEEEEEEEEG----GGHHHHHCGGGHHHHHHHHHHTCEEEECCCSSTTCSEEEEEEEECHH-------------------
T ss_pred             ceEEEEEech----hhcceeECCCcHHHHHHHHHHCCeEEEcCCCCCCCCceEEEEEcCHH-------------------
Confidence            3589999999    999999999999999999999999999874   57899999999999                   


Q ss_pred             hHHHHHHHHHHHHhhhhhhcccccCCCCCCCCCeEEEEEeccCcccceecCCchhHHHHHHhhCceEEeccCCCCCCCcc
Q psy11929         91 SVDNVCTAYNFMCRSLEDYHINRNRMENCSPQPLQLKLVIPATHCGSLIGKGGCKIKDIRDLSGANVQVASDMLPMSTER  170 (433)
Q Consensus        91 a~~~v~~A~~~I~~~~~~~~~~~~~~~~~~~~~~~~~l~ip~~~vg~iIGk~G~~Ik~I~~~sga~I~i~~~~~~~~~er  170 (433)
                         ++.+|+.+|.+.+.+... +   ........+.+|+||..++|+||||+|++|++|+++|||+|.++++..|..+++
T Consensus        59 ---~v~~A~~~I~~~~~e~~~-~---~~~~~~~~~~~i~vp~~~~g~iIGkgG~~I~~i~~~tga~I~i~~~~~~~~~~~  131 (163)
T 3krm_A           59 ---AQFKAQGRIYGKLKEENF-F---GPKEEVKLETHIRVPASAAGRVIGKGGKTVNELQNLTAAEVVVPRDQTPDENDQ  131 (163)
T ss_dssp             ---HHHHHHHHHHHHHHHTTS-S---CSSCCCCEEEEEEEETTTHHHHHCGGGHHHHHHHHHHCCEEECCTTCCCCTTSE
T ss_pred             ---HHHHHHHHHHHHHhcccc-c---ccccCCceEEEEEcChhheeeEEcCCChHHHHHHHHhCCeEEECCCCCCCCCCc
Confidence               999999999998876421 0   111244678899999999999999999999999999999999998766665554


Q ss_pred             -EEEEEccHHHHHHHHHHHHHHHHh
Q psy11929        171 -IVTVHGNPDTISQAIYQICLVLIE  194 (433)
Q Consensus       171 -~v~I~G~~~~v~~A~~~I~~~l~e  194 (433)
                       .|+|+|++++|.+|+.+|.+++.+
T Consensus       132 ~~v~I~G~~~~v~~A~~~I~~~i~~  156 (163)
T 3krm_A          132 VIVKIIGHFYASQMAQRKIRDILAQ  156 (163)
T ss_dssp             EEEEEEECHHHHHHHHHHHHHHHHH
T ss_pred             eEEEEEeCHHHHHHHHHHHHHHHHH
Confidence             899999999999999999999998

>2anr_A Neuro-oncological ventral antigen 1; protein-RNA complex, KH domain, hairpin, RNA-binding protein complex; HET: 5BU; 1.94A {Homo sapiens} PDB: 2ann_A*

Probab=99.94  E-value=7e-27  Score=210.88  Aligned_cols=157  Identities=26%  Similarity=0.454  Sum_probs=132.5

Q ss_pred             CceEEEEEEeccCCcccccceeeecCchHHHHHHHHhCCeEEEeCC-----CCCcceEEEecccCCCCCCccccCCCCCc
Q psy11929         12 DTLITMRCLFHSSVNVNEISCLIGPGGCIVRRLRKESGAKISITDG-----ACPDRIVTVSGSVDNSSTSSVETGYPGHT   86 (433)
Q Consensus        12 ~~~~~~rilvp~~~~~~~vg~IIGk~G~~Ik~I~~~tga~I~v~~~-----~~~eRvv~I~G~~~~~~~~~v~~~~~~~~   86 (433)
                      ..+++++|+||.    +++|.||||+|++||+|+++|||+|+|++.     ++.+|+|+|+|+.+               
T Consensus         3 ~~~~~~~i~vp~----~~ig~iIGkgG~~Ik~i~~~tg~~I~i~~~~~~~~~~~er~v~I~G~~~---------------   63 (178)
T 2anr_A            3 GSQYFLKVLIPS----YAAGSIIGKGGQTIVQLQKETGATIKLSKSKDFYPGTTERVCLIQGTIE---------------   63 (178)
T ss_dssp             CCCEEEEEEEEH----HHHHHHHCGGGHHHHHHHHHHCCEEEECCTTCBCTTSSEEEEEEEECHH---------------
T ss_pred             CCCEEEEEEECh----hHeeeeECCCcHHHHHHHHHhCCeEEEecCCCCCCCCCCceEEEEeCHH---------------
Confidence            467999999999    999999999999999999999999999863     57899999999999               


Q ss_pred             cccchHHHHHHHHHHHHhhhhhhcccccCC----------CCCCCCCeEEEEEeccCcccceecCCchhHHHHHHhhCce
Q psy11929         87 LWVTSVDNVCTAYNFMCRSLEDYHINRNRM----------ENCSPQPLQLKLVIPATHCGSLIGKGGCKIKDIRDLSGAN  156 (433)
Q Consensus        87 ~~~~a~~~v~~A~~~I~~~~~~~~~~~~~~----------~~~~~~~~~~~l~ip~~~vg~iIGk~G~~Ik~I~~~sga~  156 (433)
                             ++.+|+.+|.+++.+........          ........+++|+||.+++|+||||+|++|++|+++|||+
T Consensus        64 -------~v~~A~~~I~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~Vp~~~vg~iIGkgG~~Ik~i~~~tga~  136 (178)
T 2anr_A           64 -------ALNAVHGFIAEKIREMPQNVAKTEPVSILQPQTTVNPDRANQVKIIVPNSTAGLIIGKGGATVKAIMEQSGAW  136 (178)
T ss_dssp             -------HHHHHHHHHHHHHTCCCCC-----------------CGGGGEEEEEEEHHHHHHHHCGGGHHHHHHHHHSSCE
T ss_pred             -------HHHHHHHHHHHHHhccCCccccCCcccccCCccCCCCCCceEEEEEEchhheeeeECCCcHHHHHHHHHHCCE
Confidence                   99999999999887643211000          0011234789999999999999999999999999999999


Q ss_pred             EEeccC-CCCCCCccEEEEEccHHHHHHHHHHHHHHHHh
Q psy11929        157 VQVASD-MLPMSTERIVTVHGNPDTISQAIYQICLVLIE  194 (433)
Q Consensus       157 I~i~~~-~~~~~~er~v~I~G~~~~v~~A~~~I~~~l~e  194 (433)
                      |.+.++ ..+.+.++.|+|+|+++++.+|+.+|.++|++
T Consensus       137 I~i~~~~~~~~~~~~~v~I~G~~~~v~~A~~~I~~~i~e  175 (178)
T 2anr_A          137 VQLSQKPDGINLQNRVVTVSGEPEQNRKAVELIIQKIQE  175 (178)
T ss_dssp             EEECCCC----CCEEEEEEESSHHHHHHHHHHHHHHHHS
T ss_pred             EEEeCCCCCCCCCceEEEEEcCHHHHHHHHHHHHHHHHh
Confidence            999864 24566889999999999999999999999998

>2anr_A Neuro-oncological ventral antigen 1; protein-RNA complex, KH domain, hairpin, RNA-binding protein complex; HET: 5BU; 1.94A {Homo sapiens} PDB: 2ann_A*

Probab=99.94  E-value=2.3e-26  Score=207.46  Aligned_cols=169  Identities=26%  Similarity=0.385  Sum_probs=135.4

Q ss_pred             CCCeEEEEEeccCcccceecCCchhHHHHHHhhCceEEecc--CCCCCCCccEEEEEccHHHHHHHHHHHHHHHHhhccc
Q psy11929        121 PQPLQLKLVIPATHCGSLIGKGGCKIKDIRDLSGANVQVAS--DMLPMSTERIVTVHGNPDTISQAIYQICLVLIECTLQ  198 (433)
Q Consensus       121 ~~~~~~~l~ip~~~vg~iIGk~G~~Ik~I~~~sga~I~i~~--~~~~~~~er~v~I~G~~~~v~~A~~~I~~~l~e~~~~  198 (433)
                      ...++++|+||..++|.||||+|++|++|+++|||+|+|.+  +..+++.+|.|+|+|+.+++.+|+.+|.+++.+   .
T Consensus         3 ~~~~~~~i~vp~~~ig~iIGkgG~~Ik~i~~~tg~~I~i~~~~~~~~~~~er~v~I~G~~~~v~~A~~~I~~~~~~---~   79 (178)
T 2anr_A            3 GSQYFLKVLIPSYAAGSIIGKGGQTIVQLQKETGATIKLSKSKDFYPGTTERVCLIQGTIEALNAVHGFIAEKIRE---M   79 (178)
T ss_dssp             CCCEEEEEEEEHHHHHHHHCGGGHHHHHHHHHHCCEEEECCTTCBCTTSSEEEEEEEECHHHHHHHHHHHHHHHTC---C
T ss_pred             CCCEEEEEEEChhHeeeeECCCcHHHHHHHHHhCCeEEEecCCCCCCCCCCceEEEEeCHHHHHHHHHHHHHHHhc---c
Confidence            45789999999999999999999999999999999999986  346778999999999999999999999999987   2


Q ss_pred             cCCCcccccCCCCCCCCCccccCCcccccCCCCCCCcccccCCCCCCCCccccccCcCCCCCCCCCccccccccCCCccc
Q psy11929        199 VVKGAVIPYEPKTMNAGPVILSGGQAYTLHGEYAVPVQEVAGKKQPHPLAGLAVLGIEGIGSTSLTPAALAALSGSRVKS  278 (433)
Q Consensus       199 ~~~~~~~~~~p~~~~~~p~~~~g~~~~~~~g~~~~P~~~~~~~~~~~p~~~~~~~~~~~~~~p~~~~~~~~~~~~~~~~~  278 (433)
                      +....    ..     .+.            .+ +++.                                          
T Consensus        80 ~~~~~----~~-----~~~------------~~-~~~~------------------------------------------   95 (178)
T 2anr_A           80 PQNVA----KT-----EPV------------SI-LQPQ------------------------------------------   95 (178)
T ss_dssp             CCC-----------------------------------------------------------------------------
T ss_pred             CCccc----cC-----Ccc------------cc-cCCc------------------------------------------
Confidence            21100    00     000            00 0000                                          


Q ss_pred             CCCCCCCCceEEEEEeCcccccccccCCCchHHHHHhHhCCeEEEccCCC---CCceEEEEEeCHHHHHHHHHHHHHHHH
Q psy11929        279 GGKDTGDDFVETEIVLTDDIAGCVIGKAGSRLLEIRQISGAQINIHTGTE---SHKKMFHIQGCQEAVSLAQYLINMCIE  355 (433)
Q Consensus       279 ~~~~~~~~~~t~~i~VP~~~vG~IIGkgG~~Ik~I~~~sGA~I~I~~~~~---~~er~V~IsGt~e~v~~A~~lI~~~i~  355 (433)
                       .........+.+|.||.+++|+||||+|++|++|++.|||+|+|.+...   +.++.|+|+|+++++++|+.+|.++|.
T Consensus        96 -~~~~~~~~~~~~i~Vp~~~vg~iIGkgG~~Ik~i~~~tga~I~i~~~~~~~~~~~~~v~I~G~~~~v~~A~~~I~~~i~  174 (178)
T 2anr_A           96 -TTVNPDRANQVKIIVPNSTAGLIIGKGGATVKAIMEQSGAWVQLSQKPDGINLQNRVVTVSGEPEQNRKAVELIIQKIQ  174 (178)
T ss_dssp             -----CGGGGEEEEEEEHHHHHHHHCGGGHHHHHHHHHSSCEEEECCCC----CCEEEEEEESSHHHHHHHHHHHHHHHH
T ss_pred             -cCCCCCCceEEEEEEchhheeeeECCCcHHHHHHHHHHCCEEEEeCCCCCCCCCceEEEEEcCHHHHHHHHHHHHHHHH
Confidence             0000123568899999999999999999999999999999999998643   678999999999999999999999997


Q ss_pred             hc
Q psy11929        356 LQ  357 (433)
Q Consensus       356 ~~  357 (433)
                      +.
T Consensus       175 e~  176 (178)
T 2anr_A          175 ED  176 (178)
T ss_dssp             SC
T ss_pred             hC
Confidence            64

>2jvz_A KH type-splicing, FAR upstream element-binding protein 2; RNA binding protein, KH domain, KSRP, posttranscriptional regulation, mRNA decay; NMR {Homo sapiens}

Probab=99.93  E-value=1.9e-25  Score=198.68  Aligned_cols=158  Identities=22%  Similarity=0.341  Sum_probs=130.5

Q ss_pred             eEEEEEeccCcccceecCCchhHHHHHHhhCceEEeccCC-CCCCCccEEEEEccHHHHHHHHHHHHHHHHhhccccCCC
Q psy11929        124 LQLKLVIPATHCGSLIGKGGCKIKDIRDLSGANVQVASDM-LPMSTERIVTVHGNPDTISQAIYQICLVLIECTLQVVKG  202 (433)
Q Consensus       124 ~~~~l~ip~~~vg~iIGk~G~~Ik~I~~~sga~I~i~~~~-~~~~~er~v~I~G~~~~v~~A~~~I~~~l~e~~~~~~~~  202 (433)
                      ++.+|+||..++|.||||+|++|++|+++|||+|.+.++. .+...+|.|+|+|+++++.+|+.+|.+++.+.   ... 
T Consensus         2 ~~~~~~Vp~~~~g~iIGk~G~~Ik~i~~~tg~~I~i~~~~~~~~~~~r~v~I~G~~~~v~~A~~~I~~ii~e~---~~~-   77 (164)
T 2jvz_A            2 TVQEIMIPAGKAGLVIGKGGETIKQLQERAGVKMILIQDGSQNTNVDKPLRIIGDPYKVQQACEMVMDILRER---DQG-   77 (164)
T ss_dssp             EEEEEEECTTCHHHHTCTTTHHHHHHHHTSCSEEEECCCTTSSSSSCEEEEEEECHHHHHHHHHHHHHHTTCS---SSC-
T ss_pred             eEEEEEechhheeEEECCChHHHHHHHHHhCCeEEEecCCCCCCCCceEEEEEcCHHHHHHHHHHHHHHHHhc---cCC-
Confidence            5789999999999999999999999999999999998642 35678899999999999999999999998761   100 


Q ss_pred             cccccCCCCCCCCCccccCCcccccCCCCCCCcccccCCCCCCCCccccccCcCCCCCCCCCccccccccCCCcccCCCC
Q psy11929        203 AVIPYEPKTMNAGPVILSGGQAYTLHGEYAVPVQEVAGKKQPHPLAGLAVLGIEGIGSTSLTPAALAALSGSRVKSGGKD  282 (433)
Q Consensus       203 ~~~~~~p~~~~~~p~~~~g~~~~~~~g~~~~P~~~~~~~~~~~p~~~~~~~~~~~~~~p~~~~~~~~~~~~~~~~~~~~~  282 (433)
                         .|.|.                  ..                                     |.             
T Consensus        78 ---~~~~~------------------~~-------------------------------------~~-------------   86 (164)
T 2jvz_A           78 ---GFGDR------------------NE-------------------------------------YG-------------   86 (164)
T ss_dssp             ---CCSSC------------------SS-------------------------------------CT-------------
T ss_pred             ---CCCCc------------------cc-------------------------------------cC-------------
Confidence               00000                  00                                     00             


Q ss_pred             CCCCceEEEEEeCcccccccccCCCchHHHHHhHhCCeEEEccCCC-CCceEEEEEeCHHHHHHHHHHHHHHHHhc
Q psy11929        283 TGDDFVETEIVLTDDIAGCVIGKAGSRLLEIRQISGAQINIHTGTE-SHKKMFHIQGCQEAVSLAQYLINMCIELQ  357 (433)
Q Consensus       283 ~~~~~~t~~i~VP~~~vG~IIGkgG~~Ik~I~~~sGA~I~I~~~~~-~~er~V~IsGt~e~v~~A~~lI~~~i~~~  357 (433)
                       .....+.+|.||.+++|+||||+|.+|++|++.|||+|+|++..+ +.++.|+|+|++++++.|+.+|.++++..
T Consensus        87 -~~~~~~~~i~vp~~~~g~iIGk~G~~I~~i~~~tg~~I~i~~~~~~~~~~~v~I~G~~~~v~~A~~~I~~~i~~~  161 (164)
T 2jvz_A           87 -SRIGGGIDVPVPRHSVGVVIGRSGEMIKKIQNDAGVRIQFKQDDGTGPEKIAHIMGPPDRCEHAARIINDLLQSL  161 (164)
T ss_dssp             -TSCSSSBCCEEETTTHHHHHCSSSHHHHHHHHHTCCEEEECCCCTTSSEEEEEEESCHHHHHHHHHHHHHHHHHH
T ss_pred             -CCCCceEEEEEChhhccccCCCCcHhHHHHHHHHCCeEEEeCCCCCCCcEEEEEEcCHHHHHHHHHHHHHHHhhh
Confidence             001234688999999999999999999999999999999998765 66899999999999999999999999764

>1j4w_A FUSE binding protein; single-stranded DNA binding protein; HET: DNA; NMR {Homo sapiens} SCOP: d.51.1.1 d.51.1.1

Probab=99.93  E-value=1.1e-25  Score=202.40  Aligned_cols=153  Identities=21%  Similarity=0.378  Sum_probs=127.3

Q ss_pred             eEEEEEEeccCCcccccceeeecCchHHHHHHHHhCCeEEEeC--CCCCcceEEEecccCCCCCCccccCCCCCccccch
Q psy11929         14 LITMRCLFHSSVNVNEISCLIGPGGCIVRRLRKESGAKISITD--GACPDRIVTVSGSVDNSSTSSVETGYPGHTLWVTS   91 (433)
Q Consensus        14 ~~~~rilvp~~~~~~~vg~IIGk~G~~Ik~I~~~tga~I~v~~--~~~~eRvv~I~G~~~~~~~~~v~~~~~~~~~~~~a   91 (433)
                      ..+++|+||.    +++|.||||+|++||+|+++|||+|+|.+  +++.+|+|+|+|+++                    
T Consensus         2 ~~~~~~~vp~----~~vg~iIGkgG~~Ik~i~~~tg~~I~i~~~~~~~~~r~v~I~G~~~--------------------   57 (174)
T 1j4w_A            2 SHMIDVPIPR----FAVGIVIGRNGEMIKKIQNDAGVRIQFKPDDGTTPERIAQITGPPD--------------------   57 (174)
T ss_dssp             CEEEEEEEEH----HHHHHHHCGGGHHHHHHHHHHCCEEEEECCTTSCSEEEEEEEECHH--------------------
T ss_pred             CeEEEEEECh----hheeeeecCCchHHHHHHHHhCCEEEEecCCCCCCccEEEEEeCHH--------------------
Confidence            4689999999    99999999999999999999999999985  367899999999999                    


Q ss_pred             HHHHHHHHHHHHhhhhhhcccccCCC----------------CCCCCCeEEEEEeccCcccceecCCchhHHHHHHhhCc
Q psy11929         92 VDNVCTAYNFMCRSLEDYHINRNRME----------------NCSPQPLQLKLVIPATHCGSLIGKGGCKIKDIRDLSGA  155 (433)
Q Consensus        92 ~~~v~~A~~~I~~~~~~~~~~~~~~~----------------~~~~~~~~~~l~ip~~~vg~iIGk~G~~Ik~I~~~sga  155 (433)
                        ++.+|+.+|.+++.+.........                .......+++|+||.+++|+||||+|++|++|+++|||
T Consensus        58 --~v~~A~~~I~~~~~~~~~~~~~~~~p~~~~~~~~~~~~~~~~~~~~~~~~i~vp~~~~g~iIGkgG~~Ik~I~~~tga  135 (174)
T 1j4w_A           58 --RAQHAAEIITDLLRSVQAGNPGGPGPGGRGRGRGQGNWNMGPPGGLQEFNFIVPTGKTGLIIGKGGETIKSISQQSGA  135 (174)
T ss_dssp             --HHHHHHHHHHHHHHHHC-----------------------------CEEEEEEETTTHHHHHCGGGHHHHHHHHHHCC
T ss_pred             --HHHHHHHHHHHHHHhcccCCCCCCCCCCCCCCCCCCccccCCCCCcEEEEEEEChHHcCeeECCCchHHHHHHHHHCC
Confidence              999999999998877532110000                00123468899999999999999999999999999999


Q ss_pred             eEEeccCCC--CCCCccEEEEEccHHHHHHHHHHHHHHH
Q psy11929        156 NVQVASDML--PMSTERIVTVHGNPDTISQAIYQICLVL  192 (433)
Q Consensus       156 ~I~i~~~~~--~~~~er~v~I~G~~~~v~~A~~~I~~~l  192 (433)
                      +|.|.++..  .++.++.|+|+|+++++.+|+.+|.++|
T Consensus       136 ~I~i~~~~~~~~~~~~~~v~I~G~~~~v~~A~~~I~~~i  174 (174)
T 1j4w_A          136 RIELQRNPPPNADPNMKLFTIRGTPQQIDYARQLIEEKI  174 (174)
T ss_dssp             EEEEECCCTTTSCTTEEEEEEECCHHHHHHHHHHHHHHC
T ss_pred             EEEECCCCCCCCCCCceEEEEECCHHHHHHHHHHHHHhC
Confidence            999986532  2467899999999999999999998764

>2jzx_A Poly(RC)-binding protein 2; PCBP2, KH domains, RNA binding, DNA-binding, nucleus, phosph ribonucleoprotein, RNA-binding, RNA binding protein; NMR {Homo sapiens}

Probab=99.93  E-value=2.1e-25  Score=197.72  Aligned_cols=156  Identities=26%  Similarity=0.381  Sum_probs=131.3

Q ss_pred             CCCeEEEEEeccCcccceecCCchhHHHHHHhhCceEEeccCCCCCCCccEEEEEccHHHHHHHHHHHHHHHHhhccccC
Q psy11929        121 PQPLQLKLVIPATHCGSLIGKGGCKIKDIRDLSGANVQVASDMLPMSTERIVTVHGNPDTISQAIYQICLVLIECTLQVV  200 (433)
Q Consensus       121 ~~~~~~~l~ip~~~vg~iIGk~G~~Ik~I~~~sga~I~i~~~~~~~~~er~v~I~G~~~~v~~A~~~I~~~l~e~~~~~~  200 (433)
                      +.+++++|+||..++|.||||+|++|++|+++|||+|.++++   ++.+|.|+|.|+.+++.+|+.+|.+++.+..   .
T Consensus         2 ~~~~~~~~~vp~~~~g~iIGkgG~~Ik~i~~~tg~~I~i~~~---~~~~r~v~I~G~~~~v~~A~~~I~~~i~e~~---~   75 (160)
T 2jzx_A            2 NVTLTIRLLMHGKEVGSIIGKKGESVKKMREESGARINISEG---NCPERIITLAGPTNAIFKAFAMIIDKLEEDI---S   75 (160)
T ss_dssp             CCEEEEEEEEEHHHHHHHHCGGGHHHHHHHHHHCSEEEEECC---TTTEEEEEEEEEHHHHHHHHHHHHHHHHHHH---T
T ss_pred             CccEEEEEEEchhheeeeECCCcHHHHHHHHHHCCEEEEcCC---CCCceEEEEEeCHHHHHHHHHHHHHHHHhhc---c
Confidence            356789999999999999999999999999999999999864   4678999999999999999999999988721   1


Q ss_pred             CCcccccCCCCCCCCCccccCCcccccCCCCCCCcccccCCCCCCCCccccccCcCCCCCCCCCccccccccCCCcccCC
Q psy11929        201 KGAVIPYEPKTMNAGPVILSGGQAYTLHGEYAVPVQEVAGKKQPHPLAGLAVLGIEGIGSTSLTPAALAALSGSRVKSGG  280 (433)
Q Consensus       201 ~~~~~~~~p~~~~~~p~~~~g~~~~~~~g~~~~P~~~~~~~~~~~p~~~~~~~~~~~~~~p~~~~~~~~~~~~~~~~~~~  280 (433)
                      .       +.                       +..                                            
T Consensus        76 ~-------~~-----------------------~~~--------------------------------------------   81 (160)
T 2jzx_A           76 S-------SM-----------------------TNS--------------------------------------------   81 (160)
T ss_dssp             S-------CC-----------------------CSS--------------------------------------------
T ss_pred             c-------cC-----------------------CCC--------------------------------------------
Confidence            0       00                       000                                            


Q ss_pred             CCCCCCceEEEEEeCcccccccccCCCchHHHHHhHhCCeEEEccCCC--CCceEEEEEeCHHHHHHHHHHHHHHHHh
Q psy11929        281 KDTGDDFVETEIVLTDDIAGCVIGKAGSRLLEIRQISGAQINIHTGTE--SHKKMFHIQGCQEAVSLAQYLINMCIEL  356 (433)
Q Consensus       281 ~~~~~~~~t~~i~VP~~~vG~IIGkgG~~Ik~I~~~sGA~I~I~~~~~--~~er~V~IsGt~e~v~~A~~lI~~~i~~  356 (433)
                      ........+.+|.||.+++|+||||+|++|++|++.|||+|+|++...  +.++.|+|+|+++++++|+.+|.+++.+
T Consensus        82 ~~~~~~~~~~~i~vp~~~~g~iIGkgG~~Ik~i~~~tga~I~i~~~~~~~~~~~~v~I~G~~~~v~~A~~~I~~~i~e  159 (160)
T 2jzx_A           82 TAASRPPVTLRLVVPASQCGSLIGKGGCKIKEIRESTGAQVQVAGDMLPNSTERAITIAGIPQSIIECVKQICVVMLE  159 (160)
T ss_dssp             SCCCCCSEEEEEEEEHHHHHHHHCGGGHHHHHHHHHHSSEECCCCCCSTTCCEEEEEEEECHHHHHHHHHHHHHHHHH
T ss_pred             ccCCCCCEEEEEEEChhheeeEECCCCHHHHHHHHHhCCeEEECCCCCCCCCceEEEEEcCHHHHHHHHHHHHHHHhc
Confidence            000112468899999999999999999999999999999999986432  7889999999999999999999998864

>2jvz_A KH type-splicing, FAR upstream element-binding protein 2; RNA binding protein, KH domain, KSRP, posttranscriptional regulation, mRNA decay; NMR {Homo sapiens}

Probab=99.93  E-value=1.8e-25  Score=198.85  Aligned_cols=153  Identities=21%  Similarity=0.315  Sum_probs=130.1

Q ss_pred             EEEEEEeccCCcccccceeeecCchHHHHHHHHhCCeEEEeCC----CCCcceEEEecccCCCCCCccccCCCCCccccc
Q psy11929         15 ITMRCLFHSSVNVNEISCLIGPGGCIVRRLRKESGAKISITDG----ACPDRIVTVSGSVDNSSTSSVETGYPGHTLWVT   90 (433)
Q Consensus        15 ~~~rilvp~~~~~~~vg~IIGk~G~~Ik~I~~~tga~I~v~~~----~~~eRvv~I~G~~~~~~~~~v~~~~~~~~~~~~   90 (433)
                      ++++|+||.    +++|.||||+|++||+|+++|||+|+|.+.    +..+|+|+|+|+++                   
T Consensus         2 ~~~~~~Vp~----~~~g~iIGk~G~~Ik~i~~~tg~~I~i~~~~~~~~~~~r~v~I~G~~~-------------------   58 (164)
T 2jvz_A            2 TVQEIMIPA----GKAGLVIGKGGETIKQLQERAGVKMILIQDGSQNTNVDKPLRIIGDPY-------------------   58 (164)
T ss_dssp             EEEEEEECT----TCHHHHTCTTTHHHHHHHHTSCSEEEECCCTTSSSSSCEEEEEEECHH-------------------
T ss_pred             eEEEEEech----hheeEEECCChHHHHHHHHHhCCeEEEecCCCCCCCCceEEEEEcCHH-------------------
Confidence            688999999    999999999999999999999999999753    46789999999988                   


Q ss_pred             hHHHHHHHHHHHHhhhhhhccc-ccCCC-CCCCCCeEEEEEeccCcccceecCCchhHHHHHHhhCceEEeccCCCCCCC
Q psy11929         91 SVDNVCTAYNFMCRSLEDYHIN-RNRME-NCSPQPLQLKLVIPATHCGSLIGKGGCKIKDIRDLSGANVQVASDMLPMST  168 (433)
Q Consensus        91 a~~~v~~A~~~I~~~~~~~~~~-~~~~~-~~~~~~~~~~l~ip~~~vg~iIGk~G~~Ik~I~~~sga~I~i~~~~~~~~~  168 (433)
                         ++.+|..+|.+++.+.... +.... .......+++|.||..++|+||||+|++|++|+++|||+|.|.++ .+.+.
T Consensus        59 ---~v~~A~~~I~~ii~e~~~~~~~~~~~~~~~~~~~~~i~vp~~~~g~iIGk~G~~I~~i~~~tg~~I~i~~~-~~~~~  134 (164)
T 2jvz_A           59 ---KVQQACEMVMDILRERDQGGFGDRNEYGSRIGGGIDVPVPRHSVGVVIGRSGEMIKKIQNDAGVRIQFKQD-DGTGP  134 (164)
T ss_dssp             ---HHHHHHHHHHHHTTCSSSCCCSSCSSCTTSCSSSBCCEEETTTHHHHHCSSSHHHHHHHHHTCCEEEECCC-CTTSS
T ss_pred             ---HHHHHHHHHHHHHHhccCCCCCCccccCCCCCceEEEEEChhhccccCCCCcHhHHHHHHHHCCeEEEeCC-CCCCC
Confidence               9999999999988764321 11110 011123568899999999999999999999999999999999864 24566


Q ss_pred             ccEEEEEccHHHHHHHHHHHHHHHHh
Q psy11929        169 ERIVTVHGNPDTISQAIYQICLVLIE  194 (433)
Q Consensus       169 er~v~I~G~~~~v~~A~~~I~~~l~e  194 (433)
                      ++.|+|+|+++++..|+.+|.+++.+
T Consensus       135 ~~~v~I~G~~~~v~~A~~~I~~~i~~  160 (164)
T 2jvz_A          135 EKIAHIMGPPDRCEHAARIINDLLQS  160 (164)
T ss_dssp             EEEEEEESCHHHHHHHHHHHHHHHHH
T ss_pred             cEEEEEEcCHHHHHHHHHHHHHHHhh
Confidence            89999999999999999999999987

>1j4w_A FUSE binding protein; single-stranded DNA binding protein; HET: DNA; NMR {Homo sapiens} SCOP: d.51.1.1 d.51.1.1

Probab=99.92  E-value=3.6e-25  Score=198.90  Aligned_cols=169  Identities=28%  Similarity=0.423  Sum_probs=127.7

Q ss_pred             CeEEEEEeccCcccceecCCchhHHHHHHhhCceEEeccCCCCCCCccEEEEEccHHHHHHHHHHHHHHHHhhccccCCC
Q psy11929        123 PLQLKLVIPATHCGSLIGKGGCKIKDIRDLSGANVQVASDMLPMSTERIVTVHGNPDTISQAIYQICLVLIECTLQVVKG  202 (433)
Q Consensus       123 ~~~~~l~ip~~~vg~iIGk~G~~Ik~I~~~sga~I~i~~~~~~~~~er~v~I~G~~~~v~~A~~~I~~~l~e~~~~~~~~  202 (433)
                      ..+++|+||.+++|.||||+|++|++|+++|||+|+|.++ .+.+.+|.|+|+|++++|.+|+.+|.+++.+..   . +
T Consensus         2 ~~~~~~~vp~~~vg~iIGkgG~~Ik~i~~~tg~~I~i~~~-~~~~~~r~v~I~G~~~~v~~A~~~I~~~~~~~~---~-~   76 (174)
T 1j4w_A            2 SHMIDVPIPRFAVGIVIGRNGEMIKKIQNDAGVRIQFKPD-DGTTPERIAQITGPPDRAQHAAEIITDLLRSVQ---A-G   76 (174)
T ss_dssp             CEEEEEEEEHHHHHHHHCGGGHHHHHHHHHHCCEEEEECC-TTSCSEEEEEEEECHHHHHHHHHHHHHHHHHHC------
T ss_pred             CeEEEEEEChhheeeeecCCchHHHHHHHHhCCEEEEecC-CCCCCccEEEEEeCHHHHHHHHHHHHHHHHhcc---c-C
Confidence            3578999999999999999999999999999999999853 346788999999999999999999999998721   0 0


Q ss_pred             cccccCCCCCCCCCccccCCcccccCCCCCCCcccccCCCCCCCCccccccCcCCCCCCCCCccccccccCCCcccCCCC
Q psy11929        203 AVIPYEPKTMNAGPVILSGGQAYTLHGEYAVPVQEVAGKKQPHPLAGLAVLGIEGIGSTSLTPAALAALSGSRVKSGGKD  282 (433)
Q Consensus       203 ~~~~~~p~~~~~~p~~~~g~~~~~~~g~~~~P~~~~~~~~~~~p~~~~~~~~~~~~~~p~~~~~~~~~~~~~~~~~~~~~  282 (433)
                         .+.+.    .|    ++.++                            +.....|.+                   .
T Consensus        77 ---~~~~~----~p----~~~~~----------------------------~~~~~~~~~-------------------~   98 (174)
T 1j4w_A           77 ---NPGGP----GP----GGRGR----------------------------GRGQGNWNM-------------------G   98 (174)
T ss_dssp             --------------------------------------------------------------------------------
T ss_pred             ---CCCCC----CC----CCCCC----------------------------CCCCCcccc-------------------C
Confidence               00000    00    00000                            000000000                   0


Q ss_pred             CCCCceEEEEEeCcccccccccCCCchHHHHHhHhCCeEEEccCCC----CCceEEEEEeCHHHHHHHHHHHHHHH
Q psy11929        283 TGDDFVETEIVLTDDIAGCVIGKAGSRLLEIRQISGAQINIHTGTE----SHKKMFHIQGCQEAVSLAQYLINMCI  354 (433)
Q Consensus       283 ~~~~~~t~~i~VP~~~vG~IIGkgG~~Ik~I~~~sGA~I~I~~~~~----~~er~V~IsGt~e~v~~A~~lI~~~i  354 (433)
                      +.....+.+|.||.+++|+||||+|++|++|++.|||+|+|++...    +.++.|+|+|+++++++|+.+|.++|
T Consensus        99 ~~~~~~~~~i~vp~~~~g~iIGkgG~~Ik~I~~~tga~I~i~~~~~~~~~~~~~~v~I~G~~~~v~~A~~~I~~~i  174 (174)
T 1j4w_A           99 PPGGLQEFNFIVPTGKTGLIIGKGGETIKSISQQSGARIELQRNPPPNADPNMKLFTIRGTPQQIDYARQLIEEKI  174 (174)
T ss_dssp             -----CEEEEEEETTTHHHHHCGGGHHHHHHHHHHCCEEEEECCCTTTSCTTEEEEEEECCHHHHHHHHHHHHHHC
T ss_pred             CCCCcEEEEEEEChHHcCeeECCCchHHHHHHHHHCCEEEECCCCCCCCCCCceEEEEECCHHHHHHHHHHHHHhC
Confidence            0113467899999999999999999999999999999999987642    67899999999999999999999874

>3n89_A Defective in GERM LINE development protein 3, ISO; KH domains, RNA binding, cell cycle; 2.79A {Caenorhabditis elegans}

Probab=99.92  E-value=1.2e-24  Score=213.99  Aligned_cols=221  Identities=12%  Similarity=0.083  Sum_probs=167.3

Q ss_pred             CCCceEEEEEEeccCCcccccceeeecCc--hHHHHHHHHhCCeEEEeCCC-------CCcceEEEecccCCCCCCcccc
Q psy11929         10 DEDTLITMRCLFHSSVNVNEISCLIGPGG--CIVRRLRKESGAKISITDGA-------CPDRIVTVSGSVDNSSTSSVET   80 (433)
Q Consensus        10 ~~~~~~~~rilvp~~~~~~~vg~IIGk~G--~~Ik~I~~~tga~I~v~~~~-------~~eRvv~I~G~~~~~~~~~v~~   80 (433)
                      .....+++.+.||.    .+++.||||+|  ++|++|+++|||+|+|++.+       .....|+|+|.++         
T Consensus        25 ~~~~~VTl~v~Ip~----~~Hs~IIGkgG~~sNIkkImeEtgv~I~fPD~~~~~~~~~~ks~~VtItG~~e---------   91 (376)
T 3n89_A           25 INPTRVTLNMEFES----QYYSLMTSDNGDHENVASIMAETNTLIQLPDRSVGGTTPDPFAQQVTITGYFG---------   91 (376)
T ss_dssp             CCTTEEEEEEECCG----GGHHHHHSCCSSSCSHHHHHHHHTCEEECCCCCCCSSSCCTTTTEEEEEEEHH---------
T ss_pred             ecCCEEEEEEEEch----hhhhhhccCCChHHHHHHHHHHhCCeEECCCCcccccCCcCCCCeEEEEcCHH---------
Confidence            34678999999999    99999999999  99999999999999999854       3457899999999         


Q ss_pred             CCCCCccccchHHHHHHHHHHHHhhhhhhcccccCCCCCCCCCeEEEEEeccCcccceecCCchhHHHHHHhhCceEEec
Q psy11929         81 GYPGHTLWVTSVDNVCTAYNFMCRSLEDYHINRNRMENCSPQPLQLKLVIPATHCGSLIGKGGCKIKDIRDLSGANVQVA  160 (433)
Q Consensus        81 ~~~~~~~~~~a~~~v~~A~~~I~~~~~~~~~~~~~~~~~~~~~~~~~l~ip~~~vg~iIGk~G~~Ik~I~~~sga~I~i~  160 (433)
                                   +|.+|..+|.+.+                ++++.+.+|...++.  ...+..|.+ ++.++++|.|+
T Consensus        92 -------------nVE~AR~~I~~l~----------------Pl~i~~elp~~~i~~--~~l~~~I~q-q~~y~V~I~Fp  139 (376)
T 3n89_A           92 -------------DVDRARMLMRRNC----------------HFTVFMALSKMKMPL--HELQAHVRQ-NPIQNVEMSFV  139 (376)
T ss_dssp             -------------HHHHHHHHHHHSC----------------EEEEEEECTTCSSCH--HHHHHHHHH-CCCTTCEEEEE
T ss_pred             -------------HHHHHHHHHHhcC----------------CceEEEEccccccCc--chhhhhhcc-ceeCceEEEeC
Confidence                         9999999998632                445666666644332  111334544 56799999997


Q ss_pred             cCCC-CCCCccEEEEEccHHHHHHHHHHHHHHHHhhccccCCCcccccCCCCCCCCCccccCCcccccCCCCCCCccccc
Q psy11929        161 SDML-PMSTERIVTVHGNPDTISQAIYQICLVLIECTLQVVKGAVIPYEPKTMNAGPVILSGGQAYTLHGEYAVPVQEVA  239 (433)
Q Consensus       161 ~~~~-~~~~er~v~I~G~~~~v~~A~~~I~~~l~e~~~~~~~~~~~~~~p~~~~~~p~~~~g~~~~~~~g~~~~P~~~~~  239 (433)
                      .... .......|+|+|...++.+|++.+..++....+..                                        
T Consensus       140 ~~~~~~~~~sd~V~IrG~~~nv~~akeA~~~Ll~~l~~~e----------------------------------------  179 (376)
T 3n89_A          140 DAPEKNGIVTTYLRITAREKNQHELIEAAKRLNEILFRES----------------------------------------  179 (376)
T ss_dssp             EEC-----CEEEEEEEEEGGGHHHHHHHHHHHHHHHCC------------------------------------------
T ss_pred             CcccccCCCCCEEEEEcChhhHHHHHHHHHHHHHHHHhhh----------------------------------------
Confidence            5311 11235689999999888877777766665511000                                        


Q ss_pred             CCCCCCCCccccccCcCCCCCCCCCccccccccCCCcccCCCCCCCCceEEEEEeCcccccccccCCC--chHHHHHhHh
Q psy11929        240 GKKQPHPLAGLAVLGIEGIGSTSLTPAALAALSGSRVKSGGKDTGDDFVETEIVLTDDIAGCVIGKAG--SRLLEIRQIS  317 (433)
Q Consensus       240 ~~~~~~p~~~~~~~~~~~~~~p~~~~~~~~~~~~~~~~~~~~~~~~~~~t~~i~VP~~~vG~IIGkgG--~~Ik~I~~~s  317 (433)
                                                                ......++.+|.|+..++..||||+|  ..|++|+++|
T Consensus       180 ------------------------------------------~~~~~~~s~~v~V~~~~H~~IIGk~G~n~~IkkIr~eT  217 (376)
T 3n89_A          180 ------------------------------------------PAPENNFTLHFTLSTYYVDQVLGSSSTAQLMPVIERET  217 (376)
T ss_dssp             ------------------------------------------CCCSSCEEEEEEEEGGGHHHHTCCTTSCCHHHHHHHHH
T ss_pred             ------------------------------------------cccccceEEEEEeCHHHHHHhhcCCCcchHHHHHHHhh
Confidence                                                      00123578899999999999999999  5569999999


Q ss_pred             CCeEEEccCCC-----CCceEEEEEeCHHHHHHHHHHHHHHHHhc
Q psy11929        318 GAQINIHTGTE-----SHKKMFHIQGCQEAVSLAQYLINMCIELQ  357 (433)
Q Consensus       318 GA~I~I~~~~~-----~~er~V~IsGt~e~v~~A~~lI~~~i~~~  357 (433)
                      ||+|.|++..+     .+...|+|+|++++|..|+..|+++|--.
T Consensus       218 Gv~I~FP~~~d~~d~~~~~~~ItItGs~e~V~~Ark~I~~lLPv~  262 (376)
T 3n89_A          218 TTIISYPCYNNRNETRGNIYEIKVVGNIDNVLKARRYIMDLLPIS  262 (376)
T ss_dssp             TCEEECC---------CCEEEEEEESCHHHHHHHHHHHHHTSEEE
T ss_pred             CCEEECCCCCCcccccCCceEEEEEeCHHHHHHHHHHHHhhCCEE
Confidence            99999997643     24578999999999999999999988543

>2qnd_A FMR1 protein; KH domain, eukaryotic KH domains, tandem KH domains, type I domains, fragIle X mental retardation protein, RNA BI protein; 1.90A {Homo sapiens} PDB: 2fmr_A

Probab=99.78  E-value=8.8e-19  Score=151.94  Aligned_cols=133  Identities=23%  Similarity=0.378  Sum_probs=106.3

Q ss_pred             CeEEEEEeccCcccceecCCchhHHHHHHhhCceEEeccCCCCCCCccEEEEEccHHHHHHHHHHHHHHHHhhccccCCC
Q psy11929        123 PLQLKLVIPATHCGSLIGKGGCKIKDIRDLSGANVQVASDMLPMSTERIVTVHGNPDTISQAIYQICLVLIECTLQVVKG  202 (433)
Q Consensus       123 ~~~~~l~ip~~~vg~iIGk~G~~Ik~I~~~sga~I~i~~~~~~~~~er~v~I~G~~~~v~~A~~~I~~~l~e~~~~~~~~  202 (433)
                      .++.+|+||...+|.+||++|++|+.|++++|++|....+    ..++.+...+++++|.+|..++     +        
T Consensus         3 ~~~~~~~Vp~~~vG~~IG~~G~~I~~i~~e~gI~ii~~~~----~~~~~i~~~~~p~~v~~~~~~l-----~--------   65 (144)
T 2qnd_A            3 RFHEQFIVREDLMGLAIGTHGANIQQARKVPGVTAIDLDE----DTCTFHIYGEDQDAVKKARSFL-----E--------   65 (144)
T ss_dssp             -CEEEEECCGGGHHHHHCGGGHHHHHHHTSTTEEEEEEET----TTTEEEEEESSHHHHHHHHHHH-----C--------
T ss_pred             ceEEEEEECCcceeeEECCChhHHHHHHHHHCCeEeccCC----CchheeeccCCHHHHHHHHHhh-----h--------
Confidence            4678999999999999999999999999999954433322    2344555556799998885431     1        


Q ss_pred             cccccCCCCCCCCCccccCCcccccCCCCCCCcccccCCCCCCCCccccccCcCCCCCCCCCccccccccCCCcccCCCC
Q psy11929        203 AVIPYEPKTMNAGPVILSGGQAYTLHGEYAVPVQEVAGKKQPHPLAGLAVLGIEGIGSTSLTPAALAALSGSRVKSGGKD  282 (433)
Q Consensus       203 ~~~~~~p~~~~~~p~~~~g~~~~~~~g~~~~P~~~~~~~~~~~p~~~~~~~~~~~~~~p~~~~~~~~~~~~~~~~~~~~~  282 (433)
                                                                                                      
T Consensus        66 --------------------------------------------------------------------------------   65 (144)
T 2qnd_A           66 --------------------------------------------------------------------------------   65 (144)
T ss_dssp             --------------------------------------------------------------------------------
T ss_pred             --------------------------------------------------------------------------------
Confidence                                                                                            


Q ss_pred             CCCCceEEEEEeCcccccccccCCCchHHHHHhHhCC-eEEEccCCC----CCc--eEEEEEeCHHHHHHHHHHHHHHHH
Q psy11929        283 TGDDFVETEIVLTDDIAGCVIGKAGSRLLEIRQISGA-QINIHTGTE----SHK--KMFHIQGCQEAVSLAQYLINMCIE  355 (433)
Q Consensus       283 ~~~~~~t~~i~VP~~~vG~IIGkgG~~Ik~I~~~sGA-~I~I~~~~~----~~e--r~V~IsGt~e~v~~A~~lI~~~i~  355 (433)
                          ....++.||.+++|++|||+|.+|+.|++.||| +|+|++..+    .++  +.|+|+|++++++.|+.||.++|.
T Consensus        66 ----~~e~~v~Vp~~~~g~~IGK~G~nIr~i~~~tG~~~I~i~~~~~~~~~~~~~~~~vtI~G~~~~v~~Ak~li~~~l~  141 (144)
T 2qnd_A           66 ----FAEDVIQVPRNLVGKVIGKNGKLIQEIVDKSGVVRVRIEAENEKNVPQEEGMVPFVFVGTKDSIANATVLLDYHLN  141 (144)
T ss_dssp             ----EEEEEEEEEGGGHHHHHCGGGHHHHHHHHHHTCSEEEEEEECTTCCCCCTTEEEEEEEEEHHHHHHHHHHHHHHHH
T ss_pred             ----cceEEEEECHHHcCeeECCCCHHHHHHHHHHCCEEEEEcCCCCCCccccCCeeEEEEEeCHHHHHHHHHHHHHHHH
Confidence                002589999999999999999999999999997 899987543    123  358999999999999999999997


Q ss_pred             h
Q psy11929        356 L  356 (433)
Q Consensus       356 ~  356 (433)
                      +
T Consensus       142 ~  142 (144)
T 2qnd_A          142 Y  142 (144)
T ss_dssp             T
T ss_pred             h
Confidence            5

>2qnd_A FMR1 protein; KH domain, eukaryotic KH domains, tandem KH domains, type I domains, fragIle X mental retardation protein, RNA BI protein; 1.90A {Homo sapiens} PDB: 2fmr_A

Probab=99.77  E-value=7.8e-19  Score=152.24  Aligned_cols=134  Identities=22%  Similarity=0.276  Sum_probs=106.7

Q ss_pred             eEEEEEEeccCCcccccceeeecCchHHHHHHHHhCCeEEEeC-CCCCcceEEEecccCCCCCCccccCCCCCccccchH
Q psy11929         14 LITMRCLFHSSVNVNEISCLIGPGGCIVRRLRKESGAKISITD-GACPDRIVTVSGSVDNSSTSSVETGYPGHTLWVTSV   92 (433)
Q Consensus        14 ~~~~rilvp~~~~~~~vg~IIGk~G~~Ik~I~~~tga~I~v~~-~~~~eRvv~I~G~~~~~~~~~v~~~~~~~~~~~~a~   92 (433)
                      .++.+++||.    +.+|++||++|++|++|++++|  |++.. ...+++++...++++                     
T Consensus         3 ~~~~~~~Vp~----~~vG~~IG~~G~~I~~i~~e~g--I~ii~~~~~~~~~i~~~~~p~---------------------   55 (144)
T 2qnd_A            3 RFHEQFIVRE----DLMGLAIGTHGANIQQARKVPG--VTAIDLDEDTCTFHIYGEDQD---------------------   55 (144)
T ss_dssp             -CEEEEECCG----GGHHHHHCGGGHHHHHHHTSTT--EEEEEEETTTTEEEEEESSHH---------------------
T ss_pred             ceEEEEEECC----cceeeEECCChhHHHHHHHHHC--CeEeccCCCchheeeccCCHH---------------------
Confidence            5688999999    9999999999999999999999  55433 233555555555677                     


Q ss_pred             HHHHHHHHHHHhhhhhhcccccCCCCCCCCCeEEEEEeccCcccceecCCchhHHHHHHhhCc-eEEeccCCCC--CCCc
Q psy11929         93 DNVCTAYNFMCRSLEDYHINRNRMENCSPQPLQLKLVIPATHCGSLIGKGGCKIKDIRDLSGA-NVQVASDMLP--MSTE  169 (433)
Q Consensus        93 ~~v~~A~~~I~~~~~~~~~~~~~~~~~~~~~~~~~l~ip~~~vg~iIGk~G~~Ik~I~~~sga-~I~i~~~~~~--~~~e  169 (433)
                       ++.+|..++ ...                  ..++.||..++|++|||+|++|+.|++.||+ +|.|.++...  ..++
T Consensus        56 -~v~~~~~~l-~~~------------------e~~v~Vp~~~~g~~IGK~G~nIr~i~~~tG~~~I~i~~~~~~~~~~~~  115 (144)
T 2qnd_A           56 -AVKKARSFL-EFA------------------EDVIQVPRNLVGKVIGKNGKLIQEIVDKSGVVRVRIEAENEKNVPQEE  115 (144)
T ss_dssp             -HHHHHHHHH-CEE------------------EEEEEEEGGGHHHHHCGGGHHHHHHHHHHTCSEEEEEEECTTCCCCCT
T ss_pred             -HHHHHHHhh-hcc------------------eEEEEECHHHcCeeECCCCHHHHHHHHHHCCEEEEEcCCCCCCccccC
Confidence             888876543 110                  2789999999999999999999999999997 9999864221  2233


Q ss_pred             c--EEEEEccHHHHHHHHHHHHHHHHh
Q psy11929        170 R--IVTVHGNPDTISQAIYQICLVLIE  194 (433)
Q Consensus       170 r--~v~I~G~~~~v~~A~~~I~~~l~e  194 (433)
                      +  .|+|+|++++|+.|+.+|..+|.+
T Consensus       116 ~~~~vtI~G~~~~v~~Ak~li~~~l~~  142 (144)
T 2qnd_A          116 GMVPFVFVGTKDSIANATVLLDYHLNY  142 (144)
T ss_dssp             TEEEEEEEEEHHHHHHHHHHHHHHHHT
T ss_pred             CeeEEEEEeCHHHHHHHHHHHHHHHHh
Confidence            3  589999999999999999999875

>2e3u_A PH-DIM2P, hypothetical protein PH1566; PRE-ribosomal RNA processing factor, RNA binding protein; 2.30A {Pyrococcus horikoshii} PDB: 3aev_B

Probab=99.71  E-value=2.5e-17  Score=151.80  Aligned_cols=149  Identities=20%  Similarity=0.197  Sum_probs=111.8

Q ss_pred             ceEEEEEEeccCCcccccceeeecCchHHHHHHHHhCCeEEEeCCCCCcceEEEecccCCCCCCccccCCCCCccccchH
Q psy11929         13 TLITMRCLFHSSVNVNEISCLIGPGGCIVRRLRKESGAKISITDGACPDRIVTVSGSVDNSSTSSVETGYPGHTLWVTSV   92 (433)
Q Consensus        13 ~~~~~rilvp~~~~~~~vg~IIGk~G~~Ik~I~~~tga~I~v~~~~~~eRvv~I~G~~~~~~~~~v~~~~~~~~~~~~a~   92 (433)
                      ..-+.++.||.    ..+|.|||++|++|+.|+++|||+|++..   .++.|+|.++..-                 ...
T Consensus        32 aP~i~~i~IP~----~kig~lIG~gGk~Ik~I~e~tgvkI~I~~---~~g~V~I~~~~~t-----------------~d~   87 (219)
T 2e3u_A           32 FKQEEYVKIPK----DRIAVLIGKKGQTKKEIEKRTKTKITIDS---ETGEVWITSTKET-----------------EDP   87 (219)
T ss_dssp             -CCEEEEECCH----HHHHHHHCGGGHHHHHHHHHHTEEEEECT---TTCEEEEEECTTC-----------------CSH
T ss_pred             CCEEEEEEeCH----HHhhhhhcccHHHHHHHHHHHCcEEEEEc---CCCEEEEecCCCC-----------------CCH
Confidence            34567999999    99999999999999999999999999984   3567999987620                 001


Q ss_pred             HHHHHHHHHHHhhhhhhcccccCCCCCCCCCeEEEEEecc-----------CcccceecCCchhHHHHHHhhCceEEecc
Q psy11929         93 DNVCTAYNFMCRSLEDYHINRNRMENCSPQPLQLKLVIPA-----------THCGSLIGKGGCKIKDIRDLSGANVQVAS  161 (433)
Q Consensus        93 ~~v~~A~~~I~~~~~~~~~~~~~~~~~~~~~~~~~l~ip~-----------~~vg~iIGk~G~~Ik~I~~~sga~I~i~~  161 (433)
                      +++.+|.++|..+...+........ ..+....-.+.++.           ..+|+||||+|++|+.|++.|||+|.|. 
T Consensus        88 ~~i~kA~~~I~~i~rg~~~e~g~~l-l~dd~~~e~i~i~~~~v~~~~~~~~r~~GriIGk~G~tik~ie~~Tg~~I~v~-  165 (219)
T 2e3u_A           88 LAVWKARDIVLAIGRGFSPERAFRL-LNEGEYLEIINLTDIIIGNEKNALPRVRGRIIGRKGRTRQIIEEMSGASVSVY-  165 (219)
T ss_dssp             HHHHHHHHHHHHHHTTCCHHHHGGG-GSTTCEEEEEEGGGCC------CHHHHHHHHHCGGGHHHHHHHHHHCCEEEEE-
T ss_pred             HHHHHHHHHHHHHhccCCcccccee-ccCCccceeEEcccccccCCchhhhhhhheeECCCchHHHHHHHHhCceEEEC-
Confidence            2899999999887632110000000 00111112233332           2689999999999999999999999996 


Q ss_pred             CCCCCCCccEEEEEccHHHHHHHHHHHHHHHHh
Q psy11929        162 DMLPMSTERIVTVHGNPDTISQAIYQICLVLIE  194 (433)
Q Consensus       162 ~~~~~~~er~v~I~G~~~~v~~A~~~I~~~l~e  194 (433)
                             ++.|+|.|+.++++.|..+|.+++..
T Consensus       166 -------~~~v~i~G~~~~i~~A~~~i~~li~g  191 (219)
T 2e3u_A          166 -------GKTVAIIGNPIQIEIAKTAIEKLARG  191 (219)
T ss_dssp             -------TTEEEEEECHHHHHHHHHHHHHHHTT
T ss_pred             -------CeEEEEEeCHHHHHHHHHHHHHHHcC
Confidence                   46799999999999999999999976

>2e3u_A PH-DIM2P, hypothetical protein PH1566; PRE-ribosomal RNA processing factor, RNA binding protein; 2.30A {Pyrococcus horikoshii} PDB: 3aev_B

Probab=99.67  E-value=1.6e-16  Score=146.33  Aligned_cols=145  Identities=20%  Similarity=0.180  Sum_probs=111.4

Q ss_pred             CCCeEEEEEeccCcccceecCCchhHHHHHHhhCceEEeccCCCCCCCccEEEEEcc-----HHHHHHHHHHHHHHHHhh
Q psy11929        121 PQPLQLKLVIPATHCGSLIGKGGCKIKDIRDLSGANVQVASDMLPMSTERIVTVHGN-----PDTISQAIYQICLVLIEC  195 (433)
Q Consensus       121 ~~~~~~~l~ip~~~vg~iIGk~G~~Ik~I~~~sga~I~i~~~~~~~~~er~v~I~G~-----~~~v~~A~~~I~~~l~e~  195 (433)
                      ..+...++.||.+.+|.|||++|++|+.|+++||++|.+..+      ++.|+|.++     ++++.+|..+|..+.+. 
T Consensus        31 ~aP~i~~i~IP~~kig~lIG~gGk~Ik~I~e~tgvkI~I~~~------~g~V~I~~~~~t~d~~~i~kA~~~I~~i~rg-  103 (219)
T 2e3u_A           31 FFKQEEYVKIPKDRIAVLIGKKGQTKKEIEKRTKTKITIDSE------TGEVWITSTKETEDPLAVWKARDIVLAIGRG-  103 (219)
T ss_dssp             --CCEEEEECCHHHHHHHHCGGGHHHHHHHHHHTEEEEECTT------TCEEEEEECTTCCSHHHHHHHHHHHHHHHTT-
T ss_pred             CCCEEEEEEeCHHHhhhhhcccHHHHHHHHHHHCcEEEEEcC------CCEEEEecCCCCCCHHHHHHHHHHHHHHhcc-
Confidence            345567899999999999999999999999999999999743      577888885     69999999999998854 


Q ss_pred             ccccCCCcccccCCCCCCCCCccccCCcccccCCCCCCCcccccCCCCCCCCccccccCcCCCCCCCCCccccccccCCC
Q psy11929        196 TLQVVKGAVIPYEPKTMNAGPVILSGGQAYTLHGEYAVPVQEVAGKKQPHPLAGLAVLGIEGIGSTSLTPAALAALSGSR  275 (433)
Q Consensus       196 ~~~~~~~~~~~~~p~~~~~~p~~~~g~~~~~~~g~~~~P~~~~~~~~~~~p~~~~~~~~~~~~~~p~~~~~~~~~~~~~~  275 (433)
                        ..+......+..                                                                  
T Consensus       104 --~~~e~g~~ll~d------------------------------------------------------------------  115 (219)
T 2e3u_A          104 --FSPERAFRLLNE------------------------------------------------------------------  115 (219)
T ss_dssp             --CCHHHHGGGGST------------------------------------------------------------------
T ss_pred             --CCccccceeccC------------------------------------------------------------------
Confidence              111000000000                                                                  


Q ss_pred             cccCCCCCCCCceEEEEEe-----------CcccccccccCCCchHHHHHhHhCCeEEEccCCCCCceEEEEEeCHHHHH
Q psy11929        276 VKSGGKDTGDDFVETEIVL-----------TDDIAGCVIGKAGSRLLEIRQISGAQINIHTGTESHKKMFHIQGCQEAVS  344 (433)
Q Consensus       276 ~~~~~~~~~~~~~t~~i~V-----------P~~~vG~IIGkgG~~Ik~I~~~sGA~I~I~~~~~~~er~V~IsGt~e~v~  344 (433)
                                ......+.+           +...+|+||||+|.+|+.|++.|||+|.|++      +.|+|.|++++++
T Consensus       116 ----------d~~~e~i~i~~~~v~~~~~~~~r~~GriIGk~G~tik~ie~~Tg~~I~v~~------~~v~i~G~~~~i~  179 (219)
T 2e3u_A          116 ----------GEYLEIINLTDIIIGNEKNALPRVRGRIIGRKGRTRQIIEEMSGASVSVYG------KTVAIIGNPIQIE  179 (219)
T ss_dssp             ----------TCEEEEEEGGGCC------CHHHHHHHHHCGGGHHHHHHHHHHCCEEEEET------TEEEEEECHHHHH
T ss_pred             ----------CccceeEEcccccccCCchhhhhhhheeECCCchHHHHHHHHhCceEEECC------eEEEEEeCHHHHH
Confidence                      000001111           2347899999999999999999999999975      5699999999999


Q ss_pred             HHHHHHHHHHHh
Q psy11929        345 LAQYLINMCIEL  356 (433)
Q Consensus       345 ~A~~lI~~~i~~  356 (433)
                      .|+.+|.++|..
T Consensus       180 ~A~~~i~~li~g  191 (219)
T 2e3u_A          180 IAKTAIEKLARG  191 (219)
T ss_dssp             HHHHHHHHHHTT
T ss_pred             HHHHHHHHHHcC
Confidence            999999999954

>1zzk_A Heterogeneous nuclear ribonucleoprotein K; KH domian, alpha-beta fold, DNA binding protein; 0.95A {Homo sapiens} SCOP: d.51.1.1 PDB: 1zzj_A 1zzi_A

Probab=99.62  E-value=1.7e-15  Score=118.38  Aligned_cols=72  Identities=35%  Similarity=0.622  Sum_probs=67.2

Q ss_pred             CceEEEEEeCcccccccccCCCchHHHHHhHhCCeEEEccCCC-CCceEEEEEeCHHHHHHHHHHHHHHHHhc
Q psy11929        286 DFVETEIVLTDDIAGCVIGKAGSRLLEIRQISGAQINIHTGTE-SHKKMFHIQGCQEAVSLAQYLINMCIELQ  357 (433)
Q Consensus       286 ~~~t~~i~VP~~~vG~IIGkgG~~Ik~I~~~sGA~I~I~~~~~-~~er~V~IsGt~e~v~~A~~lI~~~i~~~  357 (433)
                      ...+.+|.||.+++|+||||+|++|++|+++|||+|+|++... +.+|.|+|+|+++++++|+.+|.+++.+.
T Consensus         5 ~~~~~~i~Vp~~~vg~iIGkgG~~Ik~I~~~tga~I~i~~~~~~~~~~~v~I~G~~~~v~~A~~~I~~~i~~~   77 (82)
T 1zzk_A            5 PIITTQVTIPKDLAGSIIGKGGQRIKQIRHESGASIKIDEPLEGSEDRIITITGTQDQIQNAQYLLQNSVKQY   77 (82)
T ss_dssp             CCEEEEEEEETTTGGGGTCGGGHHHHHHHHHHCCEEEECCTTSCSSEEEEEEEECHHHHHHHHHHHHHHHHHH
T ss_pred             CeEEEEEEEChHhcCeeECCCchHHHHHHHHHCCEEEEcCCCCCCCceEEEEEeCHHHHHHHHHHHHHHHHhc
Confidence            4788999999999999999999999999999999999998654 78899999999999999999999999764

>2p2r_A Poly(RC)-binding protein 2; protein-DNA complex, RNA and DNA binding protein/DNA complex; 1.60A {Homo sapiens}

Probab=99.61  E-value=8e-16  Score=118.54  Aligned_cols=72  Identities=40%  Similarity=0.716  Sum_probs=67.0

Q ss_pred             CceEEEEEeCcccccccccCCCchHHHHHhHhCCeEEEccCCC-CCceEEEEEeCHHHHHHHHHHHHHHHHhc
Q psy11929        286 DFVETEIVLTDDIAGCVIGKAGSRLLEIRQISGAQINIHTGTE-SHKKMFHIQGCQEAVSLAQYLINMCIELQ  357 (433)
Q Consensus       286 ~~~t~~i~VP~~~vG~IIGkgG~~Ik~I~~~sGA~I~I~~~~~-~~er~V~IsGt~e~v~~A~~lI~~~i~~~  357 (433)
                      ...+.+|.||.+++|+||||+|++|++|++.|||+|+|+++.+ +.+|.|+|+|+++++++|+.+|.+++.++
T Consensus         3 ~~~~~~i~Ip~~~vg~iIGkgG~~Ik~I~~~tga~I~i~~~~~~~~~~~v~I~G~~~~v~~A~~~I~~~i~~E   75 (76)
T 2p2r_A            3 QTTSHELTIPNDLIGCIIGRQGAKINEIRQMSGAQIKIANPVEGSTDRQVTITGSAASISLAQYLINVRLSSE   75 (76)
T ss_dssp             CCEEEEEEEEHHHHHHHHCGGGHHHHHHHHHHCCEEEECCCCTTCSEEEEEEEECHHHHHHHHHHHHHHHTTC
T ss_pred             CceEEEEEEChHHcceEECCCChHHHHHHHHHCCEEEEcCCCCCCCeEEEEEEeCHHHHHHHHHHHHHHHHcc
Confidence            3678899999999999999999999999999999999998655 78999999999999999999999999764

>1wvn_A Poly(RC)-binding protein 1; KH domain, RNA binding domain, RNA binding protein; 2.10A {Homo sapiens} SCOP: d.51.1.1

Probab=99.60  E-value=1.2e-15  Score=119.24  Aligned_cols=72  Identities=39%  Similarity=0.671  Sum_probs=66.1

Q ss_pred             CceEEEEEeCcccccccccCCCchHHHHHhHhCCeEEEccCCC-CCceEEEEEeCHHHHHHHHHHHHHHHHhc
Q psy11929        286 DFVETEIVLTDDIAGCVIGKAGSRLLEIRQISGAQINIHTGTE-SHKKMFHIQGCQEAVSLAQYLINMCIELQ  357 (433)
Q Consensus       286 ~~~t~~i~VP~~~vG~IIGkgG~~Ik~I~~~sGA~I~I~~~~~-~~er~V~IsGt~e~v~~A~~lI~~~i~~~  357 (433)
                      ...+.+|.||.+++|+||||+|++|++|+++|||+|+|++..+ +.+|.|+|+|+++++++|+.+|.+++.++
T Consensus         4 ~~~~~~i~Ip~~~vg~IIGkgG~~Ik~I~~~sga~I~i~~~~~~~~~r~v~I~G~~~~v~~A~~~I~~~i~~~   76 (82)
T 1wvn_A            4 SQTTHELTIPNNLIGCIIGRQGANINEIRQMSGAQIKIANPVEGSSGRQVTITGSAASISLAQYLINARLSSE   76 (82)
T ss_dssp             TCEEEEEEEEGGGHHHHHCGGGHHHHHHHHHHCCEEEECCCCTTCSEEEEEEEECHHHHHHHHHHHHHHTC--
T ss_pred             CcEEEEEEEchHhccceeCCCchhHHHHHHHhCCEEEEecCCCCCCceEEEEEcCHHHHHHHHHHHHHHHHhh
Confidence            4788999999999999999999999999999999999998654 78999999999999999999999999765

>1tua_A Hypothetical protein APE0754; structural genomics, protein structure initiative, MCSG, four layers alpha-beta sandwich, PSI; 1.50A {Aeropyrum pernix} SCOP: d.51.1.1 d.51.1.1

Probab=99.60  E-value=2.2e-15  Score=135.43  Aligned_cols=140  Identities=16%  Similarity=0.238  Sum_probs=111.1

Q ss_pred             EEEEEeccCCcccccceeeecCchHHHHHHHHhCCeEEEeCCCCCcceEEEe-----cccCCCCCCccccCCCCCccccc
Q psy11929         16 TMRCLFHSSVNVNEISCLIGPGGCIVRRLRKESGAKISITDGACPDRIVTVS-----GSVDNSSTSSVETGYPGHTLWVT   90 (433)
Q Consensus        16 ~~rilvp~~~~~~~vg~IIGk~G~~Ik~I~~~tga~I~v~~~~~~eRvv~I~-----G~~~~~~~~~v~~~~~~~~~~~~   90 (433)
                      .++++||.    +.+|.|||++|++++.|++++||+|.+..   .++.|+|.     |.+.                   
T Consensus         5 ~~~i~VP~----~rvg~liGk~g~~~k~i~e~~g~~i~id~---~~~~V~i~t~~~t~dp~-------------------   58 (191)
T 1tua_A            5 RIYVKVKP----ERLGAVIGPRGEVKAEIMRRTGTVITVDT---ENSMVIVEPEAEGIPPV-------------------   58 (191)
T ss_dssp             CEEEECCG----GGHHHHHCGGGHHHHHHHHHHTEEEEEET---TTTEEEEEESSTTSCHH-------------------
T ss_pred             ceEEECCH----HHhhHHHhcCHhHHHHHHHHHCcEEEEEc---CCCeEEEEeCCCCCCHH-------------------
Confidence            36899999    99999999999999999999999999975   57888998     4444                   


Q ss_pred             hHHHHHHHHHHHHhhhhhhcccccCCCCCCCCCeEEE-EEecc----------CcccceecCCchhHHHHHHhhCceEEe
Q psy11929         91 SVDNVCTAYNFMCRSLEDYHINRNRMENCSPQPLQLK-LVIPA----------THCGSLIGKGGCKIKDIRDLSGANVQV  159 (433)
Q Consensus        91 a~~~v~~A~~~I~~~~~~~~~~~~~~~~~~~~~~~~~-l~ip~----------~~vg~iIGk~G~~Ik~I~~~sga~I~i  159 (433)
                         ++.+|.++|......+...-.  .....+...+. +.++.          ...|+||||+|.+|+.|+..|||+|.|
T Consensus        59 ---~i~KA~dlI~ai~rgf~~e~A--~~Ll~Dd~~~e~i~i~~~~~~~~~~~~r~~GrIIGk~G~tik~iE~~Tg~~I~v  133 (191)
T 1tua_A           59 ---NLMKAAEVVKAISLGFPPEKA--FRLLEEDQILVVVDLKQVVGDSQNHLKRIKGRIIGEGGRARRTIEEMTDTYINV  133 (191)
T ss_dssp             ---HHHHHHHHHHHHHHTCCHHHH--GGGGSTTEEEEEEETHHHHTTCHHHHHHHHHHHHCGGGHHHHHHHHHHTCEEEE
T ss_pred             ---HHHHHHHHHHHHHcCCCHHHh--hhcccCcceeEEEEcccccccCchhHHHHhhheeCCCccHHHHHHHHHCceEEE
Confidence               899999999877665421100  00001223333 33442          358999999999999999999999999


Q ss_pred             ccCCCCCCCccEEEEEccHHHHHHHHHHHHHHHHh
Q psy11929        160 ASDMLPMSTERIVTVHGNPDTISQAIYQICLVLIE  194 (433)
Q Consensus       160 ~~~~~~~~~er~v~I~G~~~~v~~A~~~I~~~l~e  194 (433)
                      .        ++.|.|.|+.++++.|...|.+++..
T Consensus       134 ~--------~~~v~i~G~~~~i~~Ar~~i~~li~g  160 (191)
T 1tua_A          134 G--------EYEVAIIGDYERAMAAKQAIEMLAEG  160 (191)
T ss_dssp             C--------SSEEEEEEEHHHHHHHHHHHHHHHTT
T ss_pred             c--------CCEEEEEeChHHHHHHHHHHHHHHcC
Confidence            6        35899999999999999999999865

>2axy_A Poly(RC)-binding protein 2; protein-DNA complex, DNA binding protein-DNA complex; 1.70A {Homo sapiens} SCOP: d.51.1.1 PDB: 2pqu_A 2py9_A 1ztg_A 3vke_A*

Probab=99.58  E-value=1.2e-15  Score=116.42  Aligned_cols=71  Identities=37%  Similarity=0.800  Sum_probs=66.9

Q ss_pred             CceEEEEEEeccCCcccccceeeecCchHHHHHHHHhCCeEEEeCCCCCcceEEEecccCCCCCCccccCCCCCccccch
Q psy11929         12 DTLITMRCLFHSSVNVNEISCLIGPGGCIVRRLRKESGAKISITDGACPDRIVTVSGSVDNSSTSSVETGYPGHTLWVTS   91 (433)
Q Consensus        12 ~~~~~~rilvp~~~~~~~vg~IIGk~G~~Ik~I~~~tga~I~v~~~~~~eRvv~I~G~~~~~~~~~v~~~~~~~~~~~~a   91 (433)
                      ...++++|+||.    +++|.||||+|++||+|+++|||+|+|++.++++|+|+|+|+++                    
T Consensus         2 ~~~~~~~i~ip~----~~ig~iIGkgG~~Ik~I~~~tga~I~i~~~~~~er~v~I~G~~~--------------------   57 (73)
T 2axy_A            2 NVTLTIRLLMHG----KEVGSIIGKKGESVKKMREESGARINISEGNCPERIITLAGPTN--------------------   57 (73)
T ss_dssp             CCCEEEEEEEEH----HHHHHHHCGGGHHHHHHHHHHCCEEEECSSCCSEEEEEEEECHH--------------------
T ss_pred             CceEEEEEEECh----hHeeeEECCCCHHHHHHHHHHCCEEEEecCCCCcEEEEEEeCHH--------------------
Confidence            356899999999    99999999999999999999999999999888999999999998                    


Q ss_pred             HHHHHHHHHHHHhhhhh
Q psy11929         92 VDNVCTAYNFMCRSLED  108 (433)
Q Consensus        92 ~~~v~~A~~~I~~~~~~  108 (433)
                        ++.+|..+|.+++.+
T Consensus        58 --~v~~A~~~I~~~l~e   72 (73)
T 2axy_A           58 --AIFKAFAMIIDKLEE   72 (73)
T ss_dssp             --HHHHHHHHHHHHHHC
T ss_pred             --HHHHHHHHHHHHHhc
Confidence              999999999998864

>1dtj_A RNA-binding neurooncological ventral antigen 2; KH domain, alpha-beta fold RNA-binding motif, immune system; 2.00A {Homo sapiens} SCOP: d.51.1.1 PDB: 1dt4_A

Probab=99.58  E-value=2.7e-15  Score=115.59  Aligned_cols=70  Identities=29%  Similarity=0.532  Sum_probs=63.7

Q ss_pred             ceEEEEEeCcccccccccCCCchHHHHHhHhCCeEEEccCCC----CCceEEEEEeCHHHHHHHHHHHHHHHHh
Q psy11929        287 FVETEIVLTDDIAGCVIGKAGSRLLEIRQISGAQINIHTGTE----SHKKMFHIQGCQEAVSLAQYLINMCIEL  356 (433)
Q Consensus       287 ~~t~~i~VP~~~vG~IIGkgG~~Ik~I~~~sGA~I~I~~~~~----~~er~V~IsGt~e~v~~A~~lI~~~i~~  356 (433)
                      ..+.+|.||.+++|+||||+|++|++|++.|||+|+|++..+    +.+|.|+|+|+++++++|+.+|.+++.+
T Consensus         2 ~~~~~i~Ip~~~vg~IIGkgG~~Ik~I~~~tga~I~i~~~~~~~~~~~~~~v~I~G~~~~v~~A~~~I~~~i~e   75 (76)
T 1dtj_A            2 KELVEMAVPENLVGAILGKGGKTLVEYQELTGARIQISKKGEFLPGTRNRRVTITGSPAATQAAQYLISQRVTY   75 (76)
T ss_dssp             CEEEEEEEETTTHHHHHCSTTHHHHHHHHHHCCEEEECCTTCCSTTCCEEEEEEEESHHHHHHHHHHHHHHCC-
T ss_pred             ceEEEEEEChHHcceEECCCchHHHHHHHHhCCEEEECcCCCCCCCCceeEEEEEeCHHHHHHHHHHHHHHHhc
Confidence            457899999999999999999999999999999999998632    6789999999999999999999998864

>2axy_A Poly(RC)-binding protein 2; protein-DNA complex, DNA binding protein-DNA complex; 1.70A {Homo sapiens} SCOP: d.51.1.1 PDB: 2pqu_A 2py9_A 1ztg_A 3vke_A*

Probab=99.58  E-value=2.5e-15  Score=114.76  Aligned_cols=70  Identities=26%  Similarity=0.395  Sum_probs=65.7

Q ss_pred             CceEEEEEeCcccccccccCCCchHHHHHhHhCCeEEEccCCCCCceEEEEEeCHHHHHHHHHHHHHHHHh
Q psy11929        286 DFVETEIVLTDDIAGCVIGKAGSRLLEIRQISGAQINIHTGTESHKKMFHIQGCQEAVSLAQYLINMCIEL  356 (433)
Q Consensus       286 ~~~t~~i~VP~~~vG~IIGkgG~~Ik~I~~~sGA~I~I~~~~~~~er~V~IsGt~e~v~~A~~lI~~~i~~  356 (433)
                      ...+.+|.||.+++|+||||+|++|++|+++|||+|+|++.. ..+|.|+|+|+++++++|+.+|.++|.+
T Consensus         3 ~~~~~~i~ip~~~ig~iIGkgG~~Ik~I~~~tga~I~i~~~~-~~er~v~I~G~~~~v~~A~~~I~~~l~e   72 (73)
T 2axy_A            3 VTLTIRLLMHGKEVGSIIGKKGESVKKMREESGARINISEGN-CPERIITLAGPTNAIFKAFAMIIDKLEE   72 (73)
T ss_dssp             CCEEEEEEEEHHHHHHHHCGGGHHHHHHHHHHCCEEEECSSC-CSEEEEEEEECHHHHHHHHHHHHHHHHC
T ss_pred             ceEEEEEEEChhHeeeEECCCCHHHHHHHHHHCCEEEEecCC-CCcEEEEEEeCHHHHHHHHHHHHHHHhc
Confidence            357899999999999999999999999999999999999875 6799999999999999999999999975

>1j5k_A Heterogeneous nuclear ribonucleoprotein K; single-stranded DNA binding protein, transcription factor, hnRNP K, CT element, C-MYC oncogene; NMR {Homo sapiens} SCOP: d.51.1.1 PDB: 1khm_A

Probab=99.57  E-value=3e-15  Score=118.90  Aligned_cols=74  Identities=35%  Similarity=0.635  Sum_probs=68.3

Q ss_pred             CCCceEEEEEeCcccccccccCCCchHHHHHhHhCCeEEEccCCC-CCceEEEEEeCHHHHHHHHHHHHHHHHhc
Q psy11929        284 GDDFVETEIVLTDDIAGCVIGKAGSRLLEIRQISGAQINIHTGTE-SHKKMFHIQGCQEAVSLAQYLINMCIELQ  357 (433)
Q Consensus       284 ~~~~~t~~i~VP~~~vG~IIGkgG~~Ik~I~~~sGA~I~I~~~~~-~~er~V~IsGt~e~v~~A~~lI~~~i~~~  357 (433)
                      .....+.+|.||.+++|+||||+|++|++|+++|||+|+|++... +.+|.|+|+|+++++++|+.+|.+++.+.
T Consensus        10 ~~~~~~~~i~Ip~~~vg~IIGkgG~~Ik~I~~~tga~I~I~~~~~~~~~~~v~I~G~~e~v~~A~~~I~~~i~e~   84 (89)
T 1j5k_A           10 GGPIITTQVTIPKDLAGSIIGKGGQRIKQIRHESGASIKIDEPLEGSEDRIITITGTQDQIQNAQYLLQNSVKQY   84 (89)
T ss_dssp             CCCEEEEEEEEEHHHHHHHHCGGGHHHHHHHHHTCCEEEECSCCSSSSEEEEEEEEEHHHHHHHHHHHHHHHHHH
T ss_pred             CCCeEEEEEEEChhhcceeECCCCHhHHHHHHHhCCeEEecCCCCCCCccEEEEEcCHHHHHHHHHHHHHHHHhh
Confidence            346889999999999999999999999999999999999998654 78899999999999999999999999764

>1x4n_A FAR upstream element binding protein 1; KH domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Mus musculus} SCOP: d.51.1.1 PDB: 2opu_A

Probab=99.56  E-value=1e-14  Score=116.48  Aligned_cols=73  Identities=25%  Similarity=0.444  Sum_probs=68.1

Q ss_pred             CceEEEEEeCcccccccccCCCchHHHHHhHhCCeEEEccCCC-CCceEEEEEeCHHHHHHHHHHHHHHHHhcc
Q psy11929        286 DFVETEIVLTDDIAGCVIGKAGSRLLEIRQISGAQINIHTGTE-SHKKMFHIQGCQEAVSLAQYLINMCIELQK  358 (433)
Q Consensus       286 ~~~t~~i~VP~~~vG~IIGkgG~~Ik~I~~~sGA~I~I~~~~~-~~er~V~IsGt~e~v~~A~~lI~~~i~~~~  358 (433)
                      ...+.+|.||.+++|+||||+|++|++|+++|||+|+|++..+ ..+|.|+|+|+++++++|+.+|.++++...
T Consensus        13 ~~~~~~i~Ip~~~vG~IIGkgG~~Ik~I~~~tga~I~I~~~~~g~~~r~v~I~G~~e~v~~A~~~I~~~i~~~~   86 (92)
T 1x4n_A           13 SVMTEEYKVPDGMVGFIIGRGGEQISRIQQESGCKIQIAPDSGGLPERSCMLTGTPESVQSAKRLLDQIVEKGR   86 (92)
T ss_dssp             CCEEEEEEEEHHHHHHHHCSSSHHHHHHHHHSCCEEEECSCCTTCSEEEEEEEECHHHHHHHHHHHHHHHHHTT
T ss_pred             CCEEEEEEEChHHcceeECCCchHHHHHHHHhCCEEEEcCCCCCCCccEEEEEeCHHHHHHHHHHHHHHHHhcc
Confidence            4688999999999999999999999999999999999998765 778999999999999999999999998754

>1tua_A Hypothetical protein APE0754; structural genomics, protein structure initiative, MCSG, four layers alpha-beta sandwich, PSI; 1.50A {Aeropyrum pernix} SCOP: d.51.1.1 d.51.1.1

Probab=99.56  E-value=1e-14  Score=131.10  Aligned_cols=139  Identities=22%  Similarity=0.253  Sum_probs=111.4

Q ss_pred             EEEEeccCcccceecCCchhHHHHHHhhCceEEeccCCCCCCCccEEEEE-----ccHHHHHHHHHHHHHHHHhhccccC
Q psy11929        126 LKLVIPATHCGSLIGKGGCKIKDIRDLSGANVQVASDMLPMSTERIVTVH-----GNPDTISQAIYQICLVLIECTLQVV  200 (433)
Q Consensus       126 ~~l~ip~~~vg~iIGk~G~~Ik~I~~~sga~I~i~~~~~~~~~er~v~I~-----G~~~~v~~A~~~I~~~l~e~~~~~~  200 (433)
                      .+++||...+|.|||++|++++.|++.+|++|.+..      .++.|+|.     |++.++.+|..+|..+.+.   +++
T Consensus         6 ~~i~VP~~rvg~liGk~g~~~k~i~e~~g~~i~id~------~~~~V~i~t~~~t~dp~~i~KA~dlI~ai~rg---f~~   76 (191)
T 1tua_A            6 IYVKVKPERLGAVIGPRGEVKAEIMRRTGTVITVDT------ENSMVIVEPEAEGIPPVNLMKAAEVVKAISLG---FPP   76 (191)
T ss_dssp             EEEECCGGGHHHHHCGGGHHHHHHHHHHTEEEEEET------TTTEEEEEESSTTSCHHHHHHHHHHHHHHHHT---CCH
T ss_pred             eEEECCHHHhhHHHhcCHhHHHHHHHHHCcEEEEEc------CCCeEEEEeCCCCCCHHHHHHHHHHHHHHHcC---CCH
Confidence            689999999999999999999999999999999974      37788998     9999999999999998876   221


Q ss_pred             CCcccccCCCCCCCCCccccCCcccccCCCCCCCcccccCCCCCCCCccccccCcCCCCCCCCCccccccccCCCcccCC
Q psy11929        201 KGAVIPYEPKTMNAGPVILSGGQAYTLHGEYAVPVQEVAGKKQPHPLAGLAVLGIEGIGSTSLTPAALAALSGSRVKSGG  280 (433)
Q Consensus       201 ~~~~~~~~p~~~~~~p~~~~g~~~~~~~g~~~~P~~~~~~~~~~~p~~~~~~~~~~~~~~p~~~~~~~~~~~~~~~~~~~  280 (433)
                      ..+.-.+.                                                                        
T Consensus        77 e~A~~Ll~------------------------------------------------------------------------   84 (191)
T 1tua_A           77 EKAFRLLE------------------------------------------------------------------------   84 (191)
T ss_dssp             HHHGGGGS------------------------------------------------------------------------
T ss_pred             HHhhhccc------------------------------------------------------------------------
Confidence            11000000                                                                        


Q ss_pred             CCCCCCceEEEEEe----------CcccccccccCCCchHHHHHhHhCCeEEEccCCCCCceEEEEEeCHHHHHHHHHHH
Q psy11929        281 KDTGDDFVETEIVL----------TDDIAGCVIGKAGSRLLEIRQISGAQINIHTGTESHKKMFHIQGCQEAVSLAQYLI  350 (433)
Q Consensus       281 ~~~~~~~~t~~i~V----------P~~~vG~IIGkgG~~Ik~I~~~sGA~I~I~~~~~~~er~V~IsGt~e~v~~A~~lI  350 (433)
                          .......+.+          +....|+||||+|.+|+.|+..|||+|.|.+      +.|.|.|++++++.|+..|
T Consensus        85 ----Dd~~~e~i~i~~~~~~~~~~~~r~~GrIIGk~G~tik~iE~~Tg~~I~v~~------~~v~i~G~~~~i~~Ar~~i  154 (191)
T 1tua_A           85 ----EDQILVVVDLKQVVGDSQNHLKRIKGRIIGEGGRARRTIEEMTDTYINVGE------YEVAIIGDYERAMAAKQAI  154 (191)
T ss_dssp             ----TTEEEEEEETHHHHTTCHHHHHHHHHHHHCGGGHHHHHHHHHHTCEEEECS------SEEEEEEEHHHHHHHHHHH
T ss_pred             ----CcceeEEEEcccccccCchhHHHHhhheeCCCccHHHHHHHHHCceEEEcC------CEEEEEeChHHHHHHHHHH
Confidence                0001111222          2347899999999999999999999999986      3699999999999999999


Q ss_pred             HHHHH
Q psy11929        351 NMCIE  355 (433)
Q Consensus       351 ~~~i~  355 (433)
                      ..+|.
T Consensus       155 ~~li~  159 (191)
T 1tua_A          155 EMLAE  159 (191)
T ss_dssp             HHHHT
T ss_pred             HHHHc
Confidence            99995

>2dgr_A Ring finger and KH domain-containing protein 1; structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.56  E-value=6.2e-15  Score=115.03  Aligned_cols=69  Identities=22%  Similarity=0.301  Sum_probs=63.8

Q ss_pred             CceEEEEEeCcccccccccCCCchHHHHHhHhCCeEEEccCCCCCceEEEEEeCHHHHHHHHHHHHHHHHh
Q psy11929        286 DFVETEIVLTDDIAGCVIGKAGSRLLEIRQISGAQINIHTGTESHKKMFHIQGCQEAVSLAQYLINMCIEL  356 (433)
Q Consensus       286 ~~~t~~i~VP~~~vG~IIGkgG~~Ik~I~~~sGA~I~I~~~~~~~er~V~IsGt~e~v~~A~~lI~~~i~~  356 (433)
                      .+.+.+|.||.+++|+||||+|++||+|+++|||+|+|++..  +++.|+|+|+++++++|+.+|.+++..
T Consensus         8 ~~~~~~i~VP~~~vG~IIGkgG~tIk~Iqe~Tga~I~I~~~~--~~~~v~ItG~~e~v~~A~~~I~~~i~~   76 (83)
T 2dgr_A            8 GQTTIQVRVPYRVVGLVVGPKGATIKRIQQRTHTYIVTPGRD--KEPVFAVTGMPENVDRAREEIEAHITL   76 (83)
T ss_dssp             CSEEEEEECCHHHHHHHHTTTTSSHHHHHHHTTCEEECCCSS--SCCEEEEEECTTTHHHHHHHHHHHHHS
T ss_pred             CceEEEEEeChHHeeeeECCCchHHHHHHHHhCCeEEecCCC--CCCeEEEEcCHHHHHHHHHHHHHHHhc
Confidence            578899999999999999999999999999999999999754  468999999999999999999998764

>3n89_A Defective in GERM LINE development protein 3, ISO; KH domains, RNA binding, cell cycle; 2.79A {Caenorhabditis elegans}

Probab=99.55  E-value=6.4e-15  Score=144.99  Aligned_cols=189  Identities=8%  Similarity=0.048  Sum_probs=126.7

Q ss_pred             CCCCeEEEEEeccCcccceecCCc--hhHHHHHHhhCceEEeccCC----CCCCCccEEEEEccHHHHHHHHHHHHHHHH
Q psy11929        120 SPQPLQLKLVIPATHCGSLIGKGG--CKIKDIRDLSGANVQVASDM----LPMSTERIVTVHGNPDTISQAIYQICLVLI  193 (433)
Q Consensus       120 ~~~~~~~~l~ip~~~vg~iIGk~G--~~Ik~I~~~sga~I~i~~~~----~~~~~er~v~I~G~~~~v~~A~~~I~~~l~  193 (433)
                      ....+++++.||..+++.||||+|  ++|++|+++|||+|+|+...    .+......|+|+|.+++|++|+.+|.+++-
T Consensus        26 ~~~~VTl~v~Ip~~~Hs~IIGkgG~~sNIkkImeEtgv~I~fPD~~~~~~~~~~ks~~VtItG~~enVE~AR~~I~~l~P  105 (376)
T 3n89_A           26 NPTRVTLNMEFESQYYSLMTSDNGDHENVASIMAETNTLIQLPDRSVGGTTPDPFAQQVTITGYFGDVDRARMLMRRNCH  105 (376)
T ss_dssp             CTTEEEEEEECCGGGHHHHHSCCSSSCSHHHHHHHHTCEEECCCCCCCSSSCCTTTTEEEEEEEHHHHHHHHHHHHHSCE
T ss_pred             cCCEEEEEEEEchhhhhhhccCCChHHHHHHHHHHhCCeEECCCCcccccCCcCCCCeEEEEcCHHHHHHHHHHHHhcCC
Confidence            367899999999999999999999  99999999999999998643    122455789999999999999998876321


Q ss_pred             hhccccCCCcccccCCCCCCCCCccccCCcccccCCCCCCCcccccCCCCCCCCccccccCcCCCCCCCCCccccccccC
Q psy11929        194 ECTLQVVKGAVIPYEPKTMNAGPVILSGGQAYTLHGEYAVPVQEVAGKKQPHPLAGLAVLGIEGIGSTSLTPAALAALSG  273 (433)
Q Consensus       194 e~~~~~~~~~~~~~~p~~~~~~p~~~~g~~~~~~~g~~~~P~~~~~~~~~~~p~~~~~~~~~~~~~~p~~~~~~~~~~~~  273 (433)
                      -                                                                               
T Consensus       106 l-------------------------------------------------------------------------------  106 (376)
T 3n89_A          106 F-------------------------------------------------------------------------------  106 (376)
T ss_dssp             E-------------------------------------------------------------------------------
T ss_pred             c-------------------------------------------------------------------------------
Confidence            1                                                                               


Q ss_pred             CCcccCCCCCCCCceEEEEEeCcccccccccCCCchHHHHHhHhCCeEEEccCCC---CCceEEEEEeCHHHHHHHHHHH
Q psy11929        274 SRVKSGGKDTGDDFVETEIVLTDDIAGCVIGKAGSRLLEIRQISGAQINIHTGTE---SHKKMFHIQGCQEAVSLAQYLI  350 (433)
Q Consensus       274 ~~~~~~~~~~~~~~~t~~i~VP~~~vG~IIGkgG~~Ik~I~~~sGA~I~I~~~~~---~~er~V~IsGt~e~v~~A~~lI  350 (433)
                                     +..+.+|...++.  ...+..|.+ ++..+++|.++...+   .....|+|+|.+.+++.|+..+
T Consensus       107 ---------------~i~~elp~~~i~~--~~l~~~I~q-q~~y~V~I~Fp~~~~~~~~~sd~V~IrG~~~nv~~akeA~  168 (376)
T 3n89_A          107 ---------------TVFMALSKMKMPL--HELQAHVRQ-NPIQNVEMSFVDAPEKNGIVTTYLRITAREKNQHELIEAA  168 (376)
T ss_dssp             ---------------EEEEECTTCSSCH--HHHHHHHHH-CCCTTCEEEEEEEC-----CEEEEEEEEEGGGHHHHHHHH
T ss_pred             ---------------eEEEEccccccCc--chhhhhhcc-ceeCceEEEeCCcccccCCCCCEEEEEcChhhHHHHHHHH
Confidence                           1222333322111  011123333 467899999866543   2367899999997776665555


Q ss_pred             HHHHHhccccCCCCCCCCCccccccccccchhccccccccccCCCCCcceecccc--H--HHHHHhhhccccccceee
Q psy11929        351 NMCIELQKNNTTNTSDNPEPADLDAAISAFMTASVNSSLIEKPTPHPGSMVTLGG--L--SELLANIAASNVKSTVQT  424 (433)
Q Consensus       351 ~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~vP~~~~G~iiGkgG--~--~e~~~~~~~~~~~~~~~~  424 (433)
                      ..++..-...... .        ...+         +..+.||..+...||||||  +  +.+ +..|++.+..|-..
T Consensus       169 ~~Ll~~l~~~e~~-~--------~~~~---------s~~v~V~~~~H~~IIGk~G~n~~IkkI-r~eTGv~I~FP~~~  227 (376)
T 3n89_A          169 KRLNEILFRESPA-P--------ENNF---------TLHFTLSTYYVDQVLGSSSTAQLMPVI-ERETTTIISYPCYN  227 (376)
T ss_dssp             HHHHHHHCC--CC-C--------SSCE---------EEEEEEEGGGHHHHTCCTTSCCHHHHH-HHHHTCEEECC---
T ss_pred             HHHHHHHHhhhcc-c--------ccce---------EEEEEeCHHHHHHhhcCCCcchHHHHH-HHhhCCEEECCCCC
Confidence            5544332111100 0        0011         2457899999999999999  3  777 55689999888643

>2hh3_A KH-type splicing regulatory protein; KH-RNA binding domain, RNA binding protein; NMR {Homo sapiens}

Probab=99.53  E-value=1.5e-14  Score=118.31  Aligned_cols=72  Identities=21%  Similarity=0.352  Sum_probs=65.4

Q ss_pred             eEEEEEeCcccccccccCCCchHHHHHhHhCCeEEEccCCC-CCceEEEEEeCHHHHHHHHHHHHHHHHhccc
Q psy11929        288 VETEIVLTDDIAGCVIGKAGSRLLEIRQISGAQINIHTGTE-SHKKMFHIQGCQEAVSLAQYLINMCIELQKN  359 (433)
Q Consensus       288 ~t~~i~VP~~~vG~IIGkgG~~Ik~I~~~sGA~I~I~~~~~-~~er~V~IsGt~e~v~~A~~lI~~~i~~~~~  359 (433)
                      .+.+|.||.+++|+||||+|++|++|+++|||+|+|+++.. ..+|.|+|+|+++++++|+.+|++++.+...
T Consensus        11 ~~~~i~Ip~~~iG~IIGkgG~~Ik~I~~~TGakI~I~~~~~~~~er~V~I~G~~e~v~~A~~~I~~ii~~~~~   83 (106)
T 2hh3_A           11 GGIDVPVPRHSVGVVIGRSGEMIKKIQNDAGVRIQFKQDDGTGPEKIAHIMGPPDRCEHAARIINDLLQSLRS   83 (106)
T ss_dssp             -CEEEEEETTTHHHHHTTTTHHHHHHHHHHTCEEEECSSCSSSSEEEEEEESSHHHHHHHHHHHHHHHHHHC-
T ss_pred             eEEEEEECHHHcCccCCCCcHHHHHHHHHHCcEEEEecCCCCCceeEEEEEeCHHHHHHHHHHHHHHHhcccc
Confidence            36899999999999999999999999999999999987655 7789999999999999999999999987544

>1ec6_A RNA-binding protein NOVA-2; KH domain, alpha-beta fold, RNA-binding motif, protein/RNA structure, RNA binding protein/RNA complex; 2.40A {Homo sapiens} SCOP: d.51.1.1

Probab=99.52  E-value=1.1e-14  Score=115.13  Aligned_cols=73  Identities=29%  Similarity=0.534  Sum_probs=66.2

Q ss_pred             ceEEEEEeCcccccccccCCCchHHHHHhHhCCeEEEccCCC----CCceEEEEEeCHHHHHHHHHHHHHHHHhccc
Q psy11929        287 FVETEIVLTDDIAGCVIGKAGSRLLEIRQISGAQINIHTGTE----SHKKMFHIQGCQEAVSLAQYLINMCIELQKN  359 (433)
Q Consensus       287 ~~t~~i~VP~~~vG~IIGkgG~~Ik~I~~~sGA~I~I~~~~~----~~er~V~IsGt~e~v~~A~~lI~~~i~~~~~  359 (433)
                      ..+.+|.||.+++|+||||+|++|++|++.|||+|+|++..+    +.+|.|+|+|++++++.|+.+|.+++.+...
T Consensus         2 k~t~~i~IP~~~vG~IIGkgG~~Ik~I~~~tga~I~I~~~~~~~~g~~~r~v~I~G~~~~v~~A~~~I~~~i~~~~~   78 (87)
T 1ec6_A            2 KELVEIAVPENLVGAILGKGGKTLVEYQELTGARIQISKKGEFLPGTRNRRVTITGSPAATQAAQYLISQRVTYEQG   78 (87)
T ss_dssp             CSEEEEEEEHHHHHHHHCGGGHHHHHHHHHHCCEEEECCTTCBSTTSCEEEEEEESSHHHHHHHHHHHHHHHHHHHH
T ss_pred             ceEEEEEEChHHcCeeECCCcHhHHHHHHHhCCEEEEccCCCCCCCCCceEEEEEcCHHHHHHHHHHHHHHHhcccc
Confidence            357899999999999999999999999999999999998642    6789999999999999999999999987543

>2opv_A KHSRP protein; KH domain, RNA binding protein, KSRP; NMR {Homo sapiens}

Probab=99.51  E-value=6.1e-14  Score=110.28  Aligned_cols=70  Identities=21%  Similarity=0.281  Sum_probs=64.6

Q ss_pred             CceEEEEEeCcccccccccCCCchHHHHHhHhCCeEEEccCCC---CCceEEEEEeCHHHHHHHHHHHHHHHH
Q psy11929        286 DFVETEIVLTDDIAGCVIGKAGSRLLEIRQISGAQINIHTGTE---SHKKMFHIQGCQEAVSLAQYLINMCIE  355 (433)
Q Consensus       286 ~~~t~~i~VP~~~vG~IIGkgG~~Ik~I~~~sGA~I~I~~~~~---~~er~V~IsGt~e~v~~A~~lI~~~i~  355 (433)
                      ...+.+|.||.+++|+||||+|++|++|+++|||+|.|.+...   +.+|.|+|+|+++++++|+.+|.+++.
T Consensus        12 ~~~~~~i~Ip~~~ig~IIGkgG~~Ik~I~~~tga~I~i~~~~~~~~~~er~v~I~G~~~~v~~A~~~I~~i~~   84 (85)
T 2opv_A           12 NGTVQEIMIPAGKAGLVIGKGGETIKQLQERAGVKMILIQDGSQNTNVDKPLRIIGDPYKVQQACEMVMDILR   84 (85)
T ss_dssp             SSEEEEEEECTTTHHHHHTTTTHHHHHHHHHHTCEEEECSSSCSSTTSCEEEEEEECHHHHHHHHHHHHHHHT
T ss_pred             CCEEEEEEeChhheeeeECCCCHHHHHHHHHHCCEEEEcCCCCCCCCCceEEEEEeCHHHHHHHHHHHHHHhc
Confidence            4577899999999999999999999999999999999998653   678999999999999999999999874

>2hh2_A KH-type splicing regulatory protein; KH-RNA binding domain, RNA binding protein; NMR {Homo sapiens}

Probab=99.51  E-value=2.2e-14  Score=117.75  Aligned_cols=71  Identities=28%  Similarity=0.382  Sum_probs=65.3

Q ss_pred             EEEEEeCcccccccccCCCchHHHHHhHhCCeEEEccCCC----CCceEEEEEeCHHHHHHHHHHHHHHHHhccc
Q psy11929        289 ETEIVLTDDIAGCVIGKAGSRLLEIRQISGAQINIHTGTE----SHKKMFHIQGCQEAVSLAQYLINMCIELQKN  359 (433)
Q Consensus       289 t~~i~VP~~~vG~IIGkgG~~Ik~I~~~sGA~I~I~~~~~----~~er~V~IsGt~e~v~~A~~lI~~~i~~~~~  359 (433)
                      +.+|.||.+++|+||||+|++|++|+++|||+|+|.+..+    ..+|.|+|+|+++++++|+.+|.++|.+...
T Consensus         8 ~~~i~IP~~~vG~IIGkgG~~Ik~I~~~TGa~I~I~~~~~~~~~~~~r~V~I~G~~e~v~~A~~~I~~~i~e~~~   82 (107)
T 2hh2_A            8 EMTFSIPTHKCGLVIGRGGENVKAINQQTGAFVEISRQLPPNGDPNFKLFIIRGSPQQIDHAKQLIEEKIEGPLC   82 (107)
T ss_dssp             CEEEEEEGGGTTTTSTTTTCHHHHHHHHSSSEEEECCCCCTTCCTTEEEEEEESCHHHHHHHHHHHHHHSCSCCC
T ss_pred             eEEEEECHHHcCccCCCCcHHHHHHHHHhCCEEEEcCccCCCCCCCceEEEEECCHHHHHHHHHHHHHHHhcccc
Confidence            6899999999999999999999999999999999998743    4689999999999999999999999987643

>1x4m_A FAR upstream element binding protein 1; KH domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Mus musculus} SCOP: d.51.1.1

Probab=99.51  E-value=4.1e-14  Score=113.43  Aligned_cols=73  Identities=23%  Similarity=0.295  Sum_probs=67.1

Q ss_pred             CCceEEEEEeCcccccccccCCCchHHHHHhHhCCeEEEccCCC---CCceEEEEEeCHHHHHHHHHHHHHHHHhc
Q psy11929        285 DDFVETEIVLTDDIAGCVIGKAGSRLLEIRQISGAQINIHTGTE---SHKKMFHIQGCQEAVSLAQYLINMCIELQ  357 (433)
Q Consensus       285 ~~~~t~~i~VP~~~vG~IIGkgG~~Ik~I~~~sGA~I~I~~~~~---~~er~V~IsGt~e~v~~A~~lI~~~i~~~  357 (433)
                      ....+.+|.||.+++|+||||+|++|++|+++|||+|+|.+...   ..+|.|+|+|+++++++|+.+|.+++.+.
T Consensus        12 p~~~~~~i~Ip~~~vG~IIGkgG~~Ik~I~~~tga~I~I~~~~~~~~~~~r~v~I~G~~~~v~~A~~~I~~~i~~~   87 (94)
T 1x4m_A           12 PGNAVQEIMIPASKAGLVIGKGGETIKQLQERAGVKMVMIQDGPQNTGADKPLRITGDPYKVQQAKEMVLELIRDQ   87 (94)
T ss_dssp             CCCEEEEEEECHHHHHHHSCSSSSHHHHHHHHHTSEEEECCSCCCSSCSCEEEEEEECTTTHHHHHHHHHHHHCCC
T ss_pred             CCcEEEEEEEChhhcceEECCCCHHHHHHHHHHCCeEEecCCCCCCCCCceEEEEEeCHHHHHHHHHHHHHHHhcc
Confidence            35788999999999999999999999999999999999998653   57899999999999999999999999753

>1zzk_A Heterogeneous nuclear ribonucleoprotein K; KH domian, alpha-beta fold, DNA binding protein; 0.95A {Homo sapiens} SCOP: d.51.1.1 PDB: 1zzj_A 1zzi_A

Probab=99.47  E-value=2e-13  Score=106.61  Aligned_cols=73  Identities=36%  Similarity=0.565  Sum_probs=67.7

Q ss_pred             CCCeEEEEEeccCcccceecCCchhHHHHHHhhCceEEeccCCCCCCCccEEEEEccHHHHHHHHHHHHHHHHh
Q psy11929        121 PQPLQLKLVIPATHCGSLIGKGGCKIKDIRDLSGANVQVASDMLPMSTERIVTVHGNPDTISQAIYQICLVLIE  194 (433)
Q Consensus       121 ~~~~~~~l~ip~~~vg~iIGk~G~~Ik~I~~~sga~I~i~~~~~~~~~er~v~I~G~~~~v~~A~~~I~~~l~e  194 (433)
                      ...++++|.||.+++|.||||+|++|++|+++|||+|.+.+ ..+++.+|.|+|+|+++++.+|+.+|.+++.+
T Consensus         4 g~~~~~~i~Vp~~~vg~iIGkgG~~Ik~I~~~tga~I~i~~-~~~~~~~~~v~I~G~~~~v~~A~~~I~~~i~~   76 (82)
T 1zzk_A            4 GPIITTQVTIPKDLAGSIIGKGGQRIKQIRHESGASIKIDE-PLEGSEDRIITITGTQDQIQNAQYLLQNSVKQ   76 (82)
T ss_dssp             CCCEEEEEEEETTTGGGGTCGGGHHHHHHHHHHCCEEEECC-TTSCSSEEEEEEEECHHHHHHHHHHHHHHHHH
T ss_pred             CCeEEEEEEEChHhcCeeECCCchHHHHHHHHHCCEEEEcC-CCCCCCceEEEEEeCHHHHHHHHHHHHHHHHh
Confidence            45789999999999999999999999999999999999985 34677899999999999999999999999987

>2p2r_A Poly(RC)-binding protein 2; protein-DNA complex, RNA and DNA binding protein/DNA complex; 1.60A {Homo sapiens}

Probab=99.46  E-value=8.6e-14  Score=107.06  Aligned_cols=72  Identities=39%  Similarity=0.589  Sum_probs=67.0

Q ss_pred             CCeEEEEEeccCcccceecCCchhHHHHHHhhCceEEeccCCCCCCCccEEEEEccHHHHHHHHHHHHHHHHh
Q psy11929        122 QPLQLKLVIPATHCGSLIGKGGCKIKDIRDLSGANVQVASDMLPMSTERIVTVHGNPDTISQAIYQICLVLIE  194 (433)
Q Consensus       122 ~~~~~~l~ip~~~vg~iIGk~G~~Ik~I~~~sga~I~i~~~~~~~~~er~v~I~G~~~~v~~A~~~I~~~l~e  194 (433)
                      ..++.+|+||.+++|.||||+|++|++|+++|||+|.+.+ ..+++.+|.|+|+|+++++.+|+.+|.+++.+
T Consensus         3 ~~~~~~i~Ip~~~vg~iIGkgG~~Ik~I~~~tga~I~i~~-~~~~~~~~~v~I~G~~~~v~~A~~~I~~~i~~   74 (76)
T 2p2r_A            3 QTTSHELTIPNDLIGCIIGRQGAKINEIRQMSGAQIKIAN-PVEGSTDRQVTITGSAASISLAQYLINVRLSS   74 (76)
T ss_dssp             CCEEEEEEEEHHHHHHHHCGGGHHHHHHHHHHCCEEEECC-CCTTCSEEEEEEEECHHHHHHHHHHHHHHHTT
T ss_pred             CceEEEEEEChHHcceEECCCChHHHHHHHHHCCEEEEcC-CCCCCCeEEEEEEeCHHHHHHHHHHHHHHHHc
Confidence            4678999999999999999999999999999999999986 35678899999999999999999999999875

>1wvn_A Poly(RC)-binding protein 1; KH domain, RNA binding domain, RNA binding protein; 2.10A {Homo sapiens} SCOP: d.51.1.1

Probab=99.46  E-value=1.1e-13  Score=108.15  Aligned_cols=73  Identities=34%  Similarity=0.525  Sum_probs=66.9

Q ss_pred             CCCeEEEEEeccCcccceecCCchhHHHHHHhhCceEEeccCCCCCCCccEEEEEccHHHHHHHHHHHHHHHHh
Q psy11929        121 PQPLQLKLVIPATHCGSLIGKGGCKIKDIRDLSGANVQVASDMLPMSTERIVTVHGNPDTISQAIYQICLVLIE  194 (433)
Q Consensus       121 ~~~~~~~l~ip~~~vg~iIGk~G~~Ik~I~~~sga~I~i~~~~~~~~~er~v~I~G~~~~v~~A~~~I~~~l~e  194 (433)
                      ...++++|+||.+++|.||||+|++|++|+++|||+|.+.+. .++..+|.|+|+|+++++.+|+.+|.+++.+
T Consensus         3 g~~~~~~i~Ip~~~vg~IIGkgG~~Ik~I~~~sga~I~i~~~-~~~~~~r~v~I~G~~~~v~~A~~~I~~~i~~   75 (82)
T 1wvn_A            3 GSQTTHELTIPNNLIGCIIGRQGANINEIRQMSGAQIKIANP-VEGSSGRQVTITGSAASISLAQYLINARLSS   75 (82)
T ss_dssp             TTCEEEEEEEEGGGHHHHHCGGGHHHHHHHHHHCCEEEECCC-CTTCSEEEEEEEECHHHHHHHHHHHHHHTC-
T ss_pred             CCcEEEEEEEchHhccceeCCCchhHHHHHHHhCCEEEEecC-CCCCCceEEEEEcCHHHHHHHHHHHHHHHHh
Confidence            457889999999999999999999999999999999999863 4677899999999999999999999999887

>2cte_A Vigilin; K homology type I domain, RNA-binding, cell sterol metabolism, beta-alpha-alpha-beta-BETA-alpha structure, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.51.1.1

Probab=99.46  E-value=1.4e-13  Score=110.28  Aligned_cols=76  Identities=17%  Similarity=0.283  Sum_probs=67.9

Q ss_pred             CCceEEEEEeCcccccccccCCCchHHHHHhHhCCeEEEccCCCCCceEEEEEeCHHHHHHHHHHHHHHHHhccccC
Q psy11929        285 DDFVETEIVLTDDIAGCVIGKAGSRLLEIRQISGAQINIHTGTESHKKMFHIQGCQEAVSLAQYLINMCIELQKNNT  361 (433)
Q Consensus       285 ~~~~t~~i~VP~~~vG~IIGkgG~~Ik~I~~~sGA~I~I~~~~~~~er~V~IsGt~e~v~~A~~lI~~~i~~~~~~~  361 (433)
                      ..+++.+|.||.+++|.|||+||.+|++|+++|||+|+|++.. ..++.|+|+|+++++++|+.+|.+++.....+.
T Consensus        14 ~~~~t~~i~Ip~~~ig~IIG~gG~~Ik~I~~etg~~I~i~~~~-~~~~~V~I~G~~e~v~~A~~~I~~i~~~~~~~~   89 (94)
T 2cte_A           14 QTQASATVAIPKEHHRFVIGKNGEKLQDLELKTATKIQIPRPD-DPSNQIKITGTKEGIEKARHEVLLISAEQDKRS   89 (94)
T ss_dssp             CSCEEEEEECCTTTHHHHHCSSSCHHHHHHHHTTCCCBCCCTT-SSCCEEEEEECHHHHHHHHHHHHHHHHHHHTCC
T ss_pred             CCceEEEEEEChHHeeeeECCCChhHHHHHHHHCCEEEeCCCC-CCCCeEEEEECHHHHHHHHHHHHHHhhcccccc
Confidence            4578999999999999999999999999999999999999765 345899999999999999999999998765433

>1we8_A Tudor and KH domain containing protein; structural genomics, riken structural genomics/proteomics initiative, RSGI, RNA binding protein; NMR {Mus musculus} SCOP: d.51.1.1

Probab=99.46  E-value=1e-13  Score=113.23  Aligned_cols=72  Identities=25%  Similarity=0.353  Sum_probs=66.0

Q ss_pred             CceEEEEEeCcccccccccCCCchHHHHHhHhCCeEEEccCCC---CCceEEEEEeCHHHHHHHHHHHHHHHHhc
Q psy11929        286 DFVETEIVLTDDIAGCVIGKAGSRLLEIRQISGAQINIHTGTE---SHKKMFHIQGCQEAVSLAQYLINMCIELQ  357 (433)
Q Consensus       286 ~~~t~~i~VP~~~vG~IIGkgG~~Ik~I~~~sGA~I~I~~~~~---~~er~V~IsGt~e~v~~A~~lI~~~i~~~  357 (433)
                      ...+.+|.||.+++|+||||+|++|++|+++|||+|+|++..+   +.++.|+|+|+++++++|+.+|.+++...
T Consensus        13 ap~~~~i~Ip~~~ig~IIGkgG~~Ik~I~~~tga~I~I~~~~~~~~~~~~~V~I~G~~~~v~~A~~~I~~~i~e~   87 (104)
T 1we8_A           13 TPVFEQLSVPQRSVGRIIGRGGETIRSICKASGAKITCDKESEGTLLLSRLIKISGTQKEVAAAKHLILEKVSED   87 (104)
T ss_dssp             CEEEEEEEEETTTHHHHHTTTSHHHHHHHHHHCCEEEECCSSCCSSSSEEEEEEEEEHHHHHHHHHHHHHHHHHH
T ss_pred             CCEEEEEEEChhheeeeECCCCHHHHHHHHHHCCEEEEecCCCCCCCCcceEEEEcCHHHHHHHHHHHHHHHhhC
Confidence            3578899999999999999999999999999999999998654   36899999999999999999999999764

>1dtj_A RNA-binding neurooncological ventral antigen 2; KH domain, alpha-beta fold RNA-binding motif, immune system; 2.00A {Homo sapiens} SCOP: d.51.1.1 PDB: 1dt4_A

Probab=99.45  E-value=1.3e-13  Score=106.15  Aligned_cols=71  Identities=28%  Similarity=0.566  Sum_probs=64.6

Q ss_pred             eEEEEEeccCcccceecCCchhHHHHHHhhCceEEeccC--CCCCCCccEEEEEccHHHHHHHHHHHHHHHHh
Q psy11929        124 LQLKLVIPATHCGSLIGKGGCKIKDIRDLSGANVQVASD--MLPMSTERIVTVHGNPDTISQAIYQICLVLIE  194 (433)
Q Consensus       124 ~~~~l~ip~~~vg~iIGk~G~~Ik~I~~~sga~I~i~~~--~~~~~~er~v~I~G~~~~v~~A~~~I~~~l~e  194 (433)
                      .+++|.||.+++|.||||+|++|++|+++|||+|.|.++  ..+++.++.|+|+|+++++.+|+.+|.+++.+
T Consensus         3 ~~~~i~Ip~~~vg~IIGkgG~~Ik~I~~~tga~I~i~~~~~~~~~~~~~~v~I~G~~~~v~~A~~~I~~~i~e   75 (76)
T 1dtj_A            3 ELVEMAVPENLVGAILGKGGKTLVEYQELTGARIQISKKGEFLPGTRNRRVTITGSPAATQAAQYLISQRVTY   75 (76)
T ss_dssp             EEEEEEEETTTHHHHHCSTTHHHHHHHHHHCCEEEECCTTCCSTTCCEEEEEEEESHHHHHHHHHHHHHHCC-
T ss_pred             eEEEEEEChHHcceEECCCchHHHHHHHHhCCEEEECcCCCCCCCCceeEEEEEeCHHHHHHHHHHHHHHHhc
Confidence            578999999999999999999999999999999999863  45677899999999999999999999998754

>1j5k_A Heterogeneous nuclear ribonucleoprotein K; single-stranded DNA binding protein, transcription factor, hnRNP K, CT element, C-MYC oncogene; NMR {Homo sapiens} SCOP: d.51.1.1 PDB: 1khm_A

Probab=99.45  E-value=6.4e-14  Score=111.13  Aligned_cols=77  Identities=29%  Similarity=0.469  Sum_probs=67.7

Q ss_pred             CCCCCCceEEEEEEeccCCcccccceeeecCchHHHHHHHHhCCeEEEeCC--CCCcceEEEecccCCCCCCccccCCCC
Q psy11929          7 GKIDEDTLITMRCLFHSSVNVNEISCLIGPGGCIVRRLRKESGAKISITDG--ACPDRIVTVSGSVDNSSTSSVETGYPG   84 (433)
Q Consensus         7 ~~~~~~~~~~~rilvp~~~~~~~vg~IIGk~G~~Ik~I~~~tga~I~v~~~--~~~eRvv~I~G~~~~~~~~~v~~~~~~   84 (433)
                      +.+.....++++|+||.    +++|.||||+|++||+|+++|||+|+|++.  +..+|+|+|+|+++             
T Consensus         6 ~~~~~~~~~~~~i~Ip~----~~vg~IIGkgG~~Ik~I~~~tga~I~I~~~~~~~~~~~v~I~G~~e-------------   68 (89)
T 1j5k_A            6 YGDLGGPIITTQVTIPK----DLAGSIIGKGGQRIKQIRHESGASIKIDEPLEGSEDRIITITGTQD-------------   68 (89)
T ss_dssp             ----CCCEEEEEEEEEH----HHHHHHHCGGGHHHHHHHHHTCCEEEECSCCSSSSEEEEEEEEEHH-------------
T ss_pred             CCCCCCCeEEEEEEECh----hhcceeECCCCHhHHHHHHHhCCeEEecCCCCCCCccEEEEEcCHH-------------
Confidence            33445678999999999    999999999999999999999999999874  67899999999998             


Q ss_pred             CccccchHHHHHHHHHHHHhhhhhh
Q psy11929         85 HTLWVTSVDNVCTAYNFMCRSLEDY  109 (433)
Q Consensus        85 ~~~~~~a~~~v~~A~~~I~~~~~~~  109 (433)
                               ++.+|..+|.+++.+.
T Consensus        69 ---------~v~~A~~~I~~~i~e~   84 (89)
T 1j5k_A           69 ---------QIQNAQYLLQNSVKQY   84 (89)
T ss_dssp             ---------HHHHHHHHHHHHHHHH
T ss_pred             ---------HHHHHHHHHHHHHHhh
Confidence                     9999999999988774

>2ctl_A Vigilin; K homology type I domain, RNA-binding, cell sterol metabolism, beta-alpha-alpha-beta-BETA-alpha structure, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.51.1.1

Probab=99.45  E-value=2.8e-13  Score=109.07  Aligned_cols=74  Identities=14%  Similarity=0.193  Sum_probs=67.1

Q ss_pred             CceEEEEEeCcccccccccCCCchHHHHHhHhCCeEEEccCCC--CCceEEEEEeCHHHHHHHHHHHHHHHHhccc
Q psy11929        286 DFVETEIVLTDDIAGCVIGKAGSRLLEIRQISGAQINIHTGTE--SHKKMFHIQGCQEAVSLAQYLINMCIELQKN  359 (433)
Q Consensus       286 ~~~t~~i~VP~~~vG~IIGkgG~~Ik~I~~~sGA~I~I~~~~~--~~er~V~IsGt~e~v~~A~~lI~~~i~~~~~  359 (433)
                      ..++.+|.||.+++|.|||++|++|++|+++|||+|+|++..+  ..+|.|+|+|+++++++|+.+|..++.....
T Consensus        15 ~~~~~~i~Ip~~~ig~IIGkgG~~Ik~I~~etg~~I~i~~~g~~~~~~~~V~I~G~~e~v~~A~~~I~~iv~e~e~   90 (97)
T 2ctl_A           15 RSFKLSVTVDPKYHPKIIGRKGAVITQIRLEHDVNIQFPDKDDGNQPQDQITITGYEKNTEAARDAILRIVGELEQ   90 (97)
T ss_dssp             TTCEEEEECCTTTHHHHSCSSSCHHHHHHHHHTCEEECCCTTTCSSCSSEEEEESCHHHHHHHHHHHHHHHHHHHH
T ss_pred             cceeEEEEECHHHhhhcCCCCchhHHHHHHHHCCEEEecCCCCCCCCccEEEEEeCHHHHHHHHHHHHHHHHHHHh
Confidence            4578999999999999999999999999999999999998764  4679999999999999999999999876543

>2opv_A KHSRP protein; KH domain, RNA binding protein, KSRP; NMR {Homo sapiens}

Probab=99.44  E-value=4.5e-13  Score=105.29  Aligned_cols=74  Identities=26%  Similarity=0.427  Sum_probs=66.7

Q ss_pred             CCCeEEEEEeccCcccceecCCchhHHHHHHhhCceEEeccCCC-CCCCccEEEEEccHHHHHHHHHHHHHHHHh
Q psy11929        121 PQPLQLKLVIPATHCGSLIGKGGCKIKDIRDLSGANVQVASDML-PMSTERIVTVHGNPDTISQAIYQICLVLIE  194 (433)
Q Consensus       121 ~~~~~~~l~ip~~~vg~iIGk~G~~Ik~I~~~sga~I~i~~~~~-~~~~er~v~I~G~~~~v~~A~~~I~~~l~e  194 (433)
                      ......+|.||.+++|.||||+|++|++|+++|||+|.+.++.. +.+.+|.|+|+|+++++.+|+.+|.+++.+
T Consensus        11 ~~~~~~~i~Ip~~~ig~IIGkgG~~Ik~I~~~tga~I~i~~~~~~~~~~er~v~I~G~~~~v~~A~~~I~~i~~e   85 (85)
T 2opv_A           11 QNGTVQEIMIPAGKAGLVIGKGGETIKQLQERAGVKMILIQDGSQNTNVDKPLRIIGDPYKVQQACEMVMDILRE   85 (85)
T ss_dssp             CSSEEEEEEECTTTHHHHHTTTTHHHHHHHHHHTCEEEECSSSCSSTTSCEEEEEEECHHHHHHHHHHHHHHHTC
T ss_pred             CCCEEEEEEeChhheeeeECCCCHHHHHHHHHHCCEEEEcCCCCCCCCCceEEEEEeCHHHHHHHHHHHHHHhcC
Confidence            45678899999999999999999999999999999999987543 457899999999999999999999998764

>1vig_A Vigilin; RNA-binding protein, ribonucleoprotein; NMR {Homo sapiens} SCOP: d.51.1.1 PDB: 1vih_A

Probab=99.43  E-value=1.9e-13  Score=103.67  Aligned_cols=68  Identities=18%  Similarity=0.260  Sum_probs=62.3

Q ss_pred             CceEEEEEeCcccccccccCCCchHHHHHhHhCCeEEEccCCCCCceEEEEEeCHHHHHHHHHHHHHHH
Q psy11929        286 DFVETEIVLTDDIAGCVIGKAGSRLLEIRQISGAQINIHTGTESHKKMFHIQGCQEAVSLAQYLINMCI  354 (433)
Q Consensus       286 ~~~t~~i~VP~~~vG~IIGkgG~~Ik~I~~~sGA~I~I~~~~~~~er~V~IsGt~e~v~~A~~lI~~~i  354 (433)
                      ...+.+|.||.+++|.|||++|++|++|+++|||+|.|+++. ..+|.|+|+|+++++++|+.+|.+.+
T Consensus         3 ~~~~~~i~I~~~~ig~iIG~gG~~I~~I~e~tg~~I~i~~~g-~~~~~V~I~G~~~~v~~A~~~I~~i~   70 (71)
T 1vig_A            3 RMDYVEINIDHKFHRHLIGKSGANINRIKDQYKVSVRIPPDS-EKSNLIRIEGDPQGVQQAKRELLELA   70 (71)
T ss_dssp             CCEEEEEEECSSHHHHHTCSSCCHHHHHHHHTCCEEECCCCC-SSSEEEEEEESSHHHHHHHHHHHHTC
T ss_pred             ceEEEEEEECHHHhhhhcCCCCccHHHHHHHHCCEEEECCCC-CcccEEEEEcCHHHHHHHHHHHHHHh
Confidence            456889999999999999999999999999999999999876 46789999999999999999998753

>2ctm_A Vigilin; K homology type I domain, RNA-binding, cell sterol metabolism, beta-alpha-alpha-beta-BETA-alpha structure, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.51.1.1

Probab=99.43  E-value=4.7e-13  Score=107.23  Aligned_cols=73  Identities=18%  Similarity=0.187  Sum_probs=66.8

Q ss_pred             CCceEEEEEeCcccccccccCCCchHHHHHhHhCCeEEEccCCCCCceEEEEEeCHHHHHHHHHHHHHHHHhc
Q psy11929        285 DDFVETEIVLTDDIAGCVIGKAGSRLLEIRQISGAQINIHTGTESHKKMFHIQGCQEAVSLAQYLINMCIELQ  357 (433)
Q Consensus       285 ~~~~t~~i~VP~~~vG~IIGkgG~~Ik~I~~~sGA~I~I~~~~~~~er~V~IsGt~e~v~~A~~lI~~~i~~~  357 (433)
                      ...++.+|.||.+++|.|||++|++|++|+++|||+|+|++..+..++.|+|+|+++++++|+.+|.+++.+.
T Consensus        14 ~~~vt~~i~Ip~~~ig~IIG~gG~~Ir~I~e~tg~~I~i~~~g~~~~~~V~I~G~~e~v~~A~~~I~~i~~e~   86 (95)
T 2ctm_A           14 EQMVSEDVPLDHRVHARIIGARGKAIRKIMDEFKVDIRFPQSGAPDPNCVTVTGLPENVEEAIDHILNLEEEY   86 (95)
T ss_dssp             TTCCCEEEECCTTTHHHHHCSSSCHHHHHHHHHTCEEECCCTTCSCTTEEEEESCHHHHHHHHHHHHHHHHHH
T ss_pred             cccEEEEEEECHHHccccCCCCcchHHHHHHHHCCeEEecCCCCCCCcEEEEEcCHHHHHHHHHHHHHHHHHH
Confidence            4578899999999999999999999999999999999998865456789999999999999999999988764

>2hh2_A KH-type splicing regulatory protein; KH-RNA binding domain, RNA binding protein; NMR {Homo sapiens}

Probab=99.42  E-value=2.4e-13  Score=111.49  Aligned_cols=70  Identities=27%  Similarity=0.536  Sum_probs=64.1

Q ss_pred             EEEEEeccCcccceecCCchhHHHHHHhhCceEEeccCCCC--CCCccEEEEEccHHHHHHHHHHHHHHHHh
Q psy11929        125 QLKLVIPATHCGSLIGKGGCKIKDIRDLSGANVQVASDMLP--MSTERIVTVHGNPDTISQAIYQICLVLIE  194 (433)
Q Consensus       125 ~~~l~ip~~~vg~iIGk~G~~Ik~I~~~sga~I~i~~~~~~--~~~er~v~I~G~~~~v~~A~~~I~~~l~e  194 (433)
                      +++|+||.+++|+||||+|++||+|+++|||+|+|.++..+  +..+|.|+|+|+.++|.+|+.+|.+++.+
T Consensus         8 ~~~i~IP~~~vG~IIGkgG~~Ik~I~~~TGa~I~I~~~~~~~~~~~~r~V~I~G~~e~v~~A~~~I~~~i~e   79 (107)
T 2hh2_A            8 EMTFSIPTHKCGLVIGRGGENVKAINQQTGAFVEISRQLPPNGDPNFKLFIIRGSPQQIDHAKQLIEEKIEG   79 (107)
T ss_dssp             CEEEEEEGGGTTTTSTTTTCHHHHHHHHSSSEEEECCCCCTTCCTTEEEEEEESCHHHHHHHHHHHHHHSCS
T ss_pred             eEEEEECHHHcCccCCCCcHHHHHHHHHhCCEEEEcCccCCCCCCCceEEEEECCHHHHHHHHHHHHHHHhc
Confidence            78999999999999999999999999999999999875432  35789999999999999999999999887

>1x4n_A FAR upstream element binding protein 1; KH domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Mus musculus} SCOP: d.51.1.1 PDB: 2opu_A

Probab=99.42  E-value=5.3e-13  Score=106.48  Aligned_cols=73  Identities=25%  Similarity=0.413  Sum_probs=67.4

Q ss_pred             CCCeEEEEEeccCcccceecCCchhHHHHHHhhCceEEeccCCCCCCCccEEEEEccHHHHHHHHHHHHHHHHh
Q psy11929        121 PQPLQLKLVIPATHCGSLIGKGGCKIKDIRDLSGANVQVASDMLPMSTERIVTVHGNPDTISQAIYQICLVLIE  194 (433)
Q Consensus       121 ~~~~~~~l~ip~~~vg~iIGk~G~~Ik~I~~~sga~I~i~~~~~~~~~er~v~I~G~~~~v~~A~~~I~~~l~e  194 (433)
                      ...++.+|.||.+++|.||||+|++|++|+++|||+|.|.++. ++..+|.|+|+|+++++.+|+.+|.+++.+
T Consensus        12 ~~~~~~~i~Ip~~~vG~IIGkgG~~Ik~I~~~tga~I~I~~~~-~g~~~r~v~I~G~~e~v~~A~~~I~~~i~~   84 (92)
T 1x4n_A           12 RSVMTEEYKVPDGMVGFIIGRGGEQISRIQQESGCKIQIAPDS-GGLPERSCMLTGTPESVQSAKRLLDQIVEK   84 (92)
T ss_dssp             CCCEEEEEEEEHHHHHHHHCSSSHHHHHHHHHSCCEEEECSCC-TTCSEEEEEEEECHHHHHHHHHHHHHHHHH
T ss_pred             CCCEEEEEEEChHHcceeECCCchHHHHHHHHhCCEEEEcCCC-CCCCccEEEEEeCHHHHHHHHHHHHHHHHh
Confidence            4568899999999999999999999999999999999998643 466889999999999999999999999988

>1ec6_A RNA-binding protein NOVA-2; KH domain, alpha-beta fold, RNA-binding motif, protein/RNA structure, RNA binding protein/RNA complex; 2.40A {Homo sapiens} SCOP: d.51.1.1

Probab=99.41  E-value=2.8e-13  Score=106.99  Aligned_cols=71  Identities=28%  Similarity=0.566  Sum_probs=66.1

Q ss_pred             eEEEEEeccCcccceecCCchhHHHHHHhhCceEEeccC--CCCCCCccEEEEEccHHHHHHHHHHHHHHHHh
Q psy11929        124 LQLKLVIPATHCGSLIGKGGCKIKDIRDLSGANVQVASD--MLPMSTERIVTVHGNPDTISQAIYQICLVLIE  194 (433)
Q Consensus       124 ~~~~l~ip~~~vg~iIGk~G~~Ik~I~~~sga~I~i~~~--~~~~~~er~v~I~G~~~~v~~A~~~I~~~l~e  194 (433)
                      .+++|+||.+++|.||||+|++|++|+++|||+|.|.++  ..+++.++.|+|+|+++++.+|+.+|.+++.+
T Consensus         3 ~t~~i~IP~~~vG~IIGkgG~~Ik~I~~~tga~I~I~~~~~~~~g~~~r~v~I~G~~~~v~~A~~~I~~~i~~   75 (87)
T 1ec6_A            3 ELVEIAVPENLVGAILGKGGKTLVEYQELTGARIQISKKGEFLPGTRNRRVTITGSPAATQAAQYLISQRVTY   75 (87)
T ss_dssp             SEEEEEEEHHHHHHHHCGGGHHHHHHHHHHCCEEEECCTTCBSTTSCEEEEEEESSHHHHHHHHHHHHHHHHH
T ss_pred             eEEEEEEChHHcCeeECCCcHhHHHHHHHhCCEEEEccCCCCCCCCCceEEEEEcCHHHHHHHHHHHHHHHhc
Confidence            578999999999999999999999999999999999864  45677899999999999999999999999987

>1x4m_A FAR upstream element binding protein 1; KH domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Mus musculus} SCOP: d.51.1.1

Probab=99.41  E-value=3e-13  Score=108.40  Aligned_cols=73  Identities=16%  Similarity=0.315  Sum_probs=66.5

Q ss_pred             CCceEEEEEEeccCCcccccceeeecCchHHHHHHHHhCCeEEEeCCC----CCcceEEEecccCCCCCCccccCCCCCc
Q psy11929         11 EDTLITMRCLFHSSVNVNEISCLIGPGGCIVRRLRKESGAKISITDGA----CPDRIVTVSGSVDNSSTSSVETGYPGHT   86 (433)
Q Consensus        11 ~~~~~~~rilvp~~~~~~~vg~IIGk~G~~Ik~I~~~tga~I~v~~~~----~~eRvv~I~G~~~~~~~~~v~~~~~~~~   86 (433)
                      ....++++|+||.    +++|.||||+|++||+|+++|||+|+|.+.+    ..+|+|+|+|+++               
T Consensus        11 ~p~~~~~~i~Ip~----~~vG~IIGkgG~~Ik~I~~~tga~I~I~~~~~~~~~~~r~v~I~G~~~---------------   71 (94)
T 1x4m_A           11 GPGNAVQEIMIPA----SKAGLVIGKGGETIKQLQERAGVKMVMIQDGPQNTGADKPLRITGDPY---------------   71 (94)
T ss_dssp             CCCCEEEEEEECH----HHHHHHSCSSSSHHHHHHHHHTSEEEECCSCCCSSCSCEEEEEEECTT---------------
T ss_pred             CCCcEEEEEEECh----hhcceEECCCCHHHHHHHHHHCCeEEecCCCCCCCCCceEEEEEeCHH---------------
Confidence            4567899999999    9999999999999999999999999998854    3789999999888               


Q ss_pred             cccchHHHHHHHHHHHHhhhhhh
Q psy11929         87 LWVTSVDNVCTAYNFMCRSLEDY  109 (433)
Q Consensus        87 ~~~~a~~~v~~A~~~I~~~~~~~  109 (433)
                             ++.+|+.+|.+++.+.
T Consensus        72 -------~v~~A~~~I~~~i~~~   87 (94)
T 1x4m_A           72 -------KVQQAKEMVLELIRDQ   87 (94)
T ss_dssp             -------THHHHHHHHHHHHCCC
T ss_pred             -------HHHHHHHHHHHHHhcc
Confidence                   9999999999988763

>1vig_A Vigilin; RNA-binding protein, ribonucleoprotein; NMR {Homo sapiens} SCOP: d.51.1.1 PDB: 1vih_A

Probab=99.38  E-value=5.4e-13  Score=101.09  Aligned_cols=68  Identities=13%  Similarity=0.185  Sum_probs=62.8

Q ss_pred             ceEEEEEEeccCCcccccceeeecCchHHHHHHHHhCCeEEEeCCCCCcceEEEecccCCCCCCccccCCCCCccccchH
Q psy11929         13 TLITMRCLFHSSVNVNEISCLIGPGGCIVRRLRKESGAKISITDGACPDRIVTVSGSVDNSSTSSVETGYPGHTLWVTSV   92 (433)
Q Consensus        13 ~~~~~rilvp~~~~~~~vg~IIGk~G~~Ik~I~~~tga~I~v~~~~~~eRvv~I~G~~~~~~~~~v~~~~~~~~~~~~a~   92 (433)
                      ...+..|.||.    .++|.|||++|++|++|+++|||+|+|++.+..+|.|+|+|+.+                     
T Consensus         3 ~~~~~~i~I~~----~~ig~iIG~gG~~I~~I~e~tg~~I~i~~~g~~~~~V~I~G~~~---------------------   57 (71)
T 1vig_A            3 RMDYVEINIDH----KFHRHLIGKSGANINRIKDQYKVSVRIPPDSEKSNLIRIEGDPQ---------------------   57 (71)
T ss_dssp             CCEEEEEEECS----SHHHHHTCSSCCHHHHHHHHTCCEEECCCCCSSSEEEEEEESSH---------------------
T ss_pred             ceEEEEEEECH----HHhhhhcCCCCccHHHHHHHHCCEEEECCCCCcccEEEEEcCHH---------------------
Confidence            45788999999    99999999999999999999999999999887889999999988                     


Q ss_pred             HHHHHHHHHHHhhh
Q psy11929         93 DNVCTAYNFMCRSL  106 (433)
Q Consensus        93 ~~v~~A~~~I~~~~  106 (433)
                       ++.+|..+|.+++
T Consensus        58 -~v~~A~~~I~~i~   70 (71)
T 1vig_A           58 -GVQQAKRELLELA   70 (71)
T ss_dssp             -HHHHHHHHHHHTC
T ss_pred             -HHHHHHHHHHHHh
Confidence             9999999998753

>2dgr_A Ring finger and KH domain-containing protein 1; structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.36  E-value=4.5e-13  Score=104.47  Aligned_cols=70  Identities=16%  Similarity=0.281  Sum_probs=63.3

Q ss_pred             CCceEEEEEEeccCCcccccceeeecCchHHHHHHHHhCCeEEEeCCCCCcceEEEecccCCCCCCccccCCCCCccccc
Q psy11929         11 EDTLITMRCLFHSSVNVNEISCLIGPGGCIVRRLRKESGAKISITDGACPDRIVTVSGSVDNSSTSSVETGYPGHTLWVT   90 (433)
Q Consensus        11 ~~~~~~~rilvp~~~~~~~vg~IIGk~G~~Ik~I~~~tga~I~v~~~~~~eRvv~I~G~~~~~~~~~v~~~~~~~~~~~~   90 (433)
                      ....++++|.||.    +++|+||||+|++||+|+++|||+|+|+..+ ++|+|+|+|+++                   
T Consensus         6 ~~~~~~~~i~VP~----~~vG~IIGkgG~tIk~Iqe~Tga~I~I~~~~-~~~~v~ItG~~e-------------------   61 (83)
T 2dgr_A            6 SGGQTTIQVRVPY----RVVGLVVGPKGATIKRIQQRTHTYIVTPGRD-KEPVFAVTGMPE-------------------   61 (83)
T ss_dssp             SCCSEEEEEECCH----HHHHHHHTTTTSSHHHHHHHTTCEEECCCSS-SCCEEEEEECTT-------------------
T ss_pred             CCCceEEEEEeCh----HHeeeeECCCchHHHHHHHHhCCeEEecCCC-CCCeEEEEcCHH-------------------
Confidence            3456899999999    9999999999999999999999999998644 479999999999                   


Q ss_pred             hHHHHHHHHHHHHhhhh
Q psy11929         91 SVDNVCTAYNFMCRSLE  107 (433)
Q Consensus        91 a~~~v~~A~~~I~~~~~  107 (433)
                         ++.+|+.+|.+++.
T Consensus        62 ---~v~~A~~~I~~~i~   75 (83)
T 2dgr_A           62 ---NVDRAREEIEAHIT   75 (83)
T ss_dssp             ---THHHHHHHHHHHHH
T ss_pred             ---HHHHHHHHHHHHHh
Confidence               99999999998654

>2hh3_A KH-type splicing regulatory protein; KH-RNA binding domain, RNA binding protein; NMR {Homo sapiens}

Probab=99.35  E-value=1.4e-12  Score=106.54  Aligned_cols=71  Identities=27%  Similarity=0.398  Sum_probs=64.2

Q ss_pred             CeEEEEEeccCcccceecCCchhHHHHHHhhCceEEeccCCCCCCCccEEEEEccHHHHHHHHHHHHHHHHh
Q psy11929        123 PLQLKLVIPATHCGSLIGKGGCKIKDIRDLSGANVQVASDMLPMSTERIVTVHGNPDTISQAIYQICLVLIE  194 (433)
Q Consensus       123 ~~~~~l~ip~~~vg~iIGk~G~~Ik~I~~~sga~I~i~~~~~~~~~er~v~I~G~~~~v~~A~~~I~~~l~e  194 (433)
                      ..+++|+||.++++.||||+|++||+|+++|||+|+|.++. +...+|.|+|+|+++++++|+.+|.+++.+
T Consensus        10 ~~~~~i~Ip~~~iG~IIGkgG~~Ik~I~~~TGakI~I~~~~-~~~~er~V~I~G~~e~v~~A~~~I~~ii~~   80 (106)
T 2hh3_A           10 GGGIDVPVPRHSVGVVIGRSGEMIKKIQNDAGVRIQFKQDD-GTGPEKIAHIMGPPDRCEHAARIINDLLQS   80 (106)
T ss_dssp             --CEEEEEETTTHHHHHTTTTHHHHHHHHHHTCEEEECSSC-SSSSEEEEEEESSHHHHHHHHHHHHHHHHH
T ss_pred             CeEEEEEECHHHcCccCCCCcHHHHHHHHHHCcEEEEecCC-CCCceeEEEEEeCHHHHHHHHHHHHHHHhc
Confidence            34789999999999999999999999999999999998642 456789999999999999999999999988

>1we8_A Tudor and KH domain containing protein; structural genomics, riken structural genomics/proteomics initiative, RSGI, RNA binding protein; NMR {Mus musculus} SCOP: d.51.1.1

Probab=99.35  E-value=1.6e-12  Score=106.13  Aligned_cols=74  Identities=24%  Similarity=0.427  Sum_probs=66.6

Q ss_pred             CCCCceEEEEEEeccCCcccccceeeecCchHHHHHHHHhCCeEEEeCCC----CCcceEEEecccCCCCCCccccCCCC
Q psy11929          9 IDEDTLITMRCLFHSSVNVNEISCLIGPGGCIVRRLRKESGAKISITDGA----CPDRIVTVSGSVDNSSTSSVETGYPG   84 (433)
Q Consensus         9 ~~~~~~~~~rilvp~~~~~~~vg~IIGk~G~~Ik~I~~~tga~I~v~~~~----~~eRvv~I~G~~~~~~~~~v~~~~~~   84 (433)
                      -.....++++|+||.    +++|.||||+|++||+|+++|||+|+|.+..    ..+|.|+|+|+.+             
T Consensus         9 ~s~~ap~~~~i~Ip~----~~ig~IIGkgG~~Ik~I~~~tga~I~I~~~~~~~~~~~~~V~I~G~~~-------------   71 (104)
T 1we8_A            9 LTENTPVFEQLSVPQ----RSVGRIIGRGGETIRSICKASGAKITCDKESEGTLLLSRLIKISGTQK-------------   71 (104)
T ss_dssp             CSSSCEEEEEEEEET----TTHHHHHTTTSHHHHHHHHHHCCEEEECCSSCCSSSSEEEEEEEEEHH-------------
T ss_pred             cCCCCCEEEEEEECh----hheeeeECCCCHHHHHHHHHHCCEEEEecCCCCCCCCcceEEEEcCHH-------------
Confidence            345667899999999    9999999999999999999999999998742    2589999999999             


Q ss_pred             CccccchHHHHHHHHHHHHhhhhh
Q psy11929         85 HTLWVTSVDNVCTAYNFMCRSLED  108 (433)
Q Consensus        85 ~~~~~~a~~~v~~A~~~I~~~~~~  108 (433)
                               ++.+|+.+|.+++.+
T Consensus        72 ---------~v~~A~~~I~~~i~e   86 (104)
T 1we8_A           72 ---------EVAAAKHLILEKVSE   86 (104)
T ss_dssp             ---------HHHHHHHHHHHHHHH
T ss_pred             ---------HHHHHHHHHHHHHhh
Confidence                     999999999998865

>2cte_A Vigilin; K homology type I domain, RNA-binding, cell sterol metabolism, beta-alpha-alpha-beta-BETA-alpha structure, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.51.1.1

Probab=99.33  E-value=8.1e-13  Score=105.81  Aligned_cols=73  Identities=15%  Similarity=0.191  Sum_probs=67.1

Q ss_pred             CCceEEEEEEeccCCcccccceeeecCchHHHHHHHHhCCeEEEeCCCCCcceEEEecccCCCCCCccccCCCCCccccc
Q psy11929         11 EDTLITMRCLFHSSVNVNEISCLIGPGGCIVRRLRKESGAKISITDGACPDRIVTVSGSVDNSSTSSVETGYPGHTLWVT   90 (433)
Q Consensus        11 ~~~~~~~rilvp~~~~~~~vg~IIGk~G~~Ik~I~~~tga~I~v~~~~~~eRvv~I~G~~~~~~~~~v~~~~~~~~~~~~   90 (433)
                      ++..++.+|.||.    .++|.|||++|++||+|+++|||+|+|++.+..++.|+|+|+++                   
T Consensus        13 l~~~~t~~i~Ip~----~~ig~IIG~gG~~Ik~I~~etg~~I~i~~~~~~~~~V~I~G~~e-------------------   69 (94)
T 2cte_A           13 LQTQASATVAIPK----EHHRFVIGKNGEKLQDLELKTATKIQIPRPDDPSNQIKITGTKE-------------------   69 (94)
T ss_dssp             CCSCEEEEEECCT----TTHHHHHCSSSCHHHHHHHHTTCCCBCCCTTSSCCEEEEEECHH-------------------
T ss_pred             hCCceEEEEEECh----HHeeeeECCCChhHHHHHHHHCCEEEeCCCCCCCCeEEEEECHH-------------------
Confidence            4567999999999    99999999999999999999999999998766678999999988                   


Q ss_pred             hHHHHHHHHHHHHhhhhhh
Q psy11929         91 SVDNVCTAYNFMCRSLEDY  109 (433)
Q Consensus        91 a~~~v~~A~~~I~~~~~~~  109 (433)
                         ++.+|..+|.+++.+.
T Consensus        70 ---~v~~A~~~I~~i~~~~   85 (94)
T 2cte_A           70 ---GIEKARHEVLLISAEQ   85 (94)
T ss_dssp             ---HHHHHHHHHHHHHHHH
T ss_pred             ---HHHHHHHHHHHHhhcc
Confidence               9999999999988774

>2ctk_A Vigilin; K homology type I domain, RNA-binding, cell sterol metabolism, beta-alpha-alpha-beta-BETA-alpha structure, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.51.1.1

Probab=99.32  E-value=2.3e-12  Score=104.99  Aligned_cols=70  Identities=17%  Similarity=0.179  Sum_probs=64.3

Q ss_pred             ceEEEEEeCcccccccccCCCchHHHHHhHhCCeEEEccCCCCCceEEEEEeCHHHHHHHHHHHHHHHHhc
Q psy11929        287 FVETEIVLTDDIAGCVIGKAGSRLLEIRQISGAQINIHTGTESHKKMFHIQGCQEAVSLAQYLINMCIELQ  357 (433)
Q Consensus       287 ~~t~~i~VP~~~vG~IIGkgG~~Ik~I~~~sGA~I~I~~~~~~~er~V~IsGt~e~v~~A~~lI~~~i~~~  357 (433)
                      ..+.+|.||.+++|.|||+||++|++|+++|||+|+|+++. ...+.|+|+|+++++++|+.+|.+++...
T Consensus        16 p~~~~i~Ip~~~ig~IIG~gG~~Ir~I~eetg~~I~I~~~g-~~~~~V~I~G~~e~v~~A~~~I~~i~~e~   85 (104)
T 2ctk_A           16 PVTIEVEVPFDLHRYVIGQKGSGIRKMMDEFEVNIHVPAPE-LQSDIIAITGLAANLDRAKAGLLERVKEL   85 (104)
T ss_dssp             CEEEEEECCHHHHHHHHCSSSHHHHHHHHHTCCEEECCCTT-TTCCEEEEEECHHHHHHHHHHHHHHHHHH
T ss_pred             CEEEEEEEChHHccceeCCCchHHHHHHHHHCCEEEecCCC-CCcceEEEEcCHHHHHHHHHHHHHHHhhH
Confidence            47889999999999999999999999999999999999866 35579999999999999999999998764

>2ctl_A Vigilin; K homology type I domain, RNA-binding, cell sterol metabolism, beta-alpha-alpha-beta-BETA-alpha structure, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.51.1.1

Probab=99.32  E-value=3.8e-12  Score=102.36  Aligned_cols=73  Identities=19%  Similarity=0.236  Sum_probs=66.5

Q ss_pred             CCeEEEEEeccCcccceecCCchhHHHHHHhhCceEEeccCCCCCCCccEEEEEccHHHHHHHHHHHHHHHHh
Q psy11929        122 QPLQLKLVIPATHCGSLIGKGGCKIKDIRDLSGANVQVASDMLPMSTERIVTVHGNPDTISQAIYQICLVLIE  194 (433)
Q Consensus       122 ~~~~~~l~ip~~~vg~iIGk~G~~Ik~I~~~sga~I~i~~~~~~~~~er~v~I~G~~~~v~~A~~~I~~~l~e  194 (433)
                      ..+++.|.||..+++.|||++|++|++|+++|||+|.|+++..+...++.|+|+|+.+++.+|+.+|..++.+
T Consensus        15 ~~~~~~i~Ip~~~ig~IIGkgG~~Ik~I~~etg~~I~i~~~g~~~~~~~~V~I~G~~e~v~~A~~~I~~iv~e   87 (97)
T 2ctl_A           15 RSFKLSVTVDPKYHPKIIGRKGAVITQIRLEHDVNIQFPDKDDGNQPQDQITITGYEKNTEAARDAILRIVGE   87 (97)
T ss_dssp             TTCEEEEECCTTTHHHHSCSSSCHHHHHHHHHTCEEECCCTTTCSSCSSEEEEESCHHHHHHHHHHHHHHHHH
T ss_pred             cceeEEEEECHHHhhhcCCCCchhHHHHHHHHCCEEEecCCCCCCCCccEEEEEeCHHHHHHHHHHHHHHHHH
Confidence            4578999999999999999999999999999999999997544455789999999999999999999999887

>2ctj_A Vigilin; K homology type I domain, RNA-binding, cell sterol metabolism, beta-alpha-alpha-beta-BETA-alpha structure, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.51.1.1

Probab=99.29  E-value=7.4e-12  Score=100.10  Aligned_cols=77  Identities=18%  Similarity=0.242  Sum_probs=69.0

Q ss_pred             CCCceEEEEEeCcccccccccCCCchHHHHHhHh-CCeEEEccCCCCCceEEEEEeCHHHHHHHHHHHHHHHHhccccC
Q psy11929        284 GDDFVETEIVLTDDIAGCVIGKAGSRLLEIRQIS-GAQINIHTGTESHKKMFHIQGCQEAVSLAQYLINMCIELQKNNT  361 (433)
Q Consensus       284 ~~~~~t~~i~VP~~~vG~IIGkgG~~Ik~I~~~s-GA~I~I~~~~~~~er~V~IsGt~e~v~~A~~lI~~~i~~~~~~~  361 (433)
                      .....+.+|.||.++++.|||++|.+|++|+++| ||+|.|+++. +..+.|+|+|+.+++++|+.+|.+++.......
T Consensus        13 ~~~~vt~~i~Ip~~~i~~iIG~gGk~Ir~I~eetggv~I~i~~~g-~~~~~V~I~G~~~~v~~A~~~I~~iv~e~e~~~   90 (95)
T 2ctj_A           13 LANIAEVEVSIPAKLHNSLIGTKGRLIRSIMEECGGVHIHFPVEG-SGSDTVVIRGPSSDVEKAKKQLLHLAEEKQTKS   90 (95)
T ss_dssp             CCSSCCEEEECCHHHHHHHHCSSSHHHHHHHHHHTSCEEECCCTT-TTCCEEEEESCHHHHHHHHHHHHHHHHHHSCCS
T ss_pred             HhhcEEEEEEECHHHHhhhCCCCchhHHHHHHHcCCCEEEeCCCC-CCcceEEEEcCHHHHHHHHHHHHHHHhhhhhcc
Confidence            4567889999999999999999999999999999 9999999865 567799999999999999999999998765443

>2ctm_A Vigilin; K homology type I domain, RNA-binding, cell sterol metabolism, beta-alpha-alpha-beta-BETA-alpha structure, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.51.1.1

Probab=99.27  E-value=4.2e-12  Score=101.67  Aligned_cols=76  Identities=20%  Similarity=0.283  Sum_probs=68.4

Q ss_pred             CCCceEEEEEEeccCCcccccceeeecCchHHHHHHHHhCCeEEEeCCC-CCcceEEEecccCCCCCCccccCCCCCccc
Q psy11929         10 DEDTLITMRCLFHSSVNVNEISCLIGPGGCIVRRLRKESGAKISITDGA-CPDRIVTVSGSVDNSSTSSVETGYPGHTLW   88 (433)
Q Consensus        10 ~~~~~~~~rilvp~~~~~~~vg~IIGk~G~~Ik~I~~~tga~I~v~~~~-~~eRvv~I~G~~~~~~~~~v~~~~~~~~~~   88 (433)
                      ++...+++.|.||.    .++|.|||++|++||+|+++|||+|+|++.+ ..+|.|+|+|.++                 
T Consensus        12 ~l~~~vt~~i~Ip~----~~ig~IIG~gG~~Ir~I~e~tg~~I~i~~~g~~~~~~V~I~G~~e-----------------   70 (95)
T 2ctm_A           12 ELEQMVSEDVPLDH----RVHARIIGARGKAIRKIMDEFKVDIRFPQSGAPDPNCVTVTGLPE-----------------   70 (95)
T ss_dssp             CTTTCCCEEEECCT----TTHHHHHCSSSCHHHHHHHHHTCEEECCCTTCSCTTEEEEESCHH-----------------
T ss_pred             hhcccEEEEEEECH----HHccccCCCCcchHHHHHHHHCCeEEecCCCCCCCcEEEEEcCHH-----------------
Confidence            45667899999999    9999999999999999999999999999864 3578999999988                 


Q ss_pred             cchHHHHHHHHHHHHhhhhhhcc
Q psy11929         89 VTSVDNVCTAYNFMCRSLEDYHI  111 (433)
Q Consensus        89 ~~a~~~v~~A~~~I~~~~~~~~~  111 (433)
                           ++.+|+.+|..++.++..
T Consensus        71 -----~v~~A~~~I~~i~~e~~~   88 (95)
T 2ctm_A           71 -----NVEEAIDHILNLEEEYLA   88 (95)
T ss_dssp             -----HHHHHHHHHHHHHHHHHT
T ss_pred             -----HHHHHHHHHHHHHHHHHH
Confidence                 999999999998887644

>2ctf_A Vigilin; K homology type I domain, RNA-binding, cell sterol metabolism, beta-alpha-alpha-beta-BETA-alpha structure, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.51.1.1

Probab=99.21  E-value=2.9e-12  Score=103.87  Aligned_cols=81  Identities=17%  Similarity=0.187  Sum_probs=68.9

Q ss_pred             HHHHHHHHHHhhhhhhcccccCCCCCCCCCeEEEEEeccCcccceecCCchhHHHHHHh-hCceEEeccCCCCCCCccEE
Q psy11929         94 NVCTAYNFMCRSLEDYHINRNRMENCSPQPLQLKLVIPATHCGSLIGKGGCKIKDIRDL-SGANVQVASDMLPMSTERIV  172 (433)
Q Consensus        94 ~v~~A~~~I~~~~~~~~~~~~~~~~~~~~~~~~~l~ip~~~vg~iIGk~G~~Ik~I~~~-sga~I~i~~~~~~~~~er~v  172 (433)
                      +|.+|+.+|.+.+.              ..++.+|.||..+++.|||++|++|++|+++ ++++|.|++      .++.|
T Consensus        11 ~V~~A~~~i~~~~~--------------~~~t~~i~vp~~~h~~IIG~~G~~Ik~i~~~~~~v~I~fp~------~~~~I   70 (102)
T 2ctf_A           11 KLGQALTEVYAKAN--------------SFTVSSVAAPSWLHRFIIGKKGQNLAKITQQMPKVHIEFTE------GEDKI   70 (102)
T ss_dssp             CCCCSCCCCCCCCC--------------CCEEEEEECCSTTHHHHHTTTTCHHHHHHHHCSSSEEEECS------SSCEE
T ss_pred             HHHHHHHHHHHHhc--------------CeEEEEEEeCHHHHhhhcCCCCccHHHHHHHcCCcEEEeCC------CCCEE
Confidence            66666666554432              2378999999999999999999999999997 589999985      36799


Q ss_pred             EEEccHHHHHHHHHHHHHHHHh
Q psy11929        173 TVHGNPDTISQAIYQICLVLIE  194 (433)
Q Consensus       173 ~I~G~~~~v~~A~~~I~~~l~e  194 (433)
                      +|+|+++.|.+|..+|..++.+
T Consensus        71 tI~G~~~~V~~a~~~I~~~v~e   92 (102)
T 2ctf_A           71 TLEGPTEDVSVAQEQIEGMVKD   92 (102)
T ss_dssp             EEEECHHHHHHHHHHHHHHHHH
T ss_pred             EEECCHHHHHHHHHHHHHHHHH
Confidence            9999999999999999999887

>2ctk_A Vigilin; K homology type I domain, RNA-binding, cell sterol metabolism, beta-alpha-alpha-beta-BETA-alpha structure, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.51.1.1

Probab=99.21  E-value=9.1e-12  Score=101.43  Aligned_cols=71  Identities=15%  Similarity=0.222  Sum_probs=64.9

Q ss_pred             ceEEEEEEeccCCcccccceeeecCchHHHHHHHHhCCeEEEeCCCCCcceEEEecccCCCCCCccccCCCCCccccchH
Q psy11929         13 TLITMRCLFHSSVNVNEISCLIGPGGCIVRRLRKESGAKISITDGACPDRIVTVSGSVDNSSTSSVETGYPGHTLWVTSV   92 (433)
Q Consensus        13 ~~~~~rilvp~~~~~~~vg~IIGk~G~~Ik~I~~~tga~I~v~~~~~~eRvv~I~G~~~~~~~~~v~~~~~~~~~~~~a~   92 (433)
                      ..++..|.||.    .++|.|||++|++||+|+++|||+|+|++.+...+.|+|+|+.+                     
T Consensus        15 ap~~~~i~Ip~----~~ig~IIG~gG~~Ir~I~eetg~~I~I~~~g~~~~~V~I~G~~e---------------------   69 (104)
T 2ctk_A           15 VPVTIEVEVPF----DLHRYVIGQKGSGIRKMMDEFEVNIHVPAPELQSDIIAITGLAA---------------------   69 (104)
T ss_dssp             SCEEEEEECCH----HHHHHHHCSSSHHHHHHHHHTCCEEECCCTTTTCCEEEEEECHH---------------------
T ss_pred             CCEEEEEEECh----HHccceeCCCchHHHHHHHHHCCEEEecCCCCCcceEEEEcCHH---------------------
Confidence            46788999999    99999999999999999999999999999876778999999988                     


Q ss_pred             HHHHHHHHHHHhhhhhh
Q psy11929         93 DNVCTAYNFMCRSLEDY  109 (433)
Q Consensus        93 ~~v~~A~~~I~~~~~~~  109 (433)
                       ++.+|+.+|..++.+.
T Consensus        70 -~v~~A~~~I~~i~~e~   85 (104)
T 2ctk_A           70 -NLDRAKAGLLERVKEL   85 (104)
T ss_dssp             -HHHHHHHHHHHHHHHH
T ss_pred             -HHHHHHHHHHHHHhhH
Confidence             9999999999887663

>2ctf_A Vigilin; K homology type I domain, RNA-binding, cell sterol metabolism, beta-alpha-alpha-beta-BETA-alpha structure, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.51.1.1

Probab=99.18  E-value=6.2e-11  Score=96.06  Aligned_cols=69  Identities=26%  Similarity=0.343  Sum_probs=62.3

Q ss_pred             ceEEEEEeCcccccccccCCCchHHHHHhH-hCCeEEEccCCCCCceEEEEEeCHHHHHHHHHHHHHHHHhccc
Q psy11929        287 FVETEIVLTDDIAGCVIGKAGSRLLEIRQI-SGAQINIHTGTESHKKMFHIQGCQEAVSLAQYLINMCIELQKN  359 (433)
Q Consensus       287 ~~t~~i~VP~~~vG~IIGkgG~~Ik~I~~~-sGA~I~I~~~~~~~er~V~IsGt~e~v~~A~~lI~~~i~~~~~  359 (433)
                      ..+.+|.||.++++.|||++|++|++|++. ++++|.|++.    ++.|+|+|++++|++|+..|+.++.+-..
T Consensus        26 ~~t~~i~vp~~~h~~IIG~~G~~Ik~i~~~~~~v~I~fp~~----~~~ItI~G~~~~V~~a~~~I~~~v~el~~   95 (102)
T 2ctf_A           26 FTVSSVAAPSWLHRFIIGKKGQNLAKITQQMPKVHIEFTEG----EDKITLEGPTEDVSVAQEQIEGMVKDLIN   95 (102)
T ss_dssp             CEEEEEECCSTTHHHHHTTTTCHHHHHHHHCSSSEEEECSS----SCEEEEEECHHHHHHHHHHHHHHHHHHHH
T ss_pred             eEEEEEEeCHHHHhhhcCCCCccHHHHHHHcCCcEEEeCCC----CCEEEEECCHHHHHHHHHHHHHHHHHHHh
Confidence            478999999999999999999999999996 6999999983    47999999999999999999999876443

>2ctj_A Vigilin; K homology type I domain, RNA-binding, cell sterol metabolism, beta-alpha-alpha-beta-BETA-alpha structure, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.51.1.1

Probab=99.13  E-value=3.6e-11  Score=96.13  Aligned_cols=75  Identities=19%  Similarity=0.259  Sum_probs=68.9

Q ss_pred             CCCCceEEEEEEeccCCcccccceeeecCchHHHHHHHHh-CCeEEEeCCCCCcceEEEecccCCCCCCccccCCCCCcc
Q psy11929          9 IDEDTLITMRCLFHSSVNVNEISCLIGPGGCIVRRLRKES-GAKISITDGACPDRIVTVSGSVDNSSTSSVETGYPGHTL   87 (433)
Q Consensus         9 ~~~~~~~~~rilvp~~~~~~~vg~IIGk~G~~Ik~I~~~t-ga~I~v~~~~~~eRvv~I~G~~~~~~~~~v~~~~~~~~~   87 (433)
                      ...+..++..|.||.    .+++.|||++|++||+|+++| ||+|+|++.+...+.|+|+|+.+                
T Consensus        11 ~e~~~~vt~~i~Ip~----~~i~~iIG~gGk~Ir~I~eetggv~I~i~~~g~~~~~V~I~G~~~----------------   70 (95)
T 2ctj_A           11 KDLANIAEVEVSIPA----KLHNSLIGTKGRLIRSIMEECGGVHIHFPVEGSGSDTVVIRGPSS----------------   70 (95)
T ss_dssp             CCCCSSCCEEEECCH----HHHHHHHCSSSHHHHHHHHHHTSCEEECCCTTTTCCEEEEESCHH----------------
T ss_pred             HHHhhcEEEEEEECH----HHHhhhCCCCchhHHHHHHHcCCCEEEeCCCCCCcceEEEEcCHH----------------
Confidence            346677899999999    999999999999999999999 99999999888888999999999                


Q ss_pred             ccchHHHHHHHHHHHHhhhhhh
Q psy11929         88 WVTSVDNVCTAYNFMCRSLEDY  109 (433)
Q Consensus        88 ~~~a~~~v~~A~~~I~~~~~~~  109 (433)
                            ++.+|+.+|.+++.+.
T Consensus        71 ------~v~~A~~~I~~iv~e~   86 (95)
T 2ctj_A           71 ------DVEKAKKQLLHLAEEK   86 (95)
T ss_dssp             ------HHHHHHHHHHHHHHHH
T ss_pred             ------HHHHHHHHHHHHHhhh
Confidence                  9999999999988774

>2cpq_A FragIle X mental retardation syndrome related protein 1, isoform B'; KH domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.51.1.1

Probab=98.96  E-value=6.4e-10  Score=87.34  Aligned_cols=64  Identities=27%  Similarity=0.500  Sum_probs=57.6

Q ss_pred             CCceEEEEEeCcccccccccCCCchHHHHHhHhCCe-EEEccCCCCCceEEEEEe-CHHHHHHHHHHHHH
Q psy11929        285 DDFVETEIVLTDDIAGCVIGKAGSRLLEIRQISGAQ-INIHTGTESHKKMFHIQG-CQEAVSLAQYLINM  352 (433)
Q Consensus       285 ~~~~t~~i~VP~~~vG~IIGkgG~~Ik~I~~~sGA~-I~I~~~~~~~er~V~IsG-t~e~v~~A~~lI~~  352 (433)
                      ...+..+|.||.+++|.|||++|.+|++|+++|||+ |.|.++    +..|+|.| +.+++++|+.+|..
T Consensus        12 ~~~~i~~i~I~~dkIg~vIG~gGk~Ik~I~e~tGv~~IdI~ed----dG~V~I~g~~~ea~~~A~~~I~~   77 (91)
T 2cpq_A           12 AAAFHEEFVVREDLMGLAIGTHGSNIQQARKVPGVTAIELDED----TGTFRIYGESADAVKKARGFLEF   77 (91)
T ss_dssp             SCSEEEEEECCHHHHHHHHTTTTHHHHHHHTSTTEEEEEEETT----TTEEEEEESSHHHHHHHHHHHSC
T ss_pred             cCceEEEEEEChHHhhhhcCCCcHHHHHHHHHhCCeEEEEEcC----CCEEEEEECCHHHHHHHHHHHHh
Confidence            356889999999999999999999999999999998 999763    37899999 79999999999844

>2cpq_A FragIle X mental retardation syndrome related protein 1, isoform B'; KH domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.51.1.1

Probab=98.68  E-value=2.8e-08  Score=77.97  Aligned_cols=65  Identities=18%  Similarity=0.356  Sum_probs=57.6

Q ss_pred             CCCeEEEEEeccCcccceecCCchhHHHHHHhhCce-EEeccCCCCCCCccEEEEEc-cHHHHHHHHHHHHHH
Q psy11929        121 PQPLQLKLVIPATHCGSLIGKGGCKIKDIRDLSGAN-VQVASDMLPMSTERIVTVHG-NPDTISQAIYQICLV  191 (433)
Q Consensus       121 ~~~~~~~l~ip~~~vg~iIGk~G~~Ik~I~~~sga~-I~i~~~~~~~~~er~v~I~G-~~~~v~~A~~~I~~~  191 (433)
                      ...+...|.||.+++|.+||++|.+|++|+++||++ |.+..      .+..|+|.| +.+++++|+.+|..+
T Consensus        12 ~~~~i~~i~I~~dkIg~vIG~gGk~Ik~I~e~tGv~~IdI~e------ddG~V~I~g~~~ea~~~A~~~I~~i   78 (91)
T 2cpq_A           12 AAAFHEEFVVREDLMGLAIGTHGSNIQQARKVPGVTAIELDE------DTGTFRIYGESADAVKKARGFLEFV   78 (91)
T ss_dssp             SCSEEEEEECCHHHHHHHHTTTTHHHHHHHTSTTEEEEEEET------TTTEEEEEESSHHHHHHHHHHHSCC
T ss_pred             cCceEEEEEEChHHhhhhcCCCcHHHHHHHHHhCCeEEEEEc------CCCEEEEEECCHHHHHHHHHHHHhh
Confidence            566888999999999999999999999999999998 99964      258999999 899999998887543

>2yqr_A KIAA0907 protein; structure genomics, KH domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=98.63  E-value=1.1e-07  Score=78.69  Aligned_cols=73  Identities=16%  Similarity=0.178  Sum_probs=59.4

Q ss_pred             CceEEEEEeCcc-------cccccccCCCchHHHHHhHhCCeEEEccCCC-----------CCceEEEEEeC-HHHHHHH
Q psy11929        286 DFVETEIVLTDD-------IAGCVIGKAGSRLLEIRQISGAQINIHTGTE-----------SHKKMFHIQGC-QEAVSLA  346 (433)
Q Consensus       286 ~~~t~~i~VP~~-------~vG~IIGkgG~~Ik~I~~~sGA~I~I~~~~~-----------~~er~V~IsGt-~e~v~~A  346 (433)
                      ...+.+++||-+       ++|.|||++|.+||+|+++|||+|.|.....           .++-.|.|++. ++++++|
T Consensus        10 ~~~~~ki~ip~~~~~p~fn~ig~IIGpgG~tiK~I~~eTG~kI~I~G~gS~~~e~~~~~e~~e~l~V~I~a~~~e~i~~A   89 (119)
T 2yqr_A           10 HYVQDKLFVGLEHAVPTFNVKEKVEGPGCSYLQHIQIETGAKVFLRGKGSGCIEPASGREAFEPMYIYISHPKPEGLAAA   89 (119)
T ss_dssp             SCEEEEEECCCTTSCTTTCHHHHHSCGGGHHHHHHHHHHCCEEEEESBTTTCCCTTTSSCCSSBCEEEEEESSHHHHHHH
T ss_pred             eEEEEEEEcCCccCCCCCCeeeeEECCCChHHHHHHHHHCCEEEEecCCccccccccccccCCCcEEEEEeCCHHHHHHH
Confidence            457788888876       7899999999999999999999999974321           24457777765 8999999


Q ss_pred             HHHHHHHHHhcc
Q psy11929        347 QYLINMCIELQK  358 (433)
Q Consensus       347 ~~lI~~~i~~~~  358 (433)
                      +.+|.+++....
T Consensus        90 ~~~Ie~Ll~~v~  101 (119)
T 2yqr_A           90 KKLCENLLQTVH  101 (119)
T ss_dssp             HHHHHHHHHHHH
T ss_pred             HHHHHHHhhchH
Confidence            999999987643

>2yqr_A KIAA0907 protein; structure genomics, KH domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=98.63  E-value=8.8e-08  Score=79.28  Aligned_cols=75  Identities=16%  Similarity=0.230  Sum_probs=58.1

Q ss_pred             ceEEEEEEeccC--Cc-ccccceeeecCchHHHHHHHHhCCeEEEeCCCC------------CcceEEEecccCCCCCCc
Q psy11929         13 TLITMRCLFHSS--VN-VNEISCLIGPGGCIVRRLRKESGAKISITDGAC------------PDRIVTVSGSVDNSSTSS   77 (433)
Q Consensus        13 ~~~~~rilvp~~--~~-~~~vg~IIGk~G~~Ik~I~~~tga~I~v~~~~~------------~eRvv~I~G~~~~~~~~~   77 (433)
                      ..+..|+.||..  .| .+++|.|||++|.+||+|+++|||+|.|...++            ++-.|.|++...      
T Consensus        10 ~~~~~ki~ip~~~~~p~fn~ig~IIGpgG~tiK~I~~eTG~kI~I~G~gS~~~e~~~~~e~~e~l~V~I~a~~~------   83 (119)
T 2yqr_A           10 HYVQDKLFVGLEHAVPTFNVKEKVEGPGCSYLQHIQIETGAKVFLRGKGSGCIEPASGREAFEPMYIYISHPKP------   83 (119)
T ss_dssp             SCEEEEEECCCTTSCTTTCHHHHHSCGGGHHHHHHHHHHCCEEEEESBTTTCCCTTTSSCCSSBCEEEEEESSH------
T ss_pred             eEEEEEEEcCCccCCCCCCeeeeEECCCChHHHHHHHHHCCEEEEecCCccccccccccccCCCcEEEEEeCCH------
Confidence            467889999874  23 679999999999999999999999999975332            233566665433      


Q ss_pred             cccCCCCCccccchHHHHHHHHHHHHhhhhh
Q psy11929         78 VETGYPGHTLWVTSVDNVCTAYNFMCRSLED  108 (433)
Q Consensus        78 v~~~~~~~~~~~~a~~~v~~A~~~I~~~~~~  108 (433)
                                     +++.+|+.+|.+++.+
T Consensus        84 ---------------e~i~~A~~~Ie~Ll~~   99 (119)
T 2yqr_A           84 ---------------EGLAAAKKLCENLLQT   99 (119)
T ss_dssp             ---------------HHHHHHHHHHHHHHHH
T ss_pred             ---------------HHHHHHHHHHHHHhhc
Confidence                           3889999999888765

>1k1g_A SF1-BO isoform; splicing, branch point sequence, protein/RNA recognition, complex E, KH domain, QUA2 homology; NMR {Homo sapiens} SCOP: d.51.1.1

Probab=98.58  E-value=1.3e-07  Score=79.85  Aligned_cols=71  Identities=21%  Similarity=0.243  Sum_probs=61.2

Q ss_pred             CceEEEEEeCcc------cccccccCCCchHHHHHhHhCCeEEEccCCC-----------------CCceEEEEEeC-HH
Q psy11929        286 DFVETEIVLTDD------IAGCVIGKAGSRLLEIRQISGAQINIHTGTE-----------------SHKKMFHIQGC-QE  341 (433)
Q Consensus       286 ~~~t~~i~VP~~------~vG~IIGkgG~~Ik~I~~~sGA~I~I~~~~~-----------------~~er~V~IsGt-~e  341 (433)
                      ...+.+|.||.+      ++|.|||.+|.+||+|+++|||+|.|.....                 .++-.|.|+++ .+
T Consensus         5 ~k~~~kv~IP~~~~P~~n~iG~IIGP~G~tiK~Iq~eTG~kI~IrgkgS~~~~~~~~~~~~~~~~~~e~lhV~I~a~~~e   84 (131)
T 1k1g_A            5 TRVSDKVMIPQDEYPEINFVGLLIGPRGNTLKNIEKECNAKIMIRGKGSVKEGKVGRKDGQMLPGEDEPLHALVTANTME   84 (131)
T ss_dssp             CCEEEEEECCTTTCCSHHHHHHHHCSSSHHHHHHHHHSCCEEEEEESTTSSSSSSSSCCCCCSCCSSCCEEEEEEESSHH
T ss_pred             ceEEEEEEECCccccCcceeeeEECCCcHHHHHHHHHHCCeEEecCCcccccccccccccccccccCCCeEEEEEECCHH
Confidence            467889999988      8999999999999999999999999976321                 23668889995 78


Q ss_pred             HHHHHHHHHHHHHHh
Q psy11929        342 AVSLAQYLINMCIEL  356 (433)
Q Consensus       342 ~v~~A~~lI~~~i~~  356 (433)
                      .+++|..+|..++..
T Consensus        85 ~~~~A~~~I~~ll~~   99 (131)
T 1k1g_A           85 NVKKAVEQIRNILKQ   99 (131)
T ss_dssp             HHHHHHHHHHHHHTT
T ss_pred             HHHHHHHHHHHHHhc
Confidence            999999999999864

>1k1g_A SF1-BO isoform; splicing, branch point sequence, protein/RNA recognition, complex E, KH domain, QUA2 homology; NMR {Homo sapiens} SCOP: d.51.1.1

Probab=98.58  E-value=7.7e-08  Score=81.23  Aligned_cols=71  Identities=24%  Similarity=0.322  Sum_probs=56.5

Q ss_pred             ceEEEEEEeccCCccc------ccceeeecCchHHHHHHHHhCCeEEEeCCCC------------------CcceEEEec
Q psy11929         13 TLITMRCLFHSSVNVN------EISCLIGPGGCIVRRLRKESGAKISITDGAC------------------PDRIVTVSG   68 (433)
Q Consensus        13 ~~~~~rilvp~~~~~~------~vg~IIGk~G~~Ik~I~~~tga~I~v~~~~~------------------~eRvv~I~G   68 (433)
                      ..++.++.||.    +      ++|.|||++|.+||+|+++|||+|.|...++                  .+-.|.|++
T Consensus         5 ~k~~~kv~IP~----~~~P~~n~iG~IIGP~G~tiK~Iq~eTG~kI~IrgkgS~~~~~~~~~~~~~~~~~~e~lhV~I~a   80 (131)
T 1k1g_A            5 TRVSDKVMIPQ----DEYPEINFVGLLIGPRGNTLKNIEKECNAKIMIRGKGSVKEGKVGRKDGQMLPGEDEPLHALVTA   80 (131)
T ss_dssp             CCEEEEEECCT----TTCCSHHHHHHHHCSSSHHHHHHHHHSCCEEEEEESTTSSSSSSSSCCCCCSCCSSCCEEEEEEE
T ss_pred             ceEEEEEEECC----ccccCcceeeeEECCCcHHHHHHHHHHCCeEEecCCcccccccccccccccccccCCCeEEEEEE
Confidence            46889999997    6      8999999999999999999999999976321                  133455555


Q ss_pred             ccCCCCCCccccCCCCCccccchHHHHHHHHHHHHhhhhh
Q psy11929         69 SVDNSSTSSVETGYPGHTLWVTSVDNVCTAYNFMCRSLED  108 (433)
Q Consensus        69 ~~~~~~~~~v~~~~~~~~~~~~a~~~v~~A~~~I~~~~~~  108 (433)
                      ...                     +.+.+|+.+|..++.+
T Consensus        81 ~~~---------------------e~~~~A~~~I~~ll~~   99 (131)
T 1k1g_A           81 NTM---------------------ENVKKAVEQIRNILKQ   99 (131)
T ss_dssp             SSH---------------------HHHHHHHHHHHHHHTT
T ss_pred             CCH---------------------HHHHHHHHHHHHHHhc
Confidence            433                     4899999999988765

>2bl5_A MGC83862 protein, quaking protein; STAR proteins, GSG proteins, RNA binding; NMR {Xenopus laevis} SCOP: d.51.1.1

Probab=98.30  E-value=8.7e-07  Score=75.19  Aligned_cols=77  Identities=17%  Similarity=0.187  Sum_probs=55.2

Q ss_pred             EEEEEEeccC-Cc-ccccceeeecCchHHHHHHHHhCCeEEEeCCCCC--------------------cceEEEecccCC
Q psy11929         15 ITMRCLFHSS-VN-VNEISCLIGPGGCIVRRLRKESGAKISITDGACP--------------------DRIVTVSGSVDN   72 (433)
Q Consensus        15 ~~~rilvp~~-~~-~~~vg~IIGk~G~~Ik~I~~~tga~I~v~~~~~~--------------------eRvv~I~G~~~~   72 (433)
                      ++-|+.||.+ .| .+++|.|||++|.++|+|+++|||+|.|...|+.                    .--|.|++....
T Consensus         2 ~~~Ki~IP~~~~P~~NfiG~IiGPrG~t~K~ie~eTg~kI~IrGkGS~kd~~~e~~~~g~~~~~~~~epLHV~Isa~~~~   81 (140)
T 2bl5_A            2 LQEKLYVPVKEYPDFNFVGRILGPRGLTAKQLEAETGCKIMVRGKGSMRDKKKEEQNRGKPNWEHLNEDLHVLITVEDAQ   81 (140)
T ss_dssp             EEEEEECCTTTCSSSCHHHHHTTTTHHHHHHHHHHHSEEEEEESTTSSCCHHHHHTSTTSHHHHTTTSCCEEEEEECSCC
T ss_pred             ceeEEEcCcccCCCCCeeeEEECCCcchHHHHHHHHCCeEEEecCCCcccccccccccCCCCccccCCCcEEEEEecCch
Confidence            5678888862 12 4569999999999999999999999999875421                    115667775431


Q ss_pred             CCCCccccCCCCCccccchHHHHHHHHHHHHhhhh
Q psy11929         73 SSTSSVETGYPGHTLWVTSVDNVCTAYNFMCRSLE  107 (433)
Q Consensus        73 ~~~~~v~~~~~~~~~~~~a~~~v~~A~~~I~~~~~  107 (433)
                                      ..|...+.+|+.+|..++.
T Consensus        82 ----------------~~~~~~l~~A~~~I~~lL~  100 (140)
T 2bl5_A           82 ----------------NRAELKLKRAVEEVKKLLV  100 (140)
T ss_dssp             ----------------HHHHHHHHHHHHHHHHHSS
T ss_pred             ----------------hhHHHHHHHHHHHHHHHCC
Confidence                            1122367888888887765

>2bl5_A MGC83862 protein, quaking protein; STAR proteins, GSG proteins, RNA binding; NMR {Xenopus laevis} SCOP: d.51.1.1

Probab=98.09  E-value=3.4e-06  Score=71.57  Aligned_cols=69  Identities=10%  Similarity=0.120  Sum_probs=54.4

Q ss_pred             eEEEEEeCccc------ccccccCCCchHHHHHhHhCCeEEEccCCC-------------------CCceEEEEEeC-HH
Q psy11929        288 VETEIVLTDDI------AGCVIGKAGSRLLEIRQISGAQINIHTGTE-------------------SHKKMFHIQGC-QE  341 (433)
Q Consensus       288 ~t~~i~VP~~~------vG~IIGkgG~~Ik~I~~~sGA~I~I~~~~~-------------------~~er~V~IsGt-~e  341 (433)
                      .+.+++||.+.      +|.|||.+|.++|+|+++|||+|.|.....                   .++--|.|++. ++
T Consensus         2 ~~~Ki~IP~~~~P~~NfiG~IiGPrG~t~K~ie~eTg~kI~IrGkGS~kd~~~e~~~~g~~~~~~~~epLHV~Isa~~~~   81 (140)
T 2bl5_A            2 LQEKLYVPVKEYPDFNFVGRILGPRGLTAKQLEAETGCKIMVRGKGSMRDKKKEEQNRGKPNWEHLNEDLHVLITVEDAQ   81 (140)
T ss_dssp             EEEEEECCTTTCSSSCHHHHHTTTTHHHHHHHHHHHSEEEEEESTTSSCCHHHHHTSTTSHHHHTTTSCCEEEEEECSCC
T ss_pred             ceeEEEcCcccCCCCCeeeEEECCCcchHHHHHHHHCCeEEEecCCCcccccccccccCCCCccccCCCcEEEEEecCch
Confidence            35677787544      999999999999999999999999997542                   12237889985 32


Q ss_pred             -----HHHHHHHHHHHHHHh
Q psy11929        342 -----AVSLAQYLINMCIEL  356 (433)
Q Consensus       342 -----~v~~A~~lI~~~i~~  356 (433)
                           .+++|..+|..+|..
T Consensus        82 ~~~~~~l~~A~~~I~~lL~p  101 (140)
T 2bl5_A           82 NRAELKLKRAVEEVKKLLVP  101 (140)
T ss_dssp             HHHHHHHHHHHHHHHHHSSC
T ss_pred             hhHHHHHHHHHHHHHHHCCC
Confidence                 689999999998853

>3v69_A Protein filia; RNA-binding, embryogenesis, KH domain, RNA binding, P binding; 2.20A {Mus musculus}

Probab=98.08  E-value=8.4e-06  Score=67.79  Aligned_cols=71  Identities=8%  Similarity=0.112  Sum_probs=64.8

Q ss_pred             EEEEEeCcccccccccCCCchHHHHHhHhCCeEEEccCCCCCceEEEEEeCHHHHHHHHHHHHHHHHhccc
Q psy11929        289 ETEIVLTDDIAGCVIGKAGSRLLEIRQISGAQINIHTGTESHKKMFHIQGCQEAVSLAQYLINMCIELQKN  359 (433)
Q Consensus       289 t~~i~VP~~~vG~IIGkgG~~Ik~I~~~sGA~I~I~~~~~~~er~V~IsGt~e~v~~A~~lI~~~i~~~~~  359 (433)
                      ...|.+....++.|+|++|+.|+.|+..|.|.|++..-..+++-.|+|.|++....+|+.+|+...+..+.
T Consensus        57 PlVF~vE~~lve~IFGp~Gs~Ip~IE~~SqTLIqV~~~~s~g~tEVtIfG~~~~Q~rak~MI~sLA~~hr~  127 (140)
T 3v69_A           57 PKRLYVEPRLLEIMFGKDGEHIPHLESMLHTLIHVNVWGPERRAEIWIFGPPPFRRDVDRMLTDLAHYCRM  127 (140)
T ss_dssp             CEEEEECGGGHHHHHCGGGTTHHHHHHHHTSEEEEECCCTTSCEEEEEESCHHHHHHHHHHHHHHHHHHHH
T ss_pred             CeEEEEehhhhhcccCCCcCccchHHhhcceeEEEeccCCCCcEEEEEECCHHHHHHHHHHHHHHHHHHHH
Confidence            46789999999999999999999999999999999987557789999999999999999999998877654

>3u1k_A Polyribonucleotide nucleotidyltransferase 1, MITO; RNAse PH, KH domain, exoribonuclease; HET: CIT; 2.13A {Homo sapiens}

Probab=97.95  E-value=1.2e-05  Score=84.70  Aligned_cols=62  Identities=16%  Similarity=0.183  Sum_probs=53.9

Q ss_pred             eEEEEEeCcccccccccCCCchHHHHHhHhCCeEEEccCCCCCceEEEEEeC-HHHHHHHHHHHHHHH
Q psy11929        288 VETEIVLTDDIAGCVIGKAGSRLLEIRQISGAQINIHTGTESHKKMFHIQGC-QEAVSLAQYLINMCI  354 (433)
Q Consensus       288 ~t~~i~VP~~~vG~IIGkgG~~Ik~I~~~sGA~I~I~~~~~~~er~V~IsGt-~e~v~~A~~lI~~~i  354 (433)
                      ....|.||.+++|.|||+||++||.|+++|||+|.|.++     -.|.|.|+ ++..++|+.+|.+++
T Consensus       567 ~~~~~~I~~~kI~~vIG~gG~~Ik~I~e~tg~~I~I~d~-----G~V~I~~~~~~~~~~A~~~I~~i~  629 (630)
T 3u1k_A          567 VVETVQVPLSKRAKFVGPGGYNLKKLQAETGVTISQVDE-----ETFSVFAPTPSAMHEARDFITEIC  629 (630)
T ss_dssp             EEEEEECCHHHHHHHHCGGGHHHHHHHHHHCCEEEECSS-----SEEEEEESSHHHHHHHHHHTTC--
T ss_pred             eEEEEEeChhHhheeECCCChhHHHHHHHHCCEEEEcCC-----cEEEEEeCCHHHHHHHHHHHHHHh
Confidence            357899999999999999999999999999999999864     57899887 688999999987654

>3u1k_A Polyribonucleotide nucleotidyltransferase 1, MITO; RNAse PH, KH domain, exoribonuclease; HET: CIT; 2.13A {Homo sapiens}

Probab=97.87  E-value=1.9e-05  Score=83.21  Aligned_cols=94  Identities=15%  Similarity=0.280  Sum_probs=66.9

Q ss_pred             hHHHHHHHHHHHHhhhhhhcccccCCCCCCCCCeEEEEEeccCcccceecCCchhHHHHHHhhCceEEeccCCCCCCCcc
Q psy11929         91 SVDNVCTAYNFMCRSLEDYHINRNRMENCSPQPLQLKLVIPATHCGSLIGKGGCKIKDIRDLSGANVQVASDMLPMSTER  170 (433)
Q Consensus        91 a~~~v~~A~~~I~~~~~~~~~~~~~~~~~~~~~~~~~l~ip~~~vg~iIGk~G~~Ik~I~~~sga~I~i~~~~~~~~~er  170 (433)
                      +.+...+++..|.+.+++.-... ........+....+-||.+++|.|||++|++||+|+++|||+|.|..       +-
T Consensus       535 aL~~A~~g~~~I~~~m~~al~~~-~~~~~~~ap~~~~~~I~~~kI~~vIG~gG~~Ik~I~e~tg~~I~I~d-------~G  606 (630)
T 3u1k_A          535 AIQQASVAKKEILQIMNKTISKP-RASRKENGPVVETVQVPLSKRAKFVGPGGYNLKKLQAETGVTISQVD-------EE  606 (630)
T ss_dssp             HHHHHHHHHHHHHHHHHHHCSSC-CSSCCTTCCEEEEEECCHHHHHHHHCGGGHHHHHHHHHHCCEEEECS-------SS
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHH-HhhhcccCCeEEEEEeChhHhheeECCCChhHHHHHHHHCCEEEEcC-------Cc
Confidence            33444455555555555432211 11122345677889999999999999999999999999999999974       46


Q ss_pred             EEEEEcc-HHHHHHHHHHHHHHH
Q psy11929        171 IVTVHGN-PDTISQAIYQICLVL  192 (433)
Q Consensus       171 ~v~I~G~-~~~v~~A~~~I~~~l  192 (433)
                      .|.|.|. .+.+.+|+.+|..++
T Consensus       607 ~V~I~~~~~~~~~~A~~~I~~i~  629 (630)
T 3u1k_A          607 TFSVFAPTPSAMHEARDFITEIC  629 (630)
T ss_dssp             EEEEEESSHHHHHHHHHHTTC--
T ss_pred             EEEEEeCCHHHHHHHHHHHHHHh
Confidence            8999885 688899999887654

>2cxc_A NUSA; transcription termination, RNA binding protein, archaeal NUS domain, structural genomics, NPPSFA; 2.00A {Aeropyrum pernix} PDB: 2cy1_A

Probab=97.64  E-value=4e-05  Score=65.36  Aligned_cols=104  Identities=20%  Similarity=0.263  Sum_probs=71.8

Q ss_pred             EEEEEEeccCCcccccceeeecCchHHHHHHHHhCCeEEEeCCCCCcceEEEecccCCCCCCccccCCCCCccccchHHH
Q psy11929         15 ITMRCLFHSSVNVNEISCLIGPGGCIVRRLRKESGAKISITDGACPDRIVTVSGSVDNSSTSSVETGYPGHTLWVTSVDN   94 (433)
Q Consensus        15 ~~~rilvp~~~~~~~vg~IIGk~G~~Ik~I~~~tga~I~v~~~~~~eRvv~I~G~~~~~~~~~v~~~~~~~~~~~~a~~~   94 (433)
                      =.+.++|+.    ..+|+.||++|++|+.|+++.|-+|.+-.-..                                  .
T Consensus        36 dr~i~vVk~----g~vGa~IG~~G~ri~~i~~elgekIdIV~~s~----------------------------------d   77 (144)
T 2cxc_A           36 NRLIFLVSE----GEAGRAIGRGGRLIKLLREALGKNIEVVEYSS----------------------------------D   77 (144)
T ss_dssp             TEEEEEECT----TCHHHHHCGGGHHHHHHHHHHSSEEEEEECCS----------------------------------S
T ss_pred             CEEEEEEeC----CCccccCccCchHHHHHHHHhCCeeEEEEcCC----------------------------------C
Confidence            357889988    99999999999999999999999998865211                                  0


Q ss_pred             HHHHHHHHHhhhhhhcccccCCCCCCCCCeEEEEEeccCcccceecCCchhHHHHHHhhCceEEec
Q psy11929         95 VCTAYNFMCRSLEDYHINRNRMENCSPQPLQLKLVIPATHCGSLIGKGGCKIKDIRDLSGANVQVA  160 (433)
Q Consensus        95 v~~A~~~I~~~~~~~~~~~~~~~~~~~~~~~~~l~ip~~~vg~iIGk~G~~Ik~I~~~sga~I~i~  160 (433)
                      .   ..+|...+....-.-- .-...+....+.+.||..+.+..|||+|.+++-..+-||.+|.|.
T Consensus        78 ~---~~fI~naLsPA~V~~V-~i~~~~~~~~~~V~V~~~q~slAIGk~G~NvrLa~~Ltg~~idI~  139 (144)
T 2cxc_A           78 L---ERIVKNLFPGVKIESI-NVRERNGVKQVVIKVSEDDKGAAIGKGGKNVKRARLVLSKLFGVE  139 (144)
T ss_dssp             H---HHHHHHHSTTSCEEEE-EEEEETTEEEEEEEECTTTHHHHHCGGGHHHHHHHHHHHHHHCEE
T ss_pred             H---HHHHHHhcCCceEEEE-EEeecCCcEEEEEEEChHHhhhccCCCCHHHHHHHHHhCCeeCce
Confidence            0   1122221111000000 000002345678899999999999999999999999999887664

>3v69_A Protein filia; RNA-binding, embryogenesis, KH domain, RNA binding, P binding; 2.20A {Mus musculus}

Probab=97.49  E-value=0.00024  Score=59.09  Aligned_cols=68  Identities=12%  Similarity=0.078  Sum_probs=59.4

Q ss_pred             EEEEEeccCcccceecCCchhHHHHHHhhCceEEeccCCCCCCCccEEEEEccHHHHHHHHHHHHHHHHh
Q psy11929        125 QLKLVIPATHCGSLIGKGGCKIKDIRDLSGANVQVASDMLPMSTERIVTVHGNPDTISQAIYQICLVLIE  194 (433)
Q Consensus       125 ~~~l~ip~~~vg~iIGk~G~~Ik~I~~~sga~I~i~~~~~~~~~er~v~I~G~~~~v~~A~~~I~~~l~e  194 (433)
                      .+.|.+.+.+++.|+|++|+.|+.|+..|++.|++..-  ..+..-.|+|.|++..-.+|+.+|..+..-
T Consensus        57 PlVF~vE~~lve~IFGp~Gs~Ip~IE~~SqTLIqV~~~--~s~g~tEVtIfG~~~~Q~rak~MI~sLA~~  124 (140)
T 3v69_A           57 PKRLYVEPRLLEIMFGKDGEHIPHLESMLHTLIHVNVW--GPERRAEIWIFGPPPFRRDVDRMLTDLAHY  124 (140)
T ss_dssp             CEEEEECGGGHHHHHCGGGTTHHHHHHHHTSEEEEECC--CTTSCEEEEEESCHHHHHHHHHHHHHHHHH
T ss_pred             CeEEEEehhhhhcccCCCcCccchHHhhcceeEEEecc--CCCCcEEEEEECCHHHHHHHHHHHHHHHHH
Confidence            46789999999999999999999999999999999853  224567899999999999999999887654

>2cxc_A NUSA; transcription termination, RNA binding protein, archaeal NUS domain, structural genomics, NPPSFA; 2.00A {Aeropyrum pernix} PDB: 2cy1_A

Probab=97.29  E-value=0.00013  Score=62.18  Aligned_cols=38  Identities=32%  Similarity=0.558  Sum_probs=34.8

Q ss_pred             eEEEEEeccCcccceecCCchhHHHHHHhhCceEEecc
Q psy11929        124 LQLKLVIPATHCGSLIGKGGCKIKDIRDLSGANVQVAS  161 (433)
Q Consensus       124 ~~~~l~ip~~~vg~iIGk~G~~Ik~I~~~sga~I~i~~  161 (433)
                      -.+.++|+...+|..||++|++|+.|+++.|-+|.+-.
T Consensus        36 dr~i~vVk~g~vGa~IG~~G~ri~~i~~elgekIdIV~   73 (144)
T 2cxc_A           36 NRLIFLVSEGEAGRAIGRGGRLIKLLREALGKNIEVVE   73 (144)
T ss_dssp             TEEEEEECTTCHHHHHCGGGHHHHHHHHHHSSEEEEEE
T ss_pred             CEEEEEEeCCCccccCccCchHHHHHHHHhCCeeEEEE
Confidence            46788999999999999999999999999999998864

>4aid_A Polyribonucleotide nucleotidyltransferase; transferase-peptide complex; 2.60A {Caulobacter vibrioides} PDB: 4aim_A 4am3_A

Probab=97.22  E-value=0.00018  Score=76.70  Aligned_cols=64  Identities=20%  Similarity=0.267  Sum_probs=11.1

Q ss_pred             EEEEEeCcccccccccCCCchHHHHHhHhCCeEEEccCCCCCceEEEEEeC-HHHHHHHHHHHHHHHHhc
Q psy11929        289 ETEIVLTDDIAGCVIGKAGSRLLEIRQISGAQINIHTGTESHKKMFHIQGC-QEAVSLAQYLINMCIELQ  357 (433)
Q Consensus       289 t~~i~VP~~~vG~IIGkgG~~Ik~I~~~sGA~I~I~~~~~~~er~V~IsGt-~e~v~~A~~lI~~~i~~~  357 (433)
                      ..++.||.+++|.|||+||.+||.|+++||++|.|.+.     -.|.|.++ .++.++|+.+|..++...
T Consensus       571 ~~~~~i~~~ki~~vig~gg~~i~~i~~~tg~~idi~dd-----G~v~I~~~~~~~~~~A~~~i~~i~~~~  635 (726)
T 4aid_A          571 IETINIPTDKIREVIGSGGKVIREIVATTGAKVDINDD-----GVVKVSASDGAKIKAAIDWIKSITDEA  635 (726)
T ss_dssp             ------------------------------------------------CCSCHHHHHHHHHC--------
T ss_pred             EEEEeCCHHHHHhhcCCCchhHHHHHHHHCCceeEECC-----ceEEEEeCCHHHHHHHHHHHHHHhhhh
Confidence            45789999999999999999999999999999999864     35677666 788999999998887643

>4aid_A Polyribonucleotide nucleotidyltransferase; transferase-peptide complex; 2.60A {Caulobacter vibrioides} PDB: 4aim_A 4am3_A

Probab=97.13  E-value=0.00025  Score=75.58  Aligned_cols=96  Identities=21%  Similarity=0.258  Sum_probs=25.0

Q ss_pred             hHHHHHHHHHHHHhhhhhhcccccCCCCCCCCCeEEEEEeccCcccceecCCchhHHHHHHhhCceEEeccCCCCCCCcc
Q psy11929         91 SVDNVCTAYNFMCRSLEDYHINRNRMENCSPQPLQLKLVIPATHCGSLIGKGGCKIKDIRDLSGANVQVASDMLPMSTER  170 (433)
Q Consensus        91 a~~~v~~A~~~I~~~~~~~~~~~~~~~~~~~~~~~~~l~ip~~~vg~iIGk~G~~Ik~I~~~sga~I~i~~~~~~~~~er  170 (433)
                      +++...+++..|.+.+++.-... ........+....+.||.++++.|||+||.+||+|.++||++|.+..       +.
T Consensus       538 aL~~A~~g~~~I~~~m~~al~~~-r~~~~~~ap~~~~~~i~~~ki~~vig~gg~~i~~i~~~tg~~idi~d-------dG  609 (726)
T 4aid_A          538 ALAQAKEGRAHILGEMNKAMDAP-RADVGDFAPKIETINIPTDKIREVIGSGGKVIREIVATTGAKVDIND-------DG  609 (726)
T ss_dssp             HHHHHHHHHHHHHHHHHTTCSSC-CSSCCSSCCC----------------------------------------------
T ss_pred             HHHHHHHHHHHHHHHHHHHHHhh-hhhhcccCCeEEEEeCCHHHHHhhcCCCchhHHHHHHHHCCceeEEC-------Cc
Confidence            44455555666666555432111 11112234556778999999999999999999999999999999963       45


Q ss_pred             EEEEEc-cHHHHHHHHHHHHHHHHh
Q psy11929        171 IVTVHG-NPDTISQAIYQICLVLIE  194 (433)
Q Consensus       171 ~v~I~G-~~~~v~~A~~~I~~~l~e  194 (433)
                      .|.|.+ +.+++++|+..|..++.+
T Consensus       610 ~v~I~~~~~~~~~~A~~~i~~i~~~  634 (726)
T 4aid_A          610 VVKVSASDGAKIKAAIDWIKSITDE  634 (726)
T ss_dssp             ----CCSCHHHHHHHHHC-------
T ss_pred             eEEEEeCCHHHHHHHHHHHHHHhhh
Confidence            677776 588899999999888765

>1k0r_A NUSA; two component arrangement, S1 domain, two K-homology domains., structural genomics, PSI, protein structure initiative; 1.70A {Mycobacterium tuberculosis} SCOP: b.40.4.5 d.52.3.1 d.52.3.1 d.202.1.1

Probab=95.79  E-value=0.0089  Score=58.39  Aligned_cols=97  Identities=26%  Similarity=0.351  Sum_probs=66.2

Q ss_pred             ccccceeeecCchHHHHHHHHh-CCeEEEeCCCCCcceEEEecccCCCCCCccccCCCCCccccchHHHHHHHHHHHHhh
Q psy11929         27 VNEISCLIGPGGCIVRRLRKES-GAKISITDGACPDRIVTVSGSVDNSSTSSVETGYPGHTLWVTSVDNVCTAYNFMCRS  105 (433)
Q Consensus        27 ~~~vg~IIGk~G~~Ik~I~~~t-ga~I~v~~~~~~eRvv~I~G~~~~~~~~~v~~~~~~~~~~~~a~~~v~~A~~~I~~~  105 (433)
                      ++-+|+.||++|++|+.|.++. |=+|.|-.-.           .+                       .   ..+|...
T Consensus       248 iDpvGacIG~~G~rI~~i~~eL~gekIDIi~~s-----------~d-----------------------p---~~fi~na  290 (366)
T 1k0r_A          248 LNAKGACIGPMGQRVRNVMSELSGEKIDIIDYD-----------DD-----------------------P---ARFVANA  290 (366)
T ss_dssp             CCHHHHHHCGGGHHHHHHHHHTTTCEEEEEECC-----------SS-----------------------H---HHHHHHH
T ss_pred             CCCcccccCCcchHHHHHHHHhCCCeEEEEEcC-----------CC-----------------------H---HHHHHHh
Confidence            4668999999999999999998 8888886511           01                       0   1122222


Q ss_pred             hhhhcccccCCCCCCCCCeEEEEEeccCcccceecCCchhHHHHHHhhCceEEeccC
Q psy11929        106 LEDYHINRNRMENCSPQPLQLKLVIPATHCGSLIGKGGCKIKDIRDLSGANVQVASD  162 (433)
Q Consensus       106 ~~~~~~~~~~~~~~~~~~~~~~l~ip~~~vg~iIGk~G~~Ik~I~~~sga~I~i~~~  162 (433)
                      +....-.  .-.........+.+.||..+.+..|||+|.+++-..+-||.+|.|..+
T Consensus       291 lsPA~V~--~V~~~~~~~~~a~V~V~~~qlslAIGk~GqNvrLA~~Ltg~~idI~~~  345 (366)
T 1k0r_A          291 LSPAKVV--SVSVIDQTARAARVVVPDFQLSLAIGKEGQNARLAARLTGWRIDIRGD  345 (366)
T ss_dssp             TTTSCCS--EEEEEETTTTEEEEEECGGGHHHHHCGGGHHHHHHHHHHCCEEEEEES
T ss_pred             cCCccee--EEEEEcCCCcEEEEEEChHHhhhccCCCcHHHHHHHHHHCCeeeeeEH
Confidence            1110000  000000124468899999999999999999999999999999999753

>2asb_A Transcription elongation protein NUSA; protein-RNA complex, transcription/RNA complex; 1.50A {Mycobacterium tuberculosis} SCOP: b.40.4.5 d.52.3.1 d.52.3.1 PDB: 2atw_A

Probab=95.60  E-value=0.011  Score=54.74  Aligned_cols=96  Identities=25%  Similarity=0.341  Sum_probs=63.9

Q ss_pred             ccccceeeecCchHHHHHH-HHhCCeEEEeCCCCCcceEEEecccCCCCCCccccCCCCCccccchHHHHHHHHHHHHhh
Q psy11929         27 VNEISCLIGPGGCIVRRLR-KESGAKISITDGACPDRIVTVSGSVDNSSTSSVETGYPGHTLWVTSVDNVCTAYNFMCRS  105 (433)
Q Consensus        27 ~~~vg~IIGk~G~~Ik~I~-~~tga~I~v~~~~~~eRvv~I~G~~~~~~~~~v~~~~~~~~~~~~a~~~v~~A~~~I~~~  105 (433)
                      ++-+|+-||++|++|+.|. +-.|=+|.|-.-..           +                          ...+|...
T Consensus       125 iDpvGacIG~~G~rI~~i~~eL~gekIDIi~~s~-----------d--------------------------p~~fi~na  167 (251)
T 2asb_A          125 LNAKGACIGPMGQRVRNVMSELSGEKIDIIDYDD-----------D--------------------------PARFVANA  167 (251)
T ss_dssp             CCHHHHHHCGGGHHHHHHHHHTTTCEEEEEECCS-----------S--------------------------HHHHHHHH
T ss_pred             CCHHHHHhCCCchHHHHHHHHhCCCeEEEEEecC-----------C--------------------------HHHHHHhc
Confidence            5678999999999999994 55688888865210           1                          00112221


Q ss_pred             hhhhcccccCCCCCCCCCeEEEEEeccCcccceecCCchhHHHHHHhhCceEEecc
Q psy11929        106 LEDYHINRNRMENCSPQPLQLKLVIPATHCGSLIGKGGCKIKDIRDLSGANVQVAS  161 (433)
Q Consensus       106 ~~~~~~~~~~~~~~~~~~~~~~l~ip~~~vg~iIGk~G~~Ik~I~~~sga~I~i~~  161 (433)
                      |....-.  .-.........+.+.||..+.+..|||+|.+++-..+-||.+|.|..
T Consensus       168 lsPA~V~--~V~i~~~~~~~a~V~V~~~qlslAIGk~GqNvrLA~~Ltg~~idI~~  221 (251)
T 2asb_A          168 LSPAKVV--SVSVIDQTARAARVVVPDFQLSLAIGKEGQNARLAARLTGWRIDIRG  221 (251)
T ss_dssp             TTTSCCS--EEEEEETTTTEEEEEECGGGHHHHHCGGGHHHHHHHHHHSCEEEEEE
T ss_pred             cCCcceE--EEEEEcCCCcEEEEEEChHHhhhhhcCCcCcHHHHHHHHCCEecceE
Confidence            1110000  00000011246789999999999999999999999999999999975

>2asb_A Transcription elongation protein NUSA; protein-RNA complex, transcription/RNA complex; 1.50A {Mycobacterium tuberculosis} SCOP: b.40.4.5 d.52.3.1 d.52.3.1 PDB: 2atw_A

Probab=95.34  E-value=0.022  Score=52.62  Aligned_cols=41  Identities=22%  Similarity=0.302  Sum_probs=37.6

Q ss_pred             eEEEEEeCcccccccccCCCchHHHHHhHhCCeEEEccCCC
Q psy11929        288 VETEIVLTDDIAGCVIGKAGSRLLEIRQISGAQINIHTGTE  328 (433)
Q Consensus       288 ~t~~i~VP~~~vG~IIGkgG~~Ik~I~~~sGA~I~I~~~~~  328 (433)
                      .+..+.||.+..+.-|||+|+|++--.+.||.+|.|....+
T Consensus       184 ~~a~V~V~~~qlslAIGk~GqNvrLA~~Ltg~~idI~~~~~  224 (251)
T 2asb_A          184 RAARVVVPDFQLSLAIGKEGQNARLAARLTGWRIDIRGDAP  224 (251)
T ss_dssp             TEEEEEECGGGHHHHHCGGGHHHHHHHHHHSCEEEEEESSC
T ss_pred             cEEEEEEChHHhhhhhcCCcCcHHHHHHHHCCEecceEHHH
Confidence            46899999999999999999999999999999999986654

>1k0r_A NUSA; two component arrangement, S1 domain, two K-homology domains., structural genomics, PSI, protein structure initiative; 1.70A {Mycobacterium tuberculosis} SCOP: b.40.4.5 d.52.3.1 d.52.3.1 d.202.1.1

Probab=95.31  E-value=0.022  Score=55.66  Aligned_cols=42  Identities=21%  Similarity=0.277  Sum_probs=38.0

Q ss_pred             ceEEEEEeCcccccccccCCCchHHHHHhHhCCeEEEccCCC
Q psy11929        287 FVETEIVLTDDIAGCVIGKAGSRLLEIRQISGAQINIHTGTE  328 (433)
Q Consensus       287 ~~t~~i~VP~~~vG~IIGkgG~~Ik~I~~~sGA~I~I~~~~~  328 (433)
                      .....+.||.+..+..|||+|.|++-..+.||.+|.|....+
T Consensus       306 ~~~a~V~V~~~qlslAIGk~GqNvrLA~~Ltg~~idI~~~~~  347 (366)
T 1k0r_A          306 ARAARVVVPDFQLSLAIGKEGQNARLAARLTGWRIDIRGDAP  347 (366)
T ss_dssp             TTEEEEEECGGGHHHHHCGGGHHHHHHHHHHCCEEEEEESSC
T ss_pred             CcEEEEEEChHHhhhccCCCcHHHHHHHHHHCCeeeeeEHHH
Confidence            456899999999999999999999999999999999976653

>3cdi_A Polynucleotide phosphorylase; mRNA turnover, RNAse, RNA degradation, kinase, transferase; 2.60A {Escherichia coli} PDB: 1sro_A

Probab=94.71  E-value=0.012  Score=62.85  Aligned_cols=62  Identities=24%  Similarity=0.244  Sum_probs=0.0

Q ss_pred             EEEEEeCcccccccccCCCchHHHHHhHhCCeEEEccCCCCCceEEEEEeC-HHHHHHHHHHHHHHHH
Q psy11929        289 ETEIVLTDDIAGCVIGKAGSRLLEIRQISGAQINIHTGTESHKKMFHIQGC-QEAVSLAQYLINMCIE  355 (433)
Q Consensus       289 t~~i~VP~~~vG~IIGkgG~~Ik~I~~~sGA~I~I~~~~~~~er~V~IsGt-~e~v~~A~~lI~~~i~  355 (433)
                      ...+.||.++++.+||+||.+|+.|.+++|+.|.|.++     ..|.|++. .+..++|..+|...+.
T Consensus       561 ~~~~~i~~~ki~~~ig~gGk~I~~I~~~~G~~IdI~~d-----g~v~I~~~~~~~~~~a~~~i~~i~~  623 (723)
T 3cdi_A          561 IHTIKINPDKIKDVIGKGGSVIRALTEETGTTIEIEDD-----GTVKIAATDGEKAKHAIRRIEEITA  623 (723)
T ss_dssp             --------------------------------------------------------------------
T ss_pred             EEEEEECHHHhcccccccceeeeeeehhhCceEEecCC-----ccEEEecCCHHHHHHHHHHHHHHhh
Confidence            35788999999999999999999999999999988863     46777665 4667778777776654

>1e3p_A Guanosine pentaphosphate synthetase; polyribonucleotide transferase, ATP-GTP diphosphotransferase RNA processing, RNA degradation; 2.5A {Streptomyces antibioticus} SCOP: a.4.9.1 b.40.4.5 d.14.1.4 d.14.1.4 d.52.3.1 d.101.1.1 d.101.1.1 PDB: 1e3h_A

Probab=94.17  E-value=0.0054  Score=65.91  Aligned_cols=93  Identities=15%  Similarity=0.188  Sum_probs=33.2

Q ss_pred             hHHHHHHHHHHHHhhhhhhcccccCCCCCCCCCeEEEEEeccCcccceecCCchhHHHHHHhhCceEEeccCCCCCCCcc
Q psy11929         91 SVDNVCTAYNFMCRSLEDYHINRNRMENCSPQPLQLKLVIPATHCGSLIGKGGCKIKDIRDLSGANVQVASDMLPMSTER  170 (433)
Q Consensus        91 a~~~v~~A~~~I~~~~~~~~~~~~~~~~~~~~~~~~~l~ip~~~vg~iIGk~G~~Ik~I~~~sga~I~i~~~~~~~~~er  170 (433)
                      +.+...+++..|.+.+.+.-...  .......+....+.||.+.++.+||++|.+||+|.+++|+.|.+..       +.
T Consensus       567 aL~~A~~~~~~I~~~m~~al~~~--~~~~~~ap~~~~~~I~~~ki~~vIG~gGk~Ik~I~~~~G~~IdI~~-------dG  637 (757)
T 1e3p_A          567 ALKQARDARLHILDVMMEAIDTP--DEMSPNAPRIITVKIPVDKIGEVIGPKRQMINQIQEDTGAEITIED-------DG  637 (757)
T ss_dssp             HHHHHHHHHHHHHHHHHHHCSSC--CCCCTTSCBCCCC------------------CTTCCCCCSCC-------------
T ss_pred             HHHHHHHHHHHHHHHHHHHhccc--ccccccCceeEEEEEChHHeehcccccceeeehhhHhhCCEEEecC-------Cc
Confidence            34445555555555555422211  1111233444567899999999999999999999999999998863       45


Q ss_pred             EEEEEc-cHHHHHHHHHHHHHHH
Q psy11929        171 IVTVHG-NPDTISQAIYQICLVL  192 (433)
Q Consensus       171 ~v~I~G-~~~~v~~A~~~I~~~l  192 (433)
                      .|.|.. +....++|+..|..+.
T Consensus       638 ~v~Is~~~~~~~~~a~~~i~~i~  660 (757)
T 1e3p_A          638 TIYIGAADGPAAEAARATINGIA  660 (757)
T ss_dssp             --CCCBSSHHHHCC---------
T ss_pred             eEEEecCCHHHHHHHHHHHHHhc
Confidence            677766 4566666766665543

>1e3p_A Guanosine pentaphosphate synthetase; polyribonucleotide transferase, ATP-GTP diphosphotransferase RNA processing, RNA degradation; 2.5A {Streptomyces antibioticus} SCOP: a.4.9.1 b.40.4.5 d.14.1.4 d.14.1.4 d.52.3.1 d.101.1.1 d.101.1.1 PDB: 1e3h_A

Probab=93.90  E-value=0.0073  Score=64.88  Aligned_cols=59  Identities=25%  Similarity=0.268  Sum_probs=19.5

Q ss_pred             EEEeCcccccccccCCCchHHHHHhHhCCeEEEccCCCCCceEEEEEeC-HHHHHHHHHHHHHHH
Q psy11929        291 EIVLTDDIAGCVIGKAGSRLLEIRQISGAQINIHTGTESHKKMFHIQGC-QEAVSLAQYLINMCI  354 (433)
Q Consensus       291 ~i~VP~~~vG~IIGkgG~~Ik~I~~~sGA~I~I~~~~~~~er~V~IsGt-~e~v~~A~~lI~~~i  354 (433)
                      .|.||.+++|.+||++|.+|+.|++++|+.|.|.+.     ..|.|++. .+..++|+..|..+.
T Consensus       601 ~~~I~~~ki~~vIG~gGk~Ik~I~~~~G~~IdI~~d-----G~v~Is~~~~~~~~~a~~~i~~i~  660 (757)
T 1e3p_A          601 TVKIPVDKIGEVIGPKRQMINQIQEDTGAEITIEDD-----GTIYIGAADGPAAEAARATINGIA  660 (757)
T ss_dssp             CC------------------CTTCCCCCSCC-------------CCCBSSHHHHCC---------
T ss_pred             EEEEChHHeehcccccceeeehhhHhhCCEEEecCC-----ceEEEecCCHHHHHHHHHHHHHhc
Confidence            577999999999999999999999999999999852     56777766 456677777776654

>3cdi_A Polynucleotide phosphorylase; mRNA turnover, RNAse, RNA degradation, kinase, transferase; 2.60A {Escherichia coli} PDB: 1sro_A

Probab=93.88  E-value=0.019  Score=61.37  Aligned_cols=96  Identities=17%  Similarity=0.243  Sum_probs=9.5

Q ss_pred             hHHHHHHHHHHHHhhhhhhcccccCCCCCCCCCeEEEEEeccCcccceecCCchhHHHHHHhhCceEEeccCCCCCCCcc
Q psy11929         91 SVDNVCTAYNFMCRSLEDYHINRNRMENCSPQPLQLKLVIPATHCGSLIGKGGCKIKDIRDLSGANVQVASDMLPMSTER  170 (433)
Q Consensus        91 a~~~v~~A~~~I~~~~~~~~~~~~~~~~~~~~~~~~~l~ip~~~vg~iIGk~G~~Ik~I~~~sga~I~i~~~~~~~~~er  170 (433)
                      +.+...+++..|.+.+.+.-.... .......+....+.||.++++.+||++|.+|+.|.+++|+.|.+..       +.
T Consensus       528 ~l~~A~~~~~~I~~~m~~al~~~~-~~~~~~ap~~~~~~i~~~ki~~~ig~gGk~I~~I~~~~G~~IdI~~-------dg  599 (723)
T 3cdi_A          528 ALNQAKGARLHILGVMEQAINAPR-GDISEFAPRIHTIKINPDKIKDVIGKGGSVIRALTEETGTTIEIED-------DG  599 (723)
T ss_dssp             HHHHHHHHHHHHHHHHHHHCC-----------------------------------------------------------
T ss_pred             HHHHHHHHHHHHHHHHHHHhhhcc-hhccccCceEEEEEECHHHhcccccccceeeeeeehhhCceEEecC-------Cc
Confidence            334444555555555544211110 1111234556778899999999999999999999999999998863       45


Q ss_pred             EEEEEc-cHHHHHHHHHHHHHHHHh
Q psy11929        171 IVTVHG-NPDTISQAIYQICLVLIE  194 (433)
Q Consensus       171 ~v~I~G-~~~~v~~A~~~I~~~l~e  194 (433)
                      .+.|.+ +.+.+++|...|..++.+
T Consensus       600 ~v~I~~~~~~~~~~a~~~i~~i~~~  624 (723)
T 3cdi_A          600 TVKIAATDGEKAKHAIRRIEEITAE  624 (723)
T ss_dssp             -------------------------
T ss_pred             cEEEecCCHHHHHHHHHHHHHHhhh
Confidence            677766 456677787777665543

>1hh2_P NUSA, N utilization substance protein A; transcription regulation, termination; 2.1A {Thermotoga maritima} SCOP: b.40.4.5 d.52.3.1 d.52.3.1 d.202.1.1 PDB: 1l2f_A

Probab=93.82  E-value=0.065  Score=52.05  Aligned_cols=96  Identities=23%  Similarity=0.380  Sum_probs=65.0

Q ss_pred             ccccceeeecCchHHHHHHHHh-CCeEEEeCCCCCcceEEEecccCCCCCCccccCCCCCccccchHHHHHHHHHHHHhh
Q psy11929         27 VNEISCLIGPGGCIVRRLRKES-GAKISITDGACPDRIVTVSGSVDNSSTSSVETGYPGHTLWVTSVDNVCTAYNFMCRS  105 (433)
Q Consensus        27 ~~~vg~IIGk~G~~Ik~I~~~t-ga~I~v~~~~~~eRvv~I~G~~~~~~~~~v~~~~~~~~~~~~a~~~v~~A~~~I~~~  105 (433)
                      ++-+|+.||.+|.+|+.|.++. |=+|.+-.-.           .+                       .   ..+|...
T Consensus       244 iDpvGacvg~~G~ri~~i~~el~ge~Idii~~s-----------~d-----------------------~---~~fi~na  286 (344)
T 1hh2_P          244 VDPIGACIGEGGSRIAAILKELKGEKLDVLKWS-----------DD-----------------------P---KQLIANA  286 (344)
T ss_dssp             SCHHHHHHCTTSTTHHHHHHHTTTCEEEEEECC-----------SS-----------------------H---HHHHHHH
T ss_pred             ccccceeeccCCcEeHHHHHHhCCCeeeEEecC-----------CC-----------------------H---HHHHHHh
Confidence            5678999999999999999998 7888775411           01                       0   0122221


Q ss_pred             hhhhcccccCCCCCCCCCeEEEEEeccCcccceecCCchhHHHHHHhhCceEEecc
Q psy11929        106 LEDYHINRNRMENCSPQPLQLKLVIPATHCGSLIGKGGCKIKDIRDLSGANVQVAS  161 (433)
Q Consensus       106 ~~~~~~~~~~~~~~~~~~~~~~l~ip~~~vg~iIGk~G~~Ik~I~~~sga~I~i~~  161 (433)
                      |....-.  .-.-.......+.+.||..+.+.-|||+|.+++--..-||.+|.|..
T Consensus       287 l~Pa~v~--~v~~~d~~~~~~~v~v~~~~~s~AIGk~G~Nvrla~~Ltg~~idi~s  340 (344)
T 1hh2_P          287 LAPATVI--EVEILDKENKAARVLVPPTQLSLAIGKGGQNARLAAKLTGWKIDIKP  340 (344)
T ss_dssp             TCSSCCS--EEEEEETTTTEEEEEECTTSHHHHHCGGGHHHHHHHHHHSCEEEEEE
T ss_pred             cCccEEE--EEEEEcCCCCEEEEEEChHHcchhhcCCCccHHHHHHHHCCEeceee
Confidence            1110000  00000022346789999999999999999999999999999999864

>1hh2_P NUSA, N utilization substance protein A; transcription regulation, termination; 2.1A {Thermotoga maritima} SCOP: b.40.4.5 d.52.3.1 d.52.3.1 d.202.1.1 PDB: 1l2f_A

Probab=93.49  E-value=0.13  Score=49.98  Aligned_cols=40  Identities=18%  Similarity=0.241  Sum_probs=36.4

Q ss_pred             ceEEEEEeCcccccccccCCCchHHHHHhHhCCeEEEccC
Q psy11929        287 FVETEIVLTDDIAGCVIGKAGSRLLEIRQISGAQINIHTG  326 (433)
Q Consensus       287 ~~t~~i~VP~~~vG~IIGkgG~~Ik~I~~~sGA~I~I~~~  326 (433)
                      ..+..+.||.+..+.-|||+|+|++--.+.||.+|.|...
T Consensus       302 ~~~~~v~v~~~~~s~AIGk~G~Nvrla~~Ltg~~idi~s~  341 (344)
T 1hh2_P          302 NKAARVLVPPTQLSLAIGKGGQNARLAAKLTGWKIDIKPI  341 (344)
T ss_dssp             TTEEEEEECTTSHHHHHCGGGHHHHHHHHHHSCEEEEEEC
T ss_pred             CCEEEEEEChHHcchhhcCCCccHHHHHHHHCCEeceeec
Confidence            4568999999999999999999999999999999998653

---

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	433
d1dtja_	74	d.51.1.1 (A:) Neuro-oncological ventral antigen 2,	6e-15
d1dtja_	74	d.51.1.1 (A:) Neuro-oncological ventral antigen 2,	4e-09
d1dtja_	74	d.51.1.1 (A:) Neuro-oncological ventral antigen 2,	8e-07
d2axya1	71	d.51.1.1 (A:11-81) Poly(RC)-binding protein 2 {Hum	9e-15
d2axya1	71	d.51.1.1 (A:11-81) Poly(RC)-binding protein 2 {Hum	3e-11
d2axya1	71	d.51.1.1 (A:11-81) Poly(RC)-binding protein 2 {Hum	5e-09
d1x4na1	79	d.51.1.1 (A:8-86) Far upstream binding element, FB	2e-14
d1x4na1	79	d.51.1.1 (A:8-86) Far upstream binding element, FB	6e-10
d1x4na1	79	d.51.1.1 (A:8-86) Far upstream binding element, FB	1e-08
d2ctla1	84	d.51.1.1 (A:8-91) Vigilin {Human (Homo sapiens) [T	1e-13
d2ctla1	84	d.51.1.1 (A:8-91) Vigilin {Human (Homo sapiens) [T	2e-06
d2ctla1	84	d.51.1.1 (A:8-91) Vigilin {Human (Homo sapiens) [T	5e-06
d1j4wa2	71	d.51.1.1 (A:104-174) Far upstream binding element,	3e-13
d1j4wa2	71	d.51.1.1 (A:104-174) Far upstream binding element,	3e-08
d1j4wa2	71	d.51.1.1 (A:104-174) Far upstream binding element,	3e-06
d1wvna1	70	d.51.1.1 (A:5-74) Poly(RC)-binding protein 1 {Huma	3e-13
d1wvna1	70	d.51.1.1 (A:5-74) Poly(RC)-binding protein 1 {Huma	4e-09
d1wvna1	70	d.51.1.1 (A:5-74) Poly(RC)-binding protein 1 {Huma	7e-07
d1j4wa1	74	d.51.1.1 (A:1-74) Far upstream binding element, FB	4e-13
d1j4wa1	74	d.51.1.1 (A:1-74) Far upstream binding element, FB	2e-08
d1j4wa1	74	d.51.1.1 (A:1-74) Far upstream binding element, FB	7e-06
d1we8a_	104	d.51.1.1 (A:) Tudor and KH domain containing prote	9e-13
d1we8a_	104	d.51.1.1 (A:) Tudor and KH domain containing prote	4e-08
d1we8a_	104	d.51.1.1 (A:) Tudor and KH domain containing prote	4e-07
d1zzka1	75	d.51.1.1 (A:11-85) HnRNP K, KH3 {Human (Homo sapie	1e-12
d1zzka1	75	d.51.1.1 (A:11-85) HnRNP K, KH3 {Human (Homo sapie	9e-10
d1zzka1	75	d.51.1.1 (A:11-85) HnRNP K, KH3 {Human (Homo sapie	2e-06
d1x4ma1	81	d.51.1.1 (A:8-88) Far upstream binding element, FB	3e-12
d1x4ma1	81	d.51.1.1 (A:8-88) Far upstream binding element, FB	3e-07
d1x4ma1	81	d.51.1.1 (A:8-88) Far upstream binding element, FB	3e-05
d2ctea1	81	d.51.1.1 (A:8-88) Vigilin {Human (Homo sapiens) [T	3e-12
d2ctea1	81	d.51.1.1 (A:8-88) Vigilin {Human (Homo sapiens) [T	4e-08
d2ctea1	81	d.51.1.1 (A:8-88) Vigilin {Human (Homo sapiens) [T	1e-07
d2ctka1	91	d.51.1.1 (A:8-98) Vigilin {Human (Homo sapiens) [T	2e-11
d2ctka1	91	d.51.1.1 (A:8-98) Vigilin {Human (Homo sapiens) [T	1e-07
d2ctka1	91	d.51.1.1 (A:8-98) Vigilin {Human (Homo sapiens) [T	3e-07
d1viga_	71	d.51.1.1 (A:) Vigilin {Human (Homo sapiens) [TaxId	2e-10
d1viga_	71	d.51.1.1 (A:) Vigilin {Human (Homo sapiens) [TaxId	3e-07
d1viga_	71	d.51.1.1 (A:) Vigilin {Human (Homo sapiens) [TaxId	9e-06
d2ctma1	81	d.51.1.1 (A:8-88) Vigilin {Human (Homo sapiens) [T	2e-09
d2ctma1	81	d.51.1.1 (A:8-88) Vigilin {Human (Homo sapiens) [T	1e-07
d2ctma1	81	d.51.1.1 (A:8-88) Vigilin {Human (Homo sapiens) [T	3e-04
d2ba0a3	84	d.51.1.1 (A:136-219) Exosome complex RNA-binding p	3e-08
d2ba0a3	84	d.51.1.1 (A:136-219) Exosome complex RNA-binding p	8e-06
d2ba0a3	84	d.51.1.1 (A:136-219) Exosome complex RNA-binding p	3e-04
d2ctja1	82	d.51.1.1 (A:8-89) Vigilin {Human (Homo sapiens) [T	4e-08
d2ctja1	82	d.51.1.1 (A:8-89) Vigilin {Human (Homo sapiens) [T	1e-05
d2ctja1	82	d.51.1.1 (A:8-89) Vigilin {Human (Homo sapiens) [T	3e-05
d1e3ha4	54	d.52.3.1 (A:579-632) Polynucleotide phosphorylase/	4e-07
d1e3ha4	54	d.52.3.1 (A:579-632) Polynucleotide phosphorylase/	4e-04
d1tuaa1	84	d.51.1.1 (A:1-84) Hypothetical protein APE0754 {Ae	3e-05
d1tuaa1	84	d.51.1.1 (A:1-84) Hypothetical protein APE0754 {Ae	4e-04
d2cpqa1	78	d.51.1.1 (A:212-289) Fragile X mental retardation	1e-04
d2cpqa1	78	d.51.1.1 (A:212-289) Fragile X mental retardation	2e-04
d2cpqa1	78	d.51.1.1 (A:212-289) Fragile X mental retardation	0.001
d2z0sa2	87	d.51.1.1 (A:148-234) Exosome complex RNA-binding p	2e-04
d2z0sa2	87	d.51.1.1 (A:148-234) Exosome complex RNA-binding p	8e-04
d2je6i3	69	d.51.1.1 (I:153-221) Exosome complex RNA-binding p	7e-04
d2je6i3	69	d.51.1.1 (I:153-221) Exosome complex RNA-binding p	8e-04
d2ctfa1	90	d.51.1.1 (A:7-96) Vigilin {Human (Homo sapiens) [T	0.002

>d1dtja_ d.51.1.1 (A:) Neuro-oncological ventral antigen 2, nova-2, KH3 {Human (Homo sapiens) [TaxId: 9606]} Length = 74

class: Alpha and beta proteins (a+b)
fold: Eukaryotic type KH-domain (KH-domain type I)
superfamily: Eukaryotic type KH-domain (KH-domain type I)
family: Eukaryotic type KH-domain (KH-domain type I)
domain: Neuro-oncological ventral antigen 2, nova-2, KH3
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 67.2 bits (164), Expect = 6e-15
 Identities = 20/65 (30%), Positives = 38/65 (58%), Gaps = 2/65 (3%)

Query: 126 LKLVIPATHCGSLIGKGGCKIKDIRDLSGANVQV--ASDMLPMSTERIVTVHGNPDTISQ 183
           +++ +P    G+++GKGG  + + ++L+GA +Q+    + LP +  R VT+ G+P     
Sbjct: 5   VEMAVPENLVGAILGKGGKTLVEYQELTGARIQISKKGEFLPGTRNRRVTITGSPAATQA 64

Query: 184 AIYQI 188
           A Y I
Sbjct: 65  AQYLI 69

>d1dtja_ d.51.1.1 (A:) Neuro-oncological ventral antigen 2, nova-2, KH3 {Human (Homo sapiens) [TaxId: 9606]} Length = 74

class: Alpha and beta proteins (a+b)
fold: Eukaryotic type KH-domain (KH-domain type I)
superfamily: Eukaryotic type KH-domain (KH-domain type I)
family: Eukaryotic type KH-domain (KH-domain type I)
domain: Neuro-oncological ventral antigen 2, nova-2, KH3
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 50.6 bits (121), Expect = 4e-09
 Identities = 20/66 (30%), Positives = 36/66 (54%), Gaps = 4/66 (6%)

Query: 290 TEIVLTDDIAGCVIGKAGSRLLEIRQISGAQINIHTGTE----SHKKMFHIQGCQEAVSL 345
            E+ + +++ G ++GK G  L+E ++++GA+I I    E    +  +   I G   A   
Sbjct: 5   VEMAVPENLVGAILGKGGKTLVEYQELTGARIQISKKGEFLPGTRNRRVTITGSPAATQA 64

Query: 346 AQYLIN 351
           AQYLI+
Sbjct: 65  AQYLIS 70

>d1dtja_ d.51.1.1 (A:) Neuro-oncological ventral antigen 2, nova-2, KH3 {Human (Homo sapiens) [TaxId: 9606]} Length = 74

class: Alpha and beta proteins (a+b)
fold: Eukaryotic type KH-domain (KH-domain type I)
superfamily: Eukaryotic type KH-domain (KH-domain type I)
family: Eukaryotic type KH-domain (KH-domain type I)
domain: Neuro-oncological ventral antigen 2, nova-2, KH3
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 44.0 bits (104), Expect = 8e-07
 Identities = 14/53 (26%), Positives = 26/53 (49%), Gaps = 5/53 (9%)

Query: 25 VNVNEISCLIGPGGCIVRRLRKESGAKISITDG-----ACPDRIVTVSGSVDN 72
          V  N +  ++G GG  +   ++ +GA+I I+          +R VT++GS   
Sbjct: 9  VPENLVGAILGKGGKTLVEYQELTGARIQISKKGEFLPGTRNRRVTITGSPAA 61

>d2axya1 d.51.1.1 (A:11-81) Poly(RC)-binding protein 2 {Human (Homo sapiens) [TaxId: 9606]} Length = 71

class: Alpha and beta proteins (a+b)
fold: Eukaryotic type KH-domain (KH-domain type I)
superfamily: Eukaryotic type KH-domain (KH-domain type I)
family: Eukaryotic type KH-domain (KH-domain type I)
domain: Poly(RC)-binding protein 2
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 66.7 bits (163), Expect = 9e-15
 Identities = 24/72 (33%), Positives = 39/72 (54%), Gaps = 3/72 (4%)

Query: 123 PLQLKLVIPATHCGSLIGKGGCKIKDIRDLSGANVQVASDMLPMSTERIVTVHGNPDTIS 182
            L ++L++     GS+IGK G  +K +R+ SGA + ++    P   ERI+T+ G  + I 
Sbjct: 3   TLTIRLLMHGKEVGSIIGKKGESVKKMREESGARINISEGNCP---ERIITLAGPTNAIF 59

Query: 183 QAIYQICLVLIE 194
           +A   I   L E
Sbjct: 60  KAFAMIIDKLEE 71

>d2axya1 d.51.1.1 (A:11-81) Poly(RC)-binding protein 2 {Human (Homo sapiens) [TaxId: 9606]} Length = 71

class: Alpha and beta proteins (a+b)
fold: Eukaryotic type KH-domain (KH-domain type I)
superfamily: Eukaryotic type KH-domain (KH-domain type I)
family: Eukaryotic type KH-domain (KH-domain type I)
domain: Poly(RC)-binding protein 2
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 56.7 bits (137), Expect = 3e-11
 Identities = 23/61 (37%), Positives = 41/61 (67%), Gaps = 4/61 (6%)

Query: 12 DTLITMRCLFHSSVNVNEISCLIGPGGCIVRRLRKESGAKISITDGACPDRIVTVSGSVD 71
          +  +T+R L H      E+  +IG  G  V+++R+ESGA+I+I++G CP+RI+T++G  +
Sbjct: 1  NVTLTIRLLMHGK----EVGSIIGKKGESVKKMREESGARINISEGNCPERIITLAGPTN 56

Query: 72 N 72
           
Sbjct: 57 A 57

>d2axya1 d.51.1.1 (A:11-81) Poly(RC)-binding protein 2 {Human (Homo sapiens) [TaxId: 9606]} Length = 71

class: Alpha and beta proteins (a+b)
fold: Eukaryotic type KH-domain (KH-domain type I)
superfamily: Eukaryotic type KH-domain (KH-domain type I)
family: Eukaryotic type KH-domain (KH-domain type I)
domain: Poly(RC)-binding protein 2
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 50.5 bits (121), Expect = 5e-09
 Identities = 18/68 (26%), Positives = 35/68 (51%), Gaps = 1/68 (1%)

Query: 288 VETEIVLTDDIAGCVIGKAGSRLLEIRQISGAQINIHTGTESHKKMFHIQGCQEAVSLAQ 347
           +   +++     G +IGK G  + ++R+ SGA+INI  G    +++  + G   A+  A 
Sbjct: 4   LTIRLLMHGKEVGSIIGKKGESVKKMREESGARINISEG-NCPERIITLAGPTNAIFKAF 62

Query: 348 YLINMCIE 355
            +I   +E
Sbjct: 63  AMIIDKLE 70

>d1x4na1 d.51.1.1 (A:8-86) Far upstream binding element, FBP {Mouse (Mus musculus) [TaxId: 10090]} Length = 79

class: Alpha and beta proteins (a+b)
fold: Eukaryotic type KH-domain (KH-domain type I)
superfamily: Eukaryotic type KH-domain (KH-domain type I)
family: Eukaryotic type KH-domain (KH-domain type I)
domain: Far upstream binding element, FBP
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 66.0 bits (161), Expect = 2e-14
 Identities = 16/75 (21%), Positives = 34/75 (45%), Gaps = 1/75 (1%)

Query: 121 PQPLQLKLVIPATHCGSLIGKGGCKIKDIRDLSGANVQVASDMLPMSTERIVTVHGNPDT 180
              +  +  +P    G +IG+GG +I  I+  SG  +Q+ +       ER   + G P++
Sbjct: 5   RSVMTEEYKVPDGMVGFIIGRGGEQISRIQQESGCKIQI-APDSGGLPERSCMLTGTPES 63

Query: 181 ISQAIYQICLVLIEC 195
           +  A   +  ++ + 
Sbjct: 64  VQSAKRLLDQIVEKG 78

>d1x4na1 d.51.1.1 (A:8-86) Far upstream binding element, FBP {Mouse (Mus musculus) [TaxId: 10090]} Length = 79

class: Alpha and beta proteins (a+b)
fold: Eukaryotic type KH-domain (KH-domain type I)
superfamily: Eukaryotic type KH-domain (KH-domain type I)
family: Eukaryotic type KH-domain (KH-domain type I)
domain: Far upstream binding element, FBP
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 53.3 bits (128), Expect = 6e-10
 Identities = 18/69 (26%), Positives = 35/69 (50%), Gaps = 1/69 (1%)

Query: 288 VETEIVLTDDIAGCVIGKAGSRLLEIRQISGAQINIH-TGTESHKKMFHIQGCQEAVSLA 346
           +  E  + D + G +IG+ G ++  I+Q SG +I I        ++   + G  E+V  A
Sbjct: 8   MTEEYKVPDGMVGFIIGRGGEQISRIQQESGCKIQIAPDSGGLPERSCMLTGTPESVQSA 67

Query: 347 QYLINMCIE 355
           + L++  +E
Sbjct: 68  KRLLDQIVE 76

>d1x4na1 d.51.1.1 (A:8-86) Far upstream binding element, FBP {Mouse (Mus musculus) [TaxId: 10090]} Length = 79

class: Alpha and beta proteins (a+b)
fold: Eukaryotic type KH-domain (KH-domain type I)
superfamily: Eukaryotic type KH-domain (KH-domain type I)
family: Eukaryotic type KH-domain (KH-domain type I)
domain: Far upstream binding element, FBP
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 49.8 bits (119), Expect = 1e-08
 Identities = 16/51 (31%), Positives = 28/51 (54%), Gaps = 2/51 (3%)

Query: 24 SVNVNEISCLIGPGGCIVRRLRKESGAKISI--TDGACPDRIVTVSGSVDN 72
           V    +  +IG GG  + R+++ESG KI I    G  P+R   ++G+ ++
Sbjct: 13 KVPDGMVGFIIGRGGEQISRIQQESGCKIQIAPDSGGLPERSCMLTGTPES 63

>d2ctla1 d.51.1.1 (A:8-91) Vigilin {Human (Homo sapiens) [TaxId: 9606]} Length = 84

class: Alpha and beta proteins (a+b)
fold: Eukaryotic type KH-domain (KH-domain type I)
superfamily: Eukaryotic type KH-domain (KH-domain type I)
family: Eukaryotic type KH-domain (KH-domain type I)
domain: Vigilin
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 64.1 bits (156), Expect = 1e-13
 Identities = 13/64 (20%), Positives = 23/64 (35%)

Query: 125 QLKLVIPATHCGSLIGKGGCKIKDIRDLSGANVQVASDMLPMSTERIVTVHGNPDTISQA 184
           +L + +   +   +IG+ G  I  IR     N+Q          +  +T+ G       A
Sbjct: 11  KLSVTVDPKYHPKIIGRKGAVITQIRLEHDVNIQFPDKDDGNQPQDQITITGYEKNTEAA 70

Query: 185 IYQI 188
              I
Sbjct: 71  RDAI 74

>d2ctla1 d.51.1.1 (A:8-91) Vigilin {Human (Homo sapiens) [TaxId: 9606]} Length = 84

class: Alpha and beta proteins (a+b)
fold: Eukaryotic type KH-domain (KH-domain type I)
superfamily: Eukaryotic type KH-domain (KH-domain type I)
family: Eukaryotic type KH-domain (KH-domain type I)
domain: Vigilin
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 43.3 bits (102), Expect = 2e-06
 Identities = 12/74 (16%), Positives = 27/74 (36%), Gaps = 3/74 (4%)

Query: 288 VETEIVLTDDIAGCVIGKAGSRLLEIRQISGAQINIH--TGTESHKKMFHIQGCQEAVSL 345
            +  + +       +IG+ G+ + +IR      I           +    I G ++    
Sbjct: 10  FKLSVTVDPKYHPKIIGRKGAVITQIRLEHDVNIQFPDKDDGNQPQDQITITGYEKNTEA 69

Query: 346 AQYLINMCI-ELQK 358
           A+  I   + EL++
Sbjct: 70  ARDAILRIVGELEQ 83

>d2ctla1 d.51.1.1 (A:8-91) Vigilin {Human (Homo sapiens) [TaxId: 9606]} Length = 84

class: Alpha and beta proteins (a+b)
fold: Eukaryotic type KH-domain (KH-domain type I)
superfamily: Eukaryotic type KH-domain (KH-domain type I)
family: Eukaryotic type KH-domain (KH-domain type I)
domain: Vigilin
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 42.1 bits (99), Expect = 5e-06
 Identities = 13/52 (25%), Positives = 23/52 (44%), Gaps = 3/52 (5%)

Query: 24 SVNVNEISCLIGPGGCIVRRLRKESGAKISI---TDGACPDRIVTVSGSVDN 72
          +V+      +IG  G ++ ++R E    I      DG  P   +T++G   N
Sbjct: 15 TVDPKYHPKIIGRKGAVITQIRLEHDVNIQFPDKDDGNQPQDQITITGYEKN 66

>d1j4wa2 d.51.1.1 (A:104-174) Far upstream binding element, FBP {Human (Homo sapiens) [TaxId: 9606]} Length = 71

class: Alpha and beta proteins (a+b)
fold: Eukaryotic type KH-domain (KH-domain type I)
superfamily: Eukaryotic type KH-domain (KH-domain type I)
family: Eukaryotic type KH-domain (KH-domain type I)
domain: Far upstream binding element, FBP
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 62.6 bits (152), Expect = 3e-13
 Identities = 20/66 (30%), Positives = 31/66 (46%), Gaps = 2/66 (3%)

Query: 125 QLKLVIPATHCGSLIGKGGCKIKDIRDLSGANVQVASDMLPM--STERIVTVHGNPDTIS 182
           +   ++P    G +IGKGG  IK I   SGA +++  +  P      ++ T+ G P  I 
Sbjct: 2   EFNFIVPTGKTGLIIGKGGETIKSISQQSGARIELQRNPPPNADPNMKLFTIRGTPQQID 61

Query: 183 QAIYQI 188
            A   I
Sbjct: 62  YARQLI 67

>d1j4wa2 d.51.1.1 (A:104-174) Far upstream binding element, FBP {Human (Homo sapiens) [TaxId: 9606]} Length = 71

class: Alpha and beta proteins (a+b)
fold: Eukaryotic type KH-domain (KH-domain type I)
superfamily: Eukaryotic type KH-domain (KH-domain type I)
family: Eukaryotic type KH-domain (KH-domain type I)
domain: Far upstream binding element, FBP
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 48.0 bits (114), Expect = 3e-08
 Identities = 19/67 (28%), Positives = 31/67 (46%), Gaps = 4/67 (5%)

Query: 289 ETEIVLTDDIAGCVIGKAGSRLLEIRQISGAQINIHTGTE----SHKKMFHIQGCQEAVS 344
           E   ++     G +IGK G  +  I Q SGA+I +          + K+F I+G  + + 
Sbjct: 2   EFNFIVPTGKTGLIIGKGGETIKSISQQSGARIELQRNPPPNADPNMKLFTIRGTPQQID 61

Query: 345 LAQYLIN 351
            A+ LI 
Sbjct: 62  YARQLIE 68

>d1j4wa2 d.51.1.1 (A:104-174) Far upstream binding element, FBP {Human (Homo sapiens) [TaxId: 9606]} Length = 71

class: Alpha and beta proteins (a+b)
fold: Eukaryotic type KH-domain (KH-domain type I)
superfamily: Eukaryotic type KH-domain (KH-domain type I)
family: Eukaryotic type KH-domain (KH-domain type I)
domain: Far upstream binding element, FBP
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 42.6 bits (100), Expect = 3e-06
 Identities = 11/53 (20%), Positives = 25/53 (47%), Gaps = 5/53 (9%)

Query: 25 VNVNEISCLIGPGGCIVRRLRKESGAKISI-----TDGACPDRIVTVSGSVDN 72
          V   +   +IG GG  ++ + ++SGA+I +      +     ++ T+ G+   
Sbjct: 7  VPTGKTGLIIGKGGETIKSISQQSGARIELQRNPPPNADPNMKLFTIRGTPQQ 59

>d1wvna1 d.51.1.1 (A:5-74) Poly(RC)-binding protein 1 {Human (Homo sapiens) [TaxId: 9606]} Length = 70

class: Alpha and beta proteins (a+b)
fold: Eukaryotic type KH-domain (KH-domain type I)
superfamily: Eukaryotic type KH-domain (KH-domain type I)
family: Eukaryotic type KH-domain (KH-domain type I)
domain: Poly(RC)-binding protein 1
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 62.5 bits (152), Expect = 3e-13
 Identities = 23/63 (36%), Positives = 38/63 (60%), Gaps = 1/63 (1%)

Query: 126 LKLVIPATHCGSLIGKGGCKIKDIRDLSGANVQVASDMLPMSTERIVTVHGNPDTISQAI 185
            +L IP    G +IG+ G  I +IR +SGA +++ ++ +  S+ R VT+ G+  +IS A 
Sbjct: 4   HELTIPNNLIGCIIGRQGANINEIRQMSGAQIKI-ANPVEGSSGRQVTITGSAASISLAQ 62

Query: 186 YQI 188
           Y I
Sbjct: 63  YLI 65

>d1wvna1 d.51.1.1 (A:5-74) Poly(RC)-binding protein 1 {Human (Homo sapiens) [TaxId: 9606]} Length = 70

class: Alpha and beta proteins (a+b)
fold: Eukaryotic type KH-domain (KH-domain type I)
superfamily: Eukaryotic type KH-domain (KH-domain type I)
family: Eukaryotic type KH-domain (KH-domain type I)
domain: Poly(RC)-binding protein 1
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 50.6 bits (121), Expect = 4e-09
 Identities = 28/63 (44%), Positives = 41/63 (65%), Gaps = 1/63 (1%)

Query: 290 TEIVLTDDIAGCVIGKAGSRLLEIRQISGAQINIHTGTE-SHKKMFHIQGCQEAVSLAQY 348
            E+ + +++ GC+IG+ G+ + EIRQ+SGAQI I    E S  +   I G   ++SLAQY
Sbjct: 4   HELTIPNNLIGCIIGRQGANINEIRQMSGAQIKIANPVEGSSGRQVTITGSAASISLAQY 63

Query: 349 LIN 351
           LIN
Sbjct: 64  LIN 66

>d1wvna1 d.51.1.1 (A:5-74) Poly(RC)-binding protein 1 {Human (Homo sapiens) [TaxId: 9606]} Length = 70

class: Alpha and beta proteins (a+b)
fold: Eukaryotic type KH-domain (KH-domain type I)
superfamily: Eukaryotic type KH-domain (KH-domain type I)
family: Eukaryotic type KH-domain (KH-domain type I)
domain: Poly(RC)-binding protein 1
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 44.4 bits (105), Expect = 7e-07
 Identities = 17/51 (33%), Positives = 28/51 (54%), Gaps = 2/51 (3%)

Query: 24 SVNVNEISCLIGPGGCIVRRLRKESGAKISITD--GACPDRIVTVSGSVDN 72
          ++  N I C+IG  G  +  +R+ SGA+I I +       R VT++GS  +
Sbjct: 7  TIPNNLIGCIIGRQGANINEIRQMSGAQIKIANPVEGSSGRQVTITGSAAS 57

>d1j4wa1 d.51.1.1 (A:1-74) Far upstream binding element, FBP {Human (Homo sapiens) [TaxId: 9606]} Length = 74

class: Alpha and beta proteins (a+b)
fold: Eukaryotic type KH-domain (KH-domain type I)
superfamily: Eukaryotic type KH-domain (KH-domain type I)
family: Eukaryotic type KH-domain (KH-domain type I)
domain: Far upstream binding element, FBP
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 62.2 bits (151), Expect = 4e-13
 Identities = 20/64 (31%), Positives = 30/64 (46%), Gaps = 1/64 (1%)

Query: 125 QLKLVIPATHCGSLIGKGGCKIKDIRDLSGANVQVASDMLPMSTERIVTVHGNPDTISQA 184
            + + IP    G +IG+ G  IK I++ +G  +Q   D    + ERI  + G PD    A
Sbjct: 4   MIDVPIPRFAVGIVIGRNGEMIKKIQNDAGVRIQFKPDD-GTTPERIAQITGPPDRAQHA 62

Query: 185 IYQI 188
              I
Sbjct: 63  AEII 66

>d1j4wa1 d.51.1.1 (A:1-74) Far upstream binding element, FBP {Human (Homo sapiens) [TaxId: 9606]} Length = 74

class: Alpha and beta proteins (a+b)
fold: Eukaryotic type KH-domain (KH-domain type I)
superfamily: Eukaryotic type KH-domain (KH-domain type I)
family: Eukaryotic type KH-domain (KH-domain type I)
domain: Far upstream binding element, FBP
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 48.7 bits (116), Expect = 2e-08
 Identities = 12/66 (18%), Positives = 28/66 (42%), Gaps = 1/66 (1%)

Query: 291 EIVLTDDIAGCVIGKAGSRLLEIRQISGAQINIHTGTE-SHKKMFHIQGCQEAVSLAQYL 349
           ++ +     G VIG+ G  + +I+  +G +I        + +++  I G  +    A  +
Sbjct: 6   DVPIPRFAVGIVIGRNGEMIKKIQNDAGVRIQFKPDDGTTPERIAQITGPPDRAQHAAEI 65

Query: 350 INMCIE 355
           I   + 
Sbjct: 66  ITDLLR 71

>d1j4wa1 d.51.1.1 (A:1-74) Far upstream binding element, FBP {Human (Homo sapiens) [TaxId: 9606]} Length = 74

class: Alpha and beta proteins (a+b)
fold: Eukaryotic type KH-domain (KH-domain type I)
superfamily: Eukaryotic type KH-domain (KH-domain type I)
family: Eukaryotic type KH-domain (KH-domain type I)
domain: Far upstream binding element, FBP
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 41.4 bits (97), Expect = 7e-06
 Identities = 12/50 (24%), Positives = 27/50 (54%), Gaps = 2/50 (4%)

Query: 25 VNVNEISCLIGPGGCIVRRLRKESGAKI--SITDGACPDRIVTVSGSVDN 72
          +    +  +IG  G ++++++ ++G +I     DG  P+RI  ++G  D 
Sbjct: 9  IPRFAVGIVIGRNGEMIKKIQNDAGVRIQFKPDDGTTPERIAQITGPPDR 58

>d1we8a_ d.51.1.1 (A:) Tudor and KH domain containing protein, Tdrkh {Mouse (Mus musculus) [TaxId: 10090]} Length = 104

class: Alpha and beta proteins (a+b)
fold: Eukaryotic type KH-domain (KH-domain type I)
superfamily: Eukaryotic type KH-domain (KH-domain type I)
family: Eukaryotic type KH-domain (KH-domain type I)
domain: Tudor and KH domain containing protein, Tdrkh
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 61.9 bits (150), Expect = 9e-13
 Identities = 18/74 (24%), Positives = 33/74 (44%), Gaps = 1/74 (1%)

Query: 122 QPLQLKLVIPATHCGSLIGKGGCKIKDIRDLSGANVQVASDMLPM-STERIVTVHGNPDT 180
            P+  +L +P    G +IG+GG  I+ I   SGA +    +        R++ + G    
Sbjct: 13  TPVFEQLSVPQRSVGRIIGRGGETIRSICKASGAKITCDKESEGTLLLSRLIKISGTQKE 72

Query: 181 ISQAIYQICLVLIE 194
           ++ A + I   + E
Sbjct: 73  VAAAKHLILEKVSE 86

>d1we8a_ d.51.1.1 (A:) Tudor and KH domain containing protein, Tdrkh {Mouse (Mus musculus) [TaxId: 10090]} Length = 104

class: Alpha and beta proteins (a+b)
fold: Eukaryotic type KH-domain (KH-domain type I)
superfamily: Eukaryotic type KH-domain (KH-domain type I)
family: Eukaryotic type KH-domain (KH-domain type I)
domain: Tudor and KH domain containing protein, Tdrkh
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 48.8 bits (116), Expect = 4e-08
 Identities = 22/81 (27%), Positives = 38/81 (46%), Gaps = 3/81 (3%)

Query: 278 SGGKDTGDDFVETEIVLTDDIAGCVIGKAGSRLLEIRQISGAQINIH---TGTESHKKMF 334
           S G  T +  V  ++ +     G +IG+ G  +  I + SGA+I       GT    ++ 
Sbjct: 5   SSGILTENTPVFEQLSVPQRSVGRIIGRGGETIRSICKASGAKITCDKESEGTLLLSRLI 64

Query: 335 HIQGCQEAVSLAQYLINMCIE 355
            I G Q+ V+ A++LI   + 
Sbjct: 65  KISGTQKEVAAAKHLILEKVS 85

>d1we8a_ d.51.1.1 (A:) Tudor and KH domain containing protein, Tdrkh {Mouse (Mus musculus) [TaxId: 10090]} Length = 104

class: Alpha and beta proteins (a+b)
fold: Eukaryotic type KH-domain (KH-domain type I)
superfamily: Eukaryotic type KH-domain (KH-domain type I)
family: Eukaryotic type KH-domain (KH-domain type I)
domain: Tudor and KH domain containing protein, Tdrkh
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 46.1 bits (109), Expect = 4e-07
 Identities = 18/71 (25%), Positives = 32/71 (45%), Gaps = 8/71 (11%)

Query: 6  DGKIDEDTLITMRCLFHSSVNVNEISCLIGPGGCIVRRLRKESGAKISITDGACP----D 61
           G + E+T +  +      V    +  +IG GG  +R + K SGAKI+    +       
Sbjct: 6  SGILTENTPVFEQLS----VPQRSVGRIIGRGGETIRSICKASGAKITCDKESEGTLLLS 61

Query: 62 RIVTVSGSVDN 72
          R++ +SG+   
Sbjct: 62 RLIKISGTQKE 72

>d1zzka1 d.51.1.1 (A:11-85) HnRNP K, KH3 {Human (Homo sapiens) [TaxId: 9606]} Length = 75

class: Alpha and beta proteins (a+b)
fold: Eukaryotic type KH-domain (KH-domain type I)
superfamily: Eukaryotic type KH-domain (KH-domain type I)
family: Eukaryotic type KH-domain (KH-domain type I)
domain: HnRNP K, KH3
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 60.7 bits (147), Expect = 1e-12
 Identities = 26/63 (41%), Positives = 39/63 (61%), Gaps = 1/63 (1%)

Query: 126 LKLVIPATHCGSLIGKGGCKIKDIRDLSGANVQVASDMLPMSTERIVTVHGNPDTISQAI 185
            ++ IP    GS+IGKGG +IK IR  SGA++++  + L  S +RI+T+ G  D I  A 
Sbjct: 6   TQVTIPKDLAGSIIGKGGQRIKQIRHESGASIKI-DEPLEGSEDRIITITGTQDQIQNAQ 64

Query: 186 YQI 188
           Y +
Sbjct: 65  YLL 67

>d1zzka1 d.51.1.1 (A:11-85) HnRNP K, KH3 {Human (Homo sapiens) [TaxId: 9606]} Length = 75

class: Alpha and beta proteins (a+b)
fold: Eukaryotic type KH-domain (KH-domain type I)
superfamily: Eukaryotic type KH-domain (KH-domain type I)
family: Eukaryotic type KH-domain (KH-domain type I)
domain: HnRNP K, KH3
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 52.6 bits (126), Expect = 9e-10
 Identities = 24/69 (34%), Positives = 39/69 (56%), Gaps = 1/69 (1%)

Query: 288 VETEIVLTDDIAGCVIGKAGSRLLEIRQISGAQINIH-TGTESHKKMFHIQGCQEAVSLA 346
           + T++ +  D+AG +IGK G R+ +IR  SGA I I      S  ++  I G Q+ +  A
Sbjct: 4   ITTQVTIPKDLAGSIIGKGGQRIKQIRHESGASIKIDEPLEGSEDRIITITGTQDQIQNA 63

Query: 347 QYLINMCIE 355
           QYL+   ++
Sbjct: 64  QYLLQNSVK 72

>d1zzka1 d.51.1.1 (A:11-85) HnRNP K, KH3 {Human (Homo sapiens) [TaxId: 9606]} Length = 75

class: Alpha and beta proteins (a+b)
fold: Eukaryotic type KH-domain (KH-domain type I)
superfamily: Eukaryotic type KH-domain (KH-domain type I)
family: Eukaryotic type KH-domain (KH-domain type I)
domain: HnRNP K, KH3
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 43.3 bits (102), Expect = 2e-06
 Identities = 17/51 (33%), Positives = 29/51 (56%), Gaps = 2/51 (3%)

Query: 24 SVNVNEISCLIGPGGCIVRRLRKESGAKISI--TDGACPDRIVTVSGSVDN 72
          ++  +    +IG GG  ++++R ESGA I I        DRI+T++G+ D 
Sbjct: 9  TIPKDLAGSIIGKGGQRIKQIRHESGASIKIDEPLEGSEDRIITITGTQDQ 59

>d1x4ma1 d.51.1.1 (A:8-88) Far upstream binding element, FBP {Mouse (Mus musculus) [TaxId: 10090]} Length = 81

class: Alpha and beta proteins (a+b)
fold: Eukaryotic type KH-domain (KH-domain type I)
superfamily: Eukaryotic type KH-domain (KH-domain type I)
family: Eukaryotic type KH-domain (KH-domain type I)
domain: Far upstream binding element, FBP
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 59.6 bits (144), Expect = 3e-12
 Identities = 18/78 (23%), Positives = 39/78 (50%), Gaps = 1/78 (1%)

Query: 118 NCSPQPLQLKLVIPATHCGSLIGKGGCKIKDIRDLSGANVQVASDM-LPMSTERIVTVHG 176
              P     +++IPA+  G +IGKGG  IK +++ +G  + +  D       ++ + + G
Sbjct: 2   GDGPGNAVQEIMIPASKAGLVIGKGGETIKQLQERAGVKMVMIQDGPQNTGADKPLRITG 61

Query: 177 NPDTISQAIYQICLVLIE 194
           +P  + QA   +  ++ +
Sbjct: 62  DPYKVQQAKEMVLELIRD 79

>d1x4ma1 d.51.1.1 (A:8-88) Far upstream binding element, FBP {Mouse (Mus musculus) [TaxId: 10090]} Length = 81

class: Alpha and beta proteins (a+b)
fold: Eukaryotic type KH-domain (KH-domain type I)
superfamily: Eukaryotic type KH-domain (KH-domain type I)
family: Eukaryotic type KH-domain (KH-domain type I)
domain: Far upstream binding element, FBP
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 45.7 bits (108), Expect = 3e-07
 Identities = 17/75 (22%), Positives = 31/75 (41%), Gaps = 3/75 (4%)

Query: 284 GDDFVETEIVLTDDIAGCVIGKAGSRLLEIRQISGAQINI---HTGTESHKKMFHIQGCQ 340
           G      EI++    AG VIGK G  + ++++ +G ++ +           K   I G  
Sbjct: 4   GPGNAVQEIMIPASKAGLVIGKGGETIKQLQERAGVKMVMIQDGPQNTGADKPLRITGDP 63

Query: 341 EAVSLAQYLINMCIE 355
             V  A+ ++   I 
Sbjct: 64  YKVQQAKEMVLELIR 78

>d1x4ma1 d.51.1.1 (A:8-88) Far upstream binding element, FBP {Mouse (Mus musculus) [TaxId: 10090]} Length = 81

class: Alpha and beta proteins (a+b)
fold: Eukaryotic type KH-domain (KH-domain type I)
superfamily: Eukaryotic type KH-domain (KH-domain type I)
family: Eukaryotic type KH-domain (KH-domain type I)
domain: Far upstream binding element, FBP
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 39.9 bits (93), Expect = 3e-05
 Identities = 9/52 (17%), Positives = 25/52 (48%), Gaps = 4/52 (7%)

Query: 25 VNVNEISCLIGPGGCIVRRLRKESGAKISI----TDGACPDRIVTVSGSVDN 72
          +  ++   +IG GG  +++L++ +G K+ +          D+ + ++G    
Sbjct: 14 IPASKAGLVIGKGGETIKQLQERAGVKMVMIQDGPQNTGADKPLRITGDPYK 65

>d2ctea1 d.51.1.1 (A:8-88) Vigilin {Human (Homo sapiens) [TaxId: 9606]} Length = 81

class: Alpha and beta proteins (a+b)
fold: Eukaryotic type KH-domain (KH-domain type I)
superfamily: Eukaryotic type KH-domain (KH-domain type I)
family: Eukaryotic type KH-domain (KH-domain type I)
domain: Vigilin
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 59.7 bits (145), Expect = 3e-12
 Identities = 14/62 (22%), Positives = 29/62 (46%), Gaps = 3/62 (4%)

Query: 127 KLVIPATHCGSLIGKGGCKIKDIRDLSGANVQVASDMLPMSTERIVTVHGNPDTISQAIY 186
            + IP  H   +IGK G K++D+   +   +Q+     P      + + G  + I +A +
Sbjct: 13  TVAIPKEHHRFVIGKNGEKLQDLELKTATKIQIPR---PDDPSNQIKITGTKEGIEKARH 69

Query: 187 QI 188
           ++
Sbjct: 70  EV 71

>d2ctea1 d.51.1.1 (A:8-88) Vigilin {Human (Homo sapiens) [TaxId: 9606]} Length = 81

class: Alpha and beta proteins (a+b)
fold: Eukaryotic type KH-domain (KH-domain type I)
superfamily: Eukaryotic type KH-domain (KH-domain type I)
family: Eukaryotic type KH-domain (KH-domain type I)
domain: Vigilin
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 48.2 bits (115), Expect = 4e-08
 Identities = 9/49 (18%), Positives = 21/49 (42%)

Query: 24 SVNVNEISCLIGPGGCIVRRLRKESGAKISITDGACPDRIVTVSGSVDN 72
          ++       +IG  G  ++ L  ++  KI I     P   + ++G+ + 
Sbjct: 15 AIPKEHHRFVIGKNGEKLQDLELKTATKIQIPRPDDPSNQIKITGTKEG 63

>d2ctea1 d.51.1.1 (A:8-88) Vigilin {Human (Homo sapiens) [TaxId: 9606]} Length = 81

class: Alpha and beta proteins (a+b)
fold: Eukaryotic type KH-domain (KH-domain type I)
superfamily: Eukaryotic type KH-domain (KH-domain type I)
family: Eukaryotic type KH-domain (KH-domain type I)
domain: Vigilin
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 46.6 bits (111), Expect = 1e-07
 Identities = 12/71 (16%), Positives = 27/71 (38%), Gaps = 1/71 (1%)

Query: 285 DDFVETEIVLTDDIAGCVIGKAGSRLLEIRQISGAQINIHTGTESHKKMFHIQGCQEAVS 344
                  + +  +    VIGK G +L ++   +  +I I    +       I G +E + 
Sbjct: 7   QTQASATVAIPKEHHRFVIGKNGEKLQDLELKTATKIQIP-RPDDPSNQIKITGTKEGIE 65

Query: 345 LAQYLINMCIE 355
            A++ + +   
Sbjct: 66  KARHEVLLISA 76

>d2ctka1 d.51.1.1 (A:8-98) Vigilin {Human (Homo sapiens) [TaxId: 9606]} Length = 91

class: Alpha and beta proteins (a+b)
fold: Eukaryotic type KH-domain (KH-domain type I)
superfamily: Eukaryotic type KH-domain (KH-domain type I)
family: Eukaryotic type KH-domain (KH-domain type I)
domain: Vigilin
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 58.3 bits (141), Expect = 2e-11
 Identities = 13/66 (19%), Positives = 29/66 (43%), Gaps = 3/66 (4%)

Query: 123 PLQLKLVIPATHCGSLIGKGGCKIKDIRDLSGANVQVASDMLPMSTERIVTVHGNPDTIS 182
           P+ +++ +P      +IG+ G  I+ + D    N+ V +   P     I+ + G    + 
Sbjct: 9   PVTIEVEVPFDLHRYVIGQKGSGIRKMMDEFEVNIHVPA---PELQSDIIAITGLAANLD 65

Query: 183 QAIYQI 188
           +A   +
Sbjct: 66  RAKAGL 71

>d2ctka1 d.51.1.1 (A:8-98) Vigilin {Human (Homo sapiens) [TaxId: 9606]} Length = 91

class: Alpha and beta proteins (a+b)
fold: Eukaryotic type KH-domain (KH-domain type I)
superfamily: Eukaryotic type KH-domain (KH-domain type I)
family: Eukaryotic type KH-domain (KH-domain type I)
domain: Vigilin
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 47.1 bits (112), Expect = 1e-07
 Identities = 10/49 (20%), Positives = 19/49 (38%)

Query: 24 SVNVNEISCLIGPGGCIVRRLRKESGAKISITDGACPDRIVTVSGSVDN 72
           V  +    +IG  G  +R++  E    I +        I+ ++G   N
Sbjct: 15 EVPFDLHRYVIGQKGSGIRKMMDEFEVNIHVPAPELQSDIIAITGLAAN 63

>d2ctka1 d.51.1.1 (A:8-98) Vigilin {Human (Homo sapiens) [TaxId: 9606]} Length = 91

class: Alpha and beta proteins (a+b)
fold: Eukaryotic type KH-domain (KH-domain type I)
superfamily: Eukaryotic type KH-domain (KH-domain type I)
family: Eukaryotic type KH-domain (KH-domain type I)
domain: Vigilin
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 46.0 bits (109), Expect = 3e-07
 Identities = 16/74 (21%), Positives = 30/74 (40%), Gaps = 2/74 (2%)

Query: 288 VETEIVLTDDIAGCVIGKAGSRLLEIRQISGAQINIHTGTESHKKMFHIQGCQEAVSLAQ 347
           V  E+ +  D+   VIG+ GS + ++       I++    E    +  I G    +  A+
Sbjct: 10  VTIEVEVPFDLHRYVIGQKGSGIRKMMDEFEVNIHVP-APELQSDIIAITGLAANLDRAK 68

Query: 348 YLINMCI-ELQKNN 360
             +   + ELQ   
Sbjct: 69  AGLLERVKELQAEQ 82

>d1viga_ d.51.1.1 (A:) Vigilin {Human (Homo sapiens) [TaxId: 9606]} Length = 71

class: Alpha and beta proteins (a+b)
fold: Eukaryotic type KH-domain (KH-domain type I)
superfamily: Eukaryotic type KH-domain (KH-domain type I)
family: Eukaryotic type KH-domain (KH-domain type I)
domain: Vigilin
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 54.4 bits (131), Expect = 2e-10
 Identities = 15/62 (24%), Positives = 28/62 (45%), Gaps = 3/62 (4%)

Query: 127 KLVIPATHCGSLIGKGGCKIKDIRDLSGANVQVASDMLPMSTERIVTVHGNPDTISQAIY 186
           ++ I       LIGK G  I  I+D    +V++  D        ++ + G+P  + QA  
Sbjct: 8   EINIDHKFHRHLIGKSGANINRIKDQYKVSVRIPPD---SEKSNLIRIEGDPQGVQQAKR 64

Query: 187 QI 188
           ++
Sbjct: 65  EL 66

>d1viga_ d.51.1.1 (A:) Vigilin {Human (Homo sapiens) [TaxId: 9606]} Length = 71

class: Alpha and beta proteins (a+b)
fold: Eukaryotic type KH-domain (KH-domain type I)
superfamily: Eukaryotic type KH-domain (KH-domain type I)
family: Eukaryotic type KH-domain (KH-domain type I)
domain: Vigilin
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 45.5 bits (108), Expect = 3e-07
 Identities = 7/49 (14%), Positives = 19/49 (38%)

Query: 24 SVNVNEISCLIGPGGCIVRRLRKESGAKISITDGACPDRIVTVSGSVDN 72
          +++      LIG  G  + R++ +    + I   +    ++ + G    
Sbjct: 10 NIDHKFHRHLIGKSGANINRIKDQYKVSVRIPPDSEKSNLIRIEGDPQG 58

>d1viga_ d.51.1.1 (A:) Vigilin {Human (Homo sapiens) [TaxId: 9606]} Length = 71

class: Alpha and beta proteins (a+b)
fold: Eukaryotic type KH-domain (KH-domain type I)
superfamily: Eukaryotic type KH-domain (KH-domain type I)
family: Eukaryotic type KH-domain (KH-domain type I)
domain: Vigilin
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 41.3 bits (97), Expect = 9e-06
 Identities = 13/67 (19%), Positives = 27/67 (40%), Gaps = 1/67 (1%)

Query: 285 DDFVETEIVLTDDIAGCVIGKAGSRLLEIRQISGAQINIHTGTESHKKMFHIQGCQEAVS 344
           +     EI +       +IGK+G+ +  I+      + I   +E    +  I+G  + V 
Sbjct: 2   NRMDYVEINIDHKFHRHLIGKSGANINRIKDQYKVSVRIPPDSE-KSNLIRIEGDPQGVQ 60

Query: 345 LAQYLIN 351
            A+  + 
Sbjct: 61  QAKRELL 67

>d2ctma1 d.51.1.1 (A:8-88) Vigilin {Human (Homo sapiens) [TaxId: 9606]} Length = 81

class: Alpha and beta proteins (a+b)
fold: Eukaryotic type KH-domain (KH-domain type I)
superfamily: Eukaryotic type KH-domain (KH-domain type I)
family: Eukaryotic type KH-domain (KH-domain type I)
domain: Vigilin
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 51.7 bits (124), Expect = 2e-09
 Identities = 15/62 (24%), Positives = 25/62 (40%), Gaps = 2/62 (3%)

Query: 127 KLVIPATHCGSLIGKGGCKIKDIRDLSGANVQVASDMLPMSTERIVTVHGNPDTISQAIY 186
            + +       +IG  G  I+ I D    +++      P      VTV G P+ + +AI 
Sbjct: 13  DVPLDHRVHARIIGARGKAIRKIMDEFKVDIRFPQSGAPD--PNCVTVTGLPENVEEAID 70

Query: 187 QI 188
            I
Sbjct: 71  HI 72

>d2ctma1 d.51.1.1 (A:8-88) Vigilin {Human (Homo sapiens) [TaxId: 9606]} Length = 81

class: Alpha and beta proteins (a+b)
fold: Eukaryotic type KH-domain (KH-domain type I)
superfamily: Eukaryotic type KH-domain (KH-domain type I)
family: Eukaryotic type KH-domain (KH-domain type I)
domain: Vigilin
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 46.7 bits (111), Expect = 1e-07
 Identities = 13/71 (18%), Positives = 21/71 (29%)

Query: 285 DDFVETEIVLTDDIAGCVIGKAGSRLLEIRQISGAQINIHTGTESHKKMFHIQGCQEAVS 344
           +  V  ++ L   +   +IG  G  + +I       I              + G  E V 
Sbjct: 7   EQMVSEDVPLDHRVHARIIGARGKAIRKIMDEFKVDIRFPQSGAPDPNCVTVTGLPENVE 66

Query: 345 LAQYLINMCIE 355
            A   I    E
Sbjct: 67  EAIDHILNLEE 77

>d2ctma1 d.51.1.1 (A:8-88) Vigilin {Human (Homo sapiens) [TaxId: 9606]} Length = 81

class: Alpha and beta proteins (a+b)
fold: Eukaryotic type KH-domain (KH-domain type I)
superfamily: Eukaryotic type KH-domain (KH-domain type I)
family: Eukaryotic type KH-domain (KH-domain type I)
domain: Vigilin
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 37.1 bits (86), Expect = 3e-04
 Identities = 13/50 (26%), Positives = 22/50 (44%), Gaps = 1/50 (2%)

Query: 24 SVNVNEISCLIGPGGCIVRRLRKESGAKISITDGACPD-RIVTVSGSVDN 72
           ++    + +IG  G  +R++  E    I       PD   VTV+G  +N
Sbjct: 15 PLDHRVHARIIGARGKAIRKIMDEFKVDIRFPQSGAPDPNCVTVTGLPEN 64

>d2ba0a3 d.51.1.1 (A:136-219) Exosome complex RNA-binding protein 1, ECR1 {Archaeoglobus fulgidus [TaxId: 2234]} Length = 84

class: Alpha and beta proteins (a+b)
fold: Eukaryotic type KH-domain (KH-domain type I)
superfamily: Eukaryotic type KH-domain (KH-domain type I)
family: Eukaryotic type KH-domain (KH-domain type I)
domain: Exosome complex RNA-binding protein 1, ECR1
species: Archaeoglobus fulgidus [TaxId: 2234]

 Score = 48.6 bits (116), Expect = 3e-08
 Identities = 15/65 (23%), Positives = 26/65 (40%), Gaps = 7/65 (10%)

Query: 130 IPATHCGSLIGKGGCKIKDIRDLSGANVQVASDMLPMSTERIVTVHGNPDTISQAIYQIC 189
           I       +IGK G  IK ++      + V  +        ++ V+G+   +S A   I 
Sbjct: 7   INPARVPRVIGKKGSMIKLLKSELDVQIVVGQN-------GLIWVNGDRRKVSIAEEAIY 59

Query: 190 LVLIE 194
           L+  E
Sbjct: 60  LIEQE 64

>d2ba0a3 d.51.1.1 (A:136-219) Exosome complex RNA-binding protein 1, ECR1 {Archaeoglobus fulgidus [TaxId: 2234]} Length = 84

class: Alpha and beta proteins (a+b)
fold: Eukaryotic type KH-domain (KH-domain type I)
superfamily: Eukaryotic type KH-domain (KH-domain type I)
family: Eukaryotic type KH-domain (KH-domain type I)
domain: Exosome complex RNA-binding protein 1, ECR1
species: Archaeoglobus fulgidus [TaxId: 2234]

 Score = 41.6 bits (98), Expect = 8e-06
 Identities = 9/49 (18%), Positives = 23/49 (46%), Gaps = 4/49 (8%)

Query: 24 SVNVNEISCLIGPGGCIVRRLRKESGAKISITDGACPDRIVTVSGSVDN 72
          ++N   +  +IG  G +++ L+ E   +I +      + ++ V+G    
Sbjct: 6  AINPARVPRVIGKKGSMIKLLKSELDVQIVVGQ----NGLIWVNGDRRK 50

>d2ba0a3 d.51.1.1 (A:136-219) Exosome complex RNA-binding protein 1, ECR1 {Archaeoglobus fulgidus [TaxId: 2234]} Length = 84

class: Alpha and beta proteins (a+b)
fold: Eukaryotic type KH-domain (KH-domain type I)
superfamily: Eukaryotic type KH-domain (KH-domain type I)
family: Eukaryotic type KH-domain (KH-domain type I)
domain: Exosome complex RNA-binding protein 1, ECR1
species: Archaeoglobus fulgidus [TaxId: 2234]

 Score = 37.4 bits (87), Expect = 3e-04
 Identities = 13/56 (23%), Positives = 24/56 (42%), Gaps = 5/56 (8%)

Query: 300 GCVIGKAGSRLLEIRQISGAQINIHTGTESHKKMFHIQGCQEAVSLAQYLINMCIE 355
             VIGK GS +  ++     QI +         +  + G +  VS+A+  I +  +
Sbjct: 13  PRVIGKKGSMIKLLKSELDVQIVV-----GQNGLIWVNGDRRKVSIAEEAIYLIEQ 63

>d2ctja1 d.51.1.1 (A:8-89) Vigilin {Human (Homo sapiens) [TaxId: 9606]} Length = 82

class: Alpha and beta proteins (a+b)
fold: Eukaryotic type KH-domain (KH-domain type I)
superfamily: Eukaryotic type KH-domain (KH-domain type I)
family: Eukaryotic type KH-domain (KH-domain type I)
domain: Vigilin
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 47.9 bits (114), Expect = 4e-08
 Identities = 17/65 (26%), Positives = 29/65 (44%), Gaps = 2/65 (3%)

Query: 125 QLKLVIPATHCGSLIGKGGCKIKDIRDLSGANVQVASDMLPMSTERIVTVHGNPDTISQA 184
           ++++ IPA    SLIG  G  I+ I +  G  V +    +  S    V + G    + +A
Sbjct: 11  EVEVSIPAKLHNSLIGTKGRLIRSIMEECG-GVHI-HFPVEGSGSDTVVIRGPSSDVEKA 68

Query: 185 IYQIC 189
             Q+ 
Sbjct: 69  KKQLL 73

>d2ctja1 d.51.1.1 (A:8-89) Vigilin {Human (Homo sapiens) [TaxId: 9606]} Length = 82

class: Alpha and beta proteins (a+b)
fold: Eukaryotic type KH-domain (KH-domain type I)
superfamily: Eukaryotic type KH-domain (KH-domain type I)
family: Eukaryotic type KH-domain (KH-domain type I)
domain: Vigilin
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 41.0 bits (96), Expect = 1e-05
 Identities = 14/72 (19%), Positives = 25/72 (34%), Gaps = 2/72 (2%)

Query: 285 DDFVETEIVLTDDIAGCVIGKAGSRLLEIRQIS-GAQINIHTGTESHKKMFHIQGCQEAV 343
            +  E E+ +   +   +IG  G  +  I +   G  I+      S      I+G    V
Sbjct: 7   ANIAEVEVSIPAKLHNSLIGTKGRLIRSIMEECGGVHIHFPVE-GSGSDTVVIRGPSSDV 65

Query: 344 SLAQYLINMCIE 355
             A+  +    E
Sbjct: 66  EKAKKQLLHLAE 77

>d2ctja1 d.51.1.1 (A:8-89) Vigilin {Human (Homo sapiens) [TaxId: 9606]} Length = 82

class: Alpha and beta proteins (a+b)
fold: Eukaryotic type KH-domain (KH-domain type I)
superfamily: Eukaryotic type KH-domain (KH-domain type I)
family: Eukaryotic type KH-domain (KH-domain type I)
domain: Vigilin
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 39.8 bits (93), Expect = 3e-05
 Identities = 11/50 (22%), Positives = 19/50 (38%), Gaps = 1/50 (2%)

Query: 24 SVNVNEISCLIGPGGCIVRRLRKES-GAKISITDGACPDRIVTVSGSVDN 72
          S+     + LIG  G ++R + +E  G  I           V + G   +
Sbjct: 15 SIPAKLHNSLIGTKGRLIRSIMEECGGVHIHFPVEGSGSDTVVIRGPSSD 64

>d1e3ha4 d.52.3.1 (A:579-632) Polynucleotide phosphorylase/guanosine pentaphosphate synthase (PNPase/GPSI), domain 6 {Streptomyces antibioticus [TaxId: 1890]} Length = 54

class: Alpha and beta proteins (a+b)
fold: Alpha-lytic protease prodomain-like
superfamily: Prokaryotic type KH domain (KH-domain type II)
family: Prokaryotic type KH domain (KH-domain type II)
domain: Polynucleotide phosphorylase/guanosine pentaphosphate synthase (PNPase/GPSI), domain 6
species: Streptomyces antibioticus [TaxId: 1890]

 Score = 44.3 bits (105), Expect = 4e-07
 Identities = 11/45 (24%), Positives = 28/45 (62%), Gaps = 4/45 (8%)

Query: 25 VNVNEISCLIGPGGCIVRRLRKESGAKISITDGACPDRIVTVSGS 69
          + V++I  +IGP   ++ ++++++GA+I+I D    D  + +  +
Sbjct: 9  IPVDKIGEVIGPKRQMINQIQEDTGAEITIED----DGTIYIGAA 49

>d1e3ha4 d.52.3.1 (A:579-632) Polynucleotide phosphorylase/guanosine pentaphosphate synthase (PNPase/GPSI), domain 6 {Streptomyces antibioticus [TaxId: 1890]} Length = 54

class: Alpha and beta proteins (a+b)
fold: Alpha-lytic protease prodomain-like
superfamily: Prokaryotic type KH domain (KH-domain type II)
family: Prokaryotic type KH domain (KH-domain type II)
domain: Polynucleotide phosphorylase/guanosine pentaphosphate synthase (PNPase/GPSI), domain 6
species: Streptomyces antibioticus [TaxId: 1890]

 Score = 36.2 bits (84), Expect = 4e-04
 Identities = 11/40 (27%), Positives = 19/40 (47%)

Query: 123 PLQLKLVIPATHCGSLIGKGGCKIKDIRDLSGANVQVASD 162
           P  + + IP    G +IG     I  I++ +GA + +  D
Sbjct: 2   PRIITVKIPVDKIGEVIGPKRQMINQIQEDTGAEITIEDD 41

>d1tuaa1 d.51.1.1 (A:1-84) Hypothetical protein APE0754 {Aeropyrum pernix [TaxId: 56636]} Length = 84

class: Alpha and beta proteins (a+b)
fold: Eukaryotic type KH-domain (KH-domain type I)
superfamily: Eukaryotic type KH-domain (KH-domain type I)
family: Eukaryotic type KH-domain (KH-domain type I)
domain: Hypothetical protein APE0754
species: Aeropyrum pernix [TaxId: 56636]

 Score = 40.2 bits (94), Expect = 3e-05
 Identities = 7/38 (18%), Positives = 18/38 (47%)

Query: 125 QLKLVIPATHCGSLIGKGGCKIKDIRDLSGANVQVASD 162
           ++ + +     G++IG  G    +I   +G  + V ++
Sbjct: 4   RIYVKVKPERLGAVIGPRGEVKAEIMRRTGTVITVDTE 41

>d1tuaa1 d.51.1.1 (A:1-84) Hypothetical protein APE0754 {Aeropyrum pernix [TaxId: 56636]} Length = 84

class: Alpha and beta proteins (a+b)
fold: Eukaryotic type KH-domain (KH-domain type I)
superfamily: Eukaryotic type KH-domain (KH-domain type I)
family: Eukaryotic type KH-domain (KH-domain type I)
domain: Hypothetical protein APE0754
species: Aeropyrum pernix [TaxId: 56636]

 Score = 37.1 bits (86), Expect = 4e-04
 Identities = 7/31 (22%), Positives = 15/31 (48%)

Query: 24 SVNVNEISCLIGPGGCIVRRLRKESGAKISI 54
           V    +  +IGP G +   + + +G  I++
Sbjct: 8  KVKPERLGAVIGPRGEVKAEIMRRTGTVITV 38

>d2cpqa1 d.51.1.1 (A:212-289) Fragile X mental retardation syndrome related protein 1, FXR1 {Human (Homo sapiens) [TaxId: 9606]} Length = 78

class: Alpha and beta proteins (a+b)
fold: Eukaryotic type KH-domain (KH-domain type I)
superfamily: Eukaryotic type KH-domain (KH-domain type I)
family: Eukaryotic type KH-domain (KH-domain type I)
domain: Fragile X mental retardation syndrome related protein 1, FXR1
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 38.3 bits (89), Expect = 1e-04
 Identities = 16/66 (24%), Positives = 28/66 (42%), Gaps = 4/66 (6%)

Query: 291 EIVLTDDIAGCVIGKAGSRLLEIRQISGAQINIHTGTESHKKMFHIQGC-QEAVSLAQYL 349
           E V+ +D+ G  IG  GS + + R++ G         +     F I G   +AV  A+  
Sbjct: 11  EFVVREDLMGLAIGTHGSNIQQARKVPGVTAIE---LDEDTGTFRIYGESADAVKKARGF 67

Query: 350 INMCIE 355
           +    +
Sbjct: 68  LEFVED 73

>d2cpqa1 d.51.1.1 (A:212-289) Fragile X mental retardation syndrome related protein 1, FXR1 {Human (Homo sapiens) [TaxId: 9606]} Length = 78

class: Alpha and beta proteins (a+b)
fold: Eukaryotic type KH-domain (KH-domain type I)
superfamily: Eukaryotic type KH-domain (KH-domain type I)
family: Eukaryotic type KH-domain (KH-domain type I)
domain: Fragile X mental retardation syndrome related protein 1, FXR1
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 37.6 bits (87), Expect = 2e-04
 Identities = 11/67 (16%), Positives = 20/67 (29%), Gaps = 4/67 (5%)

Query: 122 QPLQLKLVIPATHCGSLIGKGGCKIKDIRDLSGANVQVASDMLPMSTERIVTVHGNPDTI 181
                + V+     G  IG  G  I+  R + G       +     T        + D +
Sbjct: 6   AAFHEEFVVREDLMGLAIGTHGSNIQQARKVPGVTAIELDED----TGTFRIYGESADAV 61

Query: 182 SQAIYQI 188
            +A   +
Sbjct: 62  KKARGFL 68

>d2cpqa1 d.51.1.1 (A:212-289) Fragile X mental retardation syndrome related protein 1, FXR1 {Human (Homo sapiens) [TaxId: 9606]} Length = 78

class: Alpha and beta proteins (a+b)
fold: Eukaryotic type KH-domain (KH-domain type I)
superfamily: Eukaryotic type KH-domain (KH-domain type I)
family: Eukaryotic type KH-domain (KH-domain type I)
domain: Fragile X mental retardation syndrome related protein 1, FXR1
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 35.6 bits (82), Expect = 0.001
 Identities = 9/45 (20%), Positives = 15/45 (33%), Gaps = 2/45 (4%)

Query: 25 VNVNEISCLIGPGGCIVRRLRKESGAKISITDGACPDRIVTVSGS 69
          V  + +   IG  G  +++ RK  G      D         + G 
Sbjct: 14 VREDLMGLAIGTHGSNIQQARKVPGVTAIELD--EDTGTFRIYGE 56

>d2z0sa2 d.51.1.1 (A:148-234) Exosome complex RNA-binding protein 1, ECR1 {Aeropyrum pernix [TaxId: 56636]} Length = 87

class: Alpha and beta proteins (a+b)
fold: Eukaryotic type KH-domain (KH-domain type I)
superfamily: Eukaryotic type KH-domain (KH-domain type I)
family: Eukaryotic type KH-domain (KH-domain type I)
domain: Exosome complex RNA-binding protein 1, ECR1
species: Aeropyrum pernix [TaxId: 56636]

 Score = 37.4 bits (87), Expect = 2e-04
 Identities = 5/46 (10%), Positives = 20/46 (43%), Gaps = 4/46 (8%)

Query: 24 SVNVNEISCLIGPGGCIVRRLRKESGAKISITDGACPDRIVTVSGS 69
           ++  ++  +IG    +++ L +++  KI +      +  + +   
Sbjct: 6  EISPAKVPRVIGRKMSMLKTLEEKTECKIFVAR----NGRIHLECP 47

>d2z0sa2 d.51.1.1 (A:148-234) Exosome complex RNA-binding protein 1, ECR1 {Aeropyrum pernix [TaxId: 56636]} Length = 87

class: Alpha and beta proteins (a+b)
fold: Eukaryotic type KH-domain (KH-domain type I)
superfamily: Eukaryotic type KH-domain (KH-domain type I)
family: Eukaryotic type KH-domain (KH-domain type I)
domain: Exosome complex RNA-binding protein 1, ECR1
species: Aeropyrum pernix [TaxId: 56636]

 Score = 36.2 bits (84), Expect = 8e-04
 Identities = 12/59 (20%), Positives = 22/59 (37%), Gaps = 6/59 (10%)

Query: 130 IPATHCGSLIGKGGCKIKDIRDLSGANVQVASDMLPMSTERIVTVHGNPDTISQAIYQI 188
           I       +IG+    +K + + +   + VA +       RI     N D  + A+  I
Sbjct: 7   ISPAKVPRVIGRKMSMLKTLEEKTECKIFVARN------GRIHLECPNEDLEAIAVMAI 59

>d2je6i3 d.51.1.1 (I:153-221) Exosome complex RNA-binding protein 1, ECR1 {Sulfolobus solfataricus [TaxId: 2287]} Length = 69

class: Alpha and beta proteins (a+b)
fold: Eukaryotic type KH-domain (KH-domain type I)
superfamily: Eukaryotic type KH-domain (KH-domain type I)
family: Eukaryotic type KH-domain (KH-domain type I)
domain: Exosome complex RNA-binding protein 1, ECR1
species: Sulfolobus solfataricus [TaxId: 2287]

 Score = 35.9 bits (83), Expect = 7e-04
 Identities = 6/46 (13%), Positives = 17/46 (36%), Gaps = 4/46 (8%)

Query: 24 SVNVNEISCLIGPGGCIVRRLRKESGAKISITDGACPDRIVTVSGS 69
           +   ++  +IG    +   L  +SG  I + +    +  +  +  
Sbjct: 6  DIMPVKVPRVIGKNKSMYETLTSKSGCSIFVAN----NGRIWATCP 47

>d2je6i3 d.51.1.1 (I:153-221) Exosome complex RNA-binding protein 1, ECR1 {Sulfolobus solfataricus [TaxId: 2287]} Length = 69

class: Alpha and beta proteins (a+b)
fold: Eukaryotic type KH-domain (KH-domain type I)
superfamily: Eukaryotic type KH-domain (KH-domain type I)
family: Eukaryotic type KH-domain (KH-domain type I)
domain: Exosome complex RNA-binding protein 1, ECR1
species: Sulfolobus solfataricus [TaxId: 2287]

 Score = 35.5 bits (82), Expect = 8e-04
 Identities = 12/59 (20%), Positives = 21/59 (35%), Gaps = 6/59 (10%)

Query: 130 IPATHCGSLIGKGGCKIKDIRDLSGANVQVASDMLPMSTERIVTVHGNPDTISQAIYQI 188
           I       +IGK     + +   SG ++ VA++       RI     +  +    I  I
Sbjct: 7   IMPVKVPRVIGKNKSMYETLTSKSGCSIFVANN------GRIWATCPSRFSEEILIEAI 59

>d2ctfa1 d.51.1.1 (A:7-96) Vigilin {Human (Homo sapiens) [TaxId: 9606]} Length = 90

class: Alpha and beta proteins (a+b)
fold: Eukaryotic type KH-domain (KH-domain type I)
superfamily: Eukaryotic type KH-domain (KH-domain type I)
family: Eukaryotic type KH-domain (KH-domain type I)
domain: Vigilin
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 35.2 bits (81), Expect = 0.002
 Identities = 14/62 (22%), Positives = 23/62 (37%), Gaps = 5/62 (8%)

Query: 127 KLVIPATHCGSLIGKGGCKIKDIRDLSGANVQVASDMLPMSTERIVTVHGNPDTISQAIY 186
            +  P+     +IGK G  +  I       V +         E  +T+ G  + +S A  
Sbjct: 24  SVAAPSWLHRFIIGKKGQNLAKITQQMP-KVHIEFTE----GEDKITLEGPTEDVSVAQE 78

Query: 187 QI 188
           QI
Sbjct: 79  QI 80

Homologous Domains Detected by HHsearch

Original result of HHsearch against SCOP70(version1.75) database

ID	Length	Definition	Probability
Query	433
d1wvna1	70	Poly(RC)-binding protein 1 {Human (Homo sapiens) [	99.66
d1zzka1	75	HnRNP K, KH3 {Human (Homo sapiens) [TaxId: 9606]}	99.66
d1j4wa2	71	Far upstream binding element, FBP {Human (Homo sap	99.64
d2axya1	71	Poly(RC)-binding protein 2 {Human (Homo sapiens) [	99.63
d1j4wa1	74	Far upstream binding element, FBP {Human (Homo sap	99.63
d1dtja_	74	Neuro-oncological ventral antigen 2, nova-2, KH3 {	99.62
d2axya1	71	Poly(RC)-binding protein 2 {Human (Homo sapiens) [	99.61
d1x4ma1	81	Far upstream binding element, FBP {Mouse (Mus musc	99.61
d1x4na1	79	Far upstream binding element, FBP {Mouse (Mus musc	99.59
d1we8a_	104	Tudor and KH domain containing protein, Tdrkh {Mou	99.55
d1zzka1	75	HnRNP K, KH3 {Human (Homo sapiens) [TaxId: 9606]}	99.52
d1wvna1	70	Poly(RC)-binding protein 1 {Human (Homo sapiens) [	99.52
d1dtja_	74	Neuro-oncological ventral antigen 2, nova-2, KH3 {	99.51
d1j4wa2	71	Far upstream binding element, FBP {Human (Homo sap	99.51
d2ctma1	81	Vigilin {Human (Homo sapiens) [TaxId: 9606]}	99.51
d2ctea1	81	Vigilin {Human (Homo sapiens) [TaxId: 9606]}	99.5
d2ctla1	84	Vigilin {Human (Homo sapiens) [TaxId: 9606]}	99.49
d1x4ma1	81	Far upstream binding element, FBP {Mouse (Mus musc	99.49
d1j4wa1	74	Far upstream binding element, FBP {Human (Homo sap	99.48
d1viga_	71	Vigilin {Human (Homo sapiens) [TaxId: 9606]}	99.47
d2ctja1	82	Vigilin {Human (Homo sapiens) [TaxId: 9606]}	99.46
d1x4na1	79	Far upstream binding element, FBP {Mouse (Mus musc	99.44
d1we8a_	104	Tudor and KH domain containing protein, Tdrkh {Mou	99.44
d2ctla1	84	Vigilin {Human (Homo sapiens) [TaxId: 9606]}	99.42
d2ctea1	81	Vigilin {Human (Homo sapiens) [TaxId: 9606]}	99.39
d2ctka1	91	Vigilin {Human (Homo sapiens) [TaxId: 9606]}	99.38
d1viga_	71	Vigilin {Human (Homo sapiens) [TaxId: 9606]}	99.36
d2ctma1	81	Vigilin {Human (Homo sapiens) [TaxId: 9606]}	99.36
d2ctja1	82	Vigilin {Human (Homo sapiens) [TaxId: 9606]}	99.35
d2cpqa1	78	Fragile X mental retardation syndrome related prot	99.28
d2ctka1	91	Vigilin {Human (Homo sapiens) [TaxId: 9606]}	99.26
d2ctfa1	90	Vigilin {Human (Homo sapiens) [TaxId: 9606]}	99.26
d2ba0a3	84	Exosome complex RNA-binding protein 1, ECR1 {Archa	99.24
d2ctfa1	90	Vigilin {Human (Homo sapiens) [TaxId: 9606]}	99.23
d2ba0a3	84	Exosome complex RNA-binding protein 1, ECR1 {Archa	99.1
d2cpqa1	78	Fragile X mental retardation syndrome related prot	99.06
d1tuaa1	84	Hypothetical protein APE0754 {Aeropyrum pernix [Ta	98.95
d2je6i3	69	Exosome complex RNA-binding protein 1, ECR1 {Sulfo	98.85
d2z0sa2	87	Exosome complex RNA-binding protein 1, ECR1 {Aerop	98.79
d1tuaa1	84	Hypothetical protein APE0754 {Aeropyrum pernix [Ta	98.77
d2je6i3	69	Exosome complex RNA-binding protein 1, ECR1 {Sulfo	98.74
d2z0sa2	87	Exosome complex RNA-binding protein 1, ECR1 {Aerop	98.61
d1e3ha4	54	Polynucleotide phosphorylase/guanosine pentaphosph	98.61
d1tuaa2	104	Hypothetical protein APE0754 {Aeropyrum pernix [Ta	98.55
d1e3ha4	54	Polynucleotide phosphorylase/guanosine pentaphosph	98.49
d1tuaa2	104	Hypothetical protein APE0754 {Aeropyrum pernix [Ta	98.39
d1k1ga_	122	RNA splicing factor 1 {Human (Homo sapiens) [TaxId	98.1
d2bl5a1	134	Quaking protein A (Xqua) {African clawed frog (Xen	98.01
d1k1ga_	122	RNA splicing factor 1 {Human (Homo sapiens) [TaxId	97.98
d2bl5a1	134	Quaking protein A (Xqua) {African clawed frog (Xen	97.57
d1hh2p3	68	Transcription factor NusA, C-terminal domains {The	95.33
d2asba3	67	Transcription factor NusA, C-terminal domains {Myc	95.31
d2asba3	67	Transcription factor NusA, C-terminal domains {Myc	94.7
d1hh2p3	68	Transcription factor NusA, C-terminal domains {The	94.64
d1wh9a_	92	Ribosomal protein S3 N-terminal domain {Mouse (Mus	87.15
d2ja9a2	85	Ribosomal RNA-processing protein 40, RRP40 {Saccha	84.46
d1egaa2	113	GTPase Era C-terminal domain {Escherichia coli [Ta	84.11

>d1wvna1 d.51.1.1 (A:5-74) Poly(RC)-binding protein 1 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Eukaryotic type KH-domain (KH-domain type I)
superfamily: Eukaryotic type KH-domain (KH-domain type I)
family: Eukaryotic type KH-domain (KH-domain type I)
domain: Poly(RC)-binding protein 1
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.66  E-value=5.8e-17  Score=120.97  Aligned_cols=68  Identities=41%  Similarity=0.709  Sum_probs=64.1

Q ss_pred             ceEEEEEeCcccccccccCCCchHHHHHhHhCCeEEEccCCC-CCceEEEEEeCHHHHHHHHHHHHHHH
Q psy11929        287 FVETEIVLTDDIAGCVIGKAGSRLLEIRQISGAQINIHTGTE-SHKKMFHIQGCQEAVSLAQYLINMCI  354 (433)
Q Consensus       287 ~~t~~i~VP~~~vG~IIGkgG~~Ik~I~~~sGA~I~I~~~~~-~~er~V~IsGt~e~v~~A~~lI~~~i  354 (433)
                      +.|.+|.||..++|+||||+|.+|++|++.|||+|.|+++.+ +++|.|+|+|+++++++|+.+|+++|
T Consensus         1 q~T~~i~VP~~~vg~iIGk~G~~I~~I~~~tga~I~i~~~~~~~~~r~v~I~G~~~~v~~A~~~I~~~i   69 (70)
T d1wvna1           1 QTTHELTIPNNLIGCIIGRQGANINEIRQMSGAQIKIANPVEGSSGRQVTITGSAASISLAQYLINARL   69 (70)
T ss_dssp             CEEEEEEEEGGGHHHHHCGGGHHHHHHHHHHCCEEEECCCCTTCSEEEEEEEECHHHHHHHHHHHHHHT
T ss_pred             CeEEEEEEChHhcceeECCCChHHHHHHHHcCcEEEEcCCCCCCCcEEEEEEeCHHHHHHHHHHHHHHc
Confidence            357899999999999999999999999999999999988776 88999999999999999999999886

>d1zzka1 d.51.1.1 (A:11-85) HnRNP K, KH3 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Eukaryotic type KH-domain (KH-domain type I)
superfamily: Eukaryotic type KH-domain (KH-domain type I)
family: Eukaryotic type KH-domain (KH-domain type I)
domain: HnRNP K, KH3
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.66  E-value=1.4e-16  Score=120.56  Aligned_cols=72  Identities=35%  Similarity=0.622  Sum_probs=67.3

Q ss_pred             CceEEEEEeCcccccccccCCCchHHHHHhHhCCeEEEccCCC-CCceEEEEEeCHHHHHHHHHHHHHHHHhc
Q psy11929        286 DFVETEIVLTDDIAGCVIGKAGSRLLEIRQISGAQINIHTGTE-SHKKMFHIQGCQEAVSLAQYLINMCIELQ  357 (433)
Q Consensus       286 ~~~t~~i~VP~~~vG~IIGkgG~~Ik~I~~~sGA~I~I~~~~~-~~er~V~IsGt~e~v~~A~~lI~~~i~~~  357 (433)
                      ...|.+|.||..++|+||||+|++|++|+++|||+|+|+++.+ +.+|.|+|+|+++++++|+.+|+++|++.
T Consensus         2 p~~t~~i~VP~~~vg~iIG~~G~~I~~I~~~sga~I~i~~~~~~~~~r~i~I~G~~~~v~~A~~~I~~~i~e~   74 (75)
T d1zzka1           2 PIITTQVTIPKDLAGSIIGKGGQRIKQIRHESGASIKIDEPLEGSEDRIITITGTQDQIQNAQYLLQNSVKQY   74 (75)
T ss_dssp             CCEEEEEEEETTTGGGGTCGGGHHHHHHHHHHCCEEEECCTTSCSSEEEEEEEECHHHHHHHHHHHHHHHHHH
T ss_pred             CcEEEEEEEChHhcCeeECCCCchHHHHHhhcCCeEEEccCCCCCCceEEEEEeCHHHHHHHHHHHHHHHHhc
Confidence            3578899999999999999999999999999999999988776 88999999999999999999999999863

>d1j4wa2 d.51.1.1 (A:104-174) Far upstream binding element, FBP {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Eukaryotic type KH-domain (KH-domain type I)
superfamily: Eukaryotic type KH-domain (KH-domain type I)
family: Eukaryotic type KH-domain (KH-domain type I)
domain: Far upstream binding element, FBP
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.64  E-value=1.2e-16  Score=119.52  Aligned_cols=66  Identities=30%  Similarity=0.519  Sum_probs=60.9

Q ss_pred             EEEEEeCcccccccccCCCchHHHHHhHhCCeEEEccCCC----CCceEEEEEeCHHHHHHHHHHHHHHH
Q psy11929        289 ETEIVLTDDIAGCVIGKAGSRLLEIRQISGAQINIHTGTE----SHKKMFHIQGCQEAVSLAQYLINMCI  354 (433)
Q Consensus       289 t~~i~VP~~~vG~IIGkgG~~Ik~I~~~sGA~I~I~~~~~----~~er~V~IsGt~e~v~~A~~lI~~~i  354 (433)
                      +++|.||..++|+||||+|++|++|++.|||+|+|++..+    +.+|.|+|+|++++|++|+.+|+++|
T Consensus         2 ~~~~~IP~~~vg~IIGk~G~~Ik~I~~~sga~I~i~~~~~~~~~~~~r~v~I~G~~~~v~~A~~~I~e~i   71 (71)
T d1j4wa2           2 EFNFIVPTGKTGLIIGKGGETIKSISQQSGARIELQRNPPPNADPNMKLFTIRGTPQQIDYARQLIEEKI   71 (71)
T ss_dssp             EEEEEEETTTHHHHHCGGGHHHHHHHHHHCCEEEEECCCTTTSCTTEEEEEEECCHHHHHHHHHHHHHHC
T ss_pred             EEEEEEChHhcceEECCCCcChHHHHhhcCcEEEEeecCCCCCCCCeEEEEEEeCHHHHHHHHHHHHhhC
Confidence            4689999999999999999999999999999999986544    67899999999999999999999874

>d2axya1 d.51.1.1 (A:11-81) Poly(RC)-binding protein 2 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Eukaryotic type KH-domain (KH-domain type I)
superfamily: Eukaryotic type KH-domain (KH-domain type I)
family: Eukaryotic type KH-domain (KH-domain type I)
domain: Poly(RC)-binding protein 2
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.63  E-value=1e-16  Score=119.91  Aligned_cols=70  Identities=37%  Similarity=0.801  Sum_probs=66.6

Q ss_pred             ceEEEEEEeccCCcccccceeeecCchHHHHHHHHhCCeEEEeCCCCCcceEEEecccCCCCCCccccCCCCCccccchH
Q psy11929         13 TLITMRCLFHSSVNVNEISCLIGPGGCIVRRLRKESGAKISITDGACPDRIVTVSGSVDNSSTSSVETGYPGHTLWVTSV   92 (433)
Q Consensus        13 ~~~~~rilvp~~~~~~~vg~IIGk~G~~Ik~I~~~tga~I~v~~~~~~eRvv~I~G~~~~~~~~~v~~~~~~~~~~~~a~   92 (433)
                      ..+++||+||.    +++|+||||+|++|++|+++|||+|+|++.+.++|+|+|+|+++                     
T Consensus         2 ~~vt~~i~vp~----~~~g~IIGk~G~~I~~I~~~tga~I~i~~~~~~er~v~I~G~~~---------------------   56 (71)
T d2axya1           2 VTLTIRLLMHG----KEVGSIIGKKGESVKKMREESGARINISEGNCPERIITLAGPTN---------------------   56 (71)
T ss_dssp             CCEEEEEEEEH----HHHHHHHCGGGHHHHHHHHHHCCEEEECSSCCSEEEEEEEECHH---------------------
T ss_pred             ccEEEEEEECH----HHcCeEECCCChhHHHHHHHhCCEEEEcCCCCCcceEEEEECHH---------------------
Confidence            46899999999    99999999999999999999999999999888999999999999                     


Q ss_pred             HHHHHHHHHHHhhhhh
Q psy11929         93 DNVCTAYNFMCRSLED  108 (433)
Q Consensus        93 ~~v~~A~~~I~~~~~~  108 (433)
                       ++.+|+.+|.++++|
T Consensus        57 -~v~~A~~~I~~~l~E   71 (71)
T d2axya1          57 -AIFKAFAMIIDKLEE   71 (71)
T ss_dssp             -HHHHHHHHHHHHHHC
T ss_pred             -HHHHHHHHHHHHhcC
Confidence             999999999998764

>d1j4wa1 d.51.1.1 (A:1-74) Far upstream binding element, FBP {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Eukaryotic type KH-domain (KH-domain type I)
superfamily: Eukaryotic type KH-domain (KH-domain type I)
family: Eukaryotic type KH-domain (KH-domain type I)
domain: Far upstream binding element, FBP
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.63  E-value=1.7e-16  Score=119.87  Aligned_cols=71  Identities=17%  Similarity=0.263  Sum_probs=66.2

Q ss_pred             ceEEEEEeCcccccccccCCCchHHHHHhHhCCeEEEccCCC-CCceEEEEEeCHHHHHHHHHHHHHHHHhc
Q psy11929        287 FVETEIVLTDDIAGCVIGKAGSRLLEIRQISGAQINIHTGTE-SHKKMFHIQGCQEAVSLAQYLINMCIELQ  357 (433)
Q Consensus       287 ~~t~~i~VP~~~vG~IIGkgG~~Ik~I~~~sGA~I~I~~~~~-~~er~V~IsGt~e~v~~A~~lI~~~i~~~  357 (433)
                      ..+++|.||..++|+||||+|++|++|+++|||+|+|++..+ +.+|.|+|+|+++++++|+.+|.++|++.
T Consensus         2 ~~~~~i~VP~~~vg~iIGk~G~~I~~I~~~tga~I~i~~~~~~~~~r~v~I~G~~~~v~~A~~~I~~~i~~~   73 (74)
T d1j4wa1           2 SHMIDVPIPRFAVGIVIGRNGEMIKKIQNDAGVRIQFKPDDGTTPERIAQITGPPDRAQHAAEIITDLLRSV   73 (74)
T ss_dssp             CEEEEEEEEHHHHHHHHCGGGHHHHHHHHHHCCEEEEECCTTSCSEEEEEEEECHHHHHHHHHHHHHHHHHH
T ss_pred             CeEEEEEeCHHHCCeeECCCCcHHHHHHHHcCCEEEeccCCCCCCeeEEEEEeCHHHHHHHHHHHHHHHHhc
Confidence            357899999999999999999999999999999999998776 78999999999999999999999999763

>d1dtja_ d.51.1.1 (A:) Neuro-oncological ventral antigen 2, nova-2, KH3 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Eukaryotic type KH-domain (KH-domain type I)
superfamily: Eukaryotic type KH-domain (KH-domain type I)
family: Eukaryotic type KH-domain (KH-domain type I)
domain: Neuro-oncological ventral antigen 2, nova-2, KH3
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.62  E-value=3.3e-16  Score=118.17  Aligned_cols=67  Identities=30%  Similarity=0.573  Sum_probs=62.3

Q ss_pred             eEEEEEeCcccccccccCCCchHHHHHhHhCCeEEEccCCC----CCceEEEEEeCHHHHHHHHHHHHHHH
Q psy11929        288 VETEIVLTDDIAGCVIGKAGSRLLEIRQISGAQINIHTGTE----SHKKMFHIQGCQEAVSLAQYLINMCI  354 (433)
Q Consensus       288 ~t~~i~VP~~~vG~IIGkgG~~Ik~I~~~sGA~I~I~~~~~----~~er~V~IsGt~e~v~~A~~lI~~~i  354 (433)
                      .+.+|.||..++|+||||+|++|++|++.|||+|+|++..+    +.+|.|+|+|+++++++|+.+|+++|
T Consensus         3 ~~i~i~VP~~~vg~iIGk~G~~Ik~I~~~sga~I~i~~~~~~~~~~~~r~v~I~G~~~~v~~A~~~I~~~i   73 (74)
T d1dtja_           3 ELVEMAVPENLVGAILGKGGKTLVEYQELTGARIQISKKGEFLPGTRNRRVTITGSPAATQAAQYLISQRV   73 (74)
T ss_dssp             EEEEEEEETTTHHHHHCSTTHHHHHHHHHHCCEEEECCTTCCSTTCCEEEEEEEESHHHHHHHHHHHHHHC
T ss_pred             EEEEEEeCHHHcceeECCCChhHHHHHHHcCCEEEEccCCCCCCCCCceEEEEEeCHHHHHHHHHHHHHHc
Confidence            46799999999999999999999999999999999987654    67899999999999999999999876

>d2axya1 d.51.1.1 (A:11-81) Poly(RC)-binding protein 2 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Eukaryotic type KH-domain (KH-domain type I)
superfamily: Eukaryotic type KH-domain (KH-domain type I)
family: Eukaryotic type KH-domain (KH-domain type I)
domain: Poly(RC)-binding protein 2
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.61  E-value=3e-16  Score=117.34  Aligned_cols=69  Identities=26%  Similarity=0.415  Sum_probs=64.8

Q ss_pred             ceEEEEEeCcccccccccCCCchHHHHHhHhCCeEEEccCCCCCceEEEEEeCHHHHHHHHHHHHHHHHh
Q psy11929        287 FVETEIVLTDDIAGCVIGKAGSRLLEIRQISGAQINIHTGTESHKKMFHIQGCQEAVSLAQYLINMCIEL  356 (433)
Q Consensus       287 ~~t~~i~VP~~~vG~IIGkgG~~Ik~I~~~sGA~I~I~~~~~~~er~V~IsGt~e~v~~A~~lI~~~i~~  356 (433)
                      .++.+|.||..++|+||||+|.+|++|++.|||+|+|+++. ..+|.|+|+|+++++.+|+.+|.++|++
T Consensus         3 ~vt~~i~vp~~~~g~IIGk~G~~I~~I~~~tga~I~i~~~~-~~er~v~I~G~~~~v~~A~~~I~~~l~E   71 (71)
T d2axya1           3 TLTIRLLMHGKEVGSIIGKKGESVKKMREESGARINISEGN-CPERIITLAGPTNAIFKAFAMIIDKLEE   71 (71)
T ss_dssp             CEEEEEEEEHHHHHHHHCGGGHHHHHHHHHHCCEEEECSSC-CSEEEEEEEECHHHHHHHHHHHHHHHHC
T ss_pred             cEEEEEEECHHHcCeEECCCChhHHHHHHHhCCEEEEcCCC-CCcceEEEEECHHHHHHHHHHHHHHhcC
Confidence            56889999999999999999999999999999999998866 6789999999999999999999999863

>d1x4ma1 d.51.1.1 (A:8-88) Far upstream binding element, FBP {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: Eukaryotic type KH-domain (KH-domain type I)
superfamily: Eukaryotic type KH-domain (KH-domain type I)
family: Eukaryotic type KH-domain (KH-domain type I)
domain: Far upstream binding element, FBP
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.61  E-value=4.9e-16  Score=119.31  Aligned_cols=72  Identities=24%  Similarity=0.302  Sum_probs=66.5

Q ss_pred             CceEEEEEeCcccccccccCCCchHHHHHhHhCCeEEEccCCC---CCceEEEEEeCHHHHHHHHHHHHHHHHhc
Q psy11929        286 DFVETEIVLTDDIAGCVIGKAGSRLLEIRQISGAQINIHTGTE---SHKKMFHIQGCQEAVSLAQYLINMCIELQ  357 (433)
Q Consensus       286 ~~~t~~i~VP~~~vG~IIGkgG~~Ik~I~~~sGA~I~I~~~~~---~~er~V~IsGt~e~v~~A~~lI~~~i~~~  357 (433)
                      ...+.+|.||..++|+||||+|++|++|+++|||+|+|++..+   +.+|.|+|+|++++|++|+.+|.++|.++
T Consensus         6 ~~~~~~i~Vp~~~~g~iIGk~G~~Ik~I~~~tga~I~i~~~~~~~~~~~r~v~I~G~~~~v~~A~~~I~~~i~e~   80 (81)
T d1x4ma1           6 GNAVQEIMIPASKAGLVIGKGGETIKQLQERAGVKMVMIQDGPQNTGADKPLRITGDPYKVQQAKEMVLELIRDQ   80 (81)
T ss_dssp             CCEEEEEEECHHHHHHHSCSSSSHHHHHHHHHTSEEEECCSCCCSSCSCEEEEEEECTTTHHHHHHHHHHHHCCC
T ss_pred             ccEEEEEEECHHHcCeeECCCCchHHHHHHHhCCeEEEccCCCCCCCCceEEEEEeCHHHHHHHHHHHHHHHHhc
Confidence            5789999999999999999999999999999999999987543   77999999999999999999999999653

>d1x4na1 d.51.1.1 (A:8-86) Far upstream binding element, FBP {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: Eukaryotic type KH-domain (KH-domain type I)
superfamily: Eukaryotic type KH-domain (KH-domain type I)
family: Eukaryotic type KH-domain (KH-domain type I)
domain: Far upstream binding element, FBP
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.59  E-value=1.5e-15  Score=116.05  Aligned_cols=72  Identities=25%  Similarity=0.438  Sum_probs=67.7

Q ss_pred             CceEEEEEeCcccccccccCCCchHHHHHhHhCCeEEEccCCC-CCceEEEEEeCHHHHHHHHHHHHHHHHhc
Q psy11929        286 DFVETEIVLTDDIAGCVIGKAGSRLLEIRQISGAQINIHTGTE-SHKKMFHIQGCQEAVSLAQYLINMCIELQ  357 (433)
Q Consensus       286 ~~~t~~i~VP~~~vG~IIGkgG~~Ik~I~~~sGA~I~I~~~~~-~~er~V~IsGt~e~v~~A~~lI~~~i~~~  357 (433)
                      ...+.+|.||..++|+|||++|.+|++|++.|||+|+|+++.+ +.+|.|+|+|++++|++|+.+|.++|++.
T Consensus         6 ~~~t~~i~IP~~~~g~iIG~~G~~i~~I~~~tg~~I~i~~~~~~~~~r~v~I~G~~~~v~~A~~~I~~~i~e~   78 (79)
T d1x4na1           6 SVMTEEYKVPDGMVGFIIGRGGEQISRIQQESGCKIQIAPDSGGLPERSCMLTGTPESVQSAKRLLDQIVEKG   78 (79)
T ss_dssp             CCEEEEEEEEHHHHHHHHCSSSHHHHHHHHHSCCEEEECSCCTTCSEEEEEEEECHHHHHHHHHHHHHHHHHT
T ss_pred             CcEEEEEEEChHhhcceECCCchhHHHHHHHhCCEEEEcCCCCCCCceEEEEEeCHHHHHHHHHHHHHHHHcc
Confidence            4688999999999999999999999999999999999998776 88999999999999999999999999863

>d1we8a_ d.51.1.1 (A:) Tudor and KH domain containing protein, Tdrkh {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: Eukaryotic type KH-domain (KH-domain type I)
superfamily: Eukaryotic type KH-domain (KH-domain type I)
family: Eukaryotic type KH-domain (KH-domain type I)
domain: Tudor and KH domain containing protein, Tdrkh
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.55  E-value=6.3e-15  Score=118.51  Aligned_cols=74  Identities=24%  Similarity=0.359  Sum_probs=67.5

Q ss_pred             CCceEEEEEeCcccccccccCCCchHHHHHhHhCCeEEEccCCC---CCceEEEEEeCHHHHHHHHHHHHHHHHhcc
Q psy11929        285 DDFVETEIVLTDDIAGCVIGKAGSRLLEIRQISGAQINIHTGTE---SHKKMFHIQGCQEAVSLAQYLINMCIELQK  358 (433)
Q Consensus       285 ~~~~t~~i~VP~~~vG~IIGkgG~~Ik~I~~~sGA~I~I~~~~~---~~er~V~IsGt~e~v~~A~~lI~~~i~~~~  358 (433)
                      ...++.+|.||..++|+||||+|.+|++|++.|||+|+|++..+   ..+|.|+|+|++++|++|+.+|+++|.+..
T Consensus        12 ~~~v~~~i~IP~~~vg~vIGk~G~~Ik~I~~~tga~I~i~~~~~~~~~~~r~v~I~G~~~~v~~A~~~I~~~i~e~~   88 (104)
T d1we8a_          12 NTPVFEQLSVPQRSVGRIIGRGGETIRSICKASGAKITCDKESEGTLLLSRLIKISGTQKEVAAAKHLILEKVSEDE   88 (104)
T ss_dssp             SCEEEEEEEEETTTHHHHHTTTSHHHHHHHHHHCCEEEECCSSCCSSSSEEEEEEEEEHHHHHHHHHHHHHHHHHHH
T ss_pred             CCCEEEEEEECHHHhcceECCCCcchHHHHHHcCCEEEECCCCCCCCCCccEEEEEeCHHHHHHHHHHHHHHHhCcH
Confidence            35678899999999999999999999999999999999987654   578999999999999999999999997653

>d1zzka1 d.51.1.1 (A:11-85) HnRNP K, KH3 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Eukaryotic type KH-domain (KH-domain type I)
superfamily: Eukaryotic type KH-domain (KH-domain type I)
family: Eukaryotic type KH-domain (KH-domain type I)
domain: HnRNP K, KH3
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.52  E-value=2e-14  Score=108.48  Aligned_cols=72  Identities=36%  Similarity=0.589  Sum_probs=66.4

Q ss_pred             CCeEEEEEeccCcccceecCCchhHHHHHHhhCceEEeccCCCCCCCccEEEEEccHHHHHHHHHHHHHHHHh
Q psy11929        122 QPLQLKLVIPATHCGSLIGKGGCKIKDIRDLSGANVQVASDMLPMSTERIVTVHGNPDTISQAIYQICLVLIE  194 (433)
Q Consensus       122 ~~~~~~l~ip~~~vg~iIGk~G~~Ik~I~~~sga~I~i~~~~~~~~~er~v~I~G~~~~v~~A~~~I~~~l~e  194 (433)
                      +.++.++.||..++|+|||++|++|++|+++|||+|.+.++ .+.+.+|.|+|+|++++|.+|+.+|.+++++
T Consensus         2 p~~t~~i~VP~~~vg~iIG~~G~~I~~I~~~sga~I~i~~~-~~~~~~r~i~I~G~~~~v~~A~~~I~~~i~e   73 (75)
T d1zzka1           2 PIITTQVTIPKDLAGSIIGKGGQRIKQIRHESGASIKIDEP-LEGSEDRIITITGTQDQIQNAQYLLQNSVKQ   73 (75)
T ss_dssp             CCEEEEEEEETTTGGGGTCGGGHHHHHHHHHHCCEEEECCT-TSCSSEEEEEEEECHHHHHHHHHHHHHHHHH
T ss_pred             CcEEEEEEEChHhcCeeECCCCchHHHHHhhcCCeEEEccC-CCCCCceEEEEEeCHHHHHHHHHHHHHHHHh
Confidence            35788999999999999999999999999999999999753 4567899999999999999999999999987

>d1wvna1 d.51.1.1 (A:5-74) Poly(RC)-binding protein 1 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Eukaryotic type KH-domain (KH-domain type I)
superfamily: Eukaryotic type KH-domain (KH-domain type I)
family: Eukaryotic type KH-domain (KH-domain type I)
domain: Poly(RC)-binding protein 1
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.52  E-value=6.6e-15  Score=109.58  Aligned_cols=67  Identities=30%  Similarity=0.468  Sum_probs=62.3

Q ss_pred             eEEEEEEeccCCcccccceeeecCchHHHHHHHHhCCeEEEeCC--CCCcceEEEecccCCCCCCccccCCCCCccccch
Q psy11929         14 LITMRCLFHSSVNVNEISCLIGPGGCIVRRLRKESGAKISITDG--ACPDRIVTVSGSVDNSSTSSVETGYPGHTLWVTS   91 (433)
Q Consensus        14 ~~~~rilvp~~~~~~~vg~IIGk~G~~Ik~I~~~tga~I~v~~~--~~~eRvv~I~G~~~~~~~~~v~~~~~~~~~~~~a   91 (433)
                      +++.+|+||.    +++|+||||+|.+|++|+++|||+|+|++.  ++++|+|+|+|+++                    
T Consensus         1 q~T~~i~VP~----~~vg~iIGk~G~~I~~I~~~tga~I~i~~~~~~~~~r~v~I~G~~~--------------------   56 (70)
T d1wvna1           1 QTTHELTIPN----NLIGCIIGRQGANINEIRQMSGAQIKIANPVEGSSGRQVTITGSAA--------------------   56 (70)
T ss_dssp             CEEEEEEEEG----GGHHHHHCGGGHHHHHHHHHHCCEEEECCCCTTCSEEEEEEEECHH--------------------
T ss_pred             CeEEEEEECh----HhcceeECCCChHHHHHHHHcCcEEEEcCCCCCCCcEEEEEEeCHH--------------------
Confidence            4789999999    999999999999999999999999999874  67899999999999                    


Q ss_pred             HHHHHHHHHHHHhhh
Q psy11929         92 VDNVCTAYNFMCRSL  106 (433)
Q Consensus        92 ~~~v~~A~~~I~~~~  106 (433)
                        ++.+|..+|.+++
T Consensus        57 --~v~~A~~~I~~~i   69 (70)
T d1wvna1          57 --SISLAQYLINARL   69 (70)
T ss_dssp             --HHHHHHHHHHHHT
T ss_pred             --HHHHHHHHHHHHc
Confidence              9999999998765

>d1dtja_ d.51.1.1 (A:) Neuro-oncological ventral antigen 2, nova-2, KH3 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Eukaryotic type KH-domain (KH-domain type I)
superfamily: Eukaryotic type KH-domain (KH-domain type I)
family: Eukaryotic type KH-domain (KH-domain type I)
domain: Neuro-oncological ventral antigen 2, nova-2, KH3
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.51  E-value=1.4e-14  Score=109.03  Aligned_cols=69  Identities=29%  Similarity=0.599  Sum_probs=62.8

Q ss_pred             eEEEEEeccCcccceecCCchhHHHHHHhhCceEEeccC--CCCCCCccEEEEEccHHHHHHHHHHHHHHH
Q psy11929        124 LQLKLVIPATHCGSLIGKGGCKIKDIRDLSGANVQVASD--MLPMSTERIVTVHGNPDTISQAIYQICLVL  192 (433)
Q Consensus       124 ~~~~l~ip~~~vg~iIGk~G~~Ik~I~~~sga~I~i~~~--~~~~~~er~v~I~G~~~~v~~A~~~I~~~l  192 (433)
                      ..++|+||+.++|.||||+|++|++|+++|||+|+|.++  ..+.+++|+|+|+|++++|.+|+.+|.++|
T Consensus         3 ~~i~i~VP~~~vg~iIGk~G~~Ik~I~~~sga~I~i~~~~~~~~~~~~r~v~I~G~~~~v~~A~~~I~~~i   73 (74)
T d1dtja_           3 ELVEMAVPENLVGAILGKGGKTLVEYQELTGARIQISKKGEFLPGTRNRRVTITGSPAATQAAQYLISQRV   73 (74)
T ss_dssp             EEEEEEEETTTHHHHHCSTTHHHHHHHHHHCCEEEECCTTCCSTTCCEEEEEEEESHHHHHHHHHHHHHHC
T ss_pred             EEEEEEeCHHHcceeECCCChhHHHHHHHcCCEEEEccCCCCCCCCCceEEEEEeCHHHHHHHHHHHHHHc
Confidence            367999999999999999999999999999999999863  456678999999999999999999998875

>d1j4wa2 d.51.1.1 (A:104-174) Far upstream binding element, FBP {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Eukaryotic type KH-domain (KH-domain type I)
superfamily: Eukaryotic type KH-domain (KH-domain type I)
family: Eukaryotic type KH-domain (KH-domain type I)
domain: Far upstream binding element, FBP
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.51  E-value=1.1e-14  Score=108.68  Aligned_cols=68  Identities=28%  Similarity=0.486  Sum_probs=61.2

Q ss_pred             EEEEEeccCcccceecCCchhHHHHHHhhCceEEeccCC--CCCCCccEEEEEccHHHHHHHHHHHHHHH
Q psy11929        125 QLKLVIPATHCGSLIGKGGCKIKDIRDLSGANVQVASDM--LPMSTERIVTVHGNPDTISQAIYQICLVL  192 (433)
Q Consensus       125 ~~~l~ip~~~vg~iIGk~G~~Ik~I~~~sga~I~i~~~~--~~~~~er~v~I~G~~~~v~~A~~~I~~~l  192 (433)
                      .++|+||+.++|+||||+|++|++|+++|||+|+|+++.  .+.+.+|.|+|+|++++|.+|+.+|.++|
T Consensus         2 ~~~~~IP~~~vg~IIGk~G~~Ik~I~~~sga~I~i~~~~~~~~~~~~r~v~I~G~~~~v~~A~~~I~e~i   71 (71)
T d1j4wa2           2 EFNFIVPTGKTGLIIGKGGETIKSISQQSGARIELQRNPPPNADPNMKLFTIRGTPQQIDYARQLIEEKI   71 (71)
T ss_dssp             EEEEEEETTTHHHHHCGGGHHHHHHHHHHCCEEEEECCCTTTSCTTEEEEEEECCHHHHHHHHHHHHHHC
T ss_pred             EEEEEEChHhcceEECCCCcChHHHHhhcCcEEEEeecCCCCCCCCeEEEEEEeCHHHHHHHHHHHHhhC
Confidence            468999999999999999999999999999999998643  34567899999999999999999998864

>d2ctma1 d.51.1.1 (A:8-88) Vigilin {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Eukaryotic type KH-domain (KH-domain type I)
superfamily: Eukaryotic type KH-domain (KH-domain type I)
family: Eukaryotic type KH-domain (KH-domain type I)
domain: Vigilin
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.51  E-value=2e-14  Score=110.06  Aligned_cols=73  Identities=18%  Similarity=0.187  Sum_probs=66.4

Q ss_pred             CCceEEEEEeCcccccccccCCCchHHHHHhHhCCeEEEccCCCCCceEEEEEeCHHHHHHHHHHHHHHHHhc
Q psy11929        285 DDFVETEIVLTDDIAGCVIGKAGSRLLEIRQISGAQINIHTGTESHKKMFHIQGCQEAVSLAQYLINMCIELQ  357 (433)
Q Consensus       285 ~~~~t~~i~VP~~~vG~IIGkgG~~Ik~I~~~sGA~I~I~~~~~~~er~V~IsGt~e~v~~A~~lI~~~i~~~  357 (433)
                      ...++.++.||..++|+|||++|++|++|++.|||+|+|++..+.+.+.|+|+|++++|++|+.+|.+++++.
T Consensus         7 ~~~~t~~i~Vp~~~~~~iIG~~G~~i~~I~~~tg~~I~~p~~~~~~~~~v~I~G~~~~V~~A~~~I~~i~~e~   79 (81)
T d2ctma1           7 EQMVSEDVPLDHRVHARIIGARGKAIRKIMDEFKVDIRFPQSGAPDPNCVTVTGLPENVEEAIDHILNLEEEY   79 (81)
T ss_dssp             TTCCCEEEECCTTTHHHHHCSSSCHHHHHHHHHTCEEECCCTTCSCTTEEEEESCHHHHHHHHHHHHHHHHHH
T ss_pred             hcCEEEEEEECHHHHhhccCCCCccHHHHHHHhCCEEEeCCccCCCCCEEEEeCCHHHHHHHHHHHHHHHHHH
Confidence            3567889999999999999999999999999999999999876555679999999999999999999988763

>d2ctea1 d.51.1.1 (A:8-88) Vigilin {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Eukaryotic type KH-domain (KH-domain type I)
superfamily: Eukaryotic type KH-domain (KH-domain type I)
family: Eukaryotic type KH-domain (KH-domain type I)
domain: Vigilin
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.50  E-value=1.5e-14  Score=110.89  Aligned_cols=72  Identities=18%  Similarity=0.285  Sum_probs=66.7

Q ss_pred             CCceEEEEEeCcccccccccCCCchHHHHHhHhCCeEEEccCCCCCceEEEEEeCHHHHHHHHHHHHHHHHhc
Q psy11929        285 DDFVETEIVLTDDIAGCVIGKAGSRLLEIRQISGAQINIHTGTESHKKMFHIQGCQEAVSLAQYLINMCIELQ  357 (433)
Q Consensus       285 ~~~~t~~i~VP~~~vG~IIGkgG~~Ik~I~~~sGA~I~I~~~~~~~er~V~IsGt~e~v~~A~~lI~~~i~~~  357 (433)
                      ....+.+|.||..++|+|||++|.+|++|++.|||+|+|++.. +.++.|+|+|++++|++|+.+|++++++.
T Consensus         7 ~~~~t~~i~Ip~~~~~~iIG~~G~~i~~I~~~tg~~I~~p~~~-~~~~~v~I~G~~~~v~~A~~~I~~iv~e~   78 (81)
T d2ctea1           7 QTQASATVAIPKEHHRFVIGKNGEKLQDLELKTATKIQIPRPD-DPSNQIKITGTKEGIEKARHEVLLISAEQ   78 (81)
T ss_dssp             CSCEEEEEECCTTTHHHHHCSSSCHHHHHHHHTTCCCBCCCTT-SSCCEEEEEECHHHHHHHHHHHHHHHHHH
T ss_pred             cCceEEEEEECHHHHhhccCCCChhHHHHHHHhCCEEEECCCC-CCCCEEEEEeCHHHHHHHHHHHHHHHHHH
Confidence            3568899999999999999999999999999999999998876 67789999999999999999999998764

>d2ctla1 d.51.1.1 (A:8-91) Vigilin {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Eukaryotic type KH-domain (KH-domain type I)
superfamily: Eukaryotic type KH-domain (KH-domain type I)
family: Eukaryotic type KH-domain (KH-domain type I)
domain: Vigilin
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.49  E-value=3.3e-14  Score=109.67  Aligned_cols=71  Identities=14%  Similarity=0.194  Sum_probs=65.4

Q ss_pred             ceEEEEEeCcccccccccCCCchHHHHHhHhCCeEEEccCCC--CCceEEEEEeCHHHHHHHHHHHHHHHHhc
Q psy11929        287 FVETEIVLTDDIAGCVIGKAGSRLLEIRQISGAQINIHTGTE--SHKKMFHIQGCQEAVSLAQYLINMCIELQ  357 (433)
Q Consensus       287 ~~t~~i~VP~~~vG~IIGkgG~~Ik~I~~~sGA~I~I~~~~~--~~er~V~IsGt~e~v~~A~~lI~~~i~~~  357 (433)
                      .++.+|.||..++|+|||++|++|++|++.|||+|+|++...  ..++.|+|+|++++|++|+.+|.+.+.+-
T Consensus         9 ~~~~~i~Vp~~~~~~iIG~~G~~i~~I~~~t~~~I~~~~~~~~~~~~~~i~I~G~~e~v~~A~~~I~~~i~e~   81 (84)
T d2ctla1           9 SFKLSVTVDPKYHPKIIGRKGAVITQIRLEHDVNIQFPDKDDGNQPQDQITITGYEKNTEAARDAILRIVGEL   81 (84)
T ss_dssp             TCEEEEECCTTTHHHHSCSSSCHHHHHHHHHTCEEECCCTTTCSSCSSEEEEESCHHHHHHHHHHHHHHHHHH
T ss_pred             cEEEEEEECHHHHhhhcCCCchhHHHHHHHhCCEEEECCCCCCCCCcceEEEECCHHHHHHHHHHHHHHHHhH
Confidence            567899999999999999999999999999999999987655  77899999999999999999999998753

>d1x4ma1 d.51.1.1 (A:8-88) Far upstream binding element, FBP {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: Eukaryotic type KH-domain (KH-domain type I)
superfamily: Eukaryotic type KH-domain (KH-domain type I)
family: Eukaryotic type KH-domain (KH-domain type I)
domain: Far upstream binding element, FBP
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.49  E-value=1.8e-14  Score=110.43  Aligned_cols=74  Identities=24%  Similarity=0.469  Sum_probs=68.2

Q ss_pred             CCCeEEEEEeccCcccceecCCchhHHHHHHhhCceEEeccC-CCCCCCccEEEEEccHHHHHHHHHHHHHHHHh
Q psy11929        121 PQPLQLKLVIPATHCGSLIGKGGCKIKDIRDLSGANVQVASD-MLPMSTERIVTVHGNPDTISQAIYQICLVLIE  194 (433)
Q Consensus       121 ~~~~~~~l~ip~~~vg~iIGk~G~~Ik~I~~~sga~I~i~~~-~~~~~~er~v~I~G~~~~v~~A~~~I~~~l~e  194 (433)
                      ...++.+|+||..++|+||||+|++|++|+++|||+|.|+++ ..+.+.+|.|+|+|++++|.+|+.+|.++|++
T Consensus         5 ~~~~~~~i~Vp~~~~g~iIGk~G~~Ik~I~~~tga~I~i~~~~~~~~~~~r~v~I~G~~~~v~~A~~~I~~~i~e   79 (81)
T d1x4ma1           5 PGNAVQEIMIPASKAGLVIGKGGETIKQLQERAGVKMVMIQDGPQNTGADKPLRITGDPYKVQQAKEMVLELIRD   79 (81)
T ss_dssp             CCCEEEEEEECHHHHHHHSCSSSSHHHHHHHHHTSEEEECCSCCCSSCSCEEEEEEECTTTHHHHHHHHHHHHCC
T ss_pred             CccEEEEEEECHHHcCeeECCCCchHHHHHHHhCCeEEEccCCCCCCCCceEEEEEeCHHHHHHHHHHHHHHHHh
Confidence            567899999999999999999999999999999999999864 35567899999999999999999999999976

>d1j4wa1 d.51.1.1 (A:1-74) Far upstream binding element, FBP {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Eukaryotic type KH-domain (KH-domain type I)
superfamily: Eukaryotic type KH-domain (KH-domain type I)
family: Eukaryotic type KH-domain (KH-domain type I)
domain: Far upstream binding element, FBP
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.48  E-value=3.1e-14  Score=107.11  Aligned_cols=71  Identities=30%  Similarity=0.426  Sum_probs=65.2

Q ss_pred             CeEEEEEeccCcccceecCCchhHHHHHHhhCceEEeccCCCCCCCccEEEEEccHHHHHHHHHHHHHHHHh
Q psy11929        123 PLQLKLVIPATHCGSLIGKGGCKIKDIRDLSGANVQVASDMLPMSTERIVTVHGNPDTISQAIYQICLVLIE  194 (433)
Q Consensus       123 ~~~~~l~ip~~~vg~iIGk~G~~Ik~I~~~sga~I~i~~~~~~~~~er~v~I~G~~~~v~~A~~~I~~~l~e  194 (433)
                      ...++|.||.+++|.||||+|++|++|+++|||+|+|.++ .+.+.+|.|+|+|++++|.+|+.+|.++|++
T Consensus         2 ~~~~~i~VP~~~vg~iIGk~G~~I~~I~~~tga~I~i~~~-~~~~~~r~v~I~G~~~~v~~A~~~I~~~i~~   72 (74)
T d1j4wa1           2 SHMIDVPIPRFAVGIVIGRNGEMIKKIQNDAGVRIQFKPD-DGTTPERIAQITGPPDRAQHAAEIITDLLRS   72 (74)
T ss_dssp             CEEEEEEEEHHHHHHHHCGGGHHHHHHHHHHCCEEEEECC-TTSCSEEEEEEEECHHHHHHHHHHHHHHHHH
T ss_pred             CeEEEEEeCHHHCCeeECCCCcHHHHHHHHcCCEEEeccC-CCCCCeeEEEEEeCHHHHHHHHHHHHHHHHh
Confidence            4578999999999999999999999999999999999854 3566789999999999999999999999986

>d1viga_ d.51.1.1 (A:) Vigilin {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Eukaryotic type KH-domain (KH-domain type I)
superfamily: Eukaryotic type KH-domain (KH-domain type I)
family: Eukaryotic type KH-domain (KH-domain type I)
domain: Vigilin
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.47  E-value=3.1e-14  Score=106.19  Aligned_cols=68  Identities=18%  Similarity=0.260  Sum_probs=62.5

Q ss_pred             CceEEEEEeCcccccccccCCCchHHHHHhHhCCeEEEccCCCCCceEEEEEeCHHHHHHHHHHHHHHH
Q psy11929        286 DFVETEIVLTDDIAGCVIGKAGSRLLEIRQISGAQINIHTGTESHKKMFHIQGCQEAVSLAQYLINMCI  354 (433)
Q Consensus       286 ~~~t~~i~VP~~~vG~IIGkgG~~Ik~I~~~sGA~I~I~~~~~~~er~V~IsGt~e~v~~A~~lI~~~i  354 (433)
                      ...+.+|.||..++++|||++|++|++|+++|||+|+|+++. ++++.|+|+|++++|++|+.+|++++
T Consensus         3 ~~~~~ei~V~~~~~~~iIG~~G~~i~~I~~~tg~~I~i~~~~-~~~~~v~I~G~~~~v~~A~~~I~~i~   70 (71)
T d1viga_           3 RMDYVEINIDHKFHRHLIGKSGANINRIKDQYKVSVRIPPDS-EKSNLIRIEGDPQGVQQAKRELLELA   70 (71)
T ss_dssp             CCEEEEEEECSSHHHHHTCSSCCHHHHHHHHTCCEEECCCCC-SSSEEEEEEESSHHHHHHHHHHHHTC
T ss_pred             ceEEEEEEECHHHhcccCCCCCchHHHHHHHhCCEEEeCCCC-CCCCEEEEECCHHHHHHHHHHHHHHh
Confidence            456789999999999999999999999999999999998766 67789999999999999999998753

>d2ctja1 d.51.1.1 (A:8-89) Vigilin {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Eukaryotic type KH-domain (KH-domain type I)
superfamily: Eukaryotic type KH-domain (KH-domain type I)
family: Eukaryotic type KH-domain (KH-domain type I)
domain: Vigilin
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.46  E-value=4e-14  Score=108.69  Aligned_cols=73  Identities=19%  Similarity=0.264  Sum_probs=65.8

Q ss_pred             CCceEEEEEeCcccccccccCCCchHHHHHhH-hCCeEEEccCCCCCceEEEEEeCHHHHHHHHHHHHHHHHhcc
Q psy11929        285 DDFVETEIVLTDDIAGCVIGKAGSRLLEIRQI-SGAQINIHTGTESHKKMFHIQGCQEAVSLAQYLINMCIELQK  358 (433)
Q Consensus       285 ~~~~t~~i~VP~~~vG~IIGkgG~~Ik~I~~~-sGA~I~I~~~~~~~er~V~IsGt~e~v~~A~~lI~~~i~~~~  358 (433)
                      .+..+.+|.||..++|+||||+|++|++|++. ++++|++++.. +.++.|+|+|++++|++|+.+|++++++.+
T Consensus         7 ~~~~t~~i~Vp~~~~~~iIGk~G~~I~~I~~~~~~~~I~~~~~~-~~~~~v~I~G~~~~v~~A~~~I~~~v~e~~   80 (82)
T d2ctja1           7 ANIAEVEVSIPAKLHNSLIGTKGRLIRSIMEECGGVHIHFPVEG-SGSDTVVIRGPSSDVEKAKKQLLHLAEEKQ   80 (82)
T ss_dssp             CSSCCEEEECCHHHHHHHHCSSSHHHHHHHHHHTSCEEECCCTT-TTCCEEEEESCHHHHHHHHHHHHHHHHHHS
T ss_pred             cCcEEEEEEECHHHHhhcCCCCCccHHHHHHHcCCcEEEEeCCC-CCCceEEEeCCHHHHHHHHHHHHHHHhhhh
Confidence            35678999999999999999999999999977 59999998766 677999999999999999999999998653

>d1x4na1 d.51.1.1 (A:8-86) Far upstream binding element, FBP {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: Eukaryotic type KH-domain (KH-domain type I)
superfamily: Eukaryotic type KH-domain (KH-domain type I)
family: Eukaryotic type KH-domain (KH-domain type I)
domain: Far upstream binding element, FBP
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.44  E-value=1.2e-13  Score=105.10  Aligned_cols=73  Identities=25%  Similarity=0.409  Sum_probs=67.6

Q ss_pred             CCCeEEEEEeccCcccceecCCchhHHHHHHhhCceEEeccCCCCCCCccEEEEEccHHHHHHHHHHHHHHHHh
Q psy11929        121 PQPLQLKLVIPATHCGSLIGKGGCKIKDIRDLSGANVQVASDMLPMSTERIVTVHGNPDTISQAIYQICLVLIE  194 (433)
Q Consensus       121 ~~~~~~~l~ip~~~vg~iIGk~G~~Ik~I~~~sga~I~i~~~~~~~~~er~v~I~G~~~~v~~A~~~I~~~l~e  194 (433)
                      ...++.+|.||..++|+|||++|.+|++|+++|||+|.|++. .+++.+|.|+|+|++++|.+|+.+|.++|.+
T Consensus         5 ~~~~t~~i~IP~~~~g~iIG~~G~~i~~I~~~tg~~I~i~~~-~~~~~~r~v~I~G~~~~v~~A~~~I~~~i~e   77 (79)
T d1x4na1           5 RSVMTEEYKVPDGMVGFIIGRGGEQISRIQQESGCKIQIAPD-SGGLPERSCMLTGTPESVQSAKRLLDQIVEK   77 (79)
T ss_dssp             CCCEEEEEEEEHHHHHHHHCSSSHHHHHHHHHSCCEEEECSC-CTTCSEEEEEEEECHHHHHHHHHHHHHHHHH
T ss_pred             CCcEEEEEEEChHhhcceECCCchhHHHHHHHhCCEEEEcCC-CCCCCceEEEEEeCHHHHHHHHHHHHHHHHc
Confidence            467899999999999999999999999999999999999863 3567899999999999999999999999987

>d1we8a_ d.51.1.1 (A:) Tudor and KH domain containing protein, Tdrkh {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: Eukaryotic type KH-domain (KH-domain type I)
superfamily: Eukaryotic type KH-domain (KH-domain type I)
family: Eukaryotic type KH-domain (KH-domain type I)
domain: Tudor and KH domain containing protein, Tdrkh
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.44  E-value=9e-14  Score=111.64  Aligned_cols=77  Identities=25%  Similarity=0.422  Sum_probs=69.1

Q ss_pred             CCCCCCCceEEEEEEeccCCcccccceeeecCchHHHHHHHHhCCeEEEeCC----CCCcceEEEecccCCCCCCccccC
Q psy11929          6 DGKIDEDTLITMRCLFHSSVNVNEISCLIGPGGCIVRRLRKESGAKISITDG----ACPDRIVTVSGSVDNSSTSSVETG   81 (433)
Q Consensus         6 ~~~~~~~~~~~~rilvp~~~~~~~vg~IIGk~G~~Ik~I~~~tga~I~v~~~----~~~eRvv~I~G~~~~~~~~~v~~~   81 (433)
                      ++..+.+..++.+|+||.    .++|+||||+|.+||+|+++|||+|+|++.    ...+|+|+|+|+++          
T Consensus         6 ~~~~~~~~~v~~~i~IP~----~~vg~vIGk~G~~Ik~I~~~tga~I~i~~~~~~~~~~~r~v~I~G~~~----------   71 (104)
T d1we8a_           6 SGILTENTPVFEQLSVPQ----RSVGRIIGRGGETIRSICKASGAKITCDKESEGTLLLSRLIKISGTQK----------   71 (104)
T ss_dssp             CCCCSSSCEEEEEEEEET----TTHHHHHTTTSHHHHHHHHHHCCEEEECCSSCCSSSSEEEEEEEEEHH----------
T ss_pred             CCccCCCCCEEEEEEECH----HHhcceECCCCcchHHHHHHcCCEEEECCCCCCCCCCccEEEEEeCHH----------
Confidence            444566778999999999    999999999999999999999999999763    34689999999999          


Q ss_pred             CCCCccccchHHHHHHHHHHHHhhhhh
Q psy11929         82 YPGHTLWVTSVDNVCTAYNFMCRSLED  108 (433)
Q Consensus        82 ~~~~~~~~~a~~~v~~A~~~I~~~~~~  108 (433)
                                  +|.+|+.+|.+++.+
T Consensus        72 ------------~v~~A~~~I~~~i~e   86 (104)
T d1we8a_          72 ------------EVAAAKHLILEKVSE   86 (104)
T ss_dssp             ------------HHHHHHHHHHHHHHH
T ss_pred             ------------HHHHHHHHHHHHHhC
Confidence                        999999999999876

>d2ctla1 d.51.1.1 (A:8-91) Vigilin {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Eukaryotic type KH-domain (KH-domain type I)
superfamily: Eukaryotic type KH-domain (KH-domain type I)
family: Eukaryotic type KH-domain (KH-domain type I)
domain: Vigilin
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.42  E-value=1.8e-13  Score=105.43  Aligned_cols=73  Identities=19%  Similarity=0.236  Sum_probs=67.9

Q ss_pred             CCeEEEEEeccCcccceecCCchhHHHHHHhhCceEEeccCCCCCCCccEEEEEccHHHHHHHHHHHHHHHHh
Q psy11929        122 QPLQLKLVIPATHCGSLIGKGGCKIKDIRDLSGANVQVASDMLPMSTERIVTVHGNPDTISQAIYQICLVLIE  194 (433)
Q Consensus       122 ~~~~~~l~ip~~~vg~iIGk~G~~Ik~I~~~sga~I~i~~~~~~~~~er~v~I~G~~~~v~~A~~~I~~~l~e  194 (433)
                      ..+++++.||..++++|||++|++|++|+++|||+|.|++...+...++.|+|+|+.++|.+|..+|.+++.+
T Consensus         8 ~~~~~~i~Vp~~~~~~iIG~~G~~i~~I~~~t~~~I~~~~~~~~~~~~~~i~I~G~~e~v~~A~~~I~~~i~e   80 (84)
T d2ctla1           8 RSFKLSVTVDPKYHPKIIGRKGAVITQIRLEHDVNIQFPDKDDGNQPQDQITITGYEKNTEAARDAILRIVGE   80 (84)
T ss_dssp             TTCEEEEECCTTTHHHHSCSSSCHHHHHHHHHTCEEECCCTTTCSSCSSEEEEESCHHHHHHHHHHHHHHHHH
T ss_pred             ccEEEEEEECHHHHhhhcCCCchhHHHHHHHhCCEEEECCCCCCCCCcceEEEECCHHHHHHHHHHHHHHHHh
Confidence            3567899999999999999999999999999999999987666778889999999999999999999999987

>d2ctea1 d.51.1.1 (A:8-88) Vigilin {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Eukaryotic type KH-domain (KH-domain type I)
superfamily: Eukaryotic type KH-domain (KH-domain type I)
family: Eukaryotic type KH-domain (KH-domain type I)
domain: Vigilin
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.39  E-value=1.1e-13  Score=105.92  Aligned_cols=73  Identities=15%  Similarity=0.191  Sum_probs=68.4

Q ss_pred             CCceEEEEEEeccCCcccccceeeecCchHHHHHHHHhCCeEEEeCCCCCcceEEEecccCCCCCCccccCCCCCccccc
Q psy11929         11 EDTLITMRCLFHSSVNVNEISCLIGPGGCIVRRLRKESGAKISITDGACPDRIVTVSGSVDNSSTSSVETGYPGHTLWVT   90 (433)
Q Consensus        11 ~~~~~~~rilvp~~~~~~~vg~IIGk~G~~Ik~I~~~tga~I~v~~~~~~eRvv~I~G~~~~~~~~~v~~~~~~~~~~~~   90 (433)
                      ....++.+|.||.    .++|+|||++|++|++|+++|||+|+|++.+..++.|+|+|+++                   
T Consensus         6 ~~~~~t~~i~Ip~----~~~~~iIG~~G~~i~~I~~~tg~~I~~p~~~~~~~~v~I~G~~~-------------------   62 (81)
T d2ctea1           6 LQTQASATVAIPK----EHHRFVIGKNGEKLQDLELKTATKIQIPRPDDPSNQIKITGTKE-------------------   62 (81)
T ss_dssp             CCSCEEEEEECCT----TTHHHHHCSSSCHHHHHHHHTTCCCBCCCTTSSCCEEEEEECHH-------------------
T ss_pred             hcCceEEEEEECH----HHHhhccCCCChhHHHHHHHhCCEEEECCCCCCCCEEEEEeCHH-------------------
Confidence            4566899999999    99999999999999999999999999999888999999999999                   


Q ss_pred             hHHHHHHHHHHHHhhhhhh
Q psy11929         91 SVDNVCTAYNFMCRSLEDY  109 (433)
Q Consensus        91 a~~~v~~A~~~I~~~~~~~  109 (433)
                         +|.+|..+|.+++++.
T Consensus        63 ---~v~~A~~~I~~iv~e~   78 (81)
T d2ctea1          63 ---GIEKARHEVLLISAEQ   78 (81)
T ss_dssp             ---HHHHHHHHHHHHHHHH
T ss_pred             ---HHHHHHHHHHHHHHHH
Confidence               9999999999988774

>d2ctka1 d.51.1.1 (A:8-98) Vigilin {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Eukaryotic type KH-domain (KH-domain type I)
superfamily: Eukaryotic type KH-domain (KH-domain type I)
family: Eukaryotic type KH-domain (KH-domain type I)
domain: Vigilin
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.38  E-value=3.2e-13  Score=105.61  Aligned_cols=70  Identities=17%  Similarity=0.179  Sum_probs=65.1

Q ss_pred             ceEEEEEeCcccccccccCCCchHHHHHhHhCCeEEEccCCCCCceEEEEEeCHHHHHHHHHHHHHHHHhc
Q psy11929        287 FVETEIVLTDDIAGCVIGKAGSRLLEIRQISGAQINIHTGTESHKKMFHIQGCQEAVSLAQYLINMCIELQ  357 (433)
Q Consensus       287 ~~t~~i~VP~~~vG~IIGkgG~~Ik~I~~~sGA~I~I~~~~~~~er~V~IsGt~e~v~~A~~lI~~~i~~~  357 (433)
                      .++.+|.||..++|+|||++|.+|++|++.|||+|.|++.. +.++.|+|+|++++|++|+.+|.+++.+.
T Consensus         9 ~vt~~i~Vp~~~~~~iIG~~G~~i~~I~~~tg~~I~~p~~~-~~~~~v~I~G~~~~V~~A~~~I~~~v~e~   78 (91)
T d2ctka1           9 PVTIEVEVPFDLHRYVIGQKGSGIRKMMDEFEVNIHVPAPE-LQSDIIAITGLAANLDRAKAGLLERVKEL   78 (91)
T ss_dssp             CEEEEEECCHHHHHHHHCSSSHHHHHHHHHTCCEEECCCTT-TTCCEEEEEECHHHHHHHHHHHHHHHHHH
T ss_pred             CEEEEEEECHHHHhHhcCCCchhHHHHHHHhCCEEEECCCC-CCcceEEEECCHHHHHHHHHHHHHHHHHH
Confidence            57899999999999999999999999999999999998876 56789999999999999999999999754

>d1viga_ d.51.1.1 (A:) Vigilin {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Eukaryotic type KH-domain (KH-domain type I)
superfamily: Eukaryotic type KH-domain (KH-domain type I)
family: Eukaryotic type KH-domain (KH-domain type I)
domain: Vigilin
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.36  E-value=4.5e-13  Score=99.70  Aligned_cols=69  Identities=13%  Similarity=0.193  Sum_probs=63.8

Q ss_pred             CceEEEEEEeccCCcccccceeeecCchHHHHHHHHhCCeEEEeCCCCCcceEEEecccCCCCCCccccCCCCCccccch
Q psy11929         12 DTLITMRCLFHSSVNVNEISCLIGPGGCIVRRLRKESGAKISITDGACPDRIVTVSGSVDNSSTSSVETGYPGHTLWVTS   91 (433)
Q Consensus        12 ~~~~~~rilvp~~~~~~~vg~IIGk~G~~Ik~I~~~tga~I~v~~~~~~eRvv~I~G~~~~~~~~~v~~~~~~~~~~~~a   91 (433)
                      +.....+|.||.    +++++|||++|++|++|+++|||+|+|++++.+++.|+|+|+++                    
T Consensus         2 ~~~~~~ei~V~~----~~~~~iIG~~G~~i~~I~~~tg~~I~i~~~~~~~~~v~I~G~~~--------------------   57 (71)
T d1viga_           2 NRMDYVEINIDH----KFHRHLIGKSGANINRIKDQYKVSVRIPPDSEKSNLIRIEGDPQ--------------------   57 (71)
T ss_dssp             CCCEEEEEEECS----SHHHHHTCSSCCHHHHHHHHTCCEEECCCCCSSSEEEEEEESSH--------------------
T ss_pred             CceEEEEEEECH----HHhcccCCCCCchHHHHHHHhCCEEEeCCCCCCCCEEEEECCHH--------------------
Confidence            445778899999    99999999999999999999999999999888899999999999                    


Q ss_pred             HHHHHHHHHHHHhhh
Q psy11929         92 VDNVCTAYNFMCRSL  106 (433)
Q Consensus        92 ~~~v~~A~~~I~~~~  106 (433)
                        +|.+|.++|.++.
T Consensus        58 --~v~~A~~~I~~i~   70 (71)
T d1viga_          58 --GVQQAKRELLELA   70 (71)
T ss_dssp             --HHHHHHHHHHHTC
T ss_pred             --HHHHHHHHHHHHh
Confidence              9999999998753

>d2ctma1 d.51.1.1 (A:8-88) Vigilin {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Eukaryotic type KH-domain (KH-domain type I)
superfamily: Eukaryotic type KH-domain (KH-domain type I)
family: Eukaryotic type KH-domain (KH-domain type I)
domain: Vigilin
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.36  E-value=2.7e-13  Score=103.68  Aligned_cols=74  Identities=20%  Similarity=0.302  Sum_probs=66.9

Q ss_pred             CCCceEEEEEEeccCCcccccceeeecCchHHHHHHHHhCCeEEEeCCC-CCcceEEEecccCCCCCCccccCCCCCccc
Q psy11929         10 DEDTLITMRCLFHSSVNVNEISCLIGPGGCIVRRLRKESGAKISITDGA-CPDRIVTVSGSVDNSSTSSVETGYPGHTLW   88 (433)
Q Consensus        10 ~~~~~~~~rilvp~~~~~~~vg~IIGk~G~~Ik~I~~~tga~I~v~~~~-~~eRvv~I~G~~~~~~~~~v~~~~~~~~~~   88 (433)
                      +.+..++..+.||.    .++++|||++|++|++|+++|||+|+|++.+ ..++.|+|+|+++                 
T Consensus         5 e~~~~~t~~i~Vp~----~~~~~iIG~~G~~i~~I~~~tg~~I~~p~~~~~~~~~v~I~G~~~-----------------   63 (81)
T d2ctma1           5 ELEQMVSEDVPLDH----RVHARIIGARGKAIRKIMDEFKVDIRFPQSGAPDPNCVTVTGLPE-----------------   63 (81)
T ss_dssp             CTTTCCCEEEECCT----TTHHHHHCSSSCHHHHHHHHHTCEEECCCTTCSCTTEEEEESCHH-----------------
T ss_pred             HhhcCEEEEEEECH----HHHhhccCCCCccHHHHHHHhCCEEEeCCccCCCCCEEEEeCCHH-----------------
Confidence            45667788999999    9999999999999999999999999998864 3568999999999                 


Q ss_pred             cchHHHHHHHHHHHHhhhhhh
Q psy11929         89 VTSVDNVCTAYNFMCRSLEDY  109 (433)
Q Consensus        89 ~~a~~~v~~A~~~I~~~~~~~  109 (433)
                           +|.+|.++|.++++++
T Consensus        64 -----~V~~A~~~I~~i~~e~   79 (81)
T d2ctma1          64 -----NVEEAIDHILNLEEEY   79 (81)
T ss_dssp             -----HHHHHHHHHHHHHHHH
T ss_pred             -----HHHHHHHHHHHHHHHH
Confidence                 9999999999998875

>d2ctja1 d.51.1.1 (A:8-89) Vigilin {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Eukaryotic type KH-domain (KH-domain type I)
superfamily: Eukaryotic type KH-domain (KH-domain type I)
family: Eukaryotic type KH-domain (KH-domain type I)
domain: Vigilin
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.35  E-value=2.6e-13  Score=104.01  Aligned_cols=74  Identities=19%  Similarity=0.273  Sum_probs=68.0

Q ss_pred             CCCceEEEEEEeccCCcccccceeeecCchHHHHHHHH-hCCeEEEeCCCCCcceEEEecccCCCCCCccccCCCCCccc
Q psy11929         10 DEDTLITMRCLFHSSVNVNEISCLIGPGGCIVRRLRKE-SGAKISITDGACPDRIVTVSGSVDNSSTSSVETGYPGHTLW   88 (433)
Q Consensus        10 ~~~~~~~~rilvp~~~~~~~vg~IIGk~G~~Ik~I~~~-tga~I~v~~~~~~eRvv~I~G~~~~~~~~~v~~~~~~~~~~   88 (433)
                      +....++..|.||.    .++|+||||+|++|++|+++ ++|+|++++.+..++.|+|+|+++                 
T Consensus         5 e~~~~~t~~i~Vp~----~~~~~iIGk~G~~I~~I~~~~~~~~I~~~~~~~~~~~v~I~G~~~-----------------   63 (82)
T d2ctja1           5 DLANIAEVEVSIPA----KLHNSLIGTKGRLIRSIMEECGGVHIHFPVEGSGSDTVVIRGPSS-----------------   63 (82)
T ss_dssp             CCCSSCCEEEECCH----HHHHHHHCSSSHHHHHHHHHHTSCEEECCCTTTTCCEEEEESCHH-----------------
T ss_pred             hhcCcEEEEEEECH----HHHhhcCCCCCccHHHHHHHcCCcEEEEeCCCCCCceEEEeCCHH-----------------
Confidence            45567889999999    99999999999999999988 599999999888999999999999                 


Q ss_pred             cchHHHHHHHHHHHHhhhhhh
Q psy11929         89 VTSVDNVCTAYNFMCRSLEDY  109 (433)
Q Consensus        89 ~~a~~~v~~A~~~I~~~~~~~  109 (433)
                           +|.+|..+|.+++++.
T Consensus        64 -----~v~~A~~~I~~~v~e~   79 (82)
T d2ctja1          64 -----DVEKAKKQLLHLAEEK   79 (82)
T ss_dssp             -----HHHHHHHHHHHHHHHH
T ss_pred             -----HHHHHHHHHHHHHhhh
Confidence                 9999999999998875

>d2cpqa1 d.51.1.1 (A:212-289) Fragile X mental retardation syndrome related protein 1, FXR1 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Eukaryotic type KH-domain (KH-domain type I)
superfamily: Eukaryotic type KH-domain (KH-domain type I)
family: Eukaryotic type KH-domain (KH-domain type I)
domain: Fragile X mental retardation syndrome related protein 1, FXR1
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.28  E-value=1e-12  Score=99.28  Aligned_cols=64  Identities=25%  Similarity=0.415  Sum_probs=57.5

Q ss_pred             CceEEEEEeCcccccccccCCCchHHHHHhHhCCeEEEccCCCCCceEEEEEe-CHHHHHHHHHHHHH
Q psy11929        286 DFVETEIVLTDDIAGCVIGKAGSRLLEIRQISGAQINIHTGTESHKKMFHIQG-CQEAVSLAQYLINM  352 (433)
Q Consensus       286 ~~~t~~i~VP~~~vG~IIGkgG~~Ik~I~~~sGA~I~I~~~~~~~er~V~IsG-t~e~v~~A~~lI~~  352 (433)
                      ..++.+|.||.+++|+|||+||++|++|++.|||+|.+.+.   +++.|+|.| +++++++|+.||+.
T Consensus         6 ~~~t~~i~Ip~~~ig~vIG~gG~~I~~I~~~tGa~i~i~~~---~~g~v~I~g~~~eav~~A~~~Ie~   70 (78)
T d2cpqa1           6 AAFHEEFVVREDLMGLAIGTHGSNIQQARKVPGVTAIELDE---DTGTFRIYGESADAVKKARGFLEF   70 (78)
T ss_dssp             CSEEEEEECCHHHHHHHHTTTTHHHHHHHTSTTEEEEEEET---TTTEEEEEESSHHHHHHHHHHHSC
T ss_pred             CCceEEEEECHHHHHHHcCCChHHHHHHHHhcCcEEEEecC---CCceEEEEECCHHHHHHHHHHHHH
Confidence            46788999999999999999999999999999999998764   347899999 69999999999953

>d2ctka1 d.51.1.1 (A:8-98) Vigilin {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Eukaryotic type KH-domain (KH-domain type I)
superfamily: Eukaryotic type KH-domain (KH-domain type I)
family: Eukaryotic type KH-domain (KH-domain type I)
domain: Vigilin
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.26  E-value=1.8e-12  Score=101.20  Aligned_cols=72  Identities=15%  Similarity=0.200  Sum_probs=67.1

Q ss_pred             CceEEEEEEeccCCcccccceeeecCchHHHHHHHHhCCeEEEeCCCCCcceEEEecccCCCCCCccccCCCCCccccch
Q psy11929         12 DTLITMRCLFHSSVNVNEISCLIGPGGCIVRRLRKESGAKISITDGACPDRIVTVSGSVDNSSTSSVETGYPGHTLWVTS   91 (433)
Q Consensus        12 ~~~~~~rilvp~~~~~~~vg~IIGk~G~~Ik~I~~~tga~I~v~~~~~~eRvv~I~G~~~~~~~~~v~~~~~~~~~~~~a   91 (433)
                      ...++..|.||.    .++++|||++|.+|++|+++|||+|.|++.+..++.|+|+|+.+                    
T Consensus         7 ~~~vt~~i~Vp~----~~~~~iIG~~G~~i~~I~~~tg~~I~~p~~~~~~~~v~I~G~~~--------------------   62 (91)
T d2ctka1           7 LVPVTIEVEVPF----DLHRYVIGQKGSGIRKMMDEFEVNIHVPAPELQSDIIAITGLAA--------------------   62 (91)
T ss_dssp             SSCEEEEEECCH----HHHHHHHCSSSHHHHHHHHHTCCEEECCCTTTTCCEEEEEECHH--------------------
T ss_pred             hCCEEEEEEECH----HHHhHhcCCCchhHHHHHHHhCCEEEECCCCCCcceEEEECCHH--------------------
Confidence            347899999999    99999999999999999999999999999888899999999999                    


Q ss_pred             HHHHHHHHHHHHhhhhhh
Q psy11929         92 VDNVCTAYNFMCRSLEDY  109 (433)
Q Consensus        92 ~~~v~~A~~~I~~~~~~~  109 (433)
                        +|.+|..+|.+++.++
T Consensus        63 --~V~~A~~~I~~~v~e~   78 (91)
T d2ctka1          63 --NLDRAKAGLLERVKEL   78 (91)
T ss_dssp             --HHHHHHHHHHHHHHHH
T ss_pred             --HHHHHHHHHHHHHHHH
Confidence              9999999999988764

>d2ctfa1 d.51.1.1 (A:7-96) Vigilin {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Eukaryotic type KH-domain (KH-domain type I)
superfamily: Eukaryotic type KH-domain (KH-domain type I)
family: Eukaryotic type KH-domain (KH-domain type I)
domain: Vigilin
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.26  E-value=8.9e-12  Score=96.84  Aligned_cols=68  Identities=25%  Similarity=0.336  Sum_probs=62.2

Q ss_pred             CceEEEEEeCcccccccccCCCchHHHHHhH-hCCeEEEccCCCCCceEEEEEeCHHHHHHHHHHHHHHHHhc
Q psy11929        286 DFVETEIVLTDDIAGCVIGKAGSRLLEIRQI-SGAQINIHTGTESHKKMFHIQGCQEAVSLAQYLINMCIELQ  357 (433)
Q Consensus       286 ~~~t~~i~VP~~~vG~IIGkgG~~Ik~I~~~-sGA~I~I~~~~~~~er~V~IsGt~e~v~~A~~lI~~~i~~~  357 (433)
                      ...+.++.||..++++|||++|++|++|+++ +|++|.+++..    ..|+|+|++++|++|+.+|++++.+-
T Consensus        19 ~~~t~~v~VP~~~h~~iIG~~G~~I~~i~~~~~~v~I~~~~~~----~~v~i~G~~~~ve~Ak~~I~~iv~el   87 (90)
T d2ctfa1          19 SFTVSSVAAPSWLHRFIIGKKGQNLAKITQQMPKVHIEFTEGE----DKITLEGPTEDVSVAQEQIEGMVKDL   87 (90)
T ss_dssp             CCEEEEEECCSTTHHHHHTTTTCHHHHHHHHCSSSEEEECSSS----CEEEEEECHHHHHHHHHHHHHHHHHH
T ss_pred             CcEEEEEEcCHHHHhhcCCCCchhHHHHHHHcCCcEEeeCCCC----ceEEEeCCHHHHHHHHHHHHHHHHHH
Confidence            4689999999999999999999999999999 58999998754    78999999999999999999998753

>d2ba0a3 d.51.1.1 (A:136-219) Exosome complex RNA-binding protein 1, ECR1 {Archaeoglobus fulgidus [TaxId: 2234]}

class: Alpha and beta proteins (a+b)
fold: Eukaryotic type KH-domain (KH-domain type I)
superfamily: Eukaryotic type KH-domain (KH-domain type I)
family: Eukaryotic type KH-domain (KH-domain type I)
domain: Exosome complex RNA-binding protein 1, ECR1
species: Archaeoglobus fulgidus [TaxId: 2234]

Probab=99.24  E-value=5.4e-12  Score=96.50  Aligned_cols=63  Identities=21%  Similarity=0.242  Sum_probs=57.5

Q ss_pred             EEEEeCcccccccccCCCchHHHHHhHhCCeEEEccCCCCCceEEEEEeCHHHHHHHHHHHHHHHHhc
Q psy11929        290 TEIVLTDDIAGCVIGKAGSRLLEIRQISGAQINIHTGTESHKKMFHIQGCQEAVSLAQYLINMCIELQ  357 (433)
Q Consensus       290 ~~i~VP~~~vG~IIGkgG~~Ik~I~~~sGA~I~I~~~~~~~er~V~IsGt~e~v~~A~~lI~~~i~~~  357 (433)
                      ..+.||.+++|.|||++|++|++|+++|||+|.|++.     ..|+|+|++++++.|+.+|+..+++.
T Consensus         3 ~vi~Ip~~~ig~IIG~gG~~I~~I~~~tg~~I~i~~~-----g~v~I~G~~e~v~~A~~~I~~i~~ea   65 (84)
T d2ba0a3           3 RIVAINPARVPRVIGKKGSMIKLLKSELDVQIVVGQN-----GLIWVNGDRRKVSIAEEAIYLIEQEA   65 (84)
T ss_dssp             EEEECCGGGHHHHHCGGGHHHHHHHHHHTCEEEECTT-----SEEEEESCHHHHHHHHHHHHHHHHCS
T ss_pred             EEEEEChhhcceeeCCcHHHHHHHHHHHCCEEEECCC-----CEEEEEeCHHHHHHHHHHHHHHHHhc
Confidence            4688999999999999999999999999999999753     57999999999999999998888653

>d2ctfa1 d.51.1.1 (A:7-96) Vigilin {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Eukaryotic type KH-domain (KH-domain type I)
superfamily: Eukaryotic type KH-domain (KH-domain type I)
family: Eukaryotic type KH-domain (KH-domain type I)
domain: Vigilin
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.23  E-value=1.3e-12  Score=101.63  Aligned_cols=68  Identities=19%  Similarity=0.215  Sum_probs=62.3

Q ss_pred             CCCeEEEEEeccCcccceecCCchhHHHHHHhh-CceEEeccCCCCCCCccEEEEEccHHHHHHHHHHHHHHHHh
Q psy11929        121 PQPLQLKLVIPATHCGSLIGKGGCKIKDIRDLS-GANVQVASDMLPMSTERIVTVHGNPDTISQAIYQICLVLIE  194 (433)
Q Consensus       121 ~~~~~~~l~ip~~~vg~iIGk~G~~Ik~I~~~s-ga~I~i~~~~~~~~~er~v~I~G~~~~v~~A~~~I~~~l~e  194 (433)
                      ...++..+.||..+++.|||++|++|++|++++ +++|.++.+      +..|+|+|++++|++|+.+|.+++.+
T Consensus        18 ~~~~t~~v~VP~~~h~~iIG~~G~~I~~i~~~~~~v~I~~~~~------~~~v~i~G~~~~ve~Ak~~I~~iv~e   86 (90)
T d2ctfa1          18 NSFTVSSVAAPSWLHRFIIGKKGQNLAKITQQMPKVHIEFTEG------EDKITLEGPTEDVSVAQEQIEGMVKD   86 (90)
T ss_dssp             CCCEEEEEECCSTTHHHHHTTTTCHHHHHHHHCSSSEEEECSS------SCEEEEEECHHHHHHHHHHHHHHHHH
T ss_pred             CCcEEEEEEcCHHHHhhcCCCCchhHHHHHHHcCCcEEeeCCC------CceEEEeCCHHHHHHHHHHHHHHHHH
Confidence            457899999999999999999999999999995 899999753      57899999999999999999999987

>d2ba0a3 d.51.1.1 (A:136-219) Exosome complex RNA-binding protein 1, ECR1 {Archaeoglobus fulgidus [TaxId: 2234]}

class: Alpha and beta proteins (a+b)
fold: Eukaryotic type KH-domain (KH-domain type I)
superfamily: Eukaryotic type KH-domain (KH-domain type I)
family: Eukaryotic type KH-domain (KH-domain type I)
domain: Exosome complex RNA-binding protein 1, ECR1
species: Archaeoglobus fulgidus [TaxId: 2234]

Probab=99.10  E-value=4.6e-11  Score=91.21  Aligned_cols=62  Identities=24%  Similarity=0.299  Sum_probs=57.4

Q ss_pred             EEEEeccCcccceecCCchhHHHHHHhhCceEEeccCCCCCCCccEEEEEccHHHHHHHHHHHHHHHHh
Q psy11929        126 LKLVIPATHCGSLIGKGGCKIKDIRDLSGANVQVASDMLPMSTERIVTVHGNPDTISQAIYQICLVLIE  194 (433)
Q Consensus       126 ~~l~ip~~~vg~iIGk~G~~Ik~I~~~sga~I~i~~~~~~~~~er~v~I~G~~~~v~~A~~~I~~~l~e  194 (433)
                      ..+.||.+++|+|||++|++|++|+++|||+|.+.+       +..|+|.|+++++.+|+.+|..++.+
T Consensus         3 ~vi~Ip~~~ig~IIG~gG~~I~~I~~~tg~~I~i~~-------~g~v~I~G~~e~v~~A~~~I~~i~~e   64 (84)
T d2ba0a3           3 RIVAINPARVPRVIGKKGSMIKLLKSELDVQIVVGQ-------NGLIWVNGDRRKVSIAEEAIYLIEQE   64 (84)
T ss_dssp             EEEECCGGGHHHHHCGGGHHHHHHHHHHTCEEEECT-------TSEEEEESCHHHHHHHHHHHHHHHHC
T ss_pred             EEEEEChhhcceeeCCcHHHHHHHHHHHCCEEEECC-------CCEEEEEeCHHHHHHHHHHHHHHHHh
Confidence            357899999999999999999999999999999974       46899999999999999999999887

>d2cpqa1 d.51.1.1 (A:212-289) Fragile X mental retardation syndrome related protein 1, FXR1 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Eukaryotic type KH-domain (KH-domain type I)
superfamily: Eukaryotic type KH-domain (KH-domain type I)
family: Eukaryotic type KH-domain (KH-domain type I)
domain: Fragile X mental retardation syndrome related protein 1, FXR1
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.06  E-value=7e-11  Score=88.95  Aligned_cols=64  Identities=17%  Similarity=0.291  Sum_probs=57.2

Q ss_pred             CCCeEEEEEeccCcccceecCCchhHHHHHHhhCceEEeccCCCCCCCccEEEEEc-cHHHHHHHHHHHH
Q psy11929        121 PQPLQLKLVIPATHCGSLIGKGGCKIKDIRDLSGANVQVASDMLPMSTERIVTVHG-NPDTISQAIYQIC  189 (433)
Q Consensus       121 ~~~~~~~l~ip~~~vg~iIGk~G~~Ik~I~~~sga~I~i~~~~~~~~~er~v~I~G-~~~~v~~A~~~I~  189 (433)
                      ...++.+|.||.+++|+|||++|++|++|+++|||+|.+..+     .++.|+|.| +++++++|+.+|.
T Consensus         5 ~~~~t~~i~Ip~~~ig~vIG~gG~~I~~I~~~tGa~i~i~~~-----~~g~v~I~g~~~eav~~A~~~Ie   69 (78)
T d2cpqa1           5 AAAFHEEFVVREDLMGLAIGTHGSNIQQARKVPGVTAIELDE-----DTGTFRIYGESADAVKKARGFLE   69 (78)
T ss_dssp             SCSEEEEEECCHHHHHHHHTTTTHHHHHHHTSTTEEEEEEET-----TTTEEEEEESSHHHHHHHHHHHS
T ss_pred             cCCceEEEEECHHHHHHHcCCChHHHHHHHHhcCcEEEEecC-----CCceEEEEECCHHHHHHHHHHHH
Confidence            456788999999999999999999999999999999988643     357899999 7999999999984

>d1tuaa1 d.51.1.1 (A:1-84) Hypothetical protein APE0754 {Aeropyrum pernix [TaxId: 56636]}

class: Alpha and beta proteins (a+b)
fold: Eukaryotic type KH-domain (KH-domain type I)
superfamily: Eukaryotic type KH-domain (KH-domain type I)
family: Eukaryotic type KH-domain (KH-domain type I)
domain: Hypothetical protein APE0754
species: Aeropyrum pernix [TaxId: 56636]

Probab=98.95  E-value=7.7e-11  Score=89.71  Aligned_cols=62  Identities=19%  Similarity=0.183  Sum_probs=52.3

Q ss_pred             EEEEeCcccccccccCCCchHHHHHhHhCCeEEEccCCCCCceEEEE-----EeCHHHHHHHHHHHHHHHH
Q psy11929        290 TEIVLTDDIAGCVIGKAGSRLLEIRQISGAQINIHTGTESHKKMFHI-----QGCQEAVSLAQYLINMCIE  355 (433)
Q Consensus       290 ~~i~VP~~~vG~IIGkgG~~Ik~I~~~sGA~I~I~~~~~~~er~V~I-----sGt~e~v~~A~~lI~~~i~  355 (433)
                      .++.||.+++|.|||++|++|++|+++|||+|+|++..    ..+.+     +|.+.++++|+.+|.++-.
T Consensus         5 i~i~ip~~~ig~vIG~gG~~Ik~i~~~tg~~I~Id~d~----g~v~i~~~~~~~~~~a~~~a~~iI~aI~r   71 (84)
T d1tuaa1           5 IYVKVKPERLGAVIGPRGEVKAEIMRRTGTVITVDTEN----SMVIVEPEAEGIPPVNLMKAAEVVKAISL   71 (84)
T ss_dssp             EEEECCGGGHHHHHCGGGHHHHHHHHHHTEEEEEETTT----TEEEEEESSTTSCHHHHHHHHHHHHHHHH
T ss_pred             EEEEeCHHHcCeeecCCchhHHHHHHHHCCEEEEEcCC----CeEEEecCCccccHHHHHHHHHHHHHHhC
Confidence            46899999999999999999999999999999997654    33444     4568889999999987654

>d2je6i3 d.51.1.1 (I:153-221) Exosome complex RNA-binding protein 1, ECR1 {Sulfolobus solfataricus [TaxId: 2287]}

class: Alpha and beta proteins (a+b)
fold: Eukaryotic type KH-domain (KH-domain type I)
superfamily: Eukaryotic type KH-domain (KH-domain type I)
family: Eukaryotic type KH-domain (KH-domain type I)
domain: Exosome complex RNA-binding protein 1, ECR1
species: Sulfolobus solfataricus [TaxId: 2287]

Probab=98.85  E-value=5.3e-11  Score=87.40  Aligned_cols=60  Identities=17%  Similarity=0.025  Sum_probs=46.7

Q ss_pred             EEEeCcccccccccCCCchHHHHHhHhCCeEEEccCCCCCceEEEEEeC-HHHHHHHHHHHHHHHH
Q psy11929        291 EIVLTDDIAGCVIGKAGSRLLEIRQISGAQINIHTGTESHKKMFHIQGC-QEAVSLAQYLINMCIE  355 (433)
Q Consensus       291 ~i~VP~~~vG~IIGkgG~~Ik~I~~~sGA~I~I~~~~~~~er~V~IsGt-~e~v~~A~~lI~~~i~  355 (433)
                      -+.||.+++|.||||+|++|++|+++|||+|.|.++     ..|+|+|. +++++.|+.+|....+
T Consensus         4 vi~Ip~~~ig~iIGkgG~~Ik~i~~~tg~~I~i~~~-----g~v~I~g~~~~~v~~A~~~I~~i~~   64 (69)
T d2je6i3           4 VIDIMPVKVPRVIGKNKSMYETLTSKSGCSIFVANN-----GRIWATCPSRFSEEILIEAIRKIEN   64 (69)
T ss_dssp             EEECCGGGHHHHHCGGGHHHHHHHTTC---CEECTT-----SEEEC-----CTTCCTHHHHTTTTT
T ss_pred             EEEEChhhccceECCchhHHHHHHHHHCCEEEEcCC-----CEEEEEeCCHHHHHHHHHHHHHHHH
Confidence            578999999999999999999999999999999753     46999996 6789999999976544

>d2z0sa2 d.51.1.1 (A:148-234) Exosome complex RNA-binding protein 1, ECR1 {Aeropyrum pernix [TaxId: 56636]}

class: Alpha and beta proteins (a+b)
fold: Eukaryotic type KH-domain (KH-domain type I)
superfamily: Eukaryotic type KH-domain (KH-domain type I)
family: Eukaryotic type KH-domain (KH-domain type I)
domain: Exosome complex RNA-binding protein 1, ECR1
species: Aeropyrum pernix [TaxId: 56636]

Probab=98.79  E-value=7.5e-09  Score=78.71  Aligned_cols=63  Identities=16%  Similarity=0.168  Sum_probs=55.7

Q ss_pred             EEEEeCcccccccccCCCchHHHHHhHhCCeEEEccCCCCCceEEEEEeC-HHHHHHHHHHHHHHHHhc
Q psy11929        290 TEIVLTDDIAGCVIGKAGSRLLEIRQISGAQINIHTGTESHKKMFHIQGC-QEAVSLAQYLINMCIELQ  357 (433)
Q Consensus       290 ~~i~VP~~~vG~IIGkgG~~Ik~I~~~sGA~I~I~~~~~~~er~V~IsGt-~e~v~~A~~lI~~~i~~~  357 (433)
                      ..+.||.+++|.|||++|++|+.|+..|||+|.|.+..     .|.|.|. .+.+..|..+|....++.
T Consensus         3 ~vi~I~~~ki~~vIG~gG~~ik~i~~~t~~~I~I~d~G-----~V~I~g~~~~~~~~A~~~I~~I~~ea   66 (87)
T d2z0sa2           3 KIVEISPAKVPRVIGRKMSMLKTLEEKTECKIFVARNG-----RIHLECPNEDLEAIAVMAIKIIDEEA   66 (87)
T ss_dssp             EEEECCGGGSGGGTCGGGHHHHHHHHHHCCEEEEETTT-----EEEEECSCHHHHHHHHHHHHHHHHCS
T ss_pred             EEEEEChhhcceeECCCCcHHHHHHHHHCCEEEECCCc-----EEEEEeCCHHHHHHHHHHHHHHHHhc
Confidence            36789999999999999999999999999999997643     6999995 789999999998876643

>d1tuaa1 d.51.1.1 (A:1-84) Hypothetical protein APE0754 {Aeropyrum pernix [TaxId: 56636]}

class: Alpha and beta proteins (a+b)
fold: Eukaryotic type KH-domain (KH-domain type I)
superfamily: Eukaryotic type KH-domain (KH-domain type I)
family: Eukaryotic type KH-domain (KH-domain type I)
domain: Hypothetical protein APE0754
species: Aeropyrum pernix [TaxId: 56636]

Probab=98.77  E-value=5.3e-09  Score=79.30  Aligned_cols=68  Identities=15%  Similarity=0.269  Sum_probs=51.6

Q ss_pred             EEEeccCCcccccceeeecCchHHHHHHHHhCCeEEEeCCCCCcceEEEecccCCCCCCccccCCCCCccccchHHHHHH
Q psy11929         18 RCLFHSSVNVNEISCLIGPGGCIVRRLRKESGAKISITDGACPDRIVTVSGSVDNSSTSSVETGYPGHTLWVTSVDNVCT   97 (433)
Q Consensus        18 rilvp~~~~~~~vg~IIGk~G~~Ik~I~~~tga~I~v~~~~~~eRvv~I~G~~~~~~~~~v~~~~~~~~~~~~a~~~v~~   97 (433)
                      .+-||.    +++|.||||+|++||+|+++|||+|+|..   ++..+.+.+.....                 ...++.+
T Consensus         6 ~i~ip~----~~ig~vIG~gG~~Ik~i~~~tg~~I~Id~---d~g~v~i~~~~~~~-----------------~~~a~~~   61 (84)
T d1tuaa1           6 YVKVKP----ERLGAVIGPRGEVKAEIMRRTGTVITVDT---ENSMVIVEPEAEGI-----------------PPVNLMK   61 (84)
T ss_dssp             EEECCG----GGHHHHHCGGGHHHHHHHHHHTEEEEEET---TTTEEEEEESSTTS-----------------CHHHHHH
T ss_pred             EEEeCH----HHcCeeecCCchhHHHHHHHHCCEEEEEc---CCCeEEEecCCccc-----------------cHHHHHH
Confidence            467888    99999999999999999999999999975   33456666654411                 1227888


Q ss_pred             HHHHHHhhhhhh
Q psy11929         98 AYNFMCRSLEDY  109 (433)
Q Consensus        98 A~~~I~~~~~~~  109 (433)
                      |.++|.++...+
T Consensus        62 a~~iI~aI~rGf   73 (84)
T d1tuaa1          62 AAEVVKAISLGF   73 (84)
T ss_dssp             HHHHHHHHHHTC
T ss_pred             HHHHHHHHhCCC
Confidence            888887765443

>d2je6i3 d.51.1.1 (I:153-221) Exosome complex RNA-binding protein 1, ECR1 {Sulfolobus solfataricus [TaxId: 2287]}

class: Alpha and beta proteins (a+b)
fold: Eukaryotic type KH-domain (KH-domain type I)
superfamily: Eukaryotic type KH-domain (KH-domain type I)
family: Eukaryotic type KH-domain (KH-domain type I)
domain: Exosome complex RNA-binding protein 1, ECR1
species: Sulfolobus solfataricus [TaxId: 2287]

Probab=98.74  E-value=4.5e-10  Score=82.36  Aligned_cols=60  Identities=10%  Similarity=0.080  Sum_probs=43.8

Q ss_pred             EEeccCCcccccceeeecCchHHHHHHHHhCCeEEEeCCCCCcceEEEecc-cCCCCCCccccCCCCCccccchHHHHHH
Q psy11929         19 CLFHSSVNVNEISCLIGPGGCIVRRLRKESGAKISITDGACPDRIVTVSGS-VDNSSTSSVETGYPGHTLWVTSVDNVCT   97 (433)
Q Consensus        19 ilvp~~~~~~~vg~IIGk~G~~Ik~I~~~tga~I~v~~~~~~eRvv~I~G~-~~~~~~~~v~~~~~~~~~~~~a~~~v~~   97 (433)
                      +.||.    +++|.||||+|++||+|+++|||+|+|.+.    ..|+|.|. .+                      ++.+
T Consensus         5 i~Ip~----~~ig~iIGkgG~~Ik~i~~~tg~~I~i~~~----g~v~I~g~~~~----------------------~v~~   54 (69)
T d2je6i3           5 IDIMP----VKVPRVIGKNKSMYETLTSKSGCSIFVANN----GRIWATCPSRF----------------------SEEI   54 (69)
T ss_dssp             EECCG----GGHHHHHCGGGHHHHHHHTTC---CEECTT----SEEEC-----C----------------------TTCC
T ss_pred             EEECh----hhccceECCchhHHHHHHHHHCCEEEEcCC----CEEEEEeCCHH----------------------HHHH
Confidence            55677    999999999999999999999999999763    35899996 45                      6778


Q ss_pred             HHHHHHhhhhh
Q psy11929         98 AYNFMCRSLED  108 (433)
Q Consensus        98 A~~~I~~~~~~  108 (433)
                      |..+|..+.++
T Consensus        55 A~~~I~~i~~e   65 (69)
T d2je6i3          55 LIEAIRKIENE   65 (69)
T ss_dssp             THHHHTTTTTT
T ss_pred             HHHHHHHHHHh
Confidence            88888765544

>d2z0sa2 d.51.1.1 (A:148-234) Exosome complex RNA-binding protein 1, ECR1 {Aeropyrum pernix [TaxId: 56636]}

class: Alpha and beta proteins (a+b)
fold: Eukaryotic type KH-domain (KH-domain type I)
superfamily: Eukaryotic type KH-domain (KH-domain type I)
family: Eukaryotic type KH-domain (KH-domain type I)
domain: Exosome complex RNA-binding protein 1, ECR1
species: Aeropyrum pernix [TaxId: 56636]

Probab=98.61  E-value=3.6e-08  Score=74.85  Aligned_cols=61  Identities=18%  Similarity=0.230  Sum_probs=55.0

Q ss_pred             EEEeccCcccceecCCchhHHHHHHhhCceEEeccCCCCCCCccEEEEEc-cHHHHHHHHHHHHHHHHh
Q psy11929        127 KLVIPATHCGSLIGKGGCKIKDIRDLSGANVQVASDMLPMSTERIVTVHG-NPDTISQAIYQICLVLIE  194 (433)
Q Consensus       127 ~l~ip~~~vg~iIGk~G~~Ik~I~~~sga~I~i~~~~~~~~~er~v~I~G-~~~~v~~A~~~I~~~l~e  194 (433)
                      .+.||.+++|.|||++|++|+.|+++|||+|.|.+       +-.|.|.| +.+.+..|+.+|..+.++
T Consensus         4 vi~I~~~ki~~vIG~gG~~ik~i~~~t~~~I~I~d-------~G~V~I~g~~~~~~~~A~~~I~~I~~e   65 (87)
T d2z0sa2           4 IVEISPAKVPRVIGRKMSMLKTLEEKTECKIFVAR-------NGRIHLECPNEDLEAIAVMAIKIIDEE   65 (87)
T ss_dssp             EEECCGGGSGGGTCGGGHHHHHHHHHHCCEEEEET-------TTEEEEECSCHHHHHHHHHHHHHHHHC
T ss_pred             EEEEChhhcceeECCCCcHHHHHHHHHCCEEEECC-------CcEEEEEeCCHHHHHHHHHHHHHHHHh
Confidence            46899999999999999999999999999999974       34799999 588999999999998777

>d1e3ha4 d.52.3.1 (A:579-632) Polynucleotide phosphorylase/guanosine pentaphosphate synthase (PNPase/GPSI), domain 6 {Streptomyces antibioticus [TaxId: 1890]}

class: Alpha and beta proteins (a+b)
fold: Alpha-lytic protease prodomain-like
superfamily: Prokaryotic type KH domain (KH-domain type II)
family: Prokaryotic type KH domain (KH-domain type II)
domain: Polynucleotide phosphorylase/guanosine pentaphosphate synthase (PNPase/GPSI), domain 6
species: Streptomyces antibioticus [TaxId: 1890]

Probab=98.61  E-value=1.2e-09  Score=75.38  Aligned_cols=48  Identities=21%  Similarity=0.465  Sum_probs=16.4

Q ss_pred             EEEEEeccCCcccccceeeecCchHHHHHHHHhCCeEEEeCCCCCcceEEEecccC
Q psy11929         16 TMRCLFHSSVNVNEISCLIGPGGCIVRRLRKESGAKISITDGACPDRIVTVSGSVD   71 (433)
Q Consensus        16 ~~rilvp~~~~~~~vg~IIGk~G~~Ik~I~~~tga~I~v~~~~~~eRvv~I~G~~~   71 (433)
                      ..+|.||.    +++|.|||++|++||.|+++|||+|++.+    ++.|+|+|...
T Consensus         4 ~~~i~Ip~----~kig~vIG~GG~~Ik~I~~~tga~I~i~d----dg~v~I~a~~~   51 (54)
T d1e3ha4           4 IITVKIPV----DKIGEVIGPKRQMINQIQEDTGAEITIED----DGTIYIGAADG   51 (54)
T ss_dssp             CC-------------------------CHHHHSCCCC------------CCCCBSS
T ss_pred             EEEEEeCH----HHeeEEECCccHHHHHHHHHHCCEEEEeC----CeEEEEEecCc
Confidence            45678888    99999999999999999999999999985    56788888765

>d1tuaa2 d.51.1.1 (A:85-188) Hypothetical protein APE0754 {Aeropyrum pernix [TaxId: 56636]}

class: Alpha and beta proteins (a+b)
fold: Eukaryotic type KH-domain (KH-domain type I)
superfamily: Eukaryotic type KH-domain (KH-domain type I)
family: Eukaryotic type KH-domain (KH-domain type I)
domain: Hypothetical protein APE0754
species: Aeropyrum pernix [TaxId: 56636]

Probab=98.55  E-value=2.1e-08  Score=78.77  Aligned_cols=53  Identities=28%  Similarity=0.303  Sum_probs=48.5

Q ss_pred             cccccccCCCchHHHHHhHhCCeEEEccCCCCCceEEEEEeCHHHHHHHHHHHHHHHHh
Q psy11929        298 IAGCVIGKAGSRLLEIRQISGAQINIHTGTESHKKMFHIQGCQEAVSLAQYLINMCIEL  356 (433)
Q Consensus       298 ~vG~IIGkgG~~Ik~I~~~sGA~I~I~~~~~~~er~V~IsGt~e~v~~A~~lI~~~i~~  356 (433)
                      +.|+|||++|.+|+.|++.|||.|.|.+.      .|.|.|++++++.|..+|..++..
T Consensus        23 ~~GrIIG~gGktik~Ie~~Tg~~I~I~d~------~v~iig~~e~i~~A~~~Ie~li~~   75 (104)
T d1tuaa2          23 IKGRIIGEGGRARRTIEEMTDTYINVGEY------EVAIIGDYERAMAAKQAIEMLAEG   75 (104)
T ss_dssp             HHHHHHCGGGHHHHHHHHHHTCEEEECSS------EEEEEEEHHHHHHHHHHHHHHHTT
T ss_pred             HhcceeCCCcHHHHHHHHHHCCeEEEeCC------eEEEEECchhHHHHHHHHHHHHcC
Confidence            57999999999999999999999999764      488889999999999999999964

>d1e3ha4 d.52.3.1 (A:579-632) Polynucleotide phosphorylase/guanosine pentaphosphate synthase (PNPase/GPSI), domain 6 {Streptomyces antibioticus [TaxId: 1890]}

class: Alpha and beta proteins (a+b)
fold: Alpha-lytic protease prodomain-like
superfamily: Prokaryotic type KH domain (KH-domain type II)
family: Prokaryotic type KH domain (KH-domain type II)
domain: Polynucleotide phosphorylase/guanosine pentaphosphate synthase (PNPase/GPSI), domain 6
species: Streptomyces antibioticus [TaxId: 1890]

Probab=98.49  E-value=3.9e-09  Score=72.82  Aligned_cols=45  Identities=24%  Similarity=0.326  Sum_probs=13.5

Q ss_pred             EEEEeCcccccccccCCCchHHHHHhHhCCeEEEccCCCCCceEEEEEeC
Q psy11929        290 TEIVLTDDIAGCVIGKAGSRLLEIRQISGAQINIHTGTESHKKMFHIQGC  339 (433)
Q Consensus       290 ~~i~VP~~~vG~IIGkgG~~Ik~I~~~sGA~I~I~~~~~~~er~V~IsGt  339 (433)
                      .+|.||.+++|.|||+||.+||+|+++|||+|.|.++     ..|+|.|+
T Consensus         5 ~~i~Ip~~kig~vIG~GG~~Ik~I~~~tga~I~i~dd-----g~v~I~a~   49 (54)
T d1e3ha4           5 ITVKIPVDKIGEVIGPKRQMINQIQEDTGAEITIEDD-----GTIYIGAA   49 (54)
T ss_dssp             C---------------------CHHHHSCCCC-------------CCCCB
T ss_pred             EEEEeCHHHeeEEECCccHHHHHHHHHHCCEEEEeCC-----eEEEEEec
Confidence            4788999999999999999999999999999999753     45666664

>d1tuaa2 d.51.1.1 (A:85-188) Hypothetical protein APE0754 {Aeropyrum pernix [TaxId: 56636]}

class: Alpha and beta proteins (a+b)
fold: Eukaryotic type KH-domain (KH-domain type I)
superfamily: Eukaryotic type KH-domain (KH-domain type I)
family: Eukaryotic type KH-domain (KH-domain type I)
domain: Hypothetical protein APE0754
species: Aeropyrum pernix [TaxId: 56636]

Probab=98.39  E-value=1.5e-07  Score=73.86  Aligned_cols=53  Identities=23%  Similarity=0.344  Sum_probs=48.0

Q ss_pred             cccceecCCchhHHHHHHhhCceEEeccCCCCCCCccEEEEEccHHHHHHHHHHHHHHHHh
Q psy11929        134 HCGSLIGKGGCKIKDIRDLSGANVQVASDMLPMSTERIVTVHGNPDTISQAIYQICLVLIE  194 (433)
Q Consensus       134 ~vg~iIGk~G~~Ik~I~~~sga~I~i~~~~~~~~~er~v~I~G~~~~v~~A~~~I~~~l~e  194 (433)
                      ..|+|||++|.+|+.|++.|||+|.|.        +..+.|.|+++++..|+.+|..++.+
T Consensus        23 ~~GrIIG~gGktik~Ie~~Tg~~I~I~--------d~~v~iig~~e~i~~A~~~Ie~li~~   75 (104)
T d1tuaa2          23 IKGRIIGEGGRARRTIEEMTDTYINVG--------EYEVAIIGDYERAMAAKQAIEMLAEG   75 (104)
T ss_dssp             HHHHHHCGGGHHHHHHHHHHTCEEEEC--------SSEEEEEEEHHHHHHHHHHHHHHHTT
T ss_pred             HhcceeCCCcHHHHHHHHHHCCeEEEe--------CCeEEEEECchhHHHHHHHHHHHHcC
Confidence            369999999999999999999999996        34688889999999999999999876

>d1k1ga_ d.51.1.1 (A:) RNA splicing factor 1 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Eukaryotic type KH-domain (KH-domain type I)
superfamily: Eukaryotic type KH-domain (KH-domain type I)
family: Eukaryotic type KH-domain (KH-domain type I)
domain: RNA splicing factor 1
species: Human (Homo sapiens) [TaxId: 9606]

Probab=98.10  E-value=2.5e-06  Score=68.90  Aligned_cols=44  Identities=27%  Similarity=0.465  Sum_probs=36.7

Q ss_pred             eEEEEEEeccCC--cccccceeeecCchHHHHHHHHhCCeEEEeCC
Q psy11929         14 LITMRCLFHSSV--NVNEISCLIGPGGCIVRRLRKESGAKISITDG   57 (433)
Q Consensus        14 ~~~~rilvp~~~--~~~~vg~IIGk~G~~Ik~I~~~tga~I~v~~~   57 (433)
                      .++-+|+||.+-  ..+++|.|||++|.++|+|+++|||+|.|-..
T Consensus         2 k~~~Ki~iP~~~~P~fNfvG~IlGPrG~t~K~Le~eTgckI~IrGr   47 (122)
T d1k1ga_           2 RVSDKVMIPQDEYPEINFVGLLIGPRGNTLKNIEKECNAKIMIRGK   47 (122)
T ss_dssp             CEEEEEECCTTTCCSHHHHHHHHCSSSHHHHHHHHHSCCEEEEEES
T ss_pred             ceeEEEecCCccCCCCCeeeeEeCCCCchHHHHHHHHCCEEEEEec
Confidence            467889998721  34569999999999999999999999999653

>d2bl5a1 d.51.1.1 (A:1-134) Quaking protein A (Xqua) {African clawed frog (Xenopus laevis) [TaxId: 8355]}

class: Alpha and beta proteins (a+b)
fold: Eukaryotic type KH-domain (KH-domain type I)
superfamily: Eukaryotic type KH-domain (KH-domain type I)
family: Eukaryotic type KH-domain (KH-domain type I)
domain: Quaking protein A (Xqua)
species: African clawed frog (Xenopus laevis) [TaxId: 8355]

Probab=98.01  E-value=4e-06  Score=68.47  Aligned_cols=44  Identities=20%  Similarity=0.408  Sum_probs=36.7

Q ss_pred             EEEEEEeccCC--cccccceeeecCchHHHHHHHHhCCeEEEeCCC
Q psy11929         15 ITMRCLFHSSV--NVNEISCLIGPGGCIVRRLRKESGAKISITDGA   58 (433)
Q Consensus        15 ~~~rilvp~~~--~~~~vg~IIGk~G~~Ik~I~~~tga~I~v~~~~   58 (433)
                      +.-|++||.+-  ..+++|.|||++|.++|+|+++|||+|.|-..|
T Consensus         2 l~eKv~IP~~~~P~~NfvG~IiGPrG~t~K~le~eTg~kI~IrGrG   47 (134)
T d2bl5a1           2 LQEKLYVPVKEYPDFNFVGRILGPRGLTAKQLEAETGCKIMVRGKG   47 (134)
T ss_dssp             EEEEEECCTTTCSSSCHHHHHTTTTHHHHHHHHHHHSEEEEEESTT
T ss_pred             cceEEeCCCCCCCCCCeeEEEECCCCchHHHHHHHHCCEEEEEecC
Confidence            56788888632  346899999999999999999999999997643

>d1k1ga_ d.51.1.1 (A:) RNA splicing factor 1 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Eukaryotic type KH-domain (KH-domain type I)
superfamily: Eukaryotic type KH-domain (KH-domain type I)
family: Eukaryotic type KH-domain (KH-domain type I)
domain: RNA splicing factor 1
species: Human (Homo sapiens) [TaxId: 9606]

Probab=97.98  E-value=1.3e-05  Score=64.62  Aligned_cols=70  Identities=21%  Similarity=0.229  Sum_probs=55.9

Q ss_pred             ceEEEEEeCccc------ccccccCCCchHHHHHhHhCCeEEEccCCC-----------------CCceEEEEEeC-HHH
Q psy11929        287 FVETEIVLTDDI------AGCVIGKAGSRLLEIRQISGAQINIHTGTE-----------------SHKKMFHIQGC-QEA  342 (433)
Q Consensus       287 ~~t~~i~VP~~~------vG~IIGkgG~~Ik~I~~~sGA~I~I~~~~~-----------------~~er~V~IsGt-~e~  342 (433)
                      ..+.+++||-+.      +|.|||.+|+++|+|+++|||+|.|-....                 ..+=-|.|++. ++.
T Consensus         2 k~~~Ki~iP~~~~P~fNfvG~IlGPrG~t~K~Le~eTgckI~IrGrGS~kd~~~~~~~~~~~~~~~epLHv~I~a~~~~~   81 (122)
T d1k1ga_           2 RVSDKVMIPQDEYPEINFVGLLIGPRGNTLKNIEKECNAKIMIRGKGSVKEGKVGRKDGQMLPGEDEPLHALVTANTMEN   81 (122)
T ss_dssp             CEEEEEECCTTTCCSHHHHHHHHCSSSHHHHHHHHHSCCEEEEEESTTSSSSSSSSCCCCCSCCSSCCEEEEEEESSHHH
T ss_pred             ceeEEEecCCccCCCCCeeeeEeCCCCchHHHHHHHHCCEEEEEecCCcccccccccCCCCCCCCCCCceEEEecCChhh
Confidence            356788888764      899999999999999999999999963211                 22335777776 678


Q ss_pred             HHHHHHHHHHHHHh
Q psy11929        343 VSLAQYLINMCIEL  356 (433)
Q Consensus       343 v~~A~~lI~~~i~~  356 (433)
                      ++.|..+|..+|..
T Consensus        82 ~~~A~~~i~~ll~~   95 (122)
T d1k1ga_          82 VKKAVEQIRNILKQ   95 (122)
T ss_dssp             HHHHHHHHHHHHTT
T ss_pred             HHHHHHHHHHHHHh
Confidence            99999999999964

>d2bl5a1 d.51.1.1 (A:1-134) Quaking protein A (Xqua) {African clawed frog (Xenopus laevis) [TaxId: 8355]}

class: Alpha and beta proteins (a+b)
fold: Eukaryotic type KH-domain (KH-domain type I)
superfamily: Eukaryotic type KH-domain (KH-domain type I)
family: Eukaryotic type KH-domain (KH-domain type I)
domain: Quaking protein A (Xqua)
species: African clawed frog (Xenopus laevis) [TaxId: 8355]

Probab=97.57  E-value=6e-05  Score=61.26  Aligned_cols=67  Identities=10%  Similarity=0.136  Sum_probs=52.4

Q ss_pred             EEEEEeCc------ccccccccCCCchHHHHHhHhCCeEEEccCCC-------------------CCceEEEEEeCH---
Q psy11929        289 ETEIVLTD------DIAGCVIGKAGSRLLEIRQISGAQINIHTGTE-------------------SHKKMFHIQGCQ---  340 (433)
Q Consensus       289 t~~i~VP~------~~vG~IIGkgG~~Ik~I~~~sGA~I~I~~~~~-------------------~~er~V~IsGt~---  340 (433)
                      +.+++||.      +++|.|||.+|.++|+|+++|||+|.|-....                   .++=-|.|++..   
T Consensus         3 ~eKv~IP~~~~P~~NfvG~IiGPrG~t~K~le~eTg~kI~IrGrGS~k~~~~~~~~~~~~~~~~~~epLHv~I~a~~~~~   82 (134)
T d2bl5a1           3 QEKLYVPVKEYPDFNFVGRILGPRGLTAKQLEAETGCKIMVRGKGSMRDKKKEEQNRGKPNWEHLNEDLHVLITVEDAQN   82 (134)
T ss_dssp             EEEEECCTTTCSSSCHHHHHTTTTHHHHHHHHHHHSEEEEEESTTSSCCHHHHHTSTTSHHHHTTTSCCEEEEEECSCCH
T ss_pred             ceEEeCCCCCCCCCCeeEEEECCCCchHHHHHHHHCCEEEEEecCCCcCccccccccCCCCCcCCCCCCEEEEEecCcHH
Confidence            45777774      47899999999999999999999999976431                   245568888762   


Q ss_pred             ---HHHHHHHHHHHHHHH
Q psy11929        341 ---EAVSLAQYLINMCIE  355 (433)
Q Consensus       341 ---e~v~~A~~lI~~~i~  355 (433)
                         ..+.+|..+|..+|.
T Consensus        83 ~a~~kl~~A~~~I~~lL~  100 (134)
T d2bl5a1          83 RAELKLKRAVEEVKKLLV  100 (134)
T ss_dssp             HHHHHHHHHHHHHHHHSS
T ss_pred             HHHHHHHHHHHHHHHHcC
Confidence               347889899988774

>d1hh2p3 d.52.3.1 (P:277-344) Transcription factor NusA, C-terminal domains {Thermotoga maritima [TaxId: 2336]}

class: Alpha and beta proteins (a+b)
fold: Alpha-lytic protease prodomain-like
superfamily: Prokaryotic type KH domain (KH-domain type II)
family: Prokaryotic type KH domain (KH-domain type II)
domain: Transcription factor NusA, C-terminal domains
species: Thermotoga maritima [TaxId: 2336]

Probab=95.33  E-value=0.006  Score=43.03  Aligned_cols=41  Identities=17%  Similarity=0.230  Sum_probs=36.9

Q ss_pred             ceEEEEEeCcccccccccCCCchHHHHHhHhCCeEEEccCC
Q psy11929        287 FVETEIVLTDDIAGCVIGKAGSRLLEIRQISGAQINIHTGT  327 (433)
Q Consensus       287 ~~t~~i~VP~~~vG~IIGkgG~~Ik~I~~~sGA~I~I~~~~  327 (433)
                      .....+.||.+..+..|||+|.|++-..+.||.+|.|..-.
T Consensus        26 ~~~~~v~V~~~qls~AIGk~G~NvrLas~Ltg~~idI~s~~   66 (68)
T d1hh2p3          26 NKAARVLVPPTQLSLAIGKGGQNARLAAKLTGWKIDIKPIM   66 (68)
T ss_dssp             TTEEEEEECTTSHHHHHCGGGHHHHHHHHHHSCEEEEEECC
T ss_pred             CCEEEEEECcccccccccCCcchHHHHHHHHCCEEeeEEcc
Confidence            34688999999999999999999999999999999987643

>d2asba3 d.52.3.1 (A:263-329) Transcription factor NusA, C-terminal domains {Mycobacterium tuberculosis [TaxId: 1773]}

class: Alpha and beta proteins (a+b)
fold: Alpha-lytic protease prodomain-like
superfamily: Prokaryotic type KH domain (KH-domain type II)
family: Prokaryotic type KH domain (KH-domain type II)
domain: Transcription factor NusA, C-terminal domains
species: Mycobacterium tuberculosis [TaxId: 1773]

Probab=95.31  E-value=0.0056  Score=43.04  Aligned_cols=40  Identities=23%  Similarity=0.290  Sum_probs=36.6

Q ss_pred             ceEEEEEeCcccccccccCCCchHHHHHhHhCCeEEEccC
Q psy11929        287 FVETEIVLTDDIAGCVIGKAGSRLLEIRQISGAQINIHTG  326 (433)
Q Consensus       287 ~~t~~i~VP~~~vG~IIGkgG~~Ik~I~~~sGA~I~I~~~  326 (433)
                      .....+.||.+.....|||+|.|++-..+.||.+|.|...
T Consensus        25 ~~~~~v~V~~~qls~AIGk~G~NvrLas~Ltg~~IdI~~e   64 (67)
T d2asba3          25 ARAARVVVPDFQLSLAIGKEGQNARLAARLTGWRIDIRGD   64 (67)
T ss_dssp             TTEEEEEECGGGHHHHHCGGGHHHHHHHHHHSCEEEEEES
T ss_pred             CcEEEEEECcccccchhcCCceeHHHHHHHHCCEEEEEeC
Confidence            4578899999999999999999999999999999998754

>d2asba3 d.52.3.1 (A:263-329) Transcription factor NusA, C-terminal domains {Mycobacterium tuberculosis [TaxId: 1773]}

class: Alpha and beta proteins (a+b)
fold: Alpha-lytic protease prodomain-like
superfamily: Prokaryotic type KH domain (KH-domain type II)
family: Prokaryotic type KH domain (KH-domain type II)
domain: Transcription factor NusA, C-terminal domains
species: Mycobacterium tuberculosis [TaxId: 1773]

Probab=94.70  E-value=0.01  Score=41.69  Aligned_cols=38  Identities=24%  Similarity=0.276  Sum_probs=35.1

Q ss_pred             EEEEEEeccCCcccccceeeecCchHHHHHHHHhCCeEEEeC
Q psy11929         15 ITMRCLFHSSVNVNEISCLIGPGGCIVRRLRKESGAKISITD   56 (433)
Q Consensus        15 ~~~rilvp~~~~~~~vg~IIGk~G~~Ik~I~~~tga~I~v~~   56 (433)
                      -.+.+.||.    .+.+..|||+|.++|-..+-||.+|.|-.
T Consensus        26 ~~~~v~V~~----~qls~AIGk~G~NvrLas~Ltg~~IdI~~   63 (67)
T d2asba3          26 RAARVVVPD----FQLSLAIGKEGQNARLAARLTGWRIDIRG   63 (67)
T ss_dssp             TEEEEEECG----GGHHHHHCGGGHHHHHHHHHHSCEEEEEE
T ss_pred             cEEEEEECc----ccccchhcCCceeHHHHHHHHCCEEEEEe
Confidence            367789999    99999999999999999999999999965

>d1hh2p3 d.52.3.1 (P:277-344) Transcription factor NusA, C-terminal domains {Thermotoga maritima [TaxId: 2336]}

class: Alpha and beta proteins (a+b)
fold: Alpha-lytic protease prodomain-like
superfamily: Prokaryotic type KH domain (KH-domain type II)
family: Prokaryotic type KH domain (KH-domain type II)
domain: Transcription factor NusA, C-terminal domains
species: Thermotoga maritima [TaxId: 2336]

Probab=94.64  E-value=0.011  Score=41.72  Aligned_cols=37  Identities=35%  Similarity=0.427  Sum_probs=34.5

Q ss_pred             EEEEEeccCCcccccceeeecCchHHHHHHHHhCCeEEEeC
Q psy11929         16 TMRCLFHSSVNVNEISCLIGPGGCIVRRLRKESGAKISITD   56 (433)
Q Consensus        16 ~~rilvp~~~~~~~vg~IIGk~G~~Ik~I~~~tga~I~v~~   56 (433)
                      .+.+.||.    .+.+..|||+|.+||-..+-||.+|.|..
T Consensus        28 ~~~v~V~~----~qls~AIGk~G~NvrLas~Ltg~~idI~s   64 (68)
T d1hh2p3          28 AARVLVPP----TQLSLAIGKGGQNARLAAKLTGWKIDIKP   64 (68)
T ss_dssp             EEEEEECT----TSHHHHHCGGGHHHHHHHHHHSCEEEEEE
T ss_pred             EEEEEECc----ccccccccCCcchHHHHHHHHCCEEeeEE
Confidence            57789999    99999999999999999999999999864

>d1wh9a_ d.52.3.1 (A:) Ribosomal protein S3 N-terminal domain {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: Alpha-lytic protease prodomain-like
superfamily: Prokaryotic type KH domain (KH-domain type II)
family: Prokaryotic type KH domain (KH-domain type II)
domain: Ribosomal protein S3 N-terminal domain
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=87.15  E-value=0.1  Score=38.79  Aligned_cols=32  Identities=13%  Similarity=0.229  Sum_probs=26.5

Q ss_pred             EEEEEeccCCcccccceeeecCchHHHHHHHHhCCe
Q psy11929         16 TMRCLFHSSVNVNEISCLIGPGGCIVRRLRKESGAK   51 (433)
Q Consensus        16 ~~rilvp~~~~~~~vg~IIGk~G~~Ik~I~~~tga~   51 (433)
                      .+++.++.    ..-|.|||++|+.|++|+++-.-+
T Consensus        36 ~i~I~I~t----arPGivIGrkG~~I~~L~~~l~k~   67 (92)
T d1wh9a_          36 RTEIIILA----TRTQNVLGEKGRRIRELTAVVQKR   67 (92)
T ss_dssp             CEEEEEEE----SCHHHHHCGGGHHHHHHHHHHHHH
T ss_pred             eEEEEEEe----CCCceeeccCchhHHHHHHHHHHH
Confidence            35677777    999999999999999999875443

>d2ja9a2 d.51.1.1 (A:152-236) Ribosomal RNA-processing protein 40, RRP40 {Saccharomyces cerevisiae [TaxId: 4932]}

class: Alpha and beta proteins (a+b)
fold: Eukaryotic type KH-domain (KH-domain type I)
superfamily: Eukaryotic type KH-domain (KH-domain type I)
family: Eukaryotic type KH-domain (KH-domain type I)
domain: Ribosomal RNA-processing protein 40, RRP40
species: Saccharomyces cerevisiae [TaxId: 4932]

Probab=84.46  E-value=0.89  Score=32.87  Aligned_cols=58  Identities=10%  Similarity=-0.013  Sum_probs=46.4

Q ss_pred             EEEeCcccccccccCCCc-hHHHHHhHhCCeEEEccCCCCCceEEEEEeC-HHHHHHHHHHHHHH
Q psy11929        291 EIVLTDDIAGCVIGKAGS-RLLEIRQISGAQINIHTGTESHKKMFHIQGC-QEAVSLAQYLINMC  353 (433)
Q Consensus       291 ~i~VP~~~vG~IIGkgG~-~Ik~I~~~sGA~I~I~~~~~~~er~V~IsGt-~e~v~~A~~lI~~~  353 (433)
                      -+.||..++..+||++++ .++.|.+.+++.|-|-...     .|-|.|. ++..-.+...|..+
T Consensus         4 v~~vs~~~~rrll~~~~~~ml~~l~~~~~~eI~VG~NG-----rIWi~~~~~~~~i~i~~aI~~~   63 (85)
T d2ja9a2           4 IIDVNLNFARQLLFNNDFPLLKVLAAHTKFEVAIGLNG-----KIWVKCEELSNTLACYRTIMEC   63 (85)
T ss_dssp             EEECCHHHHHHHHHCTTCCHHHHHHTTCCCEEEEETTT-----EEEEECSSHHHHHHHHHHHHHH
T ss_pred             EEEecHHHHHHHHcCCCChHHHHHHhhcCceEEEecCc-----EEEEECCCHHHHHHHHHHHHHH
Confidence            567999999999999998 7999999999999999876     5778884 66655555555443

>d1egaa2 d.52.3.1 (A:183-295) GTPase Era C-terminal domain {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a+b)
fold: Alpha-lytic protease prodomain-like
superfamily: Prokaryotic type KH domain (KH-domain type II)
family: Prokaryotic type KH domain (KH-domain type II)
domain: GTPase Era C-terminal domain
species: Escherichia coli [TaxId: 562]

Probab=84.11  E-value=0.23  Score=38.25  Aligned_cols=34  Identities=18%  Similarity=0.208  Sum_probs=27.9

Q ss_pred             CceEEEEEEeccCCcccccceeeecCchHHHHHHHHh
Q psy11929         12 DTLITMRCLFHSSVNVNEISCLIGPGGCIVRRLRKES   48 (433)
Q Consensus        12 ~~~~~~rilvp~~~~~~~vg~IIGk~G~~Ik~I~~~t   48 (433)
                      .-.+...|+|+..   ++-+.|||++|++||+|..++
T Consensus        46 ~~~I~a~I~V~~~---sqk~IiIGk~G~~ik~I~~~a   79 (113)
T d1egaa2          46 GYDINGLILVERE---GQKKMVIGNKGAKIKTIGIEA   79 (113)
T ss_dssp             SEEEEEEEEESSH---HHHHHHHCGGGHHHHHHHHHH
T ss_pred             eEEEEEEEEECCc---chhhhhhcccchHHHHHHHHH
Confidence            3458888999883   778999999999999987654