Citrus Sinensis ID: 006943

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Local Sequence Feature Prediction

Residue Number Marker
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100-------110-------120-------130-------140-------150-------160-------170-------180-------190-------200-------210-------220-------230-------240-------250-------260-------270-------280-------290-------300-------310-------320-------330-------340-------350-------360-------370-------380-------390-------400-------410-------420-------430-------440-------450-------460-------470-------480-------490-------500-------510-------520-------530-------540-------550-------560-------570-------580-------590-------600-------610-------620----
Protein Sequence
MGDSGKRYRSQRDNDRDGKNQKRRINEKDEKGNEESVIYRILCPDGVIGSVIGKSGKVINSIRQETRARVKVVDPFPGAKDRVVTIYSHVKDKEDVEVDDEFNDKEPLCAAQDALLKVHAAIANAVANATDNDKKRKEKEECQILVPSSQSANIIGKAGATIKRLRSKTRTSIKVTPKDASEPTHSCAMEFDNFVLISGESEAVKKALFAISAIMYKFSPREDIPLETTVREAPPSIIIPSDVPIYPPGGLYPNADPILPSRSVPSILGAARVPDLQGYADTGNTWPVYSTGLSLVSGLVGASQSEELVIRVLCPFNKIGRVIGKGGGTIKSIRQASGAQIDVDDTKDNRDECVITVTAIESPDDIKSMAVEAVLLLQTKINDEDDDTVTIRLLVSSKVIGCIIGKSGSIINEIRKRTKADVRISKGDKPKCADANDELVEVVGEVGSVRDALVQIILRLRDDALKDRDGSRNPPVGADHIYSSGTGISMPPLLPSIPPVGPLGYDQRADSGSGIGMLSSSSLYGYGSLSMGDSPYGSMSSYSSKLYGGLPPPLTLEVLVPANAVGKVIGKAGSNLANIRKISGATIEMSDSKSSRGDRVALISGTPEQKRAAENLIQAFIMAT
Secondary Structure (PSIPRED)
ccccccccccccccccccccccccccccccccccccEEEEEEEEcccccEEEccccHHHHHHHHHccccEEEcccccccccEEEEEEcccccccccccccccccccccHHHHHHHHHHHHHHHHHHcccccccccccccEEEEEEEEccccEEEEccccHHHHHHHHHccccEEEEcccccccccccccccccEEEEEEcHHHHHHHHHHHHHHHHHccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccEEEEEEcccccccccccccccHHHHHHHHHccEEEEcccccccccEEEEEEccccHHHHHHHHHHHHHHHHccccccccccEEEEEEEEcccccEEEcccccHHHHHHHHHcccEEEcccccccccccccEEEEEEccHHHHHHHHHHHHHHHccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccEEEEEEEcccccEEEcccccHHHHHHHHHccEEEEcccccccccEEEEEEccHHHHHHHHHHHHHHHHcc
Secondary Structure Prediction (SSPRO)
cccccccccccccccccccccccccccccccccccEEEEEEEEccccEEEEEccccHHHHHHHHHcccEEEEcccccccccEEEEEEccHHHHHHHHHHHHHcccccccHHHHHHHHHHHHHHHcccccccccccccccEEEEEEEEcccEEEEEccccHHHHHHHHHcccEEEEEcccccccccccccccccEEEEEccHHHHHHHHHHHHHHHHHccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccEEEEEEEccccEEEEEcccccEHHHHHHHcccEEEEcccccccccEEEEEEccccHHHHHHHHHHHHHHHHHHccccccccEEEEEEEEcccEEEEEcccccHHHHHHHHcccEEEEccccccccccccccEEEEEccHHHHHHHHHHHHHHHHHccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccEEEEEEccccccEEEcccccHHHHHHHHcccEEEEEccccccccEEEEEEccHHHHHHHHHHHHHHHHcc
Coil and Loop (DISEMBL)
mgdsgkryrsqrdndrdgknqkRRINekdekgneeSVIYRIlcpdgvigsvigksGKVINSIRQETRarvkvvdpfpgakdRVVTIYSHvkdkedvevddefndkeplCAAQDALLKVHAAIANAVANatdndkkrkekeecqilvpssqsaniiGKAGATIKRLRSKtrtsikvtpkdasepthscamefdnfvliSGESEAVKKALFAISAIMykfsprediplettvreappsiiipsdvpiyppgglypnadpilpsrsvpsilgaarvpdlqgyadtgntwpvystGLSLVsglvgasqseELVIRVLCpfnkigrvigkgggTIKSIRQasgaqidvddtkdnrdeCVITVTAIESPDDIKSMAVEAVLLLQTkindedddtVTIRLLVSSKVIGCIIGKSGSIINEIRKRTKAdvriskgdkpkcadanDELVEVVGEVGSVRDALVQIILRLRDDalkdrdgsrnppvgadhiyssgtgismppllpsippvgplgydqradsgsgigmlsssslygygslsmgdspygsmssyssklygglpppltlevlvpANAVGKVIGKAGSNLANIRKISGatiemsdskssrgdrvalisgtPEQKRAAENLIQAFIMAT
Flexible Loop (DISEMBL)
mgdsgkryrsqrdndrdgknqkrrinekdekgneesviYRILcpdgvigsvigksgkvinsirqetrarvkvvdpfpgakdrvvTIYSHVKDKEDVEVDDEFNDKEPLCAAQDALLKVHAAIANAVanatdndkkrkEKEEcqilvpssqsaniigkagatikrlrsktrtsikvtpkdasepthscAMEFDNFVLISGESEAVKKALFAISAIMYKFSPREDIPLETTVREAPPSIIIPSDVPIYPPGGLYPNADPILPSRSVPSILGAARVPDLQGYADTGNTWPVYSTGLSLVSGLVGASQSEELVIRVLCPFNKIGRVIGKGGGTIKSIRqasgaqidvddtkdnrdECVITvtaiespddikSMAVEAVLLLqtkindedddtVTIRLLVsskvigciigksgsiineirkrtkadvriskgdkpkcadandELVEVVgevgsvrdALVQIILRLrddalkdrdgsrnppvgaDHIYSSGTGISMPPLLPSIPPVGPLGYDQRADSGSGIGMLSSSSLYGYGSLSMGDSPYGSMSSYSSKLYGGLPPPLTLEVLVPANAVGKVigkagsnlaniRKISgatiemsdskssrgdRVALISGTPEQKRAAENLIQAFIMAT
Low Complexity Region (SEG)
MGDSGKRYRSQRDNDRDGKNQKRRINEKDEKGNEESVIYRILCPDGVIGSVIGKSGKVINSIRQETRARVKVVDPFPGAKDRVVTIYSHvkdkedvevddefndkePLCAAQDALLKVHaaianavanaTDNDKKRKEKEECQILVPSSQSANIIGKAGATIKRLRSKTRTSIKVTPKDASEPTHSCAMEFDNFVLISGESEAVKKALFAISAIMYKFSPREDIPLETTVREAppsiiipsdvpiyppGGLYPNADPILPSRSVPSILGAARVPDLQGYADTGNTWPVYSTGLSLVSGLVGASQSEELVIRVLCPFNKIGRVIGKGGGTIKSIRQASGAQIDVDDTKDNRDECVITVTAIESPDDIKSMAVEAVLLLQTKINDEDDDTVTIRLLVsskvigciigksgsiiNEIRKRTKADVRISKGDKPKCADANDELvevvgevgsvRDALVQIIlrlrddalkdrdGSRNPPVGADHIYSSGTgismppllpsippvgplgYDQRAdsgsgigmlsssslygygslsmgdspygsmssyssklygglpppltlevlvpANAVGKVIGKAGSNLANIRKISGATIEMSDSKSSRGDRVALISGTPEQKRAAENLIQAFIMAT
Disordered region (IsUnstruct)
************************************VIYRILCPDGVIGSVIGKSGKVINSIRQETRARVKVVDPFPGAKDRVVTIYSHVKDKEDVEVDDEFNDKEPLCAAQDALLKVHAAIANAVA***********************************************************CAMEFDNFVLISGESEAVKKALFAISAIMYKFSPREDIPLETTVREAPPSIIIPSDVPIYPPGGLYPNADPILPSRSVPSILGAARVPDLQGYADTGNTWPVYSTGLSLVSGLVGASQSEELVIRVLCPFNKIGRVIGKGGGTIKSIRQASGAQIDVDDTKDNRDECVITVTAIESPDDIKSMAVEAVLLLQTKINDEDDDTVTIRLLVSSKVIGCIIGKSGSIINEIRKRTKADVR********CADANDELVEVVGEVGSVRDALVQIILRLRD***********************************************************************************LYGGLPPPLTLEVLVPANAVGKVIGKAGSNLANIRKI******************************************
Disordered Region (DISOPRED)
*************************************IYRILCPDGVIGSVIGKSGKVINSIRQETRARVKVVDPFPGAKDRVVTIYSHVKDKEDVEVDD*F*D*EPLCAAQDALLKVHA********************ECQILVPSSQSANIIGKAGATIKRLRSKTRTSIKVTP*********CAMEFDNFVLISGESEAVKKALFAISAIMYKFSPREDIPLET*************************************SILGAARVP*******************************EELVIRVLCPFNKIGRVIGKGGGTIKSIRQASG*****D****NRDECVITVTAIESPDDIKSMAVEAV*****************RLLVSSKVIGCIIGKSGSIINEIRKRTKADVRISKGDKPKCADANDELVEVVGEVGSVRDALVQIILRLRDDAL***********GADHIYSSGTGISMPPLLPSIPPVGPLGYDQRADSGSGIGMLSSSSL********************SKLYGGLPPPLTLEVLVPANAVGKVIGKAGSNLANIRKISGATIEMS****SRGDRVALISGTPEQKRAAENLIQAFIMA*
Disordered Region (DISEMBL)
************************INEKDEKGNEESVIYRILCPDGVIGSVIGKSGKVINSIRQETRARVKVVDPFPGAKDRVVTIYSHVKDKEDVEVDDEFNDKEPLCAAQDALLKVHAAIANAVANA**************ILVPSSQSANIIGKAGATIKRLRS****************THSCAMEFDNFVLISGESEAVKKALFAISAIMYKFSPREDIPLETTVREAPPSIIIPSDVPIYPPGGLYPNADPILPSRSVPSILGAARVPDLQGYADTGNTWPVYSTGLSLVSGLVGASQSEELVIRVLCPFNKIGRVIGKGGGTIKSIRQASGAQIDVDDTKDNRDECVITVTAIESPDDIKSMAVEAVLLLQTKINDEDDDTVTIRLLVSSKVIGCIIGKSGSIINEIRKRTKADVRISKGDKPKCADANDELVEVVGEVGSVRDALVQIILRLRDDALKDRDGSRNPPVGADHIYSSGTGISMPPLLPSIPPVGPLGYDQRADSGSGIGMLSSSSLYGYGSLSMGDSPYGSMSSYSSKLYGGLPPPLTLEVLVPANAVGKVIGKAGSNLANIRKISGATI*************ALISGTPEQKRAAENLIQAFIMAT
Disordered Region (DISPRO)
********************************NEESVIYRILCPDGVIGSVIGKSGKVINSIRQETRARVKVVDPFPGAKDRVVTIYSHVKDKEDVEVDDEFNDKEPLCAAQDALLKVHAAIANAVAN*******RKEKEECQILVPSSQSANIIGKAGATIKRLRSKTRTSIKVTPKDASEPTHSCAMEFDNFVLISGESEAVKKALFAISAIMYKFSPREDIPLETTVREAPPSIIIPSDVPIYPPGGLYPNADPILPSRSVPSI**A**********************************SEELVIRVLCPFNKIGRVIGKGGGTIKSIRQASGAQIDVDDTKDNRDECVITVTAIESPDDIKSMAVEAVLLLQTKINDEDDDTVTIRLLVSSKVIGCIIGKSGSIINEIRKRTKADVRISKGDKPKCADANDELVEVVGEVGSVRDALVQIILRLRDDALKDRDGSRNP**GADH*****TGISMPPLLPSIPPVGPLGYDQRADSGSGIGMLSSSSLYGYGSL*M*D******************PPLTLEVLVPANAVGKVIGKAGSNLANIRKISGATIEMSDSKSSRGDRVALISGTPEQKRAAENLIQAFIMA*
Transmembrane Helix (TMHMM)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
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Transmembrane Helix (MEMSAT)
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TM Helix, Signal Peptide (MEMSAT_SVM)
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TM Helix, Signal Peptide (Phobius)
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Signal Peptide (SignalP HMM Mode)
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Signal Peptide (SignalP NN Mode)
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Coiled Coils (COILS)
MGDSGKRYRSQRDNDRDGKNQKRRINEKDEKGNEESVIYRILCPDGVIGSVIGKSGKVINSIRQETRARVKVVDPFPGAKDRVVTIYSHVKDKEDVEVDDEFNDKEPLCAAQDALLKVHAAIANAVANATDNDKKRKEKEECQILVPSSQSANIIGKAGATIKRLRSKTRTSIKVTPKDASEPTHSCAMEFDNFVLISGESEAVKKALFAISAIMYKFSPREDIPLETTVREAPPSIIIPSDVPIYPPGGLYPNADPILPSRSVPSILGAARVPDLQGYADTGNTWPVYSTGLSLVSGLVGASQSEELVIRVLCPFNKIGRVIGKGGGTIKSIRQASGAQIDVDDTKDNRDECVITVTAIESPDDIKSMAVEAVLLLQTKINDEDDDTVTIRLLVSSKVIGCIIGKSGSIINEIRKRTKADVRISKGDKPKCADANDELVEVVGEVGSVRDALVQIILRLRDDALKDRDGSRNPPVGADHIYSSGTGISMPPLLPSIPPVGPLGYDQRADSGSGIGMLSSSSLYGYGSLSMGDSPYGSMSSYSSKLYGGLPPPLTLEVLVPANAVGKVIGKAGSNLANIRKISGATIEMSDSKSSRGDRVALISGTPEQKRAAENLIQAFIMAT
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	624	2.2.26 [Sep-21-2011]
P58223	606	KH domain-containing prot	no	no	0.948	0.976	0.539	1e-179
P57721	371	Poly(rC)-binding protein	yes	no	0.459	0.773	0.283	4e-19
P57722	371	Poly(rC)-binding protein	yes	no	0.459	0.773	0.283	5e-19
Q0VCU0	403	Poly(rC)-binding protein	no	no	0.443	0.687	0.276	1e-15
Q5SF07	592	Insulin-like growth facto	no	no	0.445	0.469	0.247	1e-15
P57724	403	Poly(rC)-binding protein	no	no	0.455	0.704	0.273	4e-15
P57723	403	Poly(rC)-binding protein	no	no	0.443	0.687	0.273	4e-15
O19048	356	Poly(rC)-binding protein	no	no	0.475	0.834	0.265	7e-15
P60335	356	Poly(rC)-binding protein	no	no	0.475	0.834	0.265	7e-15
Q15365	356	Poly(rC)-binding protein	no	no	0.475	0.834	0.265	7e-15

>sp|P58223|Y4837_ARATH KH domain-containing protein At4g18375 OS=Arabidopsis thaliana GN=At4g18375 PE=2 SV=1

 Score =  629 bits (1623), Expect = e-179,   Method: Compositional matrix adjust.
 Identities = 344/638 (53%), Positives = 441/638 (69%), Gaps = 46/638 (7%)

Query: 1   MGDSGKRYRSQRDNDRDGKNQKRRINEKDEKGNEESVIYRILCPDGVIGSVIGKSGKVIN 60
           M +  KR + QR+N    +NQKRRI+  D+   +E V+YRILCP  V+G VIGKSGKVIN
Sbjct: 1   MVERKKRKQIQRNNSESNRNQKRRISH-DKINRDELVVYRILCPIDVVGGVIGKSGKVIN 59

Query: 61  SIRQETRARVKVVDPFPGAKDRVVTIYSHVKDKEDVEVDDEFNDKEPLCAAQDALLKVHA 120
           +IR  T+A++KV D   G   RV+TIY  VK+K++ E+    ++ EPLC AQDALLKV+ 
Sbjct: 60  AIRHNTKAKIKVFDQLHGCSQRVITIYCSVKEKQE-EIGFTKSENEPLCCAQDALLKVYD 118

Query: 121 AI-ANAVANATDNDKKRKEKEECQILVPSSQSANIIGKAGATIKRLRSKTRTSIKVTPKD 179
           AI A+   N T  +  R + +EC++LVP SQS+++IGKAG  IKR+R +TR S+KV  KD
Sbjct: 119 AIVASDEENNTKTNVDRDDNKECRLLVPFSQSSSLIGKAGENIKRIRRRTRASVKVVSKD 178

Query: 180 ASEPTHSCAMEFDNFVLISGESEAVKKALFAISAIMYKFSPREDIPLETTVREAP-PSII 238
            S+P+H CAME+DN V+ISGE E+VK+ALFA+SAIMYK +PRE+IPL++T ++ P  S+I
Sbjct: 179 VSDPSHVCAMEYDNVVVISGEPESVKQALFAVSAIMYKINPRENIPLDSTSQDVPAASVI 238

Query: 239 IPSDV--PIYPPGGLYPNADPILPSRS-VPSILGAARVPDLQGYADT-GNTWPVYSTGLS 294
           +PSD+   +YP  G Y N D IL   + VPS   A  V D QGYA+T  N  PV+++ L 
Sbjct: 239 VPSDLSNSVYPQTGFYSNQDHILQQGAGVPSYFNALSVSDFQGYAETAANPVPVFASSLP 298

Query: 295 LVSGLVGASQSEELVIRVLCPFNKIGRVIGKGGGTIKSIRQASGAQIDVDD--TKDNRDE 352
           +  G  G+S+SEELV +VLCP   I RVIGKGG TIK IR+ASG+ I+V+D  TK   DE
Sbjct: 299 VTHGFGGSSRSEELVFKVLCPLCNIMRVIGKGGSTIKRIREASGSCIEVNDSRTKCGDDE 358

Query: 353 CVITVTAIESPDDIKSMAVEAVLLLQTKINDEDDDTVTIRLLVSSKVIGCIIGKSGSIIN 412
           CVI VTA ESPDD+KSMAVEAVLLLQ  INDED + V ++LLVSSKVIGC+IGKSGS+IN
Sbjct: 359 CVIIVTATESPDDMKSMAVEAVLLLQEYINDEDAENVKMQLLVSSKVIGCVIGKSGSVIN 418

Query: 413 EIRKRTKADVRISKGDKPKCADANDELVEVVGEVGSVRDALVQIILRLRDDALKDRD--G 470
           EIRKRT A++ ISKG K       D+LVEV GEV SVRDAL+QI+LRLR+D L D+D   
Sbjct: 419 EIRKRTNANICISKGKK-------DDLVEVSGEVSSVRDALIQIVLRLREDVLGDKDSVA 471

Query: 471 SRNPPVGADHIY----SSGTGISMPPLLPSIPPVGPLGYDQRADSGSGIGMLSSSSLYGY 526
           +R PP   D+      SS  G ++P  + S                    M S+S  +GY
Sbjct: 472 TRKPPARTDNCSFLSGSSNAGYTLPSFMSS--------------------MASTSGFHGY 511

Query: 527 GSLSMGDSPYGSMSSYSSKLYGGLPPPLTLEVLVPANAVGKVIGKAGSNLANIRKISGAT 586
           GS   GD+  GS   YS   YG LP    LE+L+PA+A+ KV+GK G NL NIR+ISGA 
Sbjct: 512 GSFPAGDNVLGSTGPYS---YGRLPSSSALEILIPAHAMSKVMGKGGGNLENIRRISGAM 568

Query: 587 IEMSDSKSSRGDRVALISGTPEQKRAAENLIQAFIMAT 624
           IE+S SK+S GD +AL+SGT EQ R AENL+QAF+M+T
Sbjct: 569 IEISASKTSHGDHIALLSGTLEQMRCAENLVQAFVMST 606

Arabidopsis thaliana (taxid: 3702)

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

 Score = 96.7 bits (239), Expect = 4e-19,   Method: Compositional matrix adjust.
 Identities = 96/339 (28%), Positives = 155/339 (45%), Gaps = 52/339 (15%)

Query: 308 LVIRVLCPFNKIGRVIGKGGGTIKSIRQASGAQIDVDDTKDNRDECVITVTAIESPDD-- 365
           L IR+L    ++G +IGK G T+K +R+ SGA+I++ +   N  E ++T+T    P D  
Sbjct: 46  LTIRLLMHGKEVGSIIGKKGETVKKMREESGARINISE--GNCPERIVTITG---PTDAI 100

Query: 366 IKSMAVEAVLLLQTKINDEDDDT------VTIRLLVSSKVIGCIIGKSGSIINEIRKRTK 419
            K+ A+ A    +  IN   +        VT+RL+V +   G +IGK GS I EIR+ T 
Sbjct: 101 FKAFAMIAYKFEEDIINSMSNSPATSKPPVTLRLVVPASQCGSLIGKGGSKIKEIRESTG 160

Query: 420 ADVRISKGDKPKCADANDELVEVVGEVGSVRDALVQIILRLRDDALKDRDGSRNP-PVGA 478
           A V+++ GD     ++ +  V + G   ++   + QI + + +   K       P P   
Sbjct: 161 AQVQVA-GDM--LPNSTERAVTISGTPDAIIQCVKQICVVMLESPPKGATIPYRPKPAST 217

Query: 479 DHIYSSGTG--------ISMPPLLPSI-------PPVGPLGYDQRADSGSGIGMLSSSSL 523
             I++ G          I  P  L  +        P  PLG    A  G  + + SS   
Sbjct: 218 PVIFAGGQAYTIQGQYAIPHPDQLTKLHQLAMQQTPFPPLGQTNPAFPGEKLPLHSSEEA 277

Query: 524 YGYGSLSMGDSPYGSMSSYSSKLYGGL---PPPLTLEVLVPANAVGKVIGKAGSNLANIR 580
                  MG S              GL   PP  T E+ +P + +G +IG+ G+ +  IR
Sbjct: 278 QNL----MGQS-------------SGLDASPPASTHELTIPNDLIGCIIGRQGTKINEIR 320

Query: 581 KISGATIEMSDSKSSRGDRVALISGTPEQKRAAENLIQA 619
           ++SGA I+++++     +R   I+GTP     A+ LI A
Sbjct: 321 QMSGAQIKIANATEGSSERQITITGTPANISLAQYLINA 359

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

Homo sapiens (taxid: 9606)

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

 Score = 96.7 bits (239), Expect = 5e-19,   Method: Compositional matrix adjust.
 Identities = 96/339 (28%), Positives = 155/339 (45%), Gaps = 52/339 (15%)

Query: 308 LVIRVLCPFNKIGRVIGKGGGTIKSIRQASGAQIDVDDTKDNRDECVITVTAIESPDD-- 365
           L IR+L    ++G +IGK G T+K +R+ SGA+I++ +   N  E ++T+T    P D  
Sbjct: 46  LTIRLLMHGKEVGSIIGKKGETVKKMREESGARINISE--GNCPERIVTITG---PTDAI 100

Query: 366 IKSMAVEAVLLLQTKINDEDDDT------VTIRLLVSSKVIGCIIGKSGSIINEIRKRTK 419
            K+ A+ A    +  IN   +        VT+RL+V +   G +IGK GS I EIR+ T 
Sbjct: 101 FKAFAMIAYKFEEDIINSMSNSPATSKPPVTLRLVVPASQCGSLIGKGGSKIKEIRESTG 160

Query: 420 ADVRISKGDKPKCADANDELVEVVGEVGSVRDALVQIILRLRDDALKDRDGSRNP-PVGA 478
           A V+++ GD     ++ +  V + G   ++   + QI + + +   K       P P   
Sbjct: 161 AQVQVA-GDM--LPNSTERAVTISGTPDAIIQCVKQICVVMLESPPKGATIPYRPKPAST 217

Query: 479 DHIYSSGTG--------ISMPPLLPSI-------PPVGPLGYDQRADSGSGIGMLSSSSL 523
             I++ G          I  P  L  +        P  PLG    A  G  + + SS   
Sbjct: 218 PVIFAGGQAYTIQGQYAIPHPDQLTKLHQLAMQQTPFPPLGQTNPAFPGEKLPLHSSEEA 277

Query: 524 YGYGSLSMGDSPYGSMSSYSSKLYGGL---PPPLTLEVLVPANAVGKVIGKAGSNLANIR 580
                  MG S              GL   PP  T E+ +P + +G +IG+ G+ +  IR
Sbjct: 278 QNL----MGQS-------------SGLDASPPASTHELTIPNDLIGCIIGRQGTKINEIR 320

Query: 581 KISGATIEMSDSKSSRGDRVALISGTPEQKRAAENLIQA 619
           ++SGA I+++++     +R   I+GTP     A+ LI A
Sbjct: 321 QMSGAQIKIANATEGSSERQITITGTPANISLAQYLINA 359

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

Mus musculus (taxid: 10090)

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

 Score = 85.5 bits (210), Expect = 1e-15,   Method: Compositional matrix adjust.
 Identities = 91/329 (27%), Positives = 155/329 (47%), Gaps = 52/329 (15%)

Query: 308 LVIRVLCPFNKIGRVIGKGGGTIKSIRQASGAQIDVDDTKDNRDECVITVTAIESPDDIK 367
           L +R+L    ++G +IGK G T+K IR+ S A+I + +   +  E + T+T         
Sbjct: 18  LTLRMLMHGKEVGSIIGKKGETVKRIREQSSARITISE--GSCPERITTITGS------T 69

Query: 368 SMAVEAVLLLQTKINDED------------DDTVTIRLLVSSKVIGCIIGKSGSIINEIR 415
           +    AV ++  K+ DED               VT+RL++ +   G +IGK+G+ I EIR
Sbjct: 70  AAVFHAVSMIAFKL-DEDLCAAPANGGNVSRPPVTLRLVIPASQCGSLIGKAGTKIKEIR 128

Query: 416 KRTKADVRISKGDKPKCADANDELVEVVGEVGSVRDALVQIILRLRDDALKDRDGSRNPP 475
           + T A V+++    P   ++ +  V V G    V DA++  + ++    L+      +PP
Sbjct: 129 ETTGAQVQVAGDLLP---NSTERAVTVSG----VPDAIILCVRQICAVILE------SPP 175

Query: 476 VGADHIYSSGTGISMPPLLPSIPPVGPLGYDQRADSGSGIGMLSSSSLYGYGSLSMGDSP 535
            GA   Y     +S+  +L        L  +Q        G ++ + +     LS    P
Sbjct: 176 KGATIPYHPS--LSLGTVL--------LSTNQGFSVQGQYGTVTPAEVTKLQQLSGHAVP 225

Query: 536 YGSMSSYSSKLYGGLPPPL---TLEVLVPANAVGKVIGKAGSNLANIRKISGATIEMSDS 592
           + S S     +  GL P     + E LVP + +G VIG+ GS ++ IR++SGA I++ + 
Sbjct: 226 FASPS-----MVPGLDPSTQTSSQEFLVPNDLIGCVIGRQGSKISEIRQMSGAHIKIGNQ 280

Query: 593 KSSRGDRVALISGTPEQKRAAENLIQAFI 621
               G+R   I+G+P     A+ LI A +
Sbjct: 281 AEGAGERHVTITGSPVSIALAQYLITACL 309

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

Bos taurus (taxid: 9913)

>sp|Q5SF07|IF2B2_MOUSE Insulin-like growth factor 2 mRNA-binding protein 2 OS=Mus musculus GN=Igf2bp2 PE=1 SV=1

 Score = 85.1 bits (209), Expect = 1e-15,   Method: Compositional matrix adjust.
 Identities = 81/327 (24%), Positives = 150/327 (45%), Gaps = 49/327 (14%)

Query: 310 IRVLCPFNKIGRVIGKGGGTIKSIRQASGAQIDVDDTKDNRDECVITVTAIESPDDIKSM 369
           +R+L P   +G +IGK G TIK+I + + +++D+   K+N       VT   +P+   S 
Sbjct: 189 LRILVPTQFVGAIIGKEGLTIKNITKQTQSRVDIHR-KENSGAAEKPVTIHATPEGT-SE 246

Query: 370 AVEAVLLLQTKINDEDD--DTVTIRLLVSSKVIGCIIGKSGSIINEIRKRTKADVRISKG 427
           A   +L +  K  DE    + V +++L  +  +G +IGK G  + +I   T   + IS  
Sbjct: 247 ACRMILEIMQKEADETKLAEEVPLKILAHNGFVGRLIGKEGRNLKKIEHETGTKITISSL 306

Query: 428 DKPKCADANDELVEVVGEVGSVRDALVQIILRLRD----DALK-DRDGSRNPPVGADHIY 482
                 +  +  + V G + +  +A ++I+ +LR+    D L  ++  +  P +    + 
Sbjct: 307 QDLSIYNP-ERTITVRGTIEACANAEIEIMKKLREAFENDMLAVNQQANLIPGLNLSALG 365

Query: 483 SSGTGISMPPLLPSIPPVGPLGYDQRADSGSGIGMLSSSSLYGYGSLSMGDSPYGSMSSY 542
              TG+S+ P     PP GP G             +  S  Y          P+ + S Y
Sbjct: 366 IFSTGLSVLP-----PPAGPRG-------------VPPSPPY---------HPFATHSGY 398

Query: 543 SSKLYG-----------GLPPPLTLEVLVPANAVGKVIGKAGSNLANIRKISGATIEMSD 591
            S LY              P   T+ + +P  AVG +IGK G+++  + + +GA+I+++ 
Sbjct: 399 FSSLYPHHHFGPFPHHHSYPEQETVSLFIPTQAVGAIIGKKGAHIKQLARFAGASIKIAP 458

Query: 592 SKS-SRGDRVALISGTPEQKRAAENLI 617
           ++     +R+ +I+G PE +  A+  I
Sbjct: 459 AEGPDVSERMVIITGPPEAQFKAQGRI 485

Binds to the 5'-UTR of the insulin-like growth factor 2 (IGF2) mRNAs. Binding is isoform-specific. May regulate translation of target mRNAs.

Mus musculus (taxid: 10090)

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

 Score = 84.0 bits (206), Expect = 4e-15,   Method: Compositional matrix adjust.
 Identities = 92/336 (27%), Positives = 157/336 (46%), Gaps = 52/336 (15%)

Query: 301 GASQSEELVIRVLCPFNKIGRVIGKGGGTIKSIRQASGAQIDVDDTKDNRDECVITVTAI 360
           G   S  L +R+L    ++G +IGK G T+K IR+ S A+I + +   +  E + T+T  
Sbjct: 11  GPELSITLTLRMLMHGKEVGSIIGKKGETVKRIREQSSARITISE--GSCPERITTITGS 68

Query: 361 ESPDDIKSMAVEAVLLLQTKINDED------------DDTVTIRLLVSSKVIGCIIGKSG 408
                  +    AV ++  K+ DED               VT+RL++ +   G +IGK+G
Sbjct: 69  ------TAAVFHAVSMIAFKL-DEDLCAAPANGGSVSRPPVTLRLVIPASQCGSLIGKAG 121

Query: 409 SIINEIRKRTKADVRISKGDKPKCADANDELVEVVGEVGSVRDALVQIILRLRDDALKDR 468
           + I EIR+ T A V+++    P   ++ +  V V G    V DA++  + ++    L+  
Sbjct: 122 TKIKEIRETTGAQVQVAGDLLP---NSTERAVTVSG----VPDAIILCVRQICAVILE-- 172

Query: 469 DGSRNPPVGADHIYSSGTGISMPPLLPSIPPVGPLGYDQRADSGSGIGMLSSSSLYGYGS 528
               +PP GA   Y     +S+  +L        L  +Q        G ++ + +     
Sbjct: 173 ----SPPKGATIPYHPS--LSLGTVL--------LSANQGFSVQGQYGAVTPAEVTKLQQ 218

Query: 529 LSMGDSPYGSMSSYSSKLYGGLPPPL---TLEVLVPANAVGKVIGKAGSNLANIRKISGA 585
           LS    P+ S S     +  G+ P     + E LVP + +G VIG+ GS ++ IR++SGA
Sbjct: 219 LSGHAVPFASPS-----VVPGMDPSTQTSSQEFLVPNDLIGCVIGRQGSKISEIRQMSGA 273

Query: 586 TIEMSDSKSSRGDRVALISGTPEQKRAAENLIQAFI 621
            I++ +     G+R   I+G+P     A+ LI A +
Sbjct: 274 HIKIGNQAEGAGERHVTITGSPVSIALAQYLITACL 309

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

Mus musculus (taxid: 10090)

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

 Score = 83.6 bits (205), Expect = 4e-15,   Method: Compositional matrix adjust.
 Identities = 90/329 (27%), Positives = 155/329 (47%), Gaps = 52/329 (15%)

Query: 308 LVIRVLCPFNKIGRVIGKGGGTIKSIRQASGAQIDVDDTKDNRDECVITVTAIESPDDIK 367
           L +R+L    ++G +IGK G T+K IR+ S A+I + +   +  E + T+T         
Sbjct: 18  LTLRMLMHGKEVGSIIGKKGETVKRIREQSSARITISE--GSCPERITTITGS------T 69

Query: 368 SMAVEAVLLLQTKINDED------------DDTVTIRLLVSSKVIGCIIGKSGSIINEIR 415
           +    AV ++  K+ DED               VT+RL++ +   G +IGK+G+ I EIR
Sbjct: 70  AAVFHAVSMIAFKL-DEDLCAAPANGGNVSRPPVTLRLVIPASQCGSLIGKAGTKIKEIR 128

Query: 416 KRTKADVRISKGDKPKCADANDELVEVVGEVGSVRDALVQIILRLRDDALKDRDGSRNPP 475
           + T A V+++    P   ++ +  V V G    V DA++  + ++    L+      +PP
Sbjct: 129 ETTGAQVQVAGDLLP---NSTERAVTVSG----VPDAIILCVRQICAVILE------SPP 175

Query: 476 VGADHIYSSGTGISMPPLLPSIPPVGPLGYDQRADSGSGIGMLSSSSLYGYGSLSMGDSP 535
            GA   Y     +S+  +L        L  +Q        G ++ + +     LS    P
Sbjct: 176 KGATIPYHPS--LSLGTVL--------LSANQGFSVQGQYGAVTPAEVTKLQQLSSHAVP 225

Query: 536 YGSMSSYSSKLYGGLPPPL---TLEVLVPANAVGKVIGKAGSNLANIRKISGATIEMSDS 592
           + + S     +  GL P     + E LVP + +G VIG+ GS ++ IR++SGA I++ + 
Sbjct: 226 FATPS-----VVPGLDPGTQTSSQEFLVPNDLIGCVIGRQGSKISEIRQMSGAHIKIGNQ 280

Query: 593 KSSRGDRVALISGTPEQKRAAENLIQAFI 621
               G+R   I+G+P     A+ LI A +
Sbjct: 281 AEGAGERHVTITGSPVSIALAQYLITACL 309

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

Homo sapiens (taxid: 9606)

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

 Score = 82.8 bits (203), Expect = 7e-15,   Method: Compositional matrix adjust.
 Identities = 92/347 (26%), Positives = 158/347 (45%), Gaps = 50/347 (14%)

Query: 308 LVIRVLCPFNKIGRVIGKGGGTIKSIRQASGAQIDVDDTKDNRDECVITVTAIESPDDIK 367
           L IR+L    ++G +IGK G ++K IR+ SGA+I++ +   N  E +IT+T    P +  
Sbjct: 14  LTIRLLMHGKEVGSIIGKKGESVKRIREESGARINISE--GNCPERIITLTG---PTNAI 68

Query: 368 SMAVEAVL-LLQTKINDEDDDT-------VTIRLLVSSKVIGCIIGKSGSIINEIRKRTK 419
             A   ++  L+  IN    ++       VT+RL+V +   G +IGK G  I EIR+ T 
Sbjct: 69  FKAFAMIIDKLEEDINSSMTNSTAASRPPVTLRLVVPATQCGSLIGKGGCKIKEIRESTG 128

Query: 420 ADVRISKGDKPKCADANDELVEVVGEVGSVRDALVQIILRLRDDALKDRDG--------- 470
           A V+++    P   ++ +  + + G   SV + + QI L + +   +   G         
Sbjct: 129 AQVQVAGDMLP---NSTERAITIAGVPQSVTECVKQICLVMLETLSQSPQGRVMTIPYQP 185

Query: 471 --SRNPPV---GADHI-----YSSGTG-ISMPPL-------LPSIPPVGPLGYDQRADSG 512
             + +P +   G D       Y   T  +  PPL         +I P+     +Q A   
Sbjct: 186 MPASSPVICAGGQDRCSDAAGYPHATHDLEGPPLDAYSIQGQHTISPLDLAKLNQVARQQ 245

Query: 513 SGIGMLSSSSLYGYGSLSMGDSPYGSMSSYSSKLYGGLPPPLTLEVLVPANAVGKVIGKA 572
           S   M+   +  G+  +   DS    +  Y + L        T E+ +P N +G +IG+ 
Sbjct: 246 SHFAMMHGGT--GFAGI---DSSSPEVKGYWASLDAST--QTTHELTIPNNLIGCIIGRQ 298

Query: 573 GSNLANIRKISGATIEMSDSKSSRGDRVALISGTPEQKRAAENLIQA 619
           G+N+  IR++SGA I++++       R   I+G+      A+ LI A
Sbjct: 299 GANINEIRQMSGAQIKIANPVEGSSGRQVTITGSAASISLAQYLINA 345

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 = 82.8 bits (203), Expect = 7e-15,   Method: Compositional matrix adjust.
 Identities = 92/347 (26%), Positives = 158/347 (45%), Gaps = 50/347 (14%)

Query: 308 LVIRVLCPFNKIGRVIGKGGGTIKSIRQASGAQIDVDDTKDNRDECVITVTAIESPDDIK 367
           L IR+L    ++G +IGK G ++K IR+ SGA+I++ +   N  E +IT+T    P +  
Sbjct: 14  LTIRLLMHGKEVGSIIGKKGESVKRIREESGARINISE--GNCPERIITLTG---PTNAI 68

Query: 368 SMAVEAVL-LLQTKINDEDDDT-------VTIRLLVSSKVIGCIIGKSGSIINEIRKRTK 419
             A   ++  L+  IN    ++       VT+RL+V +   G +IGK G  I EIR+ T 
Sbjct: 69  FKAFAMIIDKLEEDINSSMTNSTAASRPPVTLRLVVPATQCGSLIGKGGCKIKEIRESTG 128

Query: 420 ADVRISKGDKPKCADANDELVEVVGEVGSVRDALVQIILRLRDDALKDRDG--------- 470
           A V+++    P   ++ +  + + G   SV + + QI L + +   +   G         
Sbjct: 129 AQVQVAGDMLP---NSTERAITIAGVPQSVTECVKQICLVMLETLSQSPQGRVMTIPYQP 185

Query: 471 --SRNPPV---GADHI-----YSSGTG-ISMPPL-------LPSIPPVGPLGYDQRADSG 512
             + +P +   G D       Y   T  +  PPL         +I P+     +Q A   
Sbjct: 186 MPASSPVICAGGQDRCSDAAGYPHATHDLEGPPLDAYSIQGQHTISPLDLAKLNQVARQQ 245

Query: 513 SGIGMLSSSSLYGYGSLSMGDSPYGSMSSYSSKLYGGLPPPLTLEVLVPANAVGKVIGKA 572
           S   M+   +  G+  +   DS    +  Y + L        T E+ +P N +G +IG+ 
Sbjct: 246 SHFAMMHGGT--GFAGI---DSSSPEVKGYWASLDAST--QTTHELTIPNNLIGCIIGRQ 298

Query: 573 GSNLANIRKISGATIEMSDSKSSRGDRVALISGTPEQKRAAENLIQA 619
           G+N+  IR++SGA I++++       R   I+G+      A+ LI A
Sbjct: 299 GANINEIRQMSGAQIKIANPVEGSSGRQVTITGSAASISLAQYLINA 345

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 = 82.8 bits (203), Expect = 7e-15,   Method: Compositional matrix adjust.
 Identities = 92/347 (26%), Positives = 158/347 (45%), Gaps = 50/347 (14%)

Query: 308 LVIRVLCPFNKIGRVIGKGGGTIKSIRQASGAQIDVDDTKDNRDECVITVTAIESPDDIK 367
           L IR+L    ++G +IGK G ++K IR+ SGA+I++ +   N  E +IT+T    P +  
Sbjct: 14  LTIRLLMHGKEVGSIIGKKGESVKRIREESGARINISE--GNCPERIITLTG---PTNAI 68

Query: 368 SMAVEAVL-LLQTKINDEDDDT-------VTIRLLVSSKVIGCIIGKSGSIINEIRKRTK 419
             A   ++  L+  IN    ++       VT+RL+V +   G +IGK G  I EIR+ T 
Sbjct: 69  FKAFAMIIDKLEEDINSSMTNSTAASRPPVTLRLVVPATQCGSLIGKGGCKIKEIRESTG 128

Query: 420 ADVRISKGDKPKCADANDELVEVVGEVGSVRDALVQIILRLRDDALKDRDG--------- 470
           A V+++    P   ++ +  + + G   SV + + QI L + +   +   G         
Sbjct: 129 AQVQVAGDMLP---NSTERAITIAGVPQSVTECVKQICLVMLETLSQSPQGRVMTIPYQP 185

Query: 471 --SRNPPV---GADHI-----YSSGTG-ISMPPL-------LPSIPPVGPLGYDQRADSG 512
             + +P +   G D       Y   T  +  PPL         +I P+     +Q A   
Sbjct: 186 MPASSPVICAGGQDRCSDAAGYPHATHDLEGPPLDAYSIQGQHTISPLDLAKLNQVARQQ 245

Query: 513 SGIGMLSSSSLYGYGSLSMGDSPYGSMSSYSSKLYGGLPPPLTLEVLVPANAVGKVIGKA 572
           S   M+   +  G+  +   DS    +  Y + L        T E+ +P N +G +IG+ 
Sbjct: 246 SHFAMMHGGT--GFAGI---DSSSPEVKGYWASLDAST--QTTHELTIPNNLIGCIIGRQ 298

Query: 573 GSNLANIRKISGATIEMSDSKSSRGDRVALISGTPEQKRAAENLIQA 619
           G+N+  IR++SGA I++++       R   I+G+      A+ LI A
Sbjct: 299 GANINEIRQMSGAQIKIANPVEGSSGRQVTITGSAASISLAQYLINA 345

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	624
356525090	625	PREDICTED: KH domain-containing protein	0.998	0.996	0.753	0.0
225443912	623	PREDICTED: KH domain-containing protein	0.998	1.0	0.778	0.0
147818880	637	hypothetical protein VITISV_042181 [Viti	0.998	0.978	0.760	0.0
224076902	623	predicted protein [Populus trichocarpa]	0.993	0.995	0.738	0.0
357447239	631	Heterogeneous nuclear ribonucleoprotein	0.996	0.985	0.696	0.0
449433573	625	PREDICTED: KH domain-containing protein	0.995	0.993	0.727	0.0
297791069	643	KH domain-containing protein [Arabidopsi	0.950	0.922	0.628	0.0
449525363	531	PREDICTED: KH domain-containing protein	0.823	0.967	0.705	0.0
15237393	644	RNA-binding KH domain-containing protein	0.956	0.927	0.605	0.0
21553916	644	unknown [Arabidopsis thaliana]	0.956	0.927	0.607	0.0

>gi|356525090|ref|XP_003531160.1| PREDICTED: KH domain-containing protein At4g18375-like [Glycine max]

 Score =  973 bits (2514), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 472/626 (75%), Positives = 558/626 (89%), Gaps = 3/626 (0%)

Query: 1   MGDSGKRYRSQRDNDRDGKNQKRRINEKDEKGNEESVIYRILCPDGVIGSVIGKSGKVIN 60
           MG++GKRY SQRD+D D K+QKRR+ ++D++GN+E ++YRILCPD VIGSVIGK+GKVIN
Sbjct: 1   MGETGKRYHSQRDHDGDRKHQKRRMTDRDDRGNDELIVYRILCPDEVIGSVIGKNGKVIN 60

Query: 61  SIRQETRARVKVVDPFPGAKDRVVTIYSHVKDKEDVEVDDEFNDKEPLCAAQDALLKVHA 120
           SIRQETRA+VKVVDPFPG+KDRV+TIY +VK+KEDVE+DDEF  KEPLCAAQDALLKVH 
Sbjct: 61  SIRQETRAKVKVVDPFPGSKDRVITIYCYVKEKEDVEIDDEFAGKEPLCAAQDALLKVHV 120

Query: 121 AIANAVANATDNDKKRKEKEECQILVPSSQSANIIGKAGATIKRLRSKTRTSIKVTPKDA 180
           AIAN++A   D++KKRK+++ECQILVPSSQSANIIGKAGATIK+LRSKTR +IKVT KDA
Sbjct: 121 AIANSIAAIGDSEKKRKDRDECQILVPSSQSANIIGKAGATIKKLRSKTRANIKVTAKDA 180

Query: 181 SEPTHSCAMEFDNFVLISGESEAVKKALFAISAIMYKFSPREDIPLETTVREAPPSIIIP 240
           ++PTHSCAMEFDNFV+I+GESEAVK+ALFA+S+IMYKF PREDI L+T V EAPPSIIIP
Sbjct: 181 ADPTHSCAMEFDNFVVITGESEAVKRALFAVSSIMYKFGPREDISLDTAVPEAPPSIIIP 240

Query: 241 SDVPIYPPGGLYPNADPILPSRSVPSILGAARVPDLQGYADTGNTWPVYSTGLSLVSGLV 300
           SDVP+YPPGGLYP +DPI+  R+VP I+GA  VPDLQGYAD GN+WP+YS+ L +VSG V
Sbjct: 241 SDVPVYPPGGLYPASDPIVTPRAVPQIIGATNVPDLQGYADAGNSWPMYSSALPVVSG-V 299

Query: 301 GASQSEELVIRVLCPFNKIGRVIGKGGGTIKSIRQASGAQIDVDDTKDNRDECVITVTAI 360
           GAS+SEEL+IR+LCP +KIGRVIGKGG TIKS+RQASGA I+VDD+K N DEC+I +T  
Sbjct: 300 GASRSEELIIRMLCPSDKIGRVIGKGGSTIKSMRQASGAHIEVDDSKANFDECLIIITTT 359

Query: 361 ESPDDIKSMAVEAVLLLQTKINDEDDDTVTIRLLVSSKVIGCIIGKSGSIINEIRKRTKA 420
           ESP D+KSMAVEAVLL+Q KINDEDD TV+IRLLV SKVIGCIIGKSGSIINEIRKRTKA
Sbjct: 360 ESPSDLKSMAVEAVLLMQGKINDEDDTTVSIRLLVPSKVIGCIIGKSGSIINEIRKRTKA 419

Query: 421 DVRISKGDKPKCADANDELVEVVGEVGSVRDALVQIILRLRDDALKDRDGSRNPPVGADH 480
           DVRISKGDKPKCADANDELVEV G V  VRDAL+QIILRLRDD L++RD   NP +GA+ 
Sbjct: 420 DVRISKGDKPKCADANDELVEVGGSVDCVRDALIQIILRLRDDVLRERDTGHNPSIGAES 479

Query: 481 IYSSGTGISMPPLLPSIPPV-GPLGYDQRADSGSGIGMLSSSSLY-GYGSLSMGDSPYGS 538
           +Y    G+S+P ++ S+PPV  P+ YD RA+SG+G+GMLS SS Y GYGSL MGD+ YGS
Sbjct: 480 LYPGSAGLSLPSMMHSVPPVAAPMVYDHRAESGAGLGMLSPSSPYGGYGSLPMGDNGYGS 539

Query: 539 MSSYSSKLYGGLPPPLTLEVLVPANAVGKVIGKAGSNLANIRKISGATIEMSDSKSSRGD 598
           MSSY++KLYGGLPPP TL++L+PANAVGKV+GK G+N+ANIRKISGA+IE+SD+KS+RGD
Sbjct: 540 MSSYATKLYGGLPPPSTLDMLIPANAVGKVLGKGGANIANIRKISGASIEISDNKSARGD 599

Query: 599 RVALISGTPEQKRAAENLIQAFIMAT 624
           R+ALISGTPEQKRAAENLIQAFIMAT
Sbjct: 600 RIALISGTPEQKRAAENLIQAFIMAT 625

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|225443912|ref|XP_002278367.1| PREDICTED: KH domain-containing protein At4g18375 [Vitis vinifera]

 Score =  927 bits (2395), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 486/624 (77%), Positives = 567/624 (90%), Gaps = 1/624 (0%)

Query: 1   MGDSGKRYRSQRDNDRDGKNQKRRINEKDEKGNEESVIYRILCPDGVIGSVIGKSGKVIN 60
           MG++GKR+RSQRD D D K QKRR+NE+DEKG++E ++YRILCPDGVIGSVIGKSGKVIN
Sbjct: 1   MGETGKRFRSQRDQDGDNKIQKRRVNERDEKGSDELIVYRILCPDGVIGSVIGKSGKVIN 60

Query: 61  SIRQETRARVKVVDPFPGAKDRVVTIYSHVKDKEDVEVDDEFNDKEPLCAAQDALLKVHA 120
           SIRQ+TRA++KVVDPFPGAKDRV+TIY +VK+KE+VEVDDEFNDK+PLC AQDALLKVHA
Sbjct: 61  SIRQDTRAKIKVVDPFPGAKDRVITIYCYVKEKEEVEVDDEFNDKQPLCPAQDALLKVHA 120

Query: 121 AIANAVANATDNDKKRKEKEECQILVPSSQSANIIGKAGATIKRLRSKTRTSIKVTPKDA 180
           AI NAVA+  ++DKK+K+KEECQILVPSSQSAN+IGKAGATIKRLRSKTR +IK+T KD+
Sbjct: 121 AIVNAVASLENSDKKKKDKEECQILVPSSQSANVIGKAGATIKRLRSKTRANIKITAKDS 180

Query: 181 SEPTHSCAMEFDNFVLISGESEAVKKALFAISAIMYKFSPREDIPLETTVREAPPSIIIP 240
           ++P+HSCAMEFDNFVLI+G+SEAVKKALFAISAIMYKF+PRE+IPL+TTV EAPPSIIIP
Sbjct: 181 TDPSHSCAMEFDNFVLIAGDSEAVKKALFAISAIMYKFTPREEIPLDTTVPEAPPSIIIP 240

Query: 241 SDVPIYPPGGLYPNADPILPSRSVPSILGAARVPDLQGYADTGNTWPVYSTGLSLVSGLV 300
           SDVPIYP GG YP+AD I+ +RSVP +L A  VP+LQGY+D G+TWPVYS+ L +VSG  
Sbjct: 241 SDVPIYPAGGFYPSADSIVSARSVPPVLAATHVPELQGYSDMGSTWPVYSSNLPVVSGY- 299

Query: 301 GASQSEELVIRVLCPFNKIGRVIGKGGGTIKSIRQASGAQIDVDDTKDNRDECVITVTAI 360
           GAS+SEEL+IRVLCPF+KIGRVIG+GG +IKS+R+ASGA ++VDDTK +RDEC+ITVT+ 
Sbjct: 300 GASRSEELIIRVLCPFDKIGRVIGRGGSSIKSVREASGAHVEVDDTKADRDECLITVTST 359

Query: 361 ESPDDIKSMAVEAVLLLQTKINDEDDDTVTIRLLVSSKVIGCIIGKSGSIINEIRKRTKA 420
           ES DD+KSMAVEAVLLLQ KINDEDDDTV IRLLV SK+IGCIIGKSGSIINEIRKRT+A
Sbjct: 360 ESVDDLKSMAVEAVLLLQAKINDEDDDTVAIRLLVPSKIIGCIIGKSGSIINEIRKRTRA 419

Query: 421 DVRISKGDKPKCADANDELVEVVGEVGSVRDALVQIILRLRDDALKDRDGSRNPPVGADH 480
           DVRISK ++PKCADANDEL+EVVGEVGSVRDALVQI+LRLRDDALKDRD   N   G D 
Sbjct: 420 DVRISKSERPKCADANDELIEVVGEVGSVRDALVQIVLRLRDDALKDRDTGHNTSAGTDS 479

Query: 481 IYSSGTGISMPPLLPSIPPVGPLGYDQRADSGSGIGMLSSSSLYGYGSLSMGDSPYGSMS 540
           +YS G G+S+  +LPS PPV PL YDQRA++GSG+G+LSSSSLYGYGSLS+G++ YGSMS
Sbjct: 480 LYSGGAGLSVSSVLPSAPPVAPLSYDQRAETGSGLGLLSSSSLYGYGSLSVGENAYGSMS 539

Query: 541 SYSSKLYGGLPPPLTLEVLVPANAVGKVIGKAGSNLANIRKISGATIEMSDSKSSRGDRV 600
           SYSSKLYGGLP P T ++++PANAVGKV+GK G+N+ANIRKISGA IE+SDSKSSRGDRV
Sbjct: 540 SYSSKLYGGLPTPSTFDMVIPANAVGKVMGKGGANIANIRKISGAVIEISDSKSSRGDRV 599

Query: 601 ALISGTPEQKRAAENLIQAFIMAT 624
           ALISGTPEQKR AENLIQAFIMAT
Sbjct: 600 ALISGTPEQKRTAENLIQAFIMAT 623

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|147818880|emb|CAN73780.1| hypothetical protein VITISV_042181 [Vitis vinifera]

 Score =  917 bits (2369), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 485/638 (76%), Positives = 566/638 (88%), Gaps = 15/638 (2%)

Query: 1   MGDSGKRYRSQRDNDRDGKNQKRRINEKDEKGNEESVIYRILCPDGVIGSVIGKSGKVIN 60
           MG++GKR+RSQRD D D K QKRR+NE+DEKG++E ++YRILCPDGVIGSVIGKSGKVIN
Sbjct: 1   MGETGKRFRSQRDQDGDNKIQKRRVNERDEKGSDELIVYRILCPDGVIGSVIGKSGKVIN 60

Query: 61  SIRQETRARVKVVDPFPGAKDRVVTIYSHVKDKEDVEVDDEFNDKEPLCAAQDALLKVHA 120
           SIRQ+TRA++KVVDPFPGAKDRV+TIY +VK+KE+VEVDDEFNDK+PLC AQDALLKVHA
Sbjct: 61  SIRQDTRAKIKVVDPFPGAKDRVITIYCYVKEKEEVEVDDEFNDKQPLCPAQDALLKVHA 120

Query: 121 AIANAVANATDNDKKRKEKEECQILVPSSQSANIIGKAGATIKRLRSKTRTSIKVTPKDA 180
           AI NAVA+  ++DKK+K+KEECQILVPSSQSAN+IGKAGATIKRLRSKTR +IK+T KD+
Sbjct: 121 AIVNAVASLENSDKKKKDKEECQILVPSSQSANVIGKAGATIKRLRSKTRANIKITAKDS 180

Query: 181 SEPTHSCAMEFDNFVLISGESEAVKKALFAISAIMYKFSPREDIPLETTVREAPPSIIIP 240
           ++P+HSCAMEFDNFVLI+G+SEAVKKALFAISAIMYKF+PRE+IPL+TTV EAPPSIIIP
Sbjct: 181 TDPSHSCAMEFDNFVLIAGDSEAVKKALFAISAIMYKFTPREEIPLDTTVPEAPPSIIIP 240

Query: 241 SDVPIYPPGGLYPNADPILPSRSVPSILGAARVPDLQGYADTGNTWPVYSTGLSLVSGLV 300
           SDVPIYP GG YP+AD I+ +RSVP +L A  VP+LQGY+D G+TWPVYS+ L +VSG  
Sbjct: 241 SDVPIYPAGGFYPSADSIVSARSVPPVLAATHVPELQGYSDMGSTWPVYSSNLPVVSGY- 299

Query: 301 GASQSEELVIRVLCPFNKIGRVIGKGGGTIKSIRQASGAQIDVDDTKDNRDECVITVTAI 360
           GAS+SEEL+IRVLCPF+KIGRVIG+GG +IKS+R+ASGA ++VDDTK +RDEC+ITVT+ 
Sbjct: 300 GASRSEELIIRVLCPFDKIGRVIGRGGSSIKSVREASGAHVEVDDTKADRDECLITVTST 359

Query: 361 ESPDDIKSMAVEAVLLLQTKINDEDDDTVTIRLLVSSKVIGCIIGKSGSIINEIRKRTKA 420
           ES DD+KSMAVEAVLLLQ KINDEDDDTV IRLLV SK+IGCIIGKSGSIINEIRKRT+A
Sbjct: 360 ESVDDLKSMAVEAVLLLQAKINDEDDDTVAIRLLVPSKIIGCIIGKSGSIINEIRKRTRA 419

Query: 421 DVRISKGDKPKCADANDELVEVVGEVGSVRDALVQIILRLRDDALKDRDGSRNPPVGADH 480
           DVRISK ++PKCADANDEL+EVVGEVGSVRDALVQI+LRLRDDALKDRD   N   G D 
Sbjct: 420 DVRISKSERPKCADANDELIEVVGEVGSVRDALVQIVLRLRDDALKDRDTGHNTSAGTDS 479

Query: 481 IYSSGTGISMPPLLPSIPPVGPLGYDQRADSGSGIGMLSSSSLYGYGSL----------- 529
           +YS G G+S+  +LPS PPV PL YDQRA++GSG+G+LSSSSLYGYGSL           
Sbjct: 480 LYSGGAGLSVSSVLPSAPPVAPLSYDQRAETGSGLGLLSSSSLYGYGSLSLFFAVKVVVV 539

Query: 530 ---SMGDSPYGSMSSYSSKLYGGLPPPLTLEVLVPANAVGKVIGKAGSNLANIRKISGAT 586
               +G++ YGSMSSYSSKLYGGLP P T ++++PANAVGKV+GK G+N+ANIRKISGA 
Sbjct: 540 FNGEVGENAYGSMSSYSSKLYGGLPTPSTFDMVIPANAVGKVMGKGGANIANIRKISGAV 599

Query: 587 IEMSDSKSSRGDRVALISGTPEQKRAAENLIQAFIMAT 624
           IE+SDSKSSRGDRVALISGTPEQKR AENLIQAFIMAT
Sbjct: 600 IEISDSKSSRGDRVALISGTPEQKRTAENLIQAFIMAT 637

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|224076902|ref|XP_002305041.1| predicted protein [Populus trichocarpa] gi|222848005|gb|EEE85552.1| predicted protein [Populus trichocarpa]

 Score =  884 bits (2284), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 463/627 (73%), Positives = 537/627 (85%), Gaps = 7/627 (1%)

Query: 1   MGDSGKRYRSQRDNDRDGKNQKRRINEKDEKG--NEESVIYRILCPDGVIGSVIGKSGKV 58
           M +SGKR R QRD D D  NQKR    KD KG  N+E V+YRILCPD VIGSVIGKSGKV
Sbjct: 1   MVESGKRSRPQRDYDGDTNNQKR---HKDNKGTDNDELVVYRILCPDEVIGSVIGKSGKV 57

Query: 59  INSIRQETRARVKVVDPFPGAKDRVVTIYSHVKDKEDVEVDDEFNDKEPLCAAQDALLKV 118
           INSIR E+RARVKVVDPFPGA  RV+TIY +VK+K D +VDD+F+  +PLC AQDALLKV
Sbjct: 58  INSIRNESRARVKVVDPFPGAMYRVITIYCNVKEKGDADVDDDFHQADPLCPAQDALLKV 117

Query: 119 HAAIANAVANATDNDKKRKEKEECQILVPSSQSANIIGKAGATIKRLRSKTRTSIKVTPK 178
           HAAI+NAVA   D+DK+ ++K+ECQILVP+SQSANIIGKAGATIK+LRSKTR +IK+T K
Sbjct: 118 HAAISNAVAALGDSDKRCRDKKECQILVPTSQSANIIGKAGATIKKLRSKTRANIKITAK 177

Query: 179 DASEPTHSCAMEFDNFVLISGESEAVKKALFAISAIMYKFSPREDIPLETTVREAPPSII 238
           DAS+PTHSCAM+FDNF+LI+GESEAVKKALFA+SAIMYKFSP+E+IPLETTV EAPPSII
Sbjct: 178 DASDPTHSCAMDFDNFLLITGESEAVKKALFAVSAIMYKFSPKEEIPLETTVPEAPPSII 237

Query: 239 IPSDVPIYPPGGLYPNADPILPSRSVPSILGAARVPDLQGYADTGNTWPVYSTGLSLVSG 298
           I SDVPIY PGG YPNADPI+ SRSVP ILGA  +P+ QGY D  ++WP+YS+ + +V  
Sbjct: 238 ISSDVPIYQPGGFYPNADPIVSSRSVPPILGATHIPEFQGYGDMRSSWPIYSSTVPVVPS 297

Query: 299 LVGASQSEELVIRVLCPFNKIGRVIGKGGGTIKSIRQASGAQIDVDDTKDNRDECVITVT 358
               S+S EL+IR+LCPF+KIGRVIGKGG TIKSIRQ SGA+I+VDDTK +RDEC+ITV 
Sbjct: 298 FGNTSRS-ELIIRLLCPFDKIGRVIGKGGSTIKSIRQVSGARIEVDDTKADRDECIITVI 356

Query: 359 AIESPDDIKSMAVEAVLLLQTKINDEDDDTVTIRLLVSSKVIGCIIGKSGSIINEIRKRT 418
           A ESPDD+KSMAVEA+LLLQ KINDED+D V IR LV SKVIGCIIGKSG+I+NEIRKRT
Sbjct: 357 ATESPDDLKSMAVEAILLLQGKINDEDNDIVGIRFLVPSKVIGCIIGKSGAIVNEIRKRT 416

Query: 419 KADVRISKGDKPKCADANDELVEVVGEVGSVRDALVQIILRLRDDALKDRDGSRNPPVGA 478
            ADV ISK DK KCAD+NDELVEV GEVGSVRDALVQI+LRLRDD LK++DG  N  VG 
Sbjct: 417 NADVCISKVDKLKCADSNDELVEVAGEVGSVRDALVQIVLRLRDDVLKEKDGGLNSSVGT 476

Query: 479 DHIYSSGTGISMPPLLPSIPPVGPLGYDQRADSGSGIGMLSSSSLYGYGSLSMGDSPYGS 538
           D +Y    GIS+P +LPS+PPV P+GYDQRA+SGSG+G+ SSSSLYGYGSL MG++ YGS
Sbjct: 477 DSVYPVHAGISIPSILPSVPPVAPMGYDQRAESGSGLGLFSSSSLYGYGSLPMGENSYGS 536

Query: 539 MSSYS-SKLYGGLPPPLTLEVLVPANAVGKVIGKAGSNLANIRKISGATIEMSDSKSSRG 597
           ++SYS SKLY GLPPP TLE+LVPANAVGKVIGK G+N+ANIRKISGA IE+SD+KS+RG
Sbjct: 537 LASYSLSKLYEGLPPPSTLEMLVPANAVGKVIGKGGANIANIRKISGAMIEISDAKSARG 596

Query: 598 DRVALISGTPEQKRAAENLIQAFIMAT 624
           DR+A ISG PEQK+AAENLIQAFIMAT
Sbjct: 597 DRIAYISGKPEQKQAAENLIQAFIMAT 623

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|357447239|ref|XP_003593895.1| Heterogeneous nuclear ribonucleoprotein K [Medicago truncatula] gi|357447243|ref|XP_003593897.1| Heterogeneous nuclear ribonucleoprotein K [Medicago truncatula] gi|355482943|gb|AES64146.1| Heterogeneous nuclear ribonucleoprotein K [Medicago truncatula] gi|355482945|gb|AES64148.1| Heterogeneous nuclear ribonucleoprotein K [Medicago truncatula]

 Score =  869 bits (2245), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 441/633 (69%), Positives = 538/633 (84%), Gaps = 11/633 (1%)

Query: 1   MGDSGKRYRSQRDNDR-----DGKNQKRRINEKDEKGNEESVIYRILCPDGVIGSVIGKS 55
           MG++GKR R QRD DR     D KNQKRR+N++DE+   E + YRILCP+ VIGSVIGK+
Sbjct: 1   MGENGKRNRQQRDGDRGGRNWDNKNQKRRVNDRDERDKGELIAYRILCPNEVIGSVIGKN 60

Query: 56  GKVINSIRQETRARVKVVDPFPGAKDRVVTIYSHVKDKEDVEVDDEFNDKEPLCAAQDAL 115
           GKVINSIRQE+RA+VKVVDPFPGAK RV+TI+ HVK+KE++E++DEF++++PLCAAQDAL
Sbjct: 61  GKVINSIRQESRAKVKVVDPFPGAKHRVITIFCHVKNKEEIEIEDEFDNEKPLCAAQDAL 120

Query: 116 LKVHAAIANAVANATDNDKKRKEKEECQILVPSSQSANIIGKAGATIKRLRSKTRTSIKV 175
           +KVH+AI+N++  A D++KKRK K+ECQILVPSSQSA +IGKAGATIK+LR KTRT+IKV
Sbjct: 121 IKVHSAISNSIETAGDSEKKRKNKDECQILVPSSQSAILIGKAGATIKQLRVKTRTNIKV 180

Query: 176 TPKDASEPTHSCAMEFDNFVLISGESEAVKKALFAISAIMYKFSPREDIPLETTVREAPP 235
            PKDA++P HSCAMEFDNFVL+ GESEAVK+ALFA+S IMYKFSP+EDIPL+TTV E P 
Sbjct: 181 VPKDAADPEHSCAMEFDNFVLV-GESEAVKRALFAVSTIMYKFSPKEDIPLDTTVPETPH 239

Query: 236 SIIIPSDVPIYPPGGLYPNADPILPSRSVPSILGAARVPDLQ-GYADTGNTWPVYSTGLS 294
           SIIIPS++PIYPPGGLYP +DPI+  RS P ++GA  + DL  GYADTGNTWP+YS+ L 
Sbjct: 240 SIIIPSELPIYPPGGLYPASDPIVQPRSFPQLIGATTMQDLHGGYADTGNTWPLYSSPLP 299

Query: 295 LVSGLVGASQSEELVIRVLCPFNKIGRVIGKGGGTIKSIRQASGAQIDVDDTKDNRDECV 354
           +VS L GASQSEEL++R+LCP +KIG++IGKGGGTIK +RQASGA+I+VDD+K   DEC+
Sbjct: 300 VVSSL-GASQSEELIVRMLCPSDKIGQLIGKGGGTIKRMRQASGARIEVDDSKARHDECL 358

Query: 355 ITVTAIESPDDIKSMAVEAVLLLQTKINDEDDDTVTIRLLVSSKVIGCIIGKSGSIINEI 414
           IT+TA ES  D+KS+AVEAVLLLQ KINDEDD  V+IRLLV SKVIGCIIG+SG+IINEI
Sbjct: 359 ITITATESTSDLKSVAVEAVLLLQEKINDEDDAPVSIRLLVPSKVIGCIIGRSGAIINEI 418

Query: 415 RKRTKADVRISKGDKPKCADANDELVEVVGEVGSVRDALVQIILRLRDDALKDRDGSRNP 474
           RKRTKAD++IS+ +KPK AD NDELVEVVGEV  VRDAL+QI+LRLR+D LK++D   N 
Sbjct: 419 RKRTKADIQISRSNKPKYADDNDELVEVVGEVDCVRDALIQIVLRLREDVLKNKDIDHNR 478

Query: 475 PVGADHIYSSGTGISMPPLLPSIPPVGP-LGYDQRADSGSGIGMLSSSSLYGYGSLSMGD 533
            +G++ +Y+S + +S PP+L SIP   P L YDQR  SG+G+GM SS S YGY S SM D
Sbjct: 479 HIGSESLYASSSVLSAPPMLSSIPATAPALAYDQRTGSGTGLGMHSSRSHYGYDSYSMED 538

Query: 534 SPYGSMSSYSSKLYGG--LPPPLTLEVLVPANAVGKVIGKAGSNLANIRKISGATIEMSD 591
           + YGSMSSY++ LY G  LPP  TLE++VPANAVGKV+GK G+NLANIRKISGAT+E+S+
Sbjct: 539 NGYGSMSSYATNLYEGHRLPPLSTLEMVVPANAVGKVMGKGGANLANIRKISGATVEISE 598

Query: 592 SKSSRGDRVALISGTPEQKRAAENLIQAFIMAT 624
           SKS RGDRVALISGT E+KRAAENLIQAFIMAT
Sbjct: 599 SKSYRGDRVALISGTSEEKRAAENLIQAFIMAT 631

Source: Medicago truncatula

Species: Medicago truncatula

Genus: Medicago

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|449433573|ref|XP_004134572.1| PREDICTED: KH domain-containing protein At4g18375-like [Cucumis sativus]

 Score =  857 bits (2214), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 453/623 (72%), Positives = 538/623 (86%), Gaps = 2/623 (0%)

Query: 4   SGKRYRSQRDNDRDGKNQKRRINEKDEKGNEESVIYRILCPDGVIGSVIGKSGKVINSIR 63
           SGKR   QRD + D K  KRRI E+D+  ++E V+YRILCPD VIGSVIGKSGKVINSIR
Sbjct: 3   SGKRPYGQRDYNGDNKGYKRRITEQDDWVSDELVVYRILCPDEVIGSVIGKSGKVINSIR 62

Query: 64  QETRARVKVVDPFPGAKDRVVTIYSHVKDKEDVEVDDEFNDKEPLCAAQDALLKVHAAIA 123
           QETRA++KVVDPFPGAKDRV+TI+  VKDKEDVEVDDEFND++ LCAAQDALLKVHAAIA
Sbjct: 63  QETRAKIKVVDPFPGAKDRVITIFCFVKDKEDVEVDDEFNDRQTLCAAQDALLKVHAAIA 122

Query: 124 NAVANATDNDKKRKEKEECQILVPSSQSANIIGKAGATIKRLRSKTRTSIKVTPKDASEP 183
           NA+A+A D D+K+++KE+CQIL+PSSQSAN+IGKAG+TIK+LRSKTRTSIK++PKDA++P
Sbjct: 123 NALASAGDLDRKQRDKEQCQILIPSSQSANVIGKAGSTIKKLRSKTRTSIKISPKDATDP 182

Query: 184 THSCAMEFDNFVLISGESEAVKKALFAISAIMYKFSPREDIPLETTVREAPPSIIIPSDV 243
            HSCAM+FDNF +I+GE E V++ALFAIS+IMYKF PRE+IPL+T V EAPP+IIIPSDV
Sbjct: 183 IHSCAMDFDNFAVIAGEPEGVRRALFAISSIMYKFPPREEIPLDTNVNEAPPNIIIPSDV 242

Query: 244 PIYPPGGLYPNADPILPSRSVPSILGAARVPDLQGYADTGNTWPVYSTGLSLV-SGLVGA 302
           P+Y  GGLYP+ADPILP RS+P +LGA  V DL  Y ++GN WP+YS+ L +V  G+ G 
Sbjct: 243 PLYSAGGLYPSADPILPPRSIPPMLGAQHVQDLHDYPESGNAWPLYSSSLPVVPGGISGH 302

Query: 303 SQSEELVIRVLCPFNKIGRVIGKGGGTIKSIRQASGAQIDVDDTKDNRDECVITVTAIES 362
             SEELV+RVLCPF+ IGRVIGKGGGTIKSIRQASGA+++VDDTK + DEC+IT+++ ES
Sbjct: 303 PPSEELVVRVLCPFDNIGRVIGKGGGTIKSIRQASGARVEVDDTKRDCDECIITISSFES 362

Query: 363 PDDIKSMAVEAVLLLQTKINDEDDDTVTIRLLVSSKVIGCIIGKSGSIINEIRKRTKADV 422
            DD+KSMAVE VLLLQ KIND++  TV +RLL+ SKVIGCIIGKSGSIINEIRK T+AD+
Sbjct: 363 LDDLKSMAVETVLLLQEKINDDEGGTVIMRLLIPSKVIGCIIGKSGSIINEIRKSTRADI 422

Query: 423 RISKGDKPKCADANDELVEVVGEVGSVRDALVQIILRLRDDALKDRDGSRNPPVGADHIY 482
           RISKGDK KCA ++DELVEV G+VG VRDALVQI+LRLRDDALK+RD   N  +  D +Y
Sbjct: 423 RISKGDKLKCASSSDELVEVTGKVGCVRDALVQIVLRLRDDALKERDVGHNSAIVTDSMY 482

Query: 483 SSGTGISMPPLLPSIPP-VGPLGYDQRADSGSGIGMLSSSSLYGYGSLSMGDSPYGSMSS 541
           SSG+  SMP +LPS+ P   P+GYDQRA+SGSG+G+LSSS LYG GSLSMGD+ YG MSS
Sbjct: 483 SSGSSFSMPSVLPSVSPGAPPMGYDQRAESGSGLGVLSSSGLYGSGSLSMGDNGYGYMSS 542

Query: 542 YSSKLYGGLPPPLTLEVLVPANAVGKVIGKAGSNLANIRKISGATIEMSDSKSSRGDRVA 601
           YSSKLYGGLPPP +LE+L+PANA GKVIGK G+N+ANIRKISGA IE+SDSKSSRGDR+A
Sbjct: 543 YSSKLYGGLPPPSSLEMLIPANAAGKVIGKGGANIANIRKISGALIEISDSKSSRGDRIA 602

Query: 602 LISGTPEQKRAAENLIQAFIMAT 624
           LISGT EQKR AENLIQAFIMAT
Sbjct: 603 LISGTSEQKRTAENLIQAFIMAT 625

Source: Cucumis sativus

Species: Cucumis sativus

Genus: Cucumis

Family: Cucurbitaceae

Order: Cucurbitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|297791069|ref|XP_002863419.1| KH domain-containing protein [Arabidopsis lyrata subsp. lyrata] gi|297309254|gb|EFH39678.1| KH domain-containing protein [Arabidopsis lyrata subsp. lyrata]

 Score =  716 bits (1848), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 387/616 (62%), Positives = 486/616 (78%), Gaps = 23/616 (3%)

Query: 27  EKDEKGNEESVIYRILCPDGVIGSVIGKSGKVINSIRQETRARVKVVDPFPGAKDRVVTI 86
           EK +  ++  V+YRILCP GV+GSVIGKSGKVIN IRQETRAR+KVVDPFPG  +RV+TI
Sbjct: 33  EKTDNKDDLVVVYRILCPSGVMGSVIGKSGKVINLIRQETRARIKVVDPFPGCSERVITI 92

Query: 87  YSHVKDKEDVEVD---DEFNDKEPLCAAQDALLKVHAAIANAVANATDNDK-KRKEKEEC 142
           +  V +K+D+ +D    E N   PLC+AQDALLKVH AI  ++A A +N K  R +  EC
Sbjct: 93  FCSVTEKKDI-IDIEHSELNYSIPLCSAQDALLKVHDAIVASLATAAENTKIDRDDIREC 151

Query: 143 QILVPSSQSANIIGKAGATIKRLRSKTRTSIKVTPKDASEPTHSCAMEFDNFVLISGESE 202
           ++LVPSSQ +N+IGK+G+ IK++RS+TR ++KV  KD S+P+H+CAM+FDN VLISGESE
Sbjct: 152 RLLVPSSQCSNVIGKSGSIIKKIRSRTRANVKVVSKDVSDPSHTCAMDFDNIVLISGESE 211

Query: 203 AVKKALFAISAIMYKFSPREDIPLETTVREAPPSIIIPSDVPIYPPGGLYPNADPILPS- 261
           +VKKALFA+SAIMYK SPRE IPL+TTV+E P SIIIPSD+ IYP GGLYPN DPI    
Sbjct: 212 SVKKALFAVSAIMYKVSPREQIPLDTTVQEVPASIIIPSDLSIYPQGGLYPNQDPIFQHG 271

Query: 262 RSVPSILGAARVPDLQGYADT-GNTWPVYS-TGLSLVSGLVGASQSEELVIRVLCPFNKI 319
            +V S +G   +P  QGY ++  N  PV+S + L +V G  G+S+SE+LVI+V+C  +KI
Sbjct: 272 ANVSSFIGT--LP--QGYGESAANPMPVFSASALPVVHGFGGSSKSEKLVIKVICSSSKI 327

Query: 320 GRVIGKGGGTIKSIRQASGAQIDVDDTKDNR-DECVITVTAIESPDDIKSMAVEAVLLLQ 378
           GRVIGKGG TIK IRQASG+ I+V+D++ N  D+CVITVTA ESPDD+KSMAVEAVLLLQ
Sbjct: 328 GRVIGKGGSTIKGIRQASGSHIEVNDSRANHDDDCVITVTATESPDDLKSMAVEAVLLLQ 387

Query: 379 TKINDEDDDTVTIRLLVSSKVIGCIIGKSGSIINEIRKRTKADVRISKG-DKPKCADAND 437
            KINDED++ V ++LLV SKVIGCIIGKSGSII+EIRKRTKA++ ISKG +KPKCAD ND
Sbjct: 388 EKINDEDEEKVKMQLLVPSKVIGCIIGKSGSIISEIRKRTKANIHISKGNNKPKCADPND 447

Query: 438 ELVEVVGEVGSVRDALVQIILRLRDDALKDRD-GSRN-PPVGAD--HIYSSG---TGISM 490
           ELVE+ GEV  VRDAL+QI+LRLRDD L+DR+ GSRN PP  ++  + +SSG   TG+++
Sbjct: 448 ELVEISGEVSDVRDALIQIVLRLRDDVLRDREIGSRNQPPARSENNNFFSSGSSNTGLAL 507

Query: 491 P-PLLPSIPPVGPLGYDQRADSGSGIGML-SSSSLYGYGSLSMGDSPYGSMSSYSSKLYG 548
           P   + S+P V  + +D+R ++GS + ML SS  LYGYGS  +G++ YGS SSYSS LYG
Sbjct: 508 PSSFMSSVPQVASVDFDRRPETGSSMSMLPSSGGLYGYGSFPVGNNSYGSKSSYSSNLYG 567

Query: 549 GLPPPLTLEVLVPANAVGKVIGKAGSNLANIRKISGATIEMSDSKSSRGDRVALISGTPE 608
           GLP   T+EV +PANAVGKV+G+ G NL NIR+ISGA IE+SDSK+S G R+ALISGTPE
Sbjct: 568 GLPQSTTMEVRIPANAVGKVMGRGGGNLDNIRRISGAMIEISDSKNSHGGRIALISGTPE 627

Query: 609 QKRAAENLIQAFIMAT 624
           QKR AENL QAFIM+T
Sbjct: 628 QKRTAENLFQAFIMST 643

Source: Arabidopsis lyrata subsp. lyrata

Species: Arabidopsis lyrata

Genus: Arabidopsis

Family: Brassicaceae

Order: Brassicales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|449525363|ref|XP_004169687.1| PREDICTED: KH domain-containing protein At4g18375-like, partial [Cucumis sativus]

 Score =  704 bits (1818), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 364/516 (70%), Positives = 441/516 (85%), Gaps = 2/516 (0%)

Query: 4   SGKRYRSQRDNDRDGKNQKRRINEKDEKGNEESVIYRILCPDGVIGSVIGKSGKVINSIR 63
           SGKR   QRD + D K  KRRI E+D+  ++E V+YRILCPD VIGSVIGKSGKVINSIR
Sbjct: 3   SGKRPYGQRDYNGDNKGYKRRITEQDDWVSDELVVYRILCPDEVIGSVIGKSGKVINSIR 62

Query: 64  QETRARVKVVDPFPGAKDRVVTIYSHVKDKEDVEVDDEFNDKEPLCAAQDALLKVHAAIA 123
           QETRA++KVVDPFPGAKDRV+TI+  VKDKEDVEVDDEFND++ LCAAQDALLKVHAAIA
Sbjct: 63  QETRAKIKVVDPFPGAKDRVITIFCFVKDKEDVEVDDEFNDRQTLCAAQDALLKVHAAIA 122

Query: 124 NAVANATDNDKKRKEKEECQILVPSSQSANIIGKAGATIKRLRSKTRTSIKVTPKDASEP 183
           NA+A+A D D+K+++KE+CQIL+PSSQSAN+IGKAG+TIK+LRSKTRTSIK++PKDA++P
Sbjct: 123 NALASAGDLDRKQRDKEQCQILIPSSQSANVIGKAGSTIKKLRSKTRTSIKISPKDATDP 182

Query: 184 THSCAMEFDNFVLISGESEAVKKALFAISAIMYKFSPREDIPLETTVREAPPSIIIPSDV 243
            HSCAM+FDNF +I+GE E V++ALFAIS+IMYKF PRE+IPL+T V EAPP+IIIPSDV
Sbjct: 183 IHSCAMDFDNFAVIAGEPEGVRRALFAISSIMYKFPPREEIPLDTNVNEAPPNIIIPSDV 242

Query: 244 PIYPPGGLYPNADPILPSRSVPSILGAARVPDLQGYADTGNTWPVYSTGLSLV-SGLVGA 302
           P+Y  GGLYP+ADPILP RS+P +LGA  V DL  Y ++GN WP+YS+ L +V  G+ G 
Sbjct: 243 PLYSAGGLYPSADPILPPRSIPPMLGAQHVQDLHDYPESGNAWPLYSSSLPVVPGGISGH 302

Query: 303 SQSEELVIRVLCPFNKIGRVIGKGGGTIKSIRQASGAQIDVDDTKDNRDECVITVTAIES 362
             SEELV+RVLCPF+ IGRVIGKGGGTIKSIRQASGA+++VDDTK + DEC+IT+++ ES
Sbjct: 303 PPSEELVVRVLCPFDNIGRVIGKGGGTIKSIRQASGARVEVDDTKRDCDECIITISSFES 362

Query: 363 PDDIKSMAVEAVLLLQTKINDEDDDTVTIRLLVSSKVIGCIIGKSGSIINEIRKRTKADV 422
            DD+KSMAVE VLLLQ KIND++  TV +RLL+ SKVIGCIIGKSGSIINEIRK T+AD+
Sbjct: 363 LDDLKSMAVETVLLLQEKINDDEGGTVIMRLLIPSKVIGCIIGKSGSIINEIRKSTRADI 422

Query: 423 RISKGDKPKCADANDELVEVVGEVGSVRDALVQIILRLRDDALKDRDGSRNPPVGADHIY 482
           RISKGDK KCA ++DELVEV G+VG VRDALVQI+LRLRDDALK+RD   N  +  D +Y
Sbjct: 423 RISKGDKLKCASSSDELVEVTGKVGCVRDALVQIVLRLRDDALKERDVGHNSAIVTDSMY 482

Query: 483 SSGTGISMPPLLPSIPP-VGPLGYDQRADSGSGIGM 517
           SSG+  SMP +LPS+ P   P+GYDQRA+SGSG+G+
Sbjct: 483 SSGSSFSMPSVLPSVSPGAPPMGYDQRAESGSGLGV 518

Source: Cucumis sativus

Species: Cucumis sativus

Genus: Cucumis

Family: Cucurbitaceae

Order: Cucurbitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|15237393|ref|NP_199431.1| RNA-binding KH domain-containing protein [Arabidopsis thaliana] gi|9757739|dbj|BAB08264.1| unnamed protein product [Arabidopsis thaliana] gi|14532588|gb|AAK64022.1| unknown protein [Arabidopsis thaliana] gi|21280941|gb|AAM44907.1| unknown protein [Arabidopsis thaliana] gi|332007968|gb|AED95351.1| RNA-binding KH domain-containing protein [Arabidopsis thaliana]

 Score =  690 bits (1780), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 378/624 (60%), Positives = 484/624 (77%), Gaps = 27/624 (4%)

Query: 19  KNQKRRINEKDEKGNEESVIYRILCPDGVIGSVIGKSGKVINSIRQETRARVKVVDPFPG 78
           ++++++I+ KD+      V+YRILCP GV+GSVIGKSGKVIN IRQETRAR+KVVDPFPG
Sbjct: 30  ESEEKKIDNKDDL----VVVYRILCPSGVMGSVIGKSGKVINLIRQETRARIKVVDPFPG 85

Query: 79  AKDRVVTIYSHVKDKEDVEVDDEFNDKE---PLCAAQDALLKVHAAIANAVANATDNDK- 134
             +RV+TI+  V +K+D+ VD E+++ +   PLC+AQ ALLKVH AI  ++A A +N K 
Sbjct: 86  CSERVITIFCSVSEKKDI-VDIEYSELDYSVPLCSAQAALLKVHDAIVASLATAAENTKI 144

Query: 135 KRKEKEECQILVPSSQSANIIGKAGATIKRLRSKTRTSIKVTPKDASEPTHSCAMEFDNF 194
            R +  EC++LVPSSQ + +IGK+G+ IK +R +TR ++KV  KD S+P+H+CAM+FDN 
Sbjct: 145 DRDDFRECRLLVPSSQCSIVIGKSGSIIKNIRGRTRANVKVVSKDVSDPSHTCAMDFDNI 204

Query: 195 VLISGESEAVKKALFAISAIMYKFSPREDIPLETTVREAPPSIIIPSDVPIYPPGGLYPN 254
           V+ISGE+E+VKKALFA+SAIMYK SPRE IPL+TTV+E P SIIIPSD+ IYP  GLYP+
Sbjct: 205 VMISGETESVKKALFAVSAIMYKVSPREQIPLDTTVQEVPASIIIPSDLSIYPQAGLYPS 264

Query: 255 ADPILPS-RSVPSILGAARVPDLQGYADT-GNTWPVYS-TGLSLVSGLVGASQSEELVIR 311
            D I     +V S +G   +P  QGY +   N  PV+S + L +V G  G+S+SE+L I+
Sbjct: 265 QDSIFQHGANVSSFIGT--LP--QGYGENAANPVPVFSASALPVVHGFGGSSRSEKLAIK 320

Query: 312 VLCPFNKIGRVIGKGGGTIKSIRQASGAQIDVDDTKDNR-DECVITVTAIESPDDIKSMA 370
           V+C  +KIGRVIGKGG TIK IRQASG+ I+V+D++ N  D+CVITVTA ESPDD+KSMA
Sbjct: 321 VICSSSKIGRVIGKGGLTIKGIRQASGSHIEVNDSRTNHDDDCVITVTATESPDDLKSMA 380

Query: 371 VEAVLLLQTKINDEDDDTVTIRLLVSSKVIGCIIGKSGSIINEIRKRTKADVRISKGDK- 429
           VEAVLLLQ KINDED+D V ++LLVSSKVIGCIIGKSGSII+EIRKRTKAD+ ISKG+  
Sbjct: 381 VEAVLLLQEKINDEDEDKVKMQLLVSSKVIGCIIGKSGSIISEIRKRTKADIHISKGNNT 440

Query: 430 PKCADANDELVEVVGEVGSVRDALVQIILRLRDDALKDRD-GSRN-PPVGAD-----HIY 482
           PKCAD NDELVE+ GEV +VRDAL+QI+LRLRDD L+DR+ GSRN PP  ++        
Sbjct: 441 PKCADPNDELVEISGEVSNVRDALIQIVLRLRDDVLRDRETGSRNQPPARSENNNFFSSS 500

Query: 483 SSGTGISMP-PLLPSIPPVGPLGYDQRADSGSGIGML-SSSSLYGYGSLSMGDSPYGSMS 540
           SS TG+++P   + S+P V  + +++R ++GS + ML SS  +YGYGS  +G++ YGS S
Sbjct: 501 SSNTGLALPQSFMSSVPQVASVDFNRRPETGSSMSMLPSSGGIYGYGSFPVGNTSYGSNS 560

Query: 541 SYSSKLYGGLPPPLTLEVLVPANAVGKVIGKAGSNLANIRKISGATIEMSDSKSSRGDRV 600
           SYSS LYGGLP   T+EV +PANAVGKV+G+ G NL NIR+ISGA IE+SDSK+S G RV
Sbjct: 561 SYSSNLYGGLPQSTTMEVRIPANAVGKVMGRGGGNLDNIRRISGAMIEISDSKNSHGGRV 620

Query: 601 ALISGTPEQKRAAENLIQAFIMAT 624
           ALISGT EQKR AENL QAFIM+T
Sbjct: 621 ALISGTSEQKRTAENLFQAFIMST 644

Source: Arabidopsis thaliana

Species: Arabidopsis thaliana

Genus: Arabidopsis

Family: Brassicaceae

Order: Brassicales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|21553916|gb|AAM62999.1| unknown [Arabidopsis thaliana]

 Score =  689 bits (1778), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 379/624 (60%), Positives = 484/624 (77%), Gaps = 27/624 (4%)

Query: 19  KNQKRRINEKDEKGNEESVIYRILCPDGVIGSVIGKSGKVINSIRQETRARVKVVDPFPG 78
           ++++++I+ KD+      V+YRILCP GV+GSVIGKSGKVIN IRQETRAR+KVVDPFPG
Sbjct: 30  ESEEKKIDNKDDL----VVVYRILCPSGVMGSVIGKSGKVINLIRQETRARIKVVDPFPG 85

Query: 79  AKDRVVTIYSHVKDKEDVEVDDEFNDKE---PLCAAQDALLKVHAAIANAVANATDNDK- 134
             +RV+TI+  V +K+D+ VD E+++ +   PLC+AQ ALLKVH AI  ++A A +N K 
Sbjct: 86  CSERVITIFCSVSEKKDI-VDIEYSELDYSVPLCSAQAALLKVHDAIVASLATAAENTKI 144

Query: 135 KRKEKEECQILVPSSQSANIIGKAGATIKRLRSKTRTSIKVTPKDASEPTHSCAMEFDNF 194
            R +  EC++LVPSSQ + +IGK+G+ IK +R +TR ++KV  KDAS+P+H+CAM+FDN 
Sbjct: 145 DRDDFRECRLLVPSSQCSIVIGKSGSIIKNIRGRTRANVKVVSKDASDPSHTCAMDFDNI 204

Query: 195 VLISGESEAVKKALFAISAIMYKFSPREDIPLETTVREAPPSIIIPSDVPIYPPGGLYPN 254
           V+ISGE+E+VKKALFA+SAIMYK SPRE IPL+TTV+E P SIIIPSD+ IYP  GLYP+
Sbjct: 205 VMISGETESVKKALFAVSAIMYKVSPREQIPLDTTVQEVPASIIIPSDLSIYPQAGLYPS 264

Query: 255 ADPILPS-RSVPSILGAARVPDLQGYADT-GNTWPVYS-TGLSLVSGLVGASQSEELVIR 311
            D I     +V S +G   +P  QGY +   N  PV+S + L +V G  G+S+SE+L I+
Sbjct: 265 QDSIFQHGANVSSFIGT--LP--QGYGENAANPLPVFSASALPVVHGFGGSSRSEKLAIK 320

Query: 312 VLCPFNKIGRVIGKGGGTIKSIRQASGAQIDVDDTKDNR-DECVITVTAIESPDDIKSMA 370
           V+C  +KIGRVIGKGG TIK IRQASG+ I+V+D++ N  D+CVITVTA ESPDD+KSMA
Sbjct: 321 VICASSKIGRVIGKGGLTIKGIRQASGSHIEVNDSRTNHDDDCVITVTATESPDDLKSMA 380

Query: 371 VEAVLLLQTKINDEDDDTVTIRLLVSSKVIGCIIGKSGSIINEIRKRTKADVRISKGDK- 429
           VEAVLLLQ KINDED+D V ++LLVSSKVIGCIIGKSGSII+EIRKRTKAD+ ISKG+  
Sbjct: 381 VEAVLLLQEKINDEDEDKVKMQLLVSSKVIGCIIGKSGSIISEIRKRTKADIHISKGNNT 440

Query: 430 PKCADANDELVEVVGEVGSVRDALVQIILRLRDDALKDRD-GSRN-PPVGAD-----HIY 482
           PK AD NDELVE+ GEV +VRDAL+QI+LRLRDD L+DR+ GSRN PP  ++        
Sbjct: 441 PKSADPNDELVEISGEVSNVRDALIQIVLRLRDDVLRDRETGSRNQPPARSENNNFFSSS 500

Query: 483 SSGTGISMP-PLLPSIPPVGPLGYDQRADSGSGIGML-SSSSLYGYGSLSMGDSPYGSMS 540
           SS TG+++P   + S+P V  + +D+R ++GS + ML SS  +YGYGS  +G++ YGS S
Sbjct: 501 SSNTGLALPQSFMSSVPQVASVDFDRRPETGSSMSMLPSSGGIYGYGSFPVGNTSYGSNS 560

Query: 541 SYSSKLYGGLPPPLTLEVLVPANAVGKVIGKAGSNLANIRKISGATIEMSDSKSSRGDRV 600
           SYSS LYGGLP   T+EV +PANAVGKV+G+ G NL NIR+ISGA IE+SDSK+S G RV
Sbjct: 561 SYSSNLYGGLPQSTTMEVRIPANAVGKVMGRGGGNLDNIRRISGAMIEISDSKNSHGGRV 620

Query: 601 ALISGTPEQKRAAENLIQAFIMAT 624
           ALISGT EQKR AENL QAFIM+T
Sbjct: 621 ALISGTSEQKRTAENLFQAFIMST 644

Source: Arabidopsis thaliana

Species: Arabidopsis thaliana

Genus: Arabidopsis

Family: Brassicaceae

Order: Brassicales

Phylum: Streptophyta

Superkingdom: Eukaryota

---

Prediction of Gene Ontology (GO) Terms

Close Homologs with Gene Ontology terms Detected by BLAST

Original result of BLAST against Gene Ontology (AMIGO)

ID	Length	Definition	Q cover	H cover	Identity	E-value
Query	624
TAIR|locus:2161413	644	AT5G46190 "AT5G46190" [Arabido	0.772	0.748	0.502	8.2e-138
TAIR|locus:2831364	606	AT4G18375 "AT4G18375" [Arabido	0.764	0.787	0.468	5.8e-122
TAIR|locus:2150956	548	AT5G15270 "AT5G15270" [Arabido	0.325	0.370	0.322	6.1e-43
TAIR|locus:2035807	479	AT1G14170 "AT1G14170" [Arabido	0.328	0.427	0.316	1.8e-39
TAIR|locus:2168367	652	RCF3 "AT5G53060" [Arabidopsis	0.272	0.260	0.32	2.9e-35
TAIR|locus:2017612	621	AT1G51580 "AT1G51580" [Arabido	0.243	0.244	0.301	1.9e-32
TAIR|locus:2084908	577	FLK "AT3G04610" [Arabidopsis t	0.293	0.317	0.3	4.8e-19
TAIR|locus:2066020	632	AT2G22600 "AT2G22600" [Arabido	0.306	0.302	0.252	1.6e-17
UNIPROTKB|J3QT27	322	PCBP3 "Poly(rC)-binding protei	0.184	0.357	0.310	3.8e-10
UNIPROTKB|P57721	371	PCBP3 "Poly(rC)-binding protei	0.344	0.579	0.256	4.6e-11

TAIR|locus:2161413 AT5G46190 "AT5G46190" [Arabidopsis thaliana (taxid:3702)]

 Score = 1137 (405.3 bits), Expect = 8.2e-138, Sum P(2) = 8.2e-138
 Identities = 254/505 (50%), Positives = 328/505 (64%)

Query:     1 MGDSGKRYRSQ-RDNDRDG-KNQKRRIN-EKDEK--GNEES--VIYRILCPDGVIGSVIG 53
             M + GKR  ++ RDN+ D  +NQ+RR++ E +EK   N++   V+YRILCP GV+GSVIG
Sbjct:     1 MVERGKRTHNRFRDNNNDNNRNQRRRLSYESEEKKIDNKDDLVVVYRILCPSGVMGSVIG 60

Query:    54 KSGKVINSIRQETRARVKVVDPFPGAKDRVVTIYSHXXXXXXXXXXXXXXX--XXPLCAA 111
             KSGKVIN IRQETRAR+KVVDPFPG  +RV+TI+                     PLC+A
Sbjct:    61 KSGKVINLIRQETRARIKVVDPFPGCSERVITIFCSVSEKKDIVDIEYSELDYSVPLCSA 120

Query:   112 QDALLKVHXXXXXXXXXXTDNDK-KRKEKEECQILVPSSQSANIIGKAGATIKRLRSKTR 170
             Q ALLKVH           +N K  R +  EC++LVPSSQ + +IGK+G+ IK +R +TR
Sbjct:   121 QAALLKVHDAIVASLATAAENTKIDRDDFRECRLLVPSSQCSIVIGKSGSIIKNIRGRTR 180

Query:   171 TSIKVTPKDASEPTHSCAMEFDNFVLISGESEAVKKALFAISAIMYKFSPREDIPLETTV 230
              ++KV  KD S+P+H+CAM+FDN V+ISGE+E+VKKALFA+SAIMYK SPRE IPL+TTV
Sbjct:   181 ANVKVVSKDVSDPSHTCAMDFDNIVMISGETESVKKALFAVSAIMYKVSPREQIPLDTTV 240

Query:   231 REAXXXXXXXXXXXXXXXGGLYPNADPILP-SRSVPSILGAARVPDLQGYADTG-NTWPV 288
             +E                 GLYP+ D I     +V S +G   +P  QGY +   N  PV
Sbjct:   241 QEVPASIIIPSDLSIYPQAGLYPSQDSIFQHGANVSSFIGT--LP--QGYGENAANPVPV 296

Query:   289 YS-TGLSLVSGLVGASQSEELVIRVLCPFNKIGRVIGKGGGTIKSIRQASGAQIDVDDTK 347
             +S + L +V G  G+S+SE+L I+V+C  +KIGRVIGKGG TIK IRQASG+ I+V+D++
Sbjct:   297 FSASALPVVHGFGGSSRSEKLAIKVICSSSKIGRVIGKGGLTIKGIRQASGSHIEVNDSR 356

Query:   348 DNRDE-CVITVTAIESPDDIKSMAVEAVLLLQTKINDEDDDTVTIRLLVXXXXXXXXXXX 406
              N D+ CVITVTA ESPDD+KSMAVEAVLLLQ KINDED+D V ++LLV           
Sbjct:   357 TNHDDDCVITVTATESPDDLKSMAVEAVLLLQEKINDEDEDKVKMQLLVSSKVIGCIIGK 416

Query:   407 XXXXXNEIRKRTKADVRISKGDK-PKCADANDELXXXXXXXXXXRDALVQIIXXXXXXXX 465
                  +EIRKRTKAD+ ISKG+  PKCAD NDEL          RDAL+QI+        
Sbjct:   417 SGSIISEIRKRTKADIHISKGNNTPKCADPNDELVEISGEVSNVRDALIQIVLRLRDDVL 476

Query:   466 XXX-XGSRN-PPVGADH--IYSSGT 486
                  GSRN PP  +++   +SS +
Sbjct:   477 RDRETGSRNQPPARSENNNFFSSSS 501

GO:0003676 "nucleic acid binding" evidence=ISS

GO:0003723 "RNA binding" evidence=IEA

GO:0005634 "nucleus" evidence=ISM

GO:0008150 "biological_process" evidence=ND

TAIR|locus:2831364 AT4G18375 "AT4G18375" [Arabidopsis thaliana (taxid:3702)]

 Score = 1012 (361.3 bits), Expect = 5.8e-122, Sum P(2) = 5.8e-122
 Identities = 233/497 (46%), Positives = 298/497 (59%)

Query:     1 MGDSGKRYRSQRDNDRDGKNQKRRINEKDEKGNEESVIYRILCPDGVIGSVIGKSGKVIN 60
             M +  KR + QR+N    +NQKRRI+  D+   +E V+YRILCP  V+G VIGKSGKVIN
Sbjct:     1 MVERKKRKQIQRNNSESNRNQKRRISH-DKINRDELVVYRILCPIDVVGGVIGKSGKVIN 59

Query:    61 SIRQETRARVKVVDPFPGAKDRVVTIYSHXXXXXXXXXXXXXXXXXPLCAAQDALLKVHX 120
             +IR  T+A++KV D   G   RV+TIY                   PLC AQDALLKV+ 
Sbjct:    60 AIRHNTKAKIKVFDQLHGCSQRVITIYC-SVKEKQEEIGFTKSENEPLCCAQDALLKVYD 118

Query:   121 XXXXXXXXX-TDNDKKRKEKEECQILVPSSQSANIIGKAGATIKRLRSKTRTSIKVTPKD 179
                       T  +  R + +EC++LVP SQS+++IGKAG  IKR+R +TR S+KV  KD
Sbjct:   119 AIVASDEENNTKTNVDRDDNKECRLLVPFSQSSSLIGKAGENIKRIRRRTRASVKVVSKD 178

Query:   180 ASEPTHSCAMEFDNFVLISGESEAVKKALFAISAIMYKFSPREDIPLETTVRE---AXXX 236
              S+P+H CAME+DN V+ISGE E+VK+ALFA+SAIMYK +PRE+IPL++T ++   A   
Sbjct:   179 VSDPSHVCAMEYDNVVVISGEPESVKQALFAVSAIMYKINPRENIPLDSTSQDVPAASVI 238

Query:   237 XXXXXXXXXXXXGGLYPNADPILPSRS-VPSILGAARVPDLQGYADTG-NTWPVYSTGLS 294
                          G Y N D IL   + VPS   A  V D QGYA+T  N  PV+++ L 
Sbjct:   239 VPSDLSNSVYPQTGFYSNQDHILQQGAGVPSYFNALSVSDFQGYAETAANPVPVFASSLP 298

Query:   295 LVSGLVGASQSEELVIRVLCPFNKIGRVIGKGGGTIKSIRQASGAQIDVDD--TKDNRDE 352
             +  G  G+S+SEELV +VLCP   I RVIGKGG TIK IR+ASG+ I+V+D  TK   DE
Sbjct:   299 VTHGFGGSSRSEELVFKVLCPLCNIMRVIGKGGSTIKRIREASGSCIEVNDSRTKCGDDE 358

Query:   353 CVITVTAIESPDDIKSMAVEAVLLLQTKINDEDDDTVTIRLLVXXXXXXXXXXXXXXXXN 412
             CVI VTA ESPDD+KSMAVEAVLLLQ  INDED + V ++LLV                N
Sbjct:   359 CVIIVTATESPDDMKSMAVEAVLLLQEYINDEDAENVKMQLLVSSKVIGCVIGKSGSVIN 418

Query:   413 EIRKRTKADVRISKGDKPKCADANDELXXXXXXXXXXRDALVQIIXXXXXXXXXX--XXG 470
             EIRKRT A++ ISKG K       D+L          RDAL+QI+               
Sbjct:   419 EIRKRTNANICISKGKK-------DDLVEVSGEVSSVRDALIQIVLRLREDVLGDKDSVA 471

Query:   471 SRNPPVGADHI-YSSGT 486
             +R PP   D+  + SG+
Sbjct:   472 TRKPPARTDNCSFLSGS 488

GO:0003676 "nucleic acid binding" evidence=ISS

GO:0003723 "RNA binding" evidence=IEA

GO:0005737 "cytoplasm" evidence=ISM

GO:0008150 "biological_process" evidence=ND

TAIR|locus:2150956 AT5G15270 "AT5G15270" [Arabidopsis thaliana (taxid:3702)]

 Score = 294 (108.6 bits), Expect = 6.1e-43, Sum P(2) = 6.1e-43
 Identities = 69/214 (32%), Positives = 116/214 (54%)

Query:     6 KRYRSQRDNDRDGKNQKR-RINEKDEKG-NEESVIYRILCPDGVIGSVIGKSGKVINSIR 63
             KR R Q D D +G +++R R +++D    + +  ++R LCP   IGSVIG+ G ++  +R
Sbjct:    17 KRSRPQSDYDDNGGSKRRYRGDDRDSLVIDRDDTVFRYLCPVKKIGSVIGRGGDIVKQLR 76

Query:    64 QETRARVKVVDPFPGAKDRVVTIYSHXXXXXXXXXXXXXXXXXPLCAAQDALLKVHXXXX 123
              +TR+++++ +  PG  +RV+TIYS                   L  AQDAL ++H    
Sbjct:    77 NDTRSKIRIGEAIPGCDERVITIYSPSDETNAFGDGEKV-----LSPAQDALFRIHDRVV 131

Query:   124 XXXXXXTDNDKKRKEKEECQILVPSSQSANIIGKAGATIKRLRSKTRTSIKVTPKDASEP 183
                    D+ +  K+    ++LVPS Q   I+G+ G  ++ +RS+T   I++  KD + P
Sbjct:   132 ADDARSEDSPEGEKQVT-AKLLVPSDQIGCILGRGGQIVQNIRSETGAQIRIV-KDRNMP 189

Query:   184 THSCAMEFDNFVLISGESEAVKKALFAISAIMYK 217
                CA+  D  + ISGE   VKKAL  I++ +++
Sbjct:   190 L--CALNSDELIQISGEVLIVKKALLQIASRLHE 221

GO:0003676 "nucleic acid binding" evidence=ISS

GO:0003723 "RNA binding" evidence=IEA

GO:0005634 "nucleus" evidence=ISM

GO:0008150 "biological_process" evidence=ND

TAIR|locus:2035807 AT1G14170 "AT1G14170" [Arabidopsis thaliana (taxid:3702)]

 Score = 278 (102.9 bits), Expect = 1.8e-39, Sum P(2) = 1.8e-39
 Identities = 69/218 (31%), Positives = 113/218 (51%)

Query:     5 GKRYRSQRDNDRDGKNQKRRINEKDEKG--NEESVIYRILCPDGVIGSVIGKSGKVINSI 62
             GKR   Q +   +G +++R ++++ ++     E  +YR LCP    GS+IGK G++   I
Sbjct:    10 GKRSNLQSEFTGNGGSKRRNLHDETDQNVIASEDTVYRYLCPVKKTGSIIGKGGEIAKQI 69

Query:    63 RQETRARVKVVDPFPGAKDRVVTIYSHXXXXXXXXXXXXXXXXXPLCAAQDALLKVHXXX 122
             R ET++ +++ +  PG ++RVVT+YS                   +C A DAL KVH   
Sbjct:    70 RSETKSNMRINEALPGCEERVVTMYSTNEELNHFGDDGEL-----VCPALDALFKVHDMV 124

Query:   123 XXXXXXX--TDNDKKRKEKEECQI--LVPSSQSANIIGKAGATIKRLRSKTRTSIKVTPK 178
                      TD+D    EK+   +  LVPS Q   +IGK G  I+ LR+ T   I+V  K
Sbjct:   125 VADADQDDGTDDDNDLGEKQTVTVRMLVPSDQIGCVIGKGGQVIQNLRNDTNAQIRVI-K 183

Query:   179 DASEPTHSCAMEFDNFVLISGESEAVKKALFAISAIMY 216
             D   P  +  +  D  +LI GE   V++AL+ ++++++
Sbjct:   184 DHL-PACALTLSHDELLLIIGEPLVVREALYQVASLLH 220

GO:0003676 "nucleic acid binding" evidence=ISS

GO:0003723 "RNA binding" evidence=IEA

GO:0005634 "nucleus" evidence=ISM

GO:0009737 "response to abscisic acid stimulus" evidence=IDA

TAIR|locus:2168367 RCF3 "AT5G53060" [Arabidopsis thaliana (taxid:3702)]

 Score = 212 (79.7 bits), Expect = 2.9e-35, Sum P(3) = 2.9e-35
 Identities = 56/175 (32%), Positives = 86/175 (49%)

Query:   305 SEELVIRVLCPFNKIGRVIGKGGGTIKSIRQASGAQIDVDDTKDNRDECVITVTAIESPD 364
             SEELV ++LCP +KI RV+G+  G I  ++   G  + V D     DE +IT+++ E+PD
Sbjct:   322 SEELVFQILCPADKIVRVVGESQGIIDLLQNEIGVDVRVSDPVAGSDEQIITISSEEAPD 381

Query:   365 DIKSMAVEAVLLLQTKIND---EDDDTVTIRLLVXXXXXXXXXXXXXXXXNEIRKRTKAD 421
             D    A EA+L +QT+I D   + D+ +T RLLV                +EI + T   
Sbjct:   382 DPFFPAQEALLHIQTQIIDLIPDKDNLITTRLLVPSRDSICLEGKAGSV-SEISRLTGTS 440

Query:   422 VRI-SKGDKPKCADANDELXXXXXXXXXXRDALVQIIXXXXXXXXXXXXGSRNPP 475
             V+I ++ + P+CA  ND +          R+ALV++                 PP
Sbjct:   441 VQILAREEIPRCASINDVVIQITGEIRAAREALVELTLLLRSHMFKELSQKETPP 495

GO:0003676 "nucleic acid binding" evidence=ISS

GO:0003723 "RNA binding" evidence=IEA

GO:0005634 "nucleus" evidence=ISM

GO:0008150 "biological_process" evidence=ND

TAIR|locus:2017612 AT1G51580 "AT1G51580" [Arabidopsis thaliana (taxid:3702)]

 Score = 193 (73.0 bits), Expect = 1.9e-32, Sum P(4) = 1.9e-32
 Identities = 47/156 (30%), Positives = 80/156 (51%)

Query:   306 EELVIRVLCPFNKIGRVIGKGGGTIKSIRQASGAQIDVDDTKDNRDECVITVTAIESPDD 365
             EE+  R+LCP +K+G +IGKGG  +++++  SGA I V D   + +E +I ++A E+ + 
Sbjct:   274 EEVAFRLLCPADKVGSLIGKGGAVVRALQNESGASIKVSDPTHDSEERIIVISARENLER 333

Query:   366 IKSMAVEAVLLLQTKIND---EDDDTVTIRLLVXXXXXXXXXXXXXXXXNEIRKRTKADV 422
               S+A + V+ +  +I +   E    V  RLLV                +E+R+ T A +
Sbjct:   334 RHSLAQDGVMRVHNRIVEIGFEPSAAVVARLLVHSPYIGRLLGKGGHLISEMRRATGASI 393

Query:   423 RI-SKGDKPKCADANDELXXXXXXXXXXRDALVQII 457
             R+ +K    K    +DE+          +DAL QI+
Sbjct:   394 RVFAKDQATKYESQHDEIVQVIGNLKTVQDALFQIL 429

GO:0003676 "nucleic acid binding" evidence=ISS

GO:0003723 "RNA binding" evidence=IEA

TAIR|locus:2084908 FLK "AT3G04610" [Arabidopsis thaliana (taxid:3702)]

 Score = 198 (74.8 bits), Expect = 4.8e-19, Sum P(2) = 4.8e-19
 Identities = 60/200 (30%), Positives = 95/200 (47%)

Query:    27 EKDEKGNEESVIYRILCPDGVIGSVIGKSGKVINSIRQETRARVKVVDPFPGAKDRVVTI 86
             EK   G     ++R+L P   +GS+IG+ G VI  I +ETRAR+K++D  PG  +R V +
Sbjct:   177 EKRWPGWPGETVFRMLVPAQKVGSIIGRKGDVIKKIVEETRARIKILDGPPGTTERAVMV 236

Query:    87 YSHXXXXXXXXXXXXXXXXXPLCAAQDALLKVHXXXXXXXXXXTDNDKKRKEKEECQILV 146
                                  L  + D LL+VH            +      K   ++LV
Sbjct:   237 SGKEEPESS------------LPPSMDGLLRVHMRIVDGLDGEA-SQAPPPSKVSTRLLV 283

Query:   147 PSSQSANIIGKAGATIKRLRSKTRTSIKVTPKDASEPTHSCAMEFDNFVLISGESEAVKK 206
             P+SQ+ ++IGK G T+K ++  +   ++V     SE     A++ D  V + GE  +V +
Sbjct:   284 PASQAGSLIGKQGGTVKAIQEASACIVRVL---GSEDLPVFALQDDRVVEVVGEPTSVHR 340

Query:   207 ALFAISAIMYKFS-PREDIP 225
             AL  I++ + KF   R  IP
Sbjct:   341 ALELIASHLRKFLVDRSIIP 360

GO:0003676 "nucleic acid binding" evidence=ISS

GO:0003723 "RNA binding" evidence=IEA

GO:0005737 "cytoplasm" evidence=ISM

GO:0005634 "nucleus" evidence=IDA

GO:0009911 "positive regulation of flower development" evidence=IMP

TAIR|locus:2066020 AT2G22600 "AT2G22600" [Arabidopsis thaliana (taxid:3702)]

 Score = 147 (56.8 bits), Expect = 1.6e-17, Sum P(3) = 1.6e-17
 Identities = 53/210 (25%), Positives = 87/210 (41%)

Query:    34 EESVIYRILCPDGVIGSVIGKSGKVINSIRQETRARVKVVDPFPGAKDRVVTIYSHXXXX 93
             +E+ I R++C   VIG +IG +G V++ +R+ET  ++    P  G+   VV I       
Sbjct:    23 DETAI-RVVCHASVIGGIIGSNGYVVSKLRRETGTKIHCESPVNGSDHWVVFIVGSTAVN 81

Query:    94 XXXXXXXXXXXXXP-------LC---AAQDALLKVHXXXXXXXXXXTDNDKKRKEKEE-- 141
                                   C   AAQ AL++V                   E EE  
Sbjct:    82 QSILLTDRVGEFSGGEHEDWVTCEVSAAQTALIRVLERSWVVLAAKDGGGVVDGEDEEAY 141

Query:   142 CQILVPSSQSANIIGKAGATIKRLRSKTRTSIKVTPKDASEPTHSCAMEFDNFVLISGES 201
             C IL   +Q   ++G  G  ++ +R  +   I+V P     P   C  + D  + I+G+ 
Sbjct:   142 CGILADRNQIGAVLGLGGKNVEWMRRNSGAMIRVLPP----PI--CGTKNDELIQITGDV 195

Query:   202 EAVKKALFAISAIMYKFSPREDIPLETTVR 231
              AVKKAL  +S+ +   +P    P   +++
Sbjct:   196 LAVKKALVMVSSYIQNNAPLNGYPPPLSIK 225

GO:0003676 "nucleic acid binding" evidence=ISS

GO:0003723 "RNA binding" evidence=IEA

GO:0005634 "nucleus" evidence=ISM

GO:0008150 "biological_process" evidence=ND

UNIPROTKB|J3QT27 PCBP3 "Poly(rC)-binding protein 3" [Homo sapiens (taxid:9606)]

 Score = 122 (48.0 bits), Expect = 3.8e-10, Sum P(2) = 3.8e-10
 Identities = 40/129 (31%), Positives = 64/129 (49%)

Query:   308 LVIRVLCPFNKIGRVIGKGGGTIKSIRQASGAQIDVDDTKDNRDECVITVTAIESPDD-- 365
             L IR+L    ++G +IGK G T+K +R+ SGA+I++ +   N  E ++T+T    P D  
Sbjct:    22 LTIRLLMHGKEVGSIIGKKGETVKKMREESGARINISE--GNCPERIVTITG---PTDAI 76

Query:   366 IKSMAVEAVLLLQTKINDEDDDT------VTIRLLVXXXXXXXXXXXXXXXXNEIRKRTK 419
              K+ A+ A    +  IN   +        VT+RL+V                 EIR+ T 
Sbjct:    77 FKAFAMIAYKFEEDIINSMSNSPATSKPPVTLRLVVPASQCGSLIGKGGSKIKEIRESTG 136

Query:   420 ADVRISKGD 428
             A V+++ GD
Sbjct:   137 AQVQVA-GD 144

GO:0003723 "RNA binding" evidence=IEA

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

 Score = 135 (52.6 bits), Expect = 4.6e-11, Sum P(2) = 4.6e-11
 Identities = 60/234 (25%), Positives = 99/234 (42%)

Query:   143 QILVPSSQSANIIGKAGATIKRLRSKTRTSIKVTPKDASEPTHSCAMEFDNFVLISGESE 202
             +++VP+SQ  ++IGK G+ IK +R  T   ++V        T       +  V ISG  +
Sbjct:   133 RLVVPASQCGSLIGKGGSKIKEIRESTGAQVQVAGDMLPNST-------ERAVTISGTPD 185

Query:   203 AVKKALFAISAIMYKFSPREDIPLETTVREAXXXXXXXXXXXXXXXGGL-YPNADPILPS 261
             A+ + +  I  +M + SP +   +    + A               G    P+ D +   
Sbjct:   186 AIIQCVKQICVVMLE-SPPKGATIPYRPKPASTPVIFAGGQAYTIQGQYAIPHPDQLTKL 244

Query:   262 RSVPSILGAARVPDL--QGYADTGNTWPVYST--GLSLVSGLVGASQSEELVIRVLC-PF 316
               +   +     P L     A  G   P++S+    +L+    G   S       L  P 
Sbjct:   245 HQLA--MQQTPFPPLGQTNPAFPGEKLPLHSSEEAQNLMGQSSGLDASPPASTHELTIPN 302

Query:   317 NKIGRVIGKGGGTIKSIRQASGAQIDVDDTKDNRDECVITVTAIESPDDIKSMA 370
             + IG +IG+ G  I  IRQ SGAQI + +  +   E  IT+T   +P +I S+A
Sbjct:   303 DLIGCIIGRQGTKINEIRQMSGAQIKIANATEGSSERQITITG--TPANI-SLA 353

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

---

Prediction of Enzyme Commission (EC) Number

EC Number Prediction by Annotation Transfer from SWISS-PROT Entries

Original result of BLAST against SWISS-PROT

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

EC Number Prediction by Ezypred Server

Original result from Ezypred Server

Fail to connect to Ezypred Server

EC Number Prediction by EFICAz Software

Prediction Level	EC number	Confidence of Prediction
3rd Layer	2.7.7	LOW CONFIDENCE prediction!

---

Prediction of Functionally Associated Proteins

Functionally Associated Proteins Detected by STRING

Original result from the STRING server

Fail to connect to STRING server

---

Conserved Domains and Related Protein Families

Conserved Domains Detected by RPS-BLAST

Original result of RPS-BLAST against CDD database part I

ID	Length	Definition	E-value
Query	624
cd02396	65	cd02396, PCBP_like_KH, K homology RNA-binding doma	2e-18
cd00105	64	cd00105, KH-I, K homology RNA-binding domain, type	6e-14
cd02396	65	cd02396, PCBP_like_KH, K homology RNA-binding doma	5e-13
cd00105	64	cd00105, KH-I, K homology RNA-binding domain, type	1e-12
cd02396	65	cd02396, PCBP_like_KH, K homology RNA-binding doma	2e-12
cd02396	65	cd02396, PCBP_like_KH, K homology RNA-binding doma	2e-12
pfam00013	59	pfam00013, KH_1, KH domain	9e-11
cd00105	64	cd00105, KH-I, K homology RNA-binding domain, type	1e-10
cd00105	64	cd00105, KH-I, K homology RNA-binding domain, type	2e-10
cd00105	64	cd00105, KH-I, K homology RNA-binding domain, type	4e-10
smart00322	68	smart00322, KH, K homology RNA-binding domain	4e-10
cd02396	65	cd02396, PCBP_like_KH, K homology RNA-binding doma	1e-09
pfam00013	59	pfam00013, KH_1, KH domain	1e-09
pfam00013	59	pfam00013, KH_1, KH domain	3e-09
pfam00013	59	pfam00013, KH_1, KH domain	7e-09
smart00322	68	smart00322, KH, K homology RNA-binding domain	7e-09
smart00322	68	smart00322, KH, K homology RNA-binding domain	1e-08
pfam13014	42	pfam13014, KH_3, KH domain	1e-08
pfam00013	59	pfam00013, KH_1, KH domain	3e-08
pfam13014	42	pfam13014, KH_3, KH domain	5e-08
smart00322	68	smart00322, KH, K homology RNA-binding domain	8e-08
smart00322	68	smart00322, KH, K homology RNA-binding domain	4e-07
pfam13014	42	pfam13014, KH_3, KH domain	5e-07
cd02394	62	cd02394, vigilin_like_KH, K homology RNA-binding d	5e-07
pfam13014	42	pfam13014, KH_3, KH domain	7e-06
TIGR03591	684	TIGR03591, polynuc_phos, polyribonucleotide nucleo	1e-04
PRK11824	693	PRK11824, PRK11824, polynucleotide phosphorylase/p	1e-04
cd02393	61	cd02393, PNPase_KH, Polynucleotide phosphorylase (	1e-04
cd02394	62	cd02394, vigilin_like_KH, K homology RNA-binding d	2e-04
cd02394	62	cd02394, vigilin_like_KH, K homology RNA-binding d	6e-04
cd02394	62	cd02394, vigilin_like_KH, K homology RNA-binding d	7e-04
COG1185	692	COG1185, Pnp, Polyribonucleotide nucleotidyltransf	7e-04
pfam13014	42	pfam13014, KH_3, KH domain	0.002
TIGR02696	719	TIGR02696, pppGpp_PNP, guanosine pentaphosphate sy	0.003
cd02393	61	cd02393, PNPase_KH, Polynucleotide phosphorylase (	0.004

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

 Score = 79.1 bits (196), Expect = 2e-18
 Identities = 29/68 (42%), Positives = 41/68 (60%), Gaps = 3/68 (4%)

Query: 390 TIRLLVSSKVIGCIIGKSGSIINEIRKRTKADVRISKGDKPKCADANDELVEVVGEVGSV 449
           T+RLLV S   G IIGK GS I EIR+ T A +R+SK   P      + +V + G+  +V
Sbjct: 1   TLRLLVPSSQAGSIIGKGGSTIKEIREETGAKIRVSKSVLPGS---TERVVTISGKPSAV 57

Query: 450 RDALVQII 457
           + AL+ I+
Sbjct: 58  QKALLLIL 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 = 66.4 bits (163), Expect = 6e-14
 Identities = 29/64 (45%), Positives = 42/64 (65%)

Query: 555 TLEVLVPANAVGKVIGKAGSNLANIRKISGATIEMSDSKSSRGDRVALISGTPEQKRAAE 614
           T  VLVP++ VG++IGK GS +  IR+ +GA I++ DS S   +R+  I+GTPE    A+
Sbjct: 1   TERVLVPSSLVGRIIGKGGSTIKEIREETGAKIKIPDSGSGSEERIVTITGTPEAVEKAK 60

Query: 615 NLIQ 618
            LI 
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 = 64.0 bits (157), Expect = 5e-13
 Identities = 23/49 (46%), Positives = 31/49 (63%), Gaps = 1/49 (2%)

Query: 39 YRILCPDGVIGSVIGKSGKVINSIRQETRARVKVVDPF-PGAKDRVVTI 86
           R+L P    GS+IGK G  I  IR+ET A+++V     PG+ +RVVTI
Sbjct: 2  LRLLVPSSQAGSIIGKGGSTIKEIREETGAKIRVSKSVLPGSTERVVTI 50

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 = 62.6 bits (153), Expect = 1e-12
 Identities = 27/67 (40%), Positives = 44/67 (65%), Gaps = 3/67 (4%)

Query: 309 VIRVLCPFNKIGRVIGKGGGTIKSIRQASGAQIDVDDTKDNRDECVITVTAIESPDDIKS 368
             RVL P + +GR+IGKGG TIK IR+ +GA+I + D+    +E ++T+T   +P+ ++ 
Sbjct: 1   TERVLVPSSLVGRIIGKGGSTIKEIREETGAKIKIPDSGSGSEERIVTITG--TPEAVE- 57

Query: 369 MAVEAVL 375
            A E +L
Sbjct: 58  KAKELIL 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 = 62.1 bits (152), Expect = 2e-12
 Identities = 29/72 (40%), Positives = 41/72 (56%), Gaps = 7/72 (9%)

Query: 141 ECQILVPSSQSANIIGKAGATIKRLRSKTRTSIKVTPKDASEPTHSCAMEFDNFVLISGE 200
             ++LVPSSQ+ +IIGK G+TIK +R +T   I+V+       T       +  V ISG+
Sbjct: 1   TLRLLVPSSQAGSIIGKGGSTIKEIREETGAKIRVSKSVLPGST-------ERVVTISGK 53

Query: 201 SEAVKKALFAIS 212
             AV+KAL  I 
Sbjct: 54  PSAVQKALLLIL 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|239089 cd02396, PCBP_like_KH, K homology RNA-binding domain, PCBP_like

 Score = 62.1 bits (152), Expect = 2e-12
 Identities = 21/52 (40%), Positives = 33/52 (63%), Gaps = 1/52 (1%)

Query: 309 VIRVLCPFNKIGRVIGKGGGTIKSIRQASGAQIDVDDT-KDNRDECVITVTA 359
            +R+L P ++ G +IGKGG TIK IR+ +GA+I V  +      E V+T++ 
Sbjct: 1   TLRLLVPSSQAGSIIGKGGSTIKEIREETGAKIRVSKSVLPGSTERVVTISG 52

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|215657 pfam00013, KH_1, KH domain

 Score = 57.2 bits (139), Expect = 9e-11
 Identities = 27/63 (42%), Positives = 37/63 (58%), Gaps = 4/63 (6%)

Query: 555 TLEVLVPANAVGKVIGKAGSNLANIRKISGATIEMSDSKSSRGDRVALISGTPEQKRAAE 614
           T  +L+P + VG++IGK GSN+  IR+ +G  I + D      D    ISGTPEQ   A+
Sbjct: 1   TERILIPPDKVGRIIGKGGSNIKEIREETGVKIRIPDD----RDDTVTISGTPEQVEKAK 56

Query: 615 NLI 617
            LI
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 = 56.8 bits (138), Expect = 1e-10
 Identities = 24/60 (40%), Positives = 36/60 (60%), Gaps = 3/60 (5%)

Query: 38 IYRILCPDGVIGSVIGKSGKVINSIRQETRARVKVVDPFPGAKDRVVTIYSHVKDKEDVE 97
            R+L P  ++G +IGK G  I  IR+ET A++K+ D   G+++R+VTI       E VE
Sbjct: 1  TERVLVPSSLVGRIIGKGGSTIKEIREETGAKIKIPDSGSGSEERIVTITG---TPEAVE 57

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

 Score = 56.8 bits (138), Expect = 2e-10
 Identities = 26/71 (36%), Positives = 36/71 (50%), Gaps = 8/71 (11%)

Query: 141 ECQILVPSSQSANIIGKAGATIKRLRSKTRTSIKVTPKDASEPTHSCAMEFDNFVLISGE 200
             ++LVPSS    IIGK G+TIK +R +T   IK+    +           +  V I+G 
Sbjct: 1   TERVLVPSSLVGRIIGKGGSTIKEIREETGAKIKIPDSGSGSE--------ERIVTITGT 52

Query: 201 SEAVKKALFAI 211
            EAV+KA   I
Sbjct: 53  PEAVEKAKELI 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|238053 cd00105, KH-I, K homology RNA-binding domain, type I

 Score = 55.6 bits (135), Expect = 4e-10
 Identities = 24/67 (35%), Positives = 35/67 (52%), Gaps = 4/67 (5%)

Query: 390 TIRLLVSSKVIGCIIGKSGSIINEIRKRTKADVRISKGDKPKCADANDELVEVVGEVGSV 449
           T R+LV S ++G IIGK GS I EIR+ T A ++I          + + +V + G   +V
Sbjct: 1   TERVLVPSSLVGRIIGKGGSTIKEIREETGAKIKIPDSGS----GSEERIVTITGTPEAV 56

Query: 450 RDALVQI 456
             A   I
Sbjct: 57  EKAKELI 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|197652 smart00322, KH, K homology RNA-binding domain

 Score = 55.8 bits (135), Expect = 4e-10
 Identities = 27/69 (39%), Positives = 40/69 (57%), Gaps = 2/69 (2%)

Query: 553 PLTLEVLVPANAVGKVIGKAGSNLANIRKISGATIEMSDSKSSRGDRVALISGTPEQKRA 612
           P+T+EVL+PA+ VG +IGK GS +  I + +G  I++    S   +RV  I+G PE    
Sbjct: 2   PVTIEVLIPADKVGLIIGKGGSTIKKIEEETGVKIDIPGPGSE--ERVVEITGPPENVEK 59

Query: 613 AENLIQAFI 621
           A  LI   +
Sbjct: 60  AAELILEIL 68

Length = 68

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

 Score = 54.4 bits (132), Expect = 1e-09
 Identities = 27/65 (41%), Positives = 37/65 (56%), Gaps = 1/65 (1%)

Query: 555 TLEVLVPANAVGKVIGKAGSNLANIRKISGATIEMSDS-KSSRGDRVALISGTPEQKRAA 613
           TL +LVP++  G +IGK GS +  IR+ +GA I +S S      +RV  ISG P   + A
Sbjct: 1   TLRLLVPSSQAGSIIGKGGSTIKEIREETGAKIRVSKSVLPGSTERVVTISGKPSAVQKA 60

Query: 614 ENLIQ 618
             LI 
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|215657 pfam00013, KH_1, KH domain

 Score = 54.1 bits (131), Expect = 1e-09
 Identities = 21/59 (35%), Positives = 38/59 (64%), Gaps = 6/59 (10%)

Query: 309 VIRVLCPFNKIGRVIGKGGGTIKSIRQASGAQIDVDDTKDNRDECVITVTAIESPDDIK 367
             R+L P +K+GR+IGKGG  IK IR+ +G +I + D +D+     +T++   +P+ ++
Sbjct: 1   TERILIPPDKVGRIIGKGGSNIKEIREETGVKIRIPDDRDD----TVTISG--TPEQVE 53

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 = 52.9 bits (128), Expect = 3e-09
 Identities = 23/67 (34%), Positives = 30/67 (44%), Gaps = 8/67 (11%)

Query: 390 TIRLLVSSKVIGCIIGKSGSIINEIRKRTKADVRISKGDKPKCADANDELVEVVGEVGSV 449
           T R+L+    +G IIGK GS I EIR+ T   +RI            D+ V + G    V
Sbjct: 1   TERILIPPDKVGRIIGKGGSNIKEIREETGVKIRIPDDR--------DDTVTISGTPEQV 52

Query: 450 RDALVQI 456
             A   I
Sbjct: 53  EKAKELI 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 = 51.8 bits (125), Expect = 7e-09
 Identities = 23/71 (32%), Positives = 33/71 (46%), Gaps = 12/71 (16%)

Query: 141 ECQILVPSSQSANIIGKAGATIKRLRSKTRTSIKVTPKDASEPTHSCAMEFDNFVLISGE 200
             +IL+P  +   IIGK G+ IK +R +T   I++                D+ V ISG 
Sbjct: 1   TERILIPPDKVGRIIGKGGSNIKEIREETGVKIRIPDDR------------DDTVTISGT 48

Query: 201 SEAVKKALFAI 211
            E V+KA   I
Sbjct: 49  PEQVEKAKELI 59

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 = 52.3 bits (126), Expect = 7e-09
 Identities = 24/70 (34%), Positives = 35/70 (50%), Gaps = 5/70 (7%)

Query: 306 EELVIRVLCPFNKIGRVIGKGGGTIKSIRQASGAQIDVDDTKDNRDECVITVTAIESPDD 365
           + + I VL P +K+G +IGKGG TIK I + +G +ID+           IT      P +
Sbjct: 1   DPVTIEVLIPADKVGLIIGKGGSTIKKIEEETGVKIDIPGPGSEERVVEIT-----GPPE 55

Query: 366 IKSMAVEAVL 375
               A E +L
Sbjct: 56  NVEKAAELIL 65

Length = 68

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

 Score = 51.5 bits (124), Expect = 1e-08
 Identities = 21/78 (26%), Positives = 36/78 (46%), Gaps = 10/78 (12%)

Query: 138 EKEECQILVPSSQSANIIGKAGATIKRLRSKTRTSIKVTPKDASEPTHSCAMEFDNFVLI 197
           +    ++L+P+ +   IIGK G+TIK++  +T   I +                +  V I
Sbjct: 1   DPVTIEVLIPADKVGLIIGKGGSTIKKIEEETGVKIDIPGPG----------SEERVVEI 50

Query: 198 SGESEAVKKALFAISAIM 215
           +G  E V+KA   I  I+
Sbjct: 51  TGPPENVEKAAELILEIL 68

Length = 68

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

 Score = 50.6 bits (122), Expect = 1e-08
 Identities = 17/41 (41%), Positives = 27/41 (65%)

Query: 318 KIGRVIGKGGGTIKSIRQASGAQIDVDDTKDNRDECVITVT 358
            +G +IGKGG TIK IR+ +GA+I +   +    E ++T+T
Sbjct: 1   LVGAIIGKGGETIKEIREETGAKIQIPKPEPGSGERIVTIT 41

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|215657 pfam00013, KH_1, KH domain

 Score = 50.3 bits (121), Expect = 3e-08
 Identities = 22/60 (36%), Positives = 30/60 (50%), Gaps = 7/60 (11%)

Query: 38 IYRILCPDGVIGSVIGKSGKVINSIRQETRARVKVVDPFPGAKDRVVTIYSHVKDKEDVE 97
            RIL P   +G +IGK G  I  IR+ET  ++++ D     +D  VTI       E VE
Sbjct: 1  TERILIPPDKVGRIIGKGGSNIKEIREETGVKIRIPDD----RDDTVTISG---TPEQVE 53

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

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

 Score = 49.1 bits (118), Expect = 5e-08
 Identities = 18/39 (46%), Positives = 30/39 (76%)

Query: 48 IGSVIGKSGKVINSIRQETRARVKVVDPFPGAKDRVVTI 86
          +G++IGK G+ I  IR+ET A++++  P PG+ +R+VTI
Sbjct: 2  VGAIIGKGGETIKEIREETGAKIQIPKPEPGSGERIVTI 40

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 = 49.2 bits (118), Expect = 8e-08
 Identities = 19/60 (31%), Positives = 32/60 (53%), Gaps = 2/60 (3%)

Query: 35 ESVIYRILCPDGVIGSVIGKSGKVINSIRQETRARVKVVDPFPGAKDRVVTIYSHVKDKE 94
          + V   +L P   +G +IGK G  I  I +ET  ++ +    PG+++RVV I    ++ E
Sbjct: 1  DPVTIEVLIPADKVGLIIGKGGSTIKKIEEETGVKIDIPG--PGSEERVVEITGPPENVE 58

Length = 68

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

 Score = 47.3 bits (113), Expect = 4e-07
 Identities = 22/70 (31%), Positives = 33/70 (47%), Gaps = 6/70 (8%)

Query: 387 DTVTIRLLVSSKVIGCIIGKSGSIINEIRKRTKADVRISKGDKPKCADANDELVEVVGEV 446
           D VTI +L+ +  +G IIGK GS I +I + T   + I            + +VE+ G  
Sbjct: 1   DPVTIEVLIPADKVGLIIGKGGSTIKKIEEETGVKIDIPGPGS------EERVVEITGPP 54

Query: 447 GSVRDALVQI 456
            +V  A   I
Sbjct: 55  ENVEKAAELI 64

Length = 68

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

 Score = 46.0 bits (110), Expect = 5e-07
 Identities = 15/45 (33%), Positives = 23/45 (51%), Gaps = 4/45 (8%)

Query: 400 IGCIIGKSGSIINEIRKRTKADVRISKGDKPKCADANDELVEVVG 444
           +G IIGK G  I EIR+ T A ++I          + + +V + G
Sbjct: 2   VGAIIGKGGETIKEIREETGAKIQIP----KPEPGSGERIVTITG 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 = 46.7 bits (112), Expect = 5e-07
 Identities = 16/71 (22%), Positives = 30/71 (42%), Gaps = 10/71 (14%)

Query: 141 ECQILVPSSQSANIIGKAGATIKRLRSKTRTSIKVTPKDASEPTHSCAMEFDNFVLISGE 200
             ++ +P      IIGK G+ I+++  +T   I+     +            + + I+G 
Sbjct: 1   TEEVEIPKKLHRFIIGKKGSNIRKIMEETGVKIRFPDPGSK----------SDTITITGP 50

Query: 201 SEAVKKALFAI 211
            E V+KA   I
Sbjct: 51  KENVEKAKEEI 61

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 = 42.9 bits (102), Expect = 7e-06
 Identities = 15/41 (36%), Positives = 25/41 (60%)

Query: 565 VGKVIGKAGSNLANIRKISGATIEMSDSKSSRGDRVALISG 605
           VG +IGK G  +  IR+ +GA I++   +   G+R+  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|234271 TIGR03591, polynuc_phos, polyribonucleotide nucleotidyltransferase

 Score = 45.2 bits (108), Expect = 1e-04
 Identities = 14/29 (48%), Positives = 20/29 (68%)

Query: 318 KIGRVIGKGGGTIKSIRQASGAQIDVDDT 346
           KI  VIG GG  I+ I + +GA+ID++D 
Sbjct: 561 KIRDVIGPGGKVIREITEETGAKIDIEDD 589

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

>gnl|CDD|236995 PRK11824, PRK11824, polynucleotide phosphorylase/polyadenylase; Provisional

 Score = 44.7 bits (107), Expect = 1e-04
 Identities = 15/29 (51%), Positives = 22/29 (75%)

Query: 317 NKIGRVIGKGGGTIKSIRQASGAQIDVDD 345
           +KI  VIG GG TI+ I + +GA+ID++D
Sbjct: 563 DKIRDVIGPGGKTIREITEETGAKIDIED 591

Length = 693

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

 Score = 39.8 bits (94), Expect = 1e-04
 Identities = 15/28 (53%), Positives = 20/28 (71%)

Query: 318 KIGRVIGKGGGTIKSIRQASGAQIDVDD 345
           KI  VIG GG TIK I + +G +ID++D
Sbjct: 12  KIRDVIGPGGKTIKKIIEETGVKIDIED 39

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|239087 cd02394, vigilin_like_KH, K homology RNA-binding domain_vigilin_like

 Score = 39.4 bits (93), Expect = 2e-04
 Identities = 14/48 (29%), Positives = 19/48 (39%)

Query: 309 VIRVLCPFNKIGRVIGKGGGTIKSIRQASGAQIDVDDTKDNRDECVIT 356
              V  P      +IGK G  I+ I + +G +I   D     D   IT
Sbjct: 1   TEEVEIPKKLHRFIIGKKGSNIRKIMEETGVKIRFPDPGSKSDTITIT 48

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 = 37.9 bits (89), Expect = 6e-04
 Identities = 16/67 (23%), Positives = 28/67 (41%), Gaps = 6/67 (8%)

Query: 390 TIRLLVSSKVIGCIIGKSGSIINEIRKRTKADVRISKGDKPKCADANDELVEVVGEVGSV 449
           T  + +  K+   IIGK GS I +I + T   +R           +  + + + G   +V
Sbjct: 1   TEEVEIPKKLHRFIIGKKGSNIRKIMEETGVKIRFPD------PGSKSDTITITGPKENV 54

Query: 450 RDALVQI 456
             A  +I
Sbjct: 55  EKAKEEI 61

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 = 37.9 bits (89), Expect = 7e-04
 Identities = 18/48 (37%), Positives = 26/48 (54%), Gaps = 5/48 (10%)

Query: 50 SVIGKSGKVINSIRQETRARVKVVDPFPGAKDRVVTIYSHVKDKEDVE 97
           +IGK G  I  I +ET  +++   P PG+K   +TI      KE+VE
Sbjct: 13 FIIGKKGSNIRKIMEETGVKIRF--PDPGSKSDTITI---TGPKENVE 55

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

 Score = 42.2 bits (100), Expect = 7e-04
 Identities = 15/28 (53%), Positives = 21/28 (75%)

Query: 318 KIGRVIGKGGGTIKSIRQASGAQIDVDD 345
           KI  VIG GG TIK+I + +G +ID++D
Sbjct: 562 KIRDVIGPGGKTIKAITEETGVKIDIED 589

Length = 692

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

 Score = 36.4 bits (85), Expect = 0.002
 Identities = 14/46 (30%), Positives = 21/46 (45%), Gaps = 8/46 (17%)

Query: 154 IIGKAGATIKRLRSKTRTSIKVTPKDASEPTHSCAMEFDNFVLISG 199
           IIGK G TIK +R +T   I++   +            +  V I+G
Sbjct: 5   IIGKGGETIKEIREETGAKIQIPKPEPGSG--------ERIVTITG 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|131743 TIGR02696, pppGpp_PNP, guanosine pentaphosphate synthetase I/polynucleotide phosphorylase

 Score = 40.2 bits (94), Expect = 0.003
 Identities = 16/37 (43%), Positives = 23/37 (62%)

Query: 309 VIRVLCPFNKIGRVIGKGGGTIKSIRQASGAQIDVDD 345
           +I V  P +KIG VIG  G  I  I+  +GA+I ++D
Sbjct: 579 IITVKIPVDKIGEVIGPKGKMINQIQDETGAEISIED 615

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. Length = 719

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

 Score = 35.6 bits (83), Expect = 0.004
 Identities = 18/50 (36%), Positives = 23/50 (46%), Gaps = 8/50 (16%)

Query: 48 IGSVIGKSGKVINSIRQETRARVKVVDPFPGAKDRVVTIYSHVKDKEDVE 97
          I  VIG  GK I  I +ET  ++ + D      D  V I +   DKE  E
Sbjct: 13 IRDVIGPGGKTIKKIIEETGVKIDIED------DGTVYIAA--SDKEAAE 54

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

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	624
KOG2190	485	consensus PolyC-binding proteins alphaCP-1 and rel	100.0
KOG2193	584	consensus IGF-II mRNA-binding protein IMP, contain	100.0
KOG1676	600	consensus K-homology type RNA binding proteins [RN	100.0
KOG1676	600	consensus K-homology type RNA binding proteins [RN	100.0
KOG2193	584	consensus IGF-II mRNA-binding protein IMP, contain	100.0
KOG2192	390	consensus PolyC-binding hnRNP-K protein HRB57A/hnR	100.0
KOG2192	390	consensus PolyC-binding hnRNP-K protein HRB57A/hnR	100.0
KOG2190	485	consensus PolyC-binding proteins alphaCP-1 and rel	99.97
KOG2191	402	consensus RNA-binding protein NOVA1/PASILLA and re	99.94
KOG2191	402	consensus RNA-binding protein NOVA1/PASILLA and re	99.93
TIGR03665	172	arCOG04150 arCOG04150 universal archaeal KH domain	99.62
PRK13763	180	putative RNA-processing protein; Provisional	99.56
TIGR03665	172	arCOG04150 arCOG04150 universal archaeal KH domain	99.51
PRK13763	180	putative RNA-processing protein; Provisional	99.5
KOG2208	753	consensus Vigilin [Lipid transport and metabolism]	99.48
KOG2208	753	consensus Vigilin [Lipid transport and metabolism]	99.47
cd02396	65	PCBP_like_KH K homology RNA-binding domain, PCBP_l	99.45
KOG2279	608	consensus Kinase anchor protein AKAP149, contains	99.34
cd02394	62	vigilin_like_KH K homology RNA-binding domain_vigi	99.32
PF00013	60	KH_1: KH domain syndrome, contains KH motifs.; Int	99.31
cd02396	65	PCBP_like_KH K homology RNA-binding domain, PCBP_l	99.3
cd02393	61	PNPase_KH Polynucleotide phosphorylase (PNPase) K	99.27
cd00105	64	KH-I K homology RNA-binding domain, type I. KH bin	99.26
KOG2279	608	consensus Kinase anchor protein AKAP149, contains	99.21
cd02394	62	vigilin_like_KH K homology RNA-binding domain_vigi	99.11
cd02393	61	PNPase_KH Polynucleotide phosphorylase (PNPase) K	99.05
PF00013	60	KH_1: KH domain syndrome, contains KH motifs.; Int	99.03
cd00105	64	KH-I K homology RNA-binding domain, type I. KH bin	98.98
PF13014	43	KH_3: KH domain	98.94
PF13014	43	KH_3: KH domain	98.91
smart00322	69	KH K homology RNA-binding domain.	98.9
smart00322	69	KH K homology RNA-binding domain.	98.71
COG1094	194	Predicted RNA-binding protein (contains KH domains	98.65
COG1094	194	Predicted RNA-binding protein (contains KH domains	98.6
cd02395	120	SF1_like-KH Splicing factor 1 (SF1) K homology RNA	98.42
cd02395	120	SF1_like-KH Splicing factor 1 (SF1) K homology RNA	98.14
KOG2113	394	consensus Predicted RNA binding protein, contains	98.12
TIGR02696	719	pppGpp_PNP guanosine pentaphosphate synthetase I/p	97.95
PRK08406	140	transcription elongation factor NusA-like protein;	97.92
PRK08406	140	transcription elongation factor NusA-like protein;	97.85
TIGR02696	719	pppGpp_PNP guanosine pentaphosphate synthetase I/p	97.8
KOG2113	394	consensus Predicted RNA binding protein, contains	97.73
TIGR03591	684	polynuc_phos polyribonucleotide nucleotidyltransfe	97.51
KOG0119	554	consensus Splicing factor 1/branch point binding p	97.38
TIGR03591	684	polynuc_phos polyribonucleotide nucleotidyltransfe	97.31
TIGR01952	141	nusA_arch NusA family KH domain protein, archaeal.	97.26
TIGR01952	141	nusA_arch NusA family KH domain protein, archaeal.	97.25
KOG0336	629	consensus ATP-dependent RNA helicase [RNA processi	97.17
PLN00207	891	polyribonucleotide nucleotidyltransferase; Provisi	97.13
KOG0336	629	consensus ATP-dependent RNA helicase [RNA processi	97.0
KOG0119	554	consensus Splicing factor 1/branch point binding p	96.99
KOG1588	259	consensus RNA-binding protein Sam68 and related KH	96.97
COG0195	190	NusA Transcription elongation factor [Transcriptio	96.93
COG1185	692	Pnp Polyribonucleotide nucleotidyltransferase (pol	96.87
KOG1588	259	consensus RNA-binding protein Sam68 and related KH	96.86
COG0195	190	NusA Transcription elongation factor [Transcriptio	96.73
PLN00207	891	polyribonucleotide nucleotidyltransferase; Provisi	96.71
cd02134	61	NusA_KH NusA_K homology RNA-binding domain (KH). N	96.58
COG1185	692	Pnp Polyribonucleotide nucleotidyltransferase (pol	96.51
KOG2814	345	consensus Transcription coactivator complex, P50 c	96.4
KOG2814	345	consensus Transcription coactivator complex, P50 c	96.36
PRK00106	535	hypothetical protein; Provisional	96.36
TIGR03319	514	YmdA_YtgF conserved hypothetical protein YmdA/YtgF	96.33
cd02134	61	NusA_KH NusA_K homology RNA-binding domain (KH). N	96.33
PRK04163	235	exosome complex RNA-binding protein Rrp4; Provisio	96.28
PRK12704	520	phosphodiesterase; Provisional	96.27
PRK11824	693	polynucleotide phosphorylase/polyadenylase; Provis	96.26
PF14611	210	SLS: Mitochondrial inner-membrane-bound regulator	96.16
PRK11824	693	polynucleotide phosphorylase/polyadenylase; Provis	95.86
PRK12328	374	nusA transcription elongation factor NusA; Provisi	95.84
KOG4369	2131	consensus RTK signaling protein MASK/UNC-44 [Signa	95.69
TIGR01953	341	NusA transcription termination factor NusA. This m	95.66
TIGR01953	341	NusA transcription termination factor NusA. This m	95.53
PRK02821	77	hypothetical protein; Provisional	95.4
PRK00106	535	hypothetical protein; Provisional	95.37
TIGR03319	514	YmdA_YtgF conserved hypothetical protein YmdA/YtgF	95.35
PRK12327	362	nusA transcription elongation factor NusA; Provisi	95.35
PRK12329	449	nusA transcription elongation factor NusA; Provisi	95.33
PRK02821	77	hypothetical protein; Provisional	95.32
PRK12704	520	phosphodiesterase; Provisional	95.31
PRK12328	374	nusA transcription elongation factor NusA; Provisi	95.31
PRK00468	75	hypothetical protein; Provisional	95.3
PRK12327	362	nusA transcription elongation factor NusA; Provisi	95.28
PRK00468	75	hypothetical protein; Provisional	95.22
COG5176	269	MSL5 Splicing factor (branch point binding protein	95.1
PRK12329	449	nusA transcription elongation factor NusA; Provisi	94.99
COG5176	269	MSL5 Splicing factor (branch point binding protein	94.91
PRK09202	470	nusA transcription elongation factor NusA; Validat	94.88
PRK04163	235	exosome complex RNA-binding protein Rrp4; Provisio	94.84
PRK09202	470	nusA transcription elongation factor NusA; Validat	94.72
COG1837	76	Predicted RNA-binding protein (contains KH domain)	94.67
COG1837	76	Predicted RNA-binding protein (contains KH domain)	94.43
PRK01064	78	hypothetical protein; Provisional	94.35
PRK12705	508	hypothetical protein; Provisional	94.24
PF14611	210	SLS: Mitochondrial inner-membrane-bound regulator	94.0
PRK01064	78	hypothetical protein; Provisional	94.0
PRK12705	508	hypothetical protein; Provisional	91.9
COG5166	657	Uncharacterized conserved protein [Function unknow	91.39
KOG1067	760	consensus Predicted RNA-binding polyribonucleotide	90.96
KOG3273	252	consensus Predicted RNA-binding protein Pno1p inte	90.65
KOG2874	356	consensus rRNA processing protein [Translation, ri	90.6
KOG1067	760	consensus Predicted RNA-binding polyribonucleotide	89.92
PF13083	73	KH_4: KH domain; PDB: 3GKU_B.	89.9
PF13083	73	KH_4: KH domain; PDB: 3GKU_B.	88.53
PF13184	69	KH_5: NusA-like KH domain; PDB: 1HH2_P 1L2F_A 2ATW	87.18
COG1855	604	ATPase (PilT family) [General function prediction	87.07
cd02409	68	KH-II KH-II (K homology RNA-binding domain, type I	86.95
cd02409	68	KH-II KH-II (K homology RNA-binding domain, type I	86.93
COG1855	604	ATPase (PilT family) [General function prediction	86.65
PF13184	69	KH_5: NusA-like KH domain; PDB: 1HH2_P 1L2F_A 2ATW	85.65
COG1097	239	RRP4 RNA-binding protein Rrp4 and related proteins	84.45
PF07650	78	KH_2: KH domain syndrome, contains KH motifs.; Int	84.4
cd02413	81	40S_S3_KH K homology RNA-binding (KH) domain of th	84.15
COG1097	239	RRP4 RNA-binding protein Rrp4 and related proteins	83.73
KOG2874	356	consensus rRNA processing protein [Translation, ri	83.43
cd02414	77	jag_KH jag_K homology RNA-binding domain. The KH d	83.23
PRK13764	602	ATPase; Provisional	83.23
KOG3273	252	consensus Predicted RNA-binding protein Pno1p inte	82.58
PF07650	78	KH_2: KH domain syndrome, contains KH motifs.; Int	81.51
cd02410	145	archeal_CPSF_KH The archaeal cleavage and polyaden	81.33
PRK13764	602	ATPase; Provisional	81.24
cd02414	77	jag_KH jag_K homology RNA-binding domain. The KH d	80.65

>KOG2190 consensus PolyC-binding proteins alphaCP-1 and related KH domain proteins [RNA processing and modification; General function prediction only]

Probab=100.00  E-value=8.1e-42  Score=361.80  Aligned_cols=361  Identities=38%  Similarity=0.627  Sum_probs=281.8

Q ss_pred             CCCceEEEEEEecCcccceeccCCchHHHHHHHhcCCeEEeeCCCCCCCceEEEEEccCCcccccccccccCCCCcccHH
Q 006943           32 GNEESVIYRILCPDGVIGSVIGKSGKVINSIRQETRARVKVVDPFPGAKDRVVTIYSHVKDKEDVEVDDEFNDKEPLCAA  111 (624)
Q Consensus        32 ~~~~~~~~~ilvp~~~~g~vIGk~G~~I~~i~~etg~~I~v~~~~~~~~er~i~I~G~~~~~~~~~~~~~~~~~~~~~~a  111 (624)
                      ..+...++||||+.+.+|.||||+|..|++||++|.++|+|.+..++++||+++|+|....             ..+|++
T Consensus        38 ~p~~t~~~RlL~~~kevG~IIGk~G~~vkkir~~t~s~i~i~~~~~~c~eRIiti~g~~~~-------------~~~~~~  104 (485)
T KOG2190|consen   38 GPDETLTYRLLCHVKEVGSIIGKKGDIVKKIRKETESKIRVNESLPGCPERIITITGNRVE-------------LNLSPA  104 (485)
T ss_pred             CCCCcceEEEEeccccceeEEccCcHHHHHHhhcccccceeecCCCCCCcceEEEeccccc-------------ccCCch
Confidence            3344555999999999999999999999999999999999999999999999999997222             147899


Q ss_pred             HHHHHHHHHHHHHhhhccC----CCcccCC-CceeEEEEEeccceeEEEeCCchHHHHHHHhcCCeEEEccCCCCCCCCc
Q 006943          112 QDALLKVHAAIANAVANAT----DNDKKRK-EKEECQILVPSSQSANIIGKAGATIKRLRSKTRTSIKVTPKDASEPTHS  186 (624)
Q Consensus       112 ~~ai~~v~~~i~~~~~~~~----~~~~~~~-~~~~~~llvp~~~~g~iIGk~G~~Ik~I~~~sga~I~i~~~~~~~~~~~  186 (624)
                      ++|++++++.+...++...    |...... ..++||||||++++|.||||+|++||+|+++|||+|+|.++.       
T Consensus       105 ~~al~ka~~~iv~~~~~d~~~~~d~~~~~~~~~v~~RLlVp~sq~GslIGK~G~~Ik~Ire~TgA~I~v~~~~-------  177 (485)
T KOG2190|consen  105 TDALFKAFDMIVFKLEEDDEAAEDNGEDASGPEVTCRLLVPSSQVGSLIGKGGSLIKEIREETGAKIRVSSDM-------  177 (485)
T ss_pred             HHHHHHHHHHHhhcccccccccccCCccccCCceEEEEEechhheeeeeccCcHHHHHHHHhcCceEEecCCC-------
Confidence            9999999999998755321    1111112 258999999999999999999999999999999999999862       


Q ss_pred             ccccCCceEEEecCHHHHHHHHHHHHHHHhhcCCCCCCCCCCccCCCCCCccCCCCCCCCCCCCCCCCCCCCCCCCCCCC
Q 006943          187 CAMEFDNFVLISGESEAVKKALFAISAIMYKFSPREDIPLETTVREAPPSIIIPSDVPIYPPGGLYPNADPILPSRSVPS  266 (624)
Q Consensus       187 ~~~~~~r~V~I~G~~~~V~~A~~~I~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~~~~~  266 (624)
                      .|.+++|.|+|.|.+++|.+|+.+|..+|++.......+.....             ++.|   ..+...++        
T Consensus       178 lP~ster~V~IsG~~~av~~al~~Is~~L~~~~~~~~~~~~st~-------------~y~P---~~~~~~~~--------  233 (485)
T KOG2190|consen  178 LPNSTERAVTISGEPDAVKKALVQISSRLLENPPRSPPPLVSTI-------------PYRP---SASQGGPV--------  233 (485)
T ss_pred             CCcccceeEEEcCchHHHHHHHHHHHHHHHhcCCcCCCCCCCcc-------------cCCC---cccccCcc--------
Confidence            24478999999999999999999999999886543111111110             0000   00000000        


Q ss_pred             ccCCCCCCCCCCCCCCCCCCCCCCCCCccccCCCCCCCCccEEEEEEecCCccceeeccCcchHHHHHhHhCCeEEEcCC
Q 006943          267 ILGAARVPDLQGYADTGNTWPVYSTGLSLVSGLVGASQSEELVIRVLCPFNKIGRVIGKGGGTIKSIRQASGAQIDVDDT  346 (624)
Q Consensus       267 ~~g~~~~p~~~~~~~~~~~~~~~~~~~p~~~~~~~~~~~~~~~~~i~vp~~~vg~IIGk~G~~Ik~I~~~tga~I~v~~~  346 (624)
                                         .+......+.++.+.....+.++.+++.+|...++.|||++|..|+.|+.++++.|.+.+.
T Consensus       234 -------------------~~s~~~~~~~~~~~~~~~~~~e~~~~~~~p~~~~~~v~g~~~~~i~~l~~~~~~~i~v~~~  294 (485)
T KOG2190|consen  234 -------------------LPSTAQTSPDAHPFGGIVPEEELVFKLICPSDKVGSVIGKGGLVIRALRNETGASISVGDS  294 (485)
T ss_pred             -------------------ccccccCCcccccccccccchhhhhhhcCchhhceeeecCCCccchhhhhhcCCceEeccc
Confidence                               0001111111222223455677889999999999999999999999999999999999876


Q ss_pred             CCCCCceEEEEeecCCchhHHHHHHHHHHHHhhccCCCCCC----cEEEEEEecCCeeeEEEcCCCchHHHHHHhcCceE
Q 006943          347 KDNRDECVITVTAIESPDDIKSMAVEAVLLLQTKINDEDDD----TVTIRLLVSSKVIGCIIGKSGSIINEIRKRTKADV  422 (624)
Q Consensus       347 ~~~~~er~i~I~G~~~~~~a~~~~~~~i~~~~~~~~~~~~~----~~~~~l~vp~~~~g~iIGk~G~~Ik~I~~~tga~I  422 (624)
                      ...   |+|+++..+..++..+++++++.+.+..+.+...+    .++.+|+||.+++++||||+|.+|.+|++.|||.|
T Consensus       295 ~~~---~~i~~s~~e~~~~~~s~a~~a~~~~~~~~~~~~~~~~~~~v~~~l~vps~~igciiGk~G~~iseir~~tgA~I  371 (485)
T KOG2190|consen  295 RTD---RIVTISARENPEDRYSMAQEALLLVQPRISENAGDDLTQTVTQRLLVPSDLIGCIIGKGGAKISEIRQRTGASI  371 (485)
T ss_pred             cCc---ceeeeccccCcccccccchhhhhhccccccccccccccceeeeeeccCccccceeecccccchHHHHHhcCCce
Confidence            553   89999998888888999999999988887654433    48899999999999999999999999999999999


Q ss_pred             EEeCCCCCCCCCCCCcEEEEEeehHHHHHHHHHHHHHH
Q 006943          423 RISKGDKPKCADANDELVEVVGEVGSVRDALVQIILRL  460 (624)
Q Consensus       423 ~i~~~~~p~~~~~~~~~v~I~G~~~~v~~A~~~I~~~l  460 (624)
                      +|.....-  ....++.++|+|...+...+...+...+
T Consensus       372 ~I~~~~~~--~~~~e~~~~I~~~~~~~~~~~~~~~~~~  407 (485)
T KOG2190|consen  372 SILNKEEV--SGVREALVQITGMLREDLLAQYLIRARL  407 (485)
T ss_pred             EEcccccc--CCcceeEEEecchhHHHHhhhhhccccc
Confidence            99875431  1367999999999999998877765444

>KOG2193 consensus IGF-II mRNA-binding protein IMP, contains RRM and KH domains [RNA processing and modification; General function prediction only]

Probab=100.00  E-value=6.3e-43  Score=344.31  Aligned_cols=366  Identities=23%  Similarity=0.383  Sum_probs=270.6

Q ss_pred             CCCCCCceEEEEEEecCcccceeccCCchHHHHHHHhcCCeEEeeC-CCCCCCceEEEEEccCCcccccccccccCCCCc
Q 006943           29 DEKGNEESVIYRILCPDGVIGSVIGKSGKVINSIRQETRARVKVVD-PFPGAKDRVVTIYSHVKDKEDVEVDDEFNDKEP  107 (624)
Q Consensus        29 ~~~~~~~~~~~~ilvp~~~~g~vIGk~G~~I~~i~~etg~~I~v~~-~~~~~~er~i~I~G~~~~~~~~~~~~~~~~~~~  107 (624)
                      -++......++|+|||..++|+||||.|++||.|.+.|.|||+|+. ...|..||+|||.+.+|.+              
T Consensus       191 ~~~~q~~D~PlR~lVptqyvgaIIGkeG~TIknItkqTqsriD~hrken~Gaaek~itvh~tpEg~--------------  256 (584)
T KOG2193|consen  191 HHKQQLKDWPLRLLVPTQYVGAIIGKEGATIKNITKQTQSRIDVHRKENAGAAEKIITVHSTPEGT--------------  256 (584)
T ss_pred             cccccccCcceeeeeccceeEEEecCCCccccCcchhhhheeeeeecccCCcccCceEEecCccch--------------
Confidence            3445577899999999999999999999999999999999999986 5679999999999999984              


Q ss_pred             ccHHHHHHHHHHHHHHHhhhccCCCcccCCCceeEEEEEeccceeEEEeCCchHHHHHHHhcCCeEEEccCCCCCCCCcc
Q 006943          108 LCAAQDALLKVHAAIANAVANATDNDKKRKEKEECQILVPSSQSANIIGKAGATIKRLRSKTRTSIKVTPKDASEPTHSC  187 (624)
Q Consensus       108 ~~~a~~ai~~v~~~i~~~~~~~~~~~~~~~~~~~~~llvp~~~~g~iIGk~G~~Ik~I~~~sga~I~i~~~~~~~~~~~~  187 (624)
                       +.|+..|+.++..-+.        +.+....+.++++.++.++|+||||.|.+||+|+.+||++|.|.+.-..     .
T Consensus       257 -s~Ac~~ILeimqkEA~--------~~k~~~e~pLk~lAHN~lvGRLIGKeGrnlKkIeq~TgTkITis~lqel-----s  322 (584)
T KOG2193|consen  257 -SKACKMILEIMQKEAV--------DDKVAEEIPLKILAHNNLVGRLIGKEGRNLKKIEQDTGTKITISKLQEL-----S  322 (584)
T ss_pred             -HHHHHHHHHHHHHhhh--------ccchhhhcchhhhhhcchhhhhhhhccccHHHHHhhcCCceeeeehhhh-----c
Confidence             3344444444433211        1223457899999999999999999999999999999999999874221     1


Q ss_pred             cccCCceEEEecCHHHHHHHHHHHHHHHhhcCCCCCCCCCCccCCCCCCccCCCCCCCCCCCCCCCCCCCCCCCCCCCCc
Q 006943          188 AMEFDNFVLISGESEAVKKALFAISAIMYKFSPREDIPLETTVREAPPSIIIPSDVPIYPPGGLYPNADPILPSRSVPSI  267 (624)
Q Consensus       188 ~~~~~r~V~I~G~~~~V~~A~~~I~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~~~~~~  267 (624)
                      -...||+|+|+|+.++|..|..+|...|+++.+.+. ..-...++.||-+.       ++.-|.++..+.+.|+...|+.
T Consensus       323 ~ynpERTItVkGsiEac~~AE~eImkKlre~yEnDl-~a~s~q~~l~P~l~-------~~~l~~f~ssS~~~~Ph~~Ps~  394 (584)
T KOG2193|consen  323 LYNPERTITVKGSIEACVQAEAEIMKKLRECYENDL-AAMSLQCHLPPGLN-------LPALGLFPSSSAVSPPHFPPSP  394 (584)
T ss_pred             ccCccceEEecccHHHHHHHHHHHHHHHHHHHhhhH-HHhhccCCCCcccC-------ccccCCCCcccccCCCCCCCCc
Confidence            224599999999999999999999999999887652 11112222222221       1222333333333333222221


Q ss_pred             c-CCCCCCCCCCCCCCCCCCCCCCCCCccccCCCCCCCCccEEEEEEecCCccceeeccCcchHHHHHhHhCCeEEEcCC
Q 006943          268 L-GAARVPDLQGYADTGNTWPVYSTGLSLVSGLVGASQSEELVIRVLCPFNKIGRVIGKGGGTIKSIRQASGAQIDVDDT  346 (624)
Q Consensus       268 ~-g~~~~p~~~~~~~~~~~~~~~~~~~p~~~~~~~~~~~~~~~~~i~vp~~~vg~IIGk~G~~Ik~I~~~tga~I~v~~~  346 (624)
                      . ++.+.|..+.                         ..+...+++.||...+|.||||+|.+||+|...+||.|+|..+
T Consensus       395 v~~a~p~~~~hq-------------------------~pe~e~V~~fiP~~~vGAiIGkkG~hIKql~RfagASiKIapp  449 (584)
T KOG2193|consen  395 VTFASPYPLFHQ-------------------------NPEQEQVRMFIPAQAVGAIIGKKGQHIKQLSRFAGASIKIAPP  449 (584)
T ss_pred             cccCCCchhhhc-------------------------CcchhheeeeccHHHHHHHHhhcchhHHHHHHhccceeeecCC
Confidence            1 1111111111                         1144578899999999999999999999999999999999865


Q ss_pred             C-CCCCceEEEEeecCCchhHHHHHHHHHHHHhhccCCC------CCCcEEEEEEecCCeeeEEEcCCCchHHHHHHhcC
Q 006943          347 K-DNRDECVITVTAIESPDDIKSMAVEAVLLLQTKINDE------DDDTVTIRLLVSSKVIGCIIGKSGSIINEIRKRTK  419 (624)
Q Consensus       347 ~-~~~~er~i~I~G~~~~~~a~~~~~~~i~~~~~~~~~~------~~~~~~~~l~vp~~~~g~iIGk~G~~Ik~I~~~tg  419 (624)
                      + ++..+|.|+|+|+.   .+   ..+|.-+++.++.++      ....+..++.||...+|+||||||.++++|+.-|+
T Consensus       450 E~pdvseRMViItGpp---ea---qfKAQgrifgKikEenf~~PkeevklethirVPs~~aGRvIGKGGktVnELQnlt~  523 (584)
T KOG2193|consen  450 EIPDVSERMVIITGPP---EA---QFKAQGRIFGKIKEENFFLPKEEVKLETHIRVPSSAAGRVIGKGGKTVNELQNLTS  523 (584)
T ss_pred             CCCCcceeEEEecCCh---HH---HHhhhhhhhhhhhhhccCCchhhheeeeeeeccchhhhhhhccccccHHHHhcccc
Confidence            4 45689999999972   23   245555666666553      23445667999999999999999999999999999


Q ss_pred             ceEEEeCCCCCCCCCCCCcEEEEEeehHHHHHHHHHHHHHHhhc
Q 006943          420 ADVRISKGDKPKCADANDELVEVVGEVGSVRDALVQIILRLRDD  463 (624)
Q Consensus       420 a~I~i~~~~~p~~~~~~~~~v~I~G~~~~v~~A~~~I~~~l~e~  463 (624)
                      |-|.|+++..|.  .++.-+|.|.|..-+.+.|...|...+.+.
T Consensus       524 AeV~vPrdqtpd--End~vivriiGhfyatq~aQrki~~iv~qv  565 (584)
T KOG2193|consen  524 AEVVVPRDQTPD--ENDQVIVRIIGHFYATQNAQRKIAHIVNQV  565 (584)
T ss_pred             ceEEccccCCCC--ccceeeeeeechhhcchHHHHHHHHHHHHH
Confidence            999999988663  234456999999999999988887777664

>KOG1676 consensus K-homology type RNA binding proteins [RNA processing and modification]

Probab=100.00  E-value=1e-41  Score=353.19  Aligned_cols=325  Identities=23%  Similarity=0.375  Sum_probs=257.5

Q ss_pred             CceeEEEEEeccceeEEEeCCchHHHHHHHhcCCeEEEccCCCCCCCCcccccCCceEEEecCHHHHHHHHHHHHHHHhh
Q 006943          138 EKEECQILVPSSQSANIIGKAGATIKRLRSKTRTSIKVTPKDASEPTHSCAMEFDNFVLISGESEAVKKALFAISAIMYK  217 (624)
Q Consensus       138 ~~~~~~llvp~~~~g~iIGk~G~~Ik~I~~~sga~I~i~~~~~~~~~~~~~~~~~r~V~I~G~~~~V~~A~~~I~~~l~~  217 (624)
                      ..++.+.-||...+|+||||+|+.|..|+.+|||+|++......        ...|.+.++|.+++|+.|+.+|.+++..
T Consensus        52 ~~~~~~~~VPd~~VglvIGrgG~qI~~iqq~SgCrvq~~~~~s~--------~~~r~~~~~G~pe~v~~aK~li~evv~r  123 (600)
T KOG1676|consen   52 TVQTERYKVPDEAVGLVIGRGGSQIQAIQQKSGCRVQIAADPSG--------IGYRSVDLTGSPENVEVAKQLIGEVVSR  123 (600)
T ss_pred             cccccccCCCchhceeEeeccHHHhhhhhhhcCCccccCCCCCC--------cccccccccCCcccHHHHHHhhhhhhhc
Confidence            45778899999999999999999999999999999998765432        3689999999999999999999888742


Q ss_pred             cCCCCCCCCCCccCCCCCCccCCCCCCCCCCCCCCCCCCCCCCCCCCCCccCCCCCCCCCCCCCCCCCCCCCCCCCcccc
Q 006943          218 FSPREDIPLETTVREAPPSIIIPSDVPIYPPGGLYPNADPILPSRSVPSILGAARVPDLQGYADTGNTWPVYSTGLSLVS  297 (624)
Q Consensus       218 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~~~~~~~g~~~~p~~~~~~~~~~~~~~~~~~~p~~~  297 (624)
                      ...                           .++                            |.                 
T Consensus       124 ~~~---------------------------~~~----------------------------~~-----------------  131 (600)
T KOG1676|consen  124 GRP---------------------------PGG----------------------------FP-----------------  131 (600)
T ss_pred             cCC---------------------------CCC----------------------------cc-----------------
Confidence            110                           000                            00                 


Q ss_pred             CCCCCCCCccEEEEEEecCCccceeeccCcchHHHHHhHhCCeEEEcCCCC--CCCceEEEEeec-CCchhHHHHHHHHH
Q 006943          298 GLVGASQSEELVIRVLCPFNKIGRVIGKGGGTIKSIRQASGAQIDVDDTKD--NRDECVITVTAI-ESPDDIKSMAVEAV  374 (624)
Q Consensus       298 ~~~~~~~~~~~~~~i~vp~~~vg~IIGk~G~~Ik~I~~~tga~I~v~~~~~--~~~er~i~I~G~-~~~~~a~~~~~~~i  374 (624)
                         .+-.+..++..++||...+|+||||+|++||+|++++||++.+-....  ....+-+.|+|. .+++.|+.++.++|
T Consensus       132 ---~~q~~~~ttqeI~IPa~k~GlIIGKgGETikqlqe~sg~k~i~iqd~~~~~~~~KplritGdp~~ve~a~~lV~dil  208 (600)
T KOG1676|consen  132 ---DNQGSVETTQEILIPANKCGLIIGKGGETIKQLQEQSGVKMILVQDGSIATGADKPLRITGDPDKVEQAKQLVADIL  208 (600)
T ss_pred             ---ccCCccceeeeeccCccceeeEeccCccHHHHHHhhcCCceEEEecCCcCCCCCCceeecCCHHHHHHHHHHHHHHH
Confidence               001135678999999999999999999999999999999988764322  225667888885 67888888888887


Q ss_pred             HHHhhccCCC-------CCCcEEEEEEecCCeeeEEEcCCCchHHHHHHhcCceEEEeCCCCCCCCCCCCcEEEEEeehH
Q 006943          375 LLLQTKINDE-------DDDTVTIRLLVSSKVIGCIIGKSGSIINEIRKRTKADVRISKGDKPKCADANDELVEVVGEVG  447 (624)
Q Consensus       375 ~~~~~~~~~~-------~~~~~~~~l~vp~~~~g~iIGk~G~~Ik~I~~~tga~I~i~~~~~p~~~~~~~~~v~I~G~~~  447 (624)
                      ..-.+.....       .....+.+|.||++.||.||||+|++||+|+.+||++|+|.+++.|   .+.+|.+.|.|+.+
T Consensus       209 ~e~~~~~~g~~~~~g~~~g~~~~~~V~VPr~~VG~IIGkgGE~IKklq~etG~KIQfkpDd~p---~speR~~~IiG~~d  285 (600)
T KOG1676|consen  209 REEDDEVPGSGGHAGVRGGGSATREVKVPRSKVGIIIGKGGEMIKKLQNETGAKIQFKPDDDP---SSPERPAQIIGTVD  285 (600)
T ss_pred             HhcccCCCccccccCcCccccceeEEeccccceeeEEecCchHHHHHhhccCceeEeecCCCC---CCccceeeeecCHH
Confidence            6432222111       1233489999999999999999999999999999999999999988   47799999999999


Q ss_pred             HHHHHHHHHHHHHhhccccCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
Q 006943          448 SVRDALVQIILRLRDDALKDRDGSRNPPVGADHIYSSGTGISMPPLLPSIPPVGPLGYDQRADSGSGIGMLSSSSLYGYG  527 (624)
Q Consensus       448 ~v~~A~~~I~~~l~e~~~~~~~~~~~p~~~~~~~~~~~~~~~~p~~~~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~  527 (624)
                      +|+.|.++|.+.|.+.....                                              +.+           
T Consensus       286 ~ie~Aa~lI~eii~~~~~~~----------------------------------------------~~~-----------  308 (600)
T KOG1676|consen  286 QIEHAAELINEIIAEAEAGA----------------------------------------------GGG-----------  308 (600)
T ss_pred             HHHHHHHHHHHHHHHHhccC----------------------------------------------CCC-----------
Confidence            99999988888776642110                                              000           


Q ss_pred             CCCCCCCCCCCCCCcccccCCCCCCCcEEEEEeccccccceeccCCchHHHHHHHhCCEEEEeCCC--CCCCCeEEEEEc
Q 006943          528 SLSMGDSPYGSMSSYSSKLYGGLPPPLTLEVLVPANAVGKVIGKAGSNLANIRKISGATIEMSDSK--SSRGDRVALISG  605 (624)
Q Consensus       528 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~VP~~~vg~IIGkgG~~I~~I~~~sGa~I~i~~~~--~~~~~r~v~I~G  605 (624)
                            ...|.+.           ....+++.||.++||+||||||+|||.|.++|||++.+.+..  .+.++++|+|+|
T Consensus       309 ------~~~G~P~-----------~~~~fy~~VPa~KcGLvIGrGGEtIK~in~qSGA~~el~r~~p~~~~~ektf~IrG  371 (600)
T KOG1676|consen  309 ------MGGGAPG-----------LVAQFYMKVPADKCGLVIGRGGETIKQINQQSGARCELSRQPPNGNPKEKTFVIRG  371 (600)
T ss_pred             ------cCCCCcc-----------ceeeEEEeccccccccccCCCccchhhhcccCCccccccCCCCCCCccceEEEEec
Confidence                  0000000           011789999999999999999999999999999999999873  345789999999


Q ss_pred             CHHHHHHHHHHHHHHHh
Q 006943          606 TPEQKRAAENLIQAFIM  622 (624)
Q Consensus       606 t~e~v~~A~~lI~~~i~  622 (624)
                      ++.||+.|+.||.+.+.
T Consensus       372 ~~~QIdhAk~LIr~kvg  388 (600)
T KOG1676|consen  372 DKRQIDHAKQLIRDKVG  388 (600)
T ss_pred             CcccchHHHHHHHHHhc
Confidence            99999999999998874

>KOG1676 consensus K-homology type RNA binding proteins [RNA processing and modification]

Probab=100.00  E-value=1.4e-38  Score=330.03  Aligned_cols=333  Identities=21%  Similarity=0.325  Sum_probs=257.1

Q ss_pred             CCceEEEEEEecCcccceeccCCchHHHHHHHhcCCeEEeeCCCCCCCceEEEEEccCCcccccccccccCCCCcccHHH
Q 006943           33 NEESVIYRILCPDGVIGSVIGKSGKVINSIRQETRARVKVVDPFPGAKDRVVTIYSHVKDKEDVEVDDEFNDKEPLCAAQ  112 (624)
Q Consensus        33 ~~~~~~~~ilvp~~~~g~vIGk~G~~I~~i~~etg~~I~v~~~~~~~~er~i~I~G~~~~~~~~~~~~~~~~~~~~~~a~  112 (624)
                      .+..++.+..||.+.+|+||||+|+-|..|..++||+|.+.....+...|.+.++|.++++++               | 
T Consensus        50 s~~~~~~~~~VPd~~VglvIGrgG~qI~~iqq~SgCrvq~~~~~s~~~~r~~~~~G~pe~v~~---------------a-  113 (600)
T KOG1676|consen   50 SDTVQTERYKVPDEAVGLVIGRGGSQIQAIQQKSGCRVQIAADPSGIGYRSVDLTGSPENVEV---------------A-  113 (600)
T ss_pred             cccccccccCCCchhceeEeeccHHHhhhhhhhcCCccccCCCCCCcccccccccCCcccHHH---------------H-
Confidence            446788899999999999999999999999999999999877767889999999999999764               2 


Q ss_pred             HHHHHHHHHHHHhhh-ccCCCcccCCCceeEEEEEeccceeEEEeCCchHHHHHHHhcCCeEEEccCCCCCCCCcccccC
Q 006943          113 DALLKVHAAIANAVA-NATDNDKKRKEKEECQILVPSSQSANIIGKAGATIKRLRSKTRTSIKVTPKDASEPTHSCAMEF  191 (624)
Q Consensus       113 ~ai~~v~~~i~~~~~-~~~~~~~~~~~~~~~~llvp~~~~g~iIGk~G~~Ik~I~~~sga~I~i~~~~~~~~~~~~~~~~  191 (624)
                         .+++..+.+... ..+-........++..|+||.+.+|.||||+|++||.|++.|||++.+..+....      ...
T Consensus       114 ---K~li~evv~r~~~~~~~~~~q~~~~ttqeI~IPa~k~GlIIGKgGETikqlqe~sg~k~i~iqd~~~~------~~~  184 (600)
T KOG1676|consen  114 ---KQLIGEVVSRGRPPGGFPDNQGSVETTQEILIPANKCGLIIGKGGETIKQLQEQSGVKMILVQDGSIA------TGA  184 (600)
T ss_pred             ---HHhhhhhhhccCCCCCccccCCccceeeeeccCccceeeEeccCccHHHHHHhhcCCceEEEecCCcC------CCC
Confidence               233333433221 1111112225568999999999999999999999999999999999998865322      136


Q ss_pred             CceEEEecCHHHHHHHHHHHHHHHhhcCCCCCCCCCCccCCCCCCccCCCCCCCCCCCCCCCCCCCCCCCCCCCCccCCC
Q 006943          192 DNFVLISGESEAVKKALFAISAIMYKFSPREDIPLETTVREAPPSIIIPSDVPIYPPGGLYPNADPILPSRSVPSILGAA  271 (624)
Q Consensus       192 ~r~V~I~G~~~~V~~A~~~I~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~~~~~~~g~~  271 (624)
                      ++.+.|+|.+++|+.|+.+|.++|++....  .+-.                                            
T Consensus       185 ~KplritGdp~~ve~a~~lV~dil~e~~~~--~~g~--------------------------------------------  218 (600)
T KOG1676|consen  185 DKPLRITGDPDKVEQAKQLVADILREEDDE--VPGS--------------------------------------------  218 (600)
T ss_pred             CCceeecCCHHHHHHHHHHHHHHHHhcccC--CCcc--------------------------------------------
Confidence            788999999999999999999999863221  0000                                            


Q ss_pred             CCCCCCCCCCCCCCCCCCCCCCccccCCCCCCCCccEEEEEEecCCccceeeccCcchHHHHHhHhCCeEEEcCCCC-CC
Q 006943          272 RVPDLQGYADTGNTWPVYSTGLSLVSGLVGASQSEELVIRVLCPFNKIGRVIGKGGGTIKSIRQASGAQIDVDDTKD-NR  350 (624)
Q Consensus       272 ~~p~~~~~~~~~~~~~~~~~~~p~~~~~~~~~~~~~~~~~i~vp~~~vg~IIGk~G~~Ik~I~~~tga~I~v~~~~~-~~  350 (624)
                          ...+                     +.......+++|.||...||.||||+|++||+|+.+||++|+|...+. ..
T Consensus       219 ----~~~~---------------------g~~~g~~~~~~V~VPr~~VG~IIGkgGE~IKklq~etG~KIQfkpDd~p~s  273 (600)
T KOG1676|consen  219 ----GGHA---------------------GVRGGGSATREVKVPRSKVGIIIGKGGEMIKKLQNETGAKIQFKPDDDPSS  273 (600)
T ss_pred             ----cccc---------------------CcCccccceeEEeccccceeeEEecCchHHHHHhhccCceeEeecCCCCCC
Confidence                0000                     001112237899999999999999999999999999999999975544 77


Q ss_pred             CceEEEEeec-CCchhHHHHHHHHHHHHhhccCCC---CCCcE--EEEEEecCCeeeEEEcCCCchHHHHHHhcCceEEE
Q 006943          351 DECVITVTAI-ESPDDIKSMAVEAVLLLQTKINDE---DDDTV--TIRLLVSSKVIGCIIGKSGSIINEIRKRTKADVRI  424 (624)
Q Consensus       351 ~er~i~I~G~-~~~~~a~~~~~~~i~~~~~~~~~~---~~~~~--~~~l~vp~~~~g~iIGk~G~~Ik~I~~~tga~I~i  424 (624)
                      .||.+.|.|+ +.++.|.+.+.++|......-...   .....  .+.|.||.+.||.||||+|++||.|..+|||+|.+
T Consensus       274 peR~~~IiG~~d~ie~Aa~lI~eii~~~~~~~~~~~~~G~P~~~~~fy~~VPa~KcGLvIGrGGEtIK~in~qSGA~~el  353 (600)
T KOG1676|consen  274 PERPAQIIGTVDQIEHAAELINEIIAEAEAGAGGGMGGGAPGLVAQFYMKVPADKCGLVIGRGGETIKQINQQSGARCEL  353 (600)
T ss_pred             ccceeeeecCHHHHHHHHHHHHHHHHHHhccCCCCcCCCCccceeeEEEeccccccccccCCCccchhhhcccCCccccc
Confidence            9999999997 445555555555555444321100   11112  67899999999999999999999999999999999


Q ss_pred             eCCCCCCCCCCCCcEEEEEeehHHHHHHHHHHHHHHhhc
Q 006943          425 SKGDKPKCADANDELVEVVGEVGSVRDALVQIILRLRDD  463 (624)
Q Consensus       425 ~~~~~p~~~~~~~~~v~I~G~~~~v~~A~~~I~~~l~e~  463 (624)
                      +++  +...+..+++++|+|+..+|..|..+|-.++-+.
T Consensus       354 ~r~--~p~~~~~ektf~IrG~~~QIdhAk~LIr~kvg~~  390 (600)
T KOG1676|consen  354 SRQ--PPNGNPKEKTFVIRGDKRQIDHAKQLIRDKVGDI  390 (600)
T ss_pred             cCC--CCCCCccceEEEEecCcccchHHHHHHHHHhccc
Confidence            987  3344688999999999999999999998887663

>KOG2193 consensus IGF-II mRNA-binding protein IMP, contains RRM and KH domains [RNA processing and modification; General function prediction only]

Probab=100.00  E-value=5.9e-39  Score=316.30  Aligned_cols=312  Identities=24%  Similarity=0.404  Sum_probs=255.3

Q ss_pred             ceeEEEEEeccceeEEEeCCchHHHHHHHhcCCeEEEccCCCCCCCCcccccCCceEEEecCHHHHHHHHHHHHHHHhhc
Q 006943          139 KEECQILVPSSQSANIIGKAGATIKRLRSKTRTSIKVTPKDASEPTHSCAMEFDNFVLISGESEAVKKALFAISAIMYKF  218 (624)
Q Consensus       139 ~~~~~llvp~~~~g~iIGk~G~~Ik~I~~~sga~I~i~~~~~~~~~~~~~~~~~r~V~I~G~~~~V~~A~~~I~~~l~~~  218 (624)
                      ...+|+|||..++|.||||.|.+||.|...|-|+|.|..+...       ...|+.|+|.|+++...+|+++|+++|.+.
T Consensus       198 D~PlR~lVptqyvgaIIGkeG~TIknItkqTqsriD~hrken~-------Gaaek~itvh~tpEg~s~Ac~~ILeimqkE  270 (584)
T KOG2193|consen  198 DWPLRLLVPTQYVGAIIGKEGATIKNITKQTQSRIDVHRKENA-------GAAEKIITVHSTPEGTSKACKMILEIMQKE  270 (584)
T ss_pred             CcceeeeeccceeEEEecCCCccccCcchhhhheeeeeecccC-------CcccCceEEecCccchHHHHHHHHHHHHHh
Confidence            3578999999999999999999999999999999999876432       357999999999999999999999999764


Q ss_pred             CCCCCCCCCCccCCCCCCccCCCCCCCCCCCCCCCCCCCCCCCCCCCCccCCCCCCCCCCCCCCCCCCCCCCCCCccccC
Q 006943          219 SPREDIPLETTVREAPPSIIIPSDVPIYPPGGLYPNADPILPSRSVPSILGAARVPDLQGYADTGNTWPVYSTGLSLVSG  298 (624)
Q Consensus       219 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~~~~~~~g~~~~p~~~~~~~~~~~~~~~~~~~p~~~~  298 (624)
                      ..+..                                                                           
T Consensus       271 A~~~k---------------------------------------------------------------------------  275 (584)
T KOG2193|consen  271 AVDDK---------------------------------------------------------------------------  275 (584)
T ss_pred             hhccc---------------------------------------------------------------------------
Confidence            43211                                                                           


Q ss_pred             CCCCCCCccEEEEEEecCCccceeeccCcchHHHHHhHhCCeEEEcCCC---CCCCceEEEEeecCCchhHHHHHHHHHH
Q 006943          299 LVGASQSEELVIRVLCPFNKIGRVIGKGGGTIKSIRQASGAQIDVDDTK---DNRDECVITVTAIESPDDIKSMAVEAVL  375 (624)
Q Consensus       299 ~~~~~~~~~~~~~i~vp~~~vg~IIGk~G~~Ik~I~~~tga~I~v~~~~---~~~~er~i~I~G~~~~~~a~~~~~~~i~  375 (624)
                           ...+++++++-.+.++|++|||.|.+||+|+++||++|.|..-.   .-..||.|++.|+  +|.++.+-.+++.
T Consensus       276 -----~~~e~pLk~lAHN~lvGRLIGKeGrnlKkIeq~TgTkITis~lqels~ynpERTItVkGs--iEac~~AE~eImk  348 (584)
T KOG2193|consen  276 -----VAEEIPLKILAHNNLVGRLIGKEGRNLKKIEQDTGTKITISKLQELSLYNPERTITVKGS--IEACVQAEAEIMK  348 (584)
T ss_pred             -----hhhhcchhhhhhcchhhhhhhhccccHHHHHhhcCCceeeeehhhhcccCccceEEeccc--HHHHHHHHHHHHH
Confidence                 12467889999999999999999999999999999999998532   2347999999995  5555444344444


Q ss_pred             HHhhccCCC-------------------------------------------------CCCcEEEEEEecCCeeeEEEcC
Q 006943          376 LLQTKINDE-------------------------------------------------DDDTVTIRLLVSSKVIGCIIGK  406 (624)
Q Consensus       376 ~~~~~~~~~-------------------------------------------------~~~~~~~~l~vp~~~~g~iIGk  406 (624)
                      .+.+.+..+                                                 ....-.++|.||...+|.|||+
T Consensus       349 Klre~yEnDl~a~s~q~~l~P~l~~~~l~~f~ssS~~~~Ph~~Ps~v~~a~p~~~~hq~pe~e~V~~fiP~~~vGAiIGk  428 (584)
T KOG2193|consen  349 KLRECYENDLAAMSLQCHLPPGLNLPALGLFPSSSAVSPPHFPPSPVTFASPYPLFHQNPEQEQVRMFIPAQAVGAIIGK  428 (584)
T ss_pred             HHHHHHhhhHHHhhccCCCCcccCccccCCCCcccccCCCCCCCCccccCCCchhhhcCcchhheeeeccHHHHHHHHhh
Confidence            333221110                                                 0122357899999999999999


Q ss_pred             CCchHHHHHHhcCceEEEeCCCCCCCCCCCCcEEEEEeehHHHHHHHHHHHHHHhhccccCCCCCCCCCCCCCCCCCCCC
Q 006943          407 SGSIINEIRKRTKADVRISKGDKPKCADANDELVEVVGEVGSVRDALVQIILRLRDDALKDRDGSRNPPVGADHIYSSGT  486 (624)
Q Consensus       407 ~G~~Ik~I~~~tga~I~i~~~~~p~~~~~~~~~v~I~G~~~~v~~A~~~I~~~l~e~~~~~~~~~~~p~~~~~~~~~~~~  486 (624)
                      +|..||.|.+.+||.|+|.+...|   +..+|+|+|+|++++..+|...|..+|.|.-+..                   
T Consensus       429 kG~hIKql~RfagASiKIappE~p---dvseRMViItGppeaqfKAQgrifgKikEenf~~-------------------  486 (584)
T KOG2193|consen  429 KGQHIKQLSRFAGASIKIAPPEIP---DVSERMVIITGPPEAQFKAQGRIFGKIKEENFFL-------------------  486 (584)
T ss_pred             cchhHHHHHHhccceeeecCCCCC---CcceeEEEecCChHHHHhhhhhhhhhhhhhccCC-------------------
Confidence            999999999999999999986666   5789999999999999999999999998853211                   


Q ss_pred             CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCcccccCCCCCCCcEEEEEecccccc
Q 006943          487 GISMPPLLPSIPPVGPLGYDQRADSGSGIGMLSSSSLYGYGSLSMGDSPYGSMSSYSSKLYGGLPPPLTLEVLVPANAVG  566 (624)
Q Consensus       487 ~~~~p~~~~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~VP~~~vg  566 (624)
                          |.-                                                         ......+|.||...+|
T Consensus       487 ----Pke---------------------------------------------------------evklethirVPs~~aG  505 (584)
T KOG2193|consen  487 ----PKE---------------------------------------------------------EVKLETHIRVPSSAAG  505 (584)
T ss_pred             ----chh---------------------------------------------------------hheeeeeeeccchhhh
Confidence                000                                                         1134788999999999


Q ss_pred             ceeccCCchHHHHHHHhCCEEEEeCCCCC--CCCeEEEEEcCHHHHHHHHHHHHHHHh
Q 006943          567 KVIGKAGSNLANIRKISGATIEMSDSKSS--RGDRVALISGTPEQKRAAENLIQAFIM  622 (624)
Q Consensus       567 ~IIGkgG~~I~~I~~~sGa~I~i~~~~~~--~~~r~v~I~Gt~e~v~~A~~lI~~~i~  622 (624)
                      +||||||.++++|++.|+|.|.|+++..+  .+.-+|.|.|...+++.|+..|.++++
T Consensus       506 RvIGKGGktVnELQnlt~AeV~vPrdqtpdEnd~vivriiGhfyatq~aQrki~~iv~  563 (584)
T KOG2193|consen  506 RVIGKGGKTVNELQNLTSAEVVVPRDQTPDENDQVIVRIIGHFYATQNAQRKIAHIVN  563 (584)
T ss_pred             hhhccccccHHHHhccccceEEccccCCCCccceeeeeeechhhcchHHHHHHHHHHH
Confidence            99999999999999999999999988633  344678899999999999999998875

>KOG2192 consensus PolyC-binding hnRNP-K protein HRB57A/hnRNP, contains KH domain [RNA processing and modification; General function prediction only]

Probab=100.00  E-value=5e-37  Score=286.03  Aligned_cols=317  Identities=28%  Similarity=0.433  Sum_probs=228.0

Q ss_pred             cCCCCCCCCccEEEEEEecCCccceeeccCcchHHHHHhHhCCeEEEcCCCCCCCceEEEEeecCCchhHHHHHHHHHHH
Q 006943          297 SGLVGASQSEELVIRVLCPFNKIGRVIGKGGGTIKSIRQASGAQIDVDDTKDNRDECVITVTAIESPDDIKSMAVEAVLL  376 (624)
Q Consensus       297 ~~~~~~~~~~~~~~~i~vp~~~vg~IIGk~G~~Ik~I~~~tga~I~v~~~~~~~~er~i~I~G~~~~~~a~~~~~~~i~~  376 (624)
                      .++..+.....+.+++++.++.+|+||||+|++||.|+.++++.|+|+++..  ++|+++|+..  .+.....+++++-.
T Consensus        37 d~~~qa~k~~r~e~ril~~sk~agavigkgg~nik~lr~d~na~v~vpds~~--peri~tisad--~~ti~~ilk~iip~  112 (390)
T KOG2192|consen   37 DMEEQAFKRSRVELRILLQSKNAGAVIGKGGKNIKALRTDYNASVSVPDSSG--PERILTISAD--IETIGEILKKIIPT  112 (390)
T ss_pred             hhHHHHhhhcceeEEEEEecccccceeccccccHHHHhhhccceeeccCCCC--CceeEEEecc--HHHHHHHHHHHhhh
Confidence            3344455667799999999999999999999999999999999999987654  7999999986  23333334444444


Q ss_pred             HhhccCCCCCCcEEEEEEecCCeeeEEEcCCCchHHHHHHhcCceEEEeCCCCCCCCCCCCcEEEEEeehHHHHHHHHHH
Q 006943          377 LQTKINDEDDDTVTIRLLVSSKVIGCIIGKSGSIINEIRKRTKADVRISKGDKPKCADANDELVEVVGEVGSVRDALVQI  456 (624)
Q Consensus       377 ~~~~~~~~~~~~~~~~l~vp~~~~g~iIGk~G~~Ik~I~~~tga~I~i~~~~~p~~~~~~~~~v~I~G~~~~v~~A~~~I  456 (624)
                      +.+...  ..+++.++|+|..++.|.|||++|+.||+|++++.|+++|..   .+|..++||+|.|.|.+..|..+++.|
T Consensus       113 lee~f~--~~~pce~rllihqs~ag~iigrngskikelrekcsarlkift---~c~p~stdrv~l~~g~~k~v~~~i~~i  187 (390)
T KOG2192|consen  113 LEEGFQ--LPSPCELRLLIHQSLAGGIIGRNGSKIKELREKCSARLKIFT---ECCPHSTDRVVLIGGKPKRVVECIKII  187 (390)
T ss_pred             hhhCCC--CCCchhhhhhhhhhhccceecccchhHHHHHHhhhhhhhhhh---ccCCCCcceEEEecCCcchHHHHHHHH
Confidence            444332  457899999999999999999999999999999999999876   455679999999999999999999999


Q ss_pred             HHHHhhccccCCCCCCCCCCCCCCC-CCCCC-------CCCCCCCCCCC--CCCC----CCCCCCCCCCC-CCCCC--CC
Q 006943          457 ILRLRDDALKDRDGSRNPPVGADHI-YSSGT-------GISMPPLLPSI--PPVG----PLGYDQRADSG-SGIGM--LS  519 (624)
Q Consensus       457 ~~~l~e~~~~~~~~~~~p~~~~~~~-~~~~~-------~~~~p~~~~~~--~~~~----~~~~~~~~~~~-~~~g~--~~  519 (624)
                      ++.|.|...+....+|.|.++.+.+ |+|+.       +...|......  |+.+    -+.|++.+..+ ...+|  .+
T Consensus       188 l~~i~e~pikgsa~py~p~fyd~t~dyggf~M~f~d~pg~pgpapqrggqgpp~~~~sdlmay~r~GrpG~rydg~vdFs  267 (390)
T KOG2192|consen  188 LDLISESPIKGSAQPYDPNFYDETYDYGGFTMMFDDRPGRPGPAPQRGGQGPPPPRGSDLMAYDRRGRPGDRYDGMVDFS  267 (390)
T ss_pred             HHHhhcCCcCCcCCcCCccccCcccccCCceeecCCCCCCCCCCCCCCCCCCCCCCccccceeccCCCCCcccccccccc
Confidence            9999999999999999988755433 33321       11111100000  1111    12344433221 11111  11


Q ss_pred             C-------CCCCCCCCCCCCCCCC-CCCCCcccc----cCCCC-CCCcEEEEEeccccccceeccCCchHHHHHHHhCCE
Q 006943          520 S-------SSLYGYGSLSMGDSPY-GSMSSYSSK----LYGGL-PPPLTLEVLVPANAVGKVIGKAGSNLANIRKISGAT  586 (624)
Q Consensus       520 ~-------~~~~~~~~~~~~~~~~-~~~~~~~~~----~~~~~-~~~~~~~i~VP~~~vg~IIGkgG~~I~~I~~~sGa~  586 (624)
                      .       -..|.++.|.++-.+- |.-..+...    .+|.+ .+.+|..|+||.+.-|.||||||+.|++|++++||.
T Consensus       268 ~detw~saidtw~~SewqmaYePQgGs~ydysyAG~~GsYGdlGGPitTaQvtip~dlggsiigkggqri~~ir~esGA~  347 (390)
T KOG2192|consen  268 ADETWPSAIDTWSPSEWQMAYEPQGGSGYDYSYAGGYGSYGDLGGPITTAQVTIPKDLGGSIIGKGGQRIKQIRHESGAS  347 (390)
T ss_pred             ccccCCCcCCCcCccccccccCCCCCCCCCccccccccccCCCCCceeeeeEecccccCcceecccchhhhhhhhccCce
Confidence            1       1112222232221110 100011100    12221 345789999999999999999999999999999999


Q ss_pred             EEEeCCCCCCCCeEEEEEcCHHHHHHHHHHHHHHHh
Q 006943          587 IEMSDSKSSRGDRVALISGTPEQKRAAENLIQAFIM  622 (624)
Q Consensus       587 I~i~~~~~~~~~r~v~I~Gt~e~v~~A~~lI~~~i~  622 (624)
                      |+|..+..++.+|+++|+||.+|++.|++|+++++.
T Consensus       348 IkidepleGsedrIitItGTqdQIqnAQYLlQn~Vk  383 (390)
T KOG2192|consen  348 IKIDEPLEGSEDRIITITGTQDQIQNAQYLLQNSVK  383 (390)
T ss_pred             EEecCcCCCCCceEEEEeccHHHHhhHHHHHHHHHH
Confidence            999999989999999999999999999999999874

>KOG2192 consensus PolyC-binding hnRNP-K protein HRB57A/hnRNP, contains KH domain [RNA processing and modification; General function prediction only]

Probab=100.00  E-value=1.3e-35  Score=276.55  Aligned_cols=307  Identities=25%  Similarity=0.383  Sum_probs=216.5

Q ss_pred             CCCCCCcCCCCCCccccccCCC-CCCCCCceEEEEEEecCcccceeccCCchHHHHHHHhcCCeEEeeCCCCCCCceEEE
Q 006943            7 RYRSQRDNDRDGKNQKRRINEK-DEKGNEESVIYRILCPDGVIGSVIGKSGKVINSIRQETRARVKVVDPFPGAKDRVVT   85 (624)
Q Consensus         7 r~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~~ilvp~~~~g~vIGk~G~~I~~i~~etg~~I~v~~~~~~~~er~i~   85 (624)
                      |.++.++.++-+   +|+..+. .+......+.+|||+.++.+|+||||+|+|||.|+.++++.|.|++.  ..++|+++
T Consensus        20 ~~~~~e~g~~~g---krp~~d~~~qa~k~~r~e~ril~~sk~agavigkgg~nik~lr~d~na~v~vpds--~~peri~t   94 (390)
T KOG2192|consen   20 TFPNTETGGEFG---KRPAEDMEEQAFKRSRVELRILLQSKNAGAVIGKGGKNIKALRTDYNASVSVPDS--SGPERILT   94 (390)
T ss_pred             cCCCCccccccc---CCcchhhHHHHhhhcceeEEEEEecccccceeccccccHHHHhhhccceeeccCC--CCCceeEE
Confidence            444455555444   3443332 22234567999999999999999999999999999999999999986  67999999


Q ss_pred             EEccCCcccccccccccCCCCcccHHHHHHHHHHHHHHHhhhccCCCcccCCCceeEEEEEeccceeEEEeCCchHHHHH
Q 006943           86 IYSHVKDKEDVEVDDEFNDKEPLCAAQDALLKVHAAIANAVANATDNDKKRKEKEECQILVPSSQSANIIGKAGATIKRL  165 (624)
Q Consensus        86 I~G~~~~~~~~~~~~~~~~~~~~~~a~~ai~~v~~~i~~~~~~~~~~~~~~~~~~~~~llvp~~~~g~iIGk~G~~Ik~I  165 (624)
                      |+...+                      .+..+++.+.-.+++.    ....+.+++||||+.+++|.|||++|++||+|
T Consensus        95 isad~~----------------------ti~~ilk~iip~lee~----f~~~~pce~rllihqs~ag~iigrngskikel  148 (390)
T KOG2192|consen   95 ISADIE----------------------TIGEILKKIIPTLEEG----FQLPSPCELRLLIHQSLAGGIIGRNGSKIKEL  148 (390)
T ss_pred             EeccHH----------------------HHHHHHHHHhhhhhhC----CCCCCchhhhhhhhhhhccceecccchhHHHH
Confidence            987754                      4555666665555542    22345699999999999999999999999999


Q ss_pred             HHhcCCeEEEccCCCCCCCCcccccCCceEEEecCHHHHHHHHHHHHHHHhhcCCCCCCCCCCccCCCCCCccCCCCCCC
Q 006943          166 RSKTRTSIKVTPKDASEPTHSCAMEFDNFVLISGESEAVKKALFAISAIMYKFSPREDIPLETTVREAPPSIIIPSDVPI  245 (624)
Q Consensus       166 ~~~sga~I~i~~~~~~~~~~~~~~~~~r~V~I~G~~~~V~~A~~~I~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  245 (624)
                      ++++.|+++|+.       .+||+++||+|.|.|.+.+|..+++.|.++|.+.      |+....+++.|+|++++    
T Consensus       149 rekcsarlkift-------~c~p~stdrv~l~~g~~k~v~~~i~~il~~i~e~------pikgsa~py~p~fyd~t----  211 (390)
T KOG2192|consen  149 REKCSARLKIFT-------ECCPHSTDRVVLIGGKPKRVVECIKIILDLISES------PIKGSAQPYDPNFYDET----  211 (390)
T ss_pred             HHhhhhhhhhhh-------ccCCCCcceEEEecCCcchHHHHHHHHHHHhhcC------CcCCcCCcCCccccCcc----
Confidence            999999999985       6899999999999999999999999999999654      56666677777887765    


Q ss_pred             CCCCCCCCCCCC--CCCCCC-CCCccCCC-------------CCCCCC-----CCCC---CCCCCCCCC-----CCCcc-
Q 006943          246 YPPGGLYPNADP--ILPSRS-VPSILGAA-------------RVPDLQ-----GYAD---TGNTWPVYS-----TGLSL-  295 (624)
Q Consensus       246 ~~~~g~~~~~~~--~~~~~~-~~~~~g~~-------------~~p~~~-----~~~~---~~~~~~~~~-----~~~p~-  295 (624)
                      |..|||.+.++.  ..|-++ .+...|..             .-|+..     .+..   -.+..+.|+     ...+. 
T Consensus       212 ~dyggf~M~f~d~pg~pgpapqrggqgpp~~~~sdlmay~r~GrpG~rydg~vdFs~detw~saidtw~~SewqmaYePQ  291 (390)
T KOG2192|consen  212 YDYGGFTMMFDDRPGRPGPAPQRGGQGPPPPRGSDLMAYDRRGRPGDRYDGMVDFSADETWPSAIDTWSPSEWQMAYEPQ  291 (390)
T ss_pred             cccCCceeecCCCCCCCCCCCCCCCCCCCCCCccccceeccCCCCCccccccccccccccCCCcCCCcCccccccccCCC
Confidence            566666433221  111111 01111110             001100     0000   000011111     11111 


Q ss_pred             --------ccCC---CCCCCCccEEEEEEecCCccceeeccCcchHHHHHhHhCCeEEEcCCCCCCCceEEEEeecC
Q 006943          296 --------VSGL---VGASQSEELVIRVLCPFNKIGRVIGKGGGTIKSIRQASGAQIDVDDTKDNRDECVITVTAIE  361 (624)
Q Consensus       296 --------~~~~---~~~~~~~~~~~~i~vp~~~vg~IIGk~G~~Ik~I~~~tga~I~v~~~~~~~~er~i~I~G~~  361 (624)
                              .++.   .+....--.+..+.||.+.-|.||||+|+.|++|+.++||.|++.++..+.++|+++|+|++
T Consensus       292 gGs~ydysyAG~~GsYGdlGGPitTaQvtip~dlggsiigkggqri~~ir~esGA~IkidepleGsedrIitItGTq  368 (390)
T KOG2192|consen  292 GGSGYDYSYAGGYGSYGDLGGPITTAQVTIPKDLGGSIIGKGGQRIKQIRHESGASIKIDEPLEGSEDRIITITGTQ  368 (390)
T ss_pred             CCCCCCccccccccccCCCCCceeeeeEecccccCcceecccchhhhhhhhccCceEEecCcCCCCCceEEEEeccH
Confidence                    1110   01122223577889999999999999999999999999999999999999999999999984

>KOG2190 consensus PolyC-binding proteins alphaCP-1 and related KH domain proteins [RNA processing and modification; General function prediction only]

Probab=99.97  E-value=1.9e-29  Score=267.78  Aligned_cols=313  Identities=28%  Similarity=0.356  Sum_probs=203.9

Q ss_pred             ccEEEEEEecCCccceeeccCcchHHHHHhHhCCeEEEcCCCCCCCceEEEEeec------CCchhHHHHHHHHHHHHhh
Q 006943          306 EELVIRVLCPFNKIGRVIGKGGGTIKSIRQASGAQIDVDDTKDNRDECVITVTAI------ESPDDIKSMAVEAVLLLQT  379 (624)
Q Consensus       306 ~~~~~~i~vp~~~vg~IIGk~G~~Ik~I~~~tga~I~v~~~~~~~~er~i~I~G~------~~~~~a~~~~~~~i~~~~~  379 (624)
                      ...++|++|+.+.+|.||||+|.+|++|+.++.++|+|.+...+|.+|+++|+|+      ....+|+..+.+++....+
T Consensus        41 ~t~~~RlL~~~kevG~IIGk~G~~vkkir~~t~s~i~i~~~~~~c~eRIiti~g~~~~~~~~~~~~al~ka~~~iv~~~~  120 (485)
T KOG2190|consen   41 ETLTYRLLCHVKEVGSIIGKKGDIVKKIRKETESKIRVNESLPGCPERIITITGNRVELNLSPATDALFKAFDMIVFKLE  120 (485)
T ss_pred             CcceEEEEeccccceeEEccCcHHHHHHhhcccccceeecCCCCCCcceEEEecccccccCCchHHHHHHHHHHHhhccc
Confidence            3445999999999999999999999999999999999999999999999999992      0113344444444433211


Q ss_pred             -ccC---C----CCCCcEEEEEEecCCeeeEEEcCCCchHHHHHHhcCceEEEeCCCCCCCCCCCCcEEEEEeehHHHHH
Q 006943          380 -KIN---D----EDDDTVTIRLLVSSKVIGCIIGKSGSIINEIRKRTKADVRISKGDKPKCADANDELVEVVGEVGSVRD  451 (624)
Q Consensus       380 -~~~---~----~~~~~~~~~l~vp~~~~g~iIGk~G~~Ik~I~~~tga~I~i~~~~~p~~~~~~~~~v~I~G~~~~v~~  451 (624)
                       ...   +    ....+++++|+||.+++|+||||+|+.||+|+++|||+|++.++.+|.   .++|.|+|.|.+++|.+
T Consensus       121 ~d~~~~~d~~~~~~~~~v~~RLlVp~sq~GslIGK~G~~Ik~Ire~TgA~I~v~~~~lP~---ster~V~IsG~~~av~~  197 (485)
T KOG2190|consen  121 EDDEAAEDNGEDASGPEVTCRLLVPSSQVGSLIGKGGSLIKEIREETGAKIRVSSDMLPN---STERAVTISGEPDAVKK  197 (485)
T ss_pred             ccccccccCCccccCCceEEEEEechhheeeeeccCcHHHHHHHHhcCceEEecCCCCCc---ccceeEEEcCchHHHHH
Confidence             110   0    122358999999999999999999999999999999999999998886   56888999999999999


Q ss_pred             HHHHHHHHHhhccc-----cCCCCCCCCCCCCCCCCCCCCCCCCC----CCCCC--CCCC-CCCCCCCCCCCCCCCCCCC
Q 006943          452 ALVQIILRLRDDAL-----KDRDGSRNPPVGADHIYSSGTGISMP----PLLPS--IPPV-GPLGYDQRADSGSGIGMLS  519 (624)
Q Consensus       452 A~~~I~~~l~e~~~-----~~~~~~~~p~~~~~~~~~~~~~~~~p----~~~~~--~~~~-~~~~~~~~~~~~~~~g~~~  519 (624)
                      |+..|+..|.++..     ......|.|.......+....+...+    .....  .+.. .............+.++..
T Consensus       198 al~~Is~~L~~~~~~~~~~~~st~~y~P~~~~~~~~~~s~~~~~~~~~~~~~~~~~~e~~~~~~~p~~~~~~v~g~~~~~  277 (485)
T KOG2190|consen  198 ALVQISSRLLENPPRSPPPLVSTIPYRPSASQGGPVLPSTAQTSPDAHPFGGIVPEEELVFKLICPSDKVGSVIGKGGLV  277 (485)
T ss_pred             HHHHHHHHHHhcCCcCCCCCCCcccCCCcccccCccccccccCCcccccccccccchhhhhhhcCchhhceeeecCCCcc
Confidence            99999999998542     22233455511111111000000000    00000  0000 0000000000000000000


Q ss_pred             CC--------CCCCCCCCCC---CCCCCCCCC---Cc-------------ccccCCCCCCCcEEEEEeccccccceeccC
Q 006943          520 SS--------SLYGYGSLSM---GDSPYGSMS---SY-------------SSKLYGGLPPPLTLEVLVPANAVGKVIGKA  572 (624)
Q Consensus       520 ~~--------~~~~~~~~~~---~~~~~~~~~---~~-------------~~~~~~~~~~~~~~~i~VP~~~vg~IIGkg  572 (624)
                      ..        ...-..++..   .........   +.             ......+ ...++.++.||++++|+||||+
T Consensus       278 i~~l~~~~~~~i~v~~~~~~~~i~~s~~e~~~~~~s~a~~a~~~~~~~~~~~~~~~~-~~~v~~~l~vps~~igciiGk~  356 (485)
T KOG2190|consen  278 IRALRNETGASISVGDSRTDRIVTISARENPEDRYSMAQEALLLVQPRISENAGDDL-TQTVTQRLLVPSDLIGCIIGKG  356 (485)
T ss_pred             chhhhhhcCCceEeccccCcceeeeccccCcccccccchhhhhhccccccccccccc-cceeeeeeccCccccceeeccc
Confidence            00        0000000000   000000000   00             0000111 3457899999999999999999


Q ss_pred             CchHHHHHHHhCCEEEEeCCCC--CCCCeEEEEEcCHHHHHHHHHHHHHHHh
Q 006943          573 GSNLANIRKISGATIEMSDSKS--SRGDRVALISGTPEQKRAAENLIQAFIM  622 (624)
Q Consensus       573 G~~I~~I~~~sGa~I~i~~~~~--~~~~r~v~I~Gt~e~v~~A~~lI~~~i~  622 (624)
                      |.+|.+||+.|||.|+|.+...  ...+++++|+|+..+...|+++|...+.
T Consensus       357 G~~iseir~~tgA~I~I~~~~~~~~~~e~~~~I~~~~~~~~~~~~~~~~~~~  408 (485)
T KOG2190|consen  357 GAKISEIRQRTGASISILNKEEVSGVREALVQITGMLREDLLAQYLIRARLS  408 (485)
T ss_pred             ccchHHHHHhcCCceEEccccccCCcceeEEEecchhHHHHhhhhhcccccc
Confidence            9999999999999999999876  6789999999999999999999977654

>KOG2191 consensus RNA-binding protein NOVA1/PASILLA and related KH domain proteins [RNA processing and modification; General function prediction only]

Probab=99.94  E-value=9.8e-26  Score=217.13  Aligned_cols=233  Identities=27%  Similarity=0.370  Sum_probs=169.6

Q ss_pred             eEEEEEEecCcccceeccCCchHHHHHHHhcCCeEEeeC---CCCCCCceEEEEEccCCcccccccccccCCCCcccHHH
Q 006943           36 SVIYRILCPDGVIGSVIGKSGKVINSIRQETRARVKVVD---PFPGAKDRVVTIYSHVKDKEDVEVDDEFNDKEPLCAAQ  112 (624)
Q Consensus        36 ~~~~~ilvp~~~~g~vIGk~G~~I~~i~~etg~~I~v~~---~~~~~~er~i~I~G~~~~~~~~~~~~~~~~~~~~~~a~  112 (624)
                      .+.++||||+..+|.||||+|++|.+|+++|||+|++++   .+||+.||+|.|.|..+                     
T Consensus        38 ~y~ikvLips~AaGsIIGKGG~ti~~lqk~tgariklSks~dfyPGTTeRvcli~Gt~e---------------------   96 (402)
T KOG2191|consen   38 QYFLKVLIPSYAAGSIIGKGGQTIVQLQKETGARIKLSKSKDFYPGTTERVCLIQGTVE---------------------   96 (402)
T ss_pred             ceEEEEEeecccccceeccchHHHHHHHhccCcEEEeccccccCCCccceEEEEeccHH---------------------
Confidence            499999999999999999999999999999999999964   68999999999999954                     


Q ss_pred             HHHHHHHHHHHHhhhccCCCc---------ccCCCceeEEEEEeccceeEEEeCCchHHHHHHHhcCCeEEEccCCCCCC
Q 006943          113 DALLKVHAAIANAVANATDND---------KKRKEKEECQILVPSSQSANIIGKAGATIKRLRSKTRTSIKVTPKDASEP  183 (624)
Q Consensus       113 ~ai~~v~~~i~~~~~~~~~~~---------~~~~~~~~~~llvp~~~~g~iIGk~G~~Ik~I~~~sga~I~i~~~~~~~~  183 (624)
                       +|+.+++.|.+.+.+..+..         ...+..-.++|+||++.+|.||||+|.+||.|+|++||.|+|.+....  
T Consensus        97 -ai~av~efI~dKire~p~~~~k~v~~~~pqt~~r~kqikivvPNstag~iigkggAtiK~~~Eqsga~iqisPqkpt--  173 (402)
T KOG2191|consen   97 -ALNAVHEFIADKIREKPQAVAKPVDILQPQTPDRIKQIKIVVPNSTAGMIIGKGGATIKAIQEQSGAWIQISPQKPT--  173 (402)
T ss_pred             -HHHHHHHHHHHHHHHhHHhhcCCccccCCCCccccceeEEeccCCcccceecCCcchHHHHHHhhCcceEecccCCC--
Confidence             67888888888776643211         112333568999999999999999999999999999999999963211  


Q ss_pred             CCcccccCCceEEEecCHHHHHHHHHHHHHHHhhcCCCCCCCCCCccCCCCCCccCCCCCCCCCCCCCCCCCCCCCCCCC
Q 006943          184 THSCAMEFDNFVLISGESEAVKKALFAISAIMYKFSPREDIPLETTVREAPPSIIIPSDVPIYPPGGLYPNADPILPSRS  263 (624)
Q Consensus       184 ~~~~~~~~~r~V~I~G~~~~V~~A~~~I~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~~  263 (624)
                         .-.-.||+|++.|++++..+|+.+|++.|.+.+....+-....           ..... +...+            
T Consensus       174 ---~~sLqervvt~sge~e~~~~A~~~IL~Ki~eDpqs~scln~sy-----------a~vsG-pvaNs------------  226 (402)
T KOG2191|consen  174 ---GISLQERVVTVSGEPEQNMKAVSLILQKIQEDPQSGSCLNISY-----------ANVSG-PVANS------------  226 (402)
T ss_pred             ---CccceeEEEEecCCHHHHHHHHHHHHHHhhcCCcccceeccch-----------hcccC-ccccc------------
Confidence               1124689999999999999999999999977654432210000           00000 00000            


Q ss_pred             CCCccCCCCCCCCCCCCCCCCCCCCCCCCCccccCCCCCCCCccEEEEEEecCCccceeeccCcchHHHHHhHhCCeEEE
Q 006943          264 VPSILGAARVPDLQGYADTGNTWPVYSTGLSLVSGLVGASQSEELVIRVLCPFNKIGRVIGKGGGTIKSIRQASGAQIDV  343 (624)
Q Consensus       264 ~~~~~g~~~~p~~~~~~~~~~~~~~~~~~~p~~~~~~~~~~~~~~~~~i~vp~~~vg~IIGk~G~~Ik~I~~~tga~I~v  343 (624)
                               -|...+|...+..                  .+.......-++....|..-|.+|.+.-.|-.-+|..+.+
T Consensus       227 ---------nPtGspya~~~~~------------------~~astas~~sva~~~iG~a~gaG~~~~a~l~~~~G~l~~i  279 (402)
T KOG2191|consen  227 ---------NPTGSPYAYQAHV------------------LPASTASTISVAAGLIGGANGAGGAFGAALSGFTGALIAI  279 (402)
T ss_pred             ---------CCCCCCCCCCCcc------------------ccccchhhccccccccccccccccccceeeecccccceee
Confidence                     0111111111111                  1112233456788899999999999999999999998888


Q ss_pred             cCC
Q 006943          344 DDT  346 (624)
Q Consensus       344 ~~~  346 (624)
                      .+.
T Consensus       280 tq~  282 (402)
T KOG2191|consen  280 TQA  282 (402)
T ss_pred             ccc
Confidence            753

>KOG2191 consensus RNA-binding protein NOVA1/PASILLA and related KH domain proteins [RNA processing and modification; General function prediction only]

Probab=99.93  E-value=3.9e-24  Score=206.17  Aligned_cols=262  Identities=26%  Similarity=0.368  Sum_probs=187.9

Q ss_pred             cEEEEEEecCCccceeeccCcchHHHHHhHhCCeEEEcCCC---CCCCceEEEEeec-CCchhHHHHHHHHHHHHhh---
Q 006943          307 ELVIRVLCPFNKIGRVIGKGGGTIKSIRQASGAQIDVDDTK---DNRDECVITVTAI-ESPDDIKSMAVEAVLLLQT---  379 (624)
Q Consensus       307 ~~~~~i~vp~~~vg~IIGk~G~~Ik~I~~~tga~I~v~~~~---~~~~er~i~I~G~-~~~~~a~~~~~~~i~~~~~---  379 (624)
                      .+.++|+||+..+|.||||+|++|.+|+++|||+|++++..   +++.||++.|.|+ +++......+.+-|...-.   
T Consensus        38 ~y~ikvLips~AaGsIIGKGG~ti~~lqk~tgariklSks~dfyPGTTeRvcli~Gt~eai~av~efI~dKire~p~~~~  117 (402)
T KOG2191|consen   38 QYFLKVLIPSYAAGSIIGKGGQTIVQLQKETGARIKLSKSKDFYPGTTERVCLIQGTVEALNAVHEFIADKIREKPQAVA  117 (402)
T ss_pred             ceEEEEEeecccccceeccchHHHHHHHhccCcEEEeccccccCCCccceEEEEeccHHHHHHHHHHHHHHHHHhHHhhc
Confidence            38999999999999999999999999999999999998654   4679999999997 2222222223332221111   


Q ss_pred             ccCCC-----CCCcEEEEEEecCCeeeEEEcCCCchHHHHHHhcCceEEEeCCCCCCCCCCCCcEEEEEeehHHHHHHHH
Q 006943          380 KINDE-----DDDTVTIRLLVSSKVIGCIIGKSGSIINEIRKRTKADVRISKGDKPKCADANDELVEVVGEVGSVRDALV  454 (624)
Q Consensus       380 ~~~~~-----~~~~~~~~l~vp~~~~g~iIGk~G~~Ik~I~~~tga~I~i~~~~~p~~~~~~~~~v~I~G~~~~v~~A~~  454 (624)
                      +..+-     .+....+++.||++.+|.||||+|.+||.|++++||.|+|++. .|....-.+|+|++.|++++..+|+.
T Consensus       118 k~v~~~~pqt~~r~kqikivvPNstag~iigkggAtiK~~~Eqsga~iqisPq-kpt~~sLqervvt~sge~e~~~~A~~  196 (402)
T KOG2191|consen  118 KPVDILQPQTPDRIKQIKIVVPNSTAGMIIGKGGATIKAIQEQSGAWIQISPQ-KPTGISLQERVVTVSGEPEQNMKAVS  196 (402)
T ss_pred             CCccccCCCCccccceeEEeccCCcccceecCCcchHHHHHHhhCcceEeccc-CCCCccceeEEEEecCCHHHHHHHHH
Confidence            11110     1112348899999999999999999999999999999999963 35555678999999999999999999


Q ss_pred             HHHHHHhhccccCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
Q 006943          455 QIILRLRDDALKDRDGSRNPPVGADHIYSSGTGISMPPLLPSIPPVGPLGYDQRADSGSGIGMLSSSSLYGYGSLSMGDS  534 (624)
Q Consensus       455 ~I~~~l~e~~~~~~~~~~~p~~~~~~~~~~~~~~~~p~~~~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~~~~~~~  534 (624)
                      +|+++|.|+.....+...        .|+...+   |-                                  .++.....
T Consensus       197 ~IL~Ki~eDpqs~scln~--------sya~vsG---pv----------------------------------aNsnPtGs  231 (402)
T KOG2191|consen  197 LILQKIQEDPQSGSCLNI--------SYANVSG---PV----------------------------------ANSNPTGS  231 (402)
T ss_pred             HHHHHhhcCCcccceecc--------chhcccC---cc----------------------------------cccCCCCC
Confidence            999999998654433210        0100000   00                                  00000000


Q ss_pred             CCCCCCCcccccCCCCCCCcEEEEEeccccccceeccCCchHHHHHHHhCCEEEEeCCCC---CCCCeEEEEEcCHHHHH
Q 006943          535 PYGSMSSYSSKLYGGLPPPLTLEVLVPANAVGKVIGKAGSNLANIRKISGATIEMSDSKS---SRGDRVALISGTPEQKR  611 (624)
Q Consensus       535 ~~~~~~~~~~~~~~~~~~~~~~~i~VP~~~vg~IIGkgG~~I~~I~~~sGa~I~i~~~~~---~~~~r~v~I~Gt~e~v~  611 (624)
                      +|+..       .+.++...+..+.++...+|..-|.+|.++..|...+|+.|.+++.-+   +...+ .-+.|.+-+++
T Consensus       232 pya~~-------~~~~~astas~~sva~~~iG~a~gaG~~~~a~l~~~~G~l~~itq~l~~m~g~gy~-~n~~g~~ls~~  303 (402)
T KOG2191|consen  232 PYAYQ-------AHVLPASTASTISVAAGLIGGANGAGGAFGAALSGFTGALIAITQALNTMAGYGYN-TNILGLGLSIL  303 (402)
T ss_pred             CCCCC-------Cccccccchhhccccccccccccccccccceeeecccccceeeccccccccccccc-ccccchhhhhh
Confidence            11100       112334456778899999999999999999999999999999987643   33445 77889999999


Q ss_pred             HHHHHHHHHHh
Q 006943          612 AAENLIQAFIM  622 (624)
Q Consensus       612 ~A~~lI~~~i~  622 (624)
                      .|.-+|...+.
T Consensus       304 aa~g~L~~~~~  314 (402)
T KOG2191|consen  304 AAEGVLAAKVA  314 (402)
T ss_pred             hhhhHHHHhhc
Confidence            99988887664

>TIGR03665 arCOG04150 arCOG04150 universal archaeal KH domain protein

Probab=99.62  E-value=2.3e-15  Score=140.50  Aligned_cols=137  Identities=22%  Similarity=0.301  Sum_probs=103.5

Q ss_pred             EEecCCeeeEEEcCCCchHHHHHHhcCceEEEeCCCCCCCCCCCCcEEEE---EeehHHHHHHHHHHHHHHhhccccCCC
Q 006943          393 LLVSSKVIGCIIGKSGSIINEIRKRTKADVRISKGDKPKCADANDELVEV---VGEVGSVRDALVQIILRLRDDALKDRD  469 (624)
Q Consensus       393 l~vp~~~~g~iIGk~G~~Ik~I~~~tga~I~i~~~~~p~~~~~~~~~v~I---~G~~~~v~~A~~~I~~~l~e~~~~~~~  469 (624)
                      +.||.+.+|.|||++|++|++|+++|||+|++..+         +..|.|   +++++++.+|...|..........+ +
T Consensus         2 i~Ip~~kig~vIG~gG~~Ik~I~~~tgv~I~Id~~---------~g~V~I~~~t~d~~~i~kA~~~I~~i~~gf~~e~-A   71 (172)
T TIGR03665         2 VKIPKDRIGVLIGKGGETKKEIEERTGVKLDIDSE---------TGEVKIEEEDEDPLAVMKAREVVKAIGRGFSPEK-A   71 (172)
T ss_pred             ccCCHHHhhhHhCCchhHHHHHHHHhCcEEEEEcC---------CceEEEecCCCCHHHHHHHHHHHHHHHcCCCHHH-H
Confidence            56899999999999999999999999999999742         345788   7899999999988866443210000 0


Q ss_pred             CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCcccccCCC
Q 006943          470 GSRNPPVGADHIYSSGTGISMPPLLPSIPPVGPLGYDQRADSGSGIGMLSSSSLYGYGSLSMGDSPYGSMSSYSSKLYGG  549 (624)
Q Consensus       470 ~~~~p~~~~~~~~~~~~~~~~p~~~~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  549 (624)
                                        +.+                                                        .+.
T Consensus        72 ------------------~~l--------------------------------------------------------~gd   77 (172)
T TIGR03665        72 ------------------LKL--------------------------------------------------------LDD   77 (172)
T ss_pred             ------------------HHh--------------------------------------------------------cCC
Confidence                              000                                                        000


Q ss_pred             CCCCcEEEEEecc---------ccccceeccCCchHHHHHHHhCCEEEEeCCCCCCCCeEEEEEcCHHHHHHHHHHHHHH
Q 006943          550 LPPPLTLEVLVPA---------NAVGKVIGKAGSNLANIRKISGATIEMSDSKSSRGDRVALISGTPEQKRAAENLIQAF  620 (624)
Q Consensus       550 ~~~~~~~~i~VP~---------~~vg~IIGkgG~~I~~I~~~sGa~I~i~~~~~~~~~r~v~I~Gt~e~v~~A~~lI~~~  620 (624)
                        .-....+.|++         ..+|+|||++|++++.|+..|||+|.|++       ..|.|.|++++++.|+.+|+.+
T Consensus        78 --~y~~~Vi~I~~~~~~~~~~~~~~griIG~~G~t~~~ie~~t~~~i~i~~-------~~v~i~G~~~~~~~A~~~i~~l  148 (172)
T TIGR03665        78 --DYMLEVIDLKEYGKSPNALRRIKGRIIGEGGKTRRIIEELTGVSISVYG-------KTVGIIGDPEQVQIAREAIEML  148 (172)
T ss_pred             --cceEEEEEhhhccCCHHHHHHHHhhhcCCCcHHHHHHHHHHCCeEEEcC-------CEEEEECCHHHHHHHHHHHHHH
Confidence              00011122222         46899999999999999999999999984       5699999999999999999998


Q ss_pred             Hh
Q 006943          621 IM  622 (624)
Q Consensus       621 i~  622 (624)
                      |.
T Consensus       149 i~  150 (172)
T TIGR03665       149 IE  150 (172)
T ss_pred             Hc
Confidence            84

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=99.56  E-value=2.9e-14  Score=134.08  Aligned_cols=139  Identities=22%  Similarity=0.246  Sum_probs=105.7

Q ss_pred             EEEEEEecCCeeeEEEcCCCchHHHHHHhcCceEEEeCCCCCCCCCCCCcEEEEE----eehHHHHHHHHHHHHHHhhcc
Q 006943          389 VTIRLLVSSKVIGCIIGKSGSIINEIRKRTKADVRISKGDKPKCADANDELVEVV----GEVGSVRDALVQIILRLRDDA  464 (624)
Q Consensus       389 ~~~~l~vp~~~~g~iIGk~G~~Ik~I~~~tga~I~i~~~~~p~~~~~~~~~v~I~----G~~~~v~~A~~~I~~~l~e~~  464 (624)
                      ....+.||.+.++.|||++|++|+.|+++|||+|++..+         +..|.|.    ++++++.+|..+|.+.+....
T Consensus         3 ~~~~i~IP~~kig~iIG~gGk~Ik~I~e~tg~~I~i~~~---------~g~V~I~~~~~~d~~~i~kA~~~I~ai~~gf~   73 (180)
T PRK13763          3 MMEYVKIPKDRIGVLIGKKGETKKEIEERTGVKLEIDSE---------TGEVIIEPTDGEDPLAVLKARDIVKAIGRGFS   73 (180)
T ss_pred             ceEEEEcCHHHhhhHhccchhHHHHHHHHHCcEEEEECC---------CCeEEEEeCCCCCHHHHHHHHHHHHHHhcCCC
Confidence            457899999999999999999999999999999999742         3567885    899999999988876554210


Q ss_pred             ccCC--CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCc
Q 006943          465 LKDR--DGSRNPPVGADHIYSSGTGISMPPLLPSIPPVGPLGYDQRADSGSGIGMLSSSSLYGYGSLSMGDSPYGSMSSY  542 (624)
Q Consensus       465 ~~~~--~~~~~p~~~~~~~~~~~~~~~~p~~~~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~~~~~~~~~~~~~~~  542 (624)
                      ..+.  ..+       +.++                                                            
T Consensus        74 ~e~A~~l~g-------d~y~------------------------------------------------------------   86 (180)
T PRK13763         74 PEKALRLLD-------DDYV------------------------------------------------------------   86 (180)
T ss_pred             HHHHHHHhC-------CCce------------------------------------------------------------
Confidence            0000  000       0000                                                            


Q ss_pred             ccccCCCCCCCcEEEEE---------eccccccceeccCCchHHHHHHHhCCEEEEeCCCCCCCCeEEEEEcCHHHHHHH
Q 006943          543 SSKLYGGLPPPLTLEVL---------VPANAVGKVIGKAGSNLANIRKISGATIEMSDSKSSRGDRVALISGTPEQKRAA  613 (624)
Q Consensus       543 ~~~~~~~~~~~~~~~i~---------VP~~~vg~IIGkgG~~I~~I~~~sGa~I~i~~~~~~~~~r~v~I~Gt~e~v~~A  613 (624)
                                  ...+.         .....+|+|||++|++++.|++.|||+|.|.+       ..|.|.|++++++.|
T Consensus        87 ------------~~Vi~i~~~~~~~~~~~r~~griIG~~G~~~k~ie~~t~~~i~i~~-------~~v~i~G~~~~~~~A  147 (180)
T PRK13763         87 ------------LEVIDLSDYGDSPNALRRIKGRIIGEGGKTRRIIEELTGVDISVYG-------KTVAIIGDPEQVEIA  147 (180)
T ss_pred             ------------EEEEEhhhccCChhHHHHHhhheeCCCcHHHHHHHHHHCcEEEEcC-------CEEEEEeCHHHHHHH
Confidence                        00000         11247899999999999999999999999984       339999999999999


Q ss_pred             HHHHHHHHh
Q 006943          614 ENLIQAFIM  622 (624)
Q Consensus       614 ~~lI~~~i~  622 (624)
                      +..|+.++.
T Consensus       148 ~~~I~~li~  156 (180)
T PRK13763        148 REAIEMLIE  156 (180)
T ss_pred             HHHHHHHHc
Confidence            999999874

>TIGR03665 arCOG04150 arCOG04150 universal archaeal KH domain protein

Probab=99.51  E-value=6.7e-14  Score=130.70  Aligned_cols=136  Identities=24%  Similarity=0.262  Sum_probs=95.9

Q ss_pred             EEecCcccceeccCCchHHHHHHHhcCCeEEeeCCCCCCCceEEEEE---ccCCcccccccccccCCCCcccHHHHHHHH
Q 006943           41 ILCPDGVIGSVIGKSGKVINSIRQETRARVKVVDPFPGAKDRVVTIY---SHVKDKEDVEVDDEFNDKEPLCAAQDALLK  117 (624)
Q Consensus        41 ilvp~~~~g~vIGk~G~~I~~i~~etg~~I~v~~~~~~~~er~i~I~---G~~~~~~~~~~~~~~~~~~~~~~a~~ai~~  117 (624)
                      |.||.+.+|.|||++|++|++|+++|||+|.+.+     .+..|.|.   ++++                      ++.+
T Consensus         2 i~Ip~~kig~vIG~gG~~Ik~I~~~tgv~I~Id~-----~~g~V~I~~~t~d~~----------------------~i~k   54 (172)
T TIGR03665         2 VKIPKDRIGVLIGKGGETKKEIEERTGVKLDIDS-----ETGEVKIEEEDEDPL----------------------AVMK   54 (172)
T ss_pred             ccCCHHHhhhHhCCchhHHHHHHHHhCcEEEEEc-----CCceEEEecCCCCHH----------------------HHHH
Confidence            5689999999999999999999999999999975     23568884   2222                      3333


Q ss_pred             HHHHHHHhhhccC-C-CcccCCCceeEE-EEEec---------cceeEEEeCCchHHHHHHHhcCCeEEEccCCCCCCCC
Q 006943          118 VHAAIANAVANAT-D-NDKKRKEKEECQ-ILVPS---------SQSANIIGKAGATIKRLRSKTRTSIKVTPKDASEPTH  185 (624)
Q Consensus       118 v~~~i~~~~~~~~-~-~~~~~~~~~~~~-llvp~---------~~~g~iIGk~G~~Ik~I~~~sga~I~i~~~~~~~~~~  185 (624)
                      +.+.|..-..... + ...-..+.++++ +-|+.         ...|+|||++|++++.|++.|||+|.|..        
T Consensus        55 A~~~I~~i~~gf~~e~A~~l~gd~y~~~Vi~I~~~~~~~~~~~~~~griIG~~G~t~~~ie~~t~~~i~i~~--------  126 (172)
T TIGR03665        55 AREVVKAIGRGFSPEKALKLLDDDYMLEVIDLKEYGKSPNALRRIKGRIIGEGGKTRRIIEELTGVSISVYG--------  126 (172)
T ss_pred             HHHHHHHHHcCCCHHHHHHhcCCcceEEEEEhhhccCCHHHHHHHHhhhcCCCcHHHHHHHHHHCCeEEEcC--------
Confidence            3333322111100 0 000011223333 23333         37999999999999999999999999852        


Q ss_pred             cccccCCceEEEecCHHHHHHHHHHHHHHHhhc
Q 006943          186 SCAMEFDNFVLISGESEAVKKALFAISAIMYKF  218 (624)
Q Consensus       186 ~~~~~~~r~V~I~G~~~~V~~A~~~I~~~l~~~  218 (624)
                             ..|.|.|.+++|..|..+|.+++...
T Consensus       127 -------~~v~i~G~~~~~~~A~~~i~~li~~~  152 (172)
T TIGR03665       127 -------KTVGIIGDPEQVQIAREAIEMLIEGA  152 (172)
T ss_pred             -------CEEEEECCHHHHHHHHHHHHHHHcCC
Confidence                   56999999999999999999998543

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=99.50  E-value=1.4e-13  Score=129.38  Aligned_cols=141  Identities=21%  Similarity=0.251  Sum_probs=98.0

Q ss_pred             EEEEEEecCcccceeccCCchHHHHHHHhcCCeEEeeCCCCCCCceEEEEE----ccCCcccccccccccCCCCcccHHH
Q 006943           37 VIYRILCPDGVIGSVIGKSGKVINSIRQETRARVKVVDPFPGAKDRVVTIY----SHVKDKEDVEVDDEFNDKEPLCAAQ  112 (624)
Q Consensus        37 ~~~~ilvp~~~~g~vIGk~G~~I~~i~~etg~~I~v~~~~~~~~er~i~I~----G~~~~~~~~~~~~~~~~~~~~~~a~  112 (624)
                      +...+.||.+.++.|||++|++|+.|+++|||+|.+.+.     +..|.|.    +.++                     
T Consensus         3 ~~~~i~IP~~kig~iIG~gGk~Ik~I~e~tg~~I~i~~~-----~g~V~I~~~~~~d~~---------------------   56 (180)
T PRK13763          3 MMEYVKIPKDRIGVLIGKKGETKKEIEERTGVKLEIDSE-----TGEVIIEPTDGEDPL---------------------   56 (180)
T ss_pred             ceEEEEcCHHHhhhHhccchhHHHHHHHHHCcEEEEECC-----CCeEEEEeCCCCCHH---------------------
Confidence            567899999999999999999999999999999999762     3567776    2222                     


Q ss_pred             HHHHHHHHHHHHhhhccC-CC-cccCCCceeEEE-EEe---------ccceeEEEeCCchHHHHHHHhcCCeEEEccCCC
Q 006943          113 DALLKVHAAIANAVANAT-DN-DKKRKEKEECQI-LVP---------SSQSANIIGKAGATIKRLRSKTRTSIKVTPKDA  180 (624)
Q Consensus       113 ~ai~~v~~~i~~~~~~~~-~~-~~~~~~~~~~~l-lvp---------~~~~g~iIGk~G~~Ik~I~~~sga~I~i~~~~~  180 (624)
                       ++.++.+.|.+-..... +. ..-..+.+.+++ -+.         ...+|+|||++|++++.|++.|||+|.|..   
T Consensus        57 -~i~kA~~~I~ai~~gf~~e~A~~l~gd~y~~~Vi~i~~~~~~~~~~~r~~griIG~~G~~~k~ie~~t~~~i~i~~---  132 (180)
T PRK13763         57 -AVLKARDIVKAIGRGFSPEKALRLLDDDYVLEVIDLSDYGDSPNALRRIKGRIIGEGGKTRRIIEELTGVDISVYG---  132 (180)
T ss_pred             -HHHHHHHHHHHHhcCCCHHHHHHHhCCCceEEEEEhhhccCChhHHHHHhhheeCCCcHHHHHHHHHHCcEEEEcC---
Confidence             22222222221111100 00 000111223222 111         137999999999999999999999999863   


Q ss_pred             CCCCCcccccCCceEEEecCHHHHHHHHHHHHHHHhhcC
Q 006943          181 SEPTHSCAMEFDNFVLISGESEAVKKALFAISAIMYKFS  219 (624)
Q Consensus       181 ~~~~~~~~~~~~r~V~I~G~~~~V~~A~~~I~~~l~~~~  219 (624)
                                  +.|.|.|.++++..|...|..+++...
T Consensus       133 ------------~~v~i~G~~~~~~~A~~~I~~li~g~~  159 (180)
T PRK13763        133 ------------KTVAIIGDPEQVEIAREAIEMLIEGAP  159 (180)
T ss_pred             ------------CEEEEEeCHHHHHHHHHHHHHHHcCCC
Confidence                        348999999999999999999996543

>KOG2208 consensus Vigilin [Lipid transport and metabolism]

Probab=99.48  E-value=1.1e-13  Score=156.19  Aligned_cols=363  Identities=18%  Similarity=0.222  Sum_probs=245.4

Q ss_pred             CceEEEEEEecCcccceeccCCchHHHHHHHhcCCeEEeeCCCCCCCceEEEEEccCCcccccccccccCCCCcccHHHH
Q 006943           34 EESVIYRILCPDGVIGSVIGKSGKVINSIRQETRARVKVVDPFPGAKDRVVTIYSHVKDKEDVEVDDEFNDKEPLCAAQD  113 (624)
Q Consensus        34 ~~~~~~~ilvp~~~~g~vIGk~G~~I~~i~~etg~~I~v~~~~~~~~er~i~I~G~~~~~~~~~~~~~~~~~~~~~~a~~  113 (624)
                      .-.+..++.+....+..+||++|.++..++.++.+.|+|++..  .....+.+.|....+..               +.-
T Consensus       198 ~r~~~~k~~v~~~~~~~~~g~g~~~~~~~~d~~~~~i~ip~sn--~~~~~~~i~~~~~~~~~---------------~~~  260 (753)
T KOG2208|consen  198 ERSVFEKMNVGITLHSHIIGRGGSNISIIMDETKVHIHIPDSN--KSSPSNKIDGRLNSSSS---------------INV  260 (753)
T ss_pred             ceeEEEEeeccccchhhhccccccccccccccceeEEEccccc--ccchhhhhcccccccee---------------hhh
Confidence            3358889999999999999999999999999999999998753  23344455454333210               111


Q ss_pred             HHHHHHHHHHHhhhccCCCcccCCCceeEEEEEeccceeEEEeCCchHHHHHHHhcCCeEEEccCCCCCCCCcccccCCc
Q 006943          114 ALLKVHAAIANAVANATDNDKKRKEKEECQILVPSSQSANIIGKAGATIKRLRSKTRTSIKVTPKDASEPTHSCAMEFDN  193 (624)
Q Consensus       114 ai~~v~~~i~~~~~~~~~~~~~~~~~~~~~llvp~~~~g~iIGk~G~~Ik~I~~~sga~I~i~~~~~~~~~~~~~~~~~r  193 (624)
                      -+...+..+              +....+.+.++..++-+++|..|+.+..|+...-=...+.+.         +.+.+.
T Consensus       261 ~i~~~~~~l--------------e~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~~~---------~~s~~~  317 (753)
T KOG2208|consen  261 EIQEALTRL--------------ESEFDYDEIIYRRLPRFIRGIPGEEINQLRDYMPEVDSIFQN---------YPSKDD  317 (753)
T ss_pred             hhHHHHHHh--------------cChhhhhhhhhccccccccccccchhhHHHhhcchhhhhhcc---------ccccce
Confidence            112222221              223445567788888999999999999998865544433332         125677


Q ss_pred             eEEEecCHHHHHHHHHHHHHHHhhcCCCCCCCCCCccCCCCCCccCCCCCCCCCCCCCCCCCCCCCCCCCCCCccCCCCC
Q 006943          194 FVLISGESEAVKKALFAISAIMYKFSPREDIPLETTVREAPPSIIIPSDVPIYPPGGLYPNADPILPSRSVPSILGAARV  273 (624)
Q Consensus       194 ~V~I~G~~~~V~~A~~~I~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~~~~~~~g~~~~  273 (624)
                      .+.+.|....+..+......++..+..                                                     
T Consensus       318 ~~~~~~~~~~~~~~~~~~~~~~~~~~~-----------------------------------------------------  344 (753)
T KOG2208|consen  318 SIVLSGFEVGAVLAKRDKTLLLKNSEE-----------------------------------------------------  344 (753)
T ss_pred             eEeecccccchhhhhhHHHHHHHHhhc-----------------------------------------------------
Confidence            888999988777666655444432111                                                     


Q ss_pred             CCCCCCCCCCCCCCCCCCCCccccCCCCCCCCccEEEEEEecCCccceeeccCcchHHHHHhHhCCeEEEcCCCCCCCce
Q 006943          274 PDLQGYADTGNTWPVYSTGLSLVSGLVGASQSEELVIRVLCPFNKIGRVIGKGGGTIKSIRQASGAQIDVDDTKDNRDEC  353 (624)
Q Consensus       274 p~~~~~~~~~~~~~~~~~~~p~~~~~~~~~~~~~~~~~i~vp~~~vg~IIGk~G~~Ik~I~~~tga~I~v~~~~~~~~er  353 (624)
                                                      +.....+.+...++..|+||+|.+|.+|+++++|.+.++...  ....
T Consensus       345 --------------------------------nn~~i~~~i~~~~~~~v~GK~~~ni~ki~e~~~~~i~~~~~~--~~~~  390 (753)
T KOG2208|consen  345 --------------------------------NNENIKREIFPEELKFVIGKKGANIEKIREESQVKIDLPKQG--SNNK  390 (753)
T ss_pred             --------------------------------cceeeEEeecHHhhhhhcCCCCccHHHHHHhhhhceeccccc--CCCC
Confidence                                            124556778889999999999999999999999999998733  3455


Q ss_pred             EEEEeec-CCchhHHHHHHHHHHHHhhccCCCCCCcEEEEEEecCCeeeEEEcCCCchHHHHHHhcC-ceEEEeCCCCCC
Q 006943          354 VITVTAI-ESPDDIKSMAVEAVLLLQTKINDEDDDTVTIRLLVSSKVIGCIIGKSGSIINEIRKRTK-ADVRISKGDKPK  431 (624)
Q Consensus       354 ~i~I~G~-~~~~~a~~~~~~~i~~~~~~~~~~~~~~~~~~l~vp~~~~g~iIGk~G~~Ik~I~~~tg-a~I~i~~~~~p~  431 (624)
                      .+.+++. .+.+.+...+.+.+..+.       +..+...+.+|...+.++||.+|..|++|..+++ .+|++....   
T Consensus       391 ~v~~~~~~~~~~ka~~~v~~~~~ei~-------n~~~~~~~~iP~k~~~~iig~~g~~i~~I~~k~~~v~i~f~~~~---  460 (753)
T KOG2208|consen  391 KVVITGVSANDEKAVEDVEKIIAEIL-------NSIVKEEVQIPTKSHKRIIGTKGALINYIMGKHGGVHIKFQNNN---  460 (753)
T ss_pred             CeEEeccccchhHHHHHHHHHHHhhh-------cccccceeecCccchhhhhccccccHHHHHhhcCcEEEecCCCC---
Confidence            6777775 344445444444333322       1245667999999999999999999999999999 667776533   


Q ss_pred             CCCCCCcEEEEEeehHHHHHHHHHHHHHHhhccccCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
Q 006943          432 CADANDELVEVVGEVGSVRDALVQIILRLRDDALKDRDGSRNPPVGADHIYSSGTGISMPPLLPSIPPVGPLGYDQRADS  511 (624)
Q Consensus       432 ~~~~~~~~v~I~G~~~~v~~A~~~I~~~l~e~~~~~~~~~~~p~~~~~~~~~~~~~~~~p~~~~~~~~~~~~~~~~~~~~  511 (624)
                         +....+++.|....+..+..+......+..... .                                          
T Consensus       461 ---~~~~~~~~~~~~~dv~~~~~~~~~~~~~a~~~~-~------------------------------------------  494 (753)
T KOG2208|consen  461 ---NSSDMVTIRGISKDVEKSVSLLKALKADAKNLK-F------------------------------------------  494 (753)
T ss_pred             ---cccccceEeccccccchhHHHHHhhhhhhhcch-h------------------------------------------
Confidence               234457788888888877655543332210000 0                                          


Q ss_pred             CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCcccccCCCCCCCcEEEEEeccccccceeccCCchHHHHHHHhCCEEEEeC
Q 006943          512 GSGIGMLSSSSLYGYGSLSMGDSPYGSMSSYSSKLYGGLPPPLTLEVLVPANAVGKVIGKAGSNLANIRKISGATIEMSD  591 (624)
Q Consensus       512 ~~~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~VP~~~vg~IIGkgG~~I~~I~~~sGa~I~i~~  591 (624)
                                                             ....+.....|..+.+..+|+.|..+...    +....++.
T Consensus       495 ---------------------------------------~~~~~~d~~~~~~~~~~~~g~~~~i~d~~----~~~~i~~~  531 (753)
T KOG2208|consen  495 ---------------------------------------RDVVTKDKLLPVKYIGKEIGKNGTIRDSL----GDKSIFPP  531 (753)
T ss_pred             ---------------------------------------hhhhhccccchHHhhcccccCceeeeccC----Cceeeccc
Confidence                                                   00124566678888888888887766554    44555554


Q ss_pred             CCCCCCCeEEEEEcCHHHHHHHHHHHHHHHhh
Q 006943          592 SKSSRGDRVALISGTPEQKRAAENLIQAFIMA  623 (624)
Q Consensus       592 ~~~~~~~r~v~I~Gt~e~v~~A~~lI~~~i~~  623 (624)
                      ... .....++|.|-.+.|..|+..+..++.+
T Consensus       532 ~~~-~~~~~i~i~gk~~~v~~a~~~L~~~~~~  562 (753)
T KOG2208|consen  532 NED-EDHEKITIEGKLELVLEAPAELKALIEA  562 (753)
T ss_pred             ccc-cccceeeecccccchhhhHHHHHhcchh
Confidence            422 3456799999999999999999887654

>KOG2208 consensus Vigilin [Lipid transport and metabolism]

Probab=99.47  E-value=2.8e-13  Score=152.87  Aligned_cols=396  Identities=20%  Similarity=0.189  Sum_probs=230.1

Q ss_pred             EEEEEEecCcccceeccCCchHHHHHHHhcCCeEEeeCCCCCCCceEEEEEccCCcccccccccccCCCCcccHHHHHHH
Q 006943           37 VIYRILCPDGVIGSVIGKSGKVINSIRQETRARVKVVDPFPGAKDRVVTIYSHVKDKEDVEVDDEFNDKEPLCAAQDALL  116 (624)
Q Consensus        37 ~~~~ilvp~~~~g~vIGk~G~~I~~i~~etg~~I~v~~~~~~~~er~i~I~G~~~~~~~~~~~~~~~~~~~~~~a~~ai~  116 (624)
                      +...+-+-+.++.+|+||+|.+|.+|+++++|.|.+++  .+..+..+.++|...+++               .|.+.+.
T Consensus       347 ~~i~~~i~~~~~~~v~GK~~~ni~ki~e~~~~~i~~~~--~~~~~~~v~~~~~~~~~~---------------ka~~~v~  409 (753)
T KOG2208|consen  347 ENIKREIFPEELKFVIGKKGANIEKIREESQVKIDLPK--QGSNNKKVVITGVSANDE---------------KAVEDVE  409 (753)
T ss_pred             eeeEEeecHHhhhhhcCCCCccHHHHHHhhhhceeccc--ccCCCCCeEEeccccchh---------------HHHHHHH
Confidence            67778888999999999999999999999999999987  367888999999988743               3555555


Q ss_pred             HHHHHHHHhhhccCCCcccCCCceeEEEEEeccceeEEEeCCchHHHHHHHhcC-CeEEEccCCCCCCCCcccccCCceE
Q 006943          117 KVHAAIANAVANATDNDKKRKEKEECQILVPSSQSANIIGKAGATIKRLRSKTR-TSIKVTPKDASEPTHSCAMEFDNFV  195 (624)
Q Consensus       117 ~v~~~i~~~~~~~~~~~~~~~~~~~~~llvp~~~~g~iIGk~G~~Ik~I~~~sg-a~I~i~~~~~~~~~~~~~~~~~r~V  195 (624)
                      .++..+..             +.+.-.+.+|...+.+|||.+|..|..|++++| ..|......          .....+
T Consensus       410 ~~~~ei~n-------------~~~~~~~~iP~k~~~~iig~~g~~i~~I~~k~~~v~i~f~~~~----------~~~~~~  466 (753)
T KOG2208|consen  410 KIIAEILN-------------SIVKEEVQIPTKSHKRIIGTKGALINYIMGKHGGVHIKFQNNN----------NSSDMV  466 (753)
T ss_pred             HHHHhhhc-------------ccccceeecCccchhhhhccccccHHHHHhhcCcEEEecCCCC----------cccccc
Confidence            55555432             134556899999999999999999999999999 455444322          234557


Q ss_pred             EEecCHHHHHHHHHHHHHHHhhcCCCCCCCCCCccCCCCCCccCCCCCCCCCCCCCCCCCCCCCCCCCCCCccCCCCCCC
Q 006943          196 LISGESEAVKKALFAISAIMYKFSPREDIPLETTVREAPPSIIIPSDVPIYPPGGLYPNADPILPSRSVPSILGAARVPD  275 (624)
Q Consensus       196 ~I~G~~~~V~~A~~~I~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~~~~~~~g~~~~p~  275 (624)
                      ++.|....|..++..+..+.......                                                      
T Consensus       467 ~~~~~~~dv~~~~~~~~~~~~~a~~~------------------------------------------------------  492 (753)
T KOG2208|consen  467 TIRGISKDVEKSVSLLKALKADAKNL------------------------------------------------------  492 (753)
T ss_pred             eEeccccccchhHHHHHhhhhhhhcc------------------------------------------------------
Confidence            88898888888777666555321110                                                      


Q ss_pred             CCCCCCCCCCCCCCCCCCccccCCCCCCCCccEEEEEEecCCccceeeccCcchHHHHHhHhCCeEEEcCCCCCCCceEE
Q 006943          276 LQGYADTGNTWPVYSTGLSLVSGLVGASQSEELVIRVLCPFNKIGRVIGKGGGTIKSIRQASGAQIDVDDTKDNRDECVI  355 (624)
Q Consensus       276 ~~~~~~~~~~~~~~~~~~p~~~~~~~~~~~~~~~~~i~vp~~~vg~IIGk~G~~Ik~I~~~tga~I~v~~~~~~~~er~i  355 (624)
                                                 ......+...+.|..+.+..+|+.|..+....++....+..+.     .+..+
T Consensus       493 ---------------------------~~~~~~~~d~~~~~~~~~~~~g~~~~i~d~~~~~~i~~~~~~~-----~~~~i  540 (753)
T KOG2208|consen  493 ---------------------------KFRDVVTKDKLLPVKYIGKEIGKNGTIRDSLGDKSIFPPNEDE-----DHEKI  540 (753)
T ss_pred             ---------------------------hhhhhhhccccchHHhhcccccCceeeeccCCceeeccccccc-----cccee
Confidence                                       0001123345567777777777776655555544444433322     34468


Q ss_pred             EEeec-CCchhHHHHHHHHHHHHhhccCCCCCCcEEEEEEecCCee-eEEEcCCCchHHHHHHhcCceEEEeCCCCCCCC
Q 006943          356 TVTAI-ESPDDIKSMAVEAVLLLQTKINDEDDDTVTIRLLVSSKVI-GCIIGKSGSIINEIRKRTKADVRISKGDKPKCA  433 (624)
Q Consensus       356 ~I~G~-~~~~~a~~~~~~~i~~~~~~~~~~~~~~~~~~l~vp~~~~-g~iIGk~G~~Ik~I~~~tga~I~i~~~~~p~~~  433 (624)
                      +|.|. +.+.       ++.+.+...+.... ......+.+|..++ -++++++....+..+...|+.+.+++...    
T Consensus       541 ~i~gk~~~v~-------~a~~~L~~~~~~~~-~~~~~~v~~~~~~~~~~l~~~~~~~~~~~e~~~gv~~~fp~~~~----  608 (753)
T KOG2208|consen  541 TIEGKLELVL-------EAPAELKALIEALI-KATLLEVNNPPGQHRPFLIGKGIENRTYVEVFGGVVVPFPRSPT----  608 (753)
T ss_pred             eecccccchh-------hhHHHHHhcchhhh-hhhhhhccCcchheeeeeeccccccccceeecCcccccCCCCCC----
Confidence            88885 2232       23333322221111 12234455666665 45555555566666666667888876433    


Q ss_pred             CCCCcEEEEEeehHHHHHHHHHHHHHHhhccccCCCCC-CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
Q 006943          434 DANDELVEVVGEVGSVRDALVQIILRLRDDALKDRDGS-RNPPVGADHIYSSGTGISMPPLLPSIPPVGPLGYDQRADSG  512 (624)
Q Consensus       434 ~~~~~~v~I~G~~~~v~~A~~~I~~~l~e~~~~~~~~~-~~p~~~~~~~~~~~~~~~~p~~~~~~~~~~~~~~~~~~~~~  512 (624)
                        +.+-+.|.|....++.|...+.+..... ....... .-|... .....+..+...+...          +..     
T Consensus       609 --~~~e~~i~g~~~~v~aa~~~~~~i~~~~-~~~~~~~~~i~~~~-~~~~~~~~g~~~~~~t----------~~~-----  669 (753)
T KOG2208|consen  609 --SSDEVSIKGAKDEVKAAKGRLEEIVEYL-SAYATTNTKIPDKF-HRSIVGYRGHIIEEIT----------SKF-----  669 (753)
T ss_pred             --chhhhccchhHHHHHHhhccchhhhhhc-ccccceeeeccccc-ceeeecCCCcccccce----------eec-----
Confidence              2334789999999999977665444322 1111000 000000 0000000111111000          000     


Q ss_pred             CCCCCCCCCCCCCCCCCCCCCCCCCCCC-CcccccCCCCCCCcEEEEEeccccccceeccCCchHHHHHHHhCCEEEEeC
Q 006943          513 SGIGMLSSSSLYGYGSLSMGDSPYGSMS-SYSSKLYGGLPPPLTLEVLVPANAVGKVIGKAGSNLANIRKISGATIEMSD  591 (624)
Q Consensus       513 ~~~g~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~i~VP~~~vg~IIGkgG~~I~~I~~~sGa~I~i~~  591 (624)
                      .+.|..+....  .++... ....+... .......-.....++.++.+|.++++.+||++|.+++++..++++.+.+++
T Consensus       670 ~~~~~~~~~~~--~~s~~~-~~~~~~~~~~e~~~~~~~~~~~~~~~~~~p~~~~~~~ig~~g~~~r~~~~~~~~~~~~~~  746 (753)
T KOG2208|consen  670 GVGGYFGDAPT--EGSVNT-IHVSGEKMQSEIAKIALEAKNLVTKEIEIPRSLHRYLIGPKGSNLRQLEKEFNVNIVVPN  746 (753)
T ss_pred             CccceeCCCCC--ccccCc-chhhhhhhhhhhcccccccccceeeEEeccHHHhhhccCCCCccHHHHHHHhccceecCC
Confidence            00000000000  000000 00000000 000111111223579999999999999999999999999999999999987


Q ss_pred             C
Q 006943          592 S  592 (624)
Q Consensus       592 ~  592 (624)
                      +
T Consensus       747 ~  747 (753)
T KOG2208|consen  747 P  747 (753)
T ss_pred             c
Confidence            3

>cd02396 PCBP_like_KH K homology RNA-binding domain, PCBP_like

Probab=99.45  E-value=2.1e-13  Score=106.11  Aligned_cols=63  Identities=41%  Similarity=0.616  Sum_probs=59.0

Q ss_pred             EEEEeccccccceeccCCchHHHHHHHhCCEEEEeCCCC-CCCCeEEEEEcCHHHHHHHHHHHH
Q 006943          556 LEVLVPANAVGKVIGKAGSNLANIRKISGATIEMSDSKS-SRGDRVALISGTPEQKRAAENLIQ  618 (624)
Q Consensus       556 ~~i~VP~~~vg~IIGkgG~~I~~I~~~sGa~I~i~~~~~-~~~~r~v~I~Gt~e~v~~A~~lI~  618 (624)
                      .++.||.+.+|+|||++|++|++|+++|||+|++.+... +..+|.|+|+|++++++.|..||+
T Consensus         2 ~r~~ip~~~vg~iIG~~G~~i~~i~~~tga~I~i~~~~~~~~~~r~v~I~G~~~~v~~A~~~I~   65 (65)
T cd02396           2 LRLLVPSSQAGSIIGKGGSTIKEIREETGAKIRVSKSVLPGSTERVVTISGKPSAVQKALLLIL   65 (65)
T ss_pred             EEEEECHHHcCeeECCCcHHHHHHHHHHCCEEEEcCCCCCCCCceEEEEEeCHHHHHHHHHhhC
Confidence            689999999999999999999999999999999998765 578899999999999999999984

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 Kinase anchor protein AKAP149, contains KH and Tudor RNA-binding domains [Signal transduction mechanisms]

Probab=99.34  E-value=1.3e-11  Score=127.94  Aligned_cols=286  Identities=20%  Similarity=0.262  Sum_probs=176.4

Q ss_pred             CCCccEEEEEEecCCccceeeccCcchHHHHHhHhCCeEEEcCCCCCCCceEEEEeec-CCchhHHHHHHHHHHHHhhcc
Q 006943          303 SQSEELVIRVLCPFNKIGRVIGKGGGTIKSIRQASGAQIDVDDTKDNRDECVITVTAI-ESPDDIKSMAVEAVLLLQTKI  381 (624)
Q Consensus       303 ~~~~~~~~~i~vp~~~vg~IIGk~G~~Ik~I~~~tga~I~v~~~~~~~~er~i~I~G~-~~~~~a~~~~~~~i~~~~~~~  381 (624)
                      ..++++..++.|+..++.+++|+.|++|+.|+..++++|.+....-+ +++..++.|- ..+-.+.....+.+   .   
T Consensus        63 e~~k~v~~e~Vv~~e~vkli~gr~gsnik~l~~~t~aKi~L~~ed~g-~e~~~~~~~~p~~v~~a~a~~~~~~---~---  135 (608)
T KOG2279|consen   63 KPQKDIEIEMVVPQEAVKLIIGRQGSNIKQLRKQTGAKIDLDTEDVG-DERVLLISGFPVQVCKAKAAIHQIL---T---  135 (608)
T ss_pred             CchhheeeeEeecccceeeeeccccCCcchhhcccccceecCcccCC-cccchhhccCCCCCChHHHHHHHHH---h---
Confidence            44577889999999999999999999999999999999999754433 4566666653 22222222221111   1   


Q ss_pred             CCCCCCcEEEEEEecCCeeeEEEcCCCchHHHHHHhcCceEEEeCCCCCCCCCCCCcEEEEEeehHHHHHHHHHHHHHHh
Q 006943          382 NDEDDDTVTIRLLVSSKVIGCIIGKSGSIINEIRKRTKADVRISKGDKPKCADANDELVEVVGEVGSVRDALVQIILRLR  461 (624)
Q Consensus       382 ~~~~~~~~~~~l~vp~~~~g~iIGk~G~~Ik~I~~~tga~I~i~~~~~p~~~~~~~~~v~I~G~~~~v~~A~~~I~~~l~  461 (624)
                         .+.++...+.+|...+++|+|++|.+++.|+.-++|+|.+.....    ....+...|.|...-++.|..++.+++.
T Consensus       136 ---~~~pvk~~lsvpqr~~~~i~grgget~~si~~ss~aki~~d~ngr----~g~~~~~~i~~qqk~~~~a~~~~~~~~~  208 (608)
T KOG2279|consen  136 ---ENTPVSEQLSVPQRSVGRIIGRGGETIRSICKSSGAKITCDKNGR----LGLSRLIKISGQQKEVAAAKHLILEKVS  208 (608)
T ss_pred             ---cCCcccccccchhhhcccccccchhhhcchhcccccccccccccc----cccccceecccccchHHHHHhhhhcccc
Confidence               345788889999999999999999999999999999999976521    3457778888888888889888888886


Q ss_pred             hccccCCCCC-----CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC-
Q 006943          462 DDALKDRDGS-----RNPPVGADHIYSSGTGISMPPLLPSIPPVGPLGYDQRADSGSGIGMLSSSSLYGYGSLSMGDSP-  535 (624)
Q Consensus       462 e~~~~~~~~~-----~~p~~~~~~~~~~~~~~~~p~~~~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~~~~~~~~-  535 (624)
                      ++-..-+...     ..|.....+.+  +.++.-|..               ...+...+....+...|.+...+...+ 
T Consensus       209 edeelv~~~~e~~q~rvprk~p~n~~--~~~m~~~~~---------------s~~~h~~~~t~~s~spg~~~~~~eg~dm  271 (608)
T KOG2279|consen  209 EDEELVKRIAESAQTRVPRKQPINVR--REDMTEPGG---------------AGEPHLWKNTSSSMSPGAPLVTKEGGDM  271 (608)
T ss_pred             chhHHhhhchhhcccCCCCCCCcccc--chhhccccc---------------CCccccCccchhccCCCCCCcccCCCcc
Confidence            6432221110     11110000000  000000000               000000000000000000000000000 


Q ss_pred             ------CCCCCCcccccCCCCCCCcEEEEEeccccccceeccCCchHHHHHHHhCCEEEEeCCCCCCC---CeEEEEEcC
Q 006943          536 ------YGSMSSYSSKLYGGLPPPLTLEVLVPANAVGKVIGKAGSNLANIRKISGATIEMSDSKSSRG---DRVALISGT  606 (624)
Q Consensus       536 ------~~~~~~~~~~~~~~~~~~~~~~i~VP~~~vg~IIGkgG~~I~~I~~~sGa~I~i~~~~~~~~---~r~v~I~Gt  606 (624)
                            .+......-...-........+|.+|...+|.+||+.|+.++.+...|++.+.|.-..-...   -.++.+.|+
T Consensus       272 ~v~vsk~~s~~~~~d~s~~k~~~l~i~e~e~p~~lsg~lig~~gey~s~yssasn~~~hi~t~pyt~~v~~~qic~~egk  351 (608)
T KOG2279|consen  272 AVVVSKEGSWEKPSDDSFQKSEALAIPEMEMPEILSGDLIGHAGEYLSVYSSASNHPNHIWTQPYTSRVLQLQICVNEGK  351 (608)
T ss_pred             eeEEecccccCCccccccccccccccceeecCcccccchhhhhhhhhhhhhhccCccceEEeccccchhhhhhhheecch
Confidence                  00000000000000112357899999999999999999999999999999999986543222   267889999


Q ss_pred             HHHHHHHHHHHHH
Q 006943          607 PEQKRAAENLIQA  619 (624)
Q Consensus       607 ~e~v~~A~~lI~~  619 (624)
                      ..-++.+-.||..
T Consensus       352 qh~~n~vl~ml~~  364 (608)
T KOG2279|consen  352 QHYENSVLEMLTV  364 (608)
T ss_pred             hHHHHHHHhhhhc
Confidence            9999999999873

>cd02394 vigilin_like_KH K homology RNA-binding domain_vigilin_like

Probab=99.32  E-value=2.8e-12  Score=98.96  Aligned_cols=61  Identities=30%  Similarity=0.393  Sum_probs=56.5

Q ss_pred             EEEEeccccccceeccCCchHHHHHHHhCCEEEEeCCCCCCCCeEEEEEcCHHHHHHHHHHHH
Q 006943          556 LEVLVPANAVGKVIGKAGSNLANIRKISGATIEMSDSKSSRGDRVALISGTPEQKRAAENLIQ  618 (624)
Q Consensus       556 ~~i~VP~~~vg~IIGkgG~~I~~I~~~sGa~I~i~~~~~~~~~r~v~I~Gt~e~v~~A~~lI~  618 (624)
                      .++.||.+++|+|||++|++|++|+++|||+|.|++..  ..++.|+|+|++++++.|+.+|+
T Consensus         2 ~~i~Vp~~~~~~iIG~~G~~i~~i~~~~g~~I~i~~~~--~~~~~v~I~G~~~~v~~A~~~i~   62 (62)
T cd02394           2 EEVEIPKKLHRFIIGKKGSNIRKIMEETGVKIRFPDPG--SKSDTITITGPKENVEKAKEEIL   62 (62)
T ss_pred             eEEEeCHHHhhhccCCCCCcHHHHHHHhCCEEEcCCCC--CCCCEEEEEcCHHHHHHHHHHhC
Confidence            57899999999999999999999999999999999875  46788999999999999999874

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=98.53  Aligned_cols=60  Identities=38%  Similarity=0.673  Sum_probs=55.5

Q ss_pred             EEEEEeccccccceeccCCchHHHHHHHhCCEEEEeCCCCCCCCeEEEEEcCHHHHHHHHHHH
Q 006943          555 TLEVLVPANAVGKVIGKAGSNLANIRKISGATIEMSDSKSSRGDRVALISGTPEQKRAAENLI  617 (624)
Q Consensus       555 ~~~i~VP~~~vg~IIGkgG~~I~~I~~~sGa~I~i~~~~~~~~~r~v~I~Gt~e~v~~A~~lI  617 (624)
                      |.+|.||.+++|+|||++|++|++|+++|||+|.|++.  + ....|+|+|++++|+.|+.+|
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            57899999999999999999999999999999999977  2 445899999999999999987

; 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 ....

>cd02396 PCBP_like_KH K homology RNA-binding domain, PCBP_like

Probab=99.30  E-value=6.4e-12  Score=97.77  Aligned_cols=64  Identities=44%  Similarity=0.614  Sum_probs=57.8

Q ss_pred             eEEEEEeccceeEEEeCCchHHHHHHHhcCCeEEEccCCCCCCCCcccccCCceEEEecCHHHHHHHHHHH
Q 006943          141 ECQILVPSSQSANIIGKAGATIKRLRSKTRTSIKVTPKDASEPTHSCAMEFDNFVLISGESEAVKKALFAI  211 (624)
Q Consensus       141 ~~~llvp~~~~g~iIGk~G~~Ik~I~~~sga~I~i~~~~~~~~~~~~~~~~~r~V~I~G~~~~V~~A~~~I  211 (624)
                      +++|+||.+.+|.|||++|++|++|+++|||+|.+.+...       +..++|+|+|.|++++|.+|+.+|
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 TLRLLVPSSQAGSIIGKGGSTIKEIREETGAKIRVSKSVL-------PGSTERVVTISGKPSAVQKALLLI   64 (65)
T ss_pred             CEEEEECHHHcCeeECCCcHHHHHHHHHHCCEEEEcCCCC-------CCCCceEEEEEeCHHHHHHHHHhh
Confidence            4789999999999999999999999999999999987532       236789999999999999999887

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

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

Probab=99.27  E-value=1.2e-11  Score=94.60  Aligned_cols=58  Identities=22%  Similarity=0.462  Sum_probs=53.8

Q ss_pred             EEEEEeccccccceeccCCchHHHHHHHhCCEEEEeCCCCCCCCeEEEEEcC-HHHHHHHHHHHH
Q 006943          555 TLEVLVPANAVGKVIGKAGSNLANIRKISGATIEMSDSKSSRGDRVALISGT-PEQKRAAENLIQ  618 (624)
Q Consensus       555 ~~~i~VP~~~vg~IIGkgG~~I~~I~~~sGa~I~i~~~~~~~~~r~v~I~Gt-~e~v~~A~~lI~  618 (624)
                      +..+.||.+++|+|||++|++|++|+++|||+|.|+++      +.|+|+|+ +++++.|+.+|+
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            67899999999999999999999999999999999862      56999998 999999999984

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=99.26  E-value=1.5e-11  Score=95.61  Aligned_cols=63  Identities=44%  Similarity=0.724  Sum_probs=58.7

Q ss_pred             EEEEeccccccceeccCCchHHHHHHHhCCEEEEeCCCCCCCCeEEEEEcCHHHHHHHHHHHH
Q 006943          556 LEVLVPANAVGKVIGKAGSNLANIRKISGATIEMSDSKSSRGDRVALISGTPEQKRAAENLIQ  618 (624)
Q Consensus       556 ~~i~VP~~~vg~IIGkgG~~I~~I~~~sGa~I~i~~~~~~~~~r~v~I~Gt~e~v~~A~~lI~  618 (624)
                      .++.||.+++++|||++|++|++|++.|||+|.|++...+..++.|+|+|+.++++.|+.+|+
T Consensus         2 ~~i~ip~~~~~~vIG~~G~~i~~I~~~s~~~I~i~~~~~~~~~~~v~i~G~~~~v~~a~~~i~   64 (64)
T cd00105           2 ERVLVPSSLVGRIIGKGGSTIKEIREETGAKIKIPDSGSGSEERIVTITGTPEAVEKAKELIL   64 (64)
T ss_pred             EEEEEchhhcceeECCCCHHHHHHHHHHCCEEEEcCCCCCCCceEEEEEcCHHHHHHHHHHhC
Confidence            579999999999999999999999999999999998766667899999999999999999874

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.

>KOG2279 consensus Kinase anchor protein AKAP149, contains KH and Tudor RNA-binding domains [Signal transduction mechanisms]

Probab=99.21  E-value=3.1e-11  Score=125.22  Aligned_cols=225  Identities=24%  Similarity=0.308  Sum_probs=167.0

Q ss_pred             CCCceeEEEEEeccceeEEEeCCchHHHHHHHhcCCeEEEccCCCCCCCCcccccCCceEEEecCHHHHHHHHHHHHHHH
Q 006943          136 RKEKEECQILVPSSQSANIIGKAGATIKRLRSKTRTSIKVTPKDASEPTHSCAMEFDNFVLISGESEAVKKALFAISAIM  215 (624)
Q Consensus       136 ~~~~~~~~llvp~~~~g~iIGk~G~~Ik~I~~~sga~I~i~~~~~~~~~~~~~~~~~r~V~I~G~~~~V~~A~~~I~~~l  215 (624)
                      ..+.+.++++|+...+..++|+.|.+|+.|+..++++|.+..++.         ..+++..+.|.+.+|..|..++...+
T Consensus        64 ~~k~v~~e~Vv~~e~vkli~gr~gsnik~l~~~t~aKi~L~~ed~---------g~e~~~~~~~~p~~v~~a~a~~~~~~  134 (608)
T KOG2279|consen   64 PQKDIEIEMVVPQEAVKLIIGRQGSNIKQLRKQTGAKIDLDTEDV---------GDERVLLISGFPVQVCKAKAAIHQIL  134 (608)
T ss_pred             chhheeeeEeecccceeeeeccccCCcchhhcccccceecCcccC---------CcccchhhccCCCCCChHHHHHHHHH
Confidence            345688899999999999999999999999999999999988764         34666777779999999999988877


Q ss_pred             hhcCCCCCCCCCCccCCCCCCccCCCCCCCCCCCCCCCCCCCCCCCCCCCCccCCCCCCCCCCCCCCCCCCCCCCCCCcc
Q 006943          216 YKFSPREDIPLETTVREAPPSIIIPSDVPIYPPGGLYPNADPILPSRSVPSILGAARVPDLQGYADTGNTWPVYSTGLSL  295 (624)
Q Consensus       216 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~~~~~~~g~~~~p~~~~~~~~~~~~~~~~~~~p~  295 (624)
                      ...                                                                             
T Consensus       135 ~~~-----------------------------------------------------------------------------  137 (608)
T KOG2279|consen  135 TEN-----------------------------------------------------------------------------  137 (608)
T ss_pred             hcC-----------------------------------------------------------------------------
Confidence            431                                                                             


Q ss_pred             ccCCCCCCCCccEEEEEEecCCccceeeccCcchHHHHHhHhCCeEEEcCCCCCCCceEEEEeecCCch-hHHHHHHHHH
Q 006943          296 VSGLVGASQSEELVIRVLCPFNKIGRVIGKGGGTIKSIRQASGAQIDVDDTKDNRDECVITVTAIESPD-DIKSMAVEAV  374 (624)
Q Consensus       296 ~~~~~~~~~~~~~~~~i~vp~~~vg~IIGk~G~~Ik~I~~~tga~I~v~~~~~~~~er~i~I~G~~~~~-~a~~~~~~~i  374 (624)
                                ..+.....+|...+++|+|++|++++.|+.-++++|.+..+......+.+.|.+..+.. .+..+.-+-+
T Consensus       138 ----------~pvk~~lsvpqr~~~~i~grgget~~si~~ss~aki~~d~ngr~g~~~~~~i~~qqk~~~~a~~~~~~~~  207 (608)
T KOG2279|consen  138 ----------TPVSEQLSVPQRSVGRIIGRGGETIRSICKSSGAKITCDKNGRLGLSRLIKISGQQKEVAAAKHLILEKV  207 (608)
T ss_pred             ----------CcccccccchhhhcccccccchhhhcchhcccccccccccccccccccceecccccchHHHHHhhhhccc
Confidence                      12344566899999999999999999999999999999877555567788888865443 2332222222


Q ss_pred             HHHh---hccC--------------------------C---------------------C--------------------
Q 006943          375 LLLQ---TKIN--------------------------D---------------------E--------------------  384 (624)
Q Consensus       375 ~~~~---~~~~--------------------------~---------------------~--------------------  384 (624)
                      +.-.   +.+.                          .                     +                    
T Consensus       208 ~edeelv~~~~e~~q~rvprk~p~n~~~~~m~~~~~s~~~h~~~~t~~s~spg~~~~~~eg~dm~v~vsk~~s~~~~~d~  287 (608)
T KOG2279|consen  208 SEDEELVKRIAESAQTRVPRKQPINVRREDMTEPGGAGEPHLWKNTSSSMSPGAPLVTKEGGDMAVVVSKEGSWEKPSDD  287 (608)
T ss_pred             cchhHHhhhchhhcccCCCCCCCccccchhhcccccCCccccCccchhccCCCCCCcccCCCcceeEEecccccCCcccc
Confidence            1100   0000                          0                     0                    


Q ss_pred             ----CCCcEEEEEEecCCeeeEEEcCCCchHHHHHHhcCceEEEeCCCCCCCCCCCCcEEEEEeehHHHHHHHHHHH
Q 006943          385 ----DDDTVTIRLLVSSKVIGCIIGKSGSIINEIRKRTKADVRISKGDKPKCADANDELVEVVGEVGSVRDALVQII  457 (624)
Q Consensus       385 ----~~~~~~~~l~vp~~~~g~iIGk~G~~Ik~I~~~tga~I~i~~~~~p~~~~~~~~~v~I~G~~~~v~~A~~~I~  457 (624)
                          .......+|.+|...+|.|||+.|++++.+...+++.++|........ --.-.++.+.|...-+..+..++-
T Consensus       288 s~~k~~~l~i~e~e~p~~lsg~lig~~gey~s~yssasn~~~hi~t~pyt~~-v~~~qic~~egkqh~~n~vl~ml~  363 (608)
T KOG2279|consen  288 SFQKSEALAIPEMEMPEILSGDLIGHAGEYLSVYSSASNHPNHIWTQPYTSR-VLQLQICVNEGKQHYENSVLEMLT  363 (608)
T ss_pred             ccccccccccceeecCcccccchhhhhhhhhhhhhhccCccceEEeccccch-hhhhhhheecchhHHHHHHHhhhh
Confidence                012234678999999999999999999999999999999875432100 011256889999999988876654

>cd02394 vigilin_like_KH K homology RNA-binding domain_vigilin_like

Probab=99.11  E-value=1.1e-10  Score=90.02  Aligned_cols=60  Identities=27%  Similarity=0.399  Sum_probs=54.7

Q ss_pred             EEEEEeccceeEEEeCCchHHHHHHHhcCCeEEEccCCCCCCCCcccccCCceEEEecCHHHHHHHHHHH
Q 006943          142 CQILVPSSQSANIIGKAGATIKRLRSKTRTSIKVTPKDASEPTHSCAMEFDNFVLISGESEAVKKALFAI  211 (624)
Q Consensus       142 ~~llvp~~~~g~iIGk~G~~Ik~I~~~sga~I~i~~~~~~~~~~~~~~~~~r~V~I~G~~~~V~~A~~~I  211 (624)
                      .+|.||..++++|||++|++|++|+++|||+|.|+...          +.++.|+|+|+.++|..|+.+|
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            57899999999999999999999999999999998643          4578999999999999999876

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=99.05  E-value=8e-10  Score=84.43  Aligned_cols=58  Identities=21%  Similarity=0.257  Sum_probs=52.1

Q ss_pred             EEEEEEecCCeeeEEEcCCCchHHHHHHhcCceEEEeCCCCCCCCCCCCcEEEEEee-hHHHHHHHHHH
Q 006943          389 VTIRLLVSSKVIGCIIGKSGSIINEIRKRTKADVRISKGDKPKCADANDELVEVVGE-VGSVRDALVQI  456 (624)
Q Consensus       389 ~~~~l~vp~~~~g~iIGk~G~~Ik~I~~~tga~I~i~~~~~p~~~~~~~~~v~I~G~-~~~v~~A~~~I  456 (624)
                      ....+.||..++++|||++|++|++|+++|||+|.++.          ++.|.|+|+ .++++.|+.+|
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            56789999999999999999999999999999999964          456999998 89999998765

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.

>PF00013 KH_1: KH domain syndrome, contains KH motifs

Probab=99.03  E-value=1.5e-10  Score=88.65  Aligned_cols=60  Identities=38%  Similarity=0.500  Sum_probs=53.9

Q ss_pred             eEEEEEeccceeEEEeCCchHHHHHHHhcCCeEEEccCCCCCCCCcccccCCceEEEecCHHHHHHHHHHH
Q 006943          141 ECQILVPSSQSANIIGKAGATIKRLRSKTRTSIKVTPKDASEPTHSCAMEFDNFVLISGESEAVKKALFAI  211 (624)
Q Consensus       141 ~~~llvp~~~~g~iIGk~G~~Ik~I~~~sga~I~i~~~~~~~~~~~~~~~~~r~V~I~G~~~~V~~A~~~I  211 (624)
                      |.+|.||.+++++|||++|++|++|+++|||+|.|+..           ..+..|+|+|+.++|.+|+++|
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-----------DERDIVTISGSPEQVEKAKKMI   60 (60)
T ss_dssp             EEEEEEEHHHHHHHHTGGGHHHHHHHHHHTSEEEEEST-----------TEEEEEEEEESHHHHHHHHHHH
T ss_pred             CEEEEECHHHcCEEECCCCCcHHHhhhhcCeEEEEcCC-----------CCcEEEEEEeCHHHHHHHHhhC
Confidence            57899999999999999999999999999999999752           1245899999999999999876

; 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=98.98  E-value=1.7e-09  Score=83.97  Aligned_cols=62  Identities=37%  Similarity=0.583  Sum_probs=55.3

Q ss_pred             EEEEecCCeeeEEEcCCCchHHHHHHhcCceEEEeCCCCCCCCCCCCcEEEEEeehHHHHHHHHHH
Q 006943          391 IRLLVSSKVIGCIIGKSGSIINEIRKRTKADVRISKGDKPKCADANDELVEVVGEVGSVRDALVQI  456 (624)
Q Consensus       391 ~~l~vp~~~~g~iIGk~G~~Ik~I~~~tga~I~i~~~~~p~~~~~~~~~v~I~G~~~~v~~A~~~I  456 (624)
                      .++.||..++++|||++|++|++|+++|||+|.|++...    ...++.|.|.|+.+++..|..+|
T Consensus         2 ~~i~ip~~~~~~vIG~~G~~i~~I~~~s~~~I~i~~~~~----~~~~~~v~i~G~~~~v~~a~~~i   63 (64)
T cd00105           2 ERVLVPSSLVGRIIGKGGSTIKEIREETGAKIKIPDSGS----GSEERIVTITGTPEAVEKAKELI   63 (64)
T ss_pred             EEEEEchhhcceeECCCCHHHHHHHHHHCCEEEEcCCCC----CCCceEEEEEcCHHHHHHHHHHh
Confidence            579999999999999999999999999999999986433    35688999999999999998665

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=98.94  E-value=1.5e-09  Score=76.78  Aligned_cols=42  Identities=38%  Similarity=0.722  Sum_probs=37.9

Q ss_pred             cccceeccCCchHHHHHHHhCCEEEEeC-CCCCCCCeEEEEEc
Q 006943          564 AVGKVIGKAGSNLANIRKISGATIEMSD-SKSSRGDRVALISG  605 (624)
Q Consensus       564 ~vg~IIGkgG~~I~~I~~~sGa~I~i~~-~~~~~~~r~v~I~G  605 (624)
                      +||+|||++|++|++|+++|||+|+|++ ..++..++.|+|+|
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 34456789999998

>PF13014 KH_3: KH domain

Probab=98.91  E-value=2.2e-09  Score=75.92  Aligned_cols=42  Identities=43%  Similarity=0.753  Sum_probs=39.0

Q ss_pred             ccceeccCCchHHHHHHHhcCCeEEeeC-CCCCCCceEEEEEc
Q 006943           47 VIGSVIGKSGKVINSIRQETRARVKVVD-PFPGAKDRVVTIYS   88 (624)
Q Consensus        47 ~~g~vIGk~G~~I~~i~~etg~~I~v~~-~~~~~~er~i~I~G   88 (624)
                      ++|+||||+|++|++|+++|+|+|.|++ ..++..+|.|+|+|
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            5899999999999999999999999998 56788999999987

>smart00322 KH K homology RNA-binding domain

Probab=98.90  E-value=8.1e-09  Score=81.00  Aligned_cols=66  Identities=39%  Similarity=0.703  Sum_probs=60.2

Q ss_pred             cEEEEEeccccccceeccCCchHHHHHHHhCCEEEEeCCCCCCCCeEEEEEcCHHHHHHHHHHHHHHH
Q 006943          554 LTLEVLVPANAVGKVIGKAGSNLANIRKISGATIEMSDSKSSRGDRVALISGTPEQKRAAENLIQAFI  621 (624)
Q Consensus       554 ~~~~i~VP~~~vg~IIGkgG~~I~~I~~~sGa~I~i~~~~~~~~~r~v~I~Gt~e~v~~A~~lI~~~i  621 (624)
                      .+.++.||.+++|.+||++|.+|++|++.||++|.+.....  ....++|.|++++++.|..+|.+.+
T Consensus         3 ~~~~i~i~~~~~~~liG~~G~~i~~i~~~~~~~i~~~~~~~--~~~~v~i~g~~~~v~~a~~~i~~~~   68 (69)
T smart00322        3 VTIEVLIPADKVGLIIGKGGSTIKKIEEETGVKIDIPEDGS--EERVVEITGPPENVEKAAELILEIL   68 (69)
T ss_pred             eEEEEEEcchhcceeECCCchHHHHHHHHHCCEEEECCCCC--CccEEEEEcCHHHHHHHHHHHHHHh
Confidence            47899999999999999999999999999999999986643  5678999999999999999999876

>smart00322 KH K homology RNA-binding domain

Probab=98.71  E-value=7.8e-08  Score=75.32  Aligned_cols=67  Identities=31%  Similarity=0.477  Sum_probs=59.5

Q ss_pred             ceeEEEEEeccceeEEEeCCchHHHHHHHhcCCeEEEccCCCCCCCCcccccCCceEEEecCHHHHHHHHHHHHHHH
Q 006943          139 KEECQILVPSSQSANIIGKAGATIKRLRSKTRTSIKVTPKDASEPTHSCAMEFDNFVLISGESEAVKKALFAISAIM  215 (624)
Q Consensus       139 ~~~~~llvp~~~~g~iIGk~G~~Ik~I~~~sga~I~i~~~~~~~~~~~~~~~~~r~V~I~G~~~~V~~A~~~I~~~l  215 (624)
                      .++.++.||..++++|||++|++|++|++.|||+|.+....          .....|.|.|+.+++..|..+|.+.+
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            36788999999999999999999999999999999997532          24688999999999999999998775

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

Probab=98.65  E-value=5.5e-07  Score=83.24  Aligned_cols=145  Identities=28%  Similarity=0.333  Sum_probs=99.7

Q ss_pred             ceEEEEEEecCcccceeccCCchHHHHHHHhcCCeEEeeCCCCCCCceEEEEEccCCcccccccccccCCCCcccHHHHH
Q 006943           35 ESVIYRILCPDGVIGSVIGKSGKVINSIRQETRARVKVVDPFPGAKDRVVTIYSHVKDKEDVEVDDEFNDKEPLCAAQDA  114 (624)
Q Consensus        35 ~~~~~~ilvp~~~~g~vIGk~G~~I~~i~~etg~~I~v~~~~~~~~er~i~I~G~~~~~~~~~~~~~~~~~~~~~~a~~a  114 (624)
                      ....+.+.||.+..+.+||+.|+..+.|.+.+++++.+.     ..+..|+|...... .+           |     -+
T Consensus         6 ~~~~~~v~iPk~R~~~lig~~g~v~k~ie~~~~~~~~iD-----~~~~~V~i~~~~~t-~D-----------p-----~~   63 (194)
T COG1094           6 EKSSEAVKIPKDRIGVLIGKWGEVKKAIEEKTGVKLRID-----SKTGSVTIRTTRKT-ED-----------P-----LA   63 (194)
T ss_pred             ccceeeeecCchhheeeecccccchHHHHhhcCeEEEEE-----CCCCeEEEEecCCC-CC-----------h-----HH
Confidence            345677999999999999999999999999999999995     35677888877321 10           0     12


Q ss_pred             HHHHHHH---HHHhhhccCCCcccCCCceeEEE-----EEe------ccceeEEEeCCchHHHHHHHhcCCeEEEccCCC
Q 006943          115 LLKVHAA---IANAVANATDNDKKRKEKEECQI-----LVP------SSQSANIIGKAGATIKRLRSKTRTSIKVTPKDA  180 (624)
Q Consensus       115 i~~v~~~---i~~~~~~~~~~~~~~~~~~~~~l-----lvp------~~~~g~iIGk~G~~Ik~I~~~sga~I~i~~~~~  180 (624)
                      ++++.+.   |.-.+... +...-..+.+.|.+     ++.      ....|+|||++|.+-+.|++-|||.|.|..   
T Consensus        64 ~~ka~d~VkAIgrGF~pe-~A~~LL~d~~~levIdi~~~~~~~~~~l~R~kgRIIG~~GkTr~~IE~lt~~~I~V~g---  139 (194)
T COG1094          64 LLKARDVVKAIGRGFPPE-KALKLLEDDYYLEVIDLKDVVTLSGDHLRRIKGRIIGREGKTRRAIEELTGVYISVYG---  139 (194)
T ss_pred             HHHHHHHHHHHhcCCCHH-HHHHHhcCCcEEEEEEHHHhccCchhhhhHhhceeeCCCchHHHHHHHHhCCeEEEeC---
Confidence            2222222   11111110 00000111222211     111      234699999999999999999999999864   


Q ss_pred             CCCCCcccccCCceEEEecCHHHHHHHHHHHHHHHhh
Q 006943          181 SEPTHSCAMEFDNFVLISGESEAVKKALFAISAIMYK  217 (624)
Q Consensus       181 ~~~~~~~~~~~~r~V~I~G~~~~V~~A~~~I~~~l~~  217 (624)
                                  ..|.|-|..++|..|..+|..++.-
T Consensus       140 ------------~tVaiiG~~~~v~iAr~AVemli~G  164 (194)
T COG1094         140 ------------KTVAIIGGFEQVEIAREAVEMLING  164 (194)
T ss_pred             ------------cEEEEecChhhhHHHHHHHHHHHcC
Confidence                        5699999999999999999999954

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

Probab=98.60  E-value=9e-07  Score=81.85  Aligned_cols=139  Identities=22%  Similarity=0.312  Sum_probs=97.9

Q ss_pred             EEEEEEecCCccceeeccCcchHHHHHhHhCCeEEEcCCCCCCCceEEEEeecCCchh--HHHHHHHHHHHHhhccCCC-
Q 006943          308 LVIRVLCPFNKIGRVIGKGGGTIKSIRQASGAQIDVDDTKDNRDECVITVTAIESPDD--IKSMAVEAVLLLQTKINDE-  384 (624)
Q Consensus       308 ~~~~i~vp~~~vg~IIGk~G~~Ik~I~~~tga~I~v~~~~~~~~er~i~I~G~~~~~~--a~~~~~~~i~~~~~~~~~~-  384 (624)
                      ....+.||.+..+.+||+.|++.+.|.+.+++++.++..     +..|.|..++...+  +...+.+.+..+-..++.+ 
T Consensus         8 ~~~~v~iPk~R~~~lig~~g~v~k~ie~~~~~~~~iD~~-----~~~V~i~~~~~t~Dp~~~~ka~d~VkAIgrGF~pe~   82 (194)
T COG1094           8 SSEAVKIPKDRIGVLIGKWGEVKKAIEEKTGVKLRIDSK-----TGSVTIRTTRKTEDPLALLKARDVVKAIGRGFPPEK   82 (194)
T ss_pred             ceeeeecCchhheeeecccccchHHHHhhcCeEEEEECC-----CCeEEEEecCCCCChHHHHHHHHHHHHHhcCCCHHH
Confidence            356789999999999999999999999999999999643     34577776532222  2223344444332222110 


Q ss_pred             ----CCCcEEEE-EEe------c----CCeeeEEEcCCCchHHHHHHhcCceEEEeCCCCCCCCCCCCcEEEEEeehHHH
Q 006943          385 ----DDDTVTIR-LLV------S----SKVIGCIIGKSGSIINEIRKRTKADVRISKGDKPKCADANDELVEVVGEVGSV  449 (624)
Q Consensus       385 ----~~~~~~~~-l~v------p----~~~~g~iIGk~G~~Ik~I~~~tga~I~i~~~~~p~~~~~~~~~v~I~G~~~~v  449 (624)
                          .++.+.+. +.+      +    ....|+|||++|.+.+.|++-|||.|.+..           ..|.|-|.+++|
T Consensus        83 A~~LL~d~~~levIdi~~~~~~~~~~l~R~kgRIIG~~GkTr~~IE~lt~~~I~V~g-----------~tVaiiG~~~~v  151 (194)
T COG1094          83 ALKLLEDDYYLEVIDLKDVVTLSGDHLRRIKGRIIGREGKTRRAIEELTGVYISVYG-----------KTVAIIGGFEQV  151 (194)
T ss_pred             HHHHhcCCcEEEEEEHHHhccCchhhhhHhhceeeCCCchHHHHHHHHhCCeEEEeC-----------cEEEEecChhhh
Confidence                01122222 211      1    234699999999999999999999999973           458999999999


Q ss_pred             HHHHHHHHHHHhh
Q 006943          450 RDALVQIILRLRD  462 (624)
Q Consensus       450 ~~A~~~I~~~l~e  462 (624)
                      ..|...|...+..
T Consensus       152 ~iAr~AVemli~G  164 (194)
T COG1094         152 EIAREAVEMLING  164 (194)
T ss_pred             HHHHHHHHHHHcC
Confidence            9999888877754

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

Probab=98.42  E-value=7.1e-07  Score=77.70  Aligned_cols=61  Identities=26%  Similarity=0.358  Sum_probs=50.6

Q ss_pred             cccccceeccCCchHHHHHHHhCCEEEEeCCCCC-----------------CCCeEEEEEcC---HHHHHHHHHHHHHHH
Q 006943          562 ANAVGKVIGKAGSNLANIRKISGATIEMSDSKSS-----------------RGDRVALISGT---PEQKRAAENLIQAFI  621 (624)
Q Consensus       562 ~~~vg~IIGkgG~~I~~I~~~sGa~I~i~~~~~~-----------------~~~r~v~I~Gt---~e~v~~A~~lI~~~i  621 (624)
                      -+++|.|||++|.+||+|+++|||+|.|......                 ...-.|.|++.   .++++.|..+|+.++
T Consensus        14 ~N~IG~IIGPgG~tiK~i~~eTg~kI~Irg~gs~~~~~~~~~~~~~~~~~~~eplhV~I~a~~~~~e~~~~A~~~I~~ll   93 (120)
T cd02395          14 YNFVGLILGPRGNTLKQLEKETGAKISIRGKGSMKDGKKEEELRGPKYAHLNEPLHVLITAETPPEEALAKAVEAIEELL   93 (120)
T ss_pred             CCeeEEEECCCChHHHHHHHHHCCEEEEecCcccccccccccccCcccccCCCCcEEEEEeCCcHHHHHHHHHHHHHHHh
Confidence            3788999999999999999999999999976311                 11246889985   599999999999987


Q ss_pred             h
Q 006943          622 M  622 (624)
Q Consensus       622 ~  622 (624)
                      .
T Consensus        94 ~   94 (120)
T cd02395          94 K   94 (120)
T ss_pred             c
Confidence            5

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=98.14  E-value=9.1e-06  Score=70.82  Aligned_cols=72  Identities=28%  Similarity=0.320  Sum_probs=53.9

Q ss_pred             ccceeEEEeCCchHHHHHHHhcCCeEEEccCCCCCCC--------Cccc-ccCCceEEEecCH---HHHHHHHHHHHHHH
Q 006943          148 SSQSANIIGKAGATIKRLRSKTRTSIKVTPKDASEPT--------HSCA-MEFDNFVLISGES---EAVKKALFAISAIM  215 (624)
Q Consensus       148 ~~~~g~iIGk~G~~Ik~I~~~sga~I~i~~~~~~~~~--------~~~~-~~~~r~V~I~G~~---~~V~~A~~~I~~~l  215 (624)
                      .+++|.|||++|++||+|+++|||+|.|..+......        +... ....-.|.|++..   +++.+|+.+|..++
T Consensus        14 ~N~IG~IIGPgG~tiK~i~~eTg~kI~Irg~gs~~~~~~~~~~~~~~~~~~~eplhV~I~a~~~~~e~~~~A~~~I~~ll   93 (120)
T cd02395          14 YNFVGLILGPRGNTLKQLEKETGAKISIRGKGSMKDGKKEEELRGPKYAHLNEPLHVLITAETPPEEALAKAVEAIEELL   93 (120)
T ss_pred             CCeeEEEECCCChHHHHHHHHHCCEEEEecCcccccccccccccCcccccCCCCcEEEEEeCCcHHHHHHHHHHHHHHHh
Confidence            4678999999999999999999999999976321100        0011 1233578899965   99999999999999


Q ss_pred             hhcC
Q 006943          216 YKFS  219 (624)
Q Consensus       216 ~~~~  219 (624)
                      ....
T Consensus        94 ~~~~   97 (120)
T cd02395          94 KPAI   97 (120)
T ss_pred             ccCC
Confidence            7543

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 Predicted RNA binding protein, contains KH domain [General function prediction only]

Probab=98.12  E-value=6.3e-06  Score=80.38  Aligned_cols=155  Identities=24%  Similarity=0.306  Sum_probs=109.8

Q ss_pred             CcEEEEEEecCCeeeEEEcCCCchHHHHHHhcCceEEEeCCCCCCCCCCCCcEEEEEeehHHHHHHHHHHHHHHhhcccc
Q 006943          387 DTVTIRLLVSSKVIGCIIGKSGSIINEIRKRTKADVRISKGDKPKCADANDELVEVVGEVGSVRDALVQIILRLRDDALK  466 (624)
Q Consensus       387 ~~~~~~l~vp~~~~g~iIGk~G~~Ik~I~~~tga~I~i~~~~~p~~~~~~~~~v~I~G~~~~v~~A~~~I~~~l~e~~~~  466 (624)
                      +.++..+.||..+++.+.|++|++||.|+.+|...|.-+..       ..+-++.++|..+.|..|+..|... .+++-.
T Consensus        24 ~nvt~sv~vps~~v~~ivg~qg~kikalr~KTqtyi~tPsr-------~eePiF~vTg~~edv~~aRrei~sa-aeH~~l   95 (394)
T KOG2113|consen   24 QNVTESVEVPSEHVAEIVGRQGCKIKALRAKTQTYIKTPSR-------GEEPIFPVTGRHEDVRRARREIPSA-AEHFGL   95 (394)
T ss_pred             CccceeeecCcccceeecccCccccchhhhhhcceeccCCC-------CCCCcceeccCchhHHHHhhcCccc-cceeee
Confidence            56888899999999999999999999999999999887643       2346788999999999998655321 011000


Q ss_pred             CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCccccc
Q 006943          467 DRDGSRNPPVGADHIYSSGTGISMPPLLPSIPPVGPLGYDQRADSGSGIGMLSSSSLYGYGSLSMGDSPYGSMSSYSSKL  546 (624)
Q Consensus       467 ~~~~~~~p~~~~~~~~~~~~~~~~p~~~~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  546 (624)
                                   ..|.+                                           ++..+.+.+.         
T Consensus        96 -------------~~~s~-------------------------------------------s~Sgg~~~~s---------  110 (394)
T KOG2113|consen   96 -------------IRASR-------------------------------------------SFSGGTNGAS---------  110 (394)
T ss_pred             -------------eeecc-------------------------------------------cccCCCcccc---------
Confidence                         00000                                           0000000000         


Q ss_pred             CCCCCCCcEEEEEeccccccceeccCCchHHHHHHHhCCEEEEeCCCCCCCCeEEEEEcCHHH-HHHHH-HHHHHH
Q 006943          547 YGGLPPPLTLEVLVPANAVGKVIGKAGSNLANIRKISGATIEMSDSKSSRGDRVALISGTPEQ-KRAAE-NLIQAF  620 (624)
Q Consensus       547 ~~~~~~~~~~~i~VP~~~vg~IIGkgG~~I~~I~~~sGa~I~i~~~~~~~~~r~v~I~Gt~e~-v~~A~-~lI~~~  620 (624)
                         .+.+.+.++.+|-..+|.|.|..|.+|+.|++.+...|.-+-+.   .+-++-++|.+.. +++|. ..|++.
T Consensus       111 ---~s~qt~sy~svP~rvvglvv~~~~~ti~~iqq~tnt~I~T~v~~---~~~Vf~Vtg~~~nC~kra~s~eie~t  180 (394)
T KOG2113|consen  111 ---ASGQTTSYVSVPLRVVGLVVGPKGATIKRIQQFTNTYIATPVRC---GEPVFCVTGAPKNCVKRARSCEIEQT  180 (394)
T ss_pred             ---ccCCCceeeeccceeeeeccccccCccchheecccceEeeeccC---CCceEEEecCCcchhhhccccchhhh
Confidence               11234778899999999999999999999999999999777553   4567889998888 56666 455443

>TIGR02696 pppGpp_PNP guanosine pentaphosphate synthetase I/polynucleotide phosphorylase

Probab=97.95  E-value=4.3e-05  Score=85.30  Aligned_cols=62  Identities=27%  Similarity=0.476  Sum_probs=56.8

Q ss_pred             EEEEEeccccccceeccCCchHHHHHHHhCCEEEEeCCCCCCCCeEEEEEc-CHHHHHHHHHHHHHHHh
Q 006943          555 TLEVLVPANAVGKVIGKAGSNLANIRKISGATIEMSDSKSSRGDRVALISG-TPEQKRAAENLIQAFIM  622 (624)
Q Consensus       555 ~~~i~VP~~~vg~IIGkgG~~I~~I~~~sGa~I~i~~~~~~~~~r~v~I~G-t~e~v~~A~~lI~~~i~  622 (624)
                      ..++.||.+++|.|||+||.+|+.|.++|||+|.|.++      ..|.|.+ +.+++++|+.+|+.++.
T Consensus       579 ~~~~~I~~~ki~~vIG~gGk~I~~i~~~tg~~Idi~d~------G~V~I~a~d~~~~~~A~~~I~~i~~  641 (719)
T TIGR02696       579 IITVKIPVDKIGEVIGPKGKMINQIQDETGAEISIEDD------GTVYIGAADGPSAEAARAMINAIAN  641 (719)
T ss_pred             eEEEEeChHHhhheeCCCcHhHHHHHHHHCCEEEEecC------cEEEEEeCCHHHHHHHHHHHHHhhC
Confidence            77899999999999999999999999999999999963      5588888 68999999999998875

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.

>PRK08406 transcription elongation factor NusA-like protein; Validated

Probab=97.92  E-value=2.6e-05  Score=70.08  Aligned_cols=101  Identities=21%  Similarity=0.318  Sum_probs=70.3

Q ss_pred             EEEEEEecCcccceeccCCchHHHHHHHhcCCeEEeeCCCCCCCceEEEEEccCCcccccccccccCCCCcccHHHHHHH
Q 006943           37 VIYRILCPDGVIGSVIGKSGKVINSIRQETRARVKVVDPFPGAKDRVVTIYSHVKDKEDVEVDDEFNDKEPLCAAQDALL  116 (624)
Q Consensus        37 ~~~~ilvp~~~~g~vIGk~G~~I~~i~~etg~~I~v~~~~~~~~er~i~I~G~~~~~~~~~~~~~~~~~~~~~~a~~ai~  116 (624)
                      -.+.++++...+|+.||++|++|+.|++..|-+|.|-+-           +   ++                      ..
T Consensus        32 ~~vi~vV~~~~vG~~IG~~G~rI~~i~e~lgekIdVve~-----------s---~d----------------------~~   75 (140)
T PRK08406         32 DRIIFVVKEGDMGLAIGKGGENVKRLEEKLGKDIELVEY-----------S---DD----------------------PE   75 (140)
T ss_pred             CEEEEEEeCCCccccCCcCchHHHHHHHHhCCceEEEEc-----------C---CC----------------------HH
Confidence            456788899999999999999999999999988887441           1   11                      01


Q ss_pred             HHHHHHHHhhhccC--CC-cccCCCceeEEEEEeccceeEEEeCCchHHHHHHHhcCCeEEEc
Q 006943          117 KVHAAIANAVANAT--DN-DKKRKEKEECQILVPSSQSANIIGKAGATIKRLRSKTRTSIKVT  176 (624)
Q Consensus       117 ~v~~~i~~~~~~~~--~~-~~~~~~~~~~~llvp~~~~g~iIGk~G~~Ik~I~~~sga~I~i~  176 (624)
                      ..   +.+.+....  +- ..+..+...+.+.|+...+|.+|||+|.+++.++.-++-.+.|.
T Consensus        76 ~f---I~n~l~Pa~V~~v~I~~~~~~~~~~V~V~~~d~g~aIGK~G~ni~la~~L~~~~~di~  135 (140)
T PRK08406         76 EF---IKNIFAPAAVRSVTIKKKNGDKVAYVEVAPEDKGIAIGKNGKNIERAKDLAKRHFDID  135 (140)
T ss_pred             HH---HHHHcCCCEEEEEEEEecCCcEEEEEEECccccchhhCCCCHHHHHHHHHhCCccCCe
Confidence            11   111111110  00 00112234566789999999999999999999999999888664

>PRK08406 transcription elongation factor NusA-like protein; Validated

Probab=97.85  E-value=3.1e-05  Score=69.53  Aligned_cols=101  Identities=21%  Similarity=0.323  Sum_probs=71.6

Q ss_pred             EEEEEecCCccceeeccCcchHHHHHhHhCCeEEEcCCCCCCCceEEEEeecCCchhHHHHHHHHHHHHhhc-c-CCCCC
Q 006943          309 VIRVLCPFNKIGRVIGKGGGTIKSIRQASGAQIDVDDTKDNRDECVITVTAIESPDDIKSMAVEAVLLLQTK-I-NDEDD  386 (624)
Q Consensus       309 ~~~i~vp~~~vg~IIGk~G~~Ik~I~~~tga~I~v~~~~~~~~er~i~I~G~~~~~~a~~~~~~~i~~~~~~-~-~~~~~  386 (624)
                      .+.|.|+...+|..||++|++|+.|++..|-+|.+-.-            .    ++....+..++.-..-. + -...+
T Consensus        33 ~vi~vV~~~~vG~~IG~~G~rI~~i~e~lgekIdVve~------------s----~d~~~fI~n~l~Pa~V~~v~I~~~~   96 (140)
T PRK08406         33 RIIFVVKEGDMGLAIGKGGENVKRLEEKLGKDIELVEY------------S----DDPEEFIKNIFAPAAVRSVTIKKKN   96 (140)
T ss_pred             EEEEEEeCCCccccCCcCchHHHHHHHHhCCceEEEEc------------C----CCHHHHHHHHcCCCEEEEEEEEecC
Confidence            56788899999999999999999999999888887321            1    12223333333211100 0 00122


Q ss_pred             CcEEEEEEecCCeeeEEEcCCCchHHHHHHhcCceEEEe
Q 006943          387 DTVTIRLLVSSKVIGCIIGKSGSIINEIRKRTKADVRIS  425 (624)
Q Consensus       387 ~~~~~~l~vp~~~~g~iIGk~G~~Ik~I~~~tga~I~i~  425 (624)
                      ....+.+.|+....|.+|||+|.+++.++.-+|-++.+.
T Consensus        97 ~~~~~~V~V~~~d~g~aIGK~G~ni~la~~L~~~~~di~  135 (140)
T PRK08406         97 GDKVAYVEVAPEDKGIAIGKNGKNIERAKDLAKRHFDID  135 (140)
T ss_pred             CcEEEEEEECccccchhhCCCCHHHHHHHHHhCCccCCe
Confidence            335677889999999999999999999999999877653

>TIGR02696 pppGpp_PNP guanosine pentaphosphate synthetase I/polynucleotide phosphorylase

Probab=97.80  E-value=9.2e-05  Score=82.74  Aligned_cols=94  Identities=23%  Similarity=0.341  Sum_probs=73.8

Q ss_pred             ccHHHHHHHHHHHHHHHhhhccCCCcccCCCceeEEEEEeccceeEEEeCCchHHHHHHHhcCCeEEEccCCCCCCCCcc
Q 006943          108 LCAAQDALLKVHAAIANAVANATDNDKKRKEKEECQILVPSSQSANIIGKAGATIKRLRSKTRTSIKVTPKDASEPTHSC  187 (624)
Q Consensus       108 ~~~a~~ai~~v~~~i~~~~~~~~~~~~~~~~~~~~~llvp~~~~g~iIGk~G~~Ik~I~~~sga~I~i~~~~~~~~~~~~  187 (624)
                      +..|++++.++++.+.+.+... . .....-.....+.||.+..+.|||++|++||.|.++|||+|.|..          
T Consensus       548 L~~A~~g~~~Il~~m~~al~~p-~-~~s~~aP~~~~~~I~~~ki~~vIG~gGk~I~~i~~~tg~~Idi~d----------  615 (719)
T TIGR02696       548 LKQARDARLAILDVMAEAIDTP-D-EMSPYAPRIITVKIPVDKIGEVIGPKGKMINQIQDETGAEISIED----------  615 (719)
T ss_pred             HHHHHHHHHHHHHHHHHHHhCc-c-ccccCCCeeEEEEeChHHhhheeCCCcHhHHHHHHHHCCEEEEec----------
Confidence            5567778888877776666654 2 112222345668999999999999999999999999999999853          


Q ss_pred             cccCCceEEEecC-HHHHHHHHHHHHHHHhh
Q 006943          188 AMEFDNFVLISGE-SEAVKKALFAISAIMYK  217 (624)
Q Consensus       188 ~~~~~r~V~I~G~-~~~V~~A~~~I~~~l~~  217 (624)
                          +..|.|.+. .+++.+|+.+|..++..
T Consensus       616 ----~G~V~I~a~d~~~~~~A~~~I~~i~~~  642 (719)
T TIGR02696       616 ----DGTVYIGAADGPSAEAARAMINAIANP  642 (719)
T ss_pred             ----CcEEEEEeCCHHHHHHHHHHHHHhhCc
Confidence                567899886 79999999999988853

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.

>KOG2113 consensus Predicted RNA binding protein, contains KH domain [General function prediction only]

Probab=97.73  E-value=5.3e-05  Score=74.09  Aligned_cols=141  Identities=30%  Similarity=0.372  Sum_probs=100.9

Q ss_pred             CceeEEEEEeccceeEEEeCCchHHHHHHHhcCCeEEEccCCCCCCCCcccccCCceEEEecCHHHHHHHHHHHHHHHhh
Q 006943          138 EKEECQILVPSSQSANIIGKAGATIKRLRSKTRTSIKVTPKDASEPTHSCAMEFDNFVLISGESEAVKKALFAISAIMYK  217 (624)
Q Consensus       138 ~~~~~~llvp~~~~g~iIGk~G~~Ik~I~~~sga~I~i~~~~~~~~~~~~~~~~~r~V~I~G~~~~V~~A~~~I~~~l~~  217 (624)
                      ..++..+.||..+++.+.|++|.+||.|+.+|...|.-+.+.           .+-+..++|..+.|..|++.|...-+-
T Consensus        24 ~nvt~sv~vps~~v~~ivg~qg~kikalr~KTqtyi~tPsr~-----------eePiF~vTg~~edv~~aRrei~saaeH   92 (394)
T KOG2113|consen   24 QNVTESVEVPSEHVAEIVGRQGCKIKALRAKTQTYIKTPSRG-----------EEPIFPVTGRHEDVRRARREIPSAAEH   92 (394)
T ss_pred             CccceeeecCcccceeecccCccccchhhhhhcceeccCCCC-----------CCCcceeccCchhHHHHhhcCccccce
Confidence            678999999999999999999999999999999999765432           345788999999999999877442211


Q ss_pred             cCCCCCCCCCCccCCCCCCccCCCCCCCCCCCCCCCCCCCCCCCCCCCCccCCCCCCCCCCCCCCCCCCCCCCCCCcccc
Q 006943          218 FSPREDIPLETTVREAPPSIIIPSDVPIYPPGGLYPNADPILPSRSVPSILGAARVPDLQGYADTGNTWPVYSTGLSLVS  297 (624)
Q Consensus       218 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~~~~~~~g~~~~p~~~~~~~~~~~~~~~~~~~p~~~  297 (624)
                      +.-      .    .+.                              ++     ...+..+|                  
T Consensus        93 ~~l------~----~~s------------------------------~s-----~Sgg~~~~------------------  109 (394)
T KOG2113|consen   93 FGL------I----RAS------------------------------RS-----FSGGTNGA------------------  109 (394)
T ss_pred             eee------e----eec------------------------------cc-----ccCCCccc------------------
Confidence            000      0    000                              00     00000000                  


Q ss_pred             CCCCCCCCccEEEEEEecCCccceeeccCcchHHHHHhHhCCeEEEcCCCCCCCceEEEEeec
Q 006943          298 GLVGASQSEELVIRVLCPFNKIGRVIGKGGGTIKSIRQASGAQIDVDDTKDNRDECVITVTAI  360 (624)
Q Consensus       298 ~~~~~~~~~~~~~~i~vp~~~vg~IIGk~G~~Ik~I~~~tga~I~v~~~~~~~~er~i~I~G~  360 (624)
                           ..+.+.+....+|...+|.|.|.+|.+|+.|++.++..|.-.-.   +.+.++.++|-
T Consensus       110 -----s~s~qt~sy~svP~rvvglvv~~~~~ti~~iqq~tnt~I~T~v~---~~~~Vf~Vtg~  164 (394)
T KOG2113|consen  110 -----SASGQTTSYVSVPLRVVGLVVGPKGATIKRIQQFTNTYIATPVR---CGEPVFCVTGA  164 (394)
T ss_pred             -----cccCCCceeeeccceeeeeccccccCccchheecccceEeeecc---CCCceEEEecC
Confidence                 11223455677899999999999999999999999999886532   35678899984

>TIGR03591 polynuc_phos polyribonucleotide nucleotidyltransferase

Probab=97.51  E-value=0.00032  Score=79.83  Aligned_cols=62  Identities=23%  Similarity=0.374  Sum_probs=54.4

Q ss_pred             EEEEEeccccccceeccCCchHHHHHHHhCCEEEEeCCCCCCCCeEEEEEc-CHHHHHHHHHHHHHHHh
Q 006943          555 TLEVLVPANAVGKVIGKAGSNLANIRKISGATIEMSDSKSSRGDRVALISG-TPEQKRAAENLIQAFIM  622 (624)
Q Consensus       555 ~~~i~VP~~~vg~IIGkgG~~I~~I~~~sGa~I~i~~~~~~~~~r~v~I~G-t~e~v~~A~~lI~~~i~  622 (624)
                      ..++.||.+.+|.|||+||.+|+.|.++|||+|.|.++      ..|.|.+ ..+.++.|+.+|+.+..
T Consensus       552 ~~~~~I~~~kI~~vIG~gGk~Ik~I~~~tg~~I~i~dd------G~V~i~~~~~~~~~~a~~~I~~~~~  614 (684)
T TIGR03591       552 IETIKINPDKIRDVIGPGGKVIREITEETGAKIDIEDD------GTVKIAASDGEAAEAAIKMIEGITA  614 (684)
T ss_pred             EEEEecCHHHHHhhcCCCcHHHHHHHHHHCCEEEEecC------eEEEEEECcHHHHHHHHHHHHhhhc
Confidence            77899999999999999999999999999999999863      4466666 67889999999988753

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 Splicing factor 1/branch point binding protein (RRM superfamily) [RNA processing and modification]

Probab=97.38  E-value=0.0015  Score=68.29  Aligned_cols=79  Identities=28%  Similarity=0.360  Sum_probs=58.3

Q ss_pred             ceeEEEEEec------cceeEEEeCCchHHHHHHHhcCCeEEEccCCCCCC-------CCcccccCCc-eEEEecC-HHH
Q 006943          139 KEECQILVPS------SQSANIIGKAGATIKRLRSKTRTSIKVTPKDASEP-------THSCAMEFDN-FVLISGE-SEA  203 (624)
Q Consensus       139 ~~~~~llvp~------~~~g~iIGk~G~~Ik~I~~~sga~I~i~~~~~~~~-------~~~~~~~~~r-~V~I~G~-~~~  203 (624)
                      .++-+|.||.      +++|+|||..|.|+|+|+++|||+|.|..+.....       +...+...|. -+.|+++ -++
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            5666777774      68999999999999999999999999998432110       1112222222 4667776 589


Q ss_pred             HHHHHHHHHHHHhh
Q 006943          204 VKKALFAISAIMYK  217 (624)
Q Consensus       204 V~~A~~~I~~~l~~  217 (624)
                      |.+|++.|..+|.+
T Consensus       217 i~~Ai~vienli~~  230 (554)
T KOG0119|consen  217 IKKAIAVIENLIQS  230 (554)
T ss_pred             HHHHHHHHHHHHHh
Confidence            99999999999975

>TIGR03591 polynuc_phos polyribonucleotide nucleotidyltransferase

Probab=97.31  E-value=0.00057  Score=77.80  Aligned_cols=93  Identities=18%  Similarity=0.269  Sum_probs=68.1

Q ss_pred             cHHHHHHHHHHHHHHHhhhccCCCcccCCCceeEEEEEeccceeEEEeCCchHHHHHHHhcCCeEEEccCCCCCCCCccc
Q 006943          109 CAAQDALLKVHAAIANAVANATDNDKKRKEKEECQILVPSSQSANIIGKAGATIKRLRSKTRTSIKVTPKDASEPTHSCA  188 (624)
Q Consensus       109 ~~a~~ai~~v~~~i~~~~~~~~~~~~~~~~~~~~~llvp~~~~g~iIGk~G~~Ik~I~~~sga~I~i~~~~~~~~~~~~~  188 (624)
                      ..|.++..++++.+.+.+....... ...-.....+.||.+.++.|||++|++||+|+++|||+|.|..           
T Consensus       521 ~~a~~~~~~I~~~m~~~l~~~~~~~-~~~~p~~~~~~I~~~kI~~vIG~gGk~Ik~I~~~tg~~I~i~d-----------  588 (684)
T TIGR03591       521 EQAKEGRLHILGEMNKVISEPRAEL-SPYAPRIETIKINPDKIRDVIGPGGKVIREITEETGAKIDIED-----------  588 (684)
T ss_pred             HHHHHHHHHHHHHHHHHHhhhhccc-cccCCeEEEEecCHHHHHhhcCCCcHHHHHHHHHHCCEEEEec-----------
Confidence            3455666666666665555432111 1112345668999999999999999999999999999999953           


Q ss_pred             ccCCceEEEecC-HHHHHHHHHHHHHHHh
Q 006943          189 MEFDNFVLISGE-SEAVKKALFAISAIMY  216 (624)
Q Consensus       189 ~~~~r~V~I~G~-~~~V~~A~~~I~~~l~  216 (624)
                         +..|.|.+. .+.+.+|+.+|..+..
T Consensus       589 ---dG~V~i~~~~~~~~~~a~~~I~~~~~  614 (684)
T TIGR03591       589 ---DGTVKIAASDGEAAEAAIKMIEGITA  614 (684)
T ss_pred             ---CeEEEEEECcHHHHHHHHHHHHhhhc
Confidence               456778775 6888999999888764

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).

>TIGR01952 nusA_arch NusA family KH domain protein, archaeal

Probab=97.26  E-value=0.0009  Score=59.95  Aligned_cols=100  Identities=18%  Similarity=0.343  Sum_probs=70.0

Q ss_pred             EEEEEecCCccceeeccCcchHHHHHhHhCCeEEEcCCCCCCCceEEEEeecCCchhHHHHHHHHHHH--Hhh-ccCCCC
Q 006943          309 VIRVLCPFNKIGRVIGKGGGTIKSIRQASGAQIDVDDTKDNRDECVITVTAIESPDDIKSMAVEAVLL--LQT-KINDED  385 (624)
Q Consensus       309 ~~~i~vp~~~vg~IIGk~G~~Ik~I~~~tga~I~v~~~~~~~~er~i~I~G~~~~~~a~~~~~~~i~~--~~~-~~~~~~  385 (624)
                      .+-|.|....+|..||++|++|+.|++..|=+|.+-.-..                +-...+..++.-  +.. .+.+ .
T Consensus        34 riifvV~~g~vG~~IG~~G~rIk~i~el~gekIdVVeys~----------------D~~~fI~N~l~PA~V~~V~i~~-~   96 (141)
T TIGR01952        34 RVVFVVKEGEMGAAIGKGGENVKRLEELIGKSIELIEYSE----------------NLEEFVANKLAPAEVKNVTVSE-F   96 (141)
T ss_pred             EEEEEEcCCCccccCCCCchHHHHHHHhcCCeeEEEEcCC----------------CHHHHHHHcCCCceEEEEEEEc-C
Confidence            6668899999999999999999999988888888732111                111112222210  111 0111 2


Q ss_pred             CCcEEEEEEecCCeeeEEEcCCCchHHHHHHhcCceEEEe
Q 006943          386 DDTVTIRLLVSSKVIGCIIGKSGSIINEIRKRTKADVRIS  425 (624)
Q Consensus       386 ~~~~~~~l~vp~~~~g~iIGk~G~~Ik~I~~~tga~I~i~  425 (624)
                      ++.....+.||....+..|||+|.+++...+-+|-++.+.
T Consensus        97 ~~~~~a~V~V~~~d~~~AIGk~G~Ni~la~~l~~~~~dI~  136 (141)
T TIGR01952        97 NGKKVAYVEVHPRDKGIAIGKGGKNIERAKELAKRHHDID  136 (141)
T ss_pred             CCCEEEEEEEChhhhhhhhCCCchhHHHHHHHhcCccCCe
Confidence            3346677899999999999999999999999998876653

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.

>TIGR01952 nusA_arch NusA family KH domain protein, archaeal

Probab=97.25  E-value=0.00063  Score=60.93  Aligned_cols=100  Identities=18%  Similarity=0.321  Sum_probs=69.6

Q ss_pred             EEEEEecCcccceeccCCchHHHHHHHhcCCeEEeeCCCCCCCceEEEEEccCCcccccccccccCCCCcccHHHHHHHH
Q 006943           38 IYRILCPDGVIGSVIGKSGKVINSIRQETRARVKVVDPFPGAKDRVVTIYSHVKDKEDVEVDDEFNDKEPLCAAQDALLK  117 (624)
Q Consensus        38 ~~~ilvp~~~~g~vIGk~G~~I~~i~~etg~~I~v~~~~~~~~er~i~I~G~~~~~~~~~~~~~~~~~~~~~~a~~ai~~  117 (624)
                      -+-+++....+|+.||++|++|+.|++..|=+|.|-+-           +..++                          
T Consensus        34 riifvV~~g~vG~~IG~~G~rIk~i~el~gekIdVVey-----------s~D~~--------------------------   76 (141)
T TIGR01952        34 RVVFVVKEGEMGAAIGKGGENVKRLEELIGKSIELIEY-----------SENLE--------------------------   76 (141)
T ss_pred             EEEEEEcCCCccccCCCCchHHHHHHHhcCCeeEEEEc-----------CCCHH--------------------------
Confidence            66778999999999999999999998888988887441           11110                          


Q ss_pred             HHHHHHHhhhccC--C-CcccCCCceeEEEEEeccceeEEEeCCchHHHHHHHhcCCeEEEc
Q 006943          118 VHAAIANAVANAT--D-NDKKRKEKEECQILVPSSQSANIIGKAGATIKRLRSKTRTSIKVT  176 (624)
Q Consensus       118 v~~~i~~~~~~~~--~-~~~~~~~~~~~~llvp~~~~g~iIGk~G~~Ik~I~~~sga~I~i~  176 (624)
                        +.+...+....  . ...+..+.....+.|+..+.+..|||+|.+++...+-++-++.|.
T Consensus        77 --~fI~N~l~PA~V~~V~i~~~~~~~~a~V~V~~~d~~~AIGk~G~Ni~la~~l~~~~~dI~  136 (141)
T TIGR01952        77 --EFVANKLAPAEVKNVTVSEFNGKKVAYVEVHPRDKGIAIGKGGKNIERAKELAKRHHDID  136 (141)
T ss_pred             --HHHHHcCCCceEEEEEEEcCCCCEEEEEEEChhhhhhhhCCCchhHHHHHHHhcCccCCe
Confidence              11111111110  0 000112345567889999999999999999999999999888664

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.

>KOG0336 consensus ATP-dependent RNA helicase [RNA processing and modification]

Probab=97.17  E-value=0.00081  Score=68.82  Aligned_cols=64  Identities=23%  Similarity=0.316  Sum_probs=56.5

Q ss_pred             EEEEEeccccccceeccCCchHHHHHHHhCCEEEEeCCCCCCCCeEEEEEcCHHHHHHHHHHHHHHH
Q 006943          555 TLEVLVPANAVGKVIGKAGSNLANIRKISGATIEMSDSKSSRGDRVALISGTPEQKRAAENLIQAFI  621 (624)
Q Consensus       555 ~~~i~VP~~~vg~IIGkgG~~I~~I~~~sGa~I~i~~~~~~~~~r~v~I~Gt~e~v~~A~~lI~~~i  621 (624)
                      ..-+.|-+++||.|||++|++|++||..|.++|+|.+.+   .+..|+|-|..+--.+|+.-|..++
T Consensus        48 plcf~iks~mvg~vigrggskik~iq~~tnt~iqii~~~---~e~kv~ifg~~~m~~kaka~id~~~  111 (629)
T KOG0336|consen   48 PLCFSIKSEMVGKVIGRGGSKIKRIQNDTNTRIQIIKCD---LEVKVTIFGINHMRKKAKASIDRGQ  111 (629)
T ss_pred             chhhhhhhhhhheeeccCcchhhhhhcccceeEEEeccC---ceeEEEEechHHHHHHHHhhHhhhh
Confidence            556778999999999999999999999999999999874   4678999999988888888887665

>PLN00207 polyribonucleotide nucleotidyltransferase; Provisional

Probab=97.13  E-value=0.00097  Score=76.43  Aligned_cols=62  Identities=19%  Similarity=0.318  Sum_probs=55.5

Q ss_pred             EEEEEeccccccceeccCCchHHHHHHHhCCE-EEEeCCCCCCCCeEEEEEc-CHHHHHHHHHHHHHHHh
Q 006943          555 TLEVLVPANAVGKVIGKAGSNLANIRKISGAT-IEMSDSKSSRGDRVALISG-TPEQKRAAENLIQAFIM  622 (624)
Q Consensus       555 ~~~i~VP~~~vg~IIGkgG~~I~~I~~~sGa~-I~i~~~~~~~~~r~v~I~G-t~e~v~~A~~lI~~~i~  622 (624)
                      ...+.||.++++.|||.||.+|+.|.++||+. |.|.++      -.|.|.+ +.+.++.|+.+|+++..
T Consensus       686 i~~~~i~~~ki~~vIG~GGktIk~I~eetg~~~Idi~dd------g~V~I~a~d~~~i~~A~~~I~~l~~  749 (891)
T PLN00207        686 IHIMKVKPEKVNMIIGSGGKKVKSIIEETGVEAIDTQDD------GTVKITAKDLSSLEKSKAIISSLTM  749 (891)
T ss_pred             eEEEEcCHHHHHHHhcCCchhHHHHHHHHCCCccCcCCC------eeEEEEeCCHHHHHHHHHHHHHHhc
Confidence            78899999999999999999999999999999 988863      4577877 68899999999998864

>KOG0336 consensus ATP-dependent RNA helicase [RNA processing and modification]

Probab=97.00  E-value=0.0013  Score=67.44  Aligned_cols=57  Identities=21%  Similarity=0.377  Sum_probs=50.2

Q ss_pred             CCCceEEEEEEecCcccceeccCCchHHHHHHHhcCCeEEeeCCCCCCCceEEEEEccCC
Q 006943           32 GNEESVIYRILCPDGVIGSVIGKSGKVINSIRQETRARVKVVDPFPGAKDRVVTIYSHVK   91 (624)
Q Consensus        32 ~~~~~~~~~ilvp~~~~g~vIGk~G~~I~~i~~etg~~I~v~~~~~~~~er~i~I~G~~~   91 (624)
                      .+.++.++.|.+-+.++|.|||++|++|+.|+..|+++|.+-.   ...+-.|+|.|...
T Consensus        42 ag~~e~plcf~iks~mvg~vigrggskik~iq~~tnt~iqii~---~~~e~kv~ifg~~~   98 (629)
T KOG0336|consen   42 AGGGEFPLCFSIKSEMVGKVIGRGGSKIKRIQNDTNTRIQIIK---CDLEVKVTIFGINH   98 (629)
T ss_pred             cCCCCCchhhhhhhhhhheeeccCcchhhhhhcccceeEEEec---cCceeEEEEechHH
Confidence            4667899999999999999999999999999999999999976   45677899988754

>KOG0119 consensus Splicing factor 1/branch point binding protein (RRM superfamily) [RNA processing and modification]

Probab=96.99  E-value=0.0017  Score=67.85  Aligned_cols=62  Identities=29%  Similarity=0.405  Sum_probs=49.5

Q ss_pred             cccccceeccCCchHHHHHHHhCCEEEEeCCCC---------------CC-CCeEEEEEc-CHHHHHHHHHHHHHHHhh
Q 006943          562 ANAVGKVIGKAGSNLANIRKISGATIEMSDSKS---------------SR-GDRVALISG-TPEQKRAAENLIQAFIMA  623 (624)
Q Consensus       562 ~~~vg~IIGkgG~~I~~I~~~sGa~I~i~~~~~---------------~~-~~r~v~I~G-t~e~v~~A~~lI~~~i~~  623 (624)
                      -++||+|||..|.+.|+|.++|||+|.|--...               .. .+=-+.|++ |.|.|++|..+|+.+|.+
T Consensus       152 ~NFvGLiiGPRG~TqK~lE~etgAKI~IRGkgSvkEgk~~~~d~~~~~~~~epLH~~Isadt~eki~~Ai~vienli~~  230 (554)
T KOG0119|consen  152 INFVGLIIGPRGNTQKRLERETGAKIAIRGKGSVKEGKGRSDDLSYIPKENEPLHCLISADTQEKIKKAIAVIENLIQS  230 (554)
T ss_pred             cceeEEEecCCccHHHHHHHHhCCeEEEeccccccccccCCcccccccccccceeEEEecchHHHHHHHHHHHHHHHHh
Confidence            478999999999999999999999999975210               11 112356777 788899999999999974

>KOG1588 consensus RNA-binding protein Sam68 and related KH domain proteins [RNA processing and modification]

Probab=96.97  E-value=0.0036  Score=60.87  Aligned_cols=77  Identities=17%  Similarity=0.346  Sum_probs=54.2

Q ss_pred             CccEEEEEEecCC------ccceeeccCcchHHHHHhHhCCeEEEcCCCC------------------CCCceEEEEeec
Q 006943          305 SEELVIRVLCPFN------KIGRVIGKGGGTIKSIRQASGAQIDVDDTKD------------------NRDECVITVTAI  360 (624)
Q Consensus       305 ~~~~~~~i~vp~~------~vg~IIGk~G~~Ik~I~~~tga~I~v~~~~~------------------~~~er~i~I~G~  360 (624)
                      ...++.+|+||.+      +||+|+|.+|.++|+|+++|||+|-|--...                  -+..-.|.|...
T Consensus        89 ~vk~~~Kv~vPv~~yP~fNFVGRILGPrGnSlkrLe~eTgCki~IrGrgSmrD~~KEE~lR~~p~yeHL~epLHVlIe~~  168 (259)
T KOG1588|consen   89 PVKLTEKVLVPVKEYPKFNFVGRILGPRGNSLKRLEEETGCKIMIRGRGSMRDKAKEEELRGDPGYEHLNEPLHVLIETE  168 (259)
T ss_pred             ceeEEEEEEeccCCCCCCccccccccCCcchHHHHHHHHCCeEEEecCCcccchHHHHHhhcCcchHHhCCCcEEEEEEe
Confidence            4567888999864      8999999999999999999999999942100                  012223444443


Q ss_pred             CCchhHHHHHHHHHHHHhhcc
Q 006943          361 ESPDDIKSMAVEAVLLLQTKI  381 (624)
Q Consensus       361 ~~~~~a~~~~~~~i~~~~~~~  381 (624)
                      .....|...+..|++.|...+
T Consensus       169 ~p~~ea~~rl~~AleeI~klL  189 (259)
T KOG1588|consen  169 APPAEAYARLAYALEEIKKLL  189 (259)
T ss_pred             CCHHHHHHHHHHHHHHHHHhc
Confidence            334567677778888777544

>COG0195 NusA Transcription elongation factor [Transcription]

Probab=96.93  E-value=0.0017  Score=61.29  Aligned_cols=101  Identities=24%  Similarity=0.355  Sum_probs=70.4

Q ss_pred             EEEEEecCCccceeeccCcchHHHHHhHhCCeEEEcCCCCCCCceEEEEeecCCchhHHHHHHHHHHH--HhhccCCCCC
Q 006943          309 VIRVLCPFNKIGRVIGKGGGTIKSIRQASGAQIDVDDTKDNRDECVITVTAIESPDDIKSMAVEAVLL--LQTKINDEDD  386 (624)
Q Consensus       309 ~~~i~vp~~~vg~IIGk~G~~Ik~I~~~tga~I~v~~~~~~~~er~i~I~G~~~~~~a~~~~~~~i~~--~~~~~~~~~~  386 (624)
                      .+.+.+-.+.+|..||++|++|+.|+++.|=+|.|-.            .+ +   +....+..++.-  +..-.....+
T Consensus        77 v~~~~~~~d~vG~~iG~~G~rvk~i~~eLgekIdVVe------------~s-~---d~~~fI~nal~Pa~v~~V~~~~~d  140 (190)
T COG0195          77 VVSNVVKIDPVGACIGKRGSRVKAVSEELGEKIDVVE------------WS-E---DPAEFIKNALAPAEVLSVNIKEDD  140 (190)
T ss_pred             eEEeecCcCchhhhccCCChHHHHHHHHhCCceEEEE------------eC-C---CHHHHHHHhcCcceEeEEEEEeCC
Confidence            4455667788899999999999999999996676622            11 1   112223344331  1100001112


Q ss_pred             CcEEEEEEecCCeeeEEEcCCCchHHHHHHhcCceEEEeC
Q 006943          387 DTVTIRLLVSSKVIGCIIGKSGSIINEIRKRTKADVRISK  426 (624)
Q Consensus       387 ~~~~~~l~vp~~~~g~iIGk~G~~Ik~I~~~tga~I~i~~  426 (624)
                      +. ...+.||....+.+|||+|.+++-+.+-||-++.|..
T Consensus       141 ~~-~~~v~V~~~~~~~aIGk~G~Nvrla~~Ltg~~i~I~~  179 (190)
T COG0195         141 GH-VAIVVVPPDQLSLAIGKGGQNVRLASQLTGWEIDIET  179 (190)
T ss_pred             Cc-EEEEEECHHHHhhccCcccHHHHHHHHHhCCEEEEEe
Confidence            22 6778899999999999999999999999999999864

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

Probab=96.87  E-value=0.0031  Score=69.23  Aligned_cols=62  Identities=21%  Similarity=0.384  Sum_probs=54.9

Q ss_pred             EEEEEeccccccceeccCCchHHHHHHHhCCEEEEeCCCCCCCCeEEEEEcCH-HHHHHHHHHHHHHHh
Q 006943          555 TLEVLVPANAVGKVIGKAGSNLANIRKISGATIEMSDSKSSRGDRVALISGTP-EQKRAAENLIQAFIM  622 (624)
Q Consensus       555 ~~~i~VP~~~vg~IIGkgG~~I~~I~~~sGa~I~i~~~~~~~~~r~v~I~Gt~-e~v~~A~~lI~~~i~  622 (624)
                      ..++.|+.+.++-|||++|.+|++|.++|||+|.|.++      -.|.|.++. +.+..|+.+|.++..
T Consensus       553 i~t~~i~~dKI~dvIG~gGk~I~~I~eetg~~Idiedd------Gtv~i~~s~~~~~~~ak~~I~~i~~  615 (692)
T COG1185         553 IETIKIDPDKIRDVIGPGGKTIKAITEETGVKIDIEDD------GTVKIAASDGESAKKAKERIEAITR  615 (692)
T ss_pred             eEEEccCHHHHhhccCCcccchhhhhhhhCcEEEecCC------CcEEEEecchHHHHHHHHHHHHHHh
Confidence            67899999999999999999999999999999999943      338888865 778999999998764

>KOG1588 consensus RNA-binding protein Sam68 and related KH domain proteins [RNA processing and modification]

Probab=96.86  E-value=0.0038  Score=60.72  Aligned_cols=81  Identities=19%  Similarity=0.238  Sum_probs=56.1

Q ss_pred             ceeEEEEEecc------ceeEEEeCCchHHHHHHHhcCCeEEEccCCCCCC---------CCcccccCCc---eEEEecC
Q 006943          139 KEECQILVPSS------QSANIIGKAGATIKRLRSKTRTSIKVTPKDASEP---------THSCAMEFDN---FVLISGE  200 (624)
Q Consensus       139 ~~~~~llvp~~------~~g~iIGk~G~~Ik~I~~~sga~I~i~~~~~~~~---------~~~~~~~~~r---~V~I~G~  200 (624)
                      ..+.+++||-.      ++|.|+|++|.++|+|+++|||+|.|..+..-..         -+.+++-++.   .|+..++
T Consensus        91 k~~~Kv~vPv~~yP~fNFVGRILGPrGnSlkrLe~eTgCki~IrGrgSmrD~~KEE~lR~~p~yeHL~epLHVlIe~~~p  170 (259)
T KOG1588|consen   91 KLTEKVLVPVKEYPKFNFVGRILGPRGNSLKRLEEETGCKIMIRGRGSMRDKAKEEELRGDPGYEHLNEPLHVLIETEAP  170 (259)
T ss_pred             eEEEEEEeccCCCCCCccccccccCCcchHHHHHHHHCCeEEEecCCcccchHHHHHhhcCcchHHhCCCcEEEEEEeCC
Confidence            46678899875      8999999999999999999999999998643211         1122222222   3556666


Q ss_pred             HHH----HHHHHHHHHHHHhhcC
Q 006943          201 SEA----VKKALFAISAIMYKFS  219 (624)
Q Consensus       201 ~~~----V~~A~~~I~~~l~~~~  219 (624)
                      +.-    +..|+..|..+|.-..
T Consensus       171 ~~ea~~rl~~AleeI~klL~P~~  193 (259)
T KOG1588|consen  171 PAEAYARLAYALEEIKKLLVPDH  193 (259)
T ss_pred             HHHHHHHHHHHHHHHHHhcCCCC
Confidence            543    3468888888875433

>COG0195 NusA Transcription elongation factor [Transcription]

Probab=96.73  E-value=0.0039  Score=58.80  Aligned_cols=100  Identities=26%  Similarity=0.364  Sum_probs=69.0

Q ss_pred             EEEEEecCcccceeccCCchHHHHHHHhcCCeEEeeCCCCCCCceEEEEEccCCcccccccccccCCCCcccHHHHHHHH
Q 006943           38 IYRILCPDGVIGSVIGKSGKVINSIRQETRARVKVVDPFPGAKDRVVTIYSHVKDKEDVEVDDEFNDKEPLCAAQDALLK  117 (624)
Q Consensus        38 ~~~ilvp~~~~g~vIGk~G~~I~~i~~etg~~I~v~~~~~~~~er~i~I~G~~~~~~~~~~~~~~~~~~~~~~a~~ai~~  117 (624)
                      .+-+.+-.+.+|..||++|++|+.|.++.|=+|.|-+-           +   ++                 ++      
T Consensus        77 v~~~~~~~d~vG~~iG~~G~rvk~i~~eLgekIdVVe~-----------s---~d-----------------~~------  119 (190)
T COG0195          77 VVSNVVKIDPVGACIGKRGSRVKAVSEELGEKIDVVEW-----------S---ED-----------------PA------  119 (190)
T ss_pred             eEEeecCcCchhhhccCCChHHHHHHHHhCCceEEEEe-----------C---CC-----------------HH------
Confidence            45556666789999999999999999999988877432           1   11                 00      


Q ss_pred             HHHHHHHhhhccC--C-CcccCCCceeEEEEEeccceeEEEeCCchHHHHHHHhcCCeEEEcc
Q 006943          118 VHAAIANAVANAT--D-NDKKRKEKEECQILVPSSQSANIIGKAGATIKRLRSKTRTSIKVTP  177 (624)
Q Consensus       118 v~~~i~~~~~~~~--~-~~~~~~~~~~~~llvp~~~~g~iIGk~G~~Ik~I~~~sga~I~i~~  177 (624)
                        +.+.+.+....  . .....++. ...+.||+++.+..|||+|.+++-+.+-||-++.|..
T Consensus       120 --~fI~nal~Pa~v~~V~~~~~d~~-~~~v~V~~~~~~~aIGk~G~Nvrla~~Ltg~~i~I~~  179 (190)
T COG0195         120 --EFIKNALAPAEVLSVNIKEDDGH-VAIVVVPPDQLSLAIGKGGQNVRLASQLTGWEIDIET  179 (190)
T ss_pred             --HHHHHhcCcceEeEEEEEeCCCc-EEEEEECHHHHhhccCcccHHHHHHHHHhCCEEEEEe
Confidence              11111111100  0 00001122 6778899999999999999999999999999999975

>PLN00207 polyribonucleotide nucleotidyltransferase; Provisional

Probab=96.71  E-value=0.0026  Score=72.98  Aligned_cols=94  Identities=19%  Similarity=0.220  Sum_probs=68.5

Q ss_pred             ccHHHHHHHHHHHHHHHhhhccCCCcccCCCceeEEEEEeccceeEEEeCCchHHHHHHHhcCCe-EEEccCCCCCCCCc
Q 006943          108 LCAAQDALLKVHAAIANAVANATDNDKKRKEKEECQILVPSSQSANIIGKAGATIKRLRSKTRTS-IKVTPKDASEPTHS  186 (624)
Q Consensus       108 ~~~a~~ai~~v~~~i~~~~~~~~~~~~~~~~~~~~~llvp~~~~g~iIGk~G~~Ik~I~~~sga~-I~i~~~~~~~~~~~  186 (624)
                      +..|.+++..+++.+.+.+...-.. ....-.....+.||.+.++.|||++|.+||.|.++||++ |.+.          
T Consensus       654 L~~A~~g~~~Il~~M~~~i~~pr~~-~s~~aP~i~~~~i~~~ki~~vIG~GGktIk~I~eetg~~~Idi~----------  722 (891)
T PLN00207        654 LLQAKDGRKHILAEMSKCSPPPSKR-LSKYAPLIHIMKVKPEKVNMIIGSGGKKVKSIIEETGVEAIDTQ----------  722 (891)
T ss_pred             HHHHHHHHHHHHHHHHHHHhhhhhh-hcccCCeeEEEEcCHHHHHHHhcCCchhHHHHHHHHCCCccCcC----------
Confidence            3455666666666655544432111 111223556789999999999999999999999999999 8764          


Q ss_pred             ccccCCceEEEecC-HHHHHHHHHHHHHHHh
Q 006943          187 CAMEFDNFVLISGE-SEAVKKALFAISAIMY  216 (624)
Q Consensus       187 ~~~~~~r~V~I~G~-~~~V~~A~~~I~~~l~  216 (624)
                          ++-.|.|.+. .+++.+|+.+|..+..
T Consensus       723 ----ddg~V~I~a~d~~~i~~A~~~I~~l~~  749 (891)
T PLN00207        723 ----DDGTVKITAKDLSSLEKSKAIISSLTM  749 (891)
T ss_pred             ----CCeeEEEEeCCHHHHHHHHHHHHHHhc
Confidence                3566888885 7999999999988874

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

Probab=96.58  E-value=0.0031  Score=48.02  Aligned_cols=36  Identities=33%  Similarity=0.585  Sum_probs=33.8

Q ss_pred             cEEEEEeccccccceeccCCchHHHHHHHhCCEEEE
Q 006943          554 LTLEVLVPANAVGKVIGKAGSNLANIRKISGATIEM  589 (624)
Q Consensus       554 ~~~~i~VP~~~vg~IIGkgG~~I~~I~~~sGa~I~i  589 (624)
                      ....+.||++..|.+|||+|.||+.+++.+|-+|.|
T Consensus        25 ~~~~v~V~~~~~~~aIGk~G~nI~~~~~l~~~~I~v   60 (61)
T cd02134          25 KRARVVVPDDQLGLAIGKGGQNVRLASKLLGEKIDI   60 (61)
T ss_pred             cEEEEEECcccceeeECCCCHHHHHHHHHHCCCeEE
Confidence            488999999999999999999999999999988876

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.

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

Probab=96.51  E-value=0.0065  Score=66.79  Aligned_cols=98  Identities=24%  Similarity=0.283  Sum_probs=73.2

Q ss_pred             ccHHHHHHHHHHHHHHHhhhccCCCcccCCCceeEEEEEeccceeEEEeCCchHHHHHHHhcCCeEEEccCCCCCCCCcc
Q 006943          108 LCAAQDALLKVHAAIANAVANATDNDKKRKEKEECQILVPSSQSANIIGKAGATIKRLRSKTRTSIKVTPKDASEPTHSC  187 (624)
Q Consensus       108 ~~~a~~ai~~v~~~i~~~~~~~~~~~~~~~~~~~~~llvp~~~~g~iIGk~G~~Ik~I~~~sga~I~i~~~~~~~~~~~~  187 (624)
                      +.+|.+|-++++..+.+.+...- .+......-...+-|+.....-+||++|.+|++|.++|||+|.+.           
T Consensus       521 L~QAk~aRlhIL~~M~~ai~~pr-~els~~aPri~t~~i~~dKI~dvIG~gGk~I~~I~eetg~~Idie-----------  588 (692)
T COG1185         521 LEQAKGARLHILIVMNEAISEPR-KELSPYAPRIETIKIDPDKIRDVIGPGGKTIKAITEETGVKIDIE-----------  588 (692)
T ss_pred             HHHHHHHHHHHHHHHHHHHhhhh-hhhhccCCceEEEccCHHHHhhccCCcccchhhhhhhhCcEEEec-----------
Confidence            45666777777776666655431 111122233456789999999999999999999999999999996           


Q ss_pred             cccCCceEEEecCH-HHHHHHHHHHHHHHhhcCC
Q 006943          188 AMEFDNFVLISGES-EAVKKALFAISAIMYKFSP  220 (624)
Q Consensus       188 ~~~~~r~V~I~G~~-~~V~~A~~~I~~~l~~~~~  220 (624)
                         ++..|.|.+.. +.+.+|+..|..+.++...
T Consensus       589 ---ddGtv~i~~s~~~~~~~ak~~I~~i~~e~ev  619 (692)
T COG1185         589 ---DDGTVKIAASDGESAKKAKERIEAITREVEV  619 (692)
T ss_pred             ---CCCcEEEEecchHHHHHHHHHHHHHHhhccc
Confidence               25669999986 8889999999999976543

>KOG2814 consensus Transcription coactivator complex, P50 component (LigT RNA ligase/phosphodiesterase family) [Transcription]

Probab=96.40  E-value=0.0042  Score=62.09  Aligned_cols=68  Identities=19%  Similarity=0.263  Sum_probs=57.6

Q ss_pred             cEEEEEeccccccceeccCCchHHHHHHHhCCEEEEeCCCCCCCCeEEEEEc-CHHHHHHHHHHHHHHHhh
Q 006943          554 LTLEVLVPANAVGKVIGKAGSNLANIRKISGATIEMSDSKSSRGDRVALISG-TPEQKRAAENLIQAFIMA  623 (624)
Q Consensus       554 ~~~~i~VP~~~vg~IIGkgG~~I~~I~~~sGa~I~i~~~~~~~~~r~v~I~G-t~e~v~~A~~lI~~~i~~  623 (624)
                      ....+.|++.++|.|||+.|.+.+.|+++|+++|.++.+.+.  ...|+|+| ..++|.+|...|.-+|.+
T Consensus        57 ~~~si~v~s~~~~~lig~~g~trkkle~Etq~~i~lp~p~~n--~~~i~i~~~~~~~V~~a~~Ri~~~ids  125 (345)
T KOG2814|consen   57 FSSSILVRSSFIGWLIGKQGKTRKKLEEETQTNIFLPRPNTN--KEEIKIIGISRNCVIQALERIAKLIDS  125 (345)
T ss_pred             chhhhhhhHHHhhhhhcccchHHHHHHHhhccceEccCCCCC--cceEEEeehhHHHHHHHHHHHHHHHHh
Confidence            467789999999999999999999999999999999988533  33455555 789999999999888764

>KOG2814 consensus Transcription coactivator complex, P50 component (LigT RNA ligase/phosphodiesterase family) [Transcription]

Probab=96.36  E-value=0.0042  Score=62.12  Aligned_cols=72  Identities=28%  Similarity=0.289  Sum_probs=57.3

Q ss_pred             ceeEEEEEeccceeEEEeCCchHHHHHHHhcCCeEEEccCCCCCCCCcccccCCceEEEecCHHHHHHHHHHHHHHHhhc
Q 006943          139 KEECQILVPSSQSANIIGKAGATIKRLRSKTRTSIKVTPKDASEPTHSCAMEFDNFVLISGESEAVKKALFAISAIMYKF  218 (624)
Q Consensus       139 ~~~~~llvp~~~~g~iIGk~G~~Ik~I~~~sga~I~i~~~~~~~~~~~~~~~~~r~V~I~G~~~~V~~A~~~I~~~l~~~  218 (624)
                      .....++|+++..++|||++|.|.++|+++|+|+|.++....         ..+.++.+.+..++|.+|...|..+|.++
T Consensus        56 ~~~~si~v~s~~~~~lig~~g~trkkle~Etq~~i~lp~p~~---------n~~~i~i~~~~~~~V~~a~~Ri~~~ids~  126 (345)
T KOG2814|consen   56 DFSSSILVRSSFIGWLIGKQGKTRKKLEEETQTNIFLPRPNT---------NKEEIKIIGISRNCVIQALERIAKLIDSD  126 (345)
T ss_pred             cchhhhhhhHHHhhhhhcccchHHHHHHHhhccceEccCCCC---------CcceEEEeehhHHHHHHHHHHHHHHHHhh
Confidence            355678999999999999999999999999999998875321         23344444455799999999999888654


Q ss_pred             C
Q 006943          219 S  219 (624)
Q Consensus       219 ~  219 (624)
                      .
T Consensus       127 r  127 (345)
T KOG2814|consen  127 R  127 (345)
T ss_pred             h
Confidence            4

>PRK00106 hypothetical protein; Provisional

Probab=96.36  E-value=0.0094  Score=65.28  Aligned_cols=65  Identities=25%  Similarity=0.539  Sum_probs=55.8

Q ss_pred             CcEEEEEecc-ccccceeccCCchHHHHHHHhCCEEEEeCCCCCCCCeEEEEEc-CHHHHHHHHHHHHHHHh
Q 006943          553 PLTLEVLVPA-NAVGKVIGKAGSNLANIRKISGATIEMSDSKSSRGDRVALISG-TPEQKRAAENLIQAFIM  622 (624)
Q Consensus       553 ~~~~~i~VP~-~~vg~IIGkgG~~I~~I~~~sGa~I~i~~~~~~~~~r~v~I~G-t~e~v~~A~~lI~~~i~  622 (624)
                      .++..|.+|+ ++-|+||||.|.||+.+...||++|.|++.+     ..|+||| .|---+.|+.-++.+|.
T Consensus       224 ~tvs~v~lp~demkGriIGreGrNir~~E~~tGvdliiddtp-----~~v~lS~fdpvRReiAr~~le~Li~  290 (535)
T PRK00106        224 QTITTVHLPDDNMKGRIIGREGRNIRTLESLTGIDVIIDDTP-----EVVVLSGFDPIRREIARMTLESLIK  290 (535)
T ss_pred             heeeeEEcCChHhhcceeCCCcchHHHHHHHhCceEEEcCCC-----CeEEEeCCChHHHHHHHHHHHHHHH
Confidence            3477889999 5559999999999999999999999999753     4588999 88888999988888775

>TIGR03319 YmdA_YtgF conserved hypothetical protein YmdA/YtgF

Probab=96.33  E-value=0.0086  Score=65.92  Aligned_cols=65  Identities=22%  Similarity=0.503  Sum_probs=55.5

Q ss_pred             CcEEEEEeccc-cccceeccCCchHHHHHHHhCCEEEEeCCCCCCCCeEEEEEc-CHHHHHHHHHHHHHHHh
Q 006943          553 PLTLEVLVPAN-AVGKVIGKAGSNLANIRKISGATIEMSDSKSSRGDRVALISG-TPEQKRAAENLIQAFIM  622 (624)
Q Consensus       553 ~~~~~i~VP~~-~vg~IIGkgG~~I~~I~~~sGa~I~i~~~~~~~~~r~v~I~G-t~e~v~~A~~lI~~~i~  622 (624)
                      .++..|.+|++ +-|+||||.|.||+.+...||++|.|++.+     ..|+||| .|---+.|+.-|+.+|.
T Consensus       203 ~~~~~v~lp~d~~kgriigreGrnir~~e~~tgvd~iiddtp-----~~v~ls~fdp~rreia~~~l~~li~  269 (514)
T TIGR03319       203 TTVSVVNLPNDEMKGRIIGREGRNIRALETLTGVDLIIDDTP-----EAVILSGFDPVRREIARMALEKLIQ  269 (514)
T ss_pred             heeeeEEcCChhhhccccCCCcchHHHHHHHhCceEEEcCCC-----CeEEecCCchHHHHHHHHHHHHHHH
Confidence            35778899994 559999999999999999999999999753     4588999 78888999988888775

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

Probab=96.33  E-value=0.0054  Score=46.71  Aligned_cols=37  Identities=22%  Similarity=0.434  Sum_probs=34.2

Q ss_pred             eEEEEEEecCcccceeccCCchHHHHHHHhcCCeEEe
Q 006943           36 SVIYRILCPDGVIGSVIGKSGKVINSIRQETRARVKV   72 (624)
Q Consensus        36 ~~~~~ilvp~~~~g~vIGk~G~~I~~i~~etg~~I~v   72 (624)
                      ...+.+.||.+..|.+|||+|.+|+.+++.++-+|.|
T Consensus        24 ~~~~~v~V~~~~~~~aIGk~G~nI~~~~~l~~~~I~v   60 (61)
T cd02134          24 EKRARVVVPDDQLGLAIGKGGQNVRLASKLLGEKIDI   60 (61)
T ss_pred             CcEEEEEECcccceeeECCCCHHHHHHHHHHCCCeEE
Confidence            3688999999999999999999999999999988876

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.

>PRK04163 exosome complex RNA-binding protein Rrp4; Provisional

Probab=96.28  E-value=0.0085  Score=59.17  Aligned_cols=60  Identities=25%  Similarity=0.325  Sum_probs=52.3

Q ss_pred             EEEEEeccccccceeccCCchHHHHHHHhCCEEEEeCCCCCCCCeEEEEEcC-HHHHHHHHHHHHHH
Q 006943          555 TLEVLVPANAVGKVIGKAGSNLANIRKISGATIEMSDSKSSRGDRVALISGT-PEQKRAAENLIQAF  620 (624)
Q Consensus       555 ~~~i~VP~~~vg~IIGkgG~~I~~I~~~sGa~I~i~~~~~~~~~r~v~I~Gt-~e~v~~A~~lI~~~  620 (624)
                      -+.+.||.++++.+||++|.+|+.|.+.+++.|.|...      -.|.|+++ .+++++|+.+|+.+
T Consensus       146 G~~~~V~~~~i~~lig~~g~~i~~l~~~~~~~I~ig~N------G~VwI~~~~~~~~~~a~~~I~~~  206 (235)
T PRK04163        146 GTIVEIKPVKVPRVIGKKGSMINMLKEETGCDIIVGQN------GRIWIKGPDEEDEEIAIEAIKKI  206 (235)
T ss_pred             CEEEEECHHHHHhhcCCCChhHhhhhhhhCcEEEEcCC------cEEEEeeCCHHHHHHHHHHHHHH
Confidence            36789999999999999999999999999999999854      44888885 66889999999865

>PRK12704 phosphodiesterase; Provisional

Probab=96.27  E-value=0.011  Score=65.25  Aligned_cols=65  Identities=20%  Similarity=0.483  Sum_probs=53.6

Q ss_pred             CcEEEEEecc-ccccceeccCCchHHHHHHHhCCEEEEeCCCCCCCCeEEEEEc-CHHHHHHHHHHHHHHHh
Q 006943          553 PLTLEVLVPA-NAVGKVIGKAGSNLANIRKISGATIEMSDSKSSRGDRVALISG-TPEQKRAAENLIQAFIM  622 (624)
Q Consensus       553 ~~~~~i~VP~-~~vg~IIGkgG~~I~~I~~~sGa~I~i~~~~~~~~~r~v~I~G-t~e~v~~A~~lI~~~i~  622 (624)
                      .++..|.+|+ ++-|+||||.|.||+.+...||++|.|++.+     ..|+||| .|---+.|+.-++.++.
T Consensus       209 ~~~~~v~lp~d~mkgriigreGrnir~~e~~tgvd~iiddtp-----~~v~ls~~~~~rre~a~~~l~~l~~  275 (520)
T PRK12704        209 TTVSVVNLPNDEMKGRIIGREGRNIRALETLTGVDLIIDDTP-----EAVILSGFDPIRREIARLALEKLVQ  275 (520)
T ss_pred             hceeeeecCCchhhcceeCCCcchHHHHHHHhCCeEEEcCCC-----CeEEEecCChhhHHHHHHHHHHHHh
Confidence            3467788998 4559999999999999999999999999753     4588999 77777788877777654

>PRK11824 polynucleotide phosphorylase/polyadenylase; Provisional

Probab=96.26  E-value=0.0074  Score=69.06  Aligned_cols=62  Identities=24%  Similarity=0.429  Sum_probs=53.2

Q ss_pred             EEEEEeccccccceeccCCchHHHHHHHhCCEEEEeCCCCCCCCeEEEEEc-CHHHHHHHHHHHHHHHh
Q 006943          555 TLEVLVPANAVGKVIGKAGSNLANIRKISGATIEMSDSKSSRGDRVALISG-TPEQKRAAENLIQAFIM  622 (624)
Q Consensus       555 ~~~i~VP~~~vg~IIGkgG~~I~~I~~~sGa~I~i~~~~~~~~~r~v~I~G-t~e~v~~A~~lI~~~i~  622 (624)
                      ...+.||.+.++.+||.||.+|+.|.++||+.|.+.++      -.|.|.+ ..+.++.|+.+|+.+..
T Consensus       555 ~~~~~I~~~kI~~vIG~gg~~ik~I~~~~~~~idi~d~------G~v~i~~~~~~~~~~a~~~I~~~~~  617 (693)
T PRK11824        555 IETIKIPPDKIRDVIGPGGKTIREITEETGAKIDIEDD------GTVKIAATDGEAAEAAKERIEGITA  617 (693)
T ss_pred             heeecCCHHHHHHHhcCCchhHHHHHHHHCCccccCCC------ceEEEEcccHHHHHHHHHHHHHhcc
Confidence            56778899999999999999999999999998887542      4488888 68889999999998753

>PF14611 SLS: Mitochondrial inner-membrane-bound regulator

Probab=96.16  E-value=0.25  Score=48.02  Aligned_cols=63  Identities=13%  Similarity=0.269  Sum_probs=50.6

Q ss_pred             EEEEecCCeeeEEEcCCCchHHHHHHhcCceEEEeCCCCCCCCCCCCcEEEEEeehHHHHHHHHHHHHHHhh
Q 006943          391 IRLLVSSKVIGCIIGKSGSIINEIRKRTKADVRISKGDKPKCADANDELVEVVGEVGSVRDALVQIILRLRD  462 (624)
Q Consensus       391 ~~l~vp~~~~g~iIGk~G~~Ik~I~~~tga~I~i~~~~~p~~~~~~~~~v~I~G~~~~v~~A~~~I~~~l~e  462 (624)
                      +.+.++....-.++..+|..+++|....||+|.+..         .+..+.|+|+...+..+...|.+.+..
T Consensus        28 l~v~l~~~~~~LLl~~~~~~L~~l~~~~~~~I~~~~---------~~~~i~I~g~k~~~~~i~~~i~~~l~~   90 (210)
T PF14611_consen   28 LDVWLQPDEFFLLLTGNGRILENLAARNGAKIEVSR---------SENRIRITGTKSTAEYIEASINEILSN   90 (210)
T ss_pred             eEEEecchheeeeecCCchHHHHHHHhcCceEEEec---------CCcEEEEEccHHHHHHHHHHHHHHHhh
Confidence            445566888899999999999999888999999975         245688999998888887766655543

>PRK11824 polynucleotide phosphorylase/polyadenylase; Provisional

Probab=95.86  E-value=0.012  Score=67.39  Aligned_cols=95  Identities=22%  Similarity=0.294  Sum_probs=67.7

Q ss_pred             ccHHHHHHHHHHHHHHHhhhccCCCcccCCCceeEEEEEeccceeEEEeCCchHHHHHHHhcCCeEEEccCCCCCCCCcc
Q 006943          108 LCAAQDALLKVHAAIANAVANATDNDKKRKEKEECQILVPSSQSANIIGKAGATIKRLRSKTRTSIKVTPKDASEPTHSC  187 (624)
Q Consensus       108 ~~~a~~ai~~v~~~i~~~~~~~~~~~~~~~~~~~~~llvp~~~~g~iIGk~G~~Ik~I~~~sga~I~i~~~~~~~~~~~~  187 (624)
                      +..|.++..++++.+.+.+...-.... ........+.|+.+.++.+||++|.+||+|.++||++|.+.           
T Consensus       523 l~~a~~g~~~I~~~M~~aI~~~r~~~~-~~ap~~~~~~I~~~kI~~vIG~gg~~ik~I~~~~~~~idi~-----------  590 (693)
T PRK11824        523 LEQAKEGRLHILGKMNEAISEPRAELS-PYAPRIETIKIPPDKIRDVIGPGGKTIREITEETGAKIDIE-----------  590 (693)
T ss_pred             HHHHHHHHHHHHHHHHHHhcCChhhhc-ccCchheeecCCHHHHHHHhcCCchhHHHHHHHHCCccccC-----------
Confidence            335667777777776665543211111 11123345667999999999999999999999999988763           


Q ss_pred             cccCCceEEEecC-HHHHHHHHHHHHHHHhh
Q 006943          188 AMEFDNFVLISGE-SEAVKKALFAISAIMYK  217 (624)
Q Consensus       188 ~~~~~r~V~I~G~-~~~V~~A~~~I~~~l~~  217 (624)
                         ++..|.|.+. .+++.+|+.+|..+..+
T Consensus       591 ---d~G~v~i~~~~~~~~~~a~~~I~~~~~~  618 (693)
T PRK11824        591 ---DDGTVKIAATDGEAAEAAKERIEGITAE  618 (693)
T ss_pred             ---CCceEEEEcccHHHHHHHHHHHHHhccc
Confidence               3566888885 78999999999887743

>PRK12328 nusA transcription elongation factor NusA; Provisional

Probab=95.84  E-value=0.017  Score=59.92  Aligned_cols=94  Identities=24%  Similarity=0.300  Sum_probs=64.8

Q ss_pred             cccceeccCCchHHHHHHHhc-CCeEEeeCCCCCCCceEEEEEccCCcccccccccccCCCCcccHHHHHHHHHHHHHHH
Q 006943           46 GVIGSVIGKSGKVINSIRQET-RARVKVVDPFPGAKDRVVTIYSHVKDKEDVEVDDEFNDKEPLCAAQDALLKVHAAIAN  124 (624)
Q Consensus        46 ~~~g~vIGk~G~~I~~i~~et-g~~I~v~~~~~~~~er~i~I~G~~~~~~~~~~~~~~~~~~~~~~a~~ai~~v~~~i~~  124 (624)
                      +-+|+.||++|.+|+.|.++. |=+|.|-+-..              +                         ..+.+..
T Consensus       251 DPvGacIG~~G~rI~~I~~eL~gEkIDvI~~s~--------------D-------------------------~~~fI~N  291 (374)
T PRK12328        251 DPIGATVGVKGVRINAVSKELNGENIDCIEYSN--------------V-------------------------PEIFIAR  291 (374)
T ss_pred             ChHHhhcCCCcchHHHHHHHhCCCeEEEEEcCC--------------C-------------------------HHHHHHH
Confidence            458999999999999999998 78888743210              0                         0011222


Q ss_pred             hhhccC-CCcccCCCceeEEEEEeccceeEEEeCCchHHHHHHHhcCCeEEEccC
Q 006943          125 AVANAT-DNDKKRKEKEECQILVPSSQSANIIGKAGATIKRLRSKTRTSIKVTPK  178 (624)
Q Consensus       125 ~~~~~~-~~~~~~~~~~~~~llvp~~~~g~iIGk~G~~Ik~I~~~sga~I~i~~~  178 (624)
                      ++.... ..-.-..+.....+.||..+.+..|||+|.+++-...-||.+|.|..-
T Consensus       292 al~Pa~V~~V~i~~~~~~~~V~V~~~qlslAIGk~GqNvrLA~~LtGwkIDI~s~  346 (374)
T PRK12328        292 ALAPAIISSVKIEEEEKKAIVTLLSDQKSKAIGKNGINIRLASMLTGYEIELNEI  346 (374)
T ss_pred             hCCCceeeEEEEcCCCcEEEEEEChHHhhhhhcCCChhHHHHHHHhCCEEEEEEC
Confidence            221110 000000123466789999999999999999999999999999999874

>KOG4369 consensus RTK signaling protein MASK/UNC-44 [Signal transduction mechanisms]

Probab=95.69  E-value=0.0073  Score=68.86  Aligned_cols=70  Identities=30%  Similarity=0.359  Sum_probs=61.5

Q ss_pred             CCcEEEEEeccccccceeccCCchHHHHHHHhCCEEEEeC-CCCCCCCeEEEEEcCHHHHHHHHHHHHHHH
Q 006943          552 PPLTLEVLVPANAVGKVIGKAGSNLANIRKISGATIEMSD-SKSSRGDRVALISGTPEQKRAAENLIQAFI  621 (624)
Q Consensus       552 ~~~~~~i~VP~~~vg~IIGkgG~~I~~I~~~sGa~I~i~~-~~~~~~~r~v~I~Gt~e~v~~A~~lI~~~i  621 (624)
                      +.....+.+|.....+|||+||.||+.+|.-|||.|.|.+ ..+...+|.+.+.|+++.+..|..+|.-.|
T Consensus      1338 ~~~~~k~~~P~~a~SRVig~ggsnVna~r~~tga~ielekmq~~Nqaers~~~kg~p~~~r~a~~~I~~~i 1408 (2131)
T KOG4369|consen 1338 PANQGKGDGPLYASSRVIGDGGSNVNAARLGTGALIELEKMQPDNQAERSKAPKGRPPSQRVATSPIGLPI 1408 (2131)
T ss_pred             cccccccccchhhhhhhhccCcchhhhHhhccceEEehhhcCCccchhhhcccCCCChhhhhhhcccccee
Confidence            4456788999999999999999999999999999999998 444567999999999999999998886544

>TIGR01953 NusA transcription termination factor NusA

Probab=95.66  E-value=0.024  Score=58.86  Aligned_cols=93  Identities=25%  Similarity=0.374  Sum_probs=64.2

Q ss_pred             cccceeccCCchHHHHHHHhc-CCeEEeeCCCCCCCceEEEEEccCCcccccccccccCCCCcccHHHHHHHHHHHHHHH
Q 006943           46 GVIGSVIGKSGKVINSIRQET-RARVKVVDPFPGAKDRVVTIYSHVKDKEDVEVDDEFNDKEPLCAAQDALLKVHAAIAN  124 (624)
Q Consensus        46 ~~~g~vIGk~G~~I~~i~~et-g~~I~v~~~~~~~~er~i~I~G~~~~~~~~~~~~~~~~~~~~~~a~~ai~~v~~~i~~  124 (624)
                      +-+|+.||++|++|+.|.++. |=+|.|-+-..              +                         ..+.+..
T Consensus       243 Dpvga~vG~~G~ri~~i~~el~ge~Idiv~~s~--------------d-------------------------~~~fi~n  283 (341)
T TIGR01953       243 DPVGACVGPKGSRIQAISKELNGEKIDIIEYSD--------------D-------------------------PAEFIAN  283 (341)
T ss_pred             CcceeeECCCCchHHHHHHHhCCCeEEEEEcCC--------------C-------------------------HHHHHHH
Confidence            458999999999999999998 78888743210              0                         0011112


Q ss_pred             hhhccC-CCc-ccCCCceeEEEEEeccceeEEEeCCchHHHHHHHhcCCeEEEcc
Q 006943          125 AVANAT-DND-KKRKEKEECQILVPSSQSANIIGKAGATIKRLRSKTRTSIKVTP  177 (624)
Q Consensus       125 ~~~~~~-~~~-~~~~~~~~~~llvp~~~~g~iIGk~G~~Ik~I~~~sga~I~i~~  177 (624)
                      ++.... ..- -...+.....+.||..+.+..|||+|.+++-...-||.+|.|..
T Consensus       284 al~Pa~v~~v~i~~~~~~~~~v~V~~~~~~~aIGk~G~Nv~la~~l~g~~IdI~s  338 (341)
T TIGR01953       284 ALSPAKVISVEVLDEDKHSAEVVVPDDQLSLAIGKGGQNVRLASKLTGWNIDVKT  338 (341)
T ss_pred             hcCCceEEEEEEEcCCCcEEEEEEChHHcchhhcCCChhHHHHHHHhCCEEEEEe
Confidence            111110 000 00012246788999999999999999999999999999999975

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.

>TIGR01953 NusA transcription termination factor NusA

Probab=95.53  E-value=0.047  Score=56.75  Aligned_cols=92  Identities=23%  Similarity=0.410  Sum_probs=64.5

Q ss_pred             CccceeeccCcchHHHHHhHh-CCeEEEcCCCCCCCceEEEEeecCCchhHHHHHHHHHHH--Hhhc-cCCCCCCcEEEE
Q 006943          317 NKIGRVIGKGGGTIKSIRQAS-GAQIDVDDTKDNRDECVITVTAIESPDDIKSMAVEAVLL--LQTK-INDEDDDTVTIR  392 (624)
Q Consensus       317 ~~vg~IIGk~G~~Ik~I~~~t-ga~I~v~~~~~~~~er~i~I~G~~~~~~a~~~~~~~i~~--~~~~-~~~~~~~~~~~~  392 (624)
                      +-+|..||++|++|+.|.++. |=+|.|-.-...             +   ...+..|+.-  +..- +.+.  ......
T Consensus       243 Dpvga~vG~~G~ri~~i~~el~ge~Idiv~~s~d-------------~---~~fi~nal~Pa~v~~v~i~~~--~~~~~~  304 (341)
T TIGR01953       243 DPVGACVGPKGSRIQAISKELNGEKIDIIEYSDD-------------P---AEFIANALSPAKVISVEVLDE--DKHSAE  304 (341)
T ss_pred             CcceeeECCCCchHHHHHHHhCCCeEEEEEcCCC-------------H---HHHHHHhcCCceEEEEEEEcC--CCcEEE
Confidence            567999999999999999999 777776321111             1   1112222221  1110 1111  224688


Q ss_pred             EEecCCeeeEEEcCCCchHHHHHHhcCceEEEeC
Q 006943          393 LLVSSKVIGCIIGKSGSIINEIRKRTKADVRISK  426 (624)
Q Consensus       393 l~vp~~~~g~iIGk~G~~Ik~I~~~tga~I~i~~  426 (624)
                      +.||..+.+..|||+|.+++-...-||.+|.|..
T Consensus       305 v~V~~~~~~~aIGk~G~Nv~la~~l~g~~IdI~s  338 (341)
T TIGR01953       305 VVVPDDQLSLAIGKGGQNVRLASKLTGWNIDVKT  338 (341)
T ss_pred             EEEChHHcchhhcCCChhHHHHHHHhCCEEEEEe
Confidence            9999999999999999999999999999999864

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.

>PRK02821 hypothetical protein; Provisional

Probab=95.40  E-value=0.027  Score=44.74  Aligned_cols=33  Identities=21%  Similarity=0.378  Sum_probs=28.3

Q ss_pred             CCcEEEEEEecCCeeeEEEcCCCchHHHHHHhc
Q 006943          386 DDTVTIRLLVSSKVIGCIIGKSGSIINEIRKRT  418 (624)
Q Consensus       386 ~~~~~~~l~vp~~~~g~iIGk~G~~Ik~I~~~t  418 (624)
                      +..+.+++.+.+..+|+||||+|.+|+.|+.--
T Consensus        28 ~~~~~i~l~v~~~D~GrVIGk~Gr~i~AIRtlv   60 (77)
T PRK02821         28 RRGRTLEVRVHPDDLGKVIGRGGRTATALRTVV   60 (77)
T ss_pred             CCcEEEEEEEChhhCcceeCCCCchHHHHHHHH
Confidence            445778999999999999999999999887643

>PRK00106 hypothetical protein; Provisional

Probab=95.37  E-value=0.068  Score=58.70  Aligned_cols=57  Identities=25%  Similarity=0.286  Sum_probs=43.2

Q ss_pred             cEEEEEEecC-CeeeEEEcCCCchHHHHHHhcCceEEEeCCCCCCCCCCCCcEEEEEe-ehHHHHHHH
Q 006943          388 TVTIRLLVSS-KVIGCIIGKSGSIINEIRKRTKADVRISKGDKPKCADANDELVEVVG-EVGSVRDAL  453 (624)
Q Consensus       388 ~~~~~l~vp~-~~~g~iIGk~G~~Ik~I~~~tga~I~i~~~~~p~~~~~~~~~v~I~G-~~~~v~~A~  453 (624)
                      .+.-.+.+|+ .+-|+|||+.|.+||-++.-||+.+-|..         +...|.|+| +|---+-|.
T Consensus       224 ~tvs~v~lp~demkGriIGreGrNir~~E~~tGvdliidd---------tp~~v~lS~fdpvRReiAr  282 (535)
T PRK00106        224 QTITTVHLPDDNMKGRIIGREGRNIRTLESLTGIDVIIDD---------TPEVVVLSGFDPIRREIAR  282 (535)
T ss_pred             heeeeEEcCChHhhcceeCCCcchHHHHHHHhCceEEEcC---------CCCeEEEeCCChHHHHHHH
Confidence            3445578888 67799999999999999999999999964         344577888 554444443

>TIGR03319 YmdA_YtgF conserved hypothetical protein YmdA/YtgF

Probab=95.35  E-value=0.062  Score=59.27  Aligned_cols=56  Identities=23%  Similarity=0.256  Sum_probs=42.4

Q ss_pred             EEEEEEecC-CeeeEEEcCCCchHHHHHHhcCceEEEeCCCCCCCCCCCCcEEEEEe-ehHHHHHHH
Q 006943          389 VTIRLLVSS-KVIGCIIGKSGSIINEIRKRTKADVRISKGDKPKCADANDELVEVVG-EVGSVRDAL  453 (624)
Q Consensus       389 ~~~~l~vp~-~~~g~iIGk~G~~Ik~I~~~tga~I~i~~~~~p~~~~~~~~~v~I~G-~~~~v~~A~  453 (624)
                      +.-.+.+|+ .+-|+|||+.|.+||-++..||+.+-|..         +...|.|+| +|---+-|.
T Consensus       204 ~~~~v~lp~d~~kgriigreGrnir~~e~~tgvd~iidd---------tp~~v~ls~fdp~rreia~  261 (514)
T TIGR03319       204 TVSVVNLPNDEMKGRIIGREGRNIRALETLTGVDLIIDD---------TPEAVILSGFDPVRREIAR  261 (514)
T ss_pred             eeeeEEcCChhhhccccCCCcchHHHHHHHhCceEEEcC---------CCCeEEecCCchHHHHHHH
Confidence            444578887 57799999999999999999999999964         344577887 454334443

>PRK12327 nusA transcription elongation factor NusA; Provisional

Probab=95.35  E-value=0.035  Score=58.08  Aligned_cols=94  Identities=22%  Similarity=0.332  Sum_probs=64.9

Q ss_pred             cccceeccCCchHHHHHHHhc-CCeEEeeCCCCCCCceEEEEEccCCcccccccccccCCCCcccHHHHHHHHHHHHHHH
Q 006943           46 GVIGSVIGKSGKVINSIRQET-RARVKVVDPFPGAKDRVVTIYSHVKDKEDVEVDDEFNDKEPLCAAQDALLKVHAAIAN  124 (624)
Q Consensus        46 ~~~g~vIGk~G~~I~~i~~et-g~~I~v~~~~~~~~er~i~I~G~~~~~~~~~~~~~~~~~~~~~~a~~ai~~v~~~i~~  124 (624)
                      +-+|+.||++|.+|+.|.++. |=+|.|-+-..              +                         ..+.+..
T Consensus       245 DpvGa~iG~~G~rI~~i~~el~gekIdiv~~s~--------------d-------------------------~~~fi~n  285 (362)
T PRK12327        245 DAKGACVGPKGQRVQNIVSELKGEKIDIIDWSE--------------D-------------------------PAEFVAN  285 (362)
T ss_pred             CchheeECCCChhHHHHHHHhCCCeEEEEEcCC--------------C-------------------------HHHHHHH
Confidence            458999999999999999998 78888743210              0                         0011122


Q ss_pred             hhhccC-CCc-ccCCCceeEEEEEeccceeEEEeCCchHHHHHHHhcCCeEEEccC
Q 006943          125 AVANAT-DND-KKRKEKEECQILVPSSQSANIIGKAGATIKRLRSKTRTSIKVTPK  178 (624)
Q Consensus       125 ~~~~~~-~~~-~~~~~~~~~~llvp~~~~g~iIGk~G~~Ik~I~~~sga~I~i~~~  178 (624)
                      ++.... ..- -...+...+.+.||..+.+..|||+|.+++--..-||.+|.|...
T Consensus       286 al~Pa~v~~v~i~~~~~~~~~v~V~~~~~~~AIGk~G~Nv~la~~L~~~~idi~s~  341 (362)
T PRK12327        286 ALSPAKVVSVEVDDEEEKAARVVVPDYQLSLAIGKEGQNARLAARLTGWKIDIKSE  341 (362)
T ss_pred             hCCCceEEEEEEEcCCCcEEEEEEChhhcchhhcCCChhHHHHHHHHCCeeeEEEH
Confidence            221110 000 000123467899999999999999999999999999999999864

>PRK12329 nusA transcription elongation factor NusA; Provisional

Probab=95.33  E-value=0.027  Score=59.50  Aligned_cols=93  Identities=28%  Similarity=0.387  Sum_probs=63.6

Q ss_pred             cccceeccCCchHHHHHHHhc-CCeEEeeCCCCCCCceEEEEEccCCcccccccccccCCCCcccHHHHHHHHHHHHHHH
Q 006943           46 GVIGSVIGKSGKVINSIRQET-RARVKVVDPFPGAKDRVVTIYSHVKDKEDVEVDDEFNDKEPLCAAQDALLKVHAAIAN  124 (624)
Q Consensus        46 ~~~g~vIGk~G~~I~~i~~et-g~~I~v~~~~~~~~er~i~I~G~~~~~~~~~~~~~~~~~~~~~~a~~ai~~v~~~i~~  124 (624)
                      +-+|+.||++|.+|+.|.++. |=+|.|-.-..              +                         ....|..
T Consensus       277 DPvGacVG~kG~RI~~I~~eL~gEkIDVI~ys~--------------D-------------------------p~~fI~N  317 (449)
T PRK12329        277 DPVGACIGARGSRIQAVVNELRGEKIDVIRWSP--------------D-------------------------PATYIAN  317 (449)
T ss_pred             ChhhccCCCCcchHHHHHHHhCCCeEEEEEcCC--------------C-------------------------HHHHHHH
Confidence            558999999999999999998 78888743210              0                         0011111


Q ss_pred             hhhccC-CCc-ccCCCceeEEEEEeccceeEEEeCCchHHHHHHHhcCCeEEEcc
Q 006943          125 AVANAT-DND-KKRKEKEECQILVPSSQSANIIGKAGATIKRLRSKTRTSIKVTP  177 (624)
Q Consensus       125 ~~~~~~-~~~-~~~~~~~~~~llvp~~~~g~iIGk~G~~Ik~I~~~sga~I~i~~  177 (624)
                      ++.... ..- ....+.....+.||..+.+..|||+|.+++--..-||.+|.|..
T Consensus       318 aLsPA~V~~V~i~~~~~k~a~V~V~~~qlslAIGK~GqNvrLAs~Ltg~~idI~s  372 (449)
T PRK12329        318 ALSPARVDEVRLVDPEGRHAHVLVPPDQLSLAIGKEGQNVRLAARLTGWKIDIKD  372 (449)
T ss_pred             hcCCceeeEEEEEcCCCcEEEEEEChHhcchhhcCCChhHHHHHHHHCCEecccc
Confidence            111110 000 00011235679999999999999999999999999999998864

>PRK02821 hypothetical protein; Provisional

Probab=95.32  E-value=0.032  Score=44.39  Aligned_cols=53  Identities=15%  Similarity=0.322  Sum_probs=36.5

Q ss_pred             HHHHHHHHhhhccCCCc----ccCCCceeEEEEEeccceeEEEeCCchHHHHHHHhc
Q 006943          117 KVHAAIANAVANATDND----KKRKEKEECQILVPSSQSANIIGKAGATIKRLRSKT  169 (624)
Q Consensus       117 ~v~~~i~~~~~~~~~~~----~~~~~~~~~~llvp~~~~g~iIGk~G~~Ik~I~~~s  169 (624)
                      .+++.++..+-..++.-    ....+.+.+.|.+...-+|.||||+|.+|+.|+.--
T Consensus         4 ~lv~~ivk~LVd~Pe~V~V~~~~~~~~~~i~l~v~~~D~GrVIGk~Gr~i~AIRtlv   60 (77)
T PRK02821          4 DAVEHLVRGIVDNPDDVRVDSHTNRRGRTLEVRVHPDDLGKVIGRGGRTATALRTVV   60 (77)
T ss_pred             HHHHHHHHHhCCCCCeEEEEEEECCCcEEEEEEEChhhCcceeCCCCchHHHHHHHH
Confidence            34455555554433211    123345778899999999999999999999998743

>PRK12704 phosphodiesterase; Provisional

Probab=95.31  E-value=0.063  Score=59.27  Aligned_cols=56  Identities=23%  Similarity=0.249  Sum_probs=42.7

Q ss_pred             EEEEEEecC-CeeeEEEcCCCchHHHHHHhcCceEEEeCCCCCCCCCCCCcEEEEEe-ehHHHHHHH
Q 006943          389 VTIRLLVSS-KVIGCIIGKSGSIINEIRKRTKADVRISKGDKPKCADANDELVEVVG-EVGSVRDAL  453 (624)
Q Consensus       389 ~~~~l~vp~-~~~g~iIGk~G~~Ik~I~~~tga~I~i~~~~~p~~~~~~~~~v~I~G-~~~~v~~A~  453 (624)
                      +.-.+.+|+ .+-|+|||+.|.+||-++.-||+.|-|..         +...|.|+| ++-.-+.|.
T Consensus       210 ~~~~v~lp~d~mkgriigreGrnir~~e~~tgvd~iidd---------tp~~v~ls~~~~~rre~a~  267 (520)
T PRK12704        210 TVSVVNLPNDEMKGRIIGREGRNIRALETLTGVDLIIDD---------TPEAVILSGFDPIRREIAR  267 (520)
T ss_pred             ceeeeecCCchhhcceeCCCcchHHHHHHHhCCeEEEcC---------CCCeEEEecCChhhHHHHH
Confidence            334577887 67799999999999999999999999964         345677898 454433443

>PRK12328 nusA transcription elongation factor NusA; Provisional

Probab=95.31  E-value=0.011  Score=61.38  Aligned_cols=94  Identities=17%  Similarity=0.207  Sum_probs=65.0

Q ss_pred             CccceeeccCcchHHHHHhHh-CCeEEEcCCCCCCCceEEEEeecCCchhHHHHHHHHHHH--HhhccCCCCCCcEEEEE
Q 006943          317 NKIGRVIGKGGGTIKSIRQAS-GAQIDVDDTKDNRDECVITVTAIESPDDIKSMAVEAVLL--LQTKINDEDDDTVTIRL  393 (624)
Q Consensus       317 ~~vg~IIGk~G~~Ik~I~~~t-ga~I~v~~~~~~~~er~i~I~G~~~~~~a~~~~~~~i~~--~~~~~~~~~~~~~~~~l  393 (624)
                      +-+|..||++|++|+.|.++. |=+|.|-.-..                +....+..++.-  +..-..+  ++.....+
T Consensus       251 DPvGacIG~~G~rI~~I~~eL~gEkIDvI~~s~----------------D~~~fI~Nal~Pa~V~~V~i~--~~~~~~~V  312 (374)
T PRK12328        251 DPIGATVGVKGVRINAVSKELNGENIDCIEYSN----------------VPEIFIARALAPAIISSVKIE--EEEKKAIV  312 (374)
T ss_pred             ChHHhhcCCCcchHHHHHHHhCCCeEEEEEcCC----------------CHHHHHHHhCCCceeeEEEEc--CCCcEEEE
Confidence            567999999999999999999 77777632111                111112222210  0010001  22346788


Q ss_pred             EecCCeeeEEEcCCCchHHHHHHhcCceEEEeCCC
Q 006943          394 LVSSKVIGCIIGKSGSIINEIRKRTKADVRISKGD  428 (624)
Q Consensus       394 ~vp~~~~g~iIGk~G~~Ik~I~~~tga~I~i~~~~  428 (624)
                      .||..+.+..|||+|.+++-..+-||.+|.|..-.
T Consensus       313 ~V~~~qlslAIGk~GqNvrLA~~LtGwkIDI~s~~  347 (374)
T PRK12328        313 TLLSDQKSKAIGKNGINIRLASMLTGYEIELNEIG  347 (374)
T ss_pred             EEChHHhhhhhcCCChhHHHHHHHhCCEEEEEECC
Confidence            99999999999999999999999999999997543

>PRK00468 hypothetical protein; Provisional

Probab=95.30  E-value=0.029  Score=44.49  Aligned_cols=32  Identities=22%  Similarity=0.379  Sum_probs=28.6

Q ss_pred             CCCceeEEEEEeccceeEEEeCCchHHHHHHH
Q 006943          136 RKEKEECQILVPSSQSANIIGKAGATIKRLRS  167 (624)
Q Consensus       136 ~~~~~~~~llvp~~~~g~iIGk~G~~Ik~I~~  167 (624)
                      ..+.+.++|.+..+-+|.||||+|.+|+.|+.
T Consensus        26 ~~~~~~~~l~v~~~D~GrVIGk~Gr~i~AIRt   57 (75)
T PRK00468         26 GEQSVILELKVAPEDMGKVIGKQGRIAKAIRT   57 (75)
T ss_pred             CCCeEEEEEEEChhhCcceecCCChhHHHHHH
Confidence            34568889999999999999999999999986

>PRK12327 nusA transcription elongation factor NusA; Provisional

Probab=95.28  E-value=0.055  Score=56.61  Aligned_cols=92  Identities=21%  Similarity=0.344  Sum_probs=64.5

Q ss_pred             CccceeeccCcchHHHHHhHh-CCeEEEcCCCCCCCceEEEEeecCCchhHHHHHHHHHHH--Hhh-ccCCCCCCcEEEE
Q 006943          317 NKIGRVIGKGGGTIKSIRQAS-GAQIDVDDTKDNRDECVITVTAIESPDDIKSMAVEAVLL--LQT-KINDEDDDTVTIR  392 (624)
Q Consensus       317 ~~vg~IIGk~G~~Ik~I~~~t-ga~I~v~~~~~~~~er~i~I~G~~~~~~a~~~~~~~i~~--~~~-~~~~~~~~~~~~~  392 (624)
                      +-+|..||++|.+|+.|.++. |=+|.|-.-..                +....+..++.-  +.. .+.+  +......
T Consensus       245 DpvGa~iG~~G~rI~~i~~el~gekIdiv~~s~----------------d~~~fi~nal~Pa~v~~v~i~~--~~~~~~~  306 (362)
T PRK12327        245 DAKGACVGPKGQRVQNIVSELKGEKIDIIDWSE----------------DPAEFVANALSPAKVVSVEVDD--EEEKAAR  306 (362)
T ss_pred             CchheeECCCChhHHHHHHHhCCCeEEEEEcCC----------------CHHHHHHHhCCCceEEEEEEEc--CCCcEEE
Confidence            568999999999999999999 77777632111                111112222220  111 0111  2234678


Q ss_pred             EEecCCeeeEEEcCCCchHHHHHHhcCceEEEeC
Q 006943          393 LLVSSKVIGCIIGKSGSIINEIRKRTKADVRISK  426 (624)
Q Consensus       393 l~vp~~~~g~iIGk~G~~Ik~I~~~tga~I~i~~  426 (624)
                      +.||..+.+..|||+|.+++-...-||.+|.|..
T Consensus       307 v~V~~~~~~~AIGk~G~Nv~la~~L~~~~idi~s  340 (362)
T PRK12327        307 VVVPDYQLSLAIGKEGQNARLAARLTGWKIDIKS  340 (362)
T ss_pred             EEEChhhcchhhcCCChhHHHHHHHHCCeeeEEE
Confidence            9999999999999999999999999999999865

>PRK00468 hypothetical protein; Provisional

Probab=95.22  E-value=0.021  Score=45.22  Aligned_cols=34  Identities=35%  Similarity=0.581  Sum_probs=30.4

Q ss_pred             CCceEEEEEEecCcccceeccCCchHHHHHHHhc
Q 006943           33 NEESVIYRILCPDGVIGSVIGKSGKVINSIRQET   66 (624)
Q Consensus        33 ~~~~~~~~ilvp~~~~g~vIGk~G~~I~~i~~et   66 (624)
                      .+..+.+++.|...-.|.||||+|.+|+.||.--
T Consensus        26 ~~~~~~~~l~v~~~D~GrVIGk~Gr~i~AIRtvv   59 (75)
T PRK00468         26 GEQSVILELKVAPEDMGKVIGKQGRIAKAIRTVV   59 (75)
T ss_pred             CCCeEEEEEEEChhhCcceecCCChhHHHHHHHH
Confidence            4456899999999999999999999999999764

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

Probab=95.10  E-value=0.039  Score=51.33  Aligned_cols=39  Identities=36%  Similarity=0.594  Sum_probs=33.2

Q ss_pred             cEEEEEec------cccccceeccCCchHHHHHHHhCCEEEEeCC
Q 006943          554 LTLEVLVP------ANAVGKVIGKAGSNLANIRKISGATIEMSDS  592 (624)
Q Consensus       554 ~~~~i~VP------~~~vg~IIGkgG~~I~~I~~~sGa~I~i~~~  592 (624)
                      ++-++.||      .++||.+||..|.+++++++.|+|+|.|-..
T Consensus       148 ~q~KiYIPV~eyPe~NFVGLliGPRG~Tlk~le~~s~akIaIRG~  192 (269)
T COG5176         148 YQNKIYIPVQEYPESNFVGLLIGPRGSTLKQLERISRAKIAIRGS  192 (269)
T ss_pred             ccceEEeehhhCcccceeEEEecCCcchHHHHHHHhCCeEEEecc
Confidence            34556665      4789999999999999999999999999755

>PRK12329 nusA transcription elongation factor NusA; Provisional

Probab=94.99  E-value=0.052  Score=57.37  Aligned_cols=92  Identities=22%  Similarity=0.335  Sum_probs=63.8

Q ss_pred             CccceeeccCcchHHHHHhHh-CCeEEEcCCCCCCCceEEEEeecCCchhHHHHHHHHHH--HHhhc-cCCCCCCcEEEE
Q 006943          317 NKIGRVIGKGGGTIKSIRQAS-GAQIDVDDTKDNRDECVITVTAIESPDDIKSMAVEAVL--LLQTK-INDEDDDTVTIR  392 (624)
Q Consensus       317 ~~vg~IIGk~G~~Ik~I~~~t-ga~I~v~~~~~~~~er~i~I~G~~~~~~a~~~~~~~i~--~~~~~-~~~~~~~~~~~~  392 (624)
                      +-+|..||++|..|+.|.++. |=+|.|-.-..             ++   ...+..++.  .+..- +.+  .......
T Consensus       277 DPvGacVG~kG~RI~~I~~eL~gEkIDVI~ys~-------------Dp---~~fI~NaLsPA~V~~V~i~~--~~~k~a~  338 (449)
T PRK12329        277 DPVGACIGARGSRIQAVVNELRGEKIDVIRWSP-------------DP---ATYIANALSPARVDEVRLVD--PEGRHAH  338 (449)
T ss_pred             ChhhccCCCCcchHHHHHHHhCCCeEEEEEcCC-------------CH---HHHHHHhcCCceeeEEEEEc--CCCcEEE
Confidence            568999999999999999999 77777632111             11   111222221  11110 111  1224578


Q ss_pred             EEecCCeeeEEEcCCCchHHHHHHhcCceEEEeC
Q 006943          393 LLVSSKVIGCIIGKSGSIINEIRKRTKADVRISK  426 (624)
Q Consensus       393 l~vp~~~~g~iIGk~G~~Ik~I~~~tga~I~i~~  426 (624)
                      +.||..+.+..|||+|.+++-...-||.+|.|..
T Consensus       339 V~V~~~qlslAIGK~GqNvrLAs~Ltg~~idI~s  372 (449)
T PRK12329        339 VLVPPDQLSLAIGKEGQNVRLAARLTGWKIDIKD  372 (449)
T ss_pred             EEEChHhcchhhcCCChhHHHHHHHHCCEecccc
Confidence            9999999999999999999999999999998864

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

Probab=94.91  E-value=0.04  Score=51.25  Aligned_cols=41  Identities=29%  Similarity=0.469  Sum_probs=34.4

Q ss_pred             ceeEEEEEe------ccceeEEEeCCchHHHHHHHhcCCeEEEccCC
Q 006943          139 KEECQILVP------SSQSANIIGKAGATIKRLRSKTRTSIKVTPKD  179 (624)
Q Consensus       139 ~~~~~llvp------~~~~g~iIGk~G~~Ik~I~~~sga~I~i~~~~  179 (624)
                      ..+-++.||      .+++|.|||+.|.++|+|++.|+|+|-|-...
T Consensus       147 k~q~KiYIPV~eyPe~NFVGLliGPRG~Tlk~le~~s~akIaIRG~g  193 (269)
T COG5176         147 KYQNKIYIPVQEYPESNFVGLLIGPRGSTLKQLERISRAKIAIRGSG  193 (269)
T ss_pred             cccceEEeehhhCcccceeEEEecCCcchHHHHHHHhCCeEEEeccc
Confidence            345566666      57899999999999999999999999998753

>PRK09202 nusA transcription elongation factor NusA; Validated

Probab=94.88  E-value=0.033  Score=60.43  Aligned_cols=92  Identities=24%  Similarity=0.378  Sum_probs=63.9

Q ss_pred             CccceeeccCcchHHHHHhHh-CCeEEEcCCCCCCCceEEEEeecCCchhHHHHHHHHHH--HHhhccCCCCCCcEEEEE
Q 006943          317 NKIGRVIGKGGGTIKSIRQAS-GAQIDVDDTKDNRDECVITVTAIESPDDIKSMAVEAVL--LLQTKINDEDDDTVTIRL  393 (624)
Q Consensus       317 ~~vg~IIGk~G~~Ik~I~~~t-ga~I~v~~~~~~~~er~i~I~G~~~~~~a~~~~~~~i~--~~~~~~~~~~~~~~~~~l  393 (624)
                      +-+|..||++|++|+.|.++. |=+|.|-.-..             ++   ...+..++.  .+...+.+..  .-.+.+
T Consensus       245 Dpvga~vG~~G~ri~~i~~el~ge~Idiv~~s~-------------d~---~~fi~nal~pa~v~~v~~~~~--~~~~~v  306 (470)
T PRK09202        245 DPVGACVGMRGSRIQAISNELGGEKIDIILWSD-------------DP---AQFIINALSPAEVSSVVVDED--EHSADV  306 (470)
T ss_pred             ChhHccCCCCCchHHHHHHHhCCCeEEEEEcCC-------------CH---HHHHHHhCCCCEEEEEEEeCC--CCEEEE
Confidence            467999999999999999999 77777632111             11   111222221  0111111111  236789


Q ss_pred             EecCCeeeEEEcCCCchHHHHHHhcCceEEEeC
Q 006943          394 LVSSKVIGCIIGKSGSIINEIRKRTKADVRISK  426 (624)
Q Consensus       394 ~vp~~~~g~iIGk~G~~Ik~I~~~tga~I~i~~  426 (624)
                      .||..+.+..|||+|.+++-..+-||.+|.|..
T Consensus       307 ~V~~~~~~~AIGk~G~Nvrla~~l~g~~idi~~  339 (470)
T PRK09202        307 VVPDDQLSLAIGKNGQNVRLASKLTGWKIDIMT  339 (470)
T ss_pred             EECcchHHHhhCCCCeeHHHHHHHHCCeEEEEE
Confidence            999999999999999999999999999999965

>PRK04163 exosome complex RNA-binding protein Rrp4; Provisional

Probab=94.84  E-value=0.049  Score=53.83  Aligned_cols=63  Identities=25%  Similarity=0.324  Sum_probs=53.3

Q ss_pred             EEEEeccceeEEEeCCchHHHHHHHhcCCeEEEccCCCCCCCCcccccCCceEEEecCH-HHHHHHHHHHHHHHhhcC
Q 006943          143 QILVPSSQSANIIGKAGATIKRLRSKTRTSIKVTPKDASEPTHSCAMEFDNFVLISGES-EAVKKALFAISAIMYKFS  219 (624)
Q Consensus       143 ~llvp~~~~g~iIGk~G~~Ik~I~~~sga~I~i~~~~~~~~~~~~~~~~~r~V~I~G~~-~~V~~A~~~I~~~l~~~~  219 (624)
                      .+.||..+++.|||++|..|+.|.++++++|.+-.              +-.|.|.+.. +++.+|..+|..+-++..
T Consensus       148 ~~~V~~~~i~~lig~~g~~i~~l~~~~~~~I~ig~--------------NG~VwI~~~~~~~~~~a~~~I~~~e~~~~  211 (235)
T PRK04163        148 IVEIKPVKVPRVIGKKGSMINMLKEETGCDIIVGQ--------------NGRIWIKGPDEEDEEIAIEAIKKIEREAH  211 (235)
T ss_pred             EEEECHHHHHhhcCCCChhHhhhhhhhCcEEEEcC--------------CcEEEEeeCCHHHHHHHHHHHHHHHhhhh
Confidence            58899999999999999999999999999998843              4568899984 588899998887765543

>PRK09202 nusA transcription elongation factor NusA; Validated

Probab=94.72  E-value=0.065  Score=58.14  Aligned_cols=94  Identities=21%  Similarity=0.327  Sum_probs=64.5

Q ss_pred             cccceeccCCchHHHHHHHhc-CCeEEeeCCCCCCCceEEEEEccCCcccccccccccCCCCcccHHHHHHHHHHHHHHH
Q 006943           46 GVIGSVIGKSGKVINSIRQET-RARVKVVDPFPGAKDRVVTIYSHVKDKEDVEVDDEFNDKEPLCAAQDALLKVHAAIAN  124 (624)
Q Consensus        46 ~~~g~vIGk~G~~I~~i~~et-g~~I~v~~~~~~~~er~i~I~G~~~~~~~~~~~~~~~~~~~~~~a~~ai~~v~~~i~~  124 (624)
                      +-+|+.||++|++|+.|.++. |=+|.|-.-.              ++                         ....+..
T Consensus       245 Dpvga~vG~~G~ri~~i~~el~ge~Idiv~~s--------------~d-------------------------~~~fi~n  285 (470)
T PRK09202        245 DPVGACVGMRGSRIQAISNELGGEKIDIILWS--------------DD-------------------------PAQFIIN  285 (470)
T ss_pred             ChhHccCCCCCchHHHHHHHhCCCeEEEEEcC--------------CC-------------------------HHHHHHH
Confidence            348999999999999999998 7888874321              00                         0011222


Q ss_pred             hhhccC-CCcccCCCceeEEEEEeccceeEEEeCCchHHHHHHHhcCCeEEEccC
Q 006943          125 AVANAT-DNDKKRKEKEECQILVPSSQSANIIGKAGATIKRLRSKTRTSIKVTPK  178 (624)
Q Consensus       125 ~~~~~~-~~~~~~~~~~~~~llvp~~~~g~iIGk~G~~Ik~I~~~sga~I~i~~~  178 (624)
                      ++.... ..-.-......+.+.||..+.+.-|||+|.+++-..+-||.+|.|...
T Consensus       286 al~pa~v~~v~~~~~~~~~~v~V~~~~~~~AIGk~G~Nvrla~~l~g~~idi~~~  340 (470)
T PRK09202        286 ALSPAEVSSVVVDEDEHSADVVVPDDQLSLAIGKNGQNVRLASKLTGWKIDIMTE  340 (470)
T ss_pred             hCCCCEEEEEEEeCCCCEEEEEECcchHHHhhCCCCeeHHHHHHHHCCeEEEEEh
Confidence            222110 000000112367789999999999999999999999999999999763

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

Probab=94.67  E-value=0.065  Score=42.31  Aligned_cols=31  Identities=26%  Similarity=0.495  Sum_probs=28.7

Q ss_pred             CCceeEEEEEeccceeEEEeCCchHHHHHHH
Q 006943          137 KEKEECQILVPSSQSANIIGKAGATIKRLRS  167 (624)
Q Consensus       137 ~~~~~~~llvp~~~~g~iIGk~G~~Ik~I~~  167 (624)
                      .....++|.++..-+|.+|||+|.+|+.|+.
T Consensus        27 ~~~~~~~l~v~~~D~GkvIGk~GRti~AIRT   57 (76)
T COG1837          27 EKTVTIELRVAPEDMGKVIGKQGRTIQAIRT   57 (76)
T ss_pred             CCeEEEEEEECcccccceecCCChhHHHHHH
Confidence            5678899999999999999999999999986

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

Probab=94.43  E-value=0.044  Score=43.24  Aligned_cols=34  Identities=32%  Similarity=0.511  Sum_probs=30.8

Q ss_pred             CCceEEEEEEecCcccceeccCCchHHHHHHHhc
Q 006943           33 NEESVIYRILCPDGVIGSVIGKSGKVINSIRQET   66 (624)
Q Consensus        33 ~~~~~~~~ilvp~~~~g~vIGk~G~~I~~i~~et   66 (624)
                      .+..+.+++-+.+...|.||||+|.+|+.||.--
T Consensus        26 ~~~~~~~~l~v~~~D~GkvIGk~GRti~AIRTll   59 (76)
T COG1837          26 GEKTVTIELRVAPEDMGKVIGKQGRTIQAIRTLL   59 (76)
T ss_pred             cCCeEEEEEEECcccccceecCCChhHHHHHHHH
Confidence            3678999999999999999999999999999763

>PRK01064 hypothetical protein; Provisional

Probab=94.35  E-value=0.092  Score=41.92  Aligned_cols=32  Identities=31%  Similarity=0.442  Sum_probs=28.8

Q ss_pred             CCceeEEEEEeccceeEEEeCCchHHHHHHHh
Q 006943          137 KEKEECQILVPSSQSANIIGKAGATIKRLRSK  168 (624)
Q Consensus       137 ~~~~~~~llvp~~~~g~iIGk~G~~Ik~I~~~  168 (624)
                      .+.+.+++.+...-.|.+|||+|.+|+.|+.-
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            45688899999999999999999999999874

>PRK12705 hypothetical protein; Provisional

Probab=94.24  E-value=0.054  Score=59.07  Aligned_cols=64  Identities=22%  Similarity=0.499  Sum_probs=50.2

Q ss_pred             cEEEEEeccccc-cceeccCCchHHHHHHHhCCEEEEeCCCCCCCCeEEEEEc-CHHHHHHHHHHHHHHHh
Q 006943          554 LTLEVLVPANAV-GKVIGKAGSNLANIRKISGATIEMSDSKSSRGDRVALISG-TPEQKRAAENLIQAFIM  622 (624)
Q Consensus       554 ~~~~i~VP~~~v-g~IIGkgG~~I~~I~~~sGa~I~i~~~~~~~~~r~v~I~G-t~e~v~~A~~lI~~~i~  622 (624)
                      +...|.+|++-. |+||||.|.||+.+...||+.|.|++.+     ..|+|++ .|.--+.|..-+..+|.
T Consensus       198 tvs~v~lp~demkGriIGreGrNir~~E~~tGvdliiddtp-----~~V~ls~fdp~rreia~~~l~~Li~  263 (508)
T PRK12705        198 SVSVVPIPSDAMKGRIIGREGRNIRAFEGLTGVDLIIDDTP-----EAVVISSFNPIRREIARLTLEKLLA  263 (508)
T ss_pred             eeeeeecCChHhhccccCccchhHHHHHHhhCCceEecCCc-----cchhhcccCccchHHHHHHHHHHHh
Confidence            466788888555 9999999999999999999999999764     3367777 56666777766666653

>PF14611 SLS: Mitochondrial inner-membrane-bound regulator

Probab=94.00  E-value=1  Score=43.65  Aligned_cols=126  Identities=14%  Similarity=0.156  Sum_probs=82.2

Q ss_pred             EEEecCCccceeeccCcchHHHHHhHhCCeEEEcCCCCCCCceEEEEeecCCchhHHHHHHHHHHHHhhccCCCCCCcEE
Q 006943          311 RVLCPFNKIGRVIGKGGGTIKSIRQASGAQIDVDDTKDNRDECVITVTAIESPDDIKSMAVEAVLLLQTKINDEDDDTVT  390 (624)
Q Consensus       311 ~i~vp~~~vg~IIGk~G~~Ik~I~~~tga~I~v~~~~~~~~er~i~I~G~~~~~~a~~~~~~~i~~~~~~~~~~~~~~~~  390 (624)
                      .+.++....-.+...+|..++.|....||+|.+...     +..|.|+|++   .++..+...+..+...+       .+
T Consensus        29 ~v~l~~~~~~LLl~~~~~~L~~l~~~~~~~I~~~~~-----~~~i~I~g~k---~~~~~i~~~i~~~l~~i-------~~   93 (210)
T PF14611_consen   29 DVWLQPDEFFLLLTGNGRILENLAARNGAKIEVSRS-----ENRIRITGTK---STAEYIEASINEILSNI-------RT   93 (210)
T ss_pred             EEEecchheeeeecCCchHHHHHHHhcCceEEEecC-----CcEEEEEccH---HHHHHHHHHHHHHHhhc-------EE
Confidence            445567888899999999999998889999999753     3479999973   33333444444444333       44


Q ss_pred             EEEEecCCeeeEEE-c---CCCchHHHHHHhcCceEEEeCCCCCCCCCCCCcEEEEE-----eehHHHHHHHHHHHHHH
Q 006943          391 IRLLVSSKVIGCII-G---KSGSIINEIRKRTKADVRISKGDKPKCADANDELVEVV-----GEVGSVRDALVQIILRL  460 (624)
Q Consensus       391 ~~l~vp~~~~g~iI-G---k~G~~Ik~I~~~tga~I~i~~~~~p~~~~~~~~~v~I~-----G~~~~v~~A~~~I~~~l  460 (624)
                      .++.++.-..-.-. +   .....++.|++.|++.|...++.         ..+.|.     -....+..|...+...+
T Consensus        94 ~~i~l~~~~~~~~~~~~~~~~~~~l~~i~~~t~~~ie~~~~~---------~~~~i~~~~~~~~~~~~~~a~RlL~~a~  163 (210)
T PF14611_consen   94 EEIDLSPIISKHSEKKNSQFTPDLLEEIQKLTNVYIEKNPDG---------NKLKISWLASPENEKRADRAKRLLLWAL  163 (210)
T ss_pred             EEEecchhhhhhcccccccccHHHHHHHHHHHcEEEEECCCC---------CeEEEEEEeeccccchHHHHHHHHHHhc
Confidence            55555532211111 1   13557999999999999987532         224444     35677778877766555

>PRK01064 hypothetical protein; Provisional

Probab=94.00  E-value=0.062  Score=42.87  Aligned_cols=34  Identities=32%  Similarity=0.617  Sum_probs=30.4

Q ss_pred             CCceEEEEEEecCcccceeccCCchHHHHHHHhc
Q 006943           33 NEESVIYRILCPDGVIGSVIGKSGKVINSIRQET   66 (624)
Q Consensus        33 ~~~~~~~~ilvp~~~~g~vIGk~G~~I~~i~~et   66 (624)
                      .+..+.+++.|.+...|.+|||+|.+|+.||.-.
T Consensus        26 ~~~~~~~~l~v~~~D~g~vIGk~G~~i~air~l~   59 (78)
T PRK01064         26 GTHTIIYELTVAKPDIGKIIGKEGRTIKAIRTLL   59 (78)
T ss_pred             CCCEEEEEEEECcccceEEECCCCccHHHHHHHH
Confidence            3567999999999999999999999999999753

>PRK12705 hypothetical protein; Provisional

Probab=91.90  E-value=0.33  Score=53.10  Aligned_cols=38  Identities=26%  Similarity=0.335  Sum_probs=32.0

Q ss_pred             EEEEEEecC-CeeeEEEcCCCchHHHHHHhcCceEEEeC
Q 006943          389 VTIRLLVSS-KVIGCIIGKSGSIINEIRKRTKADVRISK  426 (624)
Q Consensus       389 ~~~~l~vp~-~~~g~iIGk~G~~Ik~I~~~tga~I~i~~  426 (624)
                      +.-.+.+|+ .+-|+|||+.|.+||.++..||+.+-|..
T Consensus       198 tvs~v~lp~demkGriIGreGrNir~~E~~tGvdliidd  236 (508)
T PRK12705        198 SVSVVPIPSDAMKGRIIGREGRNIRAFEGLTGVDLIIDD  236 (508)
T ss_pred             eeeeeecCChHhhccccCccchhHHHHHHhhCCceEecC
Confidence            334467776 56799999999999999999999999975

>COG5166 Uncharacterized conserved protein [Function unknown]

Probab=91.39  E-value=1.1  Score=47.83  Aligned_cols=103  Identities=15%  Similarity=0.159  Sum_probs=69.3

Q ss_pred             EEEecCCccceeeccCcchHHHHHhHh----CCeEEEcCCCCCCCceEEEEeecCCchhHHHHHHHHHHHHhhccCCCCC
Q 006943          311 RVLCPFNKIGRVIGKGGGTIKSIRQAS----GAQIDVDDTKDNRDECVITVTAIESPDDIKSMAVEAVLLLQTKINDEDD  386 (624)
Q Consensus       311 ~i~vp~~~vg~IIGk~G~~Ik~I~~~t----ga~I~v~~~~~~~~er~i~I~G~~~~~~a~~~~~~~i~~~~~~~~~~~~  386 (624)
                      -+.+|.+..+.|+|++......+++..    ...|.|...    ..++.++.+...          .+.++...-+--..
T Consensus       500 ~I~~PrKn~~ni~~~KNd~~~~V~~~c~f~~Kgdirf~~~----~~sI~~v~~~~~----------~I~rv~kne~v~~~  565 (657)
T COG5166         500 LIEAPRKNQDNISGKKNDKLDKVKQQCRFNLKGDIRFCPQ----STSIFTVDIYSD----------EIERVIKNETVLLE  565 (657)
T ss_pred             EEECCccCccchhcccccHHHHHhhhcccccccceEEcCC----ceEEEEEccccc----------HHHHHhhccceEEe
Confidence            366999999999999999999998665    345666432    456888887532          22222211111123


Q ss_pred             CcEEEEEEecCCeeeEEEc---CCCchHHHHHHhcCceEEEeCC
Q 006943          387 DTVTIRLLVSSKVIGCIIG---KSGSIINEIRKRTKADVRISKG  427 (624)
Q Consensus       387 ~~~~~~l~vp~~~~g~iIG---k~G~~Ik~I~~~tga~I~i~~~  427 (624)
                      -++...+.+|...|+..+|   -.|++|..+..-..-.|.+...
T Consensus       566 ~p~~~~~y~~se~h~~g~gena~R~~ni~~~t~~y~~~ie~~~t  609 (657)
T COG5166         566 FPAEMHFYVPSEIHKKGIGENAFRGENIQRVTKLYNSYIEFSTT  609 (657)
T ss_pred             cccccccccchhhhhccCCcccccccchhhhhhhhhccceeecC
Confidence            3456678889999999999   6788888877776666666543

>KOG1067 consensus Predicted RNA-binding polyribonucleotide nucleotidyltransferase [General function prediction only]

Probab=90.96  E-value=0.42  Score=51.41  Aligned_cols=65  Identities=22%  Similarity=0.200  Sum_probs=53.0

Q ss_pred             CceeEEEEEeccceeEEEeCCchHHHHHHHhcCCeEEEccCCCCCCCCcccccCCceEEEecC-HHHHHHHHHHHHHHHh
Q 006943          138 EKEECQILVPSSQSANIIGKAGATIKRLRSKTRTSIKVTPKDASEPTHSCAMEFDNFVLISGE-SEAVKKALFAISAIMY  216 (624)
Q Consensus       138 ~~~~~~llvp~~~~g~iIGk~G~~Ik~I~~~sga~I~i~~~~~~~~~~~~~~~~~r~V~I~G~-~~~V~~A~~~I~~~l~  216 (624)
                      ..+...|.|+.+....+||++|...|+|+.+||+.-.+               ++..+.|-.+ ..+.++|+..|..++.
T Consensus       595 ~P~~~tlkv~~sk~~~lIGp~G~~~kki~~EtGai~~v---------------De~t~~i~A~~~~am~~Ak~~I~~i~~  659 (760)
T KOG1067|consen  595 SPVLETLKVSPSKRATLIGPGGVLKKKIEVETGAISQV---------------DEGTFSIFAPTQAAMEEAKEFIDGIIK  659 (760)
T ss_pred             CceeeEEeecchhhheeecCccceeeeEeeeccceeee---------------cCceEEEEecCHHHHHHHHHHHHHHhc
Confidence            45667789999999999999999999999999955444               3566777776 5667899999988875


Q ss_pred             h
Q 006943          217 K  217 (624)
Q Consensus       217 ~  217 (624)
                      +
T Consensus       660 ~  660 (760)
T KOG1067|consen  660 D  660 (760)
T ss_pred             C
Confidence            4

>KOG3273 consensus Predicted RNA-binding protein Pno1p interacting with Nob1p and involved in 26S proteasome assembly [Posttranslational modification, protein turnover, chaperones]

Probab=90.65  E-value=0.12  Score=47.87  Aligned_cols=54  Identities=26%  Similarity=0.451  Sum_probs=49.4

Q ss_pred             cccccceeccCCchHHHHHHHhCCEEEEeCCCCCCCCeEEEEEcCHHHHHHHHHHHHHHHh
Q 006943          562 ANAVGKVIGKAGSNLANIRKISGATIEMSDSKSSRGDRVALISGTPEQKRAAENLIQAFIM  622 (624)
Q Consensus       562 ~~~vg~IIGkgG~~I~~I~~~sGa~I~i~~~~~~~~~r~v~I~Gt~e~v~~A~~lI~~~i~  622 (624)
                      +..+|+|+||+|.+--.|.+.|.++|-+.+.       .|-|-|+.+.+..|+.-|+.+|+
T Consensus       177 sRAIGRiaGk~GkTkfaIEn~trtrIVlad~-------kIHiLG~~~niriAR~avcsLIl  230 (252)
T KOG3273|consen  177 SRAIGRIAGKGGKTKFAIENVTRTRIVLADS-------KIHILGAFQNIRIARDAVCSLIL  230 (252)
T ss_pred             HHHHHHhhcCCCcceeeeeccceeEEEecCc-------eEEEeecchhhHHHHHhhHhhhc
Confidence            5678999999999999999999999999864       49999999999999999999886

>KOG2874 consensus rRNA processing protein [Translation, ribosomal structure and biogenesis; Cell cycle control, cell division, chromosome partitioning]

Probab=90.60  E-value=0.39  Score=46.97  Aligned_cols=53  Identities=26%  Similarity=0.275  Sum_probs=47.0

Q ss_pred             eEEEeCCchHHHHHHHhcCCeEEEccCCCCCCCCcccccCCceEEEecCHHHHHHHHHHHHHHHhhcC
Q 006943          152 ANIIGKAGATIKRLRSKTRTSIKVTPKDASEPTHSCAMEFDNFVLISGESEAVKKALFAISAIMYKFS  219 (624)
Q Consensus       152 g~iIGk~G~~Ik~I~~~sga~I~i~~~~~~~~~~~~~~~~~r~V~I~G~~~~V~~A~~~I~~~l~~~~  219 (624)
                      -+|||++|.+++.|+--|.|.|-|..               .+|.+.|...++..+...+.++++...
T Consensus       161 qRLiGpng~TLKAlelLT~CYilVqG---------------~TVsaiGpfkGlkevr~IV~DcM~NiH  213 (356)
T KOG2874|consen  161 QRLIGPNGSTLKALELLTNCYILVQG---------------NTVSAIGPFKGLKEVRKIVEDCMKNIH  213 (356)
T ss_pred             HHhcCCCchhHHHHHHHhhcEEEeeC---------------cEEEeecCcchHHHHHHHHHHHHhccc
Confidence            46999999999999999999998875               458999999999999999999997543

>KOG1067 consensus Predicted RNA-binding polyribonucleotide nucleotidyltransferase [General function prediction only]

Probab=89.92  E-value=0.62  Score=50.15  Aligned_cols=67  Identities=19%  Similarity=0.206  Sum_probs=52.6

Q ss_pred             CCCcEEEEEEecCCeeeEEEcCCCchHHHHHHhcCceEEEeCCCCCCCCCCCCcEEEEEe-ehHHHHHHHHHHHHHHhh
Q 006943          385 DDDTVTIRLLVSSKVIGCIIGKSGSIINEIRKRTKADVRISKGDKPKCADANDELVEVVG-EVGSVRDALVQIILRLRD  462 (624)
Q Consensus       385 ~~~~~~~~l~vp~~~~g~iIGk~G~~Ik~I~~~tga~I~i~~~~~p~~~~~~~~~v~I~G-~~~~v~~A~~~I~~~l~e  462 (624)
                      ...++...|.|+.+....+||.+|...|+|+.+||+.-++.           +..+.|.- ++.+.++|...|...+..
T Consensus       593 ~y~P~~~tlkv~~sk~~~lIGp~G~~~kki~~EtGai~~vD-----------e~t~~i~A~~~~am~~Ak~~I~~i~~~  660 (760)
T KOG1067|consen  593 EYSPVLETLKVSPSKRATLIGPGGVLKKKIEVETGAISQVD-----------EGTFSIFAPTQAAMEEAKEFIDGIIKD  660 (760)
T ss_pred             ccCceeeEEeecchhhheeecCccceeeeEeeeccceeeec-----------CceEEEEecCHHHHHHHHHHHHHHhcC
Confidence            45678899999999999999999999999999999644443           44566666 677788898777655543

>PF13083 KH_4: KH domain; PDB: 3GKU_B

Probab=89.90  E-value=0.13  Score=40.60  Aligned_cols=34  Identities=18%  Similarity=0.374  Sum_probs=28.8

Q ss_pred             CCceeEEEEEeccceeEEEeCCchHHHHHHHhcC
Q 006943          137 KEKEECQILVPSSQSANIIGKAGATIKRLRSKTR  170 (624)
Q Consensus       137 ~~~~~~~llvp~~~~g~iIGk~G~~Ik~I~~~sg  170 (624)
                      .+...+.+-+.....|.||||+|.+++.|+--.+
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            3456778889999999999999999999987544

>PF13083 KH_4: KH domain; PDB: 3GKU_B

Probab=88.53  E-value=0.24  Score=39.13  Aligned_cols=33  Identities=21%  Similarity=0.307  Sum_probs=28.0

Q ss_pred             ceEEEEEEecCcccceeccCCchHHHHHHHhcC
Q 006943           35 ESVIYRILCPDGVIGSVIGKSGKVINSIRQETR   67 (624)
Q Consensus        35 ~~~~~~ilvp~~~~g~vIGk~G~~I~~i~~etg   67 (624)
                      +...+.+-|..+..|.||||+|.+++.||.-.+
T Consensus        27 ~~~~i~v~i~~ed~g~lIGk~G~tl~ALq~l~~   59 (73)
T PF13083_consen   27 DGDTIVVNIDGEDAGRLIGKHGKTLNALQYLVN   59 (73)
T ss_dssp             TTTEEEEEEESCCCHHHCTTHHHHHHHHHHHHH
T ss_pred             CceEEEEEECCCccceEECCCCeeHHHHHHHHH
Confidence            345677888999999999999999999997654

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

Probab=87.18  E-value=0.59  Score=36.46  Aligned_cols=38  Identities=32%  Similarity=0.484  Sum_probs=30.4

Q ss_pred             EEEEEecccc-----ccceeccCCchHHHHHHHh-CCEEEEeCC
Q 006943          555 TLEVLVPANA-----VGKVIGKAGSNLANIRKIS-GATIEMSDS  592 (624)
Q Consensus       555 ~~~i~VP~~~-----vg~IIGkgG~~I~~I~~~s-Ga~I~i~~~  592 (624)
                      ...+.|-...     +|..||++|.+|+.|+++. |-+|.|-.-
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            5667777777     8999999999999999999 899987654

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

Probab=87.07  E-value=1.4  Score=46.78  Aligned_cols=40  Identities=30%  Similarity=0.496  Sum_probs=36.3

Q ss_pred             eeEEEEEeccceeEEEeCCchHHHHHHHhcCCeEEEccCC
Q 006943          140 EECQILVPSSQSANIIGKAGATIKRLRSKTRTSIKVTPKD  179 (624)
Q Consensus       140 ~~~~llvp~~~~g~iIGk~G~~Ik~I~~~sga~I~i~~~~  179 (624)
                      -...+.||..+++.+|||+|.+|++|+++.|-+|.|.+.+
T Consensus       486 ~~avv~vpe~~i~~vigk~g~~i~~ie~klgi~I~v~~~e  525 (604)
T COG1855         486 GRAVVKVPEKYIPKVIGKGGKRIKEIEKKLGIKIDVKPLE  525 (604)
T ss_pred             CeEEEEeCHHHhhHHhhcccchHHHHHHHhCCceEEEEcc
Confidence            3467899999999999999999999999999999998754

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

Probab=86.95  E-value=0.84  Score=34.94  Aligned_cols=34  Identities=26%  Similarity=0.404  Sum_probs=27.0

Q ss_pred             EEEEEEecCcccceeccCCchHHHHHHHhcCCeE
Q 006943           37 VIYRILCPDGVIGSVIGKSGKVINSIRQETRARV   70 (624)
Q Consensus        37 ~~~~ilvp~~~~g~vIGk~G~~I~~i~~etg~~I   70 (624)
                      ....+.+.....|.+|||+|.+++.|+..++-.+
T Consensus        25 ~~~~i~~~~~~~g~lIGk~G~~l~~l~~l~~~~~   58 (68)
T cd02409          25 IEIIIVVARGQPGLVIGKKGQNIRALQKLLQKLL   58 (68)
T ss_pred             EEEEEEECCCCCceEECCCCccHHHHHHHHHHHc
Confidence            4555666665789999999999999999987443

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.

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

Probab=86.93  E-value=1  Score=34.45  Aligned_cols=33  Identities=27%  Similarity=0.491  Sum_probs=27.2

Q ss_pred             EEEEEeccccccceeccCCchHHHHHHHhCCEE
Q 006943          555 TLEVLVPANAVGKVIGKAGSNLANIRKISGATI  587 (624)
Q Consensus       555 ~~~i~VP~~~vg~IIGkgG~~I~~I~~~sGa~I  587 (624)
                      ...+.+.....|.+||++|++|+.|+..++-.+
T Consensus        26 ~~~i~~~~~~~g~lIGk~G~~l~~l~~l~~~~~   58 (68)
T cd02409          26 EIIIVVARGQPGLVIGKKGQNIRALQKLLQKLL   58 (68)
T ss_pred             EEEEEECCCCCceEECCCCccHHHHHHHHHHHc
Confidence            556666665689999999999999999998554

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.

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

Probab=86.65  E-value=0.54  Score=49.69  Aligned_cols=39  Identities=33%  Similarity=0.483  Sum_probs=36.4

Q ss_pred             EEEEEeccccccceeccCCchHHHHHHHhCCEEEEeCCC
Q 006943          555 TLEVLVPANAVGKVIGKAGSNLANIRKISGATIEMSDSK  593 (624)
Q Consensus       555 ~~~i~VP~~~vg~IIGkgG~~I~~I~~~sGa~I~i~~~~  593 (624)
                      ...+.||+.+++.||||+|.+|++|.+..|-+|.|....
T Consensus       487 ~avv~vpe~~i~~vigk~g~~i~~ie~klgi~I~v~~~e  525 (604)
T COG1855         487 RAVVKVPEKYIPKVIGKGGKRIKEIEKKLGIKIDVKPLE  525 (604)
T ss_pred             eEEEEeCHHHhhHHhhcccchHHHHHHHhCCceEEEEcc
Confidence            678999999999999999999999999999999998664

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

Probab=85.65  E-value=0.58  Score=36.49  Aligned_cols=35  Identities=31%  Similarity=0.630  Sum_probs=27.3

Q ss_pred             EEEecCcc-----cceeccCCchHHHHHHHhc-CCeEEeeC
Q 006943           40 RILCPDGV-----IGSVIGKSGKVINSIRQET-RARVKVVD   74 (624)
Q Consensus        40 ~ilvp~~~-----~g~vIGk~G~~I~~i~~et-g~~I~v~~   74 (624)
                      .+.+-+..     +|..||++|+.|+.|.++. |-+|.|-+
T Consensus         6 kvaV~~~~~~~d~vG~~iG~~G~rik~i~~~L~gekIdvV~   46 (69)
T PF13184_consen    6 KVAVKSGDPNIDPVGACIGKKGSRIKAISEELNGEKIDVVE   46 (69)
T ss_dssp             EEEEEESSTTS-HHHHHH-CCCCCHHHHHHHTTT-EEEEEE
T ss_pred             EEEEEcCCCCcCcceecCccccHHHHHHHHHhCCCeEEEEE
Confidence            45555555     8999999999999999999 88988743

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

Probab=84.45  E-value=2.4  Score=41.18  Aligned_cols=48  Identities=31%  Similarity=0.486  Sum_probs=40.7

Q ss_pred             EEEEEeccccccceeccCCchHHHHHHHhCCEEEEeCCCCCCCCeEEEEEcCHH
Q 006943          555 TLEVLVPANAVGKVIGKAGSNLANIRKISGATIEMSDSKSSRGDRVALISGTPE  608 (624)
Q Consensus       555 ~~~i~VP~~~vg~IIGkgG~~I~~I~~~sGa~I~i~~~~~~~~~r~v~I~Gt~e  608 (624)
                      -+-+.|+...|.++||++|++++.|.+.++|+|-+....     + |-|.|..+
T Consensus       147 G~iv~i~p~kVpRvig~~~sm~~~l~~~~~~~I~VG~NG-----~-IWV~~~~~  194 (239)
T COG1097         147 GQIVKIPPSKVPRVIGKKGSMLNMLKEKTGCEIIVGQNG-----R-IWVDGENE  194 (239)
T ss_pred             CEEEEEchhhcceEecCCCcHHHHhhhhcCeEEEEecCC-----E-EEecCCCc
Confidence            357899999999999999999999999999999998652     3 66666555

>PF07650 KH_2: KH domain syndrome, contains KH motifs

Probab=84.40  E-value=0.59  Score=37.37  Aligned_cols=34  Identities=35%  Similarity=0.462  Sum_probs=28.8

Q ss_pred             EEEEEecCcccceeccCCchHHHHHHHhcCCeEE
Q 006943           38 IYRILCPDGVIGSVIGKSGKVINSIRQETRARVK   71 (624)
Q Consensus        38 ~~~ilvp~~~~g~vIGk~G~~I~~i~~etg~~I~   71 (624)
                      ...+.+.....|.|||++|++|++|+++.+-.+.
T Consensus        26 ~~~i~i~~~~~~ivIGk~G~~ik~i~~~~~k~l~   59 (78)
T PF07650_consen   26 QIIIVIKASQPGIVIGKKGSNIKKIREELRKELE   59 (78)
T ss_dssp             EEEEEEEESSHHHHHTGGGHHHHHHHHHHHHHHH
T ss_pred             eEEEEEeCCCccHhHHhhhHHHHHHHHHHHHHHh
Confidence            4577888999999999999999999988765553

; 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 ....

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

Probab=84.15  E-value=1  Score=36.39  Aligned_cols=35  Identities=17%  Similarity=0.288  Sum_probs=30.4

Q ss_pred             EEEEecCcccceeccCCchHHHHHHHhcCCeEEee
Q 006943           39 YRILCPDGVIGSVIGKSGKVINSIRQETRARVKVV   73 (624)
Q Consensus        39 ~~ilvp~~~~g~vIGk~G~~I~~i~~etg~~I~v~   73 (624)
                      +++.+.....|.|||++|++|++|+++-.-...+.
T Consensus        32 i~I~I~tarPg~vIG~~G~~i~~L~~~L~k~~~~~   66 (81)
T cd02413          32 TEIIIRATRTQNVLGEKGRRIRELTSLVQKRFNFP   66 (81)
T ss_pred             EEEEEEeCCCceEECCCchhHHHHHHHHHHHhCCC
Confidence            78889999999999999999999999876666553

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.

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

Probab=83.73  E-value=2.3  Score=41.38  Aligned_cols=59  Identities=31%  Similarity=0.455  Sum_probs=46.9

Q ss_pred             EEEEeccceeEEEeCCchHHHHHHHhcCCeEEEccCCCCCCCCcccccCCceEEEecCHHH-HHHHHHHHHHHH
Q 006943          143 QILVPSSQSANIIGKAGATIKRLRSKTRTSIKVTPKDASEPTHSCAMEFDNFVLISGESEA-VKKALFAISAIM  215 (624)
Q Consensus       143 ~llvp~~~~g~iIGk~G~~Ik~I~~~sga~I~i~~~~~~~~~~~~~~~~~r~V~I~G~~~~-V~~A~~~I~~~l  215 (624)
                      -+.|++..+.++||++|+.++-|.+.++|+|-|-.+              ..|-|.|+.+. ...|..+|..+=
T Consensus       149 iv~i~p~kVpRvig~~~sm~~~l~~~~~~~I~VG~N--------------G~IWV~~~~~~~e~~~~~aI~~ie  208 (239)
T COG1097         149 IVKIPPSKVPRVIGKKGSMLNMLKEKTGCEIIVGQN--------------GRIWVDGENESLEELAIEAIRKIE  208 (239)
T ss_pred             EEEEchhhcceEecCCCcHHHHhhhhcCeEEEEecC--------------CEEEecCCCcchHHHHHHHHHHHh
Confidence            478999999999999999999999999999988653              45778888763 555665555443

>KOG2874 consensus rRNA processing protein [Translation, ribosomal structure and biogenesis; Cell cycle control, cell division, chromosome partitioning]

Probab=83.43  E-value=2.1  Score=42.05  Aligned_cols=51  Identities=14%  Similarity=0.272  Sum_probs=46.7

Q ss_pred             cceeccCCchHHHHHHHhCCEEEEeCCCCCCCCeEEEEEcCHHHHHHHHHHHHHHHhh
Q 006943          566 GKVIGKAGSNLANIRKISGATIEMSDSKSSRGDRVALISGTPEQKRAAENLIQAFIMA  623 (624)
Q Consensus       566 g~IIGkgG~~I~~I~~~sGa~I~i~~~~~~~~~r~v~I~Gt~e~v~~A~~lI~~~i~~  623 (624)
                      -++||.+|.+++.|+-.|.|-|-|..       .+|.+.|....++.++..+.+++.+
T Consensus       161 qRLiGpng~TLKAlelLT~CYilVqG-------~TVsaiGpfkGlkevr~IV~DcM~N  211 (356)
T KOG2874|consen  161 QRLIGPNGSTLKALELLTNCYILVQG-------NTVSAIGPFKGLKEVRKIVEDCMKN  211 (356)
T ss_pred             HHhcCCCchhHHHHHHHhhcEEEeeC-------cEEEeecCcchHHHHHHHHHHHHhc
Confidence            58999999999999999999999984       3489999999999999999999876

>cd02414 jag_KH jag_K homology RNA-binding domain

Probab=83.23  E-value=1.2  Score=35.59  Aligned_cols=33  Identities=18%  Similarity=0.335  Sum_probs=26.9

Q ss_pred             eEEEEEeccceeEEEeCCchHHHHHHHhcCCeE
Q 006943          141 ECQILVPSSQSANIIGKAGATIKRLRSKTRTSI  173 (624)
Q Consensus       141 ~~~llvp~~~~g~iIGk~G~~Ik~I~~~sga~I  173 (624)
                      .+.+-+.....|.||||.|++++.||--...-+
T Consensus        25 ~i~i~i~~~~~g~LIGk~G~tL~AlQ~L~~~~~   57 (77)
T cd02414          25 TVEVNISGDDIGLLIGKRGKTLDALQYLANLVL   57 (77)
T ss_pred             EEEEEEecCCCCeEECCCCccHHHHHHHHHHHH
Confidence            456777888999999999999999987655443

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.

>PRK13764 ATPase; Provisional

Probab=83.23  E-value=1.1  Score=50.21  Aligned_cols=41  Identities=32%  Similarity=0.455  Sum_probs=37.7

Q ss_pred             CcEEEEEeccccccceeccCCchHHHHHHHhCCEEEEeCCC
Q 006943          553 PLTLEVLVPANAVGKVIGKAGSNLANIRKISGATIEMSDSK  593 (624)
Q Consensus       553 ~~~~~i~VP~~~vg~IIGkgG~~I~~I~~~sGa~I~i~~~~  593 (624)
                      .....|.||+..++.+|||+|.+|++|.+..|.+|.|....
T Consensus       480 ~~~~~v~~~~~~~~~~~~k~~~~~~~~~~~~~~~i~v~~~~  520 (602)
T PRK13764        480 DNKAVVYVPEKDIPKVIGKGGKRIKKIEKKLGIDIDVRPLD  520 (602)
T ss_pred             CCeEEEEEChhhhhHHhccCcchHHHHHHHhCCceEEEEcc
Confidence            45788999999999999999999999999999999998654

>KOG3273 consensus Predicted RNA-binding protein Pno1p interacting with Nob1p and involved in 26S proteasome assembly [Posttranslational modification, protein turnover, chaperones]

Probab=82.58  E-value=0.69  Score=43.04  Aligned_cols=56  Identities=27%  Similarity=0.312  Sum_probs=49.2

Q ss_pred             eccceeEEEeCCchHHHHHHHhcCCeEEEccCCCCCCCCcccccCCceEEEecCHHHHHHHHHHHHHHHhh
Q 006943          147 PSSQSANIIGKAGATIKRLRSKTRTSIKVTPKDASEPTHSCAMEFDNFVLISGESEAVKKALFAISAIMYK  217 (624)
Q Consensus       147 p~~~~g~iIGk~G~~Ik~I~~~sga~I~i~~~~~~~~~~~~~~~~~r~V~I~G~~~~V~~A~~~I~~~l~~  217 (624)
                      -+..+|+|+||+|.+--.|++-|-++|.+.               +-.|.|-|..+++.-|...|+.+|--
T Consensus       176 lsRAIGRiaGk~GkTkfaIEn~trtrIVla---------------d~kIHiLG~~~niriAR~avcsLIlG  231 (252)
T KOG3273|consen  176 LSRAIGRIAGKGGKTKFAIENVTRTRIVLA---------------DSKIHILGAFQNIRIARDAVCSLILG  231 (252)
T ss_pred             HHHHHHHhhcCCCcceeeeeccceeEEEec---------------CceEEEeecchhhHHHHHhhHhhhcc
Confidence            356789999999999999999999999875               34589999999999999999999843

>PF07650 KH_2: KH domain syndrome, contains KH motifs

Probab=81.51  E-value=0.97  Score=36.13  Aligned_cols=34  Identities=32%  Similarity=0.474  Sum_probs=29.0

Q ss_pred             cEEEEEeccccccceeccCCchHHHHHHHhCCEE
Q 006943          554 LTLEVLVPANAVGKVIGKAGSNLANIRKISGATI  587 (624)
Q Consensus       554 ~~~~i~VP~~~vg~IIGkgG~~I~~I~~~sGa~I  587 (624)
                      ....+.+-...-|.|||++|++|++|++..+-.+
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            3678888999999999999999999988775544

; 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 ....

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

Probab=81.33  E-value=9  Score=34.36  Aligned_cols=38  Identities=21%  Similarity=0.447  Sum_probs=33.1

Q ss_pred             eeEEEEEeccceeEEEeCCchHHHHHHHhcCCeEEEcc
Q 006943          140 EECQILVPSSQSANIIGKAGATIKRLRSKTRTSIKVTP  177 (624)
Q Consensus       140 ~~~~llvp~~~~g~iIGk~G~~Ik~I~~~sga~I~i~~  177 (624)
                      .+-.+.|-...-|.+||++|.++++|..+||-+-.|..
T Consensus        76 ~tGEV~IeaeKPG~ViGk~g~~~reI~~~tgW~p~vvR  113 (145)
T cd02410          76 DTGEVIIEAEKPGLVIGKGGSTLREITRETGWAPKVVR  113 (145)
T ss_pred             CCcEEEEEEcCCeEEEecCchhHHHHHHHhCCeeEEEe
Confidence            34567777888899999999999999999999988875

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=81.24  E-value=3.7  Score=46.14  Aligned_cols=41  Identities=32%  Similarity=0.582  Sum_probs=37.0

Q ss_pred             ceeEEEEEeccceeEEEeCCchHHHHHHHhcCCeEEEccCC
Q 006943          139 KEECQILVPSSQSANIIGKAGATIKRLRSKTRTSIKVTPKD  179 (624)
Q Consensus       139 ~~~~~llvp~~~~g~iIGk~G~~Ik~I~~~sga~I~i~~~~  179 (624)
                      .-...+.||...++.+|||+|.+|++|+++.|.+|.|.+.+
T Consensus       480 ~~~~~v~~~~~~~~~~~~k~~~~~~~~~~~~~~~i~v~~~~  520 (602)
T PRK13764        480 DNKAVVYVPEKDIPKVIGKGGKRIKKIEKKLGIDIDVRPLD  520 (602)
T ss_pred             CCeEEEEEChhhhhHHhccCcchHHHHHHHhCCceEEEEcc
Confidence            34567899999999999999999999999999999998754

>cd02414 jag_KH jag_K homology RNA-binding domain

Probab=80.65  E-value=1.8  Score=34.51  Aligned_cols=34  Identities=24%  Similarity=0.406  Sum_probs=27.3

Q ss_pred             EEEEEecCCccceeeccCcchHHHHHhHhCCeEE
Q 006943          309 VIRVLCPFNKIGRVIGKGGGTIKSIRQASGAQID  342 (624)
Q Consensus       309 ~~~i~vp~~~vg~IIGk~G~~Ik~I~~~tga~I~  342 (624)
                      .+.+.+..+..|.+|||+|+++..|+--.+.-++
T Consensus        25 ~i~i~i~~~~~g~LIGk~G~tL~AlQ~L~~~~~~   58 (77)
T cd02414          25 TVEVNISGDDIGLLIGKRGKTLDALQYLANLVLN   58 (77)
T ss_pred             EEEEEEecCCCCeEECCCCccHHHHHHHHHHHHh
Confidence            4556677888999999999999999977665444

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.

---

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

ID	Length	Definition	E-value
Query	624
3krm_A	163	Imp1 Kh34 Length = 163		2e-05
2p2r_A	76	Crystal Structure Of The Third Kh Domain Of Human P		2e-05
1j5k_A	89	Complex Of The Kh3 Domain Of Hnrnp K With A Single_		7e-05
2ann_A	178	Crystal Structure (I) Of Nova-1 Kh1KH2 DOMAIN TANDE		7e-05
2anr_A	178	Crystal Structure (Ii) Of Nova-1 Kh1KH2 DOMAIN TAND		9e-05
1zzi_A	82	Crystal Structure Analysis Of The Third Kh Domain O		9e-05
1wvn_A	82	Crsytal Structure Of Domain 3 Of Human Alpha Polyc		1e-04

>pdb|3KRM|A Chain A, Imp1 Kh34 Length = 163

Iteration: 1
 Score = 47.4 bits (111), Expect = 2e-05,   Method: Compositional matrix adjust.
 Identities = 33/97 (34%), Positives = 48/97 (49%), Gaps = 10/97 (10%)
Query: 138 EKEECQILVPSSQSANIIGKAGATIKRLRSKTRTSIKVTPKDASEPTHSCAMEFDNFVLI 197
           E+E  Q+ +P+     IIGK G  IK+L      SIK+ P +   P     M     V+I
Sbjct: 1   EQEMVQVFIPAQAVGAIIGKKGQHIKQLSRFASASIKIAPPET--PDSKVRM-----VII 53
Query: 198 SGESEAVKKALFAISAIMYK---FSPREDIPLETTVR 231
           +G  EA  KA   I   + +   F P+E++ LET +R
Sbjct: 54  TGPPEAQFKAQGRIYGKLKEENFFGPKEEVKLETHIR 90

>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 = 47.4 bits (111), Expect = 2e-05,   Method: Compositional matrix adjust.
 Identities = 20/48 (41%), Positives = 32/48 (66%)
Query: 39 YRILCPDGVIGSVIGKSGKVINSIRQETRARVKVVDPFPGAKDRVVTI 86
          + +  P+ +IG +IG+ G  IN IRQ + A++K+ +P  G+ DR VTI
Sbjct: 7  HELTIPNDLIGCIIGRQGAKINEIRQXSGAQIKIANPVEGSTDRQVTI 54

>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 = 45.8 bits (107), Expect = 7e-05,   Method: Compositional matrix adjust.
 Identities = 19/47 (40%), Positives = 32/47 (68%)
Query: 40 RILCPDGVIGSVIGKSGKVINSIRQETRARVKVVDPFPGAKDRVVTI 86
          ++  P  + GS+IGK G+ I  IR E+ A +K+ +P  G++DR++TI
Sbjct: 17 QVTIPKDLAGSIIGKGGQRIKQIRHESGASIKIDEPLEGSEDRIITI 63

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

Iteration: 1
 Score = 45.8 bits (107), Expect = 7e-05,   Method: Compositional matrix adjust.
 Identities = 46/189 (24%), Positives = 76/189 (40%), Gaps = 47/189 (24%)
Query: 38  IYRILCPDGVIGSVIGKSGKVINSIRQETRARVKVV---DPFPGAKDRVVTIYSHXXXXX 94
             ++L P    GS+IGK G+ I  +++ET A +K+    D +PG  +RV  I        
Sbjct: 7   FLKVLIPSYAAGSIIGKGGQTIVQLQKETGATIKLSKSKDFYPGTTERVCLIQGTI---- 62
Query: 95  XXXXXXXXXXXXPLCAAQDALLKVHXXXXXXXXXXTDNDKKRK--------------EKE 140
                             +AL  VH            N  K +                 
Sbjct: 63  ------------------EALNAVHGFIAEKIREMPQNVAKTEPVSILQPQTTVNPDRAN 104
Query: 141 ECQILVPSSQSANIIGKAGATIKRLRSKTRTSIKVTPKDASEPTHSCAMEFDN-FVLISG 199
           + +I+VP+S +  IIGK GAT+K +  ++   ++++ K          +   N  V +SG
Sbjct: 105 QVKIIVPNSTAGLIIGKGGATVKAIMEQSGAWVQLSQKPD-------GINLQNRVVTVSG 157
Query: 200 ESEAVKKAL 208
           E E  +KA+
Sbjct: 158 EPEQNRKAV 166

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

Iteration: 1
 Score = 45.4 bits (106), Expect = 9e-05,   Method: Compositional matrix adjust.
 Identities = 47/189 (24%), Positives = 77/189 (40%), Gaps = 47/189 (24%)
Query: 38  IYRILCPDGVIGSVIGKSGKVINSIRQETRARVKVV---DPFPGAKDRVVTIYSHXXXXX 94
             ++L P    GS+IGK G+ I  +++ET A +K+    D +PG  +RV  I        
Sbjct: 7   FLKVLIPSYAAGSIIGKGGQTIVQLQKETGATIKLSKSKDFYPGTTERVCLIQGTI---- 62
Query: 95  XXXXXXXXXXXXPLCAAQDALLKVHXXXXXXXXXXTDNDKKRK--------------EKE 140
                             +AL  VH            N  K +                 
Sbjct: 63  ------------------EALNAVHGFIAEKIREXPQNVAKTEPVSILQPQTTVNPDRAN 104
Query: 141 ECQILVPSSQSANIIGKAGATIKRLRSKTRTSIKVTPKDASEPTHSCAMEFDN-FVLISG 199
           + +I+VP+S +  IIGK GAT+K +  ++   ++++ K          +   N  V +SG
Sbjct: 105 QVKIIVPNSTAGLIIGKGGATVKAIXEQSGAWVQLSQKPD-------GINLQNRVVTVSG 157
Query: 200 ESEAVKKAL 208
           E E  +KA+
Sbjct: 158 EPEQNRKAV 166

>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 = 45.4 bits (106), Expect = 9e-05,   Method: Compositional matrix adjust.
 Identities = 19/47 (40%), Positives = 32/47 (68%)
Query: 40 RILCPDGVIGSVIGKSGKVINSIRQETRARVKVVDPFPGAKDRVVTI 86
          ++  P  + GS+IGK G+ I  IR E+ A +K+ +P  G++DR++TI
Sbjct: 10 QVTIPKDLAGSIIGKGGQRIKQIRHESGASIKIDEPLEGSEDRIITI 56

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

Iteration: 1
 Score = 45.1 bits (105), Expect = 1e-04,   Method: Compositional matrix adjust.
 Identities = 19/48 (39%), Positives = 31/48 (64%)
Query: 39 YRILCPDGVIGSVIGKSGKVINSIRQETRARVKVVDPFPGAKDRVVTI 86
          + +  P+ +IG +IG+ G  IN IRQ + A++K+ +P  G+  R VTI
Sbjct: 8  HELTIPNNLIGCIIGRQGANINEIRQMSGAQIKIANPVEGSSGRQVTI 55

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Length	Definition	E-value
Query	624
2anr_A	178	Neuro-oncological ventral antigen 1; protein-RNA c	8e-35
2anr_A	178	Neuro-oncological ventral antigen 1; protein-RNA c	1e-28
2anr_A	178	Neuro-oncological ventral antigen 1; protein-RNA c	6e-14
2anr_A	178	Neuro-oncological ventral antigen 1; protein-RNA c	4e-12
2anr_A	178	Neuro-oncological ventral antigen 1; protein-RNA c	6e-11
2anr_A	178	Neuro-oncological ventral antigen 1; protein-RNA c	9e-09
2jzx_A	160	Poly(RC)-binding protein 2; PCBP2, KH domains, RNA	2e-34
2jzx_A	160	Poly(RC)-binding protein 2; PCBP2, KH domains, RNA	7e-29
2jzx_A	160	Poly(RC)-binding protein 2; PCBP2, KH domains, RNA	7e-12
2jzx_A	160	Poly(RC)-binding protein 2; PCBP2, KH domains, RNA	5e-11
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-08
3krm_A	163	Insulin-like growth factor 2 mRNA-binding protein	4e-33
3krm_A	163	Insulin-like growth factor 2 mRNA-binding protein	9e-30
3krm_A	163	Insulin-like growth factor 2 mRNA-binding protein	9e-12
3krm_A	163	Insulin-like growth factor 2 mRNA-binding protein	5e-11
3krm_A	163	Insulin-like growth factor 2 mRNA-binding protein	3e-10
3krm_A	163	Insulin-like growth factor 2 mRNA-binding protein	1e-07
1j4w_A	174	FUSE binding protein; single-stranded DNA binding	4e-30
1j4w_A	174	FUSE binding protein; single-stranded DNA binding	1e-28
1j4w_A	174	FUSE binding protein; single-stranded DNA binding	8e-18
1j4w_A	174	FUSE binding protein; single-stranded DNA binding	2e-13
1j4w_A	174	FUSE binding protein; single-stranded DNA binding	4e-12
1j4w_A	174	FUSE binding protein; single-stranded DNA binding	4e-09
2jvz_A	164	KH type-splicing, FAR upstream element-binding pro	3e-28
2jvz_A	164	KH type-splicing, FAR upstream element-binding pro	1e-26
2jvz_A	164	KH type-splicing, FAR upstream element-binding pro	5e-14
2jvz_A	164	KH type-splicing, FAR upstream element-binding pro	4e-12
2jvz_A	164	KH type-splicing, FAR upstream element-binding pro	1e-11
2jvz_A	164	KH type-splicing, FAR upstream element-binding pro	6e-10
1zzk_A	82	Heterogeneous nuclear ribonucleoprotein K; KH domi	1e-22
1zzk_A	82	Heterogeneous nuclear ribonucleoprotein K; KH domi	1e-14
1zzk_A	82	Heterogeneous nuclear ribonucleoprotein K; KH domi	9e-13
1zzk_A	82	Heterogeneous nuclear ribonucleoprotein K; KH domi	8e-10
1zzk_A	82	Heterogeneous nuclear ribonucleoprotein K; KH domi	8e-10
1wvn_A	82	Poly(RC)-binding protein 1; KH domain, RNA binding	6e-22
1wvn_A	82	Poly(RC)-binding protein 1; KH domain, RNA binding	1e-12
1wvn_A	82	Poly(RC)-binding protein 1; KH domain, RNA binding	5e-12
1wvn_A	82	Poly(RC)-binding protein 1; KH domain, RNA binding	2e-10
1wvn_A	82	Poly(RC)-binding protein 1; KH domain, RNA binding	6e-09
1j5k_A	89	Heterogeneous nuclear ribonucleoprotein K; single-	1e-20
1j5k_A	89	Heterogeneous nuclear ribonucleoprotein K; single-	1e-14
1j5k_A	89	Heterogeneous nuclear ribonucleoprotein K; single-	9e-13
1j5k_A	89	Heterogeneous nuclear ribonucleoprotein K; single-	4e-10
1j5k_A	89	Heterogeneous nuclear ribonucleoprotein K; single-	5e-10
2p2r_A	76	Poly(RC)-binding protein 2; protein-DNA complex, R	7e-20
2p2r_A	76	Poly(RC)-binding protein 2; protein-DNA complex, R	9e-14
2p2r_A	76	Poly(RC)-binding protein 2; protein-DNA complex, R	1e-12
2p2r_A	76	Poly(RC)-binding protein 2; protein-DNA complex, R	5e-11
2p2r_A	76	Poly(RC)-binding protein 2; protein-DNA complex, R	8e-09
1x4n_A	92	FAR upstream element binding protein 1; KH domain,	1e-18
1x4n_A	92	FAR upstream element binding protein 1; KH domain,	1e-10
1x4n_A	92	FAR upstream element binding protein 1; KH domain,	3e-10
1x4n_A	92	FAR upstream element binding protein 1; KH domain,	2e-08
1x4n_A	92	FAR upstream element binding protein 1; KH domain,	1e-07
2axy_A	73	Poly(RC)-binding protein 2; protein-DNA complex, D	8e-18
2axy_A	73	Poly(RC)-binding protein 2; protein-DNA complex, D	2e-14
2axy_A	73	Poly(RC)-binding protein 2; protein-DNA complex, D	7e-13
2axy_A	73	Poly(RC)-binding protein 2; protein-DNA complex, D	4e-11
2axy_A	73	Poly(RC)-binding protein 2; protein-DNA complex, D	2e-10
1dtj_A	76	RNA-binding neurooncological ventral antigen 2; KH	2e-17
1dtj_A	76	RNA-binding neurooncological ventral antigen 2; KH	8e-12
1dtj_A	76	RNA-binding neurooncological ventral antigen 2; KH	8e-12
1dtj_A	76	RNA-binding neurooncological ventral antigen 2; KH	6e-11
1dtj_A	76	RNA-binding neurooncological ventral antigen 2; KH	1e-10
1ec6_A	87	RNA-binding protein NOVA-2; KH domain, alpha-beta	2e-17
1ec6_A	87	RNA-binding protein NOVA-2; KH domain, alpha-beta	2e-11
1ec6_A	87	RNA-binding protein NOVA-2; KH domain, alpha-beta	5e-11
1ec6_A	87	RNA-binding protein NOVA-2; KH domain, alpha-beta	1e-10
1ec6_A	87	RNA-binding protein NOVA-2; KH domain, alpha-beta	3e-10
1x4m_A	94	FAR upstream element binding protein 1; KH domain,	5e-17
1x4m_A	94	FAR upstream element binding protein 1; KH domain,	7e-12
1x4m_A	94	FAR upstream element binding protein 1; KH domain,	2e-09
1x4m_A	94	FAR upstream element binding protein 1; KH domain,	2e-09
1x4m_A	94	FAR upstream element binding protein 1; KH domain,	5e-09
2hh3_A	106	KH-type splicing regulatory protein; KH-RNA bindin	3e-16
2hh3_A	106	KH-type splicing regulatory protein; KH-RNA bindin	4e-10
2hh3_A	106	KH-type splicing regulatory protein; KH-RNA bindin	4e-10
2hh3_A	106	KH-type splicing regulatory protein; KH-RNA bindin	4e-09
2hh3_A	106	KH-type splicing regulatory protein; KH-RNA bindin	1e-08
2hh2_A	107	KH-type splicing regulatory protein; KH-RNA bindin	3e-16
2hh2_A	107	KH-type splicing regulatory protein; KH-RNA bindin	8e-11
2hh2_A	107	KH-type splicing regulatory protein; KH-RNA bindin	1e-09
2hh2_A	107	KH-type splicing regulatory protein; KH-RNA bindin	5e-09
2hh2_A	107	KH-type splicing regulatory protein; KH-RNA bindin	2e-07
2opv_A	85	KHSRP protein; KH domain, RNA binding protein, KSR	5e-16
2opv_A	85	KHSRP protein; KH domain, RNA binding protein, KSR	4e-12
2opv_A	85	KHSRP protein; KH domain, RNA binding protein, KSR	1e-10
2opv_A	85	KHSRP protein; KH domain, RNA binding protein, KSR	2e-10
2opv_A	85	KHSRP protein; KH domain, RNA binding protein, KSR	2e-09
1we8_A	104	Tudor and KH domain containing protein; structural	3e-13
1we8_A	104	Tudor and KH domain containing protein; structural	9e-12
1we8_A	104	Tudor and KH domain containing protein; structural	3e-08
1we8_A	104	Tudor and KH domain containing protein; structural	1e-07
1we8_A	104	Tudor and KH domain containing protein; structural	2e-07
2qnd_A	144	FMR1 protein; KH domain, eukaryotic KH domains, ta	2e-12
2qnd_A	144	FMR1 protein; KH domain, eukaryotic KH domains, ta	2e-06
2qnd_A	144	FMR1 protein; KH domain, eukaryotic KH domains, ta	2e-04
2qnd_A	144	FMR1 protein; KH domain, eukaryotic KH domains, ta	5e-04
1vt4_I	1221	APAF-1 related killer DARK; drosophila apoptosome,	3e-11
2dgr_A	83	Ring finger and KH domain-containing protein 1; st	3e-10
2dgr_A	83	Ring finger and KH domain-containing protein 1; st	5e-06
2dgr_A	83	Ring finger and KH domain-containing protein 1; st	2e-05
2cte_A	94	Vigilin; K homology type I domain, RNA-binding, ce	7e-09
2cte_A	94	Vigilin; K homology type I domain, RNA-binding, ce	2e-08
2cte_A	94	Vigilin; K homology type I domain, RNA-binding, ce	1e-07
2cte_A	94	Vigilin; K homology type I domain, RNA-binding, ce	2e-06
2cte_A	94	Vigilin; K homology type I domain, RNA-binding, ce	2e-05
2e3u_A	219	PH-DIM2P, hypothetical protein PH1566; PRE-ribosom	4e-08
2e3u_A	219	PH-DIM2P, hypothetical protein PH1566; PRE-ribosom	4e-07
3n89_A	376	Defective in GERM LINE development protein 3, ISO;	5e-08
2ctl_A	97	Vigilin; K homology type I domain, RNA-binding, ce	1e-07
2ctl_A	97	Vigilin; K homology type I domain, RNA-binding, ce	5e-07
2ctl_A	97	Vigilin; K homology type I domain, RNA-binding, ce	4e-06
2ctl_A	97	Vigilin; K homology type I domain, RNA-binding, ce	8e-05
2ctl_A	97	Vigilin; K homology type I domain, RNA-binding, ce	2e-04
2ctm_A	95	Vigilin; K homology type I domain, RNA-binding, ce	2e-07
2ctm_A	95	Vigilin; K homology type I domain, RNA-binding, ce	8e-06
2ctm_A	95	Vigilin; K homology type I domain, RNA-binding, ce	3e-05
1tua_A	191	Hypothetical protein APE0754; structural genomics,	7e-07
1tua_A	191	Hypothetical protein APE0754; structural genomics,	5e-05
1vig_A	71	Vigilin; RNA-binding protein, ribonucleoprotein; N	2e-06
1vig_A	71	Vigilin; RNA-binding protein, ribonucleoprotein; N	4e-06
1vig_A	71	Vigilin; RNA-binding protein, ribonucleoprotein; N	4e-06
1vig_A	71	Vigilin; RNA-binding protein, ribonucleoprotein; N	6e-05
2ctk_A	104	Vigilin; K homology type I domain, RNA-binding, ce	4e-06
2ctk_A	104	Vigilin; K homology type I domain, RNA-binding, ce	5e-06
2ctk_A	104	Vigilin; K homology type I domain, RNA-binding, ce	6e-06
2ctk_A	104	Vigilin; K homology type I domain, RNA-binding, ce	1e-04
2ctk_A	104	Vigilin; K homology type I domain, RNA-binding, ce	2e-04
1e3p_A	757	Guanosine pentaphosphate synthetase; polyribonucle	2e-05
3cdi_A	723	Polynucleotide phosphorylase; mRNA turnover, RNAse	2e-05
3u1k_A	630	Polyribonucleotide nucleotidyltransferase 1, MITO;	2e-05
4aid_A	726	Polyribonucleotide nucleotidyltransferase; transfe	2e-05

>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 =  129 bits (325), Expect = 8e-35
 Identities = 46/176 (26%), Positives = 84/176 (47%), Gaps = 19/176 (10%)

Query: 305 SEELVIRVLCPFNKIGRVIGKGGGTIKSIRQASGAQIDVDDTKD---NRDECVITVTA-I 360
             +  ++VL P    G +IGKGG TI  +++ +GA I +  +KD      E V  +   I
Sbjct: 3   GSQYFLKVLIPSYAAGSIIGKGGQTIVQLQKETGATIKLSKSKDFYPGTTERVCLIQGTI 62

Query: 361 ESPDDIKSMAVEAVL-------------LLQTKINDEDDDTVTIRLLVSSKVIGCIIGKS 407
           E+ + +     E +              +LQ +     D    ++++V +   G IIGK 
Sbjct: 63  EALNAVHGFIAEKIREMPQNVAKTEPVSILQPQTTVNPDRANQVKIIVPNSTAGLIIGKG 122

Query: 408 GSIINEIRKRTKADVRISKGDKPKCADANDELVEVVGEVGSVRDALVQIILRLRDD 463
           G+ +  I +++ A V++S+  KP   +  + +V V GE    R A+  II ++++D
Sbjct: 123 GATVKAIMEQSGAWVQLSQ--KPDGINLQNRVVTVSGEPEQNRKAVELIIQKIQED 176

>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 =  111 bits (280), Expect = 1e-28
 Identities = 42/187 (22%), Positives = 79/187 (42%), Gaps = 23/187 (12%)

Query: 35  ESVIYRILCPDGVIGSVIGKSGKVINSIRQETRARVKVV---DPFPGAKDRVVTIYSHVK 91
                ++L P    GS+IGK G+ I  +++ET A +K+    D +PG  +RV  I     
Sbjct: 4   SQYFLKVLIPSYAAGSIIGKGGQTIVQLQKETGATIKLSKSKDFYPGTTERVCLIQG--- 60

Query: 92  DKEDVEVDDEFNDKEPLCAAQDALLKVHAAIANAVANATDNDKKRKE---KEECQILVPS 148
             E +                + + ++   +A     +    +         + +I+VP+
Sbjct: 61  TIEALN--------AVHGFIAEKIREMPQNVAKTEPVSILQPQTTVNPDRANQVKIIVPN 112

Query: 149 SQSANIIGKAGATIKRLRSKTRTSIKVTPKDASEPTHSCAMEFDNFVLISGESEAVKKAL 208
           S +  IIGK GAT+K +  ++   ++++ K             +  V +SGE E  +KA+
Sbjct: 113 STAGLIIGKGGATVKAIMEQSGAWVQLSQKP------DGINLQNRVVTVSGEPEQNRKAV 166

Query: 209 FAISAIM 215
             I   +
Sbjct: 167 ELIIQKI 173

>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 = 69.5 bits (170), Expect = 6e-14
 Identities = 51/245 (20%), Positives = 85/245 (34%), Gaps = 78/245 (31%)

Query: 143 QILVPSSQSANIIGKAGATIKRLRSKTRTSIKVTPKDASEPTHSCAMEFDNFVLISGESE 202
           ++L+PS  + +IIGK G TI +L+ +T  +IK++      P  +     +   LI G  E
Sbjct: 9   KVLIPSYAAGSIIGKGGQTIVQLQKETGATIKLSKSKDFYPGTT-----ERVCLIQGTIE 63

Query: 203 AVKKALFAISAIMYKFSPREDIPLETTVREAPPSIIIPSDVPIYPPGGLYPNADPILPSR 262
           A+      I+                 +RE P ++     V I  P              
Sbjct: 64  ALNAVHGFIAEK---------------IREMPQNVAKTEPVSILQPQTTVNPDRANQVKI 108

Query: 263 SVPSILGAARVPDLQGYADTGNTWPVYSTGLSLVSGLVGASQSEELVIRVLCPFNKIGRV 322
            VP+                           S    ++G                     
Sbjct: 109 IVPN---------------------------STAGLIIG--------------------- 120

Query: 323 IGKGGGTIKSIRQASGAQIDVDDTKD--NRDECVITVTAIESPDDIKSMAVEAVLLLQTK 380
             KGG T+K+I + SGA + +    D  N    V+TV+    P+  +    +AV L+  K
Sbjct: 121 --KGGATVKAIMEQSGAWVQLSQKPDGINLQNRVVTVSG--EPEQNR----KAVELIIQK 172

Query: 381 INDED 385
           I ++ 
Sbjct: 173 IQEDP 177

>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 = 64.1 bits (156), Expect = 4e-12
 Identities = 29/75 (38%), Positives = 40/75 (53%), Gaps = 3/75 (4%)

Query: 550 LPPPLTLEVLVPANAVGKVIGKAGSNLANIRKISGATIEMSDSKSSRG---DRVALISGT 606
           L     L+VL+P+ A G +IGK G  +  ++K +GATI++S SK       +RV LI GT
Sbjct: 2   LGSQYFLKVLIPSYAAGSIIGKGGQTIVQLQKETGATIKLSKSKDFYPGTTERVCLIQGT 61

Query: 607 PEQKRAAENLIQAFI 621
            E   A    I   I
Sbjct: 62  IEALNAVHGFIAEKI 76

>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 = 60.6 bits (147), Expect = 6e-11
 Identities = 25/90 (27%), Positives = 43/90 (47%), Gaps = 2/90 (2%)

Query: 534 SPYGSMSSYSSKLYGGLPPPLTLEVLVPANAVGKVIGKAGSNLANIRKISGATIEMSDSK 593
           +    +S    +          ++++VP +  G +IGK G+ +  I + SGA +++S   
Sbjct: 84  AKTEPVSILQPQTTVNPDRANQVKIIVPNSTAGLIIGKGGATVKAIMEQSGAWVQLSQKP 143

Query: 594 S--SRGDRVALISGTPEQKRAAENLIQAFI 621
              +  +RV  +SG PEQ R A  LI   I
Sbjct: 144 DGINLQNRVVTVSGEPEQNRKAVELIIQKI 173

>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 = 54.5 bits (131), Expect = 9e-09
 Identities = 14/78 (17%), Positives = 34/78 (43%), Gaps = 2/78 (2%)

Query: 11  QRDNDRDGKNQKRRINEKDEKGNEESVIYRILCPDGVIGSVIGKSGKVINSIRQETRARV 70
           +   +         +  +     + +   +I+ P+   G +IGK G  + +I +++ A V
Sbjct: 78  EMPQNVAKTEPVSILQPQTTVNPDRANQVKIIVPNSTAGLIIGKGGATVKAIMEQSGAWV 137

Query: 71  KVV--DPFPGAKDRVVTI 86
           ++         ++RVVT+
Sbjct: 138 QLSQKPDGINLQNRVVTV 155

>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 =  127 bits (320), Expect = 2e-34
 Identities = 44/164 (26%), Positives = 81/164 (49%), Gaps = 10/164 (6%)

Query: 304 QSEELVIRVLCPFNKIGRVIGKGGGTIKSIRQASGAQIDVDDTKDNRDECVITVTAIESP 363
           ++  L IR+L    ++G +IGK G ++K +R+ SGA+I++ +   N  E +IT+    + 
Sbjct: 1   KNVTLTIRLLMHGKEVGSIIGKKGESVKKMREESGARINISE--GNCPERIITLAGPTNA 58

Query: 364 -----DDIKSMAVEAVLLLQTKINDEDDDTVTIRLLVSSKVIGCIIGKSGSIINEIRKRT 418
                  I     E +    T         VT+RL+V +   G +IGK G  I EIR+ T
Sbjct: 59  IFKAFAMIIDKLEEDISSSMTNSTAASRPPVTLRLVVPASQCGSLIGKGGCKIKEIREST 118

Query: 419 KADVRISKGDKPKCADANDELVEVVGEVGSVRDALVQIILRLRD 462
            A V+++    P   ++ +  + + G   S+ + + QI + + +
Sbjct: 119 GAQVQVAGDMLP---NSTERAITIAGIPQSIIECVKQICVVMLE 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 =  111 bits (280), Expect = 7e-29
 Identities = 35/183 (19%), Positives = 76/183 (41%), Gaps = 28/183 (15%)

Query: 34  EESVIYRILCPDGVIGSVIGKSGKVINSIRQETRARVKVVDPFPGAKDRVVTIYSHVKDK 93
             ++  R+L     +GS+IGK G+ +  +R+E+ AR+ + +      +R++T+       
Sbjct: 2   NVTLTIRLLMHGKEVGSIIGKKGESVKKMREESGARINISE--GNCPERIITLAG----- 54

Query: 94  EDVEVDDEFNDKEPLCAAQDALLKVHAAIANAVANATDNDKKRKEKE-ECQILVPSSQSA 152
                        P  A   A   +   +   ++++  N           +++VP+SQ  
Sbjct: 55  -------------PTNAIFKAFAMIIDKLEEDISSSMTNSTAASRPPVTLRLVVPASQCG 101

Query: 153 NIIGKAGATIKRLRSKTRTSIKVTPKDASEPTHSCAMEFDNFVLISGESEAVKKALFAIS 212
           ++IGK G  IK +R  T   ++V                +  + I+G  +++ + +  I 
Sbjct: 102 SLIGKGGCKIKEIRESTGAQVQVAGDM-------LPNSTERAITIAGIPQSIIECVKQIC 154

Query: 213 AIM 215
            +M
Sbjct: 155 VVM 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 = 62.9 bits (153), Expect = 7e-12
 Identities = 19/69 (27%), Positives = 35/69 (50%), Gaps = 2/69 (2%)

Query: 553 PLTLEVLVPANAVGKVIGKAGSNLANIRKISGATIEMSDSKSSRGDRVALISGTPEQKRA 612
            LT+ +L+    VG +IGK G ++  +R+ SGA I +S+      +R+  ++G       
Sbjct: 4   TLTIRLLMHGKEVGSIIGKKGESVKKMREESGARINISEGNCP--ERIITLAGPTNAIFK 61

Query: 613 AENLIQAFI 621
           A  +I   +
Sbjct: 62  AFAMIIDKL 70

>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 = 60.6 bits (147), Expect = 5e-11
 Identities = 22/75 (29%), Positives = 39/75 (52%), Gaps = 1/75 (1%)

Query: 548 GGLPPPLTLEVLVPANAVGKVIGKAGSNLANIRKISGATIEMS-DSKSSRGDRVALISGT 606
               PP+TL ++VPA+  G +IGK G  +  IR+ +GA ++++ D   +  +R   I+G 
Sbjct: 83  AASRPPVTLRLVVPASQCGSLIGKGGCKIKEIRESTGAQVQVAGDMLPNSTERAITIAGI 142

Query: 607 PEQKRAAENLIQAFI 621
           P+        I   +
Sbjct: 143 PQSIIECVKQICVVM 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 = 56.3 bits (136), Expect = 2e-09
 Identities = 26/84 (30%), Positives = 42/84 (50%), Gaps = 7/84 (8%)

Query: 301 GASQSEELVIRVLCPFNKIGRVIGKGGGTIKSIRQASGAQIDVD-DTKDNRDECVITVTA 359
            A+    + +R++ P ++ G +IGKGG  IK IR+++GAQ+ V  D   N  E  IT+  
Sbjct: 82  TAASRPPVTLRLVVPASQCGSLIGKGGCKIKEIRESTGAQVQVAGDMLPNSTERAITIA- 140

Query: 360 IESPDDIKSMAVEAVLLLQTKIND 383
              P  I     E V  +   + +
Sbjct: 141 -GIPQSII----ECVKQICVVMLE 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 = 54.0 bits (130), Expect = 1e-08
 Identities = 21/59 (35%), Positives = 31/59 (52%), Gaps = 1/59 (1%)

Query: 29  DEKGNEESVIYRILCPDGVIGSVIGKSGKVINSIRQETRARVKVV-DPFPGAKDRVVTI 86
               +   V  R++ P    GS+IGK G  I  IR+ T A+V+V  D  P + +R +TI
Sbjct: 81  STAASRPPVTLRLVVPASQCGSLIGKGGCKIKEIRESTGAQVQVAGDMLPNSTERAITI 139

>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 =  123 bits (311), Expect = 4e-33
 Identities = 31/159 (19%), Positives = 70/159 (44%), Gaps = 3/159 (1%)

Query: 306 EELVIRVLCPFNKIGRVIGKGGGTIKSIRQASGAQIDVDDTKD-NRDECVITVTAIESPD 364
           E+ +++V  P   +G +IGK G  IK + + + A I +   +  +    ++ +T      
Sbjct: 1   EQEMVQVFIPAQAVGAIIGKKGQHIKQLSRFASASIKIAPPETPDSKVRMVIITGPPEAQ 60

Query: 365 DIKSMAVEAVLLLQTKINDEDDDTVTIRLLVSSKVIGCIIGKSGSIINEIRKRTKADVRI 424
                 +   L  +     +++  +   + V +   G +IGK G  +NE++  T A+V +
Sbjct: 61  FKAQGRIYGKLKEENFFGPKEEVKLETHIRVPASAAGRVIGKGGKTVNELQNLTAAEVVV 120

Query: 425 SKGDKPKCADANDELVEVVGEVGSVRDALVQIILRLRDD 463
            +   P   + +  +V+++G   + + A  +I   L   
Sbjct: 121 PRDQTP--DENDQVIVKIIGHFYASQMAQRKIRDILAQV 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 =  114 bits (287), Expect = 9e-30
 Identities = 41/189 (21%), Positives = 69/189 (36%), Gaps = 29/189 (15%)

Query: 35  ESVIYRILCPDGVIGSVIGKSGKVINSIRQETRARVKVVDPF-PGAKDRVVTIYSHVKDK 93
           E  + ++  P   +G++IGK G+ I  + +   A +K+  P  P +K R+V I       
Sbjct: 1   EQEMVQVFIPAQAVGAIIGKKGQHIKQLSRFASASIKIAPPETPDSKVRMVIIT------ 54

Query: 94  EDVEVDDEFNDKEPLCAAQDALLKVHAAIANAVANATDNDKKRKEKEECQILVPSSQSAN 153
                              +A  K    I   +        K + K E  I VP+S +  
Sbjct: 55  ----------------GPPEAQFKAQGRIYGKLKEENFFGPKEEVKLETHIRVPASAAGR 98

Query: 154 IIGKAGATIKRLRSKTRTSIKVTPKDASEPTHSCAMEFDNFVLISGESEAVKKALFAISA 213
           +IGK G T+  L++ T   + V      +            V I G   A + A   I  
Sbjct: 99  VIGKGGKTVNELQNLTAAEVVVPRDQTPDEND------QVIVKIIGHFYASQMAQRKIRD 152

Query: 214 IMYKFSPRE 222
           I+ +   + 
Sbjct: 153 ILAQVKQQH 161

>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 = 62.9 bits (153), Expect = 9e-12
 Identities = 19/69 (27%), Positives = 40/69 (57%), Gaps = 1/69 (1%)

Query: 554 LTLEVLVPANAVGKVIGKAGSNLANIRKISGATIEMSDSKSS-RGDRVALISGTPEQKRA 612
             ++V +PA AVG +IGK G ++  + + + A+I+++  ++     R+ +I+G PE +  
Sbjct: 3   EMVQVFIPAQAVGAIIGKKGQHIKQLSRFASASIKIAPPETPDSKVRMVIITGPPEAQFK 62

Query: 613 AENLIQAFI 621
           A+  I   +
Sbjct: 63  AQGRIYGKL 71

>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 = 60.6 bits (147), Expect = 5e-11
 Identities = 16/73 (21%), Positives = 32/73 (43%), Gaps = 2/73 (2%)

Query: 551 PPPLTLEVLVPANAVGKVIGKAGSNLANIRKISGATIEMSDSK--SSRGDRVALISGTPE 608
              L   + VPA+A G+VIGK G  +  ++ ++ A + +   +        +  I G   
Sbjct: 82  EVKLETHIRVPASAAGRVIGKGGKTVNELQNLTAAEVVVPRDQTPDENDQVIVKIIGHFY 141

Query: 609 QKRAAENLIQAFI 621
             + A+  I+  +
Sbjct: 142 ASQMAQRKIRDIL 154

>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 = 58.2 bits (141), Expect = 3e-10
 Identities = 19/92 (20%), Positives = 37/92 (40%), Gaps = 8/92 (8%)

Query: 298 GLVGASQSEELVIRVLCPFNKIGRVIGKGGGTIKSIRQASGAQIDV--DDTKDNRDECVI 355
              G  +  +L   +  P +  GRVIGKGG T+  ++  + A++ V  D T D  D+ ++
Sbjct: 75  NFFGPKEEVKLETHIRVPASAAGRVIGKGGKTVNELQNLTAAEVVVPRDQTPDENDQVIV 134

Query: 356 TVTAIESPDDIKSMAVEAVLLLQTKINDEDDD 387
            +         +     A   ++  +      
Sbjct: 135 KIIG--HFYASQ----MAQRKIRDILAQVKQQ 160

>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 = 50.5 bits (121), Expect = 1e-07
 Identities = 19/68 (27%), Positives = 28/68 (41%), Gaps = 4/68 (5%)

Query: 23  RRINEKDEKGN--EESVIYRILCPDGVIGSVIGKSGKVINSIRQETRARVKVV--DPFPG 78
            ++ E++  G   E  +   I  P    G VIGK GK +N ++  T A V V        
Sbjct: 69  GKLKEENFFGPKEEVKLETHIRVPASAAGRVIGKGGKTVNELQNLTAAEVVVPRDQTPDE 128

Query: 79  AKDRVVTI 86
               +V I
Sbjct: 129 NDQVIVKI 136

>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 =  115 bits (290), Expect = 4e-30
 Identities = 36/180 (20%), Positives = 62/180 (34%), Gaps = 33/180 (18%)

Query: 307 ELVIRVLCPFNKIGRVIGKGGGTIKSIRQASGAQIDVDDTKDNRDECVITVTAIESPDDI 366
             +I V  P   +G VIG+ G  IK I+  +G +I          E +  +T    PD  
Sbjct: 2   SHMIDVPIPRFAVGIVIGRNGEMIKKIQNDAGVRIQFKPDDGTTPERIAQITG--PPDRA 59

Query: 367 KSMAVEAVLLLQTKINDEDD--------------------------DTVTIRLLVSSKVI 400
           +     A  ++   +                                      +V +   
Sbjct: 60  Q----HAAEIITDLLRSVQAGNPGGPGPGGRGRGRGQGNWNMGPPGGLQEFNFIVPTGKT 115

Query: 401 GCIIGKSGSIINEIRKRTKADVRISKGDKPKCADANDELVEVVGEVGSVRDALVQIILRL 460
           G IIGK G  I  I +++ A + + + + P  AD N +L  + G    +  A   I  ++
Sbjct: 116 GLIIGKGGETIKSISQQSGARIELQR-NPPPNADPNMKLFTIRGTPQQIDYARQLIEEKI 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 =  111 bits (280), Expect = 1e-28
 Identities = 32/180 (17%), Positives = 61/180 (33%), Gaps = 7/180 (3%)

Query: 36  SVIYRILCPDGVIGSVIGKSGKVINSIRQETRARVKVVDPFPGAKDRVVTIYSHVKDKED 95
           S +  +  P   +G VIG++G++I  I+ +   R++         +R+  I       + 
Sbjct: 2   SHMIDVPIPRFAVGIVIGRNGEMIKKIQNDAGVRIQFKPDDGTTPERIAQITGPPDRAQH 61

Query: 96  VEVDDEFNDKEPLCAAQDALLKVHAAIANAVANATDNDKKRKEKEECQILVPSSQSANII 155
               +   D      A +                  N       +E   +VP+ ++  II
Sbjct: 62  AA--EIITDLLRSVQAGNPGGPGPGGRGRGRGQGNWNMGPPGGLQEFNFIVPTGKTGLII 119

Query: 156 GKAGATIKRLRSKTRTSIKVTPKDASEPTHSCAMEFDNFVLISGESEAVKKALFAISAIM 215
           GK G TIK +  ++   I++            A        I G  + +  A   I   +
Sbjct: 120 GKGGETIKSISQQSGARIELQRNPP-----PNADPNMKLFTIRGTPQQIDYARQLIEEKI 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 = 80.3 bits (198), Expect = 8e-18
 Identities = 48/242 (19%), Positives = 80/242 (33%), Gaps = 76/242 (31%)

Query: 143 QILVPSSQSANIIGKAGATIKRLRSKTRTSIKVTPKDASEPTHSCAMEFDNFVLISGESE 202
            + +P      +IG+ G  IK++++     I+  P D + P        +    I+G  +
Sbjct: 6   DVPIPRFAVGIVIGRNGEMIKKIQNDAGVRIQFKPDDGTTP--------ERIAQITGPPD 57

Query: 203 AVKKALFAISAIMYKFSPREDIPLETTVREAPPSIIIPSDVPIYPPGGLYPNADPILPSR 262
             + A   I+ ++                                              R
Sbjct: 58  RAQHAAEIITDLL----------------------------------------------R 71

Query: 263 SVPSILGAARVPDLQGYADTGNTWPVYSTGLSLVSGLVGASQSEELVIRVLCPFNKIGRV 322
           SV +       P  +G       W           G  G  Q    ++    P  K G +
Sbjct: 72  SVQAGNPGGPGPGGRGRGRGQGNWN---------MGPPGGLQEFNFIV----PTGKTGLI 118

Query: 323 IGKGGGTIKSIRQASGAQIDVDDTKD---NRDECVITVTAIESPDDIKSMAVEAVLLLQT 379
           IGKGG TIKSI Q SGA+I++        + +  + T+    +P  I      A  L++ 
Sbjct: 119 IGKGGETIKSISQQSGARIELQRNPPPNADPNMKLFTIRG--TPQQID----YARQLIEE 172

Query: 380 KI 381
           KI
Sbjct: 173 KI 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 = 68.0 bits (166), Expect = 2e-13
 Identities = 19/68 (27%), Positives = 36/68 (52%)

Query: 555 TLEVLVPANAVGKVIGKAGSNLANIRKISGATIEMSDSKSSRGDRVALISGTPEQKRAAE 614
            ++V +P  AVG VIG+ G  +  I+  +G  I+      +  +R+A I+G P++ + A 
Sbjct: 4   MIDVPIPRFAVGIVIGRNGEMIKKIQNDAGVRIQFKPDDGTTPERIAQITGPPDRAQHAA 63

Query: 615 NLIQAFIM 622
            +I   + 
Sbjct: 64  EIITDLLR 71

>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 = 64.1 bits (156), Expect = 4e-12
 Identities = 25/95 (26%), Positives = 38/95 (40%), Gaps = 3/95 (3%)

Query: 530 SMGDSPYGSMSSYSSKLYGGLPPPLTLEVLVPANAVGKVIGKAGSNLANIRKISGATIEM 589
             G    G      +   G          +VP    G +IGK G  + +I + SGA IE+
Sbjct: 80  GPGPGGRGRGRGQGNWNMGPPGGLQEFNFIVPTGKTGLIIGKGGETIKSISQQSGARIEL 139

Query: 590 SDSK---SSRGDRVALISGTPEQKRAAENLIQAFI 621
             +    +    ++  I GTP+Q   A  LI+  I
Sbjct: 140 QRNPPPNADPNMKLFTIRGTPQQIDYARQLIEEKI 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 = 55.3 bits (133), Expect = 4e-09
 Identities = 18/81 (22%), Positives = 33/81 (40%), Gaps = 3/81 (3%)

Query: 9   RSQRDNDRDGKNQKRRINEKDEKGNEESVIYRILCPDGVIGSVIGKSGKVINSIRQETRA 68
            +       G+ + R     +         +  + P G  G +IGK G+ I SI Q++ A
Sbjct: 76  GNPGGPGPGGRGRGRGQGNWNMGPPGGLQEFNFIVPTGKTGLIIGKGGETIKSISQQSGA 135

Query: 69  RVKV---VDPFPGAKDRVVTI 86
           R+++     P      ++ TI
Sbjct: 136 RIELQRNPPPNADPNMKLFTI 156

>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 =  109 bits (275), Expect = 3e-28
 Identities = 29/180 (16%), Positives = 65/180 (36%), Gaps = 26/180 (14%)

Query: 38  IYRILCPDGVIGSVIGKSGKVINSIRQETRARVKVVD--PFPGAKDRVVTIYSHVKDKED 95
           +  I+ P G  G VIGK G+ I  +++    ++ ++         D+ + I         
Sbjct: 3   VQEIMIPAGKAGLVIGKGGETIKQLQERAGVKMILIQDGSQNTNVDKPLRIIG------- 55

Query: 96  VEVDDEFNDKEPLCAAQDALLKVHAAIANAVANATDNDKKRKEKEECQILVPSSQSANII 155
                   D   +  A + ++ +     +       N+   +      + VP      +I
Sbjct: 56  --------DPYKVQQACEMVMDILRER-DQGGFGDRNEYGSRIGGGIDVPVPRHSVGVVI 106

Query: 156 GKAGATIKRLRSKTRTSIKVTPKDASEPTHSCAMEFDNFVLISGESEAVKKALFAISAIM 215
           G++G  IK++++     I+    D + P        +    I G  +  + A   I+ ++
Sbjct: 107 GRSGEMIKKIQNDAGVRIQFKQDDGTGP--------EKIAHIMGPPDRCEHAARIINDLL 158

>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 =  105 bits (264), Expect = 1e-26
 Identities = 29/162 (17%), Positives = 65/162 (40%), Gaps = 12/162 (7%)

Query: 309 VIRVLCPFNKIGRVIGKGGGTIKSIRQASGAQIDV--DDTKDNRDECVITVTA-IESPDD 365
           V  ++ P  K G VIGKGG TIK +++ +G ++ +  D +++   +  + +         
Sbjct: 3   VQEIMIPAGKAGLVIGKGGETIKQLQERAGVKMILIQDGSQNTNVDKPLRIIGDPYKVQQ 62

Query: 366 IKSMAVEAVLLLQTKINDEDDD-----TVTIRLLVSSKVIGCIIGKSGSIINEIRKRTKA 420
              M ++ +         + ++        I + V    +G +IG+SG +I +I+     
Sbjct: 63  ACEMVMDILRERDQGGFGDRNEYGSRIGGGIDVPVPRHSVGVVIGRSGEMIKKIQNDAGV 122

Query: 421 DVRISKGDKPKCADANDELVEVVGEVGSVRDALVQIILRLRD 462
            ++             +++  ++G       A   I   L+ 
Sbjct: 123 RIQFK----QDDGTGPEKIAHIMGPPDRCEHAARIINDLLQS 160

>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 = 69.4 bits (170), Expect = 5e-14
 Identities = 19/74 (25%), Positives = 37/74 (50%)

Query: 548 GGLPPPLTLEVLVPANAVGKVIGKAGSNLANIRKISGATIEMSDSKSSRGDRVALISGTP 607
            G      ++V VP ++VG VIG++G  +  I+  +G  I+      +  +++A I G P
Sbjct: 85  YGSRIGGGIDVPVPRHSVGVVIGRSGEMIKKIQNDAGVRIQFKQDDGTGPEKIAHIMGPP 144

Query: 608 EQKRAAENLIQAFI 621
           ++   A  +I   +
Sbjct: 145 DRCEHAARIINDLL 158

>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 = 63.7 bits (155), Expect = 4e-12
 Identities = 17/84 (20%), Positives = 29/84 (34%), Gaps = 6/84 (7%)

Query: 301 GASQSEELVIRVLCPFNKIGRVIGKGGGTIKSIRQASGAQIDVDDTKDNRDECVITVTAI 360
                    I V  P + +G VIG+ G  IK I+  +G +I          E +  +   
Sbjct: 84  EYGSRIGGGIDVPVPRHSVGVVIGRSGEMIKKIQNDAGVRIQFKQDDGTGPEKIAHIMG- 142

Query: 361 ESPDDIKSMAVEAVLLLQTKINDE 384
             PD  +     A  ++   +   
Sbjct: 143 -PPDRCE----HAARIINDLLQSL 161

>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 = 62.1 bits (151), Expect = 1e-11
 Identities = 16/69 (23%), Positives = 32/69 (46%), Gaps = 2/69 (2%)

Query: 555 TLEVLVPANAVGKVIGKAGSNLANIRKISGATIEMSDSKSSRG--DRVALISGTPEQKRA 612
             E+++PA   G VIGK G  +  +++ +G  + +    S     D+   I G P + + 
Sbjct: 3   VQEIMIPAGKAGLVIGKGGETIKQLQERAGVKMILIQDGSQNTNVDKPLRIIGDPYKVQQ 62

Query: 613 AENLIQAFI 621
           A  ++   +
Sbjct: 63  ACEMVMDIL 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 = 57.5 bits (139), Expect = 6e-10
 Identities = 13/59 (22%), Positives = 28/59 (47%)

Query: 28  KDEKGNEESVIYRILCPDGVIGSVIGKSGKVINSIRQETRARVKVVDPFPGAKDRVVTI 86
           ++E G+       +  P   +G VIG+SG++I  I+ +   R++         +++  I
Sbjct: 82  RNEYGSRIGGGIDVPVPRHSVGVVIGRSGEMIKKIQNDAGVRIQFKQDDGTGPEKIAHI 140

>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 = 91.2 bits (227), Expect = 1e-22
 Identities = 25/74 (33%), Positives = 43/74 (58%)

Query: 548 GGLPPPLTLEVLVPANAVGKVIGKAGSNLANIRKISGATIEMSDSKSSRGDRVALISGTP 607
           G + P +T +V +P +  G +IGK G  +  IR  SGA+I++ +      DR+  I+GT 
Sbjct: 1   GAMGPIITTQVTIPKDLAGSIIGKGGQRIKQIRHESGASIKIDEPLEGSEDRIITITGTQ 60

Query: 608 EQKRAAENLIQAFI 621
           +Q + A+ L+Q  +
Sbjct: 61  DQIQNAQYLLQNSV 74

>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 = 68.5 bits (168), Expect = 1e-14
 Identities = 26/87 (29%), Positives = 41/87 (47%), Gaps = 6/87 (6%)

Query: 302 ASQSEELVIRVLCPFNKIGRVIGKGGGTIKSIRQASGAQIDVDDTKDNRDECVITVTAIE 361
            +    +  +V  P +  G +IGKGG  IK IR  SGA I +D+  +  ++ +IT+T   
Sbjct: 1   GAMGPIITTQVTIPKDLAGSIIGKGGQRIKQIRHESGASIKIDEPLEGSEDRIITITG-- 58

Query: 362 SPDDIKSMAVEAVLLLQTKINDEDDDT 388
           + D I+     A  LLQ  +       
Sbjct: 59  TQDQIQ----NAQYLLQNSVKQYSGKF 81

>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 = 63.1 bits (154), Expect = 9e-13
 Identities = 19/51 (37%), Positives = 33/51 (64%)

Query: 36 SVIYRILCPDGVIGSVIGKSGKVINSIRQETRARVKVVDPFPGAKDRVVTI 86
           +  ++  P  + GS+IGK G+ I  IR E+ A +K+ +P  G++DR++TI
Sbjct: 6  IITTQVTIPKDLAGSIIGKGGQRIKQIRHESGASIKIDEPLEGSEDRIITI 56

>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 = 54.6 bits (132), Expect = 8e-10
 Identities = 15/76 (19%), Positives = 35/76 (46%), Gaps = 4/76 (5%)

Query: 387 DTVTIRLLVSSKVIGCIIGKSGSIINEIRKRTKADVRISKGDKPKCADANDELVEVVGEV 446
             +T ++ +   + G IIGK G  I +IR  + A ++I +        + D ++ + G  
Sbjct: 5   PIITTQVTIPKDLAGSIIGKGGQRIKQIRHESGASIKIDE----PLEGSEDRIITITGTQ 60

Query: 447 GSVRDALVQIILRLRD 462
             +++A   +   ++ 
Sbjct: 61  DQIQNAQYLLQNSVKQ 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 = 54.6 bits (132), Expect = 8e-10
 Identities = 18/80 (22%), Positives = 38/80 (47%), Gaps = 8/80 (10%)

Query: 142 CQILVPSSQSANIIGKAGATIKRLRSKTRTSIKVTPKDASEPTHSCAMEFDNFVLISGES 201
            Q+ +P   + +IIGK G  IK++R ++  SIK+                D  + I+G  
Sbjct: 9   TQVTIPKDLAGSIIGKGGQRIKQIRHESGASIKIDEPLEGSE--------DRIITITGTQ 60

Query: 202 EAVKKALFAISAIMYKFSPR 221
           + ++ A + +   + ++S +
Sbjct: 61  DQIQNAQYLLQNSVKQYSGK 80

>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 = 89.3 bits (222), Expect = 6e-22
 Identities = 23/74 (31%), Positives = 41/74 (55%)

Query: 550 LPPPLTLEVLVPANAVGKVIGKAGSNLANIRKISGATIEMSDSKSSRGDRVALISGTPEQ 609
           L    T E+ +P N +G +IG+ G+N+  IR++SGA I++++       R   I+G+   
Sbjct: 2   LGSQTTHELTIPNNLIGCIIGRQGANINEIRQMSGAQIKIANPVEGSSGRQVTITGSAAS 61

Query: 610 KRAAENLIQAFIMA 623
              A+ LI A + +
Sbjct: 62  ISLAQYLINARLSS 75

>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 = 62.7 bits (153), Expect = 1e-12
 Identities = 23/80 (28%), Positives = 36/80 (45%), Gaps = 6/80 (7%)

Query: 305 SEELVIRVLCPFNKIGRVIGKGGGTIKSIRQASGAQIDVDDTKDNRDECVITVTAIESPD 364
             +    +  P N IG +IG+ G  I  IRQ SGAQI + +  +      +T+T   S  
Sbjct: 3   GSQTTHELTIPNNLIGCIIGRQGANINEIRQMSGAQIKIANPVEGSSGRQVTITG--SAA 60

Query: 365 DIKSMAVEAVLLLQTKINDE 384
            I      A  L+  +++ E
Sbjct: 61  SISL----AQYLINARLSSE 76

>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 = 60.8 bits (148), Expect = 5e-12
 Identities = 19/52 (36%), Positives = 31/52 (59%)

Query: 35 ESVIYRILCPDGVIGSVIGKSGKVINSIRQETRARVKVVDPFPGAKDRVVTI 86
              + +  P+ +IG +IG+ G  IN IRQ + A++K+ +P  G+  R VTI
Sbjct: 4  SQTTHELTIPNNLIGCIIGRQGANINEIRQMSGAQIKIANPVEGSSGRQVTI 55

>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 = 56.1 bits (136), Expect = 2e-10
 Identities = 23/77 (29%), Positives = 38/77 (49%), Gaps = 4/77 (5%)

Query: 387 DTVTIRLLVSSKVIGCIIGKSGSIINEIRKRTKADVRISKGDKPKCADANDELVEVVGEV 446
              T  L + + +IGCIIG+ G+ INEIR+ + A ++I+         ++   V + G  
Sbjct: 4   SQTTHELTIPNNLIGCIIGRQGANINEIRQMSGAQIKIAN----PVEGSSGRQVTITGSA 59

Query: 447 GSVRDALVQIILRLRDD 463
            S+  A   I  RL  +
Sbjct: 60  ASISLAQYLINARLSSE 76

>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 = 52.3 bits (126), Expect = 6e-09
 Identities = 16/78 (20%), Positives = 33/78 (42%), Gaps = 8/78 (10%)

Query: 138 EKEECQILVPSSQSANIIGKAGATIKRLRSKTRTSIKVTPKDASEPTHSCAMEFDNFVLI 197
            +   ++ +P++    IIG+ GA I  +R  +   IK+                   V I
Sbjct: 4   SQTTHELTIPNNLIGCIIGRQGANINEIRQMSGAQIKIANPVEGSS--------GRQVTI 55

Query: 198 SGESEAVKKALFAISAIM 215
           +G + ++  A + I+A +
Sbjct: 56  TGSAASISLAQYLINARL 73

>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 = 85.8 bits (213), Expect = 1e-20
 Identities = 30/85 (35%), Positives = 47/85 (55%), Gaps = 4/85 (4%)

Query: 537 GSMSSYSSKLYGGLPPPLTLEVLVPANAVGKVIGKAGSNLANIRKISGATIEMSDSKSSR 596
           GS  SY     GG  P +T +V +P +  G +IGK G  +  IR  SGA+I++ +     
Sbjct: 1   GSHMSYGD--LGG--PIITTQVTIPKDLAGSIIGKGGQRIKQIRHESGASIKIDEPLEGS 56

Query: 597 GDRVALISGTPEQKRAAENLIQAFI 621
            DR+  I+GT +Q + A+ L+Q  +
Sbjct: 57  EDRIITITGTQDQIQNAQYLLQNSV 81

>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 = 1e-14
 Identities = 27/88 (30%), Positives = 41/88 (46%), Gaps = 6/88 (6%)

Query: 301 GASQSEELVIRVLCPFNKIGRVIGKGGGTIKSIRQASGAQIDVDDTKDNRDECVITVTAI 360
           G      +  +V  P +  G +IGKGG  IK IR  SGA I +D+  +  ++ +IT+T  
Sbjct: 7   GDLGGPIITTQVTIPKDLAGSIIGKGGQRIKQIRHESGASIKIDEPLEGSEDRIITITG- 65

Query: 361 ESPDDIKSMAVEAVLLLQTKINDEDDDT 388
            + D I+     A  LLQ  +       
Sbjct: 66  -TQDQIQ----NAQYLLQNSVKQYSGKF 88

>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 = 63.1 bits (154), Expect = 9e-13
 Identities = 19/53 (35%), Positives = 33/53 (62%)

Query: 34 EESVIYRILCPDGVIGSVIGKSGKVINSIRQETRARVKVVDPFPGAKDRVVTI 86
             +  ++  P  + GS+IGK G+ I  IR E+ A +K+ +P  G++DR++TI
Sbjct: 11 GPIITTQVTIPKDLAGSIIGKGGQRIKQIRHESGASIKIDEPLEGSEDRIITI 63

>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 = 55.8 bits (135), Expect = 4e-10
 Identities = 16/81 (19%), Positives = 36/81 (44%), Gaps = 4/81 (4%)

Query: 382 NDEDDDTVTIRLLVSSKVIGCIIGKSGSIINEIRKRTKADVRISKGDKPKCADANDELVE 441
            D     +T ++ +   + G IIGK G  I +IR  + A ++I +        + D ++ 
Sbjct: 7   GDLGGPIITTQVTIPKDLAGSIIGKGGQRIKQIRHESGASIKIDE----PLEGSEDRIIT 62

Query: 442 VVGEVGSVRDALVQIILRLRD 462
           + G    +++A   +   ++ 
Sbjct: 63  ITGTQDQIQNAQYLLQNSVKQ 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 = 55.4 bits (134), Expect = 5e-10
 Identities = 18/84 (21%), Positives = 38/84 (45%), Gaps = 8/84 (9%)

Query: 138 EKEECQILVPSSQSANIIGKAGATIKRLRSKTRTSIKVTPKDASEPTHSCAMEFDNFVLI 197
                Q+ +P   + +IIGK G  IK++R ++  SIK+                D  + I
Sbjct: 12  PIITTQVTIPKDLAGSIIGKGGQRIKQIRHESGASIKIDEPLEGSE--------DRIITI 63

Query: 198 SGESEAVKKALFAISAIMYKFSPR 221
           +G  + ++ A + +   + ++S +
Sbjct: 64  TGTQDQIQNAQYLLQNSVKQYSGK 87

>2p2r_A Poly(RC)-binding protein 2; protein-DNA complex, RNA and DNA binding protein/DNA complex; 1.60A {Homo sapiens} Length = 76

 Score = 83.1 bits (206), Expect = 7e-20
 Identities = 19/71 (26%), Positives = 38/71 (53%)

Query: 551 PPPLTLEVLVPANAVGKVIGKAGSNLANIRKISGATIEMSDSKSSRGDRVALISGTPEQK 610
               + E+ +P + +G +IG+ G+ +  IR++SGA I++++      DR   I+G+    
Sbjct: 2   AQTTSHELTIPNDLIGCIIGRQGAKINEIRQMSGAQIKIANPVEGSTDRQVTITGSAASI 61

Query: 611 RAAENLIQAFI 621
             A+ LI   +
Sbjct: 62  SLAQYLINVRL 72

>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 = 9e-14
 Identities = 22/81 (27%), Positives = 39/81 (48%), Gaps = 6/81 (7%)

Query: 304 QSEELVIRVLCPFNKIGRVIGKGGGTIKSIRQASGAQIDVDDTKDNRDECVITVTAIESP 363
           +++     +  P + IG +IG+ G  I  IRQ SGAQI + +  +   +  +T+T   S 
Sbjct: 1   KAQTTSHELTIPNDLIGCIIGRQGAKINEIRQMSGAQIKIANPVEGSTDRQVTITG--SA 58

Query: 364 DDIKSMAVEAVLLLQTKINDE 384
             I      A  L+  +++ E
Sbjct: 59  ASIS----LAQYLINVRLSSE 75

>2p2r_A Poly(RC)-binding protein 2; protein-DNA complex, RNA and DNA binding protein/DNA complex; 1.60A {Homo sapiens} Length = 76

 Score = 62.3 bits (152), Expect = 1e-12
 Identities = 20/53 (37%), Positives = 34/53 (64%)

Query: 34 EESVIYRILCPDGVIGSVIGKSGKVINSIRQETRARVKVVDPFPGAKDRVVTI 86
           ++  + +  P+ +IG +IG+ G  IN IRQ + A++K+ +P  G+ DR VTI
Sbjct: 2  AQTTSHELTIPNDLIGCIIGRQGAKINEIRQMSGAQIKIANPVEGSTDRQVTI 54

>2p2r_A Poly(RC)-binding protein 2; protein-DNA complex, RNA and DNA binding protein/DNA complex; 1.60A {Homo sapiens} Length = 76

 Score = 57.7 bits (140), Expect = 5e-11
 Identities = 24/76 (31%), Positives = 40/76 (52%), Gaps = 4/76 (5%)

Query: 388 TVTIRLLVSSKVIGCIIGKSGSIINEIRKRTKADVRISKGDKPKCADANDELVEVVGEVG 447
           T +  L + + +IGCIIG+ G+ INEIR+ + A ++I+         + D  V + G   
Sbjct: 4   TTSHELTIPNDLIGCIIGRQGAKINEIRQMSGAQIKIAN----PVEGSTDRQVTITGSAA 59

Query: 448 SVRDALVQIILRLRDD 463
           S+  A   I +RL  +
Sbjct: 60  SISLAQYLINVRLSSE 75

>2p2r_A Poly(RC)-binding protein 2; protein-DNA complex, RNA and DNA binding protein/DNA complex; 1.60A {Homo sapiens} Length = 76

 Score = 51.5 bits (124), Expect = 8e-09
 Identities = 16/80 (20%), Positives = 33/80 (41%), Gaps = 8/80 (10%)

Query: 136 RKEKEECQILVPSSQSANIIGKAGATIKRLRSKTRTSIKVTPKDASEPTHSCAMEFDNFV 195
           + +    ++ +P+     IIG+ GA I  +R  +   IK+                D  V
Sbjct: 1   KAQTTSHELTIPNDLIGCIIGRQGAKINEIRQMSGAQIKIANPVEGST--------DRQV 52

Query: 196 LISGESEAVKKALFAISAIM 215
            I+G + ++  A + I+  +
Sbjct: 53  TITGSAASISLAQYLINVRL 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 = 80.2 bits (198), Expect = 1e-18
 Identities = 20/71 (28%), Positives = 39/71 (54%)

Query: 551 PPPLTLEVLVPANAVGKVIGKAGSNLANIRKISGATIEMSDSKSSRGDRVALISGTPEQK 610
              +T E  VP   VG +IG+ G  ++ I++ SG  I+++       +R  +++GTPE  
Sbjct: 12  RSVMTEEYKVPDGMVGFIIGRGGEQISRIQQESGCKIQIAPDSGGLPERSCMLTGTPESV 71

Query: 611 RAAENLIQAFI 621
           ++A+ L+   +
Sbjct: 72  QSAKRLLDQIV 82

>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 = 57.4 bits (139), Expect = 1e-10
 Identities = 19/85 (22%), Positives = 32/85 (37%), Gaps = 6/85 (7%)

Query: 301 GASQSEELVIRVLCPFNKIGRVIGKGGGTIKSIRQASGAQIDVDDTKDNRDECVITVTAI 360
              Q   +      P   +G +IG+GG  I  I+Q SG +I +        E    +T  
Sbjct: 8   HQQQRSVMTEEYKVPDGMVGFIIGRGGEQISRIQQESGCKIQIAPDSGGLPERSCMLTG- 66

Query: 361 ESPDDIKSMAVEAVLLLQTKINDED 385
            +P+ ++     A  LL   +    
Sbjct: 67  -TPESVQ----SAKRLLDQIVEKGR 86

>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 = 56.3 bits (136), Expect = 3e-10
 Identities = 13/47 (27%), Positives = 27/47 (57%)

Query: 40 RILCPDGVIGSVIGKSGKVINSIRQETRARVKVVDPFPGAKDRVVTI 86
              PDG++G +IG+ G+ I+ I+QE+  ++++     G  +R   +
Sbjct: 18 EYKVPDGMVGFIIGRGGEQISRIQQESGCKIQIAPDSGGLPERSCML 64

>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 = 51.3 bits (123), Expect = 2e-08
 Identities = 16/73 (21%), Positives = 32/73 (43%), Gaps = 8/73 (10%)

Query: 143 QILVPSSQSANIIGKAGATIKRLRSKTRTSIKVTPKDASEPTHSCAMEFDNFVLISGESE 202
           +  VP      IIG+ G  I R++ ++   I++ P     P        +   +++G  E
Sbjct: 18  EYKVPDGMVGFIIGRGGEQISRIQQESGCKIQIAPDSGGLP--------ERSCMLTGTPE 69

Query: 203 AVKKALFAISAIM 215
           +V+ A   +  I+
Sbjct: 70  SVQSAKRLLDQIV 82

>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 = 48.6 bits (116), Expect = 1e-07
 Identities = 14/75 (18%), Positives = 31/75 (41%), Gaps = 4/75 (5%)

Query: 382 NDEDDDTVTIRLLVSSKVIGCIIGKSGSIINEIRKRTKADVRISKGDKPKCADANDELVE 441
           + +    +T    V   ++G IIG+ G  I+ I++ +   ++I+           +    
Sbjct: 8   HQQQRSVMTEEYKVPDGMVGFIIGRGGEQISRIQQESGCKIQIAPDSG----GLPERSCM 63

Query: 442 VVGEVGSVRDALVQI 456
           + G   SV+ A   +
Sbjct: 64  LTGTPESVQSAKRLL 78

>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 = 76.9 bits (190), Expect = 8e-18
 Identities = 25/79 (31%), Positives = 45/79 (56%), Gaps = 6/79 (7%)

Query: 385 DDDTVTIRLLVSSKVIGCIIGKSGSIINEIRKRTKADVRISKGDKPKCADANDELVEVVG 444
            + T+TIRLL+  K +G IIGK G  + ++R+ + A + IS+G+ P      + ++ + G
Sbjct: 1   KNVTLTIRLLMHGKEVGSIIGKKGESVKKMREESGARINISEGNCP------ERIITLAG 54

Query: 445 EVGSVRDALVQIILRLRDD 463
              ++  A   II +L +D
Sbjct: 55  PTNAIFKAFAMIIDKLEED 73

>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 = 67.3 bits (165), Expect = 2e-14
 Identities = 19/70 (27%), Positives = 35/70 (50%), Gaps = 2/70 (2%)

Query: 552 PPLTLEVLVPANAVGKVIGKAGSNLANIRKISGATIEMSDSKSSRGDRVALISGTPEQKR 611
             LT+ +L+    VG +IGK G ++  +R+ SGA I +S+      +R+  ++G      
Sbjct: 3   VTLTIRLLMHGKEVGSIIGKKGESVKKMREESGARINISEGNCP--ERIITLAGPTNAIF 60

Query: 612 AAENLIQAFI 621
            A  +I   +
Sbjct: 61  KAFAMIIDKL 70

>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 = 63.1 bits (154), Expect = 7e-13
 Identities = 22/81 (27%), Positives = 45/81 (55%), Gaps = 8/81 (9%)

Query: 304 QSEELVIRVLCPFNKIGRVIGKGGGTIKSIRQASGAQIDVDDTKDNRDECVITVTAIESP 363
           ++  L IR+L    ++G +IGK G ++K +R+ SGA+I++ +   N  E +IT+      
Sbjct: 1   KNVTLTIRLLMHGKEVGSIIGKKGESVKKMREESGARINISE--GNCPERIITLAG--PT 56

Query: 364 DDIKSMAVEAVLLLQTKINDE 384
           + I     +A  ++  K+ ++
Sbjct: 57  NAIF----KAFAMIIDKLEED 73

>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 = 58.1 bits (141), Expect = 4e-11
 Identities = 14/52 (26%), Positives = 31/52 (59%), Gaps = 2/52 (3%)

Query: 35 ESVIYRILCPDGVIGSVIGKSGKVINSIRQETRARVKVVDPFPGAKDRVVTI 86
           ++  R+L     +GS+IGK G+ +  +R+E+ AR+ + +      +R++T+
Sbjct: 3  VTLTIRLLMHGKEVGSIIGKKGESVKKMREESGARINISE--GNCPERIITL 52

>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 = 56.5 bits (137), Expect = 2e-10
 Identities = 15/73 (20%), Positives = 35/73 (47%), Gaps = 10/73 (13%)

Query: 143 QILVPSSQSANIIGKAGATIKRLRSKTRTSIKVTPKDASEPTHSCAMEFDNFVLISGESE 202
           ++L+   +  +IIGK G ++K++R ++   I ++  +  E            + ++G + 
Sbjct: 8   RLLMHGKEVGSIIGKKGESVKKMREESGARINISEGNCPERI----------ITLAGPTN 57

Query: 203 AVKKALFAISAIM 215
           A+ KA   I   +
Sbjct: 58  AIFKAFAMIIDKL 70

>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 = 76.2 bits (188), Expect = 2e-17
 Identities = 22/70 (31%), Positives = 38/70 (54%), Gaps = 3/70 (4%)

Query: 555 TLEVLVPANAVGKVIGKAGSNLANIRKISGATIEMSDSKSSR---GDRVALISGTPEQKR 611
            +E+ VP N VG ++GK G  L   ++++GA I++S          +R   I+G+P   +
Sbjct: 4   LVEMAVPENLVGAILGKGGKTLVEYQELTGARIQISKKGEFLPGTRNRRVTITGSPAATQ 63

Query: 612 AAENLIQAFI 621
           AA+ LI   +
Sbjct: 64  AAQYLISQRV 73

>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 = 60.0 bits (146), Expect = 8e-12
 Identities = 18/79 (22%), Positives = 38/79 (48%), Gaps = 9/79 (11%)

Query: 309 VIRVLCPFNKIGRVIGKGGGTIKSIRQASGAQIDVDDTKD---NRDECVITVTAIESPDD 365
           ++ +  P N +G ++GKGG T+   ++ +GA+I +    +         +T+T   SP  
Sbjct: 4   LVEMAVPENLVGAILGKGGKTLVEYQELTGARIQISKKGEFLPGTRNRRVTITG--SPAA 61

Query: 366 IKSMAVEAVLLLQTKINDE 384
            ++    A  L+  ++  E
Sbjct: 62  TQA----AQYLISQRVTYE 76

>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 = 60.0 bits (146), Expect = 8e-12
 Identities = 17/74 (22%), Positives = 32/74 (43%), Gaps = 1/74 (1%)

Query: 389 VTIRLLVSSKVIGCIIGKSGSIINEIRKRTKADVRISKGDKPKCADANDELVEVVGEVGS 448
             + + V   ++G I+GK G  + E ++ T A ++ISK          +  V + G   +
Sbjct: 3   ELVEMAVPENLVGAILGKGGKTLVEYQELTGARIQISK-KGEFLPGTRNRRVTITGSPAA 61

Query: 449 VRDALVQIILRLRD 462
            + A   I  R+  
Sbjct: 62  TQAAQYLISQRVTY 75

>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 = 57.7 bits (140), Expect = 6e-11
 Identities = 15/54 (27%), Positives = 32/54 (59%), Gaps = 3/54 (5%)

Query: 36 SVIYRILCPDGVIGSVIGKSGKVINSIRQETRARVKVV---DPFPGAKDRVVTI 86
            +  +  P+ ++G+++GK GK +   ++ T AR+++    +  PG ++R VTI
Sbjct: 2  KELVEMAVPENLVGAILGKGGKTLVEYQELTGARIQISKKGEFLPGTRNRRVTI 55

>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 = 56.9 bits (138), Expect = 1e-10
 Identities = 20/77 (25%), Positives = 34/77 (44%), Gaps = 5/77 (6%)

Query: 139 KEECQILVPSSQSANIIGKAGATIKRLRSKTRTSIKVTPKDASEPTHSCAMEFDNFVLIS 198
           KE  ++ VP +    I+GK G T+   +  T   I+++ K    P        +  V I+
Sbjct: 2   KELVEMAVPENLVGAILGKGGKTLVEYQELTGARIQISKKGEFLP-----GTRNRRVTIT 56

Query: 199 GESEAVKKALFAISAIM 215
           G   A + A + IS  +
Sbjct: 57  GSPAATQAAQYLISQRV 73

>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 = 76.6 bits (189), Expect = 2e-17
 Identities = 22/72 (30%), Positives = 38/72 (52%), Gaps = 3/72 (4%)

Query: 555 TLEVLVPANAVGKVIGKAGSNLANIRKISGATIEMSDSKSSR---GDRVALISGTPEQKR 611
            +E+ VP N VG ++GK G  L   ++++GA I++S          +R   I+G+P   +
Sbjct: 4   LVEIAVPENLVGAILGKGGKTLVEYQELTGARIQISKKGEFLPGTRNRRVTITGSPAATQ 63

Query: 612 AAENLIQAFIMA 623
           AA+ LI   +  
Sbjct: 64  AAQYLISQRVTY 75

>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 = 59.3 bits (144), Expect = 2e-11
 Identities = 17/75 (22%), Positives = 33/75 (44%), Gaps = 1/75 (1%)

Query: 389 VTIRLLVSSKVIGCIIGKSGSIINEIRKRTKADVRISKGDKPKCADANDELVEVVGEVGS 448
             + + V   ++G I+GK G  + E ++ T A ++ISK          +  V + G   +
Sbjct: 3   ELVEIAVPENLVGAILGKGGKTLVEYQELTGARIQISK-KGEFLPGTRNRRVTITGSPAA 61

Query: 449 VRDALVQIILRLRDD 463
            + A   I  R+  +
Sbjct: 62  TQAAQYLISQRVTYE 76

>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 = 58.1 bits (141), Expect = 5e-11
 Identities = 16/54 (29%), Positives = 32/54 (59%), Gaps = 3/54 (5%)

Query: 36 SVIYRILCPDGVIGSVIGKSGKVINSIRQETRARVKVV---DPFPGAKDRVVTI 86
            +  I  P+ ++G+++GK GK +   ++ T AR+++    +  PG ++R VTI
Sbjct: 2  KELVEIAVPENLVGAILGKGGKTLVEYQELTGARIQISKKGEFLPGTRNRRVTI 55

>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 = 57.0 bits (138), Expect = 1e-10
 Identities = 18/78 (23%), Positives = 36/78 (46%), Gaps = 9/78 (11%)

Query: 310 IRVLCPFNKIGRVIGKGGGTIKSIRQASGAQIDVDDTKDNRD---ECVITVTAIESPDDI 366
           + +  P N +G ++GKGG T+   ++ +GA+I +    +         +T+T   SP   
Sbjct: 5   VEIAVPENLVGAILGKGGKTLVEYQELTGARIQISKKGEFLPGTRNRRVTITG--SPAAT 62

Query: 367 KSMAVEAVLLLQTKINDE 384
           +     A  L+  ++  E
Sbjct: 63  Q----AAQYLISQRVTYE 76

>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 = 55.8 bits (135), Expect = 3e-10
 Identities = 21/77 (27%), Positives = 34/77 (44%), Gaps = 5/77 (6%)

Query: 139 KEECQILVPSSQSANIIGKAGATIKRLRSKTRTSIKVTPKDASEPTHSCAMEFDNFVLIS 198
           KE  +I VP +    I+GK G T+   +  T   I+++ K    P        +  V I+
Sbjct: 2   KELVEIAVPENLVGAILGKGGKTLVEYQELTGARIQISKKGEFLP-----GTRNRRVTIT 56

Query: 199 GESEAVKKALFAISAIM 215
           G   A + A + IS  +
Sbjct: 57  GSPAATQAAQYLISQRV 73

>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 = 5e-17
 Identities = 19/77 (24%), Positives = 37/77 (48%), Gaps = 2/77 (2%)

Query: 547 YGGLPPPLTLEVLVPANAVGKVIGKAGSNLANIRKISGATIEMSDSKSSRG--DRVALIS 604
           +G  P     E+++PA+  G VIGK G  +  +++ +G  + M          D+   I+
Sbjct: 8   HGDGPGNAVQEIMIPASKAGLVIGKGGETIKQLQERAGVKMVMIQDGPQNTGADKPLRIT 67

Query: 605 GTPEQKRAAENLIQAFI 621
           G P + + A+ ++   I
Sbjct: 68  GDPYKVQQAKEMVLELI 84

>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 = 60.9 bits (148), Expect = 7e-12
 Identities = 20/88 (22%), Positives = 40/88 (45%), Gaps = 8/88 (9%)

Query: 301 GASQSEELVIRVLCPFNKIGRVIGKGGGTIKSIRQASGAQIDV--DDTKDNRDECVITVT 358
                   V  ++ P +K G VIGKGG TIK +++ +G ++ +  D  ++   +  + +T
Sbjct: 8   HGDGPGNAVQEIMIPASKAGLVIGKGGETIKQLQERAGVKMVMIQDGPQNTGADKPLRIT 67

Query: 359 AIESPDDIKSMAVEAVLLLQTKINDEDD 386
               P  ++     A  ++   I D+  
Sbjct: 68  G--DPYKVQQ----AKEMVLELIRDQGS 89

>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 = 54.0 bits (130), Expect = 2e-09
 Identities = 12/57 (21%), Positives = 25/57 (43%), Gaps = 2/57 (3%)

Query: 32 GNEESVIYRILCPDGVIGSVIGKSGKVINSIRQETRARVKVV--DPFPGAKDRVVTI 86
              + +  I+ P    G VIGK G+ I  +++    ++ ++   P     D+ + I
Sbjct: 10 DGPGNAVQEIMIPASKAGLVIGKGGETIKQLQERAGVKMVMIQDGPQNTGADKPLRI 66

>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 = 54.0 bits (130), Expect = 2e-09
 Identities = 16/73 (21%), Positives = 36/73 (49%), Gaps = 6/73 (8%)

Query: 143 QILVPSSQSANIIGKAGATIKRLRSKTRTSIKVTPKDASEPTHSCAMEFDNFVLISGESE 202
           +I++P+S++  +IGK G TIK+L+ +    + +                D  + I+G+  
Sbjct: 18  EIMIPASKAGLVIGKGGETIKQLQERAGVKMVMIQDGPQNTGA------DKPLRITGDPY 71

Query: 203 AVKKALFAISAIM 215
            V++A   +  ++
Sbjct: 72  KVQQAKEMVLELI 84

>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 = 52.8 bits (127), Expect = 5e-09
 Identities = 13/78 (16%), Positives = 33/78 (42%), Gaps = 2/78 (2%)

Query: 386 DDTVTIRLLVSSKVIGCIIGKSGSIINEIRKRTKADVRISKGDKPKCADANDELVEVVGE 445
                  +++ +   G +IGK G  I ++++R    + + +          D+ + + G+
Sbjct: 12  PGNAVQEIMIPASKAGLVIGKGGETIKQLQERAGVKMVMIQ--DGPQNTGADKPLRITGD 69

Query: 446 VGSVRDALVQIILRLRDD 463
              V+ A   ++  +RD 
Sbjct: 70  PYKVQQAKEMVLELIRDQ 87

>2hh3_A KH-type splicing regulatory protein; KH-RNA binding domain, RNA binding protein; NMR {Homo sapiens} Length = 106

 Score = 74.1 bits (182), Expect = 3e-16
 Identities = 19/74 (25%), Positives = 37/74 (50%)

Query: 548 GGLPPPLTLEVLVPANAVGKVIGKAGSNLANIRKISGATIEMSDSKSSRGDRVALISGTP 607
            G      ++V VP ++VG VIG++G  +  I+  +G  I+      +  +++A I G P
Sbjct: 5   TGSRIGGGIDVPVPRHSVGVVIGRSGEMIKKIQNDAGVRIQFKQDDGTGPEKIAHIMGPP 64

Query: 608 EQKRAAENLIQAFI 621
           ++   A  +I   +
Sbjct: 65  DRCEHAARIINDLL 78

>2hh3_A KH-type splicing regulatory protein; KH-RNA binding domain, RNA binding protein; NMR {Homo sapiens} Length = 106

 Score = 56.3 bits (136), Expect = 4e-10
 Identities = 18/89 (20%), Positives = 31/89 (34%), Gaps = 6/89 (6%)

Query: 298 GLVGASQSEELVIRVLCPFNKIGRVIGKGGGTIKSIRQASGAQIDVDDTKDNRDECVITV 357
           G +         I V  P + +G VIG+ G  IK I+  +G +I          E +  +
Sbjct: 1   GAMATGSRIGGGIDVPVPRHSVGVVIGRSGEMIKKIQNDAGVRIQFKQDDGTGPEKIAHI 60

Query: 358 TAIESPDDIKSMAVEAVLLLQTKINDEDD 386
                PD  +     A  ++   +     
Sbjct: 61  MG--PPDRCEH----AARIINDLLQSLRS 83

>2hh3_A KH-type splicing regulatory protein; KH-RNA binding domain, RNA binding protein; NMR {Homo sapiens} Length = 106

 Score = 56.3 bits (136), Expect = 4e-10
 Identities = 15/83 (18%), Positives = 31/83 (37%), Gaps = 8/83 (9%)

Query: 143 QILVPSSQSANIIGKAGATIKRLRSKTRTSIKVTPKDASEPTHSCAMEFDNFVLISGESE 202
            + VP      +IG++G  IK++++     I+    D + P        +    I G  +
Sbjct: 14  DVPVPRHSVGVVIGRSGEMIKKIQNDAGVRIQFKQDDGTGP--------EKIAHIMGPPD 65

Query: 203 AVKKALFAISAIMYKFSPREDIP 225
             + A   I+ ++         P
Sbjct: 66  RCEHAARIINDLLQSLRSGPPGP 88

>2hh3_A KH-type splicing regulatory protein; KH-RNA binding domain, RNA binding protein; NMR {Homo sapiens} Length = 106

 Score = 53.6 bits (129), Expect = 4e-09
 Identities = 11/47 (23%), Positives = 23/47 (48%)

Query: 40 RILCPDGVIGSVIGKSGKVINSIRQETRARVKVVDPFPGAKDRVVTI 86
           +  P   +G VIG+SG++I  I+ +   R++         +++  I
Sbjct: 14 DVPVPRHSVGVVIGRSGEMIKKIQNDAGVRIQFKQDDGTGPEKIAHI 60

>2hh3_A KH-type splicing regulatory protein; KH-RNA binding domain, RNA binding protein; NMR {Homo sapiens} Length = 106

 Score = 51.7 bits (124), Expect = 1e-08
 Identities = 19/99 (19%), Positives = 37/99 (37%), Gaps = 7/99 (7%)

Query: 390 TIRLLVSSKVIGCIIGKSGSIINEIRKRTKADVRISKGDKPKCADANDELVEVVGEVGSV 449
            I + V    +G +IG+SG +I +I+      ++  + D        +++  ++G     
Sbjct: 12  GIDVPVPRHSVGVVIGRSGEMIKKIQNDAGVRIQFKQDD----GTGPEKIAHIMGPPDRC 67

Query: 450 RDA---LVQIILRLRDDALKDRDGSRNPPVGADHIYSSG 485
             A   +  ++  LR        G   PP G       G
Sbjct: 68  EHAARIINDLLQSLRSGPPGPPGGPGMPPGGRGRGRGQG 106

>2hh2_A KH-type splicing regulatory protein; KH-RNA binding domain, RNA binding protein; NMR {Homo sapiens} Length = 107

 Score = 73.8 bits (181), Expect = 3e-16
 Identities = 24/77 (31%), Positives = 41/77 (53%), Gaps = 3/77 (3%)

Query: 548 GGLPPPLTLEVLVPANAVGKVIGKAGSNLANIRKISGATIEMSDSKSSRGD---RVALIS 604
           G + P   +   +P +  G VIG+ G N+  I + +GA +E+S      GD   ++ +I 
Sbjct: 1   GAMAPGGEMTFSIPTHKCGLVIGRGGENVKAINQQTGAFVEISRQLPPNGDPNFKLFIIR 60

Query: 605 GTPEQKRAAENLIQAFI 621
           G+P+Q   A+ LI+  I
Sbjct: 61  GSPQQIDHAKQLIEEKI 77

>2hh2_A KH-type splicing regulatory protein; KH-RNA binding domain, RNA binding protein; NMR {Homo sapiens} Length = 107

 Score = 58.3 bits (141), Expect = 8e-11
 Identities = 20/86 (23%), Positives = 37/86 (43%), Gaps = 9/86 (10%)

Query: 302 ASQSEELVIRVLCPFNKIGRVIGKGGGTIKSIRQASGAQIDVDDTKD---NRDECVITVT 358
            + +    +    P +K G VIG+GG  +K+I Q +GA +++        + +  +  + 
Sbjct: 1   GAMAPGGEMTFSIPTHKCGLVIGRGGENVKAINQQTGAFVEISRQLPPNGDPNFKLFIIR 60

Query: 359 AIESPDDIKSMAVEAVLLLQTKINDE 384
              SP  I      A  L++ KI   
Sbjct: 61  G--SPQQID----HAKQLIEEKIEGP 80

>2hh2_A KH-type splicing regulatory protein; KH-RNA binding domain, RNA binding protein; NMR {Homo sapiens} Length = 107

 Score = 54.9 bits (132), Expect = 1e-09
 Identities = 19/95 (20%), Positives = 34/95 (35%), Gaps = 1/95 (1%)

Query: 390 TIRLLVSSKVIGCIIGKSGSIINEIRKRTKADVRISKGDKPKCADANDELVEVVGEVGSV 449
            +   + +   G +IG+ G  +  I ++T A V IS+   P   D N +L  + G    +
Sbjct: 8   EMTFSIPTHKCGLVIGRGGENVKAINQQTGAFVEISR-QLPPNGDPNFKLFIIRGSPQQI 66

Query: 450 RDALVQIILRLRDDALKDRDGSRNPPVGADHIYSS 484
             A   I  ++         G   P         +
Sbjct: 67  DHAKQLIEEKIEGPLCPVGPGPGGPGPAGPMGPFN 101

>2hh2_A KH-type splicing regulatory protein; KH-RNA binding domain, RNA binding protein; NMR {Homo sapiens} Length = 107

 Score = 53.3 bits (128), Expect = 5e-09
 Identities = 11/77 (14%), Positives = 29/77 (37%), Gaps = 5/77 (6%)

Query: 139 KEECQILVPSSQSANIIGKAGATIKRLRSKTRTSIKVTPKDASEPTHSCAMEFDNFVLIS 198
             E    +P+ +   +IG+ G  +K +  +T   ++++ +       +         +I 
Sbjct: 6   GGEMTFSIPTHKCGLVIGRGGENVKAINQQTGAFVEISRQLPPNGDPN-----FKLFIIR 60

Query: 199 GESEAVKKALFAISAIM 215
           G  + +  A   I   +
Sbjct: 61  GSPQQIDHAKQLIEEKI 77

>2hh2_A KH-type splicing regulatory protein; KH-RNA binding domain, RNA binding protein; NMR {Homo sapiens} Length = 107

 Score = 49.1 bits (117), Expect = 2e-07
 Identities = 13/51 (25%), Positives = 23/51 (45%), Gaps = 3/51 (5%)

Query: 39 YRILCPDGVIGSVIGKSGKVINSIRQETRARVKV---VDPFPGAKDRVVTI 86
               P    G VIG+ G+ + +I Q+T A V++   + P      ++  I
Sbjct: 9  MTFSIPTHKCGLVIGRGGENVKAINQQTGAFVEISRQLPPNGDPNFKLFII 59

>2opv_A KHSRP protein; KH domain, RNA binding protein, KSRP; NMR {Homo sapiens} Length = 85

 Score = 72.4 bits (178), Expect = 5e-16
 Identities = 17/77 (22%), Positives = 36/77 (46%), Gaps = 2/77 (2%)

Query: 547 YGGLPPPLTLEVLVPANAVGKVIGKAGSNLANIRKISGATIEMS--DSKSSRGDRVALIS 604
             G       E+++PA   G VIGK G  +  +++ +G  + +    S+++  D+   I 
Sbjct: 7   ANGGQNGTVQEIMIPAGKAGLVIGKGGETIKQLQERAGVKMILIQDGSQNTNVDKPLRII 66

Query: 605 GTPEQKRAAENLIQAFI 621
           G P + + A  ++   +
Sbjct: 67  GDPYKVQQACEMVMDIL 83

>2opv_A KHSRP protein; KH domain, RNA binding protein, KSRP; NMR {Homo sapiens} Length = 85

 Score = 61.6 bits (150), Expect = 4e-12
 Identities = 17/85 (20%), Positives = 39/85 (45%), Gaps = 8/85 (9%)

Query: 301 GASQSEELVIRVLCPFNKIGRVIGKGGGTIKSIRQASGAQIDV--DDTKDNRDECVITVT 358
                   V  ++ P  K G VIGKGG TIK +++ +G ++ +  D +++   +  + + 
Sbjct: 7   ANGGQNGTVQEIMIPAGKAGLVIGKGGETIKQLQERAGVKMILIQDGSQNTNVDKPLRII 66

Query: 359 AIESPDDIKSMAVEAVLLLQTKIND 383
               P  ++    +A  ++   + +
Sbjct: 67  G--DPYKVQ----QACEMVMDILRE 85

>2opv_A KHSRP protein; KH domain, RNA binding protein, KSRP; NMR {Homo sapiens} Length = 85

 Score = 57.0 bits (138), Expect = 1e-10
 Identities = 13/60 (21%), Positives = 27/60 (45%), Gaps = 2/60 (3%)

Query: 29 DEKGNEESVIYRILCPDGVIGSVIGKSGKVINSIRQETRARVKVV--DPFPGAKDRVVTI 86
          +  G +   +  I+ P G  G VIGK G+ I  +++    ++ ++         D+ + I
Sbjct: 6  NANGGQNGTVQEIMIPAGKAGLVIGKGGETIKQLQERAGVKMILIQDGSQNTNVDKPLRI 65

>2opv_A KHSRP protein; KH domain, RNA binding protein, KSRP; NMR {Homo sapiens} Length = 85

 Score = 56.6 bits (137), Expect = 2e-10
 Identities = 16/73 (21%), Positives = 35/73 (47%), Gaps = 6/73 (8%)

Query: 143 QILVPSSQSANIIGKAGATIKRLRSKTRTSIKVTPKDASEPTHSCAMEFDNFVLISGESE 202
           +I++P+ ++  +IGK G TIK+L+ +    + +    +           D  + I G+  
Sbjct: 17  EIMIPAGKAGLVIGKGGETIKQLQERAGVKMILIQDGSQNTNV------DKPLRIIGDPY 70

Query: 203 AVKKALFAISAIM 215
            V++A   +  I+
Sbjct: 71  KVQQACEMVMDIL 83

>2opv_A KHSRP protein; KH domain, RNA binding protein, KSRP; NMR {Homo sapiens} Length = 85

 Score = 53.9 bits (130), Expect = 2e-09
 Identities = 13/77 (16%), Positives = 35/77 (45%), Gaps = 2/77 (2%)

Query: 386 DDTVTIRLLVSSKVIGCIIGKSGSIINEIRKRTKADVRISKGDKPKCADANDELVEVVGE 445
            +     +++ +   G +IGK G  I ++++R    + + +          D+ + ++G+
Sbjct: 11  QNGTVQEIMIPAGKAGLVIGKGGETIKQLQERAGVKMILIQDGSQ--NTNVDKPLRIIGD 68

Query: 446 VGSVRDALVQIILRLRD 462
              V+ A   ++  LR+
Sbjct: 69  PYKVQQACEMVMDILRE 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 = 65.2 bits (159), Expect = 3e-13
 Identities = 23/71 (32%), Positives = 38/71 (53%), Gaps = 2/71 (2%)

Query: 553 PLTLEVLVPANAVGKVIGKAGSNLANIRKISGATIEMSDSKSSRG--DRVALISGTPEQK 610
           P+  ++ VP  +VG++IG+ G  + +I K SGA I             R+  ISGT ++ 
Sbjct: 14  PVFEQLSVPQRSVGRIIGRGGETIRSICKASGAKITCDKESEGTLLLSRLIKISGTQKEV 73

Query: 611 RAAENLIQAFI 621
            AA++LI   +
Sbjct: 74  AAAKHLILEKV 84

>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 = 9e-12
 Identities = 20/84 (23%), Positives = 45/84 (53%), Gaps = 4/84 (4%)

Query: 303 SQSEELVIRVLCPFNKIGRVIGKGGGTIKSIRQASGAQIDVDDTKDNRDECVITVTAIES 362
           +++  +  ++  P   +GR+IG+GG TI+SI +ASGA+I  D   +        +    +
Sbjct: 10  TENTPVFEQLSVPQRSVGRIIGRGGETIRSICKASGAKITCDKESEGTLLLSRLIKISGT 69

Query: 363 PDDIKSMAVEAVLLLQTKINDEDD 386
             ++ +    A  L+  K++++++
Sbjct: 70  QKEVAA----AKHLILEKVSEDEE 89

>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 = 50.6 bits (121), Expect = 3e-08
 Identities = 13/57 (22%), Positives = 25/57 (43%), Gaps = 2/57 (3%)

Query: 32 GNEESVIYRILCPDGVIGSVIGKSGKVINSIRQETRARVKVVDPFPG--AKDRVVTI 86
               V  ++  P   +G +IG+ G+ I SI + + A++       G     R++ I
Sbjct: 10 TENTPVFEQLSVPQRSVGRIIGRGGETIRSICKASGAKITCDKESEGTLLLSRLIKI 66

>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 = 49.4 bits (118), Expect = 1e-07
 Identities = 16/73 (21%), Positives = 25/73 (34%), Gaps = 6/73 (8%)

Query: 143 QILVPSSQSANIIGKAGATIKRLRSKTRTSIKVTPKDASEPTHSCAMEFDNFVLISGESE 202
           Q+ VP      IIG+ G TI+ +   +   I    +                + ISG  +
Sbjct: 18  QLSVPQRSVGRIIGRGGETIRSICKASGAKITCDKESEGTLLL------SRLIKISGTQK 71

Query: 203 AVKKALFAISAIM 215
            V  A   I   +
Sbjct: 72  EVAAAKHLILEKV 84

>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 = 48.7 bits (116), Expect = 2e-07
 Identities = 18/80 (22%), Positives = 35/80 (43%), Gaps = 2/80 (2%)

Query: 385 DDDTVTIRLLVSSKVIGCIIGKSGSIINEIRKRTKADVRISKGDKPKCADANDELVEVVG 444
           ++  V  +L V  + +G IIG+ G  I  I K + A +      + +       L+++ G
Sbjct: 11  ENTPVFEQLSVPQRSVGRIIGRGGETIRSICKASGAKITCD--KESEGTLLLSRLIKISG 68

Query: 445 EVGSVRDALVQIILRLRDDA 464
               V  A   I+ ++ +D 
Sbjct: 69  TQKEVAAAKHLILEKVSEDE 88

>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 = 63.9 bits (155), Expect = 2e-12
 Identities = 32/158 (20%), Positives = 59/158 (37%), Gaps = 26/158 (16%)

Query: 302 ASQSEELVIRVLCPFNKIGRVIGKGGGTIKSIRQASGAQ-IDVDDTKDNRDECVITVTAI 360
           +   E+ ++      + +G  IG  G  I+  R+  G   ID+D+     D C   +   
Sbjct: 2   SRFHEQFIV----REDLMGLAIGTHGANIQQARKVPGVTAIDLDE-----DTCTFHIYG- 51

Query: 361 ESPDDIKSMAVEAVLLLQTKINDEDDDTVTIRLLVSSKVIGCIIGKSGSIINEIRKRTKA 420
               D    A   +            +     + V   ++G +IGK+G +I EI  ++  
Sbjct: 52  -EDQDAVKKARSFL------------EFAEDVIQVPRNLVGKVIGKNGKLIQEIVDKSGV 98

Query: 421 -DVRISKGDKPKCADANDEL-VEVVGEVGSVRDALVQI 456
             VRI   ++         +    VG   S+ +A V +
Sbjct: 99  VRVRIEAENEKNVPQEEGMVPFVFVGTKDSIANATVLL 136

>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 = 46.9 bits (111), Expect = 2e-06
 Identities = 28/176 (15%), Positives = 51/176 (28%), Gaps = 42/176 (23%)

Query: 40  RILCPDGVIGSVIGKSGKVINSIRQETRARVKVVDPFPGAKDRVVTIYSHVKDKEDVEVD 99
           + +  + ++G  IG  G  I   R+        +D           IY   +D       
Sbjct: 7   QFIVREDLMGLAIGTHGANIQQARKVPGVTAIDLDE----DTCTFHIYGEDQD------- 55

Query: 100 DEFNDKEPLCAAQDALLKVHAAIANAVANATDNDKKRKEKEECQILVPSSQSANIIGKAG 159
                                        A    +   E  E  I VP +    +IGK G
Sbjct: 56  -----------------------------AVKKARSFLEFAEDVIQVPRNLVGKVIGKNG 86

Query: 160 ATIKRLRSKTRTSIKVTPKDASEPTHSCAMEFDNFVLISGESEAVKKALFAISAIM 215
             I+ +  K+   ++V  +  +E           FV   G  +++  A   +   +
Sbjct: 87  KLIQEIVDKSG-VVRVRIEAENEKNVPQEEGMVPFV-FVGTKDSIANATVLLDYHL 140

>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 = 14/71 (19%), Positives = 27/71 (38%), Gaps = 5/71 (7%)

Query: 553 PLTLEVLVPANAVGKVIGKAGSNLANIRKISGATIEMSDSKSSRGDRVALISG-TPEQKR 611
               + +V  + +G  IG  G+N+   RK+ G T    D  +        I G   +  +
Sbjct: 3   RFHEQFIVREDLMGLAIGTHGANIQQARKVPGVTAIDLDEDT----CTFHIYGEDQDAVK 58

Query: 612 AAENLIQAFIM 622
            A + ++    
Sbjct: 59  KARSFLEFAED 69

>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 = 40.0 bits (93), Expect = 5e-04
 Identities = 20/72 (27%), Positives = 25/72 (34%), Gaps = 6/72 (8%)

Query: 553 PLTLEVLVPANAVGKVIGKAGSNLANIRKISGATI-----EMSDSKSSRGDRVAL-ISGT 606
                + VP N VGKVIGK G  +  I   SG        E   +       V     GT
Sbjct: 66  FAEDVIQVPRNLVGKVIGKNGKLIQEIVDKSGVVRVRIEAENEKNVPQEEGMVPFVFVGT 125

Query: 607 PEQKRAAENLIQ 618
            +    A  L+ 
Sbjct: 126 KDSIANATVLLD 137

>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 = 66.0 bits (160), Expect = 3e-11
 Identities = 72/484 (14%), Positives = 128/484 (26%), Gaps = 178/484 (36%)

Query: 6   KRYRSQRD---NDRDGKNQ---KRRINEKDEKGNEESVIYRI-----LCPDGVIGSVIGK 54
           + Y  QRD   ND    NQ   K  ++           +  +     +  DGV+GS  GK
Sbjct: 110 RMYIEQRDRLYND----NQVFAKYNVSRLQPYLKLRQALLELRPAKNVLIDGVLGS--GK 163

Query: 55  SGKVINSIRQETRARVKVVDPFPGA----------KDRVV-----TIYSHVKDKEDVEVD 99
           +   ++          KV                     V      +   +        D
Sbjct: 164 TWVALDVCLSY-----KVQCKMDFKIFWLNLKNCNSPETVLEMLQKLLYQIDPNWTSRSD 218

Query: 100 DEFNDKEPLCAAQDAL-----LKVHAA-------IANA-VANATDNDKKRKEKEECQILV 146
              N K  + + Q  L      K +         + NA   NA +          C+IL+
Sbjct: 219 HSSNIKLRIHSIQAELRRLLKSKPYENCLLVLLNVQNAKAWNAFNL--------SCKILL 270

Query: 147 PSSQSANIIGKAGATIKRLRSKTRTSIKVTPKDASEPTHSCAMEFDNFVLISGESEAVKK 206
                         T       TR         A+  TH   ++  +  L   E ++   
Sbjct: 271 --------------T-------TRFKQVTDFLSAATTTHIS-LDHHSMTLTPDEVKS--- 305

Query: 207 ALFAISAIMYKFSPREDIPLETTVREAPPSIIIPSDVPIYPPGGLYPNADPILPSRSVPS 266
            L        K+       L+            P D+P               P     S
Sbjct: 306 -LLL------KY-------LD----------CRPQDLP--------REVLTTNPR--RLS 331

Query: 267 ILGAARVPDLQGYADTGNTWPVYSTGLSLVSGLVGASQSEELVIRVLCPFNKIGRVIGKG 326
           I+  +    ++    T + W   +                          +K+  +I   
Sbjct: 332 IIAES----IRDGLATWDNWKHVN-------------------------CDKLTTII--- 359

Query: 327 GGTIKSIRQASGAQIDVDDTKDNRDECVITVTAIESPDDIKSMAVEAVL-LLQTKINDED 385
                   ++S   ++  + +   D   +       P          +L L+   +   D
Sbjct: 360 --------ESSLNVLEPAEYRKMFDRLSVF------PPSAHIP--TILLSLIWFDVIKSD 403

Query: 386 DDTVTIRLLVSSKVIGCIIGKSGSI-INEI--RKRTKADVR-------ISKGDKPKCADA 435
              V  +L   S V      K  +I I  I    + K +         +   + PK  D+
Sbjct: 404 VMVVVNKLHKYSLVEKQ--PKESTISIPSIYLELKVKLENEYALHRSIVDHYNIPKTFDS 461

Query: 436 NDEL 439
           +D +
Sbjct: 462 DDLI 465

>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 = 55.7 bits (134), Expect = 3e-10
 Identities = 20/74 (27%), Positives = 32/74 (43%), Gaps = 3/74 (4%)

Query: 548 GGLPPPLTLEVLVPANAVGKVIGKAGSNLANIRKISGATIEMSDSKSSRGDRVALISGTP 607
           G      T++V VP   VG V+G  G+ +  I++ +   I          + V  ++G P
Sbjct: 4   GSSGGQTTIQVRVPYRVVGLVVGPKGATIKRIQQRTHTYIVTPGRDK---EPVFAVTGMP 60

Query: 608 EQKRAAENLIQAFI 621
           E    A   I+A I
Sbjct: 61  ENVDRAREEIEAHI 74

>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 = 43.8 bits (103), Expect = 5e-06
 Identities = 24/72 (33%), Positives = 33/72 (45%), Gaps = 11/72 (15%)

Query: 143 QILVPSSQSANIIGKAGATIKRLRSKTRTSIKVTPKDASEPTHSCAMEFDNFVLISGESE 202
           Q+ VP      ++G  GATIKR++ +T T I VTP    EP             ++G  E
Sbjct: 13  QVRVPYRVVGLVVGPKGATIKRIQQRTHTYI-VTPGRDKEPV----------FAVTGMPE 61

Query: 203 AVKKALFAISAI 214
            V +A   I A 
Sbjct: 62  NVDRAREEIEAH 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 = 42.2 bits (99), Expect = 2e-05
 Identities = 21/78 (26%), Positives = 33/78 (42%), Gaps = 3/78 (3%)

Query: 302 ASQSEELVIRVLCPFNKIGRVIGKGGGTIKSIRQASGAQIDVDDTKDNRDECVITVTAIE 361
            S   +  I+V  P+  +G V+G  G TIK I+Q +   I            V  VT + 
Sbjct: 4   GSSGGQTTIQVRVPYRVVGLVVGPKGATIKRIQQRTHTYIVTPGRDKEP---VFAVTGMP 60

Query: 362 SPDDIKSMAVEAVLLLQT 379
              D     +EA + L++
Sbjct: 61  ENVDRAREEIEAHITLRS 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 = 52.4 bits (126), Expect = 7e-09
 Identities = 17/82 (20%), Positives = 28/82 (34%), Gaps = 2/82 (2%)

Query: 540 SSYSSKLYGGLPPPLTLEVLVPANAVGKVIGKAGSNLANIRKISGATIEMSDSKSSRGDR 599
           S  S  +   L    +  V +P      VIGK G  L ++   +   I++          
Sbjct: 3   SGSSGDIVARLQTQASATVAIPKEHHRFVIGKNGEKLQDLELKTATKIQIPRPDD--PSN 60

Query: 600 VALISGTPEQKRAAENLIQAFI 621
              I+GT E    A + +    
Sbjct: 61  QIKITGTKEGIEKARHEVLLIS 82

>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 = 50.9 bits (122), Expect = 2e-08
 Identities = 19/79 (24%), Positives = 33/79 (41%), Gaps = 10/79 (12%)

Query: 143 QILVPSSQSANIIGKAGATIKRLRSKTRTSIKVTPKDASEPTHSCAMEFDNFVLISGESE 202
            + +P      +IGK G  ++ L  KT T I++   D          +  N + I+G  E
Sbjct: 20  TVAIPKEHHRFVIGKNGEKLQDLELKTATKIQIPRPD----------DPSNQIKITGTKE 69

Query: 203 AVKKALFAISAIMYKFSPR 221
            ++KA   +  I  +   R
Sbjct: 70  GIEKARHEVLLISAEQDKR 88

>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 = 48.6 bits (116), Expect = 1e-07
 Identities = 16/65 (24%), Positives = 26/65 (40%)

Query: 292 GLSLVSGLVGASQSEELVIRVLCPFNKIGRVIGKGGGTIKSIRQASGAQIDVDDTKDNRD 351
           G S  SG + A    +    V  P      VIGK G  ++ +   +  +I +    D  +
Sbjct: 1   GSSGSSGDIVARLQTQASATVAIPKEHHRFVIGKNGEKLQDLELKTATKIQIPRPDDPSN 60

Query: 352 ECVIT 356
           +  IT
Sbjct: 61  QIKIT 65

>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 = 45.5 bits (108), Expect = 2e-06
 Identities = 14/100 (14%), Positives = 35/100 (35%), Gaps = 11/100 (11%)

Query: 378 QTKINDEDDDTVTIRLLVSSKVIGCIIGKSGSIINEIRKRTKADVRISKGDKPKCADAND 437
              I        +  + +  +    +IGK+G  + ++  +T   ++I + D P       
Sbjct: 6   SGDIVARLQTQASATVAIPKEHHRFVIGKNGEKLQDLELKTATKIQIPRPDDP------S 59

Query: 438 ELVEVVGEVGSVRDALVQIILRLRDDALKDRDGSRNPPVG 477
             +++ G    +  A  ++          ++D    P  G
Sbjct: 60  NQIKITGTKEGIEKARHEV-----LLISAEQDKRSGPSSG 94

>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 = 42.4 bits (100), Expect = 2e-05
 Identities = 13/64 (20%), Positives = 26/64 (40%), Gaps = 5/64 (7%)

Query: 34 EESVIYRILCPDGVIGSVIGKSGKVINSIRQETRARVKVVDPFPGAKDRVVTIYSHVKDK 93
          +      +  P      VIGK+G+ +  +  +T  ++++  P P      + I      K
Sbjct: 14 QTQASATVAIPKEHHRFVIGKNGEKLQDLELKTATKIQI--PRPDDPSNQIKITG---TK 68

Query: 94 EDVE 97
          E +E
Sbjct: 69 EGIE 72

>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 = 53.6 bits (128), Expect = 4e-08
 Identities = 32/215 (14%), Positives = 66/215 (30%), Gaps = 26/215 (12%)

Query: 1   MGDSGKRYRSQRDNDRDGKNQKRRINEKDEKGNEESVIYRILCPDGVIGSVIGKSGKVIN 60
           MG+  ++   + +N          + ++DE          +  P   I  +IGK G+   
Sbjct: 1   MGEEFEKLMKKFENVNK---DGEIVEDEDEWEEFFKQEEYVKIPKDRIAVLIGKKGQTKK 57

Query: 61  SIRQETRARVKVVDPFPGAKDRVVTIYSHVKDKEDVEVDDEFNDKEPLCAAQDALLKVHA 120
            I + T+ ++ +       +   V I +  K+ ED     +  D         +  +   
Sbjct: 58  EIEKRTKTKITIDS-----ETGEVWI-TSTKETEDPLAVWKARDIVLAIGRGFSPERAFR 111

Query: 121 AIANAVANATDNDKKRKEKEECQILVPSSQSANIIGKAGATIKRLRSKTRTSIKVTPKDA 180
            +        +           +          IIG+ G T + +   +  S+ V     
Sbjct: 112 LLNEGE--YLEIINLTDIIIGNEKNALPRVRGRIIGRKGRTRQIIEEMSGASVSV----- 164

Query: 181 SEPTHSCAMEFDNFVLISGESEAVKKALFAISAIM 215
                     +   V I G    ++ A  AI  + 
Sbjct: 165 ----------YGKTVAIIGNPIQIEIAKTAIEKLA 189

>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 = 50.1 bits (119), Expect = 4e-07
 Identities = 35/177 (19%), Positives = 61/177 (34%), Gaps = 22/177 (12%)

Query: 311 RVLCPFNKIGRVIGKGGGTIKSIRQASGAQIDVD---------DTKDNRDECVITVTAIE 361
            V  P ++I  +IGK G T K I + +  +I +D          TK+  D   +      
Sbjct: 37  YVKIPKDRIAVLIGKKGQTKKEIEKRTKTKITIDSETGEVWITSTKETEDPLAVWKARDI 96

Query: 362 SPDDIKSMAVEAVLLL-----QTKINDEDDDTVTIRLLVSSKVIGCIIGKSGSIINEIRK 416
                +  + E    L       +I +  D  +        +V G IIG+ G     I +
Sbjct: 97  VLAIGRGFSPERAFRLLNEGEYLEIINLTDIIIGNEKNALPRVRGRIIGRKGRTRQIIEE 156

Query: 417 RTKADVRISK------GDKPKCADANDELVEVVG--EVGSVRDALVQIILRLRDDAL 465
            + A V +        G+  +   A   + ++      GSV   L +    L  +  
Sbjct: 157 MSGASVSVYGKTVAIIGNPIQIEIAKTAIEKLARGSPHGSVYRYLERRKKDLELEGA 213

>3n89_A Defective in GERM LINE development protein 3, ISO; KH domains, RNA binding, cell cycle; 2.79A {Caenorhabditis elegans} Length = 376

 Score = 54.6 bits (130), Expect = 5e-08
 Identities = 36/304 (11%), Positives = 87/304 (28%), Gaps = 33/304 (10%)

Query: 143 QILVPSSQSANIIGKAG--ATIKRLRSKTRTSIKVTPKDASEPTHSCAMEFDNFVLISGE 200
            +   S   + +    G    +  + ++T T I++          +    F   V I+G 
Sbjct: 33  NMEFESQYYSLMTSDNGDHENVASIMAETNTLIQLPD---RSVGGTTPDPFAQQVTITGY 89

Query: 201 SEAVKKALFAISAIMYKFSPREDIPLETTVREAPPSIIIPSDVPIYPPGGLYPNADPILP 260
              V +A   +         R +      +       +   ++  +       N +    
Sbjct: 90  FGDVDRARMLM---------RRNCHFTVFM-ALSKMKMPLHELQAHVRQNPIQNVEMSFV 139

Query: 261 SRSVPSILGAARVPDLQGYADTGNTWPVY---STGLSLVSGLVGASQSEELVIRVLC--P 315
                + +    +        T      +        L   L   S + E    +     
Sbjct: 140 DAPEKNGIVTTYLRI------TAREKNQHELIEAAKRLNEILFRESPAPENNFTLHFTLS 193

Query: 316 FNKIGRVIGKGGG--TIKSIRQASGAQIDVDDTKDNRDEC--VITVTAIESPDDIKSMAV 371
              + +V+G       +  I + +   I      +  +    +  +  + + D++   A 
Sbjct: 194 TYYVDQVLGSSSTAQLMPVIERETTTIISYPCYNNRNETRGNIYEIKVVGNIDNVL-KAR 252

Query: 372 EAVLLLQ--TKINDEDDDTVTIRLLVSSKVIGCIIGKSGSIINEIRKRTKADVRISKGDK 429
             ++ L   +   +  +  +     VS + I  II +SG I+       +    +S    
Sbjct: 253 RYIMDLLPISMCFNIKNTDMAEPSRVSDRNIHMIIDESGIILKMTPSVYEPADLLSGEVP 312

Query: 430 PKCA 433
             CA
Sbjct: 313 LNCA 316

>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 = 49.1 bits (117), Expect = 1e-07
 Identities = 18/90 (20%), Positives = 38/90 (42%), Gaps = 8/90 (8%)

Query: 129 ATDNDKKRKEKE-ECQILVPSSQSANIIGKAGATIKRLRSKTRTSIKVTPKDASEPTHSC 187
           ++   + R  +  +  + V       IIG+ GA I ++R +   +I+   KD        
Sbjct: 5   SSGEQEDRALRSFKLSVTVDPKYHPKIIGRKGAVITQIRLEHDVNIQFPDKDDGN----- 59

Query: 188 AMEFDNFVLISGESEAVKKALFAISAIMYK 217
             +  + + I+G  +  + A  AI  I+ +
Sbjct: 60  --QPQDQITITGYEKNTEAARDAILRIVGE 87

>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 = 47.1 bits (112), Expect = 5e-07
 Identities = 16/68 (23%), Positives = 27/68 (39%), Gaps = 1/68 (1%)

Query: 555 TLEVLVPANAVGKVIGKAGSNLANIRKISGATIEMSDS-KSSRGDRVALISGTPEQKRAA 613
            L V V      K+IG+ G+ +  IR      I+  D    ++      I+G  +   AA
Sbjct: 18  KLSVTVDPKYHPKIIGRKGAVITQIRLEHDVNIQFPDKDDGNQPQDQITITGYEKNTEAA 77

Query: 614 ENLIQAFI 621
            + I   +
Sbjct: 78  RDAILRIV 85

>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 = 44.8 bits (106), Expect = 4e-06
 Identities = 17/90 (18%), Positives = 38/90 (42%), Gaps = 6/90 (6%)

Query: 378 QTKINDEDDDTVTIRLLVSSKVIGCIIGKSGSIINEIRKRTKADVRISKGDKPKCADAND 437
             +  D    +  + + V  K    IIG+ G++I +IR     +++    D     +   
Sbjct: 6   SGEQEDRALRSFKLSVTVDPKYHPKIIGRKGAVITQIRLEHDVNIQFPDKDDG---NQPQ 62

Query: 438 ELVEVVGE---VGSVRDALVQIILRLRDDA 464
           + + + G      + RDA+++I+  L   +
Sbjct: 63  DQITITGYEKNTEAARDAILRIVGELEQMS 92

>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 = 41.0 bits (96), Expect = 8e-05
 Identities = 15/81 (18%), Positives = 29/81 (35%), Gaps = 7/81 (8%)

Query: 310 IRVLCPFNKIGRVIGKGGGTIKSIRQASGAQIDVDDTKD-NRDECVITVTAIESPDDIKS 368
           + V        ++IG+ G  I  IR      I   D  D N+ +  IT+T      + + 
Sbjct: 19  LSVTVDPKYHPKIIGRKGAVITQIRLEHDVNIQFPDKDDGNQPQDQITITG--YEKNTE- 75

Query: 369 MAVEAVLLLQTKINDEDDDTV 389
               A   +   + + +  + 
Sbjct: 76  ---AARDAILRIVGELEQMSG 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 = 40.2 bits (94), Expect = 2e-04
 Identities = 12/62 (19%), Positives = 21/62 (33%), Gaps = 3/62 (4%)

Query: 26 NEKDEKGNEESVIYRILCPDGVIGSVIGKSGKVINSIRQETRARVKVVDPF-PGAKDRVV 84
           ++D       +   +         +IG+ G VI  IR E    ++  D          +
Sbjct: 8  EQEDRALRSFKLSVTV--DPKYHPKIIGRKGAVITQIRLEHDVNIQFPDKDDGNQPQDQI 65

Query: 85 TI 86
          TI
Sbjct: 66 TI 67

>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 = 48.6 bits (116), Expect = 2e-07
 Identities = 24/88 (27%), Positives = 39/88 (44%), Gaps = 6/88 (6%)

Query: 380 KINDEDDDTVTIRLLVSSKVIGCIIGKSGSIINEIRKRTKADVRISKGDKPKCADANDEL 439
           +I  E +  V+  + +  +V   IIG  G  I +I    K D+R      P+    +   
Sbjct: 8   RIVGELEQMVSEDVPLDHRVHARIIGARGKAIRKIMDEFKVDIRF-----PQSGAPDPNC 62

Query: 440 VEVVGEVGSVRDALVQIILRLRDDALKD 467
           V V G   +V +A +  IL L ++ L D
Sbjct: 63  VTVTGLPENVEEA-IDHILNLEEEYLAD 89

>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 = 43.6 bits (103), Expect = 8e-06
 Identities = 16/81 (19%), Positives = 34/81 (41%), Gaps = 9/81 (11%)

Query: 134 KKRKEKEECQILVPSSQSANIIGKAGATIKRLRSKTRTSIKVTPKDASEPTHSCAMEFDN 193
            + ++     + +     A IIG  G  I+++  + +  I+     A +P         N
Sbjct: 11  GELEQMVSEDVPLDHRVHARIIGARGKAIRKIMDEFKVDIRFPQSGAPDP---------N 61

Query: 194 FVLISGESEAVKKALFAISAI 214
            V ++G  E V++A+  I  +
Sbjct: 62  CVTVTGLPENVEEAIDHILNL 82

>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 = 42.1 bits (99), Expect = 3e-05
 Identities = 16/79 (20%), Positives = 30/79 (37%), Gaps = 1/79 (1%)

Query: 543 SSKLYGGLPPPLTLEVLVPANAVGKVIGKAGSNLANIRKISGATIEMSDSKSSRGDRVAL 602
           S ++ G L   ++ +V +      ++IG  G  +  I       I    S +   + V  
Sbjct: 6   SGRIVGELEQMVSEDVPLDHRVHARIIGARGKAIRKIMDEFKVDIRFPQSGAPDPNCVT- 64

Query: 603 ISGTPEQKRAAENLIQAFI 621
           ++G PE    A + I    
Sbjct: 65  VTGLPENVEEAIDHILNLE 83

>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 = 49.2 bits (117), Expect = 7e-07
 Identities = 30/167 (17%), Positives = 59/167 (35%), Gaps = 31/167 (18%)

Query: 310 IRVLCPFNKIGRVIGKGGGTIKSIRQASGAQIDVDDTKDNRDECVITVTAIESP------ 363
           I V     ++G VIG  G     I + +G  I VD   +N    V        P      
Sbjct: 6   IYVKVKPERLGAVIGPRGEVKAEIMRRTGTVITVDT--ENSMVIVEPEAEGIPPVNLMKA 63

Query: 364 -DDIKSMAVEAVLLLQTKINDEDDDTVTIRLL--------VSSKVIGCIIGKSGSIINEI 414
            + +K++++        ++ +ED   V + L            ++ G IIG+ G     I
Sbjct: 64  AEVVKAISLGFPPEKAFRLLEEDQILVVVDLKQVVGDSQNHLKRIKGRIIGEGGRARRTI 123

Query: 415 RKRTKADVRISKGDKPKCADANDELVEVVGE---VGSVRDALVQIIL 458
            + T   + +            +  V ++G+     + + A+  +  
Sbjct: 124 EEMTDTYINVG-----------EYEVAIIGDYERAMAAKQAIEMLAE 159

>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 = 43.5 bits (102), Expect = 5e-05
 Identities = 32/181 (17%), Positives = 58/181 (32%), Gaps = 36/181 (19%)

Query: 41  ILCPDGVIGSVIGKSGKVINSIRQETRARVKVVDPFPGAKDRVVTIYSHVKDKEDVEVDD 100
           +      +G+VIG  G+V   I + T   + V       ++ +V +            + 
Sbjct: 8   VKVKPERLGAVIGPRGEVKAEIMRRTGTVITVDT-----ENSMVIVEP----------EA 52

Query: 101 EFNDKEPLCAAQDALLKVHAAIANAVANATDNDKKRKEKEECQILVPSSQS------ANI 154
           E      L  A + +  +        A     + +     + + +V  SQ+        I
Sbjct: 53  EGIPPVNLMKAAEVVKAISLGFPPEKAFRLLEEDQILVVVDLKQVVGDSQNHLKRIKGRI 112

Query: 155 IGKAGATIKRLRSKTRTSIKVTPKDASEPTHSCAMEFDNFVLISGESEAVKKALFAISAI 214
           IG+ G   + +   T T I V                +  V I G+ E    A  AI  +
Sbjct: 113 IGEGGRARRTIEEMTDTYINV---------------GEYEVAIIGDYERAMAAKQAIEML 157

Query: 215 M 215
            
Sbjct: 158 A 158

>1vig_A Vigilin; RNA-binding protein, ribonucleoprotein; NMR {Homo sapiens} SCOP: d.51.1.1 PDB: 1vih_A Length = 71

 Score = 45.0 bits (107), Expect = 2e-06
 Identities = 15/65 (23%), Positives = 32/65 (49%), Gaps = 10/65 (15%)

Query: 143 QILVPSSQSANIIGKAGATIKRLRSKTRTSIKVTPKDASEPTHSCAMEFDNFVLISGESE 202
           +I +      ++IGK+GA I R++ + + S+++ P               N + I G+ +
Sbjct: 8   EINIDHKFHRHLIGKSGANINRIKDQYKVSVRIPPDSEK----------SNLIRIEGDPQ 57

Query: 203 AVKKA 207
            V++A
Sbjct: 58  GVQQA 62

>1vig_A Vigilin; RNA-binding protein, ribonucleoprotein; NMR {Homo sapiens} SCOP: d.51.1.1 PDB: 1vih_A Length = 71

 Score = 43.9 bits (104), Expect = 4e-06
 Identities = 11/67 (16%), Positives = 27/67 (40%), Gaps = 2/67 (2%)

Query: 555 TLEVLVPANAVGKVIGKAGSNLANIRKISGATIEMSDSKSSRGDRVALISGTPEQKRAAE 614
            +E+ +       +IGK+G+N+  I+     ++ +          +  I G P+  + A+
Sbjct: 6   YVEINIDHKFHRHLIGKSGANINRIKDQYKVSVRIPPDSE--KSNLIRIEGDPQGVQQAK 63

Query: 615 NLIQAFI 621
             +    
Sbjct: 64  RELLELA 70

>1vig_A Vigilin; RNA-binding protein, ribonucleoprotein; NMR {Homo sapiens} SCOP: d.51.1.1 PDB: 1vih_A Length = 71

 Score = 43.9 bits (104), Expect = 4e-06
 Identities = 7/52 (13%), Positives = 16/52 (30%)

Query: 305 SEELVIRVLCPFNKIGRVIGKGGGTIKSIRQASGAQIDVDDTKDNRDECVIT 356
           +    + +         +IGK G  I  I+      + +    +  +   I 
Sbjct: 2   NRMDYVEINIDHKFHRHLIGKSGANINRIKDQYKVSVRIPPDSEKSNLIRIE 53

>1vig_A Vigilin; RNA-binding protein, ribonucleoprotein; NMR {Homo sapiens} SCOP: d.51.1.1 PDB: 1vih_A Length = 71

 Score = 40.4 bits (95), Expect = 6e-05
 Identities = 17/71 (23%), Positives = 35/71 (49%), Gaps = 6/71 (8%)

Query: 386 DDTVTIRLLVSSKVIGCIIGKSGSIINEIRKRTKADVRISKGDKPKCADANDELVEVVGE 445
           +    + + +  K    +IGKSG+ IN I+ + K  VRI     P  ++ ++  + + G+
Sbjct: 2   NRMDYVEINIDHKFHRHLIGKSGANINRIKDQYKVSVRI-----PPDSEKSNL-IRIEGD 55

Query: 446 VGSVRDALVQI 456
              V+ A  ++
Sbjct: 56  PQGVQQAKREL 66

>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 = 44.8 bits (106), Expect = 4e-06
 Identities = 15/69 (21%), Positives = 28/69 (40%), Gaps = 2/69 (2%)

Query: 553 PLTLEVLVPANAVGKVIGKAGSNLANIRKISGATIEMSDSKSSRGDRVALISGTPEQKRA 612
           P+T+EV VP +    VIG+ GS +  +       I +   +      +  I+G       
Sbjct: 16  PVTIEVEVPFDLHRYVIGQKGSGIRKMMDEFEVNIHVPAPEL--QSDIIAITGLAANLDR 73

Query: 613 AENLIQAFI 621
           A+  +   +
Sbjct: 74  AKAGLLERV 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 = 44.8 bits (106), Expect = 5e-06
 Identities = 15/99 (15%), Positives = 37/99 (37%), Gaps = 16/99 (16%)

Query: 143 QILVPSSQSANIIGKAGATIKRLRSKTRTSIKVTPKDASEPTHSCAMEFDNFVLISGESE 202
           ++ VP      +IG+ G+ I+++  +   +I V   +             + + I+G + 
Sbjct: 20  EVEVPFDLHRYVIGQKGSGIRKMMDEFEVNIHVPAPE----------LQSDIIAITGLAA 69

Query: 203 AVKKALFAISAIMYKFSPREDIPLETTVREAPPSIIIPS 241
            + +A   +   +      +++  E   R        PS
Sbjct: 70  NLDRAKAGLLERV------KELQAEQEDRALRSFKSGPS 102

>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 = 44.4 bits (105), Expect = 6e-06
 Identities = 14/47 (29%), Positives = 19/47 (40%)

Query: 310 IRVLCPFNKIGRVIGKGGGTIKSIRQASGAQIDVDDTKDNRDECVIT 356
           I V  PF+    VIG+ G  I+ +       I V   +   D   IT
Sbjct: 19  IEVEVPFDLHRYVIGQKGSGIRKMMDEFEVNIHVPAPELQSDIIAIT 65

>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 = 40.6 bits (95), Expect = 1e-04
 Identities = 14/83 (16%), Positives = 36/83 (43%), Gaps = 6/83 (7%)

Query: 380 KINDEDDDTVTIRLLVSSKVIGCIIGKSGSIINEIRKRTKADVRISKGDKPKCADANDEL 439
           K   E    VTI + V   +   +IG+ GS I ++    + ++ +         +   ++
Sbjct: 8   KEALEALVPVTIEVEVPFDLHRYVIGQKGSGIRKMMDEFEVNIHVPA------PELQSDI 61

Query: 440 VEVVGEVGSVRDALVQIILRLRD 462
           + + G   ++  A   ++ R+++
Sbjct: 62  IAITGLAANLDRAKAGLLERVKE 84

>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 = 40.2 bits (94), Expect = 2e-04
 Identities = 13/59 (22%), Positives = 22/59 (37%), Gaps = 2/59 (3%)

Query: 28 KDEKGNEESVIYRILCPDGVIGSVIGKSGKVINSIRQETRARVKVVDPFPGAKDRVVTI 86
          K+       V   +  P  +   VIG+ G  I  +  E    + V  P P  +  ++ I
Sbjct: 8  KEALEALVPVTIEVEVPFDLHRYVIGQKGSGIRKMMDEFEVNIHV--PAPELQSDIIAI 64

>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 Length = 757

 Score = 46.8 bits (112), Expect = 2e-05
 Identities = 12/28 (42%), Positives = 18/28 (64%)

Query: 318 KIGRVIGKGGGTIKSIRQASGAQIDVDD 345
           KIG VIG     I  I++ +GA+I ++D
Sbjct: 608 KIGEVIGPKRQMINQIQEDTGAEITIED 635

>3cdi_A Polynucleotide phosphorylase; mRNA turnover, RNAse, RNA degradation, kinase, transferase; 2.60A {Escherichia coli} PDB: 1sro_A Length = 723

 Score = 46.7 bits (112), Expect = 2e-05
 Identities = 12/28 (42%), Positives = 20/28 (71%)

Query: 318 KIGRVIGKGGGTIKSIRQASGAQIDVDD 345
           KI  VIGKGG  I+++ + +G  I+++D
Sbjct: 570 KIKDVIGKGGSVIRALTEETGTTIEIED 597

>3u1k_A Polyribonucleotide nucleotidyltransferase 1, MITO; RNAse PH, KH domain, exoribonuclease; HET: CIT; 2.13A {Homo sapiens} Length = 630

 Score = 46.7 bits (112), Expect = 2e-05
 Identities = 8/29 (27%), Positives = 14/29 (48%)

Query: 318 KIGRVIGKGGGTIKSIRQASGAQIDVDDT 346
           K  + +G GG  +K ++  +G  I   D 
Sbjct: 577 KRAKFVGPGGYNLKKLQAETGVTISQVDE 605

>4aid_A Polyribonucleotide nucleotidyltransferase; transferase-peptide complex; 2.60A {Caulobacter vibrioides} PDB: 4aim_A 4am3_A Length = 726

 Score = 46.7 bits (112), Expect = 2e-05
 Identities = 13/29 (44%), Positives = 19/29 (65%)

Query: 318 KIGRVIGKGGGTIKSIRQASGAQIDVDDT 346
           KI  VIG GG  I+ I   +GA++D++D 
Sbjct: 580 KIREVIGSGGKVIREIVATTGAKVDINDD 608

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	624
3krm_A	163	Insulin-like growth factor 2 mRNA-binding protein	99.92
2anr_A	178	Neuro-oncological ventral antigen 1; protein-RNA c	99.91
2jzx_A	160	Poly(RC)-binding protein 2; PCBP2, KH domains, RNA	99.91
2jvz_A	164	KH type-splicing, FAR upstream element-binding pro	99.91
3krm_A	163	Insulin-like growth factor 2 mRNA-binding protein	99.91
2jzx_A	160	Poly(RC)-binding protein 2; PCBP2, KH domains, RNA	99.9
1j4w_A	174	FUSE binding protein; single-stranded DNA binding	99.9
2anr_A	178	Neuro-oncological ventral antigen 1; protein-RNA c	99.9
3n89_A	376	Defective in GERM LINE development protein 3, ISO;	99.9
1j4w_A	174	FUSE binding protein; single-stranded DNA binding	99.89
3n89_A	376	Defective in GERM LINE development protein 3, ISO;	99.89
2jvz_A	164	KH type-splicing, FAR upstream element-binding pro	99.88
2qnd_A	144	FMR1 protein; KH domain, eukaryotic KH domains, ta	99.76
2qnd_A	144	FMR1 protein; KH domain, eukaryotic KH domains, ta	99.7
1zzk_A	82	Heterogeneous nuclear ribonucleoprotein K; KH domi	99.62
2e3u_A	219	PH-DIM2P, hypothetical protein PH1566; PRE-ribosom	99.61
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	99.59
1x4n_A	92	FAR upstream element binding protein 1; KH domain,	99.56
1dtj_A	76	RNA-binding neurooncological ventral antigen 2; KH	99.55
1j5k_A	89	Heterogeneous nuclear ribonucleoprotein K; single-	99.54
2axy_A	73	Poly(RC)-binding protein 2; protein-DNA complex, D	99.54
2e3u_A	219	PH-DIM2P, hypothetical protein PH1566; PRE-ribosom	99.54
2hh2_A	107	KH-type splicing regulatory protein; KH-RNA bindin	99.51
1ec6_A	87	RNA-binding protein NOVA-2; KH domain, alpha-beta	99.51
2hh3_A	106	KH-type splicing regulatory protein; KH-RNA bindin	99.5
1x4m_A	94	FAR upstream element binding protein 1; KH domain,	99.5
2dgr_A	83	Ring finger and KH domain-containing protein 1; st	99.49
1tua_A	191	Hypothetical protein APE0754; structural genomics,	99.48
2opv_A	85	KHSRP protein; KH domain, RNA binding protein, KSR	99.48
2ctm_A	95	Vigilin; K homology type I domain, RNA-binding, ce	99.42
2axy_A	73	Poly(RC)-binding protein 2; protein-DNA complex, D	99.42
1vig_A	71	Vigilin; RNA-binding protein, ribonucleoprotein; N	99.41
1we8_A	104	Tudor and KH domain containing protein; structural	99.41
2ctl_A	97	Vigilin; K homology type I domain, RNA-binding, ce	99.39
1tua_A	191	Hypothetical protein APE0754; structural genomics,	99.38
2cte_A	94	Vigilin; K homology type I domain, RNA-binding, ce	99.38
2p2r_A	76	Poly(RC)-binding protein 2; protein-DNA complex, R	99.36
1zzk_A	82	Heterogeneous nuclear ribonucleoprotein K; KH domi	99.35
1dtj_A	76	RNA-binding neurooncological ventral antigen 2; KH	99.35
1wvn_A	82	Poly(RC)-binding protein 1; KH domain, RNA binding	99.35
1j5k_A	89	Heterogeneous nuclear ribonucleoprotein K; single-	99.31
1ec6_A	87	RNA-binding protein NOVA-2; KH domain, alpha-beta	99.31
2dgr_A	83	Ring finger and KH domain-containing protein 1; st	99.29
1x4n_A	92	FAR upstream element binding protein 1; KH domain,	99.28
2opv_A	85	KHSRP protein; KH domain, RNA binding protein, KSR	99.28
2ctk_A	104	Vigilin; K homology type I domain, RNA-binding, ce	99.27
1x4m_A	94	FAR upstream element binding protein 1; KH domain,	99.26
2hh2_A	107	KH-type splicing regulatory protein; KH-RNA bindin	99.25
2ctj_A	95	Vigilin; K homology type I domain, RNA-binding, ce	99.25
2hh3_A	106	KH-type splicing regulatory protein; KH-RNA bindin	99.24
2ctm_A	95	Vigilin; K homology type I domain, RNA-binding, ce	99.22
1vig_A	71	Vigilin; RNA-binding protein, ribonucleoprotein; N	99.21
2cte_A	94	Vigilin; K homology type I domain, RNA-binding, ce	99.19
1we8_A	104	Tudor and KH domain containing protein; structural	99.19
2ctl_A	97	Vigilin; K homology type I domain, RNA-binding, ce	99.16
2ctf_A	102	Vigilin; K homology type I domain, RNA-binding, ce	99.14
2ctj_A	95	Vigilin; K homology type I domain, RNA-binding, ce	99.05
2ctk_A	104	Vigilin; K homology type I domain, RNA-binding, ce	99.04
2ctf_A	102	Vigilin; K homology type I domain, RNA-binding, ce	98.97
2cpq_A	91	FragIle X mental retardation syndrome related prot	98.95
1k1g_A	131	SF1-BO isoform; splicing, branch point sequence, p	98.68
2cpq_A	91	FragIle X mental retardation syndrome related prot	98.65
2yqr_A	119	KIAA0907 protein; structure genomics, KH domain, s	98.62
1k1g_A	131	SF1-BO isoform; splicing, branch point sequence, p	98.36
2yqr_A	119	KIAA0907 protein; structure genomics, KH domain, s	98.3
2bl5_A	140	MGC83862 protein, quaking protein; STAR proteins,	98.09
3u1k_A	630	Polyribonucleotide nucleotidyltransferase 1, MITO;	98.0
3v69_A	140	Protein filia; RNA-binding, embryogenesis, KH doma	97.98
2bl5_A	140	MGC83862 protein, quaking protein; STAR proteins,	97.98
3u1k_A	630	Polyribonucleotide nucleotidyltransferase 1, MITO;	97.74
4aid_A	726	Polyribonucleotide nucleotidyltransferase; transfe	97.39
2cxc_A	144	NUSA; transcription termination, RNA binding prote	97.36
3v69_A	140	Protein filia; RNA-binding, embryogenesis, KH doma	97.24
4aid_A	726	Polyribonucleotide nucleotidyltransferase; transfe	97.17
2cxc_A	144	NUSA; transcription termination, RNA binding prote	97.15
1k0r_A	366	NUSA; two component arrangement, S1 domain, two K-	95.27
2asb_A	251	Transcription elongation protein NUSA; protein-RNA	95.22
3cdi_A	723	Polynucleotide phosphorylase; mRNA turnover, RNAse	95.14
1e3p_A	757	Guanosine pentaphosphate synthetase; polyribonucle	94.61
3cdi_A	723	Polynucleotide phosphorylase; mRNA turnover, RNAse	94.5
1e3p_A	757	Guanosine pentaphosphate synthetase; polyribonucle	94.47
1k0r_A	366	NUSA; two component arrangement, S1 domain, two K-	94.14
2asb_A	251	Transcription elongation protein NUSA; protein-RNA	93.68
1hh2_P	344	NUSA, N utilization substance protein A; transcrip	92.93
1hh2_P	344	NUSA, N utilization substance protein A; transcrip	89.73

>3krm_A Insulin-like growth factor 2 mRNA-binding protein 1; KH domain, cell projection, cytoplasm, nucleus, phosphoprotein, translation regulation; 2.75A {Homo sapiens}

Probab=99.92  E-value=7.6e-25  Score=203.58  Aligned_cols=153  Identities=22%  Similarity=0.413  Sum_probs=128.9

Q ss_pred             cEEEEEEecCCeeeEEEcCCCchHHHHHHhcCceEEEeCCCCCCCCCCCCcEEEEEeehHHHHHHHHHHHHHHhhccccC
Q 006943          388 TVTIRLLVSSKVIGCIIGKSGSIINEIRKRTKADVRISKGDKPKCADANDELVEVVGEVGSVRDALVQIILRLRDDALKD  467 (624)
Q Consensus       388 ~~~~~l~vp~~~~g~iIGk~G~~Ik~I~~~tga~I~i~~~~~p~~~~~~~~~v~I~G~~~~v~~A~~~I~~~l~e~~~~~  467 (624)
                      +.+++|+||.+++|.|||++|++|++|+++|||+|+|+++..|   +..+|+|+|+|+++++.+|+.+|.+.+.+.....
T Consensus         2 ~~~~~~~ip~~~~g~iIGk~G~~Ik~i~~~tg~~I~i~~~~~~---~~~~r~v~I~G~~e~v~~A~~~I~~~~~e~~~~~   78 (163)
T 3krm_A            2 QEMVQVFIPAQAVGAIIGKKGQHIKQLSRFASASIKIAPPETP---DSKVRMVIITGPPEAQFKAQGRIYGKLKEENFFG   78 (163)
T ss_dssp             CEEEEEEEEGGGHHHHHCGGGHHHHHHHHHHTCEEEECCCSST---TCSEEEEEEEECHHHHHHHHHHHHHHHHHTTSSC
T ss_pred             ceEEEEEechhhcceeECCCcHHHHHHHHHHCCeEEEcCCCCC---CCCceEEEEEcCHHHHHHHHHHHHHHHhcccccc
Confidence            3578999999999999999999999999999999999876544   4678999999999999999999998887641100


Q ss_pred             CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCcccccC
Q 006943          468 RDGSRNPPVGADHIYSSGTGISMPPLLPSIPPVGPLGYDQRADSGSGIGMLSSSSLYGYGSLSMGDSPYGSMSSYSSKLY  547 (624)
Q Consensus       468 ~~~~~~p~~~~~~~~~~~~~~~~p~~~~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  547 (624)
                            |.                                                                        
T Consensus        79 ------~~------------------------------------------------------------------------   80 (163)
T 3krm_A           79 ------PK------------------------------------------------------------------------   80 (163)
T ss_dssp             ------SS------------------------------------------------------------------------
T ss_pred             ------cc------------------------------------------------------------------------
Confidence                  00                                                                        


Q ss_pred             CCCCCCcEEEEEeccccccceeccCCchHHHHHHHhCCEEEEeCCC-CCCC-CeEEEEEcCHHHHHHHHHHHHHHHhh
Q 006943          548 GGLPPPLTLEVLVPANAVGKVIGKAGSNLANIRKISGATIEMSDSK-SSRG-DRVALISGTPEQKRAAENLIQAFIMA  623 (624)
Q Consensus       548 ~~~~~~~~~~i~VP~~~vg~IIGkgG~~I~~I~~~sGa~I~i~~~~-~~~~-~r~v~I~Gt~e~v~~A~~lI~~~i~~  623 (624)
                        .....+.++.||.+++|+||||+|++|++|++.|||+|+|+++. +..+ ++.|+|+|++++|+.|+.+|+++|..
T Consensus        81 --~~~~~~~~i~vp~~~~g~iIGkgG~~I~~i~~~tga~I~i~~~~~~~~~~~~~v~I~G~~~~v~~A~~~I~~~i~~  156 (163)
T 3krm_A           81 --EEVKLETHIRVPASAAGRVIGKGGKTVNELQNLTAAEVVVPRDQTPDENDQVIVKIIGHFYASQMAQRKIRDILAQ  156 (163)
T ss_dssp             --CCCCEEEEEEEETTTHHHHHCGGGHHHHHHHHHHCCEEECCTTCCCCTTSEEEEEEEECHHHHHHHHHHHHHHHHH
T ss_pred             --cCCceEEEEEcChhheeeEEcCCChHHHHHHHHhCCeEEECCCCCCCCCCceEEEEEeCHHHHHHHHHHHHHHHHH
Confidence              00123779999999999999999999999999999999998764 2233 34899999999999999999999864

>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=99.91  E-value=6.5e-25  Score=207.02  Aligned_cols=159  Identities=28%  Similarity=0.424  Sum_probs=125.0

Q ss_pred             CCceEEEEEEecCcccceeccCCchHHHHHHHhcCCeEEeeCC---CCCCCceEEEEEccCCcccccccccccCCCCccc
Q 006943           33 NEESVIYRILCPDGVIGSVIGKSGKVINSIRQETRARVKVVDP---FPGAKDRVVTIYSHVKDKEDVEVDDEFNDKEPLC  109 (624)
Q Consensus        33 ~~~~~~~~ilvp~~~~g~vIGk~G~~I~~i~~etg~~I~v~~~---~~~~~er~i~I~G~~~~~~~~~~~~~~~~~~~~~  109 (624)
                      .++.++++|+||.+++|.||||+|++|++|+++|||+|.|++.   .+++.+|+|+|+|..+++                
T Consensus         2 l~~~~~~~i~vp~~~ig~iIGkgG~~Ik~i~~~tg~~I~i~~~~~~~~~~~er~v~I~G~~~~v----------------   65 (178)
T 2anr_A            2 LGSQYFLKVLIPSYAAGSIIGKGGQTIVQLQKETGATIKLSKSKDFYPGTTERVCLIQGTIEAL----------------   65 (178)
T ss_dssp             -CCCEEEEEEEEHHHHHHHHCGGGHHHHHHHHHHCCEEEECCTTCBCTTSSEEEEEEEECHHHH----------------
T ss_pred             CCCCEEEEEEEChhHeeeeECCCcHHHHHHHHHhCCeEEEecCCCCCCCCCCceEEEEeCHHHH----------------
Confidence            4667999999999999999999999999999999999999763   467899999999986653                


Q ss_pred             HHHHHHHHHHHHHHHhhhccCCC--------------cccCCCceeEEEEEeccceeEEEeCCchHHHHHHHhcCCeEEE
Q 006943          110 AAQDALLKVHAAIANAVANATDN--------------DKKRKEKEECQILVPSSQSANIIGKAGATIKRLRSKTRTSIKV  175 (624)
Q Consensus       110 ~a~~ai~~v~~~i~~~~~~~~~~--------------~~~~~~~~~~~llvp~~~~g~iIGk~G~~Ik~I~~~sga~I~i  175 (624)
                            .++.+.|.+.+....+.              ........+++|+||.+++|+||||+|++|++|+++|||+|+|
T Consensus        66 ------~~A~~~I~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~Vp~~~vg~iIGkgG~~Ik~i~~~tga~I~i  139 (178)
T 2anr_A           66 ------NAVHGFIAEKIREMPQNVAKTEPVSILQPQTTVNPDRANQVKIIVPNSTAGLIIGKGGATVKAIMEQSGAWVQL  139 (178)
T ss_dssp             ------HHHHHHHHHHHTCCCCC-----------------CGGGGEEEEEEEHHHHHHHHCGGGHHHHHHHHHSSCEEEE
T ss_pred             ------HHHHHHHHHHHhccCCccccCCcccccCCccCCCCCCceEEEEEEchhheeeeECCCcHHHHHHHHHHCCEEEE
Confidence                  22223333322221110              0012235789999999999999999999999999999999999


Q ss_pred             ccCCCCCCCCcccccCCceEEEecCHHHHHHHHHHHHHHHhhcC
Q 006943          176 TPKDASEPTHSCAMEFDNFVLISGESEAVKKALFAISAIMYKFS  219 (624)
Q Consensus       176 ~~~~~~~~~~~~~~~~~r~V~I~G~~~~V~~A~~~I~~~l~~~~  219 (624)
                      .+..      .++.++++.|+|+|++++|.+|+.+|.++|++.+
T Consensus       140 ~~~~------~~~~~~~~~v~I~G~~~~v~~A~~~I~~~i~e~p  177 (178)
T 2anr_A          140 SQKP------DGINLQNRVVTVSGEPEQNRKAVELIIQKIQEDP  177 (178)
T ss_dssp             CCCC----------CCEEEEEEESSHHHHHHHHHHHHHHHHSCC
T ss_pred             eCCC------CCCCCCceEEEEEcCHHHHHHHHHHHHHHHHhCC
Confidence            8643      2344678999999999999999999999997643

>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=99.91  E-value=9.3e-25  Score=202.32  Aligned_cols=157  Identities=29%  Similarity=0.542  Sum_probs=131.2

Q ss_pred             CCcEEEEEEecCCeeeEEEcCCCchHHHHHHhcCceEEEeCCCCCCCCCCCCcEEEEEeehHHHHHHHHHHHHHHhhccc
Q 006943          386 DDTVTIRLLVSSKVIGCIIGKSGSIINEIRKRTKADVRISKGDKPKCADANDELVEVVGEVGSVRDALVQIILRLRDDAL  465 (624)
Q Consensus       386 ~~~~~~~l~vp~~~~g~iIGk~G~~Ik~I~~~tga~I~i~~~~~p~~~~~~~~~v~I~G~~~~v~~A~~~I~~~l~e~~~  465 (624)
                      +.+++++|.||..++|.|||++|++|++|+++|||+|+|++..      ..++.|+|+|+.++|.+|+.+|.+.+.+...
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 NVTLTIRLLMHGKEVGSIIGKKGESVKKMREESGARINISEGN------CPERIITLAGPTNAIFKAFAMIIDKLEEDIS   75 (160)
T ss_dssp             CCEEEEEEEEEHHHHHHHHCGGGHHHHHHHHHHCSEEEEECCT------TTEEEEEEEEEHHHHHHHHHHHHHHHHHHHT
T ss_pred             CccEEEEEEEchhheeeeECCCcHHHHHHHHHHCCEEEEcCCC------CCceEEEEEeCHHHHHHHHHHHHHHHHhhcc
Confidence            4578899999999999999999999999999999999998642      4578999999999999999999988877532


Q ss_pred             cCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCcccc
Q 006943          466 KDRDGSRNPPVGADHIYSSGTGISMPPLLPSIPPVGPLGYDQRADSGSGIGMLSSSSLYGYGSLSMGDSPYGSMSSYSSK  545 (624)
Q Consensus       466 ~~~~~~~~p~~~~~~~~~~~~~~~~p~~~~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  545 (624)
                      .....                                 +                               .         
T Consensus        76 ~~~~~---------------------------------~-------------------------------~---------   82 (160)
T 2jzx_A           76 SSMTN---------------------------------S-------------------------------T---------   82 (160)
T ss_dssp             SCCCS---------------------------------S-------------------------------S---------
T ss_pred             ccCCC---------------------------------C-------------------------------c---------
Confidence            11000                                 0                               0         


Q ss_pred             cCCCCCCCcEEEEEeccccccceeccCCchHHHHHHHhCCEEEEeCCC-CCCCCeEEEEEcCHHHHHHHHHHHHHHHhh
Q 006943          546 LYGGLPPPLTLEVLVPANAVGKVIGKAGSNLANIRKISGATIEMSDSK-SSRGDRVALISGTPEQKRAAENLIQAFIMA  623 (624)
Q Consensus       546 ~~~~~~~~~~~~i~VP~~~vg~IIGkgG~~I~~I~~~sGa~I~i~~~~-~~~~~r~v~I~Gt~e~v~~A~~lI~~~i~~  623 (624)
                        .......+.++.||.+++|+||||+|++|++|++.|||+|+|++.. +...++.|+|+|++++++.|+.+|.+++..
T Consensus        83 --~~~~~~~~~~i~vp~~~~g~iIGkgG~~Ik~i~~~tga~I~i~~~~~~~~~~~~v~I~G~~~~v~~A~~~I~~~i~e  159 (160)
T 2jzx_A           83 --AASRPPVTLRLVVPASQCGSLIGKGGCKIKEIRESTGAQVQVAGDMLPNSTERAITIAGIPQSIIECVKQICVVMLE  159 (160)
T ss_dssp             --CCCCCSEEEEEEEEHHHHHHHHCGGGHHHHHHHHHHSSEECCCCCCSTTCCEEEEEEEECHHHHHHHHHHHHHHHHH
T ss_pred             --cCCCCCEEEEEEEChhheeeEECCCCHHHHHHHHHhCCeEEECCCCCCCCCceEEEEEcCHHHHHHHHHHHHHHHhc
Confidence              0000124899999999999999999999999999999999998642 446789999999999999999999999875

>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=99.91  E-value=2.3e-24  Score=200.63  Aligned_cols=159  Identities=21%  Similarity=0.400  Sum_probs=128.5

Q ss_pred             EEEEEEecCCeeeEEEcCCCchHHHHHHhcCceEEEeCCCCCCCCCCCCcEEEEEeehHHHHHHHHHHHHHHhhccccCC
Q 006943          389 VTIRLLVSSKVIGCIIGKSGSIINEIRKRTKADVRISKGDKPKCADANDELVEVVGEVGSVRDALVQIILRLRDDALKDR  468 (624)
Q Consensus       389 ~~~~l~vp~~~~g~iIGk~G~~Ik~I~~~tga~I~i~~~~~p~~~~~~~~~v~I~G~~~~v~~A~~~I~~~l~e~~~~~~  468 (624)
                      ++.+|.||.+++|.|||++|++||+|+++|||+|++.++..  .....+++|+|+|++++|.+|+.+|.+.+.+....  
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 TVQEIMIPAGKAGLVIGKGGETIKQLQERAGVKMILIQDGS--QNTNVDKPLRIIGDPYKVQQACEMVMDILRERDQG--   77 (164)
T ss_dssp             EEEEEEECTTCHHHHTCTTTHHHHHHHHTSCSEEEECCCTT--SSSSSCEEEEEEECHHHHHHHHHHHHHHTTCSSSC--
T ss_pred             eEEEEEechhheeEEECCChHHHHHHHHHhCCeEEEecCCC--CCCCCceEEEEEcCHHHHHHHHHHHHHHHHhccCC--
Confidence            57899999999999999999999999999999999986431  12356889999999999999999998877653110  


Q ss_pred             CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCcccccCC
Q 006943          469 DGSRNPPVGADHIYSSGTGISMPPLLPSIPPVGPLGYDQRADSGSGIGMLSSSSLYGYGSLSMGDSPYGSMSSYSSKLYG  548 (624)
Q Consensus       469 ~~~~~p~~~~~~~~~~~~~~~~p~~~~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  548 (624)
                        .+.+.                                                          ..|+.          
T Consensus        78 --~~~~~----------------------------------------------------------~~~~~----------   87 (164)
T 2jvz_A           78 --GFGDR----------------------------------------------------------NEYGS----------   87 (164)
T ss_dssp             --CCSSC----------------------------------------------------------SSCTT----------
T ss_pred             --CCCCc----------------------------------------------------------cccCC----------
Confidence              00000                                                          00000          


Q ss_pred             CCCCCcEEEEEeccccccceeccCCchHHHHHHHhCCEEEEeCCCCCCCCeEEEEEcCHHHHHHHHHHHHHHHhh
Q 006943          549 GLPPPLTLEVLVPANAVGKVIGKAGSNLANIRKISGATIEMSDSKSSRGDRVALISGTPEQKRAAENLIQAFIMA  623 (624)
Q Consensus       549 ~~~~~~~~~i~VP~~~vg~IIGkgG~~I~~I~~~sGa~I~i~~~~~~~~~r~v~I~Gt~e~v~~A~~lI~~~i~~  623 (624)
                        ....+.++.||.+++|+||||+|.+|++|++.|||+|+|++..+...++.|+|+|++++++.|+.+|+++|..
T Consensus        88 --~~~~~~~i~vp~~~~g~iIGk~G~~I~~i~~~tg~~I~i~~~~~~~~~~~v~I~G~~~~v~~A~~~I~~~i~~  160 (164)
T 2jvz_A           88 --RIGGGIDVPVPRHSVGVVIGRSGEMIKKIQNDAGVRIQFKQDDGTGPEKIAHIMGPPDRCEHAARIINDLLQS  160 (164)
T ss_dssp             --SCSSSBCCEEETTTHHHHHCSSSHHHHHHHHHTCCEEEECCCCTTSSEEEEEEESCHHHHHHHHHHHHHHHHH
T ss_pred             --CCCceEEEEEChhhccccCCCCcHhHHHHHHHHCCeEEEeCCCCCCCcEEEEEEcCHHHHHHHHHHHHHHHhh
Confidence              0012567899999999999999999999999999999999876666689999999999999999999998863

>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=99.91  E-value=2.5e-24  Score=200.07  Aligned_cols=156  Identities=24%  Similarity=0.339  Sum_probs=125.4

Q ss_pred             EEEEEEecCcccceeccCCchHHHHHHHhcCCeEEeeCC-CCCCCceEEEEEccCCcccccccccccCCCCcccHHHHHH
Q 006943           37 VIYRILCPDGVIGSVIGKSGKVINSIRQETRARVKVVDP-FPGAKDRVVTIYSHVKDKEDVEVDDEFNDKEPLCAAQDAL  115 (624)
Q Consensus        37 ~~~~ilvp~~~~g~vIGk~G~~I~~i~~etg~~I~v~~~-~~~~~er~i~I~G~~~~~~~~~~~~~~~~~~~~~~a~~ai  115 (624)
                      -+++|+||.+++|.||||+|++|++|+++|||+|.|++. .+++.+|+|+|+|+++++                  .+|.
T Consensus         3 ~~~~~~ip~~~~g~iIGk~G~~Ik~i~~~tg~~I~i~~~~~~~~~~r~v~I~G~~e~v------------------~~A~   64 (163)
T 3krm_A            3 EMVQVFIPAQAVGAIIGKKGQHIKQLSRFASASIKIAPPETPDSKVRMVIITGPPEAQ------------------FKAQ   64 (163)
T ss_dssp             EEEEEEEEGGGHHHHHCGGGHHHHHHHHHHTCEEEECCCSSTTCSEEEEEEEECHHHH------------------HHHH
T ss_pred             eEEEEEechhhcceeECCCcHHHHHHHHHHCCeEEEcCCCCCCCCceEEEEEcCHHHH------------------HHHH
Confidence            589999999999999999999999999999999999874 678899999999987652                  3455


Q ss_pred             HHHHHHHHHhhhccCCCcccCCCceeEEEEEeccceeEEEeCCchHHHHHHHhcCCeEEEccCCCCCCCCcccccCCceE
Q 006943          116 LKVHAAIANAVANATDNDKKRKEKEECQILVPSSQSANIIGKAGATIKRLRSKTRTSIKVTPKDASEPTHSCAMEFDNFV  195 (624)
Q Consensus       116 ~~v~~~i~~~~~~~~~~~~~~~~~~~~~llvp~~~~g~iIGk~G~~Ik~I~~~sga~I~i~~~~~~~~~~~~~~~~~r~V  195 (624)
                      ..+++.+.+..    ..........+++|+||.+++|+||||+|++|++|+++|||+|.|.....+.      ..+++.|
T Consensus        65 ~~I~~~~~e~~----~~~~~~~~~~~~~i~vp~~~~g~iIGkgG~~I~~i~~~tga~I~i~~~~~~~------~~~~~~v  134 (163)
T 3krm_A           65 GRIYGKLKEEN----FFGPKEEVKLETHIRVPASAAGRVIGKGGKTVNELQNLTAAEVVVPRDQTPD------ENDQVIV  134 (163)
T ss_dssp             HHHHHHHHHTT----SSCSSCCCCEEEEEEEETTTHHHHHCGGGHHHHHHHHHHCCEEECCTTCCCC------TTSEEEE
T ss_pred             HHHHHHHhccc----ccccccCCceEEEEEcChhheeeEEcCCChHHHHHHHHhCCeEEECCCCCCC------CCCceEE
Confidence            55555443321    1111223457889999999999999999999999999999999997643211      1334589


Q ss_pred             EEecCHHHHHHHHHHHHHHHhhcCC
Q 006943          196 LISGESEAVKKALFAISAIMYKFSP  220 (624)
Q Consensus       196 ~I~G~~~~V~~A~~~I~~~l~~~~~  220 (624)
                      +|+|++++|.+|+.+|.+++++...
T Consensus       135 ~I~G~~~~v~~A~~~I~~~i~~~~~  159 (163)
T 3krm_A          135 KIIGHFYASQMAQRKIRDILAQVKQ  159 (163)
T ss_dssp             EEEECHHHHHHHHHHHHHHHHHHTC
T ss_pred             EEEeCHHHHHHHHHHHHHHHHHHHH
Confidence            9999999999999999999987554

>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=99.90  E-value=4.5e-24  Score=197.74  Aligned_cols=156  Identities=21%  Similarity=0.417  Sum_probs=126.2

Q ss_pred             ceEEEEEEecCcccceeccCCchHHHHHHHhcCCeEEeeCCCCCCCceEEEEEccCCcccccccccccCCCCcccHHHHH
Q 006943           35 ESVIYRILCPDGVIGSVIGKSGKVINSIRQETRARVKVVDPFPGAKDRVVTIYSHVKDKEDVEVDDEFNDKEPLCAAQDA  114 (624)
Q Consensus        35 ~~~~~~ilvp~~~~g~vIGk~G~~I~~i~~etg~~I~v~~~~~~~~er~i~I~G~~~~~~~~~~~~~~~~~~~~~~a~~a  114 (624)
                      ..++++|+||.+.+|.||||+|++|++|+++|||+|.|++.  ++.+|+|+|+|+.+++                  .+|
T Consensus         3 ~~~~~~~~vp~~~~g~iIGkgG~~Ik~i~~~tg~~I~i~~~--~~~~r~v~I~G~~~~v------------------~~A   62 (160)
T 2jzx_A            3 VTLTIRLLMHGKEVGSIIGKKGESVKKMREESGARINISEG--NCPERIITLAGPTNAI------------------FKA   62 (160)
T ss_dssp             CEEEEEEEEEHHHHHHHHCGGGHHHHHHHHHHCSEEEEECC--TTTEEEEEEEEEHHHH------------------HHH
T ss_pred             ccEEEEEEEchhheeeeECCCcHHHHHHHHHHCCEEEEcCC--CCCceEEEEEeCHHHH------------------HHH
Confidence            46899999999999999999999999999999999999885  6789999999996653                  234


Q ss_pred             HHHHHHHHHHhhhcc-CCCcccCCCceeEEEEEeccceeEEEeCCchHHHHHHHhcCCeEEEccCCCCCCCCcccccCCc
Q 006943          115 LLKVHAAIANAVANA-TDNDKKRKEKEECQILVPSSQSANIIGKAGATIKRLRSKTRTSIKVTPKDASEPTHSCAMEFDN  193 (624)
Q Consensus       115 i~~v~~~i~~~~~~~-~~~~~~~~~~~~~~llvp~~~~g~iIGk~G~~Ik~I~~~sga~I~i~~~~~~~~~~~~~~~~~r  193 (624)
                      ...+.+.+.+.+... ..+.......++++|+||.+++|+||||+|++|++|+++|||+|+|.+..       ++.++++
T Consensus        63 ~~~I~~~i~e~~~~~~~~~~~~~~~~~~~~i~vp~~~~g~iIGkgG~~Ik~i~~~tga~I~i~~~~-------~~~~~~~  135 (160)
T 2jzx_A           63 FAMIIDKLEEDISSSMTNSTAASRPPVTLRLVVPASQCGSLIGKGGCKIKEIRESTGAQVQVAGDM-------LPNSTER  135 (160)
T ss_dssp             HHHHHHHHHHHHTSCCCSSSCCCCCSEEEEEEEEHHHHHHHHCGGGHHHHHHHHHHSSEECCCCCC-------STTCCEE
T ss_pred             HHHHHHHHHhhccccCCCCccCCCCCEEEEEEEChhheeeEECCCCHHHHHHHHHhCCeEEECCCC-------CCCCCce
Confidence            454554444433221 11111123358999999999999999999999999999999999997532       2346789


Q ss_pred             eEEEecCHHHHHHHHHHHHHHHhh
Q 006943          194 FVLISGESEAVKKALFAISAIMYK  217 (624)
Q Consensus       194 ~V~I~G~~~~V~~A~~~I~~~l~~  217 (624)
                      .|+|+|++++|.+|+.+|.+++.+
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            999999999999999999998865

>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=99.90  E-value=6.8e-24  Score=199.22  Aligned_cols=170  Identities=25%  Similarity=0.406  Sum_probs=126.3

Q ss_pred             cEEEEEEecCCeeeEEEcCCCchHHHHHHhcCceEEEeCCCCCCCCCCCCcEEEEEeehHHHHHHHHHHHHHHhhccccC
Q 006943          388 TVTIRLLVSSKVIGCIIGKSGSIINEIRKRTKADVRISKGDKPKCADANDELVEVVGEVGSVRDALVQIILRLRDDALKD  467 (624)
Q Consensus       388 ~~~~~l~vp~~~~g~iIGk~G~~Ik~I~~~tga~I~i~~~~~p~~~~~~~~~v~I~G~~~~v~~A~~~I~~~l~e~~~~~  467 (624)
                      ..+++|.||.+++|.||||+|++|++|+++|||+|+|.+.. +   ...+++|+|+|++++|.+|+.+|.+.+.+.....
T Consensus         2 ~~~~~~~vp~~~vg~iIGkgG~~Ik~i~~~tg~~I~i~~~~-~---~~~~r~v~I~G~~~~v~~A~~~I~~~~~~~~~~~   77 (174)
T 1j4w_A            2 SHMIDVPIPRFAVGIVIGRNGEMIKKIQNDAGVRIQFKPDD-G---TTPERIAQITGPPDRAQHAAEIITDLLRSVQAGN   77 (174)
T ss_dssp             CEEEEEEEEHHHHHHHHCGGGHHHHHHHHHHCCEEEEECCT-T---SCSEEEEEEEECHHHHHHHHHHHHHHHHHHC---
T ss_pred             CeEEEEEEChhheeeeecCCchHHHHHHHHhCCEEEEecCC-C---CCCccEEEEEeCHHHHHHHHHHHHHHHHhcccCC
Confidence            46789999999999999999999999999999999998632 2   3568999999999999999999988887642100


Q ss_pred             CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCcccccC
Q 006943          468 RDGSRNPPVGADHIYSSGTGISMPPLLPSIPPVGPLGYDQRADSGSGIGMLSSSSLYGYGSLSMGDSPYGSMSSYSSKLY  547 (624)
Q Consensus       468 ~~~~~~p~~~~~~~~~~~~~~~~p~~~~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  547 (624)
                          +.++              .|.           +        .+++..       ...|..                
T Consensus        78 ----~~~~--------------~p~-----------~--------~~~~~~-------~~~~~~----------------   97 (174)
T 1j4w_A           78 ----PGGP--------------GPG-----------G--------RGRGRG-------QGNWNM----------------   97 (174)
T ss_dssp             --------------------------------------------------------------------------------
T ss_pred             ----CCCC--------------CCC-----------C--------CCCCCC-------CCcccc----------------
Confidence                0000              000           0        000000       000000                


Q ss_pred             CCCCCCcEEEEEeccccccceeccCCchHHHHHHHhCCEEEEeCCCC---CCCCeEEEEEcCHHHHHHHHHHHHHHH
Q 006943          548 GGLPPPLTLEVLVPANAVGKVIGKAGSNLANIRKISGATIEMSDSKS---SRGDRVALISGTPEQKRAAENLIQAFI  621 (624)
Q Consensus       548 ~~~~~~~~~~i~VP~~~vg~IIGkgG~~I~~I~~~sGa~I~i~~~~~---~~~~r~v~I~Gt~e~v~~A~~lI~~~i  621 (624)
                      +......+.++.||.+++|+||||+|++|++|++.|||+|+|++..+   +..++.|+|+|++++++.|+.||+++|
T Consensus        98 ~~~~~~~~~~i~vp~~~~g~iIGkgG~~Ik~I~~~tga~I~i~~~~~~~~~~~~~~v~I~G~~~~v~~A~~~I~~~i  174 (174)
T 1j4w_A           98 GPPGGLQEFNFIVPTGKTGLIIGKGGETIKSISQQSGARIELQRNPPPNADPNMKLFTIRGTPQQIDYARQLIEEKI  174 (174)
T ss_dssp             ------CEEEEEEETTTHHHHHCGGGHHHHHHHHHHCCEEEEECCCTTTSCTTEEEEEEECCHHHHHHHHHHHHHHC
T ss_pred             CCCCCcEEEEEEEChHHcCeeECCCchHHHHHHHHHCCEEEECCCCCCCCCCCceEEEEECCHHHHHHHHHHHHHhC
Confidence            00011348899999999999999999999999999999999997632   356799999999999999999999875

>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=99.90  E-value=5.3e-24  Score=200.80  Aligned_cols=171  Identities=26%  Similarity=0.403  Sum_probs=130.7

Q ss_pred             CCcEEEEEEecCCeeeEEEcCCCchHHHHHHhcCceEEEeCCCCCCCCCCCCcEEEEEeehHHHHHHHHHHHHHHhhccc
Q 006943          386 DDTVTIRLLVSSKVIGCIIGKSGSIINEIRKRTKADVRISKGDKPKCADANDELVEVVGEVGSVRDALVQIILRLRDDAL  465 (624)
Q Consensus       386 ~~~~~~~l~vp~~~~g~iIGk~G~~Ik~I~~~tga~I~i~~~~~p~~~~~~~~~v~I~G~~~~v~~A~~~I~~~l~e~~~  465 (624)
                      ...++++|.||.+++|.||||+|++|++|+++|||+|+|++.... .....+|+|+|+|++++|.+|+.+|.+.+.+...
T Consensus         3 ~~~~~~~i~vp~~~ig~iIGkgG~~Ik~i~~~tg~~I~i~~~~~~-~~~~~er~v~I~G~~~~v~~A~~~I~~~~~~~~~   81 (178)
T 2anr_A            3 GSQYFLKVLIPSYAAGSIIGKGGQTIVQLQKETGATIKLSKSKDF-YPGTTERVCLIQGTIEALNAVHGFIAEKIREMPQ   81 (178)
T ss_dssp             CCCEEEEEEEEHHHHHHHHCGGGHHHHHHHHHHCCEEEECCTTCB-CTTSSEEEEEEEECHHHHHHHHHHHHHHHTCCCC
T ss_pred             CCCEEEEEEEChhHeeeeECCCcHHHHHHHHHhCCeEEEecCCCC-CCCCCCceEEEEeCHHHHHHHHHHHHHHHhccCC
Confidence            456899999999999999999999999999999999999864321 1135689999999999999999999888765421


Q ss_pred             cCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCcccc
Q 006943          466 KDRDGSRNPPVGADHIYSSGTGISMPPLLPSIPPVGPLGYDQRADSGSGIGMLSSSSLYGYGSLSMGDSPYGSMSSYSSK  545 (624)
Q Consensus       466 ~~~~~~~~p~~~~~~~~~~~~~~~~p~~~~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  545 (624)
                      .....        + .      ..   ..+      +                        .        .         
T Consensus        82 ~~~~~--------~-~------~~---~~~------~------------------------~--------~---------   96 (178)
T 2anr_A           82 NVAKT--------E-P------VS---ILQ------P------------------------Q--------T---------   96 (178)
T ss_dssp             C-------------------------------------------------------------------------------
T ss_pred             ccccC--------C-c------cc---ccC------C------------------------c--------c---------
Confidence            10000        0 0      00   000      0                        0        0         


Q ss_pred             cCCCCCCCcEEEEEeccccccceeccCCchHHHHHHHhCCEEEEeCCCC--CCCCeEEEEEcCHHHHHHHHHHHHHHHhh
Q 006943          546 LYGGLPPPLTLEVLVPANAVGKVIGKAGSNLANIRKISGATIEMSDSKS--SRGDRVALISGTPEQKRAAENLIQAFIMA  623 (624)
Q Consensus       546 ~~~~~~~~~~~~i~VP~~~vg~IIGkgG~~I~~I~~~sGa~I~i~~~~~--~~~~r~v~I~Gt~e~v~~A~~lI~~~i~~  623 (624)
                       ........+.+|.||.+++|+||||+|++|++|++.|||+|+|++...  ...++.|+|+|++++|+.|+.+|.++|..
T Consensus        97 -~~~~~~~~~~~i~Vp~~~vg~iIGkgG~~Ik~i~~~tga~I~i~~~~~~~~~~~~~v~I~G~~~~v~~A~~~I~~~i~e  175 (178)
T 2anr_A           97 -TVNPDRANQVKIIVPNSTAGLIIGKGGATVKAIMEQSGAWVQLSQKPDGINLQNRVVTVSGEPEQNRKAVELIIQKIQE  175 (178)
T ss_dssp             ----CGGGGEEEEEEEHHHHHHHHCGGGHHHHHHHHHSSCEEEECCCC----CCEEEEEEESSHHHHHHHHHHHHHHHHS
T ss_pred             -CCCCCCceEEEEEEchhheeeeECCCcHHHHHHHHHHCCEEEEeCCCCCCCCCceEEEEEcCHHHHHHHHHHHHHHHHh
Confidence             000011358899999999999999999999999999999999997642  34679999999999999999999999864

>3n89_A Defective in GERM LINE development protein 3, ISO; KH domains, RNA binding, cell cycle; 2.79A {Caenorhabditis elegans}

Probab=99.90  E-value=6.2e-24  Score=216.96  Aligned_cols=227  Identities=14%  Similarity=0.167  Sum_probs=159.5

Q ss_pred             CCCceeEEEEEeccceeEEEeCCc--hHHHHHHHhcCCeEEEccCCCCCCCCcccccCCceEEEecCHHHHHHHHHHHHH
Q 006943          136 RKEKEECQILVPSSQSANIIGKAG--ATIKRLRSKTRTSIKVTPKDASEPTHSCAMEFDNFVLISGESEAVKKALFAISA  213 (624)
Q Consensus       136 ~~~~~~~~llvp~~~~g~iIGk~G--~~Ik~I~~~sga~I~i~~~~~~~~~~~~~~~~~r~V~I~G~~~~V~~A~~~I~~  213 (624)
                      ..+.+|+.+.||..+|++||||+|  ++|++|+++|||+|+|+..+...   ..+......|+|+|.+++|++|+.+|.+
T Consensus        26 ~~~~VTl~v~Ip~~~Hs~IIGkgG~~sNIkkImeEtgv~I~fPD~~~~~---~~~~~ks~~VtItG~~enVE~AR~~I~~  102 (376)
T 3n89_A           26 NPTRVTLNMEFESQYYSLMTSDNGDHENVASIMAETNTLIQLPDRSVGG---TTPDPFAQQVTITGYFGDVDRARMLMRR  102 (376)
T ss_dssp             CTTEEEEEEECCGGGHHHHHSCCSSSCSHHHHHHHHTCEEECCCCCCCS---SSCCTTTTEEEEEEEHHHHHHHHHHHHH
T ss_pred             cCCEEEEEEEEchhhhhhhccCCChHHHHHHHHHHhCCeEECCCCcccc---cCCcCCCCeEEEEcCHHHHHHHHHHHHh
Confidence            467899999999999999999999  99999999999999997644100   1122455789999999999999998877


Q ss_pred             HHhhcCCCCCCCCCCccCCCCCCccCCCCCCCCCCCCCCCCCCCCCCCCCCCCccCCCCCCCCCCCCCCCCCCCCCCCCC
Q 006943          214 IMYKFSPREDIPLETTVREAPPSIIIPSDVPIYPPGGLYPNADPILPSRSVPSILGAARVPDLQGYADTGNTWPVYSTGL  293 (624)
Q Consensus       214 ~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~~~~~~~g~~~~p~~~~~~~~~~~~~~~~~~~  293 (624)
                      ++                                                                              
T Consensus       103 l~------------------------------------------------------------------------------  104 (376)
T 3n89_A          103 NC------------------------------------------------------------------------------  104 (376)
T ss_dssp             SC------------------------------------------------------------------------------
T ss_pred             cC------------------------------------------------------------------------------
Confidence            43                                                                              


Q ss_pred             ccccCCCCCCCCccEEEEEEecCCccceeeccCcchHHHHHhHhCCeEEEcCCCC--CCCceEEEEeecC-CchhHHHHH
Q 006943          294 SLVSGLVGASQSEELVIRVLCPFNKIGRVIGKGGGTIKSIRQASGAQIDVDDTKD--NRDECVITVTAIE-SPDDIKSMA  370 (624)
Q Consensus       294 p~~~~~~~~~~~~~~~~~i~vp~~~vg~IIGk~G~~Ik~I~~~tga~I~v~~~~~--~~~er~i~I~G~~-~~~~a~~~~  370 (624)
                                   .+++.+.+|...++.  ..-+..|.+ ++.++++|.|+....  +.....|+|+|++ ++++++.++
T Consensus       105 -------------Pl~i~~elp~~~i~~--~~l~~~I~q-q~~y~V~I~Fp~~~~~~~~~sd~V~IrG~~~nv~~akeA~  168 (376)
T 3n89_A          105 -------------HFTVFMALSKMKMPL--HELQAHVRQ-NPIQNVEMSFVDAPEKNGIVTTYLRITAREKNQHELIEAA  168 (376)
T ss_dssp             -------------EEEEEEECTTCSSCH--HHHHHHHHH-CCCTTCEEEEEEEC-----CEEEEEEEEEGGGHHHHHHHH
T ss_pred             -------------CceEEEEccccccCc--chhhhhhcc-ceeCceEEEeCCcccccCCCCCEEEEEcChhhHHHHHHHH
Confidence                         235556666543332  111234544 567899999964322  1125679999963 344444333


Q ss_pred             HHHHHHHhhccCCCCCCcEEEEEEecCCeeeEEEcCCC--chHHHHHHhcCceEEEeCCCCCCCCCCCCcEEEEEeehHH
Q 006943          371 VEAVLLLQTKINDEDDDTVTIRLLVSSKVIGCIIGKSG--SIINEIRKRTKADVRISKGDKPKCADANDELVEVVGEVGS  448 (624)
Q Consensus       371 ~~~i~~~~~~~~~~~~~~~~~~l~vp~~~~g~iIGk~G--~~Ik~I~~~tga~I~i~~~~~p~~~~~~~~~v~I~G~~~~  448 (624)
                      ...+..+.+. .......+++.|.|+..+|..|||++|  ..|++|+++|||+|.|++.+.+.........|+|+|..++
T Consensus       169 ~~Ll~~l~~~-e~~~~~~~s~~v~V~~~~H~~IIGk~G~n~~IkkIr~eTGv~I~FP~~~d~~d~~~~~~~ItItGs~e~  247 (376)
T 3n89_A          169 KRLNEILFRE-SPAPENNFTLHFTLSTYYVDQVLGSSSTAQLMPVIERETTTIISYPCYNNRNETRGNIYEIKVVGNIDN  247 (376)
T ss_dssp             HHHHHHHCC---CCCSSCEEEEEEEEGGGHHHHTCCTTSCCHHHHHHHHHTCEEECC---------CCEEEEEEESCHHH
T ss_pred             HHHHHHHHhh-hcccccceEEEEEeCHHHHHHhhcCCCcchHHHHHHHhhCCEEECCCCCCcccccCCceEEEEEeCHHH
Confidence            3333333322 122345789999999999999999999  5679999999999999865443211133567999999999


Q ss_pred             HHHHHHHHHHHH
Q 006943          449 VRDALVQIILRL  460 (624)
Q Consensus       449 v~~A~~~I~~~l  460 (624)
                      |.+|..+|.+.|
T Consensus       248 V~~Ark~I~~lL  259 (376)
T 3n89_A          248 VLKARRYIMDLL  259 (376)
T ss_dssp             HHHHHHHHHHTS
T ss_pred             HHHHHHHHHhhC
Confidence            999999998877

>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=99.89  E-value=2.3e-23  Score=195.54  Aligned_cols=160  Identities=19%  Similarity=0.290  Sum_probs=120.5

Q ss_pred             eEEEEEEecCcccceeccCCchHHHHHHHhcCCeEEeeCCCCCCCceEEEEEccCCcccccccccccCCCCcccHHHHHH
Q 006943           36 SVIYRILCPDGVIGSVIGKSGKVINSIRQETRARVKVVDPFPGAKDRVVTIYSHVKDKEDVEVDDEFNDKEPLCAAQDAL  115 (624)
Q Consensus        36 ~~~~~ilvp~~~~g~vIGk~G~~I~~i~~etg~~I~v~~~~~~~~er~i~I~G~~~~~~~~~~~~~~~~~~~~~~a~~ai  115 (624)
                      ..+++|+||.+++|.||||+|++|++|+++|||+|.|.+..++..+|+|+|+|+.+++.               .|.+.|
T Consensus         2 ~~~~~~~vp~~~vg~iIGkgG~~Ik~i~~~tg~~I~i~~~~~~~~~r~v~I~G~~~~v~---------------~A~~~I   66 (174)
T 1j4w_A            2 SHMIDVPIPRFAVGIVIGRNGEMIKKIQNDAGVRIQFKPDDGTTPERIAQITGPPDRAQ---------------HAAEII   66 (174)
T ss_dssp             CEEEEEEEEHHHHHHHHCGGGHHHHHHHHHHCCEEEEECCTTSCSEEEEEEEECHHHHH---------------HHHHHH
T ss_pred             CeEEEEEEChhheeeeecCCchHHHHHHHHhCCEEEEecCCCCCCccEEEEEeCHHHHH---------------HHHHHH
Confidence            46899999999999999999999999999999999998766678899999999977633               233333


Q ss_pred             HHHHHHHHHhhhcc----------C--CCc-ccCCCceeEEEEEeccceeEEEeCCchHHHHHHHhcCCeEEEccCCCCC
Q 006943          116 LKVHAAIANAVANA----------T--DND-KKRKEKEECQILVPSSQSANIIGKAGATIKRLRSKTRTSIKVTPKDASE  182 (624)
Q Consensus       116 ~~v~~~i~~~~~~~----------~--~~~-~~~~~~~~~~llvp~~~~g~iIGk~G~~Ik~I~~~sga~I~i~~~~~~~  182 (624)
                      ..++..........          .  +.. ..+...++++|+||.+++|+||||+|++|++|+++|||+|+|....   
T Consensus        67 ~~~~~~~~~~~~~~~~p~~~~~~~~~~~~~~~~~~~~~~~~i~vp~~~~g~iIGkgG~~Ik~I~~~tga~I~i~~~~---  143 (174)
T 1j4w_A           67 TDLLRSVQAGNPGGPGPGGRGRGRGQGNWNMGPPGGLQEFNFIVPTGKTGLIIGKGGETIKSISQQSGARIELQRNP---  143 (174)
T ss_dssp             HHHHHHHC-----------------------------CEEEEEEETTTHHHHHCGGGHHHHHHHHHHCCEEEEECCC---
T ss_pred             HHHHHhcccCCCCCCCCCCCCCCCCCCccccCCCCCcEEEEEEEChHHcCeeECCCchHHHHHHHHHCCEEEECCCC---
Confidence            33332211000000          0  000 0112357889999999999999999999999999999999998642   


Q ss_pred             CCCcccccCCceEEEecCHHHHHHHHHHHHHHH
Q 006943          183 PTHSCAMEFDNFVLISGESEAVKKALFAISAIM  215 (624)
Q Consensus       183 ~~~~~~~~~~r~V~I~G~~~~V~~A~~~I~~~l  215 (624)
                        +.+..++++.|+|+|++++|.+|+.+|.++|
T Consensus       144 --~~~~~~~~~~v~I~G~~~~v~~A~~~I~~~i  174 (174)
T 1j4w_A          144 --PPNADPNMKLFTIRGTPQQIDYARQLIEEKI  174 (174)
T ss_dssp             --TTTSCTTEEEEEEECCHHHHHHHHHHHHHHC
T ss_pred             --CCCCCCCceEEEEECCHHHHHHHHHHHHHhC
Confidence              1233467899999999999999999998764

>3n89_A Defective in GERM LINE development protein 3, ISO; KH domains, RNA binding, cell cycle; 2.79A {Caenorhabditis elegans}

Probab=99.89  E-value=4.1e-23  Score=210.94  Aligned_cols=220  Identities=9%  Similarity=0.078  Sum_probs=151.6

Q ss_pred             CCccEEEEEEecCCccceeeccCc--chHHHHHhHhCCeEEEcCCC--C---CCCceEEEEeec-CCchhHHHHHHHHHH
Q 006943          304 QSEELVIRVLCPFNKIGRVIGKGG--GTIKSIRQASGAQIDVDDTK--D---NRDECVITVTAI-ESPDDIKSMAVEAVL  375 (624)
Q Consensus       304 ~~~~~~~~i~vp~~~vg~IIGk~G--~~Ik~I~~~tga~I~v~~~~--~---~~~er~i~I~G~-~~~~~a~~~~~~~i~  375 (624)
                      ..+.+++.+.||..+|+.||||+|  ++|++|+++|||+|+|++..  .   ......|+|+|. ++++.|+.    .| 
T Consensus        26 ~~~~VTl~v~Ip~~~Hs~IIGkgG~~sNIkkImeEtgv~I~fPD~~~~~~~~~~ks~~VtItG~~enVE~AR~----~I-  100 (376)
T 3n89_A           26 NPTRVTLNMEFESQYYSLMTSDNGDHENVASIMAETNTLIQLPDRSVGGTTPDPFAQQVTITGYFGDVDRARM----LM-  100 (376)
T ss_dssp             CTTEEEEEEECCGGGHHHHHSCCSSSCSHHHHHHHHTCEEECCCCCCCSSSCCTTTTEEEEEEEHHHHHHHHH----HH-
T ss_pred             cCCEEEEEEEEchhhhhhhccCCChHHHHHHHHHHhCCeEECCCCcccccCCcCCCCeEEEEcCHHHHHHHHH----HH-
Confidence            457899999999999999999999  99999999999999998765  1   123457999996 44444433    22 


Q ss_pred             HHhhccCCCCCCcEEEEEEecCCeeeEEEcCCCchHHHHHHhcCceEEEeCCCCCCCCCCCCcEEEEEeehHHHHHHHHH
Q 006943          376 LLQTKINDEDDDTVTIRLLVSSKVIGCIIGKSGSIINEIRKRTKADVRISKGDKPKCADANDELVEVVGEVGSVRDALVQ  455 (624)
Q Consensus       376 ~~~~~~~~~~~~~~~~~l~vp~~~~g~iIGk~G~~Ik~I~~~tga~I~i~~~~~p~~~~~~~~~v~I~G~~~~v~~A~~~  455 (624)
                        ...      .++++.+.+|...+..  ...+..|.+ ++.++++|.|+.....  .......|+|+|...+|.+|...
T Consensus       101 --~~l------~Pl~i~~elp~~~i~~--~~l~~~I~q-q~~y~V~I~Fp~~~~~--~~~~sd~V~IrG~~~nv~~akeA  167 (376)
T 3n89_A          101 --RRN------CHFTVFMALSKMKMPL--HELQAHVRQ-NPIQNVEMSFVDAPEK--NGIVTTYLRITAREKNQHELIEA  167 (376)
T ss_dssp             --HHS------CEEEEEEECTTCSSCH--HHHHHHHHH-CCCTTCEEEEEEEC-------CEEEEEEEEEGGGHHHHHHH
T ss_pred             --Hhc------CCceEEEEccccccCc--chhhhhhcc-ceeCceEEEeCCcccc--cCCCCCEEEEEcChhhHHHHHHH
Confidence              221      2567778887643322  111234544 5689999999654211  01124568999999777665554


Q ss_pred             HHHHHhhccccCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
Q 006943          456 IILRLRDDALKDRDGSRNPPVGADHIYSSGTGISMPPLLPSIPPVGPLGYDQRADSGSGIGMLSSSSLYGYGSLSMGDSP  535 (624)
Q Consensus       456 I~~~l~e~~~~~~~~~~~p~~~~~~~~~~~~~~~~p~~~~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~~~~~~~~  535 (624)
                      +...|......+. .                                                                 
T Consensus       168 ~~~Ll~~l~~~e~-~-----------------------------------------------------------------  181 (376)
T 3n89_A          168 AKRLNEILFRESP-A-----------------------------------------------------------------  181 (376)
T ss_dssp             HHHHHHHHCC--C-C-----------------------------------------------------------------
T ss_pred             HHHHHHHHHhhhc-c-----------------------------------------------------------------
Confidence            4433332111100 0                                                                 


Q ss_pred             CCCCCCcccccCCCCCCCcEEEEEeccccccceeccCC--chHHHHHHHhCCEEEEeCCCCC----CCCeEEEEEcCHHH
Q 006943          536 YGSMSSYSSKLYGGLPPPLTLEVLVPANAVGKVIGKAG--SNLANIRKISGATIEMSDSKSS----RGDRVALISGTPEQ  609 (624)
Q Consensus       536 ~~~~~~~~~~~~~~~~~~~~~~i~VP~~~vg~IIGkgG--~~I~~I~~~sGa~I~i~~~~~~----~~~r~v~I~Gt~e~  609 (624)
                                    ....++.+|.|+.+++..|||++|  ..|++|+++|||+|.+++..+.    .+...|+|+|++++
T Consensus       182 --------------~~~~~s~~v~V~~~~H~~IIGk~G~n~~IkkIr~eTGv~I~FP~~~d~~d~~~~~~~ItItGs~e~  247 (376)
T 3n89_A          182 --------------PENNFTLHFTLSTYYVDQVLGSSSTAQLMPVIERETTTIISYPCYNNRNETRGNIYEIKVVGNIDN  247 (376)
T ss_dssp             --------------CSSCEEEEEEEEGGGHHHHTCCTTSCCHHHHHHHHHTCEEECC---------CCEEEEEEESCHHH
T ss_pred             --------------cccceEEEEEeCHHHHHHhhcCCCcchHHHHHHHhhCCEEECCCCCCcccccCCceEEEEEeCHHH
Confidence                          011248999999999999999999  4569999999999999976431    23468999999999


Q ss_pred             HHHHHHHHHHHH
Q 006943          610 KRAAENLIQAFI  621 (624)
Q Consensus       610 v~~A~~lI~~~i  621 (624)
                      |..|+.+|+++|
T Consensus       248 V~~Ark~I~~lL  259 (376)
T 3n89_A          248 VLKARRYIMDLL  259 (376)
T ss_dssp             HHHHHHHHHHTS
T ss_pred             HHHHHHHHHhhC
Confidence            999999999875

>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=99.88  E-value=1.1e-22  Score=189.23  Aligned_cols=152  Identities=18%  Similarity=0.310  Sum_probs=119.6

Q ss_pred             EEEEEEecCcccceeccCCchHHHHHHHhcCCeEEeeCC--CCCCCceEEEEEccCCcccccccccccCCCCcccHHHHH
Q 006943           37 VIYRILCPDGVIGSVIGKSGKVINSIRQETRARVKVVDP--FPGAKDRVVTIYSHVKDKEDVEVDDEFNDKEPLCAAQDA  114 (624)
Q Consensus        37 ~~~~ilvp~~~~g~vIGk~G~~I~~i~~etg~~I~v~~~--~~~~~er~i~I~G~~~~~~~~~~~~~~~~~~~~~~a~~a  114 (624)
                      ++++|+||.+++|.||||+|++|++|+++|||+|.|.+.  .++..+|+|+|+|+.+++.                  .|
T Consensus         2 ~~~~~~Vp~~~~g~iIGk~G~~Ik~i~~~tg~~I~i~~~~~~~~~~~r~v~I~G~~~~v~------------------~A   63 (164)
T 2jvz_A            2 TVQEIMIPAGKAGLVIGKGGETIKQLQERAGVKMILIQDGSQNTNVDKPLRIIGDPYKVQ------------------QA   63 (164)
T ss_dssp             EEEEEEECTTCHHHHTCTTTHHHHHHHHTSCSEEEECCCTTSSSSSCEEEEEEECHHHHH------------------HH
T ss_pred             eEEEEEechhheeEEECCChHHHHHHHHHhCCeEEEecCCCCCCCCceEEEEEcCHHHHH------------------HH
Confidence            688999999999999999999999999999999999753  3567899999999866532                  23


Q ss_pred             HHHHHHHHHHhhhccCCCc------ccCCCceeEEEEEeccceeEEEeCCchHHHHHHHhcCCeEEEccCCCCCCCCccc
Q 006943          115 LLKVHAAIANAVANATDND------KKRKEKEECQILVPSSQSANIIGKAGATIKRLRSKTRTSIKVTPKDASEPTHSCA  188 (624)
Q Consensus       115 i~~v~~~i~~~~~~~~~~~------~~~~~~~~~~llvp~~~~g~iIGk~G~~Ik~I~~~sga~I~i~~~~~~~~~~~~~  188 (624)
                      +..+.+    .+.......      ......++++|+||.+++|+||||+|++|++|+++|||+|.|.+.+        +
T Consensus        64 ~~~I~~----ii~e~~~~~~~~~~~~~~~~~~~~~i~vp~~~~g~iIGk~G~~I~~i~~~tg~~I~i~~~~--------~  131 (164)
T 2jvz_A           64 CEMVMD----ILRERDQGGFGDRNEYGSRIGGGIDVPVPRHSVGVVIGRSGEMIKKIQNDAGVRIQFKQDD--------G  131 (164)
T ss_dssp             HHHHHH----HTTCSSSCCCSSCSSCTTSCSSSBCCEEETTTHHHHHCSSSHHHHHHHHHTCCEEEECCCC--------T
T ss_pred             HHHHHH----HHHhccCCCCCCccccCCCCCceEEEEEChhhccccCCCCcHhHHHHHHHHCCeEEEeCCC--------C
Confidence            333333    232211000      0111135688999999999999999999999999999999998643        1


Q ss_pred             ccCCceEEEecCHHHHHHHHHHHHHHHhhc
Q 006943          189 MEFDNFVLISGESEAVKKALFAISAIMYKF  218 (624)
Q Consensus       189 ~~~~r~V~I~G~~~~V~~A~~~I~~~l~~~  218 (624)
                      .+.++.|+|+|++++|.+|+.+|.+++++.
T Consensus       132 ~~~~~~v~I~G~~~~v~~A~~~I~~~i~~~  161 (164)
T 2jvz_A          132 TGPEKIAHIMGPPDRCEHAARIINDLLQSL  161 (164)
T ss_dssp             TSSEEEEEEESCHHHHHHHHHHHHHHHHHH
T ss_pred             CCCcEEEEEEcCHHHHHHHHHHHHHHHhhh
Confidence            246899999999999999999999998753

>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=99.76  E-value=1.4e-18  Score=156.51  Aligned_cols=134  Identities=21%  Similarity=0.253  Sum_probs=105.6

Q ss_pred             cEEEEEEecCCeeeEEEcCCCchHHHHHHhcCceEEEeCCCCCCCCCCCCcEEEEEeehHHHHHHHHHHHHHHhhccccC
Q 006943          388 TVTIRLLVSSKVIGCIIGKSGSIINEIRKRTKADVRISKGDKPKCADANDELVEVVGEVGSVRDALVQIILRLRDDALKD  467 (624)
Q Consensus       388 ~~~~~l~vp~~~~g~iIGk~G~~Ik~I~~~tga~I~i~~~~~p~~~~~~~~~v~I~G~~~~v~~A~~~I~~~l~e~~~~~  467 (624)
                      .++.+|.||...+|.+||++|++|+.|++++|+++....+       ..+.++...++++.|.+|..++     +.    
T Consensus         3 ~~~~~~~Vp~~~vG~~IG~~G~~I~~i~~e~gI~ii~~~~-------~~~~~i~~~~~p~~v~~~~~~l-----~~----   66 (144)
T 2qnd_A            3 RFHEQFIVREDLMGLAIGTHGANIQQARKVPGVTAIDLDE-------DTCTFHIYGEDQDAVKKARSFL-----EF----   66 (144)
T ss_dssp             -CEEEEECCGGGHHHHHCGGGHHHHHHHTSTTEEEEEEET-------TTTEEEEEESSHHHHHHHHHHH-----CE----
T ss_pred             ceEEEEEECCcceeeEECCChhHHHHHHHHHCCeEeccCC-------CchheeeccCCHHHHHHHHHhh-----hc----
Confidence            4678999999999999999999999999999944333221       2244554445789998885421     10    


Q ss_pred             CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCcccccC
Q 006943          468 RDGSRNPPVGADHIYSSGTGISMPPLLPSIPPVGPLGYDQRADSGSGIGMLSSSSLYGYGSLSMGDSPYGSMSSYSSKLY  547 (624)
Q Consensus       468 ~~~~~~p~~~~~~~~~~~~~~~~p~~~~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  547 (624)
                                                                                                      
T Consensus        67 --------------------------------------------------------------------------------   66 (144)
T 2qnd_A           67 --------------------------------------------------------------------------------   66 (144)
T ss_dssp             --------------------------------------------------------------------------------
T ss_pred             --------------------------------------------------------------------------------
Confidence                                                                                            


Q ss_pred             CCCCCCcEEEEEeccccccceeccCCchHHHHHHHhCC-EEEEeCCCCC---CCC--eEEEEEcCHHHHHHHHHHHHHHH
Q 006943          548 GGLPPPLTLEVLVPANAVGKVIGKAGSNLANIRKISGA-TIEMSDSKSS---RGD--RVALISGTPEQKRAAENLIQAFI  621 (624)
Q Consensus       548 ~~~~~~~~~~i~VP~~~vg~IIGkgG~~I~~I~~~sGa-~I~i~~~~~~---~~~--r~v~I~Gt~e~v~~A~~lI~~~i  621 (624)
                            ...+|.||.+.+|++|||+|+||+.|++.||| +|+|+...+.   .++  +.|+|+|++++|+.|+.||++.|
T Consensus        67 ------~e~~v~Vp~~~~g~~IGK~G~nIr~i~~~tG~~~I~i~~~~~~~~~~~~~~~~vtI~G~~~~v~~Ak~li~~~l  140 (144)
T 2qnd_A           67 ------AEDVIQVPRNLVGKVIGKNGKLIQEIVDKSGVVRVRIEAENEKNVPQEEGMVPFVFVGTKDSIANATVLLDYHL  140 (144)
T ss_dssp             ------EEEEEEEEGGGHHHHHCGGGHHHHHHHHHHTCSEEEEEEECTTCCCCCTTEEEEEEEEEHHHHHHHHHHHHHHH
T ss_pred             ------ceEEEEECHHHcCeeECCCCHHHHHHHHHHCCEEEEEcCCCCCCccccCCeeEEEEEeCHHHHHHHHHHHHHHH
Confidence                  03679999999999999999999999999997 9999975432   123  35899999999999999999998


Q ss_pred             hh
Q 006943          622 MA  623 (624)
Q Consensus       622 ~~  623 (624)
                      .+
T Consensus       141 ~~  142 (144)
T 2qnd_A          141 NY  142 (144)
T ss_dssp             HT
T ss_pred             Hh
Confidence            75

>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=99.70  E-value=3.2e-17  Score=147.62  Aligned_cols=137  Identities=15%  Similarity=0.237  Sum_probs=101.7

Q ss_pred             eEEEEEEecCcccceeccCCchHHHHHHHhcCCeEEeeCCCCCCCceEEEEEccCCcccccccccccCCCCcccHHHHHH
Q 006943           36 SVIYRILCPDGVIGSVIGKSGKVINSIRQETRARVKVVDPFPGAKDRVVTIYSHVKDKEDVEVDDEFNDKEPLCAAQDAL  115 (624)
Q Consensus        36 ~~~~~ilvp~~~~g~vIGk~G~~I~~i~~etg~~I~v~~~~~~~~er~i~I~G~~~~~~~~~~~~~~~~~~~~~~a~~ai  115 (624)
                      .++.+|+||.+.+|++||++|++|++|++++|  |.+.+. ...+++.+...+.++.                      +
T Consensus         3 ~~~~~~~Vp~~~vG~~IG~~G~~I~~i~~e~g--I~ii~~-~~~~~~~i~~~~~p~~----------------------v   57 (144)
T 2qnd_A            3 RFHEQFIVREDLMGLAIGTHGANIQQARKVPG--VTAIDL-DEDTCTFHIYGEDQDA----------------------V   57 (144)
T ss_dssp             -CEEEEECCGGGHHHHHCGGGHHHHHHHTSTT--EEEEEE-ETTTTEEEEEESSHHH----------------------H
T ss_pred             ceEEEEEECCcceeeEECCChhHHHHHHHHHC--CeEecc-CCCchheeeccCCHHH----------------------H
Confidence            46789999999999999999999999999999  444321 1234555544434433                      2


Q ss_pred             HHHHHHHHHhhhccCCCcccCCCceeEEEEEeccceeEEEeCCchHHHHHHHhcCC-eEEEccCCCCCCCCcccccCCc-
Q 006943          116 LKVHAAIANAVANATDNDKKRKEKEECQILVPSSQSANIIGKAGATIKRLRSKTRT-SIKVTPKDASEPTHSCAMEFDN-  193 (624)
Q Consensus       116 ~~v~~~i~~~~~~~~~~~~~~~~~~~~~llvp~~~~g~iIGk~G~~Ik~I~~~sga-~I~i~~~~~~~~~~~~~~~~~r-  193 (624)
                      .++.. +.   .           ..+.++.||.+++|.+|||+|.+|+.|++.||| +|+|.+.+...    . ..+++ 
T Consensus        58 ~~~~~-~l---~-----------~~e~~v~Vp~~~~g~~IGK~G~nIr~i~~~tG~~~I~i~~~~~~~----~-~~~~~~  117 (144)
T 2qnd_A           58 KKARS-FL---E-----------FAEDVIQVPRNLVGKVIGKNGKLIQEIVDKSGVVRVRIEAENEKN----V-PQEEGM  117 (144)
T ss_dssp             HHHHH-HH---C-----------EEEEEEEEEGGGHHHHHCGGGHHHHHHHHHHTCSEEEEEEECTTC----C-CCCTTE
T ss_pred             HHHHH-hh---h-----------cceEEEEECHHHcCeeECCCCHHHHHHHHHHCCEEEEEcCCCCCC----c-cccCCe
Confidence            22211 11   1           123889999999999999999999999999997 99998754221    1 12344 


Q ss_pred             -eEEEecCHHHHHHHHHHHHHHHhh
Q 006943          194 -FVLISGESEAVKKALFAISAIMYK  217 (624)
Q Consensus       194 -~V~I~G~~~~V~~A~~~I~~~l~~  217 (624)
                       .|+|+|++++|..|+.+|.++|..
T Consensus       118 ~~vtI~G~~~~v~~Ak~li~~~l~~  142 (144)
T 2qnd_A          118 VPFVFVGTKDSIANATVLLDYHLNY  142 (144)
T ss_dssp             EEEEEEEEHHHHHHHHHHHHHHHHT
T ss_pred             eEEEEEeCHHHHHHHHHHHHHHHHh
Confidence             489999999999999999999864

>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=1.3e-15  Score=123.41  Aligned_cols=72  Identities=33%  Similarity=0.586  Sum_probs=67.0

Q ss_pred             CCcEEEEEeccccccceeccCCchHHHHHHHhCCEEEEeCCCCCCCCeEEEEEcCHHHHHHHHHHHHHHHhh
Q 006943          552 PPLTLEVLVPANAVGKVIGKAGSNLANIRKISGATIEMSDSKSSRGDRVALISGTPEQKRAAENLIQAFIMA  623 (624)
Q Consensus       552 ~~~~~~i~VP~~~vg~IIGkgG~~I~~I~~~sGa~I~i~~~~~~~~~r~v~I~Gt~e~v~~A~~lI~~~i~~  623 (624)
                      +.++.+|.||.+++|+||||+|++|++|+++|||+|+|++..++..++.|+|+|++++++.|+.||++++..
T Consensus         5 ~~~~~~i~Vp~~~vg~iIGkgG~~Ik~I~~~tga~I~i~~~~~~~~~~~v~I~G~~~~v~~A~~~I~~~i~~   76 (82)
T 1zzk_A            5 PIITTQVTIPKDLAGSIIGKGGQRIKQIRHESGASIKIDEPLEGSEDRIITITGTQDQIQNAQYLLQNSVKQ   76 (82)
T ss_dssp             CCEEEEEEEETTTGGGGTCGGGHHHHHHHHHHCCEEEECCTTSCSSEEEEEEEECHHHHHHHHHHHHHHHHH
T ss_pred             CeEEEEEEEChHhcCeeECCCchHHHHHHHHHCCEEEEcCCCCCCCceEEEEEeCHHHHHHHHHHHHHHHHh
Confidence            456999999999999999999999999999999999999876677889999999999999999999999863

>2e3u_A PH-DIM2P, hypothetical protein PH1566; PRE-ribosomal RNA processing factor, RNA binding protein; 2.30A {Pyrococcus horikoshii} PDB: 3aev_B

Probab=99.61  E-value=1.5e-15  Score=145.34  Aligned_cols=142  Identities=21%  Similarity=0.254  Sum_probs=108.3

Q ss_pred             cEEEEEEecCCeeeEEEcCCCchHHHHHHhcCceEEEeCCCCCCCCCCCCcEEEEEee-----hHHHHHHHHHHHHHHhh
Q 006943          388 TVTIRLLVSSKVIGCIIGKSGSIINEIRKRTKADVRISKGDKPKCADANDELVEVVGE-----VGSVRDALVQIILRLRD  462 (624)
Q Consensus       388 ~~~~~l~vp~~~~g~iIGk~G~~Ik~I~~~tga~I~i~~~~~p~~~~~~~~~v~I~G~-----~~~v~~A~~~I~~~l~e  462 (624)
                      +...++.||...++.|||++|.+|+.|+++|||+|.+..         .++.|+|.|+     ++++.+|..+|.+..+.
T Consensus        33 P~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           33 KQEEYVKIPKDRIAVLIGKKGQTKKEIEKRTKTKITIDS---------ETGEVWITSTKETEDPLAVWKARDIVLAIGRG  103 (219)
T ss_dssp             CCEEEEECCHHHHHHHHCGGGHHHHHHHHHHTEEEEECT---------TTCEEEEEECTTCCSHHHHHHHHHHHHHHHTT
T ss_pred             CEEEEEEeCHHHhhhhhcccHHHHHHHHHHHCcEEEEEc---------CCCEEEEecCCCCCCHHHHHHHHHHHHHHhcc
Confidence            446789999999999999999999999999999999963         2567889986     69999999888776532


Q ss_pred             ccccCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCc
Q 006943          463 DALKDRDGSRNPPVGADHIYSSGTGISMPPLLPSIPPVGPLGYDQRADSGSGIGMLSSSSLYGYGSLSMGDSPYGSMSSY  542 (624)
Q Consensus       463 ~~~~~~~~~~~p~~~~~~~~~~~~~~~~p~~~~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~~~~~~~~~~~~~~~  542 (624)
                      .....-.          .++.                                                           
T Consensus       104 ~~~e~g~----------~ll~-----------------------------------------------------------  114 (219)
T 2e3u_A          104 FSPERAF----------RLLN-----------------------------------------------------------  114 (219)
T ss_dssp             CCHHHHG----------GGGS-----------------------------------------------------------
T ss_pred             CCccccc----------eecc-----------------------------------------------------------
Confidence            1000000          0000                                                           


Q ss_pred             ccccCCCCCCCcEEEEEec-----------cccccceeccCCchHHHHHHHhCCEEEEeCCCCCCCCeEEEEEcCHHHHH
Q 006943          543 SSKLYGGLPPPLTLEVLVP-----------ANAVGKVIGKAGSNLANIRKISGATIEMSDSKSSRGDRVALISGTPEQKR  611 (624)
Q Consensus       543 ~~~~~~~~~~~~~~~i~VP-----------~~~vg~IIGkgG~~I~~I~~~sGa~I~i~~~~~~~~~r~v~I~Gt~e~v~  611 (624)
                              .+.....+.|+           ...+|+||||+|.+|+.|++.|||+|.|.+       +.|+|.|++++++
T Consensus       115 --------dd~~~e~i~i~~~~v~~~~~~~~r~~GriIGk~G~tik~ie~~Tg~~I~v~~-------~~v~i~G~~~~i~  179 (219)
T 2e3u_A          115 --------EGEYLEIINLTDIIIGNEKNALPRVRGRIIGRKGRTRQIIEEMSGASVSVYG-------KTVAIIGNPIQIE  179 (219)
T ss_dssp             --------TTCEEEEEEGGGCC------CHHHHHHHHHCGGGHHHHHHHHHHCCEEEEET-------TEEEEEECHHHHH
T ss_pred             --------CCccceeEEcccccccCCchhhhhhhheeECCCchHHHHHHHHhCceEEECC-------eEEEEEeCHHHHH
Confidence                    00001112222           236899999999999999999999999974       4699999999999


Q ss_pred             HHHHHHHHHHh
Q 006943          612 AAENLIQAFIM  622 (624)
Q Consensus       612 ~A~~lI~~~i~  622 (624)
                      .|+.+|+++|.
T Consensus       180 ~A~~~i~~li~  190 (219)
T 2e3u_A          180 IAKTAIEKLAR  190 (219)
T ss_dssp             HHHHHHHHHHT
T ss_pred             HHHHHHHHHHc
Confidence            99999999985

>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=8.3e-16  Score=122.68  Aligned_cols=72  Identities=26%  Similarity=0.509  Sum_probs=67.5

Q ss_pred             CcEEEEEeccccccceeccCCchHHHHHHHhCCEEEEeCCCCCCCCeEEEEEcCHHHHHHHHHHHHHHHhhC
Q 006943          553 PLTLEVLVPANAVGKVIGKAGSNLANIRKISGATIEMSDSKSSRGDRVALISGTPEQKRAAENLIQAFIMAT  624 (624)
Q Consensus       553 ~~~~~i~VP~~~vg~IIGkgG~~I~~I~~~sGa~I~i~~~~~~~~~r~v~I~Gt~e~v~~A~~lI~~~i~~~  624 (624)
                      .++.+|.||.+++|+||||+|++|++|++.|||+|+|+++.++..++.|+|+|++++++.|+.||++++.++
T Consensus         4 ~~~~~i~Ip~~~vg~iIGkgG~~Ik~I~~~tga~I~i~~~~~~~~~~~v~I~G~~~~v~~A~~~I~~~i~~E   75 (76)
T 2p2r_A            4 TTSHELTIPNDLIGCIIGRQGAKINEIRQMSGAQIKIANPVEGSTDRQVTITGSAASISLAQYLINVRLSSE   75 (76)
T ss_dssp             CEEEEEEEEHHHHHHHHCGGGHHHHHHHHHHCCEEEECCCCTTCSEEEEEEEECHHHHHHHHHHHHHHHTTC
T ss_pred             ceEEEEEEChHHcceEECCCChHHHHHHHHHCCEEEEcCCCCCCCeEEEEEEeCHHHHHHHHHHHHHHHHcc
Confidence            468999999999999999999999999999999999998777778999999999999999999999998753

>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=99.59  E-value=1.5e-15  Score=123.05  Aligned_cols=72  Identities=31%  Similarity=0.532  Sum_probs=66.5

Q ss_pred             CCcEEEEEeccccccceeccCCchHHHHHHHhCCEEEEeCCCCCCCCeEEEEEcCHHHHHHHHHHHHHHHhh
Q 006943          552 PPLTLEVLVPANAVGKVIGKAGSNLANIRKISGATIEMSDSKSSRGDRVALISGTPEQKRAAENLIQAFIMA  623 (624)
Q Consensus       552 ~~~~~~i~VP~~~vg~IIGkgG~~I~~I~~~sGa~I~i~~~~~~~~~r~v~I~Gt~e~v~~A~~lI~~~i~~  623 (624)
                      ..++.+|.||.+++|+||||+|++|++|+++|||+|+|++..++..++.|+|+|++++++.|+.||++++..
T Consensus         4 ~~~~~~i~Ip~~~vg~IIGkgG~~Ik~I~~~sga~I~i~~~~~~~~~r~v~I~G~~~~v~~A~~~I~~~i~~   75 (82)
T 1wvn_A            4 SQTTHELTIPNNLIGCIIGRQGANINEIRQMSGAQIKIANPVEGSSGRQVTITGSAASISLAQYLINARLSS   75 (82)
T ss_dssp             TCEEEEEEEEGGGHHHHHCGGGHHHHHHHHHHCCEEEECCCCTTCSEEEEEEEECHHHHHHHHHHHHHHTC-
T ss_pred             CcEEEEEEEchHhccceeCCCchhHHHHHHHhCCEEEEecCCCCCCceEEEEEcCHHHHHHHHHHHHHHHHh
Confidence            356899999999999999999999999999999999999876677899999999999999999999998864

>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=8e-15  Score=121.32  Aligned_cols=71  Identities=28%  Similarity=0.542  Sum_probs=66.7

Q ss_pred             CcEEEEEeccccccceeccCCchHHHHHHHhCCEEEEeCCCCCCCCeEEEEEcCHHHHHHHHHHHHHHHhh
Q 006943          553 PLTLEVLVPANAVGKVIGKAGSNLANIRKISGATIEMSDSKSSRGDRVALISGTPEQKRAAENLIQAFIMA  623 (624)
Q Consensus       553 ~~~~~i~VP~~~vg~IIGkgG~~I~~I~~~sGa~I~i~~~~~~~~~r~v~I~Gt~e~v~~A~~lI~~~i~~  623 (624)
                      .++.+|.||.+++|+||||+|++|++|+++|||+|+|++..++..++.|+|+|++++++.|+.||+++|..
T Consensus        14 ~~~~~i~Ip~~~vG~IIGkgG~~Ik~I~~~tga~I~I~~~~~g~~~r~v~I~G~~e~v~~A~~~I~~~i~~   84 (92)
T 1x4n_A           14 VMTEEYKVPDGMVGFIIGRGGEQISRIQQESGCKIQIAPDSGGLPERSCMLTGTPESVQSAKRLLDQIVEK   84 (92)
T ss_dssp             CEEEEEEEEHHHHHHHHCSSSHHHHHHHHHSCCEEEECSCCTTCSEEEEEEEECHHHHHHHHHHHHHHHHH
T ss_pred             CEEEEEEEChHHcceeECCCchHHHHHHHHhCCEEEEcCCCCCCCccEEEEEeCHHHHHHHHHHHHHHHHh
Confidence            46899999999999999999999999999999999999887667789999999999999999999999864

>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=99.55  E-value=6.7e-15  Score=117.53  Aligned_cols=70  Identities=31%  Similarity=0.545  Sum_probs=63.8

Q ss_pred             cEEEEEeccccccceeccCCchHHHHHHHhCCEEEEeCCC---CCCCCeEEEEEcCHHHHHHHHHHHHHHHhh
Q 006943          554 LTLEVLVPANAVGKVIGKAGSNLANIRKISGATIEMSDSK---SSRGDRVALISGTPEQKRAAENLIQAFIMA  623 (624)
Q Consensus       554 ~~~~i~VP~~~vg~IIGkgG~~I~~I~~~sGa~I~i~~~~---~~~~~r~v~I~Gt~e~v~~A~~lI~~~i~~  623 (624)
                      .+.++.||.+++|+||||+|++|++|++.|||+|+|++..   ++..++.|+|+|++++++.|+.+|++++..
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            4889999999999999999999999999999999999763   355689999999999999999999998764

>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=99.54  E-value=6.1e-15  Score=121.28  Aligned_cols=72  Identities=33%  Similarity=0.586  Sum_probs=66.9

Q ss_pred             CCcEEEEEeccccccceeccCCchHHHHHHHhCCEEEEeCCCCCCCCeEEEEEcCHHHHHHHHHHHHHHHhh
Q 006943          552 PPLTLEVLVPANAVGKVIGKAGSNLANIRKISGATIEMSDSKSSRGDRVALISGTPEQKRAAENLIQAFIMA  623 (624)
Q Consensus       552 ~~~~~~i~VP~~~vg~IIGkgG~~I~~I~~~sGa~I~i~~~~~~~~~r~v~I~Gt~e~v~~A~~lI~~~i~~  623 (624)
                      ..++.+|.||.+++|.||||+|++|++|+++|||+|+|++..++..++.|+|+|++++++.|+.+|++++..
T Consensus        12 ~~~~~~i~Ip~~~vg~IIGkgG~~Ik~I~~~tga~I~I~~~~~~~~~~~v~I~G~~e~v~~A~~~I~~~i~e   83 (89)
T 1j5k_A           12 PIITTQVTIPKDLAGSIIGKGGQRIKQIRHESGASIKIDEPLEGSEDRIITITGTQDQIQNAQYLLQNSVKQ   83 (89)
T ss_dssp             CEEEEEEEEEHHHHHHHHCGGGHHHHHHHHHTCCEEEECSCCSSSSEEEEEEEEEHHHHHHHHHHHHHHHHH
T ss_pred             CeEEEEEEEChhhcceeECCCCHhHHHHHHHhCCeEEecCCCCCCCccEEEEEcCHHHHHHHHHHHHHHHHh
Confidence            356899999999999999999999999999999999999876677889999999999999999999999864

>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=99.54  E-value=9e-15  Score=115.39  Aligned_cols=69  Identities=28%  Similarity=0.459  Sum_probs=64.4

Q ss_pred             CcEEEEEeccccccceeccCCchHHHHHHHhCCEEEEeCCCCCCCCeEEEEEcCHHHHHHHHHHHHHHHhh
Q 006943          553 PLTLEVLVPANAVGKVIGKAGSNLANIRKISGATIEMSDSKSSRGDRVALISGTPEQKRAAENLIQAFIMA  623 (624)
Q Consensus       553 ~~~~~i~VP~~~vg~IIGkgG~~I~~I~~~sGa~I~i~~~~~~~~~r~v~I~Gt~e~v~~A~~lI~~~i~~  623 (624)
                      .++.++.||.+++|.||||+|++|++|+++|||+|+|++.  +..+|.|+|+|++++++.|+.+|.++|..
T Consensus         4 ~~~~~i~ip~~~ig~iIGkgG~~Ik~I~~~tga~I~i~~~--~~~er~v~I~G~~~~v~~A~~~I~~~l~e   72 (73)
T 2axy_A            4 TLTIRLLMHGKEVGSIIGKKGESVKKMREESGARINISEG--NCPERIITLAGPTNAIFKAFAMIIDKLEE   72 (73)
T ss_dssp             CEEEEEEEEHHHHHHHHCGGGHHHHHHHHHHCCEEEECSS--CCSEEEEEEEECHHHHHHHHHHHHHHHHC
T ss_pred             eEEEEEEEChhHeeeEECCCCHHHHHHHHHHCCEEEEecC--CCCcEEEEEEeCHHHHHHHHHHHHHHHhc
Confidence            4589999999999999999999999999999999999986  45789999999999999999999999864

>2e3u_A PH-DIM2P, hypothetical protein PH1566; PRE-ribosomal RNA processing factor, RNA binding protein; 2.30A {Pyrococcus horikoshii} PDB: 3aev_B

Probab=99.54  E-value=1.6e-14  Score=138.27  Aligned_cols=144  Identities=20%  Similarity=0.212  Sum_probs=100.3

Q ss_pred             EEEEEEecCcccceeccCCchHHHHHHHhcCCeEEeeCCCCCCCceEEEEEccCCcccccccccccCCCCcccHHHHHHH
Q 006943           37 VIYRILCPDGVIGSVIGKSGKVINSIRQETRARVKVVDPFPGAKDRVVTIYSHVKDKEDVEVDDEFNDKEPLCAAQDALL  116 (624)
Q Consensus        37 ~~~~ilvp~~~~g~vIGk~G~~I~~i~~etg~~I~v~~~~~~~~er~i~I~G~~~~~~~~~~~~~~~~~~~~~~a~~ai~  116 (624)
                      -..++.||.+.+|.|||++|++|+.|+++|||+|.+..     .++.|+|++....-.                 .+++.
T Consensus        34 ~i~~i~IP~~kig~lIG~gGk~Ik~I~e~tgvkI~I~~-----~~g~V~I~~~~~t~d-----------------~~~i~   91 (219)
T 2e3u_A           34 QEEYVKIPKDRIAVLIGKKGQTKKEIEKRTKTKITIDS-----ETGEVWITSTKETED-----------------PLAVW   91 (219)
T ss_dssp             CEEEEECCHHHHHHHHCGGGHHHHHHHHHHTEEEEECT-----TTCEEEEEECTTCCS-----------------HHHHH
T ss_pred             EEEEEEeCHHHhhhhhcccHHHHHHHHHHHCcEEEEEc-----CCCEEEEecCCCCCC-----------------HHHHH
Confidence            46699999999999999999999999999999999963     356799998752211                 12333


Q ss_pred             HHHHHHHHhhhccC--CCcccCCCceeEE-EEE-----e------ccceeEEEeCCchHHHHHHHhcCCeEEEccCCCCC
Q 006943          117 KVHAAIANAVANAT--DNDKKRKEKEECQ-ILV-----P------SSQSANIIGKAGATIKRLRSKTRTSIKVTPKDASE  182 (624)
Q Consensus       117 ~v~~~i~~~~~~~~--~~~~~~~~~~~~~-llv-----p------~~~~g~iIGk~G~~Ik~I~~~sga~I~i~~~~~~~  182 (624)
                      ++.+.|.+-.....  +...-..+...+. +-+     +      ...+|+||||+|.+|+.|++.|||+|.|.      
T Consensus        92 kA~~~I~~i~rg~~~e~g~~ll~dd~~~e~i~i~~~~v~~~~~~~~r~~GriIGk~G~tik~ie~~Tg~~I~v~------  165 (219)
T 2e3u_A           92 KARDIVLAIGRGFSPERAFRLLNEGEYLEIINLTDIIIGNEKNALPRVRGRIIGRKGRTRQIIEEMSGASVSVY------  165 (219)
T ss_dssp             HHHHHHHHHHTTCCHHHHGGGGSTTCEEEEEEGGGCC------CHHHHHHHHHCGGGHHHHHHHHHHCCEEEEE------
T ss_pred             HHHHHHHHHhccCCccccceeccCCccceeEEcccccccCCchhhhhhhheeECCCchHHHHHHHHhCceEEEC------
Confidence            33333322110000  0000001111121 222     2      23689999999999999999999999985      


Q ss_pred             CCCcccccCCceEEEecCHHHHHHHHHHHHHHHhh
Q 006943          183 PTHSCAMEFDNFVLISGESEAVKKALFAISAIMYK  217 (624)
Q Consensus       183 ~~~~~~~~~~r~V~I~G~~~~V~~A~~~I~~~l~~  217 (624)
                               ++.|.|.|+.++|..|..+|.+++..
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                     35699999999999999999999954

>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=122.06  Aligned_cols=70  Identities=29%  Similarity=0.467  Sum_probs=63.6

Q ss_pred             cEEEEEeccccccceeccCCchHHHHHHHhCCEEEEeCCCC---CCCCeEEEEEcCHHHHHHHHHHHHHHHhh
Q 006943          554 LTLEVLVPANAVGKVIGKAGSNLANIRKISGATIEMSDSKS---SRGDRVALISGTPEQKRAAENLIQAFIMA  623 (624)
Q Consensus       554 ~~~~i~VP~~~vg~IIGkgG~~I~~I~~~sGa~I~i~~~~~---~~~~r~v~I~Gt~e~v~~A~~lI~~~i~~  623 (624)
                      .+.+|.||.+++|+||||+|++|++|+++|||+|+|.+..+   +..++.|+|+|++++|+.|+.+|+++|..
T Consensus         7 ~~~~i~IP~~~vG~IIGkgG~~Ik~I~~~TGa~I~I~~~~~~~~~~~~r~V~I~G~~e~v~~A~~~I~~~i~e   79 (107)
T 2hh2_A            7 GEMTFSIPTHKCGLVIGRGGENVKAINQQTGAFVEISRQLPPNGDPNFKLFIIRGSPQQIDHAKQLIEEKIEG   79 (107)
T ss_dssp             CCEEEEEEGGGTTTTSTTTTCHHHHHHHHSSSEEEECCCCCTTCCTTEEEEEEESCHHHHHHHHHHHHHHSCS
T ss_pred             CeEEEEECHHHcCccCCCCcHHHHHHHHHhCCEEEEcCccCCCCCCCceEEEEECCHHHHHHHHHHHHHHHhc
Confidence            37899999999999999999999999999999999998742   34679999999999999999999998753

>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=99.51  E-value=2.1e-14  Score=117.72  Aligned_cols=70  Identities=31%  Similarity=0.553  Sum_probs=64.4

Q ss_pred             cEEEEEeccccccceeccCCchHHHHHHHhCCEEEEeCCC---CCCCCeEEEEEcCHHHHHHHHHHHHHHHhh
Q 006943          554 LTLEVLVPANAVGKVIGKAGSNLANIRKISGATIEMSDSK---SSRGDRVALISGTPEQKRAAENLIQAFIMA  623 (624)
Q Consensus       554 ~~~~i~VP~~~vg~IIGkgG~~I~~I~~~sGa~I~i~~~~---~~~~~r~v~I~Gt~e~v~~A~~lI~~~i~~  623 (624)
                      .+.+|.||.+++|+||||+|++|++|++.|||+|+|++..   ++..++.|+|+|++++++.|+.||+++|..
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            4889999999999999999999999999999999999863   356789999999999999999999999864

>2hh3_A KH-type splicing regulatory protein; KH-RNA binding domain, RNA binding protein; NMR {Homo sapiens}

Probab=99.50  E-value=2.5e-14  Score=121.01  Aligned_cols=69  Identities=26%  Similarity=0.544  Sum_probs=64.7

Q ss_pred             EEEEEeccccccceeccCCchHHHHHHHhCCEEEEeCCCCCCCCeEEEEEcCHHHHHHHHHHHHHHHhh
Q 006943          555 TLEVLVPANAVGKVIGKAGSNLANIRKISGATIEMSDSKSSRGDRVALISGTPEQKRAAENLIQAFIMA  623 (624)
Q Consensus       555 ~~~i~VP~~~vg~IIGkgG~~I~~I~~~sGa~I~i~~~~~~~~~r~v~I~Gt~e~v~~A~~lI~~~i~~  623 (624)
                      +.+|.||.+++|+||||+|++|++|+++|||+|+|+++.+...+|.|+|+|+++++++|+.||++++..
T Consensus        12 ~~~i~Ip~~~iG~IIGkgG~~Ik~I~~~TGakI~I~~~~~~~~er~V~I~G~~e~v~~A~~~I~~ii~~   80 (106)
T 2hh3_A           12 GIDVPVPRHSVGVVIGRSGEMIKKIQNDAGVRIQFKQDDGTGPEKIAHIMGPPDRCEHAARIINDLLQS   80 (106)
T ss_dssp             CEEEEEETTTHHHHHTTTTHHHHHHHHHHTCEEEECSSCSSSSEEEEEEESSHHHHHHHHHHHHHHHHH
T ss_pred             EEEEEECHHHcCccCCCCcHHHHHHHHHHCcEEEEecCCCCCceeEEEEEeCHHHHHHHHHHHHHHHhc
Confidence            789999999999999999999999999999999999776666789999999999999999999999864

>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=99.50  E-value=3.4e-14  Score=118.01  Aligned_cols=73  Identities=25%  Similarity=0.490  Sum_probs=66.2

Q ss_pred             CCCcEEEEEeccccccceeccCCchHHHHHHHhCCEEEEeCCCC--CCCCeEEEEEcCHHHHHHHHHHHHHHHhh
Q 006943          551 PPPLTLEVLVPANAVGKVIGKAGSNLANIRKISGATIEMSDSKS--SRGDRVALISGTPEQKRAAENLIQAFIMA  623 (624)
Q Consensus       551 ~~~~~~~i~VP~~~vg~IIGkgG~~I~~I~~~sGa~I~i~~~~~--~~~~r~v~I~Gt~e~v~~A~~lI~~~i~~  623 (624)
                      +..++.+|.||.+++|+||||+|++|++|+++|||+|+|.+...  ...+|.|+|+|++++++.|+.||++++..
T Consensus        12 p~~~~~~i~Ip~~~vG~IIGkgG~~Ik~I~~~tga~I~I~~~~~~~~~~~r~v~I~G~~~~v~~A~~~I~~~i~~   86 (94)
T 1x4m_A           12 PGNAVQEIMIPASKAGLVIGKGGETIKQLQERAGVKMVMIQDGPQNTGADKPLRITGDPYKVQQAKEMVLELIRD   86 (94)
T ss_dssp             CCCEEEEEEECHHHHHHHSCSSSSHHHHHHHHHTSEEEECCSCCCSSCSCEEEEEEECTTTHHHHHHHHHHHHCC
T ss_pred             CCcEEEEEEEChhhcceEECCCCHHHHHHHHHHCCeEEecCCCCCCCCCceEEEEEeCHHHHHHHHHHHHHHHhc
Confidence            44679999999999999999999999999999999999998643  34689999999999999999999999864

>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=99.49  E-value=1.7e-14  Score=116.18  Aligned_cols=68  Identities=28%  Similarity=0.411  Sum_probs=62.3

Q ss_pred             CCcEEEEEeccccccceeccCCchHHHHHHHhCCEEEEeCCCCCCCCeEEEEEcCHHHHHHHHHHHHHHHh
Q 006943          552 PPLTLEVLVPANAVGKVIGKAGSNLANIRKISGATIEMSDSKSSRGDRVALISGTPEQKRAAENLIQAFIM  622 (624)
Q Consensus       552 ~~~~~~i~VP~~~vg~IIGkgG~~I~~I~~~sGa~I~i~~~~~~~~~r~v~I~Gt~e~v~~A~~lI~~~i~  622 (624)
                      ...+.+|.||.+++|+||||+|++|++|+++|||+|+|++..   +++.|+|+|++++++.|+++|++++.
T Consensus         8 ~~~~~~i~VP~~~vG~IIGkgG~tIk~Iqe~Tga~I~I~~~~---~~~~v~ItG~~e~v~~A~~~I~~~i~   75 (83)
T 2dgr_A            8 GQTTIQVRVPYRVVGLVVGPKGATIKRIQQRTHTYIVTPGRD---KEPVFAVTGMPENVDRAREEIEAHIT   75 (83)
T ss_dssp             CSEEEEEECCHHHHHHHHTTTTSSHHHHHHHTTCEEECCCSS---SCCEEEEEECTTTHHHHHHHHHHHHH
T ss_pred             CceEEEEEeChHHeeeeECCCchHHHHHHHHhCCeEEecCCC---CCCeEEEEcCHHHHHHHHHHHHHHHh
Confidence            356899999999999999999999999999999999999653   35889999999999999999999775

>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=99.48  E-value=5.3e-14  Score=131.05  Aligned_cols=140  Identities=19%  Similarity=0.239  Sum_probs=109.2

Q ss_pred             EEEEecCCeeeEEEcCCCchHHHHHHhcCceEEEeCCCCCCCCCCCCcEEEEE-----eehHHHHHHHHHHHHHHhhccc
Q 006943          391 IRLLVSSKVIGCIIGKSGSIINEIRKRTKADVRISKGDKPKCADANDELVEVV-----GEVGSVRDALVQIILRLRDDAL  465 (624)
Q Consensus       391 ~~l~vp~~~~g~iIGk~G~~Ik~I~~~tga~I~i~~~~~p~~~~~~~~~v~I~-----G~~~~v~~A~~~I~~~l~e~~~  465 (624)
                      .++.||...+|.|||++|++++.|++.+|++|++..         .++.|+|.     |++.++.+|...|.+..+....
T Consensus         6 ~~i~VP~~rvg~liGk~g~~~k~i~e~~g~~i~id~---------~~~~V~i~t~~~t~dp~~i~KA~dlI~ai~rgf~~   76 (191)
T 1tua_A            6 IYVKVKPERLGAVIGPRGEVKAEIMRRTGTVITVDT---------ENSMVIVEPEAEGIPPVNLMKAAEVVKAISLGFPP   76 (191)
T ss_dssp             EEEECCGGGHHHHHCGGGHHHHHHHHHHTEEEEEET---------TTTEEEEEESSTTSCHHHHHHHHHHHHHHHHTCCH
T ss_pred             eEEECCHHHhhHHHhcCHhHHHHHHHHHCcEEEEEc---------CCCeEEEEeCCCCCCHHHHHHHHHHHHHHHcCCCH
Confidence            689999999999999999999999999999999963         36778898     9999999999888765554211


Q ss_pred             cCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCcccc
Q 006943          466 KDRDGSRNPPVGADHIYSSGTGISMPPLLPSIPPVGPLGYDQRADSGSGIGMLSSSSLYGYGSLSMGDSPYGSMSSYSSK  545 (624)
Q Consensus       466 ~~~~~~~~p~~~~~~~~~~~~~~~~p~~~~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  545 (624)
                      .+-.                                                                           .
T Consensus        77 e~A~---------------------------------------------------------------------------~   81 (191)
T 1tua_A           77 EKAF---------------------------------------------------------------------------R   81 (191)
T ss_dssp             HHHG---------------------------------------------------------------------------G
T ss_pred             HHhh---------------------------------------------------------------------------h
Confidence            1000                                                                           0


Q ss_pred             cCCCCCCCcEEEEEec----------cccccceeccCCchHHHHHHHhCCEEEEeCCCCCCCCeEEEEEcCHHHHHHHHH
Q 006943          546 LYGGLPPPLTLEVLVP----------ANAVGKVIGKAGSNLANIRKISGATIEMSDSKSSRGDRVALISGTPEQKRAAEN  615 (624)
Q Consensus       546 ~~~~~~~~~~~~i~VP----------~~~vg~IIGkgG~~I~~I~~~sGa~I~i~~~~~~~~~r~v~I~Gt~e~v~~A~~  615 (624)
                      +..  ++.....+.++          ...+|+||||+|.||+.|++.|||+|.|.+       +.|.|.|++++++.|+.
T Consensus        82 Ll~--Dd~~~e~i~i~~~~~~~~~~~~r~~GrIIGk~G~tik~iE~~Tg~~I~v~~-------~~v~i~G~~~~i~~Ar~  152 (191)
T 1tua_A           82 LLE--EDQILVVVDLKQVVGDSQNHLKRIKGRIIGEGGRARRTIEEMTDTYINVGE-------YEVAIIGDYERAMAAKQ  152 (191)
T ss_dssp             GGS--TTEEEEEEETHHHHTTCHHHHHHHHHHHHCGGGHHHHHHHHHHTCEEEECS-------SEEEEEEEHHHHHHHHH
T ss_pred             ccc--CcceeEEEEcccccccCchhHHHHhhheeCCCccHHHHHHHHHCceEEEcC-------CEEEEEeChHHHHHHHH
Confidence            000  00011222233          346899999999999999999999999974       36999999999999999


Q ss_pred             HHHHHHhh
Q 006943          616 LIQAFIMA  623 (624)
Q Consensus       616 lI~~~i~~  623 (624)
                      .|+.+|..
T Consensus       153 ~i~~li~g  160 (191)
T 1tua_A          153 AIEMLAEG  160 (191)
T ss_dssp             HHHHHHTT
T ss_pred             HHHHHHcC
Confidence            99999863

>2opv_A KHSRP protein; KH domain, RNA binding protein, KSRP; NMR {Homo sapiens}

Probab=99.48  E-value=9.8e-14  Score=113.05  Aligned_cols=70  Identities=23%  Similarity=0.418  Sum_probs=64.0

Q ss_pred             CcEEEEEeccccccceeccCCchHHHHHHHhCCEEEEeCCCC--CCCCeEEEEEcCHHHHHHHHHHHHHHHh
Q 006943          553 PLTLEVLVPANAVGKVIGKAGSNLANIRKISGATIEMSDSKS--SRGDRVALISGTPEQKRAAENLIQAFIM  622 (624)
Q Consensus       553 ~~~~~i~VP~~~vg~IIGkgG~~I~~I~~~sGa~I~i~~~~~--~~~~r~v~I~Gt~e~v~~A~~lI~~~i~  622 (624)
                      ..+.+|.||.+++|.||||+|++|++|+++|||+|.|.++..  ...+|.|+|+|++++++.|+.+|++++.
T Consensus        13 ~~~~~i~Ip~~~ig~IIGkgG~~Ik~I~~~tga~I~i~~~~~~~~~~er~v~I~G~~~~v~~A~~~I~~i~~   84 (85)
T 2opv_A           13 GTVQEIMIPAGKAGLVIGKGGETIKQLQERAGVKMILIQDGSQNTNVDKPLRIIGDPYKVQQACEMVMDILR   84 (85)
T ss_dssp             SEEEEEEECTTTHHHHHTTTTHHHHHHHHHHTCEEEECSSSCSSTTSCEEEEEEECHHHHHHHHHHHHHHHT
T ss_pred             CEEEEEEeChhheeeeECCCCHHHHHHHHHHCCEEEEcCCCCCCCCCceEEEEEeCHHHHHHHHHHHHHHhc
Confidence            358899999999999999999999999999999999998643  4578999999999999999999999875

>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=99.42  E-value=4.9e-13  Score=110.81  Aligned_cols=75  Identities=19%  Similarity=0.256  Sum_probs=66.3

Q ss_pred             CCCCCCCcEEEEEeccccccceeccCCchHHHHHHHhCCEEEEeCCCCCCCCeEEEEEcCHHHHHHHHHHHHHHHh
Q 006943          547 YGGLPPPLTLEVLVPANAVGKVIGKAGSNLANIRKISGATIEMSDSKSSRGDRVALISGTPEQKRAAENLIQAFIM  622 (624)
Q Consensus       547 ~~~~~~~~~~~i~VP~~~vg~IIGkgG~~I~~I~~~sGa~I~i~~~~~~~~~r~v~I~Gt~e~v~~A~~lI~~~i~  622 (624)
                      +..+...++.+|.||.+++|.|||++|++|++|+++|||+|+|+++.. .+++.|+|+|++++++.|+.+|+.++.
T Consensus        10 v~~l~~~vt~~i~Ip~~~ig~IIG~gG~~Ir~I~e~tg~~I~i~~~g~-~~~~~V~I~G~~e~v~~A~~~I~~i~~   84 (95)
T 2ctm_A           10 VGELEQMVSEDVPLDHRVHARIIGARGKAIRKIMDEFKVDIRFPQSGA-PDPNCVTVTGLPENVEEAIDHILNLEE   84 (95)
T ss_dssp             CCCTTTCCCEEEECCTTTHHHHHCSSSCHHHHHHHHHTCEEECCCTTC-SCTTEEEEESCHHHHHHHHHHHHHHHH
T ss_pred             HHhhcccEEEEEEECHHHccccCCCCcchHHHHHHHHCCeEEecCCCC-CCCcEEEEEcCHHHHHHHHHHHHHHHH
Confidence            344556789999999999999999999999999999999999987632 346789999999999999999999875

>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=99.42  E-value=1e-13  Score=109.27  Aligned_cols=70  Identities=20%  Similarity=0.378  Sum_probs=64.2

Q ss_pred             CceeEEEEEeccceeEEEeCCchHHHHHHHhcCCeEEEccCCCCCCCCcccccCCceEEEecCHHHHHHHHHHHHHHHhh
Q 006943          138 EKEECQILVPSSQSANIIGKAGATIKRLRSKTRTSIKVTPKDASEPTHSCAMEFDNFVLISGESEAVKKALFAISAIMYK  217 (624)
Q Consensus       138 ~~~~~~llvp~~~~g~iIGk~G~~Ik~I~~~sga~I~i~~~~~~~~~~~~~~~~~r~V~I~G~~~~V~~A~~~I~~~l~~  217 (624)
                      ..++++|+||.+++|.||||+|++|++|+++|||+|+|.+.+          ..+|+|+|.|++++|.+|+.+|.++|++
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            358899999999999999999999999999999999998642          4589999999999999999999999864

>1vig_A Vigilin; RNA-binding protein, ribonucleoprotein; NMR {Homo sapiens} SCOP: d.51.1.1 PDB: 1vih_A

Probab=99.41  E-value=1.8e-13  Score=107.15  Aligned_cols=67  Identities=16%  Similarity=0.286  Sum_probs=61.3

Q ss_pred             CcEEEEEeccccccceeccCCchHHHHHHHhCCEEEEeCCCCCCCCeEEEEEcCHHHHHHHHHHHHHHH
Q 006943          553 PLTLEVLVPANAVGKVIGKAGSNLANIRKISGATIEMSDSKSSRGDRVALISGTPEQKRAAENLIQAFI  621 (624)
Q Consensus       553 ~~~~~i~VP~~~vg~IIGkgG~~I~~I~~~sGa~I~i~~~~~~~~~r~v~I~Gt~e~v~~A~~lI~~~i  621 (624)
                      ..+.++.||.+++|.|||++|++|++|+++|||+|+|+++.  ..++.|+|+|++++++.|+.+|++++
T Consensus         4 ~~~~~i~I~~~~ig~iIG~gG~~I~~I~e~tg~~I~i~~~g--~~~~~V~I~G~~~~v~~A~~~I~~i~   70 (71)
T 1vig_A            4 MDYVEINIDHKFHRHLIGKSGANINRIKDQYKVSVRIPPDS--EKSNLIRIEGDPQGVQQAKRELLELA   70 (71)
T ss_dssp             CEEEEEEECSSHHHHHTCSSCCHHHHHHHHTCCEEECCCCC--SSSEEEEEEESSHHHHHHHHHHHHTC
T ss_pred             eEEEEEEECHHHhhhhcCCCCccHHHHHHHHCCEEEECCCC--CcccEEEEEcCHHHHHHHHHHHHHHh
Confidence            35899999999999999999999999999999999999764  36689999999999999999999864

>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=99.41  E-value=2.8e-13  Score=114.71  Aligned_cols=69  Identities=32%  Similarity=0.465  Sum_probs=63.4

Q ss_pred             cEEEEEeccccccceeccCCchHHHHHHHhCCEEEEeCCCCC--CCCeEEEEEcCHHHHHHHHHHHHHHHh
Q 006943          554 LTLEVLVPANAVGKVIGKAGSNLANIRKISGATIEMSDSKSS--RGDRVALISGTPEQKRAAENLIQAFIM  622 (624)
Q Consensus       554 ~~~~i~VP~~~vg~IIGkgG~~I~~I~~~sGa~I~i~~~~~~--~~~r~v~I~Gt~e~v~~A~~lI~~~i~  622 (624)
                      .+.+|.||.+++|.||||+|++|++|+++|||+|+|++..++  ..++.|+|+|++++++.|+.||++++.
T Consensus        15 ~~~~i~Ip~~~ig~IIGkgG~~Ik~I~~~tga~I~I~~~~~~~~~~~~~V~I~G~~~~v~~A~~~I~~~i~   85 (104)
T 1we8_A           15 VFEQLSVPQRSVGRIIGRGGETIRSICKASGAKITCDKESEGTLLLSRLIKISGTQKEVAAAKHLILEKVS   85 (104)
T ss_dssp             EEEEEEEETTTHHHHHTTTSHHHHHHHHHHCCEEEECCSSCCSSSSEEEEEEEEEHHHHHHHHHHHHHHHH
T ss_pred             EEEEEEEChhheeeeECCCCHHHHHHHHHHCCEEEEecCCCCCCCCcceEEEEcCHHHHHHHHHHHHHHHh
Confidence            589999999999999999999999999999999999986543  257999999999999999999999985

>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=99.39  E-value=8.6e-13  Score=109.88  Aligned_cols=70  Identities=23%  Similarity=0.344  Sum_probs=63.5

Q ss_pred             CcEEEEEeccccccceeccCCchHHHHHHHhCCEEEEeCCCC-CCCCeEEEEEcCHHHHHHHHHHHHHHHh
Q 006943          553 PLTLEVLVPANAVGKVIGKAGSNLANIRKISGATIEMSDSKS-SRGDRVALISGTPEQKRAAENLIQAFIM  622 (624)
Q Consensus       553 ~~~~~i~VP~~~vg~IIGkgG~~I~~I~~~sGa~I~i~~~~~-~~~~r~v~I~Gt~e~v~~A~~lI~~~i~  622 (624)
                      .++.+|.||.+++|.|||++|++|++|+++|||+|+|+++.. ...++.|+|+|++++++.|+.+|+.++.
T Consensus        16 ~~~~~i~Ip~~~ig~IIGkgG~~Ik~I~~etg~~I~i~~~g~~~~~~~~V~I~G~~e~v~~A~~~I~~iv~   86 (97)
T 2ctl_A           16 SFKLSVTVDPKYHPKIIGRKGAVITQIRLEHDVNIQFPDKDDGNQPQDQITITGYEKNTEAARDAILRIVG   86 (97)
T ss_dssp             TCEEEEECCTTTHHHHSCSSSCHHHHHHHHHTCEEECCCTTTCSSCSSEEEEESCHHHHHHHHHHHHHHHH
T ss_pred             ceeEEEEECHHHhhhcCCCCchhHHHHHHHHCCEEEecCCCCCCCCccEEEEEeCHHHHHHHHHHHHHHHH
Confidence            468999999999999999999999999999999999998653 2367899999999999999999999875

>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=99.38  E-value=1.1e-12  Score=122.05  Aligned_cols=142  Identities=20%  Similarity=0.198  Sum_probs=101.8

Q ss_pred             EEEEEecCcccceeccCCchHHHHHHHhcCCeEEeeCCCCCCCceEEEEEccCCcccccccccccCCCCcccHHHHHHHH
Q 006943           38 IYRILCPDGVIGSVIGKSGKVINSIRQETRARVKVVDPFPGAKDRVVTIYSHVKDKEDVEVDDEFNDKEPLCAAQDALLK  117 (624)
Q Consensus        38 ~~~ilvp~~~~g~vIGk~G~~I~~i~~etg~~I~v~~~~~~~~er~i~I~G~~~~~~~~~~~~~~~~~~~~~~a~~ai~~  117 (624)
                      .++++||...+|.|||++|++++.|+++++++|.+..     .++.++|+.......                 ..++.+
T Consensus         5 ~~~i~VP~~rvg~liGk~g~~~k~i~e~~g~~i~id~-----~~~~V~i~t~~~t~d-----------------p~~i~K   62 (191)
T 1tua_A            5 RIYVKVKPERLGAVIGPRGEVKAEIMRRTGTVITVDT-----ENSMVIVEPEAEGIP-----------------PVNLMK   62 (191)
T ss_dssp             CEEEECCGGGHHHHHCGGGHHHHHHHHHHTEEEEEET-----TTTEEEEEESSTTSC-----------------HHHHHH
T ss_pred             ceEEECCHHHhhHHHhcCHhHHHHHHHHHCcEEEEEc-----CCCeEEEEeCCCCCC-----------------HHHHHH
Confidence            3689999999999999999999999999999999964     577888885433211                 123444


Q ss_pred             HHHHHHHhhhccC--CCcccCCCceeEEE-EEe----------ccceeEEEeCCchHHHHHHHhcCCeEEEccCCCCCCC
Q 006943          118 VHAAIANAVANAT--DNDKKRKEKEECQI-LVP----------SSQSANIIGKAGATIKRLRSKTRTSIKVTPKDASEPT  184 (624)
Q Consensus       118 v~~~i~~~~~~~~--~~~~~~~~~~~~~l-lvp----------~~~~g~iIGk~G~~Ik~I~~~sga~I~i~~~~~~~~~  184 (624)
                      +.+.|.+-....+  +...-..+...+.+ -++          ....|+||||+|.+++.|++.|||+|.|..       
T Consensus        63 A~dlI~ai~rgf~~e~A~~Ll~Dd~~~e~i~i~~~~~~~~~~~~r~~GrIIGk~G~tik~iE~~Tg~~I~v~~-------  135 (191)
T 1tua_A           63 AAEVVKAISLGFPPEKAFRLLEEDQILVVVDLKQVVGDSQNHLKRIKGRIIGEGGRARRTIEEMTDTYINVGE-------  135 (191)
T ss_dssp             HHHHHHHHHHTCCHHHHGGGGSTTEEEEEEETHHHHTTCHHHHHHHHHHHHCGGGHHHHHHHHHHTCEEEECS-------
T ss_pred             HHHHHHHHHcCCCHHHhhhcccCcceeEEEEcccccccCchhHHHHhhheeCCCccHHHHHHHHHCceEEEcC-------
Confidence            4444322111110  00111122233332 233          236899999999999999999999999853       


Q ss_pred             CcccccCCceEEEecCHHHHHHHHHHHHHHHh
Q 006943          185 HSCAMEFDNFVLISGESEAVKKALFAISAIMY  216 (624)
Q Consensus       185 ~~~~~~~~r~V~I~G~~~~V~~A~~~I~~~l~  216 (624)
                              +.|.|.|+.+++..|...|.+++.
T Consensus       136 --------~~v~i~G~~~~i~~Ar~~i~~li~  159 (191)
T 1tua_A          136 --------YEVAIIGDYERAMAAKQAIEMLAE  159 (191)
T ss_dssp             --------SEEEEEEEHHHHHHHHHHHHHHHT
T ss_pred             --------CEEEEEeChHHHHHHHHHHHHHHc
Confidence                    479999999999999999999995

>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=99.38  E-value=6.6e-13  Score=110.13  Aligned_cols=73  Identities=21%  Similarity=0.274  Sum_probs=65.0

Q ss_pred             CCCCCCcEEEEEeccccccceeccCCchHHHHHHHhCCEEEEeCCCCCCCCeEEEEEcCHHHHHHHHHHHHHHHh
Q 006943          548 GGLPPPLTLEVLVPANAVGKVIGKAGSNLANIRKISGATIEMSDSKSSRGDRVALISGTPEQKRAAENLIQAFIM  622 (624)
Q Consensus       548 ~~~~~~~~~~i~VP~~~vg~IIGkgG~~I~~I~~~sGa~I~i~~~~~~~~~r~v~I~Gt~e~v~~A~~lI~~~i~  622 (624)
                      ..+...++.+|.||.+++|.|||+||.+|++|+++|||+|+|++..+  .++.|+|+|++++++.|+.+|++++.
T Consensus        11 ~~l~~~~t~~i~Ip~~~ig~IIG~gG~~Ik~I~~etg~~I~i~~~~~--~~~~V~I~G~~e~v~~A~~~I~~i~~   83 (94)
T 2cte_A           11 ARLQTQASATVAIPKEHHRFVIGKNGEKLQDLELKTATKIQIPRPDD--PSNQIKITGTKEGIEKARHEVLLISA   83 (94)
T ss_dssp             CCCCSCEEEEEECCTTTHHHHHCSSSCHHHHHHHHTTCCCBCCCTTS--SCCEEEEEECHHHHHHHHHHHHHHHH
T ss_pred             HHhCCceEEEEEEChHHeeeeECCCChhHHHHHHHHCCEEEeCCCCC--CCCeEEEEECHHHHHHHHHHHHHHhh
Confidence            34556789999999999999999999999999999999999997532  34789999999999999999999875

>2p2r_A Poly(RC)-binding protein 2; protein-DNA complex, RNA and DNA binding protein/DNA complex; 1.60A {Homo sapiens}

Probab=99.36  E-value=3.8e-13  Score=107.18  Aligned_cols=72  Identities=22%  Similarity=0.383  Sum_probs=65.0

Q ss_pred             CceeEEEEEeccceeEEEeCCchHHHHHHHhcCCeEEEccCCCCCCCCcccccCCceEEEecCHHHHHHHHHHHHHHHhh
Q 006943          138 EKEECQILVPSSQSANIIGKAGATIKRLRSKTRTSIKVTPKDASEPTHSCAMEFDNFVLISGESEAVKKALFAISAIMYK  217 (624)
Q Consensus       138 ~~~~~~llvp~~~~g~iIGk~G~~Ik~I~~~sga~I~i~~~~~~~~~~~~~~~~~r~V~I~G~~~~V~~A~~~I~~~l~~  217 (624)
                      ..++++|+||.+++|.||||+|++|++|+++|||+|+|...        ++.+++|.|+|+|++++|.+|+.+|.+++.+
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 QTTSHELTIPNDLIGCIIGRQGAKINEIRQMSGAQIKIANP--------VEGSTDRQVTITGSAASISLAQYLINVRLSS   74 (76)
T ss_dssp             CCEEEEEEEEHHHHHHHHCGGGHHHHHHHHHHCCEEEECCC--------CTTCSEEEEEEEECHHHHHHHHHHHHHHHTT
T ss_pred             CceEEEEEEChHHcceEECCCChHHHHHHHHHCCEEEEcCC--------CCCCCeEEEEEEeCHHHHHHHHHHHHHHHHc
Confidence            46889999999999999999999999999999999999752        2346799999999999999999999999853

>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=99.35  E-value=8.6e-13  Score=106.64  Aligned_cols=73  Identities=23%  Similarity=0.439  Sum_probs=65.5

Q ss_pred             CceeEEEEEeccceeEEEeCCchHHHHHHHhcCCeEEEccCCCCCCCCcccccCCceEEEecCHHHHHHHHHHHHHHHhh
Q 006943          138 EKEECQILVPSSQSANIIGKAGATIKRLRSKTRTSIKVTPKDASEPTHSCAMEFDNFVLISGESEAVKKALFAISAIMYK  217 (624)
Q Consensus       138 ~~~~~~llvp~~~~g~iIGk~G~~Ik~I~~~sga~I~i~~~~~~~~~~~~~~~~~r~V~I~G~~~~V~~A~~~I~~~l~~  217 (624)
                      ..++++|+||.+++|.||||+|++|++|+++|||+|+|...        ++.+++|.|+|+|++++|.+|+.+|.+++.+
T Consensus         5 ~~~~~~i~Vp~~~vg~iIGkgG~~Ik~I~~~tga~I~i~~~--------~~~~~~~~v~I~G~~~~v~~A~~~I~~~i~~   76 (82)
T 1zzk_A            5 PIITTQVTIPKDLAGSIIGKGGQRIKQIRHESGASIKIDEP--------LEGSEDRIITITGTQDQIQNAQYLLQNSVKQ   76 (82)
T ss_dssp             CCEEEEEEEETTTGGGGTCGGGHHHHHHHHHHCCEEEECCT--------TSCSSEEEEEEEECHHHHHHHHHHHHHHHHH
T ss_pred             CeEEEEEEEChHhcCeeECCCchHHHHHHHHHCCEEEEcCC--------CCCCCceEEEEEeCHHHHHHHHHHHHHHHHh
Confidence            46899999999999999999999999999999999999752        2235789999999999999999999999976


Q ss_pred             c
Q 006943          218 F  218 (624)
Q Consensus       218 ~  218 (624)
                      .
T Consensus        77 ~   77 (82)
T 1zzk_A           77 Y   77 (82)
T ss_dssp             H
T ss_pred             c
Confidence            4

>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=99.35  E-value=6.1e-13  Score=106.10  Aligned_cols=73  Identities=26%  Similarity=0.335  Sum_probs=64.3

Q ss_pred             ceeEEEEEeccceeEEEeCCchHHHHHHHhcCCeEEEccCCCCCCCCcccccCCceEEEecCHHHHHHHHHHHHHHHh
Q 006943          139 KEECQILVPSSQSANIIGKAGATIKRLRSKTRTSIKVTPKDASEPTHSCAMEFDNFVLISGESEAVKKALFAISAIMY  216 (624)
Q Consensus       139 ~~~~~llvp~~~~g~iIGk~G~~Ik~I~~~sga~I~i~~~~~~~~~~~~~~~~~r~V~I~G~~~~V~~A~~~I~~~l~  216 (624)
                      ..+++|+||.+++|.||||+|++|++|+++|||+|+|.+.+.     .++.++++.|+|+|++++|.+|+.+|.+++.
T Consensus         2 ~~~~~i~Ip~~~vg~IIGkgG~~Ik~I~~~tga~I~i~~~~~-----~~~~~~~~~v~I~G~~~~v~~A~~~I~~~i~   74 (76)
T 1dtj_A            2 KELVEMAVPENLVGAILGKGGKTLVEYQELTGARIQISKKGE-----FLPGTRNRRVTITGSPAATQAAQYLISQRVT   74 (76)
T ss_dssp             CEEEEEEEETTTHHHHHCSTTHHHHHHHHHHCCEEEECCTTC-----CSTTCCEEEEEEEESHHHHHHHHHHHHHHCC
T ss_pred             ceEEEEEEChHHcceEECCCchHHHHHHHHhCCEEEECcCCC-----CCCCCceeEEEEEeCHHHHHHHHHHHHHHHh
Confidence            367899999999999999999999999999999999987432     2334678999999999999999999999874

>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=99.35  E-value=5.9e-13  Score=107.66  Aligned_cols=74  Identities=22%  Similarity=0.339  Sum_probs=65.1

Q ss_pred             CCceeEEEEEeccceeEEEeCCchHHHHHHHhcCCeEEEccCCCCCCCCcccccCCceEEEecCHHHHHHHHHHHHHHHh
Q 006943          137 KEKEECQILVPSSQSANIIGKAGATIKRLRSKTRTSIKVTPKDASEPTHSCAMEFDNFVLISGESEAVKKALFAISAIMY  216 (624)
Q Consensus       137 ~~~~~~~llvp~~~~g~iIGk~G~~Ik~I~~~sga~I~i~~~~~~~~~~~~~~~~~r~V~I~G~~~~V~~A~~~I~~~l~  216 (624)
                      ...++++|+||.+++|.||||+|++|++|+++|||+|+|...        ++.+++|.|+|+|++++|.+|+.+|.+++.
T Consensus         3 g~~~~~~i~Ip~~~vg~IIGkgG~~Ik~I~~~sga~I~i~~~--------~~~~~~r~v~I~G~~~~v~~A~~~I~~~i~   74 (82)
T 1wvn_A            3 GSQTTHELTIPNNLIGCIIGRQGANINEIRQMSGAQIKIANP--------VEGSSGRQVTITGSAASISLAQYLINARLS   74 (82)
T ss_dssp             TTCEEEEEEEEGGGHHHHHCGGGHHHHHHHHHHCCEEEECCC--------CTTCSEEEEEEEECHHHHHHHHHHHHHHTC
T ss_pred             CCcEEEEEEEchHhccceeCCCchhHHHHHHHhCCEEEEecC--------CCCCCceEEEEEcCHHHHHHHHHHHHHHHH
Confidence            346899999999999999999999999999999999999763        233679999999999999999999999986


Q ss_pred             hc
Q 006943          217 KF  218 (624)
Q Consensus       217 ~~  218 (624)
                      +.
T Consensus        75 ~~   76 (82)
T 1wvn_A           75 SE   76 (82)
T ss_dssp             --
T ss_pred             hh
Confidence            53

>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=99.31  E-value=1.1e-12  Score=107.84  Aligned_cols=75  Identities=24%  Similarity=0.432  Sum_probs=66.8

Q ss_pred             CCceeEEEEEeccceeEEEeCCchHHHHHHHhcCCeEEEccCCCCCCCCcccccCCceEEEecCHHHHHHHHHHHHHHHh
Q 006943          137 KEKEECQILVPSSQSANIIGKAGATIKRLRSKTRTSIKVTPKDASEPTHSCAMEFDNFVLISGESEAVKKALFAISAIMY  216 (624)
Q Consensus       137 ~~~~~~~llvp~~~~g~iIGk~G~~Ik~I~~~sga~I~i~~~~~~~~~~~~~~~~~r~V~I~G~~~~V~~A~~~I~~~l~  216 (624)
                      ...++++|+||.+++|.||||+|++|++|+++|||+|+|...        ++.+++|.|+|+|++++|.+|+.+|.+++.
T Consensus        11 ~~~~~~~i~Ip~~~vg~IIGkgG~~Ik~I~~~tga~I~I~~~--------~~~~~~~~v~I~G~~e~v~~A~~~I~~~i~   82 (89)
T 1j5k_A           11 GPIITTQVTIPKDLAGSIIGKGGQRIKQIRHESGASIKIDEP--------LEGSEDRIITITGTQDQIQNAQYLLQNSVK   82 (89)
T ss_dssp             CCEEEEEEEEEHHHHHHHHCGGGHHHHHHHHHTCCEEEECSC--------CSSSSEEEEEEEEEHHHHHHHHHHHHHHHH
T ss_pred             CCeEEEEEEEChhhcceeECCCCHhHHHHHHHhCCeEEecCC--------CCCCCccEEEEEcCHHHHHHHHHHHHHHHH
Confidence            457899999999999999999999999999999999999752        233678999999999999999999999997


Q ss_pred             hcC
Q 006943          217 KFS  219 (624)
Q Consensus       217 ~~~  219 (624)
                      +.+
T Consensus        83 e~~   85 (89)
T 1j5k_A           83 QYS   85 (89)
T ss_dssp             HHC
T ss_pred             hhh
Confidence            653

>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=99.31  E-value=1.3e-12  Score=106.85  Aligned_cols=74  Identities=26%  Similarity=0.296  Sum_probs=65.4

Q ss_pred             eeEEEEEeccceeEEEeCCchHHHHHHHhcCCeEEEccCCCCCCCCcccccCCceEEEecCHHHHHHHHHHHHHHHhhc
Q 006943          140 EECQILVPSSQSANIIGKAGATIKRLRSKTRTSIKVTPKDASEPTHSCAMEFDNFVLISGESEAVKKALFAISAIMYKF  218 (624)
Q Consensus       140 ~~~~llvp~~~~g~iIGk~G~~Ik~I~~~sga~I~i~~~~~~~~~~~~~~~~~r~V~I~G~~~~V~~A~~~I~~~l~~~  218 (624)
                      ++++|+||.+++|.||||+|++|++|+++|||+|.|...+.     .++.++++.|+|+|++++|.+|+.+|.+++.+.
T Consensus         3 ~t~~i~IP~~~vG~IIGkgG~~Ik~I~~~tga~I~I~~~~~-----~~~g~~~r~v~I~G~~~~v~~A~~~I~~~i~~~   76 (87)
T 1ec6_A            3 ELVEIAVPENLVGAILGKGGKTLVEYQELTGARIQISKKGE-----FLPGTRNRRVTITGSPAATQAAQYLISQRVTYE   76 (87)
T ss_dssp             SEEEEEEEHHHHHHHHCGGGHHHHHHHHHHCCEEEECCTTC-----BSTTSCEEEEEEESSHHHHHHHHHHHHHHHHHH
T ss_pred             eEEEEEEChHHcCeeECCCcHhHHHHHHHhCCEEEEccCCC-----CCCCCCceEEEEEcCHHHHHHHHHHHHHHHhcc
Confidence            67899999999999999999999999999999999986421     234467899999999999999999999998653

>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=99.29  E-value=8.6e-13  Score=106.15  Aligned_cols=70  Identities=27%  Similarity=0.364  Sum_probs=63.2

Q ss_pred             CCCceeEEEEEeccceeEEEeCCchHHHHHHHhcCCeEEEccCCCCCCCCcccccCCceEEEecCHHHHHHHHHHHHHHH
Q 006943          136 RKEKEECQILVPSSQSANIIGKAGATIKRLRSKTRTSIKVTPKDASEPTHSCAMEFDNFVLISGESEAVKKALFAISAIM  215 (624)
Q Consensus       136 ~~~~~~~~llvp~~~~g~iIGk~G~~Ik~I~~~sga~I~i~~~~~~~~~~~~~~~~~r~V~I~G~~~~V~~A~~~I~~~l  215 (624)
                      ....++++|.||.+++|+||||+|++||+|+++|||+|+|++.           .++++|+|+|.+++|++|+.+|.+++
T Consensus         6 ~~~~~~~~i~VP~~~vG~IIGkgG~tIk~Iqe~Tga~I~I~~~-----------~~~~~v~ItG~~e~v~~A~~~I~~~i   74 (83)
T 2dgr_A            6 SGGQTTIQVRVPYRVVGLVVGPKGATIKRIQQRTHTYIVTPGR-----------DKEPVFAVTGMPENVDRAREEIEAHI   74 (83)
T ss_dssp             SCCSEEEEEECCHHHHHHHHTTTTSSHHHHHHHTTCEEECCCS-----------SSCCEEEEEECTTTHHHHHHHHHHHH
T ss_pred             CCCceEEEEEeChHHeeeeECCCchHHHHHHHHhCCeEEecCC-----------CCCCeEEEEcCHHHHHHHHHHHHHHH
Confidence            3456899999999999999999999999999999999999753           24689999999999999999999987


Q ss_pred             h
Q 006943          216 Y  216 (624)
Q Consensus       216 ~  216 (624)
                      .
T Consensus        75 ~   75 (83)
T 2dgr_A           75 T   75 (83)
T ss_dssp             H
T ss_pred             h
Confidence            4

>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=99.28  E-value=3.5e-12  Score=105.37  Aligned_cols=74  Identities=22%  Similarity=0.332  Sum_probs=66.2

Q ss_pred             CCceeEEEEEeccceeEEEeCCchHHHHHHHhcCCeEEEccCCCCCCCCcccccCCceEEEecCHHHHHHHHHHHHHHHh
Q 006943          137 KEKEECQILVPSSQSANIIGKAGATIKRLRSKTRTSIKVTPKDASEPTHSCAMEFDNFVLISGESEAVKKALFAISAIMY  216 (624)
Q Consensus       137 ~~~~~~~llvp~~~~g~iIGk~G~~Ik~I~~~sga~I~i~~~~~~~~~~~~~~~~~r~V~I~G~~~~V~~A~~~I~~~l~  216 (624)
                      ...++.+|+||.+++|.||||+|++|++|+++|||+|+|....        +...+|.|+|+|++++|.+|+.+|.+++.
T Consensus        12 ~~~~~~~i~Ip~~~vG~IIGkgG~~Ik~I~~~tga~I~I~~~~--------~g~~~r~v~I~G~~e~v~~A~~~I~~~i~   83 (92)
T 1x4n_A           12 RSVMTEEYKVPDGMVGFIIGRGGEQISRIQQESGCKIQIAPDS--------GGLPERSCMLTGTPESVQSAKRLLDQIVE   83 (92)
T ss_dssp             CCCEEEEEEEEHHHHHHHHCSSSHHHHHHHHHSCCEEEECSCC--------TTCSEEEEEEEECHHHHHHHHHHHHHHHH
T ss_pred             CCCEEEEEEEChHHcceeECCCchHHHHHHHHhCCEEEEcCCC--------CCCCccEEEEEeCHHHHHHHHHHHHHHHH
Confidence            4568899999999999999999999999999999999998642        12468999999999999999999999997


Q ss_pred             hc
Q 006943          217 KF  218 (624)
Q Consensus       217 ~~  218 (624)
                      +.
T Consensus        84 ~~   85 (92)
T 1x4n_A           84 KG   85 (92)
T ss_dssp             HT
T ss_pred             hc
Confidence            64

>2opv_A KHSRP protein; KH domain, RNA binding protein, KSRP; NMR {Homo sapiens}

Probab=99.28  E-value=5.2e-12  Score=102.78  Aligned_cols=73  Identities=22%  Similarity=0.364  Sum_probs=64.4

Q ss_pred             CceeEEEEEeccceeEEEeCCchHHHHHHHhcCCeEEEccCCCCCCCCcccccCCceEEEecCHHHHHHHHHHHHHHHh
Q 006943          138 EKEECQILVPSSQSANIIGKAGATIKRLRSKTRTSIKVTPKDASEPTHSCAMEFDNFVLISGESEAVKKALFAISAIMY  216 (624)
Q Consensus       138 ~~~~~~llvp~~~~g~iIGk~G~~Ik~I~~~sga~I~i~~~~~~~~~~~~~~~~~r~V~I~G~~~~V~~A~~~I~~~l~  216 (624)
                      ...+.+|.||.+++|.||||+|++|++|+++|||+|.|.....      .+.+.+|.|+|+|++++|.+|+.+|.++++
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 NGTVQEIMIPAGKAGLVIGKGGETIKQLQERAGVKMILIQDGS------QNTNVDKPLRIIGDPYKVQQACEMVMDILR   84 (85)
T ss_dssp             SSEEEEEEECTTTHHHHHTTTTHHHHHHHHHHTCEEEECSSSC------SSTTSCEEEEEEECHHHHHHHHHHHHHHHT
T ss_pred             CCEEEEEEeChhheeeeECCCCHHHHHHHHHHCCEEEEcCCCC------CCCCCceEEEEEeCHHHHHHHHHHHHHHhc
Confidence            4577899999999999999999999999999999999987432      123678999999999999999999999875

>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=99.27  E-value=4.7e-12  Score=106.80  Aligned_cols=67  Identities=21%  Similarity=0.261  Sum_probs=61.5

Q ss_pred             cEEEEEeccccccceeccCCchHHHHHHHhCCEEEEeCCCCCCCCeEEEEEcCHHHHHHHHHHHHHHHh
Q 006943          554 LTLEVLVPANAVGKVIGKAGSNLANIRKISGATIEMSDSKSSRGDRVALISGTPEQKRAAENLIQAFIM  622 (624)
Q Consensus       554 ~~~~i~VP~~~vg~IIGkgG~~I~~I~~~sGa~I~i~~~~~~~~~r~v~I~Gt~e~v~~A~~lI~~~i~  622 (624)
                      .+.+|.||.+++|.|||+||++|++|+++|||+|+|+++..  ..+.|+|+|++++++.|+.+|++++.
T Consensus        17 ~~~~i~Ip~~~ig~IIG~gG~~Ir~I~eetg~~I~I~~~g~--~~~~V~I~G~~e~v~~A~~~I~~i~~   83 (104)
T 2ctk_A           17 VTIEVEVPFDLHRYVIGQKGSGIRKMMDEFEVNIHVPAPEL--QSDIIAITGLAANLDRAKAGLLERVK   83 (104)
T ss_dssp             EEEEEECCHHHHHHHHCSSSHHHHHHHHHTCCEEECCCTTT--TCCEEEEEECHHHHHHHHHHHHHHHH
T ss_pred             EEEEEEEChHHccceeCCCchHHHHHHHHHCCEEEecCCCC--CcceEEEEcCHHHHHHHHHHHHHHHh
Confidence            58999999999999999999999999999999999997643  34689999999999999999999875

>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=99.26  E-value=2.6e-12  Score=106.58  Aligned_cols=76  Identities=21%  Similarity=0.349  Sum_probs=66.8

Q ss_pred             CCCceeEEEEEeccceeEEEeCCchHHHHHHHhcCCeEEEccCCCCCCCCcccccCCceEEEecCHHHHHHHHHHHHHHH
Q 006943          136 RKEKEECQILVPSSQSANIIGKAGATIKRLRSKTRTSIKVTPKDASEPTHSCAMEFDNFVLISGESEAVKKALFAISAIM  215 (624)
Q Consensus       136 ~~~~~~~~llvp~~~~g~iIGk~G~~Ik~I~~~sga~I~i~~~~~~~~~~~~~~~~~r~V~I~G~~~~V~~A~~~I~~~l  215 (624)
                      ....++.+|+||.+++|.||||+|++|++|+++|||+|+|......      ...++|.|+|+|++++|.+|+.+|.+++
T Consensus        11 ~p~~~~~~i~Ip~~~vG~IIGkgG~~Ik~I~~~tga~I~I~~~~~~------~~~~~r~v~I~G~~~~v~~A~~~I~~~i   84 (94)
T 1x4m_A           11 GPGNAVQEIMIPASKAGLVIGKGGETIKQLQERAGVKMVMIQDGPQ------NTGADKPLRITGDPYKVQQAKEMVLELI   84 (94)
T ss_dssp             CCCCEEEEEEECHHHHHHHSCSSSSHHHHHHHHHTSEEEECCSCCC------SSCSCEEEEEEECTTTHHHHHHHHHHHH
T ss_pred             CCCcEEEEEEEChhhcceEECCCCHHHHHHHHHHCCeEEecCCCCC------CCCCceEEEEEeCHHHHHHHHHHHHHHH
Confidence            3467899999999999999999999999999999999999864321      1247899999999999999999999999


Q ss_pred             hh
Q 006943          216 YK  217 (624)
Q Consensus       216 ~~  217 (624)
                      .+
T Consensus        85 ~~   86 (94)
T 1x4m_A           85 RD   86 (94)
T ss_dssp             CC
T ss_pred             hc
Confidence            65

>2hh2_A KH-type splicing regulatory protein; KH-RNA binding domain, RNA binding protein; NMR {Homo sapiens}

Probab=99.25  E-value=4.4e-12  Score=107.80  Aligned_cols=72  Identities=15%  Similarity=0.279  Sum_probs=63.3

Q ss_pred             eEEEEEeccceeEEEeCCchHHHHHHHhcCCeEEEccCCCCCCCCcccccCCceEEEecCHHHHHHHHHHHHHHHhh
Q 006943          141 ECQILVPSSQSANIIGKAGATIKRLRSKTRTSIKVTPKDASEPTHSCAMEFDNFVLISGESEAVKKALFAISAIMYK  217 (624)
Q Consensus       141 ~~~llvp~~~~g~iIGk~G~~Ik~I~~~sga~I~i~~~~~~~~~~~~~~~~~r~V~I~G~~~~V~~A~~~I~~~l~~  217 (624)
                      +++|+||.+++|.||||+|++|++|+++|||+|+|......     ....++++|+|+|+.++|.+|+.+|.+++.+
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 EMTFSIPTHKCGLVIGRGGENVKAINQQTGAFVEISRQLPP-----NGDPNFKLFIIRGSPQQIDHAKQLIEEKIEG   79 (107)
T ss_dssp             CEEEEEEGGGTTTTSTTTTCHHHHHHHHSSSEEEECCCCCT-----TCCTTEEEEEEESCHHHHHHHHHHHHHHSCS
T ss_pred             eEEEEECHHHcCccCCCCcHHHHHHHHHhCCEEEEcCccCC-----CCCCCceEEEEECCHHHHHHHHHHHHHHHhc
Confidence            78999999999999999999999999999999999874321     1224679999999999999999999999865

>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=99.25  E-value=1.5e-11  Score=101.67  Aligned_cols=73  Identities=21%  Similarity=0.303  Sum_probs=65.5

Q ss_pred             CCCCCCcEEEEEeccccccceeccCCchHHHHHHHh-CCEEEEeCCCCCCCCeEEEEEcCHHHHHHHHHHHHHHHh
Q 006943          548 GGLPPPLTLEVLVPANAVGKVIGKAGSNLANIRKIS-GATIEMSDSKSSRGDRVALISGTPEQKRAAENLIQAFIM  622 (624)
Q Consensus       548 ~~~~~~~~~~i~VP~~~vg~IIGkgG~~I~~I~~~s-Ga~I~i~~~~~~~~~r~v~I~Gt~e~v~~A~~lI~~~i~  622 (624)
                      ..+.+.++.+|.||.++++.|||++|.+|++|+++| ||+|.|+++.  ...+.|+|+|+.+++++|+.+|++++.
T Consensus        11 ~e~~~~vt~~i~Ip~~~i~~iIG~gGk~Ir~I~eetggv~I~i~~~g--~~~~~V~I~G~~~~v~~A~~~I~~iv~   84 (95)
T 2ctj_A           11 KDLANIAEVEVSIPAKLHNSLIGTKGRLIRSIMEECGGVHIHFPVEG--SGSDTVVIRGPSSDVEKAKKQLLHLAE   84 (95)
T ss_dssp             CCCCSSCCEEEECCHHHHHHHHCSSSHHHHHHHHHHTSCEEECCCTT--TTCCEEEEESCHHHHHHHHHHHHHHHH
T ss_pred             HHHhhcEEEEEEECHHHHhhhCCCCchhHHHHHHHcCCCEEEeCCCC--CCcceEEEEcCHHHHHHHHHHHHHHHh
Confidence            445667899999999999999999999999999999 9999998763  345689999999999999999999875

>2hh3_A KH-type splicing regulatory protein; KH-RNA binding domain, RNA binding protein; NMR {Homo sapiens}

Probab=99.24  E-value=6.1e-12  Score=106.30  Aligned_cols=72  Identities=18%  Similarity=0.348  Sum_probs=63.7

Q ss_pred             eeEEEEEeccceeEEEeCCchHHHHHHHhcCCeEEEccCCCCCCCCcccccCCceEEEecCHHHHHHHHHHHHHHHhhcC
Q 006943          140 EECQILVPSSQSANIIGKAGATIKRLRSKTRTSIKVTPKDASEPTHSCAMEFDNFVLISGESEAVKKALFAISAIMYKFS  219 (624)
Q Consensus       140 ~~~~llvp~~~~g~iIGk~G~~Ik~I~~~sga~I~i~~~~~~~~~~~~~~~~~r~V~I~G~~~~V~~A~~~I~~~l~~~~  219 (624)
                      .+++|+||.++++.||||+|++|++|+++|||+|+|.++..        ...+|+|+|+|++++|.+|+.+|.+++.+..
T Consensus        11 ~~~~i~Ip~~~iG~IIGkgG~~Ik~I~~~TGakI~I~~~~~--------~~~er~V~I~G~~e~v~~A~~~I~~ii~~~~   82 (106)
T 2hh3_A           11 GGIDVPVPRHSVGVVIGRSGEMIKKIQNDAGVRIQFKQDDG--------TGPEKIAHIMGPPDRCEHAARIINDLLQSLR   82 (106)
T ss_dssp             -CEEEEEETTTHHHHHTTTTHHHHHHHHHHTCEEEECSSCS--------SSSEEEEEEESSHHHHHHHHHHHHHHHHHHC
T ss_pred             eEEEEEECHHHcCccCCCCcHHHHHHHHHHCcEEEEecCCC--------CCceeEEEEEeCHHHHHHHHHHHHHHHhccc
Confidence            47899999999999999999999999999999999986431        2468999999999999999999999997643

>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=99.22  E-value=8.1e-12  Score=103.46  Aligned_cols=77  Identities=19%  Similarity=0.277  Sum_probs=67.5

Q ss_pred             cCCCceeEEEEEeccceeEEEeCCchHHHHHHHhcCCeEEEccCCCCCCCCcccccCCceEEEecCHHHHHHHHHHHHHH
Q 006943          135 KRKEKEECQILVPSSQSANIIGKAGATIKRLRSKTRTSIKVTPKDASEPTHSCAMEFDNFVLISGESEAVKKALFAISAI  214 (624)
Q Consensus       135 ~~~~~~~~~llvp~~~~g~iIGk~G~~Ik~I~~~sga~I~i~~~~~~~~~~~~~~~~~r~V~I~G~~~~V~~A~~~I~~~  214 (624)
                      ..+..++..|.||..+++.|||++|++|++|+++|||+|+|+....         .+++.|+|+|.+++|.+|+.+|..+
T Consensus        12 ~l~~~vt~~i~Ip~~~ig~IIG~gG~~Ir~I~e~tg~~I~i~~~g~---------~~~~~V~I~G~~e~v~~A~~~I~~i   82 (95)
T 2ctm_A           12 ELEQMVSEDVPLDHRVHARIIGARGKAIRKIMDEFKVDIRFPQSGA---------PDPNCVTVTGLPENVEEAIDHILNL   82 (95)
T ss_dssp             CTTTCCCEEEECCTTTHHHHHCSSSCHHHHHHHHHTCEEECCCTTC---------SCTTEEEEESCHHHHHHHHHHHHHH
T ss_pred             hhcccEEEEEEECHHHccccCCCCcchHHHHHHHHCCeEEecCCCC---------CCCcEEEEEcCHHHHHHHHHHHHHH
Confidence            3566799999999999999999999999999999999999975321         2468999999999999999999999


Q ss_pred             HhhcCC
Q 006943          215 MYKFSP  220 (624)
Q Consensus       215 l~~~~~  220 (624)
                      +.++..
T Consensus        83 ~~e~~~   88 (95)
T 2ctm_A           83 EEEYLA   88 (95)
T ss_dssp             HHHHHT
T ss_pred             HHHHHH
Confidence            877543

>1vig_A Vigilin; RNA-binding protein, ribonucleoprotein; NMR {Homo sapiens} SCOP: d.51.1.1 PDB: 1vih_A

Probab=99.21  E-value=6e-12  Score=98.50  Aligned_cols=68  Identities=24%  Similarity=0.474  Sum_probs=60.2

Q ss_pred             CceeEEEEEeccceeEEEeCCchHHHHHHHhcCCeEEEccCCCCCCCCcccccCCceEEEecCHHHHHHHHHHHHHHH
Q 006943          138 EKEECQILVPSSQSANIIGKAGATIKRLRSKTRTSIKVTPKDASEPTHSCAMEFDNFVLISGESEAVKKALFAISAIM  215 (624)
Q Consensus       138 ~~~~~~llvp~~~~g~iIGk~G~~Ik~I~~~sga~I~i~~~~~~~~~~~~~~~~~r~V~I~G~~~~V~~A~~~I~~~l  215 (624)
                      ...+..|.||..+++.|||++|++|++|+++|||+|+|+..+          ..++.|+|+|+.++|.+|+.+|..++
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            356788999999999999999999999999999999997632          24689999999999999999998754

>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=99.19  E-value=9.5e-12  Score=103.11  Aligned_cols=74  Identities=24%  Similarity=0.386  Sum_probs=65.5

Q ss_pred             CCCceeEEEEEeccceeEEEeCCchHHHHHHHhcCCeEEEccCCCCCCCCcccccCCceEEEecCHHHHHHHHHHHHHHH
Q 006943          136 RKEKEECQILVPSSQSANIIGKAGATIKRLRSKTRTSIKVTPKDASEPTHSCAMEFDNFVLISGESEAVKKALFAISAIM  215 (624)
Q Consensus       136 ~~~~~~~~llvp~~~~g~iIGk~G~~Ik~I~~~sga~I~i~~~~~~~~~~~~~~~~~r~V~I~G~~~~V~~A~~~I~~~l  215 (624)
                      ....++..|.||..++|.|||++|++|++|+++|||+|+|+..+          ..++.|+|+|++++|.+|+.+|..++
T Consensus        13 l~~~~t~~i~Ip~~~ig~IIG~gG~~Ik~I~~etg~~I~i~~~~----------~~~~~V~I~G~~e~v~~A~~~I~~i~   82 (94)
T 2cte_A           13 LQTQASATVAIPKEHHRFVIGKNGEKLQDLELKTATKIQIPRPD----------DPSNQIKITGTKEGIEKARHEVLLIS   82 (94)
T ss_dssp             CCSCEEEEEECCTTTHHHHHCSSSCHHHHHHHHTTCCCBCCCTT----------SSCCEEEEEECHHHHHHHHHHHHHHH
T ss_pred             hCCceEEEEEEChHHeeeeECCCChhHHHHHHHHCCEEEeCCCC----------CCCCeEEEEECHHHHHHHHHHHHHHh
Confidence            45578999999999999999999999999999999999997532          23578999999999999999999998


Q ss_pred             hhcC
Q 006943          216 YKFS  219 (624)
Q Consensus       216 ~~~~  219 (624)
                      .+..
T Consensus        83 ~~~~   86 (94)
T 2cte_A           83 AEQD   86 (94)
T ss_dssp             HHHH
T ss_pred             hccc
Confidence            7643

>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=99.19  E-value=1.9e-11  Score=103.46  Aligned_cols=77  Identities=25%  Similarity=0.350  Sum_probs=66.6

Q ss_pred             CCcEEEEEEecCCeeeEEEcCCCchHHHHHHhcCceEEEeCCCCCCCCCCCCcEEEEEeehHHHHHHHHHHHHHHhhcc
Q 006943          386 DDTVTIRLLVSSKVIGCIIGKSGSIINEIRKRTKADVRISKGDKPKCADANDELVEVVGEVGSVRDALVQIILRLRDDA  464 (624)
Q Consensus       386 ~~~~~~~l~vp~~~~g~iIGk~G~~Ik~I~~~tga~I~i~~~~~p~~~~~~~~~v~I~G~~~~v~~A~~~I~~~l~e~~  464 (624)
                      ..+++.+|.||.+++|.|||++|++|++|+++|||+|+|.+...+.  ...++.|+|+|+.+++.+|+.+|.+.+.+..
T Consensus        12 ~ap~~~~i~Ip~~~ig~IIGkgG~~Ik~I~~~tga~I~I~~~~~~~--~~~~~~V~I~G~~~~v~~A~~~I~~~i~e~~   88 (104)
T 1we8_A           12 NTPVFEQLSVPQRSVGRIIGRGGETIRSICKASGAKITCDKESEGT--LLLSRLIKISGTQKEVAAAKHLILEKVSEDE   88 (104)
T ss_dssp             SCEEEEEEEEETTTHHHHHTTTSHHHHHHHHHHCCEEEECCSSCCS--SSSEEEEEEEEEHHHHHHHHHHHHHHHHHHH
T ss_pred             CCCEEEEEEEChhheeeeECCCCHHHHHHHHHHCCEEEEecCCCCC--CCCcceEEEEcCHHHHHHHHHHHHHHHhhCh
Confidence            3567899999999999999999999999999999999998654321  2358999999999999999999999887653

>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=99.16  E-value=3.1e-11  Score=100.41  Aligned_cols=73  Identities=18%  Similarity=0.326  Sum_probs=63.7

Q ss_pred             CcEEEEEEecCCeeeEEEcCCCchHHHHHHhcCceEEEeCCCCCCCCCCCCcEEEEEeehHHHHHHHHHHHHHHhh
Q 006943          387 DTVTIRLLVSSKVIGCIIGKSGSIINEIRKRTKADVRISKGDKPKCADANDELVEVVGEVGSVRDALVQIILRLRD  462 (624)
Q Consensus       387 ~~~~~~l~vp~~~~g~iIGk~G~~Ik~I~~~tga~I~i~~~~~p~~~~~~~~~v~I~G~~~~v~~A~~~I~~~l~e  462 (624)
                      ..+++.|.||..+|+.|||++|++|++|+++|||+|+|+++..|   ...++.|+|+|+.+++.+|+.+|...+.+
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 RSFKLSVTVDPKYHPKIIGRKGAVITQIRLEHDVNIQFPDKDDG---NQPQDQITITGYEKNTEAARDAILRIVGE   87 (97)
T ss_dssp             TTCEEEEECCTTTHHHHSCSSSCHHHHHHHHHTCEEECCCTTTC---SSCSSEEEEESCHHHHHHHHHHHHHHHHH
T ss_pred             cceeEEEEECHHHhhhcCCCCchhHHHHHHHHCCEEEecCCCCC---CCCccEEEEEeCHHHHHHHHHHHHHHHHH
Confidence            34789999999999999999999999999999999999875543   23678999999999999999988876654

>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=99.14  E-value=7.6e-11  Score=98.81  Aligned_cols=64  Identities=27%  Similarity=0.405  Sum_probs=59.2

Q ss_pred             cEEEEEeccccccceeccCCchHHHHHHH-hCCEEEEeCCCCCCCCeEEEEEcCHHHHHHHHHHHHHHHh
Q 006943          554 LTLEVLVPANAVGKVIGKAGSNLANIRKI-SGATIEMSDSKSSRGDRVALISGTPEQKRAAENLIQAFIM  622 (624)
Q Consensus       554 ~~~~i~VP~~~vg~IIGkgG~~I~~I~~~-sGa~I~i~~~~~~~~~r~v~I~Gt~e~v~~A~~lI~~~i~  622 (624)
                      ++.+|.||..++++|||++|++|++|+++ ++++|+|++     .++.|+|+|++++|++|+.+|+.++.
T Consensus        27 ~t~~i~vp~~~h~~IIG~~G~~Ik~i~~~~~~v~I~fp~-----~~~~ItI~G~~~~V~~a~~~I~~~v~   91 (102)
T 2ctf_A           27 TVSSVAAPSWLHRFIIGKKGQNLAKITQQMPKVHIEFTE-----GEDKITLEGPTEDVSVAQEQIEGMVK   91 (102)
T ss_dssp             EEEEEECCSTTHHHHHTTTTCHHHHHHHHCSSSEEEECS-----SSCEEEEEECHHHHHHHHHHHHHHHH
T ss_pred             EEEEEEeCHHHHhhhcCCCCccHHHHHHHcCCcEEEeCC-----CCCEEEEECCHHHHHHHHHHHHHHHH
Confidence            58999999999999999999999999997 599999997     24689999999999999999999875

>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=99.05  E-value=1.2e-10  Score=96.24  Aligned_cols=76  Identities=20%  Similarity=0.269  Sum_probs=67.1

Q ss_pred             ccCCCceeEEEEEeccceeEEEeCCchHHHHHHHhc-CCeEEEccCCCCCCCCcccccCCceEEEecCHHHHHHHHHHHH
Q 006943          134 KKRKEKEECQILVPSSQSANIIGKAGATIKRLRSKT-RTSIKVTPKDASEPTHSCAMEFDNFVLISGESEAVKKALFAIS  212 (624)
Q Consensus       134 ~~~~~~~~~~llvp~~~~g~iIGk~G~~Ik~I~~~s-ga~I~i~~~~~~~~~~~~~~~~~r~V~I~G~~~~V~~A~~~I~  212 (624)
                      +..++.++..|.||..+++.|||++|++|++|+++| ||+|+|+..+          +..+.|+|.|+.++|.+|+.+|.
T Consensus        11 ~e~~~~vt~~i~Ip~~~i~~iIG~gGk~Ir~I~eetggv~I~i~~~g----------~~~~~V~I~G~~~~v~~A~~~I~   80 (95)
T 2ctj_A           11 KDLANIAEVEVSIPAKLHNSLIGTKGRLIRSIMEECGGVHIHFPVEG----------SGSDTVVIRGPSSDVEKAKKQLL   80 (95)
T ss_dssp             CCCCSSCCEEEECCHHHHHHHHCSSSHHHHHHHHHHTSCEEECCCTT----------TTCCEEEEESCHHHHHHHHHHHH
T ss_pred             HHHhhcEEEEEEECHHHHhhhCCCCchhHHHHHHHcCCCEEEeCCCC----------CCcceEEEEcCHHHHHHHHHHHH
Confidence            346778999999999999999999999999999999 9999997532          34578999999999999999999


Q ss_pred             HHHhhcC
Q 006943          213 AIMYKFS  219 (624)
Q Consensus       213 ~~l~~~~  219 (624)
                      .++.+..
T Consensus        81 ~iv~e~e   87 (95)
T 2ctj_A           81 HLAEEKQ   87 (95)
T ss_dssp             HHHHHHS
T ss_pred             HHHhhhh
Confidence            9997643

>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=99.04  E-value=1.2e-10  Score=98.07  Aligned_cols=71  Identities=15%  Similarity=0.290  Sum_probs=62.4

Q ss_pred             ceeEEEEEeccceeEEEeCCchHHHHHHHhcCCeEEEccCCCCCCCCcccccCCceEEEecCHHHHHHHHHHHHHHHhhc
Q 006943          139 KEECQILVPSSQSANIIGKAGATIKRLRSKTRTSIKVTPKDASEPTHSCAMEFDNFVLISGESEAVKKALFAISAIMYKF  218 (624)
Q Consensus       139 ~~~~~llvp~~~~g~iIGk~G~~Ik~I~~~sga~I~i~~~~~~~~~~~~~~~~~r~V~I~G~~~~V~~A~~~I~~~l~~~  218 (624)
                      ..+..|.||..+++.|||++|++|++|+++|||+|+|+..+          ...+.|+|+|+.++|.+|+.+|..++.+.
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            36788999999999999999999999999999999997632          13468999999999999999999988664


Q ss_pred             C
Q 006943          219 S  219 (624)
Q Consensus       219 ~  219 (624)
                      .
T Consensus        86 e   86 (104)
T 2ctk_A           86 Q   86 (104)
T ss_dssp             H
T ss_pred             H
Confidence            3

>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=98.97  E-value=8.5e-10  Score=92.42  Aligned_cols=68  Identities=21%  Similarity=0.257  Sum_probs=59.8

Q ss_pred             CcEEEEEEecCCeeeEEEcCCCchHHHHHHh-cCceEEEeCCCCCCCCCCCCcEEEEEeehHHHHHHHHHHHHHHhhc
Q 006943          387 DTVTIRLLVSSKVIGCIIGKSGSIINEIRKR-TKADVRISKGDKPKCADANDELVEVVGEVGSVRDALVQIILRLRDD  463 (624)
Q Consensus       387 ~~~~~~l~vp~~~~g~iIGk~G~~Ik~I~~~-tga~I~i~~~~~p~~~~~~~~~v~I~G~~~~v~~A~~~I~~~l~e~  463 (624)
                      ..++.+|.||..+|++|||++|++|++|+++ ++++|+|++         .++.|+|+|+++.|.+|..+|...+.+.
T Consensus        25 ~~~t~~i~vp~~~h~~IIG~~G~~Ik~i~~~~~~v~I~fp~---------~~~~ItI~G~~~~V~~a~~~I~~~v~el   93 (102)
T 2ctf_A           25 SFTVSSVAAPSWLHRFIIGKKGQNLAKITQQMPKVHIEFTE---------GEDKITLEGPTEDVSVAQEQIEGMVKDL   93 (102)
T ss_dssp             CCEEEEEECCSTTHHHHHTTTTCHHHHHHHHCSSSEEEECS---------SSCEEEEEECHHHHHHHHHHHHHHHHHH
T ss_pred             CeEEEEEEeCHHHHhhhcCCCCccHHHHHHHcCCcEEEeCC---------CCCEEEEECCHHHHHHHHHHHHHHHHHH
Confidence            3488999999999999999999999999997 499999975         2568999999999999999997777553

>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=98.95  E-value=4.6e-10  Score=90.70  Aligned_cols=62  Identities=27%  Similarity=0.483  Sum_probs=56.6

Q ss_pred             CcEEEEEeccccccceeccCCchHHHHHHHhCCE-EEEeCCCCCCCCeEEEEEc-CHHHHHHHHHHHHH
Q 006943          553 PLTLEVLVPANAVGKVIGKAGSNLANIRKISGAT-IEMSDSKSSRGDRVALISG-TPEQKRAAENLIQA  619 (624)
Q Consensus       553 ~~~~~i~VP~~~vg~IIGkgG~~I~~I~~~sGa~-I~i~~~~~~~~~r~v~I~G-t~e~v~~A~~lI~~  619 (624)
                      .+..++.||.+++|.|||++|.+|++|+++|||+ |.|.++     +..|+|.| +.+++++|+.+|+.
T Consensus        14 ~~i~~i~I~~dkIg~vIG~gGk~Ik~I~e~tGv~~IdI~ed-----dG~V~I~g~~~ea~~~A~~~I~~   77 (91)
T 2cpq_A           14 AFHEEFVVREDLMGLAIGTHGSNIQQARKVPGVTAIELDED-----TGTFRIYGESADAVKKARGFLEF   77 (91)
T ss_dssp             SEEEEEECCHHHHHHHHTTTTHHHHHHHTSTTEEEEEEETT-----TTEEEEEESSHHHHHHHHHHHSC
T ss_pred             ceEEEEEEChHHhhhhcCCCcHHHHHHHHHhCCeEEEEEcC-----CCEEEEEECCHHHHHHHHHHHHh
Confidence            4689999999999999999999999999999998 999852     36799999 89999999999964

>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=98.68  E-value=3.8e-08  Score=86.02  Aligned_cols=71  Identities=28%  Similarity=0.388  Sum_probs=60.0

Q ss_pred             CCcEEEEEeccc------cccceeccCCchHHHHHHHhCCEEEEeCCCC----------------CCCCeEEEEEc-CHH
Q 006943          552 PPLTLEVLVPAN------AVGKVIGKAGSNLANIRKISGATIEMSDSKS----------------SRGDRVALISG-TPE  608 (624)
Q Consensus       552 ~~~~~~i~VP~~------~vg~IIGkgG~~I~~I~~~sGa~I~i~~~~~----------------~~~~r~v~I~G-t~e  608 (624)
                      ..++.+|.||.+      ++|.|||++|.+||+|+++|||+|.|.....                ...+-.|.|++ +.+
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            456899999988      8899999999999999999999999986321                11245788999 689


Q ss_pred             HHHHHHHHHHHHHh
Q 006943          609 QKRAAENLIQAFIM  622 (624)
Q Consensus       609 ~v~~A~~lI~~~i~  622 (624)
                      .++.|..+|+.++.
T Consensus        85 ~~~~A~~~I~~ll~   98 (131)
T 1k1g_A           85 NVKKAVEQIRNILK   98 (131)
T ss_dssp             HHHHHHHHHHHHHT
T ss_pred             HHHHHHHHHHHHHh
Confidence            99999999999985

>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=98.65  E-value=1.5e-08  Score=81.85  Aligned_cols=69  Identities=22%  Similarity=0.213  Sum_probs=59.5

Q ss_pred             cccCCCceeEEEEEeccceeEEEeCCchHHHHHHHhcCCe-EEEccCCCCCCCCcccccCCceEEEec-CHHHHHHHHHH
Q 006943          133 DKKRKEKEECQILVPSSQSANIIGKAGATIKRLRSKTRTS-IKVTPKDASEPTHSCAMEFDNFVLISG-ESEAVKKALFA  210 (624)
Q Consensus       133 ~~~~~~~~~~~llvp~~~~g~iIGk~G~~Ik~I~~~sga~-I~i~~~~~~~~~~~~~~~~~r~V~I~G-~~~~V~~A~~~  210 (624)
                      .+.....+...|.||...++.+||++|++|++|+++|||+ |.|..             ++..|+|.| +.+++.+|+.+
T Consensus         8 ~~~~~~~~i~~i~I~~dkIg~vIG~gGk~Ik~I~e~tGv~~IdI~e-------------ddG~V~I~g~~~ea~~~A~~~   74 (91)
T 2cpq_A            8 TKQLAAAFHEEFVVREDLMGLAIGTHGSNIQQARKVPGVTAIELDE-------------DTGTFRIYGESADAVKKARGF   74 (91)
T ss_dssp             CSSSSCSEEEEEECCHHHHHHHHTTTTHHHHHHHTSTTEEEEEEET-------------TTTEEEEEESSHHHHHHHHHH
T ss_pred             hhhccCceEEEEEEChHHhhhhcCCCcHHHHHHHHHhCCeEEEEEc-------------CCCEEEEEECCHHHHHHHHHH
Confidence            3455667888999999999999999999999999999998 99952             358899999 79999999987


Q ss_pred             HHHH
Q 006943          211 ISAI  214 (624)
Q Consensus       211 I~~~  214 (624)
                      |..+
T Consensus        75 I~~i   78 (91)
T 2cpq_A           75 LEFV   78 (91)
T ss_dssp             HSCC
T ss_pred             HHhh
Confidence            7543

>2yqr_A KIAA0907 protein; structure genomics, KH domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=98.62  E-value=1.2e-07  Score=81.11  Aligned_cols=70  Identities=24%  Similarity=0.242  Sum_probs=55.7

Q ss_pred             cEEEEEeccc-------cccceeccCCchHHHHHHHhCCEEEEeCCCCC----------CCCeEEEEEc-CHHHHHHHHH
Q 006943          554 LTLEVLVPAN-------AVGKVIGKAGSNLANIRKISGATIEMSDSKSS----------RGDRVALISG-TPEQKRAAEN  615 (624)
Q Consensus       554 ~~~~i~VP~~-------~vg~IIGkgG~~I~~I~~~sGa~I~i~~~~~~----------~~~r~v~I~G-t~e~v~~A~~  615 (624)
                      .+.+|.||-+       ++|.|||++|.+|++|+++|||+|.|......          ..+-.|.|++ +++++++|+.
T Consensus        12 ~~~ki~ip~~~~~p~fn~ig~IIGpgG~tiK~I~~eTG~kI~I~G~gS~~~e~~~~~e~~e~l~V~I~a~~~e~i~~A~~   91 (119)
T 2yqr_A           12 VQDKLFVGLEHAVPTFNVKEKVEGPGCSYLQHIQIETGAKVFLRGKGSGCIEPASGREAFEPMYIYISHPKPEGLAAAKK   91 (119)
T ss_dssp             EEEEEECCCTTSCTTTCHHHHHSCGGGHHHHHHHHHHCCEEEEESBTTTCCCTTTSSCCSSBCEEEEEESSHHHHHHHHH
T ss_pred             EEEEEEcCCccCCCCCCeeeeEECCCChHHHHHHHHHCCEEEEecCCccccccccccccCCCcEEEEEeCCHHHHHHHHH
Confidence            4677877765       78999999999999999999999999743210          1233577775 6999999999


Q ss_pred             HHHHHHhh
Q 006943          616 LIQAFIMA  623 (624)
Q Consensus       616 lI~~~i~~  623 (624)
                      ||++++..
T Consensus        92 ~Ie~Ll~~   99 (119)
T 2yqr_A           92 LCENLLQT   99 (119)
T ss_dssp             HHHHHHHH
T ss_pred             HHHHHhhc
Confidence            99999863

>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=98.36  E-value=6e-07  Score=78.41  Aligned_cols=80  Identities=20%  Similarity=0.286  Sum_probs=62.2

Q ss_pred             CceeEEEEEecc------ceeEEEeCCchHHHHHHHhcCCeEEEccCCCCCCC--------CcccccCCceEEEecC-HH
Q 006943          138 EKEECQILVPSS------QSANIIGKAGATIKRLRSKTRTSIKVTPKDASEPT--------HSCAMEFDNFVLISGE-SE  202 (624)
Q Consensus       138 ~~~~~~llvp~~------~~g~iIGk~G~~Ik~I~~~sga~I~i~~~~~~~~~--------~~~~~~~~r~V~I~G~-~~  202 (624)
                      ..++.+|.||..      ++|.|||++|.+||+|+++|||+|.|..+......        +......+-.|.|++. .+
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            357889999988      78899999999999999999999999875321100        0001123557889995 79


Q ss_pred             HHHHHHHHHHHHHhh
Q 006943          203 AVKKALFAISAIMYK  217 (624)
Q Consensus       203 ~V~~A~~~I~~~l~~  217 (624)
                      ++.+|+.+|..+|.+
T Consensus        85 ~~~~A~~~I~~ll~~   99 (131)
T 1k1g_A           85 NVKKAVEQIRNILKQ   99 (131)
T ss_dssp             HHHHHHHHHHHHHTT
T ss_pred             HHHHHHHHHHHHHhc
Confidence            999999999999965

>2yqr_A KIAA0907 protein; structure genomics, KH domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=98.30  E-value=6.1e-07  Score=76.70  Aligned_cols=80  Identities=10%  Similarity=0.074  Sum_probs=59.2

Q ss_pred             ceeEEEEEecc-------ceeEEEeCCchHHHHHHHhcCCeEEEccCCCCCCC--CcccccCCceEEEecC-HHHHHHHH
Q 006943          139 KEECQILVPSS-------QSANIIGKAGATIKRLRSKTRTSIKVTPKDASEPT--HSCAMEFDNFVLISGE-SEAVKKAL  208 (624)
Q Consensus       139 ~~~~~llvp~~-------~~g~iIGk~G~~Ik~I~~~sga~I~i~~~~~~~~~--~~~~~~~~r~V~I~G~-~~~V~~A~  208 (624)
                      .++.+|.||-.       ++|.|||++|.+||+|+++|||+|.|..+......  ......++-.|.|.+. .+++.+|+
T Consensus        11 ~~~~ki~ip~~~~~p~fn~ig~IIGpgG~tiK~I~~eTG~kI~I~G~gS~~~e~~~~~e~~e~l~V~I~a~~~e~i~~A~   90 (119)
T 2yqr_A           11 YVQDKLFVGLEHAVPTFNVKEKVEGPGCSYLQHIQIETGAKVFLRGKGSGCIEPASGREAFEPMYIYISHPKPEGLAAAK   90 (119)
T ss_dssp             CEEEEEECCCTTSCTTTCHHHHHSCGGGHHHHHHHHHHCCEEEEESBTTTCCCTTTSSCCSSBCEEEEEESSHHHHHHHH
T ss_pred             EEEEEEEcCCccCCCCCCeeeeEECCCChHHHHHHHHHCCEEEEecCCccccccccccccCCCcEEEEEeCCHHHHHHHH
Confidence            46677888765       78999999999999999999999999865321100  0001123446778765 89999999


Q ss_pred             HHHHHHHhhc
Q 006943          209 FAISAIMYKF  218 (624)
Q Consensus       209 ~~I~~~l~~~  218 (624)
                      .+|.+++.+.
T Consensus        91 ~~Ie~Ll~~v  100 (119)
T 2yqr_A           91 KLCENLLQTV  100 (119)
T ss_dssp             HHHHHHHHHH
T ss_pred             HHHHHHhhch
Confidence            9999999754

>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=2.2e-06  Score=75.16  Aligned_cols=68  Identities=19%  Similarity=0.339  Sum_probs=53.0

Q ss_pred             EEEEEeccc------cccceeccCCchHHHHHHHhCCEEEEeCCCCC------------------CCCeEEEEEcC-HH-
Q 006943          555 TLEVLVPAN------AVGKVIGKAGSNLANIRKISGATIEMSDSKSS------------------RGDRVALISGT-PE-  608 (624)
Q Consensus       555 ~~~i~VP~~------~vg~IIGkgG~~I~~I~~~sGa~I~i~~~~~~------------------~~~r~v~I~Gt-~e-  608 (624)
                      +.+|.||-+      ++|.|||++|.++|+|+++|||+|.|....+.                  ..+--|.|++. ++ 
T Consensus         3 ~~Ki~IP~~~~P~~NfiG~IiGPrG~t~K~ie~eTg~kI~IrGkGS~kd~~~e~~~~g~~~~~~~~epLHV~Isa~~~~~   82 (140)
T 2bl5_A            3 QEKLYVPVKEYPDFNFVGRILGPRGLTAKQLEAETGCKIMVRGKGSMRDKKKEEQNRGKPNWEHLNEDLHVLITVEDAQN   82 (140)
T ss_dssp             EEEEECCTTTCSSSCHHHHHTTTTHHHHHHHHHHHSEEEEEESTTSSCCHHHHHTSTTSHHHHTTTSCCEEEEEECSCCH
T ss_pred             eeEEEcCcccCCCCCeeeEEECCCcchHHHHHHHHCCeEEEecCCCcccccccccccCCCCccccCCCcEEEEEecCchh
Confidence            556777744      48999999999999999999999999965321                  01126788883 43 


Q ss_pred             ----HHHHHHHHHHHHHh
Q 006943          609 ----QKRAAENLIQAFIM  622 (624)
Q Consensus       609 ----~v~~A~~lI~~~i~  622 (624)
                          .++.|+.+|+.++.
T Consensus        83 ~~~~~l~~A~~~I~~lL~  100 (140)
T 2bl5_A           83 RAELKLKRAVEEVKKLLV  100 (140)
T ss_dssp             HHHHHHHHHHHHHHHHSS
T ss_pred             hHHHHHHHHHHHHHHHCC
Confidence                78999999999875

>3u1k_A Polyribonucleotide nucleotidyltransferase 1, MITO; RNAse PH, KH domain, exoribonuclease; HET: CIT; 2.13A {Homo sapiens}

Probab=98.00  E-value=6.7e-06  Score=90.55  Aligned_cols=61  Identities=25%  Similarity=0.368  Sum_probs=53.9

Q ss_pred             EEEEEeccccccceeccCCchHHHHHHHhCCEEEEeCCCCCCCCeEEEEEcC-HHHHHHHHHHHHHHH
Q 006943          555 TLEVLVPANAVGKVIGKAGSNLANIRKISGATIEMSDSKSSRGDRVALISGT-PEQKRAAENLIQAFI  621 (624)
Q Consensus       555 ~~~i~VP~~~vg~IIGkgG~~I~~I~~~sGa~I~i~~~~~~~~~r~v~I~Gt-~e~v~~A~~lI~~~i  621 (624)
                      ...+.||.+++|.|||+||.+|+.|+++|||+|.|.++      ..|.|.|+ .++.++|+.+|++++
T Consensus       568 ~~~~~I~~~kI~~vIG~gG~~Ik~I~e~tg~~I~I~d~------G~V~I~~~~~~~~~~A~~~I~~i~  629 (630)
T 3u1k_A          568 VETVQVPLSKRAKFVGPGGYNLKKLQAETGVTISQVDE------ETFSVFAPTPSAMHEARDFITEIC  629 (630)
T ss_dssp             EEEEECCHHHHHHHHCGGGHHHHHHHHHHCCEEEECSS------SEEEEEESSHHHHHHHHHHTTC--
T ss_pred             EEEEEeChhHhheeECCCChhHHHHHHHHCCEEEEcCC------cEEEEEeCCHHHHHHHHHHHHHHh
Confidence            78899999999999999999999999999999999853      45899886 788999999998765

>3v69_A Protein filia; RNA-binding, embryogenesis, KH domain, RNA binding, P binding; 2.20A {Mus musculus}

Probab=97.98  E-value=1.9e-05  Score=67.51  Aligned_cols=67  Identities=13%  Similarity=0.252  Sum_probs=60.7

Q ss_pred             EEEEEeccccccceeccCCchHHHHHHHhCCEEEEeCCCCCCCCeEEEEEcCHHHHHHHHHHHHHHHh
Q 006943          555 TLEVLVPANAVGKVIGKAGSNLANIRKISGATIEMSDSKSSRGDRVALISGTPEQKRAAENLIQAFIM  622 (624)
Q Consensus       555 ~~~i~VP~~~vg~IIGkgG~~I~~I~~~sGa~I~i~~~~~~~~~r~v~I~Gt~e~v~~A~~lI~~~i~  622 (624)
                      -..+.|....++.|+|++|+.|+.|+..|.|.|+|..-.+ ++...|+|.|++..-..|+.||+.+..
T Consensus        57 PlVF~vE~~lve~IFGp~Gs~Ip~IE~~SqTLIqV~~~~s-~g~tEVtIfG~~~~Q~rak~MI~sLA~  123 (140)
T 3v69_A           57 PKRLYVEPRLLEIMFGKDGEHIPHLESMLHTLIHVNVWGP-ERRAEIWIFGPPPFRRDVDRMLTDLAH  123 (140)
T ss_dssp             CEEEEECGGGHHHHHCGGGTTHHHHHHHHTSEEEEECCCT-TSCEEEEEESCHHHHHHHHHHHHHHHH
T ss_pred             CeEEEEehhhhhcccCCCcCccchHHhhcceeEEEeccCC-CCcEEEEEECCHHHHHHHHHHHHHHHH
Confidence            4678899999999999999999999999999999998754 467789999999999999999998753

>2bl5_A MGC83862 protein, quaking protein; STAR proteins, GSG proteins, RNA binding; NMR {Xenopus laevis} SCOP: d.51.1.1

Probab=97.98  E-value=1.8e-05  Score=69.39  Aligned_cols=74  Identities=19%  Similarity=0.304  Sum_probs=52.3

Q ss_pred             EEEEEEecCC------ccceeeccCcchHHHHHhHhCCeEEEcCCCC------------------CCCceEEEEeecCCc
Q 006943          308 LVIRVLCPFN------KIGRVIGKGGGTIKSIRQASGAQIDVDDTKD------------------NRDECVITVTAIESP  363 (624)
Q Consensus       308 ~~~~i~vp~~------~vg~IIGk~G~~Ik~I~~~tga~I~v~~~~~------------------~~~er~i~I~G~~~~  363 (624)
                      ++.++.||.+      ++|.|||++|.++|+|+++|||+|.|.....                  ..+.-.|.|++....
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            4567777754      4899999999999999999999999974221                  112236888886444


Q ss_pred             hhHHHHHHHHHHHHhhcc
Q 006943          364 DDIKSMAVEAVLLLQTKI  381 (624)
Q Consensus       364 ~~a~~~~~~~i~~~~~~~  381 (624)
                      ..|...+..|+..+...+
T Consensus        82 ~~~~~~l~~A~~~I~~lL   99 (140)
T 2bl5_A           82 NRAELKLKRAVEEVKKLL   99 (140)
T ss_dssp             HHHHHHHHHHHHHHHHHS
T ss_pred             hhHHHHHHHHHHHHHHHC
Confidence            445555666666666544

>3u1k_A Polyribonucleotide nucleotidyltransferase 1, MITO; RNAse PH, KH domain, exoribonuclease; HET: CIT; 2.13A {Homo sapiens}

Probab=97.74  E-value=1.9e-05  Score=86.97  Aligned_cols=93  Identities=18%  Similarity=0.228  Sum_probs=69.6

Q ss_pred             ccHHHHHHHHHHHHHHHhhhccCCCcccCCCceeEEEEEeccceeEEEeCCchHHHHHHHhcCCeEEEccCCCCCCCCcc
Q 006943          108 LCAAQDALLKVHAAIANAVANATDNDKKRKEKEECQILVPSSQSANIIGKAGATIKRLRSKTRTSIKVTPKDASEPTHSC  187 (624)
Q Consensus       108 ~~~a~~ai~~v~~~i~~~~~~~~~~~~~~~~~~~~~llvp~~~~g~iIGk~G~~Ik~I~~~sga~I~i~~~~~~~~~~~~  187 (624)
                      +..|.+++..+++.+.+.+....... ...-.....|.||.+.++.|||++|++||.|+++|||+|.|.           
T Consensus       536 L~~A~~g~~~I~~~m~~al~~~~~~~-~~~ap~~~~~~I~~~kI~~vIG~gG~~Ik~I~e~tg~~I~I~-----------  603 (630)
T 3u1k_A          536 IQQASVAKKEILQIMNKTISKPRASR-KENGPVVETVQVPLSKRAKFVGPGGYNLKKLQAETGVTISQV-----------  603 (630)
T ss_dssp             HHHHHHHHHHHHHHHHHHCSSCCSSC-CTTCCEEEEEECCHHHHHHHHCGGGHHHHHHHHHHCCEEEEC-----------
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHhhh-cccCCeEEEEEeChhHhheeECCCChhHHHHHHHHCCEEEEc-----------
Confidence            44566777777777666665432211 122234667899999999999999999999999999999985           


Q ss_pred             cccCCceEEEecC-HHHHHHHHHHHHHHH
Q 006943          188 AMEFDNFVLISGE-SEAVKKALFAISAIM  215 (624)
Q Consensus       188 ~~~~~r~V~I~G~-~~~V~~A~~~I~~~l  215 (624)
                         ++..|.|.|+ .+++.+|+.+|..++
T Consensus       604 ---d~G~V~I~~~~~~~~~~A~~~I~~i~  629 (630)
T 3u1k_A          604 ---DEETFSVFAPTPSAMHEARDFITEIC  629 (630)
T ss_dssp             ---SSSEEEEEESSHHHHHHHHHHTTC--
T ss_pred             ---CCcEEEEEeCCHHHHHHHHHHHHHHh
Confidence               3567999998 588999999886654

>4aid_A Polyribonucleotide nucleotidyltransferase; transferase-peptide complex; 2.60A {Caulobacter vibrioides} PDB: 4aim_A 4am3_A

Probab=97.39  E-value=9e-05  Score=82.49  Aligned_cols=62  Identities=23%  Similarity=0.407  Sum_probs=11.3

Q ss_pred             EEEEEeccccccceeccCCchHHHHHHHhCCEEEEeCCCCCCCCeEEEEEc-CHHHHHHHHHHHHHHHh
Q 006943          555 TLEVLVPANAVGKVIGKAGSNLANIRKISGATIEMSDSKSSRGDRVALISG-TPEQKRAAENLIQAFIM  622 (624)
Q Consensus       555 ~~~i~VP~~~vg~IIGkgG~~I~~I~~~sGa~I~i~~~~~~~~~r~v~I~G-t~e~v~~A~~lI~~~i~  622 (624)
                      ..++.||.++++.|||+||.+|+.|.++||++|.|.++      -.|.|.+ ..++.+.|+.+|+.++.
T Consensus       571 ~~~~~i~~~ki~~vig~gg~~i~~i~~~tg~~idi~dd------G~v~I~~~~~~~~~~A~~~i~~i~~  633 (726)
T 4aid_A          571 IETINIPTDKIREVIGSGGKVIREIVATTGAKVDINDD------GVVKVSASDGAKIKAAIDWIKSITD  633 (726)
T ss_dssp             -------------------------------------------------CCSCHHHHHHHHHC------
T ss_pred             EEEEeCCHHHHHhhcCCCchhHHHHHHHHCCceeEECC------ceEEEEeCCHHHHHHHHHHHHHHhh
Confidence            56789999999999999999999999999999999853      3477766 48899999999988764

>2cxc_A NUSA; transcription termination, RNA binding protein, archaeal NUS domain, structural genomics, NPPSFA; 2.00A {Aeropyrum pernix} PDB: 2cy1_A

Probab=97.36  E-value=7.3e-05  Score=65.94  Aligned_cols=102  Identities=24%  Similarity=0.370  Sum_probs=73.9

Q ss_pred             EEEEEEecCcccceeccCCchHHHHHHHhcCCeEEeeCCCCCCCceEEEEEccCCcccccccccccCCCCcccHHHHHHH
Q 006943           37 VIYRILCPDGVIGSVIGKSGKVINSIRQETRARVKVVDPFPGAKDRVVTIYSHVKDKEDVEVDDEFNDKEPLCAAQDALL  116 (624)
Q Consensus        37 ~~~~ilvp~~~~g~vIGk~G~~I~~i~~etg~~I~v~~~~~~~~er~i~I~G~~~~~~~~~~~~~~~~~~~~~~a~~ai~  116 (624)
                      -.+.++|+...+|+.||++|++|+.|+++.|-+|.|-+-.              ++                        
T Consensus        36 dr~i~vVk~g~vGa~IG~~G~ri~~i~~elgekIdIV~~s--------------~d------------------------   77 (144)
T 2cxc_A           36 NRLIFLVSEGEAGRAIGRGGRLIKLLREALGKNIEVVEYS--------------SD------------------------   77 (144)
T ss_dssp             TEEEEEECTTCHHHHHCGGGHHHHHHHHHHSSEEEEEECC--------------SS------------------------
T ss_pred             CEEEEEEeCCCccccCccCchHHHHHHHHhCCeeEEEEcC--------------CC------------------------
Confidence            5678899999999999999999999999999999885421              01                        


Q ss_pred             HHHHHHHHhhhccC--C-CcccCCCceeEEEEEeccceeEEEeCCchHHHHHHHhcCCeEEEcc
Q 006943          117 KVHAAIANAVANAT--D-NDKKRKEKEECQILVPSSQSANIIGKAGATIKRLRSKTRTSIKVTP  177 (624)
Q Consensus       117 ~v~~~i~~~~~~~~--~-~~~~~~~~~~~~llvp~~~~g~iIGk~G~~Ik~I~~~sga~I~i~~  177 (624)
                       ..+.+...+.+..  . ...+.++.....+.||..+.+..|||+|.+++-...-||.+|.|..
T Consensus        78 -~~~fI~naLsPA~V~~V~i~~~~~~~~~~V~V~~~q~slAIGk~G~NvrLa~~Ltg~~idI~~  140 (144)
T 2cxc_A           78 -LERIVKNLFPGVKIESINVRERNGVKQVVIKVSEDDKGAAIGKGGKNVKRARLVLSKLFGVEK  140 (144)
T ss_dssp             -HHHHHHHHSTTSCEEEEEEEEETTEEEEEEEECTTTHHHHHCGGGHHHHHHHHHHHHHHCEEE
T ss_pred             -HHHHHHHhcCCceEEEEEEeecCCcEEEEEEEChHHhhhccCCCCHHHHHHHHHhCCeeCceE
Confidence             0011222222110  0 0000133567788999999999999999999999999999887753

>3v69_A Protein filia; RNA-binding, embryogenesis, KH domain, RNA binding, P binding; 2.20A {Mus musculus}

Probab=97.24  E-value=0.00031  Score=60.11  Aligned_cols=69  Identities=19%  Similarity=0.149  Sum_probs=60.7

Q ss_pred             eeEEEEEeccceeEEEeCCchHHHHHHHhcCCeEEEccCCCCCCCCcccccCCceEEEecCHHHHHHHHHHHHHHHhh
Q 006943          140 EECQILVPSSQSANIIGKAGATIKRLRSKTRTSIKVTPKDASEPTHSCAMEFDNFVLISGESEAVKKALFAISAIMYK  217 (624)
Q Consensus       140 ~~~~llvp~~~~g~iIGk~G~~Ik~I~~~sga~I~i~~~~~~~~~~~~~~~~~r~V~I~G~~~~V~~A~~~I~~~l~~  217 (624)
                      -++.+.+...+++.|+|++|+.|+.|+..|++.|+|...+.         ++.-.|+|.|++..=..|+.+|..+..-
T Consensus        56 dPlVF~vE~~lve~IFGp~Gs~Ip~IE~~SqTLIqV~~~~s---------~g~tEVtIfG~~~~Q~rak~MI~sLA~~  124 (140)
T 3v69_A           56 DPKRLYVEPRLLEIMFGKDGEHIPHLESMLHTLIHVNVWGP---------ERRAEIWIFGPPPFRRDVDRMLTDLAHY  124 (140)
T ss_dssp             SCEEEEECGGGHHHHHCGGGTTHHHHHHHHTSEEEEECCCT---------TSCEEEEEESCHHHHHHHHHHHHHHHHH
T ss_pred             CCeEEEEehhhhhcccCCCcCccchHHhhcceeEEEeccCC---------CCcEEEEEECCHHHHHHHHHHHHHHHHH
Confidence            46788999999999999999999999999999999987542         3456799999999999999999887743

>4aid_A Polyribonucleotide nucleotidyltransferase; transferase-peptide complex; 2.60A {Caulobacter vibrioides} PDB: 4aim_A 4am3_A

Probab=97.17  E-value=0.00019  Score=79.92  Aligned_cols=96  Identities=18%  Similarity=0.260  Sum_probs=26.3

Q ss_pred             ccHHHHHHHHHHHHHHHhhhccCCCcccCCCceeEEEEEeccceeEEEeCCchHHHHHHHhcCCeEEEccCCCCCCCCcc
Q 006943          108 LCAAQDALLKVHAAIANAVANATDNDKKRKEKEECQILVPSSQSANIIGKAGATIKRLRSKTRTSIKVTPKDASEPTHSC  187 (624)
Q Consensus       108 ~~~a~~ai~~v~~~i~~~~~~~~~~~~~~~~~~~~~llvp~~~~g~iIGk~G~~Ik~I~~~sga~I~i~~~~~~~~~~~~  187 (624)
                      +..|.+++..+++.+.+.+...-...+ ..-.....+.||.+.++.|||++|++||+|.++||++|.|.           
T Consensus       539 L~~A~~g~~~I~~~m~~al~~~r~~~~-~~ap~~~~~~i~~~ki~~vig~gg~~i~~i~~~tg~~idi~-----------  606 (726)
T 4aid_A          539 LAQAKEGRAHILGEMNKAMDAPRADVG-DFAPKIETINIPTDKIREVIGSGGKVIREIVATTGAKVDIN-----------  606 (726)
T ss_dssp             HHHHHHHHHHHHHHHHTTCSSCCSSCC-SSCCC-----------------------------------------------
T ss_pred             HHHHHHHHHHHHHHHHHHHHhhhhhhc-ccCCeEEEEeCCHHHHHhhcCCCchhHHHHHHHHCCceeEE-----------
Confidence            445666666666666555543211111 11123456899999999999999999999999999999885           


Q ss_pred             cccCCceEEEecC-HHHHHHHHHHHHHHHhhc
Q 006943          188 AMEFDNFVLISGE-SEAVKKALFAISAIMYKF  218 (624)
Q Consensus       188 ~~~~~r~V~I~G~-~~~V~~A~~~I~~~l~~~  218 (624)
                         ++..|.|.+. .+++.+|+.+|..++.+.
T Consensus       607 ---ddG~v~I~~~~~~~~~~A~~~i~~i~~~~  635 (726)
T 4aid_A          607 ---DDGVVKVSASDGAKIKAAIDWIKSITDEA  635 (726)
T ss_dssp             ----------CCSCHHHHHHHHHC--------
T ss_pred             ---CCceEEEEeCCHHHHHHHHHHHHHHhhhh
Confidence               2456788877 789999999998887543

>2cxc_A NUSA; transcription termination, RNA binding protein, archaeal NUS domain, structural genomics, NPPSFA; 2.00A {Aeropyrum pernix} PDB: 2cy1_A

Probab=97.15  E-value=4.6e-05  Score=67.22  Aligned_cols=101  Identities=23%  Similarity=0.305  Sum_probs=72.0

Q ss_pred             EEEEEecCCccceeeccCcchHHHHHhHhCCeEEEcCCCCCCCceEEEEeecCCchhHHHHHHHHHH--HHhhccCCCCC
Q 006943          309 VIRVLCPFNKIGRVIGKGGGTIKSIRQASGAQIDVDDTKDNRDECVITVTAIESPDDIKSMAVEAVL--LLQTKINDEDD  386 (624)
Q Consensus       309 ~~~i~vp~~~vg~IIGk~G~~Ik~I~~~tga~I~v~~~~~~~~er~i~I~G~~~~~~a~~~~~~~i~--~~~~~~~~~~~  386 (624)
                      ...|.|+...+|..||++|+.|+.|+++.|-+|.+-.-..             +.   ...+..++.  .+..-.....+
T Consensus        37 r~i~vVk~g~vGa~IG~~G~ri~~i~~elgekIdIV~~s~-------------d~---~~fI~naLsPA~V~~V~i~~~~  100 (144)
T 2cxc_A           37 RLIFLVSEGEAGRAIGRGGRLIKLLREALGKNIEVVEYSS-------------DL---ERIVKNLFPGVKIESINVRERN  100 (144)
T ss_dssp             EEEEEECTTCHHHHHCGGGHHHHHHHHHHSSEEEEEECCS-------------SH---HHHHHHHSTTSCEEEEEEEEET
T ss_pred             EEEEEEeCCCccccCccCchHHHHHHHHhCCeeEEEEcCC-------------CH---HHHHHHhcCCceEEEEEEeecC
Confidence            6678899999999999999999999999999998743211             11   111222221  00000000013


Q ss_pred             CcEEEEEEecCCeeeEEEcCCCchHHHHHHhcCceEEEe
Q 006943          387 DTVTIRLLVSSKVIGCIIGKSGSIINEIRKRTKADVRIS  425 (624)
Q Consensus       387 ~~~~~~l~vp~~~~g~iIGk~G~~Ik~I~~~tga~I~i~  425 (624)
                      +.....+.||..+.+..|||+|.+++-..+-||.+|.|.
T Consensus       101 ~~~~~~V~V~~~q~slAIGk~G~NvrLa~~Ltg~~idI~  139 (144)
T 2cxc_A          101 GVKQVVIKVSEDDKGAAIGKGGKNVKRARLVLSKLFGVE  139 (144)
T ss_dssp             TEEEEEEEECTTTHHHHHCGGGHHHHHHHHHHHHHHCEE
T ss_pred             CcEEEEEEEChHHhhhccCCCCHHHHHHHHHhCCeeCce
Confidence            456788999999999999999999999999999887664

>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=95.27  E-value=0.019  Score=58.25  Aligned_cols=95  Identities=21%  Similarity=0.281  Sum_probs=67.0

Q ss_pred             cccceeccCCchHHHHHHHhc-CCeEEeeCCCCCCCceEEEEEccCCcccccccccccCCCCcccHHHHHHHHHHHHHHH
Q 006943           46 GVIGSVIGKSGKVINSIRQET-RARVKVVDPFPGAKDRVVTIYSHVKDKEDVEVDDEFNDKEPLCAAQDALLKVHAAIAN  124 (624)
Q Consensus        46 ~~~g~vIGk~G~~I~~i~~et-g~~I~v~~~~~~~~er~i~I~G~~~~~~~~~~~~~~~~~~~~~~a~~ai~~v~~~i~~  124 (624)
                      +-+|+.||++|++|+.|.++. |=+|.|-+-.              ++                         ....+..
T Consensus       249 DpvGacIG~~G~rI~~i~~eL~gekIDIi~~s--------------~d-------------------------p~~fi~n  289 (366)
T 1k0r_A          249 NAKGACIGPMGQRVRNVMSELSGEKIDIIDYD--------------DD-------------------------PARFVAN  289 (366)
T ss_dssp             CHHHHHHCGGGHHHHHHHHHTTTCEEEEEECC--------------SS-------------------------HHHHHHH
T ss_pred             CCcccccCCcchHHHHHHHHhCCCeEEEEEcC--------------CC-------------------------HHHHHHH
Confidence            558999999999999999998 8899885421              11                         0111222


Q ss_pred             hhhccC-CCc-ccCCCceeEEEEEeccceeEEEeCCchHHHHHHHhcCCeEEEccCC
Q 006943          125 AVANAT-DND-KKRKEKEECQILVPSSQSANIIGKAGATIKRLRSKTRTSIKVTPKD  179 (624)
Q Consensus       125 ~~~~~~-~~~-~~~~~~~~~~llvp~~~~g~iIGk~G~~Ik~I~~~sga~I~i~~~~  179 (624)
                      ++.... ..- .-........+.||..+.+..|||+|.+++-...-||.+|.|....
T Consensus       290 alsPA~V~~V~~~~~~~~~a~V~V~~~qlslAIGk~GqNvrLA~~Ltg~~idI~~~~  346 (366)
T 1k0r_A          290 ALSPAKVVSVSVIDQTARAARVVVPDFQLSLAIGKEGQNARLAARLTGWRIDIRGDA  346 (366)
T ss_dssp             HTTTSCCSEEEEEETTTTEEEEEECGGGHHHHHCGGGHHHHHHHHHHCCEEEEEESS
T ss_pred             hcCCcceeEEEEEcCCCcEEEEEEChHHhhhccCCCcHHHHHHHHHHCCeeeeeEHH
Confidence            222210 000 0001235678999999999999999999999999999999998643

>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=95.22  E-value=0.016  Score=55.53  Aligned_cols=94  Identities=20%  Similarity=0.284  Sum_probs=64.7

Q ss_pred             cccceeccCCchHHHHHH-HhcCCeEEeeCCCCCCCceEEEEEccCCcccccccccccCCCCcccHHHHHHHHHHHHHHH
Q 006943           46 GVIGSVIGKSGKVINSIR-QETRARVKVVDPFPGAKDRVVTIYSHVKDKEDVEVDDEFNDKEPLCAAQDALLKVHAAIAN  124 (624)
Q Consensus        46 ~~~g~vIGk~G~~I~~i~-~etg~~I~v~~~~~~~~er~i~I~G~~~~~~~~~~~~~~~~~~~~~~a~~ai~~v~~~i~~  124 (624)
                      +-+|+-||++|++|+.|. +-.|=+|.|-+-.              ++                         ....+..
T Consensus       126 DpvGacIG~~G~rI~~i~~eL~gekIDIi~~s--------------~d-------------------------p~~fi~n  166 (251)
T 2asb_A          126 NAKGACIGPMGQRVRNVMSELSGEKIDIIDYD--------------DD-------------------------PARFVAN  166 (251)
T ss_dssp             CHHHHHHCGGGHHHHHHHHHTTTCEEEEEECC--------------SS-------------------------HHHHHHH
T ss_pred             CHHHHHhCCCchHHHHHHHHhCCCeEEEEEec--------------CC-------------------------HHHHHHh
Confidence            458999999999999995 5568899884421              01                         0112222


Q ss_pred             hhhccC-CCcc-cCCCceeEEEEEeccceeEEEeCCchHHHHHHHhcCCeEEEccC
Q 006943          125 AVANAT-DNDK-KRKEKEECQILVPSSQSANIIGKAGATIKRLRSKTRTSIKVTPK  178 (624)
Q Consensus       125 ~~~~~~-~~~~-~~~~~~~~~llvp~~~~g~iIGk~G~~Ik~I~~~sga~I~i~~~  178 (624)
                      ++.... ..-. .......+.+.||..+.+.-|||+|.+++--..-||.+|.|...
T Consensus       167 alsPA~V~~V~i~~~~~~~a~V~V~~~qlslAIGk~GqNvrLA~~Ltg~~idI~~~  222 (251)
T 2asb_A          167 ALSPAKVVSVSVIDQTARAARVVVPDFQLSLAIGKEGQNARLAARLTGWRIDIRGD  222 (251)
T ss_dssp             HTTTSCCSEEEEEETTTTEEEEEECGGGHHHHHCGGGHHHHHHHHHHSCEEEEEES
T ss_pred             ccCCcceEEEEEEcCCCcEEEEEEChHHhhhhhcCCcCcHHHHHHHHCCEecceEH
Confidence            332210 0000 00112467889999999999999999999999999999999864

>3cdi_A Polynucleotide phosphorylase; mRNA turnover, RNAse, RNA degradation, kinase, transferase; 2.60A {Escherichia coli} PDB: 1sro_A

Probab=95.14  E-value=0.0074  Score=67.53  Aligned_cols=61  Identities=25%  Similarity=0.388  Sum_probs=0.0

Q ss_pred             EEEEEeccccccceeccCCchHHHHHHHhCCEEEEeCCCCCCCCeEEEEEc-CHHHHHHHHHHHHHHH
Q 006943          555 TLEVLVPANAVGKVIGKAGSNLANIRKISGATIEMSDSKSSRGDRVALISG-TPEQKRAAENLIQAFI  621 (624)
Q Consensus       555 ~~~i~VP~~~vg~IIGkgG~~I~~I~~~sGa~I~i~~~~~~~~~r~v~I~G-t~e~v~~A~~lI~~~i  621 (624)
                      ...+.||.++++.|||+||.+|+.|.+++|+.|.|.++      ..|.|++ ..+..+.|+.+|+.++
T Consensus       561 ~~~~~i~~~ki~~~ig~gGk~I~~I~~~~G~~IdI~~d------g~v~I~~~~~~~~~~a~~~i~~i~  622 (723)
T 3cdi_A          561 IHTIKINPDKIKDVIGKGGSVIRALTEETGTTIEIEDD------GTVKIAATDGEKAKHAIRRIEEIT  622 (723)
T ss_dssp             --------------------------------------------------------------------
T ss_pred             EEEEEECHHHhcccccccceeeeeeehhhCceEEecCC------ccEEEecCCHHHHHHHHHHHHHHh
Confidence            56789999999999999999999999999999988852      4477766 4667788888887664

>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=94.61  E-value=0.0039  Score=70.07  Aligned_cols=61  Identities=26%  Similarity=0.437  Sum_probs=21.0

Q ss_pred             EEEEEeccccccceeccCCchHHHHHHHhCCEEEEeCCCCCCCCeEEEEEcC-HHHHHHHHHHHHHHH
Q 006943          555 TLEVLVPANAVGKVIGKAGSNLANIRKISGATIEMSDSKSSRGDRVALISGT-PEQKRAAENLIQAFI  621 (624)
Q Consensus       555 ~~~i~VP~~~vg~IIGkgG~~I~~I~~~sGa~I~i~~~~~~~~~r~v~I~Gt-~e~v~~A~~lI~~~i  621 (624)
                      ...+.||.+++|.|||++|.+|+.|++++|+.|.|.+      +..|.|++. .+..+.|+.+|+.+.
T Consensus       599 ~~~~~I~~~ki~~vIG~gGk~Ik~I~~~~G~~IdI~~------dG~v~Is~~~~~~~~~a~~~i~~i~  660 (757)
T 1e3p_A          599 IITVKIPVDKIGEVIGPKRQMINQIQEDTGAEITIED------DGTIYIGAADGPAAEAARATINGIA  660 (757)
T ss_dssp             CCCC------------------CTTCCCCCSCC--------------CCCBSSHHHHCC---------
T ss_pred             eEEEEEChHHeehcccccceeeehhhHhhCCEEEecC------CceEEEecCCHHHHHHHHHHHHHhc
Confidence            3457899999999999999999999999999999984      245777774 677788887777654

>3cdi_A Polynucleotide phosphorylase; mRNA turnover, RNAse, RNA degradation, kinase, transferase; 2.60A {Escherichia coli} PDB: 1sro_A

Probab=94.50  E-value=0.012  Score=65.73  Aligned_cols=94  Identities=24%  Similarity=0.328  Sum_probs=12.1

Q ss_pred             ccHHHHHHHHHHHHHHHhhhccCCCcccCCCceeEEEEEeccceeEEEeCCchHHHHHHHhcCCeEEEccCCCCCCCCcc
Q 006943          108 LCAAQDALLKVHAAIANAVANATDNDKKRKEKEECQILVPSSQSANIIGKAGATIKRLRSKTRTSIKVTPKDASEPTHSC  187 (624)
Q Consensus       108 ~~~a~~ai~~v~~~i~~~~~~~~~~~~~~~~~~~~~llvp~~~~g~iIGk~G~~Ik~I~~~sga~I~i~~~~~~~~~~~~  187 (624)
                      +..|.++...+++.+.+.+....... ...-.....+-||....+.+||++|.+|+.|.++||+.|.|..          
T Consensus       529 l~~A~~~~~~I~~~m~~al~~~~~~~-~~~ap~~~~~~i~~~ki~~~ig~gGk~I~~I~~~~G~~IdI~~----------  597 (723)
T 3cdi_A          529 LNQAKGARLHILGVMEQAINAPRGDI-SEFAPRIHTIKINPDKIKDVIGKGGSVIRALTEETGTTIEIED----------  597 (723)
T ss_dssp             HHHHHHHHHHHHHHHHHHCC------------------------------------------------------------
T ss_pred             HHHHHHHHHHHHHHHHHHhhhcchhc-cccCceEEEEEECHHHhcccccccceeeeeeehhhCceEEecC----------
Confidence            34556666666666666554431111 1112234567899999999999999999999999999998753          


Q ss_pred             cccCCceEEEecC-HHHHHHHHHHHHHHHh
Q 006943          188 AMEFDNFVLISGE-SEAVKKALFAISAIMY  216 (624)
Q Consensus       188 ~~~~~r~V~I~G~-~~~V~~A~~~I~~~l~  216 (624)
                          +..|.|.+. .+.+.+|..+|..++.
T Consensus       598 ----dg~v~I~~~~~~~~~~a~~~i~~i~~  623 (723)
T 3cdi_A          598 ----DGTVKIAATDGEKAKHAIRRIEEITA  623 (723)
T ss_dssp             ------------------------------
T ss_pred             ----CccEEEecCCHHHHHHHHHHHHHHhh
Confidence                455777765 5677788877766653

>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=94.47  E-value=0.0059  Score=68.56  Aligned_cols=92  Identities=21%  Similarity=0.317  Sum_probs=36.2

Q ss_pred             ccHHHHHHHHHHHHHHHhhhccCCCcccCCCceeEEEEEeccceeEEEeCCchHHHHHHHhcCCeEEEccCCCCCCCCcc
Q 006943          108 LCAAQDALLKVHAAIANAVANATDNDKKRKEKEECQILVPSSQSANIIGKAGATIKRLRSKTRTSIKVTPKDASEPTHSC  187 (624)
Q Consensus       108 ~~~a~~ai~~v~~~i~~~~~~~~~~~~~~~~~~~~~llvp~~~~g~iIGk~G~~Ik~I~~~sga~I~i~~~~~~~~~~~~  187 (624)
                      +..|.++...+++.+.+.+... .... ..-.....+.||....+.+||++|++|+.|.+++|+.|.|..          
T Consensus       568 L~~A~~~~~~I~~~m~~al~~~-~~~~-~~ap~~~~~~I~~~ki~~vIG~gGk~Ik~I~~~~G~~IdI~~----------  635 (757)
T 1e3p_A          568 LKQARDARLHILDVMMEAIDTP-DEMS-PNAPRIITVKIPVDKIGEVIGPKRQMINQIQEDTGAEITIED----------  635 (757)
T ss_dssp             HHHHHHHHHHHHHHHHHHCSSC-CCCC-TTSCBCCCC------------------CTTCCCCCSCC--------------
T ss_pred             HHHHHHHHHHHHHHHHHHhccc-cccc-ccCceeEEEEEChHHeehcccccceeeehhhHhhCCEEEecC----------
Confidence            4456677777777766666543 2111 111223357899999999999999999999999999998853          


Q ss_pred             cccCCceEEEecC-HHHHHHHHHHHHHHH
Q 006943          188 AMEFDNFVLISGE-SEAVKKALFAISAIM  215 (624)
Q Consensus       188 ~~~~~r~V~I~G~-~~~V~~A~~~I~~~l  215 (624)
                          +..|.|... .++..+|+..|..+.
T Consensus       636 ----dG~v~Is~~~~~~~~~a~~~i~~i~  660 (757)
T 1e3p_A          636 ----DGTIYIGAADGPAAEAARATINGIA  660 (757)
T ss_dssp             --------CCCBSSHHHHCC---------
T ss_pred             ----CceEEEecCCHHHHHHHHHHHHHhc
Confidence                455777765 566777766665543

>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=94.14  E-value=0.013  Score=59.55  Aligned_cols=93  Identities=22%  Similarity=0.300  Sum_probs=66.1

Q ss_pred             CccceeeccCcchHHHHHhHh-CCeEEEcCCCCCCCceEEEEeecCCchhHHHHHHHHHHH--Hhhc-cCCCCCCcEEEE
Q 006943          317 NKIGRVIGKGGGTIKSIRQAS-GAQIDVDDTKDNRDECVITVTAIESPDDIKSMAVEAVLL--LQTK-INDEDDDTVTIR  392 (624)
Q Consensus       317 ~~vg~IIGk~G~~Ik~I~~~t-ga~I~v~~~~~~~~er~i~I~G~~~~~~a~~~~~~~i~~--~~~~-~~~~~~~~~~~~  392 (624)
                      +-+|..||++|++|+.|.++. |=+|.|-.-             ++++   ...+..++.-  +..- +.+  ++.....
T Consensus       249 DpvGacIG~~G~rI~~i~~eL~gekIDIi~~-------------s~dp---~~fi~nalsPA~V~~V~~~~--~~~~~a~  310 (366)
T 1k0r_A          249 NAKGACIGPMGQRVRNVMSELSGEKIDIIDY-------------DDDP---ARFVANALSPAKVVSVSVID--QTARAAR  310 (366)
T ss_dssp             CHHHHHHCGGGHHHHHHHHHTTTCEEEEEEC-------------CSSH---HHHHHHHTTTSCCSEEEEEE--TTTTEEE
T ss_pred             CCcccccCCcchHHHHHHHHhCCCeEEEEEc-------------CCCH---HHHHHHhcCCcceeEEEEEc--CCCcEEE
Confidence            578999999999999999999 888887321             1111   1222333220  1110 111  1245688


Q ss_pred             EEecCCeeeEEEcCCCchHHHHHHhcCceEEEeCC
Q 006943          393 LLVSSKVIGCIIGKSGSIINEIRKRTKADVRISKG  427 (624)
Q Consensus       393 l~vp~~~~g~iIGk~G~~Ik~I~~~tga~I~i~~~  427 (624)
                      +.||..+.+..|||+|.+++-..+-||.+|.|...
T Consensus       311 V~V~~~qlslAIGk~GqNvrLA~~Ltg~~idI~~~  345 (366)
T 1k0r_A          311 VVVPDFQLSLAIGKEGQNARLAARLTGWRIDIRGD  345 (366)
T ss_dssp             EEECGGGHHHHHCGGGHHHHHHHHHHCCEEEEEES
T ss_pred             EEEChHHhhhccCCCcHHHHHHHHHHCCeeeeeEH
Confidence            99999999999999999999999999999999754

>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=93.68  E-value=0.031  Score=53.64  Aligned_cols=94  Identities=23%  Similarity=0.342  Sum_probs=64.1

Q ss_pred             CccceeeccCcchHHHH-HhHhCCeEEEcCCCCCCCceEEEEeecCCchhHHHHHHHHHHH--Hhhc-cCCCCCCcEEEE
Q 006943          317 NKIGRVIGKGGGTIKSI-RQASGAQIDVDDTKDNRDECVITVTAIESPDDIKSMAVEAVLL--LQTK-INDEDDDTVTIR  392 (624)
Q Consensus       317 ~~vg~IIGk~G~~Ik~I-~~~tga~I~v~~~~~~~~er~i~I~G~~~~~~a~~~~~~~i~~--~~~~-~~~~~~~~~~~~  392 (624)
                      +-+|..||++|++|+.| ++-.|=+|.|-.-..             +.   ...+..++.-  +..- +.++  ......
T Consensus       126 DpvGacIG~~G~rI~~i~~eL~gekIDIi~~s~-------------dp---~~fi~nalsPA~V~~V~i~~~--~~~~a~  187 (251)
T 2asb_A          126 NAKGACIGPMGQRVRNVMSELSGEKIDIIDYDD-------------DP---ARFVANALSPAKVVSVSVIDQ--TARAAR  187 (251)
T ss_dssp             CHHHHHHCGGGHHHHHHHHHTTTCEEEEEECCS-------------SH---HHHHHHHTTTSCCSEEEEEET--TTTEEE
T ss_pred             CHHHHHhCCCchHHHHHHHHhCCCeEEEEEecC-------------CH---HHHHHhccCCcceEEEEEEcC--CCcEEE
Confidence            56899999999999999 555577787732111             11   1122233220  0000 1111  224678


Q ss_pred             EEecCCeeeEEEcCCCchHHHHHHhcCceEEEeCCC
Q 006943          393 LLVSSKVIGCIIGKSGSIINEIRKRTKADVRISKGD  428 (624)
Q Consensus       393 l~vp~~~~g~iIGk~G~~Ik~I~~~tga~I~i~~~~  428 (624)
                      +.||..+.+..|||+|.+++--.+-||.+|.|....
T Consensus       188 V~V~~~qlslAIGk~GqNvrLA~~Ltg~~idI~~~~  223 (251)
T 2asb_A          188 VVVPDFQLSLAIGKEGQNARLAARLTGWRIDIRGDA  223 (251)
T ss_dssp             EEECGGGHHHHHCGGGHHHHHHHHHHSCEEEEEESS
T ss_pred             EEEChHHhhhhhcCCcCcHHHHHHHHCCEecceEHH
Confidence            999999999999999999999999999999997543

>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=92.93  E-value=0.083  Score=53.43  Aligned_cols=94  Identities=32%  Similarity=0.401  Sum_probs=65.7

Q ss_pred             cccceeccCCchHHHHHHHhc-CCeEEeeCCCCCCCceEEEEEccCCcccccccccccCCCCcccHHHHHHHHHHHHHHH
Q 006943           46 GVIGSVIGKSGKVINSIRQET-RARVKVVDPFPGAKDRVVTIYSHVKDKEDVEVDDEFNDKEPLCAAQDALLKVHAAIAN  124 (624)
Q Consensus        46 ~~~g~vIGk~G~~I~~i~~et-g~~I~v~~~~~~~~er~i~I~G~~~~~~~~~~~~~~~~~~~~~~a~~ai~~v~~~i~~  124 (624)
                      +-+|+.||.+|.+|+.+.++. |=+|.|-+-.              ++                         ....+..
T Consensus       245 DpvGacvg~~G~ri~~i~~el~ge~Idii~~s--------------~d-------------------------~~~fi~n  285 (344)
T 1hh2_P          245 DPIGACIGEGGSRIAAILKELKGEKLDVLKWS--------------DD-------------------------PKQLIAN  285 (344)
T ss_dssp             CHHHHHHCTTSTTHHHHHHHTTTCEEEEEECC--------------SS-------------------------HHHHHHH
T ss_pred             cccceeeccCCcEeHHHHHHhCCCeeeEEecC--------------CC-------------------------HHHHHHH
Confidence            458999999999999999998 7788874321              11                         1112333


Q ss_pred             hhhccC-CCccc-CCCceeEEEEEeccceeEEEeCCchHHHHHHHhcCCeEEEccC
Q 006943          125 AVANAT-DNDKK-RKEKEECQILVPSSQSANIIGKAGATIKRLRSKTRTSIKVTPK  178 (624)
Q Consensus       125 ~~~~~~-~~~~~-~~~~~~~~llvp~~~~g~iIGk~G~~Ik~I~~~sga~I~i~~~  178 (624)
                      ++.... ..-.- ..+...+.+.||..+.+.-|||+|.+++--..-||.+|.|...
T Consensus       286 al~Pa~v~~v~~~d~~~~~~~v~v~~~~~s~AIGk~G~Nvrla~~Ltg~~idi~s~  341 (344)
T 1hh2_P          286 ALAPATVIEVEILDKENKAARVLVPPTQLSLAIGKGGQNARLAAKLTGWKIDIKPI  341 (344)
T ss_dssp             HTCSSCCSEEEEEETTTTEEEEEECTTSHHHHHCGGGHHHHHHHHHHSCEEEEEEC
T ss_pred             hcCccEEEEEEEEcCCCCEEEEEEChHHcchhhcCCCccHHHHHHHHCCEeceeec
Confidence            332210 00000 0123567899999999999999999999999999999999753

>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=89.73  E-value=0.12  Score=52.37  Aligned_cols=93  Identities=27%  Similarity=0.375  Sum_probs=64.3

Q ss_pred             CccceeeccCcchHHHHHhHh-CCeEEEcCCCCCCCceEEEEeecCCchhHHHHHHHHHH--HHhhccCCCCCCcEEEEE
Q 006943          317 NKIGRVIGKGGGTIKSIRQAS-GAQIDVDDTKDNRDECVITVTAIESPDDIKSMAVEAVL--LLQTKINDEDDDTVTIRL  393 (624)
Q Consensus       317 ~~vg~IIGk~G~~Ik~I~~~t-ga~I~v~~~~~~~~er~i~I~G~~~~~~a~~~~~~~i~--~~~~~~~~~~~~~~~~~l  393 (624)
                      +-+|+.||.+|..|+.|.++. |=+|.+-.-            . +++   ...+..++.  .+..-.. ..+......+
T Consensus       245 DpvGacvg~~G~ri~~i~~el~ge~Idii~~------------s-~d~---~~fi~nal~Pa~v~~v~~-~d~~~~~~~v  307 (344)
T 1hh2_P          245 DPIGACIGEGGSRIAAILKELKGEKLDVLKW------------S-DDP---KQLIANALAPATVIEVEI-LDKENKAARV  307 (344)
T ss_dssp             CHHHHHHCTTSTTHHHHHHHTTTCEEEEEEC------------C-SSH---HHHHHHHTCSSCCSEEEE-EETTTTEEEE
T ss_pred             cccceeeccCCcEeHHHHHHhCCCeeeEEec------------C-CCH---HHHHHHhcCccEEEEEEE-EcCCCCEEEE
Confidence            567999999999999999999 667776321            1 111   112233321  0000000 0122346889


Q ss_pred             EecCCeeeEEEcCCCchHHHHHHhcCceEEEeC
Q 006943          394 LVSSKVIGCIIGKSGSIINEIRKRTKADVRISK  426 (624)
Q Consensus       394 ~vp~~~~g~iIGk~G~~Ik~I~~~tga~I~i~~  426 (624)
                      .||..+.+.-|||+|.+++--..-||.+|.|..
T Consensus       308 ~v~~~~~s~AIGk~G~Nvrla~~Ltg~~idi~s  340 (344)
T 1hh2_P          308 LVPPTQLSLAIGKGGQNARLAAKLTGWKIDIKP  340 (344)
T ss_dssp             EECTTSHHHHHCGGGHHHHHHHHHHSCEEEEEE
T ss_pred             EEChHHcchhhcCCCccHHHHHHHHCCEeceee
Confidence            999999999999999999999999999999864

---

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	624
d1wvna1	70	d.51.1.1 (A:5-74) Poly(RC)-binding protein 1 {Huma	2e-15
d1wvna1	70	d.51.1.1 (A:5-74) Poly(RC)-binding protein 1 {Huma	1e-10
d1wvna1	70	d.51.1.1 (A:5-74) Poly(RC)-binding protein 1 {Huma	1e-10
d1wvna1	70	d.51.1.1 (A:5-74) Poly(RC)-binding protein 1 {Huma	6e-10
d1wvna1	70	d.51.1.1 (A:5-74) Poly(RC)-binding protein 1 {Huma	2e-08
d1j4wa1	74	d.51.1.1 (A:1-74) Far upstream binding element, FB	9e-15
d1j4wa1	74	d.51.1.1 (A:1-74) Far upstream binding element, FB	4e-10
d1j4wa1	74	d.51.1.1 (A:1-74) Far upstream binding element, FB	4e-09
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	9e-08
d1x4na1	79	d.51.1.1 (A:8-86) Far upstream binding element, FB	1e-14
d1x4na1	79	d.51.1.1 (A:8-86) Far upstream binding element, FB	1e-11
d1x4na1	79	d.51.1.1 (A:8-86) Far upstream binding element, FB	2e-10
d1x4na1	79	d.51.1.1 (A:8-86) Far upstream binding element, FB	3e-10
d1x4na1	79	d.51.1.1 (A:8-86) Far upstream binding element, FB	3e-10
d1zzka1	75	d.51.1.1 (A:11-85) HnRNP K, KH3 {Human (Homo sapie	1e-14
d1zzka1	75	d.51.1.1 (A:11-85) HnRNP K, KH3 {Human (Homo sapie	5e-10
d1zzka1	75	d.51.1.1 (A:11-85) HnRNP K, KH3 {Human (Homo sapie	8e-10
d1zzka1	75	d.51.1.1 (A:11-85) HnRNP K, KH3 {Human (Homo sapie	2e-09
d1zzka1	75	d.51.1.1 (A:11-85) HnRNP K, KH3 {Human (Homo sapie	2e-08
d2axya1	71	d.51.1.1 (A:11-81) Poly(RC)-binding protein 2 {Hum	5e-14
d2axya1	71	d.51.1.1 (A:11-81) Poly(RC)-binding protein 2 {Hum	3e-13
d2axya1	71	d.51.1.1 (A:11-81) Poly(RC)-binding protein 2 {Hum	8e-11
d2axya1	71	d.51.1.1 (A:11-81) Poly(RC)-binding protein 2 {Hum	3e-10
d2axya1	71	d.51.1.1 (A:11-81) Poly(RC)-binding protein 2 {Hum	2e-09
d1dtja_	74	d.51.1.1 (A:) Neuro-oncological ventral antigen 2,	8e-13
d1dtja_	74	d.51.1.1 (A:) Neuro-oncological ventral antigen 2,	3e-11
d1dtja_	74	d.51.1.1 (A:) Neuro-oncological ventral antigen 2,	1e-10
d1dtja_	74	d.51.1.1 (A:) Neuro-oncological ventral antigen 2,	6e-10
d1dtja_	74	d.51.1.1 (A:) Neuro-oncological ventral antigen 2,	6e-09
d1j4wa2	71	d.51.1.1 (A:104-174) Far upstream binding element,	9e-13
d1j4wa2	71	d.51.1.1 (A:104-174) Far upstream binding element,	9e-10
d1j4wa2	71	d.51.1.1 (A:104-174) Far upstream binding element,	2e-09
d1j4wa2	71	d.51.1.1 (A:104-174) Far upstream binding element,	1e-08
d1j4wa2	71	d.51.1.1 (A:104-174) Far upstream binding element,	3e-08
d1x4ma1	81	d.51.1.1 (A:8-88) Far upstream binding element, FB	4e-12
d1x4ma1	81	d.51.1.1 (A:8-88) Far upstream binding element, FB	2e-09
d1x4ma1	81	d.51.1.1 (A:8-88) Far upstream binding element, FB	4e-09
d1x4ma1	81	d.51.1.1 (A:8-88) Far upstream binding element, FB	4e-09
d1x4ma1	81	d.51.1.1 (A:8-88) Far upstream binding element, FB	1e-07
d1we8a_	104	d.51.1.1 (A:) Tudor and KH domain containing prote	4e-11
d1we8a_	104	d.51.1.1 (A:) Tudor and KH domain containing prote	4e-10
d1we8a_	104	d.51.1.1 (A:) Tudor and KH domain containing prote	3e-09
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
d2ctka1	91	d.51.1.1 (A:8-98) Vigilin {Human (Homo sapiens) [T	2e-10
d2ctka1	91	d.51.1.1 (A:8-98) Vigilin {Human (Homo sapiens) [T	2e-08
d2ctka1	91	d.51.1.1 (A:8-98) Vigilin {Human (Homo sapiens) [T	5e-08
d2ctka1	91	d.51.1.1 (A:8-98) Vigilin {Human (Homo sapiens) [T	2e-07
d2ctka1	91	d.51.1.1 (A:8-98) Vigilin {Human (Homo sapiens) [T	1e-06
d2ctea1	81	d.51.1.1 (A:8-88) Vigilin {Human (Homo sapiens) [T	3e-10
d2ctea1	81	d.51.1.1 (A:8-88) Vigilin {Human (Homo sapiens) [T	4e-09
d2ctea1	81	d.51.1.1 (A:8-88) Vigilin {Human (Homo sapiens) [T	2e-08
d2ctea1	81	d.51.1.1 (A:8-88) Vigilin {Human (Homo sapiens) [T	5e-08
d2ctea1	81	d.51.1.1 (A:8-88) Vigilin {Human (Homo sapiens) [T	6e-07
d2ctla1	84	d.51.1.1 (A:8-91) Vigilin {Human (Homo sapiens) [T	2e-09
d2ctla1	84	d.51.1.1 (A:8-91) Vigilin {Human (Homo sapiens) [T	9e-09
d2ctla1	84	d.51.1.1 (A:8-91) Vigilin {Human (Homo sapiens) [T	4e-08
d2ctla1	84	d.51.1.1 (A:8-91) Vigilin {Human (Homo sapiens) [T	1e-06
d2ctla1	84	d.51.1.1 (A:8-91) Vigilin {Human (Homo sapiens) [T	1e-05
d2cpqa1	78	d.51.1.1 (A:212-289) Fragile X mental retardation	2e-08
d2cpqa1	78	d.51.1.1 (A:212-289) Fragile X mental retardation	9e-05
d2ctma1	81	d.51.1.1 (A:8-88) Vigilin {Human (Homo sapiens) [T	2e-08
d2ctma1	81	d.51.1.1 (A:8-88) Vigilin {Human (Homo sapiens) [T	2e-07
d2ctma1	81	d.51.1.1 (A:8-88) Vigilin {Human (Homo sapiens) [T	3e-07
d2ctma1	81	d.51.1.1 (A:8-88) Vigilin {Human (Homo sapiens) [T	7e-06
d2ctma1	81	d.51.1.1 (A:8-88) Vigilin {Human (Homo sapiens) [T	7e-05
d1viga_	71	d.51.1.1 (A:) Vigilin {Human (Homo sapiens) [TaxId	3e-08
d1viga_	71	d.51.1.1 (A:) Vigilin {Human (Homo sapiens) [TaxId	2e-07
d1viga_	71	d.51.1.1 (A:) Vigilin {Human (Homo sapiens) [TaxId	4e-07
d1viga_	71	d.51.1.1 (A:) Vigilin {Human (Homo sapiens) [TaxId	8e-06
d1viga_	71	d.51.1.1 (A:) Vigilin {Human (Homo sapiens) [TaxId	6e-05
d1e3ha4	54	d.52.3.1 (A:579-632) Polynucleotide phosphorylase/	4e-08
d1e3ha4	54	d.52.3.1 (A:579-632) Polynucleotide phosphorylase/	1e-06
d1e3ha4	54	d.52.3.1 (A:579-632) Polynucleotide phosphorylase/	0.001
d1e3ha4	54	d.52.3.1 (A:579-632) Polynucleotide phosphorylase/	0.004
d1tuaa1	84	d.51.1.1 (A:1-84) Hypothetical protein APE0754 {Ae	6e-07
d1tuaa1	84	d.51.1.1 (A:1-84) Hypothetical protein APE0754 {Ae	6e-06
d1tuaa1	84	d.51.1.1 (A:1-84) Hypothetical protein APE0754 {Ae	2e-05
d1tuaa1	84	d.51.1.1 (A:1-84) Hypothetical protein APE0754 {Ae	0.003
d2ba0a3	84	d.51.1.1 (A:136-219) Exosome complex RNA-binding p	7e-07
d2ba0a3	84	d.51.1.1 (A:136-219) Exosome complex RNA-binding p	8e-07
d2ba0a3	84	d.51.1.1 (A:136-219) Exosome complex RNA-binding p	1e-04
d2ba0a3	84	d.51.1.1 (A:136-219) Exosome complex RNA-binding p	1e-04
d2ba0a3	84	d.51.1.1 (A:136-219) Exosome complex RNA-binding p	0.003
d2ctja1	82	d.51.1.1 (A:8-89) Vigilin {Human (Homo sapiens) [T	1e-06
d2ctja1	82	d.51.1.1 (A:8-89) Vigilin {Human (Homo sapiens) [T	6e-06
d2ctja1	82	d.51.1.1 (A:8-89) Vigilin {Human (Homo sapiens) [T	5e-05
d2ctja1	82	d.51.1.1 (A:8-89) Vigilin {Human (Homo sapiens) [T	1e-04
d2ctja1	82	d.51.1.1 (A:8-89) Vigilin {Human (Homo sapiens) [T	0.002
d1tuaa2	104	d.51.1.1 (A:85-188) Hypothetical protein APE0754 {	5e-06
d1tuaa2	104	d.51.1.1 (A:85-188) Hypothetical protein APE0754 {	0.004
d2z0sa2	87	d.51.1.1 (A:148-234) Exosome complex RNA-binding p	7e-06
d2z0sa2	87	d.51.1.1 (A:148-234) Exosome complex RNA-binding p	0.003
d2je6i3	69	d.51.1.1 (I:153-221) Exosome complex RNA-binding p	2e-05
d2je6i3	69	d.51.1.1 (I:153-221) Exosome complex RNA-binding p	2e-04
d2je6i3	69	d.51.1.1 (I:153-221) Exosome complex RNA-binding p	0.002
d2ctfa1	90	d.51.1.1 (A:7-96) Vigilin {Human (Homo sapiens) [T	3e-04

>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 = 69.1 bits (169), Expect = 2e-15
 Identities = 22/67 (32%), Positives = 39/67 (58%)

Query: 555 TLEVLVPANAVGKVIGKAGSNLANIRKISGATIEMSDSKSSRGDRVALISGTPEQKRAAE 614
           T E+ +P N +G +IG+ G+N+  IR++SGA I++++       R   I+G+      A+
Sbjct: 3   THELTIPNNLIGCIIGRQGANINEIRQMSGAQIKIANPVEGSSGRQVTITGSAASISLAQ 62

Query: 615 NLIQAFI 621
            LI A +
Sbjct: 63  YLINARL 69

>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 = 55.6 bits (134), Expect = 1e-10
 Identities = 22/72 (30%), Positives = 33/72 (45%), Gaps = 6/72 (8%)

Query: 310 IRVLCPFNKIGRVIGKGGGTIKSIRQASGAQIDVDDTKDNRDECVITVTAIESPDDIKSM 369
             +  P N IG +IG+ G  I  IRQ SGAQI + +  +      +T+T   S   I   
Sbjct: 4   HELTIPNNLIGCIIGRQGANINEIRQMSGAQIKIANPVEGSSGRQVTITG--SAASIS-- 59

Query: 370 AVEAVLLLQTKI 381
              A  L+  ++
Sbjct: 60  --LAQYLINARL 69

>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 = 55.6 bits (134), Expect = 1e-10
 Identities = 23/72 (31%), Positives = 37/72 (51%), Gaps = 4/72 (5%)

Query: 389 VTIRLLVSSKVIGCIIGKSGSIINEIRKRTKADVRISKGDKPKCADANDELVEVVGEVGS 448
            T  L + + +IGCIIG+ G+ INEIR+ + A ++I+         ++   V + G   S
Sbjct: 2   TTHELTIPNNLIGCIIGRQGANINEIRQMSGAQIKIA----NPVEGSSGRQVTITGSAAS 57

Query: 449 VRDALVQIILRL 460
           +  A   I  RL
Sbjct: 58  ISLAQYLINARL 69

>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 = 53.3 bits (128), Expect = 6e-10
 Identities = 19/50 (38%), Positives = 31/50 (62%)

Query: 37 VIYRILCPDGVIGSVIGKSGKVINSIRQETRARVKVVDPFPGAKDRVVTI 86
            + +  P+ +IG +IG+ G  IN IRQ + A++K+ +P  G+  R VTI
Sbjct: 2  TTHELTIPNNLIGCIIGRQGANINEIRQMSGAQIKIANPVEGSSGRQVTI 51

>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 = 49.4 bits (118), Expect = 2e-08
 Identities = 16/71 (22%), Positives = 31/71 (43%), Gaps = 8/71 (11%)

Query: 143 QILVPSSQSANIIGKAGATIKRLRSKTRTSIKVTPKDASEPTHSCAMEFDNFVLISGESE 202
           ++ +P++    IIG+ GA I  +R  +   IK+                   V I+G + 
Sbjct: 5   ELTIPNNLIGCIIGRQGANINEIRQMSGAQIKIANPVEGSS--------GRQVTITGSAA 56

Query: 203 AVKKALFAISA 213
           ++  A + I+A
Sbjct: 57  SISLAQYLINA 67

>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 = 67.2 bits (164), Expect = 9e-15
 Identities = 19/67 (28%), Positives = 36/67 (53%)

Query: 555 TLEVLVPANAVGKVIGKAGSNLANIRKISGATIEMSDSKSSRGDRVALISGTPEQKRAAE 614
            ++V +P  AVG VIG+ G  +  I+  +G  I+      +  +R+A I+G P++ + A 
Sbjct: 4   MIDVPIPRFAVGIVIGRNGEMIKKIQNDAGVRIQFKPDDGTTPERIAQITGPPDRAQHAA 63

Query: 615 NLIQAFI 621
            +I   +
Sbjct: 64  EIITDLL 70

>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 = 54.1 bits (130), Expect = 4e-10
 Identities = 18/75 (24%), Positives = 30/75 (40%), Gaps = 6/75 (8%)

Query: 309 VIRVLCPFNKIGRVIGKGGGTIKSIRQASGAQIDVDDTKDNRDECVITVTAIESPDDIKS 368
           +I V  P   +G VIG+ G  IK I+  +G +I          E +  +T    PD  + 
Sbjct: 4   MIDVPIPRFAVGIVIGRNGEMIKKIQNDAGVRIQFKPDDGTTPERIAQITG--PPDRAQ- 60

Query: 369 MAVEAVLLLQTKIND 383
               A  ++   +  
Sbjct: 61  ---HAAEIITDLLRS 72

>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 = 51.4 bits (123), Expect = 4e-09
 Identities = 12/51 (23%), Positives = 25/51 (49%)

Query: 36 SVIYRILCPDGVIGSVIGKSGKVINSIRQETRARVKVVDPFPGAKDRVVTI 86
          S +  +  P   +G VIG++G++I  I+ +   R++         +R+  I
Sbjct: 2  SHMIDVPIPRFAVGIVIGRNGEMIKKIQNDAGVRIQFKPDDGTTPERIAQI 52

>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 = 49.1 bits (117), Expect = 2e-08
 Identities = 14/73 (19%), Positives = 31/73 (42%), Gaps = 8/73 (10%)

Query: 143 QILVPSSQSANIIGKAGATIKRLRSKTRTSIKVTPKDASEPTHSCAMEFDNFVLISGESE 202
            + +P      +IG+ G  IK++++     I+  P D + P        +    I+G  +
Sbjct: 6   DVPIPRFAVGIVIGRNGEMIKKIQNDAGVRIQFKPDDGTTP--------ERIAQITGPPD 57

Query: 203 AVKKALFAISAIM 215
             + A   I+ ++
Sbjct: 58  RAQHAAEIITDLL 70

>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 = 47.2 bits (112), Expect = 9e-08
 Identities = 13/75 (17%), Positives = 30/75 (40%), Gaps = 4/75 (5%)

Query: 388 TVTIRLLVSSKVIGCIIGKSGSIINEIRKRTKADVRISKGDKPKCADANDELVEVVGEVG 447
           +  I + +    +G +IG++G +I +I+      ++      P      + + ++ G   
Sbjct: 2   SHMIDVPIPRFAVGIVIGRNGEMIKKIQNDAGVRIQFK----PDDGTTPERIAQITGPPD 57

Query: 448 SVRDALVQIILRLRD 462
             + A   I   LR 
Sbjct: 58  RAQHAAEIITDLLRS 72

>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 = 67.2 bits (164), Expect = 1e-14
 Identities = 20/71 (28%), Positives = 39/71 (54%)

Query: 551 PPPLTLEVLVPANAVGKVIGKAGSNLANIRKISGATIEMSDSKSSRGDRVALISGTPEQK 610
              +T E  VP   VG +IG+ G  ++ I++ SG  I+++       +R  +++GTPE  
Sbjct: 5   RSVMTEEYKVPDGMVGFIIGRGGEQISRIQQESGCKIQIAPDSGGLPERSCMLTGTPESV 64

Query: 611 RAAENLIQAFI 621
           ++A+ L+   +
Sbjct: 65  QSAKRLLDQIV 75

>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 = 58.3 bits (141), Expect = 1e-11
 Identities = 19/79 (24%), Positives = 32/79 (40%), Gaps = 6/79 (7%)

Query: 304 QSEELVIRVLCPFNKIGRVIGKGGGTIKSIRQASGAQIDVDDTKDNRDECVITVTAIESP 363
           Q   +      P   +G +IG+GG  I  I+Q SG +I +        E    +T   +P
Sbjct: 4   QRSVMTEEYKVPDGMVGFIIGRGGEQISRIQQESGCKIQIAPDSGGLPERSCMLTG--TP 61

Query: 364 DDIKSMAVEAVLLLQTKIN 382
           + ++     A  LL   + 
Sbjct: 62  ESVQ----SAKRLLDQIVE 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 = 55.2 bits (133), Expect = 2e-10
 Identities = 16/73 (21%), Positives = 32/73 (43%), Gaps = 8/73 (10%)

Query: 143 QILVPSSQSANIIGKAGATIKRLRSKTRTSIKVTPKDASEPTHSCAMEFDNFVLISGESE 202
           +  VP      IIG+ G  I R++ ++   I++ P     P        +   +++G  E
Sbjct: 11  EYKVPDGMVGFIIGRGGEQISRIQQESGCKIQIAPDSGGLP--------ERSCMLTGTPE 62

Query: 203 AVKKALFAISAIM 215
           +V+ A   +  I+
Sbjct: 63  SVQSAKRLLDQIV 75

>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 = 54.8 bits (132), Expect = 3e-10
 Identities = 15/82 (18%), Positives = 33/82 (40%), Gaps = 4/82 (4%)

Query: 382 NDEDDDTVTIRLLVSSKVIGCIIGKSGSIINEIRKRTKADVRISKGDKPKCADANDELVE 441
           + +    +T    V   ++G IIG+ G  I+ I++ +   ++I+    P      +    
Sbjct: 1   HQQQRSVMTEEYKVPDGMVGFIIGRGGEQISRIQQESGCKIQIA----PDSGGLPERSCM 56

Query: 442 VVGEVGSVRDALVQIILRLRDD 463
           + G   SV+ A   +   +   
Sbjct: 57  LTGTPESVQSAKRLLDQIVEKG 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 = 54.8 bits (132), Expect = 3e-10
 Identities = 15/64 (23%), Positives = 31/64 (48%), Gaps = 3/64 (4%)

Query: 34 EESVIYRILCPDGVIGSVIGKSGKVINSIRQETRARVKVVDPFPGAKDRVVTIYSHVKDK 93
             +      PDG++G +IG+ G+ I+ I+QE+  ++++     G  +R   +       
Sbjct: 5  RSVMTEEYKVPDGMVGFIIGRGGEQISRIQQESGCKIQIAPDSGGLPERSCMLTG---TP 61

Query: 94 EDVE 97
          E V+
Sbjct: 62 ESVQ 65

>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 = 66.8 bits (163), Expect = 1e-14
 Identities = 24/70 (34%), Positives = 41/70 (58%)

Query: 552 PPLTLEVLVPANAVGKVIGKAGSNLANIRKISGATIEMSDSKSSRGDRVALISGTPEQKR 611
           P +T +V +P +  G +IGK G  +  IR  SGA+I++ +      DR+  I+GT +Q +
Sbjct: 2   PIITTQVTIPKDLAGSIIGKGGQRIKQIRHESGASIKIDEPLEGSEDRIITITGTQDQIQ 61

Query: 612 AAENLIQAFI 621
            A+ L+Q  +
Sbjct: 62  NAQYLLQNSV 71

>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 = 53.7 bits (129), Expect = 5e-10
 Identities = 18/77 (23%), Positives = 37/77 (48%), Gaps = 8/77 (10%)

Query: 143 QILVPSSQSANIIGKAGATIKRLRSKTRTSIKVTPKDASEPTHSCAMEFDNFVLISGESE 202
           Q+ +P   + +IIGK G  IK++R ++  SIK+                D  + I+G  +
Sbjct: 7   QVTIPKDLAGSIIGKGGQRIKQIRHESGASIKIDEPLEGSE--------DRIITITGTQD 58

Query: 203 AVKKALFAISAIMYKFS 219
            ++ A + +   + ++S
Sbjct: 59  QIQNAQYLLQNSVKQYS 75

>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 = 53.3 bits (128), Expect = 8e-10
 Identities = 26/73 (35%), Positives = 39/73 (53%), Gaps = 6/73 (8%)

Query: 310 IRVLCPFNKIGRVIGKGGGTIKSIRQASGAQIDVDDTKDNRDECVITVTAIESPDDIKSM 369
            +V  P +  G +IGKGG  IK IR  SGA I +D+  +  ++ +IT+T   + D I+  
Sbjct: 6   TQVTIPKDLAGSIIGKGGQRIKQIRHESGASIKIDEPLEGSEDRIITITG--TQDQIQ-- 61

Query: 370 AVEAVLLLQTKIN 382
              A  LLQ  + 
Sbjct: 62  --NAQYLLQNSVK 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 = 52.2 bits (125), Expect = 2e-09
 Identities = 15/73 (20%), Positives = 35/73 (47%), Gaps = 4/73 (5%)

Query: 389 VTIRLLVSSKVIGCIIGKSGSIINEIRKRTKADVRISKGDKPKCADANDELVEVVGEVGS 448
           +T ++ +   + G IIGK G  I +IR  + A ++I +        + D ++ + G    
Sbjct: 4   ITTQVTIPKDLAGSIIGKGGQRIKQIRHESGASIKIDE----PLEGSEDRIITITGTQDQ 59

Query: 449 VRDALVQIILRLR 461
           +++A   +   ++
Sbjct: 60  IQNAQYLLQNSVK 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 = 49.5 bits (118), Expect = 2e-08
 Identities = 19/58 (32%), Positives = 36/58 (62%), Gaps = 3/58 (5%)

Query: 40 RILCPDGVIGSVIGKSGKVINSIRQETRARVKVVDPFPGAKDRVVTIYSHVKDKEDVE 97
          ++  P  + GS+IGK G+ I  IR E+ A +K+ +P  G++DR++TI      ++ ++
Sbjct: 7  QVTIPKDLAGSIIGKGGQRIKQIRHESGASIKIDEPLEGSEDRIITITG---TQDQIQ 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 = 65.2 bits (159), Expect = 5e-14
 Identities = 24/77 (31%), Positives = 44/77 (57%), Gaps = 6/77 (7%)

Query: 386 DDTVTIRLLVSSKVIGCIIGKSGSIINEIRKRTKADVRISKGDKPKCADANDELVEVVGE 445
           + T+TIRLL+  K +G IIGK G  + ++R+ + A + IS+G+ P      + ++ + G 
Sbjct: 1   NVTLTIRLLMHGKEVGSIIGKKGESVKKMREESGARINISEGNCP------ERIITLAGP 54

Query: 446 VGSVRDALVQIILRLRD 462
             ++  A   II +L +
Sbjct: 55  TNAIFKAFAMIIDKLEE 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 = 62.9 bits (153), Expect = 3e-13
 Identities = 19/69 (27%), Positives = 35/69 (50%), Gaps = 2/69 (2%)

Query: 553 PLTLEVLVPANAVGKVIGKAGSNLANIRKISGATIEMSDSKSSRGDRVALISGTPEQKRA 612
            LT+ +L+    VG +IGK G ++  +R+ SGA I +S+      +R+  ++G       
Sbjct: 3   TLTIRLLMHGKEVGSIIGKKGESVKKMREESGARINISEGNCP--ERIITLAGPTNAIFK 60

Query: 613 AENLIQAFI 621
           A  +I   +
Sbjct: 61  AFAMIIDKL 69

>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 = 55.9 bits (135), Expect = 8e-11
 Identities = 22/76 (28%), Positives = 42/76 (55%), Gaps = 8/76 (10%)

Query: 308 LVIRVLCPFNKIGRVIGKGGGTIKSIRQASGAQIDVDDTKDNRDECVITVTAIESPDDIK 367
           L IR+L    ++G +IGK G ++K +R+ SGA+I++ +   N  E +IT+      + I 
Sbjct: 4   LTIRLLMHGKEVGSIIGKKGESVKKMREESGARINISE--GNCPERIITLAG--PTNAIF 59

Query: 368 SMAVEAVLLLQTKIND 383
               +A  ++  K+ +
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 = 54.4 bits (131), Expect = 3e-10
 Identities = 15/73 (20%), Positives = 35/73 (47%), Gaps = 10/73 (13%)

Query: 143 QILVPSSQSANIIGKAGATIKRLRSKTRTSIKVTPKDASEPTHSCAMEFDNFVLISGESE 202
           ++L+   +  +IIGK G ++K++R ++   I ++  +  E            + ++G + 
Sbjct: 7   RLLMHGKEVGSIIGKKGESVKKMREESGARINISEGNCPERI----------ITLAGPTN 56

Query: 203 AVKKALFAISAIM 215
           A+ KA   I   +
Sbjct: 57  AIFKAFAMIIDKL 69

>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 = 52.1 bits (125), Expect = 2e-09
 Identities = 14/51 (27%), Positives = 31/51 (60%), Gaps = 2/51 (3%)

Query: 36 SVIYRILCPDGVIGSVIGKSGKVINSIRQETRARVKVVDPFPGAKDRVVTI 86
          ++  R+L     +GS+IGK G+ +  +R+E+ AR+ + +      +R++T+
Sbjct: 3  TLTIRLLMHGKEVGSIIGKKGESVKKMREESGARINISE--GNCPERIITL 51

>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 = 61.8 bits (150), Expect = 8e-13
 Identities = 22/70 (31%), Positives = 38/70 (54%), Gaps = 3/70 (4%)

Query: 555 TLEVLVPANAVGKVIGKAGSNLANIRKISGATIEMSDSKSSR---GDRVALISGTPEQKR 611
            +E+ VP N VG ++GK G  L   ++++GA I++S          +R   I+G+P   +
Sbjct: 4   LVEMAVPENLVGAILGKGGKTLVEYQELTGARIQISKKGEFLPGTRNRRVTITGSPAATQ 63

Query: 612 AAENLIQAFI 621
           AA+ LI   +
Sbjct: 64  AAQYLISQRV 73

>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 = 57.5 bits (139), Expect = 3e-11
 Identities = 17/71 (23%), Positives = 32/71 (45%), Gaps = 1/71 (1%)

Query: 390 TIRLLVSSKVIGCIIGKSGSIINEIRKRTKADVRISKGDKPKCADANDELVEVVGEVGSV 449
            + + V   ++G I+GK G  + E ++ T A ++ISK          +  V + G   + 
Sbjct: 4   LVEMAVPENLVGAILGKGGKTLVEYQELTGARIQISK-KGEFLPGTRNRRVTITGSPAAT 62

Query: 450 RDALVQIILRL 460
           + A   I  R+
Sbjct: 63  QAAQYLISQRV 73

>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 = 55.2 bits (133), Expect = 1e-10
 Identities = 20/77 (25%), Positives = 34/77 (44%), Gaps = 5/77 (6%)

Query: 139 KEECQILVPSSQSANIIGKAGATIKRLRSKTRTSIKVTPKDASEPTHSCAMEFDNFVLIS 198
           KE  ++ VP +    I+GK G T+   +  T   I+++ K    P        +  V I+
Sbjct: 2   KELVEMAVPENLVGAILGKGGKTLVEYQELTGARIQISKKGEFLPGTR-----NRRVTIT 56

Query: 199 GESEAVKKALFAISAIM 215
           G   A + A + IS  +
Sbjct: 57  GSPAATQAAQYLISQRV 73

>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 = 53.7 bits (129), Expect = 6e-10
 Identities = 17/76 (22%), Positives = 36/76 (47%), Gaps = 9/76 (11%)

Query: 309 VIRVLCPFNKIGRVIGKGGGTIKSIRQASGAQIDVDDTKD---NRDECVITVTAIESPDD 365
           ++ +  P N +G ++GKGG T+   ++ +GA+I +    +         +T+T   SP  
Sbjct: 4   LVEMAVPENLVGAILGKGGKTLVEYQELTGARIQISKKGEFLPGTRNRRVTITG--SPAA 61

Query: 366 IKSMAVEAVLLLQTKI 381
            +     A  L+  ++
Sbjct: 62  TQ----AAQYLISQRV 73

>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 = 6e-09
 Identities = 15/52 (28%), Positives = 32/52 (61%), Gaps = 3/52 (5%)

Query: 38 IYRILCPDGVIGSVIGKSGKVINSIRQETRARVKVV---DPFPGAKDRVVTI 86
          +  +  P+ ++G+++GK GK +   ++ T AR+++    +  PG ++R VTI
Sbjct: 4  LVEMAVPENLVGAILGKGGKTLVEYQELTGARIQISKKGEFLPGTRNRRVTI 55

>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 = 61.5 bits (149), Expect = 9e-13
 Identities = 22/70 (31%), Positives = 33/70 (47%), Gaps = 3/70 (4%)

Query: 555 TLEVLVPANAVGKVIGKAGSNLANIRKISGATIEMS---DSKSSRGDRVALISGTPEQKR 611
               +VP    G +IGK G  + +I + SGA IE+       +    ++  I GTP+Q  
Sbjct: 2   EFNFIVPTGKTGLIIGKGGETIKSISQQSGARIELQRNPPPNADPNMKLFTIRGTPQQID 61

Query: 612 AAENLIQAFI 621
            A  LI+  I
Sbjct: 62  YARQLIEEKI 71

>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 = 53.0 bits (127), Expect = 9e-10
 Identities = 16/75 (21%), Positives = 29/75 (38%), Gaps = 5/75 (6%)

Query: 140 EECQILVPSSQSANIIGKAGATIKRLRSKTRTSIKVTPKDASEPTHSCAMEFDNFVLISG 199
           +E   +VP+ ++  IIGK G TIK +  ++   I++          +          I G
Sbjct: 1   QEFNFIVPTGKTGLIIGKGGETIKSISQQSGARIELQRNPPPNADPN-----MKLFTIRG 55

Query: 200 ESEAVKKALFAISAI 214
             + +  A   I   
Sbjct: 56  TPQQIDYARQLIEEK 70

>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 = 51.8 bits (124), Expect = 2e-09
 Identities = 18/67 (26%), Positives = 30/67 (44%), Gaps = 1/67 (1%)

Query: 390 TIRLLVSSKVIGCIIGKSGSIINEIRKRTKADVRISKGDKPKCADANDELVEVVGEVGSV 449
               +V +   G IIGK G  I  I +++ A + + + + P  AD N +L  + G    +
Sbjct: 2   EFNFIVPTGKTGLIIGKGGETIKSISQQSGARIELQR-NPPPNADPNMKLFTIRGTPQQI 60

Query: 450 RDALVQI 456
             A   I
Sbjct: 61  DYARQLI 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 = 49.5 bits (118), Expect = 1e-08
 Identities = 25/75 (33%), Positives = 37/75 (49%), Gaps = 9/75 (12%)

Query: 310 IRVLCPFNKIGRVIGKGGGTIKSIRQASGAQIDVDDTKD---NRDECVITVTAIESPDDI 366
              + P  K G +IGKGG TIKSI Q SGA+I++        + +  + T+    +P  I
Sbjct: 3   FNFIVPTGKTGLIIGKGGETIKSISQQSGARIELQRNPPPNADPNMKLFTIRG--TPQQI 60

Query: 367 KSMAVEAVLLLQTKI 381
                 A  L++ KI
Sbjct: 61  D----YARQLIEEKI 71

>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 = 48.7 bits (116), Expect = 3e-08
 Identities = 16/51 (31%), Positives = 27/51 (52%), Gaps = 3/51 (5%)

Query: 39 YRILCPDGVIGSVIGKSGKVINSIRQETRARVKVV---DPFPGAKDRVVTI 86
          +  + P G  G +IGK G+ I SI Q++ AR+++     P      ++ TI
Sbjct: 3  FNFIVPTGKTGLIIGKGGETIKSISQQSGARIELQRNPPPNADPNMKLFTI 53

>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 = 60.0 bits (145), Expect = 4e-12
 Identities = 19/77 (24%), Positives = 37/77 (48%), Gaps = 2/77 (2%)

Query: 547 YGGLPPPLTLEVLVPANAVGKVIGKAGSNLANIRKISGATIEMSDSKSSRG--DRVALIS 604
           +G  P     E+++PA+  G VIGK G  +  +++ +G  + M          D+   I+
Sbjct: 1   HGDGPGNAVQEIMIPASKAGLVIGKGGETIKQLQERAGVKMVMIQDGPQNTGADKPLRIT 60

Query: 605 GTPEQKRAAENLIQAFI 621
           G P + + A+ ++   I
Sbjct: 61  GDPYKVQQAKEMVLELI 77

>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 = 51.9 bits (124), Expect = 2e-09
 Identities = 13/77 (16%), Positives = 33/77 (42%), Gaps = 2/77 (2%)

Query: 388 TVTIRLLVSSKVIGCIIGKSGSIINEIRKRTKADVRISKGDKPKCADANDELVEVVGEVG 447
                +++ +   G +IGK G  I ++++R    + + +          D+ + + G+  
Sbjct: 7   NAVQEIMIPASKAGLVIGKGGETIKQLQERAGVKMVMIQ--DGPQNTGADKPLRITGDPY 64

Query: 448 SVRDALVQIILRLRDDA 464
            V+ A   ++  +RD  
Sbjct: 65  KVQQAKEMVLELIRDQG 81

>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 = 51.5 bits (123), Expect = 4e-09
 Identities = 16/74 (21%), Positives = 36/74 (48%), Gaps = 6/74 (8%)

Query: 142 CQILVPSSQSANIIGKAGATIKRLRSKTRTSIKVTPKDASEPTHSCAMEFDNFVLISGES 201
            +I++P+S++  +IGK G TIK+L+ +    + +                D  + I+G+ 
Sbjct: 10  QEIMIPASKAGLVIGKGGETIKQLQERAGVKMVMIQDG------PQNTGADKPLRITGDP 63

Query: 202 EAVKKALFAISAIM 215
             V++A   +  ++
Sbjct: 64  YKVQQAKEMVLELI 77

>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 = 51.5 bits (123), Expect = 4e-09
 Identities = 18/80 (22%), Positives = 35/80 (43%), Gaps = 4/80 (5%)

Query: 305 SEELVIRVLCPFNKIGRVIGKGGGTIKSIRQASGAQIDVDDTKDNRDECVITVTAIESPD 364
               V  ++ P +K G VIGKGG TIK +++ +G ++ +             +     P 
Sbjct: 5   PGNAVQEIMIPASKAGLVIGKGGETIKQLQERAGVKMVMIQDGPQNTGADKPLRITGDPY 64

Query: 365 DIKSMAVEAVLLLQTKINDE 384
            ++    +A  ++   I D+
Sbjct: 65  KVQ----QAKEMVLELIRDQ 80

>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 = 47.3 bits (112), Expect = 1e-07
 Identities = 14/64 (21%), Positives = 28/64 (43%), Gaps = 5/64 (7%)

Query: 36 SVIYRILCPDGVIGSVIGKSGKVINSIRQETRARVKVVD--PFPGAKDRVVTIYSHVKDK 93
          + +  I+ P    G VIGK G+ I  +++    ++ ++   P     D+ + I     D 
Sbjct: 7  NAVQEIMIPASKAGLVIGKGGETIKQLQERAGVKMVMIQDGPQNTGADKPLRITG---DP 63

Query: 94 EDVE 97
            V+
Sbjct: 64 YKVQ 67

>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 = 58.1 bits (140), Expect = 4e-11
 Identities = 23/71 (32%), Positives = 39/71 (54%), Gaps = 2/71 (2%)

Query: 553 PLTLEVLVPANAVGKVIGKAGSNLANIRKISGATIEMSD--SKSSRGDRVALISGTPEQK 610
           P+  ++ VP  +VG++IG+ G  + +I K SGA I        +    R+  ISGT ++ 
Sbjct: 14  PVFEQLSVPQRSVGRIIGRGGETIRSICKASGAKITCDKESEGTLLLSRLIKISGTQKEV 73

Query: 611 RAAENLIQAFI 621
            AA++LI   +
Sbjct: 74  AAAKHLILEKV 84

>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 = 55.0 bits (132), Expect = 4e-10
 Identities = 18/84 (21%), Positives = 36/84 (42%), Gaps = 2/84 (2%)

Query: 385 DDDTVTIRLLVSSKVIGCIIGKSGSIINEIRKRTKADVRISKGDKPKCADANDELVEVVG 444
           ++  V  +L V  + +G IIG+ G  I  I K + A +      + +       L+++ G
Sbjct: 11  ENTPVFEQLSVPQRSVGRIIGRGGETIRSICKASGAKITCD--KESEGTLLLSRLIKISG 68

Query: 445 EVGSVRDALVQIILRLRDDALKDR 468
               V  A   I+ ++ +D    +
Sbjct: 69  TQKEVAAAKHLILEKVSEDEELRK 92

>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 = 52.7 bits (126), Expect = 3e-09
 Identities = 20/84 (23%), Positives = 44/84 (52%), Gaps = 4/84 (4%)

Query: 303 SQSEELVIRVLCPFNKIGRVIGKGGGTIKSIRQASGAQIDVDDTKDNRDECVITVTAIES 362
           +++  +  ++  P   +GR+IG+GG TI+SI +ASGA+I  D   +        +    +
Sbjct: 10  TENTPVFEQLSVPQRSVGRIIGRGGETIRSICKASGAKITCDKESEGTLLLSRLIKISGT 69

Query: 363 PDDIKSMAVEAVLLLQTKINDEDD 386
             ++      A  L+  K++++++
Sbjct: 70  QKEVA----AAKHLILEKVSEDEE 89

>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 = 49.6 bits (118), Expect = 4e-08
 Identities = 16/73 (21%), Positives = 26/73 (35%), Gaps = 6/73 (8%)

Query: 143 QILVPSSQSANIIGKAGATIKRLRSKTRTSIKVTPKDASEPTHSCAMEFDNFVLISGESE 202
           Q+ VP      IIG+ G TI+ +   +   I    +          +     + ISG  +
Sbjct: 18  QLSVPQRSVGRIIGRGGETIRSICKASGAKITCDKES------EGTLLLSRLIKISGTQK 71

Query: 203 AVKKALFAISAIM 215
            V  A   I   +
Sbjct: 72  EVAAAKHLILEKV 84

>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 = 46.5 bits (110), Expect = 4e-07
 Identities = 14/63 (22%), Positives = 29/63 (46%), Gaps = 5/63 (7%)

Query: 37 VIYRILCPDGVIGSVIGKSGKVINSIRQETRARVKVVDPFPGA--KDRVVTIYSHVKDKE 94
          V  ++  P   +G +IG+ G+ I SI + + A++       G     R++ I      ++
Sbjct: 15 VFEQLSVPQRSVGRIIGRGGETIRSICKASGAKITCDKESEGTLLLSRLIKISG---TQK 71

Query: 95 DVE 97
          +V 
Sbjct: 72 EVA 74

>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 = 56.0 bits (135), Expect = 2e-10
 Identities = 15/69 (21%), Positives = 28/69 (40%), Gaps = 2/69 (2%)

Query: 553 PLTLEVLVPANAVGKVIGKAGSNLANIRKISGATIEMSDSKSSRGDRVALISGTPEQKRA 612
           P+T+EV VP +    VIG+ GS +  +       I +   +      +  I+G       
Sbjct: 9   PVTIEVEVPFDLHRYVIGQKGSGIRKMMDEFEVNIHVPAPEL--QSDIIAITGLAANLDR 66

Query: 613 AENLIQAFI 621
           A+  +   +
Sbjct: 67  AKAGLLERV 75

>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 = 49.8 bits (119), Expect = 2e-08
 Identities = 11/73 (15%), Positives = 29/73 (39%), Gaps = 10/73 (13%)

Query: 143 QILVPSSQSANIIGKAGATIKRLRSKTRTSIKVTPKDASEPTHSCAMEFDNFVLISGESE 202
           ++ VP      +IG+ G+ I+++  +   +I V   +               + I+G + 
Sbjct: 13  EVEVPFDLHRYVIGQKGSGIRKMMDEFEVNIHVPAPELQSDI----------IAITGLAA 62

Query: 203 AVKKALFAISAIM 215
            + +A   +   +
Sbjct: 63  NLDRAKAGLLERV 75

>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 = 48.7 bits (116), Expect = 5e-08
 Identities = 18/78 (23%), Positives = 29/78 (37%), Gaps = 5/78 (6%)

Query: 310 IRVLCPFNKIGRVIGKGGGTIKSIRQASGAQIDVDDTKDNRDECVITVTAIESPDDIKSM 369
           I V  PF+    VIG+ G  I+ +       I V   +   D   IT        ++   
Sbjct: 12  IEVEVPFDLHRYVIGQKGSGIRKMMDEFEVNIHVPAPELQSDIIAITGL----AANLD-R 66

Query: 370 AVEAVLLLQTKINDEDDD 387
           A   +L    ++  E +D
Sbjct: 67  AKAGLLERVKELQAEQED 84

>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 = 46.7 bits (111), Expect = 2e-07
 Identities = 12/74 (16%), Positives = 34/74 (45%), Gaps = 6/74 (8%)

Query: 389 VTIRLLVSSKVIGCIIGKSGSIINEIRKRTKADVRISKGDKPKCADANDELVEVVGEVGS 448
           VTI + V   +   +IG+ GS I ++    + ++ +         +   +++ + G   +
Sbjct: 10  VTIEVEVPFDLHRYVIGQKGSGIRKMMDEFEVNIHVPA------PELQSDIIAITGLAAN 63

Query: 449 VRDALVQIILRLRD 462
           +  A   ++ R+++
Sbjct: 64  LDRAKAGLLERVKE 77

>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 = 44.4 bits (105), Expect = 1e-06
 Identities = 12/61 (19%), Positives = 23/61 (37%), Gaps = 5/61 (8%)

Query: 37 VIYRILCPDGVIGSVIGKSGKVINSIRQETRARVKVVDPFPGAKDRVVTIYSHVKDKEDV 96
          V   +  P  +   VIG+ G  I  +  E    + V  P P  +  ++ I        ++
Sbjct: 10 VTIEVEVPFDLHRYVIGQKGSGIRKMMDEFEVNIHV--PAPELQSDIIAITG---LAANL 64

Query: 97 E 97
          +
Sbjct: 65 D 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 = 54.7 bits (132), Expect = 3e-10
 Identities = 14/67 (20%), Positives = 24/67 (35%), Gaps = 2/67 (2%)

Query: 555 TLEVLVPANAVGKVIGKAGSNLANIRKISGATIEMSDSKSSRGDRVALISGTPEQKRAAE 614
           +  V +P      VIGK G  L ++   +   I++             I+GT E    A 
Sbjct: 11  SATVAIPKEHHRFVIGKNGEKLQDLELKTATKIQIPRPDD--PSNQIKITGTKEGIEKAR 68

Query: 615 NLIQAFI 621
           + +    
Sbjct: 69  HEVLLIS 75

>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 = 51.6 bits (124), Expect = 4e-09
 Identities = 18/88 (20%), Positives = 34/88 (38%), Gaps = 10/88 (11%)

Query: 134 KKRKEKEECQILVPSSQSANIIGKAGATIKRLRSKTRTSIKVTPKDASEPTHSCAMEFDN 193
            + + +    + +P      +IGK G  ++ L  KT T I++   D              
Sbjct: 4   ARLQTQASATVAIPKEHHRFVIGKNGEKLQDLELKTATKIQIPRPDDPSNQ--------- 54

Query: 194 FVLISGESEAVKKALFAISAIMYKFSPR 221
            + I+G  E ++KA   +  I  +   R
Sbjct: 55  -IKITGTKEGIEKARHEVLLISAEQDKR 81

>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 = 49.3 bits (118), Expect = 2e-08
 Identities = 16/84 (19%), Positives = 31/84 (36%), Gaps = 8/84 (9%)

Query: 302 ASQSEELVIRVLCPFNKIGRVIGKGGGTIKSIRQASGAQIDVDDTKDNRDECVITVTAIE 361
           A    +    V  P      VIGK G  ++ +   +  +I +    D  ++  IT T   
Sbjct: 4   ARLQTQASATVAIPKEHHRFVIGKNGEKLQDLELKTATKIQIPRPDDPSNQIKITGT--- 60

Query: 362 SPDDIKSMAVEAVLLLQTKINDED 385
             + I+    +A   +     ++D
Sbjct: 61  -KEGIE----KARHEVLLISAEQD 79

>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 = 48.5 bits (116), Expect = 5e-08
 Identities = 10/77 (12%), Positives = 29/77 (37%), Gaps = 6/77 (7%)

Query: 380 KINDEDDDTVTIRLLVSSKVIGCIIGKSGSIINEIRKRTKADVRISKGDKPKCADANDEL 439
            I        +  + +  +    +IGK+G  + ++  +T   ++I +       D     
Sbjct: 1   DIVARLQTQASATVAIPKEHHRFVIGKNGEKLQDLELKTATKIQIPR------PDDPSNQ 54

Query: 440 VEVVGEVGSVRDALVQI 456
           +++ G    +  A  ++
Sbjct: 55  IKITGTKEGIEKARHEV 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 = 45.1 bits (107), Expect = 6e-07
 Identities = 13/64 (20%), Positives = 26/64 (40%), Gaps = 5/64 (7%)

Query: 34 EESVIYRILCPDGVIGSVIGKSGKVINSIRQETRARVKVVDPFPGAKDRVVTIYSHVKDK 93
          +      +  P      VIGK+G+ +  +  +T  ++++  P P      + I      K
Sbjct: 7  QTQASATVAIPKEHHRFVIGKNGEKLQDLELKTATKIQI--PRPDDPSNQIKITG---TK 61

Query: 94 EDVE 97
          E +E
Sbjct: 62 EGIE 65

>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 = 52.5 bits (126), Expect = 2e-09
 Identities = 16/68 (23%), Positives = 27/68 (39%), Gaps = 1/68 (1%)

Query: 555 TLEVLVPANAVGKVIGKAGSNLANIRKISGATIEMSDSKS-SRGDRVALISGTPEQKRAA 613
            L V V      K+IG+ G+ +  IR      I+  D    ++      I+G  +   AA
Sbjct: 11  KLSVTVDPKYHPKIIGRKGAVITQIRLEHDVNIQFPDKDDGNQPQDQITITGYEKNTEAA 70

Query: 614 ENLIQAFI 621
            + I   +
Sbjct: 71  RDAILRIV 78

>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 = 50.6 bits (121), Expect = 9e-09
 Identities = 17/75 (22%), Positives = 31/75 (41%), Gaps = 7/75 (9%)

Query: 141 ECQILVPSSQSANIIGKAGATIKRLRSKTRTSIKVTPKDASEPTHSCAMEFDNFVLISGE 200
           +  + V       IIG+ GA I ++R +   +I+   KD             + + I+G 
Sbjct: 11  KLSVTVDPKYHPKIIGRKGAVITQIRLEHDVNIQFPDKDDGNQP-------QDQITITGY 63

Query: 201 SEAVKKALFAISAIM 215
            +  + A  AI  I+
Sbjct: 64  EKNTEAARDAILRIV 78

>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 = 48.7 bits (116), Expect = 4e-08
 Identities = 14/81 (17%), Positives = 32/81 (39%), Gaps = 3/81 (3%)

Query: 382 NDEDDDTVTIRLLVSSKVIGCIIGKSGSIINEIRKRTKADVRISKGDKPKCADANDELVE 441
            D    +  + + V  K    IIG+ G++I +IR     +++    D     +   + + 
Sbjct: 3   EDRALRSFKLSVTVDPKYHPKIIGRKGAVITQIRLEHDVNIQFPDKDDG---NQPQDQIT 59

Query: 442 VVGEVGSVRDALVQIILRLRD 462
           + G   +   A   I+  + +
Sbjct: 60  ITGYEKNTEAARDAILRIVGE 80

>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 = 44.5 bits (105), Expect = 1e-06
 Identities = 15/78 (19%), Positives = 28/78 (35%), Gaps = 7/78 (8%)

Query: 310 IRVLCPFNKIGRVIGKGGGTIKSIRQASGAQIDVDDTKD-NRDECVITVTAIESPDDIKS 368
           + V        ++IG+ G  I  IR      I   D  D N+ +  IT+T      + + 
Sbjct: 12  LSVTVDPKYHPKIIGRKGAVITQIRLEHDVNIQFPDKDDGNQPQDQITITG--YEKNTE- 68

Query: 369 MAVEAVLLLQTKINDEDD 386
               A   +   + + + 
Sbjct: 69  ---AARDAILRIVGELEQ 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 = 41.8 bits (98), Expect = 1e-05
 Identities = 12/59 (20%), Positives = 21/59 (35%), Gaps = 4/59 (6%)

Query: 40 RILCPDGVIGSVIGKSGKVINSIRQETRARVKVVD-PFPGAKDRVVTIYSHVKDKEDVE 97
           +         +IG+ G VI  IR E    ++  D          +TI      +++ E
Sbjct: 13 SVTVDPKYHPKIIGRKGAVITQIRLEHDVNIQFPDKDDGNQPQDQITITG---YEKNTE 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 = 49.5 bits (118), Expect = 2e-08
 Identities = 15/70 (21%), Positives = 26/70 (37%), Gaps = 3/70 (4%)

Query: 550 LPPPLTLEVLVPANAVGKVIGKAGSNLANIRKISGATIEMSDSKSSRGDRVALISGTPEQ 609
           L      E +V  + +G  IG  GSN+   RK+ G T    D          +   + + 
Sbjct: 4   LAAAFHEEFVVREDLMGLAIGTHGSNIQQARKVPGVTAIELD---EDTGTFRIYGESADA 60

Query: 610 KRAAENLIQA 619
            + A   ++ 
Sbjct: 61  VKKARGFLEF 70

>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 = 39.1 bits (91), Expect = 9e-05
 Identities = 12/49 (24%), Positives = 19/49 (38%), Gaps = 4/49 (8%)

Query: 300 VGASQSEELVIRVLCPFNKIGRVIGKGGGTIKSIRQASGAQIDVDDTKD 348
           + A+  EE V+      + +G  IG  G  I+  R+  G      D   
Sbjct: 4   LAAAFHEEFVV----REDLMGLAIGTHGSNIQQARKVPGVTAIELDEDT 48

>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 = 49.4 bits (118), Expect = 2e-08
 Identities = 20/77 (25%), Positives = 33/77 (42%), Gaps = 5/77 (6%)

Query: 380 KINDEDDDTVTIRLLVSSKVIGCIIGKSGSIINEIRKRTKADVRISKGDKPKCADANDEL 439
           +I  E +  V+  + +  +V   IIG  G  I +I    K D+R      P+    +   
Sbjct: 1   RIVGELEQMVSEDVPLDHRVHARIIGARGKAIRKIMDEFKVDIRF-----PQSGAPDPNC 55

Query: 440 VEVVGEVGSVRDALVQI 456
           V V G   +V +A+  I
Sbjct: 56  VTVTGLPENVEEAIDHI 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 = 2e-07
 Identities = 13/67 (19%), Positives = 24/67 (35%), Gaps = 1/67 (1%)

Query: 555 TLEVLVPANAVGKVIGKAGSNLANIRKISGATIEMSDSKSSRGDRVALISGTPEQKRAAE 614
           + +V +      ++IG  G  +  I       I    S +   + V  ++G PE    A 
Sbjct: 11  SEDVPLDHRVHARIIGARGKAIRKIMDEFKVDIRFPQSGAPDPNCVT-VTGLPENVEEAI 69

Query: 615 NLIQAFI 621
           + I    
Sbjct: 70  DHILNLE 76

>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 = 46.3 bits (110), Expect = 3e-07
 Identities = 15/85 (17%), Positives = 36/85 (42%), Gaps = 9/85 (10%)

Query: 134 KKRKEKEECQILVPSSQSANIIGKAGATIKRLRSKTRTSIKVTPKDASEPTHSCAMEFDN 193
            + ++     + +     A IIG  G  I+++  + +  I+  P+  +           N
Sbjct: 4   GELEQMVSEDVPLDHRVHARIIGARGKAIRKIMDEFKVDIRF-PQSGAPD--------PN 54

Query: 194 FVLISGESEAVKKALFAISAIMYKF 218
            V ++G  E V++A+  I  +  ++
Sbjct: 55  CVTVTGLPENVEEAIDHILNLEEEY 79

>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 = 42.5 bits (100), Expect = 7e-06
 Identities = 11/68 (16%), Positives = 19/68 (27%)

Query: 302 ASQSEELVIRVLCPFNKIGRVIGKGGGTIKSIRQASGAQIDVDDTKDNRDECVITVTAIE 361
               + +   V        R+IG  G  I+ I       I    +      CV      E
Sbjct: 4   GELEQMVSEDVPLDHRVHARIIGARGKAIRKIMDEFKVDIRFPQSGAPDPNCVTVTGLPE 63

Query: 362 SPDDIKSM 369
           + ++    
Sbjct: 64  NVEEAIDH 71

>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 = 39.4 bits (92), Expect = 7e-05
 Identities = 14/64 (21%), Positives = 22/64 (34%), Gaps = 4/64 (6%)

Query: 34 EESVIYRILCPDGVIGSVIGKSGKVINSIRQETRARVKVVDPFPGAKDRVVTIYSHVKDK 93
          E+ V   +     V   +IG  GK I  I  E +  ++         + V          
Sbjct: 7  EQMVSEDVPLDHRVHARIIGARGKAIRKIMDEFKVDIRFPQSGAPDPNCVTVT----GLP 62

Query: 94 EDVE 97
          E+VE
Sbjct: 63 ENVE 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 = 48.6 bits (116), Expect = 3e-08
 Identities = 11/65 (16%), Positives = 27/65 (41%), Gaps = 2/65 (3%)

Query: 555 TLEVLVPANAVGKVIGKAGSNLANIRKISGATIEMSDSKSSRGDRVALISGTPEQKRAAE 614
            +E+ +       +IGK+G+N+  I+     ++ +          +  I G P+  + A+
Sbjct: 6   YVEINIDHKFHRHLIGKSGANINRIKDQYKVSVRIPPDSE--KSNLIRIEGDPQGVQQAK 63

Query: 615 NLIQA 619
             +  
Sbjct: 64  RELLE 68

>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 = 46.3 bits (110), Expect = 2e-07
 Identities = 16/76 (21%), Positives = 36/76 (47%), Gaps = 10/76 (13%)

Query: 140 EECQILVPSSQSANIIGKAGATIKRLRSKTRTSIKVTPKDASEPTHSCAMEFDNFVLISG 199
           +  +I +      ++IGK+GA I R++ + + S+++ P            E  N + I G
Sbjct: 5   DYVEINIDHKFHRHLIGKSGANINRIKDQYKVSVRIPPD----------SEKSNLIRIEG 54

Query: 200 ESEAVKKALFAISAIM 215
           + + V++A   +  + 
Sbjct: 55  DPQGVQQAKRELLELA 70

>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 = 4e-07
 Identities = 7/47 (14%), Positives = 15/47 (31%)

Query: 310 IRVLCPFNKIGRVIGKGGGTIKSIRQASGAQIDVDDTKDNRDECVIT 356
           + +         +IGK G  I  I+      + +    +  +   I 
Sbjct: 7   VEINIDHKFHRHLIGKSGANINRIKDQYKVSVRIPPDSEKSNLIRIE 53

>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 = 41.7 bits (98), Expect = 8e-06
 Identities = 17/71 (23%), Positives = 32/71 (45%), Gaps = 6/71 (8%)

Query: 386 DDTVTIRLLVSSKVIGCIIGKSGSIINEIRKRTKADVRISKGDKPKCADANDELVEVVGE 445
           +    + + +  K    +IGKSG+ IN I+ + K  VRI    +         L+ + G+
Sbjct: 2   NRMDYVEINIDHKFHRHLIGKSGANINRIKDQYKVSVRIPPDSEK------SNLIRIEGD 55

Query: 446 VGSVRDALVQI 456
              V+ A  ++
Sbjct: 56  PQGVQQAKREL 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 = 39.3 bits (92), Expect = 6e-05
 Identities = 13/58 (22%), Positives = 23/58 (39%), Gaps = 5/58 (8%)

Query: 40 RILCPDGVIGSVIGKSGKVINSIRQETRARVKVVDPFPGAKDRVVTIYSHVKDKEDVE 97
           I         +IGKSG  IN I+ + +  V++          ++ I     D + V+
Sbjct: 8  EINIDHKFHRHLIGKSGANINRIKDQYKVSVRIPPDSEK--SNLIRIEG---DPQGVQ 60

>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 = 47.7 bits (114), Expect = 4e-08
 Identities = 18/55 (32%), Positives = 29/55 (52%), Gaps = 6/55 (10%)

Query: 309 VIRVLCPFNKIGRVIGKGGGTIKSIRQASGAQIDVDDTKDNRDECVITVTAIESP 363
           +I V  P +KIG VIG     I  I++ +GA+I ++      D+  I + A + P
Sbjct: 4   IITVKIPVDKIGEVIGPKRQMINQIQEDTGAEITIE------DDGTIYIGAADGP 52

>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 = 43.5 bits (103), Expect = 1e-06
 Identities = 15/52 (28%), Positives = 25/52 (48%), Gaps = 6/52 (11%)

Query: 37 VIYRILCPDGVIGSVIGKSGKVINSIRQETRARVKVVDPFPGAKDRVVTIYS 88
           I  +  P   IG VIG   ++IN I+++T A + + D      D  + I +
Sbjct: 3  RIITVKIPVDKIGEVIGPKRQMINQIQEDTGAEITIED------DGTIYIGA 48

>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 = 35.0 bits (81), Expect = 0.001
 Identities = 14/54 (25%), Positives = 24/54 (44%), Gaps = 6/54 (11%)

Query: 553 PLTLEVLVPANAVGKVIGKAGSNLANIRKISGATIEMSDSKSSRGDRVALISGT 606
           P  + V +P + +G+VIG     +  I++ +GA I + D      D    I   
Sbjct: 2   PRIITVKIPVDKIGEVIGPKRQMINQIQEDTGAEITIED------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 = 33.9 bits (78), Expect = 0.004
 Identities = 11/37 (29%), Positives = 20/37 (54%)

Query: 389 VTIRLLVSSKVIGCIIGKSGSIINEIRKRTKADVRIS 425
             I + +    IG +IG    +IN+I++ T A++ I 
Sbjct: 3   RIITVKIPVDKIGEVIGPKRQMINQIQEDTGAEITIE 39

>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 = 45.5 bits (108), Expect = 6e-07
 Identities = 17/65 (26%), Positives = 23/65 (35%), Gaps = 3/65 (4%)

Query: 310 IRVLCPFNKIGRVIGKGGGTIKSIRQASGAQIDVDDTKDNRDECVITVTAIESPDDIKSM 369
           I V     ++G VIG  G     I + +G  I VD         ++   A   P      
Sbjct: 5   IYVKVKPERLGAVIGPRGEVKAEIMRRTGTVITVD---TENSMVIVEPEAEGIPPVNLMK 61

Query: 370 AVEAV 374
           A E V
Sbjct: 62  AAEVV 66

>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 = 42.5 bits (100), Expect = 6e-06
 Identities = 15/64 (23%), Positives = 23/64 (35%)

Query: 556 LEVLVPANAVGKVIGKAGSNLANIRKISGATIEMSDSKSSRGDRVALISGTPEQKRAAEN 615
           + V V    +G VIG  G   A I + +G  I +    S            P     A  
Sbjct: 5   IYVKVKPERLGAVIGPRGEVKAEIMRRTGTVITVDTENSMVIVEPEAEGIPPVNLMKAAE 64

Query: 616 LIQA 619
           +++A
Sbjct: 65  VVKA 68

>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 = 41.3 bits (97), Expect = 2e-05
 Identities = 15/78 (19%), Positives = 25/78 (32%), Gaps = 8/78 (10%)

Query: 143 QILVPSSQSANIIGKAGATIKRLRSKTRTSIKVTPKDASEPTHSCAMEFDNFVLISGESE 202
            + V   +   +IG  G     +  +T T I V  +++       A              
Sbjct: 6   YVKVKPERLGAVIGPRGEVKAEIMRRTGTVITVDTENSMVIVEPEAEG--------IPPV 57

Query: 203 AVKKALFAISAIMYKFSP 220
            + KA   + AI   F P
Sbjct: 58  NLMKAAEVVKAISLGFPP 75

>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 = 34.8 bits (80), Expect = 0.003
 Identities = 9/32 (28%), Positives = 15/32 (46%)

Query: 41 ILCPDGVIGSVIGKSGKVINSIRQETRARVKV 72
          +      +G+VIG  G+V   I + T   + V
Sbjct: 7  VKVKPERLGAVIGPRGEVKAEIMRRTGTVITV 38

>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 = 45.1 bits (107), Expect = 7e-07
 Identities = 18/67 (26%), Positives = 27/67 (40%), Gaps = 9/67 (13%)

Query: 312 VLCPFNKIGRVIGKGGGTIKSIRQASGAQIDVDDTKDNRDECVITVTAIESPDDIKSMAV 371
           V     ++ RVIGK G  IK ++     QI V          +I V        +   A 
Sbjct: 5   VAINPARVPRVIGKKGSMIKLLKSELDVQIVVG------QNGLIWVNG--DRRKVSI-AE 55

Query: 372 EAVLLLQ 378
           EA+ L++
Sbjct: 56  EAIYLIE 62

>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 = 45.1 bits (107), Expect = 8e-07
 Identities = 13/62 (20%), Positives = 24/62 (38%), Gaps = 6/62 (9%)

Query: 558 VLVPANAVGKVIGKAGSNLANIRKISGATIEMSDSKSSRGDRVALISGTPEQKRAAENLI 617
           V +    V +VIGK GS +  ++      I +        + +  ++G   +   AE  I
Sbjct: 5   VAINPARVPRVIGKKGSMIKLLKSELDVQIVVGQ------NGLIWVNGDRRKVSIAEEAI 58

Query: 618 QA 619
             
Sbjct: 59  YL 60

>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 = 39.0 bits (91), Expect = 1e-04
 Identities = 16/72 (22%), Positives = 29/72 (40%), Gaps = 14/72 (19%)

Query: 144 ILVPSSQSANIIGKAGATIKRLRSKTRTSIKVTPKDASEPTHSCAMEFDNFVLISGESEA 203
           + +  ++   +IGK G+ IK L+S+    I V                +  + ++G+   
Sbjct: 5   VAINPARVPRVIGKKGSMIKLLKSELDVQIVVGQ--------------NGLIWVNGDRRK 50

Query: 204 VKKALFAISAIM 215
           V  A  AI  I 
Sbjct: 51  VSIAEEAIYLIE 62

>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 = 38.6 bits (90), Expect = 1e-04
 Identities = 10/57 (17%), Positives = 23/57 (40%), Gaps = 9/57 (15%)

Query: 41 ILCPDGVIGSVIGKSGKVINSIRQETRARVKVVDPFPGAKDRVVTIYSHVKDKEDVE 97
          +      +  VIGK G +I  ++ E   ++ V       ++ ++ +     D+  V 
Sbjct: 5  VAINPARVPRVIGKKGSMIKLLKSELDVQIVV------GQNGLIWVNG---DRRKVS 52

>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 = 34.7 bits (80), Expect = 0.003
 Identities = 13/70 (18%), Positives = 29/70 (41%), Gaps = 11/70 (15%)

Query: 395 VSSKVIGCIIGKSGSIINEIRKRTKADVRISKGDKPKCADANDELVEVVGEVGSVRDALV 454
           ++   +  +IGK GS+I  ++      + + +          + L+ V G+   V  A  
Sbjct: 7   INPARVPRVIGKKGSMIKLLKSELDVQIVVGQ----------NGLIWVNGDRRKVSIA-E 55

Query: 455 QIILRLRDDA 464
           + I  +  +A
Sbjct: 56  EAIYLIEQEA 65

>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 = 44.5 bits (105), Expect = 1e-06
 Identities = 13/67 (19%), Positives = 23/67 (34%), Gaps = 1/67 (1%)

Query: 555 TLEVLVPANAVGKVIGKAGSNLANIRKISGATIEMSDSKSSRGDRVALISGTPEQKRAAE 614
            +EV +PA     +IG  G  + +I +  G    +       G    +I G       A+
Sbjct: 11  EVEVSIPAKLHNSLIGTKGRLIRSIMEECGGVH-IHFPVEGSGSDTVVIRGPSSDVEKAK 69

Query: 615 NLIQAFI 621
             +    
Sbjct: 70  KQLLHLA 76

>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 = 42.5 bits (100), Expect = 6e-06
 Identities = 14/82 (17%), Positives = 30/82 (36%), Gaps = 5/82 (6%)

Query: 381 INDEDDDTVTIRLLVSSKVIGCIIGKSGSIINEIRKRTKADVRISKGDKPKCADANDELV 440
           I  +  +   + + + +K+   +IG  G +I  I +     V I          +  + V
Sbjct: 2   IQKDLANIAEVEVSIPAKLHNSLIGTKGRLIRSIMEE-CGGVHI----HFPVEGSGSDTV 56

Query: 441 EVVGEVGSVRDALVQIILRLRD 462
            + G    V  A  Q++    +
Sbjct: 57  VIRGPSSDVEKAKKQLLHLAEE 78

>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 = 5e-05
 Identities = 15/83 (18%), Positives = 31/83 (37%), Gaps = 11/83 (13%)

Query: 134 KKRKEKEECQILVPSSQSANIIGKAGATIKRLRSK-TRTSIKVTPKDASEPTHSCAMEFD 192
           K      E ++ +P+    ++IG  G  I+ +  +     I    + +            
Sbjct: 4   KDLANIAEVEVSIPAKLHNSLIGTKGRLIRSIMEECGGVHIHFPVEGSGS---------- 53

Query: 193 NFVLISGESEAVKKALFAISAIM 215
           + V+I G S  V+KA   +  + 
Sbjct: 54  DTVVIRGPSSDVEKAKKQLLHLA 76

>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 = 38.7 bits (90), Expect = 1e-04
 Identities = 13/48 (27%), Positives = 17/48 (35%), Gaps = 1/48 (2%)

Query: 310 IRVLCPFNKIGRVIGKGGGTIKSIRQAS-GAQIDVDDTKDNRDECVIT 356
           + V  P      +IG  G  I+SI +   G  I         D  VI 
Sbjct: 12  VEVSIPAKLHNSLIGTKGRLIRSIMEECGGVHIHFPVEGSGSDTVVIR 59

>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 = 35.2 bits (81), Expect = 0.002
 Identities = 18/68 (26%), Positives = 27/68 (39%), Gaps = 4/68 (5%)

Query: 30 EKGNEESVIYRILCPDGVIGSVIGKSGKVINSIRQETRARVKVVDPFPGAKDRVVTIYSH 89
          +K         +  P  +  S+IG  G++I SI +E    V +  P  G+    V I   
Sbjct: 3  QKDLANIAEVEVSIPAKLHNSLIGTKGRLIRSIMEEC-GGVHIHFPVEGSGSDTVVIRG- 60

Query: 90 VKDKEDVE 97
               DVE
Sbjct: 61 --PSSDVE 66

>d1tuaa2 d.51.1.1 (A:85-188) Hypothetical protein APE0754 {Aeropyrum pernix [TaxId: 56636]} 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: Hypothetical protein APE0754
species: Aeropyrum pernix [TaxId: 56636]

 Score = 43.5 bits (103), Expect = 5e-06
 Identities = 14/59 (23%), Positives = 26/59 (44%), Gaps = 10/59 (16%)

Query: 319 IGRVIGKGGGTIKSIRQASGAQIDVDDTKDNRDECVITVTAIESPDDIKSMAVEAVLLL 377
            GR+IG+GG   ++I + +   I+V +           V  I   +     A +A+ +L
Sbjct: 24  KGRIIGEGGRARRTIEEMTDTYINVGEY---------EVAIIGDYERAM-AAKQAIEML 72

>d1tuaa2 d.51.1.1 (A:85-188) Hypothetical protein APE0754 {Aeropyrum pernix [TaxId: 56636]} 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: Hypothetical protein APE0754
species: Aeropyrum pernix [TaxId: 56636]

 Score = 35.1 bits (81), Expect = 0.004
 Identities = 12/59 (20%), Positives = 25/59 (42%), Gaps = 7/59 (11%)

Query: 564 AVGKVIGKAGSNLANIRKISGATIEMSDSKSSRGDRVALISGTPEQKRAAENLIQAFIM 622
             G++IG+ G     I +++   I + + + +       I G  E+  AA+  I+    
Sbjct: 23  IKGRIIGEGGRARRTIEEMTDTYINVGEYEVA-------IIGDYERAMAAKQAIEMLAE 74

>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 = 42.4 bits (100), Expect = 7e-06
 Identities = 14/54 (25%), Positives = 23/54 (42%), Gaps = 6/54 (11%)

Query: 315 PFNKIGRVIGKGGGTIKSIRQASGAQIDVDD------TKDNRDECVITVTAIES 362
              K+ RVIG+    +K++ + +  +I V           N D   I V AI+ 
Sbjct: 8   SPAKVPRVIGRKMSMLKTLEEKTECKIFVARNGRIHLECPNEDLEAIAVMAIKI 61

>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 = 35.1 bits (81), Expect = 0.003
 Identities = 11/60 (18%), Positives = 24/60 (40%), Gaps = 5/60 (8%)

Query: 560 VPANAVGKVIGKAGSNLANIRKISGATIEMSDSKSSRGDRVALISGTPEQKRAAENLIQA 619
           +    V +VIG+  S L  + + +   I ++ +      R+ L     + +  A   I+ 
Sbjct: 7   ISPAKVPRVIGRKMSMLKTLEEKTECKIFVARN-----GRIHLECPNEDLEAIAVMAIKI 61

>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 = 40.9 bits (96), Expect = 2e-05
 Identities = 10/35 (28%), Positives = 16/35 (45%)

Query: 312 VLCPFNKIGRVIGKGGGTIKSIRQASGAQIDVDDT 346
           +     K+ RVIGK     +++   SG  I V + 
Sbjct: 5   IDIMPVKVPRVIGKNKSMYETLTSKSGCSIFVANN 39

>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 = 37.8 bits (88), Expect = 2e-04
 Identities = 11/62 (17%), Positives = 24/62 (38%), Gaps = 5/62 (8%)

Query: 558 VLVPANAVGKVIGKAGSNLANIRKISGATIEMSDSKSSRGDRVALISGTPEQKRAAENLI 617
           + +    V +VIGK  S    +   SG +I ++++      R+     +   +      I
Sbjct: 5   IDIMPVKVPRVIGKNKSMYETLTSKSGCSIFVANN-----GRIWATCPSRFSEEILIEAI 59

Query: 618 QA 619
           + 
Sbjct: 60  RK 61

>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 = 35.1 bits (81), Expect = 0.002
 Identities = 7/57 (12%), Positives = 19/57 (33%), Gaps = 8/57 (14%)

Query: 41 ILCPDGVIGSVIGKSGKVINSIRQETRARVKVVDPFPGAKDRVVTIYSHVKDKEDVE 97
          I      +  VIGK+  +  ++  ++   + V +      +  +        +   E
Sbjct: 5  IDIMPVKVPRVIGKNKSMYETLTSKSGCSIFVAN------NGRIWATC--PSRFSEE 53

>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 = 37.9 bits (88), Expect = 3e-04
 Identities = 13/71 (18%), Positives = 29/71 (40%), Gaps = 1/71 (1%)

Query: 372 EAVLLLQTKINDEDDDTVTIRLLVSSKVIGCIIGKSGSIINEIRKR-TKADVRISKGDKP 430
           E +    T++  + +      +   S +   IIGK G  + +I ++  K  +  ++G+  
Sbjct: 4   EKLGQALTEVYAKANSFTVSSVAAPSWLHRFIIGKKGQNLAKITQQMPKVHIEFTEGEDK 63

Query: 431 KCADANDELVE 441
              +   E V 
Sbjct: 64  ITLEGPTEDVS 74

Homologous Domains Detected by HHsearch

Original result of HHsearch against SCOP70(version1.75) database

ID	Length	Definition	Probability
Query	624
d1wvna1	70	Poly(RC)-binding protein 1 {Human (Homo sapiens) [	99.66
d1zzka1	75	HnRNP K, KH3 {Human (Homo sapiens) [TaxId: 9606]}	99.63
d1j4wa1	74	Far upstream binding element, FBP {Human (Homo sap	99.63
d1j4wa2	71	Far upstream binding element, FBP {Human (Homo sap	99.58
d1dtja_	74	Neuro-oncological ventral antigen 2, nova-2, KH3 {	99.57
d1x4na1	79	Far upstream binding element, FBP {Mouse (Mus musc	99.56
d1x4ma1	81	Far upstream binding element, FBP {Mouse (Mus musc	99.56
d2axya1	71	Poly(RC)-binding protein 2 {Human (Homo sapiens) [	99.54
d2axya1	71	Poly(RC)-binding protein 2 {Human (Homo sapiens) [	99.48
d2ctma1	81	Vigilin {Human (Homo sapiens) [TaxId: 9606]}	99.47
d2ctea1	81	Vigilin {Human (Homo sapiens) [TaxId: 9606]}	99.46
d1viga_	71	Vigilin {Human (Homo sapiens) [TaxId: 9606]}	99.45
d2ctla1	84	Vigilin {Human (Homo sapiens) [TaxId: 9606]}	99.45
d1zzka1	75	HnRNP K, KH3 {Human (Homo sapiens) [TaxId: 9606]}	99.45
d1we8a_	104	Tudor and KH domain containing protein, Tdrkh {Mou	99.44
d1x4ma1	81	Far upstream binding element, FBP {Mouse (Mus musc	99.43
d1j4wa1	74	Far upstream binding element, FBP {Human (Homo sap	99.43
d1j4wa2	71	Far upstream binding element, FBP {Human (Homo sap	99.43
d1dtja_	74	Neuro-oncological ventral antigen 2, nova-2, KH3 {	99.42
d1wvna1	70	Poly(RC)-binding protein 1 {Human (Homo sapiens) [	99.41
d2ctja1	82	Vigilin {Human (Homo sapiens) [TaxId: 9606]}	99.4
d1x4na1	79	Far upstream binding element, FBP {Mouse (Mus musc	99.38
d2ctma1	81	Vigilin {Human (Homo sapiens) [TaxId: 9606]}	99.34
d2ctka1	91	Vigilin {Human (Homo sapiens) [TaxId: 9606]}	99.33
d1we8a_	104	Tudor and KH domain containing protein, Tdrkh {Mou	99.33
d2ctla1	84	Vigilin {Human (Homo sapiens) [TaxId: 9606]}	99.32
d2cpqa1	78	Fragile X mental retardation syndrome related prot	99.32
d2ctea1	81	Vigilin {Human (Homo sapiens) [TaxId: 9606]}	99.28
d2ba0a3	84	Exosome complex RNA-binding protein 1, ECR1 {Archa	99.27
d2ctja1	82	Vigilin {Human (Homo sapiens) [TaxId: 9606]}	99.27
d1viga_	71	Vigilin {Human (Homo sapiens) [TaxId: 9606]}	99.26
d2ctfa1	90	Vigilin {Human (Homo sapiens) [TaxId: 9606]}	99.24
d2ctka1	91	Vigilin {Human (Homo sapiens) [TaxId: 9606]}	99.18
d2ctfa1	90	Vigilin {Human (Homo sapiens) [TaxId: 9606]}	99.09
d2cpqa1	78	Fragile X mental retardation syndrome related prot	99.03
d2ba0a3	84	Exosome complex RNA-binding protein 1, ECR1 {Archa	99.02
d1tuaa1	84	Hypothetical protein APE0754 {Aeropyrum pernix [Ta	99.0
d2je6i3	69	Exosome complex RNA-binding protein 1, ECR1 {Sulfo	98.88
d2z0sa2	87	Exosome complex RNA-binding protein 1, ECR1 {Aerop	98.83
d2je6i3	69	Exosome complex RNA-binding protein 1, ECR1 {Sulfo	98.64
d1tuaa1	84	Hypothetical protein APE0754 {Aeropyrum pernix [Ta	98.6
d1tuaa2	104	Hypothetical protein APE0754 {Aeropyrum pernix [Ta	98.59
d1e3ha4	54	Polynucleotide phosphorylase/guanosine pentaphosph	98.53
d2z0sa2	87	Exosome complex RNA-binding protein 1, ECR1 {Aerop	98.49
d1e3ha4	54	Polynucleotide phosphorylase/guanosine pentaphosph	98.48
d1tuaa2	104	Hypothetical protein APE0754 {Aeropyrum pernix [Ta	98.24
d1k1ga_	122	RNA splicing factor 1 {Human (Homo sapiens) [TaxId	98.07
d1k1ga_	122	RNA splicing factor 1 {Human (Homo sapiens) [TaxId	98.05
d2bl5a1	134	Quaking protein A (Xqua) {African clawed frog (Xen	97.55
d2bl5a1	134	Quaking protein A (Xqua) {African clawed frog (Xen	97.47
d2asba3	67	Transcription factor NusA, C-terminal domains {Myc	95.5
d1hh2p3	68	Transcription factor NusA, C-terminal domains {The	95.32
d1hh2p3	68	Transcription factor NusA, C-terminal domains {The	93.67
d2asba3	67	Transcription factor NusA, C-terminal domains {Myc	93.52
d2ja9a2	85	Ribosomal RNA-processing protein 40, RRP40 {Saccha	90.28
d1wh9a_	92	Ribosomal protein S3 N-terminal domain {Mouse (Mus	85.4

>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=5.2e-17  Score=125.22  Aligned_cols=69  Identities=32%  Similarity=0.549  Sum_probs=65.5

Q ss_pred             cEEEEEeccccccceeccCCchHHHHHHHhCCEEEEeCCCCCCCCeEEEEEcCHHHHHHHHHHHHHHHh
Q 006943          554 LTLEVLVPANAVGKVIGKAGSNLANIRKISGATIEMSDSKSSRGDRVALISGTPEQKRAAENLIQAFIM  622 (624)
Q Consensus       554 ~~~~i~VP~~~vg~IIGkgG~~I~~I~~~sGa~I~i~~~~~~~~~r~v~I~Gt~e~v~~A~~lI~~~i~  622 (624)
                      +|.+|.||.+++|+||||+|.+|++|+++|||+|.|+++.++.++|.|+|+|++++|+.|+.||++.|+
T Consensus         2 ~T~~i~VP~~~vg~iIGk~G~~I~~I~~~tga~I~i~~~~~~~~~r~v~I~G~~~~v~~A~~~I~~~is   70 (70)
T d1wvna1           2 TTHELTIPNNLIGCIIGRQGANINEIRQMSGAQIKIANPVEGSSGRQVTITGSAASISLAQYLINARLS   70 (70)
T ss_dssp             EEEEEEEEGGGHHHHHCGGGHHHHHHHHHHCCEEEECCCCTTCSEEEEEEEECHHHHHHHHHHHHHHTC
T ss_pred             eEEEEEEChHhcceeECCCChHHHHHHHHcCcEEEEcCCCCCCCcEEEEEEeCHHHHHHHHHHHHHHcC
Confidence            588999999999999999999999999999999999988888889999999999999999999999874

>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=99.63  E-value=3.4e-16  Score=122.75  Aligned_cols=71  Identities=32%  Similarity=0.559  Sum_probs=66.8

Q ss_pred             CcEEEEEeccccccceeccCCchHHHHHHHhCCEEEEeCCCCCCCCeEEEEEcCHHHHHHHHHHHHHHHhh
Q 006943          553 PLTLEVLVPANAVGKVIGKAGSNLANIRKISGATIEMSDSKSSRGDRVALISGTPEQKRAAENLIQAFIMA  623 (624)
Q Consensus       553 ~~~~~i~VP~~~vg~IIGkgG~~I~~I~~~sGa~I~i~~~~~~~~~r~v~I~Gt~e~v~~A~~lI~~~i~~  623 (624)
                      .+|.+|.||.+++|+|||++|++|++|+++|||+|+|+++.++.++|.|+|+|++++|+.|+.+|+++|..
T Consensus         3 ~~t~~i~VP~~~vg~iIG~~G~~I~~I~~~sga~I~i~~~~~~~~~r~i~I~G~~~~v~~A~~~I~~~i~e   73 (75)
T d1zzka1           3 IITTQVTIPKDLAGSIIGKGGQRIKQIRHESGASIKIDEPLEGSEDRIITITGTQDQIQNAQYLLQNSVKQ   73 (75)
T ss_dssp             CEEEEEEEETTTGGGGTCGGGHHHHHHHHHHCCEEEECCTTSCSSEEEEEEEECHHHHHHHHHHHHHHHHH
T ss_pred             cEEEEEEEChHhcCeeECCCCchHHHHHhhcCCeEEEccCCCCCCceEEEEEeCHHHHHHHHHHHHHHHHh
Confidence            45889999999999999999999999999999999999888788899999999999999999999999863

>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=1.9e-16  Score=123.69  Aligned_cols=70  Identities=27%  Similarity=0.539  Sum_probs=66.5

Q ss_pred             cEEEEEeccccccceeccCCchHHHHHHHhCCEEEEeCCCCCCCCeEEEEEcCHHHHHHHHHHHHHHHhh
Q 006943          554 LTLEVLVPANAVGKVIGKAGSNLANIRKISGATIEMSDSKSSRGDRVALISGTPEQKRAAENLIQAFIMA  623 (624)
Q Consensus       554 ~~~~i~VP~~~vg~IIGkgG~~I~~I~~~sGa~I~i~~~~~~~~~r~v~I~Gt~e~v~~A~~lI~~~i~~  623 (624)
                      .+.+|.||.+++|+||||+|++|++|+++|||+|+|++..++..+|.|+|+|++++|+.|+.+|+++|.+
T Consensus         3 ~~~~i~VP~~~vg~iIGk~G~~I~~I~~~tga~I~i~~~~~~~~~r~v~I~G~~~~v~~A~~~I~~~i~~   72 (74)
T d1j4wa1           3 HMIDVPIPRFAVGIVIGRNGEMIKKIQNDAGVRIQFKPDDGTTPERIAQITGPPDRAQHAAEIITDLLRS   72 (74)
T ss_dssp             EEEEEEEEHHHHHHHHCGGGHHHHHHHHHHCCEEEEECCTTSCSEEEEEEEECHHHHHHHHHHHHHHHHH
T ss_pred             eEEEEEeCHHHCCeeECCCCcHHHHHHHHcCCEEEeccCCCCCCeeEEEEEeCHHHHHHHHHHHHHHHHh
Confidence            3789999999999999999999999999999999999888778899999999999999999999999875

>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=99.58  E-value=8.7e-16  Score=118.72  Aligned_cols=67  Identities=33%  Similarity=0.538  Sum_probs=61.0

Q ss_pred             EEEEEeccccccceeccCCchHHHHHHHhCCEEEEeCCC---CCCCCeEEEEEcCHHHHHHHHHHHHHHH
Q 006943          555 TLEVLVPANAVGKVIGKAGSNLANIRKISGATIEMSDSK---SSRGDRVALISGTPEQKRAAENLIQAFI  621 (624)
Q Consensus       555 ~~~i~VP~~~vg~IIGkgG~~I~~I~~~sGa~I~i~~~~---~~~~~r~v~I~Gt~e~v~~A~~lI~~~i  621 (624)
                      .++|.||.+++|+||||+|++|++|++.|||+|+|+++.   ++..+|.|+|+|++++|+.|+.||+++|
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            578999999999999999999999999999999998654   2456799999999999999999999875

>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=99.57  E-value=1.3e-15  Score=118.81  Aligned_cols=69  Identities=32%  Similarity=0.564  Sum_probs=62.7

Q ss_pred             cEEEEEeccccccceeccCCchHHHHHHHhCCEEEEeCCC---CCCCCeEEEEEcCHHHHHHHHHHHHHHHh
Q 006943          554 LTLEVLVPANAVGKVIGKAGSNLANIRKISGATIEMSDSK---SSRGDRVALISGTPEQKRAAENLIQAFIM  622 (624)
Q Consensus       554 ~~~~i~VP~~~vg~IIGkgG~~I~~I~~~sGa~I~i~~~~---~~~~~r~v~I~Gt~e~v~~A~~lI~~~i~  622 (624)
                      .+.++.||.+++|+||||+|++|++|++.|||+|+|++..   ++.++|.|+|+|++++|+.|+.||+++|+
T Consensus         3 ~~i~i~VP~~~vg~iIGk~G~~Ik~I~~~sga~I~i~~~~~~~~~~~~r~v~I~G~~~~v~~A~~~I~~~is   74 (74)
T d1dtja_           3 ELVEMAVPENLVGAILGKGGKTLVEYQELTGARIQISKKGEFLPGTRNRRVTITGSPAATQAAQYLISQRVT   74 (74)
T ss_dssp             EEEEEEEETTTHHHHHCSTTHHHHHHHHHHCCEEEECCTTCCSTTCCEEEEEEEESHHHHHHHHHHHHHHCC
T ss_pred             EEEEEEeCHHHcceeECCCChhHHHHHHHcCCEEEEccCCCCCCCCCceEEEEEeCHHHHHHHHHHHHHHcC
Confidence            3689999999999999999999999999999999998754   34568999999999999999999999863

>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=99.56  E-value=2.1e-15  Score=119.36  Aligned_cols=71  Identities=28%  Similarity=0.542  Sum_probs=67.2

Q ss_pred             CcEEEEEeccccccceeccCCchHHHHHHHhCCEEEEeCCCCCCCCeEEEEEcCHHHHHHHHHHHHHHHhh
Q 006943          553 PLTLEVLVPANAVGKVIGKAGSNLANIRKISGATIEMSDSKSSRGDRVALISGTPEQKRAAENLIQAFIMA  623 (624)
Q Consensus       553 ~~~~~i~VP~~~vg~IIGkgG~~I~~I~~~sGa~I~i~~~~~~~~~r~v~I~Gt~e~v~~A~~lI~~~i~~  623 (624)
                      .++.+|.||.+++|+|||++|.+|++|++.|||+|+|+++.++..++.|+|+|++++|+.|+.+|.++|..
T Consensus         7 ~~t~~i~IP~~~~g~iIG~~G~~i~~I~~~tg~~I~i~~~~~~~~~r~v~I~G~~~~v~~A~~~I~~~i~e   77 (79)
T d1x4na1           7 VMTEEYKVPDGMVGFIIGRGGEQISRIQQESGCKIQIAPDSGGLPERSCMLTGTPESVQSAKRLLDQIVEK   77 (79)
T ss_dssp             CEEEEEEEEHHHHHHHHCSSSHHHHHHHHHSCCEEEECSCCTTCSEEEEEEEECHHHHHHHHHHHHHHHHH
T ss_pred             cEEEEEEEChHhhcceECCCchhHHHHHHHhCCEEEEcCCCCCCCceEEEEEeCHHHHHHHHHHHHHHHHc
Confidence            46899999999999999999999999999999999999988888899999999999999999999999863

>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=99.56  E-value=2e-15  Score=119.94  Aligned_cols=73  Identities=25%  Similarity=0.492  Sum_probs=65.8

Q ss_pred             CCCcEEEEEeccccccceeccCCchHHHHHHHhCCEEEEeCCC--CCCCCeEEEEEcCHHHHHHHHHHHHHHHhh
Q 006943          551 PPPLTLEVLVPANAVGKVIGKAGSNLANIRKISGATIEMSDSK--SSRGDRVALISGTPEQKRAAENLIQAFIMA  623 (624)
Q Consensus       551 ~~~~~~~i~VP~~~vg~IIGkgG~~I~~I~~~sGa~I~i~~~~--~~~~~r~v~I~Gt~e~v~~A~~lI~~~i~~  623 (624)
                      +..++.+|.||.+++|+||||+|++|++|+++|||+|+|++..  +...+|.|+|+|++++|+.|+.||+++|..
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            3467999999999999999999999999999999999998653  345789999999999999999999998853

>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=99.54  E-value=3.8e-15  Score=114.96  Aligned_cols=68  Identities=28%  Similarity=0.465  Sum_probs=63.0

Q ss_pred             CcEEEEEeccccccceeccCCchHHHHHHHhCCEEEEeCCCCCCCCeEEEEEcCHHHHHHHHHHHHHHHh
Q 006943          553 PLTLEVLVPANAVGKVIGKAGSNLANIRKISGATIEMSDSKSSRGDRVALISGTPEQKRAAENLIQAFIM  622 (624)
Q Consensus       553 ~~~~~i~VP~~~vg~IIGkgG~~I~~I~~~sGa~I~i~~~~~~~~~r~v~I~Gt~e~v~~A~~lI~~~i~  622 (624)
                      .++.+|.||.+.+|+||||+|++|++|++.|||+|+|+++.  .++|+|+|+|++++|+.|+.+|.++|.
T Consensus         3 ~vt~~i~vp~~~~g~IIGk~G~~I~~I~~~tga~I~i~~~~--~~er~v~I~G~~~~v~~A~~~I~~~l~   70 (71)
T d2axya1           3 TLTIRLLMHGKEVGSIIGKKGESVKKMREESGARINISEGN--CPERIITLAGPTNAIFKAFAMIIDKLE   70 (71)
T ss_dssp             CEEEEEEEEHHHHHHHHCGGGHHHHHHHHHHCCEEEECSSC--CSEEEEEEEECHHHHHHHHHHHHHHHH
T ss_pred             cEEEEEEECHHHcCeEECCCChhHHHHHHHhCCEEEEcCCC--CCcceEEEEECHHHHHHHHHHHHHHhc
Confidence            35899999999999999999999999999999999998763  567999999999999999999999885

>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=99.48  E-value=9.2e-15  Score=112.79  Aligned_cols=69  Identities=20%  Similarity=0.393  Sum_probs=63.3

Q ss_pred             ceeEEEEEeccceeEEEeCCchHHHHHHHhcCCeEEEccCCCCCCCCcccccCCceEEEecCHHHHHHHHHHHHHHHhh
Q 006943          139 KEECQILVPSSQSANIIGKAGATIKRLRSKTRTSIKVTPKDASEPTHSCAMEFDNFVLISGESEAVKKALFAISAIMYK  217 (624)
Q Consensus       139 ~~~~~llvp~~~~g~iIGk~G~~Ik~I~~~sga~I~i~~~~~~~~~~~~~~~~~r~V~I~G~~~~V~~A~~~I~~~l~~  217 (624)
                      .++++|+||.+++|+||||+|++|++|+++|||+|+|++..          ..+|+|+|+|++++|.+|+.+|.++|++
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            58999999999999999999999999999999999997632          3579999999999999999999999864

>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=99.47  E-value=5e-14  Score=111.62  Aligned_cols=73  Identities=18%  Similarity=0.244  Sum_probs=64.7

Q ss_pred             CCCCCcEEEEEeccccccceeccCCchHHHHHHHhCCEEEEeCCCCCCCCeEEEEEcCHHHHHHHHHHHHHHHh
Q 006943          549 GLPPPLTLEVLVPANAVGKVIGKAGSNLANIRKISGATIEMSDSKSSRGDRVALISGTPEQKRAAENLIQAFIM  622 (624)
Q Consensus       549 ~~~~~~~~~i~VP~~~vg~IIGkgG~~I~~I~~~sGa~I~i~~~~~~~~~r~v~I~Gt~e~v~~A~~lI~~~i~  622 (624)
                      .+...++.+|.||..++++|||++|++|++|+++|||+|+|++..+. +.+.|+|+|++++|++|+.+|++++.
T Consensus         5 e~~~~~t~~i~Vp~~~~~~iIG~~G~~i~~I~~~tg~~I~~p~~~~~-~~~~v~I~G~~~~V~~A~~~I~~i~~   77 (81)
T d2ctma1           5 ELEQMVSEDVPLDHRVHARIIGARGKAIRKIMDEFKVDIRFPQSGAP-DPNCVTVTGLPENVEEAIDHILNLEE   77 (81)
T ss_dssp             CTTTCCCEEEECCTTTHHHHHCSSSCHHHHHHHHHTCEEECCCTTCS-CTTEEEEESCHHHHHHHHHHHHHHHH
T ss_pred             HhhcCEEEEEEECHHHHhhccCCCCccHHHHHHHhCCEEEeCCccCC-CCCEEEEeCCHHHHHHHHHHHHHHHH
Confidence            34556789999999999999999999999999999999999876533 35679999999999999999999875

>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=99.46  E-value=4.6e-14  Score=111.84  Aligned_cols=72  Identities=21%  Similarity=0.277  Sum_probs=64.9

Q ss_pred             CCCCcEEEEEeccccccceeccCCchHHHHHHHhCCEEEEeCCCCCCCCeEEEEEcCHHHHHHHHHHHHHHHhh
Q 006943          550 LPPPLTLEVLVPANAVGKVIGKAGSNLANIRKISGATIEMSDSKSSRGDRVALISGTPEQKRAAENLIQAFIMA  623 (624)
Q Consensus       550 ~~~~~~~~i~VP~~~vg~IIGkgG~~I~~I~~~sGa~I~i~~~~~~~~~r~v~I~Gt~e~v~~A~~lI~~~i~~  623 (624)
                      +.+..+.+|.||.+++|+|||++|.+|++|+++|||+|+|++..  ...+.|+|+|++++|+.|+.+|++++..
T Consensus         6 ~~~~~t~~i~Ip~~~~~~iIG~~G~~i~~I~~~tg~~I~~p~~~--~~~~~v~I~G~~~~v~~A~~~I~~iv~e   77 (81)
T d2ctea1           6 LQTQASATVAIPKEHHRFVIGKNGEKLQDLELKTATKIQIPRPD--DPSNQIKITGTKEGIEKARHEVLLISAE   77 (81)
T ss_dssp             CCSCEEEEEECCTTTHHHHHCSSSCHHHHHHHHTTCCCBCCCTT--SSCCEEEEEECHHHHHHHHHHHHHHHHH
T ss_pred             hcCceEEEEEECHHHHhhccCCCChhHHHHHHHhCCEEEECCCC--CCCCEEEEEeCHHHHHHHHHHHHHHHHH
Confidence            34567999999999999999999999999999999999998764  4567899999999999999999998863

>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=99.45  E-value=3.7e-14  Score=109.28  Aligned_cols=67  Identities=16%  Similarity=0.286  Sum_probs=61.3

Q ss_pred             CcEEEEEeccccccceeccCCchHHHHHHHhCCEEEEeCCCCCCCCeEEEEEcCHHHHHHHHHHHHHHH
Q 006943          553 PLTLEVLVPANAVGKVIGKAGSNLANIRKISGATIEMSDSKSSRGDRVALISGTPEQKRAAENLIQAFI  621 (624)
Q Consensus       553 ~~~~~i~VP~~~vg~IIGkgG~~I~~I~~~sGa~I~i~~~~~~~~~r~v~I~Gt~e~v~~A~~lI~~~i  621 (624)
                      ..+.+|.||.+++++|||++|++|++|+++|||+|+|+++.  .+++.|+|+|++++|+.|+.+|++++
T Consensus         4 ~~~~ei~V~~~~~~~iIG~~G~~i~~I~~~tg~~I~i~~~~--~~~~~v~I~G~~~~v~~A~~~I~~i~   70 (71)
T d1viga_           4 MDYVEINIDHKFHRHLIGKSGANINRIKDQYKVSVRIPPDS--EKSNLIRIEGDPQGVQQAKRELLELA   70 (71)
T ss_dssp             CEEEEEEECSSHHHHHTCSSCCHHHHHHHHTCCEEECCCCC--SSSEEEEEEESSHHHHHHHHHHHHTC
T ss_pred             eEEEEEEECHHHhcccCCCCCchHHHHHHHhCCEEEeCCCC--CCCCEEEEECCHHHHHHHHHHHHHHh
Confidence            45889999999999999999999999999999999998754  45688999999999999999999864

>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=99.45  E-value=8.4e-14  Score=111.25  Aligned_cols=69  Identities=23%  Similarity=0.347  Sum_probs=63.4

Q ss_pred             cEEEEEeccccccceeccCCchHHHHHHHhCCEEEEeCCC-CCCCCeEEEEEcCHHHHHHHHHHHHHHHh
Q 006943          554 LTLEVLVPANAVGKVIGKAGSNLANIRKISGATIEMSDSK-SSRGDRVALISGTPEQKRAAENLIQAFIM  622 (624)
Q Consensus       554 ~~~~i~VP~~~vg~IIGkgG~~I~~I~~~sGa~I~i~~~~-~~~~~r~v~I~Gt~e~v~~A~~lI~~~i~  622 (624)
                      ++.+|.||..++++|||++|++|++|++.|||+|+|++.. .+.+++.|+|+|++++|+.|+.+|+++|.
T Consensus        10 ~~~~i~Vp~~~~~~iIG~~G~~i~~I~~~t~~~I~~~~~~~~~~~~~~i~I~G~~e~v~~A~~~I~~~i~   79 (84)
T d2ctla1          10 FKLSVTVDPKYHPKIIGRKGAVITQIRLEHDVNIQFPDKDDGNQPQDQITITGYEKNTEAARDAILRIVG   79 (84)
T ss_dssp             CEEEEECCTTTHHHHSCSSSCHHHHHHHHHTCEEECCCTTTCSSCSSEEEEESCHHHHHHHHHHHHHHHH
T ss_pred             EEEEEEECHHHHhhhcCCCchhHHHHHHHhCCEEEECCCCCCCCCcceEEEECCHHHHHHHHHHHHHHHH
Confidence            5789999999999999999999999999999999998654 44567899999999999999999999886

>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=99.45  E-value=3.9e-14  Score=110.76  Aligned_cols=72  Identities=24%  Similarity=0.436  Sum_probs=65.2

Q ss_pred             ceeEEEEEeccceeEEEeCCchHHHHHHHhcCCeEEEccCCCCCCCCcccccCCceEEEecCHHHHHHHHHHHHHHHhhc
Q 006943          139 KEECQILVPSSQSANIIGKAGATIKRLRSKTRTSIKVTPKDASEPTHSCAMEFDNFVLISGESEAVKKALFAISAIMYKF  218 (624)
Q Consensus       139 ~~~~~llvp~~~~g~iIGk~G~~Ik~I~~~sga~I~i~~~~~~~~~~~~~~~~~r~V~I~G~~~~V~~A~~~I~~~l~~~  218 (624)
                      .+|.+|.||.+++|+||||+|++|++|+++|||+|+|....        +.+++|+|+|+|++++|.+|+.+|.++++++
T Consensus         3 ~~t~~i~VP~~~vg~iIG~~G~~I~~I~~~sga~I~i~~~~--------~~~~~r~i~I~G~~~~v~~A~~~I~~~i~e~   74 (75)
T d1zzka1           3 IITTQVTIPKDLAGSIIGKGGQRIKQIRHESGASIKIDEPL--------EGSEDRIITITGTQDQIQNAQYLLQNSVKQY   74 (75)
T ss_dssp             CEEEEEEEETTTGGGGTCGGGHHHHHHHHHHCCEEEECCTT--------SCSSEEEEEEEECHHHHHHHHHHHHHHHHHH
T ss_pred             cEEEEEEEChHhcCeeECCCCchHHHHHhhcCCeEEEccCC--------CCCCceEEEEEeCHHHHHHHHHHHHHHHHhc
Confidence            57899999999999999999999999999999999997532        2357899999999999999999999999875

>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=8.8e-14  Score=115.86  Aligned_cols=70  Identities=33%  Similarity=0.482  Sum_probs=63.7

Q ss_pred             CcEEEEEeccccccceeccCCchHHHHHHHhCCEEEEeCCCC--CCCCeEEEEEcCHHHHHHHHHHHHHHHh
Q 006943          553 PLTLEVLVPANAVGKVIGKAGSNLANIRKISGATIEMSDSKS--SRGDRVALISGTPEQKRAAENLIQAFIM  622 (624)
Q Consensus       553 ~~~~~i~VP~~~vg~IIGkgG~~I~~I~~~sGa~I~i~~~~~--~~~~r~v~I~Gt~e~v~~A~~lI~~~i~  622 (624)
                      .++.+|.||.+++|+||||+|.+|++|++.|||+|+|++..+  ...+|+|+|+|++++|+.|+.+|+++|.
T Consensus        14 ~v~~~i~IP~~~vg~vIGk~G~~Ik~I~~~tga~I~i~~~~~~~~~~~r~v~I~G~~~~v~~A~~~I~~~i~   85 (104)
T d1we8a_          14 PVFEQLSVPQRSVGRIIGRGGETIRSICKASGAKITCDKESEGTLLLSRLIKISGTQKEVAAAKHLILEKVS   85 (104)
T ss_dssp             EEEEEEEEETTTHHHHHTTTSHHHHHHHHHHCCEEEECCSSCCSSSSEEEEEEEEEHHHHHHHHHHHHHHHH
T ss_pred             CEEEEEEECHHHhcceECCCCcchHHHHHHcCCEEEECCCCCCCCCCccEEEEEeCHHHHHHHHHHHHHHHh
Confidence            367899999999999999999999999999999999987643  3457999999999999999999999985

>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=99.43  E-value=2.7e-14  Score=113.23  Aligned_cols=75  Identities=21%  Similarity=0.347  Sum_probs=67.0

Q ss_pred             CCceeEEEEEeccceeEEEeCCchHHHHHHHhcCCeEEEccCCCCCCCCcccccCCceEEEecCHHHHHHHHHHHHHHHh
Q 006943          137 KEKEECQILVPSSQSANIIGKAGATIKRLRSKTRTSIKVTPKDASEPTHSCAMEFDNFVLISGESEAVKKALFAISAIMY  216 (624)
Q Consensus       137 ~~~~~~~llvp~~~~g~iIGk~G~~Ik~I~~~sga~I~i~~~~~~~~~~~~~~~~~r~V~I~G~~~~V~~A~~~I~~~l~  216 (624)
                      ...++.+|+||.+++|+||||+|++|++|+++|||+|.|.+.+      .++.+.+|+|+|+|++++|.+|+.+|.++|+
T Consensus         5 ~~~~~~~i~Vp~~~~g~iIGk~G~~Ik~I~~~tga~I~i~~~~------~~~~~~~r~v~I~G~~~~v~~A~~~I~~~i~   78 (81)
T d1x4ma1           5 PGNAVQEIMIPASKAGLVIGKGGETIKQLQERAGVKMVMIQDG------PQNTGADKPLRITGDPYKVQQAKEMVLELIR   78 (81)
T ss_dssp             CCCEEEEEEECHHHHHHHSCSSSSHHHHHHHHHTSEEEECCSC------CCSSCSCEEEEEEECTTTHHHHHHHHHHHHC
T ss_pred             CccEEEEEEECHHHcCeeECCCCchHHHHHHHhCCeEEEccCC------CCCCCCceEEEEEeCHHHHHHHHHHHHHHHH
Confidence            4578999999999999999999999999999999999998643      2234678999999999999999999999986


Q ss_pred             h
Q 006943          217 K  217 (624)
Q Consensus       217 ~  217 (624)
                      +
T Consensus        79 e   79 (81)
T d1x4ma1          79 D   79 (81)
T ss_dssp             C
T ss_pred             h
Confidence            4

>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=99.43  E-value=3.7e-14  Score=110.50  Aligned_cols=71  Identities=18%  Similarity=0.374  Sum_probs=64.2

Q ss_pred             ceeEEEEEeccceeEEEeCCchHHHHHHHhcCCeEEEccCCCCCCCCcccccCCceEEEecCHHHHHHHHHHHHHHHhh
Q 006943          139 KEECQILVPSSQSANIIGKAGATIKRLRSKTRTSIKVTPKDASEPTHSCAMEFDNFVLISGESEAVKKALFAISAIMYK  217 (624)
Q Consensus       139 ~~~~~llvp~~~~g~iIGk~G~~Ik~I~~~sga~I~i~~~~~~~~~~~~~~~~~r~V~I~G~~~~V~~A~~~I~~~l~~  217 (624)
                      ...++|+||.+++|+||||+|++|++|+++|||+|+|...+.        ...+|+|+|+|++++|.+|+.+|.++|++
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 SHMIDVPIPRFAVGIVIGRNGEMIKKIQNDAGVRIQFKPDDG--------TTPERIAQITGPPDRAQHAAEIITDLLRS   72 (74)
T ss_dssp             CEEEEEEEEHHHHHHHHCGGGHHHHHHHHHHCCEEEEECCTT--------SCSEEEEEEEECHHHHHHHHHHHHHHHHH
T ss_pred             CeEEEEEeCHHHCCeeECCCCcHHHHHHHHcCCEEEeccCCC--------CCCeeEEEEEeCHHHHHHHHHHHHHHHHh
Confidence            468899999999999999999999999999999999986532        24689999999999999999999999865

>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=99.43  E-value=4e-14  Score=109.22  Aligned_cols=70  Identities=24%  Similarity=0.411  Sum_probs=61.7

Q ss_pred             EEEEEecCCeeeEEEcCCCchHHHHHHhcCceEEEeCCCCCCCCCCCCcEEEEEeehHHHHHHHHHHHHHH
Q 006943          390 TIRLLVSSKVIGCIIGKSGSIINEIRKRTKADVRISKGDKPKCADANDELVEVVGEVGSVRDALVQIILRL  460 (624)
Q Consensus       390 ~~~l~vp~~~~g~iIGk~G~~Ik~I~~~tga~I~i~~~~~p~~~~~~~~~v~I~G~~~~v~~A~~~I~~~l  460 (624)
                      +.+|.||.+++|+|||++|++|++|+++|||+|+|+++..+.. ...+|+|+|+|++++|.+|..+|.++|
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 EFNFIVPTGKTGLIIGKGGETIKSISQQSGARIELQRNPPPNA-DPNMKLFTIRGTPQQIDYARQLIEEKI   71 (71)
T ss_dssp             EEEEEEETTTHHHHHCGGGHHHHHHHHHHCCEEEEECCCTTTS-CTTEEEEEEECCHHHHHHHHHHHHHHC
T ss_pred             EEEEEEChHhcceEECCCCcChHHHHhhcCcEEEEeecCCCCC-CCCeEEEEEEeCHHHHHHHHHHHHhhC
Confidence            3689999999999999999999999999999999988765443 367899999999999999999887653

>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=99.42  E-value=5.8e-14  Score=109.20  Aligned_cols=71  Identities=25%  Similarity=0.338  Sum_probs=62.7

Q ss_pred             eeEEEEEeccceeEEEeCCchHHHHHHHhcCCeEEEccCCCCCCCCcccccCCceEEEecCHHHHHHHHHHHHHHH
Q 006943          140 EECQILVPSSQSANIIGKAGATIKRLRSKTRTSIKVTPKDASEPTHSCAMEFDNFVLISGESEAVKKALFAISAIM  215 (624)
Q Consensus       140 ~~~~llvp~~~~g~iIGk~G~~Ik~I~~~sga~I~i~~~~~~~~~~~~~~~~~r~V~I~G~~~~V~~A~~~I~~~l  215 (624)
                      ..++|+||++++|+||||+|++|++|+++|||+|+|.+.+.     ..+.+++|+|+|+|++++|.+|+.+|.++|
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 ELVEMAVPENLVGAILGKGGKTLVEYQELTGARIQISKKGE-----FLPGTRNRRVTITGSPAATQAAQYLISQRV   73 (74)
T ss_dssp             EEEEEEEETTTHHHHHCSTTHHHHHHHHHHCCEEEECCTTC-----CSTTCCEEEEEEEESHHHHHHHHHHHHHHC
T ss_pred             EEEEEEeCHHHcceeECCCChhHHHHHHHcCCEEEEccCCC-----CCCCCCceEEEEEeCHHHHHHHHHHHHHHc
Confidence            45789999999999999999999999999999999987542     223467899999999999999999998875

>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=99.41  E-value=6.6e-14  Score=107.50  Aligned_cols=68  Identities=24%  Similarity=0.380  Sum_probs=61.2

Q ss_pred             eeEEEEEeccceeEEEeCCchHHHHHHHhcCCeEEEccCCCCCCCCcccccCCceEEEecCHHHHHHHHHHHHHHH
Q 006943          140 EECQILVPSSQSANIIGKAGATIKRLRSKTRTSIKVTPKDASEPTHSCAMEFDNFVLISGESEAVKKALFAISAIM  215 (624)
Q Consensus       140 ~~~~llvp~~~~g~iIGk~G~~Ik~I~~~sga~I~i~~~~~~~~~~~~~~~~~r~V~I~G~~~~V~~A~~~I~~~l  215 (624)
                      .|.+|+||.+++|+||||+|.+|++|+++|||+|.|.+..        +.+++|+|+|+|++++|.+|+.+|.+.|
T Consensus         2 ~T~~i~VP~~~vg~iIGk~G~~I~~I~~~tga~I~i~~~~--------~~~~~r~v~I~G~~~~v~~A~~~I~~~i   69 (70)
T d1wvna1           2 TTHELTIPNNLIGCIIGRQGANINEIRQMSGAQIKIANPV--------EGSSGRQVTITGSAASISLAQYLINARL   69 (70)
T ss_dssp             EEEEEEEEGGGHHHHHCGGGHHHHHHHHHHCCEEEECCCC--------TTCSEEEEEEEECHHHHHHHHHHHHHHT
T ss_pred             eEEEEEEChHhcceeECCCChHHHHHHHHcCcEEEEcCCC--------CCCCcEEEEEEeCHHHHHHHHHHHHHHc
Confidence            5789999999999999999999999999999999997532        2357899999999999999999998875

>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=99.40  E-value=1.7e-13  Score=108.85  Aligned_cols=70  Identities=20%  Similarity=0.303  Sum_probs=62.7

Q ss_pred             CCCcEEEEEeccccccceeccCCchHHHHHHH-hCCEEEEeCCCCCCCCeEEEEEcCHHHHHHHHHHHHHHHh
Q 006943          551 PPPLTLEVLVPANAVGKVIGKAGSNLANIRKI-SGATIEMSDSKSSRGDRVALISGTPEQKRAAENLIQAFIM  622 (624)
Q Consensus       551 ~~~~~~~i~VP~~~vg~IIGkgG~~I~~I~~~-sGa~I~i~~~~~~~~~r~v~I~Gt~e~v~~A~~lI~~~i~  622 (624)
                      .+.++.+|.||.+++|+|||++|++|++|+++ ++++|++++..  ..++.|+|+|++++|+.|+.+|++++.
T Consensus         7 ~~~~t~~i~Vp~~~~~~iIGk~G~~I~~I~~~~~~~~I~~~~~~--~~~~~v~I~G~~~~v~~A~~~I~~~v~   77 (82)
T d2ctja1           7 ANIAEVEVSIPAKLHNSLIGTKGRLIRSIMEECGGVHIHFPVEG--SGSDTVVIRGPSSDVEKAKKQLLHLAE   77 (82)
T ss_dssp             CSSCCEEEECCHHHHHHHHCSSSHHHHHHHHHHTSCEEECCCTT--TTCCEEEEESCHHHHHHHHHHHHHHHH
T ss_pred             cCcEEEEEEECHHHHhhcCCCCCccHHHHHHHcCCcEEEEeCCC--CCCceEEEeCCHHHHHHHHHHHHHHHh
Confidence            44568999999999999999999999999987 48999998764  456889999999999999999999875

>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=99.38  E-value=2.1e-13  Score=107.60  Aligned_cols=73  Identities=22%  Similarity=0.360  Sum_probs=65.8

Q ss_pred             CCceeEEEEEeccceeEEEeCCchHHHHHHHhcCCeEEEccCCCCCCCCcccccCCceEEEecCHHHHHHHHHHHHHHHh
Q 006943          137 KEKEECQILVPSSQSANIIGKAGATIKRLRSKTRTSIKVTPKDASEPTHSCAMEFDNFVLISGESEAVKKALFAISAIMY  216 (624)
Q Consensus       137 ~~~~~~~llvp~~~~g~iIGk~G~~Ik~I~~~sga~I~i~~~~~~~~~~~~~~~~~r~V~I~G~~~~V~~A~~~I~~~l~  216 (624)
                      ...++.+|+||.+++|+|||++|.+|++|+++|||+|.|.+.+.        .+++++|+|+|++++|.+|+.+|.++|.
T Consensus         5 ~~~~t~~i~IP~~~~g~iIG~~G~~i~~I~~~tg~~I~i~~~~~--------~~~~r~v~I~G~~~~v~~A~~~I~~~i~   76 (79)
T d1x4na1           5 RSVMTEEYKVPDGMVGFIIGRGGEQISRIQQESGCKIQIAPDSG--------GLPERSCMLTGTPESVQSAKRLLDQIVE   76 (79)
T ss_dssp             CCCEEEEEEEEHHHHHHHHCSSSHHHHHHHHHSCCEEEECSCCT--------TCSEEEEEEEECHHHHHHHHHHHHHHHH
T ss_pred             CCcEEEEEEEChHhhcceECCCchhHHHHHHHhCCEEEEcCCCC--------CCCceEEEEEeCHHHHHHHHHHHHHHHH
Confidence            45689999999999999999999999999999999999986432        2578999999999999999999999997


Q ss_pred             h
Q 006943          217 K  217 (624)
Q Consensus       217 ~  217 (624)
                      +
T Consensus        77 e   77 (79)
T d1x4na1          77 K   77 (79)
T ss_dssp             H
T ss_pred             c
Confidence            5

>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=99.34  E-value=4.1e-13  Score=106.24  Aligned_cols=77  Identities=23%  Similarity=0.311  Sum_probs=66.3

Q ss_pred             CCCCCcEEEEEEecCCeeeEEEcCCCchHHHHHHhcCceEEEeCCCCCCCCCCCCcEEEEEeehHHHHHHHHHHHHHHhh
Q 006943          383 DEDDDTVTIRLLVSSKVIGCIIGKSGSIINEIRKRTKADVRISKGDKPKCADANDELVEVVGEVGSVRDALVQIILRLRD  462 (624)
Q Consensus       383 ~~~~~~~~~~l~vp~~~~g~iIGk~G~~Ik~I~~~tga~I~i~~~~~p~~~~~~~~~v~I~G~~~~v~~A~~~I~~~l~e  462 (624)
                      ++.++.++.++.||..+|++|||++|++|++|+++|||+|+|++...     .+++.|+|+|++++|.+|+.+|.+.+.+
T Consensus         4 ~e~~~~~t~~i~Vp~~~~~~iIG~~G~~i~~I~~~tg~~I~~p~~~~-----~~~~~v~I~G~~~~V~~A~~~I~~i~~e   78 (81)
T d2ctma1           4 GELEQMVSEDVPLDHRVHARIIGARGKAIRKIMDEFKVDIRFPQSGA-----PDPNCVTVTGLPENVEEAIDHILNLEEE   78 (81)
T ss_dssp             CCTTTCCCEEEECCTTTHHHHHCSSSCHHHHHHHHHTCEEECCCTTC-----SCTTEEEEESCHHHHHHHHHHHHHHHHH
T ss_pred             hHhhcCEEEEEEECHHHHhhccCCCCccHHHHHHHhCCEEEeCCccC-----CCCCEEEEeCCHHHHHHHHHHHHHHHHH
Confidence            34456788899999999999999999999999999999999986443     3356899999999999999999887776


Q ss_pred             cc
Q 006943          463 DA  464 (624)
Q Consensus       463 ~~  464 (624)
                      .+
T Consensus        79 ~~   80 (81)
T d2ctma1          79 YL   80 (81)
T ss_dssp             HH
T ss_pred             Hh
Confidence            53

>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=99.33  E-value=7.3e-13  Score=107.30  Aligned_cols=68  Identities=22%  Similarity=0.294  Sum_probs=62.6

Q ss_pred             CcEEEEEeccccccceeccCCchHHHHHHHhCCEEEEeCCCCCCCCeEEEEEcCHHHHHHHHHHHHHHHh
Q 006943          553 PLTLEVLVPANAVGKVIGKAGSNLANIRKISGATIEMSDSKSSRGDRVALISGTPEQKRAAENLIQAFIM  622 (624)
Q Consensus       553 ~~~~~i~VP~~~vg~IIGkgG~~I~~I~~~sGa~I~i~~~~~~~~~r~v~I~Gt~e~v~~A~~lI~~~i~  622 (624)
                      .++.+|.||..+++.|||++|.+|++|+++|||+|.|++..  ..++.|+|+|++++|+.|+.+|++++.
T Consensus         9 ~vt~~i~Vp~~~~~~iIG~~G~~i~~I~~~tg~~I~~p~~~--~~~~~v~I~G~~~~V~~A~~~I~~~v~   76 (91)
T d2ctka1           9 PVTIEVEVPFDLHRYVIGQKGSGIRKMMDEFEVNIHVPAPE--LQSDIIAITGLAANLDRAKAGLLERVK   76 (91)
T ss_dssp             CEEEEEECCHHHHHHHHCSSSHHHHHHHHHTCCEEECCCTT--TTCCEEEEEECHHHHHHHHHHHHHHHH
T ss_pred             CEEEEEEECHHHHhHhcCCCchhHHHHHHHhCCEEEECCCC--CCcceEEEECCHHHHHHHHHHHHHHHH
Confidence            46899999999999999999999999999999999998764  446789999999999999999999885

>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=99.33  E-value=6.2e-13  Score=110.61  Aligned_cols=77  Identities=25%  Similarity=0.362  Sum_probs=67.6

Q ss_pred             CCCcEEEEEEecCCeeeEEEcCCCchHHHHHHhcCceEEEeCCCCCCCCCCCCcEEEEEeehHHHHHHHHHHHHHHhhc
Q 006943          385 DDDTVTIRLLVSSKVIGCIIGKSGSIINEIRKRTKADVRISKGDKPKCADANDELVEVVGEVGSVRDALVQIILRLRDD  463 (624)
Q Consensus       385 ~~~~~~~~l~vp~~~~g~iIGk~G~~Ik~I~~~tga~I~i~~~~~p~~~~~~~~~v~I~G~~~~v~~A~~~I~~~l~e~  463 (624)
                      ...+++.+|.||..++++|||++|.+|++|+++|||+|+|++...+.  ...+|+|+|+|++++|.+|+.+|.+.|.+.
T Consensus        11 ~~~~v~~~i~IP~~~vg~vIGk~G~~Ik~I~~~tga~I~i~~~~~~~--~~~~r~v~I~G~~~~v~~A~~~I~~~i~e~   87 (104)
T d1we8a_          11 ENTPVFEQLSVPQRSVGRIIGRGGETIRSICKASGAKITCDKESEGT--LLLSRLIKISGTQKEVAAAKHLILEKVSED   87 (104)
T ss_dssp             SSCEEEEEEEEETTTHHHHHTTTSHHHHHHHHHHCCEEEECCSSCCS--SSSEEEEEEEEEHHHHHHHHHHHHHHHHHH
T ss_pred             CCCCEEEEEEECHHHhcceECCCCcchHHHHHHcCCEEEECCCCCCC--CCCccEEEEEeCHHHHHHHHHHHHHHHhCc
Confidence            34578899999999999999999999999999999999998654332  356799999999999999999999999764

>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=99.32  E-value=5.7e-13  Score=106.27  Aligned_cols=73  Identities=23%  Similarity=0.300  Sum_probs=65.3

Q ss_pred             ceeEEEEEeccceeEEEeCCchHHHHHHHhcCCeEEEccCCCCCCCCcccccCCceEEEecCHHHHHHHHHHHHHHHhhc
Q 006943          139 KEECQILVPSSQSANIIGKAGATIKRLRSKTRTSIKVTPKDASEPTHSCAMEFDNFVLISGESEAVKKALFAISAIMYKF  218 (624)
Q Consensus       139 ~~~~~llvp~~~~g~iIGk~G~~Ik~I~~~sga~I~i~~~~~~~~~~~~~~~~~r~V~I~G~~~~V~~A~~~I~~~l~~~  218 (624)
                      ..++++.||..++++|||++|++|++|+++|||+|+|++.+.       +..+++.|+|+|+.++|.+|+.+|.+++.+.
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 SFKLSVTVDPKYHPKIIGRKGAVITQIRLEHDVNIQFPDKDD-------GNQPQDQITITGYEKNTEAARDAILRIVGEL   81 (84)
T ss_dssp             TCEEEEECCTTTHHHHSCSSSCHHHHHHHHHTCEEECCCTTT-------CSSCSSEEEEESCHHHHHHHHHHHHHHHHHH
T ss_pred             cEEEEEEECHHHHhhhcCCCchhHHHHHHHhCCEEEECCCCC-------CCCCcceEEEECCHHHHHHHHHHHHHHHHhH
Confidence            578899999999999999999999999999999999976432       2357889999999999999999999998764

>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=99.32  E-value=4e-13  Score=104.63  Aligned_cols=64  Identities=25%  Similarity=0.381  Sum_probs=57.4

Q ss_pred             CcEEEEEeccccccceeccCCchHHHHHHHhCCEEEEeCCCCCCCCeEEEEEc-CHHHHHHHHHHHHHH
Q 006943          553 PLTLEVLVPANAVGKVIGKAGSNLANIRKISGATIEMSDSKSSRGDRVALISG-TPEQKRAAENLIQAF  620 (624)
Q Consensus       553 ~~~~~i~VP~~~vg~IIGkgG~~I~~I~~~sGa~I~i~~~~~~~~~r~v~I~G-t~e~v~~A~~lI~~~  620 (624)
                      .++.+|.||.+++|+|||+||++|++|++.|||+|.+.+.    .++.|+|.| +++++++|+.||+.+
T Consensus         7 ~~t~~i~Ip~~~ig~vIG~gG~~I~~I~~~tGa~i~i~~~----~~g~v~I~g~~~eav~~A~~~Ie~~   71 (78)
T d2cpqa1           7 AFHEEFVVREDLMGLAIGTHGSNIQQARKVPGVTAIELDE----DTGTFRIYGESADAVKKARGFLEFV   71 (78)
T ss_dssp             SEEEEEECCHHHHHHHHTTTTHHHHHHHTSTTEEEEEEET----TTTEEEEEESSHHHHHHHHHHHSCC
T ss_pred             CceEEEEECHHHHHHHcCCChHHHHHHHHhcCcEEEEecC----CCceEEEEECCHHHHHHHHHHHHHh
Confidence            4588999999999999999999999999999999998765    346799999 799999999999754

>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=99.28  E-value=9.2e-13  Score=104.15  Aligned_cols=73  Identities=25%  Similarity=0.389  Sum_probs=65.6

Q ss_pred             CCCceeEEEEEeccceeEEEeCCchHHHHHHHhcCCeEEEccCCCCCCCCcccccCCceEEEecCHHHHHHHHHHHHHHH
Q 006943          136 RKEKEECQILVPSSQSANIIGKAGATIKRLRSKTRTSIKVTPKDASEPTHSCAMEFDNFVLISGESEAVKKALFAISAIM  215 (624)
Q Consensus       136 ~~~~~~~~llvp~~~~g~iIGk~G~~Ik~I~~~sga~I~i~~~~~~~~~~~~~~~~~r~V~I~G~~~~V~~A~~~I~~~l  215 (624)
                      ....++..|.||..++++|||++|.+|++|+++|||+|.|++.+          +.++.|+|+|+.++|.+|+.+|.+++
T Consensus         6 ~~~~~t~~i~Ip~~~~~~iIG~~G~~i~~I~~~tg~~I~~p~~~----------~~~~~v~I~G~~~~v~~A~~~I~~iv   75 (81)
T d2ctea1           6 LQTQASATVAIPKEHHRFVIGKNGEKLQDLELKTATKIQIPRPD----------DPSNQIKITGTKEGIEKARHEVLLIS   75 (81)
T ss_dssp             CCSCEEEEEECCTTTHHHHHCSSSCHHHHHHHHTTCCCBCCCTT----------SSCCEEEEEECHHHHHHHHHHHHHHH
T ss_pred             hcCceEEEEEECHHHHhhccCCCChhHHHHHHHhCCEEEECCCC----------CCCCEEEEEeCHHHHHHHHHHHHHHH
Confidence            45568999999999999999999999999999999999997633          45789999999999999999999998


Q ss_pred             hhc
Q 006943          216 YKF  218 (624)
Q Consensus       216 ~~~  218 (624)
                      .+.
T Consensus        76 ~e~   78 (81)
T d2ctea1          76 AEQ   78 (81)
T ss_dssp             HHH
T ss_pred             HHH
Confidence            763

>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=99.27  E-value=2.8e-12  Score=101.22  Aligned_cols=61  Identities=21%  Similarity=0.250  Sum_probs=56.1

Q ss_pred             EEEEeccccccceeccCCchHHHHHHHhCCEEEEeCCCCCCCCeEEEEEcCHHHHHHHHHHHHHHHh
Q 006943          556 LEVLVPANAVGKVIGKAGSNLANIRKISGATIEMSDSKSSRGDRVALISGTPEQKRAAENLIQAFIM  622 (624)
Q Consensus       556 ~~i~VP~~~vg~IIGkgG~~I~~I~~~sGa~I~i~~~~~~~~~r~v~I~Gt~e~v~~A~~lI~~~i~  622 (624)
                      ..+.||.+++|.|||++|++|++|+++|||+|.|+++      ..|+|+|++++++.|+.+|+.++.
T Consensus         3 ~vi~Ip~~~ig~IIG~gG~~I~~I~~~tg~~I~i~~~------g~v~I~G~~e~v~~A~~~I~~i~~   63 (84)
T d2ba0a3           3 RIVAINPARVPRVIGKKGSMIKLLKSELDVQIVVGQN------GLIWVNGDRRKVSIAEEAIYLIEQ   63 (84)
T ss_dssp             EEEECCGGGHHHHHCGGGHHHHHHHHHHTCEEEECTT------SEEEEESCHHHHHHHHHHHHHHHH
T ss_pred             EEEEEChhhcceeeCCcHHHHHHHHHHHCCEEEECCC------CEEEEEeCHHHHHHHHHHHHHHHH
Confidence            4689999999999999999999999999999999753      469999999999999999988765

>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=99.27  E-value=1.4e-12  Score=103.47  Aligned_cols=74  Identities=19%  Similarity=0.258  Sum_probs=65.2

Q ss_pred             cCCCceeEEEEEeccceeEEEeCCchHHHHHHHh-cCCeEEEccCCCCCCCCcccccCCceEEEecCHHHHHHHHHHHHH
Q 006943          135 KRKEKEECQILVPSSQSANIIGKAGATIKRLRSK-TRTSIKVTPKDASEPTHSCAMEFDNFVLISGESEAVKKALFAISA  213 (624)
Q Consensus       135 ~~~~~~~~~llvp~~~~g~iIGk~G~~Ik~I~~~-sga~I~i~~~~~~~~~~~~~~~~~r~V~I~G~~~~V~~A~~~I~~  213 (624)
                      ..++.++..|.||..+||+||||+|++|++|+++ ++|+|.++..+          +.++.|+|+|++++|.+|+.+|.+
T Consensus         5 e~~~~~t~~i~Vp~~~~~~iIGk~G~~I~~I~~~~~~~~I~~~~~~----------~~~~~v~I~G~~~~v~~A~~~I~~   74 (82)
T d2ctja1           5 DLANIAEVEVSIPAKLHNSLIGTKGRLIRSIMEECGGVHIHFPVEG----------SGSDTVVIRGPSSDVEKAKKQLLH   74 (82)
T ss_dssp             CCCSSCCEEEECCHHHHHHHHCSSSHHHHHHHHHHTSCEEECCCTT----------TTCCEEEEESCHHHHHHHHHHHHH
T ss_pred             hhcCcEEEEEEECHHHHhhcCCCCCccHHHHHHHcCCcEEEEeCCC----------CCCceEEEeCCHHHHHHHHHHHHH
Confidence            3556789999999999999999999999999987 59999886532          467899999999999999999999


Q ss_pred             HHhhc
Q 006943          214 IMYKF  218 (624)
Q Consensus       214 ~l~~~  218 (624)
                      ++++.
T Consensus        75 ~v~e~   79 (82)
T d2ctja1          75 LAEEK   79 (82)
T ss_dssp             HHHHH
T ss_pred             HHhhh
Confidence            99764

>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=99.26  E-value=1.3e-12  Score=100.43  Aligned_cols=68  Identities=24%  Similarity=0.474  Sum_probs=60.8

Q ss_pred             CceeEEEEEeccceeEEEeCCchHHHHHHHhcCCeEEEccCCCCCCCCcccccCCceEEEecCHHHHHHHHHHHHHHH
Q 006943          138 EKEECQILVPSSQSANIIGKAGATIKRLRSKTRTSIKVTPKDASEPTHSCAMEFDNFVLISGESEAVKKALFAISAIM  215 (624)
Q Consensus       138 ~~~~~~llvp~~~~g~iIGk~G~~Ik~I~~~sga~I~i~~~~~~~~~~~~~~~~~r~V~I~G~~~~V~~A~~~I~~~l  215 (624)
                      ...+++|.||..+|++|||++|++|++|+++|||+|+|++.+          ++++.|+|+|++++|.+|+.+|.++.
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            457789999999999999999999999999999999997532          46789999999999999999998763

>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=99.24  E-value=9.9e-12  Score=99.88  Aligned_cols=67  Identities=24%  Similarity=0.326  Sum_probs=60.7

Q ss_pred             CCCcEEEEEeccccccceeccCCchHHHHHHHh-CCEEEEeCCCCCCCCeEEEEEcCHHHHHHHHHHHHHHHh
Q 006943          551 PPPLTLEVLVPANAVGKVIGKAGSNLANIRKIS-GATIEMSDSKSSRGDRVALISGTPEQKRAAENLIQAFIM  622 (624)
Q Consensus       551 ~~~~~~~i~VP~~~vg~IIGkgG~~I~~I~~~s-Ga~I~i~~~~~~~~~r~v~I~Gt~e~v~~A~~lI~~~i~  622 (624)
                      ...++.+|.||..++++|||++|++|++|++++ |++|.+++.     ...|+|+|++++|+.|+.+|++++.
T Consensus        18 ~~~~t~~v~VP~~~h~~iIG~~G~~I~~i~~~~~~v~I~~~~~-----~~~v~i~G~~~~ve~Ak~~I~~iv~   85 (90)
T d2ctfa1          18 NSFTVSSVAAPSWLHRFIIGKKGQNLAKITQQMPKVHIEFTEG-----EDKITLEGPTEDVSVAQEQIEGMVK   85 (90)
T ss_dssp             CCCEEEEEECCSTTHHHHHTTTTCHHHHHHHHCSSSEEEECSS-----SCEEEEEECHHHHHHHHHHHHHHHH
T ss_pred             CCcEEEEEEcCHHHHhhcCCCCchhHHHHHHHcCCcEEeeCCC-----CceEEEeCCHHHHHHHHHHHHHHHH
Confidence            345799999999999999999999999999994 899999854     3679999999999999999999875

>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=99.18  E-value=5.5e-12  Score=102.02  Aligned_cols=70  Identities=16%  Similarity=0.293  Sum_probs=63.6

Q ss_pred             ceeEEEEEeccceeEEEeCCchHHHHHHHhcCCeEEEccCCCCCCCCcccccCCceEEEecCHHHHHHHHHHHHHHHhhc
Q 006943          139 KEECQILVPSSQSANIIGKAGATIKRLRSKTRTSIKVTPKDASEPTHSCAMEFDNFVLISGESEAVKKALFAISAIMYKF  218 (624)
Q Consensus       139 ~~~~~llvp~~~~g~iIGk~G~~Ik~I~~~sga~I~i~~~~~~~~~~~~~~~~~r~V~I~G~~~~V~~A~~~I~~~l~~~  218 (624)
                      .++..|.||..+|++|||++|.+|++|+++|||+|.|++.+          +.++.|+|+|+.++|.+|+.+|.+++.+.
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            57899999999999999999999999999999999997643          45678999999999999999999998764

>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=99.09  E-value=6.8e-11  Score=94.86  Aligned_cols=71  Identities=20%  Similarity=0.257  Sum_probs=62.0

Q ss_pred             CCCCcEEEEEEecCCeeeEEEcCCCchHHHHHHhc-CceEEEeCCCCCCCCCCCCcEEEEEeehHHHHHHHHHHHHHHhh
Q 006943          384 EDDDTVTIRLLVSSKVIGCIIGKSGSIINEIRKRT-KADVRISKGDKPKCADANDELVEVVGEVGSVRDALVQIILRLRD  462 (624)
Q Consensus       384 ~~~~~~~~~l~vp~~~~g~iIGk~G~~Ik~I~~~t-ga~I~i~~~~~p~~~~~~~~~v~I~G~~~~v~~A~~~I~~~l~e  462 (624)
                      ..++.++.++.||..+|++|||++|++|++|++++ |++|.|+.         .+..|+|+|++++|++|..+|.+.+.+
T Consensus        16 ~~~~~~t~~v~VP~~~h~~iIG~~G~~I~~i~~~~~~v~I~~~~---------~~~~v~i~G~~~~ve~Ak~~I~~iv~e   86 (90)
T d2ctfa1          16 KANSFTVSSVAAPSWLHRFIIGKKGQNLAKITQQMPKVHIEFTE---------GEDKITLEGPTEDVSVAQEQIEGMVKD   86 (90)
T ss_dssp             CCCCCEEEEEECCSTTHHHHHTTTTCHHHHHHHHCSSSEEEECS---------SSCEEEEEECHHHHHHHHHHHHHHHHH
T ss_pred             HcCCcEEEEEEcCHHHHhhcCCCCchhHHHHHHHcCCcEEeeCC---------CCceEEEeCCHHHHHHHHHHHHHHHHH
Confidence            44567999999999999999999999999999995 89999964         245799999999999999999887765


Q ss_pred             c
Q 006943          463 D  463 (624)
Q Consensus       463 ~  463 (624)
                      .
T Consensus        87 l   87 (90)
T d2ctfa1          87 L   87 (90)
T ss_dssp             H
T ss_pred             H
Confidence            3

>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=99.03  E-value=5.1e-11  Score=92.49  Aligned_cols=65  Identities=22%  Similarity=0.148  Sum_probs=57.3

Q ss_pred             CCceeEEEEEeccceeEEEeCCchHHHHHHHhcCCeEEEccCCCCCCCCcccccCCceEEEec-CHHHHHHHHHHHHH
Q 006943          137 KEKEECQILVPSSQSANIIGKAGATIKRLRSKTRTSIKVTPKDASEPTHSCAMEFDNFVLISG-ESEAVKKALFAISA  213 (624)
Q Consensus       137 ~~~~~~~llvp~~~~g~iIGk~G~~Ik~I~~~sga~I~i~~~~~~~~~~~~~~~~~r~V~I~G-~~~~V~~A~~~I~~  213 (624)
                      ...++..+.||.+++|+|||++|++|++|+++|||+|.+..            .+++.|+|.| ++++|.+|+.+|..
T Consensus         5 ~~~~t~~i~Ip~~~ig~vIG~gG~~I~~I~~~tGa~i~i~~------------~~~g~v~I~g~~~eav~~A~~~Ie~   70 (78)
T d2cpqa1           5 AAAFHEEFVVREDLMGLAIGTHGSNIQQARKVPGVTAIELD------------EDTGTFRIYGESADAVKKARGFLEF   70 (78)
T ss_dssp             SCSEEEEEECCHHHHHHHHTTTTHHHHHHHTSTTEEEEEEE------------TTTTEEEEEESSHHHHHHHHHHHSC
T ss_pred             cCCceEEEEECHHHHHHHcCCChHHHHHHHHhcCcEEEEec------------CCCceEEEEECCHHHHHHHHHHHHH
Confidence            45688899999999999999999999999999999998864            2357899999 59999999998843

>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=99.02  E-value=7e-11  Score=93.03  Aligned_cols=62  Identities=26%  Similarity=0.357  Sum_probs=56.7

Q ss_pred             EEEEeccceeEEEeCCchHHHHHHHhcCCeEEEccCCCCCCCCcccccCCceEEEecCHHHHHHHHHHHHHHHhhc
Q 006943          143 QILVPSSQSANIIGKAGATIKRLRSKTRTSIKVTPKDASEPTHSCAMEFDNFVLISGESEAVKKALFAISAIMYKF  218 (624)
Q Consensus       143 ~llvp~~~~g~iIGk~G~~Ik~I~~~sga~I~i~~~~~~~~~~~~~~~~~r~V~I~G~~~~V~~A~~~I~~~l~~~  218 (624)
                      .+.||.+.+|.||||+|++|++|+++|||+|.|..              +..|.|.|++++|.+|+.+|..++++.
T Consensus         4 vi~Ip~~~ig~IIG~gG~~I~~I~~~tg~~I~i~~--------------~g~v~I~G~~e~v~~A~~~I~~i~~ea   65 (84)
T d2ba0a3           4 IVAINPARVPRVIGKKGSMIKLLKSELDVQIVVGQ--------------NGLIWVNGDRRKVSIAEEAIYLIEQEA   65 (84)
T ss_dssp             EEECCGGGHHHHHCGGGHHHHHHHHHHTCEEEECT--------------TSEEEEESCHHHHHHHHHHHHHHHHCS
T ss_pred             EEEEChhhcceeeCCcHHHHHHHHHHHCCEEEECC--------------CCEEEEEeCHHHHHHHHHHHHHHHHhc
Confidence            57899999999999999999999999999999953              467999999999999999999988654

>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=99.00  E-value=3.6e-11  Score=94.30  Aligned_cols=61  Identities=23%  Similarity=0.365  Sum_probs=51.8

Q ss_pred             EEEEeccccccceeccCCchHHHHHHHhCCEEEEeCCCCCCCCeEEEE-----EcCHHHHHHHHHHHHHHH
Q 006943          556 LEVLVPANAVGKVIGKAGSNLANIRKISGATIEMSDSKSSRGDRVALI-----SGTPEQKRAAENLIQAFI  621 (624)
Q Consensus       556 ~~i~VP~~~vg~IIGkgG~~I~~I~~~sGa~I~i~~~~~~~~~r~v~I-----~Gt~e~v~~A~~lI~~~i  621 (624)
                      .+|.||.+++|.|||++|++|++|+++|||+|+|+.+.     ..+.+     +|.+.++++|+.+|.++-
T Consensus         5 i~i~ip~~~ig~vIG~gG~~Ik~i~~~tg~~I~Id~d~-----g~v~i~~~~~~~~~~a~~~a~~iI~aI~   70 (84)
T d1tuaa1           5 IYVKVKPERLGAVIGPRGEVKAEIMRRTGTVITVDTEN-----SMVIVEPEAEGIPPVNLMKAAEVVKAIS   70 (84)
T ss_dssp             EEEECCGGGHHHHHCGGGHHHHHHHHHHTEEEEEETTT-----TEEEEEESSTTSCHHHHHHHHHHHHHHH
T ss_pred             EEEEeCHHHcCeeecCCchhHHHHHHHHCCEEEEEcCC-----CeEEEecCCccccHHHHHHHHHHHHHHh
Confidence            57999999999999999999999999999999997543     22443     467899999999998763

>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=98.88  E-value=3.4e-11  Score=91.11  Aligned_cols=59  Identities=17%  Similarity=0.134  Sum_probs=46.3

Q ss_pred             EEEeccccccceeccCCchHHHHHHHhCCEEEEeCCCCCCCCeEEEEEcC-HHHHHHHHHHHHHHH
Q 006943          557 EVLVPANAVGKVIGKAGSNLANIRKISGATIEMSDSKSSRGDRVALISGT-PEQKRAAENLIQAFI  621 (624)
Q Consensus       557 ~i~VP~~~vg~IIGkgG~~I~~I~~~sGa~I~i~~~~~~~~~r~v~I~Gt-~e~v~~A~~lI~~~i  621 (624)
                      .+.||.+++|.||||+|++|++|+++|||+|.|.++      ..|+|+|. +++++.|+.+|+.+.
T Consensus         4 vi~Ip~~~ig~iIGkgG~~Ik~i~~~tg~~I~i~~~------g~v~I~g~~~~~v~~A~~~I~~i~   63 (69)
T d2je6i3           4 VIDIMPVKVPRVIGKNKSMYETLTSKSGCSIFVANN------GRIWATCPSRFSEEILIEAIRKIE   63 (69)
T ss_dssp             EEECCGGGHHHHHCGGGHHHHHHHTTC---CEECTT------SEEEC-----CTTCCTHHHHTTTT
T ss_pred             EEEEChhhccceECCchhHHHHHHHHHCCEEEEcCC------CEEEEEeCCHHHHHHHHHHHHHHH
Confidence            588999999999999999999999999999999643      35999995 788999999997654

>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=98.83  E-value=4.4e-09  Score=82.30  Aligned_cols=61  Identities=16%  Similarity=0.112  Sum_probs=54.4

Q ss_pred             EEEEeccccccceeccCCchHHHHHHHhCCEEEEeCCCCCCCCeEEEEEcC-HHHHHHHHHHHHHHHh
Q 006943          556 LEVLVPANAVGKVIGKAGSNLANIRKISGATIEMSDSKSSRGDRVALISGT-PEQKRAAENLIQAFIM  622 (624)
Q Consensus       556 ~~i~VP~~~vg~IIGkgG~~I~~I~~~sGa~I~i~~~~~~~~~r~v~I~Gt-~e~v~~A~~lI~~~i~  622 (624)
                      ..+.||.+.+|.|||++|++|+.|+++|||+|.|.++      -.|+|.|. .+.++.|+.+|+.+..
T Consensus         3 ~vi~I~~~ki~~vIG~gG~~ik~i~~~t~~~I~I~d~------G~V~I~g~~~~~~~~A~~~I~~I~~   64 (87)
T d2z0sa2           3 KIVEISPAKVPRVIGRKMSMLKTLEEKTECKIFVARN------GRIHLECPNEDLEAIAVMAIKIIDE   64 (87)
T ss_dssp             EEEECCGGGSGGGTCGGGHHHHHHHHHHCCEEEEETT------TEEEEECSCHHHHHHHHHHHHHHHH
T ss_pred             EEEEEChhhcceeECCCCcHHHHHHHHHCCEEEECCC------cEEEEEeCCHHHHHHHHHHHHHHHH
Confidence            4689999999999999999999999999999999754      35999995 8999999999998754

>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=98.64  E-value=5.4e-10  Score=84.40  Aligned_cols=61  Identities=21%  Similarity=0.170  Sum_probs=47.1

Q ss_pred             EEEEeccceeEEEeCCchHHHHHHHhcCCeEEEccCCCCCCCCcccccCCceEEEecC-HHHHHHHHHHHHHHHhh
Q 006943          143 QILVPSSQSANIIGKAGATIKRLRSKTRTSIKVTPKDASEPTHSCAMEFDNFVLISGE-SEAVKKALFAISAIMYK  217 (624)
Q Consensus       143 ~llvp~~~~g~iIGk~G~~Ik~I~~~sga~I~i~~~~~~~~~~~~~~~~~r~V~I~G~-~~~V~~A~~~I~~~l~~  217 (624)
                      .+.||.+.+|.||||+|++|++|+++|||+|.|..              +..|+|.|. .+++.+|..+|..+.++
T Consensus         4 vi~Ip~~~ig~iIGkgG~~Ik~i~~~tg~~I~i~~--------------~g~v~I~g~~~~~v~~A~~~I~~i~~e   65 (69)
T d2je6i3           4 VIDIMPVKVPRVIGKNKSMYETLTSKSGCSIFVAN--------------NGRIWATCPSRFSEEILIEAIRKIENE   65 (69)
T ss_dssp             EEECCGGGHHHHHCGGGHHHHHHHTTC---CEECT--------------TSEEEC-----CTTCCTHHHHTTTTTT
T ss_pred             EEEEChhhccceECCchhHHHHHHHHHCCEEEEcC--------------CCEEEEEeCCHHHHHHHHHHHHHHHHh
Confidence            47899999999999999999999999999999953              456999996 67999999999776654

>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=98.60  E-value=1.1e-08  Score=79.78  Aligned_cols=65  Identities=22%  Similarity=0.292  Sum_probs=54.2

Q ss_pred             EEEEEeccceeEEEeCCchHHHHHHHhcCCeEEEccCCCCCCCCcccccCCceEEE-----ecCHHHHHHHHHHHHHHHh
Q 006943          142 CQILVPSSQSANIIGKAGATIKRLRSKTRTSIKVTPKDASEPTHSCAMEFDNFVLI-----SGESEAVKKALFAISAIMY  216 (624)
Q Consensus       142 ~~llvp~~~~g~iIGk~G~~Ik~I~~~sga~I~i~~~~~~~~~~~~~~~~~r~V~I-----~G~~~~V~~A~~~I~~~l~  216 (624)
                      +.+.||.+.+|.||||+|++|++|+++|||+|+|..++             ..|.+     .|.+.++.+|..+|.++.+
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            35799999999999999999999999999999997532             33443     5678999999999998876


Q ss_pred             hcC
Q 006943          217 KFS  219 (624)
Q Consensus       217 ~~~  219 (624)
                      .+.
T Consensus        72 Gf~   74 (84)
T d1tuaa1          72 GFP   74 (84)
T ss_dssp             TCC
T ss_pred             CCC
Confidence            554

>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=98.59  E-value=1.3e-08  Score=82.33  Aligned_cols=53  Identities=23%  Similarity=0.365  Sum_probs=47.7

Q ss_pred             ccccceeccCCchHHHHHHHhCCEEEEeCCCCCCCCeEEEEEcCHHHHHHHHHHHHHHHh
Q 006943          563 NAVGKVIGKAGSNLANIRKISGATIEMSDSKSSRGDRVALISGTPEQKRAAENLIQAFIM  622 (624)
Q Consensus       563 ~~vg~IIGkgG~~I~~I~~~sGa~I~i~~~~~~~~~r~v~I~Gt~e~v~~A~~lI~~~i~  622 (624)
                      ...|+|||++|.+|+.|++.|||.|.|.+.       .|+|.|++++++.|+.+|+.+|.
T Consensus        22 R~~GrIIG~gGktik~Ie~~Tg~~I~I~d~-------~v~iig~~e~i~~A~~~Ie~li~   74 (104)
T d1tuaa2          22 RIKGRIIGEGGRARRTIEEMTDTYINVGEY-------EVAIIGDYERAMAAKQAIEMLAE   74 (104)
T ss_dssp             HHHHHHHCGGGHHHHHHHHHHTCEEEECSS-------EEEEEEEHHHHHHHHHHHHHHHT
T ss_pred             HHhcceeCCCcHHHHHHHHHHCCeEEEeCC-------eEEEEECchhHHHHHHHHHHHHc
Confidence            347999999999999999999999999743       48888999999999999999985

>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=98.53  E-value=2.6e-09  Score=75.56  Aligned_cols=46  Identities=26%  Similarity=0.500  Sum_probs=14.4

Q ss_pred             EEEEEeccccccceeccCCchHHHHHHHhCCEEEEeCCCCCCCCeEEEEEcC
Q 006943          555 TLEVLVPANAVGKVIGKAGSNLANIRKISGATIEMSDSKSSRGDRVALISGT  606 (624)
Q Consensus       555 ~~~i~VP~~~vg~IIGkgG~~I~~I~~~sGa~I~i~~~~~~~~~r~v~I~Gt  606 (624)
                      ..+|.||.+++|.|||+||.+||.|+++|||+|.|.++      ..|+|+|+
T Consensus         4 ~~~i~Ip~~kig~vIG~GG~~Ik~I~~~tga~I~i~dd------g~v~I~a~   49 (54)
T d1e3ha4           4 IITVKIPVDKIGEVIGPKRQMINQIQEDTGAEITIEDD------GTIYIGAA   49 (54)
T ss_dssp             CC---------------------CHHHHSCCCC--------------CCCCB
T ss_pred             EEEEEeCHHHeeEEECCccHHHHHHHHHHCCEEEEeCC------eEEEEEec
Confidence            45789999999999999999999999999999999843      55777774

>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=98.49  E-value=4.6e-08  Score=76.41  Aligned_cols=62  Identities=19%  Similarity=0.241  Sum_probs=54.7

Q ss_pred             EEEEeccceeEEEeCCchHHHHHHHhcCCeEEEccCCCCCCCCcccccCCceEEEecC-HHHHHHHHHHHHHHHhhc
Q 006943          143 QILVPSSQSANIIGKAGATIKRLRSKTRTSIKVTPKDASEPTHSCAMEFDNFVLISGE-SEAVKKALFAISAIMYKF  218 (624)
Q Consensus       143 ~llvp~~~~g~iIGk~G~~Ik~I~~~sga~I~i~~~~~~~~~~~~~~~~~r~V~I~G~-~~~V~~A~~~I~~~l~~~  218 (624)
                      .+.||.+.++.|||++|++|+.|+++|||+|.|..              +-.|.|.|. .+++..|+.+|..+.++.
T Consensus         4 vi~I~~~ki~~vIG~gG~~ik~i~~~t~~~I~I~d--------------~G~V~I~g~~~~~~~~A~~~I~~I~~ea   66 (87)
T d2z0sa2           4 IVEISPAKVPRVIGRKMSMLKTLEEKTECKIFVAR--------------NGRIHLECPNEDLEAIAVMAIKIIDEEA   66 (87)
T ss_dssp             EEECCGGGSGGGTCGGGHHHHHHHHHHCCEEEEET--------------TTEEEEECSCHHHHHHHHHHHHHHHHCS
T ss_pred             EEEEChhhcceeECCCCcHHHHHHHHHCCEEEECC--------------CcEEEEEeCCHHHHHHHHHHHHHHHHhc
Confidence            47899999999999999999999999999999963              356999996 789999999998887653

>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=98.48  E-value=5.7e-09  Score=73.75  Aligned_cols=48  Identities=31%  Similarity=0.452  Sum_probs=16.3

Q ss_pred             EEEEEecCcccceeccCCchHHHHHHHhcCCeEEeeCCCCCCCceEEEEEccCC
Q 006943           38 IYRILCPDGVIGSVIGKSGKVINSIRQETRARVKVVDPFPGAKDRVVTIYSHVK   91 (624)
Q Consensus        38 ~~~ilvp~~~~g~vIGk~G~~I~~i~~etg~~I~v~~~~~~~~er~i~I~G~~~   91 (624)
                      ..+|.||.+.+|.|||++|++||+|+++|||+|.+.+      +..|+|+|+.+
T Consensus         4 ~~~i~Ip~~kig~vIG~GG~~Ik~I~~~tga~I~i~d------dg~v~I~a~~~   51 (54)
T d1e3ha4           4 IITVKIPVDKIGEVIGPKRQMINQIQEDTGAEITIED------DGTIYIGAADG   51 (54)
T ss_dssp             CC---------------------CHHHHSCCCC--------------CCCCBSS
T ss_pred             EEEEEeCHHHeeEEECCccHHHHHHHHHHCCEEEEeC------CeEEEEEecCc
Confidence            4578999999999999999999999999999999964      46788888754

>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=98.24  E-value=2.1e-07  Score=75.17  Aligned_cols=52  Identities=29%  Similarity=0.290  Sum_probs=46.3

Q ss_pred             eeEEEeCCchHHHHHHHhcCCeEEEccCCCCCCCCcccccCCceEEEecCHHHHHHHHHHHHHHHhh
Q 006943          151 SANIIGKAGATIKRLRSKTRTSIKVTPKDASEPTHSCAMEFDNFVLISGESEAVKKALFAISAIMYK  217 (624)
Q Consensus       151 ~g~iIGk~G~~Ik~I~~~sga~I~i~~~~~~~~~~~~~~~~~r~V~I~G~~~~V~~A~~~I~~~l~~  217 (624)
                      .|.||||+|.+|+.|++.|||+|.|..               ..|.|.|.++++..|+.+|..++..
T Consensus        24 ~GrIIG~gGktik~Ie~~Tg~~I~I~d---------------~~v~iig~~e~i~~A~~~Ie~li~~   75 (104)
T d1tuaa2          24 KGRIIGEGGRARRTIEEMTDTYINVGE---------------YEVAIIGDYERAMAAKQAIEMLAEG   75 (104)
T ss_dssp             HHHHHCGGGHHHHHHHHHHTCEEEECS---------------SEEEEEEEHHHHHHHHHHHHHHHTT
T ss_pred             hcceeCCCcHHHHHHHHHHCCeEEEeC---------------CeEEEEECchhHHHHHHHHHHHHcC
Confidence            588999999999999999999999842               3477889999999999999999954

>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=98.07  E-value=3.9e-06  Score=69.97  Aligned_cols=79  Identities=22%  Similarity=0.303  Sum_probs=58.9

Q ss_pred             eeEEEEEeccc------eeEEEeCCchHHHHHHHhcCCeEEEccCCCCCC-------CCcccccCC-ceEEEecC-HHHH
Q 006943          140 EECQILVPSSQ------SANIIGKAGATIKRLRSKTRTSIKVTPKDASEP-------THSCAMEFD-NFVLISGE-SEAV  204 (624)
Q Consensus       140 ~~~~llvp~~~------~g~iIGk~G~~Ik~I~~~sga~I~i~~~~~~~~-------~~~~~~~~~-r~V~I~G~-~~~V  204 (624)
                      ++-+++||-..      +|.|||++|+++|+|+++|||+|.|..+.....       ....+..++ =-|.|++. .+.+
T Consensus         3 ~~~Ki~iP~~~~P~fNfvG~IlGPrG~t~K~Le~eTgckI~IrGrGS~kd~~~~~~~~~~~~~~~epLHv~I~a~~~~~~   82 (122)
T d1k1ga_           3 VSDKVMIPQDEYPEINFVGLLIGPRGNTLKNIEKECNAKIMIRGKGSVKEGKVGRKDGQMLPGEDEPLHALVTANTMENV   82 (122)
T ss_dssp             EEEEEECCTTTCCSHHHHHHHHCSSSHHHHHHHHHSCCEEEEEESTTSSSSSSSSCCCCCSCCSSCCEEEEEEESSHHHH
T ss_pred             eeEEEecCCccCCCCCeeeeEeCCCCchHHHHHHHHCCEEEEEecCCcccccccccCCCCCCCCCCCceEEEecCChhhH
Confidence            56788888764      899999999999999999999999988644110       011111222 24677776 6899


Q ss_pred             HHHHHHHHHHHhhc
Q 006943          205 KKALFAISAIMYKF  218 (624)
Q Consensus       205 ~~A~~~I~~~l~~~  218 (624)
                      .+|+.+|..+|...
T Consensus        83 ~~A~~~i~~ll~~~   96 (122)
T d1k1ga_          83 KKAVEQIRNILKQG   96 (122)
T ss_dssp             HHHHHHHHHHHTTT
T ss_pred             HHHHHHHHHHHHhc
Confidence            99999999999653

>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=98.05  E-value=5.7e-06  Score=68.96  Aligned_cols=69  Identities=29%  Similarity=0.404  Sum_probs=54.3

Q ss_pred             cEEEEEeccc------cccceeccCCchHHHHHHHhCCEEEEeCCCC----------C------CCCeEEEEEc-CHHHH
Q 006943          554 LTLEVLVPAN------AVGKVIGKAGSNLANIRKISGATIEMSDSKS----------S------RGDRVALISG-TPEQK  610 (624)
Q Consensus       554 ~~~~i~VP~~------~vg~IIGkgG~~I~~I~~~sGa~I~i~~~~~----------~------~~~r~v~I~G-t~e~v  610 (624)
                      .+.+|.||-+      ++|.|||.+|.++|+|+++|||+|.|--..+          .      ...=-|.|++ +++.+
T Consensus         3 ~~~Ki~iP~~~~P~fNfvG~IlGPrG~t~K~Le~eTgckI~IrGrGS~kd~~~~~~~~~~~~~~~epLHv~I~a~~~~~~   82 (122)
T d1k1ga_           3 VSDKVMIPQDEYPEINFVGLLIGPRGNTLKNIEKECNAKIMIRGKGSVKEGKVGRKDGQMLPGEDEPLHALVTANTMENV   82 (122)
T ss_dssp             EEEEEECCTTTCCSHHHHHHHHCSSSHHHHHHHHHSCCEEEEEESTTSSSSSSSSCCCCCSCCSSCCEEEEEEESSHHHH
T ss_pred             eeEEEecCCccCCCCCeeeeEeCCCCchHHHHHHHHCCEEEEEecCCcccccccccCCCCCCCCCCCceEEEecCChhhH
Confidence            4678888875      4899999999999999999999999964211          0      1122466777 68899


Q ss_pred             HHHHHHHHHHHh
Q 006943          611 RAAENLIQAFIM  622 (624)
Q Consensus       611 ~~A~~lI~~~i~  622 (624)
                      +.|..+|+.+|.
T Consensus        83 ~~A~~~i~~ll~   94 (122)
T d1k1ga_          83 KKAVEQIRNILK   94 (122)
T ss_dssp             HHHHHHHHHHHT
T ss_pred             HHHHHHHHHHHH
Confidence            999999999984

>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=97.55  E-value=9.8e-05  Score=61.95  Aligned_cols=74  Identities=20%  Similarity=0.317  Sum_probs=51.8

Q ss_pred             EEEEEEecC------CccceeeccCcchHHHHHhHhCCeEEEcCCCC------------------CCCceEEEEeecCCc
Q 006943          308 LVIRVLCPF------NKIGRVIGKGGGTIKSIRQASGAQIDVDDTKD------------------NRDECVITVTAIESP  363 (624)
Q Consensus       308 ~~~~i~vp~------~~vg~IIGk~G~~Ik~I~~~tga~I~v~~~~~------------------~~~er~i~I~G~~~~  363 (624)
                      +..++.||.      +++|.|||.+|.++|+|+++|||+|.|--...                  ..++-.|.|++....
T Consensus         2 l~eKv~IP~~~~P~~NfvG~IiGPrG~t~K~le~eTg~kI~IrGrGS~k~~~~~~~~~~~~~~~~~~epLHv~I~a~~~~   81 (134)
T d2bl5a1           2 LQEKLYVPVKEYPDFNFVGRILGPRGLTAKQLEAETGCKIMVRGKGSMRDKKKEEQNRGKPNWEHLNEDLHVLITVEDAQ   81 (134)
T ss_dssp             EEEEEECCTTTCSSSCHHHHHTTTTHHHHHHHHHHHSEEEEEESTTSSCCHHHHHTSTTSHHHHTTTSCCEEEEEECSCC
T ss_pred             cceEEeCCCCCCCCCCeeEEEECCCCchHHHHHHHHCCEEEEEecCCCcCccccccccCCCCCcCCCCCCEEEEEecCcH
Confidence            455777774      57899999999999999999999999953110                  124557888886433


Q ss_pred             hhHHHHHHHHHHHHhhcc
Q 006943          364 DDIKSMAVEAVLLLQTKI  381 (624)
Q Consensus       364 ~~a~~~~~~~i~~~~~~~  381 (624)
                      ..+...+..|+..+...+
T Consensus        82 ~~a~~kl~~A~~~I~~lL   99 (134)
T d2bl5a1          82 NRAELKLKRAVEEVKKLL   99 (134)
T ss_dssp             HHHHHHHHHHHHHHHHHS
T ss_pred             HHHHHHHHHHHHHHHHHc
Confidence            444445666666665544

>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=97.47  E-value=8.3e-05  Score=62.39  Aligned_cols=68  Identities=21%  Similarity=0.332  Sum_probs=51.1

Q ss_pred             EEEEEecc------ccccceeccCCchHHHHHHHhCCEEEEeCCCCC------------------CCCeEEEEEcC-H--
Q 006943          555 TLEVLVPA------NAVGKVIGKAGSNLANIRKISGATIEMSDSKSS------------------RGDRVALISGT-P--  607 (624)
Q Consensus       555 ~~~i~VP~------~~vg~IIGkgG~~I~~I~~~sGa~I~i~~~~~~------------------~~~r~v~I~Gt-~--  607 (624)
                      ..+|.||-      +++|.|||++|.++|+|+++|||+|.|--....                  ..+==|.|++. +  
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            45677774      578999999999999999999999999864320                  12234677764 2  


Q ss_pred             ---HHHHHHHHHHHHHHh
Q 006943          608 ---EQKRAAENLIQAFIM  622 (624)
Q Consensus       608 ---e~v~~A~~lI~~~i~  622 (624)
                         ..++.|..+|+.+|.
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               357889999998764

>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=95.50  E-value=0.0058  Score=44.18  Aligned_cols=39  Identities=26%  Similarity=0.411  Sum_probs=36.4

Q ss_pred             cEEEEEeccccccceeccCCchHHHHHHHhCCEEEEeCC
Q 006943          554 LTLEVLVPANAVGKVIGKAGSNLANIRKISGATIEMSDS  592 (624)
Q Consensus       554 ~~~~i~VP~~~vg~IIGkgG~~I~~I~~~sGa~I~i~~~  592 (624)
                      ....+.||++.....|||+|.|++-..+.||.+|.|...
T Consensus        26 ~~~~v~V~~~qls~AIGk~G~NvrLas~Ltg~~IdI~~e   64 (67)
T d2asba3          26 RAARVVVPDFQLSLAIGKEGQNARLAARLTGWRIDIRGD   64 (67)
T ss_dssp             TEEEEEECGGGHHHHHCGGGHHHHHHHHHHSCEEEEEES
T ss_pred             cEEEEEECcccccchhcCCceeHHHHHHHHCCEEEEEeC
Confidence            478999999999999999999999999999999999765

>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=95.32  E-value=0.0062  Score=44.19  Aligned_cols=39  Identities=31%  Similarity=0.454  Sum_probs=36.1

Q ss_pred             cEEEEEeccccccceeccCCchHHHHHHHhCCEEEEeCC
Q 006943          554 LTLEVLVPANAVGKVIGKAGSNLANIRKISGATIEMSDS  592 (624)
Q Consensus       554 ~~~~i~VP~~~vg~IIGkgG~~I~~I~~~sGa~I~i~~~  592 (624)
                      -...+.||++..+..|||+|.|++-..+.||.+|.|..-
T Consensus        27 ~~~~v~V~~~qls~AIGk~G~NvrLas~Ltg~~idI~s~   65 (68)
T d1hh2p3          27 KAARVLVPPTQLSLAIGKGGQNARLAAKLTGWKIDIKPI   65 (68)
T ss_dssp             TEEEEEECTTSHHHHHCGGGHHHHHHHHHHSCEEEEEEC
T ss_pred             CEEEEEECcccccccccCCcchHHHHHHHHCCEEeeEEc
Confidence            378899999999999999999999999999999999753

>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=93.67  E-value=0.025  Score=40.92  Aligned_cols=37  Identities=22%  Similarity=0.308  Sum_probs=34.0

Q ss_pred             EEEEEecCcccceeccCCchHHHHHHHhcCCeEEeeC
Q 006943           38 IYRILCPDGVIGSVIGKSGKVINSIRQETRARVKVVD   74 (624)
Q Consensus        38 ~~~ilvp~~~~g~vIGk~G~~I~~i~~etg~~I~v~~   74 (624)
                      .+.+.||.+..+..|||+|.||+-..+-||.+|.|..
T Consensus        28 ~~~v~V~~~qls~AIGk~G~NvrLas~Ltg~~idI~s   64 (68)
T d1hh2p3          28 AARVLVPPTQLSLAIGKGGQNARLAAKLTGWKIDIKP   64 (68)
T ss_dssp             EEEEEECTTSHHHHHCGGGHHHHHHHHHHSCEEEEEE
T ss_pred             EEEEEECcccccccccCCcchHHHHHHHHCCEEeeEE
Confidence            5778999999999999999999999999999999853

>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=93.52  E-value=0.025  Score=40.71  Aligned_cols=38  Identities=24%  Similarity=0.295  Sum_probs=34.6

Q ss_pred             EEEEEEecCcccceeccCCchHHHHHHHhcCCeEEeeC
Q 006943           37 VIYRILCPDGVIGSVIGKSGKVINSIRQETRARVKVVD   74 (624)
Q Consensus        37 ~~~~ilvp~~~~g~vIGk~G~~I~~i~~etg~~I~v~~   74 (624)
                      -.+.+.||.+..+..|||+|.||+=..+-||.+|.|-.
T Consensus        26 ~~~~v~V~~~qls~AIGk~G~NvrLas~Ltg~~IdI~~   63 (67)
T d2asba3          26 RAARVVVPDFQLSLAIGKEGQNARLAARLTGWRIDIRG   63 (67)
T ss_dssp             TEEEEEECGGGHHHHHCGGGHHHHHHHHHHSCEEEEEE
T ss_pred             cEEEEEECcccccchhcCCceeHHHHHHHHCCEEEEEe
Confidence            36778999999999999999999999999999999853

>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=90.28  E-value=0.2  Score=37.72  Aligned_cols=57  Identities=9%  Similarity=0.001  Sum_probs=46.4

Q ss_pred             EEEEeccccccceeccCCc-hHHHHHHHhCCEEEEeCCCCCCCCeEEEEEc-CHHHHHHHHHHHH
Q 006943          556 LEVLVPANAVGKVIGKAGS-NLANIRKISGATIEMSDSKSSRGDRVALISG-TPEQKRAAENLIQ  618 (624)
Q Consensus       556 ~~i~VP~~~vg~IIGkgG~-~I~~I~~~sGa~I~i~~~~~~~~~r~v~I~G-t~e~v~~A~~lI~  618 (624)
                      +-+.||..++..+||++++ .|+.|.+.+++.|.|-..     .| |-|.| +++..-++...|.
T Consensus         3 ~v~~vs~~~~rrll~~~~~~ml~~l~~~~~~eI~VG~N-----Gr-IWi~~~~~~~~i~i~~aI~   61 (85)
T d2ja9a2           3 MIIDVNLNFARQLLFNNDFPLLKVLAAHTKFEVAIGLN-----GK-IWVKCEELSNTLACYRTIM   61 (85)
T ss_dssp             EEEECCHHHHHHHHHCTTCCHHHHHHTTCCCEEEEETT-----TE-EEEECSSHHHHHHHHHHHH
T ss_pred             EEEEecHHHHHHHHcCCCChHHHHHHhhcCceEEEecC-----cE-EEEECCCHHHHHHHHHHHH
Confidence            4578999999999999998 899999999999999865     24 88999 5676665555444

>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=85.40  E-value=0.16  Score=38.95  Aligned_cols=33  Identities=18%  Similarity=0.295  Sum_probs=27.7

Q ss_pred             EEEEecCcccceeccCCchHHHHHHHhcCCeEE
Q 006943           39 YRILCPDGVIGSVIGKSGKVINSIRQETRARVK   71 (624)
Q Consensus        39 ~~ilvp~~~~g~vIGk~G~~I~~i~~etg~~I~   71 (624)
                      +++.|.....|.|||++|+.|++|+++-.-++.
T Consensus        37 i~I~I~tarPGivIGrkG~~I~~L~~~l~k~~~   69 (92)
T d1wh9a_          37 TEIIILATRTQNVLGEKGRRIRELTAVVQKRFG   69 (92)
T ss_dssp             EEEEEEESCHHHHHCGGGHHHHHHHHHHHHHHC
T ss_pred             EEEEEEeCCCceeeccCchhHHHHHHHHHHHHC
Confidence            567889999999999999999999987654443