Citrus Sinensis ID: 002054

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Local Sequence Feature Prediction

Residue Number Marker
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100-------110-------120-------130-------140-------150-------160-------170-------180-------190-------200-------210-------220-------230-------240-------250-------260-------270-------280-------290-------300-------310-------320-------330-------340-------350-------360-------370-------380-------390-------400-------410-------420-------430-------440-------450-------460-------470-------480-------490-------500-------510-------520-------530-------540-------550-------560-------570-------580-------590-------600-------610-------620-------630-------640-------650-------660-------670-------680-------690-------700-------710-------720-------730-------740-------750-------760-------770-------780-------790-------800-------810-------820-------830-------840-------850-------860-------870-------880-------890-------900-------910-------920-------930-------940-------950-------960-------970----
Protein Sequence
MSSLATKTHPLLNNLPPFLTWRALGFRTICSGRLGFAPCEPAPPTPAPSVAGTKVLETFKEEFEIGSRLITLETGKIARFANGAVVLGMDETKVLSTVTSSKGDSVRDFLPLTVDYQEKQFAQGVIPNTYMRREGAPKERELLVGRIIDRPIRPLFPAGFYHEVQVMASVLSSDGKQDPDIMAANATSAALMLSDIPWGGPIGMIRIGRICGQFIVNPTMDELSLSDLNLVYACTREKTLMIDVQAREISEKDLEAGLRLAHPEAVKYLEPQIRLAEKAGKQKKEYKLSMISEQTLEKVSNLAEAHIEAVFTDPSYSKFERGEALDKIGQDVKKALEEECDEESLQVLPKAVDTVRKRVIRKRIIAEGVRVDGRQLDEVRPIYCESGNLPILHGSSLFSRGDTQVLCTVTLGAPAEAQRLESLVGPPTKRFMLHYSFPPFCINEVGKRVGLNRREVGHGTLAEKALLAVLPPENDFPYTVRVNSEVMASDGSTSMATVCGGSMALMDAGIPLQEHVAGVSVGLVSEVDPSTGEIKDYRILTDILGLEDHLGDMDFKIAGTRIGVTAIQLDIKPAGIPLDIICECLEHAHKGRLQILDHMEREISAPRTQDDRNSPRLATLKYDNDTLRRLIGPLGALKRKIEEETGGRISVSDGTLTVVAKNRSVMEKVLEKVDFIIGREIEVGGIYKGVVTSVKEYGAFVEFNGGQQGLLHVSELSHEPVSRVSDVVSVGQQLSLRCIGQDVRGNIKLSLKAVSPRPEADVKGVVEGSVPVNKQATDVWASVGDVSNGQNPELPMRKNETPGVNSSTSSTPAVLIRSAAECDEEEKASGFSQSSKSTLKSTLASKSNSKPKKFTSQSDFFSSTNIQKSTSFSQREREELAECLFGTEDGDEDNKGTRVEAIVSAKNLKLGTKVAAKVYQVRARGLVLDLGGGIRGMYRFENNEKKDFVVGDELLVKCSSFTGKGIPVVSLVDS
Secondary Structure (PSIPRED)
cccccccccccccccccHHHHcccccEEEcccccccccccccccccccccccccccccEEEEEEEccEEEEEEccccccccccEEEEEEcccEEEEEEEcccccccccccccEEcccccccccccccccccccccccccccHHHHHcccccccccccccccccEEEEEEEEEccccccHHHHHHHHHHHHHHHccccccccEEEEEEEEEccEEEEcccHHHHHcccccEEEEEcccEEEEEEcccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHcccccccccccccHHHHHHHHHHHHHHHHHHHccccccHHHHHHHHHHHHHHHHHHHHHcccHHHHHHHHHHHHHHHHHHHHHHHHcccccccccccccccccEEEcccccccccccccccccccHHHHHcccccccHHHccccccccccccccccccccccccccccccccccccccccHHHHHHHccccccccccccEEEEEEccccccccHHHHHHHHHHHHHHHccccccccHHHHHccEEccccccccccccEEEEEccccccccccccccccccccccHHHHHHccccccccHHHHHHHHHHHHHHHHHHHHHHHHHHcccccccccccccEEEEEEcccccccccccccHHHHHHHHHHccEEEEEccEEEEEEccHHHHHHHHHHHHHHHccccccccEEEEEEEEEEEcEEEEEEcccccEEEEEEccccccccccccccccccEEEEEEEEEccccccEEEEcccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccEEEccccccHHHHcccccccccccccccccccccccccccccccccccccccccccccHHHHHHHHHHHHccccccccccccccccccccccccccccEEEEEEEEEEEEEEEEEcccccEEEEEEccccccccccccEEEEEEccccccccEEEEcccc
Secondary Structure Prediction (SSPRO)
cHHHHHcccHHHHccccHHHHHHcccEEEEcccccccccccccccccccccccEEcccEEEEEEEcccEEEEEccHHHEHcccEEEEEcccEEEEEEEEEcccccccccccEEEEcEHHHHHccccccccEcccccccHHHHHHHHHccccccccccccccccEEEEEEEEEccccccHHHHHHHHHHHHHHHccccccccEEEEEEEEEccEEEEcccHHHHHcccccEEEEccHHHHHHHHHcHccccHHHHHHHHHHcHHHHHHHHHHHHHHHHHHcccccccccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHccccccHHHHHHHHHHHHHHHHHHHHHccccccccccccEEEEEEEEccccccccccHEEcccccEEEEEEEcccccHHHHHHHccccccccEEEEEcccccccccccccccccccEcccHHHHHHHHHHHcccHHHccEEEEEEEEEEccccccccHHHHHHHHHHHHccccccccEEEEEEEEEEccccccccEEEEEEEEccccccHccccccEEEEcccccEEEEEEEEEEccccHHHHHHHHHHHHHHHHHHHHHHHHHHHccHHHHHHccccEEEEEEcHHHHHHHccccHHHHHHHHHHcccEEEEcccEEEEEEccHHHHHHHHHHHHHHHHcccEEcEEEEcEEEEEEEccEEEEEccccccEEEEHHHHHHHHHHHHHHHEcccEEEEEEEEEcccccEEEEHHHHcccccHcccccHHcccccHcccccccccccccccccccccccccccccccccccccccEEEEEEcHHccHHHHcccccccccccccccccccccccccccccccccccccccccccccccccHHHHHHccccccccccccccccccccccHcccccccEEEEEEEHHHHccEEEEcccccEEEEEEcccccccEEEccEEEEEEcccccccccEEEEEcc
Coil and Loop (DISEMBL)
msslatkthpllnnlppfltwralgfrticsgrlgfapcepapptpapsvagtKVLETFKEEFEIGSRLITLETGKIARFANGAVVLGMDETKVLSTVtsskgdsvrdflPLTVDYQEKQfaqgvipntymrregapkERELLVGRiidrpirplfpagfyHEVQVMASVlssdgkqdpdiMAANATSAALMlsdipwggpigmiRIGRIcgqfivnptmdelslsDLNLVYACTREKTLMIDVQAREISEKDLEAGLRLAHPEAVKYLEPQIRLAEKAGKQKKEYKLSMISEQTLEKVSNLAEAHIEavftdpsyskfergeALDKIGQDVKKALEEECDEESLQVLPKAVDTVRKRVIRKRIIAegvrvdgrqldevrpiycesgnlpilhgsslfsrgdtQVLCTVTLGAPAEAQRLeslvgpptkrfmlhysfppfcinevgkrvglnrrevghgTLAEKALLavlppendfpytvrvnsevmasdgstsmatvcggsmalmdagiplqehvaGVSVGLvsevdpstgeikdyRILTDILGledhlgdmdfkiAGTRIGVTAiqldikpagiplDIICECLEHAHKGRLQILDHMereisaprtqddrnsprlatlkydndTLRRLIGPLGALKRKieeetggrisvsdgtLTVVAKNRSVMEKVLEKVDFIIGREIEVGGIYKGVVTSVKEYGafvefnggqqgllhvselshepvsrvsDVVSVGQQLSLRCIGQDVRGNIKLSLkavsprpeadvkgvvegsvpvnkqatdvwasvgdvsngqnpelpmrknetpgvnsstsstpAVLIRSAaecdeeekasgfsqsskSTLKSTLasksnskpkkftsqsdffsstniqkstsFSQREREELAEClfgtedgdednkgTRVEAIVSAKNLKLGTKVAAKVYQVRARGLVLdlgggirgmyrfennekkdfvvgDELLVKCssftgkgipVVSLVDS
Flexible Loop (DISEMBL)
msslatkthpllnnlppFLTWRALGFRTICSGRLGFAPCEPAPPTPAPSVAGTKVLETFKEEFEIGsrlitletgkIARFANGAVVLGMDETKVLStvtsskgdsvrDFLPLTVDYQekqfaqgvipntymrregapkERELLVGRIIDRPIRPLFPAGFYHEVQVMASVLSSDGKQDPDIMAANATSAALMLSDIPWGGPIGMIRIGRICGQFIVNPTMDELSLSDLNLVYACTREKTLMIDVQAREISEKDLEAGLRLAhpeavkylepqIRLAEKAGKQKKEYKLSMISEQTLEKVSNLAEAHIEavftdpsyskfERGEALDKIGQDVKKALEeecdeeslqvlpkavdtvrkrvirkriiaegvrvdgrqldeVRPIYCESGNLPILHGSSLFSRGDTQVLCTVTLGAPAEAQRLESLVGPPTKRFMLHYSFPPFCINEVGKRVGLNRREVGHGTLAEkallavlppenDFPYTVRVNSEVMASDGSTSMATVCGGSMALMDAGIPLQEHVAGVSVGLvsevdpstgeikdYRILTDILGLEDHLGDMDFKIAGTRIGVTAIQLDIKPAGIPLDIICECLEHAHKGRLQILDHMEREIsaprtqddrnsprlatlkydndtlrrligplgalkrkieeetggrisvsdgtltvvaknrsvmeKVLEKVDFIIGREIEVGGIYKGVVTSVKEYGAFVEFNGGQQGLLHVSELSHEPVSRVSDVVSVGQQLSlrcigqdvrgniklslkavsprpeadvkgvvegsvpvnkqatdvwasvgdvsngqnpelpmrknetpgvnsstsstPAVLIRSAAECDEEekasgfsqsskstlkstlasksnskpkkftsqsdffsstniqkstsfsqrEREELAECLfgtedgdednkgTRVEAIvsaknlklgtkvaAKVYQVRARGLVLDLGGGIRGMYRFENNEKKDFVVGDELLVkcssftgkgipvvslvds
Low Complexity Region (SEG)
MSSLATKTHPLLNNLPPFLTWRALGFRTICSGRLGFapcepapptpapsvaGTKVLETFKEEFEIGSRLITLETGKIARFANGAVVLGMDETKVLSTVTSSKGDSVRDFLPLTVDYQEKQFAQGVIPNTYMRREGAPKERELLVGRIIDRPIRPLFPAGFYHEVQVMASVLSSDGKQDPDIMAANATSAALMLSDipwggpigmirigricgQFIVNPTMDELSLSDLNLVYACTREKTLMIDVQAREISEKDLEAGLRLAHPEAVKYLEPQIRLAEKAGKQKKEYKLSMISEQTLEKVSNLAEAHIEAVFTDPSYSKFERGEALDKIGQDVKKALEEECDEESLQVLPKAVDTvrkrvirkriiAEGVRVDGRQLDEVRPIYCESGNLPILHGSSLFSRGDTQVLCTVTLGAPAEAQRLESLVGPPTKRFMLHYSFPPFCINEVGKRVGLNRREVGHGTLAEKALLAVLPPENDFPYTVRVNSEVMASDGSTSMATVCGGSMALMDAGIPLQEHVAGVSVGLVSEVDPSTGEIKDYRILTDILGLEDHLGDMDFKIAGTRIGVTAIQLDIKPAGIPLDIICECLEHAHKGRLQILDHMEREISAPRTQDDRNSPRLATLKYDNDTLRRLIGPLGALKRKIEEETGGRISVSDGTLTVVAKNRSVMEKVLEKVDFIIGREIEVGGIYKGVVTSVKEYGAFVEFNGGQQGLLHVSELSHEPVSRVSDVVSVGQQLSLRCIGQDVRGNIKLSLKAVSPRPEADVKGVVEGSVPVNKQATDVWASVGDVSNGQNPELPMRKNETPGVNSSTSSTPAVLIRSAAECDEEEKASGFsqsskstlkstlasksnskPKKFTSQSDFFSSTNIQKSTSFSQREREELAECLFGTEDGDEDNKGTRVEAIVSAKNLKLGTKVAAKVYQVRARGLVLDLGGGIRGMYRFENNEKKDFVVGDELLVKCSSFTGKGIPVVSLVDS
Disordered region (IsUnstruct)
**********LLNNLPPFLTWRALGFRTICSGRLGFAPCE**********AGTKVLETFKEEFEIGSRLITLETGKIARFANGAVVLGMDETKVLSTVTSSKGDSVRDFLPLTVDYQEKQFAQGVIPNTYMRREGAPKERELLVGRIIDRPIRPLFPAGFYHEVQVMASVL*********IMAANATSAALMLSDIPWGGPIGMIRIGRICGQFIVNPTMDELSLSDLNLVYACTREKTLMIDVQAREISEKDLEAGLRLAHPEAVKYLEPQI***************************NLAEAHIEAVFTD*******************************LQVLPKAVDTVRKRVIRKRIIAEGVRVDGRQLDEVRPIYCESGNLPILHGSSLFSRGDTQVLCTVTLGAPAEAQRLESLVGPPTKRFMLHYSFPPFCINEVGKRVGLNRREVGHGTLAEKALLAVLPPENDFPYTVRVNSEVMA*****SMATVCGGSMALMDAGIPLQEHVAGVSVGLVSEVDPSTGEIKDYRILTDILGLEDHLGDMDFKIAGTRIGVTAIQLDIKPAGIPLDIICECLEHAHKGRLQILD**********************LKYDNDTLRRLIGPLGALKRKIEEETGGRISVSDGTLTVVAKNRSVMEKVLEKVDFIIGREIEVGGIYKGVVTSVKEYGAFVEFNGGQQGLLHVSELSHEPVSRVSDVVSVGQQLSLRCIGQDVRGNIKLSLKA***********************TDVWA*********************************************************************************************************************VEAIVSAKNLKLGTKVAAKVYQVRARGLVLDLGGGIRGMYRFENNEKKDFVVGDELLVKCSSFTGKGIPVVSL***
Disordered Region (DISOPRED)
***********LNNLPPFLTWRALGFRTICS***************************FKEEFEIGSRLITLETGKIARFANGAVVLGMDETKVLSTVTSSKGDSVRDFLPLTVDYQEKQFAQGVIPNTYMRREGAPKERELLVGRIIDRPIRPLFPAGFYHEVQVMASVLSSDGKQDPDIMAANATSAALMLSDIPWGGPIGMIRIGRICGQFIVNPTMDELSLSDLNLVYACTREKTLMIDVQAREISEKDLEAGLRLAHPEAVKYLEPQIRLAEKAGKQKKEYKLSMISEQTLEKVSNLAEAHIEAVFTDPSYSKFERGEALDKIGQDVKKALEEECDEESLQVLPKAVDTVRKRVIRKRIIAEGVRVDGRQLDEVRPIYCESGNLPILHGSSLFSRGDTQVLCTVTLGAPAEAQRLESLVGPPTKRFMLHYSFPPFCINEVGKRVGLNRREVGHGTLAEKALLAVLPPENDFPYTVRVNSEVMASDGSTSMATVCGGSMALMDAGIPLQEHVAGVSVGLVSEVDPSTGEIKDYRILTDILGLEDHLGDMDFKIAGTRIGVTAIQLDIKPAGIPLDIICECLEHAHKGRLQILDHMEREISAPRTQDDRNSPRLATLKYDNDTLRRLIGPLGALKRKIEEETGGRISVSDGTLTVVAKNRSVMEKVLEKVDFIIGREIEVGGIYKGVVTSVKEYGAFVEFNGGQQGLLHVSELSHEPVSRVSDVVSVGQQLSLRCIGQDVRGNIKLSLKA**********************************************************************************************************************************************************LKLGTKVAAKVYQVRARGLVLDLGGGIRGMYRFENNEKKDFVVGDELLVKCSSFTGKGIPVVSLVD*
Disordered Region (DISEMBL)
MSSLATKTHPLLNNLPPFLTWRALGFRTICSGRLGFAPCEPAPPTPAPSVAGTKVLETFKEEFEIGSRLITLETGKIARFANGAVVLGMDETKVLSTVTSSKGDSVRDFLPLTVDYQEKQFAQGVIPNTYMRREGAPKERELLVGRIIDRPIRPLFPAGFYHEVQVMASVLSSDGKQDPDIMAANATSAALMLSDIPWGGPIGMIRIGRICGQFIVNPTMDELSLSDLNLVYACTREKTLMIDVQAREISEKDLEAGLRLAHPEAVKYLEPQIRLAEKAGKQKKEYKLSMISEQTLEKVSNLAEAHIEAVFTDPSYSKFERGEALDKIGQDVKKALEEECDEESLQVLPKAVDTVRKRVIRKRIIAEGVRVDGRQLDEVRPIYCESGNLPILHGSSLFSRGDTQVLCTVTLGAPAEAQRLESLVGPPTKRFMLHYSFPPFCINEVGKRVGLNRREVGHGTLAEKALLAVLPPENDFPYTVRVNSEVMASDGSTSMATVCGGSMALMDAGIPLQEHVAGVSVGLVSEVDPSTGEIKDYRILTDILGLEDHLGDMDFKIAGTRIGVTAIQLDIKPAGIPLDIICECLEHAHKGRLQILDHMEREISAPRTQDDRNSPRLATLKYDNDTLRRLIGPLGALKRKIEEETGGRISVSDGTLTVVAKNRSVMEKVLEKVDFIIGREIEVGGIYKGVVTSVKEYGAFVEFNGGQQGLLHVSELSHEPVSRVSDVVSVGQQLSLRCIGQDVRGNIKLSLK***********GVVEGSVPVNKQATDVWASVGDVSNGQNPELPMRK**************AVLIRSAA***********************************SQSDFFSSTNIQ***********ELAECLFGTEDGDEDNKGTRVEAIVSAKNLKLGTKVAAKVYQVRARGLVLDLGGGIRGMYRFENNEKKDFVVGDELLVKCSSFTGKGIPVVSLVDS
Disordered Region (DISPRO)
*****TKTHPLLNNLPPFLTWRALGFRTICSGRLGFAPCEPAPPTPAPSVAGTKVLETFKEEFEIGSRLITLETGKIARFANGAVVLGMDETKVLSTVTSSKGDSVRDFLPLTVDYQEKQFAQGVIPNTYMRREGAPKERELLVGRIIDRPIRPLFPAGFYHEVQVMASVLSSDGKQDPDIMAANATSAALMLSDIPWGGPIGMIRIGRICGQFIVNPTMDELSLSDLNLVYACTREKTLMIDVQAREISEKDLEAGLRLAHPEAVKYLEPQIRLAEKAGKQKKEYKLSMISEQTLEKVSNLAEAHIEAVFTDPSYSKFERGEALDKIGQDVKKALEEECDEESLQVLPKAVDTVRKRVIRKRIIAEGVRVDGRQLDEVRPIYCESGNLPILHGSSLFSRGDTQVLCTVTLGAPAEAQRLESLVGPPTKRFMLHYSFPPFCINEVGKRVGLNRREVGHGTLAEKALLAVLPPENDFPYTVRVNSEVMASDG*TSMATVCGGSMALMDAGIPLQEHVAGVSVGLVSEVDPSTGEIKDYRILTDILGLEDHLGDMDFKIAGTRIGVTAIQLDIKPAGIPLDIICECLEHAHKGRLQILDHMEREISAPRTQDDRNSPRLATLKYDNDTLRRLIGPLGALKRKIEEETGGRISVSDGTLTVVAKNRSVMEKVLEKVDFIIGREIEVGGIYKGVVTSVKEYGAFVEFNGGQQGLLHVSELSHEPVSRVSDVVSVGQQLSLRCIGQDVRGNIKLSLKAVSPR****************************************************STPAVLIRSAAECDEE***************************************************************************A*VS*KNLKLGTKVAAKVYQVRARGLVLDLGGGIRGMYRFENNEKKDFVVGDELLVKCSSFTGKGIPVVSLVDS
Transmembrane Helix (TMHMM)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooHHHHHHHHHHHHHHHHHHHHHHHHHiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
Transmembrane Helix (MEMSAT)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooohhhhhhhhhhhhhhhhhhhhhhhhiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
TM Helix, Signal Peptide (MEMSAT_SVM)
SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhoooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (Phobius)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
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Signal Peptide (SignalP NN Mode)
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Coiled Coils (COILS)
MSSLATKTHPLLNNLPPFLTWRALGFRTICSGRLGFAPCEPAPPTPAPSVAGTKVLETFKEEFEIGSRLITLETGKIARFANGAVVLGMDETKVLSTVTSSKGDSVRDFLPLTVDYQEKQFAQGVIPNTYMRREGAPKERELLVGRIIDRPIRPLFPAGFYHEVQVMASVLSSDGKQDPDIMAANATSAALMLSDIPWGGPIGMIRIGRICGQFIVNPTMDELSLSDLNLVYACTREKTLMIDVQAREISEKDLEAGLRLAHPEAVKYLEPQIRLAEKAGKQKKEYKLSMISEQTLEKVSNLAEAHIEAVFTDPSYSKFERGEALDKIGQDVKKALEEECDEESLQVLPKAVDTVRKRVIRKRIIAEGVRVDGRQLDEVRPIYCESGNLPILHGSSLFSRGDTQVLCTVTLGAPAEAQRLESLVGPPTKRFMLHYSFPPFCINEVGKRVGLNRREVGHGTLAEKALLAVLPPENDFPYTVRVNSEVMASDGSTSMATVCGGSMALMDAGIPLQEHVAGVSVGLVSEVDPSTGEIKDYRILTDILGLEDHLGDMDFKIAGTRIGVTAIQLDIKPAGIPLDIICECLEHAHKGRLQILDHMEREISAPRTQDDRNSPRLATLKYDNDTLRRLIGPLGALKRKIEEETGGRISVSDGTLTVVAKNRSVMEKVLEKVDFIIGREIEVGGIYKGVVTSVKEYGAFVEFNGGQQGLLHVSELSHEPVSRVSDVVSVGQQLSLRCIGQDVRGNIKLSLKAVSPRPEADVKGVVEGSVPVNKQATDVWASVGDVSNGQNPELPMRKNETPGVNSSTSSTPAVLIRSAAECDEEEKASGFSQSSKSTLKSTLASKSNSKPKKFTSQSDFFSSTNIQKSTSFSQREREELAECLFGTEDGDEDNKGTRVEAIVSAKNLKLGTKVAAKVYQVRARGLVLDLGGGIRGMYRFENNEKKDFVVGDELLVKCSSFTGKGIPVVSLVDS
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	974	2.2.26 [Sep-21-2011]
Q9S7G6	991	Polyribonucleotide nucleo	yes	no	0.973	0.956	0.676	0.0
Q6KAI0	982	Polyribonucleotide nucleo	yes	no	0.934	0.926	0.662	0.0
B3DZ86	707	Polyribonucleotide nucleo	yes	no	0.705	0.971	0.457	1e-171
B1KRQ5	702	Polyribonucleotide nucleo	yes	no	0.698	0.968	0.429	1e-160
B9M1G5	696	Polyribonucleotide nucleo	yes	no	0.699	0.978	0.433	1e-160
Q39VA1	697	Polyribonucleotide nucleo	yes	no	0.700	0.978	0.435	1e-160
Q3A4A1	699	Polyribonucleotide nucleo	yes	no	0.697	0.971	0.422	1e-159
C5D9D5	712	Polyribonucleotide nucleo	yes	no	0.707	0.967	0.425	1e-158
Q21H65	722	Polyribonucleotide nucleo	yes	no	0.715	0.965	0.428	1e-158
Q6D9A1	706	Polyribonucleotide nucleo	yes	no	0.713	0.984	0.417	1e-158

>sp|Q9S7G6|PNP2_ARATH Polyribonucleotide nucleotidyltransferase 2, mitochondrial OS=Arabidopsis thaliana GN=PNP2 PE=2 SV=1

 Score = 1335 bits (3454), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 684/1011 (67%), Positives = 804/1011 (79%), Gaps = 63/1011 (6%)

Query: 1   MSSLATKTHPLLNNLPPFLTWRALGFRTICSGRLGFAPCEPAPPTPAPSVAGTKVLETFK 60
           MSS+  +      +LP FL WRALGFRTICSGRLGFAP  P     +P  AGTK+LE+FK
Sbjct: 1   MSSIVNRASSA--SLPNFLAWRALGFRTICSGRLGFAPSVPD----SPVSAGTKILESFK 54

Query: 61  EEFEIGSRLITLETGKIARFANGAVVLGMDETKVLSTVTSSKGDSVRDFLPLTVDYQEKQ 120
           EEFE+GSR+++ ETGKIARFANG+VVLGMDETKVLSTVT +K DS RDFLPLTVDYQEKQ
Sbjct: 55  EEFEVGSRVVSFETGKIARFANGSVVLGMDETKVLSTVTCAKTDSPRDFLPLTVDYQEKQ 114

Query: 121 FAQGVIPNTYMRREGAPKERELLVGRIIDRPIRPLFPAGFYHEVQVMASVLSSDGKQDPD 180
           +AQG+IPNTYMRREGAPKERELL GR+IDRPIRPLFP GFYHEVQ+MASVLSSDGKQDPD
Sbjct: 115 YAQGLIPNTYMRREGAPKERELLCGRLIDRPIRPLFPTGFYHEVQIMASVLSSDGKQDPD 174

Query: 181 IMAANATSAALMLSDIPWGGPIGMIRIGRICGQFIVNPTMDELSLSDLNLVYACTREKTL 240
           I+AANA+SAALMLSD+PWGGPIG+IRIGRICGQF+VNPTMDELS SDLNL+YACTR+KT+
Sbjct: 175 ILAANASSAALMLSDVPWGGPIGVIRIGRICGQFVVNPTMDELSSSDLNLIYACTRDKTM 234

Query: 241 MIDVQAREISEKDLEAGLRLAHPEAVKYLEPQIRLAEKAGKQKKEYKLSMISEQTLEKVS 300
           MIDVQ+REISEKDL A LRLAHPEAVKYL+PQIRLAEKAGKQKKEYKLSM+S++TLEKV+
Sbjct: 235 MIDVQSREISEKDLAAALRLAHPEAVKYLDPQIRLAEKAGKQKKEYKLSMLSDKTLEKVA 294

Query: 301 NLAEAHIEAVFTDPSYSKFERGEALDKIGQDVKKALEEECDEESLQVLPKAVDTVRKRVI 360
           +LA   IE+VFTDPSY KFERGEALD IG+DV+K  EEE D+ESL +LPKAVDTVRK+V+
Sbjct: 295 DLAATRIESVFTDPSYGKFERGEALDNIGKDVRKVFEEEGDQESLSILPKAVDTVRKKVV 354

Query: 361 RKRIIAEGVRVDGRQLDEVRPIYCESGNLPILHGSSLFSRGDTQVLCTVTLGAPAEAQRL 420
           R R+I++G RVDGR +DEVRPIYCES  LP LHGS+LFSRGDTQVLCTVTLGAPAEAQ L
Sbjct: 355 RSRMISDGFRVDGRHVDEVRPIYCESHYLPALHGSALFSRGDTQVLCTVTLGAPAEAQSL 414

Query: 421 ESLVGPPTKRFMLHYSFPPFCINEVGKRVGLNRREVGHGTLAEKALLAVLPPENDFPYTV 480
           +SLVGPP KRFMLHYSFPP+C NEVGKR GLNRREVGHGTLAEKALLAVLPPE  FPYT+
Sbjct: 415 DSLVGPPKKRFMLHYSFPPYCTNEVGKRGGLNRREVGHGTLAEKALLAVLPPEEAFPYTI 474

Query: 481 RVNSEVMASDGSTSMATVCGGSMALMDAGIPLQEHVAGVSVGLVSEVDPSTGEIKDYRIL 540
           R+NSEVM+SDGSTSMA+VCGGSMALMDAGIPL+ HVAGVSVGL+++VDPS+GEIKDYRI+
Sbjct: 475 RINSEVMSSDGSTSMASVCGGSMALMDAGIPLRAHVAGVSVGLITDVDPSSGEIKDYRIV 534

Query: 541 TDILGLEDHLGDMDFKIAGTRIGVTAIQLDIKPAGIPLDIICECLEHAHKGRLQILDHME 600
           TDILGLEDHLGDMDFKIAGTR GVTAIQLDIKPAGIPLDI+CE LE+A + RLQILDHME
Sbjct: 535 TDILGLEDHLGDMDFKIAGTRDGVTAIQLDIKPAGIPLDIVCESLENAREARLQILDHME 594

Query: 601 REISAPRTQDDRNSPRLATLKYDNDTLRRLIGPLGALKRKIEEETGGRISVSDGTLTVVA 660
           R I++PR QD   SPRLATLKY ND+LR LIGP+G LKRKIE ETG R+S+ +GTLT+VA
Sbjct: 595 RNINSPRGQDGAYSPRLATLKYSNDSLRTLIGPMGVLKRKIEVETGARLSIDNGTLTIVA 654

Query: 661 KNRSVMEKVLEKVDFIIGREIEVGGIYKGVVTSVKEYGAFVEFNGGQQGLLHVSELSHEP 720
           KN+ VMEK  E+VDFIIGRE+ VGG+YKG V+S+KEYGAFVEF GGQQGLLH+SELSHEP
Sbjct: 655 KNQDVMEKAQEQVDFIIGRELVVGGVYKGTVSSIKEYGAFVEFPGGQQGLLHMSELSHEP 714

Query: 721 VSRVSDVVSVGQQLSLRCIGQDVRGNIKLSLKAVSPRPEADVKGVVEGSVPVNKQATDVW 780
           VS+VSDV+ +GQ ++  CI  DVRGNIKLS KA+ P+P+        G  PV K+++ V+
Sbjct: 715 VSKVSDVLDIGQCITTMCIETDVRGNIKLSRKALLPKPKRKPASDA-GKDPVMKESSTVY 773

Query: 781 ---ASVGDVSNGQNPELPMRKNETPGVNSSTSSTPAVLIRSAAECDEEEKASGFSQSSKS 837
              +SVG++         M    TP +  S  S PAV+IR+A EC+E EK+S  + + K 
Sbjct: 774 IENSSVGEIVAS------MPSIVTP-LQKSRLSVPAVVIRTAVECNEAEKSSPVNDNDKP 826

Query: 838 TLKSTLASKSNSKPKKFTS-----------------------------QSDFFSSTNIQK 868
              +T  SK + KPK   S                             Q     S + + 
Sbjct: 827 RRAAT--SKPDRKPKSTASKLIATQKEEEALESIAPEETSAECGEILKQDGKLKSVSPKN 884

Query: 869 ST------SFSQREREELAECLFGTEDGDEDNKGTRVEAIVSAKNLKLGTKVAAKVYQVR 922
           ++      SFS+ ++  + E L  +E+  E++      A VS + LK+GT++ A V  VR
Sbjct: 885 NSTASNLVSFSKAKKSTMKENL--SENKAEES------ASVSTRKLKIGTEMTATVDHVR 936

Query: 923 ARGLVLDLGGGIRGMYRFENNEKKDFVVGDELLVKCSSFTGKGIPVVSLVD 973
           A GLVLDLGG IRGMY F+ ++ K F  GD L VKC+SF  KG+PV++LVD
Sbjct: 937 ALGLVLDLGGEIRGMYIFQGDKDK-FKKGDTLRVKCTSFNTKGVPVMALVD 986

Involved in the 3'-end maturation of mitochondrial mRNAs, rRNAs and tRNAs. Functions as a poly(A) mRNA 3'-5' degrading exonuclease and is required for the degradation of highly expressed transcripts of non-coding regions.
Arabidopsis thaliana (taxid: 3702)
EC: 2EC: .EC: 7EC: .EC: 7EC: .EC: 8

>sp|Q6KAI0|PNP2_ORYSJ Polyribonucleotide nucleotidyltransferase 2, mitochondrial OS=Oryza sativa subsp. japonica GN=PNP2 PE=2 SV=1

 Score = 1216 bits (3145), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 623/941 (66%), Positives = 745/941 (79%), Gaps = 31/941 (3%)

Query: 52  GTKVLETFKEEFEIGSRLITLETGKIARFANGAVVLGMDETKVLSTVTSSKG-DSVRDFL 110
           G KVLE+F+EEFEIG R+I+ ETGK+ARFANG+VV+ MD+T VLSTV ++K  + VRDFL
Sbjct: 54  GRKVLESFREEFEIGGRVISFETGKMARFANGSVVISMDDTHVLSTVAAAKSSEPVRDFL 113

Query: 111 PLTVDYQEKQFAQGVIPNTYMRREGAPKERELLVGRIIDRPIRPLFPAGFYHEVQVM--- 167
           PLTVDYQEKQ+AQGVIP TYMRREGAPKERELL GRIIDRPIRPLFP GFYHEVQVM   
Sbjct: 114 PLTVDYQEKQYAQGVIPTTYMRREGAPKERELLCGRIIDRPIRPLFPPGFYHEVQVMNAT 173

Query: 168 ---ASVLSSDGKQDPDIMAANATSAALMLSDIPWGGPIGMIRIGRICGQFIVNPTMDELS 224
               +V+SSDGKQDPD+MAANA+SAALMLSDIPW GPIG+IR+GRI G F++NPT+DEL 
Sbjct: 174 IIMVNVISSDGKQDPDVMAANASSAALMLSDIPWNGPIGVIRVGRIDGNFVLNPTVDELG 233

Query: 225 LSDLNLVYACTREKTLMIDVQAREISEKDLEAGLRLAHPEAVKYLEPQIRLAEKAGKQKK 284
           LSDLNLVYAC+R+KTLMIDVQAREI+E+DL+AG++LAH EAVK + PQ+RLA++AGK+KK
Sbjct: 234 LSDLNLVYACSRDKTLMIDVQAREITERDLQAGMKLAHAEAVKCINPQLRLAKRAGKKKK 293

Query: 285 EYKLSMISEQTLEKVSNLAEAHIEAVFTDPSYSKFERGEALDKIGQDVKKALEEECDEES 344
           EYK+S+IS+++ EK+  L+EA IE VFTD +Y KFERGEAL+ I Q VK  LEEECDE+S
Sbjct: 294 EYKISLISDKSYEKIRTLSEAPIEEVFTDSTYGKFERGEALENITQSVKAKLEEECDEDS 353

Query: 345 LQVLPKAVDTVRKRVIRKRIIAEGVRVDGRQLDEVRPIYCESGNLPILHGSSLFSRGDTQ 404
           L+ L KAVDTVRK+VIRKRII +G+RVDGRQLDEVRP+YCES   PILHGS+LFSRGDTQ
Sbjct: 354 LKFLHKAVDTVRKQVIRKRIIEKGLRVDGRQLDEVRPLYCESSTYPILHGSALFSRGDTQ 413

Query: 405 VLCTVTLGAPAEAQRLESLVGPPTKRFMLHYSFPPFCINEVGKRVGLNRREVGHGTLAEK 464
           VLCTVTLGAP +AQRL+S+VGPPTKRFMLHYSFPPF INEV KR GLNRREVGHGTLAEK
Sbjct: 414 VLCTVTLGAPGDAQRLDSIVGPPTKRFMLHYSFPPFSINEVAKRGGLNRREVGHGTLAEK 473

Query: 465 ALLAVLPPENDFPYTVRVNSEVMASDGSTSMATVCGGSMALMDAGIPLQEHVAGVSVGLV 524
           ALLAVLPPE +FPYTVRVNSEVMASDGSTSMA+VCGGSMALMDAGIP++EHVAGVSVGLV
Sbjct: 474 ALLAVLPPEGEFPYTVRVNSEVMASDGSTSMASVCGGSMALMDAGIPVREHVAGVSVGLV 533

Query: 525 SEVDPSTGEIKDYRILTDILGLEDHLGDMDFKIAGTRIGVTAIQLDIKPAGIPLDIICEC 584
           SEVD +TG+I  YRILTDILGLEDHLGDMDFKIAGTR G+TAIQLDIKPAGIPLDIICE 
Sbjct: 534 SEVDQTTGDISSYRILTDILGLEDHLGDMDFKIAGTRRGITAIQLDIKPAGIPLDIICES 593

Query: 585 LEHAHKGRLQILDHMEREISAPRTQDDRNSPRLATLKYDNDTLRRLIGPLGALKRKIEEE 644
           LE A K R QILD M++EIS+ R  +D +SPRLATL + +D+LR+L+      ++KIE+E
Sbjct: 594 LEPARKARNQILDRMDQEISSARAFNDGSSPRLATLSFSSDSLRKLL----FHRKKIEQE 649

Query: 645 TGGRISVSDGTLTVVAKNRSVMEKVLEKVDFIIGREIEVGGIYKGVVTSVKEYGAFVEFN 704
           TG R+SVSDGT+T+VAK + +M+K +EKV+F++GREIEVG  YKGVV+S+KEYGAFVEFN
Sbjct: 650 TGARVSVSDGTVTIVAKTQPIMDKAIEKVEFLVGREIEVGRTYKGVVSSIKEYGAFVEFN 709

Query: 705 GGQQGLLHVSELSHEPVSRVSDVVSVGQQLSLRCIGQDVRGNIKLSLKAVSPRPEADVKG 764
           GGQQGLLH+SELSH+ VS+VSDVVSVGQ LSL CIGQD+RGNIKLSLKA  P        
Sbjct: 710 GGQQGLLHISELSHDKVSKVSDVVSVGQVLSLTCIGQDLRGNIKLSLKATLPHAHEKKDL 769

Query: 765 VVEGSVPVNKQATDVWASVGDV-SNGQNPELPMRKN------ETPGVNSSTSSTPAVLIR 817
               + P+  Q    W +V ++ S   N E  + K+      ETPG      STPAV+IR
Sbjct: 770 ASNHTDPLPSQEVVGWTAVENMPSKDANAEPSISKDEDNMIEETPGC-----STPAVIIR 824

Query: 818 SAAECDEEEKASGFSQSSKSTLKSTLASKSNSKPKKFTSQSDFFSSTNIQKSTSFSQRER 877
           SAAECD ++  +   +      KS   S   SKP     +    S+     +++ +++ +
Sbjct: 825 SAAECDAQDVTNDPKKKRPKVAKS---SPKLSKPASERQEVKRTSAKKTSGASTTAKKNK 881

Query: 878 EELAECLFGTEDGDEDNKGTRVEAIVSAKN-----LKLGTKVAAKVYQVRARGLVLDLGG 932
           +E A+      D   +   + +    S  N     +KLG  V AKVYQ+RA GLVL+L  
Sbjct: 882 KEKADSSNDVLDAIPEQNKSNIMNYSSPSNFRSGSMKLGDVVTAKVYQIRAYGLVLELSD 941

Query: 933 GIRGMYRFENNEKKDFVVGDELLVKCSSFTGKGIPVVSLVD 973
           G+RGM++F  N  KDF VG+ELLVKCSSF  KGIPV SL+D
Sbjct: 942 GVRGMHKFAENGHKDFEVGEELLVKCSSFNAKGIPVFSLLD 982

Involved in the 3'-end maturation of mitochondrial mRNAs, rRNAs and tRNAs. Functions as a poly(A) mRNA 3'-5' degrading exonuclease.

Oryza sativa subsp. japonica (taxid: 39947)

EC: 2

EC: .

EC: 7

EC: .

EC: 7

EC: .

EC: 8

>sp|B3DZ86|PNP_METI4 Polyribonucleotide nucleotidyltransferase OS=Methylacidiphilum infernorum (isolate V4) GN=pnp PE=3 SV=2

 Score =  603 bits (1554), Expect = e-171,   Method: Compositional matrix adjust.
 Identities = 322/704 (45%), Positives = 463/704 (65%), Gaps = 17/704 (2%)

Query: 57  ETFKEEFEIGSRLITLETGKIARFANGAVVLGMDETKVLST---VTSSKGDSVRDFLPLT 113
           E  K +F  G + I  ETGK+A+FA+G+V +   ET VL T   VT  K D  +DFLPL 
Sbjct: 3   EYIKRKF--GDQTIVFETGKLAKFADGSVTVSYGETAVLVTAVSVTELKED--QDFLPLQ 58

Query: 114 VDYQEKQFAQGVIPNTYMRREGAPKERELLVGRIIDRPIRPLFPAGFYHEVQVMASVLSS 173
           V+Y+EK  A G  P  Y R+EG P ++E+L  R+IDRP+RPLFP G+++E Q++ ++LS+
Sbjct: 59  VEYREKAAAAGRFPGGYFRKEGRPTDKEILTSRMIDRPLRPLFPKGYFYETQILGTLLSA 118

Query: 174 DGKQDPDIMAANATSAALMLSDIPWGGPIGMIRIGRICGQFIVNPTMDELSLSDLNLVYA 233
           DG+ DPD+MA N  SAALM+SDIP+ GP+G +RIG+I G++I+NPT  E  +SD++LVY 
Sbjct: 119 DGQNDPDVMAINGASAALMVSDIPFYGPVGAVRIGQIDGRWIINPTHREREISDIDLVYV 178

Query: 234 CTREKTLMIDVQAREISEKDLEAGLRLAHPEAVKYLEPQIRLAEKAGKQKKEYKLSMISE 293
            +    LMI+  ARE  E++    L  AH    + +  Q  LAEK GK K+     ++ E
Sbjct: 179 GSEHYPLMIEGSAREFPEEEFVKALEFAHQHVQEVIAAQKELAEKVGKPKRS---CVLFE 235

Query: 294 QTLEKVSNLAEAHIEAVFTDPSY--SKFERGEALDKIGQDVKKALEEECDEESLQVLPKA 351
           + L   + LAE +  +   D  Y  SK ER + L K+ +++   + EE    + + +  +
Sbjct: 236 ENLAITNRLAELY-SSQLQDALYTSSKTERQKKLAKLKEELTAKILEEFPTATPREITSS 294

Query: 352 VDTVRKRVIRKRIIAEGVRVDGRQLDEVRPIYCESGNLPILHGSSLFSRGDTQVLCTVTL 411
            D+++K + R  ++    R DGR  +++RPI  E+  +P  HGSSLF RG+TQ LC  TL
Sbjct: 295 YDSLQKTIFRTNVLETKRRCDGRGPEDIRPIAIETSVVPRSHGSSLFCRGETQALCMATL 354

Query: 412 GAPAEAQRLESL-VGPPTKRFMLHYSFPPFCINEVGKRVGLNRREVGHGTLAEKALLAVL 470
            +  EAQ L++   G  +KRF+LHY FPPF + EVG+  G +RRE+GHG LAE++LL V+
Sbjct: 355 ASLNEAQELDAYGGGEQSKRFLLHYFFPPFSVGEVGRITGQSRREIGHGALAERSLLPVI 414

Query: 471 PPENDFPYTVRVNSEVMASDGSTSMATVCGGSMALMDAGIPLQEHVAGVSVGLVSEVDPS 530
           P E DFPY +RV+SE++ S+GSTSMATVCGGS+ALMDAG+PL+  VAG+SVGLV   +  
Sbjct: 415 PSETDFPYAIRVSSEILESNGSTSMATVCGGSLALMDAGVPLKTSVAGISVGLVKGKEED 474

Query: 531 TGEIKDYRILTDILGLEDHLGDMDFKIAGTRIGVTAIQLDIKPAGIPLDIICECLEHAHK 590
             +   Y +LTDILGLEDH GDMDFKIAGTR G+T  QLD+K  GIPLD++ + +  + K
Sbjct: 475 F-DWSRYCLLTDILGLEDHYGDMDFKIAGTRKGITGFQLDLKLRGIPLDVMAKAIFQSQK 533

Query: 591 GRLQILDHMEREISAPRTQDDRNSPRLATLKYDNDTLRRLIGPLGALKRKIEEETGGRIS 650
            R+ ILD M++ I+APR +  +++PR+  +K   D +  LIGP G   +KI  E+G  I+
Sbjct: 534 ARMVILDCMDKVINAPRAEISKHAPRIEKIKIHPDKIGLLIGPGGKTIKKISAESGAEIT 593

Query: 651 V-SDGTLTVVAKNRSVMEKVLEKVDFIIGREIEVGGIYKGVVTSVKEYGAFVEFNGGQQG 709
           +  DGT+ + + +   +E   E ++ ++G E+ VGGIY+  V SVK++G F+E  G  +G
Sbjct: 594 IEDDGTVMIYSSSADSLEAAREMIEDMVG-EVTVGGIYRSKVVSVKDFGCFIEIKGKGEG 652

Query: 710 LLHVSELSHEPVSRVSDVVSVGQQLSLRCIGQDVRGNIKLSLKA 753
           L+H+SELS  PV RV  VV VG+++ ++CIG D +G  K S KA
Sbjct: 653 LVHISELSDTPVRRVDQVVRVGEEIWVKCIGVDEKGRYKFSRKA 696

Involved in mRNA degradation. Hydrolyzes single-stranded polyribonucleotides processively in the 3'- to 5'-direction.

Methylacidiphilum infernorum (isolate V4) (taxid: 481448)

EC: 2

EC: .

EC: 7

EC: .

EC: 7

EC: .

EC: 8

>sp|B1KRQ5|PNP_SHEWM Polyribonucleotide nucleotidyltransferase OS=Shewanella woodyi (strain ATCC 51908 / MS32) GN=pnp PE=3 SV=1

 Score =  566 bits (1458), Expect = e-160,   Method: Compositional matrix adjust.
 Identities = 297/692 (42%), Positives = 446/692 (64%), Gaps = 12/692 (1%)

Query: 63  FEIGSRLITLETGKIARFANGAVVLGMDETKVLSTVTSSKGDSV-RDFLPLTVDYQEKQF 121
           FE G   +TLETG IAR AN AV+  M +T VL TV   K + V RDF PLTV+YQEK +
Sbjct: 8   FEYGQHTVTLETGVIARQANAAVLASMGDTTVLVTVVGKKAEDVGRDFFPLTVNYQEKTY 67

Query: 122 AQGVIPNTYMRREGAPKERELLVGRIIDRPIRPLFPAGFYHEVQVMASVLSSDGKQDPDI 181
           A G IP  + +REG P E E L+ R+IDRPIRPLFP GF +EVQV+ +V+S D + +PD+
Sbjct: 68  AAGKIPGGFFKREGRPSENETLIARLIDRPIRPLFPNGFKNEVQVIITVVSVDPEINPDV 127

Query: 182 MAANATSAALMLSDIPWGGPIGMIRIGRICGQFIVNPTMDELSLSDLNLVYACTREKTLM 241
           ++   TSAAL +SD+P+ GP+G+ R+G   G++++NP + +L+ SDL+LV A T+   LM
Sbjct: 128 ISMIGTSAALSISDLPFNGPLGVARVGYTNGEYVLNPNVSQLAESDLDLVVAGTQGAVLM 187

Query: 242 IDVQAREISEKDLEAGLRLAHPEAVKYLEPQIRLAEKAGKQKKEYKLSMISEQTLEKVSN 301
           ++ +A  + E+ +  G+   H +    +     L  +AGK K ++         +EK+  
Sbjct: 188 VESEAASLPEEVMLGGVVYGHDQQQVVINAINELTAEAGKTKWDWTAPAEDTDLVEKIKG 247

Query: 302 LAEAHIEAVFTDPSYSKFERGEALDKIGQDVKKALEEECDEESLQVLPKAVDTVRKRVIR 361
           LAEA +   +      K ER +A+  +       L EE  +  L+ + K + ++ K+V+R
Sbjct: 248 LAEAELTNAYQ--IADKHERRDAVIALKNAAVAKLVEENADVDLREVDKLLGSLEKKVVR 305

Query: 362 KRIIAEGVRVDGRQLDEVRPIYCESGNLPILHGSSLFSRGDTQVLCTVTLGAPAEAQRLE 421
            RII+   R+DGR+ D VR +   +G LP  HGSSLF+RG+TQ L T TLG   +AQ+++
Sbjct: 306 SRIISGSPRIDGREPDMVRALNVMAGVLPRTHGSSLFTRGETQALVTCTLGTERDAQKVD 365

Query: 422 SLVGPPTKRFMLHYSFPPFCINEVGKRVGLNRREVGHGTLAEKALLAVLPPENDFPYTVR 481
           S++G  T RFMLHY+FPP+ + E G      RRE+GHG LA + + AV+P   +FPY+VR
Sbjct: 366 SIMGEYTNRFMLHYNFPPYSVGETGMVGSPKRREIGHGKLAWRGINAVMPTAEEFPYSVR 425

Query: 482 VNSEVMASDGSTSMATVCGGSMALMDAGIPLQEHVAGVSVGLVSEVDPSTGEIKDYRILT 541
           V SE+  S+GS+SMA+VCG S+ALMDAG+P++  VAG+++GLV E D       D+ +L+
Sbjct: 426 VVSEITESNGSSSMASVCGTSLALMDAGVPIKTSVAGIAMGLVKEGD-------DFVVLS 478

Query: 542 DILGLEDHLGDMDFKIAGTRIGVTAIQLDIKPAGIPLDIICECLEHAHKGRLQILDHMER 601
           DILG EDHLGDMDFK+AGTR G+TA+Q+DIK  GI  +I+   L+ A+  R+ IL+ M++
Sbjct: 479 DILGDEDHLGDMDFKVAGTRDGITALQMDIKIEGITKEIMQIALQQAYGARVHILNVMDQ 538

Query: 602 EISAPRTQDDRNSPRLATLKYDNDTLRRLIGPLGALKRKIEEETGGRISV-SDGTLTVVA 660
            IS  R     ++PR+ TLK + + +R +IG  GA  R + EETG  I +  DGT+ + +
Sbjct: 539 AISGHREDISDHAPRITTLKINPEKIRDVIGKGGATIRALTEETGTTIELEDDGTVKIAS 598

Query: 661 KNRSVMEKVLEKVDFIIGREIEVGGIYKGVVTSVKEYGAFVEFNGGQQGLLHVSELSHEP 720
            N    ++ + +++ I   E+EVG +Y G V  + ++GAFV    G+ GL+H+S+++ E 
Sbjct: 599 ANGEATKEAIRRIEEITA-EVEVGTVYNGKVVRIVDFGAFVTILPGKDGLVHISQIAEER 657

Query: 721 VSRVSDVVSVGQQLSLRCIGQDVRGNIKLSLK 752
           V+ VSD + VGQ++ ++ +  D +G ++LS+K
Sbjct: 658 VANVSDYLQVGQEVKVKVMEVDRQGRVRLSMK 689

Involved in mRNA degradation. Hydrolyzes single-stranded polyribonucleotides processively in the 3'- to 5'-direction.

Shewanella woodyi (strain ATCC 51908 / MS32) (taxid: 392500)

EC: 2

EC: .

EC: 7

EC: .

EC: 7

EC: .

EC: 8

>sp|B9M1G5|PNP_GEOSF Polyribonucleotide nucleotidyltransferase OS=Geobacter sp. (strain FRC-32) GN=pnp PE=3 SV=1

 Score =  565 bits (1457), Expect = e-160,   Method: Compositional matrix adjust.
 Identities = 302/696 (43%), Positives = 437/696 (62%), Gaps = 15/696 (2%)

Query: 60  KEEFEIGSRLITLETGKIARFANGAVVLGMDETKVLSTVTSSK-GDSVRDFLPLTVDYQE 118
           K + E G R IT+ETGK+A+ A+GAVV+   +T+VL T  ++K     +DF PLTV+YQE
Sbjct: 4   KVQVECGGRTITIETGKMAKQASGAVVVSSGDTRVLVTAVATKTAKEGQDFFPLTVNYQE 63

Query: 119 KQFAQGVIPNTYMRREGAPKERELLVGRIIDRPIRPLFPAGFYHEVQVMASVLSSDGKQD 178
           K +A G IP  + +RE  P + E L  R+IDRPIRPLFP  F ++ Q+MA+V+S+D   D
Sbjct: 64  KAYAGGKIPGGFFKREARPSDNETLTCRLIDRPIRPLFPDNFLNDTQIMATVISADKDND 123

Query: 179 PDIMAANATSAALMLSDIPWGGPIGMIRIGRICGQFIVNPTMDELSLSDLNLVYACTREK 238
           P I++    SAALM+SDIP+ GPI  +++GRI G+F+ NP  +E+  SD+ +V A +++ 
Sbjct: 124 PGILSMVGASAALMVSDIPFQGPIAGVKVGRIDGRFVANPGFEEMEKSDIEIVVAASKDA 183

Query: 239 TLMIDVQAREISEKDLEAGLRLAHPEAVKYLEPQIRLAEKAGKQKKEYKLSMISEQTLEK 298
            +M++  A E+SE+D+   +   H      L  Q+ LAEKAG  K+E    +++E    K
Sbjct: 184 IIMVEGSAAEVSEEDMLEAIFFGHAAIQGLLAAQVELAEKAGVAKREVLPPVVNEALKAK 243

Query: 299 VSNLAEAHI-EAVFTDPSYSKFERGEALDKIGQDVKKALEEECDEESLQVLPKAVDTVRK 357
           V  LA + + EAV      SK ER   +D I  +V  AL EE  E + + +   +     
Sbjct: 244 VKELAYSRMKEAVRIK---SKVERHNTIDTITGEVLTALAEEF-EGAAKEIKGFLGDFEY 299

Query: 358 RVIRKRIIAEGVRVDGRQLDEVRPIYCESGNLPILHGSSLFSRGDTQVLCTVTLGAPAEA 417
            ++R+ II +G R+DGR    +R I  E G LP  HGS+LF+RG+TQ L   TLG   + 
Sbjct: 300 DLVREHIIKDGERIDGRDTKTIRQITTEVGLLPRAHGSALFTRGETQALVVATLGTSIDE 359

Query: 418 QRLESLVGPPTKRFMLHYSFPPFCINEVGKRVGLNRREVGHGTLAEKALLAVLPPENDFP 477
           QR++SL G   KRF+LHY+FPPF + E   R+   RRE+GHG LAE+AL  V+P    FP
Sbjct: 360 QRIDSLFGESKKRFLLHYNFPPFSVGETSFRLAPGRREIGHGMLAERALARVVPKHESFP 419

Query: 478 YTVRVNSEVMASDGSTSMATVCGGSMALMDAGIPLQEHVAGVSVGLVSEVDPSTGEIKDY 537
           YT+R+ S+++ S+GS+SMA+VCGGSM++MDAGIP++  VAG+++GL+ E D       D+
Sbjct: 420 YTIRIVSDILESNGSSSMASVCGGSMSMMDAGIPIKAPVAGIAMGLIKEGD-------DF 472

Query: 538 RILTDILGLEDHLGDMDFKIAGTRIGVTAIQLDIKPAGIPLDIICECLEHAHKGRLQILD 597
            IL+DILG EDHLGDMDFK+AGT  GVTA+Q+DIK  G+  +I+   L+ AH+GRL IL 
Sbjct: 473 AILSDILGDEDHLGDMDFKVAGTSTGVTALQMDIKIGGVTREIMGVALKQAHEGRLHILS 532

Query: 598 HMEREISAPRTQDDRNSPRLATLKYDNDTLRRLIGPLGALKRKIEEETGGRISVSD-GTL 656
            M   I   + +    +PR+ T+    D +R +IG  G   R I E TG  I + D G +
Sbjct: 533 KMAETIGTSKAELSTFAPRITTIYVKTDKIRDVIGSGGKNIRGITEATGVTIDIDDTGKI 592

Query: 657 TVVAKNRSVMEKVLEKVDFIIGREIEVGGIYKGVVTSVKEYGAFVEFNGGQQGLLHVSEL 716
            + + +++  +  ++ +  +   E E G +Y G+V  V E+GAFVE   G  GL+H+SEL
Sbjct: 593 NIASTDKAACDMAIKMIRDLTA-EAEEGKLYMGLVKKVMEFGAFVEIFPGTDGLVHISEL 651

Query: 717 SHEPVSRVSDVVSVGQQLSLRCIGQDVRGNIKLSLK 752
             E V  V+DV+  G ++ ++CIG D +G IKLS K
Sbjct: 652 DTERVKNVTDVLKEGDKVLVKCIGIDKQGKIKLSRK 687

Involved in mRNA degradation. Hydrolyzes single-stranded polyribonucleotides processively in the 3'- to 5'-direction.

Geobacter sp. (strain FRC-32) (taxid: 316067)

EC: 2

EC: .

EC: 7

EC: .

EC: 7

EC: .

EC: 8

>sp|Q39VA1|PNP_GEOMG Polyribonucleotide nucleotidyltransferase OS=Geobacter metallireducens (strain GS-15 / ATCC 53774 / DSM 7210) GN=pnp PE=3 SV=1

 Score =  565 bits (1456), Expect = e-160,   Method: Compositional matrix adjust.
 Identities = 303/695 (43%), Positives = 431/695 (62%), Gaps = 13/695 (1%)

Query: 60  KEEFEIGSRLITLETGKIARFANGAVVLGMDETKVLSTVTSSK-GDSVRDFLPLTVDYQE 118
           K   + G R IT+ TGK+A+ A+GAV++   ET VL T  + K     +DF PLTV+YQE
Sbjct: 5   KVNVDFGGRTITIATGKMAKQASGAVMVSCGETMVLVTAVALKSAKEGQDFFPLTVNYQE 64

Query: 119 KQFAQGVIPNTYMRREGAPKERELLVGRIIDRPIRPLFPAGFYHEVQVMASVLSSDGKQD 178
           K +A G IP  + +REG P E E L  R IDRPIRPLFP  F ++ Q+MA+V+S+D   D
Sbjct: 65  KAYAGGKIPGGFFKREGRPTENETLTCRFIDRPIRPLFPENFLNDTQIMATVVSADQDND 124

Query: 179 PDIMAANATSAALMLSDIPWGGPIGMIRIGRICGQFIVNPTMDELSLSDLNLVYACTREK 238
           P I+A    SAAL +SDIP+ GPI  +++GR+ G+FI NPT ++L+ SDL +V A +R+ 
Sbjct: 125 PGILAMIGASAALEVSDIPFFGPIAGVKVGRVDGKFICNPTAEQLAASDLEVVVAASRDA 184

Query: 239 TLMIDVQAREISEKDLEAGLRLAHPEAVKYLEPQIRLAEKAGKQKKEYKLSMISEQTLEK 298
            +M++  A EISE DL   +   H      ++ QI L ++AG  K+E     + E    K
Sbjct: 185 VIMVEGGAAEISEADLLEAIFFGHASVQPIIDAQIELRKQAGVPKREIAPPAVDEALGAK 244

Query: 299 VSNLAEAHIEAVFTDPSYSKFERGEALDKIGQDVKKALEEECDEESLQVLPKAVDTVRKR 358
           V  LA A ++        SK ER   +  I  +   ALE +      ++    +D     
Sbjct: 245 VKELAYAQMKDAVR--IRSKQERHNRISAIADETVAALEADFSGRGAEI-KDFLDGFEYE 301

Query: 359 VIRKRIIAEGVRVDGRQLDEVRPIYCESGNLPILHGSSLFSRGDTQVLCTVTLGAPAEAQ 418
           ++R+ I+ +G R+DGR    +RPI  E G LP +HGS+LF+RG+TQ L   TLG  ++ Q
Sbjct: 302 LVREHILKDGERIDGRDTKTIRPITSEVGILPRVHGSALFTRGETQALVAATLGTSSDEQ 361

Query: 419 RLESLVGPPTKRFMLHYSFPPFCINEVGKRVGLNRREVGHGTLAEKALLAVLPPENDFPY 478
           R++SL G   KRFMLHY+FPPF + E   R+   RRE+GHG LAE+AL  VLP  +DFPY
Sbjct: 362 RIDSLYGESRKRFMLHYNFPPFSVGETSFRLAPGRREIGHGYLAERALERVLPKHDDFPY 421

Query: 479 TVRVNSEVMASDGSTSMATVCGGSMALMDAGIPLQEHVAGVSVGLVSEVDPSTGEIKDYR 538
           T+R+ S+++ S+GS+SMA+VCGG++++MDAG+P+   VAG+++GL+ E D       D  
Sbjct: 422 TIRIVSDILESNGSSSMASVCGGALSMMDAGVPISAPVAGIAMGLIKEGD-------DIA 474

Query: 539 ILTDILGLEDHLGDMDFKIAGTRIGVTAIQLDIKPAGIPLDIICECLEHAHKGRLQILDH 598
           IL+DILG EDHLGDMDFK+AGT  GVTAIQ+DIK  G+  +I+ + LE A +GRL IL  
Sbjct: 475 ILSDILGDEDHLGDMDFKVAGTSTGVTAIQMDIKITGVTREIMGKALEQAKEGRLHILGK 534

Query: 599 MEREISAPRTQDDRNSPRLATLKYDNDTLRRLIGPLGALKRKIEEETGGRISVSD-GTLT 657
           M   ++APRT     +PR+ T+    D +R +IG  G   R I E TG  I + D G + 
Sbjct: 535 MAEALAAPRTDLSPYAPRITTIWVKTDKIRDVIGAGGKNVRGITEATGVSIDIEDTGKIN 594

Query: 658 VVAKNRSVMEKVLEKVDFIIGREIEVGGIYKGVVTSVKEYGAFVEFNGGQQGLLHVSELS 717
           + + N+   +K ++ +  +   E E G +Y G V  V ++GAFVE   G  GL+H+SEL 
Sbjct: 595 IASTNKEACDKAIKMIRDLTA-EAEEGKLYMGTVRKVMDFGAFVEIFPGTDGLVHISELD 653

Query: 718 HEPVSRVSDVVSVGQQLSLRCIGQDVRGNIKLSLK 752
            E V  V+D++  G ++ ++CIG D +G IKLS K
Sbjct: 654 TERVKDVTDILKEGDKVLVKCIGIDKQGKIKLSRK 688

Involved in mRNA degradation. Hydrolyzes single-stranded polyribonucleotides processively in the 3'- to 5'-direction.

Geobacter metallireducens (strain GS-15 / ATCC 53774 / DSM 7210) (taxid: 269799)

EC: 2

EC: .

EC: 7

EC: .

EC: 7

EC: .

EC: 8

>sp|Q3A4A1|PNP_PELCD Polyribonucleotide nucleotidyltransferase OS=Pelobacter carbinolicus (strain DSM 2380 / Gra Bd 1) GN=pnp PE=3 SV=1

 Score =  564 bits (1453), Expect = e-159,   Method: Compositional matrix adjust.
 Identities = 295/698 (42%), Positives = 452/698 (64%), Gaps = 19/698 (2%)

Query: 60  KEEFEIGSRLITLETGKIARFANGAVVLGMDETKVLSTVTSSKGDSVRD---FLPLTVDY 116
           K E +   + +TLETGK+AR A+GAVV+    TKVL T  S+K   +R+   F PLTV+Y
Sbjct: 5   KVECQFNGQTLTLETGKMARQADGAVVVSFGGTKVLCTAVSAK--QMREGQSFFPLTVNY 62

Query: 117 QEKQFAQGVIPNTYMRREGAPKERELLVGRIIDRPIRPLFPAGFYHEVQVMASVLSSDGK 176
           QEK +A G IP ++ RRE    ERE LV R+IDRP+RPLFP G+  E Q+M +V+S D +
Sbjct: 63  QEKFYAGGKIPGSFFRRERGATERETLVCRLIDRPLRPLFPKGYMFETQIMPTVISVDEQ 122

Query: 177 QDPDIMAANATSAALMLSDIPWGGPIGMIRIGRICGQFIVNPTMDELSLSDLNLVYACTR 236
            DPD +A    SAA+ +SDIP+ GP+  +R+GR+ G  I NPT+++ + SD++++ + +R
Sbjct: 123 NDPDTLAMVGASAAIAVSDIPFDGPVAAVRVGRVEGNLIANPTIEQRAESDMDIIVSGSR 182

Query: 237 EKTLMIDVQAREISEKDLEAGLRLAHPEAVKYLEPQIRLAEKAGKQKKEYKLSMISEQTL 296
           +  +M++ + R ISE+++   L  AH      ++ Q+ L + AGK+K+E+ +  I    +
Sbjct: 183 DAIIMVEGETRFISEQEMLDALFFAHEAIQPLIDVQLELVKIAGKEKREFSVPEIDPAVV 242

Query: 297 EKVSNLAEAHI-EAVFTDPSYSKFERGEALDKIGQDVKKALEEECDEESLQVLPKAVDTV 355
           EKV+ LAE  + EAV      +K +R  A+ +I  ++ + L  + +++   +  +A   +
Sbjct: 243 EKVAELAETRLSEAV---KIRTKQDRYAAVAEIKTEILETLAADFEDQEDDI-SEAFGNL 298

Query: 356 RKRVIRKRIIAEGVRVDGRQLDEVRPIYCESGNLPILHGSSLFSRGDTQVLCTVTLGAPA 415
           +KR++R+ +  + VR+DGR  + +RPI CE G LP  HGS+LF+RG+TQ L    LG   
Sbjct: 299 QKRLVRQMVARDKVRIDGRDKNTIRPITCEIGLLPRAHGSALFTRGETQALVAAALGTSK 358

Query: 416 EAQRLESLVGPPTKRFMLHYSFPPFCINEVGKRVGLNRREVGHGTLAEKALLAVLPPEND 475
           + QR++++     K+FMLHY+FPPFC+ E   R+   RRE+GHG LAE+++  VLP  +D
Sbjct: 359 DEQRMDNVQSMEFKKFMLHYNFPPFCVGETSMRLFPGRREIGHGMLAERSIAQVLPNHDD 418

Query: 476 FPYTVRVNSEVMASDGSTSMATVCGGSMALMDAGIPLQEHVAGVSVGLVSEVDPSTGEIK 535
           FPYT+RV S+++ S+GS+SMA+VCG S+ALMDAG+P+ E VAG+++GL+ E D       
Sbjct: 419 FPYTLRVVSDILESNGSSSMASVCGASLALMDAGVPVSEAVAGIAMGLIKEGD------- 471

Query: 536 DYRILTDILGLEDHLGDMDFKIAGTRIGVTAIQLDIKPAGIPLDIICECLEHAHKGRLQI 595
           D  +L+DILG EDHLGDMDFK+ GTR G+TA+Q+DIK  G+  +I+ + LE A +GRL I
Sbjct: 472 DIVVLSDILGDEDHLGDMDFKVTGTREGITALQMDIKIKGVSKEIMQQALEQAREGRLHI 531

Query: 596 LDHMEREISAPRTQDDRNSPRLATLKYDNDTLRRLIGPLGALKRKIEEETGGRISV-SDG 654
           LD M   I+APR+     +PR+ T++   D +R +IGP G   R I E TG  I +  DG
Sbjct: 532 LDKMAEAITAPRSDLSPYAPRITTIQVKPDQVRTVIGPGGKNVRGIIEATGCAIDIEDDG 591

Query: 655 TLTVVAKNRSVMEKVLEKVDFIIGREIEVGGIYKGVVTSVKEYGAFVEFNGGQQGLLHVS 714
            + + + +    +  ++ +  +  +E  VG +Y   V  + E+GAFVE   G +GL+H+S
Sbjct: 592 RINIASADGDACKAAIKMIRNLT-QEAVVGKLYMATVKKIMEFGAFVEIFPGTEGLVHIS 650

Query: 715 ELSHEPVSRVSDVVSVGQQLSLRCIGQDVRGNIKLSLK 752
           EL+ E V +V+D++  G Q+ ++C+  D +G IKLS K
Sbjct: 651 ELAKERVKKVTDILQEGDQVLVKCLDIDRQGKIKLSRK 688

Involved in mRNA degradation. Hydrolyzes single-stranded polyribonucleotides processively in the 3'- to 5'-direction.

Pelobacter carbinolicus (strain DSM 2380 / Gra Bd 1) (taxid: 338963)

EC: 2

EC: .

EC: 7

EC: .

EC: 7

EC: .

EC: 8

>sp|C5D9D5|PNP_GEOSW Polyribonucleotide nucleotidyltransferase OS=Geobacillus sp. (strain WCH70) GN=pnp PE=3 SV=1

 Score =  561 bits (1445), Expect = e-158,   Method: Compositional matrix adjust.
 Identities = 299/703 (42%), Positives = 453/703 (64%), Gaps = 14/703 (1%)

Query: 56  LETFKEEFEI--GSRLITLETGKIARFANGAVVLGMDETKVLSTVTSSKGDSVRDFLPLT 113
           +E  K  F I    R + +E G++A+ ANGAV++   +T VL+T T+SK     DF PLT
Sbjct: 1   MEQEKRIFSIDWAGRPLVVEIGQLAKQANGAVLVRYGDTVVLNTATASKEAKNVDFFPLT 60

Query: 114 VDYQEKQFAQGVIPNTYMRREGAPKERELLVGRIIDRPIRPLFPAGFYHEVQVMASVLSS 173
           V+Y+E+ +A G IP  +++REG P E+ +L  R+IDRPIRPLF  GF +EVQ+++ V+S 
Sbjct: 61  VNYEERLYAVGKIPGGFIKREGRPSEKAILASRLIDRPIRPLFAEGFRNEVQIVSMVMSV 120

Query: 174 DGKQDPDIMAANATSAALMLSDIPWGGPIGMIRIGRICGQFIVNPTMDELSLSDLNLVYA 233
           D    P++ A    S AL +SDIP+ GPI  + +GR+ G+F++NPT+++   SD++LV A
Sbjct: 121 DQDCSPEMAALFGASLALTISDIPFEGPIAGVTVGRVDGEFVINPTVEQSEKSDIHLVVA 180

Query: 234 CTREKTLMIDVQAREISEKDLEAGLRLAHPEAVKYLEPQIRLAEKAGKQKKEYKLSMISE 293
            T++   M++  A E+ E+ +   +   H E  + +  Q  +A + GK+K E  L  +  
Sbjct: 181 GTKDAINMVEAGADEVPEEVILEAIMFGHEEVKRLIAFQEEIAAQVGKEKMEVVLYELDP 240

Query: 294 QTLEKVSNLAEAHIEAVFTDPSYSKFERGEALDKIGQDV-KKALEEECDEESLQVLPKAV 352
           Q   ++  LAE  I+     P   K  R  A++++   V  K  E+E DEE+L+ + + +
Sbjct: 241 QLEAEIRQLAEEDIKRAVQVPE--KLARDAAIEEVKASVIAKYEEQEADEETLKQVNEIL 298

Query: 353 DTVRKRVIRKRIIAEGVRVDGRQLDEVRPIYCESGNLPILHGSSLFSRGDTQVLCTVTLG 412
             + K  +R+ I  E +R DGR++DE+RP+  E G LP  HGS LF+RG TQVL   TLG
Sbjct: 299 HKLVKEEVRRLITEEKIRPDGRKIDEIRPLSSEVGVLPRTHGSGLFTRGQTQVLSVCTLG 358

Query: 413 APAEAQRLESLVGPPTKRFMLHYSFPPFCINEVGKRVGLNRREVGHGTLAEKALLAVLPP 472
           A  + Q L+ L    TKRFM HY+FPPF + E G   G  RRE+GHG L E+AL  V+P 
Sbjct: 359 ALGDVQILDGLGIEETKRFMHHYNFPPFSVGETGPMRGPGRREIGHGALGERALEPVVPS 418

Query: 473 ENDFPYTVRVNSEVMASDGSTSMATVCGGSMALMDAGIPLQEHVAGVSVGLVSEVDPSTG 532
           E +FPYT+R+ SEV+ S+GSTS A++C  ++A+MDAG+P++  VAG+++GLV   D    
Sbjct: 419 EKEFPYTIRLVSEVLESNGSTSQASICASTLAMMDAGVPIKAPVAGIAMGLVKNDD---- 474

Query: 533 EIKDYRILTDILGLEDHLGDMDFKIAGTRIGVTAIQLDIKPAGIPLDIICECLEHAHKGR 592
              +Y ILTDI G+EDHLGDMDFK+AGT  GVTA+Q+DIK  G+  +I+ E L+ A KGR
Sbjct: 475 ---NYTILTDIQGIEDHLGDMDFKVAGTAKGVTALQMDIKIKGLSREILEEALQQAKKGR 531

Query: 593 LQILDHMEREISAPRTQDDRNSPRLATLKYDNDTLRRLIGPLGALKRKIEEETGGRISV- 651
           ++IL+HM + I  PR +  + +P++ T++ + + +R +IGP G    KI +ETG +I + 
Sbjct: 532 MEILEHMMQTIREPRKELSKYAPKILTMQINPEKIREVIGPSGKQINKIIDETGVKIDIE 591

Query: 652 SDGTLTVVAKNRSVMEKVLEKVDFIIGREIEVGGIYKGVVTSVKEYGAFVEFNGGQQGLL 711
            DGT+ + + N ++ +K  + ++ I+ RE+EVG IY G V  ++++GAFVE   G+ GL+
Sbjct: 592 QDGTIFISSVNEAMNQKAKQIIEDIV-REVEVGQIYLGKVKRIEKFGAFVELFNGKDGLV 650

Query: 712 HVSELSHEPVSRVSDVVSVGQQLSLRCIGQDVRGNIKLSLKAV 754
           H+SEL+ E V RV DVVS+G ++ ++ +  D +G + LS KAV
Sbjct: 651 HISELAEERVGRVEDVVSIGDEILVKVMEIDKQGRVNLSRKAV 693

Involved in mRNA degradation. Hydrolyzes single-stranded polyribonucleotides processively in the 3'- to 5'-direction.

Geobacillus sp. (strain WCH70) (taxid: 471223)

EC: 2

EC: .

EC: 7

EC: .

EC: 7

EC: .

EC: 8

>sp|Q21H65|PNP_SACD2 Polyribonucleotide nucleotidyltransferase OS=Saccharophagus degradans (strain 2-40 / ATCC 43961 / DSM 17024) GN=pnp PE=3 SV=1

 Score =  561 bits (1445), Expect = e-158,   Method: Compositional matrix adjust.
 Identities = 310/723 (42%), Positives = 449/723 (62%), Gaps = 26/723 (3%)

Query: 48  PSVAGTKVLETFKEEFEIGSRLITLETGKIARFANGAVVLGMDETKVLSTVTSSK-GDSV 106
           PS    KV    K+ F+ G+  +TLETG+IAR A+GAV+  M +T VL  VT SK     
Sbjct: 6   PSQKDKKVNPVIKK-FQYGNDTVTLETGRIARQASGAVLASMGQTSVLVAVTGSKEAKPG 64

Query: 107 RDFLPLTVDYQEKQFAQGVIPNTYMRREGAPKERELLVGRIIDRPIRPLFPAGFYHEVQV 166
           +DF PL+V YQEK +A G IP  + +RE  P E+E L  R+IDRPIRPLFP GF +EVQV
Sbjct: 65  QDFFPLSVHYQEKAYAAGKIPGGFFKREARPSEKETLTSRLIDRPIRPLFPNGFLNEVQV 124

Query: 167 MASVLSSDGKQDPDIMAANATSAALMLSDIPWGGPIGMIRIGRIC-GQFIVNPTMDELSL 225
           + +V+S++   DPDI+A   TSAAL +S IP+ GPIG  R+G      +++NPT   L  
Sbjct: 125 VCTVISAEKDVDPDIVAMIGTSAALAISGIPFNGPIGAARVGYTQESGYLLNPTYSTLKT 184

Query: 226 SDLNLVYACTREKTLMIDVQAREISEKDLEAGLRLAHPEAVKYLEPQIRLAEKAGKQKKE 285
           S+L++V A T +  LM++ +A+E+ E  +   +  AH E    ++    LA+ A K   +
Sbjct: 185 SELDMVVAGTADAVLMVESEAKELPEDIMLGAVLYAHQEMQAVVQAVAELAKDAAKPVWD 244

Query: 286 YKLSMISEQTLEKVSNLAEAHIEAVFTDP---SYSKFERGEALDKIGQDVKKALEEECDE 342
           +K         E+V+   +A +E  F D    +Y   ++ +  D++ +   +A+ E   E
Sbjct: 245 WKP--------EEVNAELKAKVEHGFADSVGVAYRITDKQKRYDRLSELRNQAVAELATE 296

Query: 343 ES---LQVLPKAVDTVRKRVIRKRIIAEGVRVDGRQLDEVRPIYCESGNLPILHGSSLFS 399
           ES      +      + K+++R R++A   R+DGR    VRP++ E G LP +HGS+LF+
Sbjct: 297 ESGVSADEVKGLFAKIEKQIVRSRVVAGEPRIDGRDSKTVRPLHVEVGVLPKVHGSALFT 356

Query: 400 RGDTQVLCTVTLGAPAEAQRLESLVGPPTKRFMLHYSFPPFCINEVGKRVGLNRREVGHG 459
           RG+TQ L   TLG+  +AQ +++L G     FMLHY+FPP+ + E G+     RRE+GHG
Sbjct: 357 RGETQALVVSTLGSARDAQIIDALEGERKDPFMLHYNFPPYSVGECGRMGATGRREIGHG 416

Query: 460 TLAEKALLAVLPPENDFPYTVRVNSEVMASDGSTSMATVCGGSMALMDAGIPLQEHVAGV 519
            LA + + AVLP E DFPYT+RV SE+  S+GS+SMA+VCG S+ALMDAG+PL+  VAG+
Sbjct: 417 RLARRGIGAVLPKEEDFPYTMRVVSEITESNGSSSMASVCGASLALMDAGVPLKAPVAGI 476

Query: 520 SVGLVSEVDPSTGEIKDYRILTDILGLEDHLGDMDFKIAGTRIGVTAIQLDIKPAGIPLD 579
           ++GLV E +        + +LTDILG EDHLGDMDFK+AGT  GVTA+Q+DIK  GI  +
Sbjct: 477 AMGLVKEDN-------GFAVLTDILGDEDHLGDMDFKVAGTADGVTALQMDIKIEGITEE 529

Query: 580 IICECLEHAHKGRLQILDHMEREISAPRTQDDRNSPRLATLKYDNDTLRRLIGPLGALKR 639
           I+   L  A   RL IL  M R I++PR +   N+P+  T+K D D +R +IG  GA  R
Sbjct: 530 IMEIALGQAMDARLHILAEMNRVIASPRKELSENAPQFHTMKIDPDKIRDIIGKGGATIR 589

Query: 640 KIEEETGGRISVSD-GTLTVVAKNRSVMEKVLEKVDFIIGREIEVGGIYKGVVTSVKEYG 698
            I EETG  I + D GT+ + A +   M+  + +++ I   E E+G +Y+G V  + ++G
Sbjct: 590 SITEETGASIDIDDNGTIKIYADDGDGMQAAIARIEEITA-EAEIGAVYQGKVVRIVDFG 648

Query: 699 AFVEFNGGQQGLLHVSELSHEPVSRVSDVVSVGQQLSLRCIGQDVRGNIKLSLKAVSPRP 758
           AFV F  G+ GL+H+S+++HE V  VSD +  GQ + ++C+  D RG IKLS+K + P P
Sbjct: 649 AFVNFLPGKDGLVHISQIAHERVQNVSDYLKEGQDIEVKCMDIDQRGRIKLSIKELLPAP 708

Query: 759 EAD 761
           EA+
Sbjct: 709 EAE 711

Involved in mRNA degradation. Hydrolyzes single-stranded polyribonucleotides processively in the 3'- to 5'-direction.

Saccharophagus degradans (strain 2-40 / ATCC 43961 / DSM 17024) (taxid: 203122)

EC: 2

EC: .

EC: 7

EC: .

EC: 7

EC: .

EC: 8

>sp|Q6D9A1|PNP_ERWCT Polyribonucleotide nucleotidyltransferase OS=Erwinia carotovora subsp. atroseptica (strain SCRI 1043 / ATCC BAA-672) GN=pnp PE=3 SV=1

 Score =  559 bits (1440), Expect = e-158,   Method: Compositional matrix adjust.
 Identities = 295/707 (41%), Positives = 447/707 (63%), Gaps = 12/707 (1%)

Query: 55  VLETFKEEFEIGSRLITLETGKIARFANGAVVLGMDETKVLSTVTSSK-GDSVRDFLPLT 113
           +L     +F+ G   +TLETG +AR A  AV++ MD+T V  TV  +K     + F PLT
Sbjct: 1   MLNPIVRKFQYGQHTVTLETGMMARQATAAVMVSMDDTAVFVTVVGAKNAKPGQSFFPLT 60

Query: 114 VDYQEKQFAQGVIPNTYMRREGAPKERELLVGRIIDRPIRPLFPAGFYHEVQVMASVLSS 173
           V+YQE+ +A G  P  + RREG P E E L  R+IDRPIRPLFP GF +EVQV+A+V+S 
Sbjct: 61  VNYQERTYAAGRFPGGFFRREGRPSEGETLTSRLIDRPIRPLFPEGFLNEVQVIATVVSV 120

Query: 174 DGKQDPDIMAANATSAALMLSDIPWGGPIGMIRIGRICGQFIVNPTMDELSLSDLNLVYA 233
           + +  PDI+A    SAAL LS IP+ GPIG+ R+G +  Q+++NPT DEL  S L+LV A
Sbjct: 121 NPQVSPDIVAMIGASAALSLSGIPFSGPIGVARVGYLNDQYVLNPTTDELKESRLDLVVA 180

Query: 234 CTREKTLMIDVQAREISEKDLEAGLRLAHPEAVKYLEPQIRLAEKAGKQKKEYKLSMISE 293
            T+   LM++ +A  +SE  +   +   H +    +E    L  +AGK K E+    ++ 
Sbjct: 181 GTQGAVLMVESEAELLSEDQMLGAVVFGHEQQQIVIENINSLVAEAGKPKWEWHAPAVNV 240

Query: 294 QTLEKVSNLAEAHIEAVFTDPSYSKFERGEALDKIGQDVKKALEEECDEESLQVLPKAVD 353
              ++V  L+EA +   +      K ER   ++ I  DV  AL+ E +  +   + + + 
Sbjct: 241 SLEQRVQALSEARLGDAYR--ITEKQERYAQVNVIKTDVVAALQAEDETLNAGEIQEILG 298

Query: 354 TVRKRVIRKRIIAEGVRVDGRQLDEVRPIYCESGNLPILHGSSLFSRGDTQVLCTVTLGA 413
            + K V+R R++A   R+DGR+ D +R +   +G LP  HGS+LF+RG+TQ L T TLG 
Sbjct: 299 NIEKNVVRGRVLAGEPRIDGREKDMIRGLDVRTGVLPRTHGSALFTRGETQALVTATLGT 358

Query: 414 PAEAQRLESLVGPPTKRFMLHYSFPPFCINEVGKRVGLNRREVGHGTLAEKALLAVLPPE 473
             +AQ ++ L G  T RF+LHY+FPP+C+ E G      RRE+GHG LA++ +LAV+P  
Sbjct: 359 ERDAQNIDELTGERTDRFLLHYNFPPYCVGETGMVGSPKRREIGHGRLAKRGVLAVMPKA 418

Query: 474 NDFPYTVRVNSEVMASDGSTSMATVCGGSMALMDAGIPLQEHVAGVSVGLVSEVDPSTGE 533
           N+FPYTVRV SE+  S+GS+SMA+VCG S+ALMDAG+P++  VAG+++GLV E D     
Sbjct: 419 NEFPYTVRVVSEITESNGSSSMASVCGASLALMDAGVPIKSAVAGIAMGLVKEGD----- 473

Query: 534 IKDYRILTDILGLEDHLGDMDFKIAGTRIGVTAIQLDIKPAGIPLDIICECLEHAHKGRL 593
             ++ +L+DILG EDHLGDMDFK+AG+R G+TA+Q+DIK  GI  +I+   L  A   RL
Sbjct: 474 --NFVVLSDILGDEDHLGDMDFKVAGSREGITALQMDIKIEGITREIMQVALNQAKGARL 531

Query: 594 QILDHMEREISAPRTQDDRNSPRLATLKYDNDTLRRLIGPLGALKRKIEEETGGRISV-S 652
            IL  ME+ IS PR      +PR+ T+K   D ++ +IG  G++ R + EETG  I +  
Sbjct: 532 HILGVMEQAISTPRGDISEFAPRIHTIKISTDKIKDVIGKGGSVIRALTEETGTTIEIED 591

Query: 653 DGTLTVVAKNRSVMEKVLEKVDFIIGREIEVGGIYKGVVTSVKEYGAFVEFNGGQQGLLH 712
           DGT+ + + +    +  + +++ I   EIEVG +Y+G VT + ++GAFV   GG++GL+H
Sbjct: 592 DGTVRIASTDGEKAKHAIRRIEEITA-EIEVGRVYQGKVTRIVDFGAFVAIGGGKEGLVH 650

Query: 713 VSELSHEPVSRVSDVVSVGQQLSLRCIGQDVRGNIKLSLKAVSPRPE 759
           +S+++ + V +V+D + +GQ++ ++ +  D +G ++LS+K  +P+ +
Sbjct: 651 ISQIADKRVEKVTDYLQMGQEVPVKVLEVDRQGRVRLSIKEANPQTQ 697

Involved in mRNA degradation. Hydrolyzes single-stranded polyribonucleotides processively in the 3'- to 5'-direction.

Erwinia carotovora subsp. atroseptica (strain SCRI 1043 / ATCC BAA-672) (taxid: 218491)

EC: 2

EC: .

EC: 7

EC: .

EC: 7

EC: .

EC: 8

Close Homologs in the Non-Redundant Database Detected by BLAST

Original result of BLAST against Nonredundant Database

GI	Length	Definition	Q cover	H cover	Identity	E-value
Query	974
359488677	964	PREDICTED: polyribonucleotide nucleotidy	0.980	0.990	0.773	0.0
224060110	961	predicted protein [Populus trichocarpa]	0.976	0.989	0.770	0.0
255567379	958	polyribonucleotide nucleotidyltransferas	0.978	0.994	0.764	0.0
449515386	955	PREDICTED: LOW QUALITY PROTEIN: polyribo	0.973	0.992	0.724	0.0
296087634	905	unnamed protein product [Vitis vinifera]	0.908	0.977	0.764	0.0
449446674	1032	PREDICTED: polyribonucleotide nucleotidy	0.985	0.930	0.686	0.0
356573319	959	PREDICTED: polyribonucleotide nucleotidy	0.947	0.962	0.711	0.0
297811589	992	hypothetical protein ARALYDRAFT_488299 [	0.976	0.958	0.682	0.0
15241441	991	polyribonucleotide nucleotidyltransferas	0.973	0.956	0.676	0.0
357150173	983	PREDICTED: LOW QUALITY PROTEIN: polyribo	0.945	0.936	0.66	0.0

>gi|359488677|ref|XP_002273777.2| PREDICTED: polyribonucleotide nucleotidyltransferase-like [Vitis vinifera]

 Score = 1524 bits (3947), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 758/980 (77%), Positives = 841/980 (85%), Gaps = 25/980 (2%)

Query: 1   MSSLATKTHPLLNNLPPFLTWRALGFRTICSGRLGFAPCEPAPPTPAPSVAGTKVLETFK 60
           M+++A++ +PLL +LP +LTWR+L +RTICSG LGFA   P+     P V G KVLETFK
Sbjct: 1   MAAMASRRNPLLTSLPLYLTWRSLRYRTICSGHLGFASSSPSISEQIP-VPGMKVLETFK 59

Query: 61  EEFEIGSRLITLETGKIARFANGAVVLGMDETKVLSTVTSSKGDSVRDFLPLTVDYQEKQ 120
           EEFEIGSR IT ETGKIARFANGAVV+ MDETKVLSTV SSKGD+ RDFLPLTVDYQEK 
Sbjct: 60  EEFEIGSRSITFETGKIARFANGAVVMSMDETKVLSTVASSKGDAARDFLPLTVDYQEKH 119

Query: 121 FAQGVIPNTYMRREGAPKERELLVGRIIDRPIRPLFPAGFYHEVQVMASVLSSDGKQDPD 180
           FAQGVIP T+MRREGAP+ERELL GR+IDRPIRPLFPAGFYHEVQVMASVLSSDGKQDPD
Sbjct: 120 FAQGVIPTTFMRREGAPRERELLCGRLIDRPIRPLFPAGFYHEVQVMASVLSSDGKQDPD 179

Query: 181 IMAANATSAALMLSDIPWGGPIGMIRIGRICGQFIVNPTMDELSLSDLNLVYACTREKTL 240
           +MAANATSAALMLSDIPWGGPIG+IRIGRICGQFIVNP+MDELSLSDLNLVYACTR+KTL
Sbjct: 180 VMAANATSAALMLSDIPWGGPIGVIRIGRICGQFIVNPSMDELSLSDLNLVYACTRDKTL 239

Query: 241 MIDVQAREISEKDLEAGLRLAHPEAVKYLEPQIRLAEKAGKQKKEYKLSMISEQTLEKVS 300
           MIDVQAREISEKDLEA LRLAHPEAV+YLEPQIRLA +AGK KKEY LSM+S+ T EKV 
Sbjct: 240 MIDVQAREISEKDLEAALRLAHPEAVRYLEPQIRLAARAGKSKKEYTLSMVSDITFEKVR 299

Query: 301 NLAEAHIEAVFTDPSYSKFERGEALDKIGQDVKKALEEECDEESLQVLPKAVDTVRKRVI 360
           NLAEA IEAVFTD +Y KFERGEALD I QDVK+ALEEECDEESL+VLPK VDTVRK V+
Sbjct: 300 NLAEAPIEAVFTDHTYGKFERGEALDLITQDVKRALEEECDEESLKVLPKVVDTVRKEVV 359

Query: 361 RKRIIAEGVRVDGRQLDEVRPIYCESGNLPILHGSSLFSRGDTQVLCTVTLGAPAEAQRL 420
           R+RIIAEG+RVDGR L+EVRP+YCESGNLPILHGSSLFSRGDTQVLCTVTLGAP +AQRL
Sbjct: 360 RRRIIAEGLRVDGRHLNEVRPLYCESGNLPILHGSSLFSRGDTQVLCTVTLGAPGDAQRL 419

Query: 421 ESLVGPPTKRFMLHYSFPPFCINEVGKRVGLNRREVGHGTLAEKALLAVLPPENDFPYTV 480
           +SLVGPPTKRFMLHYSFPPF INEVGKRVGLNRREVGHGTLAEKALLAVLPPE +FPYTV
Sbjct: 420 DSLVGPPTKRFMLHYSFPPFSINEVGKRVGLNRREVGHGTLAEKALLAVLPPEEEFPYTV 479

Query: 481 RVNSEVMASDGSTSMATVCGGSMALMDAGIPLQEHVAGVSVGLVSEVDPSTGEIKDYRIL 540
           R+NSEVMASDGSTSMATVCGGSMALMDAGIPL+EHVAG+SVGLV+EVDPST  IKDYRIL
Sbjct: 480 RINSEVMASDGSTSMATVCGGSMALMDAGIPLREHVAGISVGLVTEVDPSTNTIKDYRIL 539

Query: 541 TDILGLEDHLGDMDFKIAGTRIGVTAIQLDIKPAGIPLDIICECLEHAHKGRLQILDHME 600
           TDILGLEDHLGDMDFKIAGTR G+TAIQLDIKPAGIPLDIICECLE A +GRLQILD ME
Sbjct: 540 TDILGLEDHLGDMDFKIAGTRKGITAIQLDIKPAGIPLDIICECLEPALRGRLQILDRME 599

Query: 601 REISAPRTQDDRNSPRLATLKYDNDTLRRLIGPLGALKRKIEEETGGRISVSDGTLTVVA 660
           +EI+APRTQ  RNSPRLATLK+ ND+LRRL+GP+GALKRKIEEETG RISVSDGTLTVVA
Sbjct: 600 QEINAPRTQHYRNSPRLATLKFSNDSLRRLLGPMGALKRKIEEETGARISVSDGTLTVVA 659

Query: 661 KNRSVMEKVLEKVDFIIGREIEVGGIYKGVVTSVKEYGAFVEFNGGQQGLLHVSELSHEP 720
           KN+SVM+KV EKVDFI+GREIE+GGIYKGVVTSVKEYGAFVEFNGGQQGLLH+SELSHEP
Sbjct: 660 KNQSVMDKVQEKVDFIVGREIEIGGIYKGVVTSVKEYGAFVEFNGGQQGLLHISELSHEP 719

Query: 721 VSRVSDVVSVGQQLSLRCIGQDVRGNIKLSLKAVSPRPEADVKGVVEGSVPVNKQATDVW 780
           V RVSDVVS+GQQ+SL CIGQDVRGNIKLSLK+  PRP +D   VVEGS+P+ KQA  VW
Sbjct: 720 VVRVSDVVSIGQQISLMCIGQDVRGNIKLSLKSTLPRPGSDTNNVVEGSIPITKQAPSVW 779

Query: 781 ASVGDV------SNGQNPELPMRKNETPGVNSSTSSTPAVLIRSAAECDEEEKASGFSQS 834
           AS+GDV       N    ELP+ K+ET   +  TS  P+ LIRSAAECDEEEK++GF+QS
Sbjct: 780 ASIGDVPDSEEKQNSDLEELPVAKDETSEGSLPTSKLPSFLIRSAAECDEEEKSAGFNQS 839

Query: 835 SKSTLKSTLASKSNSKPKKFTSQSDFFSSTNIQKSTSFSQREREELAECLFGTEDGDEDN 894
           S++T K    S SN K K    Q+D       +  ++F+   + +L            D 
Sbjct: 840 SRNTSKPRSISGSNDKLKTSPPQND-----GDKHGSAFNANSQNDL-----------NDT 883

Query: 895 KGTRVEAIVSAKNLKLGTKVAAKVYQVRARGLVLDLGGGIRGMYRFE-NNEKKDFVVGDE 953
           K    E    AKNLKLG K+ AKVYQ+R  GLVLDLGGGIRGMYRFE +N+K+DF VGDE
Sbjct: 884 KEVP-ETCTGAKNLKLGMKLNAKVYQIRTHGLVLDLGGGIRGMYRFEGDNDKRDFKVGDE 942

Query: 954 LLVKCSSFTGKGIPVVSLVD 973
           L V CSSF+ KGIPV+SLV+
Sbjct: 943 LHVMCSSFSTKGIPVMSLVE 962

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|224060110|ref|XP_002300042.1| predicted protein [Populus trichocarpa] gi|222847300|gb|EEE84847.1| predicted protein [Populus trichocarpa]

 Score = 1509 bits (3906), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 751/975 (77%), Positives = 839/975 (86%), Gaps = 24/975 (2%)

Query: 5   ATKTHPLLNNLPPFLTWRALGFRTICSGRLGFAPCEPAPPTPAPSVAGTKVLETFKEEFE 64
           A++++PLLN+LP FLTWR+LGFRTICSGRLGFAP +P P  P  S AGTK LETF+EEFE
Sbjct: 3   ASRSNPLLNSLPRFLTWRSLGFRTICSGRLGFAPSDPDPEPPV-STAGTKFLETFREEFE 61

Query: 65  IGSRLITLETGKIARFANGAVVLGMDETKVLSTVTSSKGDSVRDFLPLTVDYQEKQFAQG 124
           IGSRLIT ETGKIARFANG+VVLGM+ETKVLSTVTSSKGDSVRDFLPLTVDYQEKQFAQG
Sbjct: 62  IGSRLITFETGKIARFANGSVVLGMEETKVLSTVTSSKGDSVRDFLPLTVDYQEKQFAQG 121

Query: 125 VIPNTYMRREGAPKERELLVGRIIDRPIRPLFPAGFYHEVQVMASVLSSDGKQDPDIMAA 184
           VIP+TY+RREGAPKERELL GR+IDRPIRPLFPAGFYHEVQVMASVLSSDG++DPD+MAA
Sbjct: 122 VIPSTYLRREGAPKERELLCGRLIDRPIRPLFPAGFYHEVQVMASVLSSDGRRDPDVMAA 181

Query: 185 NATSAALMLSDIPWGGPIGMIRIGRICGQFIVNPTMDELSLSDLNLVYACTREKTLMIDV 244
           NATSAALMLSDIPWGGPIG+IRIGRICGQF+VNPTMDELSLSDLNLVYACT++KTLMIDV
Sbjct: 182 NATSAALMLSDIPWGGPIGVIRIGRICGQFVVNPTMDELSLSDLNLVYACTKDKTLMIDV 241

Query: 245 QAREISEKDLEAGLRLAHPEAVKYLEPQIRLAEKAGKQKKEYKLSMISEQTLEKVSNLAE 304
           QA  I+EKDLEAGLRLAHPEAVKYLEPQIRLA KAGK KK+YKLS++S++TLEKV NL E
Sbjct: 242 QAGGIAEKDLEAGLRLAHPEAVKYLEPQIRLAAKAGKHKKDYKLSLVSDRTLEKVRNLTE 301

Query: 305 AHIEAVFTDPSYSKFERGEALDKIGQDVKKALEEECDEESLQVLPKAVDTVRKRVIRKRI 364
           A IEAVFTDPSY KFERGEALD I Q+ K+ LEEECD ESL VL K VD VRK V+R RI
Sbjct: 302 AKIEAVFTDPSYGKFERGEALDNIAQEAKRTLEEECDTESLTVLSKVVDRVRKGVVRNRI 361

Query: 365 IAEGVRVDGRQLDEVRPIYCESGNLPILHGSSLFSRGDTQVLCTVTLGAPAEAQRLESLV 424
           IAEG RVDGR+LDEVRP+YCE+G LP LHGSSLFSRGDTQVLCTVTLGAP +AQRL+SLV
Sbjct: 362 IAEGFRVDGRRLDEVRPLYCEAGYLPNLHGSSLFSRGDTQVLCTVTLGAPRDAQRLDSLV 421

Query: 425 GPPTKRFMLHYSFPPFCINEVGKRVGLNRREVGHGTLAEKALLAVLPPENDFPYTVRVNS 484
           GPPTKRFMLHYSFPPF INEVGKRVGLNRREVGHGTLAEKALLAVLPPE+DFPYTVR+NS
Sbjct: 422 GPPTKRFMLHYSFPPFSINEVGKRVGLNRREVGHGTLAEKALLAVLPPEDDFPYTVRINS 481

Query: 485 EVMASDGSTSMATVCGGSMALMDAGIPLQEHVAGVSVGLVSEVDPSTGEIKDYRILTDIL 544
           EVMASDGSTSMATVCGGS+A+MDAGIPLQEHVAGVSVGLVSEVDPSTGEIKDYRI+TDIL
Sbjct: 482 EVMASDGSTSMATVCGGSVAMMDAGIPLQEHVAGVSVGLVSEVDPSTGEIKDYRIVTDIL 541

Query: 545 GLEDHLGDMDFKIAGTRIGVTAIQLDIKPAGIPLDIICECLEHAHKGRLQILDHMEREIS 604
           GLEDHLGDMDFKIAGTR GVTA+QLDIKPAGIPLDIICECLE A KGRLQIL  M++EIS
Sbjct: 542 GLEDHLGDMDFKIAGTRKGVTAVQLDIKPAGIPLDIICECLEPALKGRLQILARMDQEIS 601

Query: 605 APRTQDDRNSPRLATLKYDNDTLRRLIGPLGALKRKIEEETGGRISVSDGTLTVVAKNRS 664
           APRTQD RNSPRLATLK+ ND LRRLIGPLG LKRKIEE+TG R+SVSD TLT++AKN++
Sbjct: 602 APRTQDHRNSPRLATLKFSNDALRRLIGPLGVLKRKIEEDTGARMSVSDETLTILAKNQT 661

Query: 665 VMEKVLEKVDFIIGREIEVGGIYKGVVTSVKEYGAFVEFNGGQQGLLHVSELSHEPVSRV 724
           V+E+V EK+DFIIGREIEVGGIYKG+V+S+KEYGAFVEFNGGQQGLLHVSELSHEPVS++
Sbjct: 662 VLERVQEKIDFIIGREIEVGGIYKGIVSSIKEYGAFVEFNGGQQGLLHVSELSHEPVSKI 721

Query: 725 SDVVSVGQQLSLRCIGQDVRGNIKLSLKAVSPRPEADVKGVVEGSVPVNKQATDVWASVG 784
           SDV+SVGQQLSL CIGQDVRGNIKLSLKA  P+ ++    V E  VPV K+A  VW SVG
Sbjct: 722 SDVISVGQQLSLMCIGQDVRGNIKLSLKATLPQLKSKKNNVTEEPVPVIKEAPKVWTSVG 781

Query: 785 DVSNGQ------NPELPMRKNETPGVNSSTSSTPAVLIRSAAECDEEEKASGFSQSSKST 838
           ++ N Q      + EL + ++    V  STSS P  LIRSAAECDEE+K    +Q SKS 
Sbjct: 782 NLPNEQEEQKLTDAELMLSRST---VKPSTSSNPGFLIRSAAECDEEDKTVSLNQGSKSN 838

Query: 839 LKSTLASKSNSKPKKFTSQSDFFSSTNIQKSTSFSQREREELAECLFGTEDGDEDNKGTR 898
            K+  A+K + K K    +SD   S     S+  S    + L          DED K   
Sbjct: 839 SKTLRATKRDRKRKTKVPESD--DSDASIYSSGHSSHTVDRL---------NDEDAK--- 884

Query: 899 VEAIVSAKNLKLGTKVAAKVYQVRARGLVLDLGGGIRGMYRFENNEKKDFVVGDELLVKC 958
           V + +SAK+LKLG K+AAKVYQ+RA GLVLDLG G+RGMYRFE N K+DF +GDELLVKC
Sbjct: 885 VVSPLSAKSLKLGMKIAAKVYQIRALGLVLDLGNGVRGMYRFETNGKRDFEIGDELLVKC 944

Query: 959 SSFTGKGIPVVSLVD 973
           +SF+ KG+PV+SLVD
Sbjct: 945 TSFSSKGLPVMSLVD 959

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|255567379|ref|XP_002524669.1| polyribonucleotide nucleotidyltransferase, putative [Ricinus communis] gi|223536030|gb|EEF37688.1| polyribonucleotide nucleotidyltransferase, putative [Ricinus communis]

 Score = 1478 bits (3827), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 746/976 (76%), Positives = 840/976 (86%), Gaps = 23/976 (2%)

Query: 1   MSSLA-TKTHPLLNNLPPFLTWRALGFRTICSGRLGFAPCEPAPPTPAPSVAGTKVLETF 59
           MS++A +K +PL+N+LP FLT R+  FRTICSGRLGFAP  P  P     VAGTKVLETF
Sbjct: 1   MSAIARSKANPLVNSLPRFLTRRSFNFRTICSGRLGFAPSYPDRP-----VAGTKVLETF 55

Query: 60  KEEFEIGSRLITLETGKIARFANGAVVLGMDETKVLSTVTSSKGDSVRDFLPLTVDYQEK 119
           KEEFEIGS++I+LETG+IARFANGAVVL MD+TKVLSTVTSSKGD+VRDFLPLTVDYQEK
Sbjct: 56  KEEFEIGSQVISLETGEIARFANGAVVLSMDQTKVLSTVTSSKGDAVRDFLPLTVDYQEK 115

Query: 120 QFAQGVIPNTYMRREGAPKERELLVGRIIDRPIRPLFPAGFYHEVQVMASVLSSDGKQDP 179
           QFAQGVIPNT+MRREGAPKERELL GR+IDRPIRPLF  GFYHEVQVMASVLSSDGKQDP
Sbjct: 116 QFAQGVIPNTFMRREGAPKERELLCGRLIDRPIRPLFAPGFYHEVQVMASVLSSDGKQDP 175

Query: 180 DIMAANATSAALMLSDIPWGGPIGMIRIGRICGQFIVNPTMDELSLSDLNLVYACTREKT 239
           D+MAANATSAALMLSDIPWGGPIG+IRIGRI GQFIVNPTMDELSLSDLNLVYACT++KT
Sbjct: 176 DVMAANATSAALMLSDIPWGGPIGVIRIGRIGGQFIVNPTMDELSLSDLNLVYACTKDKT 235

Query: 240 LMIDVQAREISEKDLEAGLRLAHPEAVKYLEPQIRLAEKAGKQKKEYKLSMISEQTLEKV 299
           LMIDVQAREISEKDLEA LRLAHPEAVKYLEPQIRLA KAGK KK+YKLSM+SE+ LEKV
Sbjct: 236 LMIDVQAREISEKDLEAALRLAHPEAVKYLEPQIRLAAKAGKDKKDYKLSMVSERILEKV 295

Query: 300 SNLAEAHIEAVFTDPSYSKFERGEALDKIGQDVKKALEEECDEESLQVLPKAVDTVRKRV 359
            NLAE  IEAVFTD SY KFERGEALD I QDVK+ LEEECDEESL VL KAVDTVRK+V
Sbjct: 296 RNLAETQIEAVFTDSSYGKFERGEALDNITQDVKRTLEEECDEESLNVLRKAVDTVRKQV 355

Query: 360 IRKRIIAEGVRVDGRQLDEVRPIYCESGNLPILHGSSLFSRGDTQVLCTVTLGAPAEAQR 419
           +R+RII+EG RVDGR+LDEVRP++C++G LPILHGSSLF+RGDTQVLCTVTLGAP +AQR
Sbjct: 356 VRRRIISEGFRVDGRRLDEVRPLFCKAGPLPILHGSSLFNRGDTQVLCTVTLGAPGDAQR 415

Query: 420 LESLVGPPTKRFMLHYSFPPFCINEVGKRVGLNRREVGHGTLAEKALLAVLPPENDFPYT 479
           LESLVGPPTKRFMLHYSFPPF INEVGKRVGLNRREVGHGTLAEKALLAVLPPE+DFPYT
Sbjct: 416 LESLVGPPTKRFMLHYSFPPFSINEVGKRVGLNRREVGHGTLAEKALLAVLPPEDDFPYT 475

Query: 480 VRVNSEVMASDGSTSMATVCGGSMALMDAGIPLQEHVAGVSVGLVSEVDPSTGEIKDYRI 539
           VR+NSEVMASDGSTSMATVCGGSMALMDAGIPL+EHVAGVSVGLVSEVDPSTGEIKDYR+
Sbjct: 476 VRINSEVMASDGSTSMATVCGGSMALMDAGIPLREHVAGVSVGLVSEVDPSTGEIKDYRV 535

Query: 540 LTDILGLEDHLGDMDFKIAGTRIGVTAIQLDIKPAGIPLDIICECLEHAHKGRLQILDHM 599
           LTDILGLEDHLGDMDFKIAGTR GVTAIQLDIKPAGIPLDIICECL+HA KGRLQILDHM
Sbjct: 536 LTDILGLEDHLGDMDFKIAGTRNGVTAIQLDIKPAGIPLDIICECLDHALKGRLQILDHM 595

Query: 600 EREISAPRTQDDRNSPRLATLKYDNDTLRRLIGPLGALKRKIEEETGGRISVSDGTLTVV 659
           E+EI+ PRTQ D+  PRLAT K+ NDTLR+LIGPLG LKRKIEEETG R+S+SDG LTV 
Sbjct: 596 EQEINVPRTQVDKTRPRLATFKFSNDTLRQLIGPLGVLKRKIEEETGARLSISDGMLTVG 655

Query: 660 AKNRSVMEKVLEKVDFIIGREIEVGGIYKGVVTSVKEYGAFVEFNGGQQGLLHVSELSHE 719
           AKN++VM+KV EK+DFIIG EIE GG+YKG+VTS+KEYGAF++FNGGQQGLLH+SELSHE
Sbjct: 656 AKNQAVMDKVQEKIDFIIGCEIETGGVYKGIVTSIKEYGAFIQFNGGQQGLLHISELSHE 715

Query: 720 PVSRVSDVVSVGQQLSLRCIGQDVRGNIKLSLKAVSPRPEADVKGVVEGSVPVNKQATDV 779
           PVS+VSDVVSVGQQLSL CIGQDVRGNIKLSLKA SP   ++   + EGSVPV K+   V
Sbjct: 716 PVSKVSDVVSVGQQLSLMCIGQDVRGNIKLSLKATSPPLGSNTNIMEEGSVPVTKELPKV 775

Query: 780 WASVGDVSNGQNPELPMRKN--ETPGVNSSTSSTPAVLIRSAAECDEEEKASGFSQSSKS 837
           WASV +VS+G++ + P  +   ++  VN STSS PA LIRS AECDEEEK +  ++ S +
Sbjct: 776 WASVENVSDGRDEQKPTAEFPLDSSMVNFSTSSAPAFLIRSIAECDEEEKDASLNRDSNN 835

Query: 838 TLKSTLASKSNSKPKKFTSQSDFFSSTNIQKSTSFSQREREELAECLFGTEDGDEDNKGT 897
             K    +K + K K  T+   + S + +  S S S  + +              +N   
Sbjct: 836 APKILWTAKRDHKLK--TNPPKYDSHSPVPNSNSLSHTKNK-------------LNNVEN 880

Query: 898 RVEAIVSAKNLKLGTKVAAKVYQVRARGLVLDLGGGIRGMYRFENNEKKDFVVGDELLVK 957
            VE+ ++A+NLKLGTKVAAKVYQ+R  GLVLDLGG +RGM+RFE N K+DF VGDEL VK
Sbjct: 881 EVESPINARNLKLGTKVAAKVYQIRKHGLVLDLGGEVRGMFRFEENGKRDFEVGDELRVK 940

Query: 958 CSSFTGKGIPVVSLVD 973
           C++F+ KGIPV+SLVD
Sbjct: 941 CTNFSSKGIPVMSLVD 956

Source: Ricinus communis

Species: Ricinus communis

Genus: Ricinus

Family: Euphorbiaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|449515386|ref|XP_004164730.1| PREDICTED: LOW QUALITY PROTEIN: polyribonucleotide nucleotidyltransferase 2, mitochondrial-like [Cucumis sativus]

 Score = 1431 bits (3703), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 711/981 (72%), Positives = 814/981 (82%), Gaps = 33/981 (3%)

Query: 1   MSSLATKTHPLLNNLPPFLTWRALGFRTICSGRLGFAPCEPAPPTPAPSVAGTKVLETFK 60
           M+S+ATK +PL + +P FLTWR+LGFRTIC GR+GF+        P  ++  TKVLETF+
Sbjct: 1   MASMATKANPLFSTIPHFLTWRSLGFRTICCGRMGFSSQSQQQVDPNTTLGRTKVLETFE 60

Query: 61  EEFEIGSRLITLETGKIARFANGAVVLGMDETKVLSTVTSSKGDSVRDFLPLTVDYQEKQ 120
           E FEIGSRL+ LETGKIARFANGA VLG++ETKVLSTV S+KGD+ RDFLPLTVDYQEKQ
Sbjct: 61  EVFEIGSRLVKLETGKIARFANGAAVLGIEETKVLSTVASAKGDAARDFLPLTVDYQEKQ 120

Query: 121 FAQGVIPNTYMRREGAPKERELLVGRIIDRPIRPLFPAGFYHEVQVMASVLSSDGKQDPD 180
           FAQGVIP T+ RREGAPKERELL GRIIDRPIRPLFPAGFYHEVQVMASVLSSDGKQDPD
Sbjct: 121 FAQGVIPGTFTRREGAPKERELLCGRIIDRPIRPLFPAGFYHEVQVMASVLSSDGKQDPD 180

Query: 181 IMAANATSAALMLSDIPWGGPIGMIRIGRICGQFIVNPTMDELSLSDLNLVYACTREKTL 240
           +MAANATSAALMLSDIPWGGPIG+IRIGRI GQF+VNPTMDEL+LSDLNL+YACTREKTL
Sbjct: 181 VMAANATSAALMLSDIPWGGPIGVIRIGRIDGQFVVNPTMDELNLSDLNLIYACTREKTL 240

Query: 241 MIDVQAREISEKDLEAGLRLAHPEAVKYLEPQIRLAEKAGKQKKEYKLSMISEQTLEKVS 300
           MIDVQAREI+EKDLEAGLRLAHPEAVK+LEPQIRLA KAGK KKEYKLSM+S+ TLEKV+
Sbjct: 241 MIDVQAREITEKDLEAGLRLAHPEAVKFLEPQIRLAAKAGKLKKEYKLSMVSDSTLEKVA 300

Query: 301 NLAEAHIEAVFTDPSYSKFERGEALDKIGQDVKKALEEECDEESLQVLPKAVDTVRKRVI 360
            LAE+ IEAVFTDPSY KFERGEAL+KI +DVKK  EEEC EE L+VLPKAVD VRK+V+
Sbjct: 301 KLAESPIEAVFTDPSYGKFERGEALEKITEDVKKVFEEECYEEGLKVLPKAVDYVRKKVV 360

Query: 361 RKRIIAEGVRVDGRQLDEVRPIYCESGNLPILHGSSLFSRGDTQVLCTVTLGAPAEAQRL 420
           R+RIIAEG R+DGR+LDEVRP+YCES  LPILHGSS+FSRGDTQVLCTVTLGAPA+AQ L
Sbjct: 361 RRRIIAEGRRLDGRRLDEVRPLYCESSYLPILHGSSIFSRGDTQVLCTVTLGAPADAQHL 420

Query: 421 ESLVGPPTKRFMLHYSFPPFCINEVGKRVGLNRREVGHGTLAEKALLAVLPPENDFPYTV 480
           +SLVGPPTKRFMLHYSFPPF INEVGKR GLNRREVGHGTLAEKALLAVLPPE++FPY V
Sbjct: 421 DSLVGPPTKRFMLHYSFPPFSINEVGKRGGLNRREVGHGTLAEKALLAVLPPESEFPYAV 480

Query: 481 RVNSEVMASDGSTSMATVCGGSMALMDAGIPLQEHVAGVSVGLVSEVDPSTGEIKDYRIL 540
           R+NSEVMASDGSTSMATVCGGSMALMDAG+PL EHVAGVSVGLVSE DPSTG IKDYRIL
Sbjct: 481 RINSEVMASDGSTSMATVCGGSMALMDAGVPLNEHVAGVSVGLVSETDPSTGAIKDYRIL 540

Query: 541 TDILGLEDHLGDMDFKIAGTRIGVTAIQLDIKPAGIPLDIICECLEHAHKGRLQILDHME 600
           TDILGLEDHLGDMDFKIAGTR GVTAIQLDIKPAGIPLDIICE LEHA KGR QILDHME
Sbjct: 541 TDILGLEDHLGDMDFKIAGTRKGVTAIQLDIKPAGIPLDIICESLEHARKGRWQILDHME 600

Query: 601 REISAPRTQDDRNSPRLATLKYDNDTLRRLIGPLGALKRKIEEETGGRISVSDGTLTVVA 660
           REI+APR +DD N PRL TLKY N+ LRRLIGPLG +K+KIE ETG RISV DGTLT++A
Sbjct: 601 REINAPRMKDDENCPRLVTLKYTNEALRRLIGPLGIVKKKIEAETGARISVGDGTLTILA 660

Query: 661 KNRSVMEKVLEKVDFIIGREIEVGGIYKGVVTSVKEYGAFVEFNGGQQGLLHVSELSHEP 720
           KN++VME V ++VDF +GREIE+GG YKGVV+SVKEYGAF+EFNGGQQGLLH+SELSH+P
Sbjct: 661 KNQAVMENVQDRVDFTLGREIEIGGTYKGVVSSVKEYGAFIEFNGGQQGLLHISELSHDP 720

Query: 721 VSRVSDVVSVGQQLSLRCIGQDVRGNIKLSLKAVSPRPEADVKGVVEGSVPVNKQATDVW 780
           VSRVSD+VSVGQ++SLRCIGQDV GNIKLSLKA+ P P+A  KG    SV     + +  
Sbjct: 721 VSRVSDIVSVGQKISLRCIGQDVHGNIKLSLKALLPVPKA--KGPNGNSV----SSLESL 774

Query: 781 ASVGDVSNGQNPELPMRKNETPGVN-------SSTSSTPAVLIRSAAECDEEEKASGFSQ 833
            SVG+V   Q P+     +  P V+       + TSS P+VLIRSA +CD EEK S  +Q
Sbjct: 775 PSVGEVYKTQ-PKTQNSTSNIPAVDKGVGSEVNPTSSVPSVLIRSAEDCDVEEKKSAVNQ 833

Query: 834 SSKSTLKSTLASKSNSKPKKFTSQSDFFSSTNIQKSTSFSQREREELAECLFGTEDGDED 893
            +K+T K    SKS+             +    +K+     R  + L +        D +
Sbjct: 834 ETKNTRKLKTTSKSDE------------NCDEEEKNLLLRNRNSKPLTQ-------NDVN 874

Query: 894 NKGTRVEAIVSAKNLKLGTKVAAKVYQVRARGLVLDLGGGIRGMYRFENNEKKDFVVGDE 953
           N    V+  ++  NL++GTKV AK+YQ+R  GLVLDLGGG+RGMYRFE + + ++ VGDE
Sbjct: 875 NNEVEVQDPLTPSNLRIGTKVKAKIYQIRLHGLVLDLGGGVRGMYRFEGDNQSNYKVGDE 934

Query: 954 LLVKCSSFTGKGIPVVSLVDS 974
           L V+CSSF+G+GIPV+SLV++
Sbjct: 935 LHVQCSSFSGRGIPVMSLVNN 955

Source: Cucumis sativus

Species: Cucumis sativus

Genus: Cucumis

Family: Cucurbitaceae

Order: Cucurbitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|296087634|emb|CBI34890.3| unnamed protein product [Vitis vinifera]

 Score = 1427 bits (3694), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 716/937 (76%), Positives = 785/937 (83%), Gaps = 52/937 (5%)

Query: 54  KVLETFKEEFEIGSRLITLETGKIARFANGAVVLGMDETKVLSTVTSSKGDSVRDFLPLT 113
           KVLETFKEEFEIGSR IT ETGKIARFANGAVV+ MDETKVLSTV SSKGD+ RDFLPLT
Sbjct: 2   KVLETFKEEFEIGSRSITFETGKIARFANGAVVMSMDETKVLSTVASSKGDAARDFLPLT 61

Query: 114 VDYQEKQFAQGVIPNTYMRREGAPKERELLVGRIIDRPIRPLFPAGFYHEVQVMASVLSS 173
           VDYQEK FAQGVIP T+MRREGAP+ERELL GR+IDRPIRPLFPAGFYHEVQVMASVLSS
Sbjct: 62  VDYQEKHFAQGVIPTTFMRREGAPRERELLCGRLIDRPIRPLFPAGFYHEVQVMASVLSS 121

Query: 174 DGKQDPDIMAANATSAALMLSDIPWGGPIGMIRIGRICGQFIVNPTMDELSLSDLNLVYA 233
           DGKQDPD+MAANATSAALMLSDIPWGGPIG+IRIGRICGQFIVNP+MDELSLSDLNLVYA
Sbjct: 122 DGKQDPDVMAANATSAALMLSDIPWGGPIGVIRIGRICGQFIVNPSMDELSLSDLNLVYA 181

Query: 234 CTREKTLMIDVQAREISEKDLEAGLRLAHPEAVKYLEPQIRLAEKAGKQKKEYKLSMISE 293
           CTR+KTLMIDVQAREISEKDLEA LRLAHPEAV+YLEPQIRLA +AGK KKEY LSM+S+
Sbjct: 182 CTRDKTLMIDVQAREISEKDLEAALRLAHPEAVRYLEPQIRLAARAGKSKKEYTLSMVSD 241

Query: 294 QTLEKVSNLAEAHIEAVFTDPSYSKFERGEALDKIGQDVKKALEEECDEESLQVLPKAVD 353
            T EKV NLAEA IEAVFTD +Y KFERGEALD I QDVK+ALEEECDEESL+VLPK VD
Sbjct: 242 ITFEKVRNLAEAPIEAVFTDHTYGKFERGEALDLITQDVKRALEEECDEESLKVLPKVVD 301

Query: 354 TVRKRVIRKRIIAEGVRVDGRQLDEVRPIYCESGNLPILHGSSLFSRGDTQVLCTVTLGA 413
           TVRK V+R+RIIAEG+RVDGR L+EVRP+YCESGNLPILHGSSLFSRGDTQVLCTVTLGA
Sbjct: 302 TVRKEVVRRRIIAEGLRVDGRHLNEVRPLYCESGNLPILHGSSLFSRGDTQVLCTVTLGA 361

Query: 414 PAEAQRLESLVGPPTKRFMLHYSFPPFCINEVGKRVGLNRREVGHGTLAEKALLAVLPPE 473
           P +AQRL+SLVGPPTKRFMLHYSFPPF INEVGKRVGLNRREVGHGTLAEKALLAVLPPE
Sbjct: 362 PGDAQRLDSLVGPPTKRFMLHYSFPPFSINEVGKRVGLNRREVGHGTLAEKALLAVLPPE 421

Query: 474 NDFPYTVRVNSEVMASDGSTSMATVCGGSMALMDAGIPLQEHVAGVSVGLVSEVDPSTGE 533
            +FPYTVR+NSEVMASDGSTSMATVCGGSMALMDAGIPL+EHVAG+SVGLV+EVDPST  
Sbjct: 422 EEFPYTVRINSEVMASDGSTSMATVCGGSMALMDAGIPLREHVAGISVGLVTEVDPSTNT 481

Query: 534 IKDYRILTDILGLEDHLGDMDFKIAGTRIGVTAIQLDIKPAGIPLDIICECLEHAHKGRL 593
           IKDYRILTDILGLEDHLGDMDFKIAGTR G+TAIQLDIKPAGIPLDIICECLE A +GRL
Sbjct: 482 IKDYRILTDILGLEDHLGDMDFKIAGTRKGITAIQLDIKPAGIPLDIICECLEPALRGRL 541

Query: 594 QILDHMEREISAPRTQDDRNSPRLATLKYDNDTLRRLIGPLGALKRKIEEETGGRISVSD 653
           QILD ME+EI+APRTQ  RNSPRLATLK+ ND+LRRL+GP+GALKRKIEEETG RISVSD
Sbjct: 542 QILDRMEQEINAPRTQHYRNSPRLATLKFSNDSLRRLLGPMGALKRKIEEETGARISVSD 601

Query: 654 GTLTVVAKNRSVMEKVLEKVDFIIGREIEVGGIYKGVVTSVKEYGAFVEFNGGQQGLLHV 713
           GTLTVVAKN+SVM+KV EKVDFI+GREIE+GGIYKGVVTSVKEYGAFVEFNGGQQGLLH+
Sbjct: 602 GTLTVVAKNQSVMDKVQEKVDFIVGREIEIGGIYKGVVTSVKEYGAFVEFNGGQQGLLHI 661

Query: 714 SELSHEPVSRVSDVVSVGQQLSLRCIGQDVRGNIKLSLKAVSPRPEADVKGVVEGSVPVN 773
           SELSHEPV RVSDVVS+GQQ+SL CIGQDVRGNIKLSLK+  PRP +D   VVEGS+P+ 
Sbjct: 662 SELSHEPVVRVSDVVSIGQQISLMCIGQDVRGNIKLSLKSTLPRPGSDTNNVVEGSIPIT 721

Query: 774 KQATDVWASVGDVSNGQNPELPMRKNETPGVNSSTSSTPAVLIRSAAECDEEEKASGFSQ 833
           KQA  VWAS+GDV                                    D EEK +   +
Sbjct: 722 KQAPSVWASIGDVP-----------------------------------DSEEKQNSDLE 746

Query: 834 SSKSTLKSTLASKSNSKPKKFTSQSDFF-SSTNIQKSTSFSQRERE--ELAECLFGTEDG 890
            S++T K    S SN K K    Q+    S+ N++KS   SQ+E++   +   L   EDG
Sbjct: 747 DSRNTSKPRSISGSNDKLKTSPPQNGMSDSAKNVKKSKISSQKEKDINSIFTILSMGEDG 806

Query: 891 DEDNKGTRV-------------EAIVSAKNLKLGTKVAAKVYQVRARGLVLDLGGGIRGM 937
           D+                    E    AKNLKLG K+ AKVYQ+R  GLVLDLGGGIRGM
Sbjct: 807 DKHGSAFNANSQNDLNDTKEVPETCTGAKNLKLGMKLNAKVYQIRTHGLVLDLGGGIRGM 866

Query: 938 YRFE-NNEKKDFVVGDELLVKCSSFTGKGIPVVSLVD 973
           YRFE +N+K+DF VGDEL V CSSF+ KGIPV+SLV+
Sbjct: 867 YRFEGDNDKRDFKVGDELHVMCSSFSTKGIPVMSLVE 903

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|449446674|ref|XP_004141096.1| PREDICTED: polyribonucleotide nucleotidyltransferase 2, mitochondrial-like [Cucumis sativus]

 Score = 1421 bits (3678), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 718/1046 (68%), Positives = 824/1046 (78%), Gaps = 86/1046 (8%)

Query: 1    MSSLATKTHPLLNNLPPFLTWRALGFRTICSGRLGFAPCEPAPPTPAPSVAGTKVLETFK 60
            M+S+ATK +PL + +P FLTWR+LGFRTIC GR+GF+        P  ++  TKVLETF+
Sbjct: 1    MASMATKANPLFSTIPHFLTWRSLGFRTICCGRMGFSSQSQQQVDPNTTLGRTKVLETFE 60

Query: 61   EEFEIGSRLITLETGKIARFANGAVVLGMDETKVLSTVTSSKGDSVRDFLPLTVDYQEKQ 120
            E FEIGSRL+ LETGKIARFANGA VLG++ETKVLSTV S+KGD+ RDFLPLTVDYQEKQ
Sbjct: 61   EVFEIGSRLVKLETGKIARFANGAAVLGIEETKVLSTVASAKGDAARDFLPLTVDYQEKQ 120

Query: 121  FAQGVIPNTYMRREGAPKERELLVGRIIDRPIRPLFPAGFYHEVQVMASVLSSDGKQDPD 180
            FAQGVIP T+ RREGAPKERELL GRIIDRPIRPLFPAGFYHEVQVMASVLSSDGKQDPD
Sbjct: 121  FAQGVIPGTFTRREGAPKERELLCGRIIDRPIRPLFPAGFYHEVQVMASVLSSDGKQDPD 180

Query: 181  IMAANATSAALMLSDIPWGGPIGMIRIGRICGQFIVNPTMDELSLSDLNLVYACTREKTL 240
            +MAANATSAALMLSDIPWGGPIG+IRIGRI GQF+VNPTMDEL+LSDLNL+YACTREKTL
Sbjct: 181  VMAANATSAALMLSDIPWGGPIGVIRIGRIDGQFVVNPTMDELNLSDLNLIYACTREKTL 240

Query: 241  MIDVQAREISEKDLEAGLRLAHPEAVKYLEPQIRLAEKAGKQKKEYKLSMISEQTLEKVS 300
            MIDVQAREI+EKDLEAGLRLAHPEAVK+LEPQIRLA KAGK KKEYKLSM+S+ TLEKV+
Sbjct: 241  MIDVQAREITEKDLEAGLRLAHPEAVKFLEPQIRLAAKAGKLKKEYKLSMVSDSTLEKVA 300

Query: 301  NLAEAHIEAVFTDPSYSKFERGEALDKIGQDVKKALEEECDEESLQVLPKAVDTVRKRVI 360
             LAE+ IEAVFTDPSY KFERGEAL+KI +DVKK  EEEC EE L+VLPKAVD VRK+V+
Sbjct: 301  KLAESPIEAVFTDPSYGKFERGEALEKITEDVKKVFEEECYEEGLKVLPKAVDYVRKKVV 360

Query: 361  RKRIIAEGVRVDGRQLDEVRPIYCESGNLPILHGSSLFSRGDTQVLCTVTLGAPAEAQRL 420
            R+RIIAEG R+DGR+LDEVRP+YCES  LPILHGSS+FSRGDTQVLCTVTLGAPA+AQ L
Sbjct: 361  RRRIIAEGRRLDGRRLDEVRPLYCESSYLPILHGSSIFSRGDTQVLCTVTLGAPADAQHL 420

Query: 421  ESLVGPPTKRFMLHYSFPPFCINEVGKRVGLNRREVGHGTLAEKALLAVLPPENDFPYTV 480
            +SLVGPPTKRFMLHYSFPPF INEVGKR GLNRREVGHGTLAEKALLAVLPPE++FPY V
Sbjct: 421  DSLVGPPTKRFMLHYSFPPFSINEVGKRGGLNRREVGHGTLAEKALLAVLPPESEFPYAV 480

Query: 481  RVNSEVMASDGSTSMATVCGGSMALMDAGIPLQEHVAGVSVGLVSEVDPSTGEIKDYRIL 540
            R+NSEVMASDGSTSMATVCGGSMALMDAG+PL EHVAGVSVGLVSE DPSTG IKDYRIL
Sbjct: 481  RINSEVMASDGSTSMATVCGGSMALMDAGVPLNEHVAGVSVGLVSETDPSTGAIKDYRIL 540

Query: 541  TDILGLEDHLGDMDFKIAGTRIGVTAIQLDIKPAGIPLDIICECLEHAHKGRLQILDHME 600
            TDILGLEDHLGDMDFKIAGTR GVTAIQLDIKPAGIPLDIICE LEHA KGR QILDHME
Sbjct: 541  TDILGLEDHLGDMDFKIAGTRKGVTAIQLDIKPAGIPLDIICESLEHARKGRWQILDHME 600

Query: 601  REISAPRTQDDRNSPRLATLKYDNDTLRRLIGPLGALKRKIEEETGGRISVSDGTLTVVA 660
            REI+APR +DD N PRL TLKY N+ LRRLIGPLG +K+KIE ETG RISV DGTLT++A
Sbjct: 601  REINAPRMKDDENCPRLVTLKYTNEALRRLIGPLGIVKKKIEAETGARISVGDGTLTILA 660

Query: 661  KNRSVMEKVLEKVDFIIGREIEVGGIYKGVVTSVKEYGAFVEFNGGQQGLLHVSELSHEP 720
            KN++VME V ++VDF +GREIE+GG YKGVV+SVKEYGAF+EFNGGQQGLLH+SELSH+P
Sbjct: 661  KNQAVMENVQDRVDFTLGREIEIGGTYKGVVSSVKEYGAFIEFNGGQQGLLHISELSHDP 720

Query: 721  VSRVSDVVSVGQQLSLRCIGQDVRGNIKLSLKAVSPRPEADVKGVVEGSVPVNKQATDVW 780
            VSRVSD+VSVGQ++SLRCIGQDV GNIKLSLKA+ P P+A  KG    SV     + +  
Sbjct: 721  VSRVSDIVSVGQKISLRCIGQDVHGNIKLSLKALLPVPKA--KGPNGNSV----SSLESL 774

Query: 781  ASVGDVSNGQNPELPMRKNETPGVN-------SSTSSTPAVLIRSAAECDEEEKASGF-- 831
             SVG+V   Q P+     +  P V+       + TSS P+VLIRSA +CD EEK S    
Sbjct: 775  PSVGEVYKTQ-PKTQNSTSNIPAVDKGVGSEVNPTSSVPSVLIRSAEDCDVEEKKSAVKN 833

Query: 832  -------------------------------SQSSKSTLKSTLASKSN----------SK 850
                                            Q +   LK+T  S  N           K
Sbjct: 834  LKLKNTQKLNNASTSDEDCDEEEKQSAVNNRKQKNTRKLKTTSKSDENCDEEEKKSAVKK 893

Query: 851  PKKFTSQSDFFSSTNIQ----------------------KSTSFSQREREELAECLFGTE 888
            PK+ T+Q    +ST+ +                       +TS S+ + + L +      
Sbjct: 894  PKRKTTQKQNTASTSAEDCNEEEKKSAVGNLKLKSTKKLNATSRSKGQSKPLTQ------ 947

Query: 889  DGDEDNKGTRVEAIVSAKNLKLGTKVAAKVYQVRARGLVLDLGGGIRGMYRFENNEKKDF 948
              D +N    V+  ++  NL++GTKV AK+YQ+R  GLVLDLGGG+RGMYRFE + + ++
Sbjct: 948  -NDVNNNEVEVQDPLTPSNLRIGTKVKAKIYQIRLHGLVLDLGGGVRGMYRFEGDNQSNY 1006

Query: 949  VVGDELLVKCSSFTGKGIPVVSLVDS 974
             VGDEL V+CSSF+G+GIPV+SLV++
Sbjct: 1007 KVGDELHVQCSSFSGRGIPVMSLVNN 1032

Source: Cucumis sativus

Species: Cucumis sativus

Genus: Cucumis

Family: Cucurbitaceae

Order: Cucurbitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|356573319|ref|XP_003554809.1| PREDICTED: polyribonucleotide nucleotidyltransferase-like [Glycine max]

 Score = 1368 bits (3540), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 711/999 (71%), Positives = 806/999 (80%), Gaps = 76/999 (7%)

Query: 7   KTHPLLNNLPPFLTWRALGFRTICSGRLGFAPCEPAPPTPAPSVAGTKVLETFKEEFEIG 66
           +T+ LL  LP FLTWRA  FRT                      A TK LETF E+FEIG
Sbjct: 3   RTNTLLRTLPHFLTWRAFRFRTF---------------------ATTKHLETFTEQFEIG 41

Query: 67  SRLITLETGKIARFANGAVVLGMDETKVLSTVTSSKG-DSVRDFLPLTVDYQEKQFAQGV 125
           S +ITLETGKIARFAN AVVL M+ T VLSTVT+SK  D+VRDFLPLTVDYQEKQFAQGV
Sbjct: 42  SSVITLETGKIARFANAAVVLAMENTNVLSTVTASKANDAVRDFLPLTVDYQEKQFAQGV 101

Query: 126 IPNTYMRREGAPKERELLVGRIIDRPIRPLFPAGFYHEVQVMASVLSSDGKQDPDIMAAN 185
           IP ++MRREGAP+ERELL GRIIDRPIRPLFP GFYHEVQVMASVLSSDGKQD D++AAN
Sbjct: 102 IPTSFMRREGAPRERELLCGRIIDRPIRPLFPPGFYHEVQVMASVLSSDGKQDTDVLAAN 161

Query: 186 ATSAALMLSDIPWGGPIGMIRIGRICGQFIVNPTMDELSLSDLNLVYACTREKTLMIDVQ 245
           ATSAALMLSDIPWGGPIGM+RIGRICGQFIVNPTMDEL LSDLNLVYACT++KTLMIDVQ
Sbjct: 162 ATSAALMLSDIPWGGPIGMVRIGRICGQFIVNPTMDELKLSDLNLVYACTKDKTLMIDVQ 221

Query: 246 AREISEKDLEAGLRLAHPEAVKYLEPQIRLAEKAGKQKKEYKLSMISEQTLEKVSNLAEA 305
           AREIS+KDLEAGLRLAHPEAVKY+EPQIRLA KAGK KKEYKLSM+S+ T+EKV N+AEA
Sbjct: 222 AREISDKDLEAGLRLAHPEAVKYIEPQIRLAAKAGKSKKEYKLSMLSDNTMEKVRNIAEA 281

Query: 306 HIEAVFTDPSYSKFERGEALDKIGQDVKKALEEECDEESLQVLPKAVDTVRKRVIRKRII 365
            IEAVFT+PSY KFERGEAL+ I QDVK+ LEEE DEESL+VL KAVDTVRK+V+RKRII
Sbjct: 282 PIEAVFTNPSYGKFERGEALENIAQDVKRVLEEEGDEESLKVLSKAVDTVRKKVVRKRII 341

Query: 366 AEGVRVDGRQLDEVRPIYCESGNLPILHGSSLFSRGDTQVLCTVTLGAPAEAQRLESLVG 425
           AEG R+DGRQLDEVRP+YCE+G + +LHGS+LFSRG+TQVLCTVTLGAP +AQRLES+VG
Sbjct: 342 AEGYRLDGRQLDEVRPLYCEAGYVSMLHGSALFSRGETQVLCTVTLGAPTDAQRLESVVG 401

Query: 426 PPTKRFMLHYSFPPFCINEVGKRVGLNRREVGHGTLAEKALLAVLPPENDFPYTVRVNSE 485
           PPTKRFMLHYSFPPFCINEVGKR GLNRREVGHGTLAEKALLAVLPPE+DFPYTVRVNSE
Sbjct: 402 PPTKRFMLHYSFPPFCINEVGKRGGLNRREVGHGTLAEKALLAVLPPEDDFPYTVRVNSE 461

Query: 486 VMASDGSTSMATVCGGSMALMDAGIPLQEHVAGVSVGLVSEVDPSTGEIKDYRILTDILG 545
           VMASDGSTSMATVCGGSMALMDAGIP++EHVAGVSVGLVSE+DPSTGEI DYRILTDILG
Sbjct: 462 VMASDGSTSMATVCGGSMALMDAGIPVREHVAGVSVGLVSELDPSTGEIADYRILTDILG 521

Query: 546 LEDHLGDMDFKIAGTRIGVTAIQLDIKPAGIPLDIICECLEHAHKGRLQILDHMEREISA 605
           LEDHLGD+DFKIAGTR GVTAIQLDIKPAGIPLDI+CECLE AHK RLQILDHME+EI+ 
Sbjct: 522 LEDHLGDIDFKIAGTRKGVTAIQLDIKPAGIPLDIVCECLEPAHKARLQILDHMEQEINV 581

Query: 606 PRTQDDRNSPRLATLKYDNDTLRRLIGPLGALKRKIEEETGGRISVSDGTLTVVAKNRSV 665
           PR ++D  SPRLATLKY+ND LRRLIGP+GALKRK+EEETG R+SV DGTLT+VAKN+SV
Sbjct: 582 PRNKNDSTSPRLATLKYNNDALRRLIGPMGALKRKMEEETGARMSVGDGTLTIVAKNQSV 641

Query: 666 MEKVLEKVDFIIGREIEVGGIYKGVVTSVKEYGAFVEFNGGQQGLLHVSELSHEPVSRVS 725
           M+K+LEK+DFI+GR+IEVGGIY G+VT++KEYGAFVEFNGGQQGLLH+SELSHEPVS+VS
Sbjct: 642 MDKILEKIDFIVGRQIEVGGIYTGIVTTIKEYGAFVEFNGGQQGLLHISELSHEPVSQVS 701

Query: 726 DVVSVGQQLSLRCIGQDVRGNIKLSLKAVSPRPEA-DVKGVVEGSVPVNKQATDVWASVG 784
           +VVSVGQ+LSL CIGQDV GNIKLSLKA SPRP   +    VE SV   K+  ++WA VG
Sbjct: 702 EVVSVGQKLSLMCIGQDVHGNIKLSLKATSPRPGGLETNDAVEESVASAKETANIWAPVG 761

Query: 785 DVSNGQNP----ELPMRKNETPGVNSSTSSTPAVLIRSAAECDEEE-------------- 826
           +VS+ Q      EL +   E     S TS  P +LIRSAAECDEEE              
Sbjct: 762 NVSSTQEQNSAHELSLGNLELGNAKSQTSQVPVILIRSAAECDEEEKSSSLNLSSKSPHV 821

Query: 827 --------KASGFSQSSKSTLKSTL-ASKSNSKP---KKFTSQSDFFSSTNIQKSTSFSQ 874
                   K+   SQ++KS     + A  S+S P   KK        S ++IQK    +Q
Sbjct: 822 DNGVQLDRKSKSRSQNAKSRRSQDVDAPSSHSGPLPYKKSKPSMQKESKSDIQKPKGDAQ 881

Query: 875 REREELAECLFGTEDGDEDNKGTRVEAIVSAKNLKLGTKVAAKVYQVRARGLVLDLGGGI 934
             +++                       V+A++LKLGT+V AKV Q+RA GLVLDLGGG+
Sbjct: 882 EPKDK-----------------------VTAEDLKLGTQVTAKVSQIRAHGLVLDLGGGL 918

Query: 935 RGMYRFENNEKKDFVVGDELLVKCSSFTGKGIPVVSLVD 973
           RGMYRFE N K+DF +GDE+ V CSSF+ KGIPV+S V+
Sbjct: 919 RGMYRFEENNKRDFKIGDEMRVVCSSFSSKGIPVLSFVN 957

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|297811589|ref|XP_002873678.1| hypothetical protein ARALYDRAFT_488299 [Arabidopsis lyrata subsp. lyrata] gi|297319515|gb|EFH49937.1| hypothetical protein ARALYDRAFT_488299 [Arabidopsis lyrata subsp. lyrata]

 Score = 1349 bits (3492), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 689/1009 (68%), Positives = 807/1009 (79%), Gaps = 58/1009 (5%)

Query: 1   MSSLATKTHPLLNNLPPFLTWRALGFRTICSGRLGFAPCEPAPPTPAPSVAGTKVLETFK 60
           MSS+  +      +LP FL WRALGFRTICSGRLGFAP  P     +P+ AGTK+LE+FK
Sbjct: 1   MSSIVNRARS--TSLPNFLAWRALGFRTICSGRLGFAPSNPD----SPASAGTKILESFK 54

Query: 61  EEFEIGSRLITLETGKIARFANGAVVLGMDETKVLSTVTSSKGDSVRDFLPLTVDYQEKQ 120
           EEFE+GSR+++ ETGKIARFANG+VVLGMD+TKVLSTVT +K DS RDFLPLTVDYQEKQ
Sbjct: 55  EEFEVGSRVVSFETGKIARFANGSVVLGMDQTKVLSTVTCAKTDSPRDFLPLTVDYQEKQ 114

Query: 121 FAQGVIPNTYMRREGAPKERELLVGRIIDRPIRPLFPAGFYHEVQVMASVLSSDGKQDPD 180
           +AQG+IPNTYMRREGAPKERELL GR+IDRPIRPLFP+GFYHEVQ+MASVLSSDGKQDPD
Sbjct: 115 YAQGLIPNTYMRREGAPKERELLCGRLIDRPIRPLFPSGFYHEVQIMASVLSSDGKQDPD 174

Query: 181 IMAANATSAALMLSDIPWGGPIGMIRIGRICGQFIVNPTMDELSLSDLNLVYACTREKTL 240
           I+AANA+SAALMLSD+PWGGPIG+IRIGRICGQF+VNPTMDELS SDLNL+YACTR+KT+
Sbjct: 175 ILAANASSAALMLSDVPWGGPIGVIRIGRICGQFVVNPTMDELSSSDLNLIYACTRDKTM 234

Query: 241 MIDVQAREISEKDLEAGLRLAHPEAVKYLEPQIRLAEKAGKQKKEYKLSMISEQTLEKVS 300
           MIDVQ+REISEKDL A LRLAHPEA+KYL+PQIRLAEKAGKQKKEYKLSM+SE+TLEKV+
Sbjct: 235 MIDVQSREISEKDLAAALRLAHPEAIKYLDPQIRLAEKAGKQKKEYKLSMLSEKTLEKVT 294

Query: 301 NLAEAHIEAVFTDPSYSKFERGEALDKIGQDVKKALEEECDEESLQVLPKAVDTVRKRVI 360
           +LA   IE+VFTDPSY KFERGEALD IG+DV+K  EEE D+ESL +LPKAVDTVRK+V+
Sbjct: 295 DLAATRIESVFTDPSYGKFERGEALDNIGKDVRKVFEEEGDQESLSILPKAVDTVRKKVV 354

Query: 361 RKRIIAEGVRVDGRQLDEVRPIYCESGNLPILHGSSLFSRGDTQVLCTVTLGAPAEAQRL 420
           R R+I++G RVDGR LDEVRPIYCES  LP LHGS+LFSRGDTQVLCTVTLGAP EAQ L
Sbjct: 355 RSRMISDGFRVDGRHLDEVRPIYCESHYLPALHGSALFSRGDTQVLCTVTLGAPGEAQSL 414

Query: 421 ESLVGPPTKRFMLHYSFPPFCINEVGKRVGLNRREVGHGTLAEKALLAVLPPENDFPYTV 480
           +SLVGPP KRFMLHYSFPP+C NEVGKR GLNRREVGHGTLAEKALLAVLPPE  FPYTV
Sbjct: 415 DSLVGPPKKRFMLHYSFPPYCTNEVGKRGGLNRREVGHGTLAEKALLAVLPPEEAFPYTV 474

Query: 481 RVNSEVMASDGSTSMATVCGGSMALMDAGIPLQEHVAGVSVGLVSEVDPSTGEIKDYRIL 540
           R+NSEVM+SDGSTSMA+VCGGSMALMDAGIPL+ HVAGVSVGL+++VDPS+GEIKDYRI+
Sbjct: 475 RINSEVMSSDGSTSMASVCGGSMALMDAGIPLRAHVAGVSVGLITDVDPSSGEIKDYRIV 534

Query: 541 TDILGLEDHLGDMDFKIAGTRIGVTAIQLDIKPAGIPLDIICECLEHAHKGRLQILDHME 600
           TDILGLEDHLGDMDFKIAGTR GVTAIQLDIKPAGIPLDI+CE LE+A + RLQILDHME
Sbjct: 535 TDILGLEDHLGDMDFKIAGTRNGVTAIQLDIKPAGIPLDIVCESLENAREARLQILDHME 594

Query: 601 REISAPRTQDDRNSPRLATLKYDNDTLRRLIGPLGALKRKIEEETGGRISVSDGTLTVVA 660
           R I++PR QD   SPRLAT KY ND+LR LIGP+G LKRKIEEETG R+S+ +GTLT+VA
Sbjct: 595 RNINSPRAQDGAYSPRLATFKYTNDSLRSLIGPMGVLKRKIEEETGARLSIDNGTLTIVA 654

Query: 661 KNRSVMEKVLEKVDFIIGREIEVGGIYKGVVTSVKEYGAFVEFNGGQQGLLHVSELSHEP 720
           KN+ VMEK  EKVDFIIGREI VGG+YKG VTS+KEYGAFVEF+GGQQGLLH+SELSHEP
Sbjct: 655 KNQDVMEKAQEKVDFIIGREIVVGGVYKGTVTSIKEYGAFVEFSGGQQGLLHMSELSHEP 714

Query: 721 VSRVSDVVSVGQQLSLRCIGQDVRGNIKLSLKAVSPRPE------ADVKGVVEGSVPVNK 774
           VS+VSDV+ +GQ ++  CI  DVRGNIKLS KA+ P+PE      A    V++ S  V  
Sbjct: 715 VSKVSDVLHIGQYITTMCIETDVRGNIKLSRKAMLPKPERKPASDAGKDSVMKESSTVYT 774

Query: 775 QATDVWASVGDVSNGQNPELPMRKNETPGVNSSTSSTPAVLIRSAAECDEEEKASGFSQS 834
           + + V  +V  + +   P  P +         S  S PAV+IR+A EC E EK+S  +++
Sbjct: 775 ETSSVGETVASMPSIVTP--PQK---------SKLSVPAVVIRTAVECHEAEKSSPVNKN 823

Query: 835 SKSTLKSTLASKSNSKPKKFTSQSDFFSSTNIQKSTSFSQREREELAECLFG-TEDG--- 890
            K   K     K + KPK   S+    ++T  ++    S    E  AEC     +DG   
Sbjct: 824 DKP--KRATTPKPDRKPKSTASK---LTATQKEEEVLESIAPEETPAECGETLKQDGKLK 878

Query: 891 ----------------DEDNKGTRVE----------AIVSAKNLKLGTKVAAKVYQVRAR 924
                            +  K TR E          A VS +NLK+GT++ AKV+++RAR
Sbjct: 879 SASPKNSSTDSNLVSSSKAKKSTRKENQSENKAEESAFVSTRNLKIGTEMTAKVHEIRAR 938

Query: 925 GLVLDLGGGIRGMYRFENNEKKDFVVGDELLVKCSSFTGKGIPVVSLVD 973
           GLVLDLGG +RGMY+F+ +E+ +F  GD L VKC+SF+ KGIPV++LVD
Sbjct: 939 GLVLDLGGELRGMYKFKEDEETEFEEGDTLQVKCTSFSTKGIPVMALVD 987

Source: Arabidopsis lyrata subsp. lyrata

Species: Arabidopsis lyrata

Genus: Arabidopsis

Family: Brassicaceae

Order: Brassicales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|15241441|ref|NP_196962.1| polyribonucleotide nucleotidyltransferase [Arabidopsis thaliana] gi|75336830|sp|Q9S7G6.1|PNP2_ARATH RecName: Full=Polyribonucleotide nucleotidyltransferase 2, mitochondrial; Short=AtmtPNPase; AltName: Full=Polynucleotide phosphorylase 2; Short=PNPase 2; Flags: Precursor gi|4971998|emb|CAB43864.1| polynucleotide phosphorylase [Arabidopsis thaliana] gi|4972000|emb|CAB43865.1| polynucleotide phosphorylase [Arabidopsis thaliana] gi|7573307|emb|CAB87625.1| polynucleotide phosphorylase [Arabidopsis thaliana] gi|332004667|gb|AED92050.1| polyribonucleotide nucleotidyltransferase [Arabidopsis thaliana]

 Score = 1335 bits (3454), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 684/1011 (67%), Positives = 804/1011 (79%), Gaps = 63/1011 (6%)

Query: 1   MSSLATKTHPLLNNLPPFLTWRALGFRTICSGRLGFAPCEPAPPTPAPSVAGTKVLETFK 60
           MSS+  +      +LP FL WRALGFRTICSGRLGFAP  P     +P  AGTK+LE+FK
Sbjct: 1   MSSIVNRASSA--SLPNFLAWRALGFRTICSGRLGFAPSVPD----SPVSAGTKILESFK 54

Query: 61  EEFEIGSRLITLETGKIARFANGAVVLGMDETKVLSTVTSSKGDSVRDFLPLTVDYQEKQ 120
           EEFE+GSR+++ ETGKIARFANG+VVLGMDETKVLSTVT +K DS RDFLPLTVDYQEKQ
Sbjct: 55  EEFEVGSRVVSFETGKIARFANGSVVLGMDETKVLSTVTCAKTDSPRDFLPLTVDYQEKQ 114

Query: 121 FAQGVIPNTYMRREGAPKERELLVGRIIDRPIRPLFPAGFYHEVQVMASVLSSDGKQDPD 180
           +AQG+IPNTYMRREGAPKERELL GR+IDRPIRPLFP GFYHEVQ+MASVLSSDGKQDPD
Sbjct: 115 YAQGLIPNTYMRREGAPKERELLCGRLIDRPIRPLFPTGFYHEVQIMASVLSSDGKQDPD 174

Query: 181 IMAANATSAALMLSDIPWGGPIGMIRIGRICGQFIVNPTMDELSLSDLNLVYACTREKTL 240
           I+AANA+SAALMLSD+PWGGPIG+IRIGRICGQF+VNPTMDELS SDLNL+YACTR+KT+
Sbjct: 175 ILAANASSAALMLSDVPWGGPIGVIRIGRICGQFVVNPTMDELSSSDLNLIYACTRDKTM 234

Query: 241 MIDVQAREISEKDLEAGLRLAHPEAVKYLEPQIRLAEKAGKQKKEYKLSMISEQTLEKVS 300
           MIDVQ+REISEKDL A LRLAHPEAVKYL+PQIRLAEKAGKQKKEYKLSM+S++TLEKV+
Sbjct: 235 MIDVQSREISEKDLAAALRLAHPEAVKYLDPQIRLAEKAGKQKKEYKLSMLSDKTLEKVA 294

Query: 301 NLAEAHIEAVFTDPSYSKFERGEALDKIGQDVKKALEEECDEESLQVLPKAVDTVRKRVI 360
           +LA   IE+VFTDPSY KFERGEALD IG+DV+K  EEE D+ESL +LPKAVDTVRK+V+
Sbjct: 295 DLAATRIESVFTDPSYGKFERGEALDNIGKDVRKVFEEEGDQESLSILPKAVDTVRKKVV 354

Query: 361 RKRIIAEGVRVDGRQLDEVRPIYCESGNLPILHGSSLFSRGDTQVLCTVTLGAPAEAQRL 420
           R R+I++G RVDGR +DEVRPIYCES  LP LHGS+LFSRGDTQVLCTVTLGAPAEAQ L
Sbjct: 355 RSRMISDGFRVDGRHVDEVRPIYCESHYLPALHGSALFSRGDTQVLCTVTLGAPAEAQSL 414

Query: 421 ESLVGPPTKRFMLHYSFPPFCINEVGKRVGLNRREVGHGTLAEKALLAVLPPENDFPYTV 480
           +SLVGPP KRFMLHYSFPP+C NEVGKR GLNRREVGHGTLAEKALLAVLPPE  FPYT+
Sbjct: 415 DSLVGPPKKRFMLHYSFPPYCTNEVGKRGGLNRREVGHGTLAEKALLAVLPPEEAFPYTI 474

Query: 481 RVNSEVMASDGSTSMATVCGGSMALMDAGIPLQEHVAGVSVGLVSEVDPSTGEIKDYRIL 540
           R+NSEVM+SDGSTSMA+VCGGSMALMDAGIPL+ HVAGVSVGL+++VDPS+GEIKDYRI+
Sbjct: 475 RINSEVMSSDGSTSMASVCGGSMALMDAGIPLRAHVAGVSVGLITDVDPSSGEIKDYRIV 534

Query: 541 TDILGLEDHLGDMDFKIAGTRIGVTAIQLDIKPAGIPLDIICECLEHAHKGRLQILDHME 600
           TDILGLEDHLGDMDFKIAGTR GVTAIQLDIKPAGIPLDI+CE LE+A + RLQILDHME
Sbjct: 535 TDILGLEDHLGDMDFKIAGTRDGVTAIQLDIKPAGIPLDIVCESLENAREARLQILDHME 594

Query: 601 REISAPRTQDDRNSPRLATLKYDNDTLRRLIGPLGALKRKIEEETGGRISVSDGTLTVVA 660
           R I++PR QD   SPRLATLKY ND+LR LIGP+G LKRKIE ETG R+S+ +GTLT+VA
Sbjct: 595 RNINSPRGQDGAYSPRLATLKYSNDSLRTLIGPMGVLKRKIEVETGARLSIDNGTLTIVA 654

Query: 661 KNRSVMEKVLEKVDFIIGREIEVGGIYKGVVTSVKEYGAFVEFNGGQQGLLHVSELSHEP 720
           KN+ VMEK  E+VDFIIGRE+ VGG+YKG V+S+KEYGAFVEF GGQQGLLH+SELSHEP
Sbjct: 655 KNQDVMEKAQEQVDFIIGRELVVGGVYKGTVSSIKEYGAFVEFPGGQQGLLHMSELSHEP 714

Query: 721 VSRVSDVVSVGQQLSLRCIGQDVRGNIKLSLKAVSPRPEADVKGVVEGSVPVNKQATDVW 780
           VS+VSDV+ +GQ ++  CI  DVRGNIKLS KA+ P+P+        G  PV K+++ V+
Sbjct: 715 VSKVSDVLDIGQCITTMCIETDVRGNIKLSRKALLPKPKRKPASDA-GKDPVMKESSTVY 773

Query: 781 ---ASVGDVSNGQNPELPMRKNETPGVNSSTSSTPAVLIRSAAECDEEEKASGFSQSSKS 837
              +SVG++         M    TP +  S  S PAV+IR+A EC+E EK+S  + + K 
Sbjct: 774 IENSSVGEIVAS------MPSIVTP-LQKSRLSVPAVVIRTAVECNEAEKSSPVNDNDKP 826

Query: 838 TLKSTLASKSNSKPKKFTS-----------------------------QSDFFSSTNIQK 868
              +T  SK + KPK   S                             Q     S + + 
Sbjct: 827 RRAAT--SKPDRKPKSTASKLIATQKEEEALESIAPEETSAECGEILKQDGKLKSVSPKN 884

Query: 869 ST------SFSQREREELAECLFGTEDGDEDNKGTRVEAIVSAKNLKLGTKVAAKVYQVR 922
           ++      SFS+ ++  + E L  +E+  E++      A VS + LK+GT++ A V  VR
Sbjct: 885 NSTASNLVSFSKAKKSTMKENL--SENKAEES------ASVSTRKLKIGTEMTATVDHVR 936

Query: 923 ARGLVLDLGGGIRGMYRFENNEKKDFVVGDELLVKCSSFTGKGIPVVSLVD 973
           A GLVLDLGG IRGMY F+ ++ K F  GD L VKC+SF  KG+PV++LVD
Sbjct: 937 ALGLVLDLGGEIRGMYIFQGDKDK-FKKGDTLRVKCTSFNTKGVPVMALVD 986

Source: Arabidopsis thaliana

Species: Arabidopsis thaliana

Genus: Arabidopsis

Family: Brassicaceae

Order: Brassicales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|357150173|ref|XP_003575367.1| PREDICTED: LOW QUALITY PROTEIN: polyribonucleotide nucleotidyltransferase-like [Brachypodium distachyon]

 Score = 1249 bits (3232), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 627/950 (66%), Positives = 763/950 (80%), Gaps = 29/950 (3%)

Query: 42  APPTPAPSVAGTKVLETFKEEFEIGSRLITLETGKIARFANGAVVLGMDETKVLSTVTSS 101
           APP P     G KVLE+F+EEFEIG RLI  ETGKIARFANG+VV+ MD+T VLSTV +S
Sbjct: 45  APPPP-----GRKVLESFREEFEIGGRLIAFETGKIARFANGSVVISMDDTHVLSTVAAS 99

Query: 102 KG-DSVRDFLPLTVDYQEKQFAQGVIPNTYMRREGAPKERELLVGRIIDRPIRPLFPAGF 160
           K  D VRDFLPLTVDYQEKQ+AQGVIP TYMRREGAPKERELL GRIIDRPIRPLFP GF
Sbjct: 100 KSSDPVRDFLPLTVDYQEKQYAQGVIPTTYMRREGAPKERELLCGRIIDRPIRPLFPRGF 159

Query: 161 YHEVQV-------MASVLSSDGKQDPDIMAANATSAALMLSDIPWGGPIGMIRIGRICGQ 213
           YHEVQV         +V+SSDGKQDPD+MAANA+SAALMLSDIPW GPIG+IR+GRI G 
Sbjct: 160 YHEVQVCTLLFXITTNVISSDGKQDPDVMAANASSAALMLSDIPWNGPIGVIRVGRIDGN 219

Query: 214 FIVNPTMDELSLSDLNLVYACTREKTLMIDVQAREISEKDLEAGLRLAHPEAVKYLEPQI 273
           F++NPT+DEL LSDLNL+YAC+R+KTLMIDVQAREI+E+DL+AG++LAH EAVKY++PQI
Sbjct: 220 FVLNPTVDELGLSDLNLIYACSRDKTLMIDVQAREITERDLQAGMKLAHSEAVKYIDPQI 279

Query: 274 RLAEKAGKQKKEYKLSMISEQTLEKVSNLAEAHIEAVFTDPSYSKFERGEALDKIGQDVK 333
           RLA++AGK+K+EYKLSMIS+ + EK+  L+EA IE VFTD +Y KFERGEAL+KI Q VK
Sbjct: 280 RLAKRAGKEKREYKLSMISDGSYEKIRTLSEAPIEEVFTDKTYGKFERGEALEKITQSVK 339

Query: 334 KALEEECDEESLQVLPKAVDTVRKRVIRKRIIAEGVRVDGRQLDEVRPIYCESGNLPILH 393
             LE+ECDEESL+ L KAVDTVRK+VIRKRII EG+R+DGRQLDEVRP+YCES   PILH
Sbjct: 340 LKLEDECDEESLKFLSKAVDTVRKQVIRKRIIKEGLRLDGRQLDEVRPLYCESSTYPILH 399

Query: 394 GSSLFSRGDTQVLCTVTLGAPAEAQRLESLVGPPTKRFMLHYSFPPFCINEVGKRVGLNR 453
           GS+LFSRGDTQVLCTVTLGAP +AQRL+S+VGPP+KRFMLHYSFPPF INEV KR GLNR
Sbjct: 400 GSALFSRGDTQVLCTVTLGAPGDAQRLDSIVGPPSKRFMLHYSFPPFSINEVAKRGGLNR 459

Query: 454 REVGHGTLAEKALLAVLPPENDFPYTVRVNSEVMASDGSTSMATVCGGSMALMDAGIPLQ 513
           REVGHGTLAEKALLAVLPPE DFPYTVR+NSEVMASDGSTSMA+VCGGSMALMDAGIP++
Sbjct: 460 REVGHGTLAEKALLAVLPPEGDFPYTVRINSEVMASDGSTSMASVCGGSMALMDAGIPVR 519

Query: 514 EHVAGVSVGLVSEVDPSTGEIKDYRILTDILGLEDHLGDMDFKIAGTRIGVTAIQLDIKP 573
           EHVAGVSVGLVSEVDP TG+I  YRILTDILGLEDHLGDMDFKIAGTR G+TAIQLDIKP
Sbjct: 520 EHVAGVSVGLVSEVDPMTGDISTYRILTDILGLEDHLGDMDFKIAGTRKGITAIQLDIKP 579

Query: 574 AGIPLDIICECLEHAHKGRLQILDHMEREISAPRTQDDRNSPRLATLKYDNDTLRRLIGP 633
           AGIPLDI+CE LE A K R QILD M++EIS+ R  +D ++PRLATL + +D+LR+L+  
Sbjct: 580 AGIPLDIVCESLEPARKARNQILDRMDQEISSARAINDGSAPRLATLSFSSDSLRKLL-- 637

Query: 634 LGALKRKIEEETGGRISVSDGTLTVVAKNRSVMEKVLEKVDFIIGREIEVGGIYKGVVTS 693
               ++KIE+ETG R+SVSDGT+T+VAK ++VM+K LEKV+F++GREIEVG  YKG+V+S
Sbjct: 638 --FHRKKIEQETGARVSVSDGTVTIVAKTQAVMDKALEKVEFLVGREIEVGKTYKGIVSS 695

Query: 694 VKEYGAFVEFNGGQQGLLHVSELSHEPVSRVSDVVSVGQQLSLRCIGQDVRGNIKLSLKA 753
           +KEYGAFV+FNGGQQGLLH+SELSHEPVS+VSD+V+VGQ LSL CIGQDVRGNIKLSLKA
Sbjct: 696 IKEYGAFVDFNGGQQGLLHISELSHEPVSKVSDIVTVGQVLSLTCIGQDVRGNIKLSLKA 755

Query: 754 VSPRPEADVKGVVEGSVPVNKQATDVWASVGDV-SNGQNPELPMRKNETPGVNSSTS-ST 811
             P P    K   E + P   Q    WA+V ++ S     E P  K+E   +  + S ST
Sbjct: 756 TLPHPPKK-KSASEDTTPSPSQNVIGWAAVDNMPSKDPGVEPPNSKDEDVTIEDTPSFST 814

Query: 812 PAVLIRSAAECDEEEKASGFSQSSKSTLKSTLASKSNSKPKKFTSQSDFFSSTNIQKSTS 871
           P+V+IRSA +CD ++ A+G ++  +S + S+  +KS+ +  K   +     +   +K++S
Sbjct: 815 PSVIIRSAVDCDAQDDANGPAK-KRSKVASSKVAKSSPRVYKQAKEQQEVRTVAAKKASS 873

Query: 872 FSQREREELAECLFGTEDG-----DEDNKGTRVEAIVS---AKNLKLGTKVAAKVYQVRA 923
            S  ++ +  +      +G     + D   T   +++    + ++KLG  V AKVYQ+RA
Sbjct: 874 TSSVKKNKKVKADDSGSNGLDNIPELDISNTLKSSVLKNFRSGSMKLGDVVTAKVYQIRA 933

Query: 924 RGLVLDLGGGIRGMYRFENNEKKDFVVGDELLVKCSSFTGKGIPVVSLVD 973
            GLVL+L  G+RGM++F  + +K+F +G+ELLVKC+SF  KG+PV SL+D
Sbjct: 934 YGLVLELSDGVRGMHKFVESSRKNFEIGEELLVKCASFNAKGVPVFSLLD 983

Source: Brachypodium distachyon

Species: Brachypodium distachyon

Genus: Brachypodium

Family: Poaceae

Order: Poales

Class: Liliopsida

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	974
TAIR|locus:2222662	991	AT5G14580 "AT5G14580" [Arabido	0.836	0.822	0.717	0.0
UNIPROTKB|P50849	705	pnp "Polyribonucleotide nucleo	0.702	0.970	0.415	8.2e-138
TIGR_CMR|CHY_1758	731	CHY_1758 "polyribonucleotide n	0.714	0.952	0.417	1.2e-136
TIGR_CMR|GSU_1593	697	GSU_1593 "polyribonucleotide n	0.699	0.977	0.419	4e-136
UNIPROTKB|Q0BWM9	713	pnp "Polyribonucleotide nucleo	0.694	0.948	0.42	6e-135
UNIPROTKB|P05055	711	pnp "polynucleotide phosphoryl	0.708	0.970	0.401	4.8e-133
TIGR_CMR|BA_3944	712	BA_3944 "polyribonucleotide nu	0.699	0.956	0.402	2.7e-132
TIGR_CMR|SO_1209	699	SO_1209 "polyribonucleotide nu	0.708	0.987	0.391	5.7e-130
UNIPROTKB|Q8TCS8	783	PNPT1 "Polyribonucleotide nucl	0.731	0.909	0.378	1.4e-128
UNIPROTKB|Q5RCW2	783	PNPT1 "Polyribonucleotide nucl	0.731	0.909	0.376	7.6e-128

TAIR|locus:2222662 AT5G14580 "AT5G14580" [Arabidopsis thaliana (taxid:3702)]

 Score = 3002 (1061.8 bits), Expect = 0., Sum P(2) = 0.
 Identities = 597/832 (71%), Positives = 685/832 (82%)

Query:     1 MSSLATKTHPLLNNLPPFLTWRALGFRTICSGRLGFXXXXXXXXXXXXXXXGTKVLETFK 60
             MSS+  +      +LP FL WRALGFRTICSGRLGF               GTK+LE+FK
Sbjct:     1 MSSIVNRASSA--SLPNFLAWRALGFRTICSGRLGFAPSVPDSPVSA----GTKILESFK 54

Query:    61 EEFEIGSRLITLETGKIARFANGAVVLGMDETKVLSTVTSSKGDSVRDFLPLTVDYQEKQ 120
             EEFE+GSR+++ ETGKIARFANG+VVLGMDETKVLSTVT +K DS RDFLPLTVDYQEKQ
Sbjct:    55 EEFEVGSRVVSFETGKIARFANGSVVLGMDETKVLSTVTCAKTDSPRDFLPLTVDYQEKQ 114

Query:   121 FAQGVIPNTYMRREGAPKERELLVGRIIDRPIRPLFPAGFYHEVQVMASVLSSDGKQDPD 180
             +AQG+IPNTYMRREGAPKERELL GR+IDRPIRPLFP GFYHEVQ+MASVLSSDGKQDPD
Sbjct:   115 YAQGLIPNTYMRREGAPKERELLCGRLIDRPIRPLFPTGFYHEVQIMASVLSSDGKQDPD 174

Query:   181 IMAANATSAALMLSDXXXXXXXXXXXXXXXXXQFIVNPTMDELSLSDLNLVYACTREKTL 240
             I+AANA+SAALMLSD                 QF+VNPTMDELS SDLNL+YACTR+KT+
Sbjct:   175 ILAANASSAALMLSDVPWGGPIGVIRIGRICGQFVVNPTMDELSSSDLNLIYACTRDKTM 234

Query:   241 MIDVQAREISEKDLEAGLRLAHPEAVKYLEPQIRLAEKAGKQKKEYKLSMISEQTLEKVS 300
             MIDVQ+REISEKDL A LRLAHPEAVKYL+PQIRLAEKAGKQKKEYKLSM+S++TLEKV+
Sbjct:   235 MIDVQSREISEKDLAAALRLAHPEAVKYLDPQIRLAEKAGKQKKEYKLSMLSDKTLEKVA 294

Query:   301 NLAEAHIEAVFTDPSYSKFERGEALDKIGQDVKKALEEECDEESLQVLPKAVDTXXXXXX 360
             +LA   IE+VFTDPSY KFERGEALD IG+DV+K  EEE D+ESL +LPKAVDT      
Sbjct:   295 DLAATRIESVFTDPSYGKFERGEALDNIGKDVRKVFEEEGDQESLSILPKAVDTVRKKVV 354

Query:   361 XXXXXAEGVRVDGRQLDEVRPIYCESGNLPILHGSSLFSRGDTQVLCTVTLGAPAEAQRL 420
                  ++G RVDGR +DEVRPIYCES  LP LHGS+LFSRGDTQVLCTVTLGAPAEAQ L
Sbjct:   355 RSRMISDGFRVDGRHVDEVRPIYCESHYLPALHGSALFSRGDTQVLCTVTLGAPAEAQSL 414

Query:   421 ESLVGPPTKRFMLHYSFPPFCINEVGKRVGLNRREVGHGTLAEKALLAVLPPENDFPYTV 480
             +SLVGPP KRFMLHYSFPP+C NEVGKR GLNRREVGHGTLAEKALLAVLPPE  FPYT+
Sbjct:   415 DSLVGPPKKRFMLHYSFPPYCTNEVGKRGGLNRREVGHGTLAEKALLAVLPPEEAFPYTI 474

Query:   481 RVNSEVMASDGSTSMATVCGGSMALMDAGIPLQEHVAGVSVGLVSEVDPSTGEIKDYRIL 540
             R+NSEVM+SDGSTSMA+VCGGSMALMDAGIPL+ HVAGVSVGL+++VDPS+GEIKDYRI+
Sbjct:   475 RINSEVMSSDGSTSMASVCGGSMALMDAGIPLRAHVAGVSVGLITDVDPSSGEIKDYRIV 534

Query:   541 TDILGLEDHLGDMDFKIAGTRIGVTAIQLDIKPAGIPLDIICECLEHAHKGRLQILDHME 600
             TDILGLEDHLGDMDFKIAGTR GVTAIQLDIKPAGIPLDI+CE LE+A + RLQILDHME
Sbjct:   535 TDILGLEDHLGDMDFKIAGTRDGVTAIQLDIKPAGIPLDIVCESLENAREARLQILDHME 594

Query:   601 REISAPRTQDDRNSPRLATLKYDNDTLRRLIGPLGALKRKIEEETGGRISVSDGTLTVVA 660
             R I++PR QD   SPRLATLKY ND+LR LIGP+G LKRKIE ETG R+S+ +GTLT+VA
Sbjct:   595 RNINSPRGQDGAYSPRLATLKYSNDSLRTLIGPMGVLKRKIEVETGARLSIDNGTLTIVA 654

Query:   661 KNRSVMEKVLEKVDFIIGREIEVGGIYKGVVTSVKEYGAFVEFNGGQQGLLHVSELSHEP 720
             KN+ VMEK  E+VDFIIGRE+ VGG+YKG V+S+KEYGAFVEF GGQQGLLH+SELSHEP
Sbjct:   655 KNQDVMEKAQEQVDFIIGRELVVGGVYKGTVSSIKEYGAFVEFPGGQQGLLHMSELSHEP 714

Query:   721 VSRVSDVVSVGQQLSLRCIGQDVRGNIKLSLKAVSPRPEADVKGVVEGSVPVNKQATDVW 780
             VS+VSDV+ +GQ ++  CI  DVRGNIKLS KA+ P+P+        G  PV K+++ V+
Sbjct:   715 VSKVSDVLDIGQCITTMCIETDVRGNIKLSRKALLPKPKRKPASDA-GKDPVMKESSTVY 773

Query:   781 ---ASVGDVSNGQNPELPMRKNETPGVNSSTSSTPAVLIRSAAECDEEEKAS 829
                +SVG++     P +      TP +  S  S PAV+IR+A EC+E EK+S
Sbjct:   774 IENSSVGEIVASM-PSIV-----TP-LQKSRLSVPAVVIRTAVECNEAEKSS 818

GO:0000175 "3'-5'-exoribonuclease activity" evidence=IGI;ISS

GO:0003676 "nucleic acid binding" evidence=ISS

GO:0003723 "RNA binding" evidence=ISS

GO:0005739 "mitochondrion" evidence=ISM

GO:0000957 "mitochondrial RNA catabolic process" evidence=IGI

GO:0000963 "mitochondrial RNA processing" evidence=IGI

GO:0004654 "polyribonucleotide nucleotidyltransferase activity" evidence=IGI

GO:0042991 "transcription factor import into nucleus" evidence=RCA

UNIPROTKB|P50849 pnp "Polyribonucleotide nucleotidyltransferase" [Bacillus subtilis subsp. subtilis str. 168 (taxid:224308)]

 Score = 1333 (474.3 bits), Expect = 8.2e-138, Sum P(2) = 8.2e-138
 Identities = 291/700 (41%), Positives = 430/700 (61%)

Query:    60 KEEFEI--GSRLITLETGKIARFANGAVVLGMDETKVLSTVTSSKGDSVRDFLPLTVDYQ 117
             K  F I    R +T+ETG++A+ ANGAV++   +T VLST T+SK     DF PLTV+Y+
Sbjct:     5 KHVFTIDWAGRTLTVETGQLAKQANGAVMIRYGDTAVLSTATASKEPKPLDFFPLTVNYE 64

Query:   118 EKQFAQGVIPNTYMRREGAPKERELLVGRIIDRPIRPLFPAGFYHEVQVMASVLSSDGKQ 177
             E+ +A G IP  +++REG P E+ +L  R+IDRPIRPLF  GF +EVQV++ V+S D   
Sbjct:    65 ERLYAVGKIPGGFIKREGRPSEKAVLASRLIDRPIRPLFADGFRNEVQVISIVMSVDQNC 124

Query:   178 DPDIMAANATSAALMLSDXXXXXXXXXXXXXXXXXQFIVNPTMDELSLSDLNLVYACTRE 237
               ++ A   +S AL +SD                 QFI+NPT+D+L  SD+NLV A T++
Sbjct:   125 SSEMAAMFGSSLALSVSDIPFEGPIAGVTVGRIDDQFIINPTVDQLEKSDINLVVAGTKD 184

Query:   238 KTLMIDVQAREISEKDLEAGLRLAHPEAVKYLEPQIRLAEKAGKQKKEYKLSMISEQTLE 297
                M++  A E+ E+ +   +   H E  + +  Q  +    GK+K E KL  I E+  E
Sbjct:   185 AINMVEAGADEVPEEIMLEAIMFGHEEIKRLIAFQEEIVAAVGKEKSEIKLFEIDEELNE 244

Query:   298 KVSNLAEAHI-EAVFTDPSYSKFERGEALDKIGQDVKKALE-EECDEESLQVLPKAVDTX 355
             KV  LAE  + +A+     + K  R +A++++   V    E EE DE++++ + + +   
Sbjct:   245 KVKALAEEDLLKAIQV---HEKHAREDAINEVKNAVVAKFEDEEHDEDTIKQVKQILSKL 301

Query:   356 XXXXXXXXXXAEGVRVDGRQLDEVRPIYCESGNLPILHGSSLFSRGDTQVLCTVTLGAPA 415
                        E VR DGR +D++RP+  E G LP  HGS LF+RG TQ L   TLGA  
Sbjct:   302 VKNEVRRLITEEKVRPDGRGVDQIRPLSSEVGLLPRTHGSGLFTRGQTQALSVCTLGALG 361

Query:   416 EAQRLESLVGPPTKRFMLHYSFPPFCINEVGKRVGLNRREVGHGTLAEKALLAVLPPEND 475
             + Q L+ L    +KRFM HY+FP F + E G   G  RRE+GHG L E+AL  V+P E D
Sbjct:   362 DVQILDGLGVEESKRFMHHYNFPQFSVGETGPMRGPGRREIGHGALGERALEPVIPSEKD 421

Query:   476 FPYTVRVNSEVMASDGSTSMATVCGGSMALMDAGIPLQEHVAGVSVGLVSEVDPSTGEIK 535
             FPYTVR+ SEV+ S+GSTS A++C  ++A+MDAG+P++  VAG+++GLV      +GE  
Sbjct:   422 FPYTVRLVSEVLESNGSTSQASICASTLAMMDAGVPIKAPVAGIAMGLVK-----SGE-- 474

Query:   536 DYRILTDILGLEDHLGDMDFKIAGTRIGVTAIQLDIKPAGIPLDIICECLEHAHKGRLQI 595
              Y +LTDI G+ED LGDMDFK+AGT  GVTA+Q+DIK  G+  +I+ E L+ A KGR++I
Sbjct:   475 HYTVLTDIQGMEDALGDMDFKVAGTEKGVTALQMDIKIEGLSREILEEALQQAKKGRMEI 534

Query:   596 LDHMEREISAPRTQDDRNSPRLATLKYDNDTLRRLIGPLGALKRKIEEETGGRISVS-DG 654
             L+ M   +S  R +  R +P++ T+  + D +R +IGP G    KI EETG +I +  DG
Sbjct:   535 LNSMLATLSESRKELSRYAPKILTMTINPDKIRDVIGPSGKQINKIIEETGVKIDIEQDG 594

Query:   655 TLTVVAKNRSVMEKVLEKVDFIIGREIEVGGIYKGVVTSVKEYGAFVEFNGGQQGLLHVS 714
             T+ + + + S  +K  + ++ ++ RE+EVG +Y G V  ++++GAFVE   G+ GL+H+S
Sbjct:   595 TIFISSTDESGNQKAKKIIEDLV-REVEVGQLYLGKVKRIEKFGAFVEIFSGKDGLVHIS 653

Query:   715 ELSHEPVSRVSDVVSVGQQLSLRCIGQDVRGNIKLSLKAV 754
             EL+ E V +V DVV +G ++ ++    D +G + LS KAV
Sbjct:   654 ELALERVGKVEDVVKIGDEILVKVTEIDKQGRVNLSRKAV 693

GO:0005515 "protein binding" evidence=IPI

TIGR_CMR|CHY_1758 CHY_1758 "polyribonucleotide nucleotidyltransferase" [Carboxydothermus hydrogenoformans Z-2901 (taxid:246194)]

 Score = 1338 (476.1 bits), Expect = 1.2e-136, P = 1.2e-136
 Identities = 305/731 (41%), Positives = 441/731 (60%)

Query:    52 GTKVLETFKEEFEIGSRLITLETGKIARFANGAVVLGMDETKVLSTVTSSKGDSVR-DFL 110
             G ++LE   +E  I  R + L  GK+A  A+G+V++   +T VL T T SK      DF 
Sbjct:     4 GRQILE---KEIMIAGRPLKLTAGKVATQASGSVLVSYGDTVVLVTATGSKEPREGIDFF 60

Query:   111 PLTVDYQEKQFAQGVIPNTYMRREGAPKERELLVGRIIDRPIRPLFPAGFYHEVQVMASV 170
             PLTVDY+E+ +A G IP  +++REG P E+ +L  R+IDRPIRPLFP GF ++V ++A+V
Sbjct:    61 PLTVDYEERFYAVGKIPGGFIKREGRPSEKAILSARLIDRPIRPLFPKGFKNDVHIVATV 120

Query:   171 LSSDGKQDPDIMAANATSAALMLSDXXXXXXXXXXXXXXXXXQFIVNPTMDELSLSDLNL 230
             LS +    P+I A N  SAAL LS                  + ++NPT+++   S L+L
Sbjct:   121 LSVNQDNPPEIAAMNGASAALTLSHLPFLGPIGAVVVGLVEDELVINPTIEQAEKSRLHL 180

Query:   231 VYACTREKTLMIDVQAREISEKDLEAGLRLAHPEAVK---YLEPQIRLAEKAGKQKKEYK 287
             V A TR+  +M++  A+E+ E+ +   +   H E  K   ++E     A K G  K+  K
Sbjct:   181 VVAGTRDAVMMVEAGAQEVPEEIMIEAITRGHEEVKKIVAFIEEFREEALKLGLAKE--K 238

Query:   288 LSMISEQTLE-KVSNLAEAH------IEAVFTDPSYSKFERGEALDKIGQDVKKALEEEC 340
             + ++ E+  E K +  AEA+      IE +  +  ++K ER E L+ + +++     E  
Sbjct:   239 MEVVVEEKAELKEAVTAEAYPLLKEAIEKIIAE-KFNKQERDEYLENLKKELTTKFLETY 297

Query:   341 DEESLQVLPKAV-DTXXXXXXXXXXXAEGVRVDGRQLDEVRPIYCESGNLPILHGSSLFS 399
              EE L +  K + D+            EG+R+DGR+ DEVRPI+CE G LP  HGS LF+
Sbjct:   298 PEEELTI--KGILDSIQKEIVRQKILKEGIRIDGRKTDEVRPIWCEVGLLPRTHGSGLFT 355

Query:   400 RGDTQVLCTVTLGAPAEAQRLESLVGPPTKRFMLHYSFPPFCINEVGKRVGLNRREVGHG 459
             RG TQVL  VTLGA  + Q L+ L    +KRFM HY+FPP+ + EV    G  RRE+GHG
Sbjct:   356 RGQTQVLSIVTLGAVGDVQILDDLGIEESKRFMHHYNFPPYSVGEVRPMRGPGRREIGHG 415

Query:   460 TLAEKALLAVLPPENDFPYTVRVNSEVMASDGSTSMATVCGGSMALMDAGIPLQEHVAGV 519
              LAE+AL  V+PPE  FPYT+R+ SEV+ S+GSTSM +VCG ++ALMDAG+P++  VAGV
Sbjct:   416 ALAERALEPVIPPEEVFPYTIRIVSEVLESNGSTSMGSVCGSTLALMDAGVPIKAPVAGV 475

Query:   520 SVGLVSEVDPSTGEIKDYRILTDILGLEDHLGDMDFKIAGTRIGVTAIQLDIKPAGIPLD 579
             ++GL+ E D       +  ILTDI G+ED LGDMDFK+AGT+ G+TA+Q+DIK AG+  D
Sbjct:   476 AMGLIKEGD-------EVAILTDIQGIEDALGDMDFKVAGTKDGITALQMDIKIAGVTRD 528

Query:   580 IICECLEHAHKGRLQILDHMEREISAPRTQDDRNSPRLATLKYDNDTLRRLIGPLGALKR 639
             I+ + L  A +GR+ IL  M   IS PR +    +PR+     D + +R +IGP G + +
Sbjct:   529 ILTKALAQAREGRMHILGKMLEVISEPRKELSPYAPRIIFTTVDPEKIRDIIGPGGKIIK 588

Query:   640 KIEEETGGRISVSD-GTLTVVAKNRSVMEKVLEKVDFIIGREIEVGGIYKGVVTSVKEYG 698
             KI +ETG +I + D G + + A ++   EK L  ++ +  +EIEVG +Y G VT + ++G
Sbjct:   589 KIIDETGVKIDIEDDGRIFIAAVDKEAGEKALNIIENLT-KEIEVGKVYLGKVTRIADFG 647

Query:   699 AFVEF-NG-----GQQGLLHVSELSHEPVSRVSDVVSVGQQLSLRCIGQDVRGNIKLSLK 752
             AFVE   G     G++GL+H+S+L+H  V RV DVV  G Q+ ++ IG D +G +KLS K
Sbjct:   648 AFVEVVPGVLGLPGKEGLVHISQLAHSRVKRVEDVVKEGDQILVKAIGYDNQGRLKLSRK 707

Query:   753 AVSPRPEADVK 763
                P  E   K
Sbjct:   708 DAIPAEEVREK 718

GO:0004654 "polyribonucleotide nucleotidyltransferase activity" evidence=ISS

GO:0006401 "RNA catabolic process" evidence=ISS

GO:0006402 "mRNA catabolic process" evidence=ISS

TIGR_CMR|GSU_1593 GSU_1593 "polyribonucleotide nucleotidyltransferase" [Geobacter sulfurreducens PCA (taxid:243231)]

 Score = 1316 (468.3 bits), Expect = 4.0e-136, Sum P(2) = 4.0e-136
 Identities = 292/696 (41%), Positives = 410/696 (58%)

Query:    60 KEEFEIGSRLITLETGKIARFANGAVVLGMDETKVLSTVTSSKGDSV-RDFLPLTVDYQE 118
             K   E G R IT+ TGK A+ A+GAVV+   +T VL T  ++K     +DF PLTV+YQE
Sbjct:     5 KVNVEFGGRTITIATGKWAKQASGAVVVSCGDTVVLVTAVATKSAREGQDFFPLTVNYQE 64

Query:   119 KQFAQGVIPNTYMRREGAPKERELLVGRIIDRPIRPLFPAGFYHEVQVMASVLSSDGKQD 178
             K +A G IP  + +REG P + E L  R IDRPIRPLFP  F ++ Q+MA+V+S+D   D
Sbjct:    65 KAYAGGKIPGGFFKREGRPSDNETLTSRFIDRPIRPLFPESFLNDTQIMATVVSADQDND 124

Query:   179 PDIMAANATSAALMLSDXXXXXXXXXXXXXXXXXQFIVNPTMDELSLSDLNLVYACTREK 238
             P I+A    SAAL +SD                 QF+ NPT+++L  SDL +V A +R+ 
Sbjct:   125 PGILAMIGASAALEVSDIPFLGPIAGVKVGRVDGQFVCNPTVEQLEKSDLEIVVAASRDA 184

Query:   239 TLMIDVQAREISEKDLEAGLRLAHPEAVKYLEPQIRLAEKAGKQKKEYKLSMISEQTLEK 298
              +M++  A E SEKD+   +   H      +E Q  L + AG  K+E   + + E    +
Sbjct:   185 VIMVEGGAAEASEKDVLEAIFFGHAAVQPIIEAQTDLRKLAGVPKREVAATSVDEALKTR 244

Query:   299 VSNLAEAHI-EAVFTDPSYSKFERGEALDKIGQDVKKALEEECDEESLQVLPKAVDTXXX 357
             V +LA A I EAV      +K ER   + +I     + L  E +    ++     D    
Sbjct:   245 VKDLAYAGIKEAVRI---VAKQERHNRIGEITAQTLETLLPEYEGRESEIKGFLGD-FEY 300

Query:   358 XXXXXXXXAEGVRVDGRQLDEVRPIYCESGNLPILHGSSLFSRGDTQVLCTVTLGAPAEA 417
                      +G R+DGR    +RPI  E   LP  HGS+LF+RG+TQ L   TLG   + 
Sbjct:   301 ELVREHIIKDGYRIDGRDTTTIRPISIEVSMLPRAHGSALFTRGETQALVASTLGTSIDE 360

Query:   418 QRLESLVGPPTKRFMLHYSFPPFCINEVGKRVGLNRREVGHGTLAEKALLAVLPPENDFP 477
             QR++SL G   KRF+LHY+FPPF + E   R+   RRE+GHG LAE+AL  V+P   DFP
Sbjct:   361 QRIDSLYGETRKRFLLHYNFPPFSVGETSFRLAPGRREIGHGMLAERALERVVPKHEDFP 420

Query:   478 YTVRVNSEVMASDGSTSMATVCGGSMALMDAGIPLQEHVAGVSVGLVSEVDPSTGEIKDY 537
             YT+R+ S+++ S+GS+SMATVCGG++A+MDAG+P++  VAG+++GL+ E     GE    
Sbjct:   421 YTIRIVSDILESNGSSSMATVCGGALAMMDAGVPIKAPVAGIAMGLIKE-----GE--GI 473

Query:   538 RILTDILGLEDHLGDMDFKIAGTRIGVTAIQLDIKPAGIPLDIICECLEHAHKGRLQILD 597
              IL+DILG EDHLGDMDFK+AGT  GVTAIQ+DIK  G+  +I+ + L  A  GRL IL 
Sbjct:   474 AILSDILGDEDHLGDMDFKVAGTEAGVTAIQMDIKITGVTREIMEKALLQARDGRLHILG 533

Query:   598 HMEREISAPRTQDDRNSPRLATLKYDNDTLRRLIGPLGALKRKIEEETGGRISVSD-GTL 656
              M + I+APRT     +PR+ T+    D +R +IG  G   R I E TG  I + D G +
Sbjct:   534 KMNQAIAAPRTDLSPYAPRITTIWVKTDKIRDVIGSGGKNIRGITEATGVSIDIEDSGRI 593

Query:   657 TVVAKNRSVMEKVLEKVDFIIGREIEVGGIYKGVVTSVKEYGAFVEFNGGQQGLLHVSEL 716
              + + ++   +K ++ +  +   E E G +Y G V  V ++GAFVE   G  GL+H+SEL
Sbjct:   594 NIASTSKEACDKAIKMIRDLTA-EAEEGKLYMGTVKKVMDFGAFVEIFPGTDGLVHISEL 652

Query:   717 SHEPVSRVSDVVSVGQQLSLRCIGQDVRGNIKLSLK 752
               E V  V+DV++ G ++ ++CIG D +G IKLS K
Sbjct:   653 DTERVKNVTDVLNEGDKVLVKCIGIDKQGKIKLSRK 688

GO:0003729 "mRNA binding" evidence=ISS

GO:0004654 "polyribonucleotide nucleotidyltransferase activity" evidence=ISS

GO:0006402 "mRNA catabolic process" evidence=ISS

UNIPROTKB|Q0BWM9 pnp "Polyribonucleotide nucleotidyltransferase" [Hyphomonas neptunium ATCC 15444 (taxid:228405)]

 Score = 1322 (470.4 bits), Expect = 6.0e-135, P = 6.0e-135
 Identities = 294/700 (42%), Positives = 431/700 (61%)

Query:    64 EIGSRLITLETGKIARFANGAVVLGMDETKVLSTVTSSK-GDSVRDFLPLTVDYQEKQFA 122
             E   R +T+ETG++AR A+GAV++   +T VL+T   +K     +DF PLTV+YQEK FA
Sbjct:    10 EWAGRTLTIETGQVARQADGAVMVQYGDTIVLATAVFAKEAKPGQDFFPLTVNYQEKYFA 69

Query:   123 QGVIPNTYMRREGAPKERELLVGRIIDRPIRPLFPAGFYHEVQVMASVLSSDGKQDPDIM 182
              G IP  + +REG P E+E L  R+IDRPIRPLF  GF HEVQV+ + LS D + D DI+
Sbjct:    70 SGRIPGGFFKREGRPTEKETLTSRLIDRPIRPLFVDGFKHEVQVVVTTLSYDLENDADII 129

Query:   183 AANATSAALMLSDXXXXXXXXXXXXXXXXXQFIVNPTMDELSLSDLNLVYACTREKTLMI 242
             A    SAAL+LS                  Q+I+NPT+ EL  S+L+LV A T +  +M+
Sbjct:   130 ALVGASAALVLSGAPFMGPIGAARVGYKDGQYIINPTIAELEESELDLVVAGTTDAVMMV 189

Query:   243 DVQAREISEKDLEAGLRLAHPEAVK-YLEPQIRLAEKAGKQKKEYKLSMISEQTLEKVSN 301
             + QA E+SE D+  G  +A  +A++  ++  I LAEKA K+   Y+    S   L+ V +
Sbjct:   190 ESQAAELSE-DVMLGAVVAGHDAMQPVIDAIIALAEKAAKEPFAYEPPDHSA-ALKSVID 247

Query:   302 LAEAHIEAVFTDPSYSKFERGEALDKIG--QDVKKALEEECDEESLQVLPKAVDTXXXXX 359
                A +       +Y    +GE    IG  +D  KA     DE    + P+   T     
Sbjct:   248 TVGADLSK-----AYKITAKGERYAAIGAAKDKAKAALLGTDEAPGVMTPEVFKTVFKEA 302

Query:   360 XXXXXXAE----GVRVDGRQLDEVRPIYCESGNLPILHGSSLFSRGDTQVLCTVTLGAPA 415
                    +    G R+DGR+LD++RPI  E+G LP  HGSSLF+RG+TQ +C  TLG   
Sbjct:   303 EASVVRGDILKTGQRIDGRKLDQIRPIVAEAGFLPRTHGSSLFTRGETQAICVATLGTSD 362

Query:   416 EAQRLESLVGPPTKRFMLHYSFPPFCINEVGKRVGLNRREVGHGTLAEKALLAVLPPEND 475
             + Q ++ L G   ++FMLHY+FPP+ + E G+  G  RRE+GHG LA +AL AVLP   D
Sbjct:   363 DEQYIDGLDGTKKEKFMLHYNFPPYSVGETGRMGGAGRREIGHGKLAWRALKAVLPKHED 422

Query:   476 FPYTVRVNSEVMASDGSTSMATVCGGSMALMDAGIPLQEHVAGVSVGLVSEVDPSTGEIK 535
             FPYT+R+ SE+  S+GS+SMATVCG S+A+MDAG+PL   V+G+++GL+ E     G   
Sbjct:   423 FPYTIRMVSEITESNGSSSMATVCGCSLAMMDAGVPLTRPVSGIAMGLILE-----GS-- 475

Query:   536 DYRILTDILGLEDHLGDMDFKIAGTRIGVTAIQLDIKPAGIPLDIICECLEHAHKGRLQI 595
             ++ +L+DILG EDHLGDMDFK+AGT  GVT++Q+DIK AGI  DI+ + LE A  GR+ I
Sbjct:   476 EFAVLSDILGDEDHLGDMDFKVAGTENGVTSLQMDIKVAGITKDIMGKALEQAKGGRMHI 535

Query:   596 LDHMEREISAPRTQDDRNSPRLATLKYDNDTLRRLIGPLGALKRKIEEETGGRISVSD-G 654
             L  M + ++A R Q   N+P++  +K   D +R +IG  G + R I +ETG ++++ D G
Sbjct:   536 LGEMGKALTASRGQLSENAPQMEIIKVPTDKIRDVIGSGGKVIRGIVDETGAKVNIDDDG 595

Query:   655 TLTVVAKNRSVMEKVLEKVDFIIGREIEVGGIYKGVVTSVKEYGAFVEFNGGQQGLLHVS 714
             T+ + A +R  ++  ++ +  I   E EVG IY+G V S+K++G FV F G + GL+HVS
Sbjct:   596 TVQISAMDRKSIDAAIKMIKGITA-EAEVGEIYEGKVVSMKDFGIFVNFFGPKDGLVHVS 654

Query:   715 ELSHEPVSRVSDVVSVGQQLSLRCIGQDVRGNIKLSLKAV 754
             +++++ +    ++V  G ++ ++ +G D RG ++LS+K V
Sbjct:   655 QMANKRIGHPKEMVKEGDKVWVKLMGFDERGKVRLSMKVV 694

GO:0004654 "polyribonucleotide nucleotidyltransferase activity" evidence=ISS

GO:0006402 "mRNA catabolic process" evidence=ISS

UNIPROTKB|P05055 pnp "polynucleotide phosphorylase monomer" [Escherichia coli K-12 (taxid:83333)]

 Score = 1304 (464.1 bits), Expect = 4.8e-133, P = 4.8e-133
 Identities = 286/712 (40%), Positives = 433/712 (60%)

Query:    55 VLETFKEEFEIGSRLITLETGKIARFANGAVVLGMDETKVLSTVTSSK-GDSVRDFLPLT 113
             +L     +F+ G   +TLETG +AR A  AV++ MD+T V  TV   K     +DF PLT
Sbjct:     1 MLNPIVRKFQYGQHTVTLETGMMARQATAAVMVSMDDTAVFVTVVGQKKAKPGQDFFPLT 60

Query:   114 VDYQEKQFAQGVIPNTYMRREGAPKERELLVGRIIDRPIRPLFPAGFYHEVQVMASVLSS 173
             V+YQE+ +A G IP ++ RREG P E E L+ R+IDRPIRPLFP GF +EVQV+A+V+S 
Sbjct:    61 VNYQERTYAAGRIPGSFFRREGRPSEGETLIARLIDRPIRPLFPEGFVNEVQVIATVVSV 120

Query:   174 DGKQDPDIMAANATSAALMLSDXXXXXXXXXXXXXXXXXQFIVNPTMDELSLSDLNLVYA 233
             + + +PDI+A    SAAL LS                  Q+++NPT DEL  S L+LV A
Sbjct:   121 NPQVNPDIVAMIGASAALSLSGIPFNGPIGAARVGYINDQYVLNPTQDELKESKLDLVVA 180

Query:   234 CTREKTLMIDVQAREISEKDLEAGLRLAHPEAVKYLEPQIRLAEKAGKQKKEYKLSMISE 293
              T    LM++ +A+ +SE  +   +   H +    ++    L ++AGK + +++   ++E
Sbjct:   181 GTEAAVLMVESEAQLLSEDQMLGAVVFGHEQQQVVIQNINELVKEAGKPRWDWQPEPVNE 240

Query:   294 QTLEKVSNLAEAHIEAVF--TDPSYSKFERGEALDKIGQDVKKAL---EEECDEESLQVL 348
                 +V+ LAEA +   +  TD    K ER   +D I  +    L   +E  DE  L  +
Sbjct:   241 ALNARVAALAEARLSDAYRITD----KQERYAQVDVIKSETIATLLAEDETLDENELGEI 296

Query:   349 PKAVDTXXXXXXXXXXXAEGVRVDGRQLDEVRPIYCESGNLPILHGSSLFSRGDTQVLCT 408
               A++            A   R+DGR+ D +R +   +G LP  HGS+LF+RG+TQ L T
Sbjct:   297 LHAIEKNVVRSRVL---AGEPRIDGREKDMIRGLDVRTGVLPRTHGSALFTRGETQALVT 353

Query:   409 VTLGAPAEAQRLESLVGPPTKRFMLHYSFPPFCINEVGKRVGLNRREVGHGTLAEKALLA 468
              TLG   +AQ L+ L+G  T  F+ HY+FPP+ + E G      RRE+GHG LA++ +LA
Sbjct:   354 ATLGTARDAQVLDELMGERTDTFLFHYNFPPYSVGETGMVGSPKRREIGHGRLAKRGVLA 413

Query:   469 VLPPENDFPYTVRVNSEVMASDGSTSMATVCGGSMALMDAGIPLQEHVAGVSVGLVSEVD 528
             V+P  + FPYTVRV SE+  S+GS+SMA+VCG S+ALMDAG+P++  VAG+++GLV E D
Sbjct:   414 VMPDMDKFPYTVRVVSEITESNGSSSMASVCGASLALMDAGVPIKAAVAGIAMGLVKEGD 473

Query:   529 PSTGEIKDYRILTDILGLEDHLGDMDFKIAGTRIGVTAIQLDIKPAGIPLDIICECLEHA 588
                    +Y +L+DILG EDHLGDMDFK+AG+R G++A+Q+DIK  GI  +I+   L  A
Sbjct:   474 -------NYVVLSDILGDEDHLGDMDFKVAGSRDGISALQMDIKIEGITKEIMQVALNQA 526

Query:   589 HKGRLQILDHMEREISAPRTQDDRNSPRLATLKYDNDTLRRLIGPLGALKRKIEEETGGR 648
                RL IL  ME+ I+APR      +PR+ T+K + D ++ +IG  G++ R + EETG  
Sbjct:   527 KGARLHILGVMEQAINAPRGDISEFAPRIHTIKINPDKIKDVIGKGGSVIRALTEETGTT 586

Query:   649 ISVSD-GTLTVVAKNRSVMEKVLEKVDFIIGREIEVGGIYKGVVTSVKEYGAFVEFNGGQ 707
             I + D GT+ + A +    +  + +++ I   EIEVG +Y G VT + ++GAFV   GG+
Sbjct:   587 IEIEDDGTVKIAATDGEKAKHAIRRIEEITA-EIEVGRVYTGKVTRIVDFGAFVAIGGGK 645

Query:   708 QGLLHVSELSHEPVSRVSDVVSVGQQLSLRCIGQDVRGNIKLSLKAVSPRPE 759
             +GL+H+S+++ + V +V+D + +GQ++ ++ +  D +G I+LS+K  + + +
Sbjct:   646 EGLVHISQIADKRVEKVTDYLQMGQEVPVKVLEVDRQGRIRLSIKEATEQSQ 697

GO:0006402 "mRNA catabolic process" evidence=IEA

GO:0006396 "RNA processing" evidence=IEA

GO:0035438 "cyclic-di-GMP binding" evidence=IDA

GO:0042802 "identical protein binding" evidence=IPI

GO:0005515 "protein binding" evidence=IPI

GO:0016020 "membrane" evidence=IDA

GO:0005829 "cytosol" evidence=IDA

GO:0006950 "response to stress" evidence=IEA

GO:0003723 "RNA binding" evidence=IEA

GO:0000175 "3'-5'-exoribonuclease activity" evidence=IEA;IDA

GO:0004654 "polyribonucleotide nucleotidyltransferase activity" evidence=IEA;IDA

TIGR_CMR|BA_3944 BA_3944 "polyribonucleotide nucleotidyltransferase" [Bacillus anthracis str. Ames (taxid:198094)]

 Score = 1297 (461.6 bits), Expect = 2.7e-132, P = 2.7e-132
 Identities = 279/693 (40%), Positives = 425/693 (61%)

Query:    64 EIGSRLITLETGKIARFANGAVVLGMDETKVLSTVTSSKGDSVRDFLPLTVDYQEKQFAQ 123
             ++  R +T+ETG++A+ ANGAV++   +T VLST T+SK     DF PLTV+Y+E+ +A 
Sbjct:    11 DLAGRQLTVETGQLAKQANGAVLVRYGDTAVLSTATASKEAKNVDFFPLTVNYEERLYAV 70

Query:   124 GVIPNTYMRREGAPKERELLVGRIIDRPIRPLFPAGFYHEVQVMASVLSSDGKQDPDIMA 183
             G IP  +++REG P E+ +L  R+IDRPIRPLF  GF +EVQV+  V+S D     ++ A
Sbjct:    71 GKIPGGFIKREGRPSEKAILASRLIDRPIRPLFADGFRNEVQVVNIVMSVDQDCSSEMAA 130

Query:   184 ANATSAALMLSDXXXXXXXXXXXXXXXXXQFIVNPTMDELSLSDLNLVYACTREKTLMID 243
                +S AL +SD                 +F++NPT+++   SD++LV A T++   M++
Sbjct:   131 MLGSSLALSISDIPFEGPIAGATVGRINGEFVINPTVEQQEQSDIHLVVAGTKDAINMVE 190

Query:   244 VQAREISEKDLEAGLRLAHPEAVKYLEPQIRLAEKAGKQKKEYKLSMISEQTLEKVSNLA 303
               A ++ E+ +   +   H E  + +  Q  + +  GK+K E KL  +     + V  +A
Sbjct:   191 AGADQVPEETMLEAIMFGHDEIKRLIAFQEEIVQAVGKEKSEVKLYEVDADLNQAVREMA 250

Query:   304 EAHIEAVFTDPSYSKFERGEALDKIGQDVKKALE-EECDEESLQVLPKAVDTXXXXXXXX 362
             E  + +      + K  R +A++++ + V +  E +E D ++L  + + +          
Sbjct:   251 EKDMHSAIQ--VHEKHAREDAINEVKKRVIEHYEAQEADADTLGQVNEILYKIVKEEVRR 308

Query:   363 XXXAEGVRVDGRQLDEVRPIYCESGNLPILHGSSLFSRGDTQVLCTVTLGAPAEAQRLES 422
                 E +R DGR+ DE+RP+  E G L   HGS LF+RG TQ L   TLGA  + Q L+ 
Sbjct:   309 LITVEKIRPDGRKGDEIRPLASEVGILSRTHGSGLFTRGQTQALSICTLGALGDVQILDG 368

Query:   423 LVGPPTKRFMLHYSFPPFCINEVGKRVGLNRREVGHGTLAEKALLAVLPPENDFPYTVRV 482
             L    +KRFM HY+FP F + E     G  RRE+GHG L E+AL  V+P E DFPYTVR+
Sbjct:   369 LGVEESKRFMHHYNFPSFSVGETRPMRGPGRREIGHGALGERALEPVIPSEKDFPYTVRL 428

Query:   483 NSEVMASDGSTSMATVCGGSMALMDAGIPLQEHVAGVSVGLVSEVDPSTGEIKDYRILTD 542
              SEV+ S+GSTS A++CG ++A+MDAG+PL+  VAG+++GLV      TGE   Y IL+D
Sbjct:   429 VSEVLESNGSTSQASICGSTLAMMDAGVPLKAPVAGIAMGLVK-----TGE--HYTILSD 481

Query:   543 ILGLEDHLGDMDFKIAGTRIGVTAIQLDIKPAGIPLDIICECLEHAHKGRLQILDHMERE 602
             I G+EDHLGDMDFK+AGT  GVTA+Q+DIK  G+  +I+ E L+ A  GR+ IL+HM   
Sbjct:   482 IQGMEDHLGDMDFKVAGTAHGVTALQMDIKIDGLSREILEEALQQAKVGRVHILNHMLSV 541

Query:   603 ISAPRTQDDRNSPRLATLKYDNDTLRRLIGPLGALKRKIEEETGGRISVS-DGTLTVVAK 661
             I+ PRT+    +P++ T+  + D +R +IGP G    KI EETG +I +  DGT+ + + 
Sbjct:   542 IAEPRTELSAYAPKIITMTINPDKIRDVIGPSGKQINKIIEETGVKIDIEQDGTVFISSI 601

Query:   662 NRSVMEKVLEKVDFIIGREIEVGGIYKGVVTSVKEYGAFVEFNGGQQGLLHVSELSHEPV 721
             N+ + +K  + ++ I+ RE++VG IY+G V  V+++GAFVE   G+ GL+H+SEL+ E V
Sbjct:   602 NQEMNDKAKKIIEDIV-REVQVGEIYEGKVKRVEKFGAFVELFSGKDGLVHISELALERV 660

Query:   722 SRVSDVVSVGQQLSLRCIGQDVRGNIKLSLKAV 754
              +V DVV +G  ++++ I  D +G + LS K +
Sbjct:   661 GKVEDVVKIGDVITVKVIEIDKQGRVNLSRKVL 693

GO:0003729 "mRNA binding" evidence=ISS

GO:0004654 "polyribonucleotide nucleotidyltransferase activity" evidence=ISS

GO:0006402 "mRNA catabolic process" evidence=ISS

TIGR_CMR|SO_1209 SO_1209 "polyribonucleotide nucleotidyltransferase" [Shewanella oneidensis MR-1 (taxid:211586)]

 Score = 1275 (453.9 bits), Expect = 5.7e-130, P = 5.7e-130
 Identities = 276/705 (39%), Positives = 426/705 (60%)

Query:    61 EEFEIGSRLITLETGKIARFANGAVVLGMDETKVLSTVTSSK-GDSVRDFLPLTVDYQEK 119
             + FE G   +TLETG IAR A+ AV+  M +T VL TV   K  ++ RDF PLTV+YQEK
Sbjct:     6 KSFEYGQHTVTLETGVIARQADAAVLASMGDTTVLVTVVGKKEAEAGRDFFPLTVNYQEK 65

Query:   120 QFAQGVIPNTYMRREGAPKERELLVGRIIDRPIRPLFPAGFYHEVQVMASVLSSDGKQDP 179
              +A G IP  + +REG P E E L+ R+IDRPIRPLFP GF +EVQV+ +V+S D + +P
Sbjct:    66 TYAAGKIPGGFFKREGRPSEEETLIARLIDRPIRPLFPNGFKNEVQVIITVVSVDPEIEP 125

Query:   180 DIMAANATSAALMLSDXXXXXXXXXXXXXXXXXQFIVNPTMDELSLSDLNLVYACTREKT 239
             DI++   TSAAL +S                  ++++NPT+ ++  S LNLV A T    
Sbjct:   126 DIISMIGTSAALAISGIPFNGPLGAARVGYINGEYVLNPTVKQIGASQLNLVVAGTESAV 185

Query:   240 LMIDVQAREISEKDLEAGLRLAHPEAVKYLEPQIRLAEKAGKQKKEYKLSMISEQTLEKV 299
             LM++ +A+ + E+ +   +   H +    ++       +AGK   ++   +  E  + ++
Sbjct:   186 LMVESEAQALPEEVMLGSVVYGHDQQQVVIKAIAEFKAEAGKPTWDWTAPVEDEALVAQI 245

Query:   300 SNLAEA-HIEAVFTDPSYSKFERGEALDKIGQDVKKALEEECDEESLQVLPKAVDTXXXX 358
               LAEA  IEA        ++ +   +    ++   A   + D   +  L  +++     
Sbjct:   246 KELAEAGFIEAYQIQVKQERYAQVAVVKAAAKEALLAANPDVDLREVDNLLGSLEKKVVR 305

Query:   359 XXXXXXXAEGVRVDGRQLDEVRPIYCESGNLPILHGSSLFSRGDTQVLCTVTLGAPAEAQ 418
                        R+DGR+ D VR +   +G LP  HGS+LF+RG+TQ L T TLG   +AQ
Sbjct:   306 GRILRGMP---RIDGREPDMVRALSVLAGVLPRTHGSALFTRGETQALVTCTLGTERDAQ 362

Query:   419 RLESLVGPPTKRFMLHYSFPPFCINEVGKRVGLNRREVGHGTLAEKALLAVLPPENDFPY 478
             +++S++G  T RFMLHY+FPP+ + E G      RRE+GHG LA + + AV+P   +FPY
Sbjct:   363 KIDSIMGERTNRFMLHYNFPPYSVGETGMVGSPKRREIGHGKLAWRGINAVMPSAEEFPY 422

Query:   479 TVRVNSEVMASDGSTSMATVCGGSMALMDAGIPLQEHVAGVSVGLVSEVDPSTGEIKDYR 538
             +VRV SE+  S+GS+SMA+VCG S+ALMDAG+P++  VAG+++GLV E D       D+ 
Sbjct:   423 SVRVVSEITESNGSSSMASVCGTSLALMDAGVPIKTSVAGIAMGLVKEGD-------DFV 475

Query:   539 ILTDILGLEDHLGDMDFKIAGTRIGVTAIQLDIKPAGIPLDIICECLEHAHKGRLQILDH 598
             +L+DILG EDHLGDMDFK+AGTR GVTA+Q+DIK  GI  +I+   L+ A+  R+ IL+ 
Sbjct:   476 VLSDILGDEDHLGDMDFKVAGTRDGVTALQMDIKIEGITKEIMEIALQQAYGARVHILNV 535

Query:   599 MEREISAPRTQDDRNSPRLATLKYDNDTLRRLIGPLGALKRKIEEETGGRISVSD-GTLT 657
             M++ I + R     ++PR+ T+K + + +R +IG  GA+ R + EETG  I + D GT+ 
Sbjct:   536 MDQAIGSHRADISDHAPRITTIKINPEKIRDVIGKGGAVIRALTEETGTTIELEDDGTVK 595

Query:   658 VVAKNRSVMEKVLEKVDFIIGREIEVGGIYKGVVTSVKEYGAFVEFNGGQQGLLHVSELS 717
             + + N    ++ + +++ I   E+EVG IY G V  + ++GAFV    G+ GL+H+S++S
Sbjct:   596 IASSNGEATKEAIRRIEEITS-EVEVGRIYNGKVIRIVDFGAFVNILPGKDGLVHISQIS 654

Query:   718 HEPVSRVSDVVSVGQQLSLRCIGQDVRGNIKLSLK-AVSPRPEAD 761
              E V+ VSD + + Q+++++ +  D +G ++LS+K A +  P A+
Sbjct:   655 DERVANVSDHLELNQEVTVKVMEVDRQGRVRLSIKEAQTKEPAAE 699

GO:0003729 "mRNA binding" evidence=ISS

GO:0004654 "polyribonucleotide nucleotidyltransferase activity" evidence=ISS

GO:0006402 "mRNA catabolic process" evidence=ISS

UNIPROTKB|Q8TCS8 PNPT1 "Polyribonucleotide nucleotidyltransferase 1, mitochondrial" [Homo sapiens (taxid:9606)]

 Score = 1262 (449.3 bits), Expect = 1.4e-128, P = 1.4e-128
 Identities = 278/735 (37%), Positives = 426/735 (57%)

Query:    64 EIGSRLITLETGKIARFANGAVVLGMDETKVLSTVTSSKGDSVRDFLPLTVDYQEKQFAQ 123
             ++G+R + + +GK+ARFA+G+ V+   +T V+ T  S    S   F+PL VDY++K  A 
Sbjct:    50 DLGNRKLEISSGKLARFADGSAVVQSGDTAVMVTAVSKTKPSPSQFMPLVVDYRQKAAAA 109

Query:   124 GVIPNTYMRREGAPKERELLVGRIIDRPIRPLFPAGFYHEVQVMASVLSSDGKQDPDIMA 183
             G IP  Y+RRE    ++E+L  RIIDR IRPLFPAG++++ QV+ ++L+ DG  +PD++A
Sbjct:   110 GRIPTNYLRREIGTSDKEILTSRIIDRSIRPLFPAGYFYDTQVLCNLLAVDGVNEPDVLA 169

Query:   184 ANATSAALMLSDXXXXXXXXXXXXXXXXXQFIVNPTMDELSLSDLNLVYA-CTREKTLMI 242
              N  S AL LSD                 +++VNPT  E+S S LNLV A   + + +M+
Sbjct:   170 INGASVALSLSDIPWNGPVGAVRIGIIDGEYVVNPTRKEMSSSTLNLVVAGAPKSQIVML 229

Query:   243 DVQAREISEKDLEAGLRLAHPEAVKYLEPQIRLAEKAGKQKKE-YKLSMISEQTLEKVSN 301
             +  A  I ++D    +++      + ++   +L ++ G  K+   KL   S + ++    
Sbjct:   230 EASAENILQQDFCHAIKVGVKYTQQIIQGIQQLVKETGVTKRTPQKLFTPSPEIVKYTHK 289

Query:   302 LAEAHIEAVFTDPSYSKFERGEALDKIGQDVKKALEEECDEESLQVLPKAVDTXXXXXXX 361
             LA   + AVFTD  + K  R EA++KI  D ++ L+E+  E     + ++ +        
Sbjct:   290 LAMERLYAVFTDYEHDKVSRDEAVNKIRLDTEEQLKEKFPEADPYEIIESFNVVAKEVFR 349

Query:   362 XXXXAEGVRVDGRQLDEVRPIYCESGNLPILHGSSLFSRGDTQVLCTVTLGAPAEAQRLE 421
                  E  R DGR L  +R + CE      LHGS+LF RG TQVLCTVT  +     + +
Sbjct:   350 SIVLNEYKRCDGRDLTSLRNVSCEVDMFKTLHGSALFQRGQTQVLCTVTFDSLESGIKSD 409

Query:   422 SLV----GPPTKRFMLHYSFPPFCINEVGKRVGLNRREVGHGTLAEKALLAVLPPENDFP 477
              ++    G   K FMLHY FPP+  NE+GK  GLNRRE+GHG LAEKAL  V+P   DFP
Sbjct:   410 QVITAINGIKDKNFMLHYEFPPYATNEIGKVTGLNRRELGHGALAEKALYPVIP--RDFP 467

Query:   478 YTVRVNSEVMASDGSTSMATVCGGSMALMDAGIPLQEHVAGVSVGLVSEVDPSTGEIKDY 537
             +T+RV SEV+ S+GS+SMA+ CGGS+ALMD+G+P+   VAGV++GLV++ DP  GEI+DY
Sbjct:   468 FTIRVTSEVLESNGSSSMASACGGSLALMDSGVPISSAVAGVAIGLVTKTDPEKGEIEDY 527

Query:   538 RILTDILGLEDHLGDMDFKIAGTRIGVTAIQLDIKPAGIPLDIICECLEHAHKGRLQILD 597
             R+LTDILG+ED+ GDMDFKIAGT  G+TA+Q DIK  GIP+ I+ E ++ A   + +IL 
Sbjct:   528 RLLTDILGIEDYNGDMDFKIAGTNKGITALQADIKLPGIPIKIVMEAIQQASVAKKEILQ 587

Query:   598 HMEREISAPRTQDDRNSPRLATLKYDNDTLRRLIGPLGALKRKIEEETGGRIS-VSDGTL 656
              M + IS PR     N P + T++       + +GP G   +K++ ETG  IS V + T 
Sbjct:   588 IMNKTISKPRASRKENGPVVETVQVPLSKRAKFVGPGGYNLKKLQAETGVTISQVDEETF 647

Query:   657 TVVAKNRSVMEKVLEKVDFIIG----REIEVGGIYKGVVTSVKEYGAFVEFNGGQQG-LL 711
             +V A   S M +  + +  I      +++E G +Y   +T +++ G  V+        LL
Sbjct:   648 SVFAPTPSAMHEARDFITEICKDDQEQQLEFGAVYTATITEIRDTGVMVKLYPNMTAVLL 707

Query:   712 HVSELSHEPVSRVSDV-VSVGQQLSLRCIGQD-VRGNIKLSLKAV-SP-----RPEADVK 763
             H ++L    +   + + + VGQ++ ++  G+D   G ++LS K + SP     R   D  
Sbjct:   708 HNTQLDQRKIKHPTALGLEVGQEIQVKYFGRDPADGRMRLSRKVLQSPATTVVRTLNDRS 767

Query:   764 GVVEGSVPVNKQATD 778
              +V G  P+++ +++
Sbjct:   768 SIVMGE-PISQSSSN 781

GO:0035458 "cellular response to interferon-beta" evidence=IDA

GO:0061014 "positive regulation of mRNA catabolic process" evidence=IMP

GO:0035927 "RNA import into mitochondrion" evidence=IDA

GO:0000964 "mitochondrial RNA 5'-end processing" evidence=IMP

GO:0000965 "mitochondrial RNA 3'-end processing" evidence=IMP

GO:0097222 "mitochondrial mRNA polyadenylation" evidence=IMP

GO:0070207 "protein homotrimerization" evidence=IDA

GO:0000175 "3'-5'-exoribonuclease activity" evidence=IDA

GO:0008266 "poly(U) RNA binding" evidence=IDA

GO:0034046 "poly(G) RNA binding" evidence=IDA

GO:0000962 "positive regulation of mitochondrial RNA catabolic process" evidence=IDA

GO:0004654 "polyribonucleotide nucleotidyltransferase activity" evidence=IDA

GO:0006401 "RNA catabolic process" evidence=IDA

GO:0043631 "RNA polyadenylation" evidence=IDA

GO:0034599 "cellular response to oxidative stress" evidence=IDA

GO:0000957 "mitochondrial RNA catabolic process" evidence=IDA

GO:0006402 "mRNA catabolic process" evidence=IDA

GO:0045926 "negative regulation of growth" evidence=IDA

GO:0071850 "mitotic cell cycle arrest" evidence=IDA

GO:2000627 "positive regulation of miRNA catabolic process" evidence=IDA

GO:0035198 "miRNA binding" evidence=IDA

GO:0005758 "mitochondrial intermembrane space" evidence=IDA

GO:0005739 "mitochondrion" evidence=IDA

GO:0051260 "protein homooligomerization" evidence=IDA

GO:0000958 "mitochondrial mRNA catabolic process" evidence=IDA

GO:0045025 "mitochondrial degradosome" evidence=IDA

GO:0035928 "rRNA import into mitochondrion" evidence=IDA

GO:0005515 "protein binding" evidence=IPI

GO:0071042 "nuclear polyadenylation-dependent mRNA catabolic process" evidence=IDA

GO:0043457 "regulation of cellular respiration" evidence=ISS

GO:0070584 "mitochondrion morphogenesis" evidence=ISS

GO:0005737 "cytoplasm" evidence=IDA

GO:2000772 "regulation of cellular senescence" evidence=IDA

GO:0005886 "plasma membrane" evidence=IDA

UNIPROTKB|Q5RCW2 PNPT1 "Polyribonucleotide nucleotidyltransferase 1, mitochondrial" [Pongo abelii (taxid:9601)]

 Score = 1255 (446.8 bits), Expect = 7.6e-128, P = 7.6e-128
 Identities = 277/735 (37%), Positives = 426/735 (57%)

Query:    64 EIGSRLITLETGKIARFANGAVVLGMDETKVLSTVTSSKGDSVRDFLPLTVDYQEKQFAQ 123
             ++G+R + + +GK+ARFA+G+ V+   +T V+ T  S    S   F+PL VDY++K  A 
Sbjct:    50 DLGNRKLEISSGKLARFADGSAVVQSGDTAVMVTAVSKTKPSPSQFMPLVVDYRQKAAAA 109

Query:   124 GVIPNTYMRREGAPKERELLVGRIIDRPIRPLFPAGFYHEVQVMASVLSSDGKQDPDIMA 183
             G IP  Y+RRE    ++E+L  RIIDR IRPLFPAG++++ QV+ ++L+ DG  +PD++A
Sbjct:   110 GRIPTNYLRREIGTSDKEILTSRIIDRSIRPLFPAGYFYDTQVLCNLLAVDGVNEPDVLA 169

Query:   184 ANATSAALMLSDXXXXXXXXXXXXXXXXXQFIVNPTMDELSLSDLNLVYA-CTREKTLMI 242
              N  S AL LSD                 + +VNPT  E+S S LNLV A   + + +M+
Sbjct:   170 INGASVALSLSDIPWNGPVGAVRIGIIDGECVVNPTRKEMSSSTLNLVVAGAPKSQIVML 229

Query:   243 DVQAREISEKDLEAGLRLAHPEAVKYLEPQIRLAEKAGKQKKE-YKLSMISEQTLEKVSN 301
             +  A  I ++D    +++      + ++   +L ++ G  K+   KL   S + ++    
Sbjct:   230 EASAENILQQDFCHAIKVGVKYTQQIIQGIQQLVKETGVTKRTPQKLFTPSPEIVKHTHK 289

Query:   302 LAEAHIEAVFTDPSYSKFERGEALDKIGQDVKKALEEECDEESLQVLPKAVDTXXXXXXX 361
             LA   + AVFTD  + K  R EA++KI  D ++ L+E+  +     + ++ +        
Sbjct:   290 LAMERLYAVFTDYEHDKVSRDEAVNKIRLDTEEQLKEKFPQADPYEIIESFNVVAKEVFR 349

Query:   362 XXXXAEGVRVDGRQLDEVRPIYCESGNLPILHGSSLFSRGDTQVLCTVTLGAPAEAQRLE 421
                  E  R DGR L  +R + CE      LHGS+LF RG TQVLCTVT  +     + +
Sbjct:   350 NIILNEYKRCDGRDLTSLRNVSCEVDMFKTLHGSALFQRGQTQVLCTVTFDSLESGIKSD 409

Query:   422 SLV----GPPTKRFMLHYSFPPFCINEVGKRVGLNRREVGHGTLAEKALLAVLPPENDFP 477
              ++    G   K FMLHY FPP+  NE+GK  GLNRRE+GHG LAEKAL  V+P   DFP
Sbjct:   410 QVITAINGIKDKNFMLHYEFPPYATNEIGKVTGLNRRELGHGALAEKALYPVIP--RDFP 467

Query:   478 YTVRVNSEVMASDGSTSMATVCGGSMALMDAGIPLQEHVAGVSVGLVSEVDPSTGEIKDY 537
             +T+RV SEV+ S+GS+SMA+ CGGS+ALMD+G+P+   VAGV++GLV++ DP  GEI+DY
Sbjct:   468 FTIRVTSEVLESNGSSSMASACGGSLALMDSGVPISSAVAGVAIGLVTKTDPEKGEIEDY 527

Query:   538 RILTDILGLEDHLGDMDFKIAGTRIGVTAIQLDIKPAGIPLDIICECLEHAHKGRLQILD 597
             R+LTDILG+ED+ GDMDFKIAGT  G+TA+Q DIK  GIP+ I+ E ++ A   + +IL 
Sbjct:   528 RLLTDILGIEDYNGDMDFKIAGTNKGITALQADIKLPGIPIKIVMEAIQQASVAKKEILQ 587

Query:   598 HMEREISAPRTQDDRNSPRLATLKYDNDTLRRLIGPLGALKRKIEEETGGRIS-VSDGTL 656
              M + IS PRT    N P + T++       + +GP G   +K++ ETG  IS V + T 
Sbjct:   588 IMNKTISKPRTSRKENGPVVETVQVPLSKRAKFVGPGGYNLKKLQAETGVTISQVDEETF 647

Query:   657 TVVAKNRSVMEKVLEKVDFIIG----REIEVGGIYKGVVTSVKEYGAFVEFNGGQQG-LL 711
             +V A   S + +  + +  I      +++E G +Y   +T +++ G  V+        LL
Sbjct:   648 SVFAPTPSALHEARDFITEICKDDQEQQLEFGAVYTATITEIRDTGVMVKLYPNMTAVLL 707

Query:   712 HVSELSHEPVSRVSDV-VSVGQQLSLRCIGQD-VRGNIKLSLKAV-SP-----RPEADVK 763
             H ++L    +   + + + VGQ++ ++  G+D   G ++LS K + SP     R   D  
Sbjct:   708 HNTQLDQRKIRHPTALGLEVGQEIQVKYFGRDPADGRMRLSRKVLQSPATTVVRTLNDRS 767

Query:   764 GVVEGSVPVNKQATD 778
              +V G  P+++ +++
Sbjct:   768 SIVMGE-PISQSSSN 781

GO:0000175 "3'-5'-exoribonuclease activity" evidence=ISS

GO:0000957 "mitochondrial RNA catabolic process" evidence=ISS

GO:0000958 "mitochondrial mRNA catabolic process" evidence=ISS

GO:0000962 "positive regulation of mitochondrial RNA catabolic process" evidence=ISS

GO:0000964 "mitochondrial RNA 5'-end processing" evidence=ISS

GO:0000965 "mitochondrial RNA 3'-end processing" evidence=ISS

GO:0004654 "polyribonucleotide nucleotidyltransferase activity" evidence=ISS

GO:0005739 "mitochondrion" evidence=ISS

GO:0006401 "RNA catabolic process" evidence=ISS

GO:0006402 "mRNA catabolic process" evidence=ISS

GO:0008266 "poly(U) RNA binding" evidence=ISS

GO:0034046 "poly(G) RNA binding" evidence=ISS

GO:0034599 "cellular response to oxidative stress" evidence=ISS

GO:0035198 "miRNA binding" evidence=ISS

GO:0035927 "RNA import into mitochondrion" evidence=ISS

GO:0035928 "rRNA import into mitochondrion" evidence=ISS

GO:0043457 "regulation of cellular respiration" evidence=ISS

GO:0043631 "RNA polyadenylation" evidence=ISS

GO:0045025 "mitochondrial degradosome" evidence=ISS

GO:0045926 "negative regulation of growth" evidence=ISS

GO:0051260 "protein homooligomerization" evidence=ISS

GO:0061014 "positive regulation of mRNA catabolic process" evidence=ISS

GO:0070207 "protein homotrimerization" evidence=ISS

GO:0070584 "mitochondrion morphogenesis" evidence=ISS

GO:0071042 "nuclear polyadenylation-dependent mRNA catabolic process" evidence=ISS

GO:0071850 "mitotic cell cycle arrest" evidence=ISS

GO:0097222 "mitochondrial mRNA polyadenylation" evidence=ISS

GO:2000627 "positive regulation of miRNA catabolic process" evidence=ISS

GO:2000772 "regulation of cellular senescence" evidence=ISS

---

Prediction of Enzyme Commission (EC) Number

EC Number Prediction by Annotation Transfer from SWISS-PROT Entries

Original result of BLAST against SWISS-PROT

ID	Name	Annotated EC number	Identity	Query coverage	Hit coverage	RBH(Q2H)	RBH(H2Q)
Q9S7G6	PNP2_ARATH	2, ., 7, ., 7, ., 8	0.6765	0.9733	0.9566	yes	no
Q6KAI0	PNP2_ORYSJ	2, ., 7, ., 7, ., 8	0.6620	0.9342	0.9266	yes	no

EC Number Prediction by Ezypred Server

Original result from Ezypred Server

Fail to connect to Ezypred Server

EC Number Prediction by EFICAz Software

Prediction Level	EC number	Confidence of Prediction
4th Layer	2.7.7.8	0.824
3rd Layer	2.7.7	0.766

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Prediction of Functionally Associated Proteins

Functionally Associated Proteins Detected by STRING

Original result from the STRING server

Fail to connect to STRING server

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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	974
PRK11824	693	PRK11824, PRK11824, polynucleotide phosphorylase/p	0.0
TIGR03591	684	TIGR03591, polynuc_phos, polyribonucleotide nucleo	0.0
COG1185	692	COG1185, Pnp, Polyribonucleotide nucleotidyltransf	0.0
TIGR02696	719	TIGR02696, pppGpp_PNP, guanosine pentaphosphate sy	1e-167
PLN00207	891	PLN00207, PLN00207, polyribonucleotide nucleotidyl	1e-155
cd11364	223	cd11364, RNase_PH_PNPase_2, Polyribonucleotide nuc	1e-137
cd11363	229	cd11363, RNase_PH_PNPase_1, Polyribonucleotide nuc	1e-116
pfam01138	129	pfam01138, RNase_PH, 3' exoribonuclease family, do	5e-30
cd11358	218	cd11358, RNase_PH, RNase PH-like 3'-5' exoribonucl	6e-29
pfam01138	129	pfam01138, RNase_PH, 3' exoribonuclease family, do	2e-26
cd04472	68	cd04472, S1_PNPase, S1_PNPase: Polynucleotide phos	2e-24
PRK03983	244	PRK03983, PRK03983, exosome complex exonuclease Rr	1e-22
cd11370	226	cd11370, RNase_PH_RRP41, RRP41 subunit of eukaryot	1e-21
TIGR02065	230	TIGR02065, ECX1, archaeal exosome-like complex exo	1e-21
COG0689	230	COG0689, Rph, RNase PH [Translation, ribosomal str	2e-21
cd11366	214	cd11366, RNase_PH_archRRP41, RRP41 subunit of arch	1e-18
COG1098	129	COG1098, VacB, Predicted RNA binding protein (cont	6e-18
PRK08059	123	PRK08059, PRK08059, general stress protein 13; Val	7e-18
pfam03726	80	pfam03726, PNPase, Polyribonucleotide nucleotidylt	8e-18
cd05692	69	cd05692, S1_RPS1_repeat_hs4, S1_RPS1_repeat_hs4: R	2e-17
COG0539	541	COG0539, RpsA, Ribosomal protein S1 [Translation,	4e-16
PRK00087	647	PRK00087, PRK00087, 4-hydroxy-3-methylbut-2-enyl d	2e-15
PRK06676	390	PRK06676, rpsA, 30S ribosomal protein S1; Reviewed	7e-15
cd05684	79	cd05684, S1_DHX8_helicase, S1_DHX8_helicase: The N	1e-14
smart00316	72	smart00316, S1, Ribosomal protein S1-like RNA-bind	3e-14
cd05686	73	cd05686, S1_pNO40, S1_pNO40: pNO40 , S1-like RNA-b	2e-13
PRK08582	139	PRK08582, PRK08582, hypothetical protein; Provisio	9e-13
cd11371	210	cd11371, RNase_PH_MTR3, MTR3 subunit of eukaryotic	5e-12
pfam00575	74	pfam00575, S1, S1 RNA binding domain	8e-12
cd11372	199	cd11372, RNase_PH_RRP46, RRP46 subunit of eukaryot	2e-11
cd05688	68	cd05688, S1_RPS1_repeat_ec3, S1_RPS1_repeat_ec3: R	2e-11
TIGR01966	236	TIGR01966, RNasePH, ribonuclease PH	2e-11
cd05685	68	cd05685, S1_Tex, S1_Tex: The C-terminal S1 domain	5e-11
PRK07400	318	PRK07400, PRK07400, 30S ribosomal protein S1; Revi	6e-11
cd11358	218	cd11358, RNase_PH, RNase PH-like 3'-5' exoribonucl	2e-10
PRK00087	647	PRK00087, PRK00087, 4-hydroxy-3-methylbut-2-enyl d	3e-10
cd00164	65	cd00164, S1_like, S1_like: Ribosomal protein S1-li	3e-10
COG2183	780	COG2183, Tex, Transcriptional accessory protein [T	4e-10
PRK06299	565	PRK06299, rpsA, 30S ribosomal protein S1; Reviewed	7e-10
pfam03725	68	pfam03725, RNase_PH_C, 3' exoribonuclease family,	8e-10
PRK06299	565	PRK06299, rpsA, 30S ribosomal protein S1; Reviewed	1e-09
PRK06676	390	PRK06676, rpsA, 30S ribosomal protein S1; Reviewed	2e-09
PRK07899	486	PRK07899, rpsA, 30S ribosomal protein S1; Reviewed	2e-09
TIGR00717	516	TIGR00717, rpsA, ribosomal protein S1	2e-09
TIGR00717	516	TIGR00717, rpsA, ribosomal protein S1	3e-09
cd05698	70	cd05698, S1_Rrp5_repeat_hs6_sc5, S1_Rrp5_repeat_hs	1e-08
PRK06299	565	PRK06299, rpsA, 30S ribosomal protein S1; Reviewed	2e-08
TIGR00717	516	TIGR00717, rpsA, ribosomal protein S1	2e-08
cd11363	229	cd11363, RNase_PH_PNPase_1, Polyribonucleotide nuc	4e-08
PRK13806	491	PRK13806, rpsA, 30S ribosomal protein S1; Provisio	4e-08
COG1093	269	COG1093, SUI2, Translation initiation factor 2, al	4e-08
cd04473	77	cd04473, S1_RecJ_like, S1_RecJ_like: The S1 domain	7e-08
cd04452	76	cd04452, S1_IF2_alpha, S1_IF2_alpha: The alpha sub	1e-07
PRK06299	565	PRK06299, rpsA, 30S ribosomal protein S1; Reviewed	2e-07
PRK12269	863	PRK12269, PRK12269, bifunctional cytidylate kinase	2e-07
PRK04282	271	PRK04282, PRK04282, exosome complex RNA-binding pr	2e-07
cd11362	227	cd11362, RNase_PH_bact, Ribonuclease PH	2e-07
PRK07899	486	PRK07899, rpsA, 30S ribosomal protein S1; Reviewed	3e-07
PRK13806	491	PRK13806, rpsA, 30S ribosomal protein S1; Provisio	5e-07
PRK07252	120	PRK07252, PRK07252, hypothetical protein; Provisio	6e-07
cd04461	83	cd04461, S1_Rrp5_repeat_hs8_sc7, S1_Rrp5_repeat_hs	8e-07
cd11365	256	cd11365, RNase_PH_archRRP42, RRP42 subunit of arch	8e-07
PRK03987	262	PRK03987, PRK03987, translation initiation factor	1e-06
cd11369	261	cd11369, RNase_PH_RRP43, RRP43 subunit of eukaryot	1e-06
cd02393	61	cd02393, PNPase_KH, Polynucleotide phosphorylase (	2e-06
PRK05807	136	PRK05807, PRK05807, hypothetical protein; Provisio	6e-06
cd05708	77	cd05708, S1_Rrp5_repeat_sc12, S1_Rrp5_repeat_sc12:	1e-05
cd05691	73	cd05691, S1_RPS1_repeat_ec6, S1_RPS1_repeat_ec6: R	1e-05
PRK12269	863	PRK12269, PRK12269, bifunctional cytidylate kinase	2e-05
COG0539	541	COG0539, RpsA, Ribosomal protein S1 [Translation,	3e-05
COG1107	715	COG1107, COG1107, Archaea-specific RecJ-like exonu	4e-05
cd05687	70	cd05687, S1_RPS1_repeat_ec1_hs1, S1_RPS1_repeat_ec	4e-05
COG0689	230	COG0689, Rph, RNase PH [Translation, ribosomal str	5e-05
pfam03725	68	pfam03725, RNase_PH_C, 3' exoribonuclease family,	5e-05
COG2123	272	COG2123, COG2123, RNase PH-related exoribonuclease	9e-05
PRK06676	390	PRK06676, rpsA, 30S ribosomal protein S1; Reviewed	1e-04
PRK00087	647	PRK00087, PRK00087, 4-hydroxy-3-methylbut-2-enyl d	2e-04
PRK00173	238	PRK00173, rph, ribonuclease PH; Reviewed	2e-04
cd11368	259	cd11368, RNase_PH_RRP45, RRP45 subunit of eukaryot	2e-04
cd05690	69	cd05690, S1_RPS1_repeat_ec5, S1_RPS1_repeat_ec5: R	5e-04
COG0539	541	COG0539, RpsA, Ribosomal protein S1 [Translation,	7e-04
COG0831	100	COG0831, UreA, Urea amidohydrolase (urease) gamma	0.001
cd11367	272	cd11367, RNase_PH_RRP42, RRP42 subunit of eukaryot	0.001
TIGR00717	516	TIGR00717, rpsA, ribosomal protein S1	0.002
cd04453	88	cd04453, S1_RNase_E, S1_RNase_E: RNase E and RNase	0.002
cd05689	72	cd05689, S1_RPS1_repeat_ec4, S1_RPS1_repeat_ec4: R	0.003
cd04471	83	cd04471, S1_RNase_R, S1_RNase_R: RNase R C-termina	0.004

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

 Score =  871 bits (2254), Expect = 0.0
 Identities = 331/701 (47%), Positives = 465/701 (66%), Gaps = 14/701 (1%)

Query: 57  ETFKEEFEIGSRLITLETGKIARFANGAVVLGMDETKVLSTVTSSKGDSV-RDFLPLTVD 115
               +  E G R +TLETGK+AR ANGAV++   +T VL TV +SK     +DF PLTVD
Sbjct: 3   NKIVKSIEFGGRTLTLETGKLARQANGAVLVRYGDTVVLVTVVASKEPKEGQDFFPLTVD 62

Query: 116 YQEKQFAQGVIPNTYMRREGAPKERELLVGRIIDRPIRPLFPAGFYHEVQVMASVLSSDG 175
           Y+EK +A G IP  + +REG P E+E L  R+IDRPIRPLFP GF +EVQV+A+VLS D 
Sbjct: 63  YEEKTYAAGKIPGGFFKREGRPSEKETLTSRLIDRPIRPLFPKGFRNEVQVVATVLSVDP 122

Query: 176 KQDPDIMAANATSAALMLSDIPWGGPIGMIRIGRICGQFIVNPTMDELSLSDLNLVYACT 235
           + DPDI+A    SAAL +S IP+ GPI  +R+G I G+F++NPT++EL  SDL+LV A T
Sbjct: 123 ENDPDILAMIGASAALSISGIPFNGPIAAVRVGYIDGEFVLNPTVEELEESDLDLVVAGT 182

Query: 236 REKTLMIDVQAREISEKDLEAGLRLAHPEAVKYLEPQIRLAEKAGKQKKEYKLSMISEQT 295
           ++  LM++ +A+E+SE+ +   +   H    + ++ Q  LA +AG  K E++   + E+ 
Sbjct: 183 KDAVLMVESEAKELSEEVMLEAIEFGHEAIQELIDAQEELAAEAGP-KWEWQPPEVDEEL 241

Query: 296 LEKVSNLAEAHIEAVFTDPSYSKFERGEALDKIGQDVKKAL-EEECDEESLQVLPKAVDT 354
              V  LAEA ++  +      K ER  ALD I ++V +AL  EE +EE  + + +A   
Sbjct: 242 KAAVKELAEAKLKEAYQIT--DKQEREAALDAIKEEVLEALAAEEEEEEDEKEIKEAFKK 299

Query: 355 VRKRVIRKRIIAEGVRVDGRQLDEVRPIYCESGNLPILHGSSLFSRGDTQVLCTVTLGAP 414
           + K+++R+RI+ EG+R+DGR+LDE+RPI  E G LP  HGS+LF+RG+TQ L   TLG  
Sbjct: 300 LEKKIVRRRILEEGIRIDGRKLDEIRPISIEVGVLPRTHGSALFTRGETQALVVATLGTL 359

Query: 415 AEAQRLESLVGPPTKRFMLHYSFPPFCINEVGKRVGLNRREVGHGTLAEKALLAVLPPEN 474
            + Q ++ L G   KRFMLHY+FPP+ + E G+     RRE+GHG LAE+AL  VLP E 
Sbjct: 360 RDEQIIDGLEGEYKKRFMLHYNFPPYSVGETGRVGSPGRREIGHGALAERALEPVLPSEE 419

Query: 475 DFPYTVRVNSEVMASDGSTSMATVCGGSMALMDAGIPLQEHVAGVSVGLVSEVDPSTGEI 534
           +FPYT+RV SE++ S+GS+SMA+VCG S+ALMDAG+P++  VAG+++GL+ E D      
Sbjct: 420 EFPYTIRVVSEILESNGSSSMASVCGSSLALMDAGVPIKAPVAGIAMGLIKEGD------ 473

Query: 535 KDYRILTDILGLEDHLGDMDFKIAGTRIGVTAIQLDIKPAGIPLDIICECLEHAHKGRLQ 594
             Y +LTDILG EDHLGDMDFK+AGTR G+TA+Q+DIK  GI  +I+ E LE A +GRL 
Sbjct: 474 -KYAVLTDILGDEDHLGDMDFKVAGTRDGITALQMDIKIDGITREILEEALEQAKEGRLH 532

Query: 595 ILDHMEREISAPRTQDDRNSPRLATLKYDNDTLRRLIGPLGALKRKIEEETGGRISVSD- 653
           IL  M   IS PR +    +PR+ T+K   D +R +IGP G   R+I EETG +I + D 
Sbjct: 533 ILGKMNEAISEPRAELSPYAPRIETIKIPPDKIRDVIGPGGKTIREITEETGAKIDIEDD 592

Query: 654 GTLTVVAKNRSVMEKVLEKVDFIIGREIEVGGIYKGVVTSVKEYGAFVEFNGGQQGLLHV 713
           GT+ + A +    E   E+++ I   E EVG IY+G V  + ++GAFVE   G+ GL+H+
Sbjct: 593 GTVKIAATDGEAAEAAKERIEGIT-AEPEVGEIYEGKVVRIVDFGAFVEILPGKDGLVHI 651

Query: 714 SELSHEPVSRVSDVVSVGQQLSLRCIGQDVRGNIKLSLKAV 754
           SE++ E V +V DV+  G ++ ++ +  D RG I+LS KAV
Sbjct: 652 SEIADERVEKVEDVLKEGDEVKVKVLEIDKRGRIRLSRKAV 692

Length = 693

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

 Score =  828 bits (2142), Expect = 0.0
 Identities = 331/693 (47%), Positives = 468/693 (67%), Gaps = 16/693 (2%)

Query: 64  EIGSRLITLETGKIARFANGAVVLGMDETKVLSTVTSSK-GDSVRDFLPLTVDYQEKQFA 122
           E G R +TLETGKIAR A+GAVV+   +T VL TV ++K     +DF PLTV+YQEK +A
Sbjct: 1   EYGGRTLTLETGKIARQADGAVVVRYGDTVVLVTVVAAKEAKEGQDFFPLTVNYQEKFYA 60

Query: 123 QGVIPNTYMRREGAPKERELLVGRIIDRPIRPLFPAGFYHEVQVMASVLSSDGKQDPDIM 182
            G IP  + +REG P E+E L  R+IDRPIRPLFP GF +EVQV+A+VLS D + DPDI+
Sbjct: 61  AGKIPGGFFKREGRPSEKETLTSRLIDRPIRPLFPKGFRNEVQVVATVLSYDPENDPDIL 120

Query: 183 AANATSAALMLSDIPWGGPIGMIRIGRICGQFIVNPTMDELSLSDLNLVYACTREKTLMI 242
           A    SAAL +S IP+ GPI  +R+G I GQ+++NPT+DEL  SDL+LV A T++  LM+
Sbjct: 121 AIIGASAALAISGIPFNGPIAAVRVGYIDGQYVLNPTVDELEKSDLDLVVAGTKDAVLMV 180

Query: 243 DVQAREISEKDLEAGLRLAHPEAVKYLEPQIRLAEKAGKQKKEYKLSMISEQTLEKVSNL 302
           + +A+E+SE+ +   +   H E    +E    LAE+AGK+K E+    + E+   KV  L
Sbjct: 181 ESEAKELSEEVMLGAIEFGHEEIQPVIEAIEELAEEAGKEKWEFVAPEVDEELKAKVKEL 240

Query: 303 A-EAHIEAVFTDPSYSKFERGEALDKIGQDVKKALEEECDEE----SLQVLPKAVDTVRK 357
           A EA ++  +      K ER  ALD I ++V +AL EE +EE      + + +A   + K
Sbjct: 241 AYEAGLKEAYQITE--KQERYAALDAIKEEVLEALAEEEEEEEEADREKEIKEAFKDLEK 298

Query: 358 RVIRKRIIAEGVRVDGRQLDEVRPIYCESGNLPILHGSSLFSRGDTQVLCTVTLGAPAEA 417
           +++R+RI+ EG R+DGR LD +RPI  E G LP  HGS+LF+RG+TQ L   TLG   + 
Sbjct: 299 KIVRERILKEGKRIDGRDLDTIRPISIEVGVLPRTHGSALFTRGETQALVVTTLGTERDE 358

Query: 418 QRLESLVGPPTKRFMLHYSFPPFCINEVGKRVGLNRREVGHGTLAEKALLAVLPPENDFP 477
           Q ++ L G   KRFMLHY+FPP+ + EVG+  G  RRE+GHG LAE+AL AVLP E +FP
Sbjct: 359 QIIDDLEGEYRKRFMLHYNFPPYSVGEVGRVGGPGRREIGHGALAERALKAVLPSEEEFP 418

Query: 478 YTVRVNSEVMASDGSTSMATVCGGSMALMDAGIPLQEHVAGVSVGLVSEVDPSTGEIKDY 537
           YT+RV SE++ S+GS+SMA+VCGGS+ALMDAG+P++  VAG+++GL+ E D      + +
Sbjct: 419 YTIRVVSEILESNGSSSMASVCGGSLALMDAGVPIKAPVAGIAMGLIKEGD------ERF 472

Query: 538 RILTDILGLEDHLGDMDFKIAGTRIGVTAIQLDIKPAGIPLDIICECLEHAHKGRLQILD 597
            +L+DILG EDHLGDMDFK+AGTR G+TA+Q+DIK  GI  +I+ + LE A +GRL IL 
Sbjct: 473 AVLSDILGDEDHLGDMDFKVAGTRDGITALQMDIKIDGITREIMEQALEQAKEGRLHILG 532

Query: 598 HMEREISAPRTQDDRNSPRLATLKYDNDTLRRLIGPLGALKRKIEEETGGRISVSD-GTL 656
            M + IS PR +    +PR+ T+K + D +R +IGP G + R+I EETG +I + D GT+
Sbjct: 533 EMNKVISEPRAELSPYAPRIETIKINPDKIRDVIGPGGKVIREITEETGAKIDIEDDGTV 592

Query: 657 TVVAKNRSVMEKVLEKVDFIIGREIEVGGIYKGVVTSVKEYGAFVEFNGGQQGLLHVSEL 716
            + A +    E  ++ ++ I   E EVG IY+G V  + ++GAFVE   G+ GL+H+SE+
Sbjct: 593 KIAASDGEAAEAAIKMIEGIT-AEPEVGKIYEGKVVRIMDFGAFVEILPGKDGLVHISEI 651

Query: 717 SHEPVSRVSDVVSVGQQLSLRCIGQDVRGNIKL 749
           ++E V +V DV+  G ++ ++ +  D +G IKL
Sbjct: 652 ANERVEKVEDVLKEGDEVKVKVLEIDKQGRIKL 684

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

 Score =  738 bits (1907), Expect = 0.0
 Identities = 323/702 (46%), Positives = 458/702 (65%), Gaps = 12/702 (1%)

Query: 56  LETFKEEFEIGSRLITLETGKIARFANGAVVLGMDETKVLSTVTSSKGDSVRDFLPLTVD 115
                +  E G R +TLETGKIAR ANGAV++   +T VL+TV +SK    +DF PLTV+
Sbjct: 2   FNKIVKTIEWGGRTLTLETGKIARQANGAVLVRYGDTVVLATVVASKPKEGQDFFPLTVN 61

Query: 116 YQEKQFAQGVIPNTYMRREGAPKERELLVGRIIDRPIRPLFPAGFYHEVQVMASVLSSDG 175
           Y+EK +A G IP  + +REG P E+E+L  R+IDRPIRPLFP GF +EVQ++ +VLS D 
Sbjct: 62  YEEKTYAAGKIPGGFFKREGRPSEKEILTSRLIDRPIRPLFPKGFRNEVQIVNTVLSVDP 121

Query: 176 KQDPDIMAANATSAALMLSDIPWGGPIGMIRIGRICGQFIVNPTMDELSLSDLNLVYACT 235
           + DPDI+A    SAAL LS IP+ GPIG +R+G I G F++NPT++EL  S L+LV A T
Sbjct: 122 ENDPDILAMVGASAALSLSGIPFLGPIGAVRVGYIDGIFVLNPTLEELEESKLDLVVAGT 181

Query: 236 REKTLMIDVQAREISEKDLEAGLRLAHPEAVKYLEPQIRLAEKAGKQKKEYKLSMISEQT 295
           ++   M++ +A E+ E+ +   +   H      +  Q  LA + GK+K E +   + E+ 
Sbjct: 182 KDAVNMVESEADELDEEVMLEAVEFGHEAIQSVINAQEELALEVGKKKWELEPPSLDEEL 241

Query: 296 LEKVSNLAEAHIEAVFTDPSYSKFERGEALDKIGQDVKKALEEECDEESLQVLPKAVDTV 355
             KV +LAE  ++         K ER  ALD I + +++ L  E +E SL+ +   ++ +
Sbjct: 242 EAKVRDLAEDELKEAVG--IREKQERSAALDAIKEKIEEELSGE-EESSLKEIKAILEKL 298

Query: 356 RKRVIRKRIIAEGVRVDGRQLDEVRPIYCESGNLPILHGSSLFSRGDTQVLCTVTLGAPA 415
            K+ +R+ I+   VR+DGR  DEVRPI  E G LP  HGS+LF+RG+TQ L  VTLG P 
Sbjct: 299 EKKPVRRLILEGKVRIDGRFGDEVRPIGIEVGVLPRTHGSALFTRGETQALVVVTLGTPR 358

Query: 416 EAQRLESLVGPPTKRFMLHYSFPPFCINEVGKRVGLNRREVGHGTLAEKALLAVLPPEND 475
           +AQ ++ L G   KRF+LHY+FPPF + E G+     RRE+GHG LAE+AL  VLP E +
Sbjct: 359 DAQVIDILEGEYKKRFLLHYNFPPFSVGETGRMGSPGRREIGHGALAERALAPVLPSEEE 418

Query: 476 FPYTVRVNSEVMASDGSTSMATVCGGSMALMDAGIPLQEHVAGVSVGLVSEVDPSTGEIK 535
           FPYT+RV SE++ S+GS+SMA+VCGGS+ALMDAG+P++  VAG+++GL+ E D       
Sbjct: 419 FPYTIRVVSEILESNGSSSMASVCGGSLALMDAGVPIKAPVAGIAMGLIKEGD------- 471

Query: 536 DYRILTDILGLEDHLGDMDFKIAGTRIGVTAIQLDIKPAGIPLDIICECLEHAHKGRLQI 595
            Y +L+DILG EDHLGDMDFK+AGT  G+TA+Q+DIK  GI  +I+ + LE A   RL I
Sbjct: 472 KYAVLSDILGDEDHLGDMDFKVAGTDDGITALQMDIKIKGITKEIMKKALEQAKGARLHI 531

Query: 596 LDHMEREISAPRTQDDRNSPRLATLKYDNDTLRRLIGPLGALKRKIEEETGGRISVS-DG 654
           L  M   IS PR +    +PR+ T+K D D +R +IGP G   + I EETG +I +  DG
Sbjct: 532 LIVMNEAISEPRKELSPYAPRIETIKIDPDKIRDVIGPGGKTIKAITEETGVKIDIEDDG 591

Query: 655 TLTVVAKNRSVMEKVLEKVDFIIGREIEVGGIYKGVVTSVKEYGAFVEFNGGQQGLLHVS 714
           T+ + A +    +K  E+++ I  RE+EVG +Y+G V  + ++GAFVE   G+ GL+H+S
Sbjct: 592 TVKIAASDGESAKKAKERIEAIT-REVEVGEVYEGTVVRIVDFGAFVELLPGKDGLVHIS 650

Query: 715 ELSHEPVSRVSDVVSVGQQLSLRCIGQDVRGNIKLSLKAVSP 756
           +L+ E V +V DV+  G ++ ++ I  D +G I+LS+KAV  
Sbjct: 651 QLAKERVEKVEDVLKEGDEVKVKVIEIDKQGRIRLSIKAVLE 692

Length = 692

>gnl|CDD|131743 TIGR02696, pppGpp_PNP, guanosine pentaphosphate synthetase I/polynucleotide phosphorylase

 Score =  505 bits (1302), Expect = e-167
 Identities = 283/714 (39%), Positives = 406/714 (56%), Gaps = 39/714 (5%)

Query: 66  GSRLITLETGKIARFANGAVVLGMD-ETKVLSTVTSSKG--DSVRDFLPLTVDYQEKQFA 122
           G+R I  ETG++AR A G+VV  +D ET +LS  T+SK   D   DF PLTVD +E+ +A
Sbjct: 15  GTRTIRFETGRLARQAAGSVVAYLDDETMLLSATTASKQPKDQF-DFFPLTVDVEERMYA 73

Query: 123 QGVIPNTYMRREGAPKERELLVGRIIDRPIRPLFPAGFYHEVQVMASVLSSDGKQDPDIM 182
            G IP ++ RREG P    +L  R+IDRP+RP F  G  +EVQV+ +VLS +     D++
Sbjct: 74  AGRIPGSFFRREGRPSTDAILTCRLIDRPLRPSFVKGLRNEVQVVVTVLSLNPDHLYDVV 133

Query: 183 AANATSAALMLSDIPWGGPIGMIRIGRICGQFIVNPTMDELSLSDLNLVYAC-------- 234
           A NA SA+  L+ +P+ GPIG +R+  I GQ++  PT ++L  +  ++V A         
Sbjct: 134 AINAASASTQLAGLPFSGPIGGVRVALIDGQWVAFPTHEQLEGAVFDMVVAGRVLENGDV 193

Query: 235 --------TREKTL-MIDVQAREISEKDLEAGLRLAHPEAVKYLEPQIRLAEKAGKQKKE 285
                     EKT  ++   A   +E+ +  GL  A P        Q  LAEKA K   E
Sbjct: 194 AIMMVEAEATEKTWDLVKGGAEAPTEEVVAEGLEAAKPFIKVLCRAQADLAEKAAKPTGE 253

Query: 286 YKLSM-ISEQTLEKVSNLAEAHIEAVFTDPSYSKFERGEALDKIGQDVKKALEEECDEES 344
           + L     +   E V    +  + A  T     K ER EALD++   V   L E+  E  
Sbjct: 254 FPLFPDYQDDVYEAVEGAVKDELSAALT--IAGKQEREEALDEVKALVAAKLAEQF-EGR 310

Query: 345 LQVLPKAVDTVRKRVIRKRIIAEGVRVDGRQLDEVRPIYCESGNLPILHGSSLFSRGDTQ 404
            + +  A   V K+++R+R++ EGVR+DGR + ++RP+  E   +P +HGS+LF RG+TQ
Sbjct: 311 EKEISAAYRAVTKKLVRERVLTEGVRIDGRGVTDIRPLDAEVQVIPRVHGSALFERGETQ 370

Query: 405 VLCTVTLGAPAEAQRLESLVGPPTKRFMLHYSFPPFCINEVGKRVGL-NRREVGHGTLAE 463
           +L   TL      Q+++SL    +KR+M HY+FPP+   E G RVG   RRE+GHG LAE
Sbjct: 371 ILGVTTLNMLKMEQQIDSLSPETSKRYMHHYNFPPYSTGETG-RVGSPKRREIGHGALAE 429

Query: 464 KALLAVLPPENDFPYTVRVNSEVMASDGSTSMATVCGGSMALMDAGIPLQEHVAGVSVGL 523
           +AL+ VLP   +FPY +R  SE + S+GSTSM +VC  +++L++AG+PL+  VAG+++GL
Sbjct: 430 RALVPVLPSREEFPYAIRQVSEALGSNGSTSMGSVCASTLSLLNAGVPLKAPVAGIAMGL 489

Query: 524 VSEVDPSTGEIKDYRILTDILGLEDHLGDMDFKIAGTRIGVTAIQLDIKPAGIPLDIICE 583
           +S+     GE + Y  LTDILG ED  GDMDFK+AGT   VTA+QLD K  GIP  ++  
Sbjct: 490 ISDE--VDGETR-YVALTDILGAEDAFGDMDFKVAGTSEFVTALQLDTKLDGIPASVLAS 546

Query: 584 CLEHAHKGRLQILDHMEREISAPRTQDDRNSPRLATLKYDNDTLRRLIGPLGALKRKIEE 643
            L+ A   RL ILD M   I  P       +PR+ T+K   D +  +IGP G +  +I++
Sbjct: 547 ALKQARDARLAILDVMAEAIDTPDEMSP-YAPRIITVKIPVDKIGEVIGPKGKMINQIQD 605

Query: 644 ETGGRISVS-DGTLTVVAKNRSVMEKVLEKVDFIIG-REIEVGGIYKGVVTSVKEYGAFV 701
           ETG  IS+  DGT+ + A +    E     ++ I      EVG  + G V     +GAFV
Sbjct: 606 ETGAEISIEDDGTVYIGAADGPSAEAARAMINAIANPTMPEVGERFLGTVVKTTAFGAFV 665

Query: 702 EFNGGQQGLLHVSELSH----EPVSRVSDVVSVGQQLSLRCIGQDVRGNIKLSL 751
               G+ GLLH+S++      + V  V DV+SVGQ++ +     D RG  KLSL
Sbjct: 666 SLLPGKDGLLHISQIRKLAGGKRVENVEDVLSVGQKIQVEIADIDDRG--KLSL 717

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|215104 PLN00207, PLN00207, polyribonucleotide nucleotidyltransferase; Provisional

 Score =  480 bits (1237), Expect = e-155
 Identities = 283/835 (33%), Positives = 425/835 (50%), Gaps = 71/835 (8%)

Query: 40  EPAPPTPAPSVAGTKVLETFKEEFEIGSRLITLETGKIARFANGAVVLGMDETKVLSTV- 98
           E   P P            F  +  +G R I +ETG I R A+G+V +   ET V ++V 
Sbjct: 71  EGPGPFPQQ----------FSVKIPVGDRHILVETGHIGRQASGSVTVTDGETIVYTSVC 120

Query: 99  TSSKGDSVRDFLPLTVDYQEKQFAQGVIPNTYMRREGAPKERELLVGRIIDRPIRPLFPA 158
            +       DF PL+V YQE+  A G     + +REG  K+ E+L+ R+IDRP+RP  P 
Sbjct: 121 LADVPSEPSDFFPLSVHYQERFSAAGRTSGGFFKREGRTKDHEVLICRLIDRPLRPTMPK 180

Query: 159 GFYHEVQVMASVLSSDGKQDPDIMAANATSAALMLSDIPWGGPIGMIRIGRICGQFIVNP 218
           GFYHE Q+++ VLS DG   PD +A  A   A+ LS++P    I  +R+G I G+FIVNP
Sbjct: 181 GFYHETQILSWVLSYDGLHSPDSLAVTAAGIAVALSEVPNLKAIAGVRVGLIGGKFIVNP 240

Query: 219 TMDELSLSDLNLVYACTREKTLMIDVQAREISEKDLEAGLRLAHPEAVKYLEPQIR-LAE 277
           T  E+  S+L+L+ A T    LMI+     + E+ L   + +   +AV+ +  +I  L +
Sbjct: 241 TTKEMEESELDLIMAGTDSAILMIEGYCNFLPEEKLLEAVEVGQ-DAVRAICKEIEVLVK 299

Query: 278 KAGKQKKEYKLSMISEQTLEKVSNLA-----------------------EAHIEAVFTDP 314
           K GK K    + +   +  + V  +A                       E  + ++ T+ 
Sbjct: 300 KCGKPKMLDAIKLPPPELYKHVKEIAGDELVKALQIRGKIPRRKALSSLEEKVLSILTEE 359

Query: 315 SYSKFERGEALDKIGQDVKKALEE--------ECDEESLQVLP----------KAVDT-- 354
            Y   +      +   D+ +  +E        E DE  + + P            VD   
Sbjct: 360 GYVSKDESFGTSETRADLLEDEDEDEEVVVDGEVDEGDVHIKPIPRKSSPLLFSEVDVKL 419

Query: 355 ----VRKRVIRKRIIAEGVRVDGRQLDEVRPIYCESGNLPILHGSSLFSRGDTQVLCTVT 410
               V  + +R+RI+  G R DGR  DE+RPI    G LP  HGS+LF+RG+TQ L  VT
Sbjct: 420 VFKEVTSKFLRRRIVEGGKRSDGRTPDEIRPINSSCGLLPRAHGSALFTRGETQALAVVT 479

Query: 411 LGAPAEAQRLESLVGP-PTKRFMLHYSFPPFCINEVGKRVGLNRREVGHGTLAEKALLAV 469
           LG    AQR+++LV     KRF L YSFPP C+ EVG+    +RRE+GHG LAE+AL  +
Sbjct: 480 LGDKQMAQRIDNLVDADEVKRFYLQYSFPPSCVGEVGRIGAPSRREIGHGMLAERALEPI 539

Query: 470 LPPENDFPYTVRVNSEVMASDGSTSMATVCGGSMALMDAGIPLQEHVAGVSVGLVSEVDP 529
           LP E+DFPYT+RV S +  S+GS+SMA+VCGG +AL DAG+P++  +AG+++G+V + + 
Sbjct: 540 LPSEDDFPYTIRVESTITESNGSSSMASVCGGCLALQDAGVPVKCPIAGIAMGMVLDTEE 599

Query: 530 STGEIKDYRILTDILGLEDHLGDMDFKIAGTRIGVTAIQLDIKPAGIPLDIICECLEHAH 589
             G+     IL+DI G ED  GDMDFK+AG   G+TA Q+DIK  GI L I+   L  A 
Sbjct: 600 FGGDGSPL-ILSDITGSEDASGDMDFKVAGNEDGITAFQMDIKVGGITLPIMERALLQAK 658

Query: 590 KGRLQILDHMEREISAPRTQDDRNSPRLATLKYDNDTLRRLIGPLGALKRKIEEETG-GR 648
            GR  IL  M +    P  +  + +P +  +K   + +  +IG  G   + I EETG   
Sbjct: 659 DGRKHILAEMSKCSPPPSKRLSKYAPLIHIMKVKPEKVNMIIGSGGKKVKSIIEETGVEA 718

Query: 649 ISVS-DGTLTVVAKNRSVMEKVLEKVDFIIGREIEVGGIYKGV-VTSVKEYGAFVEFNGG 706
           I    DGT+ + AK+ S +EK    +  +      VG IY+   + S+  YGAFVE   G
Sbjct: 719 IDTQDDGTVKITAKDLSSLEKSKAIISSLT-MVPTVGDIYRNCEIKSIAPYGAFVEIAPG 777

Query: 707 QQGLLHVSELSHEPVSRVSDVVSVGQQLSLRCIGQDVRGNIKLSLKAVSPRPEADVKGVV 766
           ++GL H+SELS   +++  D   VG ++ ++ I  + +G ++LS +A+ P   ++     
Sbjct: 778 REGLCHISELSSNWLAKPEDAFKVGDRIDVKLIEVNDKGQLRLSRRALLPEANSEKSSQK 837

Query: 767 EGSVPVNKQATDVWASVGDVSNGQNPELPMRKNETPGVNSSTSSTPAVLIRSAAE 821
           +          D       V+    P     + E     ++         R+ + 
Sbjct: 838 QQG----GSTKDKAPQKKYVNTSSRPR-RAAQAEKNSAENAAVPKKKDYKRATSG 887

Length = 891

>gnl|CDD|206769 cd11364, RNase_PH_PNPase_2, Polyribonucleotide nucleotidyltransferase, repeat 2

 Score =  408 bits (1052), Expect = e-137
 Identities = 143/229 (62%), Positives = 182/229 (79%), Gaps = 6/229 (2%)

Query: 378 EVRPIYCESGNLPILHGSSLFSRGDTQVLCTVTLGAPAEAQRLESLVGPPTKRFMLHYSF 437
           E+RPI CE G LP  HGS+LF+RG+TQVLCTVTLG   +AQ+++SL G  +KRFMLHY+F
Sbjct: 1   EIRPISCEVGLLPRTHGSALFTRGETQVLCTVTLGTLEDAQKIDSLGGEKSKRFMLHYNF 60

Query: 438 PPFCINEVGKRVGLNRREVGHGTLAEKALLAVLPPENDFPYTVRVNSEVMASDGSTSMAT 497
           PP+ + E G+  G  RRE+GHG LAE+ALL VLP   DFPYT+RV SEV+ S+GS+SMA+
Sbjct: 61  PPYSVGETGRVGGPGRREIGHGALAERALLPVLPSPEDFPYTIRVVSEVLESNGSSSMAS 120

Query: 498 VCGGSMALMDAGIPLQEHVAGVSVGLVSEVDPSTGEIKDYRILTDILGLEDHLGDMDFKI 557
           VCGGS+ALMDAG+P++  VAG+++GL++E       I DYR+LTDILGLEDHLGDMDFK+
Sbjct: 121 VCGGSLALMDAGVPIKAPVAGIAMGLITE------GIDDYRVLTDILGLEDHLGDMDFKV 174

Query: 558 AGTRIGVTAIQLDIKPAGIPLDIICECLEHAHKGRLQILDHMEREISAP 606
           AGTR G+TA+Q+DIK  GI L+I+ E L+ A +GRL ILD ME+ IS P
Sbjct: 175 AGTRDGITALQMDIKIPGITLEIMREALQQAKEGRLHILDIMEKAISEP 223

Polyribonucleotide nucleotidyltransferase (PNPase) is a member of the RNase_PH family, named after the bacterial Ribonuclease PH, a 3'-5' exoribonuclease. Structurally, all members of this family form hexameric rings. In the case of PNPase the complex is a trimer, since each monomer contains two tandem copies of the domain. PNPase is involved in mRNA degradation in a 3'-5' direction and in quality control of ribosomal RNA precursors, with the second repeat containing the active site. PNPase is part of the RNA degradosome complex and binds to the scaffolding domain of the endoribonuclease RNase E. Length = 223

>gnl|CDD|206768 cd11363, RNase_PH_PNPase_1, Polyribonucleotide nucleotidyltransferase, repeat 1

 Score =  356 bits (916), Expect = e-116
 Identities = 116/229 (50%), Positives = 159/229 (69%), Gaps = 1/229 (0%)

Query: 59  FKEEFEIGSRLITLETGKIARFANGAVVLGMDETKVLSTVTSSKG-DSVRDFLPLTVDYQ 117
              E  +G R +T ETGK+A+ A+G+VV+   +T VL T  SSK      DF PLTVDY+
Sbjct: 1   KVFEVLVGGRTLTFETGKLAKQADGSVVVQYGDTVVLVTAVSSKKPKEGIDFFPLTVDYR 60

Query: 118 EKQFAQGVIPNTYMRREGAPKERELLVGRIIDRPIRPLFPAGFYHEVQVMASVLSSDGKQ 177
           EK +A G IP  + +REG P E+E+L  R+IDRPIRPLFP GF +EVQV+A+VLS DG  
Sbjct: 61  EKLYAAGKIPGGFFKREGRPSEKEILTSRLIDRPIRPLFPKGFRNEVQVIATVLSVDGVN 120

Query: 178 DPDIMAANATSAALMLSDIPWGGPIGMIRIGRICGQFIVNPTMDELSLSDLNLVYACTRE 237
           DPD++A N  SAAL LSDIP+ GP+G +R+GRI G+F+VNPT +EL  SDL+LV A T++
Sbjct: 121 DPDVLAINGASAALSLSDIPFNGPVGAVRVGRIDGEFVVNPTREELEESDLDLVVAGTKD 180

Query: 238 KTLMIDVQAREISEKDLEAGLRLAHPEAVKYLEPQIRLAEKAGKQKKEY 286
             LM++  A+E+SE+D+   ++  H    + +  Q  LA + GK+K+EY
Sbjct: 181 AVLMVEAGAKEVSEEDMLEAIKFGHEAIQQLIAAQEELAAEVGKEKREY 229

Polyribonucleotide nucleotidyltransferase (PNPase) is a member of the RNase_PH family, named after the bacterial Ribonuclease PH, a 3'-5' exoribonuclease. Structurally, all members of this family form hexameric rings. In the case of PNPase the complex is a trimer, since each monomer contains two tandem copies of the domain. PNPase is involved in mRNA degradation in a 3'-5' direction and in quality control of ribosomal RNA precursors. It is part of the RNA degradosome complex and binds to the scaffolding domain of the endoribonuclease RNase E. Length = 229

>gnl|CDD|216323 pfam01138, RNase_PH, 3' exoribonuclease family, domain 1

 Score =  115 bits (289), Expect = 5e-30
 Identities = 44/134 (32%), Positives = 64/134 (47%), Gaps = 5/134 (3%)

Query: 378 EVRPIYCESGNLPILHGSSLFSRGDTQVLCTVTLGAPAEAQRLESLVGPPTKRFMLHYSF 437
           E+RPI  E+G L    GS+L   GDT+VL TVT       +  +   G       + Y  
Sbjct: 1   ELRPIEIETGVLSQADGSALVELGDTKVLATVTGPIEPPQKERDFFPG----ELTVEYEE 56

Query: 438 PPFCINEVGKRVGLNRREVGHGTLAEKALLAVLPPENDFPYTVRVNSEVMASDGSTSMAT 497
            PF   E       + RE+    L ++AL   +P E    + +R++  V++ DGS   A 
Sbjct: 57  SPFASGER-PEGRPSEREIELSRLIDRALRPSIPLEGYPRWEIRIDVTVLSDDGSLLDAA 115

Query: 498 VCGGSMALMDAGIP 511
           +   S+AL DAGIP
Sbjct: 116 INAASLALADAGIP 129

This family includes 3'-5' exoribonucleases. Ribonuclease PH contains a single copy of this domain, and removes nucleotide residues following the -CCA terminus of tRNA. Polyribonucleotide nucleotidyltransferase (PNPase) contains two tandem copies of the domain. PNPase is involved in mRNA degradation in a 3'-5' direction. The exosome is a 3'-5' exoribonuclease complex that is required for 3' processing of the 5.8S rRNA. Three of its five protein components contain a copy of this domain. A hypothetical protein from S. pombe appears to belong to an uncharacterized subfamily. This subfamily is found in both eukaryotes and archaebacteria. Length = 129

>gnl|CDD|206766 cd11358, RNase_PH, RNase PH-like 3'-5' exoribonucleases

 Score =  115 bits (289), Expect = 6e-29
 Identities = 58/233 (24%), Positives = 90/233 (38%), Gaps = 33/233 (14%)

Query: 380 RPIYCESGNLPILHGSSLFSRGDTQVLCTVTLGAPAEAQRLESLVGPPTKRFMLHYSFPP 439
           RP+  E+G L    GS+L   G+T+V+C VT            L  P      ++    P
Sbjct: 2   RPVEIETGVLNQADGSALVKLGNTKVICAVTGPIVEPD----KLERPDKGTLYVNVEISP 57

Query: 440 FCINEVGKRVGLNRREVGHGTLAEKALLAV--LPPENDFP-YTVRVNSEVMASDGSTSMA 496
             + E  ++      E+    L E+ + A   L      P + + V+ +V++ DG    A
Sbjct: 58  GAVGE-RRQGPPGDEEMEISRLLERTIEASVILDKSTRKPSWVLYVDIQVLSRDGGLLDA 116

Query: 497 TVCGGSMALMDAGIPLQ-------------EHVAGVSVGLVSEVDPSTGEIKDYRILTDI 543
                  AL DAGIP               + +  VSVG +S          D  +L D 
Sbjct: 117 CWNAAIAALKDAGIPRVFVDERSPPLLLMKDLIVAVSVGGIS----------DGVLLLDP 166

Query: 544 LGLEDHLGDMDFKIAGTRIG-VTAIQLDIKPAGIPLDIICECLEHAHKGRLQI 595
            G E+ L D    +A  + G +  +      +    +I  ECLE A K  L +
Sbjct: 167 TGEEEELADSTLTVAVDKSGKLCLLSKVGGGSLDTEEIK-ECLELAKKRSLHL 218

RNase PH-like 3'-5' exoribonucleases are enzymes that catalyze the 3' to 5' processing and decay of RNA substrates. Evolutionarily related members can be fond in prokaryotes, archaea, and eukaryotes. Bacterial ribonuclease PH contains a single copy of this domain, and removes nucleotide residues following the -CCA terminus of tRNA. Polyribonucleotide nucleotidyltransferase (PNPase) contains two tandem copies of the domain and is involved in mRNA degradation in a 3'-5' direction. Archaeal exosomes contain two individually encoded RNase PH-like 3'-5' exoribonucleases and are required for 3' processing of the 5.8S rRNA. The eukaryotic exosome core is composed of six individually encoded RNase PH-like subunits, but it is not a phosphorolytic enzyme per se; it directly associates with Rrp44 and Rrp6, which are hydrolytic exoribonucleases related to bacterial RNase II/R and RNase D. All members of the RNase PH-like family form ring structures by oligomerization of six domains or subunits, except for a total of 3 subunits with tandem repeats in the case of PNPase, with a central channel through which the RNA substrate must pass to gain access to the phosphorolytic active sites. Length = 218

>gnl|CDD|216323 pfam01138, RNase_PH, 3' exoribonuclease family, domain 1

 Score =  104 bits (263), Expect = 2e-26
 Identities = 55/136 (40%), Positives = 75/136 (55%), Gaps = 15/136 (11%)

Query: 68  RLITLETGKIARFANGAVVLGMDETKVLSTVTSSKGDSV--RDFLP--LTVDYQEKQFAQ 123
           R I +ETG +   A+G+ ++ + +TKVL+TVT         RDF P  LTV+Y+E  FA 
Sbjct: 3   RPIEIETG-VLSQADGSALVELGDTKVLATVTGPIEPPQKERDFFPGELTVEYEESPFAS 61

Query: 124 GVIPNTYMRREGAPKERELLVGRIIDRPIRPLFPAGFYH--EVQVMASVLSSDGKQDPDI 181
           G  P      EG P ERE+ + R+IDR +RP  P   Y   E+++  +VLS DG      
Sbjct: 62  GERP------EGRPSEREIELSRLIDRALRPSIPLEGYPRWEIRIDVTVLSDDG--SLLD 113

Query: 182 MAANATSAALMLSDIP 197
            A NA S AL  + IP
Sbjct: 114 AAINAASLALADAGIP 129

This family includes 3'-5' exoribonucleases. Ribonuclease PH contains a single copy of this domain, and removes nucleotide residues following the -CCA terminus of tRNA. Polyribonucleotide nucleotidyltransferase (PNPase) contains two tandem copies of the domain. PNPase is involved in mRNA degradation in a 3'-5' direction. The exosome is a 3'-5' exoribonuclease complex that is required for 3' processing of the 5.8S rRNA. Three of its five protein components contain a copy of this domain. A hypothetical protein from S. pombe appears to belong to an uncharacterized subfamily. This subfamily is found in both eukaryotes and archaebacteria. Length = 129

>gnl|CDD|239918 cd04472, S1_PNPase, S1_PNPase: Polynucleotide phosphorylase (PNPase), ), S1-like RNA-binding domain

 Score = 96.8 bits (242), Expect = 2e-24
 Identities = 33/67 (49%), Positives = 46/67 (68%)

Query: 684 GGIYKGVVTSVKEYGAFVEFNGGQQGLLHVSELSHEPVSRVSDVVSVGQQLSLRCIGQDV 743
           G IY+G V  +K++GAFVE   G+ GL+H+SELS E V +V DV+ VG ++ ++ I  D 
Sbjct: 1   GKIYEGKVVKIKDFGAFVEILPGKDGLVHISELSDERVEKVEDVLKVGDEVKVKVIEVDD 60

Query: 744 RGNIKLS 750
           RG I LS
Sbjct: 61  RGRISLS 67

PNPase is a polyribonucleotide nucleotidyl transferase that degrades mRNA. It is a trimeric multidomain protein. The C-terminus contains the S1 domain which binds ssRNA. This family is classified based on the S1 domain. PNPase nonspecifically removes the 3' nucleotides from mRNA, but is stalled by double-stranded RNA structures such as a stem-loop. Evidence shows that a minimum of 7-10 unpaired nucleotides at the 3' end, is required for PNPase degradation. It is suggested that PNPase also dephosphorylates the RNA 5' end. This additional activity may regulate the 5'-dependent activity of RNaseE in vivo. Length = 68

>gnl|CDD|235187 PRK03983, PRK03983, exosome complex exonuclease Rrp41; Provisional

 Score = 97.4 bits (243), Expect = 1e-22
 Identities = 82/244 (33%), Positives = 124/244 (50%), Gaps = 23/244 (9%)

Query: 362 KRIIAEGVRVDGRQLDEVRPIYCESGNLPILHGSSLFSRGDTQVLCTVTLGAPAEAQRLE 421
           K I+ +G+R+DGR+ DE+RPI  E G L    GS+    G+ +++  V    P E     
Sbjct: 7   KLILEDGLRLDGRKPDELRPIKIEVGVLKNADGSAYLEWGNNKIIAAVY--GPREMHP-R 63

Query: 422 SLVGPPTKRFMLHYSFPPFCINEVGKRVGLNRREVGHGTLAEKALLAVLPPENDFPYTV- 480
            L  P      + Y+  PF ++E  KR G +RR +    +  +AL   +  E  FP TV 
Sbjct: 64  HLQLPDRAVLRVRYNMAPFSVDE-RKRPGPDRRSIEISKVIREALEPAIMLEL-FPRTVI 121

Query: 481 RVNSEVMASDGSTSMATVCGGSMALMDAGIPLQEHVAGVSVGLVSEVDPSTGEIKDYRIL 540
            V  EV+ +D  T +A +   S+AL DAGIP+++ VAG +VG V  V           I+
Sbjct: 122 DVFIEVLQADAGTRVAGITAASLALADAGIPMRDLVAGCAVGKVDGV-----------IV 170

Query: 541 TDILGLEDHLGDMDFKIAGT-RIG-VTAIQLDIKPAGIPLDIICECLEHAHKGRLQILDH 598
            D+   ED+ G+ D  +A   R+G +T +QLD     +  +   E LE A KG  +I   
Sbjct: 171 LDLNKEEDNYGEADMPVAIMPRLGEITLLQLD---GNLTREEFLEALELAKKGIKRIYQ- 226

Query: 599 MERE 602
           ++RE
Sbjct: 227 LQRE 230

Length = 244

>gnl|CDD|206775 cd11370, RNase_PH_RRP41, RRP41 subunit of eukaryotic exosome

 Score = 94.5 bits (236), Expect = 1e-21
 Identities = 61/247 (24%), Positives = 106/247 (42%), Gaps = 37/247 (14%)

Query: 368 GVRVDGRQLDEVRPIYCESGNLPILHGSSLFSRGDTQVLCTVTLGAPAEAQRLESLVGPP 427
           G+R+DGR+ +E+R I C  G      GS+   +G+T+VL  V    P E +         
Sbjct: 1   GLRLDGRRPNELRRIRCRIGVFSSADGSAYLEQGNTKVLAAVY--GPHEPRN-------- 50

Query: 428 TKRFMLH--------YSFPPFCINEVGKRVGLNRREVGHGTLAEKALLAVLPPENDFPYT 479
            +   LH        YS   F   E  +R   +RR         +   AV+     +P +
Sbjct: 51  -RSQALHDRAVVNCEYSMATFSTGERKRRGKGDRRSTELSLAIRQTFEAVILTHL-YPRS 108

Query: 480 -VRVNSEVMASDGSTSMATVCGGSMALMDAGIPLQEHVAGVSVGLVSEVDPSTGEIKDYR 538
            + +  +V+ +DG    A +   ++AL+DAGIP++++V   S G +              
Sbjct: 109 QIDIYVQVLQADGGLLAACINAATLALIDAGIPMKDYVCACSAGYLDST----------- 157

Query: 539 ILTDILGLEDHLGDMDFKIA--GTRIGVTAIQLDIKPAGIPLDIICECLEHAHKGRLQIL 596
            L D+  LE+     D  +A       V  +Q++ +   + LD + + LE A +G   I 
Sbjct: 158 PLLDLNYLEESGDLPDLTVAVLPKSDKVVLLQMESR---LHLDRLEKVLELAIEGCKVIR 214

Query: 597 DHMEREI 603
           + M+  +
Sbjct: 215 EIMDEVV 221

The RRP41 subunit of eukaryotic exosome is a member of the RNase_PH family, named after the bacterial Ribonuclease PH, a 3'-5' exoribonuclease. Structurally all members of this family form hexameric rings (trimers of Rrp41-Rrp45, Rrp46-Rrp43, and Mtr3-Rrp42 dimers). The eukaryotic exosome core is composed of six individually encoded RNase PH-like subunits and three additional proteins (Rrp4, Csl4 and Rrp40) that form a stable cap and contain RNA-binding domains. The RNase PH-like subunits are no longer phosphorolytic enzymes, the exosome directly associates with Rrp44 and Rrp6, hydrolytic exoribonucleases related to bacterial RNase II/R and RNase D. The exosome plays an important role in RNA turnover. It plays a crucial role in the maturation of stable RNA species such as rRNA, snRNA and snoRNA, quality control of mRNA, and the degradation of RNA processing by-products and non-coding transcripts. Length = 226

>gnl|CDD|131120 TIGR02065, ECX1, archaeal exosome-like complex exonuclease 1

 Score = 94.0 bits (234), Expect = 1e-21
 Identities = 77/212 (36%), Positives = 109/212 (51%), Gaps = 19/212 (8%)

Query: 362 KRIIAEGVRVDGRQLDEVRPIYCESGNLPILHGSSLFSRGDTQVLCTVTLGAPAEAQRLE 421
           K I+ +GVR+DGR+ DE+RPI  E+G L    GS+    G T++L  V    P EA    
Sbjct: 1   KLILEDGVRLDGRKPDELRPIKIEAGVLKNADGSAYLEFGGTKILAAVY--GPREAHP-R 57

Query: 422 SLVGPPTKRFMLHYSFPPFCINEVGKRVGLNRREVGHGTLAEKALLAVLPPENDFPYTV- 480
            L  P      + Y   PF  +E  KR G +RRE+    +  +AL   +  E  FP TV 
Sbjct: 58  HLQLPDRAVLRVRYHMAPFSTDE-RKRPGPSRREIEISKVIREALEPAILLE-QFPRTVI 115

Query: 481 RVNSEVMASDGSTSMATVCGGSMALMDAGIPLQEHVAGVSVGLVSEVDPSTGEIKDYRIL 540
            V  EV+ +DG T  A +   S+AL DAGIP+++ V GV+VG V           D  ++
Sbjct: 116 DVFIEVLQADGGTRCAGLTAASLALADAGIPMRDLVVGVAVGKV-----------DGVVV 164

Query: 541 TDILGLEDHLGDMDFKIAGT-RIG-VTAIQLD 570
            D+   ED  G+ D  +A   + G +T +QLD
Sbjct: 165 LDLSEEEDMYGEADMPVAIMPKTGEITLLQLD 196

This family contains the archaeal protein orthologous to the eukaryotic exosome protein Rrp41. It is somewhat more distantly related to the bacterial protein ribonuclease PH. An exosome-like complex has been demonstrated experimentally for the Archaea in Sulfolobus solfataricus, so members of this family are designated exosome complex exonuclease 1, after usage in SwissProt [Transcription, Degradation of RNA]. Length = 230

>gnl|CDD|223761 COG0689, Rph, RNase PH [Translation, ribosomal structure and biogenesis]

 Score = 93.9 bits (234), Expect = 2e-21
 Identities = 79/247 (31%), Positives = 116/247 (46%), Gaps = 31/247 (12%)

Query: 367 EGVRVDGRQLDEVRPIYCESGNLPILHGSSLFSRGDTQVLCTVTLGAPAEA----QRLES 422
           +G+R DGR+ DE+RPI    G L    GSSL   G+T+V+CTV+   P E      R   
Sbjct: 6   DGMRPDGRKPDELRPIKITRGVLKHAEGSSLIEFGNTKVICTVS--GPREPVPRFLRGTG 63

Query: 423 LVGPPTKRFMLHYSFPPFCINEVGKRVGLNRREVGHGTLAEKALLAV----LPPENDFPY 478
             G  T      Y   P   +E  KR     R      L  +AL AV    L PE+    
Sbjct: 64  K-GWLTAE----YGMLPRSTDERKKREADRGRTKEISRLIGRALRAVIDLELLPES---- 114

Query: 479 TVRVNSEVMASDGSTSMATVCGGSMALMDAGIPLQEHVAGVSVGLVSEVDPSTGEIKDYR 538
           T+ ++ +V+ +DG T  A++ G S+AL DAGIPL++ VA +SVG+V  V           
Sbjct: 115 TIDIDCDVLQADGGTRTASITGASLALADAGIPLRDLVAAISVGIVDGV----------- 163

Query: 539 ILTDILGLEDHLGDMDFKIAGT-RIGVTAIQLDIKPAGIPLDIICECLEHAHKGRLQILD 597
           I+ D+   ED   + D  +  T   G+  IQ   +      D + E L+ A KG  ++ +
Sbjct: 164 IVLDLDYEEDSAAEADMNVVMTGNGGLVEIQGLAEDGPFTEDELLELLDLAIKGCNELRE 223

Query: 598 HMEREIS 604
                ++
Sbjct: 224 LQREALA 230

Length = 230

>gnl|CDD|206771 cd11366, RNase_PH_archRRP41, RRP41 subunit of archaeal exosome

 Score = 85.5 bits (212), Expect = 1e-18
 Identities = 69/228 (30%), Positives = 111/228 (48%), Gaps = 23/228 (10%)

Query: 378 EVRPIYCESGNLPILHGSSLFSRGDTQVLCTVTLGAPAEAQRLESLVGPPTKRFMLHYSF 437
           E+RPI  E G L    GS+    G+ +++  V    P E      L  P      + Y+ 
Sbjct: 1   ELRPIKIEVGVLKNADGSAYVEWGNNKIIAAVYG--PREVHP-RHLQLPDRAVIRVRYNM 57

Query: 438 PPFCINEVGKRVGLNRREVGHGTLAEKALLAVLPPENDFPYT-VRVNSEVMASDGSTSMA 496
            PF ++E  KR G +RRE+    + ++AL   +  E +FP T + V  EV+ +D  T +A
Sbjct: 58  APFSVDE-RKRPGPDRREIEISKVIKEALEPAIILE-EFPRTAIDVFVEVLQADAGTRVA 115

Query: 497 TVCGGSMALMDAGIPLQEHVAGVSVGLVSEVDPSTGEIKDYRILTDILGLEDHLGDMDFK 556
            +   S+AL DAGIP+++ VA  + G V              I+ D+   ED+ G+ D  
Sbjct: 116 GLNAASLALADAGIPMRDLVAACAAGKVDGK-----------IVLDLNKEEDNYGEADMP 164

Query: 557 IAGT-RIG-VTAIQLDIKPAGIPLDIICECLEHAHKGRLQILDHMERE 602
           IA    +G +T +QLD     +  D   + +E A KG  +I + +++E
Sbjct: 165 IAMMPNLGEITLLQLD---GDLTPDEFKQAIELAKKGCKRIYE-LQKE 208

The RRP41 subunit of the archaeal exosome is a member of the RNase_PH family, named after the bacterial Ribonuclease PH, a 3'-5' exoribonuclease. Structurally all members of this family form hexameric rings (trimers of dimers). In archaea, the ring is formed by three Rrp41:Rrp42 dimers. The central chamber within the ring contains three phosphorolytic active sites located in an Rrp41 pocket at the interface between Rrp42 and Rrp41. The ring is capped by three copies of Rrp4 and/or Csl4 which contain putative RNA interaction domains. The archaeal exosome degrades single-stranded RNA (ssRNA) in the 3'-5' direction, but also can catalyze the reverse reaction of adding nucleoside diphosphates to the 3'-end of RNA which has been shown to lead to the formation of poly-A-rich tails on RNA. Length = 214

>gnl|CDD|224023 COG1098, VacB, Predicted RNA binding protein (contains ribosomal protein S1 domain) [Translation, ribosomal structure and biogenesis]

 Score = 80.8 bits (200), Expect = 6e-18
 Identities = 30/79 (37%), Positives = 49/79 (62%)

Query: 681 IEVGGIYKGVVTSVKEYGAFVEFNGGQQGLLHVSELSHEPVSRVSDVVSVGQQLSLRCIG 740
           ++VG   KG +T +  YGAFVE  GG+ GL+H+SE++   V  + D + VGQ++ ++ + 
Sbjct: 3   MKVGSKLKGKITGITPYGAFVELEGGKTGLVHISEIADGFVKDIHDHLKVGQEVKVKVLD 62

Query: 741 QDVRGNIKLSLKAVSPRPE 759
            D  G I LS++ +   PE
Sbjct: 63  IDENGKISLSIRKLEEEPE 81

Length = 129

>gnl|CDD|181215 PRK08059, PRK08059, general stress protein 13; Validated

 Score = 80.1 bits (198), Expect = 7e-18
 Identities = 32/81 (39%), Positives = 50/81 (61%), Gaps = 1/81 (1%)

Query: 681 IEVGGIYKGVVTSVKEYGAFVEFNGGQQGLLHVSELSHEPVSRVSDVVSVGQQLSLRCIG 740
            EVG +  G VT ++ YGAFV  +   QGL+H+SE++H  V  + D +SVG ++ ++ + 
Sbjct: 5   YEVGSVVTGKVTGIQPYGAFVALDEETQGLVHISEITHGFVKDIHDFLSVGDEVKVKVLS 64

Query: 741 QDV-RGNIKLSLKAVSPRPEA 760
            D  +G I LS++A    PEA
Sbjct: 65  VDEEKGKISLSIRATEEAPEA 85

Length = 123

>gnl|CDD|217697 pfam03726, PNPase, Polyribonucleotide nucleotidyltransferase, RNA binding domain

 Score = 78.5 bits (194), Expect = 8e-18
 Identities = 30/80 (37%), Positives = 41/80 (51%), Gaps = 2/80 (2%)

Query: 295 TLEKVSNLAEAHIEAVFTDPSYSKFERGEALDKIGQDVKKALEEECDEESLQVLPKAVDT 354
             EKV+ LAE  +   +T     K ER  ALD+I  DV  A   E DE   + +      
Sbjct: 2   LEEKVAALAEERLSEAYTI--TGKQERYAALDEIKADVVAAFAAEDDELDEKEIKAIFKA 59

Query: 355 VRKRVIRKRIIAEGVRVDGR 374
           + K+V+R RI+  G R+DGR
Sbjct: 60  LEKKVVRSRILDGGPRIDGR 79

This family contains the RNA binding domain of Polyribonucleotide nucleotidyltransferase (PNPase) PNPase is involved in mRNA degradation in a 3'-5' direction. Length = 80

>gnl|CDD|240197 cd05692, S1_RPS1_repeat_hs4, S1_RPS1_repeat_hs4: Ribosomal protein S1 (RPS1) domain

 Score = 77.3 bits (191), Expect = 2e-17
 Identities = 29/69 (42%), Positives = 46/69 (66%)

Query: 684 GGIYKGVVTSVKEYGAFVEFNGGQQGLLHVSELSHEPVSRVSDVVSVGQQLSLRCIGQDV 743
           G + +G VT +K +GAFVE  GG  GL+H+S+++H+ V  V DV+  G ++ ++ +  D 
Sbjct: 1   GSVVEGTVTRLKPFGAFVELGGGISGLVHISQIAHKRVKDVKDVLKEGDKVKVKVLSIDA 60

Query: 744 RGNIKLSLK 752
           RG I LS+K
Sbjct: 61  RGRISLSIK 69

RPS1 is a component of the small ribosomal subunit thought to be involved in the recognition and binding of mRNA's during translation initiation. The bacterial RPS1 domain architecture consists of 4-6 tandem S1 domains. In some bacteria, the tandem S1 array is located C-terminal to a 4-hydroxy-3-methylbut-2-enyl diphosphate reductase (HMBPP reductase) domain. While RPS1 is found primarily in bacteria, proteins with tandem RPS1-like domains have been identified in plants and humans, however these lack the N-terminal HMBPP reductase domain. This CD includes S1 repeat 4 (hs4) of the H. sapiens RPS1 homolog. Autoantibodies to double-stranded DNA from patients with systemic lupus erythematosus cross-react with the human RPS1 homolog. Length = 69

>gnl|CDD|223613 COG0539, RpsA, Ribosomal protein S1 [Translation, ribosomal structure and biogenesis]

 Score = 82.4 bits (204), Expect = 4e-16
 Identities = 92/361 (25%), Positives = 137/361 (37%), Gaps = 82/361 (22%)

Query: 657 TVVAKNRSVMEKVLEKVDFIIGREIEVGGIYKGVVTSVKEYGAFVEFNGGQQGLLHVSEL 716
            VV   R+V+E+   +    +  ++EVG + +GVV ++ +YGAFV+  GG  GLLH+SE+
Sbjct: 166 NVVLSRRAVLEEERSEQREELLNKLEVGEVVEGVVKNITDYGAFVDI-GGVDGLLHISEI 224

Query: 717 SHEPVSRVSDVVSVGQQLSLRCIGQDV-RGNIKLSLKAVSPRP------EADVKGVVEGS 769
           S + V   S+VV VG ++ ++ I  D  RG + LSLK +   P      +  V   VEG 
Sbjct: 225 SWKRVDHPSEVVKVGDEVKVKVISLDEERGRVSLSLKQLEEDPWEGIEKKYPVGDKVEGK 284

Query: 770 VP--VNKQA-TDVWASV-GDVSNGQNPELPMRKNETPGVNSSTSSTPAVLIRSAAECDEE 825
           V    +  A  ++   V G V      E+   K   P           V +    + D E
Sbjct: 285 VTNLTDYGAFVEIEEGVEGLVH---VSEISWTKKNVPSEVVKVGQEVEVKV---LDIDPE 338

Query: 826 EKASGFSQSSKSTL---------KSTLASKSNSKPKKFTSQSDFFSSTNIQKSTSFSQRE 876
            +    S   K            K  +      K K  T    F                
Sbjct: 339 RRR--ISLGLKQLKENPWEEFADKHPVGDVVEGKVKSITDFGAF---------------- 380

Query: 877 REELAECLFG------------TEDGDEDNKGTRVEAIV------------SAKNL---- 908
             EL   + G             E+ ++  KG  VEA V              K L    
Sbjct: 381 -VELEGGIDGLVHLSDLSWDRPGEEAEKYKKGDEVEAKVLAVDKEKERISLGIKQLEESP 439

Query: 909 --------KLGTKVAAKVYQVRARGLVLDLGGGIRGMYRFENNEKKDFVVGDELLVKCSS 960
                   K G+ V  KV  V+ +G  ++LGGG+ G+ R     +    VGDE+     S
Sbjct: 440 WEEFSEKYKKGSVVKGKVKSVKDKGAFVELGGGVEGLIRLSELSRDVLKVGDEVEAVVVS 499

Query: 961 F 961
            
Sbjct: 500 I 500

Length = 541

>gnl|CDD|234623 PRK00087, PRK00087, 4-hydroxy-3-methylbut-2-enyl diphosphate reductase/S1 RNA-binding domain protein; Reviewed

 Score = 80.4 bits (199), Expect = 2e-15
 Identities = 40/120 (33%), Positives = 64/120 (53%), Gaps = 8/120 (6%)

Query: 658 VVAKNRSVMEKVLEKVDFIIGREIEVGGIYKGVVTSVKEYGAFVEFNGGQQGLLHVSELS 717
           VV   ++++E+  EK        +E G + +G V  + ++GAFV+  GG  GLLHVSE+S
Sbjct: 452 VVLSRKAILEEEKEKKKEETWNSLEEGDVVEGEVKRLTDFGAFVDI-GGVDGLLHVSEIS 510

Query: 718 HEPVSRVSDVVSVGQQLSLRCIGQD-VRGNIKLSLKAVSPRPEADVK------GVVEGSV 770
              V + SDV+ VG ++ +  +  D     + LSLK + P P  +V+       +V G V
Sbjct: 511 WGRVEKPSDVLKVGDEIKVYILDIDKENKKLSLSLKKLLPDPWENVEEKYPVGSIVLGKV 570

Length = 647

>gnl|CDD|235851 PRK06676, rpsA, 30S ribosomal protein S1; Reviewed

 Score = 77.2 bits (191), Expect = 7e-15
 Identities = 43/120 (35%), Positives = 68/120 (56%), Gaps = 8/120 (6%)

Query: 658 VVAKNRSVMEKVLEKVDFIIGREIEVGGIYKGVVTSVKEYGAFVEFNGGQQGLLHVSELS 717
           V+   R+V+E+        +   ++ G + +G V  + ++GAFV+  GG  GL+H+SELS
Sbjct: 167 VILSRRAVVEEERAAKKEELLSSLKEGDVVEGTVARLTDFGAFVDI-GGVDGLVHISELS 225

Query: 718 HEPVSRVSDVVSVGQQLSLRCIGQDV-RGNIKLSLKAVSPRPEADVKG------VVEGSV 770
           HE V + S+VVSVGQ++ ++ +  D     I LSLK   P P   V+       V+EG+V
Sbjct: 226 HERVEKPSEVVSVGQEVEVKVLSIDWETERISLSLKDTLPGPWEGVEEKLPEGDVIEGTV 285

Length = 390

>gnl|CDD|240189 cd05684, S1_DHX8_helicase, S1_DHX8_helicase: The N-terminal S1 domain of human ATP-dependent RNA helicase DHX8, a DEAH (Asp-Glu-Ala-His) box polypeptide

 Score = 69.2 bits (170), Expect = 1e-14
 Identities = 33/75 (44%), Positives = 48/75 (64%), Gaps = 5/75 (6%)

Query: 684 GGIYKGVVTSVKEYGAFVEFNG---GQQGLLHVSELSHE-PVSRVSDVVSVGQQLSLRCI 739
           G IYKG VTS+ ++G FV+  G    ++GL+H+S+LS E  V+  SDVV  GQ++ ++ I
Sbjct: 1   GKIYKGKVTSIMDFGCFVQLEGLKGRKEGLVHISQLSFEGRVANPSDVVKRGQKVKVKVI 60

Query: 740 GQDVRGNIKLSLKAV 754
                G I LS+K V
Sbjct: 61  SIQ-NGKISLSMKDV 74

The DEAH-box RNA helicases are thought to play key roles in pre-mRNA splicing and DHX8 facilitates nuclear export of spliced mRNA by releasing the RNA from the spliceosome. DHX8 is also known as HRH1 (human RNA helicase 1) in Homo sapiens and PRP22 in Saccharomyces cerevisiae. Length = 79

>gnl|CDD|197648 smart00316, S1, Ribosomal protein S1-like RNA-binding domain

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

Query: 682 EVGGIYKGVVTSVKEYGAFVEFNGGQQGLLHVSELSHEPVSRVSDVVSVGQQLSLRCIG- 740
           EVG + +G VT +   GAFV+   G +GL+ +SELS + V    +V+ VG ++ ++ +  
Sbjct: 1   EVGDVVEGTVTEITPGGAFVDLGNGVEGLIPISELSDKRVKDPEEVLKVGDEVKVKVLSV 60

Query: 741 QDVRGNIKLSLK 752
            + +G I LSLK
Sbjct: 61  DEEKGRIILSLK 72

Length = 72

>gnl|CDD|240191 cd05686, S1_pNO40, S1_pNO40: pNO40 , S1-like RNA-binding domain

 Score = 66.0 bits (161), Expect = 2e-13
 Identities = 31/72 (43%), Positives = 48/72 (66%), Gaps = 1/72 (1%)

Query: 682 EVGGIYKGVVTSVKEYGAFVEFNG-GQQGLLHVSELSHEPVSRVSDVVSVGQQLSLRCIG 740
            +  I+KG V SV EYGAFV+  G  +QGL+H S +S   V   S+VV VG+++ ++ IG
Sbjct: 2   ALYQIFKGEVASVTEYGAFVKIPGCRKQGLVHKSHMSSCRVDDPSEVVDVGEKVWVKVIG 61

Query: 741 QDVRGNIKLSLK 752
           ++++  +KLSL 
Sbjct: 62  REMKDKMKLSLS 73

pNO40 is a nucleolar protein of unknown function with an N-terminal S1 RNA binding domain, a CCHC type zinc finger, and clusters of basic amino acids representing a potential nucleolar targeting signal. pNO40 was identified through a yeast two-hybrid interaction screen of a human kidney cDNA library using the pinin (pnn) protein as bait. pNO40 is thought to play a role in ribosome maturation and/or biogenesis. Length = 73

>gnl|CDD|236305 PRK08582, PRK08582, hypothetical protein; Provisional

 Score = 66.2 bits (162), Expect = 9e-13
 Identities = 29/79 (36%), Positives = 48/79 (60%)

Query: 681 IEVGGIYKGVVTSVKEYGAFVEFNGGQQGLLHVSELSHEPVSRVSDVVSVGQQLSLRCIG 740
           IEVG   +G VT +  +GAFVE   G+ GL+H+SE++   V  ++D + VG ++ ++ + 
Sbjct: 3   IEVGSKLQGKVTGITNFGAFVELPEGKTGLVHISEVADNYVKDINDHLKVGDEVEVKVLN 62

Query: 741 QDVRGNIKLSLKAVSPRPE 759
            +  G I LS+K    RP+
Sbjct: 63  VEDDGKIGLSIKKAKDRPK 81

Length = 139

>gnl|CDD|206776 cd11371, RNase_PH_MTR3, MTR3 subunit of eukaryotic exosome

 Score = 65.7 bits (161), Expect = 5e-12
 Identities = 46/163 (28%), Positives = 74/163 (45%), Gaps = 12/163 (7%)

Query: 379 VRPIYCESGNLPILHGSSLFSRGDTQVLCTVTLGAPAEAQRLESLVGPPTKRFMLHYSFP 438
           +RPI+ ++G +    GS+    G+T+V+C+V    P   +   S  G    R      F 
Sbjct: 1   IRPIFLKTGVVSQAKGSAYVELGNTKVICSVYGPRPIPGRTEFSDRG----RLNCEVKFA 56

Query: 439 PFCINEVGKRVGLNRREVGHGTLAEKALLAVLPPENDFP-YTVRVNSEVMASDGST-SMA 496
           PF      +R G +  E    +L  +AL   +  E  +P   + V   V+ SDGS  + A
Sbjct: 57  PFA-TPGRRRHGQDSEERELSSLLHQALEPAVRLEK-YPKSQIDVFVTVLESDGSVLAAA 114

Query: 497 TVCGGSMALMDAGIPLQEHVAGVSVGLVSE---VDPSTGEIKD 536
                S+AL DAGI + + V   S  L+ +   +DP+  E + 
Sbjct: 115 ITAA-SLALADAGIEMYDLVTACSAALIGDELLLDPTREEEEA 156

The MTR3 subunit of eukaryotic exosome is a member of the RNase_PH family, named after the bacterial Ribonuclease PH, a 3'-5' exoribonuclease. Structurally all members of this family form hexameric rings (trimers of Rrp41-Rrp45, Rrp46-Rrp43, and Mtr3-Rrp42 dimers). The eukaryotic exosome core is composed of six individually encoded RNase PH-like subunits and three additional proteins (Rrp4, Csl4 and Rrp40) that form a stable cap and contain RNA-binding domains. The RNase PH-like subunits are no longer phosphorolytic enzymes, the exosome directly associates with Rrp44 and Rrp6, hydrolytic exoribonucleases related to bacterial RNase II/R and RNase D. The exosome plays an important role in RNA turnover. It plays a crucial role in the maturation of stable RNA species such as rRNA, snRNA and snoRNA, quality control of mRNA, and the degradation of RNA processing by-products and non-coding transcripts. Length = 210

>gnl|CDD|216000 pfam00575, S1, S1 RNA binding domain

 Score = 61.1 bits (149), Expect = 8e-12
 Identities = 26/74 (35%), Positives = 44/74 (59%), Gaps = 1/74 (1%)

Query: 680 EIEVGGIYKGVVTSVKEYGAFVEFNGGQQGLLHVSELSHEPVSRVSDVVSVGQQLSLRCI 739
           + E G + KG VT V + GAFV+   G +G + +SE+S + V    +V+ VG ++ ++ +
Sbjct: 1   KPEEGDVVKGTVTRVTKGGAFVDLGNGVEGFIPISEISDDRVEDPDEVLKVGDEVEVKVL 60

Query: 740 GQDV-RGNIKLSLK 752
             D  RG I LS++
Sbjct: 61  KVDKERGRIILSIR 74

The S1 domain occurs in a wide range of RNA associated proteins. It is structurally similar to cold shock protein which binds nucleic acids. The S1 domain has an OB-fold structure. Length = 74

>gnl|CDD|206777 cd11372, RNase_PH_RRP46, RRP46 subunit of eukaryotic exosome

 Score = 64.1 bits (157), Expect = 2e-11
 Identities = 49/174 (28%), Positives = 76/174 (43%), Gaps = 39/174 (22%)

Query: 380 RPIYCESGNLPILHGSSLFSRGDTQVLCTVTLGAPAEAQRLESLVGPPTKRFMLHYSFPP 439
           RP+ CE G L    GS+ FS+GDT VL  V    P E +  + L   P +          
Sbjct: 2   RPLSCELGLLSRADGSARFSQGDTSVLAAVY--GPIEVKLRKEL---PDR---------- 46

Query: 440 FCINEVGKRVGLNRREVGHGTLAEKALLA----VLPP---ENDFPYT-VRVNSEVMASDG 491
               EV     + R + G   + EK L       L P    +  P T + V  +V+  DG
Sbjct: 47  -ATLEV-----IVRPKSGLPGVKEKLLELLLRSTLEPIILLHLHPRTLISVVLQVLQDDG 100

Query: 492 S---TSMATVCGGSMALMDAGIPLQEHVAGVSVGLVSE----VDPSTGEIKDYR 538
           S    ++   C   +AL+DAG+P++   A V+  +  +    +DP+  E K+ +
Sbjct: 101 SLLACAINAAC---LALLDAGVPMKGLFAAVTCAITEDGEIILDPTAEEEKEAK 151

The RRP46 subunit of eukaryotic exosome is a member of the RNase_PH family, named after the bacterial Ribonuclease PH, a 3'-5' exoribonuclease. Structurally all members of this family form hexameric rings (trimers of Rrp41-Rrp45, Rrp46-Rrp43, and Mtr3-Rrp42 dimers). The eukaryotic exosome core is composed of six individually encoded RNase PH-like subunits and three additional proteins (Rrp4, Csl4 and Rrp40) that form a stable cap and contain RNA-binding domains. The RNase PH-like subunits are no longer phosphorolytic enzymes, the exosome directly associates with Rrp44 and Rrp6, hydrolytic exoribonucleases related to bacterial RNase II/R and RNase D. The exosome plays an important role in RNA turnover. It plays a crucial role in the maturation of stable RNA species such as rRNA, snRNA and snoRNA, quality control of mRNA, and the degradation of RNA processing by-products and non-coding transcripts. Length = 199

>gnl|CDD|240193 cd05688, S1_RPS1_repeat_ec3, S1_RPS1_repeat_ec3: Ribosomal protein S1 (RPS1) domain

 Score = 59.9 bits (146), Expect = 2e-11
 Identities = 25/70 (35%), Positives = 44/70 (62%), Gaps = 2/70 (2%)

Query: 683 VGGIYKGVVTSVKEYGAFVEFNGGQQGLLHVSELSHEPVSRVSDVVSVGQQLSLRCIGQD 742
            G + +G V S+ ++GAFV+  GG  GLLH+S++S   V   S+VV+VG ++ ++ +  D
Sbjct: 1   EGDVVEGTVKSITDFGAFVDL-GGVDGLLHISDMSWGRVKHPSEVVNVGDEVEVKVLKID 59

Query: 743 VRGNIKLSLK 752
            +   ++SL 
Sbjct: 60  -KERKRISLG 68

RPS1 is a component of the small ribosomal subunit thought to be involved in the recognition and binding of mRNA's during translation initiation. The bacterial RPS1 domain architecture consists of 4-6 tandem S1 domains. In some bacteria, the tandem S1 array is located C-terminal to a 4-hydroxy-3-methylbut-2-enyl diphosphate reductase (HMBPP reductase) domain. While RPS1 is found primarily in bacteria, proteins with tandem RPS1-like domains have been identified in plants and humans, however these lack the N-terminal HMBPP reductase domain. This CD includes S1 repeat 3 (ec3) of the Escherichia coli RPS1. Autoantibodies to double-stranded DNA from patients with systemic lupus erythematosus cross-react with the human RPS1 homolog. Length = 68

>gnl|CDD|131021 TIGR01966, RNasePH, ribonuclease PH

 Score = 64.7 bits (158), Expect = 2e-11
 Identities = 58/215 (26%), Positives = 88/215 (40%), Gaps = 42/215 (19%)

Query: 370 RVDGRQLDEVRPIYCESGNLPILHGSSLFSRGDTQVLCTVTLGAPAEAQRLESLVGPPTK 429
           R DGR+ D++RP+      L    GS L   G+T+VLCT ++         E  V PP  
Sbjct: 1   RPDGRKPDQLRPVSITRDFLKHAEGSVLIEFGNTKVLCTASV---------EEKV-PPFL 50

Query: 430 R------FMLHYSFPPFCINEVGKRVGLNRREVGHGT----LAEKALLAVLPPENDFPYT 479
           R          Y   P       +R     ++ G       L  +AL AV+  E     T
Sbjct: 51  RGSGEGWITAEYGMLPRATQTRNRRESAKGKQSGRTQEIQRLIGRALRAVVDLEALGERT 110

Query: 480 VRVNSEVMASDGSTSMATVCGGSMALMDA-----------GIPLQEHVAGVSVGLVSEVD 528
           + ++ +V+ +DG T  A++ G  +AL DA             P+++ VA VSVG+V    
Sbjct: 111 IWIDCDVIQADGGTRTASITGAFVALADAISKLHKRGILKESPIRDFVAAVSVGIVDGE- 169

Query: 529 PSTGEIKDYRILTDILGLEDHLGDMDFKIAGTRIG 563
                      + D+   ED   D+D  +  T  G
Sbjct: 170 ----------PVLDLDYEEDSAADVDMNVVMTGSG 194

This bacterial enzyme, ribonuclease PH, performs the final 3'-trimming and modification of tRNA precursors. This model is restricted absolutely to bacteria. Related families outside the model include proteins described as probable exosome complex exonucleases (rRNA processing) and polyribonucleotide nucleotidyltransferases (mRNA degradation). The most divergent member within the family is RNase PH from Deinococcus radiodurans [Transcription, RNA processing]. Length = 236

>gnl|CDD|240190 cd05685, S1_Tex, S1_Tex: The C-terminal S1 domain of a transcription accessory factor called Tex, which has been characterized in Bordetella pertussis and Pseudomonas aeruginosa

 Score = 58.8 bits (143), Expect = 5e-11
 Identities = 31/68 (45%), Positives = 45/68 (66%), Gaps = 1/68 (1%)

Query: 684 GGIYKGVVTSVKEYGAFVEFNGGQQGLLHVSELSHEPVSRVSDVVSVGQQLSLRCIGQDV 743
           G + +GVVT+V ++GAFV+    Q GL+H+S+++   VS  SDVVSVG  + ++ I  D 
Sbjct: 1   GMVLEGVVTNVTDFGAFVDIGVKQDGLIHISKMADRFVSHPSDVVSVGDIVEVKVISIDE 60

Query: 744 -RGNIKLS 750
            RG I LS
Sbjct: 61  ERGRISLS 68

The tex gene is essential in Bortella pertusis and is named for its role in toxin expression. Tex has two functional domains, an N-terminal domain homologous to the Escherichia coli maltose repression protein, which is a poorly defined transcriptional factor, and a C-terminal S1 RNA-binding domain. Tex is found in prokaryotes, eukaryotes, and archaea. Length = 68

>gnl|CDD|180960 PRK07400, PRK07400, 30S ribosomal protein S1; Reviewed

 Score = 64.4 bits (157), Expect = 6e-11
 Identities = 37/107 (34%), Positives = 59/107 (55%), Gaps = 10/107 (9%)

Query: 658 VVAKNRSVMEKVLEKVDFIIGREIEVGGIYKGVVTSVKEYGAFVEFNGGQQGLLHVSELS 717
           V++  R+++E+ + +        +EVG +  G V  +K YGAF++  GG  GLLH+SE+S
Sbjct: 179 VLSHRRALVERKMNR--------LEVGEVVVGTVRGIKPYGAFIDI-GGVSGLLHISEIS 229

Query: 718 HEPVSRVSDVVSVGQQLSLRCIGQDV-RGNIKLSLKAVSPRPEADVK 763
           HE +     V +V  ++ +  I  D  RG I LS K + P P   +K
Sbjct: 230 HEHIETPHSVFNVNDEMKVMIIDLDAERGRISLSTKQLEPEPGDMLK 276

Length = 318

>gnl|CDD|206766 cd11358, RNase_PH, RNase PH-like 3'-5' exoribonucleases

 Score = 61.6 bits (150), Expect = 2e-10
 Identities = 49/196 (25%), Positives = 78/196 (39%), Gaps = 32/196 (16%)

Query: 68  RLITLETGKIARFANGAVVLGMDETKVLSTVT----SSKGDSVRDFLPLTVDYQEKQFAQ 123
           R + +ETG + + A+G+ ++ +  TKV+  VT            D   L V+ +    A 
Sbjct: 2   RPVEIETGVLNQ-ADGSALVKLGNTKVICAVTGPIVEPDKLERPDKGTLYVNVEISPGAV 60

Query: 124 GVIPNTYMRREGAPKERELLVGRIIDRPIR-----PLFPAGFYHEVQVMASVLSSDGKQD 178
           G       RR+G P + E+ + R+++R I                + V   VLS DG   
Sbjct: 61  GE------RRQGPPGDEEMEISRLLERTIEASVILDKSTRKPSWVLYVDIQVLSRDG--G 112

Query: 179 PDIMAANATSAALMLSDIPWG-------------GPIGMIRIGRIC-GQFIVNPTMDELS 224
                 NA  AAL  + IP                 I  + +G I  G  +++PT +E  
Sbjct: 113 LLDACWNAAIAALKDAGIPRVFVDERSPPLLLMKDLIVAVSVGGISDGVLLLDPTGEEEE 172

Query: 225 LSDLNLVYACTREKTL 240
           L+D  L  A  +   L
Sbjct: 173 LADSTLTVAVDKSGKL 188

RNase PH-like 3'-5' exoribonucleases are enzymes that catalyze the 3' to 5' processing and decay of RNA substrates. Evolutionarily related members can be fond in prokaryotes, archaea, and eukaryotes. Bacterial ribonuclease PH contains a single copy of this domain, and removes nucleotide residues following the -CCA terminus of tRNA. Polyribonucleotide nucleotidyltransferase (PNPase) contains two tandem copies of the domain and is involved in mRNA degradation in a 3'-5' direction. Archaeal exosomes contain two individually encoded RNase PH-like 3'-5' exoribonucleases and are required for 3' processing of the 5.8S rRNA. The eukaryotic exosome core is composed of six individually encoded RNase PH-like subunits, but it is not a phosphorolytic enzyme per se; it directly associates with Rrp44 and Rrp6, which are hydrolytic exoribonucleases related to bacterial RNase II/R and RNase D. All members of the RNase PH-like family form ring structures by oligomerization of six domains or subunits, except for a total of 3 subunits with tandem repeats in the case of PNPase, with a central channel through which the RNA substrate must pass to gain access to the phosphorolytic active sites. Length = 218

>gnl|CDD|234623 PRK00087, PRK00087, 4-hydroxy-3-methylbut-2-enyl diphosphate reductase/S1 RNA-binding domain protein; Reviewed

 Score = 63.4 bits (155), Expect = 3e-10
 Identities = 28/82 (34%), Positives = 45/82 (54%), Gaps = 1/82 (1%)

Query: 683 VGGIYKGVVTSVKEYGAFVEFNGGQQGLLHVSELSHEPVSRVSDVVSVGQQLSLRCIGQD 742
           VG I  G V  +  +GAFVE   G  GL+H+S++S + + +  DV+S G+++  + +  D
Sbjct: 562 VGSIVLGKVVRIAPFGAFVELEPGVDGLVHISQISWKRIDKPEDVLSEGEEVKAKILEVD 621

Query: 743 -VRGNIKLSLKAVSPRPEADVK 763
                I+LS+K V   P    K
Sbjct: 622 PEEKRIRLSIKEVEEEPGDIEK 643

Length = 647

>gnl|CDD|238094 cd00164, S1_like, S1_like: Ribosomal protein S1-like RNA-binding domain

 Score = 56.6 bits (137), Expect = 3e-10
 Identities = 25/65 (38%), Positives = 38/65 (58%), Gaps = 1/65 (1%)

Query: 687 YKGVVTSVKEYGAFVEFNGGQQGLLHVSELSHEPVSRVSDVVSVGQQLSLRCIGQDVR-G 745
             G V S+ ++G FVE   G +GL+H+SELS + V   S+V  VG ++ ++ +  D   G
Sbjct: 1   VTGKVVSITKFGVFVELEDGVEGLVHISELSDKFVKDPSEVFKVGDEVEVKVLEVDPEKG 60

Query: 746 NIKLS 750
            I LS
Sbjct: 61  RISLS 65

Found in a wide variety of RNA-associated proteins. Originally identified in S1 ribosomal protein. This superfamily also contains the Cold Shock Domain (CSD), which is a homolog of the S1 domain. Both domains are members of the Oligonucleotide/oligosaccharide Binding (OB) fold. Length = 65

>gnl|CDD|225094 COG2183, Tex, Transcriptional accessory protein [Transcription]

 Score = 63.4 bits (155), Expect = 4e-10
 Identities = 28/91 (30%), Positives = 47/91 (51%), Gaps = 1/91 (1%)

Query: 663 RSVMEKVLEKVDFIIGREIEVGGIYKGVVTSVKEYGAFVEFNGGQQGLLHVSELSHEPVS 722
           R                +++ G I +G V +V ++GAFV+    Q GL+H+S+LS + V 
Sbjct: 638 RDEFHTPTLDEGVESITDLKPGMILEGTVRNVVDFGAFVDIGVHQDGLVHISQLSDKFVK 697

Query: 723 RVSDVVSVGQQLSLRCIGQDV-RGNIKLSLK 752
             ++VV VG  + ++ I  D  R  I LS++
Sbjct: 698 DPNEVVKVGDIVKVKVIEVDTARKRIALSMR 728

Length = 780

>gnl|CDD|235775 PRK06299, rpsA, 30S ribosomal protein S1; Reviewed

 Score = 62.5 bits (153), Expect = 7e-10
 Identities = 32/107 (29%), Positives = 63/107 (58%), Gaps = 2/107 (1%)

Query: 658 VVAKNRSVMEKVLEKVDFIIGREIEVGGIYKGVVTSVKEYGAFVEFNGGQQGLLHVSELS 717
           +V   R+V+E+   +    +   +E G + +GVV ++ +YGAFV+  GG  GLLH++++S
Sbjct: 176 IVVSRRAVLEEERAEEREELLENLEEGQVVEGVVKNITDYGAFVDL-GGVDGLLHITDIS 234

Query: 718 HEPVSRVSDVVSVGQQLSLRCIGQDV-RGNIKLSLKAVSPRPEADVK 763
            + V+  S+VV+VG ++ ++ +  D  +  + L LK +   P   ++
Sbjct: 235 WKRVNHPSEVVNVGDEVKVKVLKFDKEKKRVSLGLKQLGEDPWEAIE 281

Length = 565

>gnl|CDD|217696 pfam03725, RNase_PH_C, 3' exoribonuclease family, domain 2

 Score = 55.3 bits (134), Expect = 8e-10
 Identities = 24/66 (36%), Positives = 41/66 (62%), Gaps = 3/66 (4%)

Query: 200 GPIGMIRIGRICGQFIVNPTMDELSL--SDLNLVYACTREKTLMIDVQ-AREISEKDLEA 256
           GP+  + +G+I G+ +++PT++E SL  SDL +V A T E   ++      E++E++L  
Sbjct: 1   GPVAAVTVGKIDGELVLDPTLEEESLADSDLTIVVAGTGEIVALMKEGGGAELTEEELLE 60

Query: 257 GLRLAH 262
            L LAH
Sbjct: 61  ALELAH 66

This family includes 3'-5' exoribonucleases. Ribonuclease PH contains a single copy of this domain, and removes nucleotide residues following the -CCA terminus of tRNA. Polyribonucleotide nucleotidyltransferase (PNPase) contains two tandem copies of the domain. PNPase is involved in mRNA degradation in a 3'-5' direction. The exosome is a 3'-5' exoribonuclease complex that is required for 3' processing of the 5.8S rRNA. Three of its five protein components contain a copy of this domain. A hypothetical protein from S. pombe appears to belong to an uncharacterized subfamily. This subfamily is found in both eukaryotes and archaebacteria. Length = 68

>gnl|CDD|235775 PRK06299, rpsA, 30S ribosomal protein S1; Reviewed

 Score = 61.7 bits (151), Expect = 1e-09
 Identities = 47/116 (40%), Positives = 62/116 (53%), Gaps = 11/116 (9%)

Query: 677 IGREIEVGGIYKGVVTSVKEYGAFVEFNGGQQGLLHVSELSHEPVSR-VSDVVSVGQQLS 735
           I ++  VG   KG VT++ +YGAFVE   G +GL+HVSE+S    ++  S VVSVGQ++ 
Sbjct: 280 IEKKYPVGSKVKGKVTNITDYGAFVELEEGIEGLVHVSEMSWTKKNKHPSKVVSVGQEVE 339

Query: 736 LRCIGQDV-RGNIKLSLKAVSPRP-----EADVKG-VVEGSVPVNKQATDVWASVG 784
           +  +  D  +  I L LK     P     E    G VVEG V   K  TD  A VG
Sbjct: 340 VMVLEIDEEKRRISLGLKQCKENPWEEFAEKYPVGDVVEGKV---KNITDFGAFVG 392

Length = 565

>gnl|CDD|235851 PRK06676, rpsA, 30S ribosomal protein S1; Reviewed

 Score = 60.7 bits (148), Expect = 2e-09
 Identities = 25/86 (29%), Positives = 52/86 (60%), Gaps = 1/86 (1%)

Query: 677 IGREIEVGGIYKGVVTSVKEYGAFVEFNGGQQGLLHVSELSHEPVSRVSDVVSVGQQLSL 736
           +  ++  G + +G V  + ++GAFVE   G +GL+H+S++SH+ ++  S+V+  GQ++ +
Sbjct: 271 VEEKLPEGDVIEGTVKRLTDFGAFVEVLPGVEGLVHISQISHKHIATPSEVLEEGQEVKV 330

Query: 737 RCIGQDVRGN-IKLSLKAVSPRPEAD 761
           + +  +     I LS+KA+   P  +
Sbjct: 331 KVLEVNEEEKRISLSIKALEEAPAEE 356

Length = 390

>gnl|CDD|236126 PRK07899, rpsA, 30S ribosomal protein S1; Reviewed

 Score = 61.2 bits (149), Expect = 2e-09
 Identities = 34/76 (44%), Positives = 50/76 (65%), Gaps = 2/76 (2%)

Query: 684 GGIYKGVVTSVKEYGAFVEFNGGQQGLLHVSELSHEPVSRVSDVVSVGQQLSLRCIGQDV 743
           G + KGVV+S+  +GAFV+  GG  GL+HVSELS + +   S+VV VGQ++++  +  D+
Sbjct: 209 GQVRKGVVSSIVNFGAFVDL-GGVDGLVHVSELSWKHIDHPSEVVEVGQEVTVEVLDVDM 267

Query: 744 -RGNIKLSLKAVSPRP 758
            R  + LSLKA    P
Sbjct: 268 DRERVSLSLKATQEDP 283

Length = 486

>gnl|CDD|233102 TIGR00717, rpsA, ribosomal protein S1

 Score = 60.9 bits (148), Expect = 2e-09
 Identities = 30/84 (35%), Positives = 43/84 (51%), Gaps = 2/84 (2%)

Query: 677 IGREIEVGGIYKGVVTSVKEYGAFVEFNGGQQGLLHVSELSHE-PVSRVSDVVSVGQQLS 735
           I ++  VG    G VT++ +YG FVE   G +GL+HVSE+S     S  S VV  G ++ 
Sbjct: 266 IEKKFPVGDKITGRVTNLTDYGVFVEIEEGIEGLVHVSEMSWVKKNSHPSKVVKKGDEVE 325

Query: 736 LRCIGQDV-RGNIKLSLKAVSPRP 758
           +  +  D  R  + L LK     P
Sbjct: 326 VMILDIDPERRRLSLGLKQCKANP 349

This model describes ribosomal protein S1, RpsA. This protein is found in most bacterial genomes in a single copy, but is not present in the Mycoplasmas. It is heterogeneous with respect to the number of repeats of the S1 RNA binding domain described by PFAM model pfam00575: six repeats in E. coli and most other bacteria, four in Bacillus subtilis and some other species. rpsA is an essential gene in E. coli but not in B. subtilis. It is associated with the cytidylate kinase gene cmk in many species, and fused to it in Treponema pallidum. RpsA is proposed (Medline:97323001) to assist in mRNA degradation. This model provides trusted hits to most long form (6 repeat) examples of RpsA. Among homologs with only four repeats are some to which other (perhaps secondary) functions have been assigned [Protein synthesis, Ribosomal proteins: synthesis and modification]. Length = 516

>gnl|CDD|233102 TIGR00717, rpsA, ribosomal protein S1

 Score = 60.5 bits (147), Expect = 3e-09
 Identities = 27/71 (38%), Positives = 42/71 (59%), Gaps = 1/71 (1%)

Query: 683 VGGIYKGVVTSVKEYGAFVEFNGGQQGLLHVSELSHEPVSRVSDVVSVGQQLSLRCIGQD 742
           VG + KG VT +K++GAFVE  GG +GL+  SELS       +D + VG ++  + +  D
Sbjct: 446 VGSVVKGKVTEIKDFGAFVELPGGVEGLIRNSELSENRDEDKTDEIKVGDEVEAKVVDID 505

Query: 743 VR-GNIKLSLK 752
            +   + LS+K
Sbjct: 506 KKNRKVSLSVK 516

This model describes ribosomal protein S1, RpsA. This protein is found in most bacterial genomes in a single copy, but is not present in the Mycoplasmas. It is heterogeneous with respect to the number of repeats of the S1 RNA binding domain described by PFAM model pfam00575: six repeats in E. coli and most other bacteria, four in Bacillus subtilis and some other species. rpsA is an essential gene in E. coli but not in B. subtilis. It is associated with the cytidylate kinase gene cmk in many species, and fused to it in Treponema pallidum. RpsA is proposed (Medline:97323001) to assist in mRNA degradation. This model provides trusted hits to most long form (6 repeat) examples of RpsA. Among homologs with only four repeats are some to which other (perhaps secondary) functions have been assigned [Protein synthesis, Ribosomal proteins: synthesis and modification]. Length = 516

>gnl|CDD|240203 cd05698, S1_Rrp5_repeat_hs6_sc5, S1_Rrp5_repeat_hs6_sc5: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits

 Score = 52.2 bits (126), Expect = 1e-08
 Identities = 22/72 (30%), Positives = 29/72 (40%), Gaps = 5/72 (6%)

Query: 684 GGIYKGVVTSVKEYGAFVEFNGGQQGLLHVSELSHEPVSRVSDVVSVGQQLS---LRCIG 740
           G    G +  VK  G  V F    +G L  SELS   +    +   VGQ +    L C  
Sbjct: 1   GLKTHGTIVKVKPNGCIVSFYNNVKGFLPKSELSEAFIKDPEEHFRVGQVVKVKVLSCDP 60

Query: 741 QDVRGNIKLSLK 752
           +  R  + LS K
Sbjct: 61  EQQR--LLLSCK 70

Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in Saccharomyces cerevisiae Rrp5 and 14 S1 repeats in Homo sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in protein-protein interactions. Mutational studies have shown that each region represents a specific functional domain. Deletions within the S1-containing region inhibit pre-rRNA processing at either site A3 or A2, whereas deletions within the TPR region confer an inability to support cleavage of A0-A2. This CD includes H. sapiens S1 repeat 6 (hs6) and S. cerevisiae S1 repeat 5 (sc5). Rrp5 is found in eukaryotes but not in prokaryotes or archaea. Length = 70

>gnl|CDD|235775 PRK06299, rpsA, 30S ribosomal protein S1; Reviewed

 Score = 57.5 bits (140), Expect = 2e-08
 Identities = 30/72 (41%), Positives = 42/72 (58%), Gaps = 1/72 (1%)

Query: 683 VGGIYKGVVTSVKEYGAFVEFNGGQQGLLHVSELSHEPVSRVSDVVSVGQQLSLRCIGQD 742
            G I  G VT VK+ GAFVE   G +GL+  SELS + V   ++V+ VG ++  + I  D
Sbjct: 460 KGSIVTGTVTEVKDKGAFVELEDGVEGLIRASELSRDRVEDATEVLKVGDEVEAKVINID 519

Query: 743 VRGN-IKLSLKA 753
            +   I LS+KA
Sbjct: 520 RKNRRISLSIKA 531

Length = 565

>gnl|CDD|233102 TIGR00717, rpsA, ribosomal protein S1

 Score = 57.8 bits (140), Expect = 2e-08
 Identities = 31/84 (36%), Positives = 53/84 (63%), Gaps = 2/84 (2%)

Query: 681 IEVGGIYKGVVTSVKEYGAFVEFNGGQQGLLHVSELSHEPVSRVSDVVSVGQQLSLRCIG 740
           ++ G + KGVV ++ ++GAFV+  GG  GLLH++++S + V   S+ V VGQ++ ++ I 
Sbjct: 185 LKEGDVVKGVVKNITDFGAFVDL-GGVDGLLHITDMSWKRVKHPSEYVKVGQEVKVKVIK 243

Query: 741 QDV-RGNIKLSLKAVSPRPEADVK 763
            D  +G I LSLK +   P   ++
Sbjct: 244 FDKEKGRISLSLKQLGEDPWEAIE 267

This model describes ribosomal protein S1, RpsA. This protein is found in most bacterial genomes in a single copy, but is not present in the Mycoplasmas. It is heterogeneous with respect to the number of repeats of the S1 RNA binding domain described by PFAM model pfam00575: six repeats in E. coli and most other bacteria, four in Bacillus subtilis and some other species. rpsA is an essential gene in E. coli but not in B. subtilis. It is associated with the cytidylate kinase gene cmk in many species, and fused to it in Treponema pallidum. RpsA is proposed (Medline:97323001) to assist in mRNA degradation. This model provides trusted hits to most long form (6 repeat) examples of RpsA. Among homologs with only four repeats are some to which other (perhaps secondary) functions have been assigned [Protein synthesis, Ribosomal proteins: synthesis and modification]. Length = 516

>gnl|CDD|206768 cd11363, RNase_PH_PNPase_1, Polyribonucleotide nucleotidyltransferase, repeat 1

 Score = 54.4 bits (132), Expect = 4e-08
 Identities = 55/244 (22%), Positives = 91/244 (37%), Gaps = 58/244 (23%)

Query: 380 RPIYCESGNLPIL-HGSSLFSRGDTQVLCTVTLGAPAEAQRLESLVGPPTKRFMLHYSFP 438
           R +  E+G L     GS +   GDT VL T       +                    F 
Sbjct: 10  RTLTFETGKLAKQADGSVVVQYGDTVVLVTAVSSKKPKEGI----------------DFF 53

Query: 439 PFCIN------EVGKRVG-LNRREVGHGTLAEKALLAV---------LPPENDFPYTVRV 482
           P  ++        GK  G   +RE   G  +EK +L           L P+  F   V+V
Sbjct: 54  PLTVDYREKLYAAGKIPGGFFKRE---GRPSEKEILTSRLIDRPIRPLFPKG-FRNEVQV 109

Query: 483 NSEVMASDG--STSMATVCGGSMALMDAGIPLQEHVAGVSVGLVSE---VDPSTGEIKDY 537
            + V++ DG     +  + G S AL  + IP    V  V VG +     V+P+  E+++ 
Sbjct: 110 IATVLSVDGVNDPDVLAINGASAALSLSDIPFNGPVGAVRVGRIDGEFVVNPTREELEE- 168

Query: 538 RILTDILGLEDHLGDMDFKIAGTRIGVTAIQLDIKPAGIPLDIICECLEHAHKGRLQILD 597
                         D+D  +AGT+  V  ++   K   +  + + E ++  H+   Q++ 
Sbjct: 169 -------------SDLDLVVAGTKDAVLMVEAGAKE--VSEEDMLEAIKFGHEAIQQLIA 213

Query: 598 HMER 601
             E 
Sbjct: 214 AQEE 217

Polyribonucleotide nucleotidyltransferase (PNPase) is a member of the RNase_PH family, named after the bacterial Ribonuclease PH, a 3'-5' exoribonuclease. Structurally, all members of this family form hexameric rings. In the case of PNPase the complex is a trimer, since each monomer contains two tandem copies of the domain. PNPase is involved in mRNA degradation in a 3'-5' direction and in quality control of ribosomal RNA precursors. It is part of the RNA degradosome complex and binds to the scaffolding domain of the endoribonuclease RNase E. Length = 229

>gnl|CDD|237516 PRK13806, rpsA, 30S ribosomal protein S1; Provisional

 Score = 56.7 bits (137), Expect = 4e-08
 Identities = 31/102 (30%), Positives = 49/102 (48%), Gaps = 11/102 (10%)

Query: 680 EIEVGGIYKGVVTSVKEYGAFVEFNGGQQGLLHVSELSHEPVSRVSDVVSVGQQLSLRCI 739
            ++ G + +G VT +  +GAFVE   G +G++H+SELS   V +  + VSVG  + ++ +
Sbjct: 199 TVKEGDVVEGTVTRLAPFGAFVELAPGVEGMVHISELSWSRVQKADEAVSVGDTVRVKVL 258

Query: 740 GQDVRGN-----IKLSLKAVSPRPEADVKG------VVEGSV 770
           G +         I LS+K     P   V         V G V
Sbjct: 259 GIERAKKGKGLRISLSIKQAGGDPWDTVGDRLKAGDKVTGKV 300

Length = 491

>gnl|CDD|224018 COG1093, SUI2, Translation initiation factor 2, alpha subunit (eIF-2alpha) [Translation, ribosomal structure and biogenesis]

 Score = 55.0 bits (133), Expect = 4e-08
 Identities = 30/79 (37%), Positives = 46/79 (58%), Gaps = 3/79 (3%)

Query: 682 EVGGIYKGVVTSVKEYGAFVEFN--GGQQGLLHVSELSHEPVSRVSDVVSVGQQLSLRCI 739
           E G I  G V  V +YGA+VE +   G++G +H+SE++   V  + D V  GQ++  + +
Sbjct: 10  EEGEIVVGTVKQVADYGAYVELDEYPGKEGFIHISEVASGWVKNIRDYVKEGQKVVAKVL 69

Query: 740 GQD-VRGNIKLSLKAVSPR 757
             D  RG+I LSLK V+  
Sbjct: 70  RVDPKRGHIDLSLKRVTEH 88

Length = 269

>gnl|CDD|239919 cd04473, S1_RecJ_like, S1_RecJ_like: The S1 domain of the archaea-specific RecJ-like exonuclease

 Score = 50.3 bits (121), Expect = 7e-08
 Identities = 24/72 (33%), Positives = 36/72 (50%), Gaps = 8/72 (11%)

Query: 679 REIEVGGIYKGVVTSVKEYGAFVEFNGGQQGLLHVSELSHEPVSRVSDVVSVGQQLSLRC 738
            ++EVG +YKG V  V +YG FV+ N   +GL+H S L  +          VG ++ ++ 
Sbjct: 12  EDLEVGKLYKGKVNGVAKYGVFVDLNDHVRGLIHRSNLLRDY--------EVGDEVIVQV 63

Query: 739 IGQDVRGNIKLS 750
                 GNI L 
Sbjct: 64  TDIPENGNIDLI 75

The function of this family is not fully understood. In Escherichia coli, RecJ degrades single-stranded DNA in the 5'-3' direction and participates in homologous recombination and mismatch repair. Length = 77

>gnl|CDD|239899 cd04452, S1_IF2_alpha, S1_IF2_alpha: The alpha subunit of translation Initiation Factor 2, S1-like RNA-binding domain

 Score = 49.5 bits (119), Expect = 1e-07
 Identities = 23/74 (31%), Positives = 39/74 (52%), Gaps = 3/74 (4%)

Query: 682 EVGGIYKGVVTSVKEYGAFVEFN--GGQQGLLHVSELSHEPVSRVSDVVSVGQQLSLRCI 739
           E G +    V S+ + GA+V     G  +G++ +SELS   +  +  +V VG++  ++ I
Sbjct: 2   EEGELVVVTVKSIADMGAYVSLLEYGNIEGMILLSELSRRRIRSIRKLVKVGRKEVVKVI 61

Query: 740 GQDV-RGNIKLSLK 752
             D  +G I LS K
Sbjct: 62  RVDKEKGYIDLSKK 75

S1-like RNA-binding domains are found in a wide variety of RNA-associated proteins. Eukaryotic and archaeal Initiation Factor 2 (e- and aIF2, respectively) are heterotrimeric proteins with three subunits (alpha, beta, and gamma). IF2 plays a crucial role in the process of translation initiation. The IF2 gamma subunit contains a GTP-binding site. The IF2 beta and gamma subunits together are thought to be responsible for binding methionyl-initiator tRNA. The ternary complex consisting of IF2, GTP, and the methionyl-initiator tRNA binds to the small subunit of the ribosome, as part of a pre-initiation complex that scans the mRNA to find the AUG start codon. The IF2-bound GTP is hydrolyzed to GDP when the methionyl-initiator tRNA binds the AUG start codon, at which time the IF2 is released with its bound GDP. The large ribosomal subunit then joins with the small subunit to complete the initiation complex, which is competent to begin translation. The IF2a subunit is a major site of control of the translation initiation process, via phosphorylation of a specific serine residue. This alpha subunit is well conserved in eukaryotes and archaea but is not present in bacteria. IF2 is a cold-shock-inducible protein. Length = 76

>gnl|CDD|235775 PRK06299, rpsA, 30S ribosomal protein S1; Reviewed

 Score = 54.4 bits (132), Expect = 2e-07
 Identities = 26/96 (27%), Positives = 47/96 (48%), Gaps = 8/96 (8%)

Query: 683 VGGIYKGVVTSVKEYGAFVEFNGGQQGLLHVSELSH-EPVSRVSDVVSVGQQLSLRCIGQ 741
           VG + +G V ++ ++GAFV   GG  GL+H+S++S  +      ++   G ++    +  
Sbjct: 373 VGDVVEGKVKNITDFGAFVGLEGGIDGLVHLSDISWDKKGEEAVELYKKGDEVEAVVLKV 432

Query: 742 DV-RGNIKLSLKAVSPRP----EADVK--GVVEGSV 770
           DV +  I L +K +   P        K   +V G+V
Sbjct: 433 DVEKERISLGIKQLEEDPFEEFAKKHKKGSIVTGTV 468

Length = 565

>gnl|CDD|105491 PRK12269, PRK12269, bifunctional cytidylate kinase/ribosomal protein S1; Provisional

 Score = 55.1 bits (132), Expect = 2e-07
 Identities = 33/97 (34%), Positives = 54/97 (55%), Gaps = 6/97 (6%)

Query: 683 VGGIYKGVVTSVKEYGAFVEFNGGQQGLLHVSELSH-EPVSRVSDVVSVGQQLSLRCIGQ 741
           V  + KG VT + ++GAF+E   G +GL H+SE S  +  S+ SD+V +G ++    +G 
Sbjct: 578 VNDVVKGRVTKIADFGAFIELAEGIEGLAHISEFSWVKKTSKPSDMVKIGDEVECMILGY 637

Query: 742 DVR-GNIKLSLKAVSPRPEADVKGVVEGSVPVNKQAT 777
           D++ G + L LK V+  P  +    +E   PV  + T
Sbjct: 638 DIQAGRVSLGLKQVTANPWEE----IEARYPVGARFT 670

Length = 863

>gnl|CDD|235268 PRK04282, PRK04282, exosome complex RNA-binding protein Rrp42; Provisional

 Score = 53.3 bits (129), Expect = 2e-07
 Identities = 26/65 (40%), Positives = 39/65 (60%), Gaps = 3/65 (4%)

Query: 352 VDTVRKRVIRKRIIAEGVRVDGRQLDEVRPIYCESGNLPILHGSSLFSRGDTQVLCTV-- 409
           +  ++K  I   ++ +G R+DGR+LDE RPI  E+G +    GS+L   G+TQVL  V  
Sbjct: 8   IPEIKKDYIL-SLLKKGKRIDGRKLDEYRPIEIETGVIKKAEGSALVKLGNTQVLAGVKL 66

Query: 410 TLGAP 414
            +G P
Sbjct: 67  EIGEP 71

Length = 271

>gnl|CDD|206767 cd11362, RNase_PH_bact, Ribonuclease PH

 Score = 52.6 bits (127), Expect = 2e-07
 Identities = 57/205 (27%), Positives = 80/205 (39%), Gaps = 44/205 (21%)

Query: 378 EVRPIYCESGNLPILHGSSLFSRGDTQVLCTVTLGAPAEAQRLESLVGPPTKR------- 430
           ++RPI    G      GS L   GDT+VLCT ++         E  V PP  R       
Sbjct: 1   QLRPISITRGFNKHAEGSVLIEFGDTKVLCTASV---------EEKV-PPFLRGKGKGWV 50

Query: 431 ----FMLHYSFPPFCINEVGKRVGLNRREVGHGTLAEKALLAVLPPENDFPYTVRVNSEV 486
                ML  S       E  K    + R      L  ++L A +  E     T+ ++ +V
Sbjct: 51  TAEYSMLPRSTHERTQREASKG-KQSGRTQEIQRLIGRSLRAAVDLEALGERTITIDCDV 109

Query: 487 MASDGSTSMATVCGGSMALMDA-----------GIPLQEHVAGVSVGLVSEVDPSTGEIK 535
           + +DG T  A++ G  +AL DA             PL+  VA VSVG+V           
Sbjct: 110 LQADGGTRTASITGAYVALADAVDKLVEKGVLEENPLKHFVAAVSVGIV----------- 158

Query: 536 DYRILTDILGLEDHLGDMDFKIAGT 560
           D   L D+   ED   D+D  +  T
Sbjct: 159 DGEPLLDLDYEEDSAADVDMNVVMT 183

Ribonuclease PH (RNase PH)-like 3'-5' exoribonucleases are enzymes that catalyze the 3' to 5' processing and decay of RNA substrates. Structurally all members of this family form hexameric rings (trimers of dimers). Bacterial RNase PH forms a homohexameric ring, and removes nucleotide residues following the -CCA terminus of tRNA. Length = 227

>gnl|CDD|236126 PRK07899, rpsA, 30S ribosomal protein S1; Reviewed

 Score = 53.5 bits (129), Expect = 3e-07
 Identities = 29/71 (40%), Positives = 41/71 (57%), Gaps = 1/71 (1%)

Query: 683 VGGIYKGVVTSVKEYGAFVEFNGGQQGLLHVSELSHEPVSRVSDVVSVGQQLSLRCIGQD 742
           +G I  G VT +  +GAFV    G +GL+H+SEL+   V     VV VG ++ ++ I  D
Sbjct: 293 IGQIVPGKVTKLVPFGAFVRVEEGIEGLVHISELAERHVEVPEQVVQVGDEVFVKVIDID 352

Query: 743 V-RGNIKLSLK 752
           + R  I LSLK
Sbjct: 353 LERRRISLSLK 363

Length = 486

>gnl|CDD|237516 PRK13806, rpsA, 30S ribosomal protein S1; Provisional

 Score = 53.2 bits (128), Expect = 5e-07
 Identities = 31/88 (35%), Positives = 48/88 (54%), Gaps = 2/88 (2%)

Query: 677 IGREIEVGGIYKGVVTSVKEYGAFVEFNGGQQGLLHVSELSH-EPVSRVSDVVSVGQQLS 735
           +G  ++ G    G V  +  +GAFVE   G +GL+HVSE+S    V++  DVV+ G  ++
Sbjct: 286 VGDRLKAGDKVTGKVVRLAPFGAFVEILPGIEGLVHVSEMSWTRRVNKPEDVVAPGDAVA 345

Query: 736 LRCIGQDV-RGNIKLSLKAVSPRPEADV 762
           ++    D  +  I LSL+     P ADV
Sbjct: 346 VKIKDIDPAKRRISLSLRDAEGDPWADV 373

Length = 491

>gnl|CDD|180908 PRK07252, PRK07252, hypothetical protein; Provisional

 Score = 48.9 bits (117), Expect = 6e-07
 Identities = 19/62 (30%), Positives = 37/62 (59%)

Query: 681 IEVGGIYKGVVTSVKEYGAFVEFNGGQQGLLHVSELSHEPVSRVSDVVSVGQQLSLRCIG 740
           +++G   KG +T +K YGAFV    G  GL+H+SE+    +  +  ++ VG+++ ++ + 
Sbjct: 1   MKIGDKLKGTITGIKPYGAFVALENGTTGLIHISEIKTGFIDNIHQLLKVGEEVLVQVVD 60

Query: 741 QD 742
            D
Sbjct: 61  FD 62

Length = 120

>gnl|CDD|239908 cd04461, S1_Rrp5_repeat_hs8_sc7, S1_Rrp5_repeat_hs8_sc7: Rrp5 Homo sapiens S1 repeat 8 (hs8) and Saccharomyces cerevisiae S1 repeat 7 (sc7)-like domains

 Score = 47.6 bits (114), Expect = 8e-07
 Identities = 21/59 (35%), Positives = 30/59 (50%), Gaps = 2/59 (3%)

Query: 680 EIEVGGIYKGVVTSVKEYGAFVEFNGGQQGLLHVSELSHEPVSRVSDVVSVGQQLSLRC 738
           +++ G +  G V ++  YG FVEF GG  GL   S +S E V+  S     GQ  S+  
Sbjct: 11  DLKPGMVVHGYVRNITPYGVFVEFLGGLTGLAPKSYISDEFVTDPSFGFKKGQ--SVTA 67

Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits. Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in S. cerevisiae Rrp5 and 14 S1 repeats in H. sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in protein-protein interactions. Mutational studies have shown that each region represents a specific functional domain. Deletions within the S1-containing region inhibit pre-rRNA processing at either site A3 or A2, whereas deletions within the TPR region confer an inability to support cleavage of A0-A2. This CD includes H. sapiens S1 repeat 8 and S. cerevisiae S1 repeat 7. Rrp5 is found in eukaryotes but not in prokaryotes or archaea. Length = 83

>gnl|CDD|206770 cd11365, RNase_PH_archRRP42, RRP42 subunit of archaeal exosome

 Score = 51.1 bits (123), Expect = 8e-07
 Identities = 24/60 (40%), Positives = 35/60 (58%), Gaps = 1/60 (1%)

Query: 353 DTVRKRVIRKRIIAEGVRVDGRQLDEVRPIYCESGNLPILHGSSLFSRGDTQVLCTVTLG 412
             +++  I   ++ +G R+DGR LDE R I  E+G +P   GS+L   G+TQVL  V L 
Sbjct: 1   PKIKRDYIL-SLLEKGKRIDGRGLDEYRDIEIETGVIPKAEGSALVKLGNTQVLAGVKLE 59

The RRP42 subunit of the archaeal exosome is a member of the RNase_PH family, named after the bacterial Ribonuclease PH, a 3'-5' exoribonuclease. Structurally all members of this family form hexameric rings (trimers of dimers). In archaea, the ring is formed by three Rrp41:Rrp42 dimers. The central chamber within the ring contains three phosphorolytic active sites located in an Rrp41 pocket at the interface between Rrp42 and Rrp41. The ring is capped by three copies of Rrp4 and/or Csl4 which contain putative RNA interaction domains. The archaeal exosome degrades single-stranded RNA (ssRNA) in the 3'-5' direction, but also can catalyze the reverse reaction of adding nucleoside diphosphates to the 3'-end of RNA which has been shown to lead to the formation of poly-A-rich tails on RNA. It is required for 3' processing of the 5.8S rRNA. Length = 256

>gnl|CDD|235188 PRK03987, PRK03987, translation initiation factor IF-2 subunit alpha; Validated

 Score = 51.0 bits (123), Expect = 1e-06
 Identities = 29/77 (37%), Positives = 46/77 (59%), Gaps = 3/77 (3%)

Query: 682 EVGGIYKGVVTSVKEYGAFVEFN--GGQQGLLHVSELSHEPVSRVSDVVSVGQQLSLRCI 739
           E G +  G V  VK++GAFV  +   G++G +H+SE++   V  + D V  GQ++  + I
Sbjct: 7   EEGELVVGTVKEVKDFGAFVTLDEYPGKEGFIHISEVASGWVKNIRDHVKEGQKVVCKVI 66

Query: 740 GQD-VRGNIKLSLKAVS 755
             D  +G+I LSLK V+
Sbjct: 67  RVDPRKGHIDLSLKRVN 83

Length = 262

>gnl|CDD|206774 cd11369, RNase_PH_RRP43, RRP43 subunit of eukaryotic exosome

 Score = 50.6 bits (122), Expect = 1e-06
 Identities = 28/82 (34%), Positives = 38/82 (46%), Gaps = 9/82 (10%)

Query: 362 KRIIAEGVRVDGRQLDEVRPIYCESGNLPILHGSSLFSRGDTQVLCTVTL--GAPAEAQR 419
           +R +AE VR DGR+LDE RP     G++    GS+L   G+T VLC +      PA    
Sbjct: 10  RRFLAENVRPDGRELDEFRPTSVNVGSISTADGSALVKLGNTTVLCGIKAEVATPAADT- 68

Query: 420 LESLVGPPTKRFMLHYSFPPFC 441
                 P     + +   PP C
Sbjct: 69  ------PDEGYLVPNVDLPPLC 84

The RRP43 subunit of eukaryotic exosome is a member of the RNase_PH family, named after the bacterial Ribonuclease PH, a 3'-5' exoribonuclease. Structurally all members of this family form hexameric rings (trimers of Rrp41-Rrp45, Rrp46-Rrp43, and Mtr3-Rrp42 dimers). The eukaryotic exosome core is composed of six individually encoded RNase PH-like subunits and three additional proteins (Rrp4, Csl4 and Rrp40) that form a stable cap and contain RNA-binding domains. The RNase PH-like subunits are no longer phosphorolytic enzymes, the exosome directly associates with Rrp44 and Rrp6, hydrolytic exoribonucleases related to bacterial RNase II/R and RNase D. The exosome plays an important role in RNA turnover. It plays a crucial role in the maturation of stable RNA species such as rRNA, snRNA and snoRNA, quality control of mRNA, and the degradation of RNA processing by-products and non-coding transcripts. Length = 261

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

 Score = 45.2 bits (108), Expect = 2e-06
 Identities = 23/61 (37%), Positives = 37/61 (60%), Gaps = 1/61 (1%)

Query: 615 PRLATLKYDNDTLRRLIGPLGALKRKIEEETGGRISVS-DGTLTVVAKNRSVMEKVLEKV 673
           PR+ T+K   D +R +IGP G   +KI EETG +I +  DGT+ + A ++   EK  + +
Sbjct: 1   PRIETMKIPPDKIRDVIGPGGKTIKKIIEETGVKIDIEDDGTVYIAASDKEAAEKAKKMI 60

Query: 674 D 674
           +
Sbjct: 61  E 61

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|235614 PRK05807, PRK05807, hypothetical protein; Provisional

 Score = 46.3 bits (110), Expect = 6e-06
 Identities = 24/86 (27%), Positives = 46/86 (53%), Gaps = 2/86 (2%)

Query: 681 IEVGGIYKGVVTSVKEYGAFVEFNGGQQGLLHVSELSHEPVSRVSDVVSVGQQLSLRCIG 740
           ++ G I +G V ++  +GAFVE  G + GL+H+SE++   V  + + +    ++ ++ I 
Sbjct: 3   LKAGSILEGTVVNITNFGAFVEVEG-KTGLVHISEVADTYVKDIREHLKEQDKVKVKVIS 61

Query: 741 QDVRGNIKLSLK-AVSPRPEADVKGV 765
            D  G I LS+K A+  +       +
Sbjct: 62  IDDNGKISLSIKQAMKQKKSVKPAEI 87

Length = 136

>gnl|CDD|240213 cd05708, S1_Rrp5_repeat_sc12, S1_Rrp5_repeat_sc12: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits

 Score = 43.9 bits (104), Expect = 1e-05
 Identities = 25/74 (33%), Positives = 39/74 (52%), Gaps = 2/74 (2%)

Query: 682 EVGGIYKGVVTSVKEYGAFVEFNG-GQQGLLHVSELSHEPVSRVSDVVSVGQQLSLRCIG 740
           +VG    G V  V++YG F++ +G    GL H SE+S   V+  S +  VG ++  + + 
Sbjct: 1   KVGQKIDGTVRRVEDYGVFIDIDGTNVSGLCHKSEISDNRVADASKLFRVGDKVRAKVLK 60

Query: 741 QDV-RGNIKLSLKA 753
            D  +  I L LKA
Sbjct: 61  IDAEKKRISLGLKA 74

Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in Saccharomyces cerevisiae Rrp5 and 14 S1 repeats in Homo sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in protein-protein interactions. Mutational studies have shown that each region represents a specific functional domain. Deletions within the S1-containing region inhibit pre-rRNA processing at either site A3 or A2, whereas deletions within the TPR region confer an inability to support cleavage of A0-A2. This CD includes S. cerevisiae S1 repeat 12 (sc12). Rrp5 is found in eukaryotes but not in prokaryotes or archaea. Length = 77

>gnl|CDD|240196 cd05691, S1_RPS1_repeat_ec6, S1_RPS1_repeat_ec6: Ribosomal protein S1 (RPS1) domain

 Score = 43.8 bits (104), Expect = 1e-05
 Identities = 24/72 (33%), Positives = 35/72 (48%), Gaps = 1/72 (1%)

Query: 684 GGIYKGVVTSVKEYGAFVEFNGGQQGLLHVSELSHEPVSRVSDVVSVGQQLSLRCIGQDV 743
           G I  G VT V   GA V+   G +G L  +ELS + V   ++   VG ++  +    D 
Sbjct: 1   GSIVTGKVTEVDAKGATVKLGDGVEGFLRAAELSRDRVEDATERFKVGDEVEAKITNVDR 60

Query: 744 RG-NIKLSLKAV 754
           +   I LS+KA 
Sbjct: 61  KNRKISLSIKAK 72

RPS1 is a component of the small ribosomal subunit thought to be involved in the recognition and binding of mRNA's during translation initiation. The bacterial RPS1 domain architecture consists of 4-6 tandem S1 domains. In some bacteria, the tandem S1 array is located C-terminal to a 4-hydroxy-3-methylbut-2-enyl diphosphate reductase (HMBPP reductase) domain. While RPS1 is found primarily in bacteria, proteins with tandem RPS1-like domains have been identified in plants and humans, however these lack the N-terminal HMBPP reductase domain. This CD includes S1 repeat 6 (ec6) of the Escherichia coli RPS1. Autoantibodies to double-stranded DNA from patients with systemic lupus erythematosus cross-react with the human RPS1 homolog. Length = 73

>gnl|CDD|105491 PRK12269, PRK12269, bifunctional cytidylate kinase/ribosomal protein S1; Provisional

 Score = 48.2 bits (114), Expect = 2e-05
 Identities = 43/133 (32%), Positives = 61/133 (45%), Gaps = 11/133 (8%)

Query: 648 RISVSD---GTLTVVAKNRSVMEKVLEKVDFIIGREIEVGGIYKGVVTSVKEYGAFVEFN 704
           RIS S    G   +V   R  +E+   +        + +     GVV S   +GAF++  
Sbjct: 455 RISQSKQHRGNDNIVINRRRYLEERARQAREEFFNSVHIEDSVSGVVKSFTSFGAFIDL- 513

Query: 705 GGQQGLLHVSELSHEPVSRVSDVVSVGQQLSLRCIGQD-VRGNIKLSLKAVSPRP----- 758
           GG  GLLHV+++S   V+R  + V  GQ + L+ I  D     I LSLK   P P     
Sbjct: 514 GGFDGLLHVNDMSWGHVARPREFVKKGQTIELKVIRLDQAEKRINLSLKHFQPDPWLEFE 573

Query: 759 -EADVKGVVEGSV 770
            +  V  VV+G V
Sbjct: 574 NKFGVNDVVKGRV 586

Length = 863

>gnl|CDD|223613 COG0539, RpsA, Ribosomal protein S1 [Translation, ribosomal structure and biogenesis]

 Score = 47.3 bits (113), Expect = 3e-05
 Identities = 30/78 (38%), Positives = 43/78 (55%), Gaps = 8/78 (10%)

Query: 677 IGREIEVGGIYKGVVTSVKEYGAFVEFNGGQQGLLHVSELSHEPVSRVSDVVSVGQQLSL 736
              + + G + KG V SVK+ GAFVE  GG +GL+ +SELS        DV+ VG ++  
Sbjct: 443 FSEKYKKGSVVKGKVKSVKDKGAFVELGGGVEGLIRLSELS-------RDVLKVGDEVEA 495

Query: 737 RCIGQDVRGN-IKLSLKA 753
             +  D +   I LS+KA
Sbjct: 496 VVVSIDKKNRKILLSIKA 513

Length = 541

>gnl|CDD|224032 COG1107, COG1107, Archaea-specific RecJ-like exonuclease, contains DnaJ-type Zn finger domain [DNA replication, recombination, and repair]

 Score = 47.0 bits (112), Expect = 4e-05
 Identities = 28/91 (30%), Positives = 47/91 (51%), Gaps = 10/91 (10%)

Query: 679 REIEVGGIYKGVVTSVKEYGAFVEFNGGQQGLLHVSELSHEP--------VSRVSDVVSV 730
            ++E G  YKG+V+ V++YG FVE N   +GL+H  +L  +P        + +VSDV   
Sbjct: 118 EDVEAGKYYKGIVSRVEKYGVFVELNSHVRGLIHRRDLGGDPDYAVGDEIIVQVSDVRPE 177

Query: 731 GQQLSLRCIGQDVRGNIKLSLKAVSPRPEAD 761
             ++    +G D    +++  K + PR   D
Sbjct: 178 KGEIDFEPVGLDRYREVQVE-KEL-PRTLID 206

Length = 715

>gnl|CDD|240192 cd05687, S1_RPS1_repeat_ec1_hs1, S1_RPS1_repeat_ec1_hs1: Ribosomal protein S1 (RPS1) domain

 Score = 42.1 bits (100), Expect = 4e-05
 Identities = 22/70 (31%), Positives = 37/70 (52%), Gaps = 1/70 (1%)

Query: 684 GGIYKGVVTSVKEYGAFVEFNGGQQGLLHVSELSHEPVSRVSDVVSVGQQLSLRCIG-QD 742
           G I KG V SV +    V+     +G++ +SE S +P+    D V VG ++ +  +  +D
Sbjct: 1   GDIVKGTVVSVDDDEVLVDIGYKSEGIIPISEFSDDPIENGEDEVKVGDEVEVYVLRVED 60

Query: 743 VRGNIKLSLK 752
             GN+ LS +
Sbjct: 61  EEGNVVLSKR 70

RPS1 is a component of the small ribosomal subunit thought to be involved in the recognition and binding of mRNA's during translation initiation. The bacterial RPS1 domain architecture consists of 4-6 tandem S1 domains. In some bacteria, the tandem S1 array is located C-terminal to a 4-hydroxy-3-methylbut-2-enyl diphosphate reductase (HMBPP reductase) domain. While RPS1 is found primarily in bacteria, proteins with tandem RPS1-like domains have been identified in plants and humans, however these lack the N-terminal HMBPP reductase domain. This CD includes S1 repeat 1 of the Escherichia coli and Homo sapiens RPS1 (ec1 and hs1, respectively). Autoantibodies to double-stranded DNA from patients with systemic lupus erythematosus cross-react with the human RPS1 homolog. Length = 70

>gnl|CDD|223761 COG0689, Rph, RNase PH [Translation, ribosomal structure and biogenesis]

 Score = 45.4 bits (108), Expect = 5e-05
 Identities = 52/226 (23%), Positives = 91/226 (40%), Gaps = 36/226 (15%)

Query: 68  RLITLETGKIARFANGAVVLGMDETKVLSTVTSSKGDSVRDFL------PLTVDYQEKQF 121
           R I +  G + + A G+ ++    TKV+ TV+  + + V  FL       LT +Y     
Sbjct: 19  RPIKITRG-VLKHAEGSSLIEFGNTKVICTVSGPR-EPVPRFLRGTGKGWLTAEYGMLPR 76

Query: 122 AQGVIPNTYMRREGAPKERELLVGRIIDRPIRP-----LFPAGFYHEVQVMASVLSSDGK 176
           +     +   +RE A + R   + R+I R +R      L P      + +   VL +DG 
Sbjct: 77  ST----DERKKRE-ADRGRTKEISRLIGRALRAVIDLELLPE---STIDIDCDVLQADG- 127

Query: 177 QDPDIMAA--NATSAALMLSDIPWGGPIGMIRIGRICGQFIVNPTMDELS--LSDLNLVY 232
                  A     S AL  + IP    +  I +G + G  +++   +E S   +D+N+V 
Sbjct: 128 ---GTRTASITGASLALADAGIPLRDLVAAISVGIVDGVIVLDLDYEEDSAAEADMNVVM 184

Query: 233 ACTREKTLMIDVQ----AREISEKDLEAGLRLAHPEAVKYLEPQIR 274
                   ++++Q        +E +L   L LA     +  E Q  
Sbjct: 185 TGNGG---LVEIQGLAEDGPFTEDELLELLDLAIKGCNELRELQRE 227

Length = 230

>gnl|CDD|217696 pfam03725, RNase_PH_C, 3' exoribonuclease family, domain 2

 Score = 41.8 bits (99), Expect = 5e-05
 Identities = 21/78 (26%), Positives = 34/78 (43%), Gaps = 14/78 (17%)

Query: 516 VAGVSVGLVSEVDPSTGEIKDYRILTDILGLEDHL--GDMDFKIAGTRIGVTAIQLDIKP 573
           VA V+VG +           D  ++ D    E+ L   D+   +AGT   V  ++     
Sbjct: 3   VAAVTVGKI-----------DGELVLDPTLEEESLADSDLTIVVAGTGEIVALMKEGGG- 50

Query: 574 AGIPLDIICECLEHAHKG 591
           A +  + + E LE AH+G
Sbjct: 51  AELTEEELLEALELAHEG 68

This family includes 3'-5' exoribonucleases. Ribonuclease PH contains a single copy of this domain, and removes nucleotide residues following the -CCA terminus of tRNA. Polyribonucleotide nucleotidyltransferase (PNPase) contains two tandem copies of the domain. PNPase is involved in mRNA degradation in a 3'-5' direction. The exosome is a 3'-5' exoribonuclease complex that is required for 3' processing of the 5.8S rRNA. Three of its five protein components contain a copy of this domain. A hypothetical protein from S. pombe appears to belong to an uncharacterized subfamily. This subfamily is found in both eukaryotes and archaebacteria. Length = 68

>gnl|CDD|225034 COG2123, COG2123, RNase PH-related exoribonuclease [Translation, ribosomal structure and biogenesis]

 Score = 45.0 bits (107), Expect = 9e-05
 Identities = 22/56 (39%), Positives = 34/56 (60%)

Query: 357 KRVIRKRIIAEGVRVDGRQLDEVRPIYCESGNLPILHGSSLFSRGDTQVLCTVTLG 412
           KR     ++ +G+R+DGR  DE RP+  E+G +P  +GS+L   G+TQV+  V   
Sbjct: 11  KREYILNLLKKGIRIDGRSFDEFRPLEIETGVIPKANGSALVKLGNTQVVVGVKAE 66

Length = 272

>gnl|CDD|235851 PRK06676, rpsA, 30S ribosomal protein S1; Reviewed

 Score = 45.6 bits (109), Expect = 1e-04
 Identities = 28/94 (29%), Positives = 50/94 (53%), Gaps = 7/94 (7%)

Query: 666 MEKVLEKVDFIIGREIEVGGIYKGVVTSVKEYGAFVEFNG-GQQGLLHVSELSHEPVSRV 724
            E+ L  V     +E+EVG +  G V  V++   FV   G   +G++ +SELS++ +  +
Sbjct: 5   FEESLNSV-----KEVEVGDVVTGEVLKVEDKQVFVNIEGYKVEGVIPISELSNDHIEDI 59

Query: 725 SDVVSVGQQLSLRCIGQDV-RGNIKLSLKAVSPR 757
           +DVV VG +L +  +  +   GN+ LS + +   
Sbjct: 60  NDVVKVGDELEVYVLKVEDGEGNLLLSKRRLEAE 93

Length = 390

>gnl|CDD|234623 PRK00087, PRK00087, 4-hydroxy-3-methylbut-2-enyl diphosphate reductase/S1 RNA-binding domain protein; Reviewed

 Score = 45.3 bits (108), Expect = 2e-04
 Identities = 23/77 (29%), Positives = 42/77 (54%), Gaps = 1/77 (1%)

Query: 679 REIEVGGIYKGVVTSVKEYGAFVEFNGGQQGLLHVSELSHEPVSRVSDVVSVGQQLSLRC 738
           ++I  G I KG V SV E   FV+     +G++ + EL+ + +S + + V VG ++ ++ 
Sbjct: 298 KQIRRGDIVKGTVVSVNENEVFVDVGYKSEGVIPLRELTLDEISSLKESVKVGDEIEVKV 357

Query: 739 IG-QDVRGNIKLSLKAV 754
           +  +D  G + LS K  
Sbjct: 358 LKLEDEDGYVVLSKKEA 374

Length = 647

>gnl|CDD|178914 PRK00173, rph, ribonuclease PH; Reviewed

 Score = 43.9 bits (105), Expect = 2e-04
 Identities = 18/44 (40%), Positives = 24/44 (54%), Gaps = 4/44 (9%)

Query: 370 RVDGRQLDEVRPIYCESGNLPILH--GSSLFSRGDTQVLCTVTL 411
           R DGR  D++RP+          H  GS L   GDT+VLCT ++
Sbjct: 2   RPDGRAADQLRPVTITRN--FTKHAEGSVLVEFGDTKVLCTASV 43

Length = 238

>gnl|CDD|206773 cd11368, RNase_PH_RRP45, RRP45 subunit of eukaryotic exosome

 Score = 43.7 bits (104), Expect = 2e-04
 Identities = 19/46 (41%), Positives = 26/46 (56%), Gaps = 3/46 (6%)

Query: 365 IAEGVRVDGRQLDEVRPIYCESGNLPILHGSSLFSRGDTQVLCTVT 410
           + EG+R+DGR LDE RPI        + +G    S G T+VL  V+
Sbjct: 13  LKEGLRLDGRGLDEFRPI---KITFGLEYGCVEVSLGKTRVLAQVS 55

The RRP45 subunit of eukaryotic exosome is a member of the RNase_PH family, named after the bacterial Ribonuclease PH, a 3'-5' exoribonuclease. Structurally all members of this family form hexameric rings (trimers of Rrp41-Rrp45, Rrp46-Rrp43, and Mtr3-Rrp42 dimers). The eukaryotic exosome core is composed of six individually encoded RNase PH-like subunits and three additional proteins (Rrp4, Csl4 and Rrp40) that form a stable cap and contain RNA-binding domains. The RNase PH-like subunits are no longer phosphorolytic enzymes, the exosome directly associates with Rrp44 and Rrp6, hydrolytic exoribonucleases related to bacterial RNase II/R and RNase D. The exosome plays an important role in RNA turnover. It plays a crucial role in the maturation of stable RNA species such as rRNA, snRNA and snoRNA, quality control of mRNA, and the degradation of RNA processing by-products and non-coding transcripts. Length = 259

>gnl|CDD|240195 cd05690, S1_RPS1_repeat_ec5, S1_RPS1_repeat_ec5: Ribosomal protein S1 (RPS1) domain

 Score = 39.0 bits (91), Expect = 5e-04
 Identities = 17/52 (32%), Positives = 32/52 (61%), Gaps = 1/52 (1%)

Query: 684 GGIYKGVVTSVKEYGAFVEFNGGQQGLLHVSELS-HEPVSRVSDVVSVGQQL 734
           G +  G + S+ ++G FV  +GG  GL+H+S++S  + V   S++   GQ++
Sbjct: 1   GTVVSGKIKSITDFGIFVGLDGGIDGLVHISDISWTQRVRHPSEIYKKGQEV 52

RPS1 is a component of the small ribosomal subunit thought to be involved in the recognition and binding of mRNA's during translation initiation. The bacterial RPS1 domain architecture consists of 4-6 tandem S1 domains. In some bacteria, the tandem S1 array is located C-terminal to a 4-hydroxy-3-methylbut-2-enyl diphosphate reductase (HMBPP reductase) domain. While RPS1 is found primarily in bacteria, proteins with tandem RPS1-like domains have been identified in plants and humans, however these lack the N-terminal HMBPP reductase domain. This CD includes S1 repeat 5 (ec5) of the Escherichia coli RPS1. Autoantibodies to double-stranded DNA from patients with systemic lupus erythematosus cross-react with the human RPS1 homolog. Length = 69

>gnl|CDD|223613 COG0539, RpsA, Ribosomal protein S1 [Translation, ribosomal structure and biogenesis]

 Score = 43.1 bits (102), Expect = 7e-04
 Identities = 26/74 (35%), Positives = 43/74 (58%), Gaps = 4/74 (5%)

Query: 680 EIEVGGIYKGVVTSVKEYGAFVEFNGGQQGLLHVSELSHEPVSRVSDVVSVGQQLSLRCI 739
           E E G + KG V S+++ G  V+  G  +G++ +SE S+EP   V DVV VG ++ +  +
Sbjct: 18  EFEPGDVVKGTVVSIEKDGVLVDIGGKSEGVIPISEFSNEP---VEDVVQVGDEVEVLVL 74

Query: 740 G-QDVRGNIKLSLK 752
             +D  G + LS +
Sbjct: 75  RVEDGEGELVLSRR 88

Length = 541

>gnl|CDD|223901 COG0831, UreA, Urea amidohydrolase (urease) gamma subunit [Amino acid transport and metabolism]

 Score = 38.8 bits (91), Expect = 0.001
 Identities = 25/87 (28%), Positives = 41/87 (47%), Gaps = 7/87 (8%)

Query: 236 REK-TLMIDVQAREISEKDLEAGLRLAHPEAVKYLEPQIRLAEKAGKQKKE---YKLSMI 291
           REK  L+I   A E++ +    GL+L +PEAV  +   I    + GK   E       ++
Sbjct: 6   REKDKLLI-FTAAELARRRKARGLKLNYPEAVALISAFILEGARDGKTVAELMSEGRHVL 64

Query: 292 S-EQTLEKVSN-LAEAHIEAVFTDPSY 316
           + +  +E V   + E  +EA F D + 
Sbjct: 65  TRDDVMEGVPEMIHEIQVEATFPDGTK 91

Length = 100

>gnl|CDD|206772 cd11367, RNase_PH_RRP42, RRP42 subunit of eukaryotic exosome

 Score = 41.4 bits (98), Expect = 0.001
 Identities = 17/45 (37%), Positives = 25/45 (55%)

Query: 365 IAEGVRVDGRQLDEVRPIYCESGNLPILHGSSLFSRGDTQVLCTV 409
           + + +R DGR   + RPI  E+G L   +GS+    G+T VL  V
Sbjct: 14  VEQNIRNDGRSRLDYRPIELETGVLSNTNGSARVRLGNTDVLVGV 58

The RRP42 subunit of eukaryotic exosome is a member of the RNase_PH family, named after the bacterial Ribonuclease PH, a 3'-5' exoribonuclease. Structurally all members of this family form hexameric rings (trimers of Rrp41-Rrp45, Rrp46-Rrp43, and Mtr3-Rrp42 dimers). The eukaryotic exosome core is composed of six individually encoded RNase PH-like subunits and three additional proteins (Rrp4, Csl4 and Rrp40) that form a stable cap and contain RNA-binding domains. The RNase PH-like subunits are no longer phosphorolytic enzymes, the exosome directly associates with Rrp44 and Rrp6, hydrolytic exoribonucleases related to bacterial RNase II/R and RNase D. The exosome plays an important role in RNA turnover. It plays a crucial role in the maturation of stable RNA species such as rRNA, snRNA and snoRNA, quality control of mRNA, and the degradation of RNA processing by-products and non-coding transcripts. Length = 272

>gnl|CDD|233102 TIGR00717, rpsA, ribosomal protein S1

 Score = 42.0 bits (99), Expect = 0.002
 Identities = 27/96 (28%), Positives = 45/96 (46%), Gaps = 12/96 (12%)

Query: 683 VGGIYKGVVTSVKEYGAFVEFNGGQQGLLHVSELSHEPVSRVSDVV-SVGQQLSLRCIGQ 741
           VG    G +  + ++GAFVE  GG  GL+H+S++S +   R +D +   G ++    +  
Sbjct: 359 VGDRVTGKIKKITDFGAFVELEGGIDGLIHLSDISWDKDGREADHLYKKGDEIEAVVLAV 418

Query: 742 DVRGN-IKLSLKAVSPRP----------EADVKGVV 766
           D     I L +K ++  P           + VKG V
Sbjct: 419 DKEKKRISLGVKQLTENPWEKFAAKYKVGSVVKGKV 454

This model describes ribosomal protein S1, RpsA. This protein is found in most bacterial genomes in a single copy, but is not present in the Mycoplasmas. It is heterogeneous with respect to the number of repeats of the S1 RNA binding domain described by PFAM model pfam00575: six repeats in E. coli and most other bacteria, four in Bacillus subtilis and some other species. rpsA is an essential gene in E. coli but not in B. subtilis. It is associated with the cytidylate kinase gene cmk in many species, and fused to it in Treponema pallidum. RpsA is proposed (Medline:97323001) to assist in mRNA degradation. This model provides trusted hits to most long form (6 repeat) examples of RpsA. Among homologs with only four repeats are some to which other (perhaps secondary) functions have been assigned [Protein synthesis, Ribosomal proteins: synthesis and modification]. Length = 516

>gnl|CDD|239900 cd04453, S1_RNase_E, S1_RNase_E: RNase E and RNase G, S1-like RNA-binding domain

 Score = 38.3 bits (90), Expect = 0.002
 Identities = 18/62 (29%), Positives = 31/62 (50%), Gaps = 5/62 (8%)

Query: 678 GREIEVGGIYKGVVTSV--KEYGAFVEFNGGQQGLLHVSELSHE---PVSRVSDVVSVGQ 732
            RE  VG IY G V  +      AFV+   G+ G LH+S++         +++ ++  GQ
Sbjct: 2   NREPIVGNIYLGRVKKIVPGLQAAFVDIGLGKNGFLHLSDILPAYFKKHKKIAKLLKEGQ 61

Query: 733 QL 734
           ++
Sbjct: 62  EI 63

RNase E is an essential endoribonuclease in the processing and degradation of RNA. In addition to its role in mRNA degradation, RNase E has also been implicated in the processing of rRNA, and the maturation of tRNA, 10Sa RNA and the M1 precursor of RNase P. RNase E associates with PNPase (3' to 5' exonuclease), Rhl B (DEAD-box RNA helicase) and enolase (glycolytic enzyme) to form the RNA degradosome. RNase E tends to cut mRNA within single-stranded regions that are rich in A/U nucleotides. The N-terminal region of RNase E contains the catalytic site. Within the conserved N-terminal domain of RNAse E and RNase G, there is an S1-like subdomain, which is an ancient single-stranded RNA-binding domain. S1 domain is an RNA-binding module originally identified in the ribosomal protein S1. The S1 domain is required for RNA cleavage by RNase E. RNase G is paralogous to RNase E with an N-terminal catalytic domain that is highly homologous to that of RNase E. RNase G not only shares sequence similarity with RNase E, but also functionally overlaps with RNase E. In Escherichia coli, RNase G is involved in the maturation of the 5' end of the 16S rRNA. RNase G plays a secondary role in mRNA decay. Length = 88

>gnl|CDD|240194 cd05689, S1_RPS1_repeat_ec4, S1_RPS1_repeat_ec4: Ribosomal protein S1 (RPS1) domain

 Score = 37.2 bits (86), Expect = 0.003
 Identities = 15/28 (53%), Positives = 21/28 (75%)

Query: 689 GVVTSVKEYGAFVEFNGGQQGLLHVSEL 716
           G VT++ +YG FVE   G +GL+HVSE+
Sbjct: 9   GKVTNLTDYGCFVELEEGVEGLVHVSEM 36

RPS1 is a component of the small ribosomal subunit thought to be involved in the recognition and binding of mRNA's during translation initiation. The bacterial RPS1 domain architecture consists of 4-6 tandem S1 domains. In some bacteria, the tandem S1 array is located C-terminal to a 4-hydroxy-3-methylbut-2-enyl diphosphate reductase (HMBPP reductase) domain. While RPS1 is found primarily in bacteria, proteins with tandem RPS1-like domains have been identified in plants and humans, however these lack the N-terminal HMBPP reductase domain. This CD includes S1 repeat 4 (ec4) of the Escherichia coli RPS1. Autoantibodies to double-stranded DNA from patients with systemic lupus erythematosus cross-react with the human RPS1 homolog. Length = 72

>gnl|CDD|239917 cd04471, S1_RNase_R, S1_RNase_R: RNase R C-terminal S1 domain

 Score = 37.0 bits (87), Expect = 0.004
 Identities = 16/35 (45%), Positives = 22/35 (62%), Gaps = 1/35 (2%)

Query: 683 VGGIYKGVVTSVKEYGAFVE-FNGGQQGLLHVSEL 716
           VG  + GV++ V  +G FVE  N   +GL+HVS L
Sbjct: 1   VGEEFDGVISGVTSFGLFVELDNLTVEGLVHVSTL 35

RNase R is a processive 3' to 5' exoribonuclease, which is a homolog of RNase II. RNase R degrades RNA with secondary structure having a 3' overhang of at least 7 nucleotides. RNase R and PNPase play an important role in the degradation of RNA with extensive secondary structure, such as rRNA, tRNA, and certain mRNA which contains repetitive extragenic palindromic sequences. The C-terminal S1 domain binds ssRNA. Length = 83

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	974
COG1185	692	Pnp Polyribonucleotide nucleotidyltransferase (pol	100.0
TIGR02696	719	pppGpp_PNP guanosine pentaphosphate synthetase I/p	100.0
KOG1067	760	consensus Predicted RNA-binding polyribonucleotide	100.0
PLN00207	891	polyribonucleotide nucleotidyltransferase; Provisi	100.0
PRK11824	693	polynucleotide phosphorylase/polyadenylase; Provis	100.0
TIGR03591	684	polynuc_phos polyribonucleotide nucleotidyltransfe	100.0
COG0539	541	RpsA Ribosomal protein S1 [Translation, ribosomal	100.0
PRK12269	863	bifunctional cytidylate kinase/ribosomal protein S	100.0
TIGR02065	230	ECX1 archaeal exosome-like complex exonuclease 1.	100.0
PRK03983	244	exosome complex exonuclease Rrp41; Provisional	100.0
PRK00173	238	rph ribonuclease PH; Reviewed	100.0
TIGR01966	236	RNasePH ribonuclease PH. This bacterial enzyme, ri	100.0
PRK11824	693	polynucleotide phosphorylase/polyadenylase; Provis	100.0
PRK04282	271	exosome complex RNA-binding protein Rrp42; Provisi	100.0
PRK06299	565	rpsA 30S ribosomal protein S1; Reviewed	100.0
TIGR03591	684	polynuc_phos polyribonucleotide nucleotidyltransfe	100.0
TIGR00717	516	rpsA ribosomal protein S1. This model provides tru	100.0
COG0539	541	RpsA Ribosomal protein S1 [Translation, ribosomal	100.0
TIGR02065	230	ECX1 archaeal exosome-like complex exonuclease 1.	100.0
COG0689	230	Rph RNase PH [Translation, ribosomal structure and	100.0
PLN00207	891	polyribonucleotide nucleotidyltransferase; Provisi	100.0
PRK13806	491	rpsA 30S ribosomal protein S1; Provisional	100.0
PRK00173	238	rph ribonuclease PH; Reviewed	100.0
PRK07899	486	rpsA 30S ribosomal protein S1; Reviewed	100.0
KOG1068	245	consensus Exosomal 3'-5' exoribonuclease complex,	100.0
TIGR01966	236	RNasePH ribonuclease PH. This bacterial enzyme, ri	100.0
PRK03983	244	exosome complex exonuclease Rrp41; Provisional	100.0
COG2123	272	RNase PH-related exoribonuclease [Translation, rib	99.98
PRK12269	863	bifunctional cytidylate kinase/ribosomal protein S	99.97
COG1185	692	Pnp Polyribonucleotide nucleotidyltransferase (pol	99.97
COG0689	230	Rph RNase PH [Translation, ribosomal structure and	99.97
PRK06299	565	rpsA 30S ribosomal protein S1; Reviewed	99.97
TIGR02696	719	pppGpp_PNP guanosine pentaphosphate synthetase I/p	99.97
PRK06676	390	rpsA 30S ribosomal protein S1; Reviewed	99.97
TIGR00717	516	rpsA ribosomal protein S1. This model provides tru	99.96
PRK00087	647	4-hydroxy-3-methylbut-2-enyl diphosphate reductase	99.96
PRK13806	491	rpsA 30S ribosomal protein S1; Provisional	99.95
PRK07400	318	30S ribosomal protein S1; Reviewed	99.95
KOG1069	217	consensus Exosomal 3'-5' exoribonuclease complex,	99.95
KOG1614	291	consensus Exosomal 3'-5' exoribonuclease complex,	99.95
PRK04282	271	exosome complex RNA-binding protein Rrp42; Provisi	99.94
KOG1613	298	consensus Exosomal 3'-5' exoribonuclease complex,	99.94
KOG1069	217	consensus Exosomal 3'-5' exoribonuclease complex,	99.92
COG2123	272	RNase PH-related exoribonuclease [Translation, rib	99.92
KOG1067	760	consensus Predicted RNA-binding polyribonucleotide	99.9
KOG1068	245	consensus Exosomal 3'-5' exoribonuclease complex,	99.9
KOG1612	288	consensus Exosomal 3'-5' exoribonuclease complex,	99.88
PF01138	132	RNase_PH: 3' exoribonuclease family, domain 1 This	99.88
PRK07899	486	rpsA 30S ribosomal protein S1; Reviewed	99.86
PRK06676	390	rpsA 30S ribosomal protein S1; Reviewed	99.83
PRK00087	647	4-hydroxy-3-methylbut-2-enyl diphosphate reductase	99.78
COG1098	129	VacB Predicted RNA binding protein (contains ribos	99.72
PF01138	132	RNase_PH: 3' exoribonuclease family, domain 1 This	99.71
KOG1614	291	consensus Exosomal 3'-5' exoribonuclease complex,	99.63
PRK07400	318	30S ribosomal protein S1; Reviewed	99.61
KOG1070	1710	consensus rRNA processing protein Rrp5 [RNA proces	99.53
KOG1070	1710	consensus rRNA processing protein Rrp5 [RNA proces	99.52
COG2996	287	Predicted RNA-bindining protein (contains S1 and H	99.51
PTZ00248	319	eukaryotic translation initiation factor 2 subunit	99.51
PRK08582	139	hypothetical protein; Provisional	99.48
cd05704	72	S1_Rrp5_repeat_hs13 S1_Rrp5_repeat_hs13: Rrp5 is a	99.48
cd05705	74	S1_Rrp5_repeat_hs14 S1_Rrp5_repeat_hs14: Rrp5 is a	99.44
cd05686	73	S1_pNO40 S1_pNO40: pNO40 , S1-like RNA-binding dom	99.4
cd05698	70	S1_Rrp5_repeat_hs6_sc5 S1_Rrp5_repeat_hs6_sc5: Rrp	99.36
cd05696	71	S1_Rrp5_repeat_hs4 S1_Rrp5_repeat_hs4: Rrp5 is a t	99.35
PF00575	74	S1: S1 RNA binding domain; InterPro: IPR003029 Rib	99.34
cd04461	83	S1_Rrp5_repeat_hs8_sc7 S1_Rrp5_repeat_hs8_sc7: Rrp	99.33
cd05703	73	S1_Rrp5_repeat_hs12_sc9 S1_Rrp5_repeat_hs12_sc9: R	99.32
cd04452	76	S1_IF2_alpha S1_IF2_alpha: The alpha subunit of tr	99.32
COG1098	129	VacB Predicted RNA binding protein (contains ribos	99.31
cd05684	79	S1_DHX8_helicase S1_DHX8_helicase: The N-terminal	99.31
PRK05807	136	hypothetical protein; Provisional	99.31
cd05706	73	S1_Rrp5_repeat_sc10 S1_Rrp5_repeat_sc10: Rrp5 is a	99.31
PRK07252	120	hypothetical protein; Provisional	99.31
PHA02945	88	interferon resistance protein; Provisional	99.3
cd05697	69	S1_Rrp5_repeat_hs5 S1_Rrp5_repeat_hs5: Rrp5 is a t	99.29
PF03726	83	PNPase: Polyribonucleotide nucleotidyltransferase,	99.29
cd05707	68	S1_Rrp5_repeat_sc11 S1_Rrp5_repeat_sc11: Rrp5 is a	99.27
cd05694	74	S1_Rrp5_repeat_hs2_sc2 S1_Rrp5_repeat_hs2_sc2: Rrp	99.25
cd05691	73	S1_RPS1_repeat_ec6 S1_RPS1_repeat_ec6: Ribosomal p	99.24
cd05692	69	S1_RPS1_repeat_hs4 S1_RPS1_repeat_hs4: Ribosomal p	99.24
cd05690	69	S1_RPS1_repeat_ec5 S1_RPS1_repeat_ec5: Ribosomal p	99.23
cd05708	77	S1_Rrp5_repeat_sc12 S1_Rrp5_repeat_sc12: Rrp5 is a	99.22
COG1093	269	SUI2 Translation initiation factor 2, alpha subuni	99.22
cd05687	70	S1_RPS1_repeat_ec1_hs1 S1_RPS1_repeat_ec1_hs1: Rib	99.2
PRK08059	123	general stress protein 13; Validated	99.2
cd05689	72	S1_RPS1_repeat_ec4 S1_RPS1_repeat_ec4: Ribosomal p	99.17
KOG1612	288	consensus Exosomal 3'-5' exoribonuclease complex,	99.17
cd05789	86	S1_Rrp4 S1_Rrp4: Rrp4 S1-like RNA-binding domain.	99.15
cd04472	68	S1_PNPase S1_PNPase: Polynucleotide phosphorylase	99.14
cd05694	74	S1_Rrp5_repeat_hs2_sc2 S1_Rrp5_repeat_hs2_sc2: Rrp	99.12
cd05685	68	S1_Tex S1_Tex: The C-terminal S1 domain of a trans	99.11
KOG1613	298	consensus Exosomal 3'-5' exoribonuclease complex,	99.11
cd05695	66	S1_Rrp5_repeat_hs3 S1_Rrp5_repeat_hs3: Rrp5 is a t	99.1
cd04453	88	S1_RNase_E S1_RNase_E: RNase E and RNase G, S1-lik	99.1
cd05705	74	S1_Rrp5_repeat_hs14 S1_Rrp5_repeat_hs14: Rrp5 is a	99.09
cd04465	67	S1_RPS1_repeat_ec2_hs2 S1_RPS1_repeat_ec2_hs2: Rib	99.08
cd05693	100	S1_Rrp5_repeat_hs1_sc1 S1_Rrp5_repeat_hs1_sc1: Rrp	99.06
cd05703	73	S1_Rrp5_repeat_hs12_sc9 S1_Rrp5_repeat_hs12_sc9: R	99.03
PRK03987	262	translation initiation factor IF-2 subunit alpha;	99.02
PF00575	74	S1: S1 RNA binding domain; InterPro: IPR003029 Rib	99.01
cd05688	68	S1_RPS1_repeat_ec3 S1_RPS1_repeat_ec3: Ribosomal p	99.01
cd04471	83	S1_RNase_R S1_RNase_R: RNase R C-terminal S1 domai	98.98
smart00316	72	S1 Ribosomal protein S1-like RNA-binding domain.	98.97
cd04454	82	S1_Rrp4_like S1_Rrp4_like: Rrp4-like, S1-like RNA-	98.97
cd04473	77	S1_RecJ_like S1_RecJ_like: The S1 domain of the ar	98.95
COG2183	780	Tex Transcriptional accessory protein [Transcripti	98.95
PRK08582	139	hypothetical protein; Provisional	98.94
cd04461	83	S1_Rrp5_repeat_hs8_sc7 S1_Rrp5_repeat_hs8_sc7: Rrp	98.94
cd05696	71	S1_Rrp5_repeat_hs4 S1_Rrp5_repeat_hs4: Rrp5 is a t	98.93
cd05697	69	S1_Rrp5_repeat_hs5 S1_Rrp5_repeat_hs5: Rrp5 is a t	98.93
cd05695	66	S1_Rrp5_repeat_hs3 S1_Rrp5_repeat_hs3: Rrp5 is a t	98.93
cd05704	72	S1_Rrp5_repeat_hs13 S1_Rrp5_repeat_hs13: Rrp5 is a	98.91
cd05706	73	S1_Rrp5_repeat_sc10 S1_Rrp5_repeat_sc10: Rrp5 is a	98.91
cd05702	70	S1_Rrp5_repeat_hs11_sc8 S1_Rrp5_repeat_hs11_sc8: R	98.9
cd04473	77	S1_RecJ_like S1_RecJ_like: The S1 domain of the ar	98.89
cd05698	70	S1_Rrp5_repeat_hs6_sc5 S1_Rrp5_repeat_hs6_sc5: Rrp	98.88
cd05686	73	S1_pNO40 S1_pNO40: pNO40 , S1-like RNA-binding dom	98.87
cd05707	68	S1_Rrp5_repeat_sc11 S1_Rrp5_repeat_sc11: Rrp5 is a	98.86
PRK05807	136	hypothetical protein; Provisional	98.85
PF03725	68	RNase_PH_C: 3' exoribonuclease family, domain 2 Th	98.84
cd05689	72	S1_RPS1_repeat_ec4 S1_RPS1_repeat_ec4: Ribosomal p	98.83
cd05690	69	S1_RPS1_repeat_ec5 S1_RPS1_repeat_ec5: Ribosomal p	98.8
cd02393	61	PNPase_KH Polynucleotide phosphorylase (PNPase) K	98.79
cd00164	65	S1_like S1_like: Ribosomal protein S1-like RNA-bin	98.77
cd05692	69	S1_RPS1_repeat_hs4 S1_RPS1_repeat_hs4: Ribosomal p	98.77
PRK07252	120	hypothetical protein; Provisional	98.75
cd05708	77	S1_Rrp5_repeat_sc12 S1_Rrp5_repeat_sc12: Rrp5 is a	98.74
PTZ00248	319	eukaryotic translation initiation factor 2 subunit	98.74
cd05789	86	S1_Rrp4 S1_Rrp4: Rrp4 S1-like RNA-binding domain.	98.72
cd05691	73	S1_RPS1_repeat_ec6 S1_RPS1_repeat_ec6: Ribosomal p	98.71
cd05693	100	S1_Rrp5_repeat_hs1_sc1 S1_Rrp5_repeat_hs1_sc1: Rrp	98.71
cd04460	99	S1_RpoE S1_RpoE: RpoE, S1-like RNA-binding domain.	98.69
cd05687	70	S1_RPS1_repeat_ec1_hs1 S1_RPS1_repeat_ec1_hs1: Rib	98.68
cd05684	79	S1_DHX8_helicase S1_DHX8_helicase: The N-terminal	98.68
cd04452	76	S1_IF2_alpha S1_IF2_alpha: The alpha subunit of tr	98.67
smart00316	72	S1 Ribosomal protein S1-like RNA-binding domain.	98.66
PRK13763	180	putative RNA-processing protein; Provisional	98.65
cd04465	67	S1_RPS1_repeat_ec2_hs2 S1_RPS1_repeat_ec2_hs2: Rib	98.65
cd05702	70	S1_Rrp5_repeat_hs11_sc8 S1_Rrp5_repeat_hs11_sc8: R	98.64
PRK08059	123	general stress protein 13; Validated	98.63
cd05685	68	S1_Tex S1_Tex: The C-terminal S1 domain of a trans	98.63
cd04471	83	S1_RNase_R S1_RNase_R: RNase R C-terminal S1 domai	98.61
cd04453	88	S1_RNase_E S1_RNase_E: RNase E and RNase G, S1-lik	98.61
PRK04163	235	exosome complex RNA-binding protein Rrp4; Provisio	98.61
PRK09521	189	exosome complex RNA-binding protein Csl4; Provisio	98.6
TIGR03665	172	arCOG04150 arCOG04150 universal archaeal KH domain	98.6
cd04472	68	S1_PNPase S1_PNPase: Polynucleotide phosphorylase	98.58
cd04455	67	S1_NusA S1_NusA: N-utilizing substance A protein (	98.5
cd04454	82	S1_Rrp4_like S1_Rrp4_like: Rrp4-like, S1-like RNA-	98.47
TIGR02063	709	RNase_R ribonuclease R. This family consists of an	98.43
cd04455	67	S1_NusA S1_NusA: N-utilizing substance A protein (	98.43
PHA02945	88	interferon resistance protein; Provisional	98.43
cd05688	68	S1_RPS1_repeat_ec3 S1_RPS1_repeat_ec3: Ribosomal p	98.41
cd05791	92	S1_CSL4 S1_CSL4: CSL4, S1-like RNA-binding domain.	98.37
PF03725	68	RNase_PH_C: 3' exoribonuclease family, domain 2 Th	98.35
PRK09521	189	exosome complex RNA-binding protein Csl4; Provisio	98.34
COG1093	269	SUI2 Translation initiation factor 2, alpha subuni	98.34
TIGR00448	179	rpoE DNA-directed RNA polymerase (rpoE), archaeal	98.3
PRK03987	262	translation initiation factor IF-2 subunit alpha;	98.26
PRK09202	470	nusA transcription elongation factor NusA; Validat	98.2
PRK11642	813	exoribonuclease R; Provisional	98.18
TIGR00358	654	3_prime_RNase VacB and RNase II family 3'-5' exori	98.18
cd00164	65	S1_like S1_like: Ribosomal protein S1-like RNA-bin	98.17
COG1095	183	RPB7 DNA-directed RNA polymerase, subunit E' [Tran	98.16
PRK09202	470	nusA transcription elongation factor NusA; Validat	98.11
PRK08563	187	DNA-directed RNA polymerase subunit E'; Provisiona	98.06
cd04460	99	S1_RpoE S1_RpoE: RpoE, S1-like RNA-binding domain.	97.93
PHA02858	86	EIF2a-like PKR inhibitor; Provisional	97.9
cd02395	120	SF1_like-KH Splicing factor 1 (SF1) K homology RNA	97.89
PRK04163	235	exosome complex RNA-binding protein Rrp4; Provisio	97.83
COG2183	780	Tex Transcriptional accessory protein [Transcripti	97.8
TIGR02063	709	RNase_R ribonuclease R. This family consists of an	97.79
PF13509	61	S1_2: S1 domain; PDB: 3GO5_A.	97.79
TIGR01953	341	NusA transcription termination factor NusA. This m	97.74
PRK12327	362	nusA transcription elongation factor NusA; Provisi	97.71
TIGR01953	341	NusA transcription termination factor NusA. This m	97.65
PRK12327	362	nusA transcription elongation factor NusA; Provisi	97.58
PRK11642	813	exoribonuclease R; Provisional	97.56
cd02394	62	vigilin_like_KH K homology RNA-binding domain_vigi	97.56
TIGR00757	414	RNaseEG ribonuclease, Rne/Rng family. The C-termin	97.55
KOG2916	304	consensus Translation initiation factor 2, alpha s	97.54
cd05790	86	S1_Rrp40 S1_Rrp40: Rrp40 S1-like RNA-binding domai	97.49
cd05791	92	S1_CSL4 S1_CSL4: CSL4, S1-like RNA-binding domain.	97.49
COG1097	239	RRP4 RNA-binding protein Rrp4 and related proteins	97.48
COG2996	287	Predicted RNA-bindining protein (contains S1 and H	97.45
TIGR00448	179	rpoE DNA-directed RNA polymerase (rpoE), archaeal	97.38
PF00013	60	KH_1: KH domain syndrome, contains KH motifs.; Int	97.36
TIGR00358	654	3_prime_RNase VacB and RNase II family 3'-5' exori	97.36
PRK05054	644	exoribonuclease II; Provisional	97.27
cd04462	88	S1_RNAPII_Rpb7 S1_RNAPII_Rpb7: Eukaryotic RNA poly	97.25
COG1096	188	Predicted RNA-binding protein (consists of S1 doma	97.23
cd05699	72	S1_Rrp5_repeat_hs7 S1_Rrp5_repeat_hs7: Rrp5 is a t	97.18
COG1095	183	RPB7 DNA-directed RNA polymerase, subunit E' [Tran	97.16
PRK08563	187	DNA-directed RNA polymerase subunit E'; Provisiona	97.15
cd05790	86	S1_Rrp40 S1_Rrp40: Rrp40 S1-like RNA-binding domai	97.01
PTZ00162	176	DNA-directed RNA polymerase II subunit 7; Provisio	96.99
cd04462	88	S1_RNAPII_Rpb7 S1_RNAPII_Rpb7: Eukaryotic RNA poly	96.93
TIGR02062	639	RNase_B exoribonuclease II. This family consists o	96.75
PF13509	61	S1_2: S1 domain; PDB: 3GO5_A.	96.74
cd00105	64	KH-I K homology RNA-binding domain, type I. KH bin	96.72
PF10447	82	EXOSC1: Exosome component EXOSC1/CSL4; InterPro: I	96.71
COG0557	706	VacB Exoribonuclease R [Transcription]	96.7
COG1107	715	Archaea-specific RecJ-like exonuclease, contains D	96.65
PF10447	82	EXOSC1: Exosome component EXOSC1/CSL4; InterPro: I	96.59
PRK05054	644	exoribonuclease II; Provisional	96.46
TIGR00757	414	RNaseEG ribonuclease, Rne/Rng family. The C-termin	96.34
PRK12328	374	nusA transcription elongation factor NusA; Provisi	96.25
smart00322	69	KH K homology RNA-binding domain.	96.22
cd05699	72	S1_Rrp5_repeat_hs7 S1_Rrp5_repeat_hs7: Rrp5 is a t	96.16
TIGR03665	172	arCOG04150 arCOG04150 universal archaeal KH domain	96.1
PRK12328	374	nusA transcription elongation factor NusA; Provisi	95.96
PRK11712	489	ribonuclease G; Provisional	95.95
PRK13763	180	putative RNA-processing protein; Provisional	95.91
COG1107	715	Archaea-specific RecJ-like exonuclease, contains D	95.9
PRK10811	1068	rne ribonuclease E; Reviewed	95.9
cd02396	65	PCBP_like_KH K homology RNA-binding domain, PCBP_l	95.89
PRK12329	449	nusA transcription elongation factor NusA; Provisi	95.89
PHA02858	86	EIF2a-like PKR inhibitor; Provisional	95.72
PTZ00162	176	DNA-directed RNA polymerase II subunit 7; Provisio	95.58
COG1097	239	RRP4 RNA-binding protein Rrp4 and related proteins	95.29
KOG1856	1299	consensus Transcription elongation factor SPT6 [RN	95.27
TIGR02062	639	RNase_B exoribonuclease II. This family consists o	95.17
COG0557	706	VacB Exoribonuclease R [Transcription]	95.14
PRK12329	449	nusA transcription elongation factor NusA; Provisi	94.55
KOG2191	402	consensus RNA-binding protein NOVA1/PASILLA and re	94.29
PF13014	43	KH_3: KH domain	93.26
KOG3409	193	consensus Exosomal 3'-5' exoribonuclease complex,	92.78
KOG0119	554	consensus Splicing factor 1/branch point binding p	92.68
COG1530	487	CafA Ribonucleases G and E [Translation, ribosomal	92.5
KOG1676	600	consensus K-homology type RNA binding proteins [RN	91.93
PRK10811	1068	rne ribonuclease E; Reviewed	91.27
PF10246	104	MRP-S35: Mitochondrial ribosomal protein MRP-S35;	90.84
KOG1856	1299	consensus Transcription elongation factor SPT6 [RN	90.51
PRK12442	87	translation initiation factor IF-1; Reviewed	90.4
COG1094	194	Predicted RNA-binding protein (contains KH domains	90.16
KOG3409	193	consensus Exosomal 3'-5' exoribonuclease complex,	90.06
TIGR00008	68	infA translation initiation factor IF-1. This fami	89.66
COG1096	188	Predicted RNA-binding protein (consists of S1 doma	89.24
PRK11712	489	ribonuclease G; Provisional	88.33
TIGR03319	514	YmdA_YtgF conserved hypothetical protein YmdA/YtgF	88.18
COG1094	194	Predicted RNA-binding protein (contains KH domains	87.99
PRK00106	535	hypothetical protein; Provisional	87.42
KOG3298	170	consensus DNA-directed RNA polymerase subunit E' [	87.24
KOG2193	584	consensus IGF-II mRNA-binding protein IMP, contain	86.83
KOG1676	600	consensus K-homology type RNA binding proteins [RN	86.08
PRK12704	520	phosphodiesterase; Provisional	85.87
KOG2916	304	consensus Translation initiation factor 2, alpha s	85.82
cd02134	61	NusA_KH NusA_K homology RNA-binding domain (KH). N	84.29
KOG3298	170	consensus DNA-directed RNA polymerase subunit E' [	83.61
PF08292	122	RNA_pol_Rbc25: RNA polymerase III subunit Rpc25; I	83.3
PF00313	66	CSD: 'Cold-shock' DNA-binding domain; InterPro: IP	81.97

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

Probab=100.00  E-value=9.7e-166  Score=1415.99  Aligned_cols=690  Identities=47%  Similarity=0.768  Sum_probs=672.4

Q ss_pred             cceeeeeeEEECCeEEEEEeCccCcCCCcEEEEEeCCeEEEEEEEeCCCCCCCCceeeEeeccccccccCCCCCcccccc
Q 002054           55 VLETFKEEFEIGSRLITLETGKIARFANGAVVLGMDETKVLSTVTSSKGDSVRDFLPLTVDYQEKQFAQGVIPNTYMRRE  134 (974)
Q Consensus        55 ~~~~~~~~~~~~~r~i~~etg~~a~~A~GSa~v~~G~T~Vl~tv~~~~~~~~~~f~pL~v~y~e~~~a~g~ip~~~~~Re  134 (974)
                      ||+....+++||||++++|||++|+||+|||+++||+|.|||||++.+.+++.|||||||+|+||+||+|||||||+|||
T Consensus         1 ~~~~~~~~~~~~~~~l~~etg~~A~qa~gav~~~~gdt~vl~t~~~~~~~~~~dF~PLtV~y~Ek~yaaGkiPGgf~kRE   80 (692)
T COG1185           1 MFNKIVKTIEWGGRTLTLETGKIARQANGAVLVRYGDTVVLATVVASKPKEGQDFFPLTVNYEEKTYAAGKIPGGFFKRE   80 (692)
T ss_pred             CCcceEEEEEECCeeEEEEcchhhhhcCccEEEEECCeEEEEEEeecCCCCCCCccceeEeeeeehhccCcCCCcccccC
Confidence            46778889999999999999999999999999999999999999999878899999999999999999999999999999


Q ss_pred             CCCCchhhhHHHhhcCCccccccCCCCCceEEEEEEEeccCCCChhhHHHHHHHHHhhcCCCCCCCCeEEEEEEEECCEE
Q 002054          135 GAPKERELLVGRIIDRPIRPLFPAGFYHEVQVMASVLSSDGKQDPDIMAANATSAALMLSDIPWGGPIGMIRIGRICGQF  214 (974)
Q Consensus       135 g~p~~~eil~~RlidR~lrplfp~~~~~~~~i~~~vl~~dg~~~~~~~ai~aAs~AL~~s~iP~~~~v~av~vg~i~g~~  214 (974)
                      |||+++|||+|||||||||||||++|++++||+++|+|+|+.++|+++|++|||+||++|+|||.+||+|||||++||+|
T Consensus        81 Grpse~e~L~sRLIDRpiRPlFp~g~~~evqIv~tvls~D~~~~pdi~a~~gaSaAl~is~iPf~gpi~~vrvg~idg~~  160 (692)
T COG1185          81 GRPSEKEILTSRLIDRPIRPLFPKGFRNEVQIVNTVLSVDPENDPDILAMVGASAALSLSGIPFLGPIGAVRVGYIDGIF  160 (692)
T ss_pred             CCCCccchhhhhhcccccccccchhhccceEEEEEEEEECCCCCHHHHHHHHHHHHHhccCCCccCccceEEEEEECCEE
Confidence            99999999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             EEcCCHHHHhcCccceeEeeeCCeEEEEEecCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCccccccccCCCHH
Q 002054          215 IVNPTMDELSLSDLNLVYACTREKTLMIDVQAREISEKDLEAGLRLAHPEAVKYLEPQIRLAEKAGKQKKEYKLSMISEQ  294 (974)
Q Consensus       215 vldPt~~e~~~s~~~l~v~~t~~~i~mie~~~~~~~e~~~~~al~~a~~~~~~i~~~~~~~~~~~g~~k~~~~~~~~~~~  294 (974)
                      |+|||++|.+.|++||+|+||.++|+|+|+++++++|++|++||.+||+.++.++++|+++..++|++++++.....+++
T Consensus       161 vlNPt~~e~~~s~lDlvVAGT~~aV~MVE~~a~~l~E~~ml~Av~fg~~~~~~~~~~qe~l~~~~g~~~~~~~~~~~~~~  240 (692)
T COG1185         161 VLNPTLEELEESKLDLVVAGTKDAVNMVESEADELDEEVMLEAVEFGHEAIQSVINAQEELALEVGKKKWELEPPSLDEE  240 (692)
T ss_pred             EECCChHHhhhcceeeEecCChhhhheeecccccCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCccccccccCccHH
Confidence            99999999999999999999999999999999999999999999999999999999999999999988889888889999


Q ss_pred             HHHHHHHHHHHHHHhhhcCCCCChhHHHHHHHHHHHHHHHHhhhccchhhhchHHHHHHHHHHHHHHHHHHhcCCcCCCC
Q 002054          295 TLEKVSNLAEAHIEAVFTDPSYSKFERGEALDKIGQDVKKALEEECDEESLQVLPKAVDTVRKRVIRKRIIAEGVRVDGR  374 (974)
Q Consensus       295 ~~~~~~~~~~~~~~~~~~~~~~~k~~r~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~r~~il~~~~R~DGR  374 (974)
                      +...+++.+.+++.+++.+  .+|++|..+++++++++.+.|..++ .....++..+|+.++++.+|.+|++.++|+|||
T Consensus       241 l~~~i~~~~~~~l~~a~~i--~~K~eR~~~~~~~~~~i~~~~~~~e-~~~~~~~~~~~~~l~~~~vR~~Il~~~vR~DGR  317 (692)
T COG1185         241 LEAKVRDLAEDELKEAVGI--REKQERSAALDAIKEKIEEELSGEE-ESSLKEIKAILEKLEKKPVRRLILEGKVRIDGR  317 (692)
T ss_pred             HHHHHHHHhHHHHHHHhcc--cchhhhhhhHHHHHHHHHHHHhhhc-cccHHHHHHHHHHHhHHHHHHHHhcCCcccCCC
Confidence            9999999999999999988  5999999999999999999997542 122578999999999999999999999999999


Q ss_pred             CCCCccCeEEEeCCCCCCCcceEEEeCCeEEEEEEEeCCCchhhhccccCCCCceeEEEEEecCCCCccccccccCCCch
Q 002054          375 QLDEVRPIYCESGNLPILHGSSLFSRGDTQVLCTVTLGAPAEAQRLESLVGPPTKRFMLHYSFPPFCINEVGKRVGLNRR  454 (974)
Q Consensus       375 ~~~e~R~I~ie~g~l~~a~GSal~~~G~T~Vl~~Vtl~~p~~~~~~d~~~~~~~~~~~v~~~f~p~s~~e~~~~~~~~rr  454 (974)
                      ..+++|||.|++|+||++|||++|+||+||.++++|||++.++|.+|.+.++..++|++||||||||+||++|.++|+||
T Consensus       318 ~~~~VRpi~~ev~~lpr~HGS~LFtRGeTQal~v~TLG~~~d~Qvid~l~~e~~krfm~hYNFPp~SvGE~g~~g~p~RR  397 (692)
T COG1185         318 FGDEVRPIGIEVGVLPRTHGSALFTRGETQALVVVTLGTPRDAQVIDILEGEYKKRFLLHYNFPPFSVGETGRMGSPGRR  397 (692)
T ss_pred             CcceeeeeeEEecCCCCccchhhhccCCCcceEEEEcCCcchhhhhhhccchhhhheeeeccCCCCCccccCCCCCCCcc
Confidence            99999999999999999999999999999999999999999999999999888999999999999999999999999999


Q ss_pred             hhhHHHHHHHHhhhcCCCCCCCCeEEEEEEEEEcCCCChhhHHHHHHHHHHHHcCCCccccccceeeeeeccCCCCCCcc
Q 002054          455 EVGHGTLAEKALLAVLPPENDFPYTVRVNSEVMASDGSTSMATVCGGSMALMDAGIPLQEHVAGVSVGLVSEVDPSTGEI  534 (974)
Q Consensus       455 e~~~~~l~eral~~vi~~~~~~p~tI~V~v~VLesdGs~~~A~v~aa~lAL~dagvPi~~~vagvs~gli~~~d~~~~~~  534 (974)
                      |+|||+|++|++.+++|..+.|||+||++++|++||||++||++|+++|||||||||++.+|||++|||+.++|      
T Consensus       398 EiGHG~LA~Ral~~vlp~~e~fpytiRvVsEi~eSNGSsSmaSVCg~sLaLmdAGVPIk~pVAGIAMGLI~eg~------  471 (692)
T COG1185         398 EIGHGALAERALAPVLPSEEEFPYTIRVVSEILESNGSSSMASVCGGSLALMDAGVPIKAPVAGIAMGLIKEGD------  471 (692)
T ss_pred             cccCchhhHHHHhhhCCchhcCCceeeeeehhhcccCcccchhhhhhHHHHHhCCCcccccccchhccceecCC------
Confidence            99999999999999999989999999999999999999999999999999999999999999999999999865      


Q ss_pred             cceEEEecCCccccccCCccEEEEeeCCceEEEEeeccCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCCCCCCCC
Q 002054          535 KDYRILTDILGLEDHLGDMDFKIAGTRIGVTAIQLDIKPAGIPLDIICECLEHAHKGRLQILDHMEREISAPRTQDDRNS  614 (974)
Q Consensus       535 ~~~~iL~Dp~~~Ee~~~d~d~~Va~t~~gI~alq~~~k~~~i~~e~l~~al~~A~~~~~~I~~~m~~~i~~~~~~~~~~~  614 (974)
                       +|.+|+||.++|||+|||||+||||.+|||++|||+|..|++.++|.+||.||+.+|.||+..|.+++++||.++++||
T Consensus       472 -~~~vLsDI~G~EDhlGDMDFKVAGT~~GiTAlQMDiKi~Git~eim~~AL~QAk~aRlhIL~~M~~ai~~pr~els~~a  550 (692)
T COG1185         472 -KYAVLSDILGDEDHLGDMDFKVAGTDDGITALQMDIKIKGITKEIMKKALEQAKGARLHILIVMNEAISEPRKELSPYA  550 (692)
T ss_pred             -ceEeeccccccccccCCceeEEecCCCcceeeeeeeeecCCCHHHHHHHHHHHHHHHHHHHHHHHHHHhhhhhhhhccC
Confidence             8999999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             CcceeeeeccchhhhhcCCCccchhhhhhhhCceEEee-CCEEEEEecCHHHHHHHHHHHHHHhhcccccCcEEEEEEEE
Q 002054          615 PRLATLKYDNDTLRRLIGPLGALKRKIEEETGGRISVS-DGTLTVVAKNRSVMEKVLEKVDFIIGREIEVGGIYKGVVTS  693 (974)
Q Consensus       615 p~~~~~~i~~~ki~~vIg~gGk~i~~i~~~~g~~Idi~-dg~v~i~~~~~~~~~~a~~~i~~l~~~~~~~G~i~~G~V~~  693 (974)
                      |++.+++|+++||+++|||||++|++|+++||++|||+ ||+|++++.+.+..++|+++|+.++ .++++|++|.|+|++
T Consensus       551 Pri~t~~i~~dKI~dvIG~gGk~I~~I~eetg~~IdieddGtv~i~~s~~~~~~~ak~~I~~i~-~e~evg~iy~G~V~r  629 (692)
T COG1185         551 PRIETIKIDPDKIRDVIGPGGKTIKAITEETGVKIDIEDDGTVKIAASDGESAKKAKERIEAIT-REVEVGEVYEGTVVR  629 (692)
T ss_pred             CceEEEccCHHHHhhccCCcccchhhhhhhhCcEEEecCCCcEEEEecchHHHHHHHHHHHHHH-hhcccccEEEEEEEE
Confidence            99999999999999999999999999999999999997 8999999999999999999999998 799999999999999


Q ss_pred             EeeceEEEEEcCCeEEEEecccCCCccccccccccccCCEEEEEEEEEccCCceEEEEeccC
Q 002054          694 VKEYGAFVEFNGGQQGLLHVSELSHEPVSRVSDVVSVGQQLSLRCIGQDVRGNIKLSLKAVS  755 (974)
Q Consensus       694 i~~~G~fV~l~~g~~Glvhisels~~~v~~~~~~~~vGd~V~vkVl~id~~gri~LS~K~~~  755 (974)
                      +.+||+||+|.||.+||||+|++++.++.++++++++||.|.||++++|++||+.||+|...
T Consensus       630 i~~fGaFv~l~~gkdgl~hiS~~~~~rv~kv~dvlk~Gd~v~Vkv~~iD~~Gri~ls~~~~~  691 (692)
T COG1185         630 IVDFGAFVELLPGKDGLVHISQLAKERVEKVEDVLKEGDEVKVKVIEIDKQGRIRLSIKAVL  691 (692)
T ss_pred             EeecceEEEecCCcceeEEehhhhhhhhhcccceeecCceEEEEEeeecccCCccceehhcc
Confidence            99999999999999999999999999999999999999999999999999999999999764

>TIGR02696 pppGpp_PNP guanosine pentaphosphate synthetase I/polynucleotide phosphorylase

Probab=100.00  E-value=6.2e-163  Score=1431.09  Aligned_cols=686  Identities=40%  Similarity=0.643  Sum_probs=652.7

Q ss_pred             eeeeeeEEECCeEEEEEeCccCcCCCcEEEEEe-CCeEEEEEEEeCCC-CCCCCceeeEeeccccccccCCCCCcccccc
Q 002054           57 ETFKEEFEIGSRLITLETGKIARFANGAVVLGM-DETKVLSTVTSSKG-DSVRDFLPLTVDYQEKQFAQGVIPNTYMRRE  134 (974)
Q Consensus        57 ~~~~~~~~~~~r~i~~etg~~a~~A~GSa~v~~-G~T~Vl~tv~~~~~-~~~~~f~pL~v~y~e~~~a~g~ip~~~~~Re  134 (974)
                      +.....+++|++++.||||++|+||||||++++ |+|+|||||+..++ +.+.||+||+|+|+||+||+|||||||+|||
T Consensus         6 ~~~~~~~~~~~~~~~~etG~~A~qA~Gav~v~~~G~t~vl~t~~~~~~~~~~~dF~PLtV~y~Ek~yA~GkiPggf~kRE   85 (719)
T TIGR02696         6 EAVIDNGRFGTRTIRFETGRLARQAAGSVVAYLDDETMLLSATTASKQPKDQFDFFPLTVDVEERMYAAGRIPGSFFRRE   85 (719)
T ss_pred             eeEEEEEEECCEEEEEEcchhHhhCCceEEEEecCCeEEEEEEEecCCCCCCCCCcceeEeeeehhhhcCccCCceeccC
Confidence            344556777777999999999999999999999 99999999998777 7789999999999999999999999999999


Q ss_pred             CCCCchhhhHHHhhcCCccccccCCCCCceEEEEEEEeccCCCChhhHHHHHHHHHhhcCCCCCCCCeEEEEEEEECCEE
Q 002054          135 GAPKERELLVGRIIDRPIRPLFPAGFYHEVQVMASVLSSDGKQDPDIMAANATSAALMLSDIPWGGPIGMIRIGRICGQF  214 (974)
Q Consensus       135 g~p~~~eil~~RlidR~lrplfp~~~~~~~~i~~~vl~~dg~~~~~~~ai~aAs~AL~~s~iP~~~~v~av~vg~i~g~~  214 (974)
                      |+|+++|||++||||||||||||++|+++|||+|+|||+|+.++||++|+||||+||++|+|||+|||+|||||++||+|
T Consensus        86 grps~~eiL~sRliDR~iRPLFp~~~~~e~qi~~~vls~D~~~~pdvla~~~ASaAl~iSdiPf~gPv~~vrVg~i~g~~  165 (719)
T TIGR02696        86 GRPSTDAILTCRLIDRPLRPSFVKGLRNEVQVVVTVLSLNPDHLYDVVAINAASASTQLAGLPFSGPIGGVRVALIDGQW  165 (719)
T ss_pred             CCCChhhhHHHHhhCCCCccCCCCCCCcceEEEEEEEEcCCCCChHHHHHHHHHHHHHhcCCCCCCceEEEEEEEECCEE
Confidence            99999999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             EEcCCHHHHhcCccceeEeeeC----C-eEEEEEe------------cCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 002054          215 IVNPTMDELSLSDLNLVYACTR----E-KTLMIDV------------QAREISEKDLEAGLRLAHPEAVKYLEPQIRLAE  277 (974)
Q Consensus       215 vldPt~~e~~~s~~~l~v~~t~----~-~i~mie~------------~~~~~~e~~~~~al~~a~~~~~~i~~~~~~~~~  277 (974)
                      |+|||++|++.|+|||+||||+    + +++|||+            +++++||++|.+||++||++++.++++|+++.+
T Consensus       166 viNPt~~~~~~s~ldLvvagt~~~~~~~~i~MiE~~a~~~~~~~~~~~a~e~~e~~~~~Ai~~a~~~i~~~~~~~~~l~~  245 (719)
T TIGR02696       166 VAFPTHEQLEGAVFDMVVAGRVLENGDVAIMMVEAEATEKTWDLVKGGAEAPTEEVVAEGLEAAKPFIKVLCRAQADLAE  245 (719)
T ss_pred             EECcCHHHHhhCeeeEEEEeeecCCCCccEEEEecCCccccccccccCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            9999999999999999999997    6 8999998            899999999999999999999999999999999


Q ss_pred             HhCCcccccc-ccCCCHHHHHHHHHHHHHHHHhhhcCCCCChhHHHHHHHHHHHHHHHHhhhccchhhhchHHHHHHHHH
Q 002054          278 KAGKQKKEYK-LSMISEQTLEKVSNLAEAHIEAVFTDPSYSKFERGEALDKIGQDVKKALEEECDEESLQVLPKAVDTVR  356 (974)
Q Consensus       278 ~~g~~k~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~k~~r~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  356 (974)
                      ++||+|+++. ....+++|.+.+++++.++|++++.+  .+|.+|+++++++++++.++|.+. .+.+..++..+|++++
T Consensus       246 ~~gk~k~~~~~~~~~~~~l~~~v~~~~~~~~~~~~~~--~~K~~R~~~~~~~~~~~~~~~~~~-~~~~~~~i~~~~~~~~  322 (719)
T TIGR02696       246 KAAKPTGEFPLFPDYQDDVYEAVEGAVKDELSAALTI--AGKQEREEALDEVKALVAAKLAEQ-FEGREKEISAAYRAVT  322 (719)
T ss_pred             HhCCCccccCCCCCCCHHHHHHHHHHHHHHHHHHHhc--cchHHHHHHHHHHHHHHHHHhhcc-ccccHHHHHHHHHHHH
Confidence            9999999998 77788999999999999999999987  499999999999999999999653 2123367999999999


Q ss_pred             HHHHHHHHHhcCCcCCCCCCCCccCeEEEeCCCCCCCcceEEEeCCeEEEEEEEeCCCchhhhccccCCCCceeEEEEEe
Q 002054          357 KRVIRKRIIAEGVRVDGRQLDEVRPIYCESGNLPILHGSSLFSRGDTQVLCTVTLGAPAEAQRLESLVGPPTKRFMLHYS  436 (974)
Q Consensus       357 ~~~~r~~il~~~~R~DGR~~~e~R~I~ie~g~l~~a~GSal~~~G~T~Vl~~Vtl~~p~~~~~~d~~~~~~~~~~~v~~~  436 (974)
                      ++.+|+++|++|+|+|||.++|+|||+|++|++|++||||+|++|+|||+|++++|.+.++|..+.+.+++.++|+|||+
T Consensus       323 k~~~r~~il~~g~R~DGR~~~eiR~i~~~~g~l~~a~GSa~~~~G~Tqvl~~~tlG~~~~~q~~~~l~~~~~~~~~~~Yn  402 (719)
T TIGR02696       323 KKLVRERVLTEGVRIDGRGVTDIRPLDAEVQVIPRVHGSALFERGETQILGVTTLNMLKMEQQIDSLSPETSKRYMHHYN  402 (719)
T ss_pred             HHHHHHHHhcCCCCCCCCCccccccceeecCCCCCCCceEEEEecCcEEEEEEeCCCchhhhhcccccccccceEEEEEe
Confidence            99999999999999999999999999999999999999999999999999999998888888888888888999999999


Q ss_pred             cCCCCccccccccCCCchhhhHHHHHHHHhhhcCCCCCCCCeEEEEEEEEEcCCCChhhHHHHHHHHHHHHcCCCccccc
Q 002054          437 FPPFCINEVGKRVGLNRREVGHGTLAEKALLAVLPPENDFPYTVRVNSEVMASDGSTSMATVCGGSMALMDAGIPLQEHV  516 (974)
Q Consensus       437 f~p~s~~e~~~~~~~~rre~~~~~l~eral~~vi~~~~~~p~tI~V~v~VLesdGs~~~A~v~aa~lAL~dagvPi~~~v  516 (974)
                      |||||++++++.++++|||++|++|++|+|++++|..+.|||+|+++++||++|||++|||+||++||||||||||+++|
T Consensus       403 fpPFSt~er~~~~~~~RReighg~La~rALe~vI~~~e~fP~TIrvvseVLeSdGSss~AsIcaasLALmDAGVPmkd~V  482 (719)
T TIGR02696       403 FPPYSTGETGRVGSPKRREIGHGALAERALVPVLPSREEFPYAIRQVSEALGSNGSTSMGSVCASTLSLLNAGVPLKAPV  482 (719)
T ss_pred             CCCCcccCCCCCCCCCccHHHHHHHHHHHHHHhhCcHhhCCCEEEEEEEeeccCCcHHHHHHHHHHHHHHHcCcchhhee
Confidence            99999999999999999999999999999999999658999999999999999999999999999999999999999999


Q ss_pred             cceeeeeeccCCCCCCccc-ceEEEecCCccccccCCccEEEEeeCCceEEEEeeccCCCCCHHHHHHHHHHHHHHHHHH
Q 002054          517 AGVSVGLVSEVDPSTGEIK-DYRILTDILGLEDHLGDMDFKIAGTRIGVTAIQLDIKPAGIPLDIICECLEHAHKGRLQI  595 (974)
Q Consensus       517 agvs~gli~~~d~~~~~~~-~~~iL~Dp~~~Ee~~~d~d~~Va~t~~gI~alq~~~k~~~i~~e~l~~al~~A~~~~~~I  595 (974)
                      |||+||++.+.+    +.. +|.+|+||++.||++|+|||+|++|.+|||++|||++..|++.++|.+||++|+++|.+|
T Consensus       483 Agis~Gli~e~~----~~~~~~~iL~Di~g~ED~~Gdmdfkvagt~~gIt~lQmd~ki~gi~~e~l~~aL~~A~~g~~~I  558 (719)
T TIGR02696       483 AGIAMGLISDEV----DGETRYVALTDILGAEDAFGDMDFKVAGTSEFVTALQLDTKLDGIPASVLASALKQARDARLAI  558 (719)
T ss_pred             eEEEEEEecccc----CCCcceeEEeCCCchhhhcCCceEEEEecCCCEEEEEEEeeECCCCHHHHHHHHHHHHHHHHHH
Confidence            999999996521    011 689999999999999999999999999999999999999999999999999999999999


Q ss_pred             HHHHHHHhcCCCCCCCCCCCcceeeeeccchhhhhcCCCccchhhhhhhhCceEEee-CCEEEEEecCHHHHHHHHHHHH
Q 002054          596 LDHMEREISAPRTQDDRNSPRLATLKYDNDTLRRLIGPLGALKRKIEEETGGRISVS-DGTLTVVAKNRSVMEKVLEKVD  674 (974)
Q Consensus       596 ~~~m~~~i~~~~~~~~~~~p~~~~~~i~~~ki~~vIg~gGk~i~~i~~~~g~~Idi~-dg~v~i~~~~~~~~~~a~~~i~  674 (974)
                      ++.|++++..| .++++|||++.+++|+|+||+++||||||+||+|+++||++|||+ +|+|.|++.+++.+++|+++|+
T Consensus       559 l~~m~~al~~p-~~~s~~aP~~~~~~I~~~ki~~vIG~gGk~I~~i~~~tg~~Idi~d~G~V~I~a~d~~~~~~A~~~I~  637 (719)
T TIGR02696       559 LDVMAEAIDTP-DEMSPYAPRIITVKIPVDKIGEVIGPKGKMINQIQDETGAEISIEDDGTVYIGAADGPSAEAARAMIN  637 (719)
T ss_pred             HHHHHHHHhCc-cccccCCCeeEEEEeChHHhhheeCCCcHhHHHHHHHHCCEEEEecCcEEEEEeCCHHHHHHHHHHHH
Confidence            99999999999 999999999999999999999999999999999999999999998 8999999999999999999999


Q ss_pred             HHhhc-ccccCcEEEEEEEEEeeceEEEEEcCCeEEEEecccCC----CccccccccccccCCEEEEEEEEEccCCceEE
Q 002054          675 FIIGR-EIEVGGIYKGVVTSVKEYGAFVEFNGGQQGLLHVSELS----HEPVSRVSDVVSVGQQLSLRCIGQDVRGNIKL  749 (974)
Q Consensus       675 ~l~~~-~~~~G~i~~G~V~~i~~~G~fV~l~~g~~Glvhisels----~~~v~~~~~~~~vGd~V~vkVl~id~~gri~L  749 (974)
                      .++.. ++++|++|+|+|++|++||+||+|.+|.+||||+||++    +.++.++.++|++||.|+|||+++|.+||+.|
T Consensus       638 ~i~~~~~~~vG~i~~GkV~~I~dfGaFVel~~G~eGLvHISeisdls~~~rv~~~~dv~kvGd~V~VKVl~ID~~gKI~L  717 (719)
T TIGR02696       638 AIANPTMPEVGERFLGTVVKTTAFGAFVSLLPGKDGLLHISQIRKLAGGKRVENVEDVLSVGQKIQVEIADIDDRGKLSL  717 (719)
T ss_pred             HhhCcCcCCCCCEEEEEEEEEECceEEEEecCCceEEEEhhhccccccccCcCCHHHcCCCCCEEEEEEEEECCCCCeee
Confidence            99843 68999999999999999999999999999999999996    46899999999999999999999998899998


Q ss_pred             E
Q 002054          750 S  750 (974)
Q Consensus       750 S  750 (974)
                      +
T Consensus       718 ~  718 (719)
T TIGR02696       718 V  718 (719)
T ss_pred             c
Confidence            6

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.

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

Probab=100.00  E-value=3.6e-162  Score=1333.00  Aligned_cols=734  Identities=52%  Similarity=0.819  Sum_probs=701.2

Q ss_pred             CCCCccccccccCccccccCCCCCCCCCCCCCCCCCcccccccc-eeeeeeEEECCeEEEEEeCccCcCCCcEEEEEeCC
Q 002054           13 NNLPPFLTWRALGFRTICSGRLGFAPCEPAPPTPAPSVAGTKVL-ETFKEEFEIGSRLITLETGKIARFANGAVVLGMDE   91 (974)
Q Consensus        13 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~r~i~~etg~~a~~A~GSa~v~~G~   91 (974)
                      -+++.++.|++.+|++.|+|+.+++++-++++      .+.+.. +...+++.+|+|.+.||||++|+||+|||++++|+
T Consensus         6 csls~l~~~~a~kf~~~~l~r~~~~~~~~~~~------~~s~t~~~~vsveipfGnR~i~~etGklaRfAngsvvv~~Ge   79 (760)
T KOG1067|consen    6 CSLSNLLARRALKFRTILLGRLRALPQLQVRA------LGSSTGPNAVSVEIPFGNREILFETGKLARFANGSVVVQMGE   79 (760)
T ss_pred             eeehhhhcccccCcceeeccCccCCCCCCccc------cccccCccceeeeeccCCeEEEEecchhhhhcCCcEEEccCC
Confidence            47899999999999999999999888777664      333322 33455666699999999999999999999999999


Q ss_pred             eEEEEEEEeCCCCCCCCceeeEeeccccccccCCCCCccccccCCCCchhhhHHHhhcCCccccccCCCCCceEEEEEEE
Q 002054           92 TKVLSTVTSSKGDSVRDFLPLTVDYQEKQFAQGVIPNTYMRREGAPKERELLVGRIIDRPIRPLFPAGFYHEVQVMASVL  171 (974)
Q Consensus        92 T~Vl~tv~~~~~~~~~~f~pL~v~y~e~~~a~g~ip~~~~~Reg~p~~~eil~~RlidR~lrplfp~~~~~~~~i~~~vl  171 (974)
                      |.|++||+....|...+|+||.|+|+||+||+|+||++|+||||+|+++|+|+.|||||+|||+||++|++++|+.|++|
T Consensus        80 T~Vm~Tv~~a~~PSp~qFlPL~VdYqeK~aAvGRip~~fmRREg~tkdkEiL~~rLidrsirplfp~g~~~etqi~~n~L  159 (760)
T KOG1067|consen   80 TAVMTTVVLADKPSPPQFLPLVVDYQEKFAAVGRIPGNFMRREGRTKDKEILTGRLIDRPIRPLFPKGFYHETQILCNVL  159 (760)
T ss_pred             eEEEEEEEecCCCCccccceEEEehhhhhhhhccCCCcccccccCCcchhheeeeccccccccCCcccchhHHHHHhhhe
Confidence            99999999988866667999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             eccCCCChhhHHHHHHHHHhhcCCCCCCCCeEEEEEEEECCEEEEcCCHHHHhcCccceeEeeeCCeEEEEEecCCCCCH
Q 002054          172 SSDGKQDPDIMAANATSAALMLSDIPWGGPIGMIRIGRICGQFIVNPTMDELSLSDLNLVYACTREKTLMIDVQAREISE  251 (974)
Q Consensus       172 ~~dg~~~~~~~ai~aAs~AL~~s~iP~~~~v~av~vg~i~g~~vldPt~~e~~~s~~~l~v~~t~~~i~mie~~~~~~~e  251 (974)
                      ++||-.+||++|+|+|++||++|+|||++|+++||+|+++|+||+|||..|++.|+|||++|||++.++|+|+.++.+++
T Consensus       160 s~dG~~~pdvlainaas~Al~lsdvpw~gpig~vRigLi~Ge~vVNPT~kEmssS~Lnlvvagt~~~~vmle~~s~~i~q  239 (760)
T KOG1067|consen  160 SSDGVHDPDVLAINAASAALSLSDVPWNGPIGAVRIGLIDGEFVVNPTRKEMSSSQLNLVVAGTKSQTVMLEGSSNNILQ  239 (760)
T ss_pred             ecccccCchHHHHhHHHHHhhhccCCCCCceeeeEeeeecceEEeCcchhhhhhccceeEEEeccceEEEEEcccccccH
Confidence            99999999999999999999999999999999999999999999999999999999999999998889999999999999


Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHhCCccccc-cccCCCHHHHHHHHHHHHHHHHhhhcCCCCChhHHHHHHHHHHH
Q 002054          252 KDLEAGLRLAHPEAVKYLEPQIRLAEKAGKQKKEY-KLSMISEQTLEKVSNLAEAHIEAVFTDPSYSKFERGEALDKIGQ  330 (974)
Q Consensus       252 ~~~~~al~~a~~~~~~i~~~~~~~~~~~g~~k~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~k~~r~~~~~~~~~  330 (974)
                      ++|.+||+.+++++++++..++.+++++||+|+++ .....++||..++++++.++|+++|++++|||.+|++|+++|+.
T Consensus       240 qdl~~Aikvg~~~~q~~i~~i~~L~k~~Gk~Kr~~~~~~~p~pel~K~v~~la~erl~~vftd~shdK~sR~eAvn~i~~  319 (760)
T KOG1067|consen  240 QDLLHAIKVGVKEAQQIIQGIERLAKKYGKQKREPQKLFLPDPELVKHVHKLAMERLYAVFTDYSHDKISRDEAVNKIRL  319 (760)
T ss_pred             HHHHHHHHhccHHHHHHHHHHHHHHHHhCccccchhhhcCCCHHHHHHHHHHHHHHHHHHhcccccccchhhhHHhhhcc
Confidence            99999999999999999999999999999999998 46778899999999999999999999999999999999999998


Q ss_pred             HHHHHhhhccchhhhchHHHHHHHHHHHHHHHHHHhcCCcCCCCCCCCccCeEEEeCCCCCCCcceEEEeCCeEEEEEEE
Q 002054          331 DVKKALEEECDEESLQVLPKAVDTVRKRVIRKRIIAEGVRVDGRQLDEVRPIYCESGNLPILHGSSLFSRGDTQVLCTVT  410 (974)
Q Consensus       331 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~r~~il~~~~R~DGR~~~e~R~I~ie~g~l~~a~GSal~~~G~T~Vl~~Vt  410 (974)
                      +..+++.|++++....++.+.|+.+.++.+|++|+++|+|+|||.++|+|+|+|+++++++.|||++|+||+|||+|+||
T Consensus       320 ~~e~~~~e~~pe~e~~~i~~~fn~vskkv~Rs~i~~~gkR~DGR~ldelR~I~ce~~m~~~lHGSaLFqRGqTQvlctVt  399 (760)
T KOG1067|consen  320 DDEDKVKEEFPEQEPSEIIESFNTVSKKVFRSRILEEGKRCDGRDLDELRNISCEVDMLKTLHGSALFQRGQTQVLCTVT  399 (760)
T ss_pred             chHHHHHhhcCCccHHHHHHHHHHHHHHHHHHHHHhcccccCCcchhhhcccceecCccccccchhhhhcCceeEEEEEE
Confidence            88888877776666778999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             eCCCchhhhccccCCCCce-eEEEEEecCCCCccccccccCCCchhhhHHHHHHHHhhhcCCCCCCCCeEEEEEEEEEcC
Q 002054          411 LGAPAEAQRLESLVGPPTK-RFMLHYSFPPFCINEVGKRVGLNRREVGHGTLAEKALLAVLPPENDFPYTVRVNSEVMAS  489 (974)
Q Consensus       411 l~~p~~~~~~d~~~~~~~~-~~~v~~~f~p~s~~e~~~~~~~~rre~~~~~l~eral~~vi~~~~~~p~tI~V~v~VLes  489 (974)
                      |+.+..+|+.|++.+++++ +||+||+|||||++|.++.|+++|||+||++|+||||.+++|  ++|||||||+++||+|
T Consensus       400 l~s~e~a~klD~l~~~~~~~~FmLhY~FPPyat~Evgkig~~nRRE~GhgaLAEkaL~~vlP--~dfPftIRv~SeVleS  477 (760)
T KOG1067|consen  400 LDSLESAQKLDSLIGPDNGINFMLHYEFPPYATNEVGKIGGLNRRELGHGALAEKALLPVLP--EDFPFTIRVTSEVLES  477 (760)
T ss_pred             cCCHHHhhhhhhhccCccCceEEEEeccCCccccccccccCCcccccCchhHhhhhhhccCc--ccCceEEEEeeeeeec
Confidence            9999999999999888776 999999999999999999999999999999999999999999  7999999999999999


Q ss_pred             CCChhhHHHHHHHHHHHHcCCCccccccceeeeeeccCCCCCCcccceEEEecCCccccccCCccEEEEeeCCceEEEEe
Q 002054          490 DGSTSMATVCGGSMALMDAGIPLQEHVAGVSVGLVSEVDPSTGEIKDYRILTDILGLEDHLGDMDFKIAGTRIGVTAIQL  569 (974)
Q Consensus       490 dGs~~~A~v~aa~lAL~dagvPi~~~vagvs~gli~~~d~~~~~~~~~~iL~Dp~~~Ee~~~d~d~~Va~t~~gI~alq~  569 (974)
                      |||++||++|++||||||||||++.++|||+|||+.+-||+.+++.+|.+|+||+|.||+.|||||+||||++|+|++  
T Consensus       478 nGSsSMASvCGGslALmDaGvPv~a~vAGvaiGlvt~td~e~g~i~dyriltDIlGiEd~~GDMDFKiAGt~dGvTA~--  555 (760)
T KOG1067|consen  478 NGSSSMASVCGGSLALMDAGVPVSAHVAGVAIGLVTKTDPEKGEIEDYRILTDILGIEDYNGDMDFKIAGTNDGVTAL--  555 (760)
T ss_pred             CCcchHHhhhcchhhhhhcCCccccccceeEEEeEeccCcccCCcccceeehhhcchhhhcCCcceeeccccCcceec--
Confidence            999999999999999999999999999999999999999999999999999999999999999999999999999998  


Q ss_pred             eccCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCCCCCCCCCcceeeeeccchhhhhcCCCccchhhhhhhhCceE
Q 002054          570 DIKPAGIPLDIICECLEHAHKGRLQILDHMEREISAPRTQDDRNSPRLATLKYDNDTLRRLIGPLGALKRKIEEETGGRI  649 (974)
Q Consensus       570 ~~k~~~i~~e~l~~al~~A~~~~~~I~~~m~~~i~~~~~~~~~~~p~~~~~~i~~~ki~~vIg~gGk~i~~i~~~~g~~I  649 (974)
                           ||+++++++++++|+.++.+|++.|.+++..||...++|+|++++++++|+|...+|||||++.|.|+.|||+.-
T Consensus       556 -----gi~l~Iv~eal~~a~~ar~~Il~~m~k~i~~Pr~~~~~y~P~~~tlkv~~sk~~~lIGp~G~~~kki~~EtGai~  630 (760)
T KOG1067|consen  556 -----GIPLKIVMEALQKAREARLQILDIMEKNINSPRGSDKEYSPVLETLKVSPSKRATLIGPGGVLKKKIEVETGAIS  630 (760)
T ss_pred             -----CCcHHHHHHHHHhhhHHHHHHHHHHHhhcCCcccCccccCceeeEEeecchhhheeecCccceeeeEeeecccee
Confidence                 699999999999999999999999999999999999999999999999999999999999999999999999655


Q ss_pred             EeeCCEEEEEecCHHHHHHHHHHHHHHhhc----ccccCcEEEEEEEEEeeceEEEEEcCCeEEEEecccCCCccccccc
Q 002054          650 SVSDGTLTVVAKNRSVMEKVLEKVDFIIGR----EIEVGGIYKGVVTSVKEYGAFVEFNGGQQGLLHVSELSHEPVSRVS  725 (974)
Q Consensus       650 di~dg~v~i~~~~~~~~~~a~~~i~~l~~~----~~~~G~i~~G~V~~i~~~G~fV~l~~g~~Glvhisels~~~v~~~~  725 (974)
                      .+|+|+++|++++..+|++|++.|..++..    +++.|.+|+++|+++.++|+||+|+|+..||+|+|||+.+++.+|+
T Consensus       631 ~vDe~t~~i~A~~~~am~~Ak~~I~~i~~~~~~~~l~~g~vy~~tIt~~rd~G~~V~l~p~~~~Llh~sqL~~e~iakps  710 (760)
T KOG1067|consen  631 QVDEGTFSIFAPTQAAMEEAKEFIDGIIKDDQVQDLEFGGVYTATITEIRDTGVMVELYPMQQGLLHNSQLDQEKIAKPS  710 (760)
T ss_pred             eecCceEEEEecCHHHHHHHHHHHHHHhcCccccceEeeeEEEEEEeeecccceEEEecCCchhhccchhcccccccChH
Confidence            578999999999999999999999999865    6889999999999999999999999999999999999999999999


Q ss_pred             cccccCCEEEEEEEEEccCCceEEEEeccCCCcccc
Q 002054          726 DVVSVGQQLSLRCIGQDVRGNIKLSLKAVSPRPEAD  761 (974)
Q Consensus       726 ~~~~vGd~V~vkVl~id~~gri~LS~K~~~~~~~~~  761 (974)
                      +.+++||.|.||.++.|+.|.+.||.|+++++|...
T Consensus       711 d~levGq~I~vk~ie~d~~g~~~ls~ralLp~p~~~  746 (760)
T KOG1067|consen  711 DLLEVGQEIQVKYIERDPRGGIMLSSRALLPDPATK  746 (760)
T ss_pred             HHHhhcceeEEEEEeecCccceeehhhhhcCCcccC
Confidence            999999999999999999999999999999887554

>PLN00207 polyribonucleotide nucleotidyltransferase; Provisional

Probab=100.00  E-value=1.3e-157  Score=1410.93  Aligned_cols=702  Identities=39%  Similarity=0.623  Sum_probs=662.5

Q ss_pred             eeeeeeEEECCeEEEEEeCccCcCCCcEEEEEeCCeEEEEEEEeCCC-CCCCCceeeEeeccccccccCCCCCccccccC
Q 002054           57 ETFKEEFEIGSRLITLETGKIARFANGAVVLGMDETKVLSTVTSSKG-DSVRDFLPLTVDYQEKQFAQGVIPNTYMRREG  135 (974)
Q Consensus        57 ~~~~~~~~~~~r~i~~etg~~a~~A~GSa~v~~G~T~Vl~tv~~~~~-~~~~~f~pL~v~y~e~~~a~g~ip~~~~~Reg  135 (974)
                      +.++..+++|+|++.+|||++|+||+|||++++|+|.|||||+..++ +.+.||+||+|+|+||+||+|||||||+||||
T Consensus        78 ~~~~~~~~~g~~~~~~etG~~a~qA~gav~v~~g~t~vl~t~~~~~~~~~~~dF~PLtV~y~Ek~~AaGkipggf~kREg  157 (891)
T PLN00207         78 QQFSVKIPVGDRHILVETGHIGRQASGSVTVTDGETIVYTSVCLADVPSEPSDFFPLSVHYQERFSAAGRTSGGFFKREG  157 (891)
T ss_pred             cceEEEEEECCEEEEEEhhHHHHhCCCcEEEEECCeEEEEEEEeccCCCCCCCccceeEeeeeehhhcCccCCceeccCC
Confidence            34666788888899999999999999999999999999999998777 67899999999999999999999999999999


Q ss_pred             CCCchhhhHHHhhcCCccccccCCCCCceEEEEEEEeccCCCChhhHHHHHHHHHhhcCCCCCCCCeEEEEEEEECCEEE
Q 002054          136 APKERELLVGRIIDRPIRPLFPAGFYHEVQVMASVLSSDGKQDPDIMAANATSAALMLSDIPWGGPIGMIRIGRICGQFI  215 (974)
Q Consensus       136 ~p~~~eil~~RlidR~lrplfp~~~~~~~~i~~~vl~~dg~~~~~~~ai~aAs~AL~~s~iP~~~~v~av~vg~i~g~~v  215 (974)
                      +|+++|||++|||||+|||+||++|++++||+++||++||+++|+++||||||+||++|||||++||+|||||++||++|
T Consensus       158 rp~d~eiL~sRlIdR~lRPlfp~~~~~etQI~i~VLsaDg~~~pd~~AInAASaAL~~SgIP~~gpVaAVrVG~idg~~V  237 (891)
T PLN00207        158 RTKDHEVLICRLIDRPLRPTMPKGFYHETQILSWVLSYDGLHSPDSLAVTAAGIAVALSEVPNLKAIAGVRVGLIGGKFI  237 (891)
T ss_pred             CCChHHHHHHHHHCccchhhccccCCCCcEEEEEEEeeCCCCChhhHHHHHHHHHHHhhCCCccCceEEEEEEEECCEEE
Confidence            99999999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             EcCCHHHHhcCccceeEeeeCCeEEEEEecCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCccccccccCCCHHH
Q 002054          216 VNPTMDELSLSDLNLVYACTREKTLMIDVQAREISEKDLEAGLRLAHPEAVKYLEPQIRLAEKAGKQKKEYKLSMISEQT  295 (974)
Q Consensus       216 ldPt~~e~~~s~~~l~v~~t~~~i~mie~~~~~~~e~~~~~al~~a~~~~~~i~~~~~~~~~~~g~~k~~~~~~~~~~~~  295 (974)
                      ||||++|++.|++||+|+||+++|+|||+++++++|++|.+||++||++|++++++|+++++++|++|+++.....+++|
T Consensus       238 lnPt~~E~~~s~ldLvvagt~~~IvMIE~~a~e~see~l~~Al~~a~~aik~i~~~~~el~~~~gk~k~~~~~~~~~~~l  317 (891)
T PLN00207        238 VNPTTKEMEESELDLIMAGTDSAILMIEGYCNFLPEEKLLEAVEVGQDAVRAICKEIEVLVKKCGKPKMLDAIKLPPPEL  317 (891)
T ss_pred             ECCCHHHHhcCCeeEEEEEcCCeEEEEEcCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCCccCCCCCCCHHH
Confidence            99999999999999999999999999999999999999999999999999999999999999999999999888889999


Q ss_pred             HHHHHHHHHHHHHhhhcCCCCChhHHHHHHHHHHHHHHHHhhhcc---------------------chh-----------
Q 002054          296 LEKVSNLAEAHIEAVFTDPSYSKFERGEALDKIGQDVKKALEEEC---------------------DEE-----------  343 (974)
Q Consensus       296 ~~~~~~~~~~~~~~~~~~~~~~k~~r~~~~~~~~~~~~~~~~~~~---------------------~~~-----------  343 (974)
                      .+.+++++.++|++++.+  .+|++|++++++|++++.+.|.++.                     ..+           
T Consensus       318 ~~~v~~~~~~~~~~~~~~--~~K~~R~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  395 (891)
T PLN00207        318 YKHVKEIAGDELVKALQI--RGKIPRRKALSSLEEKVLSILTEEGYVSKDESFGTSETRADLLEDEDEDEEVVVDGEVDE  395 (891)
T ss_pred             HHHHHHHHHHHHHHHHhc--cchHHHHHHHHHHHHHHHHHhhccccccccccccccccccccccccccchhccccccccc
Confidence            999999999999999988  4999999999999999999885431                     000           


Q ss_pred             -----------------hhchHHHHHHHHHHHHHHHHHHhcCCcCCCCCCCCccCeEEEeCCCCCCCcceEEEeCCeEEE
Q 002054          344 -----------------SLQVLPKAVDTVRKRVIRKRIIAEGVRVDGRQLDEVRPIYCESGNLPILHGSSLFSRGDTQVL  406 (974)
Q Consensus       344 -----------------~~~~~~~~~~~~~~~~~r~~il~~~~R~DGR~~~e~R~I~ie~g~l~~a~GSal~~~G~T~Vl  406 (974)
                                       ...++..+|++++++.+|++++++|+|+|||.++|+|||+|++|++|++||||+|++|+||||
T Consensus       396 ~~~~~~~~~~~~~~~~~~~~~i~~~~~~~~k~~~R~~i~~~g~R~DGR~~~eiRpI~~e~G~Lp~A~GSAlf~~G~TqVL  475 (891)
T PLN00207        396 GDVHIKPIPRKSSPLLFSEVDVKLVFKEVTSKFLRRRIVEGGKRSDGRTPDEIRPINSSCGLLPRAHGSALFTRGETQAL  475 (891)
T ss_pred             ccccccccccccccccccHHHHHHHHHHHHHHHHHHHHhcCCCCCCCCCcCccceEEEEeCCcCCCCceEEEEECCeEEE
Confidence                             124589999999999999999999999999999999999999999999999999999999999


Q ss_pred             EEEEeCCCchhhhccccCC-CCceeEEEEEecCCCCccccccccCCCchhhhHHHHHHHHhhhcCCCCCCCCeEEEEEEE
Q 002054          407 CTVTLGAPAEAQRLESLVG-PPTKRFMLHYSFPPFCINEVGKRVGLNRREVGHGTLAEKALLAVLPPENDFPYTVRVNSE  485 (974)
Q Consensus       407 ~~Vtl~~p~~~~~~d~~~~-~~~~~~~v~~~f~p~s~~e~~~~~~~~rre~~~~~l~eral~~vi~~~~~~p~tI~V~v~  485 (974)
                      |+|++|...+.|..+.+.+ +..++|++||+|||||+++++|.+++++||++|++|++|+|++++|..+.|||+|+|+++
T Consensus       476 atVtlGp~~~~q~~d~l~~~~~~~~f~~~y~fPPfs~ge~~r~g~psrREi~hg~L~eRALrpvip~~~~fP~tIrV~~~  555 (891)
T PLN00207        476 AVVTLGDKQMAQRIDNLVDADEVKRFYLQYSFPPSCVGEVGRIGAPSRREIGHGMLAERALEPILPSEDDFPYTIRVEST  555 (891)
T ss_pred             EEEEecCccccccccccccccceeeEEEEEEcCCCCCccccCCCCCCHHHHHHHHHHHHHHHHhCCcccCCCEEEEEEEE
Confidence            9999885556666666543 567899999999999999999999999999999999999999999986689999999999


Q ss_pred             EEcCCCChhhHHHHHHHHHHHHcCCCccccccceeeeeeccCCCCCCcccceEEEecCCccccccCCccEEEEeeCCceE
Q 002054          486 VMASDGSTSMATVCGGSMALMDAGIPLQEHVAGVSVGLVSEVDPSTGEIKDYRILTDILGLEDHLGDMDFKIAGTRIGVT  565 (974)
Q Consensus       486 VLesdGs~~~A~v~aa~lAL~dagvPi~~~vagvs~gli~~~d~~~~~~~~~~iL~Dp~~~Ee~~~d~d~~Va~t~~gI~  565 (974)
                      ||++|||++||++||++||||||||||+++|+||+||++.+.++..+ .+++.+|+||++.|++.|+|||+|++|.+||+
T Consensus       556 VLesDGSssmAaV~aaSLALmDAGIPmk~~VAGvsvGli~d~~~~~~-~g~~~IL~Dp~g~Ed~~gdmDfkVAgT~~gIt  634 (891)
T PLN00207        556 ITESNGSSSMASVCGGCLALQDAGVPVKCPIAGIAMGMVLDTEEFGG-DGSPLILSDITGSEDASGDMDFKVAGNEDGIT  634 (891)
T ss_pred             EEeCCCChHHHHHHHHHHHHHhcCCCccCceeEEEEEEEecccccCC-CCcEEEEeCCCHHHHhcCCceEEEEecccceE
Confidence            99999999999999999999999999999999999999954221111 12577999999999999999999999999999


Q ss_pred             EEEeeccCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCCCCCCCCCcceeeeeccchhhhhcCCCccchhhhhhhh
Q 002054          566 AIQLDIKPAGIPLDIICECLEHAHKGRLQILDHMEREISAPRTQDDRNSPRLATLKYDNDTLRRLIGPLGALKRKIEEET  645 (974)
Q Consensus       566 alq~~~k~~~i~~e~l~~al~~A~~~~~~I~~~m~~~i~~~~~~~~~~~p~~~~~~i~~~ki~~vIg~gGk~i~~i~~~~  645 (974)
                      ++||+++..+++.++|.+||++|++++.+|++.|++++++||.++++|||++.+++|+|+||+++||+||++||+|+++|
T Consensus       635 ~iqmd~k~~gis~e~l~eAL~~A~~g~~~Il~~M~~~i~~pr~~~s~~aP~i~~~~i~~~ki~~vIG~GGktIk~I~eet  714 (891)
T PLN00207        635 AFQMDIKVGGITLPIMERALLQAKDGRKHILAEMSKCSPPPSKRLSKYAPLIHIMKVKPEKVNMIIGSGGKKVKSIIEET  714 (891)
T ss_pred             EEEEecccCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHhhhhhhhcccCCeeEEEEcCHHHHHHHhcCCchhHHHHHHHH
Confidence            99999999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             Cce-EEee-CCEEEEEecCHHHHHHHHHHHHHHhhcccccCcEEE-EEEEEEeeceEEEEEcCCeEEEEecccCCCcccc
Q 002054          646 GGR-ISVS-DGTLTVVAKNRSVMEKVLEKVDFIIGREIEVGGIYK-GVVTSVKEYGAFVEFNGGQQGLLHVSELSHEPVS  722 (974)
Q Consensus       646 g~~-Idi~-dg~v~i~~~~~~~~~~a~~~i~~l~~~~~~~G~i~~-G~V~~i~~~G~fV~l~~g~~Glvhisels~~~v~  722 (974)
                      |++ ||++ +|.|.|++.+.+.+++|+++|+.+. .++++|++|+ |+|++|.+||+||+|.+|.+||||+|+++|+++.
T Consensus       715 g~~~Idi~ddg~V~I~a~d~~~i~~A~~~I~~l~-~~~~vG~iy~~g~V~~I~~FGaFVeL~~g~EGLVHISeLs~~rv~  793 (891)
T PLN00207        715 GVEAIDTQDDGTVKITAKDLSSLEKSKAIISSLT-MVPTVGDIYRNCEIKSIAPYGAFVEIAPGREGLCHISELSSNWLA  793 (891)
T ss_pred             CCCccCcCCCeeEEEEeCCHHHHHHHHHHHHHHh-cCcCCCcEEECcEEEEEeccEEEEEeCCCCEEEEEhhhcCCcccc
Confidence            999 9997 8999999999999999999999998 5899999996 6999999999999999999999999999999999


Q ss_pred             ccccccccCCEEEEEEEEEccCCceEEEEeccCCCccccc
Q 002054          723 RVSDVVSVGQQLSLRCIGQDVRGNIKLSLKAVSPRPEADV  762 (974)
Q Consensus       723 ~~~~~~~vGd~V~vkVl~id~~gri~LS~K~~~~~~~~~~  762 (974)
                      +++++|++||.|+|+|+++|.+|||.||+|+++++||.+.
T Consensus       794 ~~~dv~kvGD~V~VkVi~ID~~grI~LSlK~l~~~Pw~~~  833 (891)
T PLN00207        794 KPEDAFKVGDRIDVKLIEVNDKGQLRLSRRALLPEANSEK  833 (891)
T ss_pred             CHHHhcCCCCEEEEEEEEECCCCcEEEEEeccccCchhhh
Confidence            9999999999999999999988999999999999999874

>PRK11824 polynucleotide phosphorylase/polyadenylase; Provisional

Probab=100.00  E-value=3.1e-147  Score=1333.31  Aligned_cols=690  Identities=48%  Similarity=0.794  Sum_probs=663.3

Q ss_pred             cceeeeeeEEECCeEEEEEeCccCcCCCcEEEEEeCCeEEEEEEEeCCC-CCCCCceeeEeeccccccccCCCCCccccc
Q 002054           55 VLETFKEEFEIGSRLITLETGKIARFANGAVVLGMDETKVLSTVTSSKG-DSVRDFLPLTVDYQEKQFAQGVIPNTYMRR  133 (974)
Q Consensus        55 ~~~~~~~~~~~~~r~i~~etg~~a~~A~GSa~v~~G~T~Vl~tv~~~~~-~~~~~f~pL~v~y~e~~~a~g~ip~~~~~R  133 (974)
                      |++.++.++++|+|+++++||++|+||||||++++|+|+|||||+++.+ +++.+|+||+|+|+|++||+|||||||+||
T Consensus         1 ~~~~~~~~~~~~~r~i~~e~G~ia~qAdGSa~v~~G~T~VlatV~~~~~~~~~~df~pL~v~y~e~~~A~gkiP~~f~kr   80 (693)
T PRK11824          1 MFNKIVKSIEFGGRTLTLETGKLARQANGAVLVRYGDTVVLVTVVASKEPKEGQDFFPLTVDYEEKTYAAGKIPGGFFKR   80 (693)
T ss_pred             CCceEEEEEEECCccEEEEECCcCCCCCeEEEEEECCeEEEEEEEcCCCCCCCCCeeeeEEEEEehhhhccCCCcccccC
Confidence            3566677888899999999999999999999999999999999999998 667899999999999999999999999999


Q ss_pred             cCCCCchhhhHHHhhcCCccccccCCCCCceEEEEEEEeccCCCChhhHHHHHHHHHhhcCCCCCCCCeEEEEEEEECCE
Q 002054          134 EGAPKERELLVGRIIDRPIRPLFPAGFYHEVQVMASVLSSDGKQDPDIMAANATSAALMLSDIPWGGPIGMIRIGRICGQ  213 (974)
Q Consensus       134 eg~p~~~eil~~RlidR~lrplfp~~~~~~~~i~~~vl~~dg~~~~~~~ai~aAs~AL~~s~iP~~~~v~av~vg~i~g~  213 (974)
                      ||+|+++|+|++|+|||+|||+||++|++++||+|+||++||+++|++||+||||+||++|+|||++||+|||||++||+
T Consensus        81 eg~pse~eil~srlIdR~lrplfp~~~~~~i~I~~~VL~~Dg~~~~d~aai~aAsaAL~~s~IP~~~~v~av~vg~i~g~  160 (693)
T PRK11824         81 EGRPSEKETLTSRLIDRPIRPLFPKGFRNEVQVVATVLSVDPENDPDILAMIGASAALSISGIPFNGPIAAVRVGYIDGE  160 (693)
T ss_pred             CCCCChHHHHHHHHHhhhHHHhCCCCCCeEEEEEEEEEeCCCCCcHHHHHHHHHHHHHHhcCCCcCCCeEEEEEEEECCE
Confidence            99999999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             EEEcCCHHHHhcCccceeEeeeCCeEEEEEecCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCccccccccCCCH
Q 002054          214 FIVNPTMDELSLSDLNLVYACTREKTLMIDVQAREISEKDLEAGLRLAHPEAVKYLEPQIRLAEKAGKQKKEYKLSMISE  293 (974)
Q Consensus       214 ~vldPt~~e~~~s~~~l~v~~t~~~i~mie~~~~~~~e~~~~~al~~a~~~~~~i~~~~~~~~~~~g~~k~~~~~~~~~~  293 (974)
                      +|+|||.+|++.|++||+|++|.+.++|+|++++++++++|.+||++||++|+++++.|+++++++| +|+++.....++
T Consensus       161 ~ivdPt~~E~~~s~~~l~va~t~~~i~mie~~~~~l~e~~l~~al~~a~~~~~~i~~~~~~~~~~~~-~~~~~~~~~~~~  239 (693)
T PRK11824        161 FVLNPTVEELEESDLDLVVAGTKDAVLMVESEAKELSEEVMLEAIEFGHEAIQELIDAQEELAAEAG-PKWEWQPPEVDE  239 (693)
T ss_pred             EEEcCCHHHHhhCcceEEEEEccCceEEEECCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHhcC-CCcccCCCCCCH
Confidence            9999999999999999999999999999999999999999999999999999999999999999999 999998888899


Q ss_pred             HHHHHHHHHHHHHHHhhhcCCCCChhHHHHHHHHHHHHHHHHhhhc-cchhhhchHHHHHHHHHHHHHHHHHHhcCCcCC
Q 002054          294 QTLEKVSNLAEAHIEAVFTDPSYSKFERGEALDKIGQDVKKALEEE-CDEESLQVLPKAVDTVRKRVIRKRIIAEGVRVD  372 (974)
Q Consensus       294 ~~~~~~~~~~~~~~~~~~~~~~~~k~~r~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~r~~il~~~~R~D  372 (974)
                      ++.+.+++++.+++++++..  ++|.+|+++++++++++.++|.++ ..+.+..++..+|++++++.+|++++++|+|+|
T Consensus       240 ~~~~~~~~~~~~~~~~~~~~--~~k~~r~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~r~~il~~g~R~D  317 (693)
T PRK11824        240 ELKAAVKELAEAKLKEAYQI--TDKQEREAALDAIKEEVLEALAAEEEEEEDEKEIKEAFKKLEKKIVRRRILEEGIRID  317 (693)
T ss_pred             HHHHHHHHHHHHHHHHHHhc--cccHHHHHHHHHHHHHHHHHhhhcccccccHHHHHHHHHHHHHHHHHHHHhcCCCCCC
Confidence            99999999999999999987  599999999999999999999653 233445689999999999999999999999999


Q ss_pred             CCCCCCccCeEEEeCCCCCCCcceEEEeCCeEEEEEEEeCCCchhhhccccCCCCceeEEEEEecCCCCccccccccCCC
Q 002054          373 GRQLDEVRPIYCESGNLPILHGSSLFSRGDTQVLCTVTLGAPAEAQRLESLVGPPTKRFMLHYSFPPFCINEVGKRVGLN  452 (974)
Q Consensus       373 GR~~~e~R~I~ie~g~l~~a~GSal~~~G~T~Vl~~Vtl~~p~~~~~~d~~~~~~~~~~~v~~~f~p~s~~e~~~~~~~~  452 (974)
                      ||.++|+|||+|++|++|++||||+|++|+|||+|+||+|.|.++|..+.+.+.+.++|++||+|||||+++++|.++|+
T Consensus       318 GR~~~e~Rpi~~~~g~l~~a~GSal~~~G~T~Vl~~vt~g~~~~~~~~~~~~~~~~~~~~~~y~~~pfs~~e~~~~~~~~  397 (693)
T PRK11824        318 GRKLDEIRPISIEVGVLPRTHGSALFTRGETQALVVATLGTLRDEQIIDGLEGEYKKRFMLHYNFPPYSVGETGRVGSPG  397 (693)
T ss_pred             CCCcCcccceEEEeCCCCCCCceEEEEECCeEEEEEEecCCCcccccccccCCCCcEEEEEEEEcCCCCCCCcCCCCCCC
Confidence            99999999999999999999999999999999999999988888887777767788999999999999999999999999


Q ss_pred             chhhhHHHHHHHHhhhcCCCCCCCCeEEEEEEEEEcCCCChhhHHHHHHHHHHHHcCCCccccccceeeeeeccCCCCCC
Q 002054          453 RREVGHGTLAEKALLAVLPPENDFPYTVRVNSEVMASDGSTSMATVCGGSMALMDAGIPLQEHVAGVSVGLVSEVDPSTG  532 (974)
Q Consensus       453 rre~~~~~l~eral~~vi~~~~~~p~tI~V~v~VLesdGs~~~A~v~aa~lAL~dagvPi~~~vagvs~gli~~~d~~~~  532 (974)
                      |||++|++|++|+|++++|.++.|||+|+|+++||++|||++|||+||+++|||||||||+++|+|++||++++++    
T Consensus       398 rre~~~~~li~ral~~vi~~~~~~p~~I~v~~~VLe~dGs~~~Aai~aaslAL~dAgvP~~~~Va~vs~gli~~~~----  473 (693)
T PRK11824        398 RREIGHGALAERALEPVLPSEEEFPYTIRVVSEILESNGSSSMASVCGSSLALMDAGVPIKAPVAGIAMGLIKEGD----  473 (693)
T ss_pred             hhHHHHHHHHHHHHHHhcCcccCCCEEEEEEEEEEecCCCHHHHHHHHHHHHHHhcCCCccCceeEEEEEEEcCCC----
Confidence            9999999999999999999878999999999999999999999999999999999999999999999999997532    


Q ss_pred             cccceEEEecCCccccccCCccEEEEeeCCceEEEEeeccCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCCCCCC
Q 002054          533 EIKDYRILTDILGLEDHLGDMDFKIAGTRIGVTAIQLDIKPAGIPLDIICECLEHAHKGRLQILDHMEREISAPRTQDDR  612 (974)
Q Consensus       533 ~~~~~~iL~Dp~~~Ee~~~d~d~~Va~t~~gI~alq~~~k~~~i~~e~l~~al~~A~~~~~~I~~~m~~~i~~~~~~~~~  612 (974)
                         +|.+|+||++.||+++||||+|++|.+|||++|+++|.++++.++|.+|+++|+++|.+|++.|++++++||.++++
T Consensus       474 ---~~~il~D~~~~Ed~~~d~d~~va~t~~gi~~lq~d~k~~~i~~~~l~~al~~a~~g~~~I~~~M~~aI~~~r~~~~~  550 (693)
T PRK11824        474 ---KYAVLTDILGDEDHLGDMDFKVAGTRDGITALQMDIKIDGITREILEEALEQAKEGRLHILGKMNEAISEPRAELSP  550 (693)
T ss_pred             ---ceEEEcCCChhhHhhCCceEEEEecCCceEEEEEecccCCcCHHHHHHHHHHHHHHHHHHHHHHHHHhcCChhhhcc
Confidence               67899999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             CCCcceeeeeccchhhhhcCCCccchhhhhhhhCceEEee-CCEEEEEecCHHHHHHHHHHHHHHhhcccccCcEEEEEE
Q 002054          613 NSPRLATLKYDNDTLRRLIGPLGALKRKIEEETGGRISVS-DGTLTVVAKNRSVMEKVLEKVDFIIGREIEVGGIYKGVV  691 (974)
Q Consensus       613 ~~p~~~~~~i~~~ki~~vIg~gGk~i~~i~~~~g~~Idi~-dg~v~i~~~~~~~~~~a~~~i~~l~~~~~~~G~i~~G~V  691 (974)
                      ++|++..++|+|+||+++||+||++||+|+++||++||++ +|.+.+++.+.+.+++|+++|+.+. .++++|++|.|+|
T Consensus       551 ~ap~~~~~~I~~~kI~~vIG~gg~~ik~I~~~~~~~idi~d~G~v~i~~~~~~~~~~a~~~I~~~~-~~~~vG~v~~G~V  629 (693)
T PRK11824        551 YAPRIETIKIPPDKIRDVIGPGGKTIREITEETGAKIDIEDDGTVKIAATDGEAAEAAKERIEGIT-AEPEVGEIYEGKV  629 (693)
T ss_pred             cCchheeecCCHHHHHHHhcCCchhHHHHHHHHCCccccCCCceEEEEcccHHHHHHHHHHHHHhc-ccCcCCeEEEEEE
Confidence            9999999999999999999999999999999999999997 8999999999999999999999988 6899999999999


Q ss_pred             EEEeeceEEEEEcCCeEEEEecccCCCccccccccccccCCEEEEEEEEEccCCceEEEEeccC
Q 002054          692 TSVKEYGAFVEFNGGQQGLLHVSELSHEPVSRVSDVVSVGQQLSLRCIGQDVRGNIKLSLKAVS  755 (974)
Q Consensus       692 ~~i~~~G~fV~l~~g~~Glvhisels~~~v~~~~~~~~vGd~V~vkVl~id~~gri~LS~K~~~  755 (974)
                      ++|.+||+||+|.++.+||+|+|++++++++++.++|++||.|+|+|+++|.+|++.||+|.++
T Consensus       630 ~~I~~fGafVei~~~~~GllhiSels~~~v~~~~~v~kvGD~V~VkV~~iD~~grI~LS~k~~~  693 (693)
T PRK11824        630 VRIVDFGAFVEILPGKDGLVHISEIADERVEKVEDVLKEGDEVKVKVLEIDKRGRIRLSRKAVL  693 (693)
T ss_pred             EEEECCeEEEEECCCCEEEEEeeeccCccccCccceeCCCCEEEEEEEEECCCCcEEEEEEecC
Confidence            9999999999999999999999999999999999999999999999999998899999999763

>TIGR03591 polynuc_phos polyribonucleotide nucleotidyltransferase

Probab=100.00  E-value=7.4e-147  Score=1326.46  Aligned_cols=675  Identities=48%  Similarity=0.803  Sum_probs=648.1

Q ss_pred             CCeEEEEEeCccCcCCCcEEEEEeCCeEEEEEEEeCCC-CCCCCceeeEeeccccccccCCCCCccccccCCCCchhhhH
Q 002054           66 GSRLITLETGKIARFANGAVVLGMDETKVLSTVTSSKG-DSVRDFLPLTVDYQEKQFAQGVIPNTYMRREGAPKERELLV  144 (974)
Q Consensus        66 ~~r~i~~etg~~a~~A~GSa~v~~G~T~Vl~tv~~~~~-~~~~~f~pL~v~y~e~~~a~g~ip~~~~~Reg~p~~~eil~  144 (974)
                      |+|+++++||++|+||||||++++|+|+|||||+++.+ +++.+|+||+|+|+|++||+|||||+|+||||+|+++|+|+
T Consensus         3 ~~R~i~ie~G~la~~AdGSa~v~~G~T~VlatV~~~~~~~~~~df~pL~vey~e~~~A~gkipg~f~kReg~p~~~eil~   82 (684)
T TIGR03591         3 GGRTLTLETGKIARQADGAVVVRYGDTVVLVTVVAAKEAKEGQDFFPLTVNYQEKFYAAGKIPGGFFKREGRPSEKETLT   82 (684)
T ss_pred             CCccEEEEECCcCCCCCeEEEEEECCeEEEEEEEcCCCCCCCCceEeEEEEEEehhhhccCCCCCcccCCCCCCHHHHHH
Confidence            67899999999999999999999999999999999988 66789999999999999999999999999999999999999


Q ss_pred             HHhhcCCccccccCCCCCceEEEEEEEeccCCCChhhHHHHHHHHHhhcCCCCCCCCeEEEEEEEECCEEEEcCCHHHHh
Q 002054          145 GRIIDRPIRPLFPAGFYHEVQVMASVLSSDGKQDPDIMAANATSAALMLSDIPWGGPIGMIRIGRICGQFIVNPTMDELS  224 (974)
Q Consensus       145 ~RlidR~lrplfp~~~~~~~~i~~~vl~~dg~~~~~~~ai~aAs~AL~~s~iP~~~~v~av~vg~i~g~~vldPt~~e~~  224 (974)
                      +|+|||+|||+||++|++++||+|+||++||+++|++||+||||+||++|+|||++||+|||||++||++|+|||.+|++
T Consensus        83 srlIdR~lrplfp~~~~~~i~V~~~VLs~Dg~~~~d~aai~aAsaAL~~s~IP~~~~v~av~vg~idg~~ildPt~~E~~  162 (684)
T TIGR03591        83 SRLIDRPIRPLFPKGFRNEVQVVATVLSYDPENDPDILAIIGASAALAISGIPFNGPIAAVRVGYIDGQYVLNPTVDELE  162 (684)
T ss_pred             HHHHhhHHHHhcCCCCCceEEEEEEEEecCcCCchHHHHHHHHHHHHHhcCCCcCCCeEEEEEEEECCEEEEcCCHHHHh
Confidence            99999999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             cCccceeEeeeCCeEEEEEecCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCccccccccCCCHHHHHHHHHHHH
Q 002054          225 LSDLNLVYACTREKTLMIDVQAREISEKDLEAGLRLAHPEAVKYLEPQIRLAEKAGKQKKEYKLSMISEQTLEKVSNLAE  304 (974)
Q Consensus       225 ~s~~~l~v~~t~~~i~mie~~~~~~~e~~~~~al~~a~~~~~~i~~~~~~~~~~~g~~k~~~~~~~~~~~~~~~~~~~~~  304 (974)
                      .|++||+|+++.++++|+|++++++++++|.+||++||++|++++++|+++++++|++|+++.....+++|.+.+++++.
T Consensus       163 ~s~~~l~va~t~~~i~mie~~~~~i~e~~l~~al~~a~~~~~~i~~~~~~~~~~~~~~k~~~~~~~~~~~~~~~~~~~~~  242 (684)
T TIGR03591       163 KSDLDLVVAGTKDAVLMVESEAKELSEEVMLGAIEFGHEEIQPVIEAIEELAEEAGKEKWEFVAPEVDEELKAKVKELAY  242 (684)
T ss_pred             hCCceEEEEccCCcEEEEEcCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCCccCCCCCCCHHHHHHHHHHhh
Confidence            99999999999999999999999999999999999999999999999999999999999999888889999999999999


Q ss_pred             H-HHHhhhcCCCCChhHHHHHHHHHHHHHHHHhhhcc--ch--hhhchHHHHHHHHHHHHHHHHHHhcCCcCCCCCCCCc
Q 002054          305 A-HIEAVFTDPSYSKFERGEALDKIGQDVKKALEEEC--DE--ESLQVLPKAVDTVRKRVIRKRIIAEGVRVDGRQLDEV  379 (974)
Q Consensus       305 ~-~~~~~~~~~~~~k~~r~~~~~~~~~~~~~~~~~~~--~~--~~~~~~~~~~~~~~~~~~r~~il~~~~R~DGR~~~e~  379 (974)
                      + ++++++..  .+|.+|+++++++++++.++|.+..  .+  .+...+..+|++++++.+|++++++|+|+|||.++|+
T Consensus       243 ~~~~~~~~~~--~~k~~r~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~r~~il~~g~R~DGR~~~e~  320 (684)
T TIGR03591       243 EAGLKEAYQI--TEKQERYAALDAIKEEVLEALAEEEEEEEEADREKEIKEAFKDLEKKIVRERILKEGKRIDGRDLDTI  320 (684)
T ss_pred             hHHHHHHhhc--cchHHHHHHHHHHHHHHHHHhhhhcccccccccHHHHHHHHHHHHHHHHHHHHhcCCCCCCCCCCCCc
Confidence            9 89999987  5999999999999999999996531  11  2345799999999999999999999999999999999


Q ss_pred             cCeEEEeCCCCCCCcceEEEeCCeEEEEEEEeCCCchhhhccccCCCCceeEEEEEecCCCCccccccccCCCchhhhHH
Q 002054          380 RPIYCESGNLPILHGSSLFSRGDTQVLCTVTLGAPAEAQRLESLVGPPTKRFMLHYSFPPFCINEVGKRVGLNRREVGHG  459 (974)
Q Consensus       380 R~I~ie~g~l~~a~GSal~~~G~T~Vl~~Vtl~~p~~~~~~d~~~~~~~~~~~v~~~f~p~s~~e~~~~~~~~rre~~~~  459 (974)
                      |||+|++|++|++||||+|++|+|||||+||+|.|.+.|..+.+.+...++|++||+|||||+++++|.++|+|||++|+
T Consensus       321 Rpi~~~~g~l~~a~GSa~~~~G~Tqvl~~vt~g~~~~~~~~~~~~~~~~~~~~~~y~~~pfs~~e~~~~g~~~rrei~~~  400 (684)
T TIGR03591       321 RPISIEVGVLPRTHGSALFTRGETQALVVTTLGTERDEQIIDDLEGEYRKRFMLHYNFPPYSVGEVGRVGGPGRREIGHG  400 (684)
T ss_pred             CceEEEeCCCCCCCceEEEEeCCeEEEEEEecCCcccccCCcccCCCccEEEEEEEEcCCCCCCCcCCCCCCChHHHHHH
Confidence            99999999999999999999999999999999988887877888778889999999999999999999999999999999


Q ss_pred             HHHHHHhhhcCCCCCCCCeEEEEEEEEEcCCCChhhHHHHHHHHHHHHcCCCccccccceeeeeeccCCCCCCcccceEE
Q 002054          460 TLAEKALLAVLPPENDFPYTVRVNSEVMASDGSTSMATVCGGSMALMDAGIPLQEHVAGVSVGLVSEVDPSTGEIKDYRI  539 (974)
Q Consensus       460 ~l~eral~~vi~~~~~~p~tI~V~v~VLesdGs~~~A~v~aa~lAL~dagvPi~~~vagvs~gli~~~d~~~~~~~~~~i  539 (974)
                      +|++|+|++++|..+.|||+|+|+++||++|||++|||+||++||||||||||+++|+|++||++++++      .+|.+
T Consensus       401 ~l~~ral~~~i~~~~~~p~tI~v~~~VLesdGs~~~Aai~aaslAL~dAgvP~~~~Vagvs~gli~~~~------~~~~i  474 (684)
T TIGR03591       401 ALAERALKAVLPSEEEFPYTIRVVSEILESNGSSSMASVCGGSLALMDAGVPIKAPVAGIAMGLIKEGD------ERFAV  474 (684)
T ss_pred             HHHHHHHHHhcCccccCCeEEEEEEEEEeCCCChHHHHHHHHHHHHHhcCCCCcCCEEEEEEEEEcCCC------cceEE
Confidence            999999999999778999999999999999999999999999999999999999999999999997521      04789


Q ss_pred             EecCCccccccCCccEEEEeeCCceEEEEeeccCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCCCCCCCCCccee
Q 002054          540 LTDILGLEDHLGDMDFKIAGTRIGVTAIQLDIKPAGIPLDIICECLEHAHKGRLQILDHMEREISAPRTQDDRNSPRLAT  619 (974)
Q Consensus       540 L~Dp~~~Ee~~~d~d~~Va~t~~gI~alq~~~k~~~i~~e~l~~al~~A~~~~~~I~~~m~~~i~~~~~~~~~~~p~~~~  619 (974)
                      |+||++.||+++||+|+|++|.+|||++|++++..+++.++|.+|+++|++++.+|++.|++++.+++.++++|||++.+
T Consensus       475 l~D~~~~Ed~~~d~d~~va~t~~gI~~lq~d~k~~~i~~~~l~~al~~a~~~~~~I~~~m~~~l~~~~~~~~~~~p~~~~  554 (684)
T TIGR03591       475 LSDILGDEDHLGDMDFKVAGTRDGITALQMDIKIDGITREIMEQALEQAKEGRLHILGEMNKVISEPRAELSPYAPRIET  554 (684)
T ss_pred             EeCCChHHHhcCCceEEEEEcCCceEEEEEEcCcCCcCHHHHHHHHHHHHHHHHHHHHHHHHHHhhhhccccccCCeEEE
Confidence            99999999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             eeeccchhhhhcCCCccchhhhhhhhCceEEee-CCEEEEEecCHHHHHHHHHHHHHHhhcccccCcEEEEEEEEEeece
Q 002054          620 LKYDNDTLRRLIGPLGALKRKIEEETGGRISVS-DGTLTVVAKNRSVMEKVLEKVDFIIGREIEVGGIYKGVVTSVKEYG  698 (974)
Q Consensus       620 ~~i~~~ki~~vIg~gGk~i~~i~~~~g~~Idi~-dg~v~i~~~~~~~~~~a~~~i~~l~~~~~~~G~i~~G~V~~i~~~G  698 (974)
                      ++|||+||+++||||||+||+|+++||++|||+ +|+|++++.+++.+++|+++|+.+. ..+++|++|.|+|++|.+||
T Consensus       555 ~~I~~~kI~~vIG~gGk~Ik~I~~~tg~~I~i~ddG~V~i~~~~~~~~~~a~~~I~~~~-~~~~~G~i~~G~V~~I~~~G  633 (684)
T TIGR03591       555 IKINPDKIRDVIGPGGKVIREITEETGAKIDIEDDGTVKIAASDGEAAEAAIKMIEGIT-AEPEVGKIYEGKVVRIMDFG  633 (684)
T ss_pred             EecCHHHHHhhcCCCcHHHHHHHHHHCCEEEEecCeEEEEEECcHHHHHHHHHHHHhhh-cccccCcEEEEEEEEEeCCE
Confidence            999999999999999999999999999999998 8999999999999999999999887 57899999999999999999


Q ss_pred             EEEEEcCCeEEEEecccCCCccccccccccccCCEEEEEEEEEccCCceEE
Q 002054          699 AFVEFNGGQQGLLHVSELSHEPVSRVSDVVSVGQQLSLRCIGQDVRGNIKL  749 (974)
Q Consensus       699 ~fV~l~~g~~Glvhisels~~~v~~~~~~~~vGd~V~vkVl~id~~gri~L  749 (974)
                      +||++.++.+||||+|+++++++.++.++|++||.|+|||+++|.+|++.|
T Consensus       634 afVei~~g~~GllHiSei~~~~v~~~~~~~kvGD~V~VkVi~id~~gki~L  684 (684)
T TIGR03591       634 AFVEILPGKDGLVHISEIANERVEKVEDVLKEGDEVKVKVLEIDKQGRIKL  684 (684)
T ss_pred             EEEEECCCcEEEEEHHHcCCCcccChhhccCCCCEEEEEEEEECCCCCccC
Confidence            999999999999999999999999999999999999999999998788765

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).

>COG0539 RpsA Ribosomal protein S1 [Translation, ribosomal structure and biogenesis]

Probab=100.00  E-value=7.8e-47  Score=434.03  Aligned_cols=298  Identities=24%  Similarity=0.337  Sum_probs=272.3

Q ss_pred             EEEecCHHHHHHHHHHHHHHhhcccccCcEEEEEEEEEeeceEEEEEcCCeEEEEecccCCCccccccccccccCCEEEE
Q 002054          657 TVVAKNRSVMEKVLEKVDFIIGREIEVGGIYKGVVTSVKEYGAFVEFNGGQQGLLHVSELSHEPVSRVSDVVSVGQQLSL  736 (974)
Q Consensus       657 ~i~~~~~~~~~~a~~~i~~l~~~~~~~G~i~~G~V~~i~~~G~fV~l~~g~~Glvhisels~~~v~~~~~~~~vGd~V~v  736 (974)
                      ++..+.+..++......+......+++|++++|+|++|++||+||+|. |++||||+|||||.++.+|+++|++||+|+|
T Consensus       166 ~vv~SrR~~~e~~~~~~r~e~~~~l~~G~vV~G~V~~It~~GafVdig-GvdGLlHiseiS~~rv~~P~~vvkvGd~Vkv  244 (541)
T COG0539         166 NVVLSRRAVLEEERSEQREELLNKLEVGEVVEGVVKNITDYGAFVDIG-GVDGLLHISEISWKRVDHPSEVVKVGDEVKV  244 (541)
T ss_pred             cEEEEhHHHhhHHHHHHHHHHHhcCCCCceEEEEEEEeecCcEEEEec-CeeeEEehhhccccccCCHHHhcccCCEEEE
Confidence            556667778876554444333378999999999999999999999995 6999999999999999999999999999999


Q ss_pred             EEEEEcc-CCceEEEEeccCCCccccc---------------CceEEEEEeecCCcceeeEEeeccCCCCCCCCCCCCCC
Q 002054          737 RCIGQDV-RGNIKLSLKAVSPRPEADV---------------KGVVEGSVPVNKQATDVWASVGDVSNGQNPELPMRKNE  800 (974)
Q Consensus       737 kVl~id~-~gri~LS~K~~~~~~~~~~---------------g~~~~G~vv~i~~gv~~~~~~~~l~~~~~~~lp~~~~~  800 (974)
                      +|+++|. ++|+.||+|++.++||...               ....+|+|+++.+|++||+|+|+++|.+... |.    
T Consensus       245 kVi~~D~e~~RVsLSlK~l~~dPw~~i~~~~~~g~~v~G~Vt~i~~~GafVei~~GvEGlvhvSEisw~~~~~-P~----  319 (541)
T COG0539         245 KVISLDEERGRVSLSLKQLEEDPWEGIEKKYPVGDKVEGKVTNLTDYGAFVEIEEGVEGLVHVSEISWTKKNV-PS----  319 (541)
T ss_pred             EEEEEccCCCeEEEEehhcccCcHHHHhhhcCCCCEEEEEEEEeecCcEEEEecCCccceeechhhcccccCC-HH----
Confidence            9999997 8999999999999999972               3457899999999999999999999998655 66    


Q ss_pred             CCCcccCCCCcceEEEeecccccccccccccccccccccccccccccCCCCCCCcEEEEEec------------------
Q 002054          801 TPGVNSSTSSTPAVLIRSAAECDEEEKASGFSQSSKSTLKSTLASKSNSKPKKFTSQSDFFS------------------  862 (974)
Q Consensus       801 ~~~~~~~~G~~v~v~Ir~~l~iD~~~r~i~ls~k~~~~~~~~~~~~~~~~~~G~~v~g~V~~------------------  862 (974)
                         +.+++||+|.|.|   +++|+++|||+|++|++.++|  |..+.+.+++|++++|.|++                  
T Consensus       320 ---evv~~Gq~V~V~V---l~id~e~rRIsL~iKq~~~~p--w~~~~~~~~~g~~v~g~v~~~t~~g~fv~le~gidG~v  391 (541)
T COG0539         320 ---EVVKVGQEVEVKV---LDIDPERRRISLGLKQLKENP--WEEFADKHPVGDVVEGKVKSITDFGAFVELEGGIDGLV  391 (541)
T ss_pred             ---HhcccCCEEEEEE---EeeCchhceEEeeehhhhcCh--hhhhhhhcCCCCeEEEEEeeecccceEEccCCCccceE
Confidence               8999999999999   999999999999999999999  99999999999999999998                  


Q ss_pred             -----ccCcCCC--cccccCCeEEEEEEEeecCCCCcC-cccccccccc--ccccCCCCCEEEEEEEEEeCCeEEEEeCC
Q 002054          863 -----STNIQKS--TSFSQREREELAECLFGTEDGDED-NKGTRVEAIV--SAKNLKLGTKVAAKVYQVRARGLVLDLGG  932 (974)
Q Consensus       863 -----~~~~~~~--~~~k~Gq~v~~~Vl~vd~e~~~i~-slK~~~~~p~--~~~~~~vG~vV~G~V~~I~~~GvFV~L~~  932 (974)
                           +|.....  ..||+|++++++|+.+|+++++++ ++|++..+||  ....|++|++|+|+|+++.++|+||+|++
T Consensus       392 h~~d~sw~~~~~~~~~~k~Gd~v~~~vl~vd~~~~~isLgiKql~~~p~~~~~~~~~~~~~v~~~v~~i~~~G~~v~l~~  471 (541)
T COG0539         392 HLSDLSWDRPGEEAEKYKKGDEVEAKVLAVDKEKERISLGIKQLEESPWEEFSEKYKKGSVVKGKVKSVKDKGAFVELGG  471 (541)
T ss_pred             EHHhcCccccCcHHHhhccCcEEEEEEEEEecccceeeeehhhhccCchhhhHhhccCCCeEEEEEEEEccCceEEEecC
Confidence                 8876544  389999999999999999999999 9999999999  57779999999999999999999999999


Q ss_pred             CeEEEEecccCCCCCCCCCCEEEEEEEEEeCCCcee
Q 002054          933 GIRGMYRFENNEKKDFVVGDELLVKCSSFTGKGIPV  968 (974)
Q Consensus       933 gv~Glih~se~~~~~f~vGd~V~vkVl~id~~~~~~  968 (974)
                      ++.||++.+++....|++||.|+|+|+++|+++.-+
T Consensus       472 ~v~G~i~~~~~~~~~~~~gd~v~a~v~~id~k~~ki  507 (541)
T COG0539         472 GVEGLIRLSELSRDVLKVGDEVEAVVVSIDKKNRKI  507 (541)
T ss_pred             ceeeeeecchhhhhhccCCCEEEEEEEEEcCCCCEE
Confidence            999999999998889999999999999999887654

>PRK12269 bifunctional cytidylate kinase/ribosomal protein S1; Provisional

Probab=100.00  E-value=7.7e-39  Score=391.78  Aligned_cols=302  Identities=20%  Similarity=0.254  Sum_probs=261.6

Q ss_pred             EEecCHHHHHH-HHHHHHHHhhcccccCcEEEEEEEEEeeceEEEEEcCCeEEEEecccCCCccccccccccccCCEEEE
Q 002054          658 VVAKNRSVMEK-VLEKVDFIIGREIEVGGIYKGVVTSVKEYGAFVEFNGGQQGLLHVSELSHEPVSRVSDVVSVGQQLSL  736 (974)
Q Consensus       658 i~~~~~~~~~~-a~~~i~~l~~~~~~~G~i~~G~V~~i~~~G~fV~l~~g~~Glvhisels~~~v~~~~~~~~vGd~V~v  736 (974)
                      +..+.+..+++ +.+.++.+. .++++|++++|+|+++.+||+||++ +|++||||+|+++|.++.++.+.|++||+++|
T Consensus       468 iVlSrr~~l~e~~~~~~ee~~-~~l~~G~~V~G~Vk~i~~~G~fVdl-~Gv~Gfvp~SeiS~~~v~~~~~~~kvGq~v~v  545 (863)
T PRK12269        468 IVINRRRYLEERARQAREEFF-NSVHIEDSVSGVVKSFTSFGAFIDL-GGFDGLLHVNDMSWGHVARPREFVKKGQTIEL  545 (863)
T ss_pred             EEEEHHHHHHHHHHHHHHHHH-hcCCCCCEEEEEEEEEeCCcEEEEE-CCEEEEEEchhccccccCCHHHhccCCCEEEE
Confidence            44445554443 445555555 6799999999999999999999999 68999999999999999999999999999999


Q ss_pred             EEEEEcc-CCceEEEEeccCCCcccc------cCce---------EEEEEeecCCcceeeEEeeccCCCCCCCCCCCCCC
Q 002054          737 RCIGQDV-RGNIKLSLKAVSPRPEAD------VKGV---------VEGSVPVNKQATDVWASVGDVSNGQNPELPMRKNE  800 (974)
Q Consensus       737 kVl~id~-~gri~LS~K~~~~~~~~~------~g~~---------~~G~vv~i~~gv~~~~~~~~l~~~~~~~lp~~~~~  800 (974)
                      +|+++|+ ++++.||+|++.++||..      .|++         .+|.|+++.+|++|++|+++++|.....+|.    
T Consensus       546 kVi~iD~e~~rI~LSlK~l~~~p~~~~~~~~~vG~iV~G~V~~I~~fG~fVeL~~gveGLvhiSEls~~~~~~~p~----  621 (863)
T PRK12269        546 KVIRLDQAEKRINLSLKHFQPDPWLEFENKFGVNDVVKGRVTKIADFGAFIELAEGIEGLAHISEFSWVKKTSKPS----  621 (863)
T ss_pred             EEEEEecCCCeEEEEEeccccchhhhhhccCCCCCEEEEEEEEEeCCeEEEEecCCceeeeEHHHhcCccccCCHH----
Confidence            9999998 789999999999999975      2333         4677778888999999999999954344454    


Q ss_pred             CCCcccCCCCcceEEEeecccccccccccccccccccccccccccccCCCCCCCcEEEEEec------------------
Q 002054          801 TPGVNSSTSSTPAVLIRSAAECDEEEKASGFSQSSKSTLKSTLASKSNSKPKKFTSQSDFFS------------------  862 (974)
Q Consensus       801 ~~~~~~~~G~~v~v~Ir~~l~iD~~~r~i~ls~k~~~~~~~~~~~~~~~~~~G~~v~g~V~~------------------  862 (974)
                         +.+++||.|.++|   +++|+++++++||+++..++|  |....+.+++|++++|+|++                  
T Consensus       622 ---~~~kvGd~V~vkV---l~iD~e~~rIsLS~K~l~~~P--w~~~~~~~~vG~~v~G~V~~i~~~G~fV~l~~gV~GlI  693 (863)
T PRK12269        622 ---DMVKIGDEVECMI---LGYDIQAGRVSLGLKQVTANP--WEEIEARYPVGARFTRRIVKVTNAGAFIEMEEGIDGFL  693 (863)
T ss_pred             ---HcCCCCCEEEEEE---EEEecccCceEEEehhcccCc--hHHHHHhCCCCCEEEEEEEEEecceEEEEeCCCcEEEE
Confidence               7899999999999   999999999999999999998  99999999999999999988                  


Q ss_pred             -----ccCcC---CCcccccCCeEEEEEEEeecCCCCcC-ccccccccccc--cccCCCCCEEEEEEEEEeCCeEEEEeC
Q 002054          863 -----STNIQ---KSTSFSQREREELAECLFGTEDGDED-NKGTRVEAIVS--AKNLKLGTKVAAKVYQVRARGLVLDLG  931 (974)
Q Consensus       863 -----~~~~~---~~~~~k~Gq~v~~~Vl~vd~e~~~i~-slK~~~~~p~~--~~~~~vG~vV~G~V~~I~~~GvFV~L~  931 (974)
                           +|...   .+..|++||.|+++|+++|++++++. |+|++..+||.  .++|++|++|+|+|.++++||+||+|+
T Consensus       694 h~sels~~~~~~~~~~~~kvGq~VkvkVl~ID~e~rrI~LS~K~l~~dpw~~~~~~~~vG~iV~GkV~~v~~~GvFVeL~  773 (863)
T PRK12269        694 HVDDLSWVKRTRPADHELEVGKEIECMVIECDPQARRIRLGVKQLSDNPWQVFANAYGVGSTVEGEVSSVTDFGIFVRVP  773 (863)
T ss_pred             EhHHhhccccccchhhccCCCCEEEEEEEEEeccCCEEEEEecccccChHHHHHhhCCCCCEEEEEEEEEecCeEEEEcC
Confidence                 56543   23479999999999999999999999 99999999994  667999999999999999999999999


Q ss_pred             CCeEEEEecccCCC----------CCCCCCCEEEEEEEEEeC-CCceeeeecC
Q 002054          932 GGIRGMYRFENNEK----------KDFVVGDELLVKCSSFTG-KGIPVVSLVD  973 (974)
Q Consensus       932 ~gv~Glih~se~~~----------~~f~vGd~V~vkVl~id~-~~~~~~~~~~  973 (974)
                      +|+.||+|.++++.          +.|++||+|+|+|+++|. ++...+|+.+
T Consensus       774 ~gVeGlI~~s~lsdd~~~~~~~~~~~f~vGD~V~v~Vl~iD~~~rkI~LSlk~  826 (863)
T PRK12269        774 GGVEGLVRKQHLVENRDGDPGEALRKYAVGDRVKAVIVDMNVKDRKVAFSVRD  826 (863)
T ss_pred             CCeEEEEEHHHcCCcccccchhhccccCCCCEEEEEEEEEEcCCCEEEEEEec
Confidence            99999999998742          248999999999999997 4566777653

>TIGR02065 ECX1 archaeal exosome-like complex exonuclease 1

Probab=100.00  E-value=2.4e-38  Score=338.73  Aligned_cols=224  Identities=32%  Similarity=0.471  Sum_probs=202.4

Q ss_pred             HHHhcCCcCCCCCCCCccCeEEEeCCCCCCCcceEEEeCCeEEEEEEEeCCCchhhhccccCCCCceeEEEEEecCCCCc
Q 002054          363 RIIAEGVRVDGRQLDEVRPIYCESGNLPILHGSSLFSRGDTQVLCTVTLGAPAEAQRLESLVGPPTKRFMLHYSFPPFCI  442 (974)
Q Consensus       363 ~il~~~~R~DGR~~~e~R~I~ie~g~l~~a~GSal~~~G~T~Vl~~Vtl~~p~~~~~~d~~~~~~~~~~~v~~~f~p~s~  442 (974)
                      .++++|+|+|||.++|+|++.+++|.++++||||+|++|+|+|+|+|+  +|.+..... ...++++.+.++|+++||++
T Consensus         2 ~~~~~~~R~DGR~~~e~R~~~~~~g~~~~a~GSa~~~~G~T~Vl~~V~--gp~e~~~~~-~~~~~~~~l~v~~~~~~~a~   78 (230)
T TIGR02065         2 LILEDGVRLDGRKPDELRPIKIEAGVLKNADGSAYVEFGGTKIIAAVY--GPREMHPRH-LQLPDRAVLRVRYHMAPFST   78 (230)
T ss_pred             cccCCCcCCCCCCcccccCeEEEECCCCCCCeEEEEEECCcEEEEEEe--CCCcccccc-ccCCCceEEEEEEEeCCccc
Confidence            367899999999999999999999999999999999999999999999  887643221 22367889999999999999


Q ss_pred             cccccccCCCchhhhHHHHHHHHhhhcCCCCCCCCe-EEEEEEEEEcCCCChhhHHHHHHHHHHHHcCCCccccccceee
Q 002054          443 NEVGKRVGLNRREVGHGTLAEKALLAVLPPENDFPY-TVRVNSEVMASDGSTSMATVCGGSMALMDAGIPLQEHVAGVSV  521 (974)
Q Consensus       443 ~e~~~~~~~~rre~~~~~l~eral~~vi~~~~~~p~-tI~V~v~VLesdGs~~~A~v~aa~lAL~dagvPi~~~vagvs~  521 (974)
                      .+.++ ++++++|+.++++++|+|+++++. +.||+ +|+|.++||++|||.++|++||+++||+||||||+++|+|+++
T Consensus        79 ~~~~~-~~~~~~~~~~s~~l~~~l~~~i~~-~~~p~~~i~i~v~vl~~DG~~~~aai~aa~lAL~dagIp~~~~v~avtv  156 (230)
T TIGR02065        79 DERKR-PGPSRREIEISKVIREALEPAILL-EQFPRTAIDVFIEVLQADAGTRCAGLTAASLALADAGIPMRDLVVGVAV  156 (230)
T ss_pred             CCccC-CCCCccHHHHHHHHHHHHHHHhCh-hhcCCeEEEEEEEEEEcCCCHHHHHHHHHHHHHHHcCCccccceeeEEE
Confidence            76554 568999999999999999999998 68897 4999999999999999999999999999999999999999999


Q ss_pred             eeeccCCCCCCcccceEEEecCCccccccCCccEEEEe--eCCceEEEEeeccCCCCCHHHHHHHHHHHHHHHHHHHHHH
Q 002054          522 GLVSEVDPSTGEIKDYRILTDILGLEDHLGDMDFKIAG--TRIGVTAIQLDIKPAGIPLDIICECLEHAHKGRLQILDHM  599 (974)
Q Consensus       522 gli~~~d~~~~~~~~~~iL~Dp~~~Ee~~~d~d~~Va~--t~~gI~alq~~~k~~~i~~e~l~~al~~A~~~~~~I~~~m  599 (974)
                      |++++           .+++||+..|+..++++++|+.  +.+.|+.+++++   .++++.|.+|++.|++++.++.++|
T Consensus       157 ~~~~~-----------~~v~Dpt~~Ee~~~~~~l~va~~~~~~~i~~i~~~g---~~~~e~~~~~l~~a~~~~~~l~~~~  222 (230)
T TIGR02065       157 GKVDG-----------VVVLDLNEEEDMYGEADMPVAMMPKLGEITLLQLDG---DMTPDEFRQALDLAVKGIKIIYQIQ  222 (230)
T ss_pred             EEECC-----------eEEECCCHHHhhcCCCceEEEEeCCCCCEEEEEEec---CcCHHHHHHHHHHHHHHHHHHHHHH
Confidence            99864           6999999999999999999997  445699999985   5999999999999999999999999


Q ss_pred             HHHhcC
Q 002054          600 EREISA  605 (974)
Q Consensus       600 ~~~i~~  605 (974)
                      ++++.+
T Consensus       223 ~~~l~~  228 (230)
T TIGR02065       223 REALKN  228 (230)
T ss_pred             HHHHHh
Confidence            999865

This family contains the archaeal protein orthologous to the eukaryotic exosome protein Rrp41. It is somewhat more distantly related to the bacterial protein ribonuclease PH. An exosome-like complex has been demonstrated experimentally for the Archaea in Sulfolobus solfataricus, so members of this family are designated exosome complex exonuclease 1, after usage in SwissProt.

>PRK03983 exosome complex exonuclease Rrp41; Provisional

Probab=100.00  E-value=1e-37  Score=336.91  Aligned_cols=225  Identities=33%  Similarity=0.522  Sum_probs=203.9

Q ss_pred             HHHhcCCcCCCCCCCCccCeEEEeCCCCCCCcceEEEeCCeEEEEEEEeCCCchhhhccccCCCCceeEEEEEecCCCCc
Q 002054          363 RIIAEGVRVDGRQLDEVRPIYCESGNLPILHGSSLFSRGDTQVLCTVTLGAPAEAQRLESLVGPPTKRFMLHYSFPPFCI  442 (974)
Q Consensus       363 ~il~~~~R~DGR~~~e~R~I~ie~g~l~~a~GSal~~~G~T~Vl~~Vtl~~p~~~~~~d~~~~~~~~~~~v~~~f~p~s~  442 (974)
                      .++++|+|+|||.++|+|++++++|.+++++|||+|++|+|+|+|+|+  +|.+.... ....++.+.+.++|+|+||++
T Consensus         8 ~~~~~~~R~DGR~~~~~R~i~i~~G~l~~a~GSa~v~~G~T~Vl~~V~--gp~e~~~~-~~~~~~~~~l~v~~~~~p~~~   84 (244)
T PRK03983          8 LILEDGLRLDGRKPDELRPIKIEVGVLKNADGSAYLEWGNNKIIAAVY--GPREMHPR-HLQLPDRAVLRVRYNMAPFSV   84 (244)
T ss_pred             hhccCCCCCCCCCcCcccceEEEeCCCCCCCeEEEEEECCeEEEEEEe--cCCccccc-cccCCCcEEEEEEEEcCCCcc
Confidence            578999999999999999999999999999999999999999999999  88764322 223467899999999999999


Q ss_pred             cccccccCCCchhhhHHHHHHHHhhhcCCCCCCCCeE-EEEEEEEEcCCCChhhHHHHHHHHHHHHcCCCccccccceee
Q 002054          443 NEVGKRVGLNRREVGHGTLAEKALLAVLPPENDFPYT-VRVNSEVMASDGSTSMATVCGGSMALMDAGIPLQEHVAGVSV  521 (974)
Q Consensus       443 ~e~~~~~~~~rre~~~~~l~eral~~vi~~~~~~p~t-I~V~v~VLesdGs~~~A~v~aa~lAL~dagvPi~~~vagvs~  521 (974)
                      .+.+ .+++++++++++++++++|+++++. +.||++ |+|.++||++|||+++||+||+++||+||||||+++++++++
T Consensus        85 ~~~~-~~~~~~~~~~~s~~l~~~l~~~i~~-~~~p~~~I~I~i~VL~~DG~~~~aai~Aa~lAL~dagIp~~~~v~avtv  162 (244)
T PRK03983         85 DERK-RPGPDRRSIEISKVIREALEPAIML-ELFPRTVIDVFIEVLQADAGTRVAGITAASLALADAGIPMRDLVAGCAV  162 (244)
T ss_pred             cccc-CCCCChhHHHHHHHHHHHHHHhccH-HhCCCeEEEEEEEEEECCCCHHHHHHHHHHHHHHhcCCccccceeEEEE
Confidence            7754 4468899999999999999999997 678885 999999999999999999999999999999999999999999


Q ss_pred             eeeccCCCCCCcccceEEEecCCccccccCCccEEEEee-CCc-eEEEEeeccCCCCCHHHHHHHHHHHHHHHHHHHHHH
Q 002054          522 GLVSEVDPSTGEIKDYRILTDILGLEDHLGDMDFKIAGT-RIG-VTAIQLDIKPAGIPLDIICECLEHAHKGRLQILDHM  599 (974)
Q Consensus       522 gli~~~d~~~~~~~~~~iL~Dp~~~Ee~~~d~d~~Va~t-~~g-I~alq~~~k~~~i~~e~l~~al~~A~~~~~~I~~~m  599 (974)
                      |++++           .+|+||+..|+..++++++|+++ ..| |+++|+++   .++.+++.+|++.|++++.+|.+.|
T Consensus       163 ~~~~~-----------~~i~DPt~~Ee~~~~~~l~va~~~~~~~I~~l~~~G---~~~~~~~~~~i~~A~~~~~~i~~~i  228 (244)
T PRK03983        163 GKVDG-----------VIVLDLNKEEDNYGEADMPVAIMPRLGEITLLQLDG---NLTREEFLEALELAKKGIKRIYQLQ  228 (244)
T ss_pred             EEECC-----------EEEECCCHHHhccCCceEEEEEECCCCCEEEEEEec---CcCHHHHHHHHHHHHHHHHHHHHHH
Confidence            99864           69999999999999999999997 345 99999985   5999999999999999999999999


Q ss_pred             HHHhcCC
Q 002054          600 EREISAP  606 (974)
Q Consensus       600 ~~~i~~~  606 (974)
                      ++++.+.
T Consensus       229 ~~~l~~~  235 (244)
T PRK03983        229 REALKSK  235 (244)
T ss_pred             HHHHHHH
Confidence            9998753

>PRK00173 rph ribonuclease PH; Reviewed

Probab=100.00  E-value=1.4e-36  Score=326.40  Aligned_cols=218  Identities=27%  Similarity=0.373  Sum_probs=197.0

Q ss_pred             CcCCCCCCCCccCeEEEeCCCCCCCcceEEEeCCeEEEEEEEeC--CCchhhhccccCCCCceeEEEEEecCCCCccccc
Q 002054          369 VRVDGRQLDEVRPIYCESGNLPILHGSSLFSRGDTQVLCTVTLG--APAEAQRLESLVGPPTKRFMLHYSFPPFCINEVG  446 (974)
Q Consensus       369 ~R~DGR~~~e~R~I~ie~g~l~~a~GSal~~~G~T~Vl~~Vtl~--~p~~~~~~d~~~~~~~~~~~v~~~f~p~s~~e~~  446 (974)
                      +|+|||+++|+|++.|++|++++++|||+|++|+|+|+|+|+..  .|..      ...++++.++++|+++||++.+++
T Consensus         1 ~R~DGR~~~e~R~i~~~~g~~~~a~GSa~v~~G~T~Vla~V~~~~~~p~~------~~~~~~g~l~v~~~~~p~a~~~~~   74 (238)
T PRK00173          1 MRPDGRAADQLRPVTITRNFTKHAEGSVLVEFGDTKVLCTASVEEGVPRF------LKGQGQGWVTAEYGMLPRATHTRN   74 (238)
T ss_pred             CCCCCCCcccccCeEEEeCCCCCCCeeEEEEecCcEEEEEEEcCCCCCCc------cCCCCcEEEEEEEecCCCCCcccc
Confidence            59999999999999999999999999999999999999999943  2322      224578999999999999998863


Q ss_pred             c----ccCCCchhhhHHHHHHHHhhhcCCCCCCCC-eEEEEEEEEEcCCCChhhHHHHHHHHHHHHc-----------CC
Q 002054          447 K----RVGLNRREVGHGTLAEKALLAVLPPENDFP-YTVRVNSEVMASDGSTSMATVCGGSMALMDA-----------GI  510 (974)
Q Consensus       447 ~----~~~~~rre~~~~~l~eral~~vi~~~~~~p-~tI~V~v~VLesdGs~~~A~v~aa~lAL~da-----------gv  510 (974)
                      +    .|.++++++.++++++|+|+++++. +.|| ++|+|+++||++|||.++||++|+++||+||           ++
T Consensus        75 ~~~~~~g~~~~~~~~~sr~i~r~lr~~i~l-~~l~~~~i~v~v~VL~~DG~~~~aai~Aa~~AL~da~~~~~~~~~~~~i  153 (238)
T PRK00173         75 DREAAKGKQGGRTQEIQRLIGRSLRAVVDL-KALGERTITIDCDVIQADGGTRTASITGAYVALADALNKLVARGKLKKN  153 (238)
T ss_pred             cccccCCCCCccHHHHHHHHHHHHHHhcCH-HHcCCeEEEEEEEEEeCCCCHHHHHHHHHHHHHHHhhhhhhccCcccCC
Confidence            2    3467888999999999999999998 4555 5799999999999999999999999999999           99


Q ss_pred             CccccccceeeeeeccCCCCCCcccceEEEecCCccccccCCccEEEEeeCCc-eEEEEeeccCCCCCHHHHHHHHHHHH
Q 002054          511 PLQEHVAGVSVGLVSEVDPSTGEIKDYRILTDILGLEDHLGDMDFKIAGTRIG-VTAIQLDIKPAGIPLDIICECLEHAH  589 (974)
Q Consensus       511 Pi~~~vagvs~gli~~~d~~~~~~~~~~iL~Dp~~~Ee~~~d~d~~Va~t~~g-I~alq~~~k~~~i~~e~l~~al~~A~  589 (974)
                      ||+++|+++++|++++           .+|+||+.+|+..++++++|+.+..| |+++|+++++.+++.++|.+|++.|+
T Consensus       154 p~~~~~~~vt~~~~~~-----------~~lvDpt~~Ee~~~~~~l~v~~~~~~~i~~v~~~g~g~~~~~e~l~~~i~~A~  222 (238)
T PRK00173        154 PLKDQVAAVSVGIVDG-----------EPVLDLDYEEDSAAETDMNVVMTGSGGFVEVQGTAEGAPFSREELDALLDLAE  222 (238)
T ss_pred             cccCceeEEEEEEECC-----------EEEECCCHHHHhcCCceEEEEECCCCCEEEEEccCCCCCcCHHHHHHHHHHHH
Confidence            9999999999999964           69999999999999999999999876 99999987767899999999999999


Q ss_pred             HHHHHHHHHHHHHhc
Q 002054          590 KGRLQILDHMEREIS  604 (974)
Q Consensus       590 ~~~~~I~~~m~~~i~  604 (974)
                      +++.+|.+.|++++.
T Consensus       223 ~~~~~l~~~~~~~l~  237 (238)
T PRK00173        223 KGIAELVALQKAALA  237 (238)
T ss_pred             HHHHHHHHHHHHHhc
Confidence            999999999999875

>TIGR01966 RNasePH ribonuclease PH

Probab=100.00  E-value=1.4e-35  Score=318.56  Aligned_cols=218  Identities=27%  Similarity=0.381  Sum_probs=194.4

Q ss_pred             cCCCCCCCCccCeEEEeCCCCCCCcceEEEeCCeEEEEEEEeCCCchhhhccccCCCCceeEEEEEecCCCCcccc-ccc
Q 002054          370 RVDGRQLDEVRPIYCESGNLPILHGSSLFSRGDTQVLCTVTLGAPAEAQRLESLVGPPTKRFMLHYSFPPFCINEV-GKR  448 (974)
Q Consensus       370 R~DGR~~~e~R~I~ie~g~l~~a~GSal~~~G~T~Vl~~Vtl~~p~~~~~~d~~~~~~~~~~~v~~~f~p~s~~e~-~~~  448 (974)
                      |+|||+++|+|++++++|++++++|||+|++|+|+|+|+|+...+.+..    ...++++.+.++|+|+||++.+. +|.
T Consensus         1 R~DGR~~~e~R~i~i~~G~~~~A~GSa~v~~G~T~Vla~V~~~~~~p~~----~~~~~~g~l~v~~~~~p~a~~~~~~r~   76 (236)
T TIGR01966         1 RPDGRKPDQLRPVSITRDFLKHAEGSVLIEFGNTKVLCTASVEEKVPPF----LRGSGEGWITAEYGMLPRATQTRNRRE   76 (236)
T ss_pred             CCCCCCCCCccCeEEEeCCcCCCCceEEEEecCCEEEEEEEccCccCCc----ccCCCcEEEEEEEecCCCCCCCCcccc
Confidence            8999999999999999999999999999999999999999955443311    11346789999999999999876 232


Q ss_pred             ---cCCCchhhhHHHHHHHHhhhcCCCCCCCC-eEEEEEEEEEcCCCChhhHHHHHHHHHHHHc-----------CCCcc
Q 002054          449 ---VGLNRREVGHGTLAEKALLAVLPPENDFP-YTVRVNSEVMASDGSTSMATVCGGSMALMDA-----------GIPLQ  513 (974)
Q Consensus       449 ---~~~~rre~~~~~l~eral~~vi~~~~~~p-~tI~V~v~VLesdGs~~~A~v~aa~lAL~da-----------gvPi~  513 (974)
                         |.+++++.+++++++|+|+++++. +.|| ++|+|+++||++|||.++||+||+++||+||           |+||+
T Consensus        77 ~~~g~~~~~~~e~~~~i~r~lr~~i~l-~~l~~~~i~I~v~VL~~DG~~~~aai~Aa~aAL~da~~~~~~~~~~~~ip~~  155 (236)
T TIGR01966        77 SAKGKQSGRTQEIQRLIGRALRAVVDL-EALGERTIWIDCDVIQADGGTRTASITGAFVALADAISKLHKRGILKESPIR  155 (236)
T ss_pred             ccCCCCCccHHHHHHHHHHHHHHhcCH-hhcCCeEEEEEEEEEeCCCCHHHHHHHHHHHHHHHHHHhhhhcCcccCCCcc
Confidence               566668889999999999999998 5565 5799999999999999999999999999999           99999


Q ss_pred             ccccceeeeeeccCCCCCCcccceEEEecCCccccccCCccEEEEeeCCc-eEEEEeeccCCCCCHHHHHHHHHHHHHHH
Q 002054          514 EHVAGVSVGLVSEVDPSTGEIKDYRILTDILGLEDHLGDMDFKIAGTRIG-VTAIQLDIKPAGIPLDIICECLEHAHKGR  592 (974)
Q Consensus       514 ~~vagvs~gli~~~d~~~~~~~~~~iL~Dp~~~Ee~~~d~d~~Va~t~~g-I~alq~~~k~~~i~~e~l~~al~~A~~~~  592 (974)
                      ++|+++++|++++           .+|+||+..|+..++..++++.+..+ |+.+|+++..+.+++++|.+|++.|++++
T Consensus       156 ~~~~~vt~~~~~~-----------~~v~Dpt~~Ee~~~~~~l~l~~~~~~~i~~i~~~g~~~~~~~~~l~~~i~~a~~~~  224 (236)
T TIGR01966       156 DFVAAVSVGIVDG-----------EPVLDLDYEEDSAADVDMNVVMTGSGGFVEVQGTAEEGPFSRDELNKLLDLAKKGI  224 (236)
T ss_pred             CceeEEEEEEECC-----------EEEECCChhHHhccCceEEEEEcCCCCEEEEEecCCCCCcCHHHHHHHHHHHHHHH
Confidence            9999999999975           69999999999999999999988776 99999976667899999999999999999


Q ss_pred             HHHHHHHHHHh
Q 002054          593 LQILDHMEREI  603 (974)
Q Consensus       593 ~~I~~~m~~~i  603 (974)
                      .+|.+.|++++
T Consensus       225 ~~l~~~~~~~l  235 (236)
T TIGR01966       225 RELIELQKQAL  235 (236)
T ss_pred             HHHHHHHHHHh
Confidence            99999999986

This bacterial enzyme, ribonuclease PH, performs the final 3'-trimming and modification of tRNA precursors. This model is restricted absolutely to bacteria. Related families outside the model include proteins described as probable exosome complex exonucleases (rRNA processing) and polyribonucleotide nucleotidyltransferases (mRNA degradation). The most divergent member within the family is RNase PH from Deinococcus radiodurans.

>PRK11824 polynucleotide phosphorylase/polyadenylase; Provisional

Probab=100.00  E-value=1.4e-34  Score=351.54  Aligned_cols=211  Identities=23%  Similarity=0.337  Sum_probs=186.4

Q ss_pred             cCeEEEeCCCC-CCCcceEEEeCCeEEEEEEEeCCCchhhhccccCCCCceeEEEEEecCCCCcc-----ccccccCCCc
Q 002054          380 RPIYCESGNLP-ILHGSSLFSRGDTQVLCTVTLGAPAEAQRLESLVGPPTKRFMLHYSFPPFCIN-----EVGKRVGLNR  453 (974)
Q Consensus       380 R~I~ie~g~l~-~a~GSal~~~G~T~Vl~~Vtl~~p~~~~~~d~~~~~~~~~~~v~~~f~p~s~~-----e~~~~~~~~r  453 (974)
                      |++++++|.++ +|||||++++|+|+|+|+|+  +|.+++     .+.++.+++++|...+|+.+     ..+|.|.|++
T Consensus        14 r~i~~e~G~ia~qAdGSa~v~~G~T~VlatV~--~~~~~~-----~~~df~pL~v~y~e~~~A~gkiP~~f~kreg~pse   86 (693)
T PRK11824         14 RTLTLETGKLARQANGAVLVRYGDTVVLVTVV--ASKEPK-----EGQDFFPLTVDYEEKTYAAGKIPGGFFKREGRPSE   86 (693)
T ss_pred             ccEEEEECCcCCCCCeEEEEEECCeEEEEEEE--cCCCCC-----CCCCeeeeEEEEEehhhhccCCCcccccCCCCCCh
Confidence            78999999996 69999999999999999999  555532     23456778889988888755     4567889999


Q ss_pred             hhhhHHHHHHHHhhhcCCCCCCCCeEEEEEEEEEcCCCChh--hHHHHHHHHHHHHcCCCccccccceeeeeeccCCCCC
Q 002054          454 REVGHGTLAEKALLAVLPPENDFPYTVRVNSEVMASDGSTS--MATVCGGSMALMDAGIPLQEHVAGVSVGLVSEVDPST  531 (974)
Q Consensus       454 re~~~~~l~eral~~vi~~~~~~p~tI~V~v~VLesdGs~~--~A~v~aa~lAL~dagvPi~~~vagvs~gli~~~d~~~  531 (974)
                      +|+.++++++|+|++++|  +.|.|.|+|+++||++||+.+  +||+||+++||+++|||+.++|+||++|++++     
T Consensus        87 ~eil~srlIdR~lrplfp--~~~~~~i~I~~~VL~~Dg~~~~d~aai~aAsaAL~~s~IP~~~~v~av~vg~i~g-----  159 (693)
T PRK11824         87 KETLTSRLIDRPIRPLFP--KGFRNEVQVVATVLSVDPENDPDILAMIGASAALSISGIPFNGPIAAVRVGYIDG-----  159 (693)
T ss_pred             HHHHHHHHHhhhHHHhCC--CCCCeEEEEEEEEEeCCCCCcHHHHHHHHHHHHHHhcCCCcCCCeEEEEEEEECC-----
Confidence            999999999999999999  469999999999999999773  48999999999999999999999999999975     


Q ss_pred             CcccceEEEecCCccccccCCccEEEEeeCCceEEEEeeccCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCCCCC
Q 002054          532 GEIKDYRILTDILGLEDHLGDMDFKIAGTRIGVTAIQLDIKPAGIPLDIICECLEHAHKGRLQILDHMEREISAPRTQDD  611 (974)
Q Consensus       532 ~~~~~~~iL~Dp~~~Ee~~~d~d~~Va~t~~gI~alq~~~k~~~i~~e~l~~al~~A~~~~~~I~~~m~~~i~~~~~~~~  611 (974)
                            .+++||+..|+..++++++|++|.+.+++++..+  .+++++.|.+||+.|++++.+|.+.|++.+++.. ++.
T Consensus       160 ------~~ivdPt~~E~~~s~~~l~va~t~~~i~mie~~~--~~l~e~~l~~al~~a~~~~~~i~~~~~~~~~~~~-~~~  230 (693)
T PRK11824        160 ------EFVLNPTVEELEESDLDLVVAGTKDAVLMVESEA--KELSEEVMLEAIEFGHEAIQELIDAQEELAAEAG-PKW  230 (693)
T ss_pred             ------EEEEcCCHHHHhhCcceEEEEEccCceEEEECCC--CCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHhcC-CCc
Confidence                  6999999999999999999999998888888654  4699999999999999999999999999998877 433


Q ss_pred             CC
Q 002054          612 RN  613 (974)
Q Consensus       612 ~~  613 (974)
                      ++
T Consensus       231 ~~  232 (693)
T PRK11824        231 EW  232 (693)
T ss_pred             cc
Confidence            33

>PRK04282 exosome complex RNA-binding protein Rrp42; Provisional

Probab=100.00  E-value=2.4e-35  Score=323.28  Aligned_cols=232  Identities=20%  Similarity=0.313  Sum_probs=204.5

Q ss_pred             HHHHHHHHHHHHHHhcCCcCCCCCCCCccCeEEEeCCCCCCCcceEEEeCCeEEEEEEEeC--CCchhhhccccCCCCce
Q 002054          352 VDTVRKRVIRKRIIAEGVRVDGRQLDEVRPIYCESGNLPILHGSSLFSRGDTQVLCTVTLG--APAEAQRLESLVGPPTK  429 (974)
Q Consensus       352 ~~~~~~~~~r~~il~~~~R~DGR~~~e~R~I~ie~g~l~~a~GSal~~~G~T~Vl~~Vtl~--~p~~~~~~d~~~~~~~~  429 (974)
                      .++.+++.++ ..+++|+|+|||.++|+|++++++|.+++++|||+++.|+|+|+|+|+.+  .|..       ..++++
T Consensus         8 ~~~~e~~~i~-~~l~~~~R~DGR~~~e~R~i~i~~g~l~~a~GSa~v~~G~T~vl~~V~~~~~~p~~-------~~~~~g   79 (271)
T PRK04282          8 IPEIKKDYIL-SLLKKGKRIDGRKLDEYRPIEIETGVIKKAEGSALVKLGNTQVLAGVKLEIGEPFP-------DTPNEG   79 (271)
T ss_pred             hhHHHHHHHH-HHHhcCCCCCCCCCccccCeEEEeCCccCCCcEEEEEECCCEEEEEEEEEEecCCC-------CCCCCC
Confidence            5567777776 56689999999999999999999999999999999999999999999954  2322       136789


Q ss_pred             eEEEEEecCCCCccccccccCCCchhhhHHHHHHHHhhhcCCC--------CCCCCeEEEEEEEEEcCCCChhhHHHHHH
Q 002054          430 RFMLHYSFPPFCINEVGKRVGLNRREVGHGTLAEKALLAVLPP--------ENDFPYTVRVNSEVMASDGSTSMATVCGG  501 (974)
Q Consensus       430 ~~~v~~~f~p~s~~e~~~~~~~~rre~~~~~l~eral~~vi~~--------~~~~p~tI~V~v~VLesdGs~~~A~v~aa  501 (974)
                      ++.++|+|+|++...+ +.+.+++++..++++++|+|++..+.        ..++.|+|+|+++||++|||+++||++|+
T Consensus        80 ~i~~~v~~~~~a~~~~-~~~~~~~~~~~l~~~l~r~l~~~~~~dl~~L~I~~g~~~w~i~Vdv~VL~~dG~~~daa~~Aa  158 (271)
T PRK04282         80 VLIVNAELLPLASPTF-EPGPPDENAIELARVVDRGIRESKAIDLEKLVIEPGKKVWVVFIDVYVLDHDGNLLDASMLAA  158 (271)
T ss_pred             EEEEEEEECCCcCccc-cCCCCCHHHHHHHHHHHHHHhccCCccHHHcEEecCcEEEEEEEEEEEECCCCCHHHHHHHHH
Confidence            9999999999998765 45678889999999999998664221        13568999999999999999999999999


Q ss_pred             HHHHHHcCCC--------------------ccccccceeeeeeccCCCCCCcccceEEEecCCccccccCCccEEEEeeC
Q 002054          502 SMALMDAGIP--------------------LQEHVAGVSVGLVSEVDPSTGEIKDYRILTDILGLEDHLGDMDFKIAGTR  561 (974)
Q Consensus       502 ~lAL~dagvP--------------------i~~~vagvs~gli~~~d~~~~~~~~~~iL~Dp~~~Ee~~~d~d~~Va~t~  561 (974)
                      ++||+|+++|                    |+++|.++++|++++           .+|+||+..|+..++..++|+.+.
T Consensus       159 ~aAL~~~~iP~~~~~~~~~~~~~~~~~~l~~~~~p~~vt~~~~~~-----------~~v~Dpt~~Ee~~~~~~l~va~~~  227 (271)
T PRK04282        159 VAALLNTKVPAVEEGEDGVVDKLGEDFPLPVNDKPVTVTFAKIGN-----------YLIVDPTLEEESVMDARITITTDE  227 (271)
T ss_pred             HHHHHhCCCCcEEEcCCceeccCCCcccCCCCCeeEEEEEEEECC-----------EEEECCCHHHHhhcCceEEEEECC
Confidence            9999999995                    999999999999964           699999999999999999999999


Q ss_pred             Cc-eEEEEeeccCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHhc
Q 002054          562 IG-VTAIQLDIKPAGIPLDIICECLEHAHKGRLQILDHMEREIS  604 (974)
Q Consensus       562 ~g-I~alq~~~k~~~i~~e~l~~al~~A~~~~~~I~~~m~~~i~  604 (974)
                      +| ++.++..+ +++++.+.|.+|+++|+++++++.+.|+++++
T Consensus       228 ~g~i~~l~~~g-~~~~~~~~l~~~i~~A~~~~~~l~~~~~~~l~  270 (271)
T PRK04282        228 DGNIVAIQKSG-IGSFTEEEVDKAIDIALEKAKELREKLKEALG  270 (271)
T ss_pred             CCcEEEEEcCC-CCCCCHHHHHHHHHHHHHHHHHHHHHHHHHhc
Confidence            85 88998864 36799999999999999999999999999884

>PRK06299 rpsA 30S ribosomal protein S1; Reviewed

Probab=100.00  E-value=1.7e-35  Score=356.58  Aligned_cols=281  Identities=22%  Similarity=0.304  Sum_probs=248.7

Q ss_pred             cccccCcEEEEEEEEEeeceEEEEEcCCeEEEEecccCCCccccccccccccCCEEEEEEEEEcc-CCceEEEEeccCCC
Q 002054          679 REIEVGGIYKGVVTSVKEYGAFVEFNGGQQGLLHVSELSHEPVSRVSDVVSVGQQLSLRCIGQDV-RGNIKLSLKAVSPR  757 (974)
Q Consensus       679 ~~~~~G~i~~G~V~~i~~~G~fV~l~~g~~Glvhisels~~~v~~~~~~~~vGd~V~vkVl~id~-~gri~LS~K~~~~~  757 (974)
                      .++++|+++.|+|+++.++|+||++. |.+||+|+||++|.++.++.+.|++||.|+|+|+++|. ++++.||+|.+.++
T Consensus       197 ~~l~~G~iv~g~V~~v~~~G~~V~i~-g~~glv~~se~s~~~~~~~~~~~kvG~~v~v~V~~~d~~~~~i~lS~k~~~~~  275 (565)
T PRK06299        197 ENLEEGQVVEGVVKNITDYGAFVDLG-GVDGLLHITDISWKRVNHPSEVVNVGDEVKVKVLKFDKEKKRVSLGLKQLGED  275 (565)
T ss_pred             hcCCCCCEEEEEEEEEeCCeEEEEEC-CEEEEEEHHHhcccccCCHhhcCCCCCEEEEEEEEEeCCCCeEEEEEEecccC
Confidence            57899999999999999999999996 99999999999999999999999999999999999997 78999999999999


Q ss_pred             cccc------cCce---------EEEEEeecCCcceeeEEeeccCCCCCCCCCCCCCCCCCcccCCCCcceEEEeecccc
Q 002054          758 PEAD------VKGV---------VEGSVPVNKQATDVWASVGDVSNGQNPELPMRKNETPGVNSSTSSTPAVLIRSAAEC  822 (974)
Q Consensus       758 ~~~~------~g~~---------~~G~vv~i~~gv~~~~~~~~l~~~~~~~lp~~~~~~~~~~~~~G~~v~v~Ir~~l~i  822 (974)
                      ||..      .|..         .+|.++++.+|+++|+|+++++|.....+|.       ..+++||.+.+.|   +++
T Consensus       276 p~~~~~~~~~~G~~v~g~V~~i~~~G~fV~l~~~v~Glv~~sel~~~~~~~~~~-------~~~~~G~~v~v~V---~~i  345 (565)
T PRK06299        276 PWEAIEKKYPVGSKVKGKVTNITDYGAFVELEEGIEGLVHVSEMSWTKKNKHPS-------KVVSVGQEVEVMV---LEI  345 (565)
T ss_pred             hhHHHHhhCCCCCEEEEEEEEEeCCeEEEEeCCCCEEEEEHHHcCccccccCHH-------HhcCCCCEEEEEE---EEE
Confidence            9975      2433         4567777788999999999999865333443       5689999999999   999


Q ss_pred             cccccccccccccccccccccccccCCCCCCCcEEEEEec-----------------------ccC---cCCCcccccCC
Q 002054          823 DEEEKASGFSQSSKSTLKSTLASKSNSKPKKFTSQSDFFS-----------------------STN---IQKSTSFSQRE  876 (974)
Q Consensus       823 D~~~r~i~ls~k~~~~~~~~~~~~~~~~~~G~~v~g~V~~-----------------------~~~---~~~~~~~k~Gq  876 (974)
                      |++++++.||+++...+|  |......+++|+++.|.|.+                       +|.   ......|++||
T Consensus       346 d~~~~~i~ls~k~~~~~p--~~~~~~~~~~G~~v~g~V~~v~~~G~fV~l~~~v~g~i~~s~l~~~~~~~~~~~~~~~Gd  423 (565)
T PRK06299        346 DEEKRRISLGLKQCKENP--WEEFAEKYPVGDVVEGKVKNITDFGAFVGLEGGIDGLVHLSDISWDKKGEEAVELYKKGD  423 (565)
T ss_pred             cCCCCEEEEehHHhccch--hhhHHHhCCCCCEEEEEEEEEecceEEEECCCCCEEEEEHHHcCccccccChHhhCCCCC
Confidence            999999999999888888  88888888899999999987                       443   22335899999


Q ss_pred             eEEEEEEEeecCCCCcC-cccccccccc--ccccCCCCCEEEEEEEEEeCCeEEEEeCCCeEEEEecccCC-------CC
Q 002054          877 REELAECLFGTEDGDED-NKGTRVEAIV--SAKNLKLGTKVAAKVYQVRARGLVLDLGGGIRGMYRFENNE-------KK  946 (974)
Q Consensus       877 ~v~~~Vl~vd~e~~~i~-slK~~~~~p~--~~~~~~vG~vV~G~V~~I~~~GvFV~L~~gv~Glih~se~~-------~~  946 (974)
                      .|+++|+.+|++++++. |+|++..+||  ..+++++|++|.|+|+++.++|+||++++|+.||||.+++.       .+
T Consensus       424 ~v~v~Il~vd~~~~~i~ls~k~~~~~p~~~~~~~~~~G~vV~G~V~~v~~~G~fV~l~~gi~g~i~~se~s~~~~~~~~~  503 (565)
T PRK06299        424 EVEAVVLKVDVEKERISLGIKQLEEDPFEEFAKKHKKGSIVTGTVTEVKDKGAFVELEDGVEGLIRASELSRDRVEDATE  503 (565)
T ss_pred             EEEEEEEEEeCCCCEEEEEEehhhcCchhHHHhhcCCCCEEEEEEEEEecCceEEecCCCcEEEEEHHHhcchhccCccc
Confidence            99999999999999999 9999999999  47789999999999999999999999999999999999773       45


Q ss_pred             CCCCCCEEEEEEEEEeC-CCceeeeec
Q 002054          947 DFVVGDELLVKCSSFTG-KGIPVVSLV  972 (974)
Q Consensus       947 ~f~vGd~V~vkVl~id~-~~~~~~~~~  972 (974)
                      .|++||.|+|+|+++|. ++...+|+.
T Consensus       504 ~~~~Gd~v~~~V~~vd~~~~~i~LS~k  530 (565)
T PRK06299        504 VLKVGDEVEAKVINIDRKNRRISLSIK  530 (565)
T ss_pred             cCCCCCEEEEEEEEEccccCEEEEEee
Confidence            79999999999999996 477777764

>TIGR03591 polynuc_phos polyribonucleotide nucleotidyltransferase

Probab=100.00  E-value=9.2e-35  Score=352.22  Aligned_cols=213  Identities=21%  Similarity=0.316  Sum_probs=189.2

Q ss_pred             cCeEEEeCCC-CCCCcceEEEeCCeEEEEEEEeCCCchhhhccccCCCCceeEEEEEecCCCCcc-----ccccccCCCc
Q 002054          380 RPIYCESGNL-PILHGSSLFSRGDTQVLCTVTLGAPAEAQRLESLVGPPTKRFMLHYSFPPFCIN-----EVGKRVGLNR  453 (974)
Q Consensus       380 R~I~ie~g~l-~~a~GSal~~~G~T~Vl~~Vtl~~p~~~~~~d~~~~~~~~~~~v~~~f~p~s~~-----e~~~~~~~~r  453 (974)
                      |++++++|.+ ++|+|||++++|+|+|+|+|+  +|.+.+     .+.++.+++++|...+|+.+     ..+|.|.|++
T Consensus         5 R~i~ie~G~la~~AdGSa~v~~G~T~VlatV~--~~~~~~-----~~~df~pL~vey~e~~~A~gkipg~f~kReg~p~~   77 (684)
T TIGR03591         5 RTLTLETGKIARQADGAVVVRYGDTVVLVTVV--AAKEAK-----EGQDFFPLTVNYQEKFYAAGKIPGGFFKREGRPSE   77 (684)
T ss_pred             ccEEEEECCcCCCCCeEEEEEECCeEEEEEEE--cCCCCC-----CCCceEeEEEEEEehhhhccCCCCCcccCCCCCCH
Confidence            7999999999 579999999999999999999  665532     23456788889988777665     4567889999


Q ss_pred             hhhhHHHHHHHHhhhcCCCCCCCCeEEEEEEEEEcCCCChh--hHHHHHHHHHHHHcCCCccccccceeeeeeccCCCCC
Q 002054          454 REVGHGTLAEKALLAVLPPENDFPYTVRVNSEVMASDGSTS--MATVCGGSMALMDAGIPLQEHVAGVSVGLVSEVDPST  531 (974)
Q Consensus       454 re~~~~~l~eral~~vi~~~~~~p~tI~V~v~VLesdGs~~--~A~v~aa~lAL~dagvPi~~~vagvs~gli~~~d~~~  531 (974)
                      +|+.++++++|+|++++|  ..|.|.|+|+++||++||+.+  .||+||+++||+++|||++++|+||++|++++     
T Consensus        78 ~eil~srlIdR~lrplfp--~~~~~~i~V~~~VLs~Dg~~~~d~aai~aAsaAL~~s~IP~~~~v~av~vg~idg-----  150 (684)
T TIGR03591        78 KETLTSRLIDRPIRPLFP--KGFRNEVQVVATVLSYDPENDPDILAIIGASAALAISGIPFNGPIAAVRVGYIDG-----  150 (684)
T ss_pred             HHHHHHHHHhhHHHHhcC--CCCCceEEEEEEEEecCcCCchHHHHHHHHHHHHHhcCCCcCCCeEEEEEEEECC-----
Confidence            999999999999999999  579999999999999999974  49999999999999999999999999999965     


Q ss_pred             CcccceEEEecCCccccccCCccEEEEeeCCceEEEEeeccCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCCCCC
Q 002054          532 GEIKDYRILTDILGLEDHLGDMDFKIAGTRIGVTAIQLDIKPAGIPLDIICECLEHAHKGRLQILDHMEREISAPRTQDD  611 (974)
Q Consensus       532 ~~~~~~~iL~Dp~~~Ee~~~d~d~~Va~t~~gI~alq~~~k~~~i~~e~l~~al~~A~~~~~~I~~~m~~~i~~~~~~~~  611 (974)
                            .+++||+..|+..++++++|+++.+++++++..+  ..+++++|.+||+.|++++.+|++.|++.+++...++.
T Consensus       151 ------~~ildPt~~E~~~s~~~l~va~t~~~i~mie~~~--~~i~e~~l~~al~~a~~~~~~i~~~~~~~~~~~~~~k~  222 (684)
T TIGR03591       151 ------QYVLNPTVDELEKSDLDLVVAGTKDAVLMVESEA--KELSEEVMLGAIEFGHEEIQPVIEAIEELAEEAGKEKW  222 (684)
T ss_pred             ------EEEEcCCHHHHhhCCceEEEEccCCcEEEEEcCC--CCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCCc
Confidence                  6999999999999999999999998888888754  47999999999999999999999999999998876554


Q ss_pred             CCC
Q 002054          612 RNS  614 (974)
Q Consensus       612 ~~~  614 (974)
                      .+.
T Consensus       223 ~~~  225 (684)
T TIGR03591       223 EFV  225 (684)
T ss_pred             cCC
Confidence            443

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).

>TIGR00717 rpsA ribosomal protein S1

Probab=100.00  E-value=1.1e-34  Score=346.34  Aligned_cols=300  Identities=22%  Similarity=0.317  Sum_probs=253.8

Q ss_pred             EEecCHHHHHHHHHH-HHHHhhcccccCcEEEEEEEEEeeceEEEEEcCCeEEEEecccCCCccccccccccccCCEEEE
Q 002054          658 VVAKNRSVMEKVLEK-VDFIIGREIEVGGIYKGVVTSVKEYGAFVEFNGGQQGLLHVSELSHEPVSRVSDVVSVGQQLSL  736 (974)
Q Consensus       658 i~~~~~~~~~~a~~~-i~~l~~~~~~~G~i~~G~V~~i~~~G~fV~l~~g~~Glvhisels~~~v~~~~~~~~vGd~V~v  736 (974)
                      +..+.+..++.+.+. ..... ..+++|++++|+|+++.++|+||++ +|.+||+|.++++|.++.++.+.|++||.++|
T Consensus       162 iv~Srk~~l~~~~~~~~~~~~-~~l~~G~~v~g~V~~i~~~G~~V~l-~g~~g~lp~~e~s~~~~~~~~~~~~vG~~v~v  239 (516)
T TIGR00717       162 IVVSRRAYLEEERSQAREELL-ENLKEGDVVKGVVKNITDFGAFVDL-GGVDGLLHITDMSWKRVKHPSEYVKVGQEVKV  239 (516)
T ss_pred             EEEEHHHHHHHHHHHHHHHHH-HhccCCCEEEEEEEEEECCeEEEEE-CCEEEEEEHHHcCCCCCCCHHHhccCCCEEEE
Confidence            334455555544322 22322 5789999999999999999999999 58999999999999999999999999999999


Q ss_pred             EEEEEcc-CCceEEEEeccCCCcccc------cCce---------EEEEEeecCCcceeeEEeeccCCCCCCCCCCCCCC
Q 002054          737 RCIGQDV-RGNIKLSLKAVSPRPEAD------VKGV---------VEGSVPVNKQATDVWASVGDVSNGQNPELPMRKNE  800 (974)
Q Consensus       737 kVl~id~-~gri~LS~K~~~~~~~~~------~g~~---------~~G~vv~i~~gv~~~~~~~~l~~~~~~~lp~~~~~  800 (974)
                      +|+++|. ++++.||+|.+.++||..      .|..         .+|.++++.+|+.+|+|+++++|......|.    
T Consensus       240 ~Vl~~d~~~~~i~lS~k~~~~~p~~~~~~~~~~G~i~~g~V~~v~~~G~fV~l~~~v~g~v~~sels~~~~~~~~~----  315 (516)
T TIGR00717       240 KVIKFDKEKGRISLSLKQLGEDPWEAIEKKFPVGDKITGRVTNLTDYGVFVEIEEGIEGLVHVSEMSWVKKNSHPS----  315 (516)
T ss_pred             EEEEEECCCCcEEEEEEecchhHHHHHHhhccCCCEEEEEEEEeeCCcEEEEeCCCCEEEEEHHHcCCccccCCHH----
Confidence            9999998 689999999998888864      3444         4566777778999999999999864333332    


Q ss_pred             CCCcccCCCCcceEEEeecccccccccccccccccccccccccccccCCCCCCCcEEEEEec------------------
Q 002054          801 TPGVNSSTSSTPAVLIRSAAECDEEEKASGFSQSSKSTLKSTLASKSNSKPKKFTSQSDFFS------------------  862 (974)
Q Consensus       801 ~~~~~~~~G~~v~v~Ir~~l~iD~~~r~i~ls~k~~~~~~~~~~~~~~~~~~G~~v~g~V~~------------------  862 (974)
                         ..+++||.+.+.|   +++|++++++.||+++...+|  |......+++|++++|+|.+                  
T Consensus       316 ---~~~~vG~~v~v~V---~~id~~~~~i~lS~k~~~~~p--~~~~~~~~~~G~~v~g~V~~v~~~G~fV~l~~~v~glv  387 (516)
T TIGR00717       316 ---KVVKKGDEVEVMI---LDIDPERRRLSLGLKQCKANP--WEQFEEKHPVGDRVTGKIKKITDFGAFVELEGGIDGLI  387 (516)
T ss_pred             ---HhccCCCEEEEEE---EEEcCCCCEEEEEehhcccCc--HHHHHHhCCCCCEEEEEEEEEecceEEEECCCCCEEEE
Confidence               5689999999999   999999999999999888888  88887788899999999988                  


Q ss_pred             -----ccCcC---CCcccccCCeEEEEEEEeecCCCCcC-cccccccccc--ccccCCCCCEEEEEEEEEeCCeEEEEeC
Q 002054          863 -----STNIQ---KSTSFSQREREELAECLFGTEDGDED-NKGTRVEAIV--SAKNLKLGTKVAAKVYQVRARGLVLDLG  931 (974)
Q Consensus       863 -----~~~~~---~~~~~k~Gq~v~~~Vl~vd~e~~~i~-slK~~~~~p~--~~~~~~vG~vV~G~V~~I~~~GvFV~L~  931 (974)
                           +|...   ....|++||.|+++|+.+|++++++. |+|++..+||  ..+++++|++++|+|++++++|+||+|+
T Consensus       388 ~~s~ls~~~~~~~~~~~~~~G~~V~~~Vl~vd~~~~~i~ls~K~~~~~p~~~~~~~~~~G~~v~g~V~~v~~~G~fV~l~  467 (516)
T TIGR00717       388 HLSDISWDKDGREADHLYKKGDEIEAVVLAVDKEKKRISLGVKQLTENPWEKFAAKYKVGSVVKGKVTEIKDFGAFVELP  467 (516)
T ss_pred             EHHHCcCcccCCCHhHccCCCCEEEEEEEEEeCcCCEEEEeeccccCCchhhhhhccCcceEEEEEEEEEecceEEEEcC
Confidence                 45432   22579999999999999999999998 9999999999  4677999999999999999999999999


Q ss_pred             CCeEEEEecccCC-------CCCCCCCCEEEEEEEEEeC-CCceeeee
Q 002054          932 GGIRGMYRFENNE-------KKDFVVGDELLVKCSSFTG-KGIPVVSL  971 (974)
Q Consensus       932 ~gv~Glih~se~~-------~~~f~vGd~V~vkVl~id~-~~~~~~~~  971 (974)
                      +++.||||.++++       .+.|++||+|+|+|+++|. ++...+|+
T Consensus       468 ~~~~Glv~~s~l~~~~~~~~~~~~~~Gd~v~~~V~~id~~~~~i~ls~  515 (516)
T TIGR00717       468 GGVEGLIRNSELSENRDEDKTDEIKVGDEVEAKVVDIDKKNRKVSLSV  515 (516)
T ss_pred             CCeEEEEEHHHcCccccccccccCCCCCEEEEEEEEEeCCCCEEEEEE
Confidence            9999999999863       4579999999999999997 46666765

This model provides trusted hits to most long form (6 repeat) examples of RpsA. Among homologs with only four repeats are some to which other (perhaps secondary) functions have been assigned.

>COG0539 RpsA Ribosomal protein S1 [Translation, ribosomal structure and biogenesis]

Probab=100.00  E-value=3.2e-35  Score=338.36  Aligned_cols=286  Identities=19%  Similarity=0.214  Sum_probs=250.2

Q ss_pred             ecCHHHHHHHHHHHHHHhhcccccCcEEEEEEEEEeeceEEEEEcCCeEEEEecccCCCccccccccccccCCEEEEEEE
Q 002054          660 AKNRSVMEKVLEKVDFIIGREIEVGGIYKGVVTSVKEYGAFVEFNGGQQGLLHVSELSHEPVSRVSDVVSVGQQLSLRCI  739 (974)
Q Consensus       660 ~~~~~~~~~a~~~i~~l~~~~~~~G~i~~G~V~~i~~~G~fV~l~~g~~Glvhisels~~~v~~~~~~~~vGd~V~vkVl  739 (974)
                      +..+...++++..++    ..++.|++++|+|+...+.|+.|++. |++||+|.|+++..++++...+  +|.++.++++
T Consensus        86 S~~k~~~~~~w~~l~----~~~e~~~~V~~~v~~~vKGG~~Vdi~-gvr~FlP~S~v~~r~v~d~~~~--~Gk~~~~kii  158 (541)
T COG0539          86 SRRKAERERAWEKLE----EAFENGEIVEGKITGKVKGGLTVDIE-GVRAFLPGSLVDVRPVRDLDPL--IGKELEFKIL  158 (541)
T ss_pred             eHHHHHHHHhHHHHH----HHHhcCCeEEEEEEEEecCcEEEEEC-CEEEeccHHHhccccccccccc--CCceEEEEEE
Confidence            344455555655555    35689999999999999999999995 6999999999999999887765  5999999999


Q ss_pred             EEcc-CCceEEEEeccCCCccc----------ccC---------ceEEEEEeecCCcceeeEEeeccCCCCCCCCCCCCC
Q 002054          740 GQDV-RGNIKLSLKAVSPRPEA----------DVK---------GVVEGSVPVNKQATDVWASVGDVSNGQNPELPMRKN  799 (974)
Q Consensus       740 ~id~-~gri~LS~K~~~~~~~~----------~~g---------~~~~G~vv~i~~gv~~~~~~~~l~~~~~~~lp~~~~  799 (974)
                      ++|. ++++.+|+|++++....          +.|         .+.+|+|+++ .|++|++|+++|+|.+ ..+|.   
T Consensus       159 e~d~~~n~vv~SrR~~~e~~~~~~r~e~~~~l~~G~vV~G~V~~It~~GafVdi-gGvdGLlHiseiS~~r-v~~P~---  233 (541)
T COG0539         159 ELDKKRNNVVLSRRAVLEEERSEQREELLNKLEVGEVVEGVVKNITDYGAFVDI-GGVDGLLHISEISWKR-VDHPS---  233 (541)
T ss_pred             EEccccCcEEEEhHHHhhHHHHHHHHHHHhcCCCCceEEEEEEEeecCcEEEEe-cCeeeEEehhhccccc-cCCHH---
Confidence            9998 78999999988763222          123         4556777777 4599999999999987 56777   


Q ss_pred             CCCCcccCCCCcceEEEeecccccccccccccccccccccccccccccCCCCCCCcEEEEEec-----------------
Q 002054          800 ETPGVNSSTSSTPAVLIRSAAECDEEEKASGFSQSSKSTLKSTLASKSNSKPKKFTSQSDFFS-----------------  862 (974)
Q Consensus       800 ~~~~~~~~~G~~v~v~Ir~~l~iD~~~r~i~ls~k~~~~~~~~~~~~~~~~~~G~~v~g~V~~-----------------  862 (974)
                          +.+++||.|.|+|   +++|++++|++||+|++.++|  |....+.+++|+.+.|+|.+                 
T Consensus       234 ----~vvkvGd~VkvkV---i~~D~e~~RVsLSlK~l~~dP--w~~i~~~~~~g~~v~G~Vt~i~~~GafVei~~GvEGl  304 (541)
T COG0539         234 ----EVVKVGDEVKVKV---ISLDEERGRVSLSLKQLEEDP--WEGIEKKYPVGDKVEGKVTNLTDYGAFVEIEEGVEGL  304 (541)
T ss_pred             ----HhcccCCEEEEEE---EEEccCCCeEEEEehhcccCc--HHHHhhhcCCCCEEEEEEEEeecCcEEEEecCCccce
Confidence                8999999999999   999999999999999999999  99999999999999999988                 


Q ss_pred             ------ccCcC--CCcccccCCeEEEEEEEeecCCCCcC-cccccccccc--ccccCCCCCEEEEEEEEEeCCeEEEEeC
Q 002054          863 ------STNIQ--KSTSFSQREREELAECLFGTEDGDED-NKGTRVEAIV--SAKNLKLGTKVAAKVYQVRARGLVLDLG  931 (974)
Q Consensus       863 ------~~~~~--~~~~~k~Gq~v~~~Vl~vd~e~~~i~-slK~~~~~p~--~~~~~~vG~vV~G~V~~I~~~GvFV~L~  931 (974)
                            +|.+.  .+..+++||.|+++||++|+++++++ |+|++..+||  +...|++|++++|+|+++++||+||.|+
T Consensus       305 vhvSEisw~~~~~P~evv~~Gq~V~V~Vl~id~e~rRIsL~iKq~~~~pw~~~~~~~~~g~~v~g~v~~~t~~g~fv~le  384 (541)
T COG0539         305 VHVSEISWTKKNVPSEVVKVGQEVEVKVLDIDPERRRISLGLKQLKENPWEEFADKHPVGDVVEGKVKSITDFGAFVELE  384 (541)
T ss_pred             eechhhcccccCCHHHhcccCCEEEEEEEeeCchhceEEeeehhhhcChhhhhhhhcCCCCeEEEEEeeecccceEEccC
Confidence                  78654  34699999999999999999999999 9999999999  5677999999999999999999999999


Q ss_pred             CCeEEEEecccCC-------CCCCCCCCEEEEEEEEEeCCCc
Q 002054          932 GGIRGMYRFENNE-------KKDFVVGDELLVKCSSFTGKGI  966 (974)
Q Consensus       932 ~gv~Glih~se~~-------~~~f~vGd~V~vkVl~id~~~~  966 (974)
                      +|++||+|.+++.       ...|+.||+++++|+.+|.++.
T Consensus       385 ~gidG~vh~~d~sw~~~~~~~~~~k~Gd~v~~~vl~vd~~~~  426 (541)
T COG0539         385 GGIDGLVHLSDLSWDRPGEEAEKYKKGDEVEAKVLAVDKEKE  426 (541)
T ss_pred             CCccceEEHHhcCccccCcHHHhhccCcEEEEEEEEEecccc
Confidence            9999999999774       2379999999999999998854

>TIGR02065 ECX1 archaeal exosome-like complex exonuclease 1

Probab=100.00  E-value=8.4e-35  Score=311.43  Aligned_cols=203  Identities=19%  Similarity=0.311  Sum_probs=180.7

Q ss_pred             CeEEEEEeCccCcCCCcEEEEEeCCeEEEEEEEeCCC-CC----CCCceeeEeeccccccccCCCCCccccccCCCCchh
Q 002054           67 SRLITLETGKIARFANGAVVLGMDETKVLSTVTSSKG-DS----VRDFLPLTVDYQEKQFAQGVIPNTYMRREGAPKERE  141 (974)
Q Consensus        67 ~r~i~~etg~~a~~A~GSa~v~~G~T~Vl~tv~~~~~-~~----~~~f~pL~v~y~e~~~a~g~ip~~~~~Reg~p~~~e  141 (974)
                      =|++++++|.+ .+|||||++++|+|+|+|+|++|++ ..    ..++.+|+|+|....||.      +.+|+++|+++|
T Consensus        18 ~R~~~~~~g~~-~~a~GSa~~~~G~T~Vl~~V~gp~e~~~~~~~~~~~~~l~v~~~~~~~a~------~~~~~~~~~~~~   90 (230)
T TIGR02065        18 LRPIKIEAGVL-KNADGSAYVEFGGTKIIAAVYGPREMHPRHLQLPDRAVLRVRYHMAPFST------DERKRPGPSRRE   90 (230)
T ss_pred             ccCeEEEECCC-CCCCeEEEEEECCcEEEEEEeCCCccccccccCCCceEEEEEEEeCCccc------CCccCCCCCccH
Confidence            48899999999 8999999999999999999999876 22    246778999998877655      355568899999


Q ss_pred             hhHHHhhcCCccccccCCCCC--ceEEEEEEEeccCCCChhhHHHHHHHHHhhcCCCCCCCCeEEEEEEEECCEEEEcCC
Q 002054          142 LLVGRIIDRPIRPLFPAGFYH--EVQVMASVLSSDGKQDPDIMAANATSAALMLSDIPWGGPIGMIRIGRICGQFIVNPT  219 (974)
Q Consensus       142 il~~RlidR~lrplfp~~~~~--~~~i~~~vl~~dg~~~~~~~ai~aAs~AL~~s~iP~~~~v~av~vg~i~g~~vldPt  219 (974)
                      ++++|+|+|+|||+++.++++  .++|.++||+.||+..  ++|+|||++||++|||||+++|+||++|+++|++|+|||
T Consensus        91 ~~~s~~l~~~l~~~i~~~~~p~~~i~i~v~vl~~DG~~~--~aai~aa~lAL~dagIp~~~~v~avtv~~~~~~~v~Dpt  168 (230)
T TIGR02065        91 IEISKVIREALEPAILLEQFPRTAIDVFIEVLQADAGTR--CAGLTAASLALADAGIPMRDLVVGVAVGKVDGVVVLDLN  168 (230)
T ss_pred             HHHHHHHHHHHHHHhChhhcCCeEEEEEEEEEEcCCCHH--HHHHHHHHHHHHHcCCccccceeeEEEEEECCeEEECCC
Confidence            999999999999999988755  4555577999999754  999999999999999999999999999999999999999


Q ss_pred             HHHHhcCccceeEee--eCCeEEEEEecCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Q 002054          220 MDELSLSDLNLVYAC--TREKTLMIDVQAREISEKDLEAGLRLAHPEAVKYLEPQIRLAEKA  279 (974)
Q Consensus       220 ~~e~~~s~~~l~v~~--t~~~i~mie~~~~~~~e~~~~~al~~a~~~~~~i~~~~~~~~~~~  279 (974)
                      .+|++.++.+++|+.  +.+.++|+|..+ .+++++|.+||++|+++|++++++|++.+++.
T Consensus       169 ~~Ee~~~~~~l~va~~~~~~~i~~i~~~g-~~~~e~~~~~l~~a~~~~~~l~~~~~~~l~~~  229 (230)
T TIGR02065       169 EEEDMYGEADMPVAMMPKLGEITLLQLDG-DMTPDEFRQALDLAVKGIKIIYQIQREALKNK  229 (230)
T ss_pred             HHHhhcCCCceEEEEeCCCCCEEEEEEec-CcCHHHHHHHHHHHHHHHHHHHHHHHHHHHhh
Confidence            999999999999997  456699999998 69999999999999999999999999988653

This family contains the archaeal protein orthologous to the eukaryotic exosome protein Rrp41. It is somewhat more distantly related to the bacterial protein ribonuclease PH. An exosome-like complex has been demonstrated experimentally for the Archaea in Sulfolobus solfataricus, so members of this family are designated exosome complex exonuclease 1, after usage in SwissProt.

>COG0689 Rph RNase PH [Translation, ribosomal structure and biogenesis]

Probab=100.00  E-value=1.4e-34  Score=301.45  Aligned_cols=224  Identities=34%  Similarity=0.475  Sum_probs=201.6

Q ss_pred             HhcCCcCCCCCCCCccCeEEEeCCCCCCCcceEEEeCCeEEEEEEEeCCCchhhhccccCCCCceeEEEEEecCCCCccc
Q 002054          365 IAEGVRVDGRQLDEVRPIYCESGNLPILHGSSLFSRGDTQVLCTVTLGAPAEAQRLESLVGPPTKRFMLHYSFPPFCINE  444 (974)
Q Consensus       365 l~~~~R~DGR~~~e~R~I~ie~g~l~~a~GSal~~~G~T~Vl~~Vtl~~p~~~~~~d~~~~~~~~~~~v~~~f~p~s~~e  444 (974)
                      ..+++|+|||.++|+|+|.++.|++++++||++|++|+|+|+|+|+  ||.+.. ...+.++..+.++++|++.|||+.+
T Consensus         4 ~~~~~R~dgR~~delR~i~~~~~~~~~a~GS~~~~~G~tkVic~vs--Gp~e~~-p~~l~~~~~g~~t~ey~m~p~sT~~   80 (230)
T COG0689           4 SEDGMRPDGRKPDELRPIKITRGVLKHAEGSSLIEFGNTKVICTVS--GPREPV-PRFLRGTGKGWLTAEYGMLPRSTDE   80 (230)
T ss_pred             cccCcCCCCCCcccccceEEEeccccCCCccEEEEeCCeEEEEEEe--cCCCCC-ChhhcCCCceEEEEEEecccccccc
Confidence            4689999999999999999999999999999999999999999999  888743 3345567889999999999999966


Q ss_pred             cccccCCCc-hhhhHHHHHHHHhhhcCCCCCCCCe-EEEEEEEEEcCCCChhhHHHHHHHHHHHHcCCCccccccceeee
Q 002054          445 VGKRVGLNR-REVGHGTLAEKALLAVLPPENDFPY-TVRVNSEVMASDGSTSMATVCGGSMALMDAGIPLQEHVAGVSVG  522 (974)
Q Consensus       445 ~~~~~~~~r-re~~~~~l~eral~~vi~~~~~~p~-tI~V~v~VLesdGs~~~A~v~aa~lAL~dagvPi~~~vagvs~g  522 (974)
                      +.+. .+.+ |++++++++.++|++++.+ +.||. +|.|+++|++.||++..|+++|+++||+|||+||+++++|+|+|
T Consensus        81 R~~~-~~~~gR~~eisrli~~al~~~i~L-~~~p~~~I~i~~dVlqaDggTrta~It~A~lAL~DAgipl~~~vaaiSvg  158 (230)
T COG0689          81 RKKR-EADRGRTKEISRLIGRALRAVIDL-ELLPESTIDIDCDVLQADGGTRTASITGASLALADAGIPLRDLVAAISVG  158 (230)
T ss_pred             cccc-cccccchhHHHHHHHHHHHHHhhh-hhcCccEEEEEEEEEECCCCeeeehhhHHHHHHHHcCCchhhheeEeEEE
Confidence            5444 3444 9999999999999999999 79998 59999999999999999999999999999999999999999999


Q ss_pred             eeccCCCCCCcccceEEEecCCccccccCCccEEEEeeCCc-eEEEEeeccCCCCCHHHHHHHHHHHHHHHHHHHHHHHH
Q 002054          523 LVSEVDPSTGEIKDYRILTDILGLEDHLGDMDFKIAGTRIG-VTAIQLDIKPAGIPLDIICECLEHAHKGRLQILDHMER  601 (974)
Q Consensus       523 li~~~d~~~~~~~~~~iL~Dp~~~Ee~~~d~d~~Va~t~~g-I~alq~~~k~~~i~~e~l~~al~~A~~~~~~I~~~m~~  601 (974)
                      ++++           .+++|++..||..+..|.+|+.+.+| +.-+|.-...+.+++++|.++|+.|.+++.++.+.|++
T Consensus       159 i~~~-----------~~~lDl~~~Eds~~~~d~~v~~~~~~~~~ei~~~~~~~~~~~del~~lL~la~~g~~~~~~~~~~  227 (230)
T COG0689         159 IVDG-----------VIVLDLDYEEDSAAEADMNVVMTGNGGLVEIQGLAEDGPFTEDELLELLDLAIKGCNELRELQRE  227 (230)
T ss_pred             EECC-----------ceEecCcchhhcccccCceEEEEecCCeEEEEEEeccCCcCHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            9986           59999999999999888888877765 56666666667899999999999999999999999999


Q ss_pred             Hhc
Q 002054          602 EIS  604 (974)
Q Consensus       602 ~i~  604 (974)
                      +|.
T Consensus       228 al~  230 (230)
T COG0689         228 ALA  230 (230)
T ss_pred             HhC
Confidence            873

>PLN00207 polyribonucleotide nucleotidyltransferase; Provisional

Probab=100.00  E-value=6.7e-35  Score=352.01  Aligned_cols=217  Identities=23%  Similarity=0.310  Sum_probs=194.9

Q ss_pred             CeEEEEEeCccCcCCCcEEEEEeCCeEEEEEEE-eCCC-CCCCCceeeEeeccccccccCCCCCccc---cccCCCCchh
Q 002054           67 SRLITLETGKIARFANGAVVLGMDETKVLSTVT-SSKG-DSVRDFLPLTVDYQEKQFAQGVIPNTYM---RREGAPKERE  141 (974)
Q Consensus        67 ~r~i~~etg~~a~~A~GSa~v~~G~T~Vl~tv~-~~~~-~~~~~f~pL~v~y~e~~~a~g~ip~~~~---~Reg~p~~~e  141 (974)
                      -|++.+++|.++ .|+|||++++|+|+|||+|+ ++.+ ....+|+ +.++|.+++|..+++|..+.   +|+|+|++||
T Consensus       448 iRpI~~e~G~Lp-~A~GSAlf~~G~TqVLatVtlGp~~~~q~~d~l-~~~~~~~~f~~~y~fPPfs~ge~~r~g~psrRE  525 (891)
T PLN00207        448 IRPINSSCGLLP-RAHGSALFTRGETQALAVVTLGDKQMAQRIDNL-VDADEVKRFYLQYSFPPSCVGEVGRIGAPSRRE  525 (891)
T ss_pred             cceEEEEeCCcC-CCCceEEEEECCeEEEEEEEecCcccccccccc-ccccceeeEEEEEEcCCCCCccccCCCCCCHHH
Confidence            478999999995 59999999999999999997 6655 4455666 78899999999999999765   8899999999


Q ss_pred             hhHHHhhcCCccccccCC--CCCceEEEEEEEeccCCCChhhHHHHHHHHHhhcCCCCCCCCeEEEEEEEE-C-------
Q 002054          142 LLVGRIIDRPIRPLFPAG--FYHEVQVMASVLSSDGKQDPDIMAANATSAALMLSDIPWGGPIGMIRIGRI-C-------  211 (974)
Q Consensus       142 il~~RlidR~lrplfp~~--~~~~~~i~~~vl~~dg~~~~~~~ai~aAs~AL~~s~iP~~~~v~av~vg~i-~-------  211 (974)
                      ++++||++|+|||+||..  |.+.++|+++||++||+.+  +||+||||+||++|||||+++|+||+||++ +       
T Consensus       526 i~hg~L~eRALrpvip~~~~fP~tIrV~~~VLesDGSss--mAaV~aaSLALmDAGIPmk~~VAGvsvGli~d~~~~~~~  603 (891)
T PLN00207        526 IGHGMLAERALEPILPSEDDFPYTIRVESTITESNGSSS--MASVCGGCLALQDAGVPVKCPIAGIAMGMVLDTEEFGGD  603 (891)
T ss_pred             HHHHHHHHHHHHHhCCcccCCCEEEEEEEEEEeCCCChH--HHHHHHHHHHHHhcCCCccCceeEEEEEEEecccccCCC
Confidence            999999999999999976  9999999999999999966  999999999999999999999999999999 3       


Q ss_pred             CEE--EEcCCHHHHhcCccceeEeeeCCeEEEEEecC--CCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCcccccc
Q 002054          212 GQF--IVNPTMDELSLSDLNLVYACTREKTLMIDVQA--REISEKDLEAGLRLAHPEAVKYLEPQIRLAEKAGKQKKEYK  287 (974)
Q Consensus       212 g~~--vldPt~~e~~~s~~~l~v~~t~~~i~mie~~~--~~~~e~~~~~al~~a~~~~~~i~~~~~~~~~~~g~~k~~~~  287 (974)
                      |++  ++||+..|+..+++||.|+||.++|+|+|+++  ++++++.|.+||++|++++..|++.|++.+.+-.++...+.
T Consensus       604 g~~~IL~Dp~g~Ed~~gdmDfkVAgT~~gIt~iqmd~k~~gis~e~l~eAL~~A~~g~~~Il~~M~~~i~~pr~~~s~~a  683 (891)
T PLN00207        604 GSPLILSDITGSEDASGDMDFKVAGNEDGITAFQMDIKVGGITLPIMERALLQAKDGRKHILAEMSKCSPPPSKRLSKYA  683 (891)
T ss_pred             CcEEEEeCCCHHHHhcCCceEEEEecccceEEEEEecccCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHhhhhhhhcccC
Confidence            354  46999999999999999999999999999854  56899999999999999999999999999877655444443

>PRK13806 rpsA 30S ribosomal protein S1; Provisional

Probab=100.00  E-value=2.2e-33  Score=330.69  Aligned_cols=277  Identities=14%  Similarity=0.078  Sum_probs=238.3

Q ss_pred             cccccCcEEEEEEEEEeeceEEEEEcCCeEEEEecccCCCccccccccccccCCEEEEEEEEEcc-CCceEEEEeccCCC
Q 002054          679 REIEVGGIYKGVVTSVKEYGAFVEFNGGQQGLLHVSELSHEPVSRVSDVVSVGQQLSLRCIGQDV-RGNIKLSLKAVSPR  757 (974)
Q Consensus       679 ~~~~~G~i~~G~V~~i~~~G~fV~l~~g~~Glvhisels~~~v~~~~~~~~vGd~V~vkVl~id~-~gri~LS~K~~~~~  757 (974)
                      ..++.|++++|+|+++.++|++|++. |..||+|.|++++.+..++...  +|+.++|+|+++|. ++++.||+|+++..
T Consensus       111 ~~~~~g~~v~g~V~~~~~~G~~V~i~-g~~~flP~s~~~~~~~~~~~~~--vG~~i~~~V~~id~~~~~v~lSrk~~~~~  187 (491)
T PRK13806        111 EAYENGVPVEGKVTGTCKGGFNVEVL-GRRAFCPVSQIDLRYVEDPESY--VGQTFQFLITRVEENGRNIVVSRRALLER  187 (491)
T ss_pred             HHHhCCCEEEEEEEEEEcCCEEEEEC-CEEEEEEHHHhccccCCChHHc--CCCeEEEEEEEEECCCCeEEEEeehhhhh
Confidence            45789999999999999999999995 8999999999999988888774  89999999999998 67999999988643


Q ss_pred             ----ccc------ccCce---------EEEEEeecCCcceeeEEeeccCCCCCCCCCCCCCCCCCcccCCCCcceEEEee
Q 002054          758 ----PEA------DVKGV---------VEGSVPVNKQATDVWASVGDVSNGQNPELPMRKNETPGVNSSTSSTPAVLIRS  818 (974)
Q Consensus       758 ----~~~------~~g~~---------~~G~vv~i~~gv~~~~~~~~l~~~~~~~lp~~~~~~~~~~~~~G~~v~v~Ir~  818 (974)
                          +|.      +.|..         .+|.|+++..|+++|+|+++++|.+. ..|.       +.+++||.+.++|  
T Consensus       188 ~~~~~~~~~~~~l~~G~iv~G~V~~v~~~G~fV~l~~gv~g~v~~sels~~~~-~~~~-------~~~~vGd~i~vkV--  257 (491)
T PRK13806        188 EQKEALEAFMETVKEGDVVEGTVTRLAPFGAFVELAPGVEGMVHISELSWSRV-QKAD-------EAVSVGDTVRVKV--  257 (491)
T ss_pred             hhHHHHHHHHhhCCCCCEEEEEEEEEeCCeEEEEcCCCcEEEEEHHHCCCccc-cChh-------HhcCCCCEEEEEE--
Confidence                222      13433         45677777778999999999999753 2333       6789999999999  


Q ss_pred             cccccccc----cccccccccccccccccccccCCCCCCCcEEEEEec-----------------------ccCcC---C
Q 002054          819 AAECDEEE----KASGFSQSSKSTLKSTLASKSNSKPKKFTSQSDFFS-----------------------STNIQ---K  868 (974)
Q Consensus       819 ~l~iD~~~----r~i~ls~k~~~~~~~~~~~~~~~~~~G~~v~g~V~~-----------------------~~~~~---~  868 (974)
                       +++|+++    +++.||+++..++|  |......+++|+++.|.|.+                       +|...   .
T Consensus       258 -l~id~~~~~~~~ri~lS~K~~~~~p--~~~~~~~~~~G~~v~G~V~~v~~~G~fV~l~~gv~Glvh~sels~~~~~~~~  334 (491)
T PRK13806        258 -LGIERAKKGKGLRISLSIKQAGGDP--WDTVGDRLKAGDKVTGKVVRLAPFGAFVEILPGIEGLVHVSEMSWTRRVNKP  334 (491)
T ss_pred             -EEEecccCCcceEEEEEehhhhccc--chhhhccCCCCCEEEEEEEEEeCceEEEEeCCCcEEEEEHHHcCcccccCCH
Confidence             9999987    47999999998888  99999999999999999988                       56432   2


Q ss_pred             CcccccCCeEEEEEEEeecCCCCcC-cccccccccc--ccccCCCCCEEEEEEEEEeCCeEEEEeCCCeEEEEecccCC-
Q 002054          869 STSFSQREREELAECLFGTEDGDED-NKGTRVEAIV--SAKNLKLGTKVAAKVYQVRARGLVLDLGGGIRGMYRFENNE-  944 (974)
Q Consensus       869 ~~~~k~Gq~v~~~Vl~vd~e~~~i~-slK~~~~~p~--~~~~~~vG~vV~G~V~~I~~~GvFV~L~~gv~Glih~se~~-  944 (974)
                      ...|++||.|+++|+++|++++++. |+|++..+||  ...+|++|++|+|+|+++++||+||++++|+.||||.++++ 
T Consensus       335 ~~~~~~Gd~v~vkVl~iD~e~~ri~Ls~K~~~~~p~~~~~~~~~vG~~v~G~V~~i~~~G~FV~l~~gv~Gli~~se~s~  414 (491)
T PRK13806        335 EDVVAPGDAVAVKIKDIDPAKRRISLSLRDAEGDPWADVAERFAPGTTVTGTVEKRAQFGLFVNLAPGVTGLLPASVISR  414 (491)
T ss_pred             HHcCCCCCEEEEEEEEEEccCCEEEEEEeecccChhHHhhhhCCCCCEEEEEEEEEecCceEEEcCCCcEEEEEHHHcCc
Confidence            3479999999999999999999999 9999999999  47799999999999999999999999999999999999874 


Q ss_pred             ------CCCCCCCCEEEEEEEEEeCCC-ceeeee
Q 002054          945 ------KKDFVVGDELLVKCSSFTGKG-IPVVSL  971 (974)
Q Consensus       945 ------~~~f~vGd~V~vkVl~id~~~-~~~~~~  971 (974)
                            .+.|++||+|+|+|+++|+++ +..+|+
T Consensus       415 ~~~~~~~~~~~~Gd~v~~~V~~id~e~~ri~Ls~  448 (491)
T PRK13806        415 AGKPATYEKLKPGDSVTLVVEEIDTAKRKISLAP  448 (491)
T ss_pred             ccccchhhcCCCCCEEEEEEEEEeCCCCEEEEEe
Confidence                  357999999999999999765 444443

>PRK00173 rph ribonuclease PH; Reviewed

Probab=100.00  E-value=1.6e-33  Score=302.75  Aligned_cols=201  Identities=20%  Similarity=0.273  Sum_probs=178.9

Q ss_pred             CeEEEEEeCccCcCCCcEEEEEeCCeEEEEEEEeCCC-CC---CCCceeeEeeccccccccCCCCCccccc------cCC
Q 002054           67 SRLITLETGKIARFANGAVVLGMDETKVLSTVTSSKG-DS---VRDFLPLTVDYQEKQFAQGVIPNTYMRR------EGA  136 (974)
Q Consensus        67 ~r~i~~etg~~a~~A~GSa~v~~G~T~Vl~tv~~~~~-~~---~~~f~pL~v~y~e~~~a~g~ip~~~~~R------eg~  136 (974)
                      =|++++++|.+ ++|+|||++++|+|+|+|+|+++.+ |.   ..+..+|+|+|.-.       |..+.+|      .|+
T Consensus        11 ~R~i~~~~g~~-~~a~GSa~v~~G~T~Vla~V~~~~~~p~~~~~~~~g~l~v~~~~~-------p~a~~~~~~~~~~~g~   82 (238)
T PRK00173         11 LRPVTITRNFT-KHAEGSVLVEFGDTKVLCTASVEEGVPRFLKGQGQGWVTAEYGML-------PRATHTRNDREAAKGK   82 (238)
T ss_pred             ccCeEEEeCCC-CCCCeeEEEEecCcEEEEEEEcCCCCCCccCCCCcEEEEEEEecC-------CCCCcccccccccCCC
Confidence            48899999998 8999999999999999999998776 42   34678999999544       4444444      378


Q ss_pred             CCchhhhHHHhhcCCccccccCCCCCc--eEEEEEEEeccCCCChhhHHHHHHHHHhhcC-----------CCCCCCCeE
Q 002054          137 PKERELLVGRIIDRPIRPLFPAGFYHE--VQVMASVLSSDGKQDPDIMAANATSAALMLS-----------DIPWGGPIG  203 (974)
Q Consensus       137 p~~~eil~~RlidR~lrplfp~~~~~~--~~i~~~vl~~dg~~~~~~~ai~aAs~AL~~s-----------~iP~~~~v~  203 (974)
                      |++++++++|+|+|+|||+||..++++  ++|+++||++||+..  .||+|||++||+++           ++||+++++
T Consensus        83 ~~~~~~~~sr~i~r~lr~~i~l~~l~~~~i~v~v~VL~~DG~~~--~aai~Aa~~AL~da~~~~~~~~~~~~ip~~~~~~  160 (238)
T PRK00173         83 QGGRTQEIQRLIGRSLRAVVDLKALGERTITIDCDVIQADGGTR--TASITGAYVALADALNKLVARGKLKKNPLKDQVA  160 (238)
T ss_pred             CCccHHHHHHHHHHHHHHhcCHHHcCCeEEEEEEEEEeCCCCHH--HHHHHHHHHHHHHhhhhhhccCcccCCcccCcee
Confidence            999999999999999999999877766  899999999999985  99999999999977           999999999


Q ss_pred             EEEEEEECCEEEEcCCHHHHhcCccceeEeeeCCe-EEEEEe--cCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 002054          204 MIRIGRICGQFIVNPTMDELSLSDLNLVYACTREK-TLMIDV--QAREISEKDLEAGLRLAHPEAVKYLEPQIRLAE  277 (974)
Q Consensus       204 av~vg~i~g~~vldPt~~e~~~s~~~l~v~~t~~~-i~mie~--~~~~~~e~~~~~al~~a~~~~~~i~~~~~~~~~  277 (974)
                      +|++|+++|++|+|||.+|++.++.+|+|+++.++ |+|++.  ++..+++++|.+|+++|++.+++++++|++.++
T Consensus       161 ~vt~~~~~~~~lvDpt~~Ee~~~~~~l~v~~~~~~~i~~v~~~g~g~~~~~e~l~~~i~~A~~~~~~l~~~~~~~l~  237 (238)
T PRK00173        161 AVSVGIVDGEPVLDLDYEEDSAAETDMNVVMTGSGGFVEVQGTAEGAPFSREELDALLDLAEKGIAELVALQKAALA  237 (238)
T ss_pred             EEEEEEECCEEEECCCHHHHhcCCceEEEEECCCCCEEEEEccCCCCCcCHHHHHHHHHHHHHHHHHHHHHHHHHhc
Confidence            99999999999999999999999999999999865 999997  355799999999999999999999999988664

>PRK07899 rpsA 30S ribosomal protein S1; Reviewed

Probab=100.00  E-value=3.2e-33  Score=324.76  Aligned_cols=281  Identities=19%  Similarity=0.166  Sum_probs=235.6

Q ss_pred             cccccCcEEEEEEEEEeeceEEEEEcCCeEEEEecccCCCccccccccccccCCEEEEEEEEEcc-CCceEEEEeccC-C
Q 002054          679 REIEVGGIYKGVVTSVKEYGAFVEFNGGQQGLLHVSELSHEPVSRVSDVVSVGQQLSLRCIGQDV-RGNIKLSLKAVS-P  756 (974)
Q Consensus       679 ~~~~~G~i~~G~V~~i~~~G~fV~l~~g~~Glvhisels~~~v~~~~~~~~vGd~V~vkVl~id~-~gri~LS~K~~~-~  756 (974)
                      ..++.|++++|+|+++.++|+||+|.++.+|+||.+|+++.+..++++.|++||.|+|+|+++|. +|++.||+|.+. .
T Consensus        31 ~~~~~GdiV~G~V~~v~~~gv~VdIg~k~eG~Ip~~Els~~~~~~~~~~~~vGd~Ie~~V~~~~~~~g~liLS~k~~~~~  110 (486)
T PRK07899         31 KYFNDGDIVEGTVVKVDRDEVLLDIGYKTEGVIPSRELSIKHDVDPNEVVEVGDEVEALVLQKEDKEGRLILSKKRAQYE  110 (486)
T ss_pred             hcCCCCCEEEEEEEEEECCcEEEEECCCcEEEEEHHHhcccccCChhhcCCCCCEEEEEEEEEECCCCeEEEEehhhccc
Confidence            46899999999999999999999998889999999999999999999999999999999999986 689999999875 5


Q ss_pred             Ccccc------cCceEEEEEeecCC-------cceeeEEeeccCCCCCCCCCCCCCCCCCcccCCCCcceEEEeeccccc
Q 002054          757 RPEAD------VKGVVEGSVPVNKQ-------ATDVWASVGDVSNGQNPELPMRKNETPGVNSSTSSTPAVLIRSAAECD  823 (974)
Q Consensus       757 ~~~~~------~g~~~~G~vv~i~~-------gv~~~~~~~~l~~~~~~~lp~~~~~~~~~~~~~G~~v~v~Ir~~l~iD  823 (974)
                      .+|..      .|..+.|+|+.+..       |+++|+|.+++++.+...+         . -.+|+.+.++|   +++|
T Consensus       111 ~~w~~ie~~~e~g~~V~G~V~~v~k~G~~VdlGi~gflP~Sel~~~~~~~~---------~-~~vGq~V~vkV---leid  177 (486)
T PRK07899        111 RAWGTIEKIKEKDGVVTGTVIEVVKGGLILDIGLRGFLPASLVEMRRVRDL---------Q-PYIGQEIEAKI---IELD  177 (486)
T ss_pred             chHHHHHHHhcCCCEEEEEEEEEECCeEEEEECCEEEEEhhHhcccccCCh---------h-hcCCCEEEEEE---EEEE
Confidence            66764      35555555444322       7999999999988542111         1 14899999999   9999


Q ss_pred             cccccccccccccccc--ccccccccCCCCCCCcEEEEEec----------------------ccCc--CCCcccccCCe
Q 002054          824 EEEKASGFSQSSKSTL--KSTLASKSNSKPKKFTSQSDFFS----------------------STNI--QKSTSFSQRER  877 (974)
Q Consensus       824 ~~~r~i~ls~k~~~~~--~~~~~~~~~~~~~G~~v~g~V~~----------------------~~~~--~~~~~~k~Gq~  877 (974)
                      ++++++.||.+...+.  ...|......+++|++++|.|++                      +|..  +.+..|++||.
T Consensus       178 ~~~~~ivLSrr~~l~~~~~~~~~~~~~~lk~G~iv~G~V~~i~~~G~FVdlggv~Glv~~Sels~~~v~~~~~~~kvGd~  257 (486)
T PRK07899        178 KNRNNVVLSRRAWLEQTQSEVRSEFLNQLQKGQVRKGVVSSIVNFGAFVDLGGVDGLVHVSELSWKHIDHPSEVVEVGQE  257 (486)
T ss_pred             CCCCEEEEEhHHHHHhhhHHHHHHHHHhccCCCEEEEEEEEEECCeEEEEECCEEEEEEHHHCCCcccCCHHHhcCCCCE
Confidence            9999999999854321  12266777788999999999988                      5643  23357999999


Q ss_pred             EEEEEEEeecCCCCcC-cccccccccc--ccccCCCCCEEEEEEEEEeCCeEEEEeCCCeEEEEecccCCC-------CC
Q 002054          878 EELAECLFGTEDGDED-NKGTRVEAIV--SAKNLKLGTKVAAKVYQVRARGLVLDLGGGIRGMYRFENNEK-------KD  947 (974)
Q Consensus       878 v~~~Vl~vd~e~~~i~-slK~~~~~p~--~~~~~~vG~vV~G~V~~I~~~GvFV~L~~gv~Glih~se~~~-------~~  947 (974)
                      |+++|+.+|++++++. |+|++..+||  ...++++|++++|+|++|++||+||+|.+|+.||+|+++++.       +.
T Consensus       258 V~vkVl~iD~e~~rI~LSlK~~~~dPw~~~~~~~~vG~vv~G~V~~I~~fGvFVeL~~gieGLvh~SeLs~~~v~~~~~~  337 (486)
T PRK07899        258 VTVEVLDVDMDRERVSLSLKATQEDPWQQFARTHAIGQIVPGKVTKLVPFGAFVRVEEGIEGLVHISELAERHVEVPEQV  337 (486)
T ss_pred             EEEEEEEEECCCCEEEEEEeeccccchhhhHHhcCCCCEEEEEEEEEeccEEEEEeCCCcEEEEEHHHcCcccccCccce
Confidence            9999999999999998 9999999999  456789999999999999999999999999999999998752       35


Q ss_pred             CCCCCEEEEEEEEEeC-CCceeeeec
Q 002054          948 FVVGDELLVKCSSFTG-KGIPVVSLV  972 (974)
Q Consensus       948 f~vGd~V~vkVl~id~-~~~~~~~~~  972 (974)
                      |++||+|+|+|+++|. +++..+|+.
T Consensus       338 ~kvGd~V~VkIi~ID~e~rrI~LSlK  363 (486)
T PRK07899        338 VQVGDEVFVKVIDIDLERRRISLSLK  363 (486)
T ss_pred             eCCCCEEEEEEEEEECCCCEEEEEEE
Confidence            8999999999999995 566667764

>KOG1068 consensus Exosomal 3'-5' exoribonuclease complex, subunit Rrp41 and related exoribonucleases [Translation, ribosomal structure and biogenesis]

Probab=100.00  E-value=3.1e-33  Score=289.34  Aligned_cols=225  Identities=27%  Similarity=0.425  Sum_probs=204.2

Q ss_pred             HHhcCCcCCCCCCCCccCeEEEeCCCCCCCcceEEEeCCeEEEEEEEeCCCchhhhccccCCCCceeEEEEEecCCCCcc
Q 002054          364 IIAEGVRVDGRQLDEVRPIYCESGNLPILHGSSLFSRGDTQVLCTVTLGAPAEAQRLESLVGPPTKRFMLHYSFPPFCIN  443 (974)
Q Consensus       364 il~~~~R~DGR~~~e~R~I~ie~g~l~~a~GSal~~~G~T~Vl~~Vtl~~p~~~~~~d~~~~~~~~~~~v~~~f~p~s~~  443 (974)
                      +-++|.|.|||.++|+|+|.+..|++.+++|||++++|||+|+|.|+  ||++.+..... .++...+++.|++.+|+++
T Consensus         8 ~seeg~r~dgRr~~elR~i~~~~g~~~~a~GSay~E~GnTKVl~aV~--GPre~~~~~~~-~~~~a~lnc~~~~a~Fst~   84 (245)
T KOG1068|consen    8 LSEEGLRTDGRRPNELRRIYARIGVLTQADGSAYMEQGNTKVLCAVY--GPREIRGKSAR-RPDKAVLNCEVSSAQFSTG   84 (245)
T ss_pred             cCccccccCCCChhHhhhhhhhcCccccCCccchhhcCCeEEEEEEe--CCccccccccc-ccccceEEEEEeeeccccc
Confidence            45799999999999999999999999999999999999999999999  99997643333 5677889999999999999


Q ss_pred             ccccccCCCchhhhHHHHHHHHhhhcCCCCCCCCe-EEEEEEEEEcCCCChhhHHHHHHHHHHHHcCCCccccccceeee
Q 002054          444 EVGKRVGLNRREVGHGTLAEKALLAVLPPENDFPY-TVRVNSEVMASDGSTSMATVCGGSMALMDAGIPLQEHVAGVSVG  522 (974)
Q Consensus       444 e~~~~~~~~rre~~~~~l~eral~~vi~~~~~~p~-tI~V~v~VLesdGs~~~A~v~aa~lAL~dagvPi~~~vagvs~g  522 (974)
                      ++++....++|+.+++.+++++|+++|.. +.||+ +|.|.++||++||+.+.||+||+++||.||||||++++.|+++|
T Consensus        85 ~r~~~~~~~rr~~e~s~~L~~afe~~I~~-~lyPrsqIDI~v~VleddG~~laa~inaatlAL~daGI~m~D~i~~~t~~  163 (245)
T KOG1068|consen   85 DRKKRPKGDRREKELSLMLQQAFEPVILL-ELYPRSQIDIYVQVLEDDGSNLAAAINAATLALADAGIPMYDLITACTAG  163 (245)
T ss_pred             hhccCCCccHHHHHHHHHHHHHHHHHHHh-hhCccccceEEEEEEECCCccHHHHHHHHHHHHHHcCCChhhhhhhceee
Confidence            98877777899999999999999999998 79999 59999999999999999999999999999999999999999999


Q ss_pred             eeccCCCCCCcccceEEEecCCccccccCCccEEEE--eeCCceEEEEeeccCCCCCHHHHHHHHHHHHHHHHHHHHHHH
Q 002054          523 LVSEVDPSTGEIKDYRILTDILGLEDHLGDMDFKIA--GTRIGVTAIQLDIKPAGIPLDIICECLEHAHKGRLQILDHME  600 (974)
Q Consensus       523 li~~~d~~~~~~~~~~iL~Dp~~~Ee~~~d~d~~Va--~t~~gI~alq~~~k~~~i~~e~l~~al~~A~~~~~~I~~~m~  600 (974)
                      +.++           ..++|++..||......++|+  ++.+.|..+|++.+   ++.+.|...++.|.++|+++.+.|+
T Consensus       164 l~~~-----------~~l~Dl~~~eesa~~~~ltVa~l~~~~~i~~l~~~~~---~~~d~l~~vl~~a~~~c~~v~~~l~  229 (245)
T KOG1068|consen  164 LADG-----------TPLLDLTSLEESARAPGLTVAALPNREEIALLQLDER---LHCDHLETVLELAIAGCKRVYERLR  229 (245)
T ss_pred             ecCC-----------ccccccccchhhccCCceEEEEecCcceEEEEEecCC---CCHHHHHHHHHHHHHHHHHHHHHHH
Confidence            9975           699999999998877667776  55666999999864   9999999999999999999999999


Q ss_pred             HHhcCC
Q 002054          601 REISAP  606 (974)
Q Consensus       601 ~~i~~~  606 (974)
                      ..+.+.
T Consensus       230 ~~l~~~  235 (245)
T KOG1068|consen  230 LVLREH  235 (245)
T ss_pred             HHHHHH
Confidence            887653

>TIGR01966 RNasePH ribonuclease PH

Probab=100.00  E-value=4.9e-32  Score=291.12  Aligned_cols=203  Identities=21%  Similarity=0.250  Sum_probs=173.4

Q ss_pred             CeEEEEEeCccCcCCCcEEEEEeCCeEEEEEEEeCCC-CCC---CCceeeEeeccccccccCCCCCcccccc---CCCCc
Q 002054           67 SRLITLETGKIARFANGAVVLGMDETKVLSTVTSSKG-DSV---RDFLPLTVDYQEKQFAQGVIPNTYMRRE---GAPKE  139 (974)
Q Consensus        67 ~r~i~~etg~~a~~A~GSa~v~~G~T~Vl~tv~~~~~-~~~---~~f~pL~v~y~e~~~a~g~ip~~~~~Re---g~p~~  139 (974)
                      =|++++++|.+ ++|+|||++++|+|+|||+|+++.. |..   .+..+|+|+|.-..+|..    .+.+|+   |+|++
T Consensus        10 ~R~i~i~~G~~-~~A~GSa~v~~G~T~Vla~V~~~~~~p~~~~~~~~g~l~v~~~~~p~a~~----~~~~r~~~~g~~~~   84 (236)
T TIGR01966        10 LRPVSITRDFL-KHAEGSVLIEFGNTKVLCTASVEEKVPPFLRGSGEGWITAEYGMLPRATQ----TRNRRESAKGKQSG   84 (236)
T ss_pred             ccCeEEEeCCc-CCCCceEEEEecCCEEEEEEEccCccCCcccCCCcEEEEEEEecCCCCCC----CCccccccCCCCCc
Confidence            48899999976 9999999999999999999997665 321   245678888854443331    112444   78888


Q ss_pred             hhhhHHHhhcCCccccccCCCCCce--EEEEEEEeccCCCChhhHHHHHHHHHhhcC-----------CCCCCCCeEEEE
Q 002054          140 RELLVGRIIDRPIRPLFPAGFYHEV--QVMASVLSSDGKQDPDIMAANATSAALMLS-----------DIPWGGPIGMIR  206 (974)
Q Consensus       140 ~eil~~RlidR~lrplfp~~~~~~~--~i~~~vl~~dg~~~~~~~ai~aAs~AL~~s-----------~iP~~~~v~av~  206 (974)
                      ++++++|+|+|+|||+|+.+++++.  +|+++||++||+..  +||+|||++||+++           +|||++++++|+
T Consensus        85 ~~~e~~~~i~r~lr~~i~l~~l~~~~i~I~v~VL~~DG~~~--~aai~Aa~aAL~da~~~~~~~~~~~~ip~~~~~~~vt  162 (236)
T TIGR01966        85 RTQEIQRLIGRALRAVVDLEALGERTIWIDCDVIQADGGTR--TASITGAFVALADAISKLHKRGILKESPIRDFVAAVS  162 (236)
T ss_pred             cHHHHHHHHHHHHHHhcCHhhcCCeEEEEEEEEEeCCCCHH--HHHHHHHHHHHHHHHHhhhhcCcccCCCccCceeEEE
Confidence            9999999999999999998777666  88999999999885  99999999999977           999999999999


Q ss_pred             EEEECCEEEEcCCHHHHhcCccceeEeeeCCe-EEEEEec--CCCCCHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 002054          207 IGRICGQFIVNPTMDELSLSDLNLVYACTREK-TLMIDVQ--AREISEKDLEAGLRLAHPEAVKYLEPQIRLA  276 (974)
Q Consensus       207 vg~i~g~~vldPt~~e~~~s~~~l~v~~t~~~-i~mie~~--~~~~~e~~~~~al~~a~~~~~~i~~~~~~~~  276 (974)
                      +|++++++|+|||.+|++.++.+|+++.+.++ |+|+|..  +..+++++|.+|+++|+++++++++.|++.+
T Consensus       163 ~~~~~~~~v~Dpt~~Ee~~~~~~l~l~~~~~~~i~~i~~~g~~~~~~~~~l~~~i~~a~~~~~~l~~~~~~~l  235 (236)
T TIGR01966       163 VGIVDGEPVLDLDYEEDSAADVDMNVVMTGSGGFVEVQGTAEEGPFSRDELNKLLDLAKKGIRELIELQKQAL  235 (236)
T ss_pred             EEEECCEEEECCChhHHhccCceEEEEEcCCCCEEEEEecCCCCCcCHHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence            99999999999999999998777777777655 9999973  5789999999999999999999999988754

This bacterial enzyme, ribonuclease PH, performs the final 3'-trimming and modification of tRNA precursors. This model is restricted absolutely to bacteria. Related families outside the model include proteins described as probable exosome complex exonucleases (rRNA processing) and polyribonucleotide nucleotidyltransferases (mRNA degradation). The most divergent member within the family is RNase PH from Deinococcus radiodurans.

>PRK03983 exosome complex exonuclease Rrp41; Provisional

Probab=100.00  E-value=4e-32  Score=293.31  Aligned_cols=204  Identities=18%  Similarity=0.310  Sum_probs=175.8

Q ss_pred             CeEEEEEeCccCcCCCcEEEEEeCCeEEEEEEEeCCC-CCCCCc----eeeEeeccccccccCCCCCccccccCCCCchh
Q 002054           67 SRLITLETGKIARFANGAVVLGMDETKVLSTVTSSKG-DSVRDF----LPLTVDYQEKQFAQGVIPNTYMRREGAPKERE  141 (974)
Q Consensus        67 ~r~i~~etg~~a~~A~GSa~v~~G~T~Vl~tv~~~~~-~~~~~f----~pL~v~y~e~~~a~g~ip~~~~~Reg~p~~~e  141 (974)
                      =|++++++|.+ ++|||||++++|+|+|+|+|++|++ ......    ..|.+.|.-..++.     . .+++++|++++
T Consensus        24 ~R~i~i~~G~l-~~a~GSa~v~~G~T~Vl~~V~gp~e~~~~~~~~~~~~~l~v~~~~~p~~~-----~-~~~~~~~~~~~   96 (244)
T PRK03983         24 LRPIKIEVGVL-KNADGSAYLEWGNNKIIAAVYGPREMHPRHLQLPDRAVLRVRYNMAPFSV-----D-ERKRPGPDRRS   96 (244)
T ss_pred             ccceEEEeCCC-CCCCeEEEEEECCeEEEEEEecCCccccccccCCCcEEEEEEEEcCCCcc-----c-cccCCCCChhH
Confidence            47899999999 8999999999999999999999887 322222    34666665443333     2 23456799999


Q ss_pred             hhHHHhhcCCccccccCCCCCc--eEEEEEEEeccCCCChhhHHHHHHHHHhhcCCCCCCCCeEEEEEEEECCEEEEcCC
Q 002054          142 LLVGRIIDRPIRPLFPAGFYHE--VQVMASVLSSDGKQDPDIMAANATSAALMLSDIPWGGPIGMIRIGRICGQFIVNPT  219 (974)
Q Consensus       142 il~~RlidR~lrplfp~~~~~~--~~i~~~vl~~dg~~~~~~~ai~aAs~AL~~s~iP~~~~v~av~vg~i~g~~vldPt  219 (974)
                      ++++|+|+|+|||+++.++++.  ++|.++||+.||+..  ++|+|||++||+++||||+++++||+|++++|++++|||
T Consensus        97 ~~~s~~l~~~l~~~i~~~~~p~~~I~I~i~VL~~DG~~~--~aai~Aa~lAL~dagIp~~~~v~avtv~~~~~~~i~DPt  174 (244)
T PRK03983         97 IEISKVIREALEPAIMLELFPRTVIDVFIEVLQADAGTR--VAGITAASLALADAGIPMRDLVAGCAVGKVDGVIVLDLN  174 (244)
T ss_pred             HHHHHHHHHHHHHhccHHhCCCeEEEEEEEEEECCCCHH--HHHHHHHHHHHHhcCCccccceeEEEEEEECCEEEECCC
Confidence            9999999999999999887777  555566999999855  999999999999999999999999999999999999999


Q ss_pred             HHHHhcCccceeEeeeC--CeEEEEEecCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHhC
Q 002054          220 MDELSLSDLNLVYACTR--EKTLMIDVQAREISEKDLEAGLRLAHPEAVKYLEPQIRLAEKAG  280 (974)
Q Consensus       220 ~~e~~~s~~~l~v~~t~--~~i~mie~~~~~~~e~~~~~al~~a~~~~~~i~~~~~~~~~~~g  280 (974)
                      .+|++.++.+|+|+++.  +.|+|+|..| .+++++|.+|+++|++++++++++|++.+++..
T Consensus       175 ~~Ee~~~~~~l~va~~~~~~~I~~l~~~G-~~~~~~~~~~i~~A~~~~~~i~~~i~~~l~~~~  236 (244)
T PRK03983        175 KEEDNYGEADMPVAIMPRLGEITLLQLDG-NLTREEFLEALELAKKGIKRIYQLQREALKSKY  236 (244)
T ss_pred             HHHhccCCceEEEEEECCCCCEEEEEEec-CcCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            99999999999999983  4499999998 699999999999999999999999999776544

>COG2123 RNase PH-related exoribonuclease [Translation, ribosomal structure and biogenesis]

Probab=99.98  E-value=7.2e-31  Score=275.58  Aligned_cols=228  Identities=21%  Similarity=0.310  Sum_probs=201.3

Q ss_pred             HHHHHHHHHHhcCCcCCCCCCCCccCeEEEeCCCCCCCcceEEEeCCeEEEEEEEeC--CCchhhhccccCCCCceeEEE
Q 002054          356 RKRVIRKRIIAEGVRVDGRQLDEVRPIYCESGNLPILHGSSLFSRGDTQVLCTVTLG--APAEAQRLESLVGPPTKRFML  433 (974)
Q Consensus       356 ~~~~~r~~il~~~~R~DGR~~~e~R~I~ie~g~l~~a~GSal~~~G~T~Vl~~Vtl~--~p~~~~~~d~~~~~~~~~~~v  433 (974)
                      .++.+. ..++.|.|+|||.++|+|+|.+++|+++.++|||+++.|+|||+|+|+.+  .|.++       .|++|.+.+
T Consensus        11 ~~~~i~-~ll~~g~R~DGR~~~efR~ieI~~~vi~ka~GSa~VklG~Tqvv~gvK~eig~Pf~D-------tP~eG~~~~   82 (272)
T COG2123          11 KREYIL-NLLKKGIRIDGRSFDEFRPLEIETGVIPKANGSALVKLGNTQVVVGVKAEIGEPFPD-------TPNEGVLVV   82 (272)
T ss_pred             HHHHHH-HHhccCcccCCCCcccccceEEEeCceecCCCcEEEEecCeEEEEEEEcccCCCCCC-------CCCCceEEe
Confidence            344443 67789999999999999999999999999999999999999999999954  56664       378999999


Q ss_pred             EEecCCCCccccccccCCCchhhhHHHHHHHHhhh--------cCCCCCCCCeEEEEEEEEEcCCCChhhHHHHHHHHHH
Q 002054          434 HYSFPPFCINEVGKRVGLNRREVGHGTLAEKALLA--------VLPPENDFPYTVRVNSEVMASDGSTSMATVCGGSMAL  505 (974)
Q Consensus       434 ~~~f~p~s~~e~~~~~~~~rre~~~~~l~eral~~--------vi~~~~~~p~tI~V~v~VLesdGs~~~A~v~aa~lAL  505 (974)
                      +.++.|.++..+- .|.|+.+.+++.++++|.++.        +.+...++.|.|+++++||++|||..+||..|+.+||
T Consensus        83 n~El~Plas~~fE-~Gppde~aielsrvvdr~lr~s~aiDlekL~I~~g~kvwvv~vDv~vld~DGnl~Da~~lA~~aAL  161 (272)
T COG2123          83 NVELSPLASPSFE-PGPPDELAIELSRVVDRGLRESKAIDLEKLCIEEGKKVWVVFVDVHVLDYDGNLIDAASLAAVAAL  161 (272)
T ss_pred             eeeeecccccccc-CCCCchhHHHHHHHHHHHHHhccCcchhheeEecCCEEEEEEEEEEEEcCCCCHHHHHHHHHHHHH
Confidence            9999999887653 456677888999999999843        1222257899999999999999999999999999999


Q ss_pred             HHcCCC----------------------ccccccceeeeeeccCCCCCCcccceEEEecCCccccccCCccEEEEeeCCc
Q 002054          506 MDAGIP----------------------LQEHVAGVSVGLVSEVDPSTGEIKDYRILTDILGLEDHLGDMDFKIAGTRIG  563 (974)
Q Consensus       506 ~dagvP----------------------i~~~vagvs~gli~~~d~~~~~~~~~~iL~Dp~~~Ee~~~d~d~~Va~t~~g  563 (974)
                      +++++|                      +.+++..++++.+++           .+++||+.+|+..+|..++|..+.+|
T Consensus       162 ~~t~vP~~~~~~~~~~v~~~~~~~~pl~~~~~pi~vt~a~ig~-----------~lvvDPsleEe~v~d~~ltit~~~~~  230 (272)
T COG2123         162 LNTRVPKAVEVGDGEIVIEVEEEPVPLPVSNPPISVTFAKIGN-----------VLVVDPSLEEELVADGRLTITVNEDG  230 (272)
T ss_pred             HhcCCCceeecCCcceeecccCCCcccccCCCceEEEEEEECC-----------EEEeCCCcchhhhcCceEEEEECCCC
Confidence            999988                      678999999999986           79999999999999999999999998


Q ss_pred             -eEEEEeeccCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHhc
Q 002054          564 -VTAIQLDIKPAGIPLDIICECLEHAHKGRLQILDHMEREIS  604 (974)
Q Consensus       564 -I~alq~~~k~~~i~~e~l~~al~~A~~~~~~I~~~m~~~i~  604 (974)
                       |+++|..+ ++.++++.+.+|++.|.+.+.++.+.+.++|+
T Consensus       231 ~Iv~iqK~g-~~~~~~~~~~~~~~~A~~~~~kl~~~~~~~L~  271 (272)
T COG2123         231 EIVAIQKVG-GGSITESDLEKALKTALSKAEKLREALKEALK  271 (272)
T ss_pred             cEEEEEEcC-CCcCCHHHHHHHHHHHHHHHHHHHHHHHHhhc
Confidence             99999976 57899999999999999999999999998875

>PRK12269 bifunctional cytidylate kinase/ribosomal protein S1; Provisional

Probab=99.97  E-value=4.1e-31  Score=324.03  Aligned_cols=278  Identities=13%  Similarity=0.100  Sum_probs=234.2

Q ss_pred             cccccCcEEEEEEEEEe--eceEEEEEcCCeEEEEecccCCCccccccccccccCCEEEEEEEEEcc------CCceEEE
Q 002054          679 REIEVGGIYKGVVTSVK--EYGAFVEFNGGQQGLLHVSELSHEPVSRVSDVVSVGQQLSLRCIGQDV------RGNIKLS  750 (974)
Q Consensus       679 ~~~~~G~i~~G~V~~i~--~~G~fV~l~~g~~Glvhisels~~~v~~~~~~~~vGd~V~vkVl~id~------~gri~LS  750 (974)
                      ..++.|++++|+|+++.  +.|++|++..+.+||||.||++..+..++...  +|+.++++|+.+|.      ++++.||
T Consensus       394 ~a~~~g~~V~G~Vv~v~~~kgG~~Vdig~~~~gfiP~se~~~~~~~~~~~~--vG~~ie~~V~~~~~~~~~~~~~~iVlS  471 (863)
T PRK12269        394 DAERDGTPVEGRIVRLTEKKSGFEVDLGAGMMAFLPISQSDCQKVDAPESL--IGLTSKFYIERISQSKQHRGNDNIVIN  471 (863)
T ss_pred             HHHhCCCeEEEEEEEEEeecCEEEEEECCCcEEEEEHHHhccccccchHHh--CCCeEEEEEEEEecccccCCCCeEEEE
Confidence            34689999999999985  36999999768999999999987777666643  69999999999864      3689999


Q ss_pred             EeccCCC--------ccc--ccCce---------EEEEEeecCCcceeeEEeeccCCCCCCCCCCCCCCCCCcccCCCCc
Q 002054          751 LKAVSPR--------PEA--DVKGV---------VEGSVPVNKQATDVWASVGDVSNGQNPELPMRKNETPGVNSSTSST  811 (974)
Q Consensus       751 ~K~~~~~--------~~~--~~g~~---------~~G~vv~i~~gv~~~~~~~~l~~~~~~~lp~~~~~~~~~~~~~G~~  811 (974)
                      +|.++..        -+.  +.|..         .+|.|+++ +|+++|+|+++++|.+. ..|.       +.+++||+
T Consensus       472 rr~~l~e~~~~~~ee~~~~l~~G~~V~G~Vk~i~~~G~fVdl-~Gv~Gfvp~SeiS~~~v-~~~~-------~~~kvGq~  542 (863)
T PRK12269        472 RRRYLEERARQAREEFFNSVHIEDSVSGVVKSFTSFGAFIDL-GGFDGLLHVNDMSWGHV-ARPR-------EFVKKGQT  542 (863)
T ss_pred             HHHHHHHHHHHHHHHHHhcCCCCCEEEEEEEEEeCCcEEEEE-CCEEEEEEchhcccccc-CCHH-------HhccCCCE
Confidence            9876431        111  12333         34666677 68999999999999763 2333       67899999


Q ss_pred             ceEEEeecccccccccccccccccccccccccccccCCCCCCCcEEEEEec-----------------------ccCc--
Q 002054          812 PAVLIRSAAECDEEEKASGFSQSSKSTLKSTLASKSNSKPKKFTSQSDFFS-----------------------STNI--  866 (974)
Q Consensus       812 v~v~Ir~~l~iD~~~r~i~ls~k~~~~~~~~~~~~~~~~~~G~~v~g~V~~-----------------------~~~~--  866 (974)
                      +.++|   +++|++++++.||+++..++|  |....+.+++|++++|.|.+                       +|..  
T Consensus       543 v~vkV---i~iD~e~~rI~LSlK~l~~~p--~~~~~~~~~vG~iV~G~V~~I~~fG~fVeL~~gveGLvhiSEls~~~~~  617 (863)
T PRK12269        543 IELKV---IRLDQAEKRINLSLKHFQPDP--WLEFENKFGVNDVVKGRVTKIADFGAFIELAEGIEGLAHISEFSWVKKT  617 (863)
T ss_pred             EEEEE---EEEecCCCeEEEEEeccccch--hhhhhccCCCCCEEEEEEEEEeCCeEEEEecCCceeeeEHHHhcCcccc
Confidence            99999   999999999999999998888  99988999999999999988                       7743  


Q ss_pred             -CCCcccccCCeEEEEEEEeecCCCCcC-cccccccccc--ccccCCCCCEEEEEEEEEeCCeEEEEeCCCeEEEEeccc
Q 002054          867 -QKSTSFSQREREELAECLFGTEDGDED-NKGTRVEAIV--SAKNLKLGTKVAAKVYQVRARGLVLDLGGGIRGMYRFEN  942 (974)
Q Consensus       867 -~~~~~~k~Gq~v~~~Vl~vd~e~~~i~-slK~~~~~p~--~~~~~~vG~vV~G~V~~I~~~GvFV~L~~gv~Glih~se  942 (974)
                       +....|++||+|+++|+.+|+++++++ |+|++..|||  ..++|++|++|+|+|+++++||+||+|++|+.||+|.++
T Consensus       618 ~~p~~~~kvGd~V~vkVl~iD~e~~rIsLS~K~l~~~Pw~~~~~~~~vG~~v~G~V~~i~~~G~fV~l~~gV~GlIh~se  697 (863)
T PRK12269        618 SKPSDMVKIGDEVECMILGYDIQAGRVSLGLKQVTANPWEEIEARYPVGARFTRRIVKVTNAGAFIEMEEGIDGFLHVDD  697 (863)
T ss_pred             CCHHHcCCCCCEEEEEEEEEecccCceEEEehhcccCchHHHHHhCCCCCEEEEEEEEEecceEEEEeCCCcEEEEEhHH
Confidence             334589999999999999999999999 9999999999  467899999999999999999999999999999999997


Q ss_pred             CC--------CCCCCCCCEEEEEEEEEeCC-Cceeeeec
Q 002054          943 NE--------KKDFVVGDELLVKCSSFTGK-GIPVVSLV  972 (974)
Q Consensus       943 ~~--------~~~f~vGd~V~vkVl~id~~-~~~~~~~~  972 (974)
                      +.        ...|++||.|+|+|+++|++ ++..+|+.
T Consensus       698 ls~~~~~~~~~~~~kvGq~VkvkVl~ID~e~rrI~LS~K  736 (863)
T PRK12269        698 LSWVKRTRPADHELEVGKEIECMVIECDPQARRIRLGVK  736 (863)
T ss_pred             hhccccccchhhccCCCCEEEEEEEEEeccCCEEEEEec
Confidence            64        23699999999999999965 56666754

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

Probab=99.97  E-value=6.7e-31  Score=303.74  Aligned_cols=344  Identities=21%  Similarity=0.272  Sum_probs=257.0

Q ss_pred             cCeEEEeCCCC-CCCcceEEEeCCeEEEEEEEeCCCchhhhccccCCCCceeEEEEEecCCCCccc-----cccccCCCc
Q 002054          380 RPIYCESGNLP-ILHGSSLFSRGDTQVLCTVTLGAPAEAQRLESLVGPPTKRFMLHYSFPPFCINE-----VGKRVGLNR  453 (974)
Q Consensus       380 R~I~ie~g~l~-~a~GSal~~~G~T~Vl~~Vtl~~p~~~~~~d~~~~~~~~~~~v~~~f~p~s~~e-----~~~~~~~~r  453 (974)
                      |++.+|+|.+. +|+||++++.|+|.||++|+...+.+        +.++.+++++|+-..|+.|.     ++|.|.|+.
T Consensus        14 ~~l~~etg~~A~qa~gav~~~~gdt~vl~t~~~~~~~~--------~~dF~PLtV~y~Ek~yaaGkiPGgf~kREGrpse   85 (692)
T COG1185          14 RTLTLETGKIARQANGAVLVRYGDTVVLATVVASKPKE--------GQDFFPLTVNYEEKTYAAGKIPGGFFKREGRPSE   85 (692)
T ss_pred             eeEEEEcchhhhhcCccEEEEECCeEEEEEEeecCCCC--------CCCccceeEeeeeehhccCcCCCcccccCCCCCc
Confidence            78999999998 79999999999999999999543333        56888999999999999865     689999999


Q ss_pred             hhhhHHHHHHHHhhhcCCCCCCCCeEEEEEEEEEcCCCCh--hhHHHHHHHHHHHHcCCCccccccceeeeeeccCCCCC
Q 002054          454 REVGHGTLAEKALLAVLPPENDFPYTVRVNSEVMASDGST--SMATVCGGSMALMDAGIPLQEHVAGVSVGLVSEVDPST  531 (974)
Q Consensus       454 re~~~~~l~eral~~vi~~~~~~p~tI~V~v~VLesdGs~--~~A~v~aa~lAL~dagvPi~~~vagvs~gli~~~d~~~  531 (974)
                      +|+..++|++|.++|++|  +.|-+.++|.++|++.|+..  ...+++|+|+||.-+++|+..+++|+.+|++++     
T Consensus        86 ~e~L~sRLIDRpiRPlFp--~g~~~evqIv~tvls~D~~~~pdi~a~~gaSaAl~is~iPf~gpi~~vrvg~idg-----  158 (692)
T COG1185          86 KEILTSRLIDRPIRPLFP--KGFRNEVQIVNTVLSVDPENDPDILAMVGASAALSLSGIPFLGPIGAVRVGYIDG-----  158 (692)
T ss_pred             cchhhhhhcccccccccc--hhhccceEEEEEEEEECCCCCHHHHHHHHHHHHHhccCCCccCccceEEEEEECC-----
Confidence            999999999999999999  57888999999999999865  489999999999999999999999999999976     


Q ss_pred             CcccceEEEecCCccccccCCccEEEEeeCCceEEEEeeccCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCCCCC
Q 002054          532 GEIKDYRILTDILGLEDHLGDMDFKIAGTRIGVTAIQLDIKPAGIPLDIICECLEHAHKGRLQILDHMEREISAPRTQDD  611 (974)
Q Consensus       532 ~~~~~~~iL~Dp~~~Ee~~~d~d~~Va~t~~gI~alq~~~k~~~i~~e~l~~al~~A~~~~~~I~~~m~~~i~~~~~~~~  611 (974)
                            .++++|+..|-+.+++|+.||||.+.|.++..+.+  .++++++.+|+..+++..+.+.+++++......+...
T Consensus       159 ------~~vlNPt~~e~~~s~lDlvVAGT~~aV~MVE~~a~--~l~E~~ml~Av~fg~~~~~~~~~~qe~l~~~~g~~~~  230 (692)
T COG1185         159 ------IFVLNPTLEELEESKLDLVVAGTKDAVNMVESEAD--ELDEEVMLEAVEFGHEAIQSVINAQEELALEVGKKKW  230 (692)
T ss_pred             ------EEEECCChHHhhhcceeeEecCChhhhheeecccc--cCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCccc
Confidence                  79999999999999999999999999988888765  7999999999999999999999999988776653333


Q ss_pred             CCCCc--ceee-----eeccchhhhhcCCCccchhh-----hhhhhCceEEeeCCEEEEEecCHHHHHHHHHHHH-HHhh
Q 002054          612 RNSPR--LATL-----KYDNDTLRRLIGPLGALKRK-----IEEETGGRISVSDGTLTVVAKNRSVMEKVLEKVD-FIIG  678 (974)
Q Consensus       612 ~~~p~--~~~~-----~i~~~ki~~vIg~gGk~i~~-----i~~~~g~~Idi~dg~v~i~~~~~~~~~~a~~~i~-~l~~  678 (974)
                      +..|.  -..+     .+-.+++.+.++..+|.-|.     +.++.-.++.   +.   .......+......++ ..++
T Consensus       231 ~~~~~~~~~~l~~~i~~~~~~~l~~a~~i~~K~eR~~~~~~~~~~i~~~~~---~~---e~~~~~~~~~~~~~l~~~~vR  304 (692)
T COG1185         231 ELEPPSLDEELEAKVRDLAEDELKEAVGIREKQERSAALDAIKEKIEEELS---GE---EESSLKEIKAILEKLEKKPVR  304 (692)
T ss_pred             cccccCccHHHHHHHHHHhHHHHHHHhcccchhhhhhhHHHHHHHHHHHHh---hh---ccccHHHHHHHHHHHhHHHHH
Confidence            32221  0111     01123355555555544442     1111111111   00   0111122222222221 1111


Q ss_pred             c-ccccCcEEEE-EEEEEeeceEEEEEcCCeEEEEecccCCCccccccccccccCCEEEEEEEEEcc--CCceEEEEecc
Q 002054          679 R-EIEVGGIYKG-VVTSVKEYGAFVEFNGGQQGLLHVSELSHEPVSRVSDVVSVGQQLSLRCIGQDV--RGNIKLSLKAV  754 (974)
Q Consensus       679 ~-~~~~G~i~~G-~V~~i~~~G~fV~l~~g~~Glvhisels~~~v~~~~~~~~vGd~V~vkVl~id~--~gri~LS~K~~  754 (974)
                      . -+.-+-..+| ....|++.++-|.+.|    ..|.|.|..+...++..+...|+...+++++...  .++..|+++-.
T Consensus       305 ~~Il~~~vR~DGR~~~~VRpi~~ev~~lp----r~HGS~LFtRGeTQal~v~TLG~~~d~Qvid~l~~e~~krfm~hYNF  380 (692)
T COG1185         305 RLILEGKVRIDGRFGDEVRPIGIEVGVLP----RTHGSALFTRGETQALVVVTLGTPRDAQVIDILEGEYKKRFLLHYNF  380 (692)
T ss_pred             HHHhcCCcccCCCCcceeeeeeEEecCCC----CccchhhhccCCCcceEEEEcCCcchhhhhhhccchhhhheeeeccC
Confidence            1 1233334445 4555667777776665    4899999998888999999999999999988654  35677777765


Q ss_pred             CC
Q 002054          755 SP  756 (974)
Q Consensus       755 ~~  756 (974)
                      -+
T Consensus       381 Pp  382 (692)
T COG1185         381 PP  382 (692)
T ss_pred             CC
Confidence            44

>COG0689 Rph RNase PH [Translation, ribosomal structure and biogenesis]

Probab=99.97  E-value=3.4e-31  Score=276.29  Aligned_cols=200  Identities=22%  Similarity=0.309  Sum_probs=174.8

Q ss_pred             CeEEEEEeCccCcCCCcEEEEEeCCeEEEEEEEeCCC--C---CCCCceeeEeeccccccccCCCCCccccccC-CCCc-
Q 002054           67 SRLITLETGKIARFANGAVVLGMDETKVLSTVTSSKG--D---SVRDFLPLTVDYQEKQFAQGVIPNTYMRREG-APKE-  139 (974)
Q Consensus        67 ~r~i~~etg~~a~~A~GSa~v~~G~T~Vl~tv~~~~~--~---~~~~f~pL~v~y~e~~~a~g~ip~~~~~Reg-~p~~-  139 (974)
                      -|++.++.|++ ++|+||+++++|||+|+|+|++|++  |   .+.+..|++++|       ++.|.+...|.- .++. 
T Consensus        18 lR~i~~~~~~~-~~a~GS~~~~~G~tkVic~vsGp~e~~p~~l~~~~~g~~t~ey-------~m~p~sT~~R~~~~~~~g   89 (230)
T COG0689          18 LRPIKITRGVL-KHAEGSSLIEFGNTKVICTVSGPREPVPRFLRGTGKGWLTAEY-------GMLPRSTDERKKREADRG   89 (230)
T ss_pred             ccceEEEeccc-cCCCccEEEEeCCeEEEEEEecCCCCCChhhcCCCceEEEEEE-------eccccccccccccccccc
Confidence            58999999999 8999999999999999999999988  2   256778999999       667766655532 2333 


Q ss_pred             hhhhHHHhhcCCccccccCCCCC--ceEEEEEEEeccCCCChhhHHHHHHHHHhhcCCCCCCCCeEEEEEEEECCEEEEc
Q 002054          140 RELLVGRIIDRPIRPLFPAGFYH--EVQVMASVLSSDGKQDPDIMAANATSAALMLSDIPWGGPIGMIRIGRICGQFIVN  217 (974)
Q Consensus       140 ~eil~~RlidR~lrplfp~~~~~--~~~i~~~vl~~dg~~~~~~~ai~aAs~AL~~s~iP~~~~v~av~vg~i~g~~vld  217 (974)
                      |+.++||+|.|+||+.+....++  .++|.|+|+++||+++  +||||||++||+++++|+.+.|+||+||.++|++++|
T Consensus        90 R~~eisrli~~al~~~i~L~~~p~~~I~i~~dVlqaDggTr--ta~It~A~lAL~DAgipl~~~vaaiSvgi~~~~~~lD  167 (230)
T COG0689          90 RTKEISRLIGRALRAVIDLELLPESTIDIDCDVLQADGGTR--TASITGASLALADAGIPLRDLVAAISVGIVDGVIVLD  167 (230)
T ss_pred             chhHHHHHHHHHHHHHhhhhhcCccEEEEEEEEEECCCCee--eehhhHHHHHHHHcCCchhhheeEeEEEEECCceEec
Confidence            89999999999999977755554  5566699999999999  9999999999999999999999999999999999999


Q ss_pred             CCHHHHhcCccceeEeeeCCe-EEEEEe--cCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 002054          218 PTMDELSLSDLNLVYACTREK-TLMIDV--QAREISEKDLEAGLRLAHPEAVKYLEPQIRLA  276 (974)
Q Consensus       218 Pt~~e~~~s~~~l~v~~t~~~-i~mie~--~~~~~~e~~~~~al~~a~~~~~~i~~~~~~~~  276 (974)
                      |++.|++.+..|++|+++.++ ++-|++  +.+.|++++|.++|++|.++|+++++.|++++
T Consensus       168 l~~~Eds~~~~d~~v~~~~~~~~~ei~~~~~~~~~~~del~~lL~la~~g~~~~~~~~~~al  229 (230)
T COG0689         168 LDYEEDSAAEADMNVVMTGNGGLVEIQGLAEDGPFTEDELLELLDLAIKGCNELRELQREAL  229 (230)
T ss_pred             CcchhhcccccCceEEEEecCCeEEEEEEeccCCcCHHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence            999999999999999999876 555554  33459999999999999999999999999875

>PRK06299 rpsA 30S ribosomal protein S1; Reviewed

Probab=99.97  E-value=2.5e-30  Score=311.75  Aligned_cols=298  Identities=19%  Similarity=0.191  Sum_probs=244.7

Q ss_pred             CCEEEEEecCHHHHHHHHHHHHHHhhcccccCcEEEEEEEEEeeceEEEEEcCCeEEEEecccCCCccccccccccccCC
Q 002054          653 DGTLTVVAKNRSVMEKVLEKVDFIIGREIEVGGIYKGVVTSVKEYGAFVEFNGGQQGLLHVSELSHEPVSRVSDVVSVGQ  732 (974)
Q Consensus       653 dg~v~i~~~~~~~~~~a~~~i~~l~~~~~~~G~i~~G~V~~i~~~G~fV~l~~g~~Glvhisels~~~v~~~~~~~~vGd  732 (974)
                      +|.+.++.. +...+.+++.+.    ..++.|++++|+|+++.++|+||++. |+.||+|.|++++.+..++.  +.+||
T Consensus        89 ~~~i~lS~k-~~~~~~~~~~l~----~~~~~g~~v~g~V~~~~~~G~~V~~~-g~~gfip~s~~~~~~~~~~~--~~vG~  160 (565)
T PRK06299         89 FGETVLSRE-KAKRLEAWDKLE----KAFENGEIVEGVINGKVKGGFTVDLN-GVEAFLPGSQVDVRPVRDTD--PLEGK  160 (565)
T ss_pred             CCcEEEech-HHHHHHHHHHHH----HHhhCCCEEEEEEEEEECCEEEEEEC-CEEEEEEHHHccCcCCCChH--HhCCC
Confidence            355555432 222333444333    34678999999999999999999996 99999999999998877766  45899


Q ss_pred             EEEEEEEEEcc-CCceEEEEeccCCCc----ccc------cCce---------EEEEEeecCCcceeeEEeeccCCCCCC
Q 002054          733 QLSLRCIGQDV-RGNIKLSLKAVSPRP----EAD------VKGV---------VEGSVPVNKQATDVWASVGDVSNGQNP  792 (974)
Q Consensus       733 ~V~vkVl~id~-~gri~LS~K~~~~~~----~~~------~g~~---------~~G~vv~i~~gv~~~~~~~~l~~~~~~  792 (974)
                      .++|+|+++|. ++++.||+|.+...+    |..      .|.+         .+|.++++. |+++++|+++++|.+. 
T Consensus       161 ~i~~~V~~~d~~~~~i~lS~k~~~~~~~~~~~~~~~~~l~~G~iv~g~V~~v~~~G~~V~i~-g~~glv~~se~s~~~~-  238 (565)
T PRK06299        161 ELEFKVIKLDKKRNNIVVSRRAVLEEERAEEREELLENLEEGQVVEGVVKNITDYGAFVDLG-GVDGLLHITDISWKRV-  238 (565)
T ss_pred             EEEEEEEEEECCCCEEEEEhHHhhhhhhhhHHHHHHhcCCCCCEEEEEEEEEeCCeEEEEEC-CEEEEEEHHHhccccc-
Confidence            99999999998 679999999886533    221      3444         456666775 8999999999999752 


Q ss_pred             CCCCCCCCCCCcccCCCCcceEEEeecccccccccccccccccccccccccccccCCCCCCCcEEEEEec----------
Q 002054          793 ELPMRKNETPGVNSSTSSTPAVLIRSAAECDEEEKASGFSQSSKSTLKSTLASKSNSKPKKFTSQSDFFS----------  862 (974)
Q Consensus       793 ~lp~~~~~~~~~~~~~G~~v~v~Ir~~l~iD~~~r~i~ls~k~~~~~~~~~~~~~~~~~~G~~v~g~V~~----------  862 (974)
                      .+|.       +.+++||.+.++|   +++|++++++.||+++..++|  |......+++|+++.|.|.+          
T Consensus       239 ~~~~-------~~~kvG~~v~v~V---~~~d~~~~~i~lS~k~~~~~p--~~~~~~~~~~G~~v~g~V~~i~~~G~fV~l  306 (565)
T PRK06299        239 NHPS-------EVVNVGDEVKVKV---LKFDKEKKRVSLGLKQLGEDP--WEAIEKKYPVGSKVKGKVTNITDYGAFVEL  306 (565)
T ss_pred             CCHh-------hcCCCCCEEEEEE---EEEeCCCCeEEEEEEecccCh--hHHHHhhCCCCCEEEEEEEEEeCCeEEEEe
Confidence            2333       6789999999999   999999999999999988888  98888889999999999877          


Q ss_pred             -------------ccCcCC---CcccccCCeEEEEEEEeecCCCCcC-cccccccccc--ccccCCCCCEEEEEEEEEeC
Q 002054          863 -------------STNIQK---STSFSQREREELAECLFGTEDGDED-NKGTRVEAIV--SAKNLKLGTKVAAKVYQVRA  923 (974)
Q Consensus       863 -------------~~~~~~---~~~~k~Gq~v~~~Vl~vd~e~~~i~-slK~~~~~p~--~~~~~~vG~vV~G~V~~I~~  923 (974)
                                   +|....   ...|++||.++++|+++|++++++. |+|++..+||  ...+|++|++|.|+|+++++
T Consensus       307 ~~~v~Glv~~sel~~~~~~~~~~~~~~~G~~v~v~V~~id~~~~~i~ls~k~~~~~p~~~~~~~~~~G~~v~g~V~~v~~  386 (565)
T PRK06299        307 EEGIEGLVHVSEMSWTKKNKHPSKVVSVGQEVEVMVLEIDEEKRRISLGLKQCKENPWEEFAEKYPVGDVVEGKVKNITD  386 (565)
T ss_pred             CCCCEEEEEHHHcCccccccCHHHhcCCCCEEEEEEEEEcCCCCEEEEehHHhccchhhhHHHhCCCCCEEEEEEEEEec
Confidence                         454322   2368999999999999999999998 9999999999  46679999999999999999


Q ss_pred             CeEEEEeCCCeEEEEecccCC--------CCCCCCCCEEEEEEEEEeCC-Cceeeeec
Q 002054          924 RGLVLDLGGGIRGMYRFENNE--------KKDFVVGDELLVKCSSFTGK-GIPVVSLV  972 (974)
Q Consensus       924 ~GvFV~L~~gv~Glih~se~~--------~~~f~vGd~V~vkVl~id~~-~~~~~~~~  972 (974)
                      +|+||+|++++.||+|.++++        .+.|++||.|+|+|+++|.+ +...+|+.
T Consensus       387 ~G~fV~l~~~v~g~i~~s~l~~~~~~~~~~~~~~~Gd~v~v~Il~vd~~~~~i~ls~k  444 (565)
T PRK06299        387 FGAFVGLEGGIDGLVHLSDISWDKKGEEAVELYKKGDEVEAVVLKVDVEKERISLGIK  444 (565)
T ss_pred             ceEEEECCCCCEEEEEHHHcCccccccChHhhCCCCCEEEEEEEEEeCCCCEEEEEEe
Confidence            999999999999999999875        24689999999999999964 66667764

>TIGR02696 pppGpp_PNP guanosine pentaphosphate synthetase I/polynucleotide phosphorylase

Probab=99.97  E-value=1.7e-29  Score=299.78  Aligned_cols=213  Identities=15%  Similarity=0.135  Sum_probs=187.2

Q ss_pred             cCeEEEeCCCC-CCCcceEEEe-CCeEEEEEEEeC-CCchhhhccccCCCCceeEEEEEecCCCCccc-----cccccCC
Q 002054          380 RPIYCESGNLP-ILHGSSLFSR-GDTQVLCTVTLG-APAEAQRLESLVGPPTKRFMLHYSFPPFCINE-----VGKRVGL  451 (974)
Q Consensus       380 R~I~ie~g~l~-~a~GSal~~~-G~T~Vl~~Vtl~-~p~~~~~~d~~~~~~~~~~~v~~~f~p~s~~e-----~~~~~~~  451 (974)
                      |++.+++|-+. +|+||++++. |+|.|||||+.. .|.+        +.++.+++|+|.-..|+.|.     ++|.|+|
T Consensus        17 ~~~~~etG~~A~qA~Gav~v~~~G~t~vl~t~~~~~~~~~--------~~dF~PLtV~y~Ek~yA~GkiPggf~kREgrp   88 (719)
T TIGR02696        17 RTIRFETGRLARQAAGSVVAYLDDETMLLSATTASKQPKD--------QFDFFPLTVDVEERMYAAGRIPGSFFRREGRP   88 (719)
T ss_pred             EEEEEEcchhHhhCCceEEEEecCCeEEEEEEEecCCCCC--------CCCCcceeEeeeehhhhcCccCCceeccCCCC
Confidence            47999999998 7999999999 999999999943 2222        45788999999999999865     5899999


Q ss_pred             CchhhhHHHHHHHHhhhcCCCCCCCCeEEEEEEEEEcCCCCh--hhHHHHHHHHHHHHcCCCccccccceeeeeeccCCC
Q 002054          452 NRREVGHGTLAEKALLAVLPPENDFPYTVRVNSEVMASDGST--SMATVCGGSMALMDAGIPLQEHVAGVSVGLVSEVDP  529 (974)
Q Consensus       452 ~rre~~~~~l~eral~~vi~~~~~~p~tI~V~v~VLesdGs~--~~A~v~aa~lAL~dagvPi~~~vagvs~gli~~~d~  529 (974)
                      +.+|+..++|++|.|+|++|  +.|.|.++|.++||+.|+..  ...+++|||+||+-++||+..|++||.+|++++   
T Consensus        89 s~~eiL~sRliDR~iRPLFp--~~~~~e~qi~~~vls~D~~~~pdvla~~~ASaAl~iSdiPf~gPv~~vrVg~i~g---  163 (719)
T TIGR02696        89 STDAILTCRLIDRPLRPSFV--KGLRNEVQVVVTVLSLNPDHLYDVVAINAASASTQLAGLPFSGPIGGVRVALIDG---  163 (719)
T ss_pred             ChhhhHHHHhhCCCCccCCC--CCCCcceEEEEEEEEcCCCCChHHHHHHHHHHHHHhcCCCCCCceEEEEEEEECC---
Confidence            99999999999999999999  68999999999999999854  588999999999999999999999999999976   


Q ss_pred             CCCcccceEEEecCCccccccCCccEEEEeeC----C-ceEEEEee----------ccCCCCCHHHHHHHHHHHHHHHHH
Q 002054          530 STGEIKDYRILTDILGLEDHLGDMDFKIAGTR----I-GVTAIQLD----------IKPAGIPLDIICECLEHAHKGRLQ  594 (974)
Q Consensus       530 ~~~~~~~~~iL~Dp~~~Ee~~~d~d~~Va~t~----~-gI~alq~~----------~k~~~i~~e~l~~al~~A~~~~~~  594 (974)
                              .++++|+..|-..+++|+.|+||.    + .|+++.+.          .....++++.|.+||..|+++.+.
T Consensus       164 --------~~viNPt~~~~~~s~ldLvvagt~~~~~~~~i~MiE~~a~~~~~~~~~~~a~e~~e~~~~~Ai~~a~~~i~~  235 (719)
T TIGR02696       164 --------QWVAFPTHEQLEGAVFDMVVAGRVLENGDVAIMMVEAEATEKTWDLVKGGAEAPTEEVVAEGLEAAKPFIKV  235 (719)
T ss_pred             --------EEEECcCHHHHhhCeeeEEEEeeecCCCCccEEEEecCCccccccccccCCCCCCHHHHHHHHHHHHHHHHH
Confidence                    699999999999999999999997    5 78888862          133579999999999999999999


Q ss_pred             HHHHHHHHhcCCCCCCCCC
Q 002054          595 ILDHMEREISAPRTQDDRN  613 (974)
Q Consensus       595 I~~~m~~~i~~~~~~~~~~  613 (974)
                      +++.+++..++..+++..+
T Consensus       236 ~~~~~~~l~~~~gk~k~~~  254 (719)
T TIGR02696       236 LCRAQADLAEKAAKPTGEF  254 (719)
T ss_pred             HHHHHHHHHHHhCCCcccc
Confidence            9999999877666544443

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.

>PRK06676 rpsA 30S ribosomal protein S1; Reviewed

Probab=99.97  E-value=5.2e-30  Score=295.61  Aligned_cols=280  Identities=20%  Similarity=0.204  Sum_probs=231.7

Q ss_pred             cccccCcEEEEEEEEEeeceEEEEE-cCCeEEEEecccCCCccccccccccccCCEEEEEEEEEcc-CCceEEEEeccCC
Q 002054          679 REIEVGGIYKGVVTSVKEYGAFVEF-NGGQQGLLHVSELSHEPVSRVSDVVSVGQQLSLRCIGQDV-RGNIKLSLKAVSP  756 (974)
Q Consensus       679 ~~~~~G~i~~G~V~~i~~~G~fV~l-~~g~~Glvhisels~~~v~~~~~~~~vGd~V~vkVl~id~-~gri~LS~K~~~~  756 (974)
                      .++++|+++.|+|+++.++|+||++ .++.+|+||.+|+++.+..++...|++||.|+|+|+++|. ++++.||+|.+..
T Consensus        13 ~~~~~G~iv~G~V~~i~~~g~~V~i~~~~~~g~lp~~e~~~~~~~~~~~~~~vGd~v~~~V~~v~~~~~~i~lS~k~~~~   92 (390)
T PRK06676         13 KEVEVGDVVTGEVLKVEDKQVFVNIEGYKVEGVIPISELSNDHIEDINDVVKVGDELEVYVLKVEDGEGNLLLSKRRLEA   92 (390)
T ss_pred             hcccCCCEEEEEEEEEECCeEEEEEecCCcEEEEEHHHhccccccCcccccCCCCEEEEEEEEEECCCCCEEEEHHHhhh
Confidence            4789999999999999999999999 7799999999999999999999999999999999999987 5789999998654


Q ss_pred             -Ccccc------cCceEE---------EEEeecCCcceeeEEeeccCCCCCCCCCCCCCCCCCcccCCCCcceEEEeecc
Q 002054          757 -RPEAD------VKGVVE---------GSVPVNKQATDVWASVGDVSNGQNPELPMRKNETPGVNSSTSSTPAVLIRSAA  820 (974)
Q Consensus       757 -~~~~~------~g~~~~---------G~vv~i~~gv~~~~~~~~l~~~~~~~lp~~~~~~~~~~~~~G~~v~v~Ir~~l  820 (974)
                       .+|..      .|....         |+++++ +|+++|+|++++++... ..|        ..+ +|+.+.++|   +
T Consensus        93 ~~~~~~~~~~~~~G~~v~g~V~~v~~~G~~V~~-~G~~gflp~~el~~~~~-~~~--------~~~-vG~~v~~~V---l  158 (390)
T PRK06676         93 EKAWDKLEEKFEEGEVVEVKVTEVVKGGLVVDV-EGVRGFIPASLISTRFV-EDF--------SDF-KGKTLEVKI---I  158 (390)
T ss_pred             hhhHHHHHHhccCCCEEEEEEEEEECCeEEEEE-CCEEEEEEHHHcCCccC-CCh--------HHc-CCCEEEEEE---E
Confidence             34543      354444         555565 47899999999998642 111        122 899999999   9


Q ss_pred             cccccccccccccccccccc--cccccccCCCCCCCcEEEEEec----------------------ccC--cCCCccccc
Q 002054          821 ECDEEEKASGFSQSSKSTLK--STLASKSNSKPKKFTSQSDFFS----------------------STN--IQKSTSFSQ  874 (974)
Q Consensus       821 ~iD~~~r~i~ls~k~~~~~~--~~~~~~~~~~~~G~~v~g~V~~----------------------~~~--~~~~~~~k~  874 (974)
                      ++|++++++.+|++......  ..|......+..|+++.|.|.+                      +|.  ......|++
T Consensus       159 ~~d~~~~~i~lS~k~~~~~~~~~~~~~~~~~~~~G~~v~g~V~~v~~~G~fV~l~~v~g~v~~sels~~~~~~~~~~~~v  238 (390)
T PRK06676        159 ELDPEKNRVILSRRAVVEEERAAKKEELLSSLKEGDVVEGTVARLTDFGAFVDIGGVDGLVHISELSHERVEKPSEVVSV  238 (390)
T ss_pred             EEECCCCEEEEEeHHHhhhhhhhHHHHHHhhCCCCCEEEEEEEEEecceEEEEeCCeEEEEEHHHcCccccCCHHHhcCC
Confidence            99999999999999754321  1244555667899999999888                      332  122346899


Q ss_pred             CCeEEEEEEEeecCCCCcC-cccccccccc--ccccCCCCCEEEEEEEEEeCCeEEEEeCCCeEEEEecccCC-------
Q 002054          875 REREELAECLFGTEDGDED-NKGTRVEAIV--SAKNLKLGTKVAAKVYQVRARGLVLDLGGGIRGMYRFENNE-------  944 (974)
Q Consensus       875 Gq~v~~~Vl~vd~e~~~i~-slK~~~~~p~--~~~~~~vG~vV~G~V~~I~~~GvFV~L~~gv~Glih~se~~-------  944 (974)
                      ||.++++|+.+|++++++. |+|++..+||  ..+++++|++++|+|+++++||+||++++|+.||+|.++++       
T Consensus       239 Gd~i~~~Vl~vd~~~~~i~lS~k~~~~~~~~~~~~~~~~G~~v~g~V~~i~~~G~fV~l~~gi~Glv~~se~~~~~~~~~  318 (390)
T PRK06676        239 GQEVEVKVLSIDWETERISLSLKDTLPGPWEGVEEKLPEGDVIEGTVKRLTDFGAFVEVLPGVEGLVHISQISHKHIATP  318 (390)
T ss_pred             CCEEEEEEEEEeCCCCEEEEEEeecccCccccchhhhcCCcEEEEEEEEEeCceEEEEECCCCeEEEEhHHcCccccCCh
Confidence            9999999999999999998 9999999999  46789999999999999999999999999999999999874       


Q ss_pred             CCCCCCCCEEEEEEEEEeC-CCceeeeec
Q 002054          945 KKDFVVGDELLVKCSSFTG-KGIPVVSLV  972 (974)
Q Consensus       945 ~~~f~vGd~V~vkVl~id~-~~~~~~~~~  972 (974)
                      .+.|++||+|+|+|+++|+ ++...+|+.
T Consensus       319 ~~~~~~Gd~v~v~V~~id~e~~~i~ls~k  347 (390)
T PRK06676        319 SEVLEEGQEVKVKVLEVNEEEKRISLSIK  347 (390)
T ss_pred             hhccCCCCEEEEEEEEEECCCCEEEEEEE
Confidence            2458999999999999995 566666654

>TIGR00717 rpsA ribosomal protein S1

Probab=99.96  E-value=4.9e-28  Score=289.17  Aligned_cols=278  Identities=18%  Similarity=0.187  Sum_probs=232.1

Q ss_pred             cccccCcEEEEEEEEEeeceEEEEEcCCeEEEEecccCCCccccccccccccCCEEEEEEEEEcc-CCceEEEEeccCCC
Q 002054          679 REIEVGGIYKGVVTSVKEYGAFVEFNGGQQGLLHVSELSHEPVSRVSDVVSVGQQLSLRCIGQDV-RGNIKLSLKAVSPR  757 (974)
Q Consensus       679 ~~~~~G~i~~G~V~~i~~~G~fV~l~~g~~Glvhisels~~~v~~~~~~~~vGd~V~vkVl~id~-~gri~LS~K~~~~~  757 (974)
                      ..++.|++++|+|+++.+.|++|++. |.+||+|.|+++..+.++..  ..+|+.++|+|+++|. ++++.||+|.++..
T Consensus        96 ~a~~~g~~v~g~V~~~~~~g~~V~i~-g~~~flP~s~~~~~~~~~~~--~~vG~~i~~~v~~~~~~~~~iv~Srk~~l~~  172 (516)
T TIGR00717        96 KAYEEGSIVEGKIVGKVKGGFIVDLN-GVEAFLPGSQVDVKPIKDLD--SLIGKTLKFKIIKLDQKRNNIVVSRRAYLEE  172 (516)
T ss_pred             HHhhCCCeEEEEEEEEECCEEEEEEC-CEEEEEeHHHhcCcccCchh--hhCCCEEEEEEEEEECCCCcEEEEHHHHHHH
Confidence            34689999999999999999999995 99999999999876555433  4689999999999998 56899999987543


Q ss_pred             c----------ccccCceE---------EEEEeecCCcceeeEEeeccCCCCCCCCCCCCCCCCCcccCCCCcceEEEee
Q 002054          758 P----------EADVKGVV---------EGSVPVNKQATDVWASVGDVSNGQNPELPMRKNETPGVNSSTSSTPAVLIRS  818 (974)
Q Consensus       758 ~----------~~~~g~~~---------~G~vv~i~~gv~~~~~~~~l~~~~~~~lp~~~~~~~~~~~~~G~~v~v~Ir~  818 (974)
                      .          ..+.|..+         +|.++++ +|+++|+|.++++|... ..|.       +.+++||.+.+.|  
T Consensus       173 ~~~~~~~~~~~~l~~G~~v~g~V~~i~~~G~~V~l-~g~~g~lp~~e~s~~~~-~~~~-------~~~~vG~~v~v~V--  241 (516)
T TIGR00717       173 ERSQAREELLENLKEGDVVKGVVKNITDFGAFVDL-GGVDGLLHITDMSWKRV-KHPS-------EYVKVGQEVKVKV--  241 (516)
T ss_pred             HHHHHHHHHHHhccCCCEEEEEEEEEECCeEEEEE-CCEEEEEEHHHcCCCCC-CCHH-------HhccCCCEEEEEE--
Confidence            2          11234444         4555565 47999999999998652 2232       6789999999999  


Q ss_pred             cccccccccccccccccccccccccccccCCCCCCCcEEEEEec-----------------------ccCcCCC---ccc
Q 002054          819 AAECDEEEKASGFSQSSKSTLKSTLASKSNSKPKKFTSQSDFFS-----------------------STNIQKS---TSF  872 (974)
Q Consensus       819 ~l~iD~~~r~i~ls~k~~~~~~~~~~~~~~~~~~G~~v~g~V~~-----------------------~~~~~~~---~~~  872 (974)
                       +++|++++++.+|++...++|  |......++.|++++|.|.+                       +|.....   ..|
T Consensus       242 -l~~d~~~~~i~lS~k~~~~~p--~~~~~~~~~~G~i~~g~V~~v~~~G~fV~l~~~v~g~v~~sels~~~~~~~~~~~~  318 (516)
T TIGR00717       242 -IKFDKEKGRISLSLKQLGEDP--WEAIEKKFPVGDKITGRVTNLTDYGVFVEIEEGIEGLVHVSEMSWVKKNSHPSKVV  318 (516)
T ss_pred             -EEEECCCCcEEEEEEecchhH--HHHHHhhccCCCEEEEEEEEeeCCcEEEEeCCCCEEEEEHHHcCCccccCCHHHhc
Confidence             999999999999999888888  88877788999999999888                       4432222   358


Q ss_pred             ccCCeEEEEEEEeecCCCCcC-cccccccccc--ccccCCCCCEEEEEEEEEeCCeEEEEeCCCeEEEEecccCC-----
Q 002054          873 SQREREELAECLFGTEDGDED-NKGTRVEAIV--SAKNLKLGTKVAAKVYQVRARGLVLDLGGGIRGMYRFENNE-----  944 (974)
Q Consensus       873 k~Gq~v~~~Vl~vd~e~~~i~-slK~~~~~p~--~~~~~~vG~vV~G~V~~I~~~GvFV~L~~gv~Glih~se~~-----  944 (974)
                      ++||.++++|+++|++++++. |+|++..+||  ..+++++|++++|+|+++++||+||+|++|++||+|.++++     
T Consensus       319 ~vG~~v~v~V~~id~~~~~i~lS~k~~~~~p~~~~~~~~~~G~~v~g~V~~v~~~G~fV~l~~~v~glv~~s~ls~~~~~  398 (516)
T TIGR00717       319 KKGDEVEVMILDIDPERRRLSLGLKQCKANPWEQFEEKHPVGDRVTGKIKKITDFGAFVELEGGIDGLIHLSDISWDKDG  398 (516)
T ss_pred             cCCCEEEEEEEEEcCCCCEEEEEehhcccCcHHHHHHhCCCCCEEEEEEEEEecceEEEECCCCCEEEEEHHHCcCcccC
Confidence            999999999999999999998 9999999999  46679999999999999999999999999999999999874     


Q ss_pred             ---CCCCCCCCEEEEEEEEEeC-CCceeeeecC
Q 002054          945 ---KKDFVVGDELLVKCSSFTG-KGIPVVSLVD  973 (974)
Q Consensus       945 ---~~~f~vGd~V~vkVl~id~-~~~~~~~~~~  973 (974)
                         ...|++||+|.|+|+++|+ ++...+|+.+
T Consensus       399 ~~~~~~~~~G~~V~~~Vl~vd~~~~~i~ls~K~  431 (516)
T TIGR00717       399 READHLYKKGDEIEAVVLAVDKEKKRISLGVKQ  431 (516)
T ss_pred             CCHhHccCCCCEEEEEEEEEeCcCCEEEEeecc
Confidence               2569999999999999996 5677787753

This model provides trusted hits to most long form (6 repeat) examples of RpsA. Among homologs with only four repeats are some to which other (perhaps secondary) functions have been assigned.

>PRK00087 4-hydroxy-3-methylbut-2-enyl diphosphate reductase/S1 RNA-binding domain protein; Reviewed

Probab=99.96  E-value=5.7e-28  Score=293.77  Aligned_cols=280  Identities=17%  Similarity=0.199  Sum_probs=232.2

Q ss_pred             cccccCcEEEEEEEEEeeceEEEEEcCCeEEEEecccCCCccccccccccccCCEEEEEEEEEcc-CCceEEEEeccC-C
Q 002054          679 REIEVGGIYKGVVTSVKEYGAFVEFNGGQQGLLHVSELSHEPVSRVSDVVSVGQQLSLRCIGQDV-RGNIKLSLKAVS-P  756 (974)
Q Consensus       679 ~~~~~G~i~~G~V~~i~~~G~fV~l~~g~~Glvhisels~~~v~~~~~~~~vGd~V~vkVl~id~-~gri~LS~K~~~-~  756 (974)
                      ..+++|+++.|+|.++.+.|+||++.++.+|+||.+++++....++.+.|++||.|+|+|+++|. +|++.||+|... .
T Consensus       298 ~~l~~G~iV~G~V~~v~~~gv~Vdig~~~~G~lp~~els~~~~~~~~~~~~vGd~V~v~V~~vd~~~g~i~LS~k~~~~~  377 (647)
T PRK00087        298 KQIRRGDIVKGTVVSVNENEVFVDVGYKSEGVIPLRELTLDEISSLKESVKVGDEIEVKVLKLEDEDGYVVLSKKEADRE  377 (647)
T ss_pred             hhccCCCEEEEEEEEEECCEEEEEECCCeEEEEEHHHhcccccCChhhccCCCCEEEEEEEEEECCCCcEEEEeehhcch
Confidence            46899999999999999999999998889999999999999999999999999999999999976 789999999875 3


Q ss_pred             Ccccc------cCceEE---------EEEeecCCcceeeEEeeccCCCCCCCCCCCCCCCCCcccCCCCcceEEEeeccc
Q 002054          757 RPEAD------VKGVVE---------GSVPVNKQATDVWASVGDVSNGQNPELPMRKNETPGVNSSTSSTPAVLIRSAAE  821 (974)
Q Consensus       757 ~~~~~------~g~~~~---------G~vv~i~~gv~~~~~~~~l~~~~~~~lp~~~~~~~~~~~~~G~~v~v~Ir~~l~  821 (974)
                      .+|..      .|....         |.+++++ |+++|+|.+++++..... |        .. .+|+.+.+.|   ++
T Consensus       378 ~~~~~l~~~~~~G~iv~g~V~~v~~~G~~V~lg-gi~gfiP~sel~~~~~~d-~--------~~-~vG~~v~v~V---l~  443 (647)
T PRK00087        378 KAWKELEEAFENGEPVKGKVKEVVKGGLLVDYG-GVRAFLPASHVELGYVED-L--------SE-YKGQELEVKI---IE  443 (647)
T ss_pred             hHHHHHHHHhhCCCEEEEEEEEEECCeEEEEEC-CEEEEEEHHHhCccccCC-H--------HH-hCCCEEEEEE---EE
Confidence            45653      355544         4555553 589999999998864211 1        12 2899999999   99


Q ss_pred             ccccccc-cccccccccc--cccccccccCCCCCCCcEEEEEec----------------------ccCc--CCCccccc
Q 002054          822 CDEEEKA-SGFSQSSKST--LKSTLASKSNSKPKKFTSQSDFFS----------------------STNI--QKSTSFSQ  874 (974)
Q Consensus       822 iD~~~r~-i~ls~k~~~~--~~~~~~~~~~~~~~G~~v~g~V~~----------------------~~~~--~~~~~~k~  874 (974)
                      +|+++++ +.+|.+....  ....+......+.+|+++.|.|.+                      +|..  +....|++
T Consensus       444 vd~e~~~~l~lS~k~~~~~~~~~~~~~~~~~l~~G~iV~g~V~~v~~~G~fV~l~gv~Gll~~sels~~~~~~~~~~~~v  523 (647)
T PRK00087        444 FNRKRRKKVVLSRKAILEEEKEKKKEETWNSLEEGDVVEGEVKRLTDFGAFVDIGGVDGLLHVSEISWGRVEKPSDVLKV  523 (647)
T ss_pred             EEcCCCcEEEEEeHHHhhhhhhhHHHHHHHhCCCCCEEEEEEEEEeCCcEEEEECCEEEEEEHHHcCccccCCHHHhcCC
Confidence            9999998 9999887542  111245555667899999999887                      3321  22347999


Q ss_pred             CCeEEEEEEEeecCCCCcC-ccccccccccc--cccCCCCCEEEEEEEEEeCCeEEEEeCCCeEEEEecccCC-------
Q 002054          875 REREELAECLFGTEDGDED-NKGTRVEAIVS--AKNLKLGTKVAAKVYQVRARGLVLDLGGGIRGMYRFENNE-------  944 (974)
Q Consensus       875 Gq~v~~~Vl~vd~e~~~i~-slK~~~~~p~~--~~~~~vG~vV~G~V~~I~~~GvFV~L~~gv~Glih~se~~-------  944 (974)
                      ||.++++|+++|++++++. |+|++..+||.  .++|++|+++.|+|+++++||+||+|++|+.||+|.++++       
T Consensus       524 Gd~V~vkV~~id~~~~~I~lS~K~~~~~p~~~~~~~~~~G~~v~g~V~~i~~~G~fV~l~~~i~Gli~~sel~~~~~~~~  603 (647)
T PRK00087        524 GDEIKVYILDIDKENKKLSLSLKKLLPDPWENVEEKYPVGSIVLGKVVRIAPFGAFVELEPGVDGLVHISQISWKRIDKP  603 (647)
T ss_pred             CCEEEEEEEEEECCCCEEEEEeeccccChhhhhhhhccCCeEEEEEEEEEECCeEEEEECCCCEEEEEhhhcCccccCCH
Confidence            9999999999999999999 99999999993  5789999999999999999999999999999999999875       


Q ss_pred             CCCCCCCCEEEEEEEEEeC-CCceeeeec
Q 002054          945 KKDFVVGDELLVKCSSFTG-KGIPVVSLV  972 (974)
Q Consensus       945 ~~~f~vGd~V~vkVl~id~-~~~~~~~~~  972 (974)
                      .+.|++||+|+|+|+++|. ++...+|+.
T Consensus       604 ~~~~kvGd~V~vkV~~id~e~~rI~lslk  632 (647)
T PRK00087        604 EDVLSEGEEVKAKILEVDPEEKRIRLSIK  632 (647)
T ss_pred             hhcCCCCCEEEEEEEEEeCCCCEEEEEEe
Confidence            2368999999999999995 577777764

>PRK13806 rpsA 30S ribosomal protein S1; Provisional

Probab=99.95  E-value=5.4e-27  Score=276.53  Aligned_cols=277  Identities=19%  Similarity=0.176  Sum_probs=223.4

Q ss_pred             ccccCcEEEEEEEEEeeceEEEEEcCCeEEEEecccCCCccccccccccccCCEEEEEEEEEccCCceEEEEeccCCCcc
Q 002054          680 EIEVGGIYKGVVTSVKEYGAFVEFNGGQQGLLHVSELSHEPVSRVSDVVSVGQQLSLRCIGQDVRGNIKLSLKAVSPRPE  759 (974)
Q Consensus       680 ~~~~G~i~~G~V~~i~~~G~fV~l~~g~~Glvhisels~~~v~~~~~~~~vGd~V~vkVl~id~~gri~LS~K~~~~~~~  759 (974)
                      .++.|++++|+|+++.+.|+||+++.+.+|++|.+|+++..-   ...+++||.|+|+|++++ .+.+.||++......|
T Consensus        31 ~~~~G~~v~G~V~~v~~~~v~Vdig~k~eg~ip~~e~~~~~~---~~~~~~G~~i~~~Vi~~~-~~~~~lS~~~~~~~~~  106 (491)
T PRK13806         31 ELRVGDKITGTVIAITEDSVFVDTGSKVDGVVDRAELLDADG---ELTVAVGDEVELYVVSVN-GQEIRLSKALSGQGGA  106 (491)
T ss_pred             cCCCCCEEEEEEEEEECCEEEEEECCCcEEEEEHHHhcCccc---cccccCCCEEEEEEEEEc-CCEEEEEhHHhhhhhH
Confidence            388999999999999999999999778999999999975321   234899999999999986 4679999875544445


Q ss_pred             cc------cCceEEEEEeec--------CCcceeeEEeeccCCCCCCCCCCCCCCCCCcccCCCCcceEEEeeccccccc
Q 002054          760 AD------VKGVVEGSVPVN--------KQATDVWASVGDVSNGQNPELPMRKNETPGVNSSTSSTPAVLIRSAAECDEE  825 (974)
Q Consensus       760 ~~------~g~~~~G~vv~i--------~~gv~~~~~~~~l~~~~~~~lp~~~~~~~~~~~~~G~~v~v~Ir~~l~iD~~  825 (974)
                      ..      .|..+.|.|...        ..|+.+|+|.+++++... ..|        .. .+|+.+.++|   +++|++
T Consensus       107 ~~l~~~~~~g~~v~g~V~~~~~~G~~V~i~g~~~flP~s~~~~~~~-~~~--------~~-~vG~~i~~~V---~~id~~  173 (491)
T PRK13806        107 AMLEEAYENGVPVEGKVTGTCKGGFNVEVLGRRAFCPVSQIDLRYV-EDP--------ES-YVGQTFQFLI---TRVEEN  173 (491)
T ss_pred             HHHHHHHhCCCEEEEEEEEEEcCCEEEEECCEEEEEEHHHhccccC-CCh--------HH-cCCCeEEEEE---EEEECC
Confidence            44      356655555443        138999999999998642 111        12 2899999999   999999


Q ss_pred             cccccccccccccc--ccccccccCCCCCCCcEEEEEec-----------------------ccCc--CCCcccccCCeE
Q 002054          826 EKASGFSQSSKSTL--KSTLASKSNSKPKKFTSQSDFFS-----------------------STNI--QKSTSFSQRERE  878 (974)
Q Consensus       826 ~r~i~ls~k~~~~~--~~~~~~~~~~~~~G~~v~g~V~~-----------------------~~~~--~~~~~~k~Gq~v  878 (974)
                      ++++.+|.++....  ...|......+..|++++|.|..                       +|..  +.+..|++||.+
T Consensus       174 ~~~v~lSrk~~~~~~~~~~~~~~~~~l~~G~iv~G~V~~v~~~G~fV~l~~gv~g~v~~sels~~~~~~~~~~~~vGd~i  253 (491)
T PRK13806        174 GRNIVVSRRALLEREQKEALEAFMETVKEGDVVEGTVTRLAPFGAFVELAPGVEGMVHISELSWSRVQKADEAVSVGDTV  253 (491)
T ss_pred             CCeEEEEeehhhhhhhHHHHHHHHhhCCCCCEEEEEEEEEeCCeEEEEcCCCcEEEEEHHHCCCccccChhHhcCCCCEE
Confidence            99999999876432  22355556678899999999887                       5542  334579999999


Q ss_pred             EEEEEEeecCCC----CcC-cccccccccc--ccccCCCCCEEEEEEEEEeCCeEEEEeCCCeEEEEecccCCC------
Q 002054          879 ELAECLFGTEDG----DED-NKGTRVEAIV--SAKNLKLGTKVAAKVYQVRARGLVLDLGGGIRGMYRFENNEK------  945 (974)
Q Consensus       879 ~~~Vl~vd~e~~----~i~-slK~~~~~p~--~~~~~~vG~vV~G~V~~I~~~GvFV~L~~gv~Glih~se~~~------  945 (974)
                      +++|+++|.+++    ++. |+|++..+||  ..++|++|+++.|+|+++++||+||+|++|+.||+|.|+++.      
T Consensus       254 ~vkVl~id~~~~~~~~ri~lS~K~~~~~p~~~~~~~~~~G~~v~G~V~~v~~~G~fV~l~~gv~Glvh~sels~~~~~~~  333 (491)
T PRK13806        254 RVKVLGIERAKKGKGLRISLSIKQAGGDPWDTVGDRLKAGDKVTGKVVRLAPFGAFVEILPGIEGLVHVSEMSWTRRVNK  333 (491)
T ss_pred             EEEEEEEecccCCcceEEEEEehhhhcccchhhhccCCCCCEEEEEEEEEeCceEEEEeCCCcEEEEEHHHcCcccccCC
Confidence            999999999874    577 9999999999  467999999999999999999999999999999999998752      


Q ss_pred             --CCCCCCCEEEEEEEEEeC-CCceeeeecC
Q 002054          946 --KDFVVGDELLVKCSSFTG-KGIPVVSLVD  973 (974)
Q Consensus       946 --~~f~vGd~V~vkVl~id~-~~~~~~~~~~  973 (974)
                        +.|++||+|+|+|+++|+ +++..+|+..
T Consensus       334 ~~~~~~~Gd~v~vkVl~iD~e~~ri~Ls~K~  364 (491)
T PRK13806        334 PEDVVAPGDAVAVKIKDIDPAKRRISLSLRD  364 (491)
T ss_pred             HHHcCCCCCEEEEEEEEEEccCCEEEEEEee
Confidence              358999999999999997 4667777653

>PRK07400 30S ribosomal protein S1; Reviewed

Probab=99.95  E-value=3.9e-27  Score=262.36  Aligned_cols=230  Identities=18%  Similarity=0.275  Sum_probs=181.7

Q ss_pred             EecCHHHHHHHHHHHHHHhhcccccCcEEEEEEEEEeeceEEEEEcCCeEEEEecccCCCccccccccccccCCEEEEEE
Q 002054          659 VAKNRSVMEKVLEKVDFIIGREIEVGGIYKGVVTSVKEYGAFVEFNGGQQGLLHVSELSHEPVSRVSDVVSVGQQLSLRC  738 (974)
Q Consensus       659 ~~~~~~~~~~a~~~i~~l~~~~~~~G~i~~G~V~~i~~~G~fV~l~~g~~Glvhisels~~~v~~~~~~~~vGd~V~vkV  738 (974)
                      +..+.+.+++..+..+    ..++.|+++.|+|+++.++|+||+|+++.+||+|.+|+++.++.++.+.|++||.++|+|
T Consensus        11 ~~~~~~~f~~~le~~~----~~~~~G~iv~G~V~~i~~~g~~Vdig~k~~g~lp~sEis~~~~~~~~~~~~~G~~v~~~V   86 (318)
T PRK07400         11 IGFTHEDFAALLDKYD----YHFKPGDIVNGTVFSLEPRGALIDIGAKTAAFMPIQEMSINRVEGPEEVLQPNETREFFI   86 (318)
T ss_pred             cCCCHHHHHHHHHhhH----hhcCCCCEEEEEEEEEECCEEEEEECCCeEEEEEHHHhccccccCHHHccCCCCEEEEEE
Confidence            3445556665554332    348999999999999999999999987899999999999999999999999999999999


Q ss_pred             EEEcc-CCceEEEEeccCC-Ccccc------cCce---------EEEEEeecCCcceeeEEeeccCCCCCCCCCCCCCCC
Q 002054          739 IGQDV-RGNIKLSLKAVSP-RPEAD------VKGV---------VEGSVPVNKQATDVWASVGDVSNGQNPELPMRKNET  801 (974)
Q Consensus       739 l~id~-~gri~LS~K~~~~-~~~~~------~g~~---------~~G~vv~i~~gv~~~~~~~~l~~~~~~~lp~~~~~~  801 (974)
                      +++|. +|++.||+|.+.. .+|..      .+..         ..|.|+++ +|+++|+|+++++|...    .     
T Consensus        87 i~~~~~~~~i~lS~k~~~~~~~w~~l~~~~~~~~~V~g~V~~~~~~G~~V~l-~Gv~gfip~s~ls~~~~----~-----  156 (318)
T PRK07400         87 LSDENEDGQLTLSIRRIEYMRAWERVRQLQKEDATVRSEVFATNRGGALVRI-EGLRGFIPGSHISTRKP----K-----  156 (318)
T ss_pred             EEEeCCCCeEEEehhhhhhhhHHHHHHHhccCCCEEEEEEEEEECCeEEEEE-CCEEEEEEHHHcCccCC----c-----
Confidence            99987 6899999998753 67775      1333         35667777 58999999999998531    1     


Q ss_pred             CCcccCCCCcceEEEeecccccccccccccccccccccccccccccCCCCCCCcEEEEEecccCcCCCcccccCCeEEEE
Q 002054          802 PGVNSSTSSTPAVLIRSAAECDEEEKASGFSQSSKSTLKSTLASKSNSKPKKFTSQSDFFSSTNIQKSTSFSQREREELA  881 (974)
Q Consensus       802 ~~~~~~~G~~v~v~Ir~~l~iD~~~r~i~ls~k~~~~~~~~~~~~~~~~~~G~~v~g~V~~~~~~~~~~~~k~Gq~v~~~  881 (974)
                        + ..+|+.+.++|   +++|++++++.||+|+...                                           
T Consensus       157 --~-~~vG~~i~~kV---l~id~~~~~i~lS~K~~~~-------------------------------------------  187 (318)
T PRK07400        157 --E-ELVGEELPLKF---LEVDEERNRLVLSHRRALV-------------------------------------------  187 (318)
T ss_pred             --c-ccCCCEEEEEE---EEEEcccCEEEEEhhHhhh-------------------------------------------
Confidence              1 23677777777   7777776666666663321                                           


Q ss_pred             EEEeecCCCCcCccccccccccccccCCCCCEEEEEEEEEeCCeEEEEeCCCeEEEEecccCC-------CCCCCCCCEE
Q 002054          882 ECLFGTEDGDEDNKGTRVEAIVSAKNLKLGTKVAAKVYQVRARGLVLDLGGGIRGMYRFENNE-------KKDFVVGDEL  954 (974)
Q Consensus       882 Vl~vd~e~~~i~slK~~~~~p~~~~~~~vG~vV~G~V~~I~~~GvFV~L~~gv~Glih~se~~-------~~~f~vGd~V  954 (974)
                                         .+ ...++++|++|.|+|++|++||+||+++ |+.||+|.++++       .+.|++||.|
T Consensus       188 -------------------~~-~~~~~k~G~vv~G~V~~I~~~G~fV~i~-gv~Gllhisels~~~~~~~~~~~~vGd~V  246 (318)
T PRK07400        188 -------------------ER-KMNRLEVGEVVVGTVRGIKPYGAFIDIG-GVSGLLHISEISHEHIETPHSVFNVNDEM  246 (318)
T ss_pred             -------------------hh-hhccCCCCCEEEEEEEEEECCeEEEEEC-CEEEEEEHHHcccccccChhhccCCCCEE
Confidence                               11 2466899999999999999999999995 899999999775       3458999999


Q ss_pred             EEEEEEEeC-CCceeeeec
Q 002054          955 LVKCSSFTG-KGIPVVSLV  972 (974)
Q Consensus       955 ~vkVl~id~-~~~~~~~~~  972 (974)
                      +|+|+++|. ++...+|+.
T Consensus       247 kvkVl~iD~e~~rI~LS~K  265 (318)
T PRK07400        247 KVMIIDLDAERGRISLSTK  265 (318)
T ss_pred             EEEEEEEeCCCCEEEEEEe
Confidence            999999996 667777764

>KOG1069 consensus Exosomal 3'-5' exoribonuclease complex, subunit Rrp46 [Translation, ribosomal structure and biogenesis]

Probab=99.95  E-value=2.6e-27  Score=236.20  Aligned_cols=202  Identities=23%  Similarity=0.328  Sum_probs=176.2

Q ss_pred             CccCeEEEeCCCCCCCcceEEEeCCeEEEEEEEeCCCchhhhccccCCCCceeEEEEEecCCCCccccccccCCCchhhh
Q 002054          378 EVRPIYCESGNLPILHGSSLFSRGDTQVLCTVTLGAPAEAQRLESLVGPPTKRFMLHYSFPPFCINEVGKRVGLNRREVG  457 (974)
Q Consensus       378 e~R~I~ie~g~l~~a~GSal~~~G~T~Vl~~Vtl~~p~~~~~~d~~~~~~~~~~~v~~~f~p~s~~e~~~~~~~~rre~~  457 (974)
                      .+|++.|+.|+|+++||||.|++|+|+|+|+|+  ||.|.+..++.    ..+..+++.+.|.+..       ++++|..
T Consensus         4 ~lr~~~cei~iLsr~dGSs~fsqgdT~V~c~V~--GP~dvk~r~E~----~~katleVi~rp~~G~-------~~~~eK~   70 (217)
T KOG1069|consen    4 RLRGIACEISILSRPDGSSEFSQGDTKVICSVY--GPIDVKARQED----PEKATLEVIWRPKSGV-------NGTVEKV   70 (217)
T ss_pred             hhhhhhhhhceecCCCCccceecCCcEEEEEee--CCcchhhcccC----chhceEEEEEecccCc-------chHHHHH
Confidence            789999999999999999999999999999999  99998765543    4567899999888753       5789999


Q ss_pred             HHHHHHHHhhhcCCCCCCCCeE-EEEEEEEEcCCCChhhHHHHHHHHHHHHcCCCccccccceeeeeeccCCCCCCcccc
Q 002054          458 HGTLAEKALLAVLPPENDFPYT-VRVNSEVMASDGSTSMATVCGGSMALMDAGIPLQEHVAGVSVGLVSEVDPSTGEIKD  536 (974)
Q Consensus       458 ~~~l~eral~~vi~~~~~~p~t-I~V~v~VLesdGs~~~A~v~aa~lAL~dagvPi~~~vagvs~gli~~~d~~~~~~~~  536 (974)
                      +++++++.|.+.+.+ +.||+| |+|.++|+++|||.+.+|+|||++||.||||||+++++|+++.+.+++         
T Consensus        71 ~e~iI~~tl~~~I~l-~l~Prt~iqVsiqvv~ddgs~LacaINaAclALvDaGIpl~~mfcai~~~~~~d~---------  140 (217)
T KOG1069|consen   71 LERIIRKTLSKAIIL-ELYPRTTIQVSIQVVEDDGSTLACAINAACLALVDAGIPLRSMFCAISCALHEDG---------  140 (217)
T ss_pred             HHHHHHHHHHHhhee-eecCCceEEEEEEEEecCCcchHHHHHHHHHHHHhcCCchHHhhhhceEEEecCc---------
Confidence            999999999999998 899995 999999999999999999999999999999999999999999999863         


Q ss_pred             eEEEecCCcccccc--CCccEEEEeeCC---ceEEEEeeccCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHhcCC
Q 002054          537 YRILTDILGLEDHL--GDMDFKIAGTRI---GVTAIQLDIKPAGIPLDIICECLEHAHKGRLQILDHMEREISAP  606 (974)
Q Consensus       537 ~~iL~Dp~~~Ee~~--~d~d~~Va~t~~---gI~alq~~~k~~~i~~e~l~~al~~A~~~~~~I~~~m~~~i~~~  606 (974)
                       .+++||+..++..  +...+++.++..   +++.+  +. .+.++.++|..+++.|..++.+++.++++.+.+.
T Consensus       141 -~lv~Dpt~~qek~~~~~~~lsf~~~~~~~~~vi~s--~t-~G~~~~d~lf~~le~a~~~~~~~f~f~r~~~q~~  211 (217)
T KOG1069|consen  141 -VLVLDPTAKQEKISTARATLSFEGGSLGEPKVIIS--ET-NGEKSEDQLFYVLELAQAAAQSLFPFYREVLQRK  211 (217)
T ss_pred             -cEEECCcHHhhhhhhceEEEEEecCCCCCcceEEE--ec-cCCCCHHHHHHHHHhhHHHHHHHHHHHHHHHHhh
Confidence             6999999999984  445666654433   34443  33 3679999999999999999999999999999764

>KOG1614 consensus Exosomal 3'-5' exoribonuclease complex, subunit Rrp45 [Translation, ribosomal structure and biogenesis]

Probab=99.95  E-value=3.2e-26  Score=233.56  Aligned_cols=233  Identities=21%  Similarity=0.272  Sum_probs=200.8

Q ss_pred             HHHHHHHHHhcCCcCCCCCCCCccCeEEEeCCCCCCCcceEEEeCCeEEEEEEEeC--CCchhhhccccCCCCceeEEEE
Q 002054          357 KRVIRKRIIAEGVRVDGRQLDEVRPIYCESGNLPILHGSSLFSRGDTQVLCTVTLG--APAEAQRLESLVGPPTKRFMLH  434 (974)
Q Consensus       357 ~~~~r~~il~~~~R~DGR~~~e~R~I~ie~g~l~~a~GSal~~~G~T~Vl~~Vtl~--~p~~~~~~d~~~~~~~~~~~v~  434 (974)
                      ++++. ..|+.|.|.|||+++|+|.+.+++|   .-.||+.++.|+|+|+|.|+..  .|...       .|.+|.|.+.
T Consensus        11 ~~fvl-~alk~g~R~DgR~l~efR~lei~fG---ke~gs~~vt~G~Tkvm~~vt~~ia~Py~d-------RP~eG~~~I~   79 (291)
T KOG1614|consen   11 SKFVL-NALKAGLRFDGRSLEEFRDLEIEFG---KEYGSVLVTMGNTKVMARVTAQIAQPYID-------RPHEGSFSIF   79 (291)
T ss_pred             HHHHH-HHHHhcccccccchhhhhceEEEec---cccccEEEEecCeeEEEEeehhhcCcccC-------CCCCCeeeee
Confidence            44454 6778999999999999999999999   5789999999999999999943  45443       4788999999


Q ss_pred             EecCCCCccccccccCCCchhhhHHHHHHHHhh----------hcCCCCCCCCeEEEEEEEEEcCCCChhhHHHHHHHHH
Q 002054          435 YSFPPFCINEVGKRVGLNRREVGHGTLAEKALL----------AVLPPENDFPYTVRVNSEVMASDGSTSMATVCGGSMA  504 (974)
Q Consensus       435 ~~f~p~s~~e~~~~~~~~rre~~~~~l~eral~----------~vi~~~~~~p~tI~V~v~VLesdGs~~~A~v~aa~lA  504 (974)
                      .++.|.+...+. .|..+..+..++++++++++          |+.-  .+-.|.||+++++|+.|||+.+||..|+.+|
T Consensus        80 telsPmA~~sfE-~Gr~~~~~v~l~Rliek~~R~S~aiD~EsLCI~a--G~kvW~IRiDlhiLd~DGnlvDaA~iAviaa  156 (291)
T KOG1614|consen   80 TELSPMASPSFE-PGRKGESEVELSRLIEKALRRSKAIDTESLCIRA--GEKVWLIRIDLHILDHDGNLVDAACIAVIAA  156 (291)
T ss_pred             eccccccccccC-CCCccchHHHHHHHHHHHHHhccccchHHHHhhh--CCeEEEEEEEEEEEcCCCCeehhHHHHHHHH
Confidence            999999886653 34456778899999999983          3444  3678999999999999999999999999999


Q ss_pred             HHHcCCC-----------------------ccccccceeeeeeccCCCCCCcccceEEEecCCccccccCCccEEEEeeC
Q 002054          505 LMDAGIP-----------------------LQEHVAGVSVGLVSEVDPSTGEIKDYRILTDILGLEDHLGDMDFKIAGTR  561 (974)
Q Consensus       505 L~dagvP-----------------------i~~~vagvs~gli~~~d~~~~~~~~~~iL~Dp~~~Ee~~~d~d~~Va~t~  561 (974)
                      ||+.+-|                       |+++|.++++|+++.+         ..+++||+..|+.++|..++|+.++
T Consensus       157 L~hFrrPdvTv~g~ev~ihp~eEr~PvPL~I~HmPIC~tf~ffnkG---------~ivviDpt~~Ee~~~dGs~vVt~Nk  227 (291)
T KOG1614|consen  157 LMHFRRPDVTVGGEEVIIHPVEEREPVPLSIHHMPICFTFGFFNKG---------EIVVIDPTEKEEAVMDGSMVVTMNK  227 (291)
T ss_pred             HHhcCCCCcccccceeEecChhccCCcceeeeeccceEEEEEecCc---------eEEEeCCcHHHHhccCceEEEEEcC
Confidence            9999943                       8999999999999863         2899999999999999999999999


Q ss_pred             Cc-eEEEEeeccCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCCCCCCC
Q 002054          562 IG-VTAIQLDIKPAGIPLDIICECLEHAHKGRLQILDHMEREISAPRTQDDRN  613 (974)
Q Consensus       562 ~g-I~alq~~~k~~~i~~e~l~~al~~A~~~~~~I~~~m~~~i~~~~~~~~~~  613 (974)
                      ++ +|++|..++ -.+...++..|...|...+..+.+.+.+++++...+.+.+
T Consensus       228 ~rEVc~i~k~G~-~~~~~~~i~~C~k~A~~~a~~vt~ii~e~l~~d~~~r~~~  279 (291)
T KOG1614|consen  228 NREVCAIQKSGG-EILDESVIERCYKLAKDRAVEVTGIILEALEEDQRERSAQ  279 (291)
T ss_pred             CccEEEEecCCC-ccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhh
Confidence            88 999999764 5788999999999999999999999999999876655543

>PRK04282 exosome complex RNA-binding protein Rrp42; Provisional

Probab=99.94  E-value=5.3e-26  Score=249.55  Aligned_cols=201  Identities=24%  Similarity=0.293  Sum_probs=172.4

Q ss_pred             CeEEEEEeCccCcCCCcEEEEEeCCeEEEEEEEeCCC-CC--CCCceeeEeeccccccccCCCCCccccccCCCCchhhh
Q 002054           67 SRLITLETGKIARFANGAVVLGMDETKVLSTVTSSKG-DS--VRDFLPLTVDYQEKQFAQGVIPNTYMRREGAPKERELL  143 (974)
Q Consensus        67 ~r~i~~etg~~a~~A~GSa~v~~G~T~Vl~tv~~~~~-~~--~~~f~pL~v~y~e~~~a~g~ip~~~~~Reg~p~~~eil  143 (974)
                      -|++.+++|.+ ++|+|||++++|+|+|+|+|+.+.. |.  ..+-.-++++|.-..+|..     + .|.|+|++++++
T Consensus        34 ~R~i~i~~g~l-~~a~GSa~v~~G~T~vl~~V~~~~~~p~~~~~~~g~i~~~v~~~~~a~~-----~-~~~~~~~~~~~~  106 (271)
T PRK04282         34 YRPIEIETGVI-KKAEGSALVKLGNTQVLAGVKLEIGEPFPDTPNEGVLIVNAELLPLASP-----T-FEPGPPDENAIE  106 (271)
T ss_pred             ccCeEEEeCCc-cCCCcEEEEEECCCEEEEEEEEEEecCCCCCCCCCEEEEEEEECCCcCc-----c-ccCCCCCHHHHH
Confidence            48899999999 9999999999999999999996543 21  1233446777665554432     1 256899999999


Q ss_pred             HHHhhcCCccccc----------cCCCCCceEEEEEEEeccCCCChhhHHHHHHHHHhhcCCCC----------------
Q 002054          144 VGRIIDRPIRPLF----------PAGFYHEVQVMASVLSSDGKQDPDIMAANATSAALMLSDIP----------------  197 (974)
Q Consensus       144 ~~RlidR~lrplf----------p~~~~~~~~i~~~vl~~dg~~~~~~~ai~aAs~AL~~s~iP----------------  197 (974)
                      ++|+++|+||+.+          |..+.|.++|.++||+.||+..  .||++||++||+++++|                
T Consensus       107 l~~~l~r~l~~~~~~dl~~L~I~~g~~~w~i~Vdv~VL~~dG~~~--daa~~Aa~aAL~~~~iP~~~~~~~~~~~~~~~~  184 (271)
T PRK04282        107 LARVVDRGIRESKAIDLEKLVIEPGKKVWVVFIDVYVLDHDGNLL--DASMLAAVAALLNTKVPAVEEGEDGVVDKLGED  184 (271)
T ss_pred             HHHHHHHHHhccCCccHHHcEEecCcEEEEEEEEEEEECCCCCHH--HHHHHHHHHHHHhCCCCcEEEcCCceeccCCCc
Confidence            9999999999963          4455779999999999999855  79999999999999995                


Q ss_pred             ----CCCCeEEEEEEEECCEEEEcCCHHHHhcCccceeEeeeCC-eEEEEEe-cCCCCCHHHHHHHHHHHHHHHHHHHHH
Q 002054          198 ----WGGPIGMIRIGRICGQFIVNPTMDELSLSDLNLVYACTRE-KTLMIDV-QAREISEKDLEAGLRLAHPEAVKYLEP  271 (974)
Q Consensus       198 ----~~~~v~av~vg~i~g~~vldPt~~e~~~s~~~l~v~~t~~-~i~mie~-~~~~~~e~~~~~al~~a~~~~~~i~~~  271 (974)
                          |++++.+|++|++++++|+|||.+|++.++.+++|+.+++ .+++++. ++..+++++|.+|+++|++.++++++.
T Consensus       185 ~~l~~~~~p~~vt~~~~~~~~v~Dpt~~Ee~~~~~~l~va~~~~g~i~~l~~~g~~~~~~~~l~~~i~~A~~~~~~l~~~  264 (271)
T PRK04282        185 FPLPVNDKPVTVTFAKIGNYLIVDPTLEEESVMDARITITTDEDGNIVAIQKSGIGSFTEEEVDKAIDIALEKAKELREK  264 (271)
T ss_pred             ccCCCCCeeEEEEEEEECCEEEECCCHHHHhhcCceEEEEECCCCcEEEEEcCCCCCCCHHHHHHHHHHHHHHHHHHHHH
Confidence                9999999999999999999999999999999999999988 5888885 456799999999999999999999999


Q ss_pred             HHHHH
Q 002054          272 QIRLA  276 (974)
Q Consensus       272 ~~~~~  276 (974)
                      +++.+
T Consensus       265 ~~~~l  269 (271)
T PRK04282        265 LKEAL  269 (271)
T ss_pred             HHHHh
Confidence            98876

>KOG1613 consensus Exosomal 3'-5' exoribonuclease complex, subunit Rrp43 [Translation, ribosomal structure and biogenesis]

Probab=99.94  E-value=4.6e-26  Score=231.74  Aligned_cols=243  Identities=21%  Similarity=0.305  Sum_probs=191.7

Q ss_pred             HHHHHHHHHHHHHHHHHHhcCCcCCCCCCCCccCeEEEeCCCCCCCcceEEEeCCeEEEEEEEeC--CCchhhhccccCC
Q 002054          348 LPKAVDTVRKRVIRKRIIAEGVRVDGRQLDEVRPIYCESGNLPILHGSSLFSRGDTQVLCTVTLG--APAEAQRLESLVG  425 (974)
Q Consensus       348 ~~~~~~~~~~~~~r~~il~~~~R~DGR~~~e~R~I~ie~g~l~~a~GSal~~~G~T~Vl~~Vtl~--~p~~~~~~d~~~~  425 (974)
                      -.++|+++.|+.|.+++|++|+|+|||.+.|+|.+.++.|.+++++|||+++.|+|.|+|+++.+  .|..+       .
T Consensus        15 ~p~~fkrI~Pe~~l~rhLse~~RpdgR~lgefRdt~in~g~IsTangSal~K~G~ttvi~~Ik~ei~epstd-------a   87 (298)
T KOG1613|consen   15 PPEVFKRISPELYLQRHLSEGIRPDGRKLGEFRDTAINAGNISTANGSALLKSGKTTVICGIKAEIAEPSTD-------A   87 (298)
T ss_pred             CHHHHhhcCHHHHHHHHhhcccCcchhhhhHHhhhheecCceeccCcHHHHhcCCcEEEEEeeeeecccccC-------C
Confidence            45789999999999999999999999999999999999999999999999999999999999965  45542       3


Q ss_pred             CCceeEEEEEecCCCCccccccccCCCchhhhHHHHHHHHh----------hhcCCCCCCCCeEEEEEEEEEcCCCChhh
Q 002054          426 PPTKRFMLHYSFPPFCINEVGKRVGLNRREVGHGTLAEKAL----------LAVLPPENDFPYTVRVNSEVMASDGSTSM  495 (974)
Q Consensus       426 ~~~~~~~v~~~f~p~s~~e~~~~~~~~rre~~~~~l~eral----------~~vi~~~~~~p~tI~V~v~VLesdGs~~~  495 (974)
                      ++++.+..+|.+||.|+..+ |.|.|+..+.-++..+...+          +|+.+  .+..|.++.++.||+.||+.++
T Consensus        88 pdeg~Iv~n~~lpplcs~r~-RpG~p~dea~viSq~LhdtIl~S~ii~~k~Lci~~--gKaawvlYadIicLd~dG~~fD  164 (298)
T KOG1613|consen   88 PDEGDIVPNYALPPLCSSRF-RPGPPTDEAQVISQKLHDTILHSRIIPKKALCIKA--GKAAWVLYADIICLDYDGPVFD  164 (298)
T ss_pred             CCCcceeecccCCcccccCC-CCCCCchHHHHHHHHHHHHHHhcCCcchhhheeec--cceeeEEEEEEEEEcCCCcHHH
Confidence            67899999999999999764 57777777755554443333          34444  4688999999999999999999


Q ss_pred             HHHHHHHHHHHHcCCCcc---c-----------cccceee-----------eee-ccCCCCCC-cccceEEEecCCcccc
Q 002054          496 ATVCGGSMALMDAGIPLQ---E-----------HVAGVSV-----------GLV-SEVDPSTG-EIKDYRILTDILGLED  548 (974)
Q Consensus       496 A~v~aa~lAL~dagvPi~---~-----------~vagvs~-----------gli-~~~d~~~~-~~~~~~iL~Dp~~~Ee  548 (974)
                      ||++|.++||.+-.+|.-   .           ..+..+.           .+. .+.+.+-. -..+.-++.|||.+||
T Consensus       165 a~w~al~aAlknvklP~a~ide~~~~~~~t~e~~ic~~tlt~p~~ln~e~r~~~~~n~~fS~~~vl~~~li~adpT~eEE  244 (298)
T KOG1613|consen  165 ACWNALMAALKNVKLPRAFIDERASDLRMTIEEIICDQTLTVPLMLNAENRAFASQNSDFSEEEVLDDVLIAADPTEEEE  244 (298)
T ss_pred             HHHHHHHHHHhcCCCceeeecccchhhhhhHHHHHHhhhhcchhhhccccccccccCCCccHHHhhcceeEecCCCchhh
Confidence            999999999999999921   1           1111100           000 00000000 0113356699999999


Q ss_pred             ccCCccEEEEeeCCc-eEEEEeeccCCCCCHHHHHHHHHHHHHHHHHHHHHHH
Q 002054          549 HLGDMDFKIAGTRIG-VTAIQLDIKPAGIPLDIICECLEHAHKGRLQILDHME  600 (974)
Q Consensus       549 ~~~d~d~~Va~t~~g-I~alq~~~k~~~i~~e~l~~al~~A~~~~~~I~~~m~  600 (974)
                      ++.+..++|..+..| ++.+.+-++..-++++.+++|++.|+.+.+++-+.|.
T Consensus       245 ~l~~~~lTIvldss~n~v~l~k~GG~al~~~~~iK~c~elar~Rakelk~~~~  297 (298)
T KOG1613|consen  245 TLITSTLTIVLDSSGNYVQLTKVGGGALITPEMIKRCLELARVRAKELKTRFN  297 (298)
T ss_pred             hhhhceEEEEEcCCCCEEEEEecCcccccCHHHHHHHHHHHHHHHHHHHHHhc
Confidence            999999999988877 8888887776778889999999999999999887764

>KOG1069 consensus Exosomal 3'-5' exoribonuclease complex, subunit Rrp46 [Translation, ribosomal structure and biogenesis]

Probab=99.92  E-value=5.9e-25  Score=219.40  Aligned_cols=193  Identities=22%  Similarity=0.250  Sum_probs=167.0

Q ss_pred             eEEEEEeCccCcCCCcEEEEEeCCeEEEEEEEeCCCC----CCCCceeeEeeccccccccCCCCCccccccCCCCchhhh
Q 002054           68 RLITLETGKIARFANGAVVLGMDETKVLSTVTSSKGD----SVRDFLPLTVDYQEKQFAQGVIPNTYMRREGAPKERELL  143 (974)
Q Consensus        68 r~i~~etg~~a~~A~GSa~v~~G~T~Vl~tv~~~~~~----~~~~f~pL~v~y~e~~~a~g~ip~~~~~Reg~p~~~eil  143 (974)
                      |++..|.|.| +++|||+-+++|+|+|+|+|+||.+.    +.-+-..|.|-||++.              |-+...|..
T Consensus         6 r~~~cei~iL-sr~dGSs~fsqgdT~V~c~V~GP~dvk~r~E~~~katleVi~rp~~--------------G~~~~~eK~   70 (217)
T KOG1069|consen    6 RGIACEISIL-SRPDGSSEFSQGDTKVICSVYGPIDVKARQEDPEKATLEVIWRPKS--------------GVNGTVEKV   70 (217)
T ss_pred             hhhhhhhcee-cCCCCccceecCCcEEEEEeeCCcchhhcccCchhceEEEEEeccc--------------CcchHHHHH
Confidence            6788999999 89999999999999999999999882    2334567999999987              888999999


Q ss_pred             HHHhhcCCccccccCCC--CCceEEEEEEEeccCCCChhhHHHHHHHHHhhcCCCCCCCCeEEEEEEEE-CCEEEEcCCH
Q 002054          144 VGRIIDRPIRPLFPAGF--YHEVQVMASVLSSDGKQDPDIMAANATSAALMLSDIPWGGPIGMIRIGRI-CGQFIVNPTM  220 (974)
Q Consensus       144 ~~RlidR~lrplfp~~~--~~~~~i~~~vl~~dg~~~~~~~ai~aAs~AL~~s~iP~~~~v~av~vg~i-~g~~vldPt~  220 (974)
                      .+|+|.+.|.+++-...  +..+||+++|++.||+..  ++|||||++||.|+||||+.+.+|+.+.+. ||.+|+|||.
T Consensus        71 ~e~iI~~tl~~~I~l~l~Prt~iqVsiqvv~ddgs~L--acaINaAclALvDaGIpl~~mfcai~~~~~~d~~lv~Dpt~  148 (217)
T KOG1069|consen   71 LERIIRKTLSKAIILELYPRTTIQVSIQVVEDDGSTL--ACAINAACLALVDAGIPLRSMFCAISCALHEDGVLVLDPTA  148 (217)
T ss_pred             HHHHHHHHHHHhheeeecCCceEEEEEEEEecCCcch--HHHHHHHHHHHHhcCCchHHhhhhceEEEecCccEEECCcH
Confidence            99999999988544333  447889999999999876  999999999999999999999999999998 5699999999


Q ss_pred             HHHhcCc--cceeEeee---CCeEEEEEecCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 002054          221 DELSLSD--LNLVYACT---REKTLMIDVQAREISEKDLEAGLRLAHPEAVKYLEPQIRLAEK  278 (974)
Q Consensus       221 ~e~~~s~--~~l~v~~t---~~~i~mie~~~~~~~e~~~~~al~~a~~~~~~i~~~~~~~~~~  278 (974)
                      .|++.+.  ..|.+.++   ..+++|.|..| ++++++|..++++|..+++.++.++++..++
T Consensus       149 ~qek~~~~~~~lsf~~~~~~~~~vi~s~t~G-~~~~d~lf~~le~a~~~~~~~f~f~r~~~q~  210 (217)
T KOG1069|consen  149 KQEKISTARATLSFEGGSLGEPKVIISETNG-EKSEDQLFYVLELAQAAAQSLFPFYREVLQR  210 (217)
T ss_pred             HhhhhhhceEEEEEecCCCCCcceEEEeccC-CCCHHHHHHHHHhhHHHHHHHHHHHHHHHHh
Confidence            9999654  44555333   34599999998 5999999999999999999999999998865

>COG2123 RNase PH-related exoribonuclease [Translation, ribosomal structure and biogenesis]

Probab=99.92  E-value=2.6e-24  Score=226.34  Aligned_cols=192  Identities=27%  Similarity=0.350  Sum_probs=170.3

Q ss_pred             eEEEEEeCccCcCCCcEEEEEeCCeEEEEEEEeCCC-C----C-------CCCceeeEeeccccccccCCCCCccccccC
Q 002054           68 RLITLETGKIARFANGAVVLGMDETKVLSTVTSSKG-D----S-------VRDFLPLTVDYQEKQFAQGVIPNTYMRREG  135 (974)
Q Consensus        68 r~i~~etg~~a~~A~GSa~v~~G~T~Vl~tv~~~~~-~----~-------~~~f~pL~v~y~e~~~a~g~ip~~~~~Reg  135 (974)
                      |++.+++|++ +.|+|||+|++|+|+|+|+++.+.. |    +       +.++.||...++|.               |
T Consensus        34 R~ieI~~~vi-~ka~GSa~VklG~Tqvv~gvK~eig~Pf~DtP~eG~~~~n~El~Plas~~fE~---------------G   97 (272)
T COG2123          34 RPLEIETGVI-PKANGSALVKLGNTQVVVGVKAEIGEPFPDTPNEGVLVVNVELSPLASPSFEP---------------G   97 (272)
T ss_pred             cceEEEeCce-ecCCCcEEEEecCeEEEEEEEcccCCCCCCCCCCceEEeeeeeeccccccccC---------------C
Confidence            7899999999 8899999999999999999998765 2    1       13567888888777               9


Q ss_pred             CCCchhhhHHHhhcCCccc----------cccCCCCCceEEEEEEEeccCCCChhhHHHHHHHHHhhcCCCC--------
Q 002054          136 APKERELLVGRIIDRPIRP----------LFPAGFYHEVQVMASVLSSDGKQDPDIMAANATSAALMLSDIP--------  197 (974)
Q Consensus       136 ~p~~~eil~~RlidR~lrp----------lfp~~~~~~~~i~~~vl~~dg~~~~~~~ai~aAs~AL~~s~iP--------  197 (974)
                      +|++++++++|++||.||.          .+++.+.+-++++++||++||+.-  .||..|+.+||+...+|        
T Consensus        98 ppde~aielsrvvdr~lr~s~aiDlekL~I~~g~kvwvv~vDv~vld~DGnl~--Da~~lA~~aAL~~t~vP~~~~~~~~  175 (272)
T COG2123          98 PPDELAIELSRVVDRGLRESKAIDLEKLCIEEGKKVWVVFVDVHVLDYDGNLI--DAASLAAVAALLNTRVPKAVEVGDG  175 (272)
T ss_pred             CCchhHHHHHHHHHHHHHhccCcchhheeEecCCEEEEEEEEEEEEcCCCCHH--HHHHHHHHHHHHhcCCCceeecCCc
Confidence            9999999999999999999          566788889999999999999766  89999999999988766        


Q ss_pred             --------------CCCCeEEEEEEEECCEEEEcCCHHHHhcCccceeEeeeCCe--EEEEEecCCCCCHHHHHHHHHHH
Q 002054          198 --------------WGGPIGMIRIGRICGQFIVNPTMDELSLSDLNLVYACTREK--TLMIDVQAREISEKDLEAGLRLA  261 (974)
Q Consensus       198 --------------~~~~v~av~vg~i~g~~vldPt~~e~~~s~~~l~v~~t~~~--i~mie~~~~~~~e~~~~~al~~a  261 (974)
                                    +.+++-+|+++++|+.+++|||.+|+..++..++++.++++  +.|..+++..++++++.+|++.|
T Consensus       176 ~~v~~~~~~~~pl~~~~~pi~vt~a~ig~~lvvDPsleEe~v~d~~ltit~~~~~~Iv~iqK~g~~~~~~~~~~~~~~~A  255 (272)
T COG2123         176 EIVIEVEEEPVPLPVSNPPISVTFAKIGNVLVVDPSLEEELVADGRLTITVNEDGEIVAIQKVGGGSITESDLEKALKTA  255 (272)
T ss_pred             ceeecccCCCcccccCCCceEEEEEEECCEEEeCCCcchhhhcCceEEEEECCCCcEEEEEEcCCCcCCHHHHHHHHHHH
Confidence                          67788899999999999999999999999999999999987  45556677889999999999999


Q ss_pred             HHHHHHHHHHHHHHHH
Q 002054          262 HPEAVKYLEPQIRLAE  277 (974)
Q Consensus       262 ~~~~~~i~~~~~~~~~  277 (974)
                      .+...++++.+.+.++
T Consensus       256 ~~~~~kl~~~~~~~L~  271 (272)
T COG2123         256 LSKAEKLREALKEALK  271 (272)
T ss_pred             HHHHHHHHHHHHHhhc
Confidence            9999999998877653

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

Probab=99.90  E-value=7.6e-23  Score=228.51  Aligned_cols=208  Identities=21%  Similarity=0.330  Sum_probs=183.7

Q ss_pred             ccCeEEEeCCCC-CCCcceEEEeCCeEEEEEEEeC-CCchhhhccccCCCCceeEEEEEecCCCCccc-----cccccCC
Q 002054          379 VRPIYCESGNLP-ILHGSSLFSRGDTQVLCTVTLG-APAEAQRLESLVGPPTKRFMLHYSFPPFCINE-----VGKRVGL  451 (974)
Q Consensus       379 ~R~I~ie~g~l~-~a~GSal~~~G~T~Vl~~Vtl~-~p~~~~~~d~~~~~~~~~~~v~~~f~p~s~~e-----~~~~~~~  451 (974)
                      -|.|.+++|.+. .|+||+.++.|+|.|+++|++. .|.+         +.+-++++||....+++|.     .+|.+++
T Consensus        55 nR~i~~etGklaRfAngsvvv~~GeT~Vm~Tv~~a~~PSp---------~qFlPL~VdYqeK~aAvGRip~~fmRREg~t  125 (760)
T KOG1067|consen   55 NREILFETGKLARFANGSVVVQMGETAVMTTVVLADKPSP---------PQFLPLVVDYQEKFAAVGRIPGNFMRREGRT  125 (760)
T ss_pred             CeEEEEecchhhhhcCCcEEEccCCeEEEEEEEecCCCCc---------cccceEEEehhhhhhhhccCCCcccccccCC
Confidence            488999999998 5999999999999999999976 4555         3477899999998887764     5788999


Q ss_pred             CchhhhHHHHHHHHhhhcCCCCCCCCeEEEEEEEEEcCCCCh--hhHHHHHHHHHHHHcCCCccccccceeeeeeccCCC
Q 002054          452 NRREVGHGTLAEKALLAVLPPENDFPYTVRVNSEVMASDGST--SMATVCGGSMALMDAGIPLQEHVAGVSVGLVSEVDP  529 (974)
Q Consensus       452 ~rre~~~~~l~eral~~vi~~~~~~p~tI~V~v~VLesdGs~--~~A~v~aa~lAL~dagvPi~~~vagvs~gli~~~d~  529 (974)
                      +.+|+..++|++|.++|.+|  +.|-+..++.+.+|.+||-.  ...++||+++||+-+.||+..++.++.+|++++   
T Consensus       126 kdkEiL~~rLidrsirplfp--~g~~~etqi~~n~Ls~dG~~~pdvlainaas~Al~lsdvpw~gpig~vRigLi~G---  200 (760)
T KOG1067|consen  126 KDKEILTGRLIDRPIRPLFP--KGFYHETQILCNVLSSDGVHDPDVLAINAASAALSLSDVPWNGPIGAVRIGLIDG---  200 (760)
T ss_pred             cchhheeeeccccccccCCc--ccchhHHHHHhhheecccccCchHHHHhHHHHHhhhccCCCCCceeeeEeeeecc---
Confidence            99999999999999999999  57877899999999999944  467899999999999999999999999999986   


Q ss_pred             CCCcccceEEEecCCccccccCCccEEEEeeCCceEEEEeeccCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCCC
Q 002054          530 STGEIKDYRILTDILGLEDHLGDMDFKIAGTRIGVTAIQLDIKPAGIPLDIICECLEHAHKGRLQILDHMEREISAPRTQ  609 (974)
Q Consensus       530 ~~~~~~~~~iL~Dp~~~Ee~~~d~d~~Va~t~~gI~alq~~~k~~~i~~e~l~~al~~A~~~~~~I~~~m~~~i~~~~~~  609 (974)
                              .++++||..|.+.++.++.+|+|++.+.++..  +...|..+.|..|+.++++.+.+++..+....++..+.
T Consensus       201 --------e~vVNPT~kEmssS~Lnlvvagt~~~~vmle~--~s~~i~qqdl~~Aikvg~~~~q~~i~~i~~L~k~~Gk~  270 (760)
T KOG1067|consen  201 --------EFVVNPTRKEMSSSQLNLVVAGTKSQTVMLEG--SSNNILQQDLLHAIKVGVKEAQQIIQGIERLAKKYGKQ  270 (760)
T ss_pred             --------eEEeCcchhhhhhccceeEEEeccceEEEEEc--ccccccHHHHHHHHHhccHHHHHHHHHHHHHHHHhCcc
Confidence                    69999999999999999999999877766554  44579999999999999999999999988888777654


Q ss_pred             C
Q 002054          610 D  610 (974)
Q Consensus       610 ~  610 (974)
                      +
T Consensus       271 K  271 (760)
T KOG1067|consen  271 K  271 (760)
T ss_pred             c
Confidence            4

>KOG1068 consensus Exosomal 3'-5' exoribonuclease complex, subunit Rrp41 and related exoribonucleases [Translation, ribosomal structure and biogenesis]

Probab=99.90  E-value=2.9e-23  Score=215.48  Aligned_cols=204  Identities=23%  Similarity=0.260  Sum_probs=168.2

Q ss_pred             eEEEEEeCccCcCCCcEEEEEeCCeEEEEEEEeCCCCCCC-----CceeeEeeccccccccCCCCCccccccCCCCchhh
Q 002054           68 RLITLETGKIARFANGAVVLGMDETKVLSTVTSSKGDSVR-----DFLPLTVDYQEKQFAQGVIPNTYMRREGAPKEREL  142 (974)
Q Consensus        68 r~i~~etg~~a~~A~GSa~v~~G~T~Vl~tv~~~~~~~~~-----~f~pL~v~y~e~~~a~g~ip~~~~~Reg~p~~~ei  142 (974)
                      |++...+|++ .+|+||||+++|||+|||+|+||++..+.     +..-+.|.|.-..|++|-     .++..+-+.++.
T Consensus        24 R~i~~~~g~~-~~a~GSay~E~GnTKVl~aV~GPre~~~~~~~~~~~a~lnc~~~~a~Fst~~-----r~~~~~~~rr~~   97 (245)
T KOG1068|consen   24 RRIYARIGVL-TQADGSAYMEQGNTKVLCAVYGPREIRGKSARRPDKAVLNCEVSSAQFSTGD-----RKKRPKGDRREK   97 (245)
T ss_pred             hhhhhhcCcc-ccCCccchhhcCCeEEEEEEeCCcccccccccccccceEEEEEeeeccccch-----hccCCCccHHHH
Confidence            6899999988 89999999999999999999999984332     345589999777776652     122234456899


Q ss_pred             hHHHhhcCCccccccCCCCC--ceEEEEEEEeccCCCChhhHHHHHHHHHhhcCCCCCCCCeEEEEEEEECCEEEEcCCH
Q 002054          143 LVGRIIDRPIRPLFPAGFYH--EVQVMASVLSSDGKQDPDIMAANATSAALMLSDIPWGGPIGMIRIGRICGQFIVNPTM  220 (974)
Q Consensus       143 l~~RlidR~lrplfp~~~~~--~~~i~~~vl~~dg~~~~~~~ai~aAs~AL~~s~iP~~~~v~av~vg~i~g~~vldPt~  220 (974)
                      +++.++.+.+.|.+-...++  .+.|.++||+.||++.  ++|||||.+||+++||||++.|.|+++|+.+|.+++||++
T Consensus        98 e~s~~L~~afe~~I~~~lyPrsqIDI~v~VleddG~~l--aa~inaatlAL~daGI~m~D~i~~~t~~l~~~~~l~Dl~~  175 (245)
T KOG1068|consen   98 ELSLMLQQAFEPVILLELYPRSQIDIYVQVLEDDGSNL--AAAINAATLALADAGIPMYDLITACTAGLADGTPLLDLTS  175 (245)
T ss_pred             HHHHHHHHHHHHHHHhhhCccccceEEEEEEECCCccH--HHHHHHHHHHHHHcCCChhhhhhhceeeecCCcccccccc
Confidence            99999999999865555544  4555578888888777  9999999999999999999999999999999999999999


Q ss_pred             HHHhcCccceeEe--eeCCeEEEEEecCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHhC
Q 002054          221 DELSLSDLNLVYA--CTREKTLMIDVQAREISEKDLEAGLRLAHPEAVKYLEPQIRLAEKAG  280 (974)
Q Consensus       221 ~e~~~s~~~l~v~--~t~~~i~mie~~~~~~~e~~~~~al~~a~~~~~~i~~~~~~~~~~~g  280 (974)
                      -|++...-.++|+  +..+.+..+|.++. ++.+.+...|++|.++|+++.+.++..+.++-
T Consensus       176 ~eesa~~~~ltVa~l~~~~~i~~l~~~~~-~~~d~l~~vl~~a~~~c~~v~~~l~~~l~~~l  236 (245)
T KOG1068|consen  176 LEESARAPGLTVAALPNREEIALLQLDER-LHCDHLETVLELAIAGCKRVYERLRLVLREHL  236 (245)
T ss_pred             chhhccCCceEEEEecCcceEEEEEecCC-CCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            9988855444444  55556999999886 99999999999999999999999988776653

>KOG1612 consensus Exosomal 3'-5' exoribonuclease complex, subunit Rrp42 [Translation, ribosomal structure and biogenesis]

Probab=99.88  E-value=2.7e-21  Score=199.06  Aligned_cols=220  Identities=20%  Similarity=0.262  Sum_probs=179.7

Q ss_pred             hcCCcCCCCCCCCccCeEEEeCCCCCCCcceEEEeCC-eEEEEEEEe--CCCchhhhccccCCCCceeEEEEEecCCCCc
Q 002054          366 AEGVRVDGRQLDEVRPIYCESGNLPILHGSSLFSRGD-TQVLCTVTL--GAPAEAQRLESLVGPPTKRFMLHYSFPPFCI  442 (974)
Q Consensus       366 ~~~~R~DGR~~~e~R~I~ie~g~l~~a~GSal~~~G~-T~Vl~~Vtl--~~p~~~~~~d~~~~~~~~~~~v~~~f~p~s~  442 (974)
                      +..+|.|||..+++|||.+++|+||+++|||.++.|+ |-++++|+.  |.|.+++       +.++.+.+.+.+.|.+.
T Consensus        18 e~~iR~DGR~~~~~Rpi~vetdVlp~tNGSaRVk~g~~tdiivgVKaEvg~~~~~~-------p~egk~~~~VD~S~sas   90 (288)
T KOG1612|consen   18 EPDIRNDGRSCHQFRPIEVETDVLPGTNGSARVKLGDGTDIIVGVKAEVGSPDDET-------PVEGKYLFFVDCSPSAS   90 (288)
T ss_pred             CcccccCCcCccccceEEEEeccccCCCCcEEEEecCCceEEEEEeeeccCccccC-------CCCCeEEEEEEecCCcC
Confidence            5689999999999999999999999999999999999 999999994  4677754       67788999999999998


Q ss_pred             cccccccCCCchh--hhHHHHHHHHhhh--------cCCCCCCCCeEEEEEEEEEcCCCChhhHHHHHHHHHHHHcCCCc
Q 002054          443 NEVGKRVGLNRRE--VGHGTLAEKALLA--------VLPPENDFPYTVRVNSEVMASDGSTSMATVCGGSMALMDAGIPL  512 (974)
Q Consensus       443 ~e~~~~~~~~rre--~~~~~l~eral~~--------vi~~~~~~p~tI~V~v~VLesdGs~~~A~v~aa~lAL~dagvPi  512 (974)
                      .++.-+   +..|  .++.+.++|+|..        -+...+.|.|.|+|++.|+++|||+++|...|+.+||.+..+|-
T Consensus        91 p~f~gR---ggde~~~eltsaLq~~l~~~~sgv~ls~L~lt~~~~W~i~VDvlVi~s~gn~~dAiS~Ai~~AL~~T~lPk  167 (288)
T KOG1612|consen   91 PQFQGR---GGDELVEELTSALQRVLNSLGSGVDLSKLQLTPGYCWKIYVDVLVISSDGNLLDAISIAIYAALNNTRLPK  167 (288)
T ss_pred             ccccCC---ChhhHHHHHHHHHHHHHhCcCcccchhheeccCCeeEEEEEeEEEEecCCCHHHHHHHHHHHHHhcccCCc
Confidence            876422   3333  2456677777755        11122469999999999999999999999999999999999992


Q ss_pred             cc---------------------------cccceeeeeeccCCCCCCcccceEEEecCCccccccCCccEEEEeeCCceE
Q 002054          513 QE---------------------------HVAGVSVGLVSEVDPSTGEIKDYRILTDILGLEDHLGDMDFKIAGTRIGVT  565 (974)
Q Consensus       513 ~~---------------------------~vagvs~gli~~~d~~~~~~~~~~iL~Dp~~~Ee~~~d~d~~Va~t~~gI~  565 (974)
                      -.                           ++.-+++..+.           +.+|+||+.+|+.+....+.|..+..|++
T Consensus       168 v~v~~dd~~~~~i~~s~~~Yd~~~~~~~~~P~ivtlskIG-----------~~~lVD~T~eEe~~a~s~l~Isv~a~giv  236 (288)
T KOG1612|consen  168 VIVAFDDDGEVEILLSDEEYDLMVKLVENVPLIVTLSKIG-----------TNMLVDPTAEEESVANSGLLISVSAGGIV  236 (288)
T ss_pred             cccccccCCceeeccCcccchhhhhhcccCCEEEEEEeec-----------ceEEccCCccHHHhhhcceEEEEecCcce
Confidence            11                           33333444332           47999999999999999999999999977


Q ss_pred             EEEeeccCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHhcCC
Q 002054          566 AIQLDIKPAGIPLDIICECLEHAHKGRLQILDHMEREISAP  606 (974)
Q Consensus       566 alq~~~k~~~i~~e~l~~al~~A~~~~~~I~~~m~~~i~~~  606 (974)
                      .+....+.+++.++.+.++++++++-...+...+.+.|.+.
T Consensus       237 s~~r~VG~G~l~~s~i~~mle~~~~~~e~l~~~l~k~L~~~  277 (288)
T KOG1612|consen  237 SCTRSVGLGDLDPSSIPEMLEQGKAVVETLAPDLVKSLENE  277 (288)
T ss_pred             EEEEEecCCCCChhhHHHHHHHHHHHHHhhhHHHHHHhhhh
Confidence            77666555669999999999999999999988888888764

>PF01138 RNase_PH: 3' exoribonuclease family, domain 1 This Prosite family only includes Ribonuclease PH; InterPro: IPR001247 The PH (phosphorolytic) domain is responsible for 3'-5' exoribonuclease activity, although in some proteins this domain has lost its catalytic function

Probab=99.88  E-value=4.7e-22  Score=194.81  Aligned_cols=131  Identities=31%  Similarity=0.482  Sum_probs=114.6

Q ss_pred             CccCeEEEeCCCCCCCcceEEEeCCeEEEEEEEeCCCchhhhccccCCCCceeEEEEEecCCCCccccccccCCCchhhh
Q 002054          378 EVRPIYCESGNLPILHGSSLFSRGDTQVLCTVTLGAPAEAQRLESLVGPPTKRFMLHYSFPPFCINEVGKRVGLNRREVG  457 (974)
Q Consensus       378 e~R~I~ie~g~l~~a~GSal~~~G~T~Vl~~Vtl~~p~~~~~~d~~~~~~~~~~~v~~~f~p~s~~e~~~~~~~~rre~~  457 (974)
                      |+|++.+++|+++++||||+|++|+|+|+|+|+  +|.+....... ....+.+.++|+++|++..++++.+.+++++..
T Consensus         1 e~R~i~i~~~~~~~a~GSa~v~~G~T~V~~~V~--~~~~~~~~~~~-~~~~g~~~v~v~~~~~~~~~~~~~~~~~~~~~~   77 (132)
T PF01138_consen    1 ELRPISIETGVLPRADGSARVSLGNTKVICSVK--GPIEPPPSNER-DDAEGRLTVEVEFSPFASPSFRRGGRPDEEERE   77 (132)
T ss_dssp             CBEEEEEEESSSSSSSEEEEEEETTEEEEEEEE--EEEEGCSCSTT-SSSSEEEEEEEEECCCGSTSSSSSSSTHHHHHH
T ss_pred             CCccEEEEeCCCCCCCeEEEEEECCeEEEEEEE--ecccccchhcc-cCCCceEEEEEEeccccccccccccccchhHHH
Confidence            789999999999999999999999999999999  55553111111 123488999999999999998777889999999


Q ss_pred             HHHHHHHHhhhcCCCCCCCCeEEEEEEEEEcCCC-ChhhHHHHHHHHHHHHcCCC
Q 002054          458 HGTLAEKALLAVLPPENDFPYTVRVNSEVMASDG-STSMATVCGGSMALMDAGIP  511 (974)
Q Consensus       458 ~~~l~eral~~vi~~~~~~p~tI~V~v~VLesdG-s~~~A~v~aa~lAL~dagvP  511 (974)
                      ++++++++|++++..+..+.|+|+|+++||++|| |+++||++|+++||+|+|||
T Consensus        78 l~~~l~~~l~~~~~~~~~~~~~i~v~v~vl~~dG~~~~~a~~~A~~~AL~~~~iP  132 (132)
T PF01138_consen   78 LSSLLERALRSSILLEGYPRWQIHVDVQVLSDDGGNLLDAAINAACLALLDAGIP  132 (132)
T ss_dssp             HHHHHHHHHHHTBSTTTTSSEEEEEEEEEEECSSSSHHHHHHHHHHHHHHHHTCS
T ss_pred             HHHHHhhhccccccccccCceEEEEEEEEEecCCCCHHHHHHHHHHHHHHhcCCC
Confidence            9999999999999984444589999999999999 99999999999999999998

An active PH domain uses inorganic phosphate as a nucleophile, adding it across the phosphodiester bond between the end two nucleotides in order to release ribonucleoside 5'-diphosphate (rNDP) from the 3' end of the RNA substrate. PH domains can be found in bacterial/organelle RNases and PNPases (polynucleotide phosphorylases) [], as well as in archaeal and eukaryotic RNA exosomes [, ], the later acting as nano-compartments for the degradation or processing of RNA (including mRNA, rRNA, snRNA and snoRNA). Bacterial/organelle PNPases share a common barrel structure with RNA exosomes, consisting of a hexameric ring of PH domains that act as a degradation chamber, and an S1-domain/KH-domain containing cap that binds the RNA substrate (and sometimes accessory proteins) in order to regulate and restrict entry into the degradation chamber []. Unstructured RNA substrates feed in through the pore made by the S1 domains, are degraded by the PH domain ring, and exit as nucleotides via the PH pore at the opposite end of the barrel [, ]. This entry represents the phosphorolytic (PH) domain 1, which has a core 2-layer alpha/beta structure with a left-handed crossover, similar to that found in ribosomal protein S5. This domain is found in bacterial/organelle PNPases and in archaeal/eukaryotic exosomes []. More information about these proteins can be found at Protein of the Month: RNA Exosomes [].; PDB: 2C38_G 2BR2_O 2C37_M 3L7Z_A 2JEB_A 2C39_A 2JEA_A 2JE6_A 3U1K_A 4AM3_B ....

>PRK07899 rpsA 30S ribosomal protein S1; Reviewed

Probab=99.86  E-value=2.8e-21  Score=225.20  Aligned_cols=226  Identities=16%  Similarity=0.151  Sum_probs=181.2

Q ss_pred             CCEEEEEecCHHHHHHHHHHHHHHhhcccccCcEEEEEEEEEeeceEEEEEcCCeEEEEecccCCCccccccccccccCC
Q 002054          653 DGTLTVVAKNRSVMEKVLEKVDFIIGREIEVGGIYKGVVTSVKEYGAFVEFNGGQQGLLHVSELSHEPVSRVSDVVSVGQ  732 (974)
Q Consensus       653 dg~v~i~~~~~~~~~~a~~~i~~l~~~~~~~G~i~~G~V~~i~~~G~fV~l~~g~~Glvhisels~~~v~~~~~~~~vGd  732 (974)
                      +|.+.++... .....++..++.+    .+.|++++|+|+++.++|+||++  |++||+|.|++++.++.++..+  +||
T Consensus        97 ~g~liLS~k~-~~~~~~w~~ie~~----~e~g~~V~G~V~~v~k~G~~Vdl--Gi~gflP~Sel~~~~~~~~~~~--vGq  167 (486)
T PRK07899         97 EGRLILSKKR-AQYERAWGTIEKI----KEKDGVVTGTVIEVVKGGLILDI--GLRGFLPASLVEMRRVRDLQPY--IGQ  167 (486)
T ss_pred             CCeEEEEehh-hcccchHHHHHHH----hcCCCEEEEEEEEEECCeEEEEE--CCEEEEEhhHhcccccCChhhc--CCC
Confidence            4566655432 2234455555432    46899999999999999999999  6899999999999888887763  899


Q ss_pred             EEEEEEEEEcc-CCceEEEEeccCC----Ccccc------cCce---------EEEEEeecCCcceeeEEeeccCCCCCC
Q 002054          733 QLSLRCIGQDV-RGNIKLSLKAVSP----RPEAD------VKGV---------VEGSVPVNKQATDVWASVGDVSNGQNP  792 (974)
Q Consensus       733 ~V~vkVl~id~-~gri~LS~K~~~~----~~~~~------~g~~---------~~G~vv~i~~gv~~~~~~~~l~~~~~~  792 (974)
                      .|+|+|+++|. ++++.||+|.++.    .+|..      .|.+         .+|.|+++ .|+++|+|+++++|.+. 
T Consensus       168 ~V~vkVleid~~~~~ivLSrr~~l~~~~~~~~~~~~~~lk~G~iv~G~V~~i~~~G~FVdl-ggv~Glv~~Sels~~~v-  245 (486)
T PRK07899        168 EIEAKIIELDKNRNNVVLSRRAWLEQTQSEVRSEFLNQLQKGQVRKGVVSSIVNFGAFVDL-GGVDGLVHVSELSWKHI-  245 (486)
T ss_pred             EEEEEEEEEECCCCEEEEEhHHHHHhhhHHHHHHHHHhccCCCEEEEEEEEEECCeEEEEE-CCEEEEEEHHHCCCccc-
Confidence            99999999998 6799999997543    23332      3433         45777777 47999999999999752 


Q ss_pred             CCCCCCCCCCCcccCCCCcceEEEeecccccccccccccccccccccccccccccCCCCCCCcEEEEEec----------
Q 002054          793 ELPMRKNETPGVNSSTSSTPAVLIRSAAECDEEEKASGFSQSSKSTLKSTLASKSNSKPKKFTSQSDFFS----------  862 (974)
Q Consensus       793 ~lp~~~~~~~~~~~~~G~~v~v~Ir~~l~iD~~~r~i~ls~k~~~~~~~~~~~~~~~~~~G~~v~g~V~~----------  862 (974)
                      .+|.       +.+++||.|.++|   +++|+++++|.||+++..++|  |..+.+.+++|+++.|.|.+          
T Consensus       246 ~~~~-------~~~kvGd~V~vkV---l~iD~e~~rI~LSlK~~~~dP--w~~~~~~~~vG~vv~G~V~~I~~fGvFVeL  313 (486)
T PRK07899        246 DHPS-------EVVEVGQEVTVEV---LDVDMDRERVSLSLKATQEDP--WQQFARTHAIGQIVPGKVTKLVPFGAFVRV  313 (486)
T ss_pred             CCHH-------HhcCCCCEEEEEE---EEEECCCCEEEEEEeeccccc--hhhhHHhcCCCCEEEEEEEEEeccEEEEEe
Confidence            3333       6789999999999   999999999999999999998  98888889999999999888          


Q ss_pred             -------------ccC--cCCCcccccCCeEEEEEEEeecCCCCcC-cccccccc
Q 002054          863 -------------STN--IQKSTSFSQREREELAECLFGTEDGDED-NKGTRVEA  901 (974)
Q Consensus       863 -------------~~~--~~~~~~~k~Gq~v~~~Vl~vd~e~~~i~-slK~~~~~  901 (974)
                                   +|.  ......|++||.|+++|+++|.+++++. |+|++..+
T Consensus       314 ~~gieGLvh~SeLs~~~v~~~~~~~kvGd~V~VkIi~ID~e~rrI~LSlK~~~~~  368 (486)
T PRK07899        314 EEGIEGLVHISELAERHVEVPEQVVQVGDEVFVKVIDIDLERRRISLSLKQANEG  368 (486)
T ss_pred             CCCcEEEEEHHHcCcccccCccceeCCCCEEEEEEEEEECCCCEEEEEEEEcccC
Confidence                         222  1223468999999999999999999999 99987654

>PRK06676 rpsA 30S ribosomal protein S1; Reviewed

Probab=99.83  E-value=6.7e-20  Score=211.72  Aligned_cols=208  Identities=19%  Similarity=0.165  Sum_probs=174.0

Q ss_pred             cccccCcEEEEEEEEEeeceEEEEEcCCeEEEEecccCCCccccccccccccCCEEEEEEEEEcc-CCceEEEEeccCCC
Q 002054          679 REIEVGGIYKGVVTSVKEYGAFVEFNGGQQGLLHVSELSHEPVSRVSDVVSVGQQLSLRCIGQDV-RGNIKLSLKAVSPR  757 (974)
Q Consensus       679 ~~~~~G~i~~G~V~~i~~~G~fV~l~~g~~Glvhisels~~~v~~~~~~~~vGd~V~vkVl~id~-~gri~LS~K~~~~~  757 (974)
                      ..++.|+++.|+|+++.++|+||++ +|.+||||++|+++.+..++.++  +||.++|+|+++|. ++++.||+|.+...
T Consensus       101 ~~~~~G~~v~g~V~~v~~~G~~V~~-~G~~gflp~~el~~~~~~~~~~~--vG~~v~~~Vl~~d~~~~~i~lS~k~~~~~  177 (390)
T PRK06676        101 EKFEEGEVVEVKVTEVVKGGLVVDV-EGVRGFIPASLISTRFVEDFSDF--KGKTLEVKIIELDPEKNRVILSRRAVVEE  177 (390)
T ss_pred             HhccCCCEEEEEEEEEECCeEEEEE-CCEEEEEEHHHcCCccCCChHHc--CCCEEEEEEEEEECCCCEEEEEeHHHhhh
Confidence            3468999999999999999999999 57899999999999988887764  89999999999998 68999999987543


Q ss_pred             ----ccc------ccCceE---------EEEEeecCCcceeeEEeeccCCCCCCCCCCCCCCCCCcccCCCCcceEEEee
Q 002054          758 ----PEA------DVKGVV---------EGSVPVNKQATDVWASVGDVSNGQNPELPMRKNETPGVNSSTSSTPAVLIRS  818 (974)
Q Consensus       758 ----~~~------~~g~~~---------~G~vv~i~~gv~~~~~~~~l~~~~~~~lp~~~~~~~~~~~~~G~~v~v~Ir~  818 (974)
                          +|.      ..|..+         .|.|+.+ .|+++|+|+++++|.+. ..|.       +.+++||.+.++|  
T Consensus       178 ~~~~~~~~~~~~~~~G~~v~g~V~~v~~~G~fV~l-~~v~g~v~~sels~~~~-~~~~-------~~~~vGd~i~~~V--  246 (390)
T PRK06676        178 ERAAKKEELLSSLKEGDVVEGTVARLTDFGAFVDI-GGVDGLVHISELSHERV-EKPS-------EVVSVGQEVEVKV--  246 (390)
T ss_pred             hhhhHHHHHHhhCCCCCEEEEEEEEEecceEEEEe-CCeEEEEEHHHcCcccc-CCHH-------HhcCCCCEEEEEE--
Confidence                222      134444         4566666 47999999999998642 2232       6689999999999  


Q ss_pred             cccccccccccccccccccccccccccccCCCCCCCcEEEEEec-----------------------ccCc--CCCcccc
Q 002054          819 AAECDEEEKASGFSQSSKSTLKSTLASKSNSKPKKFTSQSDFFS-----------------------STNI--QKSTSFS  873 (974)
Q Consensus       819 ~l~iD~~~r~i~ls~k~~~~~~~~~~~~~~~~~~G~~v~g~V~~-----------------------~~~~--~~~~~~k  873 (974)
                       +++|++++++.||+++..++|  |......+++|++++|.|.+                       +|..  +....|+
T Consensus       247 -l~vd~~~~~i~lS~k~~~~~~--~~~~~~~~~~G~~v~g~V~~i~~~G~fV~l~~gi~Glv~~se~~~~~~~~~~~~~~  323 (390)
T PRK06676        247 -LSIDWETERISLSLKDTLPGP--WEGVEEKLPEGDVIEGTVKRLTDFGAFVEVLPGVEGLVHISQISHKHIATPSEVLE  323 (390)
T ss_pred             -EEEeCCCCEEEEEEeecccCc--cccchhhhcCCcEEEEEEEEEeCceEEEEECCCCeEEEEhHHcCccccCChhhccC
Confidence             999999999999999988888  88888889999999999888                       2221  1224689


Q ss_pred             cCCeEEEEEEEeecCCCCcC-cccccccccc
Q 002054          874 QREREELAECLFGTEDGDED-NKGTRVEAIV  903 (974)
Q Consensus       874 ~Gq~v~~~Vl~vd~e~~~i~-slK~~~~~p~  903 (974)
                      +||.|+++|+.+|++++++. |+|++..+||
T Consensus       324 ~Gd~v~v~V~~id~e~~~i~ls~k~~~~~~~  354 (390)
T PRK06676        324 EGQEVKVKVLEVNEEEKRISLSIKALEEAPA  354 (390)
T ss_pred             CCCEEEEEEEEEECCCCEEEEEEEecccChh
Confidence            99999999999999999999 9999999999

>PRK00087 4-hydroxy-3-methylbut-2-enyl diphosphate reductase/S1 RNA-binding domain protein; Reviewed

Probab=99.78  E-value=1.4e-18  Score=211.78  Aligned_cols=228  Identities=21%  Similarity=0.181  Sum_probs=182.9

Q ss_pred             CCEEEEEecCHHHHHHHHHHHHHHhhcccccCcEEEEEEEEEeeceEEEEEcCCeEEEEecccCCCccccccccccccCC
Q 002054          653 DGTLTVVAKNRSVMEKVLEKVDFIIGREIEVGGIYKGVVTSVKEYGAFVEFNGGQQGLLHVSELSHEPVSRVSDVVSVGQ  732 (974)
Q Consensus       653 dg~v~i~~~~~~~~~~a~~~i~~l~~~~~~~G~i~~G~V~~i~~~G~fV~l~~g~~Glvhisels~~~v~~~~~~~~vGd  732 (974)
                      +|++.++.... ....+++.+.    ..++.|+++.|+|+++.++|+||+++ +.+||+|.+|+++.+..++..+  +|+
T Consensus       364 ~g~i~LS~k~~-~~~~~~~~l~----~~~~~G~iv~g~V~~v~~~G~~V~lg-gi~gfiP~sel~~~~~~d~~~~--vG~  435 (647)
T PRK00087        364 DGYVVLSKKEA-DREKAWKELE----EAFENGEPVKGKVKEVVKGGLLVDYG-GVRAFLPASHVELGYVEDLSEY--KGQ  435 (647)
T ss_pred             CCcEEEEeehh-cchhHHHHHH----HHhhCCCEEEEEEEEEECCeEEEEEC-CEEEEEEHHHhCccccCCHHHh--CCC
Confidence            56666665432 2334444433    34689999999999999999999995 6999999999999988887764  899


Q ss_pred             EEEEEEEEEcc-CCc-eEEEEeccCC--------Ccccc--cCceE---------EEEEeecCCcceeeEEeeccCCCCC
Q 002054          733 QLSLRCIGQDV-RGN-IKLSLKAVSP--------RPEAD--VKGVV---------EGSVPVNKQATDVWASVGDVSNGQN  791 (974)
Q Consensus       733 ~V~vkVl~id~-~gr-i~LS~K~~~~--------~~~~~--~g~~~---------~G~vv~i~~gv~~~~~~~~l~~~~~  791 (974)
                      .++|+|+++|+ +++ +.||+|....        ..|..  .|+.+         +|.|+++ +|+++|+|.++++|.+.
T Consensus       436 ~v~v~Vl~vd~e~~~~l~lS~k~~~~~~~~~~~~~~~~~l~~G~iV~g~V~~v~~~G~fV~l-~gv~Gll~~sels~~~~  514 (647)
T PRK00087        436 ELEVKIIEFNRKRRKKVVLSRKAILEEEKEKKKEETWNSLEEGDVVEGEVKRLTDFGAFVDI-GGVDGLLHVSEISWGRV  514 (647)
T ss_pred             EEEEEEEEEEcCCCcEEEEEeHHHhhhhhhhHHHHHHHhCCCCCEEEEEEEEEeCCcEEEEE-CCEEEEEEHHHcCcccc
Confidence            99999999998 567 9999998753        12322  34444         4566666 68999999999998652


Q ss_pred             CCCCCCCCCCCCcccCCCCcceEEEeecccccccccccccccccccccccccccccCCCCCCCcEEEEEec---------
Q 002054          792 PELPMRKNETPGVNSSTSSTPAVLIRSAAECDEEEKASGFSQSSKSTLKSTLASKSNSKPKKFTSQSDFFS---------  862 (974)
Q Consensus       792 ~~lp~~~~~~~~~~~~~G~~v~v~Ir~~l~iD~~~r~i~ls~k~~~~~~~~~~~~~~~~~~G~~v~g~V~~---------  862 (974)
                       ..|.       +.+++||.+.++|   +++|++++++.||+++..++|  |......+++|+++.|.|.+         
T Consensus       515 -~~~~-------~~~~vGd~V~vkV---~~id~~~~~I~lS~K~~~~~p--~~~~~~~~~~G~~v~g~V~~i~~~G~fV~  581 (647)
T PRK00087        515 -EKPS-------DVLKVGDEIKVYI---LDIDKENKKLSLSLKKLLPDP--WENVEEKYPVGSIVLGKVVRIAPFGAFVE  581 (647)
T ss_pred             -CCHH-------HhcCCCCEEEEEE---EEEECCCCEEEEEeeccccCh--hhhhhhhccCCeEEEEEEEEEECCeEEEE
Confidence             2222       6789999999999   999999999999999999888  88888888899999999887         


Q ss_pred             --------------ccC--cCCCcccccCCeEEEEEEEeecCCCCcC-ccccccccc
Q 002054          863 --------------STN--IQKSTSFSQREREELAECLFGTEDGDED-NKGTRVEAI  902 (974)
Q Consensus       863 --------------~~~--~~~~~~~k~Gq~v~~~Vl~vd~e~~~i~-slK~~~~~p  902 (974)
                                    +|.  .+....|++||.|+++|+++|.+++++. |+|++..+|
T Consensus       582 l~~~i~Gli~~sel~~~~~~~~~~~~kvGd~V~vkV~~id~e~~rI~lslk~~~~~~  638 (647)
T PRK00087        582 LEPGVDGLVHISQISWKRIDKPEDVLSEGEEVKAKILEVDPEEKRIRLSIKEVEEEP  638 (647)
T ss_pred             ECCCCEEEEEhhhcCccccCCHhhcCCCCCEEEEEEEEEeCCCCEEEEEEeecccCc
Confidence                          222  1223478999999999999999999999 999998887

>COG1098 VacB Predicted RNA binding protein (contains ribosomal protein S1 domain) [Translation, ribosomal structure and biogenesis]

Probab=99.72  E-value=4.4e-18  Score=158.00  Aligned_cols=81  Identities=37%  Similarity=0.722  Sum_probs=77.4

Q ss_pred             ccccCcEEEEEEEEEeeceEEEEEcCCeEEEEecccCCCccccccccccccCCEEEEEEEEEccCCceEEEEeccCCCcc
Q 002054          680 EIEVGGIYKGVVTSVKEYGAFVEFNGGQQGLLHVSELSHEPVSRVSDVVSVGQQLSLRCIGQDVRGNIKLSLKAVSPRPE  759 (974)
Q Consensus       680 ~~~~G~i~~G~V~~i~~~G~fV~l~~g~~Glvhisels~~~v~~~~~~~~vGd~V~vkVl~id~~gri~LS~K~~~~~~~  759 (974)
                      .+++|++++|+|++|++|||||+|.+|..|||||||+++.+++++.+++++||.|+|||+++|++|+|.||+|++.+.|.
T Consensus         2 ~~kvG~~l~GkItgI~~yGAFV~l~~g~tGLVHISEIa~~fVkdI~d~L~vG~eV~vKVl~ide~GKisLSIr~~~e~pe   81 (129)
T COG1098           2 SMKVGSKLKGKITGITPYGAFVELEGGKTGLVHISEIADGFVKDIHDHLKVGQEVKVKVLDIDENGKISLSIRKLEEEPE   81 (129)
T ss_pred             CccccceEEEEEEeeEecceEEEecCCCcceEEehHhhhhhHHhHHHHhcCCCEEEEEEEeeccCCCcceehHHhhhCcc
Confidence            47899999999999999999999999999999999999999999999999999999999999999999999999988765


Q ss_pred             c
Q 002054          760 A  760 (974)
Q Consensus       760 ~  760 (974)
                      .
T Consensus        82 ~   82 (129)
T COG1098          82 K   82 (129)
T ss_pred             c
Confidence            4

>PF01138 RNase_PH: 3' exoribonuclease family, domain 1 This Prosite family only includes Ribonuclease PH; InterPro: IPR001247 The PH (phosphorolytic) domain is responsible for 3'-5' exoribonuclease activity, although in some proteins this domain has lost its catalytic function

Probab=99.71  E-value=2.6e-17  Score=161.20  Aligned_cols=122  Identities=31%  Similarity=0.396  Sum_probs=105.3

Q ss_pred             eEEEEEeCccCcCCCcEEEEEeCCeEEEEEEEeCCCC-C-CC-Ccee--eEeeccccccccCCCCCccccccCCCCchhh
Q 002054           68 RLITLETGKIARFANGAVVLGMDETKVLSTVTSSKGD-S-VR-DFLP--LTVDYQEKQFAQGVIPNTYMRREGAPKEREL  142 (974)
Q Consensus        68 r~i~~etg~~a~~A~GSa~v~~G~T~Vl~tv~~~~~~-~-~~-~f~p--L~v~y~e~~~a~g~ip~~~~~Reg~p~~~ei  142 (974)
                      |++.+++|.+ .+|+|||++++|+|+|+|+|++|.+. + .. +..+  +++++.-..++.++.     +|+|+++..+.
T Consensus         3 R~i~i~~~~~-~~a~GSa~v~~G~T~V~~~V~~~~~~~~~~~~~~~~g~~~v~v~~~~~~~~~~-----~~~~~~~~~~~   76 (132)
T PF01138_consen    3 RPISIETGVL-PRADGSARVSLGNTKVICSVKGPIEPPPSNERDDAEGRLTVEVEFSPFASPSF-----RRGGRPDEEER   76 (132)
T ss_dssp             EEEEEEESSS-SSSSEEEEEEETTEEEEEEEEEEEEGCSCSTTSSSSEEEEEEEEECCCGSTSS-----SSSSSTHHHHH
T ss_pred             ccEEEEeCCC-CCCCeEEEEEECCeEEEEEEEecccccchhcccCCCceEEEEEEecccccccc-----ccccccchhHH
Confidence            8999999999 89999999999999999999999872 2 22 4333  888888777776654     56689999999


Q ss_pred             hHHHhhcCCcccccc--CCCCCceEEEEEEEeccC-CCChhhHHHHHHHHHhhcCCCC
Q 002054          143 LVGRIIDRPIRPLFP--AGFYHEVQVMASVLSSDG-KQDPDIMAANATSAALMLSDIP  197 (974)
Q Consensus       143 l~~RlidR~lrplfp--~~~~~~~~i~~~vl~~dg-~~~~~~~ai~aAs~AL~~s~iP  197 (974)
                      ++++++++.|++.+.  ..+++.++|.++||+.|| +..  .+|+|||++||++++||
T Consensus        77 ~l~~~l~~~l~~~~~~~~~~~~~i~v~v~vl~~dG~~~~--~a~~~A~~~AL~~~~iP  132 (132)
T PF01138_consen   77 ELSSLLERALRSSILLEGYPRWQIHVDVQVLSDDGGNLL--DAAINAACLALLDAGIP  132 (132)
T ss_dssp             HHHHHHHHHHHHTBSTTTTSSEEEEEEEEEEECSSSSHH--HHHHHHHHHHHHHHTCS
T ss_pred             HHHHHHhhhccccccccccCceEEEEEEEEEecCCCCHH--HHHHHHHHHHHHhcCCC
Confidence            999999999999665  455789999999999999 666  99999999999999998

An active PH domain uses inorganic phosphate as a nucleophile, adding it across the phosphodiester bond between the end two nucleotides in order to release ribonucleoside 5'-diphosphate (rNDP) from the 3' end of the RNA substrate. PH domains can be found in bacterial/organelle RNases and PNPases (polynucleotide phosphorylases) [], as well as in archaeal and eukaryotic RNA exosomes [, ], the later acting as nano-compartments for the degradation or processing of RNA (including mRNA, rRNA, snRNA and snoRNA). Bacterial/organelle PNPases share a common barrel structure with RNA exosomes, consisting of a hexameric ring of PH domains that act as a degradation chamber, and an S1-domain/KH-domain containing cap that binds the RNA substrate (and sometimes accessory proteins) in order to regulate and restrict entry into the degradation chamber []. Unstructured RNA substrates feed in through the pore made by the S1 domains, are degraded by the PH domain ring, and exit as nucleotides via the PH pore at the opposite end of the barrel [, ]. This entry represents the phosphorolytic (PH) domain 1, which has a core 2-layer alpha/beta structure with a left-handed crossover, similar to that found in ribosomal protein S5. This domain is found in bacterial/organelle PNPases and in archaeal/eukaryotic exosomes []. More information about these proteins can be found at Protein of the Month: RNA Exosomes [].; PDB: 2C38_G 2BR2_O 2C37_M 3L7Z_A 2JEB_A 2C39_A 2JEA_A 2JE6_A 3U1K_A 4AM3_B ....

>KOG1614 consensus Exosomal 3'-5' exoribonuclease complex, subunit Rrp45 [Translation, ribosomal structure and biogenesis]

Probab=99.63  E-value=1e-14  Score=149.90  Aligned_cols=204  Identities=21%  Similarity=0.249  Sum_probs=158.6

Q ss_pred             eEEEEEeCccCcCCCcEEEEEeCCeEEEEEEEeCCC-C----CCCCceeeEeeccccccccCCCCCcccccc-CCCCchh
Q 002054           68 RLITLETGKIARFANGAVVLGMDETKVLSTVTSSKG-D----SVRDFLPLTVDYQEKQFAQGVIPNTYMRRE-GAPKERE  141 (974)
Q Consensus        68 r~i~~etg~~a~~A~GSa~v~~G~T~Vl~tv~~~~~-~----~~~~f~pL~v~y~e~~~a~g~ip~~~~~Re-g~p~~~e  141 (974)
                      |.++++.|+. .   ||+.+++|+|+|+|.++.+.- |    +..+-+-+..+..+-++.         .-| |++++.+
T Consensus        33 R~lei~fGke-~---gs~~vt~G~Tkvm~~vt~~ia~Py~dRP~eG~~~I~telsPmA~~---------sfE~Gr~~~~~   99 (291)
T KOG1614|consen   33 RDLEIEFGKE-Y---GSVLVTMGNTKVMARVTAQIAQPYIDRPHEGSFSIFTELSPMASP---------SFEPGRKGESE   99 (291)
T ss_pred             hceEEEeccc-c---ccEEEEecCeeEEEEeehhhcCcccCCCCCCeeeeeecccccccc---------ccCCCCccchH
Confidence            5789999988 4   999999999999999998754 2    222223333333322211         112 8999999


Q ss_pred             hhHHHhhcCCccc----------cccCCCCCceEEEEEEEeccCCCChhhHHHHHHHHHhhcCC----------------
Q 002054          142 LLVGRIIDRPIRP----------LFPAGFYHEVQVMASVLSSDGKQDPDIMAANATSAALMLSD----------------  195 (974)
Q Consensus       142 il~~RlidR~lrp----------lfp~~~~~~~~i~~~vl~~dg~~~~~~~ai~aAs~AL~~s~----------------  195 (974)
                      ++++|+|++.+|-          ..-..-.+.+.|+.++|+.||+.-  .||..||.+||+-=.                
T Consensus       100 v~l~Rliek~~R~S~aiD~EsLCI~aG~kvW~IRiDlhiLd~DGnlv--DaA~iAviaaL~hFrrPdvTv~g~ev~ihp~  177 (291)
T KOG1614|consen  100 VELSRLIEKALRRSKAIDTESLCIRAGEKVWLIRIDLHILDHDGNLV--DAACIAVIAALMHFRRPDVTVGGEEVIIHPV  177 (291)
T ss_pred             HHHHHHHHHHHHhccccchHHHHhhhCCeEEEEEEEEEEEcCCCCee--hhHHHHHHHHHHhcCCCCcccccceeEecCh
Confidence            9999999999997          223444667888899999999987  899999999998644                


Q ss_pred             -----CC--CCCCeEEEEEEEEC--CEEEEcCCHHHHhcCccceeEeeeCCe-EEEEEecCC-CCCHHHHHHHHHHHHHH
Q 002054          196 -----IP--WGGPIGMIRIGRIC--GQFIVNPTMDELSLSDLNLVYACTREK-TLMIDVQAR-EISEKDLEAGLRLAHPE  264 (974)
Q Consensus       196 -----iP--~~~~v~av~vg~i~--g~~vldPt~~e~~~s~~~l~v~~t~~~-i~mie~~~~-~~~e~~~~~al~~a~~~  264 (974)
                           +|  ++....+++.|..|  +-.|+|||.+|+...|.-++|+.++.. |+.++..|+ -+++.+++.+.+.|..-
T Consensus       178 eEr~PvPL~I~HmPIC~tf~ffnkG~ivviDpt~~Ee~~~dGs~vVt~Nk~rEVc~i~k~G~~~~~~~~i~~C~k~A~~~  257 (291)
T KOG1614|consen  178 EEREPVPLSIHHMPICFTFGFFNKGEIVVIDPTEKEEAVMDGSMVVTMNKNREVCAIQKSGGEILDESVIERCYKLAKDR  257 (291)
T ss_pred             hccCCcceeeeeccceEEEEEecCceEEEeCCcHHHHhccCceEEEEEcCCccEEEEecCCCccccHHHHHHHHHHHHHH
Confidence                 33  56778899999986  557899999999999999999999887 777776554 48999999999999999


Q ss_pred             HHHHHHHHHHHHHHhCCccccc
Q 002054          265 AVKYLEPQIRLAEKAGKQKKEY  286 (974)
Q Consensus       265 ~~~i~~~~~~~~~~~g~~k~~~  286 (974)
                      +.++...+.+.+++.-+++..+
T Consensus       258 a~~vt~ii~e~l~~d~~~r~~~  279 (291)
T KOG1614|consen  258 AVEVTGIILEALEEDQRERSAQ  279 (291)
T ss_pred             HHHHHHHHHHHHHHHHHHhhhh
Confidence            9999998888887765444333

>PRK07400 30S ribosomal protein S1; Reviewed

Probab=99.61  E-value=4.4e-15  Score=165.99  Aligned_cols=169  Identities=19%  Similarity=0.201  Sum_probs=129.9

Q ss_pred             CCEEEEEecCHHHHHHHHHHHHHHhhcccccCcEEEEEEEEEeeceEEEEEcCCeEEEEecccCCCccccccccccccCC
Q 002054          653 DGTLTVVAKNRSVMEKVLEKVDFIIGREIEVGGIYKGVVTSVKEYGAFVEFNGGQQGLLHVSELSHEPVSRVSDVVSVGQ  732 (974)
Q Consensus       653 dg~v~i~~~~~~~~~~a~~~i~~l~~~~~~~G~i~~G~V~~i~~~G~fV~l~~g~~Glvhisels~~~v~~~~~~~~vGd  732 (974)
                      +|.+.++.... ....+++.+..    ..+.|++++|+|+++.++|+||++ +|++||||+|++++.+..   +.+ +|+
T Consensus        93 ~~~i~lS~k~~-~~~~~w~~l~~----~~~~~~~V~g~V~~~~~~G~~V~l-~Gv~gfip~s~ls~~~~~---~~~-vG~  162 (318)
T PRK07400         93 DGQLTLSIRRI-EYMRAWERVRQ----LQKEDATVRSEVFATNRGGALVRI-EGLRGFIPGSHISTRKPK---EEL-VGE  162 (318)
T ss_pred             CCeEEEehhhh-hhhhHHHHHHH----hccCCCEEEEEEEEEECCeEEEEE-CCEEEEEEHHHcCccCCc---ccc-CCC
Confidence            46666654432 12234444332    346799999999999999999999 699999999999986433   333 999


Q ss_pred             EEEEEEEEEcc-CCceEEEEeccCCCc-cc--ccCc---------eEEEEEeecCCcceeeEEeeccCCCCCCCCCCCCC
Q 002054          733 QLSLRCIGQDV-RGNIKLSLKAVSPRP-EA--DVKG---------VVEGSVPVNKQATDVWASVGDVSNGQNPELPMRKN  799 (974)
Q Consensus       733 ~V~vkVl~id~-~gri~LS~K~~~~~~-~~--~~g~---------~~~G~vv~i~~gv~~~~~~~~l~~~~~~~lp~~~~  799 (974)
                      .|.|+|+++|+ ++++.||+|....+. +.  +.|.         ..+|.|+++ .|++|++|+++++|.+. ..|    
T Consensus       163 ~i~~kVl~id~~~~~i~lS~K~~~~~~~~~~~k~G~vv~G~V~~I~~~G~fV~i-~gv~Gllhisels~~~~-~~~----  236 (318)
T PRK07400        163 ELPLKFLEVDEERNRLVLSHRRALVERKMNRLEVGEVVVGTVRGIKPYGAFIDI-GGVSGLLHISEISHEHI-ETP----  236 (318)
T ss_pred             EEEEEEEEEEcccCEEEEEhhHhhhhhhhccCCCCCEEEEEEEEEECCeEEEEE-CCEEEEEEHHHcccccc-cCh----
Confidence            99999999998 689999999765432 21  2344         345667776 58999999999999763 223    


Q ss_pred             CCCCcccCCCCcceEEEeeccccccccccccccccccccccccccc
Q 002054          800 ETPGVNSSTSSTPAVLIRSAAECDEEEKASGFSQSSKSTLKSTLAS  845 (974)
Q Consensus       800 ~~~~~~~~~G~~v~v~Ir~~l~iD~~~r~i~ls~k~~~~~~~~~~~  845 (974)
                         .+.+++||.+++.|   +++|.+++++.||+++..++|  |..
T Consensus       237 ---~~~~~vGd~VkvkV---l~iD~e~~rI~LS~K~l~~~P--~~~  274 (318)
T PRK07400        237 ---HSVFNVNDEMKVMI---IDLDAERGRISLSTKQLEPEP--GDM  274 (318)
T ss_pred             ---hhccCCCCEEEEEE---EEEeCCCCEEEEEEeccccCh--hhh
Confidence               37899999999999   999999999999999999998  644

>KOG1070 consensus rRNA processing protein Rrp5 [RNA processing and modification]

Probab=99.53  E-value=2.9e-13  Score=165.30  Aligned_cols=275  Identities=18%  Similarity=0.158  Sum_probs=202.3

Q ss_pred             cccccCcEEEEEEEEEeeceEEEEEcCCeEEEEecccCCCcc--ccccccccccCCEEEEEEEEEcc------------C
Q 002054          679 REIEVGGIYKGVVTSVKEYGAFVEFNGGQQGLLHVSELSHEP--VSRVSDVVSVGQQLSLRCIGQDV------------R  744 (974)
Q Consensus       679 ~~~~~G~i~~G~V~~i~~~G~fV~l~~g~~Glvhisels~~~--v~~~~~~~~vGd~V~vkVl~id~------------~  744 (974)
                      .++.+|.++.++|++|.++++-|.+..+..|.||+||+-+..  +.+|.+.|++||.|.|+|++.-.            .
T Consensus       881 ~~~~igsiv~a~v~svKp~~L~v~l~~~~~gri~isev~d~~~eitDp~~k~~vG~~I~vrviG~~D~k~lpith~i~k~  960 (1710)
T KOG1070|consen  881 EDLSIGSIVRAYVKSVKPDQLNVLLAANHHGRIHISEVLDNLHEITDPLDKFKVGDGIFVRVIGGHDVKDLPITHLISKE  960 (1710)
T ss_pred             cceeeeeEEEEEEeeecccceEEeccccccCceehHHhhccccccCChhhhcccCCeEEEEEEcCCccccCccccccchh
Confidence            368899999999999999999999999999999999998764  66899999999999999999621            1


Q ss_pred             CceEEEEeccCCC--ccc-------ccCceEEEEEeec---------CCcceeeEEeeccCCC-CCCCCCCCCCCCCCcc
Q 002054          745 GNIKLSLKAVSPR--PEA-------DVKGVVEGSVPVN---------KQATDVWASVGDVSNG-QNPELPMRKNETPGVN  805 (974)
Q Consensus       745 gri~LS~K~~~~~--~~~-------~~g~~~~G~vv~i---------~~gv~~~~~~~~l~~~-~~~~lp~~~~~~~~~~  805 (974)
                      .-..||+|....+  +..       ..|+.+.|.|...         ...+++.+++.+++.. ....+|       ...
T Consensus       961 ~v~ElSvkps~les~~~~t~s~~q~~~gq~vtGfV~nv~ke~~w~~isp~v~~RIplld~s~~~~~le~~-------e~~ 1033 (1710)
T KOG1070|consen  961 QVLELSVKPSELESDEFNTTSTKQFKAGQEVTGFVNNVSKEWLWVRISPFVDGRIPLLDTSLDLHVLELP-------ESL 1033 (1710)
T ss_pred             hhhhhccChhhhccccccccchhhhhcCCeEEEEEEccccceeEEEccccccceeeeeeccchhhhhhCc-------hhh
Confidence            2345666643222  111       1377888877643         3457888888888843 222233       378


Q ss_pred             cCCCCcceEEEeecccccccccccccccccccccccccccccCCCCCCCcEEEEEec-----------------------
Q 002054          806 SSTSSTPAVLIRSAAECDEEEKASGFSQSSKSTLKSTLASKSNSKPKKFTSQSDFFS-----------------------  862 (974)
Q Consensus       806 ~~~G~~v~v~Ir~~l~iD~~~r~i~ls~k~~~~~~~~~~~~~~~~~~G~~v~g~V~~-----------------------  862 (974)
                      |..|+.+.++|   +..|..  +....++....++        ...+|++.-|+|.+                       
T Consensus      1034 F~~g~al~~~V---~~~~~~--~tv~~iG~~~~~k--------~~s~G~~l~Grv~kv~~~~~~l~~~~~~~G~~~~i~~ 1100 (1710)
T KOG1070|consen 1034 FPLGKALDEYV---VRNDKS--KTVRAIGFSKSDK--------NPSPGDILFGRVSKVLPGYLILQLPFKVFGRVSFIED 1100 (1710)
T ss_pred             cccccceeeEE---ecccce--eEEEecccccCCC--------CCCcchhhcceeeeeccceeEEecCCccccceEEeee
Confidence            99999999999   777732  2222222221111        11156665555544                       


Q ss_pred             ---ccCcCCCcccccCCeEEEEEEEeecCCCCcC-ccccccc--ccc--------ccccCCCCCEEEEEEEEEeCCeEEE
Q 002054          863 ---STNIQKSTSFSQREREELAECLFGTEDGDED-NKGTRVE--AIV--------SAKNLKLGTKVAAKVYQVRARGLVL  928 (974)
Q Consensus       863 ---~~~~~~~~~~k~Gq~v~~~Vl~vd~e~~~i~-slK~~~~--~p~--------~~~~~~vG~vV~G~V~~I~~~GvFV  928 (974)
                         +|.-..-..|..+|.+...+|.++..++.+. |++....  .|.        ..++++.|++|.|.|.++.+.|+|+
T Consensus      1101 ~~d~~~~~P~~~f~~~~~v~~~~L~vs~~n~~leLslr~sr~~~t~~~~kd~~iks~eDlk~g~iv~G~V~nv~~~glfi 1180 (1710)
T KOG1070|consen 1101 MSDSYSMTPVEHFTKIQIVYVCVLSVSALNKGLELSLRESRTKITPVDSKDGSIKSIEDLKIGDIVRGFVKNVETKGLFI 1180 (1710)
T ss_pred             hhccccCChHHhcccccEEEEEEEEEecccccceeecccccccCccccccCCcccchhhcccCceeEEEEEEecCCcEEE
Confidence               4444444589999999999999999998665 7763322  221        5789999999999999999999999


Q ss_pred             EeCCCeEEEEecccCC-------CCCCCCCCEEEEEEEEEeCCC-ceeeeecC
Q 002054          929 DLGGGIRGMYRFENNE-------KKDFVVGDELLVKCSSFTGKG-IPVVSLVD  973 (974)
Q Consensus       929 ~L~~gv~Glih~se~~-------~~~f~vGd~V~vkVl~id~~~-~~~~~~~~  973 (974)
                      .|..++.++++++++.       +.+|.+|+-|.++|++++++- ..-++|..
T Consensus      1181 ~ls~~v~a~v~is~~~ds~~k~w~k~~~~gklv~~rv~~ve~~s~riel~Lk~ 1233 (1710)
T KOG1070|consen 1181 ALSRKVEAFVPISGLSDSFEKEWEKHLPVGKLVTGRVLSVEEDSKRIELSLKN 1233 (1710)
T ss_pred             EEccceEEEEEccccccchhhhhhccCCccceeeeEEEEeeccCceEEEEEec
Confidence            9999999999998663       668999999999999999876 55566643

>KOG1070 consensus rRNA processing protein Rrp5 [RNA processing and modification]

Probab=99.52  E-value=1.6e-13  Score=167.44  Aligned_cols=273  Identities=13%  Similarity=0.088  Sum_probs=204.6

Q ss_pred             cccccCcEEEEEEEEEeeceEEEEEcCCeEEEEecccCCCc--cccccccccccCCEEEEEEEEEccCCceEEEEecc--
Q 002054          679 REIEVGGIYKGVVTSVKEYGAFVEFNGGQQGLLHVSELSHE--PVSRVSDVVSVGQQLSLRCIGQDVRGNIKLSLKAV--  754 (974)
Q Consensus       679 ~~~~~G~i~~G~V~~i~~~G~fV~l~~g~~Glvhisels~~--~v~~~~~~~~vGd~V~vkVl~id~~gri~LS~K~~--  754 (974)
                      .+++.|+.|+|.|.++....++|.+.|.++|.+|+-+++.+  ..++|...|++|+.+++.|...|..+    +....  
T Consensus       983 ~q~~~gq~vtGfV~nv~ke~~w~~isp~v~~RIplld~s~~~~~le~~e~~F~~g~al~~~V~~~~~~~----tv~~iG~ 1058 (1710)
T KOG1070|consen  983 KQFKAGQEVTGFVNNVSKEWLWVRISPFVDGRIPLLDTSLDLHVLELPESLFPLGKALDEYVVRNDKSK----TVRAIGF 1058 (1710)
T ss_pred             hhhhcCCeEEEEEEccccceeEEEccccccceeeeeeccchhhhhhCchhhcccccceeeEEeccccee----EEEeccc
Confidence            36889999999999999999999999999999999999843  46789999999999999999987322    11111  


Q ss_pred             -CCCcccccCceEEEEEeec---------CCcceeeEEee-ccCCCCCCCCCCCCCCCCCcccCCCCcceEEEeeccccc
Q 002054          755 -SPRPEADVKGVVEGSVPVN---------KQATDVWASVG-DVSNGQNPELPMRKNETPGVNSSTSSTPAVLIRSAAECD  823 (974)
Q Consensus       755 -~~~~~~~~g~~~~G~vv~i---------~~gv~~~~~~~-~l~~~~~~~lp~~~~~~~~~~~~~G~~v~v~Ir~~l~iD  823 (974)
                       .......+|....|.+..+         ..++.|..++- ++++.. ..+|.       ..+..++.+.+-+   +.++
T Consensus      1059 ~~~~k~~s~G~~l~Grv~kv~~~~~~l~~~~~~~G~~~~i~~~~d~~-~~~P~-------~~f~~~~~v~~~~---L~vs 1127 (1710)
T KOG1070|consen 1059 SKSDKNPSPGDILFGRVSKVLPGYLILQLPFKVFGRVSFIEDMSDSY-SMTPV-------EHFTKIQIVYVCV---LSVS 1127 (1710)
T ss_pred             ccCCCCCCcchhhcceeeeeccceeEEecCCccccceEEeeehhccc-cCChH-------HhcccccEEEEEE---EEEe
Confidence             1111112455555555543         33344433333 555544 23444       6777788877777   9999


Q ss_pred             ccccccccccccccc------cccccccccCCCCCCCcEEEEEec----------cc---------------CcCCCccc
Q 002054          824 EEEKASGFSQSSKST------LKSTLASKSNSKPKKFTSQSDFFS----------ST---------------NIQKSTSF  872 (974)
Q Consensus       824 ~~~r~i~ls~k~~~~------~~~~~~~~~~~~~~G~~v~g~V~~----------~~---------------~~~~~~~~  872 (974)
                      ..++.+.||++....      .....++..+....|+.+.|+|+|          +.               ...-+.+|
T Consensus      1128 ~~n~~leLslr~sr~~~t~~~~kd~~iks~eDlk~g~iv~G~V~nv~~~glfi~ls~~v~a~v~is~~~ds~~k~w~k~~ 1207 (1710)
T KOG1070|consen 1128 ALNKGLELSLRESRTKITPVDSKDGSIKSIEDLKIGDIVRGFVKNVETKGLFIALSRKVEAFVPISGLSDSFEKEWEKHL 1207 (1710)
T ss_pred             cccccceeecccccccCccccccCCcccchhhcccCceeEEEEEEecCCcEEEEEccceEEEEEccccccchhhhhhccC
Confidence            999989999984321      122356677888899999999998          00               01112489


Q ss_pred             ccCCeEEEEEEEeecCCCCcC-ccccccc-ccc----ccccCCCCCEEEEEEEEEeCCeEEEEeCCCe--EEEEecccCC
Q 002054          873 SQREREELAECLFGTEDGDED-NKGTRVE-AIV----SAKNLKLGTKVAAKVYQVRARGLVLDLGGGI--RGMYRFENNE  944 (974)
Q Consensus       873 k~Gq~v~~~Vl~vd~e~~~i~-slK~~~~-~p~----~~~~~~vG~vV~G~V~~I~~~GvFV~L~~gv--~Glih~se~~  944 (974)
                      .+||.|.++|+.+++..+++. ++|.... ++.    .+.++++||...|+|.++.+||+||+++.++  .|+||.++..
T Consensus      1208 ~~gklv~~rv~~ve~~s~riel~Lk~s~~~d~~~~~~~~~~l~~gd~~~g~v~~~~~~G~fi~l~~tv~~~g~~~~~e~~ 1287 (1710)
T KOG1070|consen 1208 PVGKLVTGRVLSVEEDSKRIELSLKNSDIKDTVKLLKDSKDLKKGDREDGTVEVVDPFGLFIKLDVTVNMVGLCHISEEA 1287 (1710)
T ss_pred             CccceeeeEEEEeeccCceEEEEEeccccCCchhhhhhhhhhhccccccceEEEecCCceEEEecCcceecccccceeec
Confidence            999999999999999999999 9887432 222    4788999999999999999999999999855  9999999653


Q ss_pred             -------CCCCCCCCEEEEEEEEEeCCCc
Q 002054          945 -------KKDFVVGDELLVKCSSFTGKGI  966 (974)
Q Consensus       945 -------~~~f~vGd~V~vkVl~id~~~~  966 (974)
                             ...|..|+.|.|.|++++.++.
T Consensus      1288 d~~~e~it~~~~~~~~V~a~~lk~~~ek~ 1316 (1710)
T KOG1070|consen 1288 DDRGENITALYYAGDRVKACVLKEDSEKK 1316 (1710)
T ss_pred             chhhhhcccceeccceeeeEeeeccchhh
Confidence                   4568999999999999997664

>COG2996 Predicted RNA-bindining protein (contains S1 and HTH domains) [General function prediction only]

Probab=99.51  E-value=8.1e-13  Score=138.92  Aligned_cols=208  Identities=16%  Similarity=0.150  Sum_probs=153.8

Q ss_pred             cccCcEEEEEEEEEeeceEEEEEcCCe-EEEEecccCCCccccccccccccCCEEEEEEEEEccCCceEEEEeccCCCcc
Q 002054          681 IEVGGIYKGVVTSVKEYGAFVEFNGGQ-QGLLHVSELSHEPVSRVSDVVSVGQQLSLRCIGQDVRGNIKLSLKAVSPRPE  759 (974)
Q Consensus       681 ~~~G~i~~G~V~~i~~~G~fV~l~~g~-~Glvhisels~~~v~~~~~~~~vGd~V~vkVl~id~~gri~LS~K~~~~~~~  759 (974)
                      ..+|++....|.+..+||+|++=..+- .-++|.++...+       .+.+||+|+|.++- |.++++.++++.    |.
T Consensus         3 ~~iG~~~~l~V~~~~~~g~fL~~~~~~~~ilL~k~~~~~~-------e~evGdev~vFiY~-D~~~rl~aTt~~----p~   70 (287)
T COG2996           3 IKIGQINSLEVVEFSDFGYFLDAGEDGTTILLPKSEPEED-------ELEVGDEVTVFIYV-DSEDRLIATTRE----PK   70 (287)
T ss_pred             ccccceEEEEEEEeeceeEEEecCCCceEEeccccCCcCC-------ccccCcEEEEEEEE-CCCCceeheeec----ce
Confidence            478999999999999999999975432 678888876433       37899999999876 889999999875    66


Q ss_pred             cccCceEEEEEeecCCcceeeEEeeccCCCCCCCCCCCCCCCC--CcccCCCCcceEEEeeccccccccccccccccccc
Q 002054          760 ADVKGVVEGSVPVNKQATDVWASVGDVSNGQNPELPMRKNETP--GVNSSTSSTPAVLIRSAAECDEEEKASGFSQSSKS  837 (974)
Q Consensus       760 ~~~g~~~~G~vv~i~~gv~~~~~~~~l~~~~~~~lp~~~~~~~--~~~~~~G~~v~v~Ir~~l~iD~~~r~i~ls~k~~~  837 (974)
                      ..+|.-..+.|++.   ....+.|.+++..+...+|..+ ...  .-.+++||.  ++|+  +.+|..+| |.-.+..  
T Consensus        71 ~tvg~~g~~~Vv~v---~~~lGaFlD~Gl~KDl~vp~~e-lp~~~~~wpq~Gd~--l~v~--l~~Dkk~R-i~g~~a~--  139 (287)
T COG2996          71 ATVGEYGWLKVVEV---NKDLGAFLDWGLPKDLLVPLDE-LPTLKSLWPQKGDK--LLVY--LYVDKKGR-IWGTLAI--  139 (287)
T ss_pred             EeecceeEEEEEEE---cCCcceEEecCCCcceeeehhh-cccccccCCCCCCE--EEEE--EEEccCCc-EEEEecc--
Confidence            67788888888883   2378888888877655555411 111  123678887  4443  56666653 2111110  


Q ss_pred             ccccccccccCCCCCCCcEEEEEecccCcCCCcccccCCeEEEEEEEeecCCCCcCccccccccccccccCC---CCCEE
Q 002054          838 TLKSTLASKSNSKPKKFTSQSDFFSSTNIQKSTSFSQREREELAECLFGTEDGDEDNKGTRVEAIVSAKNLK---LGTKV  914 (974)
Q Consensus       838 ~~~~~~~~~~~~~~~G~~v~g~V~~~~~~~~~~~~k~Gq~v~~~Vl~vd~e~~~i~slK~~~~~p~~~~~~~---vG~vV  914 (974)
                      .                                                         +.+..   .+..+.   .+|.|
T Consensus       140 ~---------------------------------------------------------~~l~~---l~~~~~~~l~nq~v  159 (287)
T COG2996         140 E---------------------------------------------------------KILEN---LATPAYNNLKNQEV  159 (287)
T ss_pred             h---------------------------------------------------------hHHHh---cCCccchhhhcCee
Confidence            0                                                         00000   012222   59999


Q ss_pred             EEEEEEEeCCeEEEEeCCCeEEEEecccCCCCCCCCCCEEEEEEEEEeCCCceeeeec
Q 002054          915 AAKVYQVRARGLVLDLGGGIRGMYRFENNEKKDFVVGDELLVKCSSFTGKGIPVVSLV  972 (974)
Q Consensus       915 ~G~V~~I~~~GvFV~L~~gv~Glih~se~~~~~f~vGd~V~vkVl~id~~~~~~~~~~  972 (974)
                      .|+|+++..-|.||-+++++-||||.||. ..+++.||+++++|+.+.++|..++|+.
T Consensus       160 ~~tVYr~~~~G~fv~~e~~~~GfIh~sEr-~~~prlG~~l~~rVi~~reDg~lnLSl~  216 (287)
T COG2996         160 DATVYRLLESGTFVITENGYLGFIHKSER-FAEPRLGERLTARVIGVREDGKLNLSLR  216 (287)
T ss_pred             eeEEEEEeccceEEEEcCCeEEEEcchhh-cccccCCceEEEEEEEEccCCeeecccc
Confidence            99999999999999999999999999998 6789999999999999999999999984

>PTZ00248 eukaryotic translation initiation factor 2 subunit 1; Provisional

Probab=99.51  E-value=4.1e-14  Score=155.42  Aligned_cols=93  Identities=25%  Similarity=0.331  Sum_probs=87.4

Q ss_pred             cccCcEEEEEEEEEeeceEEEEEc--CCeEEEEecccCCCccccccccccccCCEEEEEEEEEcc-CCceEEEEeccCCC
Q 002054          681 IEVGGIYKGVVTSVKEYGAFVEFN--GGQQGLLHVSELSHEPVSRVSDVVSVGQQLSLRCIGQDV-RGNIKLSLKAVSPR  757 (974)
Q Consensus       681 ~~~G~i~~G~V~~i~~~G~fV~l~--~g~~Glvhisels~~~v~~~~~~~~vGd~V~vkVl~id~-~gri~LS~K~~~~~  757 (974)
                      +++|+++.|+|++|.+||+||+|.  +|++||||+|||||.++.++.+++++||.|.|+|+.+|+ +|+|.||+|++.++
T Consensus        15 P~~GdvV~g~V~~I~d~GafV~L~EY~gvEGlIhiSElS~~ri~~i~d~vkvGd~v~vkVl~VD~ekg~IdLS~K~v~~~   94 (319)
T PTZ00248         15 PEEDDLVMVKVVRITEMGAYVSLLEYDDIEGMILMSELSKRRIRSINKLIRVGRHEVVVVLRVDKEKGYIDLSKKRVSPE   94 (319)
T ss_pred             CCCCCEEEEEEEEEeCCeEEEEecCCCCcEEEEEHHHhcccccCCHHHhcCCCCEEEEEEEEEeCCCCEEEEEeeecccc
Confidence            458999999999999999999996  689999999999999999999999999999999999998 79999999999999


Q ss_pred             cccc------cCceEEEEEeec
Q 002054          758 PEAD------VKGVVEGSVPVN  773 (974)
Q Consensus       758 ~~~~------~g~~~~G~vv~i  773 (974)
                      ||..      .|..+.|.+..+
T Consensus        95 pw~~~~e~~~~g~~v~~~V~~i  116 (319)
T PTZ00248         95 DIEACEEKFSKSKKVHSIMRHI  116 (319)
T ss_pred             hHHHHHHhCcCCCEEEEEEEEc
Confidence            9987      478899988886

>PRK08582 hypothetical protein; Provisional

Probab=99.48  E-value=1.2e-13  Score=135.97  Aligned_cols=82  Identities=35%  Similarity=0.672  Sum_probs=78.1

Q ss_pred             ccccCcEEEEEEEEEeeceEEEEEcCCeEEEEecccCCCccccccccccccCCEEEEEEEEEccCCceEEEEeccCCCcc
Q 002054          680 EIEVGGIYKGVVTSVKEYGAFVEFNGGQQGLLHVSELSHEPVSRVSDVVSVGQQLSLRCIGQDVRGNIKLSLKAVSPRPE  759 (974)
Q Consensus       680 ~~~~G~i~~G~V~~i~~~G~fV~l~~g~~Glvhisels~~~v~~~~~~~~vGd~V~vkVl~id~~gri~LS~K~~~~~~~  759 (974)
                      .+++|++|.|+|++|++||+||+|.++.+||||+|++++.++.++.+.|++||.|+|+|+++|.+|+|.||+|++..+||
T Consensus         2 ~~kvG~iv~G~V~~I~~fG~fV~L~~~~~GlVhiSels~~~v~~~~~~l~vGD~VkvkV~~id~~gkI~LSlk~~~~~~~   81 (139)
T PRK08582          2 SIEVGSKLQGKVTGITNFGAFVELPEGKTGLVHISEVADNYVKDINDHLKVGDEVEVKVLNVEDDGKIGLSIKKAKDRPK   81 (139)
T ss_pred             CCcCCCEEEEEEEEEECCeEEEEECCCCEEEEEeeccCcccccccccccCCCCEEEEEEEEECCCCcEEEEEEecccCch
Confidence            36899999999999999999999999999999999999999999999999999999999999988999999999999898


Q ss_pred             cc
Q 002054          760 AD  761 (974)
Q Consensus       760 ~~  761 (974)
                      ..
T Consensus        82 ~~   83 (139)
T PRK08582         82 RQ   83 (139)
T ss_pred             hh
Confidence            65

>cd05704 S1_Rrp5_repeat_hs13 S1_Rrp5_repeat_hs13: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits

Probab=99.48  E-value=9e-14  Score=121.81  Aligned_cols=71  Identities=25%  Similarity=0.346  Sum_probs=67.2

Q ss_pred             cccCcEEEEEEEEEee-ceEEEEEcCCeEEEEecccCCCccccccccccccCCEEEEEEEEEccCCceEEEEe
Q 002054          681 IEVGGIYKGVVTSVKE-YGAFVEFNGGQQGLLHVSELSHEPVSRVSDVVSVGQQLSLRCIGQDVRGNIKLSLK  752 (974)
Q Consensus       681 ~~~G~i~~G~V~~i~~-~G~fV~l~~g~~Glvhisels~~~v~~~~~~~~vGd~V~vkVl~id~~gri~LS~K  752 (974)
                      +++|++|.|+|+++.+ ||+||+|.++.+|++|+|+++++++.++.+.|++||.|+|+|+++|. +++.||+|
T Consensus         1 l~~G~iv~G~V~~i~~~~g~~v~l~~~~~Glvhis~~s~~~~~~~~~~~~~Gd~v~~kV~~~~~-~~i~LSl~   72 (72)
T cd05704           1 LEEGAVTLGMVTKVIPHSGLTVQLPFGKTGLVSIFHLSDSYTENPLEGFKPGKIVRCCILSKKD-GKYQLSLR   72 (72)
T ss_pred             CCCCCEEEEEEEEeeCCcEEEEECCCCCEEEEEHHHhcCcccCCHHHhCCCCCEEEEEEEEecC-CEEEEEeC
Confidence            4689999999999986 89999999999999999999999999999999999999999999985 99999986

Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in Saccharomyces cerevisiae Rrp5 and 14 S1 repeats in Homo sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in protein-protein interactions. Mutational studies have shown that each region represents a specific functional domain. Deletions within the S1-containing region inhibit pre-rRNA processing at either site A3 or A2, whereas deletions within the TPR region confer an inability to support cleavage of A0-A2. This CD includes H. sapiens S1 repeat 13 (hs13). Rrp5 is found in eukaryotes but not in prokaryotes or archaea.

>cd05705 S1_Rrp5_repeat_hs14 S1_Rrp5_repeat_hs14: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits

Probab=99.44  E-value=2.4e-13  Score=119.64  Aligned_cols=70  Identities=21%  Similarity=0.375  Sum_probs=64.7

Q ss_pred             cccCcEEEEEEEEEeeceEEEEEcCCeEEEEecccCCCcccccc---ccccccCCEEEEEEEEEcc-CCceEEE
Q 002054          681 IEVGGIYKGVVTSVKEYGAFVEFNGGQQGLLHVSELSHEPVSRV---SDVVSVGQQLSLRCIGQDV-RGNIKLS  750 (974)
Q Consensus       681 ~~~G~i~~G~V~~i~~~G~fV~l~~g~~Glvhisels~~~v~~~---~~~~~vGd~V~vkVl~id~-~gri~LS  750 (974)
                      +++|+++.|+|+++.+||+||++.++++||||+++++|.++.++   .+.|++||.++|+|+++|+ +++|.||
T Consensus         1 ~k~G~~V~g~V~~i~~~G~fV~l~~~v~G~v~~~~ls~~~~~~~~~~~~~~~~G~~v~~kVl~id~~~~~i~LS   74 (74)
T cd05705           1 IKEGQLLRGYVSSVTKQGVFFRLSSSIVGRVLFQNVTKYFVSDPSLYNKYLPEGKLLTAKVLSVNSEKNLVELS   74 (74)
T ss_pred             CCCCCEEEEEEEEEeCCcEEEEeCCCCEEEEEHHHccCccccChhhHhcccCCCCEEEEEEEEEECCCCEEecC
Confidence            47899999999999999999999999999999999999997775   5889999999999999997 6888876

Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in Saccharomyces cerevisiae Rrp5 and 14 S1 repeats in Homo sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in protein-protein interactions. Mutational studies have shown that each region represents a specific functional domain. Deletions within the S1-containing region inhibit pre-rRNA processing at either site A3 or A2, whereas deletions within the TPR region confer an inability to support cleavage of A0-A2. This CD includes H. sapiens S1 repeat 14 (hs14). Rrp5 is found in eukaryotes but not in prokaryotes or archaea.

>cd05686 S1_pNO40 S1_pNO40: pNO40 , S1-like RNA-binding domain

Probab=99.40  E-value=1.1e-12  Score=115.26  Aligned_cols=71  Identities=44%  Similarity=0.700  Sum_probs=65.4

Q ss_pred             cccCcEEEEEEEEEeeceEEEEEcC-CeEEEEecccCCCccccccccccccCCEEEEEEEEEccCCceEEEE
Q 002054          681 IEVGGIYKGVVTSVKEYGAFVEFNG-GQQGLLHVSELSHEPVSRVSDVVSVGQQLSLRCIGQDVRGNIKLSL  751 (974)
Q Consensus       681 ~~~G~i~~G~V~~i~~~G~fV~l~~-g~~Glvhisels~~~v~~~~~~~~vGd~V~vkVl~id~~gri~LS~  751 (974)
                      +++|++|+|+|+++.+||+||++.+ +.+||+|+|++++.++.++.+.|++||.|+|+|+++|..+++.||+
T Consensus         1 ~~~g~~~~g~V~~i~~fG~fv~l~~~~~eGlvh~sel~~~~~~~~~~~~~~Gd~v~vkv~~vd~~~ki~ls~   72 (73)
T cd05686           1 PALYQIFKGEVASVTEYGAFVKIPGCRKQGLVHKSHMSSCRVDDPSEVVDVGEKVWVKVIGREMKDKMKLSL   72 (73)
T ss_pred             CcCCCEEEEEEEEEEeeeEEEEECCCCeEEEEEchhhCCCcccCHhhEECCCCEEEEEEEEECCCCcEEEEe
Confidence            3689999999999999999999943 2699999999999999999999999999999999999877999986

pNO40 is a nucleolar protein of unknown function with an N-terminal S1 RNA binding domain, a CCHC type zinc finger, and clusters of basic amino acids representing a potential nucleolar targeting signal. pNO40 was identified through a yeast two-hybrid interaction screen of a human kidney cDNA library using the pinin (pnn) protein as bait. pNO40 is thought to play a role in ribosome maturation and/or biogenesis.

>cd05698 S1_Rrp5_repeat_hs6_sc5 S1_Rrp5_repeat_hs6_sc5: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits

Probab=99.36  E-value=2e-12  Score=112.35  Aligned_cols=69  Identities=29%  Similarity=0.399  Sum_probs=66.1

Q ss_pred             CcEEEEEEEEEeeceEEEEEcCCeEEEEecccCCCccccccccccccCCEEEEEEEEEcc-CCceEEEEe
Q 002054          684 GGIYKGVVTSVKEYGAFVEFNGGQQGLLHVSELSHEPVSRVSDVVSVGQQLSLRCIGQDV-RGNIKLSLK  752 (974)
Q Consensus       684 G~i~~G~V~~i~~~G~fV~l~~g~~Glvhisels~~~v~~~~~~~~vGd~V~vkVl~id~-~gri~LS~K  752 (974)
                      |++|.|+|+++.++|+||+|+++.+||+|+|+++++++.++.+.|++||.++|+|+++|. ++++.||+|
T Consensus         1 g~~~~g~V~~v~~~G~~V~l~~~~~gli~~s~l~~~~~~~~~~~~~~G~~i~v~v~~~d~~~~~i~ls~k   70 (70)
T cd05698           1 GLKTHGTIVKVKPNGCIVSFYNNVKGFLPKSELSEAFIKDPEEHFRVGQVVKVKVLSCDPEQQRLLLSCK   70 (70)
T ss_pred             CCEEEEEEEEEecCcEEEEECCCCEEEEEHHHcChhhcCCHHHcccCCCEEEEEEEEEcCCCCEEEEEeC
Confidence            789999999999999999999899999999999999999999999999999999999998 789999986

Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in Saccharomyces cerevisiae Rrp5 and 14 S1 repeats in Homo sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in protein-protein interactions. Mutational studies have shown that each region represents a specific functional domain. Deletions within the S1-containing region inhibit pre-rRNA processing at either site A3 or A2, whereas deletions within the TPR region confer an inability to support cleavage of A0-A2. This CD includes H. sapiens S1 repeat 6 (hs6) and S. cerevisiae S1 repeat 5 (sc5). Rrp5 is found in eukaryotes but not in prokaryotes or archaea.

>cd05696 S1_Rrp5_repeat_hs4 S1_Rrp5_repeat_hs4: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits

Probab=99.35  E-value=2e-12  Score=112.93  Aligned_cols=68  Identities=32%  Similarity=0.488  Sum_probs=64.3

Q ss_pred             CcEEE-EEEEEE-eeceEEEEEcCCeEEEEecccCCCccccccccccccCCEEEEEEEEEcc-CCceEEEE
Q 002054          684 GGIYK-GVVTSV-KEYGAFVEFNGGQQGLLHVSELSHEPVSRVSDVVSVGQQLSLRCIGQDV-RGNIKLSL  751 (974)
Q Consensus       684 G~i~~-G~V~~i-~~~G~fV~l~~g~~Glvhisels~~~v~~~~~~~~vGd~V~vkVl~id~-~gri~LS~  751 (974)
                      |++|+ |+|+++ .+||+||++.++.+||+|+|++++.+..++.+.|++||.++|+|+++|+ ++++.||+
T Consensus         1 G~v~~~g~V~~v~~~~G~~V~l~~gv~G~i~~s~l~~~~~~~~~~~~~vG~~v~~kV~~id~~~~~i~lS~   71 (71)
T cd05696           1 GAVVDSVKVTKVEPDLGAVFELKDGLLGFVHISHLSDDKVPSDTGPFKAGTTHKARIIGYSPMDGLLQLSL   71 (71)
T ss_pred             CcEeeeeEEEEEccCceEEEEeCCCCEEEEEHHHCCcchhcCcccccCCCCEEEEEEEEEeCCCCEEEEeC
Confidence            78999 899999 6999999999999999999999999999999999999999999999998 78999985

Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in Saccharomyces cerevisiae Rrp5 and 14 S1 repeats in Homo sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in protein-protein interactions. Mutational studies have shown that each region represents a specific functional domain. Deletions within the S1-containing region inhibit pre-rRNA processing at either site A3 or A2, whereas deletions within the TPR region confer an inability to support cleavage of A0-A2. This CD includes H. sapiens S1 repeat 4 (hs4). Rrp5 is found in eukaryotes but not in prokaryotes or archaea.

>PF00575 S1: S1 RNA binding domain; InterPro: IPR003029 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms

Probab=99.34  E-value=4e-12  Score=111.68  Aligned_cols=72  Identities=39%  Similarity=0.724  Sum_probs=68.9

Q ss_pred             cccCcEEEEEEEEEeeceEEEEEcCCeEEEEecccCCCccccccccccccCCEEEEEEEEEcc-CCceEEEEe
Q 002054          681 IEVGGIYKGVVTSVKEYGAFVEFNGGQQGLLHVSELSHEPVSRVSDVVSVGQQLSLRCIGQDV-RGNIKLSLK  752 (974)
Q Consensus       681 ~~~G~i~~G~V~~i~~~G~fV~l~~g~~Glvhisels~~~v~~~~~~~~vGd~V~vkVl~id~-~gri~LS~K  752 (974)
                      +++|+++.|+|+++.++|+||+|.++.+||||.+++++.+..++...+++||.++|+|+++|. ++++.||+|
T Consensus         2 ~~~G~iv~g~V~~v~~~g~~V~l~~~~~g~ip~~~l~~~~~~~~~~~~~~G~~v~v~v~~vd~~~~~i~lS~k   74 (74)
T PF00575_consen    2 LKEGDIVEGKVTSVEDFGVFVDLGNGIEGFIPISELSDDRIDDPSEVYKIGQTVRVKVIKVDKEKGRIRLSLK   74 (74)
T ss_dssp             SSTTSEEEEEEEEEETTEEEEEESTSSEEEEEGGGSSSSEESSSHGTCETTCEEEEEEEEEETTTTEEEEEST
T ss_pred             CCCCCEEEEEEEEEECCEEEEEECCcEEEEEEeehhcCccccccccccCCCCEEEEEEEEEECCCCeEEEEEC
Confidence            689999999999999999999998899999999999999999999999999999999999998 678999986

The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites [, ]. About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits. Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome [, ]. The S1 domain was originally identified in ribosomal protein S1 but is found in a large number of RNA-associated proteins. The structure of the S1 RNA-binding domain from the Escherichia coli polynucleotide phosphorylase has been determined using NMR methods and consists of a five-stranded antiparallel beta barrel. Conserved residues on one face of the barrel and adjacent loops form the putative RNA-binding site []. The structure of the S1 domain is very similar to that of cold shock proteins. This suggests that they may both be derived from an ancient nucleic acid-binding protein []. More information about these proteins can be found at Protein of the Month: RNA Exosomes []. This entry does not include translation initiation factor IF-1 S1 domains.; GO: 0003723 RNA binding; PDB: 3L7Z_F 2JE6_I 2JEA_I 2JEB_I 1E3P_A 2Y0S_E 1WI5_A 2BH8_A 2CQO_A 2EQS_A ....

>cd04461 S1_Rrp5_repeat_hs8_sc7 S1_Rrp5_repeat_hs8_sc7: Rrp5 Homo sapiens S1 repeat 8 (hs8) and Saccharomyces cerevisiae S1 repeat 7 (sc7)-like domains

Probab=99.33  E-value=2.9e-12  Score=115.40  Aligned_cols=73  Identities=33%  Similarity=0.459  Sum_probs=69.4

Q ss_pred             cccccCcEEEEEEEEEeeceEEEEEcCCeEEEEecccCCCccccccccccccCCEEEEEEEEEcc-CCceEEEE
Q 002054          679 REIEVGGIYKGVVTSVKEYGAFVEFNGGQQGLLHVSELSHEPVSRVSDVVSVGQQLSLRCIGQDV-RGNIKLSL  751 (974)
Q Consensus       679 ~~~~~G~i~~G~V~~i~~~G~fV~l~~g~~Glvhisels~~~v~~~~~~~~vGd~V~vkVl~id~-~gri~LS~  751 (974)
                      .++++|++|.|+|+++.++|+||++.++.+||+|+++++++++.++.+.|++||.|+|+|+++|. ++++.||+
T Consensus        10 ~~~~~G~i~~g~V~~v~~~G~fv~l~~~~~g~v~~~el~~~~~~~~~~~~~~Gd~v~vkV~~id~~~~~i~lsl   83 (83)
T cd04461          10 SDLKPGMVVHGYVRNITPYGVFVEFLGGLTGLAPKSYISDEFVTDPSFGFKKGQSVTAKVTSVDEEKQRFLLSL   83 (83)
T ss_pred             HhCCCCCEEEEEEEEEeeceEEEEcCCCCEEEEEHHHCCcccccCHHHhcCCCCEEEEEEEEEcCCCCEEEEeC
Confidence            46899999999999999999999999999999999999999999999999999999999999998 79999985

Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits. Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in S. cerevisiae Rrp5 and 14 S1 repeats in H. sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in protein-protein interactions. Mutational studies have shown that each region represents a specific functional domain. Deletions within the S1-containing region inhibit pre-rRNA processing at either site A3 or A2, whereas deletions within the TPR region confer an inability to support cleavage of A0-A2. This CD includes H. sapiens S1 repeat 8 and S. cerevisiae S1 repeat 7. Rrp5 is found in eukaryotes but not in prokaryotes or archaea.

>cd05703 S1_Rrp5_repeat_hs12_sc9 S1_Rrp5_repeat_hs12_sc9: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits

Probab=99.32  E-value=4.4e-12  Score=111.43  Aligned_cols=69  Identities=20%  Similarity=0.344  Sum_probs=65.2

Q ss_pred             CcEEEEEEEEEeeceEEEEEcCCeEEEEecccCCCcc--ccccccccccCCEEEEEEEEEcc-CCceEEEEe
Q 002054          684 GGIYKGVVTSVKEYGAFVEFNGGQQGLLHVSELSHEP--VSRVSDVVSVGQQLSLRCIGQDV-RGNIKLSLK  752 (974)
Q Consensus       684 G~i~~G~V~~i~~~G~fV~l~~g~~Glvhisels~~~--v~~~~~~~~vGd~V~vkVl~id~-~gri~LS~K  752 (974)
                      |+++.|+|+++.++|+||+|.++++|++|++++++.+  .+++.+.|++||.|+|+|+++|+ +++|.||+|
T Consensus         1 G~~V~g~V~~i~~~g~~V~l~~~i~G~i~~~~ls~~~~~~~~~~~~~~vG~~v~~kV~~id~~~~~i~Ls~k   72 (73)
T cd05703           1 GQEVTGFVNNVSKEFVWLTISPDVKGRIPLLDLSDDVSVLEHPEKKFPIGQALKAKVVGVDKEHKLLRLSAR   72 (73)
T ss_pred             CCEEEEEEEEEeCCEEEEEeCCCcEEEEEHHHcCCccccccCHHHhCCCCCEEEEEEEEEeCCCCEEEEEec
Confidence            7899999999999999999999999999999999864  88999999999999999999998 689999987

Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in Saccharomyces cerevisiae Rrp5 and 14 S1 repeats in Homo sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in protein-protein interactions. Mutational studies have shown that each region represents a specific functional domain. Deletions within the S1-containing region inhibit pre-rRNA processing at either site A3 or A2, whereas deletions within the TPR region confer an inability to support cleavage of A0-A2. This CD includes H. sapiens S1 repeat 12 (hs12) and S. cerevisiae S1 repeat 9 (sc9). Rrp5 is found in eukaryotes but not in prokaryotes or archaea.

>cd04452 S1_IF2_alpha S1_IF2_alpha: The alpha subunit of translation Initiation Factor 2, S1-like RNA-binding domain

Probab=99.32  E-value=6.3e-12  Score=110.94  Aligned_cols=73  Identities=30%  Similarity=0.464  Sum_probs=67.9

Q ss_pred             cccCcEEEEEEEEEeeceEEEEEcC--CeEEEEecccCCCccccccccccccCCEEEEEEEEEcc-CCceEEEEec
Q 002054          681 IEVGGIYKGVVTSVKEYGAFVEFNG--GQQGLLHVSELSHEPVSRVSDVVSVGQQLSLRCIGQDV-RGNIKLSLKA  753 (974)
Q Consensus       681 ~~~G~i~~G~V~~i~~~G~fV~l~~--g~~Glvhisels~~~v~~~~~~~~vGd~V~vkVl~id~-~gri~LS~K~  753 (974)
                      ++.|++|.|+|+++.++|+||++.+  +.+||+|+|+++++++.++.+.|++||.|+|+|+++|. ++++.||+|+
T Consensus         1 ~~~G~~~~g~V~~v~~~g~~v~l~~~~~~~gll~~s~l~~~~~~~~~~~~~~Gd~v~vkv~~~d~~~~~i~ls~k~   76 (76)
T cd04452           1 PEEGELVVVTVKSIADMGAYVSLLEYGNIEGMILLSELSRRRIRSIRKLVKVGRKEVVKVIRVDKEKGYIDLSKKR   76 (76)
T ss_pred             CCCCCEEEEEEEEEEccEEEEEEcCCCCeEEEEEhHHcCCcccCCHHHeeCCCCEEEEEEEEEECCCCEEEEEEcC
Confidence            4689999999999999999999963  69999999999999999999999999999999999997 6899999874

S1-like RNA-binding domains are found in a wide variety of RNA-associated proteins. Eukaryotic and archaeal Initiation Factor 2 (e- and aIF2, respectively) are heterotrimeric proteins with three subunits (alpha, beta, and gamma). IF2 plays a crucial role in the process of translation initiation. The IF2 gamma subunit contains a GTP-binding site. The IF2 beta and gamma subunits together are thought to be responsible for binding methionyl-initiator tRNA. The ternary complex consisting of IF2, GTP, and the methionyl-initiator tRNA binds to the small subunit of the ribosome, as part of a pre-initiation complex that scans the mRNA to find the AUG start codon. The IF2-bound GTP is hydrolyzed to GDP when the methionyl-initiator tRNA binds the AUG start codon, at which time the IF2 is released with its bound GDP. The large ribosomal subunit then joins with the small subunit to c

>COG1098 VacB Predicted RNA binding protein (contains ribosomal protein S1 domain) [Translation, ribosomal structure and biogenesis]

Probab=99.31  E-value=1.8e-12  Score=120.85  Aligned_cols=67  Identities=24%  Similarity=0.435  Sum_probs=62.2

Q ss_pred             cCCCCCEEEEEEEEEeCCeEEEEeCCCeEEEEecccCC-------CCCCCCCCEEEEEEEEEeCCCceeeeecC
Q 002054          907 NLKLGTKVAAKVYQVRARGLVLDLGGGIRGMYRFENNE-------KKDFVVGDELLVKCSSFTGKGIPVVSLVD  973 (974)
Q Consensus       907 ~~~vG~vV~G~V~~I~~~GvFV~L~~gv~Glih~se~~-------~~~f~vGd~V~vkVl~id~~~~~~~~~~~  973 (974)
                      .+++|++++|+|..|++||+||+|++|=.||||+|+..       ++.+++||+|+|+|+++|++|++-+|+.+
T Consensus         2 ~~kvG~~l~GkItgI~~yGAFV~l~~g~tGLVHISEIa~~fVkdI~d~L~vG~eV~vKVl~ide~GKisLSIr~   75 (129)
T COG1098           2 SMKVGSKLKGKITGITPYGAFVELEGGKTGLVHISEIADGFVKDIHDHLKVGQEVKVKVLDIDENGKISLSIRK   75 (129)
T ss_pred             CccccceEEEEEEeeEecceEEEecCCCcceEEehHhhhhhHHhHHHHhcCCCEEEEEEEeeccCCCcceehHH
Confidence            57899999999999999999999999999999999774       56799999999999999999999999754

>cd05684 S1_DHX8_helicase S1_DHX8_helicase: The N-terminal S1 domain of human ATP-dependent RNA helicase DHX8, a DEAH (Asp-Glu-Ala-His) box polypeptide

Probab=99.31  E-value=8.8e-12  Score=111.17  Aligned_cols=74  Identities=43%  Similarity=0.741  Sum_probs=68.6

Q ss_pred             CcEEEEEEEEEeeceEEEEEc---CCeEEEEecccCCCccc-cccccccccCCEEEEEEEEEccCCceEEEEeccCCCc
Q 002054          684 GGIYKGVVTSVKEYGAFVEFN---GGQQGLLHVSELSHEPV-SRVSDVVSVGQQLSLRCIGQDVRGNIKLSLKAVSPRP  758 (974)
Q Consensus       684 G~i~~G~V~~i~~~G~fV~l~---~g~~Glvhisels~~~v-~~~~~~~~vGd~V~vkVl~id~~gri~LS~K~~~~~~  758 (974)
                      |++|.|+|+++.+||+||+|.   ++.+||+|++++++++. .++.+.|++||.|+|+|+++| ++++.||+|++.++.
T Consensus         1 G~~~~g~V~~v~~~G~fv~l~~~~~~~~gll~~s~l~~~~~~~~~~~~~~~Gd~v~v~v~~vd-~~~i~~s~k~~~~~~   78 (79)
T cd05684           1 GKIYKGKVTSIMDFGCFVQLEGLKGRKEGLVHISQLSFEGRVANPSDVVKRGQKVKVKVISIQ-NGKISLSMKDVDQDT   78 (79)
T ss_pred             CCEEEEEEEEEEeeeEEEEEeCCCCCcEEEEEhHhccCCCCcCChhheeCCCCEEEEEEEEEe-CCEEEEEEEecccCC
Confidence            789999999999999999997   46899999999999986 899999999999999999999 999999999987653

The DEAH-box RNA helicases are thought to play key roles in pre-mRNA splicing and DHX8 facilitates nuclear export of spliced mRNA by releasing the RNA from the spliceosome. DHX8 is also known as HRH1 (human RNA helicase 1) in Homo sapiens and PRP22 in Saccharomyces cerevisiae.

>PRK05807 hypothetical protein; Provisional

Probab=99.31  E-value=8.5e-12  Score=122.65  Aligned_cols=75  Identities=31%  Similarity=0.603  Sum_probs=71.4

Q ss_pred             ccccCcEEEEEEEEEeeceEEEEEcCCeEEEEecccCCCccccccccccccCCEEEEEEEEEccCCceEEEEeccC
Q 002054          680 EIEVGGIYKGVVTSVKEYGAFVEFNGGQQGLLHVSELSHEPVSRVSDVVSVGQQLSLRCIGQDVRGNIKLSLKAVS  755 (974)
Q Consensus       680 ~~~~G~i~~G~V~~i~~~G~fV~l~~g~~Glvhisels~~~v~~~~~~~~vGd~V~vkVl~id~~gri~LS~K~~~  755 (974)
                      .+++|++|+|+|++|.++|+||+| ++.+||||+|++++.++.++.+.|++||.|+|+|+++|.+|+|.||+|.+.
T Consensus         2 ~~~vG~vv~G~Vt~i~~~GafV~L-~~~~Glvhiseis~~~v~~~~~~~kvGd~V~VkV~~id~~gkI~LSlk~~~   76 (136)
T PRK05807          2 TLKAGSILEGTVVNITNFGAFVEV-EGKTGLVHISEVADTYVKDIREHLKEQDKVKVKVISIDDNGKISLSIKQAM   76 (136)
T ss_pred             CccCCCEEEEEEEEEECCeEEEEE-CCEEEEEEhhhcccccccCccccCCCCCEEEEEEEEECCCCcEEEEEEecc
Confidence            367999999999999999999999 689999999999999999999999999999999999998899999999976

>cd05706 S1_Rrp5_repeat_sc10 S1_Rrp5_repeat_sc10: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits

Probab=99.31  E-value=8.7e-12  Score=109.32  Aligned_cols=72  Identities=21%  Similarity=0.286  Sum_probs=67.6

Q ss_pred             cccCcEEEEEEEEEeeceEEEEEcCCeEEEEecccCCCccccccccccccCCEEEEEEEEEcc-CCceEEEEe
Q 002054          681 IEVGGIYKGVVTSVKEYGAFVEFNGGQQGLLHVSELSHEPVSRVSDVVSVGQQLSLRCIGQDV-RGNIKLSLK  752 (974)
Q Consensus       681 ~~~G~i~~G~V~~i~~~G~fV~l~~g~~Glvhisels~~~v~~~~~~~~vGd~V~vkVl~id~-~gri~LS~K  752 (974)
                      +++|+++.|+|+++.++|+||+|.++.+|++|++++++++..++.+.|++||.++|+|+++|. ++++.||+|
T Consensus         1 ~~~G~iv~g~V~~v~~~gi~v~l~~~~~g~v~~s~l~~~~~~~~~~~~~~Gd~v~~~V~~~d~~~~~i~ls~~   73 (73)
T cd05706           1 LKVGDILPGRVTKVNDRYVLVQLGNKVTGPSFITDALDDYSEALPYKFKKNDIVRACVLSVDVPNKKIALSLR   73 (73)
T ss_pred             CCCCCEEEEEEEEEeCCeEEEEeCCCcEEEEEhhhccCccccccccccCCCCEEEEEEEEEeCCCCEEEEEEC
Confidence            368999999999999999999999999999999999999888888999999999999999998 689999975

Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in Saccharomyces cerevisiae Rrp5 and 14 S1 repeats in Homo sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in protein-protein interactions. Mutational studies have shown that each region represents a specific functional domain. Deletions within the S1-containing region inhibit pre-rRNA processing at either site A3 or A2, whereas deletions within the TPR region confer an inability to support cleavage of A0-A2. This CD includes S. cerevisiae S1 repeat 10 (sc10). Rrp5 is found in eukaryotes but not in prokaryotes or archaea.

>PRK07252 hypothetical protein; Provisional

Probab=99.31  E-value=8.6e-12  Score=119.86  Aligned_cols=76  Identities=30%  Similarity=0.645  Sum_probs=72.3

Q ss_pred             ccCcEEEEEEEEEeeceEEEEEcCCeEEEEecccCCCccccccccccccCCEEEEEEEEEcc-CCceEEEEeccCCC
Q 002054          682 EVGGIYKGVVTSVKEYGAFVEFNGGQQGLLHVSELSHEPVSRVSDVVSVGQQLSLRCIGQDV-RGNIKLSLKAVSPR  757 (974)
Q Consensus       682 ~~G~i~~G~V~~i~~~G~fV~l~~g~~Glvhisels~~~v~~~~~~~~vGd~V~vkVl~id~-~gri~LS~K~~~~~  757 (974)
                      ++|++|.|+|++|.++|+||+|.++.+||+|+|+++++++.++.+.|++||.|+|+|+++|. ++++.||+|.+.++
T Consensus         2 kvG~iv~G~V~~V~~~G~fVei~~~~~GllhiseLs~~~~~~~~~~~~vGD~V~VkI~~iD~~~~ri~lSlk~~~~~   78 (120)
T PRK07252          2 KIGDKLKGTITGIKPYGAFVALENGTTGLIHISEIKTGFIDNIHQLLKVGEEVLVQVVDFDEYTGKASLSLRTLEEE   78 (120)
T ss_pred             CCCCEEEEEEEEEeCcEEEEEECCCCEEEEEHHHcCCccccChhhccCCCCEEEEEEEEEeCCCCEEEEEEeecccC
Confidence            57999999999999999999999899999999999999999999999999999999999998 79999999998764

>PHA02945 interferon resistance protein; Provisional

Probab=99.30  E-value=1.1e-11  Score=109.43  Aligned_cols=74  Identities=22%  Similarity=0.366  Sum_probs=68.4

Q ss_pred             ccccCcEEEEEEEEEeeceEEEEE--cCCeEEEEecccC--CCccccccccccccCCEEEEEEEEEcc-CCceEEEEecc
Q 002054          680 EIEVGGIYKGVVTSVKEYGAFVEF--NGGQQGLLHVSEL--SHEPVSRVSDVVSVGQQLSLRCIGQDV-RGNIKLSLKAV  754 (974)
Q Consensus       680 ~~~~G~i~~G~V~~i~~~G~fV~l--~~g~~Glvhisel--s~~~v~~~~~~~~vGd~V~vkVl~id~-~gri~LS~K~~  754 (974)
                      -|++|+++.|+|+. .+||+||.|  ++|.+||+|+|++  +..|+++ ++++ +||++.|||+.+|+ +|.|.||+|++
T Consensus         8 ~P~~GelvigtV~~-~d~ga~v~L~EY~g~eg~i~~seveva~~wvK~-rd~l-~GqkvV~KVirVd~~kg~IDlSlK~V   84 (88)
T PHA02945          8 LPNVGDVLKGKVYE-NGYALYIDLFDYPHSEAILAESVQMHMNRYFKY-RDKL-VGKTVKVKVIRVDYTKGYIDVNYKRM   84 (88)
T ss_pred             CCCCCcEEEEEEEe-cCceEEEEecccCCcEEEEEeehhhhccceEee-eeEe-cCCEEEEEEEEECCCCCEEEeEeeEc
Confidence            36899999999999 999999999  4689999999955  9999999 9999 99999999999998 79999999987


Q ss_pred             CC
Q 002054          755 SP  756 (974)
Q Consensus       755 ~~  756 (974)
                      .+
T Consensus        85 ~~   86 (88)
T PHA02945         85 CR   86 (88)
T ss_pred             cc
Confidence            54

>cd05697 S1_Rrp5_repeat_hs5 S1_Rrp5_repeat_hs5: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits

Probab=99.29  E-value=7.8e-12  Score=108.47  Aligned_cols=68  Identities=21%  Similarity=0.389  Sum_probs=64.7

Q ss_pred             CcEEEEEEEEEeeceEEEEEcCCeEEEEecccCCCccccccccccccCCEEEEEEEEEcc-CCceEEEE
Q 002054          684 GGIYKGVVTSVKEYGAFVEFNGGQQGLLHVSELSHEPVSRVSDVVSVGQQLSLRCIGQDV-RGNIKLSL  751 (974)
Q Consensus       684 G~i~~G~V~~i~~~G~fV~l~~g~~Glvhisels~~~v~~~~~~~~vGd~V~vkVl~id~-~gri~LS~  751 (974)
                      |++|+|+|+++.++|+||++.++.+||+|++++++.+..++.+.|++||.++|+|+++|. ++++.||+
T Consensus         1 G~~v~g~V~~v~~~Gv~V~l~~~v~g~i~~~~l~~~~~~~~~~~~~~Gd~i~~~V~~id~~~~~i~ls~   69 (69)
T cd05697           1 GQVVKGTIRKLRPSGIFVKLSDHIKGLVPPMHLADVRLKHPEKKFKPGLKVKCRVLSVEPERKRLVLTL   69 (69)
T ss_pred             CCEEEEEEEEEeccEEEEEecCCcEEEEEHHHCCCccccCHHHcCCCCCEEEEEEEEEECCCCEEEEEC
Confidence            789999999999999999999899999999999999999999999999999999999998 78999984

Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in Saccharomyces cerevisiae Rrp5 and 14 S1 repeats in Homo sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in protein-protein interactions. Mutational studies have shown that each region represents a specific functional domain. Deletions within the S1-containing region inhibit pre-rRNA processing at either site A3 or A2, whereas deletions within the TPR region confer an inability to support cleavage of A0-A2. This CD includes H. sapiens S1 repeat 5 (hs5) and S. cerevisiae S1 repeat 5 (sc5). Rrp5 is found in eukaryotes but not in prokaryotes or archaea.

>PF03726 PNPase: Polyribonucleotide nucleotidyltransferase, RNA binding domain; InterPro: IPR015848 The PH (phosphorolytic) domain is responsible for 3'-5' exoribonuclease activity, although in some proteins this domain has lost its catalytic function

Probab=99.29  E-value=1.7e-11  Score=110.54  Aligned_cols=80  Identities=38%  Similarity=0.573  Sum_probs=72.4

Q ss_pred             HHHHHHHHHHHHHHHhhhcCCCCChhHHHHHHHHHHHHHHHHhhhc---cchhhhchHHHHHHHHHHHHHHHHHHhcCCc
Q 002054          294 QTLEKVSNLAEAHIEAVFTDPSYSKFERGEALDKIGQDVKKALEEE---CDEESLQVLPKAVDTVRKRVIRKRIIAEGVR  370 (974)
Q Consensus       294 ~~~~~~~~~~~~~~~~~~~~~~~~k~~r~~~~~~~~~~~~~~~~~~---~~~~~~~~~~~~~~~~~~~~~r~~il~~~~R  370 (974)
                      +|.+.|++++.++|++++.+  ++|++|++++++|++++.+.|.++   .++.....+..+|+.++++.+|++||++|+|
T Consensus         1 el~~~v~~~~~~~l~~a~~~--~~K~eR~~a~~~i~~~~~~~~~~~~~e~~~~~~~~i~~~~~~l~k~~vR~~Il~~~~R   78 (83)
T PF03726_consen    1 ELKEAVKELAGEKLKEALQI--PDKQEREEALDAIKEEVIEELEEEYEEEDEEDEKEIKEAFEELEKKIVREMILEEGIR   78 (83)
T ss_dssp             HHHHHHHHHHHHHHHHHHTS--SSHHHHHHHHHHHHHHHHHHHHCCCHHSTTSHHHHHHHHHHHHHHHHHHHHHHCTSBT
T ss_pred             CHHHHHHHHHHHHHHHHHcc--cchHHHHHHHHHHHHHHHHHHHHhhcccchhhHHHHHHHHHHHHHHHHHHHHHCCCCC
Confidence            58899999999999999988  699999999999999999999843   2456677899999999999999999999999


Q ss_pred             CCCCC
Q 002054          371 VDGRQ  375 (974)
Q Consensus       371 ~DGR~  375 (974)
                      +|||+
T Consensus        79 ~DGR~   83 (83)
T PF03726_consen   79 IDGRK   83 (83)
T ss_dssp             TTS-B
T ss_pred             CCCCC
Confidence            99995

An active PH domain uses inorganic phosphate as a nucleophile, adding it across the phosphodiester bond between the end two nucleotides in order to release ribonucleoside 5'-diphosphate (rNDP) from the 3' end of the RNA substrate. PH domains can be found in bacterial/organelle RNases and PNPases (polynucleotide phosphorylases) [], as well as in archaeal and eukaryotic RNA exosomes [, ], the later acting as nano-compartments for the degradation or processing of RNA (including mRNA, rRNA, snRNA and snoRNA). Bacterial/organelle PNPases share a common barrel structure with RNA exosomes, consisting of a hexameric ring of PH domains that act as a degradation chamber, and an S1-domain/KH-domain containing cap that binds the RNA substrate (and sometimes accessory proteins) in order to regulate and restrict entry into the degradation chamber []. Unstructured RNA substrates feed in through the pore made by the S1 domains, are degraded by the PH domain ring, and exit as nucleotides via the PH pore at the opposite end of the barrel [, ]. This entry represents an RNA-binding phosphorolytic (PH) domain found in bacterial and organelle PNPases, but not in exosomes. It usually occurs in combination with PH domain 1 (IPR001247 from INTERPRO) and PH domain 2 (IPR015847 from INTERPRO), both of which are found in PNPases and exosomes. The core structure of the RNA-binding PH domain consists of a DNA/RNA-binding 3-helical bundle. More information about these proteins can be found at Protein of the Month: RNA Exosomes [].; GO: 0000175 3'-5'-exoribonuclease activity, 0003723 RNA binding, 0006396 RNA processing; PDB: 1E3H_A 1E3P_A 3U1K_B 3GCM_A 3GLL_A 3GME_A 4AM3_B 4AID_C 4AIM_A 1WHU_A ....

>cd05707 S1_Rrp5_repeat_sc11 S1_Rrp5_repeat_sc11: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits

Probab=99.27  E-value=9.3e-12  Score=107.66  Aligned_cols=67  Identities=27%  Similarity=0.458  Sum_probs=64.0

Q ss_pred             CcEEEEEEEEEeeceEEEEEcCCeEEEEecccCCCccccccccccccCCEEEEEEEEEcc-CCceEEE
Q 002054          684 GGIYKGVVTSVKEYGAFVEFNGGQQGLLHVSELSHEPVSRVSDVVSVGQQLSLRCIGQDV-RGNIKLS  750 (974)
Q Consensus       684 G~i~~G~V~~i~~~G~fV~l~~g~~Glvhisels~~~v~~~~~~~~vGd~V~vkVl~id~-~gri~LS  750 (974)
                      |++|.|+|+++.++|+||+|.++.+||+|++++++++..++.+.|++||.|+|+|+++|+ ++++.||
T Consensus         1 G~~v~g~V~~v~~~Gv~V~l~~~~~G~v~~s~l~~~~~~~~~~~~~~Gd~v~~~v~~~d~~~~~i~ls   68 (68)
T cd05707           1 GDVVRGFVKNIANNGVFVTLGRGVDARVRVSELSDSYLKDWKKRFKVGQLVKGKIVSIDPDNGRIEMT   68 (68)
T ss_pred             CCEEEEEEEEEECccEEEEeCCCCEEEEEHHHCCchhhcCHhhccCCCCEEEEEEEEEeCCCCEEecC
Confidence            789999999999999999999999999999999999999999999999999999999998 7888876

Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in Saccharomyces cerevisiae Rrp5 and 14 S1 repeats in Homo sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in protein-protein interactions. Mutational studies have shown that each region represents a specific functional domain. Deletions within the S1-containing region inhibit pre-rRNA processing at either site A3 or A2, whereas deletions within the TPR region confer an inability to support cleavage of A0-A2. This CD includes S. cerevisiae S1 repeat 11 (sc11). Rrp5 is found in eukaryotes but not in prokaryotes or archaea.

>cd05694 S1_Rrp5_repeat_hs2_sc2 S1_Rrp5_repeat_hs2_sc2: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits

Probab=99.25  E-value=2.8e-11  Score=106.52  Aligned_cols=71  Identities=21%  Similarity=0.268  Sum_probs=64.3

Q ss_pred             ccccCcEEEEEEEEEeeceEEEEEc-CCeEEEEecccCCCccccccccccccCCEEEEEEEEEcc-CCceEEEEeccCC
Q 002054          680 EIEVGGIYKGVVTSVKEYGAFVEFN-GGQQGLLHVSELSHEPVSRVSDVVSVGQQLSLRCIGQDV-RGNIKLSLKAVSP  756 (974)
Q Consensus       680 ~~~~G~i~~G~V~~i~~~G~fV~l~-~g~~Glvhisels~~~v~~~~~~~~vGd~V~vkVl~id~-~gri~LS~K~~~~  756 (974)
                      +++.|+++.|+|++|.++|+||++. ++++||+|.+++++.      +.+++||.+.|+|+++|+ ++++.||+|+..+
T Consensus         1 dl~~G~~v~g~V~si~d~G~~v~~g~~gv~Gfl~~~~~~~~------~~~~~Gq~v~~~V~~vd~~~~~v~ls~k~~~~   73 (74)
T cd05694           1 DLVEGMVLSGCVSSVEDHGYILDIGIPGTTGFLPKKDAGNF------SKLKVGQLLLCVVEKVKDDGRVVSLSADPSKV   73 (74)
T ss_pred             CCCCCCEEEEEEEEEeCCEEEEEeCCCCcEEEEEHHHCCcc------cccCCCCEEEEEEEEEECCCCEEEEEEeeccc
Confidence            4689999999999999999999995 589999999999986      569999999999999998 6789999998653

Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in Saccharomyces cerevisiae Rrp5 and 14 S1 repeats in Homo sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in protein-protein interactions. Mutational studies have shown that each region represents a specific functional domain. Deletions within the S1-containing region inhibit pre-rRNA processing at either site A3 or A2, whereas deletions within the TPR region confer an inability to support cleavage of A0-A2. This CD includes H. sapiens S1 repeat 2 (hs2) and S. cerevisiae S1 repeat 2 (sc2). Rrp5 is found in eukaryotes but not in prokaryotes or archaea.

>cd05691 S1_RPS1_repeat_ec6 S1_RPS1_repeat_ec6: Ribosomal protein S1 (RPS1) domain

Probab=99.24  E-value=2.7e-11  Score=105.87  Aligned_cols=71  Identities=34%  Similarity=0.513  Sum_probs=67.5

Q ss_pred             CcEEEEEEEEEeeceEEEEEcCCeEEEEecccCCCccccccccccccCCEEEEEEEEEcc-CCceEEEEecc
Q 002054          684 GGIYKGVVTSVKEYGAFVEFNGGQQGLLHVSELSHEPVSRVSDVVSVGQQLSLRCIGQDV-RGNIKLSLKAV  754 (974)
Q Consensus       684 G~i~~G~V~~i~~~G~fV~l~~g~~Glvhisels~~~v~~~~~~~~vGd~V~vkVl~id~-~gri~LS~K~~  754 (974)
                      |+++.|+|+++.++|+||++.++.+|++|+++++++++.++.+.|++||.++|+|+++|. ++++.||+|.+
T Consensus         1 G~~v~g~V~~v~~~g~~v~l~~~~~g~i~~~~~~~~~~~~~~~~~~~Gd~v~~~v~~~d~~~~~i~ls~k~~   72 (73)
T cd05691           1 GSIVTGKVTEVDAKGATVKLGDGVEGFLRAAELSRDRVEDATERFKVGDEVEAKITNVDRKNRKISLSIKAK   72 (73)
T ss_pred             CCEEEEEEEEEECCeEEEEeCCCCEEEEEHHHCCCccccCHHHccCCCCEEEEEEEEEeCCCCEEEEEEEEc
Confidence            789999999999999999999999999999999999999999999999999999999998 58899999875

RPS1 is a component of the small ribosomal subunit thought to be involved in the recognition and binding of mRNA's during translation initiation. The bacterial RPS1 domain architecture consists of 4-6 tandem S1 domains. In some bacteria, the tandem S1 array is located C-terminal to a 4-hydroxy-3-methylbut-2-enyl diphosphate reductase (HMBPP reductase) domain. While RPS1 is found primarily in bacteria, proteins with tandem RPS1-like domains have been identified in plants and humans, however these lack the N-terminal HMBPP reductase domain. This CD includes S1 repeat 6 (ec6) of the Escherichia coli RPS1. Autoantibodies to double-stranded DNA from patients with systemic lupus erythematosus cross-react with the human RPS1 homolog.

>cd05692 S1_RPS1_repeat_hs4 S1_RPS1_repeat_hs4: Ribosomal protein S1 (RPS1) domain

Probab=99.24  E-value=3.2e-11  Score=103.78  Aligned_cols=69  Identities=42%  Similarity=0.815  Sum_probs=65.9

Q ss_pred             CcEEEEEEEEEeeceEEEEEcCCeEEEEecccCCCccccccccccccCCEEEEEEEEEccCCceEEEEe
Q 002054          684 GGIYKGVVTSVKEYGAFVEFNGGQQGLLHVSELSHEPVSRVSDVVSVGQQLSLRCIGQDVRGNIKLSLK  752 (974)
Q Consensus       684 G~i~~G~V~~i~~~G~fV~l~~g~~Glvhisels~~~v~~~~~~~~vGd~V~vkVl~id~~gri~LS~K  752 (974)
                      |++|.|+|+++.++|+||++.++.+||+|+++++++++.++.+.|++||.++|+|+++|.++++.||+|
T Consensus         1 G~~~~g~V~~i~~~g~~v~i~~~~~g~l~~~~l~~~~~~~~~~~~~~Gd~v~v~v~~~~~~~~i~ls~k   69 (69)
T cd05692           1 GSVVEGTVTRLKPFGAFVELGGGISGLVHISQIAHKRVKDVKDVLKEGDKVKVKVLSIDARGRISLSIK   69 (69)
T ss_pred             CCEEEEEEEEEEeeeEEEEECCCCEEEEEhHHcCCcccCCHHHccCCCCEEEEEEEEECCCCcEEEEEC
Confidence            789999999999999999999899999999999999999999999999999999999998889999986

RPS1 is a component of the small ribosomal subunit thought to be involved in the recognition and binding of mRNA's during translation initiation. The bacterial RPS1 domain architecture consists of 4-6 tandem S1 domains. In some bacteria, the tandem S1 array is located C-terminal to a 4-hydroxy-3-methylbut-2-enyl diphosphate reductase (HMBPP reductase) domain. While RPS1 is found primarily in bacteria, proteins with tandem RPS1-like domains have been identified in plants and humans, however these lack the N-terminal HMBPP reductase domain. This CD includes S1 repeat 4 (hs4) of the H. sapiens RPS1 homolog. Autoantibodies to double-stranded DNA from patients with systemic lupus erythematosus cross-react with the human RPS1 homolog.

>cd05690 S1_RPS1_repeat_ec5 S1_RPS1_repeat_ec5: Ribosomal protein S1 (RPS1) domain

Probab=99.23  E-value=2.4e-11  Score=105.13  Aligned_cols=67  Identities=33%  Similarity=0.654  Sum_probs=61.9

Q ss_pred             CcEEEEEEEEEeeceEEEEEcCCeEEEEecccCCC-ccccccccccccCCEEEEEEEEEcc-CCceEEE
Q 002054          684 GGIYKGVVTSVKEYGAFVEFNGGQQGLLHVSELSH-EPVSRVSDVVSVGQQLSLRCIGQDV-RGNIKLS  750 (974)
Q Consensus       684 G~i~~G~V~~i~~~G~fV~l~~g~~Glvhisels~-~~v~~~~~~~~vGd~V~vkVl~id~-~gri~LS  750 (974)
                      |++|.|+|+++.+||+||+|.++.+||+|+++++| .+..++.+.|++||.|+|+|+++|. ++++.||
T Consensus         1 G~~~~g~V~~i~~~G~fv~l~~~~~Glv~~~~l~~~~~~~~~~~~~~~G~~v~v~v~~id~~~~~i~l~   69 (69)
T cd05690           1 GTVVSGKIKSITDFGIFVGLDGGIDGLVHISDISWTQRVRHPSEIYKKGQEVEAVVLNIDVERERISLG   69 (69)
T ss_pred             CCEEEEEEEEEEeeeEEEEeCCCCEEEEEHHHCCCccccCChhhEECCCCEEEEEEEEEECCcCEEeCC
Confidence            78999999999999999999999999999999996 5778888999999999999999997 6788774

RPS1 is a component of the small ribosomal subunit thought to be involved in the recognition and binding of mRNA's during translation initiation. The bacterial RPS1 domain architecture consists of 4-6 tandem S1 domains. In some bacteria, the tandem S1 array is located C-terminal to a 4-hydroxy-3-methylbut-2-enyl diphosphate reductase (HMBPP reductase) domain. While RPS1 is found primarily in bacteria, proteins with tandem RPS1-like domains have been identified in plants and humans, however these lack the N-terminal HMBPP reductase domain. This CD includes S1 repeat 5 (ec5) of the Escherichia coli RPS1. Autoantibodies to double-stranded DNA from patients with systemic lupus erythematosus cross-react with the human RPS1 homolog.

>cd05708 S1_Rrp5_repeat_sc12 S1_Rrp5_repeat_sc12: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits

Probab=99.22  E-value=5e-11  Score=105.28  Aligned_cols=73  Identities=34%  Similarity=0.610  Sum_probs=68.1

Q ss_pred             ccCcEEEEEEEEEeeceEEEEEcC-CeEEEEecccCCCccccccccccccCCEEEEEEEEEcc-CCceEEEEecc
Q 002054          682 EVGGIYKGVVTSVKEYGAFVEFNG-GQQGLLHVSELSHEPVSRVSDVVSVGQQLSLRCIGQDV-RGNIKLSLKAV  754 (974)
Q Consensus       682 ~~G~i~~G~V~~i~~~G~fV~l~~-g~~Glvhisels~~~v~~~~~~~~vGd~V~vkVl~id~-~gri~LS~K~~  754 (974)
                      ++|++|.|+|+++.++|+||+|.+ +.+|++|++++++++..++.+.|++||.|+|+|+++|. ++++.||+|..
T Consensus         1 ~~g~~v~g~V~~i~~~g~~v~l~~~~~~g~i~~~~l~~~~~~~~~~~~~~Gd~v~v~i~~vd~~~~~i~ls~k~~   75 (77)
T cd05708           1 KVGQKIDGTVRRVEDYGVFIDIDGTNVSGLCHKSEISDNRVADASKLFRVGDKVRAKVLKIDAEKKRISLGLKAS   75 (77)
T ss_pred             CCCCEEEEEEEEEEcceEEEEECCCCeEEEEEHHHCCCCccCCHhHeecCCCEEEEEEEEEeCCCCEEEEEEEee
Confidence            469999999999999999999975 79999999999999988899999999999999999998 78999999874

Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in Saccharomyces cerevisiae Rrp5 and 14 S1 repeats in Homo sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in protein-protein interactions. Mutational studies have shown that each region represents a specific functional domain. Deletions within the S1-containing region inhibit pre-rRNA processing at either site A3 or A2, whereas deletions within the TPR region confer an inability to support cleavage of A0-A2. This CD includes S. cerevisiae S1 repeat 12 (sc12). Rrp5 is found in eukaryotes but not in prokaryotes or archaea.

>COG1093 SUI2 Translation initiation factor 2, alpha subunit (eIF-2alpha) [Translation, ribosomal structure and biogenesis]

Probab=99.22  E-value=9.2e-12  Score=130.58  Aligned_cols=78  Identities=38%  Similarity=0.613  Sum_probs=73.7

Q ss_pred             ccccCcEEEEEEEEEeeceEEEEE--cCCeEEEEecccCCCccccccccccccCCEEEEEEEEEcc-CCceEEEEeccCC
Q 002054          680 EIEVGGIYKGVVTSVKEYGAFVEF--NGGQQGLLHVSELSHEPVSRVSDVVSVGQQLSLRCIGQDV-RGNIKLSLKAVSP  756 (974)
Q Consensus       680 ~~~~G~i~~G~V~~i~~~G~fV~l--~~g~~Glvhisels~~~v~~~~~~~~vGd~V~vkVl~id~-~gri~LS~K~~~~  756 (974)
                      -+++|+++-|+|++|.+||+||.|  ++|.+||+|+||++..|++++.+++++||.+-||||.+|+ +|.|.||+|.+.+
T Consensus         8 ~PeeGEiVv~tV~~V~~~GAyv~L~EY~g~Eg~ihiSEvas~wVknIrd~vkegqkvV~kVlrVd~~rg~IDLSlkrV~~   87 (269)
T COG1093           8 YPEEGEIVVGTVKQVADYGAYVELDEYPGKEGFIHISEVASGWVKNIRDYVKEGQKVVAKVLRVDPKRGHIDLSLKRVTE   87 (269)
T ss_pred             CCCCCcEEEEEEEEeeccccEEEeeccCCeeeeEEHHHHHHHHHHHHHHHhhcCCeEEEEEEEEcCCCCeEeeehhhCCH
Confidence            378999999999999999999999  5799999999999999999999999999999999999999 7999999998865


Q ss_pred             C
Q 002054          757 R  757 (974)
Q Consensus       757 ~  757 (974)
                      +
T Consensus        88 ~   88 (269)
T COG1093          88 H   88 (269)
T ss_pred             H
Confidence            3

>cd05687 S1_RPS1_repeat_ec1_hs1 S1_RPS1_repeat_ec1_hs1: Ribosomal protein S1 (RPS1) domain

Probab=99.20  E-value=5.4e-11  Score=103.42  Aligned_cols=69  Identities=30%  Similarity=0.531  Sum_probs=65.7

Q ss_pred             CcEEEEEEEEEeeceEEEEEcCCeEEEEecccCCCccccccccccccCCEEEEEEEEEcc-CCceEEEEe
Q 002054          684 GGIYKGVVTSVKEYGAFVEFNGGQQGLLHVSELSHEPVSRVSDVVSVGQQLSLRCIGQDV-RGNIKLSLK  752 (974)
Q Consensus       684 G~i~~G~V~~i~~~G~fV~l~~g~~Glvhisels~~~v~~~~~~~~vGd~V~vkVl~id~-~gri~LS~K  752 (974)
                      |+++.|+|.++.++|+||++.++.+|++|.+|+++.+..++.+.|++||.++|+|+++|+ ++++.||+|
T Consensus         1 G~iv~g~V~~i~~~~~~v~l~~~~~g~l~~~e~~~~~~~~~~~~~~~Gd~i~~~i~~~~~~~~~i~lS~~   70 (70)
T cd05687           1 GDIVKGTVVSVDDDEVLVDIGYKSEGIIPISEFSDDPIENGEDEVKVGDEVEVYVLRVEDEEGNVVLSKR   70 (70)
T ss_pred             CCEEEEEEEEEeCCEEEEEeCCCceEEEEHHHhCccccCCHhHcCCCCCEEEEEEEEEECCCCeEEEEeC
Confidence            789999999999999999998899999999999999999999999999999999999996 689999986

RPS1 is a component of the small ribosomal subunit thought to be involved in the recognition and binding of mRNA's during translation initiation. The bacterial RPS1 domain architecture consists of 4-6 tandem S1 domains. In some bacteria, the tandem S1 array is located C-terminal to a 4-hydroxy-3-methylbut-2-enyl diphosphate reductase (HMBPP reductase) domain. While RPS1 is found primarily in bacteria, proteins with tandem RPS1-like domains have been identified in plants and humans, however these lack the N-terminal HMBPP reductase domain. This CD includes S1 repeat 1 of the Escherichia coli and Homo sapiens RPS1 (ec1 and hs1, respectively). Autoantibodies to double-stranded DNA from patients with systemic lupus erythematosus cross-react with the human RPS1 homolog.

>PRK08059 general stress protein 13; Validated

Probab=99.20  E-value=5.9e-11  Score=115.01  Aligned_cols=80  Identities=38%  Similarity=0.713  Sum_probs=75.1

Q ss_pred             cccccCcEEEEEEEEEeeceEEEEEcCCeEEEEecccCCCccccccccccccCCEEEEEEEEEcc-CCceEEEEeccCCC
Q 002054          679 REIEVGGIYKGVVTSVKEYGAFVEFNGGQQGLLHVSELSHEPVSRVSDVVSVGQQLSLRCIGQDV-RGNIKLSLKAVSPR  757 (974)
Q Consensus       679 ~~~~~G~i~~G~V~~i~~~G~fV~l~~g~~Glvhisels~~~v~~~~~~~~vGd~V~vkVl~id~-~gri~LS~K~~~~~  757 (974)
                      .++++|++|.|+|+++.++|+||++.++.+|++|+++++++++.++.+.|++||.|+|+|+++|. ++++.||+|.+..+
T Consensus         3 ~~~k~G~iv~G~V~~i~~~G~fV~i~~~~~Gli~~sel~~~~~~~~~~~~~vGD~I~vkI~~id~~~~~i~lslk~~~~~   82 (123)
T PRK08059          3 SQYEVGSVVTGKVTGIQPYGAFVALDEETQGLVHISEITHGFVKDIHDFLSVGDEVKVKVLSVDEEKGKISLSIRATEEA   82 (123)
T ss_pred             ccCCCCCEEEEEEEEEecceEEEEECCCCEEEEEHHHCCcccccCHHHcCCCCCEEEEEEEEEECCCCeEEEEEEEcccC
Confidence            45889999999999999999999999999999999999999999999999999999999999987 79999999998776


Q ss_pred             c
Q 002054          758 P  758 (974)
Q Consensus       758 ~  758 (974)
                      |
T Consensus        83 ~   83 (123)
T PRK08059         83 P   83 (123)
T ss_pred             c
Confidence            6

>cd05689 S1_RPS1_repeat_ec4 S1_RPS1_repeat_ec4: Ribosomal protein S1 (RPS1) domain

Probab=99.17  E-value=8.8e-11  Score=102.65  Aligned_cols=70  Identities=36%  Similarity=0.554  Sum_probs=62.3

Q ss_pred             cccCcEEEEEEEEEeeceEEEEEcCCeEEEEecccCCCc-cccccccccccCCEEEEEEEEEcc-CCceEEE
Q 002054          681 IEVGGIYKGVVTSVKEYGAFVEFNGGQQGLLHVSELSHE-PVSRVSDVVSVGQQLSLRCIGQDV-RGNIKLS  750 (974)
Q Consensus       681 ~~~G~i~~G~V~~i~~~G~fV~l~~g~~Glvhisels~~-~v~~~~~~~~vGd~V~vkVl~id~-~gri~LS  750 (974)
                      +.+|++|.|+|+++.+||+||+|.++.+||+|+++++|. +..++.+.|++||.|+|+|+++|. ++++.|+
T Consensus         1 ~~~g~~~~g~V~~i~~~G~fv~l~~~~~Gl~~~~~l~~~~~~~~~~~~~~~Gd~v~v~v~~id~~~~~i~~~   72 (72)
T cd05689           1 YPEGTRLFGKVTNLTDYGCFVELEEGVEGLVHVSEMDWTNKNIHPSKVVSLGDEVEVMVLDIDEERRRISLG   72 (72)
T ss_pred             CcCCCEEEEEEEEEEeeEEEEEcCCCCEEEEEEEeccCcccccCcccEeCCCCEEEEEEEEeeCCcCEEeCC
Confidence            368999999999999999999999899999999999875 455777889999999999999997 5777764

RPS1 is a component of the small ribosomal subunit thought to be involved in the recognition and binding of mRNA's during translation initiation. The bacterial RPS1 domain architecture consists of 4-6 tandem S1 domains. In some bacteria, the tandem S1 array is located C-terminal to a 4-hydroxy-3-methylbut-2-enyl diphosphate reductase (HMBPP reductase) domain. While RPS1 is found primarily in bacteria, proteins with tandem RPS1-like domains have been identified in plants and humans, however these lack the N-terminal HMBPP reductase domain. This CD includes S1 repeat 4 (ec4) of the Escherichia coli RPS1. Autoantibodies to double-stranded DNA from patients with systemic lupus erythematosus cross-react with the human RPS1 homolog.

>KOG1612 consensus Exosomal 3'-5' exoribonuclease complex, subunit Rrp42 [Translation, ribosomal structure and biogenesis]

Probab=99.17  E-value=2.6e-09  Score=111.30  Aligned_cols=201  Identities=18%  Similarity=0.220  Sum_probs=140.9

Q ss_pred             CeEEEEEeCccCcCCCcEEEEEeCC-eEEEEEEEeCCC-C----CCCCceeeEeeccccccccCCCCCccccccCC--CC
Q 002054           67 SRLITLETGKIARFANGAVVLGMDE-TKVLSTVTSSKG-D----SVRDFLPLTVDYQEKQFAQGVIPNTYMRREGA--PK  138 (974)
Q Consensus        67 ~r~i~~etg~~a~~A~GSa~v~~G~-T~Vl~tv~~~~~-~----~~~~f~pL~v~y~e~~~a~g~ip~~~~~Reg~--p~  138 (974)
                      =|+|.+|||++ ++++|||.|++|+ |-||++|+..-+ |    +.....-+.||......      ..|-.|+|-  ++
T Consensus        31 ~Rpi~vetdVl-p~tNGSaRVk~g~~tdiivgVKaEvg~~~~~~p~egk~~~~VD~S~sas------p~f~gRggde~~~  103 (288)
T KOG1612|consen   31 FRPIEVETDVL-PGTNGSARVKLGDGTDIIVGVKAEVGSPDDETPVEGKYLFFVDCSPSAS------PQFQGRGGDELVE  103 (288)
T ss_pred             cceEEEEeccc-cCCCCcEEEEecCCceEEEEEeeeccCccccCCCCCeEEEEEEecCCcC------ccccCCChhhHHH
Confidence            37999999999 9999999999999 889999998765 2    12233456677643321      124455442  33


Q ss_pred             chhhhHHHhhcC-Cccc-----cccCCCCCceEEEEEEEeccCCCChhhHHHHHHHHHhhcCCCC---------------
Q 002054          139 ERELLVGRIIDR-PIRP-----LFPAGFYHEVQVMASVLSSDGKQDPDIMAANATSAALMLSDIP---------------  197 (974)
Q Consensus       139 ~~eil~~RlidR-~lrp-----lfp~~~~~~~~i~~~vl~~dg~~~~~~~ai~aAs~AL~~s~iP---------------  197 (974)
                      +-.-.++|+... ..-+     .|-++|.+.+.|++.|++.||+..  .|--.|+.+||.+.-+|               
T Consensus       104 eltsaLq~~l~~~~sgv~ls~L~lt~~~~W~i~VDvlVi~s~gn~~--dAiS~Ai~~AL~~T~lPkv~v~~dd~~~~~i~  181 (288)
T KOG1612|consen  104 ELTSALQRVLNSLGSGVDLSKLQLTPGYCWKIYVDVLVISSDGNLL--DAISIAIYAALNNTRLPKVIVAFDDDGEVEIL  181 (288)
T ss_pred             HHHHHHHHHHhCcCcccchhheeccCCeeEEEEEeEEEEecCCCHH--HHHHHHHHHHHhcccCCccccccccCCceeec
Confidence            333344454433 1101     455669999999999999999654  55567888999887666               


Q ss_pred             ------------CCCCeEEEEEEEECCEEEEcCCHHHHhcCccceeEeeeCCeE-EEE-EecCCCCCHHHHHHHHHHHHH
Q 002054          198 ------------WGGPIGMIRIGRICGQFIVNPTMDELSLSDLNLVYACTREKT-LMI-DVQAREISEKDLEAGLRLAHP  263 (974)
Q Consensus       198 ------------~~~~v~av~vg~i~g~~vldPt~~e~~~s~~~l~v~~t~~~i-~mi-e~~~~~~~e~~~~~al~~a~~  263 (974)
                                  ...+..=+++.+|+..+++|||.+|++.+..-+.|+-+..++ ..+ ..+.+.+..+-..++|+.|.+
T Consensus       182 ~s~~~Yd~~~~~~~~~P~ivtlskIG~~~lVD~T~eEe~~a~s~l~Isv~a~givs~~r~VG~G~l~~s~i~~mle~~~~  261 (288)
T KOG1612|consen  182 LSDEEYDLMVKLVENVPLIVTLSKIGTNMLVDPTAEEESVANSGLLISVSAGGIVSCTRSVGLGDLDPSSIPEMLEQGKA  261 (288)
T ss_pred             cCcccchhhhhhcccCCEEEEEEeecceEEccCCccHHHhhhcceEEEEecCcceEEEEEecCCCCChhhHHHHHHHHHH
Confidence                        112334578899999999999999999999999998887773 333 334444777788888888888


Q ss_pred             HHHHHHHHHHHHH
Q 002054          264 EAVKYLEPQIRLA  276 (974)
Q Consensus       264 ~~~~i~~~~~~~~  276 (974)
                      -.+.+.....+.+
T Consensus       262 ~~e~l~~~l~k~L  274 (288)
T KOG1612|consen  262 VVETLAPDLVKSL  274 (288)
T ss_pred             HHHhhhHHHHHHh
Confidence            7776665544433

>cd05789 S1_Rrp4 S1_Rrp4: Rrp4 S1-like RNA-binding domain

Probab=99.15  E-value=1.1e-10  Score=105.80  Aligned_cols=75  Identities=23%  Similarity=0.252  Sum_probs=68.6

Q ss_pred             ccccCcEEEEEEEEEeeceEEEEEcCCeEEEEecccCCC----ccccccccccccCCEEEEEEEEEccCCceEEEEecc
Q 002054          680 EIEVGGIYKGVVTSVKEYGAFVEFNGGQQGLLHVSELSH----EPVSRVSDVVSVGQQLSLRCIGQDVRGNIKLSLKAV  754 (974)
Q Consensus       680 ~~~~G~i~~G~V~~i~~~G~fV~l~~g~~Glvhisels~----~~v~~~~~~~~vGd~V~vkVl~id~~gri~LS~K~~  754 (974)
                      .+++|+++.|+|+++.++|++|++.++.+|++|+|++++    .+..++.+.+++||.++|+|+++|+++++.||+|..
T Consensus         3 ~p~~GdiV~g~V~~i~~~g~~v~i~~~~~G~l~~se~~~~~~~~~~~~~~~~l~vGd~i~~~V~~~~~~~~i~LS~~~~   81 (86)
T cd05789           3 IPEVGDVVIGRVTEVGFKRWKVDINSPYDAVLPLSEVNLPRTDEDELNMRSYLDEGDLIVAEVQSVDSDGSVSLHTRSL   81 (86)
T ss_pred             cCCCCCEEEEEEEEECCCEEEEECCCCeEEEEEHHHccCCCCccchHHHHhhCCCCCEEEEEEEEECCCCCEEEEeCcc
Confidence            368999999999999999999999989999999999986    455777888999999999999998889999999874

S1-like RNA-binding domains are found in a wide variety of RNA-associated proteins. Rrp4 protein is a subunit of the exosome complex. The exosome plays a central role in 3' to 5' RNA processing and degradation in eukarytes and archaea. Its functions include the removal of incorrectly processed RNA and the maintenance of proper levels of mRNA, rRNA and a number of small RNA species. In Saccharomyces cerevisiae, the exosome includes nine core components, six of which are homologous to bacterial RNase PH. These form a hexameric ring structure. The other three subunits (RrP4, Rrp40, and Csl4) contain an S1 RNA binding domain and are part of the "S1 pore structure".

>cd04472 S1_PNPase S1_PNPase: Polynucleotide phosphorylase (PNPase), ), S1-like RNA-binding domain

Probab=99.14  E-value=1.7e-10  Score=99.28  Aligned_cols=68  Identities=49%  Similarity=0.824  Sum_probs=64.4

Q ss_pred             CcEEEEEEEEEeeceEEEEEcCCeEEEEecccCCCccccccccccccCCEEEEEEEEEccCCceEEEE
Q 002054          684 GGIYKGVVTSVKEYGAFVEFNGGQQGLLHVSELSHEPVSRVSDVVSVGQQLSLRCIGQDVRGNIKLSL  751 (974)
Q Consensus       684 G~i~~G~V~~i~~~G~fV~l~~g~~Glvhisels~~~v~~~~~~~~vGd~V~vkVl~id~~gri~LS~  751 (974)
                      |++|.|+|+++.++|+||++.++.+||+|+++++++++.++.+.|++||.|+|+|+++|.++++.||+
T Consensus         1 g~~~~g~V~~v~~~G~~v~l~~~~~g~l~~~~l~~~~~~~~~~~~~~Gd~v~v~v~~~d~~~~i~ls~   68 (68)
T cd04472           1 GKIYEGKVVKIKDFGAFVEILPGKDGLVHISELSDERVEKVEDVLKVGDEVKVKVIEVDDRGRISLSR   68 (68)
T ss_pred             CCEEEEEEEEEEEeEEEEEeCCCCEEEEEhHHcCCccccCHHHccCCCCEEEEEEEEECCCCcEEeeC
Confidence            78999999999999999999888999999999999999888899999999999999999888999985

PNPase is a polyribonucleotide nucleotidyl transferase that degrades mRNA. It is a trimeric multidomain protein. The C-terminus contains the S1 domain which binds ssRNA. This family is classified based on the S1 domain. PNPase nonspecifically removes the 3' nucleotides from mRNA, but is stalled by double-stranded RNA structures such as a stem-loop. Evidence shows that a minimum of 7-10 unpaired nucleotides at the 3' end, is required for PNPase degradation. It is suggested that PNPase also dephosphorylates the RNA 5' end. This additional activity may regulate the 5'-dependent activity of RNaseE in vivo.

>cd05694 S1_Rrp5_repeat_hs2_sc2 S1_Rrp5_repeat_hs2_sc2: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits

Probab=99.12  E-value=2.6e-10  Score=100.37  Aligned_cols=65  Identities=25%  Similarity=0.371  Sum_probs=58.1

Q ss_pred             cCCCCCEEEEEEEEEeCCeEEEEeC-CCeEEEEecccCCC-CCCCCCCEEEEEEEEEeCCCce-eeee
Q 002054          907 NLKLGTKVAAKVYQVRARGLVLDLG-GGIRGMYRFENNEK-KDFVVGDELLVKCSSFTGKGIP-VVSL  971 (974)
Q Consensus       907 ~~~vG~vV~G~V~~I~~~GvFV~L~-~gv~Glih~se~~~-~~f~vGd~V~vkVl~id~~~~~-~~~~  971 (974)
                      +++.|++|.|+|++|++||+||+++ +|+.||+|.++++. ..|++||.+.|+|+++|+++.. .+|+
T Consensus         1 dl~~G~~v~g~V~si~d~G~~v~~g~~gv~Gfl~~~~~~~~~~~~~Gq~v~~~V~~vd~~~~~v~ls~   68 (74)
T cd05694           1 DLVEGMVLSGCVSSVEDHGYILDIGIPGTTGFLPKKDAGNFSKLKVGQLLLCVVEKVKDDGRVVSLSA   68 (74)
T ss_pred             CCCCCCEEEEEEEEEeCCEEEEEeCCCCcEEEEEHHHCCcccccCCCCEEEEEEEEEECCCCEEEEEE
Confidence            5789999999999999999999997 69999999999975 6799999999999999987765 4444

Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in Saccharomyces cerevisiae Rrp5 and 14 S1 repeats in Homo sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in protein-protein interactions. Mutational studies have shown that each region represents a specific functional domain. Deletions within the S1-containing region inhibit pre-rRNA processing at either site A3 or A2, whereas deletions within the TPR region confer an inability to support cleavage of A0-A2. This CD includes H. sapiens S1 repeat 2 (hs2) and S. cerevisiae S1 repeat 2 (sc2). Rrp5 is found in eukaryotes but not in prokaryotes or archaea.

>cd05685 S1_Tex S1_Tex: The C-terminal S1 domain of a transcription accessory factor called Tex, which has been characterized in Bordetella pertussis and Pseudomonas aeruginosa

Probab=99.11  E-value=1.5e-10  Score=99.27  Aligned_cols=67  Identities=46%  Similarity=0.736  Sum_probs=63.3

Q ss_pred             CcEEEEEEEEEeeceEEEEEcCCeEEEEecccCCCccccccccccccCCEEEEEEEEEcc-CCceEEE
Q 002054          684 GGIYKGVVTSVKEYGAFVEFNGGQQGLLHVSELSHEPVSRVSDVVSVGQQLSLRCIGQDV-RGNIKLS  750 (974)
Q Consensus       684 G~i~~G~V~~i~~~G~fV~l~~g~~Glvhisels~~~v~~~~~~~~vGd~V~vkVl~id~-~gri~LS  750 (974)
                      |++|.|+|+++.++|+||++.++.+||+|.++++++++.++.+.|++||.++|+|+++|. ++++.||
T Consensus         1 g~~~~g~V~~i~~~G~fv~l~~~~~g~~~~~~l~~~~~~~~~~~~~~Gd~v~v~i~~vd~~~~~i~ls   68 (68)
T cd05685           1 GMVLEGVVTNVTDFGAFVDIGVKQDGLIHISKMADRFVSHPSDVVSVGDIVEVKVISIDEERGRISLS   68 (68)
T ss_pred             CCEEEEEEEEEecccEEEEcCCCCEEEEEHHHCCCccccCHHHhcCCCCEEEEEEEEEECCCCEEecC
Confidence            789999999999999999999899999999999999998999999999999999999998 7888875

The tex gene is essential in Bortella pertusis and is named for its role in toxin expression. Tex has two functional domains, an N-terminal domain homologous to the Escherichia coli maltose repression protein, which is a poorly defined transcriptional factor, and a C-terminal S1 RNA-binding domain. Tex is found in prokaryotes, eukaryotes, and archaea.

>KOG1613 consensus Exosomal 3'-5' exoribonuclease complex, subunit Rrp43 [Translation, ribosomal structure and biogenesis]

Probab=99.11  E-value=3.5e-10  Score=116.55  Aligned_cols=195  Identities=19%  Similarity=0.173  Sum_probs=133.5

Q ss_pred             eEEEEEeCccCcCCCcEEEEEeCCeEEEEEEEeCCC-CC--CCCceeeEeeccccccccCCCCCccccccCCCCchhhhH
Q 002054           68 RLITLETGKIARFANGAVVLGMDETKVLSTVTSSKG-DS--VRDFLPLTVDYQEKQFAQGVIPNTYMRREGAPKERELLV  144 (974)
Q Consensus        68 r~i~~etg~~a~~A~GSa~v~~G~T~Vl~tv~~~~~-~~--~~~f~pL~v~y~e~~~a~g~ip~~~~~Reg~p~~~eil~  144 (974)
                      |...++.|-+ ..||||++++.|+|.|+|++++..- |.  ..+-.++..+|.-..--..      .-|-|+|++.+.-+
T Consensus        47 Rdt~in~g~I-sTangSal~K~G~ttvi~~Ik~ei~epstdapdeg~Iv~n~~lpplcs~------r~RpG~p~dea~vi  119 (298)
T KOG1613|consen   47 RDTAINAGNI-STANGSALLKSGKTTVICGIKAEIAEPSTDAPDEGDIVPNYALPPLCSS------RFRPGPPTDEAQVI  119 (298)
T ss_pred             hhhheecCce-eccCcHHHHhcCCcEEEEEeeeeecccccCCCCCcceeecccCCccccc------CCCCCCCchHHHHH
Confidence            5678889999 8999999999999999999998753 21  1233344444421111111      12459999988777


Q ss_pred             HHhhcCCccc----------cccCCCCCceEEEEEEEeccCCCChhhHHHHHHHHHhhcCCCC---CCCC----------
Q 002054          145 GRIIDRPIRP----------LFPAGFYHEVQVMASVLSSDGKQDPDIMAANATSAALMLSDIP---WGGP----------  201 (974)
Q Consensus       145 ~RlidR~lrp----------lfp~~~~~~~~i~~~vl~~dg~~~~~~~ai~aAs~AL~~s~iP---~~~~----------  201 (974)
                      |.-+-.+|..          ++++.+.|-....+.+|++||..-  .+|.+|+.+||..-.+|   |+..          
T Consensus       120 Sq~LhdtIl~S~ii~~k~Lci~~gKaawvlYadIicLd~dG~~f--Da~w~al~aAlknvklP~a~ide~~~~~~~t~e~  197 (298)
T KOG1613|consen  120 SQKLHDTILHSRIIPKKALCIKAGKAAWVLYADIICLDYDGPVF--DACWNALMAALKNVKLPRAFIDERASDLRMTIEE  197 (298)
T ss_pred             HHHHHHHHHhcCCcchhhheeeccceeeEEEEEEEEEcCCCcHH--HHHHHHHHHHHhcCCCceeeecccchhhhhhHHH
Confidence            6665444443          677777777778899999999877  89999999999887777   2221          


Q ss_pred             ----------------eEEE-------EEE-EECCEEE-EcCCHHHHhcCccceeEeeeCCe--EEEEEe-cCCCCCHHH
Q 002054          202 ----------------IGMI-------RIG-RICGQFI-VNPTMDELSLSDLNLVYACTREK--TLMIDV-QAREISEKD  253 (974)
Q Consensus       202 ----------------v~av-------~vg-~i~g~~v-ldPt~~e~~~s~~~l~v~~t~~~--i~mie~-~~~~~~e~~  253 (974)
                                      .-++       +-. ..|+.++ .|||-+|+..++..+++.....+  +-+... ++.-.+.+.
T Consensus       198 ~ic~~tlt~p~~ln~e~r~~~~~n~~fS~~~vl~~~li~adpT~eEE~l~~~~lTIvldss~n~v~l~k~GG~al~~~~~  277 (298)
T KOG1613|consen  198 IICDQTLTVPLMLNAENRAFASQNSDFSEEEVLDDVLIAADPTEEEETLITSTLTIVLDSSGNYVQLTKVGGGALITPEM  277 (298)
T ss_pred             HHHhhhhcchhhhccccccccccCCCccHHHhhcceeEecCCCchhhhhhhceEEEEEcCCCCEEEEEecCcccccCHHH
Confidence                            1111       111 2355555 89999999998888877776654  333443 444466688


Q ss_pred             HHHHHHHHHHHHHHHHHH
Q 002054          254 LEAGLRLAHPEAVKYLEP  271 (974)
Q Consensus       254 ~~~al~~a~~~~~~i~~~  271 (974)
                      +..++++|..-.+++-..
T Consensus       278 iK~c~elar~Rakelk~~  295 (298)
T KOG1613|consen  278 IKRCLELARVRAKELKTR  295 (298)
T ss_pred             HHHHHHHHHHHHHHHHHH
Confidence            889999998877766544

>cd05695 S1_Rrp5_repeat_hs3 S1_Rrp5_repeat_hs3: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits

Probab=99.10  E-value=2.4e-10  Score=98.37  Aligned_cols=65  Identities=23%  Similarity=0.267  Sum_probs=58.8

Q ss_pred             CcEEEEEEEEEeeceEEEEEcCCeEEEEecccCCCccccccccccccCCEEEEEEEEEcc-CCceEEE
Q 002054          684 GGIYKGVVTSVKEYGAFVEFNGGQQGLLHVSELSHEPVSRVSDVVSVGQQLSLRCIGQDV-RGNIKLS  750 (974)
Q Consensus       684 G~i~~G~V~~i~~~G~fV~l~~g~~Glvhisels~~~v~~~~~~~~vGd~V~vkVl~id~-~gri~LS  750 (974)
                      |++++|+|+++.++|+||+|.++++||+|.++++..+..  .+.|++||.++|+|+++|+ ++++.||
T Consensus         1 G~~V~g~V~~i~~~G~~v~l~~~v~g~v~~~~l~~~~~~--~~~~~~G~~i~~kVi~id~~~~~i~LS   66 (66)
T cd05695           1 GMLVNARVKKVLSNGLILDFLSSFTGTVDFLHLDPEKSS--KSTYKEGQKVRARILYVDPSTKVVGLS   66 (66)
T ss_pred             CCEEEEEEEEEeCCcEEEEEcCCceEEEEHHHcCCccCc--ccCcCCCCEEEEEEEEEeCCCCEEecC
Confidence            789999999999999999998899999999999876544  7779999999999999998 6788876

Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in Saccharomyces cerevisiae Rrp5 and 14 S1 repeats in Homo sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in protein-protein interactions. Mutational studies have shown that each region represents a specific functional domain. Deletions within the S1-containing region inhibit pre-rRNA processing at either site A3 or A2, whereas deletions within the TPR region confer an inability to support cleavage of A0-A2. This CD includes H. sapiens S1 repeat 3 (hs3). Rrp5 is found in eukaryotes but not in prokaryotes or archaea.

>cd04453 S1_RNase_E S1_RNase_E: RNase E and RNase G, S1-like RNA-binding domain

Probab=99.10  E-value=2.8e-10  Score=103.60  Aligned_cols=73  Identities=26%  Similarity=0.487  Sum_probs=63.3

Q ss_pred             cccccCcEEEEEEEEEeec--eEEEEEcCCeEEEEecccCCC---ccccccccccccCCEEEEEEEEEccCC-ceEEEE
Q 002054          679 REIEVGGIYKGVVTSVKEY--GAFVEFNGGQQGLLHVSELSH---EPVSRVSDVVSVGQQLSLRCIGQDVRG-NIKLSL  751 (974)
Q Consensus       679 ~~~~~G~i~~G~V~~i~~~--G~fV~l~~g~~Glvhisels~---~~v~~~~~~~~vGd~V~vkVl~id~~g-ri~LS~  751 (974)
                      ..+++|++|.|+|++|.++  |+||+|.++.+||||+||++|   .++.++.+.+++||.|.|+|+....++ -..||.
T Consensus         3 ~~~~~G~iy~g~V~~i~~~~~GaFV~l~~g~~Gllh~seis~~~~~~v~~~~~~~~~Gd~v~VqV~~~~~~~K~~~lt~   81 (88)
T cd04453           3 REPIVGNIYLGRVKKIVPGLQAAFVDIGLGKNGFLHLSDILPAYFKKHKKIAKLLKEGQEILVQVVKEPIGTKGPRLTT   81 (88)
T ss_pred             CcCCCCCEEEEEEEEeccCCcEEEEEeCCCCEEEEEhHHcCchhccccCCHHHcCCCCCEEEEEEEEecCCCCCceEEE
Confidence            3578999999999999997  999999989999999999999   678888999999999999999976533 344443

RNase E is an essential endoribonuclease in the processing and degradation of RNA. In addition to its role in mRNA degradation, RNase E has also been implicated in the processing of rRNA, and the maturation of tRNA, 10Sa RNA and the M1 precursor of RNase P. RNase E associates with PNPase (3' to 5' exonuclease), Rhl B (DEAD-box RNA helicase) and enolase (glycolytic enzyme) to form the RNA degradosome. RNase E tends to cut mRNA within single-stranded regions that are rich in A/U nucleotides. The N-terminal region of RNase E contains the catalytic site. Within the conserved N-terminal domain of RNAse E and RNase G, there is an S1-like subdomain, which is an ancient single-stranded RNA-binding domain. S1 domain is an RNA-binding module originally identified in the ribosomal protein S1. The S1 domain is required for RNA cleavage by RNase E. RNase G is paralogous to RNase E with an N-terminal catalytic domain th

>cd05705 S1_Rrp5_repeat_hs14 S1_Rrp5_repeat_hs14: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits

Probab=99.09  E-value=3.2e-10  Score=99.90  Aligned_cols=59  Identities=25%  Similarity=0.288  Sum_probs=53.1

Q ss_pred             CCCCCEEEEEEEEEeCCeEEEEeCCCeEEEEecccCC----------CCCCCCCCEEEEEEEEEeCCCc
Q 002054          908 LKLGTKVAAKVYQVRARGLVLDLGGGIRGMYRFENNE----------KKDFVVGDELLVKCSSFTGKGI  966 (974)
Q Consensus       908 ~~vG~vV~G~V~~I~~~GvFV~L~~gv~Glih~se~~----------~~~f~vGd~V~vkVl~id~~~~  966 (974)
                      +++|++|.|+|++|++||+||+|++++.|++|.+++.          .+.|++||.|+|+|+++|+++.
T Consensus         1 ~k~G~~V~g~V~~i~~~G~fV~l~~~v~G~v~~~~ls~~~~~~~~~~~~~~~~G~~v~~kVl~id~~~~   69 (74)
T cd05705           1 IKEGQLLRGYVSSVTKQGVFFRLSSSIVGRVLFQNVTKYFVSDPSLYNKYLPEGKLLTAKVLSVNSEKN   69 (74)
T ss_pred             CCCCCEEEEEEEEEeCCcEEEEeCCCCEEEEEHHHccCccccChhhHhcccCCCCEEEEEEEEEECCCC
Confidence            5799999999999999999999999999999988663          2578999999999999998654

Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in Saccharomyces cerevisiae Rrp5 and 14 S1 repeats in Homo sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in protein-protein interactions. Mutational studies have shown that each region represents a specific functional domain. Deletions within the S1-containing region inhibit pre-rRNA processing at either site A3 or A2, whereas deletions within the TPR region confer an inability to support cleavage of A0-A2. This CD includes H. sapiens S1 repeat 14 (hs14). Rrp5 is found in eukaryotes but not in prokaryotes or archaea.

>cd04465 S1_RPS1_repeat_ec2_hs2 S1_RPS1_repeat_ec2_hs2: Ribosomal protein S1 (RPS1) domain

Probab=99.08  E-value=4.1e-10  Score=97.09  Aligned_cols=66  Identities=33%  Similarity=0.515  Sum_probs=60.8

Q ss_pred             CcEEEEEEEEEeeceEEEEEcCCeEEEEecccCCCccccccccccccCCEEEEEEEEEcc-CCceEEEEe
Q 002054          684 GGIYKGVVTSVKEYGAFVEFNGGQQGLLHVSELSHEPVSRVSDVVSVGQQLSLRCIGQDV-RGNIKLSLK  752 (974)
Q Consensus       684 G~i~~G~V~~i~~~G~fV~l~~g~~Glvhisels~~~v~~~~~~~~vGd~V~vkVl~id~-~gri~LS~K  752 (974)
                      |++++|+|+++.++|+||++ ++.+||+|.|++++.+..++.+.  +||.++|+|+++|. ++++.||+|
T Consensus         1 G~iv~g~V~~v~~~G~~v~l-~g~~gfip~s~~~~~~~~~~~~~--vG~~i~~~i~~vd~~~~~i~lS~k   67 (67)
T cd04465           1 GEIVEGKVTEKVKGGLIVDI-EGVRAFLPASQVDLRPVEDLDEY--VGKELKFKIIEIDRERNNIVLSRR   67 (67)
T ss_pred             CCEEEEEEEEEECCeEEEEE-CCEEEEEEHHHCCCcccCChHHh--CCCEEEEEEEEEeCCCCEEEEEcC
Confidence            78999999999999999999 79999999999999888777663  89999999999998 789999986

RPS1 is a component of the small ribosomal subunit thought to be involved in the recognition and binding of mRNA's during translation initiation. The bacterial RPS1 domain architecture consists of 4-6 tandem S1 domains. In some bacteria, the tandem S1 array is located C-terminal to a 4-hydroxy-3-methylbut-2-enyl diphosphate reductase (HMBPP reductase) domain.While RPS1 is found primarily in bacteria, proteins with tandem RPS1-like domains have been identified in plants and humans, however these lack the N-terminal HMBPP reductase domain. This CD includes S1 repeat 2 of the Escherichia coli and Homo sapiens RPS1 (ec2 and hs2, respectively). Autoantibodies to double-stranded DNA from patients with systemic lupus erythematosus cross-react with the human RPS1 homolog.

>cd05693 S1_Rrp5_repeat_hs1_sc1 S1_Rrp5_repeat_hs1_sc1: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits

Probab=99.06  E-value=2.2e-10  Score=106.87  Aligned_cols=74  Identities=22%  Similarity=0.395  Sum_probs=66.4

Q ss_pred             cccCcEEEEEEEEEeeceEEEEEcCCeEEEEecccCCCccc-------------------cccccccccCCEEEEEEEEE
Q 002054          681 IEVGGIYKGVVTSVKEYGAFVEFNGGQQGLLHVSELSHEPV-------------------SRVSDVVSVGQQLSLRCIGQ  741 (974)
Q Consensus       681 ~~~G~i~~G~V~~i~~~G~fV~l~~g~~Glvhisels~~~v-------------------~~~~~~~~vGd~V~vkVl~i  741 (974)
                      +++|+++.|+|++|.++|+||+|+++.+|++|++++++++.                   .++.+.|++||.|+|+|+++
T Consensus         1 L~~G~vV~G~V~~v~~~gl~v~L~~g~~G~v~~seis~~~~~~~~~~~~~~~~~~~~~~~~~~~~~f~vGd~V~~kVi~~   80 (100)
T cd05693           1 LSEGMLVLGQVKEITKLDLVISLPNGLTGYVPITNISDAYTERLEELDEESEEEDDEEELPDLEDLFSVGQLVRCKVVSL   80 (100)
T ss_pred             CCCCCEEEEEEEEEcCCCEEEECCCCcEEEEEHHHhhHHHHHHHHHhhhhccccccccccCCHHHhccCCCEEEEEEEEc
Confidence            46899999999999999999999999999999999998753                   34778899999999999999


Q ss_pred             cc----CCceEEEEecc
Q 002054          742 DV----RGNIKLSLKAV  754 (974)
Q Consensus       742 d~----~gri~LS~K~~  754 (974)
                      |+    +++|.||+|..
T Consensus        81 d~~~~~~~~i~LSlr~~   97 (100)
T cd05693          81 DKSKSGKKRIELSLEPE   97 (100)
T ss_pred             cCCcCCCcEEEEEecHH
Confidence            98    46999999853

Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in Saccharomyces cerevisiae Rrp5 and 14 S1 repeats in Homo sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in protein-protein interactions. Mutational studies have shown that each region represents a specific functional domain. Deletions within the S1-containing region inhibit pre-rRNA processing at either site A3 or A2, whereas deletions within the TPR region confer an inability to support cleavage of A0-A2. This CD includes H. sapiens S1 repeat 1 (hs1) and S. cerevisiae S1 repeat 1 (sc1). Rrp5 is found in eukaryotes but not in prokaryotes or archaea.

>cd05703 S1_Rrp5_repeat_hs12_sc9 S1_Rrp5_repeat_hs12_sc9: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits

Probab=99.03  E-value=1.1e-09  Score=96.24  Aligned_cols=62  Identities=19%  Similarity=0.244  Sum_probs=54.5

Q ss_pred             CCEEEEEEEEEeCCeEEEEeCCCeEEEEecccCCC---------CCCCCCCEEEEEEEEEeCCC-ceeeeec
Q 002054          911 GTKVAAKVYQVRARGLVLDLGGGIRGMYRFENNEK---------KDFVVGDELLVKCSSFTGKG-IPVVSLV  972 (974)
Q Consensus       911 G~vV~G~V~~I~~~GvFV~L~~gv~Glih~se~~~---------~~f~vGd~V~vkVl~id~~~-~~~~~~~  972 (974)
                      |++|+|+|+++.++|+||+|++++.|++|.++++.         +.|++||.|+|+|+++|+++ +..+|+.
T Consensus         1 G~~V~g~V~~i~~~g~~V~l~~~i~G~i~~~~ls~~~~~~~~~~~~~~vG~~v~~kV~~id~~~~~i~Ls~k   72 (73)
T cd05703           1 GQEVTGFVNNVSKEFVWLTISPDVKGRIPLLDLSDDVSVLEHPEKKFPIGQALKAKVVGVDKEHKLLRLSAR   72 (73)
T ss_pred             CCEEEEEEEEEeCCEEEEEeCCCcEEEEEHHHcCCccccccCHHHhCCCCCEEEEEEEEEeCCCCEEEEEec
Confidence            89999999999999999999999999999998742         24999999999999999765 5666664

Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in Saccharomyces cerevisiae Rrp5 and 14 S1 repeats in Homo sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in protein-protein interactions. Mutational studies have shown that each region represents a specific functional domain. Deletions within the S1-containing region inhibit pre-rRNA processing at either site A3 or A2, whereas deletions within the TPR region confer an inability to support cleavage of A0-A2. This CD includes H. sapiens S1 repeat 12 (hs12) and S. cerevisiae S1 repeat 9 (sc9). Rrp5 is found in eukaryotes but not in prokaryotes or archaea.

>PRK03987 translation initiation factor IF-2 subunit alpha; Validated

Probab=99.02  E-value=7.1e-10  Score=120.49  Aligned_cols=78  Identities=37%  Similarity=0.605  Sum_probs=72.6

Q ss_pred             ccccCcEEEEEEEEEeeceEEEEEcC--CeEEEEecccCCCccccccccccccCCEEEEEEEEEcc-CCceEEEEeccCC
Q 002054          680 EIEVGGIYKGVVTSVKEYGAFVEFNG--GQQGLLHVSELSHEPVSRVSDVVSVGQQLSLRCIGQDV-RGNIKLSLKAVSP  756 (974)
Q Consensus       680 ~~~~G~i~~G~V~~i~~~G~fV~l~~--g~~Glvhisels~~~v~~~~~~~~vGd~V~vkVl~id~-~gri~LS~K~~~~  756 (974)
                      -+++|+++.|+|++|.++|+||+|..  +.+||+|+|+++++++.++.+.|++||.|.|+|+++|. ++++.||+|.+.+
T Consensus         5 ~P~~GdiV~G~V~~I~~~G~fV~L~e~~gieGlI~iSEls~~~i~~i~~~~kvGd~V~vkVi~VD~~k~~I~LSlK~v~~   84 (262)
T PRK03987          5 WPEEGELVVGTVKEVKDFGAFVTLDEYPGKEGFIHISEVASGWVKNIRDHVKEGQKVVCKVIRVDPRKGHIDLSLKRVNE   84 (262)
T ss_pred             CCCCCCEEEEEEEEEECCEEEEEECCCCCcEEEEEHHHcCcccccCHHHhCCCCCEEEEEEEEEecccCeEEEEEEeccc
Confidence            37899999999999999999999964  79999999999999999999999999999999999998 6899999998765


Q ss_pred             C
Q 002054          757 R  757 (974)
Q Consensus       757 ~  757 (974)
                      +
T Consensus        85 ~   85 (262)
T PRK03987         85 H   85 (262)
T ss_pred             c
Confidence            4

>PF00575 S1: S1 RNA binding domain; InterPro: IPR003029 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms

Probab=99.01  E-value=2.1e-09  Score=94.40  Aligned_cols=65  Identities=29%  Similarity=0.396  Sum_probs=58.6

Q ss_pred             cCCCCCEEEEEEEEEeCCeEEEEeCCCeEEEEecccCCC-------CCCCCCCEEEEEEEEEeCCCc-eeeee
Q 002054          907 NLKLGTKVAAKVYQVRARGLVLDLGGGIRGMYRFENNEK-------KDFVVGDELLVKCSSFTGKGI-PVVSL  971 (974)
Q Consensus       907 ~~~vG~vV~G~V~~I~~~GvFV~L~~gv~Glih~se~~~-------~~f~vGd~V~vkVl~id~~~~-~~~~~  971 (974)
                      ++++|+++.|+|.++.++|+||+|++++.|++|.+++..       ..|++||+|+|+|+++|.++. ..+|+
T Consensus         1 k~~~G~iv~g~V~~v~~~g~~V~l~~~~~g~ip~~~l~~~~~~~~~~~~~~G~~v~v~v~~vd~~~~~i~lS~   73 (74)
T PF00575_consen    1 KLKEGDIVEGKVTSVEDFGVFVDLGNGIEGFIPISELSDDRIDDPSEVYKIGQTVRVKVIKVDKEKGRIRLSL   73 (74)
T ss_dssp             -SSTTSEEEEEEEEEETTEEEEEESTSSEEEEEGGGSSSSEESSSHGTCETTCEEEEEEEEEETTTTEEEEES
T ss_pred             CCCCCCEEEEEEEEEECCEEEEEECCcEEEEEEeehhcCccccccccccCCCCEEEEEEEEEECCCCeEEEEE
Confidence            378999999999999999999999999999999998863       579999999999999998876 77765

The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites [, ]. About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits. Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome [, ]. The S1 domain was originally identified in ribosomal protein S1 but is found in a large number of RNA-associated proteins. The structure of the S1 RNA-binding domain from the Escherichia coli polynucleotide phosphorylase has been determined using NMR methods and consists of a five-stranded antiparallel beta barrel. Conserved residues on one face of the barrel and adjacent loops form the putative RNA-binding site []. The structure of the S1 domain is very similar to that of cold shock proteins. This suggests that they may both be derived from an ancient nucleic acid-binding protein []. More information about these proteins can be found at Protein of the Month: RNA Exosomes []. This entry does not include translation initiation factor IF-1 S1 domains.; GO: 0003723 RNA binding; PDB: 3L7Z_F 2JE6_I 2JEA_I 2JEB_I 1E3P_A 2Y0S_E 1WI5_A 2BH8_A 2CQO_A 2EQS_A ....

>cd05688 S1_RPS1_repeat_ec3 S1_RPS1_repeat_ec3: Ribosomal protein S1 (RPS1) domain

Probab=99.01  E-value=1.1e-09  Score=94.12  Aligned_cols=67  Identities=37%  Similarity=0.707  Sum_probs=62.4

Q ss_pred             cCcEEEEEEEEEeeceEEEEEcCCeEEEEecccCCCccccccccccccCCEEEEEEEEEcc-CCceEEE
Q 002054          683 VGGIYKGVVTSVKEYGAFVEFNGGQQGLLHVSELSHEPVSRVSDVVSVGQQLSLRCIGQDV-RGNIKLS  750 (974)
Q Consensus       683 ~G~i~~G~V~~i~~~G~fV~l~~g~~Glvhisels~~~v~~~~~~~~vGd~V~vkVl~id~-~gri~LS  750 (974)
                      +|+++.|+|+++.++|+||++. +.+|++|.+++++.++.++.+.|++||.|+|+|+++|. ++++.||
T Consensus         1 ~g~~~~g~V~~v~~~g~~v~l~-~~~g~l~~~e~~~~~~~~~~~~~~~Gd~v~v~i~~vd~~~~~i~ls   68 (68)
T cd05688           1 EGDVVEGTVKSITDFGAFVDLG-GVDGLLHISDMSWGRVKHPSEVVNVGDEVEVKVLKIDKERKRISLG   68 (68)
T ss_pred             CCCEEEEEEEEEEeeeEEEEEC-CeEEEEEhHHCCCccccCHhHEECCCCEEEEEEEEEECCCCEEecC
Confidence            4899999999999999999996 79999999999998898999999999999999999997 6888875

RPS1 is a component of the small ribosomal subunit thought to be involved in the recognition and binding of mRNA's during translation initiation. The bacterial RPS1 domain architecture consists of 4-6 tandem S1 domains. In some bacteria, the tandem S1 array is located C-terminal to a 4-hydroxy-3-methylbut-2-enyl diphosphate reductase (HMBPP reductase) domain. While RPS1 is found primarily in bacteria, proteins with tandem RPS1-like domains have been identified in plants and humans, however these lack the N-terminal HMBPP reductase domain. This CD includes S1 repeat 3 (ec3) of the Escherichia coli RPS1. Autoantibodies to double-stranded DNA from patients with systemic lupus erythematosus cross-react with the human RPS1 homolog.

>cd04471 S1_RNase_R S1_RNase_R: RNase R C-terminal S1 domain

Probab=98.98  E-value=2.6e-09  Score=95.82  Aligned_cols=69  Identities=33%  Similarity=0.661  Sum_probs=61.0

Q ss_pred             cCcEEEEEEEEEeeceEEEEEcC-CeEEEEecccCCCcccc-----------ccccccccCCEEEEEEEEEcc-CCceEE
Q 002054          683 VGGIYKGVVTSVKEYGAFVEFNG-GQQGLLHVSELSHEPVS-----------RVSDVVSVGQQLSLRCIGQDV-RGNIKL  749 (974)
Q Consensus       683 ~G~i~~G~V~~i~~~G~fV~l~~-g~~Glvhisels~~~v~-----------~~~~~~~vGd~V~vkVl~id~-~gri~L  749 (974)
                      +|++++|+|+++.++|+||++.+ +.+|++|.++++++++.           +....|++||.|+|+|+++|. ++++.|
T Consensus         1 ~g~~~~g~V~~v~~~G~fv~l~~~~~~G~v~~~~l~~~~~~~d~~~~~~~~~~~~~~~~~gd~v~v~v~~vd~~~~~i~~   80 (83)
T cd04471           1 VGEEFDGVISGVTSFGLFVELDNLTVEGLVHVSTLGDDYYEFDEENHALVGERTGKVFRLGDKVKVRVVRVDLDRRKIDF   80 (83)
T ss_pred             CCCEEEEEEEeEEeeeEEEEecCCCEEEEEEEEecCCCcEEEcccceEEEeccCCCEEcCCCEEEEEEEEeccccCEEEE
Confidence            48999999999999999999987 89999999999876532           345789999999999999997 789998


Q ss_pred             EE
Q 002054          750 SL  751 (974)
Q Consensus       750 S~  751 (974)
                      ++
T Consensus        81 ~l   82 (83)
T cd04471          81 EL   82 (83)
T ss_pred             EE
Confidence            85

RNase R is a processive 3' to 5' exoribonuclease, which is a homolog of RNase II. RNase R degrades RNA with secondary structure having a 3' overhang of at least 7 nucleotides. RNase R and PNPase play an important role in the degradation of RNA with extensive secondary structure, such as rRNA, tRNA, and certain mRNA which contains repetitive extragenic palindromic sequences. The C-terminal S1 domain binds ssRNA.

>smart00316 S1 Ribosomal protein S1-like RNA-binding domain

Probab=98.97  E-value=2.1e-09  Score=92.56  Aligned_cols=71  Identities=39%  Similarity=0.729  Sum_probs=66.0

Q ss_pred             ccCcEEEEEEEEEeeceEEEEEcCCeEEEEecccCCCccccccccccccCCEEEEEEEEEcc-CCceEEEEe
Q 002054          682 EVGGIYKGVVTSVKEYGAFVEFNGGQQGLLHVSELSHEPVSRVSDVVSVGQQLSLRCIGQDV-RGNIKLSLK  752 (974)
Q Consensus       682 ~~G~i~~G~V~~i~~~G~fV~l~~g~~Glvhisels~~~v~~~~~~~~vGd~V~vkVl~id~-~gri~LS~K  752 (974)
                      ++|+++.|+|+++.++|+||++.++.+|++|.+++.+.+..++.+.|++||.++|+|+++|. ++++.||++
T Consensus         1 ~~G~~v~g~V~~v~~~g~~v~i~~~~~g~l~~~~~~~~~~~~~~~~~~~G~~v~~~V~~~~~~~~~i~ls~~   72 (72)
T smart00316        1 EVGDVVEGTVTEITPFGAFVDLGNGVEGLIPISELSDKRVKDPEEVLKVGDEVKVKVLSVDEEKGRIILSLK   72 (72)
T ss_pred             CCCCEEEEEEEEEEccEEEEEeCCCCEEEEEHHHCCccccCCHHHeecCCCEEEEEEEEEeCCCCEEEEEeC
Confidence            36999999999999999999998899999999999998888888889999999999999998 489999975

>cd04454 S1_Rrp4_like S1_Rrp4_like: Rrp4-like, S1-like RNA-binding domain

Probab=98.97  E-value=1.9e-09  Score=96.79  Aligned_cols=73  Identities=19%  Similarity=0.172  Sum_probs=69.3

Q ss_pred             cccCcEEEEEEEEEeeceEEEEEcCCeEEEEecccCCCccccccccccccCCEEEEEEEEEccCCceEEEEec
Q 002054          681 IEVGGIYKGVVTSVKEYGAFVEFNGGQQGLLHVSELSHEPVSRVSDVVSVGQQLSLRCIGQDVRGNIKLSLKA  753 (974)
Q Consensus       681 ~~~G~i~~G~V~~i~~~G~fV~l~~g~~Glvhisels~~~v~~~~~~~~vGd~V~vkVl~id~~gri~LS~K~  753 (974)
                      +++|+++.|+|+++.+.|++|++..+.+|++|+++++..+..++.+.|++||.+.|+|+++|..+++.||++.
T Consensus         4 p~~GdiV~G~V~~v~~~~~~V~i~~~~~g~l~~~~~~~~~~~~~~~~~~~GD~i~~~V~~~~~~~~i~LS~~~   76 (82)
T cd04454           4 PDVGDIVIGIVTEVNSRFWKVDILSRGTARLEDSSATEKDKKEIRKSLQPGDLILAKVISLGDDMNVLLTTAD   76 (82)
T ss_pred             CCCCCEEEEEEEEEcCCEEEEEeCCCceEEeechhccCcchHHHHhcCCCCCEEEEEEEEeCCCCCEEEEECC
Confidence            6899999999999999999999988999999999999988888999999999999999999877899999986

S1-like RNA-binding domains are found in a wide variety of RNA-associated proteins. Rrp4 protein, and Rrp40 and Csl4 proteins, also represented in this group, are subunits of the exosome complex. The exosome plays a central role in 3' to 5' RNA processing and degradation in eukarytes and archaea. Its functions include the removal of incorrectly processed RNA and the maintenance of proper levels of mRNA, rRNA and a number of small RNA species. In Saccharomyces cerevisiae, the exosome includes nine core components, six of which are homologous to bacterial RNase PH. These form a hexameric ring structure. The other three subunits (RrP4, Rrp40, and Csl4) contain an S1 RNA binding domain and are part of the "S1 pore structure".

>cd04473 S1_RecJ_like S1_RecJ_like: The S1 domain of the archaea-specific RecJ-like exonuclease

Probab=98.95  E-value=4.2e-09  Score=93.53  Aligned_cols=68  Identities=28%  Similarity=0.449  Sum_probs=62.8

Q ss_pred             ccccCCCCCEEEEEEEEEeCCeEEEEeCCCeEEEEecccCCCCCCCCCCEEEEEEEEEeCCCceeeeec
Q 002054          904 SAKNLKLGTKVAAKVYQVRARGLVLDLGGGIRGMYRFENNEKKDFVVGDELLVKCSSFTGKGIPVVSLV  972 (974)
Q Consensus       904 ~~~~~~vG~vV~G~V~~I~~~GvFV~L~~gv~Glih~se~~~~~f~vGd~V~vkVl~id~~~~~~~~~~  972 (974)
                      ...++++|+.+.|+|+++++||+||++++++.||+|.+++ .+.|++||+++++|.++.+++...+|++
T Consensus        10 ~~~~~~~G~~~~g~V~~i~~~G~fV~l~~~~~Glv~~se~-~~~~~iGd~v~v~I~~i~e~~~i~l~~~   77 (77)
T cd04473          10 TMEDLEVGKLYKGKVNGVAKYGVFVDLNDHVRGLIHRSNL-LRDYEVGDEVIVQVTDIPENGNIDLIPV   77 (77)
T ss_pred             chhhCCCCCEEEEEEEeEecceEEEEECCCcEEEEEchhc-cCcCCCCCEEEEEEEEECCCCcEEEEEC
Confidence            4677999999999999999999999999999999999998 5679999999999999987888888875

The function of this family is not fully understood. In Escherichia coli, RecJ degrades single-stranded DNA in the 5'-3' direction and participates in homologous recombination and mismatch repair.

>COG2183 Tex Transcriptional accessory protein [Transcription]

Probab=98.95  E-value=8e-10  Score=131.85  Aligned_cols=78  Identities=35%  Similarity=0.574  Sum_probs=73.9

Q ss_pred             ccccCcEEEEEEEEEeeceEEEEEcCCeEEEEecccCCCccccccccccccCCEEEEEEEEEcc-CCceEEEEeccCCC
Q 002054          680 EIEVGGIYKGVVTSVKEYGAFVEFNGGQQGLLHVSELSHEPVSRVSDVVSVGQQLSLRCIGQDV-RGNIKLSLKAVSPR  757 (974)
Q Consensus       680 ~~~~G~i~~G~V~~i~~~G~fV~l~~g~~Glvhisels~~~v~~~~~~~~vGd~V~vkVl~id~-~gri~LS~K~~~~~  757 (974)
                      ++++|+++.|+|+++.+||+||+|+-+.+|+||+|++++.++.+|.+++++||.|+|+|+++|. +++|.|||+.....
T Consensus       655 dLk~Gm~leg~Vrnv~~fgafVdIgv~qDglvHis~ls~~fv~~P~~vv~vGdiV~v~V~~vD~~r~rI~Lsmr~~~~~  733 (780)
T COG2183         655 DLKPGMILEGTVRNVVDFGAFVDIGVHQDGLVHISQLSDKFVKDPNEVVKVGDIVKVKVIEVDTARKRIALSMRLDEEE  733 (780)
T ss_pred             hccCCCEEEEEEEEeeeccceEEeccccceeeeHHHhhhhhcCChHHhcccCCEEEEEEEEEecccCeeeeEeeccCCc
Confidence            7899999999999999999999998899999999999999999999999999999999999998 78999999976543

>PRK08582 hypothetical protein; Provisional

Probab=98.94  E-value=3.5e-09  Score=104.53  Aligned_cols=66  Identities=24%  Similarity=0.390  Sum_probs=60.6

Q ss_pred             cCCCCCEEEEEEEEEeCCeEEEEeCCCeEEEEecccCC-------CCCCCCCCEEEEEEEEEeCCCceeeeec
Q 002054          907 NLKLGTKVAAKVYQVRARGLVLDLGGGIRGMYRFENNE-------KKDFVVGDELLVKCSSFTGKGIPVVSLV  972 (974)
Q Consensus       907 ~~~vG~vV~G~V~~I~~~GvFV~L~~gv~Glih~se~~-------~~~f~vGd~V~vkVl~id~~~~~~~~~~  972 (974)
                      .+++|++|.|+|++|++||+||+|++++.||+|++++.       .+.|++||+|+|+|+++|.++...+|+.
T Consensus         2 ~~kvG~iv~G~V~~I~~fG~fV~L~~~~~GlVhiSels~~~v~~~~~~l~vGD~VkvkV~~id~~gkI~LSlk   74 (139)
T PRK08582          2 SIEVGSKLQGKVTGITNFGAFVELPEGKTGLVHISEVADNYVKDINDHLKVGDEVEVKVLNVEDDGKIGLSIK   74 (139)
T ss_pred             CCcCCCEEEEEEEEEECCeEEEEECCCCEEEEEeeccCcccccccccccCCCCEEEEEEEEECCCCcEEEEEE
Confidence            37899999999999999999999999999999999885       3579999999999999998888888874

>cd04461 S1_Rrp5_repeat_hs8_sc7 S1_Rrp5_repeat_hs8_sc7: Rrp5 Homo sapiens S1 repeat 8 (hs8) and Saccharomyces cerevisiae S1 repeat 7 (sc7)-like domains

Probab=98.94  E-value=2.3e-09  Score=96.54  Aligned_cols=68  Identities=24%  Similarity=0.301  Sum_probs=59.9

Q ss_pred             ccccCCCCCEEEEEEEEEeCCeEEEEeCCCeEEEEecccCC-------CCCCCCCCEEEEEEEEEeC-CCceeeee
Q 002054          904 SAKNLKLGTKVAAKVYQVRARGLVLDLGGGIRGMYRFENNE-------KKDFVVGDELLVKCSSFTG-KGIPVVSL  971 (974)
Q Consensus       904 ~~~~~~vG~vV~G~V~~I~~~GvFV~L~~gv~Glih~se~~-------~~~f~vGd~V~vkVl~id~-~~~~~~~~  971 (974)
                      .+.++++|+++.|+|+++.+||+||+|++++.||+|.++++       .+.|++||+|+|+|+++|. ++...+||
T Consensus         8 ~~~~~~~G~i~~g~V~~v~~~G~fv~l~~~~~g~v~~~el~~~~~~~~~~~~~~Gd~v~vkV~~id~~~~~i~lsl   83 (83)
T cd04461           8 NFSDLKPGMVVHGYVRNITPYGVFVEFLGGLTGLAPKSYISDEFVTDPSFGFKKGQSVTAKVTSVDEEKQRFLLSL   83 (83)
T ss_pred             hHHhCCCCCEEEEEEEEEeeceEEEEcCCCCEEEEEHHHCCcccccCHHHhcCCCCEEEEEEEEEcCCCCEEEEeC
Confidence            36779999999999999999999999999999999999874       3469999999999999997 46666664

Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits. Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in S. cerevisiae Rrp5 and 14 S1 repeats in H. sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in protein-protein interactions. Mutational studies have shown that each region represents a specific functional domain. Deletions within the S1-containing region inhibit pre-rRNA processing at either site A3 or A2, whereas deletions within the TPR region confer an inability to support cleavage of A0-A2. This CD includes H. sapiens S1 repeat 8 and S. cerevisiae S1 repeat 7. Rrp5 is found in eukaryotes but not in prokaryotes or archaea.

>cd05696 S1_Rrp5_repeat_hs4 S1_Rrp5_repeat_hs4: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits

Probab=98.93  E-value=3.4e-09  Score=92.61  Aligned_cols=61  Identities=23%  Similarity=0.346  Sum_probs=52.8

Q ss_pred             CCEEE-EEEEEE-eCCeEEEEeCCCeEEEEecccCC-------CCCCCCCCEEEEEEEEEeCCC-ceeeee
Q 002054          911 GTKVA-AKVYQV-RARGLVLDLGGGIRGMYRFENNE-------KKDFVVGDELLVKCSSFTGKG-IPVVSL  971 (974)
Q Consensus       911 G~vV~-G~V~~I-~~~GvFV~L~~gv~Glih~se~~-------~~~f~vGd~V~vkVl~id~~~-~~~~~~  971 (974)
                      |++++ |+|.++ .+||+||+|++|+.||+|.|+++       .+.|++||+++|+|+++|+++ +..+||
T Consensus         1 G~v~~~g~V~~v~~~~G~~V~l~~gv~G~i~~s~l~~~~~~~~~~~~~vG~~v~~kV~~id~~~~~i~lS~   71 (71)
T cd05696           1 GAVVDSVKVTKVEPDLGAVFELKDGLLGFVHISHLSDDKVPSDTGPFKAGTTHKARIIGYSPMDGLLQLSL   71 (71)
T ss_pred             CcEeeeeEEEEEccCceEEEEeCCCCEEEEEHHHCCcchhcCcccccCCCCEEEEEEEEEeCCCCEEEEeC
Confidence            78999 999999 79999999999999999999774       346999999999999999766 555553

Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in Saccharomyces cerevisiae Rrp5 and 14 S1 repeats in Homo sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in protein-protein interactions. Mutational studies have shown that each region represents a specific functional domain. Deletions within the S1-containing region inhibit pre-rRNA processing at either site A3 or A2, whereas deletions within the TPR region confer an inability to support cleavage of A0-A2. This CD includes H. sapiens S1 repeat 4 (hs4). Rrp5 is found in eukaryotes but not in prokaryotes or archaea.

>cd05697 S1_Rrp5_repeat_hs5 S1_Rrp5_repeat_hs5: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits

Probab=98.93  E-value=3.4e-09  Score=91.86  Aligned_cols=61  Identities=21%  Similarity=0.321  Sum_probs=53.5

Q ss_pred             CCEEEEEEEEEeCCeEEEEeCCCeEEEEecccCC-------CCCCCCCCEEEEEEEEEeCC-Cceeeee
Q 002054          911 GTKVAAKVYQVRARGLVLDLGGGIRGMYRFENNE-------KKDFVVGDELLVKCSSFTGK-GIPVVSL  971 (974)
Q Consensus       911 G~vV~G~V~~I~~~GvFV~L~~gv~Glih~se~~-------~~~f~vGd~V~vkVl~id~~-~~~~~~~  971 (974)
                      |++++|+|.+|.++|+||+|++++.||+|.++++       .+.|++||+++|+|+++|.+ +...+||
T Consensus         1 G~~v~g~V~~v~~~Gv~V~l~~~v~g~i~~~~l~~~~~~~~~~~~~~Gd~i~~~V~~id~~~~~i~ls~   69 (69)
T cd05697           1 GQVVKGTIRKLRPSGIFVKLSDHIKGLVPPMHLADVRLKHPEKKFKPGLKVKCRVLSVEPERKRLVLTL   69 (69)
T ss_pred             CCEEEEEEEEEeccEEEEEecCCcEEEEEHHHCCCccccCHHHcCCCCCEEEEEEEEEECCCCEEEEEC
Confidence            8999999999999999999999999999999774       24699999999999999974 5555554

Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in Saccharomyces cerevisiae Rrp5 and 14 S1 repeats in Homo sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in protein-protein interactions. Mutational studies have shown that each region represents a specific functional domain. Deletions within the S1-containing region inhibit pre-rRNA processing at either site A3 or A2, whereas deletions within the TPR region confer an inability to support cleavage of A0-A2. This CD includes H. sapiens S1 repeat 5 (hs5) and S. cerevisiae S1 repeat 5 (sc5). Rrp5 is found in eukaryotes but not in prokaryotes or archaea.

>cd05695 S1_Rrp5_repeat_hs3 S1_Rrp5_repeat_hs3: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits

Probab=98.93  E-value=4e-09  Score=90.78  Aligned_cols=57  Identities=23%  Similarity=0.313  Sum_probs=52.1

Q ss_pred             CCEEEEEEEEEeCCeEEEEeCCCeEEEEecccCC-----CCCCCCCCEEEEEEEEEeCCCce
Q 002054          911 GTKVAAKVYQVRARGLVLDLGGGIRGMYRFENNE-----KKDFVVGDELLVKCSSFTGKGIP  967 (974)
Q Consensus       911 G~vV~G~V~~I~~~GvFV~L~~gv~Glih~se~~-----~~~f~vGd~V~vkVl~id~~~~~  967 (974)
                      |++|+|+|.++.++|+||+|.++++|++|.+++.     .+.|++||+|+|+|+++|++++.
T Consensus         1 G~~V~g~V~~i~~~G~~v~l~~~v~g~v~~~~l~~~~~~~~~~~~G~~i~~kVi~id~~~~~   62 (66)
T cd05695           1 GMLVNARVKKVLSNGLILDFLSSFTGTVDFLHLDPEKSSKSTYKEGQKVRARILYVDPSTKV   62 (66)
T ss_pred             CCEEEEEEEEEeCCcEEEEEcCCceEEEEHHHcCCccCcccCcCCCCEEEEEEEEEeCCCCE
Confidence            8999999999999999999988999999999885     24599999999999999987765

Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in Saccharomyces cerevisiae Rrp5 and 14 S1 repeats in Homo sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in protein-protein interactions. Mutational studies have shown that each region represents a specific functional domain. Deletions within the S1-containing region inhibit pre-rRNA processing at either site A3 or A2, whereas deletions within the TPR region confer an inability to support cleavage of A0-A2. This CD includes H. sapiens S1 repeat 3 (hs3). Rrp5 is found in eukaryotes but not in prokaryotes or archaea.

>cd05704 S1_Rrp5_repeat_hs13 S1_Rrp5_repeat_hs13: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits

Probab=98.91  E-value=4.2e-09  Score=92.32  Aligned_cols=63  Identities=24%  Similarity=0.192  Sum_probs=55.6

Q ss_pred             CCCCCEEEEEEEEEeC-CeEEEEeCCCeEEEEecccCC-------CCCCCCCCEEEEEEEEEeCCCceeeee
Q 002054          908 LKLGTKVAAKVYQVRA-RGLVLDLGGGIRGMYRFENNE-------KKDFVVGDELLVKCSSFTGKGIPVVSL  971 (974)
Q Consensus       908 ~~vG~vV~G~V~~I~~-~GvFV~L~~gv~Glih~se~~-------~~~f~vGd~V~vkVl~id~~~~~~~~~  971 (974)
                      +++|++|.|+|++|.+ ||+||+|++|..|++|+|++.       .+.|++||.|+|+|+++|. +..-+|+
T Consensus         1 l~~G~iv~G~V~~i~~~~g~~v~l~~~~~Glvhis~~s~~~~~~~~~~~~~Gd~v~~kV~~~~~-~~i~LSl   71 (72)
T cd05704           1 LEEGAVTLGMVTKVIPHSGLTVQLPFGKTGLVSIFHLSDSYTENPLEGFKPGKIVRCCILSKKD-GKYQLSL   71 (72)
T ss_pred             CCCCCEEEEEEEEeeCCcEEEEECCCCCEEEEEHHHhcCcccCCHHHhCCCCCEEEEEEEEecC-CEEEEEe
Confidence            4689999999999986 899999999999999999774       2458999999999999996 6666765

Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in Saccharomyces cerevisiae Rrp5 and 14 S1 repeats in Homo sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in protein-protein interactions. Mutational studies have shown that each region represents a specific functional domain. Deletions within the S1-containing region inhibit pre-rRNA processing at either site A3 or A2, whereas deletions within the TPR region confer an inability to support cleavage of A0-A2. This CD includes H. sapiens S1 repeat 13 (hs13). Rrp5 is found in eukaryotes but not in prokaryotes or archaea.

>cd05706 S1_Rrp5_repeat_sc10 S1_Rrp5_repeat_sc10: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits

Probab=98.91  E-value=7.8e-09  Score=90.60  Aligned_cols=64  Identities=22%  Similarity=0.228  Sum_probs=55.9

Q ss_pred             CCCCCEEEEEEEEEeCCeEEEEeCCCeEEEEecccCC-------CCCCCCCCEEEEEEEEEeCC-Cceeeee
Q 002054          908 LKLGTKVAAKVYQVRARGLVLDLGGGIRGMYRFENNE-------KKDFVVGDELLVKCSSFTGK-GIPVVSL  971 (974)
Q Consensus       908 ~~vG~vV~G~V~~I~~~GvFV~L~~gv~Glih~se~~-------~~~f~vGd~V~vkVl~id~~-~~~~~~~  971 (974)
                      +++|++|.|+|++++++|+||+|++++.|++|.+++.       .+.|++||.|+|+|+++|.+ +...+|+
T Consensus         1 ~~~G~iv~g~V~~v~~~gi~v~l~~~~~g~v~~s~l~~~~~~~~~~~~~~Gd~v~~~V~~~d~~~~~i~ls~   72 (73)
T cd05706           1 LKVGDILPGRVTKVNDRYVLVQLGNKVTGPSFITDALDDYSEALPYKFKKNDIVRACVLSVDVPNKKIALSL   72 (73)
T ss_pred             CCCCCEEEEEEEEEeCCeEEEEeCCCcEEEEEhhhccCccccccccccCCCCEEEEEEEEEeCCCCEEEEEE
Confidence            4789999999999999999999999999999999774       23599999999999999985 4555554

Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in Saccharomyces cerevisiae Rrp5 and 14 S1 repeats in Homo sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in protein-protein interactions. Mutational studies have shown that each region represents a specific functional domain. Deletions within the S1-containing region inhibit pre-rRNA processing at either site A3 or A2, whereas deletions within the TPR region confer an inability to support cleavage of A0-A2. This CD includes S. cerevisiae S1 repeat 10 (sc10). Rrp5 is found in eukaryotes but not in prokaryotes or archaea.

>cd05702 S1_Rrp5_repeat_hs11_sc8 S1_Rrp5_repeat_hs11_sc8: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits

Probab=98.90  E-value=3.6e-09  Score=92.14  Aligned_cols=64  Identities=28%  Similarity=0.307  Sum_probs=58.9

Q ss_pred             CcEEEEEEEEEeeceEEEEEcCCeEEEEecccCCCcc--ccccccccccCCEEEEEEEEEccCCce
Q 002054          684 GGIYKGVVTSVKEYGAFVEFNGGQQGLLHVSELSHEP--VSRVSDVVSVGQQLSLRCIGQDVRGNI  747 (974)
Q Consensus       684 G~i~~G~V~~i~~~G~fV~l~~g~~Glvhisels~~~--v~~~~~~~~vGd~V~vkVl~id~~gri  747 (974)
                      |+++.|+|+++.++|+||++.++.+|++|++++++++  ..++.+.|++||.|+|+|+++|..+..
T Consensus         1 G~iV~g~V~~i~~~gi~v~l~~~i~g~i~~~~i~~~~~~~~~~~~~~~~Gd~i~~kVl~~d~~~~~   66 (70)
T cd05702           1 GDLVKAKVKSVKPTQLNVQLADNVHGRIHVSEVFDEWPDGKNPLSKFKIGQKIKARVIGGHDAKTH   66 (70)
T ss_pred             CCEEEEEEEEEECCcEEEEeCCCcEEEEEHHHhccccccccChhHhCCCCCEEEEEEEEEeCcccc
Confidence            7899999999999999999999999999999999885  788889999999999999999875443

Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in Saccharomyces cerevisiae Rrp5 and 14 S1 repeats in Homo sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in protein-protein interactions. Mutational studies have shown that each region represents a specific functional domain. Deletions within the S1-containing region inhibit pre-rRNA processing at either site A3 or A2, whereas deletions within the TPR region confer an inability to support cleavage of A0-A2. This CD includes H. sapiens S1 repeat 11 (hs11) and S. cerevisiae S1 repeat 8 (sc8). Rrp5 is found in eukaryotes but not in prokaryotes or archaea.

>cd04473 S1_RecJ_like S1_RecJ_like: The S1 domain of the archaea-specific RecJ-like exonuclease

Probab=98.89  E-value=8.1e-09  Score=91.72  Aligned_cols=65  Identities=37%  Similarity=0.626  Sum_probs=59.0

Q ss_pred             cccccCcEEEEEEEEEeeceEEEEEcCCeEEEEecccCCCccccccccccccCCEEEEEEEEEccCCceEEEE
Q 002054          679 REIEVGGIYKGVVTSVKEYGAFVEFNGGQQGLLHVSELSHEPVSRVSDVVSVGQQLSLRCIGQDVRGNIKLSL  751 (974)
Q Consensus       679 ~~~~~G~i~~G~V~~i~~~G~fV~l~~g~~Glvhisels~~~v~~~~~~~~vGd~V~vkVl~id~~gri~LS~  751 (974)
                      .++++|++|.|+|+++.+||+||++.++.+||+|.|++.        +.+++||.++|+|.++..+|++.||+
T Consensus        12 ~~~~~G~~~~g~V~~i~~~G~fV~l~~~~~Glv~~se~~--------~~~~iGd~v~v~I~~i~e~~~i~l~~   76 (77)
T cd04473          12 EDLEVGKLYKGKVNGVAKYGVFVDLNDHVRGLIHRSNLL--------RDYEVGDEVIVQVTDIPENGNIDLIP   76 (77)
T ss_pred             hhCCCCCEEEEEEEeEecceEEEEECCCcEEEEEchhcc--------CcCCCCCEEEEEEEEECCCCcEEEEE
Confidence            468999999999999999999999999999999999974        34999999999999995589999985

The function of this family is not fully understood. In Escherichia coli, RecJ degrades single-stranded DNA in the 5'-3' direction and participates in homologous recombination and mismatch repair.

>cd05698 S1_Rrp5_repeat_hs6_sc5 S1_Rrp5_repeat_hs6_sc5: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits

Probab=98.88  E-value=6.3e-09  Score=90.36  Aligned_cols=61  Identities=20%  Similarity=0.310  Sum_probs=54.0

Q ss_pred             CCEEEEEEEEEeCCeEEEEeCCCeEEEEecccCC-------CCCCCCCCEEEEEEEEEeCC-Cceeeee
Q 002054          911 GTKVAAKVYQVRARGLVLDLGGGIRGMYRFENNE-------KKDFVVGDELLVKCSSFTGK-GIPVVSL  971 (974)
Q Consensus       911 G~vV~G~V~~I~~~GvFV~L~~gv~Glih~se~~-------~~~f~vGd~V~vkVl~id~~-~~~~~~~  971 (974)
                      |+++.|+|.+++++|+||+|.+++.||+|.+++.       .+.|++||+++|+|+++|++ +...+|+
T Consensus         1 g~~~~g~V~~v~~~G~~V~l~~~~~gli~~s~l~~~~~~~~~~~~~~G~~i~v~v~~~d~~~~~i~ls~   69 (70)
T cd05698           1 GLKTHGTIVKVKPNGCIVSFYNNVKGFLPKSELSEAFIKDPEEHFRVGQVVKVKVLSCDPEQQRLLLSC   69 (70)
T ss_pred             CCEEEEEEEEEecCcEEEEECCCCEEEEEHHHcChhhcCCHHHcccCCCEEEEEEEEEcCCCCEEEEEe
Confidence            8999999999999999999999999999999874       33599999999999999984 5666665

Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in Saccharomyces cerevisiae Rrp5 and 14 S1 repeats in Homo sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in protein-protein interactions. Mutational studies have shown that each region represents a specific functional domain. Deletions within the S1-containing region inhibit pre-rRNA processing at either site A3 or A2, whereas deletions within the TPR region confer an inability to support cleavage of A0-A2. This CD includes H. sapiens S1 repeat 6 (hs6) and S. cerevisiae S1 repeat 5 (sc5). Rrp5 is found in eukaryotes but not in prokaryotes or archaea.

>cd05686 S1_pNO40 S1_pNO40: pNO40 , S1-like RNA-binding domain

Probab=98.87  E-value=1.3e-08  Score=89.44  Aligned_cols=63  Identities=21%  Similarity=0.186  Sum_probs=54.3

Q ss_pred             CCCCEEEEEEEEEeCCeEEEEeCC-CeEEEEecccCCC-------CCCCCCCEEEEEEEEEeCCCceeeee
Q 002054          909 KLGTKVAAKVYQVRARGLVLDLGG-GIRGMYRFENNEK-------KDFVVGDELLVKCSSFTGKGIPVVSL  971 (974)
Q Consensus       909 ~vG~vV~G~V~~I~~~GvFV~L~~-gv~Glih~se~~~-------~~f~vGd~V~vkVl~id~~~~~~~~~  971 (974)
                      .+|++++|+|.+|++||+||+|++ +..||+|.+++..       +.|++||+|+|+|+++|.+++.-+|+
T Consensus         2 ~~g~~~~g~V~~i~~fG~fv~l~~~~~eGlvh~sel~~~~~~~~~~~~~~Gd~v~vkv~~vd~~~ki~ls~   72 (73)
T cd05686           2 ALYQIFKGEVASVTEYGAFVKIPGCRKQGLVHKSHMSSCRVDDPSEVVDVGEKVWVKVIGREMKDKMKLSL   72 (73)
T ss_pred             cCCCEEEEEEEEEEeeeEEEEECCCCeEEEEEchhhCCCcccCHhhEECCCCEEEEEEEEECCCCcEEEEe
Confidence            589999999999999999999954 3799999998852       34799999999999999988666654

pNO40 is a nucleolar protein of unknown function with an N-terminal S1 RNA binding domain, a CCHC type zinc finger, and clusters of basic amino acids representing a potential nucleolar targeting signal. pNO40 was identified through a yeast two-hybrid interaction screen of a human kidney cDNA library using the pinin (pnn) protein as bait. pNO40 is thought to play a role in ribosome maturation and/or biogenesis.

>cd05707 S1_Rrp5_repeat_sc11 S1_Rrp5_repeat_sc11: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits

Probab=98.86  E-value=7.3e-09  Score=89.56  Aligned_cols=56  Identities=27%  Similarity=0.326  Sum_probs=50.9

Q ss_pred             CCEEEEEEEEEeCCeEEEEeCCCeEEEEecccCC-------CCCCCCCCEEEEEEEEEeCCCc
Q 002054          911 GTKVAAKVYQVRARGLVLDLGGGIRGMYRFENNE-------KKDFVVGDELLVKCSSFTGKGI  966 (974)
Q Consensus       911 G~vV~G~V~~I~~~GvFV~L~~gv~Glih~se~~-------~~~f~vGd~V~vkVl~id~~~~  966 (974)
                      |++|.|+|+++.++|+||+|.+++.||+|.++++       .+.|++||.|+|+|+++|+++.
T Consensus         1 G~~v~g~V~~v~~~Gv~V~l~~~~~G~v~~s~l~~~~~~~~~~~~~~Gd~v~~~v~~~d~~~~   63 (68)
T cd05707           1 GDVVRGFVKNIANNGVFVTLGRGVDARVRVSELSDSYLKDWKKRFKVGQLVKGKIVSIDPDNG   63 (68)
T ss_pred             CCEEEEEEEEEECccEEEEeCCCCEEEEEHHHCCchhhcCHhhccCCCCEEEEEEEEEeCCCC
Confidence            7899999999999999999999999999999874       3459999999999999998543

Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in Saccharomyces cerevisiae Rrp5 and 14 S1 repeats in Homo sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in protein-protein interactions. Mutational studies have shown that each region represents a specific functional domain. Deletions within the S1-containing region inhibit pre-rRNA processing at either site A3 or A2, whereas deletions within the TPR region confer an inability to support cleavage of A0-A2. This CD includes S. cerevisiae S1 repeat 11 (sc11). Rrp5 is found in eukaryotes but not in prokaryotes or archaea.

>PRK05807 hypothetical protein; Provisional

Probab=98.85  E-value=1.3e-08  Score=100.20  Aligned_cols=65  Identities=20%  Similarity=0.328  Sum_probs=59.1

Q ss_pred             cCCCCCEEEEEEEEEeCCeEEEEeCCCeEEEEecccCC-------CCCCCCCCEEEEEEEEEeCCCceeeeec
Q 002054          907 NLKLGTKVAAKVYQVRARGLVLDLGGGIRGMYRFENNE-------KKDFVVGDELLVKCSSFTGKGIPVVSLV  972 (974)
Q Consensus       907 ~~~vG~vV~G~V~~I~~~GvFV~L~~gv~Glih~se~~-------~~~f~vGd~V~vkVl~id~~~~~~~~~~  972 (974)
                      .+++|++|+|+|+.|++||+||+| ++..||+|++++.       ...|++||+|+|+|+++|.++...+|+.
T Consensus         2 ~~~vG~vv~G~Vt~i~~~GafV~L-~~~~Glvhiseis~~~v~~~~~~~kvGd~V~VkV~~id~~gkI~LSlk   73 (136)
T PRK05807          2 TLKAGSILEGTVVNITNFGAFVEV-EGKTGLVHISEVADTYVKDIREHLKEQDKVKVKVISIDDNGKISLSIK   73 (136)
T ss_pred             CccCCCEEEEEEEEEECCeEEEEE-CCEEEEEEhhhcccccccCccccCCCCCEEEEEEEEECCCCcEEEEEE
Confidence            478999999999999999999999 6899999999885       4568999999999999999888888874

>PF03725 RNase_PH_C: 3' exoribonuclease family, domain 2 This Prosite family only includes Ribonuclease PH; InterPro: IPR015847 The PH (phosphorolytic) domain is responsible for 3'-5' exoribonuclease activity, although in some proteins this domain has lost its catalytic function

Probab=98.84  E-value=1.1e-08  Score=88.53  Aligned_cols=65  Identities=31%  Similarity=0.437  Sum_probs=50.8

Q ss_pred             CCeEEEEEEEECCEEEEcCCHHHHhcCccceeEeee--CCeEEEEEecCCC-CCHHHHHHHHHHHHHH
Q 002054          200 GPIGMIRIGRICGQFIVNPTMDELSLSDLNLVYACT--REKTLMIDVQARE-ISEKDLEAGLRLAHPE  264 (974)
Q Consensus       200 ~~v~av~vg~i~g~~vldPt~~e~~~s~~~l~v~~t--~~~i~mie~~~~~-~~e~~~~~al~~a~~~  264 (974)
                      ++++|||+|++||++|+|||.+|+..++.+|+++.+  .+.+.|++.++.. +++++|.+||++|+++
T Consensus         1 ~~~~avt~~~i~~~~v~Dpt~~Ee~~~~~~l~~~~~~~~~~~~~~~~~g~~~~~~~~l~~~i~~A~~~   68 (68)
T PF03725_consen    1 DPPVAVTVGIIDGELVVDPTAEEESLSDSSLTLAVDGTGNICTLQKSGGGSELSEDQLEEAIELAKKA   68 (68)
T ss_dssp             SEEEEEEEEEETTEEEES--HHHHHHSSEEEEEEEETTSSEEEEEEEEESSEEEHHHHHHHHHHHHHH
T ss_pred             CCeEEEEEEEECCEEEECCCHHHHhhcCCcEEEEEECCCCEEEEEEcCCCCCCCHHHHHHHHHHHhcC
Confidence            579999999999999999999998776655555544  5555666666554 9999999999999985

An active PH domain uses inorganic phosphate as a nucleophile, adding it across the phosphodiester bond between the end two nucleotides in order to release ribonucleoside 5'-diphosphate (rNDP) from the 3' end of the RNA substrate. PH domains can be found in bacterial/organelle RNases and PNPases (polynucleotide phosphorylases) [], as well as in archaeal and eukaryotic RNA exosomes [, ], the later acting as nano-compartments for the degradation or processing of RNA (including mRNA, rRNA, snRNA and snoRNA). Bacterial/organelle PNPases share a common barrel structure with RNA exosomes, consisting of a hexameric ring of PH domains that act as a degradation chamber, and an S1-domain/KH-domain containing cap that binds the RNA substrate (and sometimes accessory proteins) in order to regulate and restrict entry into the degradation chamber []. Unstructured RNA substrates feed in through the pore made by the S1 domains, are degraded by the PH domain ring, and exit as nucleotides via the PH pore at the opposite end of the barrel [, ]. This entry represents the phosphorolytic (PH) domain 2, which has a core 3-layer alpha/beta/alpha structure. This domain is found in bacterial/organelle PNPases and in archaeal/eukaryotic exosomes []. More information about these proteins can be found at Protein of the Month: RNA Exosomes [].; GO: 0003723 RNA binding, 0006396 RNA processing; PDB: 1E3H_A 1E3P_A 2NN6_E 2WNR_A 3U1K_B 2BA0_H 2BA1_H 3M85_G 3M7N_H 3H1C_K ....

>cd05689 S1_RPS1_repeat_ec4 S1_RPS1_repeat_ec4: Ribosomal protein S1 (RPS1) domain

Probab=98.83  E-value=1.4e-08  Score=88.83  Aligned_cols=59  Identities=22%  Similarity=0.318  Sum_probs=53.0

Q ss_pred             CCCCCEEEEEEEEEeCCeEEEEeCCCeEEEEecccCCC--------CCCCCCCEEEEEEEEEeCCCc
Q 002054          908 LKLGTKVAAKVYQVRARGLVLDLGGGIRGMYRFENNEK--------KDFVVGDELLVKCSSFTGKGI  966 (974)
Q Consensus       908 ~~vG~vV~G~V~~I~~~GvFV~L~~gv~Glih~se~~~--------~~f~vGd~V~vkVl~id~~~~  966 (974)
                      |++|+++.|+|.+|++||+||+|++++.||+|.+++..        +.|++||+|+|+|+++|.+..
T Consensus         1 ~~~g~~~~g~V~~i~~~G~fv~l~~~~~Gl~~~~~l~~~~~~~~~~~~~~~Gd~v~v~v~~id~~~~   67 (72)
T cd05689           1 YPEGTRLFGKVTNLTDYGCFVELEEGVEGLVHVSEMDWTNKNIHPSKVVSLGDEVEVMVLDIDEERR   67 (72)
T ss_pred             CcCCCEEEEEEEEEEeeEEEEEcCCCCEEEEEEEeccCcccccCcccEeCCCCEEEEEEEEeeCCcC
Confidence            68999999999999999999999999999999998741        247999999999999997654

RPS1 is a component of the small ribosomal subunit thought to be involved in the recognition and binding of mRNA's during translation initiation. The bacterial RPS1 domain architecture consists of 4-6 tandem S1 domains. In some bacteria, the tandem S1 array is located C-terminal to a 4-hydroxy-3-methylbut-2-enyl diphosphate reductase (HMBPP reductase) domain. While RPS1 is found primarily in bacteria, proteins with tandem RPS1-like domains have been identified in plants and humans, however these lack the N-terminal HMBPP reductase domain. This CD includes S1 repeat 4 (ec4) of the Escherichia coli RPS1. Autoantibodies to double-stranded DNA from patients with systemic lupus erythematosus cross-react with the human RPS1 homolog.

>cd05690 S1_RPS1_repeat_ec5 S1_RPS1_repeat_ec5: Ribosomal protein S1 (RPS1) domain

Probab=98.80  E-value=1.4e-08  Score=87.74  Aligned_cols=56  Identities=21%  Similarity=0.359  Sum_probs=50.3

Q ss_pred             CCEEEEEEEEEeCCeEEEEeCCCeEEEEecccCC--------CCCCCCCCEEEEEEEEEeCCCc
Q 002054          911 GTKVAAKVYQVRARGLVLDLGGGIRGMYRFENNE--------KKDFVVGDELLVKCSSFTGKGI  966 (974)
Q Consensus       911 G~vV~G~V~~I~~~GvFV~L~~gv~Glih~se~~--------~~~f~vGd~V~vkVl~id~~~~  966 (974)
                      |+++.|+|.+|++||+||+|++++.||+|.++++        .+.|++||+|+|+|+++|.+..
T Consensus         1 G~~~~g~V~~i~~~G~fv~l~~~~~Glv~~~~l~~~~~~~~~~~~~~~G~~v~v~v~~id~~~~   64 (69)
T cd05690           1 GTVVSGKIKSITDFGIFVGLDGGIDGLVHISDISWTQRVRHPSEIYKKGQEVEAVVLNIDVERE   64 (69)
T ss_pred             CCEEEEEEEEEEeeeEEEEeCCCCEEEEEHHHCCCccccCChhhEECCCCEEEEEEEEEECCcC
Confidence            7899999999999999999999999999999874        2348999999999999997643

RPS1 is a component of the small ribosomal subunit thought to be involved in the recognition and binding of mRNA's during translation initiation. The bacterial RPS1 domain architecture consists of 4-6 tandem S1 domains. In some bacteria, the tandem S1 array is located C-terminal to a 4-hydroxy-3-methylbut-2-enyl diphosphate reductase (HMBPP reductase) domain. While RPS1 is found primarily in bacteria, proteins with tandem RPS1-like domains have been identified in plants and humans, however these lack the N-terminal HMBPP reductase domain. This CD includes S1 repeat 5 (ec5) of the Escherichia coli RPS1. Autoantibodies to double-stranded DNA from patients with systemic lupus erythematosus cross-react with the human RPS1 homolog.

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

Probab=98.79  E-value=6.6e-09  Score=87.99  Aligned_cols=59  Identities=39%  Similarity=0.644  Sum_probs=55.9

Q ss_pred             CcceeeeeccchhhhhcCCCccchhhhhhhhCceEEee-CCEEEEEecCHHHHHHHHHHH
Q 002054          615 PRLATLKYDNDTLRRLIGPLGALKRKIEEETGGRISVS-DGTLTVVAKNRSVMEKVLEKV  673 (974)
Q Consensus       615 p~~~~~~i~~~ki~~vIg~gGk~i~~i~~~~g~~Idi~-dg~v~i~~~~~~~~~~a~~~i  673 (974)
                      |++..++|++++++.+||+||++|++|+++||++|+++ +|.|.|++.+++.++.|++++
T Consensus         1 P~~~~i~Ip~~~ig~iIGkgG~~ik~I~~~tg~~I~i~~~g~v~I~G~~~~~v~~A~~~I   60 (61)
T cd02393           1 PRIETMKIPPDKIRDVIGPGGKTIKKIIEETGVKIDIEDDGTVYIAASDKEAAEKAKKMI   60 (61)
T ss_pred             CeEEEEEeChhheeeeECCCchHHHHHHHHHCCEEEeCCCCEEEEEeCCHHHHHHHHHHh
Confidence            78899999999999999999999999999999999998 799999999899999998765

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.

>cd00164 S1_like S1_like: Ribosomal protein S1-like RNA-binding domain

Probab=98.77  E-value=1.5e-08  Score=85.40  Aligned_cols=64  Identities=39%  Similarity=0.693  Sum_probs=59.1

Q ss_pred             EEEEEEEEeeceEEEEEcCCeEEEEecccCCCccccccccccccCCEEEEEEEEEcc-CCceEEE
Q 002054          687 YKGVVTSVKEYGAFVEFNGGQQGLLHVSELSHEPVSRVSDVVSVGQQLSLRCIGQDV-RGNIKLS  750 (974)
Q Consensus       687 ~~G~V~~i~~~G~fV~l~~g~~Glvhisels~~~v~~~~~~~~vGd~V~vkVl~id~-~gri~LS  750 (974)
                      +.|+|+++.++|+||++.++.+|++|.+++++.+..++.+.|++||.|+|+|+++|. ++++.||
T Consensus         1 v~g~V~~v~~~g~~v~l~~~~~g~~~~~~~~~~~~~~~~~~~~~G~~v~~~v~~~d~~~~~i~ls   65 (65)
T cd00164           1 VTGKVVSITKFGVFVELEDGVEGLVHISELSDKFVKDPSEVFKVGDEVEVKVLEVDPEKGRISLS   65 (65)
T ss_pred             CEEEEEEEEeeeEEEEecCCCEEEEEHHHCCCccccCHhhEeCCCCEEEEEEEEEcCCcCEEecC
Confidence            579999999999999999899999999999999888888899999999999999997 6788775

Found in a wide variety of RNA-associated proteins. Originally identified in S1 ribosomal protein. This superfamily also contains the Cold Shock Domain (CSD), which is a homolog of the S1 domain. Both domains are members of the Oligonucleotide/oligosaccharide Binding (OB) fold.

>cd05692 S1_RPS1_repeat_hs4 S1_RPS1_repeat_hs4: Ribosomal protein S1 (RPS1) domain

Probab=98.77  E-value=3.6e-08  Score=84.63  Aligned_cols=61  Identities=28%  Similarity=0.480  Sum_probs=55.5

Q ss_pred             CCEEEEEEEEEeCCeEEEEeCCCeEEEEecccCCC-------CCCCCCCEEEEEEEEEeCCCceeeee
Q 002054          911 GTKVAAKVYQVRARGLVLDLGGGIRGMYRFENNEK-------KDFVVGDELLVKCSSFTGKGIPVVSL  971 (974)
Q Consensus       911 G~vV~G~V~~I~~~GvFV~L~~gv~Glih~se~~~-------~~f~vGd~V~vkVl~id~~~~~~~~~  971 (974)
                      |+++.|+|.+++++|+||++++++.||+|.++++.       +.|++||.|+|+|+++|.++...+|+
T Consensus         1 G~~~~g~V~~i~~~g~~v~i~~~~~g~l~~~~l~~~~~~~~~~~~~~Gd~v~v~v~~~~~~~~i~ls~   68 (69)
T cd05692           1 GSVVEGTVTRLKPFGAFVELGGGISGLVHISQIAHKRVKDVKDVLKEGDKVKVKVLSIDARGRISLSI   68 (69)
T ss_pred             CCEEEEEEEEEEeeeEEEEECCCCEEEEEhHHcCCcccCCHHHccCCCCEEEEEEEEECCCCcEEEEE
Confidence            79999999999999999999999999999998853       34899999999999999977887775

RPS1 is a component of the small ribosomal subunit thought to be involved in the recognition and binding of mRNA's during translation initiation. The bacterial RPS1 domain architecture consists of 4-6 tandem S1 domains. In some bacteria, the tandem S1 array is located C-terminal to a 4-hydroxy-3-methylbut-2-enyl diphosphate reductase (HMBPP reductase) domain. While RPS1 is found primarily in bacteria, proteins with tandem RPS1-like domains have been identified in plants and humans, however these lack the N-terminal HMBPP reductase domain. This CD includes S1 repeat 4 (hs4) of the H. sapiens RPS1 homolog. Autoantibodies to double-stranded DNA from patients with systemic lupus erythematosus cross-react with the human RPS1 homolog.

>PRK07252 hypothetical protein; Provisional

Probab=98.75  E-value=3.8e-08  Score=94.79  Aligned_cols=65  Identities=25%  Similarity=0.460  Sum_probs=58.2

Q ss_pred             CCCCEEEEEEEEEeCCeEEEEeCCCeEEEEecccCC-------CCCCCCCCEEEEEEEEEeC-CCceeeeecC
Q 002054          909 KLGTKVAAKVYQVRARGLVLDLGGGIRGMYRFENNE-------KKDFVVGDELLVKCSSFTG-KGIPVVSLVD  973 (974)
Q Consensus       909 ~vG~vV~G~V~~I~~~GvFV~L~~gv~Glih~se~~-------~~~f~vGd~V~vkVl~id~-~~~~~~~~~~  973 (974)
                      ++|+++.|+|.+|+++|+||+|++++.||+|.+++.       .+.|++||.|+|+|+++|. .+...+|+.+
T Consensus         2 kvG~iv~G~V~~V~~~G~fVei~~~~~GllhiseLs~~~~~~~~~~~~vGD~V~VkI~~iD~~~~ri~lSlk~   74 (120)
T PRK07252          2 KIGDKLKGTITGIKPYGAFVALENGTTGLIHISEIKTGFIDNIHQLLKVGEEVLVQVVDFDEYTGKASLSLRT   74 (120)
T ss_pred             CCCCEEEEEEEEEeCcEEEEEECCCCEEEEEHHHcCCccccChhhccCCCCEEEEEEEEEeCCCCEEEEEEee
Confidence            589999999999999999999999999999999874       3469999999999999998 6777788754

>cd05708 S1_Rrp5_repeat_sc12 S1_Rrp5_repeat_sc12: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits

Probab=98.74  E-value=4.2e-08  Score=86.51  Aligned_cols=65  Identities=26%  Similarity=0.410  Sum_probs=57.1

Q ss_pred             CCCCEEEEEEEEEeCCeEEEEeCC-CeEEEEecccCCC-------CCCCCCCEEEEEEEEEeC-CCceeeeecC
Q 002054          909 KLGTKVAAKVYQVRARGLVLDLGG-GIRGMYRFENNEK-------KDFVVGDELLVKCSSFTG-KGIPVVSLVD  973 (974)
Q Consensus       909 ~vG~vV~G~V~~I~~~GvFV~L~~-gv~Glih~se~~~-------~~f~vGd~V~vkVl~id~-~~~~~~~~~~  973 (974)
                      ++|+++.|+|.+++++|+||+|.+ ++.|++|.+++..       +.|++||.|+|+|+++|. ++...+|+..
T Consensus         1 ~~g~~v~g~V~~i~~~g~~v~l~~~~~~g~i~~~~l~~~~~~~~~~~~~~Gd~v~v~i~~vd~~~~~i~ls~k~   74 (77)
T cd05708           1 KVGQKIDGTVRRVEDYGVFIDIDGTNVSGLCHKSEISDNRVADASKLFRVGDKVRAKVLKIDAEKKRISLGLKA   74 (77)
T ss_pred             CCCCEEEEEEEEEEcceEEEEECCCCeEEEEEHHHCCCCccCCHhHeecCCCEEEEEEEEEeCCCCEEEEEEEe
Confidence            479999999999999999999986 8999999998853       357999999999999998 6777777754

Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in Saccharomyces cerevisiae Rrp5 and 14 S1 repeats in Homo sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in protein-protein interactions. Mutational studies have shown that each region represents a specific functional domain. Deletions within the S1-containing region inhibit pre-rRNA processing at either site A3 or A2, whereas deletions within the TPR region confer an inability to support cleavage of A0-A2. This CD includes S. cerevisiae S1 repeat 12 (sc12). Rrp5 is found in eukaryotes but not in prokaryotes or archaea.

>PTZ00248 eukaryotic translation initiation factor 2 subunit 1; Provisional

Probab=98.74  E-value=2e-08  Score=111.00  Aligned_cols=70  Identities=20%  Similarity=0.169  Sum_probs=60.3

Q ss_pred             cccccCC-CCCEEEEEEEEEeCCeEEEEeC--CCeEEEEecccCC-------CCCCCCCCEEEEEEEEEeCC-Cceeeee
Q 002054          903 VSAKNLK-LGTKVAAKVYQVRARGLVLDLG--GGIRGMYRFENNE-------KKDFVVGDELLVKCSSFTGK-GIPVVSL  971 (974)
Q Consensus       903 ~~~~~~~-vG~vV~G~V~~I~~~GvFV~L~--~gv~Glih~se~~-------~~~f~vGd~V~vkVl~id~~-~~~~~~~  971 (974)
                      |..++|+ +|++|.|+|++|.+||+||+|.  +|+.||+|.|++.       .+.+++||+|.|+|++||++ |..-+|+
T Consensus         9 ~~~~~~P~~GdvV~g~V~~I~d~GafV~L~EY~gvEGlIhiSElS~~ri~~i~d~vkvGd~v~vkVl~VD~ekg~IdLS~   88 (319)
T PTZ00248          9 FYEQKFPEEDDLVMVKVVRITEMGAYVSLLEYDDIEGMILMSELSKRRIRSINKLIRVGRHEVVVVLRVDKEKGYIDLSK   88 (319)
T ss_pred             chhhhCCCCCCEEEEEEEEEeCCeEEEEecCCCCcEEEEEHHHhcccccCCHHHhcCCCCEEEEEEEEEeCCCCEEEEEe
Confidence            4567788 8999999999999999999997  5999999999885       44699999999999999864 5566776


Q ss_pred             c
Q 002054          972 V  972 (974)
Q Consensus       972 ~  972 (974)
                      .
T Consensus        89 K   89 (319)
T PTZ00248         89 K   89 (319)
T ss_pred             e
Confidence            4

>cd05789 S1_Rrp4 S1_Rrp4: Rrp4 S1-like RNA-binding domain

Probab=98.72  E-value=5.1e-08  Score=88.32  Aligned_cols=65  Identities=14%  Similarity=0.181  Sum_probs=58.9

Q ss_pred             CCCCCEEEEEEEEEeCCeEEEEeCCCeEEEEecccCCC-----------CCCCCCCEEEEEEEEEeCCCceeeeec
Q 002054          908 LKLGTKVAAKVYQVRARGLVLDLGGGIRGMYRFENNEK-----------KDFVVGDELLVKCSSFTGKGIPVVSLV  972 (974)
Q Consensus       908 ~~vG~vV~G~V~~I~~~GvFV~L~~gv~Glih~se~~~-----------~~f~vGd~V~vkVl~id~~~~~~~~~~  972 (974)
                      .++|++|.|+|.++.++|+||++++++.|++|.+++..           +.|++||.|+|+|+++|+++...+|+.
T Consensus         4 p~~GdiV~g~V~~i~~~g~~v~i~~~~~G~l~~se~~~~~~~~~~~~~~~~l~vGd~i~~~V~~~~~~~~i~LS~~   79 (86)
T cd05789           4 PEVGDVVIGRVTEVGFKRWKVDINSPYDAVLPLSEVNLPRTDEDELNMRSYLDEGDLIVAEVQSVDSDGSVSLHTR   79 (86)
T ss_pred             CCCCCEEEEEEEEECCCEEEEECCCCeEEEEEHHHccCCCCccchHHHHhhCCCCCEEEEEEEEECCCCCEEEEeC
Confidence            47999999999999999999999999999999998742           148999999999999999888888864

S1-like RNA-binding domains are found in a wide variety of RNA-associated proteins. Rrp4 protein is a subunit of the exosome complex. The exosome plays a central role in 3' to 5' RNA processing and degradation in eukarytes and archaea. Its functions include the removal of incorrectly processed RNA and the maintenance of proper levels of mRNA, rRNA and a number of small RNA species. In Saccharomyces cerevisiae, the exosome includes nine core components, six of which are homologous to bacterial RNase PH. These form a hexameric ring structure. The other three subunits (RrP4, Rrp40, and Csl4) contain an S1 RNA binding domain and are part of the "S1 pore structure".

>cd05691 S1_RPS1_repeat_ec6 S1_RPS1_repeat_ec6: Ribosomal protein S1 (RPS1) domain

Probab=98.71  E-value=5.4e-08  Score=84.95  Aligned_cols=62  Identities=32%  Similarity=0.491  Sum_probs=55.2

Q ss_pred             CCEEEEEEEEEeCCeEEEEeCCCeEEEEecccCC-------CCCCCCCCEEEEEEEEEeCC-Cceeeeec
Q 002054          911 GTKVAAKVYQVRARGLVLDLGGGIRGMYRFENNE-------KKDFVVGDELLVKCSSFTGK-GIPVVSLV  972 (974)
Q Consensus       911 G~vV~G~V~~I~~~GvFV~L~~gv~Glih~se~~-------~~~f~vGd~V~vkVl~id~~-~~~~~~~~  972 (974)
                      |++|.|+|++++++|+||+|.+++.|++|.+++.       .+.|++||.++|+|+++|.+ +...+|+.
T Consensus         1 G~~v~g~V~~v~~~g~~v~l~~~~~g~i~~~~~~~~~~~~~~~~~~~Gd~v~~~v~~~d~~~~~i~ls~k   70 (73)
T cd05691           1 GSIVTGKVTEVDAKGATVKLGDGVEGFLRAAELSRDRVEDATERFKVGDEVEAKITNVDRKNRKISLSIK   70 (73)
T ss_pred             CCEEEEEEEEEECCeEEEEeCCCCEEEEEHHHCCCccccCHHHccCCCCEEEEEEEEEeCCCCEEEEEEE
Confidence            8999999999999999999999999999999874       23589999999999999987 56777764

RPS1 is a component of the small ribosomal subunit thought to be involved in the recognition and binding of mRNA's during translation initiation. The bacterial RPS1 domain architecture consists of 4-6 tandem S1 domains. In some bacteria, the tandem S1 array is located C-terminal to a 4-hydroxy-3-methylbut-2-enyl diphosphate reductase (HMBPP reductase) domain. While RPS1 is found primarily in bacteria, proteins with tandem RPS1-like domains have been identified in plants and humans, however these lack the N-terminal HMBPP reductase domain. This CD includes S1 repeat 6 (ec6) of the Escherichia coli RPS1. Autoantibodies to double-stranded DNA from patients with systemic lupus erythematosus cross-react with the human RPS1 homolog.

>cd05693 S1_Rrp5_repeat_hs1_sc1 S1_Rrp5_repeat_hs1_sc1: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits

Probab=98.71  E-value=2.8e-08  Score=92.70  Aligned_cols=65  Identities=26%  Similarity=0.290  Sum_probs=57.6

Q ss_pred             CCCCCEEEEEEEEEeCCeEEEEeCCCeEEEEecccCCC--------------------------CCCCCCCEEEEEEEEE
Q 002054          908 LKLGTKVAAKVYQVRARGLVLDLGGGIRGMYRFENNEK--------------------------KDFVVGDELLVKCSSF  961 (974)
Q Consensus       908 ~~vG~vV~G~V~~I~~~GvFV~L~~gv~Glih~se~~~--------------------------~~f~vGd~V~vkVl~i  961 (974)
                      +++|++|.|+|++|.++|+||.|++|+.|++|.+++..                          +.|++||.|+|+|+++
T Consensus         1 L~~G~vV~G~V~~v~~~gl~v~L~~g~~G~v~~seis~~~~~~~~~~~~~~~~~~~~~~~~~~~~~f~vGd~V~~kVi~~   80 (100)
T cd05693           1 LSEGMLVLGQVKEITKLDLVISLPNGLTGYVPITNISDAYTERLEELDEESEEEDDEEELPDLEDLFSVGQLVRCKVVSL   80 (100)
T ss_pred             CCCCCEEEEEEEEEcCCCEEEECCCCcEEEEEHHHhhHHHHHHHHHhhhhccccccccccCCHHHhccCCCEEEEEEEEc
Confidence            57999999999999999999999999999999997742                          4599999999999999


Q ss_pred             eCC----Cceeeeec
Q 002054          962 TGK----GIPVVSLV  972 (974)
Q Consensus       962 d~~----~~~~~~~~  972 (974)
                      |.+    +...+||.
T Consensus        81 d~~~~~~~~i~LSlr   95 (100)
T cd05693          81 DKSKSGKKRIELSLE   95 (100)
T ss_pred             cCCcCCCcEEEEEec
Confidence            985    56677764

Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in Saccharomyces cerevisiae Rrp5 and 14 S1 repeats in Homo sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in protein-protein interactions. Mutational studies have shown that each region represents a specific functional domain. Deletions within the S1-containing region inhibit pre-rRNA processing at either site A3 or A2, whereas deletions within the TPR region confer an inability to support cleavage of A0-A2. This CD includes H. sapiens S1 repeat 1 (hs1) and S. cerevisiae S1 repeat 1 (sc1). Rrp5 is found in eukaryotes but not in prokaryotes or archaea.

>cd04460 S1_RpoE S1_RpoE: RpoE, S1-like RNA-binding domain

Probab=98.69  E-value=6.8e-08  Score=90.04  Aligned_cols=75  Identities=25%  Similarity=0.451  Sum_probs=64.2

Q ss_pred             cEEEEEEEEEeeceEEEEEcCCeEEEEecccCCCcccccc-----------ccccccCCEEEEEEEEEccC------Cce
Q 002054          685 GIYKGVVTSVKEYGAFVEFNGGQQGLLHVSELSHEPVSRV-----------SDVVSVGQQLSLRCIGQDVR------GNI  747 (974)
Q Consensus       685 ~i~~G~V~~i~~~G~fV~l~~g~~Glvhisels~~~v~~~-----------~~~~~vGd~V~vkVl~id~~------gri  747 (974)
                      ++|.|+|+++.++|+||++. +.+|++|+++++++++...           ...|++||.|+|+|.++|..      +++
T Consensus         1 ~vv~g~V~~i~~~GifV~l~-~v~G~v~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~Gd~v~vkI~~vd~~~~~~~~~~i   79 (99)
T cd04460           1 EVVEGEVVEVVDFGAFVRIG-PVDGLLHISQIMDDYISYDPKNKRLIGEETKRVLKVGDVVRARIVAVSLKERRPRESKI   79 (99)
T ss_pred             CEEEEEEEEEEeccEEEEEc-CeEEEEEEEEccCCceEechhheeecccCcCCEECCCCEEEEEEEEEeHHHCcCCCceE
Confidence            47999999999999999997 5999999999998876533           47799999999999999962      589


Q ss_pred             EEEEeccCCCccc
Q 002054          748 KLSLKAVSPRPEA  760 (974)
Q Consensus       748 ~LS~K~~~~~~~~  760 (974)
                      .||+|+....||.
T Consensus        80 ~ls~k~~~~g~~~   92 (99)
T cd04460          80 GLTMRQPGLGKLE   92 (99)
T ss_pred             EEEEecCCCCcHH
Confidence            9999987665544

S1-like RNA-binding domains are found in a wide variety of RNA-associated proteins. RpoE is subunit E of archaeal RNA polymerase. Archaeal cells contain a single RNA polymerase made up of 12 subunits, which are homologous to the 12 subunits (RPB1-12) of eukaryotic RNA polymerase II. RpoE is homologous to Rpa43 of eukaryotic RNA polymerase I, RPB7 of eukaryotic RNA polymerase II, and Rpc25 of eukaryotic RNA polymerase III. RpoE is composed of two domains, the N-terminal RNP (ribonucleoprotein) domain and the C-terminal S1 domain. This S1 domain binds ssRNA and ssDNA. This family is classified based on the C-terminal S1 domain. The function of RpoE is not fully understood. In eukaryotes, RPB7 and RPB4 form a heterodimer that reversibly associates with the RNA polymerase II core.

>cd05687 S1_RPS1_repeat_ec1_hs1 S1_RPS1_repeat_ec1_hs1: Ribosomal protein S1 (RPS1) domain

Probab=98.68  E-value=8.9e-08  Score=83.15  Aligned_cols=61  Identities=25%  Similarity=0.328  Sum_probs=54.1

Q ss_pred             CCEEEEEEEEEeCCeEEEEeCCCeEEEEecccCC-------CCCCCCCCEEEEEEEEEeCC-Cceeeee
Q 002054          911 GTKVAAKVYQVRARGLVLDLGGGIRGMYRFENNE-------KKDFVVGDELLVKCSSFTGK-GIPVVSL  971 (974)
Q Consensus       911 G~vV~G~V~~I~~~GvFV~L~~gv~Glih~se~~-------~~~f~vGd~V~vkVl~id~~-~~~~~~~  971 (974)
                      |++|+|+|.++.++|+||+|+.++.|++|.+++.       .+.|++||.++|+|+++|++ +...+|+
T Consensus         1 G~iv~g~V~~i~~~~~~v~l~~~~~g~l~~~e~~~~~~~~~~~~~~~Gd~i~~~i~~~~~~~~~i~lS~   69 (70)
T cd05687           1 GDIVKGTVVSVDDDEVLVDIGYKSEGIIPISEFSDDPIENGEDEVKVGDEVEVYVLRVEDEEGNVVLSK   69 (70)
T ss_pred             CCEEEEEEEEEeCCEEEEEeCCCceEEEEHHHhCccccCCHhHcCCCCCEEEEEEEEEECCCCeEEEEe
Confidence            8999999999999999999998999999999884       34699999999999999954 5666665

RPS1 is a component of the small ribosomal subunit thought to be involved in the recognition and binding of mRNA's during translation initiation. The bacterial RPS1 domain architecture consists of 4-6 tandem S1 domains. In some bacteria, the tandem S1 array is located C-terminal to a 4-hydroxy-3-methylbut-2-enyl diphosphate reductase (HMBPP reductase) domain. While RPS1 is found primarily in bacteria, proteins with tandem RPS1-like domains have been identified in plants and humans, however these lack the N-terminal HMBPP reductase domain. This CD includes S1 repeat 1 of the Escherichia coli and Homo sapiens RPS1 (ec1 and hs1, respectively). Autoantibodies to double-stranded DNA from patients with systemic lupus erythematosus cross-react with the human RPS1 homolog.

>cd05684 S1_DHX8_helicase S1_DHX8_helicase: The N-terminal S1 domain of human ATP-dependent RNA helicase DHX8, a DEAH (Asp-Glu-Ala-His) box polypeptide

Probab=98.68  E-value=9.2e-08  Score=85.25  Aligned_cols=61  Identities=21%  Similarity=0.242  Sum_probs=54.5

Q ss_pred             CCEEEEEEEEEeCCeEEEEeC---CCeEEEEecccCCCC--------CCCCCCEEEEEEEEEeCCCceeeeec
Q 002054          911 GTKVAAKVYQVRARGLVLDLG---GGIRGMYRFENNEKK--------DFVVGDELLVKCSSFTGKGIPVVSLV  972 (974)
Q Consensus       911 G~vV~G~V~~I~~~GvFV~L~---~gv~Glih~se~~~~--------~f~vGd~V~vkVl~id~~~~~~~~~~  972 (974)
                      |+++.|+|.++++||+||+|+   +++.||+|.++++..        .|++||+|+|+|+++| ++...+|+.
T Consensus         1 G~~~~g~V~~v~~~G~fv~l~~~~~~~~gll~~s~l~~~~~~~~~~~~~~~Gd~v~v~v~~vd-~~~i~~s~k   72 (79)
T cd05684           1 GKIYKGKVTSIMDFGCFVQLEGLKGRKEGLVHISQLSFEGRVANPSDVVKRGQKVKVKVISIQ-NGKISLSMK   72 (79)
T ss_pred             CCEEEEEEEEEEeeeEEEEEeCCCCCcEEEEEhHhccCCCCcCChhheeCCCCEEEEEEEEEe-CCEEEEEEE
Confidence            789999999999999999998   479999999988533        3699999999999999 888888874

The DEAH-box RNA helicases are thought to play key roles in pre-mRNA splicing and DHX8 facilitates nuclear export of spliced mRNA by releasing the RNA from the spliceosome. DHX8 is also known as HRH1 (human RNA helicase 1) in Homo sapiens and PRP22 in Saccharomyces cerevisiae.

>cd04452 S1_IF2_alpha S1_IF2_alpha: The alpha subunit of translation Initiation Factor 2, S1-like RNA-binding domain

Probab=98.67  E-value=1.4e-07  Score=83.14  Aligned_cols=64  Identities=22%  Similarity=0.221  Sum_probs=54.8

Q ss_pred             CCCCEEEEEEEEEeCCeEEEEeCC--CeEEEEecccCCCC-------CCCCCCEEEEEEEEEeCC-Cceeeeec
Q 002054          909 KLGTKVAAKVYQVRARGLVLDLGG--GIRGMYRFENNEKK-------DFVVGDELLVKCSSFTGK-GIPVVSLV  972 (974)
Q Consensus       909 ~vG~vV~G~V~~I~~~GvFV~L~~--gv~Glih~se~~~~-------~f~vGd~V~vkVl~id~~-~~~~~~~~  972 (974)
                      ++|+++.|+|.++.+||+||+|.+  ++.||+|.+++...       .|++||.|+|+|+++|.+ +...+|+.
T Consensus         2 ~~G~~~~g~V~~v~~~g~~v~l~~~~~~~gll~~s~l~~~~~~~~~~~~~~Gd~v~vkv~~~d~~~~~i~ls~k   75 (76)
T cd04452           2 EEGELVVVTVKSIADMGAYVSLLEYGNIEGMILLSELSRRRIRSIRKLVKVGRKEVVKVIRVDKEKGYIDLSKK   75 (76)
T ss_pred             CCCCEEEEEEEEEEccEEEEEEcCCCCeEEEEEhHHcCCcccCCHHHeeCCCCEEEEEEEEEECCCCEEEEEEc
Confidence            589999999999999999999975  69999999988532       379999999999999974 55666653

S1-like RNA-binding domains are found in a wide variety of RNA-associated proteins. Eukaryotic and archaeal Initiation Factor 2 (e- and aIF2, respectively) are heterotrimeric proteins with three subunits (alpha, beta, and gamma). IF2 plays a crucial role in the process of translation initiation. The IF2 gamma subunit contains a GTP-binding site. The IF2 beta and gamma subunits together are thought to be responsible for binding methionyl-initiator tRNA. The ternary complex consisting of IF2, GTP, and the methionyl-initiator tRNA binds to the small subunit of the ribosome, as part of a pre-initiation complex that scans the mRNA to find the AUG start codon. The IF2-bound GTP is hydrolyzed to GDP when the methionyl-initiator tRNA binds the AUG start codon, at which time the IF2 is released with its bound GDP. The large ribosomal subunit then joins with the small subunit to c

>smart00316 S1 Ribosomal protein S1-like RNA-binding domain

Probab=98.66  E-value=1.2e-07  Score=81.59  Aligned_cols=63  Identities=32%  Similarity=0.500  Sum_probs=57.0

Q ss_pred             CCCCEEEEEEEEEeCCeEEEEeCCCeEEEEecccCCCC-------CCCCCCEEEEEEEEEeCC-Cceeeee
Q 002054          909 KLGTKVAAKVYQVRARGLVLDLGGGIRGMYRFENNEKK-------DFVVGDELLVKCSSFTGK-GIPVVSL  971 (974)
Q Consensus       909 ~vG~vV~G~V~~I~~~GvFV~L~~gv~Glih~se~~~~-------~f~vGd~V~vkVl~id~~-~~~~~~~  971 (974)
                      ++|+++.|+|.+++++|+||++++++.|++|.+++...       .|++||.|.|+|+++|.+ +...+|+
T Consensus         1 ~~G~~v~g~V~~v~~~g~~v~i~~~~~g~l~~~~~~~~~~~~~~~~~~~G~~v~~~V~~~~~~~~~i~ls~   71 (72)
T smart00316        1 EVGDVVEGTVTEITPFGAFVDLGNGVEGLIPISELSDKRVKDPEEVLKVGDEVKVKVLSVDEEKGRIILSL   71 (72)
T ss_pred             CCCCEEEEEEEEEEccEEEEEeCCCCEEEEEHHHCCccccCCHHHeecCCCEEEEEEEEEeCCCCEEEEEe
Confidence            47999999999999999999999999999999988643       499999999999999987 7777776

>PRK13763 putative RNA-processing protein; Provisional

Probab=98.65  E-value=4.2e-08  Score=101.28  Aligned_cols=83  Identities=25%  Similarity=0.373  Sum_probs=74.7

Q ss_pred             cceeeeeccchhhhhcCCCccchhhhhhhhCceEEee-C-CEEEEE---ecCHHHHHHHHHHHHHHhhc-ccc-----cC
Q 002054          616 RLATLKYDNDTLRRLIGPLGALKRKIEEETGGRISVS-D-GTLTVV---AKNRSVMEKVLEKVDFIIGR-EIE-----VG  684 (974)
Q Consensus       616 ~~~~~~i~~~ki~~vIg~gGk~i~~i~~~~g~~Idi~-d-g~v~i~---~~~~~~~~~a~~~i~~l~~~-~~~-----~G  684 (974)
                      .+..++||+++++.+||+||++|+.|++++|++|+++ + |.|.|.   +.+...+++|+++++.+... +++     .|
T Consensus         3 ~~~~i~IP~~kig~iIG~gGk~Ik~I~e~tg~~I~i~~~~g~V~I~~~~~~d~~~i~kA~~~I~ai~~gf~~e~A~~l~g   82 (180)
T PRK13763          3 MMEYVKIPKDRIGVLIGKKGETKKEIEERTGVKLEIDSETGEVIIEPTDGEDPLAVLKARDIVKAIGRGFSPEKALRLLD   82 (180)
T ss_pred             ceEEEEcCHHHhhhHhccchhHHHHHHHHHCcEEEEECCCCeEEEEeCCCCCHHHHHHHHHHHHHHhcCCCHHHHHHHhC
Confidence            4678899999999999999999999999999999997 5 999999   89999999999999988742 456     79


Q ss_pred             cEEEEEEEEEeece
Q 002054          685 GIYKGVVTSVKEYG  698 (974)
Q Consensus       685 ~i~~G~V~~i~~~G  698 (974)
                      +.|.++|.++.+|+
T Consensus        83 d~y~~~Vi~i~~~~   96 (180)
T PRK13763         83 DDYVLEVIDLSDYG   96 (180)
T ss_pred             CCceEEEEEhhhcc
Confidence            99999999998873

>cd04465 S1_RPS1_repeat_ec2_hs2 S1_RPS1_repeat_ec2_hs2: Ribosomal protein S1 (RPS1) domain

Probab=98.65  E-value=1.3e-07  Score=81.44  Aligned_cols=60  Identities=27%  Similarity=0.340  Sum_probs=51.6

Q ss_pred             CCEEEEEEEEEeCCeEEEEeCCCeEEEEecccCCCCC-----CCCCCEEEEEEEEEeC-CCceeeee
Q 002054          911 GTKVAAKVYQVRARGLVLDLGGGIRGMYRFENNEKKD-----FVVGDELLVKCSSFTG-KGIPVVSL  971 (974)
Q Consensus       911 G~vV~G~V~~I~~~GvFV~L~~gv~Glih~se~~~~~-----f~vGd~V~vkVl~id~-~~~~~~~~  971 (974)
                      |++|+|+|.++.++|+||++ +|+.||+|.++++...     ..+||+++|+|+++|+ ++..++|.
T Consensus         1 G~iv~g~V~~v~~~G~~v~l-~g~~gfip~s~~~~~~~~~~~~~vG~~i~~~i~~vd~~~~~i~lS~   66 (67)
T cd04465           1 GEIVEGKVTEKVKGGLIVDI-EGVRAFLPASQVDLRPVEDLDEYVGKELKFKIIEIDRERNNIVLSR   66 (67)
T ss_pred             CCEEEEEEEEEECCeEEEEE-CCEEEEEEHHHCCCcccCChHHhCCCEEEEEEEEEeCCCCEEEEEc
Confidence            78999999999999999999 7999999999885332     2489999999999997 56666664

RPS1 is a component of the small ribosomal subunit thought to be involved in the recognition and binding of mRNA's during translation initiation. The bacterial RPS1 domain architecture consists of 4-6 tandem S1 domains. In some bacteria, the tandem S1 array is located C-terminal to a 4-hydroxy-3-methylbut-2-enyl diphosphate reductase (HMBPP reductase) domain.While RPS1 is found primarily in bacteria, proteins with tandem RPS1-like domains have been identified in plants and humans, however these lack the N-terminal HMBPP reductase domain. This CD includes S1 repeat 2 of the Escherichia coli and Homo sapiens RPS1 (ec2 and hs2, respectively). Autoantibodies to double-stranded DNA from patients with systemic lupus erythematosus cross-react with the human RPS1 homolog.

>cd05702 S1_Rrp5_repeat_hs11_sc8 S1_Rrp5_repeat_hs11_sc8: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits

Probab=98.64  E-value=1.1e-07  Score=82.78  Aligned_cols=58  Identities=19%  Similarity=0.247  Sum_probs=51.9

Q ss_pred             CCEEEEEEEEEeCCeEEEEeCCCeEEEEecccCCC---------CCCCCCCEEEEEEEEEeCCCcee
Q 002054          911 GTKVAAKVYQVRARGLVLDLGGGIRGMYRFENNEK---------KDFVVGDELLVKCSSFTGKGIPV  968 (974)
Q Consensus       911 G~vV~G~V~~I~~~GvFV~L~~gv~Glih~se~~~---------~~f~vGd~V~vkVl~id~~~~~~  968 (974)
                      |++|.|+|.++.++|+||+|++++.|++|.+++..         +.|++||.|+|+|+++|..+.-.
T Consensus         1 G~iV~g~V~~i~~~gi~v~l~~~i~g~i~~~~i~~~~~~~~~~~~~~~~Gd~i~~kVl~~d~~~~~~   67 (70)
T cd05702           1 GDLVKAKVKSVKPTQLNVQLADNVHGRIHVSEVFDEWPDGKNPLSKFKIGQKIKARVIGGHDAKTHR   67 (70)
T ss_pred             CCEEEEEEEEEECCcEEEEeCCCcEEEEEHHHhccccccccChhHhCCCCCEEEEEEEEEeCccccc
Confidence            89999999999999999999999999999997742         34999999999999999877543

Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in Saccharomyces cerevisiae Rrp5 and 14 S1 repeats in Homo sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in protein-protein interactions. Mutational studies have shown that each region represents a specific functional domain. Deletions within the S1-containing region inhibit pre-rRNA processing at either site A3 or A2, whereas deletions within the TPR region confer an inability to support cleavage of A0-A2. This CD includes H. sapiens S1 repeat 11 (hs11) and S. cerevisiae S1 repeat 8 (sc8). Rrp5 is found in eukaryotes but not in prokaryotes or archaea.

>PRK08059 general stress protein 13; Validated

Probab=98.63  E-value=1.2e-07  Score=91.96  Aligned_cols=68  Identities=25%  Similarity=0.344  Sum_probs=59.9

Q ss_pred             cccCCCCCEEEEEEEEEeCCeEEEEeCCCeEEEEecccCC-------CCCCCCCCEEEEEEEEEeC-CCceeeeec
Q 002054          905 AKNLKLGTKVAAKVYQVRARGLVLDLGGGIRGMYRFENNE-------KKDFVVGDELLVKCSSFTG-KGIPVVSLV  972 (974)
Q Consensus       905 ~~~~~vG~vV~G~V~~I~~~GvFV~L~~gv~Glih~se~~-------~~~f~vGd~V~vkVl~id~-~~~~~~~~~  972 (974)
                      +.++++|+++.|+|.++.++|+||++++++.||+|.++++       .+.|++||.|+|+|+++|. ++...+|+.
T Consensus         2 ~~~~k~G~iv~G~V~~i~~~G~fV~i~~~~~Gli~~sel~~~~~~~~~~~~~vGD~I~vkI~~id~~~~~i~lslk   77 (123)
T PRK08059          2 MSQYEVGSVVTGKVTGIQPYGAFVALDEETQGLVHISEITHGFVKDIHDFLSVGDEVKVKVLSVDEEKGKISLSIR   77 (123)
T ss_pred             cccCCCCCEEEEEEEEEecceEEEEECCCCEEEEEHHHCCcccccCHHHcCCCCCEEEEEEEEEECCCCeEEEEEE
Confidence            3568999999999999999999999999999999999874       3458999999999999986 667777764

>cd05685 S1_Tex S1_Tex: The C-terminal S1 domain of a transcription accessory factor called Tex, which has been characterized in Bordetella pertussis and Pseudomonas aeruginosa

Probab=98.63  E-value=1.1e-07  Score=81.38  Aligned_cols=58  Identities=24%  Similarity=0.290  Sum_probs=51.2

Q ss_pred             CCEEEEEEEEEeCCeEEEEeCCCeEEEEecccCCCC-------CCCCCCEEEEEEEEEeCC-Ccee
Q 002054          911 GTKVAAKVYQVRARGLVLDLGGGIRGMYRFENNEKK-------DFVVGDELLVKCSSFTGK-GIPV  968 (974)
Q Consensus       911 G~vV~G~V~~I~~~GvFV~L~~gv~Glih~se~~~~-------~f~vGd~V~vkVl~id~~-~~~~  968 (974)
                      |+++.|+|.+++++|+||+++++..||+|.+++...       .|++||.|+|+|+++|.+ +...
T Consensus         1 g~~~~g~V~~i~~~G~fv~l~~~~~g~~~~~~l~~~~~~~~~~~~~~Gd~v~v~i~~vd~~~~~i~   66 (68)
T cd05685           1 GMVLEGVVTNVTDFGAFVDIGVKQDGLIHISKMADRFVSHPSDVVSVGDIVEVKVISIDEERGRIS   66 (68)
T ss_pred             CCEEEEEEEEEecccEEEEcCCCCEEEEEHHHCCCccccCHHHhcCCCCEEEEEEEEEECCCCEEe
Confidence            789999999999999999999999999999988533       479999999999999984 4433

The tex gene is essential in Bortella pertusis and is named for its role in toxin expression. Tex has two functional domains, an N-terminal domain homologous to the Escherichia coli maltose repression protein, which is a poorly defined transcriptional factor, and a C-terminal S1 RNA-binding domain. Tex is found in prokaryotes, eukaryotes, and archaea.

>cd04471 S1_RNase_R S1_RNase_R: RNase R C-terminal S1 domain

Probab=98.61  E-value=1.6e-07  Score=84.20  Aligned_cols=62  Identities=19%  Similarity=0.304  Sum_probs=54.5

Q ss_pred             CCCEEEEEEEEEeCCeEEEEeCC-CeEEEEecccCCC------------------CCCCCCCEEEEEEEEEeC-CCceee
Q 002054          910 LGTKVAAKVYQVRARGLVLDLGG-GIRGMYRFENNEK------------------KDFVVGDELLVKCSSFTG-KGIPVV  969 (974)
Q Consensus       910 vG~vV~G~V~~I~~~GvFV~L~~-gv~Glih~se~~~------------------~~f~vGd~V~vkVl~id~-~~~~~~  969 (974)
                      +|+++.|+|.+|+++|+||+|++ ++.|++|.++++.                  ..|++||+|+|+|+++|. ++...+
T Consensus         1 ~g~~~~g~V~~v~~~G~fv~l~~~~~~G~v~~~~l~~~~~~~d~~~~~~~~~~~~~~~~~gd~v~v~v~~vd~~~~~i~~   80 (83)
T cd04471           1 VGEEFDGVISGVTSFGLFVELDNLTVEGLVHVSTLGDDYYEFDEENHALVGERTGKVFRLGDKVKVRVVRVDLDRRKIDF   80 (83)
T ss_pred             CCCEEEEEEEeEEeeeEEEEecCCCEEEEEEEEecCCCcEEEcccceEEEeccCCCEEcCCCEEEEEEEEeccccCEEEE
Confidence            48999999999999999999998 8999999998742                  457999999999999997 466666


Q ss_pred             ee
Q 002054          970 SL  971 (974)
Q Consensus       970 ~~  971 (974)
                      ++
T Consensus        81 ~l   82 (83)
T cd04471          81 EL   82 (83)
T ss_pred             EE
Confidence            65

RNase R is a processive 3' to 5' exoribonuclease, which is a homolog of RNase II. RNase R degrades RNA with secondary structure having a 3' overhang of at least 7 nucleotides. RNase R and PNPase play an important role in the degradation of RNA with extensive secondary structure, such as rRNA, tRNA, and certain mRNA which contains repetitive extragenic palindromic sequences. The C-terminal S1 domain binds ssRNA.

>cd04453 S1_RNase_E S1_RNase_E: RNase E and RNase G, S1-like RNA-binding domain

Probab=98.61  E-value=1.3e-07  Score=86.21  Aligned_cols=61  Identities=18%  Similarity=0.220  Sum_probs=54.1

Q ss_pred             ccCCCCCEEEEEEEEEeCC--eEEEEeCCCeEEEEecccCC----------CCCCCCCCEEEEEEEEEeCCCc
Q 002054          906 KNLKLGTKVAAKVYQVRAR--GLVLDLGGGIRGMYRFENNE----------KKDFVVGDELLVKCSSFTGKGI  966 (974)
Q Consensus       906 ~~~~vG~vV~G~V~~I~~~--GvFV~L~~gv~Glih~se~~----------~~~f~vGd~V~vkVl~id~~~~  966 (974)
                      ..+.+|+++.|+|.+|.+|  |+||+|++|..||+|.+++.          .+.|++||+|.|+|+....+++
T Consensus         3 ~~~~~G~iy~g~V~~i~~~~~GaFV~l~~g~~Gllh~seis~~~~~~v~~~~~~~~~Gd~v~VqV~~~~~~~K   75 (88)
T cd04453           3 REPIVGNIYLGRVKKIVPGLQAAFVDIGLGKNGFLHLSDILPAYFKKHKKIAKLLKEGQEILVQVVKEPIGTK   75 (88)
T ss_pred             CcCCCCCEEEEEEEEeccCCcEEEEEeCCCCEEEEEhHHcCchhccccCCHHHcCCCCCEEEEEEEEecCCCC
Confidence            3578999999999999997  99999999999999999874          3469999999999999876654

RNase E is an essential endoribonuclease in the processing and degradation of RNA. In addition to its role in mRNA degradation, RNase E has also been implicated in the processing of rRNA, and the maturation of tRNA, 10Sa RNA and the M1 precursor of RNase P. RNase E associates with PNPase (3' to 5' exonuclease), Rhl B (DEAD-box RNA helicase) and enolase (glycolytic enzyme) to form the RNA degradosome. RNase E tends to cut mRNA within single-stranded regions that are rich in A/U nucleotides. The N-terminal region of RNase E contains the catalytic site. Within the conserved N-terminal domain of RNAse E and RNase G, there is an S1-like subdomain, which is an ancient single-stranded RNA-binding domain. S1 domain is an RNA-binding module originally identified in the ribosomal protein S1. The S1 domain is required for RNA cleavage by RNase E. RNase G is paralogous to RNase E with an N-terminal catalytic domain th

>PRK04163 exosome complex RNA-binding protein Rrp4; Provisional

Probab=98.61  E-value=9.9e-08  Score=102.73  Aligned_cols=88  Identities=24%  Similarity=0.302  Sum_probs=77.7

Q ss_pred             ccccCcEEEEEEEEEeeceEEEEEcCCeEEEEecccCCCccc----cccccccccCCEEEEEEEEEccCCceEEEEeccC
Q 002054          680 EIEVGGIYKGVVTSVKEYGAFVEFNGGQQGLLHVSELSHEPV----SRVSDVVSVGQQLSLRCIGQDVRGNIKLSLKAVS  755 (974)
Q Consensus       680 ~~~~G~i~~G~V~~i~~~G~fV~l~~g~~Glvhisels~~~v----~~~~~~~~vGd~V~vkVl~id~~gri~LS~K~~~  755 (974)
                      .+++|+++.|+|+++.++|+||+|.++.+|+||++++++.++    .++.+.|++||.|+|||+++++.+++.||+|+. 
T Consensus        60 ~P~vGDiViG~V~~i~~~~~~vdI~~~~~g~L~~s~i~~~~~~~d~~~~~~~~~~GDlV~akV~~i~~~~~~~LS~k~~-  138 (235)
T PRK04163         60 IPKVGDLVIGKVTDVTFSGWEVDINSPYKAYLPVSEVLGRPVNVEGTDLRKYLDIGDYIIAKVKDVDRTRDVVLTLKGK-  138 (235)
T ss_pred             cCCCCCEEEEEEEEEeCceEEEEeCCCceeEEEHHHcCCCccccchhhhHhhCCCCCEEEEEEEEECCCCcEEEEEcCC-
Confidence            369999999999999999999999888999999999999987    788999999999999999999878899999752 


Q ss_pred             CCcccccCceEEEEEeec
Q 002054          756 PRPEADVKGVVEGSVPVN  773 (974)
Q Consensus       756 ~~~~~~~g~~~~G~vv~i  773 (974)
                           ..|....|.+..+
T Consensus       139 -----~lG~L~~G~~~~V  151 (235)
T PRK04163        139 -----GLGKIEGGTIVEI  151 (235)
T ss_pred             -----CCCccCCCEEEEE
Confidence                 3566666776664

>PRK09521 exosome complex RNA-binding protein Csl4; Provisional

Probab=98.60  E-value=8.8e-08  Score=99.91  Aligned_cols=73  Identities=26%  Similarity=0.382  Sum_probs=67.3

Q ss_pred             cccccCcEEEEEEEEEeeceEEEEEc----------CCeEEEEecccCCCccccccccccccCCEEEEEEEEEccCCceE
Q 002054          679 REIEVGGIYKGVVTSVKEYGAFVEFN----------GGQQGLLHVSELSHEPVSRVSDVVSVGQQLSLRCIGQDVRGNIK  748 (974)
Q Consensus       679 ~~~~~G~i~~G~V~~i~~~G~fV~l~----------~g~~Glvhisels~~~v~~~~~~~~vGd~V~vkVl~id~~gri~  748 (974)
                      ..+++|+++.|+|+++.++|+||+|.          ++.+|++|++++++.+..++.+.|++||.|+|+|++++  +++.
T Consensus        60 ~~~~~GdiV~GkV~~i~~~g~~V~I~~~~~~~~~l~~~~~G~l~~s~i~~~~~~~~~~~~~~GD~V~akV~~i~--~~i~  137 (189)
T PRK09521         60 PLLKKGDIVYGRVVDVKEQRALVRIVSIEGSERELATSKLAYIHISQVSDGYVESLTDAFKIGDIVRAKVISYT--DPLQ  137 (189)
T ss_pred             CCCCCCCEEEEEEEEEcCCeEEEEEEEecccccccCCCceeeEEhhHcChhhhhhHHhccCCCCEEEEEEEecC--CcEE
Confidence            35789999999999999999999994          36889999999999988889999999999999999998  8999


Q ss_pred             EEEec
Q 002054          749 LSLKA  753 (974)
Q Consensus       749 LS~K~  753 (974)
                      ||+|+
T Consensus       138 LS~k~  142 (189)
T PRK09521        138 LSTKG  142 (189)
T ss_pred             EEEec
Confidence            99985

>TIGR03665 arCOG04150 arCOG04150 universal archaeal KH domain protein

Probab=98.60  E-value=5.5e-08  Score=99.76  Aligned_cols=78  Identities=29%  Similarity=0.391  Sum_probs=70.6

Q ss_pred             eeeccchhhhhcCCCccchhhhhhhhCceEEee-C-CEEEE--EecCHHHHHHHHHHHHHHhhc-ccc-----cCcEEEE
Q 002054          620 LKYDNDTLRRLIGPLGALKRKIEEETGGRISVS-D-GTLTV--VAKNRSVMEKVLEKVDFIIGR-EIE-----VGGIYKG  689 (974)
Q Consensus       620 ~~i~~~ki~~vIg~gGk~i~~i~~~~g~~Idi~-d-g~v~i--~~~~~~~~~~a~~~i~~l~~~-~~~-----~G~i~~G  689 (974)
                      ++||+++|+.+||+||++|+.|++++|++|+++ + |.|.|  ...+...+++|+++|+.+... .++     .|+.|.+
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~~l~gd~y~~   81 (172)
T TIGR03665         2 VKIPKDRIGVLIGKGGETKKEIEERTGVKLDIDSETGEVKIEEEDEDPLAVMKAREVVKAIGRGFSPEKALKLLDDDYML   81 (172)
T ss_pred             ccCCHHHhhhHhCCchhHHHHHHHHhCcEEEEEcCCceEEEecCCCCHHHHHHHHHHHHHHHcCCCHHHHHHhcCCcceE
Confidence            578999999999999999999999999999998 4 99999  788999999999999988742 466     7999999


Q ss_pred             EEEEEeec
Q 002054          690 VVTSVKEY  697 (974)
Q Consensus       690 ~V~~i~~~  697 (974)
                      .|.++.+|
T Consensus        82 ~Vi~I~~~   89 (172)
T TIGR03665        82 EVIDLKEY   89 (172)
T ss_pred             EEEEhhhc
Confidence            99999887

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.

>cd04472 S1_PNPase S1_PNPase: Polynucleotide phosphorylase (PNPase), ), S1-like RNA-binding domain

Probab=98.58  E-value=2.4e-07  Score=79.59  Aligned_cols=60  Identities=23%  Similarity=0.343  Sum_probs=53.5

Q ss_pred             CCEEEEEEEEEeCCeEEEEeCCCeEEEEecccCCC-------CCCCCCCEEEEEEEEEeCCCceeee
Q 002054          911 GTKVAAKVYQVRARGLVLDLGGGIRGMYRFENNEK-------KDFVVGDELLVKCSSFTGKGIPVVS  970 (974)
Q Consensus       911 G~vV~G~V~~I~~~GvFV~L~~gv~Glih~se~~~-------~~f~vGd~V~vkVl~id~~~~~~~~  970 (974)
                      |+++.|+|.++++||+||+++++..||+|.++++.       +.|++||.|+|+|+++|+.+...+|
T Consensus         1 g~~~~g~V~~v~~~G~~v~l~~~~~g~l~~~~l~~~~~~~~~~~~~~Gd~v~v~v~~~d~~~~i~ls   67 (68)
T cd04472           1 GKIYEGKVVKIKDFGAFVEILPGKDGLVHISELSDERVEKVEDVLKVGDEVKVKVIEVDDRGRISLS   67 (68)
T ss_pred             CCEEEEEEEEEEEeEEEEEeCCCCEEEEEhHHcCCccccCHHHccCCCCEEEEEEEEECCCCcEEee
Confidence            78999999999999999999999999999998753       2479999999999999986676665

PNPase is a polyribonucleotide nucleotidyl transferase that degrades mRNA. It is a trimeric multidomain protein. The C-terminus contains the S1 domain which binds ssRNA. This family is classified based on the S1 domain. PNPase nonspecifically removes the 3' nucleotides from mRNA, but is stalled by double-stranded RNA structures such as a stem-loop. Evidence shows that a minimum of 7-10 unpaired nucleotides at the 3' end, is required for PNPase degradation. It is suggested that PNPase also dephosphorylates the RNA 5' end. This additional activity may regulate the 5'-dependent activity of RNaseE in vivo.

>cd04455 S1_NusA S1_NusA: N-utilizing substance A protein (NusA), S1-like RNA-binding domain

Probab=98.50  E-value=3.9e-07  Score=78.71  Aligned_cols=63  Identities=19%  Similarity=0.234  Sum_probs=54.9

Q ss_pred             ccCcEEEEEEEEEeeceEEEEEcCCeEEEEecccCCCccccccccccccCCEEEEEEEEEcc---CCceEEEE
Q 002054          682 EVGGIYKGVVTSVKEYGAFVEFNGGQQGLLHVSELSHEPVSRVSDVVSVGQQLSLRCIGQDV---RGNIKLSL  751 (974)
Q Consensus       682 ~~G~i~~G~V~~i~~~G~fV~l~~g~~Glvhisels~~~v~~~~~~~~vGd~V~vkVl~id~---~gri~LS~  751 (974)
                      +.|++++|+|.++.++|+||++. +.+|+||.+|++.      .+.|++||.|+|.|++++.   .++|.||+
T Consensus         2 ~~g~iV~G~V~~~~~~~~~vdig-~~eg~lp~~e~~~------~~~~~~Gd~v~v~v~~v~~~~~~~~i~lSr   67 (67)
T cd04455           2 REGEIVTGIVKRVDRGNVIVDLG-KVEAILPKKEQIP------GESYRPGDRIKAYVLEVRKTSKGPQIILSR   67 (67)
T ss_pred             CCCCEEEEEEEEEcCCCEEEEcC-CeEEEeeHHHCCC------CCcCCCCCEEEEEEEEEecCCCCCEEEEeC
Confidence            47999999999999999999995 5999999999973      3468999999999999986   24788884

S1-like RNA-binding domains are found in a wide variety of RNA-associated proteins. NusA is a transcription elongation factor containing an N-terminal catalytic domain and three RNA binding domains (RBD's). The RBD's include one S1 domain and two KH domains that form an RNA binding surface. DNA transcription by RNA polymerase (RNAP) includes three phases - initiation, elongation, and termination. During initiation, sigma factors bind RNAP and target RNAP to specific promoters. During elongation, N-utilization substances (NusA, B, E, and G) replace sigma factors and regulate pausing, termination, and antitermination. NusA is cold-shock-inducible.

>cd04454 S1_Rrp4_like S1_Rrp4_like: Rrp4-like, S1-like RNA-binding domain

Probab=98.47  E-value=8.3e-07  Score=79.71  Aligned_cols=65  Identities=20%  Similarity=0.176  Sum_probs=59.1

Q ss_pred             CCCCEEEEEEEEEeCCeEEEEeCCCeEEEEecccCC-------CCCCCCCCEEEEEEEEEeCCCceeeeecC
Q 002054          909 KLGTKVAAKVYQVRARGLVLDLGGGIRGMYRFENNE-------KKDFVVGDELLVKCSSFTGKGIPVVSLVD  973 (974)
Q Consensus       909 ~vG~vV~G~V~~I~~~GvFV~L~~gv~Glih~se~~-------~~~f~vGd~V~vkVl~id~~~~~~~~~~~  973 (974)
                      ++|++|.|+|.++.+.|++|++..+..|++|.+++.       .+.|++||.+.|+|+++|.++.+.+|...
T Consensus         5 ~~GdiV~G~V~~v~~~~~~V~i~~~~~g~l~~~~~~~~~~~~~~~~~~~GD~i~~~V~~~~~~~~i~LS~~~   76 (82)
T cd04454           5 DVGDIVIGIVTEVNSRFWKVDILSRGTARLEDSSATEKDKKEIRKSLQPGDLILAKVISLGDDMNVLLTTAD   76 (82)
T ss_pred             CCCCEEEEEEEEEcCCEEEEEeCCCceEEeechhccCcchHHHHhcCCCCCEEEEEEEEeCCCCCEEEEECC
Confidence            699999999999999999999999999999999874       34599999999999999998888888753

S1-like RNA-binding domains are found in a wide variety of RNA-associated proteins. Rrp4 protein, and Rrp40 and Csl4 proteins, also represented in this group, are subunits of the exosome complex. The exosome plays a central role in 3' to 5' RNA processing and degradation in eukarytes and archaea. Its functions include the removal of incorrectly processed RNA and the maintenance of proper levels of mRNA, rRNA and a number of small RNA species. In Saccharomyces cerevisiae, the exosome includes nine core components, six of which are homologous to bacterial RNase PH. These form a hexameric ring structure. The other three subunits (RrP4, Rrp40, and Csl4) contain an S1 RNA binding domain and are part of the "S1 pore structure".

>TIGR02063 RNase_R ribonuclease R

Probab=98.43  E-value=9.2e-07  Score=110.05  Aligned_cols=72  Identities=29%  Similarity=0.637  Sum_probs=63.5

Q ss_pred             ccccCcEEEEEEEEEeeceEEEEEcC-CeEEEEecccCCCccc-----------cccccccccCCEEEEEEEEEcc-CCc
Q 002054          680 EIEVGGIYKGVVTSVKEYGAFVEFNG-GQQGLLHVSELSHEPV-----------SRVSDVVSVGQQLSLRCIGQDV-RGN  746 (974)
Q Consensus       680 ~~~~G~i~~G~V~~i~~~G~fV~l~~-g~~Glvhisels~~~v-----------~~~~~~~~vGd~V~vkVl~id~-~gr  746 (974)
                      ..++|++|+|+|++|++||+||+|.+ +.+||||+|+++++++           ++....|++||.|+|+|.++|. +|+
T Consensus       624 ~~~iG~~~~g~V~~v~~fGifV~L~~~~~eGlvhis~l~~d~~~~d~~~~~l~g~~~~~~~~lGd~V~Vkv~~vd~~~~~  703 (709)
T TIGR02063       624 SEKIGEEFEGVISGVTSFGLFVELENNTIEGLVHISTLKDDYYVFDEKGLALVGERTGKVFRLGDRVKVRVVKADLDTGK  703 (709)
T ss_pred             hccCCcEEEEEEEEEEeCCEEEEecCCceEEEEEeeecCCCcEEEcccceEEEeccCCcEECCCCEEEEEEEEEecccCe
Confidence            45789999999999999999999987 7999999999987654           2345679999999999999997 799


Q ss_pred             eEEEE
Q 002054          747 IKLSL  751 (974)
Q Consensus       747 i~LS~  751 (974)
                      |.|++
T Consensus       704 I~~~l  708 (709)
T TIGR02063       704 IDFEL  708 (709)
T ss_pred             EEEEE
Confidence            99985

This family consists of an exoribonuclease, ribonuclease R, also called VacB. It is one of the eight exoribonucleases reported in E. coli and is broadly distributed throughout the bacteria. In E. coli, double mutants of this protein and polynucleotide phosphorylase are not viable. Scoring between trusted and noise cutoffs to the model are shorter, divergent forms from the Chlamydiae, and divergent forms from the Campylobacterales (including Helicobacter pylori) and Leptospira interrogans.

>cd04455 S1_NusA S1_NusA: N-utilizing substance A protein (NusA), S1-like RNA-binding domain

Probab=98.43  E-value=1e-06  Score=76.01  Aligned_cols=55  Identities=16%  Similarity=0.268  Sum_probs=50.3

Q ss_pred             CCCCEEEEEEEEEeCCeEEEEeCCCeEEEEecccCC-CCCCCCCCEEEEEEEEEeCC
Q 002054          909 KLGTKVAAKVYQVRARGLVLDLGGGIRGMYRFENNE-KKDFVVGDELLVKCSSFTGK  964 (974)
Q Consensus       909 ~vG~vV~G~V~~I~~~GvFV~L~~gv~Glih~se~~-~~~f~vGd~V~vkVl~id~~  964 (974)
                      +.|++|+|+|.++.++|+||+++ ++.|++|.+++. .+.|++||+|+|.|++++.+
T Consensus         2 ~~g~iV~G~V~~~~~~~~~vdig-~~eg~lp~~e~~~~~~~~~Gd~v~v~v~~v~~~   57 (67)
T cd04455           2 REGEIVTGIVKRVDRGNVIVDLG-KVEAILPKKEQIPGESYRPGDRIKAYVLEVRKT   57 (67)
T ss_pred             CCCCEEEEEEEEEcCCCEEEEcC-CeEEEeeHHHCCCCCcCCCCCEEEEEEEEEecC
Confidence            47999999999999999999996 499999999884 56899999999999999964

S1-like RNA-binding domains are found in a wide variety of RNA-associated proteins. NusA is a transcription elongation factor containing an N-terminal catalytic domain and three RNA binding domains (RBD's). The RBD's include one S1 domain and two KH domains that form an RNA binding surface. DNA transcription by RNA polymerase (RNAP) includes three phases - initiation, elongation, and termination. During initiation, sigma factors bind RNAP and target RNAP to specific promoters. During elongation, N-utilization substances (NusA, B, E, and G) replace sigma factors and regulate pausing, termination, and antitermination. NusA is cold-shock-inducible.

>PHA02945 interferon resistance protein; Provisional

Probab=98.43  E-value=7.5e-07  Score=79.11  Aligned_cols=62  Identities=19%  Similarity=0.218  Sum_probs=52.6

Q ss_pred             CCCCEEEEEEEEEeCCeEEEEeCC--CeEEEEecccC--C------CCCCCCCCEEEEEEEEEeCCCcee-eeec
Q 002054          909 KLGTKVAAKVYQVRARGLVLDLGG--GIRGMYRFENN--E------KKDFVVGDELLVKCSSFTGKGIPV-VSLV  972 (974)
Q Consensus       909 ~vG~vV~G~V~~I~~~GvFV~L~~--gv~Glih~se~--~------~~~f~vGd~V~vkVl~id~~~~~~-~~~~  972 (974)
                      .+|++|.|+|+. ++||+||.|++  |+.||+|.|+.  .      .+.+ +||+|.|+|+.+|+....+ +||.
T Consensus        10 ~~GelvigtV~~-~d~ga~v~L~EY~g~eg~i~~seveva~~wvK~rd~l-~GqkvV~KVirVd~~kg~IDlSlK   82 (88)
T PHA02945         10 NVGDVLKGKVYE-NGYALYIDLFDYPHSEAILAESVQMHMNRYFKYRDKL-VGKTVKVKVIRVDYTKGYIDVNYK   82 (88)
T ss_pred             CCCcEEEEEEEe-cCceEEEEecccCCcEEEEEeehhhhccceEeeeeEe-cCCEEEEEEEEECCCCCEEEeEee
Confidence            689999999999 99999999998  99999999955  3      4456 9999999999999775443 4553

>cd05688 S1_RPS1_repeat_ec3 S1_RPS1_repeat_ec3: Ribosomal protein S1 (RPS1) domain

Probab=98.41  E-value=8.8e-07  Score=75.97  Aligned_cols=55  Identities=27%  Similarity=0.418  Sum_probs=49.3

Q ss_pred             CCCEEEEEEEEEeCCeEEEEeCCCeEEEEecccCC-------CCCCCCCCEEEEEEEEEeCCC
Q 002054          910 LGTKVAAKVYQVRARGLVLDLGGGIRGMYRFENNE-------KKDFVVGDELLVKCSSFTGKG  965 (974)
Q Consensus       910 vG~vV~G~V~~I~~~GvFV~L~~gv~Glih~se~~-------~~~f~vGd~V~vkVl~id~~~  965 (974)
                      +|+++.|+|.+++++|+||+++ ++.|++|.+++.       .+.|++||+|+|+|+++|.+.
T Consensus         1 ~g~~~~g~V~~v~~~g~~v~l~-~~~g~l~~~e~~~~~~~~~~~~~~~Gd~v~v~i~~vd~~~   62 (68)
T cd05688           1 EGDVVEGTVKSITDFGAFVDLG-GVDGLLHISDMSWGRVKHPSEVVNVGDEVEVKVLKIDKER   62 (68)
T ss_pred             CCCEEEEEEEEEEeeeEEEEEC-CeEEEEEhHHCCCccccCHhHEECCCCEEEEEEEEEECCC
Confidence            5899999999999999999997 799999999773       345899999999999999754

RPS1 is a component of the small ribosomal subunit thought to be involved in the recognition and binding of mRNA's during translation initiation. The bacterial RPS1 domain architecture consists of 4-6 tandem S1 domains. In some bacteria, the tandem S1 array is located C-terminal to a 4-hydroxy-3-methylbut-2-enyl diphosphate reductase (HMBPP reductase) domain. While RPS1 is found primarily in bacteria, proteins with tandem RPS1-like domains have been identified in plants and humans, however these lack the N-terminal HMBPP reductase domain. This CD includes S1 repeat 3 (ec3) of the Escherichia coli RPS1. Autoantibodies to double-stranded DNA from patients with systemic lupus erythematosus cross-react with the human RPS1 homolog.

>cd05791 S1_CSL4 S1_CSL4: CSL4, S1-like RNA-binding domain

Probab=98.37  E-value=1e-06  Score=81.01  Aligned_cols=73  Identities=16%  Similarity=0.179  Sum_probs=66.1

Q ss_pred             cccCcEEEEEEEEEeeceEEEEE--------cCCeEEEEecccCCCcccc--ccccccccCCEEEEEEEEEccCCceEEE
Q 002054          681 IEVGGIYKGVVTSVKEYGAFVEF--------NGGQQGLLHVSELSHEPVS--RVSDVVSVGQQLSLRCIGQDVRGNIKLS  750 (974)
Q Consensus       681 ~~~G~i~~G~V~~i~~~G~fV~l--------~~g~~Glvhisels~~~v~--~~~~~~~vGd~V~vkVl~id~~gri~LS  750 (974)
                      +++|+++.|+|+++....++|+|        .....|++|++++...+.+  ++.+.|++||.|++||++.+....+.||
T Consensus         4 P~~GDiVig~V~~v~~~~~~v~I~~v~~~~l~~~~~g~l~~~dv~~~~~d~~~~~~~f~~GDiV~AkVis~~~~~~~~Ls   83 (92)
T cd05791           4 PKVGSIVIARVTRINPRFAKVDILCVGGRPLKESFRGVIRKEDIRATEKDKVEMYKCFRPGDIVRAKVISLGDASSYYLS   83 (92)
T ss_pred             CCCCCEEEEEEEEEcCCEEEEEEEEecCeecCCCcccEEEHHHccccccchHHHHhhcCCCCEEEEEEEEcCCCCCcEEE
Confidence            68999999999999999999999        6678999999999877776  6788899999999999999876789999


Q ss_pred             Eec
Q 002054          751 LKA  753 (974)
Q Consensus       751 ~K~  753 (974)
                      ++.
T Consensus        84 t~~   86 (92)
T cd05791          84 TAE   86 (92)
T ss_pred             ecC
Confidence            875

S1-like RNA-binding domains are found in a wide variety of RNA-associated proteins. ScCSL4 protein is a subunit of the exosome complex. The exosome plays a central role in 3' to 5' RNA processing and degradation in eukarytes and archaea. Its functions include the removal of incorrectly processed RNA and the maintenance of proper levels of mRNA, rRNA and a number of small RNA species. In S. cerevisiae, the exosome includes nine core components, six of which are homologous to bacterial RNase PH. These form a hexameric ring structure. The other three subunits (RrP4, Rrp40, and Csl4) contain an S1 RNA binding domain and are part of the "S1 pore structure".

>PF03725 RNase_PH_C: 3' exoribonuclease family, domain 2 This Prosite family only includes Ribonuclease PH; InterPro: IPR015847 The PH (phosphorolytic) domain is responsible for 3'-5' exoribonuclease activity, although in some proteins this domain has lost its catalytic function

Probab=98.35  E-value=7.9e-07  Score=76.90  Aligned_cols=67  Identities=22%  Similarity=0.331  Sum_probs=54.6

Q ss_pred             ccccceeeeeeccCCCCCCcccceEEEecCCccccccCCccEEEEeeCCc-eEEEEeeccCCCCCHHHHHHHHHHHHHH
Q 002054          514 EHVAGVSVGLVSEVDPSTGEIKDYRILTDILGLEDHLGDMDFKIAGTRIG-VTAIQLDIKPAGIPLDIICECLEHAHKG  591 (974)
Q Consensus       514 ~~vagvs~gli~~~d~~~~~~~~~~iL~Dp~~~Ee~~~d~d~~Va~t~~g-I~alq~~~k~~~i~~e~l~~al~~A~~~  591 (974)
                      ++|+++++|++++           .+++||+.+||.+++..++++.+.++ ++.++..+...+++++.|.+|++.|+++
T Consensus         1 ~~~~avt~~~i~~-----------~~v~Dpt~~Ee~~~~~~l~~~~~~~~~~~~~~~~~g~~~~~~~~l~~~i~~A~~~   68 (68)
T PF03725_consen    1 DPPVAVTVGIIDG-----------ELVVDPTAEEESLSDSSLTLAVDGTGNICTLQKSGGGSELSEDQLEEAIELAKKA   68 (68)
T ss_dssp             SEEEEEEEEEETT-----------EEEES--HHHHHHSSEEEEEEEETTSSEEEEEEEEESSEEEHHHHHHHHHHHHHH
T ss_pred             CCeEEEEEEEECC-----------EEEECCCHHHHhhcCCcEEEEEECCCCEEEEEEcCCCCCCCHHHHHHHHHHHhcC
Confidence            5799999999975           59999999999999999999988777 6555555443459999999999999975

An active PH domain uses inorganic phosphate as a nucleophile, adding it across the phosphodiester bond between the end two nucleotides in order to release ribonucleoside 5'-diphosphate (rNDP) from the 3' end of the RNA substrate. PH domains can be found in bacterial/organelle RNases and PNPases (polynucleotide phosphorylases) [], as well as in archaeal and eukaryotic RNA exosomes [, ], the later acting as nano-compartments for the degradation or processing of RNA (including mRNA, rRNA, snRNA and snoRNA). Bacterial/organelle PNPases share a common barrel structure with RNA exosomes, consisting of a hexameric ring of PH domains that act as a degradation chamber, and an S1-domain/KH-domain containing cap that binds the RNA substrate (and sometimes accessory proteins) in order to regulate and restrict entry into the degradation chamber []. Unstructured RNA substrates feed in through the pore made by the S1 domains, are degraded by the PH domain ring, and exit as nucleotides via the PH pore at the opposite end of the barrel [, ]. This entry represents the phosphorolytic (PH) domain 2, which has a core 3-layer alpha/beta/alpha structure. This domain is found in bacterial/organelle PNPases and in archaeal/eukaryotic exosomes []. More information about these proteins can be found at Protein of the Month: RNA Exosomes [].; GO: 0003723 RNA binding, 0006396 RNA processing; PDB: 1E3H_A 1E3P_A 2NN6_E 2WNR_A 3U1K_B 2BA0_H 2BA1_H 3M85_G 3M7N_H 3H1C_K ....

>PRK09521 exosome complex RNA-binding protein Csl4; Provisional

Probab=98.34  E-value=2.9e-06  Score=88.63  Aligned_cols=93  Identities=14%  Similarity=0.125  Sum_probs=71.8

Q ss_pred             cccCCeEEEEE---EEeecCCCCcCccccccccccc--cccCCCCCEEEEEEEEEeCCeEEEEeC----------CCeEE
Q 002054          872 FSQREREELAE---CLFGTEDGDEDNKGTRVEAIVS--AKNLKLGTKVAAKVYQVRARGLVLDLG----------GGIRG  936 (974)
Q Consensus       872 ~k~Gq~v~~~V---l~vd~e~~~i~slK~~~~~p~~--~~~~~vG~vV~G~V~~I~~~GvFV~L~----------~gv~G  936 (974)
                      |..+..+.+.+   +++|.+++++.      .+||.  ...+++|++|.|+|++|.++|+||+|.          .++.|
T Consensus        27 y~~~~~i~as~~G~~~id~~~~~Is------v~P~~~~~~~~~~GdiV~GkV~~i~~~g~~V~I~~~~~~~~~l~~~~~G  100 (189)
T PRK09521         27 YEDNGEVYASVVGKVFIDDINRKIS------VIPFKKTPPLLKKGDIVYGRVVDVKEQRALVRIVSIEGSERELATSKLA  100 (189)
T ss_pred             EeeCCEEEEEeeEEEEEcCCCCEEE------EecCcCCCCCCCCCCEEEEEEEEEcCCeEEEEEEEecccccccCCCcee
Confidence            33445555555   45566665543      25773  456789999999999999999999984          37899


Q ss_pred             EEecccCC-------CCCCCCCCEEEEEEEEEeCCCceeeeec
Q 002054          937 MYRFENNE-------KKDFVVGDELLVKCSSFTGKGIPVVSLV  972 (974)
Q Consensus       937 lih~se~~-------~~~f~vGd~V~vkVl~id~~~~~~~~~~  972 (974)
                      ++|.+++.       .+.|++||.|.|+|++++  +...+|..
T Consensus       101 ~l~~s~i~~~~~~~~~~~~~~GD~V~akV~~i~--~~i~LS~k  141 (189)
T PRK09521        101 YIHISQVSDGYVESLTDAFKIGDIVRAKVISYT--DPLQLSTK  141 (189)
T ss_pred             eEEhhHcChhhhhhHHhccCCCCEEEEEEEecC--CcEEEEEe
Confidence            99999774       456999999999999999  67777764

>COG1093 SUI2 Translation initiation factor 2, alpha subunit (eIF-2alpha) [Translation, ribosomal structure and biogenesis]

Probab=98.34  E-value=5.4e-07  Score=95.21  Aligned_cols=63  Identities=22%  Similarity=0.282  Sum_probs=55.9

Q ss_pred             CCCCEEEEEEEEEeCCeEEEEeCC--CeEEEEecccCC-------CCCCCCCCEEEEEEEEEeCCCcee-eee
Q 002054          909 KLGTKVAAKVYQVRARGLVLDLGG--GIRGMYRFENNE-------KKDFVVGDELLVKCSSFTGKGIPV-VSL  971 (974)
Q Consensus       909 ~vG~vV~G~V~~I~~~GvFV~L~~--gv~Glih~se~~-------~~~f~vGd~V~vkVl~id~~~~~~-~~~  971 (974)
                      .+|++|-|+|++|.+||+||.|++  |+.||+|+||..       .+.+++||+|.|+|+.||++...+ +||
T Consensus        10 eeGEiVv~tV~~V~~~GAyv~L~EY~g~Eg~ihiSEvas~wVknIrd~vkegqkvV~kVlrVd~~rg~IDLSl   82 (269)
T COG1093          10 EEGEIVVGTVKQVADYGAYVELDEYPGKEGFIHISEVASGWVKNIRDYVKEGQKVVAKVLRVDPKRGHIDLSL   82 (269)
T ss_pred             CCCcEEEEEEEEeeccccEEEeeccCCeeeeEEHHHHHHHHHHHHHHHhhcCCeEEEEEEEEcCCCCeEeeeh
Confidence            489999999999999999999987  899999999885       567999999999999999876543 454

>TIGR00448 rpoE DNA-directed RNA polymerase (rpoE), archaeal and eukaryotic form

Probab=98.30  E-value=2.7e-06  Score=87.99  Aligned_cols=76  Identities=26%  Similarity=0.472  Sum_probs=64.5

Q ss_pred             ccccCcEEEEEEEEEeeceEEEEEcCCeEEEEecccCCCcccc-----------ccccccccCCEEEEEEEEEcc-----
Q 002054          680 EIEVGGIYKGVVTSVKEYGAFVEFNGGQQGLLHVSELSHEPVS-----------RVSDVVSVGQQLSLRCIGQDV-----  743 (974)
Q Consensus       680 ~~~~G~i~~G~V~~i~~~G~fV~l~~g~~Glvhisels~~~v~-----------~~~~~~~vGd~V~vkVl~id~-----  743 (974)
                      .+.+|++++|+|++++++|+||++. ..+|++|.+++.+++..           +....+++||.|++||.++|.     
T Consensus        78 ~p~~gEvv~G~V~~v~~~GifV~lg-~~~gi~~~~~l~~~~~~~d~~~~~~~~~~~~~~~~~Gd~VrvrV~~v~~~~~~~  156 (179)
T TIGR00448        78 KPELGEIVEGEVIEIVEFGAFVSLG-PFDGLFHVSQVTDDYCYYDPKESALIGKETKKVLDEGDKVRARIVALSLKDRRP  156 (179)
T ss_pred             eccCCCEEEEEEEEEEeeEEEEEeC-CceEEEEcHHhCCCceEEccccceEEEccCCeEEcCCCEEEEEEEEEEccCCCC
Confidence            5678999999999999999999995 59999999999876542           234679999999999999983     


Q ss_pred             -CCceEEEEeccCC
Q 002054          744 -RGNIKLSLKAVSP  756 (974)
Q Consensus       744 -~gri~LS~K~~~~  756 (974)
                       ..+|.||+|+...
T Consensus       157 ~~~~I~lt~k~~~L  170 (179)
T TIGR00448       157 EGSKIGLTMRQPLL  170 (179)
T ss_pred             CcceEEEEeccCcC
Confidence             4689999998543

This family seems to be confined to the archea and eukaryotic taxa and are quite dissimilar to E.coli rpoE.

>PRK03987 translation initiation factor IF-2 subunit alpha; Validated

Probab=98.26  E-value=2.5e-06  Score=92.98  Aligned_cols=65  Identities=20%  Similarity=0.277  Sum_probs=56.8

Q ss_pred             CCCCCEEEEEEEEEeCCeEEEEeCC--CeEEEEecccCC-------CCCCCCCCEEEEEEEEEeCC-Cceeeeec
Q 002054          908 LKLGTKVAAKVYQVRARGLVLDLGG--GIRGMYRFENNE-------KKDFVVGDELLVKCSSFTGK-GIPVVSLV  972 (974)
Q Consensus       908 ~~vG~vV~G~V~~I~~~GvFV~L~~--gv~Glih~se~~-------~~~f~vGd~V~vkVl~id~~-~~~~~~~~  972 (974)
                      .++|++|.|+|.+|.+||+||+|.+  |+.||+|.|++.       .+.|++||.|.|+|+++|.+ +...+|+.
T Consensus         6 P~~GdiV~G~V~~I~~~G~fV~L~e~~gieGlI~iSEls~~~i~~i~~~~kvGd~V~vkVi~VD~~k~~I~LSlK   80 (262)
T PRK03987          6 PEEGELVVGTVKEVKDFGAFVTLDEYPGKEGFIHISEVASGWVKNIRDHVKEGQKVVCKVIRVDPRKGHIDLSLK   80 (262)
T ss_pred             CCCCCEEEEEEEEEECCEEEEEECCCCCcEEEEEHHHcCcccccCHHHhCCCCCEEEEEEEEEecccCeEEEEEE
Confidence            4689999999999999999999986  899999999875       33589999999999999985 45677764

>PRK09202 nusA transcription elongation factor NusA; Validated

Probab=98.20  E-value=2.2e-06  Score=100.49  Aligned_cols=95  Identities=12%  Similarity=0.118  Sum_probs=75.8

Q ss_pred             ccccCCeEEEEEEEeecCCCCcCcccccccccc-------ccccCC--CCCEEEEEEEEEeCCeEEEEeCCCeEEEEecc
Q 002054          871 SFSQREREELAECLFGTEDGDEDNKGTRVEAIV-------SAKNLK--LGTKVAAKVYQVRARGLVLDLGGGIRGMYRFE  941 (974)
Q Consensus       871 ~~k~Gq~v~~~Vl~vd~e~~~i~slK~~~~~p~-------~~~~~~--vG~vV~G~V~~I~~~GvFV~L~~gv~Glih~s  941 (974)
                      .+++|+.++..|...+..+.-+.+.|+....-|       .+..|+  +|++|+|+|+++.++|+||+|+ |+.||+|.+
T Consensus        86 ~~~vGD~ie~~I~~~~fgRia~q~aKq~i~Qkire~ere~i~~eyk~~~GeIV~G~V~ri~~~giiVDLg-gvea~LP~s  164 (470)
T PRK09202         86 DAEVGDYIEEEIESVDFGRIAAQTAKQVIVQKIREAERERVYEEYKDRVGEIITGVVKRVERGNIIVDLG-RAEAILPRK  164 (470)
T ss_pred             cccCCCeEEEEEccccCChHHHHHHHHHHHHHHHHHHHHHHHHHHHhhcCCEEEEEEEEEecCCEEEEEC-CeEEEecHH
Confidence            578999999998777633322225555433333       377787  9999999999999999999995 899999999


Q ss_pred             cC-CCCCCCCCCEEEEEEEEEeCCCc
Q 002054          942 NN-EKKDFVVGDELLVKCSSFTGKGI  966 (974)
Q Consensus       942 e~-~~~~f~vGd~V~vkVl~id~~~~  966 (974)
                      ++ +...|++||+|+|.|++|+.++.
T Consensus       165 E~ip~E~~~~GdrIka~I~~Vd~~~k  190 (470)
T PRK09202        165 EQIPRENFRPGDRVRAYVYEVRKEAR  190 (470)
T ss_pred             HcCCCccCCCCCEEEEEEEEEecCCC
Confidence            87 57789999999999999998654

>PRK11642 exoribonuclease R; Provisional

Probab=98.18  E-value=8e-06  Score=102.16  Aligned_cols=73  Identities=29%  Similarity=0.533  Sum_probs=63.4

Q ss_pred             cccCcEEEEEEEEEeeceEEEEEcCC-eEEEEecccCCCcccc-----------ccccccccCCEEEEEEEEEcc-CCce
Q 002054          681 IEVGGIYKGVVTSVKEYGAFVEFNGG-QQGLLHVSELSHEPVS-----------RVSDVVSVGQQLSLRCIGQDV-RGNI  747 (974)
Q Consensus       681 ~~~G~i~~G~V~~i~~~G~fV~l~~g-~~Glvhisels~~~v~-----------~~~~~~~vGd~V~vkVl~id~-~gri  747 (974)
                      -++|++|+|+|++|++||+||+|.+. ++||||++++.++++.           +....|++||.|+|+|.++|. +++|
T Consensus       641 ~~iGe~f~G~Is~V~~fGifVeL~~~~vEGlV~vs~L~~d~y~~d~~~~~L~g~~~~~~~~lGD~V~VkV~~vD~~~rkI  720 (813)
T PRK11642        641 DQVGNVFKGVISSVTGFGFFVRLDDLFIDGLVHVSSLDNDYYRFDQVGQRLIGESSGQTYRLGDRVEVRVEAVNMDERKI  720 (813)
T ss_pred             ccCCcEEEEEEEEeecCceEEEECCCCeeeeEEEeecCCcceEecchheEEecccCCcEECCCCEEEEEEEEeecCCCeE
Confidence            37899999999999999999999764 9999999999887532           234679999999999999997 7899


Q ss_pred             EEEEec
Q 002054          748 KLSLKA  753 (974)
Q Consensus       748 ~LS~K~  753 (974)
                      .|++-.
T Consensus       721 ~f~l~~  726 (813)
T PRK11642        721 DFSLIS  726 (813)
T ss_pred             EEEEec
Confidence            999853

>TIGR00358 3_prime_RNase VacB and RNase II family 3'-5' exoribonucleases

Probab=98.18  E-value=7.7e-06  Score=100.75  Aligned_cols=71  Identities=25%  Similarity=0.534  Sum_probs=62.0

Q ss_pred             cccCcEEEEEEEEEeeceEEEEEc-CCeEEEEecccCCCccc-----------cccccccccCCEEEEEEEEEcc-CCce
Q 002054          681 IEVGGIYKGVVTSVKEYGAFVEFN-GGQQGLLHVSELSHEPV-----------SRVSDVVSVGQQLSLRCIGQDV-RGNI  747 (974)
Q Consensus       681 ~~~G~i~~G~V~~i~~~G~fV~l~-~g~~Glvhisels~~~v-----------~~~~~~~~vGd~V~vkVl~id~-~gri  747 (974)
                      -++|++|+|+|++|++||+||+|. .+++||||++++.++++           ++....|++||.|+|+|.++|. +++|
T Consensus       570 ~~iG~~~~g~I~~v~~~GifV~L~~~~veGlV~~s~l~~d~y~~d~~~~~l~g~~~~~~~~lGD~V~Vki~~vd~~~~~I  649 (654)
T TIGR00358       570 DKVGTEFSGEISSVTRFGMFVRLDDNGIDGLIHISTLHNDYYVFDQEKMALIGKGTGKVYRIGDRVTVKLTEVNMETRSI  649 (654)
T ss_pred             hCCCcEEEEEEEeEEcCcEEEEecCCceEEEEEeEeCCCcceEEeccccEEEeccCCcEECCCCEEEEEEEEEecccCeE
Confidence            368999999999999999999997 68999999999988752           2334679999999999999997 7899


Q ss_pred             EEEE
Q 002054          748 KLSL  751 (974)
Q Consensus       748 ~LS~  751 (974)
                      .+++
T Consensus       650 ~f~l  653 (654)
T TIGR00358       650 IFEL  653 (654)
T ss_pred             EEEE
Confidence            8875

This model is defined to identify a pair of paralogous 3-prime exoribonucleases in E. coli, plus the set of proteins apparently orthologous to one or the other in other eubacteria. VacB was characterized originally as required for the expression of virulence genes, but is now recognized as the exoribonuclease RNase R (Rnr). Its paralog in E. coli and H. influenzae is designated exoribonuclease II (Rnb). Both are involved in the degradation of mRNA, and consequently have strong pleiotropic effects that may be difficult to disentangle. Both these proteins share domain-level similarity (RNB, S1) with a considerable number of other proteins, and full-length similarity scoring below the trusted cutoff to proteins associated with various phenotypes but uncertain biochemistry; it may be that these latter proteins are also 3-prime exoribonucleases.

>cd00164 S1_like S1_like: Ribosomal protein S1-like RNA-binding domain

Probab=98.17  E-value=4.1e-06  Score=70.45  Aligned_cols=52  Identities=27%  Similarity=0.440  Sum_probs=46.7

Q ss_pred             EEEEEEEEeCCeEEEEeCCCeEEEEecccCC-------CCCCCCCCEEEEEEEEEeCCC
Q 002054          914 VAAKVYQVRARGLVLDLGGGIRGMYRFENNE-------KKDFVVGDELLVKCSSFTGKG  965 (974)
Q Consensus       914 V~G~V~~I~~~GvFV~L~~gv~Glih~se~~-------~~~f~vGd~V~vkVl~id~~~  965 (974)
                      +.|+|.++.++|+||++++++.|++|.+++.       ...|++||.|+|+|+++|.++
T Consensus         1 v~g~V~~v~~~g~~v~l~~~~~g~~~~~~~~~~~~~~~~~~~~~G~~v~~~v~~~d~~~   59 (65)
T cd00164           1 VTGKVVSITKFGVFVELEDGVEGLVHISELSDKFVKDPSEVFKVGDEVEVKVLEVDPEK   59 (65)
T ss_pred             CEEEEEEEEeeeEEEEecCCCEEEEEHHHCCCccccCHhhEeCCCCEEEEEEEEEcCCc
Confidence            4799999999999999999999999999874       346999999999999999744

Found in a wide variety of RNA-associated proteins. Originally identified in S1 ribosomal protein. This superfamily also contains the Cold Shock Domain (CSD), which is a homolog of the S1 domain. Both domains are members of the Oligonucleotide/oligosaccharide Binding (OB) fold.

>COG1095 RPB7 DNA-directed RNA polymerase, subunit E' [Transcription]

Probab=98.16  E-value=4.6e-06  Score=84.46  Aligned_cols=76  Identities=28%  Similarity=0.497  Sum_probs=64.0

Q ss_pred             cccccCcEEEEEEEEEeeceEEEEEcCCeEEEEecccCCCcccc----------c-cccccccCCEEEEEEEEEcc----
Q 002054          679 REIEVGGIYKGVVTSVKEYGAFVEFNGGQQGLLHVSELSHEPVS----------R-VSDVVSVGQQLSLRCIGQDV----  743 (974)
Q Consensus       679 ~~~~~G~i~~G~V~~i~~~G~fV~l~~g~~Glvhisels~~~v~----------~-~~~~~~vGd~V~vkVl~id~----  743 (974)
                      ..+..|++++|.|+++.+||+||.+. -.+||+|+||+.++++.          + ...++++||.|++||++.+.    
T Consensus        77 fkP~~gEVV~GeVv~~~~~G~fV~ig-p~dglvh~sqi~dd~~~~d~~~~~~~g~~tk~~i~~gd~VR~RIv~~s~~~~~  155 (183)
T COG1095          77 FKPFRGEVVEGEVVEVVEFGAFVRIG-PLDGLVHVSQIMDDYIDYDEKNKVLIGEETKRVLKVGDKVRARIVGVSLKSRR  155 (183)
T ss_pred             EEeccccEEEEEEEEEeecceEEEec-cccccccHhhccCcccccCcccceeeecccceEEecCCEEEEEEEEEecccCc
Confidence            36788999999999999999999996 69999999999998432          2 34479999999999999875    


Q ss_pred             --CCceEEEEeccC
Q 002054          744 --RGNIKLSLKAVS  755 (974)
Q Consensus       744 --~gri~LS~K~~~  755 (974)
                        .-+|.|+||+..
T Consensus       156 ~~~~~I~lTmrq~~  169 (183)
T COG1095         156 PRESKIGLTMRQPG  169 (183)
T ss_pred             cccceEEEEecccc
Confidence              147899999854

>PRK09202 nusA transcription elongation factor NusA; Validated

Probab=98.11  E-value=4.4e-06  Score=97.97  Aligned_cols=68  Identities=24%  Similarity=0.272  Sum_probs=61.0

Q ss_pred             cccc--cCcEEEEEEEEEeeceEEEEEcCCeEEEEecccCCCccccccccccccCCEEEEEEEEEcc-CC--ceEEEEec
Q 002054          679 REIE--VGGIYKGVVTSVKEYGAFVEFNGGQQGLLHVSELSHEPVSRVSDVVSVGQQLSLRCIGQDV-RG--NIKLSLKA  753 (974)
Q Consensus       679 ~~~~--~G~i~~G~V~~i~~~G~fV~l~~g~~Glvhisels~~~v~~~~~~~~vGd~V~vkVl~id~-~g--ri~LS~K~  753 (974)
                      ..++  .|++++|+|.++.++|+||++ ++.+||||.++++      |.+.|++||.|+|+|+++|. ++  +|.||++.
T Consensus       128 ~eyk~~~GeIV~G~V~ri~~~giiVDL-ggvea~LP~sE~i------p~E~~~~GdrIka~I~~Vd~~~kg~qIilSRt~  200 (470)
T PRK09202        128 EEYKDRVGEIITGVVKRVERGNIIVDL-GRAEAILPRKEQI------PRENFRPGDRVRAYVYEVRKEARGPQIILSRTH  200 (470)
T ss_pred             HHHHhhcCCEEEEEEEEEecCCEEEEE-CCeEEEecHHHcC------CCccCCCCCEEEEEEEEEecCCCCCeEEEEeCc
Confidence            4565  999999999999999999999 6899999999995      66789999999999999987 23  79999975

>PRK08563 DNA-directed RNA polymerase subunit E'; Provisional

Probab=98.06  E-value=1.4e-05  Score=83.29  Aligned_cols=75  Identities=28%  Similarity=0.500  Sum_probs=63.8

Q ss_pred             cccccCcEEEEEEEEEeeceEEEEEcCCeEEEEecccCCCcccc-----------ccccccccCCEEEEEEEEEccC---
Q 002054          679 REIEVGGIYKGVVTSVKEYGAFVEFNGGQQGLLHVSELSHEPVS-----------RVSDVVSVGQQLSLRCIGQDVR---  744 (974)
Q Consensus       679 ~~~~~G~i~~G~V~~i~~~G~fV~l~~g~~Glvhisels~~~v~-----------~~~~~~~vGd~V~vkVl~id~~---  744 (974)
                      ..+.+|+++.|+|+++.++|+||++. ..+|++|.+++.+++..           +....+++||.|+++|.++|.+   
T Consensus        77 f~P~~GEVv~g~V~~v~~~Gi~V~lg-~~~g~v~~~~l~~~~~~~d~~~~~~~~~~~~~~i~~Gd~VrvrV~~v~~~~~~  155 (187)
T PRK08563         77 FKPELQEVVEGEVVEVVEFGAFVRIG-PVDGLLHISQIMDDYISYDPKNGRLIGKESKRVLKVGDVVRARIVAVSLKERR  155 (187)
T ss_pred             EeccCCCEEEEEEEEEEccEEEEEEe-CceEEEEcHHcCCCceEEccccceEEEccCCeEEcCCCEEEEEEEEEEcccCC
Confidence            35789999999999999999999996 59999999999877532           3456799999999999999862   


Q ss_pred             ---CceEEEEecc
Q 002054          745 ---GNIKLSLKAV  754 (974)
Q Consensus       745 ---gri~LS~K~~  754 (974)
                         .++.||+|+.
T Consensus       156 ~~~~~I~ls~~~~  168 (187)
T PRK08563        156 PRGSKIGLTMRQP  168 (187)
T ss_pred             CCCCEEEEEecCC
Confidence               3788999874

>cd04460 S1_RpoE S1_RpoE: RpoE, S1-like RNA-binding domain

Probab=97.93  E-value=3.8e-05  Score=71.61  Aligned_cols=52  Identities=19%  Similarity=0.291  Sum_probs=46.0

Q ss_pred             CEEEEEEEEEeCCeEEEEeCCCeEEEEecccCCC------------------CCCCCCCEEEEEEEEEeCC
Q 002054          912 TKVAAKVYQVRARGLVLDLGGGIRGMYRFENNEK------------------KDFVVGDELLVKCSSFTGK  964 (974)
Q Consensus       912 ~vV~G~V~~I~~~GvFV~L~~gv~Glih~se~~~------------------~~f~vGd~V~vkVl~id~~  964 (974)
                      +++.|+|.+|.++|+||+|+ ++.||+|.+++..                  ..|++||.|+|+|.++|.+
T Consensus         1 ~vv~g~V~~i~~~GifV~l~-~v~G~v~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~Gd~v~vkI~~vd~~   70 (99)
T cd04460           1 EVVEGEVVEVVDFGAFVRIG-PVDGLLHISQIMDDYISYDPKNKRLIGEETKRVLKVGDVVRARIVAVSLK   70 (99)
T ss_pred             CEEEEEEEEEEeccEEEEEc-CeEEEEEEEEccCCceEechhheeecccCcCCEECCCCEEEEEEEEEeHH
Confidence            47899999999999999998 5999999997641                  3479999999999999975

S1-like RNA-binding domains are found in a wide variety of RNA-associated proteins. RpoE is subunit E of archaeal RNA polymerase. Archaeal cells contain a single RNA polymerase made up of 12 subunits, which are homologous to the 12 subunits (RPB1-12) of eukaryotic RNA polymerase II. RpoE is homologous to Rpa43 of eukaryotic RNA polymerase I, RPB7 of eukaryotic RNA polymerase II, and Rpc25 of eukaryotic RNA polymerase III. RpoE is composed of two domains, the N-terminal RNP (ribonucleoprotein) domain and the C-terminal S1 domain. This S1 domain binds ssRNA and ssDNA. This family is classified based on the C-terminal S1 domain. The function of RpoE is not fully understood. In eukaryotes, RPB7 and RPB4 form a heterodimer that reversibly associates with the RNA polymerase II core.

>PHA02858 EIF2a-like PKR inhibitor; Provisional

Probab=97.90  E-value=2.2e-05  Score=69.01  Aligned_cols=70  Identities=17%  Similarity=0.312  Sum_probs=64.2

Q ss_pred             ccccCcEEEEEEEEEeeceEEEEEcC-CeEEEEe-cccCCCccccccccccccCCEEEEEEEEEcc-CCceEEEE
Q 002054          680 EIEVGGIYKGVVTSVKEYGAFVEFNG-GQQGLLH-VSELSHEPVSRVSDVVSVGQQLSLRCIGQDV-RGNIKLSL  751 (974)
Q Consensus       680 ~~~~G~i~~G~V~~i~~~G~fV~l~~-g~~Glvh-isels~~~v~~~~~~~~vGd~V~vkVl~id~-~gri~LS~  751 (974)
                      -|++|+++. .|+.+.+.|++|.|.. +.+|++. .+|++.+++++..+.+ +|..+.|+|+.+|. +|-|.||.
T Consensus        13 ~P~v~dvv~-~Vv~i~d~~~YV~LleY~iegmIl~~selsr~rirsi~kll-VGk~e~v~ViRVDk~KGYIDLs~   85 (86)
T PHA02858         13 FPNINEVTK-GIVFVKDNIFYVKLIDYGLEALIVNYVNVNADRAEKLKKKL-VGKTINVQVIRTDKLKGYIDVRH   85 (86)
T ss_pred             cCCCCeEEE-EEEEEeccEEEEEEecCccceEEecHHHHhHHHHHhhhhhh-cCCeeEEEEEEECCCCCEEEeEc
Confidence            478999999 8889999999999954 6899988 9999999999999999 99999999999998 89999984

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

Probab=97.89  E-value=1.5e-05  Score=76.83  Aligned_cols=54  Identities=22%  Similarity=0.478  Sum_probs=50.3

Q ss_pred             cchhhhhcCCCccchhhhhhhhCceEEee-C-----------------------CEEEEEecC--HHHHHHHHHHHHHHh
Q 002054          624 NDTLRRLIGPLGALKRKIEEETGGRISVS-D-----------------------GTLTVVAKN--RSVMEKVLEKVDFII  677 (974)
Q Consensus       624 ~~ki~~vIg~gGk~i~~i~~~~g~~Idi~-d-----------------------g~v~i~~~~--~~~~~~a~~~i~~l~  677 (974)
                      -.+|+.+|||||+++|.|+++||++|+|. +                       +.|.|++.+  .+.+++|.+.|+.++
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            36899999999999999999999999997 5                       789999999  999999999999887

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.

>PRK04163 exosome complex RNA-binding protein Rrp4; Provisional

Probab=97.83  E-value=6.7e-05  Score=80.97  Aligned_cols=65  Identities=22%  Similarity=0.247  Sum_probs=58.1

Q ss_pred             CCCCCEEEEEEEEEeCCeEEEEeCCCeEEEEecccCCC-----------CCCCCCCEEEEEEEEEeCCCceeeeec
Q 002054          908 LKLGTKVAAKVYQVRARGLVLDLGGGIRGMYRFENNEK-----------KDFVVGDELLVKCSSFTGKGIPVVSLV  972 (974)
Q Consensus       908 ~~vG~vV~G~V~~I~~~GvFV~L~~gv~Glih~se~~~-----------~~f~vGd~V~vkVl~id~~~~~~~~~~  972 (974)
                      .++||+|.|+|.+++++|+||+++.++.|++|.+++..           ..|++||.|.|+|+++++++.+.+|+.
T Consensus        61 P~vGDiViG~V~~i~~~~~~vdI~~~~~g~L~~s~i~~~~~~~d~~~~~~~~~~GDlV~akV~~i~~~~~~~LS~k  136 (235)
T PRK04163         61 PKVGDLVIGKVTDVTFSGWEVDINSPYKAYLPVSEVLGRPVNVEGTDLRKYLDIGDYIIAKVKDVDRTRDVVLTLK  136 (235)
T ss_pred             CCCCCEEEEEEEEEeCceEEEEeCCCceeEEEHHHcCCCccccchhhhHhhCCCCCEEEEEEEEECCCCcEEEEEc
Confidence            37999999999999999999999999999999997642           248999999999999999888888865

>COG2183 Tex Transcriptional accessory protein [Transcription]

Probab=97.80  E-value=2.5e-05  Score=94.21  Aligned_cols=69  Identities=23%  Similarity=0.246  Sum_probs=59.8

Q ss_pred             ccccCCCCCEEEEEEEEEeCCeEEEEeCCCeEEEEecccC-------CCCCCCCCCEEEEEEEEEeCCCce-eeeec
Q 002054          904 SAKNLKLGTKVAAKVYQVRARGLVLDLGGGIRGMYRFENN-------EKKDFVVGDELLVKCSSFTGKGIP-VVSLV  972 (974)
Q Consensus       904 ~~~~~~vG~vV~G~V~~I~~~GvFV~L~~gv~Glih~se~-------~~~~f~vGd~V~vkVl~id~~~~~-~~~~~  972 (974)
                      ...++++|+++.|+|+++.+||+||+++=..+|++|+|++       |.+.+++||.|+|+|++||.+++- -+|+.
T Consensus       652 ~i~dLk~Gm~leg~Vrnv~~fgafVdIgv~qDglvHis~ls~~fv~~P~~vv~vGdiV~v~V~~vD~~r~rI~Lsmr  728 (780)
T COG2183         652 SITDLKPGMILEGTVRNVVDFGAFVDIGVHQDGLVHISQLSDKFVKDPNEVVKVGDIVKVKVIEVDTARKRIALSMR  728 (780)
T ss_pred             hHhhccCCCEEEEEEEEeeeccceEEeccccceeeeHHHhhhhhcCChHHhcccCCEEEEEEEEEecccCeeeeEee
Confidence            4669999999999999999999999999999999999966       356788999999999999976543 34544

>TIGR02063 RNase_R ribonuclease R

Probab=97.79  E-value=5.1e-05  Score=94.68  Aligned_cols=65  Identities=23%  Similarity=0.329  Sum_probs=56.4

Q ss_pred             cCCCCCEEEEEEEEEeCCeEEEEeCC-CeEEEEecccCCC------------------CCCCCCCEEEEEEEEEeC-CCc
Q 002054          907 NLKLGTKVAAKVYQVRARGLVLDLGG-GIRGMYRFENNEK------------------KDFVVGDELLVKCSSFTG-KGI  966 (974)
Q Consensus       907 ~~~vG~vV~G~V~~I~~~GvFV~L~~-gv~Glih~se~~~------------------~~f~vGd~V~vkVl~id~-~~~  966 (974)
                      .-++|++++|+|.+|++||+||+|++ ++.||+|+++++.                  +.|++||+|+|+|.++|. ++.
T Consensus       624 ~~~iG~~~~g~V~~v~~fGifV~L~~~~~eGlvhis~l~~d~~~~d~~~~~l~g~~~~~~~~lGd~V~Vkv~~vd~~~~~  703 (709)
T TIGR02063       624 SEKIGEEFEGVISGVTSFGLFVELENNTIEGLVHISTLKDDYYVFDEKGLALVGERTGKVFRLGDRVKVRVVKADLDTGK  703 (709)
T ss_pred             hccCCcEEEEEEEEEEeCCEEEEecCCceEEEEEeeecCCCcEEEcccceEEEeccCCcEECCCCEEEEEEEEEecccCe
Confidence            34689999999999999999999998 8999999997741                  358999999999999997 566


Q ss_pred             eeeee
Q 002054          967 PVVSL  971 (974)
Q Consensus       967 ~~~~~  971 (974)
                      ..++|
T Consensus       704 I~~~l  708 (709)
T TIGR02063       704 IDFEL  708 (709)
T ss_pred             EEEEE
Confidence            66665

This family consists of an exoribonuclease, ribonuclease R, also called VacB. It is one of the eight exoribonucleases reported in E. coli and is broadly distributed throughout the bacteria. In E. coli, double mutants of this protein and polynucleotide phosphorylase are not viable. Scoring between trusted and noise cutoffs to the model are shorter, divergent forms from the Chlamydiae, and divergent forms from the Campylobacterales (including Helicobacter pylori) and Leptospira interrogans.

>PF13509 S1_2: S1 domain; PDB: 3GO5_A

Probab=97.79  E-value=8.4e-05  Score=62.98  Aligned_cols=61  Identities=26%  Similarity=0.390  Sum_probs=38.8

Q ss_pred             cCcEEEEEEEEEeeceEEEEEcCCeEEEEecccCCCccccccccccccCCEEEEEEEEEccCCceEEEEe
Q 002054          683 VGGIYKGVVTSVKEYGAFVEFNGGQQGLLHVSELSHEPVSRVSDVVSVGQQLSLRCIGQDVRGNIKLSLK  752 (974)
Q Consensus       683 ~G~i~~G~V~~i~~~G~fV~l~~g~~Glvhisels~~~v~~~~~~~~vGd~V~vkVl~id~~gri~LS~K  752 (974)
                      +|++.+.+|+++.++|+|++...+.+-|||.+|+...        +++||.|.|.|+. |.++++..|+|
T Consensus         1 iG~~~~L~V~~~~~~g~fL~~~~~~~vlLp~~e~~~~--------~~~Gd~v~VFvY~-D~~~rl~AT~k   61 (61)
T PF13509_consen    1 IGQINTLKVVDKNEFGYFLDDGEGKEVLLPKSEVPEP--------LKVGDEVEVFVYL-DKEGRLVATTK   61 (61)
T ss_dssp             --------EEEE-SSEEEEEETT-EEEEEEGGG--------------TTSEEEEEEEE--TTS-EEEE--
T ss_pred             CCCCcceEEEEEeCCEEEEECCCCCEEEechHHcCCC--------CCCCCEEEEEEEE-CCCCCEEEecC
Confidence            5889999999999999999987779999999998654        8999999999998 88899999876

>TIGR01953 NusA transcription termination factor NusA

Probab=97.74  E-value=4.2e-05  Score=86.43  Aligned_cols=94  Identities=16%  Similarity=0.173  Sum_probs=69.1

Q ss_pred             cccccCCeEEEEEEEeecCCCCcCcccccc-----cccc--ccccC--CCCCEEEEEEEEEeCCe-EEEEeCCCeEEEEe
Q 002054          870 TSFSQREREELAECLFGTEDGDEDNKGTRV-----EAIV--SAKNL--KLGTKVAAKVYQVRARG-LVLDLGGGIRGMYR  939 (974)
Q Consensus       870 ~~~k~Gq~v~~~Vl~vd~e~~~i~slK~~~-----~~p~--~~~~~--~vG~vV~G~V~~I~~~G-vFV~L~~gv~Glih  939 (974)
                      ..+++||.++..+..-+..+.-+.+.|+..     ..-+  .+..|  +.|++|+|+|.++.+.| +||+++ ++.|++|
T Consensus        82 ~~~~vGD~I~~~I~~~~fgR~aaq~aKqvi~Qkire~ere~i~~ey~~k~GeiV~G~V~~v~~~g~v~VdiG-~~ea~LP  160 (341)
T TIGR01953        82 PDVQIGDEVKKEIPPENFGRIAAQTAKQVILQKIREAERERVYDEFSSKEGEIISGTVKRVNRRGNLYVELG-KTEGILP  160 (341)
T ss_pred             cccccCCEEEEEecccCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhcCCEEEEEEEEEecCCcEEEEEC-CeEEEec
Confidence            468889998877743332221111455421     1111  35566  59999999999999988 799995 9999999


Q ss_pred             cccC-CCCCCCCCCEEEEEEEEEeCC
Q 002054          940 FENN-EKKDFVVGDELLVKCSSFTGK  964 (974)
Q Consensus       940 ~se~-~~~~f~vGd~V~vkVl~id~~  964 (974)
                      .+++ +.+.|++||+++|.|++|+.+
T Consensus       161 ~~E~ip~E~~~~Gd~ik~~V~~V~~~  186 (341)
T TIGR01953       161 KKEQIPGEKFRIGDRIKAYVYEVRKT  186 (341)
T ss_pred             HHHcCCCcCCCCCCEEEEEEEEEEcC
Confidence            9987 467899999999999999954

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.

>PRK12327 nusA transcription elongation factor NusA; Provisional

Probab=97.71  E-value=4.8e-05  Score=86.47  Aligned_cols=95  Identities=12%  Similarity=0.101  Sum_probs=69.2

Q ss_pred             cccccCCeEEEEEEEeecCCCCcCccccccccc-------cccccC--CCCCEEEEEEEEEeCCeEEEEeCCCeEEEEec
Q 002054          870 TSFSQREREELAECLFGTEDGDEDNKGTRVEAI-------VSAKNL--KLGTKVAAKVYQVRARGLVLDLGGGIRGMYRF  940 (974)
Q Consensus       870 ~~~k~Gq~v~~~Vl~vd~e~~~i~slK~~~~~p-------~~~~~~--~vG~vV~G~V~~I~~~GvFV~L~~gv~Glih~  940 (974)
                      ...++|+.++..+-..+..+..+...|+....-       -.+..|  +.|++|+|+|+++.+.|+||+++ ++.|++|.
T Consensus        85 ~~~~vGD~i~~~I~~~~fgR~aaq~akqvI~Qkire~ere~v~~ef~~k~GeiV~G~V~~~~~~~~~Vdlg-~vEa~LP~  163 (362)
T PRK12327         85 PAYELGDVIEIEVTPKDFGRIAAQTAKQVIMQRLREAEREIIYNEFSEREGDIVTGVVQRRDNRFVYVNLG-KIEAVLPP  163 (362)
T ss_pred             ccccCCCEEEEecCcCCCChHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCEEEEEEEEEeCCcEEEEeC-CeEEEecH
Confidence            356788888776644333322222333321111       136777  99999999999999999999996 69999997


Q ss_pred             ccC-CCCCCCCCCEEEEEEEEEeCCC
Q 002054          941 ENN-EKKDFVVGDELLVKCSSFTGKG  965 (974)
Q Consensus       941 se~-~~~~f~vGd~V~vkVl~id~~~  965 (974)
                      +++ +...|++||+++|.|++|+.+.
T Consensus       164 ~E~ip~e~~~~Gd~Ika~V~~V~~~~  189 (362)
T PRK12327        164 AEQIPGETYKHGDRIKVYVVKVEKTT  189 (362)
T ss_pred             HHcCCCCCCCCCCEEEEEEEEEecCC
Confidence            755 6788999999999999999543

>TIGR01953 NusA transcription termination factor NusA

Probab=97.65  E-value=0.00023  Score=80.50  Aligned_cols=66  Identities=24%  Similarity=0.342  Sum_probs=57.8

Q ss_pred             ccCcEEEEEEEEEeece-EEEEEcCCeEEEEecccCCCccccccccccccCCEEEEEEEEEcc---CCceEEEEecc
Q 002054          682 EVGGIYKGVVTSVKEYG-AFVEFNGGQQGLLHVSELSHEPVSRVSDVVSVGQQLSLRCIGQDV---RGNIKLSLKAV  754 (974)
Q Consensus       682 ~~G~i~~G~V~~i~~~G-~fV~l~~g~~Glvhisels~~~v~~~~~~~~vGd~V~vkVl~id~---~gri~LS~K~~  754 (974)
                      +.|++++|+|.++.+.| +||++ ++.+|+||.+|...      .+.|++||.++|.|++++.   .+.+.||++..
T Consensus       130 k~GeiV~G~V~~v~~~g~v~Vdi-G~~ea~LP~~E~ip------~E~~~~Gd~ik~~V~~V~~~~kg~qIivSRt~~  199 (341)
T TIGR01953       130 KEGEIISGTVKRVNRRGNLYVEL-GKTEGILPKKEQIP------GEKFRIGDRIKAYVYEVRKTAKGPQIILSRTHP  199 (341)
T ss_pred             hcCCEEEEEEEEEecCCcEEEEE-CCeEEEecHHHcCC------CcCCCCCCEEEEEEEEEEcCCCCCeEEEEeCcH
Confidence            59999999999999988 69999 68999999999873      4559999999999999985   24799999863

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.

>PRK12327 nusA transcription elongation factor NusA; Provisional

Probab=97.58  E-value=0.00031  Score=80.02  Aligned_cols=68  Identities=21%  Similarity=0.317  Sum_probs=58.5

Q ss_pred             ccc--ccCcEEEEEEEEEeeceEEEEEcCCeEEEEecccCCCccccccccccccCCEEEEEEEEEcc--CC-ceEEEEec
Q 002054          679 REI--EVGGIYKGVVTSVKEYGAFVEFNGGQQGLLHVSELSHEPVSRVSDVVSVGQQLSLRCIGQDV--RG-NIKLSLKA  753 (974)
Q Consensus       679 ~~~--~~G~i~~G~V~~i~~~G~fV~l~~g~~Glvhisels~~~v~~~~~~~~vGd~V~vkVl~id~--~g-ri~LS~K~  753 (974)
                      .++  +.|++++|+|.++.++|+||++ ++.+|+||.+++..      .+.|++||.++|.|++++.  +| .|.||+..
T Consensus       128 ~ef~~k~GeiV~G~V~~~~~~~~~Vdl-g~vEa~LP~~E~ip------~e~~~~Gd~Ika~V~~V~~~~kgp~IivSRt~  200 (362)
T PRK12327        128 NEFSEREGDIVTGVVQRRDNRFVYVNL-GKIEAVLPPAEQIP------GETYKHGDRIKVYVVKVEKTTKGPQIFVSRTH  200 (362)
T ss_pred             HHHHHhcCCEEEEEEEEEeCCcEEEEe-CCeEEEecHHHcCC------CCCCCCCCEEEEEEEEEecCCCCCeEEEEeCC
Confidence            346  8999999999999999999999 57999999888743      5669999999999999986  33 69999854

>PRK11642 exoribonuclease R; Provisional

Probab=97.56  E-value=0.00019  Score=90.00  Aligned_cols=65  Identities=17%  Similarity=0.283  Sum_probs=55.4

Q ss_pred             CCCCEEEEEEEEEeCCeEEEEeCC-CeEEEEecccCC------------------CCCCCCCCEEEEEEEEEeC-CCcee
Q 002054          909 KLGTKVAAKVYQVRARGLVLDLGG-GIRGMYRFENNE------------------KKDFVVGDELLVKCSSFTG-KGIPV  968 (974)
Q Consensus       909 ~vG~vV~G~V~~I~~~GvFV~L~~-gv~Glih~se~~------------------~~~f~vGd~V~vkVl~id~-~~~~~  968 (974)
                      ++|++++|+|.+|++||+||+|++ ++.||||.+++.                  .+.|++||+|+|+|.++|. ++...
T Consensus       642 ~iGe~f~G~Is~V~~fGifVeL~~~~vEGlV~vs~L~~d~y~~d~~~~~L~g~~~~~~~~lGD~V~VkV~~vD~~~rkI~  721 (813)
T PRK11642        642 QVGNVFKGVISSVTGFGFFVRLDDLFIDGLVHVSSLDNDYYRFDQVGQRLIGESSGQTYRLGDRVEVRVEAVNMDERKID  721 (813)
T ss_pred             cCCcEEEEEEEEeecCceEEEECCCCeeeeEEEeecCCcceEecchheEEecccCCcEECCCCEEEEEEEEeecCCCeEE
Confidence            789999999999999999999998 599999999663                  2459999999999999996 45566


Q ss_pred             eeecC
Q 002054          969 VSLVD  973 (974)
Q Consensus       969 ~~~~~  973 (974)
                      ++++.
T Consensus       722 f~l~~  726 (813)
T PRK11642        722 FSLIS  726 (813)
T ss_pred             EEEec
Confidence            66653

>cd02394 vigilin_like_KH K homology RNA-binding domain_vigilin_like

Probab=97.56  E-value=0.00014  Score=61.53  Aligned_cols=55  Identities=31%  Similarity=0.430  Sum_probs=47.4

Q ss_pred             eeeeeccchhhhhcCCCccchhhhhhhhCceEEee-----CCEEEEEecCHHHHHHHHHHH
Q 002054          618 ATLKYDNDTLRRLIGPLGALKRKIEEETGGRISVS-----DGTLTVVAKNRSVMEKVLEKV  673 (974)
Q Consensus       618 ~~~~i~~~ki~~vIg~gGk~i~~i~~~~g~~Idi~-----dg~v~i~~~~~~~~~~a~~~i  673 (974)
                      ..+.||+++++.+||++|++|++|++++|++|++.     ++.|.|.++ .+.+..|..++
T Consensus         2 ~~i~Vp~~~~~~iIG~~G~~i~~i~~~~g~~I~i~~~~~~~~~v~I~G~-~~~v~~A~~~i   61 (62)
T cd02394           2 EEVEIPKKLHRFIIGKKGSNIRKIMEETGVKIRFPDPGSKSDTITITGP-KENVEKAKEEI   61 (62)
T ss_pred             eEEEeCHHHhhhccCCCCCcHHHHHHHhCCEEEcCCCCCCCCEEEEEcC-HHHHHHHHHHh
Confidence            46789999999999999999999999999999985     378999987 56777776654

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.

>TIGR00757 RNaseEG ribonuclease, Rne/Rng family

Probab=97.55  E-value=0.00018  Score=83.69  Aligned_cols=63  Identities=27%  Similarity=0.467  Sum_probs=54.5

Q ss_pred             ccccCcEEEEEEEEEeec--eEEEEEcCCeEEEEecccCCCc------------cccccccccccCCEEEEEEEEEcc
Q 002054          680 EIEVGGIYKGVVTSVKEY--GAFVEFNGGQQGLLHVSELSHE------------PVSRVSDVVSVGQQLSLRCIGQDV  743 (974)
Q Consensus       680 ~~~~G~i~~G~V~~i~~~--G~fV~l~~g~~Glvhisels~~------------~v~~~~~~~~vGd~V~vkVl~id~  743 (974)
                      ...+|.+|.|+|+++.++  ||||+|+.+..||+|++++.+.            +..++.+.+++||.|.|.|.. ++
T Consensus        22 ~~~vGnIY~GrV~~i~p~l~aAFVdiG~~k~gfL~~~d~~~~~~~~~~~~~~~~~~~~i~~~l~~G~~IlVQV~K-e~   98 (414)
T TIGR00757        22 RQLKGNIYKGRVTRILPSLQAAFVDIGLEKNGFLHASDIGPNYECLAPAEAKREAGPSISELLRPGQSVLVQVVK-EP   98 (414)
T ss_pred             cCCCCCEEEEEEeeecCCCceEEEEcCCCceEEEEHHHcCchhhccccccccccccCCHHHhCcCCCEEEEEEee-CC
Confidence            456899999999999999  9999999999999999999653            234566779999999999999 54

The C-terminal half of RNase E (excluded from the seed alignment for this model) lacks ribonuclease activity but participates in mRNA degradation by organizing the degradosome.

>KOG2916 consensus Translation initiation factor 2, alpha subunit (eIF-2alpha) [Translation, ribosomal structure and biogenesis]

Probab=97.54  E-value=4.7e-05  Score=80.28  Aligned_cols=78  Identities=31%  Similarity=0.463  Sum_probs=73.2

Q ss_pred             ccccCcEEEEEEEEEeeceEEEEE--cCCeEEEEecccCCCccccccccccccCCEEEEEEEEEcc-CCceEEEEeccCC
Q 002054          680 EIEVGGIYKGVVTSVKEYGAFVEF--NGGQQGLLHVSELSHEPVSRVSDVVSVGQQLSLRCIGQDV-RGNIKLSLKAVSP  756 (974)
Q Consensus       680 ~~~~G~i~~G~V~~i~~~G~fV~l--~~g~~Glvhisels~~~v~~~~~~~~vGd~V~vkVl~id~-~gri~LS~K~~~~  756 (974)
                      -+++++++-+.|.+|.+-|+||.|  ++.++|++-.||||.+|++++..+.++|..=-|.|+.+|. +|-|.||.+.+.+
T Consensus        13 yPev~e~VmvnV~sIaemGayv~LlEYnniEGmiLlsELSrRRIRSI~klirVGr~E~vvVlrVDkekGYIDLSkrrVs~   92 (304)
T KOG2916|consen   13 YPEVEEIVMVNVRSIAEMGAYVKLLEYNNIEGMILLSELSRRRIRSIQKLIRVGRNEPVVVLRVDKEKGYIDLSKRRVSP   92 (304)
T ss_pred             CCCcccEEEEEeeEehhccceEeeeecCCcccchhhhHHHHHHHHHHHHHHhcCCcceEEEEEEcCCCCceechhccCCH
Confidence            479999999999999999999999  4689999999999999999999999999999999999998 8999999998876


Q ss_pred             C
Q 002054          757 R  757 (974)
Q Consensus       757 ~  757 (974)
                      +
T Consensus        93 e   93 (304)
T KOG2916|consen   93 E   93 (304)
T ss_pred             H
Confidence            4

>cd05790 S1_Rrp40 S1_Rrp40: Rrp40 S1-like RNA-binding domain

Probab=97.49  E-value=0.00049  Score=62.27  Aligned_cols=73  Identities=16%  Similarity=0.115  Sum_probs=63.8

Q ss_pred             cccCcEEEEEEEEEeeceEEEEEcCCeEEEEecccCCCccccccccccccCCEEEEEEEEEccCCceEEEEecc
Q 002054          681 IEVGGIYKGVVTSVKEYGAFVEFNGGQQGLLHVSELSHEPVSRVSDVVSVGQQLSLRCIGQDVRGNIKLSLKAV  754 (974)
Q Consensus       681 ~~~G~i~~G~V~~i~~~G~fV~l~~g~~Glvhisels~~~v~~~~~~~~vGd~V~vkVl~id~~gri~LS~K~~  754 (974)
                      +++|+.+-|+|+++....++|+|.....|++|.+++... .++....|++||-|-++|..+|+.....||+...
T Consensus         4 P~~gD~VIG~V~~~~~~~~~VdI~s~~~a~L~~~~f~ga-tk~~rp~L~~GDlV~ArV~~~~~~~~~eLtc~~~   76 (86)
T cd05790           4 PAKGDHVIGIVVAKAGDFFKVDIGGSEPASLSYLAFEGA-TKRNRPNLNVGDLVYARVVKANRDMEPELSCVDS   76 (86)
T ss_pred             CCCCCEEEEEEEEEcCCeEEEEcCCCcceEechHHcccc-cccccccCCCCCEEEEEEEecCCCCCeEEEEeCC
Confidence            789999999999999999999998888999999887543 4445667999999999999999888899999863

S1-like RNA-binding domains are found in a wide variety of RNA-associated proteins. Rrp4 protein is a subunit of the exosome complex. The exosome plays a central role in 3' to 5' RNA processing and degradation in eukarytes and archaea. Its functions include the removal of incorrectly processed RNA and the maintenance of proper levels of mRNA, rRNA and a number of small RNA species. In Saccharomyces cerevisiae, the exosome includes nine core components, six of which are homologous to bacterial RNase PH. These form a hexameric ring structure. The other three subunits (RrP4, Rrp40, and Csl4) contain an S1 RNA binding domain and are part of the "S1 pore structure".

>cd05791 S1_CSL4 S1_CSL4: CSL4, S1-like RNA-binding domain

Probab=97.49  E-value=0.00041  Score=63.84  Aligned_cols=64  Identities=28%  Similarity=0.307  Sum_probs=55.9

Q ss_pred             CCCCEEEEEEEEEeCCeEEEEe--------CCCeEEEEecccCC---------CCCCCCCCEEEEEEEEEeCCCceeeee
Q 002054          909 KLGTKVAAKVYQVRARGLVLDL--------GGGIRGMYRFENNE---------KKDFVVGDELLVKCSSFTGKGIPVVSL  971 (974)
Q Consensus       909 ~vG~vV~G~V~~I~~~GvFV~L--------~~gv~Glih~se~~---------~~~f~vGd~V~vkVl~id~~~~~~~~~  971 (974)
                      ++|++|-|+|.+++...++|++        ...+.|++|.++..         .+.|++||-|+|+|++++......+|.
T Consensus         5 ~~GDiVig~V~~v~~~~~~v~I~~v~~~~l~~~~~g~l~~~dv~~~~~d~~~~~~~f~~GDiV~AkVis~~~~~~~~Lst   84 (92)
T cd05791           5 KVGSIVIARVTRINPRFAKVDILCVGGRPLKESFRGVIRKEDIRATEKDKVEMYKCFRPGDIVRAKVISLGDASSYYLST   84 (92)
T ss_pred             CCCCEEEEEEEEEcCCEEEEEEEEecCeecCCCcccEEEHHHccccccchHHHHhhcCCCCEEEEEEEEcCCCCCcEEEe
Confidence            7999999999999999999999        77899999988652         356999999999999998766677776


Q ss_pred             c
Q 002054          972 V  972 (974)
Q Consensus       972 ~  972 (974)
                      .
T Consensus        85 ~   85 (92)
T cd05791          85 A   85 (92)
T ss_pred             c
Confidence            4

S1-like RNA-binding domains are found in a wide variety of RNA-associated proteins. ScCSL4 protein is a subunit of the exosome complex. The exosome plays a central role in 3' to 5' RNA processing and degradation in eukarytes and archaea. Its functions include the removal of incorrectly processed RNA and the maintenance of proper levels of mRNA, rRNA and a number of small RNA species. In S. cerevisiae, the exosome includes nine core components, six of which are homologous to bacterial RNase PH. These form a hexameric ring structure. The other three subunits (RrP4, Rrp40, and Csl4) contain an S1 RNA binding domain and are part of the "S1 pore structure".

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

Probab=97.48  E-value=0.00041  Score=73.38  Aligned_cols=88  Identities=20%  Similarity=0.305  Sum_probs=74.4

Q ss_pred             ccccCcEEEEEEEEEeeceEEEEEcCCeEEEEecccCCCccc----cccccccccCCEEEEEEEEEccCCceEEEEeccC
Q 002054          680 EIEVGGIYKGVVTSVKEYGAFVEFNGGQQGLLHVSELSHEPV----SRVSDVVSVGQQLSLRCIGQDVRGNIKLSLKAVS  755 (974)
Q Consensus       680 ~~~~G~i~~G~V~~i~~~G~fV~l~~g~~Glvhisels~~~v----~~~~~~~~vGd~V~vkVl~id~~gri~LS~K~~~  755 (974)
                      .+++||++-|+|..+...++.|+|.....+++|.|++-++.+    .+...+|++||-|.+||..+|..+...|++|.. 
T Consensus        61 iP~~gD~VIG~I~~v~~~~W~VDI~sp~~A~L~ls~~~~r~~~~~~~~~r~~l~vGD~v~AkV~~vd~~~~~~L~~k~~-  139 (239)
T COG1097          61 IPEVGDVVIGKIIEVGPSGWKVDIGSPYPALLSLSDFLRRKFENAEKDLRPFLNVGDLVYAKVVDVDRDGEVELTLKDE-  139 (239)
T ss_pred             cCCCCCEEEEEEEEEcccceEEEcCCccceEeehhhhhcccccccccccccccccCCEEEEEEEEccCCCceEEEeecC-
Confidence            479999999999999999999999888999999999966553    467788999999999999999999999999653 


Q ss_pred             CCcccccCceEEEEEeec
Q 002054          756 PRPEADVKGVVEGSVPVN  773 (974)
Q Consensus       756 ~~~~~~~g~~~~G~vv~i  773 (974)
                           ..|....|.++.+
T Consensus       140 -----~~GkL~~G~iv~i  152 (239)
T COG1097         140 -----GLGKLKNGQIVKI  152 (239)
T ss_pred             -----CCccccCCEEEEE
Confidence                 3444556666663

>COG2996 Predicted RNA-bindining protein (contains S1 and HTH domains) [General function prediction only]

Probab=97.45  E-value=0.00016  Score=77.21  Aligned_cols=94  Identities=23%  Similarity=0.290  Sum_probs=71.2

Q ss_pred             cCcEEEEEEEEEeeceEEEEEcCCeEEEEecccCCCccccccccccccCCEEEEEEEEEccCCceEEEEeccCCCccccc
Q 002054          683 VGGIYKGVVTSVKEYGAFVEFNGGQQGLLHVSELSHEPVSRVSDVVSVGQQLSLRCIGQDVRGNIKLSLKAVSPRPEADV  762 (974)
Q Consensus       683 ~G~i~~G~V~~i~~~G~fV~l~~g~~Glvhisels~~~v~~~~~~~~vGd~V~vkVl~id~~gri~LS~K~~~~~~~~~~  762 (974)
                      .|+.+.|+|.++...|.||-+.+++-||||-||....        .++|+.++++|+++.++|+|.||++....+.-..-
T Consensus       155 ~nq~v~~tVYr~~~~G~fv~~e~~~~GfIh~sEr~~~--------prlG~~l~~rVi~~reDg~lnLSl~p~~~E~l~~d  226 (287)
T COG2996         155 KNQEVDATVYRLLESGTFVITENGYLGFIHKSERFAE--------PRLGERLTARVIGVREDGKLNLSLRPRAHEMLDED  226 (287)
T ss_pred             hcCeeeeEEEEEeccceEEEEcCCeEEEEcchhhccc--------ccCCceEEEEEEEEccCCeeecccccccHHhhhhh
Confidence            4899999999999999999999999999999997655        78899999999999889999999987644332222


Q ss_pred             CceEEEEEeecCCcceeeEEeeccCC
Q 002054          763 KGVVEGSVPVNKQATDVWASVGDVSN  788 (974)
Q Consensus       763 g~~~~G~vv~i~~gv~~~~~~~~l~~  788 (974)
                      .++......+    ..|+.++++=+.
T Consensus       227 aq~Il~yL~~----~gG~mpf~DKSs  248 (287)
T COG2996         227 AQMILTYLES----NGGFMPFNDKSS  248 (287)
T ss_pred             HHHHHHHHHH----cCCccccCCCCC
Confidence            2222222223    456666665443

>TIGR00448 rpoE DNA-directed RNA polymerase (rpoE), archaeal and eukaryotic form

Probab=97.38  E-value=0.0006  Score=70.68  Aligned_cols=53  Identities=23%  Similarity=0.419  Sum_probs=47.2

Q ss_pred             CCCCEEEEEEEEEeCCeEEEEeCCCeEEEEecccCC------------------CCCCCCCCEEEEEEEEEe
Q 002054          909 KLGTKVAAKVYQVRARGLVLDLGGGIRGMYRFENNE------------------KKDFVVGDELLVKCSSFT  962 (974)
Q Consensus       909 ~vG~vV~G~V~~I~~~GvFV~L~~gv~Glih~se~~------------------~~~f~vGd~V~vkVl~id  962 (974)
                      .+|+++.|+|.+++++|+||+++ .++|++|.+++.                  ...|+.||+|++||.++|
T Consensus        80 ~~gEvv~G~V~~v~~~GifV~lg-~~~gi~~~~~l~~~~~~~d~~~~~~~~~~~~~~~~~Gd~VrvrV~~v~  150 (179)
T TIGR00448        80 ELGEIVEGEVIEIVEFGAFVSLG-PFDGLFHVSQVTDDYCYYDPKESALIGKETKKVLDEGDKVRARIVALS  150 (179)
T ss_pred             cCCCEEEEEEEEEEeeEEEEEeC-CceEEEEcHHhCCCceEEccccceEEEccCCeEEcCCCEEEEEEEEEE
Confidence            47999999999999999999995 699999999652                  135899999999999998

This family seems to be confined to the archea and eukaryotic taxa and are quite dissimilar to E.coli rpoE.

>PF00013 KH_1: KH domain syndrome, contains KH motifs

Probab=97.36  E-value=0.00031  Score=59.10  Aligned_cols=55  Identities=27%  Similarity=0.455  Sum_probs=48.4

Q ss_pred             eeeeeccchhhhhcCCCccchhhhhhhhCceEEeeC----CEEEEEecCHHHHHHHHHHH
Q 002054          618 ATLKYDNDTLRRLIGPLGALKRKIEEETGGRISVSD----GTLTVVAKNRSVMEKVLEKV  673 (974)
Q Consensus       618 ~~~~i~~~ki~~vIg~gGk~i~~i~~~~g~~Idi~d----g~v~i~~~~~~~~~~a~~~i  673 (974)
                      ..+.+|++.++.+||++|.++++|++++|++|.+.+    ..+.+.+ +.+..++|+++|
T Consensus         2 ~~i~vp~~~~~~iIG~~G~~i~~I~~~t~~~I~i~~~~~~~~v~I~G-~~~~v~~A~~~I   60 (60)
T PF00013_consen    2 ERIEVPSSLVGRIIGKKGSNIKEIEEETGVKIQIPDDDERDIVTISG-SPEQVEKAKKMI   60 (60)
T ss_dssp             EEEEEEHHHHHHHHTGGGHHHHHHHHHHTSEEEEESTTEEEEEEEEE-SHHHHHHHHHHH
T ss_pred             EEEEECHHHcCEEECCCCCcHHHhhhhcCeEEEEcCCCCcEEEEEEe-CHHHHHHHHhhC
Confidence            467899999999999999999999999999999984    4788888 888999887754

; 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 ....

>TIGR00358 3_prime_RNase VacB and RNase II family 3'-5' exoribonucleases

Probab=97.36  E-value=0.00046  Score=85.27  Aligned_cols=59  Identities=24%  Similarity=0.423  Sum_probs=51.8

Q ss_pred             CCCCEEEEEEEEEeCCeEEEEeC-CCeEEEEecccCCC------------------CCCCCCCEEEEEEEEEeCCCce
Q 002054          909 KLGTKVAAKVYQVRARGLVLDLG-GGIRGMYRFENNEK------------------KDFVVGDELLVKCSSFTGKGIP  967 (974)
Q Consensus       909 ~vG~vV~G~V~~I~~~GvFV~L~-~gv~Glih~se~~~------------------~~f~vGd~V~vkVl~id~~~~~  967 (974)
                      ++|++++|+|.+|++||+||+|+ .++.||+|.++++.                  ..|++||+|+|+|.++|.....
T Consensus       571 ~iG~~~~g~I~~v~~~GifV~L~~~~veGlV~~s~l~~d~y~~d~~~~~l~g~~~~~~~~lGD~V~Vki~~vd~~~~~  648 (654)
T TIGR00358       571 KVGTEFSGEISSVTRFGMFVRLDDNGIDGLIHISTLHNDYYVFDQEKMALIGKGTGKVYRIGDRVTVKLTEVNMETRS  648 (654)
T ss_pred             CCCcEEEEEEEeEEcCcEEEEecCCceEEEEEeEeCCCcceEEeccccEEEeccCCcEECCCCEEEEEEEEEecccCe
Confidence            57999999999999999999998 58999999996641                  4599999999999999965543

This model is defined to identify a pair of paralogous 3-prime exoribonucleases in E. coli, plus the set of proteins apparently orthologous to one or the other in other eubacteria. VacB was characterized originally as required for the expression of virulence genes, but is now recognized as the exoribonuclease RNase R (Rnr). Its paralog in E. coli and H. influenzae is designated exoribonuclease II (Rnb). Both are involved in the degradation of mRNA, and consequently have strong pleiotropic effects that may be difficult to disentangle. Both these proteins share domain-level similarity (RNB, S1) with a considerable number of other proteins, and full-length similarity scoring below the trusted cutoff to proteins associated with various phenotypes but uncertain biochemistry; it may be that these latter proteins are also 3-prime exoribonucleases.

>PRK05054 exoribonuclease II; Provisional

Probab=97.27  E-value=0.0014  Score=80.77  Aligned_cols=70  Identities=13%  Similarity=0.167  Sum_probs=56.7

Q ss_pred             ccC--cEEEEEEEEEeeceEEEEEcC-CeEEEEecccCCCcc--c--c--------ccccccccCCEEEEEEEEEcc-CC
Q 002054          682 EVG--GIYKGVVTSVKEYGAFVEFNG-GQQGLLHVSELSHEP--V--S--------RVSDVVSVGQQLSLRCIGQDV-RG  745 (974)
Q Consensus       682 ~~G--~i~~G~V~~i~~~G~fV~l~~-g~~Glvhisels~~~--v--~--------~~~~~~~vGd~V~vkVl~id~-~g  745 (974)
                      ++|  +.|.|.|+++++||+||+|.. +++||||++.|.+++  +  .        .-...|++||.|+|+|.++|. ++
T Consensus       558 ~~G~~~~f~g~I~~v~~~G~fV~l~~~~veglV~~~~l~~~~~~y~~~~~~~~~~~~~~~~~~lGd~V~V~v~~vd~~~~  637 (644)
T PRK05054        558 KAGTDTRFAAEIIDISRGGMRVRLLENGAVAFIPASFLHAVRDELVCNQENGTVQIKGETVYKLGDVIDVTLAEVRMETR  637 (644)
T ss_pred             ccCCCeEEEEEEEeeecCcEEEEEeCCceEEEEEccccCCCccceEEccccceEEEeCCEEEcCCCEEEEEEEEEccccC
Confidence            565  599999999999999999954 799999999997642  1  0        112469999999999999997 77


Q ss_pred             ceEEEE
Q 002054          746 NIKLSL  751 (974)
Q Consensus       746 ri~LS~  751 (974)
                      +|.++.
T Consensus       638 ~i~~~~  643 (644)
T PRK05054        638 SIIARP  643 (644)
T ss_pred             eEEEEE
Confidence            887764

>cd04462 S1_RNAPII_Rpb7 S1_RNAPII_Rpb7: Eukaryotic RNA polymerase II (RNAPII) Rpb7 subunit C-terminal S1 domain

Probab=97.25  E-value=0.0011  Score=60.45  Aligned_cols=60  Identities=22%  Similarity=0.280  Sum_probs=49.2

Q ss_pred             cCcEEEEEEEEEeeceEEEEEcCCeEEEEecccCCCcccccc-----------ccccccCCEEEEEEEEEcc
Q 002054          683 VGGIYKGVVTSVKEYGAFVEFNGGQQGLLHVSELSHEPVSRV-----------SDVVSVGQQLSLRCIGQDV  743 (974)
Q Consensus       683 ~G~i~~G~V~~i~~~G~fV~l~~g~~Glvhisels~~~v~~~-----------~~~~~vGd~V~vkVl~id~  743 (974)
                      .|++++|+|+++.++|+||.+. ..++|+|.+++..+..-++           ...++.|+.|++||+++..
T Consensus         1 kgEVi~g~V~~v~~~G~~v~~G-pl~~f~~~~~ip~~~~~~~~~~~~~~~~~~~~~i~~g~~VR~rV~~v~~   71 (88)
T cd04462           1 KGEVVDAIVTSVNKTGFFAEVG-PLSIFISRHLIPSDMEFDPNASPPCFTSNEDIVIKKDTEVRLKIIGTRV   71 (88)
T ss_pred             CCcEEEEEEEEEeccEEEEEEc-CceEEEEeeecCccceECCcCCCCeEeCCCcEEECCCCEEEEEEEEEEE
Confidence            4899999999999999999994 6889999999976543322           3348899999999998753

RNAPII is composed of 12 subunits (Rpb1-12). Rpb4 and Rpb7 form a heterodimer that associate with the RNAPII core. Rpb7 is a homolog of the Rpc25 of RNA polymerase III, RpoE of the archaeal RNA polymerase, and Rpa43 of eukaryotic RNA polymerase I. Rpb7 has two domains, an N-terminal ribonucleoprotein (RNP) domain and a C-terminal S1 domain, both of which bind single-stranded RNA. It is possible that the S1 domain interacts with the nascent RNA transcript, assisted by the RNP domain. In yeast, Rpb4/Rpb7 is necessary for promoter-directed transcription initiation. They also play a role in regulating transcription-coupled repair in the Rad26-dependent pathway, in efficient mRNA export, and in transcription termination.

>COG1096 Predicted RNA-binding protein (consists of S1 domain and a Zn-ribbon domain) [Translation, ribosomal structure and biogenesis]

Probab=97.23  E-value=0.00034  Score=71.12  Aligned_cols=72  Identities=32%  Similarity=0.409  Sum_probs=62.6

Q ss_pred             ccccCcEEEEEEEEEeeceEEEEEcC----------CeEEEEecccCCCccccccccccccCCEEEEEEEEEccCCceEE
Q 002054          680 EIEVGGIYKGVVTSVKEYGAFVEFNG----------GQQGLLHVSELSHEPVSRVSDVVSVGQQLSLRCIGQDVRGNIKL  749 (974)
Q Consensus       680 ~~~~G~i~~G~V~~i~~~G~fV~l~~----------g~~Glvhisels~~~v~~~~~~~~vGd~V~vkVl~id~~gri~L  749 (974)
                      -++.|+++-|.|+++....+.|++..          ...|-+|+|+..+.++++.++.|++||.|+++|++.-  -.+.|
T Consensus        61 ~~K~GdiV~grV~~v~~~~a~V~i~~ve~~~r~~~~~~~~~ihvs~~~~~~~~~~~d~f~~GDivrA~Vis~~--~~~~L  138 (188)
T COG1096          61 LPKGGDIVYGRVTDVREQRALVRIVGVEGKERELATSGAADIHVSQVRDGYVEKLSDAFRIGDIVRARVISTG--DPIQL  138 (188)
T ss_pred             CCCCCCEEEEEEeeccceEEEEEEEEEecccccCCCCceeeEEEEecccccccccccccccccEEEEEEEecC--CCeEE
Confidence            47899999999999999999998852          1457799999999999999999999999999999963  46788


Q ss_pred             EEec
Q 002054          750 SLKA  753 (974)
Q Consensus       750 S~K~  753 (974)
                      |.+.
T Consensus       139 st~~  142 (188)
T COG1096         139 STKG  142 (188)
T ss_pred             EecC
Confidence            8664

>cd05699 S1_Rrp5_repeat_hs7 S1_Rrp5_repeat_hs7: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits

Probab=97.18  E-value=0.0011  Score=57.69  Aligned_cols=66  Identities=24%  Similarity=0.313  Sum_probs=55.5

Q ss_pred             CcEEEEEEEEEeeceEEEEEcC-CeEEEEecccCCCccccc---cccccccCCEE-EEEEEEEcc-CCceEEEEe
Q 002054          684 GGIYKGVVTSVKEYGAFVEFNG-GQQGLLHVSELSHEPVSR---VSDVVSVGQQL-SLRCIGQDV-RGNIKLSLK  752 (974)
Q Consensus       684 G~i~~G~V~~i~~~G~fV~l~~-g~~Glvhisels~~~v~~---~~~~~~vGd~V-~vkVl~id~-~gri~LS~K  752 (974)
                      |++++|+|..-++.+++|++.+ +..|+++..+|++ .+++   ....+++||++ ++.|+  |. .+.+.||.|
T Consensus         1 G~lV~~~V~EKt~D~l~v~l~~~~l~a~l~~~HLsD-~~~k~~~~~~klrvG~~L~~~lvL--~~~~r~i~lt~K   72 (72)
T cd05699           1 GKLVDARVLKKTLNGLEVAILPEEIRAFLPTMHLSD-HVSNCPLLWHCLQEGDTIPNLMCL--SNYKGRIILTKK   72 (72)
T ss_pred             CceEEEEEEEEcCCcEEEEecCCCcEEEEEccccCC-chhhCHHHHhhhhcCCCccceEEE--eccccEEEEecC
Confidence            7899999999999999999987 8999999999999 4433   33458999999 99999  55 567888865

Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in Saccharomyces cerevisiae Rrp5 and 14 S1 repeats in Homo sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in protein-protein interactions. Mutational studies have shown that each region represents a specific functional domain. Deletions within the S1-containing region inhibit pre-rRNA processing at either site A3 or A2, whereas deletions within the TPR region confer an inability to support cleavage of A0-A2. This CD includes H. sapiens S1 repeat 7 (hs7). Rrp5 is found in eukaryotes but not in prokaryotes or archaea.

>COG1095 RPB7 DNA-directed RNA polymerase, subunit E' [Transcription]

Probab=97.16  E-value=0.0007  Score=68.91  Aligned_cols=57  Identities=21%  Similarity=0.278  Sum_probs=49.9

Q ss_pred             CCCCEEEEEEEEEeCCeEEEEeCCCeEEEEecccCC------------------CCCCCCCCEEEEEEEEEeCCCc
Q 002054          909 KLGTKVAAKVYQVRARGLVLDLGGGIRGMYRFENNE------------------KKDFVVGDELLVKCSSFTGKGI  966 (974)
Q Consensus       909 ~vG~vV~G~V~~I~~~GvFV~L~~gv~Glih~se~~------------------~~~f~vGd~V~vkVl~id~~~~  966 (974)
                      -.|++|.|.|.++.+||+||.++ -++||+|.+++.                  +..+++||.|+|||++++.+..
T Consensus        80 ~~gEVV~GeVv~~~~~G~fV~ig-p~dglvh~sqi~dd~~~~d~~~~~~~g~~tk~~i~~gd~VR~RIv~~s~~~~  154 (183)
T COG1095          80 FRGEVVEGEVVEVVEFGAFVRIG-PLDGLVHVSQIMDDYIDYDEKNKVLIGEETKRVLKVGDKVRARIVGVSLKSR  154 (183)
T ss_pred             ccccEEEEEEEEEeecceEEEec-cccccccHhhccCcccccCcccceeeecccceEEecCCEEEEEEEEEecccC
Confidence            47999999999999999999998 889999999653                  2268999999999999987654

>PRK08563 DNA-directed RNA polymerase subunit E'; Provisional

Probab=97.15  E-value=0.0016  Score=68.01  Aligned_cols=57  Identities=19%  Similarity=0.274  Sum_probs=49.3

Q ss_pred             CCCCCEEEEEEEEEeCCeEEEEeCCCeEEEEecccCCC------------------CCCCCCCEEEEEEEEEeCCC
Q 002054          908 LKLGTKVAAKVYQVRARGLVLDLGGGIRGMYRFENNEK------------------KDFVVGDELLVKCSSFTGKG  965 (974)
Q Consensus       908 ~~vG~vV~G~V~~I~~~GvFV~L~~gv~Glih~se~~~------------------~~f~vGd~V~vkVl~id~~~  965 (974)
                      -.+|+++.|+|.++.++|+||+++ .++|++|.++++.                  ..++.||.|+++|.+++.+.
T Consensus        79 P~~GEVv~g~V~~v~~~Gi~V~lg-~~~g~v~~~~l~~~~~~~d~~~~~~~~~~~~~~i~~Gd~VrvrV~~v~~~~  153 (187)
T PRK08563         79 PELQEVVEGEVVEVVEFGAFVRIG-PVDGLLHISQIMDDYISYDPKNGRLIGKESKRVLKVGDVVRARIVAVSLKE  153 (187)
T ss_pred             ccCCCEEEEEEEEEEccEEEEEEe-CceEEEEcHHcCCCceEEccccceEEEccCCeEEcCCCEEEEEEEEEEccc
Confidence            348999999999999999999997 5999999997642                  23689999999999999653

>cd05790 S1_Rrp40 S1_Rrp40: Rrp40 S1-like RNA-binding domain

Probab=97.01  E-value=0.0036  Score=56.74  Aligned_cols=66  Identities=23%  Similarity=0.260  Sum_probs=60.2

Q ss_pred             CCCCEEEEEEEEEeCCeEEEEeCCCeEEEEecccCC------CCCCCCCCEEEEEEEEEeCCCceeeeecCC
Q 002054          909 KLGTKVAAKVYQVRARGLVLDLGGGIRGMYRFENNE------KKDFVVGDELLVKCSSFTGKGIPVVSLVDS  974 (974)
Q Consensus       909 ~vG~vV~G~V~~I~~~GvFV~L~~gv~Glih~se~~------~~~f~vGd~V~vkVl~id~~~~~~~~~~~~  974 (974)
                      ++||.|-|+|..+...+-+|++..-..|++|.+.++      ...|++||-|-|+|.++|+...+.++.+|+
T Consensus         5 ~~gD~VIG~V~~~~~~~~~VdI~s~~~a~L~~~~f~gatk~~rp~L~~GDlV~ArV~~~~~~~~~eLtc~~~   76 (86)
T cd05790           5 AKGDHVIGIVVAKAGDFFKVDIGGSEPASLSYLAFEGATKRNRPNLNVGDLVYARVVKANRDMEPELSCVDS   76 (86)
T ss_pred             CCCCEEEEEEEEEcCCeEEEEcCCCcceEechHHcccccccccccCCCCCEEEEEEEecCCCCCeEEEEeCC
Confidence            689999999999999999999998889999998763      346999999999999999999999999884

S1-like RNA-binding domains are found in a wide variety of RNA-associated proteins. Rrp4 protein is a subunit of the exosome complex. The exosome plays a central role in 3' to 5' RNA processing and degradation in eukarytes and archaea. Its functions include the removal of incorrectly processed RNA and the maintenance of proper levels of mRNA, rRNA and a number of small RNA species. In Saccharomyces cerevisiae, the exosome includes nine core components, six of which are homologous to bacterial RNase PH. These form a hexameric ring structure. The other three subunits (RrP4, Rrp40, and Csl4) contain an S1 RNA binding domain and are part of the "S1 pore structure".

>PTZ00162 DNA-directed RNA polymerase II subunit 7; Provisional

Probab=96.99  E-value=0.0026  Score=65.67  Aligned_cols=74  Identities=15%  Similarity=0.132  Sum_probs=57.7

Q ss_pred             cccccCcEEEEEEEEEeeceEEEEEcCCeEEEEecccCCCccc------------cccccccccCCEEEEEEEEEcc---
Q 002054          679 REIEVGGIYKGVVTSVKEYGAFVEFNGGQQGLLHVSELSHEPV------------SRVSDVVSVGQQLSLRCIGQDV---  743 (974)
Q Consensus       679 ~~~~~G~i~~G~V~~i~~~G~fV~l~~g~~Glvhisels~~~v------------~~~~~~~~vGd~V~vkVl~id~---  743 (974)
                      ..+-.|++++|+|+++.++|+||.+++ .++|+|.+++.++..            ++-+..++.|+.|++||.++..   
T Consensus        77 FrPf~gEVv~g~V~~v~~~G~~v~~Gp-~~ifI~~~~l~~~~~fd~~~~~~~~~~~~~~~~i~~g~~VR~rV~~v~~~~~  155 (176)
T PTZ00162         77 FKPFKDEVLDAIVTDVNKLGFFAQAGP-LKAFVSRSAIPPDFVYDSDSAYPCYISSDGQIQIKPNTEVRLRLQGVRYDAS  155 (176)
T ss_pred             EecCCCCEEEEEEEEEecceEEEEeeC-eEEEEcHHHCCCccEECCCCCcceEecCCCcEEECCCCEEEEEEEEEEecCC
Confidence            357899999999999999999999964 669999999975421            1123469999999999999754   


Q ss_pred             CCceEEEEec
Q 002054          744 RGNIKLSLKA  753 (974)
Q Consensus       744 ~gri~LS~K~  753 (974)
                      +.+..+|||+
T Consensus       156 ~~~~i~T~~~  165 (176)
T PTZ00162        156 NLFAIATINS  165 (176)
T ss_pred             CcEEEEEecC
Confidence            2346667775

>cd04462 S1_RNAPII_Rpb7 S1_RNAPII_Rpb7: Eukaryotic RNA polymerase II (RNAPII) Rpb7 subunit C-terminal S1 domain

Probab=96.93  E-value=0.0041  Score=56.78  Aligned_cols=55  Identities=16%  Similarity=0.074  Sum_probs=46.2

Q ss_pred             CCCEEEEEEEEEeCCeEEEEeCCCeEEEEecccCC------------------CCCCCCCCEEEEEEEEEeCCC
Q 002054          910 LGTKVAAKVYQVRARGLVLDLGGGIRGMYRFENNE------------------KKDFVVGDELLVKCSSFTGKG  965 (974)
Q Consensus       910 vG~vV~G~V~~I~~~GvFV~L~~gv~Glih~se~~------------------~~~f~vGd~V~vkVl~id~~~  965 (974)
                      +|+++.|+|+++.++|+||.++ .++||+|.+.++                  ...++.|+.|++||+++.-+.
T Consensus         1 kgEVi~g~V~~v~~~G~~v~~G-pl~~f~~~~~ip~~~~~~~~~~~~~~~~~~~~~i~~g~~VR~rV~~v~~~~   73 (88)
T cd04462           1 KGEVVDAIVTSVNKTGFFAEVG-PLSIFISRHLIPSDMEFDPNASPPCFTSNEDIVIKKDTEVRLKIIGTRVDA   73 (88)
T ss_pred             CCcEEEEEEEEEeccEEEEEEc-CceEEEEeeecCccceECCcCCCCeEeCCCcEEECCCCEEEEEEEEEEEcc
Confidence            5899999999999999999996 788999988443                  123789999999999887543

RNAPII is composed of 12 subunits (Rpb1-12). Rpb4 and Rpb7 form a heterodimer that associate with the RNAPII core. Rpb7 is a homolog of the Rpc25 of RNA polymerase III, RpoE of the archaeal RNA polymerase, and Rpa43 of eukaryotic RNA polymerase I. Rpb7 has two domains, an N-terminal ribonucleoprotein (RNP) domain and a C-terminal S1 domain, both of which bind single-stranded RNA. It is possible that the S1 domain interacts with the nascent RNA transcript, assisted by the RNP domain. In yeast, Rpb4/Rpb7 is necessary for promoter-directed transcription initiation. They also play a role in regulating transcription-coupled repair in the Rad26-dependent pathway, in efficient mRNA export, and in transcription termination.

>TIGR02062 RNase_B exoribonuclease II

Probab=96.75  E-value=0.0067  Score=74.78  Aligned_cols=69  Identities=12%  Similarity=0.224  Sum_probs=54.8

Q ss_pred             ccC--cEEEEEEEEEeeceEEEEE-cCCeEEEEecccCCC--ccc-----c---cc--ccccccCCEEEEEEEEEcc-CC
Q 002054          682 EVG--GIYKGVVTSVKEYGAFVEF-NGGQQGLLHVSELSH--EPV-----S---RV--SDVVSVGQQLSLRCIGQDV-RG  745 (974)
Q Consensus       682 ~~G--~i~~G~V~~i~~~G~fV~l-~~g~~Glvhisels~--~~v-----~---~~--~~~~~vGd~V~vkVl~id~-~g  745 (974)
                      ++|  +.|+|.|+++.+||+||+| ..+++||||++.+.+  +++     .   ..  ...|++||.|+|+|.++|. ++
T Consensus       554 ~~g~~~~f~g~I~~v~~~g~~v~l~~~~~~g~v~~~~l~~~~~~~~~~~~~~~~~l~g~~~~~lgd~v~V~v~~vd~~~~  633 (639)
T TIGR02062       554 KAAKNTRFAAEIVDISRGGMRVRLLENGAIAFIPAAFLHANREELVCNQENGTVQIKGETVYKIGDVIDVVLTEVRMETR  633 (639)
T ss_pred             ccCCCcEEEEEEEeeeCCcEEEEEecCceEEEEEhhhcCCCCcceEEcccccEEEEeccEEEecCCEEEEEEEEeccccC
Confidence            454  5999999999999999999 457999999999976  221     1   11  1269999999999999997 67


Q ss_pred             ceEEE
Q 002054          746 NIKLS  750 (974)
Q Consensus       746 ri~LS  750 (974)
                      +|.+.
T Consensus       634 ~i~~~  638 (639)
T TIGR02062       634 SIIAR  638 (639)
T ss_pred             cEeee
Confidence            77653

This family consists of exoribonuclease II, the product of the rnb gene, as found in a number of gamma proteobacteria. In Escherichia coli, it is one of eight different exoribonucleases. It is involved in mRNA degradation and tRNA precursor end processing.

>PF13509 S1_2: S1 domain; PDB: 3GO5_A

Probab=96.74  E-value=0.0067  Score=51.41  Aligned_cols=60  Identities=25%  Similarity=0.258  Sum_probs=37.1

Q ss_pred             CCCEEEEEEEEEeCCeEEEEeCCCeEEEEecccCCCCCCCCCCEEEEEEEEEeCCCceeeee
Q 002054          910 LGTKVAAKVYQVRARGLVLDLGGGIRGMYRFENNEKKDFVVGDELLVKCSSFTGKGIPVVSL  971 (974)
Q Consensus       910 vG~vV~G~V~~I~~~GvFV~L~~gv~Glih~se~~~~~f~vGd~V~vkVl~id~~~~~~~~~  971 (974)
                      +|++.+.+|.++.++|+|++-+++-.=|+|.++.+ ..+++||+|.|.| -.|.++.++++.
T Consensus         1 iG~~~~L~V~~~~~~g~fL~~~~~~~vlLp~~e~~-~~~~~Gd~v~VFv-Y~D~~~rl~AT~   60 (61)
T PF13509_consen    1 IGQINTLKVVDKNEFGYFLDDGEGKEVLLPKSEVP-EPLKVGDEVEVFV-YLDKEGRLVATT   60 (61)
T ss_dssp             --------EEEE-SSEEEEEETT-EEEEEEGGG-------TTSEEEEEE-EE-TTS-EEEE-
T ss_pred             CCCCcceEEEEEeCCEEEEECCCCCEEEechHHcC-CCCCCCCEEEEEE-EECCCCCEEEec
Confidence            58999999999999999999888899999999995 6799999999976 567788887764

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

Probab=96.72  E-value=0.0023  Score=54.10  Aligned_cols=55  Identities=27%  Similarity=0.443  Sum_probs=44.2

Q ss_pred             eeeeeccchhhhhcCCCccchhhhhhhhCceEEeeC-------CEEEEEecCHHHHHHHHHHH
Q 002054          618 ATLKYDNDTLRRLIGPLGALKRKIEEETGGRISVSD-------GTLTVVAKNRSVMEKVLEKV  673 (974)
Q Consensus       618 ~~~~i~~~ki~~vIg~gGk~i~~i~~~~g~~Idi~d-------g~v~i~~~~~~~~~~a~~~i  673 (974)
                      ..+.||.+.++.+||++|++|+.|++++|+.|.+.+       ..+.+.+. .+.++.|...+
T Consensus         2 ~~i~ip~~~~~~vIG~~G~~i~~I~~~s~~~I~i~~~~~~~~~~~v~i~G~-~~~v~~a~~~i   63 (64)
T cd00105           2 ERVLVPSSLVGRIIGKGGSTIKEIREETGAKIKIPDSGSGSEERIVTITGT-PEAVEKAKELI   63 (64)
T ss_pred             EEEEEchhhcceeECCCCHHHHHHHHHHCCEEEEcCCCCCCCceEEEEEcC-HHHHHHHHHHh
Confidence            467899999999999999999999999999998852       45677765 56677666543

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.

>PF10447 EXOSC1: Exosome component EXOSC1/CSL4; InterPro: IPR019495 The exosome mediates degradation of unstable mRNAs that contain AU-rich elements (AREs) within their 3' untranslated regions []

Probab=96.71  E-value=0.0034  Score=56.30  Aligned_cols=61  Identities=25%  Similarity=0.258  Sum_probs=42.1

Q ss_pred             cccCcEEEEEEEEEeeceEEEEEcC------------------CeEEEEecccCCCccccc--cccccccCCEEEEEEEE
Q 002054          681 IEVGGIYKGVVTSVKEYGAFVEFNG------------------GQQGLLHVSELSHEPVSR--VSDVVSVGQQLSLRCIG  740 (974)
Q Consensus       681 ~~~G~i~~G~V~~i~~~G~fV~l~~------------------g~~Glvhisels~~~v~~--~~~~~~vGd~V~vkVl~  740 (974)
                      +++|+++.|+|+++.+.-++++|.-                  ...|++|.+++-......  +.+-|++||.|+++|++
T Consensus         2 P~vGdiV~~rVtrv~~~~a~v~Il~v~~~~~~~~~~~~~~l~~~f~GiIR~~DVR~te~Dkv~~~~~FrpGDIVrA~ViS   81 (82)
T PF10447_consen    2 PKVGDIVIARVTRVNPRQAKVEILCVEGKGNDSINAGDRPLKEPFQGIIRKQDVRATEKDKVKMYDCFRPGDIVRARVIS   81 (82)
T ss_dssp             --TT-EEEEEEEEE-SSEEEEEEEES----------SSS----SS-S-EEEEGGGT-SS----GGGT--SSSEEEEEEEE
T ss_pred             CCCCCEEEEEEEEEeccEEEEEEEEEEeccccccccCCcccccccEEEEEeeeecccccchhhHHhccCCCCEEEEEEee
Confidence            6899999999999999999988741                  356899999986654443  57789999999999997


Q ss_pred             E
Q 002054          741 Q  741 (974)
Q Consensus       741 i  741 (974)
                      .
T Consensus        82 l   82 (82)
T PF10447_consen   82 L   82 (82)
T ss_dssp             E
T ss_pred             C
Confidence            3

The proteins in this entry are components of the exosome 3'->5' exoribonuclease complex. They do not have exonuclease activity, but are required for the 3'-processing of the 7S pre-RNA to the mature 5.8S rRNA and for mRNA decay [, ].; PDB: 2NN6_I.

>COG0557 VacB Exoribonuclease R [Transcription]

Probab=96.70  E-value=0.0065  Score=75.98  Aligned_cols=73  Identities=30%  Similarity=0.572  Sum_probs=61.0

Q ss_pred             ccccCcEEEEEEEEEeeceEEEEEcC-CeEEEEecccCCCcccc-----------ccccccccCCEEEEEEEEEcc-CCc
Q 002054          680 EIEVGGIYKGVVTSVKEYGAFVEFNG-GQQGLLHVSELSHEPVS-----------RVSDVVSVGQQLSLRCIGQDV-RGN  746 (974)
Q Consensus       680 ~~~~G~i~~G~V~~i~~~G~fV~l~~-g~~Glvhisels~~~v~-----------~~~~~~~vGd~V~vkVl~id~-~gr  746 (974)
                      .-.+|+.++|.|+++..||+||.|.+ +++|+||++.+.++++.           .....+++||.|+|+|.++|. .++
T Consensus       619 ~~~vg~~f~g~V~~v~~~g~~V~l~~~~ieglV~~s~L~~d~y~~~~~~~~l~~~~~~~~~~lgd~v~v~v~~v~~~~~~  698 (706)
T COG0557         619 KKRVGEEFDGVVTGVTSFGFFVELPELGLEGLVHISSLPDDYYHFDERGQALVGEKSGKVYRLGDEVKVKVTSVDLDERK  698 (706)
T ss_pred             HHhcCCEEEEEEEEEEeccEEEEecccccccceEcccCCCceeeeccccceeeccccccccccCCEEEEEEEEEcccccc
Confidence            34789999999999999999999976 48999999999875432           234469999999999999987 678


Q ss_pred             eEEEEe
Q 002054          747 IKLSLK  752 (974)
Q Consensus       747 i~LS~K  752 (974)
                      +.+++-
T Consensus       699 i~~~~v  704 (706)
T COG0557         699 IDFELV  704 (706)
T ss_pred             eEEEec
Confidence            887753

>COG1107 Archaea-specific RecJ-like exonuclease, contains DnaJ-type Zn finger domain [DNA replication, recombination, and repair]

Probab=96.65  E-value=0.0044  Score=72.39  Aligned_cols=71  Identities=30%  Similarity=0.604  Sum_probs=61.6

Q ss_pred             cccccCcEEEEEEEEEeeceEEEEEcCCeEEEEecccCCCccccccccccccCCEEEEEEEEEcc-CCceEEEEeccC
Q 002054          679 REIEVGGIYKGVVTSVKEYGAFVEFNGGQQGLLHVSELSHEPVSRVSDVVSVGQQLSLRCIGQDV-RGNIKLSLKAVS  755 (974)
Q Consensus       679 ~~~~~G~i~~G~V~~i~~~G~fV~l~~g~~Glvhisels~~~v~~~~~~~~vGd~V~vkVl~id~-~gri~LS~K~~~  755 (974)
                      .+++.|..|.|+|.++.+||+||+|...+.||+|-++++..      .-+.+||.+-|++..+-+ +|.+.+....+.
T Consensus       118 ~Dve~g~~Y~g~v~~v~~~GvFv~Ln~~v~GL~~~~d~~~~------~~~~vgdeiiV~v~~vr~~~geidf~~~~~~  189 (715)
T COG1107         118 EDVEAGKYYKGIVSRVEKYGVFVELNSHVRGLIHRRDLGGD------PDYAVGDEIIVQVSDVRPEKGEIDFEPVGLD  189 (715)
T ss_pred             hhcccceeeeccccchhhhcceeecChhhhccccccccCCC------CCCCCCCeEEEEeeccCCCCCccceeecCCc
Confidence            47899999999999999999999999999999999999863      128899999999999977 588888776543

>PF10447 EXOSC1: Exosome component EXOSC1/CSL4; InterPro: IPR019495 The exosome mediates degradation of unstable mRNAs that contain AU-rich elements (AREs) within their 3' untranslated regions []

Probab=96.59  E-value=0.0047  Score=55.42  Aligned_cols=53  Identities=25%  Similarity=0.347  Sum_probs=37.5

Q ss_pred             CCCCEEEEEEEEEeCCeEEEEe------------------CCCeEEEEecccCC---------CCCCCCCCEEEEEEEEE
Q 002054          909 KLGTKVAAKVYQVRARGLVLDL------------------GGGIRGMYRFENNE---------KKDFVVGDELLVKCSSF  961 (974)
Q Consensus       909 ~vG~vV~G~V~~I~~~GvFV~L------------------~~gv~Glih~se~~---------~~~f~vGd~V~vkVl~i  961 (974)
                      ++|++|.|+|.++++..+++++                  .+.+.|++|.++..         .+.|++||-|.|+|+++
T Consensus         3 ~vGdiV~~rVtrv~~~~a~v~Il~v~~~~~~~~~~~~~~l~~~f~GiIR~~DVR~te~Dkv~~~~~FrpGDIVrA~ViSl   82 (82)
T PF10447_consen    3 KVGDIVIARVTRVNPRQAKVEILCVEGKGNDSINAGDRPLKEPFQGIIRKQDVRATEKDKVKMYDCFRPGDIVRARVISL   82 (82)
T ss_dssp             -TT-EEEEEEEEE-SSEEEEEEEES----------SSS----SS-S-EEEEGGGT-SS----GGGT--SSSEEEEEEEEE
T ss_pred             CCCCEEEEEEEEEeccEEEEEEEEEEeccccccccCCcccccccEEEEEeeeecccccchhhHHhccCCCCEEEEEEeeC
Confidence            5899999999999999998876                  23578999998542         44699999999999985

The proteins in this entry are components of the exosome 3'->5' exoribonuclease complex. They do not have exonuclease activity, but are required for the 3'-processing of the 7S pre-RNA to the mature 5.8S rRNA and for mRNA decay [, ].; PDB: 2NN6_I.

>PRK05054 exoribonuclease II; Provisional

Probab=96.46  E-value=0.0068  Score=74.85  Aligned_cols=60  Identities=18%  Similarity=0.232  Sum_probs=50.3

Q ss_pred             CCC--CEEEEEEEEEeCCeEEEEeCC-CeEEEEecccCC-------------------CCCCCCCCEEEEEEEEEeCCCc
Q 002054          909 KLG--TKVAAKVYQVRARGLVLDLGG-GIRGMYRFENNE-------------------KKDFVVGDELLVKCSSFTGKGI  966 (974)
Q Consensus       909 ~vG--~vV~G~V~~I~~~GvFV~L~~-gv~Glih~se~~-------------------~~~f~vGd~V~vkVl~id~~~~  966 (974)
                      ++|  +...|.|..+++||+||+|++ ++.||||.+.+.                   ...|+.||+|+|+|.++|....
T Consensus       558 ~~G~~~~f~g~I~~v~~~G~fV~l~~~~veglV~~~~l~~~~~~y~~~~~~~~~~~~~~~~~~lGd~V~V~v~~vd~~~~  637 (644)
T PRK05054        558 KAGTDTRFAAEIIDISRGGMRVRLLENGAVAFIPASFLHAVRDELVCNQENGTVQIKGETVYKLGDVIDVTLAEVRMETR  637 (644)
T ss_pred             ccCCCeEEEEEEEeeecCcEEEEEeCCceEEEEEccccCCCccceEEccccceEEEeCCEEEcCCCEEEEEEEEEccccC
Confidence            365  599999999999999999987 899999998552                   1258999999999999996654


Q ss_pred             ee
Q 002054          967 PV  968 (974)
Q Consensus       967 ~~  968 (974)
                      .+
T Consensus       638 ~i  639 (644)
T PRK05054        638 SI  639 (644)
T ss_pred             eE
Confidence            43

>TIGR00757 RNaseEG ribonuclease, Rne/Rng family

Probab=96.34  E-value=0.0078  Score=70.19  Aligned_cols=55  Identities=15%  Similarity=0.191  Sum_probs=48.8

Q ss_pred             ccCCCCCEEEEEEEEEeCC--eEEEEeCCCeEEEEecccCCC-------------------CCCCCCCEEEEEEEE
Q 002054          906 KNLKLGTKVAAKVYQVRAR--GLVLDLGGGIRGMYRFENNEK-------------------KDFVVGDELLVKCSS  960 (974)
Q Consensus       906 ~~~~vG~vV~G~V~~I~~~--GvFV~L~~gv~Glih~se~~~-------------------~~f~vGd~V~vkVl~  960 (974)
                      ....+|+++.|+|.+|.+.  |+||+++++-.||+|.++...                   +.+++||+|.|.|++
T Consensus        21 ~~~~vGnIY~GrV~~i~p~l~aAFVdiG~~k~gfL~~~d~~~~~~~~~~~~~~~~~~~~i~~~l~~G~~IlVQV~K   96 (414)
T TIGR00757        21 SRQLKGNIYKGRVTRILPSLQAAFVDIGLEKNGFLHASDIGPNYECLAPAEAKREAGPSISELLRPGQSVLVQVVK   96 (414)
T ss_pred             CcCCCCCEEEEEEeeecCCCceEEEEcCCCceEEEEHHHcCchhhccccccccccccCCHHHhCcCCCEEEEEEee
Confidence            3457999999999999999  999999999999999998632                   148999999999998

The C-terminal half of RNase E (excluded from the seed alignment for this model) lacks ribonuclease activity but participates in mRNA degradation by organizing the degradosome.

>PRK12328 nusA transcription elongation factor NusA; Provisional

Probab=96.25  E-value=0.014  Score=66.42  Aligned_cols=57  Identities=21%  Similarity=0.297  Sum_probs=51.1

Q ss_pred             CCCCEEEEEEEEEeCC-eEEEEeCCCeEEEEecccC-CCCCCCCCCEEEEEEEEEeCCCc
Q 002054          909 KLGTKVAAKVYQVRAR-GLVLDLGGGIRGMYRFENN-EKKDFVVGDELLVKCSSFTGKGI  966 (974)
Q Consensus       909 ~vG~vV~G~V~~I~~~-GvFV~L~~gv~Glih~se~-~~~~f~vGd~V~vkVl~id~~~~  966 (974)
                      ++|++|+|+|.++... ++||+|+ ++.|++|.++. +.+.|++||+++|.|.+|+....
T Consensus       137 ~~Geiv~g~V~r~~~~~~i~vdlg-~~ea~LP~~eqip~E~~~~Gdrik~~i~~V~~~~k  195 (374)
T PRK12328        137 KVGKIVFGTVVRVDNEENTFIEID-EIRAVLPMKNRIKGEKFKVGDVVKAVLKRVKIDKN  195 (374)
T ss_pred             hcCcEEEEEEEEEecCCCEEEEcC-CeEEEeCHHHcCCCCcCCCCCEEEEEEEEEecCCC
Confidence            6999999999999875 5999996 89999999966 68899999999999999997654

>smart00322 KH K homology RNA-binding domain

Probab=96.22  E-value=0.011  Score=49.84  Aligned_cols=60  Identities=27%  Similarity=0.327  Sum_probs=48.8

Q ss_pred             cceeeeeccchhhhhcCCCccchhhhhhhhCceEEeeC-----CEEEEEecCHHHHHHHHHHHHHH
Q 002054          616 RLATLKYDNDTLRRLIGPLGALKRKIEEETGGRISVSD-----GTLTVVAKNRSVMEKVLEKVDFI  676 (974)
Q Consensus       616 ~~~~~~i~~~ki~~vIg~gGk~i~~i~~~~g~~Idi~d-----g~v~i~~~~~~~~~~a~~~i~~l  676 (974)
                      ....+.++++.++.+||++|++|+.|++.+|++|.+..     ..+.+.+. ....+.|...+...
T Consensus         3 ~~~~i~i~~~~~~~liG~~G~~i~~i~~~~~~~i~~~~~~~~~~~v~i~g~-~~~v~~a~~~i~~~   67 (69)
T smart00322        3 VTIEVLIPADKVGLIIGKGGSTIKKIEEETGVKIDIPEDGSEERVVEITGP-PENVEKAAELILEI   67 (69)
T ss_pred             eEEEEEEcchhcceeECCCchHHHHHHHHHCCEEEECCCCCCccEEEEEcC-HHHHHHHHHHHHHH
Confidence            34577899999999999999999999999999998763     56777776 57777777766543

>cd05699 S1_Rrp5_repeat_hs7 S1_Rrp5_repeat_hs7: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits

Probab=96.16  E-value=0.017  Score=50.29  Aligned_cols=55  Identities=20%  Similarity=0.219  Sum_probs=47.7

Q ss_pred             CCEEEEEEEEEeCCeEEEEeCC-CeEEEEecccCCC---------CCCCCCCEE-EEEEEEEeCCCce
Q 002054          911 GTKVAAKVYQVRARGLVLDLGG-GIRGMYRFENNEK---------KDFVVGDEL-LVKCSSFTGKGIP  967 (974)
Q Consensus       911 G~vV~G~V~~I~~~GvFV~L~~-gv~Glih~se~~~---------~~f~vGd~V-~vkVl~id~~~~~  967 (974)
                      |++|+|+|.+-++-+++|++++ |+.|+++..+++.         ..+++||++ .+-|+  +...+.
T Consensus         1 G~lV~~~V~EKt~D~l~v~l~~~~l~a~l~~~HLsD~~~k~~~~~~klrvG~~L~~~lvL--~~~~r~   66 (72)
T cd05699           1 GKLVDARVLKKTLNGLEVAILPEEIRAFLPTMHLSDHVSNCPLLWHCLQEGDTIPNLMCL--SNYKGR   66 (72)
T ss_pred             CceEEEEEEEEcCCcEEEEecCCCcEEEEEccccCCchhhCHHHHhhhhcCCCccceEEE--eccccE
Confidence            7899999999999999999999 9999999998853         368999999 99999  555443

Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in Saccharomyces cerevisiae Rrp5 and 14 S1 repeats in Homo sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in protein-protein interactions. Mutational studies have shown that each region represents a specific functional domain. Deletions within the S1-containing region inhibit pre-rRNA processing at either site A3 or A2, whereas deletions within the TPR region confer an inability to support cleavage of A0-A2. This CD includes H. sapiens S1 repeat 7 (hs7). Rrp5 is found in eukaryotes but not in prokaryotes or archaea.

>TIGR03665 arCOG04150 arCOG04150 universal archaeal KH domain protein

Probab=96.10  E-value=0.0089  Score=61.54  Aligned_cols=51  Identities=31%  Similarity=0.438  Sum_probs=47.7

Q ss_pred             hhhhhcCCCccchhhhhhhhCceEEeeCCEEEEEecCHHHHHHHHHHHHHHh
Q 002054          626 TLRRLIGPLGALKRKIEEETGGRISVSDGTLTVVAKNRSVMEKVLEKVDFII  677 (974)
Q Consensus       626 ki~~vIg~gGk~i~~i~~~~g~~Idi~dg~v~i~~~~~~~~~~a~~~i~~l~  677 (974)
                      .++.+||+||++++.|++.||++|.+.+..|.+.+ +.+..+.|++.++.|+
T Consensus        99 ~~griIG~~G~t~~~ie~~t~~~i~i~~~~v~i~G-~~~~~~~A~~~i~~li  149 (172)
T TIGR03665        99 IKGRIIGEGGKTRRIIEELTGVSISVYGKTVGIIG-DPEQVQIAREAIEMLI  149 (172)
T ss_pred             HHhhhcCCCcHHHHHHHHHHCCeEEEcCCEEEEEC-CHHHHHHHHHHHHHHH
Confidence            68999999999999999999999999999999988 7889999999998887

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.

>PRK12328 nusA transcription elongation factor NusA; Provisional

Probab=95.96  E-value=0.035  Score=63.21  Aligned_cols=87  Identities=20%  Similarity=0.297  Sum_probs=64.8

Q ss_pred             ecCHHHHHHHHHHHHHHh--------hcc--cccCcEEEEEEEEEee-ceEEEEEcCCeEEEEecccCCCcccccccccc
Q 002054          660 AKNRSVMEKVLEKVDFII--------GRE--IEVGGIYKGVVTSVKE-YGAFVEFNGGQQGLLHVSELSHEPVSRVSDVV  728 (974)
Q Consensus       660 ~~~~~~~~~a~~~i~~l~--------~~~--~~~G~i~~G~V~~i~~-~G~fV~l~~g~~Glvhisels~~~v~~~~~~~  728 (974)
                      ...+-+++.|++.+...+        ..+  -++|+++.|+|.++.. .++||+| ++.+|++|.++..      |.+.|
T Consensus       105 ~fgRiaaq~akq~i~Qkir~~er~~i~~ey~~~~Geiv~g~V~r~~~~~~i~vdl-g~~ea~LP~~eqi------p~E~~  177 (374)
T PRK12328        105 NMGRTAANTLFKELEYHIQRLLEESIFEKYKKKVGKIVFGTVVRVDNEENTFIEI-DEIRAVLPMKNRI------KGEKF  177 (374)
T ss_pred             hCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCcEEEEEEEEEecCCCEEEEc-CCeEEEeCHHHcC------CCCcC
Confidence            344556666665542211        112  4799999999999986 4699999 5899999988765      44679


Q ss_pred             ccCCEEEEEEEEEcc--C-C-ceEEEEec
Q 002054          729 SVGQQLSLRCIGQDV--R-G-NIKLSLKA  753 (974)
Q Consensus       729 ~vGd~V~vkVl~id~--~-g-ri~LS~K~  753 (974)
                      ++||.++|.|.+++.  + | ++.||+..
T Consensus       178 ~~Gdrik~~i~~V~~~~k~gp~IilSRt~  206 (374)
T PRK12328        178 KVGDVVKAVLKRVKIDKNNGILIELSRTS  206 (374)
T ss_pred             CCCCEEEEEEEEEecCCCCCCEEEEEcCC
Confidence            999999999999986  3 3 68899854

>PRK11712 ribonuclease G; Provisional

Probab=95.95  E-value=0.015  Score=68.94  Aligned_cols=62  Identities=32%  Similarity=0.483  Sum_probs=50.7

Q ss_pred             cccCcEEEEEEEEEeec--eEEEEEcCCeEEEEecccCCCc------------cccccccccccCCEEEEEEEEEcc
Q 002054          681 IEVGGIYKGVVTSVKEY--GAFVEFNGGQQGLLHVSELSHE------------PVSRVSDVVSVGQQLSLRCIGQDV  743 (974)
Q Consensus       681 ~~~G~i~~G~V~~i~~~--G~fV~l~~g~~Glvhisels~~------------~v~~~~~~~~vGd~V~vkVl~id~  743 (974)
                      ..+|.||.|+|.+|.+.  +|||+|+.+..||+|++++...            ...++.+.+++||.|-|.|.. ++
T Consensus        36 ~~vGnIY~G~V~~v~pg~~AAFVdIG~~k~gFL~~~d~~~~~~~~~~~~~~~~~~~~i~~~l~~Gq~iLVQV~K-e~  111 (489)
T PRK11712         36 GIVGNIYKGRVSRVLPGMQAAFVDIGLDKAAFLHASDIVPHTECVAGEEQKQFVVRDISELVRQGQDIMVQVVK-DP  111 (489)
T ss_pred             cccccEEEEEEeecCCCCceeEEeeCCCccEEEEhhhccchhhhcccccccccccccHHHhccCCCEEEEEEEe-CC
Confidence            45899999999999884  8999999999999999998321            112345669999999999998 44

>PRK13763 putative RNA-processing protein; Provisional

Probab=95.91  E-value=0.011  Score=61.36  Aligned_cols=51  Identities=33%  Similarity=0.460  Sum_probs=46.6

Q ss_pred             hhhhhcCCCccchhhhhhhhCceEEeeCCEEEEEecCHHHHHHHHHHHHHHh
Q 002054          626 TLRRLIGPLGALKRKIEEETGGRISVSDGTLTVVAKNRSVMEKVLEKVDFII  677 (974)
Q Consensus       626 ki~~vIg~gGk~i~~i~~~~g~~Idi~dg~v~i~~~~~~~~~~a~~~i~~l~  677 (974)
                      ..+.+||+||++++.|++.||++|.+++..+.+.+ +.+..+.|++.++.|.
T Consensus       105 ~~griIG~~G~~~k~ie~~t~~~i~i~~~~v~i~G-~~~~~~~A~~~I~~li  155 (180)
T PRK13763        105 IKGRIIGEGGKTRRIIEELTGVDISVYGKTVAIIG-DPEQVEIAREAIEMLI  155 (180)
T ss_pred             HhhheeCCCcHHHHHHHHHHCcEEEEcCCEEEEEe-CHHHHHHHHHHHHHHH
Confidence            57899999999999999999999999988899986 7789999999998887

>COG1107 Archaea-specific RecJ-like exonuclease, contains DnaJ-type Zn finger domain [DNA replication, recombination, and repair]

Probab=95.90  E-value=0.0064  Score=71.07  Aligned_cols=61  Identities=23%  Similarity=0.440  Sum_probs=57.1

Q ss_pred             ccccCCCCCEEEEEEEEEeCCeEEEEeCCCeEEEEecccCCC-CCCCCCCEEEEEEEEEeCC
Q 002054          904 SAKNLKLGTKVAAKVYQVRARGLVLDLGGGIRGMYRFENNEK-KDFVVGDELLVKCSSFTGK  964 (974)
Q Consensus       904 ~~~~~~vG~vV~G~V~~I~~~GvFV~L~~gv~Glih~se~~~-~~f~vGd~V~vkVl~id~~  964 (974)
                      ..+++..|....|+|.++.+||+||+|+..+.||+|.+++.. ..|.+||++-+.|..+.+.
T Consensus       116 ~~~Dve~g~~Y~g~v~~v~~~GvFv~Ln~~v~GL~~~~d~~~~~~~~vgdeiiV~v~~vr~~  177 (715)
T COG1107         116 TMEDVEAGKYYKGIVSRVEKYGVFVELNSHVRGLIHRRDLGGDPDYAVGDEIIVQVSDVRPE  177 (715)
T ss_pred             chhhcccceeeeccccchhhhcceeecChhhhccccccccCCCCCCCCCCeEEEEeeccCCC
Confidence            478899999999999999999999999999999999999974 6899999999999999877

>PRK10811 rne ribonuclease E; Reviewed

Probab=95.90  E-value=0.013  Score=72.67  Aligned_cols=61  Identities=26%  Similarity=0.511  Sum_probs=51.1

Q ss_pred             cccCcEEEEEEEEEeec--eEEEEEcCCeEEEEecccCCCcccc---------ccccccccCCEEEEEEEEE
Q 002054          681 IEVGGIYKGVVTSVKEY--GAFVEFNGGQQGLLHVSELSHEPVS---------RVSDVVSVGQQLSLRCIGQ  741 (974)
Q Consensus       681 ~~~G~i~~G~V~~i~~~--G~fV~l~~g~~Glvhisels~~~v~---------~~~~~~~vGd~V~vkVl~i  741 (974)
                      ..+|.||.|+|.+|.+.  ++||+|+.+..||+|++++....+.         +..+.++.||.|-|.|.+-
T Consensus        36 ~~vGnIYkGkVenIvPGInAAFVDIG~gknGFL~L~Di~~~~f~~~~~~~~~~~i~~~Lk~GqeILVQV~KE  107 (1068)
T PRK10811         36 QKKANIYKGKITRIEPSLEAAFVDYGAERHGFLPLKEIAREYFPANYSAHGRPNIKDVLREGQEVIVQIDKE  107 (1068)
T ss_pred             cCccceEEEEEecccCCcceeEEEecCCcceEEEhhhccccccccccccccccccccccCCCCEEEEEEeec
Confidence            35899999999999884  8999999999999999999654322         2355699999999999983

>cd02396 PCBP_like_KH K homology RNA-binding domain, PCBP_like

Probab=95.89  E-value=0.015  Score=49.73  Aligned_cols=54  Identities=30%  Similarity=0.410  Sum_probs=42.6

Q ss_pred             eeeeccchhhhhcCCCccchhhhhhhhCceEEee-C-------CEEEEEecCHHHHHHHHHHH
Q 002054          619 TLKYDNDTLRRLIGPLGALKRKIEEETGGRISVS-D-------GTLTVVAKNRSVMEKVLEKV  673 (974)
Q Consensus       619 ~~~i~~~ki~~vIg~gGk~i~~i~~~~g~~Idi~-d-------g~v~i~~~~~~~~~~a~~~i  673 (974)
                      .+.++.++++.+||.+|.+|+.|++++|++|.+. +       ..+.+.+ +.+..++|..+|
T Consensus         3 r~~ip~~~vg~iIG~~G~~i~~i~~~tga~I~i~~~~~~~~~~r~v~I~G-~~~~v~~A~~~I   64 (65)
T cd02396           3 RLLVPSSQAGSIIGKGGSTIKEIREETGAKIRVSKSVLPGSTERVVTISG-KPSAVQKALLLI   64 (65)
T ss_pred             EEEECHHHcCeeECCCcHHHHHHHHHHCCEEEEcCCCCCCCCceEEEEEe-CHHHHHHHHHhh
Confidence            5778999999999999999999999999999875 1       2455555 456677776554

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

>PRK12329 nusA transcription elongation factor NusA; Provisional

Probab=95.89  E-value=0.026  Score=65.26  Aligned_cols=56  Identities=7%  Similarity=0.136  Sum_probs=50.7

Q ss_pred             CCCCEEEEEEEEEeCCeEEEEeC----C-CeEEEEecccC-CCCCCCCCCEEEEEEEEEeCC
Q 002054          909 KLGTKVAAKVYQVRARGLVLDLG----G-GIRGMYRFENN-EKKDFVVGDELLVKCSSFTGK  964 (974)
Q Consensus       909 ~vG~vV~G~V~~I~~~GvFV~L~----~-gv~Glih~se~-~~~~f~vGd~V~vkVl~id~~  964 (974)
                      ++|++|+|+|.++...+++|+|+    . ++.|++|.++. +.+.|++||+|+|.|.+|+..
T Consensus       151 ~~GeIV~G~V~r~e~~~viv~l~~~~g~~~~EaiLP~~Eqip~E~y~~Gdrika~i~~V~~~  212 (449)
T PRK12329        151 LEDTVLTARVLRFERQSVIMAVSSGFGQPEVEAELPKREQLPNDNYRANATFKVFLKEVSEG  212 (449)
T ss_pred             hcCcEEEEEEEEEcCCCEEEEecccCCCcceEEEecHHHcCCCCcCCCCCEEEEEEEEeecC
Confidence            69999999999999999999994    2 49999999966 788999999999999999875

>PHA02858 EIF2a-like PKR inhibitor; Provisional

Probab=95.72  E-value=0.029  Score=49.81  Aligned_cols=56  Identities=16%  Similarity=0.203  Sum_probs=48.4

Q ss_pred             CCCCCEEEEEEEEEeCCeEEEEeCC-CeEEEEe-cccCC-------CCCCCCCCEEEEEEEEEeCCC
Q 002054          908 LKLGTKVAAKVYQVRARGLVLDLGG-GIRGMYR-FENNE-------KKDFVVGDELLVKCSSFTGKG  965 (974)
Q Consensus       908 ~~vG~vV~G~V~~I~~~GvFV~L~~-gv~Glih-~se~~-------~~~f~vGd~V~vkVl~id~~~  965 (974)
                      -.+|+++. .|+.|++.|++|.|-+ |+.|++. .+++.       .+.+ +|-...|+|+.+|..+
T Consensus        14 P~v~dvv~-~Vv~i~d~~~YV~LleY~iegmIl~~selsr~rirsi~kll-VGk~e~v~ViRVDk~K   78 (86)
T PHA02858         14 PNINEVTK-GIVFVKDNIFYVKLIDYGLEALIVNYVNVNADRAEKLKKKL-VGKTINVQVIRTDKLK   78 (86)
T ss_pred             CCCCeEEE-EEEEEeccEEEEEEecCccceEEecHHHHhHHHHHhhhhhh-cCCeeEEEEEEECCCC
Confidence            46899999 8999999999999987 9999998 66663       4456 9999999999999764

>PTZ00162 DNA-directed RNA polymerase II subunit 7; Provisional

Probab=95.58  E-value=0.032  Score=57.68  Aligned_cols=55  Identities=11%  Similarity=0.072  Sum_probs=46.3

Q ss_pred             CCCCEEEEEEEEEeCCeEEEEeCCCeEEEEecccCC-------------------CCCCCCCCEEEEEEEEEeCC
Q 002054          909 KLGTKVAAKVYQVRARGLVLDLGGGIRGMYRFENNE-------------------KKDFVVGDELLVKCSSFTGK  964 (974)
Q Consensus       909 ~vG~vV~G~V~~I~~~GvFV~L~~gv~Glih~se~~-------------------~~~f~vGd~V~vkVl~id~~  964 (974)
                      -+|+++.|+|+++.++|+||.++ =+++++|.+.++                   ...++.|+.|++||.++.-+
T Consensus        80 f~gEVv~g~V~~v~~~G~~v~~G-p~~ifI~~~~l~~~~~fd~~~~~~~~~~~~~~~~i~~g~~VR~rV~~v~~~  153 (176)
T PTZ00162         80 FKDEVLDAIVTDVNKLGFFAQAG-PLKAFVSRSAIPPDFVYDSDSAYPCYISSDGQIQIKPNTEVRLRLQGVRYD  153 (176)
T ss_pred             CCCCEEEEEEEEEecceEEEEee-CeEEEEcHHHCCCccEECCCCCcceEecCCCcEEECCCCEEEEEEEEEEec
Confidence            48999999999999999999996 667999999553                   12478899999999888644

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

Probab=95.29  E-value=0.059  Score=57.44  Aligned_cols=65  Identities=22%  Similarity=0.328  Sum_probs=58.7

Q ss_pred             CCCCEEEEEEEEEeCCeEEEEeCCCeEEEEecccCC-----------CCCCCCCCEEEEEEEEEeCCCceeeeecC
Q 002054          909 KLGTKVAAKVYQVRARGLVLDLGGGIRGMYRFENNE-----------KKDFVVGDELLVKCSSFTGKGIPVVSLVD  973 (974)
Q Consensus       909 ~vG~vV~G~V~~I~~~GvFV~L~~gv~Glih~se~~-----------~~~f~vGd~V~vkVl~id~~~~~~~~~~~  973 (974)
                      ++||+|-|+|..+...+-.|++..-+.+++|.|++.           ...|++||-|.|+|.++|+++.+.+++.|
T Consensus        63 ~~gD~VIG~I~~v~~~~W~VDI~sp~~A~L~ls~~~~r~~~~~~~~~r~~l~vGD~v~AkV~~vd~~~~~~L~~k~  138 (239)
T COG1097          63 EVGDVVIGKIIEVGPSGWKVDIGSPYPALLSLSDFLRRKFENAEKDLRPFLNVGDLVYAKVVDVDRDGEVELTLKD  138 (239)
T ss_pred             CCCCEEEEEEEEEcccceEEEcCCccceEeehhhhhcccccccccccccccccCCEEEEEEEEccCCCceEEEeec
Confidence            699999999999999999999998899999999662           44699999999999999999999888754

>KOG1856 consensus Transcription elongation factor SPT6 [RNA processing and modification]

Probab=95.27  E-value=0.025  Score=70.75  Aligned_cols=75  Identities=27%  Similarity=0.329  Sum_probs=65.1

Q ss_pred             ccccCcEEEEEEEEEeece---EEEEEcCCeEEEEecccCCCccccccccccccCCEEEEEEEEEccCC-ceEEEEecc
Q 002054          680 EIEVGGIYKGVVTSVKEYG---AFVEFNGGQQGLLHVSELSHEPVSRVSDVVSVGQQLSLRCIGQDVRG-NIKLSLKAV  754 (974)
Q Consensus       680 ~~~~G~i~~G~V~~i~~~G---~fV~l~~g~~Glvhisels~~~v~~~~~~~~vGd~V~vkVl~id~~g-ri~LS~K~~  754 (974)
                      .+..|.++.++|++++..-   +-|.+..|+.|+||.+++|+..+.+|...+++||.|.|||+++|... -+.||+|..
T Consensus       982 t~~~g~iV~~~V~~vt~rr~~Cv~v~ld~G~~g~i~~~~~Sd~~v~~p~~~v~vgq~v~~kvi~id~e~f~v~Ls~r~s 1060 (1299)
T KOG1856|consen  982 TFYEGAIVPVTVTKVTHRRGICVRVRLDCGVTGFILAKNLSDRDVRRPENRVKVGQTVYCKVIKIDKERFSVELSCRTS 1060 (1299)
T ss_pred             HhccCceEEEeeeEEEecccceeEEEecCCCceeeeccccChhhccCHHHhhccCceEEEEeeeeeHhhhhhhhhhhhH
Confidence            4779999999999997654   56788899999999999999999999999999999999999999733 566777654

>TIGR02062 RNase_B exoribonuclease II

Probab=95.17  E-value=0.051  Score=67.16  Aligned_cols=58  Identities=16%  Similarity=0.177  Sum_probs=48.6

Q ss_pred             CCEEEEEEEEEeCCeEEEEeCC-CeEEEEecccCCC-------------------CCCCCCCEEEEEEEEEeCCCcee
Q 002054          911 GTKVAAKVYQVRARGLVLDLGG-GIRGMYRFENNEK-------------------KDFVVGDELLVKCSSFTGKGIPV  968 (974)
Q Consensus       911 G~vV~G~V~~I~~~GvFV~L~~-gv~Glih~se~~~-------------------~~f~vGd~V~vkVl~id~~~~~~  968 (974)
                      |+...|.|..++++|+||+|.+ |+.||||.+.+..                   ..|+.||+|+|+|.++|.....+
T Consensus       558 ~~~f~g~I~~v~~~g~~v~l~~~~~~g~v~~~~l~~~~~~~~~~~~~~~~~l~g~~~~~lgd~v~V~v~~vd~~~~~i  635 (639)
T TIGR02062       558 NTRFAAEIVDISRGGMRVRLLENGAIAFIPAAFLHANREELVCNQENGTVQIKGETVYKIGDVIDVVLTEVRMETRSI  635 (639)
T ss_pred             CcEEEEEEEeeeCCcEEEEEecCceEEEEEhhhcCCCCcceEEcccccEEEEeccEEEecCCEEEEEEEEeccccCcE
Confidence            4599999999999999999965 8999999885521                   13889999999999999776544

This family consists of exoribonuclease II, the product of the rnb gene, as found in a number of gamma proteobacteria. In Escherichia coli, it is one of eight different exoribonucleases. It is involved in mRNA degradation and tRNA precursor end processing.

>COG0557 VacB Exoribonuclease R [Transcription]

Probab=95.14  E-value=0.051  Score=68.08  Aligned_cols=61  Identities=23%  Similarity=0.351  Sum_probs=52.8

Q ss_pred             cccCCCCCEEEEEEEEEeCCeEEEEeCC-CeEEEEecccCC------------------CCCCCCCCEEEEEEEEEeCCC
Q 002054          905 AKNLKLGTKVAAKVYQVRARGLVLDLGG-GIRGMYRFENNE------------------KKDFVVGDELLVKCSSFTGKG  965 (974)
Q Consensus       905 ~~~~~vG~vV~G~V~~I~~~GvFV~L~~-gv~Glih~se~~------------------~~~f~vGd~V~vkVl~id~~~  965 (974)
                      +-.-.+|+..+|+|.++..+|+||.|++ +++|++|.+.++                  ...|+.||+|+++|++++..-
T Consensus       617 ~m~~~vg~~f~g~V~~v~~~g~~V~l~~~~ieglV~~s~L~~d~y~~~~~~~~l~~~~~~~~~~lgd~v~v~v~~v~~~~  696 (706)
T COG0557         617 YMKKRVGEEFDGVVTGVTSFGFFVELPELGLEGLVHISSLPDDYYHFDERGQALVGEKSGKVYRLGDEVKVKVTSVDLDE  696 (706)
T ss_pred             HHHHhcCCEEEEEEEEEEeccEEEEecccccccceEcccCCCceeeeccccceeeccccccccccCCEEEEEEEEEcccc
Confidence            4456899999999999999999999998 699999999664                  235999999999999998543

>PRK12329 nusA transcription elongation factor NusA; Provisional

Probab=94.55  E-value=0.2  Score=58.18  Aligned_cols=67  Identities=12%  Similarity=0.049  Sum_probs=55.7

Q ss_pred             cccCcEEEEEEEEEeeceEEEEEc---C--CeEEEEecccCCCccccccccccccCCEEEEEEEEEcc---CC-ceEEEE
Q 002054          681 IEVGGIYKGVVTSVKEYGAFVEFN---G--GQQGLLHVSELSHEPVSRVSDVVSVGQQLSLRCIGQDV---RG-NIKLSL  751 (974)
Q Consensus       681 ~~~G~i~~G~V~~i~~~G~fV~l~---~--g~~Glvhisels~~~v~~~~~~~~vGd~V~vkVl~id~---~g-ri~LS~  751 (974)
                      -++|+++.|+|.++...+++|++.   +  +.+|+||.++..      |.+.|++||.|+|.|.++..   +| +|.||+
T Consensus       150 ~~~GeIV~G~V~r~e~~~viv~l~~~~g~~~~EaiLP~~Eqi------p~E~y~~Gdrika~i~~V~~~~~kGpqIilSR  223 (449)
T PRK12329        150 DLEDTVLTARVLRFERQSVIMAVSSGFGQPEVEAELPKREQL------PNDNYRANATFKVFLKEVSEGPRRGPQLFVSR  223 (449)
T ss_pred             HhcCcEEEEEEEEEcCCCEEEEecccCCCcceEEEecHHHcC------CCCcCCCCCEEEEEEEEeecCCCCCCEEEEEc
Confidence            479999999999999999999983   3  389999988764      34669999999999999965   33 699998


Q ss_pred             ec
Q 002054          752 KA  753 (974)
Q Consensus       752 K~  753 (974)
                      -.
T Consensus       224 t~  225 (449)
T PRK12329        224 AN  225 (449)
T ss_pred             CC
Confidence            53

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

Probab=94.29  E-value=0.34  Score=53.41  Aligned_cols=120  Identities=20%  Similarity=0.228  Sum_probs=72.1

Q ss_pred             EeeCCceEEEEeeccCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCCCCCCCCC-cce--eeeeccchhhhhcCCC
Q 002054          558 AGTRIGVTAIQLDIKPAGIPLDIICECLEHAHKGRLQILDHMEREISAPRTQDDRNSP-RLA--TLKYDNDTLRRLIGPL  634 (974)
Q Consensus       558 a~t~~gI~alq~~~k~~~i~~e~l~~al~~A~~~~~~I~~~m~~~i~~~~~~~~~~~p-~~~--~~~i~~~ki~~vIg~g  634 (974)
                      -+|.+.||.+|-.       .+.++..++.-.+...+..+.+.+    +..-+.+..| |..  .+-+|..--+-+||+|
T Consensus        82 PGTTeRvcli~Gt-------~eai~av~efI~dKire~p~~~~k----~v~~~~pqt~~r~kqikivvPNstag~iigkg  150 (402)
T KOG2191|consen   82 PGTTERVCLIQGT-------VEALNAVHEFIADKIREKPQAVAK----PVDILQPQTPDRIKQIKIVVPNSTAGMIIGKG  150 (402)
T ss_pred             CCccceEEEEecc-------HHHHHHHHHHHHHHHHHhHHhhcC----CccccCCCCccccceeEEeccCCcccceecCC
Confidence            3677788888763       445555555433333333333222    1111122112 333  3345667789999999


Q ss_pred             ccchhhhhhhhCceEEee---------CCEEEEEecCHHHHHHHHHHHHHHhhcccccCcEEE
Q 002054          635 GALKRKIEEETGGRISVS---------DGTLTVVAKNRSVMEKVLEKVDFIIGREIEVGGIYK  688 (974)
Q Consensus       635 Gk~i~~i~~~~g~~Idi~---------dg~v~i~~~~~~~~~~a~~~i~~l~~~~~~~G~i~~  688 (974)
                      |.+||.|+|+.|..|.|.         ..+|.....+.+...+|..+|-..+..+++-+.-+.
T Consensus       151 gAtiK~~~Eqsga~iqisPqkpt~~sLqervvt~sge~e~~~~A~~~IL~Ki~eDpqs~scln  213 (402)
T KOG2191|consen  151 GATIKAIQEQSGAWIQISPQKPTGISLQERVVTVSGEPEQNMKAVSLILQKIQEDPQSGSCLN  213 (402)
T ss_pred             cchHHHHHHhhCcceEecccCCCCccceeEEEEecCCHHHHHHHHHHHHHHhhcCCcccceec
Confidence            999999999999877653         245555566777777777666443436777666543

>PF13014 KH_3: KH domain

Probab=93.26  E-value=0.042  Score=42.98  Aligned_cols=27  Identities=37%  Similarity=0.655  Sum_probs=24.1

Q ss_pred             hhhhcCCCccchhhhhhhhCceEEeeC
Q 002054          627 LRRLIGPLGALKRKIEEETGGRISVSD  653 (974)
Q Consensus       627 i~~vIg~gGk~i~~i~~~~g~~Idi~d  653 (974)
                      .+.+||++|.+|++|++++|++|.+.+
T Consensus         2 vg~iIG~~G~~I~~I~~~tg~~I~i~~   28 (43)
T PF13014_consen    2 VGRIIGKGGSTIKEIREETGAKIQIPP   28 (43)
T ss_pred             cCeEECCCChHHHHHHHHhCcEEEECC
Confidence            577999999999999999999998753

>KOG3409 consensus Exosomal 3'-5' exoribonuclease complex, subunit ski4 (Csl4) [Translation, ribosomal structure and biogenesis]

Probab=92.78  E-value=0.35  Score=48.79  Aligned_cols=58  Identities=28%  Similarity=0.348  Sum_probs=45.8

Q ss_pred             CCCCEEEEEEEEEeCCeEEEEe--------CCCeEEEEecccCC---------CCCCCCCCEEEEEEEEEeCCCc
Q 002054          909 KLGTKVAAKVYQVRARGLVLDL--------GGGIRGMYRFENNE---------KKDFVVGDELLVKCSSFTGKGI  966 (974)
Q Consensus       909 ~vG~vV~G~V~~I~~~GvFV~L--------~~gv~Glih~se~~---------~~~f~vGd~V~vkVl~id~~~~  966 (974)
                      .+|++|+++|..|...-+-+++        .+.++|++|..+..         -+.|+|||.|.|+|++.+.+..
T Consensus        67 ~~G~IVtarV~~i~~rfAkv~I~~V~d~~lk~~FrglirkqdvR~tEkdrv~v~ksFrPgDiVlAkVis~~~~~~  141 (193)
T KOG3409|consen   67 FVGAIVTARVSRINLRFAKVDILSVGDKPLKKSFRGLIRKQDVRATEKDRVKVYKSFRPGDIVLAKVISLGDGSN  141 (193)
T ss_pred             ccCcEEEEEEEeeccceeeEEEEEEcCEEhhhhhcceeehhhccccccchhhhhhccCCCcEEEEEEeecCCCCc
Confidence            4899999999999887777665        34799999998662         3469999999999999654443

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

Probab=92.68  E-value=0.5  Score=54.83  Aligned_cols=88  Identities=18%  Similarity=0.356  Sum_probs=61.8

Q ss_pred             HHHHHHHHHHHHhcCCCCCCCCCCCc---ceeeeecc------chhhhhcCCCccchhhhhhhhCceEEee------CC-
Q 002054          591 GRLQILDHMEREISAPRTQDDRNSPR---LATLKYDN------DTLRRLIGPLGALKRKIEEETGGRISVS------DG-  654 (974)
Q Consensus       591 ~~~~I~~~m~~~i~~~~~~~~~~~p~---~~~~~i~~------~ki~~vIg~gGk~i~~i~~~~g~~Idi~------dg-  654 (974)
                      .+.++++.+.+.+... +...+|-|.   -..+.|+.      +.++-+||+.|.|.|.++++||++|-|-      +| 
T Consensus       111 er~e~I~~~lk~nP~f-kpP~DYk~p~~~~~Kv~IPvke~Pd~NFvGLiiGPRG~TqK~lE~etgAKI~IRGkgSvkEgk  189 (554)
T KOG0119|consen  111 ERHEIIEEILKLNPGF-KPPADYKPPAKLHDKVYIPVKEFPDINFVGLIIGPRGNTQKRLERETGAKIAIRGKGSVKEGK  189 (554)
T ss_pred             HHHHHHHHHHHhCcCC-CCCcccCcccccccceecchhhcCCcceeEEEecCCccHHHHHHHHhCCeEEEeccccccccc
Confidence            3444555555544433 234444443   34455654      4689999999999999999999999763      22 


Q ss_pred             ----------------EEEEEecCHHHHHHHHHHHHHHhhc
Q 002054          655 ----------------TLTVVAKNRSVMEKVLEKVDFIIGR  679 (974)
Q Consensus       655 ----------------~v~i~~~~~~~~~~a~~~i~~l~~~  679 (974)
                                      ...|++.+.+.+++|.+.|+.++..
T Consensus       190 ~~~~d~~~~~~~~epLH~~Isadt~eki~~Ai~vienli~~  230 (554)
T KOG0119|consen  190 GRSDDLSYIPKENEPLHCLISADTQEKIKKAIAVIENLIQS  230 (554)
T ss_pred             cCCcccccccccccceeEEEecchHHHHHHHHHHHHHHHHh
Confidence                            2478899999999999999988853

>COG1530 CafA Ribonucleases G and E [Translation, ribosomal structure and biogenesis]

Probab=92.50  E-value=0.14  Score=61.23  Aligned_cols=62  Identities=34%  Similarity=0.431  Sum_probs=52.7

Q ss_pred             ccccCcEEEEEEEEEeec--eEEEEEcCCeEEEEecccCCCcccccc-----ccccccCCEEEEEEEEEc
Q 002054          680 EIEVGGIYKGVVTSVKEY--GAFVEFNGGQQGLLHVSELSHEPVSRV-----SDVVSVGQQLSLRCIGQD  742 (974)
Q Consensus       680 ~~~~G~i~~G~V~~i~~~--G~fV~l~~g~~Glvhisels~~~v~~~-----~~~~~vGd~V~vkVl~id  742 (974)
                      ...+|.+|.|+|++|.+.  .+||+++....||+|.+++.+ +++.+     ...++.||.+-|.|+.-.
T Consensus        34 ~~~~gniy~grv~~i~p~~~aafvdig~~r~gfl~~~~~~~-~~~~~~~~~i~~~lr~~~~~~Vqv~ke~  102 (487)
T COG1530          34 EQIVGNIYKGRVTRVLPSLEAAFVDIGLERNGFLHLSEIVP-YFRAVLEEKIKVRLRGGQATLVQVVKEP  102 (487)
T ss_pred             EeeecCceEEEecccCccchhheeeccCCccceEEecccch-hhhhcccccceeeecCCceEEEEEEeec
Confidence            456899999999999886  789999988999999999988 54433     347999999999999843

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

Probab=91.93  E-value=0.44  Score=56.61  Aligned_cols=61  Identities=23%  Similarity=0.398  Sum_probs=49.7

Q ss_pred             ceeeeeccchhhhhcCCCccchhhhhhhhCceEEee--CC------EEEEEecCHHHHHHHHHHHHHHhh
Q 002054          617 LATLKYDNDTLRRLIGPLGALKRKIEEETGGRISVS--DG------TLTVVAKNRSVMEKVLEKVDFIIG  678 (974)
Q Consensus       617 ~~~~~i~~~ki~~vIg~gGk~i~~i~~~~g~~Idi~--dg------~v~i~~~~~~~~~~a~~~i~~l~~  678 (974)
                      -..++|+..+.+-|||.+|.+||.|+.+||++|-+.  |+      .+.|.. ..+..+.|.+.|..|+.
T Consensus       231 ~~~V~VPr~~VG~IIGkgGE~IKklq~etG~KIQfkpDd~p~speR~~~IiG-~~d~ie~Aa~lI~eii~  299 (600)
T KOG1676|consen  231 TREVKVPRSKVGIIIGKGGEMIKKLQNETGAKIQFKPDDDPSSPERPAQIIG-TVDQIEHAAELINEIIA  299 (600)
T ss_pred             eeEEeccccceeeEEecCchHHHHHhhccCceeEeecCCCCCCccceeeeec-CHHHHHHHHHHHHHHHH
Confidence            456788999999999999999999999999999874  33      345554 56788888888888883

>PRK10811 rne ribonuclease E; Reviewed

Probab=91.27  E-value=0.42  Score=60.01  Aligned_cols=55  Identities=16%  Similarity=0.253  Sum_probs=46.6

Q ss_pred             CCCCEEEEEEEEEeCC--eEEEEeCCCeEEEEecccCC----------------CCCCCCCCEEEEEEEEEeC
Q 002054          909 KLGTKVAAKVYQVRAR--GLVLDLGGGIRGMYRFENNE----------------KKDFVVGDELLVKCSSFTG  963 (974)
Q Consensus       909 ~vG~vV~G~V~~I~~~--GvFV~L~~gv~Glih~se~~----------------~~~f~vGd~V~vkVl~id~  963 (974)
                      .+|+++.|+|.+|.+-  ++||+|++|-.||+|.++..                +..+++||+|-|-|.+--.
T Consensus        37 ~vGnIYkGkVenIvPGInAAFVDIG~gknGFL~L~Di~~~~f~~~~~~~~~~~i~~~Lk~GqeILVQV~KEa~  109 (1068)
T PRK10811         37 KKANIYKGKITRIEPSLEAAFVDYGAERHGFLPLKEIAREYFPANYSAHGRPNIKDVLREGQEVIVQIDKEER  109 (1068)
T ss_pred             CccceEEEEEecccCCcceeEEEecCCcceEEEhhhccccccccccccccccccccccCCCCEEEEEEeeccc
Confidence            5899999999999665  89999999999999987662                2248899999999987443

>PF10246 MRP-S35: Mitochondrial ribosomal protein MRP-S35; InterPro: IPR019375 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms

Probab=90.84  E-value=1  Score=41.79  Aligned_cols=63  Identities=16%  Similarity=0.276  Sum_probs=52.4

Q ss_pred             ccccccccCCCCCEEEEEEEEEeCCeEEEEeCCCeEEEEecccCCCCCCCCCCEEEEEEEEEe
Q 002054          900 EAIVSAKNLKLGTKVAAKVYQVRARGLVLDLGGGIRGMYRFENNEKKDFVVGDELLVKCSSFT  962 (974)
Q Consensus       900 ~~p~~~~~~~vG~vV~G~V~~I~~~GvFV~L~~gv~Glih~se~~~~~f~vGd~V~vkVl~id  962 (974)
                      .+||..-.-..|.+|.|+|..|-+--+||+++......|.......+.|..|.+|.+++.+..
T Consensus        13 ~S~fi~lG~~~gk~V~G~I~hvv~ddLYIDfG~KFhcVc~rp~~~~~~y~~G~rV~lrLkdlE   75 (104)
T PF10246_consen   13 NSPFIQLGDPEGKIVIGKIFHVVDDDLYIDFGGKFHCVCKRPAVNGEKYVRGSRVRLRLKDLE   75 (104)
T ss_pred             CChhhhcCCccCCEEEEEEEEEecCceEEEeCCceeEEEecccccccccccCCEEEEEECCHh
Confidence            345532223699999999999988899999999999999998766778999999999987654

The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites [, ]. About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits. Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome [, ]. This is a family of short mitochondrial ribosomal proteins, less than 200 amino acids long. MRP-S35 was proposed as a more appropriate name to this group of proteins [].

>KOG1856 consensus Transcription elongation factor SPT6 [RNA processing and modification]

Probab=90.51  E-value=0.33  Score=61.29  Aligned_cols=64  Identities=20%  Similarity=0.285  Sum_probs=55.1

Q ss_pred             cccCCCCCEEEEEEEEEeCCe---EEEEeCCCeEEEEecccCC-------CCCCCCCCEEEEEEEEEeCCCcee
Q 002054          905 AKNLKLGTKVAAKVYQVRARG---LVLDLGGGIRGMYRFENNE-------KKDFVVGDELLVKCSSFTGKGIPV  968 (974)
Q Consensus       905 ~~~~~vG~vV~G~V~~I~~~G---vFV~L~~gv~Glih~se~~-------~~~f~vGd~V~vkVl~id~~~~~~  968 (974)
                      -+.+-+|.+|.++|++++..-   |=|.++.|+.|+|+.++.+       ...+++||+|.|||+++|.++.+|
T Consensus       980 ~et~~~g~iV~~~V~~vt~rr~~Cv~v~ld~G~~g~i~~~~~Sd~~v~~p~~~v~vgq~v~~kvi~id~e~f~v 1053 (1299)
T KOG1856|consen  980 PETFYEGAIVPVTVTKVTHRRGICVRVRLDCGVTGFILAKNLSDRDVRRPENRVKVGQTVYCKVIKIDKERFSV 1053 (1299)
T ss_pred             hhHhccCceEEEeeeEEEecccceeEEEecCCCceeeeccccChhhccCHHHhhccCceEEEEeeeeeHhhhhh
Confidence            456899999999999997665   6678999999999999664       446889999999999999988765

>PRK12442 translation initiation factor IF-1; Reviewed

Probab=90.40  E-value=1.2  Score=40.21  Aligned_cols=64  Identities=20%  Similarity=0.261  Sum_probs=51.0

Q ss_pred             EEEEEEEEEeeceEE-EEEcCCeEEEEecccCCCccccccccccccCCEEEEEEEEEcc-CCceEEEEec
Q 002054          686 IYKGVVTSVKEYGAF-VEFNGGQQGLLHVSELSHEPVSRVSDVVSVGQQLSLRCIGQDV-RGNIKLSLKA  753 (974)
Q Consensus       686 i~~G~V~~i~~~G~f-V~l~~g~~Glvhisels~~~v~~~~~~~~vGd~V~vkVl~id~-~gri~LS~K~  753 (974)
                      .++|+|+.+.+.+.| |.|.+|..-+.|+|=    +...-.-.+-+||.|.|.+--.|. +|+|..-.|.
T Consensus         8 e~~G~V~e~Lp~~~frV~LenG~~vla~isG----KmR~~rIrIl~GD~V~VE~spYDltkGRIiyR~~~   73 (87)
T PRK12442          8 ELDGIVDEVLPDSRFRVTLENGVEVGAYASG----RMRKHRIRILAGDRVTLELSPYDLTKGRINFRHKD   73 (87)
T ss_pred             EEEEEEEEECCCCEEEEEeCCCCEEEEEecc----ceeeeeEEecCCCEEEEEECcccCCceeEEEEecC
Confidence            589999999999998 699999999999873    333223337789999999988887 7899887763

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

Probab=90.16  E-value=0.61  Score=48.40  Aligned_cols=64  Identities=27%  Similarity=0.405  Sum_probs=55.1

Q ss_pred             CCcceeeeeccchhhhhcCCCccchhhhhhhhCceEEee--CCEEEEEec----CHHHHHHHHHHHHHHh
Q 002054          614 SPRLATLKYDNDTLRRLIGPLGALKRKIEEETGGRISVS--DGTLTVVAK----NRSVMEKVLEKVDFII  677 (974)
Q Consensus       614 ~p~~~~~~i~~~ki~~vIg~gGk~i~~i~~~~g~~Idi~--dg~v~i~~~----~~~~~~~a~~~i~~l~  677 (974)
                      .+....+.||+++++-+||+.|.+-+.|.+.+++++.+|  +|.|.+...    |.-...+|.+.++.+-
T Consensus         6 ~~~~~~v~iPk~R~~~lig~~g~v~k~ie~~~~~~~~iD~~~~~V~i~~~~~t~Dp~~~~ka~d~VkAIg   75 (194)
T COG1094           6 EKSSEAVKIPKDRIGVLIGKWGEVKKAIEEKTGVKLRIDSKTGSVTIRTTRKTEDPLALLKARDVVKAIG   75 (194)
T ss_pred             ccceeeeecCchhheeeecccccchHHHHhhcCeEEEEECCCCeEEEEecCCCCChHHHHHHHHHHHHHh
Confidence            345677899999999999999999999999999998887  689998877    6678888888887665

>KOG3409 consensus Exosomal 3'-5' exoribonuclease complex, subunit ski4 (Csl4) [Translation, ribosomal structure and biogenesis]

Probab=90.06  E-value=0.92  Score=45.86  Aligned_cols=73  Identities=18%  Similarity=0.143  Sum_probs=56.0

Q ss_pred             cccCcEEEEEEEEEeeceEEEEEc--------CCeEEEEecccCCCcc--ccccccccccCCEEEEEEEEEccCCceEEE
Q 002054          681 IEVGGIYKGVVTSVKEYGAFVEFN--------GGQQGLLHVSELSHEP--VSRVSDVVSVGQQLSLRCIGQDVRGNIKLS  750 (974)
Q Consensus       681 ~~~G~i~~G~V~~i~~~G~fV~l~--------~g~~Glvhisels~~~--v~~~~~~~~vGd~V~vkVl~id~~gri~LS  750 (974)
                      +.+|+|+.++|.++...-+-|+|.        ....|++|..++-..-  --++.+-|++||.|.++|++.+...+..||
T Consensus        66 P~~G~IVtarV~~i~~rfAkv~I~~V~d~~lk~~FrglirkqdvR~tEkdrv~v~ksFrPgDiVlAkVis~~~~~~y~LT  145 (193)
T KOG3409|consen   66 PFVGAIVTARVSRINLRFAKVDILSVGDKPLKKSFRGLIRKQDVRATEKDRVKVYKSFRPGDIVLAKVISLGDGSNYLLT  145 (193)
T ss_pred             CccCcEEEEEEEeeccceeeEEEEEEcCEEhhhhhcceeehhhccccccchhhhhhccCCCcEEEEEEeecCCCCcEEEE
Confidence            689999999999998887777764        2567999988874321  223455699999999999997666678888


Q ss_pred             Eec
Q 002054          751 LKA  753 (974)
Q Consensus       751 ~K~  753 (974)
                      .-+
T Consensus       146 tAe  148 (193)
T KOG3409|consen  146 TAE  148 (193)
T ss_pred             Eec
Confidence            543

>TIGR00008 infA translation initiation factor IF-1

Probab=89.66  E-value=1.4  Score=38.17  Aligned_cols=59  Identities=25%  Similarity=0.339  Sum_probs=46.1

Q ss_pred             EEEEEEEEEeeceEE-EEEcCCeEEEEecccCCCccccccccccccCCEEEEEEEEEcc-CCceE
Q 002054          686 IYKGVVTSVKEYGAF-VEFNGGQQGLLHVSELSHEPVSRVSDVVSVGQQLSLRCIGQDV-RGNIK  748 (974)
Q Consensus       686 i~~G~V~~i~~~G~f-V~l~~g~~Glvhisels~~~v~~~~~~~~vGd~V~vkVl~id~-~gri~  748 (974)
                      .+.|+|++..+.+.| |.+.+|.+-+.|+|=    +...-.-.+.+||.|.|.+-..|. +|+|.
T Consensus         6 e~~G~V~e~L~~~~f~V~l~ng~~vla~i~G----Kmr~~rI~I~~GD~V~Ve~spyd~tkgrIi   66 (68)
T TIGR00008         6 EMEGKVTESLPNAMFRVELENGHEVLAHISG----KIRMHYIRILPGDKVKVELSPYDLTRGRIT   66 (68)
T ss_pred             EEEEEEEEECCCCEEEEEECCCCEEEEEecC----cchhccEEECCCCEEEEEECcccCCcEeEE
Confidence            578999999999998 699999999999873    232223347889999999887776 67764

This family consists of translation initiation factor IF-1 as found in bacteria and chloroplasts. This protein, about 70 residues in length, consists largely of an S1 RNA binding domain (pfam00575).

>COG1096 Predicted RNA-binding protein (consists of S1 domain and a Zn-ribbon domain) [Translation, ribosomal structure and biogenesis]

Probab=89.24  E-value=0.91  Score=46.76  Aligned_cols=58  Identities=19%  Similarity=0.173  Sum_probs=46.7

Q ss_pred             cccCCCCCEEEEEEEEEeCCeEEEEeCC----------CeEEEEecccCC-------CCCCCCCCEEEEEEEEEe
Q 002054          905 AKNLKLGTKVAAKVYQVRARGLVLDLGG----------GIRGMYRFENNE-------KKDFVVGDELLVKCSSFT  962 (974)
Q Consensus       905 ~~~~~vG~vV~G~V~~I~~~GvFV~L~~----------gv~Glih~se~~-------~~~f~vGd~V~vkVl~id  962 (974)
                      ..-.+.|++|-|.|.++....+.|++-.          -..|-+|.|+..       .+.|++||-|+|+|++.-
T Consensus        59 ~~~~K~GdiV~grV~~v~~~~a~V~i~~ve~~~r~~~~~~~~~ihvs~~~~~~~~~~~d~f~~GDivrA~Vis~~  133 (188)
T COG1096          59 PPLPKGGDIVYGRVTDVREQRALVRIVGVEGKERELATSGAADIHVSQVRDGYVEKLSDAFRIGDIVRARVISTG  133 (188)
T ss_pred             CCCCCCCCEEEEEEeeccceEEEEEEEEEecccccCCCCceeeEEEEecccccccccccccccccEEEEEEEecC
Confidence            3446889999999999999999987742          256778988552       567999999999999974

>PRK11712 ribonuclease G; Provisional

Probab=88.33  E-value=0.97  Score=54.01  Aligned_cols=55  Identities=13%  Similarity=0.128  Sum_probs=46.2

Q ss_pred             cCCCCCEEEEEEEEEeCC--eEEEEeCCCeEEEEecccCCC-------------------CCCCCCCEEEEEEEEE
Q 002054          907 NLKLGTKVAAKVYQVRAR--GLVLDLGGGIRGMYRFENNEK-------------------KDFVVGDELLVKCSSF  961 (974)
Q Consensus       907 ~~~vG~vV~G~V~~I~~~--GvFV~L~~gv~Glih~se~~~-------------------~~f~vGd~V~vkVl~i  961 (974)
                      ...+|+++.|+|.+|.+-  ++||+++.+-.||+|.++...                   +.+++||+|-|.|++=
T Consensus        35 ~~~vGnIY~G~V~~v~pg~~AAFVdIG~~k~gFL~~~d~~~~~~~~~~~~~~~~~~~~i~~~l~~Gq~iLVQV~Ke  110 (489)
T PRK11712         35 RGIVGNIYKGRVSRVLPGMQAAFVDIGLDKAAFLHASDIVPHTECVAGEEQKQFVVRDISELVRQGQDIMVQVVKD  110 (489)
T ss_pred             ccccccEEEEEEeecCCCCceeEEeeCCCccEEEEhhhccchhhhcccccccccccccHHHhccCCCEEEEEEEeC
Confidence            346999999999999775  899999999999999997621                   1288899999999863

>TIGR03319 YmdA_YtgF conserved hypothetical protein YmdA/YtgF

Probab=88.18  E-value=1.9  Score=52.13  Aligned_cols=62  Identities=21%  Similarity=0.262  Sum_probs=50.2

Q ss_pred             cceeeeeccch-hhhhcCCCccchhhhhhhhCceEEeeC--CEEEEEecCHHHHHHHHHHHHHHh
Q 002054          616 RLATLKYDNDT-LRRLIGPLGALKRKIEEETGGRISVSD--GTLTVVAKNRSVMEKVLEKVDFII  677 (974)
Q Consensus       616 ~~~~~~i~~~k-i~~vIg~gGk~i~~i~~~~g~~Idi~d--g~v~i~~~~~~~~~~a~~~i~~l~  677 (974)
                      .+.++.+|.|. -|.+||..|.|||.++.-||+.+=|||  +.|.+++.|.---+-|+..++.|+
T Consensus       204 ~~~~v~lp~d~~kgriigreGrnir~~e~~tgvd~iiddtp~~v~ls~fdp~rreia~~~l~~li  268 (514)
T TIGR03319       204 TVSVVNLPNDEMKGRIIGREGRNIRALETLTGVDLIIDDTPEAVILSGFDPVRREIARMALEKLI  268 (514)
T ss_pred             eeeeEEcCChhhhccccCCCcchHHHHHHHhCceEEEcCCCCeEEecCCchHHHHHHHHHHHHHH
Confidence            35567788865 499999999999999999999988884  688999988766666666666665

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

Probab=87.99  E-value=0.53  Score=48.86  Aligned_cols=59  Identities=34%  Similarity=0.451  Sum_probs=48.5

Q ss_pred             hhhhcCCCccchhhhhhhhCceEEeeCCEEEEEecCHHHHHHHHHHHHHHhhcccccCcEE
Q 002054          627 LRRLIGPLGALKRKIEEETGGRISVSDGTLTVVAKNRSVMEKVLEKVDFIIGREIEVGGIY  687 (974)
Q Consensus       627 i~~vIg~gGk~i~~i~~~~g~~Idi~dg~v~i~~~~~~~~~~a~~~i~~l~~~~~~~G~i~  687 (974)
                      .+.+||++|++-+.|++-||++|.+-+.+|.+.+. .+.++.|++.++.++ ...+.|.+|
T Consensus       113 kgRIIG~~GkTr~~IE~lt~~~I~V~g~tVaiiG~-~~~v~iAr~AVemli-~G~~h~~Vy  171 (194)
T COG1094         113 KGRIIGREGKTRRAIEELTGVYISVYGKTVAIIGG-FEQVEIAREAVEMLI-NGAPHGKVY  171 (194)
T ss_pred             hceeeCCCchHHHHHHHHhCCeEEEeCcEEEEecC-hhhhHHHHHHHHHHH-cCCCchhHH
Confidence            58999999999999999999999998889999875 478888888888877 444555444

>PRK00106 hypothetical protein; Provisional

Probab=87.42  E-value=2.5  Score=51.08  Aligned_cols=62  Identities=21%  Similarity=0.272  Sum_probs=51.0

Q ss_pred             cceeeeeccch-hhhhcCCCccchhhhhhhhCceEEeeC--CEEEEEecCHHHHHHHHHHHHHHh
Q 002054          616 RLATLKYDNDT-LRRLIGPLGALKRKIEEETGGRISVSD--GTLTVVAKNRSVMEKVLEKVDFII  677 (974)
Q Consensus       616 ~~~~~~i~~~k-i~~vIg~gGk~i~~i~~~~g~~Idi~d--g~v~i~~~~~~~~~~a~~~i~~l~  677 (974)
                      .+.++.+|.|. -|.+||..|.|||.++.-||+.+=|||  +.|.+++.|.---+-|+..++.|+
T Consensus       225 tvs~v~lp~demkGriIGreGrNir~~E~~tGvdliiddtp~~v~lS~fdpvRReiAr~~le~Li  289 (535)
T PRK00106        225 TITTVHLPDDNMKGRIIGREGRNIRTLESLTGIDVIIDDTPEVVVLSGFDPIRREIARMTLESLI  289 (535)
T ss_pred             eeeeEEcCChHhhcceeCCCcchHHHHHHHhCceEEEcCCCCeEEEeCCChHHHHHHHHHHHHHH
Confidence            35567788865 599999999999999999999988874  688999999777777777677665

>KOG3298 consensus DNA-directed RNA polymerase subunit E' [Transcription]

Probab=87.24  E-value=2.5  Score=42.51  Aligned_cols=62  Identities=21%  Similarity=0.275  Sum_probs=42.9

Q ss_pred             ccccCcEEEEEEEEEeeceEEEEEcCCeEEEEecccCCC----c-------cccccccccccCCEEEEEEEEEc
Q 002054          680 EIEVGGIYKGVVTSVKEYGAFVEFNGGQQGLLHVSELSH----E-------PVSRVSDVVSVGQQLSLRCIGQD  742 (974)
Q Consensus       680 ~~~~G~i~~G~V~~i~~~G~fV~l~~g~~Glvhisels~----~-------~v~~~~~~~~vGd~V~vkVl~id  742 (974)
                      .+-.|++++|.|+++...|+|++.+| .+-++-.-.+..    .       +..+-..+.++|.+|++||++.-
T Consensus        78 kpfKGEVvdgvV~~Vnk~G~F~~~GP-l~~f~sshl~ppd~~f~p~~n~P~f~~~d~s~I~~~~~VR~kiigtr  150 (170)
T KOG3298|consen   78 KPFKGEVVDGVVTKVNKMGVFARSGP-LEVFYSSHLKPPDYEFDPGENPPNFQTEDESVIQKGVEVRLKIIGTR  150 (170)
T ss_pred             eecCCcEEEEEEEEEeeeeEEEeccc-eEeeeecccCCCCcccCCCCCCCcccccccceeeeCcEEEEEEEEEE
Confidence            45679999999999999999999965 444442211111    1       11122236899999999999964

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

Probab=86.83  E-value=1.2  Score=50.77  Aligned_cols=62  Identities=31%  Similarity=0.455  Sum_probs=45.1

Q ss_pred             HHHHHHHHHHHHHHHHhcCCCCCCCCCCCcceeeeeccchhhhhcCCCccchhhhhhhhCceEEee
Q 002054          587 HAHKGRLQILDHMEREISAPRTQDDRNSPRLATLKYDNDTLRRLIGPLGALKRKIEEETGGRISVS  652 (974)
Q Consensus       587 ~A~~~~~~I~~~m~~~i~~~~~~~~~~~p~~~~~~i~~~ki~~vIg~gGk~i~~i~~~~g~~Idi~  652 (974)
                      .+.++|+.|++.|.+.-...+.  ..-.|  ..+.-.....|.+||+.|+++++|..+||++|.|.
T Consensus       255 g~s~Ac~~ILeimqkEA~~~k~--~~e~p--Lk~lAHN~lvGRLIGKeGrnlKkIeq~TgTkITis  316 (584)
T KOG2193|consen  255 GTSKACKMILEIMQKEAVDDKV--AEEIP--LKILAHNNLVGRLIGKEGRNLKKIEQDTGTKITIS  316 (584)
T ss_pred             chHHHHHHHHHHHHHhhhccch--hhhcc--hhhhhhcchhhhhhhhccccHHHHHhhcCCceeee
Confidence            5678899999999876554421  22212  22333455789999999999999999999998754

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

Probab=86.08  E-value=2.2  Score=50.88  Aligned_cols=93  Identities=17%  Similarity=0.233  Sum_probs=62.4

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHhcCCCCCCCCCCCcc---eeeeeccchhhhhcCCCccchhhhhhhhCceEEee------
Q 002054          582 CECLEHAHKGRLQILDHMEREISAPRTQDDRNSPRL---ATLKYDNDTLRRLIGPLGALKRKIEEETGGRISVS------  652 (974)
Q Consensus       582 ~~al~~A~~~~~~I~~~m~~~i~~~~~~~~~~~p~~---~~~~i~~~ki~~vIg~gGk~i~~i~~~~g~~Idi~------  652 (974)
                      .++++.|.+...+|+.   ++.+.......-.+|..   ..+.|+.+|-+-+||+||.|||.|..++|+++...      
T Consensus       284 ~d~ie~Aa~lI~eii~---~~~~~~~~~~~~G~P~~~~~fy~~VPa~KcGLvIGrGGEtIK~in~qSGA~~el~r~~p~~  360 (600)
T KOG1676|consen  284 VDQIEHAAELINEIIA---EAEAGAGGGMGGGAPGLVAQFYMKVPADKCGLVIGRGGETIKQINQQSGARCELSRQPPNG  360 (600)
T ss_pred             HHHHHHHHHHHHHHHH---HHhccCCCCcCCCCccceeeEEEeccccccccccCCCccchhhhcccCCccccccCCCCCC
Confidence            3455555544444443   34333323344455654   67789999999999999999999999999987642      


Q ss_pred             --CCEEEEEecCHHHHHHHHHHHHHHh
Q 002054          653 --DGTLTVVAKNRSVMEKVLEKVDFII  677 (974)
Q Consensus       653 --dg~v~i~~~~~~~~~~a~~~i~~l~  677 (974)
                        +.++.+..-++..++-|+..|+..+
T Consensus       361 ~~~ektf~IrG~~~QIdhAk~LIr~kv  387 (600)
T KOG1676|consen  361 NPKEKTFVIRGDKRQIDHAKQLIRDKV  387 (600)
T ss_pred             CccceEEEEecCcccchHHHHHHHHHh
Confidence              2345555566678888887776443

>PRK12704 phosphodiesterase; Provisional

Probab=85.87  E-value=2.9  Score=50.64  Aligned_cols=62  Identities=19%  Similarity=0.275  Sum_probs=49.2

Q ss_pred             cceeeeeccchh-hhhcCCCccchhhhhhhhCceEEeeC--CEEEEEecCHHHHHHHHHHHHHHh
Q 002054          616 RLATLKYDNDTL-RRLIGPLGALKRKIEEETGGRISVSD--GTLTVVAKNRSVMEKVLEKVDFII  677 (974)
Q Consensus       616 ~~~~~~i~~~ki-~~vIg~gGk~i~~i~~~~g~~Idi~d--g~v~i~~~~~~~~~~a~~~i~~l~  677 (974)
                      .+.++.+|.|.+ |.+||..|.|||.++.-||+.|=|||  +.|.+++.+...-+-|+..++.++
T Consensus       210 ~~~~v~lp~d~mkgriigreGrnir~~e~~tgvd~iiddtp~~v~ls~~~~~rre~a~~~l~~l~  274 (520)
T PRK12704        210 TVSVVNLPNDEMKGRIIGREGRNIRALETLTGVDLIIDDTPEAVILSGFDPIRREIARLALEKLV  274 (520)
T ss_pred             ceeeeecCCchhhcceeCCCcchHHHHHHHhCCeEEEcCCCCeEEEecCChhhHHHHHHHHHHHH
Confidence            355677888665 99999999999999999999988884  688888888766566666666554

>KOG2916 consensus Translation initiation factor 2, alpha subunit (eIF-2alpha) [Translation, ribosomal structure and biogenesis]

Probab=85.82  E-value=0.59  Score=50.22  Aligned_cols=58  Identities=19%  Similarity=0.139  Sum_probs=51.6

Q ss_pred             CCCCEEEEEEEEEeCCeEEEEeCC--CeEEEEecccCC-------CCCCCCCCEEEEEEEEEeCCCc
Q 002054          909 KLGTKVAAKVYQVRARGLVLDLGG--GIRGMYRFENNE-------KKDFVVGDELLVKCSSFTGKGI  966 (974)
Q Consensus       909 ~vG~vV~G~V~~I~~~GvFV~L~~--gv~Glih~se~~-------~~~f~vGd~V~vkVl~id~~~~  966 (974)
                      .++++|-+.|++|.+.|++|.|-+  ++.||+-.|+++       .+..++|-.=-|.|+.||++..
T Consensus        15 ev~e~VmvnV~sIaemGayv~LlEYnniEGmiLlsELSrRRIRSI~klirVGr~E~vvVlrVDkekG   81 (304)
T KOG2916|consen   15 EVEEIVMVNVRSIAEMGAYVKLLEYNNIEGMILLSELSRRRIRSIQKLIRVGRNEPVVVLRVDKEKG   81 (304)
T ss_pred             CcccEEEEEeeEehhccceEeeeecCCcccchhhhHHHHHHHHHHHHHHhcCCcceEEEEEEcCCCC
Confidence            589999999999999999999965  899999999996       4468899999999999997653

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

Probab=84.29  E-value=0.59  Score=39.57  Aligned_cols=36  Identities=25%  Similarity=0.279  Sum_probs=32.1

Q ss_pred             cceeeeeccchhhhhcCCCccchhhhhhhhCceEEe
Q 002054          616 RLATLKYDNDTLRRLIGPLGALKRKIEEETGGRISV  651 (974)
Q Consensus       616 ~~~~~~i~~~ki~~vIg~gGk~i~~i~~~~g~~Idi  651 (974)
                      ....+.++++.++..||++|.+|+.+..-+|.+|++
T Consensus        25 ~~~~v~V~~~~~~~aIGk~G~nI~~~~~l~~~~I~v   60 (61)
T cd02134          25 KRARVVVPDDQLGLAIGKGGQNVRLASKLLGEKIDI   60 (61)
T ss_pred             cEEEEEECcccceeeECCCCHHHHHHHHHHCCCeEE
Confidence            456778999999999999999999999999988875

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.

>KOG3298 consensus DNA-directed RNA polymerase subunit E' [Transcription]

Probab=83.61  E-value=4.3  Score=40.83  Aligned_cols=60  Identities=17%  Similarity=0.098  Sum_probs=42.1

Q ss_pred             CCCCEEEEEEEEEeCCeEEEEeCC-CeEEEEecc---------cC-C------CCCCCCCCEEEEEEEEEeCCCcee
Q 002054          909 KLGTKVAAKVYQVRARGLVLDLGG-GIRGMYRFE---------NN-E------KKDFVVGDELLVKCSSFTGKGIPV  968 (974)
Q Consensus       909 ~vG~vV~G~V~~I~~~GvFV~L~~-gv~Glih~s---------e~-~------~~~f~vGd~V~vkVl~id~~~~~~  968 (974)
                      -.|++|.|+|+++...|+|++.++ .+-=+=|..         ++ |      .+..++|.+|+++|++..-+....
T Consensus        80 fKGEVvdgvV~~Vnk~G~F~~~GPl~~f~sshl~ppd~~f~p~~n~P~f~~~d~s~I~~~~~VR~kiigtr~~~~~i  156 (170)
T KOG3298|consen   80 FKGEVVDGVVTKVNKMGVFARSGPLEVFYSSHLKPPDYEFDPGENPPNFQTEDESVIQKGVEVRLKIIGTRVDETEI  156 (170)
T ss_pred             cCCcEEEEEEEEEeeeeEEEeccceEeeeecccCCCCcccCCCCCCCcccccccceeeeCcEEEEEEEEEEEeeeeE
Confidence            389999999999999999999986 222111111         11 1      225778999999999887555443

>PF08292 RNA_pol_Rbc25: RNA polymerase III subunit Rpc25; InterPro: IPR013238 Rpc25 is a strongly conserved subunit of RNA polymerase III and has homology to Rpa43 in RNA polymerase I, Rpb7 in RNA polymerase II and the archaeal RpoE subunit

Probab=83.30  E-value=5  Score=39.04  Aligned_cols=61  Identities=16%  Similarity=0.178  Sum_probs=44.4

Q ss_pred             cCcEEEEEEEEEeeceEEEEEcCCeEEEEecccCCCc-c-----------c-cccccccccCCEEEEEEEEEcc
Q 002054          683 VGGIYKGVVTSVKEYGAFVEFNGGQQGLLHVSELSHE-P-----------V-SRVSDVVSVGQQLSLRCIGQDV  743 (974)
Q Consensus       683 ~G~i~~G~V~~i~~~G~fV~l~~g~~Glvhisels~~-~-----------v-~~~~~~~~vGd~V~vkVl~id~  743 (974)
                      +|+++.|+|.+-...|+.|.|.--.+-+||.+.|... .           . ..-.-++..|+.|++||.++..
T Consensus         3 ~gEvl~g~I~~~~~~Gi~vslgFFddI~IP~~~L~~ps~fd~~~~~W~W~~~~~~~l~~d~ge~IRFRV~~~~f   76 (122)
T PF08292_consen    3 VGEVLTGKIKSSTAEGIRVSLGFFDDIFIPPSLLPEPSRFDEEEQAWVWEYDEEQELFFDIGEEIRFRVESEIF   76 (122)
T ss_dssp             TT-EEEEEEEEEETTEEEEEECCEEEEEEECCCC-TTEEEECCCTEEEEEESSSEEEEE-TT-EEEEEEEEEEE
T ss_pred             CCCEEEEEEEecCCCcEEEEecccccEEECHHHCCCCCccCccCCEEEEECCCCceeEccCCCEEEEEEeEEEE
Confidence            6999999999999999999995556688988888642 1           1 2223347899999999999754

Rpc25 is required for transcription initiation and is not essential for the elongating properties of RNA polymerase III [].; PDB: 2CKZ_D 3AYH_B.

>PF00313 CSD: 'Cold-shock' DNA-binding domain; InterPro: IPR002059 When Escherichia coli is exposed to a temperature drop from 37 to 10 degrees centigrade, a 4-5 hour lag phase occurs, after which growth is resumed at a reduced rate []

Probab=81.97  E-value=9.7  Score=32.42  Aligned_cols=55  Identities=16%  Similarity=0.250  Sum_probs=40.1

Q ss_pred             EEEEEEEEeC---CeEEEEeCCCeEEEEecccCCC---CCCCCCCEEEEEEEEEeCCCceee
Q 002054          914 VAAKVYQVRA---RGLVLDLGGGIRGMYRFENNEK---KDFVVGDELLVKCSSFTGKGIPVV  969 (974)
Q Consensus       914 V~G~V~~I~~---~GvFV~L~~gv~Glih~se~~~---~~f~vGd~V~vkVl~id~~~~~~~  969 (974)
                      ++|+|+...+   ||....-+++-+=++|.+++..   ..+.+||+|+..+.. ++++....
T Consensus         1 ~~G~V~~~~~~kgyGFI~~~~~~~diFfh~s~~~~~~~~~l~~G~~V~F~~~~-~~~g~~A~   61 (66)
T PF00313_consen    1 MTGTVKWFDDEKGYGFITSDDGGEDIFFHISDLSGNGFRSLKEGDRVEFEVEE-GKKGPQAV   61 (66)
T ss_dssp             EEEEEEEEETTTTEEEEEETTSSSEEEEEGGGBCSSSSTS--TTSEEEEEEEE-CTTSEEEE
T ss_pred             CeEEEEEEECCCCceEEEEcccceeEEeccccccccccccCCCCCEEEEEEEE-CCCCCEEE
Confidence            4799999964   7766555556699999998853   358999999999998 66555443

During the lag phase, the expression of around 13 proteins, which contain specific DNA-binding regions [], is increased 2-10 fold. These so-called 'cold shock' proteins are thought to help the cell to survive in temperatures lower than optimum growth temperature, by contrast with heat shock proteins, which help the cell to survive in temperatures greater than the optimum, possibly by condensation of the chromosome and organisation of the prokaryotic nucleoid []. A conserved domain of about 70 amino acids has been found in prokaryotic and eukaryotic DNA-binding proteins [, , ]. This domain is known as the 'cold-shock domain' (CSD), part of which is highly similar [] to the RNP-1 RNA-binding motif.; GO: 0003677 DNA binding, 0006355 regulation of transcription, DNA-dependent; PDB: 1HZC_A 1I5F_A 1HZ9_B 1C9O_B 1HZB_B 1HZA_A 2HAX_B 2L15_A 2LSS_A 3I2Z_B ....

---

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

ID	Length	Definition	E-value
Query	974
3cdi_A	723	Crystal Structure Of E. Coli Pnpase Length = 723		1e-145
4aid_A	726	Crystal Structure Of C. Crescentus Pnpase Bound To		1e-139
4aim_A	726	Crystal Structure Of C. Crescentus Pnpase Bound To		1e-139
4am3_A	717	Crystal Structure Of C. Crescentus Pnpase Bound To		1e-139
3u1k_A	630	Crystal Structure Of Human Pnpase Length = 630		1e-131
3cdj_A	559	Crystal Structure Of The E. Coli KhS1 DOMAIN TRUNCA		1e-118
3h1c_A	549	Crystal Structure Of Polynucleotide Phosphorylase (		1e-118
3gcm_A	549	Crystal Structure Of E. Coli Polynucleotide Phospho		1e-118
1e3p_A	757	Tungstate Derivative Of Streptomyces Antibioticus P		1e-101
1e3h_A	757	Semet Derivative Of Streptomyces Antibioticus Pnpas		3e-93
3m7n_D	258	Archaeoglobus Fulgidus Exosome With Rna Bound To Th		2e-17
2ba0_F	258	Archaeal Exosome Core Length = 258		8e-17
2wnr_B	240	The Structure Of Methanothermobacter Thermautotroph		6e-15
2br2_B	248	Rnase Ph Core Of The Archaeal Exosome Length = 248		7e-15
3l7z_B	245	Crystal Structure Of The S. Solfataricus Archaeal E		7e-15
2je6_B	250	Structure Of A 9-Subunit Archaeal Exosome Length =		8e-14
2pnz_A	249	Crystal Structure Of The P. Abyssi Exosome Rnase Ph		1e-13
1sro_A	76	S1 Rna Binding Domain, Nmr, 20 Structures Length =		1e-11
1uds_A	255	Crystal Structure Of The Trna Processing Enzyme Rna		2e-10
2k4k_A	130	Solution Structure Of Gsp13 From Bacillus Subtilis		3e-10
1udn_A	255	Crystal Structure Of The Trna Processing Enzyme Rna		4e-10
1udo_A	255	Crystal Structure Of The Trna Processing Enzyme Rna		5e-10
2nn6_B	249	Structure Of The Human Rna Exosome Composed Of Rrp4		9e-10
1udq_A	255	Crystal Structure Of The Trna Processing Enzyme Rna		1e-09
3dd6_A	255	Crystal Structure Of Rph, An Exoribonuclease From B		4e-09
1r6l_A	239	Crystal Structure Of The Trna Processing Enzyme Rna		8e-09
1r6m_A	239	Crystal Structure Of The Trna Processing Enzyme Rna		1e-08
1oyp_A	245	Crystal Structure Of The Phosphorolytic Exoribonucl		2e-07
1oys_A	245	Crystal Structure Of The Phosphorolytic Exoribonucl		3e-07
4ifd_B	248	Crystal Structure Of An 11-subunit Eukaryotic Exoso		1e-06
2wp8_B	246	Yeast Rrp44 Nuclease Length = 246		1e-06
2eqs_A	103	Solution Structure Of The S1 Rna Binding Domain Of		2e-06
3bzc_A	785	Crystal Structure Of The Tex Protein From Pseudomon		3e-06
2oce_A	780	Crystal Structure Of Tex Family Protein Pa5201 From		4e-06
3b4t_A	262	Crystal Structure Of Mycobacterium Tuberculosis Rna		1e-05
3hkm_A	246	Crystal Structure Of Rice(Oryza Sativa) Rrp46 Lengt		3e-05
2cqo_A	119	Solution Structure Of The S1 Rna Binding Domain Of		3e-05
2nn6_D	237	Structure Of The Human Rna Exosome Composed Of Rrp4		5e-04

>pdb|3CDI|A Chain A, Crystal Structure Of E. Coli Pnpase Length = 723

Iteration: 1
 Score =  513 bits (1320), Expect = e-145,   Method: Compositional matrix adjust.
 Identities = 286/705 (40%), Positives = 430/705 (60%), Gaps = 22/705 (3%)
Query: 55  VLETFKEEFEIGSRLITLETGKIARFANGAVVLGMDETKVLSTVT-SSKGDSVRDFLPLT 113
           +L     +F+ G   +TLETG +AR A  AV++ MD+T V  TV    K    +DF PLT
Sbjct: 7   LLNPIVRKFQYGQHTVTLETGMMARQATAAVMVSMDDTAVFVTVVGQKKAKPGQDFFPLT 66
Query: 114 VDYQEKQFAQGVIPNTYMRREGAPKERELLVGRIIDRPIRPLFPAGFYHEVQVMASVLSS 173
           V+YQE+ +A G IP ++ RREG P E E L+ R+IDRPIRPLFP GF +EVQV+A+V+S 
Sbjct: 67  VNYQERTYAAGRIPGSFFRREGRPSEGETLIARLIDRPIRPLFPEGFVNEVQVIATVVSV 126
Query: 174 DGKQDPDIMAANATSAALMLSDXXXXXXXXXXXXXXXXXQFIVNPTMDELSLSDLNLVYA 233
           + + +PDI+A    SAAL LS                  Q+++NPT DEL  S L+LV A
Sbjct: 127 NPQVNPDIVAMIGASAALSLSGIPFNGPIGAARVGYINDQYVLNPTQDELKESKLDLVVA 186
Query: 234 CTREKTLMIDVQAREISEKDLEAGLRLAHPEAVKYLEPQIRLAEKAGKQKKEYKLSMISE 293
            T    LM++ +A+ +SE  +   +   H +    ++    L ++AGK + +++   ++E
Sbjct: 187 GTEAAVLMVESEAQLLSEDQMLGAVVFGHEQQQVVIQNINELVKEAGKPRWDWQPEPVNE 246
Query: 294 QTLEKVSNLAEAHIEAVF--TDPSYSKFERGEALDKIGQDVKKAL---EEECDEESLQVL 348
               +V+ LAEA +   +  TD    K ER   +D I  +    L   +E  DE  L  +
Sbjct: 247 ALNARVAALAEARLSDAYRITD----KQERYAQVDVIKSETIATLLAEDETLDENELGEI 302
Query: 349 PKAVDTXXXXXXXXXXXAEGVRVDGRQLDEVRPIYCESGNLPILHGSSLFSRGDTQVLCT 408
             A++            A   R+DGR+ D +R +   +G LP  HGS+LF+RG+TQ L T
Sbjct: 303 LHAIE---KNVVRSRVLAGEPRIDGREKDMIRGLDVRTGVLPRTHGSALFTRGETQALVT 359
Query: 409 VTLGAPAEAQRLESLVGPPTKRFMLHYSFPPFCINEVGKRVGLNRREVGHGTLAEKALLA 468
            TLG   +AQ L+ L+G  T  F+ HY+FPP+ + E G      RRE+GHG LA++ +LA
Sbjct: 360 ATLGTARDAQVLDELMGERTDTFLFHYNFPPYSVGETGMVGSPKRREIGHGRLAKRGVLA 419
Query: 469 VLPPENDFPYTVRVNSEVMASDGSTSMATVCGGSMALMDAGIPLQEHVAGVSVGLVSEVD 528
           V+P  + FPYTVRV SE+  S+GS+SMA+VCG S+ALMDAG+P++  VAG+++GLV E D
Sbjct: 420 VMPDMDKFPYTVRVVSEITESNGSSSMASVCGASLALMDAGVPIKAAVAGIAMGLVKEGD 479
Query: 529 PSTGEIKDYRILTDILGLEDHLGDMDFKIAGTRIGVTAIQLDIKPAGIPLDIICECLEHA 588
                  +Y +L+DILG EDHLGDMDFK+AG+R G++A+Q+DIK  GI  +I+   L  A
Sbjct: 480 -------NYVVLSDILGDEDHLGDMDFKVAGSRDGISALQMDIKIEGITKEIMQVALNQA 532
Query: 589 HKGRLQILDHMEREISAPRTQDDRNSPRLATLKYDNDTLRRLIGPLGALKRKIEEETGGR 648
              RL IL  ME+ I+APR      +PR+ T+K + D ++ +IG  G++ R + EETG  
Sbjct: 533 KGARLHILGVMEQAINAPRGDISEFAPRIHTIKINPDKIKDVIGKGGSVIRALTEETGTT 592
Query: 649 ISV-SDGTLTVVAKNRSVMEKVLEKVDFIIGREIEVGGIYKGVVTSVKEYGAFVEFNGGQ 707
           I +  DGT+ + A +    +  + +++ I   EIEVG +Y G VT + ++GAFV   GG+
Sbjct: 593 IEIEDDGTVKIAATDGEKAKHAIRRIEEITA-EIEVGRVYTGKVTRIVDFGAFVAIGGGK 651
Query: 708 QGLLHVSELSHEPVSRVSDVVSVGQQLSLRCIGQDVRGNIKLSLK 752
           +GL+H+S+++ + V +V+D + +GQ++ ++ +  D +G I+LS+K
Sbjct: 652 EGLVHISQIADKRVEKVTDYLQMGQEVPVKVLEVDRQGRIRLSIK 696

>pdb|4AID|A Chain A, Crystal Structure Of C. Crescentus Pnpase Bound To Rnase E Recognition Peptide Length = 726

Iteration: 1
 Score =  493 bits (1270), Expect = e-139,   Method: Compositional matrix adjust.
 Identities = 287/708 (40%), Positives = 419/708 (59%), Gaps = 32/708 (4%)
Query: 60  KEEFEIGSRLITLETGKIARFANGAVVLGMDETKVLSTVTSSKGDSV-RDFLPLTVDYQE 118
           ++  E G + + LETG+IAR A+GAV+  M ET VL+T   +K     +DF PLTV+YQE
Sbjct: 20  RKTIEWGGKTLVLETGRIARQADGAVLATMGETVVLATAVFAKSQKPGQDFFPLTVNYQE 79
Query: 119 KQFAQGVIPNTYMRREGAPKERELLVGRIIDRPIRPLFPAGFYHEVQVMASVLSSDGKQD 178
           K FA G IP  + +REG P E+E LV R+IDRPIRPLF  GF +EVQV+ +VL  D + D
Sbjct: 80  KTFAAGKIPGGFFKREGRPSEKETLVSRLIDRPIRPLFVKGFKNEVQVVVTVLQHDLEND 139
Query: 179 PDIMAANATSAALMLSDXXXXXXXXXXXXXXXXXQFIVNPTMDELSLSDLNLVYACTREK 238
           PDI+   A SAAL LS                   +++NPT+DE+  S ++LV A T + 
Sbjct: 140 PDILGMVAASAALCLSGAPFMGPIGAARVGWVDGAYVLNPTLDEMKESKMDLVVAGTADA 199
Query: 239 TLMIDVQAREISEKDLEAGLRLAHPEAVKYLEPQIRLAEKAGKQKKEYKLSMISEQTLEK 298
            +M++ + +E+SE+ +  G+  AH +    ++  I LAE A K+   ++    ++    K
Sbjct: 200 VMMVESEIQELSEEIVLGGVNFAHQQMQAVIDAIIDLAEHAAKEPFAFEPED-TDAIKAK 258
Query: 299 VSNLAEAHIEAVFTDPSYSKFERGEALDKIGQDVKKALEEECDEESLQVLPKAVDTXXXX 358
           + +L  A I A +      K +R EA+    +    AL    DE      P   D     
Sbjct: 259 MKDLVGADIAAAYK--IQKKQDRYEAVGAAKKKAIAALGL-SDEN-----PTGYDPLKLG 310
Query: 359 XXXXXXXAE---------GVRVDGRQLDEVRPIYCESGNLPILHGSSLFSRGDTQVLCTV 409
                  A+         G+R+DGR +  VRPI  E G LP  HGS+LF+RG+TQ +   
Sbjct: 311 AIFKELEADVVRRGILDTGLRIDGRDVKTVRPILGEVGILPRTHGSALFTRGETQAIVVA 370
Query: 410 TLGAPAEAQRLESLVGPPTKRFMLHYSFPPFCINEVGKRVGLNRREVGHGTLAEKALLAV 469
           TLG   + Q +++L G   + F+LHY+FPP+ + E G+     RRE+GHG LA +AL  +
Sbjct: 371 TLGTGDDEQFIDALEGTYKESFLLHYNFPPYSVGETGRMGSPGRREIGHGKLAWRALRPM 430
Query: 470 LPPENDFPYTVRVNSEVMASDGSTSMATVCGGSMALMDAGIPLQEHVAGVSVGLVSEVDP 529
           LP + DFPYT+R+ SE+  S+GS+SMATVCG S+A+MDAG+PL   V+G+++GL+ E D 
Sbjct: 431 LPTKEDFPYTIRLVSEITESNGSSSMATVCGSSLAMMDAGVPLVRPVSGIAMGLILEQD- 489
Query: 530 STGEIKDYRILTDILGLEDHLGDMDFKIAGTRIGVTAIQLDIKPAGIPLDIICECLEHAH 589
                  + +L+DILG EDHLGDMDFK+AGT  G+T++Q+DIK AGI   I+ + L  A 
Sbjct: 490 ------GFAVLSDILGDEDHLGDMDFKVAGTSEGLTSLQMDIKIAGITPAIMEQALAQAK 543
Query: 590 KGRLQILDHMEREISAPRTQDDRNSPRLATLKYDNDTLRRLIGPLGALKRKIEEETGGRI 649
           +GR  IL  M + + APR      +P++ T+    D +R +IG  G + R+I   TG ++
Sbjct: 544 EGRAHILGEMNKAMDAPRADVGDFAPKIETINIPTDKIREVIGSGGKVIREIVATTGAKV 603
Query: 650 SVS-DGTLTVVAKNRSVMEKVLEKVDFI--IGREIEVGGIYKGVVTSVKEYGAFVEFNGG 706
            ++ DG + V A + +   K+   +D+I  I  E EVG IY G V  V ++GAFV F G 
Sbjct: 604 DINDDGVVKVSASDGA---KIKAAIDWIKSITDEAEVGKIYDGKVVKVVDFGAFVNFFGA 660
Query: 707 QQGLLHVSELSHEPVSRVSDVVSVGQQLSLRCIGQDVRGNIKLSLKAV 754
           + GL+HVS++S+E V++ SDV+  GQ + ++ +G D RG  KLS+K V
Sbjct: 661 KDGLVHVSQISNERVAKPSDVLKEGQMVKVKLLGFDDRGKTKLSMKVV 708

>pdb|4AIM|A Chain A, Crystal Structure Of C. Crescentus Pnpase Bound To Rnase E Recognition Peptide Length = 726

Iteration: 1
 Score =  493 bits (1269), Expect = e-139,   Method: Compositional matrix adjust.
 Identities = 286/708 (40%), Positives = 419/708 (59%), Gaps = 32/708 (4%)
Query: 60  KEEFEIGSRLITLETGKIARFANGAVVLGMDETKVLSTVTSSKGDSV-RDFLPLTVDYQE 118
           ++  E G + + LETG+IAR A+GAV+  M ET VL+T   +K     +DF PLTV+YQE
Sbjct: 20  RKTIEWGGKTLVLETGRIARQADGAVLATMGETVVLATAVFAKSQKPGQDFFPLTVNYQE 79
Query: 119 KQFAQGVIPNTYMRREGAPKERELLVGRIIDRPIRPLFPAGFYHEVQVMASVLSSDGKQD 178
           K FA G IP  + +REG P E+E LV R+IDRPIRPLF  GF +EVQV+ +VL  D + D
Sbjct: 80  KTFAAGKIPGGFFKREGRPSEKETLVSRLIDRPIRPLFVKGFKNEVQVVVTVLQHDLEND 139
Query: 179 PDIMAANATSAALMLSDXXXXXXXXXXXXXXXXXQFIVNPTMDELSLSDLNLVYACTREK 238
           PDI+   A SAAL LS                   +++NPT+DE+  S ++LV A T + 
Sbjct: 140 PDILGMVAASAALCLSGAPFMGPIGAARVGWVDGAYVLNPTLDEMKESKMDLVVAGTADA 199
Query: 239 TLMIDVQAREISEKDLEAGLRLAHPEAVKYLEPQIRLAEKAGKQKKEYKLSMISEQTLEK 298
            +M++ + +E+SE+ +  G+  AH +    ++  I LAE A K+   ++    ++    K
Sbjct: 200 VMMVESEIQELSEEIVLGGVNFAHQQMQAVIDAIIDLAEHAAKEPFAFEPED-TDAIKAK 258
Query: 299 VSNLAEAHIEAVFTDPSYSKFERGEALDKIGQDVKKALEEECDEESLQVLPKAVDTXXXX 358
           + +L  A I A +      K +R EA+    +    AL    DE      P   D     
Sbjct: 259 MKDLVGADIAAAYK--IQKKQDRYEAVGAAKKKAIAALGL-SDEN-----PTGYDPLKLG 310
Query: 359 XXXXXXXAE---------GVRVDGRQLDEVRPIYCESGNLPILHGSSLFSRGDTQVLCTV 409
                  A+         G+R+DGR +  VRPI  E G LP  HGS+LF+RG+TQ +   
Sbjct: 311 AIFKELEADVVRRGILDTGLRIDGRDVKTVRPILGEVGILPRTHGSALFTRGETQAIVVA 370
Query: 410 TLGAPAEAQRLESLVGPPTKRFMLHYSFPPFCINEVGKRVGLNRREVGHGTLAEKALLAV 469
           TLG   + Q +++L G   + F+LHY+FPP+ + E G+     RRE+GHG LA +AL  +
Sbjct: 371 TLGTGDDEQFIDALEGTYKESFLLHYNFPPYSVGETGRMGSPGRREIGHGKLAWRALRPM 430
Query: 470 LPPENDFPYTVRVNSEVMASDGSTSMATVCGGSMALMDAGIPLQEHVAGVSVGLVSEVDP 529
           LP + DFPYT+R+ SE+  S+GS+SMATVCG S+A+MDAG+PL   V+G+++GL+ E D 
Sbjct: 431 LPTKEDFPYTIRLVSEITESNGSSSMATVCGSSLAMMDAGVPLVRPVSGIAMGLILEQD- 489
Query: 530 STGEIKDYRILTDILGLEDHLGDMDFKIAGTRIGVTAIQLDIKPAGIPLDIICECLEHAH 589
                  + +L+DILG EDHLGDMDFK+AGT  G+T++Q+DIK AGI   I+ + L  A 
Sbjct: 490 ------GFAVLSDILGDEDHLGDMDFKVAGTSEGLTSLQMDIKIAGITPAIMEQALAQAK 543
Query: 590 KGRLQILDHMEREISAPRTQDDRNSPRLATLKYDNDTLRRLIGPLGALKRKIEEETGGRI 649
           +GR  IL  M + + APR      +P++ T+    D +R +IG  G + R+I   TG ++
Sbjct: 544 EGRAHILGEMNKAMDAPRADVGDFAPKIETINIPTDKIREVIGSGGKVIREIVATTGAKV 603
Query: 650 SVS-DGTLTVVAKNRSVMEKVLEKVDFI--IGREIEVGGIYKGVVTSVKEYGAFVEFNGG 706
            ++ DG + V A + +   K+   +D+I  I  E E+G IY G V  V ++GAFV F G 
Sbjct: 604 DINDDGVVKVSASDGA---KIKAAIDWIKSITDEAEIGKIYDGKVVKVVDFGAFVNFFGA 660
Query: 707 QQGLLHVSELSHEPVSRVSDVVSVGQQLSLRCIGQDVRGNIKLSLKAV 754
           + GL+HVS++S+E V++ SDV+  GQ + ++ +G D RG  KLS+K V
Sbjct: 661 KDGLVHVSQISNERVAKPSDVLKEGQMVKVKLLGFDDRGKTKLSMKVV 708

>pdb|4AM3|A Chain A, Crystal Structure Of C. Crescentus Pnpase Bound To Rna Length = 717

Iteration: 1
 Score =  493 bits (1269), Expect = e-139,   Method: Compositional matrix adjust.
 Identities = 287/708 (40%), Positives = 419/708 (59%), Gaps = 32/708 (4%)
Query: 60  KEEFEIGSRLITLETGKIARFANGAVVLGMDETKVLSTVTSSKGDSV-RDFLPLTVDYQE 118
           ++  E G + + LETG+IAR A+GAV+  M ET VL+T   +K     +DF PLTV+YQE
Sbjct: 11  RKTIEWGGKTLVLETGRIARQADGAVLATMGETVVLATAVFAKSQKPGQDFFPLTVNYQE 70
Query: 119 KQFAQGVIPNTYMRREGAPKERELLVGRIIDRPIRPLFPAGFYHEVQVMASVLSSDGKQD 178
           K FA G IP  + +REG P E+E LV R+IDRPIRPLF  GF +EVQV+ +VL  D + D
Sbjct: 71  KTFAAGKIPGGFFKREGRPSEKETLVSRLIDRPIRPLFVKGFKNEVQVVVTVLQHDLEND 130
Query: 179 PDIMAANATSAALMLSDXXXXXXXXXXXXXXXXXQFIVNPTMDELSLSDLNLVYACTREK 238
           PDI+   A SAAL LS                   +++NPT+DE+  S ++LV A T + 
Sbjct: 131 PDILGMVAASAALCLSGAPFMGPIGAARVGWVDGAYVLNPTLDEMKESKMDLVVAGTADA 190
Query: 239 TLMIDVQAREISEKDLEAGLRLAHPEAVKYLEPQIRLAEKAGKQKKEYKLSMISEQTLEK 298
            +M++ + +E+SE+ +  G+  AH +    ++  I LAE A K+   ++    ++    K
Sbjct: 191 VMMVESEIQELSEEIVLGGVNFAHQQMQAVIDAIIDLAEHAAKEPFAFEPED-TDAIKAK 249
Query: 299 VSNLAEAHIEAVFTDPSYSKFERGEALDKIGQDVKKALEEECDEESLQVLPKAVDTXXXX 358
           + +L  A I A +      K +R EA+    +    AL    DE      P   D     
Sbjct: 250 MKDLVGADIAAAYK--IQKKQDRYEAVGAAKKKAIAALGL-SDEN-----PTGYDPLKLG 301
Query: 359 XXXXXXXAE---------GVRVDGRQLDEVRPIYCESGNLPILHGSSLFSRGDTQVLCTV 409
                  A+         G+R+DGR +  VRPI  E G LP  HGS+LF+RG+TQ +   
Sbjct: 302 AIFKELEADVVRRGILDTGLRIDGRDVKTVRPILGEVGILPRTHGSALFTRGETQAIVVA 361
Query: 410 TLGAPAEAQRLESLVGPPTKRFMLHYSFPPFCINEVGKRVGLNRREVGHGTLAEKALLAV 469
           TLG   + Q +++L G   + F+LHY+FPP+ + E G+     RRE+GHG LA +AL  +
Sbjct: 362 TLGTGDDEQFIDALEGTYKESFLLHYNFPPYSVGETGRMGSPGRREIGHGKLAWRALRPM 421
Query: 470 LPPENDFPYTVRVNSEVMASDGSTSMATVCGGSMALMDAGIPLQEHVAGVSVGLVSEVDP 529
           LP + DFPYT+R+ SE+  S+GS+SMATVCG S+A+MDAG+PL   V+G+++GL+ E D 
Sbjct: 422 LPTKEDFPYTIRLVSEITESNGSSSMATVCGSSLAMMDAGVPLVRPVSGIAMGLILEQD- 480
Query: 530 STGEIKDYRILTDILGLEDHLGDMDFKIAGTRIGVTAIQLDIKPAGIPLDIICECLEHAH 589
                  + +L+DILG EDHLGDMDFK+AGT  G+T++Q+DIK AGI   I+ + L  A 
Sbjct: 481 ------GFAVLSDILGDEDHLGDMDFKVAGTSEGLTSLQMDIKIAGITPAIMEQALAQAK 534
Query: 590 KGRLQILDHMEREISAPRTQDDRNSPRLATLKYDNDTLRRLIGPLGALKRKIEEETGGRI 649
           +GR  IL  M + + APR      +P++ T+    D +R +IG  G + R+I   TG ++
Sbjct: 535 EGRAHILGEMNKAMDAPRADVGDFAPKIETINIPTDKIREVIGSGGKVIREIVATTGAKV 594
Query: 650 SVS-DGTLTVVAKNRSVMEKVLEKVDFI--IGREIEVGGIYKGVVTSVKEYGAFVEFNGG 706
            ++ DG + V A + +   K+   +D+I  I  E EVG IY G V  V ++GAFV F G 
Sbjct: 595 DINDDGVVKVSASDGA---KIKAAIDWIKSITDEAEVGKIYDGKVVKVVDFGAFVNFFGA 651
Query: 707 QQGLLHVSELSHEPVSRVSDVVSVGQQLSLRCIGQDVRGNIKLSLKAV 754
           + GL+HVS++S+E V++ SDV+  GQ + ++ +G D RG  KLS+K V
Sbjct: 652 KDGLVHVSQISNERVAKPSDVLKEGQMVKVKLLGFDDRGKTKLSMKVV 699

>pdb|3U1K|A Chain A, Crystal Structure Of Human Pnpase Length = 630

Iteration: 1
 Score =  466 bits (1200), Expect = e-131,   Method: Compositional matrix adjust.
 Identities = 256/620 (41%), Positives = 370/620 (59%), Gaps = 12/620 (1%)
Query: 64  EIGSRLITLETGKIARFANGAVVLGMDETKVLSTVTSSKGDSVRDFLPLTVDYQEKQFAQ 123
           ++G+R + + +GK+ARFA+G+ V+   +T V+ T  S    S   F+PL VDY++K  A 
Sbjct: 11  DLGNRKLEISSGKLARFADGSAVVQSGDTAVMVTAVSKTKPSPSQFMPLVVDYRQKAAAA 70
Query: 124 GVIPNTYMRREGAPKERELLVGRIIDRPIRPLFPAGFYHEVQVMASVLSSDGKQDPDIMA 183
           G IP  Y+RRE    ++E+L  RIIDR IRPLFPAG++++ QV+ ++L+ DG  +PD++A
Sbjct: 71  GRIPTNYLRREVGTSDKEILTSRIIDRSIRPLFPAGYFYDTQVLCNLLAVDGVNEPDVLA 130
Query: 184 ANATSAALMLSDXXXXXXXXXXXXXXXXXQFIVNPTMDELSLSDLNLVYA-CTREKTLMI 242
            N  S AL LSD                 +++VNPT  E+S S LNLV A   + + +M+
Sbjct: 131 INGASVALSLSDIPWNGPVGAVRIGIIDGEYVVNPTRKEMSSSTLNLVVAGAPKSQIVML 190
Query: 243 DVQAREISEKDLEAGLRLAHPEAVKYLEPQIRLAEKAGKQKKE-YKLSMISEQTLEKVSN 301
           +  A  I ++D    +++      + ++   +L ++ G  K+   KL   S + ++    
Sbjct: 191 EASAENILQQDFCHAIKVGVKYTQQIIQGIQQLVKETGVTKRTPQKLFTPSPEIVKYTHK 250
Query: 302 LAEAHIEAVFTDPSYSKFERGEALDKIGQDVKKALEEECDEESLQVLPKAVDTXXXXXXX 361
           LA   + AVFTD  + K  R EA++KI  D ++ L+E+  E     + ++ +        
Sbjct: 251 LAMERLYAVFTDYEHDKVSRDEAVNKIRLDTEEQLKEKFPEADPYEIIESFNVVAKEVFR 310
Query: 362 XXXXAEGVRVDGRQLDEVRPIYCESGNLPILHGSSLFSRGDTQVLCTVTLGAPAEA---- 417
                E  R DGR L  +R + CE      LHGS+LF RG TQVLCTVT  +        
Sbjct: 311 SIVLNEYKRCDGRDLTSLRNVSCEVDMFKTLHGSALFQRGQTQVLCTVTFDSLESGIKSD 370
Query: 418 QRLESLVGPPTKRFMLHYSFPPFCINEVGKRVGLNRREVGHGTLAEKALLAVLPPENDFP 477
           Q + ++ G   K FMLHY FPP+  NE+GK  GLNRRE+GHG LAEKAL  V+P   DFP
Sbjct: 371 QVITAINGIKDKNFMLHYEFPPYATNEIGKVTGLNRRELGHGALAEKALYPVIP--RDFP 428
Query: 478 YTVRVNSEVMASDGSTSMATVCGGSMALMDAGIPLQEHVAGVSVGLVSEVDPSTGEIKDY 537
           +T+RV SEV+ S+GS+SMA+ CGGS+ALMD+G+P+   VAGV++GLV++ DP  GEI+DY
Sbjct: 429 FTIRVTSEVLESNGSSSMASACGGSLALMDSGVPISSAVAGVAIGLVTKTDPEKGEIEDY 488
Query: 538 RILTDILGLEDHLGDMDFKIAGTRIGVTAIQLDIKPAGIPLDIICECLEHAHKGRLQILD 597
           R+LTDILG+ED+ GDMDFKIAGT  G+TA+Q DIK  GIP+ I+ E ++ A   + +IL 
Sbjct: 489 RLLTDILGIEDYNGDMDFKIAGTNKGITALQADIKLPGIPIKIVMEAIQQASVAKKEILQ 548
Query: 598 HMEREISAPRTQDDRNSPRLATLKYDNDTLRRLIGPLGALKRKIEEETGGRIS-VSDGTL 656
            M + IS PR     N P + T++       + +GP G   +K++ ETG  IS V + T 
Sbjct: 549 IMNKTISKPRASRKENGPVVETVQVPLSKRAKFVGPGGYNLKKLQAETGVTISQVDEETF 608
Query: 657 TVVAKNRSVMEKVLEKVDFI 676
           +V A   S M    E  DFI
Sbjct: 609 SVFAPTPSAMH---EARDFI 625

>pdb|3CDJ|A Chain A, Crystal Structure Of The E. Coli KhS1 DOMAIN TRUNCATED Pnpase Length = 559

Iteration: 1
 Score =  422 bits (1086), Expect = e-118,   Method: Compositional matrix adjust.
 Identities = 237/559 (42%), Positives = 338/559 (60%), Gaps = 20/559 (3%)
Query: 55  VLETFKEEFEIGSRLITLETGKIARFANGAVVLGMDETKVLSTVT-SSKGDSVRDFLPLT 113
           +L     +F+ G   +TLETG +AR A  AV++ MD+T V  TV    K    +DF PLT
Sbjct: 7   LLNPIVRKFQYGQHTVTLETGMMARQATAAVMVSMDDTAVFVTVVGQKKAKPGQDFFPLT 66
Query: 114 VDYQEKQFAQGVIPNTYMRREGAPKERELLVGRIIDRPIRPLFPAGFYHEVQVMASVLSS 173
           V+YQE+ +A G IP ++ RREG P E E L+ R+IDRPIRPLFP GF +EVQV+A+V+S 
Sbjct: 67  VNYQERTYAAGRIPGSFFRREGRPSEGETLIARLIDRPIRPLFPEGFVNEVQVIATVVSV 126
Query: 174 DGKQDPDIMAANATSAALMLSDXXXXXXXXXXXXXXXXXQFIVNPTMDELSLSDLNLVYA 233
           + + +PDI+A    SAAL LS                  Q+++NPT DEL  S L+LV A
Sbjct: 127 NPQVNPDIVAMIGASAALSLSGIPFNGPIGAARVGYINDQYVLNPTQDELKESKLDLVVA 186
Query: 234 CTREKTLMIDVQAREISEKDLEAGLRLAHPEAVKYLEPQIRLAEKAGKQKKEYKLSMISE 293
            T    LM++ +A+ +SE  +   +   H +    ++    L ++AGK + +++   ++E
Sbjct: 187 GTEAAVLMVESEAQLLSEDQMLGAVVFGHEQQQVVIQNINELVKEAGKPRWDWQPEPVNE 246
Query: 294 QTLEKVSNLAEAHIEAVF--TDPSYSKFERGEALDKIGQDVKKAL---EEECDEESLQVL 348
               +V+ LAEA +   +  TD    K ER   +D I  +    L   +E  DE  L  +
Sbjct: 247 ALNARVAALAEARLSDAYRITD----KQERYAQVDVIKSETIATLLAEDETLDENELGEI 302
Query: 349 PKAVDTXXXXXXXXXXXAEGVRVDGRQLDEVRPIYCESGNLPILHGSSLFSRGDTQVLCT 408
             A++            A   R+DGR+ D +R +   +G LP  HGS+LF+RG+TQ L T
Sbjct: 303 LHAIE---KNVVRSRVLAGEPRIDGREKDMIRGLDVRTGVLPRTHGSALFTRGETQALVT 359
Query: 409 VTLGAPAEAQRLESLVGPPTKRFMLHYSFPPFCINEVGKRVGLNRREVGHGTLAEKALLA 468
            TLG   +AQ L+ L+G  T  F+ HY+FPP+ + E G      RRE+GHG LA++ +LA
Sbjct: 360 ATLGTARDAQVLDELMGERTDTFLFHYNFPPYSVGETGMVGSPKRREIGHGRLAKRGVLA 419
Query: 469 VLPPENDFPYTVRVNSEVMASDGSTSMATVCGGSMALMDAGIPLQEHVAGVSVGLVSEVD 528
           V+P  + FPYTVRV SE+  S+GS+SMA+VCG S+ALMDAG+P++  VAG+++GLV E D
Sbjct: 420 VMPDMDKFPYTVRVVSEITESNGSSSMASVCGASLALMDAGVPIKAAVAGIAMGLVKEGD 479
Query: 529 PSTGEIKDYRILTDILGLEDHLGDMDFKIAGTRIGVTAIQLDIKPAGIPLDIICECLEHA 588
                  +Y +L+DILG EDHLGDMDFK+AG+R G++A+Q+DIK  GI  +I+   L  A
Sbjct: 480 -------NYVVLSDILGDEDHLGDMDFKVAGSRDGISALQMDIKIEGITKEIMQVALNQA 532
Query: 589 HKGRLQILDHMEREISAPR 607
              RL IL  ME+ I+APR
Sbjct: 533 KGARLHILGVMEQAINAPR 551

>pdb|3H1C|A Chain A, Crystal Structure Of Polynucleotide Phosphorylase (Pnpase) Core Bound To Rnase E And Tungstate Length = 549

Iteration: 1
 Score =  422 bits (1086), Expect = e-118,   Method: Compositional matrix adjust.
 Identities = 237/559 (42%), Positives = 338/559 (60%), Gaps = 20/559 (3%)
Query: 55  VLETFKEEFEIGSRLITLETGKIARFANGAVVLGMDETKVLSTVTSSK-GDSVRDFLPLT 113
           +L     +F+ G   +TLETG +AR A  AV++ MD+T V  TV   K     +DF PLT
Sbjct: 1   MLNPIVRKFQYGQHTVTLETGMMARQATAAVMVSMDDTAVFVTVVGQKKAKPGQDFFPLT 60
Query: 114 VDYQEKQFAQGVIPNTYMRREGAPKERELLVGRIIDRPIRPLFPAGFYHEVQVMASVLSS 173
           V+YQE+ +A G IP ++ RREG P E E L+ R+IDRPIRPLFP GF +EVQV+A+V+S 
Sbjct: 61  VNYQERTYAAGRIPGSFFRREGRPSEGETLIARLIDRPIRPLFPEGFVNEVQVIATVVSV 120
Query: 174 DGKQDPDIMAANATSAALMLSDXXXXXXXXXXXXXXXXXQFIVNPTMDELSLSDLNLVYA 233
           + + +PDI+A    SAAL LS                  Q+++NPT DEL  S L+LV A
Sbjct: 121 NPQVNPDIVAMIGASAALSLSGIPFNGPIGAARVGYINDQYVLNPTQDELKESKLDLVVA 180
Query: 234 CTREKTLMIDVQAREISEKDLEAGLRLAHPEAVKYLEPQIRLAEKAGKQKKEYKLSMISE 293
            T    LM++ +A+ +SE  +   +   H +    ++    L ++AGK + +++   ++E
Sbjct: 181 GTEAAVLMVESEAQLLSEDQMLGAVVFGHEQQQVVIQNINELVKEAGKPRWDWQPEPVNE 240
Query: 294 QTLEKVSNLAEAHIEAVF--TDPSYSKFERGEALDKIGQDVKKAL---EEECDEESLQVL 348
               +V+ LAEA +   +  TD    K ER   +D I  +    L   +E  DE  L  +
Sbjct: 241 ALNARVAALAEARLSDAYRITD----KQERYAQVDVIKSETIATLLAEDETLDENELGEI 296
Query: 349 PKAVDTXXXXXXXXXXXAEGVRVDGRQLDEVRPIYCESGNLPILHGSSLFSRGDTQVLCT 408
             A++            A   R+DGR+ D +R +   +G LP  HGS+LF+RG+TQ L T
Sbjct: 297 LHAIE---KNVVRSRVLAGEPRIDGREKDMIRGLDVRTGVLPRTHGSALFTRGETQALVT 353
Query: 409 VTLGAPAEAQRLESLVGPPTKRFMLHYSFPPFCINEVGKRVGLNRREVGHGTLAEKALLA 468
            TLG   +AQ L+ L+G  T  F+ HY+FPP+ + E G      RRE+GHG LA++ +LA
Sbjct: 354 ATLGTARDAQVLDELMGERTDTFLFHYNFPPYSVGETGMVGSPKRREIGHGRLAKRGVLA 413
Query: 469 VLPPENDFPYTVRVNSEVMASDGSTSMATVCGGSMALMDAGIPLQEHVAGVSVGLVSEVD 528
           V+P  + FPYTVRV SE+  S+GS+SMA+VCG S+ALMDAG+P++  VAG+++GLV E D
Sbjct: 414 VMPDMDKFPYTVRVVSEITESNGSSSMASVCGASLALMDAGVPIKAAVAGIAMGLVKEGD 473
Query: 529 PSTGEIKDYRILTDILGLEDHLGDMDFKIAGTRIGVTAIQLDIKPAGIPLDIICECLEHA 588
                  +Y +L+DILG EDHLGDMDFK+AG+R G++A+Q+DIK  GI  +I+   L  A
Sbjct: 474 -------NYVVLSDILGDEDHLGDMDFKVAGSRDGISALQMDIKIEGITKEIMQVALNQA 526
Query: 589 HKGRLQILDHMEREISAPR 607
              RL IL  ME+ I+APR
Sbjct: 527 KGARLHILGVMEQAINAPR 545

>pdb|3GCM|A Chain A, Crystal Structure Of E. Coli Polynucleotide Phosphorylase Bound To Rna And Rnase E Length = 549

Iteration: 1
 Score =  422 bits (1084), Expect = e-118,   Method: Compositional matrix adjust.
 Identities = 237/559 (42%), Positives = 337/559 (60%), Gaps = 20/559 (3%)
Query: 55  VLETFKEEFEIGSRLITLETGKIARFANGAVVLGMDETKVLSTVTSSK-GDSVRDFLPLT 113
           +L     +F+ G   +TLETG +AR A  AV++ MD+T V  TV   K     +DF PLT
Sbjct: 1   MLNPIVRKFQYGQHTVTLETGMMARQATAAVMVSMDDTAVFVTVVGQKKAKPGQDFFPLT 60
Query: 114 VDYQEKQFAQGVIPNTYMRREGAPKERELLVGRIIDRPIRPLFPAGFYHEVQVMASVLSS 173
           V+YQE+ +A G IP ++ RREG P E E L+ R+IDRPIRPLFP GF +EVQV+A+V+S 
Sbjct: 61  VNYQERTYAAGRIPGSFFRREGRPSEGETLIARLIDRPIRPLFPEGFVNEVQVIATVVSV 120
Query: 174 DGKQDPDIMAANATSAALMLSDXXXXXXXXXXXXXXXXXQFIVNPTMDELSLSDLNLVYA 233
           + + +PDI+A    SAAL LS                  Q+++NPT DEL  S L+LV A
Sbjct: 121 NPQVNPDIVAMIGASAALSLSGIPFNGPIGAARVGYINDQYVLNPTQDELKESKLDLVVA 180
Query: 234 CTREKTLMIDVQAREISEKDLEAGLRLAHPEAVKYLEPQIRLAEKAGKQKKEYKLSMISE 293
            T    LM++ +A  +SE  +   +   H +    ++    L ++AGK + +++   ++E
Sbjct: 181 GTEAAVLMVESEAELLSEDQMLGAVVFGHEQQQVVIQNINELVKEAGKPRWDWQPEPVNE 240
Query: 294 QTLEKVSNLAEAHIEAVF--TDPSYSKFERGEALDKIGQDVKKAL---EEECDEESLQVL 348
               +V+ LAEA +   +  TD    K ER   +D I  +    L   +E  DE  L  +
Sbjct: 241 ALNARVAALAEARLSDAYRITD----KQERYAQVDVIKSETIATLLAEDETLDENELGEI 296
Query: 349 PKAVDTXXXXXXXXXXXAEGVRVDGRQLDEVRPIYCESGNLPILHGSSLFSRGDTQVLCT 408
             A++            A   R+DGR+ D +R +   +G LP  HGS+LF+RG+TQ L T
Sbjct: 297 LHAIE---KNVVRSRVLAGEPRIDGREKDMIRGLDVRTGVLPRTHGSALFTRGETQALVT 353
Query: 409 VTLGAPAEAQRLESLVGPPTKRFMLHYSFPPFCINEVGKRVGLNRREVGHGTLAEKALLA 468
            TLG   +AQ L+ L+G  T  F+ HY+FPP+ + E G      RRE+GHG LA++ +LA
Sbjct: 354 ATLGTARDAQVLDELMGERTDTFLFHYNFPPYSVGETGMVGSPKRREIGHGRLAKRGVLA 413
Query: 469 VLPPENDFPYTVRVNSEVMASDGSTSMATVCGGSMALMDAGIPLQEHVAGVSVGLVSEVD 528
           V+P  + FPYTVRV SE+  S+GS+SMA+VCG S+ALMDAG+P++  VAG+++GLV E D
Sbjct: 414 VMPDMDKFPYTVRVVSEITESNGSSSMASVCGASLALMDAGVPIKAAVAGIAMGLVKEGD 473
Query: 529 PSTGEIKDYRILTDILGLEDHLGDMDFKIAGTRIGVTAIQLDIKPAGIPLDIICECLEHA 588
                  +Y +L+DILG EDHLGDMDFK+AG+R G++A+Q+DIK  GI  +I+   L  A
Sbjct: 474 -------NYVVLSDILGDEDHLGDMDFKVAGSRDGISALQMDIKIEGITKEIMQVALNQA 526
Query: 589 HKGRLQILDHMEREISAPR 607
              RL IL  ME+ I+APR
Sbjct: 527 KGARLHILGVMEQAINAPR 545

>pdb|1E3P|A Chain A, Tungstate Derivative Of Streptomyces Antibioticus Pnpase Gpsi Enzyme Length = 757

Iteration: 1
 Score =  367 bits (941), Expect = e-101,   Method: Compositional matrix adjust.
 Identities = 254/714 (35%), Positives = 382/714 (53%), Gaps = 39/714 (5%)
Query: 65  IGSRLITLETGKIARFANGAVVLGMDE-TKVLSTVTSSKGDSVR-DFLPLTVDYQEKQFA 122
            G+R I  ETG++AR A G+ V  +D+ T VLS  T+SK    + DF PLTVD +E+ +A
Sbjct: 34  FGTRTIRFETGRLARQAAGSAVAYLDDDTMVLSATTASKNPKDQLDFFPLTVDVEERMYA 93
Query: 123 QGVIPNTYMRREGAPKERELLVGRIIDRPIRPLFPAGFYHEVQVMASVLSSDGKQDPDIM 182
            G IP ++ RREG P E  +L  R+IDRP+RP F  G  +E+QV+A++++ +     D++
Sbjct: 94  AGKIPGSFFRREGRPSEDAILTCRLIDRPLRPSFKKGLRNEIQVVATIMALNPDHLYDVV 153
Query: 183 AANATSAALMLSDXXXXXXXXXXXXXXXXXQFIVNPTMDELSLSDLNLVYAC-------- 234
           A NA SA+  L+                  Q++  PT  EL  +  ++V A         
Sbjct: 154 AINAASASTQLAGLPFSGPIGGVRVALIRGQWVAFPTHTELEDAVFDMVVAGRVLEDGDV 213
Query: 235 --------TREKTL-MIDVQAREISEKDLEAGLRLAHPEAVKYLEPQIRLAEKAGKQKKE 285
                     EKT+ ++   A   +E+ + AGL  A P      + Q  LA KA K   E
Sbjct: 214 AIMMVEAEATEKTIQLVKDGAEAPTEEVVAAGLDAAKPFIKVLCKAQADLAAKAAKPTGE 273
Query: 286 YKLSM-ISEQTLEKVSNLAEAHIEAVFTDPSYSKFERGEALDKIGQDVKKAL--EEECDE 342
           + + +   +  LE +S      + A  T     K +R   LD++     + L  E E  E
Sbjct: 274 FPVFLDYQDDVLEALSAAVRPELSAALT--IAGKQDREAELDRVKALAAEKLLPEFEGRE 331
Query: 343 ESLQVLPKAVDTXXXXXXXXXXXAEGVRVDGRQLDEVRPIYCESGNLPILHGSSLFSRGD 402
           + +    +A+             AE  R+DGR + ++R +  E   +P +HGS+LF RG+
Sbjct: 332 KEISAAYRAL---TKSLVRERVIAEKKRIDGRGVTDIRTLAAEVEAIPRVHGSALFERGE 388
Query: 403 TQVLCTVTLGAPAEAQRLESLVGPPTKRFMLHYSFPPFCINEVGKRVGLNRREVGHGTLA 462
           TQ+L   TL      Q+L++L     KR+M +Y+FPP+ + E G+     RRE+GHG LA
Sbjct: 389 TQILGVTTLNMLRMEQQLDTLSPVTRKRYMHNYNFPPYSVGETGRVGSPKRREIGHGALA 448
Query: 463 EKALLAVLPPENDFPYTVRVNSEVMASDGSTSMATVCGGSMALMDAGIPLQEHVAGVSVG 522
           E+A++ VLP   +FPY +R  SE + S+GSTSM +VC  +M+L++AG+PL+  VAG+++G
Sbjct: 449 ERAIVPVLPTREEFPYAIRQVSEALGSNGSTSMGSVCASTMSLLNAGVPLKAPVAGIAMG 508
Query: 523 LVS-EVDPSTGEIKDYRILTDILGLEDHLGDMDFKIAGTRIGVTAIQLDIKPAGIPLDII 581
           L+S E++  T     Y  LTDILG ED  GDMDFK+AGT+  VTA+QLD K  GIP  ++
Sbjct: 509 LISQEINGET----HYVALTDILGAEDAFGDMDFKVAGTKEFVTALQLDTKLDGIPASVL 564
Query: 582 CECLEHAHKGRLQILDHMEREISAPRTQDDRNSPRLATLKYDNDTLRRLIGPLGALKRKI 641
              L+ A   RL ILD M   I  P  +   N+PR+ T+K   D +  +IGP   +  +I
Sbjct: 565 AAALKQARDARLHILDVMMEAIDTP-DEMSPNAPRIITVKIPVDKIGEVIGPKRQMINQI 623
Query: 642 EEETGGRISV-SDGTLTVVAKNRSVMEKVLEKVDFIIG-REIEVGGIYKGVVTSVKEYGA 699
           +E+TG  I++  DGT+ + A +    E     ++ I      EVG    G V     +GA
Sbjct: 624 QEDTGAEITIEDDGTIYIGAADGPAAEAARATINGIANPTSPEVGERILGSVVKTTTFGA 683
Query: 700 FVEFNGGQQGLLHVSELSH----EPVSRVSDVVSVGQQLSLRCIGQDVRGNIKL 749
           FV    G+ GLLH+S++      + V  V DV+ VGQ++ +     D RG + L
Sbjct: 684 FVSLLPGKDGLLHISQIRKLAGGKRVENVEDVLGVGQKVQVEIAEIDSRGKLSL 737

>pdb|1E3H|A Chain A, Semet Derivative Of Streptomyces Antibioticus PnpaseGPSI Enzyme Length = 757

Iteration: 1
 Score =  340 bits (871), Expect = 3e-93,   Method: Compositional matrix adjust.
 Identities = 251/714 (35%), Positives = 374/714 (52%), Gaps = 39/714 (5%)
Query: 65  IGSRLITLETGKIARFANGAVVLGMDE-TKVLSTVTSSKGDSVR-DFLPLTVDYQEKQFA 122
            G+R I  ETG++AR A G+ V  +D+ T VLS  T+SK    + DF PLTVD +E+ +A
Sbjct: 34  FGTRTIRFETGRLARQAAGSAVAYLDDDTXVLSATTASKNPKDQLDFFPLTVDVEERXYA 93
Query: 123 QGVIPNTYMRREGAPKERELLVGRIIDRPIRPLFPAGFYHEVQVMASVLSSDGKQDPDIM 182
            G IP ++ RREG P E  +L  R+IDRP+RP F  G  +E+QV+A++ + +     D++
Sbjct: 94  AGKIPGSFFRREGRPSEDAILTCRLIDRPLRPSFKKGLRNEIQVVATIXALNPDHLYDVV 153
Query: 183 AANATSAALMLSDXXXXXXXXXXXXXXXXXQFIVNPTMDELS------------LSD--- 227
           A NA SA+  L+                  Q++  PT  EL             L D   
Sbjct: 154 AINAASASTQLAGLPFSGPIGGVRVALIRGQWVAFPTHTELEDAVFDXVVAGRVLEDGDV 213
Query: 228 -LNLVYACTREKTL-MIDVQAREISEKDLEAGLRLAHPEAVKYLEPQIRLAEKAGKQKKE 285
            +  V A   EKT+ ++   A   +E+ + AGL  A P      + Q  LA KA K   E
Sbjct: 214 AIXXVEAEATEKTIQLVKDGAEAPTEEVVAAGLDAAKPFIKVLCKAQADLAAKAAKPTGE 273
Query: 286 YKLSM-ISEQTLEKVSNLAEAHIEAVFTDPSYSKFERGEALDKIGQDVKKAL--EEECDE 342
           + + +   +  LE +S      + A  T     K +R   LD++     + L  E E  E
Sbjct: 274 FPVFLDYQDDVLEALSAAVRPELSAALT--IAGKQDREAELDRVKALAAEKLLPEFEGRE 331
Query: 343 ESLQVLPKAVDTXXXXXXXXXXXAEGVRVDGRQLDEVRPIYCESGNLPILHGSSLFSRGD 402
           + +    +A+             AE  R+DGR + ++R +  E   +P +HGS+LF RG+
Sbjct: 332 KEISAAYRAL---TKSLVRERVIAEKKRIDGRGVTDIRTLAAEVEAIPRVHGSALFERGE 388
Query: 403 TQVLCTVTLGAPAEAQRLESLVGPPTKRFMLHYSFPPFCINEVGKRVGLNRREVGHGTLA 462
           TQ+L   TL      Q+L++L     KR+  +Y+FPP+ + E G+     RRE+GHG LA
Sbjct: 389 TQILGVTTLNXLRXEQQLDTLSPVTRKRYXHNYNFPPYSVGETGRVGSPKRREIGHGALA 448
Query: 463 EKALLAVLPPENDFPYTVRVNSEVMASDGSTSMATVCGGSMALMDAGIPLQEHVAGVSVG 522
           E+A++ VLP   +FPY +R  SE + S+GSTS  +VC  + +L++AG+PL+  VAG++ G
Sbjct: 449 ERAIVPVLPTREEFPYAIRQVSEALGSNGSTSXGSVCASTXSLLNAGVPLKAPVAGIAXG 508
Query: 523 LVS-EVDPSTGEIKDYRILTDILGLEDHLGDMDFKIAGTRIGVTAIQLDIKPAGIPLDII 581
           L+S E++  T     Y  LTDILG ED  GD DFK+AGT+  VTA+QLD K  GIP  ++
Sbjct: 509 LISQEINGET----HYVALTDILGAEDAFGDXDFKVAGTKEFVTALQLDTKLDGIPASVL 564
Query: 582 CECLEHAHKGRLQILDHMEREISAPRTQDDRNSPRLATLKYDNDTLRRLIGPLGALKRKI 641
              L+ A   RL ILD     I  P  +   N+PR+ T+K   D +  +IGP      +I
Sbjct: 565 AAALKQARDARLHILDVXXEAIDTP-DEXSPNAPRIITVKIPVDKIGEVIGPKRQXINQI 623
Query: 642 EEETGGRISV-SDGTLTVVAKNRSVMEKVLEKVDFIIG-REIEVGGIYKGVVTSVKEYGA 699
           +E+TG  I++  DGT+ + A +    E     ++ I      EVG    G V     +GA
Sbjct: 624 QEDTGAEITIEDDGTIYIGAADGPAAEAARATINGIANPTSPEVGERILGSVVKTTTFGA 683
Query: 700 FVEFNGGQQGLLHVSELSH----EPVSRVSDVVSVGQQLSLRCIGQDVRGNIKL 749
           FV    G+ GLLH+S++      + V  V DV+ VGQ++ +     D RG + L
Sbjct: 684 FVSLLPGKDGLLHISQIRKLAGGKRVENVEDVLGVGQKVQVEIAEIDSRGKLSL 737

>pdb|3M7N|D Chain D, Archaeoglobus Fulgidus Exosome With Rna Bound To The Active Site Length = 258

Iteration: 1
 Score = 88.2 bits (217), Expect = 2e-17,   Method: Compositional matrix adjust.
 Identities = 72/242 (29%), Positives = 119/242 (49%), Gaps = 26/242 (10%)
Query: 367 EGVRVDGRQLDEVRPIYCESGNLPILHGSSLFSRGDTQVLCTVTLGAPAEAQRLESLVGP 426
           +G+R+DGR+ DE+RPI  E+  L    GS     G  +V+  V    P E    E L  P
Sbjct: 14  DGLRLDGRKFDELRPIKIEASVLKRADGSCYLEMGKNKVIAAVF--GPREVHP-EHLQDP 70
Query: 427 PTKRFMLHYSFPPFCINEVGKRVGLNRREVGHGTLAEKALLAVLPPENDFPYT-VRVNSE 485
                   Y+  PF + E  KR G +RR +    ++++A  AV+  E  FP + + +  E
Sbjct: 71  SKAIIRYRYNMAPFSVEE-RKRPGPDRRSIEISKVSKEAFEAVIMKEL-FPRSAIDIFVE 128
Query: 486 VMASDGSTSMATVCGGSMALMDAGIPLQEHVAGVSVGLVSEVDPSTGEIKDYRILTDILG 545
           V+ +D  +  A +   S+AL+DAG+P++  +  V+VG             D +++ D + 
Sbjct: 129 VLQADAGSRTACLNAASVALVDAGVPMKGMITSVAVGKA-----------DGQLVLDPMK 177
Query: 546 LEDHLGDMDFKIA-----GTRIGVTAIQLDIKPAGIPLDIICECLEHAHKGRLQILDHME 600
            ED+ G+ D   A     G    +  +Q+D +   +  D + + +E A KG LQI + M+
Sbjct: 178 EEDNFGEADMPFAFLIRNGKIESIALLQMDGR---MTRDEVKQAIELAKKGALQIYE-MQ 233
Query: 601 RE 602
           RE
Sbjct: 234 RE 235

>pdb|2BA0|F Chain F, Archaeal Exosome Core Length = 258

Iteration: 1
 Score = 86.3 bits (212), Expect = 8e-17,   Method: Compositional matrix adjust.
 Identities = 71/242 (29%), Positives = 118/242 (48%), Gaps = 26/242 (10%)
Query: 367 EGVRVDGRQLDEVRPIYCESGNLPILHGSSLFSRGDTQVLCTVTLGAPAEAQRLESLVGP 426
           +G+R+DGR+ DE+RPI  E+  L    GS     G  +V+  V    P E      L  P
Sbjct: 14  DGLRLDGRKFDELRPIKIEASVLKRADGSCYLEMGKNKVIAAVF--GPREVHP-RHLQDP 70
Query: 427 PTKRFMLHYSFPPFCINEVGKRVGLNRREVGHGTLAEKALLAVLPPENDFPYT-VRVNSE 485
                   Y+  PF + E  KR G +RR +    ++++A  AV+  E  FP + + +  E
Sbjct: 71  SKAIIRYRYNMAPFSVEE-RKRPGPDRRSIEISKVSKEAFEAVIMKEL-FPRSAIDIFVE 128
Query: 486 VMASDGSTSMATVCGGSMALMDAGIPLQEHVAGVSVGLVSEVDPSTGEIKDYRILTDILG 545
           V+ +D  +  A +   S+AL+DAG+P++  +  V+VG             D +++ D + 
Sbjct: 129 VLQADAGSRTACLNAASVALVDAGVPMKGMITSVAVGKA-----------DGQLVLDPMK 177
Query: 546 LEDHLGDMDFKIA-----GTRIGVTAIQLDIKPAGIPLDIICECLEHAHKGRLQILDHME 600
            ED+ G+ D   A     G    +  +Q+D +   +  D + + +E A KG LQI + M+
Sbjct: 178 EEDNFGEADMPFAFLIRNGKIESIALLQMDGR---MTRDEVKQAIELAKKGALQIYE-MQ 233
Query: 601 RE 602
           RE
Sbjct: 234 RE 235

>pdb|2WNR|B Chain B, The Structure Of Methanothermobacter Thermautotrophicus Exosome Core Assembly Length = 240

Iteration: 1
 Score = 80.1 bits (196), Expect = 6e-15,   Method: Compositional matrix adjust.
 Identities = 64/191 (33%), Positives = 92/191 (48%), Gaps = 17/191 (8%)
Query: 369 VRVDGRQLDEVRPIYCESGNLPILHGSSLFSRGDTQVLCTVTLGAPAEAQRLESLVGPPT 428
           VR DGR  DE+RP+  E+G L    GSS    G  ++L  V +  P EAQ +  L  P  
Sbjct: 16  VREDGRAFDELRPLKIEAGILERADGSSYLEFGGNKIL--VAVYGPREAQ-IRKLQRPDR 72
Query: 429 KRFMLHYSFPPFCINEVGKRVGLNRREVGHGTLAEKALLAVLPPENDFPYTV-RVNSEVM 487
                 Y+  PF + E  KR G +RR V    +  +AL   L  E  FP +V  V  EV+
Sbjct: 73  AVIRCRYNMAPFSVEE-RKRPGPDRRSVEISKITAEALRPALILEK-FPRSVIDVFIEVL 130
Query: 488 ASDGSTSMATVCGGSMALMDAGIPLQEHVAGVSVGLVSEVDPSTGEIKDYRILTDILGLE 547
            ++G T  A +   S+AL DAGIP+++ V   + G V +           +++ D+   E
Sbjct: 131 EAEGGTRCAGITAASVALADAGIPMRDMVVACAAGKVGD-----------QVVLDLSEEE 179
Query: 548 DHLGDMDFKIA 558
           D  G  D  +A
Sbjct: 180 DKEGQADVPVA 190

>pdb|2BR2|B Chain B, Rnase Ph Core Of The Archaeal Exosome Length = 248

Iteration: 1
 Score = 79.7 bits (195), Expect = 7e-15,   Method: Compositional matrix adjust.
 Identities = 73/239 (30%), Positives = 116/239 (48%), Gaps = 23/239 (9%)
Query: 367 EGVRVDGRQLDEVRPIYCESGNLPILHGSSLFSRGDTQVLCTVTLGAPAEAQRLESLVGP 426
           +G R DGR+ DE+R I  E G L    GS++F  G+T+ +  V    P E      L  P
Sbjct: 16  DGKRTDGRKPDELRSIKIELGVLKNADGSAIFEMGNTKAIAAVY--GPKEMHP-RHLSLP 72
Query: 427 PTKRFMLHYSFPPFCINEVGKRVGLNRREVGHGTLAEKALLAVLPPENDFPYT-VRVNSE 485
                 + Y   PF  +E  K    +RRE+    +  +AL + +  E  FP T + V +E
Sbjct: 73  DRAVLRVRYHMTPFSTDE-RKNPAPSRREIELSKVIREALESAVLVEL-FPRTAIDVFTE 130
Query: 486 VMASDGSTSMATVCGGSMALMDAGIPLQEHVAGVSVGLVSEVDPSTGEIKDYRILTDILG 545
           ++ +D  + + ++   S+AL DAGIP+++ +AGV+VG    V           I+ D+  
Sbjct: 131 ILQADAGSRLVSLMAASLALADAGIPMRDLIAGVAVGKADGV-----------IILDLNE 179
Query: 546 LEDHLGDMDFKIA--GTRIGVTAIQLDIKPAGIPLDIICECLEHAHKGRLQILDHMERE 602
            ED  G+ D  IA   +   VT  QL+     +  D   +  + A KG + I+ ++ERE
Sbjct: 180 TEDMWGEADMPIAMMPSLNQVTLFQLN---GSMTPDEFRQAFDLAVKG-INIIYNLERE 234

>pdb|3L7Z|B Chain B, Crystal Structure Of The S. Solfataricus Archaeal Exosome Length = 245

Iteration: 1
 Score = 79.7 bits (195), Expect = 7e-15,   Method: Compositional matrix adjust.
 Identities = 73/239 (30%), Positives = 116/239 (48%), Gaps = 23/239 (9%)
Query: 367 EGVRVDGRQLDEVRPIYCESGNLPILHGSSLFSRGDTQVLCTVTLGAPAEAQRLESLVGP 426
           +G R DGR+ DE+R I  E G L    GS++F  G+T+ +  V    P E      L  P
Sbjct: 13  DGKRTDGRKPDELRSIKIELGVLKNADGSAIFEMGNTKAIAAVY--GPKEMHP-RHLSLP 69
Query: 427 PTKRFMLHYSFPPFCINEVGKRVGLNRREVGHGTLAEKALLAVLPPENDFPYT-VRVNSE 485
                 + Y   PF  +E  K    +RRE+    +  +AL + +  E  FP T + V +E
Sbjct: 70  DRAVLRVRYHMTPFSTDE-RKNPAPSRREIELSKVIREALESAVLVEL-FPRTAIDVFTE 127
Query: 486 VMASDGSTSMATVCGGSMALMDAGIPLQEHVAGVSVGLVSEVDPSTGEIKDYRILTDILG 545
           ++ +D  + + ++   S+AL DAGIP+++ +AGV+VG    V           I+ D+  
Sbjct: 128 ILQADAGSRLVSLMAASLALADAGIPMRDLIAGVAVGKADGV-----------IILDLNE 176
Query: 546 LEDHLGDMDFKIA--GTRIGVTAIQLDIKPAGIPLDIICECLEHAHKGRLQILDHMERE 602
            ED  G+ D  IA   +   VT  QL+     +  D   +  + A KG + I+ ++ERE
Sbjct: 177 TEDMWGEADMPIAMMPSLNQVTLFQLN---GSMTPDEFRQAFDLAVKG-INIIYNLERE 231

>pdb|2JE6|B Chain B, Structure Of A 9-Subunit Archaeal Exosome Length = 250

Iteration: 1
 Score = 76.3 bits (186), Expect = 8e-14,   Method: Compositional matrix adjust.
 Identities = 72/239 (30%), Positives = 115/239 (48%), Gaps = 23/239 (9%)
Query: 367 EGVRVDGRQLDEVRPIYCESGNLPILHGSSLFSRGDTQVLCTVTLGAPAEAQRLESLVGP 426
           +G R DGR+ DE+R I  E G L    GS++F  G+T+ +  V    P E      L  P
Sbjct: 18  DGKRTDGRKPDELRSIKIELGVLKNADGSAIFEMGNTKAIAAVY--GPKEMHP-RHLSLP 74
Query: 427 PTKRFMLHYSFPPFCINEVGKRVGLNRREVGHGTLAEKALLAVLPPENDFPYT-VRVNSE 485
                 + Y   PF  +E  K    +RRE+    +  +AL + +  E  FP T + V +E
Sbjct: 75  DRAVLRVRYHMTPFSTDE-RKNPAPSRREIELSKVIREALESAVLVEL-FPRTAIDVFTE 132
Query: 486 VMASDGSTSMATVCGGSMALMDAGIPLQEHVAGVSVGLVSEVDPSTGEIKDYRILTDILG 545
           ++ +D  + + ++   S+AL DAGIP+++ +AGV+VG    V           I+ D+  
Sbjct: 133 ILQADAGSRLVSLMAASLALADAGIPMRDLIAGVAVGKADGV-----------IILDLNE 181
Query: 546 LEDHLGDMDFKIA--GTRIGVTAIQLDIKPAGIPLDIICECLEHAHKGRLQILDHMERE 602
            E   G+ D  IA   +   VT  QL+     +  D   +  + A KG + I+ ++ERE
Sbjct: 182 TEAMWGEADMPIAMMPSLNQVTLFQLN---GSMTPDEFRQAFDLAVKG-INIIYNLERE 236

>pdb|2PNZ|A Chain A, Crystal Structure Of The P. Abyssi Exosome Rnase Ph Ring Complexed With Udp And Gmp Length = 249

Iteration: 1
 Score = 75.9 bits (185), Expect = 1e-13,   Method: Compositional matrix adjust.
 Identities = 64/206 (31%), Positives = 101/206 (49%), Gaps = 19/206 (9%)
Query: 368 GVRVDGRQLDEVRPIYCESGNLPILHGSSLFSRGDTQVLCTVTLGAPAEAQRLESLVGPP 427
           G R+DGR+  E+RPI  E G L   +GS+    G  +++  V    P E    + L  P 
Sbjct: 15  GRRIDGRKKYELRPIKMEVGVLKNANGSAYIEWGKNKIIAAVY--GPRELHP-KHLQRPD 71
Query: 428 TKRFMLHYSFPPFCINEVGKRVGLNRREVGHGTLAEKALLAVLPPENDFPYT-VRVNSEV 486
                + Y+  PF + E  K+ G +RR +    + + AL   L  E  FP T + V  EV
Sbjct: 72  RAILRVRYNMAPFSVEE-RKKPGPDRRSIEISKVIKGALEPALILEM-FPRTAIDVFIEV 129
Query: 487 MASDGSTSMATVCGGSMALMDAGIPLQEHVAGVSVGLVSEVDPSTGEIKDYRILTDILGL 546
           + +D  T +A +   S+AL DAGIP+++ VA  + G +       GE     I+ D+   
Sbjct: 130 LQADAGTRVAGITAASLALADAGIPMRDLVAACAAGKIE------GE-----IVLDLNKE 178
Query: 547 EDHLGDMDFKIA--GTRIGVTAIQLD 570
           ED+ G+ D  +A    +  +T +Q+D
Sbjct: 179 EDNYGEADVPVAIMPLKNDITLLQMD 204

>pdb|1SRO|A Chain A, S1 Rna Binding Domain, Nmr, 20 Structures Length = 76

Iteration: 1
 Score = 68.9 bits (167), Expect = 1e-11,   Method: Compositional matrix adjust.
 Identities = 30/73 (41%), Positives = 54/73 (73%)
Query: 680 EIEVGGIYKGVVTSVKEYGAFVEFNGGQQGLLHVSELSHEPVSRVSDVVSVGQQLSLRCI 739
           EIEVG +Y G VT + ++GAFV   GG++GL+H+S+++ + V +V+D + +GQ++ ++ +
Sbjct: 2   EIEVGRVYTGKVTRIVDFGAFVAIGGGKEGLVHISQIADKRVEKVTDYLQMGQEVPVKVL 61
Query: 740 GQDVRGNIKLSLK 752
             D +G I+LS+K
Sbjct: 62  EVDRQGRIRLSIK 74

>pdb|1UDS|A Chain A, Crystal Structure Of The Trna Processing Enzyme Rnase Ph R126a Mutant From Aquifex Aeolicus Length = 255

Iteration: 1
 Score = 64.7 bits (156), Expect = 2e-10,   Method: Compositional matrix adjust.
 Identities = 57/211 (27%), Positives = 92/211 (43%), Gaps = 38/211 (18%)
Query: 369 VRVDGRQLDEVRPIYCESGNLPILHGSSLFSRGDTQVLCTVTL--GAPAEAQRLESLVGP 426
           +R DGR+ D++RP+  +   L    GS L S G T+V+CT ++    P        L G 
Sbjct: 1   MRSDGRKEDQLRPVSIQRDFLEYPEGSCLISFGKTKVICTASVIENVP------NWLKGK 54
Query: 427 PTKRFMLHYSFPPFCINE------VGKRVGLNRREVGHGTLAEKALLAVLPPENDFPYTV 480
                   YS  P    +      V  R+G    E+    +  +A+   +        T+
Sbjct: 55  GQGWITAEYSMLPRATQQRTIRESVQGRIGGRTHEIQR--MIGRAMRTAVELTKIGERTI 112
Query: 481 RVNSEVMASDGSTSMATVCGGSMALMDAGI-----------PLQEHVAGVSVGLVSEVDP 529
            V+ +V+ +DG T+ A + G  +A+ DA I           P+++ VA VSVG+V++   
Sbjct: 113 WVDCDVIQADGGTATAAITGAFVAVADAIIKLHKEGIIEETPIKDFVAAVSVGIVND--- 169
Query: 530 STGEIKDYRILTDILGLEDHLGDMDFKIAGT 560
                   RIL D+   ED    +D  + GT
Sbjct: 170 --------RILLDLNFEEDSAAQVDMNVVGT 192

>pdb|2K4K|A Chain A, Solution Structure Of Gsp13 From Bacillus Subtilis Length = 130

Iteration: 1
 Score = 64.7 bits (156), Expect = 3e-10,   Method: Compositional matrix adjust.
 Identities = 31/84 (36%), Positives = 53/84 (63%), Gaps = 1/84 (1%)
Query: 677 IGREIEVGGIYKGVVTSVKEYGAFVEFNGGQQGLLHVSELSHEPVSRVSDVVSVGQQLSL 736
           +  + EVG +Y G VT ++ YGAFV  +   QGL+H+SE++H  V  +++ +SVG ++ +
Sbjct: 1   MAAKFEVGSVYTGKVTGLQAYGAFVALDEETQGLVHISEVTHGFVKDINEHLSVGDEVQV 60
Query: 737 RCIGQD-VRGNIKLSLKAVSPRPE 759
           + +  D  +G I LS++A    PE
Sbjct: 61  KVLAVDEEKGKISLSIRATQAAPE 84

>pdb|1UDN|A Chain A, Crystal Structure Of The Trna Processing Enzyme Rnase Ph From Aquifex Aeolicus Length = 255

Iteration: 1
 Score = 63.9 bits (154), Expect = 4e-10,   Method: Compositional matrix adjust.
 Identities = 57/211 (27%), Positives = 91/211 (43%), Gaps = 38/211 (18%)
Query: 369 VRVDGRQLDEVRPIYCESGNLPILHGSSLFSRGDTQVLCTVTL--GAPAEAQRLESLVGP 426
           +R DGR+ D++RP+  +   L    GS L S G T+V+CT ++    P        L G 
Sbjct: 1   MRSDGRKEDQLRPVSIQRDFLEYPEGSCLISFGKTKVICTASVIENVP------NWLKGK 54
Query: 427 PTKRFMLHYSFPPFCINE------VGKRVGLNRREVGHGTLAEKALLAVLPPENDFPYTV 480
                   YS  P    +      V  R+G    E+    +  +A+   +        T+
Sbjct: 55  GQGWITAEYSMLPRATQQRTIRESVQGRIGGRTHEIQR--MIGRAMRTAVELTKIGERTI 112
Query: 481 RVNSEVMASDGSTSMATVCGGSMALMDAGI-----------PLQEHVAGVSVGLVSEVDP 529
            V+ +V+ +DG T  A + G  +A+ DA I           P+++ VA VSVG+V++   
Sbjct: 113 WVDCDVIQADGGTRTAAITGAFVAVADAIIKLHKEGIIEETPIKDFVAAVSVGIVND--- 169
Query: 530 STGEIKDYRILTDILGLEDHLGDMDFKIAGT 560
                   RIL D+   ED    +D  + GT
Sbjct: 170 --------RILLDLNFEEDSAAQVDMNVVGT 192

>pdb|1UDO|A Chain A, Crystal Structure Of The Trna Processing Enzyme Rnase Ph R86a Mutant From Aquifex Aeolicus Length = 255

Iteration: 1
 Score = 63.5 bits (153), Expect = 5e-10,   Method: Compositional matrix adjust.
 Identities = 57/211 (27%), Positives = 91/211 (43%), Gaps = 38/211 (18%)
Query: 369 VRVDGRQLDEVRPIYCESGNLPILHGSSLFSRGDTQVLCTVTL--GAPAEAQRLESLVGP 426
           +R DGR+ D++RP+  +   L    GS L S G T+V+CT ++    P        L G 
Sbjct: 1   MRSDGRKEDQLRPVSIQRDFLEYPEGSCLISFGKTKVICTASVIENVP------NWLKGK 54
Query: 427 PTKRFMLHYSFPPFCINE------VGKRVGLNRREVGHGTLAEKALLAVLPPENDFPYTV 480
                   YS  P    +      V  R+G    E+    +  +A+   +        T+
Sbjct: 55  GQGWITAEYSMLPRATQQRTIRESVQGRIGGATHEIQR--MIGRAMRTAVELTKIGERTI 112
Query: 481 RVNSEVMASDGSTSMATVCGGSMALMDAGI-----------PLQEHVAGVSVGLVSEVDP 529
            V+ +V+ +DG T  A + G  +A+ DA I           P+++ VA VSVG+V++   
Sbjct: 113 WVDCDVIQADGGTRTAAITGAFVAVADAIIKLHKEGIIEETPIKDFVAAVSVGIVND--- 169
Query: 530 STGEIKDYRILTDILGLEDHLGDMDFKIAGT 560
                   RIL D+   ED    +D  + GT
Sbjct: 170 --------RILLDLNFEEDSAAQVDMNVVGT 192

>pdb|2NN6|B Chain B, Structure Of The Human Rna Exosome Composed Of Rrp41, Rrp45, Rrp46, Rrp43, Mtr3, Rrp42, Csl4, Rrp4, And Rrp40 Length = 249

Iteration: 1
 Score = 62.8 bits (151), Expect = 9e-10,   Method: Compositional matrix adjust.
 Identities = 48/162 (29%), Positives = 72/162 (44%), Gaps = 10/162 (6%)
Query: 367 EGVRVDGRQLDEVRPIYCESGNLPILHGSSLFSRGDTQVLCTVTLGAPAEAQRLESLVGP 426
           +G RVDGR+  E+R I    G      GS+   +G+T+ L  V    P E +   +   P
Sbjct: 14  QGYRVDGRRAGELRKIQARMGVFAQADGSAYIEQGNTKALAVVY--GPHEIRGSRARALP 71
Query: 427 PTKRFMLHYSFPPFCINEVGKRVGLNRREVGHG----TLAEKALLAVLPPENDFPYTVRV 482
                   YS   F   E  +R   +R+    G       E A+L  L P +     V  
Sbjct: 72  DRALVNCQYSSATFSTGERKRRPHGDRKSCEMGLQLRQTFEAAILTQLHPRSQIDIYV-- 129
Query: 483 NSEVMASDGSTSMATVCGGSMALMDAGIPLQEHVAGVSVGLV 524
             +V+ +DG T  A V   ++A++DAGIP+++ V   S G V
Sbjct: 130 --QVLQADGGTYAACVNAATLAVLDAGIPMRDFVCACSAGFV 169

>pdb|1UDQ|A Chain A, Crystal Structure Of The Trna Processing Enzyme Rnase Ph T125a Mutant From Aquifex Aeolicus Length = 255

Iteration: 1
 Score = 62.0 bits (149), Expect = 1e-09,   Method: Compositional matrix adjust.
 Identities = 56/211 (26%), Positives = 90/211 (42%), Gaps = 38/211 (18%)
Query: 369 VRVDGRQLDEVRPIYCESGNLPILHGSSLFSRGDTQVLCTVTL--GAPAEAQRLESLVGP 426
           +R DGR+ D++RP+  +   L    GS L S G T+V+CT ++    P        L G 
Sbjct: 1   MRSDGRKEDQLRPVSIQRDFLEYPEGSCLISFGKTKVICTASVIENVP------NWLKGK 54
Query: 427 PTKRFMLHYSFPPFCINE------VGKRVGLNRREVGHGTLAEKALLAVLPPENDFPYTV 480
                   YS  P    +      V  R+G    E+    +  +A+   +        T+
Sbjct: 55  GQGWITAEYSMLPRATQQRTIRESVQGRIGGRTHEIQR--MIGRAMRTAVELTKIGERTI 112
Query: 481 RVNSEVMASDGSTSMATVCGGSMALMDAGI-----------PLQEHVAGVSVGLVSEVDP 529
            V+ +V+ +DG    A + G  +A+ DA I           P+++ VA VSVG+V++   
Sbjct: 113 WVDCDVIQADGGARTAAITGAFVAVADAIIKLHKEGIIEETPIKDFVAAVSVGIVND--- 169
Query: 530 STGEIKDYRILTDILGLEDHLGDMDFKIAGT 560
                   RIL D+   ED    +D  + GT
Sbjct: 170 --------RILLDLNFEEDSAAQVDMNVVGT 192

>pdb|3DD6|A Chain A, Crystal Structure Of Rph, An Exoribonuclease From Bacillus Anthracis At 1.7 A Resolution Length = 255

Iteration: 1
 Score = 60.8 bits (146), Expect = 4e-09,   Method: Compositional matrix adjust.
 Identities = 65/251 (25%), Positives = 109/251 (43%), Gaps = 42/251 (16%)
Query: 369 VRVDGRQLDEVRPIYCESGNLPILHGSSLFSRGDTQVLCTVTLGAPAEAQRLESLVGPPT 428
           +RVDGR+  E+R I+  +  L    GS L   GDT+V+C+ T+      +R+     PP 
Sbjct: 11  MRVDGREKTELRHIHIHTNYLKHPEGSVLIEVGDTKVICSATI-----EERV-----PPF 60
Query: 429 KR------FMLHYSFPPFCINEVGKRVGLNRREVGHGT----LAEKALLAVLPPENDFPY 478
            R          Y+  P    +   R     +  G       L  +AL AV+  E     
Sbjct: 61  MRGEGKGWVTAEYAMIPRATEQRTIRESSKGKVTGRTMEIQRLIGRALRAVVDLEALGER 120
Query: 479 TVRVNSEVMASDGSTSMATVCGGSMALMDA-----------GIPLQEHVAGVSVGLVSEV 527
           TV ++ +V+ +DG T  A++ G  +A++ A            IP+++++A  SVG+V E 
Sbjct: 121 TVWIDCDVIQADGGTRTASITGAYVAMVLAFEKLLQAEKVSKIPVKDYLAATSVGIVEE- 179
Query: 528 DPSTGEIKDYRILTDILGLEDHLGDMDFKIAGTRIG-VTAIQLDIKPAGIPLDIICECLE 586
                      ++ D+   ED   D+D  +  T  G    +Q   + A      + E L+
Sbjct: 180 ---------QGVVLDLNYAEDSKADVDMNVIMTGKGQFVEVQGTGEEATFSRAQLNELLD 230
Query: 587 HAHKGRLQILD 597
            A +G  Q++D
Sbjct: 231 AAEQGIFQLID 241

>pdb|1R6L|A Chain A, Crystal Structure Of The Trna Processing Enzyme Rnase Ph From Pseudomonas Aeruginosa Length = 239

Iteration: 1
 Score = 59.7 bits (143), Expect = 8e-09,   Method: Compositional matrix adjust.
 Identities = 58/209 (27%), Positives = 87/209 (41%), Gaps = 30/209 (14%)
Query: 370 RVDGRQLDEVRPIYCESGNLPILHGSSLFSRGDTQVLCTVTLGAPAEAQRLESLVGPPTK 429
           R  GR  D++RPI           GS L   GDT+V+CTV+    AE+     L G    
Sbjct: 3   RPSGRAADQLRPIRITRHYTKHAEGSVLVEFGDTKVICTVS----AESGVPRFLKGQGQG 58
Query: 430 RFMLHYSFPPFCINEVGKRVGLNRREVGHG----TLAEKALLAVLPPENDFPYTVRVNSE 485
                Y   P    E  +R     ++ G       L  ++L A L        T+ ++ +
Sbjct: 59  WLTAEYGXLPRSTGERNQREASRGKQGGRTLEIQRLIGRSLRAALDLSKLGENTLYIDCD 118
Query: 486 VMASDGSTSMATVCGGSMALMDA-----------GIPLQEHVAGVSVGLVSEVDPSTGEI 534
           V+ +DG T  A++ G ++AL+DA           G PL++ VA VSVG+   V       
Sbjct: 119 VIQADGGTRTASITGATVALIDALAVLKKRGALKGNPLKQXVAAVSVGIYQGVP------ 172
Query: 535 KDYRILTDILGLEDHLGDMDFKIAGTRIG 563
                + D+  LED   + D  +  T  G
Sbjct: 173 -----VLDLDYLEDSAAETDLNVVXTDAG 196

>pdb|1R6M|A Chain A, Crystal Structure Of The Trna Processing Enzyme Rnase Ph From Pseudomonas Aeruginosa In Complex With Phosphate Length = 239

Iteration: 1
 Score = 58.9 bits (141), Expect = 1e-08,   Method: Compositional matrix adjust.
 Identities = 61/215 (28%), Positives = 89/215 (41%), Gaps = 42/215 (19%)
Query: 370 RVDGRQLDEVRPIYCESGNLPILHGSSLFSRGDTQVLCTVTLGAPAEAQRLESLVGPPTK 429
           R  GR  D++RPI           GS L   GDT+V+CTV+    AE+     L G    
Sbjct: 3   RPSGRAADQLRPIRITRHYTKHAEGSVLVEFGDTKVICTVS----AESGVPRFLKGQGQG 58
Query: 430 RFMLHYSFPPFCINEVGKRVGLNRREVGHGT----------LAEKALLAVLPPENDFPYT 479
                Y   P      G+R   N+RE   G           L  ++L A L        T
Sbjct: 59  WLTAEYGMLP---RSTGER---NQREASRGKQGGRTLEIQRLIGRSLRAALDLSKLGENT 112
Query: 480 VRVNSEVMASDGSTSMATVCGGSMALMDA-----------GIPLQEHVAGVSVGLVSEVD 528
           + ++ +V+ +DG T  A++ G ++AL+DA           G PL++ VA VSVG+   V 
Sbjct: 113 LYIDCDVIQADGGTRTASITGATVALIDALAVLKKRGALKGNPLKQMVAAVSVGIYQGVP 172
Query: 529 PSTGEIKDYRILTDILGLEDHLGDMDFKIAGTRIG 563
                      + D+  LED   + D  +  T  G
Sbjct: 173 -----------VLDLDYLEDSAAETDLNVVMTDAG 196

>pdb|1OYP|A Chain A, Crystal Structure Of The Phosphorolytic Exoribonuclease Rnase Ph From Bacillus Subtilis Length = 245

Iteration: 1
 Score = 55.1 bits (131), Expect = 2e-07,   Method: Compositional matrix adjust.
 Identities = 50/173 (28%), Positives = 80/173 (46%), Gaps = 19/173 (10%)
Query: 369 VRVDGRQLDEVRPIYCESGNLPILHGSSLFSRGDTQVLCTVTLGAPAEAQRLESLVGPPT 428
           +R DGRQ DE+RPI  +   +    GS L + G+T+V+C     A  E +    L G   
Sbjct: 1   MRHDGRQHDELRPITFDLDFISHPEGSVLITAGNTKVICN----ASVEDRVPPFLRGGGK 56
Query: 429 KRFMLHYSFPPFCINEVGKRVG----LNRREVGHGTLAEKALLAVLPPENDFPYTVRVNS 484
                 YS  P   N+   R      ++ R +    L  +AL AV+  E     T+ ++ 
Sbjct: 57  GWITAEYSMLPRATNQRTIRESSKGKISGRTMEIQRLIGRALRAVVDLEKLGERTIWIDC 116
Query: 485 EVMASDGSTSMATVCGGSMA-------LMDAGI----PLQEHVAGVSVGLVSE 526
           +V+ +DG T  A++ G  +A       L+ AG     P+ + +A +SVG+  E
Sbjct: 117 DVIQADGGTRTASITGAFLAMAIAIGKLIKAGTIKTNPITDFLAAISVGIDKE 169

>pdb|1OYS|A Chain A, Crystal Structure Of The Phosphorolytic Exoribonuclease Rnase Ph From Bacillus Subtilis Length = 245

Iteration: 1
 Score = 54.3 bits (129), Expect = 3e-07,   Method: Compositional matrix adjust.
 Identities = 49/173 (28%), Positives = 80/173 (46%), Gaps = 19/173 (10%)
Query: 369 VRVDGRQLDEVRPIYCESGNLPILHGSSLFSRGDTQVLCTVTLGAPAEAQRLESLVGPPT 428
           +R DGRQ DE+RPI  +   +    GS L + G+T+V+C     A  E +    L G   
Sbjct: 1   MRHDGRQHDELRPITFDLDFISHPEGSVLITAGNTKVICN----ASVEDRVPPFLRGGGK 56
Query: 429 KRFMLHYSFPPFCINEV----GKRVGLNRREVGHGTLAEKALLAVLPPENDFPYTVRVNS 484
                 YS  P   N+       +  ++ R +    L  +AL AV+  E     T+ ++ 
Sbjct: 57  GWITAEYSMLPQATNQQTIQESSKGKISGRTMEIQRLIGRALRAVVDLEKLGERTIWIDC 116
Query: 485 EVMASDGSTSMATVCGGSMA-------LMDAGI----PLQEHVAGVSVGLVSE 526
           +V+ +DG T  A++ G  +A       L+ AG     P+ + +A +SVG+  E
Sbjct: 117 DVIQADGGTRTASITGAFLAMAIAIGKLIKAGTIKTNPITDFLAAISVGIDKE 169

>pdb|4IFD|B Chain B, Crystal Structure Of An 11-subunit Eukaryotic Exosome Complex Bound To Rna Length = 248

Iteration: 1
 Score = 52.4 bits (124), Expect = 1e-06,   Method: Compositional matrix adjust.
 Identities = 45/162 (27%), Positives = 77/162 (47%), Gaps = 11/162 (6%)
Query: 367 EGVRVDGRQLDEVRPIYCESGNLP-ILHGSSLFSRGDTQVLCTVTLGAPAEAQRLESLVG 425
           EG+R+DGR+ +E+R         P    GSS   +G+ +++  V    P E  RL+S + 
Sbjct: 12  EGLRLDGRRWNELRRFESSINTHPHAADGSSYMEQGNNKIITLVK--GPKEP-RLKSQMD 68
Query: 426 PPTKRFMLHYSFPPFCINEVGKRVGLNRREVGHGTLAEKALLAVLPPE---NDFPYTV-R 481
                  +  +   F   E  K    N R V      + +L+ +       N +P TV  
Sbjct: 69  TSKALLNVSVNITKFSKFERSKSSHKNERRVLE---IQTSLVRMFEKNVMLNIYPRTVID 125
Query: 482 VNSEVMASDGSTSMATVCGGSMALMDAGIPLQEHVAGVSVGL 523
           +   V+  DG    + + G ++AL+DAGI + ++++G+SVGL
Sbjct: 126 IEIHVLEQDGGIMGSLINGITLALIDAGISMFDYISGISVGL 167

>pdb|2WP8|B Chain B, Yeast Rrp44 Nuclease Length = 246

Iteration: 1
 Score = 52.4 bits (124), Expect = 1e-06,   Method: Compositional matrix adjust.
 Identities = 45/162 (27%), Positives = 77/162 (47%), Gaps = 11/162 (6%)
Query: 367 EGVRVDGRQLDEVRPIYCESGNLP-ILHGSSLFSRGDTQVLCTVTLGAPAEAQRLESLVG 425
           EG+R+DGR+ +E+R         P    GSS   +G+ +++  V    P E  RL+S + 
Sbjct: 10  EGLRLDGRRWNELRRFESSINTHPHAADGSSYMEQGNNKIITLVK--GPKEP-RLKSQMD 66
Query: 426 PPTKRFMLHYSFPPFCINEVGKRVGLNRREVGHGTLAEKALLAVLPPE---NDFPYTV-R 481
                  +  +   F   E  K    N R V      + +L+ +       N +P TV  
Sbjct: 67  TSKALLNVSVNINKFSKFERSKSSHKNERRVLE---IQTSLVRMFEKNVMLNIYPRTVID 123
Query: 482 VNSEVMASDGSTSMATVCGGSMALMDAGIPLQEHVAGVSVGL 523
           +   V+  DG    + + G ++AL+DAGI + ++++G+SVGL
Sbjct: 124 IEIHVLEQDGGIMGSLINGITLALIDAGISMFDYISGISVGL 165

>pdb|2EQS|A Chain A, Solution Structure Of The S1 Rna Binding Domain Of Human Atp-Dependent Rna Helicase Dhx8 Length = 103

Iteration: 1
 Score = 51.6 bits (122), Expect = 2e-06,   Method: Compositional matrix adjust.
 Identities = 28/66 (42%), Positives = 43/66 (65%), Gaps = 4/66 (6%)
Query: 678 GREIEVGGIYKGVVTSVKEYGAFVEFNG---GQQGLLHVSELSHEP-VSRVSDVVSVGQQ 733
           G E  +G IY G VTS+ ++G FV+  G     +GL+H+SEL  E  V+ V+DVVS GQ+
Sbjct: 7   GEEPTIGDIYNGKVTSIMQFGCFVQLEGLRKRWEGLVHISELRREGRVANVADVVSKGQR 66
Query: 734 LSLRCI 739
           + ++ +
Sbjct: 67  VKVKVL 72

>pdb|3BZC|A Chain A, Crystal Structure Of The Tex Protein From Pseudomonas Aeruginosa, Crystal Form I Length = 785

Iteration: 1
 Score = 50.8 bits (120), Expect = 3e-06,   Method: Compositional matrix adjust.
 Identities = 46/147 (31%), Positives = 76/147 (51%), Gaps = 11/147 (7%)
Query: 627 LRRLIGPLGALKR----KIEEETGGRISVSDGTLTVVAKNRSVMEKVLEKVDFIIG---- 678
           +R LIG    LKR    K  +ET G  +V+D  L  + K         +  +F  G    
Sbjct: 591 IRSLIGDSAFLKRLDPKKFTDETFGLPTVTD-ILKELDKPGRDPRPEFKTAEFQEGVESL 649
Query: 679 REIEVGGIYKGVVTSVKEYGAFVEFNGGQQGLLHVSELSHEPVSRVSDVVSVGQQLSLRC 738
           ++++ G + +GVVT+V  +GAFV+    Q GL+H+S LS + V    +VV  G  + ++ 
Sbjct: 650 KDLKPGMVLEGVVTNVTNFGAFVDIGVHQDGLVHISALSEKFVKDPYEVVKAGDIVKVKV 709
Query: 739 IGQDV-RGNIKLSLKAVSPRPEADVKG 764
           +  D+ R  + LS++ +S  P   V+G
Sbjct: 710 MEVDIPRNRVGLSMR-MSDTPGEKVEG 735

>pdb|2OCE|A Chain A, Crystal Structure Of Tex Family Protein Pa5201 From Pseudomonas Aeruginosa Length = 780

Iteration: 1
 Score = 50.8 bits (120), Expect = 4e-06,   Method: Compositional matrix adjust.
 Identities = 46/147 (31%), Positives = 76/147 (51%), Gaps = 11/147 (7%)
Query: 627 LRRLIGPLGALKR----KIEEETGGRISVSDGTLTVVAKNRSVMEKVLEKVDFIIG---- 678
           +R LIG    LKR    K  +ET G  +V+D  L  + K         +  +F  G    
Sbjct: 592 IRSLIGDSAFLKRLDPKKFTDETFGLPTVTD-ILKELDKPGRDPRPEFKTAEFQEGVESL 650
Query: 679 REIEVGGIYKGVVTSVKEYGAFVEFNGGQQGLLHVSELSHEPVSRVSDVVSVGQQLSLRC 738
           ++++ G + +GVVT+V  +GAFV+    Q GL+H+S LS + V    +VV  G  + ++ 
Sbjct: 651 KDLKPGMVLEGVVTNVTNFGAFVDIGVHQDGLVHISALSEKFVKDPYEVVKAGDIVKVKV 710
Query: 739 IGQDV-RGNIKLSLKAVSPRPEADVKG 764
           +  D+ R  + LS++ +S  P   V+G
Sbjct: 711 MEVDIPRNRVGLSMR-MSDTPGEKVEG 736

>pdb|3B4T|A Chain A, Crystal Structure Of Mycobacterium Tuberculosis Rnase Ph, The Mycobacterium Tuberculosis Structural Genomics Consortium Target Rv1340 Length = 262

Iteration: 1
 Score = 48.9 bits (115), Expect = 1e-05,   Method: Compositional matrix adjust.
 Identities = 59/212 (27%), Positives = 82/212 (38%), Gaps = 35/212 (16%)
Query: 370 RVDGRQLDEVRPIYCESGNLPILHGSSLFSRGDTQVLCT--VTLGAPAEAQRLESLVGPP 427
           R DGR   E+RP+    G      GS L   G T+VLCT  VT G P    R     G  
Sbjct: 7   REDGRLDHELRPVIITRGFTENPAGSVLIEFGHTKVLCTASVTEGVP----RWRKATG-- 60
Query: 428 TKRFMLHYSFPPFCINEVGKRVGLNRREVGH----GTLAEKALLAVLPPENDFPYTVRVN 483
                  Y+  P   +    R  +  R  G       L  ++L A +        T+ ++
Sbjct: 61  LGWLTAEYAMLPSATHSRSDRESVRGRLSGRTQEISRLIGRSLRACIDLAALGENTIAID 120
Query: 484 SEVMASDGSTSMATVCGGSMALMDAGI------------PLQEHVAGVSVGLVSEVDPST 531
            +V+ +DG T  A + G  +AL DA              PL   +A VSVG+V       
Sbjct: 121 CDVLQADGGTRTAAITGAYVALADAVTYLSAAGKLSDPRPLSCAIAAVSVGVV------- 173
Query: 532 GEIKDYRILTDILGLEDHLGDMDFKIAGTRIG 563
               D RI  D+   ED   ++D  +  T  G
Sbjct: 174 ----DGRIRVDLPYEEDSRAEVDMNVVATDTG 201

>pdb|3HKM|A Chain A, Crystal Structure Of Rice(Oryza Sativa) Rrp46 Length = 246

Iteration: 1
 Score = 48.1 bits (113), Expect = 3e-05,   Method: Compositional matrix adjust.
 Identities = 45/165 (27%), Positives = 71/165 (43%), Gaps = 23/165 (13%)
Query: 367 EGVRVDGRQLDEVRPIYCESGNLPILHGSSLFSRGDTQVLCTVTLGAPAEAQRLESLVGP 426
           E  R DGR  +++RP  C    L   HGS+ +++GDT VL  V    P   +      G 
Sbjct: 2   EESRADGRNPNQLRPFSCTRNPLDRAHGSARWAQGDTIVLAAVYGPKPGTRK------GE 55
Query: 427 PTKRFMLHYSFPPFCINEVGKR-----VGLNRREVGHGTLAEKALLAVLPPENDFPYTVR 481
             ++  +   + P    ++GK+     + L R      TL    LL V P       T  
Sbjct: 56  NPEKASIEVVWKPM-TGQIGKQEKEYEMTLKR------TLQSICLLTVHP-----NTTTS 103
Query: 482 VNSEVMASDGSTSMATVCGGSMALMDAGIPLQEHVAGVSVGLVSE 526
           V  +V+ +DGS     +     AL+ AGIPL+     +  G++ +
Sbjct: 104 VILQVVGNDGSLLPCAINACCAALVFAGIPLKHLAVAIGCGVLED 148

>pdb|2CQO|A Chain A, Solution Structure Of The S1 Rna Binding Domain Of Human Hypothetical Protein Flj11067 Length = 119

Iteration: 1
 Score = 47.8 bits (112), Expect = 3e-05,   Method: Compositional matrix adjust.
 Identities = 25/74 (33%), Positives = 49/74 (66%), Gaps = 4/74 (5%)
Query: 686 IYKGVVTSVKEYGAFVEFNGG-QQGLLHVSELSHEPVSRVSDVVSVGQQLSLRCIGQDVR 744
           I++G V  V +YGAF++  G  +QGL+H + +S   V + S++V VG ++ ++ IG++++
Sbjct: 25  IFQGEVAMVTDYGAFIKIPGCRKQGLVHRTHMSSCRVDKPSEIVDVGDKVWVKLIGREMK 84
Query: 745 GN---IKLSLKAVS 755
            +   + LS+K V+
Sbjct: 85  NDRIKVSLSMKVVN 98

>pdb|2NN6|D Chain D, Structure Of The Human Rna Exosome Composed Of Rrp41, Rrp45, Rrp46, Rrp43, Mtr3, Rrp42, Csl4, Rrp4, And Rrp40 Length = 237

Iteration: 1
 Score = 43.5 bits (101), Expect = 5e-04,   Method: Compositional matrix adjust.
 Identities = 45/164 (27%), Positives = 75/164 (45%), Gaps = 17/164 (10%)
Query: 379 VRPIYCESGNLPILHGSSLFSRGDTQVLCTVTLGAPAEAQRLESLVGPPTKRFMLHYSFP 438
           +R   CE   L    GS+ F +GDT VL  V    PAE +  + +    T   +L    P
Sbjct: 30  LRHFACEQNLLSRPDGSASFLQGDTSVLAGVY--GPAEVKVSKEIFNKATLEVILR---P 84
Query: 439 PFCINEVGKRVGLNRREVGHGTLAEKALLAVLPPENDFPYTVRVNSEVMASDGSTSMATV 498
              +  V ++   +R  +   T  E  +L  L P      ++ V  +V++  GS     +
Sbjct: 85  KIGLPGVAEK---SRERLIRNT-CEAVVLGTLHPRT----SITVVLQVVSDAGSLLACCL 136
Query: 499 CGGSMALMDAGIPLQEHVAGVSVGLVSE----VDPSTGEIKDYR 538
               MAL+DAG+P++    GV+  L S+    +DP++ + K+ R
Sbjct: 137 NAACMALVDAGVPMRALFCGVACALDSDGTLVLDPTSKQEKEAR 180

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Length	Definition	E-value
Query	974
3cdi_A	723	Polynucleotide phosphorylase; mRNA turnover, RNAse	0.0
4aid_A	726	Polyribonucleotide nucleotidyltransferase; transfe	0.0
1e3p_A	757	Guanosine pentaphosphate synthetase; polyribonucle	0.0
3u1k_A	630	Polyribonucleotide nucleotidyltransferase 1, MITO;	0.0
3gme_A	549	Polyribonucleotide nucleotidyltransferase; protein	0.0
3m7n_D	258	Probable exosome complex exonuclease 1; exosome, R	1e-110
2je6_B	250	RRP41, exosome complex exonuclease 1; nuclease, hy	1e-109
2je6_B	250	RRP41, exosome complex exonuclease 1; nuclease, hy	9e-05
2po1_A	249	Probable exosome complex exonuclease 1; RNAse PH,	1e-107
2po1_A	249	Probable exosome complex exonuclease 1; RNAse PH,	3e-05
2nn6_B	249	Exosome complex exonuclease RRP41; RNA, exosome, P	1e-103
2nn6_B	249	Exosome complex exonuclease RRP41; RNA, exosome, P	2e-05
2wnr_B	240	Probable exosome complex exonuclease 1; phosphate	1e-91
2wnr_B	240	Probable exosome complex exonuclease 1; phosphate	6e-08
3hkm_A	246	OS03G0854200 protein; RNAse PH domain, phosphoryla	3e-84
3hkm_A	246	OS03G0854200 protein; RNAse PH domain, phosphoryla	8e-07
1oys_A	245	Ribonuclease PH; transferase, tRNA processing; 2.4	6e-81
1oys_A	245	Ribonuclease PH; transferase, tRNA processing; 2.4	1e-04
2nn6_F	272	MTR3, exosome component 6; RNA, exosome, PM/SCL, p	3e-78
2nn6_F	272	MTR3, exosome component 6; RNA, exosome, PM/SCL, p	6e-11
2wp8_B	246	Exosome complex component SKI6; nucleus, hydrolase	4e-77
2wp8_B	246	Exosome complex component SKI6; nucleus, hydrolase	1e-11
3dd6_A	255	Ribonuclease PH; exoribonuclease, tRNA maturation,	7e-77
3dd6_A	255	Ribonuclease PH; exoribonuclease, tRNA maturation,	3e-04
2nn6_D	237	Exosome complex exonuclease RRP46; RNA, exosome, P	2e-71
2nn6_D	237	Exosome complex exonuclease RRP46; RNA, exosome, P	1e-14
1udn_A	255	Ribonuclease PH, RNAse PH; transferase, riken stru	4e-66
1udn_A	255	Ribonuclease PH, RNAse PH; transferase, riken stru	1e-05
1r6l_A	239	Ribonuclease PH; beta-alpha-beta-alpha fold, hexam	3e-58
3b4t_A	262	Ribonuclease PH; RNAse, tRNA nucleotidyltransferas	5e-53
3krn_A	222	Protein C14A4.5, confirmed by transcript evidence;	2e-32
3krn_A	222	Protein C14A4.5, confirmed by transcript evidence;	1e-12
2k4k_A	130	GSP13, general stress protein 13; cytoplasm, stres	1e-23
2eqs_A	103	ATP-dependent RNA helicase DHX8; S1 domain, OB-fol	6e-23
2wnr_A	271	Probable exosome complex exonuclease 2; phosphate	6e-22
2cqo_A	119	Nucleolar protein of 40 kDa; S1 domain, OB-fold, s	2e-21
3m7n_G	259	Probable exosome complex exonuclease 2; exosome, R	2e-21
2nn6_C	278	Exosome complex exonuclease RRP43; RNA, exosome, P	9e-21
2je6_A	277	RRP42, exosome complex exonuclease 2; nuclease, hy	1e-20
1whu_A	104	Polynucleotide phosphorylase; 3'-5' RNA exonucleas	3e-20
2po1_B	277	Probable exosome complex exonuclease 2; RNAse PH,	2e-19
2k52_A	80	Uncharacterized protein MJ1198; metal-binding, zin	4e-18
2a19_A	175	EIF-2- alpha, eukaryotic translation initiation fa	3e-16
1kl9_A	182	Eukaryotic translation initiation factor 2 subuni;	4e-16
2nn6_E	305	Exosome complex exonuclease RRP42; RNA, exosome, P	6e-16
2wp8_A	305	Exosome complex component RRP45; nucleus, hydrolas	7e-16
2khj_A	109	30S ribosomal protein S1; OB fold, acetylation, ph	1e-15
2nn6_A	358	Polymyositis/scleroderma autoantigen 1; RNA, exoso	1e-15
3cw2_C	266	Translation initiation factor 2 subunit alpha; AIF	1e-14
3aev_A	275	Translation initiation factor 2 subunit alpha; pro	3e-14
2khi_A	115	30S ribosomal protein S1; acetylation, phosphoprot	3e-14
1q8k_A	308	Eukaryotic translation initiation factor 2 subunit	6e-13
3bzc_A	785	TEX; helix-turn-helix, helix-hairpin-helix, S1 dom	5e-11
3psf_A	1030	Transcription elongation factor SPT6; nucleus; 2.5	8e-09
3psi_A	1219	Transcription elongation factor SPT6; nucleus; 3.3	4e-08
3h36_A	93	Polyribonucleotide nucleotidyltransferase; polyrib	6e-08
1vt4_I	1221	APAF-1 related killer DARK; drosophila apoptosome,	4e-07
1vt4_I	1221	APAF-1 related killer DARK; drosophila apoptosome,	5e-07
4ubp_A	101	Protein (urease (chain A)); bacillus pasteurii, ni	7e-07
2fvh_A	120	Urease gamma subunit; protein: UREA homolog, struc	9e-05
2qnd_A	144	FMR1 protein; KH domain, eukaryotic KH domains, ta	1e-04
3m7n_A	179	Putative uncharacterized protein AF_0206; exosome,	2e-04

>3cdi_A Polynucleotide phosphorylase; mRNA turnover, RNAse, RNA degradation, kinase, transferase; 2.60A {Escherichia coli} PDB: 1sro_A Length = 723

 Score =  890 bits (2303), Expect = 0.0
 Identities = 294/716 (41%), Positives = 446/716 (62%), Gaps = 16/716 (2%)

Query: 52  GTKVLETFKEEFEIGSRLITLETGKIARFANGAVVLGMDETKVLSTVTSSKGDSVR---D 108
              +L     +F+ G   +TLETG +AR A  AV++ MD+T V  TV   K    +   D
Sbjct: 4   DITLLNPIVRKFQYGQHTVTLETGMMARQATAAVMVSMDDTAVFVTVVGQK--KAKPGQD 61

Query: 109 FLPLTVDYQEKQFAQGVIPNTYMRREGAPKERELLVGRIIDRPIRPLFPAGFYHEVQVMA 168
           F PLTV+YQE+ +A G IP ++ RREG P E E L+ R+IDRPIRPLFP GF +EVQV+A
Sbjct: 62  FFPLTVNYQERTYAAGRIPGSFFRREGRPSEGETLIARLIDRPIRPLFPEGFVNEVQVIA 121

Query: 169 SVLSSDGKQDPDIMAANATSAALMLSDIPWGGPIGMIRIGRICGQFIVNPTMDELSLSDL 228
           +V+S + + +PDI+A    SAAL LS IP+ GPIG  R+G I  Q+++NPT DEL  S L
Sbjct: 122 TVVSVNPQVNPDIVAMIGASAALSLSGIPFNGPIGAARVGYINDQYVLNPTQDELKESKL 181

Query: 229 NLVYACTREKTLMIDVQAREISEKDLEAGLRLAHPEAVKYLEPQIRLAEKAGKQKKEYKL 288
           +LV A T    LM++ +A+ +SE  +   +   H +    ++    L ++AGK + +++ 
Sbjct: 182 DLVVAGTEAAVLMVESEAQLLSEDQMLGAVVFGHEQQQVVIQNINELVKEAGKPRWDWQP 241

Query: 289 SMISEQTLEKVSNLAEAHIEAVFTDPSYSKFERGEALDKIGQDVKKALEEECDEESLQVL 348
             ++E    +V+ LAEA +   +      K ER   +D I  +    L  E +      L
Sbjct: 242 EPVNEALNARVAALAEARLSDAYRITD--KQERYAQVDVIKSETIATLLAEDETLDENEL 299

Query: 349 PKAVDTVRKRVIRKRIIAEGVRVDGRQLDEVRPIYCESGNLPILHGSSLFSRGDTQVLCT 408
            + +  + K V+R R++A   R+DGR+ D +R +   +G LP  HGS+LF+RG+TQ L T
Sbjct: 300 GEILHAIEKNVVRSRVLAGEPRIDGREKDMIRGLDVRTGVLPRTHGSALFTRGETQALVT 359

Query: 409 VTLGAPAEAQRLESLVGPPTKRFMLHYSFPPFCINEVGKRVGLNRREVGHGTLAEKALLA 468
            TLG   +AQ L+ L+G  T  F+ HY+FPP+ + E G      RRE+GHG LA++ +LA
Sbjct: 360 ATLGTARDAQVLDELMGERTDTFLFHYNFPPYSVGETGMVGSPKRREIGHGRLAKRGVLA 419

Query: 469 VLPPENDFPYTVRVNSEVMASDGSTSMATVCGGSMALMDAGIPLQEHVAGVSVGLVSEVD 528
           V+P  + FPYTVRV SE+  S+GS+SMA+VCG S+ALMDAG+P++  VAG+++GLV E D
Sbjct: 420 VMPDMDKFPYTVRVVSEITESNGSSSMASVCGASLALMDAGVPIKAAVAGIAMGLVKEGD 479

Query: 529 PSTGEIKDYRILTDILGLEDHLGDMDFKIAGTRIGVTAIQLDIKPAGIPLDIICECLEHA 588
                  +Y +L+DILG EDHLGDMDFK+AG+R G++A+Q+DIK  GI  +I+   L  A
Sbjct: 480 -------NYVVLSDILGDEDHLGDMDFKVAGSRDGISALQMDIKIEGITKEIMQVALNQA 532

Query: 589 HKGRLQILDHMEREISAPRTQDDRNSPRLATLKYDNDTLRRLIGPLGALKRKIEEETGGR 648
              RL IL  ME+ I+APR      +PR+ T+K + D ++ +IG  G++ R + EETG  
Sbjct: 533 KGARLHILGVMEQAINAPRGDISEFAPRIHTIKINPDKIKDVIGKGGSVIRALTEETGTT 592

Query: 649 ISVS-DGTLTVVAKNRSVMEKVLEKVDFIIGREIEVGGIYKGVVTSVKEYGAFVEFNGGQ 707
           I +  DGT+ + A +    +  + +++ I   EIEVG +Y G VT + ++GAFV   GG+
Sbjct: 593 IEIEDDGTVKIAATDGEKAKHAIRRIEEIT-AEIEVGRVYTGKVTRIVDFGAFVAIGGGK 651

Query: 708 QGLLHVSELSHEPVSRVSDVVSVGQQLSLRCIGQDVRGNIKLSLKAVSPRPEADVK 763
           +GL+H+S+++ + V +V+D + +GQ++ ++ +  D +G I+LS+K  + + +    
Sbjct: 652 EGLVHISQIADKRVEKVTDYLQMGQEVPVKVLEVDRQGRIRLSIKEATEQSQPAAA 707

>4aid_A Polyribonucleotide nucleotidyltransferase; transferase-peptide complex; 2.60A {Caulobacter vibrioides} PDB: 4aim_A 4am3_A Length = 726

 Score =  887 bits (2296), Expect = 0.0
 Identities = 293/713 (41%), Positives = 434/713 (60%), Gaps = 16/713 (2%)

Query: 56  LETFKEEFEIGSRLITLETGKIARFANGAVVLGMDETKVLSTVTSSKGDSV-RDFLPLTV 114
            +  ++  E G + + LETG+IAR A+GAV+  M ET VL+T   +K     +DF PLTV
Sbjct: 16  FDIKRKTIEWGGKTLVLETGRIARQADGAVLATMGETVVLATAVFAKSQKPGQDFFPLTV 75

Query: 115 DYQEKQFAQGVIPNTYMRREGAPKERELLVGRIIDRPIRPLFPAGFYHEVQVMASVLSSD 174
           +YQEK FA G IP  + +REG P E+E LV R+IDRPIRPLF  GF +EVQV+ +VL  D
Sbjct: 76  NYQEKTFAAGKIPGGFFKREGRPSEKETLVSRLIDRPIRPLFVKGFKNEVQVVVTVLQHD 135

Query: 175 GKQDPDIMAANATSAALMLSDIPWGGPIGMIRIGRICGQFIVNPTMDELSLSDLNLVYAC 234
            + DPDI+   A SAAL LS  P+ GPIG  R+G + G +++NPT+DE+  S ++LV A 
Sbjct: 136 LENDPDILGMVAASAALCLSGAPFMGPIGAARVGWVDGAYVLNPTLDEMKESKMDLVVAG 195

Query: 235 TREKTLMIDVQAREISEKDLEAGLRLAHPEAVKYLEPQIRLAEKAGKQKKEYKLSMISEQ 294
           T +  +M++ + +E+SE+ +  G+  AH +    ++  I LAE A K+   ++       
Sbjct: 196 TADAVMMVESEIQELSEEIVLGGVNFAHQQMQAVIDAIIDLAEHAAKEPFAFEPEDTDA- 254

Query: 295 TLEKVSNLAEAHIEAVFTDPSYSKFERGEALDKIGQDVKKAL---EEECDEESLQVLPKA 351
              K+ +L  A I A +      K +R EA+    +    AL   +E         L   
Sbjct: 255 IKAKMKDLVGADIAAAYKIQK--KQDRYEAVGAAKKKAIAALGLSDENPTGYDPLKLGAI 312

Query: 352 VDTVRKRVIRKRIIAEGVRVDGRQLDEVRPIYCESGNLPILHGSSLFSRGDTQVLCTVTL 411
              +   V+R+ I+  G+R+DGR +  VRPI  E G LP  HGS+LF+RG+TQ +   TL
Sbjct: 313 FKELEADVVRRGILDTGLRIDGRDVKTVRPILGEVGILPRTHGSALFTRGETQAIVVATL 372

Query: 412 GAPAEAQRLESLVGPPTKRFMLHYSFPPFCINEVGKRVGLNRREVGHGTLAEKALLAVLP 471
           G   + Q +++L G   + F+LHY+FPP+ + E G+     RRE+GHG LA +AL  +LP
Sbjct: 373 GTGDDEQFIDALEGTYKESFLLHYNFPPYSVGETGRMGSPGRREIGHGKLAWRALRPMLP 432

Query: 472 PENDFPYTVRVNSEVMASDGSTSMATVCGGSMALMDAGIPLQEHVAGVSVGLVSEVDPST 531
            + DFPYT+R+ SE+  S+GS+SMATVCG S+A+MDAG+PL   V+G+++GL+ E D   
Sbjct: 433 TKEDFPYTIRLVSEITESNGSSSMATVCGSSLAMMDAGVPLVRPVSGIAMGLILEQD--- 489

Query: 532 GEIKDYRILTDILGLEDHLGDMDFKIAGTRIGVTAIQLDIKPAGIPLDIICECLEHAHKG 591
                + +L+DILG EDHLGDMDFK+AGT  G+T++Q+DIK AGI   I+ + L  A +G
Sbjct: 490 ----GFAVLSDILGDEDHLGDMDFKVAGTSEGLTSLQMDIKIAGITPAIMEQALAQAKEG 545

Query: 592 RLQILDHMEREISAPRTQDDRNSPRLATLKYDNDTLRRLIGPLGALKRKIEEETGGRISV 651
           R  IL  M + + APR      +P++ T+    D +R +IG  G + R+I   TG ++ +
Sbjct: 546 RAHILGEMNKAMDAPRADVGDFAPKIETINIPTDKIREVIGSGGKVIREIVATTGAKVDI 605

Query: 652 SD-GTLTVVAKNRSVMEKVLEKVDFIIGREIEVGGIYKGVVTSVKEYGAFVEFNGGQQGL 710
           +D G + V A + + ++  ++ +  I   E EVG IY G V  V ++GAFV F G + GL
Sbjct: 606 NDDGVVKVSASDGAKIKAAIDWIKSIT-DEAEVGKIYDGKVVKVVDFGAFVNFFGAKDGL 664

Query: 711 LHVSELSHEPVSRVSDVVSVGQQLSLRCIGQDVRGNIKLSLKAVSPRPEADVK 763
           +HVS++S+E V++ SDV+  GQ + ++ +G D RG  KLS+K V      D+ 
Sbjct: 665 VHVSQISNERVAKPSDVLKEGQMVKVKLLGFDDRGKTKLSMKVVDQETGEDLS 717

>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 =  844 bits (2183), Expect = 0.0
 Identities = 266/740 (35%), Positives = 403/740 (54%), Gaps = 37/740 (5%)

Query: 52  GTKVLETFKEEFEIGSRLITLETGKIARFANGAVVLGM-DETKVLSTVTSSKGDSVR--- 107
            T   E   +    G+R I  ETG++AR A G+ V  + D+T VLS  T+SK  + +   
Sbjct: 21  ETHYAEAVIDNGAFGTRTIRFETGRLARQAAGSAVAYLDDDTMVLSATTASK--NPKDQL 78

Query: 108 DFLPLTVDYQEKQFAQGVIPNTYMRREGAPKERELLVGRIIDRPIRPLFPAGFYHEVQVM 167
           DF PLTVD +E+ +A G IP ++ RREG P E  +L  R+IDRP+RP F  G  +E+QV+
Sbjct: 79  DFFPLTVDVEERMYAAGKIPGSFFRREGRPSEDAILTCRLIDRPLRPSFKKGLRNEIQVV 138

Query: 168 ASVLSSDGKQDPDIMAANATSAALMLSDIPWGGPIGMIRIGRICGQFIVNPTMDELSLSD 227
           A++++ +     D++A NA SA+  L+ +P+ GPIG +R+  I GQ++  PT  EL  + 
Sbjct: 139 ATIMALNPDHLYDVVAINAASASTQLAGLPFSGPIGGVRVALIRGQWVAFPTHTELEDAV 198

Query: 228 LNLVYACT-----REKTLMIDVQARE------------ISEKDLEAGLRLAHPEAVKYLE 270
            ++V A           +M++ +A E             +E+ + AGL  A P      +
Sbjct: 199 FDMVVAGRVLEDGDVAIMMVEAEATEKTIQLVKDGAEAPTEEVVAAGLDAAKPFIKVLCK 258

Query: 271 PQIRLAEKAGKQKKEYKLSM-ISEQTLEKVSNLAEAHIEAVFTDPSYSKFERGEALDKIG 329
            Q  LA KA K   E+ + +   +  LE +S      + A  T     K +R   LD++ 
Sbjct: 259 AQADLAAKAAKPTGEFPVFLDYQDDVLEALSAAVRPELSAALTIAG--KQDREAELDRVK 316

Query: 330 QDVKKALEEECDEESLQVLPKAVDTVRKRVIRKRIIAEGVRVDGRQLDEVRPIYCESGNL 389
               + L  E  E   + +  A   + K ++R+R+IAE  R+DGR + ++R +  E   +
Sbjct: 317 ALAAEKLLPE-FEGREKEISAAYRALTKSLVRERVIAEKKRIDGRGVTDIRTLAAEVEAI 375

Query: 390 PILHGSSLFSRGDTQVLCTVTLGAPAEAQRLESLVGPPTKRFMLHYSFPPFCINEVGKRV 449
           P +HGS+LF RG+TQ+L   TL      Q+L++L     KR+M +Y+FPP+ + E G+  
Sbjct: 376 PRVHGSALFERGETQILGVTTLNMLRMEQQLDTLSPVTRKRYMHNYNFPPYSVGETGRVG 435

Query: 450 GLNRREVGHGTLAEKALLAVLPPENDFPYTVRVNSEVMASDGSTSMATVCGGSMALMDAG 509
              RRE+GHG LAE+A++ VLP   +FPY +R  SE + S+GSTSM +VC  +M+L++AG
Sbjct: 436 SPKRREIGHGALAERAIVPVLPTREEFPYAIRQVSEALGSNGSTSMGSVCASTMSLLNAG 495

Query: 510 IPLQEHVAGVSVGLVSEVDPSTGEIKDYRILTDILGLEDHLGDMDFKIAGTRIGVTAIQL 569
           +PL+  VAG+++GL+S+          Y  LTDILG ED  GDMDFK+AGT+  VTA+QL
Sbjct: 496 VPLKAPVAGIAMGLISQEINGETH---YVALTDILGAEDAFGDMDFKVAGTKEFVTALQL 552

Query: 570 DIKPAGIPLDIICECLEHAHKGRLQILDHMEREISAPRTQDDRNSPRLATLKYDNDTLRR 629
           D K  GIP  ++   L+ A   RL ILD M   I  P      N+PR+ T+K   D +  
Sbjct: 553 DTKLDGIPASVLAAALKQARDARLHILDVMMEAIDTPDEMSP-NAPRIITVKIPVDKIGE 611

Query: 630 LIGPLGALKRKIEEETGGRISVS-DGTLTVVAKNRSVMEKVLEKVDFIIGR-EIEVGGIY 687
           +IGP   +  +I+E+TG  I++  DGT+ + A +    E     ++ I      EVG   
Sbjct: 612 VIGPKRQMINQIQEDTGAEITIEDDGTIYIGAADGPAAEAARATINGIANPTSPEVGERI 671

Query: 688 KGVVTSVKEYGAFVEFNGGQQGLLHVSELS----HEPVSRVSDVVSVGQQLSLRCIGQDV 743
            G V     +GAFV    G+ GLLH+S++      + V  V DV+ VGQ++ +     D 
Sbjct: 672 LGSVVKTTTFGAFVSLLPGKDGLLHISQIRKLAGGKRVENVEDVLGVGQKVQVEIAEIDS 731

Query: 744 RGNIKLSLKAVSPRPEADVK 763
           RG + L          +D K
Sbjct: 732 RGKLSLIPVIEGEEAASDEK 751

>3u1k_A Polyribonucleotide nucleotidyltransferase 1, MITO; RNAse PH, KH domain, exoribonuclease; HET: CIT; 2.13A {Homo sapiens} Length = 630

 Score =  794 bits (2053), Expect = 0.0
 Identities = 268/623 (43%), Positives = 388/623 (62%), Gaps = 9/623 (1%)

Query: 62  EFEIGSRLITLETGKIARFANGAVVLGMDETKVLSTVTSSKGDSVRDFLPLTVDYQEKQF 121
             ++G+R + + +GK+ARFA+G+ V+   +T V+ T  S    S   F+PL VDY++K  
Sbjct: 9   AVDLGNRKLEISSGKLARFADGSAVVQSGDTAVMVTAVSKTKPSPSQFMPLVVDYRQKAA 68

Query: 122 AQGVIPNTYMRREGAPKERELLVGRIIDRPIRPLFPAGFYHEVQVMASVLSSDGKQDPDI 181
           A G IP  Y+RRE    ++E+L  RIIDR IRPLFPAG++++ QV+ ++L+ DG  +PD+
Sbjct: 69  AAGRIPTNYLRREVGTSDKEILTSRIIDRSIRPLFPAGYFYDTQVLCNLLAVDGVNEPDV 128

Query: 182 MAANATSAALMLSDIPWGGPIGMIRIGRICGQFIVNPTMDELSLSDLNLVYACT-REKTL 240
           +A N  S AL LSDIPW GP+G +RIG I G+++VNPT  E+S S LNLV A   + + +
Sbjct: 129 LAINGASVALSLSDIPWNGPVGAVRIGIIDGEYVVNPTRKEMSSSTLNLVVAGAPKSQIV 188

Query: 241 MIDVQAREISEKDLEAGLRLAHPEAVKYLEPQIRLAEKAGKQKKE-YKLSMISEQTLEKV 299
           M++  A  I ++D    +++      + ++   +L ++ G  K+   KL   S + ++  
Sbjct: 189 MLEASAENILQQDFCHAIKVGVKYTQQIIQGIQQLVKETGVTKRTPQKLFTPSPEIVKYT 248

Query: 300 SNLAEAHIEAVFTDPSYSKFERGEALDKIGQDVKKALEEECDEESLQVLPKAVDTVRKRV 359
             LA   + AVFTD  + K  R EA++KI  D ++ L+E+  E     + ++ + V K V
Sbjct: 249 HKLAMERLYAVFTDYEHDKVSRDEAVNKIRLDTEEQLKEKFPEADPYEIIESFNVVAKEV 308

Query: 360 IRKRIIAEGVRVDGRQLDEVRPIYCESGNLPILHGSSLFSRGDTQVLCTVTLGAPAE--- 416
            R  ++ E  R DGR L  +R + CE      LHGS+LF RG TQVLCTVT  +      
Sbjct: 309 FRSIVLNEYKRCDGRDLTSLRNVSCEVDMFKTLHGSALFQRGQTQVLCTVTFDSLESGIK 368

Query: 417 -AQRLESLVGPPTKRFMLHYSFPPFCINEVGKRVGLNRREVGHGTLAEKALLAVLPPEND 475
             Q + ++ G   K FMLHY FPP+  NE+GK  GLNRRE+GHG LAEKAL  V+P   D
Sbjct: 369 SDQVITAINGIKDKNFMLHYEFPPYATNEIGKVTGLNRRELGHGALAEKALYPVIP--RD 426

Query: 476 FPYTVRVNSEVMASDGSTSMATVCGGSMALMDAGIPLQEHVAGVSVGLVSEVDPSTGEIK 535
           FP+T+RV SEV+ S+GS+SMA+ CGGS+ALMD+G+P+   VAGV++GLV++ DP  GEI+
Sbjct: 427 FPFTIRVTSEVLESNGSSSMASACGGSLALMDSGVPISSAVAGVAIGLVTKTDPEKGEIE 486

Query: 536 DYRILTDILGLEDHLGDMDFKIAGTRIGVTAIQLDIKPAGIPLDIICECLEHAHKGRLQI 595
           DYR+LTDILG+ED+ GDMDFKIAGT  G+TA+Q DIK  GIP+ I+ E ++ A   + +I
Sbjct: 487 DYRLLTDILGIEDYNGDMDFKIAGTNKGITALQADIKLPGIPIKIVMEAIQQASVAKKEI 546

Query: 596 LDHMEREISAPRTQDDRNSPRLATLKYDNDTLRRLIGPLGALKRKIEEETGGRISVSD-G 654
           L  M + IS PR     N P + T++       + +GP G   +K++ ETG  IS  D  
Sbjct: 547 LQIMNKTISKPRASRKENGPVVETVQVPLSKRAKFVGPGGYNLKKLQAETGVTISQVDEE 606

Query: 655 TLTVVAKNRSVMEKVLEKVDFII 677
           T +V A   S M +  + +  I 
Sbjct: 607 TFSVFAPTPSAMHEARDFITEIC 629

>3gme_A Polyribonucleotide nucleotidyltransferase; protein-RNA complex, cytoplasm, nucleotidyltransferase, RNA- binding, transferase, hydrolase; 2.40A {Escherichia coli E24377A} PDB: 3gll_A 3gcm_A 3h1c_A 3cdj_A Length = 549

 Score =  735 bits (1901), Expect = 0.0
 Identities = 245/555 (44%), Positives = 349/555 (62%), Gaps = 10/555 (1%)

Query: 56  LETFKEEFEIGSRLITLETGKIARFANGAVVLGMDETKVLSTVTSSK-GDSVRDFLPLTV 114
           L     +F+ G   +TLETG +AR A  AV++ MD+T V  TV   K     +DF PLTV
Sbjct: 2   LNPIVRKFQYGQHTVTLETGMMARQATAAVMVSMDDTAVFVTVVGQKKAKPGQDFFPLTV 61

Query: 115 DYQEKQFAQGVIPNTYMRREGAPKERELLVGRIIDRPIRPLFPAGFYHEVQVMASVLSSD 174
           +YQE+ +A G IP ++ RREG P E E L+ R+IDRPIRPLFP GF +EVQV+A+V+S +
Sbjct: 62  NYQERTYAAGRIPGSFFRREGRPSEGETLIARLIDRPIRPLFPEGFVNEVQVIATVVSVN 121

Query: 175 GKQDPDIMAANATSAALMLSDIPWGGPIGMIRIGRICGQFIVNPTMDELSLSDLNLVYAC 234
            + +PDI+A    SAAL LS IP+ GPIG  R+G I  Q+++NPT DEL  S L+LV A 
Sbjct: 122 PQVNPDIVAMIGASAALSLSGIPFNGPIGAARVGYINDQYVLNPTQDELKESKLDLVVAG 181

Query: 235 TREKTLMIDVQAREISEKDLEAGLRLAHPEAVKYLEPQIRLAEKAGKQKKEYKLSMISEQ 294
           T    LM++ +A  +SE  +   +   H +    ++    L ++AGK + +++   ++E 
Sbjct: 182 TEAAVLMVESEAELLSEDQMLGAVVFGHEQQQVVIQNINELVKEAGKPRWDWQPEPVNEA 241

Query: 295 TLEKVSNLAEAHIEAVFTDPSYSKFERGEALDKIGQDVKKALEEECDEESLQVLPKAVDT 354
              +V+ LAEA +   +      K ER   +D I  +    L  E +      L + +  
Sbjct: 242 LNARVAALAEARLSDAYRITD--KQERYAQVDVIKSETIATLLAEDETLDENELGEILHA 299

Query: 355 VRKRVIRKRIIAEGVRVDGRQLDEVRPIYCESGNLPILHGSSLFSRGDTQVLCTVTLGAP 414
           + K V+R R++A   R+DGR+ D +R +   +G LP  HGS+LF+RG+TQ L T TLG  
Sbjct: 300 IEKNVVRSRVLAGEPRIDGREKDMIRGLDVRTGVLPRTHGSALFTRGETQALVTATLGTA 359

Query: 415 AEAQRLESLVGPPTKRFMLHYSFPPFCINEVGKRVGLNRREVGHGTLAEKALLAVLPPEN 474
            +AQ L+ L+G  T  F+ HY+FPP+ + E G      RRE+GHG LA++ +LAV+P  +
Sbjct: 360 RDAQVLDELMGERTDTFLFHYNFPPYSVGETGMVGSPKRREIGHGRLAKRGVLAVMPDMD 419

Query: 475 DFPYTVRVNSEVMASDGSTSMATVCGGSMALMDAGIPLQEHVAGVSVGLVSEVDPSTGEI 534
            FPYTVRV SE+  S+GS+SMA+VCG S+ALMDAG+P++  VAG+++GLV E D      
Sbjct: 420 KFPYTVRVVSEITESNGSSSMASVCGASLALMDAGVPIKAAVAGIAMGLVKEGD------ 473

Query: 535 KDYRILTDILGLEDHLGDMDFKIAGTRIGVTAIQLDIKPAGIPLDIICECLEHAHKGRLQ 594
            +Y +L+DILG EDHLGDMDFK+AG+R G++A+Q+DIK  GI  +I+   L  A   RL 
Sbjct: 474 -NYVVLSDILGDEDHLGDMDFKVAGSRDGISALQMDIKIEGITKEIMQVALNQAKGARLH 532

Query: 595 ILDHMEREISAPRTQ 609
           IL  ME+ I+APR  
Sbjct: 533 ILGVMEQAINAPRGD 547

>3m7n_D Probable exosome complex exonuclease 1; exosome, RNA, exonuclease, hydrolase, nuclease, hydrolase-RN; 2.40A {Archaeoglobus fulgidus} PDB: 3m85_D 2ba0_F 2ba1_E Length = 258

 Score =  340 bits (875), Expect = e-110
 Identities = 68/272 (25%), Positives = 118/272 (43%), Gaps = 23/272 (8%)

Query: 357 KRVIRKRIIAEGVRVDGRQLDEVRPIYCESGNLPILHGSSLFSRGDTQVLCTVTLGAPAE 416
                +++I +G+R+DGR+ DE+RPI  E+  L    GS     G  +V+  V       
Sbjct: 4   FNEKPEKLIVDGLRLDGRKFDELRPIKIEASVLKRADGSCYLEMGKNKVIAAVFGP---R 60

Query: 417 AQRLESLVGPPTKRFMLHYSFPPFCINEVGKRVGLNRREVGHGTLAEKALLAVLPPENDF 476
               E L  P        Y+  PF + E  KR G +RR +    ++++A  AV+  E   
Sbjct: 61  EVHPEHLQDPSKAIIRYRYNMAPFSVEER-KRPGPDRRSIEISKVSKEAFEAVIMKELFP 119

Query: 477 PYTVRVNSEVMASDGSTSMATVCGGSMALMDAGIPLQEHVAGVSVGLVSEVDPSTGEIKD 536
              + +  EV+ +D  +  A +   S+AL+DAG+P++  +  V+VG             D
Sbjct: 120 RSAIDIFVEVLQADAGSRTACLNAASVALVDAGVPMKGMITSVAVGKA-----------D 168

Query: 537 YRILTDILGLEDHLGDMDFKIA-----GTRIGVTAIQLDIKPAGIPLDIICECLEHAHKG 591
            +++ D +  ED+ G+ D   A     G    +  +Q+D +   +  D + + +E A KG
Sbjct: 169 GQLVLDPMKEEDNFGEADMPFAFLIRNGKIESIALLQMDGR---MTRDEVKQAIELAKKG 225

Query: 592 RLQILDHMEREISAPRTQDDRNSPRLATLKYD 623
            LQI +     I     +       +     D
Sbjct: 226 ALQIYEMQREAILRRYIEVGEEMDEITEGGED 257

>2je6_B RRP41, exosome complex exonuclease 1; nuclease, hydrolase, exonuclease, phosphorolytic, exoribonuclease, RNA degradation; HET: 1PE; 1.6A {Sulfolobus solfataricus} SCOP: d.14.1.4 d.101.1.1 PDB: 2jea_B* 2jeb_B* 2br2_B 2c37_B* 2c38_B* 2c39_B* 3l7z_B Length = 250

 Score =  335 bits (862), Expect = e-109
 Identities = 65/261 (24%), Positives = 113/261 (43%), Gaps = 20/261 (7%)

Query: 351 AVDTVRKRVIRKRIIAEGVRVDGRQLDEVRPIYCESGNLPILHGSSLFSRGDTQVLCTVT 410
            +  + +    K I+ +G R DGR+ DE+R I  E G L    GS++F  G+T+ +  V 
Sbjct: 2   HMREMLQVERPKLILDDGKRTDGRKPDELRSIKIELGVLKNADGSAIFEMGNTKAIAAVY 61

Query: 411 LGAPAEAQRLESLVGPPTKRFMLHYSFPPFCINEVGKRVGLNRREVGHGTLAEKALLAVL 470
                +      L  P      + Y   PF  +E       +RRE+    +  +AL + +
Sbjct: 62  GP---KEMHPRHLSLPDRAVLRVRYHMTPFSTDERKNP-APSRREIELSKVIREALESAV 117

Query: 471 PPENDFPYTVRVNSEVMASDGSTSMATVCGGSMALMDAGIPLQEHVAGVSVGLVSEVDPS 530
             E      + V +E++ +D  + + ++   S+AL DAGIP+++ +AGV+VG        
Sbjct: 118 LVELFPRTAIDVFTEILQADAGSRLVSLMAASLALADAGIPMRDLIAGVAVGKA------ 171

Query: 531 TGEIKDYRILTDILGLEDHLGDMDFKIA--GTRIGVTAIQLDIKPAGIPLDIICECLEHA 588
                D  I+ D+   E   G+ D  IA   +   VT  QL+     +  D   +  + A
Sbjct: 172 -----DGVIILDLNETEAMWGEADMPIAMMPSLNQVTLFQLNG---SMTPDEFRQAFDLA 223

Query: 589 HKGRLQILDHMEREISAPRTQ 609
            KG   I +     + +   +
Sbjct: 224 VKGINIIYNLEREALKSKYVE 244

>2je6_B RRP41, exosome complex exonuclease 1; nuclease, hydrolase, exonuclease, phosphorolytic, exoribonuclease, RNA degradation; HET: 1PE; 1.6A {Sulfolobus solfataricus} SCOP: d.14.1.4 d.101.1.1 PDB: 2jea_B* 2jeb_B* 2br2_B 2c37_B* 2c38_B* 2c39_B* 3l7z_B Length = 250

 Score = 44.2 bits (105), Expect = 9e-05
 Identities = 37/170 (21%), Positives = 64/170 (37%), Gaps = 28/170 (16%)

Query: 68  RLITLETGKIARFANGAVVLGMDETKVLSTVT-----SSKGDSVRDFLPLTVDYQEKQFA 122
           R I +E G +   A+G+ +  M  TK ++ V        +  S+ D   L V Y    F+
Sbjct: 31  RSIKIELGVLKN-ADGSAIFEMGNTKAIAAVYGPKEMHPRHLSLPDRAVLRVRYHMTPFS 89

Query: 123 QGVIPNTYMRREGAPKERELLVGRIIDRPIRPLFPAG--FYHEVQVMASVLSSDGKQDPD 180
                    R+  AP  RE+ + ++I   +             + V   +L +D      
Sbjct: 90  TD------ERKNPAPSRREIELSKVIREALESAVLVELFPRTAIDVFTEILQADAGSR-- 141

Query: 181 IMAA-NATSAALMLSDIPWGGPIGMIRIGRICGQFIVNPTMDELSLSDLN 229
            + +  A S AL  + IP    I  + +G+           D + + DLN
Sbjct: 142 -LVSLMAASLALADAGIPMRDLIAGVAVGKA----------DGVIILDLN 180

>2po1_A Probable exosome complex exonuclease 1; RNAse PH, hydrolase/hydrolase/RNA complex; 1.94A {Pyrococcus abyssi} PDB: 2po0_A* 2pnz_A 2po2_A* Length = 249

 Score =  331 bits (850), Expect = e-107
 Identities = 65/264 (24%), Positives = 110/264 (41%), Gaps = 20/264 (7%)

Query: 355 VRKRVIRKRIIAEGVRVDGRQLDEVRPIYCESGNLPILHGSSLFSRGDTQVLCTVTLGAP 414
           + K    K I   G R+DGR+  E+RPI  E G L   +GS+    G  +++  V     
Sbjct: 2   MEKPEGLKLIDENGRRIDGRKKYELRPIKMEVGVLKNANGSAYIEWGKNKIIAAVYGP-- 59

Query: 415 AEAQRLESLVGPPTKRFMLHYSFPPFCINEVGKRVGLNRREVGHGTLAEKALLAVLPPEN 474
                 + L  P      + Y+  PF + E  K+ G +RR +    + + AL   L  E 
Sbjct: 60  -RELHPKHLQRPDRAILRVRYNMAPFSVEER-KKPGPDRRSIEISKVIKGALEPALILEM 117

Query: 475 DFPYTVRVNSEVMASDGSTSMATVCGGSMALMDAGIPLQEHVAGVSVGLVSEVDPSTGEI 534
                + V  EV+ +D  T +A +   S+AL DAGIP+++ VA  + G +          
Sbjct: 118 FPRTAIDVFIEVLQADAGTRVAGITAASLALADAGIPMRDLVAACAAGKIEGE------- 170

Query: 535 KDYRILTDILGLEDHLGDMDFKIA--GTRIGVTAIQLDIKPAGIPLDIICECLEHAHKGR 592
               I+ D+   ED+ G+ D  +A    +  +T +Q+D     +  D   E ++ A KG 
Sbjct: 171 ----IVLDLNKEEDNYGEADVPVAIMPLKNDITLLQMDGY---LTKDEFIEAVKLAIKGA 223

Query: 593 LQILDHMEREISAPRTQDDRNSPR 616
             +       +     +  +    
Sbjct: 224 KAVYQKQREALKEKYLKIAQEVEG 247

>2po1_A Probable exosome complex exonuclease 1; RNAse PH, hydrolase/hydrolase/RNA complex; 1.94A {Pyrococcus abyssi} PDB: 2po0_A* 2pnz_A 2po2_A* Length = 249

 Score = 45.7 bits (109), Expect = 3e-05
 Identities = 37/205 (18%), Positives = 79/205 (38%), Gaps = 21/205 (10%)

Query: 68  RLITLETGKIARFANGAVVLGMDETKVLSTVTSSKGDSVR-----DFLPLTVDYQEKQFA 122
           R I +E G +   ANG+  +   + K+++ V   +    +     D   L V Y    F+
Sbjct: 27  RPIKMEVGVLKN-ANGSAYIEWGKNKIIAAVYGPRELHPKHLQRPDRAILRVRYNMAPFS 85

Query: 123 QGVIPNTYMRREGAPKERELLVGRIIDRPIRPLFPAG--FYHEVQVMASVLSSDGKQDPD 180
                    R++  P  R + + ++I   + P           + V   VL +D      
Sbjct: 86  VEE------RKKPGPDRRSIEISKVIKGALEPALILEMFPRTAIDVFIEVLQADAG---T 136

Query: 181 IMAA-NATSAALMLSDIPWGGPIGMIRIGRICGQFIVNPTMDELSLS--DLNLVYACTRE 237
            +A   A S AL  + IP    +     G+I G+ +++   +E +    D+ +     + 
Sbjct: 137 RVAGITAASLALADAGIPMRDLVAACAAGKIEGEIVLDLNKEEDNYGEADVPVAIMPLKN 196

Query: 238 KTLMIDVQAREISEKDLEAGLRLAH 262
              ++ +    +++ +    ++LA 
Sbjct: 197 DITLLQMDGY-LTKDEFIEAVKLAI 220

>2nn6_B Exosome complex exonuclease RRP41; RNA, exosome, PM/SCL, phosphorolytic, hydrolase/transferase complex; 3.35A {Homo sapiens} SCOP: d.14.1.4 d.101.1.1 Length = 249

 Score =  321 bits (825), Expect = e-103
 Identities = 54/251 (21%), Positives = 99/251 (39%), Gaps = 18/251 (7%)

Query: 361 RKRIIAEGVRVDGRQLDEVRPIYCESGNLPILHGSSLFSRGDTQVLCTVTLGAPAEAQRL 420
            + +  +G RVDGR+  E+R I    G      GS+   +G+T+ L  V         R 
Sbjct: 8   LELLSDQGYRVDGRRAGELRKIQARMGVFAQADGSAYIEQGNTKALAVVYGPHEIRGSRA 67

Query: 421 ESLVGPPTKRFMLHYSFPPFCINEVGKRVGLNRREVGHGTLAEKALLAVLPPENDFPYTV 480
            +L           YS   F   E  +R   +R+    G    +   A +  +      +
Sbjct: 68  RALPD--RALVNCQYSSATFSTGERKRRPHGDRKSCEMGLQLRQTFEAAILTQLHPRSQI 125

Query: 481 RVNSEVMASDGSTSMATVCGGSMALMDAGIPLQEHVAGVSVGLVSEVDPSTGEIKDYRIL 540
            +  +V+ +DG T  A V   ++A++DAGIP+++ V   S G V           D   L
Sbjct: 126 DIYVQVLQADGGTYAACVNAATLAVLDAGIPMRDFVCACSAGFV-----------DGTAL 174

Query: 541 TDILGLEDHLGDMDFKIA--GTRIGVTAIQLDIKPAGIPLDIICECLEHAHKGRLQILDH 598
            D+  +E+  G     +A       +  +++D +   +  D +   LE A +    +   
Sbjct: 175 ADLSHVEEAAGGPQLALALLPASGQIALLEMDAR---LHEDHLERVLEAAAQAARDVHTL 231

Query: 599 MEREISAPRTQ 609
           ++R +     +
Sbjct: 232 LDRVVRQHVRE 242

>2nn6_B Exosome complex exonuclease RRP41; RNA, exosome, PM/SCL, phosphorolytic, hydrolase/transferase complex; 3.35A {Homo sapiens} SCOP: d.14.1.4 d.101.1.1 Length = 249

 Score = 46.1 bits (110), Expect = 2e-05
 Identities = 39/206 (18%), Positives = 74/206 (35%), Gaps = 21/206 (10%)

Query: 68  RLITLETGKIARFANGAVVLGMDETKVLSTVT------SSKGDSVRDFLPLTVDYQEKQF 121
           R I    G  A+ A+G+  +    TK L+ V        S+  ++ D   +   Y    F
Sbjct: 27  RKIQARMGVFAQ-ADGSAYIEQGNTKALAVVYGPHEIRGSRARALPDRALVNCQYSSATF 85

Query: 122 AQGVIPNTYMRREGAPKERELLVGRIIDRPIRPLFPAGFY--HEVQVMASVLSSDGKQDP 179
           + G       +R      +   +G  + +          +   ++ +   VL +DG    
Sbjct: 86  STG-----ERKRRPHGDRKSCEMGLQLRQTFEAAILTQLHPRSQIDIYVQVLQADGG--- 137

Query: 180 DIMAA-NATSAALMLSDIPWGGPIGMIRIGRICGQFIVNPTMDE--LSLSDLNLVYACTR 236
              A  NA + A++ + IP    +     G + G  + + +  E       L L      
Sbjct: 138 TYAACVNAATLAVLDAGIPMRDFVCACSAGFVDGTALADLSHVEEAAGGPQLALALLPAS 197

Query: 237 EKTLMIDVQAREISEKDLEAGLRLAH 262
            +  ++++ AR + E  LE  L  A 
Sbjct: 198 GQIALLEMDAR-LHEDHLERVLEAAA 222

>2wnr_B Probable exosome complex exonuclease 1; phosphate binding, 3'-5' exoribonuclease, hydrolase; 2.65A {Methanothermobacter thermautotrophicusorganism_taxid} Length = 240

 Score =  289 bits (743), Expect = 1e-91
 Identities = 65/258 (25%), Positives = 108/258 (41%), Gaps = 21/258 (8%)

Query: 355 VRKRVIRKRIIA-EGVRVDGRQLDEVRPIYCESGNLPILHGSSLFSRGDTQVLCTVTLGA 413
           +   + + ++     VR DGR  DE+RP+  E+G L    GSS    G  ++L  V    
Sbjct: 1   MITIITQDQLKTSPSVREDGRAFDELRPLKIEAGILERADGSSYLEFGGNKILVAVYGP- 59

Query: 414 PAEAQRLESLVGPPTKRFMLHYSFPPFCINEVGKRVGLNRREVGHGTLAEKALLAVLPPE 473
                ++  L  P        Y+  PF + E  KR G +RR V    +  +AL   L  E
Sbjct: 60  --REAQIRKLQRPDRAVIRCRYNMAPFSVEER-KRPGPDRRSVEISKITAEALRPALILE 116

Query: 474 NDFPYTVRVNSEVMASDGSTSMATVCGGSMALMDAGIPLQEHVAGVSVGLVSEVDPSTGE 533
                 + V  EV+ ++G T  A +   S+AL DAGIP+++ V   + G V +       
Sbjct: 117 KFPRSVIDVFIEVLEAEGGTRCAGITAASVALADAGIPMRDMVVACAAGKVGDQ------ 170

Query: 534 IKDYRILTDILGLEDHLGDMDFKIA--GTRIGVTAIQLDIKPAGIPLDIICECLEHAHKG 591
                ++ D+   ED  G  D  +A       +T +Q D     +  +     L+ A +G
Sbjct: 171 -----VVLDLSEEEDKEGQADVPVAILPRTREITLLQSD---GNLTPEEFERALDLAVEG 222

Query: 592 RLQILDHMEREISAPRTQ 609
            L+I +  +  +     +
Sbjct: 223 CLRIHEVQKEALRKRYGE 240

>2wnr_B Probable exosome complex exonuclease 1; phosphate binding, 3'-5' exoribonuclease, hydrolase; 2.65A {Methanothermobacter thermautotrophicusorganism_taxid} Length = 240

 Score = 53.7 bits (130), Expect = 6e-08
 Identities = 38/206 (18%), Positives = 75/206 (36%), Gaps = 23/206 (11%)

Query: 68  RLITLETGKIARFANGAVVLGMDETKVLSTVTSSKGDSVRDFLP------LTVDYQEKQF 121
           R + +E G + R A+G+  L     K+L  V   + ++    L       +   Y    F
Sbjct: 27  RPLKIEAGILER-ADGSSYLEFGGNKILVAVYGPR-EAQIRKLQRPDRAVIRCRYNMAPF 84

Query: 122 AQGVIPNTYMRREGAPKERELLVGRIIDRPIRPLFP--AGFYHEVQVMASVLSSDGKQDP 179
           +         R+   P  R + + +I    +RP           + V   VL ++G    
Sbjct: 85  SVEE------RKRPGPDRRSVEISKITAEALRPALILEKFPRSVIDVFIEVLEAEGG--- 135

Query: 180 DIMAA-NATSAALMLSDIPWGGPIGMIRIGRICGQFIVNPTMDELSLS--DLNLVYACTR 236
              A   A S AL  + IP    +     G++  Q +++ + +E      D+ +      
Sbjct: 136 TRCAGITAASVALADAGIPMRDMVVACAAGKVGDQVVLDLSEEEDKEGQADVPVAILPRT 195

Query: 237 EKTLMIDVQAREISEKDLEAGLRLAH 262
            +  ++      ++ ++ E  L LA 
Sbjct: 196 REITLLQSDG-NLTPEEFERALDLAV 220

>3hkm_A OS03G0854200 protein; RNAse PH domain, phosphorylase, hydrolase; 1.98A {Oryza sativa japonica group} Length = 246

 Score =  270 bits (692), Expect = 3e-84
 Identities = 50/258 (19%), Positives = 90/258 (34%), Gaps = 36/258 (13%)

Query: 367 EGVRVDGRQLDEVRPIYCESGNLPILHGSSLFSRGDTQVLCTVTLGAPAEAQRLESLVGP 426
           E  R DGR  +++RP  C    L   HGS+ +++GDT VL  V    P   +      G 
Sbjct: 2   EESRADGRNPNQLRPFSCTRNPLDRAHGSARWAQGDTIVLAAVYGPKPGTRK------GE 55

Query: 427 PTKRFMLHYSFPPFCINEVGKRVGLNRREVGHGTLAEKALLAVLPPENDFPYTVRVNSEV 486
             ++  +   + P           + ++E  +    ++ L ++         T  V  +V
Sbjct: 56  NPEKASIEVVWKPM-------TGQIGKQEKEYEMTLKRTLQSICLLTVHPNTTTSVILQV 108

Query: 487 MASDGSTSMATVCGGSMALMDAGIPLQEHVAGVSVGLVSEVDPSTGEIKDYRILTDILGL 546
           + +DGS     +     AL+ AGIPL+     +  G++ + +          IL      
Sbjct: 109 VGNDGSLLPCAINACCAALVFAGIPLKHLAVAIGCGVLEDGEV---------ILDTNKAE 159

Query: 547 EDHLG-DMDFKIAGTRIGVTAIQLDIKPAGIPLDIIC-------------ECLEHAHKGR 592
           E  L          +R   ++ + + K       +I               C+E      
Sbjct: 160 EQQLKSFAHLVFPNSRKSASSKEPNQKEEDSERGLITSITHGVMSEEDYFSCIERGLAAS 219

Query: 593 LQILDHMEREISAPRTQD 610
            +I D M   +      D
Sbjct: 220 SRISDFMRTTLQKQAPGD 237

>3hkm_A OS03G0854200 protein; RNAse PH domain, phosphorylase, hydrolase; 1.98A {Oryza sativa japonica group} Length = 246

 Score = 50.5 bits (121), Expect = 8e-07
 Identities = 38/223 (17%), Positives = 76/223 (34%), Gaps = 24/223 (10%)

Query: 68  RLITLETGKIARFANGAVVLGMDETKVLSTVTSSKGDSVRDFLP--LTVDYQEKQFAQGV 125
           R  +     + R A+G+      +T VL+ V   K  + +   P   +++   K      
Sbjct: 15  RPFSCTRNPLDR-AHGSARWAQGDTIVLAAVYGPKPGTRKGENPEKASIEVVWKPMT--- 70

Query: 126 IPNTYMRREGAPKERELLVGRIIDRPIRPLFPAGFY--HEVQVMASVLSSDGKQDPDIMA 183
                    G   ++E      + R ++ +     +      V+  V+ +DG     +  
Sbjct: 71  ---------GQIGKQEKEYEMTLKRTLQSICLLTVHPNTTTSVILQVVGNDGS---LLPC 118

Query: 184 A-NATSAALMLSDIPWGGPIGMIRIGRIC-GQFIVNPTMDELS--LSDLNLVYACTREKT 239
           A NA  AAL+ + IP       I  G +  G+ I++    E     S  +LV+  +R+  
Sbjct: 119 AINACCAALVFAGIPLKHLAVAIGCGVLEDGEVILDTNKAEEQQLKSFAHLVFPNSRKSA 178

Query: 240 LMIDVQAREISEKDLEAGLRLAHPEAVKYLEPQIRLAEKAGKQ 282
              +   +E   +            + +     I     A  +
Sbjct: 179 SSKEPNQKEEDSERGLITSITHGVMSEEDYFSCIERGLAASSR 221

>1oys_A Ribonuclease PH; transferase, tRNA processing; 2.40A {Bacillus subtilis} SCOP: d.14.1.4 d.101.1.1 PDB: 1oyp_A 1oyr_A Length = 245

 Score =  261 bits (670), Expect = 6e-81
 Identities = 61/257 (23%), Positives = 109/257 (42%), Gaps = 30/257 (11%)

Query: 369 VRVDGRQLDEVRPIYCESGNLPILHGSSLFSRGDTQVLCTVTLGAPAEAQRLESLVGPPT 428
           +R DGRQ DE+RPI  +   +    GS L + G+T+V+C  ++    E +    L G   
Sbjct: 1   MRHDGRQHDELRPITFDLDFISHPEGSVLITAGNTKVICNASV----EDRVPPFLRGGGK 56

Query: 429 KRFMLHYSFPPFCINEVGKR----VGLNRREVGHGTLAEKALLAVLPPENDFPYTVRVNS 484
                 YS  P   N+   +      ++ R +    L  +AL AV+  E     T+ ++ 
Sbjct: 57  GWITAEYSMLPQATNQQTIQESSKGKISGRTMEIQRLIGRALRAVVDLEKLGERTIWIDC 116

Query: 485 EVMASDGSTSMATVCGGSMALMDA-----------GIPLQEHVAGVSVGLVSEVDPSTGE 533
           +V+ +DG T  A++ G  +A+  A             P+ + +A +SVG+          
Sbjct: 117 DVIQADGGTRTASITGAFLAMAIAIGKLIKAGTIKTNPITDFLAAISVGID--------- 167

Query: 534 IKDYRILTDILGLEDHLGDMDFKIAGTRIG-VTAIQLDIKPAGIPLDIICECLEHAHKGR 592
            K+  IL D+   ED   ++D  +  T  G    +Q   + A    + +   L  A KG 
Sbjct: 168 -KEQGILLDLNYEEDSSAEVDMNVIMTGSGRFVELQGTGEEATFSREDLNGLLGLAEKGI 226

Query: 593 LQILDHMEREISAPRTQ 609
            +++D  +  +     +
Sbjct: 227 QELIDKQKEVLGDSLPE 243

>1oys_A Ribonuclease PH; transferase, tRNA processing; 2.40A {Bacillus subtilis} SCOP: d.14.1.4 d.101.1.1 PDB: 1oyp_A 1oyr_A Length = 245

 Score = 43.8 bits (104), Expect = 1e-04
 Identities = 48/247 (19%), Positives = 85/247 (34%), Gaps = 44/247 (17%)

Query: 68  RLITLETGKIARFANGAVVLGMDETKVLSTVTSSKGDSVRDFL------PLTVDYQEKQF 121
           R IT +         G+V++    TKV+   +    D V  FL       +T +Y     
Sbjct: 12  RPITFDLD-FISHPEGSVLITAGNTKVICNAS--VEDRVPPFLRGGGKGWITAEYSMLPQ 68

Query: 122 AQGVIPNTYMRRE---GAPKERELLVGRIIDRPIRPLFPAGFYHE--VQVMASVLSSDGK 176
           A          +E   G    R + + R+I R +R +       E  + +   V+ +DG 
Sbjct: 69  ATN----QQTIQESSKGKISGRTMEIQRLIGRALRAVVDLEKLGERTIWIDCDVIQADGG 124

Query: 177 QDPDIMAA-NATSAALM-----------LSDIPWGGPIGMIRIGRICGQFIV---NPTMD 221
                 A+      A+            +   P    +  I +G    Q I+   N   D
Sbjct: 125 TR---TASITGAFLAMAIAIGKLIKAGTIKTNPITDFLAAISVGIDKEQGILLDLNYEED 181

Query: 222 ELSLSDLNLVYACTREKTLMIDVQA----REISEKDLEAGLRLAHPEAVKYLEPQIR-LA 276
             +  D+N++   T      +++Q        S +DL   L LA     + ++ Q   L 
Sbjct: 182 SSAEVDMNVI--MTGSGRF-VELQGTGEEATFSREDLNGLLGLAEKGIQELIDKQKEVLG 238

Query: 277 EKAGKQK 283
           +   + K
Sbjct: 239 DSLPELK 245

>2nn6_F MTR3, exosome component 6; RNA, exosome, PM/SCL, phosphorolytic, hydrolase/transferase complex; 3.35A {Homo sapiens} SCOP: d.14.1.4 d.101.1.1 Length = 272

 Score =  255 bits (653), Expect = 3e-78
 Identities = 45/247 (18%), Positives = 82/247 (33%), Gaps = 21/247 (8%)

Query: 367 EGVRVDGRQLDEVRPIYCESGNLPILHGSSLFSRGDTQVLCTVTLGAPAE--------AQ 418
           E      R    +RP+Y  +G L    GS+    G T+VLC V+    AE        A 
Sbjct: 24  EEEAPGTRDPTRLRPVYARAGLLSQAKGSAYLEAGGTKVLCAVSGPRQAEGGERGGGPAG 83

Query: 419 RLESLVGPPTKRFMLHYSFPPFCINEVGKRVGLNRREVGHGTLAEKALLAVLPPENDFPY 478
                      R +  +   PF      +       E       ++AL   +        
Sbjct: 84  AGGEAPAALRGRLLCDFRRAPFAGRR-RRAPPGGCEERELALALQEALEPAVRLGRYPRA 142

Query: 479 TVRVNSEVMASDGSTSMATVCGGSMALMDAGIPLQEHVAGVSVGLVSEVDPSTGEIKDYR 538
            + V++ ++   GS   A +   ++AL DAG+ + + V G  + L               
Sbjct: 143 QLEVSALLLEDGGSALAAALTAAALALADAGVEMYDLVVGCGLSLAPG--------PAPT 194

Query: 539 ILTDILGLEDHLGDMDFKIA--GTRIGVTAIQLDIKPAGIPLDIICECLEHAHKGRLQIL 596
            L D   LE+        +A       V  +    +  G   +   E +    +G  ++ 
Sbjct: 195 WLLDPTRLEEERAAAGLTVALMPVLNQVAGLLGSGE--GGLTESWAEAVRLGLEGCQRLY 252

Query: 597 DHMEREI 603
             +++ +
Sbjct: 253 PVLQQSL 259

>2nn6_F MTR3, exosome component 6; RNA, exosome, PM/SCL, phosphorolytic, hydrolase/transferase complex; 3.35A {Homo sapiens} SCOP: d.14.1.4 d.101.1.1 Length = 272

 Score = 63.3 bits (154), Expect = 6e-11
 Identities = 37/237 (15%), Positives = 74/237 (31%), Gaps = 29/237 (12%)

Query: 68  RLITLETGKIARFANGAVVLGMDETKVLSTVTSSKGDSVRDFLPLTVDYQEKQFAQGVIP 127
           R +    G +++ A G+  L    TKVL  V+  +                   A   + 
Sbjct: 37  RPVYARAGLLSQ-AKGSAYLEAGGTKVLCAVSGPR--QAEGGERGGGPAGAGGEAPAALR 93

Query: 128 NTYM------------RREGAPKERELLVGRIIDRPIRPLFPAG--FYHEVQVMASVLSS 173
              +            RR       E  +   +   + P    G     +++V A +L  
Sbjct: 94  GRLLCDFRRAPFAGRRRRAPPGGCEERELALALQEALEPAVRLGRYPRAQLEVSALLLED 153

Query: 174 DGKQDPDIMAA-NATSAALMLSDIPWGGP---IGMIRIGRICGQFIVNPTMDE--LSLSD 227
            G     + AA  A + AL  + +         G+         ++++PT  E   + + 
Sbjct: 154 GG---SALAAALTAAALALADAGVEMYDLVVGCGLSLAPGPAPTWLLDPTRLEEERAAAG 210

Query: 228 LNLVYACTREKTLMIDVQAREISEKDLEAGLRLAHPEAVKYLEPQIR--LAEKAGKQ 282
           L +       +   +         +     +RL   E  + L P ++  L   A ++
Sbjct: 211 LTVALMPVLNQVAGLLGSGEGGLTESWAEAVRLGL-EGCQRLYPVLQQSLVRAARRR 266

>2wp8_B Exosome complex component SKI6; nucleus, hydrolase, RNA-binding, exonucle binding, mitochondrion, rRNA processing; 3.00A {Saccharomyces cerevisiae} Length = 246

 Score =  251 bits (643), Expect = 4e-77
 Identities = 56/254 (22%), Positives = 104/254 (40%), Gaps = 18/254 (7%)

Query: 364 IIAEGVRVDGRQLDEVRPIYCESGNLPIL-HGSSLFSRGDTQVLCTVTLGAPAEAQRLES 422
              EG+R+DGR+ +E+R         P    GSS   +G+ +++  V    P E  RL+S
Sbjct: 7   YSPEGLRLDGRRWNELRRFESSINTHPHAADGSSYMEQGNNKIITLVK--GPKE-PRLKS 63

Query: 423 LVGPPTKRFMLHYSFPPFCINEVGKRVGLNRREVGHGTLAEKALLAVLPPENDFPY-TVR 481
            +        +  +   F   E  K    N R V     +   +       N +P   + 
Sbjct: 64  QMDTSKALLNVSVNINKFSKFERSKSSHKNERRVLEIQTSLVRMFEKNVMLNIYPRTVID 123

Query: 482 VNSEVMASDGSTSMATVCGGSMALMDAGIPLQEHVAGVSVGLVSEVDPSTGEIKDYRILT 541
           +   V+  DG    + + G ++AL+DAGI + ++++G+SVGL               +L 
Sbjct: 124 IEIHVLEQDGGIMGSLINGITLALIDAGISMFDYISGISVGL----------YDTTPLLD 173

Query: 542 DILGLEDHLGDMDFKIAGTRIGVTAIQLDIKPAGIPLDIICECLEHAHKGRLQILDHMER 601
                E+ +  +   + G    ++ + ++ K   IPLD +   L     G  ++ D M+ 
Sbjct: 174 TNSLEENAMSTVTLGVVGKSEKLSLLLVEDK---IPLDRLENVLAIGIAGAHRVRDLMDE 230

Query: 602 EISAPRTQDDRNSP 615
           E+     +   N+ 
Sbjct: 231 ELRKHAQKRVSNAS 244

>2wp8_B Exosome complex component SKI6; nucleus, hydrolase, RNA-binding, exonucle binding, mitochondrion, rRNA processing; 3.00A {Saccharomyces cerevisiae} Length = 246

 Score = 64.6 bits (158), Expect = 1e-11
 Identities = 34/230 (14%), Positives = 81/230 (35%), Gaps = 21/230 (9%)

Query: 68  RLITLETGKIARFANGAVVLGMDETKVLSTVTSSKGDSVRDFLP-----LTVDYQEKQFA 122
           R            A+G+  +     K+++ V   K   ++  +      L V     +F+
Sbjct: 23  RRFESSINTHPHAADGSSYMEQGNNKIITLVKGPKEPRLKSQMDTSKALLNVSVNINKFS 82

Query: 123 QGVIPNTYMRREGAPKERELLVGRIIDRPIRP-LFPAGFYHEVQVMASVLSSDGKQDPDI 181
           +     +  + E    E +  + R+ ++ +   ++P      + +   VL  DG     +
Sbjct: 83  KFERSKSSHKNERRVLEIQTSLVRMFEKNVMLNIYP---RTVIDIEIHVLEQDGG---IM 136

Query: 182 MAA-NATSAALMLSDIPWGGPIGMIRIGRICGQFIVNPT-MDELSLSDLNLVYACTREKT 239
            +  N  + AL+ + I     I  I +G      +++   ++E ++S + L      EK 
Sbjct: 137 GSLINGITLALIDAGISMFDYISGISVGLYDTTPLLDTNSLEENAMSTVTLGVVGKSEK- 195

Query: 240 LMIDVQ--AREISEKDLEAGLRLAHPEAVKYLEPQIRLA-EKAGKQKKEY 286
             + +     +I    LE  L +        +   +     K  +++   
Sbjct: 196 --LSLLLVEDKIPLDRLENVLAIGI-AGAHRVRDLMDEELRKHAQKRVSN 242

>3dd6_A Ribonuclease PH; exoribonuclease, tRNA maturation, RNAse PH., transferase; 1.70A {Bacillus anthracis} Length = 255

 Score =  251 bits (642), Expect = 7e-77
 Identities = 60/266 (22%), Positives = 112/266 (42%), Gaps = 30/266 (11%)

Query: 360 IRKRIIAEGVRVDGRQLDEVRPIYCESGNLPILHGSSLFSRGDTQVLCTVTLGAPAEAQR 419
                    +RVDGR+  E+R I+  +  L    GS L   GDT+V+C+ T+    E + 
Sbjct: 2   GSSHHHHHHMRVDGREKTELRHIHIHTNYLKHPEGSVLIEVGDTKVICSATI----EERV 57

Query: 420 LESLVGPPTKRFMLHYSFPPFCINEVGKR----VGLNRREVGHGTLAEKALLAVLPPEND 475
              + G         Y+  P    +   R      +  R +    L  +AL AV+  E  
Sbjct: 58  PPFMRGEGKGWVTAEYAMIPRATEQRTIRESSKGKVTGRTMEIQRLIGRALRAVVDLEAL 117

Query: 476 FPYTVRVNSEVMASDGSTSMATVCGGSMALMD-----------AGIPLQEHVAGVSVGLV 524
              TV ++ +V+ +DG T  A++ G  +A++            + IP+++++A  SVG+ 
Sbjct: 118 GERTVWIDCDVIQADGGTRTASITGAYVAMVLAFEKLLQAEKVSKIPVKDYLAATSVGI- 176

Query: 525 SEVDPSTGEIKDYRILTDILGLEDHLGDMDFKIAGTRIG-VTAIQLDIKPAGIPLDIICE 583
                    +++  ++ D+   ED   D+D  +  T  G    +Q   + A      + E
Sbjct: 177 ---------VEEQGVVLDLNYAEDSKADVDMNVIMTGKGQFVEVQGTGEEATFSRAQLNE 227

Query: 584 CLEHAHKGRLQILDHMEREISAPRTQ 609
            L+ A +G  Q++D  +  +    + 
Sbjct: 228 LLDAAEQGIFQLIDIQKEALGDIVSH 253

>3dd6_A Ribonuclease PH; exoribonuclease, tRNA maturation, RNAse PH., transferase; 1.70A {Bacillus anthracis} Length = 255

 Score = 42.7 bits (101), Expect = 3e-04
 Identities = 46/224 (20%), Positives = 82/224 (36%), Gaps = 43/224 (19%)

Query: 68  RLITLETGKIARFANGAVVLGMDETKVLSTVTSSKGDSVRDFLP------LTVDYQEKQF 121
           R I + T  +     G+V++ + +TKV+ + T    + V  F+       +T +Y     
Sbjct: 22  RHIHIHTNYLKH-PEGSVLIEVGDTKVICSATI--EERVPPFMRGEGKGWVTAEYAMIPR 78

Query: 122 AQGVIPNTYMRRE---GAPKERELLVGRIIDRPIRPLFPAGFYHE--VQVMASVLSSDGK 176
           A          RE   G    R + + R+I R +R +       E  V +   V+ +DG 
Sbjct: 79  ATE----QRTIRESSKGKVTGRTMEIQRLIGRALRAVVDLEALGERTVWIDCDVIQADGG 134

Query: 177 QDPDIMAA-NATSAALM-----------LSDIPWGGPIGMIRIGRICGQFIV---NPTMD 221
                 A+      A++           +S IP    +    +G +  Q +V   N   D
Sbjct: 135 ---TRTASITGAYVAMVLAFEKLLQAEKVSKIPVKDYLAATSVGIVEEQGVVLDLNYAED 191

Query: 222 ELSLSDLNLVYACTREKTLMIDVQA----REISEKDLEAGLRLA 261
             +  D+N++   T +    ++VQ        S   L   L  A
Sbjct: 192 SKADVDMNVI--MTGKGQF-VEVQGTGEEATFSRAQLNELLDAA 232

>2nn6_D Exosome complex exonuclease RRP46; RNA, exosome, PM/SCL, phosphorolytic, hydrolase/transferase complex; 3.35A {Homo sapiens} SCOP: d.14.1.4 d.101.1.1 Length = 237

 Score =  235 bits (602), Expect = 2e-71
 Identities = 45/251 (17%), Positives = 74/251 (29%), Gaps = 29/251 (11%)

Query: 357 KRVIRKRIIAEGVRVDGRQLD-EVRPIYCESGNLPILHGSSLFSRGDTQVLCTVTLGAPA 415
                K     G     R     +R   CE   L    GS+ F +GDT VL  V    PA
Sbjct: 7   THTDAKIRAENGTGSSPRGPGCSLRHFACEQNLLSRPDGSASFLQGDTSVLAGVY--GPA 64

Query: 416 EAQRLESLVGPPTKRFMLHYSFPPFCINEVGKRVGLNRREVGHGTLAEKALLAVLPPEND 475
           E            K     ++     +    K       E     L      AV+     
Sbjct: 65  EV-----------KVSKEIFNKATLEVILRPKIGLPGVAEKSRERLIRNTCEAVVLGTLH 113

Query: 476 FPYTVRVNSEVMASDGSTSMATVCGGSMALMDAGIPLQEHVAGVSVGLVSEVDPSTGEIK 535
              ++ V  +V++  GS     +    MAL+DAG+P++    GV+  L            
Sbjct: 114 PRTSITVVLQVVSDAGSLLACCLNAACMALVDAGVPMRALFCGVACAL----------DS 163

Query: 536 DYRILTDILGLEDHLG--DMDFKIAGTRIGVTAIQLDIKPAGIPLDIICECLEHAHKGRL 593
           D  ++ D    ++      + F +      +                + +CL  A     
Sbjct: 164 DGTLVLDPTSKQEKEARAVLTFALDSVERKLLMSSTK---GLYSDTELQQCLAAAQAASQ 220

Query: 594 QILDHMEREIS 604
            +       + 
Sbjct: 221 HVFRFYRESLQ 231

>2nn6_D Exosome complex exonuclease RRP46; RNA, exosome, PM/SCL, phosphorolytic, hydrolase/transferase complex; 3.35A {Homo sapiens} SCOP: d.14.1.4 d.101.1.1 Length = 237

 Score = 73.6 bits (181), Expect = 1e-14
 Identities = 39/226 (17%), Positives = 74/226 (32%), Gaps = 32/226 (14%)

Query: 68  RLITLETGKIARFANGAVVLGMDETKVLSTVT----SSKGDSVRDFLPLTVDYQEKQFAQ 123
           R    E   ++R  +G+      +T VL+ V           + +   L V  +      
Sbjct: 31  RHFACEQNLLSR-PDGSASFLQGDTSVLAGVYGPAEVKVSKEIFNKATLEVILR------ 83

Query: 124 GVIPNTYMRREGAPKERELLVGRIIDRPIRPLFPAGFY--HEVQVMASVLSSDGKQDPDI 181
                    + G P   E    R+I      +     +    + V+  V+S  G     +
Sbjct: 84  --------PKIGLPGVAEKSRERLIRNTCEAVVLGTLHPRTSITVVLQVVSDAGS---LL 132

Query: 182 MAA-NATSAALMLSDIPWGGPIGMIRIGRIC-GQFIVNPTMDE--LSLSDLNLVYACTRE 237
               NA   AL+ + +P       +       G  +++PT  +   + + L         
Sbjct: 133 ACCLNAACMALVDAGVPMRALFCGVACALDSDGTLVLDPTSKQEKEARAVLTFALDSVER 192

Query: 238 KTLMIDVQAREISEKDLEAGLRLAHPEAVKYLEPQIR--LAEKAGK 281
           K LM   +    S+ +L+  L  A   A +++    R  L  +  K
Sbjct: 193 KLLMSSTKGL-YSDTELQQCLAAAQ-AASQHVFRFYRESLQRRYSK 236

>1udn_A Ribonuclease PH, RNAse PH; transferase, riken structural genomics/proteomics initiative structural genomics; 2.30A {Aquifex aeolicus} SCOP: d.14.1.4 d.101.1.1 PDB: 1udq_A 1uds_A 1udo_A Length = 255

 Score =  221 bits (565), Expect = 4e-66
 Identities = 61/264 (23%), Positives = 110/264 (41%), Gaps = 31/264 (11%)

Query: 369 VRVDGRQLDEVRPIYCESGNLPILHGSSLFSRGDTQVLCTVTLGAPAEAQRLESLVGPPT 428
           +R DGR+ D++RP+  +   L    GS L S G T+V+CT ++           L G   
Sbjct: 1   MRSDGRKEDQLRPVSIQRDFLEYPEGSCLISFGKTKVICTASV----IENVPNWLKGKGQ 56

Query: 429 KRFMLHYSFPPFCINEVGKR----VGLNRREVGHGTLAEKALLAVLPPENDFPYTVRVNS 484
                 YS  P    +   R      +  R      +  +A+   +        T+ V+ 
Sbjct: 57  GWITAEYSMLPRATQQRTIRESVQGRIGGRTHEIQRMIGRAMRTAVELTKIGERTIWVDC 116

Query: 485 EVMASDGSTSMATVCGGSMALMDAGI-----------PLQEHVAGVSVGLVSEVDPSTGE 533
           +V+ +DG T  A + G  +A+ DA I           P+++ VA VSVG+V         
Sbjct: 117 DVIQADGGTRTAAITGAFVAVADAIIKLHKEGIIEETPIKDFVAAVSVGIV--------- 167

Query: 534 IKDYRILTDILGLEDHLGDMDFKIAGTRIG-VTAIQLDIKPAGIPLDIICECLEHAHKGR 592
             + RIL D+   ED    +D  + GT  G ++ +    +      D + + L+ A KG 
Sbjct: 168 --NDRILLDLNFEEDSAAQVDMNVVGTGSGRLSEVHTMGEEYSFTKDELIKMLDLAQKGI 225

Query: 593 LQILDHMEREISAPRTQDDRNSPR 616
            ++++  ++       + +R+  +
Sbjct: 226 NELIELQKKLYVIQDGKWERSELK 249

>1udn_A Ribonuclease PH, RNAse PH; transferase, riken structural genomics/proteomics initiative structural genomics; 2.30A {Aquifex aeolicus} SCOP: d.14.1.4 d.101.1.1 PDB: 1udq_A 1uds_A 1udo_A Length = 255

 Score = 47.0 bits (112), Expect = 1e-05
 Identities = 43/254 (16%), Positives = 90/254 (35%), Gaps = 43/254 (16%)

Query: 68  RLITLETGKIARFANGAVVLGMDETKVLSTVTSSKGDSVRDFLP------LTVDYQEKQF 121
           R ++++   +     G+ ++   +TKV+ T +  +   V ++L       +T +Y     
Sbjct: 12  RPVSIQRDFLEY-PEGSCLISFGKTKVICTASVIEN--VPNWLKGKGQGWITAEYSMLPR 68

Query: 122 AQGVIPNTYMRRE---GAPKERELLVGRIIDRPIRPLFPAGFYHE--VQVMASVLSSDGK 176
           A          RE   G    R   + R+I R +R         E  + V   V+ +DG 
Sbjct: 69  ATQ----QRTIRESVQGRIGGRTHEIQRMIGRAMRTAVELTKIGERTIWVDCDVIQADGG 124

Query: 177 QDPDIMAANATSAALMLSDIPWG-----------GPIGMIRIGRICGQFIVNPTMDELSL 225
                 A      A+  + I                +  + +G +  + +++   +E S 
Sbjct: 125 TRT--AAITGAFVAVADAIIKLHKEGIIEETPIKDFVAAVSVGIVNDRILLDLNFEEDSA 182

Query: 226 --SDLNLVYACTREKTLMIDVQA----REISEKDLEAGLRLAHPEAVKYLEPQIRLAEKA 279
              D+N+V         + +V         ++ +L   L LA     + +E Q    +  
Sbjct: 183 AQVDMNVVGT---GSGRLSEVHTMGEEYSFTKDELIKMLDLAQKGINELIELQ---KKLY 236

Query: 280 GKQKKEYKLSMISE 293
             Q  +++ S + E
Sbjct: 237 VIQDGKWERSELKE 250

>1r6l_A Ribonuclease PH; beta-alpha-beta-alpha fold, hexamer, phosphate bound, transf; HET: NHE; 1.90A {Pseudomonas aeruginosa} SCOP: d.14.1.4 d.101.1.1 PDB: 1r6m_A Length = 239

 Score =  199 bits (507), Expect = 3e-58
 Identities = 62/251 (24%), Positives = 99/251 (39%), Gaps = 31/251 (12%)

Query: 370 RVDGRQLDEVRPIYCESGNLPILHGSSLFSRGDTQVLCTVTLGAPAEAQRLESLVGPPTK 429
           R  GR  D++RPI           GS L   GDT+V+CTV+     E+     L G    
Sbjct: 3   RPSGRAADQLRPIRITRHYTKHAEGSVLVEFGDTKVICTVSA----ESGVPRFLKGQGQG 58

Query: 430 RFMLHYSFPPFCINEVGKRVG----LNRREVGHGTLAEKALLAVLPPENDFPYTVRVNSE 485
                Y   P    E  +R         R +    L  ++L A L        T+ ++ +
Sbjct: 59  WLTAEYGMLPRSTGERNQREASRGKQGGRTLEIQRLIGRSLRAALDLSKLGENTLYIDCD 118

Query: 486 VMASDGSTSMATVCGGSMALMDA-----------GIPLQEHVAGVSVGLVSEVDPSTGEI 534
           V+ +DG T  A++ G ++AL+DA           G PL++ VA VSVG+           
Sbjct: 119 VIQADGGTRTASITGATVALIDALAVLKKRGALKGNPLKQMVAAVSVGIY---------- 168

Query: 535 KDYRILTDILGLEDHLGDMDFKIAGTRIG-VTAIQLDIKPAGIPLDIICECLEHAHKGRL 593
                + D+  LED   + D  +  T  G    +Q   + A      +   LE A +G  
Sbjct: 169 -QGVPVLDLDYLEDSAAETDLNVVMTDAGGFIEVQGTAEGAPFRPAELNAMLELAQQGMQ 227

Query: 594 QILDHMEREIS 604
           ++ +     ++
Sbjct: 228 ELFELQRAALA 238

>3b4t_A Ribonuclease PH; RNAse, tRNA nucleotidyltransferase, RPHA, STRU genomics, TBSGC; 2.10A {Mycobacterium tuberculosis} Length = 262

 Score =  185 bits (471), Expect = 5e-53
 Identities = 62/260 (23%), Positives = 98/260 (37%), Gaps = 24/260 (9%)

Query: 370 RVDGRQLDEVRPIYCESGNLPILHGSSLFSRGDTQVLCTVTLGAPAEAQRLESLVGPPTK 429
           R DGR   E+RP+    G      GS L   G T+VLCT ++       R  + +G  T 
Sbjct: 7   REDGRLDHELRPVIITRGFTENPAGSVLIEFGHTKVLCTASVTEGVPRWRKATGLGWLTA 66

Query: 430 RFMLHYSFPPFCINEVGKRVGLNRREVGHGTLAEKALLAVLPPENDFPYTVRVNSEVMAS 489
            + +  S      +    R  L+ R      L  ++L A +        T+ ++ +V+ +
Sbjct: 67  EYAMLPSATHSRSDRESVRGRLSGRTQEISRLIGRSLRACIDLAALGENTIAIDCDVLQA 126

Query: 490 DGSTSMATVCGGSMALMDAGI------------PLQEHVAGVSVGLVSEVDPSTGEIKDY 537
           DG T  A + G  +AL DA              PL   +A VSVG+V           D 
Sbjct: 127 DGGTRTAAITGAYVALADAVTYLSAAGKLSDPRPLSCAIAAVSVGVV-----------DG 175

Query: 538 RILTDILGLEDHLGDMDFKIAGTRIG-VTAIQLDIKPAGIPLDIICECLEHAHKGRLQIL 596
           RI  D+   ED   ++D  +  T  G +  IQ   + A      + + L+ A      + 
Sbjct: 176 RIRVDLPYEEDSRAEVDMNVVATDTGTLVEIQGTGEGATFARSTLDKLLDMALGACDTLF 235

Query: 597 DHMEREISAPRTQDDRNSPR 616
                 ++ P        P 
Sbjct: 236 AAQRDALALPYPGVLPQGPP 255

>3krn_A Protein C14A4.5, confirmed by transcript evidence; RNAse PH domain, homodimer, exosome, cell-death-related DNAS hydrolase; 3.92A {Caenorhabditis elegans} Length = 222

 Score =  124 bits (313), Expect = 2e-32
 Identities = 39/240 (16%), Positives = 73/240 (30%), Gaps = 34/240 (14%)

Query: 377 DEVRPIYCESGNLPILHGSSLFSRGDTQVLCTVTLGAPAEAQRLESLVGPPTKRFMLHYS 436
             +R + CE   L    GS+ FS+G T +  + +   P +                   +
Sbjct: 3   GRLREMRCELSFLKNADGSACFSQGATCIWASCS--GPGDVHA--------------SKA 46

Query: 437 FPPFCINEVGKRVGLN-RREVGHGTLAEKALLAVLPPENDFPY-TVRVNSEVMASDGSTS 494
                  ++  R      +      +    L   +  E  FP+ T+ V    +  DGS  
Sbjct: 47  SDEAMTLDISYRANCGDNKFNVLNNIIHSTLSNAINLE-LFPHTTISVTVHGIQDDGSMG 105

Query: 495 MATVCGGSMALMDAGIPLQEHVAGVSVGLVSE---VDPSTGEIKDYRILTDILGLEDHLG 551
              + G   AL+D G+P +    GV +  V +   +DP+  +                 G
Sbjct: 106 AVAINGACFALLDNGMPFETVFCGVLIVRVKDELIIDPTAKQEAAST------------G 153

Query: 552 DMDFKIAGTRIGVTAIQLDIKPAGIPLDIICECLEHAHKGRLQILDHMEREISAPRTQDD 611
            + F +     G   +             +      A      I D  +  +    + D+
Sbjct: 154 RVLFSVCKGSDGHPEVCAMDAIGHWDFIQLEAAWSLAQPSASAIFDFYKTVMKRKLSVDE 213

>3krn_A Protein C14A4.5, confirmed by transcript evidence; RNAse PH domain, homodimer, exosome, cell-death-related DNAS hydrolase; 3.92A {Caenorhabditis elegans} Length = 222

 Score = 67.5 bits (165), Expect = 1e-12
 Identities = 32/228 (14%), Positives = 74/228 (32%), Gaps = 30/228 (13%)

Query: 68  RLITLETGKIARFANGAVVLGMDETKVLSTVTSSKGDSVRDFLP--LTVDYQEKQFAQGV 125
           R +  E   +   A+G+       T + ++ +              +T+D   +      
Sbjct: 6   REMRCELSFLKN-ADGSACFSQGATCIWASCSGPGDVHASKASDEAMTLDISYRANCGD- 63

Query: 126 IPNTYMRREGAPKERELLVGRIIDRPI--RPLFPAGFYHEVQVMASVLSSDGKQDPDIMA 183
                  +         ++   +        LFP   +  + V    +  DG        
Sbjct: 64  ------NKF---NVLNNIIHSTL-SNAINLELFP---HTTISVTVHGIQDDG---SMGAV 107

Query: 184 A-NATSAALMLSDIPWGGPIGMIRIGRICGQFIVNPTMDELSLSDLNLVYACTREKTLMI 242
           A N    AL+ + +P+      + I R+  + I++PT  + + S   ++++  +      
Sbjct: 108 AINGACFALLDNGMPFETVFCGVLIVRVKDELIIDPTAKQEAASTGRVLFSVCKGSDGHP 167

Query: 243 DVQARE----ISEKDLEAGLRLAHPEAVKYLEPQIR--LAEKAGKQKK 284
           +V A +         LEA   LA   +   +    +  +  K    ++
Sbjct: 168 EVCAMDAIGHWDFIQLEAAWSLAQ-PSASAIFDFYKTVMKRKLSVDEQ 214

>2k4k_A GSP13, general stress protein 13; cytoplasm, stress response, RNA binding protein; NMR {Bacillus subtilis} Length = 130

 Score = 96.3 bits (240), Expect = 1e-23
 Identities = 31/88 (35%), Positives = 53/88 (60%), Gaps = 1/88 (1%)

Query: 677 IGREIEVGGIYKGVVTSVKEYGAFVEFNGGQQGLLHVSELSHEPVSRVSDVVSVGQQLSL 736
           +  + EVG +Y G VT ++ YGAFV  +   QGL+H+SE++H  V  +++ +SVG ++ +
Sbjct: 1   MAAKFEVGSVYTGKVTGLQAYGAFVALDEETQGLVHISEVTHGFVKDINEHLSVGDEVQV 60

Query: 737 RCIGQDV-RGNIKLSLKAVSPRPEADVK 763
           + +  D  +G I LS++A    PE    
Sbjct: 61  KVLAVDEEKGKISLSIRATQAAPEKKES 88

>2eqs_A ATP-dependent RNA helicase DHX8; S1 domain, OB-fold, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Length = 103

 Score = 93.2 bits (232), Expect = 6e-23
 Identities = 33/91 (36%), Positives = 50/91 (54%), Gaps = 5/91 (5%)

Query: 677 IGREIEVGGIYKGVVTSVKEYGAFVEFNGG---QQGLLHVSELSHEP-VSRVSDVVSVGQ 732
            G E  +G IY G VTS+ ++G FV+  G     +GL+H+SEL  E  V+ V+DVVS GQ
Sbjct: 6   SGEEPTIGDIYNGKVTSIMQFGCFVQLEGLRKRWEGLVHISELRREGRVANVADVVSKGQ 65

Query: 733 QLSLRCIGQDVRGNIKLSLKAVSPRPEADVK 763
           ++ ++ +         LS+K V      D+ 
Sbjct: 66  RVKVKVLSFT-GTKTSLSMKDVDQETGEDLN 95

>2wnr_A Probable exosome complex exonuclease 2; phosphate binding, 3'-5' exoribonuclease, hydrolase; 2.65A {Methanothermobacter thermautotrophicusorganism_taxid} Length = 271

 Score = 95.9 bits (239), Expect = 6e-22
 Identities = 52/268 (19%), Positives = 100/268 (37%), Gaps = 39/268 (14%)

Query: 362 KRIIAEGVRVDGRQLDEVRPIYCESGNLPILHGSSLFSRGDTQVLCTVT--LGAPAEAQR 419
             +I    R+DGR L E R I  E+G +    GSS    G+TQ++  V   +G P     
Sbjct: 17  TDLINNKERIDGRSLHEFRDISIETGVISKAEGSSRVKLGNTQIIVGVKPQIGEP----- 71

Query: 420 LESLVGPPTKRFMLHYSFPPFCINEVGKRVGLNRREVGHGTLAEKAL----------LAV 469
                 P     + +    P            + R V    + ++ +          L +
Sbjct: 72  --FPDTPEMGVILTNSELLPMASPTFEPG-PPDERSVELSRVVDRCIRESRMIDLEKLCI 128

Query: 470 LPPENDFPYTVRVNSEVMASDGSTSMATVCGGSMALMDAGIPLQEHVAGVSVGLVSEVDP 529
           +       + + ++  ++  DG+   A V     AL+D  IP  E   G  V    ++ P
Sbjct: 129 IEGSKV--WMLFLDLHIIDYDGNLFDAAVLATVAALLDTRIPAAEVEDGEVVINREKMQP 186

Query: 530 ----------STGEIKDYRILTDILGLEDHLGDMDFKIAGTRIG-VTAIQLDIKPAGIPL 578
                     +  +I +  I+ D    E+ +      I  T  G + A+Q   K    PL
Sbjct: 187 LPVNRKALMCTFAKIGN-EIVLDPSLEEEDILTARISIGVTEEGSICAMQ---KGGEGPL 242

Query: 579 DI--ICECLEHAHKGRLQILDHMEREIS 604
               + + +  A +   Q+++++++ ++
Sbjct: 243 TRDDVLKAVSIAVEKVPQLIEYLDKSMT 270

>2cqo_A Nucleolar protein of 40 kDa; S1 domain, OB-fold, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Length = 119

 Score = 89.8 bits (223), Expect = 2e-21
 Identities = 27/92 (29%), Positives = 52/92 (56%), Gaps = 4/92 (4%)

Query: 676 IIGREIEVGGIYKGVVTSVKEYGAFVEFNG-GQQGLLHVSELSHEPVSRVSDVVSVGQQL 734
            +     +  I++G V  V +YGAF++  G  +QGL+H + +S   V + S++V VG ++
Sbjct: 15  TMENLPALYTIFQGEVAMVTDYGAFIKIPGCRKQGLVHRTHMSSCRVDKPSEIVDVGDKV 74

Query: 735 SLRCIGQDV---RGNIKLSLKAVSPRPEADVK 763
            ++ IG+++   R  + LS+K V+     D+ 
Sbjct: 75  WVKLIGREMKNDRIKVSLSMKVVNQGTGKDLD 106

>3m7n_G Probable exosome complex exonuclease 2; exosome, RNA, exonuclease, hydrolase, nuclease, hydrolase-RN; 2.40A {Archaeoglobus fulgidus} PDB: 2ba1_H 2ba0_I 3m85_G Length = 259

 Score = 94.0 bits (234), Expect = 2e-21
 Identities = 48/264 (18%), Positives = 86/264 (32%), Gaps = 52/264 (19%)

Query: 362 KRIIAEGVRVDGRQLDEVRPIYCESGNLPILHGSSLFSRGDTQVLCTVT--LGAPAEAQR 419
              + +  R+DGR  DE R +      +    GS+L   GDTQV+  V    G P     
Sbjct: 15  LSKLRDNERIDGRGFDEFRKVEIIPNVIEKAEGSALVKLGDTQVVVGVKMQPGEP----- 69

Query: 420 LESLVGPPTKRFMLHYSFPPFCINEVGKRVGLNRREVGHGTLAEKAL----------LAV 469
                 P     +++    P            +   +    + ++ +          L +
Sbjct: 70  --YPDTPDRGVIIVNAELVPLASPTFEPG-PPDENSIELARVVDRGIRESEAVDLSKLVI 126

Query: 470 LPPENDFPYTVRVNSEVMASDGSTSMATVCGGSMALMDAGIP-------------LQEHV 516
              E    + V V+   +  DG+   A+      ALM+  +P             +++  
Sbjct: 127 EEGEKV--WIVFVDIHALDDDGNLLDASALAAIAALMNTKVPAERFDLGEDYLLPVRDLP 184

Query: 517 AGVSVGLVSEVDPSTGEIKDYRILTDILGLEDHLGDMDFKIAGTRIG-VTAIQLDIKPAG 575
             V+  +V             + L D    E  +GD    I   +   V A+Q   K  G
Sbjct: 185 VSVTSLIVGN-----------KYLVDPSREEMSVGDTTLTITTDKDDNVVAMQ---KSGG 230

Query: 576 IPLDI--ICECLEHAHKGRLQILD 597
             LD     E L+ +     ++ +
Sbjct: 231 YLLDEKLFDELLDVSINCARKLRE 254

>2nn6_C Exosome complex exonuclease RRP43; RNA, exosome, PM/SCL, phosphorolytic, hydrolase/transferase complex; 3.35A {Homo sapiens} SCOP: d.14.1.4 d.101.1.1 Length = 278

 Score = 92.3 bits (229), Expect = 9e-21
 Identities = 49/273 (17%), Positives = 85/273 (31%), Gaps = 36/273 (13%)

Query: 362 KRIIAEGVRVDGRQLDEVRPIYCESGNLPILHGSSLFSRGDTQVLCTVT--LGAPAEAQR 419
           +R + E  R DGR+L E R      G++    GS+L   G+T V+C V     AP     
Sbjct: 17  RRFLKENCRPDGRELGEFRTTTVNIGSISTADGSALVKLGNTTVICGVKAEFAAP----- 71

Query: 420 LESLVGPPTKRFMLHYSFPPFCINEVGKRVGLNRREVGHGTLAEKALLAVLPP------- 472
             S   P     + +   PP C +                      +             
Sbjct: 72  --STDAPDKGYVVPNVDLPPLCSSRFRSG-PPGEEAQVASQFIADVIENSQIIQKEDLCI 128

Query: 473 -ENDFPYTVRVNSEVMASDGSTSMATVCGGSMALMDAGIPLQEHVAGVSVGLVSEVDP-- 529
                 + +  +   +  DG+   A       AL +  +P        ++  V+      
Sbjct: 129 SPGKLVWVLYCDLICLDYDGNILDACTFALLAALKNVQLPEVTINEETALAEVNLKKKSY 188

Query: 530 ----------STGEIKDYRILTDILGLEDHLGDMDFKIAGTRIG-VTAIQLDIKPAGIPL 578
                     S     D  ++ D  G E+HL      I     G +  +    KP G  L
Sbjct: 189 LNIRTHPVATSFAVFDDTLLIVDPTGEEEHLATGTLTIVMDEEGKLCCLH---KPGGSGL 245

Query: 579 DI--ICECLEHAHKGRLQILDHMEREISAPRTQ 609
               + +C+  A     ++   M+  I + + +
Sbjct: 246 TGAKLQDCMSRAVTRHKEVKKLMDEVIKSMKPK 278

>2je6_A RRP42, exosome complex exonuclease 2; nuclease, hydrolase, exonuclease, phosphorolytic, exoribonuclease, RNA degradation; HET: 1PE; 1.6A {Sulfolobus solfataricus} SCOP: d.14.1.4 d.101.1.1 PDB: 2jea_A* 2jeb_A* 2br2_A 2c37_A* 2c38_A* 2c39_A* 3l7z_A Length = 277

 Score = 92.1 bits (229), Expect = 1e-20
 Identities = 44/278 (15%), Positives = 88/278 (31%), Gaps = 60/278 (21%)

Query: 362 KRIIAEGVRVDGRQLDEVRPIYCESGNLPILHGSSLFSRGDTQVLCTVT--LGAPAEAQR 419
             +  +G+R DGR+L + RP+           GS+L   G T VL      +  P     
Sbjct: 22  VSLFEKGIRQDGRKLTDYRPLSITLDYAKKADGSALVKLGTTMVLAGTKLEIDKP----- 76

Query: 420 LESLVGPPTKRFMLHYSFPPFCINEVGKRVGLNRREVGHGTLAEKAL----------LAV 469
                 P     +++    P            +   +    + +++L          L +
Sbjct: 77  --YEDTPNQGNLIVNVELLPLAYETFEPG-PPDENAIELARVVDRSLRDSKALDLTKLVI 133

Query: 470 LPPENDFPYTVRVNSEVMASDGSTSMATVCGGSMALMDAGIP------------------ 511
            P +    +TV ++  V+   G+   A       AL +  +                   
Sbjct: 134 EPGK--SVWTVWLDVYVLDYGGNVLDACTLASVAALYNTKVYKVEQHSNGISVNKNEVVG 191

Query: 512 ---LQEHVAGVSVGLVSEVDPSTGEIKDYRILTDILGLEDHLGDMDFKIAGTRIG-VTAI 567
              L   V  +SV  V           D  ++ D    E+ + D     + T    +  I
Sbjct: 192 KLPLNYPVVTISVAKV-----------DKYLVVDPDLDEESIMDAKISFSYTPDLKIVGI 240

Query: 568 QLDIKPAGIPLDI--ICECLEHAHKGRLQILDHMEREI 603
           Q   K     + +  I +    A    +++L+ +++ +
Sbjct: 241 Q---KSGKGSMSLQDIDQAENTARSTAVKLLEELKKHL 275

>1whu_A Polynucleotide phosphorylase; 3'-5' RNA exonuclease; pnpase, alpha-helical domain, structural genomics; NMR {Mus musculus} SCOP: a.4.9.1 Length = 104

 Score = 85.9 bits (213), Expect = 3e-20
 Identities = 28/94 (29%), Positives = 46/94 (48%)

Query: 282 QKKEYKLSMISEQTLEKVSNLAEAHIEAVFTDPSYSKFERGEALDKIGQDVKKALEEECD 341
                K+   S + ++    +A   + AVFTD  + K  R EA++KI  D ++ L+E+  
Sbjct: 5   SSGPQKIFTPSAEIVKYTKIIAMEKLYAVFTDYEHDKVSRDEAVNKIRLDTEEHLKEKFP 64

Query: 342 EESLQVLPKAVDTVRKRVIRKRIIAEGVRVDGRQ 375
           E     + ++ + V K V R  I+ E  R DGR 
Sbjct: 65  EVDQFEIIESFNIVAKEVFRSIILNEYKRCDGRD 98

>2po1_B Probable exosome complex exonuclease 2; RNAse PH, hydrolase/hydrolase/RNA complex; 1.94A {Pyrococcus abyssi} PDB: 2po0_B* 2pnz_B 2po2_B* Length = 277

 Score = 88.2 bits (219), Expect = 2e-19
 Identities = 50/266 (18%), Positives = 94/266 (35%), Gaps = 36/266 (13%)

Query: 362 KRIIAEGVRVDGRQLDEVRPIYCESGNLPILHGSSLFSRGDTQVLCTVT--LGAPAEAQR 419
             ++ EG R+D R  ++ RPI  E G +    GS+L   G TQVL  +   LG P     
Sbjct: 19  INLLKEGKRIDDRGFEDYRPIEIEVGVIEKAEGSALVKLGSTQVLVGIKTSLGEP----- 73

Query: 420 LESLVGPPTKRFMLHYSFPPFCINEVGKRVGLNRREVGHGTLAEKALL--------AVLP 471
                 P       +    P       +    + R +    + ++ +          ++ 
Sbjct: 74  --FPDTPNMGVMTTNVELVPLASPTF-EPGPPDERAIELARVIDRGIRESKALNLEKMVI 130

Query: 472 PENDFPYTVRVNSEVMASDGSTSMATVCGGSMALMDAGIPLQEHV-AGVSVGLVSEVDP- 529
                   V ++  V+  DG+   A       AL++A +P   +      V  + E +P 
Sbjct: 131 VPGKIVRVVFIDVHVLDHDGNLMDAIGIAAIAALLNARVPKVRYNEETGEVETLDETEPL 190

Query: 530 ---------STGEIKDYRILTDILGLEDHLGDMDFKIAGTRIG-VTAIQLDIKPAGIPLD 579
                    +  +I +  ++ D    E+ + D    I     G ++A+Q   K  G    
Sbjct: 191 PVEKIPVPVTFAKIGNI-LVVDPSLDEELVMDGKITITTDETGHISAVQ---KSEGGAFK 246

Query: 580 I--ICECLEHAHKGRLQILDHMEREI 603
           +  +   +E A K   +I   +   +
Sbjct: 247 LEEVMYAVETAFKKAEEIRKLILEAV 272

>2k52_A Uncharacterized protein MJ1198; metal-binding, zinc, zinc-finger, structural genomics, PSI-2, protein structure initiative; NMR {Methanocaldococcus jannaschii} Length = 80

 Score = 78.9 bits (195), Expect = 4e-18
 Identities = 20/81 (24%), Positives = 38/81 (46%), Gaps = 5/81 (6%)

Query: 680 EIEVGGIYKGVVTSVKEYGAFVEFNGGQQGLLHVSELSHEPVSRVSDVVSVGQQLSLRCI 739
           ++E G  YKGVVT +++YGAF+  N   +GLL   ++    +    + ++VG ++ ++ I
Sbjct: 2   DVEPGKFYKGVVTRIEKYGAFINLNEQVRGLLRPRDMISLRL----ENLNVGDEIIVQAI 57

Query: 740 GQDVRGN-IKLSLKAVSPRPE 759
                   I      +     
Sbjct: 58  DVRPEKREIDFKYIPLEHHHH 78

>2a19_A EIF-2- alpha, eukaryotic translation initiation factor 2 alpha; transferase, protein biosynthesis, protein synthesis transferase complex; HET: TPO ANP; 2.50A {Saccharomyces cerevisiae} PDB: 2a1a_A* 1q46_A Length = 175

 Score = 76.7 bits (189), Expect = 3e-16
 Identities = 21/85 (24%), Positives = 38/85 (44%), Gaps = 3/85 (3%)

Query: 682 EVGGIYKGVVTSVKEYGAFVEFN--GGQQGLLHVSELSHEPVSRVSDVVSVGQQLSLRCI 739
           E+  I    V  + E GA+V+       +G++ +SELS   +  +  ++ VG+      +
Sbjct: 14  EIDDIVMVNVQQIAEMGAYVKLLEYDNIEGMILLSELSRRRIRSIQKLIRVGKNDVAVVL 73

Query: 740 GQDV-RGNIKLSLKAVSPRPEADVK 763
             D  +G I LS + VS       +
Sbjct: 74  RVDKEKGYIDLSKRRVSSEDIIKCE 98

>1kl9_A Eukaryotic translation initiation factor 2 subuni; OB fold, helical domain; 1.90A {Homo sapiens} SCOP: a.60.14.1 b.40.4.5 Length = 182

 Score = 76.4 bits (188), Expect = 4e-16
 Identities = 23/84 (27%), Positives = 40/84 (47%), Gaps = 3/84 (3%)

Query: 682 EVGGIYKGVVTSVKEYGAFVEFN--GGQQGLLHVSELSHEPVSRVSDVVSVGQQLSLRCI 739
           EV  +    V S+ E GA+V        +G++ +SELS   +  ++ ++ +G+   +  I
Sbjct: 14  EVEDVVMVNVRSIAEMGAYVSLLEYNNIEGMILLSELSRRRIRSINKLIRIGRNECVVVI 73

Query: 740 GQDV-RGNIKLSLKAVSPRPEADV 762
             D  +G I LS + VSP      
Sbjct: 74  RVDKEKGYIDLSKRRVSPEEAIKC 97

>2nn6_E Exosome complex exonuclease RRP42; RNA, exosome, PM/SCL, phosphorolytic, hydrolase/transferase complex; 3.35A {Homo sapiens} SCOP: d.14.1.4 d.101.1.1 Length = 305

 Score = 78.9 bits (194), Expect = 6e-16
 Identities = 47/283 (16%), Positives = 84/283 (29%), Gaps = 44/283 (15%)

Query: 362 KRIIAEGVRVDGRQLDEVRPIYCESGNLPILHGSSLFSRGDTQVLCTVT--LGAPAEAQR 419
              + E +RVDGR  ++ R +  E+  +    GS+    G T +L  V   +G P     
Sbjct: 29  VHGVQEDLRVDGRGCEDYRCVEVETDVVSNTSGSARVKLGHTDILVGVKAEMGTP----- 83

Query: 420 LESLVGPPTKRFMLHYSFPPFCINEVGKRVG----------LNRREVGHGTLAEKALLAV 469
              L  P                 E   R G          L R      ++  K L   
Sbjct: 84  --KLEKPNEGYLEFFVDCSASATPEFEGRGGDDLGTEIANTLYRIFNNKSSVDLKTLCIS 141

Query: 470 LPPENDFPYTVRVNSEVMASDGSTSMATVCGGSMALMDAGIPLQEHVAGVSVGLVSEVDP 529
                +  + + V+  ++   G+   A       AL +  IP    +         E+  
Sbjct: 142 ---PREHCWVLYVDVLLLECGGNLFDAISIAVKAALFNTRIPRVRVLEDEEGSKDIELSD 198

Query: 530 STGEIK----------------DYRILTDILGLEDHLGDMDFKIAGTRIG-VTAIQLDIK 572
              +                   YR + D    E+        ++ T  G VT ++   K
Sbjct: 199 DPYDCIRLSVENVPCIVTLCKIGYRHVVDATLQEEACSLASLLVSVTSKGVVTCMR---K 255

Query: 573 PAGIPLDI--ICECLEHAHKGRLQILDHMEREISAPRTQDDRN 613
                LD   I E +E   +    +   ++  +    +   + 
Sbjct: 256 VGKGSLDPESIFEMMETGKRVGKVLHASLQSVVHKEESLGPKR 298

>2wp8_A Exosome complex component RRP45; nucleus, hydrolase, RNA-binding, exonucle binding, mitochondrion, rRNA processing; 3.00A {Saccharomyces cerevisiae} Length = 305

 Score = 78.6 bits (193), Expect = 7e-16
 Identities = 48/303 (15%), Positives = 91/303 (30%), Gaps = 55/303 (18%)

Query: 362 KRIIAEGVRVDGRQLDEVRPIYCESGNLPILHGSSLFSRGDTQVLCTVT--LGAPAEAQR 419
              + +  R+DGR  D+ R +    G      G      G+T+V C ++  +  P E + 
Sbjct: 16  LEALRQNYRLDGRSFDQFRDVEITFGK---EFGDVSVKMGNTKVHCRISCQIAQPYEDR- 71

Query: 420 LESLVGPPTKRFMLHYSFPPFCINEVGKRVGLNRREVGHGTLAEKALLAVLPP------- 472
                 P    F++     P   ++          EV    + EK++             
Sbjct: 72  ------PFEGLFVISTEISPMAGSQFENGNITGEDEVLCSRIIEKSVRRSGALDVEGLCI 125

Query: 473 -ENDFPYTVRVNSEVMASDGSTSMATVCGGSMALMDAGIP-------------------- 511
                 + VR +   +  DG    A+       LM    P                    
Sbjct: 126 VAGSKCWAVRADVHFLDCDGGFIDASCIAVMAGLMHFKKPDITVHGEQIIVHPVNEREPV 185

Query: 512 ---LQEHVAGVSVGLV---SEVDPSTGEIKDYRILTDILGLEDHLGDMDFKIAGTRIG-V 564
              +      V+          +   GE      + D    E+ L D    +   +   V
Sbjct: 186 PLGILHIPICVTFSFFNPQDTEENIKGETNSEISIIDATLKEELLRDGVLTVTLNKNREV 245

Query: 565 TAIQLDIKPAGIPLDI--ICECLEHAHKGRLQILDHMEREISAPRTQDDRNSPRLATLKY 622
             +    K  G+P+D   + +C   A+    +I D + + +       ++ +   A L  
Sbjct: 246 VQVS---KAGGLPMDALTLMKCCHEAYSIIEKITDQILQLLKE---DSEKRNKYAAMLTS 299

Query: 623 DND 625
           +N 
Sbjct: 300 ENA 302

>2khj_A 30S ribosomal protein S1; OB fold, acetylation, phosphoprotein, ribonucleoprotein, RNA-binding; NMR {Escherichia coli} Length = 109

 Score = 73.0 bits (180), Expect = 1e-15
 Identities = 28/84 (33%), Positives = 40/84 (47%), Gaps = 1/84 (1%)

Query: 677 IGREIEVGGIYKGVVTSVKEYGAFVEFNGGQQGLLHVSELSHEPVSRVSDVVSVGQQLSL 736
                + G I  G VT+V   GA VE   G +G L  SE S + V   + V+SVG ++  
Sbjct: 25  WVALNKKGAIVTGKVTAVDAKGATVELADGVEGYLRASEASRDRVEDATLVLSVGDEVEA 84

Query: 737 RCIGQDVRG-NIKLSLKAVSPRPE 759
           +  G D +   I LS++A     E
Sbjct: 85  KFTGVDRKNRAISLSVRAKDEADE 108

>2nn6_A Polymyositis/scleroderma autoantigen 1; RNA, exosome, PM/SCL, phosphorolytic, hydrolase/transferase complex; 3.35A {Homo sapiens} SCOP: d.14.1.4 d.101.1.1 Length = 358

 Score = 78.9 bits (194), Expect = 1e-15
 Identities = 54/272 (19%), Positives = 90/272 (33%), Gaps = 43/272 (15%)

Query: 362 KRIIAEGVRVDGRQLDEVRPIYCESGNLPILHGSSLFSRGDTQVLCTVT--LGAPAEAQR 419
            R I E  R+DGRQ  + R I    G     +G  +   G T+VL  V+  L +P     
Sbjct: 32  LRAIEEKKRLDGRQTYDYRNIRISFGT---DYGCCIVELGKTRVLGQVSCELVSP----- 83

Query: 420 LESLVGPPTKRFMLHYSFPPFC--INEVGKRVGLN-------RREVGHGTLAEKALLAVL 470
              L          +           E G++  L         R + +    +   L V+
Sbjct: 84  --KLNRATEGILFFNLELSQMAAPAFEPGRQSDLLVKLNRLMERCLRNSKCIDTESLCVV 141

Query: 471 PPENDFPYTVRVNSEVMASDGSTSMATVCGGSMALMDAGIP-LQEHVAGVSVGLVSEVDP 529
             E    + +RV+  ++  DG+   A      +AL     P +      V++    E DP
Sbjct: 142 AGEKV--WQIRVDLHLLNHDGNIIDAASIAAIVALCHFRRPDVSVQGDEVTLYTPEERDP 199

Query: 530 STGEIKDY-------------RILTDILGLEDHLGDMDFKIAGTRIG-VTAIQLDIKPAG 575
               I                 +L D    E+ + D    IA  +   +  IQ      G
Sbjct: 200 VPLSIHHMPICVSFAFFQQGTYLLVDPNEREERVMDGLLVIAMNKHREICTIQ---SSGG 256

Query: 576 IPLDI--ICECLEHAHKGRLQILDHMEREISA 605
           I L    +  C + A     +I + + + +  
Sbjct: 257 IMLLKDQVLRCSKIAGVKVAEITELILKALEN 288

>3cw2_C Translation initiation factor 2 subunit alpha; AIF2, intact AIF2, initiation factor 2 alpha subunit, initiation factor 2 beta subunit; 2.80A {Sulfolobus solfataricus} PDB: 2aho_B 3v11_B* Length = 266

 Score = 74.3 bits (182), Expect = 1e-14
 Identities = 26/108 (24%), Positives = 48/108 (44%), Gaps = 3/108 (2%)

Query: 675 FIIGREIEVGGIYKGVVTSVKEYGAFVEFN--GGQQGLLHVSELSHEPVSRVSDVVSVGQ 732
           +   +    G I    V  V +YG++V  +  GG Q  L  SE+S + V  + DV+   +
Sbjct: 3   YSRSKLPSEGEILIATVKQVFDYGSYVSLDEYGGLQAFLPWSEVSSKWVKNIRDVLKENR 62

Query: 733 QLSLRCIGQD-VRGNIKLSLKAVSPRPEADVKGVVEGSVPVNKQATDV 779
           ++ ++ I  D  +G + +SLK V+           +    ++K    V
Sbjct: 63  KVIVKVIRVDRRKGTVDVSLKKVTDDERRKKNLQWKKIQRLDKILELV 110

>3aev_A Translation initiation factor 2 subunit alpha; proteins-rRNA complex, 16S rRNA, RNA-binding; 2.80A {Pyrococcus horikoshii} PDB: 1yz6_A Length = 275

 Score = 73.1 bits (179), Expect = 3e-14
 Identities = 24/87 (27%), Positives = 43/87 (49%), Gaps = 3/87 (3%)

Query: 679 REIEVGGIYKGVVTSVKEYGAFVEFN--GGQQGLLHVSELSHEPVSRVSDVVSVGQQLSL 736
              E G      V  +  YGAF+E +   G++  +H+SE++   V  + D +  GQ++  
Sbjct: 7   EYPEEGEFVVATVKRIHNYGAFLELDEYPGKEAFMHISEVASTWVRNIRDYLKEGQKVVA 66

Query: 737 RCIGQD-VRGNIKLSLKAVSPRPEADV 762
           + I  D  +G+I LSL+ V+ +     
Sbjct: 67  KVIRVDPRKGHIDLSLRRVTQQQRKAK 93

>2khi_A 30S ribosomal protein S1; acetylation, phosphoprotein, ribonucleoprotein, RNA-binding; NMR {Escherichia coli} Length = 115

 Score = 68.8 bits (169), Expect = 3e-14
 Identities = 29/84 (34%), Positives = 40/84 (47%), Gaps = 2/84 (2%)

Query: 677 IGREIEVGGIYKGVVTSVKEYGAFVEFNGGQQGLLHVSELSH-EPVSRVSDVVSVGQQLS 735
           I +    G    G VT++ +YG FVE   G +GL+HVSE+         S VV+VG  + 
Sbjct: 24  IAKRYPEGTKLTGRVTNLTDYGCFVEIEEGVEGLVHVSEMDWTNKNIHPSKVVNVGDVVE 83

Query: 736 LRCIGQDV-RGNIKLSLKAVSPRP 758
           +  +  D  R  I L LK     P
Sbjct: 84  VMVLDIDEERRRISLGLKQCKANP 107

>1q8k_A Eukaryotic translation initiation factor 2 subunit 1; NMR {Homo sapiens} SCOP: a.60.14.1 b.40.4.5 d.58.51.1 Length = 308

 Score = 70.0 bits (171), Expect = 6e-13
 Identities = 24/84 (28%), Positives = 43/84 (51%), Gaps = 3/84 (3%)

Query: 682 EVGGIYKGVVTSVKEYGAFVEFN--GGQQGLLHVSELSHEPVSRVSDVVSVGQQLSLRCI 739
           EV  +    V S++E GA+V        +G++H+SELS   +  ++ ++ +G+   ++ I
Sbjct: 12  EVEDVVMVNVRSIQEMGAYVSLLEYNNIEGMIHLSELSRRRIRSINKLIRIGRNECVKVI 71

Query: 740 GQD-VRGNIKLSLKAVSPRPEADV 762
             D  +G I LS + VSP      
Sbjct: 72  RVDKEKGYIDLSKRRVSPEEAIKC 95

>3bzc_A TEX; helix-turn-helix, helix-hairpin-helix, S1 domain, YQGF domain, transcription, RNA binding protein; 2.27A {Pseudomonas aeruginosa} SCOP: a.60.2.6 a.60.2.6 a.294.1.1 b.40.4.5 c.55.3.13 PDB: 3bzk_A 2oce_A Length = 785

 Score = 65.7 bits (161), Expect = 5e-11
 Identities = 25/73 (34%), Positives = 44/73 (60%), Gaps = 1/73 (1%)

Query: 681 IEVGGIYKGVVTSVKEYGAFVEFNGGQQGLLHVSELSHEPVSRVSDVVSVGQQLSLRCIG 740
           ++ G + +GVVT+V  +GAFV+    Q GL+H+S LS + V    +VV  G  + ++ + 
Sbjct: 652 LKPGMVLEGVVTNVTNFGAFVDIGVHQDGLVHISALSEKFVKDPYEVVKAGDIVKVKVME 711

Query: 741 QDV-RGNIKLSLK 752
            D+ R  + LS++
Sbjct: 712 VDIPRNRVGLSMR 724

>3psf_A Transcription elongation factor SPT6; nucleus; 2.59A {Saccharomyces cerevisiae} Length = 1030

 Score = 58.7 bits (142), Expect = 8e-09
 Identities = 10/88 (11%), Positives = 30/88 (34%), Gaps = 2/88 (2%)

Query: 667 EKVLEKVDFIIGREIEVGGIYKGVVTSVKEYGAFVEFNGGQQGLLHVSELSHEPVSR-VS 725
           +++ + +     +    G I    V            N   + +++    +   + R  +
Sbjct: 889 DEIFQSLTGESEKTFFKGSIIPVRVERFWHNDIICTTNSEVECVVNAQRHAGAQLRRPAN 948

Query: 726 DVVSVGQQLSLRCIGQDV-RGNIKLSLK 752
           ++  +G+    + I  D      ++SL 
Sbjct: 949 EIYEIGKTYPAKVIYIDYANITAEVSLL 976

>3psi_A Transcription elongation factor SPT6; nucleus; 3.30A {Saccharomyces cerevisiae} Length = 1219

 Score = 56.4 bits (136), Expect = 4e-08
 Identities = 10/88 (11%), Positives = 30/88 (34%), Gaps = 2/88 (2%)

Query: 667 EKVLEKVDFIIGREIEVGGIYKGVVTSVKEYGAFVEFNGGQQGLLHVSELSHEPVSR-VS 725
           +++ + +     +    G I    V            N   + +++    +   + R  +
Sbjct: 886 DEIFQSLTGESEKTFFKGSIIPVRVERFWHNDIICTTNSEVECVVNAQRHAGAQLRRPAN 945

Query: 726 DVVSVGQQLSLRCIGQDV-RGNIKLSLK 752
           ++  +G+    + I  D      ++SL 
Sbjct: 946 EIYEIGKTYPAKVIYIDYANITAEVSLL 973

>3h36_A Polyribonucleotide nucleotidyltransferase; polyribonucleotide nucleotidyltransfer structural genomics, PSI-2, protein structure initiative; 1.80A {Streptococcus mutans} Length = 93

 Score = 50.5 bits (121), Expect = 6e-08
 Identities = 15/92 (16%), Positives = 34/92 (36%), Gaps = 9/92 (9%)

Query: 287 KLSMISEQTLEKVSNLAEAHI-EAVFTDPSYSKFERGEALDKIGQDVKKALEEE-CDEES 344
           +L  +      ++     A + +AV  +    K     A + + + V    EE   + E 
Sbjct: 5   ELLQVDADLQAEIVGKYNADLQKAVQIE---EKKASEIATEAVKEHVTAEYEERYAEHEE 61

Query: 345 LQVLPK----AVDTVRKRVIRKRIIAEGVRVD 372
              + +     ++ +    +R+ I  + VR D
Sbjct: 62  HDRIMRDVAEILEQMEHAEVRRLITEDKVRPD 93

>1vt4_I APAF-1 related killer DARK; drosophila apoptosome, apoptosis, programmed cell death; HET: DTP; 6.90A {Drosophila melanogaster} PDB: 3iz8_A* Length = 1221

 Score = 53.3 bits (127), Expect = 4e-07
 Identities = 100/710 (14%), Positives = 188/710 (26%), Gaps = 256/710 (36%)

Query: 54  KVLETFKEEFEIGSRLITLETGKIARFANGAVVLGMDETK-VLST-----VTSSKGDSVR 107
            +L  F++ F             +  F    V    D  K +LS      +  SK     
Sbjct: 20  DILSVFEDAF-------------VDNFDCKDV---QDMPKSILSKEEIDHIIMSKDAVSG 63

Query: 108 DFLPLTV--DYQE---KQFAQGVIPNTYMRREGAPKERELLVGRIIDRPIRPLFPAGFYH 162
                      QE   ++F + V+   Y          + L+  I     +P      Y 
Sbjct: 64  TLRLFWTLLSKQEEMVQKFVEEVLRINY----------KFLMSPIKTEQRQPSMMTRMYI 113

Query: 163 EVQVMASVLSSDGKQDPDI------MAANATSAALMLSDIPWGGPIGMIRIGRICGQFIV 216
           E +     L +D +                  A L L         G++  G   G    
Sbjct: 114 EQR---DRLYNDNQVFAKYNVSRLQPYLKLRQALLELRPAKNVLIDGVL--G--SG---- 162

Query: 217 NPTMDELSLSDLNLVYACTREKT-LMIDVQAREISEKDLEAGLRLAHPEAVKYLEPQIRL 275
                                KT + +DV             ++      + +L      
Sbjct: 163 ---------------------KTWVALDV-CLSYK-------VQCKMDFKIFWL------ 187

Query: 276 AEKAGKQKKEYKLSMISEQTLEKVSNLAEAHIEAVFT---DPSYSKFERGEALDKIGQDV 332
                            E  LE +  L    I+  +T   D S +   R  ++     ++
Sbjct: 188 --NLKNCNSP-------ETVLEMLQKLL-YQIDPNWTSRSDHSSNIKLRIHSIQ---AEL 234

Query: 333 KKALEEECDEESLQVL-----PKAVDT--VRKRVI---RKRIIAEGVRVDGRQLDEVRPI 382
           ++ L+ +  E  L VL      KA +   +  +++   R + + + +             
Sbjct: 235 RRLLKSKPYENCLLVLLNVQNAKAWNAFNLSCKILLTTRFKQVTDFLSAATTT------- 287

Query: 383 YCESGNLPILHGSSLFSRGDTQVLCTVTLGAPAEAQRLESLVGPPTKRFMLHYSFPPFCI 442
                ++ + H S   +  + + L    L    +    E L          +    P  +
Sbjct: 288 -----HISLDHHSMTLTPDEVKSLLLKYLDCRPQDLPREVLTT--------N----PRRL 330

Query: 443 NEVGK--RVGLNR----REVGHGTLAE------KAL-----------LAVLPPENDFPYT 479
           + + +  R GL      + V    L          L           L+V PP    P  
Sbjct: 331 SIIAESIRDGLATWDNWKHVNCDKLTTIIESSLNVLEPAEYRKMFDRLSVFPPSAHIPTI 390

Query: 480 V--RVNSEVMASDGSTSMATVCGGSMALMDAGIPLQEHVAGVSVGLVSEVDPSTGEIKDY 537
           +   +  +V+ SD    +  +   S+                          ST      
Sbjct: 391 LLSLIWFDVIKSDVMVVVNKLHKYSLVEKQP-------------------KEST-----I 426

Query: 538 RILTDILGLEDHLGDMDFKIAGTRIGVTAIQLDIKPAGIPLDIICECLEHA--HKGRLQI 595
            I                          +I L++K          +       H+    I
Sbjct: 427 SI---------P----------------SIYLELK---------VKLENEYALHR---SI 449

Query: 596 LDHMEREISAPRTQDDRNSPR------------LATLKYDN--DTLRRLIGPLGALKRKI 641
           +DH    I      DD   P             L  +++       R +      L++KI
Sbjct: 450 VDH--YNIPKTFDSDDLIPPYLDQYFYSHIGHHLKNIEHPERMTLFRMVFLDFRFLEQKI 507

Query: 642 EEET---GGRISVSDGTLTV-------VAKNRSVMEKVLEKV-DFIIGRE 680
             ++       S+ + TL         +  N    E+++  + DF+   E
Sbjct: 508 RHDSTAWNASGSILN-TLQQLKFYKPYICDNDPKYERLVNAILDFLPKIE 556

>1vt4_I APAF-1 related killer DARK; drosophila apoptosome, apoptosis, programmed cell death; HET: DTP; 6.90A {Drosophila melanogaster} PDB: 3iz8_A* Length = 1221

 Score = 52.9 bits (126), Expect = 5e-07
 Identities = 65/419 (15%), Positives = 112/419 (26%), Gaps = 135/419 (32%)

Query: 50  VAGTKVLETFKEEFEIGSR-LITLETGKIARFANGAVVLGMDETKVLSTVTSSKGDSVRD 108
           V   K    F     +  + L+T  T    RF      L    T  +S    S       
Sbjct: 253 VQNAKAWNAF----NLSCKILLT--T----RFKQVTDFLSAATTTHISLDHHSMT----- 297

Query: 109 FLPLTVDYQEKQFAQ--GVIPNTYMRRE---GAPKERELLVGRIIDRPIRPLFPAGFYHE 163
              LT D  +    +     P   + RE     P+   ++   I D           +  
Sbjct: 298 ---LTPDEVKSLLLKYLDCRPQD-LPREVLTTNPRRLSIIAESIRDGLATW----DNWKH 349

Query: 164 VQV--MASVLSSD-GKQDPDIMAANATSAALMLSD--IPWGGPIGMIRIGRICGQFIVNP 218
           V    + +++ S     +P          ++      IP                     
Sbjct: 350 VNCDKLTTIIESSLNVLEPAEYRKMFDRLSVFPPSAHIP--------------------- 388

Query: 219 TMDELSLSDLNLVYACTREKTLMI---DVQAREISEKDLEAGLRLAHPEAVKYLEPQIRL 275
                                L +   DV   ++    +         +  KY      L
Sbjct: 389 ------------------TILLSLIWFDVIKSDV-MVVVN--------KLHKY-----SL 416

Query: 276 AEKAGKQKKEYKLSM--ISEQTLEKVSNLAEAH---IEAVFTDPSYSKFERG-EALDK-- 327
            EK   Q KE  +S+  I  +   K+ N    H   ++      ++   +     LD+  
Sbjct: 417 VEK---QPKESTISIPSIYLELKVKLENEYALHRSIVDHYNIPKTFDSDDLIPPYLDQYF 473

Query: 328 ---IGQDVKKALEEECDEESLQVLPKAVDTVRKRVIRKRIIAEGVRVDGR--------QL 376
              IG  +K     E       V    +D    R + ++I  +    +          QL
Sbjct: 474 YSHIGHHLKNIEHPERMTLFRMVF---LDF---RFLEQKIRHDSTAWNASGSILNTLQQL 527

Query: 377 DEVRPIYCESGNLP------ILH-----GSSLFSRGDTQVLCTVTLGAP-----AEAQR 419
              +P  C++          IL        +L     T +L  + L A       EA +
Sbjct: 528 KFYKPYICDNDPKYERLVNAILDFLPKIEENLICSKYTDLL-RIALMAEDEAIFEEAHK 585

>4ubp_A Protein (urease (chain A)); bacillus pasteurii, nickel, acetohydroxamic acid, metalloenzyme, hydrolase; HET: KCX; 1.55A {Sporosarcina pasteurii} SCOP: d.8.1.1 PDB: 3ubp_A* 2ubp_A* 1ubp_A* 1s3t_A* 1ie7_A* 1ejx_A* 1a5l_A 1a5k_A 1a5n_A 1a5o_A 1ef2_C* 1ejr_A* 1ejs_A* 1ejt_A* 1eju_A* 1ejv_A* 1a5m_A* 1ejw_A* 1fwa_A* 1fwb_A* ... Length = 101

 Score = 47.5 bits (113), Expect = 7e-07
 Identities = 20/86 (23%), Positives = 32/86 (37%), Gaps = 5/86 (5%)

Query: 236 REKTLMIDVQAREISEKDLEAGLRLAHPEAVKYLEPQIRLAEKAGKQKKEYKLSMIS--- 292
            EK  +    A E+  +    GL+L +PEAV  +   I    + GK              
Sbjct: 7   AEKEKLQIFLASELLLRRKARGLKLNYPEAVAIITSFIMEGARDGKTVAMLMEEGKHVLT 66

Query: 293 -EQTLEKVSN-LAEAHIEAVFTDPSY 316
            +  +E V   + +   EA F D + 
Sbjct: 67  RDDVMEGVPEMIDDIQAEATFPDGTK 92

>2fvh_A Urease gamma subunit; protein: UREA homolog, structural genomics, PSI, protein STR initiative, TB structural genomics consortium; 1.80A {Mycobacterium tuberculosis} Length = 120

 Score = 41.9 bits (98), Expect = 9e-05
 Identities = 24/86 (27%), Positives = 38/86 (44%), Gaps = 5/86 (5%)

Query: 236 REKTLMIDVQAREISEKDLEAGLRLAHPEAVKYLEPQIRLAEKAGKQKKEYKLSMI---- 291
            E+  ++   A E++ +    GLRL HPEA+  +   I    + G+   E   S      
Sbjct: 26  HEQERLLLSYAAELARRRRARGLRLNHPEAIAVIADHILEGARDGRTVAELMASGREVLG 85

Query: 292 SEQTLEKVSN-LAEAHIEAVFTDPSY 316
            +  +E V   LAE  +EA F D + 
Sbjct: 86  RDDVMEGVPEMLAEVQVEATFPDGTK 111

>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 = 42.3 bits (99), Expect = 1e-04
 Identities = 27/125 (21%), Positives = 49/125 (39%), Gaps = 21/125 (16%)

Query: 530 STGEIKDYRILTDILGLEDHLGDMDFKIAGTRIGVTAIQLDIKPAGIPLDIICECLEHAH 589
           ++   + + +  D++GL       + + A    GVTAI LD         I  E  +   
Sbjct: 1   ASRFHEQFIVREDLMGLAIGTHGANIQQARKVPGVTAIDLD--EDTCTFHIYGEDQDAVK 58

Query: 590 KGRLQILDHMEREISAPRTQDDRNSPRLATLKYDNDTLRRLIGPLGALKRKIEEETGG-R 648
           K R   L+  E  I  PR                 + + ++IG  G L ++I +++G  R
Sbjct: 59  KAR-SFLEFAEDVIQVPR-----------------NLVGKVIGKNGKLIQEIVDKSGVVR 100

Query: 649 ISVSD 653
           + +  
Sbjct: 101 VRIEA 105

>3m7n_A Putative uncharacterized protein AF_0206; exosome, RNA, exonuclease, hydrolase, nuclease, hydrolase-RN; 2.40A {Archaeoglobus fulgidus} PDB: 2ba1_A 3m85_A Length = 179

 Score = 41.9 bits (98), Expect = 2e-04
 Identities = 31/135 (22%), Positives = 53/135 (39%), Gaps = 16/135 (11%)

Query: 639 RKIEEETGGR-ISVSDGTLTVVAKNRSVMEKVLEKVDFIIGR-EIEVGGIYKGVVTSVKE 696
              EE   G  +    G L      + +++  + KV+ I    EI  G +  G V  ++ 
Sbjct: 11  GSAEEYVKGEGVYEEGGELFAAVAGKLIIKDRVAKVESISPIPEIVKGDVVLGRVVDLRN 70

Query: 697 YGAFVEFNGGQ----------QGLLHVSELSHEPVSRVSDVVSVGQQLSLRCIGQDVRGN 746
             A +E +  +           G+LHVS +    V  +S+ V     L  R IG ++R +
Sbjct: 71  SIALIEVSSKKGENRGPSNRGIGILHVSNVDEGYVKEISEAVGYLDILKARVIGDNLRLS 130

Query: 747 IKLS----LKAVSPR 757
            K      L+A+   
Sbjct: 131 TKEEEMGVLRALCSN 145

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	974
4aid_A	726	Polyribonucleotide nucleotidyltransferase; transfe	100.0
3cdi_A	723	Polynucleotide phosphorylase; mRNA turnover, RNAse	100.0
1e3p_A	757	Guanosine pentaphosphate synthetase; polyribonucle	100.0
3u1k_A	630	Polyribonucleotide nucleotidyltransferase 1, MITO;	100.0
3gme_A	549	Polyribonucleotide nucleotidyltransferase; protein	100.0
2nn6_B	249	Exosome complex exonuclease RRP41; RNA, exosome, P	100.0
2wnr_B	240	Probable exosome complex exonuclease 1; phosphate	100.0
3m7n_D	258	Probable exosome complex exonuclease 1; exosome, R	100.0
2po1_A	249	Probable exosome complex exonuclease 1; RNAse PH,	100.0
2je6_B	250	RRP41, exosome complex exonuclease 1; nuclease, hy	100.0
3hkm_A	246	OS03G0854200 protein; RNAse PH domain, phosphoryla	100.0
3b4t_A	262	Ribonuclease PH; RNAse, tRNA nucleotidyltransferas	100.0
2wp8_B	246	Exosome complex component SKI6; nucleus, hydrolase	100.0
2po1_B	277	Probable exosome complex exonuclease 2; RNAse PH,	100.0
3dd6_A	255	Ribonuclease PH; exoribonuclease, tRNA maturation,	100.0
3m7n_G	259	Probable exosome complex exonuclease 2; exosome, R	100.0
2wnr_A	271	Probable exosome complex exonuclease 2; phosphate	100.0
1oys_A	245	Ribonuclease PH; transferase, tRNA processing; 2.4	100.0
2nn6_C	278	Exosome complex exonuclease RRP43; RNA, exosome, P	100.0
2nn6_F	272	MTR3, exosome component 6; RNA, exosome, PM/SCL, p	100.0
1udn_A	255	Ribonuclease PH, RNAse PH; transferase, riken stru	100.0
2je6_A	277	RRP42, exosome complex exonuclease 2; nuclease, hy	100.0
1r6l_A	239	Ribonuclease PH; beta-alpha-beta-alpha fold, hexam	100.0
2wp8_A	305	Exosome complex component RRP45; nucleus, hydrolas	100.0
2nn6_E	305	Exosome complex exonuclease RRP42; RNA, exosome, P	100.0
2nn6_A	358	Polymyositis/scleroderma autoantigen 1; RNA, exoso	100.0
3dd6_A	255	Ribonuclease PH; exoribonuclease, tRNA maturation,	100.0
2je6_B	250	RRP41, exosome complex exonuclease 1; nuclease, hy	100.0
2nn6_D	237	Exosome complex exonuclease RRP46; RNA, exosome, P	100.0
3b4t_A	262	Ribonuclease PH; RNAse, tRNA nucleotidyltransferas	100.0
2wp8_B	246	Exosome complex component SKI6; nucleus, hydrolase	100.0
2nn6_F	272	MTR3, exosome component 6; RNA, exosome, PM/SCL, p	100.0
1r6l_A	239	Ribonuclease PH; beta-alpha-beta-alpha fold, hexam	100.0
2wnr_A	271	Probable exosome complex exonuclease 2; phosphate	100.0
3m7n_G	259	Probable exosome complex exonuclease 2; exosome, R	100.0
3m7n_D	258	Probable exosome complex exonuclease 1; exosome, R	100.0
3krn_A	222	Protein C14A4.5, confirmed by transcript evidence;	100.0
1udn_A	255	Ribonuclease PH, RNAse PH; transferase, riken stru	100.0
2je6_A	277	RRP42, exosome complex exonuclease 2; nuclease, hy	100.0
1oys_A	245	Ribonuclease PH; transferase, tRNA processing; 2.4	100.0
3hkm_A	246	OS03G0854200 protein; RNAse PH domain, phosphoryla	100.0
2nn6_C	278	Exosome complex exonuclease RRP43; RNA, exosome, P	100.0
2po1_A	249	Probable exosome complex exonuclease 1; RNAse PH,	100.0
4aid_A	726	Polyribonucleotide nucleotidyltransferase; transfe	100.0
3krn_A	222	Protein C14A4.5, confirmed by transcript evidence;	100.0
3cdi_A	723	Polynucleotide phosphorylase; mRNA turnover, RNAse	100.0
2nn6_B	249	Exosome complex exonuclease RRP41; RNA, exosome, P	100.0
2nn6_E	305	Exosome complex exonuclease RRP42; RNA, exosome, P	100.0
2wnr_B	240	Probable exosome complex exonuclease 1; phosphate	100.0
2nn6_D	237	Exosome complex exonuclease RRP46; RNA, exosome, P	100.0
2nn6_A	358	Polymyositis/scleroderma autoantigen 1; RNA, exoso	99.98
2po1_B	277	Probable exosome complex exonuclease 2; RNAse PH,	99.97
3u1k_A	630	Polyribonucleotide nucleotidyltransferase 1, MITO;	99.97
2wp8_A	305	Exosome complex component RRP45; nucleus, hydrolas	99.97
3gme_A	549	Polyribonucleotide nucleotidyltransferase; protein	99.97
1e3p_A	757	Guanosine pentaphosphate synthetase; polyribonucle	99.96
3go5_A	285	Multidomain protein with S1 RNA-binding domains; s	99.93
1kl9_A	182	Eukaryotic translation initiation factor 2 subuni;	99.62
1y14_B	171	B16, RPB7, DNA-directed RNA polymerase II 19 kDa p	99.62
1go3_E	187	DNA-directed RNA polymerase subunit E; transferase	99.59
2b8k_G	215	B16, DNA-directed RNA polymerase II 19 kDa polypep	99.56
2eqs_A	103	ATP-dependent RNA helicase DHX8; S1 domain, OB-fol	99.55
1luz_A	88	Protein K3, protein K2; stranded anti-parallel bet	99.54
2khi_A	115	30S ribosomal protein S1; acetylation, phosphoprot	99.53
3go5_A	285	Multidomain protein with S1 RNA-binding domains; s	99.52
2k4k_A	130	GSP13, general stress protein 13; cytoplasm, stres	99.51
2a19_A	175	EIF-2- alpha, eukaryotic translation initiation fa	99.5
1whu_A	104	Polynucleotide phosphorylase; 3'-5' RNA exonucleas	99.5
2cqo_A	119	Nucleolar protein of 40 kDa; S1 domain, OB-fold, s	99.5
2k52_A	80	Uncharacterized protein MJ1198; metal-binding, zin	99.48
2khj_A	109	30S ribosomal protein S1; OB fold, acetylation, ph	99.43
2c35_B	172	Human RPB7, DNA-directed RNA polymerase II 19 kDa	99.42
1q8k_A	308	Eukaryotic translation initiation factor 2 subunit	99.34
2khj_A	109	30S ribosomal protein S1; OB fold, acetylation, ph	99.33
3aev_A	275	Translation initiation factor 2 subunit alpha; pro	99.33
2khi_A	115	30S ribosomal protein S1; acetylation, phosphoprot	99.33
3cw2_C	266	Translation initiation factor 2 subunit alpha; AIF	99.25
2k52_A	80	Uncharacterized protein MJ1198; metal-binding, zin	99.24
3h0g_G	172	DNA-directed RNA polymerase II subunit RPB7; trans	99.16
4ayb_E	180	DNA-directed RNA polymerase; transferase, multi-su	99.15
2eqs_A	103	ATP-dependent RNA helicase DHX8; S1 domain, OB-fol	99.11
2k4k_A	130	GSP13, general stress protein 13; cytoplasm, stres	99.08
1wi5_A	119	RRP5 protein homolog; S1 domain, OB-fold, structur	99.05
3h36_A	93	Polyribonucleotide nucleotidyltransferase; polyrib	99.03
3psi_A	1219	Transcription elongation factor SPT6; nucleus; 3.3	99.01
2cqo_A	119	Nucleolar protein of 40 kDa; S1 domain, OB-fold, s	99.0
1luz_A	88	Protein K3, protein K2; stranded anti-parallel bet	98.99
2cpq_A	91	FragIle X mental retardation syndrome related prot	98.98
3m7n_A	179	Putative uncharacterized protein AF_0206; exosome,	98.97
1kl9_A	182	Eukaryotic translation initiation factor 2 subuni;	98.97
2a19_A	175	EIF-2- alpha, eukaryotic translation initiation fa	98.96
2ctk_A	104	Vigilin; K homology type I domain, RNA-binding, ce	98.95
3bzc_A	785	TEX; helix-turn-helix, helix-hairpin-helix, S1 dom	98.94
2nn6_I	209	3'-5' exoribonuclease CSL4 homolog; RNA, exosome,	98.92
3psf_A	1030	Transcription elongation factor SPT6; nucleus; 2.5	98.9
1wi5_A	119	RRP5 protein homolog; S1 domain, OB-fold, structur	98.83
3aev_A	275	Translation initiation factor 2 subunit alpha; pro	98.8
2je6_I	251	RRP4, exosome complex RNA-binding protein 1; nucle	98.78
2ba0_A	229	Archeal exosome RNA binding protein RRP4; RNAse PH	98.73
2e3u_A	219	PH-DIM2P, hypothetical protein PH1566; PRE-ribosom	98.71
1we8_A	104	Tudor and KH domain containing protein; structural	98.68
2z0s_A	235	Probable exosome complex RNA-binding protein 1; al	98.68
1q8k_A	308	Eukaryotic translation initiation factor 2 subunit	98.66
1vig_A	71	Vigilin; RNA-binding protein, ribonucleoprotein; N	98.58
2ctj_A	95	Vigilin; K homology type I domain, RNA-binding, ce	98.58
3cw2_C	266	Translation initiation factor 2 subunit alpha; AIF	98.56
2opv_A	85	KHSRP protein; KH domain, RNA binding protein, KSR	98.53
3psi_A	1219	Transcription elongation factor SPT6; nucleus; 3.3	98.49
1hh2_P	344	NUSA, N utilization substance protein A; transcrip	98.46
2ctm_A	95	Vigilin; K homology type I domain, RNA-binding, ce	98.41
1go3_E	187	DNA-directed RNA polymerase subunit E; transferase	98.4
1y14_B	171	B16, RPB7, DNA-directed RNA polymerase II 19 kDa p	98.38
2ctl_A	97	Vigilin; K homology type I domain, RNA-binding, ce	98.35
3bzc_A	785	TEX; helix-turn-helix, helix-hairpin-helix, S1 dom	98.34
3psf_A	1030	Transcription elongation factor SPT6; nucleus; 2.5	98.34
2cte_A	94	Vigilin; K homology type I domain, RNA-binding, ce	98.32
2axy_A	73	Poly(RC)-binding protein 2; protein-DNA complex, D	98.27
2b8k_G	215	B16, DNA-directed RNA polymerase II 19 kDa polypep	98.27
2id0_A	644	Exoribonuclease 2; RNAse, exonuclease, hydrolyase,	98.26
4ayb_E	180	DNA-directed RNA polymerase; transferase, multi-su	98.26
2hh3_A	106	KH-type splicing regulatory protein; KH-RNA bindin	98.24
2c35_B	172	Human RPB7, DNA-directed RNA polymerase II 19 kDa	98.24
2bx2_L	517	Ribonuclease E, RNAse E; RNA-binding, RNA turnover	98.22
3ayh_B	203	DNA-directed RNA polymerase III subunit RPC8; tran	98.22
2yqr_A	119	KIAA0907 protein; structure genomics, KH domain, s	98.21
2ba0_A	229	Archeal exosome RNA binding protein RRP4; RNAse PH	98.18
2z0s_A	235	Probable exosome complex RNA-binding protein 1; al	98.16
2nn6_I	209	3'-5' exoribonuclease CSL4 homolog; RNA, exosome,	98.16
1x4m_A	94	FAR upstream element binding protein 1; KH domain,	98.16
3m7n_A	179	Putative uncharacterized protein AF_0206; exosome,	98.16
2jvz_A	164	KH type-splicing, FAR upstream element-binding pro	98.15
1k1g_A	131	SF1-BO isoform; splicing, branch point sequence, p	98.14
1hh2_P	344	NUSA, N utilization substance protein A; transcrip	98.11
2p2r_A	76	Poly(RC)-binding protein 2; protein-DNA complex, R	98.1
2ckz_B	218	C25, DNA-directed RNA polymerase III 25 KD polypep	98.09
2je6_I	251	RRP4, exosome complex RNA-binding protein 1; nucle	98.09
1x4n_A	92	FAR upstream element binding protein 1; KH domain,	98.06
2ja9_A	175	Exosome complex exonuclease RRP40; RNA-binding pro	98.05
2wp8_J	977	Exosome complex exonuclease DIS3; nucleus, hydrola	98.04
2nn6_H	308	Exosome complex exonuclease RRP4; RNA, exosome, PM	98.03
3h0g_G	172	DNA-directed RNA polymerase II subunit RPB7; trans	98.0
2bh8_A	101	1B11; transcription, molecular evolution, unique a	98.0
1zzk_A	82	Heterogeneous nuclear ribonucleoprotein K; KH domi	97.99
3krm_A	163	Insulin-like growth factor 2 mRNA-binding protein	97.99
2jzx_A	160	Poly(RC)-binding protein 2; PCBP2, KH domains, RNA	97.98
1wvn_A	82	Poly(RC)-binding protein 1; KH domain, RNA binding	97.98
1dtj_A	76	RNA-binding neurooncological ventral antigen 2; KH	97.97
2vnu_D	760	Exosome complex exonuclease RRP44; hydrolase-RNA c	97.97
2hh2_A	107	KH-type splicing regulatory protein; KH-RNA bindin	97.94
1j5k_A	89	Heterogeneous nuclear ribonucleoprotein K; single-	97.91
2bh8_A	101	1B11; transcription, molecular evolution, unique a	97.88
1ec6_A	87	RNA-binding protein NOVA-2; KH domain, alpha-beta	97.84
1k0r_A	366	NUSA; two component arrangement, S1 domain, two K-	97.73
2dgr_A	83	Ring finger and KH domain-containing protein 1; st	97.7
2id0_A	644	Exoribonuclease 2; RNAse, exonuclease, hydrolyase,	97.59
1k0r_A	366	NUSA; two component arrangement, S1 domain, two K-	97.57
2ckz_B	218	C25, DNA-directed RNA polymerase III 25 KD polypep	97.5
2ja9_A	175	Exosome complex exonuclease RRP40; RNA-binding pro	97.46
3ayh_B	203	DNA-directed RNA polymerase III subunit RPC8; tran	97.44
2jzx_A	160	Poly(RC)-binding protein 2; PCBP2, KH domains, RNA	97.39
2asb_A	251	Transcription elongation protein NUSA; protein-RNA	97.37
2asb_A	251	Transcription elongation protein NUSA; protein-RNA	97.29
1j4w_A	174	FUSE binding protein; single-stranded DNA binding	97.25
2bl5_A	140	MGC83862 protein, quaking protein; STAR proteins,	97.21
2anr_A	178	Neuro-oncological ventral antigen 1; protein-RNA c	97.16
2bx2_L	517	Ribonuclease E, RNAse E; RNA-binding, RNA turnover	97.13
2nn6_G	289	Exosome complex exonuclease RRP40; RNA, exosome, P	97.05
3krm_A	163	Insulin-like growth factor 2 mRNA-binding protein	97.04
2jvz_A	164	KH type-splicing, FAR upstream element-binding pro	97.03
2nn6_H	308	Exosome complex exonuclease RRP4; RNA, exosome, PM	96.94
2vnu_D	760	Exosome complex exonuclease RRP44; hydrolase-RNA c	96.92
2wp8_J	977	Exosome complex exonuclease DIS3; nucleus, hydrola	96.86
1j4w_A	174	FUSE binding protein; single-stranded DNA binding	96.82
2anr_A	178	Neuro-oncological ventral antigen 1; protein-RNA c	96.62
2nn6_G	289	Exosome complex exonuclease RRP40; RNA, exosome, P	96.13
2ctf_A	102	Vigilin; K homology type I domain, RNA-binding, ce	95.69
2qnd_A	144	FMR1 protein; KH domain, eukaryotic KH domains, ta	94.52
2e3u_A	219	PH-DIM2P, hypothetical protein PH1566; PRE-ribosom	93.96
1tua_A	191	Hypothetical protein APE0754; structural genomics,	93.67
3n89_A	376	Defective in GERM LINE development protein 3, ISO;	92.22
2r7d_A	469	Ribonuclease II family protein; structural genomic	92.15
1tua_A	191	Hypothetical protein APE0754; structural genomics,	92.06
3n89_A	376	Defective in GERM LINE development protein 3, ISO;	90.69
3d0f_A	106	Penicillin-binding 1 transmembrane protein MRCA; B	88.92
1wfq_A	89	UNR protein; beta-barrel, translational regulation	87.14
2qnd_A	144	FMR1 protein; KH domain, eukaryotic KH domains, ta	85.8
3v69_A	140	Protein filia; RNA-binding, embryogenesis, KH doma	85.05
2rf4_A	214	DNA-directed RNA polymerase I subunit RPA4; transf	84.32
2k5n_A	74	Putative cold-shock protein; GFT protein structure	82.01
1h95_A	79	CSD, Y-box binding protein; translation factor, tr	80.01

>4aid_A Polyribonucleotide nucleotidyltransferase; transferase-peptide complex; 2.60A {Caulobacter vibrioides} PDB: 4aim_A 4am3_A

Probab=100.00  E-value=1.6e-158  Score=1418.20  Aligned_cols=697  Identities=42%  Similarity=0.703  Sum_probs=543.9

Q ss_pred             cceeeeeeEEECCeEEEEEeCccCcCCCcEEEEEeCCeEEEEEEEeCCC-CCCCCceeeEeeccccccccCCCCCccccc
Q 002054           55 VLETFKEEFEIGSRLITLETGKIARFANGAVVLGMDETKVLSTVTSSKG-DSVRDFLPLTVDYQEKQFAQGVIPNTYMRR  133 (974)
Q Consensus        55 ~~~~~~~~~~~~~r~i~~etg~~a~~A~GSa~v~~G~T~Vl~tv~~~~~-~~~~~f~pL~v~y~e~~~a~g~ip~~~~~R  133 (974)
                      ||+.+++++++|||+++||||++|+||+|||++++|+|+|||||+++.+ +++.+|+||+|+|+||+||+|||||||+||
T Consensus        15 ~~~~~~~~~~~~~R~i~ietg~~ak~A~GSvlv~~GdT~VL~tv~~~~~~~~g~df~pltveY~ek~~a~G~iPg~~~~R   94 (726)
T 4aid_A           15 MFDIKRKTIEWGGKTLVLETGRIARQADGAVLATMGETVVLATAVFAKSQKPGQDFFPLTVNYQEKTFAAGKIPGGFFKR   94 (726)
T ss_dssp             CCCEEECCCEETTEEEEEEESSSCTTSSEEEEEEETTEEEEEEEEECSSCCTTCCSCCEEEEEEECGGGGTCCCCSTTCS
T ss_pred             ccCcEEEEEEECCeeEEEEECCccCCCCeeEEEEECCeEEEEEEEecCCCCCCCCCcCceeeeeeehhhcccCCCcccCC
Confidence            7999999999999999999999999999999999999999999999988 678999999999999999999999999999


Q ss_pred             cCCCCchhhhHHHhhcCCccccccCCCCCceEEEEEEEeccCCCChhhHHHHHHHHHhhcCCCCCCCCeEEEEEEEECCE
Q 002054          134 EGAPKERELLVGRIIDRPIRPLFPAGFYHEVQVMASVLSSDGKQDPDIMAANATSAALMLSDIPWGGPIGMIRIGRICGQ  213 (974)
Q Consensus       134 eg~p~~~eil~~RlidR~lrplfp~~~~~~~~i~~~vl~~dg~~~~~~~ai~aAs~AL~~s~iP~~~~v~av~vg~i~g~  213 (974)
                      ||+|+++++|++|||||+|||+||++|++++||+|+||++||+++|+++||||||+||++|+|||++||+|||||++||+
T Consensus        95 EGrps~~~~li~RlIdR~lRplf~~~~~~evqI~~~Vls~Dg~~~~d~~ai~gAs~AL~~s~iP~~~~vaaV~Vg~i~g~  174 (726)
T 4aid_A           95 EGRPSEKETLVSRLIDRPIRPLFVKGFKNEVQVVVTVLQHDLENDPDILGMVAASAALCLSGAPFMGPIGAARVGWVDGA  174 (726)
T ss_dssp             CCSCCHHHHHHHHHHHHHHGGGBCTTCCSCEEEEEEEEECCSSSCHHHHHHHHHHHHHHHHTCSBCCCCEEEEEEEETTE
T ss_pred             CCCCCchhhhHHHHhCCccccccccCCccceEEEEEEEecCCCCChhHHHHHHHHHHHHhcCCCcCCCeEEEEEEEECCE
Confidence            99999999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             EEEcCCHHHHhcCccceeEeeeCCeEEEEEecCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCccccccccCCCH
Q 002054          214 FIVNPTMDELSLSDLNLVYACTREKTLMIDVQAREISEKDLEAGLRLAHPEAVKYLEPQIRLAEKAGKQKKEYKLSMISE  293 (974)
Q Consensus       214 ~vldPt~~e~~~s~~~l~v~~t~~~i~mie~~~~~~~e~~~~~al~~a~~~~~~i~~~~~~~~~~~g~~k~~~~~~~~~~  293 (974)
                      +|+|||++|++.|++||+|+||+++++|+|+++++||+++|.+||++||+++++++++|+++++++||+|++|... .++
T Consensus       175 ~vldPt~~E~~~s~~dl~va~t~~~i~mve~~~~~~se~~~~~al~~a~~~i~~l~~~q~~~~~~~g~~k~~~~~~-~~~  253 (726)
T 4aid_A          175 YVLNPTLDEMKESKMDLVVAGTADAVMMVESEIQELSEEIVLGGVNFAHQQMQAVIDAIIDLAEHAAKEPFAFEPE-DTD  253 (726)
T ss_dssp             EEESCCHHHHHTCSEEEEEEECSSCEEEEEEEESSBCHHHHHHHHHHHHHHTHHHHHHHHHHHHHHCCCCCCCCCC-TTH
T ss_pred             EEECCCHHHHhhCceeEEEEEeCCeEEEEEccCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCcccCCCC-CCH
Confidence            9999999999999999999999999999999999999999999999999999999999999999999999999887 899


Q ss_pred             HHHHHHHHHHHHHHHhhhcCCCCChhHHHHHHHHHHHHHHHHhhhccc-h--hhhchHHHHHHHHHHHHHHHHHHhcCCc
Q 002054          294 QTLEKVSNLAEAHIEAVFTDPSYSKFERGEALDKIGQDVKKALEEECD-E--ESLQVLPKAVDTVRKRVIRKRIIAEGVR  370 (974)
Q Consensus       294 ~~~~~~~~~~~~~~~~~~~~~~~~k~~r~~~~~~~~~~~~~~~~~~~~-~--~~~~~~~~~~~~~~~~~~r~~il~~~~R  370 (974)
                      ++.+++++++.++|++++.+  ++|++|+++++++++++.+.|.++.. +  ....++..+|++++++.+|++|+++|+|
T Consensus       254 ~~~~~~~~~~~~~~~~~~~~--~~k~~r~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~r~~il~~g~R  331 (726)
T 4aid_A          254 AIKAKMKDLVGADIAAAYKI--QKKQDRYEAVGAAKKKAIAALGLSDENPTGYDPLKLGAIFKELEADVVRRGILDTGLR  331 (726)
T ss_dssp             HHHHHHHHHHHHHHHHHHHC--CSHHHHHHHHHHHHHHHHTTTTCCTTSSCCCCSSSHHHHHHHHHHHHHHHHHHSSSBC
T ss_pred             HHHHHHHHHHHHHHHHHHhc--cchHHHHHHHHHHHHHHHHHhhhhccccccccHHHHHHHHHHHHHHHHHHHHhcCCCC
Confidence            99999999999999999987  59999999999999999999965431 1  2456899999999999999999999999


Q ss_pred             CCCCCCCCccCeEEEeCCCCCCCcceEEEeCCeEEEEEEEeCCCchhhhccccCCCCceeEEEEEecCCCCccccccccC
Q 002054          371 VDGRQLDEVRPIYCESGNLPILHGSSLFSRGDTQVLCTVTLGAPAEAQRLESLVGPPTKRFMLHYSFPPFCINEVGKRVG  450 (974)
Q Consensus       371 ~DGR~~~e~R~I~ie~g~l~~a~GSal~~~G~T~Vl~~Vtl~~p~~~~~~d~~~~~~~~~~~v~~~f~p~s~~e~~~~~~  450 (974)
                      +|||.++|+|||+|++|+++++||||+|++|+|||||+|++|...+.++.|.+.+++.++|++||+|||||++++++.++
T Consensus       332 ~DGR~~~elRpI~ie~gvl~~a~GSAl~~~G~TkVl~~Vt~Gp~~~~~~~d~l~~~~~g~~~~~y~~~P~st~er~~~g~  411 (726)
T 4aid_A          332 IDGRDVKTVRPILGEVGILPRTHGSALFTRGETQAIVVATLGTGDDEQFIDALEGTYKESFLLHYNFPPYSVGETGRMGS  411 (726)
T ss_dssp             TTSCBTTCCCCEEEEECSSTTSSEEEEEEETTEEEEEEEEEECGGGSEEEEETTEEEEECEEEEEECCGGGGTCCCCCSS
T ss_pred             CCCCCCCCccceEEEECCCCCCCceEEEEeCCeEEEEEEEeCCCCcccccccccCCCceEEEEEEEeCCCcccccccCCC
Confidence            99999999999999999999999999999999999999988754455666667667889999999999999999999999


Q ss_pred             CCchhhhHHHHHHHHhhhcCCCCCCCCeEEEEEEEEEcCCCChhhHHHHHHHHHHHHcCCCccccccceeeeeeccCCCC
Q 002054          451 LNRREVGHGTLAEKALLAVLPPENDFPYTVRVNSEVMASDGSTSMATVCGGSMALMDAGIPLQEHVAGVSVGLVSEVDPS  530 (974)
Q Consensus       451 ~~rre~~~~~l~eral~~vi~~~~~~p~tI~V~v~VLesdGs~~~A~v~aa~lAL~dagvPi~~~vagvs~gli~~~d~~  530 (974)
                      +++||++|++|++|+|++++|..+.|||+|+|+++||++|||++|||+||+++||+||||||+++|+||+||++++++  
T Consensus       412 ~~~Reie~~~li~raL~~vI~~~~~~P~tI~V~~~VLesDGs~~~AsI~aa~lAL~DAGIPm~~~VaavsvGli~~g~--  489 (726)
T 4aid_A          412 PGRREIGHGKLAWRALRPMLPTKEDFPYTIRLVSEITESNGSSSMATVCGSSLAMMDAGVPLVRPVSGIAMGLILEQD--  489 (726)
T ss_dssp             CCHHHHHHHHHHHHHHGGGSCCTTTCCCEEEEEEEEEECSSCHHHHHHHHHHHHHHHTTCCCSSCCEEEEEEEEECSS--
T ss_pred             cchhhHHHHHHHHHHHHHhcCccccCCeEEEEEEEEEEcCCcHHHHHHHHHHHHHHhcCCccccCeeEEEEEEEcCCC--
Confidence            999999999999999999999668999999999999999999999999999999999999999999999999998643  


Q ss_pred             CCcccceEEEecCCccccccCCccEEEEeeCCceEEEEeeccCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCCCC
Q 002054          531 TGEIKDYRILTDILGLEDHLGDMDFKIAGTRIGVTAIQLDIKPAGIPLDIICECLEHAHKGRLQILDHMEREISAPRTQD  610 (974)
Q Consensus       531 ~~~~~~~~iL~Dp~~~Ee~~~d~d~~Va~t~~gI~alq~~~k~~~i~~e~l~~al~~A~~~~~~I~~~m~~~i~~~~~~~  610 (974)
                           ++.+|+||++.||++++|||+|++|.+|||++|++++.++++.++|.+||++|+++|.+|++.|+++|.++|.++
T Consensus       490 -----~~~iLlD~~~~Ed~~gd~d~~Va~t~~gIt~lQ~d~k~~~~s~e~l~~aL~~A~~g~~~I~~~m~~al~~~r~~~  564 (726)
T 4aid_A          490 -----GFAVLSDILGDEDHLGDMDFKVAGTSEGLTSLQMDIKIAGITPAIMEQALAQAKEGRAHILGEMNKAMDAPRADV  564 (726)
T ss_dssp             -----CEEEEESCCTTGGGGSSEEEEEEEETTEEEEEEEEECSSCCCHHHHHHHHHHHHHHHHHHHHHHHTTCSSCCSSC
T ss_pred             -----ceEEEecCChhHHhcCCceEEEEecCCceEEEEecCCcCCcCHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhhhh
Confidence                 678999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             CCCCCcceeeeeccchhhhhcCCCccchhhhhhhhCceEEee-CCEEEEEecCHHHHHHHHHHHHHHhhcccccCcEEEE
Q 002054          611 DRNSPRLATLKYDNDTLRRLIGPLGALKRKIEEETGGRISVS-DGTLTVVAKNRSVMEKVLEKVDFIIGREIEVGGIYKG  689 (974)
Q Consensus       611 ~~~~p~~~~~~i~~~ki~~vIg~gGk~i~~i~~~~g~~Idi~-dg~v~i~~~~~~~~~~a~~~i~~l~~~~~~~G~i~~G  689 (974)
                      ++|||++.+++|||+||+++||||||+||+|+++||++|||+ +|+|+|++.+++.+++|+++++.++ .++++|++|+|
T Consensus       565 ~~~ap~~~~~~i~~~ki~~vig~gg~~i~~i~~~tg~~idi~ddG~v~I~~~~~~~~~~A~~~i~~i~-~~~~vG~v~~G  643 (726)
T 4aid_A          565 GDFAPKIETINIPTDKIREVIGSGGKVIREIVATTGAKVDINDDGVVKVSASDGAKIKAAIDWIKSIT-DEAEVGKIYDG  643 (726)
T ss_dssp             CSSCCC-------------------------------------------CCSCHHHHHHHHHC-----------------
T ss_pred             cccCCeEEEEeCCHHHHHhhcCCCchhHHHHHHHHCCceeEECCceEEEEeCCHHHHHHHHHHHHHHh-hhhcCCcEEEE
Confidence            999999999999999999999999999999999999999997 8999999999999999999999988 68999999999


Q ss_pred             EEEEEeeceEEEEEcCCeEEEEecccCCCccccccccccccCCEEEEEEEEEccCCceEEEEeccCCCccccc
Q 002054          690 VVTSVKEYGAFVEFNGGQQGLLHVSELSHEPVSRVSDVVSVGQQLSLRCIGQDVRGNIKLSLKAVSPRPEADV  762 (974)
Q Consensus       690 ~V~~i~~~G~fV~l~~g~~Glvhisels~~~v~~~~~~~~vGd~V~vkVl~id~~gri~LS~K~~~~~~~~~~  762 (974)
                      +|++|.+||+||+|.++.+||||+||++++++.++.++|++||.|+|||+++|.+|||.||+|++.++||...
T Consensus       644 ~V~~I~~fGaFVel~~g~eGLvHiSels~~rv~~~~d~~kvGD~V~VkVi~iD~~grI~LS~K~~~~~~G~~~  716 (726)
T 4aid_A          644 KVVKVVDFGAFVNFFGAKDGLVHVSQISNERVAKPSDVLKEGQMVKVKLLGFDDRGKTKLSMKVVDQETGEDL  716 (726)
T ss_dssp             -------------------------------------------------------------------------
T ss_pred             EEEEEeccEEEEEECCCcEEEEEHHHcCcccccCccccCCCCCEEEEEEEEECCCCcEEEEEeecccCcchhh
Confidence            9999999999999999999999999999999999999999999999999999999999999999999888764

>3cdi_A Polynucleotide phosphorylase; mRNA turnover, RNAse, RNA degradation, kinase, transferase; 2.60A {Escherichia coli} PDB: 1sro_A

Probab=100.00  E-value=1.5e-152  Score=1375.30  Aligned_cols=698  Identities=42%  Similarity=0.720  Sum_probs=495.3

Q ss_pred             ccceeeeeeEEECCeEEEEEeCccCcCCCcEEEEEeCCeEEEEEEEeCCCC-CCCCceeeEeeccccccccCCCCCcccc
Q 002054           54 KVLETFKEEFEIGSRLITLETGKIARFANGAVVLGMDETKVLSTVTSSKGD-SVRDFLPLTVDYQEKQFAQGVIPNTYMR  132 (974)
Q Consensus        54 ~~~~~~~~~~~~~~r~i~~etg~~a~~A~GSa~v~~G~T~Vl~tv~~~~~~-~~~~f~pL~v~y~e~~~a~g~ip~~~~~  132 (974)
                      .||+..+.++++|||++++|||++|+||||||++++|||+|||||+++.+| ++.+|+||+|+|+|++||+|||||||+|
T Consensus         6 ~~~~~~~~~~~~~~r~i~ietg~ia~qA~GSv~v~~G~T~Vl~tv~~~~~~~~~~~f~pltv~y~ek~~a~g~ipg~f~k   85 (723)
T 3cdi_A            6 TLLNPIVRKFQYGQHTVTLETGMMARQATAAVMVSMDDTAVFVTVVGQKKAKPGQDFFPLTVNYQERTYAAGRIPGSFFR   85 (723)
T ss_dssp             --CCCEEEEEEETTEEEEEEESSSCTTSSEEEEEEETTEEEEEEEEECSSCCSSCCSCCEEEEEEECGGGGTCCCC----
T ss_pred             cccceEEEEEEECCEEEEEEeCccccCCCeeEEEEECCEEEEEEEEecCCCCCCCCeeeEEEEEeEeccccccCCCcccc
Confidence            356777889999999999999999999999999999999999999999874 6789999999999999999999999999


Q ss_pred             ccCCCCchhhhHHHhhcCCccccccCCCCCceEEEEEEEeccCCCChhhHHHHHHHHHhhcCCCCCCCCeEEEEEEEECC
Q 002054          133 REGAPKERELLVGRIIDRPIRPLFPAGFYHEVQVMASVLSSDGKQDPDIMAANATSAALMLSDIPWGGPIGMIRIGRICG  212 (974)
Q Consensus       133 Reg~p~~~eil~~RlidR~lrplfp~~~~~~~~i~~~vl~~dg~~~~~~~ai~aAs~AL~~s~iP~~~~v~av~vg~i~g  212 (974)
                      |||+|+++|+|++|||||+|||+||++|++++||+|+||++||+++|+++||||||+||++|+|||++||+|||||++||
T Consensus        86 ReGrpse~e~l~sRlIdR~lRplfp~~~~~~vqv~~~vls~Dg~~~~d~~ai~aAsaAL~~s~iP~~~pv~av~vg~i~g  165 (723)
T 3cdi_A           86 REGRPSEGETLIARLIDRPIRPLFPEGFVNEVQVIATVVSVNPQVNPDIVAMIGASAALSLSGIPFNGPIGAARVGYIND  165 (723)
T ss_dssp             ---CCCHHHHHHHHHHHHHHGGGSCTTCCSCEEEEEEEEECCTTSCHHHHHHHHHHHHHHHHTSSCCCCCCCEEEEEETT
T ss_pred             CCCCCChHHhHHHHHhCccchhcccccCcceEEEEEEEEEcCCCCCHHHHHHHHHHHHHHhcCCCCCCCeEEEEEEEECC
Confidence            99999999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             EEEEcCCHHHHhcCccceeEeeeCCeEEEEEecCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCccccccccCCC
Q 002054          213 QFIVNPTMDELSLSDLNLVYACTREKTLMIDVQAREISEKDLEAGLRLAHPEAVKYLEPQIRLAEKAGKQKKEYKLSMIS  292 (974)
Q Consensus       213 ~~vldPt~~e~~~s~~~l~v~~t~~~i~mie~~~~~~~e~~~~~al~~a~~~~~~i~~~~~~~~~~~g~~k~~~~~~~~~  292 (974)
                      ++|+|||++|++.|++||+|+|++++++|+|+++++|||++|.+||++||+++++++++|+++++++||+|++|.....+
T Consensus       166 ~~v~nPt~~e~~~s~~~lvvagt~~~i~mve~~~~~~se~~~~~al~~a~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~  245 (723)
T 3cdi_A          166 QYVLNPTQDELKESKLDLVVAGTEAAVLMVESEAQLLSEDQMLGAVVFGHEQQQVVIQNINELVKEAGKPRWDWQPEPVN  245 (723)
T ss_dssp             EEEESCCTTGGGGCSEEEEEEECSSCEEEEEEEEEEECHHHHHHHHHHHHHHTHHHHHHHHHHHHHTCCCCCCCCCCCCC
T ss_pred             EEEECcCHHHHHhCCceEEEEccCCEEEEEeCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCcccCCCCCCC
Confidence            99999999999999999999999999999999999999999999999999999999999999999999999999888888


Q ss_pred             HHHHHHHHHHHHHHHHhhhcCCCCChhHHHHHHHHHHHHHHHHhhhccchhhhchHHHHHHHHHHHHHHHHHHhcCCcCC
Q 002054          293 EQTLEKVSNLAEAHIEAVFTDPSYSKFERGEALDKIGQDVKKALEEECDEESLQVLPKAVDTVRKRVIRKRIIAEGVRVD  372 (974)
Q Consensus       293 ~~~~~~~~~~~~~~~~~~~~~~~~~k~~r~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~r~~il~~~~R~D  372 (974)
                      +++.+++++++.++|++++..  ++|++|+++++++++++.++|.++..+....++..+|++++++.+|++++++|+|+|
T Consensus       246 ~~~~~~~~~~~~~~~~~~~~~--~~k~~r~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~k~~vr~~i~~~g~R~D  323 (723)
T 3cdi_A          246 EALNARVAALAEARLSDAYRI--TDKQERYAQVDVIKSETIATLLAEDETLDENELGEILHAIEKNVVRSRVLAGEPRID  323 (723)
T ss_dssp             TTGGGSSTTTTHHHHHHHTTC--CCHHHHHHHHHHHHHHHHHHHHHHSCCCCHHHHHHHHHHHHHHHHHHHHHTTCCCTT
T ss_pred             HHHHHHHHHHHHHHHHHHHhc--cchHHHHHHHHHHHHHHHHHhhhhcccccHHHHHHHHHHHHHHHHHHHHhccCcCCC
Confidence            999999999999999999987  599999999999999999999544222234579999999999999999999999999


Q ss_pred             CCCCCCccCeEEEeCCCCCCCcceEEEeCCeEEEEEEEeCCCchhhhccccCCCCceeEEEEEecCCCCccccccccCCC
Q 002054          373 GRQLDEVRPIYCESGNLPILHGSSLFSRGDTQVLCTVTLGAPAEAQRLESLVGPPTKRFMLHYSFPPFCINEVGKRVGLN  452 (974)
Q Consensus       373 GR~~~e~R~I~ie~g~l~~a~GSal~~~G~T~Vl~~Vtl~~p~~~~~~d~~~~~~~~~~~v~~~f~p~s~~e~~~~~~~~  452 (974)
                      ||.++|+|||+|++|++|++||||+|++|+|||||+|++|...+.|..+.+.+++.++|++||+|||||+++++|.++++
T Consensus       324 GR~~~elRpI~ie~gvl~~a~GSAl~~~G~TqVL~~Vt~gp~e~~~~~d~l~~~~~g~~~~~y~~~P~st~e~~r~g~p~  403 (723)
T 3cdi_A          324 GREKDMIRGLDVRTGVLPRTHGSALFTRGETQALVTATLGTARDAQVLDELMGERTDTFLFHYNFPPYSVGETGMVGSPK  403 (723)
T ss_dssp             SCCTTCCCCEEEEESCSTTSSEEEEEEETTEEEEEEEEECC-------------CTTSEEEEEECCGGGGTCCCCC----
T ss_pred             CCCccccccceEEeCCCCCCCeEEEEEECCcEEEEEEEecCcccccCCcccCCCCceEEEEEEecCCCCccccccCCCCC
Confidence            99999999999999999999999999999999999998875444556666666788999999999999999999999999


Q ss_pred             chhhhHHHHHHHHhhhcCCCCCCCCeEEEEEEEEEcCCCChhhHHHHHHHHHHHHcCCCccccccceeeeeeccCCCCCC
Q 002054          453 RREVGHGTLAEKALLAVLPPENDFPYTVRVNSEVMASDGSTSMATVCGGSMALMDAGIPLQEHVAGVSVGLVSEVDPSTG  532 (974)
Q Consensus       453 rre~~~~~l~eral~~vi~~~~~~p~tI~V~v~VLesdGs~~~A~v~aa~lAL~dagvPi~~~vagvs~gli~~~d~~~~  532 (974)
                      +||++|+++++|+|++++|+++.|||+|+|+++||++|||++|||+||+++||+||||||+++|+|++||++++++    
T Consensus       404 ~REi~~~~li~raL~~vI~~~~~~p~tI~Vd~~VLesdGs~~~Asi~aa~lAL~dAgVPl~~~vaavs~gli~~g~----  479 (723)
T 3cdi_A          404 RREIGHGRLAKRGVLAVMPDMDKFPYTVRVVSEITESNGSSSMASVCGASLALMDAGVPIKAAVAGIAMGLVKEGD----  479 (723)
T ss_dssp             -CTTHHHHHHHHHHHTTSCCSSSSCSCEEEEEEEEECSSCHHHHHHHHHHHHHHHTTCCCSSCCEEEEEEEEEETT----
T ss_pred             HHHHHHHHHHHHHHHHhcCcccCCCEEEEEEEEEEeCCCCHHHHHHHHHHHHHhcCCCCcccceeeEEEEEEcCCC----
Confidence            9999999999999999999878999999999999999999999999999999999999999999999999997532    


Q ss_pred             cccceEEEecCCccccccCCccEEEEeeCCceEEEEeeccCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCCCCCC
Q 002054          533 EIKDYRILTDILGLEDHLGDMDFKIAGTRIGVTAIQLDIKPAGIPLDIICECLEHAHKGRLQILDHMEREISAPRTQDDR  612 (974)
Q Consensus       533 ~~~~~~iL~Dp~~~Ee~~~d~d~~Va~t~~gI~alq~~~k~~~i~~e~l~~al~~A~~~~~~I~~~m~~~i~~~~~~~~~  612 (974)
                         +|.+|+||++.||++++|+|+|++|.+|||++|++++.++++.++|.+||++|++++.+|++.|+++|.+++.++++
T Consensus       480 ---~~~iL~Dp~~~Ed~~~d~d~~Va~t~~gI~~lq~~gk~~~is~e~l~~~l~~A~~~~~~I~~~m~~al~~~~~~~~~  556 (723)
T 3cdi_A          480 ---NYVVLSDILGDEDHLGDMDFKVAGSRDGISALQMDIKIEGITKEIMQVALNQAKGARLHILGVMEQAINAPRGDISE  556 (723)
T ss_dssp             ---EEEEESSCCGGGGGGCSEEEEEEECSSCEEEEEEEECSSCCCHHHHHHHHHHHHHHHHHHHHHHHHHCC--------
T ss_pred             ---ceEEEECCChHHhhhccceeeecccCCceEEEEeCCccCCcCHHHHHHHHHHHHHHHHHHHHHHHHHhhhcchhccc
Confidence               57899999999999999999999999999999999998999999999999999999999999999999999999999


Q ss_pred             CCCcceeeeeccchhhhhcCCCccchhhhhhhhCceEEee-CCEEEEEecCHHHHHHHHHHHHHHhhcccccCcEEEEEE
Q 002054          613 NSPRLATLKYDNDTLRRLIGPLGALKRKIEEETGGRISVS-DGTLTVVAKNRSVMEKVLEKVDFIIGREIEVGGIYKGVV  691 (974)
Q Consensus       613 ~~p~~~~~~i~~~ki~~vIg~gGk~i~~i~~~~g~~Idi~-dg~v~i~~~~~~~~~~a~~~i~~l~~~~~~~G~i~~G~V  691 (974)
                      |||++.+++|||+||+++|||||++|++|+++||+.|||+ +|.+.|++.+.+.+++|.++++.+. .++++|++|+|+|
T Consensus       557 ~ap~~~~~~i~~~ki~~~ig~gGk~I~~I~~~~G~~IdI~~dg~v~I~~~~~~~~~~a~~~i~~i~-~~~~vG~i~~G~V  635 (723)
T 3cdi_A          557 FAPRIHTIKINPDKIKDVIGKGGSVIRALTEETGTTIEIEDDGTVKIAATDGEKAKHAIRRIEEIT-AEIEVGRVYTGKV  635 (723)
T ss_dssp             --------------------------------------------------------------------------------
T ss_pred             cCceEEEEEECHHHhcccccccceeeeeeehhhCceEEecCCccEEEecCCHHHHHHHHHHHHHHh-hhhhcCcEEEEEE
Confidence            9999999999999999999999999999999999999997 8999999999999999999998887 6899999999999


Q ss_pred             EEEeeceEEEEEcCCeEEEEecccCCCccccccccccccCCEEEEEEEEEccCCceEEEEeccCCCcccc
Q 002054          692 TSVKEYGAFVEFNGGQQGLLHVSELSHEPVSRVSDVVSVGQQLSLRCIGQDVRGNIKLSLKAVSPRPEAD  761 (974)
Q Consensus       692 ~~i~~~G~fV~l~~g~~Glvhisels~~~v~~~~~~~~vGd~V~vkVl~id~~gri~LS~K~~~~~~~~~  761 (974)
                      ++|.+||+||+|.+|.+||||+|+++++++++++++|++||.|+|||+++|.+|||.||+|++.++||..
T Consensus       636 ~~i~~fGaFVel~~g~eGLvHiSel~~~~v~~~~~~~~vGd~V~VkVi~vd~~grI~LS~k~~~~~~g~~  705 (723)
T 3cdi_A          636 TRIVDFGAFVAIGGGKEGLVHISQIADKRVEKVTDYLQMGQEVPVKVLEVDRQGRIRLSIKEATEQSQPA  705 (723)
T ss_dssp             ----------------------------------------------------------------------
T ss_pred             EEEecceEEEEeCCCceEEEEHHHcCCccccCcccccCCCCEEEEEEEEECCCCcEEEEEEeccCCCCcc
Confidence            9999999999999999999999999999999999999999999999999998999999999998888765

>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=100.00  E-value=3.6e-151  Score=1366.79  Aligned_cols=697  Identities=37%  Similarity=0.613  Sum_probs=587.0

Q ss_pred             eeeeeEEECCeEEEEEeCccCcCCCcEEEEEe-CCeEEEEEEEeCCC-CCCCCceeeEeeccccccccCCCCCccccccC
Q 002054           58 TFKEEFEIGSRLITLETGKIARFANGAVVLGM-DETKVLSTVTSSKG-DSVRDFLPLTVDYQEKQFAQGVIPNTYMRREG  135 (974)
Q Consensus        58 ~~~~~~~~~~r~i~~etg~~a~~A~GSa~v~~-G~T~Vl~tv~~~~~-~~~~~f~pL~v~y~e~~~a~g~ip~~~~~Reg  135 (974)
                      .++.++++|||++++|||++|+||+|||++++ |+|+|||||+++++ +++.||+||+|+|+||+||+|||||+|+||||
T Consensus        27 ~~~~~~~~~~r~i~~etg~la~qA~GSv~v~~~G~T~Vl~tv~~~~~~~~~~df~pLtv~y~ek~~a~g~iPg~f~~REG  106 (757)
T 1e3p_A           27 AVIDNGAFGTRTIRFETGRLARQAAGSAVAYLDDDTMVLSATTASKNPKDQLDFFPLTVDVEERMYAAGKIPGSFFRREG  106 (757)
T ss_dssp             EEEECGGGCEEEEEEEESSSCTTSSEEEEEEETTTEEEEEEEEEEEEECTTCSSCCEEEEEEECGGGGTCCCCSTTSSCC
T ss_pred             eEEEEEEECCEeEEEEECccccCCCeEEEEEECCCeEEEEEEEecCCCCCCCCCccEEEEEEecccccccCCCcccccCc
Confidence            44667888999999999999999999999999 99999999999988 57789999999999999999999999999999


Q ss_pred             CCCchhhhHHHhhcCCccccccCCCCCceEEEEEEEeccCCCChhhHHHHHHHHHhhcCCCCCCCCeEEEEEEEECCEEE
Q 002054          136 APKERELLVGRIIDRPIRPLFPAGFYHEVQVMASVLSSDGKQDPDIMAANATSAALMLSDIPWGGPIGMIRIGRICGQFI  215 (974)
Q Consensus       136 ~p~~~eil~~RlidR~lrplfp~~~~~~~~i~~~vl~~dg~~~~~~~ai~aAs~AL~~s~iP~~~~v~av~vg~i~g~~v  215 (974)
                      +|+++|+|++|||||+|||+||++|++++||+|+||++||+++|+++||||||+||++|+|||++||+|||||++||++|
T Consensus       107 rps~~e~l~~RlIdR~LRplfp~~~~~evqv~~~Vls~D~~~~~~~~ai~gAs~AL~~s~iP~~~~vaav~vg~~~g~~v  186 (757)
T 1e3p_A          107 RPSEDAILTCRLIDRPLRPSFKKGLRNEIQVVATIMALNPDHLYDVVAINAASASTQLAGLPFSGPIGGVRVALIRGQWV  186 (757)
T ss_dssp             SCCHHHHHHHHHHHHHHGGGBCTTBCEEEEEEEEEEECCTTSCCHHHHHHHHHHHHHHTTSSBCCCCEEEEEEEETTEEE
T ss_pred             CCChHHHHHHHHHCCcchhccccCCCCceEEEEEEEEECCCCCHHHHHHHHHHHHHhccCCCCCCceEEEEEEEECCEEE
Confidence            99999999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             EcCCHHHHhcCccceeEeee-----CCeEEEEEe------------cCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 002054          216 VNPTMDELSLSDLNLVYACT-----REKTLMIDV------------QAREISEKDLEAGLRLAHPEAVKYLEPQIRLAEK  278 (974)
Q Consensus       216 ldPt~~e~~~s~~~l~v~~t-----~~~i~mie~------------~~~~~~e~~~~~al~~a~~~~~~i~~~~~~~~~~  278 (974)
                      +|||++|++.|++||+|+||     +++++|||+            ++++|||++|.+||++||++|++++++|++++++
T Consensus       187 lnPt~~e~~~s~~dl~va~t~~~~~~~~i~mvE~q~t~~~~~~~~~~~~~~se~~l~~al~~a~~~i~~l~~~q~~~~~~  266 (757)
T 1e3p_A          187 AFPTHTELEDAVFDMVVAGRVLEDGDVAIMMVEAEATEKTIQLVKDGAEAPTEEVVAAGLDAAKPFIKVLCKAQADLAAK  266 (757)
T ss_dssp             ESCCHHHHTTEEEEEEEEEEECTTSCEEEEEEEEEECSSHHHHHHTTCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             ECCCHHHHhcCceeEEEEeccccCCCCcEEEEEEecccccccccccccCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence            99999999999999999999     677999999            7889999999999999999999999999999999


Q ss_pred             hCCccccccc-cCCCHHHHHHHHHHHHHHHHhhhcCCCCChhHHHHHHHHHHHHHHHHhhhccchhhhchHHHHHHHHHH
Q 002054          279 AGKQKKEYKL-SMISEQTLEKVSNLAEAHIEAVFTDPSYSKFERGEALDKIGQDVKKALEEECDEESLQVLPKAVDTVRK  357 (974)
Q Consensus       279 ~g~~k~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~k~~r~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  357 (974)
                      +||+|++|.. ...++++.+++++++.++|++++..  ++|++|+++++++++++.++|.+++. ....++..+|+++++
T Consensus       267 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~--~~k~~r~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~~k  343 (757)
T 1e3p_A          267 AAKPTGEFPVFLDYQDDVLEALSAAVRPELSAALTI--AGKQDREAELDRVKALAAEKLLPEFE-GREKEISAAYRALTK  343 (757)
T ss_dssp             HCCCCCCCCBCCSCCHHHHHHHHHHHHHHHHHHTTC--CSHHHHHHHHHHHHHHHHTTSTTTTC-SCHHHHHHHHHHHHH
T ss_pred             cCCCCccCCCCCCCCHHHHHHHHHHHHHHHHHHHhc--cchHHHHHHHHHHHHHHHHHhhhhcc-ccHHHHHHHHHHHHH
Confidence            9999999987 6788999999999999999999986  59999999999999999999854322 234579999999999


Q ss_pred             HHHHHHHHhcCCcCCCCCCCCccCeEEEeCCCCCCCcceEEEeCCeEEEEEEEeCCCchhhhccccCCCCceeEEEEEec
Q 002054          358 RVIRKRIIAEGVRVDGRQLDEVRPIYCESGNLPILHGSSLFSRGDTQVLCTVTLGAPAEAQRLESLVGPPTKRFMLHYSF  437 (974)
Q Consensus       358 ~~~r~~il~~~~R~DGR~~~e~R~I~ie~g~l~~a~GSal~~~G~T~Vl~~Vtl~~p~~~~~~d~~~~~~~~~~~v~~~f  437 (974)
                      +.+|++++++|+|+|||.++|+|||+|++|++|++||||+|++|+|||||+|++|...+.++.+.+.+++.++|++||+|
T Consensus       344 ~~~r~~i~~~g~R~DGR~~~elRpI~ie~gvl~~a~GSAl~~~G~TqVL~~Vt~Gp~~~~~~~d~l~~~~~g~~~~~y~f  423 (757)
T 1e3p_A          344 SLVRERVIAEKKRIDGRGVTDIRTLAAEVEAIPRVHGSALFERGETQILGVTTLNMLRMEQQLDTLSPVTRKRYMHNYNF  423 (757)
T ss_dssp             HHHHHHHHHTCBCTTSCBTTCCCCEEEEECCSSSSSEEEEEEETTEEEEEEEEEEEGGGSEECCSSSSCCEESEEEEEEC
T ss_pred             HHHHHHHhcCCCCCCCCCcccccceeEEeCCCCCCCEEEEEEECCcEEEEEEEecCCCccccccccCCCCceEEEEEEEe
Confidence            99999999999999999999999999999999999999999999999999999875555666677777889999999999


Q ss_pred             CCCCccccccccCCCchhhhHHHHHHHHhhhcCCCCCCCCeEEEEEEEEEcCCCChhhHHHHHHHHHHHHcCCCcccccc
Q 002054          438 PPFCINEVGKRVGLNRREVGHGTLAEKALLAVLPPENDFPYTVRVNSEVMASDGSTSMATVCGGSMALMDAGIPLQEHVA  517 (974)
Q Consensus       438 ~p~s~~e~~~~~~~~rre~~~~~l~eral~~vi~~~~~~p~tI~V~v~VLesdGs~~~A~v~aa~lAL~dagvPi~~~va  517 (974)
                      ||||++++++.+++++||++|+++++|+|++++|..++|||+|+|+++||++|||++|||+||+++|||||||||+++++
T Consensus       424 ~P~st~e~~~~g~~~~reie~~~li~raL~~vI~~~~~~P~tI~V~~~VLesDGs~~~Asi~aa~lAL~dAgIP~k~~Va  503 (757)
T 1e3p_A          424 PPYSVGETGRVGSPKRREIGHGALAERAIVPVLPTREEFPYAIRQVSEALGSNGSTSMGSVCASTMSLLNAGVPLKAPVA  503 (757)
T ss_dssp             CGGGGTCCCCCSSCCHHHHHHHHHHHHHHGGGCCCTTTSCEEEEEEEEEEECSSCHHHHHHHHHHHHHHHHTCCCSSCCE
T ss_pred             CCcccccccCCCCCchhHHHHHHHHHHHHHHhccccccCCEEEEEEEEEEECCCCHHHHHHHHHHHHHHHcCCCcccceE
Confidence            99999999989999999999999999999999996689999999999999999999999999999999999999999999


Q ss_pred             ceeeeeeccC-CCCCCcccceEEEecCCccccccCCccEEEEeeCCceEEEEeeccCCCCCHHHHHHHHHHHHHHHHHHH
Q 002054          518 GVSVGLVSEV-DPSTGEIKDYRILTDILGLEDHLGDMDFKIAGTRIGVTAIQLDIKPAGIPLDIICECLEHAHKGRLQIL  596 (974)
Q Consensus       518 gvs~gli~~~-d~~~~~~~~~~iL~Dp~~~Ee~~~d~d~~Va~t~~gI~alq~~~k~~~i~~e~l~~al~~A~~~~~~I~  596 (974)
                      |++||+++++ |.    ..+|.+|+||++.||++++|+|+|++|.++||++|++++.++++.++|.+||++|++++.+|+
T Consensus       504 avs~gli~eg~dg----~~~~~iLlDp~~~Ed~~gd~d~~Va~t~~~It~lQ~~gk~~gi~~e~l~~aL~~A~~~~~~I~  579 (757)
T 1e3p_A          504 GIAMGLISQEING----ETHYVALTDILGAEDAFGDMDFKVAGTKEFVTALQLDTKLDGIPASVLAAALKQARDARLHIL  579 (757)
T ss_dssp             EEEEEEEEEESSS----CEEEEEEESCCHHHHHHCSEEEEEEECSSSEEEEEEEECSSCCCHHHHHHHHHHHHHHHHHHH
T ss_pred             EEEEEEEecCCCC----ccceeEEeCCCHHHHhccCceEEEEecCCeEEEEEEcCCccccCHHHHHHHHHHHHHHHHHHH
Confidence            9999999653 21    025789999999999999999999999999999999999999999999999999999999999


Q ss_pred             HHHHHHhcCCCCCCCCCCCcceeeeeccchhhhhcCCCccchhhhhhhhCceEEee-CCEEEEEecCHHHHHHHHHHHHH
Q 002054          597 DHMEREISAPRTQDDRNSPRLATLKYDNDTLRRLIGPLGALKRKIEEETGGRISVS-DGTLTVVAKNRSVMEKVLEKVDF  675 (974)
Q Consensus       597 ~~m~~~i~~~~~~~~~~~p~~~~~~i~~~ki~~vIg~gGk~i~~i~~~~g~~Idi~-dg~v~i~~~~~~~~~~a~~~i~~  675 (974)
                      +.|+++|.++ .++++|||++.+++|||+||+++||+|||+||+|+++||+.|||+ +|.+.|+..+...+++|+++++.
T Consensus       580 ~~m~~al~~~-~~~~~~ap~~~~~~I~~~ki~~vIG~gGk~Ik~I~~~~G~~IdI~~dG~v~Is~~~~~~~~~a~~~i~~  658 (757)
T 1e3p_A          580 DVMMEAIDTP-DEMSPNAPRIITVKIPVDKIGEVIGPKRQMINQIQEDTGAEITIEDDGTIYIGAADGPAAEAARATING  658 (757)
T ss_dssp             HHHHHHCSSC-CCCCTTSCBCCCC------------------CTTCCCCCSCC--------CCCBSSHHHHCC-------
T ss_pred             HHHHHHhccc-ccccccCceeEEEEEChHHeehcccccceeeehhhHhhCCEEEecCCceEEEecCCHHHHHHHHHHHHH
Confidence            9999999999 999999999999999999999999999999999999999999998 89999999999999999888877


Q ss_pred             Hhh-cccccCcEEEEEEEEEeeceEEEEEcCCeEEEEecccC----CCccccccccccccCCEEEEEEEEEccCCceEEE
Q 002054          676 IIG-REIEVGGIYKGVVTSVKEYGAFVEFNGGQQGLLHVSEL----SHEPVSRVSDVVSVGQQLSLRCIGQDVRGNIKLS  750 (974)
Q Consensus       676 l~~-~~~~~G~i~~G~V~~i~~~G~fV~l~~g~~Glvhisel----s~~~v~~~~~~~~vGd~V~vkVl~id~~gri~LS  750 (974)
                      +.. .++++|++|+|+|++|.+||+||+|.+|.+||||+|++    +|+++++++++|++||.|+|||+++|.+|||.||
T Consensus       659 i~~p~~~~vG~i~~G~V~~i~~fGaFV~l~~g~eGLvHiSel~~~~s~~rv~~~~~~~~vGd~V~VkVi~vd~~grI~LS  738 (757)
T 1e3p_A          659 IANPTSPEVGERILGSVVKTTTFGAFVSLLPGKDGLLHISQIRKLAGGKRVENVEDVLGVGQKVQVEIAEIDSRGKLSLI  738 (757)
T ss_dssp             --------------CBEEECC-CSCEECCC---CCCCC-------------------CCSSCBCCCCCCCCCSSCC----
T ss_pred             hcchhhcccccEEEEEEEEccccEEEEEEcCCcEEEEEhHHhccccCCCcccCcccccCCCCEEEEEEEEECCCCCEEEE
Confidence            641 36899999999999999999999999999999999999    9999999999999999999999999999999999


Q ss_pred             EeccCCCccccc
Q 002054          751 LKAVSPRPEADV  762 (974)
Q Consensus       751 ~K~~~~~~~~~~  762 (974)
                      +|.+.++||...
T Consensus       739 ~k~~~~~pw~~~  750 (757)
T 1e3p_A          739 PVIEGEEAASDE  750 (757)
T ss_dssp             ------------
T ss_pred             EecCCCCchhhh
Confidence            999999999864

>3u1k_A Polyribonucleotide nucleotidyltransferase 1, MITO; RNAse PH, KH domain, exoribonuclease; HET: CIT; 2.13A {Homo sapiens}

Probab=100.00  E-value=2.2e-136  Score=1218.46  Aligned_cols=617  Identities=43%  Similarity=0.719  Sum_probs=575.2

Q ss_pred             eeeeEEECCeEEEEEeCccCcCCCcEEEEEeCCeEEEEEEEeCCCCCCCCceeeEeeccccccccCCCCCccccccCCCC
Q 002054           59 FKEEFEIGSRLITLETGKIARFANGAVVLGMDETKVLSTVTSSKGDSVRDFLPLTVDYQEKQFAQGVIPNTYMRREGAPK  138 (974)
Q Consensus        59 ~~~~~~~~~r~i~~etg~~a~~A~GSa~v~~G~T~Vl~tv~~~~~~~~~~f~pL~v~y~e~~~a~g~ip~~~~~Reg~p~  138 (974)
                      ...++++|||++++|||++++||||||++++|||+|||||+++++++..+|+||+|+|+|++||+|||||+|+||||+|+
T Consensus         6 ~~~~~~~~~R~i~ietG~~a~qA~GSa~v~~G~T~VL~tv~~~~~~~~~df~pL~v~y~~~~~a~g~iPg~f~kRegrps   85 (630)
T 3u1k_A            6 SAVAVDLGNRKLEISSGKLARFADGSAVVQSGDTAVMVTAVSKTKPSPSQFMPLVVDYRQKAAAAGRIPTNYLRREVGTS   85 (630)
T ss_dssp             EEEEEECSSSEEEEEESSSCTTSSEEEEEEETTEEEEEEEEECSSCCSSSSCCEEEEEECSEETTTTEECTTC-----CC
T ss_pred             eeEEEEECCEEEEEEeCCccccCCeeEEEEECCeEEEEEEEecCCCCCCCeeEEEEEEEecccccCCCCccccccCCCCC
Confidence            34677799999999999999999999999999999999999999833339999999999999999999999999999999


Q ss_pred             chhhhHHHhhcCCccccccCCCCCceEEEEEEEeccCCCChhhHHHHHHHHHhhcCCCCCCCCeEEEEEEEECCEEEEcC
Q 002054          139 ERELLVGRIIDRPIRPLFPAGFYHEVQVMASVLSSDGKQDPDIMAANATSAALMLSDIPWGGPIGMIRIGRICGQFIVNP  218 (974)
Q Consensus       139 ~~eil~~RlidR~lrplfp~~~~~~~~i~~~vl~~dg~~~~~~~ai~aAs~AL~~s~iP~~~~v~av~vg~i~g~~vldP  218 (974)
                      ++|+|+||||||+|||+||++|++++||+|+||++||+++|+++||||||+||++|+|||++||+|||||++||++|+||
T Consensus        86 ~~e~lisRlIdR~lRp~~~~~~~~~~qI~~~VLs~Dg~~~~~~aai~aAs~AL~~s~iP~~~~vaav~vg~i~g~~vldP  165 (630)
T 3u1k_A           86 DKEILTSRIIDRSIRPLFPAGYFYDTQVLCNLLAVDGVNEPDVLAINGASVALSLSDIPWNGPVGAVRIGIIDGEYVVNP  165 (630)
T ss_dssp             HHHHHHHHHHHHHHGGGSCTTCCCCEEEEEEEEECCSSSCHHHHHHHHHHHHHHHSSSCCCCCCEEEEEEEETTEEEESC
T ss_pred             HHHHHHHHHHhHHhhhcccccCCCceEEEEEEEECCCCCCHHHHHHHHHHHHHhccCCCcCCCeEEEEEEEECCEEEECC
Confidence            99999999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             CHHHHhcCccceeEeeeCCe-EEEEEecCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCccccccccC-CCHHHH
Q 002054          219 TMDELSLSDLNLVYACTREK-TLMIDVQAREISEKDLEAGLRLAHPEAVKYLEPQIRLAEKAGKQKKEYKLSM-ISEQTL  296 (974)
Q Consensus       219 t~~e~~~s~~~l~v~~t~~~-i~mie~~~~~~~e~~~~~al~~a~~~~~~i~~~~~~~~~~~g~~k~~~~~~~-~~~~~~  296 (974)
                      |++|++.|++||+|++++++ |+|+|++++++|+++|.+||++||+++++++++|+++++++||+|++|.... .++++.
T Consensus       166 t~~E~~~s~~dl~Va~t~~~~i~mve~~~~~~se~~~~~al~~a~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  245 (630)
T 3u1k_A          166 TRKEMSSSTLNLVVAGAPKSQIVMLEASAENILQQDFCHAIKVGVKYTQQIIQGIQQLVKETGVTKRTPQKLFTPSPEIV  245 (630)
T ss_dssp             CHHHHHTEEEEEEEEEETTTEEEEEEEEEEEECHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTCCCCCCSCCCCCCHHHH
T ss_pred             CHHHHhhCCceEEEEEccCCcEEEEECCCccCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCccCCCCCCCCHHHH
Confidence            99999999999999999865 9999999999999999999999999999999999999999999999996544 789999


Q ss_pred             HHHHHHHHHHHHhhhcCCCCChhHHHHHHHHHHHHHHHHhhhccchhhhchHHHHHHHHHHHHHHHHHHhcCCcCCCCCC
Q 002054          297 EKVSNLAEAHIEAVFTDPSYSKFERGEALDKIGQDVKKALEEECDEESLQVLPKAVDTVRKRVIRKRIIAEGVRVDGRQL  376 (974)
Q Consensus       297 ~~~~~~~~~~~~~~~~~~~~~k~~r~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~r~~il~~~~R~DGR~~  376 (974)
                      +++++++.++|++++.+..++|++|+++++++++++.++|.++.++....++..+|++++++.+|++|+++|+|+|||.+
T Consensus       246 ~~~~~~~~~~~~~~~~~~~~~k~~r~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~r~~il~~g~R~DGR~~  325 (630)
T 3u1k_A          246 KYTHKLAMERLYAVFTDYEHDKVSRDEAVNKIRLDTEEQLKEKFPEADPYEIIESFNVVAKEVFRSIVLNEYKRCDGRDL  325 (630)
T ss_dssp             HHHHHHHHHHHHHHHTCTTCCHHHHHHHHHHHHHHHHHHHHHHCCSCCHHHHHHHHHHHHHHHHHHHHHHHSCCTTSCCT
T ss_pred             HHHHHHHHHHHHHHHhccCcchHHHHHHHHHHHHHHHHHhhhhcCcccHHHHHHHHHHHHHHHHHHHHhcCCCCCCCCCC
Confidence            99999999999999987557999999999999999999997654443456899999999999999999999999999999


Q ss_pred             CCccCeEEEeCCCCCCCcceEEEeCCeEEEEEEEeCCCchhhhcccc----CCCCceeEEEEEecCCCCccccccccCCC
Q 002054          377 DEVRPIYCESGNLPILHGSSLFSRGDTQVLCTVTLGAPAEAQRLESL----VGPPTKRFMLHYSFPPFCINEVGKRVGLN  452 (974)
Q Consensus       377 ~e~R~I~ie~g~l~~a~GSal~~~G~T~Vl~~Vtl~~p~~~~~~d~~----~~~~~~~~~v~~~f~p~s~~e~~~~~~~~  452 (974)
                      +|+|||+|++|+++++||||+|++|+|||||+|+++.+.+.|+.|.+    .+++.++|++||+|||||++++++.|+++
T Consensus       326 ~elRpi~i~~g~l~~a~GSal~~~G~T~Vl~~Vt~~~~~~~~~~d~~~~~l~~~~~g~~~~~y~~~P~st~e~~~~g~~~  405 (630)
T 3u1k_A          326 TSLRNVSCEVDMFKTLHGSALFQRGQTQVLCTVTFDSLESGIKSDQVITAINGIKDKNFMLHYEFPPYATNEIGKVTGLN  405 (630)
T ss_dssp             TCCCCEEEEECCSTTSSEEEEEEETTEEEEEEEEEECGGGGSCSSHHHHHHHCCCGGGEEEEEECCGGGGTCCCCCSSCC
T ss_pred             ccccceEEEECCCCCCCceEEEEECCeEEEEEEEcCCCCchhcccccccccCCCCceEEEEEEEecCCcccccccCCCCC
Confidence            99999999999999999999999999999999998766666666653    35788999999999999999999999999


Q ss_pred             chhhhHHHHHHHHhhhcCCCCCCCCeEEEEEEEEEcCCCChhhHHHHHHHHHHHHcCCCccccccceeeeeeccCCCCCC
Q 002054          453 RREVGHGTLAEKALLAVLPPENDFPYTVRVNSEVMASDGSTSMATVCGGSMALMDAGIPLQEHVAGVSVGLVSEVDPSTG  532 (974)
Q Consensus       453 rre~~~~~l~eral~~vi~~~~~~p~tI~V~v~VLesdGs~~~A~v~aa~lAL~dagvPi~~~vagvs~gli~~~d~~~~  532 (974)
                      +||++|++|++|+|++++|  .+|||+|+|+++||++|||++|||+||+++|||||||||+++|+|++||++++.+++.+
T Consensus       406 rREi~~~~Li~raLr~vi~--~~~p~tI~V~~~VLesDGs~~~AsI~aa~lAL~dAGIPl~~~Vaavs~gli~~~~~~~g  483 (630)
T 3u1k_A          406 RRELGHGALAEKALYPVIP--RDFPFTIRVTSEVLESNGSSSMASACGGSLALMDSGVPISSAVAGVAIGLVTKTDPEKG  483 (630)
T ss_dssp             HHHHHHHHHHHHHHGGGSC--TTCSSEEEEEEEEEECSSCHHHHHHHHHHHHHHHTTCCCSSCCEEEEEEEEEEECSSSS
T ss_pred             hHHHHHHHHHHHHHHhhCc--ccCCeEEEEEEEEEEcCCCHHHHHHHHHHHHHHhCCCCcccceEEEEEEEecCCCcccc
Confidence            9999999999999999999  47999999999999999999999999999999999999999999999999984222212


Q ss_pred             cccceEEEecCCccccccCCccEEEEeeCCceEEEEeeccCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCCCCCC
Q 002054          533 EIKDYRILTDILGLEDHLGDMDFKIAGTRIGVTAIQLDIKPAGIPLDIICECLEHAHKGRLQILDHMEREISAPRTQDDR  612 (974)
Q Consensus       533 ~~~~~~iL~Dp~~~Ee~~~d~d~~Va~t~~gI~alq~~~k~~~i~~e~l~~al~~A~~~~~~I~~~m~~~i~~~~~~~~~  612 (974)
                      +.++|.+|+||++.||++++|||+|++|.+|||++|++++..+++.++|.+||++|++++.+|++.|++++.+|+.++++
T Consensus       484 ~~~~~~iLlD~~~~Ed~~~d~d~~Va~t~~gIt~lQ~~~k~~~~s~~~l~~aL~~A~~g~~~I~~~m~~al~~~~~~~~~  563 (630)
T 3u1k_A          484 EIEDYRLLTDILGIEDYNGDMDFKIAGTNKGITALQADIKLPGIPIKIVMEAIQQASVAKKEILQIMNKTISKPRASRKE  563 (630)
T ss_dssp             CEEEEEEEESCCHHHHHTSSEEEEEEECSSCEEEEEEEECSSCBCHHHHHHHHHHHHHHHHHHHHHHHHHCSSCCSSCCT
T ss_pred             cccCceEEecCCHHHHhhCcceEEEEecCCceEEEEecCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhcc
Confidence            23478999999999999999999999999999999999998899999999999999999999999999999999999999


Q ss_pred             CCCcceeeeeccchhhhhcCCCccchhhhhhhhCceEEee-CCEEEEEecCHHHHHHHHHHHHHHh
Q 002054          613 NSPRLATLKYDNDTLRRLIGPLGALKRKIEEETGGRISVS-DGTLTVVAKNRSVMEKVLEKVDFII  677 (974)
Q Consensus       613 ~~p~~~~~~i~~~ki~~vIg~gGk~i~~i~~~~g~~Idi~-dg~v~i~~~~~~~~~~a~~~i~~l~  677 (974)
                      |||++.+++|||+||+++|||||++||+|+++||++|+|+ ||+|.|++.+++.+++|+++|+.++
T Consensus       564 ~ap~~~~~~I~~~kI~~vIG~gG~~Ik~I~e~tg~~I~I~d~G~V~I~~~~~~~~~~A~~~I~~i~  629 (630)
T 3u1k_A          564 NGPVVETVQVPLSKRAKFVGPGGYNLKKLQAETGVTISQVDEETFSVFAPTPSAMHEARDFITEIC  629 (630)
T ss_dssp             TCCEEEEEECCHHHHHHHHCGGGHHHHHHHHHHCCEEEECSSSEEEEEESSHHHHHHHHHHTTC--
T ss_pred             cCCeEEEEEeChhHhheeECCCChhHHHHHHHHCCEEEEcCCcEEEEEeCCHHHHHHHHHHHHHHh
Confidence            9999999999999999999999999999999999999997 8999999999999999999887654

>3gme_A Polyribonucleotide nucleotidyltransferase; protein-RNA complex, cytoplasm, nucleotidyltransferase, RNA- binding, transferase, hydrolase; 2.40A {Escherichia coli E24377A} PDB: 3gll_A 3gcm_A 3h1c_A 3cdj_A

Probab=100.00  E-value=2.6e-130  Score=1143.13  Aligned_cols=548  Identities=45%  Similarity=0.735  Sum_probs=471.0

Q ss_pred             cceeeeeeEEECCeEEEEEeCccCcCCCcEEEEEeCCeEEEEEEEeCCC-CCCCCceeeEeeccccccccCCCCCccccc
Q 002054           55 VLETFKEEFEIGSRLITLETGKIARFANGAVVLGMDETKVLSTVTSSKG-DSVRDFLPLTVDYQEKQFAQGVIPNTYMRR  133 (974)
Q Consensus        55 ~~~~~~~~~~~~~r~i~~etg~~a~~A~GSa~v~~G~T~Vl~tv~~~~~-~~~~~f~pL~v~y~e~~~a~g~ip~~~~~R  133 (974)
                      ||+.+++++++|||+++||||++|+||+|||++++|||+|||||+++.+ +++.||+||+|+|+||+||+|||||||+||
T Consensus         1 ~~~~~~~~~~~~~R~i~ietg~~ak~A~GSvlv~~GdT~Vl~tv~~~~~~~~g~df~Pltv~Y~e~~~a~G~iPg~~~~R   80 (549)
T 3gme_A            1 MLNPIVRKFQYGQHTVTLETGMMARQATAAVMVSMDDTAVFVTVVGQKKAKPGQDFFPLTVNYQERTYAAGRIPGSFFRR   80 (549)
T ss_dssp             CCCCEEEEEEETTEEEEEEESSSCTTSSEEEEEEETTEEEEEEEEECSSCCTTCCSCCEEEEEEECGGGTTCCCSCC---
T ss_pred             CCCcEEEEEEECCEEEEEEECCccCCCCeEEEEEECCEEEEEEEEecCCCCCCCCCccceeeeeeehhhcccCCCcCcCc
Confidence            6788899999999999999999999999999999999999999999988 778999999999999999999999999999


Q ss_pred             cCCCCchhhhHHHhhcCCccccccCCCCCceEEEEEEEeccCCCChhhHHHHHHHHHhhcCCCCCCCCeEEEEEEEECCE
Q 002054          134 EGAPKERELLVGRIIDRPIRPLFPAGFYHEVQVMASVLSSDGKQDPDIMAANATSAALMLSDIPWGGPIGMIRIGRICGQ  213 (974)
Q Consensus       134 eg~p~~~eil~~RlidR~lrplfp~~~~~~~~i~~~vl~~dg~~~~~~~ai~aAs~AL~~s~iP~~~~v~av~vg~i~g~  213 (974)
                      ||+|+++|+|++|||||+|||+||++|++++||+|+||++||+++|+++||||||+||++|+|||++||+|||||++||+
T Consensus        81 EGrps~~~~l~~RlIdR~lRplfp~~~~~evqI~~~Vls~D~~~~pd~~ai~gAs~AL~~s~iP~~gpvaaV~Vg~i~g~  160 (549)
T 3gme_A           81 EGRPSEGETLIARLIDRPIRPLFPEGFVNEVQVIATVVSVNPQVNPDIVAMIGASAALSLSGIPFNGPIGAARVGYINDQ  160 (549)
T ss_dssp             --CCCHHHHHHHHHHHHHHGGGSCTTCCSCEEEEEEEEECCSSSCHHHHHHHHHHHHHHHHCSCCCCCCEEEEEEEETTE
T ss_pred             CCCCChhhhHHHHHhCCccccccccCCcccEEEEEEEEecCCCCcHHHHHHHHHHHHHhccCCCcCCCeeEEEEEEECCE
Confidence            99999999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             EEEcCCHHHHhcCccceeEeeeCCeEEEEEecCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCccccccccCCCH
Q 002054          214 FIVNPTMDELSLSDLNLVYACTREKTLMIDVQAREISEKDLEAGLRLAHPEAVKYLEPQIRLAEKAGKQKKEYKLSMISE  293 (974)
Q Consensus       214 ~vldPt~~e~~~s~~~l~v~~t~~~i~mie~~~~~~~e~~~~~al~~a~~~~~~i~~~~~~~~~~~g~~k~~~~~~~~~~  293 (974)
                      +|+|||++|++.|++||+|+||+++++|||+++++|||++|.+||++||+++++++++|+++++++||+|++|.....++
T Consensus       161 ~vlnPt~~e~~~s~~dl~va~t~~~i~mve~e~~~~se~~~~~al~~a~~~i~~l~~~q~~~~~~~~~~~~~~~~~~~~~  240 (549)
T 3gme_A          161 YVLNPTQDELKESKLDLVVAGTEAAVLMVESEAELLSEDQMLGAVVFGHEQQQVVIQNINELVKEAGKPRWDWQPEPVNE  240 (549)
T ss_dssp             EEESCCTTTTTTCSBCEEEEECSSCEEEEEEEEEEECHHHHHHHHHHHHHHTHHHHHHHHHHHHHHCCCCCCCCCCCCCH
T ss_pred             EEECCCHHHHhhCceEEEEEecCCeEEEEEccCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCcccCCCCCCCH
Confidence            99999999999999999999999999999999999999999999999999999999999999999999999999888999


Q ss_pred             HHHHHHHHHHHHHHHhhhcCCCCChhHHHHHHHHHHHHHHHHhhhccchhhhchHHHHHHHHHHHHHHHHHHhcCCcCCC
Q 002054          294 QTLEKVSNLAEAHIEAVFTDPSYSKFERGEALDKIGQDVKKALEEECDEESLQVLPKAVDTVRKRVIRKRIIAEGVRVDG  373 (974)
Q Consensus       294 ~~~~~~~~~~~~~~~~~~~~~~~~k~~r~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~r~~il~~~~R~DG  373 (974)
                      ++.+++++++.++|++++.+  ++|++|+++++++++++.++|.++.++....++..+|++++++.+|++|+++|+|+||
T Consensus       241 ~~~~~~~~~~~~~~~~~~~~--~~k~~r~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~R~~il~~g~R~DG  318 (549)
T 3gme_A          241 ALNARVAALAEARLSDAYRI--TDKQERYAQVDVIKSETIATLLAEDETLDENELGEILHAIEKNVVRSRVLAGEPRIDG  318 (549)
T ss_dssp             HHHTTC----------------CCHHHHC-----------------------------CCHHHHHHHHHHHHHTCCCTTS
T ss_pred             HHHHHHHHHHHHHHHHHHhc--cchHHHHHHHHHHHHHHHHHhhhhcccccHHHHHHHHHHHHHHHHHHHHhcCCCCCCC
Confidence            99999999999999999987  5999999999999999999997654333456899999999999999999999999999


Q ss_pred             CCCCCccCeEEEeCCCCCCCcceEEEeCCeEEEEEEEeCCCchhhhccccCCCCceeEEEEEecCCCCccccccccCCCc
Q 002054          374 RQLDEVRPIYCESGNLPILHGSSLFSRGDTQVLCTVTLGAPAEAQRLESLVGPPTKRFMLHYSFPPFCINEVGKRVGLNR  453 (974)
Q Consensus       374 R~~~e~R~I~ie~g~l~~a~GSal~~~G~T~Vl~~Vtl~~p~~~~~~d~~~~~~~~~~~v~~~f~p~s~~e~~~~~~~~r  453 (974)
                      |.++|+|||+|++|+++++||||+|++|+|||+|+||+|...+.+..+.+.+++.++|++||+|||||++++++.|++++
T Consensus       319 R~~~elRpi~i~~g~l~~a~GSal~~~G~T~Vl~~Vt~gp~~~~~~~~~l~~~~~g~~~~~y~~~P~st~e~~~~g~~~~  398 (549)
T 3gme_A          319 REKDMIRGLDVRTGVLPRTHGSALFTRGETQALVTATLGTARDAQVLDELMGERTDTFLFHYNFPPYSVGETGMVGSPKR  398 (549)
T ss_dssp             CCTTCCCCEEEEECCCSSSSEEEEEEETTEEEEEEEEEEC---------------CCEEEEEECCGGGTTCCCCSSCCCS
T ss_pred             CCCCCccceEEEECCCCCCCceEEEEECCeEEEEEEEecCcccccCccccCCCCceEEEEEEEeCCCCcCCcccCCCCCh
Confidence            99999999999999999999999999999999999998865666777777778899999999999999999999999999


Q ss_pred             hhhhHHHHHHHHhhhcCCCCCCCCeEEEEEEEEEcCCCChhhHHHHHHHHHHHHcCCCccccccceeeeeeccCCCCCCc
Q 002054          454 REVGHGTLAEKALLAVLPPENDFPYTVRVNSEVMASDGSTSMATVCGGSMALMDAGIPLQEHVAGVSVGLVSEVDPSTGE  533 (974)
Q Consensus       454 re~~~~~l~eral~~vi~~~~~~p~tI~V~v~VLesdGs~~~A~v~aa~lAL~dagvPi~~~vagvs~gli~~~d~~~~~  533 (974)
                      ||++|++|++|+|++++|+.+.|||+|+|+++||++|||++|||+||+++||+||||||+++|+|++||++++++     
T Consensus       399 Reie~~~li~raL~~vI~~~~~~P~tI~V~~~VLesDGs~~~AsI~aa~lAL~DAGvPm~~~Vaavs~Gli~~g~-----  473 (549)
T 3gme_A          399 REIGHGRLAKRGVLAVMPDMDKFPYTVRVVSEITESNGSSSMASVCGASLALMDAGVPIKAAVAGIAMGLVKEGD-----  473 (549)
T ss_dssp             SHHHHHHHHHHHHTTTCCCTTTCCCEEEEEEEEEECSSCHHHHHHHHHHHHHHHHTCCCSSCCEEEEEEEEEETT-----
T ss_pred             hHHHHHHHHHHHHHHhcCccccCCeEEEEEEEEEECCCCHHHHHHHHHHHHHHhCCCCcccceeEEEEEEEcCCC-----
Confidence            999999999999999999778999999999999999999999999999999999999999999999999998743     


Q ss_pred             ccceEEEecCCccccccCCccEEEEeeCCceEEEEeeccCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCCCCC
Q 002054          534 IKDYRILTDILGLEDHLGDMDFKIAGTRIGVTAIQLDIKPAGIPLDIICECLEHAHKGRLQILDHMEREISAPRTQDD  611 (974)
Q Consensus       534 ~~~~~iL~Dp~~~Ee~~~d~d~~Va~t~~gI~alq~~~k~~~i~~e~l~~al~~A~~~~~~I~~~m~~~i~~~~~~~~  611 (974)
                        ++.+|+||++.||++++|||+|++|.+|++++||+++.+|++.++|.+||++|++++.+|++.|++++.+||.+++
T Consensus       474 --~~~iL~D~~~~Ed~~~d~d~~Va~t~~gitalqmd~ki~G~s~~~l~~~L~~A~~g~~~I~~~m~~al~~pr~~~~  549 (549)
T 3gme_A          474 --NYVVLSDILGDEDHLGDMDFKVAGSRDGISALQMDIKIEGITKEIMQVALNQAKGARLHILGVMEQAINAPRGDIS  549 (549)
T ss_dssp             --EEEEEESCCHHHHHHSSEEEEEEECSSCEEEEEEEECCSCCCHHHHHHHHHHHHHHHHHHHHHHHHHCCSCC----
T ss_pred             --ceEEEecCChHHHccCCceEEEEecCCCeEEEEEccccCCcCHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhhhcC
Confidence              6789999999999999999999999999999999999999999999999999999999999999999999998764

>2nn6_B Exosome complex exonuclease RRP41; RNA, exosome, PM/SCL, phosphorolytic, hydrolase/transferase complex; 3.35A {Homo sapiens} SCOP: d.14.1.4 d.101.1.1

Probab=100.00  E-value=7.7e-45  Score=392.10  Aligned_cols=231  Identities=24%  Similarity=0.365  Sum_probs=210.0

Q ss_pred             HHHHhcCCcCCCCCCCCccCeEEEeCCCCCCCcceEEEeCCeEEEEEEEeCCCchhhhccccCCCCceeEEEEEecCCCC
Q 002054          362 KRIIAEGVRVDGRQLDEVRPIYCESGNLPILHGSSLFSRGDTQVLCTVTLGAPAEAQRLESLVGPPTKRFMLHYSFPPFC  441 (974)
Q Consensus       362 ~~il~~~~R~DGR~~~e~R~I~ie~g~l~~a~GSal~~~G~T~Vl~~Vtl~~p~~~~~~d~~~~~~~~~~~v~~~f~p~s  441 (974)
                      +.++++|+|+|||.++|+|||++++|+++++||||+|++|+|+|+|+|+  +|.+.+..+....+++++|++||+|+|||
T Consensus         9 ~~i~~~~~R~DGR~~~e~R~i~i~~g~l~~a~GSa~v~~G~T~Vl~~V~--g~~~~~~~~~~~~~~~g~l~~~~~~~p~a   86 (249)
T 2nn6_B            9 ELLSDQGYRVDGRRAGELRKIQARMGVFAQADGSAYIEQGNTKALAVVY--GPHEIRGSRARALPDRALVNCQYSSATFS   86 (249)
T ss_dssp             --CCBTTBCSSSSCTTSCCCEEEEESCSSSSSEEEEEEESSCEEEEEEE--EEEECCSSSCCCCCSSCCEEEEEEECTTT
T ss_pred             hhcccCCcCCCCCCcCCcCCeEEEeCCCCCCCeEEEEEECCeEEEEEEE--ccCCccccccccCCCcEEEEEEEEcCCCc
Confidence            5677999999999999999999999999999999999999999999999  67665433223457889999999999999


Q ss_pred             ccccccccCCCchhhhHHHHHHHHhhhcCCCCCCCCe-EEEEEEEEEcCCCChhhHHHHHHHHHHHHcCCCcccccccee
Q 002054          442 INEVGKRVGLNRREVGHGTLAEKALLAVLPPENDFPY-TVRVNSEVMASDGSTSMATVCGGSMALMDAGIPLQEHVAGVS  520 (974)
Q Consensus       442 ~~e~~~~~~~~rre~~~~~l~eral~~vi~~~~~~p~-tI~V~v~VLesdGs~~~A~v~aa~lAL~dagvPi~~~vagvs  520 (974)
                      ++++++.+++++|+++|+++++|+|+++++. +.||+ +|+|+++||++|||+++||+||+++||+||||||+++|++++
T Consensus        87 ~~~~~~~~~~~~~~~~~~~ll~r~l~~~i~~-~~~p~~~I~i~~~VL~~dG~~~~A~i~aa~~AL~da~iPl~~~v~avs  165 (249)
T 2nn6_B           87 TGERKRRPHGDRKSCEMGLQLRQTFEAAILT-QLHPRSQIDIYVQVLQADGGTYAACVNAATLAVLDAGIPMRDFVCACS  165 (249)
T ss_dssp             SSSCCCTTTSTHHHHHHHHHHHHHHHHTTCG-GGCTTEEEEEEEEEEECCSCHHHHHHHHHHHHHHHTCCCCSSCCEEEE
T ss_pred             ccccccCCCCCHhHHHHHHHHHHHHHHhcCH-HHCCCcEEEEEEEEEeCCCCHHHHHHHHHHHHHHhcCCcccCCeeeEE
Confidence            9998888899999999999999999999998 67885 699999999999999999999999999999999999999999


Q ss_pred             eeeeccCCCCCCcccceEEEecCCccccccCCccEEEEee--CCceEEEEeeccCCCCCHHHHHHHHHHHHHHHHHHHHH
Q 002054          521 VGLVSEVDPSTGEIKDYRILTDILGLEDHLGDMDFKIAGT--RIGVTAIQLDIKPAGIPLDIICECLEHAHKGRLQILDH  598 (974)
Q Consensus       521 ~gli~~~d~~~~~~~~~~iL~Dp~~~Ee~~~d~d~~Va~t--~~gI~alq~~~k~~~i~~e~l~~al~~A~~~~~~I~~~  598 (974)
                      +|++++           .+|+||+..||+.++++|+|+.+  .++|+++|+++   .++.++|.+|+++|++++.+|++.
T Consensus       166 ~g~~~~-----------~~l~Dp~~~Ee~~~~~~~~v~~~~~~~~i~~lq~~g---~~~~~~l~~~l~~A~~~~~~i~~~  231 (249)
T 2nn6_B          166 AGFVDG-----------TALADLSHVEEAAGGPQLALALLPASGQIALLEMDA---RLHEDHLERVLEAAAQAARDVHTL  231 (249)
T ss_dssp             EEEETT-----------EEEESCCHHHHTSSCCCEEEEEETTTTEEEEEEECS---CCBTTSHHHHHHHHHHHHHHHHHH
T ss_pred             EEEECC-----------eEEECCChHHhccCCcEEEEEEECCCCCEEEEEEEC---CcCHHHHHHHHHHHHHHHHHHHHH
Confidence            999975           69999999999999999999963  45599999985   589999999999999999999999


Q ss_pred             HHHHhcCCCCC
Q 002054          599 MEREISAPRTQ  609 (974)
Q Consensus       599 m~~~i~~~~~~  609 (974)
                      |++++.++..+
T Consensus       232 ~~~~l~~~~~~  242 (249)
T 2nn6_B          232 LDRVVRQHVRE  242 (249)
T ss_dssp             HHHHHHHHHHH
T ss_pred             HHHHHHHHHHh
Confidence            99999887543

>2wnr_B Probable exosome complex exonuclease 1; phosphate binding, 3'-5' exoribonuclease, hydrolase; 2.65A {Methanothermobacter thermautotrophicusorganism_taxid}

Probab=100.00  E-value=1.5e-43  Score=380.12  Aligned_cols=227  Identities=30%  Similarity=0.445  Sum_probs=201.9

Q ss_pred             HHHHhcCCcCCCCCCCCccCeEEEeCCCCCCCcceEEEeCCeEEEEEEEeCCCchhhhccccCCCCceeEEEEEecCCCC
Q 002054          362 KRIIAEGVRVDGRQLDEVRPIYCESGNLPILHGSSLFSRGDTQVLCTVTLGAPAEAQRLESLVGPPTKRFMLHYSFPPFC  441 (974)
Q Consensus       362 ~~il~~~~R~DGR~~~e~R~I~ie~g~l~~a~GSal~~~G~T~Vl~~Vtl~~p~~~~~~d~~~~~~~~~~~v~~~f~p~s  441 (974)
                      ++++++|+|+|||.++|+|||++++|+++++||||+|++|+|+|+|+|+  +|.+.... ....+++++|++||+|+|||
T Consensus         9 ~~~l~~~~R~DGR~~~e~R~i~i~~g~l~~a~GSa~v~~G~T~Vl~~V~--gp~e~~~~-~~~~~~~g~l~~~~~~~p~a   85 (240)
T 2wnr_B            9 QLKTSPSVREDGRAFDELRPLKIEAGILERADGSSYLEFGGNKILVAVY--GPREAQIR-KLQRPDRAVIRCRYNMAPFS   85 (240)
T ss_dssp             ------CCCTTSCCTTCCCCEEEEESCCSSSSEEEEEEETTEEEEEEEE--EEEECCSS-SSCCSSSCEEEEEEEECTTS
T ss_pred             EeecccCccCCCCCcCCccCeEEEeCCCCCCCEEEEEEECCeEEEEEEE--cCCCCCcc-cccCCCcEEEEEEEEeCCCC
Confidence            5789999999999999999999999999999999999999999999999  66553221 23457889999999999999


Q ss_pred             ccccccccCCCchhhhHHHHHHHHhhhcCCCCCCCCe-EEEEEEEEEcCCCChhhHHHHHHHHHHHHcCCCcccccccee
Q 002054          442 INEVGKRVGLNRREVGHGTLAEKALLAVLPPENDFPY-TVRVNSEVMASDGSTSMATVCGGSMALMDAGIPLQEHVAGVS  520 (974)
Q Consensus       442 ~~e~~~~~~~~rre~~~~~l~eral~~vi~~~~~~p~-tI~V~v~VLesdGs~~~A~v~aa~lAL~dagvPi~~~vagvs  520 (974)
                      +++++ .+++++|+++|+++++|+|+++++. +.||+ +|+|+++||++|||+++||+||+++||+|||+||+++|++++
T Consensus        86 ~~~~~-~~~~~~~~~~l~~ll~r~l~~~i~l-~~~p~~~I~i~~~VL~~dG~~~~a~i~aa~~AL~da~iP~~~~v~avs  163 (240)
T 2wnr_B           86 VEERK-RPGPDRRSVEISKITAEALRPALIL-EKFPRSVIDVFIEVLEAEGGTRCAGITAASVALADAGIPMRDMVVACA  163 (240)
T ss_dssp             SSSCC-CSSCCHHHHHHHHHHHHHHGGGBCG-GGSTTEEEEEEEEEEECCSCHHHHHHHHHHHHHHHTTCCBSSCCEEEE
T ss_pred             cCCcc-CCCCChhHHHHHHHHHHHHHHhcCH-HHCCCcEEEEEEEEEeCCCCHHHHHHHHHHHHHHHcCCccccceeeEE
Confidence            99876 6789999999999999999999987 68896 899999999999999999999999999999999999999999


Q ss_pred             eeeeccCCCCCCcccceEEEecCCccccccCCccEEEEe-e-CCceEEEEeeccCCCCCHHHHHHHHHHHHHHHHHHHHH
Q 002054          521 VGLVSEVDPSTGEIKDYRILTDILGLEDHLGDMDFKIAG-T-RIGVTAIQLDIKPAGIPLDIICECLEHAHKGRLQILDH  598 (974)
Q Consensus       521 ~gli~~~d~~~~~~~~~~iL~Dp~~~Ee~~~d~d~~Va~-t-~~gI~alq~~~k~~~i~~e~l~~al~~A~~~~~~I~~~  598 (974)
                      +|++++           .+|+||+..||+.++++++|+. + .++|+++|++++   ++.++|.+|+++|.+++.+|++.
T Consensus       164 ~g~~~~-----------~~l~Dp~~~Ee~~~~~~~~v~~~~~~~~i~~lq~~g~---~~~~~l~~~l~~A~~~~~~i~~~  229 (240)
T 2wnr_B          164 AGKVGD-----------QVVLDLSEEEDKEGQADVPVAILPRTREITLLQSDGN---LTPEEFERALDLAVEGCLRIHEV  229 (240)
T ss_dssp             EEESSS-----------SEEESCCSHHHHSCSEEEEEEEETTTTEEEEEEEEEC---BCHHHHHHHHHHHHHHHHHHHHH
T ss_pred             EEEECC-----------EEEeCCCHHHhccCCceEEEEEECCCCCEEEEEEEcc---cCHHHHHHHHHHHHHHHHHHHHH
Confidence            999975           5999999999999999999996 4 455999999865   99999999999999999999999


Q ss_pred             HHHHhcCCC
Q 002054          599 MEREISAPR  607 (974)
Q Consensus       599 m~~~i~~~~  607 (974)
                      |++++.++.
T Consensus       230 ~~~~l~~~~  238 (240)
T 2wnr_B          230 QKEALRKRY  238 (240)
T ss_dssp             HHHHHHC--
T ss_pred             HHHHHHHhh
Confidence            999998763

>3m7n_D Probable exosome complex exonuclease 1; exosome, RNA, exonuclease, hydrolase, nuclease, hydrolase-RN; 2.40A {Archaeoglobus fulgidus} PDB: 3m85_D 2ba0_F 2ba1_E

Probab=100.00  E-value=7.2e-44  Score=385.17  Aligned_cols=225  Identities=30%  Similarity=0.515  Sum_probs=205.2

Q ss_pred             HHHhcCCcCCCCCCCCccCeEEEeCCCCCCCcceEEEeCCeEEEEEEEeCCCchhhhccccCCCCceeEEEEEecCCCCc
Q 002054          363 RIIAEGVRVDGRQLDEVRPIYCESGNLPILHGSSLFSRGDTQVLCTVTLGAPAEAQRLESLVGPPTKRFMLHYSFPPFCI  442 (974)
Q Consensus       363 ~il~~~~R~DGR~~~e~R~I~ie~g~l~~a~GSal~~~G~T~Vl~~Vtl~~p~~~~~~d~~~~~~~~~~~v~~~f~p~s~  442 (974)
                      +++.+|+|+|||.++|+|||+|++|+++++||||+|++|+|+|+|+|+  +|.+.+. .....+++++|++||+|+|||+
T Consensus        10 ~~i~~~~R~DGR~~~e~R~i~i~~g~l~~a~GSa~v~~G~T~Vl~~V~--gp~e~~~-~~~~~~~~g~l~~~~~~~P~s~   86 (258)
T 3m7n_D           10 KLIVDGLRLDGRKFDELRPIKIEASVLKRADGSCYLEMGKNKVIAAVF--GPREVHP-EHLQDPSKAIIRYRYNMAPFSV   86 (258)
T ss_dssp             CSEETTEETTSCCTTCCCCEEEEECCCSSSSEEEEEEETTEEEEEEEE--EEEECSS-STTCCSSSCEEEEEEEECGGGS
T ss_pred             HHHhcCCCCCCCCcCCccCeEEEECCCCCCCceEEEEECCeEEEEEEE--cccCCCC-ccccCCCceEEEEEEEeCCccc
Confidence            356699999999999999999999999999999999999999999999  6766442 2234578899999999999999


Q ss_pred             cccccccCCCchhhhHHHHHHHHhhhcCCCCCCCCe-EEEEEEEEEcCCCChhhHHHHHHHHHHHHcCCCccccccceee
Q 002054          443 NEVGKRVGLNRREVGHGTLAEKALLAVLPPENDFPY-TVRVNSEVMASDGSTSMATVCGGSMALMDAGIPLQEHVAGVSV  521 (974)
Q Consensus       443 ~e~~~~~~~~rre~~~~~l~eral~~vi~~~~~~p~-tI~V~v~VLesdGs~~~A~v~aa~lAL~dagvPi~~~vagvs~  521 (974)
                      ++++ .+++++||++|+++++|+|+++++. +.||+ +|+|+++||++|||+++||+||+++||+||||||+++|+|+++
T Consensus        87 ~~r~-~~~~~~re~ei~~li~r~l~~~i~~-~~~p~~~I~V~~~VL~~DG~~~~Aai~aa~lAL~dagiP~~~~v~avsv  164 (258)
T 3m7n_D           87 EERK-RPGPDRRSIEISKVSKEAFEAVIMK-ELFPRSAIDIFVEVLQADAGSRTACLNAASVALVDAGVPMKGMITSVAV  164 (258)
T ss_dssp             SSCC-CSSCCHHHHHHHHHHHHHHHTTBCG-GGSTTEEEEEEEEEEECCTTHHHHHHHHHHHHHHHTTCCBSSEEEEEEE
T ss_pred             cccc-CCCCCHHHHHHHHHHHHHHHhhcCH-HhCCceEEEEEEEEEEcCCCHHHHHHHHHHHHHHhcCCCCCCceEEEEE
Confidence            8865 4679999999999999999999987 78975 6999999999999999999999999999999999999999999


Q ss_pred             eeeccCCCCCCcccceEEEecCCccccccCCccEEEEe-eC----CceEEEEeeccCCCCCHHHHHHHHHHHHHHHHHHH
Q 002054          522 GLVSEVDPSTGEIKDYRILTDILGLEDHLGDMDFKIAG-TR----IGVTAIQLDIKPAGIPLDIICECLEHAHKGRLQIL  596 (974)
Q Consensus       522 gli~~~d~~~~~~~~~~iL~Dp~~~Ee~~~d~d~~Va~-t~----~gI~alq~~~k~~~i~~e~l~~al~~A~~~~~~I~  596 (974)
                      |++++           .+|+||+..||+.++++|+|++ +.    ++|+++|+++   +++.++|.+|+++|++++.+|+
T Consensus       165 g~i~~-----------~~llDpt~~Ee~~~~~d~~va~~~~~~~~~~I~~lq~~g---~~~~~~l~~~l~~A~~~~~~i~  230 (258)
T 3m7n_D          165 GKADG-----------QLVLDPMKEEDNFGEADMPFAFLIRNGKIESIALLQMDG---RMTRDEVKQAIELAKKGALQIY  230 (258)
T ss_dssp             EEETT-----------EEEESCCHHHHHHSSEEEEEEEEEETTEEEEEEEEEEEE---EECHHHHHHHHHHHHHHHHHHH
T ss_pred             EEECC-----------EEEECCCHHHHhccCceEEEEEEcCCCCCCCEEEEEecC---CcCHHHHHHHHHHHHHHHHHHH
Confidence            99964           6899999999999999999999 55    4599999985   6999999999999999999999


Q ss_pred             HHHHHHhcCC
Q 002054          597 DHMEREISAP  606 (974)
Q Consensus       597 ~~m~~~i~~~  606 (974)
                      +.|++++.+.
T Consensus       231 ~~~~~~l~~~  240 (258)
T 3m7n_D          231 EMQREAILRR  240 (258)
T ss_dssp             HHHHHHHHHH
T ss_pred             HHHHHHHHHH
Confidence            9999999863

>2po1_A Probable exosome complex exonuclease 1; RNAse PH, hydrolase/hydrolase/RNA complex; 1.94A {Pyrococcus abyssi} PDB: 2po0_A* 2pnz_A 2po2_A*

Probab=100.00  E-value=2.5e-43  Score=380.33  Aligned_cols=231  Identities=29%  Similarity=0.437  Sum_probs=208.1

Q ss_pred             HHHHHHHHHhcCCcCCCCCCCCccCeEEEeCCCCCCCcceEEEeCCeEEEEEEEeCCCchhhhccccCCCCceeEEEEEe
Q 002054          357 KRVIRKRIIAEGVRVDGRQLDEVRPIYCESGNLPILHGSSLFSRGDTQVLCTVTLGAPAEAQRLESLVGPPTKRFMLHYS  436 (974)
Q Consensus       357 ~~~~r~~il~~~~R~DGR~~~e~R~I~ie~g~l~~a~GSal~~~G~T~Vl~~Vtl~~p~~~~~~d~~~~~~~~~~~v~~~  436 (974)
                      |+.+ ++++++|+|+|||.++|+|+|.+++|+++++||||+|++|+|+|+|+|+  +|.+... .....+++++|+++|+
T Consensus         5 p~~~-~~~l~~~~R~DGR~~~e~R~i~i~~g~l~~a~GSa~v~~G~T~Vl~~V~--gp~e~~~-~~~~~~~~g~l~v~~~   80 (249)
T 2po1_A            5 PEGL-KLIDENGRRIDGRKKYELRPIKMEVGVLKNANGSAYIEWGKNKIIAAVY--GPRELHP-KHLQRPDRAILRVRYN   80 (249)
T ss_dssp             -----CCSBCSSCBTTSCCTTCCCCEEEEECCCSSSSEEEEEEETTEEEEEEEE--EEEECSS-GGGCCSSSCEEEEEEE
T ss_pred             Ccce-EEecccCccCCCCCcccccCEEEEeCCcCCCCEEEEEEECCcEEEEEEE--cCcccCc-ccccCCCceEEEEEEE
Confidence            3334 5788999999999999999999999999999999999999999999999  6665432 1234578899999999


Q ss_pred             cCCCCccccccccCCCchhhhHHHHHHHHhhhcCCCCCCCC-eEEEEEEEEEcCCCChhhHHHHHHHHHHHHcCCCcccc
Q 002054          437 FPPFCINEVGKRVGLNRREVGHGTLAEKALLAVLPPENDFP-YTVRVNSEVMASDGSTSMATVCGGSMALMDAGIPLQEH  515 (974)
Q Consensus       437 f~p~s~~e~~~~~~~~rre~~~~~l~eral~~vi~~~~~~p-~tI~V~v~VLesdGs~~~A~v~aa~lAL~dagvPi~~~  515 (974)
                      |+|||+++++ .+++++||++++++++|+|+++++. +.|| |+|+|+++||++|||+++||+||+++||+||||||+++
T Consensus        81 ~~p~a~~~~~-~~~~~~~~~~~s~li~r~l~~~i~l-~~~p~~~i~I~~~VL~~dG~~~~aai~aa~~AL~da~iP~~~~  158 (249)
T 2po1_A           81 MAPFSVEERK-KPGPDRRSIEISKVIKGALEPALIL-EMFPRTAIDVFIEVLQADAGTRVAGITAASLALADAGIPMRDL  158 (249)
T ss_dssp             ECGGGSSSCC-CSSCCHHHHHHHHHHHHHHGGGBCG-GGSTTEEEEEEEEEEECCSCHHHHHHHHHHHHHHHTTCCBSSC
T ss_pred             eCCccccccc-CCCCCHHHHHHHHHHHHHHHhhccH-HHCCCCEEEEEEEEEecCCCHHHHHHHHHHHHHHhcCCCccCc
Confidence            9999999875 5679999999999999999999997 6889 58999999999999999999999999999999999999


Q ss_pred             ccceeeeeeccCCCCCCcccceEEEecCCccccccCCccEEEEe--eCCceEEEEeeccCCCCCHHHHHHHHHHHHHHHH
Q 002054          516 VAGVSVGLVSEVDPSTGEIKDYRILTDILGLEDHLGDMDFKIAG--TRIGVTAIQLDIKPAGIPLDIICECLEHAHKGRL  593 (974)
Q Consensus       516 vagvs~gli~~~d~~~~~~~~~~iL~Dp~~~Ee~~~d~d~~Va~--t~~gI~alq~~~k~~~i~~e~l~~al~~A~~~~~  593 (974)
                      |+++++|++++           .+|+||+..||+.++++|+|++  +.++|+++|++++   ++.++|.+|+++|++++.
T Consensus       159 v~avs~g~~~~-----------~~l~Dp~~~Ee~~~~~~l~va~~~~~~~i~~~~~~g~---~~~~~l~~~l~~A~~~~~  224 (249)
T 2po1_A          159 VAACAAGKIEG-----------EIVLDLNKEEDNYGEADVPVAIMPLKNDITLLQMDGY---LTKDEFIEAVKLAIKGAK  224 (249)
T ss_dssp             CEEEEEEEETT-----------EEEESCCHHHHHTCSEEEEEEEEGGGTEEEEECCEEC---CCHHHHHHHHHHHHHHHH
T ss_pred             eEEEEEEEECC-----------EEEecCcHHHhccCCceEEEEEECCCCCEEEEEEEcc---cCHHHHHHHHHHHHHHHH
Confidence            99999999974           7999999999999999999997  4556999999864   999999999999999999


Q ss_pred             HHHHHHHHHhcCCC
Q 002054          594 QILDHMEREISAPR  607 (974)
Q Consensus       594 ~I~~~m~~~i~~~~  607 (974)
                      +|++.|++++.++.
T Consensus       225 ~i~~~~~~~l~~~~  238 (249)
T 2po1_A          225 AVYQKQREALKEKY  238 (249)
T ss_dssp             HHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHH
Confidence            99999999998764

>2je6_B RRP41, exosome complex exonuclease 1; nuclease, hydrolase, exonuclease, phosphorolytic, exoribonuclease, RNA degradation; HET: 1PE; 1.6A {Sulfolobus solfataricus} SCOP: d.14.1.4 d.101.1.1 PDB: 2jea_B* 2jeb_B* 2br2_B 2c37_B* 2c38_B* 2c39_B* 3l7z_B

Probab=100.00  E-value=1.2e-42  Score=375.21  Aligned_cols=228  Identities=29%  Similarity=0.435  Sum_probs=207.8

Q ss_pred             HHHhcCCcCCCCCCCCccCeEEEeCCCCCCCcceEEEeCCeEEEEEEEeCCCchhhhccccCCCCceeEEEEEecCCCCc
Q 002054          363 RIIAEGVRVDGRQLDEVRPIYCESGNLPILHGSSLFSRGDTQVLCTVTLGAPAEAQRLESLVGPPTKRFMLHYSFPPFCI  442 (974)
Q Consensus       363 ~il~~~~R~DGR~~~e~R~I~ie~g~l~~a~GSal~~~G~T~Vl~~Vtl~~p~~~~~~d~~~~~~~~~~~v~~~f~p~s~  442 (974)
                      .++++|+|+|||.++|+|+|++++|+++++||||+|++|+|+|+|+|+  +|.+.... ....+++++++++|+++|||+
T Consensus        14 ~~l~~~~R~DGR~~~e~R~i~i~~g~~~~a~GSa~v~~G~T~Vl~~V~--g~~e~~~~-~~~~~~~g~l~v~~~~~p~a~   90 (250)
T 2je6_B           14 LILDDGKRTDGRKPDELRSIKIELGVLKNADGSAIFEMGNTKAIAAVY--GPKEMHPR-HLSLPDRAVLRVRYHMTPFST   90 (250)
T ss_dssp             SBCTTSCBTTSCCTTCCCCEEEEESCCSSSSEEEEEEETTEEEEEEEE--EEEECSSG-GGSCSSSCEEEEEEEECTTSS
T ss_pred             eecCCCccCCCCCccCcCCeEEEeCCCCCCCeEEEEEECCcEEEEEEE--cccccccc-cccCCCcEEEEEEEEeCCCcc
Confidence            468899999999999999999999999999999999999999999999  66553211 233578899999999999999


Q ss_pred             cccccccCCCchhhhHHHHHHHHhhhcCCCCCCCCe-EEEEEEEEEcCCCChhhHHHHHHHHHHHHcCCCccccccceee
Q 002054          443 NEVGKRVGLNRREVGHGTLAEKALLAVLPPENDFPY-TVRVNSEVMASDGSTSMATVCGGSMALMDAGIPLQEHVAGVSV  521 (974)
Q Consensus       443 ~e~~~~~~~~rre~~~~~l~eral~~vi~~~~~~p~-tI~V~v~VLesdGs~~~A~v~aa~lAL~dagvPi~~~vagvs~  521 (974)
                      ++++ .++++++|++++++++|+|+++++. +.||+ +|+|+++||++|||+++||+||+++||+|||+|++++|+++++
T Consensus        91 ~~~~-~g~~~~~e~~~s~li~r~l~~~i~~-~~~p~~~i~I~~~VL~~DG~~~~aai~aa~~AL~~a~iP~~~~v~avsv  168 (250)
T 2je6_B           91 DERK-NPAPSRREIELSKVIREALESAVLV-ELFPRTAIDVFTEILQADAGSRLVSLMAASLALADAGIPMRDLIAGVAV  168 (250)
T ss_dssp             SSCC-CSSCCHHHHHHHHHHHHHHHTTBCG-GGSTTEEEEEEEEEEECSSCHHHHHHHHHHHHHHHTTCCBSSCCEEEEE
T ss_pred             CCcc-CCCCChhHHHHHHHHHHHHHhhcCH-hhCCCcEEEEEEEEEeCCCCHHHHHHHHHHHHHHhcCCCccCceEEEEE
Confidence            9986 7789999999999999999999997 67884 8999999999999999999999999999999999999999999


Q ss_pred             eeeccCCCCCCcccceEEEecCCccccccCCccEEEEe--eCCceEEEEeeccCCCCCHHHHHHHHHHHHHHHHHHHHHH
Q 002054          522 GLVSEVDPSTGEIKDYRILTDILGLEDHLGDMDFKIAG--TRIGVTAIQLDIKPAGIPLDIICECLEHAHKGRLQILDHM  599 (974)
Q Consensus       522 gli~~~d~~~~~~~~~~iL~Dp~~~Ee~~~d~d~~Va~--t~~gI~alq~~~k~~~i~~e~l~~al~~A~~~~~~I~~~m  599 (974)
                      |++++           .+|+||+..||+.++++++|+.  +.++|+++|+++   +++.++|.+|+++|++++.+|++.|
T Consensus       169 g~~~~-----------~~l~Dpt~~Ee~~~~~~l~va~~~~~~~i~~v~~~g---~~~~~~l~~~l~~A~~~~~~i~~~~  234 (250)
T 2je6_B          169 GKADG-----------VIILDLNETEAMWGEADMPIAMMPSLNQVTLFQLNG---SMTPDEFRQAFDLAVKGINIIYNLE  234 (250)
T ss_dssp             EEETT-----------EEEESCCHHHHHHSSEEEEEEEEGGGTEEEEEEEEE---CBCHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             EEECC-----------EEEeCCCHHHHhcCCceEEEEEECCCCCEEEEEEEc---ccCHHHHHHHHHHHHHHHHHHHHHH
Confidence            99975           7999999999999999999997  456699999986   4899999999999999999999999


Q ss_pred             HHHhcCCCCC
Q 002054          600 EREISAPRTQ  609 (974)
Q Consensus       600 ~~~i~~~~~~  609 (974)
                      ++++.++..+
T Consensus       235 ~~~l~~~~~~  244 (250)
T 2je6_B          235 REALKSKYVE  244 (250)
T ss_dssp             HHHHHGGGC-
T ss_pred             HHHHHHHHhh
Confidence            9999987543

>3hkm_A OS03G0854200 protein; RNAse PH domain, phosphorylase, hydrolase; 1.98A {Oryza sativa japonica group}

Probab=100.00  E-value=2.7e-42  Score=370.34  Aligned_cols=218  Identities=21%  Similarity=0.289  Sum_probs=182.3

Q ss_pred             cCCcCCCCCCCCccCeEEEeCCCCCCCcceEEEeCCeEEEEEEEeCCCchhhhccccCCCCceeEEEEEecCCCCccccc
Q 002054          367 EGVRVDGRQLDEVRPIYCESGNLPILHGSSLFSRGDTQVLCTVTLGAPAEAQRLESLVGPPTKRFMLHYSFPPFCINEVG  446 (974)
Q Consensus       367 ~~~R~DGR~~~e~R~I~ie~g~l~~a~GSal~~~G~T~Vl~~Vtl~~p~~~~~~d~~~~~~~~~~~v~~~f~p~s~~e~~  446 (974)
                      +|+|+|||.++|+|||+|++|+++++||||+|++|+|+|+|+|+  +|.+....    .....+++++|+|+|+      
T Consensus         2 eg~R~DGR~~~e~R~i~i~~g~l~~a~GSa~v~~G~T~Vl~~V~--g~~~~~~~----~~~~~~~~~~~~~~P~------   69 (246)
T 3hkm_A            2 EESRADGRNPNQLRPFSCTRNPLDRAHGSARWAQGDTIVLAAVY--GPKPGTRK----GENPEKASIEVVWKPM------   69 (246)
T ss_dssp             ---CTTSCCTTCCCCEEEEECCCSSSSEEEEEEETTEEEEEEEC--CCEECCCT----TSCSSSCEEEEEEECS------
T ss_pred             CCcCCCCCCCCCcCCeEEEECCCCCCCeEEEEEECCeEEEEEEe--cCcCCCcc----cCCCccEEEEEEeCCC------
Confidence            68999999999999999999999999999999999999999999  77653211    2234567899999983      


Q ss_pred             cccCCCchhhhHHHHHHHHhhhcCCCCCCCCeEEEEEEEEEcCCCChhhHHHHHHHHHHHHcCCCccccccceeeeeecc
Q 002054          447 KRVGLNRREVGHGTLAEKALLAVLPPENDFPYTVRVNSEVMASDGSTSMATVCGGSMALMDAGIPLQEHVAGVSVGLVSE  526 (974)
Q Consensus       447 ~~~~~~rre~~~~~l~eral~~vi~~~~~~p~tI~V~v~VLesdGs~~~A~v~aa~lAL~dagvPi~~~vagvs~gli~~  526 (974)
                       .|.+++||++++++++|+|+++++.+..++|+|+|+++||++|||+++||+||+++||+||||||+++|+|+++|++.+
T Consensus        70 -~g~~~~~~~e~~~li~r~l~~l~~~~~~~~~~I~v~~~VL~~dG~~~~aai~aa~~AL~dagiP~~~~v~avs~g~~~~  148 (246)
T 3hkm_A           70 -TGQIGKQEKEYEMTLKRTLQSICLLTVHPNTTTSVILQVVGNDGSLLPCAINACCAALVFAGIPLKHLAVAIGCGVLED  148 (246)
T ss_dssp             -SSCCCTTHHHHHHHHHHHHHHHBCTTSSCSEEEEEEEEEEECSSCHHHHHHHHHHHHHHHHTCCBSSCEEEEEEEECTT
T ss_pred             -CCCCChhHHHHHHHHHHHHHHhcCccCCCcEEEEEEEEEEecCCCHHHHHHHHHHHHHHhcCCCCCCceEEEEEEEEEC
Confidence             2457889999999999999999998444469999999999999999999999999999999999999999999999953


Q ss_pred             CCCCCCcccceEEEecCCccccccCCccEEEEeeCCceEEEEeec---------------cCCCCCHHHHHHHHHHHHHH
Q 002054          527 VDPSTGEIKDYRILTDILGLEDHLGDMDFKIAGTRIGVTAIQLDI---------------KPAGIPLDIICECLEHAHKG  591 (974)
Q Consensus       527 ~d~~~~~~~~~~iL~Dp~~~Ee~~~d~d~~Va~t~~gI~alq~~~---------------k~~~i~~e~l~~al~~A~~~  591 (974)
                      +          .+|+||+..||+.++++++|++|.+++|++|+++               ..++++.++|.+|+++|+++
T Consensus       149 g----------~~llDpt~~Ee~~~~~~~~va~~~~~i~~lq~~g~~~~~~~~~~~i~~~~~g~~~~~~l~~~l~~A~~~  218 (246)
T 3hkm_A          149 G----------EVILDTNKAEEQQLKSFAHLVFPNSRKSASSKEPNQKEEDSERGLITSITHGVMSEEDYFSCIERGLAA  218 (246)
T ss_dssp             S----------CEEESCCHHHHTTCSEEEEEEEEC--------------------CCCEEEEECEEHHHHHHHHHHHHHH
T ss_pred             C----------EEEECCCHHHHhcCCeeEEEEEeCCceEEEeecccccccccccceeeeeccCCcCHHHHHHHHHHHHHH
Confidence            1          5999999999999999999999999999999976               24689999999999999999


Q ss_pred             HHHHHHHHHHHhcCCC
Q 002054          592 RLQILDHMEREISAPR  607 (974)
Q Consensus       592 ~~~I~~~m~~~i~~~~  607 (974)
                      +.+|++.|+++|++..
T Consensus       219 ~~~i~~~~~~~l~~~~  234 (246)
T 3hkm_A          219 SSRISDFMRTTLQKQA  234 (246)
T ss_dssp             HHHHHHHHHTTTC---
T ss_pred             HHHHHHHHHHHHHhhh
Confidence            9999999999998764

>3b4t_A Ribonuclease PH; RNAse, tRNA nucleotidyltransferase, RPHA, STRU genomics, TBSGC; 2.10A {Mycobacterium tuberculosis}

Probab=100.00  E-value=2.1e-41  Score=368.03  Aligned_cols=234  Identities=26%  Similarity=0.315  Sum_probs=209.3

Q ss_pred             cCCcCCCCCCCCccCeEEEeCCCCCCCcceEEEeCCeEEEEEEEeCCCchhhhccccCCCCceeEEEEEecCCCCccccc
Q 002054          367 EGVRVDGRQLDEVRPIYCESGNLPILHGSSLFSRGDTQVLCTVTLGAPAEAQRLESLVGPPTKRFMLHYSFPPFCINEVG  446 (974)
Q Consensus       367 ~~~R~DGR~~~e~R~I~ie~g~l~~a~GSal~~~G~T~Vl~~Vtl~~p~~~~~~d~~~~~~~~~~~v~~~f~p~s~~e~~  446 (974)
                      .|+|+|||.++|+|+|++++|+++++||||+|++|+|+|+|+|+.+  .....  ...+++.+.++++|+++|||++++.
T Consensus         4 ~g~R~DGR~~~e~R~i~i~~g~~~~a~GSa~v~~G~T~Vl~~V~~~--~~~p~--~~~~~~~g~l~v~~~~~p~a~~~~~   79 (262)
T 3b4t_A            4 VSKREDGRLDHELRPVIITRGFTENPAGSVLIEFGHTKVLCTASVT--EGVPR--WRKATGLGWLTAEYAMLPSATHSRS   79 (262)
T ss_dssp             -CCSTTSCCTTCCCCEEEEETSSSSSSEEEEEEETTEEEEEEEEEE--ESCC------CCSCCEEEEEEEECGGGSSSCC
T ss_pred             CCcCCCCCCCcCcCCeEEEeCCcCCCCeEEEEEECCCEEEEEEEec--CcCCC--ccCCCCceEEEEEEEeCCCcccccc
Confidence            5899999999999999999999999999999999999999999943  22110  1123577899999999999998875


Q ss_pred             cc----cCCCchhhhHHHHHHHHhhhcCCCCCCCC-eEEEEEEEEEcCCCChhhHHHHHHHHHHHHc------------C
Q 002054          447 KR----VGLNRREVGHGTLAEKALLAVLPPENDFP-YTVRVNSEVMASDGSTSMATVCGGSMALMDA------------G  509 (974)
Q Consensus       447 ~~----~~~~rre~~~~~l~eral~~vi~~~~~~p-~tI~V~v~VLesdGs~~~A~v~aa~lAL~da------------g  509 (974)
                      ++    |.+++++++++++++|+|+++++. +.|| |+|+|+++||++|||+++||+||+++||+||            +
T Consensus        80 ~Re~~~G~~~~~~~~isrli~r~lr~~i~~-~~l~~~~I~i~~~VL~~DG~~~~aai~aa~~AL~~a~~~~~~~~~~~~~  158 (262)
T 3b4t_A           80 DRESVRGRLSGRTQEISRLIGRSLRACIDL-AALGENTIAIDCDVLQADGGTRTAAITGAYVALADAVTYLSAAGKLSDP  158 (262)
T ss_dssp             CCHHHHTSCCHHHHHHHHHHHHHHHTTBCH-HHHCSEEEEEEEEEEECSSCHHHHHHHHHHHHHHHHHHHHHHTTCCSSS
T ss_pred             ccccCCCCCCHHHHHHHHHHHHHHHHhcCH-hHCCCeEEEEEEEEEeCCCCHHHHHHHHHHHHHHHhhhhhccCCccccC
Confidence            43    689999999999999999999998 5677 8999999999999999999999999999999            9


Q ss_pred             CCccccccceeeeeeccCCCCCCcccceEEEecCCccccccCCccEEEEeeCCc-eEEEEeeccCCCCCHHHHHHHHHHH
Q 002054          510 IPLQEHVAGVSVGLVSEVDPSTGEIKDYRILTDILGLEDHLGDMDFKIAGTRIG-VTAIQLDIKPAGIPLDIICECLEHA  588 (974)
Q Consensus       510 vPi~~~vagvs~gli~~~d~~~~~~~~~~iL~Dp~~~Ee~~~d~d~~Va~t~~g-I~alq~~~k~~~i~~e~l~~al~~A  588 (974)
                      +||+++|+++++|++++           .+|+||+..||+.++++++|+++.+| |+++|+++++.+++.++|.+|+++|
T Consensus       159 ip~~~~v~avsvg~~~g-----------~~l~Dpt~~Ee~~~~~~l~va~~~~g~i~~i~~~g~~~~~~~~~l~~~l~~A  227 (262)
T 3b4t_A          159 RPLSCAIAAVSVGVVDG-----------RIRVDLPYEEDSRAEVDMNVVATDTGTLVEIQGTGEGATFARSTLDKLLDMA  227 (262)
T ss_dssp             CCBCSCEEEEEEEEETT-----------EEEESCCHHHHTTCSEEEEEEEETTSCEEEEEECSSCCCBCHHHHHHHHHHH
T ss_pred             CcccCceeEEEEEEECC-----------EEEECCCHHHHhccCceEEEEEcCCCCEEEEEeeCCCCCcCHHHHHHHHHHH
Confidence            99999999999999974           69999999999999999999999876 9999999877789999999999999


Q ss_pred             HHHHHHHHHHHHHHhcCCCCCCCCCCCc
Q 002054          589 HKGRLQILDHMEREISAPRTQDDRNSPR  616 (974)
Q Consensus       589 ~~~~~~I~~~m~~~i~~~~~~~~~~~p~  616 (974)
                      ++++.+|++.|++++.+++.+.++++|.
T Consensus       228 ~~~~~~i~~~~~~~l~~~~~~~~~~~~~  255 (262)
T 3b4t_A          228 LGACDTLFAAQRDALALPYPGVLPQGPP  255 (262)
T ss_dssp             HHHHHHHHHHHHHHHTSCCSSCCC----
T ss_pred             HHHHHHHHHHHHHHHhcchhccCccCCC
Confidence            9999999999999999999999998885

>2wp8_B Exosome complex component SKI6; nucleus, hydrolase, RNA-binding, exonucle binding, mitochondrion, rRNA processing; 3.00A {Saccharomyces cerevisiae}

Probab=100.00  E-value=5.4e-42  Score=369.37  Aligned_cols=226  Identities=23%  Similarity=0.332  Sum_probs=192.8

Q ss_pred             HHHhcCCcCCCCCCCCccCeEEEeCCCCCC-CcceEEEeCCeEEEEEEEeCCCchh-hhccccCCCCceeEEEEEecCCC
Q 002054          363 RIIAEGVRVDGRQLDEVRPIYCESGNLPIL-HGSSLFSRGDTQVLCTVTLGAPAEA-QRLESLVGPPTKRFMLHYSFPPF  440 (974)
Q Consensus       363 ~il~~~~R~DGR~~~e~R~I~ie~g~l~~a-~GSal~~~G~T~Vl~~Vtl~~p~~~-~~~d~~~~~~~~~~~v~~~f~p~  440 (974)
                      .++++|+|+|||.++|+|+|++++|+++++ ||||+|++|+|+|+|+|+  +|.+. ++.+  ..++++++++||+++||
T Consensus         6 ~~~~~~~R~DGR~~~e~R~i~i~~g~l~~aa~GSa~v~~G~T~Vl~~V~--~~~~~~~~~~--~~~~~g~l~v~~~~~p~   81 (246)
T 2wp8_B            6 IYSPEGLRLDGRRWNELRRFESSINTHPHAADGSSYMEQGNNKIITLVK--GPKEPRLKSQ--MDTSKALLNVSVNINKF   81 (246)
T ss_dssp             SSCTTSCCTTSCCTTCCCCEEEEECSCTTTCSEEEEEEETTEEEEEEEE--EEEC--------CCSSSEEEEEEEEEC--
T ss_pred             hhcccCccCCCCCcCCccCeEEEeCCCCCCCCceEEEEECCeEEEEEEE--ecCCcccccc--cCCCcEEEEEEEEeCCc
Confidence            467899999999999999999999999999 999999999999999999  55552 2111  24688999999999999


Q ss_pred             Cccccccc-cCCCchhhhHHHHHHHHhhhcCCCCCCCC-eEEEEEEEEEcCCCChhhHHHHHHHHHHHHcCCCccccccc
Q 002054          441 CINEVGKR-VGLNRREVGHGTLAEKALLAVLPPENDFP-YTVRVNSEVMASDGSTSMATVCGGSMALMDAGIPLQEHVAG  518 (974)
Q Consensus       441 s~~e~~~~-~~~~rre~~~~~l~eral~~vi~~~~~~p-~tI~V~v~VLesdGs~~~A~v~aa~lAL~dagvPi~~~vag  518 (974)
                      |++++.++ +.+++||++++++++|+|+++++. +.|| |+|+|+++||++|||+++||+||+++||+||||||+++|++
T Consensus        82 a~~~~~~r~g~~~~~~~~~s~li~r~l~~~i~~-~~~p~~~I~i~~~VL~~dG~~~~aai~aa~~AL~~a~iP~~~~v~a  160 (246)
T 2wp8_B           82 SKFERSKSSHKNERRVLEIQTSLVRMFEKNVML-NIYPRTVIDIEIHVLEQDGGIMGSLINGITLALIDAGISMFDYISG  160 (246)
T ss_dssp             ------------CHHHHHHHHHHHHHHHHHBCT-TTSCSEEEEEEEEEEECCSCHHHHHHHHHHHHHHHHTCCBSSCEEE
T ss_pred             ccccccccCCCCChhHHHHHHHHHHHHHHhhhH-HHCCCeEEEEEEEEEECCCCHHHHHHHHHHHHHHHcCCcccCceeE
Confidence            99998766 566799999999999999999998 6887 57999999999999999999999999999999999999999


Q ss_pred             eeeeeeccCCCCCCcccceEEEecCCccccccCCccEEEEe--eCCceEEEEeeccCCCCCHHHHHHHHHHHHHHHHHHH
Q 002054          519 VSVGLVSEVDPSTGEIKDYRILTDILGLEDHLGDMDFKIAG--TRIGVTAIQLDIKPAGIPLDIICECLEHAHKGRLQIL  596 (974)
Q Consensus       519 vs~gli~~~d~~~~~~~~~~iL~Dp~~~Ee~~~d~d~~Va~--t~~gI~alq~~~k~~~i~~e~l~~al~~A~~~~~~I~  596 (974)
                      +++|++++           .+|+||+..|| .++++++|+.  +.++|+++|+++   .++.++|.+|+++|++++.+|+
T Consensus       161 vs~g~~~~-----------~~l~Dp~~~Ee-~~~~~l~v~~~~~~~~i~~i~~~g---~~~~~~l~~~l~~A~~~~~~i~  225 (246)
T 2wp8_B          161 ISVGLYDT-----------TPLLDTNSLEE-NAMSTVTLGVVGKSEKLSLLLVED---KIPLDRLENVLAIGIAGAHRVR  225 (246)
T ss_dssp             EEEEEETT-----------EEESSCCHHHH-HHSEEEEEEEETTSSCEEEEEECS---CEEHHHHHHHHHHHHHHHHHHH
T ss_pred             EEEEEECC-----------EEEECCCchhh-ccCceEEEEEeCCCCCEEEEEecC---CcCHHHHHHHHHHHHHHHHHHH
Confidence            99999965           79999999999 9999999975  455699999964   5899999999999999999999


Q ss_pred             HHHHHHhcCCCC
Q 002054          597 DHMEREISAPRT  608 (974)
Q Consensus       597 ~~m~~~i~~~~~  608 (974)
                      +.|++++.++.+
T Consensus       226 ~~~~~~l~~~~~  237 (246)
T 2wp8_B          226 DLMDEELRKHAQ  237 (246)
T ss_dssp             HHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHH
Confidence            999999988754

>2po1_B Probable exosome complex exonuclease 2; RNAse PH, hydrolase/hydrolase/RNA complex; 1.94A {Pyrococcus abyssi} PDB: 2po0_B* 2pnz_B 2po2_B*

Probab=100.00  E-value=4.2e-41  Score=368.57  Aligned_cols=237  Identities=20%  Similarity=0.278  Sum_probs=210.7

Q ss_pred             HHHHHHHHHHHHHHHHhcCCcCCCCCCCCccCeEEEeCCCCCCCcceEEEeCCeEEEEEEEeC--CCchhhhccccCCCC
Q 002054          350 KAVDTVRKRVIRKRIIAEGVRVDGRQLDEVRPIYCESGNLPILHGSSLFSRGDTQVLCTVTLG--APAEAQRLESLVGPP  427 (974)
Q Consensus       350 ~~~~~~~~~~~r~~il~~~~R~DGR~~~e~R~I~ie~g~l~~a~GSal~~~G~T~Vl~~Vtl~--~p~~~~~~d~~~~~~  427 (974)
                      .+++..+++.+++ .+++|+|+|||.++|+|||++++|+++++||||+|++|+|+|+|+|+++  .|..       ..++
T Consensus         8 ~~~s~~~~~~i~~-~l~~~~R~DGR~~~e~R~i~i~~g~l~~a~GSa~v~~G~T~Vl~~V~~~~~~p~~-------~~~~   79 (277)
T 2po1_B            8 EIVAGIMRDHIIN-LLKEGKRIDDRGFEDYRPIEIEVGVIEKAEGSALVKLGSTQVLVGIKTSLGEPFP-------DTPN   79 (277)
T ss_dssp             ---CCHHHHHHHH-HHHTTCCTTSCCTTCCCCEEEEECCSTTSSEEEEEEETTEEEEEEEEEEEECCCT-------TCTT
T ss_pred             cccCccHHHHHHH-HHhcCCCCCCCCCCCcCCeEEEeCCcCCCCeEEEEEECCeEEEEEEEecccCCCC-------CCCC
Confidence            4566677777775 5699999999999999999999999999999999999999999999976  3432       2467


Q ss_pred             ceeEEEEEecCCCCccccccccCCCchhhhHHHHHHHHhhh--cCCCC------CCCCeEEEEEEEEEcCCCChhhHHHH
Q 002054          428 TKRFMLHYSFPPFCINEVGKRVGLNRREVGHGTLAEKALLA--VLPPE------NDFPYTVRVNSEVMASDGSTSMATVC  499 (974)
Q Consensus       428 ~~~~~v~~~f~p~s~~e~~~~~~~~rre~~~~~l~eral~~--vi~~~------~~~p~tI~V~v~VLesdGs~~~A~v~  499 (974)
                      +++|+++|+|+|||++.+ +.|.+++|+++++++++|+|++  +++.+      .+++|+|+|+++||++|||+++||+|
T Consensus        80 ~g~l~~~~~~~p~a~~~~-~~g~~~~~~~~l~~li~r~l~~s~~idl~~L~i~pg~~~w~i~id~~VL~~dG~~~~a~i~  158 (277)
T 2po1_B           80 MGVMTTNVELVPLASPTF-EPGPPDERAIELARVIDRGIRESKALNLEKMVIVPGKIVRVVFIDVHVLDHDGNLMDAIGI  158 (277)
T ss_dssp             SCEEEEEEEECGGGCTTC-CSSSCCHHHHHHHHHHHHHHHTTTSBCGGGGEEETTTEEEEEEEEEEEEECSSCHHHHHHH
T ss_pred             ceEEEEEEEeCCCccccc-cCCCCChHHHHHHHHHHHHHhhcccccHHHccccCCcEEEEEEEEEEEECCCCCHHHHHHH
Confidence            899999999999999874 4578899999999999999987  34432      34679999999999999999999999


Q ss_pred             HHHHHHHHcC---------------------CCccccccceeeeeeccCCCCCCcccceEEEecCCccccccCCccEEEE
Q 002054          500 GGSMALMDAG---------------------IPLQEHVAGVSVGLVSEVDPSTGEIKDYRILTDILGLEDHLGDMDFKIA  558 (974)
Q Consensus       500 aa~lAL~dag---------------------vPi~~~vagvs~gli~~~d~~~~~~~~~~iL~Dp~~~Ee~~~d~d~~Va  558 (974)
                      |+++||+|||                     +||+++|+++++|++++           .+|+||+..||+.++++++|+
T Consensus       159 aa~~AL~da~~p~~~~~~~~~~~~~~~~~~~ipl~~~~~avs~g~~~~-----------~~l~Dp~~~Ee~~~~~~~~v~  227 (277)
T 2po1_B          159 AAIAALLNARVPKVRYNEETGEVETLDETEPLPVEKIPVPVTFAKIGN-----------ILVVDPSLDEELVMDGKITIT  227 (277)
T ss_dssp             HHHHHHHHCEEEEEEECTTTCCEEEEEEEEECCBCCCCEEEEEEEETT-----------EEEESCCHHHHHHCSEEEEEE
T ss_pred             HHHHHHHhcCCCcEEEeCCCceeecccccccccccCceEEEEEEEECC-----------EEEeCCCHHHHhhCCCcEEEE
Confidence            9999999999                     89999999999999975           799999999999999999999


Q ss_pred             eeCCc-eEEEEeeccCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHhcCCC
Q 002054          559 GTRIG-VTAIQLDIKPAGIPLDIICECLEHAHKGRLQILDHMEREISAPR  607 (974)
Q Consensus       559 ~t~~g-I~alq~~~k~~~i~~e~l~~al~~A~~~~~~I~~~m~~~i~~~~  607 (974)
                      ++.+| |+++|+.+. ++++.++|.+|+++|.+++.+|.+.|++++.+.+
T Consensus       228 ~~~~g~i~~lq~~g~-~~~~~~~l~~~l~~A~~~~~~l~~~~~~~l~~~~  276 (277)
T 2po1_B          228 TDETGHISAVQKSEG-GAFKLEEVMYAVETAFKKAEEIRKLILEAVEKAK  276 (277)
T ss_dssp             ECTTSCEEEEEEESS-CCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHT
T ss_pred             EcCCCCEEEEEccCC-CCCCHHHHHHHHHHHHHHHHHHHHHHHHHHhhcc
Confidence            99988 999998764 6899999999999999999999999999998653

>3dd6_A Ribonuclease PH; exoribonuclease, tRNA maturation, RNAse PH., transferase; 1.70A {Bacillus anthracis}

Probab=100.00  E-value=4.1e-41  Score=363.26  Aligned_cols=227  Identities=27%  Similarity=0.357  Sum_probs=205.1

Q ss_pred             cCCcCCCCCCCCccCeEEEeCCCCCCCcceEEEeCCeEEEEEEEeCCCchhhhccccCCCCceeEEEEEecCCCCccccc
Q 002054          367 EGVRVDGRQLDEVRPIYCESGNLPILHGSSLFSRGDTQVLCTVTLGAPAEAQRLESLVGPPTKRFMLHYSFPPFCINEVG  446 (974)
Q Consensus       367 ~~~R~DGR~~~e~R~I~ie~g~l~~a~GSal~~~G~T~Vl~~Vtl~~p~~~~~~d~~~~~~~~~~~v~~~f~p~s~~e~~  446 (974)
                      ..+|.|||.++|+|||++++|+++++||||+|++|+|+|+|+|+.+...+    +...++++++|+++|+++|||+.++.
T Consensus         9 ~~~~~~~R~~~e~R~i~i~~g~~~~A~GSa~v~~G~T~Vl~~V~~~~~~p----~~~~~~~~g~l~v~~~~~P~a~~~~~   84 (255)
T 3dd6_A            9 HHMRVDGREKTELRHIHIHTNYLKHPEGSVLIEVGDTKVICSATIEERVP----PFMRGEGKGWVTAEYAMIPRATEQRT   84 (255)
T ss_dssp             --CCCCSCCTTCCCCEEEEESCSSSSSEEEEEEETTEEEEEEEEEESCCC----GGGTTSSCCEEEEEEEECTTSSSSCC
T ss_pred             cccccCCCCcCCCCCEEEEECCCCCCCeEEEEEECCeEEEEEEEecCCCC----CCCCCCCceEEEEEEEECCCcccccc
Confidence            35799999999999999999999999999999999999999999542211    22446789999999999999999876


Q ss_pred             cc----cCCCchhhhHHHHHHHHhhhcCCCCCCCCeEEEEEEEEEcCCCChhhHHHHHHHHHHHHc-----------CCC
Q 002054          447 KR----VGLNRREVGHGTLAEKALLAVLPPENDFPYTVRVNSEVMASDGSTSMATVCGGSMALMDA-----------GIP  511 (974)
Q Consensus       447 ~~----~~~~rre~~~~~l~eral~~vi~~~~~~p~tI~V~v~VLesdGs~~~A~v~aa~lAL~da-----------gvP  511 (974)
                      ++    |.+++|+++++++++|+|+++++.+....|+|+|+++||++|||+++||+||+++||+||           +||
T Consensus        85 ~Re~~~g~~~~~~~eisrli~r~lr~~i~~~~l~~~~I~V~~~VL~~DG~~~~aai~aa~~AL~~a~~p~~~~g~~~~iP  164 (255)
T 3dd6_A           85 IRESSKGKVTGRTMEIQRLIGRALRAVVDLEALGERTVWIDCDVIQADGGTRTASITGAYVAMVLAFEKLLQAEKVSKIP  164 (255)
T ss_dssp             CCCCC-CCCCHHHHHHHHHHHHHHHHHBCHHHHCSCEEEEEEEEEECSSCHHHHHHHHHHHHHHHHHHHHHHTTSSSSCC
T ss_pred             cccccCCCCCHHHHHHHHHHHHHHHHhcChhhcCCeEEEEEEEEEECCCCHHHHHHHHHHHHHHHhhhhhhhcCcccCCC
Confidence            43    779999999999999999999998544568999999999999999999999999999999           999


Q ss_pred             ccccccceeeeeeccCCCCCCcccceEEEecCCccccccCCccEEEEeeCCc-eEEEEeeccCCCCCHHHHHHHHHHHHH
Q 002054          512 LQEHVAGVSVGLVSEVDPSTGEIKDYRILTDILGLEDHLGDMDFKIAGTRIG-VTAIQLDIKPAGIPLDIICECLEHAHK  590 (974)
Q Consensus       512 i~~~vagvs~gli~~~d~~~~~~~~~~iL~Dp~~~Ee~~~d~d~~Va~t~~g-I~alq~~~k~~~i~~e~l~~al~~A~~  590 (974)
                      |+++|+++++|++++          ..+|+||+..||+.++++++|++|.+| |+++|++++.++++.++|.+|+++|++
T Consensus       165 l~~~v~avsvg~i~g----------~~vllDpt~~Ee~~~~~~l~Va~~~~g~i~~vq~~g~~~~~~~~~l~~~l~~A~~  234 (255)
T 3dd6_A          165 VKDYLAATSVGIVEE----------QGVVLDLNYAEDSKADVDMNVIMTGKGQFVEVQGTGEEATFSRAQLNELLDAAEQ  234 (255)
T ss_dssp             BSSCEEEEEEEEETT----------TEEEESCCHHHHHTEEEEEEEEEETTSCEEEEEEEESSSCCCHHHHHHHHHHHHH
T ss_pred             ccCceeEEEEEEECC----------EEEEeCCCHHHHhhcCceEEEEEcCCCcEEEEEecCCCCCcCHHHHHHHHHHHHH
Confidence            999999999999964          245599999999999999999999998 999999987789999999999999999


Q ss_pred             HHHHHHHHHHHHhcCCC
Q 002054          591 GRLQILDHMEREISAPR  607 (974)
Q Consensus       591 ~~~~I~~~m~~~i~~~~  607 (974)
                      ++.+|++.|++++++..
T Consensus       235 ~~~~i~~~~~~~l~~~~  251 (255)
T 3dd6_A          235 GIFQLIDIQKEALGDIV  251 (255)
T ss_dssp             HHHHHHHHHHHHHGGGG
T ss_pred             HHHHHHHHHHHHHHHHH
Confidence            99999999999998764

>3m7n_G Probable exosome complex exonuclease 2; exosome, RNA, exonuclease, hydrolase, nuclease, hydrolase-RN; 2.40A {Archaeoglobus fulgidus} PDB: 2ba1_H 2ba0_I 3m85_G

Probab=100.00  E-value=1.2e-40  Score=361.36  Aligned_cols=230  Identities=18%  Similarity=0.252  Sum_probs=207.4

Q ss_pred             HHHHHHHHHHHHHHHhcCCcCCCCCCCCccCeEEEeCCCCCCCcceEEEeCCeEEEEEEEeC--CCchhhhccccCCCCc
Q 002054          351 AVDTVRKRVIRKRIIAEGVRVDGRQLDEVRPIYCESGNLPILHGSSLFSRGDTQVLCTVTLG--APAEAQRLESLVGPPT  428 (974)
Q Consensus       351 ~~~~~~~~~~r~~il~~~~R~DGR~~~e~R~I~ie~g~l~~a~GSal~~~G~T~Vl~~Vtl~--~p~~~~~~d~~~~~~~  428 (974)
                      +++..+++.+++ .+++|+|+|||.++|+|++++++|.++++||||+|++|+|+|+|+|+++  .|..       ..+++
T Consensus         5 ~ls~~e~~~i~~-~l~~~~R~DGR~~~e~R~i~i~~g~l~~a~GSa~v~~G~T~Vl~~V~~~~~~p~~-------~~~~~   76 (259)
T 3m7n_G            5 ILVDIKRDYVLS-KLRDNERIDGRGFDEFRKVEIIPNVIEKAEGSALVKLGDTQVVVGVKMQPGEPYP-------DTPDR   76 (259)
T ss_dssp             HHHHHHHHHHHH-HHHTTCCTTCCCTTCCCCEEEEETSSTTSSEEEEEEETTEEEEEEEEEEEECCCS-------SCTTS
T ss_pred             ccCHHHHHHHHH-HHhcCCCCCCCCCccccCeEEEeCCcCCCCceEEEEECCcEEEEEEEecccCCCC-------CCCCc
Confidence            577888888885 5568999999999999999999999999999999999999999999965  2321       24678


Q ss_pred             eeEEEEEecCCCCccccccccCCCchhhhHHHHHHHHhhh--cCCCC------CCCCeEEEEEEEEEcCCCChhhHHHHH
Q 002054          429 KRFMLHYSFPPFCINEVGKRVGLNRREVGHGTLAEKALLA--VLPPE------NDFPYTVRVNSEVMASDGSTSMATVCG  500 (974)
Q Consensus       429 ~~~~v~~~f~p~s~~e~~~~~~~~rre~~~~~l~eral~~--vi~~~------~~~p~tI~V~v~VLesdGs~~~A~v~a  500 (974)
                      ++++++|+++|||+++++ .|.+++++++++++++|+|++  +++.+      .+|+|+|+|+++||++|||+++||+||
T Consensus        77 g~l~v~~~~~p~a~~~~~-~g~~~~~~~~~srli~r~lr~s~~i~l~~L~i~pg~~~~~i~i~~~VL~~DG~~~~aai~a  155 (259)
T 3m7n_G           77 GVIIVNAELVPLASPTFE-PGPPDENSIELARVVDRGIRESEAVDLSKLVIEEGEKVWIVFVDIHALDDDGNLLDASALA  155 (259)
T ss_dssp             CEEEEEEECCTTSCTTCC-SSSSCHHHHHHHHHHHHHHHHTTCBCGGGGEEETTTEEEEEEEEEEEEECSSCHHHHHHHH
T ss_pred             eEEEEEEEeCCccccccc-CCCCChHHHHHHHHHHHHHhhcCCccHHHhcccCCcEEEEEEEEEEEEcCCCCHHHHHHHH
Confidence            899999999999999874 588999999999999999998  66652      245699999999999999999999999


Q ss_pred             HHHHHHHcCC-------------CccccccceeeeeeccCCCCCCcccceEEEecCCccccccCCccEEEEeeCCc-eEE
Q 002054          501 GSMALMDAGI-------------PLQEHVAGVSVGLVSEVDPSTGEIKDYRILTDILGLEDHLGDMDFKIAGTRIG-VTA  566 (974)
Q Consensus       501 a~lAL~dagv-------------Pi~~~vagvs~gli~~~d~~~~~~~~~~iL~Dp~~~Ee~~~d~d~~Va~t~~g-I~a  566 (974)
                      +++||+|+++             ||+++|+++++|++++           .+|+||+..||+.++++++|+++.+| +++
T Consensus       156 a~~AL~~a~iP~~~~~~~~~~~lp~~~~~~avtvg~~~~-----------~~l~Dpt~~Ee~~~~~~l~va~~~~g~i~~  224 (259)
T 3m7n_G          156 AIAALMNTKVPAERFDLGEDYLLPVRDLPVSVTSLIVGN-----------KYLVDPSREEMSVGDTTLTITTDKDDNVVA  224 (259)
T ss_dssp             HHHHHHTCEECTGGGTSSSCEECCBCCCCEEEEEEEETT-----------EEEESCCTTGGGGCSCEEEEEECTTSCEEE
T ss_pred             HHHHHHhCCCCeEEecCCceecccccCceeEEEEEEECC-----------EEEECCCHHHHhhCCCcEEEEEeCCCcEEE
Confidence            9999999999             7999999999999975           69999999999999999999999985 999


Q ss_pred             EEeeccCCCCCHHHHHHHHHHHHHHHHHHHHHHHH
Q 002054          567 IQLDIKPAGIPLDIICECLEHAHKGRLQILDHMER  601 (974)
Q Consensus       567 lq~~~k~~~i~~e~l~~al~~A~~~~~~I~~~m~~  601 (974)
                      +|+.++ ++++.++|.+|+++|++++.+|++.|++
T Consensus       225 i~~~g~-~~~~~~~l~~~l~~a~~~~~~l~~~~~~  258 (259)
T 3m7n_G          225 MQKSGG-YLLDEKLFDELLDVSINCARKLREKFKE  258 (259)
T ss_dssp             EEEESS-CCBCHHHHHHHHHHHHHHHHHHHHTTC-
T ss_pred             EECCCC-CCcCHHHHHHHHHHHHHHHHHHHHHHhh
Confidence            999876 7999999999999999999999998764

>2wnr_A Probable exosome complex exonuclease 2; phosphate binding, 3'-5' exoribonuclease, hydrolase; 2.65A {Methanothermobacter thermautotrophicusorganism_taxid}

Probab=100.00  E-value=8.2e-41  Score=365.33  Aligned_cols=230  Identities=19%  Similarity=0.271  Sum_probs=207.7

Q ss_pred             HHHHHHHHHHHHhcCCcCCCCCCCCccCeEEEeCCCCCCCcceEEEeCCeEEEEEEEeC--CCchhhhccccCCCCceeE
Q 002054          354 TVRKRVIRKRIIAEGVRVDGRQLDEVRPIYCESGNLPILHGSSLFSRGDTQVLCTVTLG--APAEAQRLESLVGPPTKRF  431 (974)
Q Consensus       354 ~~~~~~~r~~il~~~~R~DGR~~~e~R~I~ie~g~l~~a~GSal~~~G~T~Vl~~Vtl~--~p~~~~~~d~~~~~~~~~~  431 (974)
                      ..+++.++ .++++|+|+|||.++|+|++++++|.++++||||+|++|+|+|+|+|+++  .|..       .+++++++
T Consensus        10 ~~~~~~~~-~~l~~~~R~DGR~~~e~R~i~i~~g~l~~a~GSa~v~~G~T~Vl~~V~~~~~~p~~-------~~~~~g~l   81 (271)
T 2wnr_A           10 EITRKSIT-DLINNKERIDGRSLHEFRDISIETGVISKAEGSSRVKLGNTQIIVGVKPQIGEPFP-------DTPEMGVI   81 (271)
T ss_dssp             CHHHHHHH-HHHHTTCCTTCCCTTCCCCEEEEESCSTTSSEEEEEEETTEEEEEEEEEEEECCCT-------TCTTCCEE
T ss_pred             ccHHHHHH-HHHhcCCCCCCCCcccccCeEEEeCccCCCCeEEEEEECCeEEEEEEEeeeecCCC-------CCCCceEE
Confidence            34455555 58999999999999999999999999999999999999999999999965  3322       24688999


Q ss_pred             EEEEecCCCCccccccccCCCchhhhHHHHHHHHhhh--cCCCCC------CCCeEEEEEEEEEcCCCChhhHHHHHHHH
Q 002054          432 MLHYSFPPFCINEVGKRVGLNRREVGHGTLAEKALLA--VLPPEN------DFPYTVRVNSEVMASDGSTSMATVCGGSM  503 (974)
Q Consensus       432 ~v~~~f~p~s~~e~~~~~~~~rre~~~~~l~eral~~--vi~~~~------~~p~tI~V~v~VLesdGs~~~A~v~aa~l  503 (974)
                      +++|+++|||+++ ++.|.+++++++++++++|+|++  +++.+.      +++|+|+|+++||++|||+++||+||+++
T Consensus        82 ~v~~~~~p~a~~~-~~~g~~~~~~~~~s~li~r~lr~s~~i~l~~l~i~pg~~~~~i~i~~~VL~~DG~~~~aai~aa~~  160 (271)
T 2wnr_A           82 LTNSELLPMASPT-FEPGPPDERSVELSRVVDRCIRESRMIDLEKLCIIEGSKVWMLFLDLHIIDYDGNLFDAAVLATVA  160 (271)
T ss_dssp             EEEEEECGGGCTT-CCCSSCCHHHHHHHHHHHHHHHHTTCBCGGGGEEETTTEEEEEEEEEEEEECSSCHHHHHHHHHHH
T ss_pred             EEEEEeCCccccc-ccCCCCchHHHHHHHHHHHHHhccCCccHHHccccCCcEEEEEEEEEEEECCCCCHHHHHHHHHHH
Confidence            9999999999987 45788999999999999999998  687631      24799999999999999999999999999


Q ss_pred             HHHHcC--------------------CCccccccceeeeeeccCCCCCCcccceEEEecCCccccccCCccEEEEeeCCc
Q 002054          504 ALMDAG--------------------IPLQEHVAGVSVGLVSEVDPSTGEIKDYRILTDILGLEDHLGDMDFKIAGTRIG  563 (974)
Q Consensus       504 AL~dag--------------------vPi~~~vagvs~gli~~~d~~~~~~~~~~iL~Dp~~~Ee~~~d~d~~Va~t~~g  563 (974)
                      ||+|+|                    +||+++|+++++|++++           .+|+||+..||+.++++++|+++.+|
T Consensus       161 AL~~a~~p~~~~~~~~~~~~~~~~~~ip~~~~~~avt~g~~~~-----------~~l~Dpt~~Ee~~~~~~l~va~~~~~  229 (271)
T 2wnr_A          161 ALLDTRIPAAEVEDGEVVINREKMQPLPVNRKALMCTFAKIGN-----------EIVLDPSLEEEDILTARISIGVTEEG  229 (271)
T ss_dssp             HHHHCEEEEEEEETTEEEEEEEEEEECCBCCCEEEEEEEEETT-----------EEEESCCHHHHTTCSEEEEEEEETTS
T ss_pred             HHHhcCCCeEEecCCceeeccCcccccCccCCeEEEEEEEECC-----------EEEeCCCHHHHhcCCCcEEEEEeCCC
Confidence            999999                    99999999999999975           79999999999999999999999866


Q ss_pred             -eEEEEeeccCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHhc
Q 002054          564 -VTAIQLDIKPAGIPLDIICECLEHAHKGRLQILDHMEREIS  604 (974)
Q Consensus       564 -I~alq~~~k~~~i~~e~l~~al~~A~~~~~~I~~~m~~~i~  604 (974)
                       |+++|++++ ++++.++|.+|+++|++++.+|++.|+++++
T Consensus       230 ~i~~i~~~g~-~~~~~~~l~~~l~~a~~~~~~i~~~~~~~l~  270 (271)
T 2wnr_A          230 SICAMQKGGE-GPLTRDDVLKAVSIAVEKVPQLIEYLDKSMT  270 (271)
T ss_dssp             CEEEEEEESS-SCBCHHHHHHHHHHHHHHHHHHHHHHHHHC-
T ss_pred             CEEEEECCCC-CCCCHHHHHHHHHHHHHHHHHHHHHHHHHhC
Confidence             999999876 6899999999999999999999999999874

>1oys_A Ribonuclease PH; transferase, tRNA processing; 2.40A {Bacillus subtilis} SCOP: d.14.1.4 d.101.1.1 PDB: 1oyp_A 1oyr_A

Probab=100.00  E-value=1.6e-41  Score=365.47  Aligned_cols=229  Identities=26%  Similarity=0.337  Sum_probs=184.0

Q ss_pred             CcCCCCCCCCccCeEEEeCCCCCCCcceEEEeCCeEEEEEEEeCCCchhhhccccCCCCceeEEEEEecCCCCccccccc
Q 002054          369 VRVDGRQLDEVRPIYCESGNLPILHGSSLFSRGDTQVLCTVTLGAPAEAQRLESLVGPPTKRFMLHYSFPPFCINEVGKR  448 (974)
Q Consensus       369 ~R~DGR~~~e~R~I~ie~g~l~~a~GSal~~~G~T~Vl~~Vtl~~p~~~~~~d~~~~~~~~~~~v~~~f~p~s~~e~~~~  448 (974)
                      +|+|||.++|+|||++++|+++++||||+|++|+|+|+|+|+++  ....  ....+++++++++||+++|||++++.++
T Consensus         1 ~R~DGR~~~e~R~i~i~~g~l~~a~GSa~v~~G~T~Vl~~V~~~--~~~p--~~~~~~~~g~l~~~~~~~p~a~~~~~~R   76 (245)
T 1oys_A            1 MRHDGRQHDELRPITFDLDFISHPEGSVLITAGNTKVICNASVE--DRVP--PFLRGGGKGWITAEYSMLPQATNQQTIQ   76 (245)
T ss_dssp             CCTTSCCTTCCCCEEEECC-----CCCEEEEETTEEEEEEEEEE--SCCC--GGGTTSCCCEEEEEEEC-----------
T ss_pred             CCCCCCCCCCcCCeEEEeCCCCCCCEEEEEEECCeEEEEEEEec--cccC--CccCCCCceEEEEEEEeCCCcCcccccc
Confidence            49999999999999999999999999999999999999999954  2211  1123568899999999999999987533


Q ss_pred             ----cCCCchhhhHHHHHHHHhhhcCCCCCCCCeEEEEEEEEEcCCCChhhHHHHHHHHHHHHcC-----------CCcc
Q 002054          449 ----VGLNRREVGHGTLAEKALLAVLPPENDFPYTVRVNSEVMASDGSTSMATVCGGSMALMDAG-----------IPLQ  513 (974)
Q Consensus       449 ----~~~~rre~~~~~l~eral~~vi~~~~~~p~tI~V~v~VLesdGs~~~A~v~aa~lAL~dag-----------vPi~  513 (974)
                          |.++.++.+++++++|+|+++++.+..++|+|+|+++||++|||+++||+||+++||+|||           +||+
T Consensus        77 e~~~G~~~~~~~eis~li~r~l~~~i~~~~l~~~~i~i~~~VL~~DG~~~~aai~aa~~AL~~a~~~~~~~~~~~~ipl~  156 (245)
T 1oys_A           77 ESSKGKISGRTMEIQRLIGRALRAVVDLEKLGERTIWIDCDVIQADGGTRTASITGAFLAMAIAIGKLIKAGTIKTNPIT  156 (245)
T ss_dssp             --------CHHHHHHHHHHHHHHHTBCHHHHCSCEEEEEEEEEECSSCHHHHHHHHHHHHHHHHHHHHHHTTSSSSCCBC
T ss_pred             cccCCCCchHHHHHHHHHHHHHHHhcCHhHCCCEEEEEEEEEEeCCCCHHHHHHHHHHHHHHhccchhcccCcccccCCC
Confidence                5688999999999999999999985456679999999999999999999999999999999           9999


Q ss_pred             ccccceeeeeeccCCCCCCcccceEEEecCCccccccCCccEEEEeeCCc-eEEEEeeccCCCCCHHHHHHHHHHHHHHH
Q 002054          514 EHVAGVSVGLVSEVDPSTGEIKDYRILTDILGLEDHLGDMDFKIAGTRIG-VTAIQLDIKPAGIPLDIICECLEHAHKGR  592 (974)
Q Consensus       514 ~~vagvs~gli~~~d~~~~~~~~~~iL~Dp~~~Ee~~~d~d~~Va~t~~g-I~alq~~~k~~~i~~e~l~~al~~A~~~~  592 (974)
                      ++|+++++|++++          ..+|+||+..||+.++++++|+++.+| |+++|+++++++++.++|.+|+++|++++
T Consensus       157 ~~v~avs~g~~~g----------~~vl~Dp~~~Ee~~~~~~~~v~~~~~g~i~~iq~~g~~~~~~~~~l~~~l~~A~~~~  226 (245)
T 1oys_A          157 DFLAAISVGIDKE----------QGILLDLNYEEDSSAEVDMNVIMTGSGRFVELQGTGEEATFSREDLNGLLGLAEKGI  226 (245)
T ss_dssp             SCEEEEEEEEETT----------TEEEESCCHHHHHHEEEEEEEEEETTSCEEEEEEEESSCCCCHHHHHHHHHHHHHHH
T ss_pred             CceeEEEEEEECC----------EEEEecCCHHHHhcCCCcEEEEEcCCCcEEEEEEeCCCCCcCHHHHHHHHHHHHHHH
Confidence            9999999999963          256699999999999999999999988 99999998888999999999999999999


Q ss_pred             HHHHHHHHHHhcCCCCCCC
Q 002054          593 LQILDHMEREISAPRTQDD  611 (974)
Q Consensus       593 ~~I~~~m~~~i~~~~~~~~  611 (974)
                      .+|++.|++++.++..+++
T Consensus       227 ~~i~~~~~~~l~~~~~~~~  245 (245)
T 1oys_A          227 QELIDKQKEVLGDSLPELK  245 (245)
T ss_dssp             HHHHHHHHHHC--------
T ss_pred             HHHHHHHHHHHhhhhhhcC
Confidence            9999999999998876653

>2nn6_C Exosome complex exonuclease RRP43; RNA, exosome, PM/SCL, phosphorolytic, hydrolase/transferase complex; 3.35A {Homo sapiens} SCOP: d.14.1.4 d.101.1.1

Probab=100.00  E-value=7.2e-41  Score=367.16  Aligned_cols=239  Identities=19%  Similarity=0.311  Sum_probs=213.1

Q ss_pred             HHHHHHHHHHHHHHHHHhcCCcCCCCCCCCccCeEEEeCCCCCCCcceEEEeCCeEEEEEEEeC--CCchhhhccccCCC
Q 002054          349 PKAVDTVRKRVIRKRIIAEGVRVDGRQLDEVRPIYCESGNLPILHGSSLFSRGDTQVLCTVTLG--APAEAQRLESLVGP  426 (974)
Q Consensus       349 ~~~~~~~~~~~~r~~il~~~~R~DGR~~~e~R~I~ie~g~l~~a~GSal~~~G~T~Vl~~Vtl~--~p~~~~~~d~~~~~  426 (974)
                      .++|.++.++.|+.++|++|+|+|||.++|+|++.+++|.++++||||+|++|+|+|+|+|+.+  .|..       ..+
T Consensus         4 ~~~~~~~~~~~~~~~~l~~~~R~DGR~~~e~R~i~i~~g~l~~a~GSa~v~~G~T~Vl~~V~~~~~~p~~-------~~~   76 (278)
T 2nn6_C            4 AAGFKTVEPLEYYRRFLKENCRPDGRELGEFRTTTVNIGSISTADGSALVKLGNTTVICGVKAEFAAPST-------DAP   76 (278)
T ss_dssp             -----CCSTHHHHHHHHHTSCCTTSCCSCCCCSCCEEETCCSSSSEEEEEEETTEEEEEEEEEEECCCCS-------SST
T ss_pred             hhhhhhhCHHHHHHHHHhcCCCCCCCCcccccCeEEEeCCccCCCceEEEEeCCeEEEEEEEEEeecCCC-------CCC
Confidence            4578899999999999999999999999999999999999999999999999999999999954  1221       125


Q ss_pred             CceeEEEEEecCCCCccccccccCCCchhhhHHHHHHHHhhh--cCCCC------CCCCeEEEEEEEEEcCCCChhhHHH
Q 002054          427 PTKRFMLHYSFPPFCINEVGKRVGLNRREVGHGTLAEKALLA--VLPPE------NDFPYTVRVNSEVMASDGSTSMATV  498 (974)
Q Consensus       427 ~~~~~~v~~~f~p~s~~e~~~~~~~~rre~~~~~l~eral~~--vi~~~------~~~p~tI~V~v~VLesdGs~~~A~v  498 (974)
                      ++++++++|+++|||++++ +.|.+++++++++++++|+|++  +++.+      .+|+|+|+|+++||++|||+++||+
T Consensus        77 ~~g~l~v~~~~~p~a~~~~-~~g~~~~~~~~~s~li~r~l~~s~~i~l~~L~i~pg~~~~~i~i~~~VL~~DG~~~~aai  155 (278)
T 2nn6_C           77 DKGYVVPNVDLPPLCSSRF-RSGPPGEEAQVASQFIADVIENSQIIQKEDLCISPGKLVWVLYCDLICLDYDGNILDACT  155 (278)
T ss_dssp             TCCCCEEEEECCSSSCTTS-CSSSCCHHHHHHHHHHHHHHHHHCCSCHHHHCSSBTTBCEEEEEEEEESSCCSCTTHHHH
T ss_pred             CccEEEEEEEeCCccCccc-cCCCCcHHHHHHHHHHHHHHhccCCCCHHHCEEeCCcEEEEEEEEEEEECCCCCHHHHHH
Confidence            7899999999999999986 4578899999999999999994  67542      3689999999999999999999999


Q ss_pred             HHHHHHHHHcCC----------------------CccccccceeeeeeccCCCCCCcccceEEEecCCccccccCCccEE
Q 002054          499 CGGSMALMDAGI----------------------PLQEHVAGVSVGLVSEVDPSTGEIKDYRILTDILGLEDHLGDMDFK  556 (974)
Q Consensus       499 ~aa~lAL~dagv----------------------Pi~~~vagvs~gli~~~d~~~~~~~~~~iL~Dp~~~Ee~~~d~d~~  556 (974)
                      ||+++||+|+|+                      ||+++|+++++|++++          +.+|+||+..||+.++++++
T Consensus       156 ~aa~~AL~~a~iP~v~~~~~~~~~~~~~~~~~~lp~~~~~~avs~g~~~~----------~~~l~Dpt~~Ee~~~~~~l~  225 (278)
T 2nn6_C          156 FALLAALKNVQLPEVTINEETALAEVNLKKKSYLNIRTHPVATSFAVFDD----------TLLIVDPTGEEEHLATGTLT  225 (278)
T ss_dssp             HHHHHHHHTCCCCCCCBCSSSBCCCTTSCCCSCSCCSCCCEEEEEEECTT----------TCCEESCCTTTTTSCSEEEE
T ss_pred             HHHHHHHHhCCCCeEEEeCCCcceecCcccccccccCCceEEEEEEEECC----------ceEEECCCHHHHhhcCceEE
Confidence            999999999996                      7999999999999964          25999999999999999999


Q ss_pred             EEeeCCc-eEEEEeeccCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHhcCC
Q 002054          557 IAGTRIG-VTAIQLDIKPAGIPLDIICECLEHAHKGRLQILDHMEREISAP  606 (974)
Q Consensus       557 Va~t~~g-I~alq~~~k~~~i~~e~l~~al~~A~~~~~~I~~~m~~~i~~~  606 (974)
                      |+++.+| |+++|+.+ +.+++.++|.+|+++|++++.+|++.|++++++.
T Consensus       226 va~~~~g~i~~v~~~g-~~~~~~~~l~~~l~~a~~~~~~i~~~~~~~l~~~  275 (278)
T 2nn6_C          226 IVMDEEGKLCCLHKPG-GSGLTGAKLQDCMSRAVTRHKEVKKLMDEVIKSM  275 (278)
T ss_dssp             EEECTTCCEEEEEESC-CSCCCHHHHHHHHHHHHHHHHHHHHHHHTTTTTT
T ss_pred             EEEcCCCcEEEEEccC-CCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHhh
Confidence            9999986 99999987 4689999999999999999999999999999875

>2nn6_F MTR3, exosome component 6; RNA, exosome, PM/SCL, phosphorolytic, hydrolase/transferase complex; 3.35A {Homo sapiens} SCOP: d.14.1.4 d.101.1.1

Probab=100.00  E-value=2.3e-41  Score=369.59  Aligned_cols=227  Identities=20%  Similarity=0.269  Sum_probs=194.7

Q ss_pred             hcCCcCCCCCCCCccCeEEEeCCCCCCCcceEEEeCCeEEEEEEEeCCCchhhhccc--c--------CCCCceeEEEEE
Q 002054          366 AEGVRVDGRQLDEVRPIYCESGNLPILHGSSLFSRGDTQVLCTVTLGAPAEAQRLES--L--------VGPPTKRFMLHY  435 (974)
Q Consensus       366 ~~~~R~DGR~~~e~R~I~ie~g~l~~a~GSal~~~G~T~Vl~~Vtl~~p~~~~~~d~--~--------~~~~~~~~~v~~  435 (974)
                      ++++|+|||.++|+|+|++++|+++++||||+|++|+|+|||+|+  +|.+......  +        ..++++++++||
T Consensus        23 ~~~~R~DGR~~~e~R~i~i~~g~l~~a~GSa~v~~G~T~Vl~~V~--~~~~~~~~~~~~~~~~~~~~~~~~~~g~l~v~~  100 (272)
T 2nn6_F           23 DEEEAPGTRDPTRLRPVYARAGLLSQAKGSAYLEAGGTKVLCAVS--GPRQAEGGERGGGPAGAGGEAPAALRGRLLCDF  100 (272)
T ss_dssp             ------CCCCSSCCCCCCCCCSCCSSSSEEECCCSSSCEEEEEEE--EEECC-------------------CBCEEEEEE
T ss_pred             ccCccCCCCCccccCCeEEEeCCCCCCCeEEEEEeCCeEEEEEEE--CCCcccccccccccccccccccCCCceEEEEEE
Confidence            788999999999999999999999999999999999999999999  6665432111  0        034679999999


Q ss_pred             ecCCCCccccccccCCCchhhhHHHHHHHHhhhcCCCCCCCC-eEEEEEEEEEcCCCChhhHHHHHHHHHHHHcCCCccc
Q 002054          436 SFPPFCINEVGKRVGLNRREVGHGTLAEKALLAVLPPENDFP-YTVRVNSEVMASDGSTSMATVCGGSMALMDAGIPLQE  514 (974)
Q Consensus       436 ~f~p~s~~e~~~~~~~~rre~~~~~l~eral~~vi~~~~~~p-~tI~V~v~VLesdGs~~~A~v~aa~lAL~dagvPi~~  514 (974)
                      +|+|||+++++ .++++++|++|+++++|+|+++++. +.|| |+|+|+++||++|||+++||+||+++||+|||||+++
T Consensus       101 ~~~p~a~~~~~-~~~~~~~e~~~s~li~r~l~~~i~~-~~~p~~~I~I~~~VL~~DG~~~~aai~aa~~AL~da~iP~~~  178 (272)
T 2nn6_F          101 RRAPFAGRRRR-APPGGCEERELALALQEALEPAVRL-GRYPRAQLEVSALLLEDGGSALAAALTAAALALADAGVEMYD  178 (272)
T ss_dssp             EECTTSSSSCC-CSCCHHHHHHHHHHHHHHHTTTBCS-TTSBTCEEEEEEEEEECCSSHHHHHHHHHHHHHHHHCCCBSS
T ss_pred             EecCCCcCCcc-CCCCCHHHHHHHHHHHHHHHHhccH-HHCCceEEEEEEEEEeCCCCHHHHHHHHHHHHHHHcCCcccC
Confidence            99999999865 4789999999999999999999998 6899 6999999999999999999999999999999999999


Q ss_pred             cccceeeeeeccCCCCCCcccceEEEecCCccccccCCccEEEE--eeCCceEEEEeeccCCCCCH-HHHHHHHHHHHHH
Q 002054          515 HVAGVSVGLVSEVDPSTGEIKDYRILTDILGLEDHLGDMDFKIA--GTRIGVTAIQLDIKPAGIPL-DIICECLEHAHKG  591 (974)
Q Consensus       515 ~vagvs~gli~~~d~~~~~~~~~~iL~Dp~~~Ee~~~d~d~~Va--~t~~gI~alq~~~k~~~i~~-e~l~~al~~A~~~  591 (974)
                      +++|+++|++.+.        +..+|+||+..||+.++++++|+  ++.++|+++|+++   +++. ++|.+|+++|+++
T Consensus       179 ~v~avsvg~~~~~--------~~~~llDpt~~Ee~~~~~~l~va~~~~~~~I~~i~~~g---~~~~~~~l~~~l~~A~~~  247 (272)
T 2nn6_F          179 LVVGCGLSLAPGP--------APTWLLDPTRLEEERAAAGLTVALMPVLNQVAGLLGSG---EGGLTESWAEAVRLGLEG  247 (272)
T ss_dssp             CCEEEECCCCSCS--------SCCCCSSCCTTTGGGCSSEEEEEEETTTTEEEEEEEEC---CSSCTTTTHHHHHHHHHH
T ss_pred             cEEEEEEEEeecc--------CCeEEeCCCHHHhccCCceEEEEEeCCCCCEEEEEEec---CCCHHHHHHHHHHHHHHH
Confidence            9999999995221        22699999999999999999999  4556799999986   4899 9999999999999


Q ss_pred             HHHHHHHHHHHhcCCC
Q 002054          592 RLQILDHMEREISAPR  607 (974)
Q Consensus       592 ~~~I~~~m~~~i~~~~  607 (974)
                      +++|++.|++++.++.
T Consensus       248 ~~~i~~~~~~~l~~~~  263 (272)
T 2nn6_F          248 CQRLYPVLQQSLVRAA  263 (272)
T ss_dssp             HHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHH
Confidence            9999999999998753

>1udn_A Ribonuclease PH, RNAse PH; transferase, riken structural genomics/proteomics initiative structural genomics; 2.30A {Aquifex aeolicus} SCOP: d.14.1.4 d.101.1.1 PDB: 1udq_A 1uds_A 1udo_A

Probab=100.00  E-value=2.8e-40  Score=357.60  Aligned_cols=222  Identities=27%  Similarity=0.372  Sum_probs=203.1

Q ss_pred             CcCCCCCCCCccCeEEEeCCCCCCCcceEEEeCCeEEEEEEEeCCCchhhhccccCCCCceeEEEEEecCCCCccccccc
Q 002054          369 VRVDGRQLDEVRPIYCESGNLPILHGSSLFSRGDTQVLCTVTLGAPAEAQRLESLVGPPTKRFMLHYSFPPFCINEVGKR  448 (974)
Q Consensus       369 ~R~DGR~~~e~R~I~ie~g~l~~a~GSal~~~G~T~Vl~~Vtl~~p~~~~~~d~~~~~~~~~~~v~~~f~p~s~~e~~~~  448 (974)
                      +|+|||.++|+|+|.+++|+++++||||+|++|+|+|+|+|+.+  ...  .+...+++++++++||+++|+++.+++++
T Consensus         1 ~R~DGR~~~e~R~i~i~~g~~~~a~GSa~v~~G~T~Vl~~V~~~--~~~--p~~~~~~~~g~l~~~~~~~P~a~~~r~~R   76 (255)
T 1udn_A            1 MRSDGRKEDQLRPVSIQRDFLEYPEGSCLISFGKTKVICTASVI--ENV--PNWLKGKGQGWITAEYSMLPRATQQRTIR   76 (255)
T ss_dssp             -CTTSCCTTCCCCEEEEECCSSSSSEEEEEEETTEEEEEEEEEE--SCC--CGGGTTSSCCEEEEEEEECSCCTTSCCCC
T ss_pred             CCCCCCCCCCccCeEEEECCCCCCCEEEEEEECCEEEEEEEEcC--CcC--CCCCCCCCceEEEEEEEcCCCcccccccc
Confidence            49999999999999999999999999999999999999999954  221  12234578899999999999999987543


Q ss_pred             ----cCCCchhhhHHHHHHHHhhhcCCCCCCCCeEEEEEEEEEcCCCChhhHHHHHHHHHHHHcC-----------CCcc
Q 002054          449 ----VGLNRREVGHGTLAEKALLAVLPPENDFPYTVRVNSEVMASDGSTSMATVCGGSMALMDAG-----------IPLQ  513 (974)
Q Consensus       449 ----~~~~rre~~~~~l~eral~~vi~~~~~~p~tI~V~v~VLesdGs~~~A~v~aa~lAL~dag-----------vPi~  513 (974)
                          |.++.++++++++++|+|+++++.+..+.|+|+|+++||++|||+++||+||+++||+|||           +||+
T Consensus        77 e~~~G~~~~~~~eisrli~r~lr~~i~~~~l~~~~i~I~~~VL~~DG~~~~aai~aa~~AL~da~~~~~~~~~~~~ipl~  156 (255)
T 1udn_A           77 ESVQGRIGGRTHEIQRMIGRAMRTAVELTKIGERTIWVDCDVIQADGGTRTAAITGAFVAVADAIIKLHKEGIIEETPIK  156 (255)
T ss_dssp             SSTTCSCCHHHHHHHHHHHHHHHHHBCGGGGCSCEEEEEEEEEECSSCHHHHHHHHHHHHHHHHHHHHHHTTSSSSCCBC
T ss_pred             ccCCCCCCHHHHHHHHHHHHHHHHhcCHHHcCCeEEEEEEEEEeCCCCHHHHHHHHHHHHHHhhcchhcccCcccCCCcc
Confidence                5789999999999999999999986566689999999999999999999999999999999           9999


Q ss_pred             ccccceeeeeeccCCCCCCcccceEEEecCCccccccCCccEEEEeeCCc-eEEEEeeccCCCCCHHHHHHHHHHHHHHH
Q 002054          514 EHVAGVSVGLVSEVDPSTGEIKDYRILTDILGLEDHLGDMDFKIAGTRIG-VTAIQLDIKPAGIPLDIICECLEHAHKGR  592 (974)
Q Consensus       514 ~~vagvs~gli~~~d~~~~~~~~~~iL~Dp~~~Ee~~~d~d~~Va~t~~g-I~alq~~~k~~~i~~e~l~~al~~A~~~~  592 (974)
                      ++|+++++|++++           .+|+||+..||+.++++++|+++.+| ++.+|++++.++++.++|.+|+++|++++
T Consensus       157 ~~v~avsvg~~~g-----------~~llDpt~~Ee~~~~~~l~va~~~~g~i~~~q~~g~~~~~~~~~l~~~l~~A~~~~  225 (255)
T 1udn_A          157 DFVAAVSVGIVND-----------RILLDLNFEEDSAAQVDMNVVGTGSGRLSEVHTMGEEYSFTKDELIKMLDLAQKGI  225 (255)
T ss_dssp             CCEEEEEEEEETT-----------EEEESCCHHHHHTCSEEEEEEEETTSCEEEEEEEESSCCCCHHHHHHHHHHHHHHH
T ss_pred             CceeEEEEEEECC-----------EEEECCCHHHHhhCCCCEEEEEeCCCCEEEEEEeCCCCCcCHHHHHHHHHHHHHHH
Confidence            9999999999964           69999999999999999999999988 99999998888999999999999999999


Q ss_pred             HHHHHHHHHHhcC
Q 002054          593 LQILDHMEREISA  605 (974)
Q Consensus       593 ~~I~~~m~~~i~~  605 (974)
                      .+|++.|++++.+
T Consensus       226 ~~i~~~~~~~l~~  238 (255)
T 1udn_A          226 NELIELQKKLYVI  238 (255)
T ss_dssp             HHHHHHHHTTEEE
T ss_pred             HHHHHHHHHHHHh
Confidence            9999999999986

>2je6_A RRP42, exosome complex exonuclease 2; nuclease, hydrolase, exonuclease, phosphorolytic, exoribonuclease, RNA degradation; HET: 1PE; 1.6A {Sulfolobus solfataricus} SCOP: d.14.1.4 d.101.1.1 PDB: 2jea_A* 2jeb_A* 2br2_A 2c37_A* 2c38_A* 2c39_A* 3l7z_A

Probab=100.00  E-value=5.4e-40  Score=359.95  Aligned_cols=229  Identities=21%  Similarity=0.290  Sum_probs=206.4

Q ss_pred             HHHHHHHHHHHhcCCcCCCCCCCCccCeEEEeCCCCCCCcceEEEeCCeEEEEEEEeC--CCchhhhccccCCCCceeEE
Q 002054          355 VRKRVIRKRIIAEGVRVDGRQLDEVRPIYCESGNLPILHGSSLFSRGDTQVLCTVTLG--APAEAQRLESLVGPPTKRFM  432 (974)
Q Consensus       355 ~~~~~~r~~il~~~~R~DGR~~~e~R~I~ie~g~l~~a~GSal~~~G~T~Vl~~Vtl~--~p~~~~~~d~~~~~~~~~~~  432 (974)
                      .+++.++ ..+++|+|+|||.++|+|++++++|.++++||||+|++|+|+|+|+|+++  .|..       .++++++++
T Consensus        16 ~~~~~i~-~~l~~~~R~DGR~~~e~R~i~i~~g~l~~a~GSa~v~~G~T~Vl~~V~~~~~~p~~-------~~~~~g~l~   87 (277)
T 2je6_A           16 IKKESIV-SLFEKGIRQDGRKLTDYRPLSITLDYAKKADGSALVKLGTTMVLAGTKLEIDKPYE-------DTPNQGNLI   87 (277)
T ss_dssp             HHHHHHT-TTGGGTBCTTSCBTTCCCCEEEEETCSTTSSEEEEEEETTEEEEEEEEEEEECCCT-------TCTTCCEEE
T ss_pred             cHHHHHH-HHHhcCCCCCCCCcCcccCeEEEeCCcCCCCeEEEEEECCeEEEEEEEeeeeCCCC-------CCCCccEEE
Confidence            3444444 68999999999999999999999999999999999999999999999965  2321       246889999


Q ss_pred             EEEecCCCCccccccccCCCchhhhHHHHHHHHhhh--cCCCCC------CCCeEEEEEEEEEcCCCChhhHHHHHHHHH
Q 002054          433 LHYSFPPFCINEVGKRVGLNRREVGHGTLAEKALLA--VLPPEN------DFPYTVRVNSEVMASDGSTSMATVCGGSMA  504 (974)
Q Consensus       433 v~~~f~p~s~~e~~~~~~~~rre~~~~~l~eral~~--vi~~~~------~~p~tI~V~v~VLesdGs~~~A~v~aa~lA  504 (974)
                      ++|+++|||++++ +.|++++++++++++++|+|++  +++.+.      +++|+|+|+++||++|||+++||+||+++|
T Consensus        88 v~~~~~p~a~~~~-~~g~~~~~~~~is~li~r~lr~~~~i~~~~l~i~~g~~~~~i~i~~~VL~~DG~~~~aai~aa~~A  166 (277)
T 2je6_A           88 VNVELLPLAYETF-EPGPPDENAIELARVVDRSLRDSKALDLTKLVIEPGKSVWTVWLDVYVLDYGGNVLDACTLASVAA  166 (277)
T ss_dssp             EEEEECTTSCTTC-CCSSCCHHHHHHHHHHHHHHHHTTCSCGGGGEEETTTEEEEEEEEEEEEECCSCHHHHHHHHHHHH
T ss_pred             EEEEeCCccCccc-ccCCCChHHHHHHHHHHHHHhccCCcCHHHceeecCceEEEEEEEEEEECCCCCHHHHHHHHHHHH
Confidence            9999999999875 3678899999999999999999  465532      258999999999999999999999999999


Q ss_pred             HHHcC---------------------CCccccccceeeeeeccCCCCCCcccceEEEecCCccccccCCccEEEEeeCCc
Q 002054          505 LMDAG---------------------IPLQEHVAGVSVGLVSEVDPSTGEIKDYRILTDILGLEDHLGDMDFKIAGTRIG  563 (974)
Q Consensus       505 L~dag---------------------vPi~~~vagvs~gli~~~d~~~~~~~~~~iL~Dp~~~Ee~~~d~d~~Va~t~~g  563 (974)
                      |+|+|                     +||+++|+++++|++++           .+|+||+..||+.++++++|+++.+|
T Consensus       167 L~~a~~p~v~~~~~~~~~~~~~~~~~ip~~~~~~avsvg~~~~-----------~~l~Dpt~~Ee~~~~~~l~va~~~~g  235 (277)
T 2je6_A          167 LYNTKVYKVEQHSNGISVNKNEVVGKLPLNYPVVTISVAKVDK-----------YLVVDPDLDEESIMDAKISFSYTPDL  235 (277)
T ss_dssp             HHTCEEEEEECC---CEEEEEEEEEECCCSCCCEEEEEEEETT-----------EEEESCCHHHHHHCSEEEEEEECTTC
T ss_pred             HHhcCCCeEEecCCcceEeccCccccccccCCeEEEEEEEECC-----------EEecCCCHHHHhcCCCcEEEEEeCCC
Confidence            99999                     99999999999999975           79999999999999999999999876


Q ss_pred             -eEEEEeeccCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHhc
Q 002054          564 -VTAIQLDIKPAGIPLDIICECLEHAHKGRLQILDHMEREIS  604 (974)
Q Consensus       564 -I~alq~~~k~~~i~~e~l~~al~~A~~~~~~I~~~m~~~i~  604 (974)
                       |+++|++++ ++++.++|.+|+++|++++++|++.|+++++
T Consensus       236 ~i~~v~~~g~-~~~~~~~l~~~l~~A~~~~~~i~~~~~~~l~  276 (277)
T 2je6_A          236 KIVGIQKSGK-GSMSLQDIDQAENTARSTAVKLLEELKKHLG  276 (277)
T ss_dssp             CEEEEEEESS-SCEEHHHHHHHHHHHHHHHHHHHHHHHHHHT
T ss_pred             CEEEEECCCC-CCCCHHHHHHHHHHHHHHHHHHHHHHHHHhc
Confidence             999999876 7899999999999999999999999999874

>1r6l_A Ribonuclease PH; beta-alpha-beta-alpha fold, hexamer, phosphate bound, transf; HET: NHE; 1.90A {Pseudomonas aeruginosa} SCOP: d.14.1.4 d.101.1.1 PDB: 1r6m_A

Probab=100.00  E-value=1.4e-39  Score=349.29  Aligned_cols=222  Identities=27%  Similarity=0.341  Sum_probs=200.1

Q ss_pred             CcCCCCCCCCccCeEEEeCCCCCCCcceEEEeCCeEEEEEEEeCCCchhhhccccCCCCceeEEEEEecCCCCccccccc
Q 002054          369 VRVDGRQLDEVRPIYCESGNLPILHGSSLFSRGDTQVLCTVTLGAPAEAQRLESLVGPPTKRFMLHYSFPPFCINEVGKR  448 (974)
Q Consensus       369 ~R~DGR~~~e~R~I~ie~g~l~~a~GSal~~~G~T~Vl~~Vtl~~p~~~~~~d~~~~~~~~~~~v~~~f~p~s~~e~~~~  448 (974)
                      .|+|||.++|+|+|++++|+++++||||+|++|+|+|+|+|+.+  ...  .+...++++++++++|+++|+++.+++++
T Consensus         2 ~R~DGR~~~e~R~i~i~~g~~~~a~GSa~v~~G~T~Vl~~V~~~--~~~--p~~~~~~~~g~l~v~~~~~p~~~~~r~~R   77 (239)
T 1r6l_A            2 NRPSGRAADQLRPIRITRHYTKHAEGSVLVEFGDTKVICTVSAE--SGV--PRFLKGQGQGWLTAEYGMLPRSTGERNQR   77 (239)
T ss_dssp             CCTTCCCTTCCCCEEEESSCSSSSSEEEEEEETTEEEEEEEEEE--ESC--SSCCC---CCEEEEEEEECTTSSSSCCCC
T ss_pred             cCCCCCCCCCcCCeEEEeCCcCCCCeEEEEEECCEEEEEEEEcc--Ccc--CCccCCCCcEEEEEEEEeCCCcccccccc
Confidence            39999999999999999999999999999999999999999943  221  12233467899999999999999987433


Q ss_pred             ----cCCCchhhhHHHHHHHHhhhcCCCCCCCCeEEEEEEEEEcCCCChhhHHHHHHHHHHHHcC-----------CCcc
Q 002054          449 ----VGLNRREVGHGTLAEKALLAVLPPENDFPYTVRVNSEVMASDGSTSMATVCGGSMALMDAG-----------IPLQ  513 (974)
Q Consensus       449 ----~~~~rre~~~~~l~eral~~vi~~~~~~p~tI~V~v~VLesdGs~~~A~v~aa~lAL~dag-----------vPi~  513 (974)
                          |.++.+++.++++++|+|+++++.+....|+|+|+++||++|||+++||+||+++||+|||           +||+
T Consensus        78 e~~~G~~~~~~~~isrli~r~l~~~i~~~~l~~~~i~I~~~VL~~DG~~~~aai~aa~~AL~da~~~~~~~~~~~~ip~~  157 (239)
T 1r6l_A           78 EASRGKQGGRTLEIQRLIGRSLRAALDLSKLGENTLYIDCDVIQADGGTRTASITGATVALIDALAVLKKRGALKGNPLK  157 (239)
T ss_dssp             HHHHTSCCHHHHHHHHHHHHHHHHTBCGGGTCSEEEEEEEEEEECSSCHHHHHHHHHHHHHHHHHHHHHHTTCCSSCCBC
T ss_pred             ccCCCCCcHHHHHHHHHHHHHHHHhcCHHHcCCeEEEEEEEEEeCCCCHHHHHHHHHHHHHHHhcchhcccCcccccCcc
Confidence                6789999999999999999999986555689999999999999999999999999999999           9999


Q ss_pred             ccccceeeeeeccCCCCCCcccceEEEecCCccccccCCccEEEEeeCCc-eEEEEeeccCCCCCHHHHHHHHHHHHHHH
Q 002054          514 EHVAGVSVGLVSEVDPSTGEIKDYRILTDILGLEDHLGDMDFKIAGTRIG-VTAIQLDIKPAGIPLDIICECLEHAHKGR  592 (974)
Q Consensus       514 ~~vagvs~gli~~~d~~~~~~~~~~iL~Dp~~~Ee~~~d~d~~Va~t~~g-I~alq~~~k~~~i~~e~l~~al~~A~~~~  592 (974)
                      ++|+++++|++++           .+|+||+..||+.++++++|+++.+| ++.+|++++.++++.++|.+|+++|++++
T Consensus       158 ~~~~avs~g~~~~-----------~~l~Dpt~~Ee~~~~~~l~va~~~~g~i~~~~~~g~~~~~~~~~l~~~l~~a~~~~  226 (239)
T 1r6l_A          158 QMVAAVSVGIYQG-----------VPVLDLDYLEDSAAETDLNVVMTDAGGFIEVQGTAEGAPFRPAELNAMLELAQQGM  226 (239)
T ss_dssp             CCEEEEEEEEETT-----------EEEESCCHHHHHHCSEEEEEEEETTSCEEEEEEEESSSCCCHHHHHHHHHHHHHHH
T ss_pred             CceeEEEEEEECC-----------EEEECCCHHHHhcCCceEEEEEeCCCCEEEEEEeCCCCCcCHHHHHHHHHHHHHHH
Confidence            9999999999964           69999999999999999999999988 99999998878999999999999999999


Q ss_pred             HHHHHHHHHHhcC
Q 002054          593 LQILDHMEREISA  605 (974)
Q Consensus       593 ~~I~~~m~~~i~~  605 (974)
                      .+|++.|++++++
T Consensus       227 ~~i~~~~~~~l~~  239 (239)
T 1r6l_A          227 QELFELQRAALAE  239 (239)
T ss_dssp             HHHHHHHHHHHTC
T ss_pred             HHHHHHHHHHHhC
Confidence            9999999999863

>2wp8_A Exosome complex component RRP45; nucleus, hydrolase, RNA-binding, exonucle binding, mitochondrion, rRNA processing; 3.00A {Saccharomyces cerevisiae}

Probab=100.00  E-value=9.2e-40  Score=362.75  Aligned_cols=244  Identities=18%  Similarity=0.222  Sum_probs=187.4

Q ss_pred             HHHHHHHHHHHHhcCCcCCCCCCCCccCeEEEeCCCCCCCcceEEEeCCeEEEEEEEeC--CCchhhhccccCCCCceeE
Q 002054          354 TVRKRVIRKRIIAEGVRVDGRQLDEVRPIYCESGNLPILHGSSLFSRGDTQVLCTVTLG--APAEAQRLESLVGPPTKRF  431 (974)
Q Consensus       354 ~~~~~~~r~~il~~~~R~DGR~~~e~R~I~ie~g~l~~a~GSal~~~G~T~Vl~~Vtl~--~p~~~~~~d~~~~~~~~~~  431 (974)
                      ..++++++ ..|++|+|+|||.++|+|||+|++|   ++||||+|++|+|+|+|+|+.+  .|...       .++.+.+
T Consensus         9 ~~e~~~i~-~~l~~~~R~DGR~~~e~R~i~i~~g---~a~GSa~v~~G~T~Vl~~V~~~~~~p~~~-------~~~~g~~   77 (305)
T 2wp8_A            9 ASESKFIL-EALRQNYRLDGRSFDQFRDVEITFG---KEFGDVSVKMGNTKVHCRISCQIAQPYED-------RPFEGLF   77 (305)
T ss_dssp             HHHHHHHH-HHHTTTCCTTSCCTTCCCCEEEEEC---SSTTEEEEEETTEEEEEEEEEEEC-CCSS-------CTTCCEE
T ss_pred             cCHHHHHH-HHHhhCCCCCCCCCcccCCeEEEEc---CCCcEEEEEECCeEEEEEEeccccCCccc-------CCCCcEE
Confidence            45556666 5589999999999999999999999   8999999999999999999953  34331       3578899


Q ss_pred             EEEEecCCCCccccccccCCC-chhhhHHHHHHHHhh--hcCCCC------CCCCeEEEEEEEEEcCCCChhhHHHHHHH
Q 002054          432 MLHYSFPPFCINEVGKRVGLN-RREVGHGTLAEKALL--AVLPPE------NDFPYTVRVNSEVMASDGSTSMATVCGGS  502 (974)
Q Consensus       432 ~v~~~f~p~s~~e~~~~~~~~-rre~~~~~l~eral~--~vi~~~------~~~p~tI~V~v~VLesdGs~~~A~v~aa~  502 (974)
                      .++|+|+|++.++++ .|.++ +++++++++++|+|+  .+++.+      .+|+|+|+|+++||++|||+++||+||++
T Consensus        78 ~~~ve~~~~~~~~~~-~g~~~~~~~~~is~li~r~l~~s~~idl~~L~i~pg~~~w~I~id~~VL~~DG~~~dAai~aa~  156 (305)
T 2wp8_A           78 VISTEISPMAGSQFE-NGNITGEDEVLCSRIIEKSVRRSGALDVEGLCIVAGSKCWAVRADVHFLDCDGGFIDASCIAVM  156 (305)
T ss_dssp             EEEECCC-----------------------CHHHHHHHTTSBCGGGGEEETTTEEEEEEEEEEEEECSSCHHHHHHHHHH
T ss_pred             EEEEEECCCCCcccc-CCCCChhHHHHHHHHHHHHHhhccCcCHHHccccCCcEEEEEEEEEEEEcCCCCHHHHHHHHHH
Confidence            999999999998873 46777 999999999999998  444332      36889999999999999999999999999


Q ss_pred             HHHHHcCCC-----------------------ccccccceeeeeeccCCCCCCcccc----eEEEecCCccccccCCccE
Q 002054          503 MALMDAGIP-----------------------LQEHVAGVSVGLVSEVDPSTGEIKD----YRILTDILGLEDHLGDMDF  555 (974)
Q Consensus       503 lAL~dagvP-----------------------i~~~vagvs~gli~~~d~~~~~~~~----~~iL~Dp~~~Ee~~~d~d~  555 (974)
                      +||+|||+|                       |++.|+++++|+++.++.+ ...+.    +.+|+||++.||+.++++|
T Consensus       157 ~AL~~a~iP~~~~~~~~~~i~~~~~~~~~~l~~~~~pvavs~g~i~~~~~~-~~~~~~~~~~~~l~Dpt~~Ee~~~~~~l  235 (305)
T 2wp8_A          157 AGLMHFKKPDITVHGEQIIVHPVNEREPVPLGILHIPICVTFSFFNPQDTE-ENIKGETNSEISIIDATLKEELLRDGVL  235 (305)
T ss_dssp             HHHHHCEECCCBCTTSSCCBCCSSSSCCEECCBSCCCEEEEEEECC----------------CEEESCCHHHHHHCSEEE
T ss_pred             HHHHHhCCCeEEecCCceEecccccccccccccccCeEEEEEEEEcccccc-ccccccccCCeEEeCCCHHHHhccCCcE
Confidence            999999999                       6788999999999621100 00001    5799999999999999999


Q ss_pred             EEEeeCCc-eEEEEeeccCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCCCCC
Q 002054          556 KIAGTRIG-VTAIQLDIKPAGIPLDIICECLEHAHKGRLQILDHMEREISAPRTQDD  611 (974)
Q Consensus       556 ~Va~t~~g-I~alq~~~k~~~i~~e~l~~al~~A~~~~~~I~~~m~~~i~~~~~~~~  611 (974)
                      +|+++.+| |+++|+.+ +.+++.++|.+|+++|++++.+|++.|++++.++.....
T Consensus       236 ~Va~~~~g~i~~l~~~g-~~~~~~~~l~~~l~~A~~~~~~i~~~~~~~l~~~~~~r~  291 (305)
T 2wp8_A          236 TVTLNKNREVVQVSKAG-GLPMDALTLMKCCHEAYSIIEKITDQILQLLKEDSEKRN  291 (305)
T ss_dssp             EEEECTTSEEEEEEEEE-EEEECHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHC
T ss_pred             EEEEcCCCcEEEEEecC-CCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhh
Confidence            99999988 99999987 467999999999999999999999999999998755443

>2nn6_E Exosome complex exonuclease RRP42; RNA, exosome, PM/SCL, phosphorolytic, hydrolase/transferase complex; 3.35A {Homo sapiens} SCOP: d.14.1.4 d.101.1.1

Probab=100.00  E-value=1.9e-39  Score=360.02  Aligned_cols=236  Identities=17%  Similarity=0.179  Sum_probs=209.1

Q ss_pred             HHHHHHHHHHHHHHHHhcCCcCCCCCCCCccCeEEEeCCCCCCCcceEEEeCCeEEEEEEEeC--CCchhhhccccCCCC
Q 002054          350 KAVDTVRKRVIRKRIIAEGVRVDGRQLDEVRPIYCESGNLPILHGSSLFSRGDTQVLCTVTLG--APAEAQRLESLVGPP  427 (974)
Q Consensus       350 ~~~~~~~~~~~r~~il~~~~R~DGR~~~e~R~I~ie~g~l~~a~GSal~~~G~T~Vl~~Vtl~--~p~~~~~~d~~~~~~  427 (974)
                      ..++..+++.+++. +++|+|+|||.++|+|+|.+++|.++++||||+|++|+|+|+|+|+.+  .|.       ...++
T Consensus        18 ~~~s~~e~~~i~~~-l~~~~R~DGR~~~e~R~i~i~~g~l~~a~GSa~v~~G~T~Vl~~V~~e~~~p~-------~~~~~   89 (305)
T 2nn6_E           18 VTLSEAEKVYIVHG-VQEDLRVDGRGCEDYRCVEVETDVVSNTSGSARVKLGHTDILVGVKAEMGTPK-------LEKPN   89 (305)
T ss_dssp             -CCCHHHHHHHHHH-HHTTCCSSSCCSSCCCCCEEEECCCTTSSSEEEEEETTEEEEEECCCCCSCCC-------SSSCS
T ss_pred             cccChhHHHHHHHH-HhcCCCCCCCCCcCccCeEEEeCcccCCCcEEEEEECCeEEEEEEEEEeeCCC-------cCCCC
Confidence            34667778888855 589999999999999999999999999999999999999999999953  122       12467


Q ss_pred             ceeEEEEEecCCCCccccccccCCCchhhhHHHHHHHHhhh----------cCCCCCCCCeEEEEEEEEEcCCCChhhHH
Q 002054          428 TKRFMLHYSFPPFCINEVGKRVGLNRREVGHGTLAEKALLA----------VLPPENDFPYTVRVNSEVMASDGSTSMAT  497 (974)
Q Consensus       428 ~~~~~v~~~f~p~s~~e~~~~~~~~rre~~~~~l~eral~~----------vi~~~~~~p~tI~V~v~VLesdGs~~~A~  497 (974)
                      .+.|.++|+|+|+|++++ +.+.+++++++++++++|+|++          ++|  ..|+|+|+|+++||++|||+++||
T Consensus        90 ~g~l~~~v~~~p~a~~~~-~~r~~~~~~~~isrli~r~lr~s~~idl~~L~i~p--~~~~w~i~idv~VL~~DG~~~daa  166 (305)
T 2nn6_E           90 EGYLEFFVDCSASATPEF-EGRGGDDLGTEIANTLYRIFNNKSSVDLKTLCISP--REHCWVLYVDVLLLECGGNLFDAI  166 (305)
T ss_dssp             SCCEEEECCCCTTTCSSC-CTTSTHHHHHHHHHHHHHHHHHSCCSCSSSSCSST--TTCCCCEEEEEEECCCCSSHHHHH
T ss_pred             ceEEEEEEEeCCCcCccc-cCCCCchHHHHHHHHHHHHHhhcCcccHHHheecc--CcEEEEEEEEEEEECCCCCHHHHH
Confidence            899999999999999876 3345568999999999999998          555  478999999999999999999999


Q ss_pred             HHHHHHHHHHcCCCccc---------------------------cccceeeeeeccCCCCCCcccceEEEecCCcccccc
Q 002054          498 VCGGSMALMDAGIPLQE---------------------------HVAGVSVGLVSEVDPSTGEIKDYRILTDILGLEDHL  550 (974)
Q Consensus       498 v~aa~lAL~dagvPi~~---------------------------~vagvs~gli~~~d~~~~~~~~~~iL~Dp~~~Ee~~  550 (974)
                      +||+++||+|+++|+..                           +|+++++|++++           .+|+||+..||+.
T Consensus       167 i~aa~~AL~~a~iP~~~~~~~~~~~~~i~~~~d~~~~~~l~l~~~p~avt~g~i~~-----------~~l~Dpt~~Ee~~  235 (305)
T 2nn6_E          167 SIAVKAALFNTRIPRVRVLEDEEGSKDIELSDDPYDCIRLSVENVPCIVTLCKIGY-----------RHVVDATLQEEAC  235 (305)
T ss_dssp             HHHHHHTTTTCCCCEEEEECC------EEEEESSCCCSCCCCTTCCCCEEEEESSS-----------SEESSCCHHHHTS
T ss_pred             HHHHHHHHHhcCCCeEEEecCCCCceeeeccCcccccccccccCceEEEEEEEECC-----------EEEECCCHHHHhh
Confidence            99999999999999653                           478999999964           5999999999999


Q ss_pred             CCccEEEEeeCCc-eEEEEeeccCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCC
Q 002054          551 GDMDFKIAGTRIG-VTAIQLDIKPAGIPLDIICECLEHAHKGRLQILDHMEREISAPRT  608 (974)
Q Consensus       551 ~d~d~~Va~t~~g-I~alq~~~k~~~i~~e~l~~al~~A~~~~~~I~~~m~~~i~~~~~  608 (974)
                      ++++++|+++.+| |+++|+.+ +.+++.++|.+|+++|++++.+|++.|+++++++..
T Consensus       236 ~~~~l~Va~~~~g~i~~i~~~g-~~~l~~~~l~~~l~~A~~~~~~i~~~~~~~l~~~~~  293 (305)
T 2nn6_E          236 SLASLLVSVTSKGVVTCMRKVG-KGSLDPESIFEMMETGKRVGKVLHASLQSVVHKEES  293 (305)
T ss_dssp             CSEEEEECCCSSSCCCEEEEEE-SSCBCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHC
T ss_pred             cCCcEEEEEcCCCCEEEEEccC-CCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence            9999999999987 99999987 578999999999999999999999999999987654

>2nn6_A Polymyositis/scleroderma autoantigen 1; RNA, exosome, PM/SCL, phosphorolytic, hydrolase/transferase complex; 3.35A {Homo sapiens} SCOP: d.14.1.4 d.101.1.1

Probab=100.00  E-value=5.1e-39  Score=361.67  Aligned_cols=235  Identities=19%  Similarity=0.209  Sum_probs=206.2

Q ss_pred             HHHHHHHHHHHHHHhcCCcCCCCCCCCccCeEEEeCCCCCCCcceEEEeCCeEEEEEEEeC--CCchhhhccccCCCCce
Q 002054          352 VDTVRKRVIRKRIIAEGVRVDGRQLDEVRPIYCESGNLPILHGSSLFSRGDTQVLCTVTLG--APAEAQRLESLVGPPTK  429 (974)
Q Consensus       352 ~~~~~~~~~r~~il~~~~R~DGR~~~e~R~I~ie~g~l~~a~GSal~~~G~T~Vl~~Vtl~--~p~~~~~~d~~~~~~~~  429 (974)
                      ++..+++.+++ .|++|+|+|||.++|+|+|.|++|   ++||||+|++|+|+|+|+|+.+  .|...       .++.+
T Consensus        23 ~s~~e~~~i~~-~L~~g~R~DGR~~~e~R~i~ie~g---~A~GSa~v~~G~T~VL~tV~~e~~~p~~~-------~~~~g   91 (358)
T 2nn6_A           23 LSNCERRFLLR-AIEEKKRLDGRQTYDYRNIRISFG---TDYGCCIVELGKTRVLGQVSCELVSPKLN-------RATEG   91 (358)
T ss_dssp             CCHHHHHHHHH-HHHTTCCTTSCCTTCCCCCEEEEC---SSTTEEEEESSSCEEEEEECCEEECCCST-------TTTSC
T ss_pred             ccHhHHHHHHH-HHhcCCCCCCCCccccCCeEEEEe---cCCcEEEEEECCcEEEEEEEecccCCccc-------CCCCc
Confidence            34566777775 589999999999999999999999   8999999999999999999942  33321       26789


Q ss_pred             eEEEEEecCCCCccccccccCCCchhhhHHHHHHHHhhhc--CCCC------CCCCeEEEEEEEEEcCCCChhhHHHHHH
Q 002054          430 RFMLHYSFPPFCINEVGKRVGLNRREVGHGTLAEKALLAV--LPPE------NDFPYTVRVNSEVMASDGSTSMATVCGG  501 (974)
Q Consensus       430 ~~~v~~~f~p~s~~e~~~~~~~~rre~~~~~l~eral~~v--i~~~------~~~p~tI~V~v~VLesdGs~~~A~v~aa  501 (974)
                      .|+++|+|+|+|+++++ .|.+++++++++++++|+|++.  ++.+      ..|+|+|+|+++||++|||+++||+||+
T Consensus        92 ~l~~~v~~~p~a~~~~~-~g~~s~~e~eisrli~r~Lr~s~~idl~~LcI~pg~~~w~I~Vdv~VL~~DGn~~dAai~Aa  170 (358)
T 2nn6_A           92 ILFFNLELSQMAAPAFE-PGRQSDLLVKLNRLMERCLRNSKCIDTESLCVVAGEKVWQIRVDLHLLNHDGNIIDAASIAA  170 (358)
T ss_dssp             CEEEEEEECTTTCSSCC-SSSTHHHHTHHHHHHHHHHHHHTCBCSSSSCSBTTTBEEEEEEEEEECSCCSCCHHHHHHHH
T ss_pred             EEEEEEEecCCcccccc-CCCCCHHHHHHHHHHHHHhhhccccchHhhcccCCCccEEEEEEEEEEeCCCCHHHHHHHHH
Confidence            99999999999998864 4678999999999999999882  2221      3588999999999999999999999999


Q ss_pred             HHHHHHcCCC-----------------------ccccccceeeeeeccCCCCCCcccceEEEecCCccccccCCccEEEE
Q 002054          502 SMALMDAGIP-----------------------LQEHVAGVSVGLVSEVDPSTGEIKDYRILTDILGLEDHLGDMDFKIA  558 (974)
Q Consensus       502 ~lAL~dagvP-----------------------i~~~vagvs~gli~~~d~~~~~~~~~~iL~Dp~~~Ee~~~d~d~~Va  558 (974)
                      ++||+|||+|                       |+++|+++++|++..+         ..+|+||+..||+.++++++|+
T Consensus       171 ~aAL~da~iP~v~~~~~~v~i~~~~~~~~~~l~i~~~p~avsvgl~~~~---------~~illDPt~~Ee~~~~~~l~Va  241 (358)
T 2nn6_A          171 IVALCHFRRPDVSVQGDEVTLYTPEERDPVPLSIHHMPICVSFAFFQQG---------TYLLVDPNEREERVMDGLLVIA  241 (358)
T ss_dssp             HHHHHHCCCCCCBCCTTCCBCCHHHHTSCCCCCBCCCEEEEEEEECTTT---------SSEEESCCHHHHHHCSCEEEEE
T ss_pred             HHHHHHhCcCcEEeeCCeeEecccccccccccCccCCEEEEEEEEEeeC---------CEEEECCCHHHHhhcCccEEEE
Confidence            9999999999                       9999999999998531         2699999999999999999999


Q ss_pred             eeCCc-eEEEEeeccCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCC
Q 002054          559 GTRIG-VTAIQLDIKPAGIPLDIICECLEHAHKGRLQILDHMEREISAPRT  608 (974)
Q Consensus       559 ~t~~g-I~alq~~~k~~~i~~e~l~~al~~A~~~~~~I~~~m~~~i~~~~~  608 (974)
                      ++.+| |+++|+.+. .+++.++|.+|+++|++++.+|++.|++++.++..
T Consensus       242 ~t~~g~I~~lqk~G~-~~ls~~~l~~~l~~A~~~~~~i~~~~~~~l~~~~~  291 (358)
T 2nn6_A          242 MNKHREICTIQSSGG-IMLLKDQVLRCSKIAGVKVAEITELILKALENDQK  291 (358)
T ss_dssp             EETTTEEEEEEEESC-CCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             EcCCCeEEEEEeCCC-CCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHhHHH
Confidence            99987 999998654 57999999999999999999999999999987643

>3dd6_A Ribonuclease PH; exoribonuclease, tRNA maturation, RNAse PH., transferase; 1.70A {Bacillus anthracis}

Probab=100.00  E-value=3.2e-39  Score=348.47  Aligned_cols=205  Identities=20%  Similarity=0.261  Sum_probs=186.0

Q ss_pred             CCeEEEEEeCccCcCCCcEEEEEeCCeEEEEEEEeCCC-C---CCCCceeeEeeccccccccCCCCCcccc---cc---C
Q 002054           66 GSRLITLETGKIARFANGAVVLGMDETKVLSTVTSSKG-D---SVRDFLPLTVDYQEKQFAQGVIPNTYMR---RE---G  135 (974)
Q Consensus        66 ~~r~i~~etg~~a~~A~GSa~v~~G~T~Vl~tv~~~~~-~---~~~~f~pL~v~y~e~~~a~g~ip~~~~~---Re---g  135 (974)
                      ..|++++++|.+ ++|||||++++|+|+|||+|+++.+ |   +..+..+|+++|.       +.|+++.+   ||   |
T Consensus        20 e~R~i~i~~g~~-~~A~GSa~v~~G~T~Vl~~V~~~~~~p~~~~~~~~g~l~v~~~-------~~P~a~~~~~~Re~~~g   91 (255)
T 3dd6_A           20 ELRHIHIHTNYL-KHPEGSVLIEVGDTKVICSATIEERVPPFMRGEGKGWVTAEYA-------MIPRATEQRTIRESSKG   91 (255)
T ss_dssp             CCCCEEEEESCS-SSSSEEEEEEETTEEEEEEEEEESCCCGGGTTSSCCEEEEEEE-------ECTTSSSSCCCCCCC-C
T ss_pred             CCCCEEEEECCC-CCCCeEEEEEECCeEEEEEEEecCCCCCCCCCCCceEEEEEEE-------ECCCcccccccccccCC
Confidence            368999999988 9999999999999999999999875 3   1233445999996       45655554   66   9


Q ss_pred             CCCchhhhHHHhhcCCccccccCCCCCc--eEEEEEEEeccCCCChhhHHHHHHHHHhhcC-----------CCCCCCCe
Q 002054          136 APKERELLVGRIIDRPIRPLFPAGFYHE--VQVMASVLSSDGKQDPDIMAANATSAALMLS-----------DIPWGGPI  202 (974)
Q Consensus       136 ~p~~~eil~~RlidR~lrplfp~~~~~~--~~i~~~vl~~dg~~~~~~~ai~aAs~AL~~s-----------~iP~~~~v  202 (974)
                      +|++++++++|+|+|+|||+||.+++++  ++|+|+||++||+..  +||+|||++||+++           +|||+++|
T Consensus        92 ~~~~~~~eisrli~r~lr~~i~~~~l~~~~I~V~~~VL~~DG~~~--~aai~aa~~AL~~a~~p~~~~g~~~~iPl~~~v  169 (255)
T 3dd6_A           92 KVTGRTMEIQRLIGRALRAVVDLEALGERTVWIDCDVIQADGGTR--TASITGAYVAMVLAFEKLLQAEKVSKIPVKDYL  169 (255)
T ss_dssp             CCCHHHHHHHHHHHHHHHHHBCHHHHCSCEEEEEEEEEECSSCHH--HHHHHHHHHHHHHHHHHHHHTTSSSSCCBSSCE
T ss_pred             CCCHHHHHHHHHHHHHHHHhcChhhcCCeEEEEEEEEEECCCCHH--HHHHHHHHHHHHHhhhhhhhcCcccCCCccCce
Confidence            9999999999999999999999877655  999999999999987  99999999999999           99999999


Q ss_pred             EEEEEEEECCEEE-EcCCHHHHhcCccceeEeeeCCe-EEEEEec--CCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 002054          203 GMIRIGRICGQFI-VNPTMDELSLSDLNLVYACTREK-TLMIDVQ--AREISEKDLEAGLRLAHPEAVKYLEPQIRLAEK  278 (974)
Q Consensus       203 ~av~vg~i~g~~v-ldPt~~e~~~s~~~l~v~~t~~~-i~mie~~--~~~~~e~~~~~al~~a~~~~~~i~~~~~~~~~~  278 (974)
                      +||++|+++|++| +|||++|++.+++||+|++++++ ++|+|+.  +..|++++|.+||++|++++++|+++|++++++
T Consensus       170 ~avsvg~i~g~~vllDpt~~Ee~~~~~~l~Va~~~~g~i~~vq~~g~~~~~~~~~l~~~l~~A~~~~~~i~~~~~~~l~~  249 (255)
T 3dd6_A          170 AATSVGIVEEQGVVLDLNYAEDSKADVDMNVIMTGKGQFVEVQGTGEEATFSRAQLNELLDAAEQGIFQLIDIQKEALGD  249 (255)
T ss_dssp             EEEEEEEETTTEEEESCCHHHHHTEEEEEEEEEETTSCEEEEEEEESSSCCCHHHHHHHHHHHHHHHHHHHHHHHHHHGG
T ss_pred             eEEEEEEECCEEEEeCCCHHHHhhcCceEEEEEcCCCcEEEEEecCCCCCcCHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            9999999999999 99999999999999999999998 9999986  467999999999999999999999999999987


Q ss_pred             hC
Q 002054          279 AG  280 (974)
Q Consensus       279 ~g  280 (974)
                      .|
T Consensus       250 ~~  251 (255)
T 3dd6_A          250 IV  251 (255)
T ss_dssp             GG
T ss_pred             HH
Confidence            76

>2je6_B RRP41, exosome complex exonuclease 1; nuclease, hydrolase, exonuclease, phosphorolytic, exoribonuclease, RNA degradation; HET: 1PE; 1.6A {Sulfolobus solfataricus} SCOP: d.14.1.4 d.101.1.1 PDB: 2jea_B* 2jeb_B* 2br2_B 2c37_B* 2c38_B* 2c39_B* 3l7z_B

Probab=100.00  E-value=2.5e-38  Score=341.52  Aligned_cols=207  Identities=18%  Similarity=0.297  Sum_probs=190.6

Q ss_pred             CeEEEEEeCccCcCCCcEEEEEeCCeEEEEEEEeCCC-CC----CCCceeeEeeccccccccCCCCCccccccCCCCchh
Q 002054           67 SRLITLETGKIARFANGAVVLGMDETKVLSTVTSSKG-DS----VRDFLPLTVDYQEKQFAQGVIPNTYMRREGAPKERE  141 (974)
Q Consensus        67 ~r~i~~etg~~a~~A~GSa~v~~G~T~Vl~tv~~~~~-~~----~~~f~pL~v~y~e~~~a~g~ip~~~~~Reg~p~~~e  141 (974)
                      =|++.+++|.+ ++|+|||++++|+|+|||+|++|.+ .+    ..++.||+|+|.++.||++++     + +|+|++++
T Consensus        30 ~R~i~i~~g~~-~~a~GSa~v~~G~T~Vl~~V~g~~e~~~~~~~~~~~g~l~v~~~~~p~a~~~~-----~-~g~~~~~e  102 (250)
T 2je6_B           30 LRSIKIELGVL-KNADGSAIFEMGNTKAIAAVYGPKEMHPRHLSLPDRAVLRVRYHMTPFSTDER-----K-NPAPSRRE  102 (250)
T ss_dssp             CCCEEEEESCC-SSSSEEEEEEETTEEEEEEEEEEEECSSGGGSCSSSCEEEEEEEECTTSSSSC-----C-CSSCCHHH
T ss_pred             cCCeEEEeCCC-CCCCeEEEEEECCcEEEEEEEcccccccccccCCCcEEEEEEEEeCCCccCCc-----c-CCCCChhH
Confidence            48899999977 9999999999999999999999766 22    578999999999999999865     2 68999999


Q ss_pred             hhHHHhhcCCccccccCCCCC--ceEEEEEEEeccCCCChhhHHHHHHHHHhhcCCCCCCCCeEEEEEEEECCEEEEcCC
Q 002054          142 LLVGRIIDRPIRPLFPAGFYH--EVQVMASVLSSDGKQDPDIMAANATSAALMLSDIPWGGPIGMIRIGRICGQFIVNPT  219 (974)
Q Consensus       142 il~~RlidR~lrplfp~~~~~--~~~i~~~vl~~dg~~~~~~~ai~aAs~AL~~s~iP~~~~v~av~vg~i~g~~vldPt  219 (974)
                      ++++|+|+|+|||+||.++++  .++|+++||++||+..  +||+|||++||++++|||+++|+||++|+++|++++|||
T Consensus       103 ~~~s~li~r~l~~~i~~~~~p~~~i~I~~~VL~~DG~~~--~aai~aa~~AL~~a~iP~~~~v~avsvg~~~~~~l~Dpt  180 (250)
T 2je6_B          103 IELSKVIREALESAVLVELFPRTAIDVFTEILQADAGSR--LVSLMAASLALADAGIPMRDLIAGVAVGKADGVIILDLN  180 (250)
T ss_dssp             HHHHHHHHHHHHTTBCGGGSTTEEEEEEEEEEECSSCHH--HHHHHHHHHHHHHTTCCBSSCCEEEEEEEETTEEEESCC
T ss_pred             HHHHHHHHHHHHhhcCHhhCCCcEEEEEEEEEeCCCCHH--HHHHHHHHHHHHhcCCCccCceEEEEEEEECCEEEeCCC
Confidence            999999999999999987766  7999999999999987  999999999999999999999999999999999999999


Q ss_pred             HHHHhcCccceeEee--eCCeEEEEEecCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCcc
Q 002054          220 MDELSLSDLNLVYAC--TREKTLMIDVQAREISEKDLEAGLRLAHPEAVKYLEPQIRLAEKAGKQK  283 (974)
Q Consensus       220 ~~e~~~s~~~l~v~~--t~~~i~mie~~~~~~~e~~~~~al~~a~~~~~~i~~~~~~~~~~~g~~k  283 (974)
                      ++|++.++.||+|+.  +.++++|+|+++ +|++++|.+||++|+++++++++.|++++++..+.+
T Consensus       181 ~~Ee~~~~~~l~va~~~~~~~i~~v~~~g-~~~~~~l~~~l~~A~~~~~~i~~~~~~~l~~~~~~~  245 (250)
T 2je6_B          181 ETEAMWGEADMPIAMMPSLNQVTLFQLNG-SMTPDEFRQAFDLAVKGINIIYNLEREALKSKYVEF  245 (250)
T ss_dssp             HHHHHHSSEEEEEEEEGGGTEEEEEEEEE-CBCHHHHHHHHHHHHHHHHHHHHHHHHHHHGGGC--
T ss_pred             HHHHhcCCceEEEEEECCCCCEEEEEEEc-ccCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhh
Confidence            999999999999996  567799999998 599999999999999999999999999998876543

>2nn6_D Exosome complex exonuclease RRP46; RNA, exosome, PM/SCL, phosphorolytic, hydrolase/transferase complex; 3.35A {Homo sapiens} SCOP: d.14.1.4 d.101.1.1

Probab=100.00  E-value=1.7e-38  Score=340.20  Aligned_cols=216  Identities=20%  Similarity=0.224  Sum_probs=174.0

Q ss_pred             HHhcCCcCCCCCCC----CccCeEEEeCCCCCCCcceEEEeCCeEEEEEEEeCCCchhhhccccCCCCceeEEEEEecCC
Q 002054          364 IIAEGVRVDGRQLD----EVRPIYCESGNLPILHGSSLFSRGDTQVLCTVTLGAPAEAQRLESLVGPPTKRFMLHYSFPP  439 (974)
Q Consensus       364 il~~~~R~DGR~~~----e~R~I~ie~g~l~~a~GSal~~~G~T~Vl~~Vtl~~p~~~~~~d~~~~~~~~~~~v~~~f~p  439 (974)
                      .+.+|+|+|||.++    |+|||++++|+++++||||+|++|+|+|+|+|+  +|.+.+...    ....+..++|+|+|
T Consensus        11 ~~~~~~R~DGR~~~~~~~e~R~i~i~~g~l~~a~GSa~v~~G~T~Vl~~V~--g~~~~~~~~----~~~~~g~l~~~~~p   84 (237)
T 2nn6_D           11 AKIRAENGTGSSPRGPGCSLRHFACEQNLLSRPDGSASFLQGDTSVLAGVY--GPAEVKVSK----EIFNKATLEVILRP   84 (237)
T ss_dssp             ----------------CCCCCCEEEEESCCSSSSEEEEEEETTEEEEEEEE--EEEECC----------CCEEEEEEEEC
T ss_pred             CCccCccCCCCCCCCccccccceEEEeCCCCCCCEEEEEEECCcEEEEEEe--CCCcccccc----cCCCcEEEEEEecC
Confidence            34679999999999    999999999999999999999999999999998  666533211    12345577888888


Q ss_pred             CCccccccccCCCchhhhHHHHHHHHhhhcCCCCCCCCe-EEEEEEEEEcCCCChhhHHHHHHHHHHHHcCCCccccccc
Q 002054          440 FCINEVGKRVGLNRREVGHGTLAEKALLAVLPPENDFPY-TVRVNSEVMASDGSTSMATVCGGSMALMDAGIPLQEHVAG  518 (974)
Q Consensus       440 ~s~~e~~~~~~~~rre~~~~~l~eral~~vi~~~~~~p~-tI~V~v~VLesdGs~~~A~v~aa~lAL~dagvPi~~~vag  518 (974)
                      |+       |.+++||++|+++++|+|+++++. +.||+ +|+|+++||++|||+++||+||+++||+|||+||+++|++
T Consensus        85 ~~-------g~~~~~e~~~~~li~r~l~~~i~~-~~~p~~~I~I~~~VL~~dG~~~~aai~aa~~AL~da~iP~~~~v~a  156 (237)
T 2nn6_D           85 KI-------GLPGVAEKSRERLIRNTCEAVVLG-TLHPRTSITVVLQVVSDAGSLLACCLNAACMALVDAGVPMRALFCG  156 (237)
T ss_dssp             SS-------SCCCHHHHHHHHHHHHHHHHHCGG-GCSSSEEEEEEEEEEECSSCHHHHHHHHHHHHHHHTTCCCSSCEEE
T ss_pred             CC-------CCCCccHHHHHHHHHHHHHHHhch-hcCCceEEEEEEEEEECCCcHHHHHHHHHHHHHHHcCCCcccCeee
Confidence            74       457899999999999999999998 67885 8999999999999999999999999999999999999999


Q ss_pred             eeeeeeccCCCCCCcccceEEEecCCccccccCCccEEEEe--eCCceEEEEeeccCCCCCHHHHHHHHHHHHHHHHHHH
Q 002054          519 VSVGLVSEVDPSTGEIKDYRILTDILGLEDHLGDMDFKIAG--TRIGVTAIQLDIKPAGIPLDIICECLEHAHKGRLQIL  596 (974)
Q Consensus       519 vs~gli~~~d~~~~~~~~~~iL~Dp~~~Ee~~~d~d~~Va~--t~~gI~alq~~~k~~~i~~e~l~~al~~A~~~~~~I~  596 (974)
                      +++|++.++          .+++||+..||..++.+++|+.  +.++|+++|+.   ++++.++|.+|+++|++++.+|+
T Consensus       157 vs~g~~~~~----------~~llDp~~~Ee~~~~~~~~v~~~~~~~~i~~lq~~---g~~~~~~l~~~l~~A~~~~~~i~  223 (237)
T 2nn6_D          157 VACALDSDG----------TLVLDPTSKQEKEARAVLTFALDSVERKLLMSSTK---GLYSDTELQQCLAAAQAASQHVF  223 (237)
T ss_dssp             EEEEECTTC----------CEEESCCHHHHHHCSEEEEEEEETTTCCCCEEEEE---ESCCHHHHHHHHHHHHHHHHHHH
T ss_pred             EEEEEecCC----------cEEeCCCHHHHhccCCceEEEEcCCCCCEEEEEEe---CCcCHHHHHHHHHHHHHHHHHHH
Confidence            999999531          5999999999988655555554  44569999996   36999999999999999999999


Q ss_pred             HHHHHHhcCC
Q 002054          597 DHMEREISAP  606 (974)
Q Consensus       597 ~~m~~~i~~~  606 (974)
                      +.|++++++.
T Consensus       224 ~~~~~~l~~~  233 (237)
T 2nn6_D          224 RFYRESLQRR  233 (237)
T ss_dssp             HHHHHHHHHH
T ss_pred             HHHHHHHHHh
Confidence            9999999764

>3b4t_A Ribonuclease PH; RNAse, tRNA nucleotidyltransferase, RPHA, STRU genomics, TBSGC; 2.10A {Mycobacterium tuberculosis}

Probab=100.00  E-value=2.9e-38  Score=343.22  Aligned_cols=214  Identities=20%  Similarity=0.223  Sum_probs=192.2

Q ss_pred             CeEEEEEeCccCcCCCcEEEEEeCCeEEEEEEEeCCC-CC---CCCceeeEeeccccccccCCCCCcccccc---CCCCc
Q 002054           67 SRLITLETGKIARFANGAVVLGMDETKVLSTVTSSKG-DS---VRDFLPLTVDYQEKQFAQGVIPNTYMRRE---GAPKE  139 (974)
Q Consensus        67 ~r~i~~etg~~a~~A~GSa~v~~G~T~Vl~tv~~~~~-~~---~~~f~pL~v~y~e~~~a~g~ip~~~~~Re---g~p~~  139 (974)
                      -|++.+++|.+ ++|+|||++++|+|+|||+|+++.+ |.   +.+..+|+|+|.++.||+    ++|.+||   |+|++
T Consensus        16 ~R~i~i~~g~~-~~a~GSa~v~~G~T~Vl~~V~~~~~~p~~~~~~~~g~l~v~~~~~p~a~----~~~~~Re~~~G~~~~   90 (262)
T 3b4t_A           16 LRPVIITRGFT-ENPAGSVLIEFGHTKVLCTASVTEGVPRWRKATGLGWLTAEYAMLPSAT----HSRSDRESVRGRLSG   90 (262)
T ss_dssp             CCCEEEEETSS-SSSSEEEEEEETTEEEEEEEEEEESCC----CCSCCEEEEEEEECGGGS----SSCCCCHHHHTSCCH
T ss_pred             cCCeEEEeCCc-CCCCeEEEEEECCCEEEEEEEecCcCCCccCCCCceEEEEEEEeCCCcc----ccccccccCCCCCCH
Confidence            58999999977 9999999999999999999999876 42   245567999999999998    4688998   99999


Q ss_pred             hhhhHHHhhcCCccccccCCCCCceEEE--EEEEeccCCCChhhHHHHHHHHHhhcC------------CCCCCCCeEEE
Q 002054          140 RELLVGRIIDRPIRPLFPAGFYHEVQVM--ASVLSSDGKQDPDIMAANATSAALMLS------------DIPWGGPIGMI  205 (974)
Q Consensus       140 ~eil~~RlidR~lrplfp~~~~~~~~i~--~~vl~~dg~~~~~~~ai~aAs~AL~~s------------~iP~~~~v~av  205 (974)
                      ++++++|+|+|+|||+||.+++++.+|.  |+||++||+  +.+||+|||++||+++            +|||+++++||
T Consensus        91 ~~~~isrli~r~lr~~i~~~~l~~~~I~i~~~VL~~DG~--~~~aai~aa~~AL~~a~~~~~~~~~~~~~ip~~~~v~av  168 (262)
T 3b4t_A           91 RTQEISRLIGRSLRACIDLAALGENTIAIDCDVLQADGG--TRTAAITGAYVALADAVTYLSAAGKLSDPRPLSCAIAAV  168 (262)
T ss_dssp             HHHHHHHHHHHHHHTTBCHHHHCSEEEEEEEEEEECSSC--HHHHHHHHHHHHHHHHHHHHHHTTCCSSSCCBCSCEEEE
T ss_pred             HHHHHHHHHHHHHHHhcCHhHCCCeEEEEEEEEEeCCCC--HHHHHHHHHHHHHHHhhhhhccCCccccCCcccCceeEE
Confidence            9999999999999999998887776666  999999998  4599999999999999            99999999999


Q ss_pred             EEEEECCEEEEcCCHHHHhcCccceeEeeeCCe-EEEEEecC--CCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCc
Q 002054          206 RIGRICGQFIVNPTMDELSLSDLNLVYACTREK-TLMIDVQA--REISEKDLEAGLRLAHPEAVKYLEPQIRLAEKAGKQ  282 (974)
Q Consensus       206 ~vg~i~g~~vldPt~~e~~~s~~~l~v~~t~~~-i~mie~~~--~~~~e~~~~~al~~a~~~~~~i~~~~~~~~~~~g~~  282 (974)
                      ++|+++|++++|||++|++.++.||+|+++.++ ++|+|+.+  ..|++++|.+||++|+++++++++.|++++++..++
T Consensus       169 svg~~~g~~l~Dpt~~Ee~~~~~~l~va~~~~g~i~~i~~~g~~~~~~~~~l~~~l~~A~~~~~~i~~~~~~~l~~~~~~  248 (262)
T 3b4t_A          169 SVGVVDGRIRVDLPYEEDSRAEVDMNVVATDTGTLVEIQGTGEGATFARSTLDKLLDMALGACDTLFAAQRDALALPYPG  248 (262)
T ss_dssp             EEEEETTEEEESCCHHHHTTCSEEEEEEEETTSCEEEEEECSSCCCBCHHHHHHHHHHHHHHHHHHHHHHHHHHTSCCSS
T ss_pred             EEEEECCEEEECCCHHHHhccCceEEEEEcCCCCEEEEEeeCCCCCcCHHHHHHHHHHHHHHHHHHHHHHHHHHhcchhc
Confidence            999999999999999999999999999999865 99999987  579999999999999999999999999999866554


Q ss_pred             ccccc
Q 002054          283 KKEYK  287 (974)
Q Consensus       283 k~~~~  287 (974)
                      ...+.
T Consensus       249 ~~~~~  253 (262)
T 3b4t_A          249 VLPQG  253 (262)
T ss_dssp             CCC--
T ss_pred             cCccC
Confidence            44443

>2wp8_B Exosome complex component SKI6; nucleus, hydrolase, RNA-binding, exonucle binding, mitochondrion, rRNA processing; 3.00A {Saccharomyces cerevisiae}

Probab=100.00  E-value=6e-38  Score=337.80  Aligned_cols=210  Identities=16%  Similarity=0.092  Sum_probs=178.1

Q ss_pred             CeEEEEEeCccCcCCCcEEEEEeCCeEEEEEEEeCCC--C---CCCCceeeEeeccccccccCCCCCccccccCCCCchh
Q 002054           67 SRLITLETGKIARFANGAVVLGMDETKVLSTVTSSKG--D---SVRDFLPLTVDYQEKQFAQGVIPNTYMRREGAPKERE  141 (974)
Q Consensus        67 ~r~i~~etg~~a~~A~GSa~v~~G~T~Vl~tv~~~~~--~---~~~~f~pL~v~y~e~~~a~g~ip~~~~~Reg~p~~~e  141 (974)
                      -|++.+++|.+++.|+|||++++|+|+|||+|+++.+  +   ...++.||+++|.++.||++.    |.+|||+|++++
T Consensus        22 ~R~i~i~~g~l~~aa~GSa~v~~G~T~Vl~~V~~~~~~~~~~~~~~~~g~l~v~~~~~p~a~~~----~~~r~g~~~~~~   97 (246)
T 2wp8_B           22 LRRFESSINTHPHAADGSSYMEQGNNKIITLVKGPKEPRLKSQMDTSKALLNVSVNINKFSKFE----RSKSSHKNERRV   97 (246)
T ss_dssp             CCCEEEEECSCTTTCSEEEEEEETTEEEEEEEEEEEC------CCSSSEEEEEEEEEC------------------CHHH
T ss_pred             ccCeEEEeCCCCCCCCceEEEEECCeEEEEEEEecCCcccccccCCCcEEEEEEEEeCCccccc----ccccCCCCChhH
Confidence            5899999999954349999999999999999999876  2   246899999999999999975    788899999999


Q ss_pred             hhHHHhhcCCccccccCC-C-CCceEEEEEEEeccCCCChhhHHHHHHHHHhhcCCCCCCCCeEEEEEEEECCEEEEcCC
Q 002054          142 LLVGRIIDRPIRPLFPAG-F-YHEVQVMASVLSSDGKQDPDIMAANATSAALMLSDIPWGGPIGMIRIGRICGQFIVNPT  219 (974)
Q Consensus       142 il~~RlidR~lrplfp~~-~-~~~~~i~~~vl~~dg~~~~~~~ai~aAs~AL~~s~iP~~~~v~av~vg~i~g~~vldPt  219 (974)
                      ++++|+|+|+|||+||.. | ++.++|+++||++||+..  +||+|||++||++++|||+++|+||++|+++|++++|||
T Consensus        98 ~~~s~li~r~l~~~i~~~~~p~~~I~i~~~VL~~dG~~~--~aai~aa~~AL~~a~iP~~~~v~avs~g~~~~~~l~Dp~  175 (246)
T 2wp8_B           98 LEIQTSLVRMFEKNVMLNIYPRTVIDIEIHVLEQDGGIM--GSLINGITLALIDAGISMFDYISGISVGLYDTTPLLDTN  175 (246)
T ss_dssp             HHHHHHHHHHHHHHBCTTTSCSEEEEEEEEEEECCSCHH--HHHHHHHHHHHHHHTCCBSSCEEEEEEEEETTEEESSCC
T ss_pred             HHHHHHHHHHHHHhhhHHHCCCeEEEEEEEEEECCCCHH--HHHHHHHHHHHHHcCCcccCceeEEEEEEECCEEEECCC
Confidence            999999999999999964 4 567999999999999855  999999999999999999999999999999999999999


Q ss_pred             HHHHhcCccceeEee--eCCeEEEEEecCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCccc
Q 002054          220 MDELSLSDLNLVYAC--TREKTLMIDVQAREISEKDLEAGLRLAHPEAVKYLEPQIRLAEKAGKQKK  284 (974)
Q Consensus       220 ~~e~~~s~~~l~v~~--t~~~i~mie~~~~~~~e~~~~~al~~a~~~~~~i~~~~~~~~~~~g~~k~  284 (974)
                      ++|+ .++.||+|+.  +.++++|+|+++ .|++++|.+||++|+++++++++.|++.+++.++++.
T Consensus       176 ~~Ee-~~~~~l~v~~~~~~~~i~~i~~~g-~~~~~~l~~~l~~A~~~~~~i~~~~~~~l~~~~~~~~  240 (246)
T 2wp8_B          176 SLEE-NAMSTVTLGVVGKSEKLSLLLVED-KIPLDRLENVLAIGIAGAHRVRDLMDEELRKHAQKRV  240 (246)
T ss_dssp             HHHH-HHSEEEEEEEETTSSCEEEEEECS-CEEHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCC-
T ss_pred             chhh-ccCceEEEEEeCCCCCEEEEEecC-CcCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhh
Confidence            9999 9999999965  566799999987 5999999999999999999999999999998876554

>2nn6_F MTR3, exosome component 6; RNA, exosome, PM/SCL, phosphorolytic, hydrolase/transferase complex; 3.35A {Homo sapiens} SCOP: d.14.1.4 d.101.1.1

Probab=100.00  E-value=4.7e-38  Score=343.40  Aligned_cols=207  Identities=17%  Similarity=0.140  Sum_probs=187.3

Q ss_pred             CeEEEEEeCccCcCCCcEEEEEeCCeEEEEEEEeCCC-CCC---------------CCceeeEeeccccccccCCCCCcc
Q 002054           67 SRLITLETGKIARFANGAVVLGMDETKVLSTVTSSKG-DSV---------------RDFLPLTVDYQEKQFAQGVIPNTY  130 (974)
Q Consensus        67 ~r~i~~etg~~a~~A~GSa~v~~G~T~Vl~tv~~~~~-~~~---------------~~f~pL~v~y~e~~~a~g~ip~~~  130 (974)
                      -|++.+++|.+ .+|||||++++|+|+|||+|+++.+ +..               .++.||+|+|.++.||+++     
T Consensus        36 ~R~i~i~~g~l-~~a~GSa~v~~G~T~Vl~~V~~~~~~~~~~~~~~~~~~~~~~~~~~~g~l~v~~~~~p~a~~~-----  109 (272)
T 2nn6_F           36 LRPVYARAGLL-SQAKGSAYLEAGGTKVLCAVSGPRQAEGGERGGGPAGAGGEAPAALRGRLLCDFRRAPFAGRR-----  109 (272)
T ss_dssp             CCCCCCCCSCC-SSSSEEECCCSSSCEEEEEEEEEECC-------------------CBCEEEEEEEECTTSSSS-----
T ss_pred             cCCeEEEeCCC-CCCCeEEEEEeCCeEEEEEEECCCcccccccccccccccccccCCCceEEEEEEEecCCCcCC-----
Confidence            58899999999 5999999999999999999999887 332               3579999999999999986     


Q ss_pred             ccccCCCCchhhhHHHhhcCCccccccCCC--CCceEEEEEEEeccCCCChhhHHHHHHHHHhhcCCCCCCCCeEEEEEE
Q 002054          131 MRREGAPKERELLVGRIIDRPIRPLFPAGF--YHEVQVMASVLSSDGKQDPDIMAANATSAALMLSDIPWGGPIGMIRIG  208 (974)
Q Consensus       131 ~~Reg~p~~~eil~~RlidR~lrplfp~~~--~~~~~i~~~vl~~dg~~~~~~~ai~aAs~AL~~s~iP~~~~v~av~vg  208 (974)
                       +|+|+|+++|++++|+|+|+|||+++.+.  ++.++|+|+||++||+..  +||+|||++||++++|||+++|+||++|
T Consensus       110 -~~~~~~~~~e~~~s~li~r~l~~~i~~~~~p~~~I~I~~~VL~~DG~~~--~aai~aa~~AL~da~iP~~~~v~avsvg  186 (272)
T 2nn6_F          110 -RRAPPGGCEERELALALQEALEPAVRLGRYPRAQLEVSALLLEDGGSAL--AAALTAAALALADAGVEMYDLVVGCGLS  186 (272)
T ss_dssp             -CCCSCCHHHHHHHHHHHHHHHTTTBCSTTSBTCEEEEEEEEEECCSSHH--HHHHHHHHHHHHHHCCCBSSCCEEEECC
T ss_pred             -ccCCCCCHHHHHHHHHHHHHHHHhccHHHCCceEEEEEEEEEeCCCCHH--HHHHHHHHHHHHHcCCcccCcEEEEEEE
Confidence             56789999999999999999999777543  358999999999999755  9999999999999999999999999999


Q ss_pred             E---ECCEEEEcCCHHHHhcCccceeEe--eeCCeEEEEEecCCCCCH-HHHHHHHHHHHHHHHHHHHHHHHHHHHhCCc
Q 002054          209 R---ICGQFIVNPTMDELSLSDLNLVYA--CTREKTLMIDVQAREISE-KDLEAGLRLAHPEAVKYLEPQIRLAEKAGKQ  282 (974)
Q Consensus       209 ~---i~g~~vldPt~~e~~~s~~~l~v~--~t~~~i~mie~~~~~~~e-~~~~~al~~a~~~~~~i~~~~~~~~~~~g~~  282 (974)
                      +   ++|++|+|||++|++.+++||+|+  ++.++|+|+|+++ .|++ ++|.+||++|++++++++++|++++++.+++
T Consensus       187 ~~~~~~~~~llDpt~~Ee~~~~~~l~va~~~~~~~I~~i~~~g-~~~~~~~l~~~l~~A~~~~~~i~~~~~~~l~~~~~~  265 (272)
T 2nn6_F          187 LAPGPAPTWLLDPTRLEEERAAAGLTVALMPVLNQVAGLLGSG-EGGLTESWAEAVRLGLEGCQRLYPVLQQSLVRAARR  265 (272)
T ss_dssp             CCSCSSCCCCSSCCTTTGGGCSSEEEEEEETTTTEEEEEEEEC-CSSCTTTTHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             EeeccCCeEEeCCCHHHhccCCceEEEEEeCCCCCEEEEEEec-CCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence            9   899999999999999999999999  5677899999998 5999 9999999999999999999999999887754


Q ss_pred             c
Q 002054          283 K  283 (974)
Q Consensus       283 k  283 (974)
                      +
T Consensus       266 ~  266 (272)
T 2nn6_F          266 R  266 (272)
T ss_dssp             H
T ss_pred             h
Confidence            3

>1r6l_A Ribonuclease PH; beta-alpha-beta-alpha fold, hexamer, phosphate bound, transf; HET: NHE; 1.90A {Pseudomonas aeruginosa} SCOP: d.14.1.4 d.101.1.1 PDB: 1r6m_A

Probab=100.00  E-value=1.6e-36  Score=325.38  Aligned_cols=201  Identities=22%  Similarity=0.286  Sum_probs=179.9

Q ss_pred             CeEEEEEeCccCcCCCcEEEEEeCCeEEEEEEEeCCC-CC---CCCceeeEeeccccccccCCCCCcccc---cc---CC
Q 002054           67 SRLITLETGKIARFANGAVVLGMDETKVLSTVTSSKG-DS---VRDFLPLTVDYQEKQFAQGVIPNTYMR---RE---GA  136 (974)
Q Consensus        67 ~r~i~~etg~~a~~A~GSa~v~~G~T~Vl~tv~~~~~-~~---~~~f~pL~v~y~e~~~a~g~ip~~~~~---Re---g~  136 (974)
                      =|++.+++|.+ ++|+|||++++|+|+|||+|+++.+ |.   +.+..+|+++|       +++|+++.+   ||   |+
T Consensus        12 ~R~i~i~~g~~-~~a~GSa~v~~G~T~Vl~~V~~~~~~p~~~~~~~~g~l~v~~-------~~~p~~~~~r~~Re~~~G~   83 (239)
T 1r6l_A           12 LRPIRITRHYT-KHAEGSVLVEFGDTKVICTVSAESGVPRFLKGQGQGWLTAEY-------GMLPRSTGERNQREASRGK   83 (239)
T ss_dssp             CCCEEEESSCS-SSSSEEEEEEETTEEEEEEEEEEESCSSCCC---CCEEEEEE-------EECTTSSSSCCCCHHHHTS
T ss_pred             cCCeEEEeCCc-CCCCeEEEEEECCEEEEEEEEccCccCCccCCCCcEEEEEEE-------EeCCCccccccccccCCCC
Confidence            48899999988 9999999999999999999999876 32   23445699999       566777764   56   89


Q ss_pred             CCchhhhHHHhhcCCccccccCCCCCc--eEEEEEEEeccCCCChhhHHHHHHHHHhhcCC-----------CCCCCCeE
Q 002054          137 PKERELLVGRIIDRPIRPLFPAGFYHE--VQVMASVLSSDGKQDPDIMAANATSAALMLSD-----------IPWGGPIG  203 (974)
Q Consensus       137 p~~~eil~~RlidR~lrplfp~~~~~~--~~i~~~vl~~dg~~~~~~~ai~aAs~AL~~s~-----------iP~~~~v~  203 (974)
                      |++++++++|+|+|+|||+||.+++++  ++|+|+||++||+..  +||+|||++||++++           |||+++++
T Consensus        84 ~~~~~~~isrli~r~l~~~i~~~~l~~~~i~I~~~VL~~DG~~~--~aai~aa~~AL~da~~~~~~~~~~~~ip~~~~~~  161 (239)
T 1r6l_A           84 QGGRTLEIQRLIGRSLRAALDLSKLGENTLYIDCDVIQADGGTR--TASITGATVALIDALAVLKKRGALKGNPLKQMVA  161 (239)
T ss_dssp             CCHHHHHHHHHHHHHHHHTBCGGGTCSEEEEEEEEEEECSSCHH--HHHHHHHHHHHHHHHHHHHHTTCCSSCCBCCCEE
T ss_pred             CcHHHHHHHHHHHHHHHHhcCHHHcCCeEEEEEEEEEeCCCCHH--HHHHHHHHHHHHHhcchhcccCcccccCccCcee
Confidence            999999999999999999999888777  799999999999875  999999999999777           99999999


Q ss_pred             EEEEEEECCEEEEcCCHHHHhcCccceeEeeeCCe-EEEEEec--CCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 002054          204 MIRIGRICGQFIVNPTMDELSLSDLNLVYACTREK-TLMIDVQ--AREISEKDLEAGLRLAHPEAVKYLEPQIRLAE  277 (974)
Q Consensus       204 av~vg~i~g~~vldPt~~e~~~s~~~l~v~~t~~~-i~mie~~--~~~~~e~~~~~al~~a~~~~~~i~~~~~~~~~  277 (974)
                      ||++|+++|++++|||++|++.++.+|+|++++++ ++.+++.  +..|++++|.+|+++|+++++++++.|+++++
T Consensus       162 avs~g~~~~~~l~Dpt~~Ee~~~~~~l~va~~~~g~i~~~~~~g~~~~~~~~~l~~~l~~a~~~~~~i~~~~~~~l~  238 (239)
T 1r6l_A          162 AVSVGIYQGVPVLDLDYLEDSAAETDLNVVMTDAGGFIEVQGTAEGAPFRPAELNAMLELAQQGMQELFELQRAALA  238 (239)
T ss_dssp             EEEEEEETTEEEESCCHHHHHHCSEEEEEEEETTSCEEEEEEEESSSCCCHHHHHHHHHHHHHHHHHHHHHHHHHHT
T ss_pred             EEEEEEECCEEEECCCHHHHhcCCceEEEEEeCCCCEEEEEEeCCCCCcCHHHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence            99999999999999999999999999999999887 7778753  46799999999999999999999999998764

>2wnr_A Probable exosome complex exonuclease 2; phosphate binding, 3'-5' exoribonuclease, hydrolase; 2.65A {Methanothermobacter thermautotrophicusorganism_taxid}

Probab=100.00  E-value=4e-36  Score=328.29  Aligned_cols=201  Identities=19%  Similarity=0.254  Sum_probs=184.6

Q ss_pred             CeEEEEEeCccCcCCCcEEEEEeCCeEEEEEEEeC-CCC--CCCCceeeEeeccccccccCCCCCccccccCCCCchhhh
Q 002054           67 SRLITLETGKIARFANGAVVLGMDETKVLSTVTSS-KGD--SVRDFLPLTVDYQEKQFAQGVIPNTYMRREGAPKERELL  143 (974)
Q Consensus        67 ~r~i~~etg~~a~~A~GSa~v~~G~T~Vl~tv~~~-~~~--~~~~f~pL~v~y~e~~~a~g~ip~~~~~Reg~p~~~eil  143 (974)
                      -|++.+++|.+ ++|+|||++++|+|+|||+|+.+ .+|  ...++.||+++|.++.||+++      +|+|+|++++++
T Consensus        34 ~R~i~i~~g~l-~~a~GSa~v~~G~T~Vl~~V~~~~~~p~~~~~~~g~l~v~~~~~p~a~~~------~~~g~~~~~~~~  106 (271)
T 2wnr_A           34 FRDISIETGVI-SKAEGSSRVKLGNTQIIVGVKPQIGEPFPDTPEMGVILTNSELLPMASPT------FEPGPPDERSVE  106 (271)
T ss_dssp             CCCEEEEESCS-TTSSEEEEEEETTEEEEEEEEEEEECCCTTCTTCCEEEEEEEECGGGCTT------CCCSSCCHHHHH
T ss_pred             ccCeEEEeCcc-CCCCeEEEEEECCeEEEEEEEeeeecCCCCCCCceEEEEEEEeCCccccc------ccCCCCchHHHH
Confidence            58899999999 89999999999999999999944 343  357899999999999999975      567999999999


Q ss_pred             HHHhhcCCccc--ccc-CCC-------CCceEEEEEEEeccCCCChhhHHHHHHHHHhhcCC------------------
Q 002054          144 VGRIIDRPIRP--LFP-AGF-------YHEVQVMASVLSSDGKQDPDIMAANATSAALMLSD------------------  195 (974)
Q Consensus       144 ~~RlidR~lrp--lfp-~~~-------~~~~~i~~~vl~~dg~~~~~~~ai~aAs~AL~~s~------------------  195 (974)
                      ++|+|+|+|||  +|| +.|       .+.++|+++||++||+.  .+||+|||++||++++                  
T Consensus       107 ~s~li~r~lr~s~~i~l~~l~i~pg~~~~~i~i~~~VL~~DG~~--~~aai~aa~~AL~~a~~p~~~~~~~~~~~~~~~~  184 (271)
T 2wnr_A          107 LSRVVDRCIRESRMIDLEKLCIIEGSKVWMLFLDLHIIDYDGNL--FDAAVLATVAALLDTRIPAAEVEDGEVVINREKM  184 (271)
T ss_dssp             HHHHHHHHHHHTTCBCGGGGEEETTTEEEEEEEEEEEEECSSCH--HHHHHHHHHHHHHHCEEEEEEEETTEEEEEEEEE
T ss_pred             HHHHHHHHHhccCCccHHHccccCCcEEEEEEEEEEEECCCCCH--HHHHHHHHHHHHHhcCCCeEEecCCceeeccCcc
Confidence            99999999999  788 444       57999999999999984  5999999999999999                  


Q ss_pred             --CCCCCCeEEEEEEEECCEEEEcCCHHHHhcCccceeEeeeCCe-EEEEEecC-CCCCHHHHHHHHHHHHHHHHHHHHH
Q 002054          196 --IPWGGPIGMIRIGRICGQFIVNPTMDELSLSDLNLVYACTREK-TLMIDVQA-REISEKDLEAGLRLAHPEAVKYLEP  271 (974)
Q Consensus       196 --iP~~~~v~av~vg~i~g~~vldPt~~e~~~s~~~l~v~~t~~~-i~mie~~~-~~~~e~~~~~al~~a~~~~~~i~~~  271 (974)
                        +||+++++||++|+++|++++|||++|++.++.+|+|++++++ ++|+|+.+ +.|++++|.+|+++|+++++++++.
T Consensus       185 ~~ip~~~~~~avt~g~~~~~~l~Dpt~~Ee~~~~~~l~va~~~~~~i~~i~~~g~~~~~~~~l~~~l~~a~~~~~~i~~~  264 (271)
T 2wnr_A          185 QPLPVNRKALMCTFAKIGNEIVLDPSLEEEDILTARISIGVTEEGSICAMQKGGEGPLTRDDVLKAVSIAVEKVPQLIEY  264 (271)
T ss_dssp             EECCBCCCEEEEEEEEETTEEEESCCHHHHTTCSEEEEEEEETTSCEEEEEEESSSCBCHHHHHHHHHHHHHHHHHHHHH
T ss_pred             cccCccCCeEEEEEEEECCEEEeCCCHHHHhcCCCcEEEEEeCCCCEEEEECCCCCCCCHHHHHHHHHHHHHHHHHHHHH
Confidence              9999999999999999999999999999999999999999855 99999875 6799999999999999999999999


Q ss_pred             HHHHH
Q 002054          272 QIRLA  276 (974)
Q Consensus       272 ~~~~~  276 (974)
                      |++++
T Consensus       265 ~~~~l  269 (271)
T 2wnr_A          265 LDKSM  269 (271)
T ss_dssp             HHHHC
T ss_pred             HHHHh
Confidence            98865

>3m7n_G Probable exosome complex exonuclease 2; exosome, RNA, exonuclease, hydrolase, nuclease, hydrolase-RN; 2.40A {Archaeoglobus fulgidus} PDB: 2ba1_H 2ba0_I 3m85_G

Probab=100.00  E-value=2.7e-36  Score=327.27  Aligned_cols=199  Identities=22%  Similarity=0.247  Sum_probs=181.0

Q ss_pred             CeEEEEEeCccCcCCCcEEEEEeCCeEEEEEEEeCCC-C--CCCCceeeEeeccccccccCCCCCccccccCCCCchhhh
Q 002054           67 SRLITLETGKIARFANGAVVLGMDETKVLSTVTSSKG-D--SVRDFLPLTVDYQEKQFAQGVIPNTYMRREGAPKERELL  143 (974)
Q Consensus        67 ~r~i~~etg~~a~~A~GSa~v~~G~T~Vl~tv~~~~~-~--~~~~f~pL~v~y~e~~~a~g~ip~~~~~Reg~p~~~eil  143 (974)
                      -|++.+++|.+ ++|+|||++++|+|+|||+|+++.. |  ...+..+|+++|.++.||+++    |  |+|+|++++++
T Consensus        32 ~R~i~i~~g~l-~~a~GSa~v~~G~T~Vl~~V~~~~~~p~~~~~~~g~l~v~~~~~p~a~~~----~--~~g~~~~~~~~  104 (259)
T 3m7n_G           32 FRKVEIIPNVI-EKAEGSALVKLGDTQVVVGVKMQPGEPYPDTPDRGVIIVNAELVPLASPT----F--EPGPPDENSIE  104 (259)
T ss_dssp             CCCEEEEETSS-TTSSEEEEEEETTEEEEEEEEEEEECCCSSCTTSCEEEEEEECCTTSCTT----C--CSSSSCHHHHH
T ss_pred             ccCeEEEeCCc-CCCCceEEEEECCcEEEEEEEecccCCCCCCCCceEEEEEEEeCCccccc----c--cCCCCChHHHH
Confidence            68999999999 8999999999999999999997543 3  234567899999999999986    2  56999999999


Q ss_pred             HHHhhcCCccc--c--------ccCCCCCceEEEEEEEeccCCCChhhHHHHHHHHHhhcCCC-------------CCCC
Q 002054          144 VGRIIDRPIRP--L--------FPAGFYHEVQVMASVLSSDGKQDPDIMAANATSAALMLSDI-------------PWGG  200 (974)
Q Consensus       144 ~~RlidR~lrp--l--------fp~~~~~~~~i~~~vl~~dg~~~~~~~ai~aAs~AL~~s~i-------------P~~~  200 (974)
                      ++|+|+|+|||  +        +|..|.+.++|+|+||++||+..  +||+|||++||++++|             ||++
T Consensus       105 ~srli~r~lr~s~~i~l~~L~i~pg~~~~~i~i~~~VL~~DG~~~--~aai~aa~~AL~~a~iP~~~~~~~~~~~lp~~~  182 (259)
T 3m7n_G          105 LARVVDRGIRESEAVDLSKLVIEEGEKVWIVFVDIHALDDDGNLL--DASALAAIAALMNTKVPAERFDLGEDYLLPVRD  182 (259)
T ss_dssp             HHHHHHHHHHHTTCBCGGGGEEETTTEEEEEEEEEEEEECSSCHH--HHHHHHHHHHHHTCEECTGGGTSSSCEECCBCC
T ss_pred             HHHHHHHHHhhcCCccHHHhcccCCcEEEEEEEEEEEEcCCCCHH--HHHHHHHHHHHHhCCCCeEEecCCceecccccC
Confidence            99999999999  3        46777899999999999999876  8999999999999999             7999


Q ss_pred             CeEEEEEEEECCEEEEcCCHHHHhcCccceeEeeeCCe-EEEEEecC-CCCCHHHHHHHHHHHHHHHHHHHHHHHH
Q 002054          201 PIGMIRIGRICGQFIVNPTMDELSLSDLNLVYACTREK-TLMIDVQA-REISEKDLEAGLRLAHPEAVKYLEPQIR  274 (974)
Q Consensus       201 ~v~av~vg~i~g~~vldPt~~e~~~s~~~l~v~~t~~~-i~mie~~~-~~~~e~~~~~al~~a~~~~~~i~~~~~~  274 (974)
                      +++||++|+++|++++|||++|++.++.+|+|++++++ ++|+++.+ +.|++++|.+||++|++++++++++|++
T Consensus       183 ~~~avtvg~~~~~~l~Dpt~~Ee~~~~~~l~va~~~~g~i~~i~~~g~~~~~~~~l~~~l~~a~~~~~~l~~~~~~  258 (259)
T 3m7n_G          183 LPVSVTSLIVGNKYLVDPSREEMSVGDTTLTITTDKDDNVVAMQKSGGYLLDEKLFDELLDVSINCARKLREKFKE  258 (259)
T ss_dssp             CCEEEEEEEETTEEEESCCTTGGGGCSCEEEEEECTTSCEEEEEEESSCCBCHHHHHHHHHHHHHHHHHHHHTTC-
T ss_pred             ceeEEEEEEECCEEEECCCHHHHhhCCCcEEEEEeCCCcEEEEECCCCCCcCHHHHHHHHHHHHHHHHHHHHHHhh
Confidence            99999999999999999999999999999999999884 99998764 7899999999999999999999998765

>3m7n_D Probable exosome complex exonuclease 1; exosome, RNA, exonuclease, hydrolase, nuclease, hydrolase-RN; 2.40A {Archaeoglobus fulgidus} PDB: 3m85_D 2ba0_F 2ba1_E

Probab=100.00  E-value=7.8e-36  Score=322.38  Aligned_cols=202  Identities=20%  Similarity=0.364  Sum_probs=183.1

Q ss_pred             CeEEEEEeCccCcCCCcEEEEEeCCeEEEEEEEeCCC--CC---CCCceeeEeeccccccccCCCCCccccccCCCCchh
Q 002054           67 SRLITLETGKIARFANGAVVLGMDETKVLSTVTSSKG--DS---VRDFLPLTVDYQEKQFAQGVIPNTYMRREGAPKERE  141 (974)
Q Consensus        67 ~r~i~~etg~~a~~A~GSa~v~~G~T~Vl~tv~~~~~--~~---~~~f~pL~v~y~e~~~a~g~ip~~~~~Reg~p~~~e  141 (974)
                      =|++.+++|++ ++|+|||++++|+|+|||+|++|.+  ++   ..+..+|+++|....||.+.      +|.|+|++++
T Consensus        26 ~R~i~i~~g~l-~~a~GSa~v~~G~T~Vl~~V~gp~e~~~~~~~~~~~g~l~~~~~~~P~s~~~------r~~~~~~~re   98 (258)
T 3m7n_D           26 LRPIKIEASVL-KRADGSCYLEMGKNKVIAAVFGPREVHPEHLQDPSKAIIRYRYNMAPFSVEE------RKRPGPDRRS   98 (258)
T ss_dssp             CCCEEEEECCC-SSSSEEEEEEETTEEEEEEEEEEEECSSSTTCCSSSCEEEEEEEECGGGSSS------CCCSSCCHHH
T ss_pred             ccCeEEEECCC-CCCCceEEEEECCeEEEEEEEcccCCCCccccCCCceEEEEEEEeCCccccc------ccCCCCCHHH
Confidence            48899999999 9999999999999999999998766  22   34667899999888888753      3448899999


Q ss_pred             hhHHHhhcCCcccccc-CCC-CCceEEEEEEEeccCCCChhhHHHHHHHHHhhcCCCCCCCCeEEEEEEEECCEEEEcCC
Q 002054          142 LLVGRIIDRPIRPLFP-AGF-YHEVQVMASVLSSDGKQDPDIMAANATSAALMLSDIPWGGPIGMIRIGRICGQFIVNPT  219 (974)
Q Consensus       142 il~~RlidR~lrplfp-~~~-~~~~~i~~~vl~~dg~~~~~~~ai~aAs~AL~~s~iP~~~~v~av~vg~i~g~~vldPt  219 (974)
                      ++++|+|+|+|||+++ +.| ++.++|+|+||++||+..  +||+|||++||++++|||+++|+||++|+++|++++|||
T Consensus        99 ~ei~~li~r~l~~~i~~~~~p~~~I~V~~~VL~~DG~~~--~Aai~aa~lAL~dagiP~~~~v~avsvg~i~~~~llDpt  176 (258)
T 3m7n_D           99 IEISKVSKEAFEAVIMKELFPRSAIDIFVEVLQADAGSR--TACLNAASVALVDAGVPMKGMITSVAVGKADGQLVLDPM  176 (258)
T ss_dssp             HHHHHHHHHHHHTTBCGGGSTTEEEEEEEEEEECCTTHH--HHHHHHHHHHHHHTTCCBSSEEEEEEEEEETTEEEESCC
T ss_pred             HHHHHHHHHHHHhhcCHHhCCceEEEEEEEEEEcCCCHH--HHHHHHHHHHHHhcCCCCCCceEEEEEEEECCEEEECCC
Confidence            9999999999999985 566 556899999999999886  999999999999999999999999999999999999999


Q ss_pred             HHHHhcCccceeEee-eC----CeEEEEEecCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 002054          220 MDELSLSDLNLVYAC-TR----EKTLMIDVQAREISEKDLEAGLRLAHPEAVKYLEPQIRLAEK  278 (974)
Q Consensus       220 ~~e~~~s~~~l~v~~-t~----~~i~mie~~~~~~~e~~~~~al~~a~~~~~~i~~~~~~~~~~  278 (974)
                      ++|++.++.||+|++ +.    ++|+++|+.+ .|++++|.+||++|+++|++|++.|++.+++
T Consensus       177 ~~Ee~~~~~d~~va~~~~~~~~~~I~~lq~~g-~~~~~~l~~~l~~A~~~~~~i~~~~~~~l~~  239 (258)
T 3m7n_D          177 KEEDNFGEADMPFAFLIRNGKIESIALLQMDG-RMTRDEVKQAIELAKKGALQIYEMQREAILR  239 (258)
T ss_dssp             HHHHHHSSEEEEEEEEEETTEEEEEEEEEEEE-EECHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHhccCceEEEEEEcCCCCCCCEEEEEecC-CcCHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            999999999999999 54    5699999998 6999999999999999999999999998875

>3krn_A Protein C14A4.5, confirmed by transcript evidence; RNAse PH domain, homodimer, exosome, cell-death-related DNAS hydrolase; 3.92A {Caenorhabditis elegans}

Probab=100.00  E-value=1.5e-38  Score=336.98  Aligned_cols=197  Identities=17%  Similarity=0.260  Sum_probs=160.9

Q ss_pred             CeEEEEEeCccCcCCCcEEEEEeCCeEEEEEEEeCCC-C---CCCCceeeEeeccccccccCCCCCccccccCCCCchhh
Q 002054           67 SRLITLETGKIARFANGAVVLGMDETKVLSTVTSSKG-D---SVRDFLPLTVDYQEKQFAQGVIPNTYMRREGAPKEREL  142 (974)
Q Consensus        67 ~r~i~~etg~~a~~A~GSa~v~~G~T~Vl~tv~~~~~-~---~~~~f~pL~v~y~e~~~a~g~ip~~~~~Reg~p~~~ei  142 (974)
                      =|++++|+|++ ++|||||++++|+|+|||+|++|.+ +   ...+++||+|+|.+.              .|+|+++  
T Consensus         5 ~R~i~ie~g~l-~~A~GSa~v~~G~T~Vl~~V~~~~e~~~~~~~~~~~~l~v~~~p~--------------~G~~~~~--   67 (222)
T 3krn_A            5 LREMRCELSFL-KNADGSACFSQGATCIWASCSGPGDVHASKASDEAMTLDISYRAN--------------CGDNKFN--   67 (222)
T ss_dssp             CCCBCCBSCCC-----CCCBCCBTTCEEECCCCSSCC-------------CCCSSCC--------------CC--CCS--
T ss_pred             ccceEEEECCC-CCCCeEEEEEECCcEEEEEEECCCCCcccccCCceEEEEEEEcCC--------------CCCCCHH--
Confidence            38999999999 6899999999999999999999987 3   245789999999743              2667666  


Q ss_pred             hHHHhhcCCccccccCCCC--CceEEEEEEEeccCCCChhhHHHHHHHHHhhcCCCCCCCCeEEEEEEEECCEEEEcCCH
Q 002054          143 LVGRIIDRPIRPLFPAGFY--HEVQVMASVLSSDGKQDPDIMAANATSAALMLSDIPWGGPIGMIRIGRICGQFIVNPTM  220 (974)
Q Consensus       143 l~~RlidR~lrplfp~~~~--~~~~i~~~vl~~dg~~~~~~~ai~aAs~AL~~s~iP~~~~v~av~vg~i~g~~vldPt~  220 (974)
                      +++|+|+|+|||+++...+  +.++|+++||++||+..  +||+|||++||++|||||+++|+||+||+++|++++|||+
T Consensus        68 e~~~li~r~l~~~i~~~~~p~~~I~I~~~VL~~DG~~~--~aai~aa~~AL~dagiP~~~~v~avsvg~~~g~~llDpt~  145 (222)
T 3krn_A           68 VLNNIIHSTLSNAINLELFPHTTISVTVHGIQDDGSMG--AVAINGACFALLDNGMPFETVFCGVLIVRVKDELIIDPTA  145 (222)
T ss_dssp             SCTTHHHHC--CCSCC-----CCCCCCCEEEECCSCHH--HHHHHGGGTTTTTTTCCTTSCCCCCCCEECSSSEESSCCT
T ss_pred             HHHHHHHHHHHHhccHHhCCCcEEEEEEEEEECCCChH--HHHHHHHHHHHHHCCCCccCcEEEEEEEEECCEEEeCCCH
Confidence            8899999999997765443  47899999999999875  9999999999999999999999999999999999999999


Q ss_pred             HHHhcCccceeEee-----eCCeEEEEEecCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCcc
Q 002054          221 DELSLSDLNLVYAC-----TREKTLMIDVQAREISEKDLEAGLRLAHPEAVKYLEPQIRLAEKAGKQK  283 (974)
Q Consensus       221 ~e~~~s~~~l~v~~-----t~~~i~mie~~~~~~~e~~~~~al~~a~~~~~~i~~~~~~~~~~~g~~k  283 (974)
                      +|++.+++||+|++     +.++|+|+|+++ .|++++|.+||++|++++++++++|++++++..++.
T Consensus       146 ~Ee~~~~~~l~va~~~~~~~~~~i~~vq~~g-~~~~~~l~~~l~~a~~~~~~i~~~~~~~l~~~~~~~  212 (222)
T 3krn_A          146 KQEAASTGRVLFSVCKGSDGHPEVCAMDAIG-HWDFIQLEAAWSLAQPSASAIFDFYKTVMKRKLSVD  212 (222)
T ss_dssp             TTTTSCC-CCCCEECCCSSSSCCEEEECCBS-SCTTHHHHTHHHHTTHHHHHHHHHHHHHHHHHHHHC
T ss_pred             HHHhccCccEEEEEEccCCCCCCEEEEEEeC-CcCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcch
Confidence            99999999999999     456799999998 599999999999999999999999999998765433

>1udn_A Ribonuclease PH, RNAse PH; transferase, riken structural genomics/proteomics initiative structural genomics; 2.30A {Aquifex aeolicus} SCOP: d.14.1.4 d.101.1.1 PDB: 1udq_A 1uds_A 1udo_A

Probab=100.00  E-value=1.2e-35  Score=321.36  Aligned_cols=202  Identities=18%  Similarity=0.250  Sum_probs=182.2

Q ss_pred             CeEEEEEeCccCcCCCcEEEEEeCCeEEEEEEEeCCC-C---CCCCceeeEeeccccccccCCCCCccccc---c---CC
Q 002054           67 SRLITLETGKIARFANGAVVLGMDETKVLSTVTSSKG-D---SVRDFLPLTVDYQEKQFAQGVIPNTYMRR---E---GA  136 (974)
Q Consensus        67 ~r~i~~etg~~a~~A~GSa~v~~G~T~Vl~tv~~~~~-~---~~~~f~pL~v~y~e~~~a~g~ip~~~~~R---e---g~  136 (974)
                      =|++.+++|.+ ++|+|||++++|+|+|||+|+++.+ |   ++.+..+|+++|       ++.|.++.+|   |   |+
T Consensus        11 ~R~i~i~~g~~-~~a~GSa~v~~G~T~Vl~~V~~~~~~p~~~~~~~~g~l~~~~-------~~~P~a~~~r~~Re~~~G~   82 (255)
T 1udn_A           11 LRPVSIQRDFL-EYPEGSCLISFGKTKVICTASVIENVPNWLKGKGQGWITAEY-------SMLPRATQQRTIRESVQGR   82 (255)
T ss_dssp             CCCEEEEECCS-SSSSEEEEEEETTEEEEEEEEEESCCCGGGTTSSCCEEEEEE-------EECSCCTTSCCCCSSTTCS
T ss_pred             ccCeEEEECCC-CCCCEEEEEEECCEEEEEEEEcCCcCCCCCCCCCceEEEEEE-------EcCCCccccccccccCCCC
Confidence            48999999988 9999999999999999999999876 3   123455699999       4567666655   7   88


Q ss_pred             CCchhhhHHHhhcCCccccccCCCCCc--eEEEEEEEeccCCCChhhHHHHHHHHHhhcCC-----------CCCCCCeE
Q 002054          137 PKERELLVGRIIDRPIRPLFPAGFYHE--VQVMASVLSSDGKQDPDIMAANATSAALMLSD-----------IPWGGPIG  203 (974)
Q Consensus       137 p~~~eil~~RlidR~lrplfp~~~~~~--~~i~~~vl~~dg~~~~~~~ai~aAs~AL~~s~-----------iP~~~~v~  203 (974)
                      |++++++++|+|+|+|||+||..++++  ++|+|+||++||+..  +||+|||++||++++           |||+++++
T Consensus        83 ~~~~~~eisrli~r~lr~~i~~~~l~~~~i~I~~~VL~~DG~~~--~aai~aa~~AL~da~~~~~~~~~~~~ipl~~~v~  160 (255)
T 1udn_A           83 IGGRTHEIQRMIGRAMRTAVELTKIGERTIWVDCDVIQADGGTR--TAAITGAFVAVADAIIKLHKEGIIEETPIKDFVA  160 (255)
T ss_dssp             CCHHHHHHHHHHHHHHHHHBCGGGGCSCEEEEEEEEEECSSCHH--HHHHHHHHHHHHHHHHHHHHTTSSSSCCBCCCEE
T ss_pred             CCHHHHHHHHHHHHHHHHhcCHHHcCCeEEEEEEEEEeCCCCHH--HHHHHHHHHHHHhhcchhcccCcccCCCccCcee
Confidence            999999999999999999999887777  999999999999986  999999999999888           99999999


Q ss_pred             EEEEEEECCEEEEcCCHHHHhcCccceeEeeeCCe-EEEEEec--CCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 002054          204 MIRIGRICGQFIVNPTMDELSLSDLNLVYACTREK-TLMIDVQ--AREISEKDLEAGLRLAHPEAVKYLEPQIRLAEK  278 (974)
Q Consensus       204 av~vg~i~g~~vldPt~~e~~~s~~~l~v~~t~~~-i~mie~~--~~~~~e~~~~~al~~a~~~~~~i~~~~~~~~~~  278 (974)
                      ||++|+++|++++|||++|++.++.||+|+++.++ ++.+++.  +..|++++|.+||++|++++++++++|++++++
T Consensus       161 avsvg~~~g~~llDpt~~Ee~~~~~~l~va~~~~g~i~~~q~~g~~~~~~~~~l~~~l~~A~~~~~~i~~~~~~~l~~  238 (255)
T 1udn_A          161 AVSVGIVNDRILLDLNFEEDSAAQVDMNVVGTGSGRLSEVHTMGEEYSFTKDELIKMLDLAQKGINELIELQKKLYVI  238 (255)
T ss_dssp             EEEEEEETTEEEESCCHHHHHTCSEEEEEEEETTSCEEEEEEEESSCCCCHHHHHHHHHHHHHHHHHHHHHHHTTEEE
T ss_pred             EEEEEEECCEEEECCCHHHHhhCCCCEEEEEeCCCCEEEEEEeCCCCCcCHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence            99999999999999999999999999999999887 7777753  468999999999999999999999999988765

>2je6_A RRP42, exosome complex exonuclease 2; nuclease, hydrolase, exonuclease, phosphorolytic, exoribonuclease, RNA degradation; HET: 1PE; 1.6A {Sulfolobus solfataricus} SCOP: d.14.1.4 d.101.1.1 PDB: 2jea_A* 2jeb_A* 2br2_A 2c37_A* 2c38_A* 2c39_A* 3l7z_A

Probab=100.00  E-value=1.6e-35  Score=324.55  Aligned_cols=201  Identities=22%  Similarity=0.277  Sum_probs=184.0

Q ss_pred             CeEEEEEeCccCcCCCcEEEEEeCCeEEEEEEEeCC-CC--CCCCceeeEeeccccccccCCCCCccccccCCCCchhhh
Q 002054           67 SRLITLETGKIARFANGAVVLGMDETKVLSTVTSSK-GD--SVRDFLPLTVDYQEKQFAQGVIPNTYMRREGAPKERELL  143 (974)
Q Consensus        67 ~r~i~~etg~~a~~A~GSa~v~~G~T~Vl~tv~~~~-~~--~~~~f~pL~v~y~e~~~a~g~ip~~~~~Reg~p~~~eil  143 (974)
                      -|++.+++|.+ ++|+|||++++|+|+|||+|+++. +|  ...++.||+++|.++.||+++      +|+|+|++++++
T Consensus        39 ~R~i~i~~g~l-~~a~GSa~v~~G~T~Vl~~V~~~~~~p~~~~~~~g~l~v~~~~~p~a~~~------~~~g~~~~~~~~  111 (277)
T 2je6_A           39 YRPLSITLDYA-KKADGSALVKLGTTMVLAGTKLEIDKPYEDTPNQGNLIVNVELLPLAYET------FEPGPPDENAIE  111 (277)
T ss_dssp             CCCEEEEETCS-TTSSEEEEEEETTEEEEEEEEEEEECCCTTCTTCCEEEEEEEECTTSCTT------CCCSSCCHHHHH
T ss_pred             ccCeEEEeCCc-CCCCeEEEEEECCeEEEEEEEeeeeCCCCCCCCccEEEEEEEeCCccCcc------cccCCCChHHHH
Confidence            58999999999 899999999999999999999543 33  356899999999999999854      357999999999


Q ss_pred             HHHhhcCCccc---cccCCC-------CCceEEEEEEEeccCCCChhhHHHHHHHHHhhcCC------------------
Q 002054          144 VGRIIDRPIRP---LFPAGF-------YHEVQVMASVLSSDGKQDPDIMAANATSAALMLSD------------------  195 (974)
Q Consensus       144 ~~RlidR~lrp---lfp~~~-------~~~~~i~~~vl~~dg~~~~~~~ai~aAs~AL~~s~------------------  195 (974)
                      ++|+|+|+|||   ++++.|       ++.++|+++||++||+..  +||+|||++||++++                  
T Consensus       112 is~li~r~lr~~~~i~~~~l~i~~g~~~~~i~i~~~VL~~DG~~~--~aai~aa~~AL~~a~~p~v~~~~~~~~~~~~~~  189 (277)
T 2je6_A          112 LARVVDRSLRDSKALDLTKLVIEPGKSVWTVWLDVYVLDYGGNVL--DACTLASVAALYNTKVYKVEQHSNGISVNKNEV  189 (277)
T ss_dssp             HHHHHHHHHHHTTCSCGGGGEEETTTEEEEEEEEEEEEECCSCHH--HHHHHHHHHHHHTCEEEEEECC---CEEEEEEE
T ss_pred             HHHHHHHHHhccCCcCHHHceeecCceEEEEEEEEEEECCCCCHH--HHHHHHHHHHHHhcCCCeEEecCCcceEeccCc
Confidence            99999999999   566664       789999999999999875  999999999999999                  


Q ss_pred             ---CCCCCCeEEEEEEEECCEEEEcCCHHHHhcCccceeEeeeCCe-EEEEEecC-CCCCHHHHHHHHHHHHHHHHHHHH
Q 002054          196 ---IPWGGPIGMIRIGRICGQFIVNPTMDELSLSDLNLVYACTREK-TLMIDVQA-REISEKDLEAGLRLAHPEAVKYLE  270 (974)
Q Consensus       196 ---iP~~~~v~av~vg~i~g~~vldPt~~e~~~s~~~l~v~~t~~~-i~mie~~~-~~~~e~~~~~al~~a~~~~~~i~~  270 (974)
                         +||+++++||++|+++|++++|||++|++.++.+|+|++++++ ++|+|+.+ ..|++++|.+|+++|+++++++++
T Consensus       190 ~~~ip~~~~~~avsvg~~~~~~l~Dpt~~Ee~~~~~~l~va~~~~g~i~~v~~~g~~~~~~~~l~~~l~~A~~~~~~i~~  269 (277)
T 2je6_A          190 VGKLPLNYPVVTISVAKVDKYLVVDPDLDEESIMDAKISFSYTPDLKIVGIQKSGKGSMSLQDIDQAENTARSTAVKLLE  269 (277)
T ss_dssp             EEECCCSCCCEEEEEEEETTEEEESCCHHHHHHCSEEEEEEECTTCCEEEEEEESSSCEEHHHHHHHHHHHHHHHHHHHH
T ss_pred             cccccccCCeEEEEEEEECCEEecCCCHHHHhcCCCcEEEEEeCCCCEEEEECCCCCCCCHHHHHHHHHHHHHHHHHHHH
Confidence               9999999999999999999999999999999999999999865 99999864 579999999999999999999999


Q ss_pred             HHHHHH
Q 002054          271 PQIRLA  276 (974)
Q Consensus       271 ~~~~~~  276 (974)
                      .|++++
T Consensus       270 ~~~~~l  275 (277)
T 2je6_A          270 ELKKHL  275 (277)
T ss_dssp             HHHHHH
T ss_pred             HHHHHh
Confidence            999875

>1oys_A Ribonuclease PH; transferase, tRNA processing; 2.40A {Bacillus subtilis} SCOP: d.14.1.4 d.101.1.1 PDB: 1oyp_A 1oyr_A

Probab=100.00  E-value=1.5e-35  Score=318.94  Aligned_cols=206  Identities=18%  Similarity=0.193  Sum_probs=170.9

Q ss_pred             CeEEEEEeCccCcCCCcEEEEEeCCeEEEEEEEeCCC-C---CCCCceeeEeeccccccccCCCCCcccccc---CCCCc
Q 002054           67 SRLITLETGKIARFANGAVVLGMDETKVLSTVTSSKG-D---SVRDFLPLTVDYQEKQFAQGVIPNTYMRRE---GAPKE  139 (974)
Q Consensus        67 ~r~i~~etg~~a~~A~GSa~v~~G~T~Vl~tv~~~~~-~---~~~~f~pL~v~y~e~~~a~g~ip~~~~~Re---g~p~~  139 (974)
                      =|++.+++|.+ ++|+|||++++|+|+|||+|+++.+ |   .+.++.||+++|....||++.    +.+||   |+|++
T Consensus        11 ~R~i~i~~g~l-~~a~GSa~v~~G~T~Vl~~V~~~~~~p~~~~~~~~g~l~~~~~~~p~a~~~----~~~Re~~~G~~~~   85 (245)
T 1oys_A           11 LRPITFDLDFI-SHPEGSVLITAGNTKVICNASVEDRVPPFLRGGGKGWITAEYSMLPQATNQ----QTIQESSKGKISG   85 (245)
T ss_dssp             CCCEEEECC------CCCEEEEETTEEEEEEEEEESCCCGGGTTSCCCEEEEEEEC-----------------------C
T ss_pred             cCCeEEEeCCC-CCCCEEEEEEECCeEEEEEEEeccccCCccCCCCceEEEEEEEeCCCcCcc----cccccccCCCCch
Confidence            48999999999 7999999999999999999999887 4   356889999999999999874    47787   89999


Q ss_pred             hhhhHHHhhcCCccccccCC--CCCceEEEEEEEeccCCCChhhHHHHHHHHHhhcCC-----------CCCCCCeEEEE
Q 002054          140 RELLVGRIIDRPIRPLFPAG--FYHEVQVMASVLSSDGKQDPDIMAANATSAALMLSD-----------IPWGGPIGMIR  206 (974)
Q Consensus       140 ~eil~~RlidR~lrplfp~~--~~~~~~i~~~vl~~dg~~~~~~~ai~aAs~AL~~s~-----------iP~~~~v~av~  206 (974)
                      ++++++|+|+|+|||+++..  +.+.++|+|+||++||+..  +||+|||++||++++           +||+++|+||+
T Consensus        86 ~~~eis~li~r~l~~~i~~~~l~~~~i~i~~~VL~~DG~~~--~aai~aa~~AL~~a~~~~~~~~~~~~ipl~~~v~avs  163 (245)
T 1oys_A           86 RTMEIQRLIGRALRAVVDLEKLGERTIWIDCDVIQADGGTR--TASITGAFLAMAIAIGKLIKAGTIKTNPITDFLAAIS  163 (245)
T ss_dssp             HHHHHHHHHHHHHHHTBCHHHHCSCEEEEEEEEEECSSCHH--HHHHHHHHHHHHHHHHHHHHTTSSSSCCBCSCEEEEE
T ss_pred             HHHHHHHHHHHHHHHhcCHhHCCCEEEEEEEEEEeCCCCHH--HHHHHHHHHHHHhccchhcccCcccccCCCCceeEEE
Confidence            99999999999999999865  5678999999999999866  999999999999999           99999999999


Q ss_pred             EEEECCEEE-EcCCHHHHhcCccceeEeeeCCe-EEEEEecC--CCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Q 002054          207 IGRICGQFI-VNPTMDELSLSDLNLVYACTREK-TLMIDVQA--REISEKDLEAGLRLAHPEAVKYLEPQIRLAEKA  279 (974)
Q Consensus       207 vg~i~g~~v-ldPt~~e~~~s~~~l~v~~t~~~-i~mie~~~--~~~~e~~~~~al~~a~~~~~~i~~~~~~~~~~~  279 (974)
                      +|+++|+++ +|||++|++.++.||+|+++.++ ++++|+.+  ..|++++|.++|++|+++++++++.|++.+++.
T Consensus       164 ~g~~~g~~vl~Dp~~~Ee~~~~~~~~v~~~~~g~i~~iq~~g~~~~~~~~~l~~~l~~A~~~~~~i~~~~~~~l~~~  240 (245)
T 1oys_A          164 VGIDKEQGILLDLNYEEDSSAEVDMNVIMTGSGRFVELQGTGEEATFSREDLNGLLGLAEKGIQELIDKQKEVLGDS  240 (245)
T ss_dssp             EEEETTTEEEESCCHHHHHHEEEEEEEEEETTSCEEEEEEEESSCCCCHHHHHHHHHHHHHHHHHHHHHHHHHC---
T ss_pred             EEEECCEEEEecCCHHHHhcCCCcEEEEEcCCCcEEEEEEeCCCCCcCHHHHHHHHHHHHHHHHHHHHHHHHHHhhh
Confidence            999999999 99999999999999999999887 99999865  579999999999999999999999999887653

>3hkm_A OS03G0854200 protein; RNAse PH domain, phosphorylase, hydrolase; 1.98A {Oryza sativa japonica group}

Probab=100.00  E-value=2.1e-35  Score=316.81  Aligned_cols=198  Identities=17%  Similarity=0.146  Sum_probs=171.1

Q ss_pred             CeEEEEEeCccCcCCCcEEEEEeCCeEEEEEEEeCCC--CCCCCceeeEeeccccccccCCCCCccccccCCCCchhhhH
Q 002054           67 SRLITLETGKIARFANGAVVLGMDETKVLSTVTSSKG--DSVRDFLPLTVDYQEKQFAQGVIPNTYMRREGAPKERELLV  144 (974)
Q Consensus        67 ~r~i~~etg~~a~~A~GSa~v~~G~T~Vl~tv~~~~~--~~~~~f~pL~v~y~e~~~a~g~ip~~~~~Reg~p~~~eil~  144 (974)
                      =|++++++|.+ ++|+|||++++|+|+|||+|++|.+  +.+..+.+.+++|.   |+    |     +.|+|+++++++
T Consensus        14 ~R~i~i~~g~l-~~a~GSa~v~~G~T~Vl~~V~g~~~~~~~~~~~~~~~~~~~---~~----P-----~~g~~~~~~~e~   80 (246)
T 3hkm_A           14 LRPFSCTRNPL-DRAHGSARWAQGDTIVLAAVYGPKPGTRKGENPEKASIEVV---WK----P-----MTGQIGKQEKEY   80 (246)
T ss_dssp             CCCEEEEECCC-SSSSEEEEEEETTEEEEEEECCCEECCCTTSCSSSCEEEEE---EE----C-----SSSCCCTTHHHH
T ss_pred             cCCeEEEECCC-CCCCeEEEEEECCeEEEEEEecCcCCCcccCCCccEEEEEE---eC----C-----CCCCCChhHHHH
Confidence            48999999999 7999999999999999999998765  34445566777774   21    3     358999999999


Q ss_pred             HHhhcCCcccccc-CCC-CCceEEEEEEEeccCCCChhhHHHHHHHHHhhcCCCCCCCCeEEEEEEEE-CCEEEEcCCHH
Q 002054          145 GRIIDRPIRPLFP-AGF-YHEVQVMASVLSSDGKQDPDIMAANATSAALMLSDIPWGGPIGMIRIGRI-CGQFIVNPTMD  221 (974)
Q Consensus       145 ~RlidR~lrplfp-~~~-~~~~~i~~~vl~~dg~~~~~~~ai~aAs~AL~~s~iP~~~~v~av~vg~i-~g~~vldPt~~  221 (974)
                      +|+|+|+|||+++ .+| .+.++|+|+||++||+..  +||+|||++||++++|||+++|+||++|++ +|++++|||++
T Consensus        81 ~~li~r~l~~l~~~~~~~~~~I~v~~~VL~~dG~~~--~aai~aa~~AL~dagiP~~~~v~avs~g~~~~g~~llDpt~~  158 (246)
T 3hkm_A           81 EMTLKRTLQSICLLTVHPNTTTSVILQVVGNDGSLL--PCAINACCAALVFAGIPLKHLAVAIGCGVLEDGEVILDTNKA  158 (246)
T ss_dssp             HHHHHHHHHHHBCTTSSCSEEEEEEEEEEECSSCHH--HHHHHHHHHHHHHHTCCBSSCEEEEEEEECTTSCEEESCCHH
T ss_pred             HHHHHHHHHHhcCccCCCcEEEEEEEEEEecCCCHH--HHHHHHHHHHHHhcCCCCCCceEEEEEEEEECCEEEECCCHH
Confidence            9999999999999 455 789999999999999876  999999999999999999999999999998 89999999999


Q ss_pred             HHhcCccceeEeeeCCe------------------EEEEEecCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHhC
Q 002054          222 ELSLSDLNLVYACTREK------------------TLMIDVQAREISEKDLEAGLRLAHPEAVKYLEPQIRLAEKAG  280 (974)
Q Consensus       222 e~~~s~~~l~v~~t~~~------------------i~mie~~~~~~~e~~~~~al~~a~~~~~~i~~~~~~~~~~~g  280 (974)
                      |++.+++|++|+++.++                  ++|++. .+.|++++|.+|+++|++++++|+++|++.+++..
T Consensus       159 Ee~~~~~~~~va~~~~~i~~lq~~g~~~~~~~~~~~i~~~~-~g~~~~~~l~~~l~~A~~~~~~i~~~~~~~l~~~~  234 (246)
T 3hkm_A          159 EEQQLKSFAHLVFPNSRKSASSKEPNQKEEDSERGLITSIT-HGVMSEEDYFSCIERGLAASSRISDFMRTTLQKQA  234 (246)
T ss_dssp             HHTTCSEEEEEEEEC--------------------CCCEEE-EECEEHHHHHHHHHHHHHHHHHHHHHHHTTTC---
T ss_pred             HHhcCCeeEEEEEeCCceEEEeecccccccccccceeeeec-cCCcCHHHHHHHHHHHHHHHHHHHHHHHHHHHhhh
Confidence            99999999999998764                  444443 35699999999999999999999999998876554

>2nn6_C Exosome complex exonuclease RRP43; RNA, exosome, PM/SCL, phosphorolytic, hydrolase/transferase complex; 3.35A {Homo sapiens} SCOP: d.14.1.4 d.101.1.1

Probab=100.00  E-value=4.4e-35  Score=321.18  Aligned_cols=203  Identities=17%  Similarity=0.151  Sum_probs=186.5

Q ss_pred             CeEEEEEeCccCcCCCcEEEEEeCCeEEEEEEEeCCC-CCC--CCceeeEeeccccccccCCCCCccccccCCCCchhhh
Q 002054           67 SRLITLETGKIARFANGAVVLGMDETKVLSTVTSSKG-DSV--RDFLPLTVDYQEKQFAQGVIPNTYMRREGAPKERELL  143 (974)
Q Consensus        67 ~r~i~~etg~~a~~A~GSa~v~~G~T~Vl~tv~~~~~-~~~--~~f~pL~v~y~e~~~a~g~ip~~~~~Reg~p~~~eil  143 (974)
                      -|++.+++|.+ ++|+|||++++|+|+|||+|+++.+ |..  .++.||+++|.++.||+++    |  |+|+|++++++
T Consensus        34 ~R~i~i~~g~l-~~a~GSa~v~~G~T~Vl~~V~~~~~~p~~~~~~~g~l~v~~~~~p~a~~~----~--~~g~~~~~~~~  106 (278)
T 2nn6_C           34 FRTTTVNIGSI-STADGSALVKLGNTTVICGVKAEFAAPSTDAPDKGYVVPNVDLPPLCSSR----F--RSGPPGEEAQV  106 (278)
T ss_dssp             CCSCCEEETCC-SSSSEEEEEEETTEEEEEEEEEEECCCCSSSTTCCCCEEEEECCSSSCTT----S--CSSSCCHHHHH
T ss_pred             ccCeEEEeCCc-cCCCceEEEEeCCeEEEEEEEEEeecCCCCCCCccEEEEEEEeCCccCcc----c--cCCCCcHHHHH
Confidence            47899999999 8999999999999999999999766 332  4889999999999999975    2  56999999999


Q ss_pred             HHHhhcCCccc--cc--------cCCCCCceEEEEEEEeccCCCChhhHHHHHHHHHhhcCCC-----------------
Q 002054          144 VGRIIDRPIRP--LF--------PAGFYHEVQVMASVLSSDGKQDPDIMAANATSAALMLSDI-----------------  196 (974)
Q Consensus       144 ~~RlidR~lrp--lf--------p~~~~~~~~i~~~vl~~dg~~~~~~~ai~aAs~AL~~s~i-----------------  196 (974)
                      ++|+|+|+|||  +|        |..|++.++|+++||++||+..  +||+|||++||++++|                 
T Consensus       107 ~s~li~r~l~~s~~i~l~~L~i~pg~~~~~i~i~~~VL~~DG~~~--~aai~aa~~AL~~a~iP~v~~~~~~~~~~~~~~  184 (278)
T 2nn6_C          107 ASQFIADVIENSQIIQKEDLCISPGKLVWVLYCDLICLDYDGNIL--DACTFALLAALKNVQLPEVTINEETALAEVNLK  184 (278)
T ss_dssp             HHHHHHHHHHHHCCSCHHHHCSSBTTBCEEEEEEEEESSCCSCTT--HHHHHHHHHHHHTCCCCCCCBCSSSBCCCTTSC
T ss_pred             HHHHHHHHHhccCCCCHHHCEEeCCcEEEEEEEEEEEECCCCCHH--HHHHHHHHHHHHhCCCCeEEEeCCCcceecCcc
Confidence            99999999995  66        5678999999999999999987  9999999999999996                 


Q ss_pred             -----CCCCCeEEEEEEEECC-EEEEcCCHHHHhcCccceeEeeeCCe-EEEEEecC-CCCCHHHHHHHHHHHHHHHHHH
Q 002054          197 -----PWGGPIGMIRIGRICG-QFIVNPTMDELSLSDLNLVYACTREK-TLMIDVQA-REISEKDLEAGLRLAHPEAVKY  268 (974)
Q Consensus       197 -----P~~~~v~av~vg~i~g-~~vldPt~~e~~~s~~~l~v~~t~~~-i~mie~~~-~~~~e~~~~~al~~a~~~~~~i  268 (974)
                           ||+++++||++|+++| ++++|||++|++.++.+|+|++++++ ++|+|+.+ ..|++++|.+||++|+++++++
T Consensus       185 ~~~~lp~~~~~~avs~g~~~~~~~l~Dpt~~Ee~~~~~~l~va~~~~g~i~~v~~~g~~~~~~~~l~~~l~~a~~~~~~i  264 (278)
T 2nn6_C          185 KKSYLNIRTHPVATSFAVFDDTLLIVDPTGEEEHLATGTLTIVMDEEGKLCCLHKPGGSGLTGAKLQDCMSRAVTRHKEV  264 (278)
T ss_dssp             CCSCSCCSCCCEEEEEEECTTTCCEESCCTTTTTSCSEEEEEEECTTCCEEEEEESCCSCCCHHHHHHHHHHHHHHHHHH
T ss_pred             cccccccCCceEEEEEEEECCceEEECCCHHHHhhcCceEEEEEcCCCcEEEEEccCCCCCCHHHHHHHHHHHHHHHHHH
Confidence                 8999999999999998 99999999999999999999999885 99999977 4699999999999999999999


Q ss_pred             HHHHHHHHHH
Q 002054          269 LEPQIRLAEK  278 (974)
Q Consensus       269 ~~~~~~~~~~  278 (974)
                      ++.|++++++
T Consensus       265 ~~~~~~~l~~  274 (278)
T 2nn6_C          265 KKLMDEVIKS  274 (278)
T ss_dssp             HHHHHTTTTT
T ss_pred             HHHHHHHHHh
Confidence            9999887653

>2po1_A Probable exosome complex exonuclease 1; RNAse PH, hydrolase/hydrolase/RNA complex; 1.94A {Pyrococcus abyssi} PDB: 2po0_A* 2pnz_A 2po2_A*

Probab=100.00  E-value=2.4e-34  Score=310.11  Aligned_cols=203  Identities=18%  Similarity=0.321  Sum_probs=182.5

Q ss_pred             CeEEEEEeCccCcCCCcEEEEEeCCeEEEEEEEeCCC--C---CCCCceeeEeeccccccccCCCCCccccccCCCCchh
Q 002054           67 SRLITLETGKIARFANGAVVLGMDETKVLSTVTSSKG--D---SVRDFLPLTVDYQEKQFAQGVIPNTYMRREGAPKERE  141 (974)
Q Consensus        67 ~r~i~~etg~~a~~A~GSa~v~~G~T~Vl~tv~~~~~--~---~~~~f~pL~v~y~e~~~a~g~ip~~~~~Reg~p~~~e  141 (974)
                      -|++.+++|.+ ++|+|||++++|+|+|||+|++|.+  +   ...++.||+++|....||++..      +.+.|++++
T Consensus        26 ~R~i~i~~g~l-~~a~GSa~v~~G~T~Vl~~V~gp~e~~~~~~~~~~~g~l~v~~~~~p~a~~~~------~~~~~~~~~   98 (249)
T 2po1_A           26 LRPIKMEVGVL-KNANGSAYIEWGKNKIIAAVYGPRELHPKHLQRPDRAILRVRYNMAPFSVEER------KKPGPDRRS   98 (249)
T ss_dssp             CCCEEEEECCC-SSSSEEEEEEETTEEEEEEEEEEEECSSGGGCCSSSCEEEEEEEECGGGSSSC------CCSSCCHHH
T ss_pred             ccCEEEEeCCc-CCCCEEEEEEECCcEEEEEEEcCcccCcccccCCCceEEEEEEEeCCcccccc------cCCCCCHHH
Confidence            48899999999 8999999999999999999999766  2   2568899999999999999732      235699999


Q ss_pred             hhHHHhhcCCccccccCCCC--CceEEEEEEEeccCCCChhhHHHHHHHHHhhcCCCCCCCCeEEEEEEEECCEEEEcCC
Q 002054          142 LLVGRIIDRPIRPLFPAGFY--HEVQVMASVLSSDGKQDPDIMAANATSAALMLSDIPWGGPIGMIRIGRICGQFIVNPT  219 (974)
Q Consensus       142 il~~RlidR~lrplfp~~~~--~~~~i~~~vl~~dg~~~~~~~ai~aAs~AL~~s~iP~~~~v~av~vg~i~g~~vldPt  219 (974)
                      ++++|+|+|+|||.++...+  +.++|+++||++||+..  +||+|||++||++++|||+++|+||++|+++|++++|||
T Consensus        99 ~~~s~li~r~l~~~i~l~~~p~~~i~I~~~VL~~dG~~~--~aai~aa~~AL~da~iP~~~~v~avs~g~~~~~~l~Dp~  176 (249)
T 2po1_A           99 IEISKVIKGALEPALILEMFPRTAIDVFIEVLQADAGTR--VAGITAASLALADAGIPMRDLVAACAAGKIEGEIVLDLN  176 (249)
T ss_dssp             HHHHHHHHHHHGGGBCGGGSTTEEEEEEEEEEECCSCHH--HHHHHHHHHHHHHTTCCBSSCCEEEEEEEETTEEEESCC
T ss_pred             HHHHHHHHHHHHhhccHHHCCCCEEEEEEEEEecCCCHH--HHHHHHHHHHHHhcCCCccCceEEEEEEEECCEEEecCc
Confidence            99999999999995543222  36999999999999865  999999999999999999999999999999999999999


Q ss_pred             HHHHhcCccceeEee--eCCeEEEEEecCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Q 002054          220 MDELSLSDLNLVYAC--TREKTLMIDVQAREISEKDLEAGLRLAHPEAVKYLEPQIRLAEKA  279 (974)
Q Consensus       220 ~~e~~~s~~~l~v~~--t~~~i~mie~~~~~~~e~~~~~al~~a~~~~~~i~~~~~~~~~~~  279 (974)
                      ++|++.++.+|+|++  +.++++++|+.++ |++++|.+||++|+++++++++.|++.+++.
T Consensus       177 ~~Ee~~~~~~l~va~~~~~~~i~~~~~~g~-~~~~~l~~~l~~A~~~~~~i~~~~~~~l~~~  237 (249)
T 2po1_A          177 KEEDNYGEADVPVAIMPLKNDITLLQMDGY-LTKDEFIEAVKLAIKGAKAVYQKQREALKEK  237 (249)
T ss_dssp             HHHHHTCSEEEEEEEEGGGTEEEEECCEEC-CCHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHhccCCceEEEEEECCCCCEEEEEEEcc-cCHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            999999999999997  5677999999984 9999999999999999999999999988764

>4aid_A Polyribonucleotide nucleotidyltransferase; transferase-peptide complex; 2.60A {Caulobacter vibrioides} PDB: 4aim_A 4am3_A

Probab=100.00  E-value=5.9e-34  Score=341.85  Aligned_cols=215  Identities=19%  Similarity=0.239  Sum_probs=189.2

Q ss_pred             ccCeEEEeCCCC-CCCcceEEEeCCeEEEEEEEeCCCchhhhccccCCCCceeEEEEEecCCCCcc-----ccccccCCC
Q 002054          379 VRPIYCESGNLP-ILHGSSLFSRGDTQVLCTVTLGAPAEAQRLESLVGPPTKRFMLHYSFPPFCIN-----EVGKRVGLN  452 (974)
Q Consensus       379 ~R~I~ie~g~l~-~a~GSal~~~G~T~Vl~~Vtl~~p~~~~~~d~~~~~~~~~~~v~~~f~p~s~~-----e~~~~~~~~  452 (974)
                      -|++++++|.+. +|+||++++.|+|+|||+|+..  ..++     .+.++.+++++|....|+.|     ..+|.|.|+
T Consensus        27 ~R~i~ietg~~ak~A~GSvlv~~GdT~VL~tv~~~--~~~~-----~g~df~pltveY~ek~~a~G~iPg~~~~REGrps   99 (726)
T 4aid_A           27 GKTLVLETGRIARQADGAVLATMGETVVLATAVFA--KSQK-----PGQDFFPLTVNYQEKTFAAGKIPGGFFKREGRPS   99 (726)
T ss_dssp             TEEEEEEESSSCTTSSEEEEEEETTEEEEEEEEEC--SSCC-----TTCCSCCEEEEEEECGGGGTCCCCSTTCSCCSCC
T ss_pred             CeeEEEEECCccCCCCeeEEEEECCeEEEEEEEec--CCCC-----CCCCCcCceeeeeeehhhcccCCCcccCCCCCCC
Confidence            478999999887 5999999999999999999943  3211     13456779999987777665     346779999


Q ss_pred             chhhhHHHHHHHHhhhcCCCCCCCCeEEEEEEEEEcCCCChh--hHHHHHHHHHHHHcCCCccccccceeeeeeccCCCC
Q 002054          453 RREVGHGTLAEKALLAVLPPENDFPYTVRVNSEVMASDGSTS--MATVCGGSMALMDAGIPLQEHVAGVSVGLVSEVDPS  530 (974)
Q Consensus       453 rre~~~~~l~eral~~vi~~~~~~p~tI~V~v~VLesdGs~~--~A~v~aa~lAL~dagvPi~~~vagvs~gli~~~d~~  530 (974)
                      .||+.+++|+.|+|+|++|.  .|-|.++|+++||+.||+..  .||++||++||+++++|++++++||++|++++    
T Consensus       100 ~~~~li~RlIdR~lRplf~~--~~~~evqI~~~Vls~Dg~~~~d~~ai~gAs~AL~~s~iP~~~~vaaV~Vg~i~g----  173 (726)
T 4aid_A          100 EKETLVSRLIDRPIRPLFVK--GFKNEVQVVVTVLQHDLENDPDILGMVAASAALCLSGAPFMGPIGAARVGWVDG----  173 (726)
T ss_dssp             HHHHHHHHHHHHHHGGGBCT--TCCSCEEEEEEEEECCSSSCHHHHHHHHHHHHHHHHTCSBCCCCEEEEEEEETT----
T ss_pred             chhhhHHHHhCCcccccccc--CCccceEEEEEEEecCCCCChhHHHHHHHHHHHHhcCCCcCCCeEEEEEEEECC----
Confidence            99999999999999999995  67889999999999999764  78999999999999999999999999999875    


Q ss_pred             CCcccceEEEecCCccccccCCccEEEEeeCCceEEEEeeccCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCCCC
Q 002054          531 TGEIKDYRILTDILGLEDHLGDMDFKIAGTRIGVTAIQLDIKPAGIPLDIICECLEHAHKGRLQILDHMEREISAPRTQD  610 (974)
Q Consensus       531 ~~~~~~~~iL~Dp~~~Ee~~~d~d~~Va~t~~gI~alq~~~k~~~i~~e~l~~al~~A~~~~~~I~~~m~~~i~~~~~~~  610 (974)
                             .+++||+..|+..++++++|++|.++++++|..+  ..++.++|.+||+.|++++..|++.+++++.+..+++
T Consensus       174 -------~~vldPt~~E~~~s~~dl~va~t~~~i~mve~~~--~~~se~~~~~al~~a~~~i~~l~~~q~~~~~~~g~~k  244 (726)
T 4aid_A          174 -------AYVLNPTLDEMKESKMDLVVAGTADAVMMVESEI--QELSEEIVLGGVNFAHQQMQAVIDAIIDLAEHAAKEP  244 (726)
T ss_dssp             -------EEEESCCHHHHHTCSEEEEEEECSSCEEEEEEEE--SSBCHHHHHHHHHHHHHHTHHHHHHHHHHHHHHCCCC
T ss_pred             -------EEEECCCHHHHhhCceeEEEEEeCCeEEEEEccC--CCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCc
Confidence                   6999999999999999999999999998888654  5799999999999999999999999999999887776


Q ss_pred             CCCCC
Q 002054          611 DRNSP  615 (974)
Q Consensus       611 ~~~~p  615 (974)
                      ..+.|
T Consensus       245 ~~~~~  249 (726)
T 4aid_A          245 FAFEP  249 (726)
T ss_dssp             CCCCC
T ss_pred             ccCCC
Confidence            66654

>3krn_A Protein C14A4.5, confirmed by transcript evidence; RNAse PH domain, homodimer, exosome, cell-death-related DNAS hydrolase; 3.92A {Caenorhabditis elegans}

Probab=100.00  E-value=4.9e-36  Score=317.64  Aligned_cols=201  Identities=18%  Similarity=0.259  Sum_probs=159.8

Q ss_pred             CCCccCeEEEeCCCCCCCcceEEEeCCeEEEEEEEeCCCchhhhccccCCCCceeEEEEEecCCCCccccccccCCCchh
Q 002054          376 LDEVRPIYCESGNLPILHGSSLFSRGDTQVLCTVTLGAPAEAQRLESLVGPPTKRFMLHYSFPPFCINEVGKRVGLNRRE  455 (974)
Q Consensus       376 ~~e~R~I~ie~g~l~~a~GSal~~~G~T~Vl~~Vtl~~p~~~~~~d~~~~~~~~~~~v~~~f~p~s~~e~~~~~~~~rre  455 (974)
                      .+|+|+|++++|+++++||||+|++|+|+|+|+|+  +|.+.+..+    ...+++.++|+|+|++.       .++++ 
T Consensus         2 ~~e~R~i~ie~g~l~~A~GSa~v~~G~T~Vl~~V~--~~~e~~~~~----~~~~~~~l~v~~~p~~G-------~~~~~-   67 (222)
T 3krn_A            2 AGRLREMRCELSFLKNADGSACFSQGATCIWASCS--GPGDVHASK----ASDEAMTLDISYRANCG-------DNKFN-   67 (222)
T ss_dssp             -CCCCCBCCBSCCC----CCCBCCBTTCEEECCCC--SSCC-----------------CCCSSCCCC---------CCS-
T ss_pred             CCcccceEEEECCCCCCCeEEEEEECCcEEEEEEE--CCCCCcccc----cCCceEEEEEEEcCCCC-------CCCHH-
Confidence            57999999999999999999999999999999999  777654321    23456778999998752       23333 


Q ss_pred             hhHHHHHHHHhhhcCCCCCCCCe-EEEEEEEEEcCCCChhhHHHHHHHHHHHHcCCCccccccceeeeeeccCCCCCCcc
Q 002054          456 VGHGTLAEKALLAVLPPENDFPY-TVRVNSEVMASDGSTSMATVCGGSMALMDAGIPLQEHVAGVSVGLVSEVDPSTGEI  534 (974)
Q Consensus       456 ~~~~~l~eral~~vi~~~~~~p~-tI~V~v~VLesdGs~~~A~v~aa~lAL~dagvPi~~~vagvs~gli~~~d~~~~~~  534 (974)
                       +++++++|+|+++++. +.||+ +|+|+++||++|||+++||+||+++||+||||||+++|+|+++|++++        
T Consensus        68 -e~~~li~r~l~~~i~~-~~~p~~~I~I~~~VL~~DG~~~~aai~aa~~AL~dagiP~~~~v~avsvg~~~g--------  137 (222)
T 3krn_A           68 -VLNNIIHSTLSNAINL-ELFPHTTISVTVHGIQDDGSMGAVAINGACFALLDNGMPFETVFCGVLIVRVKD--------  137 (222)
T ss_dssp             -SCTTHHHHC--CCSCC------CCCCCCCEEEECCSCHHHHHHHGGGTTTTTTTCCTTSCCCCCCCEECSS--------
T ss_pred             -HHHHHHHHHHHHhccH-HhCCCcEEEEEEEEEECCCChHHHHHHHHHHHHHHCCCCccCcEEEEEEEEECC--------
Confidence             7899999999999998 78996 799999999999999999999999999999999999999999999754        


Q ss_pred             cceEEEecCCccccccCCccEEEEe---e--CCceEEEEeeccCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHhcCC
Q 002054          535 KDYRILTDILGLEDHLGDMDFKIAG---T--RIGVTAIQLDIKPAGIPLDIICECLEHAHKGRLQILDHMEREISAP  606 (974)
Q Consensus       535 ~~~~iL~Dp~~~Ee~~~d~d~~Va~---t--~~gI~alq~~~k~~~i~~e~l~~al~~A~~~~~~I~~~m~~~i~~~  606 (974)
                         .+|+||+..|++.++++++|++   +  .++|+++|+++   .++.++|.+|+++|++++.+|++.|++++++.
T Consensus       138 ---~~llDpt~~Ee~~~~~~l~va~~~~~~~~~~i~~vq~~g---~~~~~~l~~~l~~a~~~~~~i~~~~~~~l~~~  208 (222)
T 3krn_A          138 ---ELIIDPTAKQEAASTGRVLFSVCKGSDGHPEVCAMDAIG---HWDFIQLEAAWSLAQPSASAIFDFYKTVMKRK  208 (222)
T ss_dssp             ---SEESSCCTTTTTSCC-CCCCEECCCSSSSCCEEEECCBS---SCTTHHHHTHHHHTTHHHHHHHHHHHHHHHHH
T ss_pred             ---EEEeCCCHHHHhccCccEEEEEEccCCCCCCEEEEEEeC---CcCHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence               5999999999999999999999   4  46799999974   59999999999999999999999999999864

>3cdi_A Polynucleotide phosphorylase; mRNA turnover, RNAse, RNA degradation, kinase, transferase; 2.60A {Escherichia coli} PDB: 1sro_A

Probab=100.00  E-value=1.4e-33  Score=340.61  Aligned_cols=244  Identities=16%  Similarity=0.226  Sum_probs=198.8

Q ss_pred             CCcCCCCCCCCccCeEEEeCCCC-CCCcceEEEeCCeEEEEEEEeCCCchhhhccccCCCCceeEEEEEecCCCCccc--
Q 002054          368 GVRVDGRQLDEVRPIYCESGNLP-ILHGSSLFSRGDTQVLCTVTLGAPAEAQRLESLVGPPTKRFMLHYSFPPFCINE--  444 (974)
Q Consensus       368 ~~R~DGR~~~e~R~I~ie~g~l~-~a~GSal~~~G~T~Vl~~Vtl~~p~~~~~~d~~~~~~~~~~~v~~~f~p~s~~e--  444 (974)
                      .++.+||      ++++++|.+. +|+|||+++.|+|+|||+|+..  .+++     ++.++.+++++|.-..|+.|.  
T Consensus        14 ~~~~~~r------~i~ietg~ia~qA~GSv~v~~G~T~Vl~tv~~~--~~~~-----~~~~f~pltv~y~ek~~a~g~ip   80 (723)
T 3cdi_A           14 KFQYGQH------TVTLETGMMARQATAAVMVSMDDTAVFVTVVGQ--KKAK-----PGQDFFPLTVNYQERTYAAGRIP   80 (723)
T ss_dssp             EEEETTE------EEEEEESSSCTTSSEEEEEEETTEEEEEEEEEC--SSCC-----SSCCSCCEEEEEEECGGGGTCCC
T ss_pred             EEEECCE------EEEEEeCccccCCCeeEEEEECCEEEEEEEEec--CCCC-----CCCCeeeEEEEEeEeccccccCC
Confidence            3455555      8999999885 7999999999999999999944  2221     234667799999987777765  


Q ss_pred             ---cccccCCCchhhhHHHHHHHHhhhcCCCCCCCCeEEEEEEEEEcCCCCh--hhHHHHHHHHHHHHcCCCccccccce
Q 002054          445 ---VGKRVGLNRREVGHGTLAEKALLAVLPPENDFPYTVRVNSEVMASDGST--SMATVCGGSMALMDAGIPLQEHVAGV  519 (974)
Q Consensus       445 ---~~~~~~~~rre~~~~~l~eral~~vi~~~~~~p~tI~V~v~VLesdGs~--~~A~v~aa~lAL~dagvPi~~~vagv  519 (974)
                         .+|.|.|+.+|+..++|++|+|+|++|.  .|.|.++|+++||+.||+.  ..||++||++||+.+++|+.++++||
T Consensus        81 g~f~kReGrpse~e~l~sRlIdR~lRplfp~--~~~~~vqv~~~vls~Dg~~~~d~~ai~aAsaAL~~s~iP~~~pv~av  158 (723)
T 3cdi_A           81 GSFFRREGRPSEGETLIARLIDRPIRPLFPE--GFVNEVQVIATVVSVNPQVNPDIVAMIGASAALSLSGIPFNGPIGAA  158 (723)
T ss_dssp             C-------CCCHHHHHHHHHHHHHHGGGSCT--TCCSCEEEEEEEEECCTTSCHHHHHHHHHHHHHHHHTSSCCCCCCCE
T ss_pred             CccccCCCCCChHHhHHHHHhCccchhcccc--cCcceEEEEEEEEEcCCCCCHHHHHHHHHHHHHHhcCCCCCCCeEEE
Confidence               4678999999999999999999999994  6889999999999999997  56999999999999999999999999


Q ss_pred             eeeeeccCCCCCCcccceEEEecCCccccccCCccEEEEeeCCceEEEEeeccCCCCCHHHHHHHHHHHHHHHHHHHHHH
Q 002054          520 SVGLVSEVDPSTGEIKDYRILTDILGLEDHLGDMDFKIAGTRIGVTAIQLDIKPAGIPLDIICECLEHAHKGRLQILDHM  599 (974)
Q Consensus       520 s~gli~~~d~~~~~~~~~~iL~Dp~~~Ee~~~d~d~~Va~t~~gI~alq~~~k~~~i~~e~l~~al~~A~~~~~~I~~~m  599 (974)
                      ++|++++           .+++||+..|+..++++++|++|.+++.++|..+  ..+++++|.+||+.|+++++.|++.+
T Consensus       159 ~vg~i~g-----------~~v~nPt~~e~~~s~~~lvvagt~~~i~mve~~~--~~~se~~~~~al~~a~~~~~~l~~~~  225 (723)
T 3cdi_A          159 RVGYIND-----------QYVLNPTQDELKESKLDLVVAGTEAAVLMVESEA--QLLSEDQMLGAVVFGHEQQQVVIQNI  225 (723)
T ss_dssp             EEEEETT-----------EEEESCCTTGGGGCSEEEEEEECSSCEEEEEEEE--EEECHHHHHHHHHHHHHHTHHHHHHH
T ss_pred             EEEEECC-----------EEEECcCHHHHHhCCceEEEEccCCEEEEEeCCC--CCCCHHHHHHHHHHHHHHHHHHHHHH
Confidence            9999975           5999999999999999999999999998888654  46999999999999999999999999


Q ss_pred             HHHhcCCCCCCCCCCCccee--e-----eeccchhhhhcCCCccchh
Q 002054          600 EREISAPRTQDDRNSPRLAT--L-----KYDNDTLRRLIGPLGALKR  639 (974)
Q Consensus       600 ~~~i~~~~~~~~~~~p~~~~--~-----~i~~~ki~~vIg~gGk~i~  639 (974)
                      ++++.+..+++..+.+....  +     ..-.+++.+.+-..+|.-|
T Consensus       226 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~k~~r  272 (723)
T 3cdi_A          226 NELVKEAGKPRWDWQPEPVNEALNARVAALAEARLSDAYRITDKQER  272 (723)
T ss_dssp             HHHHHHTCCCCCCCCCCCCCTTGGGSSTTTTHHHHHHHTTCCCHHHH
T ss_pred             HHHHHHhCCCcccCCCCCCCHHHHHHHHHHHHHHHHHHHhccchHHH
Confidence            99998887766665432111  1     0122456666655555555

>2nn6_B Exosome complex exonuclease RRP41; RNA, exosome, PM/SCL, phosphorolytic, hydrolase/transferase complex; 3.35A {Homo sapiens} SCOP: d.14.1.4 d.101.1.1

Probab=100.00  E-value=2.2e-33  Score=302.71  Aligned_cols=206  Identities=18%  Similarity=0.227  Sum_probs=184.7

Q ss_pred             CeEEEEEeCccCcCCCcEEEEEeCCeEEEEEEEeCCCC------CCCCceeeEeeccccccccCCCCCccccccCCCCch
Q 002054           67 SRLITLETGKIARFANGAVVLGMDETKVLSTVTSSKGD------SVRDFLPLTVDYQEKQFAQGVIPNTYMRREGAPKER  140 (974)
Q Consensus        67 ~r~i~~etg~~a~~A~GSa~v~~G~T~Vl~tv~~~~~~------~~~~f~pL~v~y~e~~~a~g~ip~~~~~Reg~p~~~  140 (974)
                      -|++.+++|.+ ++|+|||++++|+|+|||+|++|.++      ...++.+|+++|....||++.     .+|.|+|+++
T Consensus        26 ~R~i~i~~g~l-~~a~GSa~v~~G~T~Vl~~V~g~~~~~~~~~~~~~~~g~l~~~~~~~p~a~~~-----~~~~~~~~~~   99 (249)
T 2nn6_B           26 LRKIQARMGVF-AQADGSAYIEQGNTKALAVVYGPHEIRGSRARALPDRALVNCQYSSATFSTGE-----RKRRPHGDRK   99 (249)
T ss_dssp             CCCEEEEESCS-SSSSEEEEEEESSCEEEEEEEEEEECCSSSCCCCCSSCCEEEEEEECTTTSSS-----CCCTTTSTHH
T ss_pred             cCCeEEEeCCC-CCCCeEEEEEECCeEEEEEEEccCCccccccccCCCcEEEEEEEEcCCCcccc-----cccCCCCCHh
Confidence            48999999999 89999999999999999999998763      245678999999999888863     2334789999


Q ss_pred             hhhHHHhhcCCccccccCC-CC-CceEEEEEEEeccCCCChhhHHHHHHHHHhhcCCCCCCCCeEEEEEEEECCEEEEcC
Q 002054          141 ELLVGRIIDRPIRPLFPAG-FY-HEVQVMASVLSSDGKQDPDIMAANATSAALMLSDIPWGGPIGMIRIGRICGQFIVNP  218 (974)
Q Consensus       141 eil~~RlidR~lrplfp~~-~~-~~~~i~~~vl~~dg~~~~~~~ai~aAs~AL~~s~iP~~~~v~av~vg~i~g~~vldP  218 (974)
                      +++++|+|+|+|||.++.. |. +.++|+|+||++||+..  +||+|||++||++++|||+++|+||++|+++|++++||
T Consensus       100 ~~~~~~ll~r~l~~~i~~~~~p~~~I~i~~~VL~~dG~~~--~A~i~aa~~AL~da~iPl~~~v~avs~g~~~~~~l~Dp  177 (249)
T 2nn6_B          100 SCEMGLQLRQTFEAAILTQLHPRSQIDIYVQVLQADGGTY--AACVNAATLAVLDAGIPMRDFVCACSAGFVDGTALADL  177 (249)
T ss_dssp             HHHHHHHHHHHHHHTTCGGGCTTEEEEEEEEEEECCSCHH--HHHHHHHHHHHHHTCCCCSSCCEEEEEEEETTEEEESC
T ss_pred             HHHHHHHHHHHHHHhcCHHHCCCcEEEEEEEEEeCCCCHH--HHHHHHHHHHHHhcCCcccCCeeeEEEEEECCeEEECC
Confidence            9999999999999998844 32 35889999999999877  99999999999999999999999999999999999999


Q ss_pred             CHHHHhcCccceeEee--eCCeEEEEEecCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHhCC
Q 002054          219 TMDELSLSDLNLVYAC--TREKTLMIDVQAREISEKDLEAGLRLAHPEAVKYLEPQIRLAEKAGK  281 (974)
Q Consensus       219 t~~e~~~s~~~l~v~~--t~~~i~mie~~~~~~~e~~~~~al~~a~~~~~~i~~~~~~~~~~~g~  281 (974)
                      |++|++.++.+|+|+.  +.++++++|+.+. |+.++|.+++++|.+++++|++.|++.+++..+
T Consensus       178 ~~~Ee~~~~~~~~v~~~~~~~~i~~lq~~g~-~~~~~l~~~l~~A~~~~~~i~~~~~~~l~~~~~  241 (249)
T 2nn6_B          178 SHVEEAAGGPQLALALLPASGQIALLEMDAR-LHEDHLERVLEAAAQAARDVHTLLDRVVRQHVR  241 (249)
T ss_dssp             CHHHHTSSCCCEEEEEETTTTEEEEEEECSC-CBTTSHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             ChHHhccCCcEEEEEEECCCCCEEEEEEECC-cCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            9999999999999996  4567999999974 999999999999999999999999998877643

>2nn6_E Exosome complex exonuclease RRP42; RNA, exosome, PM/SCL, phosphorolytic, hydrolase/transferase complex; 3.35A {Homo sapiens} SCOP: d.14.1.4 d.101.1.1

Probab=100.00  E-value=4.5e-33  Score=308.81  Aligned_cols=203  Identities=16%  Similarity=0.174  Sum_probs=178.9

Q ss_pred             CeEEEEEeCccCcCCCcEEEEEeCCeEEEEEEEeCCC-C----CCCCceeeEeeccccccccCCCCCccccccCCC-Cch
Q 002054           67 SRLITLETGKIARFANGAVVLGMDETKVLSTVTSSKG-D----SVRDFLPLTVDYQEKQFAQGVIPNTYMRREGAP-KER  140 (974)
Q Consensus        67 ~r~i~~etg~~a~~A~GSa~v~~G~T~Vl~tv~~~~~-~----~~~~f~pL~v~y~e~~~a~g~ip~~~~~Reg~p-~~~  140 (974)
                      =|++.+++|.+ .+|+|||++++|+|+|||+|+++.. |    ++.+|++++|+|.+.  |++    +|   +|+| +++
T Consensus        46 ~R~i~i~~g~l-~~a~GSa~v~~G~T~Vl~~V~~e~~~p~~~~~~~g~l~~~v~~~p~--a~~----~~---~~r~~~~~  115 (305)
T 2nn6_E           46 YRCVEVETDVV-SNTSGSARVKLGHTDILVGVKAEMGTPKLEKPNEGYLEFFVDCSAS--ATP----EF---EGRGGDDL  115 (305)
T ss_dssp             CCCCEEEECCC-TTSSSEEEEEETTEEEEEECCCCCSCCCSSSCSSCCEEEECCCCTT--TCS----SC---CTTSTHHH
T ss_pred             ccCeEEEeCcc-cCCCcEEEEEECCeEEEEEEEEEeeCCCcCCCCceEEEEEEEeCCC--cCc----cc---cCCCCchH
Confidence            47899999999 6999999999999999999999755 3    456888899988775  443    23   4554 589


Q ss_pred             hhhHHHhhcCCccc----------cccCCCCCceEEEEEEEeccCCCChhhHHHHHHHHHhhcCCCCCCC----------
Q 002054          141 ELLVGRIIDRPIRP----------LFPAGFYHEVQVMASVLSSDGKQDPDIMAANATSAALMLSDIPWGG----------  200 (974)
Q Consensus       141 eil~~RlidR~lrp----------lfp~~~~~~~~i~~~vl~~dg~~~~~~~ai~aAs~AL~~s~iP~~~----------  200 (974)
                      +++++|+|+|+|||          +||+.|.|.++|+|+||++||+..  .||+|||++||++++||+..          
T Consensus       116 ~~~isrli~r~lr~s~~idl~~L~i~p~~~~w~i~idv~VL~~DG~~~--daai~aa~~AL~~a~iP~~~~~~~~~~~~~  193 (305)
T 2nn6_E          116 GTEIANTLYRIFNNKSSVDLKTLCISPREHCWVLYVDVLLLECGGNLF--DAISIAVKAALFNTRIPRVRVLEDEEGSKD  193 (305)
T ss_dssp             HHHHHHHHHHHHHHSCCSCSSSSCSSTTTCCCCEEEEEEECCCCSSHH--HHHHHHHHHTTTTCCCCEEEEECC------
T ss_pred             HHHHHHHHHHHHhhcCcccHHHheeccCcEEEEEEEEEEEECCCCCHH--HHHHHHHHHHHHhcCCCeEEEecCCCCcee
Confidence            99999999999999          999999999999999999999655  78999999999999999542          


Q ss_pred             -----------------CeEEEEEEEECCEEEEcCCHHHHhcCccceeEeeeCCe-EEEEEe-cCCCCCHHHHHHHHHHH
Q 002054          201 -----------------PIGMIRIGRICGQFIVNPTMDELSLSDLNLVYACTREK-TLMIDV-QAREISEKDLEAGLRLA  261 (974)
Q Consensus       201 -----------------~v~av~vg~i~g~~vldPt~~e~~~s~~~l~v~~t~~~-i~mie~-~~~~~~e~~~~~al~~a  261 (974)
                                       +++||++|+++|++++|||++|++.++++|+|++++++ |+|+++ ++..|++++|.+||++|
T Consensus       194 i~~~~d~~~~~~l~l~~~p~avt~g~i~~~~l~Dpt~~Ee~~~~~~l~Va~~~~g~i~~i~~~g~~~l~~~~l~~~l~~A  273 (305)
T 2nn6_E          194 IELSDDPYDCIRLSVENVPCIVTLCKIGYRHVVDATLQEEACSLASLLVSVTSKGVVTCMRKVGKGSLDPESIFEMMETG  273 (305)
T ss_dssp             EEEEESSCCCSCCCCTTCCCCEEEEESSSSEESSCCHHHHTSCSEEEEECCCSSSCCCEEEEEESSCBCHHHHHHHHHHH
T ss_pred             eeccCcccccccccccCceEEEEEEEECCEEEECCCHHHHhhcCCcEEEEEcCCCCEEEEEccCCCCCCHHHHHHHHHHH
Confidence                             46799999999999999999999999999999999886 888884 45679999999999999


Q ss_pred             HHHHHHHHHHHHHHHHHhCC
Q 002054          262 HPEAVKYLEPQIRLAEKAGK  281 (974)
Q Consensus       262 ~~~~~~i~~~~~~~~~~~g~  281 (974)
                      +++++++++.|++++++..+
T Consensus       274 ~~~~~~i~~~~~~~l~~~~~  293 (305)
T 2nn6_E          274 KRVGKVLHASLQSVVHKEES  293 (305)
T ss_dssp             HHHHHHHHHHHHHHHHHHHC
T ss_pred             HHHHHHHHHHHHHHHHHHHh
Confidence            99999999999999887543

>2wnr_B Probable exosome complex exonuclease 1; phosphate binding, 3'-5' exoribonuclease, hydrolase; 2.65A {Methanothermobacter thermautotrophicusorganism_taxid}

Probab=100.00  E-value=2.1e-32  Score=293.49  Aligned_cols=203  Identities=19%  Similarity=0.276  Sum_probs=181.4

Q ss_pred             CeEEEEEeCccCcCCCcEEEEEeCCeEEEEEEEeCCC--C---CCCCceeeEeeccccccccCCCCCccccccCCCCchh
Q 002054           67 SRLITLETGKIARFANGAVVLGMDETKVLSTVTSSKG--D---SVRDFLPLTVDYQEKQFAQGVIPNTYMRREGAPKERE  141 (974)
Q Consensus        67 ~r~i~~etg~~a~~A~GSa~v~~G~T~Vl~tv~~~~~--~---~~~~f~pL~v~y~e~~~a~g~ip~~~~~Reg~p~~~e  141 (974)
                      -|++.+++|.+ ++|+|||++++|+|+|||+|++|.+  +   ...+..+|+++|....||.+..      +.|+|++++
T Consensus        26 ~R~i~i~~g~l-~~a~GSa~v~~G~T~Vl~~V~gp~e~~~~~~~~~~~g~l~~~~~~~p~a~~~~------~~~~~~~~~   98 (240)
T 2wnr_B           26 LRPLKIEAGIL-ERADGSSYLEFGGNKILVAVYGPREAQIRKLQRPDRAVIRCRYNMAPFSVEER------KRPGPDRRS   98 (240)
T ss_dssp             CCCEEEEESCC-SSSSEEEEEEETTEEEEEEEEEEEECCSSSSCCSSSCEEEEEEEECTTSSSSC------CCSSCCHHH
T ss_pred             ccCeEEEeCCC-CCCCEEEEEEECCeEEEEEEEcCCCCCcccccCCCcEEEEEEEEeCCCCcCCc------cCCCCChhH
Confidence            58999999999 7999999999999999999999765  3   2457789999999888887632      247899999


Q ss_pred             hhHHHhhcCCccccccCCCCC--ceEEEEEEEeccCCCChhhHHHHHHHHHhhcCCCCCCCCeEEEEEEEECCEEEEcCC
Q 002054          142 LLVGRIIDRPIRPLFPAGFYH--EVQVMASVLSSDGKQDPDIMAANATSAALMLSDIPWGGPIGMIRIGRICGQFIVNPT  219 (974)
Q Consensus       142 il~~RlidR~lrplfp~~~~~--~~~i~~~vl~~dg~~~~~~~ai~aAs~AL~~s~iP~~~~v~av~vg~i~g~~vldPt  219 (974)
                      ++++|+|+|+||+.++...++  .++|+++||++||+..  +||+|||++||++++|||+++++||++|++++.+++|||
T Consensus        99 ~~l~~ll~r~l~~~i~l~~~p~~~I~i~~~VL~~dG~~~--~a~i~aa~~AL~da~iP~~~~v~avs~g~~~~~~l~Dp~  176 (240)
T 2wnr_B           99 VEISKITAEALRPALILEKFPRSVIDVFIEVLEAEGGTR--CAGITAASVALADAGIPMRDMVVACAAGKVGDQVVLDLS  176 (240)
T ss_dssp             HHHHHHHHHHHGGGBCGGGSTTEEEEEEEEEEECCSCHH--HHHHHHHHHHHHHTTCCBSSCCEEEEEEESSSSEEESCC
T ss_pred             HHHHHHHHHHHHHhcCHHHCCCcEEEEEEEEEeCCCCHH--HHHHHHHHHHHHHcCCccccceeeEEEEEECCEEEeCCC
Confidence            999999999999988755444  5778889999999877  999999999999999999999999999999999999999


Q ss_pred             HHHHhcCccceeEee--eCCeEEEEEecCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Q 002054          220 MDELSLSDLNLVYAC--TREKTLMIDVQAREISEKDLEAGLRLAHPEAVKYLEPQIRLAEKA  279 (974)
Q Consensus       220 ~~e~~~s~~~l~v~~--t~~~i~mie~~~~~~~e~~~~~al~~a~~~~~~i~~~~~~~~~~~  279 (974)
                      ++|+..++.+++|+.  +.++++++++.++ |+.++|.+++++|.++++++++.|++.+++.
T Consensus       177 ~~Ee~~~~~~~~v~~~~~~~~i~~lq~~g~-~~~~~l~~~l~~A~~~~~~i~~~~~~~l~~~  237 (240)
T 2wnr_B          177 EEEDKEGQADVPVAILPRTREITLLQSDGN-LTPEEFERALDLAVEGCLRIHEVQKEALRKR  237 (240)
T ss_dssp             SHHHHSCSEEEEEEEETTTTEEEEEEEEEC-BCHHHHHHHHHHHHHHHHHHHHHHHHHHHC-
T ss_pred             HHHhccCCceEEEEEECCCCCEEEEEEEcc-cCHHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence            999999999999996  4566999999986 9999999999999999999999999987643

>2nn6_D Exosome complex exonuclease RRP46; RNA, exosome, PM/SCL, phosphorolytic, hydrolase/transferase complex; 3.35A {Homo sapiens} SCOP: d.14.1.4 d.101.1.1

Probab=100.00  E-value=1.6e-32  Score=293.88  Aligned_cols=195  Identities=18%  Similarity=0.178  Sum_probs=172.3

Q ss_pred             CeEEEEEeCccCcCCCcEEEEEeCCeEEEEEEEeCCC-CC---CCCceeeEeeccccccccCCCCCccccccCCCCchhh
Q 002054           67 SRLITLETGKIARFANGAVVLGMDETKVLSTVTSSKG-DS---VRDFLPLTVDYQEKQFAQGVIPNTYMRREGAPKEREL  142 (974)
Q Consensus        67 ~r~i~~etg~~a~~A~GSa~v~~G~T~Vl~tv~~~~~-~~---~~~f~pL~v~y~e~~~a~g~ip~~~~~Reg~p~~~ei  142 (974)
                      -|++.+++|.+ .+|+|||++++|+|+|||+|++|.+ ++   ..+.++|+++|.+.              .|+|+++|+
T Consensus        30 ~R~i~i~~g~l-~~a~GSa~v~~G~T~Vl~~V~g~~~~~~~~~~~~~g~l~~~~~p~--------------~g~~~~~e~   94 (237)
T 2nn6_D           30 LRHFACEQNLL-SRPDGSASFLQGDTSVLAGVYGPAEVKVSKEIFNKATLEVILRPK--------------IGLPGVAEK   94 (237)
T ss_dssp             CCCEEEEESCC-SSSSEEEEEEETTEEEEEEEEEEEECC------CCEEEEEEEECS--------------SSCCCHHHH
T ss_pred             ccceEEEeCCC-CCCCEEEEEEECCcEEEEEEeCCCcccccccCCCcEEEEEEecCC--------------CCCCCccHH
Confidence            58999999999 7899999999999999999999887 32   35667999998642              278999999


Q ss_pred             hHHHhhcCCcccccc-CCC-CCceEEEEEEEeccCCCChhhHHHHHHHHHhhcCCCCCCCCeEEEEEEEE-CCEEEEcCC
Q 002054          143 LVGRIIDRPIRPLFP-AGF-YHEVQVMASVLSSDGKQDPDIMAANATSAALMLSDIPWGGPIGMIRIGRI-CGQFIVNPT  219 (974)
Q Consensus       143 l~~RlidR~lrplfp-~~~-~~~~~i~~~vl~~dg~~~~~~~ai~aAs~AL~~s~iP~~~~v~av~vg~i-~g~~vldPt  219 (974)
                      +++|+|+|+|||+++ .+| ++.++|+|+||++||+..  +||+|||++||++++|||+++|+||++|++ +|++++||+
T Consensus        95 ~~~~li~r~l~~~i~~~~~p~~~I~I~~~VL~~dG~~~--~aai~aa~~AL~da~iP~~~~v~avs~g~~~~~~~llDp~  172 (237)
T 2nn6_D           95 SRERLIRNTCEAVVLGTLHPRTSITVVLQVVSDAGSLL--ACCLNAACMALVDAGVPMRALFCGVACALDSDGTLVLDPT  172 (237)
T ss_dssp             HHHHHHHHHHHHHCGGGCSSSEEEEEEEEEEECSSCHH--HHHHHHHHHHHHHTTCCCSSCEEEEEEEECTTCCEEESCC
T ss_pred             HHHHHHHHHHHHHhchhcCCceEEEEEEEEEECCCcHH--HHHHHHHHHHHHHcCCCcccCeeeEEEEEecCCcEEeCCC
Confidence            999999999999998 455 449999999999999876  999999999999999999999999999999 899999999


Q ss_pred             HHHHhcCccceeEeeeC--CeEEEEEecCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Q 002054          220 MDELSLSDLNLVYACTR--EKTLMIDVQAREISEKDLEAGLRLAHPEAVKYLEPQIRLAEKA  279 (974)
Q Consensus       220 ~~e~~~s~~~l~v~~t~--~~i~mie~~~~~~~e~~~~~al~~a~~~~~~i~~~~~~~~~~~  279 (974)
                      +.|++.++.+|+|+.+.  ++++++|+.+ .|++++|.+++++|.+++++|++.|++.+++.
T Consensus       173 ~~Ee~~~~~~~~v~~~~~~~~i~~lq~~g-~~~~~~l~~~l~~A~~~~~~i~~~~~~~l~~~  233 (237)
T 2nn6_D          173 SKQEKEARAVLTFALDSVERKLLMSSTKG-LYSDTELQQCLAAAQAASQHVFRFYRESLQRR  233 (237)
T ss_dssp             HHHHHHCSEEEEEEEETTTCCCCEEEEEE-SCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHhccCCceEEEEcCCCCCEEEEEEeC-CcCHHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence            99999976666666554  5699999976 59999999999999999999999999988764

>2nn6_A Polymyositis/scleroderma autoantigen 1; RNA, exosome, PM/SCL, phosphorolytic, hydrolase/transferase complex; 3.35A {Homo sapiens} SCOP: d.14.1.4 d.101.1.1

Probab=99.98  E-value=2.1e-32  Score=307.90  Aligned_cols=198  Identities=17%  Similarity=0.174  Sum_probs=176.3

Q ss_pred             CeEEEEEeCccCcCCCcEEEEEeCCeEEEEEEEeCCC-C----CCCCceeeEeeccccccccCCCCCcccc-ccCCCCch
Q 002054           67 SRLITLETGKIARFANGAVVLGMDETKVLSTVTSSKG-D----SVRDFLPLTVDYQEKQFAQGVIPNTYMR-REGAPKER  140 (974)
Q Consensus        67 ~r~i~~etg~~a~~A~GSa~v~~G~T~Vl~tv~~~~~-~----~~~~f~pL~v~y~e~~~a~g~ip~~~~~-Reg~p~~~  140 (974)
                      -|++.+++|    +|+|||++++|+|+|||+|+++.+ |    ++.+|++++|+|.+         +++.+ |+|+|+++
T Consensus        49 ~R~i~ie~g----~A~GSa~v~~G~T~VL~tV~~e~~~p~~~~~~~g~l~~~v~~~p---------~a~~~~~~g~~s~~  115 (358)
T 2nn6_A           49 YRNIRISFG----TDYGCCIVELGKTRVLGQVSCELVSPKLNRATEGILFFNLELSQ---------MAAPAFEPGRQSDL  115 (358)
T ss_dssp             CCCCEEEEC----SSTTEEEEESSSCEEEEEECCEEECCCSTTTTSCCEEEEEEECT---------TTCSSCCSSSTHHH
T ss_pred             cCCeEEEEe----cCCcEEEEEECCcEEEEEEEecccCCcccCCCCcEEEEEEEecC---------CccccccCCCCCHH
Confidence            478999999    899999999999999999998764 3    35677777777744         33333 56999999


Q ss_pred             hhhHHHhhcCCccc----------cccCCCCCceEEEEEEEeccCCCChhhHHHHHHHHHhhcCCCC-------------
Q 002054          141 ELLVGRIIDRPIRP----------LFPAGFYHEVQVMASVLSSDGKQDPDIMAANATSAALMLSDIP-------------  197 (974)
Q Consensus       141 eil~~RlidR~lrp----------lfp~~~~~~~~i~~~vl~~dg~~~~~~~ai~aAs~AL~~s~iP-------------  197 (974)
                      +++++|+|+|+|||          +||..+++.++|+|+||++||+..  .||++||++||+++++|             
T Consensus       116 e~eisrli~r~Lr~s~~idl~~LcI~pg~~~w~I~Vdv~VL~~DGn~~--dAai~Aa~aAL~da~iP~v~~~~~~v~i~~  193 (358)
T 2nn6_A          116 LVKLNRLMERCLRNSKCIDTESLCVVAGEKVWQIRVDLHLLNHDGNII--DAASIAAIVALCHFRRPDVSVQGDEVTLYT  193 (358)
T ss_dssp             HTHHHHHHHHHHHHHTCBCSSSSCSBTTTBEEEEEEEEEECSCCSCCH--HHHHHHHHHHHHHCCCCCCBCCTTCCBCCH
T ss_pred             HHHHHHHHHHHhhhccccchHhhcccCCCccEEEEEEEEEEeCCCCHH--HHHHHHHHHHHHHhCcCcEEeeCCeeEecc
Confidence            99999999999999          478889999999999999999776  79999999999999999             


Q ss_pred             ----------CCCCeEEEEEEEE--CCEEEEcCCHHHHhcCccceeEeeeCCe-EEEEEecC-CCCCHHHHHHHHHHHHH
Q 002054          198 ----------WGGPIGMIRIGRI--CGQFIVNPTMDELSLSDLNLVYACTREK-TLMIDVQA-REISEKDLEAGLRLAHP  263 (974)
Q Consensus       198 ----------~~~~v~av~vg~i--~g~~vldPt~~e~~~s~~~l~v~~t~~~-i~mie~~~-~~~~e~~~~~al~~a~~  263 (974)
                                |+++++||++|++  ++++++|||++|++.++.+|+|+++.++ ++|+|..+ ..|++++|.+||++|++
T Consensus       194 ~~~~~~~~l~i~~~p~avsvgl~~~~~~illDPt~~Ee~~~~~~l~Va~t~~g~I~~lqk~G~~~ls~~~l~~~l~~A~~  273 (358)
T 2nn6_A          194 PEERDPVPLSIHHMPICVSFAFFQQGTYLLVDPNEREERVMDGLLVIAMNKHREICTIQSSGGIMLLKDQVLRCSKIAGV  273 (358)
T ss_dssp             HHHTSCCCCCBCCCEEEEEEEECTTTSSEEESCCHHHHHHCSCEEEEEEETTTEEEEEEEESCCCCCHHHHHHHHHHHHH
T ss_pred             cccccccccCccCCEEEEEEEEEeeCCEEEECCCHHHHhhcCccEEEEEcCCCeEEEEEeCCCCCCCHHHHHHHHHHHHH
Confidence                      9999999999976  8999999999999999999999999886 99999544 46999999999999999


Q ss_pred             HHHHHHHHHHHHHHHh
Q 002054          264 EAVKYLEPQIRLAEKA  279 (974)
Q Consensus       264 ~~~~i~~~~~~~~~~~  279 (974)
                      ++++|++.|++++++.
T Consensus       274 ~~~~i~~~~~~~l~~~  289 (358)
T 2nn6_A          274 KVAEITELILKALEND  289 (358)
T ss_dssp             HHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHhH
Confidence            9999999999988763

>2po1_B Probable exosome complex exonuclease 2; RNAse PH, hydrolase/hydrolase/RNA complex; 1.94A {Pyrococcus abyssi} PDB: 2po0_B* 2pnz_B 2po2_B*

Probab=99.97  E-value=2e-31  Score=291.91  Aligned_cols=204  Identities=22%  Similarity=0.278  Sum_probs=183.2

Q ss_pred             CeEEEEEeCccCcCCCcEEEEEeCCeEEEEEEEe-CCCC--CCCCceeeEeeccccccccCCCCCccccccCCCCchhhh
Q 002054           67 SRLITLETGKIARFANGAVVLGMDETKVLSTVTS-SKGD--SVRDFLPLTVDYQEKQFAQGVIPNTYMRREGAPKERELL  143 (974)
Q Consensus        67 ~r~i~~etg~~a~~A~GSa~v~~G~T~Vl~tv~~-~~~~--~~~~f~pL~v~y~e~~~a~g~ip~~~~~Reg~p~~~eil  143 (974)
                      -|++.+++|.+ ++|+|||++++|+|+|||+|+. +.+|  ...+..+++++|....||.+..      +.|+|++++++
T Consensus        36 ~R~i~i~~g~l-~~a~GSa~v~~G~T~Vl~~V~~~~~~p~~~~~~~g~l~~~~~~~p~a~~~~------~~g~~~~~~~~  108 (277)
T 2po1_B           36 YRPIEIEVGVI-EKAEGSALVKLGSTQVLVGIKTSLGEPFPDTPNMGVMTTNVELVPLASPTF------EPGPPDERAIE  108 (277)
T ss_dssp             CCCEEEEECCS-TTSSEEEEEEETTEEEEEEEEEEEECCCTTCTTSCEEEEEEEECGGGCTTC------CSSSCCHHHHH
T ss_pred             cCCeEEEeCCc-CCCCeEEEEEECCeEEEEEEEecccCCCCCCCCceEEEEEEEeCCCccccc------cCCCCChHHHH
Confidence            48999999999 7899999999999999999994 4343  2346678999998888887531      34899999999


Q ss_pred             HHHhhcCCccc----------cccCCCCCceEEEEEEEeccCCCChhhHHHHHHHHHhhcCC------------------
Q 002054          144 VGRIIDRPIRP----------LFPAGFYHEVQVMASVLSSDGKQDPDIMAANATSAALMLSD------------------  195 (974)
Q Consensus       144 ~~RlidR~lrp----------lfp~~~~~~~~i~~~vl~~dg~~~~~~~ai~aAs~AL~~s~------------------  195 (974)
                      ++|+|+|+||+          ++|..+.+.++|+|+||++||+..  +||+|||++||++++                  
T Consensus       109 l~~li~r~l~~s~~idl~~L~i~pg~~~w~i~id~~VL~~dG~~~--~a~i~aa~~AL~da~~p~~~~~~~~~~~~~~~~  186 (277)
T 2po1_B          109 LARVIDRGIRESKALNLEKMVIVPGKIVRVVFIDVHVLDHDGNLM--DAIGIAAIAALLNARVPKVRYNEETGEVETLDE  186 (277)
T ss_dssp             HHHHHHHHHHTTTSBCGGGGEEETTTEEEEEEEEEEEEECSSCHH--HHHHHHHHHHHHHCEEEEEEECTTTCCEEEEEE
T ss_pred             HHHHHHHHHhhcccccHHHccccCCcEEEEEEEEEEEECCCCCHH--HHHHHHHHHHHHhcCCCcEEEeCCCceeecccc
Confidence            99999999998          356777789999999999999876  999999999999999                  


Q ss_pred             ---CCCCCCeEEEEEEEECCEEEEcCCHHHHhcCccceeEeeeCCe-EEEEEecC-CCCCHHHHHHHHHHHHHHHHHHHH
Q 002054          196 ---IPWGGPIGMIRIGRICGQFIVNPTMDELSLSDLNLVYACTREK-TLMIDVQA-REISEKDLEAGLRLAHPEAVKYLE  270 (974)
Q Consensus       196 ---iP~~~~v~av~vg~i~g~~vldPt~~e~~~s~~~l~v~~t~~~-i~mie~~~-~~~~e~~~~~al~~a~~~~~~i~~  270 (974)
                         +||+++++||++|++++.+++|||++|++.++.+|+|+++.++ ++++++.| ..|+.++|.+++++|.++++++++
T Consensus       187 ~~~ipl~~~~~avs~g~~~~~~l~Dp~~~Ee~~~~~~~~v~~~~~g~i~~lq~~g~~~~~~~~l~~~l~~A~~~~~~l~~  266 (277)
T 2po1_B          187 TEPLPVEKIPVPVTFAKIGNILVVDPSLDEELVMDGKITITTDETGHISAVQKSEGGAFKLEEVMYAVETAFKKAEEIRK  266 (277)
T ss_dssp             EEECCBCCCCEEEEEEEETTEEEESCCHHHHHHCSEEEEEEECTTSCEEEEEEESSCCCCHHHHHHHHHHHHHHHHHHHH
T ss_pred             cccccccCceEEEEEEEECCEEEeCCCHHHHhhCCCcEEEEEcCCCCEEEEEccCCCCCCHHHHHHHHHHHHHHHHHHHH
Confidence               8999999999999999999999999999999999999999877 99999864 579999999999999999999999


Q ss_pred             HHHHHHHHh
Q 002054          271 PQIRLAEKA  279 (974)
Q Consensus       271 ~~~~~~~~~  279 (974)
                      .|++.+++.
T Consensus       267 ~~~~~l~~~  275 (277)
T 2po1_B          267 LILEAVEKA  275 (277)
T ss_dssp             HHHHHHHHH
T ss_pred             HHHHHHhhc
Confidence            999988764

>3u1k_A Polyribonucleotide nucleotidyltransferase 1, MITO; RNAse PH, KH domain, exoribonuclease; HET: CIT; 2.13A {Homo sapiens}

Probab=99.97  E-value=1.1e-31  Score=319.83  Aligned_cols=214  Identities=21%  Similarity=0.261  Sum_probs=191.8

Q ss_pred             CeEEEEEeCccCcCCCcEEEEEeCCeEEEEEEEeCCC-CC-----------CCCceeeEeeccccccccCCCCCcccccc
Q 002054           67 SRLITLETGKIARFANGAVVLGMDETKVLSTVTSSKG-DS-----------VRDFLPLTVDYQEKQFAQGVIPNTYMRRE  134 (974)
Q Consensus        67 ~r~i~~etg~~a~~A~GSa~v~~G~T~Vl~tv~~~~~-~~-----------~~~f~pL~v~y~e~~~a~g~ip~~~~~Re  134 (974)
                      =|++.+++|.+ ++|+|||++++|+|+|||+|+++.. +.           +.+..+++++|....||++..     +|-
T Consensus       328 lRpi~i~~g~l-~~a~GSal~~~G~T~Vl~~Vt~~~~~~~~~~d~~~~~l~~~~~g~~~~~y~~~P~st~e~-----~~~  401 (630)
T 3u1k_A          328 LRNVSCEVDMF-KTLHGSALFQRGQTQVLCTVTFDSLESGIKSDQVITAINGIKDKNFMLHYEFPPYATNEI-----GKV  401 (630)
T ss_dssp             CCCEEEEECCS-TTSSEEEEEEETTEEEEEEEEEECGGGGSCSSHHHHHHHCCCGGGEEEEEECCGGGGTCC-----CCC
T ss_pred             ccceEEEECCC-CCCCceEEEEECCeEEEEEEEcCCCCchhcccccccccCCCCceEEEEEEEecCCccccc-----ccC
Confidence            37899999999 8999999999999999999998654 32           234458999999999998632     233


Q ss_pred             CCCCchhhhHHHhhcCCccccccCCCCCceEEEEEEEeccCCCChhhHHHHHHHHHhhcCCCCCCCCeEEEEEEEEC---
Q 002054          135 GAPKERELLVGRIIDRPIRPLFPAGFYHEVQVMASVLSSDGKQDPDIMAANATSAALMLSDIPWGGPIGMIRIGRIC---  211 (974)
Q Consensus       135 g~p~~~eil~~RlidR~lrplfp~~~~~~~~i~~~vl~~dg~~~~~~~ai~aAs~AL~~s~iP~~~~v~av~vg~i~---  211 (974)
                      |+|+.||++++||++|+|||++|..|.+.++|+|+||++||+..  +||+|||++||+++||||+++|+||++|+++   
T Consensus       402 g~~~rREi~~~~Li~raLr~vi~~~~p~tI~V~~~VLesDGs~~--~AsI~aa~lAL~dAGIPl~~~Vaavs~gli~~~~  479 (630)
T 3u1k_A          402 TGLNRRELGHGALAEKALYPVIPRDFPFTIRVTSEVLESNGSSS--MASACGGSLALMDSGVPISSAVAGVAIGLVTKTD  479 (630)
T ss_dssp             SSCCHHHHHHHHHHHHHHGGGSCTTCSSEEEEEEEEEECSSCHH--HHHHHHHHHHHHHTTCCCSSCCEEEEEEEEEEEC
T ss_pred             CCCChHHHHHHHHHHHHHHhhCcccCCeEEEEEEEEEEcCCCHH--HHHHHHHHHHHHhCCCCcccceEEEEEEEecCCC
Confidence            88999999999999999999999999999999999999999877  9999999999999999999999999999997   


Q ss_pred             ---C-----EEEEcCCHHHHhcCccceeEeeeCCeEEEEEecCC--CCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHhCC
Q 002054          212 ---G-----QFIVNPTMDELSLSDLNLVYACTREKTLMIDVQAR--EISEKDLEAGLRLAHPEAVKYLEPQIRLAEKAGK  281 (974)
Q Consensus       212 ---g-----~~vldPt~~e~~~s~~~l~v~~t~~~i~mie~~~~--~~~e~~~~~al~~a~~~~~~i~~~~~~~~~~~g~  281 (974)
                         |     .+++||++.|+..+++||.|++|.++++++|++++  .|++++|.+||++|++++++|++.|++.+++...
T Consensus       480 ~~~g~~~~~~iLlD~~~~Ed~~~d~d~~Va~t~~gIt~lQ~~~k~~~~s~~~l~~aL~~A~~g~~~I~~~m~~al~~~~~  559 (630)
T 3u1k_A          480 PEKGEIEDYRLLTDILGIEDYNGDMDFKIAGTNKGITALQADIKLPGIPIKIVMEAIQQASVAKKEILQIMNKTISKPRA  559 (630)
T ss_dssp             SSSSCEEEEEEEESCCHHHHHTSSEEEEEEECSSCEEEEEEEECSSCBCHHHHHHHHHHHHHHHHHHHHHHHHHCSSCCS
T ss_pred             cccccccCceEEecCCHHHHhhCcceEEEEecCCceEEEEecCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence               4     79999999999999999999999999999998775  6999999999999999999999999999987766


Q ss_pred             ccccccc
Q 002054          282 QKKEYKL  288 (974)
Q Consensus       282 ~k~~~~~  288 (974)
                      +..++.+
T Consensus       560 ~~~~~ap  566 (630)
T 3u1k_A          560 SRKENGP  566 (630)
T ss_dssp             SCCTTCC
T ss_pred             hhcccCC
Confidence            5555543

>2wp8_A Exosome complex component RRP45; nucleus, hydrolase, RNA-binding, exonucle binding, mitochondrion, rRNA processing; 3.00A {Saccharomyces cerevisiae}

Probab=99.97  E-value=2.8e-31  Score=294.58  Aligned_cols=202  Identities=18%  Similarity=0.178  Sum_probs=160.6

Q ss_pred             CeEEEEEeCccCcCCCcEEEEEeCCeEEEEEEEeCCC-C----CCCCceeeEeeccccccccCCCCCccccccCCCC-ch
Q 002054           67 SRLITLETGKIARFANGAVVLGMDETKVLSTVTSSKG-D----SVRDFLPLTVDYQEKQFAQGVIPNTYMRREGAPK-ER  140 (974)
Q Consensus        67 ~r~i~~etg~~a~~A~GSa~v~~G~T~Vl~tv~~~~~-~----~~~~f~pL~v~y~e~~~a~g~ip~~~~~Reg~p~-~~  140 (974)
                      -|++.+++|    +|+|||++++|+|+|||+|+++.. |    ++.++++++|+|.+..++.      |  |.|+|+ ++
T Consensus        33 ~R~i~i~~g----~a~GSa~v~~G~T~Vl~~V~~~~~~p~~~~~~~g~~~~~ve~~~~~~~~------~--~~g~~~~~~  100 (305)
T 2wp8_A           33 FRDVEITFG----KEFGDVSVKMGNTKVHCRISCQIAQPYEDRPFEGLFVISTEISPMAGSQ------F--ENGNITGED  100 (305)
T ss_dssp             CCCEEEEEC----SSTTEEEEEETTEEEEEEEEEEEC-CCSSCTTCCEEEEEECCC------------------------
T ss_pred             cCCeEEEEc----CCCcEEEEEECCeEEEEEEeccccCCcccCCCCcEEEEEEEECCCCCcc------c--cCCCCChhH
Confidence            588999999    799999999999999999998743 2    3578999999997665432      2  459999 99


Q ss_pred             hhhHHHhhcCCccc----------cccCCCCCceEEEEEEEeccCCCChhhHHHHHHHHHhhcCCCC-------------
Q 002054          141 ELLVGRIIDRPIRP----------LFPAGFYHEVQVMASVLSSDGKQDPDIMAANATSAALMLSDIP-------------  197 (974)
Q Consensus       141 eil~~RlidR~lrp----------lfp~~~~~~~~i~~~vl~~dg~~~~~~~ai~aAs~AL~~s~iP-------------  197 (974)
                      +++++|+|+|+|||          ++|..|.+.++|+|+||++||+..  +||++||++||+++++|             
T Consensus       101 ~~~is~li~r~l~~s~~idl~~L~i~pg~~~w~I~id~~VL~~DG~~~--dAai~aa~~AL~~a~iP~~~~~~~~~~i~~  178 (305)
T 2wp8_A          101 EVLCSRIIEKSVRRSGALDVEGLCIVAGSKCWAVRADVHFLDCDGGFI--DASCIAVMAGLMHFKKPDITVHGEQIIVHP  178 (305)
T ss_dssp             ------CHHHHHHHTTSBCGGGGEEETTTEEEEEEEEEEEEECSSCHH--HHHHHHHHHHHHHCEECCCBCTTSSCCBCC
T ss_pred             HHHHHHHHHHHHhhccCcCHHHccccCCcEEEEEEEEEEEEcCCCCHH--HHHHHHHHHHHHHhCCCeEEecCCceEecc
Confidence            99999999999995          467888899999999999999866  89999999999999999             


Q ss_pred             ----------CCCCeEEEEEEEEC--------------CEEEEcCCHHHHhcCccceeEeeeCCe-EEEEEecC-CCCCH
Q 002054          198 ----------WGGPIGMIRIGRIC--------------GQFIVNPTMDELSLSDLNLVYACTREK-TLMIDVQA-REISE  251 (974)
Q Consensus       198 ----------~~~~v~av~vg~i~--------------g~~vldPt~~e~~~s~~~l~v~~t~~~-i~mie~~~-~~~~e  251 (974)
                                +++.++||++|+++              +.+++|||++|+..++.+|+|+++.++ ++++++.+ ..|++
T Consensus       179 ~~~~~~~~l~~~~~pvavs~g~i~~~~~~~~~~~~~~~~~~l~Dpt~~Ee~~~~~~l~Va~~~~g~i~~l~~~g~~~~~~  258 (305)
T 2wp8_A          179 VNEREPVPLGILHIPICVTFSFFNPQDTEENIKGETNSEISIIDATLKEELLRDGVLTVTLNKNREVVQVSKAGGLPMDA  258 (305)
T ss_dssp             SSSSCCEECCBSCCCEEEEEEECC---------------CEEESCCHHHHHHCSEEEEEEECTTSEEEEEEEEEEEEECH
T ss_pred             cccccccccccccCeEEEEEEEEccccccccccccccCCeEEeCCCHHHHhccCCcEEEEEcCCCcEEEEEecCCCCCCH
Confidence                      55667799999997              899999999999999999999999887 77666544 46999


Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHhCCc
Q 002054          252 KDLEAGLRLAHPEAVKYLEPQIRLAEKAGKQ  282 (974)
Q Consensus       252 ~~~~~al~~a~~~~~~i~~~~~~~~~~~g~~  282 (974)
                      ++|.+||++|++++++|++.|++.+++.++.
T Consensus       259 ~~l~~~l~~A~~~~~~i~~~~~~~l~~~~~~  289 (305)
T 2wp8_A          259 LTLMKCCHEAYSIIEKITDQILQLLKEDSEK  289 (305)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            9999999999999999999999998876543

>3gme_A Polyribonucleotide nucleotidyltransferase; protein-RNA complex, cytoplasm, nucleotidyltransferase, RNA- binding, transferase, hydrolase; 2.40A {Escherichia coli E24377A} PDB: 3gll_A 3gcm_A 3h1c_A 3cdj_A

Probab=99.97  E-value=4.9e-30  Score=299.61  Aligned_cols=202  Identities=21%  Similarity=0.302  Sum_probs=176.7

Q ss_pred             eEEEEEeCccCcCCCcEEEEEeCCeEEEEEE-EeCCCC-C------CCCceeeEeeccccccccCCCCCccccccCCCCc
Q 002054           68 RLITLETGKIARFANGAVVLGMDETKVLSTV-TSSKGD-S------VRDFLPLTVDYQEKQFAQGVIPNTYMRREGAPKE  139 (974)
Q Consensus        68 r~i~~etg~~a~~A~GSa~v~~G~T~Vl~tv-~~~~~~-~------~~~f~pL~v~y~e~~~a~g~ip~~~~~Reg~p~~  139 (974)
                      |++.+++|.+ ++|+|||++++|+|+|||+| .+|.++ .      +.+..+++++|.-..||++.     .+|-|+|+.
T Consensus       325 Rpi~i~~g~l-~~a~GSal~~~G~T~Vl~~Vt~gp~~~~~~~~~l~~~~~g~~~~~y~~~P~st~e-----~~~~g~~~~  398 (549)
T 3gme_A          325 RGLDVRTGVL-PRTHGSALFTRGETQALVTATLGTARDAQVLDELMGERTDTFLFHYNFPPYSVGE-----TGMVGSPKR  398 (549)
T ss_dssp             CCEEEEECCC-SSSSEEEEEEETTEEEEEEEEEEC---------------CCEEEEEECCGGGTTC-----CCCSSCCCS
T ss_pred             cceEEEECCC-CCCCceEEEEECCeEEEEEEEecCcccccCccccCCCCceEEEEEEEeCCCCcCC-----cccCCCCCh
Confidence            7899999999 89999999999999999999 477542 1      23456799999988888863     223378999


Q ss_pred             hhhhHHHhhcCCcccccc--CCCCCceEEEEEEEeccCCCChhhHHHHHHHHHhhcCCCCCCCCeEEEEEEEECC----E
Q 002054          140 RELLVGRIIDRPIRPLFP--AGFYHEVQVMASVLSSDGKQDPDIMAANATSAALMLSDIPWGGPIGMIRIGRICG----Q  213 (974)
Q Consensus       140 ~eil~~RlidR~lrplfp--~~~~~~~~i~~~vl~~dg~~~~~~~ai~aAs~AL~~s~iP~~~~v~av~vg~i~g----~  213 (974)
                      ||++++|++.|+|||.+|  ..|.+.++|+|+||++||+..  +||||||++||+++||||+++|+||++|++++    .
T Consensus       399 Reie~~~li~raL~~vI~~~~~~P~tI~V~~~VLesDGs~~--~AsI~aa~lAL~DAGvPm~~~Vaavs~Gli~~g~~~~  476 (549)
T 3gme_A          399 REIGHGRLAKRGVLAVMPDMDKFPYTVRVVSEITESNGSSS--MASVCGASLALMDAGVPIKAAVAGIAMGLVKEGDNYV  476 (549)
T ss_dssp             SHHHHHHHHHHHHTTTCCCTTTCCCEEEEEEEEEECSSCHH--HHHHHHHHHHHHHHTCCCSSCCEEEEEEEEEETTEEE
T ss_pred             hHHHHHHHHHHHHHHhcCccccCCeEEEEEEEEEECCCCHH--HHHHHHHHHHHHhCCCCcccceeEEEEEEEcCCCceE
Confidence            999999999999999999  467778999999999999988  99999999999999999999999999999965    7


Q ss_pred             EEEcCCHHHHhcCccceeEeeeCCeEEEEEecC--CCCCHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 002054          214 FIVNPTMDELSLSDLNLVYACTREKTLMIDVQA--REISEKDLEAGLRLAHPEAVKYLEPQIRLAE  277 (974)
Q Consensus       214 ~vldPt~~e~~~s~~~l~v~~t~~~i~mie~~~--~~~~e~~~~~al~~a~~~~~~i~~~~~~~~~  277 (974)
                      +++||++.|+..+++||.|++|.++++.+|+++  ..|+.++|.+||++|.+++.+|++.|++.+.
T Consensus       477 iL~D~~~~Ed~~~d~d~~Va~t~~gitalqmd~ki~G~s~~~l~~~L~~A~~g~~~I~~~m~~al~  542 (549)
T 3gme_A          477 VLSDILGDEDHLGDMDFKVAGSRDGISALQMDIKIEGITKEIMQVALNQAKGARLHILGVMEQAIN  542 (549)
T ss_dssp             EEESCCHHHHHHSSEEEEEEECSSCEEEEEEEECCSCCCHHHHHHHHHHHHHHHHHHHHHHHHHCC
T ss_pred             EEecCChHHHccCCceEEEEecCCCeEEEEEccccCCcCHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            899999999999999999999999998888754  3499999999999999999999999988764

>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=99.96  E-value=2.5e-28  Score=295.81  Aligned_cols=212  Identities=21%  Similarity=0.320  Sum_probs=185.9

Q ss_pred             CeEEEEEeCccCcCCCcEEEEEeCCeEEEEEEE-eCCCC-C------CCCceeeEeeccccccccCCCCCccccccCCCC
Q 002054           67 SRLITLETGKIARFANGAVVLGMDETKVLSTVT-SSKGD-S------VRDFLPLTVDYQEKQFAQGVIPNTYMRREGAPK  138 (974)
Q Consensus        67 ~r~i~~etg~~a~~A~GSa~v~~G~T~Vl~tv~-~~~~~-~------~~~f~pL~v~y~e~~~a~g~ip~~~~~Reg~p~  138 (974)
                      =|++.+++|.+ ++|+|||++++|+|+|||+|+ +|.++ .      +.+..+++++|.-..||++.     .+|-|+|+
T Consensus       365 lRpI~ie~gvl-~~a~GSAl~~~G~TqVL~~Vt~Gp~~~~~~~d~l~~~~~g~~~~~y~f~P~st~e-----~~~~g~~~  438 (757)
T 1e3p_A          365 IRTLAAEVEAI-PRVHGSALFERGETQILGVTTLNMLRMEQQLDTLSPVTRKRYMHNYNFPPYSVGE-----TGRVGSPK  438 (757)
T ss_dssp             CCCEEEEECCS-SSSSEEEEEEETTEEEEEEEEEEEGGGSEECCSSSSCCEESEEEEEECCGGGGTC-----CCCCSSCC
T ss_pred             ccceeEEeCCC-CCCCEEEEEEECCcEEEEEEEecCCCccccccccCCCCceEEEEEEEeCCccccc-----ccCCCCCc
Confidence            37899999999 899999999999999999995 77652 2      23446799999999998853     23347899


Q ss_pred             chhhhHHHhhcCCcccccc--CCCCCceEEEEEEEeccCCCChhhHHHHHHHHHhhcCCCCCCCCeEEEEEEEE----CC
Q 002054          139 ERELLVGRIIDRPIRPLFP--AGFYHEVQVMASVLSSDGKQDPDIMAANATSAALMLSDIPWGGPIGMIRIGRI----CG  212 (974)
Q Consensus       139 ~~eil~~RlidR~lrplfp--~~~~~~~~i~~~vl~~dg~~~~~~~ai~aAs~AL~~s~iP~~~~v~av~vg~i----~g  212 (974)
                      .+|++++|++.|+|||.+|  ..|.+.++|+|+||++||+..  +||+|||++||++++||++++|+||++|++    +|
T Consensus       439 ~reie~~~li~raL~~vI~~~~~~P~tI~V~~~VLesDGs~~--~Asi~aa~lAL~dAgIP~k~~Vaavs~gli~eg~dg  516 (757)
T 1e3p_A          439 RREIGHGALAERAIVPVLPTREEFPYAIRQVSEALGSNGSTS--MGSVCASTMSLLNAGVPLKAPVAGIAMGLISQEING  516 (757)
T ss_dssp             HHHHHHHHHHHHHHGGGCCCTTTSCEEEEEEEEEEECSSCHH--HHHHHHHHHHHHHHTCCCSSCCEEEEEEEEEEESSS
T ss_pred             hhHHHHHHHHHHHHHHhccccccCCEEEEEEEEEEECCCCHH--HHHHHHHHHHHHHcCCCcccceEEEEEEEEecCCCC
Confidence            9999999999999999998  367778999999999999987  999999999999999999999999999999    55


Q ss_pred             ----EEEEcCCHHHHhcCccceeEeeeCCeEEEEEecCC--CCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCccccc
Q 002054          213 ----QFIVNPTMDELSLSDLNLVYACTREKTLMIDVQAR--EISEKDLEAGLRLAHPEAVKYLEPQIRLAEKAGKQKKEY  286 (974)
Q Consensus       213 ----~~vldPt~~e~~~s~~~l~v~~t~~~i~mie~~~~--~~~e~~~~~al~~a~~~~~~i~~~~~~~~~~~g~~k~~~  286 (974)
                          .+++||+..|+..+++||.|+++.++++.+|+.++  .|+.++|.+||++|.+++++|++.|++.+.+. .+...+
T Consensus       517 ~~~~~iLlDp~~~Ed~~gd~d~~Va~t~~~It~lQ~~gk~~gi~~e~l~~aL~~A~~~~~~I~~~m~~al~~~-~~~~~~  595 (757)
T 1e3p_A          517 ETHYVALTDILGAEDAFGDMDFKVAGTKEFVTALQLDTKLDGIPASVLAAALKQARDARLHILDVMMEAIDTP-DEMSPN  595 (757)
T ss_dssp             CEEEEEEESCCHHHHHHCSEEEEEEECSSSEEEEEEEECSSCCCHHHHHHHHHHHHHHHHHHHHHHHHHCSSC-CCCCTT
T ss_pred             ccceeEEeCCCHHHHhccCceEEEEecCCeEEEEEEcCCccccCHHHHHHHHHHHHHHHHHHHHHHHHHhccc-cccccc
Confidence                78999999999999999999999999999998764  48999999999999999999999999988766 433344


Q ss_pred             c
Q 002054          287 K  287 (974)
Q Consensus       287 ~  287 (974)
                      .
T Consensus       596 a  596 (757)
T 1e3p_A          596 A  596 (757)
T ss_dssp             S
T ss_pred             C
Confidence            3

>3go5_A Multidomain protein with S1 RNA-binding domains; structural genomics, joint center for structural genomics, JCSG; HET: MSE; 1.40A {Streptococcus pneumoniae}

Probab=99.93  E-value=3.5e-25  Score=241.42  Aligned_cols=204  Identities=14%  Similarity=0.051  Sum_probs=158.0

Q ss_pred             ccCcEEEEEEEEEeeceEEEEEcCCeEEEEecccCCCccccccccccccCCEEEEEEEEEccCCceEEEEeccCCCcccc
Q 002054          682 EVGGIYKGVVTSVKEYGAFVEFNGGQQGLLHVSELSHEPVSRVSDVVSVGQQLSLRCIGQDVRGNIKLSLKAVSPRPEAD  761 (974)
Q Consensus       682 ~~G~i~~G~V~~i~~~G~fV~l~~g~~Glvhisels~~~v~~~~~~~~vGd~V~vkVl~id~~gri~LS~K~~~~~~~~~  761 (974)
                      .+|++++|+|+++.++|+||++. +.+||||.||++.          ++||+|+|+|+. |.++|+.+|++    .||..
T Consensus         5 ~~G~~v~g~V~~~~~~G~fv~~~-g~egllp~se~~~----------~vGdevev~v~~-d~~~r~iat~~----~p~~~   68 (285)
T 3go5_A            5 NLASFIVGLIIDENDRFYFVQKD-GQTYALAKEEGQH----------TVGDTVKGFAYT-DMKQKLRLTTL----EVTAT   68 (285)
T ss_dssp             TTTEEEEEEEEEECSSEEEEEET-TEEEEEEGGGCCC----------CTTSEEEEEEEE-CTTSCEEEECS----CCCSC
T ss_pred             cCCCEEEEEEEEEECCEEEEEcC-CeEEEEEHHHCcc----------ccCCEEEEEEEE-CCCCCEEEecc----ccccc
Confidence            57999999999999999999995 8999999999943          789999999984 88889988865    47888


Q ss_pred             cCceEEEEEeecCCcce-eeEEeeccCC-CCCCCCCCCCCCCCCcccCCCCcceEEEeeccccccccccccccccccccc
Q 002054          762 VKGVVEGSVPVNKQATD-VWASVGDVSN-GQNPELPMRKNETPGVNSSTSSTPAVLIRSAAECDEEEKASGFSQSSKSTL  839 (974)
Q Consensus       762 ~g~~~~G~vv~i~~gv~-~~~~~~~l~~-~~~~~lp~~~~~~~~~~~~~G~~v~v~Ir~~l~iD~~~r~i~ls~k~~~~~  839 (974)
                      .|....|.|++    ++ .|+.|.+++. .....+|.       +.+                                 
T Consensus        69 ~G~~~~g~V~~----v~~~~GaFVdiG~~~~d~lvp~-------sel---------------------------------  104 (285)
T 3go5_A           69 QDQFGWGRVTE----VRKDLGVFVDTGLPDKEIVVSL-------DIL---------------------------------  104 (285)
T ss_dssp             SSSCEEEEEEE----EETTTEEEEECSCTTCCEEEEG-------GGS---------------------------------
T ss_pred             CCCEEEEEEEE----EccCceEEEEECCCCcEEEEEH-------HHC---------------------------------
Confidence            88777777777    55 5666666654 22211111       000                                 


Q ss_pred             ccccccccCCCCCCCcEEEEEecccCcCCCcccccCCeEEEEEEEeecCCCCcC-ccccc-ccccc--ccccCCCCCEEE
Q 002054          840 KSTLASKSNSKPKKFTSQSDFFSSTNIQKSTSFSQREREELAECLFGTEDGDED-NKGTR-VEAIV--SAKNLKLGTKVA  915 (974)
Q Consensus       840 ~~~~~~~~~~~~~G~~v~g~V~~~~~~~~~~~~k~Gq~v~~~Vl~vd~e~~~i~-slK~~-~~~p~--~~~~~~vG~vV~  915 (974)
                                             +|.+  ...+++||++. +++.+|+ ++++. |+|+. ..+||  ...+|++|++|+
T Consensus       105 -----------------------~~~~--~~~~~~Gd~v~-v~l~iD~-~~Ri~ls~k~~~~~~~~~~~~~~~~~G~~V~  157 (285)
T 3go5_A          105 -----------------------PELK--ELWPKKGDQLY-IRLEVDK-KDRIWGLLAYQEDFQRLARPAYNNMQNQNWP  157 (285)
T ss_dssp             -----------------------CSSG--GGSCCTTCEEE-EEEEECT-TSCEEEEECCHHHHHHHCCCCCSCCTTCEEE
T ss_pred             -----------------------Cccc--ccccCCCCEEE-EEEEECC-CCcEEEEehhhhhcchhhhhhhhCCCCCEEE
Confidence                                   0100  01246677774 3457776 45665 77765 45677  367899999999


Q ss_pred             EEEEEEeCCeEEE-EeCCCeEEEEecccCCCCCCCCCCEEEEEEEEEeC-CCceeeeecC
Q 002054          916 AKVYQVRARGLVL-DLGGGIRGMYRFENNEKKDFVVGDELLVKCSSFTG-KGIPVVSLVD  973 (974)
Q Consensus       916 G~V~~I~~~GvFV-~L~~gv~Glih~se~~~~~f~vGd~V~vkVl~id~-~~~~~~~~~~  973 (974)
                      |+|+++++||+|| .+++++.||||.||+. ..+++||+|+|+|++||+ +++..+|+..
T Consensus       158 g~V~~i~~~G~fV~~i~~g~~Glih~SEl~-~~l~~Gd~v~~~V~~id~~d~kI~LSlk~  216 (285)
T 3go5_A          158 AIVYRLKLSGTFVYLPENNMLGFIHPSERY-AEPRLGQVLDARVIGFREVDRTLNLSLKP  216 (285)
T ss_dssp             EEEEEEETTEEEEEETTTTEEEEECGGGCS-SCCCTTCEEEEEEEEEETTTTEEEEECSC
T ss_pred             EEEEEEeCCcEEEEEeCCCeEEEEEHHHcc-ccCCCCCEEEEEEEEEECCCCeEEEEeCh
Confidence            9999999999999 9999999999999995 679999999999999999 8999999853

>1kl9_A Eukaryotic translation initiation factor 2 subuni; OB fold, helical domain; 1.90A {Homo sapiens} SCOP: a.60.14.1 b.40.4.5

Probab=99.62  E-value=9.8e-18  Score=170.85  Aligned_cols=110  Identities=22%  Similarity=0.300  Sum_probs=84.3

Q ss_pred             cccCcEEEEEEEEEeeceEEEEE--cCCeEEEEecccCCCccccccccccccCCEEEEEEEEEcc-CCceEEEEeccCCC
Q 002054          681 IEVGGIYKGVVTSVKEYGAFVEF--NGGQQGLLHVSELSHEPVSRVSDVVSVGQQLSLRCIGQDV-RGNIKLSLKAVSPR  757 (974)
Q Consensus       681 ~~~G~i~~G~V~~i~~~G~fV~l--~~g~~Glvhisels~~~v~~~~~~~~vGd~V~vkVl~id~-~gri~LS~K~~~~~  757 (974)
                      +++|++|.|+|++|++||+||+|  .++++||||+|+++++++.++.++|++||.|+|+|+++|. +++|.||+|++.++
T Consensus        13 p~~G~iv~G~V~~I~~fGaFV~L~e~~g~eGLvhiSels~~~v~~~~~~~~vGd~V~VkVl~vD~~~~rI~LSlk~~~~~   92 (182)
T 1kl9_A           13 PEVEDVVMVNVRSIAEMGAYVSLLEYNNIEGMILLSELSRRRIRSINKLIRIGRNECVVVIRVDKEKGYIDLSKRRVSPE   92 (182)
T ss_dssp             CCTTCEEEEEEEEECSSEEEEEETTTTTEEEEEEGGGC------------CTTCEEEEEEEEEETTTTEEEEESTTCCHH
T ss_pred             CCCCCEEEEEEEEEeccEEEEEEccCCCcEEEEEHHHCCCcccCCHHHhcCCCCEEEEEEEEEECCCCEEEEEEeecCcC
Confidence            58999999999999999999999  6789999999999999999999999999999999999997 78999999999999


Q ss_pred             ccccc------CceEEEEE--------eecCCcceeeEEeeccCCCC
Q 002054          758 PEADV------KGVVEGSV--------PVNKQATDVWASVGDVSNGQ  790 (974)
Q Consensus       758 ~~~~~------g~~~~G~v--------v~i~~gv~~~~~~~~l~~~~  790 (974)
                      ||...      |..+.|.|        +.+.+|+++++|.++++|.+
T Consensus        93 p~~~~~~~~~~g~~v~g~v~~i~~~~gv~l~~giegl~h~s~~~~~~  139 (182)
T 1kl9_A           93 EAIKCEDKFTKSKTVYSILRHVAEVLEYTKDEQLESLFQRTAWVFDD  139 (182)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHTTCCSHHHHHHHHHHTHHHHHH
T ss_pred             hHHHHHHhccCCCEEEEEEEEchhhcCCcccCChhheEEeeecchhh
Confidence            99762      33333333        45555899999999888764

>1y14_B B16, RPB7, DNA-directed RNA polymerase II 19 kDa polypeptide; transferase; 2.30A {Saccharomyces cerevisiae} SCOP: b.40.4.5 d.230.1.1 PDB: 1nt9_G 1wcm_G 1pqv_G 1y1v_G 1y1w_G 1y1y_G 1y77_G* 2b63_G* 2ja5_G* 2ja6_G* 2ja7_G* 2ja8_G* 2r7z_G 2r92_G 2r93_G 2vum_G* 3fki_G 3h3v_H 3hou_G* 3hov_G* ...

Probab=99.62  E-value=3.8e-18  Score=173.31  Aligned_cols=134  Identities=11%  Similarity=0.124  Sum_probs=100.5

Q ss_pred             HHHHHHHhcCCCCCCCCCCCcceeeeeccchhhhhcCCCccchhhhhhhhCceEEee-----CCEEEEEecCHHHHHHHH
Q 002054          596 LDHMEREISAPRTQDDRNSPRLATLKYDNDTLRRLIGPLGALKRKIEEETGGRISVS-----DGTLTVVAKNRSVMEKVL  670 (974)
Q Consensus       596 ~~~m~~~i~~~~~~~~~~~p~~~~~~i~~~ki~~vIg~gGk~i~~i~~~~g~~Idi~-----dg~v~i~~~~~~~~~~a~  670 (974)
                      +..|+++++.|+.++++++|++...++++++++++||++|++|.        .+|++     +|.+.  ..+.  ...+.
T Consensus         4 l~~m~~~i~~pp~~l~~~~p~~i~~~i~~~~i~~vig~~G~~I~--------~~di~~~di~~g~i~--~~d~--~~~~~   71 (171)
T 1y14_B            4 IKDLSLNITLHPSFFGPRMKQYLKTKLLEEVEGSCTGKFGYILC--------VLDYDNIDIQRGRIL--PTDG--SAEFN   71 (171)
T ss_dssp             EEEEEEECCCCTTSCSTTHHHHHHHHHHHHHTTEEETTTEEEEE--------ECCGGGCBCC----------------CE
T ss_pred             EEEEEEEEEECHHHhCChHHHHHHHHHHHHHcCcCcCCceEEEE--------EEEecccccCccEEe--CCCC--CEEEE
Confidence            34567788999999999999999999999999999999999982        34444     35555  2222  22222


Q ss_pred             HHHHHHhhcccccCcEEEEEEEEEeeceEEEEEcCCeEEEEecccCCCcccccc----------ccccccCCEEEEEEEE
Q 002054          671 EKVDFIIGREIEVGGIYKGVVTSVKEYGAFVEFNGGQQGLLHVSELSHEPVSRV----------SDVVSVGQQLSLRCIG  740 (974)
Q Consensus       671 ~~i~~l~~~~~~~G~i~~G~V~~i~~~G~fV~l~~g~~Glvhisels~~~v~~~----------~~~~~vGd~V~vkVl~  740 (974)
                      ..++.+. ..+++|++|+|+|+++++||+||++.+ .+||||+|++++.+.-++          ++.+++||.|+|||++
T Consensus        72 ~~~~~~~-~~~~~Gev~~G~V~~v~~fG~FV~l~~-~dglvhis~l~~~~~~d~~~~~~~~~~~~~~~~~Gd~V~vkV~~  149 (171)
T 1y14_B           72 VKYRAVV-FKPFKGEVVDGTVVSCSQHGFEVQVGP-MKVFVTKHLMPQDLTFNAGSNPPSYQSSEDVITIKSRIRVKIEG  149 (171)
T ss_dssp             EEEEEEE-ECCCTTCEEEEEEEEEETTEEEEEETT-EEEEEEGGGSCTTCEECC-----CEECSSCEECTTCEEEEEEEE
T ss_pred             EEEEEEE-ccCCCCCEEEEEEEEEecCEEEEEecC-eEEEEEHHHCCCCceECcccCceEEeccceEECCCCEEEEEEEE
Confidence            2333333 468999999999999999999999988 999999999986543222          2679999999999999


Q ss_pred             Ecc
Q 002054          741 QDV  743 (974)
Q Consensus       741 id~  743 (974)
                      +|.
T Consensus       150 vd~  152 (171)
T 1y14_B          150 CIS  152 (171)
T ss_dssp             EEE
T ss_pred             EEc
Confidence            997

>1go3_E DNA-directed RNA polymerase subunit E; transferase, transferase, transcription; 1.75A {Methanococcus jannaschii} SCOP: b.40.4.5 d.230.1.1

Probab=99.59  E-value=1.5e-16  Score=163.97  Aligned_cols=131  Identities=23%  Similarity=0.336  Sum_probs=108.0

Q ss_pred             eeeeeccchhhhhcCCCccchhhh-hhhh--------Cc---eEEee-CCEEEEEecCHHHHHHHHHHHHHHhhcccccC
Q 002054          618 ATLKYDNDTLRRLIGPLGALKRKI-EEET--------GG---RISVS-DGTLTVVAKNRSVMEKVLEKVDFIIGREIEVG  684 (974)
Q Consensus       618 ~~~~i~~~ki~~vIg~gGk~i~~i-~~~~--------g~---~Idi~-dg~v~i~~~~~~~~~~a~~~i~~l~~~~~~~G  684 (974)
                      .+++|+|++|+++||   ++|+++ .+++        |+   .+|++ +|...|...+...+..  ..++.++ ..+++|
T Consensus         9 ~~i~I~P~~~~~~i~---~~I~~~L~~~~~gk~~~~~G~~i~~idi~~~g~~~I~~~d~~~~~~--~~~~~i~-~~~~~G   82 (187)
T 1go3_E            9 DVVKVPPEEFGKDLK---ETVKKILMEKYEGRLDKDVGFVLSIVDVKDIGEGKVVHGDGSAYHP--VVFETLV-YIPEMY   82 (187)
T ss_dssp             EEEEECGGGTTSCHH---HHHHHHHHHHHTTCEETTTEEEEEEEEEEEECCCBCCTTCCSEEEE--EEEEEEE-ECCCTT
T ss_pred             EEEEECHHHhCccHH---HHHHHHHHHHhCCeEcCCccEEEEEEEEeeccCCEEeCCCccEEEE--EEEEEEE-EccCCC
Confidence            578899999999997   799985 8888        88   57776 6777777766555442  2233333 468999


Q ss_pred             cEEEEEEEEEeeceEEEEEcCCeEEEEecccCCCcccc-----------ccccccccCCEEEEEEEEEcc------CCce
Q 002054          685 GIYKGVVTSVKEYGAFVEFNGGQQGLLHVSELSHEPVS-----------RVSDVVSVGQQLSLRCIGQDV------RGNI  747 (974)
Q Consensus       685 ~i~~G~V~~i~~~G~fV~l~~g~~Glvhisels~~~v~-----------~~~~~~~vGd~V~vkVl~id~------~gri  747 (974)
                      ++|+|+|+++.+||+||+|.+ .+||+|+|+++++++.           ++.+.|++||.|+|+|+++|.      .++|
T Consensus        83 ev~~G~V~~v~~~G~fV~l~~-~eglvhis~l~~~~~~~d~~~~~~~~~~~~~~~~~Gd~V~vkV~~vd~~~~~p~~~~I  161 (187)
T 1go3_E           83 ELIEGEVVDVVEFGSFVRLGP-LDGLIHVSQIMDDYVSYDPKREAIIGKETGKVLEIGDYVRARIVAISLKAERKRGSKI  161 (187)
T ss_dssp             CEEEEEEEEEETTEEEEECSS-SEEEEEGGGSCSSCEEECCC--CEEETTTCCEECTTCEEEEEEEEEECCC-----CEE
T ss_pred             CEEEEEEEEEeCcEEEEEEcC-ccEEEEhHHhCCCcceECCccceEEecCCCeEEcCCCEEEEEEEEEEcccCCCCccEE
Confidence            999999999999999999965 9999999999998875           788999999999999999997      3599


Q ss_pred             EEEEeccC
Q 002054          748 KLSLKAVS  755 (974)
Q Consensus       748 ~LS~K~~~  755 (974)
                      .||+|+..
T Consensus       162 ~lS~k~~~  169 (187)
T 1go3_E          162 ALTMRQPY  169 (187)
T ss_dssp             EEECCSTT
T ss_pred             EEEEcCCC
Confidence            99999854

>2b8k_G B16, DNA-directed RNA polymerase II 19 kDa polypeptide; DNA-dependent RNA polymerase, cellular RNA polymerase; 4.15A {Saccharomyces cerevisiae} SCOP: b.40.4.5 d.230.1.1

Probab=99.56  E-value=1.3e-17  Score=174.34  Aligned_cols=145  Identities=12%  Similarity=0.125  Sum_probs=109.9

Q ss_pred             HHHHHHHhcCCCCCCCCCCCcceeeeeccchhhhhcCCCccchhhhhhhhCceEEee-----CCEEEEEecCHHHHHHHH
Q 002054          596 LDHMEREISAPRTQDDRNSPRLATLKYDNDTLRRLIGPLGALKRKIEEETGGRISVS-----DGTLTVVAKNRSVMEKVL  670 (974)
Q Consensus       596 ~~~m~~~i~~~~~~~~~~~p~~~~~~i~~~ki~~vIg~gGk~i~~i~~~~g~~Idi~-----dg~v~i~~~~~~~~~~a~  670 (974)
                      +..|.+++..|+.++++++|++...+|++++++++||++|++|-        .+|++     +|.+.  ..+.  ...+.
T Consensus         4 L~~m~~~I~ipp~~~~~~~p~~i~~~I~~~~ig~vIg~~G~vI~--------~~dI~~~di~dG~I~--~gdg--~~~~~   71 (215)
T 2b8k_G            4 IKDLSLNITLHPSFFGPRMKQYLKTKLLEEVEGSCTGKFGYILC--------VLDYDNIDIQRGRIL--PTDG--SAEFN   71 (215)
T ss_dssp             EECCEEEEEECGGGCSSSHHHHHHHHHHHSSTTCEETTTEEEEE--------ECCSTTCBCCCEEEC--SSSC--CEEEE
T ss_pred             eHHHHhhhhcCHHHHChhHhHHHHhcCCHHHCCeEcCCCCEEEE--------EEEeeecccccceEe--CCCH--HHHHH
Confidence            34567788889899999999999999999999999999999983        33333     46555  2121  11122


Q ss_pred             HHHHHHhhcccccCcEEEEEEEEEeeceEEEEEcCCeEEEEecccCCCcccccc----------ccccccCCEEEEEEEE
Q 002054          671 EKVDFIIGREIEVGGIYKGVVTSVKEYGAFVEFNGGQQGLLHVSELSHEPVSRV----------SDVVSVGQQLSLRCIG  740 (974)
Q Consensus       671 ~~i~~l~~~~~~~G~i~~G~V~~i~~~G~fV~l~~g~~Glvhisels~~~v~~~----------~~~~~vGd~V~vkVl~  740 (974)
                      ..++.+. ..+++|++|+|+|+++++||+||+|.+ .+||||+|+|++.+.-++          ++.+++||.|+|||++
T Consensus        72 v~~~~i~-~~p~vGev~~G~V~~vt~fG~FVelg~-~dGlVhiS~l~d~~~~d~~~~~w~~~~~~~~~~~Gd~VrVkV~~  149 (215)
T 2b8k_G           72 VKYRAVV-FKPFKGEVVDGTVVSCSQHGFEVQVGP-MKVFVTKHLMPQDLTFNAGSNPPSYQSSEDVITIKSRIRVKIEG  149 (215)
T ss_dssp             EECCEEE-ECCCTTEEEEEEEEEEETTEEEEECTT-SEEEEEGGGSCSSCCCBSSCSSCEEECSSCEEETTCEEEEEEEE
T ss_pred             HHhhhhe-eccCCCCEEEEEEEEEecceEEEEecC-cEEEEEHHHCCccceeccccccceeeccccEECCCCEEEEEEEE
Confidence            2233333 468999999999999999999999987 999999999987644222          2679999999999999


Q ss_pred             Ecc-CC---ceEEEEeccC
Q 002054          741 QDV-RG---NIKLSLKAVS  755 (974)
Q Consensus       741 id~-~g---ri~LS~K~~~  755 (974)
                      +|. .+   ++. |||+..
T Consensus       150 vd~~~~~i~~Ig-Smk~~~  167 (215)
T 2b8k_G          150 CISQVSSIHAIG-SIKEDY  167 (215)
T ss_dssp             EEEETTEEEEEE-ECCSTT
T ss_pred             EEcCCCccEEEE-EcCCCC
Confidence            997 32   555 777643

>2eqs_A ATP-dependent RNA helicase DHX8; S1 domain, OB-fold, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.55  E-value=5.7e-15  Score=137.25  Aligned_cols=83  Identities=37%  Similarity=0.637  Sum_probs=76.9

Q ss_pred             cccccCcEEEEEEEEEeeceEEEEEcC---CeEEEEecccC-CCccccccccccccCCEEEEEEEEEccCCceEEEEecc
Q 002054          679 REIEVGGIYKGVVTSVKEYGAFVEFNG---GQQGLLHVSEL-SHEPVSRVSDVVSVGQQLSLRCIGQDVRGNIKLSLKAV  754 (974)
Q Consensus       679 ~~~~~G~i~~G~V~~i~~~G~fV~l~~---g~~Glvhisel-s~~~v~~~~~~~~vGd~V~vkVl~id~~gri~LS~K~~  754 (974)
                      ..+++|++|.|+|++|.+||+||+|.+   +.+||||+|++ ++.++.++.+.|++||.|+|+|+++|. ++|.||+|++
T Consensus         8 ~~~~vG~i~~G~V~~v~~fG~FV~l~~~~~~~~Glvhisel~~~~~~~~~~~~~~~Gd~V~VkV~~vd~-~~i~LSlk~~   86 (103)
T 2eqs_A            8 EEPTIGDIYNGKVTSIMQFGCFVQLEGLRKRWEGLVHISELRREGRVANVADVVSKGQRVKVKVLSFTG-TKTSLSMKDV   86 (103)
T ss_dssp             SSCCTTCEEEEEEEEECSSCEEEEECSSSSCCEEEECGGGTSSSSCCCCHHHHCCTTCEEEEEEEEEET-TEEEEESTTB
T ss_pred             ccCCCCCEEEEEEEEEeccEEEEEEcCCCCCeEEEEEHHHCCCCcccCCcccEeCCCCEEEEEEEEEEC-CeeEEEEeec
Confidence            368999999999999999999999985   89999999999 677888999999999999999999997 7999999999


Q ss_pred             CCCccccc
Q 002054          755 SPRPEADV  762 (974)
Q Consensus       755 ~~~~~~~~  762 (974)
                      .++||...
T Consensus        87 ~~~~~~~~   94 (103)
T 2eqs_A           87 DQETGEDL   94 (103)
T ss_dssp             CTTTCCBC
T ss_pred             ccCCchhc
Confidence            99999764

>1luz_A Protein K3, protein K2; stranded anti-parallel beta barrel, viral protein; 1.80A {Vaccinia virus} SCOP: b.40.4.5

Probab=99.54  E-value=7.2e-15  Score=132.38  Aligned_cols=77  Identities=21%  Similarity=0.349  Sum_probs=71.4

Q ss_pred             cccccCcEEEEEEEEEeeceEEEEEc--CCeEEEEecc-cCCCccccccccccccCCEEEEEEEEEcc-CCceEEEEecc
Q 002054          679 REIEVGGIYKGVVTSVKEYGAFVEFN--GGQQGLLHVS-ELSHEPVSRVSDVVSVGQQLSLRCIGQDV-RGNIKLSLKAV  754 (974)
Q Consensus       679 ~~~~~G~i~~G~V~~i~~~G~fV~l~--~g~~Glvhis-els~~~v~~~~~~~~vGd~V~vkVl~id~-~gri~LS~K~~  754 (974)
                      ..+++|++|.|+|+ |++||+||+|.  ++.+||+|+| +++++++.++++.+ +||.|+|+|+++|. +|+|.||+|++
T Consensus         7 ~~~~vG~~~~G~V~-v~~fG~FVel~~~~~~eGLvhis~el~~~~~~~~~~~~-~Gd~V~VkV~~vd~~~~kI~lslk~~   84 (88)
T 1luz_A            7 SLPNAGDVIKGRVY-EKDYALYIYLFDYPHFEAILAESVKMHMDRYVEYRDKL-VGKTVKVKVIRVDYTKGYIDVNYKRM   84 (88)
T ss_dssp             CCCCTTCEEEEEEE-EETTEEEEEETTCTTSEEEEGGGSSCCHHHHHHHHHHH-TTCEEEEEEEEEETTTTEEEEEEEEE
T ss_pred             cCCCCCCEEEEEEE-EEccEEEEEECCCCCeEEEEEeeHHhCcccccCHhHEe-CCCEEEEEEEEEECCCCEEEEEEeec
Confidence            35789999999999 99999999996  4899999999 99999999999999 99999999999998 79999999998


Q ss_pred             CCC
Q 002054          755 SPR  757 (974)
Q Consensus       755 ~~~  757 (974)
                      .++
T Consensus        85 ~~~   87 (88)
T 1luz_A           85 CRH   87 (88)
T ss_dssp             CSC
T ss_pred             CCC
Confidence            654

>2khi_A 30S ribosomal protein S1; acetylation, phosphoprotein, ribonucleoprotein, RNA-binding; NMR {Escherichia coli}

Probab=99.53  E-value=1.9e-14  Score=136.43  Aligned_cols=84  Identities=33%  Similarity=0.519  Sum_probs=78.7

Q ss_pred             cccccCcEEEEEEEEEeeceEEEEEcCCeEEEEecccCCCc-cccccccccccCCEEEEEEEEEcc-CCceEEEEeccCC
Q 002054          679 REIEVGGIYKGVVTSVKEYGAFVEFNGGQQGLLHVSELSHE-PVSRVSDVVSVGQQLSLRCIGQDV-RGNIKLSLKAVSP  756 (974)
Q Consensus       679 ~~~~~G~i~~G~V~~i~~~G~fV~l~~g~~Glvhisels~~-~v~~~~~~~~vGd~V~vkVl~id~-~gri~LS~K~~~~  756 (974)
                      .++++|++|.|+|+++.+||+||+|.++.+||||+|+++++ +..++.+.|++||.|+|+|+++|. +++|.||+|++.+
T Consensus        26 ~~~~~G~~~~G~V~~v~~~G~FV~l~~~~~Glvhisel~~~~~~~~~~~~~~vGd~V~vkV~~vd~~~~rI~lslk~~~~  105 (115)
T 2khi_A           26 KRYPEGTKLTGRVTNLTDYGCFVEIEEGVEGLVHVSEMDWTNKNIHPSKVVNVGDVVEVMVLDIDEERRRISLGLKQCKA  105 (115)
T ss_dssp             CSSCSSCEEEEEEEEEETTEEEEECSTTCEEEEETTSSSCSSTTCSSTTTCCTTCEEEEEEEEEETTTTEEEECCCCCCS
T ss_pred             hcCCCCCEEEEEEEEEECCEEEEEECCCCEEEEEHHHCCccccccCcccEECCCCEEEEEEEEEECCCCEEEEEEEecCc
Confidence            46899999999999999999999999999999999999984 788899999999999999999998 7999999999999


Q ss_pred             Cccccc
Q 002054          757 RPEADV  762 (974)
Q Consensus       757 ~~~~~~  762 (974)
                      +||+..
T Consensus       106 ~p~~~~  111 (115)
T 2khi_A          106 NPWQQF  111 (115)
T ss_dssp             SCCCCC
T ss_pred             CHHHHH
Confidence            999864

>3go5_A Multidomain protein with S1 RNA-binding domains; structural genomics, joint center for structural genomics, JCSG; HET: MSE; 1.40A {Streptococcus pneumoniae}

Probab=99.52  E-value=2e-14  Score=156.72  Aligned_cols=136  Identities=15%  Similarity=0.084  Sum_probs=108.0

Q ss_pred             ccccCcEEEEEEEEEe-eceEEEEEcC-CeEEEEecccCCCccccccccccccCCEEEEEEEEEccCCceEEEEecc-CC
Q 002054          680 EIEVGGIYKGVVTSVK-EYGAFVEFNG-GQQGLLHVSELSHEPVSRVSDVVSVGQQLSLRCIGQDVRGNIKLSLKAV-SP  756 (974)
Q Consensus       680 ~~~~G~i~~G~V~~i~-~~G~fV~l~~-g~~Glvhisels~~~v~~~~~~~~vGd~V~vkVl~id~~gri~LS~K~~-~~  756 (974)
                      .+++|+++.|+|++++ +||+||++.. +.+||||+||++|.+..    .+++||.+.|+ +.+|+++||.||+|+. ..
T Consensus        66 ~~~~G~~~~g~V~~v~~~~GaFVdiG~~~~d~lvp~sel~~~~~~----~~~~Gd~v~v~-l~iD~~~Ri~ls~k~~~~~  140 (285)
T 3go5_A           66 TATQDQFGWGRVTEVRKDLGVFVDTGLPDKEIVVSLDILPELKEL----WPKKGDQLYIR-LEVDKKDRIWGLLAYQEDF  140 (285)
T ss_dssp             CSCSSSCEEEEEEEEETTTEEEEECSCTTCCEEEEGGGSCSSGGG----SCCTTCEEEEE-EEECTTSCEEEEECCHHHH
T ss_pred             cccCCCEEEEEEEEEccCceEEEEECCCCcEEEEEHHHCCccccc----ccCCCCEEEEE-EEECCCCcEEEEehhhhhc
Confidence            4689999999999999 7999999975 69999999999986533    47899999766 6899989999999864 23


Q ss_pred             Ccccc------cCceE---------EEEEe-ecCCcceeeEEeeccCCCCCCCCCCCCCCCCCcccCCCCcceEEEeecc
Q 002054          757 RPEAD------VKGVV---------EGSVP-VNKQATDVWASVGDVSNGQNPELPMRKNETPGVNSSTSSTPAVLIRSAA  820 (974)
Q Consensus       757 ~~~~~------~g~~~---------~G~vv-~i~~gv~~~~~~~~l~~~~~~~lp~~~~~~~~~~~~~G~~v~v~Ir~~l  820 (974)
                      +||..      .|+.+         +|.|+ .+.+|+.||+|.++++                ..+++||.|+++|   +
T Consensus       141 ~~~~~~~~~~~~G~~V~g~V~~i~~~G~fV~~i~~g~~Glih~SEl~----------------~~l~~Gd~v~~~V---~  201 (285)
T 3go5_A          141 QRLARPAYNNMQNQNWPAIVYRLKLSGTFVYLPENNMLGFIHPSERY----------------AEPRLGQVLDARV---I  201 (285)
T ss_dssp             HHHCCCCCSCCTTCEEEEEEEEEETTEEEEEETTTTEEEEECGGGCS----------------SCCCTTCEEEEEE---E
T ss_pred             chhhhhhhhCCCCCEEEEEEEEEeCCcEEEEEeCCCeEEEEEHHHcc----------------ccCCCCCEEEEEE---E
Confidence            45543      35444         45566 6556666666666665                3468999999999   9


Q ss_pred             ccccccccccccccccccc
Q 002054          821 ECDEEEKASGFSQSSKSTL  839 (974)
Q Consensus       821 ~iD~~~r~i~ls~k~~~~~  839 (974)
                      ++|++++||+||+++....
T Consensus       202 ~id~~d~kI~LSlk~~~~~  220 (285)
T 3go5_A          202 GFREVDRTLNLSLKPRSFE  220 (285)
T ss_dssp             EEETTTTEEEEECSCCCCC
T ss_pred             EEECCCCeEEEEeChhhhh
Confidence            9999999999999976543

>2k4k_A GSP13, general stress protein 13; cytoplasm, stress response, RNA binding protein; NMR {Bacillus subtilis}

Probab=99.51  E-value=1.9e-14  Score=139.25  Aligned_cols=82  Identities=38%  Similarity=0.733  Sum_probs=77.9

Q ss_pred             cccccCcEEEEEEEEEeeceEEEEEcCCeEEEEecccCCCccccccccccccCCEEEEEEEEEcc-CCceEEEEeccCCC
Q 002054          679 REIEVGGIYKGVVTSVKEYGAFVEFNGGQQGLLHVSELSHEPVSRVSDVVSVGQQLSLRCIGQDV-RGNIKLSLKAVSPR  757 (974)
Q Consensus       679 ~~~~~G~i~~G~V~~i~~~G~fV~l~~g~~Glvhisels~~~v~~~~~~~~vGd~V~vkVl~id~-~gri~LS~K~~~~~  757 (974)
                      .++++|++|.|+|++|++||+||+|.++.+||||+|++++.++.++.+.|++||.|+|+|+++|. +|+|.||+|.+.++
T Consensus         3 ~~~~vG~iv~G~V~~i~~~G~FV~l~~~~~Glihisel~~~~~~~~~~~~~vGd~V~vkV~~vd~~~~kI~LSlk~~~~~   82 (130)
T 2k4k_A            3 AKFEVGSVYTGKVTGLQAYGAFVALDEETQGLVHISEVTHGFVKDINEHLSVGDEVQVKVLAVDEEKGKISLSIRATQAA   82 (130)
T ss_dssp             CCCCTTCEEEEEEEEEETTEEEEEEETTEEEEEEGGGTSSSCCSCGGGTCCTTCEEEEEEEEEETTTTEEEEESHHHHHS
T ss_pred             CcCCCCCEEEEEEEEEeCCeEEEEECCCcEEEEEHHHCCcccccCccccCCCCCEEEEEEEEEeCCCCEEEEEEeecccC
Confidence            46899999999999999999999999999999999999999999999999999999999999998 89999999999888


Q ss_pred             ccc
Q 002054          758 PEA  760 (974)
Q Consensus       758 ~~~  760 (974)
                      |+.
T Consensus        83 p~~   85 (130)
T 2k4k_A           83 PEK   85 (130)
T ss_dssp             CCC
T ss_pred             ccc
Confidence            865

>2a19_A EIF-2- alpha, eukaryotic translation initiation factor 2 alpha; transferase, protein biosynthesis, protein synthesis transferase complex; HET: TPO ANP; 2.50A {Saccharomyces cerevisiae} PDB: 2a1a_A* 1q46_A

Probab=99.50  E-value=1.4e-14  Score=146.83  Aligned_cols=93  Identities=24%  Similarity=0.329  Sum_probs=76.2

Q ss_pred             cccCcEEEEEEEEEeeceEEEEE--cCCeEEEEecccCCCccccccccccccCCEEEEEEEEEcc-CCceEEEEeccCCC
Q 002054          681 IEVGGIYKGVVTSVKEYGAFVEF--NGGQQGLLHVSELSHEPVSRVSDVVSVGQQLSLRCIGQDV-RGNIKLSLKAVSPR  757 (974)
Q Consensus       681 ~~~G~i~~G~V~~i~~~G~fV~l--~~g~~Glvhisels~~~v~~~~~~~~vGd~V~vkVl~id~-~gri~LS~K~~~~~  757 (974)
                      +++|++|.|+|++|++||+||+|  +++++||||+|+++++++.++.+.|++||.|+|+|+++|. +|+|.||+|++.++
T Consensus        13 p~~G~iv~G~V~~i~~fGaFV~L~e~~gveGLvhiSels~~~v~~~~~~~~vGd~V~vkVl~vd~~~~~I~LSlk~~~~~   92 (175)
T 2a19_A           13 PEIDDIVMVNVQQIAEMGAYVKLLEYDNIEGMILLSELSRRRIRSIQKLIRVGKNDVAVVLRVDKEKGYIDLSKRRVSSE   92 (175)
T ss_dssp             CCTTCEEEEEEEEEETTEEEEEETTTTTCEEEEECC--------CCCCCCCTTSEEEEEEEEEETTTTEEEEESTTCCHH
T ss_pred             CCCCCEEEEEEEEEecceEEEEEcCCCCcEEEEEHHHcCCcccCCHHHcCCCCCEEEEEEEEEECCCCeEEEEEEecCcC
Confidence            35999999999999999999999  4799999999999999999999999999999999999998 78999999999999


Q ss_pred             cccc------cCceEEEEEeec
Q 002054          758 PEAD------VKGVVEGSVPVN  773 (974)
Q Consensus       758 ~~~~------~g~~~~G~vv~i  773 (974)
                      ||..      .|..+.|.|..+
T Consensus        93 ~~~~~~~~~~~g~~v~g~V~~i  114 (175)
T 2a19_A           93 DIIKCEEKYQKSKTVHSILRYC  114 (175)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHH
T ss_pred             hHHHHHHhccCCCcceEEEEEc
Confidence            9985      355666766654

>1whu_A Polynucleotide phosphorylase; 3'-5' RNA exonuclease; pnpase, alpha-helical domain, structural genomics; NMR {Mus musculus} SCOP: a.4.9.1

Probab=99.50  E-value=1e-13  Score=128.91  Aligned_cols=92  Identities=29%  Similarity=0.321  Sum_probs=80.5

Q ss_pred             cCCCHHHHHHHHHHHHHHHHhhhcCCCCChhHHHHHHHHHHHHHHHHhhhccchhhhchHHHHHHHHHHHHHHHHHHhcC
Q 002054          289 SMISEQTLEKVSNLAEAHIEAVFTDPSYSKFERGEALDKIGQDVKKALEEECDEESLQVLPKAVDTVRKRVIRKRIIAEG  368 (974)
Q Consensus       289 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~k~~r~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~r~~il~~~  368 (974)
                      +..+++|.++|++++.++|++|+++..++|++|+++++++++++.++|.++..+.....+..+|++++++.+|++||++|
T Consensus        12 ~~~~~el~~~V~~~~~~~l~~A~~~~~~~K~eR~~al~~ik~~v~~~l~~e~~~~~~~~i~~~~~~lek~~vR~~IL~e~   91 (104)
T 1whu_A           12 FTPSAEIVKYTKIIAMEKLYAVFTDYEHDKVSRDEAVNKIRLDTEEHLKEKFPEVDQFEIIESFNIVAKEVFRSIILNEY   91 (104)
T ss_dssp             CCCCHHHHHHHHHHHHHHHHHHHSSCCSCSHHHHHHHHHHHHHHHHHHTTTCSSSCHHHHHHHHHHHHHHHHHHHHTTSS
T ss_pred             CCCCHHHHHHHHHHHHHHHHHHHHcccccHHHHHHHHHHHHHHHHHHHHhhcccccHHHHHHHHHHHHHHHHHHHHHCCC
Confidence            45678999999999999999999943469999999999999999999954322223457999999999999999999999


Q ss_pred             CcCCCCCCCCcc
Q 002054          369 VRVDGRQLDEVR  380 (974)
Q Consensus       369 ~R~DGR~~~e~R  380 (974)
                      +|+|||.++|+|
T Consensus        92 ~RiDGR~~deIr  103 (104)
T 1whu_A           92 KRCDGRDSGPSS  103 (104)
T ss_dssp             CSCCCCCSSCSC
T ss_pred             cCCCCCCccccc
Confidence            999999999998

>2cqo_A Nucleolar protein of 40 kDa; S1 domain, OB-fold, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.50  E-value=1.6e-14  Score=137.53  Aligned_cols=84  Identities=32%  Similarity=0.576  Sum_probs=77.1

Q ss_pred             cccccCcEEEEEEEEEeeceEEEEEcC-CeEEEEecccCCCccccccccccccCCEEEEEEEEEcc---CCceEEEEecc
Q 002054          679 REIEVGGIYKGVVTSVKEYGAFVEFNG-GQQGLLHVSELSHEPVSRVSDVVSVGQQLSLRCIGQDV---RGNIKLSLKAV  754 (974)
Q Consensus       679 ~~~~~G~i~~G~V~~i~~~G~fV~l~~-g~~Glvhisels~~~v~~~~~~~~vGd~V~vkVl~id~---~gri~LS~K~~  754 (974)
                      ..+++|++|.|+|++|.+||+||+|.+ +.+||||+|++++.++.++.+.|++||.|+|+|+++|.   +++|.||+|++
T Consensus        18 ~~~~vG~iv~G~V~~I~~fGaFV~l~g~~~~Glvhisel~~~~~~~~~~~~~~Gd~V~VkV~~vd~~~~~~~i~LSlk~~   97 (119)
T 2cqo_A           18 NLPALYTIFQGEVAMVTDYGAFIKIPGCRKQGLVHRTHMSSCRVDKPSEIVDVGDKVWVKLIGREMKNDRIKVSLSMKVV   97 (119)
T ss_dssp             CSCCTTCEEEEEEEEEETTEEEEECTTCSSCEEEEHHHHCSSCCSCHHHHCCTTCEEEEEEEEEEECSSCEEEEEESTTB
T ss_pred             cccCCCCEEEEEEEEEeCceEEEEECCCcEEEEEEHHHCCcccccChhhcCCCCCEEEEEEEEEeccccCceEEEEEeec
Confidence            468999999999999999999999954 36999999999999999999999999999999999996   26999999999


Q ss_pred             CCCccccc
Q 002054          755 SPRPEADV  762 (974)
Q Consensus       755 ~~~~~~~~  762 (974)
                      .++||+..
T Consensus        98 ~~~~~~~~  105 (119)
T 2cqo_A           98 NQGTGKDL  105 (119)
T ss_dssp             CSSSCCBS
T ss_pred             ccCCcccc
Confidence            99999763

>2k52_A Uncharacterized protein MJ1198; metal-binding, zinc, zinc-finger, structural genomics, PSI-2, protein structure initiative; NMR {Methanocaldococcus jannaschii}

Probab=99.48  E-value=1.4e-13  Score=121.90  Aligned_cols=73  Identities=27%  Similarity=0.559  Sum_probs=67.5

Q ss_pred             ccccCcEEEEEEEEEeeceEEEEEcCCeEEEEecccCCCccccccccccccCCEEEEEEEEEcc-CCceEEEEeccCC
Q 002054          680 EIEVGGIYKGVVTSVKEYGAFVEFNGGQQGLLHVSELSHEPVSRVSDVVSVGQQLSLRCIGQDV-RGNIKLSLKAVSP  756 (974)
Q Consensus       680 ~~~~G~i~~G~V~~i~~~G~fV~l~~g~~Glvhisels~~~v~~~~~~~~vGd~V~vkVl~id~-~gri~LS~K~~~~  756 (974)
                      ++++|++|.|+|+++.+||+||+|.++.+||+|+|++++.++    +.|++||.|+|+|+++|. +|+|.||+|.+.+
T Consensus         2 ~~~~G~iv~G~V~~v~~~G~fV~l~~~~~Gllh~sel~~~~~----~~~~~Gd~V~v~V~~vd~~~~~i~lsl~~~~~   75 (80)
T 2k52_A            2 DVEPGKFYKGVVTRIEKYGAFINLNEQVRGLLRPRDMISLRL----ENLNVGDEIIVQAIDVRPEKREIDFKYIPLEH   75 (80)
T ss_dssp             CCCTTCEEEEEEEEEETTEEEEEEETTEEEEECGGGCSSCCG----GGCCTTCEEEEEEEEEETTTTEEEEEECSCC-
T ss_pred             CCCCCCEEEEEEEEEeCCEEEEEECCCCEEEEEHHHCCcccc----eeeCCCCEEEEEEEEEECCCCEEEEEEeeccc
Confidence            578999999999999999999999989999999999998876    679999999999999998 5999999998764

>2khj_A 30S ribosomal protein S1; OB fold, acetylation, phosphoprotein, ribonucleoprotein, RNA-binding; NMR {Escherichia coli}

Probab=99.43  E-value=1.3e-13  Score=129.40  Aligned_cols=78  Identities=35%  Similarity=0.461  Sum_probs=73.5

Q ss_pred             cccccCcEEEEEEEEEeeceEEEEEcCCeEEEEecccCCCccccccccccccCCEEEEEEEEEccC-CceEEEEeccCC
Q 002054          679 REIEVGGIYKGVVTSVKEYGAFVEFNGGQQGLLHVSELSHEPVSRVSDVVSVGQQLSLRCIGQDVR-GNIKLSLKAVSP  756 (974)
Q Consensus       679 ~~~~~G~i~~G~V~~i~~~G~fV~l~~g~~Glvhisels~~~v~~~~~~~~vGd~V~vkVl~id~~-gri~LS~K~~~~  756 (974)
                      .++++|++|.|+|+++.+||+||+|.++.+||||+|++++.++.++.+.|++||.|+|+|+++|.. ++|.||+|.+.+
T Consensus        27 ~~~~~G~iv~G~V~~v~~~G~fV~l~~~~~Gll~~sel~~~~~~~~~~~~~vGd~V~v~V~~vd~~~~ki~LS~k~~~~  105 (109)
T 2khj_A           27 ALNKKGAIVTGKVTAVDAKGATVELADGVEGYLRASEASRDRVEDATLVLSVGDEVEAKFTGVDRKNRAISLSVRAKDE  105 (109)
T ss_dssp             TTCCSSSEEEEEEEEECSSCEEEECSTTCBCCBCTTCCCSSSSSSGGGSCCTTCEEEEEEEEEETTTTEEEEETTSSSS
T ss_pred             hcCCCCCEEEEEEEEEECCeEEEEECCCCEEEEEHHHcCcccccChhhccCCCCEEEEEEEEEECCCCEEEEEEeecCh
Confidence            578999999999999999999999998999999999999999999999999999999999999984 589999998754

>2c35_B Human RPB7, DNA-directed RNA polymerase II 19 kDa polypeptide; transcription, nucleotidyltransferase; 2.70A {Homo sapiens} SCOP: b.40.4.5 d.230.1.1

Probab=99.42  E-value=2.9e-15  Score=152.27  Aligned_cols=142  Identities=18%  Similarity=0.163  Sum_probs=104.4

Q ss_pred             HHHHHHhcCCCCCCCCCCCcceeeeeccchhhhhcCCCccchhhhhhhhCceEEee---CCEEEEEecCHHHHHHHHHHH
Q 002054          597 DHMEREISAPRTQDDRNSPRLATLKYDNDTLRRLIGPLGALKRKIEEETGGRISVS---DGTLTVVAKNRSVMEKVLEKV  673 (974)
Q Consensus       597 ~~m~~~i~~~~~~~~~~~p~~~~~~i~~~ki~~vIg~gGk~i~~i~~~~g~~Idi~---dg~v~i~~~~~~~~~~a~~~i  673 (974)
                      ..|++++..|+.++++++|+....++++++++++||++|++|        +.++++   +|.+.  ..+.  ...+...+
T Consensus         5 ~~m~~~I~~~p~~~~~~~~~~i~~~l~~~~~~~vi~~~G~~I--------~~~di~~i~~g~i~--~~d~--~~~~~~~~   72 (172)
T 2c35_B            5 ISLEHEILLHPRYFGPNLLNTVKQKLFTEVEGTCTGKYGFVI--------AVTTIDNIGAGVIQ--PGRG--FVLYPVKY   72 (172)
T ss_dssp             EEEEEEEEECGGGCCSCHHHHHHHHHHHHHTTCEETTTEEEE--------EEEEEEEECCCBCC--TTCS--SEEEEEEE
T ss_pred             EEEeEEEEECHHHhCChHHHHHHHHHHHHHcCcCcCCceEEE--------EEEEeeecCCeEEe--CCCC--CEEEEEEE
Confidence            345667888888999999999999999999999999999988        344443   46544  2221  11111112


Q ss_pred             HHHhhcccccCcEEEEEEEEEeeceEEEEEcCCeEEEEecccCCCcccccc------------ccccccCCEEEEEEEEE
Q 002054          674 DFIIGREIEVGGIYKGVVTSVKEYGAFVEFNGGQQGLLHVSELSHEPVSRV------------SDVVSVGQQLSLRCIGQ  741 (974)
Q Consensus       674 ~~l~~~~~~~G~i~~G~V~~i~~~G~fV~l~~g~~Glvhisels~~~v~~~------------~~~~~vGd~V~vkVl~i  741 (974)
                      +.+. ..+++|++|+|+|+++++||+||+|. ..+||||+|++++.+.-++            .+++++||.|+|||+++
T Consensus        73 ~~~~-~~~~~Gev~~G~V~~v~~fG~fV~l~-~~~glvhis~l~~~~~~d~~~~~~~~~~~~~~~~~~~Gd~V~vkV~~v  150 (172)
T 2c35_B           73 KAIV-FRPFKGEVVDAVVTQVNKVGLFTEIG-PMSCFISRHSIPSEMEFDPNSNPPCYKTMDEDIVIQQDDEIRLKIVGT  150 (172)
T ss_dssp             EEEE-ECCCTTCEEEEEEEEEETTEEEEEET-TEEEEEEGGGSCTTEEEESSSSSCEEEETTSCSEEETTCEEEEEEEEE
T ss_pred             EEEE-eeCCCCCEEEEEEEEEeCCEEEEEEC-CEEEEEEHHHCCCCcEECCCCCccEEEeCCCCEEECCCCEEEEEEEEE
Confidence            2222 35789999999999999999999995 5679999999976533222            45799999999999999


Q ss_pred             ccC-C---ceEEEEec
Q 002054          742 DVR-G---NIKLSLKA  753 (974)
Q Consensus       742 d~~-g---ri~LS~K~  753 (974)
                      |.. +   ++. |||+
T Consensus       151 d~~~~~~~~ig-sm~~  165 (172)
T 2c35_B          151 RVDKNDIFAIG-SLMD  165 (172)
T ss_dssp             EEETTEEEEEE-ECCS
T ss_pred             EcCCCCcEEEE-EecC
Confidence            973 3   343 6654

>1q8k_A Eukaryotic translation initiation factor 2 subunit 1; NMR {Homo sapiens} SCOP: a.60.14.1 b.40.4.5 d.58.51.1

Probab=99.34  E-value=8.5e-13  Score=144.71  Aligned_cols=94  Identities=27%  Similarity=0.400  Sum_probs=85.8

Q ss_pred             ccccCcEEEEEEEEEeeceEEEEEc--CCeEEEEecccCCCccccccccccccCCEEEEEEEEEcc-CCceEEEEeccCC
Q 002054          680 EIEVGGIYKGVVTSVKEYGAFVEFN--GGQQGLLHVSELSHEPVSRVSDVVSVGQQLSLRCIGQDV-RGNIKLSLKAVSP  756 (974)
Q Consensus       680 ~~~~G~i~~G~V~~i~~~G~fV~l~--~g~~Glvhisels~~~v~~~~~~~~vGd~V~vkVl~id~-~gri~LS~K~~~~  756 (974)
                      .+++|++|.|+|++|.+||+||+|.  ++++||||+|+++|+++.++.+.|++||.|+|+|+++|+ +++|.||+|.+.+
T Consensus        10 ~~~vG~iv~G~V~~I~~fGaFV~L~ey~gveGLvhiSels~~~i~~~~~~~kvGd~V~VkVl~vD~~~~rI~LSlK~~~~   89 (308)
T 1q8k_A           10 FPEVEDVVMVNVRSIQEMGAYVSLLEYNNIEGMIHLSELSRRRIRSINKLIRIGRNECVKVIRVDKEKGYIDLSKRRVSP   89 (308)
T ss_dssp             CCSSCCEEEEEEEEEETTEEEEESCTTTSCCEEECGGGTSCSSCSCCTTTCSSSCEEEEEEEEEETTTTEEEEECSSCCH
T ss_pred             CCCCCCEEEEEEEEEeCcEEEEEECCCCCeEEEEEhHHcCcccccCHHHhcCCCCEEEEEEEEEeCCCCEEEEEEEeccc
Confidence            4679999999999999999999997  789999999999999999999999999999999999998 7999999999998


Q ss_pred             Ccccc------cCceEEEEEeec
Q 002054          757 RPEAD------VKGVVEGSVPVN  773 (974)
Q Consensus       757 ~~~~~------~g~~~~G~vv~i  773 (974)
                      +||..      .|..+.|.|..+
T Consensus        90 ~p~~~~~~~~~~G~~v~G~V~~v  112 (308)
T 1q8k_A           90 EEAIKCEDKFTKSKTVYSILRHV  112 (308)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             ChHHHHHHHccCCCeeEEEEEEc
Confidence            89976      366677777774

>2khj_A 30S ribosomal protein S1; OB fold, acetylation, phosphoprotein, ribonucleoprotein, RNA-binding; NMR {Escherichia coli}

Probab=99.33  E-value=1.3e-12  Score=122.61  Aligned_cols=80  Identities=25%  Similarity=0.278  Sum_probs=64.5

Q ss_pred             cccccccccc--ccccCCCCCEEEEEEEEEeCCeEEEEeCCCeEEEEecccCC-------CCCCCCCCEEEEEEEEEeCC
Q 002054          894 NKGTRVEAIV--SAKNLKLGTKVAAKVYQVRARGLVLDLGGGIRGMYRFENNE-------KKDFVVGDELLVKCSSFTGK  964 (974)
Q Consensus       894 slK~~~~~p~--~~~~~~vG~vV~G~V~~I~~~GvFV~L~~gv~Glih~se~~-------~~~f~vGd~V~vkVl~id~~  964 (974)
                      |+|++..+||  ...++++|++|+|+|++|++||+||+|++++.||+|.+++.       .+.|++||+|+|+|+++|.+
T Consensus        13 ~iKq~~~~p~~~~~~~~~~G~iv~G~V~~v~~~G~fV~l~~~~~Gll~~sel~~~~~~~~~~~~~vGd~V~v~V~~vd~~   92 (109)
T 2khj_A           13 GLVPRGSHMFNNWVALNKKGAIVTGKVTAVDAKGATVELADGVEGYLRASEASRDRVEDATLVLSVGDEVEAKFTGVDRK   92 (109)
T ss_dssp             --------CHHHHTTTCCSSSEEEEEEEEECSSCEEEECSTTCBCCBCTTCCCSSSSSSGGGSCCTTCEEEEEEEEEETT
T ss_pred             chhhcccCHHHHHhhcCCCCCEEEEEEEEEECCeEEEEECCCCEEEEEHHHcCcccccChhhccCCCCEEEEEEEEEECC
Confidence            8999999999  57799999999999999999999999999999999999874       23699999999999999988


Q ss_pred             C-ceeeeecC
Q 002054          965 G-IPVVSLVD  973 (974)
Q Consensus       965 ~-~~~~~~~~  973 (974)
                      + ...+|+..
T Consensus        93 ~~ki~LS~k~  102 (109)
T 2khj_A           93 NRAISLSVRA  102 (109)
T ss_dssp             TTEEEEETTS
T ss_pred             CCEEEEEEee
Confidence            6 67777653

>3aev_A Translation initiation factor 2 subunit alpha; proteins-rRNA complex, 16S rRNA, RNA-binding; 2.80A {Pyrococcus horikoshii} PDB: 1yz6_A

Probab=99.33  E-value=1.2e-12  Score=141.80  Aligned_cols=93  Identities=27%  Similarity=0.461  Sum_probs=82.4

Q ss_pred             ccccCcEEEEEEEEEeeceEEEEEc--CCeEEEEecccCCCccccccccccccCCEEEEEEEEEcc-CCceEEEEeccCC
Q 002054          680 EIEVGGIYKGVVTSVKEYGAFVEFN--GGQQGLLHVSELSHEPVSRVSDVVSVGQQLSLRCIGQDV-RGNIKLSLKAVSP  756 (974)
Q Consensus       680 ~~~~G~i~~G~V~~i~~~G~fV~l~--~g~~Glvhisels~~~v~~~~~~~~vGd~V~vkVl~id~-~gri~LS~K~~~~  756 (974)
                      .+++|++|.|+|++|.+||+||+|.  ++.+||||+|+++++++.++.+.|++||.|.|+|+++|. +|+|.||+|++.+
T Consensus         8 ~p~~Gdiv~G~V~~I~~fGaFV~L~e~~gieGlIhiSels~~~v~~~~~~~kvGd~V~vkVi~vD~~~~~I~LSlk~~~~   87 (275)
T 3aev_A            8 YPEEGEFVVATVKRIHNYGAFLELDEYPGKEAFMHISEVASTWVRNIRDYLKEGQKVVAKVIRVDPRKGHIDLSLRRVTQ   87 (275)
T ss_dssp             CCCTTCEEEEEEEEEETTEEEEEETTSTTCEEEEEGGGSCSSCCSCGGGTCCTTCEEEEEEEEEETTTTEEEEESTTCCH
T ss_pred             CCCCCCEEEEEEEEEECcEEEEEECCCCCeEEEEEHHHcCcccccCHHhccCCCCEEEEEEEEEECCCCEEEEEEeecCc
Confidence            3579999999999999999999997  689999999999999999999999999999999999998 8999999999988


Q ss_pred             Ccccc------cCceEEEEEee
Q 002054          757 RPEAD------VKGVVEGSVPV  772 (974)
Q Consensus       757 ~~~~~------~g~~~~G~vv~  772 (974)
                      +||..      .|..+.|.+..
T Consensus        88 ~~~~~~~~~~~~g~~v~g~v~~  109 (275)
T 3aev_A           88 QQRKAKLQEFKRAQKAENLLRL  109 (275)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHH
T ss_pred             chhHHHHHhccCCCeEEEEEEE
Confidence            88874      24444454444

>2khi_A 30S ribosomal protein S1; acetylation, phosphoprotein, ribonucleoprotein, RNA-binding; NMR {Escherichia coli}

Probab=99.33  E-value=4.3e-12  Score=120.18  Aligned_cols=80  Identities=19%  Similarity=0.206  Sum_probs=63.5

Q ss_pred             ccccccccccc--cccCCCCCEEEEEEEEEeCCeEEEEeCCCeEEEEecccCCC--------CCCCCCCEEEEEEEEEeC
Q 002054          894 NKGTRVEAIVS--AKNLKLGTKVAAKVYQVRARGLVLDLGGGIRGMYRFENNEK--------KDFVVGDELLVKCSSFTG  963 (974)
Q Consensus       894 slK~~~~~p~~--~~~~~vG~vV~G~V~~I~~~GvFV~L~~gv~Glih~se~~~--------~~f~vGd~V~vkVl~id~  963 (974)
                      |+|++..+||.  ..++++|+++.|+|++|++||+||+|++++.||+|.|++..        +.|++||+|+|+|+++|.
T Consensus        12 ~~k~~~~~p~~~~~~~~~~G~~~~G~V~~v~~~G~FV~l~~~~~Glvhisel~~~~~~~~~~~~~~vGd~V~vkV~~vd~   91 (115)
T 2khi_A           12 SGLVPRGSHWVAIAKRYPEGTKLTGRVTNLTDYGCFVEIEEGVEGLVHVSEMDWTNKNIHPSKVVNVGDVVEVMVLDIDE   91 (115)
T ss_dssp             ---------CCCSSCSSCSSCEEEEEEEEEETTEEEEECSTTCEEEEETTSSSCSSTTCSSTTTCCTTCEEEEEEEEEET
T ss_pred             chhhcccCCHHHHhhcCCCCCEEEEEEEEEECCEEEEEECCCCEEEEEHHHCCccccccCcccEECCCCEEEEEEEEEEC
Confidence            78999999994  57899999999999999999999999999999999998743        369999999999999998


Q ss_pred             -CCceeeeecC
Q 002054          964 -KGIPVVSLVD  973 (974)
Q Consensus       964 -~~~~~~~~~~  973 (974)
                       ++...+|+.+
T Consensus        92 ~~~rI~lslk~  102 (115)
T 2khi_A           92 ERRRISLGLKQ  102 (115)
T ss_dssp             TTTEEEECCCC
T ss_pred             CCCEEEEEEEe
Confidence             5788888764

>3cw2_C Translation initiation factor 2 subunit alpha; AIF2, intact AIF2, initiation factor 2 alpha subunit, initiation factor 2 beta subunit; 2.80A {Sulfolobus solfataricus} PDB: 2aho_B 3v11_B*

Probab=99.25  E-value=1.7e-12  Score=140.20  Aligned_cols=82  Identities=29%  Similarity=0.463  Sum_probs=78.3

Q ss_pred             ccccCcEEEEEEEEEeeceEEEEEc--CCeEEEEecccCCCccccccccccccCCEEEEEEEEEcc-CCceEEEEeccCC
Q 002054          680 EIEVGGIYKGVVTSVKEYGAFVEFN--GGQQGLLHVSELSHEPVSRVSDVVSVGQQLSLRCIGQDV-RGNIKLSLKAVSP  756 (974)
Q Consensus       680 ~~~~G~i~~G~V~~i~~~G~fV~l~--~g~~Glvhisels~~~v~~~~~~~~vGd~V~vkVl~id~-~gri~LS~K~~~~  756 (974)
                      .+++|++|.|+|++|.+||+||+|.  ++.+||||+|+++++++.++.+.|++||.|.|+|+++|. +|++.||+|.+.+
T Consensus         8 ~~~vG~iv~G~V~~I~~~GaFV~l~e~~~~~GlihiSels~~~v~~~~~~~~vGd~V~VkVi~vd~~~g~I~LSlk~~~~   87 (266)
T 3cw2_C            8 LPSEGEILIATVKQVFDYGSYVSLDEYGGLQAFLPWSEVSSKWVKNIRDVLKENRKVIVKVIRVDRRKGTVDVSLKKVTD   87 (266)
T ss_dssp             SCCTTCEEEEEEEECCSSSBEEEETTTTSEECBBCGGGSSCSSCCCHHHHSCTTCEEEEEECCCCSSSCCCBEESTTSCT
T ss_pred             cCCCCCEEEEEEEEEeccEEEEEEcCCCCeEEEEEhHHcCcccccCHHHhCcCCCEEEEEEEEEeCCCCEEEEEEEecch
Confidence            5789999999999999999999997  799999999999999999999999999999999999998 8999999999999


Q ss_pred             Ccccc
Q 002054          757 RPEAD  761 (974)
Q Consensus       757 ~~~~~  761 (974)
                      +||..
T Consensus        88 ~~~~~   92 (266)
T 3cw2_C           88 DERRK   92 (266)
T ss_dssp             THHHH
T ss_pred             hhHHH
Confidence            99965

>2k52_A Uncharacterized protein MJ1198; metal-binding, zinc, zinc-finger, structural genomics, PSI-2, protein structure initiative; NMR {Methanocaldococcus jannaschii}

Probab=99.24  E-value=2.8e-11  Score=106.95  Aligned_cols=67  Identities=18%  Similarity=0.305  Sum_probs=61.9

Q ss_pred             cCCCCCEEEEEEEEEeCCeEEEEeCCCeEEEEecccCCC---CCCCCCCEEEEEEEEEeCC-CceeeeecC
Q 002054          907 NLKLGTKVAAKVYQVRARGLVLDLGGGIRGMYRFENNEK---KDFVVGDELLVKCSSFTGK-GIPVVSLVD  973 (974)
Q Consensus       907 ~~~vG~vV~G~V~~I~~~GvFV~L~~gv~Glih~se~~~---~~f~vGd~V~vkVl~id~~-~~~~~~~~~  973 (974)
                      ++++|++++|+|+++++||+||+|++++.||+|.|++..   +.|++||+|+|+|+++|++ ++..+|+..
T Consensus         2 ~~~~G~iv~G~V~~v~~~G~fV~l~~~~~Gllh~sel~~~~~~~~~~Gd~V~v~V~~vd~~~~~i~lsl~~   72 (80)
T 2k52_A            2 DVEPGKFYKGVVTRIEKYGAFINLNEQVRGLLRPRDMISLRLENLNVGDEIIVQAIDVRPEKREIDFKYIP   72 (80)
T ss_dssp             CCCTTCEEEEEEEEEETTEEEEEEETTEEEEECGGGCSSCCGGGCCTTCEEEEEEEEEETTTTEEEEEECS
T ss_pred             CCCCCCEEEEEEEEEeCCEEEEEECCCCEEEEEHHHCCcccceeeCCCCEEEEEEEEEECCCCEEEEEEee
Confidence            578999999999999999999999999999999999964   3699999999999999997 888998865

>3h0g_G DNA-directed RNA polymerase II subunit RPB7; transcription, multi-protein complex, DNA- binding, magnesium; 3.65A {Schizosaccharomyces pombe}

Probab=99.16  E-value=1.2e-13  Score=140.22  Aligned_cols=144  Identities=14%  Similarity=0.144  Sum_probs=103.6

Q ss_pred             HHH-HhcCCCCCCCCCCCcceeeeeccchhhhhcCCCccchhhhhhhhCceE-EeeCCEEEEEecCHHHHHHHHHHHHHH
Q 002054          599 MER-EISAPRTQDDRNSPRLATLKYDNDTLRRLIGPLGALKRKIEEETGGRI-SVSDGTLTVVAKNRSVMEKVLEKVDFI  676 (974)
Q Consensus       599 m~~-~i~~~~~~~~~~~p~~~~~~i~~~ki~~vIg~gGk~i~~i~~~~g~~I-di~dg~v~i~~~~~~~~~~a~~~i~~l  676 (974)
                      |.+ .+.-|+..+++++|+....+++++.++.++|++|+.|. +   +|..| ++.+|.+.  .  .+....+...++.+
T Consensus         7 l~d~~i~ipp~~~~~~~~~~i~~~l~~~~~g~vi~~~G~~I~-i---~~idi~~i~~G~I~--~--gdg~~~~~v~f~~i   78 (172)
T 3h0g_G            7 ELSLTISLHPSYFGPRMQDYLKAKLLADVEGTCSGQYGYIIC-V---LDSNTIDIDKGRVV--P--GQGFAEFEVKYRAV   78 (172)
T ss_dssp             EEEEEEECCGGGCTTTHHHHHHHHHHHHHTTCEETTTEEEEE-E---CTTTSEEECCCEEC--T--TTCCEEEEEEEEEE
T ss_pred             EecCeEEeCHHHhCccHHHHHHHHHHHHhCCcCcCCccEEEE-E---EeeeeeEeeCCEEE--C--CCCcEEEEEEEEEe
Confidence            444 56677788888889888889999999999999999998 5   32111 23366654  1  11111111112222


Q ss_pred             hhcccccCcEEEEEEEEEeeceEEEEEcCCeEEEEecccCCCccccc----------cccccccCCEEEEEEEEEccC--
Q 002054          677 IGREIEVGGIYKGVVTSVKEYGAFVEFNGGQQGLLHVSELSHEPVSR----------VSDVVSVGQQLSLRCIGQDVR--  744 (974)
Q Consensus       677 ~~~~~~~G~i~~G~V~~i~~~G~fV~l~~g~~Glvhisels~~~v~~----------~~~~~~vGd~V~vkVl~id~~--  744 (974)
                      . ..+.+|++++|+|+++++||+||++. ..+||||+|++++.+.-+          ..+.+++||.|+|||+++|.+  
T Consensus        79 v-f~p~~Gev~~G~V~~v~~fG~FV~l~-~~~glVh~s~l~~~~~~d~~~~~~~~~~~~~~~~~Gd~VrvkV~~vd~~~~  156 (172)
T 3h0g_G           79 L-WRPFRGEVVDAIVTTVNKMGFFANIG-PLNVFVSSHLVPPDMKFDPTANPPNYSGEDQVIEKGSNVRLKIVGTRTDAT  156 (172)
T ss_dssp             E-ECCCTTCEEECCCCEEETTEEECCBT-TBCCEEEGGGSCTTCCCBSSSSSCBEESSSCEECSSCCEEEEEEEEEESSS
T ss_pred             e-eccCCCCEEEEEEEEEEcceEEEEeC-CeEEEEEHHHCCCccccCcccccceEecCCcEECCCCEEEEEEEEEECCCC
Confidence            2 46899999999999999999999996 477999999997664433          356899999999999999973  


Q ss_pred             --CceEEEEec
Q 002054          745 --GNIKLSLKA  753 (974)
Q Consensus       745 --gri~LS~K~  753 (974)
                        .+|. |||+
T Consensus       157 ~~~~Ig-tm~~  166 (172)
T 3h0g_G          157 EIFAIA-TMKE  166 (172)
T ss_dssp             CEEEEE-ECCS
T ss_pred             CceEEE-EcCC
Confidence              2455 6654

>4ayb_E DNA-directed RNA polymerase; transferase, multi-subunit, transcription; 3.20A {Sulfolobus shibatae} PDB: 2y0s_E 4b1o_E 4b1p_T 2waq_E 2wb1_E 2pmz_E 3hkz_E

Probab=99.15  E-value=3.5e-12  Score=130.46  Aligned_cols=75  Identities=24%  Similarity=0.454  Sum_probs=66.8

Q ss_pred             cccccCcEEEEEEEEEeeceEEEEEcCCeEEEEecccCCCccc-----------cccccccccCCEEEEEEEEEcc----
Q 002054          679 REIEVGGIYKGVVTSVKEYGAFVEFNGGQQGLLHVSELSHEPV-----------SRVSDVVSVGQQLSLRCIGQDV----  743 (974)
Q Consensus       679 ~~~~~G~i~~G~V~~i~~~G~fV~l~~g~~Glvhisels~~~v-----------~~~~~~~~vGd~V~vkVl~id~----  743 (974)
                      ..+.+|++++|+|+++++||+||++. ..+||+|+|+++++++           ++..+.+++||.|+|||+++|.    
T Consensus        77 ~~p~~Gev~~G~V~~v~~~G~fv~l~-~~~glvh~s~l~~d~~~~d~~~~~~~g~~~~~~~~~Gd~VrvkV~~v~~~~~~  155 (180)
T 4ayb_E           77 YVPVVQEVVEGEVLQVDNYGVFVNLG-PMDGLVHISQITDDTLKYDNVRGIIFGEKSKKVIQKGDKVRARVISVASTVTG  155 (180)
T ss_dssp             ECCCTTCEEEEEEEEEETTEEEEECS-SSEEEEEGGGSCSSCEEECSSSCCEEETTTCCCCCTTCEEEEEEEEECC----
T ss_pred             eeccCCCEEEEEEeeeccceEEEEEC-CccceEEeeecCCCccccchhcceEEEeccCeEECCCCEEEEEEEEEeCCCCc
Confidence            46899999999999999999999995 5899999999999977           4678889999999999999985    


Q ss_pred             -CCceEEEEecc
Q 002054          744 -RGNIKLSLKAV  754 (974)
Q Consensus       744 -~gri~LS~K~~  754 (974)
                       .++|.||||+.
T Consensus       156 ~~~rI~ls~k~~  167 (180)
T 4ayb_E          156 RLPRIALTMRQP  167 (180)
T ss_dssp             ---CEEEECCST
T ss_pred             ccCcEEEEcCCC
Confidence             36899999974

>2eqs_A ATP-dependent RNA helicase DHX8; S1 domain, OB-fold, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.11  E-value=2.5e-10  Score=105.92  Aligned_cols=72  Identities=24%  Similarity=0.296  Sum_probs=62.6

Q ss_pred             cccccccCCCCCEEEEEEEEEeCCeEEEEeCC---CeEEEEecccCC-C-------CCCCCCCEEEEEEEEEeCCCceee
Q 002054          901 AIVSAKNLKLGTKVAAKVYQVRARGLVLDLGG---GIRGMYRFENNE-K-------KDFVVGDELLVKCSSFTGKGIPVV  969 (974)
Q Consensus       901 ~p~~~~~~~vG~vV~G~V~~I~~~GvFV~L~~---gv~Glih~se~~-~-------~~f~vGd~V~vkVl~id~~~~~~~  969 (974)
                      .+|...++++|+++.|+|++|++||+||+|++   ++.||+|.|++. .       +.|++||+|+|+|+++|. +...+
T Consensus         3 ~~~~~~~~~vG~i~~G~V~~v~~fG~FV~l~~~~~~~~Glvhisel~~~~~~~~~~~~~~~Gd~V~VkV~~vd~-~~i~L   81 (103)
T 2eqs_A            3 SGSSGEEPTIGDIYNGKVTSIMQFGCFVQLEGLRKRWEGLVHISELRREGRVANVADVVSKGQRVKVKVLSFTG-TKTSL   81 (103)
T ss_dssp             CCCCCSSCCTTCEEEEEEEEECSSCEEEEECSSSSCCEEEECGGGTSSSSCCCCHHHHCCTTCEEEEEEEEEET-TEEEE
T ss_pred             cccccccCCCCCEEEEEEEEEeccEEEEEEcCCCCCeEEEEEHHHCCCCcccCCcccEeCCCCEEEEEEEEEEC-CeeEE
Confidence            34567789999999999999999999999996   899999999993 1       359999999999999998 57777


Q ss_pred             eecC
Q 002054          970 SLVD  973 (974)
Q Consensus       970 ~~~~  973 (974)
                      |+.+
T Consensus        82 Slk~   85 (103)
T 2eqs_A           82 SMKD   85 (103)
T ss_dssp             ESTT
T ss_pred             EEee
Confidence            7753

>2k4k_A GSP13, general stress protein 13; cytoplasm, stress response, RNA binding protein; NMR {Bacillus subtilis}

Probab=99.08  E-value=3.1e-10  Score=109.71  Aligned_cols=67  Identities=24%  Similarity=0.370  Sum_probs=61.1

Q ss_pred             ccCCCCCEEEEEEEEEeCCeEEEEeCCCeEEEEecccCC-------CCCCCCCCEEEEEEEEEeC-CCceeeeec
Q 002054          906 KNLKLGTKVAAKVYQVRARGLVLDLGGGIRGMYRFENNE-------KKDFVVGDELLVKCSSFTG-KGIPVVSLV  972 (974)
Q Consensus       906 ~~~~vG~vV~G~V~~I~~~GvFV~L~~gv~Glih~se~~-------~~~f~vGd~V~vkVl~id~-~~~~~~~~~  972 (974)
                      .++++|+++.|+|++|++||+||+|++++.||||+|++.       .+.|++||+|+|+|+++|. ++...+|+.
T Consensus         3 ~~~~vG~iv~G~V~~i~~~G~FV~l~~~~~Glihisel~~~~~~~~~~~~~vGd~V~vkV~~vd~~~~kI~LSlk   77 (130)
T 2k4k_A            3 AKFEVGSVYTGKVTGLQAYGAFVALDEETQGLVHISEVTHGFVKDINEHLSVGDEVQVKVLAVDEEKGKISLSIR   77 (130)
T ss_dssp             CCCCTTCEEEEEEEEEETTEEEEEEETTEEEEEEGGGTSSSCCSCGGGTCCTTCEEEEEEEEEETTTTEEEEESH
T ss_pred             CcCCCCCEEEEEEEEEeCCeEEEEECCCcEEEEEHHHCCcccccCccccCCCCCEEEEEEEEEeCCCCEEEEEEe
Confidence            578999999999999999999999999999999999885       3569999999999999998 778888875

>1wi5_A RRP5 protein homolog; S1 domain, OB-fold, structural genomics, riken structural genomics/proteomics initiative, RSGI, unknown function; NMR {Homo sapiens} SCOP: b.40.4.5

Probab=99.05  E-value=1.2e-10  Score=110.97  Aligned_cols=77  Identities=19%  Similarity=0.264  Sum_probs=63.4

Q ss_pred             cccccCcEEEEEEEEEeeceEEEEEc-CCeEEEEecccC-CCccccccccccccCCEEEEEEEEEcc-CCceEEEEeccC
Q 002054          679 REIEVGGIYKGVVTSVKEYGAFVEFN-GGQQGLLHVSEL-SHEPVSRVSDVVSVGQQLSLRCIGQDV-RGNIKLSLKAVS  755 (974)
Q Consensus       679 ~~~~~G~i~~G~V~~i~~~G~fV~l~-~g~~Glvhisel-s~~~v~~~~~~~~vGd~V~vkVl~id~-~gri~LS~K~~~  755 (974)
                      .++++|++|.|+|++|.+||+||+|. ++..||+|.++. ++.++.++.+.|++||.|+|+|+++|. ++++.||+|+..
T Consensus        17 ~~l~~G~i~~G~V~~v~~fG~fV~l~~~~~~~l~~~~~~~~~~~~~~~~~~~~~Gd~V~vkV~~vd~~~~~i~Lslk~~~   96 (119)
T 1wi5_A           17 EALKPGMLLTGTVSSLEDHGYLVDIGVDGTRAFLPLLKAQEYIRQKNKGAKLKVGQYLNCIVEKVKGNGGVVSLSVGHSE   96 (119)
T ss_dssp             TTCCTTCEEEEEEEEECSSEEEEECCCSSCEEEEEHHHHHHHHHHHSSSCCCCTTCEEEEEEEECCTTSCEEEEECCCCC
T ss_pred             hcCCCCCEEEEEEEEEeCceEEEEECCCCeEEEEEEecccccccccCccCEeCCCCEEEEEEEEEeCCCCEEEEEEchhh
Confidence            46899999999999999999999997 456665555543 233455788999999999999999998 689999998753

>3h36_A Polyribonucleotide nucleotidyltransferase; polyribonucleotide nucleotidyltransfer structural genomics, PSI-2, protein structure initiative; 1.80A {Streptococcus mutans}

Probab=99.03  E-value=4.8e-10  Score=101.99  Aligned_cols=84  Identities=15%  Similarity=0.192  Sum_probs=64.2

Q ss_pred             ccccCCCHHHHHHHHHHHHHHHHhhhcCCCCChhHHHHHHHHHHHHHHHHhhhccchhhh------chHHHHHHHHHHHH
Q 002054          286 YKLSMISEQTLEKVSNLAEAHIEAVFTDPSYSKFERGEALDKIGQDVKKALEEECDEESL------QVLPKAVDTVRKRV  359 (974)
Q Consensus       286 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~k~~r~~~~~~~~~~~~~~~~~~~~~~~~------~~~~~~~~~~~~~~  359 (974)
                      |.++..+++|.+.|+++++++|++++.+  .+|++|+++++++++++.++|.++.++ ..      ..+..+|++++++.
T Consensus         4 ~~~~~~~~el~~~v~~~~~~~l~~a~~~--~~K~eR~~a~~~ik~~v~~~l~e~~~~-~~~~~~~~~~i~~~~~~lek~i   80 (93)
T 3h36_A            4 VELLQVDADLQAEIVGKYNADLQKAVQI--EEKKASEIATEAVKEHVTAEYEERYAE-HEEHDRIMRDVAEILEQMEHAE   80 (93)
T ss_dssp             ----CCCHHHHHHHHHHHHHHHHHHHHC--SSHHHHHHHHHHHHHHHHHHHHHHHTT-CTTHHHHHHHHHHHHHHHHHHH
T ss_pred             CCCCCCCHHHHHHHHHHHHHHHHHHHcc--cchHHHHHHHHHHHHHHHHHHHhhCcc-chhhhhhHHHHHHHHHHHHHHH
Confidence            4456678899999999999999999988  499999999999999999999654322 22      57999999999999


Q ss_pred             HHHHHHhcCCcCC
Q 002054          360 IRKRIIAEGVRVD  372 (974)
Q Consensus       360 ~r~~il~~~~R~D  372 (974)
                      +|++||++|+|+|
T Consensus        81 vR~~IL~e~~RiD   93 (93)
T 3h36_A           81 VRRLITEDKVRPD   93 (93)
T ss_dssp             HHHHC--------
T ss_pred             HHHHHHCCCCCCC
Confidence            9999999999998

>3psi_A Transcription elongation factor SPT6; nucleus; 3.30A {Saccharomyces cerevisiae}

Probab=99.01  E-value=3.1e-10  Score=143.66  Aligned_cols=76  Identities=12%  Similarity=0.097  Sum_probs=72.3

Q ss_pred             cccccCcEEEEEEEEEeeceEEEEEcCCeEEEEecccCCCcc-ccccccccccCCEEEEEEEEEcc-CCceEEEEecc
Q 002054          679 REIEVGGIYKGVVTSVKEYGAFVEFNGGQQGLLHVSELSHEP-VSRVSDVVSVGQQLSLRCIGQDV-RGNIKLSLKAV  754 (974)
Q Consensus       679 ~~~~~G~i~~G~V~~i~~~G~fV~l~~g~~Glvhisels~~~-v~~~~~~~~vGd~V~vkVl~id~-~gri~LS~K~~  754 (974)
                      .++++|++|.|+|++|++||+||+|.+|++||||+|++++++ +.++.++|++||.|+|||+++|. +++|.||+|..
T Consensus       898 ~~l~~G~iv~G~V~~V~~fGaFV~L~~gveGLVHiSelsd~~~v~~p~~v~kvGd~V~vkVl~VD~~~~rI~LSlk~~  975 (1219)
T 3psi_A          898 KTFFKGSIIPVRVERFWHNDIICTTNSEVECVVNAQRHAGAQLRRPANEIYEIGKTYPAKVIYIDYANITAEVSLLDH  975 (1219)
T ss_dssp             TTSCTTCEEEEEEEEECSSCEEEECTTSCEEEECTTSSSSTTSCSCSTTTSCTTCEEEEEEEEEEGGGTEEEEECCHH
T ss_pred             hhCCCCCEEEEEEEEEecceEEEEeCCCceEEEEHHHcCCCcccCCHHHcCCCCCEEEEEEEEEECCCCEEEEEecHH
Confidence            578999999999999999999999999999999999999998 89999999999999999999996 79999999864

>2cqo_A Nucleolar protein of 40 kDa; S1 domain, OB-fold, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.00  E-value=7.4e-10  Score=105.34  Aligned_cols=76  Identities=18%  Similarity=0.064  Sum_probs=63.4

Q ss_pred             cccccc--ccccCCCCCEEEEEEEEEeCCeEEEEeCC-CeEEEEecccCCC-------CCCCCCCEEEEEEEEEeCC---
Q 002054          898 RVEAIV--SAKNLKLGTKVAAKVYQVRARGLVLDLGG-GIRGMYRFENNEK-------KDFVVGDELLVKCSSFTGK---  964 (974)
Q Consensus       898 ~~~~p~--~~~~~~vG~vV~G~V~~I~~~GvFV~L~~-gv~Glih~se~~~-------~~f~vGd~V~vkVl~id~~---  964 (974)
                      +..++|  ....+++|+++.|+|++|++||+||+|++ ++.||+|++++..       +.|++||+|+|+|+++|.+   
T Consensus         8 ~~~~~~~~~~~~~~vG~iv~G~V~~I~~fGaFV~l~g~~~~Glvhisel~~~~~~~~~~~~~~Gd~V~VkV~~vd~~~~~   87 (119)
T 2cqo_A            8 MNSGRPETMENLPALYTIFQGEVAMVTDYGAFIKIPGCRKQGLVHRTHMSSCRVDKPSEIVDVGDKVWVKLIGREMKNDR   87 (119)
T ss_dssp             SCCCCCCCSCCSCCTTCEEEEEEEEEETTEEEEECTTCSSCEEEEHHHHCSSCCSCHHHHCCTTCEEEEEEEEEEECSSC
T ss_pred             ccccchhhhhcccCCCCEEEEEEEEEeCceEEEEECCCcEEEEEEHHHCCcccccChhhcCCCCCEEEEEEEEEeccccC
Confidence            455566  46688999999999999999999999976 5799999998753       2499999999999999974   


Q ss_pred             CceeeeecC
Q 002054          965 GIPVVSLVD  973 (974)
Q Consensus       965 ~~~~~~~~~  973 (974)
                      +...+|+.+
T Consensus        88 ~~i~LSlk~   96 (119)
T 2cqo_A           88 IKVSLSMKV   96 (119)
T ss_dssp             EEEEEESTT
T ss_pred             ceEEEEEee
Confidence            477777753

>1luz_A Protein K3, protein K2; stranded anti-parallel beta barrel, viral protein; 1.80A {Vaccinia virus} SCOP: b.40.4.5

Probab=98.99  E-value=6.1e-10  Score=100.13  Aligned_cols=67  Identities=18%  Similarity=0.180  Sum_probs=58.0

Q ss_pred             ccccCCCCCEEEEEEEEEeCCeEEEEeCC--CeEEEEecc-cCC-------CCCCCCCCEEEEEEEEEeC-CCceeeeec
Q 002054          904 SAKNLKLGTKVAAKVYQVRARGLVLDLGG--GIRGMYRFE-NNE-------KKDFVVGDELLVKCSSFTG-KGIPVVSLV  972 (974)
Q Consensus       904 ~~~~~~vG~vV~G~V~~I~~~GvFV~L~~--gv~Glih~s-e~~-------~~~f~vGd~V~vkVl~id~-~~~~~~~~~  972 (974)
                      .+...++|++++|+|+ |++||+||+|++  |+.||+|+| +++       .+.| +||+|+|+|+++|. +++.-+|+.
T Consensus         5 ~y~~~~vG~~~~G~V~-v~~fG~FVel~~~~~~eGLvhis~el~~~~~~~~~~~~-~Gd~V~VkV~~vd~~~~kI~lslk   82 (88)
T 1luz_A            5 CYSLPNAGDVIKGRVY-EKDYALYIYLFDYPHFEAILAESVKMHMDRYVEYRDKL-VGKTVKVKVIRVDYTKGYIDVNYK   82 (88)
T ss_dssp             CSCCCCTTCEEEEEEE-EETTEEEEEETTCTTSEEEEGGGSSCCHHHHHHHHHHH-TTCEEEEEEEEEETTTTEEEEEEE
T ss_pred             EecCCCCCCEEEEEEE-EEccEEEEEECCCCCeEEEEEeeHHhCcccccCHhHEe-CCCEEEEEEEEEECCCCEEEEEEe
Confidence            3556789999999999 999999999974  899999999 985       2347 99999999999997 567777775

>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=98.98  E-value=2.8e-10  Score=102.02  Aligned_cols=65  Identities=17%  Similarity=0.270  Sum_probs=59.8

Q ss_pred             CCCcceeeeeccchhhhhcCCCccchhhhhhhhCce-EEee-C-CEEEEEecCHHHHHHHHHHHHHHh
Q 002054          613 NSPRLATLKYDNDTLRRLIGPLGALKRKIEEETGGR-ISVS-D-GTLTVVAKNRSVMEKVLEKVDFII  677 (974)
Q Consensus       613 ~~p~~~~~~i~~~ki~~vIg~gGk~i~~i~~~~g~~-Idi~-d-g~v~i~~~~~~~~~~a~~~i~~l~  677 (974)
                      .++.+.+++|+|++|+++||+||++|++|+++||++ |+++ | |+|+|++.+.+++++|+++++.+-
T Consensus        12 ~~~~i~~i~I~~dkIg~vIG~gGk~Ik~I~e~tGv~~IdI~eddG~V~I~g~~~ea~~~A~~~I~~ie   79 (91)
T 2cpq_A           12 AAAFHEEFVVREDLMGLAIGTHGSNIQQARKVPGVTAIELDEDTGTFRIYGESADAVKKARGFLEFVE   79 (91)
T ss_dssp             SCSEEEEEECCHHHHHHHHTTTTHHHHHHHTSTTEEEEEEETTTTEEEEEESSHHHHHHHHHHHSCCC
T ss_pred             cCceEEEEEEChHHhhhhcCCCcHHHHHHHHHhCCeEEEEEcCCCEEEEEECCHHHHHHHHHHHHhhh
Confidence            457899999999999999999999999999999998 9998 4 999999999999999999887553

>3m7n_A Putative uncharacterized protein AF_0206; exosome, RNA, exonuclease, hydrolase, nuclease, hydrolase-RN; 2.40A {Archaeoglobus fulgidus} PDB: 2ba1_A 3m85_A

Probab=98.97  E-value=8e-10  Score=112.66  Aligned_cols=70  Identities=30%  Similarity=0.440  Sum_probs=66.3

Q ss_pred             ccccCcEEEEEEEEEeeceEEEEEcC----------CeEEEEecccCCCccccccccccccCCEEEEEEEEEccCCceEE
Q 002054          680 EIEVGGIYKGVVTSVKEYGAFVEFNG----------GQQGLLHVSELSHEPVSRVSDVVSVGQQLSLRCIGQDVRGNIKL  749 (974)
Q Consensus       680 ~~~~G~i~~G~V~~i~~~G~fV~l~~----------g~~Glvhisels~~~v~~~~~~~~vGd~V~vkVl~id~~gri~L  749 (974)
                      .++ |++|.|+|++|.++|+||+|.+          +.+|+||+||+++.++.++.+.|++||.|+|+|++    +++.|
T Consensus        55 ~p~-GdiV~G~V~~V~~~ga~V~I~~v~~~~~~~~~~~~Gll~isei~~~~~~~~~~~~~~GD~V~akVi~----~~i~L  129 (179)
T 3m7n_A           55 IVK-GDVVLGRVVDLRNSIALIEVSSKKGENRGPSNRGIGILHVSNVDEGYVKEISEAVGYLDILKARVIG----DNLRL  129 (179)
T ss_dssp             CCT-TCEEEEEEEEECSSEEEEEEEEETTCCSCCTTCEEEEEEGGGTTSSCCSSGGGTCCTTCEEEEEEEE----TTTEE
T ss_pred             cCC-CCEEEEEEEEEeCCcEEEEEccccCcccccccCeeEEEEHHHcCcchhhCHhhcCCCCCEEEEEEEC----CeEEE
Confidence            478 9999999999999999999987          89999999999999999999999999999999998    89999


Q ss_pred             EEecc
Q 002054          750 SLKAV  754 (974)
Q Consensus       750 S~K~~  754 (974)
                      |+|+.
T Consensus       130 S~k~~  134 (179)
T 3m7n_A          130 STKEE  134 (179)
T ss_dssp             ECCST
T ss_pred             EEecC
Confidence            98874

>1kl9_A Eukaryotic translation initiation factor 2 subuni; OB fold, helical domain; 1.90A {Homo sapiens} SCOP: a.60.14.1 b.40.4.5

Probab=98.97  E-value=1.5e-09  Score=110.43  Aligned_cols=66  Identities=20%  Similarity=0.161  Sum_probs=55.3

Q ss_pred             CCCCCEEEEEEEEEeCCeEEEEe--CCCeEEEEecccCC-------CCCCCCCCEEEEEEEEEeC-CCceeeeecC
Q 002054          908 LKLGTKVAAKVYQVRARGLVLDL--GGGIRGMYRFENNE-------KKDFVVGDELLVKCSSFTG-KGIPVVSLVD  973 (974)
Q Consensus       908 ~~vG~vV~G~V~~I~~~GvFV~L--~~gv~Glih~se~~-------~~~f~vGd~V~vkVl~id~-~~~~~~~~~~  973 (974)
                      .++|+++.|+|++|++||+||+|  .+|+.||+|+|+++       .+.|++||+|+|+|+++|. ++...+|+.+
T Consensus        13 p~~G~iv~G~V~~I~~fGaFV~L~e~~g~eGLvhiSels~~~v~~~~~~~~vGd~V~VkVl~vD~~~~rI~LSlk~   88 (182)
T 1kl9_A           13 PEVEDVVMVNVRSIAEMGAYVSLLEYNNIEGMILLSELSRRRIRSINKLIRIGRNECVVVIRVDKEKGYIDLSKRR   88 (182)
T ss_dssp             CCTTCEEEEEEEEECSSEEEEEETTTTTEEEEEEGGGC------------CTTCEEEEEEEEEETTTTEEEEESTT
T ss_pred             CCCCCEEEEEEEEEeccEEEEEEccCCCcEEEEEHHHCCCcccCCHHHhcCCCCEEEEEEEEEECCCCEEEEEEee
Confidence            38999999999999999999999  46899999999884       4579999999999999997 5677788754

>2a19_A EIF-2- alpha, eukaryotic translation initiation factor 2 alpha; transferase, protein biosynthesis, protein synthesis transferase complex; HET: TPO ANP; 2.50A {Saccharomyces cerevisiae} PDB: 2a1a_A* 1q46_A

Probab=98.96  E-value=2e-09  Score=109.08  Aligned_cols=69  Identities=20%  Similarity=0.182  Sum_probs=57.7

Q ss_pred             cccCC-CCCEEEEEEEEEeCCeEEEEeC--CCeEEEEecccCC-------CCCCCCCCEEEEEEEEEeC-CCceeeeecC
Q 002054          905 AKNLK-LGTKVAAKVYQVRARGLVLDLG--GGIRGMYRFENNE-------KKDFVVGDELLVKCSSFTG-KGIPVVSLVD  973 (974)
Q Consensus       905 ~~~~~-vG~vV~G~V~~I~~~GvFV~L~--~gv~Glih~se~~-------~~~f~vGd~V~vkVl~id~-~~~~~~~~~~  973 (974)
                      ...|+ +|+++.|+|++|++||+||+|+  +|+.||+|+|++.       .+.|++||+|+|+|+++|. ++...+|+.+
T Consensus         9 ~~~~p~~G~iv~G~V~~i~~fGaFV~L~e~~gveGLvhiSels~~~v~~~~~~~~vGd~V~vkVl~vd~~~~~I~LSlk~   88 (175)
T 2a19_A            9 ENKYPEIDDIVMVNVQQIAEMGAYVKLLEYDNIEGMILLSELSRRRIRSIQKLIRVGKNDVAVVLRVDKEKGYIDLSKRR   88 (175)
T ss_dssp             SSSSCCTTCEEEEEEEEEETTEEEEEETTTTTCEEEEECC--------CCCCCCCTTSEEEEEEEEEETTTTEEEEESTT
T ss_pred             hhcCCCCCCEEEEEEEEEecceEEEEEcCCCCcEEEEEHHHcCCcccCCHHHcCCCCCEEEEEEEEEECCCCeEEEEEEe
Confidence            34455 9999999999999999999995  7999999999884       4679999999999999997 5677788754

>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=98.95  E-value=6.4e-10  Score=103.15  Aligned_cols=74  Identities=16%  Similarity=0.130  Sum_probs=67.8

Q ss_pred             hcCCCCCCCCCCCcceeeeeccchhhhhcCCCccchhhhhhhhCceEEee-CC----EEEEEecCHHHHHHHHHHHHHHh
Q 002054          603 ISAPRTQDDRNSPRLATLKYDNDTLRRLIGPLGALKRKIEEETGGRISVS-DG----TLTVVAKNRSVMEKVLEKVDFII  677 (974)
Q Consensus       603 i~~~~~~~~~~~p~~~~~~i~~~ki~~vIg~gGk~i~~i~~~~g~~Idi~-dg----~v~i~~~~~~~~~~a~~~i~~l~  677 (974)
                      +...+.++++++|++..+.||+++++.+||+||++|++|+++||++|+++ +|    .|.|++.. +.+++|+++|..++
T Consensus         4 ~~~Ak~~i~~~ap~~~~i~Ip~~~ig~IIG~gG~~Ir~I~eetg~~I~I~~~g~~~~~V~I~G~~-e~v~~A~~~I~~i~   82 (104)
T 2ctk_A            4 GSSGKEALEALVPVTIEVEVPFDLHRYVIGQKGSGIRKMMDEFEVNIHVPAPELQSDIIAITGLA-ANLDRAKAGLLERV   82 (104)
T ss_dssp             CCCCCCCCCCSSCEEEEEECCHHHHHHHHCSSSHHHHHHHHHTCCEEECCCTTTTCCEEEEEECH-HHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHhhCCEEEEEEEChHHccceeCCCchHHHHHHHHHCCEEEecCCCCCcceEEEEcCH-HHHHHHHHHHHHHH
Confidence            34567889999999999999999999999999999999999999999997 66    99999985 89999999998876

>3bzc_A TEX; helix-turn-helix, helix-hairpin-helix, S1 domain, YQGF domain, transcription, RNA binding protein; 2.27A {Pseudomonas aeruginosa} SCOP: a.60.2.6 a.60.2.6 a.294.1.1 b.40.4.5 c.55.3.13 PDB: 3bzk_A 2oce_A

Probab=98.94  E-value=2.4e-10  Score=139.37  Aligned_cols=76  Identities=33%  Similarity=0.596  Sum_probs=71.8

Q ss_pred             ccccCcEEEEEEEEEeeceEEEEEcCCeEEEEecccCCCccccccccccccCCEEEEEEEEEcc-CCceEEEEeccC
Q 002054          680 EIEVGGIYKGVVTSVKEYGAFVEFNGGQQGLLHVSELSHEPVSRVSDVVSVGQQLSLRCIGQDV-RGNIKLSLKAVS  755 (974)
Q Consensus       680 ~~~~G~i~~G~V~~i~~~G~fV~l~~g~~Glvhisels~~~v~~~~~~~~vGd~V~vkVl~id~-~gri~LS~K~~~  755 (974)
                      ++++|++|.|+|++|++||+||+|..+.+||||+|++++.++.++.+.|++||.|+|+|+++|. +++|.||+|...
T Consensus       651 ~l~vG~iv~G~V~~V~~fGaFV~l~~~~eGLVhiS~Lsd~~v~d~~~~~~vGd~V~VkVi~VD~~~~rI~LSlk~~~  727 (785)
T 3bzc_A          651 DLKPGMVLEGVVTNVTNFGAFVDIGVHQDGLVHISALSEKFVKDPYEVVKAGDIVKVKVMEVDIPRNRVGLSMRMSD  727 (785)
T ss_dssp             TCCTTCBCCCEEEEEETTEEEEECSSSSEEEEETTTSCSSCCSCHHHHCCTTCCCCCBEEEEETTTTEEEECCSSCC
T ss_pred             hcCCCCEEEEEEEEEecCCeEEEeCCCcEEEEEHHHcCccccCChhheeCCCCEEEEEEEEEECCCCEEEEEEecCC
Confidence            5789999999999999999999998899999999999999999999999999999999999998 799999999644

>2nn6_I 3'-5' exoribonuclease CSL4 homolog; RNA, exosome, PM/SCL, phosphorolytic, hydrolase/transferase complex; 3.35A {Homo sapiens} SCOP: b.40.4.5 b.84.4.2

Probab=98.92  E-value=1.2e-09  Score=113.82  Aligned_cols=75  Identities=16%  Similarity=0.132  Sum_probs=68.6

Q ss_pred             ccccCcEEEEEEEEEeeceEEEEEc--------CCeEEEEecccCCCcccc--ccccccccCCEEEEEEEEEccC-CceE
Q 002054          680 EIEVGGIYKGVVTSVKEYGAFVEFN--------GGQQGLLHVSELSHEPVS--RVSDVVSVGQQLSLRCIGQDVR-GNIK  748 (974)
Q Consensus       680 ~~~~G~i~~G~V~~i~~~G~fV~l~--------~g~~Glvhisels~~~v~--~~~~~~~vGd~V~vkVl~id~~-gri~  748 (974)
                      .+++|+++.|+|+++.++|+||+|.        .+.+|+||+||+++.+.+  ++.+.|++||.|+|+|+++|.. +++.
T Consensus        78 ~p~vGDvV~G~V~~v~~~~a~V~I~~v~~~~L~~~~~GlIhisei~~~~~~~~~~~~~l~~GD~V~akVisi~~~~~~i~  157 (209)
T 2nn6_I           78 LPDVGAIVTCKVSSINSRFAKVHILYVGSMPLKNSFRGTIRKEDVRATEKDKVEIYKSFRPGDIVLAKVISLGDAQSNYL  157 (209)
T ss_dssp             CCCTTCEEEEEEEEECSSEEEEEEEESSSSCCCCSSCSCEEEEGGGTCSSCCCCGGGTCCSSSEEEEEEEEEETTTTEEE
T ss_pred             CCCCCCEEEEEEEEEECceEEEEECccccccccCCceeEEEHHHcccccccccchhhhcCCCCEEEEEEEEEeCCCCeEE
Confidence            5799999999999999999999984        467999999999999888  8999999999999999999874 5799


Q ss_pred             EEEecc
Q 002054          749 LSLKAV  754 (974)
Q Consensus       749 LS~K~~  754 (974)
                      ||+|+.
T Consensus       158 LS~k~~  163 (209)
T 2nn6_I          158 LTTAEN  163 (209)
T ss_dssp             EECCSS
T ss_pred             EEEecC
Confidence            999874

>3psf_A Transcription elongation factor SPT6; nucleus; 2.59A {Saccharomyces cerevisiae}

Probab=98.90  E-value=1.8e-10  Score=143.68  Aligned_cols=77  Identities=12%  Similarity=0.098  Sum_probs=0.0

Q ss_pred             cccccCcEEEEEEEEEeeceEEEEEcCCeEEEEecccCCCcc-ccccccccccCCEEEEEEEEEcc-CCceEEEEeccC
Q 002054          679 REIEVGGIYKGVVTSVKEYGAFVEFNGGQQGLLHVSELSHEP-VSRVSDVVSVGQQLSLRCIGQDV-RGNIKLSLKAVS  755 (974)
Q Consensus       679 ~~~~~G~i~~G~V~~i~~~G~fV~l~~g~~Glvhisels~~~-v~~~~~~~~vGd~V~vkVl~id~-~gri~LS~K~~~  755 (974)
                      .++++|++|.|+|++|++||+||+|.+|++||||+|++++.+ +.++.++|++||.|+|||+++|. +++|.||+|...
T Consensus       901 ~~l~~G~iv~G~V~~V~~fGaFV~L~~gveGLVHiSelsd~~~v~~~~~v~kvGd~V~vkVl~VD~~~~rI~LSlk~~d  979 (1030)
T 3psf_A          901 KTFFKGSIIPVRVERFWHNDIICTTNSEVECVVNAQRHAGAQLRRPANEIYEIGKTYPAKVIYIDYANITAEVSLLDHD  979 (1030)
T ss_dssp             -------------------------------------------------------------------------------
T ss_pred             HHhcCCCEEEEEEEEEccCeEEEEeCCCcEEEEEHHHcCCCcccCCHHHcCCCCCEEEEEEEEEECCCCEEEEEechHH
Confidence            578999999999999999999999999999999999999998 89999999999999999999996 799999999753

>1wi5_A RRP5 protein homolog; S1 domain, OB-fold, structural genomics, riken structural genomics/proteomics initiative, RSGI, unknown function; NMR {Homo sapiens} SCOP: b.40.4.5

Probab=98.83  E-value=9.5e-09  Score=97.74  Aligned_cols=70  Identities=24%  Similarity=0.396  Sum_probs=59.5

Q ss_pred             ccccCCCCCEEEEEEEEEeCCeEEEEeC-CCeEEEEecccC--------CCCCCCCCCEEEEEEEEEeCC-CceeeeecC
Q 002054          904 SAKNLKLGTKVAAKVYQVRARGLVLDLG-GGIRGMYRFENN--------EKKDFVVGDELLVKCSSFTGK-GIPVVSLVD  973 (974)
Q Consensus       904 ~~~~~~vG~vV~G~V~~I~~~GvFV~L~-~gv~Glih~se~--------~~~~f~vGd~V~vkVl~id~~-~~~~~~~~~  973 (974)
                      ..+++++|+++.|+|++|++||+||+|+ +++.|++|.++.        +.+.|++||+|+|+|+++|.+ +...+|+..
T Consensus        15 ~~~~l~~G~i~~G~V~~v~~fG~fV~l~~~~~~~l~~~~~~~~~~~~~~~~~~~~~Gd~V~vkV~~vd~~~~~i~Lslk~   94 (119)
T 1wi5_A           15 SAEALKPGMLLTGTVSSLEDHGYLVDIGVDGTRAFLPLLKAQEYIRQKNKGAKLKVGQYLNCIVEKVKGNGGVVSLSVGH   94 (119)
T ss_dssp             CTTTCCTTCEEEEEEEEECSSEEEEECCCSSCEEEEEHHHHHHHHHHHSSSCCCCTTCEEEEEEEECCTTSCEEEEECCC
T ss_pred             cHhcCCCCCEEEEEEEEEeCceEEEEECCCCeEEEEEEecccccccccCccCEeCCCCEEEEEEEEEeCCCCEEEEEEch
Confidence            4678999999999999999999999999 578887777652        357899999999999999975 567777653

>3aev_A Translation initiation factor 2 subunit alpha; proteins-rRNA complex, 16S rRNA, RNA-binding; 2.80A {Pyrococcus horikoshii} PDB: 1yz6_A

Probab=98.80  E-value=1.3e-08  Score=110.19  Aligned_cols=71  Identities=21%  Similarity=0.260  Sum_probs=59.5

Q ss_pred             cccccCC-CCCEEEEEEEEEeCCeEEEEeC--CCeEEEEecccCC-------CCCCCCCCEEEEEEEEEeC-CCceeeee
Q 002054          903 VSAKNLK-LGTKVAAKVYQVRARGLVLDLG--GGIRGMYRFENNE-------KKDFVVGDELLVKCSSFTG-KGIPVVSL  971 (974)
Q Consensus       903 ~~~~~~~-vG~vV~G~V~~I~~~GvFV~L~--~gv~Glih~se~~-------~~~f~vGd~V~vkVl~id~-~~~~~~~~  971 (974)
                      +....+. +|++|.|+|++|++||+||+|+  +|+.||+|.|+++       .+.|++||+|.|+|+++|+ ++...+|+
T Consensus         3 ~~~~~~p~~Gdiv~G~V~~I~~fGaFV~L~e~~gieGlIhiSels~~~v~~~~~~~kvGd~V~vkVi~vD~~~~~I~LSl   82 (275)
T 3aev_A            3 RKAREYPEEGEFVVATVKRIHNYGAFLELDEYPGKEAFMHISEVASTWVRNIRDYLKEGQKVVAKVIRVDPRKGHIDLSL   82 (275)
T ss_dssp             ----CCCCTTCEEEEEEEEEETTEEEEEETTSTTCEEEEEGGGSCSSCCSCGGGTCCTTCEEEEEEEEEETTTTEEEEES
T ss_pred             cccccCCCCCCEEEEEEEEEECcEEEEEECCCCCeEEEEEHHHcCcccccCHHhccCCCCEEEEEEEEEECCCCEEEEEE
Confidence            3344554 9999999999999999999998  5999999999885       2469999999999999998 67888887


Q ss_pred             cC
Q 002054          972 VD  973 (974)
Q Consensus       972 ~~  973 (974)
                      .+
T Consensus        83 k~   84 (275)
T 3aev_A           83 RR   84 (275)
T ss_dssp             TT
T ss_pred             ee
Confidence            64

>2je6_I RRP4, exosome complex RNA-binding protein 1; nuclease, hydrolase, exonuclease, phosphorolytic, exoribonuclease, RNA degradation; HET: 1PE; 1.6A {Sulfolobus solfataricus} SCOP: b.40.4.5 b.84.4.2 d.51.1.1 PDB: 2jea_I* 2jeb_I* 3l7z_C

Probab=98.78  E-value=4.8e-09  Score=112.26  Aligned_cols=74  Identities=23%  Similarity=0.270  Sum_probs=69.5

Q ss_pred             ccccCcEEEEEEEEEeeceEEEEEcCCeEEEEecccCCCccc---cccccccccCCEEEEEEEEEccCCceEEEEec
Q 002054          680 EIEVGGIYKGVVTSVKEYGAFVEFNGGQQGLLHVSELSHEPV---SRVSDVVSVGQQLSLRCIGQDVRGNIKLSLKA  753 (974)
Q Consensus       680 ~~~~G~i~~G~V~~i~~~G~fV~l~~g~~Glvhisels~~~v---~~~~~~~~vGd~V~vkVl~id~~gri~LS~K~  753 (974)
                      .+++|+++.|+|+++.++|+||+|..+.+|+||+|++++.+.   .++.+.|++||.|+|+|++++.++++.||+|+
T Consensus        71 ~p~~GDiV~G~V~~v~~~ga~VdI~~~~~GlL~isei~~~~~~~~~~~~~~l~vGD~V~arVi~v~~~~~i~LS~r~  147 (251)
T 2je6_I           71 YPKINDIVIGLVEDVEIYGWVVDIKAPYKAYLPASNLLGRSINVGEDLRRYLDVGDYVIARIENFDRSIDPVLSVKG  147 (251)
T ss_dssp             CCCTTCEEEEEEEEECSSEEEEECSSSSCEEEEHHHHHTSCCCTTCCCSSSCCTTCEEEEEEEEEETTEEEEEECCS
T ss_pred             CCCCCCEEEEEEEEEeCceEEEEcCCCeEEEEEHHHhcCCccccccchhhcCCCCCEEEEEEEEECCCCcEEEEEcc
Confidence            479999999999999999999999888999999999998877   88899999999999999999988999999876

>2ba0_A Archeal exosome RNA binding protein RRP4; RNAse PH, RNA degradation, exoribonuclease, S1domain, KH domain, archaeal; 2.70A {Archaeoglobus fulgidus} SCOP: b.40.4.5 b.84.4.2 d.51.1.1

Probab=98.73  E-value=1.8e-08  Score=106.55  Aligned_cols=74  Identities=23%  Similarity=0.387  Sum_probs=69.0

Q ss_pred             ccccCcEEEEEEEEEeeceEEEEEcCCeEEEEecccCCCc-cccccccccccCCEEEEEEEEEccCCceEEEEec
Q 002054          680 EIEVGGIYKGVVTSVKEYGAFVEFNGGQQGLLHVSELSHE-PVSRVSDVVSVGQQLSLRCIGQDVRGNIKLSLKA  753 (974)
Q Consensus       680 ~~~~G~i~~G~V~~i~~~G~fV~l~~g~~Glvhisels~~-~v~~~~~~~~vGd~V~vkVl~id~~gri~LS~K~  753 (974)
                      .+++|+++.|+|+++.++|+||+|....+|+||+|++++. +..++.+.|++||.|.|+|++++.++++.||+|+
T Consensus        54 ~p~~GDiV~G~V~~v~~~~a~V~I~~~~~g~l~isev~~~~~~~~~~~~l~~GD~V~arVi~v~~~~~i~LS~r~  128 (229)
T 2ba0_A           54 TPSVGDVVIGIIREVAANGWAVDIYSPYQAFLPVSENPEMKPNKKPNEVLDIGDAIIAKVLNIDPKMKVTLTMKD  128 (229)
T ss_dssp             CCCTTCEEEEEEEEECSSEEEEECSSSSCEEEEGGGCTTCCTTSCGGGTCCTTCEEEEEEEEECTTCCEEEECCS
T ss_pred             cCCCCCEEEEEEEEEeCCeEEEEeCCCeEEEEEHHHccccccccchhcccCCCCEEEEEEEEECCCCcEEEEEcc
Confidence            4799999999999999999999998789999999999974 6788999999999999999999988999999876

>2e3u_A PH-DIM2P, hypothetical protein PH1566; PRE-ribosomal RNA processing factor, RNA binding protein; 2.30A {Pyrococcus horikoshii} PDB: 3aev_B

Probab=98.71  E-value=1.1e-08  Score=107.17  Aligned_cols=76  Identities=22%  Similarity=0.236  Sum_probs=60.2

Q ss_pred             HhcCCCCCCCCCCCcceeeeeccchhhhhcCCCccchhhhhhhhCceEEee--CCEEEEEecC----HHHHHHHHHHHHH
Q 002054          602 EISAPRTQDDRNSPRLATLKYDNDTLRRLIGPLGALKRKIEEETGGRISVS--DGTLTVVAKN----RSVMEKVLEKVDF  675 (974)
Q Consensus       602 ~i~~~~~~~~~~~p~~~~~~i~~~ki~~vIg~gGk~i~~i~~~~g~~Idi~--dg~v~i~~~~----~~~~~~a~~~i~~  675 (974)
                      .+..|+.+++++||++..+.||+++++.+||+||++|+.|++++|++|+++  +|.|.+.+.+    .+.+++|+++|..
T Consensus        20 ~~~~pr~e~s~~aP~i~~i~IP~~kig~lIG~gGk~Ik~I~e~tgvkI~I~~~~g~V~I~~~~~t~d~~~i~kA~~~I~~   99 (219)
T 2e3u_A           20 EIVEDEDEWEEFFKQEEYVKIPKDRIAVLIGKKGQTKKEIEKRTKTKITIDSETGEVWITSTKETEDPLAVWKARDIVLA   99 (219)
T ss_dssp             -------------CCEEEEECCHHHHHHHHCGGGHHHHHHHHHHTEEEEECTTTCEEEEEECTTCCSHHHHHHHHHHHHH
T ss_pred             CCCCCccccCCCCCEEEEEEeCHHHhhhhhcccHHHHHHHHHHHCcEEEEEcCCCEEEEecCCCCCCHHHHHHHHHHHHH
Confidence            455788899999999999999999999999999999999999999999998  7999999887    8999999999998


Q ss_pred             Hh
Q 002054          676 II  677 (974)
Q Consensus       676 l~  677 (974)
                      +.
T Consensus       100 i~  101 (219)
T 2e3u_A          100 IG  101 (219)
T ss_dssp             HH
T ss_pred             Hh
Confidence            87

>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=98.68  E-value=1e-08  Score=95.13  Aligned_cols=76  Identities=14%  Similarity=0.230  Sum_probs=66.4

Q ss_pred             CCCCCCCCCCCcceeeeeccchhhhhcCCCccchhhhhhhhCceEEee---------CCEEEEEecCHHHHHHHHHHHHH
Q 002054          605 APRTQDDRNSPRLATLKYDNDTLRRLIGPLGALKRKIEEETGGRISVS---------DGTLTVVAKNRSVMEKVLEKVDF  675 (974)
Q Consensus       605 ~~~~~~~~~~p~~~~~~i~~~ki~~vIg~gGk~i~~i~~~~g~~Idi~---------dg~v~i~~~~~~~~~~a~~~i~~  675 (974)
                      .++.++++++|+...+.||+++++.+||+||++|++|+++||++|+|+         ++.|.|++... .+++|+++|..
T Consensus         4 ~~~~~~s~~ap~~~~i~Ip~~~ig~IIGkgG~~Ik~I~~~tga~I~I~~~~~~~~~~~~~V~I~G~~~-~v~~A~~~I~~   82 (104)
T 1we8_A            4 GSSGILTENTPVFEQLSVPQRSVGRIIGRGGETIRSICKASGAKITCDKESEGTLLLSRLIKISGTQK-EVAAAKHLILE   82 (104)
T ss_dssp             CCCCCCSSSCEEEEEEEEETTTHHHHHTTTSHHHHHHHHHHCCEEEECCSSCCSSSSEEEEEEEEEHH-HHHHHHHHHHH
T ss_pred             CCccccCCCCCEEEEEEEChhheeeeECCCCHHHHHHHHHHCCEEEEecCCCCCCCCcceEEEEcCHH-HHHHHHHHHHH
Confidence            456789999999999999999999999999999999999999999986         35788988765 78999999988


Q ss_pred             Hhhccc
Q 002054          676 IIGREI  681 (974)
Q Consensus       676 l~~~~~  681 (974)
                      ++..+.
T Consensus        83 ~i~e~~   88 (104)
T 1we8_A           83 KVSEDE   88 (104)
T ss_dssp             HHHHHH
T ss_pred             HHhhCh
Confidence            774443

>2z0s_A Probable exosome complex RNA-binding protein 1; alpha/beta protein, cytoplasm, structural genomics, NPPSFA; 3.20A {Aeropyrum pernix} SCOP: b.40.4.5 d.51.1.1

Probab=98.68  E-value=1.5e-08  Score=107.63  Aligned_cols=74  Identities=19%  Similarity=0.319  Sum_probs=67.9

Q ss_pred             ccccCcEEEEEEEEEeeceEEEEEcCCeEEEEecccCCCc----cccccccccccCCEEEEEEEEEccCCceEEEEec
Q 002054          680 EIEVGGIYKGVVTSVKEYGAFVEFNGGQQGLLHVSELSHE----PVSRVSDVVSVGQQLSLRCIGQDVRGNIKLSLKA  753 (974)
Q Consensus       680 ~~~~G~i~~G~V~~i~~~G~fV~l~~g~~Glvhisels~~----~v~~~~~~~~vGd~V~vkVl~id~~gri~LS~K~  753 (974)
                      .+++|+++.|+|+++.++|+||+|..+.+|+||+|+++++    +..++.+.|++||.|+|+|++++.++++.||+|+
T Consensus        63 ~p~~GDiV~G~V~~v~~~~~~V~I~~~~~g~l~isei~~~~~~~~~~~~~~~l~~GD~V~a~Vi~v~~~~~i~LS~k~  140 (235)
T 2z0s_A           63 VPQAGDVVIGLIQSVGIMNWFVDINSPYVAVLSVQDFLGRPFNPAVDDMQSLLKVGDYIKAKVVAFDKTRSPLLTVQG  140 (235)
T ss_dssp             CCCTTCCEEEEEEEECSSEEEEECSSSSCEEEEHHHHHTSCCCTTTTCCTTSSCTTCEEEEEEEEECTTSCEEEECCS
T ss_pred             CCCCCCEEEEEEEEEeCCeEEEEeCCCeEEEEEHHHhCCCccccchhhHhhcCCCCCEEEEEEEEECCCCcEEEEEec
Confidence            4799999999999999999999998889999999999873    4577888999999999999999988899999875

>1q8k_A Eukaryotic translation initiation factor 2 subunit 1; NMR {Homo sapiens} SCOP: a.60.14.1 b.40.4.5 d.58.51.1

Probab=98.66  E-value=5.1e-08  Score=106.93  Aligned_cols=66  Identities=21%  Similarity=0.208  Sum_probs=58.8

Q ss_pred             CCCCCEEEEEEEEEeCCeEEEEeC--CCeEEEEecccCC-------CCCCCCCCEEEEEEEEEeC-CCceeeeecC
Q 002054          908 LKLGTKVAAKVYQVRARGLVLDLG--GGIRGMYRFENNE-------KKDFVVGDELLVKCSSFTG-KGIPVVSLVD  973 (974)
Q Consensus       908 ~~vG~vV~G~V~~I~~~GvFV~L~--~gv~Glih~se~~-------~~~f~vGd~V~vkVl~id~-~~~~~~~~~~  973 (974)
                      +++|+++.|+|++|++||+||+|+  +|+.||+|.|+++       .+.|++||.|+|+|+++|+ ++..-+|+.+
T Consensus        11 ~~vG~iv~G~V~~I~~fGaFV~L~ey~gveGLvhiSels~~~i~~~~~~~kvGd~V~VkVl~vD~~~~rI~LSlK~   86 (308)
T 1q8k_A           11 PEVEDVVMVNVRSIQEMGAYVSLLEYNNIEGMIHLSELSRRRIRSINKLIRIGRNECVKVIRVDKEKGYIDLSKRR   86 (308)
T ss_dssp             CSSCCEEEEEEEEEETTEEEEESCTTTSCCEEECGGGTSCSSCSCCTTTCSSSCEEEEEEEEEETTTTEEEEECSS
T ss_pred             CCCCCEEEEEEEEEeCcEEEEEECCCCCeEEEEEhHHcCcccccCHHHhcCCCCEEEEEEEEEeCCCCEEEEEEEe
Confidence            459999999999999999999998  6999999999884       4569999999999999998 6777788754

>1vig_A Vigilin; RNA-binding protein, ribonucleoprotein; NMR {Homo sapiens} SCOP: d.51.1.1 PDB: 1vih_A

Probab=98.58  E-value=5.4e-08  Score=83.81  Aligned_cols=60  Identities=15%  Similarity=0.245  Sum_probs=54.1

Q ss_pred             ceeeeeccchhhhhcCCCccchhhhhhhhCceEEee-CC----EEEEEecCHHHHHHHHHHHHHHh
Q 002054          617 LATLKYDNDTLRRLIGPLGALKRKIEEETGGRISVS-DG----TLTVVAKNRSVMEKVLEKVDFII  677 (974)
Q Consensus       617 ~~~~~i~~~ki~~vIg~gGk~i~~i~~~~g~~Idi~-dg----~v~i~~~~~~~~~~a~~~i~~l~  677 (974)
                      ...++||+++++.+||+||++|++|+++||++|+++ +|    .|.|++. .+.+++|+++|..++
T Consensus         6 ~~~i~I~~~~ig~iIG~gG~~I~~I~e~tg~~I~i~~~g~~~~~V~I~G~-~~~v~~A~~~I~~i~   70 (71)
T 1vig_A            6 YVEINIDHKFHRHLIGKSGANINRIKDQYKVSVRIPPDSEKSNLIRIEGD-PQGVQQAKRELLELA   70 (71)
T ss_dssp             EEEEEECSSHHHHHTCSSCCHHHHHHHHTCCEEECCCCCSSSEEEEEEES-SHHHHHHHHHHHHTC
T ss_pred             EEEEEECHHHhhhhcCCCCccHHHHHHHHCCEEEECCCCCcccEEEEEcC-HHHHHHHHHHHHHHh
Confidence            457789999999999999999999999999999997 77    9999998 588999999888663

>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=98.58  E-value=3.9e-08  Score=89.49  Aligned_cols=60  Identities=25%  Similarity=0.325  Sum_probs=55.9

Q ss_pred             ceeeeeccchhhhhcCCCccchhhhhhhh-CceEEee-CC----EEEEEecCHHHHHHHHHHHHHHh
Q 002054          617 LATLKYDNDTLRRLIGPLGALKRKIEEET-GGRISVS-DG----TLTVVAKNRSVMEKVLEKVDFII  677 (974)
Q Consensus       617 ~~~~~i~~~ki~~vIg~gGk~i~~i~~~~-g~~Idi~-dg----~v~i~~~~~~~~~~a~~~i~~l~  677 (974)
                      ..+++||+++++.+||+||++||+|+++| |++|+++ +|    .|.|.+++. .+++|+++|+.++
T Consensus        18 t~~i~Ip~~~i~~iIG~gGk~Ir~I~eetggv~I~i~~~g~~~~~V~I~G~~~-~v~~A~~~I~~iv   83 (95)
T 2ctj_A           18 EVEVSIPAKLHNSLIGTKGRLIRSIMEECGGVHIHFPVEGSGSDTVVIRGPSS-DVEKAKKQLLHLA   83 (95)
T ss_dssp             CEEEECCHHHHHHHHCSSSHHHHHHHHHHTSCEEECCCTTTTCCEEEEESCHH-HHHHHHHHHHHHH
T ss_pred             EEEEEECHHHHhhhCCCCchhHHHHHHHcCCCEEEeCCCCCCcceEEEEcCHH-HHHHHHHHHHHHH
Confidence            56788999999999999999999999999 9999997 78    999999877 9999999999887

>3cw2_C Translation initiation factor 2 subunit alpha; AIF2, intact AIF2, initiation factor 2 alpha subunit, initiation factor 2 beta subunit; 2.80A {Sulfolobus solfataricus} PDB: 2aho_B 3v11_B*

Probab=98.56  E-value=4.2e-08  Score=105.87  Aligned_cols=68  Identities=25%  Similarity=0.271  Sum_probs=60.8

Q ss_pred             ccCCCCCEEEEEEEEEeCCeEEEEeC--CCeEEEEecccCCC-------CCCCCCCEEEEEEEEEeC-CCceeeeecC
Q 002054          906 KNLKLGTKVAAKVYQVRARGLVLDLG--GGIRGMYRFENNEK-------KDFVVGDELLVKCSSFTG-KGIPVVSLVD  973 (974)
Q Consensus       906 ~~~~vG~vV~G~V~~I~~~GvFV~L~--~gv~Glih~se~~~-------~~f~vGd~V~vkVl~id~-~~~~~~~~~~  973 (974)
                      ..+++|+++.|+|++|.+||+||+|+  +|+.||+|.|+++.       +.|++||+|.|+|+++|+ ++...+|+.+
T Consensus         7 ~~~~vG~iv~G~V~~I~~~GaFV~l~e~~~~~GlihiSels~~~v~~~~~~~~vGd~V~VkVi~vd~~~g~I~LSlk~   84 (266)
T 3cw2_C            7 KLPSEGEILIATVKQVFDYGSYVSLDEYGGLQAFLPWSEVSSKWVKNIRDVLKENRKVIVKVIRVDRRKGTVDVSLKK   84 (266)
T ss_dssp             SSCCTTCEEEEEEEECCSSSBEEEETTTTSEECBBCGGGSSCSSCCCHHHHSCTTCEEEEEECCCCSSSCCCBEESTT
T ss_pred             ccCCCCCEEEEEEEEEeccEEEEEEcCCCCeEEEEEhHHcCcccccCHHHhCcCCCEEEEEEEEEeCCCCEEEEEEEe
Confidence            45689999999999999999999997  79999999999853       349999999999999998 7888888764

>2opv_A KHSRP protein; KH domain, RNA binding protein, KSRP; NMR {Homo sapiens}

Probab=98.53  E-value=1.2e-07  Score=84.50  Aligned_cols=62  Identities=18%  Similarity=0.298  Sum_probs=57.1

Q ss_pred             CcceeeeeccchhhhhcCCCccchhhhhhhhCceEEee-CCE--------EEEEecCHHHHHHHHHHHHHHh
Q 002054          615 PRLATLKYDNDTLRRLIGPLGALKRKIEEETGGRISVS-DGT--------LTVVAKNRSVMEKVLEKVDFII  677 (974)
Q Consensus       615 p~~~~~~i~~~ki~~vIg~gGk~i~~i~~~~g~~Idi~-dg~--------v~i~~~~~~~~~~a~~~i~~l~  677 (974)
                      ++...+.||+++++.+||+||++|++|+++||++|+++ +|.        |.|++ +.+.+++|+++|..++
T Consensus        13 ~~~~~i~Ip~~~ig~IIGkgG~~Ik~I~~~tga~I~i~~~~~~~~~~er~v~I~G-~~~~v~~A~~~I~~i~   83 (85)
T 2opv_A           13 GTVQEIMIPAGKAGLVIGKGGETIKQLQERAGVKMILIQDGSQNTNVDKPLRIIG-DPYKVQQACEMVMDIL   83 (85)
T ss_dssp             SEEEEEEECTTTHHHHHTTTTHHHHHHHHHHTCEEEECSSSCSSTTSCEEEEEEE-CHHHHHHHHHHHHHHH
T ss_pred             CEEEEEEeChhheeeeECCCCHHHHHHHHHHCCEEEEcCCCCCCCCCceEEEEEe-CHHHHHHHHHHHHHHh
Confidence            37889999999999999999999999999999999997 676        99998 8899999999998775

>3psi_A Transcription elongation factor SPT6; nucleus; 3.30A {Saccharomyces cerevisiae}

Probab=98.49  E-value=1.4e-07  Score=119.64  Aligned_cols=68  Identities=12%  Similarity=0.173  Sum_probs=60.4

Q ss_pred             cccCCCCCEEEEEEEEEeCCeEEEEeCCCeEEEEecccCC--------CCCCCCCCEEEEEEEEEe-CCCceeeeec
Q 002054          905 AKNLKLGTKVAAKVYQVRARGLVLDLGGGIRGMYRFENNE--------KKDFVVGDELLVKCSSFT-GKGIPVVSLV  972 (974)
Q Consensus       905 ~~~~~vG~vV~G~V~~I~~~GvFV~L~~gv~Glih~se~~--------~~~f~vGd~V~vkVl~id-~~~~~~~~~~  972 (974)
                      .+++++|++|+|+|++|++||+||+|+.|+.||||+|+++        .+.|++||.|+|+|++|| ..+...+|+.
T Consensus       897 ~~~l~~G~iv~G~V~~V~~fGaFV~L~~gveGLVHiSelsd~~~v~~p~~v~kvGd~V~vkVl~VD~~~~rI~LSlk  973 (1219)
T 3psi_A          897 EKTFFKGSIIPVRVERFWHNDIICTTNSEVECVVNAQRHAGAQLRRPANEIYEIGKTYPAKVIYIDYANITAEVSLL  973 (1219)
T ss_dssp             TTTSCTTCEEEEEEEEECSSCEEEECTTSCEEEECTTSSSSTTSCSCSTTTSCTTCEEEEEEEEEEGGGTEEEEECC
T ss_pred             HhhCCCCCEEEEEEEEEecceEEEEeCCCceEEEEHHHcCCCcccCCHHHcCCCCCEEEEEEEEEECCCCEEEEEec
Confidence            4899999999999999999999999999999999999875        335899999999999999 4566777765

>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=98.46  E-value=4.3e-07  Score=100.67  Aligned_cols=94  Identities=10%  Similarity=-0.024  Sum_probs=75.0

Q ss_pred             ccccCCeEEEEEEEeecCCCCcCcccccccccc-------ccccCC--CCCEEEEEEEEEeCCeEEEEeCCCeEEEEecc
Q 002054          871 SFSQREREELAECLFGTEDGDEDNKGTRVEAIV-------SAKNLK--LGTKVAAKVYQVRARGLVLDLGGGIRGMYRFE  941 (974)
Q Consensus       871 ~~k~Gq~v~~~Vl~vd~e~~~i~slK~~~~~p~-------~~~~~~--vG~vV~G~V~~I~~~GvFV~L~~gv~Glih~s  941 (974)
                      .+++||.++..|...|..+.-+.+.|+....-+       .+.+|+  .|++|+|+|+++.++|+||+++ ++.|++|.+
T Consensus        86 ~~~vGd~ie~~I~~~dfgR~aa~~aKqvi~qkireaere~i~~e~~~~~GeIV~G~V~ri~~~~v~VDlG-k~EgiLp~s  164 (344)
T 1hh2_P           86 LAEVGSIVKKELNVKNFGRIAAQTAKQVLIQRIRELEKEKQFEKYSELKGTVTTAEVIRVMGEWADIRIG-KLETRLPKK  164 (344)
T ss_dssp             TCCTTCEEEEECCCCCSSSCSGGGHHHHHHHHHHHHTTCCSSCCTTCCTTCEEEEEEEEECSSEEEEEET-TEEEEEEGG
T ss_pred             cccCCCEEEEEEccccCccHHHHHHHHHHHHHHHHHHHHHHHHHHhhcCCCEEEEEEEEEecCcEEEEeC-CeEEEEeHH
Confidence            578999999999777765544445555331111       246666  8999999999999999999997 999999999


Q ss_pred             cC-CCCCCCCCCEEEEEEEEEeCCC
Q 002054          942 NN-EKKDFVVGDELLVKCSSFTGKG  965 (974)
Q Consensus       942 e~-~~~~f~vGd~V~vkVl~id~~~  965 (974)
                      ++ +.+.|++||+|+|.|++++.++
T Consensus       165 E~ip~E~~~vGD~Vkv~V~~V~~~~  189 (344)
T 1hh2_P          165 EWIPGEEIKAGDLVKVYIIDVVKTT  189 (344)
T ss_dssp             GSCTTCCCCTTCEEEEEEEEEEEET
T ss_pred             HcCCCcCCCCCCEEEEEEEEEEcCC
Confidence            88 5678999999999999999653

>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=98.41  E-value=3e-07  Score=83.74  Aligned_cols=62  Identities=23%  Similarity=0.265  Sum_probs=56.5

Q ss_pred             CcceeeeeccchhhhhcCCCccchhhhhhhhCceEEee-CC-----EEEEEecCHHHHHHHHHHHHHHh
Q 002054          615 PRLATLKYDNDTLRRLIGPLGALKRKIEEETGGRISVS-DG-----TLTVVAKNRSVMEKVLEKVDFII  677 (974)
Q Consensus       615 p~~~~~~i~~~ki~~vIg~gGk~i~~i~~~~g~~Idi~-dg-----~v~i~~~~~~~~~~a~~~i~~l~  677 (974)
                      +....+.||+++++.+||+||++|++|+++||++|++. +|     .|.|++. .+.+++|+++|..++
T Consensus        16 ~vt~~i~Ip~~~ig~IIG~gG~~Ir~I~e~tg~~I~i~~~g~~~~~~V~I~G~-~e~v~~A~~~I~~i~   83 (95)
T 2ctm_A           16 MVSEDVPLDHRVHARIIGARGKAIRKIMDEFKVDIRFPQSGAPDPNCVTVTGL-PENVEEAIDHILNLE   83 (95)
T ss_dssp             CCCEEEECCTTTHHHHHCSSSCHHHHHHHHHTCEEECCCTTCSCTTEEEEESC-HHHHHHHHHHHHHHH
T ss_pred             cEEEEEEECHHHccccCCCCcchHHHHHHHHCCeEEecCCCCCCCcEEEEEcC-HHHHHHHHHHHHHHH
Confidence            45678899999999999999999999999999999997 66     8999987 589999999999887

>1go3_E DNA-directed RNA polymerase subunit E; transferase, transferase, transcription; 1.75A {Methanococcus jannaschii} SCOP: b.40.4.5 d.230.1.1

Probab=98.40  E-value=6.6e-07  Score=91.74  Aligned_cols=67  Identities=15%  Similarity=0.173  Sum_probs=56.6

Q ss_pred             ccCCCCCEEEEEEEEEeCCeEEEEeCCCeEEEEecccCC------------------CCCCCCCCEEEEEEEEEeCC---
Q 002054          906 KNLKLGTKVAAKVYQVRARGLVLDLGGGIRGMYRFENNE------------------KKDFVVGDELLVKCSSFTGK---  964 (974)
Q Consensus       906 ~~~~vG~vV~G~V~~I~~~GvFV~L~~gv~Glih~se~~------------------~~~f~vGd~V~vkVl~id~~---  964 (974)
                      ....+|+++.|+|+++++||+||+|++ ++||+|.|++.                  ...|++||+|+|+|+++|.+   
T Consensus        77 ~~~~~Gev~~G~V~~v~~~G~fV~l~~-~eglvhis~l~~~~~~~d~~~~~~~~~~~~~~~~~Gd~V~vkV~~vd~~~~~  155 (187)
T 1go3_E           77 YIPEMYELIEGEVVDVVEFGSFVRLGP-LDGLIHVSQIMDDYVSYDPKREAIIGKETGKVLEIGDYVRARIVAISLKAER  155 (187)
T ss_dssp             ECCCTTCEEEEEEEEEETTEEEEECSS-SEEEEEGGGSCSSCEEECCC--CEEETTTCCEECTTCEEEEEEEEEECCC--
T ss_pred             EccCCCCEEEEEEEEEeCcEEEEEEcC-ccEEEEhHHhCCCcceECCccceEEecCCCeEEcCCCEEEEEEEEEEcccCC
Confidence            457899999999999999999999974 99999999763                  24589999999999999974   


Q ss_pred             ---CceeeeecC
Q 002054          965 ---GIPVVSLVD  973 (974)
Q Consensus       965 ---~~~~~~~~~  973 (974)
                         +...+|+.+
T Consensus       156 p~~~~I~lS~k~  167 (187)
T 1go3_E          156 KRGSKIALTMRQ  167 (187)
T ss_dssp             ---CEEEEECCS
T ss_pred             CCccEEEEEEcC
Confidence               355667654

>1y14_B B16, RPB7, DNA-directed RNA polymerase II 19 kDa polypeptide; transferase; 2.30A {Saccharomyces cerevisiae} SCOP: b.40.4.5 d.230.1.1 PDB: 1nt9_G 1wcm_G 1pqv_G 1y1v_G 1y1w_G 1y1y_G 1y77_G* 2b63_G* 2ja5_G* 2ja6_G* 2ja7_G* 2ja8_G* 2r7z_G 2r92_G 2r93_G 2vum_G* 3fki_G 3h3v_H 3hou_G* 3hov_G* ...

Probab=98.38  E-value=6.8e-07  Score=90.36  Aligned_cols=59  Identities=12%  Similarity=0.111  Sum_probs=52.0

Q ss_pred             cCCCCCEEEEEEEEEeCCeEEEEeCCCeEEEEecccCCC-----------------CCCCCCCEEEEEEEEEeCCCc
Q 002054          907 NLKLGTKVAAKVYQVRARGLVLDLGGGIRGMYRFENNEK-----------------KDFVVGDELLVKCSSFTGKGI  966 (974)
Q Consensus       907 ~~~vG~vV~G~V~~I~~~GvFV~L~~gv~Glih~se~~~-----------------~~f~vGd~V~vkVl~id~~~~  966 (974)
                      +..+|++++|+|+++++||+||+|++ .+||+|.|+++.                 +.|++||+|+|+|+++|.+..
T Consensus        80 ~~~~Gev~~G~V~~v~~fG~FV~l~~-~dglvhis~l~~~~~~d~~~~~~~~~~~~~~~~~Gd~V~vkV~~vd~~~~  155 (171)
T 1y14_B           80 KPFKGEVVDGTVVSCSQHGFEVQVGP-MKVFVTKHLMPQDLTFNAGSNPPSYQSSEDVITIKSRIRVKIEGCISQVS  155 (171)
T ss_dssp             CCCTTCEEEEEEEEEETTEEEEEETT-EEEEEEGGGSCTTCEECC-----CEECSSCEECTTCEEEEEEEEEEEETT
T ss_pred             cCCCCCEEEEEEEEEecCEEEEEecC-eEEEEEHHHCCCCceECcccCceEEeccceEECCCCEEEEEEEEEEcCCC
Confidence            34699999999999999999999998 999999997741                 348899999999999997753

>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=98.35  E-value=4.4e-07  Score=82.95  Aligned_cols=61  Identities=18%  Similarity=0.202  Sum_probs=55.5

Q ss_pred             cceeeeeccchhhhhcCCCccchhhhhhhhCceEEee-CC-------EEEEEecCHHHHHHHHHHHHHHh
Q 002054          616 RLATLKYDNDTLRRLIGPLGALKRKIEEETGGRISVS-DG-------TLTVVAKNRSVMEKVLEKVDFII  677 (974)
Q Consensus       616 ~~~~~~i~~~ki~~vIg~gGk~i~~i~~~~g~~Idi~-dg-------~v~i~~~~~~~~~~a~~~i~~l~  677 (974)
                      ....+.||+++++.+||+||++|+.|+++||++|++. +|       .|.|++. .+.+++|+.+|..++
T Consensus        17 ~~~~i~Ip~~~ig~IIGkgG~~Ik~I~~etg~~I~i~~~g~~~~~~~~V~I~G~-~e~v~~A~~~I~~iv   85 (97)
T 2ctl_A           17 FKLSVTVDPKYHPKIIGRKGAVITQIRLEHDVNIQFPDKDDGNQPQDQITITGY-EKNTEAARDAILRIV   85 (97)
T ss_dssp             CEEEEECCTTTHHHHSCSSSCHHHHHHHHHTCEEECCCTTTCSSCSSEEEEESC-HHHHHHHHHHHHHHH
T ss_pred             eeEEEEECHHHhhhcCCCCchhHHHHHHHHCCEEEecCCCCCCCCccEEEEEeC-HHHHHHHHHHHHHHH
Confidence            3578899999999999999999999999999999997 55       8999987 889999999998876

>3bzc_A TEX; helix-turn-helix, helix-hairpin-helix, S1 domain, YQGF domain, transcription, RNA binding protein; 2.27A {Pseudomonas aeruginosa} SCOP: a.60.2.6 a.60.2.6 a.294.1.1 b.40.4.5 c.55.3.13 PDB: 3bzk_A 2oce_A

Probab=98.34  E-value=2.6e-07  Score=112.81  Aligned_cols=69  Identities=22%  Similarity=0.205  Sum_probs=60.9

Q ss_pred             cccCCCCCEEEEEEEEEeCCeEEEEeCCCeEEEEecccCCC-------CCCCCCCEEEEEEEEEeC-CCceeeeecC
Q 002054          905 AKNLKLGTKVAAKVYQVRARGLVLDLGGGIRGMYRFENNEK-------KDFVVGDELLVKCSSFTG-KGIPVVSLVD  973 (974)
Q Consensus       905 ~~~~~vG~vV~G~V~~I~~~GvFV~L~~gv~Glih~se~~~-------~~f~vGd~V~vkVl~id~-~~~~~~~~~~  973 (974)
                      .+++++|+++.|+|++|++||+||+|+.+++||||+|+++.       +.|++||.|+|+|++||. ++..-+|+..
T Consensus       649 ~~~l~vG~iv~G~V~~V~~fGaFV~l~~~~eGLVhiS~Lsd~~v~d~~~~~~vGd~V~VkVi~VD~~~~rI~LSlk~  725 (785)
T 3bzc_A          649 LKDLKPGMVLEGVVTNVTNFGAFVDIGVHQDGLVHISALSEKFVKDPYEVVKAGDIVKVKVMEVDIPRNRVGLSMRM  725 (785)
T ss_dssp             STTCCTTCBCCCEEEEEETTEEEEECSSSSEEEEETTTSCSSCCSCHHHHCCTTCCCCCBEEEEETTTTEEEECCSS
T ss_pred             hhhcCCCCEEEEEEEEEecCCeEEEeCCCcEEEEEHHHcCccccCChhheeCCCCEEEEEEEEEECCCCEEEEEEec
Confidence            56799999999999999999999999989999999999853       248999999999999997 5666777754

>3psf_A Transcription elongation factor SPT6; nucleus; 2.59A {Saccharomyces cerevisiae}

Probab=98.34  E-value=5.9e-08  Score=121.27  Aligned_cols=69  Identities=13%  Similarity=0.184  Sum_probs=0.0

Q ss_pred             cccCCCCCEEEEEEEEEeCCeEEEEeCCCeEEEEecccCCC--------CCCCCCCEEEEEEEEEe-CCCceeeeecC
Q 002054          905 AKNLKLGTKVAAKVYQVRARGLVLDLGGGIRGMYRFENNEK--------KDFVVGDELLVKCSSFT-GKGIPVVSLVD  973 (974)
Q Consensus       905 ~~~~~vG~vV~G~V~~I~~~GvFV~L~~gv~Glih~se~~~--------~~f~vGd~V~vkVl~id-~~~~~~~~~~~  973 (974)
                      .++|++|++|.|+|++|++||+||+|+.|+.||||+|++..        +.|++||.|+|+|++|| .++...+|+..
T Consensus       900 ~~~l~~G~iv~G~V~~V~~fGaFV~L~~gveGLVHiSelsd~~~v~~~~~v~kvGd~V~vkVl~VD~~~~rI~LSlk~  977 (1030)
T 3psf_A          900 EKTFFKGSIIPVRVERFWHNDIICTTNSEVECVVNAQRHAGAQLRRPANEIYEIGKTYPAKVIYIDYANITAEVSLLD  977 (1030)
T ss_dssp             ------------------------------------------------------------------------------
T ss_pred             HHHhcCCCEEEEEEEEEccCeEEEEeCCCcEEEEEHHHcCCCcccCCHHHcCCCCCEEEEEEEEEECCCCEEEEEech
Confidence            47899999999999999999999999999999999998753        34999999999999999 56777777754

>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=98.32  E-value=4.8e-07  Score=82.25  Aligned_cols=62  Identities=21%  Similarity=0.299  Sum_probs=56.3

Q ss_pred             cceeeeeccchhhhhcCCCccchhhhhhhhCceEEee-----CCEEEEEecCHHHHHHHHHHHHHHhh
Q 002054          616 RLATLKYDNDTLRRLIGPLGALKRKIEEETGGRISVS-----DGTLTVVAKNRSVMEKVLEKVDFIIG  678 (974)
Q Consensus       616 ~~~~~~i~~~ki~~vIg~gGk~i~~i~~~~g~~Idi~-----dg~v~i~~~~~~~~~~a~~~i~~l~~  678 (974)
                      ....+.||+++++.+||+||++|++|+++||++|+++     ++.|.|++. .+.+++|+.+|..++.
T Consensus        17 ~t~~i~Ip~~~ig~IIG~gG~~Ik~I~~etg~~I~i~~~~~~~~~V~I~G~-~e~v~~A~~~I~~i~~   83 (94)
T 2cte_A           17 ASATVAIPKEHHRFVIGKNGEKLQDLELKTATKIQIPRPDDPSNQIKITGT-KEGIEKARHEVLLISA   83 (94)
T ss_dssp             EEEEEECCTTTHHHHHCSSSCHHHHHHHHTTCCCBCCCTTSSCCEEEEEEC-HHHHHHHHHHHHHHHH
T ss_pred             eEEEEEEChHHeeeeECCCChhHHHHHHHHCCEEEeCCCCCCCCeEEEEEC-HHHHHHHHHHHHHHhh
Confidence            4567899999999999999999999999999999996     379999998 8999999999988873

>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=98.27  E-value=1.1e-06  Score=75.88  Aligned_cols=63  Identities=21%  Similarity=0.303  Sum_probs=55.5

Q ss_pred             CCcceeeeeccchhhhhcCCCccchhhhhhhhCceEEee-CC----EEEEEecCHHHHHHHHHHHHHHh
Q 002054          614 SPRLATLKYDNDTLRRLIGPLGALKRKIEEETGGRISVS-DG----TLTVVAKNRSVMEKVLEKVDFII  677 (974)
Q Consensus       614 ~p~~~~~~i~~~ki~~vIg~gGk~i~~i~~~~g~~Idi~-dg----~v~i~~~~~~~~~~a~~~i~~l~  677 (974)
                      .+....+.+|+++++.+||+||++|++|+++||++|+++ +|    .+.|++. .+.+++|..+|..++
T Consensus         3 ~~~~~~i~ip~~~ig~iIGkgG~~Ik~I~~~tga~I~i~~~~~~er~v~I~G~-~~~v~~A~~~I~~~l   70 (73)
T 2axy_A            3 VTLTIRLLMHGKEVGSIIGKKGESVKKMREESGARINISEGNCPERIITLAGP-TNAIFKAFAMIIDKL   70 (73)
T ss_dssp             CCEEEEEEEEHHHHHHHHCGGGHHHHHHHHHHCCEEEECSSCCSEEEEEEEEC-HHHHHHHHHHHHHHH
T ss_pred             ceEEEEEEEChhHeeeEECCCCHHHHHHHHHHCCEEEEecCCCCcEEEEEEeC-HHHHHHHHHHHHHHH
Confidence            356678899999999999999999999999999999997 44    6888887 889999999888765

>2b8k_G B16, DNA-directed RNA polymerase II 19 kDa polypeptide; DNA-dependent RNA polymerase, cellular RNA polymerase; 4.15A {Saccharomyces cerevisiae} SCOP: b.40.4.5 d.230.1.1

Probab=98.27  E-value=1e-06  Score=91.92  Aligned_cols=59  Identities=12%  Similarity=0.111  Sum_probs=52.0

Q ss_pred             cCCCCCEEEEEEEEEeCCeEEEEeCCCeEEEEecccCCC-----------------CCCCCCCEEEEEEEEEeCCCc
Q 002054          907 NLKLGTKVAAKVYQVRARGLVLDLGGGIRGMYRFENNEK-----------------KDFVVGDELLVKCSSFTGKGI  966 (974)
Q Consensus       907 ~~~vG~vV~G~V~~I~~~GvFV~L~~gv~Glih~se~~~-----------------~~f~vGd~V~vkVl~id~~~~  966 (974)
                      ...+|++++|+|+++++||+||+|+. ++||+|+|+++.                 +.|++||+|+|+|+++|.+..
T Consensus        80 ~p~vGev~~G~V~~vt~fG~FVelg~-~dGlVhiS~l~d~~~~d~~~~~w~~~~~~~~~~~Gd~VrVkV~~vd~~~~  155 (215)
T 2b8k_G           80 KPFKGEVVDGTVVSCSQHGFEVQVGP-MKVFVTKHLMPQDLTFNAGSNPPSYQSSEDVITIKSRIRVKIEGCISQVS  155 (215)
T ss_dssp             CCCTTEEEEEEEEEEETTEEEEECTT-SEEEEEGGGSCSSCCCBSSCSSCEEECSSCEEETTCEEEEEEEEEEEETT
T ss_pred             ccCCCCEEEEEEEEEecceEEEEecC-cEEEEEHHHCCccceeccccccceeeccccEECCCCEEEEEEEEEEcCCC
Confidence            45799999999999999999999987 999999998741                 338899999999999997653

>2id0_A Exoribonuclease 2; RNAse, exonuclease, hydrolyase, mRNA decay, RNR family, hydrolase; 2.35A {Escherichia coli} SCOP: b.40.4.5 b.40.4.5 b.40.4.5 b.40.4.16 PDB: 2ix0_A* 2ix1_A

Probab=98.26  E-value=2.7e-06  Score=102.99  Aligned_cols=72  Identities=11%  Similarity=0.141  Sum_probs=61.9

Q ss_pred             ccccCc--EEEEEEEEEeeceEEEEEc-CCeEEEEecccCCC--cccc----------ccccccccCCEEEEEEEEEcc-
Q 002054          680 EIEVGG--IYKGVVTSVKEYGAFVEFN-GGQQGLLHVSELSH--EPVS----------RVSDVVSVGQQLSLRCIGQDV-  743 (974)
Q Consensus       680 ~~~~G~--i~~G~V~~i~~~G~fV~l~-~g~~Glvhisels~--~~v~----------~~~~~~~vGd~V~vkVl~id~-  743 (974)
                      .-++|+  +++|+|++|++||+||+|. .|.+||||+|++++  +++.          +....|++||.|+|+|+++|. 
T Consensus       555 ~~~vGe~~~f~g~V~~V~~~G~fV~L~~~gieGlVhis~l~~~~d~~~~d~~~~~l~~~~~~~~~lGD~V~VkV~~vd~~  634 (644)
T 2id0_A          555 KDKAGTDTRFAAEIVDISRGGMRVRLVDNGAIAFIPAPFLHAVRDELVCSQENGTVQIKGETVYKVTDVIDVTIAEVRME  634 (644)
T ss_dssp             GGGTTSCCCEEEEEEEEETTEEEEEETTTCCEEEEEGGGTCSCGGGEEEETTTTEEEETTEEEEETTCEEEEEEEEEETT
T ss_pred             hhccCCCceEEEEEEEEeCCceEEEEcCCcEEEEEEchhccCcCceeEEcccccEEEecCCCEeCCCCEEEEEEEEEeCC
Confidence            457899  9999999999999999994 68999999999974  3311          345679999999999999998 


Q ss_pred             CCceEEEE
Q 002054          744 RGNIKLSL  751 (974)
Q Consensus       744 ~gri~LS~  751 (974)
                      +++|.|++
T Consensus       635 ~~~I~~~l  642 (644)
T 2id0_A          635 TRSIIARP  642 (644)
T ss_dssp             TTEEEEEE
T ss_pred             CCEEEEEE
Confidence            78999986

>4ayb_E DNA-directed RNA polymerase; transferase, multi-subunit, transcription; 3.20A {Sulfolobus shibatae} PDB: 2y0s_E 4b1o_E 4b1p_T 2waq_E 2wb1_E 2pmz_E 3hkz_E

Probab=98.26  E-value=2.7e-06  Score=86.61  Aligned_cols=58  Identities=22%  Similarity=0.302  Sum_probs=50.5

Q ss_pred             ccCCCCCEEEEEEEEEeCCeEEEEeCCCeEEEEecccCC------------------CCCCCCCCEEEEEEEEEeCC
Q 002054          906 KNLKLGTKVAAKVYQVRARGLVLDLGGGIRGMYRFENNE------------------KKDFVVGDELLVKCSSFTGK  964 (974)
Q Consensus       906 ~~~~vG~vV~G~V~~I~~~GvFV~L~~gv~Glih~se~~------------------~~~f~vGd~V~vkVl~id~~  964 (974)
                      .+..+|+++.|+|+++++||+||+++ .++||+|.++++                  ...|++||+|++||+++|.+
T Consensus        77 ~~p~~Gev~~G~V~~v~~~G~fv~l~-~~~glvh~s~l~~d~~~~d~~~~~~~g~~~~~~~~~Gd~VrvkV~~v~~~  152 (180)
T 4ayb_E           77 YVPVVQEVVEGEVLQVDNYGVFVNLG-PMDGLVHISQITDDTLKYDNVRGIIFGEKSKKVIQKGDKVRARVISVAST  152 (180)
T ss_dssp             ECCCTTCEEEEEEEEEETTEEEEECS-SSEEEEEGGGSCSSCEEECSSSCCEEETTTCCCCCTTCEEEEEEEEECC-
T ss_pred             eeccCCCEEEEEEeeeccceEEEEEC-CccceEEeeecCCCccccchhcceEEEeccCeEECCCCEEEEEEEEEeCC
Confidence            34679999999999999999999997 699999999774                  23589999999999999964

>2hh3_A KH-type splicing regulatory protein; KH-RNA binding domain, RNA binding protein; NMR {Homo sapiens}

Probab=98.24  E-value=1e-06  Score=81.79  Aligned_cols=68  Identities=15%  Similarity=0.260  Sum_probs=56.4

Q ss_pred             CCCcceeeeeccchhhhhcCCCccchhhhhhhhCceEEee-CC------EEEEEecCHHHHHHHHHHHHHHhhcccc
Q 002054          613 NSPRLATLKYDNDTLRRLIGPLGALKRKIEEETGGRISVS-DG------TLTVVAKNRSVMEKVLEKVDFIIGREIE  682 (974)
Q Consensus       613 ~~p~~~~~~i~~~ki~~vIg~gGk~i~~i~~~~g~~Idi~-dg------~v~i~~~~~~~~~~a~~~i~~l~~~~~~  682 (974)
                      ..|++..+.|++++++.|||++|++|++|+++|+++|+|+ ++      .|.|+.. .+.+++|+++|+.++ .+.+
T Consensus         8 ~~~~~~~i~Ip~~~iG~IIGkgG~~Ik~I~~~TGakI~I~~~~~~~~er~V~I~G~-~e~v~~A~~~I~~ii-~~~~   82 (106)
T 2hh3_A            8 RIGGGIDVPVPRHSVGVVIGRSGEMIKKIQNDAGVRIQFKQDDGTGPEKIAHIMGP-PDRCEHAARIINDLL-QSLR   82 (106)
T ss_dssp             ----CEEEEEETTTHHHHHTTTTHHHHHHHHHHTCEEEECSSCSSSSEEEEEEESS-HHHHHHHHHHHHHHH-HHHC
T ss_pred             CCCeEEEEEECHHHcCccCCCCcHHHHHHHHHHCcEEEEecCCCCCceeEEEEEeC-HHHHHHHHHHHHHHH-hccc
Confidence            4578899999999999999999999999999999999997 33      6888876 789999999999887 3443

>2c35_B Human RPB7, DNA-directed RNA polymerase II 19 kDa polypeptide; transcription, nucleotidyltransferase; 2.70A {Homo sapiens} SCOP: b.40.4.5 d.230.1.1

Probab=98.24  E-value=2.3e-06  Score=86.58  Aligned_cols=58  Identities=21%  Similarity=0.110  Sum_probs=50.3

Q ss_pred             CCCCCEEEEEEEEEeCCeEEEEeCCCeEEEEecccCC-------------------CCCCCCCCEEEEEEEEEeCCCc
Q 002054          908 LKLGTKVAAKVYQVRARGLVLDLGGGIRGMYRFENNE-------------------KKDFVVGDELLVKCSSFTGKGI  966 (974)
Q Consensus       908 ~~vG~vV~G~V~~I~~~GvFV~L~~gv~Glih~se~~-------------------~~~f~vGd~V~vkVl~id~~~~  966 (974)
                      -.+|++++|+|+++++||+||+|+ .+.||+|.|+++                   ...|++||+|+|+|+++|.+..
T Consensus        79 ~~~Gev~~G~V~~v~~fG~fV~l~-~~~glvhis~l~~~~~~d~~~~~~~~~~~~~~~~~~~Gd~V~vkV~~vd~~~~  155 (172)
T 2c35_B           79 PFKGEVVDAVVTQVNKVGLFTEIG-PMSCFISRHSIPSEMEFDPNSNPPCYKTMDEDIVIQQDDEIRLKIVGTRVDKN  155 (172)
T ss_dssp             CCTTCEEEEEEEEEETTEEEEEET-TEEEEEEGGGSCTTEEEESSSSSCEEEETTSCSEEETTCEEEEEEEEEEEETT
T ss_pred             CCCCCEEEEEEEEEeCCEEEEEEC-CEEEEEEHHHCCCCcEECCCCCccEEEeCCCCEEECCCCEEEEEEEEEEcCCC
Confidence            469999999999999999999996 678999999764                   1148899999999999997644

>2bx2_L Ribonuclease E, RNAse E; RNA-binding, RNA turnover, RNA processing, hydrolase, endonu nuclease; 2.85A {Escherichia coli} PDB: 2c0b_L 2c4r_L 2vmk_A 2vrt_A 1slj_A 1smx_A 1sn8_A

Probab=98.22  E-value=1.7e-06  Score=100.78  Aligned_cols=72  Identities=25%  Similarity=0.465  Sum_probs=60.7

Q ss_pred             ccccCcEEEEEEEEEeec--eEEEEEcCCeEEEEecccCCCccc---------cccccccccCCEEEEEEEEEcc-CCce
Q 002054          680 EIEVGGIYKGVVTSVKEY--GAFVEFNGGQQGLLHVSELSHEPV---------SRVSDVVSVGQQLSLRCIGQDV-RGNI  747 (974)
Q Consensus       680 ~~~~G~i~~G~V~~i~~~--G~fV~l~~g~~Glvhisels~~~v---------~~~~~~~~vGd~V~vkVl~id~-~gri  747 (974)
                      ...+|.+|.|+|++|.++  ||||+++++.+||||+|++++.++         .++.+.+++||.|.|+|++.+. ++.-
T Consensus        42 ~~~vGnIY~GkV~rv~p~~~aAFVdiG~gk~gfLhisei~~~~~~~~~~~~~~~~i~d~lk~Gq~VlVQV~Ke~~g~KGa  121 (517)
T 2bx2_L           42 EQKKANIYKGKITRIEPSLEAAFVDYGAERHGFLPLKEIAREYFPANYSAHGRPNIKDVLREGQEVIVQIDKEERGNKGA  121 (517)
T ss_dssp             CCCTTCEEEEEEEEEETTTTEEEEESSSSSCEEEEGGGSCGGGCC-------CCCGGGTCCTTCEEEEEEEECCCTTCCC
T ss_pred             cCCCCCEEEEEEEEeccCCceEEEEeCCCcEEEEEHHHcChhhhccccccccccchhhhccCCCEEEEEEEeeccccCCc
Confidence            467999999999999999  999999999999999999988763         3467889999999999999654 2334


Q ss_pred             EEEE
Q 002054          748 KLSL  751 (974)
Q Consensus       748 ~LS~  751 (974)
                      .||.
T Consensus       122 ~lTt  125 (517)
T 2bx2_L          122 ALTT  125 (517)
T ss_dssp             EEES
T ss_pred             eEEe
Confidence            5553

>3ayh_B DNA-directed RNA polymerase III subunit RPC8; transcription; 2.19A {Schizosaccharomyces pombe}

Probab=98.22  E-value=1.7e-06  Score=89.75  Aligned_cols=63  Identities=13%  Similarity=0.190  Sum_probs=55.8

Q ss_pred             ccccCcEEEEEEEEEeeceEEEEEcCCeEEEEecccCCCccc-------------------cccccccccCCEEEEEEEE
Q 002054          680 EIEVGGIYKGVVTSVKEYGAFVEFNGGQQGLLHVSELSHEPV-------------------SRVSDVVSVGQQLSLRCIG  740 (974)
Q Consensus       680 ~~~~G~i~~G~V~~i~~~G~fV~l~~g~~Glvhisels~~~v-------------------~~~~~~~~vGd~V~vkVl~  740 (974)
                      .+.+|++++|+|+++++||+||+| +..+|++|++++.+++.                   ++....+++||.|++||.+
T Consensus        78 ~p~~GEv~~G~Vs~vt~~GifV~l-g~~eglv~~~~l~~d~~~fd~~~~~~v~~~~~~~~~~~~~~~~~~Gd~VrvrV~~  156 (203)
T 3ayh_B           78 RPFRGEVMLGKIKSCSEEGIRVTI-SFFDDIFIPKDMLFDPCVFRPDERAWVWKIEGEDGSEGTELYFDIDEEIRFQIES  156 (203)
T ss_dssp             CCCTTCEEEEEEEEEETTEEEEEC-SSCCCEEEEGGGBCTTEEEEGGGTEEEEEECCCTTSCCEEEECCTTCEEEEEEEE
T ss_pred             ccCCCCEEEEEEEEEeccEEEEEE-eCceEEEEcHHhCCCCceECccCceEEeecccccccccCCcEEcCCCEEEEEEEE
Confidence            578999999999999999999999 57899999999987654                   4445679999999999999


Q ss_pred             Ecc
Q 002054          741 QDV  743 (974)
Q Consensus       741 id~  743 (974)
                      +|.
T Consensus       157 v~~  159 (203)
T 3ayh_B          157 EDF  159 (203)
T ss_dssp             EEE
T ss_pred             EEc
Confidence            986

>2yqr_A KIAA0907 protein; structure genomics, KH domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=98.21  E-value=1.1e-06  Score=82.90  Aligned_cols=54  Identities=11%  Similarity=0.175  Sum_probs=50.1

Q ss_pred             chhhhhcCCCccchhhhhhhhCceEEee-----------------CCEEEEEecCHHHHHHHHHHHHHHhh
Q 002054          625 DTLRRLIGPLGALKRKIEEETGGRISVS-----------------DGTLTVVAKNRSVMEKVLEKVDFIIG  678 (974)
Q Consensus       625 ~ki~~vIg~gGk~i~~i~~~~g~~Idi~-----------------dg~v~i~~~~~~~~~~a~~~i~~l~~  678 (974)
                      ++|+++|||||++||.|+++||++|+|.                 +++|.|++.+.+.+++|+++|+.|+.
T Consensus        28 n~ig~IIGpgG~tiK~I~~eTG~kI~I~G~gS~~~e~~~~~e~~e~l~V~I~a~~~e~i~~A~~~Ie~Ll~   98 (119)
T 2yqr_A           28 NVKEKVEGPGCSYLQHIQIETGAKVFLRGKGSGCIEPASGREAFEPMYIYISHPKPEGLAAAKKLCENLLQ   98 (119)
T ss_dssp             CHHHHHSCGGGHHHHHHHHHHCCEEEEESBTTTCCCTTTSSCCSSBCEEEEEESSHHHHHHHHHHHHHHHH
T ss_pred             CeeeeEECCCChHHHHHHHHHCCEEEEecCCccccccccccccCCCcEEEEEeCCHHHHHHHHHHHHHHhh
Confidence            4899999999999999999999999994                 37999999999999999999998873

>2ba0_A Archeal exosome RNA binding protein RRP4; RNAse PH, RNA degradation, exoribonuclease, S1domain, KH domain, archaeal; 2.70A {Archaeoglobus fulgidus} SCOP: b.40.4.5 b.84.4.2 d.51.1.1

Probab=98.18  E-value=4e-06  Score=88.51  Aligned_cols=65  Identities=17%  Similarity=0.263  Sum_probs=59.2

Q ss_pred             CCCCCEEEEEEEEEeCCeEEEEeCCCeEEEEecccCCC--------CCCCCCCEEEEEEEEEeCCCceeeeec
Q 002054          908 LKLGTKVAAKVYQVRARGLVLDLGGGIRGMYRFENNEK--------KDFVVGDELLVKCSSFTGKGIPVVSLV  972 (974)
Q Consensus       908 ~~vG~vV~G~V~~I~~~GvFV~L~~gv~Glih~se~~~--------~~f~vGd~V~vkVl~id~~~~~~~~~~  972 (974)
                      .++||+|.|+|.+++++|+||+++....|++|.++...        +.|++||.|.|+|++++.++.+.+|+.
T Consensus        55 p~~GDiV~G~V~~v~~~~a~V~I~~~~~g~l~isev~~~~~~~~~~~~l~~GD~V~arVi~v~~~~~i~LS~r  127 (229)
T 2ba0_A           55 PSVGDVVIGIIREVAANGWAVDIYSPYQAFLPVSENPEMKPNKKPNEVLDIGDAIIAKVLNIDPKMKVTLTMK  127 (229)
T ss_dssp             CCTTCEEEEEEEEECSSEEEEECSSSSCEEEEGGGCTTCCTTSCGGGTCCTTCEEEEEEEEECTTCCEEEECC
T ss_pred             CCCCCEEEEEEEEEeCCeEEEEeCCCeEEEEEHHHccccccccchhcccCCCCEEEEEEEEECCCCcEEEEEc
Confidence            58999999999999999999999989999999998752        369999999999999999998888864

>2z0s_A Probable exosome complex RNA-binding protein 1; alpha/beta protein, cytoplasm, structural genomics, NPPSFA; 3.20A {Aeropyrum pernix} SCOP: b.40.4.5 d.51.1.1

Probab=98.16  E-value=2e-06  Score=91.24  Aligned_cols=66  Identities=15%  Similarity=0.186  Sum_probs=58.6

Q ss_pred             cCCCCCEEEEEEEEEeCCeEEEEeCCCeEEEEecccCCC-----------CCCCCCCEEEEEEEEEeCCCceeeeec
Q 002054          907 NLKLGTKVAAKVYQVRARGLVLDLGGGIRGMYRFENNEK-----------KDFVVGDELLVKCSSFTGKGIPVVSLV  972 (974)
Q Consensus       907 ~~~vG~vV~G~V~~I~~~GvFV~L~~gv~Glih~se~~~-----------~~f~vGd~V~vkVl~id~~~~~~~~~~  972 (974)
                      ..++||+|.|+|+++.++|+||+++.++.|++|.+++..           +.|++||.|.|+|++++.++.+.+|+.
T Consensus        63 ~p~~GDiV~G~V~~v~~~~~~V~I~~~~~g~l~isei~~~~~~~~~~~~~~~l~~GD~V~a~Vi~v~~~~~i~LS~k  139 (235)
T 2z0s_A           63 VPQAGDVVIGLIQSVGIMNWFVDINSPYVAVLSVQDFLGRPFNPAVDDMQSLLKVGDYIKAKVVAFDKTRSPLLTVQ  139 (235)
T ss_dssp             CCCTTCCEEEEEEEECSSEEEEECSSSSCEEEEHHHHHTSCCCTTTTCCTTSSCTTCEEEEEEEEECTTSCEEEECC
T ss_pred             CCCCCCEEEEEEEEEeCCeEEEEeCCCeEEEEEHHHhCCCccccchhhHhhcCCCCCEEEEEEEEECCCCcEEEEEe
Confidence            358999999999999999999999999999999997632           279999999999999999887777753

>2nn6_I 3'-5' exoribonuclease CSL4 homolog; RNA, exosome, PM/SCL, phosphorolytic, hydrolase/transferase complex; 3.35A {Homo sapiens} SCOP: b.40.4.5 b.84.4.2

Probab=98.16  E-value=2.3e-06  Score=89.09  Aligned_cols=66  Identities=24%  Similarity=0.259  Sum_probs=55.9

Q ss_pred             cCCCCCEEEEEEEEEeCCeEEEEeC--------CCeEEEEecccCC---------CCCCCCCCEEEEEEEEEeCCC-cee
Q 002054          907 NLKLGTKVAAKVYQVRARGLVLDLG--------GGIRGMYRFENNE---------KKDFVVGDELLVKCSSFTGKG-IPV  968 (974)
Q Consensus       907 ~~~vG~vV~G~V~~I~~~GvFV~L~--------~gv~Glih~se~~---------~~~f~vGd~V~vkVl~id~~~-~~~  968 (974)
                      .+++||+|.|+|.+|+++|+||+|.        .++.|++|+++..         .+.|++||.|.|+|++++.++ ...
T Consensus        78 ~p~vGDvV~G~V~~v~~~~a~V~I~~v~~~~L~~~~~GlIhisei~~~~~~~~~~~~~l~~GD~V~akVisi~~~~~~i~  157 (209)
T 2nn6_I           78 LPDVGAIVTCKVSSINSRFAKVHILYVGSMPLKNSFRGTIRKEDVRATEKDKVEIYKSFRPGDIVLAKVISLGDAQSNYL  157 (209)
T ss_dssp             CCCTTCEEEEEEEEECSSEEEEEEEESSSSCCCCSSCSCEEEEGGGTCSSCCCCGGGTCCSSSEEEEEEEEEETTTTEEE
T ss_pred             CCCCCCEEEEEEEEEECceEEEEECccccccccCCceeEEEHHHcccccccccchhhhcCCCCEEEEEEEEEeCCCCeEE
Confidence            5799999999999999999999974        5789999998663         234999999999999999876 466


Q ss_pred             eeec
Q 002054          969 VSLV  972 (974)
Q Consensus       969 ~~~~  972 (974)
                      +|..
T Consensus       158 LS~k  161 (209)
T 2nn6_I          158 LTTA  161 (209)
T ss_dssp             EECC
T ss_pred             EEEe
Confidence            6654

>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=98.16  E-value=1.9e-06  Score=78.30  Aligned_cols=65  Identities=18%  Similarity=0.291  Sum_probs=56.2

Q ss_pred             cceeeeeccchhhhhcCCCccchhhhhhhhCceEEee-CCE--------EEEEecCHHHHHHHHHHHHHHhhcccc
Q 002054          616 RLATLKYDNDTLRRLIGPLGALKRKIEEETGGRISVS-DGT--------LTVVAKNRSVMEKVLEKVDFIIGREIE  682 (974)
Q Consensus       616 ~~~~~~i~~~ki~~vIg~gGk~i~~i~~~~g~~Idi~-dg~--------v~i~~~~~~~~~~a~~~i~~l~~~~~~  682 (974)
                      ....+.||+++++.+||++|++|++|+++||++|+++ ++.        |.|.. +.+.+++|+++|..++ .+.+
T Consensus        15 ~~~~i~Ip~~~vG~IIGkgG~~Ik~I~~~tga~I~I~~~~~~~~~~~r~v~I~G-~~~~v~~A~~~I~~~i-~~~~   88 (94)
T 1x4m_A           15 AVQEIMIPASKAGLVIGKGGETIKQLQERAGVKMVMIQDGPQNTGADKPLRITG-DPYKVQQAKEMVLELI-RDQG   88 (94)
T ss_dssp             EEEEEEECHHHHHHHSCSSSSHHHHHHHHHTSEEEECCSCCCSSCSCEEEEEEE-CTTTHHHHHHHHHHHH-CCCS
T ss_pred             EEEEEEEChhhcceEECCCCHHHHHHHHHHCCeEEecCCCCCCCCCceEEEEEe-CHHHHHHHHHHHHHHH-hccC
Confidence            4567789999999999999999999999999999997 444        88988 7789999999999887 3444

>3m7n_A Putative uncharacterized protein AF_0206; exosome, RNA, exonuclease, hydrolase, nuclease, hydrolase-RN; 2.40A {Archaeoglobus fulgidus} PDB: 2ba1_A 3m85_A

Probab=98.16  E-value=3.7e-06  Score=85.56  Aligned_cols=60  Identities=17%  Similarity=0.150  Sum_probs=52.5

Q ss_pred             CCCCCEEEEEEEEEeCCeEEEEeCC----------CeEEEEecccCC-------CCCCCCCCEEEEEEEEEeCCCceeee
Q 002054          908 LKLGTKVAAKVYQVRARGLVLDLGG----------GIRGMYRFENNE-------KKDFVVGDELLVKCSSFTGKGIPVVS  970 (974)
Q Consensus       908 ~~vG~vV~G~V~~I~~~GvFV~L~~----------gv~Glih~se~~-------~~~f~vGd~V~vkVl~id~~~~~~~~  970 (974)
                      .+ ||+|.|+|++|+++|+||+|..          ++.|++|+|++.       .+.|++||.|.|+|++    +...+|
T Consensus        56 p~-GdiV~G~V~~V~~~ga~V~I~~v~~~~~~~~~~~~Gll~isei~~~~~~~~~~~~~~GD~V~akVi~----~~i~LS  130 (179)
T 3m7n_A           56 VK-GDVVLGRVVDLRNSIALIEVSSKKGENRGPSNRGIGILHVSNVDEGYVKEISEAVGYLDILKARVIG----DNLRLS  130 (179)
T ss_dssp             CT-TCEEEEEEEEECSSEEEEEEEEETTCCSCCTTCEEEEEEGGGTTSSCCSSGGGTCCTTCEEEEEEEE----TTTEEE
T ss_pred             CC-CCEEEEEEEEEeCCcEEEEEccccCcccccccCeeEEEEHHHcCcchhhCHhhcCCCCCEEEEEEEC----CeEEEE
Confidence            36 9999999999999999999987          899999999874       3469999999999998    666666


Q ss_pred             ec
Q 002054          971 LV  972 (974)
Q Consensus       971 ~~  972 (974)
                      ..
T Consensus       131 ~k  132 (179)
T 3m7n_A          131 TK  132 (179)
T ss_dssp             CC
T ss_pred             Ee
Confidence            54

>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=98.15  E-value=2.3e-06  Score=85.54  Aligned_cols=94  Identities=13%  Similarity=0.265  Sum_probs=70.1

Q ss_pred             HHHHHHHHHHHHHHhcCCCCCCCCCCCcc---eeeeeccchhhhhcCCCccchhhhhhhhCceEEee-------CCEEEE
Q 002054          589 HKGRLQILDHMEREISAPRTQDDRNSPRL---ATLKYDNDTLRRLIGPLGALKRKIEEETGGRISVS-------DGTLTV  658 (974)
Q Consensus       589 ~~~~~~I~~~m~~~i~~~~~~~~~~~p~~---~~~~i~~~ki~~vIg~gGk~i~~i~~~~g~~Idi~-------dg~v~i  658 (974)
                      ..+...|.+.|.+....+......+.|+.   ..+.+|+++++.+||+||++|++|+++||++|.+.       ++.+.|
T Consensus        61 ~~A~~~I~~ii~e~~~~~~~~~~~~~~~~~~~~~i~vp~~~~g~iIGk~G~~I~~i~~~tg~~I~i~~~~~~~~~~~v~I  140 (164)
T 2jvz_A           61 QQACEMVMDILRERDQGGFGDRNEYGSRIGGGIDVPVPRHSVGVVIGRSGEMIKKIQNDAGVRIQFKQDDGTGPEKIAHI  140 (164)
T ss_dssp             HHHHHHHHHHTTCSSSCCCSSCSSCTTSCSSSBCCEEETTTHHHHHCSSSHHHHHHHHHTCCEEEECCCCTTSSEEEEEE
T ss_pred             HHHHHHHHHHHHhccCCCCCCccccCCCCCceEEEEEChhhccccCCCCcHhHHHHHHHHCCeEEEeCCCCCCCcEEEEE
Confidence            33444555555544333333444555543   67889999999999999999999999999999986       357888


Q ss_pred             EecCHHHHHHHHHHHHHHhhcccccC
Q 002054          659 VAKNRSVMEKVLEKVDFIIGREIEVG  684 (974)
Q Consensus       659 ~~~~~~~~~~a~~~i~~l~~~~~~~G  684 (974)
                      ++. .+..+.|+..+..++ .+++.|
T Consensus       141 ~G~-~~~v~~A~~~I~~~i-~~~~~g  164 (164)
T 2jvz_A          141 MGP-PDRCEHAARIINDLL-QSLRSG  164 (164)
T ss_dssp             ESC-HHHHHHHHHHHHHHH-HHHHCC
T ss_pred             EcC-HHHHHHHHHHHHHHH-hhhhCC
Confidence            876 789999999998887 566654

>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=98.14  E-value=2.5e-06  Score=82.13  Aligned_cols=62  Identities=24%  Similarity=0.323  Sum_probs=55.1

Q ss_pred             ceeeeeccc------hhhhhcCCCccchhhhhhhhCceEEee-----------------------CCEEEEEecCHHHHH
Q 002054          617 LATLKYDND------TLRRLIGPLGALKRKIEEETGGRISVS-----------------------DGTLTVVAKNRSVME  667 (974)
Q Consensus       617 ~~~~~i~~~------ki~~vIg~gGk~i~~i~~~~g~~Idi~-----------------------dg~v~i~~~~~~~~~  667 (974)
                      ...+.||++      +|+.+|||+|++||.|+++||++|+|.                       ++.|.|++.+.+.++
T Consensus         8 ~~kv~IP~~~~P~~n~iG~IIGP~G~tiK~Iq~eTG~kI~IrgkgS~~~~~~~~~~~~~~~~~~e~lhV~I~a~~~e~~~   87 (131)
T 1k1g_A            8 SDKVMIPQDEYPEINFVGLLIGPRGNTLKNIEKECNAKIMIRGKGSVKEGKVGRKDGQMLPGEDEPLHALVTANTMENVK   87 (131)
T ss_dssp             EEEEECCTTTCCSHHHHHHHHCSSSHHHHHHHHHSCCEEEEEESTTSSSSSSSSCCCCCSCCSSCCEEEEEEESSHHHHH
T ss_pred             EEEEEECCccccCcceeeeEECCCcHHHHHHHHHHCCeEEecCCcccccccccccccccccccCCCeEEEEEECCHHHHH
Confidence            356677776      899999999999999999999999983                       458999999999999


Q ss_pred             HHHHHHHHHhh
Q 002054          668 KVLEKVDFIIG  678 (974)
Q Consensus       668 ~a~~~i~~l~~  678 (974)
                      +|+++|+.++.
T Consensus        88 ~A~~~I~~ll~   98 (131)
T 1k1g_A           88 KAVEQIRNILK   98 (131)
T ss_dssp             HHHHHHHHHHT
T ss_pred             HHHHHHHHHHh
Confidence            99999999873

>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=98.11  E-value=3.6e-06  Score=93.37  Aligned_cols=65  Identities=15%  Similarity=0.078  Sum_probs=58.0

Q ss_pred             ccCcEEEEEEEEEeeceEEEEEcCCeEEEEecccCCCccccccccccccCCEEEEEEEEEcc--C-CceEEEEec
Q 002054          682 EVGGIYKGVVTSVKEYGAFVEFNGGQQGLLHVSELSHEPVSRVSDVVSVGQQLSLRCIGQDV--R-GNIKLSLKA  753 (974)
Q Consensus       682 ~~G~i~~G~V~~i~~~G~fV~l~~g~~Glvhisels~~~v~~~~~~~~vGd~V~vkVl~id~--~-gri~LS~K~  753 (974)
                      +.|++++|+|.++.++|+||+++ +.+|+||.+|++      |.+.|++||.|+|.|++++.  + +++.||++.
T Consensus       133 ~~GeIV~G~V~ri~~~~v~VDlG-k~EgiLp~sE~i------p~E~~~vGD~Vkv~V~~V~~~~kg~~I~LSRt~  200 (344)
T 1hh2_P          133 LKGTVTTAEVIRVMGEWADIRIG-KLETRLPKKEWI------PGEEIKAGDLVKVYIIDVVKTTKGPKILVSRRV  200 (344)
T ss_dssp             CTTCEEEEEEEEECSSEEEEEET-TEEEEEEGGGSC------TTCCCCTTCEEEEEEEEEEEETTEEEEEEESSS
T ss_pred             cCCCEEEEEEEEEecCcEEEEeC-CeEEEEeHHHcC------CCcCCCCCCEEEEEEEEEEcCCCCcEEEEEeec
Confidence            38999999999999999999995 899999999996      45789999999999999986  2 478899874

>2p2r_A Poly(RC)-binding protein 2; protein-DNA complex, RNA and DNA binding protein/DNA complex; 1.60A {Homo sapiens}

Probab=98.10  E-value=3.2e-06  Score=73.58  Aligned_cols=62  Identities=18%  Similarity=0.297  Sum_probs=54.8

Q ss_pred             CcceeeeeccchhhhhcCCCccchhhhhhhhCceEEeeC-------CEEEEEecCHHHHHHHHHHHHHHh
Q 002054          615 PRLATLKYDNDTLRRLIGPLGALKRKIEEETGGRISVSD-------GTLTVVAKNRSVMEKVLEKVDFII  677 (974)
Q Consensus       615 p~~~~~~i~~~ki~~vIg~gGk~i~~i~~~~g~~Idi~d-------g~v~i~~~~~~~~~~a~~~i~~l~  677 (974)
                      .....+.||+++++.+||+||++|++|++++|++|++++       +.|.|++. .+..++|+.+|..++
T Consensus         4 ~~~~~i~Ip~~~vg~iIGkgG~~Ik~I~~~tga~I~i~~~~~~~~~~~v~I~G~-~~~v~~A~~~I~~~i   72 (76)
T 2p2r_A            4 TTSHELTIPNDLIGCIIGRQGAKINEIRQMSGAQIKIANPVEGSTDRQVTITGS-AASISLAQYLINVRL   72 (76)
T ss_dssp             CEEEEEEEEHHHHHHHHCGGGHHHHHHHHHHCCEEEECCCCTTCSEEEEEEEEC-HHHHHHHHHHHHHHH
T ss_pred             ceEEEEEEChHHcceEECCCChHHHHHHHHHCCEEEEcCCCCCCCeEEEEEEeC-HHHHHHHHHHHHHHH
Confidence            345678999999999999999999999999999999863       67889886 889999999998776

>2ckz_B C25, DNA-directed RNA polymerase III 25 KD polypeptide; multiprotein complex, nucleotidyltransferase, nuclear protein, hypothetical protein; 3.2A {Saccharomyces cerevisiae}

Probab=98.09  E-value=3.9e-06  Score=87.87  Aligned_cols=65  Identities=14%  Similarity=0.130  Sum_probs=55.7

Q ss_pred             cccccCcEEEEEEEEEeeceEEEEEcCCeEEEEecccCCCccc--------------cccccccccCCEEEEEEEEEcc
Q 002054          679 REIEVGGIYKGVVTSVKEYGAFVEFNGGQQGLLHVSELSHEPV--------------SRVSDVVSVGQQLSLRCIGQDV  743 (974)
Q Consensus       679 ~~~~~G~i~~G~V~~i~~~G~fV~l~~g~~Glvhisels~~~v--------------~~~~~~~~vGd~V~vkVl~id~  743 (974)
                      ..+.+|++++|+|+++++||+||+|.+..+|++|++++.++++              ++....+++||.|+|||.++|.
T Consensus        77 f~p~vGEv~~G~Is~Vt~fGifVeL~g~~eglv~~s~l~~d~~~fd~~~~~~vg~~~e~t~~~~~~Gd~VrvrV~~v~~  155 (218)
T 2ckz_B           77 FKPFLGEIVTGWISKCTAEGIKVSLLGIFDDIFIPQNMLFEGCYYTPEESAWIWPMDEETKLYFDVNEKIRFRIEREVF  155 (218)
T ss_dssp             ECCCTTCEEEEEEEEEETTEEEEECTTSCCCEEEETTTSCTTCEEETTTTEEEEECC--CEEEECTTCEEEEEEEEEEE
T ss_pred             ecCCCCCEEEEEEEEEccCcEEEEccCccceEEEcHHHCCCCcEEcCcCceEEeeccccCCcEEcCCCEEEEEEEEEEc
Confidence            3578999999999999999999999666899999999977653              3345669999999999999986

>2je6_I RRP4, exosome complex RNA-binding protein 1; nuclease, hydrolase, exonuclease, phosphorolytic, exoribonuclease, RNA degradation; HET: 1PE; 1.6A {Sulfolobus solfataricus} SCOP: b.40.4.5 b.84.4.2 d.51.1.1 PDB: 2jea_I* 2jeb_I* 3l7z_C

Probab=98.09  E-value=5.5e-06  Score=88.59  Aligned_cols=65  Identities=23%  Similarity=0.276  Sum_probs=57.9

Q ss_pred             CCCCCEEEEEEEEEeCCeEEEEeCCCeEEEEecccCC----------CCCCCCCCEEEEEEEEEeCCCceeeeec
Q 002054          908 LKLGTKVAAKVYQVRARGLVLDLGGGIRGMYRFENNE----------KKDFVVGDELLVKCSSFTGKGIPVVSLV  972 (974)
Q Consensus       908 ~~vG~vV~G~V~~I~~~GvFV~L~~gv~Glih~se~~----------~~~f~vGd~V~vkVl~id~~~~~~~~~~  972 (974)
                      .++||+|.|+|.++.++|+||+|++.+.|++|.+++.          .+.|++||.|.|+|++++.++.+.+|+.
T Consensus        72 p~~GDiV~G~V~~v~~~ga~VdI~~~~~GlL~isei~~~~~~~~~~~~~~l~vGD~V~arVi~v~~~~~i~LS~r  146 (251)
T 2je6_I           72 PKINDIVIGLVEDVEIYGWVVDIKAPYKAYLPASNLLGRSINVGEDLRRYLDVGDYVIARIENFDRSIDPVLSVK  146 (251)
T ss_dssp             CCTTCEEEEEEEEECSSEEEEECSSSSCEEEEHHHHHTSCCCTTCCCSSSCCTTCEEEEEEEEEETTEEEEEECC
T ss_pred             CCCCCEEEEEEEEEeCceEEEEcCCCeEEEEEHHHhcCCccccccchhhcCCCCCEEEEEEEEECCCCcEEEEEc
Confidence            4899999999999999999999999999999999653          2369999999999999999888777754

>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=98.06  E-value=7e-06  Score=74.21  Aligned_cols=63  Identities=17%  Similarity=0.260  Sum_probs=56.1

Q ss_pred             CCcceeeeeccchhhhhcCCCccchhhhhhhhCceEEeeC-------CEEEEEecCHHHHHHHHHHHHHHh
Q 002054          614 SPRLATLKYDNDTLRRLIGPLGALKRKIEEETGGRISVSD-------GTLTVVAKNRSVMEKVLEKVDFII  677 (974)
Q Consensus       614 ~p~~~~~~i~~~ki~~vIg~gGk~i~~i~~~~g~~Idi~d-------g~v~i~~~~~~~~~~a~~~i~~l~  677 (974)
                      .+....+.|++++++.+||++|++|++|+++||++|++++       +.|.|+.. .+.+++|+.+|+.++
T Consensus        13 ~~~~~~i~Ip~~~vG~IIGkgG~~Ik~I~~~tga~I~I~~~~~g~~~r~v~I~G~-~e~v~~A~~~I~~~i   82 (92)
T 1x4n_A           13 SVMTEEYKVPDGMVGFIIGRGGEQISRIQQESGCKIQIAPDSGGLPERSCMLTGT-PESVQSAKRLLDQIV   82 (92)
T ss_dssp             CCEEEEEEEEHHHHHHHHCSSSHHHHHHHHHSCCEEEECSCCTTCSEEEEEEEEC-HHHHHHHHHHHHHHH
T ss_pred             CCEEEEEEEChHHcceeECCCchHHHHHHHHhCCEEEEcCCCCCCCccEEEEEeC-HHHHHHHHHHHHHHH
Confidence            4567888999999999999999999999999999999973       37889886 789999999998877

>2ja9_A Exosome complex exonuclease RRP40; RNA-binding protein, RNA, S1 domain, KH domain, hydrolase, RNA-binding, nuclear protein; 2.20A {Saccharomyces cerevisiae} SCOP: b.40.4.5 d.51.1.1

Probab=98.05  E-value=9e-06  Score=82.07  Aligned_cols=93  Identities=11%  Similarity=0.054  Sum_probs=74.1

Q ss_pred             ccccCcEEEEEEEEEeeceEEEEEcC-CeEEEEecccCCCccccccccccccCCEEEEEEEEEccCCceEEEEeccCCCc
Q 002054          680 EIEVGGIYKGVVTSVKEYGAFVEFNG-GQQGLLHVSELSHEPVSRVSDVVSVGQQLSLRCIGQDVRGNIKLSLKAVSPRP  758 (974)
Q Consensus       680 ~~~~G~i~~G~V~~i~~~G~fV~l~~-g~~Glvhisels~~~v~~~~~~~~vGd~V~vkVl~id~~gri~LS~K~~~~~~  758 (974)
                      .+++|+++.|+|+++..++++|+|.+ ..+|++|++++. ...++....|++||.|.++|..++.++.+.||+.+.....
T Consensus         4 ~P~~gDvViG~V~~v~~~~~~VdI~~~~~~a~L~~s~~~-g~~k~~r~~l~~GDlV~ArV~~~~~~~~~~Ltc~~~~~~r   82 (175)
T 2ja9_A            4 IPSVNDFVIGVIIGTFSDSYKVSLQNFSSSVSLSYMAFP-NASKKNRPTLQVGDLVYARVCTAEKELEAEIECFDSTTGR   82 (175)
T ss_dssp             CCCTTCEEEEEEEEECSSEEEEESSTTSCCEEEETTSST-TCCSSSCCCCCTTCEEEEEEEECCTTSCCEEESSCTTTCS
T ss_pred             cCCCcCEEEEEEEEEECcEEEEEECCCCccEEEEHHHCC-chhhhhhccCCCCCEEEEEEEEecCCCceEEEeccccccc
Confidence            47899999999999999999999988 799999999986 3456778889999999999999988889999954321111


Q ss_pred             ccccCceEEEEEeec
Q 002054          759 EADVKGVVEGSVPVN  773 (974)
Q Consensus       759 ~~~~g~~~~G~vv~i  773 (974)
                      ....|....|.++++
T Consensus        83 ~~~lG~L~~G~l~~v   97 (175)
T 2ja9_A           83 DAGFGILEDGMIIDV   97 (175)
T ss_dssp             CTTCEEECSCEEEEC
T ss_pred             ccCCcCcCCCEEEEE
Confidence            123455566777765

>2wp8_J Exosome complex exonuclease DIS3; nucleus, hydrolase, RNA-binding, exonucle binding, mitochondrion, rRNA processing; 3.00A {Saccharomyces cerevisiae}

Probab=98.04  E-value=6.6e-06  Score=103.28  Aligned_cols=69  Identities=20%  Similarity=0.207  Sum_probs=60.0

Q ss_pred             CcEEEEEEEEEeeceEEEEEcC-CeEEEEecccCC--Cccc-----------cc----cccccccCCEEEEEEEEEcc--
Q 002054          684 GGIYKGVVTSVKEYGAFVEFNG-GQQGLLHVSELS--HEPV-----------SR----VSDVVSVGQQLSLRCIGQDV--  743 (974)
Q Consensus       684 G~i~~G~V~~i~~~G~fV~l~~-g~~Glvhisels--~~~v-----------~~----~~~~~~vGd~V~vkVl~id~--  743 (974)
                      |++++|+|++|.+||+||.|.+ |++|+||+|+++  ++++           ++    ....|++||.|+|+|..+|.  
T Consensus       887 ge~~~g~V~~V~~~G~fV~L~~~giEGlVhis~L~~~~d~y~fde~~~~L~g~~~~g~~~~~~~lGD~V~VkV~~vd~~~  966 (977)
T 2wp8_J          887 ESTETGYVIKVFNNGIVVLVPKFGVEGLIRLDNLTEDPNSAAFDEVEYKLTFVPTNSDKPRDVYVFDKVEVQVRSVMDPI  966 (977)
T ss_dssp             TCEEEEEEEEECSSEEEEECTTTCCEEEEEGGGTCSCGGGCEEETTTTEEEECCTTCCSCEEEETTCEEEEEECCCCCSS
T ss_pred             ceEEEEEEEEEcCCeEEEEEcCCCeEEEEEeccccCCCceeEEcccccEEEeecCCCccCcEEccCCEEEEEEEEEcCcc
Confidence            9999999999999999999987 899999999997  4431           12    35789999999999999986  


Q ss_pred             --CCceEEEEe
Q 002054          744 --RGNIKLSLK  752 (974)
Q Consensus       744 --~gri~LS~K  752 (974)
                        ++||.||+|
T Consensus       967 ~~~~kI~Lslk  977 (977)
T 2wp8_J          967 TSKRKAELLLK  977 (977)
T ss_dssp             SCCCCCCEEEC
T ss_pred             cCCCceEEEeC
Confidence              279999987

>2nn6_H Exosome complex exonuclease RRP4; RNA, exosome, PM/SCL, phosphorolytic, hydrolase/transferase complex; 3.35A {Homo sapiens} SCOP: b.40.4.5 b.84.4.2 d.51.1.1

Probab=98.03  E-value=3e-06  Score=92.91  Aligned_cols=88  Identities=19%  Similarity=0.166  Sum_probs=70.4

Q ss_pred             ccccCcEEEEEEEEEeeceEEEEEcCCeEEEEecccCCCc----cc------cccccccccCCEEEEEEEEEccCCceEE
Q 002054          680 EIEVGGIYKGVVTSVKEYGAFVEFNGGQQGLLHVSELSHE----PV------SRVSDVVSVGQQLSLRCIGQDVRGNIKL  749 (974)
Q Consensus       680 ~~~~G~i~~G~V~~i~~~G~fV~l~~g~~Glvhisels~~----~v------~~~~~~~~vGd~V~vkVl~id~~gri~L  749 (974)
                      .+++|+++.|+|+++.++|+||+|....+|++|+|+++..    +.      .++.+.|++||.|.|||++++.++++.|
T Consensus        92 ~P~vGDvViG~Vt~V~~~~a~VdI~s~~~~~l~iS~v~f~gg~iR~~~~~D~~~m~~~l~vGDlV~ArVisv~~~~~i~L  171 (308)
T 2nn6_H           92 IGEVGDIVVGRITEVQQKRWKVETNSRLDSVLLLSSMNLPGGELRRRSAEDELAMRGFLQEGDLISAEVQAVFSDGAVSL  171 (308)
T ss_dssp             CCCSSBCCCEEEEEEETTEEEEECSSSSCEEEESSCCC-------------CHHHHHHSCSSCEECCEEEEEETTTEEEE
T ss_pred             CCCCCCEEEEEEEEEeCceEEEEECCCcCCceechhhccccceeecccchhhhhhhccCCCCCEEEEEEEEcCCCCCEEE
Confidence            4799999999999999999999997678999999999753    22      2345789999999999999998889999


Q ss_pred             EEeccCCCcccccCceEEEEEeec
Q 002054          750 SLKAVSPRPEADVKGVVEGSVPVN  773 (974)
Q Consensus       750 S~K~~~~~~~~~~g~~~~G~vv~i  773 (974)
                      |+|+      ...|....|++..+
T Consensus       172 Str~------~~LGkL~~G~v~~v  189 (308)
T 2nn6_H          172 HTRS------LKYGKLGQGVLVQV  189 (308)
T ss_dssp             ECCS------STTCEECSSCEEEC
T ss_pred             EecC------cCCcccCCeEEEEE
Confidence            9885      23455555666653

>3h0g_G DNA-directed RNA polymerase II subunit RPB7; transcription, multi-protein complex, DNA- binding, magnesium; 3.65A {Schizosaccharomyces pombe}

Probab=98.00  E-value=3.2e-06  Score=85.51  Aligned_cols=60  Identities=15%  Similarity=0.075  Sum_probs=52.1

Q ss_pred             ccCCCCCEEEEEEEEEeCCeEEEEeCCCeEEEEecccCCC-----------------CCCCCCCEEEEEEEEEeCCCc
Q 002054          906 KNLKLGTKVAAKVYQVRARGLVLDLGGGIRGMYRFENNEK-----------------KDFVVGDELLVKCSSFTGKGI  966 (974)
Q Consensus       906 ~~~~vG~vV~G~V~~I~~~GvFV~L~~gv~Glih~se~~~-----------------~~f~vGd~V~vkVl~id~~~~  966 (974)
                      -.-.+|++++|+|+++++||+||+|+ .++||+|.|+++.                 ..|++||+|++||+++|.+..
T Consensus        80 f~p~~Gev~~G~V~~v~~fG~FV~l~-~~~glVh~s~l~~~~~~d~~~~~~~~~~~~~~~~~Gd~VrvkV~~vd~~~~  156 (172)
T 3h0g_G           80 WRPFRGEVVDAIVTTVNKMGFFANIG-PLNVFVSSHLVPPDMKFDPTANPPNYSGEDQVIEKGSNVRLKIVGTRTDAT  156 (172)
T ss_dssp             ECCCTTCEEECCCCEEETTEEECCBT-TBCCEEEGGGSCTTCCCBSSSSSCBEESSSCEECSSCCEEEEEEEEEESSS
T ss_pred             eccCCCCEEEEEEEEEEcceEEEEeC-CeEEEEEHHHCCCccccCcccccceEecCCcEECCCCEEEEEEEEEECCCC
Confidence            34579999999999999999999997 5789999998741                 358999999999999998763

>2bh8_A 1B11; transcription, molecular evolution, unique architecture, transcription regulation, phosphorylation; 1.9A {Escherichia coli}

Probab=98.00  E-value=2.2e-05  Score=72.22  Aligned_cols=84  Identities=20%  Similarity=0.199  Sum_probs=65.2

Q ss_pred             cccCcEEEEEEEEE---eeceEEEEEc-CCeEEEEecccCCCccccccccccccCCEEEEEEEEEccCCceEEEEeccCC
Q 002054          681 IEVGGIYKGVVTSV---KEYGAFVEFN-GGQQGLLHVSELSHEPVSRVSDVVSVGQQLSLRCIGQDVRGNIKLSLKAVSP  756 (974)
Q Consensus       681 ~~~G~i~~G~V~~i---~~~G~fV~l~-~g~~Glvhisels~~~v~~~~~~~~vGd~V~vkVl~id~~gri~LS~K~~~~  756 (974)
                      .+.++.++|+|+..   +.|| |+.-. ++.+.|+|+|++.+..+  +...+++||.|+..|..++              
T Consensus        11 ~~~~~~~~G~Vk~fn~~kGfG-FI~~~~gg~dvfvH~s~l~~~~~--~~~~l~~Ge~V~g~V~~i~--------------   73 (101)
T 2bh8_A           11 RLQSGKMTGIVKWFNADKGFG-FITPDDGSKDVFVHFSAGSSGAA--VRGNPQQGDRVEGKIKSIT--------------   73 (101)
T ss_dssp             -----CEEEEEEEEEGGGTEE-EEEESSSSCEEEEECCCSCSSSC--CCCCCCTTCEEEEEEEECC--------------
T ss_pred             ccccccceeEEEEEECCCCCE-EEEeCCCCcEEEEEEEEEecCCc--cccCCCCCCEEEEEEEEeC--------------
Confidence            45678899999988   6689 77764 45899999999998754  1234789999999887753              


Q ss_pred             CcccccCceEEEEEeecCCcceeeEEeeccCCCC
Q 002054          757 RPEADVKGVVEGSVPVNKQATDVWASVGDVSNGQ  790 (974)
Q Consensus       757 ~~~~~~g~~~~G~vv~i~~gv~~~~~~~~l~~~~  790 (974)
                               .+|.|+++..++++++|+++++|.+
T Consensus        74 ---------~fG~fv~l~~~~eGlvhis~i~~~~   98 (101)
T 2bh8_A           74 ---------DFGIFIGLDGGIDGLVHLSDISWAQ   98 (101)
T ss_dssp             ---------SEEEEECTTSCEEEEEEEEEEEECC
T ss_pred             ---------CcEEEEEcCCCceEEEEHHHCccCc
Confidence                     3899999988999999999999875

>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=97.99  E-value=9.9e-06  Score=71.57  Aligned_cols=61  Identities=15%  Similarity=0.269  Sum_probs=54.1

Q ss_pred             cceeeeeccchhhhhcCCCccchhhhhhhhCceEEeeC-------CEEEEEecCHHHHHHHHHHHHHHh
Q 002054          616 RLATLKYDNDTLRRLIGPLGALKRKIEEETGGRISVSD-------GTLTVVAKNRSVMEKVLEKVDFII  677 (974)
Q Consensus       616 ~~~~~~i~~~ki~~vIg~gGk~i~~i~~~~g~~Idi~d-------g~v~i~~~~~~~~~~a~~~i~~l~  677 (974)
                      ....+.||+++++.+||+||++|++|+++||++|++++       +.|.|+. +.+.+++|+.+|+.++
T Consensus         7 ~~~~i~Vp~~~vg~iIGkgG~~Ik~I~~~tga~I~i~~~~~~~~~~~v~I~G-~~~~v~~A~~~I~~~i   74 (82)
T 1zzk_A            7 ITTQVTIPKDLAGSIIGKGGQRIKQIRHESGASIKIDEPLEGSEDRIITITG-TQDQIQNAQYLLQNSV   74 (82)
T ss_dssp             EEEEEEEETTTGGGGTCGGGHHHHHHHHHHCCEEEECCTTSCSSEEEEEEEE-CHHHHHHHHHHHHHHH
T ss_pred             EEEEEEEChHhcCeeECCCchHHHHHHHHHCCEEEEcCCCCCCCceEEEEEe-CHHHHHHHHHHHHHHH
Confidence            45678999999999999999999999999999999873       3788888 5889999999998776

>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=97.99  E-value=1.1e-05  Score=80.49  Aligned_cols=86  Identities=15%  Similarity=0.246  Sum_probs=67.9

Q ss_pred             HHHHHHHHHHHHHHHH-hcCCCCCCCCCCCcceeeeeccchhhhhcCCCccchhhhhhhhCceEEee-CC--------EE
Q 002054          587 HAHKGRLQILDHMERE-ISAPRTQDDRNSPRLATLKYDNDTLRRLIGPLGALKRKIEEETGGRISVS-DG--------TL  656 (974)
Q Consensus       587 ~A~~~~~~I~~~m~~~-i~~~~~~~~~~~p~~~~~~i~~~ki~~vIg~gGk~i~~i~~~~g~~Idi~-dg--------~v  656 (974)
                      ++..+...|++.|.+. ...|+.    ..+....+.||+++++.+||+||++|++|+++||++|++. ++        .|
T Consensus        59 ~v~~A~~~I~~~~~e~~~~~~~~----~~~~~~~i~vp~~~~g~iIGkgG~~I~~i~~~tga~I~i~~~~~~~~~~~~~v  134 (163)
T 3krm_A           59 AQFKAQGRIYGKLKEENFFGPKE----EVKLETHIRVPASAAGRVIGKGGKTVNELQNLTAAEVVVPRDQTPDENDQVIV  134 (163)
T ss_dssp             HHHHHHHHHHHHHHHTTSSCSSC----CCCEEEEEEEETTTHHHHHCGGGHHHHHHHHHHCCEEECCTTCCCCTTSEEEE
T ss_pred             HHHHHHHHHHHHHhccccccccc----CCceEEEEEcChhheeeEEcCCChHHHHHHHHhCCeEEECCCCCCCCCCceEE
Confidence            4455666777777765 333322    2233457889999999999999999999999999999997 44        78


Q ss_pred             EEEecCHHHHHHHHHHHHHHh
Q 002054          657 TVVAKNRSVMEKVLEKVDFII  677 (974)
Q Consensus       657 ~i~~~~~~~~~~a~~~i~~l~  677 (974)
                      .|++ +.+..+.|+.+|..++
T Consensus       135 ~I~G-~~~~v~~A~~~I~~~i  154 (163)
T 3krm_A          135 KIIG-HFYASQMAQRKIRDIL  154 (163)
T ss_dssp             EEEE-CHHHHHHHHHHHHHHH
T ss_pred             EEEe-CHHHHHHHHHHHHHHH
Confidence            9998 6789999999998887

>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=97.98  E-value=1.8e-05  Score=78.80  Aligned_cols=88  Identities=22%  Similarity=0.347  Sum_probs=70.8

Q ss_pred             HHHHHHHHHHHHHHhcCCCCC--CCCCCCcceeeeeccchhhhhcCCCccchhhhhhhhCceEEee--------CCEEEE
Q 002054          589 HKGRLQILDHMEREISAPRTQ--DDRNSPRLATLKYDNDTLRRLIGPLGALKRKIEEETGGRISVS--------DGTLTV  658 (974)
Q Consensus       589 ~~~~~~I~~~m~~~i~~~~~~--~~~~~p~~~~~~i~~~ki~~vIg~gGk~i~~i~~~~g~~Idi~--------dg~v~i  658 (974)
                      .++...|++.|.+.+..++..  ..+++|....+.||+++++.+||+||++|++|++++|++|+++        ++.|.|
T Consensus        60 ~~A~~~I~~~i~e~~~~~~~~~~~~~~~~~~~~i~vp~~~~g~iIGkgG~~Ik~i~~~tga~I~i~~~~~~~~~~~~v~I  139 (160)
T 2jzx_A           60 FKAFAMIIDKLEEDISSSMTNSTAASRPPVTLRLVVPASQCGSLIGKGGCKIKEIRESTGAQVQVAGDMLPNSTERAITI  139 (160)
T ss_dssp             HHHHHHHHHHHHHHHTSCCCSSSCCCCCSEEEEEEEEHHHHHHHHCGGGHHHHHHHHHHSSEECCCCCCSTTCCEEEEEE
T ss_pred             HHHHHHHHHHHHhhccccCCCCccCCCCCEEEEEEEChhheeeEECCCCHHHHHHHHHhCCeEEECCCCCCCCCceEEEE
Confidence            445556777777776654321  2356688889999999999999999999999999999999886        367889


Q ss_pred             EecCHHHHHHHHHHHHHHh
Q 002054          659 VAKNRSVMEKVLEKVDFII  677 (974)
Q Consensus       659 ~~~~~~~~~~a~~~i~~l~  677 (974)
                      ++ +.+.+++|+..+..++
T Consensus       140 ~G-~~~~v~~A~~~I~~~i  157 (160)
T 2jzx_A          140 AG-IPQSIIECVKQICVVM  157 (160)
T ss_dssp             EE-CHHHHHHHHHHHHHHH
T ss_pred             Ec-CHHHHHHHHHHHHHHH
Confidence            88 7889999998887765

>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=97.98  E-value=8.2e-06  Score=72.09  Aligned_cols=63  Identities=16%  Similarity=0.268  Sum_probs=54.5

Q ss_pred             CcceeeeeccchhhhhcCCCccchhhhhhhhCceEEeeC-------CEEEEEecCHHHHHHHHHHHHHHhh
Q 002054          615 PRLATLKYDNDTLRRLIGPLGALKRKIEEETGGRISVSD-------GTLTVVAKNRSVMEKVLEKVDFIIG  678 (974)
Q Consensus       615 p~~~~~~i~~~ki~~vIg~gGk~i~~i~~~~g~~Idi~d-------g~v~i~~~~~~~~~~a~~~i~~l~~  678 (974)
                      +....+.||+++++.+||+||++|++|++++|++|++++       +.|.|++.. +.+++|+.+|..++.
T Consensus         5 ~~~~~i~Ip~~~vg~IIGkgG~~Ik~I~~~sga~I~i~~~~~~~~~r~v~I~G~~-~~v~~A~~~I~~~i~   74 (82)
T 1wvn_A            5 QTTHELTIPNNLIGCIIGRQGANINEIRQMSGAQIKIANPVEGSSGRQVTITGSA-ASISLAQYLINARLS   74 (82)
T ss_dssp             CEEEEEEEEGGGHHHHHCGGGHHHHHHHHHHCCEEEECCCCTTCSEEEEEEEECH-HHHHHHHHHHHHHTC
T ss_pred             cEEEEEEEchHhccceeCCCchhHHHHHHHhCCEEEEecCCCCCCceEEEEEcCH-HHHHHHHHHHHHHHH
Confidence            345678999999999999999999999999999999863       378888765 899999999988763

>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=97.97  E-value=7.4e-06  Score=71.18  Aligned_cols=59  Identities=15%  Similarity=0.234  Sum_probs=52.2

Q ss_pred             eeeeeccchhhhhcCCCccchhhhhhhhCceEEee-C---------CEEEEEecCHHHHHHHHHHHHHHh
Q 002054          618 ATLKYDNDTLRRLIGPLGALKRKIEEETGGRISVS-D---------GTLTVVAKNRSVMEKVLEKVDFII  677 (974)
Q Consensus       618 ~~~~i~~~ki~~vIg~gGk~i~~i~~~~g~~Idi~-d---------g~v~i~~~~~~~~~~a~~~i~~l~  677 (974)
                      ..+.||+++++.+||+||++|++|++++|++|+++ +         +.|.|++. .+..+.|+..|..++
T Consensus         5 ~~i~Ip~~~vg~IIGkgG~~Ik~I~~~tga~I~i~~~~~~~~~~~~~~v~I~G~-~~~v~~A~~~I~~~i   73 (76)
T 1dtj_A            5 VEMAVPENLVGAILGKGGKTLVEYQELTGARIQISKKGEFLPGTRNRRVTITGS-PAATQAAQYLISQRV   73 (76)
T ss_dssp             EEEEEETTTHHHHHCSTTHHHHHHHHHHCCEEEECCTTCCSTTCCEEEEEEEES-HHHHHHHHHHHHHHC
T ss_pred             EEEEEChHHcceEECCCchHHHHHHHHhCCEEEECcCCCCCCCCceeEEEEEeC-HHHHHHHHHHHHHHH
Confidence            46789999999999999999999999999999997 3         47888886 789999999888765

>2vnu_D Exosome complex exonuclease RRP44; hydrolase-RNA complex, RNA degradation, RNA-binding, RNA Pro; HET: 1PE; 2.30A {Saccharomyces cerevisiae} SCOP: b.40.4.5 b.40.4.5 b.40.4.5 b.40.4.16

Probab=97.97  E-value=9.8e-06  Score=99.81  Aligned_cols=68  Identities=21%  Similarity=0.196  Sum_probs=52.4

Q ss_pred             cEEEEEEEEEeeceEEEEEcC-CeEEEEecccCC--Cccc-----------cc----cccccccCCEEEEEEEEEccC--
Q 002054          685 GIYKGVVTSVKEYGAFVEFNG-GQQGLLHVSELS--HEPV-----------SR----VSDVVSVGQQLSLRCIGQDVR--  744 (974)
Q Consensus       685 ~i~~G~V~~i~~~G~fV~l~~-g~~Glvhisels--~~~v-----------~~----~~~~~~vGd~V~vkVl~id~~--  744 (974)
                      ++++|+|++|.+||+||.|.+ |++||||+|+++  ++++           .+    ....|++||.|+|+|+.+|.+  
T Consensus       671 ~~~~g~V~~V~~~G~fV~l~~~giEGlVhis~L~~~~d~~~fd~~~~~l~g~~~~~~~~~~~~lGD~V~VkV~~vd~~~~  750 (760)
T 2vnu_D          671 STETGYVIKVFNNGIVVLVPKFGVEGLIRLDNLTEDPNSAAFDEVEYKLTFVPTNSDKPRDVYVFDKVEVQVRSVMDPIT  750 (760)
T ss_dssp             SEEEEEEEEEETTEEEEEETTTTEEEEEEHHHHCSCGGGCEEETTTTEEEECCTTCSSCEEEETTCEEEEEEC-------
T ss_pred             eEEEEEEEEEECCeEEEEEeCCCcEEEEEeccccCCCceeEEcccccEEEEecCCCccCcEEecCCEEEEEEEEEECccc
Confidence            799999999999999999987 899999999996  4431           12    257899999999999999874  


Q ss_pred             --CceEEEEe
Q 002054          745 --GNIKLSLK  752 (974)
Q Consensus       745 --gri~LS~K  752 (974)
                        +||.||+|
T Consensus       751 ~~~kI~lslk  760 (760)
T 2vnu_D          751 SKRKAELLLK  760 (760)
T ss_dssp             -CCEEEC---
T ss_pred             cCCcEEEEeC
Confidence              89999986

>2hh2_A KH-type splicing regulatory protein; KH-RNA binding domain, RNA binding protein; NMR {Homo sapiens}

Probab=97.94  E-value=9.4e-06  Score=75.49  Aligned_cols=60  Identities=15%  Similarity=0.213  Sum_probs=54.0

Q ss_pred             ceeeeeccchhhhhcCCCccchhhhhhhhCceEEee-C---------CEEEEEecCHHHHHHHHHHHHHHh
Q 002054          617 LATLKYDNDTLRRLIGPLGALKRKIEEETGGRISVS-D---------GTLTVVAKNRSVMEKVLEKVDFII  677 (974)
Q Consensus       617 ~~~~~i~~~ki~~vIg~gGk~i~~i~~~~g~~Idi~-d---------g~v~i~~~~~~~~~~a~~~i~~l~  677 (974)
                      ...+.|+.++++.|||++|++|++|+++||++|+++ +         +.|.|+. +.+.+++|+.+|+.++
T Consensus         8 ~~~i~IP~~~vG~IIGkgG~~Ik~I~~~TGa~I~I~~~~~~~~~~~~r~V~I~G-~~e~v~~A~~~I~~~i   77 (107)
T 2hh2_A            8 EMTFSIPTHKCGLVIGRGGENVKAINQQTGAFVEISRQLPPNGDPNFKLFIIRG-SPQQIDHAKQLIEEKI   77 (107)
T ss_dssp             CEEEEEEGGGTTTTSTTTTCHHHHHHHHSSSEEEECCCCCTTCCTTEEEEEEES-CHHHHHHHHHHHHHHS
T ss_pred             eEEEEECHHHcCccCCCCcHHHHHHHHHhCCEEEEcCccCCCCCCCceEEEEEC-CHHHHHHHHHHHHHHH
Confidence            567899999999999999999999999999999986 3         4688887 8899999999999877

>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=97.91  E-value=9.1e-06  Score=72.99  Aligned_cols=61  Identities=15%  Similarity=0.267  Sum_probs=54.3

Q ss_pred             cceeeeeccchhhhhcCCCccchhhhhhhhCceEEeeC-------CEEEEEecCHHHHHHHHHHHHHHh
Q 002054          616 RLATLKYDNDTLRRLIGPLGALKRKIEEETGGRISVSD-------GTLTVVAKNRSVMEKVLEKVDFII  677 (974)
Q Consensus       616 ~~~~~~i~~~ki~~vIg~gGk~i~~i~~~~g~~Idi~d-------g~v~i~~~~~~~~~~a~~~i~~l~  677 (974)
                      ....+.||+++++.+||++|++|++|+++||++|++++       +.|.|+.. .+.+++|+.+|+.++
T Consensus        14 ~~~~i~Ip~~~vg~IIGkgG~~Ik~I~~~tga~I~I~~~~~~~~~~~v~I~G~-~e~v~~A~~~I~~~i   81 (89)
T 1j5k_A           14 ITTQVTIPKDLAGSIIGKGGQRIKQIRHESGASIKIDEPLEGSEDRIITITGT-QDQIQNAQYLLQNSV   81 (89)
T ss_dssp             EEEEEEEEHHHHHHHHCGGGHHHHHHHHHTCCEEEECSCCSSSSEEEEEEEEE-HHHHHHHHHHHHHHH
T ss_pred             EEEEEEEChhhcceeECCCCHhHHHHHHHhCCeEEecCCCCCCCccEEEEEcC-HHHHHHHHHHHHHHH
Confidence            45678899999999999999999999999999999863       67888887 789999999998776

>2bh8_A 1B11; transcription, molecular evolution, unique architecture, transcription regulation, phosphorylation; 1.9A {Escherichia coli}

Probab=97.88  E-value=4.9e-06  Score=76.57  Aligned_cols=43  Identities=28%  Similarity=0.651  Sum_probs=40.3

Q ss_pred             cccccCcEEEEEEEEEeeceEEEEEcCCeEEEEecccCCCccc
Q 002054          679 REIEVGGIYKGVVTSVKEYGAFVEFNGGQQGLLHVSELSHEPV  721 (974)
Q Consensus       679 ~~~~~G~i~~G~V~~i~~~G~fV~l~~g~~Glvhisels~~~v  721 (974)
                      ..+++|++|+++|+++.+||+||+|.++++||||+|+++|.++
T Consensus        57 ~~l~~Ge~V~g~V~~i~~fG~fv~l~~~~eGlvhis~i~~~~~   99 (101)
T 2bh8_A           57 GNPQQGDRVEGKIKSITDFGIFIGLDGGIDGLVHLSDISWAQA   99 (101)
T ss_dssp             CCCCTTCEEEEEEEECCSEEEEECTTSCEEEEEEEEEEEECCC
T ss_pred             cCCCCCCEEEEEEEEeCCcEEEEEcCCCceEEEEHHHCccCcC
Confidence            4689999999999999999999999889999999999998765

>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=97.84  E-value=1.7e-05  Score=70.86  Aligned_cols=59  Identities=15%  Similarity=0.234  Sum_probs=52.6

Q ss_pred             eeeeeccchhhhhcCCCccchhhhhhhhCceEEee-C---------CEEEEEecCHHHHHHHHHHHHHHh
Q 002054          618 ATLKYDNDTLRRLIGPLGALKRKIEEETGGRISVS-D---------GTLTVVAKNRSVMEKVLEKVDFII  677 (974)
Q Consensus       618 ~~~~i~~~ki~~vIg~gGk~i~~i~~~~g~~Idi~-d---------g~v~i~~~~~~~~~~a~~~i~~l~  677 (974)
                      ..+.||+++++.+||+||++|++|++++|++|+++ +         +.|.|++. .+.++.|+.+|..++
T Consensus         5 ~~i~IP~~~vG~IIGkgG~~Ik~I~~~tga~I~I~~~~~~~~g~~~r~v~I~G~-~~~v~~A~~~I~~~i   73 (87)
T 1ec6_A            5 VEIAVPENLVGAILGKGGKTLVEYQELTGARIQISKKGEFLPGTRNRRVTITGS-PAATQAAQYLISQRV   73 (87)
T ss_dssp             EEEEEEHHHHHHHHCGGGHHHHHHHHHHCCEEEECCTTCBSTTSCEEEEEEESS-HHHHHHHHHHHHHHH
T ss_pred             EEEEEChHHcCeeECCCcHhHHHHHHHhCCEEEEccCCCCCCCCCceEEEEEcC-HHHHHHHHHHHHHHH
Confidence            46789999999999999999999999999999997 3         37888886 789999999998776

>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=97.73  E-value=5.2e-05  Score=84.30  Aligned_cols=61  Identities=15%  Similarity=0.169  Sum_probs=52.7

Q ss_pred             cccCC--CCCEEEEEEEE----EeCCeEEEEeCC---CeEEEEecccC-CCCCCCCCCEEEEEEEEEeCCC
Q 002054          905 AKNLK--LGTKVAAKVYQ----VRARGLVLDLGG---GIRGMYRFENN-EKKDFVVGDELLVKCSSFTGKG  965 (974)
Q Consensus       905 ~~~~~--vG~vV~G~V~~----I~~~GvFV~L~~---gv~Glih~se~-~~~~f~vGd~V~vkVl~id~~~  965 (974)
                      +.+|+  +|++|+|+|.+    +.+.++||+|+.   ++.|++|.+++ |.+.|++||+|+|.|++|+.+.
T Consensus       123 ~~ef~~r~GeIVtG~V~r~~~~v~~~~v~VdLG~~~~k~EgiLP~~EqiP~E~~~~GDrVkvyV~~V~~~~  193 (366)
T 1k0r_A          123 YGEFSTREGEIVAGVIQRDSRANARGLVVVRIGTETKASEGVIPAAEQVPGESYEHGNRLRCYVVGVTRGA  193 (366)
T ss_dssp             ----CCCTTCEEEEEEECCHHHHHTTCEEEEECCSSSCEEEEECGGGSCTTCCCCTTCEEEEEEEEEECCS
T ss_pred             HHHHHhcCCCEEEEEEEEccccccCCeEEEEeCCCccceEEEEcHHHcCCCccCCCCCEEEEEEEEEecCC
Confidence            55666  99999999999    999999999986   59999999977 6788999999999999999863

>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=97.70  E-value=3.2e-05  Score=68.44  Aligned_cols=61  Identities=16%  Similarity=0.284  Sum_probs=51.1

Q ss_pred             cceeeeeccchhhhhcCCCccchhhhhhhhCceEEee---CC-EEEEEecCHHHHHHHHHHHHHHh
Q 002054          616 RLATLKYDNDTLRRLIGPLGALKRKIEEETGGRISVS---DG-TLTVVAKNRSVMEKVLEKVDFII  677 (974)
Q Consensus       616 ~~~~~~i~~~ki~~vIg~gGk~i~~i~~~~g~~Idi~---dg-~v~i~~~~~~~~~~a~~~i~~l~  677 (974)
                      ....+.||.++++.+||+||++||+|+++||++|.+.   ++ .+.++.. .+..++|+++|..+.
T Consensus        10 ~~~~i~VP~~~vG~IIGkgG~tIk~Iqe~Tga~I~I~~~~~~~~v~ItG~-~e~v~~A~~~I~~~i   74 (83)
T 2dgr_A           10 TTIQVRVPYRVVGLVVGPKGATIKRIQQRTHTYIVTPGRDKEPVFAVTGM-PENVDRAREEIEAHI   74 (83)
T ss_dssp             EEEEEECCHHHHHHHHTTTTSSHHHHHHHTTCEEECCCSSSCCEEEEEEC-TTTHHHHHHHHHHHH
T ss_pred             eEEEEEeChHHeeeeECCCchHHHHHHHHhCCeEEecCCCCCCeEEEEcC-HHHHHHHHHHHHHHH
Confidence            3456789999999999999999999999999999986   33 5666654 589999999998765

>2id0_A Exoribonuclease 2; RNAse, exonuclease, hydrolyase, mRNA decay, RNR family, hydrolase; 2.35A {Escherichia coli} SCOP: b.40.4.5 b.40.4.5 b.40.4.5 b.40.4.16 PDB: 2ix0_A* 2ix1_A

Probab=97.59  E-value=7.9e-05  Score=90.20  Aligned_cols=66  Identities=18%  Similarity=0.156  Sum_probs=56.6

Q ss_pred             cCCCCC--EEEEEEEEEeCCeEEEEeC-CCeEEEEecccCCC-------------------CCCCCCCEEEEEEEEEeCC
Q 002054          907 NLKLGT--KVAAKVYQVRARGLVLDLG-GGIRGMYRFENNEK-------------------KDFVVGDELLVKCSSFTGK  964 (974)
Q Consensus       907 ~~~vG~--vV~G~V~~I~~~GvFV~L~-~gv~Glih~se~~~-------------------~~f~vGd~V~vkVl~id~~  964 (974)
                      .-++|+  +++|+|.+|++||+||+|+ .|+.||||.|++..                   ..|++||+|+|+|+++|.+
T Consensus       555 ~~~vGe~~~f~g~V~~V~~~G~fV~L~~~gieGlVhis~l~~~~d~~~~d~~~~~l~~~~~~~~~lGD~V~VkV~~vd~~  634 (644)
T 2id0_A          555 KDKAGTDTRFAAEIVDISRGGMRVRLVDNGAIAFIPAPFLHAVRDELVCSQENGTVQIKGETVYKVTDVIDVTIAEVRME  634 (644)
T ss_dssp             GGGTTSCCCEEEEEEEEETTEEEEEETTTCCEEEEEGGGTCSCGGGEEEETTTTEEEETTEEEEETTCEEEEEEEEEETT
T ss_pred             hhccCCCceEEEEEEEEeCCceEEEEcCCcEEEEEEchhccCcCceeEEcccccEEEecCCCEeCCCCEEEEEEEEEeCC
Confidence            347899  9999999999999999995 59999999987741                   2489999999999999985


Q ss_pred             -Cceeeeec
Q 002054          965 -GIPVVSLV  972 (974)
Q Consensus       965 -~~~~~~~~  972 (974)
                       +...++|+
T Consensus       635 ~~~I~~~l~  643 (644)
T 2id0_A          635 TRSIIARPV  643 (644)
T ss_dssp             TTEEEEEEC
T ss_pred             CCEEEEEEc
Confidence             66777776

>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=97.57  E-value=6.6e-05  Score=83.46  Aligned_cols=66  Identities=20%  Similarity=0.222  Sum_probs=57.0

Q ss_pred             ccCcEEEEEEEE----EeeceEEEEEcC---CeEEEEecccCCCccccccccccccCCEEEEEEEEEccC---CceEEEE
Q 002054          682 EVGGIYKGVVTS----VKEYGAFVEFNG---GQQGLLHVSELSHEPVSRVSDVVSVGQQLSLRCIGQDVR---GNIKLSL  751 (974)
Q Consensus       682 ~~G~i~~G~V~~----i~~~G~fV~l~~---g~~Glvhisels~~~v~~~~~~~~vGd~V~vkVl~id~~---gri~LS~  751 (974)
                      ++|++++|+|.+    +.++++||+|+.   +.+|+||.+|+..      .+.|++||.|+|.|++++..   .+|.||+
T Consensus       129 r~GeIVtG~V~r~~~~v~~~~v~VdLG~~~~k~EgiLP~~EqiP------~E~~~~GDrVkvyV~~V~~~~kgpqI~LSR  202 (366)
T 1k0r_A          129 REGEIVAGVIQRDSRANARGLVVVRIGTETKASEGVIPAAEQVP------GESYEHGNRLRCYVVGVTRGAREPLITLSR  202 (366)
T ss_dssp             CTTCEEEEEEECCHHHHHTTCEEEEECCSSSCEEEEECGGGSCT------TCCCCTTCEEEEEEEEEECCSSSCEEEEES
T ss_pred             cCCCEEEEEEEEccccccCCeEEEEeCCCccceEEEEcHHHcCC------CccCCCCCEEEEEEEEEecCCCccEEEEEe
Confidence            499999999999    999999999965   4999999999863      57899999999999999873   3677876


Q ss_pred             ec
Q 002054          752 KA  753 (974)
Q Consensus       752 K~  753 (974)
                      ..
T Consensus       203 T~  204 (366)
T 1k0r_A          203 TH  204 (366)
T ss_dssp             SC
T ss_pred             CC
Confidence            53

>2ckz_B C25, DNA-directed RNA polymerase III 25 KD polypeptide; multiprotein complex, nucleotidyltransferase, nuclear protein, hypothetical protein; 3.2A {Saccharomyces cerevisiae}

Probab=97.50  E-value=0.00015  Score=75.76  Aligned_cols=59  Identities=19%  Similarity=0.149  Sum_probs=50.8

Q ss_pred             cCCCCCEEEEEEEEEeCCeEEEEeCCCeEEEEecccCC---------------------CCCCCCCCEEEEEEEEEeCCC
Q 002054          907 NLKLGTKVAAKVYQVRARGLVLDLGGGIRGMYRFENNE---------------------KKDFVVGDELLVKCSSFTGKG  965 (974)
Q Consensus       907 ~~~vG~vV~G~V~~I~~~GvFV~L~~gv~Glih~se~~---------------------~~~f~vGd~V~vkVl~id~~~  965 (974)
                      .-.+|+++.|+|.++++||+||+|++-++|++|.+++.                     ...|+.||+|++||.++|-..
T Consensus        78 ~p~vGEv~~G~Is~Vt~fGifVeL~g~~eglv~~s~l~~d~~~fd~~~~~~vg~~~e~t~~~~~~Gd~VrvrV~~v~~~~  157 (218)
T 2ckz_B           78 KPFLGEIVTGWISKCTAEGIKVSLLGIFDDIFIPQNMLFEGCYYTPEESAWIWPMDEETKLYFDVNEKIRFRIEREVFVD  157 (218)
T ss_dssp             CCCTTCEEEEEEEEEETTEEEEECTTSCCCEEEETTTSCTTCEEETTTTEEEEECC--CEEEECTTCEEEEEEEEEEECC
T ss_pred             cCCCCCEEEEEEEEEccCcEEEEccCccceEEEcHHHCCCCcEEcCcCceEEeeccccCCcEEcCCCEEEEEEEEEEccc
Confidence            34699999999999999999999976789999999662                     113889999999999999654

>2ja9_A Exosome complex exonuclease RRP40; RNA-binding protein, RNA, S1 domain, KH domain, hydrolase, RNA-binding, nuclear protein; 2.20A {Saccharomyces cerevisiae} SCOP: b.40.4.5 d.51.1.1

Probab=97.46  E-value=0.00031  Score=70.88  Aligned_cols=66  Identities=9%  Similarity=0.055  Sum_probs=59.5

Q ss_pred             CCCCCEEEEEEEEEeCCeEEEEeCC-CeEEEEecccCC------CCCCCCCCEEEEEEEEEeCCCceeeeecC
Q 002054          908 LKLGTKVAAKVYQVRARGLVLDLGG-GIRGMYRFENNE------KKDFVVGDELLVKCSSFTGKGIPVVSLVD  973 (974)
Q Consensus       908 ~~vG~vV~G~V~~I~~~GvFV~L~~-gv~Glih~se~~------~~~f~vGd~V~vkVl~id~~~~~~~~~~~  973 (974)
                      .++||+|-|+|..+..++.+|+++. ...|++|.+.++      ...|++||-|.|+|.+++.++.+-++.+|
T Consensus         5 P~~gDvViG~V~~v~~~~~~VdI~~~~~~a~L~~s~~~g~~k~~r~~l~~GDlV~ArV~~~~~~~~~~Ltc~~   77 (175)
T 2ja9_A            5 PSVNDFVIGVIIGTFSDSYKVSLQNFSSSVSLSYMAFPNASKKNRPTLQVGDLVYARVCTAEKELEAEIECFD   77 (175)
T ss_dssp             CCTTCEEEEEEEEECSSEEEEESSTTSCCEEEETTSSTTCCSSSCCCCCTTCEEEEEEEECCTTSCCEEESSC
T ss_pred             CCCcCEEEEEEEEEECcEEEEEECCCCccEEEEHHHCCchhhhhhccCCCCCEEEEEEEEecCCCceEEEecc
Confidence            3689999999999999999999998 799999999764      34699999999999999999988888666

>3ayh_B DNA-directed RNA polymerase III subunit RPC8; transcription; 2.19A {Schizosaccharomyces pombe}

Probab=97.44  E-value=0.00021  Score=74.06  Aligned_cols=56  Identities=11%  Similarity=0.072  Sum_probs=48.8

Q ss_pred             CCCCCEEEEEEEEEeCCeEEEEeCCCeEEEEecccCCC----------------------C----CCCCCCEEEEEEEEE
Q 002054          908 LKLGTKVAAKVYQVRARGLVLDLGGGIRGMYRFENNEK----------------------K----DFVVGDELLVKCSSF  961 (974)
Q Consensus       908 ~~vG~vV~G~V~~I~~~GvFV~L~~gv~Glih~se~~~----------------------~----~f~vGd~V~vkVl~i  961 (974)
                      -.+|+++.|+|.+++++|+||+| +.++|++|.+++..                      +    .|+.||+|++||.++
T Consensus        79 p~~GEv~~G~Vs~vt~~GifV~l-g~~eglv~~~~l~~d~~~fd~~~~~~v~~~~~~~~~~~~~~~~~~Gd~VrvrV~~v  157 (203)
T 3ayh_B           79 PFRGEVMLGKIKSCSEEGIRVTI-SFFDDIFIPKDMLFDPCVFRPDERAWVWKIEGEDGSEGTELYFDIDEEIRFQIESE  157 (203)
T ss_dssp             CCTTCEEEEEEEEEETTEEEEEC-SSCCCEEEEGGGBCTTEEEEGGGTEEEEEECCCTTSCCEEEECCTTCEEEEEEEEE
T ss_pred             cCCCCEEEEEEEEEeccEEEEEE-eCceEEEEcHHhCCCCceECccCceEEeecccccccccCCcEEcCCCEEEEEEEEE
Confidence            47999999999999999999999 48999999996521                      2    389999999999999


Q ss_pred             eCC
Q 002054          962 TGK  964 (974)
Q Consensus       962 d~~  964 (974)
                      |-.
T Consensus       158 ~~~  160 (203)
T 3ayh_B          158 DFV  160 (203)
T ss_dssp             EEC
T ss_pred             Ecc
Confidence            963

>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=97.39  E-value=0.00017  Score=71.67  Aligned_cols=64  Identities=22%  Similarity=0.318  Sum_probs=55.7

Q ss_pred             CCCcceeeeeccchhhhhcCCCccchhhhhhhhCceEEee-CC----EEEEEecCHHHHHHHHHHHHHHh
Q 002054          613 NSPRLATLKYDNDTLRRLIGPLGALKRKIEEETGGRISVS-DG----TLTVVAKNRSVMEKVLEKVDFII  677 (974)
Q Consensus       613 ~~p~~~~~~i~~~ki~~vIg~gGk~i~~i~~~~g~~Idi~-dg----~v~i~~~~~~~~~~a~~~i~~l~  677 (974)
                      +.|....+.||+++++.+||+||++|++|++++|++|+++ ++    .+.|++. .+.+++|+..+..++
T Consensus         2 ~~~~~~~~~vp~~~~g~iIGkgG~~Ik~i~~~tg~~I~i~~~~~~~r~v~I~G~-~~~v~~A~~~I~~~i   70 (160)
T 2jzx_A            2 NVTLTIRLLMHGKEVGSIIGKKGESVKKMREESGARINISEGNCPERIITLAGP-TNAIFKAFAMIIDKL   70 (160)
T ss_dssp             CCEEEEEEEEEHHHHHHHHCGGGHHHHHHHHHHCSEEEEECCTTTEEEEEEEEE-HHHHHHHHHHHHHHH
T ss_pred             CccEEEEEEEchhheeeeECCCcHHHHHHHHHHCCEEEEcCCCCCceEEEEEeC-HHHHHHHHHHHHHHH
Confidence            4678889999999999999999999999999999999997 33    7888876 678888888877655

>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=97.37  E-value=0.00034  Score=73.80  Aligned_cols=57  Identities=16%  Similarity=0.198  Sum_probs=52.0

Q ss_pred             CCCCEEEEEEEE----EeCCeEEEEeCC---CeEEEEecccC-CCCCCCCCCEEEEEEEEEeCCC
Q 002054          909 KLGTKVAAKVYQ----VRARGLVLDLGG---GIRGMYRFENN-EKKDFVVGDELLVKCSSFTGKG  965 (974)
Q Consensus       909 ~vG~vV~G~V~~----I~~~GvFV~L~~---gv~Glih~se~-~~~~f~vGd~V~vkVl~id~~~  965 (974)
                      ++|++|+|+|.+    +.+..+||+|+.   +..|++|.+++ +.+.|++||+|+|.|++|+...
T Consensus         6 r~GeIVtG~V~r~~~~v~~~~ViVdlG~~~~k~EgiLP~~Eqip~E~~~~GDrIkayV~~V~~~~   70 (251)
T 2asb_A            6 REGEIVAGVIQRDSRANARGLVVVRIGTETKASEGVIPAAEQVPGESYEHGNRLRCYVVGVTRGA   70 (251)
T ss_dssp             CTTCEEEEEEECCHHHHHTTCEEEEECSSSSCEEEEECGGGSCTTCCCCTTCEEEEEEEEEECCS
T ss_pred             cCCCEEEEEEEEccccccCCeEEEEeCCCCcceEEEEcHHHcCCCccCCCCCEEEEEEEEEEcCC
Confidence            589999999999    888899999986   59999999977 6788999999999999999763

>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=97.29  E-value=0.00028  Score=74.41  Aligned_cols=67  Identities=19%  Similarity=0.212  Sum_probs=58.5

Q ss_pred             cccCcEEEEEEEE----EeeceEEEEEcC---CeEEEEecccCCCccccccccccccCCEEEEEEEEEccC---CceEEE
Q 002054          681 IEVGGIYKGVVTS----VKEYGAFVEFNG---GQQGLLHVSELSHEPVSRVSDVVSVGQQLSLRCIGQDVR---GNIKLS  750 (974)
Q Consensus       681 ~~~G~i~~G~V~~----i~~~G~fV~l~~---g~~Glvhisels~~~v~~~~~~~~vGd~V~vkVl~id~~---gri~LS  750 (974)
                      -+.|++++|+|.+    +.+..+||+|..   +.+|+||.+|+.      |.+.|++||.|+|.|++++..   ++|.||
T Consensus         5 ~r~GeIVtG~V~r~~~~v~~~~ViVdlG~~~~k~EgiLP~~Eqi------p~E~~~~GDrIkayV~~V~~~~~gpqIiLS   78 (251)
T 2asb_A            5 TREGEIVAGVIQRDSRANARGLVVVRIGTETKASEGVIPAAEQV------PGESYEHGNRLRCYVVGVTRGAREPLITLS   78 (251)
T ss_dssp             CCTTCEEEEEEECCHHHHHTTCEEEEECSSSSCEEEEECGGGSC------TTCCCCTTCEEEEEEEEEECCSSSCEEEEE
T ss_pred             hcCCCEEEEEEEEccccccCCeEEEEeCCCCcceEEEEcHHHcC------CCccCCCCCEEEEEEEEEEcCCCCCEEEEE
Confidence            3689999999999    888999999965   499999999986      457899999999999999862   589999


Q ss_pred             Eec
Q 002054          751 LKA  753 (974)
Q Consensus       751 ~K~  753 (974)
                      +..
T Consensus        79 Rt~   81 (251)
T 2asb_A           79 RTH   81 (251)
T ss_dssp             SSC
T ss_pred             ecc
Confidence            865

>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=97.25  E-value=0.00058  Score=68.79  Aligned_cols=59  Identities=14%  Similarity=0.190  Sum_probs=51.5

Q ss_pred             ceeeeeccchhhhhcCCCccchhhhhhhhCceEEeeC----------CEEEEEecCHHHHHHHHHHHHHH
Q 002054          617 LATLKYDNDTLRRLIGPLGALKRKIEEETGGRISVSD----------GTLTVVAKNRSVMEKVLEKVDFI  676 (974)
Q Consensus       617 ~~~~~i~~~ki~~vIg~gGk~i~~i~~~~g~~Idi~d----------g~v~i~~~~~~~~~~a~~~i~~l  676 (974)
                      ...+.|++++++.+||++|++|++|++++|++|++++          +.|.|.. +.+.+++|+..|..+
T Consensus       105 ~~~i~vp~~~~g~iIGkgG~~Ik~I~~~tga~I~i~~~~~~~~~~~~~~v~I~G-~~~~v~~A~~~I~~~  173 (174)
T 1j4w_A          105 EFNFIVPTGKTGLIIGKGGETIKSISQQSGARIELQRNPPPNADPNMKLFTIRG-TPQQIDYARQLIEEK  173 (174)
T ss_dssp             EEEEEEETTTHHHHHCGGGHHHHHHHHHHCCEEEEECCCTTTSCTTEEEEEEEC-CHHHHHHHHHHHHHH
T ss_pred             EEEEEEChHHcCeeECCCchHHHHHHHHHCCEEEECCCCCCCCCCCceEEEEEC-CHHHHHHHHHHHHHh
Confidence            5677899999999999999999999999999999862          5688887 778999999888754

>2bl5_A MGC83862 protein, quaking protein; STAR proteins, GSG proteins, RNA binding; NMR {Xenopus laevis} SCOP: d.51.1.1

Probab=97.21  E-value=0.00034  Score=67.67  Aligned_cols=53  Identities=25%  Similarity=0.554  Sum_probs=46.6

Q ss_pred             chhhhhcCCCccchhhhhhhhCceEEee-CC------------------------EEEEEecCHH-----HHHHHHHHHH
Q 002054          625 DTLRRLIGPLGALKRKIEEETGGRISVS-DG------------------------TLTVVAKNRS-----VMEKVLEKVD  674 (974)
Q Consensus       625 ~ki~~vIg~gGk~i~~i~~~~g~~Idi~-dg------------------------~v~i~~~~~~-----~~~~a~~~i~  674 (974)
                      +.++.+|||+|.++|.|+++||++|.|. .|                        .|.|++.+.+     .+++|.+.|+
T Consensus        17 NfiG~IiGPrG~t~K~ie~eTg~kI~IrGkGS~kd~~~e~~~~g~~~~~~~~epLHV~Isa~~~~~~~~~~l~~A~~~I~   96 (140)
T 2bl5_A           17 NFVGRILGPRGLTAKQLEAETGCKIMVRGKGSMRDKKKEEQNRGKPNWEHLNEDLHVLITVEDAQNRAELKLKRAVEEVK   96 (140)
T ss_dssp             CHHHHHTTTTHHHHHHHHHHHSEEEEEESTTSSCCHHHHHTSTTSHHHHTTTSCCEEEEEECSCCHHHHHHHHHHHHHHH
T ss_pred             CeeeEEECCCcchHHHHHHHHCCeEEEecCCCcccccccccccCCCCccccCCCcEEEEEecCchhhHHHHHHHHHHHHH
Confidence            4699999999999999999999999987 55                        7889997764     7889999998


Q ss_pred             HHh
Q 002054          675 FII  677 (974)
Q Consensus       675 ~l~  677 (974)
                      .++
T Consensus        97 ~lL   99 (140)
T 2bl5_A           97 KLL   99 (140)
T ss_dssp             HHS
T ss_pred             HHC
Confidence            876

>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=97.16  E-value=0.0004  Score=70.24  Aligned_cols=63  Identities=24%  Similarity=0.250  Sum_probs=53.5

Q ss_pred             cceeeeeccchhhhhcCCCccchhhhhhhhCceEEee-C--------CEEEEEecCHHHHHHHHHHHHHHhhc
Q 002054          616 RLATLKYDNDTLRRLIGPLGALKRKIEEETGGRISVS-D--------GTLTVVAKNRSVMEKVLEKVDFIIGR  679 (974)
Q Consensus       616 ~~~~~~i~~~ki~~vIg~gGk~i~~i~~~~g~~Idi~-d--------g~v~i~~~~~~~~~~a~~~i~~l~~~  679 (974)
                      ....+.|++++++.+||+||++|++|++++|++|.+. +        +.|.|++.. +.+++|+..+..++..
T Consensus       104 ~~~~i~Vp~~~vg~iIGkgG~~Ik~i~~~tga~I~i~~~~~~~~~~~~~v~I~G~~-~~v~~A~~~I~~~i~e  175 (178)
T 2anr_A          104 NQVKIIVPNSTAGLIIGKGGATVKAIMEQSGAWVQLSQKPDGINLQNRVVTVSGEP-EQNRKAVELIIQKIQE  175 (178)
T ss_dssp             GEEEEEEEHHHHHHHHCGGGHHHHHHHHHSSCEEEECCCC----CCEEEEEEESSH-HHHHHHHHHHHHHHHS
T ss_pred             eEEEEEEchhheeeeECCCcHHHHHHHHHHCCEEEEeCCCCCCCCCceEEEEEcCH-HHHHHHHHHHHHHHHh
Confidence            4567889999999999999999999999999999986 3        378888765 7889999888877643

>2bx2_L Ribonuclease E, RNAse E; RNA-binding, RNA turnover, RNA processing, hydrolase, endonu nuclease; 2.85A {Escherichia coli} PDB: 2c0b_L 2c4r_L 2vmk_A 2vrt_A 1slj_A 1smx_A 1sn8_A

Probab=97.13  E-value=0.00059  Score=79.53  Aligned_cols=60  Identities=13%  Similarity=0.225  Sum_probs=52.1

Q ss_pred             ccCCCCCEEEEEEEEEeCC--eEEEEeCCCeEEEEecccCCC----------------CCCCCCCEEEEEEEEEeCCC
Q 002054          906 KNLKLGTKVAAKVYQVRAR--GLVLDLGGGIRGMYRFENNEK----------------KDFVVGDELLVKCSSFTGKG  965 (974)
Q Consensus       906 ~~~~vG~vV~G~V~~I~~~--GvFV~L~~gv~Glih~se~~~----------------~~f~vGd~V~vkVl~id~~~  965 (974)
                      ....+|+++.|+|++|.++  |+||++++|-.||+|.+++..                +.+++||+|.|.|++....+
T Consensus        41 ~~~~vGnIY~GkV~rv~p~~~aAFVdiG~gk~gfLhisei~~~~~~~~~~~~~~~~i~d~lk~Gq~VlVQV~Ke~~g~  118 (517)
T 2bx2_L           41 HEQKKANIYKGKITRIEPSLEAAFVDYGAERHGFLPLKEIAREYFPANYSAHGRPNIKDVLREGQEVIVQIDKEERGN  118 (517)
T ss_dssp             SCCCTTCEEEEEEEEEETTTTEEEEESSSSSCEEEEGGGSCGGGCC-------CCCGGGTCCTTCEEEEEEEECCCTT
T ss_pred             CcCCCCCEEEEEEEEeccCCceEEEEeCCCcEEEEEHHHcChhhhccccccccccchhhhccCCCEEEEEEEeecccc
Confidence            3467999999999999999  999999999999999998631                34889999999999977443

>2nn6_G Exosome complex exonuclease RRP40; RNA, exosome, PM/SCL, phosphorolytic, hydrolase/transferase complex; 3.35A {Homo sapiens} SCOP: b.40.4.5 b.84.4.2 d.51.1.1

Probab=97.05  E-value=0.001  Score=72.13  Aligned_cols=92  Identities=13%  Similarity=0.040  Sum_probs=74.5

Q ss_pred             ccccCcEEEEEEEEEeeceEEEEEcCCeEEEEecccCCCccccccccccccCCEEEEEEEEEccCCceEEEEeccCCCcc
Q 002054          680 EIEVGGIYKGVVTSVKEYGAFVEFNGGQQGLLHVSELSHEPVSRVSDVVSVGQQLSLRCIGQDVRGNIKLSLKAVSPRPE  759 (974)
Q Consensus       680 ~~~~G~i~~G~V~~i~~~G~fV~l~~g~~Glvhisels~~~v~~~~~~~~vGd~V~vkVl~id~~gri~LS~K~~~~~~~  759 (974)
                      -+++|+++.|+|+++....+.|+|.....|+||.+++. ...++....|++||.|.++|++++..+.+.||+..... ..
T Consensus       124 iP~vGDiVIG~Vt~v~~~~~~VdI~s~~~a~L~~~~f~-Gatk~~r~~f~~GDlV~ArV~s~~~~~~~eLsc~~~~~-k~  201 (289)
T 2nn6_G          124 VPVKGDHVIGIVTAKSGDIFKVDVGGSEPASLSYLSFE-GATKRNRPNVQVGDLIYGQFVVANKDMEPEMVCIDSCG-RA  201 (289)
T ss_dssp             CCCSSEEEEEEEEEEETTEEEEECSSSSCCCEESCSSS-CCSSCSSSSSCTTCEEEEEEEECCTTSCCEEECSBTTT-TB
T ss_pred             CCCCCCEEEEEEEEEeCcEEEEEECCCceeEEehhhcC-cchhhhhhhcCCCCEEEEEEEEcCCCCceEEEeccccc-cc
Confidence            47999999999999999999999988888999999876 34567778899999999999999888889999844211 11


Q ss_pred             cccCce-EEEEEeec
Q 002054          760 ADVKGV-VEGSVPVN  773 (974)
Q Consensus       760 ~~~g~~-~~G~vv~i  773 (974)
                      ...|.. ..|.++++
T Consensus       202 ~~lG~L~~~G~l~~V  216 (289)
T 2nn6_G          202 NGMGVIGQDGLLFKV  216 (289)
T ss_dssp             CCCCSCCSSCEEECC
T ss_pred             ccCCEecCCeEEEEE
Confidence            235666 67777764

>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=97.04  E-value=0.00056  Score=68.06  Aligned_cols=62  Identities=8%  Similarity=0.130  Sum_probs=53.2

Q ss_pred             CcceeeeeccchhhhhcCCCccchhhhhhhhCceEEeeC-C-------EEEEEecCHHHHHHHHHHHHHHh
Q 002054          615 PRLATLKYDNDTLRRLIGPLGALKRKIEEETGGRISVSD-G-------TLTVVAKNRSVMEKVLEKVDFII  677 (974)
Q Consensus       615 p~~~~~~i~~~ki~~vIg~gGk~i~~i~~~~g~~Idi~d-g-------~v~i~~~~~~~~~~a~~~i~~l~  677 (974)
                      |....+.|++++++.+||+||++|+.|++++|++|++.+ +       .|.|++ +.+.+.+|+..+..++
T Consensus         2 ~~~~~~~ip~~~~g~iIGk~G~~Ik~i~~~tg~~I~i~~~~~~~~~~r~v~I~G-~~e~v~~A~~~I~~~~   71 (163)
T 3krm_A            2 QEMVQVFIPAQAVGAIIGKKGQHIKQLSRFASASIKIAPPETPDSKVRMVIITG-PPEAQFKAQGRIYGKL   71 (163)
T ss_dssp             CEEEEEEEEGGGHHHHHCGGGHHHHHHHHHHTCEEEECCCSSTTCSEEEEEEEE-CHHHHHHHHHHHHHHH
T ss_pred             ceEEEEEechhhcceeECCCcHHHHHHHHHHCCeEEEcCCCCCCCCceEEEEEc-CHHHHHHHHHHHHHHH
Confidence            556788999999999999999999999999999999863 2       488888 6788888888887665

>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=97.03  E-value=0.00076  Score=67.06  Aligned_cols=60  Identities=18%  Similarity=0.310  Sum_probs=52.6

Q ss_pred             ceeeeeccchhhhhcCCCccchhhhhhhhCceEEee-CC--------EEEEEecCHHHHHHHHHHHHHHh
Q 002054          617 LATLKYDNDTLRRLIGPLGALKRKIEEETGGRISVS-DG--------TLTVVAKNRSVMEKVLEKVDFII  677 (974)
Q Consensus       617 ~~~~~i~~~ki~~vIg~gGk~i~~i~~~~g~~Idi~-dg--------~v~i~~~~~~~~~~a~~~i~~l~  677 (974)
                      +..+.||+++++.+||+||++|++|++++|++|++. ++        .+.|++ +.+.+++|+..+..++
T Consensus         3 ~~~~~Vp~~~~g~iIGk~G~~Ik~i~~~tg~~I~i~~~~~~~~~~~r~v~I~G-~~~~v~~A~~~I~~ii   71 (164)
T 2jvz_A            3 VQEIMIPAGKAGLVIGKGGETIKQLQERAGVKMILIQDGSQNTNVDKPLRIIG-DPYKVQQACEMVMDIL   71 (164)
T ss_dssp             EEEEEECTTCHHHHTCTTTHHHHHHHHTSCSEEEECCCTTSSSSSCEEEEEEE-CHHHHHHHHHHHHHHT
T ss_pred             EEEEEechhheeEEECCChHHHHHHHHHhCCeEEEecCCCCCCCCceEEEEEc-CHHHHHHHHHHHHHHH
Confidence            457889999999999999999999999999999885 33        688887 6788999999988776

>2nn6_H Exosome complex exonuclease RRP4; RNA, exosome, PM/SCL, phosphorolytic, hydrolase/transferase complex; 3.35A {Homo sapiens} SCOP: b.40.4.5 b.84.4.2 d.51.1.1

Probab=96.94  E-value=0.00062  Score=74.60  Aligned_cols=64  Identities=9%  Similarity=0.151  Sum_probs=55.1

Q ss_pred             CCCCCEEEEEEEEEeCCeEEEEeCCCeEEEEecccCCC-----------------CCCCCCCEEEEEEEEEeCCCceeee
Q 002054          908 LKLGTKVAAKVYQVRARGLVLDLGGGIRGMYRFENNEK-----------------KDFVVGDELLVKCSSFTGKGIPVVS  970 (974)
Q Consensus       908 ~~vG~vV~G~V~~I~~~GvFV~L~~gv~Glih~se~~~-----------------~~f~vGd~V~vkVl~id~~~~~~~~  970 (974)
                      .++||+|.|+|.++.++|+||++.....|++|.+++..                 ..|++||.|.|+|++++.++..-+|
T Consensus        93 P~vGDvViG~Vt~V~~~~a~VdI~s~~~~~l~iS~v~f~gg~iR~~~~~D~~~m~~~l~vGDlV~ArVisv~~~~~i~LS  172 (308)
T 2nn6_H           93 GEVGDIVVGRITEVQQKRWKVETNSRLDSVLLLSSMNLPGGELRRRSAEDELAMRGFLQEGDLISAEVQAVFSDGAVSLH  172 (308)
T ss_dssp             CCSSBCCCEEEEEEETTEEEEECSSSSCEEEESSCCC-------------CHHHHHHSCSSCEECCEEEEEETTTEEEEE
T ss_pred             CCCCCEEEEEEEEEeCceEEEEECCCcCCceechhhccccceeecccchhhhhhhccCCCCCEEEEEEEEcCCCCCEEEE
Confidence            58999999999999999999999977899999886520                 3599999999999999987766655


Q ss_pred             e
Q 002054          971 L  971 (974)
Q Consensus       971 ~  971 (974)
                      .
T Consensus       173 t  173 (308)
T 2nn6_H          173 T  173 (308)
T ss_dssp             C
T ss_pred             e
Confidence            4

>2vnu_D Exosome complex exonuclease RRP44; hydrolase-RNA complex, RNA degradation, RNA-binding, RNA Pro; HET: 1PE; 2.30A {Saccharomyces cerevisiae} SCOP: b.40.4.5 b.40.4.5 b.40.4.5 b.40.4.16

Probab=96.92  E-value=0.00064  Score=83.75  Aligned_cols=60  Identities=23%  Similarity=0.310  Sum_probs=46.9

Q ss_pred             CEEEEEEEEEeCCeEEEEeCC-CeEEEEecccCC------------------------CCCCCCCCEEEEEEEEEeCC--
Q 002054          912 TKVAAKVYQVRARGLVLDLGG-GIRGMYRFENNE------------------------KKDFVVGDELLVKCSSFTGK--  964 (974)
Q Consensus       912 ~vV~G~V~~I~~~GvFV~L~~-gv~Glih~se~~------------------------~~~f~vGd~V~vkVl~id~~--  964 (974)
                      +++.|+|.+|++||+||.|++ |+.||||.+++.                        ...|++||+|+|+|+++|.+  
T Consensus       671 ~~~~g~V~~V~~~G~fV~l~~~giEGlVhis~L~~~~d~~~fd~~~~~l~g~~~~~~~~~~~~lGD~V~VkV~~vd~~~~  750 (760)
T 2vnu_D          671 STETGYVIKVFNNGIVVLVPKFGVEGLIRLDNLTEDPNSAAFDEVEYKLTFVPTNSDKPRDVYVFDKVEVQVRSVMDPIT  750 (760)
T ss_dssp             SEEEEEEEEEETTEEEEEETTTTEEEEEEHHHHCSCGGGCEEETTTTEEEECCTTCSSCEEEETTCEEEEEEC-------
T ss_pred             eEEEEEEEEEECCeEEEEEeCCCcEEEEEeccccCCCceeEEcccccEEEEecCCCccCcEEecCCEEEEEEEEEECccc
Confidence            799999999999999999998 999999998652                        24589999999999999987  


Q ss_pred             --Cceeeee
Q 002054          965 --GIPVVSL  971 (974)
Q Consensus       965 --~~~~~~~  971 (974)
                        ++.-+||
T Consensus       751 ~~~kI~lsl  759 (760)
T 2vnu_D          751 SKRKAELLL  759 (760)
T ss_dssp             -CCEEEC--
T ss_pred             cCCcEEEEe
Confidence              6666655

>2wp8_J Exosome complex exonuclease DIS3; nucleus, hydrolase, RNA-binding, exonucle binding, mitochondrion, rRNA processing; 3.00A {Saccharomyces cerevisiae}

Probab=96.86  E-value=0.00086  Score=84.33  Aligned_cols=61  Identities=23%  Similarity=0.300  Sum_probs=53.8

Q ss_pred             CCEEEEEEEEEeCCeEEEEeCC-CeEEEEecccCC------------------C------CCCCCCCEEEEEEEEEeCC-
Q 002054          911 GTKVAAKVYQVRARGLVLDLGG-GIRGMYRFENNE------------------K------KDFVVGDELLVKCSSFTGK-  964 (974)
Q Consensus       911 G~vV~G~V~~I~~~GvFV~L~~-gv~Glih~se~~------------------~------~~f~vGd~V~vkVl~id~~-  964 (974)
                      |++..|+|.+|++||+||.|++ |+.||||.+++.                  .      ..|++||+|+|+|.++|.+ 
T Consensus       887 ge~~~g~V~~V~~~G~fV~L~~~giEGlVhis~L~~~~d~y~fde~~~~L~g~~~~g~~~~~~~lGD~V~VkV~~vd~~~  966 (977)
T 2wp8_J          887 ESTETGYVIKVFNNGIVVLVPKFGVEGLIRLDNLTEDPNSAAFDEVEYKLTFVPTNSDKPRDVYVFDKVEVQVRSVMDPI  966 (977)
T ss_dssp             TCEEEEEEEEECSSEEEEECTTTCCEEEEEGGGTCSCGGGCEEETTTTEEEECCTTCCSCEEEETTCEEEEEECCCCCSS
T ss_pred             ceEEEEEEEEEcCCeEEEEEcCCCeEEEEEeccccCCCceeEEcccccEEEeecCCCccCcEEccCCEEEEEEEEEcCcc
Confidence            9999999999999999999998 999999999763                  1      3589999999999999973 


Q ss_pred             ---Cceeeee
Q 002054          965 ---GIPVVSL  971 (974)
Q Consensus       965 ---~~~~~~~  971 (974)
                         ++..++|
T Consensus       967 ~~~~kI~Lsl  976 (977)
T 2wp8_J          967 TSKRKAELLL  976 (977)
T ss_dssp             SCCCCCCEEE
T ss_pred             cCCCceEEEe
Confidence               6777765

>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=96.82  E-value=0.0013  Score=66.15  Aligned_cols=59  Identities=17%  Similarity=0.264  Sum_probs=51.7

Q ss_pred             eeeeeccchhhhhcCCCccchhhhhhhhCceEEee--C-----CEEEEEecCHHHHHHHHHHHHHHh
Q 002054          618 ATLKYDNDTLRRLIGPLGALKRKIEEETGGRISVS--D-----GTLTVVAKNRSVMEKVLEKVDFII  677 (974)
Q Consensus       618 ~~~~i~~~ki~~vIg~gGk~i~~i~~~~g~~Idi~--d-----g~v~i~~~~~~~~~~a~~~i~~l~  677 (974)
                      ..+.|++++++.+||++|++|++|+++||++|+++  +     ..|.|++. .+.+++|+..|..++
T Consensus         5 ~~~~vp~~~vg~iIGkgG~~Ik~i~~~tg~~I~i~~~~~~~~~r~v~I~G~-~~~v~~A~~~I~~~~   70 (174)
T 1j4w_A            5 IDVPIPRFAVGIVIGRNGEMIKKIQNDAGVRIQFKPDDGTTPERIAQITGP-PDRAQHAAEIITDLL   70 (174)
T ss_dssp             EEEEEEHHHHHHHHCGGGHHHHHHHHHHCCEEEEECCTTSCSEEEEEEEEC-HHHHHHHHHHHHHHH
T ss_pred             EEEEEChhheeeeecCCchHHHHHHHHhCCEEEEecCCCCCCccEEEEEeC-HHHHHHHHHHHHHHH
Confidence            46789999999999999999999999999999996  2     26788776 788999999988776

>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=96.62  E-value=0.0021  Score=64.88  Aligned_cols=61  Identities=16%  Similarity=0.168  Sum_probs=51.7

Q ss_pred             ceeeeeccchhhhhcCCCccchhhhhhhhCceEEee-CC---------EEEEEecCHHHHHHHHHHHHHHhh
Q 002054          617 LATLKYDNDTLRRLIGPLGALKRKIEEETGGRISVS-DG---------TLTVVAKNRSVMEKVLEKVDFIIG  678 (974)
Q Consensus       617 ~~~~~i~~~ki~~vIg~gGk~i~~i~~~~g~~Idi~-dg---------~v~i~~~~~~~~~~a~~~i~~l~~  678 (974)
                      ...+.|++++++.+||+||++|++|+++||++|+++ ++         .+.|++. .+.+++|...+..++.
T Consensus         7 ~~~i~vp~~~ig~iIGkgG~~Ik~i~~~tg~~I~i~~~~~~~~~~~er~v~I~G~-~~~v~~A~~~I~~~~~   77 (178)
T 2anr_A            7 FLKVLIPSYAAGSIIGKGGQTIVQLQKETGATIKLSKSKDFYPGTTERVCLIQGT-IEALNAVHGFIAEKIR   77 (178)
T ss_dssp             EEEEEEEHHHHHHHHCGGGHHHHHHHHHHCCEEEECCTTCBCTTSSEEEEEEEEC-HHHHHHHHHHHHHHHT
T ss_pred             EEEEEEChhHeeeeECCCcHHHHHHHHHhCCeEEEecCCCCCCCCCCceEEEEeC-HHHHHHHHHHHHHHHh
Confidence            456789999999999999999999999999999986 33         5777765 6788899988887763

>2nn6_G Exosome complex exonuclease RRP40; RNA, exosome, PM/SCL, phosphorolytic, hydrolase/transferase complex; 3.35A {Homo sapiens} SCOP: b.40.4.5 b.84.4.2 d.51.1.1

Probab=96.13  E-value=0.0086  Score=64.95  Aligned_cols=66  Identities=18%  Similarity=0.181  Sum_probs=59.7

Q ss_pred             CCCCCEEEEEEEEEeCCeEEEEeCCCeEEEEecccCC------CCCCCCCCEEEEEEEEEeCCCceeeeecC
Q 002054          908 LKLGTKVAAKVYQVRARGLVLDLGGGIRGMYRFENNE------KKDFVVGDELLVKCSSFTGKGIPVVSLVD  973 (974)
Q Consensus       908 ~~vG~vV~G~V~~I~~~GvFV~L~~gv~Glih~se~~------~~~f~vGd~V~vkVl~id~~~~~~~~~~~  973 (974)
                      .++||+|-|+|.++......|++..-..|++|.++++      ...|++||-|.|+|++++.++.+-++.+|
T Consensus       125 P~vGDiVIG~Vt~v~~~~~~VdI~s~~~a~L~~~~f~Gatk~~r~~f~~GDlV~ArV~s~~~~~~~eLsc~~  196 (289)
T 2nn6_G          125 PVKGDHVIGIVTAKSGDIFKVDVGGSEPASLSYLSFEGATKRNRPNVQVGDLIYGQFVVANKDMEPEMVCID  196 (289)
T ss_dssp             CCSSEEEEEEEEEEETTEEEEECSSSSCCCEESCSSSCCSSCSSSSSCTTCEEEEEEEECCTTSCCEEECSB
T ss_pred             CCCCCEEEEEEEEEeCcEEEEEECCCceeEEehhhcCcchhhhhhhcCCCCEEEEEEEEcCCCCceEEEecc
Confidence            3799999999999999999999998889999998664      44699999999999999999989888866

>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=95.69  E-value=0.016  Score=53.09  Aligned_cols=61  Identities=15%  Similarity=0.197  Sum_probs=52.3

Q ss_pred             cceeeeeccchhhhhcCCCccchhhhhhh-hCceEEee--CCEEEEEecCHHHHHHHHHHHHHHh
Q 002054          616 RLATLKYDNDTLRRLIGPLGALKRKIEEE-TGGRISVS--DGTLTVVAKNRSVMEKVLEKVDFII  677 (974)
Q Consensus       616 ~~~~~~i~~~ki~~vIg~gGk~i~~i~~~-~g~~Idi~--dg~v~i~~~~~~~~~~a~~~i~~l~  677 (974)
                      ....+.+|+..-+.+||++|.+|++|+++ +++.|.+.  ++.|.|.++ .+..++|+..++.++
T Consensus        27 ~t~~i~vp~~~h~~IIG~~G~~Ik~i~~~~~~v~I~fp~~~~~ItI~G~-~~~V~~a~~~I~~~v   90 (102)
T 2ctf_A           27 TVSSVAAPSWLHRFIIGKKGQNLAKITQQMPKVHIEFTEGEDKITLEGP-TEDVSVAQEQIEGMV   90 (102)
T ss_dssp             EEEEEECCSTTHHHHHTTTTCHHHHHHHHCSSSEEEECSSSCEEEEEEC-HHHHHHHHHHHHHHH
T ss_pred             EEEEEEeCHHHHhhhcCCCCccHHHHHHHcCCcEEEeCCCCCEEEEECC-HHHHHHHHHHHHHHH
Confidence            34567788888899999999999999997 48999886  678999987 788999999888776

>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=94.52  E-value=0.036  Score=53.98  Aligned_cols=59  Identities=17%  Similarity=0.430  Sum_probs=48.6

Q ss_pred             eeeeeccchhhhhcCCCccchhhhhhhhCc-eEEee---C-------CE--EEEEecCHHHHHHHHHHHHHHh
Q 002054          618 ATLKYDNDTLRRLIGPLGALKRKIEEETGG-RISVS---D-------GT--LTVVAKNRSVMEKVLEKVDFII  677 (974)
Q Consensus       618 ~~~~i~~~ki~~vIg~gGk~i~~i~~~~g~-~Idi~---d-------g~--v~i~~~~~~~~~~a~~~i~~l~  677 (974)
                      ..+.+|++..+.+||.+|.|||.+.+.||+ +|++.   +       +.  +.+.+ +.+..+.|+..++..+
T Consensus        69 ~~v~Vp~~~~g~~IGK~G~nIr~i~~~tG~~~I~i~~~~~~~~~~~~~~~~vtI~G-~~~~v~~Ak~li~~~l  140 (144)
T 2qnd_A           69 DVIQVPRNLVGKVIGKNGKLIQEIVDKSGVVRVRIEAENEKNVPQEEGMVPFVFVG-TKDSIANATVLLDYHL  140 (144)
T ss_dssp             EEEEEEGGGHHHHHCGGGHHHHHHHHHHTCSEEEEEEECTTCCCCCTTEEEEEEEE-EHHHHHHHHHHHHHHH
T ss_pred             EEEEECHHHcCeeECCCCHHHHHHHHHHCCEEEEEcCCCCCCccccCCeeEEEEEe-CHHHHHHHHHHHHHHH
Confidence            677899999999999999999999999996 88875   1       22  55665 5678999998888766

>2e3u_A PH-DIM2P, hypothetical protein PH1566; PRE-ribosomal RNA processing factor, RNA binding protein; 2.30A {Pyrococcus horikoshii} PDB: 3aev_B

Probab=93.96  E-value=0.068  Score=55.71  Aligned_cols=51  Identities=24%  Similarity=0.369  Sum_probs=45.6

Q ss_pred             hhhhhcCCCccchhhhhhhhCceEEeeCCEEEEEecCHHHHHHHHHHHHHHh
Q 002054          626 TLRRLIGPLGALKRKIEEETGGRISVSDGTLTVVAKNRSVMEKVLEKVDFII  677 (974)
Q Consensus       626 ki~~vIg~gGk~i~~i~~~~g~~Idi~dg~v~i~~~~~~~~~~a~~~i~~l~  677 (974)
                      .++.+||++|++++.|++.||++|.+.+..+.+.+. .+.++.|+..+..++
T Consensus       139 ~~GriIGk~G~tik~ie~~Tg~~I~v~~~~v~i~G~-~~~i~~A~~~i~~li  189 (219)
T 2e3u_A          139 VRGRIIGRKGRTRQIIEEMSGASVSVYGKTVAIIGN-PIQIEIAKTAIEKLA  189 (219)
T ss_dssp             HHHHHHCGGGHHHHHHHHHHCCEEEEETTEEEEEEC-HHHHHHHHHHHHHHH
T ss_pred             hhheeECCCchHHHHHHHHhCceEEECCeEEEEEeC-HHHHHHHHHHHHHHH
Confidence            588999999999999999999999999889998874 567788998888777

>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=93.67  E-value=0.099  Score=53.22  Aligned_cols=60  Identities=28%  Similarity=0.337  Sum_probs=52.5

Q ss_pred             eeeeeccchhhhhcCCCccchhhhhhhhCceEEee--CCEEEEEe----cCHHHHHHHHHHHHHHh
Q 002054          618 ATLKYDNDTLRRLIGPLGALKRKIEEETGGRISVS--DGTLTVVA----KNRSVMEKVLEKVDFII  677 (974)
Q Consensus       618 ~~~~i~~~ki~~vIg~gGk~i~~i~~~~g~~Idi~--dg~v~i~~----~~~~~~~~a~~~i~~l~  677 (974)
                      ..+.||+++++-+||.+|.+++.|++++|++|.++  +|.+.+..    .+...+.+|.+.+..+.
T Consensus         6 ~~i~VP~~rvg~liGk~g~~~k~i~e~~g~~i~id~~~~~V~i~t~~~t~dp~~i~KA~dlI~ai~   71 (191)
T 1tua_A            6 IYVKVKPERLGAVIGPRGEVKAEIMRRTGTVITVDTENSMVIVEPEAEGIPPVNLMKAAEVVKAIS   71 (191)
T ss_dssp             EEEECCGGGHHHHHCGGGHHHHHHHHHHTEEEEEETTTTEEEEEESSTTSCHHHHHHHHHHHHHHH
T ss_pred             eEEECCHHHhhHHHhcCHhHHHHHHHHHCcEEEEEcCCCeEEEEeCCCCCCHHHHHHHHHHHHHHH
Confidence            57889999999999999999999999999999988  78998873    45678889999887665

>3n89_A Defective in GERM LINE development protein 3, ISO; KH domains, RNA binding, cell cycle; 2.79A {Caenorhabditis elegans}

Probab=92.22  E-value=0.24  Score=55.49  Aligned_cols=85  Identities=16%  Similarity=0.128  Sum_probs=62.3

Q ss_pred             HHHHHHHHHHHHHHHHHhcCCCCCCCCCCCcceeeeeccchhhhhcCCCc--cchhhhhhhhCceEEee---C-------
Q 002054          586 EHAHKGRLQILDHMEREISAPRTQDDRNSPRLATLKYDNDTLRRLIGPLG--ALKRKIEEETGGRISVS---D-------  653 (974)
Q Consensus       586 ~~A~~~~~~I~~~m~~~i~~~~~~~~~~~p~~~~~~i~~~ki~~vIg~gG--k~i~~i~~~~g~~Idi~---d-------  653 (974)
                      +.|++++..+++.+.+.      +....-+....+.|++.....+||.+|  ..|+.|.++||+.|++-   +       
T Consensus       162 ~~akeA~~~Ll~~l~~~------e~~~~~~~s~~v~V~~~~H~~IIGk~G~n~~IkkIr~eTGv~I~FP~~~d~~d~~~~  235 (376)
T 3n89_A          162 HELIEAAKRLNEILFRE------SPAPENNFTLHFTLSTYYVDQVLGSSSTAQLMPVIERETTTIISYPCYNNRNETRGN  235 (376)
T ss_dssp             HHHHHHHHHHHHHHCC--------CCCSSCEEEEEEEEGGGHHHHTCCTTSCCHHHHHHHHHTCEEECC---------CC
T ss_pred             HHHHHHHHHHHHHHHhh------hcccccceEEEEEeCHHHHHHhhcCCCcchHHHHHHHhhCCEEECCCCCCcccccCC
Confidence            35777777777776432      222233456678899999999999998  55699999999999863   2       


Q ss_pred             -CEEEEEecCHHHHHHHHHHHHHHh
Q 002054          654 -GTLTVVAKNRSVMEKVLEKVDFII  677 (974)
Q Consensus       654 -g~v~i~~~~~~~~~~a~~~i~~l~  677 (974)
                       ..+.|.+ ..+...+|++.|..++
T Consensus       236 ~~~ItItG-s~e~V~~Ark~I~~lL  259 (376)
T 3n89_A          236 IYEIKVVG-NIDNVLKARRYIMDLL  259 (376)
T ss_dssp             EEEEEEES-CHHHHHHHHHHHHHTS
T ss_pred             ceEEEEEe-CHHHHHHHHHHHHhhC
Confidence             1477776 5688999999888765

>2r7d_A Ribonuclease II family protein; structural genomics, PSI-2, structure initiative, northeast structural genomics consort NESG; 1.80A {Deinococcus radiodurans R1} SCOP: b.40.4.5 b.40.4.16 PDB: 2r7f_A

Probab=92.15  E-value=0.32  Score=56.38  Aligned_cols=58  Identities=17%  Similarity=0.324  Sum_probs=45.2

Q ss_pred             ccCcEEEEEEEEEeeceEEEEEcCCeEEEEecccCCCccccccccccccCCEEEEEEEEEcc-CCceEEEE
Q 002054          682 EVGGIYKGVVTSVKEYGAFVEFNGGQQGLLHVSELSHEPVSRVSDVVSVGQQLSLRCIGQDV-RGNIKLSL  751 (974)
Q Consensus       682 ~~G~i~~G~V~~i~~~G~fV~l~~g~~Glvhisels~~~v~~~~~~~~vGd~V~vkVl~id~-~gri~LS~  751 (974)
                      ++|+.++|.|+++         . +.+|+||++++..+  -.....+++||.|+|+|.++|. ++++.+..
T Consensus       402 ~~g~~f~g~vv~l---------~-~~~glV~v~~l~~d--~~~~~~~~lGd~V~V~v~~vd~~~~~i~f~~  460 (469)
T 2r7d_A          402 QPERVWDAVVVDR---------R-GAQATLLIPDLAFD--VQVNTPAAPGTALQVQFADIDLPQMRVRARS  460 (469)
T ss_dssp             CTTCCEEEEEEEE---------E-TTEEEEEEGGGTEE--EEEECCCCTTCEEEEEEEEEETTTTEEEEEE
T ss_pred             CCCCEEEEEEEEE---------e-CcEEEEEECCCCeE--EecCCcCCCCCEEEEEEEEEccCCCEEEEEE
Confidence            6899999987553         2 45799999999765  2234569999999999999998 77777653

>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=92.06  E-value=0.12  Score=52.66  Aligned_cols=51  Identities=22%  Similarity=0.326  Sum_probs=45.0

Q ss_pred             hhhhhcCCCccchhhhhhhhCceEEeeCCEEEEEecCHHHHHHHHHHHHHHh
Q 002054          626 TLRRLIGPLGALKRKIEEETGGRISVSDGTLTVVAKNRSVMEKVLEKVDFII  677 (974)
Q Consensus       626 ki~~vIg~gGk~i~~i~~~~g~~Idi~dg~v~i~~~~~~~~~~a~~~i~~l~  677 (974)
                      .++.+||++|++++.|+.-||++|-+.+.++.+.+. .+.++.|+..++.++
T Consensus       108 ~~GrIIGk~G~tik~iE~~Tg~~I~v~~~~v~i~G~-~~~i~~Ar~~i~~li  158 (191)
T 1tua_A          108 IKGRIIGEGGRARRTIEEMTDTYINVGEYEVAIIGD-YERAMAAKQAIEMLA  158 (191)
T ss_dssp             HHHHHHCGGGHHHHHHHHHHTCEEEECSSEEEEEEE-HHHHHHHHHHHHHHH
T ss_pred             HhhheeCCCccHHHHHHHHHCceEEEcCCEEEEEeC-hHHHHHHHHHHHHHH
Confidence            479999999999999999999999999889988774 467788888888776

>3n89_A Defective in GERM LINE development protein 3, ISO; KH domains, RNA binding, cell cycle; 2.79A {Caenorhabditis elegans}

Probab=90.69  E-value=0.27  Score=55.05  Aligned_cols=56  Identities=13%  Similarity=0.128  Sum_probs=46.6

Q ss_pred             eeeccchhhhhcCCCc--cchhhhhhhhCceEEeeCC------------EEEEEecCHHHHHHHHHHHHHH
Q 002054          620 LKYDNDTLRRLIGPLG--ALKRKIEEETGGRISVSDG------------TLTVVAKNRSVMEKVLEKVDFI  676 (974)
Q Consensus       620 ~~i~~~ki~~vIg~gG--k~i~~i~~~~g~~Idi~dg------------~v~i~~~~~~~~~~a~~~i~~l  676 (974)
                      +.|++..-+-+||+||  .+|+.|.++||++|++-|.            .|.|++. .+..++|+..+..+
T Consensus        34 v~Ip~~~Hs~IIGkgG~~sNIkkImeEtgv~I~fPD~~~~~~~~~~ks~~VtItG~-~enVE~AR~~I~~l  103 (376)
T 3n89_A           34 MEFESQYYSLMTSDNGDHENVASIMAETNTLIQLPDRSVGGTTPDPFAQQVTITGY-FGDVDRARMLMRRN  103 (376)
T ss_dssp             EECCGGGHHHHHSCCSSSCSHHHHHHHHTCEEECCCCCCCSSSCCTTTTEEEEEEE-HHHHHHHHHHHHHS
T ss_pred             EEEchhhhhhhccCCChHHHHHHHHHHhCCeEECCCCcccccCCcCCCCeEEEEcC-HHHHHHHHHHHHhc
Confidence            4577777789999999  9999999999999998522            4888875 57999999888764

>3d0f_A Penicillin-binding 1 transmembrane protein MRCA; BIG_1156.2, STR genomics, PSI-2, protein structure initiative; 1.64A {Nitrosomonas europaea atcc 19718}

Probab=88.92  E-value=2  Score=39.13  Aligned_cols=59  Identities=12%  Similarity=0.021  Sum_probs=50.8

Q ss_pred             cccccCcEEEEEEEEEeeceEEEEEcCCeEEEEecccCCCccc-----cc-cccccccCCEEEEE
Q 002054          679 REIEVGGIYKGVVTSVKEYGAFVEFNGGQQGLLHVSELSHEPV-----SR-VSDVVSVGQQLSLR  737 (974)
Q Consensus       679 ~~~~~G~i~~G~V~~i~~~G~fV~l~~g~~Glvhisels~~~v-----~~-~~~~~~vGd~V~vk  737 (974)
                      .....|+.+.+.|+++.+.++-|.+.+|..+.|+.+.+.|.+-     +. +.+.+++||.|.|+
T Consensus        29 ~~~~~~~~~~AvV~~v~~~~~~v~~~~g~~~~l~~~~~~WA~~~~~~~~~~~~~~l~~GdvI~V~   93 (106)
T 3d0f_A           29 DIGNSDDILAAVVLSATPGAVEAFRKNGETIRITGDGLKAAHRFLSNDPKIGEKRIRPGALIRVK   93 (106)
T ss_dssp             TSCTTTTCEEEEEEEEETTEEEEEETTSCEEEECGGGGSTTGGGTTTCTTTGGGSCCTTEEEEEE
T ss_pred             ccCccCCeEEEEEEEeCCCeEEEEEcCCCeEEEcHHHChhhhhcccccccchhccCCCCCEEEEE
Confidence            3456799999999999999999999888888899999998752     34 67789999999998

>1wfq_A UNR protein; beta-barrel, translational regulation, RNA chaperone, RNA/DN binding, QB fold, greek-KEY topology, structur genomics; NMR {Homo sapiens} SCOP: b.40.4.5

Probab=87.14  E-value=4.1  Score=36.07  Aligned_cols=62  Identities=16%  Similarity=0.252  Sum_probs=44.9

Q ss_pred             cccCcEEEEEEEEEeeceE-EEEEcC-CeEEEEecccCCCccccccccccccCCEEEEEEEEEccC-CceEE
Q 002054          681 IEVGGIYKGVVTSVKEYGA-FVEFNG-GQQGLLHVSELSHEPVSRVSDVVSVGQQLSLRCIGQDVR-GNIKL  749 (974)
Q Consensus       681 ~~~G~i~~G~V~~i~~~G~-fV~l~~-g~~Glvhisels~~~v~~~~~~~~vGd~V~vkVl~id~~-gri~L  749 (974)
                      +...+...|+|+... .|. |+.-.. +.+-|+|+|.|... .    ..+++||.|+..+.. +++ ||...
T Consensus        13 ~s~~~~~~G~Vkwf~-KGfGFI~~ddgg~DVFvH~s~i~~~-~----~~L~~G~~V~F~v~~-~~k~Gk~~A   77 (89)
T 1wfq_A           13 TSAALRETGVIEKLL-TSYGFIQCSERQARLFFHCSQYNGN-L----QDLKVGDDVEFEVSS-DRRTGKPIA   77 (89)
T ss_dssp             SSCCCEEEEEEEEEC-SSEEEEEETTTTEEEEEETTTCSSC-T----TTCCTTCCEEEEEEE-CSSSCCEEE
T ss_pred             CCcccccceEEEEEe-CCeeEEecCCCCccEEEEhHHhhCc-c----CCCCCCCEEEEEEEE-CCCCCCcEE
Confidence            344578899999985 444 666554 48999999999764 2    458899999999876 455 75443

>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=85.80  E-value=1.1  Score=43.44  Aligned_cols=55  Identities=15%  Similarity=0.204  Sum_probs=41.8

Q ss_pred             ceeeeeccchhhhhcCCCccchhhhhhhhCceE-Eee--CCEEEEEecCHHHHHHHHH
Q 002054          617 LATLKYDNDTLRRLIGPLGALKRKIEEETGGRI-SVS--DGTLTVVAKNRSVMEKVLE  671 (974)
Q Consensus       617 ~~~~~i~~~ki~~vIg~gGk~i~~i~~~~g~~I-di~--dg~v~i~~~~~~~~~~a~~  671 (974)
                      .+.+.|+.+..+.+||++|.+|+.|++++|+.+ ..+  ...+.+.+...+...+++.
T Consensus         5 ~~~~~Vp~~~vG~~IG~~G~~I~~i~~e~gI~ii~~~~~~~~~i~~~~~p~~v~~~~~   62 (144)
T 2qnd_A            5 HEQFIVREDLMGLAIGTHGANIQQARKVPGVTAIDLDEDTCTFHIYGEDQDAVKKARS   62 (144)
T ss_dssp             EEEEECCGGGHHHHHCGGGHHHHHHHTSTTEEEEEEETTTTEEEEEESSHHHHHHHHH
T ss_pred             EEEEEECCcceeeEECCChhHHHHHHHHHCCeEeccCCCchheeeccCCHHHHHHHHH
Confidence            467789999999999999999999999999432 122  2467777777666666643

>3v69_A Protein filia; RNA-binding, embryogenesis, KH domain, RNA binding, P binding; 2.20A {Mus musculus}

Probab=85.05  E-value=1.4  Score=41.88  Aligned_cols=59  Identities=14%  Similarity=0.102  Sum_probs=44.8

Q ss_pred             eeeeeccchhhhhcCCCccchhhhhhhhCceEEee----CC--EEEEEecCHHHHHHHHHHHHHHh
Q 002054          618 ATLKYDNDTLRRLIGPLGALKRKIEEETGGRISVS----DG--TLTVVAKNRSVMEKVLEKVDFII  677 (974)
Q Consensus       618 ~~~~i~~~ki~~vIg~gGk~i~~i~~~~g~~Idi~----dg--~v~i~~~~~~~~~~a~~~i~~l~  677 (974)
                      ..++++.+..+.+||+||..|+.|+..+++.|.++    +|  .|.|+++. ..-.+++.+|..+.
T Consensus        58 lVF~vE~~lve~IFGp~Gs~Ip~IE~~SqTLIqV~~~~s~g~tEVtIfG~~-~~Q~rak~MI~sLA  122 (140)
T 3v69_A           58 KRLYVEPRLLEIMFGKDGEHIPHLESMLHTLIHVNVWGPERRAEIWIFGPP-PFRRDVDRMLTDLA  122 (140)
T ss_dssp             EEEEECGGGHHHHHCGGGTTHHHHHHHHTSEEEEECCCTTSCEEEEEESCH-HHHHHHHHHHHHHH
T ss_pred             eEEEEehhhhhcccCCCcCccchHHhhcceeEEEeccCCCCcEEEEEECCH-HHHHHHHHHHHHHH
Confidence            36678899999999999999999999999998876    34  46666654 34445666666554

>2rf4_A DNA-directed RNA polymerase I subunit RPA4; transferase DNA/RNA, DNA-binding, phosphorylation, POL I, POLI, rpoli, nuclear protein; 3.10A {Saccharomyces cerevisiae}

Probab=84.32  E-value=1.8  Score=44.68  Aligned_cols=69  Identities=7%  Similarity=0.078  Sum_probs=50.8

Q ss_pred             cccccCcEEEEEEEEEeeceEEEEEcCCeEEEEecccCCCccccccc------------cccccCCEEEEEEEEEccCCc
Q 002054          679 REIEVGGIYKGVVTSVKEYGAFVEFNGGQQGLLHVSELSHEPVSRVS------------DVVSVGQQLSLRCIGQDVRGN  746 (974)
Q Consensus       679 ~~~~~G~i~~G~V~~i~~~G~fV~l~~g~~Glvhisels~~~v~~~~------------~~~~vGd~V~vkVl~id~~gr  746 (974)
                      ..+.+|++++|+|+.+.+.|+.+-+.+-.+.+|+...|..++.-++.            +--++|+.|++||.+++.+|.
T Consensus       125 FrPf~GevL~G~V~~~s~~~Ig~~~~G~Fn~~Ip~~~ip~~~~f~~~~~~~~~~~wv~~~~~~ig~~IRFrV~~~~~~~~  204 (214)
T 2rf4_A          125 WQPQVGDVLEGYIFIQSASHIGLLIHDAFNASIKKNNIPVDWTFVHNDGNRSLGHWVDSNGEPIDGKLRFTVRNVHTTGR  204 (214)
T ss_dssp             ECCCTTCEEEEEECCCCSSCEEEEETTTEEEEECSTTSCSSCBCCCCSCC-CCCCCBCSSCCBCCSEEEEEEEEEECCSS
T ss_pred             EecCCCCEEEEEEEEECCCcEEEEEeCCEEEEEcHHHCCCcccccccccccCCCceEcCCCCCCCCEEEEEEEEEEecCC
Confidence            36899999999999999977777666667889999888544211111            112369999999999987664


Q ss_pred             e
Q 002054          747 I  747 (974)
Q Consensus       747 i  747 (974)
                      +
T Consensus       205 ~  205 (214)
T 2rf4_A          205 V  205 (214)
T ss_dssp             S
T ss_pred             E
Confidence            3

>2k5n_A Putative cold-shock protein; GFT protein structure, PSI, nesgc, OB fold, cold shock structural genomics; NMR {Pectobacterium atrosepticum}

Probab=82.01  E-value=6.7  Score=33.41  Aligned_cols=53  Identities=15%  Similarity=0.334  Sum_probs=38.1

Q ss_pred             EEEEEEEEEee---ceEEEEEcCCeEEEEecccCCCccccccccccccCCEEEEEEEEEccCCc
Q 002054          686 IYKGVVTSVKE---YGAFVEFNGGQQGLLHVSELSHEPVSRVSDVVSVGQQLSLRCIGQDVRGN  746 (974)
Q Consensus       686 i~~G~V~~i~~---~G~fV~l~~g~~Glvhisels~~~v~~~~~~~~vGd~V~vkVl~id~~gr  746 (974)
                      ..+|+|+...+   ||....-.++.+ |+|+|.+....      .+++||.|+..+.. +++|.
T Consensus         2 ~~~G~Vkwfn~~KGfGFI~~~dg~~d-FvH~s~i~~~g------~l~~G~~V~F~~~~-g~kG~   57 (74)
T 2k5n_A            2 AMNGTITTWFKDKGFGFIKDENGDNR-YFHVIKVANPD------LIKKDAAVTFEPTT-NNKGL   57 (74)
T ss_dssp             CEEEEEEEEETTTTEEEEEESSSCEE-EEEGGGBSSGG------GCCTTCEEEEEEEE-CSSSE
T ss_pred             CcceEEEEEECCCCeEEEecCCCCce-EEEHhHcccCC------CCCCCCEEEEEEEe-CCCCc
Confidence            46899999843   555444334566 99999997653      48899999999875 55673

>1h95_A CSD, Y-box binding protein; translation factor, transcription factor, OB-fold, 5- stranded anti-parallel beta-barrel, single stranded DNA binding; NMR {Homo sapiens} SCOP: b.40.4.5

Probab=80.01  E-value=5.6  Score=34.31  Aligned_cols=62  Identities=13%  Similarity=0.213  Sum_probs=42.4

Q ss_pred             CcEEEEEEEEEee---ceEEEEEcCCeEEEEecccCCCccccccccccccCCEEEEEEEEEccCCc
Q 002054          684 GGIYKGVVTSVKE---YGAFVEFNGGQQGLLHVSELSHEPVSRVSDVVSVGQQLSLRCIGQDVRGN  746 (974)
Q Consensus       684 G~i~~G~V~~i~~---~G~fV~l~~g~~Glvhisels~~~v~~~~~~~~vGd~V~vkVl~id~~gr  746 (974)
                      ...++|+|+...+   ||....-.++.+-|+|+|.|.......-...+++||.|+..+.. +++|.
T Consensus         6 ~~~~~G~Vkwfn~~kGfGFI~~~~gg~DvFvH~s~i~~~~~~~g~~~l~~G~~V~f~~~~-~~kG~   70 (79)
T 1h95_A            6 ATKVLGTVKWFNVRNGYGFINRNDTKEDVFVHQTAIKKNNPRKYLRSVGDGETVEFDVVE-GEKGA   70 (79)
T ss_dssp             EEEEEEEEEEEETTTTEEEEEEGGGTEEEEEEGGGBCSCCCSCCSCSCCSSCEEEEEEEE-CSSSE
T ss_pred             ccccceEEEEEECCCCcEEEecCCCCccEEEEhHHccccccccccccCCCCCEEEEEEEE-CCCCc
Confidence            4568899999853   55554444468999999999764111112348899999998866 45664

---

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	974
d1e3ha6	96	d.101.1.1 (A:483-578) Polynucleotide phosphorylase	6e-38
d2je6a1	191	d.14.1.4 (A:1-191) Exosome complex exonuclease 2,E	2e-37
d2ba0g1	176	d.14.1.4 (G:3-178) Exosome complex exonuclease 2,E	4e-36
d2ba0g1	176	d.14.1.4 (G:3-178) Exosome complex exonuclease 2,E	5e-05
d2je6b1	148	d.14.1.4 (B:8-155) Exosome complex exonuclease 1,	2e-35
d1e3ha3	137	d.14.1.4 (A:346-482) Polynucleotide phosphorylase/	4e-35
d1e3ha3	137	d.14.1.4 (A:346-482) Polynucleotide phosphorylase/	8e-18
d2ba0d1	144	d.14.1.4 (D:10-153) Exosome complex exonuclease 1,	3e-34
d2nn6c1	181	d.14.1.4 (C:7-187) Exosome complex exonuclease RRP	5e-33
d2nn6c1	181	d.14.1.4 (C:7-187) Exosome complex exonuclease RRP	1e-14
d2nn6b1	145	d.14.1.4 (B:6-150) Exosome complex exonuclease RRP	7e-33
d2nn6a1	184	d.14.1.4 (A:1-184) Exosome complex exonuclease RRP	1e-32
d1r6la1	151	d.14.1.4 (A:1-151) Ribonuclease PH, domain 1 {Pseu	2e-32
d1r6la1	151	d.14.1.4 (A:1-151) Ribonuclease PH, domain 1 {Pseu	2e-05
d2nn6e1	187	d.14.1.4 (E:5-191) Exosome complex exonuclease RRP	1e-31
d2nn6e1	187	d.14.1.4 (E:5-191) Exosome complex exonuclease RRP	6e-04
d1oysa1	151	d.14.1.4 (A:1-151) Ribonuclease PH, domain 1 {Baci	4e-31
d1oysa1	151	d.14.1.4 (A:1-151) Ribonuclease PH, domain 1 {Baci	1e-05
d1e3ha2	149	d.14.1.4 (A:3-151) Polynucleotide phosphorylase/gu	1e-30
d1e3ha2	149	d.14.1.4 (A:3-151) Polynucleotide phosphorylase/gu	3e-25
d1udsa1	149	d.14.1.4 (A:2-150) Ribonuclease PH, domain 1 {Aqui	4e-29
d1udsa1	149	d.14.1.4 (A:2-150) Ribonuclease PH, domain 1 {Aqui	2e-06
d2nn6f1	147	d.14.1.4 (F:29-175) Exosome complex exonuclease MT	5e-28
d2nn6f1	147	d.14.1.4 (F:29-175) Exosome complex exonuclease MT	5e-17
d2nn6d1	122	d.14.1.4 (D:25-146) Exosome complex exonuclease RR	1e-25
d2nn6d1	122	d.14.1.4 (D:25-146) Exosome complex exonuclease RR	1e-18
d1e3ha5	111	d.101.1.1 (A:152-262) Polynucleotide phosphorylase	2e-20
d1whua_	104	a.4.9.1 (A:) Polynucleotide phosphorylase/guanosin	5e-18
d1sroa_	76	b.40.4.5 (A:) S1 RNA-binding domain of polyribonuc	9e-18
d1e3ha1	83	a.4.9.1 (A:263-345) Polynucleotide phosphorylase/g	2e-14
d1oysa2	86	d.101.1.1 (A:152-237) Ribonuclease PH, domain 2 {B	7e-14
d1oysa2	86	d.101.1.1 (A:152-237) Ribonuclease PH, domain 2 {B	3e-04
d3bzka4	94	b.40.4.5 (A:637-730) Tex S1-domain {Pseudomonas ae	1e-13
d2nn6h1	95	b.40.4.5 (H:73-167) S1-domain of Ribosomal RNA-pro	2e-13
d2z0sa1	88	b.40.4.5 (A:60-147) S1-domain of exosome complex R	5e-13
d1r6la2	88	d.101.1.1 (A:152-239) Ribonuclease PH, domain 2 {P	1e-12
d1r6la2	88	d.101.1.1 (A:152-239) Ribonuclease PH, domain 2 {P	2e-08
d1e3pa2	62	b.40.4.5 (A:656-717) S1 RNA-binding domain of poly	2e-12
d2ba0a1	83	b.40.4.5 (A:53-135) S1-domain of exosome complex R	3e-12
d1udsa2	105	d.101.1.1 (A:151-255) Ribonuclease PH, domain 2 {A	7e-12
d1udsa2	105	d.101.1.1 (A:151-255) Ribonuclease PH, domain 2 {A	1e-09
d2je6b2	86	d.101.1.1 (B:156-241) Exosome complex exonuclease	9e-12
d2je6b2	86	d.101.1.1 (B:156-241) Exosome complex exonuclease	2e-06
d2je6i1	87	b.40.4.5 (I:66-152) S1-domain of exosome complex R	2e-11
d2z0sa2	87	d.51.1.1 (A:148-234) Exosome complex RNA-binding p	3e-11
d2nn6b2	90	d.101.1.1 (B:151-240) Exosome complex exonuclease	3e-11
d2nn6b2	90	d.101.1.1 (B:151-240) Exosome complex exonuclease	3e-04
d2ba0d2	99	d.101.1.1 (D:154-252) Exosome complex exonuclease	4e-11
d2ba0d2	99	d.101.1.1 (D:154-252) Exosome complex exonuclease	4e-11
d2je6a2	84	d.101.1.1 (A:192-275) Exosome complex exonuclease	6e-11
d2je6a2	84	d.101.1.1 (A:192-275) Exosome complex exonuclease	3e-05
d2ahob2	84	b.40.4.5 (B:1-84) Eukaryotic initiation factor 2al	2e-10
d1kl9a2	86	b.40.4.5 (A:3-88) Eukaryotic initiation factor 2al	2e-09
d2nn6d2	89	d.101.1.1 (D:147-235) Exosome complex exonuclease	1e-08
d1go3e1	106	b.40.4.5 (E:79-184) C-terminal domain of RNA polym	2e-08
d2nn6g1	88	b.40.4.5 (G:107-194) S1-domain of exosome componen	5e-08
d1e3ha4	54	d.52.3.1 (A:579-632) Polynucleotide phosphorylase/	5e-08
d1tuaa2	104	d.51.1.1 (A:85-188) Hypothetical protein APE0754 {	9e-08
d1wi5a_	119	b.40.4.5 (A:) S1-domain of RRP5 protein homolog (P	9e-07
d2ja9a1	90	b.40.4.5 (A:62-151) S1-domain of exosome component	1e-06
d1tuaa1	84	d.51.1.1 (A:1-84) Hypothetical protein APE0754 {Ae	2e-06
d2je6i3	69	d.51.1.1 (I:153-221) Exosome complex RNA-binding p	4e-06
d2nn6f2	95	d.101.1.1 (F:176-270) Exosome complex exonuclease	7e-06
d1y14b1	91	b.40.4.5 (B:81-171) C-terminal domain of RNA polym	1e-05
d2ba0a3	84	d.51.1.1 (A:136-219) Exosome complex RNA-binding p	1e-05
d2cpqa1	78	d.51.1.1 (A:212-289) Fragile X mental retardation	3e-04
d4ubpa_	100	d.8.1.1 (A:) Urease, gamma-subunit {Bacillus paste	8e-04
d1e9ya2	105	d.8.1.1 (A:1-105) Urease, gamma-subunit {Helicobac	0.001
d2ctka1	91	d.51.1.1 (A:8-98) Vigilin {Human (Homo sapiens) [T	0.003
d1we8a_	104	d.51.1.1 (A:) Tudor and KH domain containing prote	0.004

>d1e3ha6 d.101.1.1 (A:483-578) Polynucleotide phosphorylase/guanosine pentaphosphate synthase (PNPase/GPSI), domains 2 and 5 {Streptomyces antibioticus [TaxId: 1890]} Length = 96

class: Alpha and beta proteins (a+b)
fold: Ribonuclease PH domain 2-like
superfamily: Ribonuclease PH domain 2-like
family: Ribonuclease PH domain 2-like
domain: Polynucleotide phosphorylase/guanosine pentaphosphate synthase (PNPase/GPSI), domains 2 and 5
species: Streptomyces antibioticus [TaxId: 1890]

 Score =  134 bits (340), Expect = 6e-38
 Identities = 44/92 (47%), Positives = 55/92 (59%), Gaps = 3/92 (3%)

Query: 516 VAGVSVGLVSEVDPSTGEIKDYRILTDILGLEDHLGDMDFKIAGTRIGVTAIQLDIKPAG 575
           VAG+++GL+S+          Y  LTDILG ED  GDMDFK+AGT+  VTA+QLD K  G
Sbjct: 3   VAGIAMGLISQEI---NGETHYVALTDILGAEDAFGDMDFKVAGTKEFVTALQLDTKLDG 59

Query: 576 IPLDIICECLEHAHKGRLQILDHMEREISAPR 607
           IP  ++   L+ A   RL ILD M   I  P 
Sbjct: 60  IPASVLAAALKQARDARLHILDVMMEAIDTPD 91

>d2je6a1 d.14.1.4 (A:1-191) Exosome complex exonuclease 2,ECX2 {Sulfolobus solfataricus [TaxId: 2287]} Length = 191

class: Alpha and beta proteins (a+b)
fold: Ribosomal protein S5 domain 2-like
superfamily: Ribosomal protein S5 domain 2-like
family: Ribonuclease PH domain 1-like
domain: Exosome complex exonuclease 2,ECX2
species: Sulfolobus solfataricus [TaxId: 2287]

 Score =  136 bits (344), Expect = 2e-37
 Identities = 36/174 (20%), Positives = 65/174 (37%), Gaps = 4/174 (2%)

Query: 352 VDTVRKRVIRKRIIAEGVRVDGRQLDEVRPIYCESGNLPILHGSSLFSRGDTQVLCTVTL 411
           +  ++K  I   +  +G+R DGR+L + RP+           GS+L   G T VL    L
Sbjct: 11  IPIIKKESIV-SLFEKGIRQDGRKLTDYRPLSITLDYAKKADGSALVKLGTTMVLAGTKL 69

Query: 412 GAPAEAQRLESLVGPPTKRFMLHYSFPPFCINEVGKRVGLNRREVGHGTLAEKAL--LAV 469
                 +   +         +L  ++  F      +      R V       KAL    +
Sbjct: 70  EIDKPYEDTPNQGNLIVNVELLPLAYETFEPGPPDENAIELARVVDRSLRDSKALDLTKL 129

Query: 470 LPPENDFPYTVRVNSEVMASDGSTSMATVCGGSMALMDAGIP-LQEHVAGVSVG 522
           +       +TV ++  V+   G+   A       AL +  +  +++H  G+SV 
Sbjct: 130 VIEPGKSVWTVWLDVYVLDYGGNVLDACTLASVAALYNTKVYKVEQHSNGISVN 183

>d2ba0g1 d.14.1.4 (G:3-178) Exosome complex exonuclease 2,ECX2 {Archaeoglobus fulgidus [TaxId: 2234]} Length = 176

class: Alpha and beta proteins (a+b)
fold: Ribosomal protein S5 domain 2-like
superfamily: Ribosomal protein S5 domain 2-like
family: Ribonuclease PH domain 1-like
domain: Exosome complex exonuclease 2,ECX2
species: Archaeoglobus fulgidus [TaxId: 2234]

 Score =  132 bits (333), Expect = 4e-36
 Identities = 34/170 (20%), Positives = 63/170 (37%), Gaps = 3/170 (1%)

Query: 351 AVDTVRKRVIRKRIIAEGVRVDGRQLDEVRPIYCESGNLPILHGSSLFSRGDTQVLCTVT 410
            +  +++  +    + +  R+DGR  DE R +      +    GS+L   GDTQV+  V 
Sbjct: 3   ILVDIKRDYVLS-KLRDNERIDGRGFDEFRKVEIIPNVIEKAEGSALVKLGDTQVVVGVK 61

Query: 411 LGAPAEAQRLESLVGPPTKRFMLHYSFPPFCINEVGKRVGLNRREVGHGTLAEKA--LLA 468
           +                    ++  + P F      +      R V  G    +A  L  
Sbjct: 62  MQPGEPYPDTPDRGVIIVNAELVPLASPTFEPGPPDENSIELARVVDRGIRESEAVDLSK 121

Query: 469 VLPPENDFPYTVRVNSEVMASDGSTSMATVCGGSMALMDAGIPLQEHVAG 518
           ++  E +  + V V+   +  DG+   A+      ALM+  +P +    G
Sbjct: 122 LVIEEGEKVWIVFVDIHALDDDGNLLDASALAAIAALMNTKVPAERFDLG 171

>d2ba0g1 d.14.1.4 (G:3-178) Exosome complex exonuclease 2,ECX2 {Archaeoglobus fulgidus [TaxId: 2234]} Length = 176

class: Alpha and beta proteins (a+b)
fold: Ribosomal protein S5 domain 2-like
superfamily: Ribosomal protein S5 domain 2-like
family: Ribonuclease PH domain 1-like
domain: Exosome complex exonuclease 2,ECX2
species: Archaeoglobus fulgidus [TaxId: 2234]

 Score = 42.8 bits (100), Expect = 5e-05
 Identities = 31/140 (22%), Positives = 52/140 (37%), Gaps = 16/140 (11%)

Query: 68  RLITLETGKIARFANGAVVLGMDETKVLSTVTSSKGDSVRDFLPLTVDYQEKQFAQGVIP 127
           R + +    I + A G+ ++ + +T+V+  V    G+   D     V     +      P
Sbjct: 31  RKVEIIPNVIEK-AEGSALVKLGDTQVVVGVKMQPGEPYPDTPDRGVIIVNAELVPLASP 89

Query: 128 NTYMRREGAPKERELLVGRIIDRPIRP----------LFPAGFYHEVQVMASVLSSDGKQ 177
                  G P E  + + R++DR IR           +        V V    L  DG  
Sbjct: 90  T---FEPGPPDENSIELARVVDRGIRESEAVDLSKLVIEEGEKVWIVFVDIHALDDDG-- 144

Query: 178 DPDIMAANATSAALMLSDIP 197
           +    +A A  AALM + +P
Sbjct: 145 NLLDASALAAIAALMNTKVP 164

>d2je6b1 d.14.1.4 (B:8-155) Exosome complex exonuclease 1, ECX1 {Sulfolobus solfataricus [TaxId: 2287]} Length = 148

class: Alpha and beta proteins (a+b)
fold: Ribosomal protein S5 domain 2-like
superfamily: Ribosomal protein S5 domain 2-like
family: Ribonuclease PH domain 1-like
domain: Exosome complex exonuclease 1, ECX1
species: Sulfolobus solfataricus [TaxId: 2287]

 Score =  129 bits (325), Expect = 2e-35
 Identities = 42/150 (28%), Positives = 69/150 (46%), Gaps = 4/150 (2%)

Query: 361 RKRIIAEGVRVDGRQLDEVRPIYCESGNLPILHGSSLFSRGDTQVLCTVTLGAPAEAQRL 420
            K I+ +G R DGR+ DE+R I  E G L    GS++F  G+T+ +  V           
Sbjct: 3   PKLILDDGKRTDGRKPDELRSIKIELGVLKNADGSAIFEMGNTKAIAAVYGPKE---MHP 59

Query: 421 ESLVGPPTKRFMLHYSFPPFCINEVGKRVGLNRREVGHGTLAEKALLAVLPPENDFPYTV 480
             L  P      + Y   PF  +E       +RRE+    +  +AL + +  E      +
Sbjct: 60  RHLSLPDRAVLRVRYHMTPFSTDERKNPAP-SRREIELSKVIREALESAVLVELFPRTAI 118

Query: 481 RVNSEVMASDGSTSMATVCGGSMALMDAGI 510
            V +E++ +D  + + ++   S+AL DAGI
Sbjct: 119 DVFTEILQADAGSRLVSLMAASLALADAGI 148

>d1e3ha3 d.14.1.4 (A:346-482) Polynucleotide phosphorylase/guanosine pentaphosphate synthase (PNPase/GPSI), domains 1 and 4 {Streptomyces antibioticus [TaxId: 1890]} Length = 137

class: Alpha and beta proteins (a+b)
fold: Ribosomal protein S5 domain 2-like
superfamily: Ribosomal protein S5 domain 2-like
family: Ribonuclease PH domain 1-like
domain: Polynucleotide phosphorylase/guanosine pentaphosphate synthase (PNPase/GPSI), domains 1 and 4
species: Streptomyces antibioticus [TaxId: 1890]

 Score =  128 bits (322), Expect = 4e-35
 Identities = 60/136 (44%), Positives = 92/136 (67%)

Query: 378 EVRPIYCESGNLPILHGSSLFSRGDTQVLCTVTLGAPAEAQRLESLVGPPTKRFMLHYSF 437
           ++R +  E   +P +HGS+LF RG+TQ+L   TL      Q+L++L     KR+M +Y+F
Sbjct: 2   DIRTLAAEVEAIPRVHGSALFERGETQILGVTTLNMLRMEQQLDTLSPVTRKRYMHNYNF 61

Query: 438 PPFCINEVGKRVGLNRREVGHGTLAEKALLAVLPPENDFPYTVRVNSEVMASDGSTSMAT 497
           PP+ + E G+     RRE+GHG LAE+A++ VLP   +FPY +R  SE + S+GSTSM +
Sbjct: 62  PPYSVGETGRVGSPKRREIGHGALAERAIVPVLPTREEFPYAIRQVSEALGSNGSTSMGS 121

Query: 498 VCGGSMALMDAGIPLQ 513
           VC  +M+L++AG+PL+
Sbjct: 122 VCASTMSLLNAGVPLK 137

>d1e3ha3 d.14.1.4 (A:346-482) Polynucleotide phosphorylase/guanosine pentaphosphate synthase (PNPase/GPSI), domains 1 and 4 {Streptomyces antibioticus [TaxId: 1890]} Length = 137

class: Alpha and beta proteins (a+b)
fold: Ribosomal protein S5 domain 2-like
superfamily: Ribosomal protein S5 domain 2-like
family: Ribonuclease PH domain 1-like
domain: Polynucleotide phosphorylase/guanosine pentaphosphate synthase (PNPase/GPSI), domains 1 and 4
species: Streptomyces antibioticus [TaxId: 1890]

 Score = 78.7 bits (193), Expect = 8e-18
 Identities = 22/134 (16%), Positives = 49/134 (36%), Gaps = 4/134 (2%)

Query: 68  RLITLETGKIARFANGAVVLGMDETKVLSTVTSSKGDSVRDFLPLTVDYQEKQFAQGV-- 125
           R +  E        +G+ +    ET++L   T +     +    L+   +++        
Sbjct: 4   RTLAAEVE-AIPRVHGSALFERGETQILGVTTLNMLRMEQQLDTLSPVTRKRYMHNYNFP 62

Query: 126 -IPNTYMRREGAPKERELLVGRIIDRPIRPLFPAGFYHEVQVMASVLSSDGKQDPDIMAA 184
                   R G+PK RE+  G + +R I P+ P        +     +        + + 
Sbjct: 63  PYSVGETGRVGSPKRREIGHGALAERAIVPVLPTREEFPYAIRQVSEALGSNGSTSMGSV 122

Query: 185 NATSAALMLSDIPW 198
            A++ +L+ + +P 
Sbjct: 123 CASTMSLLNAGVPL 136

>d2ba0d1 d.14.1.4 (D:10-153) Exosome complex exonuclease 1, ECX1 {Archaeoglobus fulgidus [TaxId: 2234]} Length = 144

class: Alpha and beta proteins (a+b)
fold: Ribosomal protein S5 domain 2-like
superfamily: Ribosomal protein S5 domain 2-like
family: Ribonuclease PH domain 1-like
domain: Exosome complex exonuclease 1, ECX1
species: Archaeoglobus fulgidus [TaxId: 2234]

 Score =  126 bits (316), Expect = 3e-34
 Identities = 43/148 (29%), Positives = 71/148 (47%), Gaps = 4/148 (2%)

Query: 363 RIIAEGVRVDGRQLDEVRPIYCESGNLPILHGSSLFSRGDTQVLCTVTLGAPAEAQRLES 422
           ++I +G+R+DGR+ DE+RPI  E+  L    GS     G  +V+  V             
Sbjct: 1   KLIVDGLRLDGRKFDELRPIKIEASVLKRADGSCYLEMGKNKVIAAVFGPRE---VHPRH 57

Query: 423 LVGPPTKRFMLHYSFPPFCINEVGKRVGLNRREVGHGTLAEKALLAVLPPENDFPYTVRV 482
           L  P        Y+  PF + E  KR G +RR +    ++++A  AV+  E      + +
Sbjct: 58  LQDPSKAIIRYRYNMAPFSVEER-KRPGPDRRSIEISKVSKEAFEAVIMKELFPRSAIDI 116

Query: 483 NSEVMASDGSTSMATVCGGSMALMDAGI 510
             EV+ +D  +  A +   S+AL+DAG+
Sbjct: 117 FVEVLQADAGSRTACLNAASVALVDAGV 144

>d2nn6c1 d.14.1.4 (C:7-187) Exosome complex exonuclease RRP43 {Human (Homo sapiens) [TaxId: 9606]} Length = 181

class: Alpha and beta proteins (a+b)
fold: Ribosomal protein S5 domain 2-like
superfamily: Ribosomal protein S5 domain 2-like
family: Ribonuclease PH domain 1-like
domain: Exosome complex exonuclease RRP43
species: Human (Homo sapiens) [TaxId: 9606]

 Score =  123 bits (310), Expect = 5e-33
 Identities = 29/160 (18%), Positives = 51/160 (31%), Gaps = 2/160 (1%)

Query: 354 TVRKRVIRKRIIAEGVRVDGRQLDEVRPIYCESGNLPILHGSSLFSRGDTQVLCTVTLGA 413
           TV      +R + E  R DGR+L E R      G++    GS+L   G+T V+C V    
Sbjct: 1   TVEPLEYYRRFLKENCRPDGRELGEFRTTTVNIGSISTADGSALVKLGNTTVICGVKAEF 60

Query: 414 PAEAQRLESLVGPPTKRFMLHYSFPPFCINEVGKRVGLNRREVGHGTL--AEKALLAVLP 471
            A +              +       F     G+   +  + +              +  
Sbjct: 61  AAPSTDAPDKGYVVPNVDLPPLCSSRFRSGPPGEEAQVASQFIADVIENSQIIQKEDLCI 120

Query: 472 PENDFPYTVRVNSEVMASDGSTSMATVCGGSMALMDAGIP 511
                 + +  +   +  DG+   A       AL +  +P
Sbjct: 121 SPGKLVWVLYCDLICLDYDGNILDACTFALLAALKNVQLP 160

>d2nn6c1 d.14.1.4 (C:7-187) Exosome complex exonuclease RRP43 {Human (Homo sapiens) [TaxId: 9606]} Length = 181

class: Alpha and beta proteins (a+b)
fold: Ribosomal protein S5 domain 2-like
superfamily: Ribosomal protein S5 domain 2-like
family: Ribonuclease PH domain 1-like
domain: Exosome complex exonuclease RRP43
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 71.0 bits (173), Expect = 1e-14
 Identities = 22/158 (13%), Positives = 46/158 (29%), Gaps = 13/158 (8%)

Query: 68  RLITLETGKIARFANGAVVLGMDETKVLSTVT-------SSKGDSVRDFLPLTVDYQEKQ 120
           R  T+  G I+  A+G+ ++ +  T V+  V        +   D       + +      
Sbjct: 27  RTTTVNIGSIST-ADGSALVKLGNTTVICGVKAEFAAPSTDAPDKGYVVPNVDLPPLCSS 85

Query: 121 FAQGVIPNTYMRREGAPKERELLVGRIIDRPIRPLFPAGFYHEVQVMASVLSSDGKQDPD 180
             +   P    +         +   +II +    + P      +      L  DG  +  
Sbjct: 86  RFRSGPPGEEAQVASQFIADVIENSQIIQKEDLCISPGKLVWVLYCDLICLDYDG--NIL 143

Query: 181 IMAANATSAALMLSDIP---WGGPIGMIRIGRICGQFI 215
                A  AAL    +P         +  +      ++
Sbjct: 144 DACTFALLAALKNVQLPEVTINEETALAEVNLKKKSYL 181

>d2nn6b1 d.14.1.4 (B:6-150) Exosome complex exonuclease RRP41 {Human (Homo sapiens) [TaxId: 9606]} Length = 145

class: Alpha and beta proteins (a+b)
fold: Ribosomal protein S5 domain 2-like
superfamily: Ribosomal protein S5 domain 2-like
family: Ribonuclease PH domain 1-like
domain: Exosome complex exonuclease RRP41
species: Human (Homo sapiens) [TaxId: 9606]

 Score =  122 bits (306), Expect = 7e-33
 Identities = 37/147 (25%), Positives = 61/147 (41%), Gaps = 2/147 (1%)

Query: 364 IIAEGVRVDGRQLDEVRPIYCESGNLPILHGSSLFSRGDTQVLCTVTLGAPAEAQRLESL 423
           +  +G RVDGR+  E+R I    G      GS+   +G+T+ L  V         R  + 
Sbjct: 1   LSDQGYRVDGRRAGELRKIQARMGVFAQADGSAYIEQGNTKALAVVYGPHEIRGSRARA- 59

Query: 424 VGPPTKRFMLHYSFPPFCINEVGKRVGLNRREVGHGTLAEKALLAVLPPENDFPYTVRVN 483
             P        YS   F   E  +R   +R+    G    +   A +  +      + + 
Sbjct: 60  -LPDRALVNCQYSSATFSTGERKRRPHGDRKSCEMGLQLRQTFEAAILTQLHPRSQIDIY 118

Query: 484 SEVMASDGSTSMATVCGGSMALMDAGI 510
            +V+ +DG T  A V   ++A++DAGI
Sbjct: 119 VQVLQADGGTYAACVNAATLAVLDAGI 145

>d2nn6a1 d.14.1.4 (A:1-184) Exosome complex exonuclease RRP45 {Human (Homo sapiens) [TaxId: 9606]} Length = 184

class: Alpha and beta proteins (a+b)
fold: Ribosomal protein S5 domain 2-like
superfamily: Ribosomal protein S5 domain 2-like
family: Ribonuclease PH domain 1-like
domain: Exosome complex exonuclease RRP45
species: Human (Homo sapiens) [TaxId: 9606]

 Score =  122 bits (307), Expect = 1e-32
 Identities = 33/174 (18%), Positives = 60/174 (34%), Gaps = 7/174 (4%)

Query: 357 KRVIRKRIIAEGVRVDGRQLDEVRPIYCESGNLPILHGSSLFSRGDTQVLCTVTLGAPAE 416
           +R + +  I E  R+DGRQ  + R I    G     +G  +   G T+VL  V+    + 
Sbjct: 11  RRFLLR-AIEEKKRLDGRQTYDYRNIRISFGTD---YGCCIVELGKTRVLGQVSCELVSP 66

Query: 417 AQRLESLVGPPTKRFMLHYSFPPFCINEVGKRVGLNRREVGHGTLAEKA--LLAVLPPEN 474
                +         +   + P F        +    R +       K     ++     
Sbjct: 67  KLNRATEGILFFNLELSQMAAPAFEPGRQSDLLVKLNRLMERCLRNSKCIDTESLCVVAG 126

Query: 475 DFPYTVRVNSEVMASDGSTSMATVCGGSMALMDAGIPLQEHVAGVSVGLVSEVD 528
           +  + +RV+  ++  DG+   A      +AL     P    V G  V L +  +
Sbjct: 127 EKVWQIRVDLHLLNHDGNIIDAASIAAIVALCHFRRPDVS-VQGDEVTLYTPEE 179

>d1r6la1 d.14.1.4 (A:1-151) Ribonuclease PH, domain 1 {Pseudomonas aeruginosa [TaxId: 287]} Length = 151

class: Alpha and beta proteins (a+b)
fold: Ribosomal protein S5 domain 2-like
superfamily: Ribosomal protein S5 domain 2-like
family: Ribonuclease PH domain 1-like
domain: Ribonuclease PH, domain 1
species: Pseudomonas aeruginosa [TaxId: 287]

 Score =  121 bits (303), Expect = 2e-32
 Identities = 41/149 (27%), Positives = 65/149 (43%), Gaps = 8/149 (5%)

Query: 370 RVDGRQLDEVRPIYCESGNLPILHGSSLFSRGDTQVLCTVTLGAPAEAQRLESLVGPPTK 429
           R  GR  D++RPI           GS L   GDT+V+CTV+     E+     L G    
Sbjct: 3   RPSGRAADQLRPIRITRHYTKHAEGSVLVEFGDTKVICTVSA----ESGVPRFLKGQGQG 58

Query: 430 RFMLHYSFPPFCINEVGKRVGLNRREVG----HGTLAEKALLAVLPPENDFPYTVRVNSE 485
                Y   P    E  +R     ++ G       L  ++L A L        T+ ++ +
Sbjct: 59  WLTAEYGMLPRSTGERNQREASRGKQGGRTLEIQRLIGRSLRAALDLSKLGENTLYIDCD 118

Query: 486 VMASDGSTSMATVCGGSMALMDAGIPLQE 514
           V+ +DG T  A++ G ++AL+DA   L++
Sbjct: 119 VIQADGGTRTASITGATVALIDALAVLKK 147

>d1r6la1 d.14.1.4 (A:1-151) Ribonuclease PH, domain 1 {Pseudomonas aeruginosa [TaxId: 287]} Length = 151

class: Alpha and beta proteins (a+b)
fold: Ribosomal protein S5 domain 2-like
superfamily: Ribosomal protein S5 domain 2-like
family: Ribonuclease PH domain 1-like
domain: Ribonuclease PH, domain 1
species: Pseudomonas aeruginosa [TaxId: 287]

 Score = 43.3 bits (101), Expect = 2e-05
 Identities = 28/136 (20%), Positives = 51/136 (37%), Gaps = 10/136 (7%)

Query: 68  RLITLETGKIARFANGAVVLGMDETKVLSTVTSSKGDSVR----DFLPLTVDYQEKQFAQ 123
           R I +      + A G+V++   +TKV+ TV++  G            LT +Y     + 
Sbjct: 13  RPIRITRH-YTKHAEGSVLVEFGDTKVICTVSAESGVPRFLKGQGQGWLTAEYGMLPRST 71

Query: 124 GVIPNTYMRREGAPKERELLVGRIIDRPIRPLFPAG--FYHEVQVMASVLSSDGKQDPDI 181
           G        R G    R L + R+I R +R          + + +   V+ +DG      
Sbjct: 72  GERNQREASR-GKQGGRTLEIQRLIGRSLRAALDLSKLGENTLYIDCDVIQADG--GTRT 128

Query: 182 MAANATSAALMLSDIP 197
            +    + AL+ +   
Sbjct: 129 ASITGATVALIDALAV 144

>d2nn6e1 d.14.1.4 (E:5-191) Exosome complex exonuclease RRP42 {Human (Homo sapiens) [TaxId: 9606]} Length = 187

class: Alpha and beta proteins (a+b)
fold: Ribosomal protein S5 domain 2-like
superfamily: Ribosomal protein S5 domain 2-like
family: Ribonuclease PH domain 1-like
domain: Exosome complex exonuclease RRP42
species: Human (Homo sapiens) [TaxId: 9606]

 Score =  119 bits (300), Expect = 1e-31
 Identities = 31/187 (16%), Positives = 52/187 (27%), Gaps = 21/187 (11%)

Query: 358 RVIRKRIIAEGVRVDGRQLDEVRPIYCESGNLPILHGSSLFSRGDTQVLCTVTLGAPAEA 417
           +V     + E +RVDGR  ++ R +  E+  +    GS+    G T +L  V        
Sbjct: 7   KVYIVHGVQEDLRVDGRGCEDYRCVEVETDVVSNTSGSARVKLGHTDILVGVKAEMGTPK 66

Query: 418 QRLESLVGPPTKRFMLHYSFPPFCINEVGKRVGLNRREVGHGTLAEKALLAVLPP----- 472
                   P                 E   R G +           +             
Sbjct: 67  LE-----KPNEGYLEFFVDCSASATPEFEGR-GGDDLGTEIANTLYRIFNNKSSVDLKTL 120

Query: 473 ---ENDFPYTVRVNSEVMASDGSTSMATVCGGSMALMDAGIPLQEHVAGVSVGLVSEVDP 529
                +  + + V+  ++   G+   A       AL +  IP       V V    E   
Sbjct: 121 CISPREHCWVLYVDVLLLECGGNLFDAISIAVKAALFNTRIPR------VRVLEDEEGSK 174

Query: 530 STGEIKD 536
              E+ D
Sbjct: 175 -DIELSD 180

>d2nn6e1 d.14.1.4 (E:5-191) Exosome complex exonuclease RRP42 {Human (Homo sapiens) [TaxId: 9606]} Length = 187

class: Alpha and beta proteins (a+b)
fold: Ribosomal protein S5 domain 2-like
superfamily: Ribosomal protein S5 domain 2-like
family: Ribonuclease PH domain 1-like
domain: Exosome complex exonuclease RRP42
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 39.7 bits (92), Expect = 6e-04
 Identities = 20/140 (14%), Positives = 41/140 (29%), Gaps = 16/140 (11%)

Query: 68  RLITLETGKIARFANGAVVLGMDETKVLSTVTSSKGDSVRDFLPLTVDYQEKQFAQGVIP 127
           R + +ET  ++   +G+  + +  T +L  V +  G    +             +     
Sbjct: 29  RCVEVETDVVSN-TSGSARVKLGHTDILVGVKAEMGTPKLEKPNEGYLEFFVDCS---AS 84

Query: 128 NTYMRREGAPKERELLVGRIIDRPIRP----------LFPAGFYHEVQVMASVLSSDGKQ 177
            T         +    +   + R              + P      + V   +L   G  
Sbjct: 85  ATPEFEGRGGDDLGTEIANTLYRIFNNKSSVDLKTLCISPREHCWVLYVDVLLLECGG-- 142

Query: 178 DPDIMAANATSAALMLSDIP 197
           +     + A  AAL  + IP
Sbjct: 143 NLFDAISIAVKAALFNTRIP 162

>d1oysa1 d.14.1.4 (A:1-151) Ribonuclease PH, domain 1 {Bacillus subtilis [TaxId: 1423]} Length = 151

class: Alpha and beta proteins (a+b)
fold: Ribosomal protein S5 domain 2-like
superfamily: Ribosomal protein S5 domain 2-like
family: Ribonuclease PH domain 1-like
domain: Ribonuclease PH, domain 1
species: Bacillus subtilis [TaxId: 1423]

 Score =  117 bits (293), Expect = 4e-31
 Identities = 36/145 (24%), Positives = 65/145 (44%)

Query: 370 RVDGRQLDEVRPIYCESGNLPILHGSSLFSRGDTQVLCTVTLGAPAEAQRLESLVGPPTK 429
           R DGRQ DE+RPI  +   +    GS L + G+T+V+C  ++             G  T 
Sbjct: 2   RHDGRQHDELRPITFDLDFISHPEGSVLITAGNTKVICNASVEDRVPPFLRGGGKGWITA 61

Query: 430 RFMLHYSFPPFCINEVGKRVGLNRREVGHGTLAEKALLAVLPPENDFPYTVRVNSEVMAS 489
            + +          +   +  ++ R +    L  +AL AV+  E     T+ ++ +V+ +
Sbjct: 62  EYSMLPQATNQQTIQESSKGKISGRTMEIQRLIGRALRAVVDLEKLGERTIWIDCDVIQA 121

Query: 490 DGSTSMATVCGGSMALMDAGIPLQE 514
           DG T  A++ G  +A+  A   L +
Sbjct: 122 DGGTRTASITGAFLAMAIAIGKLIK 146

>d1oysa1 d.14.1.4 (A:1-151) Ribonuclease PH, domain 1 {Bacillus subtilis [TaxId: 1423]} Length = 151

class: Alpha and beta proteins (a+b)
fold: Ribosomal protein S5 domain 2-like
superfamily: Ribosomal protein S5 domain 2-like
family: Ribonuclease PH domain 1-like
domain: Ribonuclease PH, domain 1
species: Bacillus subtilis [TaxId: 1423]

 Score = 44.1 bits (103), Expect = 1e-05
 Identities = 17/130 (13%), Positives = 35/130 (26%), Gaps = 4/130 (3%)

Query: 68  RLITLETGKIARFANGAVVLGMDETKVLSTVT-SSKGDSVRDFLPLTVDYQEKQFAQGVI 126
           R IT +         G+V++    TKV+   +   +               E        
Sbjct: 12  RPITFDLD-FISHPEGSVLITAGNTKVICNASVEDRVPPFLRGGGKGWITAEYSMLPQAT 70

Query: 127 PNTY--MRREGAPKERELLVGRIIDRPIRPLFPAGFYHEVQVMASVLSSDGKQDPDIMAA 184
                    +G    R + + R+I R +R +       E  +                + 
Sbjct: 71  NQQTIQESSKGKISGRTMEIQRLIGRALRAVVDLEKLGERTIWIDCDVIQADGGTRTASI 130

Query: 185 NATSAALMLS 194
                A+ ++
Sbjct: 131 TGAFLAMAIA 140

>d1e3ha2 d.14.1.4 (A:3-151) Polynucleotide phosphorylase/guanosine pentaphosphate synthase (PNPase/GPSI), domains 1 and 4 {Streptomyces antibioticus [TaxId: 1890]} Length = 149

class: Alpha and beta proteins (a+b)
fold: Ribosomal protein S5 domain 2-like
superfamily: Ribosomal protein S5 domain 2-like
family: Ribonuclease PH domain 1-like
domain: Polynucleotide phosphorylase/guanosine pentaphosphate synthase (PNPase/GPSI), domains 1 and 4
species: Streptomyces antibioticus [TaxId: 1890]

 Score =  115 bits (289), Expect = 1e-30
 Identities = 54/147 (36%), Positives = 88/147 (59%), Gaps = 2/147 (1%)

Query: 53  TKVLETFKEEFEIGSRLITLETGKIARFANGAVVLGMDETKVLSTVTSSKGDSVRD--FL 110
           T   E   +    G+R I  ETG++AR A G+ V  +D+  ++ + T++  +      F 
Sbjct: 3   THYAEAVIDNGAFGTRTIRFETGRLARQAAGSAVAYLDDDTMVLSATTASKNPKDQLDFF 62

Query: 111 PLTVDYQEKQFAQGVIPNTYMRREGAPKERELLVGRIIDRPIRPLFPAGFYHEVQVMASV 170
           PLTVD +E+ +A G IP ++ RREG P E  +L  R+IDRP+RP F  G  +E+QV+A++
Sbjct: 63  PLTVDVEERMYAAGKIPGSFFRREGRPSEDAILTCRLIDRPLRPSFKKGLRNEIQVVATI 122

Query: 171 LSSDGKQDPDIMAANATSAALMLSDIP 197
           ++ +     D++A NA SA+  L+ +P
Sbjct: 123 MALNPDHLYDVVAINAASASTQLAGLP 149

>d1e3ha2 d.14.1.4 (A:3-151) Polynucleotide phosphorylase/guanosine pentaphosphate synthase (PNPase/GPSI), domains 1 and 4 {Streptomyces antibioticus [TaxId: 1890]} Length = 149

class: Alpha and beta proteins (a+b)
fold: Ribosomal protein S5 domain 2-like
superfamily: Ribosomal protein S5 domain 2-like
family: Ribonuclease PH domain 1-like
domain: Polynucleotide phosphorylase/guanosine pentaphosphate synthase (PNPase/GPSI), domains 1 and 4
species: Streptomyces antibioticus [TaxId: 1890]

 Score =  100 bits (250), Expect = 3e-25
 Identities = 20/144 (13%), Positives = 42/144 (29%), Gaps = 3/144 (2%)

Query: 369 VRVDGRQLDEVRPIYCESGNLPIL-HGSSLFSRGDTQVLCTVTLGAPAEAQRLESLVGPP 427
             +D       R I  E+G L     GS++    D  ++ + T  +     +L+      
Sbjct: 8   AVIDNGAFGT-RTIRFETGRLARQAAGSAVAYLDDDTMVLSATTASKNPKDQLDFF-PLT 65

Query: 428 TKRFMLHYSFPPFCINEVGKRVGLNRREVGHGTLAEKALLAVLPPENDFPYTVRVNSEVM 487
                  Y+      +   +    +   +    L ++ L             V      +
Sbjct: 66  VDVEERMYAAGKIPGSFFRREGRPSEDAILTCRLIDRPLRPSFKKGLRNEIQVVATIMAL 125

Query: 488 ASDGSTSMATVCGGSMALMDAGIP 511
             D    +  +   S +   AG+P
Sbjct: 126 NPDHLYDVVAINAASASTQLAGLP 149

>d1udsa1 d.14.1.4 (A:2-150) Ribonuclease PH, domain 1 {Aquifex aeolicus [TaxId: 63363]} Length = 149

class: Alpha and beta proteins (a+b)
fold: Ribosomal protein S5 domain 2-like
superfamily: Ribosomal protein S5 domain 2-like
family: Ribonuclease PH domain 1-like
domain: Ribonuclease PH, domain 1
species: Aquifex aeolicus [TaxId: 63363]

 Score =  111 bits (278), Expect = 4e-29
 Identities = 38/149 (25%), Positives = 63/149 (42%), Gaps = 8/149 (5%)

Query: 370 RVDGRQLDEVRPIYCESGNLPILHGSSLFSRGDTQVLCTVTLGAPAEAQRLESLVGPPTK 429
           R DGR+ D++RP+  +   L    GS L S G T+V+CT ++           L G    
Sbjct: 1   RSDGRKEDQLRPVSIQRDFLEYPEGSCLISFGKTKVICTASV----IENVPNWLKGKGQG 56

Query: 430 RFMLHYSFPPFCINEVGKRVGLNRREV----GHGTLAEKALLAVLPPENDFPYTVRVNSE 485
                YS  P    +   R  +  R          +  +A+   +        T+ V+ +
Sbjct: 57  WITAEYSMLPRATQQRTIRESVQGRIGGRTHEIQRMIGRAMRTAVELTKIGERTIWVDCD 116

Query: 486 VMASDGSTSMATVCGGSMALMDAGIPLQE 514
           V+ +DG T+ A + G  +A+ DA I L +
Sbjct: 117 VIQADGGTATAAITGAFVAVADAIIKLHK 145

>d1udsa1 d.14.1.4 (A:2-150) Ribonuclease PH, domain 1 {Aquifex aeolicus [TaxId: 63363]} Length = 149

class: Alpha and beta proteins (a+b)
fold: Ribosomal protein S5 domain 2-like
superfamily: Ribosomal protein S5 domain 2-like
family: Ribonuclease PH domain 1-like
domain: Ribonuclease PH, domain 1
species: Aquifex aeolicus [TaxId: 63363]

 Score = 46.1 bits (108), Expect = 2e-06
 Identities = 21/147 (14%), Positives = 44/147 (29%), Gaps = 12/147 (8%)

Query: 68  RLITLETGKIARFANGAVVLGMDETKVLSTVTSSKGDSVR----DFLPLTVDYQEKQFAQ 123
           R ++++      +  G+ ++   +TKV+ T +  +             +T +Y     A 
Sbjct: 11  RPVSIQRD-FLEYPEGSCLISFGKTKVICTASVIENVPNWLKGKGQGWITAEYSMLPRAT 69

Query: 124 GVIPNTYMRREGAPKERELLVGRIIDRPIRPLFPAGFYHEVQVMASVLSSDGKQDPDIMA 183
                    + G    R   + R+I R +R         E  +                A
Sbjct: 70  QQRTIRESVQ-GRIGGRTHEIQRMIGRAMRTAVELTKIGERTIWVDCDVIQADGGTATAA 128

Query: 184 ANATSAALMLSDIPWGGPIGMIRIGRI 210
                 A+  + I       + + G I
Sbjct: 129 ITGAFVAVADAIIK------LHKEGII 149

>d2nn6f1 d.14.1.4 (F:29-175) Exosome complex exonuclease MTR3 {Human (Homo sapiens) [TaxId: 9606]} Length = 147

class: Alpha and beta proteins (a+b)
fold: Ribosomal protein S5 domain 2-like
superfamily: Ribosomal protein S5 domain 2-like
family: Ribonuclease PH domain 1-like
domain: Exosome complex exonuclease MTR3
species: Human (Homo sapiens) [TaxId: 9606]

 Score =  108 bits (270), Expect = 5e-28
 Identities = 30/146 (20%), Positives = 51/146 (34%), Gaps = 9/146 (6%)

Query: 373 GRQLDEVRPIYCESGNLPILHGSSLFSRGDTQVLCTVT--------LGAPAEAQRLESLV 424
            R    +RP+Y  +G L    GS+    G T+VLC V+              A       
Sbjct: 2   TRDPTRLRPVYARAGLLSQAKGSAYLEAGGTKVLCAVSGPRQAEGGERGGGPAGAGGEAP 61

Query: 425 GPPTKRFMLHYSFPPFCINEVGKRVGLNRREVGHGTLAEKALLAVLPPENDFPYTVRVNS 484
                R +  +   PF      +       E       ++AL   +         + V++
Sbjct: 62  AALRGRLLCDFRRAPFAGRR-RRAPPGGCEERELALALQEALEPAVRLGRYPRAQLEVSA 120

Query: 485 EVMASDGSTSMATVCGGSMALMDAGI 510
            ++   GS   A +   ++AL DAG+
Sbjct: 121 LLLEDGGSALAAALTAAALALADAGV 146

>d2nn6f1 d.14.1.4 (F:29-175) Exosome complex exonuclease MTR3 {Human (Homo sapiens) [TaxId: 9606]} Length = 147

class: Alpha and beta proteins (a+b)
fold: Ribosomal protein S5 domain 2-like
superfamily: Ribosomal protein S5 domain 2-like
family: Ribonuclease PH domain 1-like
domain: Exosome complex exonuclease MTR3
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 76.9 bits (188), Expect = 5e-17
 Identities = 26/139 (18%), Positives = 42/139 (30%), Gaps = 11/139 (7%)

Query: 68  RLITLETGKIARFANGAVVLGMDETKVLSTVTSSKG--DSVRDFLPLTVDYQEKQFAQGV 125
           R +    G +   A G+  L    TKVL  V+  +      R   P     +     +G 
Sbjct: 9   RPVYARAG-LLSQAKGSAYLEAGGTKVLCAVSGPRQAEGGERGGGPAGAGGEAPAALRGR 67

Query: 126 I--------PNTYMRREGAPKERELLVGRIIDRPIRPLFPAGFYHEVQVMASVLSSDGKQ 177
           +             RR       E  +   +   + P    G Y   Q+  S L  +   
Sbjct: 68  LLCDFRRAPFAGRRRRAPPGGCEERELALALQEALEPAVRLGRYPRAQLEVSALLLEDGG 127

Query: 178 DPDIMAANATSAALMLSDI 196
                A  A + AL  + +
Sbjct: 128 SALAAALTAAALALADAGV 146

>d2nn6d1 d.14.1.4 (D:25-146) Exosome complex exonuclease RRP46 {Human (Homo sapiens) [TaxId: 9606]} Length = 122

class: Alpha and beta proteins (a+b)
fold: Ribosomal protein S5 domain 2-like
superfamily: Ribosomal protein S5 domain 2-like
family: Ribonuclease PH domain 1-like
domain: Exosome complex exonuclease RRP46
species: Human (Homo sapiens) [TaxId: 9606]

 Score =  100 bits (250), Expect = 1e-25
 Identities = 29/133 (21%), Positives = 44/133 (33%), Gaps = 13/133 (9%)

Query: 378 EVRPIYCESGNLPILHGSSLFSRGDTQVLCTVTLGAPAEAQRLESLVGPPTKRFMLHYSF 437
            +R   CE   L    GS+ F +GDT VL  V                   K     ++ 
Sbjct: 3   SLRHFACEQNLLSRPDGSASFLQGDTSVLAGVYGP-------------AEVKVSKEIFNK 49

Query: 438 PPFCINEVGKRVGLNRREVGHGTLAEKALLAVLPPENDFPYTVRVNSEVMASDGSTSMAT 497
               +    K       E     L      AV+        ++ V  +V++  GS     
Sbjct: 50  ATLEVILRPKIGLPGVAEKSRERLIRNTCEAVVLGTLHPRTSITVVLQVVSDAGSLLACC 109

Query: 498 VCGGSMALMDAGI 510
           +    MAL+DAG+
Sbjct: 110 LNAACMALVDAGV 122

>d2nn6d1 d.14.1.4 (D:25-146) Exosome complex exonuclease RRP46 {Human (Homo sapiens) [TaxId: 9606]} Length = 122

class: Alpha and beta proteins (a+b)
fold: Ribosomal protein S5 domain 2-like
superfamily: Ribosomal protein S5 domain 2-like
family: Ribonuclease PH domain 1-like
domain: Exosome complex exonuclease RRP46
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 80.1 bits (197), Expect = 1e-18
 Identities = 20/129 (15%), Positives = 39/129 (30%), Gaps = 11/129 (8%)

Query: 68  RLITLETGKIARFANGAVVLGMDETKVLSTVTSSKGDSVRDFLPLTVDYQEKQFAQGVIP 127
           R    E   ++R  +G+      +T VL+ V            P  V   ++ F +  + 
Sbjct: 5   RHFACEQNLLSR-PDGSASFLQGDTSVLAGVY----------GPAEVKVSKEIFNKATLE 53

Query: 128 NTYMRREGAPKERELLVGRIIDRPIRPLFPAGFYHEVQVMASVLSSDGKQDPDIMAANAT 187
                + G P   E    R+I      +     +    +   +              NA 
Sbjct: 54  VILRPKIGLPGVAEKSRERLIRNTCEAVVLGTLHPRTSITVVLQVVSDAGSLLACCLNAA 113

Query: 188 SAALMLSDI 196
             AL+ + +
Sbjct: 114 CMALVDAGV 122

>d1e3ha5 d.101.1.1 (A:152-262) Polynucleotide phosphorylase/guanosine pentaphosphate synthase (PNPase/GPSI), domains 2 and 5 {Streptomyces antibioticus [TaxId: 1890]} Length = 111

class: Alpha and beta proteins (a+b)
fold: Ribonuclease PH domain 2-like
superfamily: Ribonuclease PH domain 2-like
family: Ribonuclease PH domain 2-like
domain: Polynucleotide phosphorylase/guanosine pentaphosphate synthase (PNPase/GPSI), domains 2 and 5
species: Streptomyces antibioticus [TaxId: 1890]

 Score = 85.4 bits (211), Expect = 2e-20
 Identities = 28/108 (25%), Positives = 45/108 (41%), Gaps = 17/108 (15%)

Query: 198 WGGPIGMIRIGRICGQFIVNPTMDELSLSDLNLVYACTREKTLMIDV------------- 244
           + GPIG +R+  I GQ++  PT  EL  +  ++V A    +   + +             
Sbjct: 1   FSGPIGGVRVALIRGQWVAFPTHTELEDAVFDMVVAGRVLEDGDVAIMMVEAEATEKTIQ 60

Query: 245 ----QAREISEKDLEAGLRLAHPEAVKYLEPQIRLAEKAGKQKKEYKL 288
                A   +E+ + AGL  A P      + Q  LA KA K   E+ +
Sbjct: 61  LVKDGAEAPTEEVVAAGLDAAKPFIKVLCKAQADLAAKAAKPTGEFPV 108

>d1whua_ a.4.9.1 (A:) Polynucleotide phosphorylase/guanosine pentaphosphate synthase (PNPase/GPSI), domain 3 {Mouse (Mus musculus) [TaxId: 10090]} Length = 104

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Polynucleotide phosphorylase/guanosine pentaphosphate synthase (PNPase/GPSI), domain 3
family: Polynucleotide phosphorylase/guanosine pentaphosphate synthase (PNPase/GPSI), domain 3
domain: Polynucleotide phosphorylase/guanosine pentaphosphate synthase (PNPase/GPSI), domain 3
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 78.3 bits (193), Expect = 5e-18
 Identities = 28/100 (28%), Positives = 46/100 (46%)

Query: 281 KQKKEYKLSMISEQTLEKVSNLAEAHIEAVFTDPSYSKFERGEALDKIGQDVKKALEEEC 340
                 K+   S + ++    +A   + AVFTD  + K  R EA++KI  D ++ L+E+ 
Sbjct: 4   GSSGPQKIFTPSAEIVKYTKIIAMEKLYAVFTDYEHDKVSRDEAVNKIRLDTEEHLKEKF 63

Query: 341 DEESLQVLPKAVDTVRKRVIRKRIIAEGVRVDGRQLDEVR 380
            E     + ++ + V K V R  I+ E  R DGR      
Sbjct: 64  PEVDQFEIIESFNIVAKEVFRSIILNEYKRCDGRDSGPSS 103

>d1sroa_ b.40.4.5 (A:) S1 RNA-binding domain of polyribonucleotide phosphorylase, PNPase {Escherichia coli [TaxId: 562]} Length = 76

class: All beta proteins
fold: OB-fold
superfamily: Nucleic acid-binding proteins
family: Cold shock DNA-binding domain-like
domain: S1 RNA-binding domain of polyribonucleotide phosphorylase, PNPase
species: Escherichia coli [TaxId: 562]

 Score = 76.3 bits (188), Expect = 9e-18
 Identities = 30/73 (41%), Positives = 54/73 (73%)

Query: 680 EIEVGGIYKGVVTSVKEYGAFVEFNGGQQGLLHVSELSHEPVSRVSDVVSVGQQLSLRCI 739
           EIEVG +Y G VT + ++GAFV   GG++GL+H+S+++ + V +V+D + +GQ++ ++ +
Sbjct: 2   EIEVGRVYTGKVTRIVDFGAFVAIGGGKEGLVHISQIADKRVEKVTDYLQMGQEVPVKVL 61

Query: 740 GQDVRGNIKLSLK 752
             D +G I+LS+K
Sbjct: 62  EVDRQGRIRLSIK 74

>d1e3ha1 a.4.9.1 (A:263-345) Polynucleotide phosphorylase/guanosine pentaphosphate synthase (PNPase/GPSI), domain 3 {Streptomyces antibioticus [TaxId: 1890]} Length = 83

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Polynucleotide phosphorylase/guanosine pentaphosphate synthase (PNPase/GPSI), domain 3
family: Polynucleotide phosphorylase/guanosine pentaphosphate synthase (PNPase/GPSI), domain 3
domain: Polynucleotide phosphorylase/guanosine pentaphosphate synthase (PNPase/GPSI), domain 3
species: Streptomyces antibioticus [TaxId: 1890]

 Score = 67.2 bits (164), Expect = 2e-14
 Identities = 23/85 (27%), Positives = 39/85 (45%), Gaps = 3/85 (3%)

Query: 292 SEQTLEKVSNLAEAHIEAVFTDPSYSKFERGEALDKIGQDVKKALEEECDEESLQVLPKA 351
            +  LE +S      + A  T     K +R   LD++     + L  E  E   + +  A
Sbjct: 2   QDDVLEALSAAVRPELSAALTIAG--KQDREAELDRVKALAAEKLLPE-FEGREKEISAA 58

Query: 352 VDTVRKRVIRKRIIAEGVRVDGRQL 376
              + K ++R+R+IAE  R+DGR +
Sbjct: 59  YRALTKSLVRERVIAEKKRIDGRGV 83

>d1oysa2 d.101.1.1 (A:152-237) Ribonuclease PH, domain 2 {Bacillus subtilis [TaxId: 1423]} Length = 86

class: Alpha and beta proteins (a+b)
fold: Ribonuclease PH domain 2-like
superfamily: Ribonuclease PH domain 2-like
family: Ribonuclease PH domain 2-like
domain: Ribonuclease PH, domain 2
species: Bacillus subtilis [TaxId: 1423]

 Score = 65.8 bits (160), Expect = 7e-14
 Identities = 21/92 (22%), Positives = 39/92 (42%), Gaps = 11/92 (11%)

Query: 510 IPLQEHVAGVSVGLVSEVDPSTGEIKDYRILTDILGLEDHLGDMDFKIAGTRIG-VTAIQ 568
            P+ + +A +SVG+           K+  IL D+   ED   ++D  +  T  G    +Q
Sbjct: 2   NPITDFLAAISVGI----------DKEQGILLDLNYEEDSSAEVDMNVIMTGSGRFVELQ 51

Query: 569 LDIKPAGIPLDIICECLEHAHKGRLQILDHME 600
              + A    + +   L  A KG  +++D  +
Sbjct: 52  GTGEEATFSREDLNGLLGLAEKGIQELIDKQK 83

>d1oysa2 d.101.1.1 (A:152-237) Ribonuclease PH, domain 2 {Bacillus subtilis [TaxId: 1423]} Length = 86

class: Alpha and beta proteins (a+b)
fold: Ribonuclease PH domain 2-like
superfamily: Ribonuclease PH domain 2-like
family: Ribonuclease PH domain 2-like
domain: Ribonuclease PH, domain 2
species: Bacillus subtilis [TaxId: 1423]

 Score = 38.0 bits (88), Expect = 3e-04
 Identities = 17/88 (19%), Positives = 33/88 (37%), Gaps = 8/88 (9%)

Query: 196 IPWGGPIGMIRIGRICGQFIVNPTM-DELSLSDLNLVYACTRE---KTLMIDVQAREISE 251
            P    +  I +G    Q I+     +E S +++++    T       L    +    S 
Sbjct: 2   NPITDFLAAISVGIDKEQGILLDLNYEEDSSAEVDMNVIMTGSGRFVELQGTGEEATFSR 61

Query: 252 KDLEAGLRLAHPEAVKYLEPQIRLAEKA 279
           +DL   L LA  + ++ L   I   ++ 
Sbjct: 62  EDLNGLLGLAE-KGIQEL---IDKQKEV 85

>d3bzka4 b.40.4.5 (A:637-730) Tex S1-domain {Pseudomonas aeruginosa [TaxId: 287]} Length = 94

class: All beta proteins
fold: OB-fold
superfamily: Nucleic acid-binding proteins
family: Cold shock DNA-binding domain-like
domain: Tex S1-domain
species: Pseudomonas aeruginosa [TaxId: 287]

 Score = 65.3 bits (159), Expect = 1e-13
 Identities = 25/77 (32%), Positives = 46/77 (59%), Gaps = 1/77 (1%)

Query: 679 REIEVGGIYKGVVTSVKEYGAFVEFNGGQQGLLHVSELSHEPVSRVSDVVSVGQQLSLRC 738
           ++++ G + +GVVT+V  +GAFV+    Q GL+H+S LS + V    +VV  G  + ++ 
Sbjct: 14  KDLKPGMVLEGVVTNVTNFGAFVDIGVHQDGLVHISALSEKFVKDPYEVVKAGDIVKVKV 73

Query: 739 IGQDV-RGNIKLSLKAV 754
           +  D+ R  + LS++  
Sbjct: 74  MEVDIPRNRVGLSMRMS 90

>d2nn6h1 b.40.4.5 (H:73-167) S1-domain of Ribosomal RNA-processing protein 4, RRP4 {Human (Homo sapiens) [TaxId: 9606]} Length = 95

class: All beta proteins
fold: OB-fold
superfamily: Nucleic acid-binding proteins
family: Cold shock DNA-binding domain-like
domain: S1-domain of Ribosomal RNA-processing protein 4, RRP4
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 64.6 bits (157), Expect = 2e-13
 Identities = 17/82 (20%), Positives = 30/82 (36%), Gaps = 10/82 (12%)

Query: 682 EVGGIYKGVVTSVKEYGAFVEFNGGQQGLLHVSELS----------HEPVSRVSDVVSVG 731
           EVG I  G +T V++    VE N     +L +S ++           E    +   +  G
Sbjct: 7   EVGDIVVGRITEVQQKRWKVETNSRLDSVLLLSSMNLPGGELRRRSAEDELAMRGFLQEG 66

Query: 732 QQLSLRCIGQDVRGNIKLSLKA 753
             +S         G + L  ++
Sbjct: 67  DLISAEVQAVFSDGAVSLHTRS 88

>d2z0sa1 b.40.4.5 (A:60-147) S1-domain of exosome complex RNA-binding protein 1, ECR1 {Aeropyrum pernix [TaxId: 56636]} Length = 88

class: All beta proteins
fold: OB-fold
superfamily: Nucleic acid-binding proteins
family: Cold shock DNA-binding domain-like
domain: S1-domain of exosome complex RNA-binding protein 1, ECR1
species: Aeropyrum pernix [TaxId: 56636]

 Score = 63.4 bits (154), Expect = 5e-13
 Identities = 14/77 (18%), Positives = 32/77 (41%), Gaps = 4/77 (5%)

Query: 682 EVGGIYKGVVTSVKEYGAFVEFNGGQQGLLHVSELSHEPVS----RVSDVVSVGQQLSLR 737
           + G +  G++ SV     FV+ N     +L V +    P +     +  ++ VG  +  +
Sbjct: 6   QAGDVVIGLIQSVGIMNWFVDINSPYVAVLSVQDFLGRPFNPAVDDMQSLLKVGDYIKAK 65

Query: 738 CIGQDVRGNIKLSLKAV 754
            +  D   +  L+++  
Sbjct: 66  VVAFDKTRSPLLTVQGE 82

>d1r6la2 d.101.1.1 (A:152-239) Ribonuclease PH, domain 2 {Pseudomonas aeruginosa [TaxId: 287]} Length = 88

class: Alpha and beta proteins (a+b)
fold: Ribonuclease PH domain 2-like
superfamily: Ribonuclease PH domain 2-like
family: Ribonuclease PH domain 2-like
domain: Ribonuclease PH, domain 2
species: Pseudomonas aeruginosa [TaxId: 287]

 Score = 62.3 bits (151), Expect = 1e-12
 Identities = 22/97 (22%), Positives = 38/97 (39%), Gaps = 12/97 (12%)

Query: 509 GIPLQEHVAGVSVGLVSEVDPSTGEIKDYRILTDILGLEDHLGDMDFKIAGTRIG-VTAI 567
           G PL++ VA VSVG+                + D+  LED   + D  +  T  G    +
Sbjct: 2   GNPLKQMVAAVSVGIY-----------QGVPVLDLDYLEDSAAETDLNVVMTDAGGFIEV 50

Query: 568 QLDIKPAGIPLDIICECLEHAHKGRLQILDHMEREIS 604
           Q   + A      +   LE A +G  ++ +     ++
Sbjct: 51  QGTAEGAPFRPAELNAMLELAQQGMQELFELQRAALA 87

>d1r6la2 d.101.1.1 (A:152-239) Ribonuclease PH, domain 2 {Pseudomonas aeruginosa [TaxId: 287]} Length = 88

class: Alpha and beta proteins (a+b)
fold: Ribonuclease PH domain 2-like
superfamily: Ribonuclease PH domain 2-like
family: Ribonuclease PH domain 2-like
domain: Ribonuclease PH, domain 2
species: Pseudomonas aeruginosa [TaxId: 287]

 Score = 50.4 bits (120), Expect = 2e-08
 Identities = 14/80 (17%), Positives = 26/80 (32%), Gaps = 3/80 (3%)

Query: 196 IPWGGPIGMIRIGRICGQFIVNPTMDELSLSDLNLVYACTREKTL---MIDVQAREISEK 252
            P    +  + +G   G  +++    E S ++ +L    T            +       
Sbjct: 3   NPLKQMVAAVSVGIYQGVPVLDLDYLEDSAAETDLNVVMTDAGGFIEVQGTAEGAPFRPA 62

Query: 253 DLEAGLRLAHPEAVKYLEPQ 272
           +L A L LA     +  E Q
Sbjct: 63  ELNAMLELAQQGMQELFELQ 82

>d1e3pa2 b.40.4.5 (A:656-717) S1 RNA-binding domain of polyribonucleotide phosphorylase, PNPase {Streptomyces antibioticus [TaxId: 1890]} Length = 62

class: All beta proteins
fold: OB-fold
superfamily: Nucleic acid-binding proteins
family: Cold shock DNA-binding domain-like
domain: S1 RNA-binding domain of polyribonucleotide phosphorylase, PNPase
species: Streptomyces antibioticus [TaxId: 1890]

 Score = 60.5 bits (147), Expect = 2e-12
 Identities = 22/61 (36%), Positives = 32/61 (52%), Gaps = 4/61 (6%)

Query: 689 GVVTSVKEYGAFVEFNGGQQGLLHVSELSH----EPVSRVSDVVSVGQQLSLRCIGQDVR 744
           G V     +GAFV    G+ GLLH+S++      + V  V DV+ VGQ++ +     D R
Sbjct: 1   GSVVKTTTFGAFVSLLPGKDGLLHISQIRKLAGGKRVENVEDVLGVGQKVQVEIAEIDSR 60

Query: 745 G 745
           G
Sbjct: 61  G 61

>d2ba0a1 b.40.4.5 (A:53-135) S1-domain of exosome complex RNA-binding protein 1, ECR1 {Archaeoglobus fulgidus [TaxId: 2234]} Length = 83

class: All beta proteins
fold: OB-fold
superfamily: Nucleic acid-binding proteins
family: Cold shock DNA-binding domain-like
domain: S1-domain of exosome complex RNA-binding protein 1, ECR1
species: Archaeoglobus fulgidus [TaxId: 2234]

 Score = 61.2 bits (148), Expect = 3e-12
 Identities = 19/78 (24%), Positives = 35/78 (44%), Gaps = 1/78 (1%)

Query: 682 EVGGIYKGVVTSVKEYGAFVEFNGGQQGLLHVSELSHE-PVSRVSDVVSVGQQLSLRCIG 740
            VG +  G++  V   G  V+     Q  L VSE     P  + ++V+ +G  +  + + 
Sbjct: 4   SVGDVVIGIIREVAANGWAVDIYSPYQAFLPVSENPEMKPNKKPNEVLDIGDAIIAKVLN 63

Query: 741 QDVRGNIKLSLKAVSPRP 758
            D +  + L++K    RP
Sbjct: 64  IDPKMKVTLTMKDRICRP 81

>d1udsa2 d.101.1.1 (A:151-255) Ribonuclease PH, domain 2 {Aquifex aeolicus [TaxId: 63363]} Length = 105

class: Alpha and beta proteins (a+b)
fold: Ribonuclease PH domain 2-like
superfamily: Ribonuclease PH domain 2-like
family: Ribonuclease PH domain 2-like
domain: Ribonuclease PH, domain 2
species: Aquifex aeolicus [TaxId: 63363]

 Score = 60.8 bits (147), Expect = 7e-12
 Identities = 24/108 (22%), Positives = 49/108 (45%), Gaps = 12/108 (11%)

Query: 510 IPLQEHVAGVSVGLVSEVDPSTGEIKDYRILTDILGLEDHLGDMDFKIAGTRIG-VTAIQ 568
            P+++ VA VSVG+V           + RIL D+   ED    +D  + GT  G ++ + 
Sbjct: 3   TPIKDFVAAVSVGIV-----------NDRILLDLNFEEDSAAQVDMNVVGTGSGRLSEVH 51

Query: 569 LDIKPAGIPLDIICECLEHAHKGRLQILDHMEREISAPRTQDDRNSPR 616
              +      D + + L+ A KG  ++++  ++       + +R+  +
Sbjct: 52  TMGEEYSFTKDELIKMLDLAQKGINELIELQKKLYVIQDGKWERSELK 99

>d1udsa2 d.101.1.1 (A:151-255) Ribonuclease PH, domain 2 {Aquifex aeolicus [TaxId: 63363]} Length = 105

class: Alpha and beta proteins (a+b)
fold: Ribonuclease PH domain 2-like
superfamily: Ribonuclease PH domain 2-like
family: Ribonuclease PH domain 2-like
domain: Ribonuclease PH, domain 2
species: Aquifex aeolicus [TaxId: 63363]

 Score = 54.2 bits (130), Expect = 1e-09
 Identities = 14/96 (14%), Positives = 38/96 (39%), Gaps = 4/96 (4%)

Query: 195 DIPWGGPIGMIRIGRICGQFIVNPTMDELSLSDLNLVYACTREKTL---MIDVQAREISE 251
           + P    +  + +G +  + +++   +E S + +++    T    L       +    ++
Sbjct: 2   ETPIKDFVAAVSVGIVNDRILLDLNFEEDSAAQVDMNVVGTGSGRLSEVHTMGEEYSFTK 61

Query: 252 KDLEAGLRLAHPEAVKYLEPQIR-LAEKAGKQKKEY 286
            +L   L LA     + +E Q +    + GK ++  
Sbjct: 62  DELIKMLDLAQKGINELIELQKKLYVIQDGKWERSE 97

>d2je6b2 d.101.1.1 (B:156-241) Exosome complex exonuclease 1, ECX1 {Sulfolobus solfataricus [TaxId: 2287]} Length = 86

class: Alpha and beta proteins (a+b)
fold: Ribonuclease PH domain 2-like
superfamily: Ribonuclease PH domain 2-like
family: Ribonuclease PH domain 2-like
domain: Exosome complex exonuclease 1, ECX1
species: Sulfolobus solfataricus [TaxId: 2287]

 Score = 59.5 bits (144), Expect = 9e-12
 Identities = 23/96 (23%), Positives = 37/96 (38%), Gaps = 16/96 (16%)

Query: 511 PLQEHVAGVSVGLVSEVDPSTGEIKDYRILTDILGLEDHLGDMDFKIAGT--RIGVTAIQ 568
           P+++ +AGV+VG             D  I+ D+   E   G+ D  IA       VT  Q
Sbjct: 1   PMRDLIAGVAVGKA-----------DGVIILDLNETEAMWGEADMPIAMMPSLNQVTLFQ 49

Query: 569 LDIKPAGIPLDIICECLEHAHKGRLQILDHMEREIS 604
           L+     +  D   +  + A KG   I +     + 
Sbjct: 50  LN---GSMTPDEFRQAFDLAVKGINIIYNLEREALK 82

>d2je6b2 d.101.1.1 (B:156-241) Exosome complex exonuclease 1, ECX1 {Sulfolobus solfataricus [TaxId: 2287]} Length = 86

class: Alpha and beta proteins (a+b)
fold: Ribonuclease PH domain 2-like
superfamily: Ribonuclease PH domain 2-like
family: Ribonuclease PH domain 2-like
domain: Exosome complex exonuclease 1, ECX1
species: Sulfolobus solfataricus [TaxId: 2287]

 Score = 44.1 bits (104), Expect = 2e-06
 Identities = 14/88 (15%), Positives = 30/88 (34%), Gaps = 5/88 (5%)

Query: 197 PWGGPIGMIRIGRICGQFIVNPTMDELSLSDLNLVYACTREKTLMIDVQAR-EISEKDLE 255
           P    I  + +G+  G  I++    E    + ++  A       +   Q    ++  +  
Sbjct: 1   PMRDLIAGVAVGKADGVIILDLNETEAMWGEADMPIAMMPSLNQVTLFQLNGSMTPDEFR 60

Query: 256 AGLRLAHPEAVKYLEPQIRLAEKAGKQK 283
               LA  + +  +     L  +A K K
Sbjct: 61  QAFDLAV-KGINII---YNLEREALKSK 84

>d2je6i1 b.40.4.5 (I:66-152) S1-domain of exosome complex RNA-binding protein 1, ECR1 {Sulfolobus solfataricus [TaxId: 2287]} Length = 87

class: All beta proteins
fold: OB-fold
superfamily: Nucleic acid-binding proteins
family: Cold shock DNA-binding domain-like
domain: S1-domain of exosome complex RNA-binding protein 1, ECR1
species: Sulfolobus solfataricus [TaxId: 2287]

 Score = 58.9 bits (142), Expect = 2e-11
 Identities = 17/76 (22%), Positives = 29/76 (38%), Gaps = 3/76 (3%)

Query: 682 EVGGIYKGVVTSVKEYGAFVEFNGGQQGLLHVSELSHEPVSRV---SDVVSVGQQLSLRC 738
           ++  I  G+V  V+ YG  V+     +  L  S L    ++        + VG  +  R 
Sbjct: 6   KINDIVIGLVEDVEIYGWVVDIKAPYKAYLPASNLLGRSINVGEDLRRYLDVGDYVIARI 65

Query: 739 IGQDVRGNIKLSLKAV 754
              D   +  LS+K  
Sbjct: 66  ENFDRSIDPVLSVKGK 81

>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 = 58.2 bits (141), Expect = 3e-11
 Identities = 16/83 (19%), Positives = 38/83 (45%), Gaps = 2/83 (2%)

Query: 616 RLATLKYDNDTLRRLIGPLGALKRKIEEETGGRISVS-DGTLTVVAKNRSVMEKVLEKVD 674
           R   ++     + R+IG   ++ + +EE+T  +I V+ +G + +   N  +    +  + 
Sbjct: 1   RGKIVEISPAKVPRVIGRKMSMLKTLEEKTECKIFVARNGRIHLECPNEDLEAIAVMAIK 60

Query: 675 FIIGREIEVGGIYKGVVTSVKEY 697
            I   E    G+ K ++  ++E 
Sbjct: 61  IID-EEAYTSGLTKRIIKFIEEE 82

>d2nn6b2 d.101.1.1 (B:151-240) Exosome complex exonuclease RRP41 {Human (Homo sapiens) [TaxId: 9606]} Length = 90

class: Alpha and beta proteins (a+b)
fold: Ribonuclease PH domain 2-like
superfamily: Ribonuclease PH domain 2-like
family: Ribonuclease PH domain 2-like
domain: Exosome complex exonuclease RRP41
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 58.1 bits (140), Expect = 3e-11
 Identities = 17/101 (16%), Positives = 37/101 (36%), Gaps = 16/101 (15%)

Query: 511 PLQEHVAGVSVGLVSEVDPSTGEIKDYRILTDILGLEDHLGDMDFKIA--GTRIGVTAIQ 568
           P+++ V   S G V           D   L D+  +E+  G     +A       +  ++
Sbjct: 1   PMRDFVCACSAGFV-----------DGTALADLSHVEEAAGGPQLALALLPASGQIALLE 49

Query: 569 LDIKPAGIPLDIICECLEHAHKGRLQILDHMEREISAPRTQ 609
           +D +   +  D +   LE A +    +   ++R +     +
Sbjct: 50  MDAR---LHEDHLERVLEAAAQAARDVHTLLDRVVRQHVRE 87

>d2nn6b2 d.101.1.1 (B:151-240) Exosome complex exonuclease RRP41 {Human (Homo sapiens) [TaxId: 9606]} Length = 90

class: Alpha and beta proteins (a+b)
fold: Ribonuclease PH domain 2-like
superfamily: Ribonuclease PH domain 2-like
family: Ribonuclease PH domain 2-like
domain: Exosome complex exonuclease RRP41
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 38.5 bits (89), Expect = 3e-04
 Identities = 14/88 (15%), Positives = 30/88 (34%), Gaps = 3/88 (3%)

Query: 197 PWGGPIGMIRIGRICGQFIVNPTMDELSLSD--LNLVYACTREKTLMIDVQAREISEKDL 254
           P    +     G + G  + + +  E +     L L       +  ++++ AR   +  L
Sbjct: 1   PMRDFVCACSAGFVDGTALADLSHVEEAAGGPQLALALLPASGQIALLEMDARLHED-HL 59

Query: 255 EAGLRLAHPEAVKYLEPQIRLAEKAGKQ 282
           E  L  A   A        R+  +  ++
Sbjct: 60  ERVLEAAAQAARDVHTLLDRVVRQHVRE 87

>d2ba0d2 d.101.1.1 (D:154-252) Exosome complex exonuclease 1, ECX1 {Archaeoglobus fulgidus [TaxId: 2234]} Length = 99

class: Alpha and beta proteins (a+b)
fold: Ribonuclease PH domain 2-like
superfamily: Ribonuclease PH domain 2-like
family: Ribonuclease PH domain 2-like
domain: Exosome complex exonuclease 1, ECX1
species: Archaeoglobus fulgidus [TaxId: 2234]

 Score = 58.6 bits (141), Expect = 4e-11
 Identities = 15/99 (15%), Positives = 39/99 (39%)

Query: 197 PWGGPIGMIRIGRICGQFIVNPTMDELSLSDLNLVYACTREKTLMIDVQAREISEKDLEA 256
           P  G I  + +G+  GQ +++P  +E +  + ++ +A       +  +   ++  +    
Sbjct: 1   PMKGMITSVAVGKADGQLVLDPMKEEDNFGEADMPFAFLIRNGKIESIALLQMDGRMTRD 60

Query: 257 GLRLAHPEAVKYLEPQIRLAEKAGKQKKEYKLSMISEQT 295
            ++ A   A K       +  +A  ++       + E T
Sbjct: 61  EVKQAIELAKKGALQIYEMQREAILRRYIEVGEEMDEIT 99

>d2ba0d2 d.101.1.1 (D:154-252) Exosome complex exonuclease 1, ECX1 {Archaeoglobus fulgidus [TaxId: 2234]} Length = 99

class: Alpha and beta proteins (a+b)
fold: Ribonuclease PH domain 2-like
superfamily: Ribonuclease PH domain 2-like
family: Ribonuclease PH domain 2-like
domain: Exosome complex exonuclease 1, ECX1
species: Archaeoglobus fulgidus [TaxId: 2234]

 Score = 58.6 bits (141), Expect = 4e-11
 Identities = 22/104 (21%), Positives = 42/104 (40%), Gaps = 19/104 (18%)

Query: 511 PLQEHVAGVSVGLVSEVDPSTGEIKDYRILTDILGLEDHLGDMDFKIAG-----TRIGVT 565
           P++  +  V+VG             D +++ D +  ED+ G+ D   A          + 
Sbjct: 1   PMKGMITSVAVGKA-----------DGQLVLDPMKEEDNFGEADMPFAFLIRNGKIESIA 49

Query: 566 AIQLDIKPAGIPLDIICECLEHAHKGRLQILDHMEREISAPRTQ 609
            +Q+D +   +  D + + +E A KG LQI +     I     +
Sbjct: 50  LLQMDGR---MTRDEVKQAIELAKKGALQIYEMQREAILRRYIE 90

>d2je6a2 d.101.1.1 (A:192-275) Exosome complex exonuclease 2, ECX2 {Sulfolobus solfataricus [TaxId: 2287]} Length = 84

class: Alpha and beta proteins (a+b)
fold: Ribonuclease PH domain 2-like
superfamily: Ribonuclease PH domain 2-like
family: Ribonuclease PH domain 2-like
domain: Exosome complex exonuclease 2, ECX2
species: Sulfolobus solfataricus [TaxId: 2287]

 Score = 57.3 bits (138), Expect = 6e-11
 Identities = 18/78 (23%), Positives = 35/78 (44%), Gaps = 2/78 (2%)

Query: 197 PWGGPIGMIRIGRICGQFIVNPTMDELSLSDLNLVYACT--REKTLMIDVQAREISEKDL 254
           P   P+  I + ++    +V+P +DE S+ D  + ++ T   +   +       +S +D+
Sbjct: 1   PLNYPVVTISVAKVDKYLVVDPDLDEESIMDAKISFSYTPDLKIVGIQKSGKGSMSLQDI 60

Query: 255 EAGLRLAHPEAVKYLEPQ 272
           +     A   AVK LE  
Sbjct: 61  DQAENTARSTAVKLLEEL 78

>d2je6a2 d.101.1.1 (A:192-275) Exosome complex exonuclease 2, ECX2 {Sulfolobus solfataricus [TaxId: 2287]} Length = 84

class: Alpha and beta proteins (a+b)
fold: Ribonuclease PH domain 2-like
superfamily: Ribonuclease PH domain 2-like
family: Ribonuclease PH domain 2-like
domain: Exosome complex exonuclease 2, ECX2
species: Sulfolobus solfataricus [TaxId: 2287]

 Score = 41.1 bits (96), Expect = 3e-05
 Identities = 18/94 (19%), Positives = 35/94 (37%), Gaps = 13/94 (13%)

Query: 511 PLQEHVAGVSVGLVSEVDPSTGEIKDYRILTDILGLEDHLGDMDFKIAGTRIG-VTAIQL 569
           PL   V  +SV  V           D  ++ D    E+ + D     + T    +  IQ 
Sbjct: 1   PLNYPVVTISVAKV-----------DKYLVVDPDLDEESIMDAKISFSYTPDLKIVGIQK 49

Query: 570 DIKPAGIPLDIICECLEHAHKGRLQILDHMEREI 603
             K   + L  I +    A    +++L+ +++ +
Sbjct: 50  SGK-GSMSLQDIDQAENTARSTAVKLLEELKKHL 82

>d2ahob2 b.40.4.5 (B:1-84) Eukaryotic initiation factor 2alpha, eIF2alpha, N-terminal domain {Sulfolobus solfataricus [TaxId: 2287]} Length = 84

class: All beta proteins
fold: OB-fold
superfamily: Nucleic acid-binding proteins
family: Cold shock DNA-binding domain-like
domain: Eukaryotic initiation factor 2alpha, eIF2alpha, N-terminal domain
species: Sulfolobus solfataricus [TaxId: 2287]

 Score = 55.8 bits (134), Expect = 2e-10
 Identities = 23/81 (28%), Positives = 41/81 (50%), Gaps = 3/81 (3%)

Query: 675 FIIGREIEVGGIYKGVVTSVKEYGAFVEFN--GGQQGLLHVSELSHEPVSRVSDVVSVGQ 732
           +   +    G I    V  V +YG++V  +  GG Q  L  SE+S + V  + DV+   +
Sbjct: 3   YSRSKLPSEGEILIATVKQVFDYGSYVSLDEYGGLQAFLPWSEVSSKWVKNIRDVLKENR 62

Query: 733 QLSLRCIGQDV-RGNIKLSLK 752
           ++ ++ I  D  +G + +SLK
Sbjct: 63  KVIVKVIRVDRRKGTVDVSLK 83

>d1kl9a2 b.40.4.5 (A:3-88) Eukaryotic initiation factor 2alpha, eIF2alpha, N-terminal domain {Human (Homo sapiens) [TaxId: 9606]} Length = 86

class: All beta proteins
fold: OB-fold
superfamily: Nucleic acid-binding proteins
family: Cold shock DNA-binding domain-like
domain: Eukaryotic initiation factor 2alpha, eIF2alpha, N-terminal domain
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 53.1 bits (127), Expect = 2e-09
 Identities = 20/74 (27%), Positives = 37/74 (50%), Gaps = 3/74 (4%)

Query: 682 EVGGIYKGVVTSVKEYGAFVEFN--GGQQGLLHVSELSHEPVSRVSDVVSVGQQLSLRCI 739
           EV  +    V S+ E GA+V        +G++ +SELS   +  ++ ++ +G+   +  I
Sbjct: 12  EVEDVVMVNVRSIAEMGAYVSLLEYNNIEGMILLSELSRRRIRSINKLIRIGRNECVVVI 71

Query: 740 GQDV-RGNIKLSLK 752
             D  +G I LS +
Sbjct: 72  RVDKEKGYIDLSKR 85

>d2nn6d2 d.101.1.1 (D:147-235) Exosome complex exonuclease RRP46 {Human (Homo sapiens) [TaxId: 9606]} Length = 89

class: Alpha and beta proteins (a+b)
fold: Ribonuclease PH domain 2-like
superfamily: Ribonuclease PH domain 2-like
family: Ribonuclease PH domain 2-like
domain: Exosome complex exonuclease RRP46
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 50.7 bits (121), Expect = 1e-08
 Identities = 11/93 (11%), Positives = 24/93 (25%), Gaps = 11/93 (11%)

Query: 511 PLQEHVAGVSVGLVSEVDPSTGEIKDYRILTDILGLEDHLGDMDFKIAGTRIGVTAIQLD 570
           P++    GV+  L            D  ++ D    ++         A   +    +   
Sbjct: 1   PMRALFCGVACALD----------SDGTLVLDPTSKQEKEARAVLTFALDSVERKLLMSS 50

Query: 571 IKPAGIPLDIICECLEHAHKGRLQILDHMEREI 603
            K        + +CL  A      +       +
Sbjct: 51  TK-GLYSDTELQQCLAAAQAASQHVFRFYRESL 82

>d1go3e1 b.40.4.5 (E:79-184) C-terminal domain of RNA polymerase II subunit RBP7 (RpoE) {Archaeon Methanococcus jannaschii [TaxId: 2190]} Length = 106

class: All beta proteins
fold: OB-fold
superfamily: Nucleic acid-binding proteins
family: Cold shock DNA-binding domain-like
domain: C-terminal domain of RNA polymerase II subunit RBP7 (RpoE)
species: Archaeon Methanococcus jannaschii [TaxId: 2190]

 Score = 50.8 bits (121), Expect = 2e-08
 Identities = 21/99 (21%), Positives = 40/99 (40%), Gaps = 18/99 (18%)

Query: 682 EVGGIYKGVVTSVKEYGAFVEFNGGQQGLLHVSELSHEPVS-----------RVSDVVSV 730
           E+  + +G V  V E+G+FV   G   GL+HVS++  + VS               V+ +
Sbjct: 2   EMYELIEGEVVDVVEFGSFVRL-GPLDGLIHVSQIMDDYVSYDPKREAIIGKETGKVLEI 60

Query: 731 GQQLSLRCIGQDV------RGNIKLSLKAVSPRPEADVK 763
           G  +  R +   +         I L+++         ++
Sbjct: 61  GDYVRARIVAISLKAERKRGSKIALTMRQPYLGKLEWIE 99

>d2nn6g1 b.40.4.5 (G:107-194) S1-domain of exosome component 3 (RRP40) {Human (Homo sapiens) [TaxId: 9606]} Length = 88

class: All beta proteins
fold: OB-fold
superfamily: Nucleic acid-binding proteins
family: Cold shock DNA-binding domain-like
domain: S1-domain of exosome component 3 (RRP40)
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 49.1 bits (117), Expect = 5e-08
 Identities = 12/78 (15%), Positives = 22/78 (28%), Gaps = 1/78 (1%)

Query: 682 EVGGIYKGVVTSVKEYGAFVEFNGGQQGLLHVSELSHEPVSRVSDVVSVGQQLSLRCIGQ 741
             G    G+VT+       V+  G +   L           R    V VG  +  + +  
Sbjct: 5   VKGDHVIGIVTAKSGDIFKVDVGGSEPASLSYLSFEG-ATKRNRPNVQVGDLIYGQFVVA 63

Query: 742 DVRGNIKLSLKAVSPRPE 759
           +     ++       R  
Sbjct: 64  NKDMEPEMVCIDSCGRAN 81

>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 = 48.1 bits (115), Expect = 5e-08
 Identities = 17/49 (34%), Positives = 30/49 (61%), Gaps = 1/49 (2%)

Query: 615 PRLATLKYDNDTLRRLIGPLGALKRKIEEETGGRISVSD-GTLTVVAKN 662
           PR+ T+K   D +  +IGP   +  +I+E+TG  I++ D GT+ + A +
Sbjct: 2   PRIITVKIPVDKIGEVIGPKRQMINQIQEDTGAEITIEDDGTIYIGAAD 50

>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 = 48.9 bits (117), Expect = 9e-08
 Identities = 13/68 (19%), Positives = 29/68 (42%), Gaps = 2/68 (2%)

Query: 629 RLIGPLGALKRKIEEETGGRISVSDGTLTVVAKNRSVMEKVLEKVDFIIGREIEVGGIYK 688
           R+IG  G  +R IEE T   I+V +  + ++           + ++ +         +Y+
Sbjct: 26  RIIGEGGRARRTIEEMTDTYINVGEYEVAIIGDYER-AMAAKQAIEMLA-EGRMHSTVYR 83

Query: 689 GVVTSVKE 696
            +   ++E
Sbjct: 84  HLERIMRE 91

>d1wi5a_ b.40.4.5 (A:) S1-domain of RRP5 protein homolog (PDCD11, KIAA0185) {Human (Homo sapiens) [TaxId: 9606]} Length = 119

class: All beta proteins
fold: OB-fold
superfamily: Nucleic acid-binding proteins
family: Cold shock DNA-binding domain-like
domain: S1-domain of RRP5 protein homolog (PDCD11, KIAA0185)
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 46.7 bits (110), Expect = 9e-07
 Identities = 14/76 (18%), Positives = 29/76 (38%), Gaps = 3/76 (3%)

Query: 680 EIEVGGIYKGVVTSVKEYGAFVEFNGGQQ-GLLHVSELSHEP-VSRVSDVVSVGQQLSLR 737
            ++ G +  G V+S++++G  V+         L + +             + VGQ L+  
Sbjct: 18  ALKPGMLLTGTVSSLEDHGYLVDIGVDGTRAFLPLLKAQEYIRQKNKGAKLKVGQYLNCI 77

Query: 738 CIGQDVRGN-IKLSLK 752
                  G  + LS+ 
Sbjct: 78  VEKVKGNGGVVSLSVG 93

>d2ja9a1 b.40.4.5 (A:62-151) S1-domain of exosome component 3 (RRP40) {Saccharomyces cerevisiae [TaxId: 4932]} Length = 90

class: All beta proteins
fold: OB-fold
superfamily: Nucleic acid-binding proteins
family: Cold shock DNA-binding domain-like
domain: S1-domain of exosome component 3 (RRP40)
species: Saccharomyces cerevisiae [TaxId: 4932]

 Score = 45.2 bits (107), Expect = 1e-06
 Identities = 7/71 (9%), Positives = 15/71 (21%)

Query: 682 EVGGIYKGVVTSVKEYGAFVEFNGGQQGLLHVSELSHEPVSRVSDVVSVGQQLSLRCIGQ 741
            V     GV+         V        +            +    + VG  +  R    
Sbjct: 6   SVNDFVIGVIIGTFSDSYKVSLQNFSSSVSLSYMAFPNASKKNRPTLQVGDLVYARVCTA 65

Query: 742 DVRGNIKLSLK 752
           +     ++   
Sbjct: 66  EKELEAEIECF 76

>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 = 44.8 bits (106), Expect = 2e-06
 Identities = 19/73 (26%), Positives = 34/73 (46%), Gaps = 4/73 (5%)

Query: 614 SPRLATLKYDNDTLRRLIGPLGALKRKIEEETGGRISVS--DGTLTVVAKNRSVMEKVLE 671
            PR+  +K   + L  +IGP G +K +I   TG  I+V   +  + V  +   +    L 
Sbjct: 2   KPRI-YVKVKPERLGAVIGPRGEVKAEIMRRTGTVITVDTENSMVIVEPEAEGIPPVNLM 60

Query: 672 KVDFIIGREIEVG 684
           K   ++ + I +G
Sbjct: 61  KAAEVV-KAISLG 72

>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 = 43.2 bits (102), Expect = 4e-06
 Identities = 12/66 (18%), Positives = 28/66 (42%), Gaps = 2/66 (3%)

Query: 619 TLKYDNDTLRRLIGPLGALKRKIEEETGGRISVS-DGTLTVVAKNRSVMEKVLEKVDFII 677
            +      + R+IG   ++   +  ++G  I V+ +G +     +R   E ++E +  I 
Sbjct: 4   VIDIMPVKVPRVIGKNKSMYETLTSKSGCSIFVANNGRIWATCPSRFSEEILIEAIRKIE 63

Query: 678 GREIEV 683
             E  +
Sbjct: 64  -NESHI 68

>d2nn6f2 d.101.1.1 (F:176-270) Exosome complex exonuclease MTR3 {Human (Homo sapiens) [TaxId: 9606]} Length = 95

class: Alpha and beta proteins (a+b)
fold: Ribonuclease PH domain 2-like
superfamily: Ribonuclease PH domain 2-like
family: Ribonuclease PH domain 2-like
domain: Exosome complex exonuclease MTR3
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 43.4 bits (102), Expect = 7e-06
 Identities = 11/96 (11%), Positives = 26/96 (27%), Gaps = 12/96 (12%)

Query: 516 VAGVSVGLVSEVDPSTGEIKDYRILTDILGLEDHLGDMDFKIA--GTRIGVTAIQLDIKP 573
           V G  + L                L D   LE+        +A       V  +    + 
Sbjct: 5   VVGCGLSLAPG--------PAPTWLLDPTRLEEERAAAGLTVALMPVLNQVAGLLGSGEG 56

Query: 574 AGIPLDIICECLEHAHKGRLQILDHMEREISAPRTQ 609
                +   E +    +G  ++   +++ +     +
Sbjct: 57  --GLTESWAEAVRLGLEGCQRLYPVLQQSLVRAARR 90

>d1y14b1 b.40.4.5 (B:81-171) C-terminal domain of RNA polymerase II subunit RBP7 (RpoE) {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]} Length = 91

class: All beta proteins
fold: OB-fold
superfamily: Nucleic acid-binding proteins
family: Cold shock DNA-binding domain-like
domain: C-terminal domain of RNA polymerase II subunit RBP7 (RpoE)
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

 Score = 42.5 bits (100), Expect = 1e-05
 Identities = 11/79 (13%), Positives = 27/79 (34%), Gaps = 12/79 (15%)

Query: 682 EVGGIYKGVVTSVKEYGAFVEFNGGQQGLLHVSELSHEPVS----------RVSDVVSVG 731
             G +  G V S  ++G  V+  G  +  +    +  +                DV+++ 
Sbjct: 2   FKGEVVDGTVVSCSQHGFEVQV-GPMKVFVTKHLMPQDLTFNAGSNPPSYQSSEDVITIK 60

Query: 732 QQLSLRCIGQDV-RGNIKL 749
            ++ ++  G      +I  
Sbjct: 61  SRIRVKIEGCISQVSSIHA 79

>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 = 42.0 bits (99), Expect = 1e-05
 Identities = 17/80 (21%), Positives = 33/80 (41%), Gaps = 3/80 (3%)

Query: 619 TLKYDNDTLRRLIGPLGALKRKIEEETGGRISVS-DGTLTVVAKNRSVMEKVLEKVDFII 677
            +  +   + R+IG  G++ + ++ E   +I V  +G + V    R V     E +  I 
Sbjct: 4   IVAINPARVPRVIGKKGSMIKLLKSELDVQIVVGQNGLIWVNGDRRKV-SIAEEAIYLIE 62

Query: 678 GREIEVGGIYKGVVTSVKEY 697
            +E    G+   V   +K  
Sbjct: 63  -QEAHTEGLTDRVAEFIKRR 81

>d2cpqa1 d.51.1.1 (A:212-289) Fragile X mental retardation syndrome related protein 1, FXR1 {Human (Homo sapiens) [TaxId: 9606]} Length = 78

class: Alpha and beta proteins (a+b)
fold: Eukaryotic type KH-domain (KH-domain type I)
superfamily: Eukaryotic type KH-domain (KH-domain type I)
family: Eukaryotic type KH-domain (KH-domain type I)
domain: Fragile X mental retardation syndrome related protein 1, FXR1
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 37.9 bits (88), Expect = 3e-04
 Identities = 11/68 (16%), Positives = 25/68 (36%), Gaps = 4/68 (5%)

Query: 619 TLKYDNDTLRRLIGPLGALKRKIEEETGGRISVS---DGTLTVVAKNRSVMEKVLEKVDF 675
                 D +   IG  G+  ++  +  G          GT  +  ++   ++K    ++F
Sbjct: 11  EFVVREDLMGLAIGTHGSNIQQARKVPGVTAIELDEDTGTFRIYGESADAVKKARGFLEF 70

Query: 676 IIGREIEV 683
           +    I+V
Sbjct: 71  VE-DFIQV 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 = 35.6 bits (82), Expect = 0.003
 Identities = 12/72 (16%), Positives = 29/72 (40%), Gaps = 5/72 (6%)

Query: 615 PRLATLKYDNDTLRRLIGPLGALKRKIEEETGGRISV----SDGTLTVVAKNRSVMEKVL 670
           P    ++   D  R +IG  G+  RK+ +E    I V        +  +    + +++  
Sbjct: 9   PVTIEVEVPFDLHRYVIGQKGSGIRKMMDEFEVNIHVPAPELQSDIIAITGLAANLDRAK 68

Query: 671 EKVDFIIGREIE 682
             +   + +E++
Sbjct: 69  AGLLERV-KELQ 79

>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 = 35.7 bits (82), Expect = 0.004
 Identities = 13/62 (20%), Positives = 25/62 (40%)

Query: 604 SAPRTQDDRNSPRLATLKYDNDTLRRLIGPLGALKRKIEEETGGRISVSDGTLTVVAKNR 663
           S        N+P    L     ++ R+IG  G   R I + +G +I+    +   +  +R
Sbjct: 3   SGSSGILTENTPVFEQLSVPQRSVGRIIGRGGETIRSICKASGAKITCDKESEGTLLLSR 62

Query: 664 SV 665
            +
Sbjct: 63  LI 64

Homologous Domains Detected by HHsearch

Original result of HHsearch against SCOP70(version1.75) database

ID	Length	Definition	Probability
Query	974
d1e3ha2	149	Polynucleotide phosphorylase/guanosine pentaphosph	100.0
d2nn6b1	145	Exosome complex exonuclease RRP41 {Human (Homo sap	99.96
d2je6b1	148	Exosome complex exonuclease 1, ECX1 {Sulfolobus so	99.96
d2ba0d1	144	Exosome complex exonuclease 1, ECX1 {Archaeoglobus	99.96
d2ba0g1	176	Exosome complex exonuclease 2,ECX2 {Archaeoglobus	99.94
d1e3ha3	137	Polynucleotide phosphorylase/guanosine pentaphosph	99.94
d1udsa1	149	Ribonuclease PH, domain 1 {Aquifex aeolicus [TaxId	99.93
d1r6la1	151	Ribonuclease PH, domain 1 {Pseudomonas aeruginosa	99.92
d2je6a1	191	Exosome complex exonuclease 2,ECX2 {Sulfolobus sol	99.92
d1oysa1	151	Ribonuclease PH, domain 1 {Bacillus subtilis [TaxI	99.91
d2nn6e1	187	Exosome complex exonuclease RRP42 {Human (Homo sap	99.9
d2nn6c1	181	Exosome complex exonuclease RRP43 {Human (Homo sap	99.89
d1e3ha6	96	Polynucleotide phosphorylase/guanosine pentaphosph	99.89
d1e3ha2	149	Polynucleotide phosphorylase/guanosine pentaphosph	99.88
d2nn6a1	184	Exosome complex exonuclease RRP45 {Human (Homo sap	99.88
d2nn6f1	147	Exosome complex exonuclease MTR3 {Human (Homo sapi	99.87
d2nn6d1	122	Exosome complex exonuclease RRP46 {Human (Homo sap	99.86
d1e3ha3	137	Polynucleotide phosphorylase/guanosine pentaphosph	99.86
d1e3ha5	111	Polynucleotide phosphorylase/guanosine pentaphosph	99.82
d1r6la2	88	Ribonuclease PH, domain 2 {Pseudomonas aeruginosa	99.78
d2nn6d1	122	Exosome complex exonuclease RRP46 {Human (Homo sap	99.78
d2je6b1	148	Exosome complex exonuclease 1, ECX1 {Sulfolobus so	99.76
d2ba0d1	144	Exosome complex exonuclease 1, ECX1 {Archaeoglobus	99.76
d2nn6b1	145	Exosome complex exonuclease RRP41 {Human (Homo sap	99.74
d1udsa1	149	Ribonuclease PH, domain 1 {Aquifex aeolicus [TaxId	99.74
d1r6la1	151	Ribonuclease PH, domain 1 {Pseudomonas aeruginosa	99.68
d1sroa_	76	S1 RNA-binding domain of polyribonucleotide phosph	99.68
d1udsa2	105	Ribonuclease PH, domain 2 {Aquifex aeolicus [TaxId	99.68
d1oysa2	86	Ribonuclease PH, domain 2 {Bacillus subtilis [TaxI	99.64
d2nn6f1	147	Exosome complex exonuclease MTR3 {Human (Homo sapi	99.64
d1oysa1	151	Ribonuclease PH, domain 1 {Bacillus subtilis [TaxI	99.63
d2je6b2	86	Exosome complex exonuclease 1, ECX1 {Sulfolobus so	99.57
d1kl9a2	86	Eukaryotic initiation factor 2alpha, eIF2alpha, N-	99.56
d2ahob2	84	Eukaryotic initiation factor 2alpha, eIF2alpha, N-	99.53
d3bzka4	94	Tex S1-domain {Pseudomonas aeruginosa [TaxId: 287]	99.52
d2je6a1	191	Exosome complex exonuclease 2,ECX2 {Sulfolobus sol	99.51
d2ba0a1	83	S1-domain of exosome complex RNA-binding protein 1	99.51
d2nn6b2	90	Exosome complex exonuclease RRP41 {Human (Homo sap	99.51
d2ba0g1	176	Exosome complex exonuclease 2,ECX2 {Archaeoglobus	99.5
d2nn6c1	181	Exosome complex exonuclease RRP43 {Human (Homo sap	99.47
d2ba0d2	99	Exosome complex exonuclease 1, ECX1 {Archaeoglobus	99.46
d1r6la2	88	Ribonuclease PH, domain 2 {Pseudomonas aeruginosa	99.46
d2nn6e1	187	Exosome complex exonuclease RRP42 {Human (Homo sap	99.46
d2je6i1	87	S1-domain of exosome complex RNA-binding protein 1	99.42
d1go3e1	106	C-terminal domain of RNA polymerase II subunit RBP	99.42
d1whua_	104	Polynucleotide phosphorylase/guanosine pentaphosph	99.41
d1sroa_	76	S1 RNA-binding domain of polyribonucleotide phosph	99.4
d2je6a2	84	Exosome complex exonuclease 2, ECX2 {Sulfolobus so	99.4
d2z0sa1	88	S1-domain of exosome complex RNA-binding protein 1	99.4
d2nn6d2	89	Exosome complex exonuclease RRP46 {Human (Homo sap	99.35
d1e3ha1	83	Polynucleotide phosphorylase/guanosine pentaphosph	99.32
d1oysa2	86	Ribonuclease PH, domain 2 {Bacillus subtilis [TaxI	99.31
d1wi5a_	119	S1-domain of RRP5 protein homolog (PDCD11, KIAA018	99.27
d2nn6a1	184	Exosome complex exonuclease RRP45 {Human (Homo sap	99.26
d1e3pa2	62	S1 RNA-binding domain of polyribonucleotide phosph	99.25
d2nn6h1	95	S1-domain of Ribosomal RNA-processing protein 4, R	99.23
d2je6b2	86	Exosome complex exonuclease 1, ECX1 {Sulfolobus so	99.22
d2je6a2	84	Exosome complex exonuclease 2, ECX2 {Sulfolobus so	99.2
d1udsa2	105	Ribonuclease PH, domain 2 {Aquifex aeolicus [TaxId	99.2
d2ba0a1	83	S1-domain of exosome complex RNA-binding protein 1	99.19
d1kl9a2	86	Eukaryotic initiation factor 2alpha, eIF2alpha, N-	99.17
d2nn6b2	90	Exosome complex exonuclease RRP41 {Human (Homo sap	99.15
d3bzka4	94	Tex S1-domain {Pseudomonas aeruginosa [TaxId: 287]	99.11
d2je6i1	87	S1-domain of exosome complex RNA-binding protein 1	99.09
d2ahob2	84	Eukaryotic initiation factor 2alpha, eIF2alpha, N-	99.06
d2nn6d2	89	Exosome complex exonuclease RRP46 {Human (Homo sap	99.05
d2ba0d2	99	Exosome complex exonuclease 1, ECX1 {Archaeoglobus	99.02
d2z0sa1	88	S1-domain of exosome complex RNA-binding protein 1	99.0
d1e3ha4	54	Polynucleotide phosphorylase/guanosine pentaphosph	99.0
d1wi5a_	119	S1-domain of RRP5 protein homolog (PDCD11, KIAA018	98.99
d2nn6c2	89	Exosome complex exonuclease RRP43 {Human (Homo sap	98.98
d2nn6e2	94	Exosome complex exonuclease RRP42 {Human (Homo sap	98.97
d2ba0g2	79	Exosome complex exonuclease 2, ECX2 {Archaeoglobus	98.97
d2nn6a2	118	Exosome complex exonuclease RRP45 {Human (Homo sap	98.95
d2ix0a3	87	Exoribonuclease 2, RNB {Escherichia coli [TaxId: 5	98.93
d1e3pa2	62	S1 RNA-binding domain of polyribonucleotide phosph	98.9
d2nn6f2	95	Exosome complex exonuclease MTR3 {Human (Homo sapi	98.87
d1go3e1	106	C-terminal domain of RNA polymerase II subunit RBP	98.87
d2ba0g2	79	Exosome complex exonuclease 2, ECX2 {Archaeoglobus	98.86
d2nn6g1	88	S1-domain of exosome component 3 (RRP40) {Human (H	98.86
d2z0sa2	87	Exosome complex RNA-binding protein 1, ECR1 {Aerop	98.81
d2nn6f2	95	Exosome complex exonuclease MTR3 {Human (Homo sapi	98.8
d2nn6e2	94	Exosome complex exonuclease RRP42 {Human (Homo sap	98.77
d1y14b1	91	C-terminal domain of RNA polymerase II subunit RBP	98.73
d2nn6c2	89	Exosome complex exonuclease RRP43 {Human (Homo sap	98.68
d2ja9a1	90	S1-domain of exosome component 3 (RRP40) {Saccharo	98.63
d2c35b1	94	C-terminal domain of RNA polymerase II subunit RBP	98.62
d2nn6h1	95	S1-domain of Ribosomal RNA-processing protein 4, R	98.62
d2nn6a2	118	Exosome complex exonuclease RRP45 {Human (Homo sap	98.6
d2cpqa1	78	Fragile X mental retardation syndrome related prot	98.58
d2ix0a3	87	Exoribonuclease 2, RNB {Escherichia coli [TaxId: 5	98.57
d1tuaa1	84	Hypothetical protein APE0754 {Aeropyrum pernix [Ta	98.56
d2nn6g1	88	S1-domain of exosome component 3 (RRP40) {Human (H	98.51
d1y14b1	91	C-terminal domain of RNA polymerase II subunit RBP	98.44
d2je6i3	69	Exosome complex RNA-binding protein 1, ECR1 {Sulfo	98.41
d2ba0a3	84	Exosome complex RNA-binding protein 1, ECR1 {Archa	98.35
d2c35b1	94	C-terminal domain of RNA polymerase II subunit RBP	98.19
d1hh2p1	72	S1 domain of NusA {Thermotoga maritima [TaxId: 233	98.11
d2ja9a1	90	S1-domain of exosome component 3 (RRP40) {Saccharo	98.07
d1hh2p1	72	S1 domain of NusA {Thermotoga maritima [TaxId: 233	98.01
d1tuaa2	104	Hypothetical protein APE0754 {Aeropyrum pernix [Ta	98.01
d1e3ha6	96	Polynucleotide phosphorylase/guanosine pentaphosph	97.91
d2nn6i1	125	Exosome component 1, EXOSC1 {Human (Homo sapiens)	97.9
d1e3ha5	111	Polynucleotide phosphorylase/guanosine pentaphosph	97.83
d2asba1	76	S1 domain of NusA {Mycobacterium tuberculosis [Tax	97.74
d2ctka1	91	Vigilin {Human (Homo sapiens) [TaxId: 9606]}	97.71
d1we8a_	104	Tudor and KH domain containing protein, Tdrkh {Mou	97.6
d1smxa_	87	S1-domain of Ribonuclease E {Escherichia coli [Tax	97.44
d2asba1	76	S1 domain of NusA {Mycobacterium tuberculosis [Tax	97.41
d1j4wa1	74	Far upstream binding element, FBP {Human (Homo sap	97.27
d1j4wa2	71	Far upstream binding element, FBP {Human (Homo sap	97.16
d1viga_	71	Vigilin {Human (Homo sapiens) [TaxId: 9606]}	97.14
d2axya1	71	Poly(RC)-binding protein 2 {Human (Homo sapiens) [	97.11
d1zzka1	75	HnRNP K, KH3 {Human (Homo sapiens) [TaxId: 9606]}	97.1
d2ctfa1	90	Vigilin {Human (Homo sapiens) [TaxId: 9606]}	97.08
d2ctma1	81	Vigilin {Human (Homo sapiens) [TaxId: 9606]}	97.04
d1dtja_	74	Neuro-oncological ventral antigen 2, nova-2, KH3 {	97.02
d1wvna1	70	Poly(RC)-binding protein 1 {Human (Homo sapiens) [	96.95
d1x4ma1	81	Far upstream binding element, FBP {Mouse (Mus musc	96.9
d2ctea1	81	Vigilin {Human (Homo sapiens) [TaxId: 9606]}	96.87
d2nn6i1	125	Exosome component 1, EXOSC1 {Human (Homo sapiens)	96.86
d1x4na1	79	Far upstream binding element, FBP {Mouse (Mus musc	96.78
d2ctla1	84	Vigilin {Human (Homo sapiens) [TaxId: 9606]}	96.71
d2ctja1	82	Vigilin {Human (Homo sapiens) [TaxId: 9606]}	96.62
d1k1ga_	122	RNA splicing factor 1 {Human (Homo sapiens) [TaxId	94.84
d1smxa_	87	S1-domain of Ribonuclease E {Escherichia coli [Tax	94.3
d1luza_	85	Viral structural mimic of eIF2alpha {Vaccinia viru	92.26
d1wfqa_	89	Cold shock domain protein E1 (UNR) {Human (Homo sa	88.26
d2bl5a1	134	Quaking protein A (Xqua) {African clawed frog (Xen	87.86
d1jjga_	102	Viral structural mimic of eIF2alpha {Myxoma virus,	86.72
d1c9oa_	66	Major cold shock protein {Bacillus caldolyticus [T	86.5
d1h95a_	79	Y-box protein 1 cold shock domain (YB1-CSD) {Human	83.69
d1mjca_	69	Major cold shock protein {Escherichia coli [TaxId:	82.8
d1k3ra1	71	Hypothetical protein MTH1 (MT0001), insert domain	81.57

>d1e3ha2 d.14.1.4 (A:3-151) Polynucleotide phosphorylase/guanosine pentaphosphate synthase (PNPase/GPSI), domains 1 and 4 {Streptomyces antibioticus [TaxId: 1890]}

class: Alpha and beta proteins (a+b)
fold: Ribosomal protein S5 domain 2-like
superfamily: Ribosomal protein S5 domain 2-like
family: Ribonuclease PH domain 1-like
domain: Polynucleotide phosphorylase/guanosine pentaphosphate synthase (PNPase/GPSI), domains 1 and 4
species: Streptomyces antibioticus [TaxId: 1890]

Probab=100.00  E-value=1.1e-38  Score=314.41  Aligned_cols=141  Identities=38%  Similarity=0.672  Sum_probs=131.7

Q ss_pred             eeeeeeEEECCeEEEEEeCccCcCCCcEEEEEeCCeEEEEEEEeCCC--CCCCCceeeEeeccccccccCCCCCcccccc
Q 002054           57 ETFKEEFEIGSRLITLETGKIARFANGAVVLGMDETKVLSTVTSSKG--DSVRDFLPLTVDYQEKQFAQGVIPNTYMRRE  134 (974)
Q Consensus        57 ~~~~~~~~~~~r~i~~etg~~a~~A~GSa~v~~G~T~Vl~tv~~~~~--~~~~~f~pL~v~y~e~~~a~g~ip~~~~~Re  134 (974)
                      +......++|+|+|++|||++|+||||||++++|+|+|||+|+.+.+  +...+|+|++++|+|++|++|++|++|.|||
T Consensus         7 ~~~~~~~~~~~R~i~ie~G~lakqA~GSalv~~G~T~vl~ta~~~~~~~~~~~~~~~~~v~~~~~~~~~~~~~~~~~rre   86 (149)
T d1e3ha2           7 EAVIDNGAFGTRTIRFETGRLARQAAGSAVAYLDDDTMVLSATTASKNPKDQLDFFPLTVDVEERMYAAGKIPGSFFRRE   86 (149)
T ss_dssp             EEEEECGGGCEEEEEEEESSSCTTSSEEEEEEETTTEEEEEEEEECSSCCTTCSSCCEEEEEEECGGGGTCCCCSTTSSC
T ss_pred             EEEEeCCcCCCcEEEEEeCcccccCCceEEEEECCcEEEEEeeecccccccccccCCceeEEEEeccccccccccccccc
Confidence            33333334688999999999999999999999999999999998766  4467899999999999999999999999999


Q ss_pred             CCCCchhhhHHHhhcCCccccccCCCCCceEEEEEEEeccCCCChhhHHHHHHHHHhhcCCCC
Q 002054          135 GAPKERELLVGRIIDRPIRPLFPAGFYHEVQVMASVLSSDGKQDPDIMAANATSAALMLSDIP  197 (974)
Q Consensus       135 g~p~~~eil~~RlidR~lrplfp~~~~~~~~i~~~vl~~dg~~~~~~~ai~aAs~AL~~s~iP  197 (974)
                      |+|+++|+|++|||||+|||+||++|++++||+|+|+++|++++++++||||||+||++||||
T Consensus        87 ~~~~~reil~~rlidR~Lrpl~p~~~~~~~qI~~~vl~~d~d~~~~~aai~aAs~AL~~agIP  149 (149)
T d1e3ha2          87 GRPSEDAILTCRLIDRPLRPSFKKGLRNEIQVVATIMALNPDHLYDVVAINAASASTQLAGLP  149 (149)
T ss_dssp             CSCCHHHHHHHHHHHHHHHHHBCTTBCSCEEEEEEEEECCTTSCCHHHHHHHHHHHHHHTTCS
T ss_pred             cccchHHHHHHHHHHHHHHhhccccCCCceEEEEEEEEeCCCCChHHHHHHHHHHHHHhcCCC
Confidence            999999999999999999999999999999999999999999999999999999999999999

>d2nn6b1 d.14.1.4 (B:6-150) Exosome complex exonuclease RRP41 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ribosomal protein S5 domain 2-like
superfamily: Ribosomal protein S5 domain 2-like
family: Ribonuclease PH domain 1-like
domain: Exosome complex exonuclease RRP41
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.96  E-value=1.2e-29  Score=248.92  Aligned_cols=143  Identities=27%  Similarity=0.400  Sum_probs=129.5

Q ss_pred             HhcCCcCCCCCCCCccCeEEEeCCCCCCCcceEEEeCCeEEEEEEEeCCCchhhhccccCCCCceeEEEEEecCCCCccc
Q 002054          365 IAEGVRVDGRQLDEVRPIYCESGNLPILHGSSLFSRGDTQVLCTVTLGAPAEAQRLESLVGPPTKRFMLHYSFPPFCINE  444 (974)
Q Consensus       365 l~~~~R~DGR~~~e~R~I~ie~g~l~~a~GSal~~~G~T~Vl~~Vtl~~p~~~~~~d~~~~~~~~~~~v~~~f~p~s~~e  444 (974)
                      .++|+|+|||.++|+|++.+++|+++++||||+|++|+|+|+|+|+  +|.+.........++++.+.++|+++||++++
T Consensus         2 ~e~g~R~DGR~~~e~R~i~i~~g~~~~a~GSa~v~~G~T~Vi~~V~--gp~~~~~~~~~~~~~~~~v~v~~~~~~~~~~~   79 (145)
T d2nn6b1           2 SDQGYRVDGRRAGELRKIQARMGVFAQADGSAYIEQGNTKALAVVY--GPHEIRGSRARALPDRALVNCQYSSATFSTGE   79 (145)
T ss_dssp             CBTTBCSSSSCTTSCCCEEEEESCSSSSSEEEEEEESSCEEEEEEE--EEEECCSSSCCCCCSSCCEEEEEEECTTTSSS
T ss_pred             CCCCccCCCCCCCCccCeEEEECCCCCCCceEEEEeCCceEEEEEE--eccccccchhhccccceeEEEEeeecCccccc
Confidence            5799999999999999999999999999999999999999999999  66654433334456788999999999999999


Q ss_pred             cccccCCCchhhhHHHHHHHHhhhcCCCCCCCCe-EEEEEEEEEcCCCChhhHHHHHHHHHHHHcCC
Q 002054          445 VGKRVGLNRREVGHGTLAEKALLAVLPPENDFPY-TVRVNSEVMASDGSTSMATVCGGSMALMDAGI  510 (974)
Q Consensus       445 ~~~~~~~~rre~~~~~l~eral~~vi~~~~~~p~-tI~V~v~VLesdGs~~~A~v~aa~lAL~dagv  510 (974)
                      ..+.+.+++++.+++.+++++|+++++. +.||+ +|+|+++||++|||+++||+||+++||+||||
T Consensus        80 ~~~~~~~~~~~~~l~~~l~~~l~~~i~~-~~~~~~~I~v~v~VL~~DG~l~~a~i~aa~lAL~daGI  145 (145)
T d2nn6b1          80 RKRRPHGDRKSCEMGLQLRQTFEAAILT-QLHPRSQIDIYVQVLQADGGTYAACVNAATLAVLDAGI  145 (145)
T ss_dssp             CCCTTTSTHHHHHHHHHHHHHHHHTTCG-GGCTTEEEEEEEEEEECCSCHHHHHHHHHHHHHHHTCC
T ss_pred             ccccCCCCchhhhHHHHHHHhhhcccch-HhhCceeeEEEEEEEeCCCCHHHHHHHHHHHHHHHcCC
Confidence            8777778889999999999999999998 67776 69999999999999999999999999999997

>d2je6b1 d.14.1.4 (B:8-155) Exosome complex exonuclease 1, ECX1 {Sulfolobus solfataricus [TaxId: 2287]}

class: Alpha and beta proteins (a+b)
fold: Ribosomal protein S5 domain 2-like
superfamily: Ribosomal protein S5 domain 2-like
family: Ribonuclease PH domain 1-like
domain: Exosome complex exonuclease 1, ECX1
species: Sulfolobus solfataricus [TaxId: 2287]

Probab=99.96  E-value=3.7e-29  Score=246.32  Aligned_cols=143  Identities=31%  Similarity=0.509  Sum_probs=128.4

Q ss_pred             HHHhcCCcCCCCCCCCccCeEEEeCCCCCCCcceEEEeCCeEEEEEEEeCCCchhhhccccCCCCceeEEEEEecCCCCc
Q 002054          363 RIIAEGVRVDGRQLDEVRPIYCESGNLPILHGSSLFSRGDTQVLCTVTLGAPAEAQRLESLVGPPTKRFMLHYSFPPFCI  442 (974)
Q Consensus       363 ~il~~~~R~DGR~~~e~R~I~ie~g~l~~a~GSal~~~G~T~Vl~~Vtl~~p~~~~~~d~~~~~~~~~~~v~~~f~p~s~  442 (974)
                      .|+++|+|+|||.++|+|++++++|+++++||||+|++|+|+|+|+|+  +|.+.... ....++++.++++|+|+||++
T Consensus         5 ~i~~~g~R~DGR~~~e~R~i~i~~g~l~~adGSa~v~~G~T~Vl~~V~--gp~e~~~~-~~~~~~~~~~~v~~~~~~~~~   81 (148)
T d2je6b1           5 LILDDGKRTDGRKPDELRSIKIELGVLKNADGSAIFEMGNTKAIAAVY--GPKEMHPR-HLSLPDRAVLRVRYHMTPFST   81 (148)
T ss_dssp             SBCTTSCBTTSCCTTCCCCEEEEESCCSSSSEEEEEEETTEEEEEEEE--EEEECSSG-GGSCSSSCEEEEEEEECTTSS
T ss_pred             EecCCCccCCCCCCCCccCeEEEECCCCCCCEEEEEEcCCccEEeecc--cCccccch-hhcCCcceEEEEEEEeccccc
Confidence            578999999999999999999999999999999999999999999999  67654321 233468899999999999999


Q ss_pred             cccccccCCCchhhhHHHHHHHHhhhcCCCCCCCCe-EEEEEEEEEcCCCChhhHHHHHHHHHHHHcCC
Q 002054          443 NEVGKRVGLNRREVGHGTLAEKALLAVLPPENDFPY-TVRVNSEVMASDGSTSMATVCGGSMALMDAGI  510 (974)
Q Consensus       443 ~e~~~~~~~~rre~~~~~l~eral~~vi~~~~~~p~-tI~V~v~VLesdGs~~~A~v~aa~lAL~dagv  510 (974)
                      ++. +.+.+.++++++.++++++|.++++. +.||+ +|+|+++||++|||+++||+||+++||+||||
T Consensus        82 ~~~-~~~~~~~~~~el~~~l~~~l~~~i~~-~~~p~~~i~v~v~VL~~DG~~~~a~i~aa~~AL~daGI  148 (148)
T d2je6b1          82 DER-KNPAPSRREIELSKVIREALESAVLV-ELFPRTAIDVFTEILQADAGSRLVSLMAASLALADAGI  148 (148)
T ss_dssp             SSC-CCSSCCHHHHHHHHHHHHHHHTTBCG-GGSTTEEEEEEEEEEECSSCHHHHHHHHHHHHHHHTTC
T ss_pred             ccc-ccccccchhHHHHHHHHHHhhccccH-HHcCCEEEEEEEEEEEcCCCHHHHHHHHHHHHHHHcCC
Confidence            874 46667889999999999999999998 68887 59999999999999999999999999999997

>d2ba0d1 d.14.1.4 (D:10-153) Exosome complex exonuclease 1, ECX1 {Archaeoglobus fulgidus [TaxId: 2234]}

class: Alpha and beta proteins (a+b)
fold: Ribosomal protein S5 domain 2-like
superfamily: Ribosomal protein S5 domain 2-like
family: Ribonuclease PH domain 1-like
domain: Exosome complex exonuclease 1, ECX1
species: Archaeoglobus fulgidus [TaxId: 2234]

Probab=99.96  E-value=6.4e-29  Score=243.41  Aligned_cols=142  Identities=31%  Similarity=0.557  Sum_probs=126.1

Q ss_pred             HHhcCCcCCCCCCCCccCeEEEeCCCCCCCcceEEEeCCeEEEEEEEeCCCchhhhccccCCCCceeEEEEEecCCCCcc
Q 002054          364 IIAEGVRVDGRQLDEVRPIYCESGNLPILHGSSLFSRGDTQVLCTVTLGAPAEAQRLESLVGPPTKRFMLHYSFPPFCIN  443 (974)
Q Consensus       364 il~~~~R~DGR~~~e~R~I~ie~g~l~~a~GSal~~~G~T~Vl~~Vtl~~p~~~~~~d~~~~~~~~~~~v~~~f~p~s~~  443 (974)
                      ++++|+|+|||.++|+||+.+++|+++++||||+|++|+|+|+|+|+  +|.+... .....++++.+.++++++||+++
T Consensus         2 ~~~~g~R~DGR~~~e~R~i~i~~g~l~~a~GSa~v~~G~T~Vl~~V~--gp~~~~~-~~~~~~~~~~~~~~~~~~~~s~~   78 (144)
T d2ba0d1           2 LIVDGLRLDGRKFDELRPIKIEASVLKRADGSCYLEMGKNKVIAAVF--GPREVHP-RHLQDPSKAIIRYRYNMAPFSVE   78 (144)
T ss_dssp             CBCSSCBTTSCCTTCCCCEEEEECCCSSSSEEEEEEETTEEEEEEEE--EEEECCS-GGGCCSSSCEEEEEEEECTTSSS
T ss_pred             cccCCcCCCCCCCCCccCeEEEECCCCCCCceEEEEEcccceEEEEe--ccchhhh-hhcccccceEEEEEEecCCcccc
Confidence            67899999999999999999999999999999999999999999999  6665321 12345678899999999999998


Q ss_pred             ccccccCCCchhhhHHHHHHHHhhhcCCCCCCCC-eEEEEEEEEEcCCCChhhHHHHHHHHHHHHcCC
Q 002054          444 EVGKRVGLNRREVGHGTLAEKALLAVLPPENDFP-YTVRVNSEVMASDGSTSMATVCGGSMALMDAGI  510 (974)
Q Consensus       444 e~~~~~~~~rre~~~~~l~eral~~vi~~~~~~p-~tI~V~v~VLesdGs~~~A~v~aa~lAL~dagv  510 (974)
                      +..+ +.+.+++.+++++++++++++++. +.|| |+|+|+++||++|||+++||+||+++||+||||
T Consensus        79 ~~~~-~~~~~~~~~l~~~l~~~l~~~i~~-~~~~~~~i~v~v~VL~~DG~~~~a~i~aa~lAL~daGI  144 (144)
T d2ba0d1          79 ERKR-PGPDRRSIEISKVSKEAFEAVIMK-ELFPRSAIDIFVEVLQADAGSRTACLNAASVALVDAGV  144 (144)
T ss_dssp             SCCC-SSCCHHHHHHHHHHHHHHHTTBCG-GGCTTEEEEEEEEEEECCTTHHHHHHHHHHHHHHHHTC
T ss_pred             cccc-cCCCchhhhhhhhhhhhhccccch-hhcCCeEEEEEEEEEccCCCHHHHHHHHHHHHHHHcCC
Confidence            7643 557889999999999999999998 4555 589999999999999999999999999999997

>d2ba0g1 d.14.1.4 (G:3-178) Exosome complex exonuclease 2,ECX2 {Archaeoglobus fulgidus [TaxId: 2234]}

class: Alpha and beta proteins (a+b)
fold: Ribosomal protein S5 domain 2-like
superfamily: Ribosomal protein S5 domain 2-like
family: Ribonuclease PH domain 1-like
domain: Exosome complex exonuclease 2,ECX2
species: Archaeoglobus fulgidus [TaxId: 2234]

Probab=99.94  E-value=1.6e-26  Score=233.93  Aligned_cols=159  Identities=19%  Similarity=0.296  Sum_probs=133.6

Q ss_pred             HHHHHHHHHHHHHHHhcCCcCCCCCCCCccCeEEEeCCCCCCCcceEEEeCCeEEEEEEEeC--CCchhhhccccCCCCc
Q 002054          351 AVDTVRKRVIRKRIIAEGVRVDGRQLDEVRPIYCESGNLPILHGSSLFSRGDTQVLCTVTLG--APAEAQRLESLVGPPT  428 (974)
Q Consensus       351 ~~~~~~~~~~r~~il~~~~R~DGR~~~e~R~I~ie~g~l~~a~GSal~~~G~T~Vl~~Vtl~--~p~~~~~~d~~~~~~~  428 (974)
                      +++..++++++ ..+++|+|+|||.++|+|++++++|.++++||||+|++|+|+|+|+|+.+  .|..       ..+++
T Consensus         3 ~ls~~e~~~i~-~~l~~~~R~DGR~~~e~R~i~i~~g~l~~a~GSa~v~~G~T~V~~~V~~~~~~p~~-------~~~~~   74 (176)
T d2ba0g1           3 ILVDIKRDYVL-SKLRDNERIDGRGFDEFRKVEIIPNVIEKAEGSALVKLGDTQVVVGVKMQPGEPYP-------DTPDR   74 (176)
T ss_dssp             SSHHHHHHHHH-HHHTTTCCTTCCCTTCCCCEEEEECCCTTSSEEEEEEETTEEEEEEEEEEEECCCT-------TCTTC
T ss_pred             HHHHHHHHHHH-HHHHhCCCCCCCCCCCccCeEEEeCccCCCCeEEEEEeCCcEEEEEEecccccccc-------ccCCC
Confidence            45677888887 56789999999999999999999999999999999999999999999943  3333       23678


Q ss_pred             eeEEEEEecCCCCccccccccCCCchhhhHHHHHHHHhhhc--CCC------CCCCCeEEEEEEEEEcCCCChhhHHHHH
Q 002054          429 KRFMLHYSFPPFCINEVGKRVGLNRREVGHGTLAEKALLAV--LPP------ENDFPYTVRVNSEVMASDGSTSMATVCG  500 (974)
Q Consensus       429 ~~~~v~~~f~p~s~~e~~~~~~~~rre~~~~~l~eral~~v--i~~------~~~~p~tI~V~v~VLesdGs~~~A~v~a  500 (974)
                      +.+.++|+++|++..... .+.+++++..+.+++++++.+.  ++.      ...+.|+|+|+++||++|||+++||+||
T Consensus        75 g~~~~~v~~~~~~~~~~~-~~~~~~~~~~~~~~l~~~~~~~~~i~~e~L~i~~~~~~~~i~i~v~VL~~DG~l~dA~~~A  153 (176)
T d2ba0g1          75 GVIIVNAELVPLASPTFE-PGPPDENSIELARVVDRGIRESEAVDLSKLVIEEGEKVWIVFVDIHALDDDGNLLDASALA  153 (176)
T ss_dssp             CEEEEEEECCTTTCTTSC-SSSCCHHHHHHHHHHHHHHHHTTCBCGGGGEEETTTEEEEEEEEEEEEECSSCHHHHHHHH
T ss_pred             ceeeeeeEeccccCcccc-CCCCCchhHHHHHHHHHhhccccccchhhccCCCCCceEEEEEEEEEEeCCCCHHHHHHHH
Confidence            899999999999998764 3567788888999999987442  211      1345689999999999999999999999


Q ss_pred             HHHHHHHcCCCccccccc
Q 002054          501 GSMALMDAGIPLQEHVAG  518 (974)
Q Consensus       501 a~lAL~dagvPi~~~vag  518 (974)
                      +++||+|+|||+.....|
T Consensus       154 ~~~AL~da~iP~~~~~~g  171 (176)
T d2ba0g1         154 AIAALMNTKVPAERFDLG  171 (176)
T ss_dssp             HHHHHTTCEECTGGGTSS
T ss_pred             HHHHHHHcCCCcEEecCC
Confidence            999999999999886543

>d1e3ha3 d.14.1.4 (A:346-482) Polynucleotide phosphorylase/guanosine pentaphosphate synthase (PNPase/GPSI), domains 1 and 4 {Streptomyces antibioticus [TaxId: 1890]}

class: Alpha and beta proteins (a+b)
fold: Ribosomal protein S5 domain 2-like
superfamily: Ribosomal protein S5 domain 2-like
family: Ribonuclease PH domain 1-like
domain: Polynucleotide phosphorylase/guanosine pentaphosphate synthase (PNPase/GPSI), domains 1 and 4
species: Streptomyces antibioticus [TaxId: 1890]

Probab=99.94  E-value=2.5e-26  Score=222.90  Aligned_cols=137  Identities=44%  Similarity=0.834  Sum_probs=119.1

Q ss_pred             CCccCeEEEeCCCCCCCcceEEEeCCeEEEEEEEeCCCchhhhccccCCCCceeEEEEEecCCCCccccccccCCCchhh
Q 002054          377 DEVRPIYCESGNLPILHGSSLFSRGDTQVLCTVTLGAPAEAQRLESLVGPPTKRFMLHYSFPPFCINEVGKRVGLNRREV  456 (974)
Q Consensus       377 ~e~R~I~ie~g~l~~a~GSal~~~G~T~Vl~~Vtl~~p~~~~~~d~~~~~~~~~~~v~~~f~p~s~~e~~~~~~~~rre~  456 (974)
                      +|+|+|+|++|+++++||||+|++|+|+|+|+|+.+.+.+....+.........+.++|.++||+++..++.+.+++++.
T Consensus         1 tE~R~i~~~~gv~~~adGSa~~~~G~T~Vl~~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~   80 (137)
T d1e3ha3           1 TDIRTLAAEVEAIPRVHGSALFERGETQILGVTTLNMLRMEQQLDTLSPVTRKRYMHNYNFPPYSVGETGRVGSPKRREI   80 (137)
T ss_dssp             TCCCCEEEEECCSSSSSEEEEEEETTEEEEEEEEEEEGGGSEECCSSSSCCEESEEEEEECCGGGGTCCCCCSSCCHHHH
T ss_pred             CCcceEEEEeCCCCCCCeeEEEEECCeEEEEEEccCccCccccccccCcceeeeeeeecccccccccccccccccccccc
Confidence            58999999999999999999999999999999994322221111222334567899999999999999999999999999


Q ss_pred             hHHHHHHHHhhhcCCCCCCCCeEEEEEEEEEcCCCChhhHHHHHHHHHHHHcCCCcc
Q 002054          457 GHGTLAEKALLAVLPPENDFPYTVRVNSEVMASDGSTSMATVCGGSMALMDAGIPLQ  513 (974)
Q Consensus       457 ~~~~l~eral~~vi~~~~~~p~tI~V~v~VLesdGs~~~A~v~aa~lAL~dagvPi~  513 (974)
                      +++++++++|+++++.+..++|+|+|+++||++|||+++||+||+++||+||||||+
T Consensus        81 ~~~~~i~~~l~~~i~~~~~~~~~I~v~v~vl~~DG~~~~aainAa~lAL~dAGIpmk  137 (137)
T d1e3ha3          81 GHGALAERAIVPVLPTREEFPYAIRQVSEALGSNGSTSMGSVCASTMSLLNAGVPLK  137 (137)
T ss_dssp             HHHHHHHHHHGGGCCCTTTSCEEEEEEEEEEECSSCHHHHHHHHHHHHHHHHTCCCS
T ss_pred             ccchHHHHHHHhccchhhcCcEEEEEEEEEecCCCCHHHHHHHHHHHHHHHcCCccC
Confidence            999999999999999866666789999999999999999999999999999999996

>d1udsa1 d.14.1.4 (A:2-150) Ribonuclease PH, domain 1 {Aquifex aeolicus [TaxId: 63363]}

class: Alpha and beta proteins (a+b)
fold: Ribosomal protein S5 domain 2-like
superfamily: Ribosomal protein S5 domain 2-like
family: Ribonuclease PH domain 1-like
domain: Ribonuclease PH, domain 1
species: Aquifex aeolicus [TaxId: 63363]

Probab=99.93  E-value=2.4e-26  Score=226.26  Aligned_cols=141  Identities=27%  Similarity=0.367  Sum_probs=118.8

Q ss_pred             cCCCCCCCCccCeEEEeCCCCCCCcceEEEeCCeEEEEEEEeCCCchhhhccccCCCCceeEEEEEecCCCCccccccc-
Q 002054          370 RVDGRQLDEVRPIYCESGNLPILHGSSLFSRGDTQVLCTVTLGAPAEAQRLESLVGPPTKRFMLHYSFPPFCINEVGKR-  448 (974)
Q Consensus       370 R~DGR~~~e~R~I~ie~g~l~~a~GSal~~~G~T~Vl~~Vtl~~p~~~~~~d~~~~~~~~~~~v~~~f~p~s~~e~~~~-  448 (974)
                      |+|||.++|+|++.+++|+++++||||++++|+|+|+|+|+.  |.+..  .....++++.++++|+++|++.+..... 
T Consensus         1 R~DGR~~~e~R~i~i~~g~l~~a~GSa~v~~G~T~V~~~V~~--~~~~~--~~~~~~~~g~~~~~~~~~~~~~~~~~~~~   76 (149)
T d1udsa1           1 RSDGRKEDQLRPVSIQRDFLEYPEGSCLISFGKTKVICTASV--IENVP--NWLKGKGQGWITAEYSMLPRATQQRTIRE   76 (149)
T ss_dssp             CTTSCCTTCCCCEEEEECCSSSSSEEEEEEETTEEEEEEEEE--ESCCC--GGGTTSSCCEEEEEEEECSEETTEECCCS
T ss_pred             CCCCCCCCCccCeEEEeCCCCCCCEEEEEEECCCEEEEEEEe--ecccc--ccccCCCceeEEeeecchhhccccccccc
Confidence            899999999999999999999999999999999999999994  33211  1223567899999999999988654322 


Q ss_pred             ---cCCCchhhhHHHHHHHHhhhcCCCCCCCCeEEEEEEEEEcCCCChhhHHHHHHHHHHHHcCCCccc
Q 002054          449 ---VGLNRREVGHGTLAEKALLAVLPPENDFPYTVRVNSEVMASDGSTSMATVCGGSMALMDAGIPLQE  514 (974)
Q Consensus       449 ---~~~~rre~~~~~l~eral~~vi~~~~~~p~tI~V~v~VLesdGs~~~A~v~aa~lAL~dagvPi~~  514 (974)
                         +.+..++..++.++++++++++..+..+.|+|+|+++||++|||+++||++|+++||+||||||+.
T Consensus        77 ~~~~~~~~~~~~~~~~l~~~l~~~i~l~~~~~~~i~v~v~VL~~DG~l~da~~~A~~~AL~dagipm~~  145 (149)
T d1udsa1          77 SVQGRIGGRTHEIQRMIGRAMRTAVELTKIGERTIWVDCDVIQADGGTATAAITGAFVAVADAIIKLHK  145 (149)
T ss_dssp             SSSCCCCHHHHHHHHHHHHHHHHHBCGGGSCSCEEEEEEEEEECSSCHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             ccccccccchhHHHHHHHhhhhheehhhhcCCceEEEEEEEEccCCCHHHHHHHHHHHHHHHhChHHHH
Confidence               334556677888999999999988444446899999999999999999999999999999999974

>d1r6la1 d.14.1.4 (A:1-151) Ribonuclease PH, domain 1 {Pseudomonas aeruginosa [TaxId: 287]}

class: Alpha and beta proteins (a+b)
fold: Ribosomal protein S5 domain 2-like
superfamily: Ribosomal protein S5 domain 2-like
family: Ribonuclease PH domain 1-like
domain: Ribonuclease PH, domain 1
species: Pseudomonas aeruginosa [TaxId: 287]

Probab=99.92  E-value=1.4e-25  Score=221.15  Aligned_cols=141  Identities=29%  Similarity=0.399  Sum_probs=117.4

Q ss_pred             CcCCCCCCCCccCeEEEeCCCCCCCcceEEEeCCeEEEEEEEeCCCchhhhccccCCCCceeEEEEEecCCCCccccccc
Q 002054          369 VRVDGRQLDEVRPIYCESGNLPILHGSSLFSRGDTQVLCTVTLGAPAEAQRLESLVGPPTKRFMLHYSFPPFCINEVGKR  448 (974)
Q Consensus       369 ~R~DGR~~~e~R~I~ie~g~l~~a~GSal~~~G~T~Vl~~Vtl~~p~~~~~~d~~~~~~~~~~~v~~~f~p~s~~e~~~~  448 (974)
                      .|+|||.++|+|++.+++|+++++||||+|++|+|+|+|+|+  +|.+..  .....++++.+.++|+++|++.......
T Consensus         2 ~R~DGR~~~e~R~i~i~~g~l~~a~GSa~v~~G~T~Vl~~V~--~~~~~~--~~~~~~~~g~~~~~~~~~~~~~~~~~~~   77 (151)
T d1r6la1           2 NRPSGRAADQLRPIRITRHYTKHAEGSVLVEFGDTKVICTVS--AESGVP--RFLKGQGQGWLTAEYGMLPRSTGERNQR   77 (151)
T ss_dssp             CCTTCCCTTCCCCEEEESSCSSSSSEEEEEEETTEEEEEEEE--EEESCS--SCCC---CCEEEEEEEECTTSSSSCCCC
T ss_pred             CCCCCCCCCCccCeEEEeCCCCCCCEEEEEEeCCCEEEEEEE--eccccc--ccccCCCceeEEEEEEecCccccccccc
Confidence            499999999999999999999999999999999999999999  443321  1123467899999999999998765322


Q ss_pred             ----cCCCchhhhHHHHHHHHhhhcCCCCCCCCe-EEEEEEEEEcCCCChhhHHHHHHHHHHHHcCCCccc
Q 002054          449 ----VGLNRREVGHGTLAEKALLAVLPPENDFPY-TVRVNSEVMASDGSTSMATVCGGSMALMDAGIPLQE  514 (974)
Q Consensus       449 ----~~~~rre~~~~~l~eral~~vi~~~~~~p~-tI~V~v~VLesdGs~~~A~v~aa~lAL~dagvPi~~  514 (974)
                          +....++..+..++++++.+.++. +.||+ +|+|+++||++|||+++|+++|+++||+||||||+.
T Consensus        78 ~~~~~~~~~~~~~~~~~l~~~~~~~~~l-~~~~~~~i~v~v~VL~~DG~~~da~~~Aa~~AL~dagip~~~  147 (151)
T d1r6la1          78 EASRGKQGGRTLEIQRLIGRSLRAALDL-SKLGENTLYIDCDVIQADGGTRTASITGATVALIDALAVLKK  147 (151)
T ss_dssp             HHHHTSCCHHHHHHHHHHHHHHHHTBCG-GGTCSEEEEEEEEEEECSSCHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             cCCCccccccchhHHHHHHhhhhhccch-hhhCceEEEEEEEEEeCCCCHHHHHHHHHHHHHHHhcHHHHH
Confidence                234456667888999999999988 56665 799999999999999999999999999999999875

>d2je6a1 d.14.1.4 (A:1-191) Exosome complex exonuclease 2,ECX2 {Sulfolobus solfataricus [TaxId: 2287]}

class: Alpha and beta proteins (a+b)
fold: Ribosomal protein S5 domain 2-like
superfamily: Ribosomal protein S5 domain 2-like
family: Ribonuclease PH domain 1-like
domain: Exosome complex exonuclease 2,ECX2
species: Sulfolobus solfataricus [TaxId: 2287]

Probab=99.92  E-value=3.1e-25  Score=227.24  Aligned_cols=160  Identities=21%  Similarity=0.324  Sum_probs=128.9

Q ss_pred             HHHHHHHHHHHHhcCCcCCCCCCCCccCeEEEeCCCCCCCcceEEEeCCeEEEEEEEeCCCchhhhccccCCCCceeEEE
Q 002054          354 TVRKRVIRKRIIAEGVRVDGRQLDEVRPIYCESGNLPILHGSSLFSRGDTQVLCTVTLGAPAEAQRLESLVGPPTKRFML  433 (974)
Q Consensus       354 ~~~~~~~r~~il~~~~R~DGR~~~e~R~I~ie~g~l~~a~GSal~~~G~T~Vl~~Vtl~~p~~~~~~d~~~~~~~~~~~v  433 (974)
                      ..++++++ .++++|+|+|||.++|+|++++++|+++++||||+|++|+|+|+|+|+..  ....   ....++.+.+.+
T Consensus        13 ~~~~~~~~-~~l~~giR~DGR~~~e~R~i~i~~g~l~~a~GSa~v~~G~T~V~a~V~~~--~~~~---~~~~~~~~~~~~   86 (191)
T d2je6a1          13 IIKKESIV-SLFEKGIRQDGRKLTDYRPLSITLDYAKKADGSALVKLGTTMVLAGTKLE--IDKP---YEDTPNQGNLIV   86 (191)
T ss_dssp             HHHHHHHT-TTGGGTBCTTSCBTTCCCCEEEEETCSTTSSEEEEEEETTEEEEEEEEEE--EECC---CTTCTTCCEEEE
T ss_pred             HHHHHHHH-HHHhcCCCCCCcCCCCccCeEEEECCccCcCceEEEEcCCceEEEEEEec--ccCc---hhccCccCcccc
Confidence            34555555 67789999999999999999999999999999999999999999999943  2211   112357789999


Q ss_pred             EEecCCCCccccccccCCCchhhhHHHHHHHHhhh----------cCCCCCCCCeEEEEEEEEEcCCCChhhHHHHHHHH
Q 002054          434 HYSFPPFCINEVGKRVGLNRREVGHGTLAEKALLA----------VLPPENDFPYTVRVNSEVMASDGSTSMATVCGGSM  503 (974)
Q Consensus       434 ~~~f~p~s~~e~~~~~~~~rre~~~~~l~eral~~----------vi~~~~~~p~tI~V~v~VLesdGs~~~A~v~aa~l  503 (974)
                      ++++++++.... +.+.+.+++..+.+++++++..          +++  .++.|+|+|+++||++|||+++|+++|+++
T Consensus        87 ~~~~~~~~~~~~-~~~~~~~~~~~l~~~l~~~~~~~~~id~~~l~i~~--~~~~w~I~v~v~VL~~DG~l~dA~~~A~~~  163 (191)
T d2je6a1          87 NVELLPLAYETF-EPGPPDENAIELARVVDRSLRDSKALDLTKLVIEP--GKSVWTVWLDVYVLDYGGNVLDACTLASVA  163 (191)
T ss_dssp             EEEECTTSCTTC-CCSSCCHHHHHHHHHHHHHHHHTTCSCGGGGEEET--TTEEEEEEEEEEEEECCSCHHHHHHHHHHH
T ss_pred             cccccccccccc-ccccCCcchhHHHHHHHHhhcchhhcccccccccC--ccccEEEEEEEEEEcCCCCHHHHHHHHHHH
Confidence            999999987653 4556677888889999988743          233  468899999999999999999999999999


Q ss_pred             HHHHcCCCc-cccccceeee
Q 002054          504 ALMDAGIPL-QEHVAGVSVG  522 (974)
Q Consensus       504 AL~dagvPi-~~~vagvs~g  522 (974)
                      ||+|+|||+ +-...|+.++
T Consensus       164 AL~da~iP~v~~~~~~~~v~  183 (191)
T d2je6a1         164 ALYNTKVYKVEQHSNGISVN  183 (191)
T ss_dssp             HHHTCEEEEEECC---CEEE
T ss_pred             HHHHcCCCeEEeecCceeec
Confidence            999999995 5566666665

>d1oysa1 d.14.1.4 (A:1-151) Ribonuclease PH, domain 1 {Bacillus subtilis [TaxId: 1423]}

class: Alpha and beta proteins (a+b)
fold: Ribosomal protein S5 domain 2-like
superfamily: Ribosomal protein S5 domain 2-like
family: Ribonuclease PH domain 1-like
domain: Ribonuclease PH, domain 1
species: Bacillus subtilis [TaxId: 1423]

Probab=99.91  E-value=2.2e-25  Score=219.67  Aligned_cols=139  Identities=28%  Similarity=0.400  Sum_probs=103.4

Q ss_pred             CcCCCCCCCCccCeEEEeCCCCCCCcceEEEeCCeEEEEEEEeCCCchhhhccccCCCCceeEEEEEecCCCCcccc---
Q 002054          369 VRVDGRQLDEVRPIYCESGNLPILHGSSLFSRGDTQVLCTVTLGAPAEAQRLESLVGPPTKRFMLHYSFPPFCINEV---  445 (974)
Q Consensus       369 ~R~DGR~~~e~R~I~ie~g~l~~a~GSal~~~G~T~Vl~~Vtl~~p~~~~~~d~~~~~~~~~~~v~~~f~p~s~~e~---  445 (974)
                      +|+|||.++|+|+++|++|+++++||||+|++|+|+|+|+|+...+.+.    ....++++.++++|+++|++....   
T Consensus         1 lR~DGR~~~e~R~i~i~~g~l~~a~GSa~v~~G~T~Vl~~V~~~~~~~~----~~~~~~~g~~~~~~~~~~~~~~~~~~~   76 (151)
T d1oysa1           1 MRHDGRQHDELRPITFDLDFISHPEGSVLITAGNTKVICNASVEDRVPP----FLRGGGKGWITAEYSMLPQATNQQTIQ   76 (151)
T ss_dssp             CCTTSCCTTCCCCEEEECC-----CCCEEEEETTEEEEEEEEEESCCCG----GGTTSCCCEEEEEEEC-----------
T ss_pred             CCCCCCCCCCccCeEEEeCCCCCCCEEEEEEEcCCEEEEEEEecccccc----cccccccceeeeeeeeccccccccccc
Confidence            6999999999999999999999999999999999999999985422221    123467889999999999988643   


Q ss_pred             -ccccCCCchhhhHHHHHHHHhhhcCCCCCCCC-eEEEEEEEEEcCCCChhhHHHHHHHHHHHHcCCCc
Q 002054          446 -GKRVGLNRREVGHGTLAEKALLAVLPPENDFP-YTVRVNSEVMASDGSTSMATVCGGSMALMDAGIPL  512 (974)
Q Consensus       446 -~~~~~~~rre~~~~~l~eral~~vi~~~~~~p-~tI~V~v~VLesdGs~~~A~v~aa~lAL~dagvPi  512 (974)
                       ...+.+...+..++.+++++|.++++. +.|| |+|+|+++||++|||+++||+||+++||+||.+++
T Consensus        77 ~~~~~~~~~~~~~~~~~l~~~l~~~i~l-~~~~~~~i~v~v~VL~~DG~l~~a~i~Aa~~AL~dA~~~~  144 (151)
T d1oysa1          77 ESSKGKISGRTMEIQRLIGRALRAVVDL-EKLGERTIWIDCDVIQADGGTRTASITGAFLAMAIAIGKL  144 (151)
T ss_dssp             --------CHHHHHHHHHHHHHHHTBCH-HHHCSCEEEEEEEEEECSSCHHHHHHHHHHHHHHHHHHHH
T ss_pred             cccCCcccchhhHHhHHHHHHhhhhhhh-hhhccceEEEEEEEEcCCCCHHHHHHHHHHHHHHHHHHHH
Confidence             223456778889999999999999987 4555 58999999999999999999999999999995543

>d2nn6e1 d.14.1.4 (E:5-191) Exosome complex exonuclease RRP42 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ribosomal protein S5 domain 2-like
superfamily: Ribosomal protein S5 domain 2-like
family: Ribonuclease PH domain 1-like
domain: Exosome complex exonuclease RRP42
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.90  E-value=4.5e-24  Score=217.83  Aligned_cols=151  Identities=18%  Similarity=0.174  Sum_probs=124.8

Q ss_pred             HHHHHHHHHHHhcCCcCCCCCCCCccCeEEEeCCCCCCCcceEEEeCCeEEEEEEEeCCCchhhhccccCCCCceeEEEE
Q 002054          355 VRKRVIRKRIIAEGVRVDGRQLDEVRPIYCESGNLPILHGSSLFSRGDTQVLCTVTLGAPAEAQRLESLVGPPTKRFMLH  434 (974)
Q Consensus       355 ~~~~~~r~~il~~~~R~DGR~~~e~R~I~ie~g~l~~a~GSal~~~G~T~Vl~~Vtl~~p~~~~~~d~~~~~~~~~~~v~  434 (974)
                      .++.+++ ..|++|+|+|||.++|+|++++++|.++++||||+|++|+|+|+|+|+..  ....   ....++++.+.++
T Consensus         5 ~E~~~i~-~~l~~~iR~DGR~~~e~R~i~i~~g~l~~a~GSa~v~~G~T~V~~~V~~~--~~~~---~~~~~~~g~~~~~   78 (187)
T d2nn6e1           5 AEKVYIV-HGVQEDLRVDGRGCEDYRCVEVETDVVSNTSGSARVKLGHTDILVGVKAE--MGTP---KLEKPNEGYLEFF   78 (187)
T ss_dssp             HHHHHHH-HHHHTTCCSSSCCSSCCCCCEEEECCCTTSSSEEEEEETTEEEEEECCCC--CSCC---CSSSCSSCCEEEE
T ss_pred             HHHHHHH-HHHhhCCCCCCcCCCCccCeEEEeCccCCCCceEEEEeCCceEEEEEEec--cccc---cccccccceeeee
Confidence            4566666 45689999999999999999999999999999999999999999999933  2211   0123567899999


Q ss_pred             EecCCCCccccccccCCCchhhhHHHHHHHHhhhcCC--------CCCCCCeEEEEEEEEEcCCCChhhHHHHHHHHHHH
Q 002054          435 YSFPPFCINEVGKRVGLNRREVGHGTLAEKALLAVLP--------PENDFPYTVRVNSEVMASDGSTSMATVCGGSMALM  506 (974)
Q Consensus       435 ~~f~p~s~~e~~~~~~~~rre~~~~~l~eral~~vi~--------~~~~~p~tI~V~v~VLesdGs~~~A~v~aa~lAL~  506 (974)
                      |+++|++...+. .+.++.++..++++++++|.....        ....+.|+|+|+++||++|||+++|+++|+++||+
T Consensus        79 v~~~~~~~~~~~-~~~~~~~~~~ls~~l~~~l~~~~~~d~~~L~i~~~~~~w~i~v~v~vL~~DG~~~da~~~A~~~AL~  157 (187)
T d2nn6e1          79 VDCSASATPEFE-GRGGDDLGTEIANTLYRIFNNKSSVDLKTLCISPREHCWVLYVDVLLLECGGNLFDAISIAVKAALF  157 (187)
T ss_dssp             CCCCTTTCSSCC-TTSTHHHHHHHHHHHHHHHHHSCCSCSSSSCSSTTTCCCCEEEEEEECCCCSSHHHHHHHHHHHTTT
T ss_pred             eeeccccccCcC-CCCcchHHHHHHHHHHHHhccccccchhhheecCCCccEEEEEEEEEeCCCCCHHHHHHHHHHHHHH
Confidence            999999987753 345667778889999999965321        11467899999999999999999999999999999


Q ss_pred             HcCCCc
Q 002054          507 DAGIPL  512 (974)
Q Consensus       507 dagvPi  512 (974)
                      |+++|.
T Consensus       158 d~~iP~  163 (187)
T d2nn6e1         158 NTRIPR  163 (187)
T ss_dssp             TCCCCE
T ss_pred             hcCCCE
Confidence            999995

>d2nn6c1 d.14.1.4 (C:7-187) Exosome complex exonuclease RRP43 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ribosomal protein S5 domain 2-like
superfamily: Ribosomal protein S5 domain 2-like
family: Ribonuclease PH domain 1-like
domain: Exosome complex exonuclease RRP43
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.89  E-value=1.6e-23  Score=212.18  Aligned_cols=152  Identities=20%  Similarity=0.274  Sum_probs=123.2

Q ss_pred             HHHHHHHHHHhcCCcCCCCCCCCccCeEEEeCCCCCCCcceEEEeCCeEEEEEEEeCCCchhhhccccCCCCceeEEEEE
Q 002054          356 RKRVIRKRIIAEGVRVDGRQLDEVRPIYCESGNLPILHGSSLFSRGDTQVLCTVTLGAPAEAQRLESLVGPPTKRFMLHY  435 (974)
Q Consensus       356 ~~~~~r~~il~~~~R~DGR~~~e~R~I~ie~g~l~~a~GSal~~~G~T~Vl~~Vtl~~p~~~~~~d~~~~~~~~~~~v~~  435 (974)
                      .|..|.+.+|++|+|+|||.++|+|++++++|.++++||||++++|+|+|+|+|+..  ...+   ....+..+.+.+++
T Consensus         3 ~p~~y~~~~l~~giR~DGR~~~e~R~~~i~~g~l~~a~GSa~v~~G~T~v~~~v~~~--~~~~---~~~~~~~~~~~~~~   77 (181)
T d2nn6c1           3 EPLEYYRRFLKENCRPDGRELGEFRTTTVNIGSISTADGSALVKLGNTTVICGVKAE--FAAP---STDAPDKGYVVPNV   77 (181)
T ss_dssp             STHHHHHHHHHTSCCTTSCCSCCCCSCCEEETCCSSSSEEEEEEETTEEEEEEEEEE--ECCC---CSSSTTCCCCEEEE
T ss_pred             CHHHHHHHHHhcCCCCCCcCCCCccCeEEEeCCcCCCCeEEEEEeCCcEEEEEEecc--cccc---ccccCCCceeeeee
Confidence            456678889999999999999999999999999999999999999999999999942  2111   11234578899999


Q ss_pred             ecCCCCccccccccCCCchhhhHHHHHHHHhhh--------cCCCCCCCCeEEEEEEEEEcCCCChhhHHHHHHHHHHHH
Q 002054          436 SFPPFCINEVGKRVGLNRREVGHGTLAEKALLA--------VLPPENDFPYTVRVNSEVMASDGSTSMATVCGGSMALMD  507 (974)
Q Consensus       436 ~f~p~s~~e~~~~~~~~rre~~~~~l~eral~~--------vi~~~~~~p~tI~V~v~VLesdGs~~~A~v~aa~lAL~d  507 (974)
                      .+++++..... .+.+..++....+++++.+..        ++.....+.|+|+|+++||++|||+++||++|+++||+|
T Consensus        78 ~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~i~~~~~~~~i~i~v~vl~~DG~l~da~~~A~~~AL~d  156 (181)
T d2nn6c1          78 DLPPLCSSRFR-SGPPGEEAQVASQFIADVIENSQIIQKEDLCISPGKLVWVLYCDLICLDYDGNILDACTFALLAALKN  156 (181)
T ss_dssp             ECCSSSCTTSC-SSSCCHHHHHHHHHHHHHHHHHCCSCHHHHCSSBTTBCEEEEEEEEESSCCSCTTHHHHHHHHHHHHT
T ss_pred             eeecccccccc-ccCCCchhhhhHHHHHHHHHhhhhhhhhhccccCCcceEEEEEEEEEecCCCCHHHHHHHHHHHHHHh
Confidence            99999887643 344456666677777776532        222225678999999999999999999999999999999


Q ss_pred             cCCCcc
Q 002054          508 AGIPLQ  513 (974)
Q Consensus       508 agvPi~  513 (974)
                      +++|+-
T Consensus       157 ~~iP~v  162 (181)
T d2nn6c1         157 VQLPEV  162 (181)
T ss_dssp             CCCCCC
T ss_pred             cCCCeE
Confidence            999973

>d1e3ha6 d.101.1.1 (A:483-578) Polynucleotide phosphorylase/guanosine pentaphosphate synthase (PNPase/GPSI), domains 2 and 5 {Streptomyces antibioticus [TaxId: 1890]}

class: Alpha and beta proteins (a+b)
fold: Ribonuclease PH domain 2-like
superfamily: Ribonuclease PH domain 2-like
family: Ribonuclease PH domain 2-like
domain: Polynucleotide phosphorylase/guanosine pentaphosphate synthase (PNPase/GPSI), domains 2 and 5
species: Streptomyces antibioticus [TaxId: 1890]

Probab=99.89  E-value=1.4e-23  Score=183.35  Aligned_cols=96  Identities=47%  Similarity=0.692  Sum_probs=88.1

Q ss_pred             ccccceeeeeeccCCCCCCcccceEEEecCCccccccCCccEEEEeeCCceEEEEeeccCCCCCHHHHHHHHHHHHHHHH
Q 002054          514 EHVAGVSVGLVSEVDPSTGEIKDYRILTDILGLEDHLGDMDFKIAGTRIGVTAIQLDIKPAGIPLDIICECLEHAHKGRL  593 (974)
Q Consensus       514 ~~vagvs~gli~~~d~~~~~~~~~~iL~Dp~~~Ee~~~d~d~~Va~t~~gI~alq~~~k~~~i~~e~l~~al~~A~~~~~  593 (974)
                      .||||++|||+.+.+.   +..+|.+|+|+.|.|||+||||||||||++|||++|||.|..|+|.+++.+||+||+++|.
T Consensus         1 APVAGIamGLi~~~~~---~~~~~~iLtDI~G~ED~~GDMDFKVAGT~~GITa~QmDiKi~Gi~~~il~~Al~qAk~gR~   77 (96)
T d1e3ha6           1 APVAGIAMGLISQEIN---GETHYVALTDILGAEDAFGDMDFKVAGTKEFVTALQLDTKLDGIPASVLAAALKQARDARL   77 (96)
T ss_dssp             SCCEEEEEEEEEEEET---TEEEEEEESSCCSHHHHHCSEEEEEEECSSCEEEEEEEECCSCCCHHHHHHHHHHHHHHHH
T ss_pred             CCcceeeeeeeeccCC---CCccEEEEeeccCchhhccCcccccccCcccceeeeeeecccCCCHHHHHHHHHHHHHHHH
Confidence            4899999999986321   1247999999999999999999999999999999999999999999999999999999999


Q ss_pred             HHHHHHHHHhcCCCCCCCCC
Q 002054          594 QILDHMEREISAPRTQDDRN  613 (974)
Q Consensus       594 ~I~~~m~~~i~~~~~~~~~~  613 (974)
                      +|++.|.+++++|| |+++|
T Consensus        78 ~IL~~M~~~i~~pr-e~sp~   96 (96)
T d1e3ha6          78 HILDVMMEAIDTPD-EMSPN   96 (96)
T ss_dssp             HHHHHHHHHCSSCC-CCCTT
T ss_pred             HHHHHHHHHhcccc-cCCCC
Confidence            99999999999998 78864

>d1e3ha2 d.14.1.4 (A:3-151) Polynucleotide phosphorylase/guanosine pentaphosphate synthase (PNPase/GPSI), domains 1 and 4 {Streptomyces antibioticus [TaxId: 1890]}

class: Alpha and beta proteins (a+b)
fold: Ribosomal protein S5 domain 2-like
superfamily: Ribosomal protein S5 domain 2-like
family: Ribonuclease PH domain 1-like
domain: Polynucleotide phosphorylase/guanosine pentaphosphate synthase (PNPase/GPSI), domains 1 and 4
species: Streptomyces antibioticus [TaxId: 1890]

Probab=99.88  E-value=2.1e-23  Score=204.49  Aligned_cols=136  Identities=13%  Similarity=0.090  Sum_probs=108.2

Q ss_pred             CcCCCCCCCCccCeEEEeCCCC-CCCcceEEEeCCeEEEEEEEeCCCchhhhccccCCCCceeEEEEEe-----cCCCCc
Q 002054          369 VRVDGRQLDEVRPIYCESGNLP-ILHGSSLFSRGDTQVLCTVTLGAPAEAQRLESLVGPPTKRFMLHYS-----FPPFCI  442 (974)
Q Consensus       369 ~R~DGR~~~e~R~I~ie~g~l~-~a~GSal~~~G~T~Vl~~Vtl~~p~~~~~~d~~~~~~~~~~~v~~~-----f~p~s~  442 (974)
                      .++|+|.+.+ |+|++|+|.++ +|||||+|++|+|+|+|+++.+...+..      ..+.....+.|.     ++++..
T Consensus         8 ~~~~~~~~~~-R~i~ie~G~lakqA~GSalv~~G~T~vl~ta~~~~~~~~~------~~~~~~~~v~~~~~~~~~~~~~~   80 (149)
T d1e3ha2           8 AVIDNGAFGT-RTIRFETGRLARQAAGSAVAYLDDDTMVLSATTASKNPKD------QLDFFPLTVDVEERMYAAGKIPG   80 (149)
T ss_dssp             EEEECGGGCE-EEEEEEESSSCTTSSEEEEEEETTTEEEEEEEEECSSCCT------TCSSCCEEEEEEECGGGGTCCCC
T ss_pred             EEEeCCcCCC-cEEEEEeCcccccCCceEEEEECCcEEEEEeeeccccccc------ccccCCceeEEEEeccccccccc
Confidence            4678888777 99999999996 6999999999999999999965333221      122334444443     344556


Q ss_pred             cccccccCCCchhhhHHHHHHHHhhhcCCCCCCCCeEEEEEEEEEcCCCChhhHHHHHHHHHHHHcCCC
Q 002054          443 NEVGKRVGLNRREVGHGTLAEKALLAVLPPENDFPYTVRVNSEVMASDGSTSMATVCGGSMALMDAGIP  511 (974)
Q Consensus       443 ~e~~~~~~~~rre~~~~~l~eral~~vi~~~~~~p~tI~V~v~VLesdGs~~~A~v~aa~lAL~dagvP  511 (974)
                      +..+|.+++++||++|++|++|+|++++|....++.+|.+++.+++.||++.+||+|||++||++||||
T Consensus        81 ~~~rre~~~~~reil~~rlidR~Lrpl~p~~~~~~~qI~~~vl~~d~d~~~~~aai~aAs~AL~~agIP  149 (149)
T d1e3ha2          81 SFFRREGRPSEDAILTCRLIDRPLRPSFKKGLRNEIQVVATIMALNPDHLYDVVAINAASASTQLAGLP  149 (149)
T ss_dssp             STTSSCCSCCHHHHHHHHHHHHHHHHHBCTTBCSCEEEEEEEEECCTTSCCHHHHHHHHHHHHHHTTCS
T ss_pred             cccccccccchHHHHHHHHHHHHHHhhccccCCCceEEEEEEEEeCCCCChHHHHHHHHHHHHHhcCCC
Confidence            778899999999999999999999999996434444566666677788899999999999999999998

>d2nn6a1 d.14.1.4 (A:1-184) Exosome complex exonuclease RRP45 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ribosomal protein S5 domain 2-like
superfamily: Ribosomal protein S5 domain 2-like
family: Ribonuclease PH domain 1-like
domain: Exosome complex exonuclease RRP45
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.88  E-value=1.4e-22  Score=206.11  Aligned_cols=147  Identities=22%  Similarity=0.255  Sum_probs=121.7

Q ss_pred             HHHHHHHHHHhcCCcCCCCCCCCccCeEEEeCCCCCCCcceEEEeCCeEEEEEEEeC--CCchhhhccccCCCCceeEEE
Q 002054          356 RKRVIRKRIIAEGVRVDGRQLDEVRPIYCESGNLPILHGSSLFSRGDTQVLCTVTLG--APAEAQRLESLVGPPTKRFML  433 (974)
Q Consensus       356 ~~~~~r~~il~~~~R~DGR~~~e~R~I~ie~g~l~~a~GSal~~~G~T~Vl~~Vtl~--~p~~~~~~d~~~~~~~~~~~v  433 (974)
                      ++++++ ..|++|+|+|||+++|+|++.+++|   .+||||+|++|+|+|+|+|+..  .|..       ..++++.+.+
T Consensus        10 e~~fi~-~~l~~~~R~DGR~~~e~R~~~i~~g---~a~GSa~v~~G~T~V~~~V~~~~~~p~~-------~~~~~g~~~~   78 (184)
T d2nn6a1          10 ERRFLL-RAIEEKKRLDGRQTYDYRNIRISFG---TDYGCCIVELGKTRVLGQVSCELVSPKL-------NRATEGILFF   78 (184)
T ss_dssp             HHHHHH-HHHHTTCCTTSCCTTCCCCCEEEEC---SSTTEEEEESSSCEEEEEECCEEECCCS-------TTTTSCCEEE
T ss_pred             HHHHHH-HHHhhCcCCCCCCCCCcCCeEEEec---CCCCEEEEEeCCCEEEEEEEeccccccc-------cCCCccceeE
Confidence            556555 5577899999999999999999998   5999999999999999999932  2322       2367789999


Q ss_pred             EEecCCCCccccccccCCCchhhhHHHHHHHHhh----------hcCCCCCCCCeEEEEEEEEEcCCCChhhHHHHHHHH
Q 002054          434 HYSFPPFCINEVGKRVGLNRREVGHGTLAEKALL----------AVLPPENDFPYTVRVNSEVMASDGSTSMATVCGGSM  503 (974)
Q Consensus       434 ~~~f~p~s~~e~~~~~~~~rre~~~~~l~eral~----------~vi~~~~~~p~tI~V~v~VLesdGs~~~A~v~aa~l  503 (974)
                      +++++|++.... +.+.++.++..+.+++++.+.          ++++  .++.|.|+|+++||++|||+++|+++|+++
T Consensus        79 ~v~~~~~~~~~~-~~~~~~~~~~~l~~~l~~~~~~~~~~d~~~L~i~~--~~~~w~i~i~v~VL~~DG~~~da~~~a~~~  155 (184)
T d2nn6a1          79 NLELSQMAAPAF-EPGRQSDLLVKLNRLMERCLRNSKCIDTESLCVVA--GEKVWQIRVDLHLLNHDGNIIDAASIAAIV  155 (184)
T ss_dssp             EEEECTTTCSSC-CSSSTHHHHTHHHHHHHHHHHHHTCBCSSSSCSBT--TTBEEEEEEEEEECSCCSCCHHHHHHHHHH
T ss_pred             EEEeccccCccc-ccCCCCchhHHHHHHHHhhhhhhhhhhhhhhcccc--ccCcEEEEEEEEEECCCCCHHHHHHHHHHH
Confidence            999999998664 345566777888888888874          2333  468999999999999999999999999999


Q ss_pred             HHHHcCCCccccc
Q 002054          504 ALMDAGIPLQEHV  516 (974)
Q Consensus       504 AL~dagvPi~~~v  516 (974)
                      ||+|+++|.....
T Consensus       156 AL~~~~iP~v~v~  168 (184)
T d2nn6a1         156 ALCHFRRPDVSVQ  168 (184)
T ss_dssp             HHHHCCCCCCBCC
T ss_pred             HHHhhCCCeEEEe
Confidence            9999999975543

>d2nn6f1 d.14.1.4 (F:29-175) Exosome complex exonuclease MTR3 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ribosomal protein S5 domain 2-like
superfamily: Ribosomal protein S5 domain 2-like
family: Ribonuclease PH domain 1-like
domain: Exosome complex exonuclease MTR3
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.87  E-value=1.7e-22  Score=197.58  Aligned_cols=136  Identities=23%  Similarity=0.331  Sum_probs=114.0

Q ss_pred             CCCCCCccCeEEEeCCCCCCCcceEEEeCCeEEEEEEEeCCCchhhhc----------cccCCCCceeEEEEEecCCCCc
Q 002054          373 GRQLDEVRPIYCESGNLPILHGSSLFSRGDTQVLCTVTLGAPAEAQRL----------ESLVGPPTKRFMLHYSFPPFCI  442 (974)
Q Consensus       373 GR~~~e~R~I~ie~g~l~~a~GSal~~~G~T~Vl~~Vtl~~p~~~~~~----------d~~~~~~~~~~~v~~~f~p~s~  442 (974)
                      .|+++|+|+|++++|+++++||||+|++|+|+|+|+|+  +|.+....          ........+.++++|+++|++.
T Consensus         2 ~R~~~e~R~i~i~~gvi~~a~GSa~v~~G~T~V~~~V~--gp~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~   79 (147)
T d2nn6f1           2 TRDPTRLRPVYARAGLLSQAKGSAYLEAGGTKVLCAVS--GPRQAEGGERGGGPAGAGGEAPAALRGRLLCDFRRAPFAG   79 (147)
T ss_dssp             CCCSSCCCCCCCCCSCCSSSSEEECCCSSSCEEEEEEE--EEECC-------------------CBCEEEEEEEECTTSS
T ss_pred             CCCCCCccceEEEeCCCCCCCEEEEEEECCeEEEEEEe--ccccccccccCCccccccccccccccceeEEEEEecCCcc
Confidence            59999999999999999999999999999999999999  55443211          1223456688999999999998


Q ss_pred             cccccccCCCchhhhHHHHHHHHhhhcCCCCCCCCeEEEEEEEEEcCCCChhhHHHHHHHHHHHHcCCC
Q 002054          443 NEVGKRVGLNRREVGHGTLAEKALLAVLPPENDFPYTVRVNSEVMASDGSTSMATVCGGSMALMDAGIP  511 (974)
Q Consensus       443 ~e~~~~~~~~rre~~~~~l~eral~~vi~~~~~~p~tI~V~v~VLesdGs~~~A~v~aa~lAL~dagvP  511 (974)
                      .+. +.+.+..++..++.++.++|.++++.+..+.|+|+|+++||++|||+++||++|+++||+||||.
T Consensus        80 ~~~-~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~i~v~v~Vl~~DG~l~~a~i~A~~~AL~daGIe  147 (147)
T d2nn6f1          80 RRR-RAPPGGCEERELALALQEALEPAVRLGRYPRAQLEVSALLLEDGGSALAAALTAAALALADAGVE  147 (147)
T ss_dssp             SSC-CCSCCHHHHHHHHHHHHHHHTTTBCSTTSBTCEEEEEEEEEECCSSHHHHHHHHHHHHHHHHCCC
T ss_pred             ccc-cccCCccchhhhhhhhhhcccccccccccCCEEEEEEEEEECCCCCHHHHHHHHHHHHHHHhCCC
Confidence            765 34556678889999999999999998655667999999999999999999999999999999984

>d2nn6d1 d.14.1.4 (D:25-146) Exosome complex exonuclease RRP46 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ribosomal protein S5 domain 2-like
superfamily: Ribosomal protein S5 domain 2-like
family: Ribonuclease PH domain 1-like
domain: Exosome complex exonuclease RRP46
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.86  E-value=9.9e-22  Score=186.41  Aligned_cols=120  Identities=28%  Similarity=0.320  Sum_probs=98.8

Q ss_pred             CCccCeEEEeCCCCCCCcceEEEeCCeEEEEEEEeCCCchhhhccccCCCCceeEEEEEecCCCCccccccccCCCchhh
Q 002054          377 DEVRPIYCESGNLPILHGSSLFSRGDTQVLCTVTLGAPAEAQRLESLVGPPTKRFMLHYSFPPFCINEVGKRVGLNRREV  456 (974)
Q Consensus       377 ~e~R~I~ie~g~l~~a~GSal~~~G~T~Vl~~Vtl~~p~~~~~~d~~~~~~~~~~~v~~~f~p~s~~e~~~~~~~~rre~  456 (974)
                      .|+|++.+++|+++++||||+|++|+|+|+|+|+  +|.+.+.....  .+...  +++++.|       +.+.++++++
T Consensus         2 ~elR~i~~~~gvl~~adGSa~~~~G~T~Vi~~V~--gP~e~~~~~~~--~~~~~--~~v~~~~-------~~~~~~~~~~   68 (122)
T d2nn6d1           2 CSLRHFACEQNLLSRPDGSASFLQGDTSVLAGVY--GPAEVKVSKEI--FNKAT--LEVILRP-------KIGLPGVAEK   68 (122)
T ss_dssp             CCCCCEEEEESCCSSSSEEEEEEETTEEEEEEEE--EEEECC--------CCEE--EEEEEEC-------SSSCCCHHHH
T ss_pred             CccceEEEEECCCCCCCeEEEEEECCcEEEEEEE--ecccccchhhC--cCCCc--eEEEeee-------ecCCCCchhh
Confidence            4899999999999999999999999999999999  88775433221  23333  4444433       3355688999


Q ss_pred             hHHHHHHHHhhhcCCCCCCCC-eEEEEEEEEEcCCCChhhHHHHHHHHHHHHcCC
Q 002054          457 GHGTLAEKALLAVLPPENDFP-YTVRVNSEVMASDGSTSMATVCGGSMALMDAGI  510 (974)
Q Consensus       457 ~~~~l~eral~~vi~~~~~~p-~tI~V~v~VLesdGs~~~A~v~aa~lAL~dagv  510 (974)
                      .++++++++|+++++. +.|| |+|+|+++||++|||.++|++||+++||+||||
T Consensus        69 ~~~~~l~~~l~~~i~~-~~~p~~~i~i~v~Vl~~DG~~~~a~ina~~lAL~dagI  122 (122)
T d2nn6d1          69 SRERLIRNTCEAVVLG-TLHPRTSITVVLQVVSDAGSLLACCLNAACMALVDAGV  122 (122)
T ss_dssp             HHHHHHHHHHHHHCGG-GCSSSEEEEEEEEEEECSSCHHHHHHHHHHHHHHHTTC
T ss_pred             HHHHHHHhhhhcccch-hhcCCeEEEEEEEEEcCCCChhHHHHHHHHHHHHHcCC
Confidence            9999999999999998 6777 579999999999999999999999999999997

>d1e3ha3 d.14.1.4 (A:346-482) Polynucleotide phosphorylase/guanosine pentaphosphate synthase (PNPase/GPSI), domains 1 and 4 {Streptomyces antibioticus [TaxId: 1890]}

class: Alpha and beta proteins (a+b)
fold: Ribosomal protein S5 domain 2-like
superfamily: Ribosomal protein S5 domain 2-like
family: Ribonuclease PH domain 1-like
domain: Polynucleotide phosphorylase/guanosine pentaphosphate synthase (PNPase/GPSI), domains 1 and 4
species: Streptomyces antibioticus [TaxId: 1890]

Probab=99.86  E-value=2.8e-22  Score=194.11  Aligned_cols=124  Identities=21%  Similarity=0.275  Sum_probs=99.7

Q ss_pred             eEEEEEeCccCcCCCcEEEEEeCCeEEEEEEEeCCC-CCC-------CCceeeEeeccccccccCCCCCccccccCCCCc
Q 002054           68 RLITLETGKIARFANGAVVLGMDETKVLSTVTSSKG-DSV-------RDFLPLTVDYQEKQFAQGVIPNTYMRREGAPKE  139 (974)
Q Consensus        68 r~i~~etg~~a~~A~GSa~v~~G~T~Vl~tv~~~~~-~~~-------~~f~pL~v~y~e~~~a~g~ip~~~~~Reg~p~~  139 (974)
                      |+|.+|+|.+ +||||||++++|+|+|||+|+++.+ +..       ..+..+.++|...     .+++++.+|++.++.
T Consensus         4 R~i~~~~gv~-~~adGSa~~~~G~T~Vl~~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-----~~~~~~~~~~~~~~~   77 (137)
T d1e3ha3           4 RTLAAEVEAI-PRVHGSALFERGETQILGVTTLNMLRMEQQLDTLSPVTRKRYMHNYNFP-----PYSVGETGRVGSPKR   77 (137)
T ss_dssp             CCEEEEECCS-SSSSEEEEEEETTEEEEEEEEEEEGGGSEECCSSSSCCEESEEEEEECC-----GGGGTCCCCCSSCCH
T ss_pred             ceEEEEeCCC-CCCCeeEEEEECCeEEEEEEccCccCccccccccCcceeeeeeeecccc-----ccccccccccccccc
Confidence            8999999999 8999999999999999999999865 221       1222334444333     345678889999999


Q ss_pred             hhhhHHHhhcCCccccccCCCCCceEEE--EEEEeccCCCChhhHHHHHHHHHhhcCCCCCC
Q 002054          140 RELLVGRIIDRPIRPLFPAGFYHEVQVM--ASVLSSDGKQDPDIMAANATSAALMLSDIPWG  199 (974)
Q Consensus       140 ~eil~~RlidR~lrplfp~~~~~~~~i~--~~vl~~dg~~~~~~~ai~aAs~AL~~s~iP~~  199 (974)
                      ++++++++++|+|+|+++..+++..+|.  ++||+.||+  +.+||+|||++||++|||||+
T Consensus        78 ~~~~~~~~i~~~l~~~i~~~~~~~~~I~v~v~vl~~DG~--~~~aainAa~lAL~dAGIpmk  137 (137)
T d1e3ha3          78 REIGHGALAERAIVPVLPTREEFPYAIRQVSEALGSNGS--TSMGSVCASTMSLLNAGVPLK  137 (137)
T ss_dssp             HHHHHHHHHHHHHGGGCCCTTTSCEEEEEEEEEEECSSC--HHHHHHHHHHHHHHHHTCCCS
T ss_pred             cccccchHHHHHHHhccchhhcCcEEEEEEEEEecCCCC--HHHHHHHHHHHHHHHcCCccC
Confidence            9999999999999999998777666666  555666665  459999999999999999995

>d1e3ha5 d.101.1.1 (A:152-262) Polynucleotide phosphorylase/guanosine pentaphosphate synthase (PNPase/GPSI), domains 2 and 5 {Streptomyces antibioticus [TaxId: 1890]}

class: Alpha and beta proteins (a+b)
fold: Ribonuclease PH domain 2-like
superfamily: Ribonuclease PH domain 2-like
family: Ribonuclease PH domain 2-like
domain: Polynucleotide phosphorylase/guanosine pentaphosphate synthase (PNPase/GPSI), domains 2 and 5
species: Streptomyces antibioticus [TaxId: 1890]

Probab=99.82  E-value=7.6e-21  Score=175.65  Aligned_cols=92  Identities=32%  Similarity=0.440  Sum_probs=84.6

Q ss_pred             CCCCeEEEEEEEECCEEEEcCCHHHHhcCccceeEeeeCC-----eEEEEEec------------CCCCCHHHHHHHHHH
Q 002054          198 WGGPIGMIRIGRICGQFIVNPTMDELSLSDLNLVYACTRE-----KTLMIDVQ------------AREISEKDLEAGLRL  260 (974)
Q Consensus       198 ~~~~v~av~vg~i~g~~vldPt~~e~~~s~~~l~v~~t~~-----~i~mie~~------------~~~~~e~~~~~al~~  260 (974)
                      |+|||+|||||++||+||+|||++|++.|+|||+||||.+     .++|+|++            +++++|+++.+||++
T Consensus         1 f~GPvgaVRVg~idge~viNPt~~el~~S~ldLvVaGt~~~~~~~~v~mie~~~~e~~~~mie~~a~e~~E~~~~~ai~~   80 (111)
T d1e3ha5           1 FSGPIGGVRVALIRGQWVAFPTHTELEDAVFDMVVAGRVLEDGDVAIMMVEAEATEKTIQLVKDGAEAPTEEVVAAGLDA   80 (111)
T ss_dssp             BCCCCEEEEEEEETTEEEESCCHHHHTTEEEEEEEEEEECTTSCEEEEEEEEEECTTHHHHHHTTCCCCCHHHHHHHHHH
T ss_pred             CCCCEEEEEEEEECCEEEECCCHHHHhcCceEEEEeecccccchHHHHHHHhcchhHHHHHHHhccccccHHHHHHHHHH
Confidence            8999999999999999999999999999999999999964     37777654            466999999999999


Q ss_pred             HHHHHHHHHHHHHHHHHHhCCcccccccc
Q 002054          261 AHPEAVKYLEPQIRLAEKAGKQKKEYKLS  289 (974)
Q Consensus       261 a~~~~~~i~~~~~~~~~~~g~~k~~~~~~  289 (974)
                      ||+.++++++.|+++.+++||+|++|+..
T Consensus        81 a~~~i~~~i~~q~el~~~~gk~k~e~p~~  109 (111)
T d1e3ha5          81 AKPFIKVLCKAQADLAAKAAKPTGEFPVF  109 (111)
T ss_dssp             HHHHHHHHHHHHHHHHHHHCCCCCCCCBC
T ss_pred             HHHHHHHHHHHHHHHHHHHCCCCCcCCCC
Confidence            99999999999999999999999998654

>d1r6la2 d.101.1.1 (A:152-239) Ribonuclease PH, domain 2 {Pseudomonas aeruginosa [TaxId: 287]}

class: Alpha and beta proteins (a+b)
fold: Ribonuclease PH domain 2-like
superfamily: Ribonuclease PH domain 2-like
family: Ribonuclease PH domain 2-like
domain: Ribonuclease PH, domain 2
species: Pseudomonas aeruginosa [TaxId: 287]

Probab=99.78  E-value=3.4e-19  Score=158.63  Aligned_cols=83  Identities=17%  Similarity=0.132  Sum_probs=78.9

Q ss_pred             CCCCCCCeEEEEEEEECCEEEEcCCHHHHhcCccceeEeeeCCe---EEEEEecCCCCCHHHHHHHHHHHHHHHHHHHHH
Q 002054          195 DIPWGGPIGMIRIGRICGQFIVNPTMDELSLSDLNLVYACTREK---TLMIDVQAREISEKDLEAGLRLAHPEAVKYLEP  271 (974)
Q Consensus       195 ~iP~~~~v~av~vg~i~g~~vldPt~~e~~~s~~~l~v~~t~~~---i~mie~~~~~~~e~~~~~al~~a~~~~~~i~~~  271 (974)
                      |+||++||||||||++||++|+|||++|++.+++||+|++|+++   .+|+++++++||+++|.+||++||+++++|+++
T Consensus         2 g~P~~~~VaavsvG~idg~~vld~~~~E~~~~~~Dl~va~t~~g~i~~iq~~ge~~~~sed~~~~al~~A~~~i~~i~~~   81 (88)
T d1r6la2           2 GNPLKQMVAAVSVGIYQGVPVLDLDYLEDSAAETDLNVVMTDAGGFIEVQGTAEGAPFRPAELNAMLELAQQGMQELFEL   81 (88)
T ss_dssp             SCCBCCCEEEEEEEEETTEEEESCCHHHHHHCSEEEEEEEETTSCEEEEEEEESSSCCCHHHHHHHHHHHHHHHHHHHHH
T ss_pred             CCCcCCCccEEEEEEECCEEEecCcHHhhccCceeEEEEEeCCCCEEeehhhcccCCCCHHHHHHHHHHHHHHHHHHHHH
Confidence            79999999999999999999999999999999999999999995   567888889999999999999999999999999


Q ss_pred             HHHHHH
Q 002054          272 QIRLAE  277 (974)
Q Consensus       272 ~~~~~~  277 (974)
                      |+++++
T Consensus        82 Qkeal~   87 (88)
T d1r6la2          82 QRAALA   87 (88)
T ss_dssp             HHHHHT
T ss_pred             HHHHhc
Confidence            999774

>d2nn6d1 d.14.1.4 (D:25-146) Exosome complex exonuclease RRP46 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ribosomal protein S5 domain 2-like
superfamily: Ribosomal protein S5 domain 2-like
family: Ribonuclease PH domain 1-like
domain: Exosome complex exonuclease RRP46
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.78  E-value=2e-19  Score=170.30  Aligned_cols=112  Identities=21%  Similarity=0.214  Sum_probs=96.8

Q ss_pred             eEEEEEeCccCcCCCcEEEEEeCCeEEEEEEEeCCC-CC---CCCceeeEeeccccccccCCCCCccccccCCCCchhhh
Q 002054           68 RLITLETGKIARFANGAVVLGMDETKVLSTVTSSKG-DS---VRDFLPLTVDYQEKQFAQGVIPNTYMRREGAPKERELL  143 (974)
Q Consensus        68 r~i~~etg~~a~~A~GSa~v~~G~T~Vl~tv~~~~~-~~---~~~f~pL~v~y~e~~~a~g~ip~~~~~Reg~p~~~eil  143 (974)
                      |++.+++|++ .+|||||++++|+|+|+|+|++|.+ +.   ..++.+++|+++++.              |.|+.++++
T Consensus         5 R~i~~~~gvl-~~adGSa~~~~G~T~Vi~~V~gP~e~~~~~~~~~~~~~~v~~~~~~--------------~~~~~~~~~   69 (122)
T d2nn6d1           5 RHFACEQNLL-SRPDGSASFLQGDTSVLAGVYGPAEVKVSKEIFNKATLEVILRPKI--------------GLPGVAEKS   69 (122)
T ss_dssp             CCEEEEESCC-SSSSEEEEEEETTEEEEEEEEEEEECC------CCEEEEEEEECSS--------------SCCCHHHHH
T ss_pred             ceEEEEECCC-CCCCeEEEEEECCcEEEEEEEecccccchhhCcCCCceEEEeeeec--------------CCCCchhhH
Confidence            8999999999 7899999999999999999999987 22   346788999886543              889999999


Q ss_pred             HHHhhcCCccccccCCC--CCceEEEEEEEeccCCCChhhHHHHHHHHHhhcCCC
Q 002054          144 VGRIIDRPIRPLFPAGF--YHEVQVMASVLSSDGKQDPDIMAANATSAALMLSDI  196 (974)
Q Consensus       144 ~~RlidR~lrplfp~~~--~~~~~i~~~vl~~dg~~~~~~~ai~aAs~AL~~s~i  196 (974)
                      ++++++|+|+|+++...  ++.++|.++||+.||+..  +||+||+++||++|||
T Consensus        70 ~~~~l~~~l~~~i~~~~~p~~~i~i~v~Vl~~DG~~~--~a~ina~~lAL~dagI  122 (122)
T d2nn6d1          70 RERLIRNTCEAVVLGTLHPRTSITVVLQVVSDAGSLL--ACCLNAACMALVDAGV  122 (122)
T ss_dssp             HHHHHHHHHHHHCGGGCSSSEEEEEEEEEEECSSCHH--HHHHHHHHHHHHHTTC
T ss_pred             HHHHHHhhhhcccchhhcCCeEEEEEEEEEcCCCChh--HHHHHHHHHHHHHcCC
Confidence            99999999999988655  456777788999988776  9999999999999997

>d2je6b1 d.14.1.4 (B:8-155) Exosome complex exonuclease 1, ECX1 {Sulfolobus solfataricus [TaxId: 2287]}

class: Alpha and beta proteins (a+b)
fold: Ribosomal protein S5 domain 2-like
superfamily: Ribosomal protein S5 domain 2-like
family: Ribonuclease PH domain 1-like
domain: Exosome complex exonuclease 1, ECX1
species: Sulfolobus solfataricus [TaxId: 2287]

Probab=99.76  E-value=4.2e-19  Score=173.80  Aligned_cols=121  Identities=26%  Similarity=0.427  Sum_probs=102.2

Q ss_pred             CeEEEEEeCccCcCCCcEEEEEeCCeEEEEEEEeCCC-C----CCCCceeeEeeccccccccCCCCCccccccCCCCchh
Q 002054           67 SRLITLETGKIARFANGAVVLGMDETKVLSTVTSSKG-D----SVRDFLPLTVDYQEKQFAQGVIPNTYMRREGAPKERE  141 (974)
Q Consensus        67 ~r~i~~etg~~a~~A~GSa~v~~G~T~Vl~tv~~~~~-~----~~~~f~pL~v~y~e~~~a~g~ip~~~~~Reg~p~~~e  141 (974)
                      -|++++++|.+ ++|||||++++|+|+|+|+|++|.+ .    ...+...++++|....++.+.      ++.+.++.++
T Consensus        21 ~R~i~i~~g~l-~~adGSa~v~~G~T~Vl~~V~gp~e~~~~~~~~~~~~~~~v~~~~~~~~~~~------~~~~~~~~~~   93 (148)
T d2je6b1          21 LRSIKIELGVL-KNADGSAIFEMGNTKAIAAVYGPKEMHPRHLSLPDRAVLRVRYHMTPFSTDE------RKNPAPSRRE   93 (148)
T ss_dssp             CCCEEEEESCC-SSSSEEEEEEETTEEEEEEEEEEEECSSGGGSCSSSCEEEEEEEECTTSSSS------CCCSSCCHHH
T ss_pred             ccCeEEEECCC-CCCCEEEEEEcCCccEEeecccCccccchhhcCCcceEEEEEEEeccccccc------cccccccchh
Confidence            58899999999 8999999999999999999999866 2    235667799999877665532      3446788999


Q ss_pred             hhHHHhhcCCccccccCCCCC--ceEEEEEEEeccCCCChhhHHHHHHHHHhhcCCC
Q 002054          142 LLVGRIIDRPIRPLFPAGFYH--EVQVMASVLSSDGKQDPDIMAANATSAALMLSDI  196 (974)
Q Consensus       142 il~~RlidR~lrplfp~~~~~--~~~i~~~vl~~dg~~~~~~~ai~aAs~AL~~s~i  196 (974)
                      ++++++++|+|+|.++...++  .++|.++||+.||+..  .+|+|||++||++|||
T Consensus        94 ~el~~~l~~~l~~~i~~~~~p~~~i~v~v~VL~~DG~~~--~a~i~aa~~AL~daGI  148 (148)
T d2je6b1          94 IELSKVIREALESAVLVELFPRTAIDVFTEILQADAGSR--LVSLMAASLALADAGI  148 (148)
T ss_dssp             HHHHHHHHHHHHTTBCGGGSTTEEEEEEEEEEECSSCHH--HHHHHHHHHHHHHTTC
T ss_pred             HHHHHHHHHHhhccccHHHcCCEEEEEEEEEEEcCCCHH--HHHHHHHHHHHHHcCC
Confidence            999999999999988866544  5677899999999877  8999999999999997

>d2ba0d1 d.14.1.4 (D:10-153) Exosome complex exonuclease 1, ECX1 {Archaeoglobus fulgidus [TaxId: 2234]}

class: Alpha and beta proteins (a+b)
fold: Ribosomal protein S5 domain 2-like
superfamily: Ribosomal protein S5 domain 2-like
family: Ribonuclease PH domain 1-like
domain: Exosome complex exonuclease 1, ECX1
species: Archaeoglobus fulgidus [TaxId: 2234]

Probab=99.76  E-value=4.8e-19  Score=172.50  Aligned_cols=120  Identities=19%  Similarity=0.338  Sum_probs=100.1

Q ss_pred             CeEEEEEeCccCcCCCcEEEEEeCCeEEEEEEEeCCC-CC----CCCceeeEeeccccccccCCCCCcccccc-CCCCch
Q 002054           67 SRLITLETGKIARFANGAVVLGMDETKVLSTVTSSKG-DS----VRDFLPLTVDYQEKQFAQGVIPNTYMRRE-GAPKER  140 (974)
Q Consensus        67 ~r~i~~etg~~a~~A~GSa~v~~G~T~Vl~tv~~~~~-~~----~~~f~pL~v~y~e~~~a~g~ip~~~~~Re-g~p~~~  140 (974)
                      -|++.+++|.+ ++|+|||++++|+|+|+|+|++|.+ +.    ..+...++++|....++.       ..|+ +.|+.+
T Consensus        17 ~R~i~i~~g~l-~~a~GSa~v~~G~T~Vl~~V~gp~~~~~~~~~~~~~~~~~~~~~~~~~s~-------~~~~~~~~~~~   88 (144)
T d2ba0d1          17 LRPIKIEASVL-KRADGSCYLEMGKNKVIAAVFGPREVHPRHLQDPSKAIIRYRYNMAPFSV-------EERKRPGPDRR   88 (144)
T ss_dssp             CCCEEEEECCC-SSSSEEEEEEETTEEEEEEEEEEEECCSGGGCCSSSCEEEEEEEECTTSS-------SSCCCSSCCHH
T ss_pred             ccCeEEEECCC-CCCCceEEEEEcccceEEEEeccchhhhhhcccccceEEEEEEecCCccc-------ccccccCCCch
Confidence            48899999999 8999999999999999999999876 22    345567888886655544       3343 678999


Q ss_pred             hhhHHHhhcCCccccccCCCCC--ceEEEEEEEeccCCCChhhHHHHHHHHHhhcCCC
Q 002054          141 ELLVGRIIDRPIRPLFPAGFYH--EVQVMASVLSSDGKQDPDIMAANATSAALMLSDI  196 (974)
Q Consensus       141 eil~~RlidR~lrplfp~~~~~--~~~i~~~vl~~dg~~~~~~~ai~aAs~AL~~s~i  196 (974)
                      +++++++++|+++|+++...++  .++|.++||+.||+..  +||+|||++||++|||
T Consensus        89 ~~~l~~~l~~~l~~~i~~~~~~~~~i~v~v~VL~~DG~~~--~a~i~aa~lAL~daGI  144 (144)
T d2ba0d1          89 SIEISKVSKEAFEAVIMKELFPRSAIDIFVEVLQADAGSR--TACLNAASVALVDAGV  144 (144)
T ss_dssp             HHHHHHHHHHHHHTTBCGGGCTTEEEEEEEEEEECCTTHH--HHHHHHHHHHHHHHTC
T ss_pred             hhhhhhhhhhhhccccchhhcCCeEEEEEEEEEccCCCHH--HHHHHHHHHHHHHcCC
Confidence            9999999999999998875544  5777788899999866  9999999999999997

>d2nn6b1 d.14.1.4 (B:6-150) Exosome complex exonuclease RRP41 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ribosomal protein S5 domain 2-like
superfamily: Ribosomal protein S5 domain 2-like
family: Ribonuclease PH domain 1-like
domain: Exosome complex exonuclease RRP41
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.74  E-value=1.3e-18  Score=169.69  Aligned_cols=122  Identities=19%  Similarity=0.266  Sum_probs=102.6

Q ss_pred             CeEEEEEeCccCcCCCcEEEEEeCCeEEEEEEEeCCC-C-----CCCCceeeEeeccccccccCCCCCccccccCCCCch
Q 002054           67 SRLITLETGKIARFANGAVVLGMDETKVLSTVTSSKG-D-----SVRDFLPLTVDYQEKQFAQGVIPNTYMRREGAPKER  140 (974)
Q Consensus        67 ~r~i~~etg~~a~~A~GSa~v~~G~T~Vl~tv~~~~~-~-----~~~~f~pL~v~y~e~~~a~g~ip~~~~~Reg~p~~~  140 (974)
                      -|++++++|.+ .+|||||++++|+|+|+|+|++|.+ +     ...+...++|+|....|+.+..     ++.+.++.+
T Consensus        16 ~R~i~i~~g~~-~~a~GSa~v~~G~T~Vi~~V~gp~~~~~~~~~~~~~~~~v~v~~~~~~~~~~~~-----~~~~~~~~~   89 (145)
T d2nn6b1          16 LRKIQARMGVF-AQADGSAYIEQGNTKALAVVYGPHEIRGSRARALPDRALVNCQYSSATFSTGER-----KRRPHGDRK   89 (145)
T ss_dssp             CCCEEEEESCS-SSSSEEEEEEESSCEEEEEEEEEEECCSSSCCCCCSSCCEEEEEEECTTTSSSC-----CCTTTSTHH
T ss_pred             ccCeEEEECCC-CCCCceEEEEeCCceEEEEEEeccccccchhhccccceeEEEEeeecCcccccc-----cccCCCCch
Confidence            48899999999 8999999999999999999999865 2     2356788999998887776531     222567788


Q ss_pred             hhhHHHhhcCCccccccC--CCCCceEEEEEEEeccCCCChhhHHHHHHHHHhhcCCC
Q 002054          141 ELLVGRIIDRPIRPLFPA--GFYHEVQVMASVLSSDGKQDPDIMAANATSAALMLSDI  196 (974)
Q Consensus       141 eil~~RlidR~lrplfp~--~~~~~~~i~~~vl~~dg~~~~~~~ai~aAs~AL~~s~i  196 (974)
                      ++++++++.|+|++.++.  .++..++|.++||+.||+..  .||+|||++||++|||
T Consensus        90 ~~~l~~~l~~~l~~~i~~~~~~~~~I~v~v~VL~~DG~l~--~a~i~aa~lAL~daGI  145 (145)
T d2nn6b1          90 SCEMGLQLRQTFEAAILTQLHPRSQIDIYVQVLQADGGTY--AACVNAATLAVLDAGI  145 (145)
T ss_dssp             HHHHHHHHHHHHHHTTCGGGCTTEEEEEEEEEEECCSCHH--HHHHHHHHHHHHHTCC
T ss_pred             hhhHHHHHHHhhhcccchHhhCceeeEEEEEEEeCCCCHH--HHHHHHHHHHHHHcCC
Confidence            999999999999998773  33556888899999999877  8999999999999997

>d1udsa1 d.14.1.4 (A:2-150) Ribonuclease PH, domain 1 {Aquifex aeolicus [TaxId: 63363]}

class: Alpha and beta proteins (a+b)
fold: Ribosomal protein S5 domain 2-like
superfamily: Ribosomal protein S5 domain 2-like
family: Ribonuclease PH domain 1-like
domain: Ribonuclease PH, domain 1
species: Aquifex aeolicus [TaxId: 63363]

Probab=99.74  E-value=5.5e-19  Score=173.09  Aligned_cols=129  Identities=17%  Similarity=0.161  Sum_probs=110.2

Q ss_pred             CeEEEEEeCccCcCCCcEEEEEeCCeEEEEEEEeCCC-C---CCCCceeeEeeccccccccCCCCCccccccCCCCchhh
Q 002054           67 SRLITLETGKIARFANGAVVLGMDETKVLSTVTSSKG-D---SVRDFLPLTVDYQEKQFAQGVIPNTYMRREGAPKEREL  142 (974)
Q Consensus        67 ~r~i~~etg~~a~~A~GSa~v~~G~T~Vl~tv~~~~~-~---~~~~f~pL~v~y~e~~~a~g~ip~~~~~Reg~p~~~ei  142 (974)
                      -|++.+++|.+ ++|||||++++|+|+|+|+|++|.+ |   ...++..++++|....++.+....+.. +.|++...+.
T Consensus        10 ~R~i~i~~g~l-~~a~GSa~v~~G~T~V~~~V~~~~~~~~~~~~~~~g~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~   87 (149)
T d1udsa1          10 LRPVSIQRDFL-EYPEGSCLISFGKTKVICTASVIENVPNWLKGKGQGWITAEYSMLPRATQQRTIRES-VQGRIGGRTH   87 (149)
T ss_dssp             CCCEEEEECCS-SSSSEEEEEEETTEEEEEEEEEESCCCGGGTTSSCCEEEEEEEECSEETTEECCCSS-SSCCCCHHHH
T ss_pred             ccCeEEEeCCC-CCCCEEEEEEECCCEEEEEEEeeccccccccCCCceeEEeeecchhhcccccccccc-cccccccchh
Confidence            58999999999 8999999999999999999999876 3   345788899999888877755443333 3388999999


Q ss_pred             hHHHhhcCCcccccc--CCCCCceEEEEEEEeccCCCChhhHHHHHHHHHhhcCCCCCC
Q 002054          143 LVGRIIDRPIRPLFP--AGFYHEVQVMASVLSSDGKQDPDIMAANATSAALMLSDIPWG  199 (974)
Q Consensus       143 l~~RlidR~lrplfp--~~~~~~~~i~~~vl~~dg~~~~~~~ai~aAs~AL~~s~iP~~  199 (974)
                      ++++++.+.+++++.  ..+.+.++|.++||+.||+..  .||+||+++||+++||||.
T Consensus        88 ~~~~~l~~~l~~~i~l~~~~~~~i~v~v~VL~~DG~l~--da~~~A~~~AL~dagipm~  144 (149)
T d1udsa1          88 EIQRMIGRAMRTAVELTKIGERTIWVDCDVIQADGGTA--TAAITGAFVAVADAIIKLH  144 (149)
T ss_dssp             HHHHHHHHHHHHHBCGGGSCSCEEEEEEEEEECSSCHH--HHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHhhhhheehhhhcCCceEEEEEEEEccCCCHH--HHHHHHHHHHHHHhChHHH
Confidence            999999999999765  445667888899999999876  9999999999999999997

>d1r6la1 d.14.1.4 (A:1-151) Ribonuclease PH, domain 1 {Pseudomonas aeruginosa [TaxId: 287]}

class: Alpha and beta proteins (a+b)
fold: Ribosomal protein S5 domain 2-like
superfamily: Ribosomal protein S5 domain 2-like
family: Ribonuclease PH domain 1-like
domain: Ribonuclease PH, domain 1
species: Pseudomonas aeruginosa [TaxId: 287]

Probab=99.68  E-value=7.1e-18  Score=165.37  Aligned_cols=129  Identities=22%  Similarity=0.265  Sum_probs=103.5

Q ss_pred             CeEEEEEeCccCcCCCcEEEEEeCCeEEEEEEEeCCC-C---CCCCceeeEeeccccccccCCCCCccccccCCCCchhh
Q 002054           67 SRLITLETGKIARFANGAVVLGMDETKVLSTVTSSKG-D---SVRDFLPLTVDYQEKQFAQGVIPNTYMRREGAPKEREL  142 (974)
Q Consensus        67 ~r~i~~etg~~a~~A~GSa~v~~G~T~Vl~tv~~~~~-~---~~~~f~pL~v~y~e~~~a~g~ip~~~~~Reg~p~~~ei  142 (974)
                      -|++.+++|.+ .+|||||++++|+|+|+|+|+++.+ |   ...+...+.++|....++.......-..| +...+.+.
T Consensus        12 ~R~i~i~~g~l-~~a~GSa~v~~G~T~Vl~~V~~~~~~~~~~~~~~~g~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~   89 (151)
T d1r6la1          12 LRPIRITRHYT-KHAEGSVLVEFGDTKVICTVSAESGVPRFLKGQGQGWLTAEYGMLPRSTGERNQREASR-GKQGGRTL   89 (151)
T ss_dssp             CCCEEEESSCS-SSSSEEEEEEETTEEEEEEEEEEESCSSCCC---CCEEEEEEEECTTSSSSCCCCHHHH-TSCCHHHH
T ss_pred             ccCeEEEeCCC-CCCCEEEEEEeCCCEEEEEEEecccccccccCCCceeEEEEEEecCccccccccccCCC-ccccccch
Confidence            48999999999 8999999999999999999999876 3   23456778888877766654433222222 56778999


Q ss_pred             hHHHhhcCCccccccCCC--CCceEEEEEEEeccCCCChhhHHHHHHHHHhhcCCCCCC
Q 002054          143 LVGRIIDRPIRPLFPAGF--YHEVQVMASVLSSDGKQDPDIMAANATSAALMLSDIPWG  199 (974)
Q Consensus       143 l~~RlidR~lrplfp~~~--~~~~~i~~~vl~~dg~~~~~~~ai~aAs~AL~~s~iP~~  199 (974)
                      ++++++.++++++++...  .+.+.|.++||+.||+..  .||+|||++||++|+|||+
T Consensus        90 ~~~~~l~~~~~~~~~l~~~~~~~i~v~v~VL~~DG~~~--da~~~Aa~~AL~dagip~~  146 (151)
T d1r6la1          90 EIQRLIGRSLRAALDLSKLGENTLYIDCDVIQADGGTR--TASITGATVALIDALAVLK  146 (151)
T ss_dssp             HHHHHHHHHHHHTBCGGGTCSEEEEEEEEEEECSSCHH--HHHHHHHHHHHHHHHHHHH
T ss_pred             hHHHHHHhhhhhccchhhhCceEEEEEEEEEeCCCCHH--HHHHHHHHHHHHHhcHHHH
Confidence            999999999999887444  346778889999998877  9999999999999999984

>d1sroa_ b.40.4.5 (A:) S1 RNA-binding domain of polyribonucleotide phosphorylase, PNPase {Escherichia coli [TaxId: 562]}

class: All beta proteins
fold: OB-fold
superfamily: Nucleic acid-binding proteins
family: Cold shock DNA-binding domain-like
domain: S1 RNA-binding domain of polyribonucleotide phosphorylase, PNPase
species: Escherichia coli [TaxId: 562]

Probab=99.68  E-value=1.1e-17  Score=144.59  Aligned_cols=76  Identities=39%  Similarity=0.808  Sum_probs=72.9

Q ss_pred             cccccCcEEEEEEEEEeeceEEEEEcCCeEEEEecccCCCccccccccccccCCEEEEEEEEEccCCceEEEEecc
Q 002054          679 REIEVGGIYKGVVTSVKEYGAFVEFNGGQQGLLHVSELSHEPVSRVSDVVSVGQQLSLRCIGQDVRGNIKLSLKAV  754 (974)
Q Consensus       679 ~~~~~G~i~~G~V~~i~~~G~fV~l~~g~~Glvhisels~~~v~~~~~~~~vGd~V~vkVl~id~~gri~LS~K~~  754 (974)
                      +++++|++|.|+|+++.+||+||+|.++.+||||+|+++|.++.+|++.|++||.|+|+|+++|+++|+.||+|+.
T Consensus         1 ad~kvG~iv~G~V~~v~~~G~fV~l~~~~~Glv~~sels~~~~~~~~~~~~~G~~v~v~Vi~id~~~ri~LS~k~a   76 (76)
T d1sroa_           1 AEIEVGRVYTGKVTRIVDFGAFVAIGGGKEGLVHISQIADKRVEKVTDYLQMGQEVPVKVLEVDRQGRIRLSIKEA   76 (76)
T ss_dssp             CCCCTTSEEEEEEEEEETTEEEEECSSSCCCBCCTTSSCSSCCSCHHHHCCTTCEEEEEEEECCTTCCCEEEECCC
T ss_pred             CCCCCCCEEEEEEEEEeCcEEEEEeCCCCEEEEEhHHhCccccCCHHHccCCCCEEEEEEEEECCCCCEEEEEEcC
Confidence            3689999999999999999999999999999999999999999999999999999999999999989999999973

>d1udsa2 d.101.1.1 (A:151-255) Ribonuclease PH, domain 2 {Aquifex aeolicus [TaxId: 63363]}

class: Alpha and beta proteins (a+b)
fold: Ribonuclease PH domain 2-like
superfamily: Ribonuclease PH domain 2-like
family: Ribonuclease PH domain 2-like
domain: Ribonuclease PH, domain 2
species: Aquifex aeolicus [TaxId: 63363]

Probab=99.68  E-value=3e-17  Score=150.39  Aligned_cols=91  Identities=15%  Similarity=0.177  Sum_probs=79.6

Q ss_pred             CCCCCCeEEEEEEEECCEEEEcCCHHHHhcCccceeEeeeCCe-EEE--EEecCCCCCHHHHHHHHHHHHHHHHHHHHHH
Q 002054          196 IPWGGPIGMIRIGRICGQFIVNPTMDELSLSDLNLVYACTREK-TLM--IDVQAREISEKDLEAGLRLAHPEAVKYLEPQ  272 (974)
Q Consensus       196 iP~~~~v~av~vg~i~g~~vldPt~~e~~~s~~~l~v~~t~~~-i~m--ie~~~~~~~e~~~~~al~~a~~~~~~i~~~~  272 (974)
                      .||++||||||||++||++|+|||++|++.+++||+|++|+++ +++  +.+++++||+++|.+||++|+++|++|+++|
T Consensus         3 ~P~~~~VaAVsvG~idg~~vldp~~~Ed~~~~~dl~va~t~~g~~~ei~~~~e~~~~see~~~eal~~a~~~i~~i~~~Q   82 (105)
T d1udsa2           3 TPIKDFVAAVSVGIVNDRILLDLNFEEDSAAQVDMNVVGTGSGRLSEVHTMGEEYSFTKDELIKMLDLAQKGINELIELQ   82 (105)
T ss_dssp             CCBCCCEEEEEEEEETTEEEESCCHHHHHTCSEEEEEEEETTSCEEEEEEEESSCCCCHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             CCccCCceEEEEEEECCEEeecCCHHHHhcCccceeEEEecCCcchhhhhhhccccccHHHHHHHHHHHHHHHHHHHHHH
Confidence            6999999999999999999999999999999999999999987 444  4455677999999999999999999999999


Q ss_pred             HHHH-HHhCCccccc
Q 002054          273 IRLA-EKAGKQKKEY  286 (974)
Q Consensus       273 ~~~~-~~~g~~k~~~  286 (974)
                      ++++ .+.|+.|+..
T Consensus        83 ke~l~~~~~~~kr~e   97 (105)
T d1udsa2          83 KKLYVIQDGKWERSE   97 (105)
T ss_dssp             HTTEEEETTEEEECS
T ss_pred             HHHHhcccCcccccc
Confidence            9964 4555555543

>d1oysa2 d.101.1.1 (A:152-237) Ribonuclease PH, domain 2 {Bacillus subtilis [TaxId: 1423]}

class: Alpha and beta proteins (a+b)
fold: Ribonuclease PH domain 2-like
superfamily: Ribonuclease PH domain 2-like
family: Ribonuclease PH domain 2-like
domain: Ribonuclease PH, domain 2
species: Bacillus subtilis [TaxId: 1423]

Probab=99.64  E-value=3.1e-16  Score=138.59  Aligned_cols=80  Identities=19%  Similarity=0.156  Sum_probs=75.5

Q ss_pred             CCCCCCeEEEEEEEECCEE-EEcCCHHHHhcCccceeEeeeCCe---EEEEEecCCCCCHHHHHHHHHHHHHHHHHHHHH
Q 002054          196 IPWGGPIGMIRIGRICGQF-IVNPTMDELSLSDLNLVYACTREK---TLMIDVQAREISEKDLEAGLRLAHPEAVKYLEP  271 (974)
Q Consensus       196 iP~~~~v~av~vg~i~g~~-vldPt~~e~~~s~~~l~v~~t~~~---i~mie~~~~~~~e~~~~~al~~a~~~~~~i~~~  271 (974)
                      .||+++|||||||+++|++ ++||+++|++.+++|++|++|+++   .+|++++++.||+++|.+||++|+++|++|++.
T Consensus         2 ~P~~~~VaavsvG~i~~~~vlldl~~~Ed~~~~~D~~va~t~~g~i~~iq~~ge~~~~s~d~~~~al~lA~~gi~~I~~~   81 (86)
T d1oysa2           2 NPITDFLAAISVGIDKEQGILLDLNYEEDSSAEVDMNVIMTGSGRFVELQGTGEEATFSREDLNGLLGLAEKGIQELIDK   81 (86)
T ss_dssp             CCBCSCEEEEEEEEETTTEEEESCCHHHHHHEEEEEEEEEETTSCEEEEEEEESSCCCCHHHHHHHHHHHHHHHHHHHHH
T ss_pred             CCccCcccEEEEEEEcCCcEECCCHHHHhcCCCcceEEEEeCCCCEEEEEEeeccCcccHHHHHHHHHHHHHHHHHHHHH
Confidence            5999999999999999875 689999999999999999999996   579999999999999999999999999999999


Q ss_pred             HHHH
Q 002054          272 QIRL  275 (974)
Q Consensus       272 ~~~~  275 (974)
                      |+++
T Consensus        82 Qkea   85 (86)
T d1oysa2          82 QKEV   85 (86)
T ss_dssp             HHHH
T ss_pred             HHHh
Confidence            9986

>d2nn6f1 d.14.1.4 (F:29-175) Exosome complex exonuclease MTR3 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ribosomal protein S5 domain 2-like
superfamily: Ribosomal protein S5 domain 2-like
family: Ribonuclease PH domain 1-like
domain: Exosome complex exonuclease MTR3
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.64  E-value=3.2e-17  Score=159.58  Aligned_cols=122  Identities=22%  Similarity=0.232  Sum_probs=99.1

Q ss_pred             CeEEEEEeCccCcCCCcEEEEEeCCeEEEEEEEeCCC-CC-C--------------CCceeeEeeccccccccCCCCCcc
Q 002054           67 SRLITLETGKIARFANGAVVLGMDETKVLSTVTSSKG-DS-V--------------RDFLPLTVDYQEKQFAQGVIPNTY  130 (974)
Q Consensus        67 ~r~i~~etg~~a~~A~GSa~v~~G~T~Vl~tv~~~~~-~~-~--------------~~f~pL~v~y~e~~~a~g~ip~~~  130 (974)
                      =|++++++|.+ .+|||||++++|+|+|+|+|++|.+ +. .              .....++++|..+.++.      .
T Consensus         8 ~R~i~i~~gvi-~~a~GSa~v~~G~T~V~~~V~gp~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~------~   80 (147)
T d2nn6f1           8 LRPVYARAGLL-SQAKGSAYLEAGGTKVLCAVSGPRQAEGGERGGGPAGAGGEAPAALRGRLLCDFRRAPFAG------R   80 (147)
T ss_dssp             CCCCCCCCSCC-SSSSEEECCCSSSCEEEEEEEEEECC-------------------CBCEEEEEEEECTTSS------S
T ss_pred             ccceEEEeCCC-CCCCEEEEEEECCeEEEEEEeccccccccccCCccccccccccccccceeEEEEEecCCcc------c
Confidence            38999999999 8999999999999999999999876 21 1              12245677776665443      3


Q ss_pred             ccccCCCCchhhhHHHhhcCCccccccCCC--CCceEEEEEEEeccCCCChhhHHHHHHHHHhhcCCCC
Q 002054          131 MRREGAPKERELLVGRIIDRPIRPLFPAGF--YHEVQVMASVLSSDGKQDPDIMAANATSAALMLSDIP  197 (974)
Q Consensus       131 ~~Reg~p~~~eil~~RlidR~lrplfp~~~--~~~~~i~~~vl~~dg~~~~~~~ai~aAs~AL~~s~iP  197 (974)
                      .++.+.+.+++.++++++++.++++++...  .+.++|.++||+.||+..  .||+|||++||++|||-
T Consensus        81 ~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~i~v~v~Vl~~DG~l~--~a~i~A~~~AL~daGIe  147 (147)
T d2nn6f1          81 RRRAPPGGCEERELALALQEALEPAVRLGRYPRAQLEVSALLLEDGGSAL--AAALTAAALALADAGVE  147 (147)
T ss_dssp             SCCCSCCHHHHHHHHHHHHHHHTTTBCSTTSBTCEEEEEEEEEECCSSHH--HHHHHHHHHHHHHHCCC
T ss_pred             cccccCCccchhhhhhhhhhcccccccccccCCEEEEEEEEEECCCCCHH--HHHHHHHHHHHHHhCCC
Confidence            455678889999999999999999988544  567778889999998866  99999999999999983

>d1oysa1 d.14.1.4 (A:1-151) Ribonuclease PH, domain 1 {Bacillus subtilis [TaxId: 1423]}

class: Alpha and beta proteins (a+b)
fold: Ribosomal protein S5 domain 2-like
superfamily: Ribosomal protein S5 domain 2-like
family: Ribonuclease PH domain 1-like
domain: Ribonuclease PH, domain 1
species: Bacillus subtilis [TaxId: 1423]

Probab=99.63  E-value=3.8e-17  Score=160.11  Aligned_cols=128  Identities=17%  Similarity=0.175  Sum_probs=87.4

Q ss_pred             CeEEEEEeCccCcCCCcEEEEEeCCeEEEEEEEeCCC-CC---CCCceeeEeeccccccccCCCCCccccccCCCCchhh
Q 002054           67 SRLITLETGKIARFANGAVVLGMDETKVLSTVTSSKG-DS---VRDFLPLTVDYQEKQFAQGVIPNTYMRREGAPKEREL  142 (974)
Q Consensus        67 ~r~i~~etg~~a~~A~GSa~v~~G~T~Vl~tv~~~~~-~~---~~~f~pL~v~y~e~~~a~g~ip~~~~~Reg~p~~~ei  142 (974)
                      -|++++++|.+ .+|||||++++|+|+|+|+|+++.+ ++   ..+...++++|.-..++.. .+.+...+.|++++.++
T Consensus        11 ~R~i~i~~g~l-~~a~GSa~v~~G~T~Vl~~V~~~~~~~~~~~~~~~g~~~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~   88 (151)
T d1oysa1          11 LRPITFDLDFI-SHPEGSVLITAGNTKVICNASVEDRVPPFLRGGGKGWITAEYSMLPQATN-QQTIQESSKGKISGRTM   88 (151)
T ss_dssp             CCCEEEECC------CCCEEEEETTEEEEEEEEEESCCCGGGTTSCCCEEEEEEEC--------------------CHHH
T ss_pred             ccCeEEEeCCC-CCCCEEEEEEEcCCEEEEEEEecccccccccccccceeeeeeeecccccc-ccccccccCCcccchhh
Confidence            48999999999 8999999999999999999997655 32   2344567777754443332 22233334478899999


Q ss_pred             hHHHhhcCCcccccc--CCCCCceEEEEEEEeccCCCChhhHHHHHHHHHhhcCCCCC
Q 002054          143 LVGRIIDRPIRPLFP--AGFYHEVQVMASVLSSDGKQDPDIMAANATSAALMLSDIPW  198 (974)
Q Consensus       143 l~~RlidR~lrplfp--~~~~~~~~i~~~vl~~dg~~~~~~~ai~aAs~AL~~s~iP~  198 (974)
                      +++++++|+|+++++  ..+.+.++|.++||+.||+..  +||+|||++||+++.+|+
T Consensus        89 ~~~~~l~~~l~~~i~l~~~~~~~i~v~v~VL~~DG~l~--~a~i~Aa~~AL~dA~~~~  144 (151)
T d1oysa1          89 EIQRLIGRALRAVVDLEKLGERTIWIDCDVIQADGGTR--TASITGAFLAMAIAIGKL  144 (151)
T ss_dssp             HHHHHHHHHHHHTBCHHHHCSCEEEEEEEEEECSSCHH--HHHHHHHHHHHHHHHHHH
T ss_pred             HHhHHHHHHhhhhhhhhhhccceEEEEEEEEcCCCCHH--HHHHHHHHHHHHHHHHHH
Confidence            999999999999876  344668999999999999877  999999999999985543

>d2je6b2 d.101.1.1 (B:156-241) Exosome complex exonuclease 1, ECX1 {Sulfolobus solfataricus [TaxId: 2287]}

class: Alpha and beta proteins (a+b)
fold: Ribonuclease PH domain 2-like
superfamily: Ribonuclease PH domain 2-like
family: Ribonuclease PH domain 2-like
domain: Exosome complex exonuclease 1, ECX1
species: Sulfolobus solfataricus [TaxId: 2287]

Probab=99.57  E-value=4.5e-15  Score=131.17  Aligned_cols=81  Identities=11%  Similarity=0.183  Sum_probs=76.4

Q ss_pred             CCCCCeEEEEEEEECCEEEEcCCHHHHhcCccceeEeeeCC--eEEEEEecCCCCCHHHHHHHHHHHHHHHHHHHHHHHH
Q 002054          197 PWGGPIGMIRIGRICGQFIVNPTMDELSLSDLNLVYACTRE--KTLMIDVQAREISEKDLEAGLRLAHPEAVKYLEPQIR  274 (974)
Q Consensus       197 P~~~~v~av~vg~i~g~~vldPt~~e~~~s~~~l~v~~t~~--~i~mie~~~~~~~e~~~~~al~~a~~~~~~i~~~~~~  274 (974)
                      ||+++|+||+||++||++|+|||++|++.++.|++|+++.+  .++|+|++| ++++++|.+|+++|+++|++|++.|++
T Consensus         1 Pm~d~V~avsvg~~d~~~llDp~~~E~~~~~~~l~va~~~~~~~i~~~~~~g-~~~~~~~~~~l~~a~~~~~~I~~~~~e   79 (86)
T d2je6b2           1 PMRDLIAGVAVGKADGVIILDLNETEAMWGEADMPIAMMPSLNQVTLFQLNG-SMTPDEFRQAFDLAVKGINIIYNLERE   79 (86)
T ss_dssp             CBSSCCEEEEEEEETTEEEESCCHHHHHHSSEEEEEEEEGGGTEEEEEEEEE-CBCHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             CCCCCeEEEEEEEECCEEEEecchhhhhcCceeEEEEEeCCCCeEEEEeecC-CCCHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            99999999999999999999999999999999999998855  499999988 599999999999999999999999999


Q ss_pred             HHHH
Q 002054          275 LAEK  278 (974)
Q Consensus       275 ~~~~  278 (974)
                      .+++
T Consensus        80 ~l~~   83 (86)
T d2je6b2          80 ALKS   83 (86)
T ss_dssp             HHHG
T ss_pred             HHHh
Confidence            8863

>d1kl9a2 b.40.4.5 (A:3-88) Eukaryotic initiation factor 2alpha, eIF2alpha, N-terminal domain {Human (Homo sapiens) [TaxId: 9606]}

class: All beta proteins
fold: OB-fold
superfamily: Nucleic acid-binding proteins
family: Cold shock DNA-binding domain-like
domain: Eukaryotic initiation factor 2alpha, eIF2alpha, N-terminal domain
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.56  E-value=2.6e-15  Score=132.75  Aligned_cols=73  Identities=27%  Similarity=0.438  Sum_probs=57.7

Q ss_pred             cccCcEEEEEEEEEeeceEEEEEc--CCeEEEEecccCCCccccccccccccCCEEEEEEEEEcc-CCceEEEEec
Q 002054          681 IEVGGIYKGVVTSVKEYGAFVEFN--GGQQGLLHVSELSHEPVSRVSDVVSVGQQLSLRCIGQDV-RGNIKLSLKA  753 (974)
Q Consensus       681 ~~~G~i~~G~V~~i~~~G~fV~l~--~g~~Glvhisels~~~v~~~~~~~~vGd~V~vkVl~id~-~gri~LS~K~  753 (974)
                      +++|+++.|+|+++.++|+||+|.  +|++||+|+||++|.++.++.+.|++||.|+|+|+++|+ +++|.||+|+
T Consensus        11 p~~G~iv~G~V~~i~~~G~fV~l~~~~~i~G~i~~sels~~~~~~~~~~~~~Gd~v~~kV~~vd~~~~ki~LS~Kq   86 (86)
T d1kl9a2          11 PEVEDVVMVNVRSIAEMGAYVSLLEYNNIEGMILLSELSRRRIRSINKLIRIGRNECVVVIRVDKEKGYIDLSKRR   86 (86)
T ss_dssp             CCTTCEEEEEEEEECSSEEEEEETTTTTEEEEEEGGGC------------CTTCEEEEEEEEEETTTTEEEEESTT
T ss_pred             CCCCCEEEEEEEEEeCCeEEEEEecCCCEEEEEEeeeccccccccceEEeecccEEEEEEEEEECCCCEEEEEeeC
Confidence            579999999999999999999996  589999999999999999999999999999999999997 8899999985

>d2ahob2 b.40.4.5 (B:1-84) Eukaryotic initiation factor 2alpha, eIF2alpha, N-terminal domain {Sulfolobus solfataricus [TaxId: 2287]}

class: All beta proteins
fold: OB-fold
superfamily: Nucleic acid-binding proteins
family: Cold shock DNA-binding domain-like
domain: Eukaryotic initiation factor 2alpha, eIF2alpha, N-terminal domain
species: Sulfolobus solfataricus [TaxId: 2287]

Probab=99.53  E-value=2.9e-15  Score=131.81  Aligned_cols=74  Identities=31%  Similarity=0.496  Sum_probs=65.1

Q ss_pred             ccccCcEEEEEEEEEeeceEEEEEc--CCeEEEEecccCCCccccccccccccCCEEEEEEEEEcc-CCceEEEEec
Q 002054          680 EIEVGGIYKGVVTSVKEYGAFVEFN--GGQQGLLHVSELSHEPVSRVSDVVSVGQQLSLRCIGQDV-RGNIKLSLKA  753 (974)
Q Consensus       680 ~~~~G~i~~G~V~~i~~~G~fV~l~--~g~~Glvhisels~~~v~~~~~~~~vGd~V~vkVl~id~-~gri~LS~K~  753 (974)
                      .+++|++++|+|+++.+||+||+|.  +|++||+|.||+++.+..++.+.|++||.|+|+|+++|. ++++.||+|+
T Consensus         8 ~p~~G~iv~G~V~~v~~~G~fV~l~~~~gi~Gli~~sels~~~~~~~~~~~~~G~~v~~kV~~vd~~~~~i~LS~Kq   84 (84)
T d2ahob2           8 LPSEGEILIATVKQVFDYGSYVSLDEYGGLQAFLPWSEVSSKWVKNIRDVLKENRKVIVKVIRVDRRKGTVDVSLKK   84 (84)
T ss_dssp             SCCTTCCCEEEEEEEETTEEEEEETTTTTEEEEECGGGCC-----CHHHHTCSSCEEECEEEEEETTTTEEEEESSS
T ss_pred             CCCCCCEEEEEEEEEECCEEEEEECCcCCEEEEEEccccccccccccceEeecccEEEEEEEEEECCCCEEEEEEcC
Confidence            4689999999999999999999996  589999999999999999999999999999999999997 7899999985

>d3bzka4 b.40.4.5 (A:637-730) Tex S1-domain {Pseudomonas aeruginosa [TaxId: 287]}

class: All beta proteins
fold: OB-fold
superfamily: Nucleic acid-binding proteins
family: Cold shock DNA-binding domain-like
domain: Tex S1-domain
species: Pseudomonas aeruginosa [TaxId: 287]

Probab=99.52  E-value=8e-15  Score=131.73  Aligned_cols=79  Identities=33%  Similarity=0.611  Sum_probs=74.9

Q ss_pred             cccccCcEEEEEEEEEeeceEEEEEcCCeEEEEecccCCCccccccccccccCCEEEEEEEEEcc-CCceEEEEeccCCC
Q 002054          679 REIEVGGIYKGVVTSVKEYGAFVEFNGGQQGLLHVSELSHEPVSRVSDVVSVGQQLSLRCIGQDV-RGNIKLSLKAVSPR  757 (974)
Q Consensus       679 ~~~~~G~i~~G~V~~i~~~G~fV~l~~g~~Glvhisels~~~v~~~~~~~~vGd~V~vkVl~id~-~gri~LS~K~~~~~  757 (974)
                      .++++|+++.|+|+++.++|+||+|.++++||||.++++++++.++.+.|++||.|+|+|+++|. +++|.||+|.. ++
T Consensus        14 ~~~k~G~iv~g~V~~v~~~G~~V~l~~~i~G~i~~~~ls~~~~~~~~~~~~vGq~v~~~V~~id~~~~~i~LS~K~~-e~   92 (94)
T d3bzka4          14 KDLKPGMVLEGVVTNVTNFGAFVDIGVHQDGLVHISALSEKFVKDPYEVVKAGDIVKVKVMEVDIPRNRVGLSMRMS-DT   92 (94)
T ss_dssp             GGCCTTCEEEEEEEEEETTEEEEECSSSSCEEEEGGGGCSSCCSCHHHHCCTTCEEEEEEEEEETTTTEEEEESCTT-CC
T ss_pred             hcCCCCCEEEEEEEEEECcEEEEEeCCCceEEeehhhhhcccccChhhhhccCcEEEEEEEEEECCCCEEEEEEecc-CC
Confidence            57899999999999999999999999999999999999999999999999999999999999998 89999999975 55


Q ss_pred             c
Q 002054          758 P  758 (974)
Q Consensus       758 ~  758 (974)
                      |
T Consensus        93 P   93 (94)
T d3bzka4          93 P   93 (94)
T ss_dssp             C
T ss_pred             C
Confidence            5

>d2je6a1 d.14.1.4 (A:1-191) Exosome complex exonuclease 2,ECX2 {Sulfolobus solfataricus [TaxId: 2287]}

class: Alpha and beta proteins (a+b)
fold: Ribosomal protein S5 domain 2-like
superfamily: Ribosomal protein S5 domain 2-like
family: Ribonuclease PH domain 1-like
domain: Exosome complex exonuclease 2,ECX2
species: Sulfolobus solfataricus [TaxId: 2287]

Probab=99.51  E-value=7.2e-15  Score=149.37  Aligned_cols=134  Identities=19%  Similarity=0.200  Sum_probs=100.1

Q ss_pred             CeEEEEEeCccCcCCCcEEEEEeCCeEEEEEEEeCCC-C--CCCCceeeEeeccccccccCCCCCccccccCCCCchhhh
Q 002054           67 SRLITLETGKIARFANGAVVLGMDETKVLSTVTSSKG-D--SVRDFLPLTVDYQEKQFAQGVIPNTYMRREGAPKERELL  143 (974)
Q Consensus        67 ~r~i~~etg~~a~~A~GSa~v~~G~T~Vl~tv~~~~~-~--~~~~f~pL~v~y~e~~~a~g~ip~~~~~Reg~p~~~eil  143 (974)
                      -|++.+++|.+ ++|+|||++++|+|+|+|+|+++.. |  ...+...+.+.+....++...      .+.+.++..+..
T Consensus        37 ~R~i~i~~g~l-~~a~GSa~v~~G~T~V~a~V~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~------~~~~~~~~~~~~  109 (191)
T d2je6a1          37 YRPLSITLDYA-KKADGSALVKLGTTMVLAGTKLEIDKPYEDTPNQGNLIVNVELLPLAYET------FEPGPPDENAIE  109 (191)
T ss_dssp             CCCEEEEETCS-TTSSEEEEEEETTEEEEEEEEEEEECCCTTCTTCCEEEEEEEECTTSCTT------CCCSSCCHHHHH
T ss_pred             ccCeEEEECCc-cCcCceEEEEcCCceEEEEEEecccCchhccCccCccccccccccccccc------cccccCCcchhH
Confidence            47899999999 8999999999999999999999865 2  223344555665544433321      223567777787


Q ss_pred             HHHhhcCCccc----------cccCCCCCceEEEEEEEeccCCCChhhHHHHHHHHHhhcCCCCC-CCCeEEEEEEE
Q 002054          144 VGRIIDRPIRP----------LFPAGFYHEVQVMASVLSSDGKQDPDIMAANATSAALMLSDIPW-GGPIGMIRIGR  209 (974)
Q Consensus       144 ~~RlidR~lrp----------lfp~~~~~~~~i~~~vl~~dg~~~~~~~ai~aAs~AL~~s~iP~-~~~v~av~vg~  209 (974)
                      +++++.|.++.          ++|..+.+.+.|.++||++||+..  .||++|+++||++++||. .-...++.++.
T Consensus       110 l~~~l~~~~~~~~~id~~~l~i~~~~~~w~I~v~v~VL~~DG~l~--dA~~~A~~~AL~da~iP~v~~~~~~~~v~~  184 (191)
T d2je6a1         110 LARVVDRSLRDSKALDLTKLVIEPGKSVWTVWLDVYVLDYGGNVL--DACTLASVAALYNTKVYKVEQHSNGISVNK  184 (191)
T ss_dssp             HHHHHHHHHHHTTCSCGGGGEEETTTEEEEEEEEEEEEECCSCHH--HHHHHHHHHHHHTCEEEEEECC---CEEEE
T ss_pred             HHHHHHHhhcchhhcccccccccCccccEEEEEEEEEEcCCCCHH--HHHHHHHHHHHHHcCCCeEEeecCceeecC
Confidence            88877766542          456778889999999999999777  899999999999999995 55666666654

>d2ba0a1 b.40.4.5 (A:53-135) S1-domain of exosome complex RNA-binding protein 1, ECR1 {Archaeoglobus fulgidus [TaxId: 2234]}

class: All beta proteins
fold: OB-fold
superfamily: Nucleic acid-binding proteins
family: Cold shock DNA-binding domain-like
domain: S1-domain of exosome complex RNA-binding protein 1, ECR1
species: Archaeoglobus fulgidus [TaxId: 2234]

Probab=99.51  E-value=1.2e-14  Score=127.42  Aligned_cols=77  Identities=22%  Similarity=0.328  Sum_probs=71.9

Q ss_pred             cccCcEEEEEEEEEeeceEEEEEcCCeEEEEecccCCCcc-ccccccccccCCEEEEEEEEEccCCceEEEEeccCCC
Q 002054          681 IEVGGIYKGVVTSVKEYGAFVEFNGGQQGLLHVSELSHEP-VSRVSDVVSVGQQLSLRCIGQDVRGNIKLSLKAVSPR  757 (974)
Q Consensus       681 ~~~G~i~~G~V~~i~~~G~fV~l~~g~~Glvhisels~~~-v~~~~~~~~vGd~V~vkVl~id~~gri~LS~K~~~~~  757 (974)
                      +++|+++.|+|+++.++|+||+|.++.+||||+||+++.+ ..++.+.|++||.|+|+|+++|+++++.||+|+....
T Consensus         3 Pk~Gd~V~G~V~~v~~~g~~V~i~~~~~g~l~~se~s~~~~~~~~~~~~~vGd~V~~kV~~vd~~~~i~LS~k~~~~~   80 (83)
T d2ba0a1           3 PSVGDVVIGIIREVAANGWAVDIYSPYQAFLPVSENPEMKPNKKPNEVLDIGDAIIAKVLNIDPKMKVTLTMKDRICR   80 (83)
T ss_dssp             CCTTCEEEEEEEEECSSEEEEECSSSSCEEEEGGGCTTCCTTSCGGGTCCTTCEEEEEEEEECTTCCEEEECCSSSCE
T ss_pred             CCCCCEEEEEEEEEECCEEEEecCCCeeEEEecccccccccccChhhhcccccEEEEEEEEECCCCCEEEEecCCCCC
Confidence            7899999999999999999999999999999999999875 7789999999999999999999889999999986543

>d2nn6b2 d.101.1.1 (B:151-240) Exosome complex exonuclease RRP41 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ribonuclease PH domain 2-like
superfamily: Ribonuclease PH domain 2-like
family: Ribonuclease PH domain 2-like
domain: Exosome complex exonuclease RRP41
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.51  E-value=1.4e-14  Score=129.08  Aligned_cols=85  Identities=16%  Similarity=0.151  Sum_probs=78.5

Q ss_pred             CCCCCeEEEEEEEECCEEEEcCCHHHHhcCccceeEe--eeCCeEEEEEecCCCCCHHHHHHHHHHHHHHHHHHHHHHHH
Q 002054          197 PWGGPIGMIRIGRICGQFIVNPTMDELSLSDLNLVYA--CTREKTLMIDVQAREISEKDLEAGLRLAHPEAVKYLEPQIR  274 (974)
Q Consensus       197 P~~~~v~av~vg~i~g~~vldPt~~e~~~s~~~l~v~--~t~~~i~mie~~~~~~~e~~~~~al~~a~~~~~~i~~~~~~  274 (974)
                      ||++.|+||++|++||++++|||++|++.++.+|+|+  ++.+.|+|+|+++ +|++++|.+++++|+++|++|++.|++
T Consensus         1 Pm~d~V~avs~g~~~~~~llDp~~~E~~~~~~~l~va~~~~~~~I~~~~~~g-~~~~~~~~~~l~~a~~~~~~i~~~~~~   79 (90)
T d2nn6b2           1 PMRDFVCACSAGFVDGTALADLSHVEEAAGGPQLALALLPASGQIALLEMDA-RLHEDHLERVLEAAAQAARDVHTLLDR   79 (90)
T ss_dssp             CCSSCCEEEEEEEETTEEEESCCHHHHTSSCCCEEEEEETTTTEEEEEEECS-CCBTTSHHHHHHHHHHHHHHHHHHHHH
T ss_pred             CCCCCeEEEEEEEECCEEeeCCccccccccccceEEEEEecCCCEEEEEEec-ccCHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            9999999999999999999999999999999888887  5566799999998 599999999999999999999999999


Q ss_pred             HHHHhCCc
Q 002054          275 LAEKAGKQ  282 (974)
Q Consensus       275 ~~~~~g~~  282 (974)
                      ++++..++
T Consensus        80 ~l~~~~~e   87 (90)
T d2nn6b2          80 VVRQHVRE   87 (90)
T ss_dssp             HHHHHHHH
T ss_pred             HHHhhhhh
Confidence            99887654

>d2ba0g1 d.14.1.4 (G:3-178) Exosome complex exonuclease 2,ECX2 {Archaeoglobus fulgidus [TaxId: 2234]}

class: Alpha and beta proteins (a+b)
fold: Ribosomal protein S5 domain 2-like
superfamily: Ribosomal protein S5 domain 2-like
family: Ribonuclease PH domain 1-like
domain: Exosome complex exonuclease 2,ECX2
species: Archaeoglobus fulgidus [TaxId: 2234]

Probab=99.50  E-value=1.1e-14  Score=146.09  Aligned_cols=125  Identities=26%  Similarity=0.268  Sum_probs=94.8

Q ss_pred             CeEEEEEeCccCcCCCcEEEEEeCCeEEEEEEEeCCC---CCCCCceeeEeeccccccccCCCCCccccccCCCCchhhh
Q 002054           67 SRLITLETGKIARFANGAVVLGMDETKVLSTVTSSKG---DSVRDFLPLTVDYQEKQFAQGVIPNTYMRREGAPKERELL  143 (974)
Q Consensus        67 ~r~i~~etg~~a~~A~GSa~v~~G~T~Vl~tv~~~~~---~~~~~f~pL~v~y~e~~~a~g~ip~~~~~Reg~p~~~eil  143 (974)
                      -|++.+++|.+ .+|+|||++++|+|+|+|+|+++..   +...+...+.+.+.-..++...      .+.|++++++..
T Consensus        30 ~R~i~i~~g~l-~~a~GSa~v~~G~T~V~~~V~~~~~~p~~~~~~~g~~~~~v~~~~~~~~~------~~~~~~~~~~~~  102 (176)
T d2ba0g1          30 FRKVEIIPNVI-EKAEGSALVKLGDTQVVVGVKMQPGEPYPDTPDRGVIIVNAELVPLASPT------FEPGPPDENSIE  102 (176)
T ss_dssp             CCCEEEEECCC-TTSSEEEEEEETTEEEEEEEEEEEECCCTTCTTCCEEEEEEECCTTTCTT------SCSSSCCHHHHH
T ss_pred             ccCeEEEeCcc-CCCCeEEEEEeCCcEEEEEEeccccccccccCCCceeeeeeEeccccCcc------ccCCCCCchhHH
Confidence            47899999999 8999999999999999999987543   2223344455554333332211      122778899999


Q ss_pred             HHHhhcCCccc--------c--ccCCCCCceEEEEEEEeccCCCChhhHHHHHHHHHhhcCCCCCCC
Q 002054          144 VGRIIDRPIRP--------L--FPAGFYHEVQVMASVLSSDGKQDPDIMAANATSAALMLSDIPWGG  200 (974)
Q Consensus       144 ~~RlidR~lrp--------l--fp~~~~~~~~i~~~vl~~dg~~~~~~~ai~aAs~AL~~s~iP~~~  200 (974)
                      +++++.+.+++        |  .|..+.+.+.|.++||+.||+..  .||+||+++||.+++||+..
T Consensus       103 ~~~~l~~~~~~~~~i~~e~L~i~~~~~~~~i~i~v~VL~~DG~l~--dA~~~A~~~AL~da~iP~~~  167 (176)
T d2ba0g1         103 LARVVDRGIRESEAVDLSKLVIEEGEKVWIVFVDIHALDDDGNLL--DASALAAIAALMNTKVPAER  167 (176)
T ss_dssp             HHHHHHHHHHHTTCBCGGGGEEETTTEEEEEEEEEEEEECSSCHH--HHHHHHHHHHHTTCEECTGG
T ss_pred             HHHHHHHhhccccccchhhccCCCCCceEEEEEEEEEEeCCCCHH--HHHHHHHHHHHHHcCCCcEE
Confidence            99999988755        1  23344567888899999999866  99999999999999999865

>d2nn6c1 d.14.1.4 (C:7-187) Exosome complex exonuclease RRP43 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ribosomal protein S5 domain 2-like
superfamily: Ribosomal protein S5 domain 2-like
family: Ribonuclease PH domain 1-like
domain: Exosome complex exonuclease RRP43
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.47  E-value=3.8e-14  Score=142.28  Aligned_cols=123  Identities=20%  Similarity=0.198  Sum_probs=96.6

Q ss_pred             CeEEEEEeCccCcCCCcEEEEEeCCeEEEEEEEeCCCCC---CCCceeeEeeccccccccCCCCCccccccCCCCchhhh
Q 002054           67 SRLITLETGKIARFANGAVVLGMDETKVLSTVTSSKGDS---VRDFLPLTVDYQEKQFAQGVIPNTYMRREGAPKERELL  143 (974)
Q Consensus        67 ~r~i~~etg~~a~~A~GSa~v~~G~T~Vl~tv~~~~~~~---~~~f~pL~v~y~e~~~a~g~ip~~~~~Reg~p~~~eil  143 (974)
                      -|++.+++|.+ ++|+|||++++|+|+|+|+|+++..++   ..+...+.+.+....++...      .+.+.+++.+.+
T Consensus        26 ~R~~~i~~g~l-~~a~GSa~v~~G~T~v~~~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~------~~~~~~~~~~~~   98 (181)
T d2nn6c1          26 FRTTTVNIGSI-STADGSALVKLGNTTVICGVKAEFAAPSTDAPDKGYVVPNVDLPPLCSSR------FRSGPPGEEAQV   98 (181)
T ss_dssp             CCSCCEEETCC-SSSSEEEEEEETTEEEEEEEEEEECCCCSSSTTCCCCEEEEECCSSSCTT------SCSSSCCHHHHH
T ss_pred             ccCeEEEeCCc-CCCCeEEEEEeCCcEEEEEEeccccccccccCCCceeeeeeeeecccccc------ccccCCCchhhh
Confidence            57899999999 899999999999999999999876521   12234455554444333321      123667788888


Q ss_pred             HHHhhcCCccc----------cccCCCCCceEEEEEEEeccCCCChhhHHHHHHHHHhhcCCCCC
Q 002054          144 VGRIIDRPIRP----------LFPAGFYHEVQVMASVLSSDGKQDPDIMAANATSAALMLSDIPW  198 (974)
Q Consensus       144 ~~RlidR~lrp----------lfp~~~~~~~~i~~~vl~~dg~~~~~~~ai~aAs~AL~~s~iP~  198 (974)
                      +++.+.|.++.          +++..+++.+.|.++||+.||+..  .||++||++||++++||.
T Consensus        99 ~~~~~~~~~~~~~~~~~~~l~i~~~~~~~~i~i~v~vl~~DG~l~--da~~~A~~~AL~d~~iP~  161 (181)
T d2nn6c1          99 ASQFIADVIENSQIIQKEDLCISPGKLVWVLYCDLICLDYDGNIL--DACTFALLAALKNVQLPE  161 (181)
T ss_dssp             HHHHHHHHHHHHCCSCHHHHCSSBTTBCEEEEEEEEESSCCSCTT--HHHHHHHHHHHHTCCCCC
T ss_pred             hHHHHHHHHHhhhhhhhhhccccCCcceEEEEEEEEEecCCCCHH--HHHHHHHHHHHHhcCCCe
Confidence            88888877663          467888999999999999999888  999999999999999996

>d2ba0d2 d.101.1.1 (D:154-252) Exosome complex exonuclease 1, ECX1 {Archaeoglobus fulgidus [TaxId: 2234]}

class: Alpha and beta proteins (a+b)
fold: Ribonuclease PH domain 2-like
superfamily: Ribonuclease PH domain 2-like
family: Ribonuclease PH domain 2-like
domain: Exosome complex exonuclease 1, ECX1
species: Archaeoglobus fulgidus [TaxId: 2234]

Probab=99.46  E-value=5.2e-14  Score=127.60  Aligned_cols=81  Identities=17%  Similarity=0.347  Sum_probs=71.9

Q ss_pred             CCCCCeEEEEEEEECCEEEEcCCHHHHhcCccceeEeeeCCeEEEEE-----ecCCCCCHHHHHHHHHHHHHHHHHHHHH
Q 002054          197 PWGGPIGMIRIGRICGQFIVNPTMDELSLSDLNLVYACTREKTLMID-----VQAREISEKDLEAGLRLAHPEAVKYLEP  271 (974)
Q Consensus       197 P~~~~v~av~vg~i~g~~vldPt~~e~~~s~~~l~v~~t~~~i~mie-----~~~~~~~e~~~~~al~~a~~~~~~i~~~  271 (974)
                      ||+++|+|||||++||++++|||+.|++.+++||+|+++.+...|+|     .. +.|++++|.+|+++|+++|++|++.
T Consensus         1 Pm~~~V~avsvG~~d~~~llDp~~~E~~~~~~~l~va~~~~~~~~~ei~~~~~~-~~~~~~~~~~~l~~a~~~~~~I~~~   79 (99)
T d2ba0d2           1 PMKGMITSVAVGKADGQLVLDPMKEEDNFGEADMPFAFLIRNGKIESIALLQMD-GRMTRDEVKQAIELAKKGALQIYEM   79 (99)
T ss_dssp             CBSSEEEEEEEEEETTEEEESCCHHHHHHSSEEEEEEEEEETTEEEEEEEEEEE-EEECHHHHHHHHHHHHHHHHHHHHH
T ss_pred             CCCCcEEEEEEEEECCEEEEcCCcchhhcccCceEEEEecCcceEEEEEEEecc-ccchHHHHHHHHHHHHHHHHHHHHH
Confidence            99999999999999999999999999999999999998776533333     33 3599999999999999999999999


Q ss_pred             HHHHHHH
Q 002054          272 QIRLAEK  278 (974)
Q Consensus       272 ~~~~~~~  278 (974)
                      |++.+++
T Consensus        80 ~~~alk~   86 (99)
T d2ba0d2          80 QREAILR   86 (99)
T ss_dssp             HHHHHHH
T ss_pred             HHHHHhh
Confidence            9988765

>d1r6la2 d.101.1.1 (A:152-239) Ribonuclease PH, domain 2 {Pseudomonas aeruginosa [TaxId: 287]}

class: Alpha and beta proteins (a+b)
fold: Ribonuclease PH domain 2-like
superfamily: Ribonuclease PH domain 2-like
family: Ribonuclease PH domain 2-like
domain: Ribonuclease PH, domain 2
species: Pseudomonas aeruginosa [TaxId: 287]

Probab=99.46  E-value=1.1e-13  Score=122.54  Aligned_cols=86  Identities=26%  Similarity=0.327  Sum_probs=82.0

Q ss_pred             CCCccccccceeeeeeccCCCCCCcccceEEEecCCccccccCCccEEEEeeCCc-eEEEEeeccCCCCCHHHHHHHHHH
Q 002054          509 GIPLQEHVAGVSVGLVSEVDPSTGEIKDYRILTDILGLEDHLGDMDFKIAGTRIG-VTAIQLDIKPAGIPLDIICECLEH  587 (974)
Q Consensus       509 gvPi~~~vagvs~gli~~~d~~~~~~~~~~iL~Dp~~~Ee~~~d~d~~Va~t~~g-I~alq~~~k~~~i~~e~l~~al~~  587 (974)
                      |+||+++||||++|++++           .+++||+..|+..+++|+.+++|.+| ++.+|+++....+|.++|.+++++
T Consensus         2 g~P~~~~VaavsvG~idg-----------~~vld~~~~E~~~~~~Dl~va~t~~g~i~~iq~~ge~~~~sed~~~~al~~   70 (88)
T d1r6la2           2 GNPLKQMVAAVSVGIYQG-----------VPVLDLDYLEDSAAETDLNVVMTDAGGFIEVQGTAEGAPFRPAELNAMLEL   70 (88)
T ss_dssp             SCCBCCCEEEEEEEEETT-----------EEEESCCHHHHHHCSEEEEEEEETTSCEEEEEEEESSSCCCHHHHHHHHHH
T ss_pred             CCCcCCCccEEEEEEECC-----------EEEecCcHHhhccCceeEEEEEeCCCCEEeehhhcccCCCCHHHHHHHHHH
Confidence            899999999999999976           79999999999999999999999997 899999998889999999999999


Q ss_pred             HHHHHHHHHHHHHHHhcC
Q 002054          588 AHKGRLQILDHMEREISA  605 (974)
Q Consensus       588 A~~~~~~I~~~m~~~i~~  605 (974)
                      |++++++|++.|++++++
T Consensus        71 A~~~i~~i~~~Qkeal~e   88 (88)
T d1r6la2          71 AQQGMQELFELQRAALAE   88 (88)
T ss_dssp             HHHHHHHHHHHHHHHHTC
T ss_pred             HHHHHHHHHHHHHHHhcC
Confidence            999999999999999864

>d2nn6e1 d.14.1.4 (E:5-191) Exosome complex exonuclease RRP42 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ribosomal protein S5 domain 2-like
superfamily: Ribosomal protein S5 domain 2-like
family: Ribonuclease PH domain 1-like
domain: Exosome complex exonuclease RRP42
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.46  E-value=4e-14  Score=143.26  Aligned_cols=121  Identities=18%  Similarity=0.131  Sum_probs=95.1

Q ss_pred             CeEEEEEeCccCcCCCcEEEEEeCCeEEEEEEEeCCC-CC--CCCceeeEeeccccccccCCCCCcccccc-CCCCchhh
Q 002054           67 SRLITLETGKIARFANGAVVLGMDETKVLSTVTSSKG-DS--VRDFLPLTVDYQEKQFAQGVIPNTYMRRE-GAPKEREL  142 (974)
Q Consensus        67 ~r~i~~etg~~a~~A~GSa~v~~G~T~Vl~tv~~~~~-~~--~~~f~pL~v~y~e~~~a~g~ip~~~~~Re-g~p~~~ei  142 (974)
                      -|++.+++|.+ .+|+|||++++|+|+|+|+|+++.. +.  ..+...+.+++.-..++..       .+. +++++++.
T Consensus        28 ~R~i~i~~g~l-~~a~GSa~v~~G~T~V~~~V~~~~~~~~~~~~~~g~~~~~v~~~~~~~~-------~~~~~~~~~~~~   99 (187)
T d2nn6e1          28 YRCVEVETDVV-SNTSGSARVKLGHTDILVGVKAEMGTPKLEKPNEGYLEFFVDCSASATP-------EFEGRGGDDLGT   99 (187)
T ss_dssp             CCCCEEEECCC-TTSSSEEEEEETTEEEEEECCCCCSCCCSSSCSSCCEEEECCCCTTTCS-------SCCTTSTHHHHH
T ss_pred             ccCeEEEeCcc-CCCCceEEEEeCCceEEEEEEeccccccccccccceeeeeeeecccccc-------CcCCCCcchHHH
Confidence            58899999999 7999999999999999999998765 21  1222335555543333332       222 45778888


Q ss_pred             hHHHhhcCCccc----------cccCCCCCceEEEEEEEeccCCCChhhHHHHHHHHHhhcCCCC
Q 002054          143 LVGRIIDRPIRP----------LFPAGFYHEVQVMASVLSSDGKQDPDIMAANATSAALMLSDIP  197 (974)
Q Consensus       143 l~~RlidR~lrp----------lfp~~~~~~~~i~~~vl~~dg~~~~~~~ai~aAs~AL~~s~iP  197 (974)
                      ++++++.|.|++          +.|..+.+.+.|.++||+.||+..  .||++|+++||.+++||
T Consensus       100 ~ls~~l~~~l~~~~~~d~~~L~i~~~~~~w~i~v~v~vL~~DG~~~--da~~~A~~~AL~d~~iP  162 (187)
T d2nn6e1         100 EIANTLYRIFNNKSSVDLKTLCISPREHCWVLYVDVLLLECGGNLF--DAISIAVKAALFNTRIP  162 (187)
T ss_dssp             HHHHHHHHHHHHSCCSCSSSSCSSTTTCCCCEEEEEEECCCCSSHH--HHHHHHHHHTTTTCCCC
T ss_pred             HHHHHHHHHhccccccchhhheecCCCccEEEEEEEEEeCCCCCHH--HHHHHHHHHHHHhcCCC
Confidence            999999999876          245677889999999999999866  99999999999999999

>d2je6i1 b.40.4.5 (I:66-152) S1-domain of exosome complex RNA-binding protein 1, ECR1 {Sulfolobus solfataricus [TaxId: 2287]}

class: All beta proteins
fold: OB-fold
superfamily: Nucleic acid-binding proteins
family: Cold shock DNA-binding domain-like
domain: S1-domain of exosome complex RNA-binding protein 1, ECR1
species: Sulfolobus solfataricus [TaxId: 2287]

Probab=99.42  E-value=6.9e-14  Score=123.69  Aligned_cols=75  Identities=23%  Similarity=0.262  Sum_probs=69.4

Q ss_pred             ccccCcEEEEEEEEEeeceEEEEEcCCeEEEEecccCCCcccc---ccccccccCCEEEEEEEEEccCCceEEEEecc
Q 002054          680 EIEVGGIYKGVVTSVKEYGAFVEFNGGQQGLLHVSELSHEPVS---RVSDVVSVGQQLSLRCIGQDVRGNIKLSLKAV  754 (974)
Q Consensus       680 ~~~~G~i~~G~V~~i~~~G~fV~l~~g~~Glvhisels~~~v~---~~~~~~~vGd~V~vkVl~id~~gri~LS~K~~  754 (974)
                      .+++|+++.|+|+++.+||+||+|.++.+||||+|+++++++.   ++.+.|++||.|.|+|+++|+++++.||+|+.
T Consensus         4 ~Pk~Gdiv~G~V~~i~~~g~fV~i~~~~~gll~~s~~~~~~~~~~~~~~~~~~~Gd~v~~kV~~vd~~~~i~LS~k~~   81 (87)
T d2je6i1           4 YPKINDIVIGLVEDVEIYGWVVDIKAPYKAYLPASNLLGRSINVGEDLRRYLDVGDYVIARIENFDRSIDPVLSVKGK   81 (87)
T ss_dssp             CCCTTCEEEEEEEEECSSEEEEECSSSSCEEEEHHHHHTSCCCTTCCCSSSCCTTCEEEEEEEEEETTEEEEEECCST
T ss_pred             cCCCCCEEEEEEEEEECCEEEEEeCCCEEEEEehHHhCCceeccccccchhhcccceEEEEEEEECCCCCEEEEEecC
Confidence            3789999999999999999999999999999999999998764   57778999999999999999989999999974

>d1go3e1 b.40.4.5 (E:79-184) C-terminal domain of RNA polymerase II subunit RBP7 (RpoE) {Archaeon Methanococcus jannaschii [TaxId: 2190]}

class: All beta proteins
fold: OB-fold
superfamily: Nucleic acid-binding proteins
family: Cold shock DNA-binding domain-like
domain: C-terminal domain of RNA polymerase II subunit RBP7 (RpoE)
species: Archaeon Methanococcus jannaschii [TaxId: 2190]

Probab=99.42  E-value=1.4e-13  Score=126.18  Aligned_cols=80  Identities=24%  Similarity=0.385  Sum_probs=70.7

Q ss_pred             cccCcEEEEEEEEEeeceEEEEEcCCeEEEEecccCCCccc-----------cccccccccCCEEEEEEEEEcc-CC---
Q 002054          681 IEVGGIYKGVVTSVKEYGAFVEFNGGQQGLLHVSELSHEPV-----------SRVSDVVSVGQQLSLRCIGQDV-RG---  745 (974)
Q Consensus       681 ~~~G~i~~G~V~~i~~~G~fV~l~~g~~Glvhisels~~~v-----------~~~~~~~~vGd~V~vkVl~id~-~g---  745 (974)
                      +++|++|+|+|++|.+||+||+|. +++||||+|+|+++++           .++.+.|++||.|+|+|+++|. ++   
T Consensus         1 p~~gei~~g~V~~v~~~G~FVel~-~ieGlv~~s~l~~~~~~~~~~~~~~~~~~~~~~~~~Gd~v~vkV~~vd~~~~~~~   79 (106)
T d1go3e1           1 PEMYELIEGEVVDVVEFGSFVRLG-PLDGLIHVSQIMDDYVSYDPKREAIIGKETGKVLEIGDYVRARIVAISLKAERKR   79 (106)
T ss_dssp             CCTTCEEEEEEEEEETTEEEEECS-SSEEEEEGGGSCSSCEEECCC--CEEETTTCCEECTTCEEEEEEEEEECCC----
T ss_pred             CCCCCEEEEEEEEEeeeEEEEEee-CeEEEEEeecccCceeeeccceeEEeecccccceeecceEEEEEEEEchhhcccc
Confidence            578999999999999999999995 7999999999999887           3778899999999999999996 33   


Q ss_pred             --ceEEEEeccCCCcccc
Q 002054          746 --NIKLSLKAVSPRPEAD  761 (974)
Q Consensus       746 --ri~LS~K~~~~~~~~~  761 (974)
                        ++.||+|+....||+.
T Consensus        80 ~~~i~ls~K~~~~~~~e~   97 (106)
T d1go3e1          80 GSKIALTMRQPYLGKLEW   97 (106)
T ss_dssp             -CEEEEECCSTTCEEHHH
T ss_pred             CceeecccccCCCCcchh
Confidence              4889999988887764

>d1whua_ a.4.9.1 (A:) Polynucleotide phosphorylase/guanosine pentaphosphate synthase (PNPase/GPSI), domain 3 {Mouse (Mus musculus) [TaxId: 10090]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Polynucleotide phosphorylase/guanosine pentaphosphate synthase (PNPase/GPSI), domain 3
family: Polynucleotide phosphorylase/guanosine pentaphosphate synthase (PNPase/GPSI), domain 3
domain: Polynucleotide phosphorylase/guanosine pentaphosphate synthase (PNPase/GPSI), domain 3
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.41  E-value=5.7e-13  Score=121.18  Aligned_cols=87  Identities=31%  Similarity=0.357  Sum_probs=79.6

Q ss_pred             CCCHHHHHHHHHHHHHHHHhhhcCCCCChhHHHHHHHHHHHHHHHHhhhccchhhhchHHHHHHHHHHHHHHHHHHhcCC
Q 002054          290 MISEQTLEKVSNLAEAHIEAVFTDPSYSKFERGEALDKIGQDVKKALEEECDEESLQVLPKAVDTVRKRVIRKRIIAEGV  369 (974)
Q Consensus       290 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~k~~r~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~r~~il~~~~  369 (974)
                      .++++|.+.|++++.++|++++++..++|++|++++++|++++.+.|.++.++.+..++..+|+.++++.+|++||++|+
T Consensus        13 ~~~eel~~~V~~~~~~ki~~a~~~~~~dK~eR~~al~~ik~ei~~~l~e~~~~~~~~~i~~af~~v~k~ivR~~IL~~~~   92 (104)
T d1whua_          13 TPSAEIVKYTKIIAMEKLYAVFTDYEHDKVSRDEAVNKIRLDTEEHLKEKFPEVDQFEIIESFNIVAKEVFRSIILNEYK   92 (104)
T ss_dssp             CCCHHHHHHHHHHHHHHHHHHHSSCCSCSHHHHHHHHHHHHHHHHHHTTTCSSSCHHHHHHHHHHHHHHHHHHHHTTSSC
T ss_pred             CCCHHHHHHHHHHHHHHHHHHHHhcccCHHHHHHHHHHHHHHHHHHHhhcccccCHHHHHHHHHHHHHHHHHHHHHcCCC
Confidence            45789999999999999999998766899999999999999999999887665566789999999999999999999999


Q ss_pred             cCCCCCC
Q 002054          370 RVDGRQL  376 (974)
Q Consensus       370 R~DGR~~  376 (974)
                      |+|||..
T Consensus        93 RiDGRd~   99 (104)
T d1whua_          93 RCDGRDS   99 (104)
T ss_dssp             SCCCCCS
T ss_pred             cCCCCCC
Confidence            9999954

>d1sroa_ b.40.4.5 (A:) S1 RNA-binding domain of polyribonucleotide phosphorylase, PNPase {Escherichia coli [TaxId: 562]}

class: All beta proteins
fold: OB-fold
superfamily: Nucleic acid-binding proteins
family: Cold shock DNA-binding domain-like
domain: S1 RNA-binding domain of polyribonucleotide phosphorylase, PNPase
species: Escherichia coli [TaxId: 562]

Probab=99.40  E-value=9.6e-14  Score=119.53  Aligned_cols=69  Identities=20%  Similarity=0.364  Sum_probs=63.7

Q ss_pred             ccCCCCCEEEEEEEEEeCCeEEEEeCCCeEEEEecccCC-------CCCCCCCCEEEEEEEEEeCCCceeeeecCC
Q 002054          906 KNLKLGTKVAAKVYQVRARGLVLDLGGGIRGMYRFENNE-------KKDFVVGDELLVKCSSFTGKGIPVVSLVDS  974 (974)
Q Consensus       906 ~~~~vG~vV~G~V~~I~~~GvFV~L~~gv~Glih~se~~-------~~~f~vGd~V~vkVl~id~~~~~~~~~~~~  974 (974)
                      +++++|++++|+|++|++||+||+|++++.||+|.+++.       .+.|++||+|+|+|+++|++++..+|+.++
T Consensus         1 ad~kvG~iv~G~V~~v~~~G~fV~l~~~~~Glv~~sels~~~~~~~~~~~~~G~~v~v~Vi~id~~~ri~LS~k~a   76 (76)
T d1sroa_           1 AEIEVGRVYTGKVTRIVDFGAFVAIGGGKEGLVHISQIADKRVEKVTDYLQMGQEVPVKVLEVDRQGRIRLSIKEA   76 (76)
T ss_dssp             CCCCTTSEEEEEEEEEETTEEEEECSSSCCCBCCTTSSCSSCCSCHHHHCCTTCEEEEEEEECCTTCCCEEEECCC
T ss_pred             CCCCCCCEEEEEEEEEeCcEEEEEeCCCCEEEEEhHHhCccccCCHHHccCCCCEEEEEEEEECCCCCEEEEEEcC
Confidence            478999999999999999999999999999999999885       234999999999999999999999999875

>d2je6a2 d.101.1.1 (A:192-275) Exosome complex exonuclease 2, ECX2 {Sulfolobus solfataricus [TaxId: 2287]}

class: Alpha and beta proteins (a+b)
fold: Ribonuclease PH domain 2-like
superfamily: Ribonuclease PH domain 2-like
family: Ribonuclease PH domain 2-like
domain: Exosome complex exonuclease 2, ECX2
species: Sulfolobus solfataricus [TaxId: 2287]

Probab=99.40  E-value=6.7e-13  Score=116.43  Aligned_cols=80  Identities=23%  Similarity=0.336  Sum_probs=75.0

Q ss_pred             CCCCCeEEEEEEEECCEEEEcCCHHHHhcCccceeEeeeCCe--EEEEEecCCCCCHHHHHHHHHHHHHHHHHHHHHHHH
Q 002054          197 PWGGPIGMIRIGRICGQFIVNPTMDELSLSDLNLVYACTREK--TLMIDVQAREISEKDLEAGLRLAHPEAVKYLEPQIR  274 (974)
Q Consensus       197 P~~~~v~av~vg~i~g~~vldPt~~e~~~s~~~l~v~~t~~~--i~mie~~~~~~~e~~~~~al~~a~~~~~~i~~~~~~  274 (974)
                      ||++++++||+|++++++++|||++|+..++.+|+|+.++++  +.|.+.++..+++++|.+|+++|++.++++++.+++
T Consensus         1 P~~~~~~~vt~~~i~~~~lvDpt~~EE~~~~~~l~v~~~~~g~i~~~~k~g~~~~~~~~i~~~i~~A~~~~~~l~~~l~~   80 (84)
T d2je6a2           1 PLNYPVVTISVAKVDKYLVVDPDLDEESIMDAKISFSYTPDLKIVGIQKSGKGSMSLQDIDQAENTARSTAVKLLEELKK   80 (84)
T ss_dssp             CCSCCCEEEEEEEETTEEEESCCHHHHHHCSEEEEEEECTTCCEEEEEEESSSCEEHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             CCCCCeEEEEEEEECCEEEecCCHHHHHhcCCceeeeecCCCceeeEEeccCCcCCHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            999999999999999999999999999999999999999987  556677778899999999999999999999999988


Q ss_pred             HH
Q 002054          275 LA  276 (974)
Q Consensus       275 ~~  276 (974)
                      .+
T Consensus        81 ~l   82 (84)
T d2je6a2          81 HL   82 (84)
T ss_dssp             HH
T ss_pred             Hh
Confidence            65

>d2z0sa1 b.40.4.5 (A:60-147) S1-domain of exosome complex RNA-binding protein 1, ECR1 {Aeropyrum pernix [TaxId: 56636]}

class: All beta proteins
fold: OB-fold
superfamily: Nucleic acid-binding proteins
family: Cold shock DNA-binding domain-like
domain: S1-domain of exosome complex RNA-binding protein 1, ECR1
species: Aeropyrum pernix [TaxId: 56636]

Probab=99.40  E-value=1.1e-13  Score=122.54  Aligned_cols=75  Identities=19%  Similarity=0.325  Sum_probs=69.6

Q ss_pred             ccccCcEEEEEEEEEeeceEEEEEcCCeEEEEecccCCCcccc----ccccccccCCEEEEEEEEEccCCceEEEEecc
Q 002054          680 EIEVGGIYKGVVTSVKEYGAFVEFNGGQQGLLHVSELSHEPVS----RVSDVVSVGQQLSLRCIGQDVRGNIKLSLKAV  754 (974)
Q Consensus       680 ~~~~G~i~~G~V~~i~~~G~fV~l~~g~~Glvhisels~~~v~----~~~~~~~vGd~V~vkVl~id~~gri~LS~K~~  754 (974)
                      .+++|+++.|+|+++.++|+||+|.++.+||||.|++++.+++    ++.++|++||.|.|+|+++|+++++.||+|+.
T Consensus         4 ~Pk~GdvV~G~V~~v~~~g~fV~i~~~~~g~l~~se~~~~~~~~~~~~~~~~~~vGd~V~~kV~~vd~~~~i~Ls~k~~   82 (88)
T d2z0sa1           4 VPQAGDVVIGLIQSVGIMNWFVDINSPYVAVLSVQDFLGRPFNPAVDDMQSLLKVGDYIKAKVVAFDKTRSPLLTVQGE   82 (88)
T ss_dssp             CCCTTCCEEEEEEEECSSEEEEECSSSSCEEEEHHHHHTSCCCTTTTCCTTSSCTTCEEEEEEEEECTTSCEEEECCSS
T ss_pred             CCCCCCEEEEEEEEEECCeEEEEeCCCeEEEEehHHhCcccccccccchhhhcccCcEEEEEEEEECCCCCEEEEEecC
Confidence            4789999999999999999999999999999999999998764    67788999999999999999989999999964

>d2nn6d2 d.101.1.1 (D:147-235) Exosome complex exonuclease RRP46 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ribonuclease PH domain 2-like
superfamily: Ribonuclease PH domain 2-like
family: Ribonuclease PH domain 2-like
domain: Exosome complex exonuclease RRP46
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.35  E-value=1.1e-12  Score=116.30  Aligned_cols=81  Identities=16%  Similarity=0.159  Sum_probs=73.3

Q ss_pred             CCCCCeEEEEEEEE-CCEEEEcCCHHHHhcCccceeEeeeCC--eEEEEEecCCCCCHHHHHHHHHHHHHHHHHHHHHHH
Q 002054          197 PWGGPIGMIRIGRI-CGQFIVNPTMDELSLSDLNLVYACTRE--KTLMIDVQAREISEKDLEAGLRLAHPEAVKYLEPQI  273 (974)
Q Consensus       197 P~~~~v~av~vg~i-~g~~vldPt~~e~~~s~~~l~v~~t~~--~i~mie~~~~~~~e~~~~~al~~a~~~~~~i~~~~~  273 (974)
                      ||+++|+||++|+. ||++|+|||++|++.++.+++++.+..  .++++++.+ .|++++|.+|+++|.++|++|+++|+
T Consensus         1 Pm~~~v~av~~~~~~dg~~vlDpt~~Ee~~~~~~~~~a~~~~~~~i~~~~~~g-~~s~~~~~~~l~~a~~~~~~I~~~~r   79 (89)
T d2nn6d2           1 PMRALFCGVACALDSDGTLVLDPTSKQEKEARAVLTFALDSVERKLLMSSTKG-LYSDTELQQCLAAAQAASQHVFRFYR   79 (89)
T ss_dssp             CCSSCEEEEEEEECTTCCEEESCCHHHHHHCSEEEEEEEETTTCCCCEEEEEE-SCCHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             CCCCCEeEEEEEEEcCCceeeCCCHHHHhhcceEEEEEEEcCCCeEEEEeecC-CcCHHHHHHHHHHHHHHHHHHHHHHH
Confidence            99999999999987 789999999999999998888887643  489999887 59999999999999999999999999


Q ss_pred             HHHHH
Q 002054          274 RLAEK  278 (974)
Q Consensus       274 ~~~~~  278 (974)
                      +.+++
T Consensus        80 ~~l~k   84 (89)
T d2nn6d2          80 ESLQR   84 (89)
T ss_dssp             HHHHH
T ss_pred             HHHHH
Confidence            96655

>d1e3ha1 a.4.9.1 (A:263-345) Polynucleotide phosphorylase/guanosine pentaphosphate synthase (PNPase/GPSI), domain 3 {Streptomyces antibioticus [TaxId: 1890]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Polynucleotide phosphorylase/guanosine pentaphosphate synthase (PNPase/GPSI), domain 3
family: Polynucleotide phosphorylase/guanosine pentaphosphate synthase (PNPase/GPSI), domain 3
domain: Polynucleotide phosphorylase/guanosine pentaphosphate synthase (PNPase/GPSI), domain 3
species: Streptomyces antibioticus [TaxId: 1890]

Probab=99.32  E-value=2.9e-12  Score=111.93  Aligned_cols=82  Identities=28%  Similarity=0.401  Sum_probs=74.8

Q ss_pred             CHHHHHHHHHHHHHHHHhhhcCCCCChhHHHHHHHHHHHHHHHHhhhccchhhhchHHHHHHHHHHHHHHHHHHhcCCcC
Q 002054          292 SEQTLEKVSNLAEAHIEAVFTDPSYSKFERGEALDKIGQDVKKALEEECDEESLQVLPKAVDTVRKRVIRKRIIAEGVRV  371 (974)
Q Consensus       292 ~~~~~~~~~~~~~~~~~~~~~~~~~~k~~r~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~r~~il~~~~R~  371 (974)
                      .+++.+.|.+++.++|.+|+.+  .+|++|+++++++++++.+.|.++. +++...+..+|++++++++|++||++|+|+
T Consensus         2 ~eel~~~v~~~~~~~l~~A~~~--~~K~eR~~al~~lk~~~~e~~~~~~-~~~~~~i~~~~~~l~k~~vR~~Il~~~~Ri   78 (83)
T d1e3ha1           2 QDDVLEALSAAVRPELSAALTI--AGKQDREAELDRVKALAAEKLLPEF-EGREKEISAAYRALTKSLVRERVIAEKKRI   78 (83)
T ss_dssp             CHHHHHHHHHHHHHHHHHHTTC--CSHHHHHHHHHHHHHHHHHHTTTTS-TTCHHHHHHHHHHHHHHHHHHHHHHTCBCT
T ss_pred             CHHHHHHHHHHHHHHHHHHHhh--cchHHHHHHHHHHHHHHHHHhcccc-chhHHHHHHHHHHHHHHHHHHHHHcCCCCC
Confidence            4689999999999999999987  5999999999999999999997764 345678999999999999999999999999


Q ss_pred             CCCCC
Q 002054          372 DGRQL  376 (974)
Q Consensus       372 DGR~~  376 (974)
                      |||++
T Consensus        79 DGR~L   83 (83)
T d1e3ha1          79 DGRGV   83 (83)
T ss_dssp             TSCBT
T ss_pred             CCCCC
Confidence            99975

>d1oysa2 d.101.1.1 (A:152-237) Ribonuclease PH, domain 2 {Bacillus subtilis [TaxId: 1423]}

class: Alpha and beta proteins (a+b)
fold: Ribonuclease PH domain 2-like
superfamily: Ribonuclease PH domain 2-like
family: Ribonuclease PH domain 2-like
domain: Ribonuclease PH, domain 2
species: Bacillus subtilis [TaxId: 1423]

Probab=99.31  E-value=2.1e-12  Score=113.62  Aligned_cols=84  Identities=25%  Similarity=0.311  Sum_probs=78.8

Q ss_pred             CCccccccceeeeeeccCCCCCCcccceEEEecCCccccccCCccEEEEeeCCc-eEEEEeeccCCCCCHHHHHHHHHHH
Q 002054          510 IPLQEHVAGVSVGLVSEVDPSTGEIKDYRILTDILGLEDHLGDMDFKIAGTRIG-VTAIQLDIKPAGIPLDIICECLEHA  588 (974)
Q Consensus       510 vPi~~~vagvs~gli~~~d~~~~~~~~~~iL~Dp~~~Ee~~~d~d~~Va~t~~g-I~alq~~~k~~~i~~e~l~~al~~A  588 (974)
                      .||+++||||++|++++          ..+++||+.+||+.+++|+.|++|++| ++.+|+++....++.++|.++++.|
T Consensus         2 ~P~~~~VaavsvG~i~~----------~~vlldl~~~Ed~~~~~D~~va~t~~g~i~~iq~~ge~~~~s~d~~~~al~lA   71 (86)
T d1oysa2           2 NPITDFLAAISVGIDKE----------QGILLDLNYEEDSSAEVDMNVIMTGSGRFVELQGTGEEATFSREDLNGLLGLA   71 (86)
T ss_dssp             CCBCSCEEEEEEEEETT----------TEEEESCCHHHHHHEEEEEEEEEETTSCEEEEEEEESSCCCCHHHHHHHHHHH
T ss_pred             CCccCcccEEEEEEEcC----------CcEECCCHHHHhcCCCcceEEEEeCCCCEEEEEEeeccCcccHHHHHHHHHHH
Confidence            59999999999999975          157889999999999999999999998 8999999998999999999999999


Q ss_pred             HHHHHHHHHHHHHHh
Q 002054          589 HKGRLQILDHMEREI  603 (974)
Q Consensus       589 ~~~~~~I~~~m~~~i  603 (974)
                      ++++.+|++.++++|
T Consensus        72 ~~gi~~I~~~Qkeal   86 (86)
T d1oysa2          72 EKGIQELIDKQKEVL   86 (86)
T ss_dssp             HHHHHHHHHHHHHHC
T ss_pred             HHHHHHHHHHHHHhC
Confidence            999999999999885

>d1wi5a_ b.40.4.5 (A:) S1-domain of RRP5 protein homolog (PDCD11, KIAA0185) {Human (Homo sapiens) [TaxId: 9606]}

class: All beta proteins
fold: OB-fold
superfamily: Nucleic acid-binding proteins
family: Cold shock DNA-binding domain-like
domain: S1-domain of RRP5 protein homolog (PDCD11, KIAA0185)
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.27  E-value=1.6e-12  Score=121.59  Aligned_cols=78  Identities=19%  Similarity=0.246  Sum_probs=71.3

Q ss_pred             cccccCcEEEEEEEEEeeceEEEEE-cCCeEEEEecccCCCcc-ccccccccccCCEEEEEEEEEcc-CCceEEEEeccC
Q 002054          679 REIEVGGIYKGVVTSVKEYGAFVEF-NGGQQGLLHVSELSHEP-VSRVSDVVSVGQQLSLRCIGQDV-RGNIKLSLKAVS  755 (974)
Q Consensus       679 ~~~~~G~i~~G~V~~i~~~G~fV~l-~~g~~Glvhisels~~~-v~~~~~~~~vGd~V~vkVl~id~-~gri~LS~K~~~  755 (974)
                      .++++|+++.|+|++|.++|+||+| .++++||||++++++.+ ..++.+.|++||.|+|+|+++|+ ++++.||+|...
T Consensus        17 ~~l~~G~iv~G~V~~i~~~G~~V~lg~~~~~G~l~~~els~~~~~~~~~~~~~vGq~v~~~V~~vd~~~~~i~LS~k~~~   96 (119)
T d1wi5a_          17 EALKPGMLLTGTVSSLEDHGYLVDIGVDGTRAFLPLLKAQEYIRQKNKGAKLKVGQYLNCIVEKVKGNGGVVSLSVGHSE   96 (119)
T ss_dssp             TTCCTTCEEEEEEEEECSSEEEEECCCSSCEEEEEHHHHHHHHHHHSSSCCCCTTCEEEEEEEECCTTSCEEEEECCCCC
T ss_pred             hhcCCCCEEEEEEEEEeccEEEEEEeccccceEEeHHHhccccccCCHHHhcccceEEEEEEEEEeCCCCEEEEEecHHH
Confidence            4789999999999999999999999 47899999999999874 77899999999999999999998 678999999765


Q ss_pred             C
Q 002054          756 P  756 (974)
Q Consensus       756 ~  756 (974)
                      .
T Consensus        97 ~   97 (119)
T d1wi5a_          97 V   97 (119)
T ss_dssp             S
T ss_pred             h
Confidence            4

>d2nn6a1 d.14.1.4 (A:1-184) Exosome complex exonuclease RRP45 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ribosomal protein S5 domain 2-like
superfamily: Ribosomal protein S5 domain 2-like
family: Ribonuclease PH domain 1-like
domain: Exosome complex exonuclease RRP45
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.26  E-value=1.7e-12  Score=130.75  Aligned_cols=120  Identities=20%  Similarity=0.227  Sum_probs=92.1

Q ss_pred             CeEEEEEeCccCcCCCcEEEEEeCCeEEEEEEEeCCC-C----CCCCceeeEeeccccccccCCCCCccccccCCCCchh
Q 002054           67 SRLITLETGKIARFANGAVVLGMDETKVLSTVTSSKG-D----SVRDFLPLTVDYQEKQFAQGVIPNTYMRREGAPKERE  141 (974)
Q Consensus        67 ~r~i~~etg~~a~~A~GSa~v~~G~T~Vl~tv~~~~~-~----~~~~f~pL~v~y~e~~~a~g~ip~~~~~Reg~p~~~e  141 (974)
                      -|++.+++|    +|+|||++++|+|+|+|+|+++.. |    +...+..++++|.  .++      +...+.|++++++
T Consensus        32 ~R~~~i~~g----~a~GSa~v~~G~T~V~~~V~~~~~~p~~~~~~~g~~~~~v~~~--~~~------~~~~~~~~~~~~~   99 (184)
T d2nn6a1          32 YRNIRISFG----TDYGCCIVELGKTRVLGQVSCELVSPKLNRATEGILFFNLELS--QMA------APAFEPGRQSDLL   99 (184)
T ss_dssp             CCCCEEEEC----SSTTEEEEESSSCEEEEEECCEEECCCSTTTTSCCEEEEEEEC--TTT------CSSCCSSSTHHHH
T ss_pred             cCCeEEEec----CCCCEEEEEeCCCEEEEEEEeccccccccCCCccceeEEEEec--ccc------CcccccCCCCchh
Confidence            467778887    489999999999999999987654 2    2334455555553  222      1223447788999


Q ss_pred             hhHHHhhcCCccc----------cccCCCCCceEEEEEEEeccCCCChhhHHHHHHHHHhhcCCCCCCC
Q 002054          142 LLVGRIIDRPIRP----------LFPAGFYHEVQVMASVLSSDGKQDPDIMAANATSAALMLSDIPWGG  200 (974)
Q Consensus       142 il~~RlidR~lrp----------lfp~~~~~~~~i~~~vl~~dg~~~~~~~ai~aAs~AL~~s~iP~~~  200 (974)
                      .++++++++.++.          +.|..+.+.+.|.++||+.||+..  .||++|+++||+++++|...
T Consensus       100 ~~l~~~l~~~~~~~~~~d~~~L~i~~~~~~w~i~i~v~VL~~DG~~~--da~~~a~~~AL~~~~iP~v~  166 (184)
T d2nn6a1         100 VKLNRLMERCLRNSKCIDTESLCVVAGEKVWQIRVDLHLLNHDGNII--DAASIAAIVALCHFRRPDVS  166 (184)
T ss_dssp             THHHHHHHHHHHHHTCBCSSSSCSBTTTBEEEEEEEEEECSCCSCCH--HHHHHHHHHHHHHCCCCCCB
T ss_pred             HHHHHHHHhhhhhhhhhhhhhhccccccCcEEEEEEEEEECCCCCHH--HHHHHHHHHHHHhhCCCeEE
Confidence            9999999877653          346777889999999999999888  99999999999999999643

>d1e3pa2 b.40.4.5 (A:656-717) S1 RNA-binding domain of polyribonucleotide phosphorylase, PNPase {Streptomyces antibioticus [TaxId: 1890]}

class: All beta proteins
fold: OB-fold
superfamily: Nucleic acid-binding proteins
family: Cold shock DNA-binding domain-like
domain: S1 RNA-binding domain of polyribonucleotide phosphorylase, PNPase
species: Streptomyces antibioticus [TaxId: 1890]

Probab=99.25  E-value=7e-14  Score=115.29  Aligned_cols=58  Identities=38%  Similarity=0.682  Sum_probs=37.0

Q ss_pred             EEEEEEeeceEEEEEcCCeEEEEecccCCC----ccccccccccccCCEEEEEEEEEccCCc
Q 002054          689 GVVTSVKEYGAFVEFNGGQQGLLHVSELSH----EPVSRVSDVVSVGQQLSLRCIGQDVRGN  746 (974)
Q Consensus       689 G~V~~i~~~G~fV~l~~g~~Glvhisels~----~~v~~~~~~~~vGd~V~vkVl~id~~gr  746 (974)
                      |+|++|.+||+||+|.++.+||||+|++++    .+++++++.|++||+|+|+|+++|+++|
T Consensus         1 G~V~~i~~fG~FV~l~~g~~Glihiseis~~~~~~~v~~~~~~~~~G~~V~vkV~~iD~~~r   62 (62)
T d1e3pa2           1 GSVVKTTTFGAFVSLLPGKDGLLHISQIRKLAGGKRVENVEDVLGVGQKVQVEIAEIDSRGK   62 (62)
T ss_dssp             CBEEECC-CSCEECCC---CCCCC-------------------CCSSCBCCCCCCCCCSSCC
T ss_pred             CEEEEEEeceEEEEecCCceEEEEHHHcccccccccccCHHHhcCCCCEEEEEEEEEcCCCC
Confidence            789999999999999999999999999986    4788999999999999999999998664

>d2nn6h1 b.40.4.5 (H:73-167) S1-domain of Ribosomal RNA-processing protein 4, RRP4 {Human (Homo sapiens) [TaxId: 9606]}

class: All beta proteins
fold: OB-fold
superfamily: Nucleic acid-binding proteins
family: Cold shock DNA-binding domain-like
domain: S1-domain of Ribosomal RNA-processing protein 4, RRP4
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.23  E-value=1.9e-12  Score=116.10  Aligned_cols=75  Identities=21%  Similarity=0.212  Sum_probs=66.7

Q ss_pred             ccccCcEEEEEEEEEeeceEEEEEcCCeEEEEecccCCCc----------cccccccccccCCEEEEEEEEEccCCceEE
Q 002054          680 EIEVGGIYKGVVTSVKEYGAFVEFNGGQQGLLHVSELSHE----------PVSRVSDVVSVGQQLSLRCIGQDVRGNIKL  749 (974)
Q Consensus       680 ~~~~G~i~~G~V~~i~~~G~fV~l~~g~~Glvhisels~~----------~v~~~~~~~~vGd~V~vkVl~id~~gri~L  749 (974)
                      .+++|+++.|+|+++.++|+||+|.++.+|+||+|++++.          ++.++.+.|++||.|.|+|+++|.+|++.|
T Consensus         5 ~P~vGdiV~G~V~~v~~~g~~V~I~~~~~g~l~is~i~~~~~~~rr~~~~~~~~~~~~~~~Gd~V~~kV~~v~~dg~i~L   84 (95)
T d2nn6h1           5 IGEVGDIVVGRITEVQQKRWKVETNSRLDSVLLLSSMNLPGGELRRRSAEDELAMRGFLQEGDLISAEVQAVFSDGAVSL   84 (95)
T ss_dssp             CCCSSBCCCEEEEEEETTEEEEECSSSSCEEEESSCCC-------------CHHHHHHSCSSCEECCEEEEEETTTEEEE
T ss_pred             cCCCCCEEEEEEEEEecCcEEEEeCCCceEEEEHHHccccccccccccchhhhhhhhhcccccEEEEEEEEECCCCCEEE
Confidence            4789999999999999999999999899999999999753          345678889999999999999999999999


Q ss_pred             EEecc
Q 002054          750 SLKAV  754 (974)
Q Consensus       750 S~K~~  754 (974)
                      |+|..
T Consensus        85 s~r~~   89 (95)
T d2nn6h1          85 HTRSL   89 (95)
T ss_dssp             ECCSS
T ss_pred             Eeccc
Confidence            99864

>d2je6b2 d.101.1.1 (B:156-241) Exosome complex exonuclease 1, ECX1 {Sulfolobus solfataricus [TaxId: 2287]}

class: Alpha and beta proteins (a+b)
fold: Ribonuclease PH domain 2-like
superfamily: Ribonuclease PH domain 2-like
family: Ribonuclease PH domain 2-like
domain: Exosome complex exonuclease 1, ECX1
species: Sulfolobus solfataricus [TaxId: 2287]

Probab=99.22  E-value=1.5e-11  Score=108.19  Aligned_cols=81  Identities=27%  Similarity=0.345  Sum_probs=75.0

Q ss_pred             CccccccceeeeeeccCCCCCCcccceEEEecCCccccccCCccEEEEeeCC--ceEEEEeeccCCCCCHHHHHHHHHHH
Q 002054          511 PLQEHVAGVSVGLVSEVDPSTGEIKDYRILTDILGLEDHLGDMDFKIAGTRI--GVTAIQLDIKPAGIPLDIICECLEHA  588 (974)
Q Consensus       511 Pi~~~vagvs~gli~~~d~~~~~~~~~~iL~Dp~~~Ee~~~d~d~~Va~t~~--gI~alq~~~k~~~i~~e~l~~al~~A  588 (974)
                      ||+++|+||++|++++           .+|+||+..|++.++++++|+.+.+  .|+.+|++++   ++.+++.+|++.|
T Consensus         1 Pm~d~V~avsvg~~d~-----------~~llDp~~~E~~~~~~~l~va~~~~~~~i~~~~~~g~---~~~~~~~~~l~~a   66 (86)
T d2je6b2           1 PMRDLIAGVAVGKADG-----------VIILDLNETEAMWGEADMPIAMMPSLNQVTLFQLNGS---MTPDEFRQAFDLA   66 (86)
T ss_dssp             CBSSCCEEEEEEEETT-----------EEEESCCHHHHHHSSEEEEEEEEGGGTEEEEEEEEEC---BCHHHHHHHHHHH
T ss_pred             CCCCCeEEEEEEEECC-----------EEEEecchhhhhcCceeEEEEEeCCCCeEEEEeecCC---CCHHHHHHHHHHH
Confidence            8999999999999975           6999999999999999999998744  4999999864   9999999999999


Q ss_pred             HHHHHHHHHHHHHHhcC
Q 002054          589 HKGRLQILDHMEREISA  605 (974)
Q Consensus       589 ~~~~~~I~~~m~~~i~~  605 (974)
                      +++|.+|++.|++++.+
T Consensus        67 ~~~~~~I~~~~~e~l~~   83 (86)
T d2je6b2          67 VKGINIIYNLEREALKS   83 (86)
T ss_dssp             HHHHHHHHHHHHHHHHG
T ss_pred             HHHHHHHHHHHHHHHHh
Confidence            99999999999999975

>d2je6a2 d.101.1.1 (A:192-275) Exosome complex exonuclease 2, ECX2 {Sulfolobus solfataricus [TaxId: 2287]}

class: Alpha and beta proteins (a+b)
fold: Ribonuclease PH domain 2-like
superfamily: Ribonuclease PH domain 2-like
family: Ribonuclease PH domain 2-like
domain: Exosome complex exonuclease 2, ECX2
species: Sulfolobus solfataricus [TaxId: 2287]

Probab=99.20  E-value=2e-11  Score=106.79  Aligned_cols=82  Identities=21%  Similarity=0.230  Sum_probs=76.9

Q ss_pred             CccccccceeeeeeccCCCCCCcccceEEEecCCccccccCCccEEEEeeCCc-eEEEEeeccCCCCCHHHHHHHHHHHH
Q 002054          511 PLQEHVAGVSVGLVSEVDPSTGEIKDYRILTDILGLEDHLGDMDFKIAGTRIG-VTAIQLDIKPAGIPLDIICECLEHAH  589 (974)
Q Consensus       511 Pi~~~vagvs~gli~~~d~~~~~~~~~~iL~Dp~~~Ee~~~d~d~~Va~t~~g-I~alq~~~k~~~i~~e~l~~al~~A~  589 (974)
                      |++++|++||+|++++           .+|+||+.+||.+++++++|+.+.+| ++++|+.++ +.++.+.|.+|++.|.
T Consensus         1 P~~~~~~~vt~~~i~~-----------~~lvDpt~~EE~~~~~~l~v~~~~~g~i~~~~k~g~-~~~~~~~i~~~i~~A~   68 (84)
T d2je6a2           1 PLNYPVVTISVAKVDK-----------YLVVDPDLDEESIMDAKISFSYTPDLKIVGIQKSGK-GSMSLQDIDQAENTAR   68 (84)
T ss_dssp             CCSCCCEEEEEEEETT-----------EEEESCCHHHHHHCSEEEEEEECTTCCEEEEEEESS-SCEEHHHHHHHHHHHH
T ss_pred             CCCCCeEEEEEEEECC-----------EEEecCCHHHHHhcCCceeeeecCCCceeeEEeccC-CcCCHHHHHHHHHHHH
Confidence            8999999999999975           69999999999999999999999987 999999865 6799999999999999


Q ss_pred             HHHHHHHHHHHHHhc
Q 002054          590 KGRLQILDHMEREIS  604 (974)
Q Consensus       590 ~~~~~I~~~m~~~i~  604 (974)
                      +.+++|.+.|++++.
T Consensus        69 ~~~~~l~~~l~~~l~   83 (84)
T d2je6a2          69 STAVKLLEELKKHLG   83 (84)
T ss_dssp             HHHHHHHHHHHHHHT
T ss_pred             HHHHHHHHHHHHHhC
Confidence            999999999999874

>d1udsa2 d.101.1.1 (A:151-255) Ribonuclease PH, domain 2 {Aquifex aeolicus [TaxId: 63363]}

class: Alpha and beta proteins (a+b)
fold: Ribonuclease PH domain 2-like
superfamily: Ribonuclease PH domain 2-like
family: Ribonuclease PH domain 2-like
domain: Ribonuclease PH, domain 2
species: Aquifex aeolicus [TaxId: 63363]

Probab=99.20  E-value=1.4e-11  Score=112.08  Aligned_cols=86  Identities=27%  Similarity=0.410  Sum_probs=80.5

Q ss_pred             CCccccccceeeeeeccCCCCCCcccceEEEecCCccccccCCccEEEEeeCCc-eEEEEeeccCCCCCHHHHHHHHHHH
Q 002054          510 IPLQEHVAGVSVGLVSEVDPSTGEIKDYRILTDILGLEDHLGDMDFKIAGTRIG-VTAIQLDIKPAGIPLDIICECLEHA  588 (974)
Q Consensus       510 vPi~~~vagvs~gli~~~d~~~~~~~~~~iL~Dp~~~Ee~~~d~d~~Va~t~~g-I~alq~~~k~~~i~~e~l~~al~~A  588 (974)
                      .||+++||||++|++++           .+++||+..|++.+++|+.|++|.+| +..+|+....+.+|.+.|.++++.|
T Consensus         3 ~P~~~~VaAVsvG~idg-----------~~vldp~~~Ed~~~~~dl~va~t~~g~~~ei~~~~e~~~~see~~~eal~~a   71 (105)
T d1udsa2           3 TPIKDFVAAVSVGIVND-----------RILLDLNFEEDSAAQVDMNVVGTGSGRLSEVHTMGEEYSFTKDELIKMLDLA   71 (105)
T ss_dssp             CCBCCCEEEEEEEEETT-----------EEEESCCHHHHHTCSEEEEEEEETTSCEEEEEEEESSCCCCHHHHHHHHHHH
T ss_pred             CCccCCceEEEEEEECC-----------EEeecCCHHHHhcCccceeEEEecCCcchhhhhhhccccccHHHHHHHHHHH
Confidence            69999999999999976           79999999999999999999999998 7889999887889999999999999


Q ss_pred             HHHHHHHHHHHHHHhcCC
Q 002054          589 HKGRLQILDHMEREISAP  606 (974)
Q Consensus       589 ~~~~~~I~~~m~~~i~~~  606 (974)
                      ++++.+|++.+++++...
T Consensus        72 ~~~i~~i~~~Qke~l~~~   89 (105)
T d1udsa2          72 QKGINELIELQKKLYVIQ   89 (105)
T ss_dssp             HHHHHHHHHHHHTTEEEE
T ss_pred             HHHHHHHHHHHHHHHhcc
Confidence            999999999999987654

>d2ba0a1 b.40.4.5 (A:53-135) S1-domain of exosome complex RNA-binding protein 1, ECR1 {Archaeoglobus fulgidus [TaxId: 2234]}

class: All beta proteins
fold: OB-fold
superfamily: Nucleic acid-binding proteins
family: Cold shock DNA-binding domain-like
domain: S1-domain of exosome complex RNA-binding protein 1, ECR1
species: Archaeoglobus fulgidus [TaxId: 2234]

Probab=99.19  E-value=2.1e-11  Score=106.47  Aligned_cols=65  Identities=18%  Similarity=0.296  Sum_probs=60.1

Q ss_pred             CCCCEEEEEEEEEeCCeEEEEeCCCeEEEEecccCC--------CCCCCCCCEEEEEEEEEeCCCceeeeecC
Q 002054          909 KLGTKVAAKVYQVRARGLVLDLGGGIRGMYRFENNE--------KKDFVVGDELLVKCSSFTGKGIPVVSLVD  973 (974)
Q Consensus       909 ~vG~vV~G~V~~I~~~GvFV~L~~gv~Glih~se~~--------~~~f~vGd~V~vkVl~id~~~~~~~~~~~  973 (974)
                      ++||+|.|+|++++++|+||++++++.||+|.++++        .+.|++||+|.|+|+++|+++...+|+.+
T Consensus         4 k~Gd~V~G~V~~v~~~g~~V~i~~~~~g~l~~se~s~~~~~~~~~~~~~vGd~V~~kV~~vd~~~~i~LS~k~   76 (83)
T d2ba0a1           4 SVGDVVIGIIREVAANGWAVDIYSPYQAFLPVSENPEMKPNKKPNEVLDIGDAIIAKVLNIDPKMKVTLTMKD   76 (83)
T ss_dssp             CTTCEEEEEEEEECSSEEEEECSSSSCEEEEGGGCTTCCTTSCGGGTCCTTCEEEEEEEEECTTCCEEEECCS
T ss_pred             CCCCEEEEEEEEEECCEEEEecCCCeeEEEecccccccccccChhhhcccccEEEEEEEEECCCCCEEEEecC
Confidence            689999999999999999999999999999999874        23599999999999999999999999875

>d1kl9a2 b.40.4.5 (A:3-88) Eukaryotic initiation factor 2alpha, eIF2alpha, N-terminal domain {Human (Homo sapiens) [TaxId: 9606]}

class: All beta proteins
fold: OB-fold
superfamily: Nucleic acid-binding proteins
family: Cold shock DNA-binding domain-like
domain: Eukaryotic initiation factor 2alpha, eIF2alpha, N-terminal domain
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.17  E-value=4.6e-11  Score=104.99  Aligned_cols=67  Identities=19%  Similarity=0.195  Sum_probs=54.9

Q ss_pred             cccC-CCCCEEEEEEEEEeCCeEEEEeC--CCeEEEEecccCC-------CCCCCCCCEEEEEEEEEeC-CCceeeee
Q 002054          905 AKNL-KLGTKVAAKVYQVRARGLVLDLG--GGIRGMYRFENNE-------KKDFVVGDELLVKCSSFTG-KGIPVVSL  971 (974)
Q Consensus       905 ~~~~-~vG~vV~G~V~~I~~~GvFV~L~--~gv~Glih~se~~-------~~~f~vGd~V~vkVl~id~-~~~~~~~~  971 (974)
                      .++| ++|++|+|+|.+|++||+||+|+  +|+.||||.+++.       .+.|++||+|+|+|+++|+ ++...+|+
T Consensus         7 ~~~~p~~G~iv~G~V~~i~~~G~fV~l~~~~~i~G~i~~sels~~~~~~~~~~~~~Gd~v~~kV~~vd~~~~ki~LS~   84 (86)
T d1kl9a2           7 QHKFPEVEDVVMVNVRSIAEMGAYVSLLEYNNIEGMILLSELSRRRIRSINKLIRIGRNECVVVIRVDKEKGYIDLSK   84 (86)
T ss_dssp             SSSSCCTTCEEEEEEEEECSSEEEEEETTTTTEEEEEEGGGC------------CTTCEEEEEEEEEETTTTEEEEES
T ss_pred             hhcCCCCCCEEEEEEEEEeCCeEEEEEecCCCEEEEEEeeeccccccccceEEeecccEEEEEEEEEECCCCEEEEEe
Confidence            3445 58999999999999999999997  4899999999873       5569999999999999995 66777775

>d2nn6b2 d.101.1.1 (B:151-240) Exosome complex exonuclease RRP41 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ribonuclease PH domain 2-like
superfamily: Ribonuclease PH domain 2-like
family: Ribonuclease PH domain 2-like
domain: Exosome complex exonuclease RRP41
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.15  E-value=1e-11  Score=110.15  Aligned_cols=84  Identities=19%  Similarity=0.326  Sum_probs=75.9

Q ss_pred             CccccccceeeeeeccCCCCCCcccceEEEecCCccccccCCccEEEE--eeCCceEEEEeeccCCCCCHHHHHHHHHHH
Q 002054          511 PLQEHVAGVSVGLVSEVDPSTGEIKDYRILTDILGLEDHLGDMDFKIA--GTRIGVTAIQLDIKPAGIPLDIICECLEHA  588 (974)
Q Consensus       511 Pi~~~vagvs~gli~~~d~~~~~~~~~~iL~Dp~~~Ee~~~d~d~~Va--~t~~gI~alq~~~k~~~i~~e~l~~al~~A  588 (974)
                      ||+++|+|+++|++++           .+++||+..|+..++.+++|+  ++.+.|+.+|+++   .++.+.+.++++.|
T Consensus         1 Pm~d~V~avs~g~~~~-----------~~llDp~~~E~~~~~~~l~va~~~~~~~I~~~~~~g---~~~~~~~~~~l~~a   66 (90)
T d2nn6b2           1 PMRDFVCACSAGFVDG-----------TALADLSHVEEAAGGPQLALALLPASGQIALLEMDA---RLHEDHLERVLEAA   66 (90)
T ss_dssp             CCSSCCEEEEEEEETT-----------EEEESCCHHHHTSSCCCEEEEEETTTTEEEEEEECS---CCBTTSHHHHHHHH
T ss_pred             CCCCCeEEEEEEEECC-----------EEeeCCccccccccccceEEEEEecCCCEEEEEEec---ccCHHHHHHHHHHH
Confidence            8999999999999975           799999999999999999997  4555699999975   49999999999999


Q ss_pred             HHHHHHHHHHHHHHhcCCCC
Q 002054          589 HKGRLQILDHMEREISAPRT  608 (974)
Q Consensus       589 ~~~~~~I~~~m~~~i~~~~~  608 (974)
                      ++++.+|++.|++++++..+
T Consensus        67 ~~~~~~i~~~~~~~l~~~~~   86 (90)
T d2nn6b2          67 AQAARDVHTLLDRVVRQHVR   86 (90)
T ss_dssp             HHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHhhhh
Confidence            99999999999999987543

>d3bzka4 b.40.4.5 (A:637-730) Tex S1-domain {Pseudomonas aeruginosa [TaxId: 287]}

class: All beta proteins
fold: OB-fold
superfamily: Nucleic acid-binding proteins
family: Cold shock DNA-binding domain-like
domain: Tex S1-domain
species: Pseudomonas aeruginosa [TaxId: 287]

Probab=99.11  E-value=5.1e-11  Score=106.48  Aligned_cols=69  Identities=23%  Similarity=0.214  Sum_probs=61.7

Q ss_pred             ccccCCCCCEEEEEEEEEeCCeEEEEeCCCeEEEEecccCC-------CCCCCCCCEEEEEEEEEeC-CCceeeeec
Q 002054          904 SAKNLKLGTKVAAKVYQVRARGLVLDLGGGIRGMYRFENNE-------KKDFVVGDELLVKCSSFTG-KGIPVVSLV  972 (974)
Q Consensus       904 ~~~~~~vG~vV~G~V~~I~~~GvFV~L~~gv~Glih~se~~-------~~~f~vGd~V~vkVl~id~-~~~~~~~~~  972 (974)
                      ..+++++|++|.|+|++|.++|+||+|++++.||||.+++.       .+.|++||.|+|+|+++|. ++...+|+.
T Consensus        12 ~~~~~k~G~iv~g~V~~v~~~G~~V~l~~~i~G~i~~~~ls~~~~~~~~~~~~vGq~v~~~V~~id~~~~~i~LS~K   88 (94)
T d3bzka4          12 SLKDLKPGMVLEGVVTNVTNFGAFVDIGVHQDGLVHISALSEKFVKDPYEVVKAGDIVKVKVMEVDIPRNRVGLSMR   88 (94)
T ss_dssp             CGGGCCTTCEEEEEEEEEETTEEEEECSSSSCEEEEGGGGCSSCCSCHHHHCCTTCEEEEEEEEEETTTTEEEEESC
T ss_pred             HHhcCCCCCEEEEEEEEEECcEEEEEeCCCceEEeehhhhhcccccChhhhhccCcEEEEEEEEEECCCCEEEEEEe
Confidence            46889999999999999999999999999999999999885       2359999999999999996 677777764

>d2je6i1 b.40.4.5 (I:66-152) S1-domain of exosome complex RNA-binding protein 1, ECR1 {Sulfolobus solfataricus [TaxId: 2287]}

class: All beta proteins
fold: OB-fold
superfamily: Nucleic acid-binding proteins
family: Cold shock DNA-binding domain-like
domain: S1-domain of exosome complex RNA-binding protein 1, ECR1
species: Sulfolobus solfataricus [TaxId: 2287]

Probab=99.09  E-value=6e-11  Score=104.44  Aligned_cols=65  Identities=23%  Similarity=0.288  Sum_probs=59.7

Q ss_pred             CCCCEEEEEEEEEeCCeEEEEeCCCeEEEEecccCC----------CCCCCCCCEEEEEEEEEeCCCceeeeecC
Q 002054          909 KLGTKVAAKVYQVRARGLVLDLGGGIRGMYRFENNE----------KKDFVVGDELLVKCSSFTGKGIPVVSLVD  973 (974)
Q Consensus       909 ~vG~vV~G~V~~I~~~GvFV~L~~gv~Glih~se~~----------~~~f~vGd~V~vkVl~id~~~~~~~~~~~  973 (974)
                      ++||+|.|+|++|++||+||+|++++.||+|.+++.          .+.|++||.|.|+|+++|+++...+|+.+
T Consensus         6 k~Gdiv~G~V~~i~~~g~fV~i~~~~~gll~~s~~~~~~~~~~~~~~~~~~~Gd~v~~kV~~vd~~~~i~LS~k~   80 (87)
T d2je6i1           6 KINDIVIGLVEDVEIYGWVVDIKAPYKAYLPASNLLGRSINVGEDLRRYLDVGDYVIARIENFDRSIDPVLSVKG   80 (87)
T ss_dssp             CTTCEEEEEEEEECSSEEEEECSSSSCEEEEHHHHHTSCCCTTCCCSSSCCTTCEEEEEEEEEETTEEEEEECCS
T ss_pred             CCCCEEEEEEEEEECCEEEEEeCCCEEEEEehHHhCCceeccccccchhhcccceEEEEEEEECCCCCEEEEEec
Confidence            679999999999999999999999999999999652          34699999999999999999999999875

>d2ahob2 b.40.4.5 (B:1-84) Eukaryotic initiation factor 2alpha, eIF2alpha, N-terminal domain {Sulfolobus solfataricus [TaxId: 2287]}

class: All beta proteins
fold: OB-fold
superfamily: Nucleic acid-binding proteins
family: Cold shock DNA-binding domain-like
domain: Eukaryotic initiation factor 2alpha, eIF2alpha, N-terminal domain
species: Sulfolobus solfataricus [TaxId: 2287]

Probab=99.06  E-value=8.5e-11  Score=102.77  Aligned_cols=63  Identities=22%  Similarity=0.282  Sum_probs=54.9

Q ss_pred             CCCCEEEEEEEEEeCCeEEEEeCC--CeEEEEecccCC-------CCCCCCCCEEEEEEEEEeCC-Cceeeee
Q 002054          909 KLGTKVAAKVYQVRARGLVLDLGG--GIRGMYRFENNE-------KKDFVVGDELLVKCSSFTGK-GIPVVSL  971 (974)
Q Consensus       909 ~vG~vV~G~V~~I~~~GvFV~L~~--gv~Glih~se~~-------~~~f~vGd~V~vkVl~id~~-~~~~~~~  971 (974)
                      ++|++|+|+|++|++||+||+|++  |+.||||.+++.       .+.|++||+|+|+|+++|.+ +...+|+
T Consensus        10 ~~G~iv~G~V~~v~~~G~fV~l~~~~gi~Gli~~sels~~~~~~~~~~~~~G~~v~~kV~~vd~~~~~i~LS~   82 (84)
T d2ahob2          10 SEGEILIATVKQVFDYGSYVSLDEYGGLQAFLPWSEVSSKWVKNIRDVLKENRKVIVKVIRVDRRKGTVDVSL   82 (84)
T ss_dssp             CTTCCCEEEEEEEETTEEEEEETTTTTEEEEECGGGCC-----CHHHHTCSSCEEECEEEEEETTTTEEEEES
T ss_pred             CCCCEEEEEEEEEECCEEEEEECCcCCEEEEEEccccccccccccceEeecccEEEEEEEEEECCCCEEEEEE
Confidence            489999999999999999999984  899999999885       33499999999999999955 5666665

>d2nn6d2 d.101.1.1 (D:147-235) Exosome complex exonuclease RRP46 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ribonuclease PH domain 2-like
superfamily: Ribonuclease PH domain 2-like
family: Ribonuclease PH domain 2-like
domain: Exosome complex exonuclease RRP46
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.05  E-value=1.7e-10  Score=101.76  Aligned_cols=83  Identities=12%  Similarity=0.151  Sum_probs=73.7

Q ss_pred             CccccccceeeeeeccCCCCCCcccceEEEecCCccccccCCccEEEEeeCC--ceEEEEeeccCCCCCHHHHHHHHHHH
Q 002054          511 PLQEHVAGVSVGLVSEVDPSTGEIKDYRILTDILGLEDHLGDMDFKIAGTRI--GVTAIQLDIKPAGIPLDIICECLEHA  588 (974)
Q Consensus       511 Pi~~~vagvs~gli~~~d~~~~~~~~~~iL~Dp~~~Ee~~~d~d~~Va~t~~--gI~alq~~~k~~~i~~e~l~~al~~A  588 (974)
                      ||+++++||++|+..++          .+++||+..|+..++.+++++.+.+  .++.+|+++   .++.+++.+|++.|
T Consensus         1 Pm~~~v~av~~~~~~dg----------~~vlDpt~~Ee~~~~~~~~~a~~~~~~~i~~~~~~g---~~s~~~~~~~l~~a   67 (89)
T d2nn6d2           1 PMRALFCGVACALDSDG----------TLVLDPTSKQEKEARAVLTFALDSVERKLLMSSTKG---LYSDTELQQCLAAA   67 (89)
T ss_dssp             CCSSCEEEEEEEECTTC----------CEEESCCHHHHHHCSEEEEEEEETTTCCCCEEEEEE---SCCHHHHHHHHHHH
T ss_pred             CCCCCEeEEEEEEEcCC----------ceeeCCCHHHHhhcceEEEEEEEcCCCeEEEEeecC---CcCHHHHHHHHHHH
Confidence            89999999999998652          5999999999999999999997643  388888875   49999999999999


Q ss_pred             HHHHHHHHHHHHHHhcCC
Q 002054          589 HKGRLQILDHMEREISAP  606 (974)
Q Consensus       589 ~~~~~~I~~~m~~~i~~~  606 (974)
                      ++++.+|+++|+++|.+.
T Consensus        68 ~~~~~~I~~~~r~~l~k~   85 (89)
T d2nn6d2          68 QAASQHVFRFYRESLQRR   85 (89)
T ss_dssp             HHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHH
Confidence            999999999999999764

>d2ba0d2 d.101.1.1 (D:154-252) Exosome complex exonuclease 1, ECX1 {Archaeoglobus fulgidus [TaxId: 2234]}

class: Alpha and beta proteins (a+b)
fold: Ribonuclease PH domain 2-like
superfamily: Ribonuclease PH domain 2-like
family: Ribonuclease PH domain 2-like
domain: Exosome complex exonuclease 1, ECX1
species: Archaeoglobus fulgidus [TaxId: 2234]

Probab=99.02  E-value=1.9e-10  Score=103.63  Aligned_cols=83  Identities=25%  Similarity=0.372  Sum_probs=73.0

Q ss_pred             CccccccceeeeeeccCCCCCCcccceEEEecCCccccccCCccEEEEeeCCc-----eEEEEeeccCCCCCHHHHHHHH
Q 002054          511 PLQEHVAGVSVGLVSEVDPSTGEIKDYRILTDILGLEDHLGDMDFKIAGTRIG-----VTAIQLDIKPAGIPLDIICECL  585 (974)
Q Consensus       511 Pi~~~vagvs~gli~~~d~~~~~~~~~~iL~Dp~~~Ee~~~d~d~~Va~t~~g-----I~alq~~~k~~~i~~e~l~~al  585 (974)
                      ||+++|+||++|++++           .+|+||+..|+..++++++++++.+.     +++.|+++   .++.+.|.+|+
T Consensus         1 Pm~~~V~avsvG~~d~-----------~~llDp~~~E~~~~~~~l~va~~~~~~~~~ei~~~~~~~---~~~~~~~~~~l   66 (99)
T d2ba0d2           1 PMKGMITSVAVGKADG-----------QLVLDPMKEEDNFGEADMPFAFLIRNGKIESIALLQMDG---RMTRDEVKQAI   66 (99)
T ss_dssp             CBSSEEEEEEEEEETT-----------EEEESCCHHHHHHSSEEEEEEEEEETTEEEEEEEEEEEE---EECHHHHHHHH
T ss_pred             CCCCcEEEEEEEEECC-----------EEEEcCCcchhhcccCceEEEEecCcceEEEEEEEeccc---cchHHHHHHHH
Confidence            8999999999999975           79999999999999999999875432     45556665   49999999999


Q ss_pred             HHHHHHHHHHHHHHHHHhcCCC
Q 002054          586 EHAHKGRLQILDHMEREISAPR  607 (974)
Q Consensus       586 ~~A~~~~~~I~~~m~~~i~~~~  607 (974)
                      +.|+++|.+|++.|++++.+++
T Consensus        67 ~~a~~~~~~I~~~~~~alk~~~   88 (99)
T d2ba0d2          67 ELAKKGALQIYEMQREAILRRY   88 (99)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHhhhh
Confidence            9999999999999999998754

>d2z0sa1 b.40.4.5 (A:60-147) S1-domain of exosome complex RNA-binding protein 1, ECR1 {Aeropyrum pernix [TaxId: 56636]}

class: All beta proteins
fold: OB-fold
superfamily: Nucleic acid-binding proteins
family: Cold shock DNA-binding domain-like
domain: S1-domain of exosome complex RNA-binding protein 1, ECR1
species: Aeropyrum pernix [TaxId: 56636]

Probab=99.00  E-value=3.4e-10  Score=99.74  Aligned_cols=66  Identities=15%  Similarity=0.223  Sum_probs=60.2

Q ss_pred             CCCCEEEEEEEEEeCCeEEEEeCCCeEEEEecccCC-----------CCCCCCCCEEEEEEEEEeCCCceeeeecCC
Q 002054          909 KLGTKVAAKVYQVRARGLVLDLGGGIRGMYRFENNE-----------KKDFVVGDELLVKCSSFTGKGIPVVSLVDS  974 (974)
Q Consensus       909 ~vG~vV~G~V~~I~~~GvFV~L~~gv~Glih~se~~-----------~~~f~vGd~V~vkVl~id~~~~~~~~~~~~  974 (974)
                      ++||+|.|+|.++++||+||+|++++.||+|.+++.           .+.|++||.|.|+|+++|+++...+|+.++
T Consensus         6 k~GdvV~G~V~~v~~~g~fV~i~~~~~g~l~~se~~~~~~~~~~~~~~~~~~vGd~V~~kV~~vd~~~~i~Ls~k~~   82 (88)
T d2z0sa1           6 QAGDVVIGLIQSVGIMNWFVDINSPYVAVLSVQDFLGRPFNPAVDDMQSLLKVGDYIKAKVVAFDKTRSPLLTVQGE   82 (88)
T ss_dssp             CTTCCEEEEEEEECSSEEEEECSSSSCEEEEHHHHHTSCCCTTTTCCTTSSCTTCEEEEEEEEECTTSCEEEECCSS
T ss_pred             CCCCEEEEEEEEEECCeEEEEeCCCeEEEEehHHhCcccccccccchhhhcccCcEEEEEEEEECCCCCEEEEEecC
Confidence            699999999999999999999999999999999652           346999999999999999999999998763

>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=99.00  E-value=7.6e-12  Score=99.12  Aligned_cols=51  Identities=33%  Similarity=0.617  Sum_probs=21.2

Q ss_pred             CCcceeeeeccchhhhhcCCCccchhhhhhhhCceEEee-CCEEEEEecCHH
Q 002054          614 SPRLATLKYDNDTLRRLIGPLGALKRKIEEETGGRISVS-DGTLTVVAKNRS  664 (974)
Q Consensus       614 ~p~~~~~~i~~~ki~~vIg~gGk~i~~i~~~~g~~Idi~-dg~v~i~~~~~~  664 (974)
                      ||++.+++||++||+.+||+||++||+|+++||++|+++ ||.|.|++.+.+
T Consensus         1 AP~~~~i~Ip~~kig~vIG~GG~~Ik~I~~~tga~I~i~ddg~v~I~a~~~~   52 (54)
T d1e3ha4           1 APRIITVKIPVDKIGEVIGPKRQMINQIQEDTGAEITIEDDGTIYIGAADGP   52 (54)
T ss_dssp             SCBCC---------------------CHHHHSCCCC--------CCCCBSSC
T ss_pred             CCeEEEEEeCHHHeeEEECCccHHHHHHHHHHCCEEEEeCCeEEEEEecCcc
Confidence            799999999999999999999999999999999999997 899999998864

>d1wi5a_ b.40.4.5 (A:) S1-domain of RRP5 protein homolog (PDCD11, KIAA0185) {Human (Homo sapiens) [TaxId: 9606]}

class: All beta proteins
fold: OB-fold
superfamily: Nucleic acid-binding proteins
family: Cold shock DNA-binding domain-like
domain: S1-domain of RRP5 protein homolog (PDCD11, KIAA0185)
species: Human (Homo sapiens) [TaxId: 9606]

Probab=98.99  E-value=3.7e-10  Score=105.14  Aligned_cols=68  Identities=25%  Similarity=0.384  Sum_probs=59.7

Q ss_pred             ccccCCCCCEEEEEEEEEeCCeEEEEeC-CCeEEEEecccC--------CCCCCCCCCEEEEEEEEEeCCCc-eeeee
Q 002054          904 SAKNLKLGTKVAAKVYQVRARGLVLDLG-GGIRGMYRFENN--------EKKDFVVGDELLVKCSSFTGKGI-PVVSL  971 (974)
Q Consensus       904 ~~~~~~vG~vV~G~V~~I~~~GvFV~L~-~gv~Glih~se~--------~~~~f~vGd~V~vkVl~id~~~~-~~~~~  971 (974)
                      ..+++++|++|+|+|++|++||+||+|+ +++.||||.+++        +.+.|++||.|+|+|++||+++. ..+|+
T Consensus        15 s~~~l~~G~iv~G~V~~i~~~G~~V~lg~~~~~G~l~~~els~~~~~~~~~~~~~vGq~v~~~V~~vd~~~~~i~LS~   92 (119)
T d1wi5a_          15 SAEALKPGMLLTGTVSSLEDHGYLVDIGVDGTRAFLPLLKAQEYIRQKNKGAKLKVGQYLNCIVEKVKGNGGVVSLSV   92 (119)
T ss_dssp             CTTTCCTTCEEEEEEEEECSSEEEEECCCSSCEEEEEHHHHHHHHHHHSSSCCCCTTCEEEEEEEECCTTSCEEEEEC
T ss_pred             CHhhcCCCCEEEEEEEEEeccEEEEEEeccccceEEeHHHhccccccCCHHHhcccceEEEEEEEEEeCCCCEEEEEe
Confidence            4678999999999999999999999996 799999999964        35689999999999999997655 66665

>d2nn6c2 d.101.1.1 (C:188-276) Exosome complex exonuclease RRP43 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ribonuclease PH domain 2-like
superfamily: Ribonuclease PH domain 2-like
family: Ribonuclease PH domain 2-like
domain: Exosome complex exonuclease RRP43
species: Human (Homo sapiens) [TaxId: 9606]

Probab=98.98  E-value=6.5e-10  Score=98.10  Aligned_cols=84  Identities=17%  Similarity=0.288  Sum_probs=76.5

Q ss_pred             ccccccceeeeeeccCCCCCCcccceEEEecCCccccccCCccEEEEeeCCc-eEEEEeeccCCCCCHHHHHHHHHHHHH
Q 002054          512 LQEHVAGVSVGLVSEVDPSTGEIKDYRILTDILGLEDHLGDMDFKIAGTRIG-VTAIQLDIKPAGIPLDIICECLEHAHK  590 (974)
Q Consensus       512 i~~~vagvs~gli~~~d~~~~~~~~~~iL~Dp~~~Ee~~~d~d~~Va~t~~g-I~alq~~~k~~~i~~e~l~~al~~A~~  590 (974)
                      ++++|.++|+|++++         + .+|+||+..||.+++.+++|+.+.+| ++.+|..++ +.++.+.|.+|++.|..
T Consensus         2 i~~~Pi~vT~~~~~~---------~-~~lvDpt~~EE~~~~~~lti~~~~~g~i~~l~k~G~-~~l~~~~l~~~~~~A~~   70 (89)
T d2nn6c2           2 IRTHPVATSFAVFDD---------T-LLIVDPTGEEEHLATGTLTIVMDEEGKLCCLHKPGG-SGLTGAKLQDCMSRAVT   70 (89)
T ss_dssp             CSCCCEEEEEEECTT---------T-CCEESCCTTTTTSCSEEEEEEECTTCCEEEEEESCC-SCCCHHHHHHHHHHHHH
T ss_pred             ccCCEEEEEEEEECC---------E-EEEEcCCHHHHhcCCceEEEEEcCCCCEEEEEecCC-cccCHHHHHHHHHHHHH
Confidence            688999999999975         2 47889999999999999999999988 999999764 67999999999999999


Q ss_pred             HHHHHHHHHHHHhcCC
Q 002054          591 GRLQILDHMEREISAP  606 (974)
Q Consensus       591 ~~~~I~~~m~~~i~~~  606 (974)
                      ++.+|.+.+++++++.
T Consensus        71 ~~~~l~~~l~~al~~~   86 (89)
T d2nn6c2          71 RHKEVKKLMDEVIKSM   86 (89)
T ss_dssp             HHHHHHHHHHTTTTTT
T ss_pred             HHHHHHHHHHHHHHhc
Confidence            9999999999999865

>d2nn6e2 d.101.1.1 (E:192-285) Exosome complex exonuclease RRP42 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ribonuclease PH domain 2-like
superfamily: Ribonuclease PH domain 2-like
family: Ribonuclease PH domain 2-like
domain: Exosome complex exonuclease RRP42
species: Human (Homo sapiens) [TaxId: 9606]

Probab=98.97  E-value=3.6e-10  Score=100.83  Aligned_cols=85  Identities=14%  Similarity=0.121  Sum_probs=78.7

Q ss_pred             CCccccccceeeeeeccCCCCCCcccceEEEecCCccccccCCccEEEEeeCCc-eEEEEeeccCCCCCHHHHHHHHHHH
Q 002054          510 IPLQEHVAGVSVGLVSEVDPSTGEIKDYRILTDILGLEDHLGDMDFKIAGTRIG-VTAIQLDIKPAGIPLDIICECLEHA  588 (974)
Q Consensus       510 vPi~~~vagvs~gli~~~d~~~~~~~~~~iL~Dp~~~Ee~~~d~d~~Va~t~~g-I~alq~~~k~~~i~~e~l~~al~~A  588 (974)
                      +|++++|..||+|++++           .+++||+..||.+++.+++|+.+.+| |+++|+.+. +.++.+.|.+|++.|
T Consensus         1 L~i~~~Pv~vT~~~i~~-----------~~lvDpt~~EE~~~~~~l~v~~~~~g~i~~l~k~G~-~~l~~~~i~~~i~~A   68 (94)
T d2nn6e2           1 LSVENVPCIVTLCKIGY-----------RHVVDATLQEEACSLASLLVSVTSKGVVTCMRKVGK-GSLDPESIFEMMETG   68 (94)
T ss_dssp             CCCTTCCCCEEEEESSS-----------SEESSCCHHHHTSCSEEEEECCCSSSCCCEEEEEES-SCBCHHHHHHHHHHH
T ss_pred             CCcCceEEEEEEEEECC-----------EEEECCCHHHHhccCceEEEEEcCCCcEEEEEecCC-CccCHHHHHHHHHHH
Confidence            47899999999999975           47889999999999999999999988 999999875 679999999999999


Q ss_pred             HHHHHHHHHHHHHHhcCC
Q 002054          589 HKGRLQILDHMEREISAP  606 (974)
Q Consensus       589 ~~~~~~I~~~m~~~i~~~  606 (974)
                      .+.+.+|.+.++++|++.
T Consensus        69 ~~~~~el~~~l~~~L~~~   86 (94)
T d2nn6e2          69 KRVGKVLHASLQSVVHKE   86 (94)
T ss_dssp             HHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHH
Confidence            999999999999999765

>d2ba0g2 d.101.1.1 (G:179-257) Exosome complex exonuclease 2, ECX2 {Archaeoglobus fulgidus [TaxId: 2234]}

class: Alpha and beta proteins (a+b)
fold: Ribonuclease PH domain 2-like
superfamily: Ribonuclease PH domain 2-like
family: Ribonuclease PH domain 2-like
domain: Exosome complex exonuclease 2, ECX2
species: Archaeoglobus fulgidus [TaxId: 2234]

Probab=98.97  E-value=6e-10  Score=96.06  Aligned_cols=77  Identities=18%  Similarity=0.190  Sum_probs=70.5

Q ss_pred             CccccccceeeeeeccCCCCCCcccceEEEecCCccccccCCccEEEEeeCCc-eEEEEeeccCCCCCHHHHHHHHHHHH
Q 002054          511 PLQEHVAGVSVGLVSEVDPSTGEIKDYRILTDILGLEDHLGDMDFKIAGTRIG-VTAIQLDIKPAGIPLDIICECLEHAH  589 (974)
Q Consensus       511 Pi~~~vagvs~gli~~~d~~~~~~~~~~iL~Dp~~~Ee~~~d~d~~Va~t~~g-I~alq~~~k~~~i~~e~l~~al~~A~  589 (974)
                      |++++|.++|+|++++           .+|+||+.+||.+++.+++|+.+.+| |+++|+.++ +.++.+.|.+|++.|.
T Consensus         1 Pv~~~Pv~vT~~~~~~-----------~~lvDpt~eEE~~~~~~iti~~~~~g~i~~~~k~G~-~~~~~~~i~~~i~~A~   68 (79)
T d2ba0g2           1 PVRDLPVSVTSLIVGN-----------KYLVDPSREEMSVGDTTLTITTDKDDNVVAMQKSGG-YLLDEKLFDELLDVSI   68 (79)
T ss_dssp             CBCCCCEEEEEEEETT-----------EEEESCCTTGGGGCSCEEEEEECTTSCEEEEEEESS-CCBCHHHHHHHHHHHH
T ss_pred             CCCCceEEEEEEEECC-----------EEEECCCHHHHhcCCceEEEEEcCCCCEEEEEccCC-CCcCHHHHHHHHHHHH
Confidence            8999999999999975           68999999999999999999999987 999999764 6799999999999999


Q ss_pred             HHHHHHHHHH
Q 002054          590 KGRLQILDHM  599 (974)
Q Consensus       590 ~~~~~I~~~m  599 (974)
                      +.+++|.+.+
T Consensus        69 ~~~~~l~e~l   78 (79)
T d2ba0g2          69 NCARKLREKF   78 (79)
T ss_dssp             HHHHHHTTTT
T ss_pred             HHHHHHHHHh
Confidence            9999986653

>d2nn6a2 d.101.1.1 (A:185-302) Exosome complex exonuclease RRP45 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ribonuclease PH domain 2-like
superfamily: Ribonuclease PH domain 2-like
family: Ribonuclease PH domain 2-like
domain: Exosome complex exonuclease RRP45
species: Human (Homo sapiens) [TaxId: 9606]

Probab=98.95  E-value=7.7e-10  Score=102.78  Aligned_cols=87  Identities=16%  Similarity=0.115  Sum_probs=79.4

Q ss_pred             CCccccccceeeeeeccCCCCCCcccceEEEecCCccccccCCccEEEEeeCCc-eEEEEeeccCCCCCHHHHHHHHHHH
Q 002054          510 IPLQEHVAGVSVGLVSEVDPSTGEIKDYRILTDILGLEDHLGDMDFKIAGTRIG-VTAIQLDIKPAGIPLDIICECLEHA  588 (974)
Q Consensus       510 vPi~~~vagvs~gli~~~d~~~~~~~~~~iL~Dp~~~Ee~~~d~d~~Va~t~~g-I~alq~~~k~~~i~~e~l~~al~~A  588 (974)
                      ++++++|.++|+|+++.++         .+|+||+..||.+++.+++|+.+.+| ||++|+.+ ++.++.+++.+|++.|
T Consensus         1 L~i~h~Pi~vT~~~~~~g~---------~~lvDPt~~EE~~~~~~ltv~~n~~gei~~l~k~G-g~~l~~~~l~~~~~~A   70 (118)
T d2nn6a2           1 LSIHHMPICVSFAFFQQGT---------YLLVDPNEREERVMDGLLVIAMNKHREICTIQSSG-GIMLLKDQVLRCSKIA   70 (118)
T ss_dssp             CCBCCCEEEEEEEECTTTS---------SEEESCCHHHHHHCSCEEEEEEETTTEEEEEEEES-CCCCCHHHHHHHHHHH
T ss_pred             CCcCceEEEEEEEEEecCC---------eEEECCCHHHHhCCCCcEEEEEeCCCcEEEEEecC-CcccCHHHHHHHHHHH
Confidence            4789999999999997532         58999999999999999999999998 99999876 4789999999999999


Q ss_pred             HHHHHHHHHHHHHHhcCC
Q 002054          589 HKGRLQILDHMEREISAP  606 (974)
Q Consensus       589 ~~~~~~I~~~m~~~i~~~  606 (974)
                      ...+.+|.+.++++|++.
T Consensus        71 ~~~~~el~~~i~~aLk~~   88 (118)
T d2nn6a2          71 GVKVAEITELILKALEND   88 (118)
T ss_dssp             HHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHH
Confidence            999999999999999765

>d2ix0a3 b.40.4.5 (A:558-644) Exoribonuclease 2, RNB {Escherichia coli [TaxId: 562]}

class: All beta proteins
fold: OB-fold
superfamily: Nucleic acid-binding proteins
family: Cold shock DNA-binding domain-like
domain: Exoribonuclease 2, RNB
species: Escherichia coli [TaxId: 562]

Probab=98.93  E-value=1.4e-09  Score=95.31  Aligned_cols=67  Identities=10%  Similarity=0.095  Sum_probs=57.6

Q ss_pred             cCcEEEEEEEEEeeceEEEEEc-CCeEEEEecccCCCcccc------------ccccccccCCEEEEEEEEEcc-CCceE
Q 002054          683 VGGIYKGVVTSVKEYGAFVEFN-GGQQGLLHVSELSHEPVS------------RVSDVVSVGQQLSLRCIGQDV-RGNIK  748 (974)
Q Consensus       683 ~G~i~~G~V~~i~~~G~fV~l~-~g~~Glvhisels~~~v~------------~~~~~~~vGd~V~vkVl~id~-~gri~  748 (974)
                      .|+.|+|+|++|++||+||+|. .+.+||||+|+|.+++..            +....|++||+|+|+|+++|+ +++|.
T Consensus         3 ~~~~F~g~Is~v~~~GifV~L~e~~~eGlI~~s~L~~d~y~~d~~~~~l~~~~~~~~~~~~Gd~V~V~v~~vd~~~r~I~   82 (87)
T d2ix0a3           3 TDTRFAAEIVDISRGGMRVRLVDNGAIAFIPAPFLHAVRDELVCSQENGTVQIKGETVYKVTDVIDVTIAEVRMETRSII   82 (87)
T ss_dssp             SCCCEEEEEEEEETTEEEEEETTTCCEEEEEGGGTCSCGGGEEEETTTTEEEETTEEEEETTCEEEEEEEEEETTTTEEE
T ss_pred             CCCEEEEEEEEEEcCeEEEEEecCCcEEEEEehhCCCceEEEeccceEEEEEEcccEEEECCCEEEEEEEEEecccCeEE
Confidence            4789999999999999999995 479999999999997642            234579999999999999998 67776


Q ss_pred             E
Q 002054          749 L  749 (974)
Q Consensus       749 L  749 (974)
                      +
T Consensus        83 ~   83 (87)
T d2ix0a3          83 A   83 (87)
T ss_dssp             E
T ss_pred             E
Confidence            4

>d1e3pa2 b.40.4.5 (A:656-717) S1 RNA-binding domain of polyribonucleotide phosphorylase, PNPase {Streptomyces antibioticus [TaxId: 1890]}

class: All beta proteins
fold: OB-fold
superfamily: Nucleic acid-binding proteins
family: Cold shock DNA-binding domain-like
domain: S1 RNA-binding domain of polyribonucleotide phosphorylase, PNPase
species: Streptomyces antibioticus [TaxId: 1890]

Probab=98.90  E-value=1.8e-11  Score=100.56  Aligned_cols=51  Identities=18%  Similarity=0.291  Sum_probs=37.4

Q ss_pred             EEEEEEeCCeEEEEeCCCeEEEEecccCC-----------CCCCCCCCEEEEEEEEEeCCCc
Q 002054          916 AKVYQVRARGLVLDLGGGIRGMYRFENNE-----------KKDFVVGDELLVKCSSFTGKGI  966 (974)
Q Consensus       916 G~V~~I~~~GvFV~L~~gv~Glih~se~~-----------~~~f~vGd~V~vkVl~id~~~~  966 (974)
                      |+|++|++||+||+|.+|++||+|+|++.           .+.|++||+|+|+|++||++++
T Consensus         1 G~V~~i~~fG~FV~l~~g~~Glihiseis~~~~~~~v~~~~~~~~~G~~V~vkV~~iD~~~r   62 (62)
T d1e3pa2           1 GSVVKTTTFGAFVSLLPGKDGLLHISQIRKLAGGKRVENVEDVLGVGQKVQVEIAEIDSRGK   62 (62)
T ss_dssp             CBEEECC-CSCEECCC---CCCCC-------------------CCSSCBCCCCCCCCCSSCC
T ss_pred             CEEEEEEeceEEEEecCCceEEEEHHHcccccccccccCHHHhcCCCCEEEEEEEEEcCCCC
Confidence            78999999999999999999999999884           3459999999999999998874

>d2nn6f2 d.101.1.1 (F:176-270) Exosome complex exonuclease MTR3 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ribonuclease PH domain 2-like
superfamily: Ribonuclease PH domain 2-like
family: Ribonuclease PH domain 2-like
domain: Exosome complex exonuclease MTR3
species: Human (Homo sapiens) [TaxId: 9606]

Probab=98.87  E-value=3.9e-10  Score=100.84  Aligned_cols=86  Identities=9%  Similarity=-0.006  Sum_probs=75.8

Q ss_pred             CCCCeEEEEEEEEC---CEEEEcCCHHHHhcCccceeEeee--CCeEEEEEecCCCCCHHHHHHHHHHHHHHHHHHHHHH
Q 002054          198 WGGPIGMIRIGRIC---GQFIVNPTMDELSLSDLNLVYACT--REKTLMIDVQAREISEKDLEAGLRLAHPEAVKYLEPQ  272 (974)
Q Consensus       198 ~~~~v~av~vg~i~---g~~vldPt~~e~~~s~~~l~v~~t--~~~i~mie~~~~~~~e~~~~~al~~a~~~~~~i~~~~  272 (974)
                      |++.|+||++|..|   +++++|||+.|++.++.+++|+..  .+.|+.++++|..++.++|.+++++|.++|++|++.|
T Consensus         1 M~D~V~acs~~~~~~~~~~~llD~~~~Ee~~~~~~~~va~~p~~~~i~~~~~~G~~~~~d~l~~~lela~~g~~~I~~i~   80 (95)
T d2nn6f2           1 MYDLVVGCGLSLAPGPAPTWLLDPTRLEEERAAAGLTVALMPVLNQVAGLLGSGEGGLTESWAEAVRLGLEGCQRLYPVL   80 (95)
T ss_dssp             BSSCCEEEECCCCSCSSCCCCSSCCTTTGGGCSSEEEEEEETTTTEEEEEEEECCSSCTTTTHHHHHHHHHHHHHHHHHH
T ss_pred             CCcEEEEEEEEeecCCCCcEEECCCHHHhcCCCCcEEEEEcCCCceeEEEEEecccchHHHHHHHHHHHHHHHHHHHHHH
Confidence            68899999999975   579999999999999989988764  4559999999987899999999999999999999999


Q ss_pred             HHHHHHhCCcc
Q 002054          273 IRLAEKAGKQK  283 (974)
Q Consensus       273 ~~~~~~~g~~k  283 (974)
                      ++.+.+..++|
T Consensus        81 ~~aL~~~~~k~   91 (95)
T d2nn6f2          81 QQSLVRAARRR   91 (95)
T ss_dssp             HHHHHHHHHHH
T ss_pred             HHHHHHHHHHh
Confidence            99888765544

>d1go3e1 b.40.4.5 (E:79-184) C-terminal domain of RNA polymerase II subunit RBP7 (RpoE) {Archaeon Methanococcus jannaschii [TaxId: 2190]}

class: All beta proteins
fold: OB-fold
superfamily: Nucleic acid-binding proteins
family: Cold shock DNA-binding domain-like
domain: C-terminal domain of RNA polymerase II subunit RBP7 (RpoE)
species: Archaeon Methanococcus jannaschii [TaxId: 2190]

Probab=98.87  E-value=2.1e-09  Score=97.91  Aligned_cols=57  Identities=18%  Similarity=0.237  Sum_probs=50.8

Q ss_pred             CCCCEEEEEEEEEeCCeEEEEeCCCeEEEEecccCCC------------------CCCCCCCEEEEEEEEEeCCCc
Q 002054          909 KLGTKVAAKVYQVRARGLVLDLGGGIRGMYRFENNEK------------------KDFVVGDELLVKCSSFTGKGI  966 (974)
Q Consensus       909 ~vG~vV~G~V~~I~~~GvFV~L~~gv~Glih~se~~~------------------~~f~vGd~V~vkVl~id~~~~  966 (974)
                      ++|+++.|+|.+|++||+||+|+ ++.||||.++++.                  +.|++||.|+|+|++||.+..
T Consensus         2 ~~gei~~g~V~~v~~~G~FVel~-~ieGlv~~s~l~~~~~~~~~~~~~~~~~~~~~~~~~Gd~v~vkV~~vd~~~~   76 (106)
T d1go3e1           2 EMYELIEGEVVDVVEFGSFVRLG-PLDGLIHVSQIMDDYVSYDPKREAIIGKETGKVLEIGDYVRARIVAISLKAE   76 (106)
T ss_dssp             CTTCEEEEEEEEEETTEEEEECS-SSEEEEEGGGSCSSCEEECCC--CEEETTTCCEECTTCEEEEEEEEEECCC-
T ss_pred             CCCCEEEEEEEEEeeeEEEEEee-CeEEEEEeecccCceeeeccceeEEeecccccceeecceEEEEEEEEchhhc
Confidence            58999999999999999999996 7999999998852                  458999999999999997653

>d2ba0g2 d.101.1.1 (G:179-257) Exosome complex exonuclease 2, ECX2 {Archaeoglobus fulgidus [TaxId: 2234]}

class: Alpha and beta proteins (a+b)
fold: Ribonuclease PH domain 2-like
superfamily: Ribonuclease PH domain 2-like
family: Ribonuclease PH domain 2-like
domain: Exosome complex exonuclease 2, ECX2
species: Archaeoglobus fulgidus [TaxId: 2234]

Probab=98.86  E-value=2.9e-09  Score=91.64  Aligned_cols=75  Identities=17%  Similarity=0.220  Sum_probs=67.3

Q ss_pred             CCCCCeEEEEEEEECCEEEEcCCHHHHhcCccceeEeeeCCe-EEEEE-ecCCCCCHHHHHHHHHHHHHHHHHHHHH
Q 002054          197 PWGGPIGMIRIGRICGQFIVNPTMDELSLSDLNLVYACTREK-TLMID-VQAREISEKDLEAGLRLAHPEAVKYLEP  271 (974)
Q Consensus       197 P~~~~v~av~vg~i~g~~vldPt~~e~~~s~~~l~v~~t~~~-i~mie-~~~~~~~e~~~~~al~~a~~~~~~i~~~  271 (974)
                      |+.+.+.+|+++++++++|+|||.+|+..++.+++|+.++++ +..++ .++..|+.++|.+++++|.+.++++.+.
T Consensus         1 Pv~~~Pv~vT~~~~~~~~lvDpt~eEE~~~~~~iti~~~~~g~i~~~~k~G~~~~~~~~i~~~i~~A~~~~~~l~e~   77 (79)
T d2ba0g2           1 PVRDLPVSVTSLIVGNKYLVDPSREEMSVGDTTLTITTDKDDNVVAMQKSGGYLLDEKLFDELLDVSINCARKLREK   77 (79)
T ss_dssp             CBCCCCEEEEEEEETTEEEESCCTTGGGGCSCEEEEEECTTSCEEEEEEESSCCBCHHHHHHHHHHHHHHHHHHTTT
T ss_pred             CCCCceEEEEEEEECCEEEECCCHHHHhcCCceEEEEEcCCCCEEEEEccCCCCcCHHHHHHHHHHHHHHHHHHHHH
Confidence            788889999999999999999999999999999999998876 66665 5566799999999999999999988654

>d2nn6g1 b.40.4.5 (G:107-194) S1-domain of exosome component 3 (RRP40) {Human (Homo sapiens) [TaxId: 9606]}

class: All beta proteins
fold: OB-fold
superfamily: Nucleic acid-binding proteins
family: Cold shock DNA-binding domain-like
domain: S1-domain of exosome component 3 (RRP40)
species: Human (Homo sapiens) [TaxId: 9606]

Probab=98.86  E-value=2e-09  Score=94.37  Aligned_cols=75  Identities=15%  Similarity=0.060  Sum_probs=69.2

Q ss_pred             ccccCcEEEEEEEEEeeceEEEEEcCCeEEEEecccCCCccccccccccccCCEEEEEEEEEccCCceEEEEeccC
Q 002054          680 EIEVGGIYKGVVTSVKEYGAFVEFNGGQQGLLHVSELSHEPVSRVSDVVSVGQQLSLRCIGQDVRGNIKLSLKAVS  755 (974)
Q Consensus       680 ~~~~G~i~~G~V~~i~~~G~fV~l~~g~~Glvhisels~~~v~~~~~~~~vGd~V~vkVl~id~~gri~LS~K~~~  755 (974)
                      .+++|+++.|+|+++..+++||+|.+...|+||++++. .++++....|++||.|.|||.++|.++++.||+.+..
T Consensus         3 ~P~~GD~ViG~V~~~~~~~~~VdI~s~~~a~L~~~~f~-g~~k~~r~~l~~GD~V~arV~~v~~~~~~~Lscvd~~   77 (88)
T d2nn6g1           3 VPVKGDHVIGIVTAKSGDIFKVDVGGSEPASLSYLSFE-GATKRNRPNVQVGDLIYGQFVVANKDMEPEMVCIDSC   77 (88)
T ss_dssp             CCCSSEEEEEEEEEEETTEEEEECSSSSCCCEESCSSS-CCSSCSSSSSCTTCEEEEEEEECCTTSCCEEECSBTT
T ss_pred             cCCCCCEEEEEEEEEeCCeEEEEcCCCeeEEEeHHHcC-ccccccCcccCCCCEEEEEEEEeCCCCCEEEEEEccc
Confidence            37899999999999999999999999999999999995 5688888999999999999999999999999987753

>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=98.81  E-value=3.2e-09  Score=92.27  Aligned_cols=61  Identities=18%  Similarity=0.271  Sum_probs=57.9

Q ss_pred             ceeeeeccchhhhhcCCCccchhhhhhhhCceEEee-CCEEEEEecCHHHHHHHHHHHHHHh
Q 002054          617 LATLKYDNDTLRRLIGPLGALKRKIEEETGGRISVS-DGTLTVVAKNRSVMEKVLEKVDFII  677 (974)
Q Consensus       617 ~~~~~i~~~ki~~vIg~gGk~i~~i~~~~g~~Idi~-dg~v~i~~~~~~~~~~a~~~i~~l~  677 (974)
                      -..++|||++|+.+||+||++|+.|+++||++|+|+ +|+|.|++.+.+.++.|+..++.+.
T Consensus         2 g~vi~I~~~ki~~vIG~gG~~ik~i~~~t~~~I~I~d~G~V~I~g~~~~~~~~A~~~I~~I~   63 (87)
T d2z0sa2           2 GKIVEISPAKVPRVIGRKMSMLKTLEEKTECKIFVARNGRIHLECPNEDLEAIAVMAIKIID   63 (87)
T ss_dssp             SEEEECCGGGSGGGTCGGGHHHHHHHHHHCCEEEEETTTEEEEECSCHHHHHHHHHHHHHHH
T ss_pred             cEEEEEChhhcceeECCCCcHHHHHHHHHCCEEEECCCcEEEEEeCCHHHHHHHHHHHHHHH
Confidence            367899999999999999999999999999999998 8999999999999999999999887

>d2nn6f2 d.101.1.1 (F:176-270) Exosome complex exonuclease MTR3 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ribonuclease PH domain 2-like
superfamily: Ribonuclease PH domain 2-like
family: Ribonuclease PH domain 2-like
domain: Exosome complex exonuclease MTR3
species: Human (Homo sapiens) [TaxId: 9606]

Probab=98.80  E-value=8.7e-10  Score=98.47  Aligned_cols=86  Identities=14%  Similarity=0.123  Sum_probs=74.1

Q ss_pred             ccccccceeeeeeccCCCCCCcccceEEEecCCccccccCCccEEEEe--eCCceEEEEeeccCCCCCHHHHHHHHHHHH
Q 002054          512 LQEHVAGVSVGLVSEVDPSTGEIKDYRILTDILGLEDHLGDMDFKIAG--TRIGVTAIQLDIKPAGIPLDIICECLEHAH  589 (974)
Q Consensus       512 i~~~vagvs~gli~~~d~~~~~~~~~~iL~Dp~~~Ee~~~d~d~~Va~--t~~gI~alq~~~k~~~i~~e~l~~al~~A~  589 (974)
                      |+++|+|+++|++++.        ...+|+||+..||+.++.+++|+.  +.+.|+.+|+++.  .++.+.|.+++++|.
T Consensus         1 M~D~V~acs~~~~~~~--------~~~~llD~~~~Ee~~~~~~~~va~~p~~~~i~~~~~~G~--~~~~d~l~~~lela~   70 (95)
T d2nn6f2           1 MYDLVVGCGLSLAPGP--------APTWLLDPTRLEEERAAAGLTVALMPVLNQVAGLLGSGE--GGLTESWAEAVRLGL   70 (95)
T ss_dssp             BSSCCEEEECCCCSCS--------SCCCCSSCCTTTGGGCSSEEEEEEETTTTEEEEEEEECC--SSCTTTTHHHHHHHH
T ss_pred             CCcEEEEEEEEeecCC--------CCcEEECCCHHHhcCCCCcEEEEEcCCCceeEEEEEecc--cchHHHHHHHHHHHH
Confidence            7899999999998742        126999999999999999999984  5556999999875  357789999999999


Q ss_pred             HHHHHHHHHHHHHhcCCC
Q 002054          590 KGRLQILDHMEREISAPR  607 (974)
Q Consensus       590 ~~~~~I~~~m~~~i~~~~  607 (974)
                      ++|..|++.|+++|.+..
T Consensus        71 ~g~~~I~~i~~~aL~~~~   88 (95)
T d2nn6f2          71 EGCQRLYPVLQQSLVRAA   88 (95)
T ss_dssp             HHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHH
Confidence            999999999999998764

>d2nn6e2 d.101.1.1 (E:192-285) Exosome complex exonuclease RRP42 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ribonuclease PH domain 2-like
superfamily: Ribonuclease PH domain 2-like
family: Ribonuclease PH domain 2-like
domain: Exosome complex exonuclease RRP42
species: Human (Homo sapiens) [TaxId: 9606]

Probab=98.77  E-value=7.5e-09  Score=92.06  Aligned_cols=83  Identities=11%  Similarity=0.081  Sum_probs=72.3

Q ss_pred             CCCCCeEEEEEEEECCEEEEcCCHHHHhcCccceeEeeeCCe-EEEEE-ecCCCCCHHHHHHHHHHHHHHHHHHHHHHHH
Q 002054          197 PWGGPIGMIRIGRICGQFIVNPTMDELSLSDLNLVYACTREK-TLMID-VQAREISEKDLEAGLRLAHPEAVKYLEPQIR  274 (974)
Q Consensus       197 P~~~~v~av~vg~i~g~~vldPt~~e~~~s~~~l~v~~t~~~-i~mie-~~~~~~~e~~~~~al~~a~~~~~~i~~~~~~  274 (974)
                      |++....+|++|++++.+|+|||++|+..++.+++|+.++++ ++.++ .++..|+.++|.+++++|.+.++++++.+++
T Consensus         2 ~i~~~Pv~vT~~~i~~~~lvDpt~~EE~~~~~~l~v~~~~~g~i~~l~k~G~~~l~~~~i~~~i~~A~~~~~el~~~l~~   81 (94)
T d2nn6e2           2 SVENVPCIVTLCKIGYRHVVDATLQEEACSLASLLVSVTSKGVVTCMRKVGKGSLDPESIFEMMETGKRVGKVLHASLQS   81 (94)
T ss_dssp             CCTTCCCCEEEEESSSSEESSCCHHHHTSCSEEEEECCCSSSCCCEEEEEESSCBCHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             CcCceEEEEEEEEECCEEEECCCHHHHhccCceEEEEEcCCCcEEEEEecCCCccCHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            445555679999999999999999999999999999999987 55554 4556799999999999999999999999999


Q ss_pred             HHHHh
Q 002054          275 LAEKA  279 (974)
Q Consensus       275 ~~~~~  279 (974)
                      .+++-
T Consensus        82 ~L~~~   86 (94)
T d2nn6e2          82 VVHKE   86 (94)
T ss_dssp             HHHHH
T ss_pred             HHHHH
Confidence            88764

>d1y14b1 b.40.4.5 (B:81-171) C-terminal domain of RNA polymerase II subunit RBP7 (RpoE) {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: All beta proteins
fold: OB-fold
superfamily: Nucleic acid-binding proteins
family: Cold shock DNA-binding domain-like
domain: C-terminal domain of RNA polymerase II subunit RBP7 (RpoE)
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=98.73  E-value=1.7e-08  Score=89.16  Aligned_cols=67  Identities=15%  Similarity=0.204  Sum_probs=57.6

Q ss_pred             ccCcEEEEEEEEEeeceEEEEEcCCeEEEEecccCCCccc----------cccccccccCCEEEEEEEEEcc-CCceEE
Q 002054          682 EVGGIYKGVVTSVKEYGAFVEFNGGQQGLLHVSELSHEPV----------SRVSDVVSVGQQLSLRCIGQDV-RGNIKL  749 (974)
Q Consensus       682 ~~G~i~~G~V~~i~~~G~fV~l~~g~~Glvhisels~~~v----------~~~~~~~~vGd~V~vkVl~id~-~gri~L  749 (974)
                      -.|++++|+|+++++||+||++. ..+||+|++++.+++.          ++..+.+++||.|+|||+++|. +++|..
T Consensus         2 f~Gev~~g~I~~v~~~G~fv~lg-~~eg~i~~~~l~~~~~~d~~~~~~~~~~~~~~~~~Gd~VrvkV~~v~~~~~~i~~   79 (91)
T d1y14b1           2 FKGEVVDGTVVSCSQHGFEVQVG-PMKVFVTKHLMPQDLTFNAGSNPPSYQSSEDVITIKSRIRVKIEGCISQVSSIHA   79 (91)
T ss_dssp             CTTCEEEEEEEEEETTEEEEEET-TEEEEEEGGGSCTTCEECC-----CEECSSCEECTTCEEEEEEEEEEEETTEEEE
T ss_pred             CCCCEEEEEEEEEEeeEEEEEEc-CeEEEEEhhhcCcceEEccccceeEecccCeEEeCCCEEEEEEEEEecccCccEE
Confidence            36999999999999999999995 6899999999988754          3456679999999999999987 566643

>d2nn6c2 d.101.1.1 (C:188-276) Exosome complex exonuclease RRP43 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ribonuclease PH domain 2-like
superfamily: Ribonuclease PH domain 2-like
family: Ribonuclease PH domain 2-like
domain: Exosome complex exonuclease RRP43
species: Human (Homo sapiens) [TaxId: 9606]

Probab=98.68  E-value=1.5e-08  Score=89.07  Aligned_cols=81  Identities=12%  Similarity=0.048  Sum_probs=69.0

Q ss_pred             CCCeEEEEEEEECCE-EEEcCCHHHHhcCccceeEeeeCCe-EEEEEe-cCCCCCHHHHHHHHHHHHHHHHHHHHHHHHH
Q 002054          199 GGPIGMIRIGRICGQ-FIVNPTMDELSLSDLNLVYACTREK-TLMIDV-QAREISEKDLEAGLRLAHPEAVKYLEPQIRL  275 (974)
Q Consensus       199 ~~~v~av~vg~i~g~-~vldPt~~e~~~s~~~l~v~~t~~~-i~mie~-~~~~~~e~~~~~al~~a~~~~~~i~~~~~~~  275 (974)
                      ++.+.+|++|+++|+ +++|||++|++.++.+++|+.+.++ ++.++. ++..|+.++|.+++++|.+.++++++++++.
T Consensus         3 ~~~Pi~vT~~~~~~~~~lvDpt~~EE~~~~~~lti~~~~~g~i~~l~k~G~~~l~~~~l~~~~~~A~~~~~~l~~~l~~a   82 (89)
T d2nn6c2           3 RTHPVATSFAVFDDTLLIVDPTGEEEHLATGTLTIVMDEEGKLCCLHKPGGSGLTGAKLQDCMSRAVTRHKEVKKLMDEV   82 (89)
T ss_dssp             SCCCEEEEEEECTTTCCEESCCTTTTTSCSEEEEEEECTTCCEEEEEESCCSCCCHHHHHHHHHHHHHHHHHHHHHHHTT
T ss_pred             cCCEEEEEEEEECCEEEEEcCCHHHHhcCCceEEEEEcCCCCEEEEEecCCcccCHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            344568999999775 6889999999999999999998887 665654 5556999999999999999999999999987


Q ss_pred             HHHh
Q 002054          276 AEKA  279 (974)
Q Consensus       276 ~~~~  279 (974)
                      +++.
T Consensus        83 l~~~   86 (89)
T d2nn6c2          83 IKSM   86 (89)
T ss_dssp             TTTT
T ss_pred             HHhc
Confidence            7643

>d2ja9a1 b.40.4.5 (A:62-151) S1-domain of exosome component 3 (RRP40) {Saccharomyces cerevisiae [TaxId: 4932]}

class: All beta proteins
fold: OB-fold
superfamily: Nucleic acid-binding proteins
family: Cold shock DNA-binding domain-like
domain: S1-domain of exosome component 3 (RRP40)
species: Saccharomyces cerevisiae [TaxId: 4932]

Probab=98.63  E-value=2.1e-08  Score=88.09  Aligned_cols=75  Identities=9%  Similarity=-0.015  Sum_probs=69.9

Q ss_pred             ccccCcEEEEEEEEEeeceEEEEEcCCeEEEEecccCCCccccccccccccCCEEEEEEEEEccCCceEEEEecc
Q 002054          680 EIEVGGIYKGVVTSVKEYGAFVEFNGGQQGLLHVSELSHEPVSRVSDVVSVGQQLSLRCIGQDVRGNIKLSLKAV  754 (974)
Q Consensus       680 ~~~~G~i~~G~V~~i~~~G~fV~l~~g~~Glvhisels~~~v~~~~~~~~vGd~V~vkVl~id~~gri~LS~K~~  754 (974)
                      .+++|++|.|+|+++..+++||+|.+...|++|.++......++....|++||.|.|||.++|.++++.||++..
T Consensus         4 ~P~~gD~ViG~V~~~~~~~~~vdI~~~~~~~L~~~~~f~g~~k~~r~~l~~GDlV~arV~~v~~~~~~~Lsc~~~   78 (90)
T d2ja9a1           4 IPSVNDFVIGVIIGTFSDSYKVSLQNFSSSVSLSYMAFPNASKKNRPTLQVGDLVYARVCTAEKELEAEIECFDS   78 (90)
T ss_dssp             CCCTTCEEEEEEEEECSSEEEEESSTTSCCEEEETTSSTTCCSSSCCCCCTTCEEEEEEEECCTTSCCEEESSCT
T ss_pred             cCCCCCEEEEEEEEEeCCcEEEEcCCcchhhhhhhhccCccccccCCccCCCCEEEEEEEEECCCCCEEEEEecc
Confidence            378999999999999999999999888999999999888888999999999999999999999999999998763

>d2c35b1 b.40.4.5 (B:78-171) C-terminal domain of RNA polymerase II subunit RBP7 (RpoE) {Human (Homo sapiens) [TaxId: 9606]}

class: All beta proteins
fold: OB-fold
superfamily: Nucleic acid-binding proteins
family: Cold shock DNA-binding domain-like
domain: C-terminal domain of RNA polymerase II subunit RBP7 (RpoE)
species: Human (Homo sapiens) [TaxId: 9606]

Probab=98.62  E-value=5.5e-08  Score=86.35  Aligned_cols=67  Identities=21%  Similarity=0.302  Sum_probs=57.1

Q ss_pred             cccCcEEEEEEEEEeeceEEEEEcCCeEEEEecccCCCccc------------cccccccccCCEEEEEEEEEcc-CCce
Q 002054          681 IEVGGIYKGVVTSVKEYGAFVEFNGGQQGLLHVSELSHEPV------------SRVSDVVSVGQQLSLRCIGQDV-RGNI  747 (974)
Q Consensus       681 ~~~G~i~~G~V~~i~~~G~fV~l~~g~~Glvhisels~~~v------------~~~~~~~~vGd~V~vkVl~id~-~gri  747 (974)
                      +-.|++++|+|+++.++|+||++. ..+||+|.+++.+++.            ++....+++||.|++||+++|. .++|
T Consensus         2 Pf~Gev~~g~V~~v~~~G~fv~lg-~~~~~v~~~~l~~d~~y~~~~~~~~~~~~~~~~~~~~Gd~VrvkV~~v~~~~~~I   80 (94)
T d2c35b1           2 PFKGEVVDAVVTQVNKVGLFTEIG-PMSCFISRHSIPSEMEFDPNSNPPCYKTMDEDIVIQQDDEIRLKIVGTRVDKNDI   80 (94)
T ss_dssp             CCTTCEEEEEEEEEETTEEEEEET-TEEEEEEGGGSCTTEEEESSSSSCEEEETTSCSEEETTCEEEEEEEEEEEETTEE
T ss_pred             CCCCCEEEEEEEEEEeeEEEEEec-CceEEEEhhhcCcceeecccccceEEEcccceEEEeCCCEEEEEEEEEecCcCcc
Confidence            346999999999999999999994 6899999999998852            2445579999999999999987 6666


Q ss_pred             E
Q 002054          748 K  748 (974)
Q Consensus       748 ~  748 (974)
                      .
T Consensus        81 ~   81 (94)
T d2c35b1          81 F   81 (94)
T ss_dssp             E
T ss_pred             e
Confidence            4

>d2nn6h1 b.40.4.5 (H:73-167) S1-domain of Ribosomal RNA-processing protein 4, RRP4 {Human (Homo sapiens) [TaxId: 9606]}

class: All beta proteins
fold: OB-fold
superfamily: Nucleic acid-binding proteins
family: Cold shock DNA-binding domain-like
domain: S1-domain of Ribosomal RNA-processing protein 4, RRP4
species: Human (Homo sapiens) [TaxId: 9606]

Probab=98.62  E-value=1.1e-08  Score=91.22  Aligned_cols=65  Identities=9%  Similarity=0.188  Sum_probs=58.4

Q ss_pred             CCCCEEEEEEEEEeCCeEEEEeCCCeEEEEecccCC-----------------CCCCCCCCEEEEEEEEEeCCCceeeee
Q 002054          909 KLGTKVAAKVYQVRARGLVLDLGGGIRGMYRFENNE-----------------KKDFVVGDELLVKCSSFTGKGIPVVSL  971 (974)
Q Consensus       909 ~vG~vV~G~V~~I~~~GvFV~L~~gv~Glih~se~~-----------------~~~f~vGd~V~vkVl~id~~~~~~~~~  971 (974)
                      ++||+|.|+|.++.++|+||+|+.+..|++|.|++.                 .+.|++||.|.|+|++||.+|...+|.
T Consensus         7 ~vGdiV~G~V~~v~~~g~~V~I~~~~~g~l~is~i~~~~~~~rr~~~~~~~~~~~~~~~Gd~V~~kV~~v~~dg~i~Ls~   86 (95)
T d2nn6h1           7 EVGDIVVGRITEVQQKRWKVETNSRLDSVLLLSSMNLPGGELRRRSAEDELAMRGFLQEGDLISAEVQAVFSDGAVSLHT   86 (95)
T ss_dssp             CSSBCCCEEEEEEETTEEEEECSSSSCEEEESSCCC-------------CHHHHHHSCSSCEECCEEEEEETTTEEEEEC
T ss_pred             CCCCEEEEEEEEEecCcEEEEeCCCceEEEEHHHccccccccccccchhhhhhhhhcccccEEEEEEEEECCCCCEEEEe
Confidence            589999999999999999999999999999999873                 123999999999999999999988887


Q ss_pred             cC
Q 002054          972 VD  973 (974)
Q Consensus       972 ~~  973 (974)
                      .+
T Consensus        87 r~   88 (95)
T d2nn6h1          87 RS   88 (95)
T ss_dssp             CS
T ss_pred             cc
Confidence            54

>d2nn6a2 d.101.1.1 (A:185-302) Exosome complex exonuclease RRP45 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ribonuclease PH domain 2-like
superfamily: Ribonuclease PH domain 2-like
family: Ribonuclease PH domain 2-like
domain: Exosome complex exonuclease RRP45
species: Human (Homo sapiens) [TaxId: 9606]

Probab=98.60  E-value=1.3e-07  Score=87.34  Aligned_cols=83  Identities=13%  Similarity=0.084  Sum_probs=72.2

Q ss_pred             CCCCCCeEEEEEEEEC--CEEEEcCCHHHHhcCccceeEeeeCCe-EEEEE-ecCCCCCHHHHHHHHHHHHHHHHHHHHH
Q 002054          196 IPWGGPIGMIRIGRIC--GQFIVNPTMDELSLSDLNLVYACTREK-TLMID-VQAREISEKDLEAGLRLAHPEAVKYLEP  271 (974)
Q Consensus       196 iP~~~~v~av~vg~i~--g~~vldPt~~e~~~s~~~l~v~~t~~~-i~mie-~~~~~~~e~~~~~al~~a~~~~~~i~~~  271 (974)
                      .++++...+|++++.+  +.+|+|||++|+..++.+++|+.+.++ |+.++ .++..|+.+++.+++++|.+.++++++.
T Consensus         1 L~i~h~Pi~vT~~~~~~g~~~lvDPt~~EE~~~~~~ltv~~n~~gei~~l~k~Gg~~l~~~~l~~~~~~A~~~~~el~~~   80 (118)
T d2nn6a2           1 LSIHHMPICVSFAFFQQGTYLLVDPNEREERVMDGLLVIAMNKHREICTIQSSGGIMLLKDQVLRCSKIAGVKVAEITEL   80 (118)
T ss_dssp             CCBCCCEEEEEEEECTTTSSEEESCCHHHHHHCSCEEEEEEETTTEEEEEEEESCCCCCHHHHHHHHHHHHHHHHHHHHH
T ss_pred             CCcCceEEEEEEEEEecCCeEEECCCHHHHhCCCCcEEEEEeCCCcEEEEEecCCcccCHHHHHHHHHHHHHHHHHHHHH
Confidence            3667777899999763  679999999999999999999999987 65555 5666799999999999999999999999


Q ss_pred             HHHHHHH
Q 002054          272 QIRLAEK  278 (974)
Q Consensus       272 ~~~~~~~  278 (974)
                      +++.+++
T Consensus        81 i~~aLk~   87 (118)
T d2nn6a2          81 ILKALEN   87 (118)
T ss_dssp             HHHHHHH
T ss_pred             HHHHHHH
Confidence            9988765

>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=98.58  E-value=1.6e-08  Score=86.48  Aligned_cols=62  Identities=15%  Similarity=0.182  Sum_probs=56.0

Q ss_pred             cceeeeeccchhhhhcCCCccchhhhhhhhCceEEee---CCEEEEEecCHHHHHHHHHHHHHHh
Q 002054          616 RLATLKYDNDTLRRLIGPLGALKRKIEEETGGRISVS---DGTLTVVAKNRSVMEKVLEKVDFII  677 (974)
Q Consensus       616 ~~~~~~i~~~ki~~vIg~gGk~i~~i~~~~g~~Idi~---dg~v~i~~~~~~~~~~a~~~i~~l~  677 (974)
                      ..+.++||+++++.+||+||++|++|++++|+++.++   +|.+.|++.+.+++++|+++|+.+.
T Consensus         8 ~t~~i~Ip~~~ig~vIG~gG~~I~~I~~~tGa~i~i~~~~~g~v~I~g~~~eav~~A~~~Ie~~~   72 (78)
T d2cpqa1           8 FHEEFVVREDLMGLAIGTHGSNIQQARKVPGVTAIELDEDTGTFRIYGESADAVKKARGFLEFVE   72 (78)
T ss_dssp             EEEEEECCHHHHHHHHTTTTHHHHHHHTSTTEEEEEEETTTTEEEEEESSHHHHHHHHHHHSCCC
T ss_pred             ceEEEEECHHHHHHHcCCChHHHHHHHHhcCcEEEEecCCCceEEEEECCHHHHHHHHHHHHHhh
Confidence            3557899999999999999999999999999998874   4899999999999999999987554

>d2ix0a3 b.40.4.5 (A:558-644) Exoribonuclease 2, RNB {Escherichia coli [TaxId: 562]}

class: All beta proteins
fold: OB-fold
superfamily: Nucleic acid-binding proteins
family: Cold shock DNA-binding domain-like
domain: Exoribonuclease 2, RNB
species: Escherichia coli [TaxId: 562]

Probab=98.57  E-value=5.2e-08  Score=85.01  Aligned_cols=60  Identities=15%  Similarity=0.157  Sum_probs=52.0

Q ss_pred             CCCEEEEEEEEEeCCeEEEEeCC-CeEEEEecccCCC-------------------CCCCCCCEEEEEEEEEeCCCceee
Q 002054          910 LGTKVAAKVYQVRARGLVLDLGG-GIRGMYRFENNEK-------------------KDFVVGDELLVKCSSFTGKGIPVV  969 (974)
Q Consensus       910 vG~vV~G~V~~I~~~GvFV~L~~-gv~Glih~se~~~-------------------~~f~vGd~V~vkVl~id~~~~~~~  969 (974)
                      .|+..+|+|.+|++||+||+|.+ +++||||.++++.                   ..|+.||+|+|+|+++|++++-++
T Consensus         3 ~~~~F~g~Is~v~~~GifV~L~e~~~eGlI~~s~L~~d~y~~d~~~~~l~~~~~~~~~~~~Gd~V~V~v~~vd~~~r~I~   82 (87)
T d2ix0a3           3 TDTRFAAEIVDISRGGMRVRLVDNGAIAFIPAPFLHAVRDELVCSQENGTVQIKGETVYKVTDVIDVTIAEVRMETRSII   82 (87)
T ss_dssp             SCCCEEEEEEEEETTEEEEEETTTCCEEEEEGGGTCSCGGGEEEETTTTEEEETTEEEEETTCEEEEEEEEEETTTTEEE
T ss_pred             CCCEEEEEEEEEEcCeEEEEEecCCcEEEEEehhCCCceEEEeccceEEEEEEcccEEEECCCEEEEEEEEEecccCeEE
Confidence            47889999999999999999976 7999999997641                   248999999999999998877554

>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=98.56  E-value=2e-08  Score=86.89  Aligned_cols=63  Identities=30%  Similarity=0.433  Sum_probs=52.3

Q ss_pred             CCcceeeeeccchhhhhcCCCccchhhhhhhhCceEEee--CCEEEEEecCH----HHHHHHHHHHHHHh
Q 002054          614 SPRLATLKYDNDTLRRLIGPLGALKRKIEEETGGRISVS--DGTLTVVAKNR----SVMEKVLEKVDFII  677 (974)
Q Consensus       614 ~p~~~~~~i~~~ki~~vIg~gGk~i~~i~~~~g~~Idi~--dg~v~i~~~~~----~~~~~a~~~i~~l~  677 (974)
                      .|++ +++||+++|+.+||+||++|++|+++||++|+|+  +|.+.+...+.    .++++|.+.+..+.
T Consensus         2 ~pri-~i~ip~~~ig~vIG~gG~~Ik~i~~~tg~~I~Id~d~g~v~i~~~~~~~~~~a~~~a~~iI~aI~   70 (84)
T d1tuaa1           2 KPRI-YVKVKPERLGAVIGPRGEVKAEIMRRTGTVITVDTENSMVIVEPEAEGIPPVNLMKAAEVVKAIS   70 (84)
T ss_dssp             CCCE-EEECCGGGHHHHHCGGGHHHHHHHHHHTEEEEEETTTTEEEEEESSTTSCHHHHHHHHHHHHHHH
T ss_pred             CCcE-EEEeCHHHcCeeecCCchhHHHHHHHHCCEEEEEcCCCeEEEecCCccccHHHHHHHHHHHHHHh
Confidence            5887 6899999999999999999999999999999996  58999887653    45556666665554

>d2nn6g1 b.40.4.5 (G:107-194) S1-domain of exosome component 3 (RRP40) {Human (Homo sapiens) [TaxId: 9606]}

class: All beta proteins
fold: OB-fold
superfamily: Nucleic acid-binding proteins
family: Cold shock DNA-binding domain-like
domain: S1-domain of exosome component 3 (RRP40)
species: Human (Homo sapiens) [TaxId: 9606]

Probab=98.51  E-value=9e-08  Score=83.63  Aligned_cols=66  Identities=20%  Similarity=0.203  Sum_probs=61.8

Q ss_pred             CCCCEEEEEEEEEeCCeEEEEeCCCeEEEEecccCC------CCCCCCCCEEEEEEEEEeCCCceeeeecCC
Q 002054          909 KLGTKVAAKVYQVRARGLVLDLGGGIRGMYRFENNE------KKDFVVGDELLVKCSSFTGKGIPVVSLVDS  974 (974)
Q Consensus       909 ~vG~vV~G~V~~I~~~GvFV~L~~gv~Glih~se~~------~~~f~vGd~V~vkVl~id~~~~~~~~~~~~  974 (974)
                      ++||+|-|+|.++..+|.||++.....|++|.++++      ...|++||.|.|||.++|+++.+.+|.+|+
T Consensus         5 ~~GD~ViG~V~~~~~~~~~VdI~s~~~a~L~~~~f~g~~k~~r~~l~~GD~V~arV~~v~~~~~~~Lscvd~   76 (88)
T d2nn6g1           5 VKGDHVIGIVTAKSGDIFKVDVGGSEPASLSYLSFEGATKRNRPNVQVGDLIYGQFVVANKDMEPEMVCIDS   76 (88)
T ss_dssp             CSSEEEEEEEEEEETTEEEEECSSSSCCCEESCSSSCCSSCSSSSSCTTCEEEEEEEECCTTSCCEEECSBT
T ss_pred             CCCCEEEEEEEEEeCCeEEEEcCCCeeEEEeHHHcCccccccCcccCCCCEEEEEEEEeCCCCCEEEEEEcc
Confidence            689999999999999999999999999999999875      457999999999999999999999999885

>d1y14b1 b.40.4.5 (B:81-171) C-terminal domain of RNA polymerase II subunit RBP7 (RpoE) {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: All beta proteins
fold: OB-fold
superfamily: Nucleic acid-binding proteins
family: Cold shock DNA-binding domain-like
domain: C-terminal domain of RNA polymerase II subunit RBP7 (RpoE)
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=98.44  E-value=2.9e-07  Score=81.04  Aligned_cols=58  Identities=12%  Similarity=0.158  Sum_probs=51.0

Q ss_pred             CCCEEEEEEEEEeCCeEEEEeCCCeEEEEecccCC-----------------CCCCCCCCEEEEEEEEEeCCCcee
Q 002054          910 LGTKVAAKVYQVRARGLVLDLGGGIRGMYRFENNE-----------------KKDFVVGDELLVKCSSFTGKGIPV  968 (974)
Q Consensus       910 vG~vV~G~V~~I~~~GvFV~L~~gv~Glih~se~~-----------------~~~f~vGd~V~vkVl~id~~~~~~  968 (974)
                      +|+++.|+|+++++||+||+++ .++||+|.+.++                 .+.|+.||+|++||+++|.+....
T Consensus         3 ~Gev~~g~I~~v~~~G~fv~lg-~~eg~i~~~~l~~~~~~d~~~~~~~~~~~~~~~~~Gd~VrvkV~~v~~~~~~i   77 (91)
T d1y14b1           3 KGEVVDGTVVSCSQHGFEVQVG-PMKVFVTKHLMPQDLTFNAGSNPPSYQSSEDVITIKSRIRVKIEGCISQVSSI   77 (91)
T ss_dssp             TTCEEEEEEEEEETTEEEEEET-TEEEEEEGGGSCTTCEECC-----CEECSSCEECTTCEEEEEEEEEEEETTEE
T ss_pred             CCCEEEEEEEEEEeeEEEEEEc-CeEEEEEhhhcCcceEEccccceeEecccCeEEeCCCEEEEEEEEEecccCcc
Confidence            7999999999999999999996 799999999664                 335999999999999999776554

>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=98.41  E-value=1.2e-08  Score=85.14  Aligned_cols=59  Identities=19%  Similarity=0.256  Sum_probs=47.4

Q ss_pred             eeeeccchhhhhcCCCccchhhhhhhhCceEEee-CCEEEEEecCHHHHHHHHHHHHHHh
Q 002054          619 TLKYDNDTLRRLIGPLGALKRKIEEETGGRISVS-DGTLTVVAKNRSVMEKVLEKVDFII  677 (974)
Q Consensus       619 ~~~i~~~ki~~vIg~gGk~i~~i~~~~g~~Idi~-dg~v~i~~~~~~~~~~a~~~i~~l~  677 (974)
                      .++||+++++.+||+||++|+.|+++||++|+++ +|++.+++.+++.+++|.++|+.+.
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 VIDIMPVKVPRVIGKNKSMYETLTSKSGCSIFVANNGRIWATCPSRFSEEILIEAIRKIE   63 (69)
T ss_dssp             EEECCGGGHHHHHCGGGHHHHHHHTTC---CEECTTSEEEC-----CTTCCTHHHHTTTT
T ss_pred             EEEEChhhccceECCchhHHHHHHHHHCCEEEEcCCCEEEEEeCCHHHHHHHHHHHHHHH
Confidence            5789999999999999999999999999999997 8999999999899999999888765

>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=98.35  E-value=2.9e-07  Score=79.64  Aligned_cols=60  Identities=20%  Similarity=0.293  Sum_probs=54.8

Q ss_pred             eeeeeccchhhhhcCCCccchhhhhhhhCceEEee-CCEEEEEecCHHHHHHHHHHHHHHhh
Q 002054          618 ATLKYDNDTLRRLIGPLGALKRKIEEETGGRISVS-DGTLTVVAKNRSVMEKVLEKVDFIIG  678 (974)
Q Consensus       618 ~~~~i~~~ki~~vIg~gGk~i~~i~~~~g~~Idi~-dg~v~i~~~~~~~~~~a~~~i~~l~~  678 (974)
                      +.++||+++++.+||+||++|+.|+++||++|+++ +|.|.|.. +.+.++.|+++|+.+..
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 RIVAINPARVPRVIGKKGSMIKLLKSELDVQIVVGQNGLIWVNG-DRRKVSIAEEAIYLIEQ   63 (84)
T ss_dssp             EEEECCGGGHHHHHCGGGHHHHHHHHHHTCEEEECTTSEEEEES-CHHHHHHHHHHHHHHHH
T ss_pred             EEEEEChhhcceeeCCcHHHHHHHHHHHCCEEEECCCCEEEEEe-CHHHHHHHHHHHHHHHH
Confidence            46789999999999999999999999999999997 89999987 56899999999988873

>d2c35b1 b.40.4.5 (B:78-171) C-terminal domain of RNA polymerase II subunit RBP7 (RpoE) {Human (Homo sapiens) [TaxId: 9606]}

class: All beta proteins
fold: OB-fold
superfamily: Nucleic acid-binding proteins
family: Cold shock DNA-binding domain-like
domain: C-terminal domain of RNA polymerase II subunit RBP7 (RpoE)
species: Human (Homo sapiens) [TaxId: 9606]

Probab=98.19  E-value=2e-06  Score=75.99  Aligned_cols=58  Identities=21%  Similarity=0.156  Sum_probs=49.6

Q ss_pred             CCCEEEEEEEEEeCCeEEEEeCCCeEEEEecccCC-------------------CCCCCCCCEEEEEEEEEeCCCcee
Q 002054          910 LGTKVAAKVYQVRARGLVLDLGGGIRGMYRFENNE-------------------KKDFVVGDELLVKCSSFTGKGIPV  968 (974)
Q Consensus       910 vG~vV~G~V~~I~~~GvFV~L~~gv~Glih~se~~-------------------~~~f~vGd~V~vkVl~id~~~~~~  968 (974)
                      +|+++.|+|++++++|+||+++ .++||+|.++++                   ...|+.||.|++||++++.+....
T Consensus         4 ~Gev~~g~V~~v~~~G~fv~lg-~~~~~v~~~~l~~d~~y~~~~~~~~~~~~~~~~~~~~Gd~VrvkV~~v~~~~~~I   80 (94)
T d2c35b1           4 KGEVVDAVVTQVNKVGLFTEIG-PMSCFISRHSIPSEMEFDPNSNPPCYKTMDEDIVIQQDDEIRLKIVGTRVDKNDI   80 (94)
T ss_dssp             TTCEEEEEEEEEETTEEEEEET-TEEEEEEGGGSCTTEEEESSSSSCEEEETTSCSEEETTCEEEEEEEEEEEETTEE
T ss_pred             CCCEEEEEEEEEEeeEEEEEec-CceEEEEhhhcCcceeecccccceEEEcccceEEEeCCCEEEEEEEEEecCcCcc
Confidence            7999999999999999999995 799999999764                   224889999999999887655443

>d1hh2p1 b.40.4.5 (P:127-198) S1 domain of NusA {Thermotoga maritima [TaxId: 2336]}

class: All beta proteins
fold: OB-fold
superfamily: Nucleic acid-binding proteins
family: Cold shock DNA-binding domain-like
domain: S1 domain of NusA
species: Thermotoga maritima [TaxId: 2336]

Probab=98.11  E-value=5.1e-06  Score=69.32  Aligned_cols=56  Identities=16%  Similarity=0.112  Sum_probs=51.5

Q ss_pred             CCCCEEEEEEEEEeCCeEEEEeCCCeEEEEecccC-CCCCCCCCCEEEEEEEEEeCCC
Q 002054          909 KLGTKVAAKVYQVRARGLVLDLGGGIRGMYRFENN-EKKDFVVGDELLVKCSSFTGKG  965 (974)
Q Consensus       909 ~vG~vV~G~V~~I~~~GvFV~L~~gv~Glih~se~-~~~~f~vGd~V~vkVl~id~~~  965 (974)
                      ++|++|+|+|.++.+.+++|+|+ +..|++|.+++ +.+.|++||+|+|-|.+|+...
T Consensus         7 ~~geiv~G~V~r~~~~~~~Vdlg-~~eaiLp~~eqip~E~~~~Gdrik~~i~~V~~~~   63 (72)
T d1hh2p1           7 LKGTVTTAEVIRVMGEWADIRIG-KLETRLPKKEWIPGEEIKAGDLVKVYIIDVVKTT   63 (72)
T ss_dssp             CTTCEEEEEEEEECSSEEEEEET-TEEEEEEGGGSCTTCCCCTTCEEEEEEEEEEEET
T ss_pred             ccCcEEEEEEEEEcCCCEEEEEC-CcEEECCHHHcCCCCCCCCCCEEEEEEEEEEEcC
Confidence            68999999999999999999997 79999999976 6889999999999999998544

>d2ja9a1 b.40.4.5 (A:62-151) S1-domain of exosome component 3 (RRP40) {Saccharomyces cerevisiae [TaxId: 4932]}

class: All beta proteins
fold: OB-fold
superfamily: Nucleic acid-binding proteins
family: Cold shock DNA-binding domain-like
domain: S1-domain of exosome component 3 (RRP40)
species: Saccharomyces cerevisiae [TaxId: 4932]

Probab=98.07  E-value=4.3e-06  Score=73.00  Aligned_cols=66  Identities=11%  Similarity=0.008  Sum_probs=59.3

Q ss_pred             CCCCEEEEEEEEEeCCeEEEEeCCCeEEEEecccCC-------CCCCCCCCEEEEEEEEEeCCCceeeeecCC
Q 002054          909 KLGTKVAAKVYQVRARGLVLDLGGGIRGMYRFENNE-------KKDFVVGDELLVKCSSFTGKGIPVVSLVDS  974 (974)
Q Consensus       909 ~vG~vV~G~V~~I~~~GvFV~L~~gv~Glih~se~~-------~~~f~vGd~V~vkVl~id~~~~~~~~~~~~  974 (974)
                      ++||+|-|+|.++...|.||+|+....|++|.+...       ...|++||.|.|+|.++|+++.+.+|.+|+
T Consensus         6 ~~gD~ViG~V~~~~~~~~~vdI~~~~~~~L~~~~~f~g~~k~~r~~l~~GDlV~arV~~v~~~~~~~Lsc~~~   78 (90)
T d2ja9a1           6 SVNDFVIGVIIGTFSDSYKVSLQNFSSSVSLSYMAFPNASKKNRPTLQVGDLVYARVCTAEKELEAEIECFDS   78 (90)
T ss_dssp             CTTCEEEEEEEEECSSEEEEESSTTSCCEEEETTSSTTCCSSSCCCCCTTCEEEEEEEECCTTSCCEEESSCT
T ss_pred             CCCCEEEEEEEEEeCCcEEEEcCCcchhhhhhhhccCccccccCCccCCCCEEEEEEEEECCCCCEEEEEecc
Confidence            689999999999999999999998899998876431       456999999999999999999999998874

>d1hh2p1 b.40.4.5 (P:127-198) S1 domain of NusA {Thermotoga maritima [TaxId: 2336]}

class: All beta proteins
fold: OB-fold
superfamily: Nucleic acid-binding proteins
family: Cold shock DNA-binding domain-like
domain: S1 domain of NusA
species: Thermotoga maritima [TaxId: 2336]

Probab=98.01  E-value=8.4e-06  Score=67.99  Aligned_cols=64  Identities=19%  Similarity=0.125  Sum_probs=55.3

Q ss_pred             cccCcEEEEEEEEEeeceEEEEEcCCeEEEEecccCCCccccccccccccCCEEEEEEEEEcc--CC-ceEEEE
Q 002054          681 IEVGGIYKGVVTSVKEYGAFVEFNGGQQGLLHVSELSHEPVSRVSDVVSVGQQLSLRCIGQDV--RG-NIKLSL  751 (974)
Q Consensus       681 ~~~G~i~~G~V~~i~~~G~fV~l~~g~~Glvhisels~~~v~~~~~~~~vGd~V~vkVl~id~--~g-ri~LS~  751 (974)
                      -++|+++.|+|.++.+..++|+| ++.+|+||.+|..      |.+.|++||.|+|-|.+++.  +| +|.||+
T Consensus         6 ~~~geiv~G~V~r~~~~~~~Vdl-g~~eaiLp~~eqi------p~E~~~~Gdrik~~i~~V~~~~kgpqI~lSR   72 (72)
T d1hh2p1           6 ELKGTVTTAEVIRVMGEWADIRI-GKLETRLPKKEWI------PGEEIKAGDLVKVYIIDVVKTTKGPKILVSR   72 (72)
T ss_dssp             CCTTCEEEEEEEEECSSEEEEEE-TTEEEEEEGGGSC------TTCCCCTTCEEEEEEEEEEEETTEEEEEEES
T ss_pred             hccCcEEEEEEEEEcCCCEEEEE-CCcEEECCHHHcC------CCCCCCCCCEEEEEEEEEEEcCCCCeEEEeC
Confidence            36899999999999999999999 5899999999874      45779999999999999976  33 677774

>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=98.01  E-value=9.8e-07  Score=78.85  Aligned_cols=60  Identities=20%  Similarity=0.324  Sum_probs=52.5

Q ss_pred             hhhhcCCCccchhhhhhhhCceEEeeCCEEEEEecCHHHHHHHHHHHHHHhhcccccCcEEE
Q 002054          627 LRRLIGPLGALKRKIEEETGGRISVSDGTLTVVAKNRSVMEKVLEKVDFIIGREIEVGGIYK  688 (974)
Q Consensus       627 i~~vIg~gGk~i~~i~~~~g~~Idi~dg~v~i~~~~~~~~~~a~~~i~~l~~~~~~~G~i~~  688 (974)
                      .+.+||+||++|+.|++.||++|+|++.++.+.+ +.+.++.|+++|+.++ ..+++|.+|.
T Consensus        24 ~GrIIG~gGktik~Ie~~Tg~~I~I~d~~v~iig-~~e~i~~A~~~Ie~li-~~~e~g~VY~   83 (104)
T d1tuaa2          24 KGRIIGEGGRARRTIEEMTDTYINVGEYEVAIIG-DYERAMAAKQAIEMLA-EGRMHSTVYR   83 (104)
T ss_dssp             HHHHHCGGGHHHHHHHHHHTCEEEECSSEEEEEE-EHHHHHHHHHHHHHHH-TTCCHHHHHH
T ss_pred             hcceeCCCcHHHHHHHHHHCCeEEEeCCeEEEEE-CchhHHHHHHHHHHHH-cCCCccHHHH
Confidence            6889999999999999999999999977777776 5678999999999998 6788887764

>d1e3ha6 d.101.1.1 (A:483-578) Polynucleotide phosphorylase/guanosine pentaphosphate synthase (PNPase/GPSI), domains 2 and 5 {Streptomyces antibioticus [TaxId: 1890]}

class: Alpha and beta proteins (a+b)
fold: Ribonuclease PH domain 2-like
superfamily: Ribonuclease PH domain 2-like
family: Ribonuclease PH domain 2-like
domain: Polynucleotide phosphorylase/guanosine pentaphosphate synthase (PNPase/GPSI), domains 2 and 5
species: Streptomyces antibioticus [TaxId: 1890]

Probab=97.91  E-value=1.8e-05  Score=68.30  Aligned_cols=76  Identities=20%  Similarity=0.256  Sum_probs=66.4

Q ss_pred             CeEEEEEEEEC------C--EEEEcCCHHHHhcCccceeEeeeCCeEEEEEecC--CCCCHHHHHHHHHHHHHHHHHHHH
Q 002054          201 PIGMIRIGRIC------G--QFIVNPTMDELSLSDLNLVYACTREKTLMIDVQA--REISEKDLEAGLRLAHPEAVKYLE  270 (974)
Q Consensus       201 ~v~av~vg~i~------g--~~vldPt~~e~~~s~~~l~v~~t~~~i~mie~~~--~~~~e~~~~~al~~a~~~~~~i~~  270 (974)
                      |||++.+|++-      +  .++.|-.-.|+...|+||-||||+++|..+|++-  ..+|.+.+.+||+.|.++...|++
T Consensus         2 PVAGIamGLi~~~~~~~~~~~iLtDI~G~ED~~GDMDFKVAGT~~GITa~QmDiKi~Gi~~~il~~Al~qAk~gR~~IL~   81 (96)
T d1e3ha6           2 PVAGIAMGLISQEINGETHYVALTDILGAEDAFGDMDFKVAGTKEFVTALQLDTKLDGIPASVLAAALKQARDARLHILD   81 (96)
T ss_dssp             CCEEEEEEEEEEEETTEEEEEEESSCCSHHHHHCSEEEEEEECSSCEEEEEEEECCSCCCHHHHHHHHHHHHHHHHHHHH
T ss_pred             CcceeeeeeeeccCCCCccEEEEeeccCchhhccCcccccccCcccceeeeeeecccCCCHHHHHHHHHHHHHHHHHHHH
Confidence            89999999982      2  2456677789999999999999999999999973  349999999999999999999999


Q ss_pred             HHHHHH
Q 002054          271 PQIRLA  276 (974)
Q Consensus       271 ~~~~~~  276 (974)
                      .|.+.+
T Consensus        82 ~M~~~i   87 (96)
T d1e3ha6          82 VMMEAI   87 (96)
T ss_dssp             HHHHHC
T ss_pred             HHHHHh
Confidence            988766

>d2nn6i1 b.40.4.5 (I:61-185) Exosome component 1, EXOSC1 {Human (Homo sapiens) [TaxId: 9606]}

class: All beta proteins
fold: OB-fold
superfamily: Nucleic acid-binding proteins
family: Cold shock DNA-binding domain-like
domain: Exosome component 1, EXOSC1
species: Human (Homo sapiens) [TaxId: 9606]

Probab=97.90  E-value=9.4e-06  Score=75.21  Aligned_cols=73  Identities=16%  Similarity=0.171  Sum_probs=61.9

Q ss_pred             cccCcEEEEEEEEEeeceEEEEEc--------CCeEEEEecccCC--CccccccccccccCCEEEEEEEEEcc-CCceEE
Q 002054          681 IEVGGIYKGVVTSVKEYGAFVEFN--------GGQQGLLHVSELS--HEPVSRVSDVVSVGQQLSLRCIGQDV-RGNIKL  749 (974)
Q Consensus       681 ~~~G~i~~G~V~~i~~~G~fV~l~--------~g~~Glvhisels--~~~v~~~~~~~~vGd~V~vkVl~id~-~gri~L  749 (974)
                      +++|+++.|+|+++.+..++|+|.        ....|++|.+++.  +....++.+.|++||.|+++|++++. +..+.|
T Consensus         5 P~vGDiVig~V~~v~~~~a~v~I~~v~~~~l~~~~~g~i~~~dvr~te~d~~~m~~~fr~GDiV~A~Vis~~~~~~~~~L   84 (125)
T d2nn6i1           5 PDVGAIVTCKVSSINSRFAKVHILYVGSMPLKNSFRGTIRKEDVRATEKDKVEIYKSFRPGDIVLAKVISLGDAQSNYLL   84 (125)
T ss_dssp             CCTTCEEEEEEEEECSSEEEEEEEESSSSCCCCSSCSCEEEEGGGTCSSCCCCGGGTCCSSSEEEEEEEEEETTTTEEEE
T ss_pred             CCCCCEEEEEEEEecCCEEEEEEeEecCcccccCccccccHHHcccchhhhhhHHHhcCCCCEEEEEEEEccCCCccEEE
Confidence            789999999999999999999994        2567999999984  34555788999999999999999976 346889


Q ss_pred             EEec
Q 002054          750 SLKA  753 (974)
Q Consensus       750 S~K~  753 (974)
                      |.++
T Consensus        85 st~~   88 (125)
T d2nn6i1          85 TTAE   88 (125)
T ss_dssp             ECCS
T ss_pred             EecC
Confidence            9765

>d1e3ha5 d.101.1.1 (A:152-262) Polynucleotide phosphorylase/guanosine pentaphosphate synthase (PNPase/GPSI), domains 2 and 5 {Streptomyces antibioticus [TaxId: 1890]}

class: Alpha and beta proteins (a+b)
fold: Ribonuclease PH domain 2-like
superfamily: Ribonuclease PH domain 2-like
family: Ribonuclease PH domain 2-like
domain: Polynucleotide phosphorylase/guanosine pentaphosphate synthase (PNPase/GPSI), domains 2 and 5
species: Streptomyces antibioticus [TaxId: 1890]

Probab=97.83  E-value=1.4e-05  Score=72.39  Aligned_cols=91  Identities=11%  Similarity=0.103  Sum_probs=73.6

Q ss_pred             ccccccceeeeeeccCCCCCCcccceEEEecCCccccccCCccEEEEeeCCc-----eEEEEeecc----------CCCC
Q 002054          512 LQEHVAGVSVGLVSEVDPSTGEIKDYRILTDILGLEDHLGDMDFKIAGTRIG-----VTAIQLDIK----------PAGI  576 (974)
Q Consensus       512 i~~~vagvs~gli~~~d~~~~~~~~~~iL~Dp~~~Ee~~~d~d~~Va~t~~g-----I~alq~~~k----------~~~i  576 (974)
                      +.+|++||.+|++++           .++++||..|-..+++|+.|+||.++     +..+...++          ...+
T Consensus         1 f~GPvgaVRVg~idg-----------e~viNPt~~el~~S~ldLvVaGt~~~~~~~~v~mie~~~~e~~~~mie~~a~e~   69 (111)
T d1e3ha5           1 FSGPIGGVRVALIRG-----------QWVAFPTHTELEDAVFDMVVAGRVLEDGDVAIMMVEAEATEKTIQLVKDGAEAP   69 (111)
T ss_dssp             BCCCCEEEEEEEETT-----------EEEESCCHHHHTTEEEEEEEEEEECTTSCEEEEEEEEEECTTHHHHHHTTCCCC
T ss_pred             CCCCEEEEEEEEECC-----------EEEECCCHHHHhcCceEEEEeecccccchHHHHHHHhcchhHHHHHHHhccccc
Confidence            468999999999975           58999999999999999999999754     333333322          2358


Q ss_pred             CHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCCCCCCC
Q 002054          577 PLDIICECLEHAHKGRLQILDHMEREISAPRTQDDRN  613 (974)
Q Consensus       577 ~~e~l~~al~~A~~~~~~I~~~m~~~i~~~~~~~~~~  613 (974)
                      +++.+.+||+.|++..+.+++.+++..++..+++.++
T Consensus        70 ~E~~~~~ai~~a~~~i~~~i~~q~el~~~~gk~k~e~  106 (111)
T d1e3ha5          70 TEEVVAAGLDAAKPFIKVLCKAQADLAAKAAKPTGEF  106 (111)
T ss_dssp             CHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCC
T ss_pred             cHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCcC
Confidence            9999999999999999999999988887766655544

>d2asba1 b.40.4.5 (A:108-183) S1 domain of NusA {Mycobacterium tuberculosis [TaxId: 1773]}

class: All beta proteins
fold: OB-fold
superfamily: Nucleic acid-binding proteins
family: Cold shock DNA-binding domain-like
domain: S1 domain of NusA
species: Mycobacterium tuberculosis [TaxId: 1773]

Probab=97.74  E-value=2.5e-05  Score=65.69  Aligned_cols=58  Identities=16%  Similarity=0.182  Sum_probs=50.3

Q ss_pred             CCCCEEEEEEEEEeCC----eEEEEeC---CCeEEEEecccC-CCCCCCCCCEEEEEEEEEeCCCc
Q 002054          909 KLGTKVAAKVYQVRAR----GLVLDLG---GGIRGMYRFENN-EKKDFVVGDELLVKCSSFTGKGI  966 (974)
Q Consensus       909 ~vG~vV~G~V~~I~~~----GvFV~L~---~gv~Glih~se~-~~~~f~vGd~V~vkVl~id~~~~  966 (974)
                      ++|++|+|+|+++...    -++|+|+   +++.|++|.++. |.+.|++||.|+|.|.+|+...+
T Consensus         3 r~geiv~G~V~r~~~~~~~~~v~vdlG~~~~~~EaiLp~~eqip~E~y~~Gdrik~~i~~V~~~~k   68 (76)
T d2asba1           3 REGEIVAGVIQRDSRANARGLVVVRIGTETKASEGVIPAAEQVPGESYEHGNRLRCYVVGVTRGAR   68 (76)
T ss_dssp             CTTCEEEEEEECCHHHHHTTCEEEEECSSSSCEEEEECGGGSCTTCCCCTTCEEEEEEEEEECCSS
T ss_pred             ccceEEEEEEEEEecCCCceEEEEECCCCCCCEEEECCHHHcCCCcccCCCCEEEEEEEEEEecCC
Confidence            6899999999998643    3899997   589999999966 78899999999999999996543

>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=97.71  E-value=3e-05  Score=67.71  Aligned_cols=69  Identities=16%  Similarity=0.144  Sum_probs=60.7

Q ss_pred             CCCCCCCCcceeeeeccchhhhhcCCCccchhhhhhhhCceEEee-----CCEEEEEecCHHHHHHHHHHHHHHh
Q 002054          608 TQDDRNSPRLATLKYDNDTLRRLIGPLGALKRKIEEETGGRISVS-----DGTLTVVAKNRSVMEKVLEKVDFII  677 (974)
Q Consensus       608 ~~~~~~~p~~~~~~i~~~ki~~vIg~gGk~i~~i~~~~g~~Idi~-----dg~v~i~~~~~~~~~~a~~~i~~l~  677 (974)
                      ..+...+|....+.||++..+.+||++|.+|++|+++||++|.+.     +..+.|.+ +.+..++|..++..++
T Consensus         2 e~l~~~~~vt~~i~Vp~~~~~~iIG~~G~~i~~I~~~tg~~I~~p~~~~~~~~v~I~G-~~~~V~~A~~~I~~~v   75 (91)
T d2ctka1           2 EALEALVPVTIEVEVPFDLHRYVIGQKGSGIRKMMDEFEVNIHVPAPELQSDIIAITG-LAANLDRAKAGLLERV   75 (91)
T ss_dssp             CCCCCSSCEEEEEECCHHHHHHHHCSSSHHHHHHHHHTCCEEECCCTTTTCCEEEEEE-CHHHHHHHHHHHHHHH
T ss_pred             hhhhhhCCEEEEEEECHHHHhHhcCCCchhHHHHHHHhCCEEEECCCCCCcceEEEEC-CHHHHHHHHHHHHHHH
Confidence            457788899999999999999999999999999999999999984     24688877 4689999999988776

>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=97.60  E-value=3.6e-05  Score=68.95  Aligned_cols=69  Identities=16%  Similarity=0.250  Sum_probs=59.6

Q ss_pred             CCCCCCCCcceeeeeccchhhhhcCCCccchhhhhhhhCceEEee-C--------CEEEEEecCHHHHHHHHHHHHHHh
Q 002054          608 TQDDRNSPRLATLKYDNDTLRRLIGPLGALKRKIEEETGGRISVS-D--------GTLTVVAKNRSVMEKVLEKVDFII  677 (974)
Q Consensus       608 ~~~~~~~p~~~~~~i~~~ki~~vIg~gGk~i~~i~~~~g~~Idi~-d--------g~v~i~~~~~~~~~~a~~~i~~l~  677 (974)
                      ..+.++.|..+.+.||.+.++.+||++|.+|++|+++||++|.+. +        ..|.|+. +.+.+++|...|..++
T Consensus         7 ~~~~~~~~v~~~i~IP~~~vg~vIGk~G~~Ik~I~~~tga~I~i~~~~~~~~~~~r~v~I~G-~~~~v~~A~~~I~~~i   84 (104)
T d1we8a_           7 GILTENTPVFEQLSVPQRSVGRIIGRGGETIRSICKASGAKITCDKESEGTLLLSRLIKISG-TQKEVAAAKHLILEKV   84 (104)
T ss_dssp             CCCSSSCEEEEEEEEETTTHHHHHTTTSHHHHHHHHHHCCEEEECCSSCCSSSSEEEEEEEE-EHHHHHHHHHHHHHHH
T ss_pred             CccCCCCCEEEEEEECHHHhcceECCCCcchHHHHHHcCCEEEECCCCCCCCCCccEEEEEe-CHHHHHHHHHHHHHHH
Confidence            346788899999999999999999999999999999999999984 1        1578877 6788999999888776

>d1smxa_ b.40.4.5 (A:) S1-domain of Ribonuclease E {Escherichia coli [TaxId: 562]}

class: All beta proteins
fold: OB-fold
superfamily: Nucleic acid-binding proteins
family: Cold shock DNA-binding domain-like
domain: S1-domain of Ribonuclease E
species: Escherichia coli [TaxId: 562]

Probab=97.44  E-value=0.00015  Score=62.37  Aligned_cols=58  Identities=28%  Similarity=0.543  Sum_probs=49.8

Q ss_pred             cEEEEEEEEEeec--eEEEEEcCCeEEEEecccCCCccc---------cccccccccCCEEEEEEEEEcc
Q 002054          685 GIYKGVVTSVKEY--GAFVEFNGGQQGLLHVSELSHEPV---------SRVSDVVSVGQQLSLRCIGQDV  743 (974)
Q Consensus       685 ~i~~G~V~~i~~~--G~fV~l~~g~~Glvhisels~~~v---------~~~~~~~~vGd~V~vkVl~id~  743 (974)
                      .||.|+|.+|.+.  ++||++..+..||||.+++...+.         .+..+.+++||.|-|.|.. |+
T Consensus         2 NIY~G~V~~V~pgl~AAFVDiG~~k~gFL~~~di~~~~~~~~~~~~~~~~i~~~l~~G~~ilVQV~K-e~   70 (87)
T d1smxa_           2 NIYKGKITRIEPSLEAAFVDYGAERHGFLPLKEIAREYFPANYSAHGRPNIKDVLREGQEVIVQIDK-EE   70 (87)
T ss_dssp             CCEEEEEEEEEGGGTEEEEESSSSSCEEEEGGGSCGGGCSSCCCSSSCCCGGGTCCTTCEEEEEEEE-CC
T ss_pred             CcEEEEEEEecCCceEEEEEeCCCccceeEecccceeeeccccccccccchhhhccCCCeEEEEEee-cc
Confidence            5899999999995  999999999999999999876543         2456779999999999998 55

>d2asba1 b.40.4.5 (A:108-183) S1 domain of NusA {Mycobacterium tuberculosis [TaxId: 1773]}

class: All beta proteins
fold: OB-fold
superfamily: Nucleic acid-binding proteins
family: Cold shock DNA-binding domain-like
domain: S1 domain of NusA
species: Mycobacterium tuberculosis [TaxId: 1773]

Probab=97.41  E-value=0.00013  Score=61.27  Aligned_cols=64  Identities=22%  Similarity=0.295  Sum_probs=52.5

Q ss_pred             ccCcEEEEEEEEEeece----EEEEEc---CCeEEEEecccCCCccccccccccccCCEEEEEEEEEcc--CC-ceEEEE
Q 002054          682 EVGGIYKGVVTSVKEYG----AFVEFN---GGQQGLLHVSELSHEPVSRVSDVVSVGQQLSLRCIGQDV--RG-NIKLSL  751 (974)
Q Consensus       682 ~~G~i~~G~V~~i~~~G----~fV~l~---~g~~Glvhisels~~~v~~~~~~~~vGd~V~vkVl~id~--~g-ri~LS~  751 (974)
                      ++|+++.|+|.++....    ++|+|.   ++.+|+||.+|.-      |.+.|+.||.|+|.|.+++.  +| +|.||+
T Consensus         3 r~geiv~G~V~r~~~~~~~~~v~vdlG~~~~~~EaiLp~~eqi------p~E~y~~Gdrik~~i~~V~~~~kGp~IilSR   76 (76)
T d2asba1           3 REGEIVAGVIQRDSRANARGLVVVRIGTETKASEGVIPAAEQV------PGESYEHGNRLRCYVVGVTRGAREPLITLSR   76 (76)
T ss_dssp             CTTCEEEEEEECCHHHHHTTCEEEEECSSSSCEEEEECGGGSC------TTCCCCTTCEEEEEEEEEECCSSSCEEEEES
T ss_pred             ccceEEEEEEEEEecCCCceEEEEECCCCCCCEEEECCHHHcC------CCcccCCCCEEEEEEEEEEecCCCCEEEEeC
Confidence            68999999999986543    899995   4799999988764      35679999999999999986  44 677774

>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=97.27  E-value=0.00016  Score=60.33  Aligned_cols=59  Identities=17%  Similarity=0.259  Sum_probs=49.8

Q ss_pred             eeeeeccchhhhhcCCCccchhhhhhhhCceEEee--C---C--EEEEEecCHHHHHHHHHHHHHHh
Q 002054          618 ATLKYDNDTLRRLIGPLGALKRKIEEETGGRISVS--D---G--TLTVVAKNRSVMEKVLEKVDFII  677 (974)
Q Consensus       618 ~~~~i~~~ki~~vIg~gGk~i~~i~~~~g~~Idi~--d---g--~v~i~~~~~~~~~~a~~~i~~l~  677 (974)
                      ..+.||.+.++.+||++|.+|++|+++||++|.+.  +   .  .+.+.. +.+..+.|.++|..++
T Consensus         5 ~~i~VP~~~vg~iIGk~G~~I~~I~~~tga~I~i~~~~~~~~~r~v~I~G-~~~~v~~A~~~I~~~i   70 (74)
T d1j4wa1           5 IDVPIPRFAVGIVIGRNGEMIKKIQNDAGVRIQFKPDDGTTPERIAQITG-PPDRAQHAAEIITDLL   70 (74)
T ss_dssp             EEEEEEHHHHHHHHCGGGHHHHHHHHHHCCEEEEECCTTSCSEEEEEEEE-CHHHHHHHHHHHHHHH
T ss_pred             EEEEeCHHHCCeeECCCCcHHHHHHHHcCCEEEeccCCCCCCeeEEEEEe-CHHHHHHHHHHHHHHH
Confidence            45678899999999999999999999999999985  1   1  477766 4688999999998776

>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=97.16  E-value=0.00027  Score=58.49  Aligned_cols=58  Identities=14%  Similarity=0.224  Sum_probs=48.1

Q ss_pred             eeeeeccchhhhhcCCCccchhhhhhhhCceEEee-C---------CEEEEEecCHHHHHHHHHHHHHH
Q 002054          618 ATLKYDNDTLRRLIGPLGALKRKIEEETGGRISVS-D---------GTLTVVAKNRSVMEKVLEKVDFI  676 (974)
Q Consensus       618 ~~~~i~~~ki~~vIg~gGk~i~~i~~~~g~~Idi~-d---------g~v~i~~~~~~~~~~a~~~i~~l  676 (974)
                      ..+.||.+.++.+||++|.+|+.|++++|++|.++ +         ..+.|.+ +.+..++|.+.|..+
T Consensus         3 ~~~~IP~~~vg~IIGk~G~~Ik~I~~~sga~I~i~~~~~~~~~~~~r~v~I~G-~~~~v~~A~~~I~e~   70 (71)
T d1j4wa2           3 FNFIVPTGKTGLIIGKGGETIKSISQQSGARIELQRNPPPNADPNMKLFTIRG-TPQQIDYARQLIEEK   70 (71)
T ss_dssp             EEEEEETTTHHHHHCGGGHHHHHHHHHHCCEEEEECCCTTTSCTTEEEEEEEC-CHHHHHHHHHHHHHH
T ss_pred             EEEEEChHhcceEECCCCcChHHHHhhcCcEEEEeecCCCCCCCCeEEEEEEe-CHHHHHHHHHHHHhh
Confidence            35778999999999999999999999999999874 1         1567776 578899998887653

>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=97.14  E-value=0.00027  Score=58.46  Aligned_cols=58  Identities=14%  Similarity=0.228  Sum_probs=49.5

Q ss_pred             eeeeccchhhhhcCCCccchhhhhhhhCceEEee-----CCEEEEEecCHHHHHHHHHHHHHHh
Q 002054          619 TLKYDNDTLRRLIGPLGALKRKIEEETGGRISVS-----DGTLTVVAKNRSVMEKVLEKVDFII  677 (974)
Q Consensus       619 ~~~i~~~ki~~vIg~gGk~i~~i~~~~g~~Idi~-----dg~v~i~~~~~~~~~~a~~~i~~l~  677 (974)
                      .+.||+...+.+||++|.+|++|++++|++|.+.     +..|.+.+. .+..++|+++|..+.
T Consensus         8 ei~V~~~~~~~iIG~~G~~i~~I~~~tg~~I~i~~~~~~~~~v~I~G~-~~~v~~A~~~I~~i~   70 (71)
T d1viga_           8 EINIDHKFHRHLIGKSGANINRIKDQYKVSVRIPPDSEKSNLIRIEGD-PQGVQQAKRELLELA   70 (71)
T ss_dssp             EEEECSSHHHHHTCSSCCHHHHHHHHTCCEEECCCCCSSSEEEEEEES-SHHHHHHHHHHHHTC
T ss_pred             EEEECHHHhcccCCCCCchHHHHHHHhCCEEEeCCCCCCCCEEEEECC-HHHHHHHHHHHHHHh
Confidence            4678999999999999999999999999999984     246888875 578999999888663

>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=97.11  E-value=0.00026  Score=58.59  Aligned_cols=62  Identities=21%  Similarity=0.304  Sum_probs=51.1

Q ss_pred             CcceeeeeccchhhhhcCCCccchhhhhhhhCceEEee-C----CEEEEEecCHHHHHHHHHHHHHHh
Q 002054          615 PRLATLKYDNDTLRRLIGPLGALKRKIEEETGGRISVS-D----GTLTVVAKNRSVMEKVLEKVDFII  677 (974)
Q Consensus       615 p~~~~~~i~~~ki~~vIg~gGk~i~~i~~~~g~~Idi~-d----g~v~i~~~~~~~~~~a~~~i~~l~  677 (974)
                      +....+.++.+..+.+||++|++|++|++++|++|.+. +    ..+.|.+ +.+..++|...|..++
T Consensus         3 ~vt~~i~vp~~~~g~IIGk~G~~I~~I~~~tga~I~i~~~~~~er~v~I~G-~~~~v~~A~~~I~~~l   69 (71)
T d2axya1           3 TLTIRLLMHGKEVGSIIGKKGESVKKMREESGARINISEGNCPERIITLAG-PTNAIFKAFAMIIDKL   69 (71)
T ss_dssp             CEEEEEEEEHHHHHHHHCGGGHHHHHHHHHHCCEEEECSSCCSEEEEEEEE-CHHHHHHHHHHHHHHH
T ss_pred             cEEEEEEECHHHcCeEECCCChhHHHHHHHhCCEEEEcCCCCCcceEEEEE-CHHHHHHHHHHHHHHh
Confidence            34456789999999999999999999999999999986 2    2566766 6788999998887654

>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=97.10  E-value=0.00037  Score=58.17  Aligned_cols=59  Identities=15%  Similarity=0.299  Sum_probs=50.1

Q ss_pred             eeeeeccchhhhhcCCCccchhhhhhhhCceEEee---C----CEEEEEecCHHHHHHHHHHHHHHh
Q 002054          618 ATLKYDNDTLRRLIGPLGALKRKIEEETGGRISVS---D----GTLTVVAKNRSVMEKVLEKVDFII  677 (974)
Q Consensus       618 ~~~~i~~~ki~~vIg~gGk~i~~i~~~~g~~Idi~---d----g~v~i~~~~~~~~~~a~~~i~~l~  677 (974)
                      ..+.||.+.++.+||++|.+|+.|++++|++|.+.   +    ..+.|.+ +.+.+++|...|..++
T Consensus         6 ~~i~VP~~~vg~iIG~~G~~I~~I~~~sga~I~i~~~~~~~~~r~i~I~G-~~~~v~~A~~~I~~~i   71 (75)
T d1zzka1           6 TQVTIPKDLAGSIIGKGGQRIKQIRHESGASIKIDEPLEGSEDRIITITG-TQDQIQNAQYLLQNSV   71 (75)
T ss_dssp             EEEEEETTTGGGGTCGGGHHHHHHHHHHCCEEEECCTTSCSSEEEEEEEE-CHHHHHHHHHHHHHHH
T ss_pred             EEEEEChHhcCeeECCCCchHHHHHhhcCCeEEEccCCCCCCceEEEEEe-CHHHHHHHHHHHHHHH
Confidence            46789999999999999999999999999999885   1    2477776 6789999998888765

>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=97.08  E-value=0.00037  Score=60.40  Aligned_cols=62  Identities=15%  Similarity=0.168  Sum_probs=52.9

Q ss_pred             CcceeeeeccchhhhhcCCCccchhhhhhhh-CceEEee--CCEEEEEecCHHHHHHHHHHHHHHh
Q 002054          615 PRLATLKYDNDTLRRLIGPLGALKRKIEEET-GGRISVS--DGTLTVVAKNRSVMEKVLEKVDFII  677 (974)
Q Consensus       615 p~~~~~~i~~~ki~~vIg~gGk~i~~i~~~~-g~~Idi~--dg~v~i~~~~~~~~~~a~~~i~~l~  677 (974)
                      +....+.+|....+.+||+||.+|++|++++ |++|++.  +..+.+.+ +.+..++|+++|+.++
T Consensus        20 ~~t~~v~VP~~~h~~iIG~~G~~I~~i~~~~~~v~I~~~~~~~~v~i~G-~~~~ve~Ak~~I~~iv   84 (90)
T d2ctfa1          20 FTVSSVAAPSWLHRFIIGKKGQNLAKITQQMPKVHIEFTEGEDKITLEG-PTEDVSVAQEQIEGMV   84 (90)
T ss_dssp             CEEEEEECCSTTHHHHHTTTTCHHHHHHHHCSSSEEEECSSSCEEEEEE-CHHHHHHHHHHHHHHH
T ss_pred             cEEEEEEcCHHHHhhcCCCCchhHHHHHHHcCCcEEeeCCCCceEEEeC-CHHHHHHHHHHHHHHH
Confidence            4566777888889999999999999999995 7999986  46777777 6788999999998877

>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=97.04  E-value=0.00041  Score=58.87  Aligned_cols=60  Identities=22%  Similarity=0.252  Sum_probs=52.0

Q ss_pred             ceeeeeccchhhhhcCCCccchhhhhhhhCceEEee------CCEEEEEecCHHHHHHHHHHHHHHh
Q 002054          617 LATLKYDNDTLRRLIGPLGALKRKIEEETGGRISVS------DGTLTVVAKNRSVMEKVLEKVDFII  677 (974)
Q Consensus       617 ~~~~~i~~~ki~~vIg~gGk~i~~i~~~~g~~Idi~------dg~v~i~~~~~~~~~~a~~~i~~l~  677 (974)
                      ...+.||+...+.+||++|.+|+.|+++||++|.+.      +..+.|.+ ..+..++|++++..+.
T Consensus        11 t~~i~Vp~~~~~~iIG~~G~~i~~I~~~tg~~I~~p~~~~~~~~~v~I~G-~~~~V~~A~~~I~~i~   76 (81)
T d2ctma1          11 SEDVPLDHRVHARIIGARGKAIRKIMDEFKVDIRFPQSGAPDPNCVTVTG-LPENVEEAIDHILNLE   76 (81)
T ss_dssp             CEEEECCTTTHHHHHCSSSCHHHHHHHHHTCEEECCCTTCSCTTEEEEES-CHHHHHHHHHHHHHHH
T ss_pred             EEEEEECHHHHhhccCCCCccHHHHHHHhCCEEEeCCccCCCCCEEEEeC-CHHHHHHHHHHHHHHH
Confidence            467899999999999999999999999999999984      13688876 5678999999998876

>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=97.02  E-value=0.00045  Score=57.51  Aligned_cols=58  Identities=17%  Similarity=0.268  Sum_probs=48.8

Q ss_pred             eeeeeccchhhhhcCCCccchhhhhhhhCceEEee-CC---------EEEEEecCHHHHHHHHHHHHHH
Q 002054          618 ATLKYDNDTLRRLIGPLGALKRKIEEETGGRISVS-DG---------TLTVVAKNRSVMEKVLEKVDFI  676 (974)
Q Consensus       618 ~~~~i~~~ki~~vIg~gGk~i~~i~~~~g~~Idi~-dg---------~v~i~~~~~~~~~~a~~~i~~l  676 (974)
                      ..+.||.+.++.+||++|.+|++|++++|++|.+. ++         .+.|.+ +.+..++|...|...
T Consensus         5 i~i~VP~~~vg~iIGk~G~~Ik~I~~~sga~I~i~~~~~~~~~~~~r~v~I~G-~~~~v~~A~~~I~~~   72 (74)
T d1dtja_           5 VEMAVPENLVGAILGKGGKTLVEYQELTGARIQISKKGEFLPGTRNRRVTITG-SPAATQAAQYLISQR   72 (74)
T ss_dssp             EEEEEETTTHHHHHCSTTHHHHHHHHHHCCEEEECCTTCCSTTCCEEEEEEEE-SHHHHHHHHHHHHHH
T ss_pred             EEEEeCHHHcceeECCCChhHHHHHHHcCCEEEEccCCCCCCCCCceEEEEEe-CHHHHHHHHHHHHHH
Confidence            45678999999999999999999999999999874 21         478877 578999999888754

>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=96.95  E-value=0.00052  Score=56.51  Aligned_cols=58  Identities=17%  Similarity=0.285  Sum_probs=48.7

Q ss_pred             eeeeeccchhhhhcCCCccchhhhhhhhCceEEeeC-------CEEEEEecCHHHHHHHHHHHHHH
Q 002054          618 ATLKYDNDTLRRLIGPLGALKRKIEEETGGRISVSD-------GTLTVVAKNRSVMEKVLEKVDFI  676 (974)
Q Consensus       618 ~~~~i~~~ki~~vIg~gGk~i~~i~~~~g~~Idi~d-------g~v~i~~~~~~~~~~a~~~i~~l  676 (974)
                      ..+.||.+.++.+||++|.+|++|++++|++|.+.+       ..+.+.+ ..+..++|..+|...
T Consensus         4 ~~i~VP~~~vg~iIGk~G~~I~~I~~~tga~I~i~~~~~~~~~r~v~I~G-~~~~v~~A~~~I~~~   68 (70)
T d1wvna1           4 HELTIPNNLIGCIIGRQGANINEIRQMSGAQIKIANPVEGSSGRQVTITG-SAASISLAQYLINAR   68 (70)
T ss_dssp             EEEEEEGGGHHHHHCGGGHHHHHHHHHHCCEEEECCCCTTCSEEEEEEEE-CHHHHHHHHHHHHHH
T ss_pred             EEEEEChHhcceeECCCChHHHHHHHHcCcEEEEcCCCCCCCcEEEEEEe-CHHHHHHHHHHHHHH
Confidence            467899999999999999999999999999999851       1477777 478999999887654

>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=96.90  E-value=0.00052  Score=58.17  Aligned_cols=61  Identities=16%  Similarity=0.233  Sum_probs=51.3

Q ss_pred             cceeeeeccchhhhhcCCCccchhhhhhhhCceEEee-C--------CEEEEEecCHHHHHHHHHHHHHHh
Q 002054          616 RLATLKYDNDTLRRLIGPLGALKRKIEEETGGRISVS-D--------GTLTVVAKNRSVMEKVLEKVDFII  677 (974)
Q Consensus       616 ~~~~~~i~~~ki~~vIg~gGk~i~~i~~~~g~~Idi~-d--------g~v~i~~~~~~~~~~a~~~i~~l~  677 (974)
                      ....+.||+++++.+||++|.+|+.|++++|++|.+. +        ..+.|... .+.+++|..+|..++
T Consensus         8 ~~~~i~Vp~~~~g~iIGk~G~~Ik~I~~~tga~I~i~~~~~~~~~~~r~v~I~G~-~~~v~~A~~~I~~~i   77 (81)
T d1x4ma1           8 AVQEIMIPASKAGLVIGKGGETIKQLQERAGVKMVMIQDGPQNTGADKPLRITGD-PYKVQQAKEMVLELI   77 (81)
T ss_dssp             EEEEEEECHHHHHHHSCSSSSHHHHHHHHHTSEEEECCSCCCSSCSCEEEEEEEC-TTTHHHHHHHHHHHH
T ss_pred             EEEEEEECHHHcCeeECCCCchHHHHHHHhCCeEEEccCCCCCCCCceEEEEEeC-HHHHHHHHHHHHHHH
Confidence            4567789999999999999999999999999999873 1        14777775 579999999998776

>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=96.87  E-value=0.00047  Score=58.50  Aligned_cols=60  Identities=22%  Similarity=0.312  Sum_probs=51.5

Q ss_pred             ceeeeeccchhhhhcCCCccchhhhhhhhCceEEee-----CCEEEEEecCHHHHHHHHHHHHHHh
Q 002054          617 LATLKYDNDTLRRLIGPLGALKRKIEEETGGRISVS-----DGTLTVVAKNRSVMEKVLEKVDFII  677 (974)
Q Consensus       617 ~~~~~i~~~ki~~vIg~gGk~i~~i~~~~g~~Idi~-----dg~v~i~~~~~~~~~~a~~~i~~l~  677 (974)
                      ...+.||++..+.+||++|.+|+.|+++||++|.+.     +..|.|.+ ..+.+++|...|..++
T Consensus        11 t~~i~Ip~~~~~~iIG~~G~~i~~I~~~tg~~I~~p~~~~~~~~v~I~G-~~~~v~~A~~~I~~iv   75 (81)
T d2ctea1          11 SATVAIPKEHHRFVIGKNGEKLQDLELKTATKIQIPRPDDPSNQIKITG-TKEGIEKARHEVLLIS   75 (81)
T ss_dssp             EEEEECCTTTHHHHHCSSSCHHHHHHHHTTCCCBCCCTTSSCCEEEEEE-CHHHHHHHHHHHHHHH
T ss_pred             EEEEEECHHHHhhccCCCChhHHHHHHHhCCEEEECCCCCCCCEEEEEe-CHHHHHHHHHHHHHHH
Confidence            467889999999999999999999999999999873     35677766 5678999999988776

>d2nn6i1 b.40.4.5 (I:61-185) Exosome component 1, EXOSC1 {Human (Homo sapiens) [TaxId: 9606]}

class: All beta proteins
fold: OB-fold
superfamily: Nucleic acid-binding proteins
family: Cold shock DNA-binding domain-like
domain: Exosome component 1, EXOSC1
species: Human (Homo sapiens) [TaxId: 9606]

Probab=96.86  E-value=0.00073  Score=62.11  Aligned_cols=58  Identities=28%  Similarity=0.344  Sum_probs=49.5

Q ss_pred             CCCCEEEEEEEEEeCCeEEEEe--------CCCeEEEEecccCC---------CCCCCCCCEEEEEEEEEeCCCc
Q 002054          909 KLGTKVAAKVYQVRARGLVLDL--------GGGIRGMYRFENNE---------KKDFVVGDELLVKCSSFTGKGI  966 (974)
Q Consensus       909 ~vG~vV~G~V~~I~~~GvFV~L--------~~gv~Glih~se~~---------~~~f~vGd~V~vkVl~id~~~~  966 (974)
                      ++||+|.|+|.++.+..++|++        ...+.|++|.++..         .+.|++||-|.|+|+++...+.
T Consensus         6 ~vGDiVig~V~~v~~~~a~v~I~~v~~~~l~~~~~g~i~~~dvr~te~d~~~m~~~fr~GDiV~A~Vis~~~~~~   80 (125)
T d2nn6i1           6 DVGAIVTCKVSSINSRFAKVHILYVGSMPLKNSFRGTIRKEDVRATEKDKVEIYKSFRPGDIVLAKVISLGDAQS   80 (125)
T ss_dssp             CTTCEEEEEEEEECSSEEEEEEEESSSSCCCCSSCSCEEEEGGGTCSSCCCCGGGTCCSSSEEEEEEEEEETTTT
T ss_pred             CCCCEEEEEEEEecCCEEEEEEeEecCcccccCccccccHHHcccchhhhhhHHHhcCCCCEEEEEEEEccCCCc
Confidence            6899999999999999999998        44688999988541         4579999999999999987544

>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=96.78  E-value=0.00072  Score=56.95  Aligned_cols=61  Identities=18%  Similarity=0.314  Sum_probs=51.5

Q ss_pred             cceeeeeccchhhhhcCCCccchhhhhhhhCceEEee---CC----EEEEEecCHHHHHHHHHHHHHHh
Q 002054          616 RLATLKYDNDTLRRLIGPLGALKRKIEEETGGRISVS---DG----TLTVVAKNRSVMEKVLEKVDFII  677 (974)
Q Consensus       616 ~~~~~~i~~~ki~~vIg~gGk~i~~i~~~~g~~Idi~---dg----~v~i~~~~~~~~~~a~~~i~~l~  677 (974)
                      ....+.||.+.++.+||++|.+|+.|.++||++|.+.   ++    .+.|.+ ..+.++.|..+|..++
T Consensus         8 ~t~~i~IP~~~~g~iIG~~G~~i~~I~~~tg~~I~i~~~~~~~~~r~v~I~G-~~~~v~~A~~~I~~~i   75 (79)
T d1x4na1           8 MTEEYKVPDGMVGFIIGRGGEQISRIQQESGCKIQIAPDSGGLPERSCMLTG-TPESVQSAKRLLDQIV   75 (79)
T ss_dssp             EEEEEEEEHHHHHHHHCSSSHHHHHHHHHSCCEEEECSCCTTCSEEEEEEEE-CHHHHHHHHHHHHHHH
T ss_pred             EEEEEEEChHhhcceECCCchhHHHHHHHhCCEEEEcCCCCCCCceEEEEEe-CHHHHHHHHHHHHHHH
Confidence            4457789999999999999999999999999999874   22    477777 5789999999988765

>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=96.71  E-value=0.001  Score=56.63  Aligned_cols=59  Identities=19%  Similarity=0.241  Sum_probs=50.6

Q ss_pred             eeeeeccchhhhhcCCCccchhhhhhhhCceEEee--------CCEEEEEecCHHHHHHHHHHHHHHh
Q 002054          618 ATLKYDNDTLRRLIGPLGALKRKIEEETGGRISVS--------DGTLTVVAKNRSVMEKVLEKVDFII  677 (974)
Q Consensus       618 ~~~~i~~~ki~~vIg~gGk~i~~i~~~~g~~Idi~--------dg~v~i~~~~~~~~~~a~~~i~~l~  677 (974)
                      ..+.||....+.+||.+|.+|+.|+++||++|.+.        +..+.|.+. .+.++.|+.+|..++
T Consensus        12 ~~i~Vp~~~~~~iIG~~G~~i~~I~~~t~~~I~~~~~~~~~~~~~~i~I~G~-~e~v~~A~~~I~~~i   78 (84)
T d2ctla1          12 LSVTVDPKYHPKIIGRKGAVITQIRLEHDVNIQFPDKDDGNQPQDQITITGY-EKNTEAARDAILRIV   78 (84)
T ss_dssp             EEEECCTTTHHHHSCSSSCHHHHHHHHHTCEEECCCTTTCSSCSSEEEEESC-HHHHHHHHHHHHHHH
T ss_pred             EEEEECHHHHhhhcCCCchhHHHHHHHhCCEEEECCCCCCCCCcceEEEECC-HHHHHHHHHHHHHHH
Confidence            46779999999999999999999999999999873        236888775 688999999888776

>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=96.62  E-value=0.0013  Score=55.66  Aligned_cols=61  Identities=25%  Similarity=0.271  Sum_probs=51.3

Q ss_pred             cceeeeeccchhhhhcCCCccchhhhhhh-hCceEEee-----CCEEEEEecCHHHHHHHHHHHHHHh
Q 002054          616 RLATLKYDNDTLRRLIGPLGALKRKIEEE-TGGRISVS-----DGTLTVVAKNRSVMEKVLEKVDFII  677 (974)
Q Consensus       616 ~~~~~~i~~~ki~~vIg~gGk~i~~i~~~-~g~~Idi~-----dg~v~i~~~~~~~~~~a~~~i~~l~  677 (974)
                      ....+.||++..+.+||++|.+|+.|+++ +++.|++.     +..|.|.+ +.+..++|+.++..++
T Consensus        10 ~t~~i~Vp~~~~~~iIGk~G~~I~~I~~~~~~~~I~~~~~~~~~~~v~I~G-~~~~v~~A~~~I~~~v   76 (82)
T d2ctja1          10 AEVEVSIPAKLHNSLIGTKGRLIRSIMEECGGVHIHFPVEGSGSDTVVIRG-PSSDVEKAKKQLLHLA   76 (82)
T ss_dssp             CCEEEECCHHHHHHHHCSSSHHHHHHHHHHTSCEEECCCTTTTCCEEEEES-CHHHHHHHHHHHHHHH
T ss_pred             EEEEEEECHHHHhhcCCCCCccHHHHHHHcCCcEEEEeCCCCCCceEEEeC-CHHHHHHHHHHHHHHH
Confidence            35678899999999999999999999987 58999874     24788877 5678999999998776

>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=94.84  E-value=0.024  Score=51.34  Aligned_cols=52  Identities=27%  Similarity=0.386  Sum_probs=45.6

Q ss_pred             hhhhhcCCCccchhhhhhhhCceEEee-C----------------------CEEEEEecCHHHHHHHHHHHHHHh
Q 002054          626 TLRRLIGPLGALKRKIEEETGGRISVS-D----------------------GTLTVVAKNRSVMEKVLEKVDFII  677 (974)
Q Consensus       626 ki~~vIg~gGk~i~~i~~~~g~~Idi~-d----------------------g~v~i~~~~~~~~~~a~~~i~~l~  677 (974)
                      .++.+|||+|.+.|.|+++||++|.|- .                      =.|.|++.+.+.++.|...++.++
T Consensus        19 fvG~IlGPrG~t~K~Le~eTgckI~IrGrGS~kd~~~~~~~~~~~~~~~epLHv~I~a~~~~~~~~A~~~i~~ll   93 (122)
T d1k1ga_          19 FVGLLIGPRGNTLKNIEKECNAKIMIRGKGSVKEGKVGRKDGQMLPGEDEPLHALVTANTMENVKKAVEQIRNIL   93 (122)
T ss_dssp             HHHHHHCSSSHHHHHHHHHSCCEEEEEESTTSSSSSSSSCCCCCSCCSSCCEEEEEEESSHHHHHHHHHHHHHHH
T ss_pred             eeeeEeCCCCchHHHHHHHHCCEEEEEecCCcccccccccCCCCCCCCCCCceEEEecCChhhHHHHHHHHHHHH
Confidence            589999999999999999999999762 1                      157899999999999999998887

>d1smxa_ b.40.4.5 (A:) S1-domain of Ribonuclease E {Escherichia coli [TaxId: 562]}

class: All beta proteins
fold: OB-fold
superfamily: Nucleic acid-binding proteins
family: Cold shock DNA-binding domain-like
domain: S1-domain of Ribonuclease E
species: Escherichia coli [TaxId: 562]

Probab=94.30  E-value=0.038  Score=46.95  Aligned_cols=49  Identities=16%  Similarity=0.307  Sum_probs=41.9

Q ss_pred             CEEEEEEEEEeCC--eEEEEeCCCeEEEEecccCC----------------CCCCCCCCEEEEEEEE
Q 002054          912 TKVAAKVYQVRAR--GLVLDLGGGIRGMYRFENNE----------------KKDFVVGDELLVKCSS  960 (974)
Q Consensus       912 ~vV~G~V~~I~~~--GvFV~L~~gv~Glih~se~~----------------~~~f~vGd~V~vkVl~  960 (974)
                      ++..|+|.+|.+-  ++||+++.+-.||+|.++..                .+.+++||+|-|.|.+
T Consensus         2 NIY~G~V~~V~pgl~AAFVDiG~~k~gFL~~~di~~~~~~~~~~~~~~~~i~~~l~~G~~ilVQV~K   68 (87)
T d1smxa_           2 NIYKGKITRIEPSLEAAFVDYGAERHGFLPLKEIAREYFPANYSAHGRPNIKDVLREGQEVIVQIDK   68 (87)
T ss_dssp             CCEEEEEEEEEGGGTEEEEESSSSSCEEEEGGGSCGGGCSSCCCSSSCCCGGGTCCTTCEEEEEEEE
T ss_pred             CcEEEEEEEecCCceEEEEEeCCCccceeEecccceeeeccccccccccchhhhccCCCeEEEEEee
Confidence            4688999999876  99999999999999998642                2358999999999876

>d1luza_ b.40.4.5 (A:) Viral structural mimic of eIF2alpha {Vaccinia virus [TaxId: 10245]}

class: All beta proteins
fold: OB-fold
superfamily: Nucleic acid-binding proteins
family: Cold shock DNA-binding domain-like
domain: Viral structural mimic of eIF2alpha
species: Vaccinia virus [TaxId: 10245]

Probab=92.26  E-value=0.18  Score=41.20  Aligned_cols=73  Identities=22%  Similarity=0.370  Sum_probs=54.5

Q ss_pred             ccccCcEEEEEEEEEeeceEEEEEc--CCeEEEEecc-cCCCccccccccccccCCEEEEEEEEEcc-CCceEEEEecc
Q 002054          680 EIEVGGIYKGVVTSVKEYGAFVEFN--GGQQGLLHVS-ELSHEPVSRVSDVVSVGQQLSLRCIGQDV-RGNIKLSLKAV  754 (974)
Q Consensus       680 ~~~~G~i~~G~V~~i~~~G~fV~l~--~g~~Glvhis-els~~~v~~~~~~~~vGd~V~vkVl~id~-~gri~LS~K~~  754 (974)
                      -+.+|++.+|.|. +.+.-.+|.|.  +|.++++--+ ++-.++..+..+.+ +|..|+|+|+.+|. +|-|.+.-|..
T Consensus         5 lPnigdVtkGiVy-~kd~~fyV~L~dY~g~ea~l~dy~~~~~d~~~klk~kL-VGKtIkvqVIR~d~lKGYIDVr~~~~   81 (85)
T d1luza_           5 LPNAGDVIKGRVY-EKDYALYIYLFDYPHFEAILAESVKMHMDRYVEYRDKL-VGKTVKVKVIRVDYTKGYIDVNYKRM   81 (85)
T ss_dssp             CCCTTCEEEEEEE-EETTEEEEEETTCTTSEEEEGGGSSCCHHHHHHHHHHH-TTCEEEEEEEEEETTTTEEEEEEEEE
T ss_pred             cCCCCceeeeEEE-EeCCEEEEEecCCCCceEEeeehhhhhhHHHHHHHHHh-cCceEEEEEEEEcceeeEEEehhhhh
Confidence            3679999999885 46677788885  4788887322 23234455555555 89999999999998 89999998864

>d1wfqa_ b.40.4.5 (A:) Cold shock domain protein E1 (UNR) {Human (Homo sapiens) [TaxId: 9606]}

class: All beta proteins
fold: OB-fold
superfamily: Nucleic acid-binding proteins
family: Cold shock DNA-binding domain-like
domain: Cold shock domain protein E1 (UNR)
species: Human (Homo sapiens) [TaxId: 9606]

Probab=88.26  E-value=1.2  Score=37.39  Aligned_cols=62  Identities=13%  Similarity=0.183  Sum_probs=44.3

Q ss_pred             ccCcEEEEEEEEEeeceEEEEEcC-CeEEEEecccCCCccccccccccccCCEEEEEEEEEccCCceE
Q 002054          682 EVGGIYKGVVTSVKEYGAFVEFNG-GQQGLLHVSELSHEPVSRVSDVVSVGQQLSLRCIGQDVRGNIK  748 (974)
Q Consensus       682 ~~G~i~~G~V~~i~~~G~fV~l~~-g~~Glvhisels~~~v~~~~~~~~vGd~V~vkVl~id~~gri~  748 (974)
                      ..+...+|+|....+.==|++-.+ +.+-|+|+|++...     ...+++||.|+..+..-+..++..
T Consensus        14 ~~~~r~~G~I~~~~~gfGFI~~~~~~~dvF~H~s~~~~~-----~~~l~~G~~VeF~v~~~~kg~k~~   76 (89)
T d1wfqa_          14 SAALRETGVIEKLLTSYGFIQCSERQARLFFHCSQYNGN-----LQDLKVGDDVEFEVSSDRRTGKPI   76 (89)
T ss_dssp             SCCCEEEEEEEEECSSEEEEEETTTTEEEEEETTTCSSC-----TTTCCTTCCEEEEEEECSSSCCEE
T ss_pred             CccceEEEEEEEecCccceEEeCCCCceEEEEeehhhcc-----CCcccCCCEEEEEEEECCCCCceE
Confidence            467789999999976323666554 46899999999543     234889999999987733335543

>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=87.86  E-value=0.2  Score=45.69  Aligned_cols=53  Identities=23%  Similarity=0.485  Sum_probs=41.2

Q ss_pred             chhhhhcCCCccchhhhhhhhCceEEee-C------------------------CEEEEEecCHH-----HHHHHHHHHH
Q 002054          625 DTLRRLIGPLGALKRKIEEETGGRISVS-D------------------------GTLTVVAKNRS-----VMEKVLEKVD  674 (974)
Q Consensus       625 ~ki~~vIg~gGk~i~~i~~~~g~~Idi~-d------------------------g~v~i~~~~~~-----~~~~a~~~i~  674 (974)
                      +.++.+|||+|.++|.|+++||++|.|- .                        =.|.|++.+.+     .++.|.+.|+
T Consensus        17 NfvG~IiGPrG~t~K~le~eTg~kI~IrGrGS~k~~~~~~~~~~~~~~~~~~epLHv~I~a~~~~~~a~~kl~~A~~~I~   96 (134)
T d2bl5a1          17 NFVGRILGPRGLTAKQLEAETGCKIMVRGKGSMRDKKKEEQNRGKPNWEHLNEDLHVLITVEDAQNRAELKLKRAVEEVK   96 (134)
T ss_dssp             CHHHHHTTTTHHHHHHHHHHHSEEEEEESTTSSCCHHHHHTSTTSHHHHTTTSCCEEEEEECSCCHHHHHHHHHHHHHHH
T ss_pred             CeeEEEECCCCchHHHHHHHHCCEEEEEecCCCcCccccccccCCCCCcCCCCCCEEEEEecCcHHHHHHHHHHHHHHHH
Confidence            4689999999999999999999999653 1                        24677776643     4677888887


Q ss_pred             HHh
Q 002054          675 FII  677 (974)
Q Consensus       675 ~l~  677 (974)
                      .++
T Consensus        97 ~lL   99 (134)
T d2bl5a1          97 KLL   99 (134)
T ss_dssp             HHS
T ss_pred             HHc
Confidence            765

>d1jjga_ b.40.4.5 (A:) Viral structural mimic of eIF2alpha {Myxoma virus, m156r [TaxId: 10273]}

class: All beta proteins
fold: OB-fold
superfamily: Nucleic acid-binding proteins
family: Cold shock DNA-binding domain-like
domain: Viral structural mimic of eIF2alpha
species: Myxoma virus, m156r [TaxId: 10273]

Probab=86.72  E-value=0.65  Score=38.73  Aligned_cols=67  Identities=18%  Similarity=0.318  Sum_probs=48.9

Q ss_pred             cccccCcEEEEEEEEEeeceEEEEEc--CCeEEEE-ecccCCCccccccccccccCCEEEEEEEEEccCCceE
Q 002054          679 REIEVGGIYKGVVTSVKEYGAFVEFN--GGQQGLL-HVSELSHEPVSRVSDVVSVGQQLSLRCIGQDVRGNIK  748 (974)
Q Consensus       679 ~~~~~G~i~~G~V~~i~~~G~fV~l~--~g~~Glv-hisels~~~v~~~~~~~~vGd~V~vkVl~id~~gri~  748 (974)
                      .++-+|++.+|.|. +.++-.+|.|.  +|.++++ .--++-.++..+..+.+ +|..|+|+|+.+| ++-|.
T Consensus        28 ~~~~~G~V~kGiVy-~rd~~fyV~L~dY~g~eail~dY~n~~~dr~~klkkkL-VGKTIkVqVIRvD-klYID   97 (102)
T d1jjga_          28 MDLSPGSVHEGIVY-FKDGIFKVRLLGYEGHECILLDYLNYRQDTLDRLKERL-VGRVIKTRVVRAD-GLYVD   97 (102)
T ss_dssp             CCCCSSCEEEEEEE-EETTEEEEECTTTSSCEEEECTTCCSSCCCCCHHHHHH-TTCEEEEEEEEEC-SSEEE
T ss_pred             cccCCCcEeeeEEE-EeCCEEEEEecCCCCceeeeeehhhhhHHHHHHHHHHh-cCceEEEEEEEec-cEEEE
Confidence            36789999999884 56777788885  4788885 33344455666666665 8999999999998 44443

>d1c9oa_ b.40.4.5 (A:) Major cold shock protein {Bacillus caldolyticus [TaxId: 1394]}

class: All beta proteins
fold: OB-fold
superfamily: Nucleic acid-binding proteins
family: Cold shock DNA-binding domain-like
domain: Major cold shock protein
species: Bacillus caldolyticus [TaxId: 1394]

Probab=86.50  E-value=1.3  Score=34.88  Aligned_cols=54  Identities=26%  Similarity=0.495  Sum_probs=38.5

Q ss_pred             EEEEEEEee-ceE-EEEEcCCeEEEEecccCCCccccccccccccCCEEEEEEEEEccCCc
Q 002054          688 KGVVTSVKE-YGA-FVEFNGGQQGLLHVSELSHEPVSRVSDVVSVGQQLSLRCIGQDVRGN  746 (974)
Q Consensus       688 ~G~V~~i~~-~G~-fV~l~~g~~Glvhisels~~~v~~~~~~~~vGd~V~vkVl~id~~gr  746 (974)
                      +|+|+-..+ .|. |+...+|.+-|+|+|.+.....    ..+..||.|++.+.. +++|.
T Consensus         3 ~G~Vk~fn~~kGfGFI~~d~g~DiF~H~s~l~~~~~----~~L~~G~~V~f~~~~-~~~G~   58 (66)
T d1c9oa_           3 RGKVKWFNNEKGYGFIEVEGGSDVFVHFTAIQGEGF----KTLEEGQEVSFEIVQ-GNRGP   58 (66)
T ss_dssp             EEEEEEEETTTTEEEEEETTEEEEEEEGGGBCSSSC----CCCCTTCEEEEEEEE-ETTEE
T ss_pred             CeEEEEEECCCCEEEEEecCCceEEEEehhcccccC----CcCCCCCEEEEEEEE-CCCCC
Confidence            688888733 333 4666778899999999965432    237889999998866 34553

>d1h95a_ b.40.4.5 (A:) Y-box protein 1 cold shock domain (YB1-CSD) {Human (Homo sapiens) [TaxId: 9606]}

class: All beta proteins
fold: OB-fold
superfamily: Nucleic acid-binding proteins
family: Cold shock DNA-binding domain-like
domain: Y-box protein 1 cold shock domain (YB1-CSD)
species: Human (Homo sapiens) [TaxId: 9606]

Probab=83.69  E-value=1.6  Score=35.69  Aligned_cols=61  Identities=13%  Similarity=0.214  Sum_probs=41.8

Q ss_pred             cEEEEEEEEEee---ceEEEEEcCCeEEEEecccCCCccccccccccccCCEEEEEEEEEccCCc
Q 002054          685 GIYKGVVTSVKE---YGAFVEFNGGQQGLLHVSELSHEPVSRVSDVVSVGQQLSLRCIGQDVRGN  746 (974)
Q Consensus       685 ~i~~G~V~~i~~---~G~fV~l~~g~~Glvhisels~~~v~~~~~~~~vGd~V~vkVl~id~~gr  746 (974)
                      ..+.|+|+-..+   ||....-.++.+-|+|.|.|...-....-..+..||.|+..+.. +++|+
T Consensus         7 ~r~~G~VKwfn~~KGfGFI~~ddg~~DvFvH~s~i~~~g~~~~~~~L~~G~~V~f~~~~-~~~G~   70 (79)
T d1h95a_           7 TKVLGTVKWFNVRNGYGFINRNDTKEDVFVHQTAIKKNNPRKYLRSVGDGETVEFDVVE-GEKGA   70 (79)
T ss_dssp             EEEEEEEEEEETTTTEEEEEEGGGTEEEEEEGGGBCSCCCSCCSCSCCSSCEEEEEEEE-CSSSE
T ss_pred             CcccEEEEEEcCCCCeEEEEECCCCccEEEEhhHcccCCCcceeeecCCCCEEEEEEEe-CCCCC
Confidence            568899988743   45444334568899999999665333233458899999998776 34553

>d1mjca_ b.40.4.5 (A:) Major cold shock protein {Escherichia coli [TaxId: 562]}

class: All beta proteins
fold: OB-fold
superfamily: Nucleic acid-binding proteins
family: Cold shock DNA-binding domain-like
domain: Major cold shock protein
species: Escherichia coli [TaxId: 562]

Probab=82.80  E-value=2.1  Score=34.04  Aligned_cols=55  Identities=18%  Similarity=0.365  Sum_probs=38.0

Q ss_pred             EEEEEEEEEe-eceE-EEEEcC-CeEEEEecccCCCccccccccccccCCEEEEEEEEEccCC
Q 002054          686 IYKGVVTSVK-EYGA-FVEFNG-GQQGLLHVSELSHEPVSRVSDVVSVGQQLSLRCIGQDVRG  745 (974)
Q Consensus       686 i~~G~V~~i~-~~G~-fV~l~~-g~~Glvhisels~~~v~~~~~~~~vGd~V~vkVl~id~~g  745 (974)
                      .++|+|+-.. ..|. |+.-.. +.+-|+|+|.+......    .+++||.|+..+.. +.+|
T Consensus         3 r~~G~Vk~f~~~kGfGFI~~d~g~~diFvH~s~l~~~~~~----~L~~G~~V~f~~~~-~~~G   60 (69)
T d1mjca_           3 KMTGIVKWFNADKGFGFITPDDGSKDVFVHFSAIQNDGYK----SLDEGQKVSFTIES-GAKG   60 (69)
T ss_dssp             CEEEEEEEEETTTTEEEEEETTSCCCEEEEGGGBCCTTTC----CCCTTCEEEEEEEC-CSSS
T ss_pred             CEEEEEEEEeCCCCEEEEEEcCCCccEEEEhHHhcccCCC----cCCCCCEEEEEEEe-CCCC
Confidence            4789998874 3343 555444 57899999999755332    37889999998755 3345

>d1k3ra1 b.40.4.10 (A:93-163) Hypothetical protein MTH1 (MT0001), insert domain {Archaeon Methanobacterium thermoautotrophicum [TaxId: 145262]}

class: All beta proteins
fold: OB-fold
superfamily: Nucleic acid-binding proteins
family: Hypothetical protein MTH1 (MT0001), insert domain
domain: Hypothetical protein MTH1 (MT0001), insert domain
species: Archaeon Methanobacterium thermoautotrophicum [TaxId: 145262]

Probab=81.57  E-value=2.1  Score=33.89  Aligned_cols=50  Identities=10%  Similarity=0.159  Sum_probs=41.6

Q ss_pred             ccCCCCCEEEEEEEEEeCCeEEEEeCCCeEEEEecccCCCCCCCCCCEEEEEEEEE
Q 002054          906 KNLKLGTKVAAKVYQVRARGLVLDLGGGIRGMYRFENNEKKDFVVGDELLVKCSSF  961 (974)
Q Consensus       906 ~~~~vG~vV~G~V~~I~~~GvFV~L~~gv~Glih~se~~~~~f~vGd~V~vkVl~i  961 (974)
                      ...++|++=+|.+.+-...|+||+++  ++-++..    +..|..|+.+++||.++
T Consensus         6 g~p~vGEiReG~~~rr~~~g~~vDiG--lD~la~~----k~~~~~~~r~tfrIvs~   55 (71)
T d1k3ra1           6 GKPVTGEYRQGLTVKRVKKGTLVDIG--ADKLALC----REKLTVNRIMSFRVVRL   55 (71)
T ss_dssp             SSCCTTCEEEEEEEEECSSSEEEESS--SSCEEEC----SSCCCSSCEEEEEEEEC
T ss_pred             CCCcccceeeEEEEEecCCcEEEEec--CCceeee----ecccccCcEEEEEEEEc
Confidence            34689999999999999999999995  4444443    35799999999999998