Citrus Sinensis ID: 001115

Local Sequence Feature Prediction

Prediction and (Method)	Result

Residue Number Marker

Protein Sequence

Secondary Structure (PSIPRED)

Secondary Structure Prediction (SSPRO)

Coil and Loop (DISEMBL)

Flexible Loop (DISEMBL)

Low Complexity Region (SEG)

Disordered region (IsUnstruct)

Disordered Region (DISOPRED)

Disordered Region (DISEMBL)

Disordered Region (DISPRO)

Transmembrane Helix (TMHMM)

Transmembrane Helix (HMMTOP)

Transmembrane Helix (MEMSAT)

TM Helix, Signal Peptide (MEMSAT_SVM)

TM Helix, Signal Peptide (Phobius)

Signal Peptide (SignalP HMM Mode)

Signal Peptide (SignalP NN Mode)

Coiled Coils (COILS)

Positional Conservation

--------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-------980-------990------1000------1010------1020------1030------1040------1050------1060------1070------1080------1090------1100------1110------1120------1130------1140------1150--

MAASSRKSQKKSSKDGPKFNKASKNQFKNSKKQINDAVEAQDLALPPDDDVPVFPRGGGHSLTQRERDEIHAEVDAEFEAVERGLHKKNKKKKKKTERKANETVDDLGSLFGDGISGKLPRYANKITLKNISAGMKLWGVVAEVNEKDLVICLPGGLRGLARAADALDPILDNEIEANEDNLLPTIFHVGQLVSCIVLQLDDDKKEIGKRKIWLSLRLSLLYKGLSLETVQEGMVLTAYVKSIEDHGYILHFGLPSFTGFLPRNNLAENSGIDVKPGLLLQGVVRSIDRTRKVVYLSSDPDTVSKCVTKDLKGISIDLLVPGMMVSTRVQSILENGVMLSFLTYFTGTVDIFHLQNTFPTTNWKNDYNQHKKVNARILFVDPTSRAVGLTLNPYLLHNRAPPSHVKVGDIYDQSKVVRVDRGLGLLLDIPSTPVSTPAYVTISDVAEEEVRKLEKKYKEGSCVRVRILGFRHLEGLATGILKASAFEGLVFTHSDVKPGMVVKGKVIAVDSFGAIVQFPGGVKALCPLPHMSEFEIVKPGKKFKVGAELVFRVLGVKSKRITVTHKKTLVKSKLAILSSYAEATDRLITHGWITKIEKHGCFVRFYNGVQGFAPRSELGLDPGCEPSSMYHVGQVVKCRIMSSIPASRRINLSFMMKPTRVSEDDLVKLGSLVSGVVDVVTPNAVVVYVIAKGYSKGTIPTEHLADHLEHATVMKSVIKPGYEFDQLLVLDNESSNLLLSAKYSLINSAQQLPSDASHIHPNSVVHGYVCNIIETGCFVRFLGRLTGFAPRSKAVDGQRADLSKTYYVGQSVRSNILDVNSETGRITLSLKQSCCSSTDASFMQEHFLLEEKIAMLQSSKHNGSELKWVEGFIIGSVIEGKVHESNDFGVVVSFEEHSDVYGFITHHQLAGATVESGSVIQAAILDVAKAERLVDLSLKTVFIDRFREANSNRQAQKKKRKREASKDLGVHQTVNAIVEIVKENYLVLSLPEYNHSIGYASVSDYNTQKFPQKQFLNGQSVIATVMALPSSSTAGRLLLLLKAISETETSSSKRAKKKSSYDVGSLVQAEITEIKPLELRLKFGIGFHGRIHITEVNDDKSNVVENLFSNFKIGQTVTARIIAKSNKPDMKKSFLWELSIKPSMLTGKWFTA

ccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccHHHHHHHHHHHHHHHHHHcccccccccccHHHHHcccccccccccccccccccccccccccccccccccccEEEEEEEEEEcccEEEEcccccEEEEEcccccccccHHHHHHccccccccccccccEEEEEEEEEEcccccccEEEEEEEccHHHHHccccccccccccEEEEEEEEEEccEEEEEEccccEEEEEcccccccccccccccccEEEEEEEEEcccccEEEEccccccccHHHHHHcccccccccccccEEEEEEEEEEccEEEEEEcccEEEEEEcccccccccccccccccccccEEEEEEEEEEccccEEEEEccHHHHcccccccccccccEEEccEEEEEEEccEEEEEcccccccccEEEEccccccHHccccccccccccEEEEEEEEEEccccEEEEEEcccccccccccccccccccEEEEEEEEEEccEEEEEEcccEEEEEEccccccccccccccccccccEEEEEEEEEEccEEEEEEcccccccHHHHHHHHHHcccccEEEEEEEEEEEcEEEEEEcccEEEEEEccccccccccccccccccccEEEEEEEEEEccccEEEEEEEEcccccccccccccccEEEEEEEEEEcccEEEEEEEcccccEEEEccccccccccccccccccccccEEEEEEEEEccccEEEEEEccccccccccccccccccccccEEEEEEEEEEccEEEEEEccccEEEEEccccccccccccccccccccEEEEEEEEEEccccEEEEEEcccccccccHHHHHHHHHHHHHHHHHHcccccccccccccccccccEEEEEEEEEEccEEEEEEcccccEEEEEEcccccccccccccEEEEEEEEEEccccEEEEEEccccccHHHHHHHHHHHHHHHHHHccccccccccEEEEEEEEEEccEEEEEEccccEEEEEEEccccccccccccccccccEEEEEEEEEcccccccEEEEEEccccccccccccccccccccccccEEEEEEEEEEccEEEEEEcccEEEEEEcccccccccccccccccccccccEEEEEEEEEEcccccccccEEEEEEcccccccccccc

cccccccccccccccccHHccccccccccccccccccccccccccccccccccccccccccccHHHHHHHHHHHHHHHHHHHcccccccccccccHHccccccccccccccccccccccccEEccccHHccccccEEEEEEEEEccccEEEEcccccEEEEEHHHHcHHHccccccccccccHHHHEccccEEEEEEEEEccccccccccEEEEEEcHHHHcccccHHHcccccEEEEEEEEEEccEEEEEEccccEEEEEcHHHcccccccccccccEEEEEEEEEcccccEEEEEccHHHHHHHHHHHHHHccHHHcccccEEEEEEEEEcccEEEEEEccccEEEEEccccccccccccHHHcEccccEEEEEEEEEcccccEEEEEEccHHcccccccHccccccEEEccEEEEEEcccEEEEEEccccccEEEEEEcccccccccccccccEccccEEEEEEEEEcccccEEEEEEcccHcccHHHHHHHcccccEEEEEEEEEcccEEEEEEccccEEEEEHHHcccccccccHHccccccEEEEEEEEEccccEEEEEcccHccccccHHHHHHHcccccEEEEEEEEEcccEEEEEEccccEEEEEHHHccHcccccHHHccccccEEEEEEEEEcccccEEEEEEccccccHHHHHHcccccEEEEEEEEEcccEEEEEEcccccEEEEEEcccccccccccccHHHHcccccEEEEEEEEcccccEEEEEEcccHcccHHccHHHHHHcccccEEEEEEEEEcccEEEEEEcccEEEEEEcHHccHHHcccHHHHcccccEEEEEEEEEcccccEEEEEEEccccccccccHHccHcHHHHHHHHHccccccHHHHHHHHHcccccEEEEEEEEEEccEEEEEEccccEEEEEEEcccccccccccccEEEEEEEEEcccccEEEEEccccccccHHHHccccccccccccHHHHHHcccccEEEEEEEEEcccEEEEEEcccccEEEEEEccccccccccHHccccccEEEEEEEEEcccccEEEEEEcccccccccccccccHccHHHcccccEEEEEEEEEcccEEEEEEccccEEEEEEEEcccccccccccccHHcccccEEEEEEEEcccccccccccEEEEEEcccccccccccc

maassrksqkksskdgpkfnkasknqfKNSKKQINDAVeaqdlalppdddvpvfprggghsltqrERDEIHAEVDAEFEAVERGLHKKNKKKKKKTERKANETVDdlgslfgdgisgklpryanKITLKNISAGMKLWGVVAEVNEKDLVICLPGGLRGLARaadaldpildneieanednllptiFHVGQLVSCIVLQLDDDKKEIGKRKIWLSLRLSLLYKGLSLETVQEGMVLTAYVKSIEDhgyilhfglpsftgflprnnlaensgidvkpgllLQGVVRSIDRTRKVVylssdpdtvskcvtkdlkgisidllvpgmMVSTRVQSILENGVMLSFLTYFTGTvdifhlqntfpttnwkndynqhkkvnarilfvdptsravgltlnpyllhnrappshvkvgdiydqskvvrvdrglgllldipstpvstpayvtISDVAEEEVRKLEKKykegscvrVRILGFRHLEGLATGILKASAfeglvfthsdvkpgmvVKGKVIAVDSfgaivqfpggvkalcplphmsefeivkpgkkfkvGAELVFRVLGVKSKRITVTHKKTLVKSKLAILSSYAEATDRLITHGWITKIEKHGCFvrfyngvqgfaprselgldpgcepssmyhvgQVVKCRimssipasrrinlsfmmkptrvseddLVKLGSLVSGVVDVVTPNAVVVYVIAKgyskgtiptehladHLEHATVMKsvikpgyefdqllvldnessnLLLSAKYSLINsaqqlpsdashihpnsvvHGYVCNIIETGCFVRFlgrltgfaprskavdgqradlsktyyvgqsvrsnildvnsetgrITLSlkqsccsstdasFMQEHFLLEEKIAMLQSskhngselkwVEGFIIGSVIegkvhesndfGVVVSFEEHSDVYGFITHHqlagatveSGSVIQAAILDVAKAERLVDLSLKTVFIDRFREANSNRQAQKKKRKReaskdlgvhQTVNAIVEIVKENYLVlslpeynhsigyasvsdyntqkfpqkqflngqSVIATVmalpssstAGRLLLLLKAISETetssskrakkkssydVGSLVQAEITEIKPLELRLKFgigfhgrihitevnddksNVVENLFSNFKIGQTVTARIIAksnkpdmkKSFLWElsikpsmltgkwfta

maassrksqkksskdgpkfnkasknqfknSKKQINDAVEAQDLALPPDDDVPVFPRGGGHSLTQRERDEIHAEVDAefeaverglhkknkkkkkkterkanetvddlgslfgdgisgklPRYANKITLKNISAGMKLWGVVAEVNEKDLVICLPGGLRGLARAADALDPILDNEIEANEDNLLPTIFHVGQLVSCIVLQLDDDKKEIGKRKIWLSLRLSLLYKGLSLETVQEGMVLTAYVKSIEDHGYILHFGLPSFTGFLPRNNLAEnsgidvkpgllLQGVVRSIDRTRKvvylssdpdtvskcvtkdLKGISIDLLVPGMMVSTRVQSILENGVMLSFLTYFTGTVDIFHLQNTFPTTNWKNDYNQHKKVNARILFVDPTSRAVGLTLNPYLlhnrappshvkvgdiydqSKVVRVDRGLGllldipstpvstpayvtiSDVAEEEVRKLekkykegscvrvRILGFRHLEGLATGILKASAFEGLVFTHSDVKPGMVVKGKVIAVDSFGAIVQFPGGVKALCPLPHMSEFEIVKPGKKFKVGAELVFRvlgvkskritvthkktlvksklaiLSSYAEATDRLITHGWITKIEKHGCFVRFYNGVQGFAPRSELGLDPGCEPSSMYHVGQVVKCRIMSSIPASRRINLSFMMKPTRVSEDDLVKLGSLVsgvvdvvtpNAVVVYVIAKGYSKGTIPTEHLADHLEHATVMKSVIKPGYEFDQLLVLDNESSNLLLSAKYSLINSAQQLPSDASHIHPNSVVHGYVCNIIETGCFVRFLGRLTGFaprskavdgqradlsktyyvgqsvrsnildvnseTGRITLSLKQSCCSSTDASFMQEHFLLEEKIAMLQSSKHNGSELKWVEGFIIGSVIEGKVHESNDFGVVVSFEEHSDVYGFITHHQLAGATVESGSVIQAAILDVAKAERLVDLSLKTVFidrfreansnrqaqkkkrkreaskdlgvhqtvNAIVEIVKENYLVLSLPEYNHSIGYASVSDYNTQKFPQKQFLNGQSVIATVMALPSSSTAGRLLLLLKAISetetssskrakkkssydvgSLVQAEITEIKPLELRLKFGIGFHGRIHitevnddksNVVENLFsnfkigqtvtariiaksnkpdmkksflwelsikpsmltgkwfta

MAAssrksqkksskDGPKFNKASKNQFKNSKKQINDAVEAQDLALppdddvpvFPRGGGHSLTQRERDEIHAEVDAEFEAVERGLHkknkkkkkkTERKANETVDDLGSLFGDGISGKLPRYANKITLKNISAGMKLWGVVAEVNEKDLVIClpgglrglaraadaldpILDNEIEANEDNLLPTIFHVGQLVSCIVLQLDDDKKEIGKRKIWlslrlsllykglslETVQEGMVLTAYVKSIEDHGYILHFGLPSFTGFLPRNNLAENSGIDVKPGLLLQGVVRSIDRTRKVVYLSSDPDTVSKCVTKDLKGISIDLLVPGMMVSTRVQSILENGVMLSFLTYFTGTVDIFHLQNTFPTTNWKNDYNQHKKVNARILFVDPTSRAVGLTLNPYLLHNRAPPSHVKVGDIYDQSKvvrvdrglgllldIPSTPVSTPAYVTISDVAEEEVRKLEKKYKEGSCVRVRILGFRHLEGLATGILKASAFEGLVFTHSDVKPGMVVKGKVIAVDSFGAIVQFPGGVKALCPLPHMSEFEIVKPGKKFKVGAELVFRVLGVKSKRITVTHKKTLVKSKLAILSSYAEATDRLITHGWITKIEKHGCFVRFYNGVQGFAPRSELGLDPGCEPSSMYHVGQVVKCRIMSSIPASRRINLSFMMKPTRVSEDdlvklgslvsgvvdvvtpnavvvyvIAKGYSKGTIPTEHLADHLEHATVMKSVIKPGYEFDQLLVLDNESSNLLLSAKYSLINSAQQLPSDASHIHPNSVVHGYVCNIIETGCFVRFLGRLTGFAPRSKAVDGQRADLSKTYYVGQSVRSNILDVNSETGRITLSLKQSCCSSTDASFMQEHFLLEEKIAMLQSSKHNGSELKWVEGFIIGSVIEGKVHESNDFGVVVSFEEHSDVYGFITHHQLAGATVESGSVIQAAILDVAKAERLVDLSLKTVFIDRFREAnsnrqaqkkkrkreaskDLGVHQTVNAIVEIVKENYLVLSLPEYNHSIGYASVSDYNTQKFPQKQFLNGQSVIATVMALPSSSTAGRLLLLLKAIsetetssskrakkkssYDVGSLVQAEITEIKPLELRLKFGIGFHGRIHITEVNDDKSNVVENLFSNFKIGQTVTARIIAKSNKPDMKKSFLWELSIKPSMLTGKWFTA

***********************************************************************************************************GSLFGDGISGKLPRYANKITLKNISAGMKLWGVVAEVNEKDLVICLPGGLRGLARAADALDPILDNEIEANEDNLLPTIFHVGQLVSCIVLQLDDDKKEIGKRKIWLSLRLSLLYKGLSLETVQEGMVLTAYVKSIEDHGYILHFGLPSFTGFLPRNNLAENSGIDVKPGLLLQGVVRSIDRTRKVVYLSSDPDTVSKCVTKDLKGISIDLLVPGMMVSTRVQSILENGVMLSFLTYFTGTVDIFHLQNTFPTTNWKNDYNQHKKVNARILFVDPTSRAVGLTLNPYLLHNRAPPSHVKVGDIYDQSKVVRVDRGLGLLLDIPSTPVSTPAYVTISDVAEEEVRKLEKKYKEGSCVRVRILGFRHLEGLATGILKASAFEGLVFTHSDVKPGMVVKGKVIAVDSFGAIVQFPGGVKALCPLPHMSEFEIVKPGKKFKVGAELVFRVLGVKSKRITVTHKKTLVKSKLAILSSYAEATDRLITHGWITKIEKHGCFVRFYNGVQGFAPRSELGLDPGCEPSSMYHVGQVVKCRIMSSIPASRRINLSFMMKPTRVSEDDLVKLGSLVSGVVDVVTPNAVVVYVIAKGYSKGTIPTEHLADHLEHATVMKSVIKPGYEFDQLLVLDNESSNLLLSAKYSLINSA*******SHIHPNSVVHGYVCNIIETGCFVRFLGRLTGFAPRSKAVDGQRADLSKTYYVGQSVRSNILDVNSETGRITLSLKQSCCSSTDASFMQEHFLLEEKIAMLQSSKHNGSELKWVEGFIIGSVIEGKVHESNDFGVVVSFEEHSDVYGFITHHQLAGATVESGSVIQAAILDVAKAERLVDLSLKTVFIDRF*********************LGVHQTVNAIVEIVKENYLVLSLPEYNHSIGYASVSDYNTQKFPQKQFLNGQSVIATVMALPSSSTAGRLLLLLKAI******************VGSLVQAEITEIKPLELRLKFGIGFHGRIHITEVNDDKSNVVENLFSNFKIGQTVTARIIAKSNK*DMKKSFLWELSIKPSMLTGKW***

*******************************************************RGGGHS*************************************************************ANKITLKNISAGMKLWGVVAEVNEKDLVICLPGGLRGLARAADALDPILDNEI***EDNLLPTIFHVGQLVSCIVL*****************LRLSLLYKGLSLETVQEGMVLTAYVKSIEDHGYILHFGLPSFTGFLPRNNLA***GIDVKPGLLLQGVVRSIDRTRKVVYLSSDPD***********GISIDLLVPGMMVSTRVQSILENGVMLSFLTYFTGTVDIFHLQN*****NWKNDYNQHKKVNARILFVDPTSRAVGLTLNPYLLHNRAPPSHVKVGDIYDQSKVVRVDRGLGLLLDIPSTPVSTPAYVTISDVAEEEVRKLEKKYKEGSCVRVRILGFRHLEGLATGILKASAFEGLVFTHSDVKPGMVVKGKVIAVDSFGAIVQFPGGVKALCPLPHMSEFEIVKPGKKFKVGAELVFRVLGVKSKRITVTHKKTLVKSKLAILSSYAEATDRLITHGWITKIEKHGCFVRFYNGVQGFAPRSELGLDPGCEPSSMYHVGQVVKCRIMSSIPASRRINLSFM***********VKLGSLVSGVVDVVTPNAVVVYVIAKGYSKGTIPTEHLADHLEHATVMKSVIKPGYEFDQLLVLDNESSNLLLSAKYSLINSAQQLPSDASHIHPNSVVHGYVCNIIETGCFVRFLGRLTGFAPRSKAVDGQRADLSKTYYVGQSVRSNILDVNSETGRITLSLKQSCCSS*DA******FLLEEKIAMLQSSKHNGSELKWVEGFIIGSVIEGKVHESNDFGVVVSFEEHSDVYGFITHHQLAGATVESGSVIQAAILDVAKAERLVDLSLKTVF*************************LGVHQTVNAIVEIVKENYLVLSLPEYNHSIGYASVS******F**KQFLNGQSVIATVMALPSSSTAGRLLL*********************YDVGSLVQAEITEIKPLELRLKFGIGFHGRIHITEVNDDKSNVVENLFSNFKIGQTVTARIIAKSNK*************************

********************KASKNQFKNSKKQINDAVEAQDLALPPDDDVPVFPRGGGHSLTQRERDEIHAEVDAEFEAVERG*****************ETVDDLGSLFGDGISGKLPRYANKITLKNISAGMKLWGVVAEVNEKDLVICLPGGLRGLARAADALDPILDNEIEANEDNLLPTIFHVGQLVSCIVLQLDDDKKEIGKRKIWLSLRLSLLYKGLSLETVQEGMVLTAYVKSIEDHGYILHFGLPSFTGFLPRNNLAENSGIDVKPGLLLQGVVRSIDRTRKVVYLSSDPDTVSKCVTKDLKGISIDLLVPGMMVSTRVQSILENGVMLSFLTYFTGTVDIFHLQNTFPTTNWKNDYNQHKKVNARILFVDPTSRAVGLTLNPYLLHNRAPPSHVKVGDIYDQSKVVRVDRGLGLLLDIPSTPVSTPAYVTISDVAEEEVRKLEKKYKEGSCVRVRILGFRHLEGLATGILKASAFEGLVFTHSDVKPGMVVKGKVIAVDSFGAIVQFPGGVKALCPLPHMSEFEIVKPGKKFKVGAELVFRVLGVKSKRITVTHKKTLVKSKLAILSSYAEATDRLITHGWITKIEKHGCFVRFYNGVQGFAPRSELGLDPGCEPSSMYHVGQVVKCRIMSSIPASRRINLSFMMKPTRVSEDDLVKLGSLVSGVVDVVTPNAVVVYVIAKGYSKGTIPTEHLADHLEHATVMKSVIKPGYEFDQLLVLDNESSNLLLSAKYSLINSAQQLPSDASHIHPNSVVHGYVCNIIETGCFVRFLGRLTGFAPRSKAVDGQRADLSKTYYVGQSVRSNILDVNSETGRITLSLKQSCCSSTDASFMQEHFLLEEKIAMLQSSKHNGSELKWVEGFIIGSVIEGKVHESNDFGVVVSFEEHSDVYGFITHHQLAGATVESGSVIQAAILDVAKAERLVDLSLKTVFIDRFREAN*****************LGVHQTVNAIVEIVKENYLVLSLPEYNHSIGYASVSDYNTQKFPQKQFLNGQSVIATVMALPSSSTAGRLLLLLKAISE******************SLVQAEITEIKPLELRLKFGIGFHGRIHITEVNDDKSNVVENLFSNFKIGQTVTARIIAKSNKPDMKKSFLWELSIKPSMLTGKWFTA

***********************************************************HSLTQRERDEIHAEVDAEFEAVER************************************PRYANKITLKNISAGMKLWGVVAEVNEKDLVICLPGGLRGLARAADALDPILDNEIEANEDNLLPTIFHVGQLVSCIVLQLDDDKKEIGKRKIWLSLRLSLLYKGLSLETVQEGMVLTAYVKSIEDHGYILHFGLPSFTGFLPRNNLAENSGIDVKPGLLLQGVVRSIDRTRKVVYLSSDPDTVSKCVTKDLKGISIDLLVPGMMVSTRVQSILENGVMLSFLTYFTGTVDIFHLQNTFPTTNWKNDYNQHKKVNARILFVDPTSRAVGLTLNPYLLHNRAPPSHVKVGDIYDQSKVVRVDRGLGLLLDIPSTPVSTPAYVTISDVAEEEVRKLEKKYKEGSCVRVRILGFRHLEGLATGILKASAFEGLVFTHSDVKPGMVVKGKVIAVDSFGAIVQFPGGVKALCPLPHMSEFEIVKPGKKFKVGAELVFRVLGVKSKRITVTHKKTLVKSKLAILSSYAEATDRLITHGWITKIEKHGCFVRFYNGVQGFAPRSELGLDPGCEPSSMYHVGQVVKCRIMSSIPASRRINLSFMMKPTRVSEDDLVKLGSLVSGVVDVVTPNAVVVYVIAKGYSKGTIPTEHLADHLEHATVMKSVIKPGYEFDQLLVLDNESSNLLLSAKYSLINSAQQLPSDASHIHPNSVVHGYVCNIIETGCFVRFLGRLTGFAPRSKAVDGQRADLSKTYYVGQSVRSNILDVNSETGRITLSLKQSCC***DASF*QEHFLLEEKIAMLQSSKHNGSELKWVEGFIIGSVIEGKVHESNDFGVVVSFEEHSDVYGFITHHQLAGATVESGSVIQAAILDVAKAERLVDLSLKTV******************RKREASKDLGVHQTVNAIVEIVKENYLVLSLPEYNHSIGYASVSDYNTQKFPQKQFLNGQSVIATVMALPSSSTAGRLLLLLKAISE*ETSSSKRAKKKSSYDVGSLVQAEITEIKPLELRLKFGIGFHGRIHITEVNDDKSNVVENLFSNFKIGQTVTARIIAKSNKPDMKKSFLWELSIKPS*********

oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo

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no confident homologs detected

Close Homologs for Annotation Transfer

Close Homologs in SWISS-PROT Database Detected by BLAST

Original result of BLAST against SWISS-PROT Database

ID	Alignment graph	Length	Definition	RBH(Q2H)	RBH(H2Q)	Q cover	H cover	Identity	E-value
Query		1152	2.2.26 [Sep-21-2011]
A7MB10		1874	Protein RRP5 homolog OS=B	yes	no	0.904	0.556	0.293	1e-107
Q14690		1871	Protein RRP5 homolog OS=H	yes	no	0.908	0.559	0.286	1e-105
Q6NS46		1862	Protein RRP5 homolog OS=M	yes	no	0.913	0.564	0.282	1e-102
O74835		1690	rRNA biogenesis protein r	yes	no	0.656	0.447	0.277	5e-58
Q05022		1729	rRNA biogenesis protein R	yes	no	0.644	0.429	0.251	9e-42
Q9ZD28		568	30S ribosomal protein S1	yes	no	0.293	0.595	0.220	2e-10
Q4L6I1		392	30S ribosomal protein S1	yes	no	0.203	0.599	0.287	2e-10
Q49XT0		393	30S ribosomal protein S1	yes	no	0.197	0.580	0.28	3e-10
Q68WL4		568	30S ribosomal protein S1	yes	no	0.293	0.595	0.218	3e-10
Q8NWM8		391	30S ribosomal protein S1	yes	no	0.283	0.836	0.236	4e-10

>sp\|A7MB10\|RRP5_BOVIN Protein RRP5 homolog OS=Bos taurus GN=PDCD11 PE=2 SV=1	Back alignment and function desciption

 Score =  391 bits (1004), Expect = e-107,   Method: Compositional matrix adjust.
 Identities = 342/1166 (29%), Positives = 553/1166 (47%), Gaps = 124/1166 (10%)

Query: 54   FPRGGGHSLTQRERDEIHA-------EVDAEFEAVERGLHKKNKKKKKKTERKANETVDD 106
            FPRGG     + E+    +       ++  E E+ +R   KK +K   KT++   ET   
Sbjct: 8    FPRGGTRKTHKSEKAFQQSVEQDNLFDISTEEESTKR---KKIQKGPAKTKKLKVETRQ- 63

Query: 107  LGSLFGDGISGKLPRYANKI-TLKNISAGMKLWGVVAEVNEKDLVICLPGGLRGLARAAD 165
                     S K  R   +I  ++++  GM++ G V EVNE +L I LP GL+G  +  +
Sbjct: 64   ---------SSKFVREKFEILNVESLCEGMRILGCVKEVNELELAISLPNGLQGYVQVTE 114

Query: 166  ALDPILD--NEIEANEDNL-----LPTIFHVGQLVSCIVLQLDDDKKEIGKRKIWLSLRL 218
              D   +  NE  A E+ L     LP +F  G LV C+V  LD  K    K+ + LSL  
Sbjct: 115  ICDAYTEKLNEQVAQEEPLQDLVGLPELFSPGMLVRCVVSSLDTTKG--SKKNVMLSLNP 172

Query: 219  SLLYKGLSLETVQEGMVLTAYVKSIEDHGYILHFGLPSFTGFLPRNNLAE-----NSGID 273
              + + LS ET++ GM+LT  V S+EDHGY++  G+     FLP     E     N G  
Sbjct: 173  KNVNRVLSAETLKPGMLLTGTVSSLEDHGYLVDIGVSGARAFLPLQKAQEYIRQKNKGAK 232

Query: 274  VKPGLLLQGVVRSIDRTRKVVYLSSDPDTVSKCVTKDLKGISIDLLVPGMMVSTRVQSIL 333
            +K G  L  ++  +  +R VV LS     VS  +  + +  +++ L+PG++V  +VQ + 
Sbjct: 233  LKVGQYLNCLIEEVKGSRGVVTLSIGHSEVSAAIATEEQSWTLNSLLPGLVVKAQVQKVT 292

Query: 334  ENGVMLSFLTYFTGTVDIFHLQNTFPTTNWKNDYNQHKKVNARILFVDPTSRAVGLTLNP 393
              G+ L FL++F+G VD  HL      T + N     ++V A +L V P +RAV L+L P
Sbjct: 293  PLGLTLKFLSFFSGLVDFMHLDPKKAGTYFSN-----QQVRACVLCVHPRTRAVRLSLRP 347

Query: 394  YLLHNRAPPSHV---KVGDIYDQSKVVRVDRGLGLLLDIPSTPVSTPAYVTISDVAEEEV 450
              L    P + +   ++G + D   V       G    +      T AY   + ++  + 
Sbjct: 348  VFLQPGRPLTRLLCQQLGAVLDDVPVQGFFGSAGATFKLKD---GTLAYARRNHLSNSKK 404

Query: 451  RKLEKKYKEGSCVRVRILGFRHLEGLATGILKASAFEGLVFTHSDVKPGMVVKGKVIAVD 510
                + +K G+  + RI+ +  ++ LA   L+ S  E     + D+KPG +VKGKV+ + 
Sbjct: 405  TFKPEAFKPGNTHKCRIIDYSQMDELALLSLRTSIIEAQFLWYHDIKPGALVKGKVLTIK 464

Query: 511  SFGAIVQFPGGVKALCPLPHMSEFEIVKPGKKFKVGAELVFRVL--GVKSKRITVTHKKT 568
              G +V+    ++ L P  H+++  I  P KK+ VG E+  RVL    K+K++ +T KKT
Sbjct: 465  PHGMVVKMGKQIRGLVPTMHLADILIKNPEKKYHVGDEVKCRVLLCDPKAKKLMMTLKKT 524

Query: 569  LVKSKLAILSSYAEATDRLITHGWITKIEKHGCFVRFYNGVQGFAPRSELGLDPGCEPSS 628
            LV+SKL  ++ Y +A   L THG+I +++ +GC V+FYN VQG  PR EL  +   +P S
Sbjct: 525  LVESKLPAITCYDDAKPGLQTHGFILRVKDYGCIVKFYNDVQGLVPRHELSAEYVPDPES 584

Query: 629  MYHVGQVVKCRIMSSIPASRRINLSFMM--KPTRVSEDD------LVKLGSLVSGVVDVV 680
            +++ GQVVK  +++  P+  R+ LSF +   P +  E         V  G L    V   
Sbjct: 585  VFYTGQVVKVVVLNCEPSKERMLLSFRLLSDPKQEGEGQSQKKKKAVSAGQLADVKVLEK 644

Query: 681  TPNAVVVYVIAKGYSKGTIPTEHLADHLEHATVMKSVIKPGYEFDQLLVLDNESSNLLLS 740
            T + + V V+      G +PT HL+DH+ +  ++   ++ G    ++L L      +LL 
Sbjct: 645  TKDGLKVAVLPHNIP-GFLPTAHLSDHVTNGPLLYHWLQTGDTLHRVLCLSVSEERVLLC 703

Query: 741  AKYSLINSAQ--QLPSDASHIHPNSVVHGYVCNIIETGCFVRFLGRLTGFAPRSKAVDGQ 798
             K +L+++ +  Q P   S IHP  ++ G+V NI + G FV+F   L+G AP++   D  
Sbjct: 704  RKPALVSAVEGGQNPKSFSEIHPGMLLIGFVKNIKDYGVFVQFPSGLSGLAPKAILSDKF 763

Query: 799  RADLSKTYYVGQSVRSNILDVNSETGRITLSLKQSCCSSTDASFMQEHF---LLEEKIAM 855
                S  +  GQ+V + + +V+ E  R+ LSL+ S C+  D +          LEE+  +
Sbjct: 764  VTSTSDHFVEGQTVVAKVTNVDEEKQRMLLSLRLSDCTLGDLATTSLLLLSQCLEERQGV 823

Query: 856  LQSSKHNGSEL-KWVEGFIIGSVIEGKVHESNDFGVVVSFEEHSDVYGFI---THHQLAG 911
                 +  S L + +     G  ++ +V E  + G V+ F E   V G +   + +  AG
Sbjct: 824  RSLMSNRDSVLIQTLAEMTPGMALDLEVQEVLEDGSVL-FSE-GPVPGLVLRASKYHRAG 881

Query: 912  ATVESGSVIQAAILDVAKAERLVDLSLKTVFIDRFREANSNRQAQKKKRKREASKDLGVH 971
              +E G   +A IL+V   +  V +SL    +        NR+A+K K+  +        
Sbjct: 882  QELEPGQKKKAVILNVDMLKLEVHVSLCHDLV--------NRKAKKLKKGSD-------- 925

Query: 972  QTVNAIVEIVKENYLVLSLPEYNHSIGYASVSDYN-TQKFPQKQFLNGQSVIATVMALPS 1030
              + AIV+ ++E++ V SL E  H   ++  S  N T +F  ++   GQ V  T+     
Sbjct: 926  --LQAIVQHLEESFAVASLVETGHLAAFSLTSHLNDTFRFDSEKLQVGQGVSLTLQTTEP 983

Query: 1031 SSTAGRLLLLLKAISETETSSSKRAK-------------------KKSSYDVGSLVQAEI 1071
              T   LLL ++  +   T    R                     KK +  +G +V   +
Sbjct: 984  GVTG--LLLAIEGPAAKRTMRQTRKDSETVDEDEEVDPALVVGTVKKHTLSIGDVVTGTV 1041

Query: 1072 TEIKPLELRLKFGIGFHGRIHITEVNDDKSNVVENLFSNFKIGQTVTARIIAKSNKPDMK 1131
              IKP  + +    G  G IH + + DD   V  +  +  K+G+ VTAR+I      DMK
Sbjct: 1042 KSIKPTHVVVTLEDGIIGCIHASHILDD-VPVGTSPTAKLKVGKKVTARVIGGR---DMK 1097

Query: 1132 K-SFL-----------WELSIKPSML 1145
               FL            ELS++PS L
Sbjct: 1098 TFKFLPISHPRFIRTIPELSVRPSEL 1123

Essential for the generation of mature 18S rRNA, specifically necessary for cleavages at sites A0, 1 and 2 of the 47S precursor. Directly interacts with U3 snoRNA.
Bos taurus (taxid: 9913)

>sp\|Q14690\|RRP5_HUMAN Protein RRP5 homolog OS=Homo sapiens GN=PDCD11 PE=1 SV=3	Back alignment and function description

>sp\|Q6NS46\|RRP5_MOUSE Protein RRP5 homolog OS=Mus musculus GN=Pdcd11 PE=2 SV=2	Back alignment and function description

>sp\|O74835\|RRP5_SCHPO rRNA biogenesis protein rrp5 OS=Schizosaccharomyces pombe (strain 972 / ATCC 24843) GN=rrp5 PE=1 SV=1	Back alignment and function description

>sp\|Q05022\|RRP5_YEAST rRNA biogenesis protein RRP5 OS=Saccharomyces cerevisiae (strain ATCC 204508 / S288c) GN=RRP5 PE=1 SV=1	Back alignment and function description

>sp\|Q9ZD28\|RS1_RICPR 30S ribosomal protein S1 OS=Rickettsia prowazekii (strain Madrid E) GN=rpsA PE=3 SV=1	Back alignment and function description

>sp\|Q4L6I1\|RS1_STAHJ 30S ribosomal protein S1 OS=Staphylococcus haemolyticus (strain JCSC1435) GN=rpsA PE=3 SV=1	Back alignment and function description

>sp\|Q49XT0\|RS1_STAS1 30S ribosomal protein S1 OS=Staphylococcus saprophyticus subsp. saprophyticus (strain ATCC 15305 / DSM 20229) GN=rpsA PE=3 SV=1	Back alignment and function description

>sp\|Q68WL4\|RS1_RICTY 30S ribosomal protein S1 OS=Rickettsia typhi (strain ATCC VR-144 / Wilmington) GN=rpsA PE=3 SV=1	Back alignment and function description

>sp\|Q8NWM8\|RS1_STAAW 30S ribosomal protein S1 OS=Staphylococcus aureus (strain MW2) GN=rpsA PE=3 SV=1	Back alignment and function description

Close Homologs in the Non-Redundant Database Detected by BLAST

Original result of BLAST against Nonredundant Database

GI	Alignment Graph	Length	Definition	Q cover	H cover	Identity	E-value
Query		1152
297739784		1862	unnamed protein product [Vitis vinifera]	0.955	0.591	0.745	0.0
359481849		1879	PREDICTED: protein RRP5 homolog [Vitis v	0.950	0.582	0.745	0.0
356533079		1885	PREDICTED: protein RRP5 homolog [Glycine	0.961	0.587	0.657	0.0
356498361		2174	PREDICTED: protein RRP5 homolog [Glycine	0.951	0.504	0.659	0.0
449453908		1898	PREDICTED: protein RRP5 homolog [Cucumis	0.961	0.583	0.628	0.0
240255326		1896	RNA binding protein [Arabidopsis thalian	0.927	0.563	0.616	0.0
12322020		1396	rRNA biogenesis protein, putative, 3' pa	0.927	0.765	0.617	0.0
10998136		1765	pre-rRNA processing protein RRP5 [Arabid	0.847	0.552	0.623	0.0
414883924		1207	TPA: hypothetical protein ZEAMMB73_95705	0.929	0.887	0.544	0.0
222636634		1898	hypothetical protein OsJ_23484 [Oryza sa	0.891	0.541	0.583	0.0

>gi\|297739784\|emb\|CBI29966.3\| unnamed protein product [Vitis vinifera]	Back alignment and taxonomy information

 Score = 1672 bits (4330), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 844/1132 (74%), Positives = 962/1132 (84%), Gaps = 31/1132 (2%)

Query: 18   KFNKASKNQFKNSKKQINDAVEAQDLALPPDDDVPVFPRGGGHSLTQRERDEIHAEVDAE 77
            K   ASK  FK   +Q N+AV ++ LAL  +DDVP FPRGGG  L+++E D I AEVDAE
Sbjct: 18   KLRGASKKPFKPRMRQ-NEAVPSESLALQMEDDVPDFPRGGGSLLSRQEHDAIRAEVDAE 76

Query: 78   FEAVERGLHKKNKKKKKKTERKANETVDDLGSLFGDGISGKLPRYANKITLKNISAGMKL 137
            FEA ER   KKNK  KK  +  A E  DD+GSLFGDGI+GKLPR+ANKITLKNIS GMKL
Sbjct: 77   FEAGERKTKKKNKNAKKTKKNYALE--DDMGSLFGDGITGKLPRFANKITLKNISPGMKL 134

Query: 138  WGVVAEVNEKDLVICLPGGLRGLARAADALDPILDNEIEANEDNLLPTIFHVGQLVSCIV 197
            WGVVAEVNEKDL I LPGGLRGL RA++A DP+  NEI+  E   LP IFH+GQLVSC+V
Sbjct: 135  WGVVAEVNEKDLGISLPGGLRGLVRASEAFDPLFSNEIKDAEGIFLPRIFHIGQLVSCVV 194

Query: 198  LQLDDDKKEIGKRKIWLSLRLSLLYKGLSLETVQEGMVLTAYVKSIEDHGYILHFGLPSF 257
            LQLDDDKKE GKR+IWLSLRLSLL+KG +L+ +QEGMVLTAYVKSIEDHGYILHFGLPSF
Sbjct: 195  LQLDDDKKEKGKRRIWLSLRLSLLHKGFTLDALQEGMVLTAYVKSIEDHGYILHFGLPSF 254

Query: 258  TGFLPRNNLAENSGIDVKPGLLLQGVVRSIDRTRKVVYLSSDPDTVSKCVTKDLKGISID 317
            TGFLP+++ AEN  I++  G +LQGV+RSID+  KVVYLSSDPDT+SKCVTKDLKGISID
Sbjct: 255  TGFLPKSSQAEN--IEINTGQILQGVIRSIDKAHKVVYLSSDPDTISKCVTKDLKGISID 312

Query: 318  LLVPGMMVSTRVQSILENGVMLSFLTYFTGTVDIFHLQNTFPTTNWKNDYNQHKKVNARI 377
            LL+PGMMV+ RVQS  ENGVMLSFLTYFTGTVDIFHLQ TFP++NWK+DYNQ+KKVNARI
Sbjct: 313  LLIPGMMVNARVQSTFENGVMLSFLTYFTGTVDIFHLQTTFPSSNWKDDYNQNKKVNARI 372

Query: 378  LFVDPTSRAVGLTLNPYLLHNRAPPSHVKVGDIYDQSKVVRVDRGLGLLLDIPSTPVSTP 437
            LF+DP++RAVGLTLNP+L++N+APP  VK GDIYD SKV+RVDRGLGLLL++PSTP STP
Sbjct: 373  LFIDPSTRAVGLTLNPHLVNNKAPPCPVKTGDIYDHSKVIRVDRGLGLLLEVPSTPASTP 432

Query: 438  AYVTISDVAEEEVRKLEKKYKEGSCVRVRILGFRHLEGLATGILKASAFEGLVFTHSDVK 497
             YVT+ DVA+EEVRK+EKKYKEGS VRVRILGFR+LEGLA G LKASAFEG VFTHSDVK
Sbjct: 433  TYVTLFDVADEEVRKMEKKYKEGSHVRVRILGFRNLEGLAMGTLKASAFEGSVFTHSDVK 492

Query: 498  PGMVVKGKVIAVDSFGAIVQFPGGVKALCPLPHMSEFEIVKPGKKFKVGAELVFRVLGVK 557
            PGMVVK KVIAVDSFGAIVQFP GVKALCPL HMSEF+IVKP KKFKVGAEL+FRVLG K
Sbjct: 493  PGMVVKAKVIAVDSFGAIVQFPSGVKALCPLRHMSEFDIVKPRKKFKVGAELIFRVLGCK 552

Query: 558  SKRITVTHKKTLVKSKLAILSSYAEATDRLITHGWITKIEKHGCFVRFYNGVQGFAPRSE 617
            SKRITVTHKKTL+KSKL I+SSY +AT+ LITHGWITKIEKHGCF+RFYNGVQGFAP SE
Sbjct: 553  SKRITVTHKKTLLKSKLGIISSYTDATEGLITHGWITKIEKHGCFIRFYNGVQGFAPSSE 612

Query: 618  LGLDPGCEPSSMYHVGQVVKCRIMSSIPASRRINLSFMMKPTRVSEDDLVKLGSLVSGVV 677
            LGL+PGC  S MYHVGQVVKCR+  S+PASRRINLSF++KPTR+SEDD+VKLGS+V GVV
Sbjct: 613  LGLEPGCNTSLMYHVGQVVKCRVKGSVPASRRINLSFIIKPTRISEDDMVKLGSVVGGVV 672

Query: 678  DVVTPNAVVVYVIAKGYSKGTIPTEHLADHLEHATVMKSVIKPGYEFDQLLVLDNESSNL 737
            D VTP+A++V V AKGY KGTI TEHLADH  HA +MKS +KPGYEFDQLLVLD E +N 
Sbjct: 673  DRVTPHAIIVNVSAKGYLKGTISTEHLADHQGHAALMKSTLKPGYEFDQLLVLDVEGNNF 732

Query: 738  LLSAKYSLINSAQQLPSDASHIHPNSVVHGYVCNIIETGCFVRFLGRLTGFAPRSKAVDG 797
            +LSAKYSLINSAQQLP D + IHPNSVVHGY+CNIIETGCFVRFLGRLTGF+PR+K +D 
Sbjct: 733  ILSAKYSLINSAQQLPLDLTQIHPNSVVHGYICNIIETGCFVRFLGRLTGFSPRNKVMDD 792

Query: 798  QRADLSKTYYVGQSVRSNILDVNSETGRITLSLKQSCCSSTDASFMQEHFLLEEKIAMLQ 857
            QRA  S+ +++GQSVRSNILDVNSETGRITLSLKQSCCSSTDASF+QE+FLLEEKIA LQ
Sbjct: 793  QRAVPSEAFFIGQSVRSNILDVNSETGRITLSLKQSCCSSTDASFIQEYFLLEEKIAKLQ 852

Query: 858  SSKHNGSELKWVEGFIIGSVIEGKVHESNDFGVVVSFEEHSDVYGFITHHQLAGATVESG 917
             S    SELKW EGF IG+VIEGK+H++ DFGVV+SFE+++DV+GFITH+QL   T E G
Sbjct: 853  LSDSEHSELKWAEGFNIGTVIEGKIHDAKDFGVVISFEKYNDVFGFITHYQL---TAERG 909

Query: 918  SVIQAAILDVAKAERLVDLSLKTVFIDRFREANSNRQAQKKKRKREASKDLGVHQTVNAI 977
            S +QA +LDVAK ERLVDLSLK  F+DR +E +SN QA KKKR+REA K+L  HQTVNAI
Sbjct: 910  STVQAVVLDVAKTERLVDLSLKPEFLDRHKEDSSNSQAGKKKRRREAYKELQPHQTVNAI 969

Query: 978  VEIVKENYLVLSLPEYNHSIGYASVSDYNTQKFPQKQFLNGQSVIATVMALPSSSTAGRL 1037
            VEIVKENYL  S                      +KQFL+GQSVIA+VMALPS ST GRL
Sbjct: 970  VEIVKENYLASSF-------------------IARKQFLHGQSVIASVMALPSPSTVGRL 1010

Query: 1038 LLLLKAISE-TETSSSKRAKKKSSYDVGSLVQAEITEIKPLELRLKFGIGFHGRIHITEV 1096
            LL+LK++SE TETSSSKRAKKKSSY+VGSLVQAEITEIKPLELRLKFGIGFHGR+HITEV
Sbjct: 1011 LLVLKSVSEATETSSSKRAKKKSSYNVGSLVQAEITEIKPLELRLKFGIGFHGRVHITEV 1070

Query: 1097 NDDKSNVVENLFSNFKIGQTVTARIIAKSNKPDMK-KSFLWELSIKPSMLTG 1147
             D+  NV+EN FSNF+IGQTV+ARI+AK+NK +   K+  WELSIKP MLTG
Sbjct: 1071 CDE--NVIENPFSNFRIGQTVSARIVAKANKSENNGKNHQWELSIKPEMLTG 1120

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Class:

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi\|359481849\|ref\|XP_002276633.2\| PREDICTED: protein RRP5 homolog [Vitis vinifera]	Back alignment and taxonomy information

>gi\|356533079\|ref\|XP_003535096.1\| PREDICTED: protein RRP5 homolog [Glycine max]	Back alignment and taxonomy information

>gi\|356498361\|ref\|XP_003518021.1\| PREDICTED: protein RRP5 homolog [Glycine max]	Back alignment and taxonomy information

>gi\|449453908\|ref\|XP_004144698.1\| PREDICTED: protein RRP5 homolog [Cucumis sativus]	Back alignment and taxonomy information

>gi\|240255326\|ref\|NP_187803.4\| RNA binding protein [Arabidopsis thaliana] gi\|332641610\|gb\|AEE75131.1\| RNA binding protein [Arabidopsis thaliana]	Back alignment and taxonomy information

>gi\|12322020\|gb\|AAG51058.1\|AC069473_20 rRNA biogenesis protein, putative, 3' partial; 75505-85642 [Arabidopsis thaliana]	Back alignment and taxonomy information

>gi\|10998136\|dbj\|BAB03107.1\| pre-rRNA processing protein RRP5 [Arabidopsis thaliana]	Back alignment and taxonomy information

>gi\|414883924\|tpg\|DAA59938.1\| TPA: hypothetical protein ZEAMMB73_957052, partial [Zea mays]	Back alignment and taxonomy information

>gi\|222636634\|gb\|EEE66766.1\| hypothetical protein OsJ_23484 [Oryza sativa Japonica Group]	Back alignment and taxonomy information

Prediction of Gene Ontology (GO) Terms

Close Homologs with Gene Ontology terms Detected by BLAST

Original result of BLAST against Gene Ontology (AMIGO)

ID	Alignment graph	Length	Definition	Q cover	H cover	Identity	E-value
Query		1152
TAIR\|locus:2088644		1896	RRP5 "Ribosomal RNA Processing	0.586	0.356	0.573	9.5e-208
MGI\|MGI:1341788		1862	Pdcd11 "programmed cell death	0.813	0.503	0.272	1.6e-87
RGD\|1304933		1876	Pdcd11 "programmed cell death	0.756	0.464	0.276	2.1e-87
UNIPROTKB\|A7MB10		1874	PDCD11 "Protein RRP5 homolog"	0.837	0.514	0.274	8.4e-87
UNIPROTKB\|G5E5C4		1874	PDCD11 "Protein RRP5 homolog"	0.837	0.514	0.274	1.1e-86
UNIPROTKB\|Q14690		1871	PDCD11 "Protein RRP5 homolog"	0.838	0.516	0.264	6.2e-84
UNIPROTKB\|F1PLK8		1870	PDCD11 "Uncharacterized protei	0.837	0.516	0.265	5.9e-83
UNIPROTKB\|F1S842		1859	LOC100157027 "Uncharacterized	0.894	0.554	0.263	7.9e-81
UNIPROTKB\|F1S843		1876	LOC100157027 "Uncharacterized	0.894	0.549	0.261	8.1e-81
UNIPROTKB\|F1P3T9		1841	PDCD11 "Uncharacterized protei	0.458	0.286	0.297	2.3e-76

TAIR\|locus:2088644 RRP5 "Ribosomal RNA Processing 5" [Arabidopsis thaliana (taxid:3702)]	Back alignment and assigned GO terms

 Score = 2009 (712.3 bits), Expect = 9.5e-208, P = 9.5e-208
 Identities = 396/690 (57%), Positives = 507/690 (73%)

Query:   457 YKEGSCVRVRILGFRHLEGLATGILKASAFEGLVFTHSDVKPGMVVKGKVIAVDSFGAIV 516
             +KEG+ +RVR+LG + +EGLA G LK SAFEG VFTHSDVKPGMV K KVI+VD+FGAIV
Sbjct:   433 FKEGNHIRVRVLGLKQMEGLAVGTLKESAFEGPVFTHSDVKPGMVTKAKVISVDTFGAIV 492

Query:   517 QFPGGVKALCPLPHMSEFEIVKPGKKFKVGAELVFRVLGVKSKRITVTHKKTLVKSKLAI 576
             QF GG+KA+CPL HMSEFE+ KP KKFKVGAELVFRVLG KSKRITVT+KKTLVKSKL I
Sbjct:   493 QFSGGLKAMCPLRHMSEFEVTKPRKKFKVGAELVFRVLGCKSKRITVTYKKTLVKSKLPI 552

Query:   577 LSSYAEATDRLITHGWITKIEKHGCFVRFYNGVQGFAPRSELGLDPGCEPSSMYHVGQVV 636
             LSSY +AT+ L+THGWITKIEKHGCFVRFYNGVQGF PR ELGL+PG +P S++HVG+VV
Sbjct:   553 LSSYTDATEGLVTHGWITKIEKHGCFVRFYNGVQGFVPRFELGLEPGSDPDSVFHVGEVV 612

Query:   637 KCRIMSSIPASRRINLSFMMKPTRVSEDXXXXXXXXXXXXXXXXXXXXXXXXXIAKGYSK 696
             KCR+ S++  ++RI L+  +K   +                             +K   K
Sbjct:   613 KCRVTSAVHGTQRITLNDSIKLGSIVSGIIDTITSQAVIVRVK-----------SKSVVK 661

Query:   697 GTIPTEHLADHLEHATVMKSVIKPGYEFDQLLVLDNESSNLLLSAKYSLINSAQQLPSDA 756
             GTI  EHLADH E A ++ S+++PGYE D+LLVLD E +N+ LS+KYSLI  A++LPSD 
Sbjct:   662 GTISAEHLADHHEQAKLIMSLLRPGYELDKLLVLDIEGNNMALSSKYSLIKLAEELPSDF 721

Query:   757 SHIHPNSVVHGYVCNIIETGCFVRFLGRLTGFAPRSKAVDGQRADLSKTYYVGQSVRSNI 816
             + + PNSVVHGYVCN+IE GCFVRFLGRLTGFAPRSKA+D  +AD+S++++VGQSVR+NI
Sbjct:   722 NQLQPNSVVHGYVCNLIENGCFVRFLGRLTGFAPRSKAIDDPKADVSESFFVGQSVRANI 781

Query:   817 LDVNSETGRITLSLKQSCCSSTDASFMQEHFLLEEKIAMLQSSKHNGSELKWVEGFIIGS 876
             +DVN E  RITLSLKQS C+S DASF+QE+FL++EKI+ LQSS    S+  WVE F IGS
Sbjct:   782 VDVNQEKSRITLSLKQSSCASVDASFVQEYFLMDEKISDLQSSDITKSDCSWVEKFSIGS 841

Query:   877 VIEGKVHESNDFGVVVSFEEHSDVYGFITHHQLAGATVESGSVIQAAILDVAKAERLVDL 936
             +I+G + E ND GVVV+F+  ++V GFI  H + GAT+  GSV+ A +LD+++AERLVDL
Sbjct:   842 LIKGTIQEQNDLGVVVNFDNINNVLGFIPQHHMGGATLVPGSVVNAVVLDISRAERLVDL 901

Query:   937 SLKTVFIDRFREAXXXXXXXXXXXXXXXXXDLGVHQTVNAIVEIVKENYLVLSLPEYNHS 996
             SL+   ++   +                  +L VHQ V+A+VEIVKE +LVLS+PE+ ++
Sbjct:   902 SLRPELLNNLTKEVSNSSKKKRKRGISK--ELEVHQRVSAVVEIVKEQHLVLSIPEHGYT 959

Query:   997 IGYASVSDYNTQKFPQKQFLNGQSVIATVMALPSSSTAGRLLLLLKAIXXXXXXXXXXXX 1056
             IGYASVSDYNTQK P KQF  GQSV+A+V A+ +  T+GRLLLLL ++            
Sbjct:   960 IGYASVSDYNTQKLPVKQFSTGQSVVASVKAVQNPLTSGRLLLLLDSVSGTSETSRSKRA 1019

Query:  1057 XX-XXYDVGSLVQAEITEIKPLELRLKFGIGFHGRIHITEVNDDKSNVVENLFSNFKIGQ 1115
                   +VGS+V AEITEIKP ELR+ FG  F GRIHITEV  + ++  +  F+ F++GQ
Sbjct:  1020 KKKSSCEVGSVVHAEITEIKPFELRVNFGNSFRGRIHITEVLVNDASTSDEPFAKFRVGQ 1079

Query:  1116 TVTARIIAKSNKPDMKKSFLWELSIKPSML 1145
             +++AR++AK    D+KK+ LWELS+KP+ML
Sbjct:  1080 SISARVVAKPCHTDIKKTQLWELSVKPAML 1109

GO:0003723 "RNA binding" evidence=IEA;ISS

GO:0005634 "nucleus" evidence=ISM

GO:0005886 "plasma membrane" evidence=IDA

GO:0005730 "nucleolus" evidence=IDA

GO:0005829 "cytosol" evidence=RCA

GO:0001510 "RNA methylation" evidence=RCA

GO:0006606 "protein import into nucleus" evidence=RCA

GO:0006364 "rRNA processing" evidence=IMP

GO:0009553 "embryo sac development" evidence=IMP

MGI\|MGI:1341788 Pdcd11 "programmed cell death 11" [Mus musculus (taxid:10090)]	Back alignment and assigned GO terms

RGD\|1304933 Pdcd11 "programmed cell death 11" [Rattus norvegicus (taxid:10116)]	Back alignment and assigned GO terms

UNIPROTKB\|A7MB10 PDCD11 "Protein RRP5 homolog" [Bos taurus (taxid:9913)]	Back alignment and assigned GO terms

UNIPROTKB\|G5E5C4 PDCD11 "Protein RRP5 homolog" [Bos taurus (taxid:9913)]	Back alignment and assigned GO terms

UNIPROTKB\|Q14690 PDCD11 "Protein RRP5 homolog" [Homo sapiens (taxid:9606)]	Back alignment and assigned GO terms

UNIPROTKB\|F1PLK8 PDCD11 "Uncharacterized protein" [Canis lupus familiaris (taxid:9615)]	Back alignment and assigned GO terms

UNIPROTKB\|F1S842 LOC100157027 "Uncharacterized protein" [Sus scrofa (taxid:9823)]	Back alignment and assigned GO terms

UNIPROTKB\|F1S843 LOC100157027 "Uncharacterized protein" [Sus scrofa (taxid:9823)]	Back alignment and assigned GO terms

UNIPROTKB\|F1P3T9 PDCD11 "Uncharacterized protein" [Gallus gallus (taxid:9031)]	Back alignment and assigned GO terms

Prediction of Enzyme Commission (EC) Number

EC Number Prediction by Annotation Transfer from SWISS-PROT Entries

Original result of BLAST against SWISS-PROT

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

EC Number Prediction by Ezypred Server

Original result from Ezypred Server

Fail to connect to Ezypred Server

EC Number Prediction by EFICAz Software

No EC number assignment, probably not an enzyme!

Prediction of Functionally Associated Proteins

Functionally Associated Proteins Detected by STRING

Original result from the STRING server

Fail to connect to STRING server

Conserved Domains and Related Protein Families

Conserved Domains Detected by RPS-BLAST

Original result of RPS-BLAST against CDD database part I

ID	Alignment Graph	Length	Definition	E-value
Query		1152
cd04461		83	cd04461, S1_Rrp5_repeat_hs8_sc7, S1_Rrp5_repeat_hs	5e-27
COG0539		541	COG0539, RpsA, Ribosomal protein S1 [Translation,	1e-26
COG0539		541	COG0539, RpsA, Ribosomal protein S1 [Translation,	3e-26
TIGR00717		516	TIGR00717, rpsA, ribosomal protein S1	5e-25
cd05694		74	cd05694, S1_Rrp5_repeat_hs2_sc2, S1_Rrp5_repeat_hs	3e-23
cd05698		70	cd05698, S1_Rrp5_repeat_hs6_sc5, S1_Rrp5_repeat_hs	3e-23
COG0539		541	COG0539, RpsA, Ribosomal protein S1 [Translation,	7e-23
cd05695		66	cd05695, S1_Rrp5_repeat_hs3, S1_Rrp5_repeat_hs3: R	5e-21
TIGR00717		516	TIGR00717, rpsA, ribosomal protein S1	3e-19
cd05702		70	cd05702, S1_Rrp5_repeat_hs11_sc8, S1_Rrp5_repeat_h	1e-17
cd05693		100	cd05693, S1_Rrp5_repeat_hs1_sc1, S1_Rrp5_repeat_hs	4e-17
TIGR00717		516	TIGR00717, rpsA, ribosomal protein S1	4e-15
PRK06299		565	PRK06299, rpsA, 30S ribosomal protein S1; Reviewed	2e-13
TIGR00717		516	TIGR00717, rpsA, ribosomal protein S1	9e-13
smart00316		72	smart00316, S1, Ribosomal protein S1-like RNA-bind	9e-13
PRK06299		565	PRK06299, rpsA, 30S ribosomal protein S1; Reviewed	4e-12
cd05698		70	cd05698, S1_Rrp5_repeat_hs6_sc5, S1_Rrp5_repeat_hs	7e-12
PRK00087		647	PRK00087, PRK00087, 4-hydroxy-3-methylbut-2-enyl d	3e-11
COG0539		541	COG0539, RpsA, Ribosomal protein S1 [Translation,	4e-11
smart00316		72	smart00316, S1, Ribosomal protein S1-like RNA-bind	4e-11
TIGR00717		516	TIGR00717, rpsA, ribosomal protein S1	1e-10
smart00316		72	smart00316, S1, Ribosomal protein S1-like RNA-bind	1e-10
cd04461		83	cd04461, S1_Rrp5_repeat_hs8_sc7, S1_Rrp5_repeat_hs	2e-10
PRK12269		863	PRK12269, PRK12269, bifunctional cytidylate kinase	2e-10
PRK12269		863	PRK12269, PRK12269, bifunctional cytidylate kinase	3e-10
PRK06299		565	PRK06299, rpsA, 30S ribosomal protein S1; Reviewed	4e-10
cd05697		69	cd05697, S1_Rrp5_repeat_hs5, S1_Rrp5_repeat_hs5: R	6e-10
PRK06299		565	PRK06299, rpsA, 30S ribosomal protein S1; Reviewed	2e-09
cd05708		77	cd05708, S1_Rrp5_repeat_sc12, S1_Rrp5_repeat_sc12:	3e-09
pfam00575		74	pfam00575, S1, S1 RNA binding domain	4e-09
PRK06676		390	PRK06676, rpsA, 30S ribosomal protein S1; Reviewed	9e-09
TIGR00717		516	TIGR00717, rpsA, ribosomal protein S1	2e-08
cd00164		65	cd00164, S1_like, S1_like: Ribosomal protein S1-li	2e-08
PRK00087		647	PRK00087, PRK00087, 4-hydroxy-3-methylbut-2-enyl d	5e-08
cd05698		70	cd05698, S1_Rrp5_repeat_hs6_sc5, S1_Rrp5_repeat_hs	9e-08
cd04461		83	cd04461, S1_Rrp5_repeat_hs8_sc7, S1_Rrp5_repeat_hs	1e-07
cd00164		65	cd00164, S1_like, S1_like: Ribosomal protein S1-li	1e-07
cd00164		65	cd00164, S1_like, S1_like: Ribosomal protein S1-li	1e-07
PRK00087		647	PRK00087, PRK00087, 4-hydroxy-3-methylbut-2-enyl d	2e-07
PRK13806		491	PRK13806, rpsA, 30S ribosomal protein S1; Provisio	3e-07
cd05696		71	cd05696, S1_Rrp5_repeat_hs4, S1_Rrp5_repeat_hs4: R	3e-07
COG0539		541	COG0539, RpsA, Ribosomal protein S1 [Translation,	4e-07
PRK06676		390	PRK06676, rpsA, 30S ribosomal protein S1; Reviewed	6e-07
cd05693		100	cd05693, S1_Rrp5_repeat_hs1_sc1, S1_Rrp5_repeat_hs	7e-07
smart00316		72	smart00316, S1, Ribosomal protein S1-like RNA-bind	7e-07
PRK13806		491	PRK13806, rpsA, 30S ribosomal protein S1; Provisio	1e-06
PRK06299		565	PRK06299, rpsA, 30S ribosomal protein S1; Reviewed	2e-06
PRK06299		565	PRK06299, rpsA, 30S ribosomal protein S1; Reviewed	2e-06
PRK00087		647	PRK00087, PRK00087, 4-hydroxy-3-methylbut-2-enyl d	3e-06
pfam00575		74	pfam00575, S1, S1 RNA binding domain	7e-06
pfam00575		74	pfam00575, S1, S1 RNA binding domain	1e-05
cd05691		73	cd05691, S1_RPS1_repeat_ec6, S1_RPS1_repeat_ec6: R	2e-05
PRK13806		491	PRK13806, rpsA, 30S ribosomal protein S1; Provisio	4e-05
COG1098		129	COG1098, VacB, Predicted RNA binding protein (cont	5e-05
PRK07899		486	PRK07899, rpsA, 30S ribosomal protein S1; Reviewed	2e-04
PRK06299		565	PRK06299, rpsA, 30S ribosomal protein S1; Reviewed	3e-04
cd05692		69	cd05692, S1_RPS1_repeat_hs4, S1_RPS1_repeat_hs4: R	3e-04
cd05707		68	cd05707, S1_Rrp5_repeat_sc11, S1_Rrp5_repeat_sc11:	4e-04
COG1185		692	COG1185, Pnp, Polyribonucleotide nucleotidyltransf	4e-04
smart00316		72	smart00316, S1, Ribosomal protein S1-like RNA-bind	6e-04
cd04461		83	cd04461, S1_Rrp5_repeat_hs8_sc7, S1_Rrp5_repeat_hs	7e-04
cd05697		69	cd05697, S1_Rrp5_repeat_hs5, S1_Rrp5_repeat_hs5: R	7e-04
PRK06676		390	PRK06676, rpsA, 30S ribosomal protein S1; Reviewed	7e-04
PRK06676		390	PRK06676, rpsA, 30S ribosomal protein S1; Reviewed	7e-04
COG1098		129	COG1098, VacB, Predicted RNA binding protein (cont	8e-04
pfam00575		74	pfam00575, S1, S1 RNA binding domain	0.002
cd05707		68	cd05707, S1_Rrp5_repeat_sc11, S1_Rrp5_repeat_sc11:	0.002
cd05706		73	cd05706, S1_Rrp5_repeat_sc10, S1_Rrp5_repeat_sc10:	0.002
cd05691		73	cd05691, S1_RPS1_repeat_ec6, S1_RPS1_repeat_ec6: R	0.003
PRK11824		693	PRK11824, PRK11824, polynucleotide phosphorylase/p	0.003
cd04452		76	cd04452, S1_IF2_alpha, S1_IF2_alpha: The alpha sub	0.003
cd04461		83	cd04461, S1_Rrp5_repeat_hs8_sc7, S1_Rrp5_repeat_hs	0.004

>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	Back alignment and domain information

 Score =  104 bits (263), Expect = 5e-27
 Identities = 37/80 (46%), Positives = 45/80 (56%)

Query: 751 QLPSDASHIHPNSVVHGYVCNIIETGCFVRFLGRLTGFAPRSKAVDGQRADLSKTYYVGQ 810
            LP++ S + P  VVHGYV NI   G FV FLG LTG AP+S   D    D S  +  GQ
Sbjct: 4   TLPTNFSDLKPGMVVHGYVRNITPYGVFVEFLGGLTGLAPKSYISDEFVTDPSFGFKKGQ 63

Query: 811 SVRSNILDVNSETGRITLSL 830
           SV + +  V+ E  R  LSL
Sbjct: 64  SVTAKVTSVDEEKQRFLLSL 83

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\|223613 COG0539, RpsA, Ribosomal protein S1 [Translation, ribosomal structure and biogenesis]	Back alignment and domain information

>gnl\|CDD\|223613 COG0539, RpsA, Ribosomal protein S1 [Translation, ribosomal structure and biogenesis]	Back alignment and domain information

>gnl\|CDD\|233102 TIGR00717, rpsA, ribosomal protein S1	Back alignment and domain information

>gnl\|CDD\|240199 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	Back alignment and domain information

>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	Back alignment and domain information

>gnl\|CDD\|223613 COG0539, RpsA, Ribosomal protein S1 [Translation, ribosomal structure and biogenesis]	Back alignment and domain information

>gnl\|CDD\|240200 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	Back alignment and domain information

>gnl\|CDD\|233102 TIGR00717, rpsA, ribosomal protein S1	Back alignment and domain information

>gnl\|CDD\|240207 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	Back alignment and domain information

>gnl\|CDD\|240198 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	Back alignment and domain information

>gnl\|CDD\|233102 TIGR00717, rpsA, ribosomal protein S1	Back alignment and domain information

>gnl\|CDD\|235775 PRK06299, rpsA, 30S ribosomal protein S1; Reviewed	Back alignment and domain information

>gnl\|CDD\|233102 TIGR00717, rpsA, ribosomal protein S1	Back alignment and domain information

>gnl\|CDD\|197648 smart00316, S1, Ribosomal protein S1-like RNA-binding domain	Back alignment and domain information

>gnl\|CDD\|235775 PRK06299, rpsA, 30S ribosomal protein S1; Reviewed	Back alignment and domain information

>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	Back alignment and domain information

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

>gnl\|CDD\|223613 COG0539, RpsA, Ribosomal protein S1 [Translation, ribosomal structure and biogenesis]	Back alignment and domain information

>gnl\|CDD\|197648 smart00316, S1, Ribosomal protein S1-like RNA-binding domain	Back alignment and domain information

>gnl\|CDD\|233102 TIGR00717, rpsA, ribosomal protein S1	Back alignment and domain information

>gnl\|CDD\|197648 smart00316, S1, Ribosomal protein S1-like RNA-binding domain	Back alignment and domain information

>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	Back alignment and domain information

>gnl\|CDD\|105491 PRK12269, PRK12269, bifunctional cytidylate kinase/ribosomal protein S1; Provisional	Back alignment and domain information

>gnl\|CDD\|105491 PRK12269, PRK12269, bifunctional cytidylate kinase/ribosomal protein S1; Provisional	Back alignment and domain information

>gnl\|CDD\|235775 PRK06299, rpsA, 30S ribosomal protein S1; Reviewed	Back alignment and domain information

>gnl\|CDD\|240202 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	Back alignment and domain information

>gnl\|CDD\|235775 PRK06299, rpsA, 30S ribosomal protein S1; Reviewed	Back alignment and domain information

>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	Back alignment and domain information

>gnl\|CDD\|216000 pfam00575, S1, S1 RNA binding domain	Back alignment and domain information

>gnl\|CDD\|235851 PRK06676, rpsA, 30S ribosomal protein S1; Reviewed	Back alignment and domain information

>gnl\|CDD\|233102 TIGR00717, rpsA, ribosomal protein S1	Back alignment and domain information

>gnl\|CDD\|238094 cd00164, S1_like, S1_like: Ribosomal protein S1-like RNA-binding domain	Back alignment and domain information

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

>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	Back alignment and domain information

>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	Back alignment and domain information

>gnl\|CDD\|238094 cd00164, S1_like, S1_like: Ribosomal protein S1-like RNA-binding domain	Back alignment and domain information

>gnl\|CDD\|238094 cd00164, S1_like, S1_like: Ribosomal protein S1-like RNA-binding domain	Back alignment and domain information

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

>gnl\|CDD\|237516 PRK13806, rpsA, 30S ribosomal protein S1; Provisional	Back alignment and domain information

>gnl\|CDD\|240201 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	Back alignment and domain information

>gnl\|CDD\|223613 COG0539, RpsA, Ribosomal protein S1 [Translation, ribosomal structure and biogenesis]	Back alignment and domain information

>gnl\|CDD\|235851 PRK06676, rpsA, 30S ribosomal protein S1; Reviewed	Back alignment and domain information

>gnl\|CDD\|240198 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	Back alignment and domain information

>gnl\|CDD\|197648 smart00316, S1, Ribosomal protein S1-like RNA-binding domain	Back alignment and domain information

>gnl\|CDD\|237516 PRK13806, rpsA, 30S ribosomal protein S1; Provisional	Back alignment and domain information

>gnl\|CDD\|235775 PRK06299, rpsA, 30S ribosomal protein S1; Reviewed	Back alignment and domain information

>gnl\|CDD\|235775 PRK06299, rpsA, 30S ribosomal protein S1; Reviewed	Back alignment and domain information

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

>gnl\|CDD\|216000 pfam00575, S1, S1 RNA binding domain	Back alignment and domain information

>gnl\|CDD\|216000 pfam00575, S1, S1 RNA binding domain	Back alignment and domain information

>gnl\|CDD\|240196 cd05691, S1_RPS1_repeat_ec6, S1_RPS1_repeat_ec6: Ribosomal protein S1 (RPS1) domain	Back alignment and domain information

>gnl\|CDD\|237516 PRK13806, rpsA, 30S ribosomal protein S1; Provisional	Back alignment and domain information

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

>gnl\|CDD\|236126 PRK07899, rpsA, 30S ribosomal protein S1; Reviewed	Back alignment and domain information

>gnl\|CDD\|235775 PRK06299, rpsA, 30S ribosomal protein S1; Reviewed	Back alignment and domain information

>gnl\|CDD\|240197 cd05692, S1_RPS1_repeat_hs4, S1_RPS1_repeat_hs4: Ribosomal protein S1 (RPS1) domain	Back alignment and domain information

>gnl\|CDD\|240212 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	Back alignment and domain information

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

>gnl\|CDD\|197648 smart00316, S1, Ribosomal protein S1-like RNA-binding domain	Back alignment and domain information

>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	Back alignment and domain information

>gnl\|CDD\|240202 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	Back alignment and domain information

>gnl\|CDD\|235851 PRK06676, rpsA, 30S ribosomal protein S1; Reviewed	Back alignment and domain information

>gnl\|CDD\|235851 PRK06676, rpsA, 30S ribosomal protein S1; Reviewed	Back alignment and domain information

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

>gnl\|CDD\|216000 pfam00575, S1, S1 RNA binding domain	Back alignment and domain information

>gnl\|CDD\|240212 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	Back alignment and domain information

>gnl\|CDD\|240211 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	Back alignment and domain information

>gnl\|CDD\|240196 cd05691, S1_RPS1_repeat_ec6, S1_RPS1_repeat_ec6: Ribosomal protein S1 (RPS1) domain	Back alignment and domain information

>gnl\|CDD\|236995 PRK11824, PRK11824, polynucleotide phosphorylase/polyadenylase; Provisional	Back alignment and domain information

>gnl\|CDD\|239899 cd04452, S1_IF2_alpha, S1_IF2_alpha: The alpha subunit of translation Initiation Factor 2, S1-like RNA-binding domain	Back alignment and domain information

>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	Back alignment and domain information

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Alignment Graph	Length	Definition	Probability
Query		1152
KOG1070		1710	consensus rRNA processing protein Rrp5 [RNA proces	100.0
KOG1070		1710	consensus rRNA processing protein Rrp5 [RNA proces	100.0
COG0539		541	RpsA Ribosomal protein S1 [Translation, ribosomal	100.0
COG0539		541	RpsA Ribosomal protein S1 [Translation, ribosomal	100.0
PRK06299		565	rpsA 30S ribosomal protein S1; Reviewed	100.0
PRK12269		863	bifunctional cytidylate kinase/ribosomal protein S	100.0
PRK06299		565	rpsA 30S ribosomal protein S1; Reviewed	100.0
PRK12269		863	bifunctional cytidylate kinase/ribosomal protein S	100.0
TIGR00717		516	rpsA ribosomal protein S1. This model provides tru	100.0
TIGR00717		516	rpsA ribosomal protein S1. This model provides tru	100.0
PRK13806		491	rpsA 30S ribosomal protein S1; Provisional	100.0
PRK13806		491	rpsA 30S ribosomal protein S1; Provisional	100.0
PRK07899		486	rpsA 30S ribosomal protein S1; Reviewed	100.0
PRK06676		390	rpsA 30S ribosomal protein S1; Reviewed	100.0
PRK07899		486	rpsA 30S ribosomal protein S1; Reviewed	100.0
PRK00087		647	4-hydroxy-3-methylbut-2-enyl diphosphate reductase	100.0
PRK06676		390	rpsA 30S ribosomal protein S1; Reviewed	100.0
PRK00087		647	4-hydroxy-3-methylbut-2-enyl diphosphate reductase	100.0
PRK07400		318	30S ribosomal protein S1; Reviewed	100.0
PRK07400		318	30S ribosomal protein S1; Reviewed	99.97
PTZ00248		319	eukaryotic translation initiation factor 2 subunit	99.44
COG1098		129	VacB Predicted RNA binding protein (contains ribos	99.42
COG2996		287	Predicted RNA-bindining protein (contains S1 and H	99.41
cd05705		74	S1_Rrp5_repeat_hs14 S1_Rrp5_repeat_hs14: Rrp5 is a	99.39
cd05694		74	S1_Rrp5_repeat_hs2_sc2 S1_Rrp5_repeat_hs2_sc2: Rrp	99.38
cd05694		74	S1_Rrp5_repeat_hs2_sc2 S1_Rrp5_repeat_hs2_sc2: Rrp	99.36
PTZ00248		319	eukaryotic translation initiation factor 2 subunit	99.34
cd05693		100	S1_Rrp5_repeat_hs1_sc1 S1_Rrp5_repeat_hs1_sc1: Rrp	99.33
cd04461		83	S1_Rrp5_repeat_hs8_sc7 S1_Rrp5_repeat_hs8_sc7: Rrp	99.32
cd05703		73	S1_Rrp5_repeat_hs12_sc9 S1_Rrp5_repeat_hs12_sc9: R	99.31
cd05705		74	S1_Rrp5_repeat_hs14 S1_Rrp5_repeat_hs14: Rrp5 is a	99.3
COG1098		129	VacB Predicted RNA binding protein (contains ribos	99.3
PF00575		74	S1: S1 RNA binding domain; InterPro: IPR003029 Rib	99.29
COG2996		287	Predicted RNA-bindining protein (contains S1 and H	99.28
cd04461		83	S1_Rrp5_repeat_hs8_sc7 S1_Rrp5_repeat_hs8_sc7: Rrp	99.28
cd05698		70	S1_Rrp5_repeat_hs6_sc5 S1_Rrp5_repeat_hs6_sc5: Rrp	99.25
cd05703		73	S1_Rrp5_repeat_hs12_sc9 S1_Rrp5_repeat_hs12_sc9: R	99.24
PF00575		74	S1: S1 RNA binding domain; InterPro: IPR003029 Rib	99.23
cd05698		70	S1_Rrp5_repeat_hs6_sc5 S1_Rrp5_repeat_hs6_sc5: Rrp	99.22
cd05696		71	S1_Rrp5_repeat_hs4 S1_Rrp5_repeat_hs4: Rrp5 is a t	99.19
cd05697		69	S1_Rrp5_repeat_hs5 S1_Rrp5_repeat_hs5: Rrp5 is a t	99.19
cd05707		68	S1_Rrp5_repeat_sc11 S1_Rrp5_repeat_sc11: Rrp5 is a	99.18
cd05704		72	S1_Rrp5_repeat_hs13 S1_Rrp5_repeat_hs13: Rrp5 is a	99.17
cd05706		73	S1_Rrp5_repeat_sc10 S1_Rrp5_repeat_sc10: Rrp5 is a	99.17
cd05697		69	S1_Rrp5_repeat_hs5 S1_Rrp5_repeat_hs5: Rrp5 is a t	99.16
cd05696		71	S1_Rrp5_repeat_hs4 S1_Rrp5_repeat_hs4: Rrp5 is a t	99.15
cd05707		68	S1_Rrp5_repeat_sc11 S1_Rrp5_repeat_sc11: Rrp5 is a	99.12
PRK08582		139	hypothetical protein; Provisional	99.11
PRK07252		120	hypothetical protein; Provisional	99.11
cd04452		76	S1_IF2_alpha S1_IF2_alpha: The alpha subunit of tr	99.09
cd05706		73	S1_Rrp5_repeat_sc10 S1_Rrp5_repeat_sc10: Rrp5 is a	99.08
cd05704		72	S1_Rrp5_repeat_hs13 S1_Rrp5_repeat_hs13: Rrp5 is a	99.08
cd05708		77	S1_Rrp5_repeat_sc12 S1_Rrp5_repeat_sc12: Rrp5 is a	99.08
cd05690		69	S1_RPS1_repeat_ec5 S1_RPS1_repeat_ec5: Ribosomal p	99.07
cd05693		100	S1_Rrp5_repeat_hs1_sc1 S1_Rrp5_repeat_hs1_sc1: Rrp	99.06
cd05686		73	S1_pNO40 S1_pNO40: pNO40 , S1-like RNA-binding dom	99.06
cd05691		73	S1_RPS1_repeat_ec6 S1_RPS1_repeat_ec6: Ribosomal p	99.04
cd05695		66	S1_Rrp5_repeat_hs3 S1_Rrp5_repeat_hs3: Rrp5 is a t	99.04
cd04452		76	S1_IF2_alpha S1_IF2_alpha: The alpha subunit of tr	99.03
PRK07252		120	hypothetical protein; Provisional	99.03
cd05690		69	S1_RPS1_repeat_ec5 S1_RPS1_repeat_ec5: Ribosomal p	99.03
cd05695		66	S1_Rrp5_repeat_hs3 S1_Rrp5_repeat_hs3: Rrp5 is a t	99.02
cd05689		72	S1_RPS1_repeat_ec4 S1_RPS1_repeat_ec4: Ribosomal p	99.02
cd05708		77	S1_Rrp5_repeat_sc12 S1_Rrp5_repeat_sc12: Rrp5 is a	99.01
cd05699		72	S1_Rrp5_repeat_hs7 S1_Rrp5_repeat_hs7: Rrp5 is a t	99.01
cd05691		73	S1_RPS1_repeat_ec6 S1_RPS1_repeat_ec6: Ribosomal p	99.0
cd05687		70	S1_RPS1_repeat_ec1_hs1 S1_RPS1_repeat_ec1_hs1: Rib	99.0
cd05687		70	S1_RPS1_repeat_ec1_hs1 S1_RPS1_repeat_ec1_hs1: Rib	98.99
cd04465		67	S1_RPS1_repeat_ec2_hs2 S1_RPS1_repeat_ec2_hs2: Rib	98.98
PRK08582		139	hypothetical protein; Provisional	98.98
cd05686		73	S1_pNO40 S1_pNO40: pNO40 , S1-like RNA-binding dom	98.96
PRK08059		123	general stress protein 13; Validated	98.95
PRK05807		136	hypothetical protein; Provisional	98.95
cd05689		72	S1_RPS1_repeat_ec4 S1_RPS1_repeat_ec4: Ribosomal p	98.93
cd04465		67	S1_RPS1_repeat_ec2_hs2 S1_RPS1_repeat_ec2_hs2: Rib	98.93
cd05692		69	S1_RPS1_repeat_hs4 S1_RPS1_repeat_hs4: Ribosomal p	98.92
cd05692		69	S1_RPS1_repeat_hs4 S1_RPS1_repeat_hs4: Ribosomal p	98.92
cd05685		68	S1_Tex S1_Tex: The C-terminal S1 domain of a trans	98.89
cd05684		79	S1_DHX8_helicase S1_DHX8_helicase: The N-terminal	98.88
PRK08059		123	general stress protein 13; Validated	98.88
PHA02945		88	interferon resistance protein; Provisional	98.87
PRK05807		136	hypothetical protein; Provisional	98.86
cd05684		79	S1_DHX8_helicase S1_DHX8_helicase: The N-terminal	98.84
cd05685		68	S1_Tex S1_Tex: The C-terminal S1 domain of a trans	98.83
cd04472		68	S1_PNPase S1_PNPase: Polynucleotide phosphorylase	98.82
smart00316		72	S1 Ribosomal protein S1-like RNA-binding domain.	98.82
cd04472		68	S1_PNPase S1_PNPase: Polynucleotide phosphorylase	98.81
PHA02945		88	interferon resistance protein; Provisional	98.8
smart00316		72	S1 Ribosomal protein S1-like RNA-binding domain.	98.79
cd05688		68	S1_RPS1_repeat_ec3 S1_RPS1_repeat_ec3: Ribosomal p	98.78
cd05688		68	S1_RPS1_repeat_ec3 S1_RPS1_repeat_ec3: Ribosomal p	98.77
PLN00207		891	polyribonucleotide nucleotidyltransferase; Provisi	98.76
cd05789		86	S1_Rrp4 S1_Rrp4: Rrp4 S1-like RNA-binding domain.	98.74
cd05702		70	S1_Rrp5_repeat_hs11_sc8 S1_Rrp5_repeat_hs11_sc8: R	98.72
cd04453		88	S1_RNase_E S1_RNase_E: RNase E and RNase G, S1-lik	98.68
COG1093		269	SUI2 Translation initiation factor 2, alpha subuni	98.66
cd04471		83	S1_RNase_R S1_RNase_R: RNase R C-terminal S1 domai	98.66
cd05789		86	S1_Rrp4 S1_Rrp4: Rrp4 S1-like RNA-binding domain.	98.65
cd04453		88	S1_RNase_E S1_RNase_E: RNase E and RNase G, S1-lik	98.63
PRK03987		262	translation initiation factor IF-2 subunit alpha;	98.62
cd05702		70	S1_Rrp5_repeat_hs11_sc8 S1_Rrp5_repeat_hs11_sc8: R	98.62
cd04473		77	S1_RecJ_like S1_RecJ_like: The S1 domain of the ar	98.62
cd04473		77	S1_RecJ_like S1_RecJ_like: The S1 domain of the ar	98.62
TIGR02696		719	pppGpp_PNP guanosine pentaphosphate synthetase I/p	98.61
PLN00207		891	polyribonucleotide nucleotidyltransferase; Provisi	98.6
COG2183		780	Tex Transcriptional accessory protein [Transcripti	98.58
cd00164		65	S1_like S1_like: Ribosomal protein S1-like RNA-bin	98.58
cd00164		65	S1_like S1_like: Ribosomal protein S1-like RNA-bin	98.57
cd04454		82	S1_Rrp4_like S1_Rrp4_like: Rrp4-like, S1-like RNA-	98.57
PRK03987		262	translation initiation factor IF-2 subunit alpha;	98.57
cd04471		83	S1_RNase_R S1_RNase_R: RNase R C-terminal S1 domai	98.56
TIGR02696		719	pppGpp_PNP guanosine pentaphosphate synthetase I/p	98.56
COG1093		269	SUI2 Translation initiation factor 2, alpha subuni	98.54
cd04454		82	S1_Rrp4_like S1_Rrp4_like: Rrp4-like, S1-like RNA-	98.53
PRK11824		693	polynucleotide phosphorylase/polyadenylase; Provis	98.48
PRK09521		189	exosome complex RNA-binding protein Csl4; Provisio	98.4
PRK11824		693	polynucleotide phosphorylase/polyadenylase; Provis	98.4
COG2183		780	Tex Transcriptional accessory protein [Transcripti	98.38
PRK09202		470	nusA transcription elongation factor NusA; Validat	98.37
PRK09521		189	exosome complex RNA-binding protein Csl4; Provisio	98.36
PRK09202		470	nusA transcription elongation factor NusA; Validat	98.3
PRK04163		235	exosome complex RNA-binding protein Rrp4; Provisio	98.28
cd04460		99	S1_RpoE S1_RpoE: RpoE, S1-like RNA-binding domain.	98.27
cd04455		67	S1_NusA S1_NusA: N-utilizing substance A protein (	98.26
TIGR03591		684	polynuc_phos polyribonucleotide nucleotidyltransfe	98.24
cd04455		67	S1_NusA S1_NusA: N-utilizing substance A protein (	98.24
TIGR03591		684	polynuc_phos polyribonucleotide nucleotidyltransfe	98.21
COG1185		692	Pnp Polyribonucleotide nucleotidyltransferase (pol	98.09
cd04460		99	S1_RpoE S1_RpoE: RpoE, S1-like RNA-binding domain.	98.08
COG1185		692	Pnp Polyribonucleotide nucleotidyltransferase (pol	97.98
PRK04163		235	exosome complex RNA-binding protein Rrp4; Provisio	97.96
TIGR01953		341	NusA transcription termination factor NusA. This m	97.94
TIGR00448		179	rpoE DNA-directed RNA polymerase (rpoE), archaeal	97.91
TIGR01953		341	NusA transcription termination factor NusA. This m	97.88
cd05699		72	S1_Rrp5_repeat_hs7 S1_Rrp5_repeat_hs7: Rrp5 is a t	97.87
PRK12327		362	nusA transcription elongation factor NusA; Provisi	97.86
TIGR00448		179	rpoE DNA-directed RNA polymerase (rpoE), archaeal	97.85
cd05791		92	S1_CSL4 S1_CSL4: CSL4, S1-like RNA-binding domain.	97.79
TIGR02063		709	RNase_R ribonuclease R. This family consists of an	97.73
KOG1067		760	consensus Predicted RNA-binding polyribonucleotide	97.65
KOG1067		760	consensus Predicted RNA-binding polyribonucleotide	97.65
TIGR02063		709	RNase_R ribonuclease R. This family consists of an	97.64
PRK12327		362	nusA transcription elongation factor NusA; Provisi	97.6
COG1095		183	RPB7 DNA-directed RNA polymerase, subunit E' [Tran	97.56
cd05791		92	S1_CSL4 S1_CSL4: CSL4, S1-like RNA-binding domain.	97.53
COG1095		183	RPB7 DNA-directed RNA polymerase, subunit E' [Tran	97.5
PRK11642		813	exoribonuclease R; Provisional	97.48
PRK11642		813	exoribonuclease R; Provisional	97.46
TIGR00358		654	3_prime_RNase VacB and RNase II family 3'-5' exori	97.45
PRK08563		187	DNA-directed RNA polymerase subunit E'; Provisiona	97.41
PRK08563		187	DNA-directed RNA polymerase subunit E'; Provisiona	97.4
TIGR00358		654	3_prime_RNase VacB and RNase II family 3'-5' exori	97.39
PF10447		82	EXOSC1: Exosome component EXOSC1/CSL4; InterPro: I	97.26
PHA02858		86	EIF2a-like PKR inhibitor; Provisional	97.11
PHA02858		86	EIF2a-like PKR inhibitor; Provisional	97.03
cd04462		88	S1_RNAPII_Rpb7 S1_RNAPII_Rpb7: Eukaryotic RNA poly	96.97
COG1107		715	Archaea-specific RecJ-like exonuclease, contains D	96.94
PRK12328		374	nusA transcription elongation factor NusA; Provisi	96.91
cd04462		88	S1_RNAPII_Rpb7 S1_RNAPII_Rpb7: Eukaryotic RNA poly	96.67
cd05701		69	S1_Rrp5_repeat_hs10 S1_Rrp5_repeat_hs10: Rrp5 is a	96.62
PF13509		61	S1_2: S1 domain; PDB: 3GO5_A.	96.52
COG1107		715	Archaea-specific RecJ-like exonuclease, contains D	96.44
COG1096		188	Predicted RNA-binding protein (consists of S1 doma	96.43
KOG2916		304	consensus Translation initiation factor 2, alpha s	96.39
PRK12329		449	nusA transcription elongation factor NusA; Provisi	96.32
COG1097		239	RRP4 RNA-binding protein Rrp4 and related proteins	96.29
PTZ00162		176	DNA-directed RNA polymerase II subunit 7; Provisio	96.26
PRK05054		644	exoribonuclease II; Provisional	96.15
COG1096		188	Predicted RNA-binding protein (consists of S1 doma	96.12
PF10447		82	EXOSC1: Exosome component EXOSC1/CSL4; InterPro: I	96.1
KOG1856		1299	consensus Transcription elongation factor SPT6 [RN	96.06
PTZ00162		176	DNA-directed RNA polymerase II subunit 7; Provisio	95.94
PRK05054		644	exoribonuclease II; Provisional	95.91
PF13509		61	S1_2: S1 domain; PDB: 3GO5_A.	95.91
KOG1856		1299	consensus Transcription elongation factor SPT6 [RN	95.9
PRK12328		374	nusA transcription elongation factor NusA; Provisi	95.74
COG1097		239	RRP4 RNA-binding protein Rrp4 and related proteins	95.74
TIGR00757		414	RNaseEG ribonuclease, Rne/Rng family. The C-termin	95.64
TIGR00757		414	RNaseEG ribonuclease, Rne/Rng family. The C-termin	95.59
cd05790		86	S1_Rrp40 S1_Rrp40: Rrp40 S1-like RNA-binding domai	95.56
cd05790		86	S1_Rrp40 S1_Rrp40: Rrp40 S1-like RNA-binding domai	95.54
cd05700		65	S1_Rrp5_repeat_hs9 S1_Rrp5_repeat_hs9: Rrp5 is a t	95.32
TIGR02062		639	RNase_B exoribonuclease II. This family consists o	95.16
TIGR02062		639	RNase_B exoribonuclease II. This family consists o	94.66
PRK12329		449	nusA transcription elongation factor NusA; Provisi	94.61
COG0557		706	VacB Exoribonuclease R [Transcription]	94.34
KOG2916		304	consensus Translation initiation factor 2, alpha s	93.9
COG0557		706	VacB Exoribonuclease R [Transcription]	93.69
KOG3409		193	consensus Exosomal 3'-5' exoribonuclease complex,	93.04
PF10246		104	MRP-S35: Mitochondrial ribosomal protein MRP-S35;	91.9
PF08292		122	RNA_pol_Rbc25: RNA polymerase III subunit Rpc25; I	91.6
PRK10811		1068	rne ribonuclease E; Reviewed	89.69
PRK10811		1068	rne ribonuclease E; Reviewed	89.36
KOG3409		193	consensus Exosomal 3'-5' exoribonuclease complex,	89.34
cd05701		69	S1_Rrp5_repeat_hs10 S1_Rrp5_repeat_hs10: Rrp5 is a	87.91
PRK11712		489	ribonuclease G; Provisional	86.88
KOG3298		170	consensus DNA-directed RNA polymerase subunit E' [	85.93
PRK11712		489	ribonuclease G; Provisional	84.82
KOG3298		170	consensus DNA-directed RNA polymerase subunit E' [	84.42
PF10246		104	MRP-S35: Mitochondrial ribosomal protein MRP-S35;	82.1

>KOG1070 consensus rRNA processing protein Rrp5 [RNA processing and modification]	Back alignment and domain information

Probab=100.00  E-value=1.6e-102  Score=935.23  Aligned_cols=1028  Identities=23%  Similarity=0.289  Sum_probs=805.4

Q ss_pred             cccCCCCCCCCCCCCCCCCCCCCchhhccchhc--ccchhhhccccc-----ccccccccccccccccccccccCCccCC
Q 001115           41 QDLALPPDDDVPVFPRGGGHSLTQRERDEIHAE--VDAEFEAVERGL-----HKKNKKKKKKTERKANETVDDLGSLFGD  113 (1152)
Q Consensus        41 ~~~~~~~~~~e~~fpRGg~~~lt~~e~~~~~~~--~d~lf~~~~~~~-----~k~~~~~~~~~~~~~~~~~~~~~~~~~~  113 (1152)
                      +..-+..++++++|||||+|.|||+|++++..|  .|.+|+....+.     .++++..++...+-.        ..+++
T Consensus        25 s~~~l~~~t~~~~fprgg~s~lt~~e~~kv~~E~~~e~l~~~~~vke~~~~~~~~~k~vk~~~s~~s--------~~~~~   96 (1710)
T KOG1070|consen   25 SKSSLKRKTAAPDFPRGGASKLTPLEIEKVEEEAFIEGLTGFGVVKEVFDDGRPKKKTVKKSASKVS--------KKFTE   96 (1710)
T ss_pred             ccccccccccccccccccccccChHHHHHHHHHHHhhhhhcccceecccCCCCccccccccchhhHH--------Hhhhc
Confidence            334456678899999999999999999999555  455555322110     111111111111100        01111


Q ss_pred             CcCCCCCeeecccccCCCCCCCEEEEEEEEEecceEEEEcCCCcEEEEeccccCChhh------cccc---cc-------
Q 001115          114 GISGKLPRYANKITLKNISAGMKLWGVVAEVNEKDLVICLPGGLRGLARAADALDPIL------DNEI---EA-------  177 (1152)
Q Consensus       114 ~~~~~~~~~ve~l~~k~l~~G~~vlG~V~~i~~~~l~vslp~~l~G~v~~~~is~~~~------~~~~---~~-------  177 (1152)
                      +....-+.++++++++++.|||+++|+|++|+..|+.+++|++++|+++.+++|+.++      +.+.   +|       
T Consensus        97 ~~~~~k~~~~~~~~~k~isPG~~llgvIs~i~~~Dl~isv~~~l~g~v~~t~lS~~~~~~~~~l~~~v~S~ed~g~~l~~  176 (1710)
T KOG1070|consen   97 NFNEEKPEIINAFQLKNISPGMLLLGVISKINGNDLKISVKGGLNGYVLNTHLSDEMLAAGEVLDTAVVSIEDHGAILDV  176 (1710)
T ss_pred             cccccchhhhhhccccccCCcceeeeeeeeccccceeEEccCcccccccccccCHhHhhhhhhhccccccccccccchhc
Confidence            1111226678999999999999999999999999999999999999999999999851      2210   10       


Q ss_pred             --cc---------cCCCCCccCCCCEEEEEEEEEecCC-cccceeEEEEecchHHHhcCCCccccCCCCEEEEEEEEEec
Q 001115          178 --NE---------DNLLPTIFHVGQLVSCIVLQLDDDK-KEIGKRKIWLSLRLSLLYKGLSLETVQEGMVLTAYVKSIED  245 (1152)
Q Consensus       178 --~~---------~~~l~~~f~vGq~v~~~V~~~~~~~-~~~~~~~i~LS~~p~~vn~~l~~~~l~~g~~l~~~V~sved  245 (1152)
                        ++         ..++.+.|++|||++|.|++..... ....++++++++.|...| +|..++|.|||+|+|.|+||+|
T Consensus       177 g~~~~~~~~e~~q~pn~~~~lKvGq~l~~~V~k~~s~~v~ks~~~~~~~t~~~t~~~-~~~~~~LvpGt~vqa~V~sv~~  255 (1710)
T KOG1070|consen  177 GLDEITGFIEKSQFPNLGAKLKVGQWLRVSVTKSTSERVVKSTKFVEVLTLNPTSCN-GLALNDLVPGTMVQAEVQSVED  255 (1710)
T ss_pred             CCccccchhhhccCchhhhhcccCceEEEEEEeccCceEEecccceeeecccchhcc-ccchhhcCCcceEEEEecceec
Confidence              11         1156688999999999999864410 111367999999999999 7999999999999999999999


Q ss_pred             CeEEEEeCCCceeeeecCCCCCCCCCCcCCCCcEEEEEEEEEeCCCCEEEEccCccccccccccccccccccccCCCcEE
Q 001115          246 HGYILHFGLPSFTGFLPRNNLAENSGIDVKPGLLLQGVVRSIDRTRKVVYLSSDPDTVSKCVTKDLKGISIDLLVPGMMV  325 (1152)
Q Consensus       246 hG~ivd~Gi~~~~gFl~~~~~~~~~~~~l~~G~~~~~~V~~~~~~~~~v~ls~~~~~~~~~~~~~~~~~~~~~l~pG~~V  325 (1152)
                      ||+++|| +.+++|||++.|+++..  .+..||.++|+|+..  +.|++.+.+-..  ..+...  -...++.+.||..+
T Consensus       256 ~Gi~~di-l~~ftG~l~~~hl~~~~--~~~~~~~~l~~vi~~--s~Rv~~~~f~~k--a~ki~~--l~~~v~ai~p~~~~  326 (1710)
T KOG1070|consen  256 HGITLDI-LNGFTGFLDKKHLPPFL--RYFENQEKLGKVIHK--SDRVFVVDFFDK--ASKILV--LKAGVDAIAPSRIE  326 (1710)
T ss_pred             CcEEEEe-cccccceeehhhCCchh--hccccHHHhhcccch--hhheeeechhhc--cceEEE--ecCccceEccCCcc
Confidence            9999999 79999999999998665  688999999997663  456665553111  111111  12356778888888


Q ss_pred             EEEEEEEeCCeEEEEeCCceEEEEeccccccCCCCCCCCccCCCCCEEEEEEEEEeC--CC-CEEEEecchhhhcCCC--
Q 001115          326 STRVQSILENGVMLSFLTYFTGTVDIFHLQNTFPTTNWKNDYNQHKKVNARILFVDP--TS-RAVGLTLNPYLLHNRA--  400 (1152)
Q Consensus       326 ~g~V~~v~~~Gl~v~~~~~~~G~v~~~~l~~~~~~~~l~~~~~~G~~v~arVl~~~~--~~-k~v~LSl~p~~~~~~~--  400 (1152)
                      .....++.+.|..++..+--.+..+..|+..... .+++.+|..+..|++|++..-|  .+ -.+.|+-.||+.....  
T Consensus       327 ~~~~~e~~k~G~~~K~~vi~~~~~~~~~~~tl~~-s~ie~k~~~~s~V~~r~l~~~~~svdt~~~~l~~L~hv~~f~~a~  405 (1710)
T KOG1070|consen  327 KVLSFEIFKIGNKVKCRVIDVLQMDSLALFTLKE-SAIEGKFSLVSDVSPRGLLKKPVSVDTEEVGLSPLPHVLGFEYAD  405 (1710)
T ss_pred             cccchhhcccCceEEEEEEEEeeccceEEeecch-hhccCceEEEeccCCceEEEecccCChhhhhccccchhhceeecC
Confidence            8888888888888888776667777777765443 4688999999999999998766  23 3789999999987432  


Q ss_pred             C----CCCCCCCCeEEceEEEEEeCCceEEEEeCCCCCCcceeeeecccchHHHhhh----ccccCCCCEEEEEEEEEec
Q 001115          401 P----PSHVKVGDIYDQSKVVRVDRGLGLLLDIPSTPVSTPAYVTISDVAEEEVRKL----EKKYKEGSCVRVRILGFRH  472 (1152)
Q Consensus       401 ~----~~~~~~G~iv~~~~V~~v~~~~G~~v~l~~~~~~i~Gfv~~s~~~~~~~~~~----~~~~~vG~~v~~rVi~~~~  472 (1152)
                      +    ....++|.++-.|..+..+-.++.++....+  -+.+|.+...+.+..+...    ...|++|+.+.|||..|.+
T Consensus       406 p~~~~~~~~di~~~vl~~~ak~~~vt~~v~~~sK~p--vis~y~~~~~~t~~~l~~v~q~~v~~~e~~te~~~rv~~v~~  483 (1710)
T KOG1070|consen  406 PSKKISDGKDIGFRVLTCKAKCGSVTLKVLCVSKLP--VISMYADAVKLTHGMLSKVPQGMVPIYEVGTEVKSRVWQVFY  483 (1710)
T ss_pred             CCcccccccceeeEEeeccceeeeeeeeeeEeecCc--ceEEEeeccccCcchhhccccCCCCceecCCcccCccceecc
Confidence            2    2456777777777777776555667776543  3689999988776665443    2359999999999999999


Q ss_pred             CCCeEEEEccccccccccccccccCCCCEEEEEEEEEeCCeEEEEeCCC-eEEEEeCCccccccccCCCCccccCCEEEE
Q 001115          473 LEGLATGILKASAFEGLVFTHSDVKPGMVVKGKVIAVDSFGAIVQFPGG-VKALCPLPHMSEFEIVKPGKKFKVGAELVF  551 (1152)
Q Consensus       473 ~~~~~~lS~k~~~~~~~~~~~~~l~~G~iv~g~V~~v~~~G~~V~i~~~-v~g~vp~~hls~~~~~~~~~~~kvG~~V~~  551 (1152)
                      .+..++|++.++.+...+++.+||+.|+.|.|+|.++++.|+.|.+..+ +.|++|..|++|.+...|...|++|..+++
T Consensus       484 v~~v~~v~~~~svl~lk~~~~nDI~iG~~V~~~I~~vt~~Gv~v~v~~~ni~g~lp~~hlsd~~~~~p~~~f~v~~~~k~  563 (1710)
T KOG1070|consen  484 VGKVVIVSVRESVLGLKFLRVNDIEIGQLVPGVIRKVTPQGVEVLVTFGNIKGVLPKEHLSDHPLQPPLRDFKVGSGVKL  563 (1710)
T ss_pred             cCcEEEEEEehHhhcccccccccccccceeeeEEEEecCCcEEEEEecCceeeecChHhhhhcccccccceeeeccccEE
Confidence            9999999999999999999999999999999999999999999999765 999999999999999999999999999999


Q ss_pred             EEEEE--eCCeEEEeechhhhhhhhhHhhhhhhccCCceEEEEEEEEecCeEEEEEcCCeEEEEeccccCCCCCCCCCCC
Q 001115          552 RVLGV--KSKRITVTHKKTLVKSKLAILSSYAEATDRLITHGWITKIEKHGCFVRFYNGVQGFAPRSELGLDPGCEPSSM  629 (1152)
Q Consensus       552 rVl~v--~~~~i~LS~K~~l~~~~~~~~~~~~~~~~G~~~~G~V~~i~~~G~~V~~~~gv~Gflp~sel~~~~~~~~~~~  629 (1152)
                      |||.+  +.+++.||+|++|++...|...+|++++||+++.|+|.++.++||||+|++|+.||+|.++|++.++.+++++
T Consensus       564 RVl~~~~~~~~v~l~~K~slv~~~~plp~d~~~~~pg~~~~G~l~~~~~~g~~V~F~g~lsGf~p~s~~sd~~v~~~~eh  643 (1710)
T KOG1070|consen  564 RVLSVNRDRNRVALTLKKSLVNTQLPLPSDFEQAIPGKITKGTLCAIKENGAFVTFTGGLSGFAPVSEMSDDFVLSDSEH  643 (1710)
T ss_pred             EEEEEEccCCeeEEEechhhhcccCCCccchhhcCCCceEEEEEeeeccCCeEEEecCccccccchhhhhhhhhcChhhh
Confidence            99999  6899999999999999889999999999999999999999999999999999999999999999999999999


Q ss_pred             ccCCCEEEEEEEEEecCCCEEEEEEeeCCCC----ccccccccCCCEEEEEEEEEeCCcEEEEEeeCCceEEEEeCCCcC
Q 001115          630 YHVGQVVKCRIMSSIPASRRINLSFMMKPTR----VSEDDLVKLGSLVSGVVDVVTPNAVVVYVIAKGYSKGTIPTEHLA  705 (1152)
Q Consensus       630 f~vGq~v~vrV~~vd~~~~ri~lS~k~~~~~----~~~~~~l~vG~iv~g~V~~v~~~g~~V~l~~~~~v~G~ip~~hls  705 (1152)
                      |.+||++.+.|+++|++++|+.++++.+.+.    ....+.+..|.+..+.+.+.+.+.++|++. ..++.|++...||.
T Consensus       644 f~vGqTv~~~i~nvd~ek~rm~l~~r~s~~~~a~~~~~~e~~~~g~v~s~~~~~~tkd~viVei~-~~~~~~v~~~~~L~  722 (1710)
T KOG1070|consen  644 FPVGQTVRAKIVNVDDEKRRMPLGLRASSCARACVKRSVENFVKGGVKSLKSIDKTKDSVIVEIV-DQGITGVGVFGELV  722 (1710)
T ss_pred             cccccEEEEEEEecCchhceeehhhhhhhhHHHHHHHHHHHhhccccccceeehhccccEEEEcc-CcceEEEEEEEEEc
Confidence            9999999999999999999999999988752    223457788988899999999999999994 24799999999999


Q ss_pred             Ccc-ccccccccc---------cCCCCeEe-EEEEeecccCceeeecchhhccccccCCCccccCCCCCEEEEEEEEEec
Q 001115          706 DHL-EHATVMKSV---------IKPGYEFD-QLLVLDNESSNLLLSAKYSLINSAQQLPSDASHIHPNSVVHGYVCNIIE  774 (1152)
Q Consensus       706 d~~-~~~~~~~~~---------lk~G~~v~-~vl~~d~~~~~i~lS~K~sl~~~~~~~~~~~~~~~~G~~v~G~V~~i~~  774 (1152)
                      |.. ..+..+..+         +.+|+... +|+.++..+.-+.+++++.       +|....++..|....++|.+|.+
T Consensus       723 dg~v~~~~~~~~kl~~~t~~~~lv~gq~~~~~i~~isl~k~lv~~s~~~~-------L~~~~~~l~k~~~~~~~v~~is~  795 (1710)
T KOG1070|consen  723 DGSVVVNKVLENKLRKNTSLLHLVVGQVTVGVILSISLKKSLVLISLCTD-------LPNNATKLLKGSYALALVRSISK  795 (1710)
T ss_pred             cCceEEccchhhhhhhcchhheeeecceeEEEEEEeehhhhhhhcccccc-------ccchHHHHhcCchhHHHHHhhhh
Confidence            832 122222222         44666666 6655554444444444443       45556778899999999999999


Q ss_pred             ceEEEEECCCeEEEEeccCCCCccccCccccccCCCEEEEEEEEEeCCCCeEEEEeeccccCCCchhhhhhhhhHHHHHH
Q 001115          775 TGCFVRFLGRLTGFAPRSKAVDGQRADLSKTYYVGQSVRSNILDVNSETGRITLSLKQSCCSSTDASFMQEHFLLEEKIA  854 (1152)
Q Consensus       775 ~GvfV~~~~~l~Glv~~s~ls~~~~~~~~~~f~~Gq~V~v~Vl~vd~e~~ri~LSlk~~~~~~~~~~~~~~~~~~~e~~~  854 (1152)
                      .|.|+.|.+++.++++.+++.+....+.. ....||.|.|+++++++......++++......+..      +   +..+
T Consensus       796 ~~~~~a~~~~~i~~v~~s~~v~s~~~d~~-~~~y~Q~v~~~~~st~~~~~~~~~a~e~p~~K~~~~------~---~~~~  865 (1710)
T KOG1070|consen  796 EGKFVAFVSNLIALVKVSHLVDSELDDLT-KAEYGQSVTVKLLSTEPKVVKDLKAVEKPKKKKEKK------F---IKVS  865 (1710)
T ss_pred             heeheeecccccceeeccccccccccccc-eeeeecccceEEEecChhHHHHHHhhcchhhcccee------E---EEec
Confidence            99999999999999999998876666544 344469999999999987777777765542211000      0   0000


Q ss_pred             HhhcCcCCCcccccccCcccccEEEEEEEEEecceEEEEecCCCCeEEEEEeEeeCC---------CcccCCCEEEEEEE
Q 001115          855 MLQSSKHNGSELKWVEGFIIGSVIEGKVHESNDFGVVVSFEEHSDVYGFITHHQLAG---------ATVESGSVIQAAIL  925 (1152)
Q Consensus       855 ~~~~~~~~~~~~~~~~~~~vG~~v~g~V~~i~~~g~~v~l~~~~~v~G~i~~s~l~~---------~~~~~G~~v~a~Vl  925 (1152)
                      .-...+++|...+..+++.+|++|.|+|++++++|+.|.+..  ++.|+||.+|+-+         .+|++||.|.|+|+
T Consensus       866 ~~~~d~~Vd~a~k~~~~~~igsiv~a~v~svKp~~L~v~l~~--~~~gri~isev~d~~~eitDp~~k~~vG~~I~vrvi  943 (1710)
T KOG1070|consen  866 SNDSDNEVDLAIKSTEDLSIGSIVRAYVKSVKPDQLNVLLAA--NHHGRIHISEVLDNLHEITDPLDKFKVGDGIFVRVI  943 (1710)
T ss_pred             cccCCCccccccccccceeeeeEEEEEEeeecccceEEeccc--cccCceehHHhhccccccCChhhhcccCCeEEEEEE
Confidence            012236677777767999999999999999999999888875  8999999999853         58999999999999


Q ss_pred             EEECCC-----------CEEEEEEcccchhhhhcccchhhhhhhccccccccccCCCCEEEEEEEEEecCEEEEEEcCCC
Q 001115          926 DVAKAE-----------RLVDLSLKTVFIDRFREANSNRQAQKKKRKREASKDLGVHQTVNAIVEIVKENYLVLSLPEYN  994 (1152)
Q Consensus       926 ~vd~~~-----------~~v~LSlk~s~~~~~~~~~~~~~~~~~~~~~~~~~~l~~G~~v~g~V~~i~~~~l~V~l~~~~  994 (1152)
                      +.++-+           ..++||+||+.++...            ....+..+++.||+++|||+++..+|+|++++|..
T Consensus       944 G~~D~k~lpith~i~k~~v~ElSvkps~les~~------------~~t~s~~q~~~gq~vtGfV~nv~ke~~w~~isp~v 1011 (1710)
T KOG1070|consen  944 GGHDVKDLPITHLISKEQVLELSVKPSELESDE------------FNTTSTKQFKAGQEVTGFVNNVSKEWLWVRISPFV 1011 (1710)
T ss_pred             cCCccccCccccccchhhhhhhccChhhhcccc------------ccccchhhhhcCCeEEEEEEccccceeEEEccccc
Confidence            996533           6799999999998432            11234468999999999999999999999997755


Q ss_pred             ce-EEEEEec-ccccccCCcCCCCCCCEEEEEEEeecCCCCccEEEEEecccccccccccccccccCCCcCCcEEEEEEE
Q 001115          995 HS-IGYASVS-DYNTQKFPQKQFLNGQSVIATVMALPSSSTAGRLLLLLKAISETETSSSKRAKKKSSYDVGSLVQAEIT 1072 (1152)
Q Consensus       995 ~~-~~~~~~s-~~~~~~~~~~~f~~Gq~v~~~V~~~d~~~~~~~l~l~~~~~~~~~~~~~~~~~~~~~~~~G~~v~~~V~ 1072 (1152)
                      .+ +.++.++ ++....++++.|+.|+++.+.|+..|.   ++.  ++.-..          .++.....+|+++.|||.
T Consensus      1012 ~~RIplld~s~~~~~le~~e~~F~~g~al~~~V~~~~~---~~t--v~~iG~----------~~~~k~~s~G~~l~Grv~ 1076 (1710)
T KOG1070|consen 1012 DGRIPLLDTSLDLHVLELPESLFPLGKALDEYVVRNDK---SKT--VRAIGF----------SKSDKNPSPGDILFGRVS 1076 (1710)
T ss_pred             cceeeeeeccchhhhhhCchhhcccccceeeEEecccc---eeE--EEeccc----------ccCCCCCCcchhhcceee
Confidence            54 5666665 444455688999999999999999883   332  332110          111223349999999999


Q ss_pred             EEeCCeEEEEeCCCeeEEEEee-eccCCccccccccccCCCCCCEEEEEEEeeecCCCCCCCceEEEEeecCC
Q 001115         1073 EIKPLELRLKFGIGFHGRIHIT-EVNDDKSNVVENLFSNFKIGQTVTARIIAKSNKPDMKKSFLWELSIKPSM 1144 (1152)
Q Consensus      1073 ~i~~~~l~V~L~~~~~G~v~~t-e~~D~~~~~~~~p~~~f~~g~~V~~~Vl~~~~~~~~~k~~~~~LSlr~s~ 1144 (1152)
                      ++.+.++.|+++.+..||++.+ ++.|+|+.   +|...|..+++|.+++|.++.  .|++   ++||+|.|+
T Consensus      1077 kv~~~~~~l~~~~~~~G~~~~i~~~~d~~~~---~P~~~f~~~~~v~~~~L~vs~--~n~~---leLslr~sr 1141 (1710)
T KOG1070|consen 1077 KVLPGYLILQLPFKVFGRVSFIEDMSDSYSM---TPVEHFTKIQIVYVCVLSVSA--LNKG---LELSLRESR 1141 (1710)
T ss_pred             eeccceeEEecCCccccceEEeeehhccccC---ChHHhcccccEEEEEEEEEec--cccc---ceeeccccc
Confidence            9999999999999999988877 99999987   899999999999999999997  6676   999999555

>KOG1070 consensus rRNA processing protein Rrp5 [RNA processing and modification]	Back alignment and domain information

>COG0539 RpsA Ribosomal protein S1 [Translation, ribosomal structure and biogenesis]	Back alignment and domain information

>COG0539 RpsA Ribosomal protein S1 [Translation, ribosomal structure and biogenesis]	Back alignment and domain information

>PRK06299 rpsA 30S ribosomal protein S1; Reviewed	Back alignment and domain information

>PRK12269 bifunctional cytidylate kinase/ribosomal protein S1; Provisional	Back alignment and domain information

>PRK06299 rpsA 30S ribosomal protein S1; Reviewed	Back alignment and domain information

>PRK12269 bifunctional cytidylate kinase/ribosomal protein S1; Provisional	Back alignment and domain information

>TIGR00717 rpsA ribosomal protein S1	Back alignment and domain information

>TIGR00717 rpsA ribosomal protein S1	Back alignment and domain information

>PRK13806 rpsA 30S ribosomal protein S1; Provisional	Back alignment and domain information

>PRK13806 rpsA 30S ribosomal protein S1; Provisional	Back alignment and domain information

>PRK07899 rpsA 30S ribosomal protein S1; Reviewed	Back alignment and domain information

>PRK06676 rpsA 30S ribosomal protein S1; Reviewed	Back alignment and domain information

>PRK07899 rpsA 30S ribosomal protein S1; Reviewed	Back alignment and domain information

>PRK00087 4-hydroxy-3-methylbut-2-enyl diphosphate reductase/S1 RNA-binding domain protein; Reviewed	Back alignment and domain information

>PRK06676 rpsA 30S ribosomal protein S1; Reviewed	Back alignment and domain information

>PRK00087 4-hydroxy-3-methylbut-2-enyl diphosphate reductase/S1 RNA-binding domain protein; Reviewed	Back alignment and domain information

>PRK07400 30S ribosomal protein S1; Reviewed	Back alignment and domain information

>PRK07400 30S ribosomal protein S1; Reviewed	Back alignment and domain information

>PTZ00248 eukaryotic translation initiation factor 2 subunit 1; Provisional	Back alignment and domain information

>COG1098 VacB Predicted RNA binding protein (contains ribosomal protein S1 domain) [Translation, ribosomal structure and biogenesis]	Back alignment and domain information

>COG2996 Predicted RNA-bindining protein (contains S1 and HTH domains) [General function prediction only]	Back alignment and domain information

>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	Back alignment and domain information

>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	Back alignment and domain information

>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	Back alignment and domain information

>PTZ00248 eukaryotic translation initiation factor 2 subunit 1; Provisional	Back alignment and domain information

>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	Back alignment and domain information

>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	Back alignment and domain information

>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	Back alignment and domain information

>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	Back alignment and domain information

>COG1098 VacB Predicted RNA binding protein (contains ribosomal protein S1 domain) [Translation, ribosomal structure and biogenesis]	Back alignment and domain information

>PF00575 S1: S1 RNA binding domain; InterPro: IPR003029 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms	Back alignment and domain information

>COG2996 Predicted RNA-bindining protein (contains S1 and HTH domains) [General function prediction only]	Back alignment and domain information

>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	Back alignment and domain information

>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	Back alignment and domain information

>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	Back alignment and domain information

>PF00575 S1: S1 RNA binding domain; InterPro: IPR003029 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms	Back alignment and domain information

>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	Back alignment and domain information

>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	Back alignment and domain information

>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	Back alignment and domain information

>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	Back alignment and domain information

>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	Back alignment and domain information

>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	Back alignment and domain information

>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	Back alignment and domain information

>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	Back alignment and domain information

>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	Back alignment and domain information

>PRK08582 hypothetical protein; Provisional	Back alignment and domain information

>PRK07252 hypothetical protein; Provisional	Back alignment and domain information

>cd04452 S1_IF2_alpha S1_IF2_alpha: The alpha subunit of translation Initiation Factor 2, S1-like RNA-binding domain	Back alignment and domain information

>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	Back alignment and domain information

>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	Back alignment and domain information

>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	Back alignment and domain information

>cd05690 S1_RPS1_repeat_ec5 S1_RPS1_repeat_ec5: Ribosomal protein S1 (RPS1) domain	Back alignment and domain information

>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	Back alignment and domain information

>cd05686 S1_pNO40 S1_pNO40: pNO40 , S1-like RNA-binding domain	Back alignment and domain information

>cd05691 S1_RPS1_repeat_ec6 S1_RPS1_repeat_ec6: Ribosomal protein S1 (RPS1) domain	Back alignment and domain information

>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	Back alignment and domain information

>cd04452 S1_IF2_alpha S1_IF2_alpha: The alpha subunit of translation Initiation Factor 2, S1-like RNA-binding domain	Back alignment and domain information

>PRK07252 hypothetical protein; Provisional	Back alignment and domain information

>cd05690 S1_RPS1_repeat_ec5 S1_RPS1_repeat_ec5: Ribosomal protein S1 (RPS1) domain	Back alignment and domain information

>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	Back alignment and domain information

>cd05689 S1_RPS1_repeat_ec4 S1_RPS1_repeat_ec4: Ribosomal protein S1 (RPS1) domain	Back alignment and domain information

>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	Back alignment and domain information

>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	Back alignment and domain information

>cd05691 S1_RPS1_repeat_ec6 S1_RPS1_repeat_ec6: Ribosomal protein S1 (RPS1) domain	Back alignment and domain information

>cd05687 S1_RPS1_repeat_ec1_hs1 S1_RPS1_repeat_ec1_hs1: Ribosomal protein S1 (RPS1) domain	Back alignment and domain information

>cd05687 S1_RPS1_repeat_ec1_hs1 S1_RPS1_repeat_ec1_hs1: Ribosomal protein S1 (RPS1) domain	Back alignment and domain information

>cd04465 S1_RPS1_repeat_ec2_hs2 S1_RPS1_repeat_ec2_hs2: Ribosomal protein S1 (RPS1) domain	Back alignment and domain information

>PRK08582 hypothetical protein; Provisional	Back alignment and domain information

>cd05686 S1_pNO40 S1_pNO40: pNO40 , S1-like RNA-binding domain	Back alignment and domain information

>PRK08059 general stress protein 13; Validated	Back alignment and domain information

>PRK05807 hypothetical protein; Provisional	Back alignment and domain information

>cd05689 S1_RPS1_repeat_ec4 S1_RPS1_repeat_ec4: Ribosomal protein S1 (RPS1) domain	Back alignment and domain information

>cd04465 S1_RPS1_repeat_ec2_hs2 S1_RPS1_repeat_ec2_hs2: Ribosomal protein S1 (RPS1) domain	Back alignment and domain information

>cd05692 S1_RPS1_repeat_hs4 S1_RPS1_repeat_hs4: Ribosomal protein S1 (RPS1) domain	Back alignment and domain information

>cd05692 S1_RPS1_repeat_hs4 S1_RPS1_repeat_hs4: Ribosomal protein S1 (RPS1) domain	Back alignment and domain information

>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	Back alignment and domain information

>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	Back alignment and domain information

>PRK08059 general stress protein 13; Validated	Back alignment and domain information

>PHA02945 interferon resistance protein; Provisional	Back alignment and domain information

>PRK05807 hypothetical protein; Provisional	Back alignment and domain information

>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	Back alignment and domain information

>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	Back alignment and domain information

>cd04472 S1_PNPase S1_PNPase: Polynucleotide phosphorylase (PNPase), ), S1-like RNA-binding domain	Back alignment and domain information

>smart00316 S1 Ribosomal protein S1-like RNA-binding domain	Back alignment and domain information

>cd04472 S1_PNPase S1_PNPase: Polynucleotide phosphorylase (PNPase), ), S1-like RNA-binding domain	Back alignment and domain information

>PHA02945 interferon resistance protein; Provisional	Back alignment and domain information

>smart00316 S1 Ribosomal protein S1-like RNA-binding domain	Back alignment and domain information

>cd05688 S1_RPS1_repeat_ec3 S1_RPS1_repeat_ec3: Ribosomal protein S1 (RPS1) domain	Back alignment and domain information

>cd05688 S1_RPS1_repeat_ec3 S1_RPS1_repeat_ec3: Ribosomal protein S1 (RPS1) domain	Back alignment and domain information

>PLN00207 polyribonucleotide nucleotidyltransferase; Provisional	Back alignment and domain information

>cd05789 S1_Rrp4 S1_Rrp4: Rrp4 S1-like RNA-binding domain	Back alignment and domain information

>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	Back alignment and domain information

>cd04453 S1_RNase_E S1_RNase_E: RNase E and RNase G, S1-like RNA-binding domain	Back alignment and domain information

>COG1093 SUI2 Translation initiation factor 2, alpha subunit (eIF-2alpha) [Translation, ribosomal structure and biogenesis]	Back alignment and domain information

>cd04471 S1_RNase_R S1_RNase_R: RNase R C-terminal S1 domain	Back alignment and domain information

>cd05789 S1_Rrp4 S1_Rrp4: Rrp4 S1-like RNA-binding domain	Back alignment and domain information

>cd04453 S1_RNase_E S1_RNase_E: RNase E and RNase G, S1-like RNA-binding domain	Back alignment and domain information

>PRK03987 translation initiation factor IF-2 subunit alpha; Validated	Back alignment and domain information

>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	Back alignment and domain information

>cd04473 S1_RecJ_like S1_RecJ_like: The S1 domain of the archaea-specific RecJ-like exonuclease	Back alignment and domain information

>cd04473 S1_RecJ_like S1_RecJ_like: The S1 domain of the archaea-specific RecJ-like exonuclease	Back alignment and domain information

>TIGR02696 pppGpp_PNP guanosine pentaphosphate synthetase I/polynucleotide phosphorylase	Back alignment and domain information

>PLN00207 polyribonucleotide nucleotidyltransferase; Provisional	Back alignment and domain information

>COG2183 Tex Transcriptional accessory protein [Transcription]	Back alignment and domain information

>cd00164 S1_like S1_like: Ribosomal protein S1-like RNA-binding domain	Back alignment and domain information

>cd00164 S1_like S1_like: Ribosomal protein S1-like RNA-binding domain	Back alignment and domain information

>cd04454 S1_Rrp4_like S1_Rrp4_like: Rrp4-like, S1-like RNA-binding domain	Back alignment and domain information

>PRK03987 translation initiation factor IF-2 subunit alpha; Validated	Back alignment and domain information

>cd04471 S1_RNase_R S1_RNase_R: RNase R C-terminal S1 domain	Back alignment and domain information

>TIGR02696 pppGpp_PNP guanosine pentaphosphate synthetase I/polynucleotide phosphorylase	Back alignment and domain information

>COG1093 SUI2 Translation initiation factor 2, alpha subunit (eIF-2alpha) [Translation, ribosomal structure and biogenesis]	Back alignment and domain information

>cd04454 S1_Rrp4_like S1_Rrp4_like: Rrp4-like, S1-like RNA-binding domain	Back alignment and domain information

>PRK11824 polynucleotide phosphorylase/polyadenylase; Provisional	Back alignment and domain information

>PRK09521 exosome complex RNA-binding protein Csl4; Provisional	Back alignment and domain information

>PRK11824 polynucleotide phosphorylase/polyadenylase; Provisional	Back alignment and domain information

>COG2183 Tex Transcriptional accessory protein [Transcription]	Back alignment and domain information

>PRK09202 nusA transcription elongation factor NusA; Validated	Back alignment and domain information

>PRK09521 exosome complex RNA-binding protein Csl4; Provisional	Back alignment and domain information

>PRK09202 nusA transcription elongation factor NusA; Validated	Back alignment and domain information

>PRK04163 exosome complex RNA-binding protein Rrp4; Provisional	Back alignment and domain information

>cd04460 S1_RpoE S1_RpoE: RpoE, S1-like RNA-binding domain	Back alignment and domain information

>cd04455 S1_NusA S1_NusA: N-utilizing substance A protein (NusA), S1-like RNA-binding domain	Back alignment and domain information

>TIGR03591 polynuc_phos polyribonucleotide nucleotidyltransferase	Back alignment and domain information

>cd04455 S1_NusA S1_NusA: N-utilizing substance A protein (NusA), S1-like RNA-binding domain	Back alignment and domain information

>TIGR03591 polynuc_phos polyribonucleotide nucleotidyltransferase	Back alignment and domain information

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

>cd04460 S1_RpoE S1_RpoE: RpoE, S1-like RNA-binding domain	Back alignment and domain information

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

>PRK04163 exosome complex RNA-binding protein Rrp4; Provisional	Back alignment and domain information

>TIGR01953 NusA transcription termination factor NusA	Back alignment and domain information

>TIGR00448 rpoE DNA-directed RNA polymerase (rpoE), archaeal and eukaryotic form	Back alignment and domain information

>TIGR01953 NusA transcription termination factor NusA	Back alignment and domain information

>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	Back alignment and domain information

>PRK12327 nusA transcription elongation factor NusA; Provisional	Back alignment and domain information

>TIGR00448 rpoE DNA-directed RNA polymerase (rpoE), archaeal and eukaryotic form	Back alignment and domain information

>cd05791 S1_CSL4 S1_CSL4: CSL4, S1-like RNA-binding domain	Back alignment and domain information

>TIGR02063 RNase_R ribonuclease R	Back alignment and domain information

>KOG1067 consensus Predicted RNA-binding polyribonucleotide nucleotidyltransferase [General function prediction only]	Back alignment and domain information

>KOG1067 consensus Predicted RNA-binding polyribonucleotide nucleotidyltransferase [General function prediction only]	Back alignment and domain information

>TIGR02063 RNase_R ribonuclease R	Back alignment and domain information

>PRK12327 nusA transcription elongation factor NusA; Provisional	Back alignment and domain information

>COG1095 RPB7 DNA-directed RNA polymerase, subunit E' [Transcription]	Back alignment and domain information

>cd05791 S1_CSL4 S1_CSL4: CSL4, S1-like RNA-binding domain	Back alignment and domain information

>COG1095 RPB7 DNA-directed RNA polymerase, subunit E' [Transcription]	Back alignment and domain information

>PRK11642 exoribonuclease R; Provisional	Back alignment and domain information

>PRK11642 exoribonuclease R; Provisional	Back alignment and domain information

>TIGR00358 3_prime_RNase VacB and RNase II family 3'-5' exoribonucleases	Back alignment and domain information

>PRK08563 DNA-directed RNA polymerase subunit E'; Provisional	Back alignment and domain information

>PRK08563 DNA-directed RNA polymerase subunit E'; Provisional	Back alignment and domain information

>TIGR00358 3_prime_RNase VacB and RNase II family 3'-5' exoribonucleases	Back alignment and domain information

>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 []	Back alignment and domain information

>PHA02858 EIF2a-like PKR inhibitor; Provisional	Back alignment and domain information

>PHA02858 EIF2a-like PKR inhibitor; Provisional	Back alignment and domain information

>cd04462 S1_RNAPII_Rpb7 S1_RNAPII_Rpb7: Eukaryotic RNA polymerase II (RNAPII) Rpb7 subunit C-terminal S1 domain	Back alignment and domain information

>COG1107 Archaea-specific RecJ-like exonuclease, contains DnaJ-type Zn finger domain [DNA replication, recombination, and repair]	Back alignment and domain information

>PRK12328 nusA transcription elongation factor NusA; Provisional	Back alignment and domain information

>cd04462 S1_RNAPII_Rpb7 S1_RNAPII_Rpb7: Eukaryotic RNA polymerase II (RNAPII) Rpb7 subunit C-terminal S1 domain	Back alignment and domain information

>cd05701 S1_Rrp5_repeat_hs10 S1_Rrp5_repeat_hs10: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits	Back alignment and domain information

>PF13509 S1_2: S1 domain; PDB: 3GO5_A	Back alignment and domain information

>COG1107 Archaea-specific RecJ-like exonuclease, contains DnaJ-type Zn finger domain [DNA replication, recombination, and repair]	Back alignment and domain information

>COG1096 Predicted RNA-binding protein (consists of S1 domain and a Zn-ribbon domain) [Translation, ribosomal structure and biogenesis]	Back alignment and domain information

>KOG2916 consensus Translation initiation factor 2, alpha subunit (eIF-2alpha) [Translation, ribosomal structure and biogenesis]	Back alignment and domain information

>PRK12329 nusA transcription elongation factor NusA; Provisional	Back alignment and domain information

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

>PTZ00162 DNA-directed RNA polymerase II subunit 7; Provisional	Back alignment and domain information

>PRK05054 exoribonuclease II; Provisional	Back alignment and domain information

>COG1096 Predicted RNA-binding protein (consists of S1 domain and a Zn-ribbon domain) [Translation, ribosomal structure and biogenesis]	Back alignment and domain information

>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 []	Back alignment and domain information

>KOG1856 consensus Transcription elongation factor SPT6 [RNA processing and modification]	Back alignment and domain information

>PTZ00162 DNA-directed RNA polymerase II subunit 7; Provisional	Back alignment and domain information

>PRK05054 exoribonuclease II; Provisional	Back alignment and domain information

>PF13509 S1_2: S1 domain; PDB: 3GO5_A	Back alignment and domain information

>KOG1856 consensus Transcription elongation factor SPT6 [RNA processing and modification]	Back alignment and domain information

>PRK12328 nusA transcription elongation factor NusA; Provisional	Back alignment and domain information

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

>TIGR00757 RNaseEG ribonuclease, Rne/Rng family	Back alignment and domain information

>TIGR00757 RNaseEG ribonuclease, Rne/Rng family	Back alignment and domain information

>cd05790 S1_Rrp40 S1_Rrp40: Rrp40 S1-like RNA-binding domain	Back alignment and domain information

>cd05790 S1_Rrp40 S1_Rrp40: Rrp40 S1-like RNA-binding domain	Back alignment and domain information

>cd05700 S1_Rrp5_repeat_hs9 S1_Rrp5_repeat_hs9: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits	Back alignment and domain information

>TIGR02062 RNase_B exoribonuclease II	Back alignment and domain information

>TIGR02062 RNase_B exoribonuclease II	Back alignment and domain information

>PRK12329 nusA transcription elongation factor NusA; Provisional	Back alignment and domain information

>COG0557 VacB Exoribonuclease R [Transcription]	Back alignment and domain information

>KOG2916 consensus Translation initiation factor 2, alpha subunit (eIF-2alpha) [Translation, ribosomal structure and biogenesis]	Back alignment and domain information

>COG0557 VacB Exoribonuclease R [Transcription]	Back alignment and domain information

>KOG3409 consensus Exosomal 3'-5' exoribonuclease complex, subunit ski4 (Csl4) [Translation, ribosomal structure and biogenesis]	Back alignment and domain information

>PF10246 MRP-S35: Mitochondrial ribosomal protein MRP-S35; InterPro: IPR019375 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms	Back alignment and domain information

>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	Back alignment and domain information

>PRK10811 rne ribonuclease E; Reviewed	Back alignment and domain information

>PRK10811 rne ribonuclease E; Reviewed	Back alignment and domain information

>KOG3409 consensus Exosomal 3'-5' exoribonuclease complex, subunit ski4 (Csl4) [Translation, ribosomal structure and biogenesis]	Back alignment and domain information

>cd05701 S1_Rrp5_repeat_hs10 S1_Rrp5_repeat_hs10: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits	Back alignment and domain information

>PRK11712 ribonuclease G; Provisional	Back alignment and domain information

>KOG3298 consensus DNA-directed RNA polymerase subunit E' [Transcription]	Back alignment and domain information

>PRK11712 ribonuclease G; Provisional	Back alignment and domain information

>KOG3298 consensus DNA-directed RNA polymerase subunit E' [Transcription]	Back alignment and domain information

>PF10246 MRP-S35: Mitochondrial ribosomal protein MRP-S35; InterPro: IPR019375 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms	Back alignment and domain information

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

ID	Alignment Graph	Length	Definition	E-value
Query		1152
1wi5_A		119	Solution Structure Of The S1 Rna Binding Domain Fro		9e-05

>pdb|1WI5|A Chain A, Solution Structure Of The S1 Rna Binding Domain From Human Hypothetical Protein Baa11502 Length = 119

Back alignment and structure

Iteration: 1

Score = 46.2 bits (108), Expect = 9e-05, Method: Compositional matrix adjust. Identities = 30/97 (30%), Positives = 46/97 (47%), Gaps = 5/97 (5%) Query: 228 ETVQEGMVLTAYVKSIEDHGYILHFGLPSFTGFLPRNNLAE-----NSGIDVKPGLLLQG 282 E ++ GM+LT V S+EDHGY++ G+ FLP E N G +K G L Sbjct: 17 EALKPGMLLTGTVSSLEDHGYLVDIGVDGTRAFLPLLKAQEYIRQKNKGAKLKVGQYLNC 76 Query: 283 VVRSIDRTRKVVYLSSDPDTVSKCVTKDLKGISIDLL 319 +V + VV LS VS + + + +++ L Sbjct: 77 IVEKVKGNGGVVSLSVGHSEVSTAIATEQQSWNLNNL 113

PyMOL of 1wi5

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Alignment Graph	Length	Definition	E-value
Query		1152
1wi5_A		119	RRP5 protein homolog; S1 domain, OB-fold, structur	2e-22
1wi5_A		119	RRP5 protein homolog; S1 domain, OB-fold, structur	2e-07
1wi5_A		119	RRP5 protein homolog; S1 domain, OB-fold, structur	8e-06
1wi5_A		119	RRP5 protein homolog; S1 domain, OB-fold, structur	4e-05
1vt4_I		1221	APAF-1 related killer DARK; drosophila apoptosome,	3e-13
1vt4_I		1221	APAF-1 related killer DARK; drosophila apoptosome,	3e-11
1vt4_I		1221	APAF-1 related killer DARK; drosophila apoptosome,	1e-06
2k4k_A		130	GSP13, general stress protein 13; cytoplasm, stres	4e-10
2k4k_A		130	GSP13, general stress protein 13; cytoplasm, stres	2e-07
2k4k_A		130	GSP13, general stress protein 13; cytoplasm, stres	3e-04
1kl9_A		182	Eukaryotic translation initiation factor 2 subuni;	2e-09
1kl9_A		182	Eukaryotic translation initiation factor 2 subuni;	3e-06
1kl9_A		182	Eukaryotic translation initiation factor 2 subuni;	1e-05
1kl9_A		182	Eukaryotic translation initiation factor 2 subuni;	2e-04
2khj_A		109	30S ribosomal protein S1; OB fold, acetylation, ph	1e-08
2khj_A		109	30S ribosomal protein S1; OB fold, acetylation, ph	2e-07
2khj_A		109	30S ribosomal protein S1; OB fold, acetylation, ph	4e-07
2khj_A		109	30S ribosomal protein S1; OB fold, acetylation, ph	7e-06
2khj_A		109	30S ribosomal protein S1; OB fold, acetylation, ph	4e-04
2a19_A		175	EIF-2- alpha, eukaryotic translation initiation fa	2e-08
2a19_A		175	EIF-2- alpha, eukaryotic translation initiation fa	4e-06
2a19_A		175	EIF-2- alpha, eukaryotic translation initiation fa	8e-05
2k52_A		80	Uncharacterized protein MJ1198; metal-binding, zin	8e-08
2k52_A		80	Uncharacterized protein MJ1198; metal-binding, zin	3e-05
2k52_A		80	Uncharacterized protein MJ1198; metal-binding, zin	1e-04
1q8k_A		308	Eukaryotic translation initiation factor 2 subunit	2e-07
1q8k_A		308	Eukaryotic translation initiation factor 2 subunit	1e-04
1q8k_A		308	Eukaryotic translation initiation factor 2 subunit	2e-04
1q8k_A		308	Eukaryotic translation initiation factor 2 subunit	8e-04
2khi_A		115	30S ribosomal protein S1; acetylation, phosphoprot	2e-06
2khi_A		115	30S ribosomal protein S1; acetylation, phosphoprot	8e-05
2khi_A		115	30S ribosomal protein S1; acetylation, phosphoprot	4e-04
3go5_A		285	Multidomain protein with S1 RNA-binding domains; s	2e-06
3go5_A		285	Multidomain protein with S1 RNA-binding domains; s	1e-05
3cw2_C		266	Translation initiation factor 2 subunit alpha; AIF	4e-06
3cw2_C		266	Translation initiation factor 2 subunit alpha; AIF	5e-04
3aev_A		275	Translation initiation factor 2 subunit alpha; pro	7e-06
3aev_A		275	Translation initiation factor 2 subunit alpha; pro	7e-04
3psi_A		1219	Transcription elongation factor SPT6; nucleus; 3.3	7e-06
3psi_A		1219	Transcription elongation factor SPT6; nucleus; 3.3	2e-05
3psi_A		1219	Transcription elongation factor SPT6; nucleus; 3.3	2e-04
3psi_A		1219	Transcription elongation factor SPT6; nucleus; 3.3	7e-04
3psf_A		1030	Transcription elongation factor SPT6; nucleus; 2.5	1e-05
3psf_A		1030	Transcription elongation factor SPT6; nucleus; 2.5	1e-05
3psf_A		1030	Transcription elongation factor SPT6; nucleus; 2.5	2e-04
3psf_A		1030	Transcription elongation factor SPT6; nucleus; 2.5	2e-04
2eqs_A		103	ATP-dependent RNA helicase DHX8; S1 domain, OB-fol	4e-05
4aid_A		726	Polyribonucleotide nucleotidyltransferase; transfe	9e-04

>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 Length = 119	Back alignment and structure

 Score = 93.2 bits (231), Expect = 2e-22
 Identities = 32/106 (30%), Positives = 50/106 (47%), Gaps = 5/106 (4%)

Query: 219 SLLYKGLSLETVQEGMVLTAYVKSIEDHGYILHFGLPSFTGFLPRNNLAE-----NSGID 273
             + + LS E ++ GM+LT  V S+EDHGY++  G+     FLP     E     N G  
Sbjct: 8   KNVNRVLSAEALKPGMLLTGTVSSLEDHGYLVDIGVDGTRAFLPLLKAQEYIRQKNKGAK 67

Query: 274 VKPGLLLQGVVRSIDRTRKVVYLSSDPDTVSKCVTKDLKGISIDLL 319
           +K G  L  +V  +     VV LS     VS  +  + +  +++ L
Sbjct: 68  LKVGQYLNCIVEKVKGNGGVVSLSVGHSEVSTAIATEQQSWNLNNL 113

PyMOL of 1wi5

>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 Length = 119	Back alignment and structure

>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 Length = 119	Back alignment and structure

>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 Length = 119	Back alignment and structure

>1vt4_I APAF-1 related killer DARK; drosophila apoptosome, apoptosis, programmed cell death; HET: DTP; 6.90A {Drosophila melanogaster} PDB: 3iz8_A* Length = 1221	Back alignment and structure

>1vt4_I APAF-1 related killer DARK; drosophila apoptosome, apoptosis, programmed cell death; HET: DTP; 6.90A {Drosophila melanogaster} PDB: 3iz8_A* Length = 1221	Back alignment and structure

>1vt4_I APAF-1 related killer DARK; drosophila apoptosome, apoptosis, programmed cell death; HET: DTP; 6.90A {Drosophila melanogaster} PDB: 3iz8_A* Length = 1221	Back alignment and structure

>2k4k_A GSP13, general stress protein 13; cytoplasm, stress response, RNA binding protein; NMR {Bacillus subtilis} Length = 130	Back alignment and structure

>2k4k_A GSP13, general stress protein 13; cytoplasm, stress response, RNA binding protein; NMR {Bacillus subtilis} Length = 130	Back alignment and structure

>2k4k_A GSP13, general stress protein 13; cytoplasm, stress response, RNA binding protein; NMR {Bacillus subtilis} Length = 130	Back alignment and structure

>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	Back alignment and structure

>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	Back alignment and structure

>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	Back alignment and structure

>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	Back alignment and structure

>2khj_A 30S ribosomal protein S1; OB fold, acetylation, phosphoprotein, ribonucleoprotein, RNA-binding; NMR {Escherichia coli} Length = 109	Back alignment and structure

>2khj_A 30S ribosomal protein S1; OB fold, acetylation, phosphoprotein, ribonucleoprotein, RNA-binding; NMR {Escherichia coli} Length = 109	Back alignment and structure

>2khj_A 30S ribosomal protein S1; OB fold, acetylation, phosphoprotein, ribonucleoprotein, RNA-binding; NMR {Escherichia coli} Length = 109	Back alignment and structure

>2khj_A 30S ribosomal protein S1; OB fold, acetylation, phosphoprotein, ribonucleoprotein, RNA-binding; NMR {Escherichia coli} Length = 109	Back alignment and structure

>2khj_A 30S ribosomal protein S1; OB fold, acetylation, phosphoprotein, ribonucleoprotein, RNA-binding; NMR {Escherichia coli} Length = 109	Back alignment and structure

>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	Back alignment and structure

>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	Back alignment and structure

>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	Back alignment and structure

>2k52_A Uncharacterized protein MJ1198; metal-binding, zinc, zinc-finger, structural genomics, PSI-2, protein structure initiative; NMR {Methanocaldococcus jannaschii} Length = 80	Back alignment and structure

>2k52_A Uncharacterized protein MJ1198; metal-binding, zinc, zinc-finger, structural genomics, PSI-2, protein structure initiative; NMR {Methanocaldococcus jannaschii} Length = 80	Back alignment and structure

>2k52_A Uncharacterized protein MJ1198; metal-binding, zinc, zinc-finger, structural genomics, PSI-2, protein structure initiative; NMR {Methanocaldococcus jannaschii} Length = 80	Back alignment and structure

>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	Back alignment and structure

>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	Back alignment and structure

>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	Back alignment and structure

>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	Back alignment and structure

>2khi_A 30S ribosomal protein S1; acetylation, phosphoprotein, ribonucleoprotein, RNA-binding; NMR {Escherichia coli} Length = 115	Back alignment and structure

>2khi_A 30S ribosomal protein S1; acetylation, phosphoprotein, ribonucleoprotein, RNA-binding; NMR {Escherichia coli} Length = 115	Back alignment and structure

>2khi_A 30S ribosomal protein S1; acetylation, phosphoprotein, ribonucleoprotein, RNA-binding; NMR {Escherichia coli} Length = 115	Back alignment and structure

>3go5_A Multidomain protein with S1 RNA-binding domains; structural genomics, joint center for structural genomics, JCSG; HET: MSE; 1.40A {Streptococcus pneumoniae} Length = 285	Back alignment and structure

>3go5_A Multidomain protein with S1 RNA-binding domains; structural genomics, joint center for structural genomics, JCSG; HET: MSE; 1.40A {Streptococcus pneumoniae} Length = 285	Back alignment and structure

>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	Back alignment and structure

>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	Back alignment and structure

>3aev_A Translation initiation factor 2 subunit alpha; proteins-rRNA complex, 16S rRNA, RNA-binding; 2.80A {Pyrococcus horikoshii} PDB: 1yz6_A Length = 275	Back alignment and structure

>3aev_A Translation initiation factor 2 subunit alpha; proteins-rRNA complex, 16S rRNA, RNA-binding; 2.80A {Pyrococcus horikoshii} PDB: 1yz6_A Length = 275	Back alignment and structure

>3psi_A Transcription elongation factor SPT6; nucleus; 3.30A {Saccharomyces cerevisiae} Length = 1219	Back alignment and structure

>3psi_A Transcription elongation factor SPT6; nucleus; 3.30A {Saccharomyces cerevisiae} Length = 1219	Back alignment and structure

>3psi_A Transcription elongation factor SPT6; nucleus; 3.30A {Saccharomyces cerevisiae} Length = 1219	Back alignment and structure

>3psi_A Transcription elongation factor SPT6; nucleus; 3.30A {Saccharomyces cerevisiae} Length = 1219	Back alignment and structure

>3psf_A Transcription elongation factor SPT6; nucleus; 2.59A {Saccharomyces cerevisiae} Length = 1030	Back alignment and structure

>3psf_A Transcription elongation factor SPT6; nucleus; 2.59A {Saccharomyces cerevisiae} Length = 1030	Back alignment and structure

>3psf_A Transcription elongation factor SPT6; nucleus; 2.59A {Saccharomyces cerevisiae} Length = 1030	Back alignment and structure

>3psf_A Transcription elongation factor SPT6; nucleus; 2.59A {Saccharomyces cerevisiae} Length = 1030	Back alignment and structure

>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	Back alignment and structure

>4aid_A Polyribonucleotide nucleotidyltransferase; transferase-peptide complex; 2.60A {Caulobacter vibrioides} PDB: 4aim_A 4am3_A Length = 726	Back alignment and structure

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Alignment Graph	Length	Definition	Probability
Query		1152
3go5_A		285	Multidomain protein with S1 RNA-binding domains; s	99.95
3go5_A		285	Multidomain protein with S1 RNA-binding domains; s	99.94
1kl9_A		182	Eukaryotic translation initiation factor 2 subuni;	99.53
2a19_A		175	EIF-2- alpha, eukaryotic translation initiation fa	99.41
2khj_A		109	30S ribosomal protein S1; OB fold, acetylation, ph	99.39
1kl9_A		182	Eukaryotic translation initiation factor 2 subuni;	99.39
2khi_A		115	30S ribosomal protein S1; acetylation, phosphoprot	99.37
1wi5_A		119	RRP5 protein homolog; S1 domain, OB-fold, structur	99.33
1luz_A		88	Protein K3, protein K2; stranded anti-parallel bet	99.32
1q8k_A		308	Eukaryotic translation initiation factor 2 subunit	99.28
2k4k_A		130	GSP13, general stress protein 13; cytoplasm, stres	99.27
2khj_A		109	30S ribosomal protein S1; OB fold, acetylation, ph	99.26
2k52_A		80	Uncharacterized protein MJ1198; metal-binding, zin	99.26
2k52_A		80	Uncharacterized protein MJ1198; metal-binding, zin	99.2
2k4k_A		130	GSP13, general stress protein 13; cytoplasm, stres	99.19
2khi_A		115	30S ribosomal protein S1; acetylation, phosphoprot	99.19
1luz_A		88	Protein K3, protein K2; stranded anti-parallel bet	99.17
2eqs_A		103	ATP-dependent RNA helicase DHX8; S1 domain, OB-fol	99.17
3aev_A		275	Translation initiation factor 2 subunit alpha; pro	99.17
2a19_A		175	EIF-2- alpha, eukaryotic translation initiation fa	99.16
2cqo_A		119	Nucleolar protein of 40 kDa; S1 domain, OB-fold, s	99.14
1q8k_A		308	Eukaryotic translation initiation factor 2 subunit	99.08
1wi5_A		119	RRP5 protein homolog; S1 domain, OB-fold, structur	99.08
2eqs_A		103	ATP-dependent RNA helicase DHX8; S1 domain, OB-fol	99.01
2cqo_A		119	Nucleolar protein of 40 kDa; S1 domain, OB-fold, s	99.01
3aev_A		275	Translation initiation factor 2 subunit alpha; pro	98.88
3cw2_C		266	Translation initiation factor 2 subunit alpha; AIF	98.86
3psi_A		1219	Transcription elongation factor SPT6; nucleus; 3.3	98.81
3bzc_A		785	TEX; helix-turn-helix, helix-hairpin-helix, S1 dom	98.72
1go3_E		187	DNA-directed RNA polymerase subunit E; transferase	98.68
3cw2_C		266	Translation initiation factor 2 subunit alpha; AIF	98.67
3psi_A		1219	Transcription elongation factor SPT6; nucleus; 3.3	98.65
3psf_A		1030	Transcription elongation factor SPT6; nucleus; 2.5	98.65
4aid_A		726	Polyribonucleotide nucleotidyltransferase; transfe	98.6
1go3_E		187	DNA-directed RNA polymerase subunit E; transferase	98.58
1e3p_A		757	Guanosine pentaphosphate synthetase; polyribonucle	98.57
4ayb_E		180	DNA-directed RNA polymerase; transferase, multi-su	98.54
3bzc_A		785	TEX; helix-turn-helix, helix-hairpin-helix, S1 dom	98.53
3cdi_A		723	Polynucleotide phosphorylase; mRNA turnover, RNAse	98.52
1e3p_A		757	Guanosine pentaphosphate synthetase; polyribonucle	98.52
2nn6_I		209	3'-5' exoribonuclease CSL4 homolog; RNA, exosome,	98.51
4aid_A		726	Polyribonucleotide nucleotidyltransferase; transfe	98.5
3psf_A		1030	Transcription elongation factor SPT6; nucleus; 2.5	98.49
1hh2_P		344	NUSA, N utilization substance protein A; transcrip	98.48
4ayb_E		180	DNA-directed RNA polymerase; transferase, multi-su	98.45
3cdi_A		723	Polynucleotide phosphorylase; mRNA turnover, RNAse	98.45
1y14_B		171	B16, RPB7, DNA-directed RNA polymerase II 19 kDa p	98.44
2nn6_I		209	3'-5' exoribonuclease CSL4 homolog; RNA, exosome,	98.42
2b8k_G		215	B16, DNA-directed RNA polymerase II 19 kDa polypep	98.4
2c35_B		172	Human RPB7, DNA-directed RNA polymerase II 19 kDa	98.4
3m7n_A		179	Putative uncharacterized protein AF_0206; exosome,	98.38
1hh2_P		344	NUSA, N utilization substance protein A; transcrip	98.37
1y14_B		171	B16, RPB7, DNA-directed RNA polymerase II 19 kDa p	98.3
2b8k_G		215	B16, DNA-directed RNA polymerase II 19 kDa polypep	98.3
3m7n_A		179	Putative uncharacterized protein AF_0206; exosome,	98.29
2c35_B		172	Human RPB7, DNA-directed RNA polymerase II 19 kDa	98.27
2je6_I		251	RRP4, exosome complex RNA-binding protein 1; nucle	98.16
3h0g_G		172	DNA-directed RNA polymerase II subunit RPB7; trans	98.14
2z0s_A		235	Probable exosome complex RNA-binding protein 1; al	98.14
2je6_I		251	RRP4, exosome complex RNA-binding protein 1; nucle	98.12
2ba0_A		229	Archeal exosome RNA binding protein RRP4; RNAse PH	98.09
2z0s_A		235	Probable exosome complex RNA-binding protein 1; al	98.08
3h0g_G		172	DNA-directed RNA polymerase II subunit RPB7; trans	98.07
2bh8_A		101	1B11; transcription, molecular evolution, unique a	98.02
2ba0_A		229	Archeal exosome RNA binding protein RRP4; RNAse PH	98.0
2bh8_A		101	1B11; transcription, molecular evolution, unique a	97.84
2id0_A		644	Exoribonuclease 2; RNAse, exonuclease, hydrolyase,	97.55
2id0_A		644	Exoribonuclease 2; RNAse, exonuclease, hydrolyase,	97.46
3ayh_B		203	DNA-directed RNA polymerase III subunit RPC8; tran	97.45
1k0r_A		366	NUSA; two component arrangement, S1 domain, two K-	97.44
3ayh_B		203	DNA-directed RNA polymerase III subunit RPC8; tran	97.37
2ckz_B		218	C25, DNA-directed RNA polymerase III 25 KD polypep	97.32
2asb_A		251	Transcription elongation protein NUSA; protein-RNA	97.3
1k0r_A		366	NUSA; two component arrangement, S1 domain, two K-	97.27
2ckz_B		218	C25, DNA-directed RNA polymerase III 25 KD polypep	97.26
2bx2_L		517	Ribonuclease E, RNAse E; RNA-binding, RNA turnover	97.22
2bx2_L		517	Ribonuclease E, RNAse E; RNA-binding, RNA turnover	97.01
2asb_A		251	Transcription elongation protein NUSA; protein-RNA	96.98
2vnu_D		760	Exosome complex exonuclease RRP44; hydrolase-RNA c	96.87
2wp8_J		977	Exosome complex exonuclease DIS3; nucleus, hydrola	96.82
2vnu_D		760	Exosome complex exonuclease RRP44; hydrolase-RNA c	96.68
2nn6_H		308	Exosome complex exonuclease RRP4; RNA, exosome, PM	96.63
2wp8_J		977	Exosome complex exonuclease DIS3; nucleus, hydrola	96.52
2ja9_A		175	Exosome complex exonuclease RRP40; RNA-binding pro	96.45
2nn6_H		308	Exosome complex exonuclease RRP4; RNA, exosome, PM	96.38
2ja9_A		175	Exosome complex exonuclease RRP40; RNA-binding pro	96.36
2nn6_G		289	Exosome complex exonuclease RRP40; RNA, exosome, P	94.55
2nn6_G		289	Exosome complex exonuclease RRP40; RNA, exosome, P	93.73
2rf4_A		214	DNA-directed RNA polymerase I subunit RPA4; transf	86.51
2rf4_A		214	DNA-directed RNA polymerase I subunit RPA4; transf	85.83

>3go5_A Multidomain protein with S1 RNA-binding domains; structural genomics, joint center for structural genomics, JCSG; HET: MSE; 1.40A {Streptococcus pneumoniae}	Back alignment and structure

Probab=99.95  E-value=3.4e-26  Score=252.57  Aligned_cols=223  Identities=17%  Similarity=0.118  Sum_probs=187.7

Q ss_pred             cCCceEEEEEEEEecCeEEEEEcCCeEEEEeccccCCCCCCCCCCCccCCCEEEEEEEEEecCCCEEEEEEeeCCCCccc
Q 001115          584 TDRLITHGWITKIEKHGCFVRFYNGVQGFAPRSELGLDPGCEPSSMYHVGQVVKCRIMSSIPASRRINLSFMMKPTRVSE  663 (1152)
Q Consensus       584 ~~G~~~~G~V~~i~~~G~~V~~~~gv~Gflp~sel~~~~~~~~~~~f~vGq~v~vrV~~vd~~~~ri~lS~k~~~~~~~~  663 (1152)
                      ..|+++.|+|+++.++|+||++ ++.+||||.+++.       .   ++||+++|.|+ .|. ++|+.+|.+.       
T Consensus         5 ~~G~~v~g~V~~~~~~G~fv~~-~g~egllp~se~~-------~---~vGdevev~v~-~d~-~~r~iat~~~-------   64 (285)
T 3go5_A            5 NLASFIVGLIIDENDRFYFVQK-DGQTYALAKEEGQ-------H---TVGDTVKGFAY-TDM-KQKLRLTTLE-------   64 (285)
T ss_dssp             TTTEEEEEEEEEECSSEEEEEE-TTEEEEEEGGGCC-------C---CTTSEEEEEEE-ECT-TSCEEEECSC-------
T ss_pred             cCCCEEEEEEEEEECCEEEEEc-CCeEEEEEHHHCc-------c---ccCCEEEEEEE-ECC-CCCEEEeccc-------
Confidence            3699999999999999999999 5999999999983       1   89999999998 576 4567777642       


Q ss_pred             cccccCCCEEEEEEEEEe-CCcEEEEEeeCC-ceEEEEeCCCcCCccccccccccccCCCCeEeEEEEeecccCceeeec
Q 001115          664 DDLVKLGSLVSGVVDVVT-PNAVVVYVIAKG-YSKGTIPTEHLADHLEHATVMKSVIKPGYEFDQLLVLDNESSNLLLSA  741 (1152)
Q Consensus       664 ~~~l~vG~iv~g~V~~v~-~~g~~V~l~~~~-~v~G~ip~~hlsd~~~~~~~~~~~lk~G~~v~~vl~~d~~~~~i~lS~  741 (1152)
                       ..+++|+++.|+|++++ ++|+||++  +. +.+||||.+++++..      ...+++||++...+.+|+ ++||.+|+
T Consensus        65 -p~~~~G~~~~g~V~~v~~~~GaFVdi--G~~~~d~lvp~sel~~~~------~~~~~~Gd~v~v~l~iD~-~~Ri~ls~  134 (285)
T 3go5_A           65 -VTATQDQFGWGRVTEVRKDLGVFVDT--GLPDKEIVVSLDILPELK------ELWPKKGDQLYIRLEVDK-KDRIWGLL  134 (285)
T ss_dssp             -CCSCSSSCEEEEEEEEETTTEEEEEC--SCTTCCEEEEGGGSCSSG------GGSCCTTCEEEEEEEECT-TSCEEEEE
T ss_pred             -ccccCCCEEEEEEEEEccCceEEEEE--CCCCcEEEEEHHHCCccc------ccccCCCCEEEEEEEECC-CCcEEEEe
Confidence             24789999999999999 79999999  65 699999999988743      235799999996678998 67899999


Q ss_pred             chh-hccccccCCCccccCCCCCEEEEEEEEEecceEEE-EECCCeEEEEeccCCCCccccCccccccCCCEEEEEEEEE
Q 001115          742 KYS-LINSAQQLPSDASHIHPNSVVHGYVCNIIETGCFV-RFLGRLTGFAPRSKAVDGQRADLSKTYYVGQSVRSNILDV  819 (1152)
Q Consensus       742 K~s-l~~~~~~~~~~~~~~~~G~~v~G~V~~i~~~GvfV-~~~~~l~Glv~~s~ls~~~~~~~~~~f~~Gq~V~v~Vl~v  819 (1152)
                      |+. ..++|...   .+.+++|+.+.|+|.+++++|+|| .+.+++.||+|.|++++        .+++||.|+|+|++|
T Consensus       135 k~~~~~~~~~~~---~~~~~~G~~V~g~V~~i~~~G~fV~~i~~g~~Glih~SEl~~--------~l~~Gd~v~~~V~~i  203 (285)
T 3go5_A          135 AYQEDFQRLARP---AYNNMQNQNWPAIVYRLKLSGTFVYLPENNMLGFIHPSERYA--------EPRLGQVLDARVIGF  203 (285)
T ss_dssp             CCHHHHHHHCCC---CCSCCTTCEEEEEEEEEETTEEEEEETTTTEEEEECGGGCSS--------CCCTTCEEEEEEEEE
T ss_pred             hhhhhcchhhhh---hhhCCCCCEEEEEEEEEeCCcEEEEEeCCCeEEEEEHHHccc--------cCCCCCEEEEEEEEE
Confidence            976 56777643   467899999999999999999999 98899999999999973        689999999999999


Q ss_pred             eCCCCeEEEEeecccc--CCCchhhhhhhh
Q 001115          820 NSETGRITLSLKQSCC--SSTDASFMQEHF  847 (1152)
Q Consensus       820 d~e~~ri~LSlk~~~~--~~~~~~~~~~~~  847 (1152)
                      |++++||.||+|+...  ...++..+.+|+
T Consensus       204 d~~d~kI~LSlk~~~~~~~~~~a~~il~~L  233 (285)
T 3go5_A          204 REVDRTLNLSLKPRSFEMLENDAQMILTYL  233 (285)
T ss_dssp             ETTTTEEEEECSCCCCCCCCHHHHHHHHHH
T ss_pred             ECCCCeEEEEeChhhhhccchHHHHHHHHH
Confidence            9999999999999743  223344444444

PyMOL of 3go5

>3go5_A Multidomain protein with S1 RNA-binding domains; structural genomics, joint center for structural genomics, JCSG; HET: MSE; 1.40A {Streptococcus pneumoniae}	Back alignment and structure

>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	Back alignment and structure

>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	Back alignment and structure

>2khj_A 30S ribosomal protein S1; OB fold, acetylation, phosphoprotein, ribonucleoprotein, RNA-binding; NMR {Escherichia coli}	Back alignment and structure

>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	Back alignment and structure

>2khi_A 30S ribosomal protein S1; acetylation, phosphoprotein, ribonucleoprotein, RNA-binding; NMR {Escherichia coli}	Back alignment and structure

>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	Back alignment and structure

>1luz_A Protein K3, protein K2; stranded anti-parallel beta barrel, viral protein; 1.80A {Vaccinia virus} SCOP: b.40.4.5	Back alignment and structure

>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	Back alignment and structure

>2k4k_A GSP13, general stress protein 13; cytoplasm, stress response, RNA binding protein; NMR {Bacillus subtilis}	Back alignment and structure

>2khj_A 30S ribosomal protein S1; OB fold, acetylation, phosphoprotein, ribonucleoprotein, RNA-binding; NMR {Escherichia coli}	Back alignment and structure

>2k52_A Uncharacterized protein MJ1198; metal-binding, zinc, zinc-finger, structural genomics, PSI-2, protein structure initiative; NMR {Methanocaldococcus jannaschii}	Back alignment and structure

>2k52_A Uncharacterized protein MJ1198; metal-binding, zinc, zinc-finger, structural genomics, PSI-2, protein structure initiative; NMR {Methanocaldococcus jannaschii}	Back alignment and structure

>2k4k_A GSP13, general stress protein 13; cytoplasm, stress response, RNA binding protein; NMR {Bacillus subtilis}	Back alignment and structure

>2khi_A 30S ribosomal protein S1; acetylation, phosphoprotein, ribonucleoprotein, RNA-binding; NMR {Escherichia coli}	Back alignment and structure

>1luz_A Protein K3, protein K2; stranded anti-parallel beta barrel, viral protein; 1.80A {Vaccinia virus} SCOP: b.40.4.5	Back alignment and structure

>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}	Back alignment and structure

>3aev_A Translation initiation factor 2 subunit alpha; proteins-rRNA complex, 16S rRNA, RNA-binding; 2.80A {Pyrococcus horikoshii} PDB: 1yz6_A	Back alignment and structure

>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	Back alignment and structure

>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}	Back alignment and structure

>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	Back alignment and structure

>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	Back alignment and structure

>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}	Back alignment and structure

>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}	Back alignment and structure

>3aev_A Translation initiation factor 2 subunit alpha; proteins-rRNA complex, 16S rRNA, RNA-binding; 2.80A {Pyrococcus horikoshii} PDB: 1yz6_A	Back alignment and structure

>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*	Back alignment and structure

>3psi_A Transcription elongation factor SPT6; nucleus; 3.30A {Saccharomyces cerevisiae}	Back alignment and structure

>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	Back alignment and structure

>1go3_E DNA-directed RNA polymerase subunit E; transferase, transferase, transcription; 1.75A {Methanococcus jannaschii} SCOP: b.40.4.5 d.230.1.1	Back alignment and structure

>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*	Back alignment and structure

>3psi_A Transcription elongation factor SPT6; nucleus; 3.30A {Saccharomyces cerevisiae}	Back alignment and structure

>3psf_A Transcription elongation factor SPT6; nucleus; 2.59A {Saccharomyces cerevisiae}	Back alignment and structure

>4aid_A Polyribonucleotide nucleotidyltransferase; transferase-peptide complex; 2.60A {Caulobacter vibrioides} PDB: 4aim_A 4am3_A	Back alignment and structure

>1go3_E DNA-directed RNA polymerase subunit E; transferase, transferase, transcription; 1.75A {Methanococcus jannaschii} SCOP: b.40.4.5 d.230.1.1	Back alignment and structure

>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	Back alignment and structure

>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	Back alignment and structure

>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	Back alignment and structure

>3cdi_A Polynucleotide phosphorylase; mRNA turnover, RNAse, RNA degradation, kinase, transferase; 2.60A {Escherichia coli} PDB: 1sro_A	Back alignment and structure

>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	Back alignment and structure

>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	Back alignment and structure

>4aid_A Polyribonucleotide nucleotidyltransferase; transferase-peptide complex; 2.60A {Caulobacter vibrioides} PDB: 4aim_A 4am3_A	Back alignment and structure

>3psf_A Transcription elongation factor SPT6; nucleus; 2.59A {Saccharomyces cerevisiae}	Back alignment and structure

>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	Back alignment and structure

>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	Back alignment and structure

>3cdi_A Polynucleotide phosphorylase; mRNA turnover, RNAse, RNA degradation, kinase, transferase; 2.60A {Escherichia coli} PDB: 1sro_A	Back alignment and structure

>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* ...	Back alignment and structure

>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	Back alignment and structure

>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	Back alignment and structure

>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	Back alignment and structure

>3m7n_A Putative uncharacterized protein AF_0206; exosome, RNA, exonuclease, hydrolase, nuclease, hydrolase-RN; 2.40A {Archaeoglobus fulgidus} PDB: 2ba1_A 3m85_A	Back alignment and structure

>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	Back alignment and structure

>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* ...	Back alignment and structure

>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	Back alignment and structure

>3m7n_A Putative uncharacterized protein AF_0206; exosome, RNA, exonuclease, hydrolase, nuclease, hydrolase-RN; 2.40A {Archaeoglobus fulgidus} PDB: 2ba1_A 3m85_A	Back alignment and structure

>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	Back alignment and structure

>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	Back alignment and structure

>3h0g_G DNA-directed RNA polymerase II subunit RPB7; transcription, multi-protein complex, DNA- binding, magnesium; 3.65A {Schizosaccharomyces pombe}	Back alignment and structure

>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	Back alignment and structure

>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	Back alignment and structure

>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	Back alignment and structure

>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	Back alignment and structure

>3h0g_G DNA-directed RNA polymerase II subunit RPB7; transcription, multi-protein complex, DNA- binding, magnesium; 3.65A {Schizosaccharomyces pombe}	Back alignment and structure

>2bh8_A 1B11; transcription, molecular evolution, unique architecture, transcription regulation, phosphorylation; 1.9A {Escherichia coli}	Back alignment and structure

>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	Back alignment and structure

>2bh8_A 1B11; transcription, molecular evolution, unique architecture, transcription regulation, phosphorylation; 1.9A {Escherichia coli}	Back alignment and structure

>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	Back alignment and structure

>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	Back alignment and structure

>3ayh_B DNA-directed RNA polymerase III subunit RPC8; transcription; 2.19A {Schizosaccharomyces pombe}	Back alignment and structure

>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	Back alignment and structure

>3ayh_B DNA-directed RNA polymerase III subunit RPC8; transcription; 2.19A {Schizosaccharomyces pombe}	Back alignment and structure

>2ckz_B C25, DNA-directed RNA polymerase III 25 KD polypeptide; multiprotein complex, nucleotidyltransferase, nuclear protein, hypothetical protein; 3.2A {Saccharomyces cerevisiae}	Back alignment and structure

>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	Back alignment and structure

>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	Back alignment and structure

>2ckz_B C25, DNA-directed RNA polymerase III 25 KD polypeptide; multiprotein complex, nucleotidyltransferase, nuclear protein, hypothetical protein; 3.2A {Saccharomyces cerevisiae}	Back alignment and structure

>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	Back alignment and structure

>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	Back alignment and structure

>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	Back alignment and structure

>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	Back alignment and structure

>2wp8_J Exosome complex exonuclease DIS3; nucleus, hydrolase, RNA-binding, exonucle binding, mitochondrion, rRNA processing; 3.00A {Saccharomyces cerevisiae}	Back alignment and structure

>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	Back alignment and structure

>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	Back alignment and structure

>2wp8_J Exosome complex exonuclease DIS3; nucleus, hydrolase, RNA-binding, exonucle binding, mitochondrion, rRNA processing; 3.00A {Saccharomyces cerevisiae}	Back alignment and structure

>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	Back alignment and structure

>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	Back alignment and structure

>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	Back alignment and structure

>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	Back alignment and structure

>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	Back alignment and structure

>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}	Back alignment and structure

>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}	Back alignment and structure

Homologous Structure Domains

Structure Domains Detected by RPS-BLAST

Original result of RPS-BLAST against SCOP70(version1.75) database

ID	Alignment Graph	Length	Definition	E-value
Query		1152
d1sroa_		76	b.40.4.5 (A:) S1 RNA-binding domain of polyribonuc	2e-14
d1sroa_		76	b.40.4.5 (A:) S1 RNA-binding domain of polyribonuc	4e-10
d1sroa_		76	b.40.4.5 (A:) S1 RNA-binding domain of polyribonuc	1e-07
d1sroa_		76	b.40.4.5 (A:) S1 RNA-binding domain of polyribonuc	7e-04
d1sroa_		76	b.40.4.5 (A:) S1 RNA-binding domain of polyribonuc	0.004
d3bzka4		94	b.40.4.5 (A:637-730) Tex S1-domain {Pseudomonas ae	5e-14
d3bzka4		94	b.40.4.5 (A:637-730) Tex S1-domain {Pseudomonas ae	2e-11
d3bzka4		94	b.40.4.5 (A:637-730) Tex S1-domain {Pseudomonas ae	8e-09
d3bzka4		94	b.40.4.5 (A:637-730) Tex S1-domain {Pseudomonas ae	3e-04
d3bzka4		94	b.40.4.5 (A:637-730) Tex S1-domain {Pseudomonas ae	8e-04
d3bzka4		94	b.40.4.5 (A:637-730) Tex S1-domain {Pseudomonas ae	0.001
d1wi5a_		119	b.40.4.5 (A:) S1-domain of RRP5 protein homolog (P	8e-10
d1wi5a_		119	b.40.4.5 (A:) S1-domain of RRP5 protein homolog (P	9e-07
d1wi5a_		119	b.40.4.5 (A:) S1-domain of RRP5 protein homolog (P	3e-04
d1wi5a_		119	b.40.4.5 (A:) S1-domain of RRP5 protein homolog (P	3e-04
d1kl9a2		86	b.40.4.5 (A:3-88) Eukaryotic initiation factor 2al	7e-09
d1kl9a2		86	b.40.4.5 (A:3-88) Eukaryotic initiation factor 2al	4e-07
d1kl9a2		86	b.40.4.5 (A:3-88) Eukaryotic initiation factor 2al	2e-06
d1kl9a2		86	b.40.4.5 (A:3-88) Eukaryotic initiation factor 2al	1e-05
d2ba0a1		83	b.40.4.5 (A:53-135) S1-domain of exosome complex R	5e-08
d2ba0a1		83	b.40.4.5 (A:53-135) S1-domain of exosome complex R	2e-05
d2ba0a1		83	b.40.4.5 (A:53-135) S1-domain of exosome complex R	3e-04
d2z0sa1		88	b.40.4.5 (A:60-147) S1-domain of exosome complex R	6e-08
d2z0sa1		88	b.40.4.5 (A:60-147) S1-domain of exosome complex R	1e-04
d2ahob2		84	b.40.4.5 (B:1-84) Eukaryotic initiation factor 2al	1e-07
d2ahob2		84	b.40.4.5 (B:1-84) Eukaryotic initiation factor 2al	4e-07
d2ahob2		84	b.40.4.5 (B:1-84) Eukaryotic initiation factor 2al	5e-07
d2ahob2		84	b.40.4.5 (B:1-84) Eukaryotic initiation factor 2al	4e-06
d1e3pa2		62	b.40.4.5 (A:656-717) S1 RNA-binding domain of poly	2e-07
d1e3pa2		62	b.40.4.5 (A:656-717) S1 RNA-binding domain of poly	7e-07
d2je6i1		87	b.40.4.5 (I:66-152) S1-domain of exosome complex R	3e-07
d2je6i1		87	b.40.4.5 (I:66-152) S1-domain of exosome complex R	1e-04
d2ix0a3		87	b.40.4.5 (A:558-644) Exoribonuclease 2, RNB {Esche	9e-04
d1y14b1		91	b.40.4.5 (B:81-171) C-terminal domain of RNA polym	0.001

>d1sroa_ b.40.4.5 (A:) S1 RNA-binding domain of polyribonucleotide phosphorylase, PNPase {Escherichia coli [TaxId: 562]} Length = 76	Back information, alignment and structure


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 = 66.7 bits (163), Expect = 2e-14
 Identities = 21/75 (28%), Positives = 40/75 (53%), Gaps = 1/75 (1%)

Query: 494 SDVKPGMVVKGKVIAVDSFGAIVQFPGGVKALCPLPHMSEFEIVKPGKKFKVGAELVFRV 553
           ++++ G V  GKV  +  FGA V   GG + L  +  +++  + K     ++G E+  +V
Sbjct: 1   AEIEVGRVYTGKVTRIVDFGAFVAIGGGKEGLVHISQIADKRVEKVTDYLQMGQEVPVKV 60

Query: 554 LGV-KSKRITVTHKK 567
           L V +  RI ++ K+
Sbjct: 61  LEVDRQGRIRLSIKE 75

PyMOL of d1sroa_

>d1sroa_ b.40.4.5 (A:) S1 RNA-binding domain of polyribonucleotide phosphorylase, PNPase {Escherichia coli [TaxId: 562]} Length = 76	Back information, alignment and structure

>d1sroa_ b.40.4.5 (A:) S1 RNA-binding domain of polyribonucleotide phosphorylase, PNPase {Escherichia coli [TaxId: 562]} Length = 76	Back information, alignment and structure

>d1sroa_ b.40.4.5 (A:) S1 RNA-binding domain of polyribonucleotide phosphorylase, PNPase {Escherichia coli [TaxId: 562]} Length = 76	Back information, alignment and structure

>d1sroa_ b.40.4.5 (A:) S1 RNA-binding domain of polyribonucleotide phosphorylase, PNPase {Escherichia coli [TaxId: 562]} Length = 76	Back information, alignment and structure

>d3bzka4 b.40.4.5 (A:637-730) Tex S1-domain {Pseudomonas aeruginosa [TaxId: 287]} Length = 94	Back information, alignment and structure

>d3bzka4 b.40.4.5 (A:637-730) Tex S1-domain {Pseudomonas aeruginosa [TaxId: 287]} Length = 94	Back information, alignment and structure

>d3bzka4 b.40.4.5 (A:637-730) Tex S1-domain {Pseudomonas aeruginosa [TaxId: 287]} Length = 94	Back information, alignment and structure

>d3bzka4 b.40.4.5 (A:637-730) Tex S1-domain {Pseudomonas aeruginosa [TaxId: 287]} Length = 94	Back information, alignment and structure

>d3bzka4 b.40.4.5 (A:637-730) Tex S1-domain {Pseudomonas aeruginosa [TaxId: 287]} Length = 94	Back information, alignment and structure

>d3bzka4 b.40.4.5 (A:637-730) Tex S1-domain {Pseudomonas aeruginosa [TaxId: 287]} Length = 94	Back information, alignment and structure

>d1wi5a_ b.40.4.5 (A:) S1-domain of RRP5 protein homolog (PDCD11, KIAA0185) {Human (Homo sapiens) [TaxId: 9606]} Length = 119	Back information, alignment and structure

>d1wi5a_ b.40.4.5 (A:) S1-domain of RRP5 protein homolog (PDCD11, KIAA0185) {Human (Homo sapiens) [TaxId: 9606]} Length = 119	Back information, alignment and structure

>d1wi5a_ b.40.4.5 (A:) S1-domain of RRP5 protein homolog (PDCD11, KIAA0185) {Human (Homo sapiens) [TaxId: 9606]} Length = 119	Back information, alignment and structure

>d1wi5a_ b.40.4.5 (A:) S1-domain of RRP5 protein homolog (PDCD11, KIAA0185) {Human (Homo sapiens) [TaxId: 9606]} Length = 119	Back information, alignment and structure

>d1kl9a2 b.40.4.5 (A:3-88) Eukaryotic initiation factor 2alpha, eIF2alpha, N-terminal domain {Human (Homo sapiens) [TaxId: 9606]} Length = 86	Back information, alignment and structure

>d1kl9a2 b.40.4.5 (A:3-88) Eukaryotic initiation factor 2alpha, eIF2alpha, N-terminal domain {Human (Homo sapiens) [TaxId: 9606]} Length = 86	Back information, alignment and structure

>d1kl9a2 b.40.4.5 (A:3-88) Eukaryotic initiation factor 2alpha, eIF2alpha, N-terminal domain {Human (Homo sapiens) [TaxId: 9606]} Length = 86	Back information, alignment and structure

>d1kl9a2 b.40.4.5 (A:3-88) Eukaryotic initiation factor 2alpha, eIF2alpha, N-terminal domain {Human (Homo sapiens) [TaxId: 9606]} Length = 86	Back information, alignment and structure

>d2ba0a1 b.40.4.5 (A:53-135) S1-domain of exosome complex RNA-binding protein 1, ECR1 {Archaeoglobus fulgidus [TaxId: 2234]} Length = 83	Back information, alignment and structure

>d2ba0a1 b.40.4.5 (A:53-135) S1-domain of exosome complex RNA-binding protein 1, ECR1 {Archaeoglobus fulgidus [TaxId: 2234]} Length = 83	Back information, alignment and structure

>d2ba0a1 b.40.4.5 (A:53-135) S1-domain of exosome complex RNA-binding protein 1, ECR1 {Archaeoglobus fulgidus [TaxId: 2234]} Length = 83	Back information, alignment and structure

>d2z0sa1 b.40.4.5 (A:60-147) S1-domain of exosome complex RNA-binding protein 1, ECR1 {Aeropyrum pernix [TaxId: 56636]} Length = 88	Back information, alignment and structure

>d2z0sa1 b.40.4.5 (A:60-147) S1-domain of exosome complex RNA-binding protein 1, ECR1 {Aeropyrum pernix [TaxId: 56636]} Length = 88	Back information, alignment and structure

>d2ahob2 b.40.4.5 (B:1-84) Eukaryotic initiation factor 2alpha, eIF2alpha, N-terminal domain {Sulfolobus solfataricus [TaxId: 2287]} Length = 84	Back information, alignment and structure

>d2ahob2 b.40.4.5 (B:1-84) Eukaryotic initiation factor 2alpha, eIF2alpha, N-terminal domain {Sulfolobus solfataricus [TaxId: 2287]} Length = 84	Back information, alignment and structure

>d2ahob2 b.40.4.5 (B:1-84) Eukaryotic initiation factor 2alpha, eIF2alpha, N-terminal domain {Sulfolobus solfataricus [TaxId: 2287]} Length = 84	Back information, alignment and structure

>d2ahob2 b.40.4.5 (B:1-84) Eukaryotic initiation factor 2alpha, eIF2alpha, N-terminal domain {Sulfolobus solfataricus [TaxId: 2287]} Length = 84	Back information, alignment and structure

>d1e3pa2 b.40.4.5 (A:656-717) S1 RNA-binding domain of polyribonucleotide phosphorylase, PNPase {Streptomyces antibioticus [TaxId: 1890]} Length = 62	Back information, alignment and structure

>d1e3pa2 b.40.4.5 (A:656-717) S1 RNA-binding domain of polyribonucleotide phosphorylase, PNPase {Streptomyces antibioticus [TaxId: 1890]} Length = 62	Back information, alignment and structure

>d2je6i1 b.40.4.5 (I:66-152) S1-domain of exosome complex RNA-binding protein 1, ECR1 {Sulfolobus solfataricus [TaxId: 2287]} Length = 87	Back information, alignment and structure

>d2je6i1 b.40.4.5 (I:66-152) S1-domain of exosome complex RNA-binding protein 1, ECR1 {Sulfolobus solfataricus [TaxId: 2287]} Length = 87	Back information, alignment and structure

>d2ix0a3 b.40.4.5 (A:558-644) Exoribonuclease 2, RNB {Escherichia coli [TaxId: 562]} Length = 87	Back information, alignment and structure

>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	Back information, alignment and structure

Homologous Domains Detected by HHsearch

Original result of HHsearch against SCOP70(version1.75) database

ID	Alignment Graph	Length	Definition	Probability
Query		1152
d1sroa_		76	S1 RNA-binding domain of polyribonucleotide phosph	99.58
d3bzka4		94	Tex S1-domain {Pseudomonas aeruginosa [TaxId: 287]	99.54
d3bzka4		94	Tex S1-domain {Pseudomonas aeruginosa [TaxId: 287]	99.5
d1kl9a2		86	Eukaryotic initiation factor 2alpha, eIF2alpha, N-	99.49
d1sroa_		76	S1 RNA-binding domain of polyribonucleotide phosph	99.49
d1wi5a_		119	S1-domain of RRP5 protein homolog (PDCD11, KIAA018	99.48
d2ahob2		84	Eukaryotic initiation factor 2alpha, eIF2alpha, N-	99.45
d1kl9a2		86	Eukaryotic initiation factor 2alpha, eIF2alpha, N-	99.42
d2ahob2		84	Eukaryotic initiation factor 2alpha, eIF2alpha, N-	99.38
d1wi5a_		119	S1-domain of RRP5 protein homolog (PDCD11, KIAA018	99.33
d2ba0a1		83	S1-domain of exosome complex RNA-binding protein 1	99.3
d2ba0a1		83	S1-domain of exosome complex RNA-binding protein 1	99.21
d1go3e1		106	C-terminal domain of RNA polymerase II subunit RBP	99.21
d2je6i1		87	S1-domain of exosome complex RNA-binding protein 1	99.17
d2z0sa1		88	S1-domain of exosome complex RNA-binding protein 1	99.15
d2z0sa1		88	S1-domain of exosome complex RNA-binding protein 1	99.1
d2je6i1		87	S1-domain of exosome complex RNA-binding protein 1	99.09
d1go3e1		106	C-terminal domain of RNA polymerase II subunit RBP	99.04
d1e3pa2		62	S1 RNA-binding domain of polyribonucleotide phosph	99.03
d1e3pa2		62	S1 RNA-binding domain of polyribonucleotide phosph	98.97
d2ix0a3		87	Exoribonuclease 2, RNB {Escherichia coli [TaxId: 5	98.67
d2nn6h1		95	S1-domain of Ribosomal RNA-processing protein 4, R	98.66
d2ix0a3		87	Exoribonuclease 2, RNB {Escherichia coli [TaxId: 5	98.64
d1y14b1		91	C-terminal domain of RNA polymerase II subunit RBP	98.54
d2nn6h1		95	S1-domain of Ribosomal RNA-processing protein 4, R	98.54
d1y14b1		91	C-terminal domain of RNA polymerase II subunit RBP	98.49
d2c35b1		94	C-terminal domain of RNA polymerase II subunit RBP	98.39
d2c35b1		94	C-terminal domain of RNA polymerase II subunit RBP	98.3
d1hh2p1		72	S1 domain of NusA {Thermotoga maritima [TaxId: 233	98.09
d2nn6g1		88	S1-domain of exosome component 3 (RRP40) {Human (H	98.05
d2nn6g1		88	S1-domain of exosome component 3 (RRP40) {Human (H	98.01
d1hh2p1		72	S1 domain of NusA {Thermotoga maritima [TaxId: 233	97.94
d2ja9a1		90	S1-domain of exosome component 3 (RRP40) {Saccharo	97.83
d2ja9a1		90	S1-domain of exosome component 3 (RRP40) {Saccharo	97.82
d2asba1		76	S1 domain of NusA {Mycobacterium tuberculosis [Tax	97.61
d2nn6i1		125	Exosome component 1, EXOSC1 {Human (Homo sapiens)	97.35
d2asba1		76	S1 domain of NusA {Mycobacterium tuberculosis [Tax	97.2
d2nn6i1		125	Exosome component 1, EXOSC1 {Human (Homo sapiens)	97.06
d1smxa_		87	S1-domain of Ribonuclease E {Escherichia coli [Tax	95.19
d1smxa_		87	S1-domain of Ribonuclease E {Escherichia coli [Tax	94.11

>d1sroa_ b.40.4.5 (A:) S1 RNA-binding domain of polyribonucleotide phosphorylase, PNPase {Escherichia coli [TaxId: 562]}	Back information, alignment and structure

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=99.58  E-value=8.8e-16  Score=133.43  Aligned_cols=76  Identities=30%  Similarity=0.480  Sum_probs=72.0

Q ss_pred             ccCCCCCEEEEEEEEEecceEEEEECCCeEEEEeccCCCCccccCccccccCCCEEEEEEEEEeCCCCeEEEEeecc
Q 001115          757 SHIHPNSVVHGYVCNIIETGCFVRFLGRLTGFAPRSKAVDGQRADLSKTYYVGQSVRSNILDVNSETGRITLSLKQS  833 (1152)
Q Consensus       757 ~~~~~G~~v~G~V~~i~~~GvfV~~~~~l~Glv~~s~ls~~~~~~~~~~f~~Gq~V~v~Vl~vd~e~~ri~LSlk~~  833 (1152)
                      +++++|+++.|+|.++++||+||+|.++++||+|.++++|.+..+|++.|++||.|.|+|+++|+ ++|+.||||++
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 AEIEVGRVYTGKVTRIVDFGAFVAIGGGKEGLVHISQIADKRVEKVTDYLQMGQEVPVKVLEVDR-QGRIRLSIKEA   76 (76)
T ss_dssp             CCCCTTSEEEEEEEEEETTEEEEECSSSCCCBCCTTSSCSSCCSCHHHHCCTTCEEEEEEEECCT-TCCCEEEECCC
T ss_pred             CCCCCCCEEEEEEEEEeCcEEEEEeCCCCEEEEEhHHhCccccCCHHHccCCCCEEEEEEEEECC-CCCEEEEEEcC
Confidence            36899999999999999999999999999999999999999999999999999999999999996 57999999974

PyMOL of d1sroa_

>d3bzka4 b.40.4.5 (A:637-730) Tex S1-domain {Pseudomonas aeruginosa [TaxId: 287]}	Back information, alignment and structure

>d3bzka4 b.40.4.5 (A:637-730) Tex S1-domain {Pseudomonas aeruginosa [TaxId: 287]}	Back information, alignment and structure

>d1kl9a2 b.40.4.5 (A:3-88) Eukaryotic initiation factor 2alpha, eIF2alpha, N-terminal domain {Human (Homo sapiens) [TaxId: 9606]}	Back information, alignment and structure

>d1sroa_ b.40.4.5 (A:) S1 RNA-binding domain of polyribonucleotide phosphorylase, PNPase {Escherichia coli [TaxId: 562]}	Back information, alignment and structure

>d1wi5a_ b.40.4.5 (A:) S1-domain of RRP5 protein homolog (PDCD11, KIAA0185) {Human (Homo sapiens) [TaxId: 9606]}	Back information, alignment and structure

>d2ahob2 b.40.4.5 (B:1-84) Eukaryotic initiation factor 2alpha, eIF2alpha, N-terminal domain {Sulfolobus solfataricus [TaxId: 2287]}	Back information, alignment and structure

>d1kl9a2 b.40.4.5 (A:3-88) Eukaryotic initiation factor 2alpha, eIF2alpha, N-terminal domain {Human (Homo sapiens) [TaxId: 9606]}	Back information, alignment and structure

>d2ahob2 b.40.4.5 (B:1-84) Eukaryotic initiation factor 2alpha, eIF2alpha, N-terminal domain {Sulfolobus solfataricus [TaxId: 2287]}	Back information, alignment and structure

>d1wi5a_ b.40.4.5 (A:) S1-domain of RRP5 protein homolog (PDCD11, KIAA0185) {Human (Homo sapiens) [TaxId: 9606]}	Back information, alignment and structure

>d2ba0a1 b.40.4.5 (A:53-135) S1-domain of exosome complex RNA-binding protein 1, ECR1 {Archaeoglobus fulgidus [TaxId: 2234]}	Back information, alignment and structure

>d2ba0a1 b.40.4.5 (A:53-135) S1-domain of exosome complex RNA-binding protein 1, ECR1 {Archaeoglobus fulgidus [TaxId: 2234]}	Back information, alignment and structure

>d1go3e1 b.40.4.5 (E:79-184) C-terminal domain of RNA polymerase II subunit RBP7 (RpoE) {Archaeon Methanococcus jannaschii [TaxId: 2190]}	Back information, alignment and structure

>d2je6i1 b.40.4.5 (I:66-152) S1-domain of exosome complex RNA-binding protein 1, ECR1 {Sulfolobus solfataricus [TaxId: 2287]}	Back information, alignment and structure

>d2z0sa1 b.40.4.5 (A:60-147) S1-domain of exosome complex RNA-binding protein 1, ECR1 {Aeropyrum pernix [TaxId: 56636]}	Back information, alignment and structure

>d2z0sa1 b.40.4.5 (A:60-147) S1-domain of exosome complex RNA-binding protein 1, ECR1 {Aeropyrum pernix [TaxId: 56636]}	Back information, alignment and structure

>d2je6i1 b.40.4.5 (I:66-152) S1-domain of exosome complex RNA-binding protein 1, ECR1 {Sulfolobus solfataricus [TaxId: 2287]}	Back information, alignment and structure

>d1go3e1 b.40.4.5 (E:79-184) C-terminal domain of RNA polymerase II subunit RBP7 (RpoE) {Archaeon Methanococcus jannaschii [TaxId: 2190]}	Back information, alignment and structure

>d1e3pa2 b.40.4.5 (A:656-717) S1 RNA-binding domain of polyribonucleotide phosphorylase, PNPase {Streptomyces antibioticus [TaxId: 1890]}	Back information, alignment and structure

>d1e3pa2 b.40.4.5 (A:656-717) S1 RNA-binding domain of polyribonucleotide phosphorylase, PNPase {Streptomyces antibioticus [TaxId: 1890]}	Back information, alignment and structure

>d2ix0a3 b.40.4.5 (A:558-644) Exoribonuclease 2, RNB {Escherichia coli [TaxId: 562]}	Back information, alignment and structure

>d2nn6h1 b.40.4.5 (H:73-167) S1-domain of Ribosomal RNA-processing protein 4, RRP4 {Human (Homo sapiens) [TaxId: 9606]}	Back information, alignment and structure

>d2ix0a3 b.40.4.5 (A:558-644) Exoribonuclease 2, RNB {Escherichia coli [TaxId: 562]}	Back information, alignment and structure

>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]}	Back information, alignment and structure

>d2nn6h1 b.40.4.5 (H:73-167) S1-domain of Ribosomal RNA-processing protein 4, RRP4 {Human (Homo sapiens) [TaxId: 9606]}	Back information, alignment and structure

>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]}	Back information, alignment and structure

>d2c35b1 b.40.4.5 (B:78-171) C-terminal domain of RNA polymerase II subunit RBP7 (RpoE) {Human (Homo sapiens) [TaxId: 9606]}	Back information, alignment and structure

>d2c35b1 b.40.4.5 (B:78-171) C-terminal domain of RNA polymerase II subunit RBP7 (RpoE) {Human (Homo sapiens) [TaxId: 9606]}	Back information, alignment and structure

>d1hh2p1 b.40.4.5 (P:127-198) S1 domain of NusA {Thermotoga maritima [TaxId: 2336]}	Back information, alignment and structure

>d2nn6g1 b.40.4.5 (G:107-194) S1-domain of exosome component 3 (RRP40) {Human (Homo sapiens) [TaxId: 9606]}	Back information, alignment and structure

>d2nn6g1 b.40.4.5 (G:107-194) S1-domain of exosome component 3 (RRP40) {Human (Homo sapiens) [TaxId: 9606]}	Back information, alignment and structure

>d1hh2p1 b.40.4.5 (P:127-198) S1 domain of NusA {Thermotoga maritima [TaxId: 2336]}	Back information, alignment and structure

>d2ja9a1 b.40.4.5 (A:62-151) S1-domain of exosome component 3 (RRP40) {Saccharomyces cerevisiae [TaxId: 4932]}	Back information, alignment and structure

>d2ja9a1 b.40.4.5 (A:62-151) S1-domain of exosome component 3 (RRP40) {Saccharomyces cerevisiae [TaxId: 4932]}	Back information, alignment and structure

>d2asba1 b.40.4.5 (A:108-183) S1 domain of NusA {Mycobacterium tuberculosis [TaxId: 1773]}	Back information, alignment and structure

>d2nn6i1 b.40.4.5 (I:61-185) Exosome component 1, EXOSC1 {Human (Homo sapiens) [TaxId: 9606]}	Back information, alignment and structure

>d2asba1 b.40.4.5 (A:108-183) S1 domain of NusA {Mycobacterium tuberculosis [TaxId: 1773]}	Back information, alignment and structure

>d2nn6i1 b.40.4.5 (I:61-185) Exosome component 1, EXOSC1 {Human (Homo sapiens) [TaxId: 9606]}	Back information, alignment and structure

>d1smxa_ b.40.4.5 (A:) S1-domain of Ribonuclease E {Escherichia coli [TaxId: 562]}	Back information, alignment and structure

>d1smxa_ b.40.4.5 (A:) S1-domain of Ribonuclease E {Escherichia coli [TaxId: 562]}	Back information, alignment and structure