Citrus Sinensis ID: 002487

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------

MLATSPGGLHIRPCYPHSSHFSLSARCKLSLSSNCPRFSTSQKSSKFRSLSLLLSRRKYSERFSVRASATGPEVSEPVLSDALPSFPQPVSVKIPFGDRQILVETGHMGRQASGAVTVTDGETIIYTSVCLADVPSEPSDFFPLNVNYQERFSAAGRTSGGFFKREGRTKDHEVLVCRLIDRPLRPTLIKGFYHETQILSWVLSYDGLHFPDALAVTAAGIAVALSEVPNSKVIAGVRVGLVGDKFIVNPTTQEMEDSQLDLLLAGSDDAILMIEGYCDFLSEEMLIQAVQVGQDAVREISNEVKALVEMCGKPKMLDTIKLPPPELYKHVEEIAGEELVKVLQIKNKIPRRKALSSLEEKVLTILSENGYVSKDETVGIVETIPDLLEDEDEDEEVVVDGEVDEGDVHIKPKSRKSTPMLFSEVDVKLVFKEVTSKFLRRRIVEGGRRSDGRFADGIRPISSRCGLLPRAHGSALFTRGETQSLAVITLGDKQMAQRIDNLESDDEVKRFYLQYSFPPSSVGEVGRIGAPSRREIGHGTLAERALEPVLPSDNDFPYTIRVESTITESNGSSSMASVCGGCLALQDAGVPIKCSIAGVAMGMVLDTDEFGGDGTPLILSDITGSEDASGDMDFKVAGNEDGITAFQMDIKVGGITLPVMKKALQQAKDGRRHILAEMLKCSPPPSNSLSKHAPLIHIMKVKPEKINLIIGSGGKKVKSIIEETGVEAIDTEDDGTVKITAKDLSSLEKSKAIISNLTMVPTVGDIYRNCEIKSIAPYGVFVEIAPGREGLCHISELSSNWLAKAEDVVKVGDLVDVKLIEVNDKGQLRLSRRALLPEADAENPPVKLPTGDPTKDAAASDKLVGSPKPKGSSSEDTVLPHKKVKVFKRPASPAKDRPYSNKDRTKKSSGKAVSSQ

cccccccccccccccccccccccccccccccccccccccccccccccccccHHHHHHccccccccccccccccccccccccccccccccEEEEEEEccEEEEEEccccccccccEEEEEEccEEEEEEEEEcccccccccccccEEccccccccccccccccccccccccccHHHHHHcccccccccccccccccEEEEEEEEEEcccccHHHHHHHHHHHHHHccccccccccEEEEEEEEccEEEEcccHHHHHcccEEEEEEEcccEEEEEEcccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHcccccccccccccHHHHHHHHHHHHHHHHHHHHccccHHHHHHHHHHHHHHHHHHHHcccccccccccccccccccccccccHHHHHcccccccccccccccccccccccccHHHHHHHHHHHHHHHHHHHHHcccccccccccccccccEEEccccccccccccccccccEEEEEEccccccccHHccccccccccccEEEEcccccccccccccccccccccccccHHHHHHcccccccccccccEEEEEEEcccccccHHHHHHHHHHHHHHHccccccccHHHHHccccccccccccccccEEEEccccccccccccccccccccccHHHHHHHcccccccHHHHHHHHHHHHHHHHHHHHHHHHHcccccccccccccEEEEEEEcccccccccccccHHHHHHHHHHcccEEccccccEEEEEEccHHHHHHHHHHHHHHHcccccccEEEccEEEEEEccEEEEEEccccccEEEEEccccccccccccccccccEEEEEEEEEcccccEEEEEcccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccc

ccccccccccccccccccccHHHHHHcHHHcccccccccEEEccccccHHHHHccccccccHHHHHHHccccHHcHHHHHcccccccccEEEEEEEcccEEEEEccHHEEccccEEEEEcccEEEEEEEEEccccccccccccEEEEEEEEHHHccccccccEEccccccHHHHHHHHHccccccccccccccccEEEEEEEEEccccccHHHHHHHHHHHHHHHccccccccEEEEEEEEEccEEEEcccHHHHHcccccEEEEccHHHHHHHHHHHHHccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHcccccccccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHccccccHHHcccccccHHHHHccccccEEEEcccccccccEEcccccccccccccHHHHHHHHHHHHHHHHHHHHHccccccccccccEEEEEEEEEcccccccccEEEcccccEEEEEEEccccccHHHHHHcccccccccEEEEEcccccccccccccccccccEccHHHHHHHHHHHHcccHHHccEEEEEEEEEEEccccccccHHHHHHHHHHHccccccccEEEEEEEEEEccccccccccEEEEEccccccHccccccEEEEcccccEEEEEEEEEEccccHHHHHHHHHHHHHHHHHHHHHHHHHHHccHHHHHHccccEEEEEEcHHHHHHHccccHHHHHHHHHHHccEEEEEccccEEEEEEccHHHHHHHHHHHHHHHccccEcEEEcccEEEEEEcccHEEEEccccccEEEHHHHHHHHHHHHHHHHccccEEEEEEEEEcccccEEEEHHHHcccccHcccHHccHHcccccccccccccccccccccccccccccccccEEEEEcccccccccccccccccccccccEEEcc

mlatspgglhirpcyphsshfslsarcklslssncprfstsqksskfRSLSLLLSRRKYSerfsvrasatgpevsepvlsdalpsfpqpvsvkipfgdrqilvetghmgrqasgavtvtdgETIIYTSVcladvpsepsdffplnvnYQERFsaagrtsggffkregrtkdhEVLVCRLidrplrptlikgfyhETQILSWVLsydglhfpdALAVTAAGIAVAlsevpnskviAGVRVGlvgdkfivnpttqemEDSQLDLLLAGSDDAILMIEGYCDFLSEEMLIQAVQVGQDAVREISNEVKALVEMcgkpkmldtiklpppelykHVEEIAGEELVKVLQIKNKIPRRKALSSLEEKVLTILSengyvskdetVGIVetipdlledededeevvvdgevdegdvhikpksrkstpmlfsEVDVKLVFKEVTSKFLRRRIVeggrrsdgrfadgirpissrcgllprahgsalftrgetQSLAVITLGDKQMAQRIDNLESDDEVKRFYLqysfppssvgevgrigapsrreighgtlaeralepvlpsdndfpytIRVESTitesngsssmasvCGGCLalqdagvpikcSIAGVAMGmvldtdefggdgtplilsditgsedasgdmdfkvagnedgiTAFQMDIKVGGITLPVMKKALQQAKDGRRHILAEMlkcspppsnslskhaplihimkvkpeKINLIIGSGGKKVKSIIEETgveaidteddgtvkITAKDLSSLEKSKAIISNltmvptvgdiyrnceiksiapygvfveiapgreglchISELSSNWLAKAEDVVKVGDLVDVklievndkgqlrlsrrallpeadaenppvklptgdptkdaaasdklvgspkpkgsssedtvlphkkvkvfkrpaspakdrpysnkdrtkkssgkavssq

mlatspgglhirpcyPHSSHFSLSARCKLSLSSNCPrfstsqksskfrslsLLLSRRKYSErfsvrasatgpevsepvlsDALPSFPQPVSVKIPFGDRQILVETGHMGRQASGAVTVTDGETIIYTSVCLADVPSEPSDFFPLNVNYQERFSaagrtsggffkregrtkdhevlvCRLIDRPLRPTLIKGFYHETQILSWVLSYDGLHFPDALAVTAAGIAVALSEVPNSKVIAGVRVGLVGDKFIVNPTTQEMEDSQLDLLLAGSDDAILMIEGYCDFLSEEMLIQAVQVGQDAVREISNEVKALVEMCGKPKMLDTIKLPPPELYKHVEEIAGEELvkvlqiknkiprrkalssleEKVLTilsengyvskdetvGIVETipdllededeDEEVVvdgevdegdvhikpksrkstpmlfsevdvklvfkevtskflrrriveggrrsdgrfadgirpissrcglLPRAHGSALFTRGETQSLAVITLGDKQMAQRIDNLESDDEVKRFYLqysfppssvgevgrIGAPSRREIGHgtlaeralepvlpsdndfpYTIRVESTITESNGSSSMASVCGGCLALQDAGVPIKCSIAGVAMGMVLDTDEFGGDGTPLILSDITGSEDASGDMDFKVAGNEDGITAFQMDIKVGGITLPVMKKALQQAKDGRRHILAEMLkcspppsnsLSKHAPLIHIMKVKPEKINLIIGSGGKKVKSIIEETgveaidteddgtvkitakdlsslekskaiisnltmvptVGDIYRNCEIKSIAPYGVFVEIAPGREGLCHISELSSNWLAKAEDVVKVGDLVDVklievndkgqlrlsrrallpeadaenppvklptgdptkdaaasdklvgspkpkgsssedtvlphkkvkvfkrpaspakdrpysnkdrtkkssgkavssq

MLATSPGGLHIRPCYPHSSHFSLSARCKLSLSSNCPrfstsqksskfrslslllsrrkysERFSVRASATGPEVSEPVLSDALPSFPQPVSVKIPFGDRQILVETGHMGRQASGAVTVTDGETIIYTSVCLADVPSEPSDFFPLNVNYQERFSAAGRTSGGFFKREGRTKDHEVLVCRLIDRPLRPTLIKGFYHETQILSWVLSYDGLHFPDalavtaagiavalSEVPNSKVIAGVRVGLVGDKFIVNPTTQEMEDSQLDLLLAGSDDAILMIEGYCDFLSEEMLIQAVQVGQDAVREISNEVKALVEMCGKPKMLDTIKLPPPELYKHVEEIAGEELVKVLQIKNKIPRRKALSSLEEKVLTILSENGYVSKDETVGIVETIPdlledededeevvvdgevdegdvHIKPKSRKSTPMLFSEVDVKLVFKEVTSKFLRRRIVEGGRRSDGRFADGIRPISSRCGLLPRAHGSALFTRGETQSLAVITLGDKQMAQRIDNLESDDEVKRFYLQYSFPPSSVGEVGRIGAPSRREIGHGTLAERALEPVLPSDNDFPYTIRVESTITESNGSSSMASVCGGCLALQDAGVPIKCSIAGVAMGMVLDTDEFGGDGTPLILSDITGSEDASGDMDFKVAGNEDGITAFQMDIKVGGITLPVMKKALQQAKDGRRHILAEMLKCSPPPSNSLSKHAPLIHIMKVKPEKINLIIGSGGKKVKSIIEETGVEAIDTEDDGTVKITAKDLSSLEKSKAIISNLTMVPTVGDIYRNCEIKSIAPYGVFVEIAPGREGLCHISELSSNWLAKAEdvvkvgdlvdvklIEVNDKGQLRLSRRALLPEADAENPPVKLPTGDPTKDAAASDKLVGSPKPKGSSSEDTVLPHKKVKVFKRPASPAKDRPYSNKDRTKKSSGKAVSSQ

*************CY**************************************************************************VSVKIPFGDRQILVETGHMGRQASGAVTVTDGETIIYTSVCLADVPSEPSDFFPLNVNYQERFSAAGRTSGGFFKREGRTKDHEVLVCRLIDRPLRPTLIKGFYHETQILSWVLSYDGLHFPDALAVTAAGIAVALSEVPNSKVIAGVRVGLVGDKFIVNPTTQEMEDSQLDLLLAGSDDAILMIEGYCDFLSEEMLIQAVQVGQDAVREISNEVKALVEMCGKPKMLDTIKLPPPELYKHVEEIAGEELVKVLQIKNKIPRRKALSSLEEKVLTILSENGYVSKDETVGIVETI************************************LFSEVDVKLVFKEVTSKFLRRRIVEGGRRSDGRFADGIRPISSRCGLLPRAHGSALFTRGETQSLAVITLGDKQMAQRID*****DEVKRFYLQYSFP************************************DFPYTIRVE************ASVCGGCLALQDAGVPIKCSIAGVAMGMVLDTDEFGGDGTPLILSDIT*********DFKVAGNEDGITAFQMDIKVGGITLPVMKKALQ*******HILA*****************PLIHIMKVKPEKINLIIGSGGKKVKSIIEETGVEAIDTEDDGTVKITAKDLSSLEKSKAIISNLTMVPTVGDIYRNCEIKSIAPYGVFVEIAPGREGLCHISELSSNWLAKAEDVVKVGDLVDVKLIEVNDKGQL****************************************************************************************

**************************************************************************************PQPVSVKIPFGDRQILVETGHMGRQASGAVTVTDGETIIYTSVCLADVPSEPSDFFPLNVNYQERFSAAGRTSGGFFKREGRTKDHEVLVCRLIDRPLRPTLIKGFYHETQILSWVLSYDGLHFPDALAVTAAGIAVALSEVPNSKVIAGVRVGLVGDKFIVNPTTQEMEDSQLDLLLAGSDDAILMIEGYCDFLSEEMLIQAVQVGQDAVREISNEVKALVEMCGKPKMLDTIKLPPPELYKHVEEIAGEELVKVLQIKNKIPRRKALSSLEEKVLTILSENGYVSKDETVGIVETIPDLLEDEDEDEEVVVDGEVDEGDVHIKPKSRKSTPMLFSEVDVKLVFKEVTSKFLRRRIVEGGRRSDGRFADGIRPISSRCGLLPRAHGSALFTRGETQSLAVITLGDKQMAQRIDNLESDDEVKRFYLQYSFPPSSVGEVGRIGAPSRREIGHGTLAERALEPVLPSDNDFPYTIRVESTITESNGSSSMASVCGGCLALQDAGVPIKCSIAGVAMGMVLDTDEFGGDGTPLILSDITGSEDASGDMDFKVAGNEDGITAFQMDIKVGGITLPVMKKALQQAKDGRRHILAEMLKCSPPPSNSLSKHAPLIHIMKVKPEKINLIIGSGGKKVKSIIEETGVEAIDTEDDGTVKITAKDLSSLEKSKAIISNLTMVPTVGDIYRNCEIKSIAPYGVFVEIAPGREGLCHISELSSNWLAKAEDVVKVGDLVDVKLIEVNDKGQLRLS*************************************************************************************

MLATSPGGLHIRPCYPHSSHFSLSARCKLSLSS**************RSLSLLLSRRKYSERFSVRASATGPEVSEPVLSDALPSFPQPVSVKIPFGDRQILVETGHMGRQASGAVTVTDGETIIYTSVCLADVPSEPSDFFPLNVNYQERFSAAGRTSGGFFKREGRTKDHEVLVCRLIDRPLRPTLIKGFYHETQILSWVLSYDGLHFPDALAVTAAGIAVALSEVPNSKVIAGVRVGLVGDKFIVNPTTQEMEDSQLDLLLAGSDDAILMIEGYCDFLSEEMLIQAVQVGQDAVREISNEVKALVEMCGKPKMLDTIKLPPPELYKHVEEIAGEELVKVLQIKNKIPRRKALSSLEEKVLTILSENGYVSKDETVGIVETIPDLLEDEDEDEEVVVDGEVDEGDVHIKPKSRKSTPMLFSEVDVKLVFKEVTSKFLRRRIVEGGRRSDGRFADGIRPISSRCGLLPRAHGSALFTRGETQSLAVITLGDKQMAQRIDNLESDDEVKRFYLQYSFPPSSVGEVGRIGAPSRREIGHGTLAERALEPVLPSDNDFPYTIRVESTITE********SVCGGCLALQDAGVPIKCSIAGVAMGMVLDTDEFGGDGTPLILSDITGSEDASGDMDFKVAGNEDGITAFQMDIKVGGITLPVMKKALQQAKDGRRHILAEMLKCSPPPSNSLSKHAPLIHIMKVKPEKINLIIGSGGKKVKSIIEETGVEAIDTEDDGTVKITAKDLSSLEKSKAIISNLTMVPTVGDIYRNCEIKSIAPYGVFVEIAPGREGLCHISELSSNWLAKAEDVVKVGDLVDVKLIEVNDKGQLRLSRRALLPEADAENPPVKLPTG**************************VLPHKKVKVFKRPA*************************

***TSPGGLHIRPCYPHSSHFSLSARCKLSLSSNCPRFSTSQKSSKFRSLSLLLSR*******S*********VSEPVLSDALPSFPQPVSVKIPFGDRQILVETGHMGRQASGAVTVTDGETIIYTSVCLADVPSEPSDFFPLNVNYQERFSAAGRTSGGFFKREGRTKDHEVLVCRLIDRPLRPTLIKGFYHETQILSWVLSYDGLHFPDALAVTAAGIAVALSEVPNSKVIAGVRVGLVGDKFIVNPTTQEMEDSQLDLLLAGSDDAILMIEGYCDFLSEEMLIQAVQVGQDAVREISNEVKALVEMCGKPKMLDTIKLPPPELYKHVEEIAGEELVKVLQIKNKIPRRKALSSLEEKVLTILSENGY*SKDETVGIVETIPDLLEDEDEDEEVVVDGEVDEGDVHIKPKSRKSTPMLFSEVDVKLVFKEVTSKFLRRRIVEGGRRSDGRFADGIRPISSRCGLLPRAHGSALFTRGETQSLAVITLGDKQMAQRIDNLESDDEVKRFYLQYSFPPSSVGEVGRIGAPSRREIGHGTLAERALEPVLPSDNDFPYTIRVESTITESNG*SSMASVCGGCLALQDAGVPIKCSIAGVAMGMVLDTDEFGGDGTPLILSDITGSEDASGDMDFKVAGNEDGITAFQMDIKVGGITLPVMKKALQQAKDGRRHILAEMLKCSPPPSNSLSKHAPLIHIMKVKPEKINLIIGSGGKKVKSIIEETGVEAIDTEDDGTVKITAKDLSSLEKSKAIISNLTMVPTVGDIYRNCEIKSIAPYGVFVEIAPGREGLCHISELSSNWLAKAEDVVKVGDLVDVKLIEVNDKGQLRLSRRALLPE*******************************************KKVKV*KR***************************

oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo

iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii

iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhhhhoooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooohhhhhhhhhhhhhhhhhhhhhhhhiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii

SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo

xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx

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		916	2.2.26 [Sep-21-2011]
Q8GZQ3		922	Polyribonucleotide nucleo	yes	no	0.971	0.965	0.718	0.0
Q69LE7		902	Probable polyribonucleoti	yes	no	0.848	0.861	0.762	0.0
Q3KKJ7		695	Polyribonucleotide nucleo	yes	no	0.745	0.982	0.485	0.0
B0BAV0		695	Polyribonucleotide nucleo	yes	no	0.745	0.982	0.487	0.0
B0B971		695	Polyribonucleotide nucleo	yes	no	0.745	0.982	0.487	0.0
O84849		695	Polyribonucleotide nucleo	yes	no	0.745	0.982	0.484	0.0
A8IGA3		724	Polyribonucleotide nucleo	yes	no	0.75	0.948	0.443	1e-168
A0LE14		701	Polyribonucleotide nucleo	yes	no	0.748	0.978	0.427	1e-164
Q13EM2		722	Polyribonucleotide nucleo	yes	no	0.75	0.951	0.432	1e-163
B3QAB0		722	Polyribonucleotide nucleo	yes	no	0.75	0.951	0.431	1e-163

>sp\|Q8GZQ3\|PNP1_ARATH Polyribonucleotide nucleotidyltransferase 1, chloroplastic OS=Arabidopsis thaliana GN=PNP1 PE=1 SV=1	Back alignment and function desciption

 Score = 1247 bits (3227), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 652/907 (71%), Positives = 739/907 (81%), Gaps = 17/907 (1%)

Query: 17  HSS--HFSLSARCKLSLSSNCPRF--STSQKSSKFRSLSLLLSRRKYSERFSVRASATGP 72
           HSS   F    R KL  S N PRF           +  SL L     + +FSVRA     
Sbjct: 10  HSSTPQFWPLRRSKLCRSRNFPRFHSGERSSGGGGKLCSLSLLSGSGAGKFSVRALVRPD 69

Query: 73  EVSEP-VLSDALPSFPQPVSVKIPFGDRQILVETGHMGRQASGAVTVTDGETIIYTSVCL 131
           +  +   + D   +FP  VSVKIPFG+R+ILVETG MGRQAS AVTVTDGETI+YTSVCL
Sbjct: 70  DTDDADSVGDGSLAFPNHVSVKIPFGNREILVETGLMGRQASSAVTVTDGETIVYTSVCL 129

Query: 132 ADVPSEPSDFFPLNVNYQERFSAAGRTSGGFFKREGRTKDHEVLVCRLIDRPLRPTLIKG 191
           ADVPSEPSDF PL V+YQERFSA GRTSGGFFKREGRTKDHEVL+CRLIDRPLRPT+ KG
Sbjct: 130 ADVPSEPSDFLPLYVHYQERFSAVGRTSGGFFKREGRTKDHEVLICRLIDRPLRPTMPKG 189

Query: 192 FYHETQILSWVLSYDGLHFPDALAVTAAGIAVALSEVPNSKVIAGVRVGLVGDKFIVNPT 251
           FY+ETQILSWVLSYDGLH PDALAVT+AGIAVALSEVPN+K IAGVRVGL+G +FIVNPT
Sbjct: 190 FYNETQILSWVLSYDGLHAPDALAVTSAGIAVALSEVPNAKAIAGVRVGLIGGEFIVNPT 249

Query: 252 TQEMEDSQLDLLLAGSDDAILMIEGYCDFLSEEMLIQAVQVGQDAVREISNEVKALVEMC 311
            +EME+SQLDL LAG+D AIL IEGY +FL EEML+QAV+VGQDAV+     ++ L +  
Sbjct: 250 VKEMEESQLDLFLAGTDTAILTIEGYSNFLPEEMLLQAVKVGQDAVQATCIAIEVLAKKY 309

Query: 312 GKPKMLDTIKLPPPELYKHVEEIAGEELVKVLQIKNKIPRRKALSSLEEKVLTILSENGY 371
           GKPKMLD I+LPPPELYKHV+E+AGEEL K LQIK+KI RRKA+SSLEEKVLTIL+E GY
Sbjct: 310 GKPKMLDAIRLPPPELYKHVKELAGEELTKALQIKSKISRRKAISSLEEKVLTILTEKGY 369

Query: 372 VSKDETVGIVETIPDLLEDEDEDEEVVVDGEVDEGDVHIKPKSRKSTPMLFSEVDVKLVF 431
           V  +   G +E  PDLLEDEDEDEEVV +GEVD+GDVHI+P  RK  P+LFSEVDVKLVF
Sbjct: 370 VIDEVAFGTIEAQPDLLEDEDEDEEVVPEGEVDQGDVHIRPIPRKPIPLLFSEVDVKLVF 429

Query: 432 KEVTSKFLRRRIVEGGRRSDGRFADGIRPISSRCGLLPRAHGSALFTRGETQSLAVITLG 491
           KEV+SK LRRRIVEGG+RSDGR  D IRPI+SRCGLLPRAHGS LFTRGETQ+LAV+TLG
Sbjct: 430 KEVSSKLLRRRIVEGGKRSDGRTLDEIRPINSRCGLLPRAHGSTLFTRGETQALAVVTLG 489

Query: 492 DKQMAQRIDNLESDDEVKRFYLQYSFPPSSVGEVGRIGAPSRREIGHGTLAERALEPVLP 551
           DKQMAQRIDNLE  DE KRFYLQY+FPPSSVGEVGRIGAPSRREIGHGTLAERALE +LP
Sbjct: 490 DKQMAQRIDNLEGSDEYKRFYLQYTFPPSSVGEVGRIGAPSRREIGHGTLAERALETILP 549

Query: 552 SDNDFPYTIRVESTITESNGSSSMASVCGGCLALQDAGVPIKCSIAGVAMGMVLDTDEFG 611
           SD+DFPYTIRVEST+ ESNGSSSMASVCGGCLALQDAGVP+KCS+AG+AMGMV DT+EFG
Sbjct: 550 SDDDFPYTIRVESTVIESNGSSSMASVCGGCLALQDAGVPVKCSVAGIAMGMVWDTEEFG 609

Query: 612 GDGTPLILSDITGSEDASGDMDFKVAGNEDGITAFQMDIKVGGITLPVMKKALQQAKDGR 671
           GDG+PLILSDITG+EDASGDMDFKVAGNEDG+TAFQMDIKVGGITL +M+KAL QAK GR
Sbjct: 610 GDGSPLILSDITGAEDASGDMDFKVAGNEDGVTAFQMDIKVGGITLEIMEKALIQAKAGR 669

Query: 672 RHILAEMLKCSPPPSNSLSKHAPLIHIMKVKPEKINLIIGSGGKKVKSIIEETGVEAIDT 731
           RHILAEM KCSPPP+ SLSK+APLI IMKV P K+  +IGSGGKKVKSIIEE+GVEAID 
Sbjct: 670 RHILAEMAKCSPPPTLSLSKYAPLILIMKVHPSKVYSLIGSGGKKVKSIIEESGVEAIDM 729

Query: 732 EDDGTVKITAKDLSSLEKSKAIISNLTMVPTVGDIYRNCEIKSIAPYGVFVEIAPGREGL 791
           +DDGTVKI A D++SLE++KAIIS LTMVP+VGDIYRNCEIKS+APYG FVEIAPGREGL
Sbjct: 730 QDDGTVKIMAIDVASLERAKAIISGLTMVPSVGDIYRNCEIKSMAPYGAFVEIAPGREGL 789

Query: 792 CHISELSSNWLAKAEDVVKVGDLVDVKLIEVNDKGQLRLSRRALLPEADAENPPVK-LPT 850
           CHISELS+ WLAK ED  KVGD +DVKLIEVN+KGQLRLS RALLPE++ +    K  P 
Sbjct: 790 CHISELSAEWLAKPEDAYKVGDRIDVKLIEVNEKGQLRLSVRALLPESETDKDSQKQQPA 849

Query: 851 GDPTKDAAASDKLVGSPK--------PKGSSSEDTVLPHKKVKVFKRPASPAKDRPYSNK 902
           GD TKD ++  K V +           K SS ++ VL  K V   +R    + D+  ++ 
Sbjct: 850 GDSTKDKSSQRKYVNTSSKDRAAAGASKVSSGDELVLKKKDV---RRATGGSSDKTMNSN 906

Query: 903 DRTKKSS 909
             T + S
Sbjct: 907 SSTNEES 913

Involved in the metabolism of all major classes of plastid RNAs. Required for efficient 3'-end processing of mRNAs and 3'-end maturation of rRNA transcripts, but is not sufficient to mediate their degradation. Mediates tRNA degradation. May function as a poly(A) mRNA 3'-5' degrading exonuclease. May be required for plastid ribosome assembly and non-coding RNA biogenesis and accumulation. Seems not required for efficient translation.
Arabidopsis thaliana (taxid: 3702)
EC: 2EC: .EC: 7EC: .EC: 7EC: .EC: 8

>sp\|Q69LE7\|PNP1_ORYSJ Probable polyribonucleotide nucleotidyltransferase 1, chloroplastic OS=Oryza sativa subsp. japonica GN=PNP1 PE=2 SV=1	Back alignment and function description

>sp\|Q3KKJ7\|PNP_CHLTA Polyribonucleotide nucleotidyltransferase OS=Chlamydia trachomatis serovar A (strain HAR-13 / ATCC VR-571B) GN=pnp PE=3 SV=1	Back alignment and function description

>sp\|B0BAV0\|PNP_CHLTB Polyribonucleotide nucleotidyltransferase OS=Chlamydia trachomatis serovar L2b (strain UCH-1/proctitis) GN=pnp PE=3 SV=1	Back alignment and function description

>sp\|B0B971\|PNP_CHLT2 Polyribonucleotide nucleotidyltransferase OS=Chlamydia trachomatis serovar L2 (strain 434/Bu / ATCC VR-902B) GN=pnp PE=3 SV=1	Back alignment and function description

>sp\|O84849\|PNP_CHLTR Polyribonucleotide nucleotidyltransferase OS=Chlamydia trachomatis (strain D/UW-3/Cx) GN=pnp PE=3 SV=1	Back alignment and function description

>sp\|A8IGA3\|PNP_AZOC5 Polyribonucleotide nucleotidyltransferase OS=Azorhizobium caulinodans (strain ATCC 43989 / DSM 5975 / ORS 571) GN=pnp PE=3 SV=2	Back alignment and function description

>sp\|A0LE14\|PNP_MAGSM Polyribonucleotide nucleotidyltransferase OS=Magnetococcus sp. (strain MC-1) GN=pnp PE=3 SV=1	Back alignment and function description

>sp\|Q13EM2\|PNP_RHOPS Polyribonucleotide nucleotidyltransferase OS=Rhodopseudomonas palustris (strain BisB5) GN=pnp PE=3 SV=1	Back alignment and function description

>sp\|B3QAB0\|PNP_RHOPT Polyribonucleotide nucleotidyltransferase OS=Rhodopseudomonas palustris (strain TIE-1) GN=pnp 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		916
255569434		948	polyribonucleotide nucleotidyltransferas	0.992	0.958	0.768	0.0
449437763		922	PREDICTED: probable polyribonucleotide n	0.983	0.977	0.730	0.0
296085901		942	unnamed protein product [Vitis vinifera]	0.960	0.934	0.773	0.0
449494763		922	PREDICTED: LOW QUALITY PROTEIN: probable	0.983	0.977	0.729	0.0
225439207		946	PREDICTED: polyribonucleotide nucleotidy	0.961	0.931	0.754	0.0
224125980		853	predicted protein [Populus trichocarpa]	0.890	0.956	0.804	0.0
2286200		897	polynucleotide phosphorylase [Pisum sati	0.822	0.839	0.812	0.0
356570339		916	PREDICTED: LOW QUALITY PROTEIN: polyribo	0.902	0.902	0.775	0.0
297828842		922	hypothetical protein ARALYDRAFT_896385 [	0.968	0.962	0.723	0.0
30678905		922	polyribonucleotide nucleotidyltransferas	0.971	0.965	0.718	0.0

>gi\|255569434\|ref\|XP_002525684.1\| polyribonucleotide nucleotidyltransferase, putative [Ricinus communis] gi\|223534984\|gb\|EEF36667.1\| polyribonucleotide nucleotidyltransferase, putative [Ricinus communis]	Back alignment and taxonomy information

 Score = 1410 bits (3651), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 719/935 (76%), Positives = 801/935 (85%), Gaps = 26/935 (2%)

Query: 1   MLAT-SPGGLHIRPCYPHSS---HFSLSARCKLSLSSNCPRFSTSQKSSKFRSLSLLLSR 56
           MLA  S   LH  P +P +S     S++ RCKL LS NCPRF  S   SKF SLSLLL  
Sbjct: 1   MLANPSTSSLHTIPYHPQTSPSFSNSITTRCKLFLSPNCPRFIHSS-FSKFPSLSLLLPC 59

Query: 57  RKYSERFSVRASATGPEVSEPVLSDALPSFPQPVSVKIPFGDRQILVETGHMGRQASGAV 116
           ++  ERFS RA    PE++E V+ D    FPQ VSVKIPFGDR ILVETGH GRQASG+V
Sbjct: 60  KR-GERFSARA-LEDPEITESVIVDGPQFFPQAVSVKIPFGDRHILVETGHTGRQASGSV 117

Query: 117 TVTDGETIIYTSVCLADVPSEPSDFFPLNVNYQERFSAAGRTSGGFFKREGRTKDHEVLV 176
            VTDGETI+YT+VCL DVPSEPSDFFPL+VNYQERFSAAGRTSGGFFKREGR KDHEVL+
Sbjct: 118 MVTDGETIVYTTVCLDDVPSEPSDFFPLSVNYQERFSAAGRTSGGFFKREGRAKDHEVLI 177

Query: 177 CRLIDRPLRPTLIKGFYHETQILSWVLSYDGLHFPDALAVTAAGIAVALSEVPNSKVIAG 236
           CRLIDRPLRPT++KGFYHETQILSWVLSYDGLH  DALAVTAAGIAVALSEVP +K IAG
Sbjct: 178 CRLIDRPLRPTMLKGFYHETQILSWVLSYDGLHSSDALAVTAAGIAVALSEVPTTKAIAG 237

Query: 237 VRVGLVGDKFIVNPTTQEMEDSQLDLLLAGSDDAILMIEGYCDFLSEEMLIQAVQVGQDA 296
           VRVGLVGDKFIVNPTT+EME+S+LDL++AG+D AILMIEGYC+FL EE L++AVQVGQDA
Sbjct: 238 VRVGLVGDKFIVNPTTKEMEESKLDLVMAGTDSAILMIEGYCNFLPEEKLLEAVQVGQDA 297

Query: 297 VREISNEVKALVEMCGKPKMLDTIKLPPPELYKHVEEIAGEELVKVLQIKNKIPRRKALS 356
           VR I NEV ALV+ CGKPKM D IKLPPPELYKHV+EIAG+ELV VLQI+NKIPRRKALS
Sbjct: 298 VRAICNEVDALVKKCGKPKMHDAIKLPPPELYKHVKEIAGDELVNVLQIRNKIPRRKALS 357

Query: 357 SLEEKVLTILSENGYVSKDETVGIVETIPDLLEDEDEDEEVVVDGEVDEGDVHIKPKSRK 416
           SLEEKV++IL+E G+VSKD + G  ET+ DLLE+E+EDEE VVDGEVDEGD+HIKP SRK
Sbjct: 358 SLEEKVISILTEEGFVSKDTSFGTTETVADLLEEEEEDEEFVVDGEVDEGDIHIKPVSRK 417

Query: 417 STPMLFSEVDVKLVFKEVTSKFLRRRIVEGGRRSDGRFADGIRPISSRCGLLPRAHGSAL 476
           S+P+L+SEVDVKLVFKEVTS+FLRRRIVEGG+RSDGR ADGIRPI+SRCGLLPRAHGSAL
Sbjct: 418 SSPLLYSEVDVKLVFKEVTSQFLRRRIVEGGKRSDGRNADGIRPINSRCGLLPRAHGSAL 477

Query: 477 FTRGETQSLAVITLGDKQMAQRIDNLESDDEVKRFYLQYSFPPSSVGEVGRIGAPSRREI 536
           FTRGETQSLAV TLGDKQMAQ++DNL   DE KRFYLQYSFPPSSVGEVGR+GAPSRREI
Sbjct: 478 FTRGETQSLAVATLGDKQMAQKVDNLVDVDEFKRFYLQYSFPPSSVGEVGRMGAPSRREI 537

Query: 537 GHGTLAERALEPVLPSDNDFPYTIRVESTITESNGSSSMASVCGGCLALQDAGVPIKCSI 596
           GHG LAERALEP+LPS+ DFPYTIRVESTITESNGSSSMASVCGGCLALQDAGVP+KCSI
Sbjct: 538 GHGMLAERALEPILPSEADFPYTIRVESTITESNGSSSMASVCGGCLALQDAGVPVKCSI 597

Query: 597 AGVAMGMVLDTDEFGGDGTPLILSDITGSEDASGDMDFKVAGNEDGITAFQMDIKVGGIT 656
           AG+AMGMVLDT+EFGGDGTPLILSDITGSEDASGDMDFKVAGNEDG+TAFQMDIKVGGIT
Sbjct: 598 AGIAMGMVLDTEEFGGDGTPLILSDITGSEDASGDMDFKVAGNEDGVTAFQMDIKVGGIT 657

Query: 657 LPVMKKALQQAKDGRRHILAEMLKCSPPPSNSLSKHAPLIHIMKVKPEKINLIIGSGGKK 716
           LPVM++AL QA+DGR+HILAEMLKCSP PS  LSKHAPLIH+MKV P+K+N+IIGSGGKK
Sbjct: 658 LPVMRRALLQARDGRKHILAEMLKCSPSPSKRLSKHAPLIHMMKVDPQKVNMIIGSGGKK 717

Query: 717 VKSIIEETGVEAIDTEDDGTVKITAKDLSSLEKSKAIISNLTMVPTVGDIYRNCEIKSIA 776
           V+SIIEETGVEAIDT+DDGT+KITAKDLSSLEKSK+IISNLTMVPTVGDIYRNCEIK+IA
Sbjct: 718 VRSIIEETGVEAIDTDDDGTIKITAKDLSSLEKSKSIISNLTMVPTVGDIYRNCEIKTIA 777

Query: 777 PYGVFVEIAPGREGLCHISELSSNWLAKAEDVVKVGDLVDVKLIEVNDKGQLRLSRRALL 836
           PYGVFVEIAPGREGLCHISEL+S+WLAKAED  KVGD VDVKLIEVN+KGQL+LSR+ALL
Sbjct: 778 PYGVFVEIAPGREGLCHISELTSSWLAKAEDAFKVGDRVDVKLIEVNEKGQLKLSRKALL 837

Query: 837 PEADAENPPVKLPTGDPTKDAAASDKL-------------VGSPK----PKGSSSEDTVL 879
           PE   ENP  K    D  K    S K+               SP+    PK ++ E+T +
Sbjct: 838 PEPTVENPDGKTTDKDYPKGTVNSSKVGITEAKIEQLKGDTSSPEVATSPKSNAVENTPV 897

Query: 880 PHKKVKVFKRPASPAKDRPYSNKDRTKKSSGKAVS 914
           P K  K++KR  S  K+ P +NKDR KK   K VS
Sbjct: 898 PQK--KIYKRTISSTKNGPNTNKDRPKKGGNKVVS 930

Source: Ricinus communis

Species: Ricinus communis

Genus: Ricinus

Family: Euphorbiaceae

Order: Malpighiales

Class:

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi\|449437763\|ref\|XP_004136660.1\| PREDICTED: probable polyribonucleotide nucleotidyltransferase 1, chloroplastic-like [Cucumis sativus]	Back alignment and taxonomy information

>gi\|296085901\|emb\|CBI31225.3\| unnamed protein product [Vitis vinifera]	Back alignment and taxonomy information

>gi\|449494763\|ref\|XP_004159640.1\| PREDICTED: LOW QUALITY PROTEIN: probable polyribonucleotide nucleotidyltransferase 1, chloroplastic-like [Cucumis sativus]	Back alignment and taxonomy information

>gi\|225439207\|ref\|XP_002270169.1\| PREDICTED: polyribonucleotide nucleotidyltransferase [Vitis vinifera]	Back alignment and taxonomy information

>gi\|224125980\|ref\|XP_002319726.1\| predicted protein [Populus trichocarpa] gi\|222858102\|gb\|EEE95649.1\| predicted protein [Populus trichocarpa]	Back alignment and taxonomy information

>gi\|2286200\|gb\|AAC50039.1\| polynucleotide phosphorylase [Pisum sativum]	Back alignment and taxonomy information

>gi\|356570339\|ref\|XP_003553347.1\| PREDICTED: LOW QUALITY PROTEIN: polyribonucleotide nucleotidyltransferase-like [Glycine max]	Back alignment and taxonomy information

>gi\|297828842\|ref\|XP_002882303.1\| hypothetical protein ARALYDRAFT_896385 [Arabidopsis lyrata subsp. lyrata] gi\|297328143\|gb\|EFH58562.1\| hypothetical protein ARALYDRAFT_896385 [Arabidopsis lyrata subsp. lyrata]	Back alignment and taxonomy information

>gi|30678905|ref|NP_187021.2| polyribonucleotide nucleotidyltransferase [Arabidopsis thaliana] gi|75151653|sp|Q8GZQ3.1|PNP1_ARATH RecName: Full=Polyribonucleotide nucleotidyltransferase 1, chloroplastic; Short=AtcpPNPase; AltName: Full=Polynucleotide phosphorylase 1; Short=PNPase 1; AltName: Full=Protein PIGMENT DEFECTIVE 326; AltName: Full=Protein RESISTANT TO INHIBITION WITH FSM 10; Flags: Precursor gi|25991185|gb|AAN76771.1|AF450480_1 polynucleotide phosphorylase [Arabidopsis thaliana] gi|332640453|gb|AEE73974.1| polyribonucleotide nucleotidyltransferase [Arabidopsis thaliana]

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		916
TAIR\|locus:2079429		922	RIF10 "AT3G03710" [Arabidopsis	0.922	0.916	0.695	6e-309
UNIPROTKB\|Q0BWM9		713	pnp "Polyribonucleotide nucleo	0.443	0.569	0.472	4.3e-143
UNIPROTKB\|P50849		705	pnp "Polyribonucleotide nucleo	0.439	0.571	0.485	1.1e-142
UNIPROTKB\|Q3IJ73		708	pnp "Polyribonucleotide nucleo	0.448	0.580	0.472	7.1e-141
TIGR_CMR\|SPO_3389		714	SPO_3389 "polyribonucleotide n	0.444	0.570	0.490	5e-140
TIGR_CMR\|CHY_1758		731	CHY_1758 "polyribonucleotide n	0.455	0.570	0.489	1.3e-139
TIGR_CMR\|GSU_1593		697	GSU_1593 "polyribonucleotide n	0.443	0.582	0.489	5.7e-139
UNIPROTKB\|Q9KU76		709	pnp "Polyribonucleotide nucleo	0.444	0.574	0.466	4e-138
TIGR_CMR\|VC_0647		709	VC_0647 "polyribonucleotide nu	0.444	0.574	0.466	4e-138
UNIPROTKB\|P05055		711	pnp "polynucleotide phosphoryl	0.444	0.572	0.461	5.1e-138

TAIR\|locus:2079429 RIF10 "AT3G03710" [Arabidopsis thaliana (taxid:3702)]	Back alignment and assigned GO terms

 Score = 2964 (1048.4 bits), Expect = 6.0e-309, P = 6.0e-309
 Identities = 597/858 (69%), Positives = 678/858 (79%)

Query:    62 RFSVRASATGPEVSEP-VLSDALPSFPQPVSVKIPFGDRQILVETGHMGRQASGAVTVTD 120
             +FSVRA     +  +   + D   +FP  VSVKIPFG+R+ILVETG MGRQAS AVTVTD
Sbjct:    59 KFSVRALVRPDDTDDADSVGDGSLAFPNHVSVKIPFGNREILVETGLMGRQASSAVTVTD 118

Query:   121 GETIIYTSVCLADVPSEPSDFFPLNVNYQERFSAAGRTSGGFFKREGRTKDHEVLVCRLI 180
             GETI+YTSVCLADVPSEPSDF PL V+YQERFSA GRTSGGFFKREGRTKDHEVL+CRLI
Sbjct:   119 GETIVYTSVCLADVPSEPSDFLPLYVHYQERFSAVGRTSGGFFKREGRTKDHEVLICRLI 178

Query:   181 DRPLRPTLIKGFYHETQILSWVLSYDGLHFPDXXXXXXXXXXXXXSEVPNSKVIAGVRVG 240
             DRPLRPT+ KGFY+ETQILSWVLSYDGLH PD             SEVPN+K IAGVRVG
Sbjct:   179 DRPLRPTMPKGFYNETQILSWVLSYDGLHAPDALAVTSAGIAVALSEVPNAKAIAGVRVG 238

Query:   241 LVGDKFIVNPTTQEMEDSQLDLLLAGSDDAILMIEGYCDFLSEEMLIQAVQVGQDAVREI 300
             L+G +FIVNPT +EME+SQLDL LAG+D AIL IEGY +FL EEML+QAV+VGQDAV+  
Sbjct:   239 LIGGEFIVNPTVKEMEESQLDLFLAGTDTAILTIEGYSNFLPEEMLLQAVKVGQDAVQAT 298

Query:   301 SNEVKALVEMCGKPKMLDTIKLPPPELYKHVEEIAGEELVKVLQIKNKIPRRKALSSLEE 360
                ++ L +  GKPKMLD I+LPPPELYKHV+E+AGEEL K LQIK+KI RRKA+SSLEE
Sbjct:   299 CIAIEVLAKKYGKPKMLDAIRLPPPELYKHVKELAGEELTKALQIKSKISRRKAISSLEE 358

Query:   361 KVLTILSENGYVSKDETVGIVETIPXXXXXXXXXXXXXXXXXXXXXXXHIKPKSRKSTPM 420
             KVLTIL+E GYV  +   G +E  P                       HI+P  RK  P+
Sbjct:   359 KVLTILTEKGYVIDEVAFGTIEAQPDLLEDEDEDEEVVPEGEVDQGDVHIRPIPRKPIPL 418

Query:   421 LFSEVDVKLVFKEVTSKFLRRRIVEGGRRSDGRFADGIRPISSRCGLLPRAHGSALFTRG 480
             LFSEVDVKLVFKEV+SK LRRRIVEGG+RSDGR  D IRPI+SRCGLLPRAHGS LFTRG
Sbjct:   419 LFSEVDVKLVFKEVSSKLLRRRIVEGGKRSDGRTLDEIRPINSRCGLLPRAHGSTLFTRG 478

Query:   481 ETQSLAVITLGDKQMAQRIDNLESDDEVKRFYLQYSFPPSSVGEVGRIGAPSRREIGHGT 540
             ETQ+LAV+TLGDKQMAQRIDNLE  DE KRFYLQY+FPPSSVGEVGRIGAPSRREIGHGT
Sbjct:   479 ETQALAVVTLGDKQMAQRIDNLEGSDEYKRFYLQYTFPPSSVGEVGRIGAPSRREIGHGT 538

Query:   541 LAERALEPVLPSDNDFPYTIRVESTITESNGSSSMASVCGGCLALQDAGVPIKCSIAGVA 600
             LAERALE +LPSD+DFPYTIRVEST+ ESNGSSSMASVCGGCLALQDAGVP+KCS+AG+A
Sbjct:   539 LAERALETILPSDDDFPYTIRVESTVIESNGSSSMASVCGGCLALQDAGVPVKCSVAGIA 598

Query:   601 MGMVLDTDEFGGDGTPLILSDITGSEDASGDMDFKVAGNEDGITAFQMDIKVGGITLPVM 660
             MGMV DT+EFGGDG+PLILSDITG+EDASGDMDFKVAGNEDG+TAFQMDIKVGGITL +M
Sbjct:   599 MGMVWDTEEFGGDGSPLILSDITGAEDASGDMDFKVAGNEDGVTAFQMDIKVGGITLEIM 658

Query:   661 KKALQQAKDGRRHILAEMLKCSPPPSNSLSKHAPLIHIMKVKPEKINLIIGSGGKKVKSI 720
             +KAL QAK GRRHILAEM KCSPPP+ SLSK+APLI IMKV P K+  +IGSGGKKVKSI
Sbjct:   659 EKALIQAKAGRRHILAEMAKCSPPPTLSLSKYAPLILIMKVHPSKVYSLIGSGGKKVKSI 718

Query:   721 IEETGVEAIDTEDDGTVKITAKDLSSLEKSKAIISNLTMVPTVGDIYRNCEIKSIAPYGV 780
             IEE+GVEAID +DDGTVKI A D++SLE++KAIIS LTMVP+VGDIYRNCEIKS+APYG 
Sbjct:   719 IEESGVEAIDMQDDGTVKIMAIDVASLERAKAIISGLTMVPSVGDIYRNCEIKSMAPYGA 778

Query:   781 FVEIAPGREGLCHISELSSNWLAKAEXXXXXXXXXXXXXIEVNDKGQLRLSRRALLPEAD 840
             FVEIAPGREGLCHISELS+ WLAK E             IEVN+KGQLRLS RALLPE++
Sbjct:   779 FVEIAPGREGLCHISELSAEWLAKPEDAYKVGDRIDVKLIEVNEKGQLRLSVRALLPESE 838

Query:   841 AENPPVKL-PTGDPTKDAAASDKLVG-SPKPKG-------SSSEDTVLPHKKVKVFKRPA 891
              +    K  P GD TKD ++  K V  S K +        SS ++ VL  K V+   R  
Sbjct:   839 TDKDSQKQQPAGDSTKDKSSQRKYVNTSSKDRAAAGASKVSSGDELVLKKKDVR---RAT 895

Query:   892 SPAKDRPYSNKDRTKKSS 909
               + D+  ++   T + S
Sbjct:   896 GGSSDKTMNSNSSTNEES 913

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

GO:0003676 "nucleic acid binding" evidence=ISS

GO:0003723 "RNA binding" evidence=ISS

GO:0004654 "polyribonucleotide nucleotidyltransferase activity" evidence=IGI

GO:0006401 "RNA catabolic process" evidence=IGI

GO:0031425 "chloroplast RNA processing" evidence=IGI

GO:0009507 "chloroplast" evidence=IDA

GO:0009570 "chloroplast stroma" evidence=IDA

GO:0010323 "negative regulation of isopentenyl diphosphate biosynthetic process, mevalonate-independent pathway" evidence=IMP

GO:0015995 "chlorophyll biosynthetic process" evidence=IMP

GO:0016120 "carotene biosynthetic process" evidence=IMP

GO:0016123 "xanthophyll biosynthetic process" evidence=IMP

GO:0016036 "cellular response to phosphate starvation" evidence=IMP

UNIPROTKB\|Q0BWM9 pnp "Polyribonucleotide nucleotidyltransferase" [Hyphomonas neptunium ATCC 15444 (taxid:228405)]	Back alignment and assigned GO terms

UNIPROTKB\|P50849 pnp "Polyribonucleotide nucleotidyltransferase" [Bacillus subtilis subsp. subtilis str. 168 (taxid:224308)]	Back alignment and assigned GO terms

UNIPROTKB\|Q3IJ73 pnp "Polyribonucleotide nucleotidyltransferase" [Pseudoalteromonas haloplanktis TAC125 (taxid:326442)]	Back alignment and assigned GO terms

TIGR_CMR\|SPO_3389 SPO_3389 "polyribonucleotide nucleotidyltransferase" [Ruegeria pomeroyi DSS-3 (taxid:246200)]	Back alignment and assigned GO terms

TIGR_CMR\|CHY_1758 CHY_1758 "polyribonucleotide nucleotidyltransferase" [Carboxydothermus hydrogenoformans Z-2901 (taxid:246194)]	Back alignment and assigned GO terms

TIGR_CMR\|GSU_1593 GSU_1593 "polyribonucleotide nucleotidyltransferase" [Geobacter sulfurreducens PCA (taxid:243231)]	Back alignment and assigned GO terms

UNIPROTKB\|Q9KU76 pnp "Polyribonucleotide nucleotidyltransferase" [Vibrio cholerae O1 biovar El Tor str. N16961 (taxid:243277)]	Back alignment and assigned GO terms

TIGR_CMR\|VC_0647 VC_0647 "polyribonucleotide nucleotidyltransferase" [Vibrio cholerae O1 biovar El Tor (taxid:686)]	Back alignment and assigned GO terms

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

ID	Name	Annotated EC number	Identity	Query coverage	Hit coverage	RBH(Q2H)	RBH(H2Q)
Q8GZQ3	PNP1_ARATH	2, ., 7, ., 7, ., 8	0.7188	0.9716	0.9652	yes	no
Q69LE7	PNP1_ORYSJ	2, ., 7, ., 7, ., 8	0.7622	0.8482	0.8614	yes	no

EC Number Prediction by Ezypred Server

Original result from Ezypred Server

Fail to connect to Ezypred Server

EC Number Prediction by EFICAz Software

Prediction Level	EC number	Confidence of Prediction
4th Layer	2.7.7.8	0.914
3rd Layer	2.7.7	0.921

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		916
PLN00207		891	PLN00207, PLN00207, polyribonucleotide nucleotidyl	0.0
PRK11824		693	PRK11824, PRK11824, polynucleotide phosphorylase/p	0.0
TIGR03591		684	TIGR03591, polynuc_phos, polyribonucleotide nucleo	0.0
COG1185		692	COG1185, Pnp, Polyribonucleotide nucleotidyltransf	0.0
TIGR02696		719	TIGR02696, pppGpp_PNP, guanosine pentaphosphate sy	1e-177
cd11364		223	cd11364, RNase_PH_PNPase_2, Polyribonucleotide nuc	1e-130
cd11363		229	cd11363, RNase_PH_PNPase_1, Polyribonucleotide nuc	3e-96
pfam01138		129	pfam01138, RNase_PH, 3' exoribonuclease family, do	2e-31
cd11358		218	cd11358, RNase_PH, RNase PH-like 3'-5' exoribonucl	4e-29
cd04472		68	cd04472, S1_PNPase, S1_PNPase: Polynucleotide phos	1e-27
TIGR02065		230	TIGR02065, ECX1, archaeal exosome-like complex exo	6e-24
PRK03983		244	PRK03983, PRK03983, exosome complex exonuclease Rr	4e-23
cd02393		61	cd02393, PNPase_KH, Polynucleotide phosphorylase (	7e-23
pfam01138		129	pfam01138, RNase_PH, 3' exoribonuclease family, do	1e-22
cd11366		214	cd11366, RNase_PH_archRRP41, RRP41 subunit of arch	3e-21
cd11370		226	cd11370, RNase_PH_RRP41, RRP41 subunit of eukaryot	8e-17
smart00316		72	smart00316, S1, Ribosomal protein S1-like RNA-bind	1e-16
COG0689		230	COG0689, Rph, RNase PH [Translation, ribosomal str	2e-16
PRK00087		647	PRK00087, PRK00087, 4-hydroxy-3-methylbut-2-enyl d	5e-14
pfam00575		74	pfam00575, S1, S1 RNA binding domain	9e-14
COG1098		129	COG1098, VacB, Predicted RNA binding protein (cont	6e-13
cd05692		69	cd05692, S1_RPS1_repeat_hs4, S1_RPS1_repeat_hs4: R	6e-13
PRK00087		647	PRK00087, PRK00087, 4-hydroxy-3-methylbut-2-enyl d	7e-13
cd00164		65	cd00164, S1_like, S1_like: Ribosomal protein S1-li	3e-12
PRK06676		390	PRK06676, rpsA, 30S ribosomal protein S1; Reviewed	7e-12
cd11372		199	cd11372, RNase_PH_RRP46, RRP46 subunit of eukaryot	7e-12
COG0539		541	COG0539, RpsA, Ribosomal protein S1 [Translation,	8e-12
PRK13806		491	PRK13806, rpsA, 30S ribosomal protein S1; Provisio	9e-12
COG0539		541	COG0539, RpsA, Ribosomal protein S1 [Translation,	1e-11
PRK13806		491	PRK13806, rpsA, 30S ribosomal protein S1; Provisio	1e-11
pfam03725		68	pfam03725, RNase_PH_C, 3' exoribonuclease family,	1e-11
cd05685		68	cd05685, S1_Tex, S1_Tex: The C-terminal S1 domain	1e-11
PRK06299		565	PRK06299, rpsA, 30S ribosomal protein S1; Reviewed	8e-11
PRK08059		123	PRK08059, PRK08059, general stress protein 13; Val	2e-10
PRK03987		262	PRK03987, PRK03987, translation initiation factor	2e-10
PRK08582		139	PRK08582, PRK08582, hypothetical protein; Provisio	3e-10
cd11358		218	cd11358, RNase_PH, RNase PH-like 3'-5' exoribonucl	5e-10
cd05688		68	cd05688, S1_RPS1_repeat_ec3, S1_RPS1_repeat_ec3: R	6e-10
TIGR00717		516	TIGR00717, rpsA, ribosomal protein S1	2e-09
cd04452		76	cd04452, S1_IF2_alpha, S1_IF2_alpha: The alpha sub	2e-09
PRK06676		390	PRK06676, rpsA, 30S ribosomal protein S1; Reviewed	3e-09
COG1093		269	COG1093, SUI2, Translation initiation factor 2, al	4e-09
PRK06299		565	PRK06299, rpsA, 30S ribosomal protein S1; Reviewed	5e-09
cd05684		79	cd05684, S1_DHX8_helicase, S1_DHX8_helicase: The N	6e-09
cd05708		77	cd05708, S1_Rrp5_repeat_sc12, S1_Rrp5_repeat_sc12:	2e-08
PRK06299		565	PRK06299, rpsA, 30S ribosomal protein S1; Reviewed	5e-08
cd05687		70	cd05687, S1_RPS1_repeat_ec1_hs1, S1_RPS1_repeat_ec	8e-08
cd05686		73	cd05686, S1_pNO40, S1_pNO40: pNO40 , S1-like RNA-b	1e-07
PRK07252		120	PRK07252, PRK07252, hypothetical protein; Provisio	1e-07
TIGR00717		516	TIGR00717, rpsA, ribosomal protein S1	2e-07
PRK07899		486	PRK07899, rpsA, 30S ribosomal protein S1; Reviewed	2e-07
pfam00013		59	pfam00013, KH_1, KH domain	5e-07
cd11362		227	cd11362, RNase_PH_bact, Ribonuclease PH	5e-07
cd05689		72	cd05689, S1_RPS1_repeat_ec4, S1_RPS1_repeat_ec4: R	8e-07
PRK06676		390	PRK06676, rpsA, 30S ribosomal protein S1; Reviewed	1e-06
PRK05807		136	PRK05807, PRK05807, hypothetical protein; Provisio	1e-06
pfam03726		80	pfam03726, PNPase, Polyribonucleotide nucleotidylt	1e-06
TIGR01966		236	TIGR01966, RNasePH, ribonuclease PH	2e-06
PRK07400		318	PRK07400, PRK07400, 30S ribosomal protein S1; Revi	2e-06
cd00105		64	cd00105, KH-I, K homology RNA-binding domain, type	3e-06
PRK06299		565	PRK06299, rpsA, 30S ribosomal protein S1; Reviewed	4e-06
cd11371		210	cd11371, RNase_PH_MTR3, MTR3 subunit of eukaryotic	6e-06
COG2183		780	COG2183, Tex, Transcriptional accessory protein [T	2e-05
PRK00087		647	PRK00087, PRK00087, 4-hydroxy-3-methylbut-2-enyl d	3e-05
COG0539		541	COG0539, RpsA, Ribosomal protein S1 [Translation,	3e-05
TIGR00717		516	TIGR00717, rpsA, ribosomal protein S1	4e-05
smart00322		68	smart00322, KH, K homology RNA-binding domain	6e-05
COG0539		541	COG0539, RpsA, Ribosomal protein S1 [Translation,	7e-05
COG0539		541	COG0539, RpsA, Ribosomal protein S1 [Translation,	1e-04
pfam03725		68	pfam03725, RNase_PH_C, 3' exoribonuclease family,	1e-04
cd05690		69	cd05690, S1_RPS1_repeat_ec5, S1_RPS1_repeat_ec5: R	1e-04
cd04471		83	cd04471, S1_RNase_R, S1_RNase_R: RNase R C-termina	1e-04
TIGR00717		516	TIGR00717, rpsA, ribosomal protein S1	2e-04
cd11365		256	cd11365, RNase_PH_archRRP42, RRP42 subunit of arch	2e-04
PRK07899		486	PRK07899, rpsA, 30S ribosomal protein S1; Reviewed	3e-04
cd11371		210	cd11371, RNase_PH_MTR3, MTR3 subunit of eukaryotic	3e-04
cd04461		83	cd04461, S1_Rrp5_repeat_hs8_sc7, S1_Rrp5_repeat_hs	3e-04
cd04473		77	cd04473, S1_RecJ_like, S1_RecJ_like: The S1 domain	4e-04
PRK12269		863	PRK12269, PRK12269, bifunctional cytidylate kinase	4e-04
TIGR03665		172	TIGR03665, arCOG04150, arCOG04150 universal archae	4e-04
PRK04282		271	PRK04282, PRK04282, exosome complex RNA-binding pr	7e-04
PRK03983		244	PRK03983, PRK03983, exosome complex exonuclease Rr	0.001
cd11366		214	cd11366, RNase_PH_archRRP41, RRP41 subunit of arch	0.001
cd05698		70	cd05698, S1_Rrp5_repeat_hs6_sc5, S1_Rrp5_repeat_hs	0.001
COG2123		272	COG2123, COG2123, RNase PH-related exoribonuclease	0.002
cd04453		88	cd04453, S1_RNase_E, S1_RNase_E: RNase E and RNase	0.003
cd05707		68	cd05707, S1_Rrp5_repeat_sc11, S1_Rrp5_repeat_sc11:	0.004

>gnl\|CDD\|215104 PLN00207, PLN00207, polyribonucleotide nucleotidyltransferase; Provisional	Back alignment and domain information

 Score = 1498 bits (3880), Expect = 0.0
 Identities = 694/889 (78%), Positives = 761/889 (85%), Gaps = 15/889 (1%)

Query: 19  SHFSLSARCKLSLSSNCPRFSTSQKSSKFRSLSLLLSRRKYS---ERFSVRASATGPEVS 75
           S      R  L  S N PRF  S +SS   S SL  +    S   +  SVRA    P  S
Sbjct: 6   SALHHLLRSPLPPSRNLPRFHDS-ESSPSISSSLPEAGLLKSSIKKARSVRALLR-PVDS 63

Query: 76  E--PVLSDALPSFPQPVSVKIPFGDRQILVETGHMGRQASGAVTVTDGETIIYTSVCLAD 133
           E    + +    FPQ  SVKIP GDR ILVETGH+GRQASG+VTVTDGETI+YTSVCLAD
Sbjct: 64  EDTSSVGEGPGPFPQQFSVKIPVGDRHILVETGHIGRQASGSVTVTDGETIVYTSVCLAD 123

Query: 134 VPSEPSDFFPLNVNYQERFSAAGRTSGGFFKREGRTKDHEVLVCRLIDRPLRPTLIKGFY 193
           VPSEPSDFFPL+V+YQERFSAAGRTSGGFFKREGRTKDHEVL+CRLIDRPLRPT+ KGFY
Sbjct: 124 VPSEPSDFFPLSVHYQERFSAAGRTSGGFFKREGRTKDHEVLICRLIDRPLRPTMPKGFY 183

Query: 194 HETQILSWVLSYDGLHFPDALAVTAAGIAVALSEVPNSKVIAGVRVGLVGDKFIVNPTTQ 253
           HETQILSWVLSYDGLH PD+LAVTAAGIAVALSEVPN K IAGVRVGL+G KFIVNPTT+
Sbjct: 184 HETQILSWVLSYDGLHSPDSLAVTAAGIAVALSEVPNLKAIAGVRVGLIGGKFIVNPTTK 243

Query: 254 EMEDSQLDLLLAGSDDAILMIEGYCDFLSEEMLIQAVQVGQDAVREISNEVKALVEMCGK 313
           EME+S+LDL++AG+D AILMIEGYC+FL EE L++AV+VGQDAVR I  E++ LV+ CGK
Sbjct: 244 EMEESELDLIMAGTDSAILMIEGYCNFLPEEKLLEAVEVGQDAVRAICKEIEVLVKKCGK 303

Query: 314 PKMLDTIKLPPPELYKHVEEIAGEELVKVLQIKNKIPRRKALSSLEEKVLTILSENGYVS 373
           PKMLD IKLPPPELYKHV+EIAG+ELVK LQI+ KIPRRKALSSLEEKVL+IL+E GYVS
Sbjct: 304 PKMLDAIKLPPPELYKHVKEIAGDELVKALQIRGKIPRRKALSSLEEKVLSILTEEGYVS 363

Query: 374 KDETVGIVETIPDLLEDEDEDEEVVVDGEVDEGDVHIKPKSRKSTPMLFSEVDVKLVFKE 433
           KDE+ G  ET  DLLEDEDEDEEVVVDGEVDEGDVHIKP  RKS+P+LFSEVDVKLVFKE
Sbjct: 364 KDESFGTSETRADLLEDEDEDEEVVVDGEVDEGDVHIKPIPRKSSPLLFSEVDVKLVFKE 423

Query: 434 VTSKFLRRRIVEGGRRSDGRFADGIRPISSRCGLLPRAHGSALFTRGETQSLAVITLGDK 493
           VTSKFLRRRIVEGG+RSDGR  D IRPI+S CGLLPRAHGSALFTRGETQ+LAV+TLGDK
Sbjct: 424 VTSKFLRRRIVEGGKRSDGRTPDEIRPINSSCGLLPRAHGSALFTRGETQALAVVTLGDK 483

Query: 494 QMAQRIDNLESDDEVKRFYLQYSFPPSSVGEVGRIGAPSRREIGHGTLAERALEPVLPSD 553
           QMAQRIDNL   DEVKRFYLQYSFPPS VGEVGRIGAPSRREIGHG LAERALEP+LPS+
Sbjct: 484 QMAQRIDNLVDADEVKRFYLQYSFPPSCVGEVGRIGAPSRREIGHGMLAERALEPILPSE 543

Query: 554 NDFPYTIRVESTITESNGSSSMASVCGGCLALQDAGVPIKCSIAGVAMGMVLDTDEFGGD 613
           +DFPYTIRVESTITESNGSSSMASVCGGCLALQDAGVP+KC IAG+AMGMVLDT+EFGGD
Sbjct: 544 DDFPYTIRVESTITESNGSSSMASVCGGCLALQDAGVPVKCPIAGIAMGMVLDTEEFGGD 603

Query: 614 GTPLILSDITGSEDASGDMDFKVAGNEDGITAFQMDIKVGGITLPVMKKALQQAKDGRRH 673
           G+PLILSDITGSEDASGDMDFKVAGNEDGITAFQMDIKVGGITLP+M++AL QAKDGR+H
Sbjct: 604 GSPLILSDITGSEDASGDMDFKVAGNEDGITAFQMDIKVGGITLPIMERALLQAKDGRKH 663

Query: 674 ILAEMLKCSPPPSNSLSKHAPLIHIMKVKPEKINLIIGSGGKKVKSIIEETGVEAIDTED 733
           ILAEM KCSPPPS  LSK+APLIHIMKVKPEK+N+IIGSGGKKVKSIIEETGVEAIDT+D
Sbjct: 664 ILAEMSKCSPPPSKRLSKYAPLIHIMKVKPEKVNMIIGSGGKKVKSIIEETGVEAIDTQD 723

Query: 734 DGTVKITAKDLSSLEKSKAIISNLTMVPTVGDIYRNCEIKSIAPYGVFVEIAPGREGLCH 793
           DGTVKITAKDLSSLEKSKAIIS+LTMVPTVGDIYRNCEIKSIAPYG FVEIAPGREGLCH
Sbjct: 724 DGTVKITAKDLSSLEKSKAIISSLTMVPTVGDIYRNCEIKSIAPYGAFVEIAPGREGLCH 783

Query: 794 ISELSSNWLAKAEDVVKVGDLVDVKLIEVNDKGQLRLSRRALLPEADAENPPVKLPTGDP 853
           ISELSSNWLAK ED  KVGD +DVKLIEVNDKGQLRLSRRALLPEA++E    K   G  
Sbjct: 784 ISELSSNWLAKPEDAFKVGDRIDVKLIEVNDKGQLRLSRRALLPEANSEKSSQKQQGGST 843

Query: 854 TKDAAASDKLVGSPKP------KGSSSEDTVLPHKKVKVFKRPASPAKD 896
              A     +  S +P      + +S+E+  +P K  K +KR  S +KD
Sbjct: 844 KDKAPQKKYVNTSSRPRRAAQAEKNSAENAAVPKK--KDYKRATSGSKD 890

Length = 891

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

>gnl\|CDD\|234271 TIGR03591, polynuc_phos, polyribonucleotide nucleotidyltransferase	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\|131743 TIGR02696, pppGpp_PNP, guanosine pentaphosphate synthetase I/polynucleotide phosphorylase	Back alignment and domain information

>gnl\|CDD\|206769 cd11364, RNase_PH_PNPase_2, Polyribonucleotide nucleotidyltransferase, repeat 2	Back alignment and domain information

>gnl\|CDD\|206768 cd11363, RNase_PH_PNPase_1, Polyribonucleotide nucleotidyltransferase, repeat 1	Back alignment and domain information

>gnl\|CDD\|216323 pfam01138, RNase_PH, 3' exoribonuclease family, domain 1	Back alignment and domain information

>gnl\|CDD\|206766 cd11358, RNase_PH, RNase PH-like 3'-5' exoribonucleases	Back alignment and domain information

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

>gnl\|CDD\|131120 TIGR02065, ECX1, archaeal exosome-like complex exonuclease 1	Back alignment and domain information

>gnl\|CDD\|235187 PRK03983, PRK03983, exosome complex exonuclease Rrp41; Provisional	Back alignment and domain information

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

>gnl\|CDD\|216323 pfam01138, RNase_PH, 3' exoribonuclease family, domain 1	Back alignment and domain information

>gnl\|CDD\|206771 cd11366, RNase_PH_archRRP41, RRP41 subunit of archaeal exosome	Back alignment and domain information

>gnl\|CDD\|206775 cd11370, RNase_PH_RRP41, RRP41 subunit of eukaryotic exosome	Back alignment and domain information

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

>gnl\|CDD\|223761 COG0689, Rph, RNase PH [Translation, ribosomal structure and biogenesis]	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\|224023 COG1098, VacB, Predicted RNA binding protein (contains ribosomal protein S1 domain) [Translation, ribosomal structure and biogenesis]	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\|234623 PRK00087, PRK00087, 4-hydroxy-3-methylbut-2-enyl diphosphate reductase/S1 RNA-binding domain protein; Reviewed	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\|235851 PRK06676, rpsA, 30S ribosomal protein S1; Reviewed	Back alignment and domain information

>gnl\|CDD\|206777 cd11372, RNase_PH_RRP46, RRP46 subunit of eukaryotic exosome	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\|237516 PRK13806, rpsA, 30S ribosomal protein S1; Provisional	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\|237516 PRK13806, rpsA, 30S ribosomal protein S1; Provisional	Back alignment and domain information

>gnl\|CDD\|217696 pfam03725, RNase_PH_C, 3' exoribonuclease family, domain 2	Back alignment and domain information

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

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

>gnl\|CDD\|181215 PRK08059, PRK08059, general stress protein 13; Validated	Back alignment and domain information

>gnl\|CDD\|235188 PRK03987, PRK03987, translation initiation factor IF-2 subunit alpha; Validated	Back alignment and domain information

>gnl\|CDD\|236305 PRK08582, PRK08582, hypothetical protein; Provisional	Back alignment and domain information

>gnl\|CDD\|206766 cd11358, RNase_PH, RNase PH-like 3'-5' exoribonucleases	Back alignment and domain information

>gnl\|CDD\|240193 cd05688, S1_RPS1_repeat_ec3, S1_RPS1_repeat_ec3: Ribosomal protein S1 (RPS1) domain	Back alignment and domain information

>gnl\|CDD\|233102 TIGR00717, rpsA, ribosomal protein S1	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\|235851 PRK06676, rpsA, 30S ribosomal protein S1; Reviewed	Back alignment and domain information

>gnl\|CDD\|224018 COG1093, SUI2, Translation initiation factor 2, alpha subunit (eIF-2alpha) [Translation, ribosomal structure and biogenesis]	Back alignment and domain information

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

>gnl\|CDD\|240189 cd05684, S1_DHX8_helicase, S1_DHX8_helicase: The N-terminal S1 domain of human ATP-dependent RNA helicase DHX8, a DEAH (Asp-Glu-Ala-His) box polypeptide	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\|235775 PRK06299, rpsA, 30S ribosomal protein S1; Reviewed	Back alignment and domain information

>gnl\|CDD\|240192 cd05687, S1_RPS1_repeat_ec1_hs1, S1_RPS1_repeat_ec1_hs1: Ribosomal protein S1 (RPS1) domain	Back alignment and domain information

>gnl\|CDD\|240191 cd05686, S1_pNO40, S1_pNO40: pNO40 , S1-like RNA-binding domain	Back alignment and domain information

>gnl\|CDD\|180908 PRK07252, PRK07252, hypothetical protein; Provisional	Back alignment and domain information

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

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

>gnl\|CDD\|215657 pfam00013, KH_1, KH domain	Back alignment and domain information

>gnl\|CDD\|206767 cd11362, RNase_PH_bact, Ribonuclease PH	Back alignment and domain information

>gnl\|CDD\|240194 cd05689, S1_RPS1_repeat_ec4, S1_RPS1_repeat_ec4: Ribosomal protein S1 (RPS1) domain	Back alignment and domain information

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

>gnl\|CDD\|235614 PRK05807, PRK05807, hypothetical protein; Provisional	Back alignment and domain information

>gnl\|CDD\|217697 pfam03726, PNPase, Polyribonucleotide nucleotidyltransferase, RNA binding domain	Back alignment and domain information

>gnl\|CDD\|131021 TIGR01966, RNasePH, ribonuclease PH	Back alignment and domain information

>gnl\|CDD\|180960 PRK07400, PRK07400, 30S ribosomal protein S1; Reviewed	Back alignment and domain information

>gnl\|CDD\|238053 cd00105, KH-I, K homology RNA-binding domain, type I	Back alignment and domain information

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

>gnl\|CDD\|206776 cd11371, RNase_PH_MTR3, MTR3 subunit of eukaryotic exosome	Back alignment and domain information

>gnl\|CDD\|225094 COG2183, Tex, Transcriptional accessory protein [Transcription]	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\|233102 TIGR00717, rpsA, ribosomal protein S1	Back alignment and domain information

>gnl\|CDD\|197652 smart00322, KH, K homology RNA-binding domain	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\|223613 COG0539, RpsA, Ribosomal protein S1 [Translation, ribosomal structure and biogenesis]	Back alignment and domain information

>gnl\|CDD\|217696 pfam03725, RNase_PH_C, 3' exoribonuclease family, domain 2	Back alignment and domain information

>gnl\|CDD\|240195 cd05690, S1_RPS1_repeat_ec5, S1_RPS1_repeat_ec5: Ribosomal protein S1 (RPS1) domain	Back alignment and domain information

>gnl\|CDD\|239917 cd04471, S1_RNase_R, S1_RNase_R: RNase R C-terminal S1 domain	Back alignment and domain information

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

>gnl\|CDD\|206770 cd11365, RNase_PH_archRRP42, RRP42 subunit of archaeal exosome	Back alignment and domain information

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

>gnl\|CDD\|206776 cd11371, RNase_PH_MTR3, MTR3 subunit of eukaryotic exosome	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\|239919 cd04473, S1_RecJ_like, S1_RecJ_like: The S1 domain of the archaea-specific RecJ-like exonuclease	Back alignment and domain information

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

>gnl\|CDD\|211858 TIGR03665, arCOG04150, arCOG04150 universal archaeal KH domain protein	Back alignment and domain information

>gnl\|CDD\|235268 PRK04282, PRK04282, exosome complex RNA-binding protein Rrp42; Provisional	Back alignment and domain information

>gnl\|CDD\|235187 PRK03983, PRK03983, exosome complex exonuclease Rrp41; Provisional	Back alignment and domain information

>gnl\|CDD\|206771 cd11366, RNase_PH_archRRP41, RRP41 subunit of archaeal exosome	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\|225034 COG2123, COG2123, RNase PH-related exoribonuclease [Translation, ribosomal structure and biogenesis]	Back alignment and domain information

>gnl\|CDD\|239900 cd04453, S1_RNase_E, S1_RNase_E: RNase E and RNase G, S1-like 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

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Alignment Graph	Length	Definition	Probability
Query		916
PLN00207		891	polyribonucleotide nucleotidyltransferase; Provisi	100.0
TIGR02696		719	pppGpp_PNP guanosine pentaphosphate synthetase I/p	100.0
COG1185		692	Pnp Polyribonucleotide nucleotidyltransferase (pol	100.0
KOG1067		760	consensus Predicted RNA-binding polyribonucleotide	100.0
PRK11824		693	polynucleotide phosphorylase/polyadenylase; Provis	100.0
TIGR03591		684	polynuc_phos polyribonucleotide nucleotidyltransfe	100.0
TIGR02065		230	ECX1 archaeal exosome-like complex exonuclease 1.	100.0
PRK03983		244	exosome complex exonuclease Rrp41; Provisional	100.0
PRK00173		238	rph ribonuclease PH; Reviewed	100.0
PLN00207		891	polyribonucleotide nucleotidyltransferase; Provisi	100.0
COG0689		230	Rph RNase PH [Translation, ribosomal structure and	100.0
KOG1068		245	consensus Exosomal 3'-5' exoribonuclease complex,	100.0
TIGR02065		230	ECX1 archaeal exosome-like complex exonuclease 1.	100.0
TIGR01966		236	RNasePH ribonuclease PH. This bacterial enzyme, ri	100.0
PRK04282		271	exosome complex RNA-binding protein Rrp42; Provisi	100.0
PRK00173		238	rph ribonuclease PH; Reviewed	100.0
PRK03983		244	exosome complex exonuclease Rrp41; Provisional	100.0
TIGR03591		684	polynuc_phos polyribonucleotide nucleotidyltransfe	100.0
TIGR01966		236	RNasePH ribonuclease PH. This bacterial enzyme, ri	100.0
PRK11824		693	polynucleotide phosphorylase/polyadenylase; Provis	99.98
COG0689		230	Rph RNase PH [Translation, ribosomal structure and	99.97
COG2123		272	RNase PH-related exoribonuclease [Translation, rib	99.97
KOG1069		217	consensus Exosomal 3'-5' exoribonuclease complex,	99.96
TIGR02696		719	pppGpp_PNP guanosine pentaphosphate synthetase I/p	99.96
PRK04282		271	exosome complex RNA-binding protein Rrp42; Provisi	99.95
COG0539		541	RpsA Ribosomal protein S1 [Translation, ribosomal	99.94
COG0539		541	RpsA Ribosomal protein S1 [Translation, ribosomal	99.94
KOG1068		245	consensus Exosomal 3'-5' exoribonuclease complex,	99.94
KOG1069		217	consensus Exosomal 3'-5' exoribonuclease complex,	99.93
KOG1614		291	consensus Exosomal 3'-5' exoribonuclease complex,	99.9
KOG1613		298	consensus Exosomal 3'-5' exoribonuclease complex,	99.9
PF01138		132	RNase_PH: 3' exoribonuclease family, domain 1 This	99.89
COG1185		692	Pnp Polyribonucleotide nucleotidyltransferase (pol	99.88
COG2123		272	RNase PH-related exoribonuclease [Translation, rib	99.88
PRK12269		863	bifunctional cytidylate kinase/ribosomal protein S	99.87
PRK07899		486	rpsA 30S ribosomal protein S1; Reviewed	99.85
PRK13806		491	rpsA 30S ribosomal protein S1; Provisional	99.85
KOG1067		760	consensus Predicted RNA-binding polyribonucleotide	99.84
PRK12269		863	bifunctional cytidylate kinase/ribosomal protein S	99.82
PRK13806		491	rpsA 30S ribosomal protein S1; Provisional	99.81
KOG1612		288	consensus Exosomal 3'-5' exoribonuclease complex,	99.79
PRK06299		565	rpsA 30S ribosomal protein S1; Reviewed	99.76
PRK06676		390	rpsA 30S ribosomal protein S1; Reviewed	99.76
COG1098		129	VacB Predicted RNA binding protein (contains ribos	99.75
PRK06299		565	rpsA 30S ribosomal protein S1; Reviewed	99.74
PF01138		132	RNase_PH: 3' exoribonuclease family, domain 1 This	99.73
PRK00087		647	4-hydroxy-3-methylbut-2-enyl diphosphate reductase	99.72
TIGR00717		516	rpsA ribosomal protein S1. This model provides tru	99.72
TIGR00717		516	rpsA ribosomal protein S1. This model provides tru	99.71
PTZ00248		319	eukaryotic translation initiation factor 2 subunit	99.67
PRK07400		318	30S ribosomal protein S1; Reviewed	99.63
PRK07899		486	rpsA 30S ribosomal protein S1; Reviewed	99.59
KOG1614		291	consensus Exosomal 3'-5' exoribonuclease complex,	99.57
PRK08582		139	hypothetical protein; Provisional	99.57
PRK07400		318	30S ribosomal protein S1; Reviewed	99.56
PRK06676		390	rpsA 30S ribosomal protein S1; Reviewed	99.52
cd05704		72	S1_Rrp5_repeat_hs13 S1_Rrp5_repeat_hs13: Rrp5 is a	99.52
cd05705		74	S1_Rrp5_repeat_hs14 S1_Rrp5_repeat_hs14: Rrp5 is a	99.5
cd05686		73	S1_pNO40 S1_pNO40: pNO40 , S1-like RNA-binding dom	99.49
cd05696		71	S1_Rrp5_repeat_hs4 S1_Rrp5_repeat_hs4: Rrp5 is a t	99.43
cd05698		70	S1_Rrp5_repeat_hs6_sc5 S1_Rrp5_repeat_hs6_sc5: Rrp	99.42
cd04461		83	S1_Rrp5_repeat_hs8_sc7 S1_Rrp5_repeat_hs8_sc7: Rrp	99.41
cd04452		76	S1_IF2_alpha S1_IF2_alpha: The alpha subunit of tr	99.41
PF00575		74	S1: S1 RNA binding domain; InterPro: IPR003029 Rib	99.41
PRK05807		136	hypothetical protein; Provisional	99.4
cd05684		79	S1_DHX8_helicase S1_DHX8_helicase: The N-terminal	99.4
PRK07252		120	hypothetical protein; Provisional	99.4
cd05706		73	S1_Rrp5_repeat_sc10 S1_Rrp5_repeat_sc10: Rrp5 is a	99.39
cd05703		73	S1_Rrp5_repeat_hs12_sc9 S1_Rrp5_repeat_hs12_sc9: R	99.39
PRK00087		647	4-hydroxy-3-methylbut-2-enyl diphosphate reductase	99.39
cd05697		69	S1_Rrp5_repeat_hs5 S1_Rrp5_repeat_hs5: Rrp5 is a t	99.38
cd05707		68	S1_Rrp5_repeat_sc11 S1_Rrp5_repeat_sc11: Rrp5 is a	99.35
PHA02945		88	interferon resistance protein; Provisional	99.35
cd05691		73	S1_RPS1_repeat_ec6 S1_RPS1_repeat_ec6: Ribosomal p	99.34
cd05690		69	S1_RPS1_repeat_ec5 S1_RPS1_repeat_ec5: Ribosomal p	99.34
PRK08059		123	general stress protein 13; Validated	99.32
cd05692		69	S1_RPS1_repeat_hs4 S1_RPS1_repeat_hs4: Ribosomal p	99.31
cd05694		74	S1_Rrp5_repeat_hs2_sc2 S1_Rrp5_repeat_hs2_sc2: Rrp	99.31
cd05708		77	S1_Rrp5_repeat_sc12 S1_Rrp5_repeat_sc12: Rrp5 is a	99.31
cd05689		72	S1_RPS1_repeat_ec4 S1_RPS1_repeat_ec4: Ribosomal p	99.3
COG1093		269	SUI2 Translation initiation factor 2, alpha subuni	99.29
cd05687		70	S1_RPS1_repeat_ec1_hs1 S1_RPS1_repeat_ec1_hs1: Rib	99.26
PF03726		83	PNPase: Polyribonucleotide nucleotidyltransferase,	99.22
cd05685		68	S1_Tex S1_Tex: The C-terminal S1 domain of a trans	99.22
cd04472		68	S1_PNPase S1_PNPase: Polynucleotide phosphorylase	99.21
cd05789		86	S1_Rrp4 S1_Rrp4: Rrp4 S1-like RNA-binding domain.	99.21
cd04453		88	S1_RNase_E S1_RNase_E: RNase E and RNase G, S1-lik	99.19
cd05695		66	S1_Rrp5_repeat_hs3 S1_Rrp5_repeat_hs3: Rrp5 is a t	99.14
PRK03987		262	translation initiation factor IF-2 subunit alpha;	99.14
COG2183		780	Tex Transcriptional accessory protein [Transcripti	99.14
cd04465		67	S1_RPS1_repeat_ec2_hs2 S1_RPS1_repeat_ec2_hs2: Rib	99.13
cd04471		83	S1_RNase_R S1_RNase_R: RNase R C-terminal S1 domai	99.12
cd05688		68	S1_RPS1_repeat_ec3 S1_RPS1_repeat_ec3: Ribosomal p	99.11
cd05693		100	S1_Rrp5_repeat_hs1_sc1 S1_Rrp5_repeat_hs1_sc1: Rrp	99.1
KOG1612		288	consensus Exosomal 3'-5' exoribonuclease complex,	99.06
smart00316		72	S1 Ribosomal protein S1-like RNA-binding domain.	99.06
cd04454		82	S1_Rrp4_like S1_Rrp4_like: Rrp4-like, S1-like RNA-	99.0
cd04473		77	S1_RecJ_like S1_RecJ_like: The S1 domain of the ar	98.98
cd05702		70	S1_Rrp5_repeat_hs11_sc8 S1_Rrp5_repeat_hs11_sc8: R	98.96
cd02393		61	PNPase_KH Polynucleotide phosphorylase (PNPase) K	98.88
cd00164		65	S1_like S1_like: Ribosomal protein S1-like RNA-bin	98.87
KOG1070		1710	consensus rRNA processing protein Rrp5 [RNA proces	98.85
KOG1613		298	consensus Exosomal 3'-5' exoribonuclease complex,	98.84
PF03725		68	RNase_PH_C: 3' exoribonuclease family, domain 2 Th	98.83
cd04460		99	S1_RpoE S1_RpoE: RpoE, S1-like RNA-binding domain.	98.77
TIGR02063		709	RNase_R ribonuclease R. This family consists of an	98.74
PRK09521		189	exosome complex RNA-binding protein Csl4; Provisio	98.74
PRK13763		180	putative RNA-processing protein; Provisional	98.73
PRK04163		235	exosome complex RNA-binding protein Rrp4; Provisio	98.69
TIGR03665		172	arCOG04150 arCOG04150 universal archaeal KH domain	98.65
PRK08563		187	DNA-directed RNA polymerase subunit E'; Provisiona	98.58
PRK11642		813	exoribonuclease R; Provisional	98.57
TIGR00358		654	3_prime_RNase VacB and RNase II family 3'-5' exori	98.55
TIGR00448		179	rpoE DNA-directed RNA polymerase (rpoE), archaeal	98.53
cd04455		67	S1_NusA S1_NusA: N-utilizing substance A protein (	98.49
cd05791		92	S1_CSL4 S1_CSL4: CSL4, S1-like RNA-binding domain.	98.41
COG1095		183	RPB7 DNA-directed RNA polymerase, subunit E' [Tran	98.34
KOG1070		1710	consensus rRNA processing protein Rrp5 [RNA proces	98.32
PHA02858		86	EIF2a-like PKR inhibitor; Provisional	98.17
PRK09202		470	nusA transcription elongation factor NusA; Validat	98.16
cd02395		120	SF1_like-KH Splicing factor 1 (SF1) K homology RNA	98.05
PF03725		68	RNase_PH_C: 3' exoribonuclease family, domain 2 Th	98.02
PRK05054		644	exoribonuclease II; Provisional	97.84
KOG2916		304	consensus Translation initiation factor 2, alpha s	97.77
COG1097		239	RRP4 RNA-binding protein Rrp4 and related proteins	97.66
TIGR00757		414	RNaseEG ribonuclease, Rne/Rng family. The C-termin	97.65
TIGR01953		341	NusA transcription termination factor NusA. This m	97.63
cd02394		62	vigilin_like_KH K homology RNA-binding domain_vigi	97.59
PRK12327		362	nusA transcription elongation factor NusA; Provisi	97.52
COG0557		706	VacB Exoribonuclease R [Transcription]	97.5
TIGR02062		639	RNase_B exoribonuclease II. This family consists o	97.48
cd05790		86	S1_Rrp40 S1_Rrp40: Rrp40 S1-like RNA-binding domai	97.46
COG1107		715	Archaea-specific RecJ-like exonuclease, contains D	97.39
cd04462		88	S1_RNAPII_Rpb7 S1_RNAPII_Rpb7: Eukaryotic RNA poly	97.29
PRK04163		235	exosome complex RNA-binding protein Rrp4; Provisio	97.26
PF10447		82	EXOSC1: Exosome component EXOSC1/CSL4; InterPro: I	97.16
PF00013		60	KH_1: KH domain syndrome, contains KH motifs.; Int	97.15
PTZ00162		176	DNA-directed RNA polymerase II subunit 7; Provisio	97.08
COG1096		188	Predicted RNA-binding protein (consists of S1 doma	97.04
COG2996		287	Predicted RNA-bindining protein (contains S1 and H	96.97
cd00105		64	KH-I K homology RNA-binding domain, type I. KH bin	96.95
cd05705		74	S1_Rrp5_repeat_hs14 S1_Rrp5_repeat_hs14: Rrp5 is a	96.84
COG1098		129	VacB Predicted RNA binding protein (contains ribos	96.69
PF13509		61	S1_2: S1 domain; PDB: 3GO5_A.	96.59
cd05699		72	S1_Rrp5_repeat_hs7 S1_Rrp5_repeat_hs7: Rrp5 is a t	96.54
cd05703		73	S1_Rrp5_repeat_hs12_sc9 S1_Rrp5_repeat_hs12_sc9: R	96.45
smart00322		69	KH K homology RNA-binding domain.	96.37
cd05695		66	S1_Rrp5_repeat_hs3 S1_Rrp5_repeat_hs3: Rrp5 is a t	96.35
COG2996		287	Predicted RNA-bindining protein (contains S1 and H	96.29
PRK10811		1068	rne ribonuclease E; Reviewed	96.11
PTZ00248		319	eukaryotic translation initiation factor 2 subunit	95.98
PRK11712		489	ribonuclease G; Provisional	95.91
cd02396		65	PCBP_like_KH K homology RNA-binding domain, PCBP_l	95.8
PF00575		74	S1: S1 RNA binding domain; InterPro: IPR003029 Rib	95.46
cd04461		83	S1_Rrp5_repeat_hs8_sc7 S1_Rrp5_repeat_hs8_sc7: Rrp	95.21
PRK12328		374	nusA transcription elongation factor NusA; Provisi	95.15
TIGR03665		172	arCOG04150 arCOG04150 universal archaeal KH domain	95.13
cd05708		77	S1_Rrp5_repeat_sc12 S1_Rrp5_repeat_sc12: Rrp5 is a	95.1
cd05706		73	S1_Rrp5_repeat_sc10 S1_Rrp5_repeat_sc10: Rrp5 is a	94.7
cd05696		71	S1_Rrp5_repeat_hs4 S1_Rrp5_repeat_hs4: Rrp5 is a t	94.52
KOG1856		1299	consensus Transcription elongation factor SPT6 [RN	94.41
cd05689		72	S1_RPS1_repeat_ec4 S1_RPS1_repeat_ec4: Ribosomal p	94.41
cd05690		69	S1_RPS1_repeat_ec5 S1_RPS1_repeat_ec5: Ribosomal p	94.39
cd05698		70	S1_Rrp5_repeat_hs6_sc5 S1_Rrp5_repeat_hs6_sc5: Rrp	94.39
cd05687		70	S1_RPS1_repeat_ec1_hs1 S1_RPS1_repeat_ec1_hs1: Rib	94.32
cd05694		74	S1_Rrp5_repeat_hs2_sc2 S1_Rrp5_repeat_hs2_sc2: Rrp	94.31
cd05704		72	S1_Rrp5_repeat_hs13 S1_Rrp5_repeat_hs13: Rrp5 is a	94.26
PRK13763		180	putative RNA-processing protein; Provisional	94.12
cd05707		68	S1_Rrp5_repeat_sc11 S1_Rrp5_repeat_sc11: Rrp5 is a	93.92
cd05697		69	S1_Rrp5_repeat_hs5 S1_Rrp5_repeat_hs5: Rrp5 is a t	93.89
PRK08582		139	hypothetical protein; Provisional	93.85
cd05789		86	S1_Rrp4 S1_Rrp4: Rrp4 S1-like RNA-binding domain.	93.67
cd04454		82	S1_Rrp4_like S1_Rrp4_like: Rrp4-like, S1-like RNA-	93.65
PRK12329		449	nusA transcription elongation factor NusA; Provisi	93.52
cd05686		73	S1_pNO40 S1_pNO40: pNO40 , S1-like RNA-binding dom	93.39
PRK07252		120	hypothetical protein; Provisional	93.37
cd05691		73	S1_RPS1_repeat_ec6 S1_RPS1_repeat_ec6: Ribosomal p	93.29
KOG1676		600	consensus K-homology type RNA binding proteins [RN	93.26
PF13014		43	KH_3: KH domain	93.21
cd05693		100	S1_Rrp5_repeat_hs1_sc1 S1_Rrp5_repeat_hs1_sc1: Rrp	93.0
PRK05807		136	hypothetical protein; Provisional	92.99
KOG2191		402	consensus RNA-binding protein NOVA1/PASILLA and re	92.77
cd04452		76	S1_IF2_alpha S1_IF2_alpha: The alpha subunit of tr	92.67
cd05688		68	S1_RPS1_repeat_ec3 S1_RPS1_repeat_ec3: Ribosomal p	92.45
COG1530		487	CafA Ribonucleases G and E [Translation, ribosomal	92.08
PRK08059		123	general stress protein 13; Validated	92.01
cd05685		68	S1_Tex S1_Tex: The C-terminal S1 domain of a trans	91.7
COG2183		780	Tex Transcriptional accessory protein [Transcripti	91.51
PRK09202		470	nusA transcription elongation factor NusA; Validat	91.43
PRK09521		189	exosome complex RNA-binding protein Csl4; Provisio	91.42
PRK12442		87	translation initiation factor IF-1; Reviewed	90.8
KOG0119		554	consensus Splicing factor 1/branch point binding p	90.79
TIGR00008		68	infA translation initiation factor IF-1. This fami	89.43
COG1094		194	Predicted RNA-binding protein (contains KH domains	89.27
smart00316		72	S1 Ribosomal protein S1-like RNA-binding domain.	88.97
KOG3409		193	consensus Exosomal 3'-5' exoribonuclease complex,	88.11
cd04472		68	S1_PNPase S1_PNPase: Polynucleotide phosphorylase	87.82
KOG3298		170	consensus DNA-directed RNA polymerase subunit E' [	87.77
cd05692		69	S1_RPS1_repeat_hs4 S1_RPS1_repeat_hs4: Ribosomal p	87.15
cd04473		77	S1_RecJ_like S1_RecJ_like: The S1 domain of the ar	86.97
cd04465		67	S1_RPS1_repeat_ec2_hs2 S1_RPS1_repeat_ec2_hs2: Rib	85.57
PHA02945		88	interferon resistance protein; Provisional	84.94
PRK03987		262	translation initiation factor IF-2 subunit alpha;	84.75
KOG1676		600	consensus K-homology type RNA binding proteins [RN	84.69
PF00313		66	CSD: 'Cold-shock' DNA-binding domain; InterPro: IP	83.42
cd05702		70	S1_Rrp5_repeat_hs11_sc8 S1_Rrp5_repeat_hs11_sc8: R	83.37
cd05684		79	S1_DHX8_helicase S1_DHX8_helicase: The N-terminal	83.32
cd04455		67	S1_NusA S1_NusA: N-utilizing substance A protein (	81.77
PRK04012		100	translation initiation factor IF-1A; Provisional	81.47

>PLN00207 polyribonucleotide nucleotidyltransferase; Provisional	Back alignment and domain information

Probab=100.00  E-value=7.5e-181  Score=1604.49  Aligned_cols=820  Identities=83%  Similarity=1.242  Sum_probs=776.8

Q ss_pred             ccceeeccccCCCCCcccCCC----CCccccccccccccccccccccccccCCCCCCc--cccCCCCCCCCCceeEEeee
Q 002487           23 LSARCKLSLSSNCPRFSTSQK----SSKFRSLSLLLSRRKYSERFSVRASATGPEVSE--PVLSDALPSFPQPVSVKIPF   96 (916)
Q Consensus        23 ~~~~~~~~~~~~~~~~~~~~~----~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~--~~~~~~~~~~~~~~~~~~~~   96 (916)
                      .--||.|++|+||||+.++.+    +.+.|..++|..+.+  +.|..|+.. +|..++  +.+.+..+.|++.+++.+++
T Consensus        10 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~--~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~~   86 (891)
T PLN00207         10 HLLRSPLPPSRNLPRFHDSESSPSISSSLPEAGLLKSSIK--KARSVRALL-RPVDSEDTSSVGEGPGPFPQQFSVKIPV   86 (891)
T ss_pred             hhccCCCCCCcCCceeecCCCCCCCCCCCccccccccccc--cccccceec-cccccccccccccCCCCCCcceEEEEEE
Confidence            346899999999998876655    456667777999888  999999887 777666  66788888889999988899


Q ss_pred             CCeeEEEEeCccccCCCceEEEEeCCeEEEEEEEecCCCCCCCCCCccccceeecccccccCCCCCcccCCCCCchhhhH
Q 002487           97 GDRQILVETGHMGRQASGAVTVTDGETIIYTSVCLADVPSEPSDFFPLNVNYQERFSAAGRTSGGFFKREGRTKDHEVLV  176 (916)
Q Consensus        97 ~~R~i~~etG~la~qAdGSa~v~~G~T~Vl~tV~~~~e~~~~~~f~pL~v~y~ek~~A~g~iPg~f~kReg~p~~~eil~  176 (916)
                      |.|+|.+|||++|+||||||++++|+|+|||||+..++++++.|||||+|+|+||+||+|||||||+||||+|+++|+|+
T Consensus        87 g~~~~~~etG~~a~qA~gav~v~~g~t~vl~t~~~~~~~~~~~dF~PLtV~y~Ek~~AaGkipggf~kREgrp~d~eiL~  166 (891)
T PLN00207         87 GDRHILVETGHIGRQASGSVTVTDGETIVYTSVCLADVPSEPSDFFPLSVHYQERFSAAGRTSGGFFKREGRTKDHEVLI  166 (891)
T ss_pred             CCEEEEEEhhHHHHhCCCcEEEEECCeEEEEEEEeccCCCCCCCccceeEeeeeehhhcCccCCceeccCCCCChHHHHH
Confidence            88899999999999999999999999999999999888999999999999999999999999999999999999999999


Q ss_pred             HHHhcCcccccccCCCcCeEEEEEEEEeecCCCChhHHHHHHHHHHhcCCCCCCCCceEEEEEEEECCEEEECCChHHHh
Q 002487          177 CRLIDRPLRPTLIKGFYHETQILSWVLSYDGLHFPDALAVTAAGIAVALSEVPNSKVIAGVRVGLVGDKFIVNPTTQEME  256 (916)
Q Consensus       177 sRlIdR~LRplfp~~~~~~iqI~~~VLs~Dg~~~~~~~ai~aAs~AL~~S~IP~~~~VaaV~vg~i~g~~ildPt~~E~~  256 (916)
                      +|||||+|||+||++|++++||+++|||+||+++++++||||||+||++|||||++||+|||||++||++|||||++|++
T Consensus       167 sRlIdR~lRPlfp~~~~~etQI~i~VLsaDg~~~pd~~AInAASaAL~~SgIP~~gpVaAVrVG~idg~~VlnPt~~E~~  246 (891)
T PLN00207        167 CRLIDRPLRPTMPKGFYHETQILSWVLSYDGLHSPDSLAVTAAGIAVALSEVPNLKAIAGVRVGLIGGKFIVNPTTKEME  246 (891)
T ss_pred             HHHHCccchhhccccCCCCcEEEEEEEeeCCCCChhhHHHHHHHHHHHhhCCCccCceEEEEEEEECCEEEECCCHHHHh
Confidence            99999999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             hCCeeEEEEeecCeEEEEEecCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCCcccCCCCCChhHHHHHHHHHH
Q 002487          257 DSQLDLLLAGSDDAILMIEGYCDFLSEEMLIQAVQVGQDAVREISNEVKALVEMCGKPKMLDTIKLPPPELYKHVEEIAG  336 (916)
Q Consensus       257 ~s~~dl~vagt~~~i~mie~~~~~~~e~~l~~al~~a~~~~~~i~~~~~~~~~~~gk~k~~~~~~~~~~~~~~~~~~~~~  336 (916)
                      .|++||+|+||.++|+|||++++++++++|.+||++||++|+.||++|+++++++|++|+++.....+++|.+.|++++.
T Consensus       247 ~s~ldLvvagt~~~IvMIE~~a~e~see~l~~Al~~a~~aik~i~~~~~el~~~~gk~k~~~~~~~~~~~l~~~v~~~~~  326 (891)
T PLN00207        247 ESELDLIMAGTDSAILMIEGYCNFLPEEKLLEAVEVGQDAVRAICKEIEVLVKKCGKPKMLDAIKLPPPELYKHVKEIAG  326 (891)
T ss_pred             cCCeeEEEEEcCCeEEEEEcCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCCccCCCCCCCHHHHHHHHHHHH
Confidence            99999999999999999999999999999999999999999999999999999999999998877789999999999999


Q ss_pred             HHHHHHHhccCchHHHHHHHHHHHHHHHHHhhcCCccccccccccccccccccCccccchhhccCcccCCccccCCCCCC
Q 002487          337 EELVKVLQIKNKIPRRKALSSLEEKVLTILSENGYVSKDETVGIVETIPDLLEDEDEDEEVVVDGEVDEGDVHIKPKSRK  416 (916)
Q Consensus       337 ~~~~~~~~~~~k~~r~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  416 (916)
                      ++|++|+++.+|++|+++++++++++++.|.++++..++..++..++++++++.++.+++.+++||+|+||+||+|.+|+
T Consensus       327 ~~~~~~~~~~~K~~R~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  406 (891)
T PLN00207        327 DELVKALQIRGKIPRRKALSSLEEKVLSILTEEGYVSKDESFGTSETRADLLEDEDEDEEVVVDGEVDEGDVHIKPIPRK  406 (891)
T ss_pred             HHHHHHHhccchHHHHHHHHHHHHHHHHHhhccccccccccccccccccccccccccchhcccccccccccccccccccc
Confidence            99999999999999999999999999999977555677888999999999987765444467899999999999999999


Q ss_pred             CCCcccchHHHHHHHHHHHHHHHHHHHhcCCCCCCCCCCCCccceEEEeCCCCCCcceeEEEeCCeEEEEEEEecCcccc
Q 002487          417 STPMLFSEVDVKLVFKEVTSKFLRRRIVEGGRRSDGRFADGIRPISSRCGLLPRAHGSALFTRGETQSLAVITLGDKQMA  496 (916)
Q Consensus       417 ~~~~~~~~~~~~~~~~~~~~~~~r~~il~~~~R~DGR~~~eiR~I~ie~g~l~~a~GSalf~~G~TqVl~~Vt~Gp~~~~  496 (916)
                      ++|.++...+++.+|++++++++|++|+++|+|+|||+++|+|||+|++|++++|||||+|++|+|||||+||+||.++.
T Consensus       407 ~~~~~~~~~~i~~~~~~~~k~~~R~~i~~~g~R~DGR~~~eiRpI~~e~G~Lp~A~GSAlf~~G~TqVLatVtlGp~~~~  486 (891)
T PLN00207        407 SSPLLFSEVDVKLVFKEVTSKFLRRRIVEGGKRSDGRTPDEIRPINSSCGLLPRAHGSALFTRGETQALAVVTLGDKQMA  486 (891)
T ss_pred             cccccccHHHHHHHHHHHHHHHHHHHHhcCCCCCCCCCcCccceEEEEeCCcCCCCceEEEEECCeEEEEEEEecCcccc
Confidence            99999998899999999999999999999999999999999999999999999999999999999999999999999888


Q ss_pred             ccccCCCCCCceeEEEEEEeeCCCCcccccCCCCCChhhHHHHHHHHHHhccccCCCCCCCeEEEEEEEEEecCCCcchh
Q 002487          497 QRIDNLESDDEVKRFYLQYSFPPSSVGEVGRIGAPSRREIGHGTLAERALEPVLPSDNDFPYTIRVESTITESNGSSSMA  576 (916)
Q Consensus       497 ~~~d~~~~~~~~~~~~~~~~fpP~s~~e~~r~g~~~rrei~~~~l~eraL~~vip~~~~fp~tI~V~~~VLesdGs~~~A  576 (916)
                      |..+.+......++|++||+|||||++++++.|+|+|||++|+++++|+|+|+||.++.|||+|+|+++||++|||++||
T Consensus       487 q~~d~l~~~~~~~~f~~~y~fPPfs~ge~~r~g~psrREi~hg~L~eRALrpvip~~~~fP~tIrV~~~VLesDGSssmA  566 (891)
T PLN00207        487 QRIDNLVDADEVKRFYLQYSFPPSCVGEVGRIGAPSRREIGHGMLAERALEPILPSEDDFPYTIRVESTITESNGSSSMA  566 (891)
T ss_pred             ccccccccccceeeEEEEEEcCCCCCccccCCCCCCHHHHHHHHHHHHHHHHhCCcccCCCEEEEEEEEEEeCCCChHHH
Confidence            88777654456789999999999999999999999999999999999999999998668999999999999999999999


Q ss_pred             HHhHHHHHHHhcCCCcccceeEEEEEEEccCCCCCCCCCceeecCCChhhhhcCCccEEEEecCCceeEEEeeccccCCC
Q 002487          577 SVCGGCLALQDAGVPIKCSIAGVAMGMVLDTDEFGGDGTPLILSDITGSEDASGDMDFKVAGNEDGITAFQMDIKVGGIT  656 (916)
Q Consensus       577 sv~aaslAL~dAGIP~~~~Vagvsvgli~~~~~~~~~~~~~iL~Dpt~~Ed~~gdmdf~Vagt~~gItalq~d~K~ggis  656 (916)
                      +|||+|||||||||||+++|+||+||++.+.++++++++|.+|+||++.|++.|+|||+||||.+|||++|||+|+++++
T Consensus       567 aV~aaSLALmDAGIPmk~~VAGvsvGli~d~~~~~~~g~~~IL~Dp~g~Ed~~gdmDfkVAgT~~gIt~iqmd~k~~gis  646 (891)
T PLN00207        567 SVCGGCLALQDAGVPVKCPIAGIAMGMVLDTEEFGGDGSPLILSDITGSEDASGDMDFKVAGNEDGITAFQMDIKVGGIT  646 (891)
T ss_pred             HHHHHHHHHHhcCCCccCceeEEEEEEEecccccCCCCcEEEEeCCCHHHHhcCCceEEEEecccceEEEEEecccCCCC
Confidence            99999999999999999999999999996544444456788999999999999999999999999999999999999999


Q ss_pred             HHHHHHHHHHHHhhhHHHHHHHHhcCCCCCCCCCCCCCeEEEEeeccceeeeeecCCchhHHHHHHHhCCceeccCCCcc
Q 002487          657 LPVMKKALQQAKDGRRHILAEMLKCSPPPSNSLSKHAPLIHIMKVKPEKINLIIGSGGKKVKSIIEETGVEAIDTEDDGT  736 (916)
Q Consensus       657 ~e~l~eaL~~A~~a~~~Il~~m~~~i~~~r~~~~~~aP~i~~~~I~~~ki~~vIG~gGk~Ik~I~~~~~v~~Idi~d~g~  736 (916)
                      .++|.+||++|+++|.+|++.|+++++.||.++++|+|++++++|+|+||+++||+||+|||+|+++||++.|||+|+|.
T Consensus       647 ~e~l~eAL~~A~~g~~~Il~~M~~~i~~pr~~~s~~aP~i~~~~i~~~ki~~vIG~GGktIk~I~eetg~~~Idi~ddg~  726 (891)
T PLN00207        647 LPIMERALLQAKDGRKHILAEMSKCSPPPSKRLSKYAPLIHIMKVKPEKVNMIIGSGGKKVKSIIEETGVEAIDTQDDGT  726 (891)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHhhhhhhhcccCCeeEEEEcCHHHHHHHhcCCchhHHHHHHHHCCCccCcCCCee
Confidence            99999999999999999999999999999999999999999999999999999999999999999999997699999999


Q ss_pred             eeEEecccccHHHHHHHHHhhhcCCCCCcEEEccEEEEEecceEEEEECCCeeeEEeccccCcccccCccccccCCCEEE
Q 002487          737 VKITAKDLSSLEKSKAIISNLTMVPTVGDIYRNCEIKSIAPYGVFVEIAPGREGLCHISELSSNWLAKAEDVVKVGDLVD  816 (916)
Q Consensus       737 v~I~~~~~~~~~~a~~~i~~l~~~~~vG~i~~G~~V~~I~~fGaFVel~~g~eGlvhiSels~~~v~~~~~~~kvGd~V~  816 (916)
                      |.|++.+.+++++|+++|+.++.++++|++|+|++|++|++||+||+|.+|++||||+|+|+|+++.++.++|++||.|+
T Consensus       727 V~I~a~d~~~i~~A~~~I~~l~~~~~vG~iy~~g~V~~I~~FGaFVeL~~g~EGLVHISeLs~~rv~~~~dv~kvGD~V~  806 (891)
T PLN00207        727 VKITAKDLSSLEKSKAIISSLTMVPTVGDIYRNCEIKSIAPYGAFVEIAPGREGLCHISELSSNWLAKPEDAFKVGDRID  806 (891)
T ss_pred             EEEEeCCHHHHHHHHHHHHHHhcCcCCCcEEECcEEEEEeccEEEEEeCCCCEEEEEhhhcCCccccCHHHhcCCCCEEE
Confidence            99999999999999999999999999999996339999999999999999999999999999999999999999999999


Q ss_pred             EEEEEEcCCCceEEEEeecCCCCCCCCCC
Q 002487          817 VKLIEVNDKGQLRLSRRALLPEADAENPP  845 (916)
Q Consensus       817 VKVi~iD~~gkI~LS~K~~~~~p~~~~~~  845 (916)
                      |||+++|.+|||.||+|+++++||..+..
T Consensus       807 VkVi~ID~~grI~LSlK~l~~~Pw~~~~~  835 (891)
T PLN00207        807 VKLIEVNDKGQLRLSRRALLPEANSEKSS  835 (891)
T ss_pred             EEEEEECCCCcEEEEEeccccCchhhhhh
Confidence            99999999899999999999999998764

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

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

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

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

>TIGR03591 polynuc_phos polyribonucleotide nucleotidyltransferase	Back alignment and domain information

>TIGR02065 ECX1 archaeal exosome-like complex exonuclease 1	Back alignment and domain information

>PRK03983 exosome complex exonuclease Rrp41; Provisional	Back alignment and domain information

>PRK00173 rph ribonuclease PH; Reviewed	Back alignment and domain information

>PLN00207 polyribonucleotide nucleotidyltransferase; Provisional	Back alignment and domain information

>COG0689 Rph RNase PH [Translation, ribosomal structure and biogenesis]	Back alignment and domain information

>KOG1068 consensus Exosomal 3'-5' exoribonuclease complex, subunit Rrp41 and related exoribonucleases [Translation, ribosomal structure and biogenesis]	Back alignment and domain information

>TIGR02065 ECX1 archaeal exosome-like complex exonuclease 1	Back alignment and domain information

>TIGR01966 RNasePH ribonuclease PH	Back alignment and domain information

>PRK04282 exosome complex RNA-binding protein Rrp42; Provisional	Back alignment and domain information

>PRK00173 rph ribonuclease PH; Reviewed	Back alignment and domain information

>PRK03983 exosome complex exonuclease Rrp41; Provisional	Back alignment and domain information

>TIGR03591 polynuc_phos polyribonucleotide nucleotidyltransferase	Back alignment and domain information

>TIGR01966 RNasePH ribonuclease PH	Back alignment and domain information

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

>COG0689 Rph RNase PH [Translation, ribosomal structure and biogenesis]	Back alignment and domain information

>COG2123 RNase PH-related exoribonuclease [Translation, ribosomal structure and biogenesis]	Back alignment and domain information

>KOG1069 consensus Exosomal 3'-5' exoribonuclease complex, subunit Rrp46 [Translation, ribosomal structure and biogenesis]	Back alignment and domain information

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

>PRK04282 exosome complex RNA-binding protein Rrp42; Provisional	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

>KOG1068 consensus Exosomal 3'-5' exoribonuclease complex, subunit Rrp41 and related exoribonucleases [Translation, ribosomal structure and biogenesis]	Back alignment and domain information

>KOG1069 consensus Exosomal 3'-5' exoribonuclease complex, subunit Rrp46 [Translation, ribosomal structure and biogenesis]	Back alignment and domain information

>KOG1614 consensus Exosomal 3'-5' exoribonuclease complex, subunit Rrp45 [Translation, ribosomal structure and biogenesis]	Back alignment and domain information

>KOG1613 consensus Exosomal 3'-5' exoribonuclease complex, subunit Rrp43 [Translation, ribosomal structure and biogenesis]	Back alignment and domain information

>PF01138 RNase_PH: 3' exoribonuclease family, domain 1 This Prosite family only includes Ribonuclease PH; InterPro: IPR001247 The PH (phosphorolytic) domain is responsible for 3'-5' exoribonuclease activity, although in some proteins this domain has lost its catalytic function	Back alignment and domain information

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

>COG2123 RNase PH-related exoribonuclease [Translation, ribosomal structure and biogenesis]	Back alignment and domain information

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

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

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

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

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

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

>KOG1612 consensus Exosomal 3'-5' exoribonuclease complex, subunit Rrp42 [Translation, ribosomal structure and biogenesis]	Back alignment and domain information

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

>PRK06676 rpsA 30S ribosomal protein S1; Reviewed	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

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

>PF01138 RNase_PH: 3' exoribonuclease family, domain 1 This Prosite family only includes Ribonuclease PH; InterPro: IPR001247 The PH (phosphorolytic) domain is responsible for 3'-5' exoribonuclease activity, although in some proteins this domain has lost its catalytic function	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

>TIGR00717 rpsA ribosomal protein S1	Back alignment and domain information

>TIGR00717 rpsA ribosomal protein S1	Back alignment and domain information

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

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

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

>KOG1614 consensus Exosomal 3'-5' exoribonuclease complex, subunit Rrp45 [Translation, ribosomal structure and biogenesis]	Back alignment and domain information

>PRK08582 hypothetical protein; Provisional	Back alignment and domain information

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

>PRK06676 rpsA 30S ribosomal protein S1; Reviewed	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

>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

>cd05686 S1_pNO40 S1_pNO40: pNO40 , S1-like RNA-binding domain	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

>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

>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

>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

>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

>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

>PRK07252 hypothetical protein; Provisional	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

>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

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

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

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

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

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

>cd05692 S1_RPS1_repeat_hs4 S1_RPS1_repeat_hs4: Ribosomal protein S1 (RPS1) domain	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

>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

>cd05689 S1_RPS1_repeat_ec4 S1_RPS1_repeat_ec4: Ribosomal protein S1 (RPS1) 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

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

>PF03726 PNPase: Polyribonucleotide nucleotidyltransferase, RNA binding domain; InterPro: IPR015848 The PH (phosphorolytic) domain is responsible for 3'-5' exoribonuclease activity, although in some proteins this domain has lost its catalytic function	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

>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

>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

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

>COG2183 Tex Transcriptional accessory protein [Transcription]	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

>cd04471 S1_RNase_R S1_RNase_R: RNase R C-terminal S1 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

>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

>KOG1612 consensus Exosomal 3'-5' exoribonuclease complex, subunit Rrp42 [Translation, ribosomal structure and biogenesis]	Back alignment and domain information

>smart00316 S1 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

>cd04473 S1_RecJ_like S1_RecJ_like: The S1 domain of the archaea-specific RecJ-like exonuclease	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

>cd02393 PNPase_KH Polynucleotide phosphorylase (PNPase) K homology RNA-binding domain (KH)	Back alignment and domain information

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

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

>KOG1613 consensus Exosomal 3'-5' exoribonuclease complex, subunit Rrp43 [Translation, ribosomal structure and biogenesis]	Back alignment and domain information

>PF03725 RNase_PH_C: 3' exoribonuclease family, domain 2 This Prosite family only includes Ribonuclease PH; InterPro: IPR015847 The PH (phosphorolytic) domain is responsible for 3'-5' exoribonuclease activity, although in some proteins this domain has lost its catalytic function	Back alignment and domain information

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

>TIGR02063 RNase_R ribonuclease R	Back alignment and domain information

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

>PRK13763 putative RNA-processing protein; Provisional	Back alignment and domain information

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

>TIGR03665 arCOG04150 arCOG04150 universal archaeal KH domain protein	Back alignment and domain information

>PRK08563 DNA-directed RNA polymerase subunit E'; 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

>TIGR00448 rpoE DNA-directed RNA polymerase (rpoE), archaeal and eukaryotic form	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

>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

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

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

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

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

>PF03725 RNase_PH_C: 3' exoribonuclease family, domain 2 This Prosite family only includes Ribonuclease PH; InterPro: IPR015847 The PH (phosphorolytic) domain is responsible for 3'-5' exoribonuclease activity, although in some proteins this domain has lost its catalytic function	Back alignment and domain information

>PRK05054 exoribonuclease II; Provisional	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

>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

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

>cd02394 vigilin_like_KH K homology RNA-binding domain_vigilin_like	Back alignment and domain information

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

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

>TIGR02062 RNase_B exoribonuclease II	Back alignment and domain information

>cd05790 S1_Rrp40 S1_Rrp40: Rrp40 S1-like RNA-binding 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

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

>PRK04163 exosome complex RNA-binding protein Rrp4; Provisional	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

>PF00013 KH_1: KH domain syndrome, contains KH motifs	Back alignment and domain information

>PTZ00162 DNA-directed RNA polymerase II subunit 7; 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

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

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

>PF13509 S1_2: S1 domain; PDB: 3GO5_A	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

>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

>smart00322 KH K homology RNA-binding 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

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

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

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

>PRK11712 ribonuclease G; Provisional	Back alignment and domain information

>cd02396 PCBP_like_KH K homology RNA-binding domain, PCBP_like	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

>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

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

>TIGR03665 arCOG04150 arCOG04150 universal archaeal KH domain protein	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

>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

>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

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

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

>cd05690 S1_RPS1_repeat_ec5 S1_RPS1_repeat_ec5: Ribosomal protein S1 (RPS1) domain	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

>cd05687 S1_RPS1_repeat_ec1_hs1 S1_RPS1_repeat_ec1_hs1: Ribosomal protein S1 (RPS1) domain	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

>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

>PRK13763 putative RNA-processing protein; Provisional	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

>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

>PRK08582 hypothetical protein; Provisional	Back alignment and domain information

>cd05789 S1_Rrp4 S1_Rrp4: Rrp4 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

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

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

>PRK07252 hypothetical protein; Provisional	Back alignment and domain information

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

>KOG1676 consensus K-homology type RNA binding proteins [RNA processing and modification]	Back alignment and domain information

>PF13014 KH_3: KH 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

>PRK05807 hypothetical protein; Provisional	Back alignment and domain information

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

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

>COG1530 CafA Ribonucleases G and E [Translation, ribosomal structure and biogenesis]	Back alignment and domain information

>PRK08059 general stress protein 13; Validated	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

>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

>PRK12442 translation initiation factor IF-1; Reviewed	Back alignment and domain information

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

>TIGR00008 infA translation initiation factor IF-1	Back alignment and domain information

>COG1094 Predicted RNA-binding protein (contains KH domains) [General function prediction only]	Back alignment and domain information

>smart00316 S1 Ribosomal protein S1-like RNA-binding domain	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

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

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

>cd05692 S1_RPS1_repeat_hs4 S1_RPS1_repeat_hs4: Ribosomal protein S1 (RPS1) domain	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

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

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

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

>KOG1676 consensus K-homology type RNA binding proteins [RNA processing and modification]	Back alignment and domain information

>PF00313 CSD: 'Cold-shock' DNA-binding domain; InterPro: IPR002059 When Escherichia coli is exposed to a temperature drop from 37 to 10 degrees centigrade, a 4-5 hour lag phase occurs, after which growth is resumed at a reduced rate []	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

>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

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

>PRK04012 translation initiation factor IF-1A; Provisional	Back alignment and domain information

Homologous Structure Templates