Psyllid ID: psy6283

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Local Sequence Feature Prediction

Residue Number Marker
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100-------110-------120-------130-------140-------150-------160-------170-------180-------190-------200-------210-------220-------230-------240-------250-------260-------270-------280-------290-------300-------310-------320-------330-------340-------350-------360-------370-------380-------390-------400-------410-------420-------430-------440-------450-------460-------470-------480-------490-------500-------510-------520-------530-------540-------550-------560-------570-------580-------590-------600-------610-------620-------630-------640-------650-------660-------670-------680-------690-------700-------710-------720-------730-------740-------750-------760-------770-------780-------790-------800-------810-------820-------830-------840-------850-------860-------870-------880-------890-------900-------910-------920-------930-------940-------950-------960-------970-------980-------990------1000------1010------1020------1030
Protein Sequence
MLILATFVPTTDNFSGGVDVFGDLIKLSIDLIDYVGKYLVLSSIPGKGHAKILTAGVGWAGAEVILTRFLDLWVGARGAEFDWKYIQNSLDSNICLIDKTNKFAAFQKLKDLKGQGVKHKYEFTADENVYEEVSEKEYTERVLKRQEDDWIDDDGGDGYVEDGREIFDDDIEDVPQKKEKHDKRKKNKNIQNPNAKDDSLPLATDHENKKVFRMFFLDAFEDIYKQPGTVYLFGKVFVKENNSHSSCCVIVQNIDRKIYLLPRSEHLKTKEPVSIAQVYSEFDQIATQYKILDFKSRKIEKKYAFNLPGVPDLSEYLEVRYSAKCPALPSDLSGDTFSHVFGTKTSFLENLLLERKIKGPSWLEFPEAEKFPSRISWCKYEVQCNQMEKIRSKQGLIYLIGIVEFIKFTMLHSSYIIKIMCELNVLPLAIQITNVCGNVLSRTLMGGRSERNEFLLLHAFHEKSYVLPDKQYGKNKKEGEETGEANKGKGRKKAAYSGGLVLEPKKGFYDKFIILMDFNSLYPSIIQEYNICFTTIPVRMLQDSDITTLCEYLPEHQVDTGILPSEIKKLVESRRQVKALMKQPNLSSDLLMQYDIRQKALKLTANSMYGCLGFPNSRFFAQPLAALVTAKGREILLNTKSLVENLNYEVIYGDTDSLMISCNVNDYDSVFKIGNQIKSECNKLYKQLELDIDGVYKYMLLLKKKKYAALSISKLSNGKMICSQEIKGVDVVRRDWSQLASEAGKFVISQILDEQSYTDYSLDDRLQNIHEHMKKIRTDLDNGFVPLTLLEITKQLTKAPEGGKVCITQIRLSRNRRGRRRRRRKKKEEKKKWKRRGGGRRRRRGKKEEEKKKKKEEEEEGGEKEEEEGGGGGGRRRRRRRRSGKEEEEKKKKEGGGGRRRRRRKKRRRSRRRRSRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRSGKEEEEEEKKKEEKKKEEEEKKKKEGKTKKEEKKKEEEEEKKKKKKEEEKEEEEKKEEEEKEEEEKKRRRIRRKR
Secondary Structure (PSIPRED)
ccEEEEEcccccccccccccccccHHHHHHHHHHcccEEEEEcccccccccEEEcccccccHHHHHHHHHHHHHccccccccHHHHHHHccccccEEccccHHHHHHHHHHHHHccccccccccccccccccccHHHHHHHHHHHcccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccEEEEEEEEccccccccccEEEEEEEEEEccccEEEEEEEEEccEEEEEEEEEccccccccccccHHHHHHHHHHHHHHcccccEEEEEEEcccccccccccccccEEEEEcccccccccccccccccccccccccHHHHHHHHHccccccccccccccccccccccHHHHHHHHcccHHHHHHcccccHHHHHHHHHHHHHHHHHHHHHHHHHccHHHHHHHHHHHcccHHHHccccHHHHHHHHHHHHHHHccccccccccccccccccccccccccccccccccccEEEEccccccccccEEEEEcccccHHHHHHHccccccccccccccccccccccccccccccccccHHHHHHHHHHHHHHHHHHccccccHHHHHccHHHHHHHHHHHHcccccccccccccccHHHHHHHHHHHHHHHHHHHHHHHHcccEEEEccccEEEEEcccccHHHHHHHHHHHHHHHHcccccEEEEEEEEEccccccccccEEEEEEEEcccccEEEccccccccccccccHHHHHHHHHHHHHHHHcccccccccHHHHHHHHHHHHHHHHHHHHccccccccEEEEEEcccccccccccccHHHHHHHHHccccccccccccEEEEEEEccccccccccHHHHHHcccHHHHHcccccccccccccHHHHHHHHHccccHHHHHHHcccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHcccHHHHHHHHHHHHHHHHHHHHHHHccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHc
Secondary Structure Prediction (SSPRO)
cEEEEEEccccccccccccHHHHHHHHHHHHHHHHccEEEEEccccccHHHHHHccccHHHHHHHHHHHHHHHHccccccEcHHHHHHHccccccHHHccccccHHHHHccccccccccccEEEccccccccccccccccccHHHcccccccccccccccccccccccccccccccccccccccccccccEEEEEcccccccccccccccEEEEEEEEccccccccccEEEEEEEEEEEccccEEEEEEEEEccEEEEEEccccccccccccccHHHHHHHHHHHHccccccccccccccHHccccccHHHHHHHHcEEEEEccccccccccccccEEcccccccccEEEEEEEEEcccccEEEEccccHHHHHHHHHHHHHHcccccHHHHHHccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHccHHHHHHHccHHHHHHHHHHHHHHHcccEEcccccccccHccccccccEEEcccccccEccEEEEccccccccccEEEEEHHcHHHHHHHHHHcEEEEEccccccccEEcccccccccccHHccHHHHHHHHHHHHHHHHHHHHHcccccHHHHHHHcHHHHHHEEEcccccccccccccccccHHHHHHHHHHHHHHHHHHHHHHHHcccEEEEEcccEEEEEcccccHHHHHHHHHHHHHHHHHcccccEEEEHHccccEEEEEccEEEEEEEEccccccccccHccccHHHHHcccHHHHHHHHHHHHHHHHHccccccccccHHHHHHHHHHHHHHHHHHcccccHHHEEEEHHHcccHHHHHccHHHHHHHHHHHHcccccccccccEEEEEEEccccccHHHHHHHHHHccccHEEEccccccccccccccHHHHHHcccccHHHHHccccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHcccccHHHHHHHHHHHHHHHHHHHHccccccHHHHcHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHcc
Coil and Loop (DISEMBL)
mlilatfvpttdnfsggvdvfGDLIKLSIDLIDYVGKYLVlssipgkghaKILTAGVGWAGAEVILTRFLDLWVgargaefdWKYIQNSldsniclidktNKFAAFQKLKdlkgqgvkhkyeftadenvyeevseKEYTERVLKRQeddwidddggdgyvedgreifdddiedvpqkkekhdkrkknkniqnpnakddslplatdhenKKVFRMFFLDAFEDiykqpgtvYLFGKVFVkennshssccVIVQNIdrkiyllprsehlktkepvsiAQVYSEFDQIATQYKILDFKSRKIEKKYafnlpgvpdlseYLEVRysakcpalpsdlsgdtfshvfgTKTSFLENLLLErkikgpswlefpeaekfpsriswcKYEVQCNQMEKIRSKQGLIYLIGIVEFIKFTMLHSSYIIKIMCELNVLPLAIQITNVCGNVLsrtlmggrseRNEFLLLHAFHeksyvlpdkqygknkkegeetgeankgkgrkkaaysgglvlepkkgfydKFIILMdfnslypsIIQEYNICFttipvrmlqdsdiTTLCeylpehqvdtgilPSEIKKLVESRRQVKALmkqpnlssdLLMQYDIRQKALKLTANsmygclgfpnsrffAQPLAALVTAKGREILLNTKSLVENLnyeviygdtdslmiscnvndydsvFKIGNQIKSECNKLYKQLELDIDGVYKYMLLLKKKKYAALSISKLsngkmicsqeikgvdVVRRDWSQLASEAGKFVISQildeqsytdysldDRLQNIHEHMKKIRTdldngfvplTLLEITKQltkapeggkvcITQIRLSRNRRGRRRRRRKKKEEKKKWkrrgggrrrrrgkkeeEKKKKKEeeeeggekeeeeggggggrrrrrrrrsgkeeeekkkkeggggrrrrrrKKRRRSRRRRSRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRrrrsgkeeeEEEKKKEEKKKEEEEKKKKEGKTKKEEKKKEEEEEKKKKKKEEEKEEEEKKEEEEKEEEEKKRRRIRRKR
Flexible Loop (DISEMBL)
mlilatfvpttdnfsggvDVFGDLIKLSIDLIDYVGKYLVLSSIPGKGHAKILTAGVGWAGAEVILTRFLDLWVGARGAEFDWKYIQNSLDSNICLIDKTNKFAAFQKLkdlkgqgvkhkyeftadenvyeevsekeytervlkrqeddwidddggdGYVEDGreifdddiedvpqkkekhdkrkknkniqnpnakddslplaTDHENKKVFRMFFLDAFEDIYKQPGTVYLFGKVFVKENNSHSSCCVIVQNIDRKIYLLprsehlktkepVSIAQVYSEFDQIATQYKILDFKSRKIEKKYAFNLPGVPDLSEYLEVRYSAKCPALPSDLSGDTFSHVFGTKTSFLENLLLERKIkgpswlefpeaekfpsriSWCKYEVQCNQMEKIRSKQGLIYLIGIVEFIKFTMLHSSYIIKIMCELNVLPLAIQITNVCGNVLSRTLMGGRSERNEFLLLHAFHeksyvlpdkqygknkkegeetgeankgkgrkkaaysgglvlepkKGFYDKFIILMDFNSLYPSIIQEYNICFTTIPVRMLQDSDITTLCEYLPehqvdtgilpSEIKKLVESRRQVKAlmkqpnlssdlLMQYDIRQKALKLTANSMYGCLGFPNSRFFAQPLAALVTAKGREILLNTKSLVENLNYEVIYGDTDSLMISCNVNDYDSVFKIGNQIKSECNKLYKQLELDIDGVYKYMLLLKKKKYAALSIsklsngkmicsqEIKGVDVVRRDWSQLASEAGKFVISQILDEQSYTDYSLDDRLQNIHEHMKKIRTDLDNGFVPLTLLEITkqltkapeggkvcitqirlsrnrrgrrrrrrkkkeekkkwkrrgggrrrrrgkkeeekkkkkeeeeeggekeeeeggggggrrrrrrrrsgkeeeekkkkeggggrrrrrrkkrrrsrrrrsrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrsgkeeeeeekkkeekkkeeeekkkkegktkkeekkkeeeeekkkkkkeeekeeeekkeeeekeeeekkrrrirrkr
Low Complexity Region (SEG)
MLILATFVPTTDNFSGGVDVFGDLIKLSIDLIDYVGKYLVLSSIPGKGHAKILTAGVGWAGAEVILTRFLDLWVGARGAEFDWKYIQNSLDSNICLIDKTNKFAAFQKLKDLKGQGVKHKYEFTADENVYEEVSEKEYTERVLKRQEddwidddggdgYVEDGREIFDDDIEDVPQkkekhdkrkknkNIQNPNAKDDSLPLATDHENKKVFRMFFLDAFEDIYKQPGTVYLFGKVFVKENNSHSSCCVIVQNIDRKIYLLPRSEHLKTKEPVSIAQVYSEFDQIATQYKILDFKSRKIEKKYAFNLPGVPDLSEYLEVRYSAKCPALPSDLSGDTFSHVFGTKTSFLENLLLERKIKGPSWLEFPEAEKFPSRISWCKYEVQCNQMEKIRSKQGLIYLIGIVEFIKFTMLHSSYIIKIMCELNVLPLAIQITNVCGNVLSRTLMGGRSERNEFLLLHAFHEKSYVLPDKQYgknkkegeetgeankgkgRKKAAYSGGLVLEPKKGFYDKFIILMDFNSLYPSIIQEYNICFTTIPVRMLQDSDITTLCEYLPEHQVDTGILPSEIKKLVESRRQVKALMKQPNLSSDLLMQYDIRQKALKLTANSMYGCLGFPNSRFFAQPLAALVTAKGREILLNTKSLVENLNYEVIYGDTDSLMISCNVNDYDSVFKIGNQIKSECNKLYKQLELDIDGVykymlllkkkkyaalsisklsNGKMICSQEIKGVDVVRRDWSQLASEAGKFVISQILDEQSYTDYSLDDRLQNIHEHMKKIRTDLDNGFVPLTLLEITKQLTKAPEGGKVCITQIRLSRNrrgrrrrrrkkkeekkkwkrrgggrrrrrgkkeeekkkkkeeeeeggekeeeeggggggrrrrrrrrsgkeeeekkkkeggggrrrrrrkkrrrsrrrrsrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrsgkeeeeeekkkeekkkeeeekkkkegktkkeekkkeeeeekkkkkkeeekeeeekkeeeekeeeekkrrrirrkr
Disordered region (IsUnstruct)
*LILATFVPTTDNFSGGVDVFGDLIKLSIDLIDYVGKYLVLSSIPGKGHAKILTAGVGWAGAEVILTRFLDLWVGARGAEFDWKYIQNSLDSNICLIDKTNKFAAFQKLKDLKGQGVKHKYEFTADENVYEEVS***YTERVL*****DWIDD****GYV************************************************KKVFRMFFLDAFEDIYKQPGTVYLFGKVFVKENNSHSSCCVIVQNIDRKIYLLPRSEHLKTKEPVSIAQVYSEFDQIATQYKILDFKSRKIEKKYAFNLPGVPDLSEYLEVRYSAKCPALPSDLSGDTFSHVFGTKTSFLENLLLERKIKGPSWLEFPEAEKFPSRISWCKYEVQCNQMEKIRSKQGLIYLIGIVEFIKFTMLHSSYIIKIMCELNVLPLAIQITNVCGNVLSRTLMGGRSERNEFLLLHAFHEKSYVL****************************YSGGLVLEPKKGFYDKFIILMDFNSLYPSIIQEYNICFTTIPVRMLQDSDITTLCEYLPEHQVDTGILPSEIKKLVE*************LSSDLLMQYDIRQKALKLTANSMYGCLGFPNSRFFAQPLAALVTAKGREILLNTKSLVENLNYEVIYGDTDSLMISCNVNDYDSVFKIGNQIKSECNKLYKQLELDIDGVYKYMLLLKKKKYAALSISKLSNGKMICSQEIKGVDVVRRDWSQLASEAGKFVISQILDEQSYTDYSLDDRLQNIHEHMKKIRTDLDNGFVPLTLLEITKQLTKAPEGGKVCITQIR***************************************************************************************************************************************************************************************************************************
Disordered Region (DISOPRED)
*LILATFVPTTDNFSGGVDVFGDLIKLSIDLIDYVGKYLVLSSIPGKGHAKILTAGVGWAGAEVILTRFLDLWVGARGAEFDWKYIQNS********************************************************************************************************************HENKKVFRMFFLDAFEDIYKQPGTVYLFGKVFVKENNSHSSCCVIVQNIDRKIYLLPRSEH******V**AQVYSEFDQIATQYKILDFKSRKIEKKYAFNLPGVPDLSEYLEVRYSAKCPALPSDLSGDTFSHVFGTKTSFLENLLLERKIKGPSWLEFPEAEKFPSRISWCKYEVQCNQMEKIRSKQGLIYLIGIVEFIKFTMLHSSYIIKIMCELNVLPLAIQITNVCGNVLSRTLMGGRSERNEFLLLHAFHEKSYVLPDKQY**************************GLVLEPKKGFYDKFIILMDFNSLYPSIIQEYNICFTTIPVRMLQDSDITTLCEYLPEHQVDTGILPSEIKKLVESRRQV***************QYDIRQKALKLTANSMYGCLGFPNSRFFAQPLAALVTAKGREILLNTKSLVENLNYEVIYGDTDSLMISCNVNDYDSVFKIGNQIKSECNKLYKQLELDIDGVYKYMLLLKKKKYAALSISKLSNGKMICSQEIKGVDVVRRDWSQLASEAGKFVISQILDEQSYTDYSLDDRLQNIHEHMKKIRTDLDNGFVPLTLLEITKQLTKA****KVCITQIRLS***************EKKKWKRR**************************************************************************************************************************************************************************************************
Disordered Region (DISEMBL)
MLILATFVPTTDNFSGGVDVFGDLIKLSIDLIDYVGKYLVLSSIPGKGHAKILTAGVGWAGAEVILTRFLDLWVGARGAEFDWKYIQNSLDSNICLIDKTNKFAAFQKLKDLKGQGVKHKYEFTADENVYEEVSEKEYTERVLKRQEDDWIDDDGGDGYVEDGREIFDDDIEDV*************KNIQNPNAKDDSLPLATDHENKKVFRMFFLDAFEDIYKQPGTVYLFGKVFVKENNSHSSCCVIVQNIDRKIYLLPRSEHLKTKEPVSIAQVYSEFDQIATQYKILDFKSRKIEKKYAFNLPGVPDLSEYLEVRYSAKCPALPSDLSGDTFSHVFGTKTSFLENLLLERKIKGPSWLEFPEAEKFPSRISWCKYEVQCNQMEKIRSKQGLIYLIGIVEFIKFTMLHSSYIIKIMCELNVLPLAIQITNVCGNVLSRTLMGGRSERNEFLLLHAFHEKSYVLPDKQYG********************AAYSGGLVLEPKKGFYDKFIILMDFNSLYPSIIQEYNICFTTIPVRMLQDSDITTLCEYLPEHQVDTGILPSEIKKLVESRRQVKALMKQPNLSSDLLMQYDIRQKALKLTANSMYGCLGFPNSRFFAQPLAALVTAKGREILLNTKSLVENLNYEVIYGDTDSLMISCNVNDYDSVFKIGNQIKSECNKLYKQLELDIDGVYKYMLLLKKKKYAALSISKLSNGKMICSQEIKGVDVVRRDWSQLASEAGKFVISQILDEQSYTDYSLDDRLQNIHEHMKKIRTDLDNGFVPLTLLEITKQLTKAPEGGKVCITQIRLS*************************************************************************************************************************************************************************************************************************
Disordered Region (DISPRO)
MLILATFVPTTDNFSGGVDVFGDLIKLSIDLIDYVGKYLVLSSIPGKGHAKILTAGVGWAGAEVILTRFLDLWVGARGAEFDWKYIQNSLDSNICLI*KTNKFAAFQKLKDLKGQGVKHKYEFTADENVY***************************************DIEDVPQKKEKHDKRKKNKNIQNPNAKDDSLPLATDHENKKVFRMFFLDAFEDIYKQPGTVYLFGKVFVKENNSHSSCCVIVQNIDRKIYLLPRSEHLKTKEPVSIAQVYSEFDQIATQYKILDFKSRKIEKKYAFNLPGVPDLSEYLEVRYSAKCPALPSDLSGDTFSHVFGTKTSFLENLLLERKIKGPSWLEFPEAEKFPSRISWCKYEVQCNQMEKIRSKQGLIYLIGIVEFIKFTMLHSSYIIKIMCELNVLPLAIQITNVCGNVLSRTLMGGRSERNEFLLLHAFHEKSYVLPDKQY*********TGEANKGKGRKKAAYSGGLVLEPKKGFYDKFIILMDFNSLYPSIIQEYNICFTTIPVRMLQDSDITTLCEYLPEHQVDTGILPSEIKKLVESRRQVKALMKQPNLSSDLLMQYDIRQKALKLTANSMYGCLGFPNSRFFAQPLAALVTAKGREILLNTKSLVENLNYEVIYGDTDSLMISCNVNDYDSVFKIGNQIKSECNKLYKQLELDIDGVYKYMLLLKKKKYAALSISKLSNGKMICSQEIKGVDVVRRDWSQLASEAGKFVISQILDEQSYTDYSLDDRLQNIHEHMKKIRTDLDNGFVPLTLLEITKQLTKAPEGGKVCITQIRLSRNRRGRRRRRRKKKEEKKKWKRRGGGRRRRRGKKEEEKKKKKEEEEEGGE***********************************************************************************************************************************************************************
Transmembrane Helix (TMHMM)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooHHHHHHHHHHHHHHHHHHiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
Transmembrane Helix (MEMSAT)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooHHHHHHHHHHHHHHHHHHHiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
TM Helix, Signal Peptide (MEMSAT_SVM)
oooooooooooooooooooooooohhhhhhhhhhhhhhhhiiiiiiiiiiiiiihhhhhhhhhhhhhhhhhooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooohhhhhhhhhhhhhhhhhhhhhhhhhhhhhiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhoooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (Phobius)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiHHHHHHHHHHHHHHHHHHHHHHooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
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Signal Peptide (SignalP NN Mode)
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Coiled Coils (COILS)
MLILATFVPTTDNFSGGVDVFGDLIKLSIDLIDYVGKYLVLSSIPGKGHAKILTAGVGWAGAEVILTRFLDLWVGARGAEFDWKYIQNSLDSNICLIDKTNKFAAFQKLKDLKGQGVKHKYEFTADENVYEEVSEKEYTERVLKRQEDDWIDDDGGDGYVEDGREIFDDDIEDVPQKKEKHDKRKKNKNIQNPNAKDDSLPLATDHENKKVFRMFFLDAFEDIYKQPGTVYLFGKVFVKENNSHSSCCVIVQNIDRKIYLLPRSEHLKTKEPVSIAQVYSEFDQIATQYKILDFKSRKIEKKYAFNLPGVPDLSEYLEVRYSAKCPALPSDLSGDTFSHVFGTKTSFLENLLLERKIKGPSWLEFPEAEKFPSRISWCKYEVQCNQMEKIRSKQGLIYLIGIVEFIKFTMLHSSYIIKIMCELNVLPLAIQITNVCGNVLSRTLMGGRSERNEFLLLHAFHEKSYVLPDKQYGKNKKEGEETGEANKGKGRKKAAYSGGLVLEPKKGFYDKFIILMDFNSLYPSIIQEYNICFTTIPVRMLQDSDITTLCEYLPEHQVDTGILPSEIKKLVESRRQVKALMKQPNLSSDLLMQYDIRQKALKLTANSMYGCLGFPNSRFFAQPLAALVTAKGREILLNTKSLVENLNYEVIYGDTDSLMISCNVNDYDSVFKIGNQIKSECNKLYKQLELDIDGVYKYMLLLKKKKYAALSISKLSNGKMICSQEIKGVDVVRRDWSQLASEAGKFVISQILDEQSYTDYSLDDRLQNIHEHMKKIRTDLDNGFVPLTLLEITKQLTKAPEGGKVCITQIRLSRNRRGRRRRRRKKKEEKKKWKRRGGGxxxxxxxxxxxxxxxxxxxxxxxxxxxxxGGGGGGRRRRRRRRSGKEEEEKKKKEGGGGRRRRRRKKRRRSRRRRSRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxR
Positional Conservation
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	Length	Definition	RBH(Q2H)	RBH(H2Q)	Q cover	H cover	Identity	E-value
Query	1030	2.2.26 [Sep-21-2011]
P26019	1488	DNA polymerase alpha cata	yes	N/A	0.400	0.277	0.562	1e-135
Q9DE46	1458	DNA polymerase alpha cata	N/A	N/A	0.385	0.272	0.582	1e-131
P09884	1462	DNA polymerase alpha cata	yes	N/A	0.382	0.269	0.585	1e-130
O89042	1451	DNA polymerase alpha cata	yes	N/A	0.369	0.262	0.605	1e-130
P33609	1465	DNA polymerase alpha cata	yes	N/A	0.383	0.269	0.585	1e-127
O48653	1534	DNA polymerase alpha cata	yes	N/A	0.372	0.250	0.461	1e-91
Q9FHA3	1524	DNA polymerase alpha cata	yes	N/A	0.389	0.263	0.451	2e-91
P28040	1405	DNA polymerase alpha cata	yes	N/A	0.4	0.293	0.431	1e-87
P27727	1339	DNA polymerase alpha cata	N/A	N/A	0.372	0.286	0.439	2e-82
O00874	1339	DNA polymerase alpha cata	N/A	N/A	0.361	0.277	0.453	1e-81

>sp|P26019|DPOLA_DROME DNA polymerase alpha catalytic subunit OS=Drosophila melanogaster GN=DNApol-alpha180 PE=1 SV=2

 Score =  481 bits (1239), Expect = e-135,   Method: Compositional matrix adjust.
 Identities = 246/437 (56%), Positives = 321/437 (73%), Gaps = 24/437 (5%)

Query: 401  GIVEFIKFTMLHSSYIIKIMCELNVLPLAIQITNVCGNVLSRTLMGGRSERNEFLLLHAF 460
             I + I  TM  +SY++++MCELN++PLA+QITN+CGN ++RTL GGRSERNEFLLLHAF
Sbjct: 759  SITKLISLTMQDNSYLLRLMCELNIMPLALQITNICGNTMTRTLQGGRSERNEFLLLHAF 818

Query: 461  HEKSYVLPDKQ-----YGKNKKEGEETGEANKGKGRKKAAYSGGLVLEPKKGFYDKFIIL 515
            HEK+Y++PDK+      G    +   +G     + +KKAAY+GGLVLEP +G Y+K+++L
Sbjct: 819  HEKNYIVPDKKPVSKRSGAGDTDATLSGADATMQTKKKAAYAGGLVLEPMRGLYEKYVLL 878

Query: 516  MDFNSLYPSIIQEYNICFTTI--PVRMLQDSD-ITTLCEYLPEHQVDTGILPSEIKKLVE 572
            MDFNSLYPSIIQEYNICFTT+  PV    D+D + TL    P+ + + GILP ++K+LVE
Sbjct: 879  MDFNSLYPSIIQEYNICFTTVQQPV----DADELPTL----PDSKTEPGILPLQLKRLVE 930

Query: 573  SRRQVKALMKQPNLSSDLLMQYDIRQKALKLTANSMYGCLGFPNSRFFAQPLAALVTAKG 632
            SR++VK LM  P+LS +L MQY IRQ ALKLTANSMYGCLGF +SRFFAQ LAALVT KG
Sbjct: 931  SRKEVKKLMAAPDLSPELQMQYHIRQMALKLTANSMYGCLGFAHSRFFAQHLAALVTHKG 990

Query: 633  REILLNTKSLVENLNYEVIYGDTDSLMISCNVNDYDSVFKIGNQIKSECNKLYKQLELDI 692
            REIL NT+ LV+ +NY+V+YGDTDSLMI+ N+ DYD V+KIG+ IK   NKLYKQLELDI
Sbjct: 991  REILTNTQQLVQKMNYDVVYGDTDSLMINTNITDYDQVYKIGHNIKQSVNKLYKQLELDI 1050

Query: 693  DGVYKYMLLLKKKKYAALSISKLSNGKMICSQEIKGVDVVRRDWSQLASEAGKFVISQIL 752
            DGV+  +LLLKKKKYAA+ +SK S G +   QE KG+D+VRRDWSQLA   GK V+ ++L
Sbjct: 1051 DGVFGCLLLLKKKKYAAIKLSKDSKGNLRREQEHKGLDIVRRDWSQLAVMVGKAVLDEVL 1110

Query: 753  DEQSYTDYSLDDRLQNIHEHMKKIRTDLDNGFVPLTLLEITKQLTKAPE--GGKVCITQI 810
             E+      L+++L  +H  ++KI+T +  G VPL L  ITKQLT+ P+       +  +
Sbjct: 1111 SEK-----PLEEKLDAVHAQLEKIKTQIAEGVVPLPLFVITKQLTRTPQEYANSASLPHV 1165

Query: 811  RLSRNRRGRRRRRRKKK 827
            +++  R  R R RR KK
Sbjct: 1166 QVAL-RMNRERNRRYKK 1181

Polymerase alpha in a complex with DNA primase is a replicative polymerase. In addition to polymerase activity, this DNA polymerase exhibits 3' to 5' exonuclease activity.
Drosophila melanogaster (taxid: 7227)
EC: 2EC: .EC: 7EC: .EC: 7EC: .EC: 7

>sp|Q9DE46|DPOLA_XENLA DNA polymerase alpha catalytic subunit OS=Xenopus laevis GN=pola1 PE=2 SV=1

 Score =  469 bits (1206), Expect = e-131,   Method: Compositional matrix adjust.
 Identities = 239/410 (58%), Positives = 311/410 (75%), Gaps = 13/410 (3%)

Query: 400  IGIVEFIKFTMLHSSYIIKIMCELNVLPLAIQITNVCGNVLSRTLMGGRSERNEFLLLHA 459
            + ++  ++ T + + +I++IMCELNVLPLA+QITN+ GNV+SRTLMGGRSERNE+LLLHA
Sbjct: 736  VHLLYMLENTWIDAKFILQIMCELNVLPLALQITNIAGNVMSRTLMGGRSERNEYLLLHA 795

Query: 460  FHEKSYVLPDKQYGKNKKE-----GEETG-EANKGKGRKKAAYSGGLVLEPKKGFYDKFI 513
            F E ++++PDK   K  ++      ++ G + NK K RKKAAY+GGLVLEPK GFYDKFI
Sbjct: 796  FTENNFIVPDKPVFKKMQQTTVEDNDDMGTDQNKNKSRKKAAYAGGLVLEPKVGFYDKFI 855

Query: 514  ILMDFNSLYPSIIQEYNICFTTIP--VRMLQDSDITTLCEYLPEHQVDTGILPSEIKKLV 571
            +L+DFNSLYPSIIQEYNICFTT+       Q  +       LP   ++ GILP EI+KLV
Sbjct: 856  LLLDFNSLYPSIIQEYNICFTTVHREAPSTQKGEDQDEIPELPHSDLEMGILPREIRKLV 915

Query: 572  ESRRQVKALMKQPNLSSDLLMQYDIRQKALKLTANSMYGCLGFPNSRFFAQPLAALVTAK 631
            E RR VK LMKQP+L+ DL +QYDIRQKALKLTANSMYGCLGF  SRF+A+PLAALVT +
Sbjct: 916  ERRRHVKQLMKQPDLNPDLYLQYDIRQKALKLTANSMYGCLGFSYSRFYAKPLAALVTHQ 975

Query: 632  GREILLNTKSLVENLNYEVIYGDTDSLMISCNVNDYDSVFKIGNQIKSECNKLYKQLELD 691
            GREILL+TK +V+ +N EVIYGDTDS+MI+ N N+ + VFK+GN++KSE NK YK LE+D
Sbjct: 976  GREILLHTKEMVQKMNLEVIYGDTDSIMINTNCNNLEEVFKLGNRVKSEINKSYKLLEID 1035

Query: 692  IDGVYKYMLLLKKKKYAALSISKLSNGKMICSQEIKGVDVVRRDWSQLASEAGKFVISQI 751
            IDG++K +LLLKKKKYAAL++    +GK +  QE+KG+D+VRRDW +LA +AG +VISQI
Sbjct: 1036 IDGIFKSLLLLKKKKYAALTVEPTGDGKYVTKQELKGLDIVRRDWCELAKQAGNYVISQI 1095

Query: 752  LDEQSYTDYSLDDRLQNIHEHMKKIRTDLDNGFVPLTLLEITKQLTKAPE 801
            L +Q       D  ++NI + + +I  ++ NG VP+T  EI K LTK P+
Sbjct: 1096 LSDQPR-----DSIVENIQKKLTEIGENVTNGTVPITQYEINKALTKDPQ 1140

Plays an essential role in the initiation of DNA replication. During the S phase of the cell cycle, the DNA polymerase alpha complex (composed of a catalytic subunit POLA1/p180, a regulatory subunit POLA2/p70 and two primase subunits PRIM1/p49 and PRIM2/p58) is recruited to DNA at the replicative forks via direct interactions with MCM10 and WDHD1. The primase subunit of the polymerase alpha complex initiates DNA synthesis by oligomerising short RNA primers on both leading and lagging strands. These primers are initially extended by the polymerase alpha catalytic subunit and subsequently transferred to polymerase delta and polymerase epsilon for processive synthesis on the lagging and leading strand, respectively. The reason this transfer occurs is because the polymerase alpha has limited processivity and lacks intrinsic 3' exonuclease activity for proofreading error, and therefore is not well suited for replicating long complexes.

Xenopus laevis (taxid: 8355)

EC: 2

EC: .

EC: 7

EC: .

EC: 7

EC: .

EC: 7

>sp|P09884|DPOLA_HUMAN DNA polymerase alpha catalytic subunit OS=Homo sapiens GN=POLA1 PE=1 SV=2

 Score =  465 bits (1197), Expect = e-130,   Method: Compositional matrix adjust.
 Identities = 242/413 (58%), Positives = 317/413 (76%), Gaps = 19/413 (4%)

Query: 402  IVEFIKFTMLHSSYIIKIMCELNVLPLAIQITNVCGNVLSRTLMGGRSERNEFLLLHAFH 461
            ++  ++ T   + +I++IMCELNVLPLA+QITN+ GN++SRTLMGGRSERNEFLLLHAF+
Sbjct: 738  LLYLLEHTWKDAKFILQIMCELNVLPLALQITNIAGNIMSRTLMGGRSERNEFLLLHAFY 797

Query: 462  EKSYVLPDKQYGK--NKKEGEET----GEANK-GKGRKKAAYSGGLVLEPKKGFYDKFII 514
            E +Y++PDKQ  +   +K G+E     G+ NK  KGRKKAAY+GGLVL+PK GFYDKFI+
Sbjct: 798  ENNYIVPDKQIFRKPQQKLGDEDEEIDGDTNKYKKGRKKAAYAGGLVLDPKVGFYDKFIL 857

Query: 515  LMDFNSLYPSIIQEYNICFTTI------PVRMLQDSDITTLCEYLPEHQVDTGILPSEIK 568
            L+DFNSLYPSIIQE+NICFTT+        ++ +D +   + E LP+  ++ GILP EI+
Sbjct: 858  LLDFNSLYPSIIQEFNICFTTVQRVASEAQKVTEDGEQEQIPE-LPDPSLEMGILPREIR 916

Query: 569  KLVESRRQVKALMKQPNLSSDLLMQYDIRQKALKLTANSMYGCLGFPNSRFFAQPLAALV 628
            KLVE R+QVK LMKQ +L+ DL++QYDIRQKALKLTANSMYGCLGF  SRF+A+PLAALV
Sbjct: 917  KLVERRKQVKQLMKQQDLNPDLILQYDIRQKALKLTANSMYGCLGFSYSRFYAKPLAALV 976

Query: 629  TAKGREILLNTKSLVENLNYEVIYGDTDSLMISCNVNDYDSVFKIGNQIKSECNKLYKQL 688
            T KGREIL++TK +V+ +N EVIYGDTDS+MI+ N  + + VFK+GN++KSE NKLYK L
Sbjct: 977  TYKGREILMHTKEMVQKMNLEVIYGDTDSIMINTNSTNLEEVFKLGNKVKSEVNKLYKLL 1036

Query: 689  ELDIDGVYKYMLLLKKKKYAALSISKLSNGKMICSQEIKGVDVVRRDWSQLASEAGKFVI 748
            E+DIDGV+K +LLLKKKKYAAL +   S+G  +  QE+KG+D+VRRDW  LA + G FVI
Sbjct: 1037 EIDIDGVFKSLLLLKKKKYAALVVEPTSDGNYVTKQELKGLDIVRRDWCDLAKDTGNFVI 1096

Query: 749  SQILDEQSYTDYSLDDRLQNIHEHMKKIRTDLDNGFVPLTLLEITKQLTKAPE 801
             QIL +QS      D  ++NI + + +I  ++ NG VP++  EI K LTK P+
Sbjct: 1097 GQILSDQSR-----DTIVENIQKRLIEIGENVLNGSVPVSQFEINKALTKDPQ 1144

Plays an essential role in the initiation of DNA replication. During the S phase of the cell cycle, the DNA polymerase alpha complex (composed of a catalytic subunit POLA1/p180, a regulatory subunit POLA2/p70 and two primase subunits PRIM1/p49 and PRIM2/p58) is recruited to DNA at the replicative forks via direct interactions with MCM10 and WDHD1. The primase subunit of the polymerase alpha complex initiates DNA synthesis by oligomerising short RNA primers on both leading and lagging strands. These primers are initially extended by the polymerase alpha catalytic subunit and subsequently transferred to polymerase delta and polymerase epsilon for processive synthesis on the lagging and leading strand, respectively. The reason this transfer occurs is because the polymerase alpha has limited processivity and lacks intrinsic 3' exonuclease activity for proofreading error, and therefore is not well suited for replicating long complexes.

Homo sapiens (taxid: 9606)

EC: 2

EC: .

EC: 7

EC: .

EC: 7

EC: .

EC: 7

>sp|O89042|DPOLA_RAT DNA polymerase alpha catalytic subunit (Fragment) OS=Rattus norvegicus GN=Pola1 PE=2 SV=1

 Score =  465 bits (1197), Expect = e-130,   Method: Compositional matrix adjust.
 Identities = 242/400 (60%), Positives = 311/400 (77%), Gaps = 19/400 (4%)

Query: 415  YIIKIMCELNVLPLAIQITNVCGNVLSRTLMGGRSERNEFLLLHAFHEKSYVLPDKQYGK 474
            +I++IMCELNVLPLA+QITN+ GN++SRTLMGGRSERNEFLLLHAF+E +Y++PDKQ  +
Sbjct: 758  FILQIMCELNVLPLALQITNIAGNIMSRTLMGGRSERNEFLLLHAFYENNYIVPDKQIFR 817

Query: 475  --NKKEGEET----GEANK-GKGRKKAAYSGGLVLEPKKGFYDKFIILMDFNSLYPSIIQ 527
               +K G+E     G+ NK  KGRKKAAY+GGLVL+PK GFYDKFI+L+DFNSLYPSIIQ
Sbjct: 818  KPQQKPGDEDEEIDGDTNKYKKGRKKAAYAGGLVLDPKVGFYDKFILLLDFNSLYPSIIQ 877

Query: 528  EYNICFTTI------PVRMLQDSDITTLCEYLPEHQVDTGILPSEIKKLVESRRQVKALM 581
            E+NICFTT+       ++  +D +   + E LP+  +D GILP EI+KLVE R+QVK LM
Sbjct: 878  EFNICFTTVQRVASETLKATEDEEQEQIPE-LPDPNLDMGILPREIRKLVERRKQVKQLM 936

Query: 582  KQPNLSSDLLMQYDIRQKALKLTANSMYGCLGFPNSRFFAQPLAALVTAKGREILLNTKS 641
            KQ +L+ DL++QYDIRQKALKLTANSMYGCLGF  SRF+A+PLAALVT KGREIL++TK 
Sbjct: 937  KQQDLNPDLVLQYDIRQKALKLTANSMYGCLGFSYSRFYAKPLAALVTYKGREILMHTKE 996

Query: 642  LVENLNYEVIYGDTDSLMISCNVNDYDSVFKIGNQIKSECNKLYKQLELDIDGVYKYMLL 701
            +V+ +N EVIYGDTDS+MI+ N  + + VFK+GN++K+E NKLYK LE+DIDGV+K +LL
Sbjct: 997  MVQKMNLEVIYGDTDSIMINTNSTNLEEVFKLGNKVKNEVNKLYKLLEIDIDGVFKSLLL 1056

Query: 702  LKKKKYAALSISKLSNGKMICSQEIKGVDVVRRDWSQLASEAGKFVISQILDEQSYTDYS 761
            LKKKKYAAL +   S+G  I  QE+KG+D+VRRDW  LA + G FVI QIL +QS     
Sbjct: 1057 LKKKKYAALVVEPTSDGNYITKQELKGLDIVRRDWCDLAKDTGNFVIGQILSDQSR---- 1112

Query: 762  LDDRLQNIHEHMKKIRTDLDNGFVPLTLLEITKQLTKAPE 801
             D  ++NI + + +I  ++ NG VP++  EI K LTK P+
Sbjct: 1113 -DTIVENIQKRLIEIGENVLNGSVPVSQFEINKALTKDPQ 1151

Plays an essential role in the initiation of DNA replication. During the S phase of the cell cycle, the DNA polymerase alpha complex (composed of a catalytic subunit POLA1/p180, a regulatory subunit POLA2/p70 and two primase subunits PRIM1/p49 and PRIM2/p58) is recruited to DNA at the replicative forks via direct interactions with MCM10 and WDHD1. The primase subunit of the polymerase alpha complex initiates DNA synthesis by oligomerising short RNA primers on both leading and lagging strands. These primers are initially extended by the polymerase alpha catalytic subunit and subsequently transferred to polymerase delta and polymerase epsilon for processive synthesis on the lagging and leading strand, respectively. The reason this transfer occurs is because the polymerase alpha has limited processivity and lacks intrinsic 3' exonuclease activity for proofreading error, and therefore is not well suited for replicating long complexes.

Rattus norvegicus (taxid: 10116)

EC: 2

EC: .

EC: 7

EC: .

EC: 7

EC: .

EC: 7

>sp|P33609|DPOLA_MOUSE DNA polymerase alpha catalytic subunit OS=Mus musculus GN=Pola1 PE=1 SV=2

 Score =  458 bits (1179), Expect = e-127,   Method: Compositional matrix adjust.
 Identities = 244/417 (58%), Positives = 316/417 (75%), Gaps = 22/417 (5%)

Query: 398  YLIGIVEFIKFTMLHSSYIIKIMCELNVLPLAIQITNVCGNVLSRTLMGGRSERNEFLLL 457
            YL+ ++E I      + +I++IMCELNVLPLA+QITN+ GN++SRTLMGGRSERNEFLLL
Sbjct: 741  YLLYLLEHI---WKDARFILQIMCELNVLPLALQITNIAGNIMSRTLMGGRSERNEFLLL 797

Query: 458  HAFHEKSYVLPDKQYGK--NKKEGEET----GEANK-GKGRKKAAYSGGLVLEPKKGFYD 510
            HAF+E +Y++PDKQ  +   +K G+E     G+ NK  KGRKKA Y+GGLVL+PK GFYD
Sbjct: 798  HAFYENNYIVPDKQIFRKPQQKLGDEDEEIDGDTNKYKKGRKKATYAGGLVLDPKVGFYD 857

Query: 511  KFIILMDFNSLYPSIIQEYNICFTTIP------VRMLQDSDITTLCEYLPEHQVDTGILP 564
            KFI+L+DFNSLYPSIIQE+NICFTT+        +  +D +   + E LP+  ++ GILP
Sbjct: 858  KFILLLDFNSLYPSIIQEFNICFTTVQRVTSEVQKATEDEEQEQIPE-LPDPNLEMGILP 916

Query: 565  SEIKKLVESRRQVKALMKQPNLSSDLLMQYDIRQKALKLTANSMYGCLGFPNSRFFAQPL 624
             EI+KLVE R+QVK LMKQ +L+ DL++QYDIRQKALKLTANSMYGCLGF  SRF+A+PL
Sbjct: 917  REIRKLVERRKQVKQLMKQQDLNPDLVLQYDIRQKALKLTANSMYGCLGFSYSRFYAKPL 976

Query: 625  AALVTAKGREILLNTKSLVENLNYEVIYGDTDSLMISCNVNDYDSVFKIGNQIKSECNKL 684
            AALVT KGREIL++TK +V+ +N EVIYGDTDS+MI+ N  + + VFK+GN++KSE NKL
Sbjct: 977  AALVTYKGREILMHTKDMVQKMNLEVIYGDTDSIMINTNSTNLEEVFKLGNKVKSEVNKL 1036

Query: 685  YKQLELDIDGVYKYMLLLKKKKYAALSISKLSNGKMICSQEIKGVDVVRRDWSQLASEAG 744
            YK LE+DID V+K +LLLKKKKYAAL +   S+G  I  QE+KG+D+VRRDW  LA + G
Sbjct: 1037 YKLLEIDIDAVFKSLLLLKKKKYAALVVEPTSDGNYITKQELKGLDIVRRDWCDLAKDTG 1096

Query: 745  KFVISQILDEQSYTDYSLDDRLQNIHEHMKKIRTDLDNGFVPLTLLEITKQLTKAPE 801
             FVI QIL +QS      D  ++NI + + +I  ++ NG VP++  EI K LTK P+
Sbjct: 1097 NFVIGQILSDQSR-----DTIVENIQKRLIEIGENVLNGSVPVSQFEINKALTKDPQ 1148

Plays an essential role in the initiation of DNA replication. During the S phase of the cell cycle, the DNA polymerase alpha complex (composed of a catalytic subunit POLA1/p180, a regulatory subunit POLA2/p70 and two primase subunits PRIM1/p49 and PRIM2/p58) is recruited to DNA at the replicative forks via direct interactions with MCM10 and WDHD1. The primase subunit of the polymerase alpha complex initiates DNA synthesis by oligomerising short RNA primers on both leading and lagging strands. These primers are initially extended by the polymerase alpha catalytic subunit and subsequently transferred to polymerase delta and polymerase epsilon for processive synthesis on the lagging and leading strand, respectively. The reason this transfer occurs is because the polymerase alpha has limited processivity and lacks intrinsic 3' exonuclease activity for proofreading error, and therefore is not well suited for replicating long complexes.

Mus musculus (taxid: 10090)

EC: 2

EC: .

EC: 7

EC: .

EC: 7

EC: .

EC: 7

>sp|O48653|DPOLA_ORYSJ DNA polymerase alpha catalytic subunit OS=Oryza sativa subsp. japonica GN=Os01g0868300 PE=2 SV=2

 Score =  338 bits (867), Expect = 1e-91,   Method: Compositional matrix adjust.
 Identities = 196/425 (46%), Positives = 276/425 (64%), Gaps = 41/425 (9%)

Query: 401  GIVEFIKFTMLHSSYIIKIMCELNVLPLAIQITNVCGNVLSRTLMGGRSERNEFLLLHAF 460
             +++ +++    +   +++M  L+VLPL  Q+TN+ GN+  +TL G R++R E+LLLHAF
Sbjct: 788  ALLKLVEYGETDACLALELMFHLSVLPLTRQLTNISGNLWGKTLQGSRAQRVEYLLLHAF 847

Query: 461  HEKSYVLPDK-----QYGKNKKEGEETGEA-----------------NKGKGRKKAAYSG 498
            H + +++PDK     ++   K++     EA                 ++GK +K  +Y+G
Sbjct: 848  HARKFIVPDKFARSKEFNSTKRKMNPDTEAARPDEADPSIDDEGHHVDQGKTKKGPSYAG 907

Query: 499  GLVLEPKKGFYDKFIILMDFNSLYPSIIQEYNICFTTIPVRMLQDSDITTLCEYLPEHQV 558
            GLVLEPKKG YDK+++L+DFNSLYPSIIQEYNICFTT  V    D ++      LP  + 
Sbjct: 908  GLVLEPKKGLYDKYVLLLDFNSLYPSIIQEYNICFTT--VDRSADGNVPN----LPASKT 961

Query: 559  DTGILPSEIKKLVESRRQVKALMKQPNLSSDL-LMQYDIRQKALKLTANSMYGCLGFPNS 617
             TG+LP  +K LVE RR VK+ +K    +S L   Q+DI+Q+ALKLTANSMYGCLGF NS
Sbjct: 962  -TGVLPELLKSLVERRRMVKSWLKT---ASGLKRQQFDIQQQALKLTANSMYGCLGFSNS 1017

Query: 618  RFFAQPLAALVTAKGREILLNTKSLVE-NLNYEVIYGDTDSLMISCNVNDYDSVFKIGNQ 676
            RF+A+PLA L+T +GREIL NT  LV+ NLN EVIYGDTDS+MI   ++D      I  +
Sbjct: 1018 RFYAKPLAELITLQGREILQNTVDLVQNNLNLEVIYGDTDSIMIHTGLDDISRAKGIAGK 1077

Query: 677  IKSECNKLYKQLELDIDGVYKYMLLLKKKKYAALSISKLSNGKMICSQEIKGVDVVRRDW 736
            +  E NK Y+ LE+D+DG+YK MLLLKKKKYAA+ ++   +G +  + E KG+D+VRRDW
Sbjct: 1078 VIQEVNKKYRCLEIDLDGIYKRMLLLKKKKYAAIKVAL--DGSLRENIERKGLDMVRRDW 1135

Query: 737  SQLASEAGKFVISQILDEQSYTDYSLDDRLQNIHEHMKKIRTDLDNGFVPLTLLEITKQL 796
            S L+ E G F ++QIL     +  S DD +++IH  + +++  +  G   L    ITK L
Sbjct: 1136 SLLSKEIGDFCLNQIL-----SGGSCDDVIESIHSSLVQVQEQMRGGQTELEKYIITKSL 1190

Query: 797  TKAPE 801
            TKAPE
Sbjct: 1191 TKAPE 1195

Polymerase alpha in a complex with DNA primase is a replicative polymerase.

Oryza sativa subsp. japonica (taxid: 39947)

EC: 2

EC: .

EC: 7

EC: .

EC: 7

EC: .

EC: 7

>sp|Q9FHA3|DPOLA_ARATH DNA polymerase alpha catalytic subunit OS=Arabidopsis thaliana GN=POLA PE=3 SV=2

 Score =  337 bits (865), Expect = 2e-91,   Method: Compositional matrix adjust.
 Identities = 202/447 (45%), Positives = 274/447 (61%), Gaps = 46/447 (10%)

Query: 402  IVEFIKFTMLHSSYIIKIMCELNVLPLAIQITNVCGNVLSRTLMGGRSERNEFLLLHAFH 461
            +VE I+     +   +++M  L+VLPL +Q+TN+ GN+  +TL G R++R E+ LLH FH
Sbjct: 780  LVELIECGETDAWLSMELMFHLSVLPLTLQLTNISGNLWGKTLQGARAQRIEYYLLHTFH 839

Query: 462  EKSYVLPDK---------------QYGKNKKEGEE-----TGEANKGKG---RKKAAYSG 498
             K ++LPDK                Y    +  +E     T E +  KG   +K  AY+G
Sbjct: 840  SKKFILPDKISQRMKEIKSSKRRMDYAPEDRNVDELDADLTLENDPSKGSKTKKGPAYAG 899

Query: 499  GLVLEPKKGFYDKFIILMDFNSLYPSIIQEYNICFTTIPVRMLQDSDITTLCEYLPEHQV 558
            GLVLEPK+G YDK+++L+DFNSLYPSIIQEYNICFTTIP    +D         LP  Q 
Sbjct: 900  GLVLEPKRGLYDKYVLLLDFNSLYPSIIQEYNICFTTIPRS--EDG-----VPRLPSSQT 952

Query: 559  DTGILPSEIKKLVESRRQVKALMKQPNLSSDLLMQY---DIRQKALKLTANSMYGCLGFP 615
              GILP  ++ LV  R+ VK  MK+     +  ++Y   DIRQ+ALKLTANSMYGCLGF 
Sbjct: 953  -PGILPKLMEHLVSIRKSVKLKMKK-----ETGLKYWELDIRQQALKLTANSMYGCLGFS 1006

Query: 616  NSRFFAQPLAALVTAKGREILLNTKSLVEN-LNYEVIYGDTDSLMISCNVNDYDSVFKIG 674
            NSRF+A+PLA L+T +GR+IL  T  LV+N LN EVIYGDTDS+MI   ++D + V  I 
Sbjct: 1007 NSRFYAKPLAELITLQGRDILQRTVDLVQNHLNLEVIYGDTDSIMIHSGLDDIEEVKAIK 1066

Query: 675  NQIKSECNKLYKQLELDIDGVYKYMLLLKKKKYAALSISKLSNGKMICSQEIKGVDVVRR 734
            +++  E NK Y+ L++D DG+YK MLLL+KKKYAA+ + +  +GK     E KGVD+VRR
Sbjct: 1067 SKVIQEVNKKYRCLKIDCDGIYKRMLLLRKKKYAAVKL-QFKDGKPCEDIERKGVDMVRR 1125

Query: 735  DWSQLASEAGKFVISQILDEQSYTDYSLDDRLQNIHEHMKKIRTDLDNGFVPLTLLEITK 794
            DWS L+ E G   +S+IL        S +D ++ IH  + KI+ ++ NG V L    ITK
Sbjct: 1126 DWSLLSKEIGDLCLSKIL-----YGGSCEDVVEAIHNELMKIKEEMRNGQVALEKYVITK 1180

Query: 795  QLTKAPEGGKVCITQIRLSRNRRGRRR 821
             LTK P       +Q  +    R R+R
Sbjct: 1181 TLTKPPAAYPDSKSQPHVQVALRMRQR 1207

Polymerase alpha in a complex with DNA primase is a replicative polymerase.

Arabidopsis thaliana (taxid: 3702)

EC: 2

EC: .

EC: 7

EC: .

EC: 7

EC: .

EC: 7

>sp|P28040|DPOA_SCHPO DNA polymerase alpha catalytic subunit OS=Schizosaccharomyces pombe (strain 972 / ATCC 24843) GN=pol1 PE=1 SV=1

 Score =  325 bits (833), Expect = 1e-87,   Method: Compositional matrix adjust.
 Identities = 185/429 (43%), Positives = 264/429 (61%), Gaps = 17/429 (3%)

Query: 401  GIVEFIKFTMLHSSYIIKIMCELNVLPLAIQITNVCGNVLSRTLMGGRSERNEFLLLHAF 460
            G+++++    + + +I  +  ++ +L L+  +TN+ GN  +RTL G R+ERNE++LLH F
Sbjct: 727  GLLDYLVHCEIDTFFIAAVAFKIQMLQLSKNLTNIAGNSWARTLTGTRAERNEYILLHEF 786

Query: 461  HEKSYVLPDKQYGKNKKE---GEETGEANKGKGRKKAAYSGGLVLEPKKGFYDKFIILMD 517
             +  Y++PDKQ    +     G E G   +  G+KK  Y GGLV EP+KG Y+  I++MD
Sbjct: 787  KKNGYIVPDKQQSIRRHAEAFGAEDGLQEESLGKKKDKYKGGLVFEPQKGLYETCILVMD 846

Query: 518  FNSLYPSIIQEYNICFTTIPVRMLQDSDITTLCEYLPEHQVDTGILPSEIKKLVESRRQV 577
            FNSLYPSIIQEYNICFTT+  R   +SD        P    + GI P  I  LVE RRQ+
Sbjct: 847  FNSLYPSIIQEYNICFTTVD-RSPSNSDSDDQIPDTPSASANQGIFPRLIANLVERRRQI 905

Query: 578  KALMKQPNLSSDLLMQYDIRQKALKLTANSMYGCLGFPNSRFFAQPLAALVTAKGREILL 637
            K L+K  + +    +Q+DI+Q+ALKLTANSMYGCLG+  SRF+A+PLA L+T KGRE L+
Sbjct: 906  KGLLKDNSATPTQRLQWDIQQQALKLTANSMYGCLGYTKSRFYARPLAVLITYKGREALM 965

Query: 638  NTKSLVENLNYEVIYGDTDSLMISCNVNDYDSVFKIGNQIKSECNKLYKQLELDIDGVYK 697
            NTK L + +  +VIYGDTDS+M++ NV D +   +IGN+ K + N+ Y +LE+DID VY+
Sbjct: 966  NTKELADQMGLQVIYGDTDSVMLNTNVTDKNHALRIGNEFKEKVNERYSKLEIDIDNVYQ 1025

Query: 698  YMLLLKKKKYAALSISKLSNGKMICSQEIKGVDVVRRDWSQLASEAGKFVISQILDEQSY 757
             MLL  KKKYAAL +   S GK   + ++KG+D+ RR++  LA EA KF + QIL  +  
Sbjct: 1026 RMLLHAKKKYAALQLD--SQGKP--NLDVKGLDMKRREFCTLAKEASKFCLDQILSGE-- 1079

Query: 758  TDYSLDDRLQNIHEHMKKIRTDLDNGFVPLTLLEITKQLTKAPE----GGKVCITQIRLS 813
                 +  ++NIH ++      + NG  P     I  +L K PE    G  +   Q+ L 
Sbjct: 1080 ---LTETVIENIHSYLMDFSEKMRNGKFPANKFIIFNRLGKNPEDYPNGKTMPFVQVALK 1136

Query: 814  RNRRGRRRR 822
            +  RG   R
Sbjct: 1137 KKARGENVR 1145

Polymerase alpha in a complex with DNA primase is a replicative polymerase.

Schizosaccharomyces pombe (strain 972 / ATCC 24843) (taxid: 284812)

EC: 2

EC: .

EC: 7

EC: .

EC: 7

EC: .

EC: 7

>sp|P27727|DPOLA_TRYBB DNA polymerase alpha catalytic subunit OS=Trypanosoma brucei brucei PE=3 SV=1

 Score =  308 bits (788), Expect = 2e-82,   Method: Compositional matrix adjust.
 Identities = 185/421 (43%), Positives = 259/421 (61%), Gaps = 37/421 (8%)

Query: 423  LNVLPLAIQITNVCGNVLSRTLMGGRSERNEFLLLHAFHEKSYVLPDKQYGKNKKEGEET 482
            L+V+PL  ++T + GN+ SRTL G RSER E+LLLHAFH   +V PDK+    K++ +  
Sbjct: 660  LDVIPLTKRLTLLAGNLWSRTLYGARSERIEYLLLHAFHNLKFVTPDKK----KRDLKRG 715

Query: 483  GEANKGKGRKKAAYSGGLVLEPKKGFYDKFIILMDFNSLYPSIIQEYNICFTTI------ 536
             E +  +G++K  Y GG+VLEPK G Y ++I+L+DFNSLYPS+IQE+N+C+TTI      
Sbjct: 716  REDDDDEGKRKTKYQGGMVLEPKSGLYSEYILLLDFNSLYPSLIQEFNVCYTTIDRDENT 775

Query: 537  ------PVRMLQDSDITTLCEY--LPEHQVDTGILPSEIKKLVESRRQVKALMKQPNLSS 588
                  P     +S I   C    LP   +   ILP  I+ LV+SRR++K +MK      
Sbjct: 776  VSAEVPP----PESLICLSCRAAGLPSPCLHKCILPKVIRGLVDSRREIKRMMKSEKDPG 831

Query: 589  DLLMQYDIRQKALKLTANSMYGCLGFPNSRFFAQPLAALVTAKGREILLNTKSLVENLN- 647
            +L M  +IRQ ALKLTANSMYGCLGF  SRF+AQPLA LVT +GR  L NT  L+  ++ 
Sbjct: 832  NLAM-LEIRQLALKLTANSMYGCLGFEYSRFYAQPLAELVTRQGRLALQNTVELIPQISP 890

Query: 648  -YEVIYGDTDSLMISCNV-NDYDSVFKIGNQIKSECNKLYKQLELDIDGVYKYMLLLKKK 705
               VIYGDTDS+MI   + +D   V  +G +IK + N+ Y+ LELDIDGV++ MLLL+KK
Sbjct: 891  SIRVIYGDTDSVMIQTGIKDDIVKVRNLGFEIKGKVNQRYQSLELDIDGVFRAMLLLRKK 950

Query: 706  KYAALSISKLSNGKMICSQEIKGVDVVRRDWSQLASEAGKFVISQILDEQSYTDYSLDDR 765
            KYAALS+        +  +E+KG+D+VRRDW  L+      V+ +IL+ +       +D 
Sbjct: 951  KYAALSVVDWQGEGKVYKREVKGLDMVRRDWCPLSQHVSDAVLKRILNAEGG-----EDI 1005

Query: 766  LQNIHEHMKKIRTDLDNGFV-PLTLLEITKQLTKAPE-----GGKVCITQIRLSRNRRGR 819
            L  + ++MK +  D+ +G V PL    I+K LTK PE     G    +  +R+ + + G 
Sbjct: 1006 LDFVIKYMKGVAQDVRSGNVYPLEEFVISKSLTKEPESYHGTGYPHAVVALRMKQRKEGV 1065

Query: 820  R 820
            R
Sbjct: 1066 R 1066

Polymerase alpha in a complex with DNA primase is a replicative polymerase.

Trypanosoma brucei brucei (taxid: 5702)

EC: 2

EC: .

EC: 7

EC: .

EC: 7

EC: .

EC: 7

>sp|O00874|DPOLA_LEIDO DNA polymerase alpha catalytic subunit OS=Leishmania donovani PE=3 SV=1

 Score =  305 bits (781), Expect = 1e-81,   Method: Compositional matrix adjust.
 Identities = 181/399 (45%), Positives = 254/399 (63%), Gaps = 27/399 (6%)

Query: 419  IMCELNVLPLAIQITNVCGNVLSRTLMGGRSERNEFLLLHAFHEKSYVLPDKQYGKNKKE 478
            ++  L+V+ L  ++T + GN+ SRTL G RSER E+LLLH FH+  ++ PD+ Y +N K 
Sbjct: 658  VVSHLDVIRLTKRLTTIAGNLWSRTLFGARSERIEYLLLHTFHDLKFITPDR-YVQNFKR 716

Query: 479  GEETGEANKGKGRKKAAYSGGLVLEPKKGFYDKFIILMDFNSLYPSIIQEYNICFTTIPV 538
            G +  E   GK  +KA Y GG+VL+PK G Y  +I+L+DFNSLYPS+IQE+NICFTT+  
Sbjct: 717  GRDDEEEEDGK--RKAKYQGGMVLDPKCGLYSDYILLLDFNSLYPSLIQEFNICFTTVDR 774

Query: 539  RMLQDSDITT----LCEY-----LPEHQVDTGILPSEIKKLVESRRQVKALMKQPNLSSD 589
                + D+      +C       L    +   +LP  IK LV+SRR+VK LMK    +++
Sbjct: 775  ESGSEIDVPPPENLICASCAAAGLSAPCLHKCVLPKVIKSLVDSRREVKRLMKIEKDANN 834

Query: 590  LLMQYDIRQKALKLTANSMYGCLGFPNSRFFAQPLAALVTAKGREILLNTKSLVENLN-- 647
            L +  +IRQKALKLTANSMYGCLGF  SRF AQPLA LVT +GR  L +T  L+  LN  
Sbjct: 835  LAL-LEIRQKALKLTANSMYGCLGFEYSRFHAQPLAELVTRQGRLALQSTVDLIPQLNPS 893

Query: 648  YEVIYGDTDSLMISCNV-NDYDSVFKIGNQIKSECNKLYKQLELDIDGVYKYMLLLKKKK 706
              VIYGDTDS+MI   + ND  +V  +G  +K++ NK Y+ LE+DIDGV++ +LLLKKKK
Sbjct: 894  LRVIYGDTDSVMIQTGIKNDIKAVRDLGLDLKAKINKRYQSLEIDIDGVFRAILLLKKKK 953

Query: 707  YAALSISKLSNGKMICSQEIKGVDVVRRDWSQLASEAGKFVISQILD---EQSYTDYSLD 763
            YAAL+++          +E+KG+D+VRRDW  L+      V+S++L+    +   DY + 
Sbjct: 954  YAALTVTDWQGEGKTYKKEVKGLDMVRRDWCPLSKCVCDSVLSRVLNAEGSEDILDYVM- 1012

Query: 764  DRLQNIHEHMKKIRTDLDNGFVPLTLLEITKQLTKAPEG 802
            + ++++ E ++  R  LDN FV      I+K LTK PE 
Sbjct: 1013 NYMRDVSEKVRAGRYTLDN-FV------ISKSLTKEPEA 1044

Polymerase alpha in a complex with DNA primase is a replicative polymerase.

Leishmania donovani (taxid: 5661)

EC: 2

EC: .

EC: 7

EC: .

EC: 7

EC: .

EC: 7

Close Homologs in the Non-Redundant Database Detected by BLAST

Original result of BLAST against Nonredundant Database

GI	Length	Definition	Q cover	H cover	Identity	E-value
Query	1030
328711134	1437	PREDICTED: DNA polymerase alpha catalyti	0.385	0.276	0.621	1e-140
357608358	1477	putative DNA polymerase alpha catalytic	0.403	0.281	0.612	1e-137
242009635	1474	DNA polymerase alpha catalytic subunit,	0.401	0.280	0.578	1e-133
195111871	1487	GI10263 [Drosophila mojavensis] gi|19391	0.403	0.279	0.562	1e-133
24648780	1488	DNA polymerase alpha 180kD [Drosophila m	0.400	0.277	0.562	1e-133
189237191	1406	PREDICTED: similar to DNA polymerase alp	0.399	0.292	0.586	1e-132
194742070	1481	GF17808 [Drosophila ananassae] gi|190626	0.4	0.278	0.573	1e-132
195498574	1492	GE24967 [Drosophila yakuba] gi|194182682	0.400	0.276	0.563	1e-132
195344386	1488	GM10998 [Drosophila sechellia] gi|194133	0.400	0.277	0.562	1e-131
195396107	1481	GJ11070 [Drosophila virilis] gi|19414338	0.403	0.280	0.556	1e-131

>gi|328711134|ref|XP_003244454.1| PREDICTED: DNA polymerase alpha catalytic subunit-like [Acyrthosiphon pisum]

 Score =  504 bits (1298), Expect = e-140,   Method: Compositional matrix adjust.
 Identities = 254/409 (62%), Positives = 322/409 (78%), Gaps = 12/409 (2%)

Query: 400  IGIVEFIKFTMLHSSYIIKIMCELNVLPLAIQITNVCGNVLSRTLMGGRSERNEFLLLHA 459
            + +++ IKFT++ +S I+++MC++NVLPLA+QIT V GN+LSRTL+GGR+ERNE+LLLHA
Sbjct: 731  VSLMQLIKFTIMDTSCIMRLMCQMNVLPLALQITKVAGNLLSRTLIGGRAERNEYLLLHA 790

Query: 460  FHEKSYVLPDKQYGK---NKKEGEETGEANKGKGRKKAAYSGGLVLEPKKGFYDKFIILM 516
            F+EK Y+LPDKQY K   NK E     E  K  GRKKA Y GGLVL+PK GFYDK I+LM
Sbjct: 791  FNEKGYILPDKQYKKRSMNKNEDNVEEENTKKNGRKKAQYLGGLVLDPKIGFYDKMILLM 850

Query: 517  DFNSLYPSIIQEYNICFTTIPVRMLQ----DSDITTLCEYLPEHQVDTGILPSEIKKLVE 572
            DFNSLYPSIIQEYNICFTT+  R L     D +I  L +  P   V  GILP+EIK LV+
Sbjct: 851  DFNSLYPSIIQEYNICFTTVSFRTLLAQEGDDEIAELLKLTPNQSVARGILPAEIKSLVD 910

Query: 573  SRRQVKALMKQPNLSSDLLMQYDIRQKALKLTANSMYGCLGFPNSRFFAQPLAALVTAKG 632
            SRR+VK LM  P +S+ L  QY++RQ ALKLTANSMYGCLGF +SRF+A+PLAAL+TAKG
Sbjct: 911  SRREVKKLMNDPKISATLKEQYNLRQTALKLTANSMYGCLGFTHSRFYAKPLAALITAKG 970

Query: 633  REILLNTKSLVENLNYEVIYGDTDSLMISCNVNDYDSVFKIGNQIKSECNKLYKQLELDI 692
            REIL++TK+LVE L+++VIYGDTDSLMI+ N  DYD V KIG +IK+E NK+YKQ+ELDI
Sbjct: 971  REILISTKALVEKLSFDVIYGDTDSLMINSNCVDYDQVMKIGYKIKAEVNKMYKQVELDI 1030

Query: 693  DGVYKYMLLLKKKKYAALSISKLSNGKMICSQEIKGVDVVRRDWSQLASEAGKFVISQIL 752
            DG++KYMLLLKKKKYAA+SISKL +G+ I  +EIKG+D+VRRDWSQL+ EAG+FV+ QIL
Sbjct: 1031 DGIFKYMLLLKKKKYAAISISKLPSGEFITKEEIKGLDIVRRDWSQLSQEAGRFVLRQIL 1090

Query: 753  DEQSYTDYSLDDRLQNIHEHMKKIRTDLDNGFVPLTLLEITKQLTKAPE 801
             +Q     S ++R+ NI   ++K+R D +   +PL LL I+K LTKAP+
Sbjct: 1091 SDQ-----SPEERVSNICAQLEKLRVDCEENNIPLGLLAISKTLTKAPQ 1134

Source: Acyrthosiphon pisum

Species: Acyrthosiphon pisum

Genus: Acyrthosiphon

Family: Aphididae

Order: Hemiptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|357608358|gb|EHJ65949.1| putative DNA polymerase alpha catalytic subunit [Danaus plexippus]

 Score =  494 bits (1273), Expect = e-137,   Method: Compositional matrix adjust.
 Identities = 265/433 (61%), Positives = 337/433 (77%), Gaps = 17/433 (3%)

Query: 402  IVEFIKFTMLHSSYIIKIMCELNVLPLAIQITNVCGNVLSRTLMGGRSERNEFLLLHAFH 461
            +++ +  +M  +SYI+KIMCELNV+PLA+QIT + GN++SRTLMGGRSERNEFLLLHAF 
Sbjct: 743  LLQLVSLSMQDASYILKIMCELNVIPLALQITQIAGNIMSRTLMGGRSERNEFLLLHAFT 802

Query: 462  EKSYVLPDKQYGK----NKKEGEETGEANKGKGRKKAAYSGGLVLEPKKGFYDKFIILMD 517
            EK+Y++PDK YGK    +  E +E G  +K + +KKAAY+GGLVL+PKKGFYDK I+LMD
Sbjct: 803  EKNYIVPDKIYGKKADGDDDEQDEAGNVSKKQAKKKAAYAGGLVLDPKKGFYDKLILLMD 862

Query: 518  FNSLYPSIIQEYNICFTTIPVR--MLQDSDITTLCEYLPEHQVDTGILPSEIKKLVESRR 575
            FNSLYPSIIQEYNICFTTI  +     D DI  L   LP    + G+LP++I+KLVESRR
Sbjct: 863  FNSLYPSIIQEYNICFTTIKRKNGASSDDDINNLV--LPAPNTEFGVLPTQIRKLVESRR 920

Query: 576  QVKALMKQPNLSSDLLMQYDIRQKALKLTANSMYGCLGFPNSRFFAQPLAALVTAKGREI 635
            +VK LMK P+L+S+L MQY+IRQ ALKLTANSMYGCLGF +SRF+A+PLAALVT KGREI
Sbjct: 921  EVKRLMKSPDLASELYMQYNIRQMALKLTANSMYGCLGFTHSRFYAKPLAALVTMKGREI 980

Query: 636  LLNTKSLVENLNYEVIYGDTDSLMISCNVNDYDSVFKIGNQIKSECNKLYKQLELDIDGV 695
            L++TK +V+ LNYEV+YGDTDSLMI+ N  DYD VFKIGN +K E NK YKQ+ELDIDGV
Sbjct: 981  LMDTKEIVQKLNYEVVYGDTDSLMINTNCLDYDYVFKIGNDLKREINKKYKQIELDIDGV 1040

Query: 696  YKYMLLLKKKKYAALSISKLSNGKMICSQEIKGVDVVRRDWSQLASEAGKFVISQILDEQ 755
            +KY+LLLKKKKYAA+ +SK  +G+ I +QE KG+D+VRRDWSQLA+EAGKF+++QIL EQ
Sbjct: 1041 FKYLLLLKKKKYAAVVVSKSKSGEFIYNQEHKGLDIVRRDWSQLAAEAGKFILTQILSEQ 1100

Query: 756  SYTDYSLDDRLQNIHEHMKKIRTDLDNGFVPLTLLEITKQLTKAP----EGGKVCITQIR 811
                 + D+RL++I  H+ K++ DL N  +PL+LL ITKQLTK P    +       Q+ 
Sbjct: 1101 -----TADERLESIQNHLNKLKEDLVNSKMPLSLLTITKQLTKNPNEYADKNNQPHVQVA 1155

Query: 812  LSRNRRGRRRRRR 824
            L  N +  RR ++
Sbjct: 1156 LRLNSKNSRRFKK 1168

Source: Danaus plexippus

Species: Danaus plexippus

Genus: Danaus

Family: Nymphalidae

Order: Lepidoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|242009635|ref|XP_002425588.1| DNA polymerase alpha catalytic subunit, putative [Pediculus humanus corporis] gi|212509481|gb|EEB12850.1| DNA polymerase alpha catalytic subunit, putative [Pediculus humanus corporis]

 Score =  484 bits (1245), Expect = e-133,   Method: Compositional matrix adjust.
 Identities = 247/427 (57%), Positives = 323/427 (75%), Gaps = 13/427 (3%)

Query: 401  GIVEFIKFTMLHSSYIIKIMCELNVLPLAIQITNVCGNVLSRTLMGGRSERNEFLLLHAF 460
             ++E I +TM  +S+I+KI+ E+N LPLA+QIT + GNV+S+TL GGRSERNEFLLLHAF
Sbjct: 737  SVIELINYTMEDASHILKIVYEINALPLALQITKIAGNVMSKTLSGGRSERNEFLLLHAF 796

Query: 461  HEKSYVLPDKQYGKNKKEGEETGEANKGKGRKKAAYSGGLVLEPKKGFYDKFIILMDFNS 520
             EK+Y++PDK + K  +  E+  EA+    +KK  Y+GGLV EPKKGFYDKFI+LMDFNS
Sbjct: 797  TEKNYLVPDKSFSKKPRMNEDEMEASSKNNKKKPQYAGGLVFEPKKGFYDKFILLMDFNS 856

Query: 521  LYPSIIQEYNICFTTIPVRMLQDSDITTLCEYLPEHQVDTGILPSEIKKLVESRRQVKAL 580
            LYPSIIQEYNICFTT+     +D +        P   +  GILP EIKKLVE+RR VK L
Sbjct: 857  LYPSIIQEYNICFTTVSRSNGEDENEINC----PPDNLPLGILPIEIKKLVETRRDVKQL 912

Query: 581  MKQPNLSSDLLMQYDIRQKALKLTANSMYGCLGFPNSRFFAQPLAALVTAKGREILLNTK 640
            MK PNLS +L MQ++IRQ ALKLTANSMYGCLGF  SRF+A+PLAALVT+KGREILLNTK
Sbjct: 913  MKSPNLSPELYMQHNIRQMALKLTANSMYGCLGFSYSRFYAKPLAALVTSKGREILLNTK 972

Query: 641  SLVENLNYEVIYGDTDSLMISCNVNDYDSVFKIGNQIKSECNKLYKQLELDIDGVYKYML 700
            ++VE +NY+VIYGDTDS+MI+ N  +YD VF IG++IK E NKLYK +ELDIDGV+KYML
Sbjct: 973  NIVEKMNYDVIYGDTDSVMINTNCINYDEVFTIGHKIKDEINKLYKYIELDIDGVFKYML 1032

Query: 701  LLKKKKYAALSISKLSNGKMICSQEIKGVDVVRRDWSQLASEAGKFVISQILDEQSYTDY 760
            LLKKKKYAA+ ++K  +G+++ ++E KG+D+VRRDW QL++E G+ +++QIL     +D 
Sbjct: 1033 LLKKKKYAAVVLTKKPSGELVATKEYKGLDIVRRDWCQLSAEVGRHILNQIL-----SDL 1087

Query: 761  SLDDRLQNIHEHMKKIRTDLDNGFVPLTLLEITKQLTKAPEG----GKVCITQIRLSRNR 816
            S +DR+ NI +H+++I  DL +  VP++LL ITKQL K PE       +   Q+ L  N 
Sbjct: 1088 SPEDRIGNIKDHLERITVDLRDRKVPISLLAITKQLAKNPEDYSDIKSLPHLQVALRMNS 1147

Query: 817  RGRRRRR 823
            +G ++ R
Sbjct: 1148 KGGKKLR 1154

Source: Pediculus humanus corporis

Species: Pediculus humanus

Genus: Pediculus

Family: Pediculidae

Order: Phthiraptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|195111871|ref|XP_002000500.1| GI10263 [Drosophila mojavensis] gi|193917094|gb|EDW15961.1| GI10263 [Drosophila mojavensis]

 Score =  482 bits (1240), Expect = e-133,   Method: Compositional matrix adjust.
 Identities = 248/441 (56%), Positives = 319/441 (72%), Gaps = 25/441 (5%)

Query: 401  GIVEFIKFTMLHSSYIIKIMCELNVLPLAIQITNVCGNVLSRTLMGGRSERNEFLLLHAF 460
             I + I  TM  +SY++++MCELN++PLA+QITN+CGN ++RTL GGRSERNEFLLLHAF
Sbjct: 754  NITKLISLTMQDASYMLRLMCELNIMPLALQITNICGNTMTRTLQGGRSERNEFLLLHAF 813

Query: 461  HEKSYVLPDK-----------QYGKNKKEGEETG-EANKGKGRKKAAYSGGLVLEPKKGF 508
            HEK+Y++PDK           Q   +   G +T   A  G  RKKAAY+GGLVLEP +G 
Sbjct: 814  HEKNYIVPDKLPQRRGAVANTQTDPDATTGNDTTVAAGSGAARKKAAYAGGLVLEPLRGL 873

Query: 509  YDKFIILMDFNSLYPSIIQEYNICFTTIPVRMLQDSDITTLCEYLPEHQVDTGILPSEIK 568
            Y+K+++LMDFNSLYPSIIQEYNICFTT  V+   D+D   +   LP+   + GILP +++
Sbjct: 874  YEKYVLLMDFNSLYPSIIQEYNICFTT--VQQPHDADQLPV---LPDSSAEPGILPMQLR 928

Query: 569  KLVESRRQVKALMKQPNLSSDLLMQYDIRQKALKLTANSMYGCLGFPNSRFFAQPLAALV 628
            +LVESRRQVK LM  P+LS +L MQY IRQ ALKLTANSMYGCLGF +SRFFAQ LAALV
Sbjct: 929  RLVESRRQVKKLMAVPDLSPELQMQYHIRQMALKLTANSMYGCLGFAHSRFFAQHLAALV 988

Query: 629  TAKGREILLNTKSLVENLNYEVIYGDTDSLMISCNVNDYDSVFKIGNQIKSECNKLYKQL 688
            T KGREIL+NT+ LV+ LNY+V+YGDTDSLMI+ N+ DYD V+KIG+ IK   NKLYKQL
Sbjct: 989  THKGREILVNTQQLVQKLNYDVVYGDTDSLMINTNITDYDQVYKIGHTIKQSVNKLYKQL 1048

Query: 689  ELDIDGVYKYMLLLKKKKYAALSISKLSNGKMICSQEIKGVDVVRRDWSQLASEAGKFVI 748
            ELDIDGV+  +LLLKKKKYAA+ ++K + G +I  QE KG+D+VRRDWSQLA   GK V+
Sbjct: 1049 ELDIDGVFACLLLLKKKKYAAVKLTKNAKGVLIREQEHKGLDIVRRDWSQLAVMVGKAVL 1108

Query: 749  SQILDEQSYTDYSLDDRLQNIHEHMKKIRTDLDNGFVPLTLLEITKQLTKAPE--GGKVC 806
             ++L     +D  L+D+L  +H  + +I+  +    VPL L  ITKQLT+AP+       
Sbjct: 1109 DEVL-----SDKPLEDKLDAVHAQLGRIKDQIAKSAVPLPLYVITKQLTRAPQEYANSAS 1163

Query: 807  ITQIRLSRNRRGRRRRRRKKK 827
            +  ++++  R  R R RR KK
Sbjct: 1164 LPHVQVAL-RMNRERNRRYKK 1183

Source: Drosophila mojavensis

Species: Drosophila mojavensis

Genus: Drosophila

Family: Drosophilidae

Order: Diptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|24648780|ref|NP_536736.2| DNA polymerase alpha 180kD [Drosophila melanogaster] gi|45644974|sp|P26019.2|DPOLA_DROME RecName: Full=DNA polymerase alpha catalytic subunit gi|23171902|gb|AAF55908.2| DNA polymerase alpha 180kD [Drosophila melanogaster]

 Score =  481 bits (1239), Expect = e-133,   Method: Compositional matrix adjust.
 Identities = 246/437 (56%), Positives = 321/437 (73%), Gaps = 24/437 (5%)

Query: 401  GIVEFIKFTMLHSSYIIKIMCELNVLPLAIQITNVCGNVLSRTLMGGRSERNEFLLLHAF 460
             I + I  TM  +SY++++MCELN++PLA+QITN+CGN ++RTL GGRSERNEFLLLHAF
Sbjct: 759  SITKLISLTMQDNSYLLRLMCELNIMPLALQITNICGNTMTRTLQGGRSERNEFLLLHAF 818

Query: 461  HEKSYVLPDKQ-----YGKNKKEGEETGEANKGKGRKKAAYSGGLVLEPKKGFYDKFIIL 515
            HEK+Y++PDK+      G    +   +G     + +KKAAY+GGLVLEP +G Y+K+++L
Sbjct: 819  HEKNYIVPDKKPVSKRSGAGDTDATLSGADATMQTKKKAAYAGGLVLEPMRGLYEKYVLL 878

Query: 516  MDFNSLYPSIIQEYNICFTTI--PVRMLQDSD-ITTLCEYLPEHQVDTGILPSEIKKLVE 572
            MDFNSLYPSIIQEYNICFTT+  PV    D+D + TL    P+ + + GILP ++K+LVE
Sbjct: 879  MDFNSLYPSIIQEYNICFTTVQQPV----DADELPTL----PDSKTEPGILPLQLKRLVE 930

Query: 573  SRRQVKALMKQPNLSSDLLMQYDIRQKALKLTANSMYGCLGFPNSRFFAQPLAALVTAKG 632
            SR++VK LM  P+LS +L MQY IRQ ALKLTANSMYGCLGF +SRFFAQ LAALVT KG
Sbjct: 931  SRKEVKKLMAAPDLSPELQMQYHIRQMALKLTANSMYGCLGFAHSRFFAQHLAALVTHKG 990

Query: 633  REILLNTKSLVENLNYEVIYGDTDSLMISCNVNDYDSVFKIGNQIKSECNKLYKQLELDI 692
            REIL NT+ LV+ +NY+V+YGDTDSLMI+ N+ DYD V+KIG+ IK   NKLYKQLELDI
Sbjct: 991  REILTNTQQLVQKMNYDVVYGDTDSLMINTNITDYDQVYKIGHNIKQSVNKLYKQLELDI 1050

Query: 693  DGVYKYMLLLKKKKYAALSISKLSNGKMICSQEIKGVDVVRRDWSQLASEAGKFVISQIL 752
            DGV+  +LLLKKKKYAA+ +SK S G +   QE KG+D+VRRDWSQLA   GK V+ ++L
Sbjct: 1051 DGVFGCLLLLKKKKYAAIKLSKDSKGNLRREQEHKGLDIVRRDWSQLAVMVGKAVLDEVL 1110

Query: 753  DEQSYTDYSLDDRLQNIHEHMKKIRTDLDNGFVPLTLLEITKQLTKAPE--GGKVCITQI 810
             E+      L+++L  +H  ++KI+T +  G VPL L  ITKQLT+ P+       +  +
Sbjct: 1111 SEK-----PLEEKLDAVHAQLEKIKTQIAEGVVPLPLFVITKQLTRTPQEYANSASLPHV 1165

Query: 811  RLSRNRRGRRRRRRKKK 827
            +++  R  R R RR KK
Sbjct: 1166 QVAL-RMNRERNRRYKK 1181

Source: Drosophila melanogaster

Species: Drosophila melanogaster

Genus: Drosophila

Family: Drosophilidae

Order: Diptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|189237191|ref|XP_967510.2| PREDICTED: similar to DNA polymerase alpha 180kD CG6349-PA [Tribolium castaneum] gi|270008175|gb|EFA04623.1| DNA polymerase alpha 180kD [Tribolium castaneum]

 Score =  481 bits (1237), Expect = e-132,   Method: Compositional matrix adjust.
 Identities = 258/440 (58%), Positives = 329/440 (74%), Gaps = 29/440 (6%)

Query: 387  MEKIRSKQGLIYLIGIVEFIKFTMLHSSYIIKIMCELNVLPLAIQITNVCGNVLSRTLMG 446
            ++  RSK+ L+ L+ +      TM  +++++KIM  LN++PLA+QIT + GNV+S+TLMG
Sbjct: 699  LKMFRSKEELLKLVSL------TMQDTAFVLKIMYSLNIIPLALQITTIAGNVMSKTLMG 752

Query: 447  GRSERNEFLLLHAFHEKSYVLPDKQYGKNKKEGEETGEANKGKGRKKAAYSGGLVLEPKK 506
            GRSERNEFLLLHAF EK+Y++PDK  GK K  GE+T         KKA YSGGLVL+PK 
Sbjct: 753  GRSERNEFLLLHAFSEKNYIVPDKSSGK-KDFGEKTA-------NKKATYSGGLVLDPKI 804

Query: 507  GFYDKFIILMDFNSLYPSIIQEYNICFTTIPVRMLQDSDITTLCEYLPEHQVDTGILPSE 566
            GFYDKFI+LMDFNSLYPSIIQEYNICFTT+P  + +D+ +      LP+  +  G+LP+E
Sbjct: 805  GFYDKFILLMDFNSLYPSIIQEYNICFTTMPPNLAEDNMV------LPDATLPAGVLPTE 858

Query: 567  IKKLVESRRQVKALMKQPNLSSDLLMQYDIRQKALKLTANSMYGCLGFPNSRFFAQPLAA 626
            IKKLVESRR VK LMK  +LS D  MQYDIRQ ALKLTANSMYGCLGF NSRF+A+ LAA
Sbjct: 859  IKKLVESRRAVKKLMKSADLSPDQRMQYDIRQMALKLTANSMYGCLGFANSRFYAKNLAA 918

Query: 627  LVTAKGREILLNTKSLVENLNYEVIYGDTDSLMISCNVNDYDSVFKIGNQIKSECNKLYK 686
            L+T KGREIL NTK +VE LN+EVIYGDTDSLMI+ N+ D+D V +IG +IK E NKLY+
Sbjct: 919  LITHKGREILTNTKEVVERLNFEVIYGDTDSLMINTNLVDFDQVAQIGTKIKQEINKLYR 978

Query: 687  QLELDIDGVYKYMLLLKKKKYAALSISKLSNGKMICSQEIKGVDVVRRDWSQLASEAGKF 746
            Q+ELDIDGV+KY+LLLKKKKYAA+++SK   G++    E KG+D+VRRDWS+LA+EAGKF
Sbjct: 979  QVELDIDGVFKYLLLLKKKKYAAVTLSKDKEGRLKTDIEYKGLDIVRRDWSRLAAEAGKF 1038

Query: 747  VISQILDEQSYTDYSLDDRLQNIHEHMKKIRTDLDNGFVPLTLLEITKQLTKA----PEG 802
            V++QIL +QS      ++R  NI  H+ ++R DL  G VPL+LL ITKQL+K     PE 
Sbjct: 1039 VLNQILSDQSS-----ENRFLNILTHLSQLREDLQEGKVPLSLLVITKQLSKNPDQYPED 1093

Query: 803  GKVCITQIRLSRNRRGRRRR 822
              +   Q+ +  N++G   R
Sbjct: 1094 NTLPHVQVAIRYNKQGGHYR 1113

Source: Tribolium castaneum

Species: Tribolium castaneum

Genus: Tribolium

Family: Tenebrionidae

Order: Coleoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|194742070|ref|XP_001953530.1| GF17808 [Drosophila ananassae] gi|190626567|gb|EDV42091.1| GF17808 [Drosophila ananassae]

 Score =  481 bits (1237), Expect = e-132,   Method: Compositional matrix adjust.
 Identities = 250/436 (57%), Positives = 326/436 (74%), Gaps = 24/436 (5%)

Query: 401  GIVEFIKFTMLHSSYIIKIMCELNVLPLAIQITNVCGNVLSRTLMGGRSERNEFLLLHAF 460
             I + I  TM  +SY++++MCELN++PLA+QITN+CGN ++RTL GGRSERNEFLLLHAF
Sbjct: 755  SITKLISLTMQDNSYLLRLMCELNIMPLALQITNICGNTMTRTLQGGRSERNEFLLLHAF 814

Query: 461  HEKSYVLPDKQYGKNKKEG---EETGEANKG-KGRKKAAYSGGLVLEPKKGFYDKFIILM 516
            HEK+Y++PDK+   N++ G   E T  A+     RKKAAY+GGLVLEP +G Y+KF++LM
Sbjct: 815  HEKNYIVPDKK-ASNRRGGGDPENTIIADATLPVRKKAAYAGGLVLEPMRGLYEKFVLLM 873

Query: 517  DFNSLYPSIIQEYNICFTTI--PVRMLQDSD-ITTLCEYLPEHQVDTGILPSEIKKLVES 573
            DFNSLYPSIIQEYNICFTT+  PV    D+D + TL    PE +V+ GILP ++K+LVES
Sbjct: 874  DFNSLYPSIIQEYNICFTTVQQPV----DADELPTL----PESKVEAGILPLQLKRLVES 925

Query: 574  RRQVKALMKQPNLSSDLLMQYDIRQKALKLTANSMYGCLGFPNSRFFAQPLAALVTAKGR 633
            R++VK LM  P+LS +L MQY IRQ ALKLTANSMYGCLGF +SRFFAQ LAALVT KGR
Sbjct: 926  RKEVKKLMAAPDLSPELQMQYHIRQMALKLTANSMYGCLGFAHSRFFAQHLAALVTHKGR 985

Query: 634  EILLNTKSLVENLNYEVIYGDTDSLMISCNVNDYDSVFKIGNQIKSECNKLYKQLELDID 693
            EIL NT+ +V+ +NY+V+YGDTDS+MI+ N+ DYD V+KIG +IK   NK+YKQLELDID
Sbjct: 986  EILTNTQQMVQKMNYDVVYGDTDSIMINTNITDYDQVYKIGREIKQSVNKMYKQLELDID 1045

Query: 694  GVYKYMLLLKKKKYAALSISKLSNGKMICSQEIKGVDVVRRDWSQLASEAGKFVISQILD 753
            GV+  +LLLKKKKYAA+ +SK S G +   QE KG+D+VRRDWSQLA   GK V+ ++L 
Sbjct: 1046 GVFACLLLLKKKKYAAVKLSKDSKGNLKREQEHKGLDIVRRDWSQLAVMVGKAVLDEVLA 1105

Query: 754  EQSYTDYSLDDRLQNIHEHMKKIRTDLDNGFVPLTLLEITKQLTKAPE--GGKVCITQIR 811
            E+      L+++L  +H  ++KI+  ++ G VPL L  ITKQLT+AP+       +  ++
Sbjct: 1106 EK-----QLEEKLDAVHTQLEKIKQQINEGAVPLPLFVITKQLTRAPQEYANSASLPHVQ 1160

Query: 812  LSRNRRGRRRRRRKKK 827
            ++  R  R R RR KK
Sbjct: 1161 VAL-RMNRERNRRYKK 1175

Source: Drosophila ananassae

Species: Drosophila ananassae

Genus: Drosophila

Family: Drosophilidae

Order: Diptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|195498574|ref|XP_002096581.1| GE24967 [Drosophila yakuba] gi|194182682|gb|EDW96293.1| GE24967 [Drosophila yakuba]

 Score =  480 bits (1235), Expect = e-132,   Method: Compositional matrix adjust.
 Identities = 247/438 (56%), Positives = 322/438 (73%), Gaps = 25/438 (5%)

Query: 401  GIVEFIKFTMLHSSYIIKIMCELNVLPLAIQITNVCGNVLSRTLMGGRSERNEFLLLHAF 460
             I + I  TM  +SY++++MCELN++PLA+QITN+CGN ++RTL GGRSERNEFLLLHAF
Sbjct: 762  SITKLISLTMQDNSYLLRLMCELNIMPLALQITNICGNTMTRTLQGGRSERNEFLLLHAF 821

Query: 461  HEKSYVLPDKQYGKNKKEGEETGEANKG------KGRKKAAYSGGLVLEPKKGFYDKFII 514
            HEK+Y++PDK+   +K+      EA         + +KKAAY+GGLVLEP +G Y+K+++
Sbjct: 822  HEKNYIVPDKKVPVSKRSAAGDAEATFSGADATLQSKKKAAYAGGLVLEPLRGLYEKYVL 881

Query: 515  LMDFNSLYPSIIQEYNICFTTI--PVRMLQDSD-ITTLCEYLPEHQVDTGILPSEIKKLV 571
            LMDFNSLYPSIIQEYNICFTT+  PV    D+D + TL    P+ + + GILP ++K+LV
Sbjct: 882  LMDFNSLYPSIIQEYNICFTTVQQPV----DADELPTL----PDSKTEAGILPLQLKRLV 933

Query: 572  ESRRQVKALMKQPNLSSDLLMQYDIRQKALKLTANSMYGCLGFPNSRFFAQPLAALVTAK 631
            ESR++VK LM  P+LS +L MQY IRQ ALKLTANSMYGCLGF +SRFFAQ LAALVT K
Sbjct: 934  ESRKEVKKLMAAPDLSPELQMQYHIRQMALKLTANSMYGCLGFAHSRFFAQHLAALVTHK 993

Query: 632  GREILLNTKSLVENLNYEVIYGDTDSLMISCNVNDYDSVFKIGNQIKSECNKLYKQLELD 691
            GREIL +T+ LV+ LNY+V+YGDTDSLMI+ N+ DYD V+KIG+ IK   NKLYKQLELD
Sbjct: 994  GREILTSTQQLVQKLNYDVVYGDTDSLMINTNITDYDQVYKIGHSIKQSVNKLYKQLELD 1053

Query: 692  IDGVYKYMLLLKKKKYAALSISKLSNGKMICSQEIKGVDVVRRDWSQLASEAGKFVISQI 751
            IDGV+  +LLLKKKKYAA+ +SK S G +   QE KG+D+VRRDWSQLA   GK V+ ++
Sbjct: 1054 IDGVFGCLLLLKKKKYAAVKLSKDSKGNLRREQEHKGLDIVRRDWSQLAVMVGKAVLDEV 1113

Query: 752  LDEQSYTDYSLDDRLQNIHEHMKKIRTDLDNGFVPLTLLEITKQLTKAPE--GGKVCITQ 809
            L E+      L+++L  +H  ++KI+T +  G VPL L  ITKQLT+ P+       +  
Sbjct: 1114 LSEK-----PLEEKLDAVHAQLEKIKTQIAEGAVPLPLFVITKQLTRTPQEYANSASLPH 1168

Query: 810  IRLSRNRRGRRRRRRKKK 827
            ++++  R  R R RR KK
Sbjct: 1169 VQVAL-RMNRERNRRYKK 1185

Source: Drosophila yakuba

Species: Drosophila yakuba

Genus: Drosophila

Family: Drosophilidae

Order: Diptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|195344386|ref|XP_002038769.1| GM10998 [Drosophila sechellia] gi|194133790|gb|EDW55306.1| GM10998 [Drosophila sechellia]

 Score =  477 bits (1228), Expect = e-131,   Method: Compositional matrix adjust.
 Identities = 246/437 (56%), Positives = 320/437 (73%), Gaps = 24/437 (5%)

Query: 401  GIVEFIKFTMLHSSYIIKIMCELNVLPLAIQITNVCGNVLSRTLMGGRSERNEFLLLHAF 460
             I + I  TM  +SY++++MCELN++PLA+QITN+CGN ++RTL GGRSERNEFLLLHAF
Sbjct: 759  SITKLISLTMQDNSYLLRLMCELNIMPLALQITNICGNTMTRTLQGGRSERNEFLLLHAF 818

Query: 461  HEKSYVLPDKQ-----YGKNKKEGEETGEANKGKGRKKAAYSGGLVLEPKKGFYDKFIIL 515
            HEK+Y++PDK+      G    +   +G     + +KKAAY+GGLVLEP +G Y+K+++L
Sbjct: 819  HEKNYIVPDKKPVSKRSGAGDTDATLSGADATMQTKKKAAYAGGLVLEPMRGLYEKYVLL 878

Query: 516  MDFNSLYPSIIQEYNICFTTI--PVRMLQDSD-ITTLCEYLPEHQVDTGILPSEIKKLVE 572
            MDFNSLYPSIIQEYNICFTT+  PV    D+D + TL    P+ + + GILP ++K+LVE
Sbjct: 879  MDFNSLYPSIIQEYNICFTTVQQPV----DADELPTL----PDSKTEPGILPLQLKRLVE 930

Query: 573  SRRQVKALMKQPNLSSDLLMQYDIRQKALKLTANSMYGCLGFPNSRFFAQPLAALVTAKG 632
            SR++VK LM   +LS +L MQY IRQ ALKLTANSMYGCLGF +SRFFAQ LAALVT KG
Sbjct: 931  SRKEVKKLMAAHDLSPELQMQYHIRQMALKLTANSMYGCLGFAHSRFFAQHLAALVTHKG 990

Query: 633  REILLNTKSLVENLNYEVIYGDTDSLMISCNVNDYDSVFKIGNQIKSECNKLYKQLELDI 692
            REIL NT+ LV+ LNY+V+YGDTDSLMI+ N+ DYD V+KIG+ IK   NKLYKQLELDI
Sbjct: 991  REILTNTQQLVQKLNYDVVYGDTDSLMINTNITDYDQVYKIGHNIKQSVNKLYKQLELDI 1050

Query: 693  DGVYKYMLLLKKKKYAALSISKLSNGKMICSQEIKGVDVVRRDWSQLASEAGKFVISQIL 752
            DGV+  +LLLKKKKYAA+ +SK S G +   QE KG+D+VRRDWSQLA   GK V+ ++L
Sbjct: 1051 DGVFGCLLLLKKKKYAAVKLSKDSKGNLRREQEHKGLDIVRRDWSQLAVMVGKAVLDEVL 1110

Query: 753  DEQSYTDYSLDDRLQNIHEHMKKIRTDLDNGFVPLTLLEITKQLTKAPE--GGKVCITQI 810
             E+      L+++L  +H  ++KI+T +  G VPL L  ITKQLT+ P+       +  +
Sbjct: 1111 SEK-----PLEEKLDAVHAQLEKIKTQIAEGVVPLPLFVITKQLTRTPQEYANSASLPHV 1165

Query: 811  RLSRNRRGRRRRRRKKK 827
            +++  R  R R RR KK
Sbjct: 1166 QVAL-RMNRERNRRYKK 1181

Source: Drosophila sechellia

Species: Drosophila sechellia

Genus: Drosophila

Family: Drosophilidae

Order: Diptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|195396107|ref|XP_002056674.1| GJ11070 [Drosophila virilis] gi|194143383|gb|EDW59786.1| GJ11070 [Drosophila virilis]

 Score =  477 bits (1228), Expect = e-131,   Method: Compositional matrix adjust.
 Identities = 243/437 (55%), Positives = 317/437 (72%), Gaps = 21/437 (4%)

Query: 401  GIVEFIKFTMLHSSYIIKIMCELNVLPLAIQITNVCGNVLSRTLMGGRSERNEFLLLHAF 460
             + + I  TM  +SY++++MCELN++PLA+QITN+CGN ++RTL GGRSERNE+LLLHAF
Sbjct: 751  NVTKLISLTMQDASYMLRLMCELNIMPLALQITNICGNTMTRTLQGGRSERNEYLLLHAF 810

Query: 461  HEKSYVLPDKQYGKNKKEGEE--------TGEANKGKGRKKAAYSGGLVLEPKKGFYDKF 512
            HEK+Y++PDK   +    G +        T  A  G  RKKAAY+GGLVLEP +G Y+K+
Sbjct: 811  HEKNYIVPDKLPARRVAAGADPDATSQDTTVAAGAGAVRKKAAYAGGLVLEPIRGLYEKY 870

Query: 513  IILMDFNSLYPSIIQEYNICFTTIPVRMLQDSDITTLCEYLPEHQVDTGILPSEIKKLVE 572
            ++LMDFNSLYPSIIQEYNICFTT+     Q  D   L   LP+   + GILP ++++LVE
Sbjct: 871  VLLMDFNSLYPSIIQEYNICFTTVQ----QPHDAEQL-PTLPDSSAEPGILPLQLRRLVE 925

Query: 573  SRRQVKALMKQPNLSSDLLMQYDIRQKALKLTANSMYGCLGFPNSRFFAQPLAALVTAKG 632
            SRR+VK LM  P+L+++L MQY IRQ ALKLTANSMYGCLGF +SRFFAQ LAALVT KG
Sbjct: 926  SRREVKKLMAAPDLAAELHMQYHIRQMALKLTANSMYGCLGFAHSRFFAQHLAALVTHKG 985

Query: 633  REILLNTKSLVENLNYEVIYGDTDSLMISCNVNDYDSVFKIGNQIKSECNKLYKQLELDI 692
            REIL+NT+ LV+ LNY+V+YGDTDSLMI+ N+ DYD V+KIG+ IK   NKLYKQLELDI
Sbjct: 986  REILVNTQQLVQKLNYDVVYGDTDSLMINTNITDYDQVYKIGHTIKQSVNKLYKQLELDI 1045

Query: 693  DGVYKYMLLLKKKKYAALSISKLSNGKMICSQEIKGVDVVRRDWSQLASEAGKFVISQIL 752
            DGV+  +LLLKKKKYAA+ +SK + G ++  QE KG+D+VRRDWSQLA   GK V+ ++L
Sbjct: 1046 DGVFACLLLLKKKKYAAVKLSKNAKGVLLREQEHKGLDIVRRDWSQLAVMVGKAVLDEVL 1105

Query: 753  DEQSYTDYSLDDRLQNIHEHMKKIRTDLDNGFVPLTLLEITKQLTKAPE--GGKVCITQI 810
                  D  L+D+L+ +H  + +I+  +    VPL L  ITKQLT+AP+       +  +
Sbjct: 1106 -----ADKPLEDKLEAVHAQLGRIKEQITQSAVPLPLYVITKQLTRAPQEYANSSSLPHV 1160

Query: 811  RLSRNRRGRRRRRRKKK 827
            +++  R  R R RR KK
Sbjct: 1161 QVAL-RMNRERNRRYKK 1176

Source: Drosophila virilis

Species: Drosophila virilis

Genus: Drosophila

Family: Drosophilidae

Order: Diptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

---

Prediction of Gene Ontology (GO) Terms

Close Homologs with Gene Ontology terms Detected by BLAST

Original result of BLAST against Gene Ontology (AMIGO)

ID	Length	Definition	Q cover	H cover	Identity	E-value
Query	1030
UNIPROTKB|Q9DE46	1458	pola1 "DNA polymerase alpha ca	0.385	0.272	0.543	8.9e-182
UNIPROTKB|A6NMQ1	1468	POLA1 "DNA polymerase" [Homo s	0.382	0.268	0.535	3.8e-179
UNIPROTKB|P09884	1462	POLA1 "DNA polymerase alpha ca	0.382	0.269	0.535	3.8e-179
ZFIN|ZDB-GENE-030114-9	1468	pola1 "polymerase (DNA directe	0.382	0.268	0.545	8e-179
UNIPROTKB|Q59J88	1441	Q59J88 "DNA polymerase" [Iguan	0.382	0.273	0.553	5.6e-178
UNIPROTKB|F6Y1C9	1467	POLA1 "DNA polymerase" [Canis	0.382	0.268	0.537	3e-177
MGI|MGI:99660	1465	Pola1 "polymerase (DNA directe	0.383	0.269	0.534	5e-177
UNIPROTKB|Q59J89	1441	Q59J89 "DNA polymerase" [Trach	0.383	0.274	0.540	2.7e-176
UNIPROTKB|E2QVU2	1357	POLA1 "Uncharacterized protein	0.382	0.290	0.536	2.7e-176
UNIPROTKB|F1NR19	1462	POLA1 "DNA polymerase" [Gallus	0.375	0.264	0.553	6.4e-175

UNIPROTKB|Q9DE46 pola1 "DNA polymerase alpha catalytic subunit" [Xenopus laevis (taxid:8355)]

 Score = 1106 (394.4 bits), Expect = 8.9e-182, Sum P(3) = 8.9e-182
 Identities = 223/410 (54%), Positives = 286/410 (69%)

Query:   400 IGIVEFIKFTMLHSSYIIKIMCELNVLPLAIQITNVCGNVLSRTLMGGRSERNEFLLLHA 459
             + ++  ++ T + + +I++IMCELNVLPLA+QITN+ GNV+SRTLMGGRSERNE+LLLHA
Sbjct:   736 VHLLYMLENTWIDAKFILQIMCELNVLPLALQITNIAGNVMSRTLMGGRSERNEYLLLHA 795

Query:   460 FHEKSYVLPDK------QYXXXXXXXXXXXXXXXXXXRKKAAYSGGLVLEPKKGFYDKFI 513
             F E ++++PDK      Q                   RKKAAY+GGLVLEPK GFYDKFI
Sbjct:   796 FTENNFIVPDKPVFKKMQQTTVEDNDDMGTDQNKNKSRKKAAYAGGLVLEPKVGFYDKFI 855

Query:   514 ILMDFNSLYPSIIQEYNICFTTI--PVRMLQDSDITTLCEYLPEHQVDTGILPSEIKKLV 571
             +L+DFNSLYPSIIQEYNICFTT+       Q  +       LP   ++ GILP EI+KLV
Sbjct:   856 LLLDFNSLYPSIIQEYNICFTTVHREAPSTQKGEDQDEIPELPHSDLEMGILPREIRKLV 915

Query:   572 ESRRQVKALMKQPNLSSDLLMQYDIRQKALKLTANSMYGCLGFPNSRFFAQPLAALVTAK 631
             E RR VK LMKQP+L+ DL +QYDIRQKALKLTANSMYGCLGF  SRF+A+PLAALVT +
Sbjct:   916 ERRRHVKQLMKQPDLNPDLYLQYDIRQKALKLTANSMYGCLGFSYSRFYAKPLAALVTHQ 975

Query:   632 GREILLNTKSLVENLNYEVIYGDTDSLMISCNVNDYDSVFKIGNQIKSECNKLYKQLELD 691
             GREILL+TK +V+ +N EVIYGDTDS+MI+ N N+ + VFK+GN++KSE NK YK LE+D
Sbjct:   976 GREILLHTKEMVQKMNLEVIYGDTDSIMINTNCNNLEEVFKLGNRVKSEINKSYKLLEID 1035

Query:   692 IDGVXXXXXXXXXXXXXXXXXXXXXNGKMICSQEIKGVDVVRRDWSQLASEAGKFVISQI 751
             IDG+                     +GK +  QE+KG+D+VRRDW +LA +AG +VISQI
Sbjct:  1036 IDGIFKSLLLLKKKKYAALTVEPTGDGKYVTKQELKGLDIVRRDWCELAKQAGNYVISQI 1095

Query:   752 LDEQSYTDYSLDDRLQNIHEHMKKIRTDLDNGFVPLTLLEITKQLTKAPE 801
             L +Q       D  ++NI + + +I  ++ NG VP+T  EI K LTK P+
Sbjct:  1096 LSDQPR-----DSIVENIQKKLTEIGENVTNGTVPITQYEINKALTKDPQ 1140

GO:0000084 "S phase of mitotic cell cycle" evidence=ISS

GO:0000166 "nucleotide binding" evidence=ISS

GO:0003677 "DNA binding" evidence=ISS

GO:0003682 "chromatin binding" evidence=ISS

GO:0003887 "DNA-directed DNA polymerase activity" evidence=ISS

GO:0005634 "nucleus" evidence=ISS

GO:0005635 "nuclear envelope" evidence=ISS

GO:0005654 "nucleoplasm" evidence=ISS

GO:0005658 "alpha DNA polymerase:primase complex" evidence=ISS

GO:0005730 "nucleolus" evidence=ISS

GO:0006260 "DNA replication" evidence=ISS

GO:0006269 "DNA replication, synthesis of RNA primer" evidence=ISS

GO:0006270 "DNA replication initiation" evidence=ISS

GO:0006271 "DNA strand elongation involved in DNA replication" evidence=ISS

GO:0006272 "leading strand elongation" evidence=ISS

GO:0006273 "lagging strand elongation" evidence=ISS

GO:0006303 "double-strand break repair via nonhomologous end joining" evidence=ISS

GO:0008283 "cell proliferation" evidence=ISS

GO:0016363 "nuclear matrix" evidence=ISS

GO:0000731 "DNA synthesis involved in DNA repair" evidence=ISS

GO:0006281 "DNA repair" evidence=ISS

GO:0000785 "chromatin" evidence=ISS

GO:0003896 "DNA primase activity" evidence=ISS

UNIPROTKB|A6NMQ1 POLA1 "DNA polymerase" [Homo sapiens (taxid:9606)]

 Score = 1087 (387.7 bits), Expect = 3.8e-179, Sum P(3) = 3.8e-179
 Identities = 221/413 (53%), Positives = 289/413 (69%)

Query:   402 IVEFIKFTMLHSSYIIKIMCELNVLPLAIQITNVCGNVLSRTLMGGRSERNEFLLLHAFH 461
             ++  ++ T   + +I++IMCELNVLPLA+QITN+ GN++SRTLMGGRSERNEFLLLHAF+
Sbjct:   744 LLYLLEHTWKDAKFILQIMCELNVLPLALQITNIAGNIMSRTLMGGRSERNEFLLLHAFY 803

Query:   462 EKSYVLPDKQYXXX-------XXXXXXXXXXXXXXXRKKAAYSGGLVLEPKKGFYDKFII 514
             E +Y++PDKQ                          RKKAAY+GGLVL+PK GFYDKFI+
Sbjct:   804 ENNYIVPDKQIFRKPQQKLGDEDEEIDGDTNKYKKGRKKAAYAGGLVLDPKVGFYDKFIL 863

Query:   515 LMDFNSLYPSIIQEYNICFTTIP------VRMLQDSDITTLCEYLPEHQVDTGILPSEIK 568
             L+DFNSLYPSIIQE+NICFTT+        ++ +D +   + E LP+  ++ GILP EI+
Sbjct:   864 LLDFNSLYPSIIQEFNICFTTVQRVASEAQKVTEDGEQEQIPE-LPDPSLEMGILPREIR 922

Query:   569 KLVESRRQVKALMKQPNLSSDLLMQYDIRQKALKLTANSMYGCLGFPNSRFFAQPLAALV 628
             KLVE R+QVK LMKQ +L+ DL++QYDIRQKALKLTANSMYGCLGF  SRF+A+PLAALV
Sbjct:   923 KLVERRKQVKQLMKQQDLNPDLILQYDIRQKALKLTANSMYGCLGFSYSRFYAKPLAALV 982

Query:   629 TAKGREILLNTKSLVENLNYEVIYGDTDSLMISCNVNDYDSVFKIGNQIKSECNKLYKQL 688
             T KGREIL++TK +V+ +N EVIYGDTDS+MI+ N  + + VFK+GN++KSE NKLYK L
Sbjct:   983 TYKGREILMHTKEMVQKMNLEVIYGDTDSIMINTNSTNLEEVFKLGNKVKSEVNKLYKLL 1042

Query:   689 ELDIDGVXXXXXXXXXXXXXXXXXXXXXNGKMICSQEIKGVDVVRRDWSQLASEAGKFVI 748
             E+DIDGV                     +G  +  QE+KG+D+VRRDW  LA + G FVI
Sbjct:  1043 EIDIDGVFKSLLLLKKKKYAALVVEPTSDGNYVTKQELKGLDIVRRDWCDLAKDTGNFVI 1102

Query:   749 SQILDEQSYTDYSLDDRLQNIHEHMKKIRTDLDNGFVPLTLLEITKQLTKAPE 801
              QIL +QS      D  ++NI + + +I  ++ NG VP++  EI K LTK P+
Sbjct:  1103 GQILSDQSR-----DTIVENIQKRLIEIGENVLNGSVPVSQFEINKALTKDPQ 1150

GO:0000166 "nucleotide binding" evidence=IEA

GO:0001882 "nucleoside binding" evidence=IEA

GO:0003677 "DNA binding" evidence=IEA

GO:0006260 "DNA replication" evidence=IEA

GO:0003887 "DNA-directed DNA polymerase activity" evidence=IEA

GO:0005634 "nucleus" evidence=IDA

GO:0005730 "nucleolus" evidence=IDA

GO:0005737 "cytoplasm" evidence=IDA

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

UNIPROTKB|P09884 POLA1 "DNA polymerase alpha catalytic subunit" [Homo sapiens (taxid:9606)]

 Score = 1087 (387.7 bits), Expect = 3.8e-179, Sum P(3) = 3.8e-179
 Identities = 221/413 (53%), Positives = 289/413 (69%)

Query:   402 IVEFIKFTMLHSSYIIKIMCELNVLPLAIQITNVCGNVLSRTLMGGRSERNEFLLLHAFH 461
             ++  ++ T   + +I++IMCELNVLPLA+QITN+ GN++SRTLMGGRSERNEFLLLHAF+
Sbjct:   738 LLYLLEHTWKDAKFILQIMCELNVLPLALQITNIAGNIMSRTLMGGRSERNEFLLLHAFY 797

Query:   462 EKSYVLPDKQYXXX-------XXXXXXXXXXXXXXXRKKAAYSGGLVLEPKKGFYDKFII 514
             E +Y++PDKQ                          RKKAAY+GGLVL+PK GFYDKFI+
Sbjct:   798 ENNYIVPDKQIFRKPQQKLGDEDEEIDGDTNKYKKGRKKAAYAGGLVLDPKVGFYDKFIL 857

Query:   515 LMDFNSLYPSIIQEYNICFTTIP------VRMLQDSDITTLCEYLPEHQVDTGILPSEIK 568
             L+DFNSLYPSIIQE+NICFTT+        ++ +D +   + E LP+  ++ GILP EI+
Sbjct:   858 LLDFNSLYPSIIQEFNICFTTVQRVASEAQKVTEDGEQEQIPE-LPDPSLEMGILPREIR 916

Query:   569 KLVESRRQVKALMKQPNLSSDLLMQYDIRQKALKLTANSMYGCLGFPNSRFFAQPLAALV 628
             KLVE R+QVK LMKQ +L+ DL++QYDIRQKALKLTANSMYGCLGF  SRF+A+PLAALV
Sbjct:   917 KLVERRKQVKQLMKQQDLNPDLILQYDIRQKALKLTANSMYGCLGFSYSRFYAKPLAALV 976

Query:   629 TAKGREILLNTKSLVENLNYEVIYGDTDSLMISCNVNDYDSVFKIGNQIKSECNKLYKQL 688
             T KGREIL++TK +V+ +N EVIYGDTDS+MI+ N  + + VFK+GN++KSE NKLYK L
Sbjct:   977 TYKGREILMHTKEMVQKMNLEVIYGDTDSIMINTNSTNLEEVFKLGNKVKSEVNKLYKLL 1036

Query:   689 ELDIDGVXXXXXXXXXXXXXXXXXXXXXNGKMICSQEIKGVDVVRRDWSQLASEAGKFVI 748
             E+DIDGV                     +G  +  QE+KG+D+VRRDW  LA + G FVI
Sbjct:  1037 EIDIDGVFKSLLLLKKKKYAALVVEPTSDGNYVTKQELKGLDIVRRDWCDLAKDTGNFVI 1096

Query:   749 SQILDEQSYTDYSLDDRLQNIHEHMKKIRTDLDNGFVPLTLLEITKQLTKAPE 801
              QIL +QS      D  ++NI + + +I  ++ NG VP++  EI K LTK P+
Sbjct:  1097 GQILSDQSR-----DTIVENIQKRLIEIGENVLNGSVPVSQFEINKALTKDPQ 1144

GO:0001882 "nucleoside binding" evidence=IEA

GO:0019048 "virus-host interaction" evidence=IEA

GO:0046872 "metal ion binding" evidence=IEA

GO:0051539 "4 iron, 4 sulfur cluster binding" evidence=IEA

GO:0046982 "protein heterodimerization activity" evidence=IEA

GO:0005634 "nucleus" evidence=IDA

GO:0006260 "DNA replication" evidence=IMP

GO:0003887 "DNA-directed DNA polymerase activity" evidence=IMP;IDA

GO:0006297 "nucleotide-excision repair, DNA gap filling" evidence=IBA

GO:0008408 "3'-5' exonuclease activity" evidence=IBA

GO:0019985 "translesion synthesis" evidence=IBA

GO:0016363 "nuclear matrix" evidence=IDA

GO:0005515 "protein binding" evidence=IPI

GO:0005658 "alpha DNA polymerase:primase complex" evidence=IDA;TAS

GO:0000166 "nucleotide binding" evidence=IDA

GO:0000785 "chromatin" evidence=IDA

GO:0006272 "leading strand elongation" evidence=IDA

GO:0006273 "lagging strand elongation" evidence=IDA

GO:0005635 "nuclear envelope" evidence=IDA

GO:0005730 "nucleolus" evidence=IDA

GO:0006303 "double-strand break repair via nonhomologous end joining" evidence=IMP

GO:0000731 "DNA synthesis involved in DNA repair" evidence=IMP

GO:0008283 "cell proliferation" evidence=IDA

GO:0003677 "DNA binding" evidence=IDA;NAS

GO:0005654 "nucleoplasm" evidence=IDA;TAS

GO:0006271 "DNA strand elongation involved in DNA replication" evidence=IMP;TAS

GO:0006281 "DNA repair" evidence=IDA

GO:0000084 "S phase of mitotic cell cycle" evidence=IDA;TAS

GO:0003682 "chromatin binding" evidence=IDA

GO:0003896 "DNA primase activity" evidence=IDA

GO:0006270 "DNA replication initiation" evidence=IDA;TAS

GO:0000082 "G1/S transition of mitotic cell cycle" evidence=TAS

GO:0000083 "regulation of transcription involved in G1/S phase of mitotic cell cycle" evidence=TAS

GO:0000216 "M/G1 transition of mitotic cell cycle" evidence=TAS

GO:0000278 "mitotic cell cycle" evidence=TAS

GO:0000722 "telomere maintenance via recombination" evidence=TAS

GO:0000723 "telomere maintenance" evidence=TAS

GO:0032201 "telomere maintenance via semi-conservative replication" evidence=TAS

GO:0006269 "DNA replication, synthesis of RNA primer" evidence=IDA

GO:0005737 "cytoplasm" evidence=IDA

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

ZFIN|ZDB-GENE-030114-9 pola1 "polymerase (DNA directed), alpha 1" [Danio rerio (taxid:7955)]

 Score = 1115 (397.6 bits), Expect = 8.0e-179, Sum P(3) = 8.0e-179
 Identities = 224/411 (54%), Positives = 288/411 (70%)

Query:   402 IVEFIKFTMLHSSYIIKIMCELNVLPLAIQITNVCGNVLSRTLMGGRSERNEFLLLHAFH 461
             ++  ++ T + +  I++IMCELNVLPLA+QITN+ GNV+SRTLMGGRSERNE+LLLHAFH
Sbjct:   747 LLYLLELTWMDAKLILQIMCELNVLPLALQITNIAGNVMSRTLMGGRSERNEYLLLHAFH 806

Query:   462 EKSYVLPDKQYXXXXXXXXX------XXXXXXXXXRKKAAYSGGLVLEPKKGFYDKFIIL 515
             E+ +++PDKQ+                        RKKAAY+GGLVL+PK GFYDKFI+L
Sbjct:   807 ERDFIVPDKQFFKKAQQDLGEDEEGDSGKGKSNKTRKKAAYAGGLVLDPKVGFYDKFILL 866

Query:   516 MDFNSLYPSIIQEYNICFTTIP-----VRMLQDSDITTLCEYLPEHQVDTGILPSEIKKL 570
             +DFNSLYPSIIQE+NICFTT+       R   + D   + E LP+  ++ GILP EI+KL
Sbjct:   867 LDFNSLYPSIIQEFNICFTTVERGATNTRKKTEEDEDEIPE-LPDQSLEMGILPKEIRKL 925

Query:   571 VESRRQVKALMKQPNLSSDLLMQYDIRQKALKLTANSMYGCLGFPNSRFFAQPLAALVTA 630
             VE RRQVK LMK+P+L+ DL +QYDIRQKALKLTANSMYGCLGF  SRF+A+PLAALVT 
Sbjct:   926 VERRRQVKQLMKEPDLNPDLYLQYDIRQKALKLTANSMYGCLGFSFSRFYAKPLAALVTH 985

Query:   631 KGREILLNTKSLVENLNYEVIYGDTDSLMISCNVNDYDSVFKIGNQIKSECNKLYKQLEL 690
             KGREIL++TK +V+ +N EVIYGDTDS+MI+ N  + + VFK+GN++KSE NKLYK LE+
Sbjct:   986 KGREILMHTKEMVQRMNLEVIYGDTDSIMINTNSTNLEEVFKLGNKVKSEVNKLYKLLEI 1045

Query:   691 DIDGVXXXXXXXXXXXXXXXXXXXXXNGKMICSQEIKGVDVVRRDWSQLASEAGKFVISQ 750
             DIDGV                     +GK    QE+KG+D+VRRDW  LA E G +VI Q
Sbjct:  1046 DIDGVFKSLLLLKKKKYAALMVEPQGDGKYTTKQELKGLDIVRRDWCDLAKECGNYVIGQ 1105

Query:   751 ILDEQSYTDYSLDDRLQNIHEHMKKIRTDLDNGFVPLTLLEITKQLTKAPE 801
             IL +Q+      D  ++NI +H+ +I   + NG +PL + EI K LTK P+
Sbjct:  1106 ILSDQNR-----DTIIENIQKHLIEIGEKVANGNIPLNMFEIHKSLTKEPQ 1151

GO:0001882 "nucleoside binding" evidence=IEA

GO:0000166 "nucleotide binding" evidence=IEA

GO:0003676 "nucleic acid binding" evidence=IEA

GO:0003677 "DNA binding" evidence=IEA

GO:0003887 "DNA-directed DNA polymerase activity" evidence=IEA;IBA

GO:0006260 "DNA replication" evidence=IEA;IBA

GO:0006139 "nucleobase-containing compound metabolic process" evidence=IEA

GO:0019985 "translesion synthesis" evidence=IBA

GO:0006303 "double-strand break repair via nonhomologous end joining" evidence=IBA

GO:0090305 "nucleic acid phosphodiester bond hydrolysis" evidence=IBA

GO:0005658 "alpha DNA polymerase:primase complex" evidence=IBA

GO:0008408 "3'-5' exonuclease activity" evidence=IBA

GO:0005634 "nucleus" evidence=IBA

GO:0006297 "nucleotide-excision repair, DNA gap filling" evidence=IBA

GO:0016740 "transferase activity" evidence=IEA

GO:0016779 "nucleotidyltransferase activity" evidence=IEA

UNIPROTKB|Q59J88 Q59J88 "DNA polymerase" [Iguana iguana (taxid:8517)]

 Score = 1117 (398.3 bits), Expect = 5.6e-178, Sum P(3) = 5.6e-178
 Identities = 228/412 (55%), Positives = 291/412 (70%)

Query:   402 IVEFIKFTMLHSSYIIKIMCELNVLPLAIQITNVCGNVLSRTLMGGRSERNEFLLLHAFH 461
             ++  ++ T   + YI++IMC+LNVLPLA+QITN+ GNV+SRTLMGGR+ERNE+LLLHAF+
Sbjct:   710 LLYMVENTWTDAKYILQIMCDLNVLPLALQITNIAGNVMSRTLMGGRAERNEYLLLHAFY 769

Query:   462 EKSYVLPDKQYXXXXXXXXXXXXXX------XXXXRKKAAYSGGLVLEPKKGFYDKFIIL 515
             EK++++PDKQ                         RKKAAYSGGLVLEPK GFYDKFI+L
Sbjct:   770 EKNFIVPDKQLFKKTQKQLEEDEDFEGDQNKSKTGRKKAAYSGGLVLEPKVGFYDKFILL 829

Query:   516 MDFNSLYPSIIQEYNICFTTIPV------RMLQDSDITTLCEYLPEHQVDTGILPSEIKK 569
             +DFNSLYPSIIQE+NICFTT+        +  +D +   + E LP+  +D GILP EI+K
Sbjct:   830 LDFNSLYPSIIQEFNICFTTVHRVSSSLHKNTEDGEEEEIPE-LPDSSLDMGILPKEIRK 888

Query:   570 LVESRRQVKALMKQPNLSSDLLMQYDIRQKALKLTANSMYGCLGFPNSRFFAQPLAALVT 629
             LVE RRQVK LMKQP+L+SDL +QYDIRQKALKLTANSMYGCLGF  SRF+A+PLAALVT
Sbjct:   889 LVERRRQVKQLMKQPDLNSDLYLQYDIRQKALKLTANSMYGCLGFSYSRFYAKPLAALVT 948

Query:   630 AKGREILLNTKSLVENLNYEVIYGDTDSLMISCNVNDYDSVFKIGNQIKSECNKLYKQLE 689
              KGREIL++TK +VE +N EVIYGDTDS+MI+ N+ + + VFK+GN+IKSE NKLYK LE
Sbjct:   949 FKGREILMHTKEMVEKMNLEVIYGDTDSIMINTNITNLEEVFKLGNKIKSEVNKLYKLLE 1008

Query:   690 LDIDGVXXXXXXXXXXXXXXXXXXXXXNGKMICSQEIKGVDVVRRDWSQLASEAGKFVIS 749
             +DIDG+                     +GK I  QE+KG+D+VRRDW  LA E G ++IS
Sbjct:  1009 IDIDGIFKSLLLLKKKKYAALVVEPTGDGKYITKQELKGLDIVRRDWCDLAKETGNYIIS 1068

Query:   750 QILDEQSYTDYSLDDRLQNIHEHMKKIRTDLDNGFVPLTLLEITKQLTKAPE 801
             QIL +Q + D  ++    NI   + +I  ++ NG VP+   EI K LTK P+
Sbjct:  1069 QILSDQ-FRDVIVE----NIQRRLIQIGENVVNGSVPIKQFEINKALTKDPQ 1115

GO:0000084 "S phase of mitotic cell cycle" evidence=ISS

GO:0000166 "nucleotide binding" evidence=ISS

GO:0003677 "DNA binding" evidence=ISS

GO:0003682 "chromatin binding" evidence=ISS

GO:0003887 "DNA-directed DNA polymerase activity" evidence=ISS

GO:0005634 "nucleus" evidence=ISS

GO:0005635 "nuclear envelope" evidence=ISS

GO:0005654 "nucleoplasm" evidence=ISS

GO:0005658 "alpha DNA polymerase:primase complex" evidence=ISS

GO:0005730 "nucleolus" evidence=ISS

GO:0006260 "DNA replication" evidence=ISS

GO:0006269 "DNA replication, synthesis of RNA primer" evidence=ISS

GO:0006270 "DNA replication initiation" evidence=ISS

GO:0006271 "DNA strand elongation involved in DNA replication" evidence=ISS

GO:0006272 "leading strand elongation" evidence=ISS

GO:0006273 "lagging strand elongation" evidence=ISS

GO:0006303 "double-strand break repair via nonhomologous end joining" evidence=ISS

GO:0008283 "cell proliferation" evidence=ISS

GO:0016363 "nuclear matrix" evidence=ISS

GO:0000731 "DNA synthesis involved in DNA repair" evidence=ISS

GO:0006281 "DNA repair" evidence=ISS

GO:0000785 "chromatin" evidence=ISS

GO:0003896 "DNA primase activity" evidence=ISS

UNIPROTKB|F6Y1C9 POLA1 "DNA polymerase" [Canis lupus familiaris (taxid:9615)]

 Score = 1083 (386.3 bits), Expect = 3.0e-177, Sum P(3) = 3.0e-177
 Identities = 222/413 (53%), Positives = 288/413 (69%)

Query:   402 IVEFIKFTMLHSSYIIKIMCELNVLPLAIQITNVCGNVLSRTLMGGRSERNEFLLLHAFH 461
             ++  ++ T   + +I++IMCELNVLPLA+QITN+ GN++SRTLMGGRSERNEFLLLHAF+
Sbjct:   744 LLYLLEHTWKDARFILQIMCELNVLPLALQITNIAGNIMSRTLMGGRSERNEFLLLHAFY 803

Query:   462 EKSYVLPDKQYXXX-------XXXXXXXXXXXXXXXRKKAAYSGGLVLEPKKGFYDKFII 514
             E +Y++PDKQ                          RKKAAY+GGLVL+PK GFYDKFI+
Sbjct:   804 ENNYIVPDKQIFRKPQQKLGDEDEELDGDANKYKKGRKKAAYAGGLVLDPKAGFYDKFIL 863

Query:   515 LMDFNSLYPSIIQEYNICFTTIP------VRMLQDSDITTLCEYLPEHQVDTGILPSEIK 568
             L+DFNSLYPSIIQE+NICFTT+        ++ +D +   + E LP+  ++ GILP EI+
Sbjct:   864 LLDFNSLYPSIIQEFNICFTTVQRVASETQKVTEDGEQEQIPE-LPDPGLEMGILPREIR 922

Query:   569 KLVESRRQVKALMKQPNLSSDLLMQYDIRQKALKLTANSMYGCLGFPNSRFFAQPLAALV 628
             KLVE R+QVK LMKQ +L+ DL++QYDIRQKALKLTANSMYGCLGF  SRF+A+PLAALV
Sbjct:   923 KLVERRKQVKQLMKQQDLNPDLVLQYDIRQKALKLTANSMYGCLGFSYSRFYAKPLAALV 982

Query:   629 TAKGREILLNTKSLVENLNYEVIYGDTDSLMISCNVNDYDSVFKIGNQIKSECNKLYKQL 688
             T KGREIL++TK +V+ +N EVIYGDTDS+MI+ N  D + V+K+GN++KSE NKLYK L
Sbjct:   983 TYKGREILMHTKEMVQKMNLEVIYGDTDSIMINTNSTDLEEVYKLGNKVKSEVNKLYKLL 1042

Query:   689 ELDIDGVXXXXXXXXXXXXXXXXXXXXXNGKMICSQEIKGVDVVRRDWSQLASEAGKFVI 748
             E+DIDGV                     +G     QE+KG+D+VRRDW  LA E G FVI
Sbjct:  1043 EIDIDGVFKSLLLLKKKKYGALVVEPTSDGNYSTKQELKGLDIVRRDWCDLAKETGNFVI 1102

Query:   749 SQILDEQSYTDYSLDDRLQNIHEHMKKIRTDLDNGFVPLTLLEITKQLTKAPE 801
              QIL +QS      D  ++NI + + +I  ++ NG VP++  EI K LTK P+
Sbjct:  1103 GQILSDQSR-----DTIVENIQKRLIEIGENVLNGSVPVSQFEINKALTKDPQ 1150

GO:0003887 "DNA-directed DNA polymerase activity" evidence=IEA

GO:0006260 "DNA replication" evidence=IEA

GO:0003677 "DNA binding" evidence=IEA

GO:0001882 "nucleoside binding" evidence=IEA

GO:0000166 "nucleotide binding" evidence=IEA

MGI|MGI:99660 Pola1 "polymerase (DNA directed), alpha 1" [Mus musculus (taxid:10090)]

 Score = 1074 (383.1 bits), Expect = 5.0e-177, Sum P(3) = 5.0e-177
 Identities = 223/417 (53%), Positives = 288/417 (69%)

Query:   398 YLIGIVEFIKFTMLHSSYIIKIMCELNVLPLAIQITNVCGNVLSRTLMGGRSERNEFLLL 457
             YL+ ++E I      + +I++IMCELNVLPLA+QITN+ GN++SRTLMGGRSERNEFLLL
Sbjct:   741 YLLYLLEHI---WKDARFILQIMCELNVLPLALQITNIAGNIMSRTLMGGRSERNEFLLL 797

Query:   458 HAFHEKSYVLPDKQYXXX-------XXXXXXXXXXXXXXXRKKAAYSGGLVLEPKKGFYD 510
             HAF+E +Y++PDKQ                          RKKA Y+GGLVL+PK GFYD
Sbjct:   798 HAFYENNYIVPDKQIFRKPQQKLGDEDEEIDGDTNKYKKGRKKATYAGGLVLDPKVGFYD 857

Query:   511 KFIILMDFNSLYPSIIQEYNICFTTIP------VRMLQDSDITTLCEYLPEHQVDTGILP 564
             KFI+L+DFNSLYPSIIQE+NICFTT+        +  +D +   + E LP+  ++ GILP
Sbjct:   858 KFILLLDFNSLYPSIIQEFNICFTTVQRVTSEVQKATEDEEQEQIPE-LPDPNLEMGILP 916

Query:   565 SEIKKLVESRRQVKALMKQPNLSSDLLMQYDIRQKALKLTANSMYGCLGFPNSRFFAQPL 624
              EI+KLVE R+QVK LMKQ +L+ DL++QYDIRQKALKLTANSMYGCLGF  SRF+A+PL
Sbjct:   917 REIRKLVERRKQVKQLMKQQDLNPDLVLQYDIRQKALKLTANSMYGCLGFSYSRFYAKPL 976

Query:   625 AALVTAKGREILLNTKSLVENLNYEVIYGDTDSLMISCNVNDYDSVFKIGNQIKSECNKL 684
             AALVT KGREIL++TK +V+ +N EVIYGDTDS+MI+ N  + + VFK+GN++KSE NKL
Sbjct:   977 AALVTYKGREILMHTKDMVQKMNLEVIYGDTDSIMINTNSTNLEEVFKLGNKVKSEVNKL 1036

Query:   685 YKQLELDIDGVXXXXXXXXXXXXXXXXXXXXXNGKMICSQEIKGVDVVRRDWSQLASEAG 744
             YK LE+DID V                     +G  I  QE+KG+D+VRRDW  LA + G
Sbjct:  1037 YKLLEIDIDAVFKSLLLLKKKKYAALVVEPTSDGNYITKQELKGLDIVRRDWCDLAKDTG 1096

Query:   745 KFVISQILDEQSYTDYSLDDRLQNIHEHMKKIRTDLDNGFVPLTLLEITKQLTKAPE 801
              FVI QIL +QS      D  ++NI + + +I  ++ NG VP++  EI K LTK P+
Sbjct:  1097 NFVIGQILSDQSR-----DTIVENIQKRLIEIGENVLNGSVPVSQFEINKALTKDPQ 1148

GO:0000084 "S phase of mitotic cell cycle" evidence=ISO

GO:0000166 "nucleotide binding" evidence=ISO

GO:0001882 "nucleoside binding" evidence=IEA

GO:0003676 "nucleic acid binding" evidence=IEA

GO:0003677 "DNA binding" evidence=ISO

GO:0003682 "chromatin binding" evidence=ISO

GO:0003690 "double-stranded DNA binding" evidence=ISO

GO:0003887 "DNA-directed DNA polymerase activity" evidence=ISO;IDA

GO:0005515 "protein binding" evidence=IPI

GO:0005634 "nucleus" evidence=ISO;IDA

GO:0005635 "nuclear envelope" evidence=ISO

GO:0005654 "nucleoplasm" evidence=ISO

GO:0005658 "alpha DNA polymerase:primase complex" evidence=ISO;IDA

GO:0005730 "nucleolus" evidence=ISO

GO:0006139 "nucleobase-containing compound metabolic process" evidence=IEA

GO:0006260 "DNA replication" evidence=ISO;IMP;IDA

GO:0006269 "DNA replication, synthesis of RNA primer" evidence=ISO

GO:0006270 "DNA replication initiation" evidence=ISO

GO:0006271 "DNA strand elongation involved in DNA replication" evidence=ISO

GO:0006272 "leading strand elongation" evidence=ISO

GO:0006273 "lagging strand elongation" evidence=ISO

GO:0006303 "double-strand break repair via nonhomologous end joining" evidence=ISO;IBA

GO:0008283 "cell proliferation" evidence=ISO

GO:0008408 "3'-5' exonuclease activity" evidence=IBA

GO:0016363 "nuclear matrix" evidence=ISO

GO:0016740 "transferase activity" evidence=IEA

GO:0016779 "nucleotidyltransferase activity" evidence=IEA

GO:0017076 "purine nucleotide binding" evidence=ISO

GO:0019103 "pyrimidine nucleotide binding" evidence=ISO

GO:0019985 "translesion synthesis" evidence=IBA

GO:0046872 "metal ion binding" evidence=IEA

GO:0046982 "protein heterodimerization activity" evidence=IPI

GO:0051536 "iron-sulfur cluster binding" evidence=IEA

GO:0051539 "4 iron, 4 sulfur cluster binding" evidence=IEA

GO:0090305 "nucleic acid phosphodiester bond hydrolysis" evidence=IBA

UNIPROTKB|Q59J89 Q59J89 "DNA polymerase" [Trachemys scripta (taxid:34903)]

 Score = 1089 (388.4 bits), Expect = 2.7e-176, Sum P(3) = 2.7e-176
 Identities = 222/411 (54%), Positives = 284/411 (69%)

Query:   402 IVEFIKFTMLHSSYIIKIMCELNVLPLAIQITNVCGNVLSRTLMGGRSERNEFLLLHAFH 461
             ++  ++ T   + +I++IMCELNVLPLA+QITN+ GNV+SRT+MGGRSERNEFLLLHAF+
Sbjct:   708 LLYMLENTWTDARFILQIMCELNVLPLALQITNISGNVMSRTMMGGRSERNEFLLLHAFY 767

Query:   462 EKSYVLPDKQYXXX------XXXXXXXXXXXXXXXRKKAAYSGGLVLEPKKGFYDKFIIL 515
             E+ Y++PDKQ                         RKKAAY+GGLVL+PK GFYD FI+L
Sbjct:   768 ERDYIVPDKQVFKKPQQKLVDEDEGVEDQNKSKIGRKKAAYAGGLVLDPKVGFYDTFILL 827

Query:   516 MDFNSLYPSIIQEYNICFTTIP-----VRMLQDSDITTLCEYLPEHQVDTGILPSEIKKL 570
             +DFNSLYPSIIQE+NICFTT+       +   +  +      LP+  ++ GILP EI+KL
Sbjct:   828 LDFNSLYPSIIQEFNICFTTVQRESSDAQKRAEDGVQEEIPELPDPSLEMGILPKEIRKL 887

Query:   571 VESRRQVKALMKQPNLSSDLLMQYDIRQKALKLTANSMYGCLGFPNSRFFAQPLAALVTA 630
             VE RRQVK LMKQP+L+ DL +QYDIRQKALKLTANSMYGCLGF  SRF+A+PLAALVT 
Sbjct:   888 VERRRQVKQLMKQPDLNPDLYLQYDIRQKALKLTANSMYGCLGFSYSRFYAKPLAALVTH 947

Query:   631 KGREILLNTKSLVENLNYEVIYGDTDSLMISCNVNDYDSVFKIGNQIKSECNKLYKQLEL 690
             KGREIL++TK +V+ +N EVIYGDTDS+MI+ N  + + VFK+GN+IKSE NKLYK LE+
Sbjct:   948 KGREILMHTKEMVQKMNLEVIYGDTDSIMINTNSTNLEEVFKLGNKIKSEVNKLYKLLEI 1007

Query:   691 DIDGVXXXXXXXXXXXXXXXXXXXXXNGKMICSQEIKGVDVVRRDWSQLASEAGKFVISQ 750
             DIDGV                     +GK +  QE+KG+D+VRRDW  LA E G +VI Q
Sbjct:  1008 DIDGVFKSLLLLKKKKYAALTVEPTGDGKYVTKQELKGLDIVRRDWCDLAKETGNYVIGQ 1067

Query:   751 ILDEQSYTDYSLDDRLQNIHEHMKKIRTDLDNGFVPLTLLEITKQLTKAPE 801
             IL +QS      D  ++NI   + +I  ++ NG VP++  EI K LTK P+
Sbjct:  1068 ILSDQSR-----DTIVENIQRRLIEIGENVINGRVPISQFEINKALTKDPQ 1113

GO:0000084 "S phase of mitotic cell cycle" evidence=ISS

GO:0000166 "nucleotide binding" evidence=ISS

GO:0003677 "DNA binding" evidence=ISS

GO:0003682 "chromatin binding" evidence=ISS

GO:0003887 "DNA-directed DNA polymerase activity" evidence=ISS

GO:0005634 "nucleus" evidence=ISS

GO:0005635 "nuclear envelope" evidence=ISS

GO:0005654 "nucleoplasm" evidence=ISS

GO:0005658 "alpha DNA polymerase:primase complex" evidence=ISS

GO:0005730 "nucleolus" evidence=ISS

GO:0006260 "DNA replication" evidence=ISS

GO:0006269 "DNA replication, synthesis of RNA primer" evidence=ISS

GO:0006270 "DNA replication initiation" evidence=ISS

GO:0006271 "DNA strand elongation involved in DNA replication" evidence=ISS

GO:0006272 "leading strand elongation" evidence=ISS

GO:0006273 "lagging strand elongation" evidence=ISS

GO:0006303 "double-strand break repair via nonhomologous end joining" evidence=ISS

GO:0008283 "cell proliferation" evidence=ISS

GO:0016363 "nuclear matrix" evidence=ISS

GO:0000731 "DNA synthesis involved in DNA repair" evidence=ISS

GO:0006281 "DNA repair" evidence=ISS

GO:0000785 "chromatin" evidence=ISS

GO:0003896 "DNA primase activity" evidence=ISS

UNIPROTKB|E2QVU2 POLA1 "Uncharacterized protein" [Canis lupus familiaris (taxid:9615)]

 Score = 1074 (383.1 bits), Expect = 2.7e-176, Sum P(3) = 2.7e-176
 Identities = 222/414 (53%), Positives = 288/414 (69%)

Query:   402 IVEFIKFTMLHSSYIIKIMCELNVLPLAIQITNVCGNVLSRTLMGGRSERNEFLLLHAFH 461
             ++  ++ T   + +I++IMCELNVLPLA+QITN+ GN++SRTLMGGRSERNEFLLLHAF+
Sbjct:   744 LLYLLEHTWKDARFILQIMCELNVLPLALQITNIAGNIMSRTLMGGRSERNEFLLLHAFY 803

Query:   462 EKSYVLPDKQYXXX-------XXXXXXXXXXXXXXXRKKAAYSGGLVLEPKK-GFYDKFI 513
             E +Y++PDKQ                          RKKAAY+GGLVL+PK  GFYDKFI
Sbjct:   804 ENNYIVPDKQIFRKPQQKLGDEDEELDGDANKYKKGRKKAAYAGGLVLDPKAAGFYDKFI 863

Query:   514 ILMDFNSLYPSIIQEYNICFTTIP------VRMLQDSDITTLCEYLPEHQVDTGILPSEI 567
             +L+DFNSLYPSIIQE+NICFTT+        ++ +D +   + E LP+  ++ GILP EI
Sbjct:   864 LLLDFNSLYPSIIQEFNICFTTVQRVASETQKVTEDGEQEQIPE-LPDPGLEMGILPREI 922

Query:   568 KKLVESRRQVKALMKQPNLSSDLLMQYDIRQKALKLTANSMYGCLGFPNSRFFAQPLAAL 627
             +KLVE R+QVK LMKQ +L+ DL++QYDIRQKALKLTANSMYGCLGF  SRF+A+PLAAL
Sbjct:   923 RKLVERRKQVKQLMKQQDLNPDLVLQYDIRQKALKLTANSMYGCLGFSYSRFYAKPLAAL 982

Query:   628 VTAKGREILLNTKSLVENLNYEVIYGDTDSLMISCNVNDYDSVFKIGNQIKSECNKLYKQ 687
             VT KGREIL++TK +V+ +N EVIYGDTDS+MI+ N  D + V+K+GN++KSE NKLYK 
Sbjct:   983 VTYKGREILMHTKEMVQKMNLEVIYGDTDSIMINTNSTDLEEVYKLGNKVKSEVNKLYKL 1042

Query:   688 LELDIDGVXXXXXXXXXXXXXXXXXXXXXNGKMICSQEIKGVDVVRRDWSQLASEAGKFV 747
             LE+DIDGV                     +G     QE+KG+D+VRRDW  LA E G FV
Sbjct:  1043 LEIDIDGVFKSLLLLKKKKYGALVVEPTSDGNYSTKQELKGLDIVRRDWCDLAKETGNFV 1102

Query:   748 ISQILDEQSYTDYSLDDRLQNIHEHMKKIRTDLDNGFVPLTLLEITKQLTKAPE 801
             I QIL +QS      D  ++NI + + +I  ++ NG VP++  EI K LTK P+
Sbjct:  1103 IGQILSDQSR-----DTIVENIQKRLIEIGENVLNGSVPVSQFEINKALTKDPQ 1151

GO:0006260 "DNA replication" evidence=IEA

GO:0003887 "DNA-directed DNA polymerase activity" evidence=IEA

GO:0003677 "DNA binding" evidence=IEA

GO:0001882 "nucleoside binding" evidence=IEA

GO:0000166 "nucleotide binding" evidence=IEA

UNIPROTKB|F1NR19 POLA1 "DNA polymerase" [Gallus gallus (taxid:9031)]

 Score = 1089 (388.4 bits), Expect = 6.4e-175, Sum P(3) = 6.4e-175
 Identities = 224/405 (55%), Positives = 281/405 (69%)

Query:   409 TMLHSSYIIKIMCELNVLPLAIQITNVCGNVLSRTLMGGRSERNEFLLLHAFHEKSYVLP 468
             T   + +I++IMCELNVLPLA+QITN+ GNV+SRT+MGGRSERNEFLLLHAF+EK Y++P
Sbjct:   736 TWTDAKFILQIMCELNVLPLALQITNISGNVMSRTMMGGRSERNEFLLLHAFYEKDYIVP 795

Query:   469 DKQYXXX------XXXXXXXXXXXXXXXRKKAAYSGGLVLEPKKGFYDKFIILMDFNSLY 522
             DKQ                         +KKAAY+GGLVL+PK GFYDKFI+L+DFNSLY
Sbjct:   796 DKQVFKKPLQKLVDEDEDFEDQNKSKIGKKKAAYAGGLVLDPKVGFYDKFILLLDFNSLY 855

Query:   523 PSIIQEYNICFTTIPVRMLQDSDITTLCEY------LPEHQVDTGILPSEIKKLVESRRQ 576
             PSIIQE+NICFTT+  R+  ++      E       LP+  ++ GILP EI+KLVE RRQ
Sbjct:   856 PSIIQEFNICFTTVQ-RLSSEAQKRAEVEEEEEIPELPDPSLEMGILPKEIRKLVERRRQ 914

Query:   577 VKALMKQPNLSSDLLMQYDIRQKALKLTANSMYGCLGFPNSRFFAQPLAALVTAKGREIL 636
             VK LMKQP+L+ DL +QYDIRQKALKLTANSMYGCLGF  SRF+A+PLAALVT KGREIL
Sbjct:   915 VKQLMKQPDLNPDLYLQYDIRQKALKLTANSMYGCLGFSYSRFYAKPLAALVTHKGREIL 974

Query:   637 LNTKSLVENLNYEVIYGDTDSLMISCNVNDYDSVFKIGNQIKSECNKLYKQLELDIDGVX 696
             ++TK +V+ +N EVIYGDTDS+MI+ N  + D VFK+GN+IKSE NKLYK LE+DIDGV 
Sbjct:   975 MHTKEMVQKMNLEVIYGDTDSIMINTNSTNLDEVFKLGNKIKSEVNKLYKLLEIDIDGVF 1034

Query:   697 XXXXXXXXXXXXXXXXXXXXNGKMICSQEIKGVDVVRRDWSQLASEAGKFVISQILDEQS 756
                                 +GK +  QE+KG+D+VRRDW  LA E G +VI QIL +Q 
Sbjct:  1035 KSLLLLKKKKYAALTVEPTGDGKYVTKQELKGLDIVRRDWCDLAKETGNYVIGQILSDQP 1094

Query:   757 YTDYSLDDRLQNIHEHMKKIRTDLDNGFVPLTLLEITKQLTKAPE 801
                   D  ++NI   + +I  ++ NG +P+   EI K LTK P+
Sbjct:  1095 R-----DIIVENIQRRLIEIGENVINGQIPVNQFEINKALTKDPQ 1134

GO:0001882 "nucleoside binding" evidence=IEA

GO:0003887 "DNA-directed DNA polymerase activity" evidence=IEA

GO:0000084 "S phase of mitotic cell cycle" evidence=IEA

GO:0000166 "nucleotide binding" evidence=IEA

GO:0000785 "chromatin" evidence=IEA

GO:0003677 "DNA binding" evidence=IEA

GO:0003682 "chromatin binding" evidence=IEA

GO:0003896 "DNA primase activity" evidence=IEA

GO:0005635 "nuclear envelope" evidence=IEA

GO:0005654 "nucleoplasm" evidence=IEA

GO:0005658 "alpha DNA polymerase:primase complex" evidence=IEA

GO:0005730 "nucleolus" evidence=IEA

GO:0005737 "cytoplasm" evidence=IEA

GO:0006270 "DNA replication initiation" evidence=IEA

GO:0006272 "leading strand elongation" evidence=IEA

GO:0006273 "lagging strand elongation" evidence=IEA

GO:0006303 "double-strand break repair via nonhomologous end joining" evidence=IEA

GO:0008283 "cell proliferation" evidence=IEA

GO:0016363 "nuclear matrix" evidence=IEA

GO:0046982 "protein heterodimerization activity" evidence=IEA

---

Prediction of Enzyme Commission (EC) Number

EC Number Prediction by Annotation Transfer from SWISS-PROT Entries

Original result of BLAST against SWISS-PROT

ID	Name	Annotated EC number	Identity	Query coverage	Hit coverage	RBH(Q2H)	RBH(H2Q)
P26019	DPOLA_DROME	2, ., 7, ., 7, ., 7	0.5629	0.4009	0.2775	yes	N/A

EC Number Prediction by EFICAz Software

Prediction Level	EC number	Confidence of Prediction
3rd Layer	2.7.7	0.691
4th Layer	2.7.7.7	0.737

---

Conserved Domains and Related Protein Families

Conserved Domains Detected by RPS-BLAST

Original result of RPS-BLAST against CDD database

ID	Length	Definition	E-value
Query	1030
cd05532	400	cd05532, POLBc_alpha, DNA polymerase type-B alpha	1e-165
TIGR00592	1172	TIGR00592, pol2, DNA polymerase (pol2)	1e-139
pfam00136	458	pfam00136, DNA_pol_B, DNA polymerase family B	1e-97
COG0417	792	COG0417, PolB, DNA polymerase elongation subunit (	7e-77
cd00145	323	cd00145, POLBc, DNA polymerase type-B family catal	1e-66
smart00486	474	smart00486, POLBc, DNA polymerase type-B family	6e-65
PRK05762	786	PRK05762, PRK05762, DNA polymerase II; Reviewed	2e-53
cd05533	393	cd05533, POLBc_delta, DNA polymerase type-B delta	3e-48
cd05536	371	cd05536, POLBc_B3, DNA polymerase type-B B3 subfam	6e-47
PTZ00166	1054	PTZ00166, PTZ00166, DNA polymerase delta catalytic	1e-42
pfam09767	159	pfam09767, DUF2053, Predicted membrane protein (DU	2e-36
cd05537	371	cd05537, POLBc_Pol_II, DNA polymerase type-II subf	2e-36
cd05534	451	cd05534, POLBc_zeta, DNA polymerase type-B zeta su	3e-35
TIGR00592	1172	TIGR00592, pol2, DNA polymerase (pol2)	3e-34
PRK05761	787	PRK05761, PRK05761, DNA polymerase I; Reviewed	1e-33
cd05530	372	cd05530, POLBc_B1, DNA polymerase type-B B1 subfam	5e-30
cd05531	352	cd05531, POLBc_B2, DNA polymerase type-B B2 subfam	3e-27
pfam02956	525	pfam02956, TT_ORF1, TT viral orf 1	6e-26
pfam02956	525	pfam02956, TT_ORF1, TT viral orf 1	8e-26
pfam02956	525	pfam02956, TT_ORF1, TT viral orf 1	2e-25
pfam02956	525	pfam02956, TT_ORF1, TT viral orf 1	2e-25
pfam02956	525	pfam02956, TT_ORF1, TT viral orf 1	4e-25
PRK12678	672	PRK12678, PRK12678, transcription termination fact	4e-25
PHA03036	1004	PHA03036, PHA03036, DNA polymerase; Provisional	1e-23
pfam02956	525	pfam02956, TT_ORF1, TT viral orf 1	2e-23
pfam02956	525	pfam02956, TT_ORF1, TT viral orf 1	4e-23
PRK12678	672	PRK12678, PRK12678, transcription termination fact	1e-18
PRK12678	672	PRK12678, PRK12678, transcription termination fact	3e-18
PRK12678	672	PRK12678, PRK12678, transcription termination fact	6e-18
PTZ00121	2084	PTZ00121, PTZ00121, MAEBL; Provisional	1e-17
PTZ00121	2084	PTZ00121, PTZ00121, MAEBL; Provisional	4e-17
PTZ00121	2084	PTZ00121, PTZ00121, MAEBL; Provisional	2e-16
PTZ00121	2084	PTZ00121, PTZ00121, MAEBL; Provisional	2e-16
PRK12678	672	PRK12678, PRK12678, transcription termination fact	3e-16
PTZ00121	2084	PTZ00121, PTZ00121, MAEBL; Provisional	1e-15
PTZ00121	2084	PTZ00121, PTZ00121, MAEBL; Provisional	1e-15
PRK12678	672	PRK12678, PRK12678, transcription termination fact	2e-15
PTZ00121	2084	PTZ00121, PTZ00121, MAEBL; Provisional	2e-15
PTZ00121	2084	PTZ00121, PTZ00121, MAEBL; Provisional	2e-15
PTZ00121	2084	PTZ00121, PTZ00121, MAEBL; Provisional	2e-15
PTZ00121	2084	PTZ00121, PTZ00121, MAEBL; Provisional	2e-15
PRK10811	1068	PRK10811, rne, ribonuclease E; Reviewed	2e-15
PTZ00121	2084	PTZ00121, PTZ00121, MAEBL; Provisional	3e-15
PRK10811	1068	PRK10811, rne, ribonuclease E; Reviewed	6e-15
PTZ00121	2084	PTZ00121, PTZ00121, MAEBL; Provisional	7e-15
cd05538	347	cd05538, POLBc_Pol_II_B, DNA polymerase type-II B	8e-15
PTZ00121	2084	PTZ00121, PTZ00121, MAEBL; Provisional	1e-14
PTZ00121	2084	PTZ00121, PTZ00121, MAEBL; Provisional	1e-14
PTZ00121	2084	PTZ00121, PTZ00121, MAEBL; Provisional	3e-14
PTZ00121	2084	PTZ00121, PTZ00121, MAEBL; Provisional	5e-14
PTZ00121	2084	PTZ00121, PTZ00121, MAEBL; Provisional	6e-14
PTZ00121	2084	PTZ00121, PTZ00121, MAEBL; Provisional	6e-14
PTZ00121	2084	PTZ00121, PTZ00121, MAEBL; Provisional	9e-14
PTZ00121	2084	PTZ00121, PTZ00121, MAEBL; Provisional	1e-13
PTZ00121	2084	PTZ00121, PTZ00121, MAEBL; Provisional	1e-13
PTZ00121	2084	PTZ00121, PTZ00121, MAEBL; Provisional	2e-13
PTZ00121	2084	PTZ00121, PTZ00121, MAEBL; Provisional	2e-13
PTZ00121	2084	PTZ00121, PTZ00121, MAEBL; Provisional	5e-13
PTZ00121	2084	PTZ00121, PTZ00121, MAEBL; Provisional	8e-13
TIGR01642	509	TIGR01642, U2AF_lg, U2 snRNP auxilliary factor, la	1e-12
PTZ00121	2084	PTZ00121, PTZ00121, MAEBL; Provisional	3e-12
pfam08648	158	pfam08648, DUF1777, Protein of unknown function (D	4e-12
pfam02956	525	pfam02956, TT_ORF1, TT viral orf 1	5e-12
pfam12254	67	pfam12254, DNA_pol_alpha_N, DNA polymerase alpha s	7e-12
pfam10243	506	pfam10243, MIP-T3, Microtubule-binding protein MIP	9e-12
TIGR01642	509	TIGR01642, U2AF_lg, U2 snRNP auxilliary factor, la	1e-11
pfam02443	237	pfam02443, Circo_capsid, Circovirus capsid protein	1e-11
TIGR01622	457	TIGR01622, SF-CC1, splicing factor, CC1-like famil	1e-11
pfam08648	158	pfam08648, DUF1777, Protein of unknown function (D	2e-11
pfam10243	506	pfam10243, MIP-T3, Microtubule-binding protein MIP	2e-11
pfam02443	237	pfam02443, Circo_capsid, Circovirus capsid protein	2e-11
pfam02443	237	pfam02443, Circo_capsid, Circovirus capsid protein	2e-11
PRK04195	482	PRK04195, PRK04195, replication factor C large sub	2e-11
TIGR01642	509	TIGR01642, U2AF_lg, U2 snRNP auxilliary factor, la	4e-11
TIGR01622	457	TIGR01622, SF-CC1, splicing factor, CC1-like famil	5e-11
pfam02443	237	pfam02443, Circo_capsid, Circovirus capsid protein	6e-11
TIGR02794	346	TIGR02794, tolA_full, TolA protein	6e-11
PTZ00121	2084	PTZ00121, PTZ00121, MAEBL; Provisional	8e-11
pfam02443	237	pfam02443, Circo_capsid, Circovirus capsid protein	9e-11
TIGR01642	509	TIGR01642, U2AF_lg, U2 snRNP auxilliary factor, la	1e-10
TIGR01642	509	TIGR01642, U2AF_lg, U2 snRNP auxilliary factor, la	2e-10
pfam02443	237	pfam02443, Circo_capsid, Circovirus capsid protein	2e-10
pfam02443	237	pfam02443, Circo_capsid, Circovirus capsid protein	2e-10
pfam02443	237	pfam02443, Circo_capsid, Circovirus capsid protein	2e-10
PRK04195	482	PRK04195, PRK04195, replication factor C large sub	2e-10
pfam02443	237	pfam02443, Circo_capsid, Circovirus capsid protein	3e-10
pfam08648	158	pfam08648, DUF1777, Protein of unknown function (D	4e-10
PRK05306	746	PRK05306, infB, translation initiation factor IF-2	5e-10
pfam08648	158	pfam08648, DUF1777, Protein of unknown function (D	6e-10
pfam13904	261	pfam13904, DUF4207, Domain of unknown function (DU	6e-10
pfam02443	237	pfam02443, Circo_capsid, Circovirus capsid protein	8e-10
pfam00260	51	pfam00260, Protamine_P1, Protamine P1	9e-10
PTZ00121	2084	PTZ00121, PTZ00121, MAEBL; Provisional	1e-09
PRK10811	1068	PRK10811, rne, ribonuclease E; Reviewed	1e-09
pfam02443	237	pfam02443, Circo_capsid, Circovirus capsid protein	1e-09
pfam02443	237	pfam02443, Circo_capsid, Circovirus capsid protein	1e-09
pfam13868	349	pfam13868, Trichoplein, Tumour suppressor, Mitosta	1e-09
PHA02528	881	PHA02528, 43, DNA polymerase; Provisional	1e-09
PTZ00121	2084	PTZ00121, PTZ00121, MAEBL; Provisional	2e-09
TIGR01642	509	TIGR01642, U2AF_lg, U2 snRNP auxilliary factor, la	2e-09
pfam10243	506	pfam10243, MIP-T3, Microtubule-binding protein MIP	2e-09
TIGR01622	457	TIGR01622, SF-CC1, splicing factor, CC1-like famil	2e-09
pfam00260	51	pfam00260, Protamine_P1, Protamine P1	3e-09
TIGR00927	1096	TIGR00927, 2A1904, K+-dependent Na+/Ca+ exchanger	3e-09
PRK04195	482	PRK04195, PRK04195, replication factor C large sub	4e-09
pfam00260	51	pfam00260, Protamine_P1, Protamine P1	4e-09
pfam00260	51	pfam00260, Protamine_P1, Protamine P1	4e-09
TIGR00592	1172	TIGR00592, pol2, DNA polymerase (pol2)	5e-09
PTZ00121	2084	PTZ00121, PTZ00121, MAEBL; Provisional	6e-09
pfam02443	237	pfam02443, Circo_capsid, Circovirus capsid protein	8e-09
TIGR01622	457	TIGR01622, SF-CC1, splicing factor, CC1-like famil	8e-09
COG1196	1163	COG1196, Smc, Chromosome segregation ATPases [Cell	8e-09
pfam08597	242	pfam08597, eIF3_subunit, Translation initiation fa	8e-09
pfam10243	506	pfam10243, MIP-T3, Microtubule-binding protein MIP	9e-09
pfam12871	97	pfam12871, PRP38_assoc, Pre-mRNA-splicing factor 3	9e-09
TIGR02794	346	TIGR02794, tolA_full, TolA protein	1e-08
pfam13868	349	pfam13868, Trichoplein, Tumour suppressor, Mitosta	1e-08
pfam12871	97	pfam12871, PRP38_assoc, Pre-mRNA-splicing factor 3	1e-08
COG3064	387	COG3064, TolA, Membrane protein involved in colici	1e-08
pfam08432	182	pfam08432, DUF1742, Fungal protein of unknown func	1e-08
PHA03328	316	PHA03328, PHA03328, nuclear egress lamina protein	1e-08
TIGR01622	457	TIGR01622, SF-CC1, splicing factor, CC1-like famil	2e-08
PRK05306	746	PRK05306, infB, translation initiation factor IF-2	2e-08
pfam12871	97	pfam12871, PRP38_assoc, Pre-mRNA-splicing factor 3	2e-08
pfam06495	182	pfam06495, Transformer, Fruit fly transformer prot	2e-08
pfam02443	237	pfam02443, Circo_capsid, Circovirus capsid protein	3e-08
TIGR01622	457	TIGR01622, SF-CC1, splicing factor, CC1-like famil	3e-08
pfam12871	97	pfam12871, PRP38_assoc, Pre-mRNA-splicing factor 3	3e-08
pfam02463	1162	pfam02463, SMC_N, RecF/RecN/SMC N terminal domain	3e-08
pfam03228	117	pfam03228, Adeno_VII, Adenoviral core protein VII	3e-08
PRK05306	746	PRK05306, infB, translation initiation factor IF-2	4e-08
pfam00260	51	pfam00260, Protamine_P1, Protamine P1	4e-08
TIGR01642	509	TIGR01642, U2AF_lg, U2 snRNP auxilliary factor, la	5e-08
pfam08648	158	pfam08648, DUF1777, Protein of unknown function (D	5e-08
TIGR02794	346	TIGR02794, tolA_full, TolA protein	5e-08
TIGR02169	1164	TIGR02169, SMC_prok_A, chromosome segregation prot	5e-08
pfam13868	349	pfam13868, Trichoplein, Tumour suppressor, Mitosta	6e-08
COG1196	1163	COG1196, Smc, Chromosome segregation ATPases [Cell	6e-08
pfam07423	214	pfam07423, DUF1510, Protein of unknown function (D	6e-08
PRK05306	746	PRK05306, infB, translation initiation factor IF-2	7e-08
COG1196	1163	COG1196, Smc, Chromosome segregation ATPases [Cell	7e-08
pfam08432	182	pfam08432, DUF1742, Fungal protein of unknown func	9e-08
PRK04195	482	PRK04195, PRK04195, replication factor C large sub	1e-07
pfam00260	51	pfam00260, Protamine_P1, Protamine P1	1e-07
pfam13868	349	pfam13868, Trichoplein, Tumour suppressor, Mitosta	1e-07
pfam08432	182	pfam08432, DUF1742, Fungal protein of unknown func	1e-07
PHA03328	316	PHA03328, PHA03328, nuclear egress lamina protein	1e-07
pfam03228	117	pfam03228, Adeno_VII, Adenoviral core protein VII	1e-07
pfam05672	171	pfam05672, MAP7, MAP7 (E-MAP-115) family	1e-07
pfam02029	431	pfam02029, Caldesmon, Caldesmon	1e-07
TIGR01622	457	TIGR01622, SF-CC1, splicing factor, CC1-like famil	2e-07
PRK04195	482	PRK04195, PRK04195, replication factor C large sub	2e-07
PRK04195	482	PRK04195, PRK04195, replication factor C large sub	2e-07
COG1196	1163	COG1196, Smc, Chromosome segregation ATPases [Cell	2e-07
pfam12871	97	pfam12871, PRP38_assoc, Pre-mRNA-splicing factor 3	2e-07
pfam12871	97	pfam12871, PRP38_assoc, Pre-mRNA-splicing factor 3	2e-07
pfam12871	97	pfam12871, PRP38_assoc, Pre-mRNA-splicing factor 3	2e-07
pfam08432	182	pfam08432, DUF1742, Fungal protein of unknown func	2e-07
PHA03328	316	PHA03328, PHA03328, nuclear egress lamina protein	2e-07
pfam03228	117	pfam03228, Adeno_VII, Adenoviral core protein VII	2e-07
pfam07423	214	pfam07423, DUF1510, Protein of unknown function (D	2e-07
PHA03334	1545	PHA03334, PHA03334, putative DNA polymerase cataly	2e-07
pfam00841	91	pfam00841, Protamine_P2, Sperm histone P2	2e-07
pfam09756	189	pfam09756, DDRGK, DDRGK domain	2e-07
PRK03918	880	PRK03918, PRK03918, chromosome segregation protein	2e-07
pfam08208	193	pfam08208, RNA_polI_A34, DNA-directed RNA polymera	2e-07
TIGR01642	509	TIGR01642, U2AF_lg, U2 snRNP auxilliary factor, la	3e-07
pfam08648	158	pfam08648, DUF1777, Protein of unknown function (D	3e-07
COG3064	387	COG3064, TolA, Membrane protein involved in colici	3e-07
pfam02463	1162	pfam02463, SMC_N, RecF/RecN/SMC N terminal domain	3e-07
pfam10243	506	pfam10243, MIP-T3, Microtubule-binding protein MIP	4e-07
PHA03328	316	PHA03328, PHA03328, nuclear egress lamina protein	4e-07
PHA03328	316	PHA03328, PHA03328, nuclear egress lamina protein	4e-07
PRK03918	880	PRK03918, PRK03918, chromosome segregation protein	4e-07
PRK03918	880	PRK03918, PRK03918, chromosome segregation protein	4e-07
pfam02463	1162	pfam02463, SMC_N, RecF/RecN/SMC N terminal domain	5e-07
pfam07420	377	pfam07420, DUF1509, Protein of unknown function (D	5e-07
TIGR02794	346	TIGR02794, tolA_full, TolA protein	6e-07
pfam08597	242	pfam08597, eIF3_subunit, Translation initiation fa	6e-07
pfam08432	182	pfam08432, DUF1742, Fungal protein of unknown func	6e-07
pfam03910	336	pfam03910, Adeno_PV, Adenovirus minor core protein	6e-07
TIGR01642	509	TIGR01642, U2AF_lg, U2 snRNP auxilliary factor, la	7e-07
pfam07423	214	pfam07423, DUF1510, Protein of unknown function (D	7e-07
pfam08208	193	pfam08208, RNA_polI_A34, DNA-directed RNA polymera	7e-07
PRK00247	429	PRK00247, PRK00247, putative inner membrane protei	7e-07
PHA03328	316	PHA03328, PHA03328, nuclear egress lamina protein	8e-07
pfam09756	189	pfam09756, DDRGK, DDRGK domain	8e-07
COG0419	908	COG0419, SbcC, ATPase involved in DNA repair [DNA	8e-07
PRK04195	482	PRK04195, PRK04195, replication factor C large sub	1e-06
TIGR00927	1096	TIGR00927, 2A1904, K+-dependent Na+/Ca+ exchanger	1e-06
COG1196	1163	COG1196, Smc, Chromosome segregation ATPases [Cell	1e-06
PHA03328	316	PHA03328, PHA03328, nuclear egress lamina protein	1e-06
PHA03328	316	PHA03328, PHA03328, nuclear egress lamina protein	1e-06
pfam02463	1162	pfam02463, SMC_N, RecF/RecN/SMC N terminal domain	1e-06
TIGR02169	1164	TIGR02169, SMC_prok_A, chromosome segregation prot	1e-06
pfam02029	431	pfam02029, Caldesmon, Caldesmon	1e-06
pfam03910	336	pfam03910, Adeno_PV, Adenovirus minor core protein	1e-06
pfam04615	728	pfam04615, Utp14, Utp14 protein	1e-06
COG4499	434	COG4499, COG4499, Predicted membrane protein [Func	1e-06
TIGR01642	509	TIGR01642, U2AF_lg, U2 snRNP auxilliary factor, la	2e-06
COG3064	387	COG3064, TolA, Membrane protein involved in colici	2e-06
pfam08432	182	pfam08432, DUF1742, Fungal protein of unknown func	2e-06
pfam07423	214	pfam07423, DUF1510, Protein of unknown function (D	2e-06
PRK00247	429	PRK00247, PRK00247, putative inner membrane protei	2e-06
pfam03344	715	pfam03344, Daxx, Daxx Family	2e-06
pfam03344	715	pfam03344, Daxx, Daxx Family	2e-06
PTZ00108	1388	PTZ00108, PTZ00108, DNA topoisomerase 2-like prote	2e-06
PRK04195	482	PRK04195, PRK04195, replication factor C large sub	3e-06
pfam13868	349	pfam13868, Trichoplein, Tumour suppressor, Mitosta	3e-06
COG1196	1163	COG1196, Smc, Chromosome segregation ATPases [Cell	3e-06
pfam02463	1162	pfam02463, SMC_N, RecF/RecN/SMC N terminal domain	3e-06
pfam02463	1162	pfam02463, SMC_N, RecF/RecN/SMC N terminal domain	3e-06
pfam03910	336	pfam03910, Adeno_PV, Adenovirus minor core protein	3e-06
PRK00247	429	PRK00247, PRK00247, putative inner membrane protei	3e-06
pfam06658	142	pfam06658, DUF1168, Protein of unknown function (D	3e-06
COG1196	1163	COG1196, Smc, Chromosome segregation ATPases [Cell	4e-06
pfam08597	242	pfam08597, eIF3_subunit, Translation initiation fa	4e-06
pfam02463	1162	pfam02463, SMC_N, RecF/RecN/SMC N terminal domain	4e-06
TIGR02168	1179	TIGR02168, SMC_prok_B, chromosome segregation prot	4e-06
PRK09510	387	PRK09510, tolA, cell envelope integrity inner memb	4e-06
PRK04195	482	PRK04195, PRK04195, replication factor C large sub	5e-06
PRK04195	482	PRK04195, PRK04195, replication factor C large sub	5e-06
pfam13904	261	pfam13904, DUF4207, Domain of unknown function (DU	5e-06
pfam08208	193	pfam08208, RNA_polI_A34, DNA-directed RNA polymera	5e-06
PRK09510	387	PRK09510, tolA, cell envelope integrity inner memb	5e-06
pfam07946	322	pfam07946, DUF1682, Protein of unknown function (D	5e-06
pfam05793	528	pfam05793, TFIIF_alpha, Transcription initiation f	5e-06
pfam14181	155	pfam14181, YqfQ, YqfQ-like protein	5e-06
PRK12705	508	PRK12705, PRK12705, hypothetical protein; Provisio	6e-06
pfam10243	506	pfam10243, MIP-T3, Microtubule-binding protein MIP	7e-06
pfam02443	237	pfam02443, Circo_capsid, Circovirus capsid protein	7e-06
pfam03910	336	pfam03910, Adeno_PV, Adenovirus minor core protein	7e-06
PRK00247	429	PRK00247, PRK00247, putative inner membrane protei	7e-06
COG0419	908	COG0419, SbcC, ATPase involved in DNA repair [DNA	7e-06
pfam06658	142	pfam06658, DUF1168, Protein of unknown function (D	7e-06
pfam08208	193	pfam08208, RNA_polI_A34, DNA-directed RNA polymera	8e-06
pfam03910	336	pfam03910, Adeno_PV, Adenovirus minor core protein	8e-06
COG4499	434	COG4499, COG4499, Predicted membrane protein [Func	8e-06
pfam05262	489	pfam05262, Borrelia_P83, Borrelia P83/100 protein	8e-06
pfam03228	117	pfam03228, Adeno_VII, Adenoviral core protein VII	9e-06
PRK04195	482	PRK04195, PRK04195, replication factor C large sub	1e-05
PRK04195	482	PRK04195, PRK04195, replication factor C large sub	1e-05
PRK04195	482	PRK04195, PRK04195, replication factor C large sub	1e-05
PRK05306	746	PRK05306, infB, translation initiation factor IF-2	1e-05
pfam13868	349	pfam13868, Trichoplein, Tumour suppressor, Mitosta	1e-05
pfam07423	214	pfam07423, DUF1510, Protein of unknown function (D	1e-05
pfam07423	214	pfam07423, DUF1510, Protein of unknown function (D	1e-05
pfam00841	91	pfam00841, Protamine_P2, Sperm histone P2	1e-05
pfam03910	336	pfam03910, Adeno_PV, Adenovirus minor core protein	1e-05
pfam14181	155	pfam14181, YqfQ, YqfQ-like protein	1e-05
PRK12705	508	PRK12705, PRK12705, hypothetical protein; Provisio	1e-05
pfam14153	185	pfam14153, Spore_coat_CotO, Spore coat protein Cot	1e-05
pfam14265	125	pfam14265, DUF4355, Domain of unknown function (DU	1e-05
PHA03169	413	PHA03169, PHA03169, hypothetical protein; Provisio	1e-05
PRK02224	880	PRK02224, PRK02224, chromosome segregation protein	1e-05
PHA00451	362	PHA00451, PHA00451, protein kinase	1e-05
COG3552	395	COG3552, CoxE, Protein containing von Willebrand f	1e-05
PRK04195	482	PRK04195, PRK04195, replication factor C large sub	2e-05
PRK04195	482	PRK04195, PRK04195, replication factor C large sub	2e-05
PRK04195	482	PRK04195, PRK04195, replication factor C large sub	2e-05
COG1196	1163	COG1196, Smc, Chromosome segregation ATPases [Cell	2e-05
COG1196	1163	COG1196, Smc, Chromosome segregation ATPases [Cell	2e-05
COG3064	387	COG3064, TolA, Membrane protein involved in colici	2e-05
pfam06495	182	pfam06495, Transformer, Fruit fly transformer prot	2e-05
TIGR02169	1164	TIGR02169, SMC_prok_A, chromosome segregation prot	2e-05
pfam05672	171	pfam05672, MAP7, MAP7 (E-MAP-115) family	2e-05
pfam03910	336	pfam03910, Adeno_PV, Adenovirus minor core protein	2e-05
COG0419	908	COG0419, SbcC, ATPase involved in DNA repair [DNA	2e-05
pfam03344	715	pfam03344, Daxx, Daxx Family	2e-05
PRK09510	387	PRK09510, tolA, cell envelope integrity inner memb	2e-05
PRK12705	508	PRK12705, PRK12705, hypothetical protein; Provisio	2e-05
PHA00451	362	PHA00451, PHA00451, protein kinase	2e-05
pfam07767	387	pfam07767, Nop53, Nop53 (60S ribosomal biogenesis)	2e-05
pfam07767	387	pfam07767, Nop53, Nop53 (60S ribosomal biogenesis)	2e-05
PRK12280	158	PRK12280, rplW, 50S ribosomal protein L23; Reviewe	2e-05
pfam00183	529	pfam00183, HSP90, Hsp90 protein	2e-05
pfam04569	89	pfam04569, DUF591, Protein of unknown function	2e-05
pfam12569	516	pfam12569, NARP1, NMDA receptor-regulated protein	2e-05
PRK00409	782	PRK00409, PRK00409, recombination and DNA strand e	2e-05
pfam08432	182	pfam08432, DUF1742, Fungal protein of unknown func	3e-05
pfam06495	182	pfam06495, Transformer, Fruit fly transformer prot	3e-05
pfam02029	431	pfam02029, Caldesmon, Caldesmon	3e-05
pfam05793	528	pfam05793, TFIIF_alpha, Transcription initiation f	3e-05
PLN02381	1066	PLN02381, PLN02381, valyl-tRNA synthetase	3e-05
COG5269	379	COG5269, ZUO1, Ribosome-associated chaperone zuoti	3e-05
pfam09507	427	pfam09507, CDC27, DNA polymerase subunit Cdc27	3e-05
pfam08619	430	pfam08619, Nha1_C, Alkali metal cation/H+ antiport	3e-05
COG2433	652	COG2433, COG2433, Uncharacterized conserved protei	3e-05
TIGR02794	346	TIGR02794, tolA_full, TolA protein	4e-05
COG3064	387	COG3064, TolA, Membrane protein involved in colici	4e-05
pfam05672	171	pfam05672, MAP7, MAP7 (E-MAP-115) family	4e-05
COG0419	908	COG0419, SbcC, ATPase involved in DNA repair [DNA	4e-05
PRK12280	158	PRK12280, rplW, 50S ribosomal protein L23; Reviewe	4e-05
pfam00183	529	pfam00183, HSP90, Hsp90 protein	4e-05
COG4942	420	COG4942, COG4942, Membrane-bound metallopeptidase	4e-05
pfam00844	244	pfam00844, Gemini_coat, Geminivirus coat protein/n	4e-05
pfam00260	51	pfam00260, Protamine_P1, Protamine P1	5e-05
pfam14265	125	pfam14265, DUF4355, Domain of unknown function (DU	5e-05
PRK14160	211	PRK14160, PRK14160, heat shock protein GrpE; Provi	5e-05
TIGR03319	514	TIGR03319, RNase_Y, ribonuclease Y	5e-05
PRK14521	186	PRK14521, rpsP, 30S ribosomal protein S16; Provisi	5e-05
pfam05762	223	pfam05762, VWA_CoxE, VWA domain containing CoxE-li	5e-05
PRK12704	520	PRK12704, PRK12704, phosphodiesterase; Provisional	5e-05
pfam03839	217	pfam03839, Sec62, Translocation protein Sec62	5e-05
pfam03985	431	pfam03985, Paf1, Paf1	5e-05
pfam05672	171	pfam05672, MAP7, MAP7 (E-MAP-115) family	6e-05
pfam08208	193	pfam08208, RNA_polI_A34, DNA-directed RNA polymera	6e-05
TIGR02168	1179	TIGR02168, SMC_prok_B, chromosome segregation prot	6e-05
pfam05262	489	pfam05262, Borrelia_P83, Borrelia P83/100 protein	6e-05
PRK12280	158	PRK12280, rplW, 50S ribosomal protein L23; Reviewe	6e-05
pfam12569	516	pfam12569, NARP1, NMDA receptor-regulated protein	6e-05
PRK12704	520	PRK12704, PRK12704, phosphodiesterase; Provisional	6e-05
pfam11861	154	pfam11861, DUF3381, Domain of unknown function (DU	6e-05
pfam00260	51	pfam00260, Protamine_P1, Protamine P1	7e-05
pfam04569	89	pfam04569, DUF591, Protein of unknown function	7e-05
PRK04195	482	PRK04195, PRK04195, replication factor C large sub	8e-05
PRK05306	746	PRK05306, infB, translation initiation factor IF-2	8e-05
pfam00906	182	pfam00906, Hepatitis_core, Hepatitis core antigen	8e-05
COG0810	244	COG0810, TonB, Periplasmic protein TonB, links inn	8e-05
COG0810	244	COG0810, TonB, Periplasmic protein TonB, links inn	8e-05
COG0419	908	COG0419, SbcC, ATPase involved in DNA repair [DNA	9e-05
pfam09507	427	pfam09507, CDC27, DNA polymerase subunit Cdc27	9e-05
TIGR02680	1353	TIGR02680, TIGR02680, TIGR02680 family protein	9e-05
PTZ00121	2084	PTZ00121, PTZ00121, MAEBL; Provisional	1e-04
pfam08648	158	pfam08648, DUF1777, Protein of unknown function (D	1e-04
pfam12871	97	pfam12871, PRP38_assoc, Pre-mRNA-splicing factor 3	1e-04
COG3064	387	COG3064, TolA, Membrane protein involved in colici	1e-04
pfam02463	1162	pfam02463, SMC_N, RecF/RecN/SMC N terminal domain	1e-04
pfam02029	431	pfam02029, Caldesmon, Caldesmon	1e-04
PRK03918	880	PRK03918, PRK03918, chromosome segregation protein	1e-04
PRK03918	880	PRK03918, PRK03918, chromosome segregation protein	1e-04
PRK03918	880	PRK03918, PRK03918, chromosome segregation protein	1e-04
PRK03918	880	PRK03918, PRK03918, chromosome segregation protein	1e-04
COG0419	908	COG0419, SbcC, ATPase involved in DNA repair [DNA	1e-04
pfam07946	322	pfam07946, DUF1682, Protein of unknown function (D	1e-04
pfam14181	155	pfam14181, YqfQ, YqfQ-like protein	1e-04
PRK14160	211	PRK14160, PRK14160, heat shock protein GrpE; Provi	1e-04
pfam05762	223	pfam05762, VWA_CoxE, VWA domain containing CoxE-li	1e-04
pfam00906	182	pfam00906, Hepatitis_core, Hepatitis core antigen	1e-04
TIGR02680	1353	TIGR02680, TIGR02680, TIGR02680 family protein	1e-04
PTZ00436	357	PTZ00436, PTZ00436, 60S ribosomal protein L19-like	1e-04
pfam06375	561	pfam06375, BLVR, Bovine leukaemia virus receptor (	1e-04
PRK10864	346	PRK10864, PRK10864, putative methyltransferase; Pr	1e-04
PRK10864	346	PRK10864, PRK10864, putative methyltransferase; Pr	1e-04
PRK05306	746	PRK05306, infB, translation initiation factor IF-2	2e-04
PHA03328	316	PHA03328, PHA03328, nuclear egress lamina protein	2e-04
pfam02463	1162	pfam02463, SMC_N, RecF/RecN/SMC N terminal domain	2e-04
PRK00247	429	PRK00247, PRK00247, putative inner membrane protei	2e-04
pfam00183	529	pfam00183, HSP90, Hsp90 protein	2e-04
COG2433	652	COG2433, COG2433, Uncharacterized conserved protei	2e-04
pfam00844	244	pfam00844, Gemini_coat, Geminivirus coat protein/n	2e-04
pfam00844	244	pfam00844, Gemini_coat, Geminivirus coat protein/n	2e-04
pfam00844	244	pfam00844, Gemini_coat, Geminivirus coat protein/n	2e-04
pfam00844	244	pfam00844, Gemini_coat, Geminivirus coat protein/n	2e-04
pfam00906	182	pfam00906, Hepatitis_core, Hepatitis core antigen	2e-04
pfam00906	182	pfam00906, Hepatitis_core, Hepatitis core antigen	2e-04
pfam00906	182	pfam00906, Hepatitis_core, Hepatitis core antigen	2e-04
pfam00906	182	pfam00906, Hepatitis_core, Hepatitis core antigen	2e-04
pfam00906	182	pfam00906, Hepatitis_core, Hepatitis core antigen	2e-04
pfam00906	182	pfam00906, Hepatitis_core, Hepatitis core antigen	2e-04
pfam00906	182	pfam00906, Hepatitis_core, Hepatitis core antigen	2e-04
pfam00906	182	pfam00906, Hepatitis_core, Hepatitis core antigen	2e-04
COG0810	244	COG0810, TonB, Periplasmic protein TonB, links inn	2e-04
COG0810	244	COG0810, TonB, Periplasmic protein TonB, links inn	2e-04
pfam06375	561	pfam06375, BLVR, Bovine leukaemia virus receptor (	2e-04
pfam01528	374	pfam01528, Herpes_glycop, Herpesvirus glycoprotein	2e-04
PTZ00372	413	PTZ00372, PTZ00372, endonuclease 4-like protein; P	2e-04
PTZ00372	413	PTZ00372, PTZ00372, endonuclease 4-like protein; P	2e-04
pfam11705	221	pfam11705, RNA_pol_3_Rpc31, DNA-directed RNA polym	2e-04
TIGR01642	509	TIGR01642, U2AF_lg, U2 snRNP auxilliary factor, la	3e-04
PRK04195	482	PRK04195, PRK04195, replication factor C large sub	3e-04
COG1196	1163	COG1196, Smc, Chromosome segregation ATPases [Cell	3e-04
pfam03228	117	pfam03228, Adeno_VII, Adenoviral core protein VII	3e-04
PRK00247	429	PRK00247, PRK00247, putative inner membrane protei	3e-04
COG0419	908	COG0419, SbcC, ATPase involved in DNA repair [DNA	3e-04
pfam14265	125	pfam14265, DUF4355, Domain of unknown function (DU	3e-04
PLN02381	1066	PLN02381, PLN02381, valyl-tRNA synthetase	3e-04
COG2433	652	COG2433, COG2433, Uncharacterized conserved protei	3e-04
PRK14521	186	PRK14521, rpsP, 30S ribosomal protein S16; Provisi	3e-04
PRK14521	186	PRK14521, rpsP, 30S ribosomal protein S16; Provisi	3e-04
pfam05762	223	pfam05762, VWA_CoxE, VWA domain containing CoxE-li	3e-04
pfam00906	182	pfam00906, Hepatitis_core, Hepatitis core antigen	3e-04
PRK10864	346	PRK10864, PRK10864, putative methyltransferase; Pr	3e-04
PLN02967	581	PLN02967, PLN02967, kinase	3e-04
pfam03064	238	pfam03064, U79_P34, HSV U79 / HCMV P34	3e-04
PRK11634	629	PRK11634, PRK11634, ATP-dependent RNA helicase Dea	3e-04
pfam04162	449	pfam04162, Gyro_capsid, Gyrovirus capsid protein (	3e-04
COG0675	364	COG0675, COG0675, Transposase and inactivated deri	3e-04
pfam02463	1162	pfam02463, SMC_N, RecF/RecN/SMC N terminal domain	4e-04
pfam03344	715	pfam03344, Daxx, Daxx Family	4e-04
TIGR02168	1179	TIGR02168, SMC_prok_B, chromosome segregation prot	4e-04
PHA00451	362	PHA00451, PHA00451, protein kinase	4e-04
PHA00451	362	PHA00451, PHA00451, protein kinase	4e-04
pfam00906	182	pfam00906, Hepatitis_core, Hepatitis core antigen	4e-04
pfam00906	182	pfam00906, Hepatitis_core, Hepatitis core antigen	4e-04
COG0810	244	COG0810, TonB, Periplasmic protein TonB, links inn	4e-04
PRK10864	346	PRK10864, PRK10864, putative methyltransferase; Pr	4e-04
pfam09073	424	pfam09073, BUD22, BUD22	4e-04
pfam14303	147	pfam14303, NAM-associated, No apical meristem-asso	4e-04
pfam05091	517	pfam05091, eIF-3_zeta, Eukaryotic translation init	4e-04
COG0576	193	COG0576, GrpE, Molecular chaperone GrpE (heat shoc	4e-04
pfam13148	379	pfam13148, DUF3987, Protein of unknown function (D	4e-04
TIGR01069	771	TIGR01069, mutS2, MutS2 family protein	4e-04
PRK04195	482	PRK04195, PRK04195, replication factor C large sub	5e-04
COG1196	1163	COG1196, Smc, Chromosome segregation ATPases [Cell	5e-04
PHA03328	316	PHA03328, PHA03328, nuclear egress lamina protein	5e-04
PRK03918	880	PRK03918, PRK03918, chromosome segregation protein	5e-04
PTZ00108	1388	PTZ00108, PTZ00108, DNA topoisomerase 2-like prote	5e-04
PRK09510	387	PRK09510, tolA, cell envelope integrity inner memb	5e-04
pfam07946	322	pfam07946, DUF1682, Protein of unknown function (D	5e-04
pfam09507	427	pfam09507, CDC27, DNA polymerase subunit Cdc27	5e-04
pfam03839	217	pfam03839, Sec62, Translocation protein Sec62	5e-04
pfam00906	182	pfam00906, Hepatitis_core, Hepatitis core antigen	5e-04
pfam05279	240	pfam05279, Asp-B-Hydro_N, Aspartyl beta-hydroxylas	5e-04
pfam11719	397	pfam11719, Drc1-Sld2, DNA replication and checkpoi	5e-04
pfam02459	548	pfam02459, Adeno_terminal, Adenoviral DNA terminal	5e-04
pfam07767	387	pfam07767, Nop53, Nop53 (60S ribosomal biogenesis)	6e-04
pfam08619	430	pfam08619, Nha1_C, Alkali metal cation/H+ antiport	6e-04
PTZ00372	413	PTZ00372, PTZ00372, endonuclease 4-like protein; P	6e-04
PRK10590	456	PRK10590, PRK10590, ATP-dependent RNA helicase Rhl	6e-04
pfam10243	506	pfam10243, MIP-T3, Microtubule-binding protein MIP	7e-04
PRK05306	746	PRK05306, infB, translation initiation factor IF-2	7e-04
COG1196	1163	COG1196, Smc, Chromosome segregation ATPases [Cell	7e-04
PRK12705	508	PRK12705, PRK12705, hypothetical protein; Provisio	7e-04
pfam07767	387	pfam07767, Nop53, Nop53 (60S ribosomal biogenesis)	7e-04
COG2433	652	COG2433, COG2433, Uncharacterized conserved protei	7e-04
pfam00844	244	pfam00844, Gemini_coat, Geminivirus coat protein/n	7e-04
pfam00844	244	pfam00844, Gemini_coat, Geminivirus coat protein/n	7e-04
pfam00906	182	pfam00906, Hepatitis_core, Hepatitis core antigen	7e-04
PRK10864	346	PRK10864, PRK10864, putative methyltransferase; Pr	7e-04
PRK11634	629	PRK11634, PRK11634, ATP-dependent RNA helicase Dea	7e-04
pfam04094	843	pfam04094, DUF390, Protein of unknown function (DU	7e-04
pfam09736	141	pfam09736, Bud13, Pre-mRNA-splicing factor of RES	7e-04
pfam07767	387	pfam07767, Nop53, Nop53 (60S ribosomal biogenesis)	8e-04
pfam11861	154	pfam11861, DUF3381, Domain of unknown function (DU	8e-04
PTZ00372	413	PTZ00372, PTZ00372, endonuclease 4-like protein; P	8e-04
pfam11241	168	pfam11241, DUF3043, Protein of unknown function (D	8e-04
pfam04514	363	pfam04514, BTV_NS2, Bluetongue virus non-structura	8e-04
pfam09731	493	pfam09731, Mitofilin, Mitochondrial inner membrane	8e-04
PTZ00399	651	PTZ00399, PTZ00399, cysteinyl-tRNA-synthetase; Pro	8e-04
PHA03307	1352	PHA03307, PHA03307, transcriptional regulator ICP4	8e-04
pfam04935	206	pfam04935, SURF6, Surfeit locus protein 6	8e-04
PRK04195	482	PRK04195, PRK04195, replication factor C large sub	9e-04
COG2433	652	COG2433, COG2433, Uncharacterized conserved protei	9e-04
pfam00844	244	pfam00844, Gemini_coat, Geminivirus coat protein/n	9e-04
PTZ00372	413	PTZ00372, PTZ00372, endonuclease 4-like protein; P	9e-04
pfam13136	301	pfam13136, DUF3984, Protein of unknown function (D	9e-04
pfam05917	417	pfam05917, DUF874, Helicobacter pylori protein of	9e-04
PRK04195	482	PRK04195, PRK04195, replication factor C large sub	0.001
TIGR02169	1164	TIGR02169, SMC_prok_A, chromosome segregation prot	0.001
pfam09756	189	pfam09756, DDRGK, DDRGK domain	0.001
PRK03918	880	PRK03918, PRK03918, chromosome segregation protein	0.001
pfam00183	529	pfam00183, HSP90, Hsp90 protein	0.001
pfam00183	529	pfam00183, HSP90, Hsp90 protein	0.001
pfam00183	529	pfam00183, HSP90, Hsp90 protein	0.001
pfam12569	516	pfam12569, NARP1, NMDA receptor-regulated protein	0.001
pfam09507	427	pfam09507, CDC27, DNA polymerase subunit Cdc27	0.001
pfam00844	244	pfam00844, Gemini_coat, Geminivirus coat protein/n	0.001
PRK12704	520	PRK12704, PRK12704, phosphodiesterase; Provisional	0.001
pfam11861	154	pfam11861, DUF3381, Domain of unknown function (DU	0.001
pfam00906	182	pfam00906, Hepatitis_core, Hepatitis core antigen	0.001
PRK10864	346	PRK10864, PRK10864, putative methyltransferase; Pr	0.001
PRK10864	346	PRK10864, PRK10864, putative methyltransferase; Pr	0.001
PRK10864	346	PRK10864, PRK10864, putative methyltransferase; Pr	0.001
pfam01528	374	pfam01528, Herpes_glycop, Herpesvirus glycoprotein	0.001
PLN02967	581	PLN02967, PLN02967, kinase	0.001
PRK11634	629	PRK11634, PRK11634, ATP-dependent RNA helicase Dea	0.001
pfam04162	449	pfam04162, Gyro_capsid, Gyrovirus capsid protein (	0.001
pfam04162	449	pfam04162, Gyro_capsid, Gyrovirus capsid protein (	0.001
pfam11719	397	pfam11719, Drc1-Sld2, DNA replication and checkpoi	0.001
pfam02459	548	pfam02459, Adeno_terminal, Adenoviral DNA terminal	0.001
PHA03307	1352	PHA03307, PHA03307, transcriptional regulator ICP4	0.001
pfam13136	301	pfam13136, DUF3984, Protein of unknown function (D	0.001
COG2801	232	COG2801, Tra5, Transposase and inactivated derivat	0.001
cd02988	192	cd02988, Phd_like_VIAF, Phosducin (Phd)-like famil	0.001
cd02988	192	cd02988, Phd_like_VIAF, Phosducin (Phd)-like famil	0.001
cd05832	106	cd05832, Ribosomal_L12p, Ribosomal protein L12p	0.001
pfam04502	321	pfam04502, DUF572, Family of unknown function (DUF	0.001
pfam10659	98	pfam10659, Trypan_glycop_C, Trypanosome variant su	0.001
pfam05764	238	pfam05764, YL1, YL1 nuclear protein	0.001
TIGR03685	105	TIGR03685, L12P_arch, 50S ribosomal protein L12P	0.001
COG5019	373	COG5019, CDC3, Septin family protein [Cell divisio	0.001
pfam13801	125	pfam13801, Metal_resist, Heavy-metal resistance	0.001
pfam13801	125	pfam13801, Metal_resist, Heavy-metal resistance	0.001
pfam14239	174	pfam14239, RRXRR, RRXRR protein	0.001
PHA03089	191	PHA03089, PHA03089, late transcription factor VLTF	0.001
pfam02841	297	pfam02841, GBP_C, Guanylate-binding protein, C-ter	0.001
pfam10243	506	pfam10243, MIP-T3, Microtubule-binding protein MIP	0.002
TIGR02794	346	TIGR02794, tolA_full, TolA protein	0.002
TIGR02794	346	TIGR02794, tolA_full, TolA protein	0.002
COG1196	1163	COG1196, Smc, Chromosome segregation ATPases [Cell	0.002
pfam02463	1162	pfam02463, SMC_N, RecF/RecN/SMC N terminal domain	0.002
pfam02029	431	pfam02029, Caldesmon, Caldesmon	0.002
PRK03918	880	PRK03918, PRK03918, chromosome segregation protein	0.002
COG0419	908	COG0419, SbcC, ATPase involved in DNA repair [DNA	0.002
pfam06658	142	pfam06658, DUF1168, Protein of unknown function (D	0.002
TIGR02168	1179	TIGR02168, SMC_prok_B, chromosome segregation prot	0.002
pfam14265	125	pfam14265, DUF4355, Domain of unknown function (DU	0.002
PHA00451	362	PHA00451, PHA00451, protein kinase	0.002
pfam00183	529	pfam00183, HSP90, Hsp90 protein	0.002
PLN02381	1066	PLN02381, PLN02381, valyl-tRNA synthetase	0.002
pfam00844	244	pfam00844, Gemini_coat, Geminivirus coat protein/n	0.002
TIGR03319	514	TIGR03319, RNase_Y, ribonuclease Y	0.002
pfam05762	223	pfam05762, VWA_CoxE, VWA domain containing CoxE-li	0.002
pfam00906	182	pfam00906, Hepatitis_core, Hepatitis core antigen	0.002
pfam00906	182	pfam00906, Hepatitis_core, Hepatitis core antigen	0.002
pfam04162	449	pfam04162, Gyro_capsid, Gyrovirus capsid protein (	0.002
pfam14303	147	pfam14303, NAM-associated, No apical meristem-asso	0.002
pfam02459	548	pfam02459, Adeno_terminal, Adenoviral DNA terminal	0.002
PRK10590	456	PRK10590, PRK10590, ATP-dependent RNA helicase Rhl	0.002
PRK10590	456	PRK10590, PRK10590, ATP-dependent RNA helicase Rhl	0.002
pfam04502	321	pfam04502, DUF572, Family of unknown function (DUF	0.002
pfam10659	98	pfam10659, Trypan_glycop_C, Trypanosome variant su	0.002
PRK05035	695	PRK05035, PRK05035, electron transport complex pro	0.002
COG5116	926	COG5116, RPN2, 26S proteasome regulatory complex c	0.002
pfam00012	598	pfam00012, HSP70, Hsp70 protein	0.002
pfam03154	979	pfam03154, Atrophin-1, Atrophin-1 family	0.002
pfam07133	164	pfam07133, Merozoite_SPAM, Merozoite surface prote	0.002
pfam10310	436	pfam10310, DUF2413, Protein of unknown function (D	0.002
pfam10211	189	pfam10211, Ax_dynein_light, Axonemal dynein light	0.002
pfam08576	98	pfam08576, DUF1764, Eukaryotic protein of unknown	0.002
pfam09805	134	pfam09805, Nop25, Nucleolar protein 12 (25kDa)	0.002
COG2268	548	COG2268, COG2268, Uncharacterized protein conserve	0.002
PTZ00266	1021	PTZ00266, PTZ00266, NIMA-related protein kinase; P	0.002
PRK07735	430	PRK07735, PRK07735, NADH dehydrogenase subunit C;	0.002
COG5137	279	COG5137, COG5137, Histone chaperone involved in ge	0.002
pfam04774	106	pfam04774, HABP4_PAI-RBP1, Hyaluronan / mRNA bindi	0.002
PTZ00121	2084	PTZ00121, PTZ00121, MAEBL; Provisional	0.003
TIGR01622	457	TIGR01622, SF-CC1, splicing factor, CC1-like famil	0.003
TIGR01622	457	TIGR01622, SF-CC1, splicing factor, CC1-like famil	0.003
TIGR00927	1096	TIGR00927, 2A1904, K+-dependent Na+/Ca+ exchanger	0.003
pfam06495	182	pfam06495, Transformer, Fruit fly transformer prot	0.003
TIGR02168	1179	TIGR02168, SMC_prok_B, chromosome segregation prot	0.003
pfam14153	185	pfam14153, Spore_coat_CotO, Spore coat protein Cot	0.003
pfam07767	387	pfam07767, Nop53, Nop53 (60S ribosomal biogenesis)	0.003
pfam09507	427	pfam09507, CDC27, DNA polymerase subunit Cdc27	0.003
pfam00906	182	pfam00906, Hepatitis_core, Hepatitis core antigen	0.003
pfam06375	561	pfam06375, BLVR, Bovine leukaemia virus receptor (	0.003
PTZ00372	413	PTZ00372, PTZ00372, endonuclease 4-like protein; P	0.003
PLN02967	581	PLN02967, PLN02967, kinase	0.003
pfam03064	238	pfam03064, U79_P34, HSV U79 / HCMV P34	0.003
pfam04162	449	pfam04162, Gyro_capsid, Gyrovirus capsid protein (	0.003
pfam11241	168	pfam11241, DUF3043, Protein of unknown function (D	0.003
COG2801	232	COG2801, Tra5, Transposase and inactivated derivat	0.003
COG2801	232	COG2801, Tra5, Transposase and inactivated derivat	0.003
cd05832	106	cd05832, Ribosomal_L12p, Ribosomal protein L12p	0.003
pfam13801	125	pfam13801, Metal_resist, Heavy-metal resistance	0.003
pfam02841	297	pfam02841, GBP_C, Guanylate-binding protein, C-ter	0.003
pfam03154	979	pfam03154, Atrophin-1, Atrophin-1 family	0.003
pfam07133	164	pfam07133, Merozoite_SPAM, Merozoite surface prote	0.003
PRK11642	813	PRK11642, PRK11642, exoribonuclease R; Provisional	0.003
pfam11917	418	pfam11917, DUF3435, Protein of unknown function (D	0.003
pfam04702	147	pfam04702, Vicilin_N, Vicilin N terminal region	0.003
PHA02644	112	PHA02644, PHA02644, hypothetical protein; Provisio	0.003
COG3351	214	COG3351, FlaD, Putative archaeal flagellar protein	0.003
PRK13766	773	PRK13766, PRK13766, Hef nuclease; Provisional	0.003
smart00435	391	smart00435, TOPEUc, DNA Topoisomerase I (eukaryota	0.003
pfam12871	97	pfam12871, PRP38_assoc, Pre-mRNA-splicing factor 3	0.004
pfam06495	182	pfam06495, Transformer, Fruit fly transformer prot	0.004
PRK00247	429	PRK00247, PRK00247, putative inner membrane protei	0.004
COG4499	434	COG4499, COG4499, Predicted membrane protein [Func	0.004
pfam03344	715	pfam03344, Daxx, Daxx Family	0.004
PRK12705	508	PRK12705, PRK12705, hypothetical protein; Provisio	0.004
PRK12280	158	PRK12280, rplW, 50S ribosomal protein L23; Reviewe	0.004
PRK14160	211	PRK14160, PRK14160, heat shock protein GrpE; Provi	0.004
TIGR03319	514	TIGR03319, RNase_Y, ribonuclease Y	0.004
PRK14521	186	PRK14521, rpsP, 30S ribosomal protein S16; Provisi	0.004
PRK12704	520	PRK12704, PRK12704, phosphodiesterase; Provisional	0.004
PTZ00372	413	PTZ00372, PTZ00372, endonuclease 4-like protein; P	0.004
pfam11705	221	pfam11705, RNA_pol_3_Rpc31, DNA-directed RNA polym	0.004
pfam03064	238	pfam03064, U79_P34, HSV U79 / HCMV P34	0.004
pfam11719	397	pfam11719, Drc1-Sld2, DNA replication and checkpoi	0.004
pfam09736	141	pfam09736, Bud13, Pre-mRNA-splicing factor of RES	0.004
pfam11241	168	pfam11241, DUF3043, Protein of unknown function (D	0.004
cd05832	106	cd05832, Ribosomal_L12p, Ribosomal protein L12p	0.004
pfam05764	238	pfam05764, YL1, YL1 nuclear protein	0.004
pfam03154	979	pfam03154, Atrophin-1, Atrophin-1 family	0.004
pfam07133	164	pfam07133, Merozoite_SPAM, Merozoite surface prote	0.004
pfam10186	307	pfam10186, Atg14, UV radiation resistance protein	0.004
TIGR01554	384	TIGR01554, major_cap_HK97, phage major capsid prot	0.004
pfam06991	277	pfam06991, Prp19_bind, Splicing factor, Prp19-bind	0.004
PRK06402	106	PRK06402, rpl12p, 50S ribosomal protein L12P; Revi	0.004
pfam12619	145	pfam12619, MCM2_N, Mini-chromosome maintenance pro	0.004
pfam06978	158	pfam06978, POP1, Ribonucleases P/MRP protein subun	0.004

>gnl|CDD|99915 cd05532, POLBc_alpha, DNA polymerase type-B alpha subfamily catalytic domain

 Score =  490 bits (1264), Expect = e-165
 Identities = 187/313 (59%), Positives = 225/313 (71%), Gaps = 10/313 (3%)

Query: 489 KGRKKAAYSGGLVLEPKKGFYDKFIILMDFNSLYPSIIQEYNICFTTIPVRMLQDSDITT 548
           K +KKA Y+GGLVLEPKKG YDKFI+L+DFNSLYPSIIQEYNICFTT+      D D   
Sbjct: 1   KKKKKAKYAGGLVLEPKKGLYDKFILLLDFNSLYPSIIQEYNICFTTVDRADPDDEDDEE 60

Query: 549 LCEYLPEHQVDTGILPSEIKKLVESRRQVKALMKQPNLSSDLLMQYDIRQKALKLTANSM 608
               LP    + GILP  I+KLVE RRQVK LMK      D   Q DIRQ ALKLTANSM
Sbjct: 61  PP--LPPSDQEKGILPRIIRKLVERRRQVKKLMKSEK-DPDKKAQLDIRQLALKLTANSM 117

Query: 609 YGCLGFPNSRFFAQPLAALVTAKGREILLNTKSLVENLNYEVIYGDTDSLMISCNVNDYD 668
           YGCLGF  SRF+A+PLAAL+T+KGREIL  TK LVE +N EVIYGDTDS+MI+    DY+
Sbjct: 118 YGCLGFSYSRFYAKPLAALITSKGREILQKTKDLVEKMNLEVIYGDTDSIMINTGTTDYE 177

Query: 669 SVFKIGNQIKSECNKLYKQLELDIDGVYKYMLLLKKKKYAALSISKLSNGKMICSQEIKG 728
              K+GN+IK E NK YK+LE+DIDGV+K +LLLKKKKYAAL +     GK    +E+KG
Sbjct: 178 EAKKLGNKIKKEVNKSYKKLEIDIDGVFKRLLLLKKKKYAALKVVDDDKGK--LKKEVKG 235

Query: 729 VDVVRRDWSQLASEAGKFVISQILDEQSYTDYSLDDRLQNIHEHMKKIRTDLDNGFVPLT 788
           +D+VRRDW  L+ E G +V+ QIL ++S      +D ++NIHE+++KI  DL NG +PL 
Sbjct: 236 LDIVRRDWCPLSKEIGNYVLDQILSDKSR-----EDIVENIHEYLRKINEDLRNGKIPLE 290

Query: 789 LLEITKQLTKAPE 801
              ITKQLTK PE
Sbjct: 291 KFIITKQLTKNPE 303

Three DNA-dependent DNA polymerases type B (alpha, delta, and epsilon) have been identified as essential for nuclear DNA replication in eukaryotes. DNA polymerase (Pol) alpha is almost exclusively required for the initiation of DNA replication and the priming of Okazaki fragments during elongation. In most organisms no specific repair role, other than check point control, has been assigned to this enzyme. Pol alpha contains both polymerase and exonuclease domains, but lacks exonuclease activity suggesting that the exonuclease domain may be for structural purposes only. Length = 400

>gnl|CDD|233037 TIGR00592, pol2, DNA polymerase (pol2)

 Score =  447 bits (1150), Expect = e-139
 Identities = 241/427 (56%), Positives = 312/427 (73%), Gaps = 12/427 (2%)

Query: 402  IVEFIKFTMLHSSYIIKIMCELNVLPLAIQITNVCGNVLSRTLMGGRSERNEFLLLHAFH 461
            +   ++ T   + +I++IMCELNVLPLA+QITN+ GN++SRTLMGGRSERNEFLLLHAF+
Sbjct: 701  LTYLLEHTWKDAMFILQIMCELNVLPLALQITNIAGNIMSRTLMGGRSERNEFLLLHAFY 760

Query: 462  EKSYVLPDKQ-YGKNKKEGEETGEANKGKGRKKAAYSGGLVLEPKKGFYDKFIILMDFNS 520
            E +Y++PDKQ + K +K G+E  E +  K  KKAAY+GGLVLEPK G YDK+++LMDFNS
Sbjct: 761  ENNYIVPDKQIFRKQQKLGDEDEEIDGYKKGKKAAYAGGLVLEPKVGLYDKYVLLMDFNS 820

Query: 521  LYPSIIQEYNICFTTIPVRMLQDSDITTLCEYLPEHQVDTGILPSEIKKLVESRRQVKAL 580
            LYPSIIQE+NICFTT+     Q  D   L E LP+ +++ GILP E++KLVE R++VK L
Sbjct: 821  LYPSIIQEFNICFTTVQ----QKVDEDELPE-LPDSELEMGILPRELRKLVERRKEVKKL 875

Query: 581  MKQPNLSSDLLMQYDIRQKALKLTANSMYGCLGFPNSRFFAQPLAALVTAKGREILLNTK 640
            MKQ +L+ DL +QYDIRQKALKLTANSMYGCLG+  SRF+A+PLAALVTAKGREIL +T+
Sbjct: 876  MKQ-DLNPDLRLQYDIRQKALKLTANSMYGCLGYSKSRFYAKPLAALVTAKGREILEHTR 934

Query: 641  SLVENLNYEVIYGDTDSLMISCNVNDYDSVFKIGNQIKSECNKLYKQLELDIDGVYKYML 700
             LVE +N EVIYGDTDS+MI+     Y+ VFKIG + KSE NKLYK LELDIDGV+K +L
Sbjct: 935  QLVEEMNLEVIYGDTDSIMINTPGTKYEEVFKIGKEFKSEVNKLYKLLELDIDGVFKRLL 994

Query: 701  LLKKKKYAALSISKLSNGKMICSQEIKGVDVVRRDWSQLASEAGKFVISQILDEQSYTDY 760
            LLKKKKYAA+ +   S+G     QE+KG+D+VRRDWS LA E GK V+  IL ++     
Sbjct: 995  LLKKKKYAAIKVEGDSDGNYTTKQEVKGLDIVRRDWSPLAKETGKKVLDTILSDK----- 1049

Query: 761  SLDDRLQNIHEHMKKIRTDLDNGFVPLTLLEITKQLTKAPEGGKVCITQIRLSRNRRGRR 820
             +++ ++ + E ++KI  ++ NG VPL    I KQLT+ P+      +   +    R   
Sbjct: 1050 DVEEAVEEVQEVLEKIGKNVLNGEVPLEKFVINKQLTRDPKDYPDGASLPHVHVALRINA 1109

Query: 821  RRRRKKK 827
            R  RK K
Sbjct: 1110 RGGRKVK 1116

All proteins in this superfamily for which functions are known are DNA polymerases.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University) [DNA metabolism, DNA replication, recombination, and repair]. Length = 1172

>gnl|CDD|215742 pfam00136, DNA_pol_B, DNA polymerase family B

 Score =  315 bits (810), Expect = 1e-97
 Identities = 131/403 (32%), Positives = 194/403 (48%), Gaps = 42/403 (10%)

Query: 447 GRSERNEFLLLHAFHEKSYVLPDKQYGKNKKEGEETGEANKGKGRKKAAYSGGLVLEPKK 506
           G+  R   LLL    E++++LPDK   ++           +    KK  Y G  VLEPKK
Sbjct: 1   GQQIRVFSLLLREAKERNFILPDKFELRSLS---------RQVNIKKEGYQGATVLEPKK 51

Query: 507 GFYDKFIILMDFNSLYPSIIQEYNICFTTI--PVRMLQDSDITTLCEYLPEHQVDT---- 560
           GFY+  ++++DF SLYPSIIQ +N+C+ T+                E L           
Sbjct: 52  GFYNNPVLVLDFASLYPSIIQAHNLCYETLVDVDAEAPKLAAERNLEVLHIVVGSLRERF 111

Query: 561 -------GILPSEIKKLVESRRQVKALMKQPNLSSDLLMQYDIRQKALKLTANSMYGCLG 613
                  GILP  ++ L+  R++ K LMK+     +L    D +Q ALK+TANS+YG  G
Sbjct: 112 VKKGVRKGILPVLLRDLLAKRKEKKKLMKESKDPEELRTLLDKQQLALKVTANSVYGFTG 171

Query: 614 FPNSRFFAQPLAALVTAKGREILLNTKSLVENL---NYEVIYGDTDSLMISCNVNDYDSV 670
             N R    P+A  VTA GRE++  TK  VE L    ++VIYGDTDS+ +     D +  
Sbjct: 172 AANGRLPCLPIAESVTAIGREMIEKTKRYVEELLNYGFKVIYGDTDSVFVKFPGVDIEEA 231

Query: 671 FKIGNQIKSECNK--LYKQLELDIDGVYKYMLLLKKKKYAALSISKLSNGKMICSQEIKG 728
            K+G ++         +K ++L+ + VYK +LL+ KK+YA L      +        IKG
Sbjct: 232 KKLGKELAKHVTSELFFKPIKLEFEKVYKPLLLISKKRYAGLKYDGKGD--------IKG 283

Query: 729 VDVVRRDWSQLASEAGKFVISQILDEQSYTDYSLDDRLQN-IHEHMKKIRTDLDNGFVPL 787
           VD+VRRDW +   E  + V+  +L ++          L+  I E +K +   L    VPL
Sbjct: 284 VDLVRRDWCEFVKEVIRKVLDLLLKDK--DVEDAAPSLKIVIIEILKSLTDKLVQNKVPL 341

Query: 788 TLLEITKQLTKAPEGGKVCITQIRLSRNRRGRRRRRRKKKEEK 830
             L ITK+L+K P   K    +          R ++R  +E  
Sbjct: 342 EDLVITKELSKPPSEYK----KKNPPHVTVALRLKKRGNEEAP 380

This region of DNA polymerase B appears to consist of more than one structural domain, possibly including elongation, DNA-binding and dNTP binding activities. Length = 458

>gnl|CDD|223494 COG0417, PolB, DNA polymerase elongation subunit (family B) [DNA replication, recombination, and repair]

 Score =  268 bits (688), Expect = 7e-77
 Identities = 129/413 (31%), Positives = 204/413 (49%), Gaps = 37/413 (8%)

Query: 416 IIKIMCELNVLPLAIQITNVCGNVLSRTLMGGRSERNEFLLLHAFHEKSYVLPDKQYGKN 475
           +++I+ +  +LPL I+++ V G  L      G   R E LLL     +  ++P       
Sbjct: 343 VLRILLKNELLPLLIELSRVSGLPLDDVTRAGSGARVEGLLLREAKRRGELIP------- 395

Query: 476 KKEGEETGEANKGKGRKKAAYSGGLVLEPKKGFYDKFIILMDFNSLYPSIIQEYNICFTT 535
                     NK +  ++  Y GGLVLEP+ G Y+  ++++DF+SLYPSII +YNI   T
Sbjct: 396 ----------NKEERPERKKYKGGLVLEPEPGLYEN-VLVLDFSSLYPSIIIKYNISPDT 444

Query: 536 IPVRMLQDSDITTLCEYLPEHQVDTGILPSEIKKLVESRRQVKALMKQPNLSSDLLMQYD 595
           +      D        +    + + G LP  +++L++ R ++K  MK+           D
Sbjct: 445 LVEEDCSDDYSPPGVGHGFC-KREKGFLPEILEELLDRRDEIKKKMKKE-KDPSERKLLD 502

Query: 596 IRQKALKLTANSMYGCLGFPNSRFFAQPLAALVTAKGREILLNTKSLVENLNYEVIYGDT 655
            RQ ALK+ ANS YG LG+ NSRF+    A  VTA GREIL  TK L E +   VIYGDT
Sbjct: 503 GRQLALKVLANSFYGYLGYSNSRFYCIECAESVTAFGREILRETKELAEEMGLRVIYGDT 562

Query: 656 DSLMISCNVNDYDSVFKIGNQIKSECN-KLYKQLELDIDGVYKYMLLL-KKKKYAALSIS 713
           DSL ++     Y+   KIG ++  E N +L   +EL+++ VYK  LL   KK+YA L   
Sbjct: 563 DSLFVTLPGATYEEAIKIGEELVEEVNERLPSGIELEVEKVYKRFLLPTAKKRYAGLLE- 621

Query: 714 KLSNGKMICSQEIKGVDVVRRDWSQLASEAGKFVISQILDEQSYTDYSLDDRLQNIHEHM 773
                K+    E+KG++ VRRDW +L  E  + V+  +L  +   +      ++++ E +
Sbjct: 622 --DGDKI----EVKGLETVRRDWPELVKEFQREVLEVLLSGRDVEEALA-KYVRDVIEKL 674

Query: 774 KKIRTDLDNGFVPLTLLEITKQLTKAPEGGKVCITQIRLSRNRRGRRRRRRKK 826
           +     ++        L I+K+LT+     K     + ++   R R    +  
Sbjct: 675 RNGEVPIE-------KLVISKRLTRPLSEYKANKPHVVVAARLRKRGINVKPG 720

Length = 792

>gnl|CDD|99912 cd00145, POLBc, DNA polymerase type-B family catalytic domain

 Score =  226 bits (578), Expect = 1e-66
 Identities = 96/268 (35%), Positives = 141/268 (52%), Gaps = 6/268 (2%)

Query: 494 AAYSGGLVLEPKKGFYDKFIILMDFNSLYPSIIQEYNICFTTIPVRMLQDSDITTLCEYL 553
             Y GG V +P  G Y+  +I++DF SLYPSII  YN+  TT+       +    +    
Sbjct: 1   EPYEGGYVFDPIPGLYE-NVIVLDFKSLYPSIIITYNLSPTTLVGNGEIAAPEDYIGVGF 59

Query: 554 PEHQVDTGILPSEIKKLVESRRQVKALMKQPNLSSDLLMQYDIRQKALKLTANSMYGCLG 613
              +   G+LP  +++L+  R + K  MK   L+ +  + YD RQ+ALK+ ANS YG LG
Sbjct: 60  RSPKDRKGLLPRILEELLNFRDEAKKRMKAAKLAPEERVLYDNRQQALKVLANSFYGYLG 119

Query: 614 FPNSRFFAQPLAALVTAKGREILLNTKSLVENLNYEVIYGDTDSLMISCNVN-DYDSVFK 672
               RF+   +AA +T+ GREI+ +T +LVE     VIYGDTDS+ +S       +   K
Sbjct: 120 AKFFRFYDPEVAASITSFGREIIQDTIALVEEHGARVIYGDTDSIFVSLPKMGTKEDAIK 179

Query: 673 IGNQIKSECNKLYKQLELDIDGVYKYMLLLKKKKYAALSISKLSNGKMICSQEIKGVDVV 732
            G +I  +       LEL+ + VY    L KKK+YA L I K   G+     +IKG++  
Sbjct: 180 EGREI-LQELADEHLLELEFEKVYLPFFLGKKKRYAGLDIWK---GQDEGKIDIKGLETR 235

Query: 733 RRDWSQLASEAGKFVISQILDEQSYTDY 760
           RRD   L  +  K V+  IL+E+   + 
Sbjct: 236 RRDSPPLVKKFQKEVLELILEEERKVEA 263

DNA-directed DNA polymerases elongate DNA by adding nucleotide triphosphate (dNTP) residues to the 5'-end of the growing chain of DNA. DNA-directed DNA polymerases are multifunctional with both synthetic (polymerase) and degradative modes (exonucleases) and play roles in the processes of DNA replication, repair, and recombination. DNA-dependent DNA polymerases can be classified in six main groups based upon their phylogenetic relationships with E. coli polymerase I (class A), E. coli polymerase II (class B), E. coli polymerase III (class C), euryarchaeota polymerase II (class D), human polymerase beta (class x), E. coli UmuC/DinB, and eukaryotic RAP 30/Xeroderma pigmentosum variant (class Y). Family B DNA polymerases include E. coli DNA polymerase II, some eubacterial phage DNA polymerases, nuclear replicative DNA polymerases (alpha, delta, epsilon, and zeta), and eukaryotic viral and plasmid-borne enzymes. DNA polymerase is made up of distinct domains and sub-domains. The polymerase domain of DNA polymerase type B (Pol domain) is responsible for the template-directed polymerization of dNTPs onto the growing primer strand of duplex DNA that is usually magnesium dependent. In general, the architecture of the Pol domain has been likened to a right hand with fingers, thumb, and palm sub-domains with a deep groove to accommodate the nucleic acid substrate. There are a few conserved motifs in the Pol domain of family B DNA polymerases. The conserved aspartic acid residues in the DTDS motifs of the palm sub-domain is crucial for binding to divalent metal ion and is suggested to be important for polymerase catalysis. Length = 323

>gnl|CDD|214691 smart00486, POLBc, DNA polymerase type-B family

 Score =  227 bits (579), Expect = 6e-65
 Identities = 110/267 (41%), Positives = 154/267 (57%), Gaps = 28/267 (10%)

Query: 417 IKIMCELNVLPLAIQITNVCGNVLSRTLMGGRSERNEFLLLHAFHEKSYVLPDKQYGKNK 476
           +K+  +LNV+PL I++  + G  L RTL  G   R E LLL    + +Y+LP K+     
Sbjct: 215 LKLFNKLNVIPLIIELARIAGIPLRRTLYYGSQIRVESLLLREAKKNNYILPSKE----- 269

Query: 477 KEGEETGEANKGKGRKKAAYSGGLVLEPKKGFYDKFIILMDFNSLYPSIIQEYNICFTTI 536
                  + ++   +KK  Y GG VLEPKKGFYD  ++++DFNSLYPSII  +N+C++T+
Sbjct: 270 ---LYDFKGSEPDLKKKVKYEGGKVLEPKKGFYDNPVLVLDFNSLYPSIIIAHNLCYSTL 326

Query: 537 PVR-------MLQDSDITTLCEY-------LPEHQVDTGILPSEIKKLVESRRQVKALMK 582
                      L   +     +Y         +  +  GILP  +KKL++ R+++K LMK
Sbjct: 327 VGVGEVVIKGDLIIPEDLLTIKYEKGNKYRFVKKNIRKGILPKLLKKLLDKRKEIKKLMK 386

Query: 583 Q-PNLSSDLLMQYDIRQKALKLTANSMYGCLGFPNSRFFAQPLAALVTAKGREILLNTKS 641
           +  + S +L    D RQ ALKLTANS+YG LGF NSR   +PLAA VTA GREIL  TK 
Sbjct: 387 KEKDESEELKKLLDSRQLALKLTANSVYGYLGFTNSRLPCKPLAASVTALGREILEKTKE 446

Query: 642 LVENLNY-----EVIYGDTDSLMISCN 663
           L+E   Y     +VIYGDTDS+ ++  
Sbjct: 447 LIEENGYPKPGFKVIYGDTDSIFVTKP 473

DNA polymerase alpha, delta, epsilon and zeta chain (eukaryota), DNA polymerases in archaea, DNA polymerase II in e. coli, mitochondrial DNA polymerases and and virus DNA polymerases. Length = 474

>gnl|CDD|235595 PRK05762, PRK05762, DNA polymerase II; Reviewed

 Score =  200 bits (511), Expect = 2e-53
 Identities = 109/366 (29%), Positives = 164/366 (44%), Gaps = 77/366 (21%)

Query: 425 VLPLAIQITNVCGNVLSRTLMGGRSERNEFLLLHAFHEKSYVLPDKQYGKNKKEGEETGE 484
           +LP  ++   V G  L R  +GG     E L L   H   YV P+         GE  GE
Sbjct: 350 LLPFLLERATVTGLPLDR--VGGSVAAFEHLYLPRAHRAGYVAPNL--------GERPGE 399

Query: 485 ANKGKGRKKAAYSGGLVLEPKKGFYDKFIILMDFNSLYPSIIQEYNICFTTIPVRMLQDS 544
           A            GG V++ K G YD  ++L DF SLYPSII+ +NI    + V  L   
Sbjct: 400 A----------SPGGYVMDSKPGLYDSVLVL-DFKSLYPSIIRTFNIDPDGL-VEGLAQP 447

Query: 545 DITTLCEYLPEHQV----------DTGILPSEIKKLVESRRQVKALMKQPNLSSDLLMQY 594
                     E  V          +   LP  +++L E R + K  M +P          
Sbjct: 448 P---------EESVAGFLGARFSREKHFLPEIVERLWEGRDEAKREMNKP---------- 488

Query: 595 DIRQKALKLTANSMYGCLGFPNSRFFAQPLAALVTAKGREILLNTKSLVENLNYEVIYGD 654
               +A+K+  N+ YG LG    RFF   LA+ +T +G EI+  T+ L+E   Y+VIYGD
Sbjct: 489 --LSQAIKIIMNAFYGVLGSSGCRFFDPRLASSITMRGHEIMKQTRELIEAQGYQVIYGD 546

Query: 655 TDSLMISCNV-NDYDSVFKIGNQIKSECNKLYKQ-----------LELDIDGVYK--YML 700
           TDS  +     +D +   KIG  +  E N+ +++           LEL+ +  Y+  +M 
Sbjct: 547 TDSTFVWLGGAHDEEDAAKIGRALVQEINQWWQEHLQQEFGLESALELEFEKHYRRFFMP 606

Query: 701 LLK------KKKYAALSISKLSNGKMICSQEIKGVDVVRRDWSQLASEAGKFVISQILDE 754
            ++      KK+YA L      +G+++     KG++ VR DW+ LA E  + +  +I   
Sbjct: 607 TIRGAEEGSKKRYAGLIQEGDGDGRIV----FKGLETVRTDWTPLAKEFQQELYERIFRG 662

Query: 755 QSYTDY 760
           + Y DY
Sbjct: 663 EPYVDY 668

Length = 786

>gnl|CDD|99916 cd05533, POLBc_delta, DNA polymerase type-B delta subfamily catalytic domain

 Score =  176 bits (449), Expect = 3e-48
 Identities = 103/321 (32%), Positives = 167/321 (52%), Gaps = 31/321 (9%)

Query: 496 YSGGLVLEPKKGFYDKFIILMDFNSLYPSIIQEYNICFTTI----PVRMLQDSDITTL-- 549
           Y G  V+EP KG+YD  I  +DF SLYPSI+  +N+C+TT+      + L   D      
Sbjct: 3   YEGATVIEPIKGYYDVPIATLDFASLYPSIMMAHNLCYTTLLNKNTAKKLPPEDYIKTPN 62

Query: 550 CEYLPEHQVDTGILPSEIKKLVESRRQVKALMKQPNLSSDLLMQYDIRQKALKLTANSMY 609
            +Y  +  V  G+LP  +++L+ +R++ K  +K+           D RQ ALK++ANS+Y
Sbjct: 63  GDYFVKSSVRKGLLPEILEELLAARKRAKKDLKEET-DPFKKAVLDGRQLALKISANSVY 121

Query: 610 GCLGFPNSRFFAQPLAALVTAKGREILLNTKSLVENL---------NYEVIYGDTDSLMI 660
           G  G    +     +++ VT+ GR+++  TK LVE           + +VIYGDTDS+M+
Sbjct: 122 GFTGATVGKLPCLEISSSVTSFGRQMIEKTKKLVEEKYTKANGYSHDAKVIYGDTDSVMV 181

Query: 661 SCNVNDYDSVFKIGNQIKSECNKLY-KQLELDIDGVYKYMLLLKKKKYAALSISKLSN-G 718
              V+D +   K+G +     +K + K ++L+ + VY   LL+ KK+YA L  +      
Sbjct: 182 KFGVSDVEEAMKLGKEAAEYVSKKFIKPIKLEFEKVYFPYLLINKKRYAGLLWTNPDKHD 241

Query: 719 KMICSQEIKGVDVVRRDWSQLASEAGKFVISQILDEQSYTDYSLDDRLQNIHEHMKKIRT 778
           KM      KG++ VRRD   L     +  +++IL E+          ++   E +K + +
Sbjct: 242 KMDT----KGIETVRRDNCLLVQNVVETCLNKILIERD---------VEGAIEFVKGVIS 288

Query: 779 DLDNGFVPLTLLEITKQLTKA 799
           DL    + ++LL ITK LTK 
Sbjct: 289 DLLQNKIDISLLVITKALTKT 309

Three DNA-dependent DNA polymerases type B (alpha, delta, and epsilon) have been identified as essential for nuclear DNA replication in eukaryotes. Presently, no direct data is available regarding the strand specificity of DNA polymerase during DNA replication in vivo. However, mutation analysis supports the hypothesis that DNA polymerase delta is the enzyme responsible for both elongation and maturation of Okazaki fragments on the lagging strand. Length = 393

>gnl|CDD|99919 cd05536, POLBc_B3, DNA polymerase type-B B3 subfamily catalytic domain

 Score =  172 bits (437), Expect = 6e-47
 Identities = 110/309 (35%), Positives = 170/309 (55%), Gaps = 26/309 (8%)

Query: 495 AYSGGLVLEPKKGFYDKFIILMDFNSLYPSIIQEYNICFTTIPVRMLQDSDITTLCEYLP 554
           +Y GG+VLEP+KG ++  I+++DF+SLYPSI+ +YNI   T+     +D D+     +  
Sbjct: 3   SYEGGIVLEPEKGLHEN-IVVLDFSSLYPSIMIKYNISPDTLVREGCEDCDVEPQVGHKF 61

Query: 555 EHQVDTGILPSEIKKLVESRRQVKALMKQPNLSSDLLMQYDIRQKALKLTANSMYGCLGF 614
                 G +PS ++ L+E RR++K  MK+ +  S+     D RQ+A+K+ ANS YG +G+
Sbjct: 62  RKDPP-GFIPSVLEDLLEERRRIKEKMKKLDPESEEYKLLDERQRAIKILANSFYGYMGW 120

Query: 615 PNSRFFAQPLAALVTAKGREILLNTKSLVENLNYEVIYGDTDSLM--ISCNVNDYDSVFK 672
            N+R++ +  A  VTA GRE +  T  + E   ++VIYGDTDSL   I         V K
Sbjct: 121 ANARWYCKECAEAVTAWGREYIKTTIKIAEEKGFKVIYGDTDSLFVKIDGADAVKKKVKK 180

Query: 673 IGNQIKSECNKLYKQLELDIDGVYKYMLLLKKKKYAALSISKLSNGKMICSQEIKGVDVV 732
           +   I  E       LEL+I+  YK    + KK+YA L      +GK+     + G++VV
Sbjct: 181 LLKYINEELP-----LELEIEKFYKRGFFVTKKRYAGL----TEDGKID----VVGLEVV 227

Query: 733 RRDWSQLASEAGKFVISQILDEQSYTDYSLDDRLQNIHEHMKKIRTDLDNGFVPLTLLEI 792
           RRDWS++A E    V+  IL E       +++ ++ + E ++K++     G VP   L I
Sbjct: 228 RRDWSEIAKETQARVLEAILKEG-----DVEEAVKIVKEVIEKLK----RGEVPPEKLVI 278

Query: 793 TKQLTKAPE 801
            KQLTK   
Sbjct: 279 WKQLTKDLS 287

Archaeal proteins that are involved in DNA replication are similar to those from eukaryotes. Some members of the archaea also possess multiple family B DNA polymerases (B1, B2 and B3). So far there is no specific function(s) has been assigned for different members of the archaea type B DNA polymerases. Phylogenetic analyses of eubacterial, archaeal, and eukaryotic family B DNA polymerases are support independent gene duplications during the evolution of archaeal and eukaryotic family B DNA polymerases. Structural comparison of the thermostable DNA polymerase type B to its mesostable homolog suggests several adaptations to high temperature such as shorter loops, disulfide bridges, and increasing electrostatic interaction at subdomain interfaces. Length = 371

>gnl|CDD|240301 PTZ00166, PTZ00166, DNA polymerase delta catalytic subunit; Provisional

 Score =  168 bits (428), Expect = 1e-42
 Identities = 105/337 (31%), Positives = 167/337 (49%), Gaps = 44/337 (13%)

Query: 486 NKGKGRKKAAYSGGLVLEPKKGFYDKFIILMDFNSLYPSIIQEYNICFTTIPVRMLQDSD 545
               G  +  Y G  VLEPKKGFYD+ I  +DF SLYPSI+  +N+C++T    ++  +D
Sbjct: 530 KYSGGGSEEKYEGATVLEPKKGFYDEPIATLDFASLYPSIMIAHNLCYST----LVPPND 585

Query: 546 ITTLCE----------YLPEHQVDTGILPSEIKKLVESRRQVKALMKQPNLSSDLLMQYD 595
                E             + +V  GILP  +++L+ +R++ K  MK       L    +
Sbjct: 586 ANNYPEDTYVTTPTGDKFVKKEVRKGILPLIVEELIAARKKAKKEMKDEK-DPLLKKVLN 644

Query: 596 IRQKALKLTANSMYGCLGFPNSRFFAQP---LAALVTAKGREILLNTKSLVENL------ 646
            RQ ALK++ANS+YG  G         P   ++  +T+ GR+++  TK LVE        
Sbjct: 645 GRQLALKISANSVYGYTGAQVGGQL--PCLEVSTSITSFGRQMIDKTKELVEKHYTKANG 702

Query: 647 ---NYEVIYGDTDSLMISCNVNDYDSVFKIGNQIKSECNKLY-KQLELDIDGVYKYMLLL 702
              +  VIYGDTDS+M+    +D      +G +     +K + K ++L+ + VY   LL+
Sbjct: 703 YKHDATVIYGDTDSVMVKFGTDDIQEAMDLGKEAAERISKKFLKPIKLEFEKVYCPYLLM 762

Query: 703 KKKKYAALSISKLSN-GKMICSQEIKGVDVVRRDWSQLASEAGKFVISQILDEQSYTDYS 761
            KK+YA L  +      K+ C    KG++ VRRD   L  +  + V+++IL E+      
Sbjct: 763 NKKRYAGLLYTNPEKYDKIDC----KGIETVRRDNCLLVQQMVETVLNKILIEKD----- 813

Query: 762 LDDRLQNIHEHMKKIRTDLDNGFVPLTLLEITKQLTK 798
               +++  E  K   +DL    + ++LL ITK L K
Sbjct: 814 ----VESAIEFTKGKISDLLQNRIDISLLVITKSLGK 846

Length = 1054

>gnl|CDD|220389 pfam09767, DUF2053, Predicted membrane protein (DUF2053)

 Score =  134 bits (340), Expect = 2e-36
 Identities = 53/107 (49%), Positives = 73/107 (68%), Gaps = 4/107 (3%)

Query: 1   MLILATFVPTTDNFSGGVDVFGDLIKLSIDLIDYVGKYLVLS--SIPGKGHAKILTAGVG 58
           +L+LATF P +D  SG  D+FG+++K+S D ID  G YLVLS  +  GKG ++IL  G+G
Sbjct: 49  LLLLATFFPVSD--SGSFDIFGEILKISADFIDLAGLYLVLSQKTNAGKGESRILAVGLG 106

Query: 59  WAGAEVILTRFLDLWVGARGAEFDWKYIQNSLDSNICLIDKTNKFAA 105
           WA AE I++R + LWVGARG EFDWKYI  S+++N+ L+        
Sbjct: 107 WAFAESIMSRLIPLWVGARGLEFDWKYILRSIEANLDLVQTLVLACL 153

This entry is of the conserved N-terminal 150 residues of proteins conserved from plants to humans. The function is unknown although some annotation suggests it to be a transmembrane protein. Length = 159

>gnl|CDD|99920 cd05537, POLBc_Pol_II, DNA polymerase type-II subfamily catalytic domain

 Score =  141 bits (358), Expect = 2e-36
 Identities = 80/293 (27%), Positives = 131/293 (44%), Gaps = 57/293 (19%)

Query: 498 GGLVLEPKKGFYDKFIILMDFNSLYPSIIQEYNICFTTIPVRMLQDSDITTLCEYLPEHQ 557
           GG V++ K G Y   ++L DF SLYPSII+ + I     P+ +++           PE  
Sbjct: 5   GGYVMDSKPGLYKNVLVL-DFKSLYPSIIRTFLI----DPLGLIEGLKAPD-----PEDL 54

Query: 558 V----------DTGILPSEIKKLVESRRQVKALMKQPNLSSDLLMQYDIRQKALKLTANS 607
           +          +  ILP  I +L  +R + K          +  +       A+K+  NS
Sbjct: 55  IPGFLGARFSREKHILPDLIARLWAARDEAK-------REKNAPLSQ-----AIKIIMNS 102

Query: 608 MYGCLGFPNSRFFAQPLAALVTAKGREILLNTKSLVENLNYEVIYGDTDSLMISCNVN-D 666
            YG LG    RFF   LA+ +T +G EI+  T++ +E   Y+VIYGDTDS  +      D
Sbjct: 103 FYGVLGSTGCRFFDPRLASSITLRGHEIMKQTRAWIEQQGYQVIYGDTDSTFVWLGEELD 162

Query: 667 YDSVFKIGNQIKSECNKLYKQ-----------LELDIDGVYKYMLLL--------KKKKY 707
                 IG ++ S+ N+ + Q           LE++ +  Y    +          KK+Y
Sbjct: 163 AAEAQAIGKELASQINQWWAQKLKEEFGLESFLEIEFETHYSRFFMPTIRGSDEGSKKRY 222

Query: 708 AALSISKLSNGKMICSQEIKGVDVVRRDWSQLASEAGKFVISQILDEQSYTDY 760
           A L     ++G        KG++ VR DW+ LA +  K +  ++ +++ Y  +
Sbjct: 223 AGLKS---TDGGD--ELVFKGLETVRSDWTPLARQFQKELYERVFNDEPYEGF 270

Bacteria contain five DNA polymerases (I, II, III, IV and V). DNA polymerase II (Pol II) is a prototype for the B-family of polymerases. The role of Pol II in a variety of cellular activities, such as repair of DNA damaged by UV irradiation or oxidation has been proven by genetic studies. DNA polymerase III is the main enzyme responsible for replication of the bacterial chromosome; however, In vivo studies have also shown that Pol II is able to participate in chromosomal DNA replication with larger role in lagging-strand replication. Length = 371

>gnl|CDD|99917 cd05534, POLBc_zeta, DNA polymerase type-B zeta subfamily catalytic domain

 Score =  140 bits (354), Expect = 3e-35
 Identities = 79/279 (28%), Positives = 119/279 (42%), Gaps = 53/279 (18%)

Query: 500 LVLEPKKGFYDKFIILMDFNSLYPSIIQEYNICFTTI----------------------- 536
           LV+EP+ GFY   +I++DF SLYPSI+  YN C++T                        
Sbjct: 40  LVMEPESGFYSDPVIVLDFQSLYPSIMIAYNYCYSTCLGRVEELNGGGKFGFLGVKLYLP 99

Query: 537 ---PVRMLQDSDITTL---CEYLPEHQVDTGILPSEIKKLVESRRQVKALMKQPNLSSDL 590
                 +L   D+T       ++ +  V  GILP  +++++++R  VK  MK+      L
Sbjct: 100 PPPLDLLLLKDDVTISPNGVMFVKKS-VRKGILPKMLEEILDTRIMVKKAMKKYKDDKKL 158

Query: 591 LMQYDIRQKALKLTANSMYGCLG------FPNSRFFAQPLAALVTAKGREILLNTKSLVE 644
               D RQ ALKL AN  YG          P        +A  +   GRE L     L+E
Sbjct: 159 QRILDARQLALKLLANVTYGYTAASFSGRMPCVE-----IADSIVQTGRETLERAIELIE 213

Query: 645 NLNY---EVIYGDTDSLMISC---NVNDYDSVFKIGNQIKSECNKLY-KQLELDIDGVYK 697
           +      +V+YGDTDSL +        +    FKIG +I           ++L  + VY 
Sbjct: 214 STPKWGAKVVYGDTDSLFVLLPGRTKEE---AFKIGKEIAEAVTAANPSPIKLKFEKVYH 270

Query: 698 YMLLLKKKKYAALSISKLSNGKMICSQEIKGVDVVRRDW 736
             +L+ KK+Y           +     + KG++ VRRD 
Sbjct: 271 PCVLVTKKRYVGYKYESPDQTEPTF--DAKGIETVRRDG 307

DNA polymerase (Pol) zeta is a member of the eukaryotic B-family of DNA polymerases and distantly related to DNA Pol delta. Pol zeta plays a major role in translesion replication and the production of either spontaneous or induced mutations. Apart from its role in translesion replication, Pol zeta also appears to be involved in somatic hypermutability in B lymphocytes, an important element for the production of high affinity antibodies in response to an antigen. Length = 451

>gnl|CDD|233037 TIGR00592, pol2, DNA polymerase (pol2)

 Score =  142 bits (358), Expect = 3e-34
 Identities = 89/319 (27%), Positives = 130/319 (40%), Gaps = 51/319 (15%)

Query: 109 LKDLKGQGVKHKYEFTADENVYEEVSEKEYTERVLKRQEDDWIDDDGGDGYV----EDGR 164
           L  +  +  +        E   E        E      +D +  D+              
Sbjct: 175 LIPVPLKRAEFAGGDVQMEGDPELKLASFDIETYFHDGKDFFPGDENPADEEIMISTTPV 234

Query: 165 EIFDDDIEDVPQKKEKH------------------DKRKKNKNIQNPNAKDDSLPLATDH 206
                D E  P+ +                     +     +     + +D  + +  + 
Sbjct: 235 IAKQWDYESEPEARVVTWKKPDKPTTGSYVESVSEEISMIKRFWDVIDQEDTDVEITVNG 294

Query: 207 EN-------KKVFRMFFLDAFEDIYKQPGTVYLFGKVFVKENNSHSSCCVIVQNIDRKIY 259
           +N        +    F+ DA+ED  ++ G V LFG+     +  H S CV V+ I+R ++
Sbjct: 295 DNFDLVYLADRQVFQFYWDAYEDPAEKLGVVLLFGR-----DVDHVSPCVQVKGINRDLF 349

Query: 260 LLPRSEHLK------TKEPVSIAQVYSEFD-QIATQYKILDFKSRKIEKKYAFNLPG--V 310
            LPR   +       T+  +++   Y EF  ++A  YK   F+++ I KKY F  P    
Sbjct: 350 FLPREGKIDFDLGKVTRRTINLPDYYLEFVSELALGYKKEKFRAKPIAKKYEFEAPDIDA 409

Query: 311 PDLSEYLEVRYS-----AKCPALPSDLSGDTFSHVFGTKTSFLENLLLERKIKGPSWLEF 365
           P  SEYLEV Y      A   ALPSDL G TF HVFG+ T  LE  LL RKIKGP WL  
Sbjct: 410 PYSSEYLEVTYELGKEFAPMEALPSDLKGQTFWHVFGSNTGNLERFLLLRKIKGPCWLAV 469

Query: 366 --PEAEKFPSRISWCKYEV 382
             P+  ++P R SWCKYE 
Sbjct: 470 KGPDELEYP-RRSWCKYEG 487

All proteins in this superfamily for which functions are known are DNA polymerases.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University) [DNA metabolism, DNA replication, recombination, and repair]. Length = 1172

>gnl|CDD|235594 PRK05761, PRK05761, DNA polymerase I; Reviewed

 Score =  139 bits (351), Expect = 1e-33
 Identities = 92/332 (27%), Positives = 152/332 (45%), Gaps = 22/332 (6%)

Query: 475 NKKEGEET-GEANKGKGRKKAAYSGGLVLEPKKGFYDKFIILMDFNSLYPSIIQEYNICF 533
            K++      E  K    K   Y GGLV +P  G +   + ++DF SLYPSII ++N+  
Sbjct: 385 WKEDILRLDHEVYKKAIIKGKKYRGGLVFQPPPGIFFN-VYVLDFASLYPSIIVKWNLSP 443

Query: 534 TTIPVRMLQDSDITTLCEYLPEHQVDTGILPSEIKKLVESRRQ--VKALMKQPNLSSDLL 591
            T+ +   +      + E       D   L S +  L+   R    K   K PNL  +  
Sbjct: 444 ETVRIPECKCHYDDEVPELGHSVCDDRPGLTSVLVGLLRDFRVKIYKKKAKDPNLDEERR 503

Query: 592 MQYDIRQKALKLTANSMYGCLGFPNSRFFAQPLAALVTAKGREILLNTKSLVENLNYEVI 651
             YD+ Q+ALK+  N+ YG  G  N + +   +A  +TA GREILL+TK   E L  +V+
Sbjct: 504 AWYDVVQRALKVFLNASYGVFGAENFKLYRIEVAESITALGREILLSTKKKAEELGLKVL 563

Query: 652 YGDTDSLMISCNVNDYDSVFKIGNQIKSECNKLYKQLELDIDGVYKYMLLLK-KKKYAAL 710
           YGDTDSL +       +S+ ++  +I+         ++L++D  Y ++     KK Y   
Sbjct: 564 YGDTDSLFVWG--PTKESLEELIKEIEERTG-----IDLEVDKTYDWVAFSGLKKNY--- 613

Query: 711 SISKLSNGKMICSQEIKGVDVVRRDWSQLASEAGKFVISQILDEQSYTDYSLDDRLQNIH 770
               L +GK+    +IKG+   +R+  +   E  + V+ ++L      +     +   I 
Sbjct: 614 -FGVLKDGKV----KIKGIVAKKRNTPEFVKELQREVL-EVLKSIRSPEDVEKVK-DEIE 666

Query: 771 EHMKKIRTDLDNGFVPLTLLEITKQLTKAPEG 802
           + +K+    L     PL  L I  +L+K  + 
Sbjct: 667 DVLKRYYEKLRAKDYPLDELAIRVRLSKPLDE 698

Length = 787

>gnl|CDD|99913 cd05530, POLBc_B1, DNA polymerase type-B B1 subfamily catalytic domain

 Score =  122 bits (309), Expect = 5e-30
 Identities = 88/318 (27%), Positives = 145/318 (45%), Gaps = 29/318 (9%)

Query: 489 KGRKKAAYSGGLVLEPKKGFYDKFIILMDFNSLYPSIIQEYNICFTTIPVRMLQDSDITT 548
           KG+K   Y G +VLEP  G +   ++++DF SLYPSII+ +N+ + T  V        T 
Sbjct: 9   KGKK---YRGAIVLEPPPGIFFN-VVVLDFASLYPSIIKVWNLSYET--VNCPHCECKTN 62

Query: 549 LCEYLPEHQVDT---GILPSEIKKLVESRRQV-KALMKQPNLSSDLLMQYDIRQKALKLT 604
               +  H V     GI    I  L + R ++ K   K  +L  ++   YD+ Q A+K+ 
Sbjct: 63  EVPEVG-HWVCKKRPGITSQIIGLLRDLRVKIYKKKAKDKSLDEEMRQWYDVVQSAMKVF 121

Query: 605 ANSMYGCLGFPNSRFFAQPLAALVTAKGREILLNTKSLVENLNYEVIYGDTDSLMISCNV 664
            N+ YG  G  N   +  P+A   TA GR I+ +T      L  +V+YGDTDSL +    
Sbjct: 122 INASYGVFGAENFPLYCPPVAESTTALGRYIITSTIKKARELGLKVLYGDTDSLFLWNPP 181

Query: 665 NDYDSVFKIGNQIKSECNKLYKQLELDIDGVYKYMLLLKKKK-YAALSISKLSNGKMICS 723
            +     ++ + ++    +L   L+L++D  Y+Y++    KK Y    +    +G +   
Sbjct: 182 QE-----QLEDLVEWVEKEL--GLDLELDKEYRYVVFSGLKKNY----LGVTKDGSV--- 227

Query: 724 QEIKGVDVVRRDWSQLASEAGKFVISQILDEQSYTDYSLDDRLQNIHEHMKKIRTDLDNG 783
            +IKG+   +R+  +   E    VI  +    S  D+      + I + +K +   L   
Sbjct: 228 -DIKGLLGKKRNTPEFVKELFYEVIEILSAVNSPEDFE--KAREKIRDIVKGVYKRLKKK 284

Query: 784 FVPLTLLEITKQLTKAPE 801
              L  L     L+K PE
Sbjct: 285 EYTLDQLAFKVMLSKPPE 302

Archaeal proteins that are involved in DNA replication are similar to those from eukaryotes. Some archaeal members also possess multiple family B DNA polymerases (B1, B2 and B3). So far there is no specific function(s) has been assigned for different members of the archaea type B DNA polymerases. Phylogenetic analyses of eubacterial, archaeal, and eukaryotic family B DNA polymerases are support independent gene duplications during the evolution of archaeal and eukaryotic family B DNA polymerases. Length = 372

>gnl|CDD|99914 cd05531, POLBc_B2, DNA polymerase type-B B2 subfamily catalytic domain

 Score =  113 bits (286), Expect = 3e-27
 Identities = 84/320 (26%), Positives = 150/320 (46%), Gaps = 40/320 (12%)

Query: 494 AAYSGGLVLEPKKGFYDKFIILMDFNSLYPSIIQEYNICFTTIPVRMLQDSDITTLCEYL 553
            A  GGLV +P+ G Y+    + DF+S+YPSII +YNI   TI  R  +  D   L   +
Sbjct: 3   LADRGGLVFQPEPGLYENVAQI-DFSSMYPSIIVKYNISPETINCRCCECRDHVYLGHRI 61

Query: 554 PEHQVDTGILPSEIKKLVESRRQVKALMKQPNLSSDLLMQYDIRQKALKLTANSMYGCLG 613
                  G LP  ++ L+E R + K L K+ +        Y  RQKALK    + +G LG
Sbjct: 62  CLK--RRGFLPEVLEPLLERRLEYKRLKKEED-------PYAGRQKALKWILVTSFGYLG 112

Query: 614 FPNSRFFAQPLAALVTAKGREILLNTKSLVENLNYEVIYGDTDSLMISCNVNDYDSVFKI 673
           + N++F    +   +TA GR+ILL  K + E + + V++G  DSL I     D + +   
Sbjct: 113 YKNAKFGRIEVHEAITAYGRKILLRAKEIAEEMGFRVLHGIVDSLWIQGR-GDIEEL--- 168

Query: 674 GNQIKSECNKLYKQ--LELDIDGVYKYMLLLKKKKYAALS---ISKLSNGKMICSQEIKG 728
                    ++ ++  + L ++G Y +++ L ++           +LS+G+M     ++G
Sbjct: 169 -------AREIEERTGIPLKLEGHYDWIVFLPERDGLGAPNRYFGRLSDGEMK----VRG 217

Query: 729 VDVVRRDWSQLASEAGKFVISQILDE-QSYTDY--SLDDRLQNIHEHMKKIRTDLDNGFV 785
           +++ RRD      +  +  +  IL   ++  +     ++ L     +++++R        
Sbjct: 218 IELRRRDTPPFVKKFQEEAL-DILASAKTPEELLKLREEALDLFRRYLQRLR------EG 270

Query: 786 PLTLLEITKQLTKAPEGGKV 805
            L  L I K+++K     KV
Sbjct: 271 DLEDLIIEKKISKRSSEYKV 290

Archaeal proteins that are involved in DNA replication are similar to those from eukaryotes. Some archaeal members also possess multiple family B DNA polymerases (B1, B2 and B3). So far there is no specific function(s) has been assigned for different members of the archaea type B DNA polymerases. Phylogenetic analyses of eubacterial, archaeal, and eukaryotic family B DNA polymerases are support independent gene duplications during the evolution of archaeal and eukaryotic family B DNA polymerases. Length = 352

>gnl|CDD|217301 pfam02956, TT_ORF1, TT viral orf 1

 Score =  113 bits (284), Expect = 6e-26
 Identities = 44/56 (78%), Positives = 48/56 (85%)

Query: 899 RRRRRRKKRRRSRRRRSRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRR 954
           R  RRR++R R RRRR RRRR RRRRRRRR RRRRR RRRRRRRRRRRRRRRR+R+
Sbjct: 4   RWWRRRRRRWRGRRRRRRRRRARRRRRRRRVRRRRRGRRRRRRRRRRRRRRRRKRK 59

TT virus (TTV), isolated initially from a Japanese patient with hepatitis of unknown aetiology, has since been found to infect both healthy and diseased individuals and numerous prevalence studies have raised questions about its role in unexplained hepatitis. ORF1 is a large 750 residue protein. The N-terminal half of this protein corresponds to the capsid protein. Length = 525

>gnl|CDD|217301 pfam02956, TT_ORF1, TT viral orf 1

 Score =  112 bits (283), Expect = 8e-26
 Identities = 42/57 (73%), Positives = 47/57 (82%)

Query: 898 GRRRRRRKKRRRSRRRRSRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRR 954
              RRRR++ R  RRRR RRR RRRRRRRR RRRRR RRRRRRRRRRRRRRRR+R++
Sbjct: 4   RWWRRRRRRWRGRRRRRRRRRARRRRRRRRVRRRRRGRRRRRRRRRRRRRRRRKRKK 60

TT virus (TTV), isolated initially from a Japanese patient with hepatitis of unknown aetiology, has since been found to infect both healthy and diseased individuals and numerous prevalence studies have raised questions about its role in unexplained hepatitis. ORF1 is a large 750 residue protein. The N-terminal half of this protein corresponds to the capsid protein. Length = 525

>gnl|CDD|217301 pfam02956, TT_ORF1, TT viral orf 1

 Score =  111 bits (280), Expect = 2e-25
 Identities = 43/57 (75%), Positives = 47/57 (82%)

Query: 897 GGRRRRRRKKRRRSRRRRSRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRR 953
              RRRRR+ R R RRRR RR RRRRRRRR RRRRR RRRRRRRRRRRRRRRR+R++
Sbjct: 4   RWWRRRRRRWRGRRRRRRRRRARRRRRRRRVRRRRRGRRRRRRRRRRRRRRRRKRKK 60

TT virus (TTV), isolated initially from a Japanese patient with hepatitis of unknown aetiology, has since been found to infect both healthy and diseased individuals and numerous prevalence studies have raised questions about its role in unexplained hepatitis. ORF1 is a large 750 residue protein. The N-terminal half of this protein corresponds to the capsid protein. Length = 525

>gnl|CDD|217301 pfam02956, TT_ORF1, TT viral orf 1

 Score =  111 bits (279), Expect = 2e-25
 Identities = 42/59 (71%), Positives = 46/59 (77%)

Query: 895 GGGGRRRRRRKKRRRSRRRRSRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRR 953
               RRRRR + RRR RRRR  RRRRRRRR RRRRR RRRRRRRRRRRRRRRR+R++  
Sbjct: 4   RWWRRRRRRWRGRRRRRRRRRARRRRRRRRVRRRRRGRRRRRRRRRRRRRRRRKRKKLI 62

TT virus (TTV), isolated initially from a Japanese patient with hepatitis of unknown aetiology, has since been found to infect both healthy and diseased individuals and numerous prevalence studies have raised questions about its role in unexplained hepatitis. ORF1 is a large 750 residue protein. The N-terminal half of this protein corresponds to the capsid protein. Length = 525

>gnl|CDD|217301 pfam02956, TT_ORF1, TT viral orf 1

 Score =  110 bits (277), Expect = 4e-25
 Identities = 43/59 (72%), Positives = 47/59 (79%)

Query: 896 GGGRRRRRRKKRRRSRRRRSRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRR 954
              RRRRRR + RR RRRR R RRRRRRRR RRRRR RRRRRRRRRRRRRRRR+R++  
Sbjct: 4   RWWRRRRRRWRGRRRRRRRRRARRRRRRRRVRRRRRGRRRRRRRRRRRRRRRRKRKKLI 62

TT virus (TTV), isolated initially from a Japanese patient with hepatitis of unknown aetiology, has since been found to infect both healthy and diseased individuals and numerous prevalence studies have raised questions about its role in unexplained hepatitis. ORF1 is a large 750 residue protein. The N-terminal half of this protein corresponds to the capsid protein. Length = 525

>gnl|CDD|237171 PRK12678, PRK12678, transcription termination factor Rho; Provisional

 Score =  111 bits (280), Expect = 4e-25
 Identities = 48/169 (28%), Positives = 68/169 (40%), Gaps = 7/169 (4%)

Query: 808 TQIRLSRNRRGRRRRRRKKKEEKKKWKRRGGGRRRRRGKKEEEKKKKKEEEEEGGEKEEE 867
            Q R  R R    RR   +K  +   +     R     + EEE++ ++    +  +++ E
Sbjct: 125 AQARERRERGEAARRGAARKAGEGGEQPATEARADAAERTEEEERDERRRRGDREDRQAE 184

Query: 868 EGGGGGGRRRRRRRRSGKEEEEKKKKEGGGGRRRRRRKKRRRSRRRRSRRRRRRRRRRRR 927
              G  GRR  R R     +   ++++G     R RR    R  RRR R RR  R    R
Sbjct: 185 AERGERGRREERGRDGDDRDRRDRREQGDRREERGRRDGGDRRGRRRRRDRRDARGDDNR 244

Query: 928 RRRRRR-------RRRRRRRRRRRRRRRRRRRRRSGKEEEEEEKKKEEK 969
             R  R       R  RR RR R R RR RR    G E E E ++ +  
Sbjct: 245 EDRGDRDGDDGEGRGGRRGRRFRDRDRRGRRGGDGGNEREPELREDDVL 293

Length = 672

>gnl|CDD|222962 PHA03036, PHA03036, DNA polymerase; Provisional

 Score =  107 bits (269), Expect = 1e-23
 Identities = 81/331 (24%), Positives = 134/331 (40%), Gaps = 71/331 (21%)

Query: 492 KKAAYSGGLVLEPKKGFYDKFIILMDFNSLYPSIIQEYNICFTTIPVRMLQDSD------ 545
            K  Y GG V  PK+  +D  +++ D+NSLYP++    N+   T+ V ++ + +      
Sbjct: 526 NKFPYEGGKVFAPKQKMFDNNVLIFDYNSLYPNVCIFGNLSPETL-VGVVVNDNRLEAEI 584

Query: 546 --------------ITTLCEYLPEHQVDT---------GILPSEIKKLVESRRQVKALMK 582
                         I   CE      V           GI+P  +K  +E R + K L+K
Sbjct: 585 NKQELRRKYPYPRYIYVHCEPRSPDLVSEIAVFDRRIEGIIPKLLKTFLEERARYKKLLK 644

Query: 583 QPNLSSDLLMQYDIRQKALKLTANSMYGCLGFPNSRFFAQPLAALVTAKGREILLNTKSL 642
           +   S +  + YD  Q   K+ ANS+YG +GF NS  ++   A   TA GR ++    S+
Sbjct: 645 EATSSVEKAI-YDSMQYTYKIVANSVYGLMGFRNSALYSYASAKSCTAIGRNMIKYLNSV 703

Query: 643 VEN--------------------------------------LNYEVIYGDTDSLMISCNV 664
           +                                          +  +YGDTDS+ +  N 
Sbjct: 704 LNGSKLINGKLILANCPINPFFKDDRSIDTNYDTNLPVEYNFTFRSVYGDTDSVFLEINT 763

Query: 665 NDYDSVFKIGNQIKSECNK--LYKQLELDIDGVYKYMLLLKKKKYAALSISKLSNGKMIC 722
            D D   KI  +++   N+  L+   +++ + VYK +++  KKKY  L     S    + 
Sbjct: 764 KDVDKSIKIAKELERIINEKVLFDNFKIEFEAVYKNLIMQSKKKYTTLKYIASSTDGSVP 823

Query: 723 SQEIKGVDVVRRDWSQLASEAGKFVISQILD 753
            +  KG    RRD S+      K   +++LD
Sbjct: 824 ERVNKGTSETRRDVSKFHKYMIKIYKTRLLD 854

Length = 1004

>gnl|CDD|217301 pfam02956, TT_ORF1, TT viral orf 1

 Score =  105 bits (264), Expect = 2e-23
 Identities = 43/51 (84%), Positives = 43/51 (84%)

Query: 907 RRRSRRRRSRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRSGK 957
           RRR RR R RRRRRRRRR RRRRRRRR RRRRR RRRRRRRRRRRRRR  K
Sbjct: 7   RRRRRRWRGRRRRRRRRRARRRRRRRRVRRRRRGRRRRRRRRRRRRRRRRK 57

TT virus (TTV), isolated initially from a Japanese patient with hepatitis of unknown aetiology, has since been found to infect both healthy and diseased individuals and numerous prevalence studies have raised questions about its role in unexplained hepatitis. ORF1 is a large 750 residue protein. The N-terminal half of this protein corresponds to the capsid protein. Length = 525

>gnl|CDD|217301 pfam02956, TT_ORF1, TT viral orf 1

 Score =  104 bits (261), Expect = 4e-23
 Identities = 42/55 (76%), Positives = 44/55 (80%)

Query: 903 RRKKRRRSRRRRSRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRSGK 957
           R  +RRR R R  RRRRRRRR RRRRRRRR RRRRR RRRRRRRRRRRRRRR  +
Sbjct: 4   RWWRRRRRRWRGRRRRRRRRRARRRRRRRRVRRRRRGRRRRRRRRRRRRRRRRKR 58

TT virus (TTV), isolated initially from a Japanese patient with hepatitis of unknown aetiology, has since been found to infect both healthy and diseased individuals and numerous prevalence studies have raised questions about its role in unexplained hepatitis. ORF1 is a large 750 residue protein. The N-terminal half of this protein corresponds to the capsid protein. Length = 525

>gnl|CDD|237171 PRK12678, PRK12678, transcription termination factor Rho; Provisional

 Score = 90.7 bits (226), Expect = 1e-18
 Identities = 29/150 (19%), Positives = 45/150 (30%)

Query: 814 RNRRGRRRRRRKKKEEKKKWKRRGGGRRRRRGKKEEEKKKKKEEEEEGGEKEEEEGGGGG 873
             R  R     ++ E+                +       +     E  +  E    G  
Sbjct: 77  ARRAARAAAAARQAEQPAAEAAAAKAEAAPAARAAAAAAAEAASAPEAAQARERRERGEA 136

Query: 874 GRRRRRRRRSGKEEEEKKKKEGGGGRRRRRRKKRRRSRRRRSRRRRRRRRRRRRRRRRRR 933
            RR   R+     E+   +       R    ++  R RR     R+    R  R RR  R
Sbjct: 137 ARRGAARKAGEGGEQPATEARADAAERTEEEERDERRRRGDREDRQAEAERGERGRREER 196

Query: 934 RRRRRRRRRRRRRRRRRRRRRSGKEEEEEE 963
            R    R RR RR +  RR   G+ +  + 
Sbjct: 197 GRDGDDRDRRDRREQGDRREERGRRDGGDR 226

Length = 672

>gnl|CDD|237171 PRK12678, PRK12678, transcription termination factor Rho; Provisional

 Score = 89.6 bits (223), Expect = 3e-18
 Identities = 38/146 (26%), Positives = 49/146 (33%), Gaps = 2/146 (1%)

Query: 813 SRNRRGRRRRRRKKKEEKKKWKRRGGGRRRRRGKKEEEKKKKKEEEEEGGEKEEEEGGGG 872
           +      R       E     +      RR RG+       +K  E       E      
Sbjct: 102 AEAAPAARAAAAAAAEAASAPEAAQARERRERGEAARRGAARKAGEGGEQPATEARADAA 161

Query: 873 --GGRRRRRRRRSGKEEEEKKKKEGGGGRRRRRRKKRRRSRRRRSRRRRRRRRRRRRRRR 930
                  R  RR   + E+++ +   G R RR  + R    R R  RR +  RR  R RR
Sbjct: 162 ERTEEEERDERRRRGDREDRQAEAERGERGRREERGRDGDDRDRRDRREQGDRREERGRR 221

Query: 931 RRRRRRRRRRRRRRRRRRRRRRRRSG 956
               RR RRRRR RR  R    R   
Sbjct: 222 DGGDRRGRRRRRDRRDARGDDNREDR 247

Length = 672

>gnl|CDD|237171 PRK12678, PRK12678, transcription termination factor Rho; Provisional

 Score = 88.8 bits (221), Expect = 6e-18
 Identities = 44/182 (24%), Positives = 68/182 (37%), Gaps = 9/182 (4%)

Query: 813 SRNRRGRRRRRRKKKEEKKKWKRRGGGRRRRRGKKEEEKKKKKEEEEEGGEKEEEEGGGG 872
           S     + R RR++ E           RR    K  E  ++   E      +  EE    
Sbjct: 120 SAPEAAQARERRERGEA---------ARRGAARKAGEGGEQPATEARADAAERTEEEERD 170

Query: 873 GGRRRRRRRRSGKEEEEKKKKEGGGGRRRRRRKKRRRSRRRRSRRRRRRRRRRRRRRRRR 932
             RRR  R     E E  ++       R    + RR  R +  RR  R RR    RR RR
Sbjct: 171 ERRRRGDREDRQAEAERGERGRREERGRDGDDRDRRDRREQGDRREERGRRDGGDRRGRR 230

Query: 933 RRRRRRRRRRRRRRRRRRRRRRSGKEEEEEEKKKEEKKKEEEEKKKKEGKTKKEEKKKEE 992
           RRR RR  R    R  R  R     E     + +  + ++   ++  +G  ++E + +E+
Sbjct: 231 RRRDRRDARGDDNREDRGDRDGDDGEGRGGRRGRRFRDRDRRGRRGGDGGNEREPELRED 290

Query: 993 EE 994
           + 
Sbjct: 291 DV 292

Length = 672

>gnl|CDD|173412 PTZ00121, PTZ00121, MAEBL; Provisional

 Score = 88.7 bits (219), Expect = 1e-17
 Identities = 55/215 (25%), Positives = 104/215 (48%), Gaps = 4/215 (1%)

Query: 819  RRRRRRKKKEEKKKWKRRGGGRRRRRGKKEEEKKKKKEE----EEEGGEKEEEEGGGGGG 874
            ++    KKK E+ K K     ++    KK  E  K + E    E E  E++ E       
Sbjct: 1315 KKADEAKKKAEEAKKKADAAKKKAEEAKKAAEAAKAEAEAAADEAEAAEEKAEAAEKKKE 1374

Query: 875  RRRRRRRRSGKEEEEKKKKEGGGGRRRRRRKKRRRSRRRRSRRRRRRRRRRRRRRRRRRR 934
              +++   + K+ EEKKK +    +    +KK    ++  + +++    +++   +++  
Sbjct: 1375 EAKKKADAAKKKAEEKKKADEAKKKAEEDKKKADELKKAAAAKKKADEAKKKAEEKKKAD 1434

Query: 935  RRRRRRRRRRRRRRRRRRRRSGKEEEEEEKKKEEKKKEEEEKKKKEGKTKKEEKKKEEEE 994
              +++    ++    +++    K+ EE +KK EE KK +E KKK E   K +E KK+ EE
Sbjct: 1435 EAKKKAEEAKKADEAKKKAEEAKKAEEAKKKAEEAKKADEAKKKAEEAKKADEAKKKAEE 1494

Query: 995  EKKKKKKEEEKEEEEKKEEEEKEEEEKKRRRIRRK 1029
             KKK  + ++  E +KK +E K+ EE K+    +K
Sbjct: 1495 AKKKADEAKKAAEAKKKADEAKKAEEAKKADEAKK 1529

Length = 2084

>gnl|CDD|173412 PTZ00121, PTZ00121, MAEBL; Provisional

 Score = 86.7 bits (214), Expect = 4e-17
 Identities = 60/223 (26%), Positives = 102/223 (45%), Gaps = 12/223 (5%)

Query: 819  RRRRRRKKKEEKKKWKRRGGGRRRRRGKKEEEKKKKKEEEEEGGEKEEEEGGGGGGRRRR 878
            +++    KK ++ K K     ++    KK  E KKK +E ++  E ++ +         +
Sbjct: 1476 KKKAEEAKKADEAKKKAEEAKKKADEAKKAAEAKKKADEAKKAEEAKKADEAKKA-EEAK 1534

Query: 879  RRRRSGKEEEEKKKKEGGGGRRRRRRKKRRRSRRRRSRRRRRRRRRRRRRRRRRRRRRRR 938
            +   + K EE+KK  E       ++ ++++++   +     +    R+    ++    R 
Sbjct: 1535 KADEAKKAEEKKKADELKKAEELKKAEEKKKAEEAKKAEEDKNMALRKAEEAKKAEEARI 1594

Query: 939  RRRRRRRRRRRRRRRRSGKEEEEEEKKKEEKKKEEEEKKK--------KEGKTKKEEKKK 990
                +     ++ +    K+ EE + K EE KK EEEKKK         E K K EE KK
Sbjct: 1595 EEVMKLYEEEKKMKAEEAKKAEEAKIKAEELKKAEEEKKKVEQLKKKEAEEKKKAEELKK 1654

Query: 991  EEEEEKKKKKKEEEKEEEEKKEEEE---KEEEEKKRRRIRRKR 1030
             EEE K K  +E +K EE+KK+ EE    EE+EKK     +K 
Sbjct: 1655 AEEENKIKAAEEAKKAEEDKKKAEEAKKAEEDEKKAAEALKKE 1697

Length = 2084

>gnl|CDD|173412 PTZ00121, PTZ00121, MAEBL; Provisional

 Score = 84.8 bits (209), Expect = 2e-16
 Identities = 58/220 (26%), Positives = 100/220 (45%), Gaps = 9/220 (4%)

Query: 819  RRRRRRKKKEEKKKWKRRGGGRRRRRGKKEEEKKKKK----EEEEEGGEKEEEEGGGGGG 874
            ++    KKK +  K K     +     K E E    +    EE+ E  EK++EE      
Sbjct: 1322 KKAEEAKKKADAAKKKAEEAKKAAEAAKAEAEAAADEAEAAEEKAEAAEKKKEEAKKKAD 1381

Query: 875  RRRRRRRRSGKEEEEKKKKEGGGGRRRRRRKKRRRSRRRRSRRRRRRRRRRRRRRRRRRR 934
              +++     K +E KKK E    +    +K     ++    +++   +++    +++  
Sbjct: 1382 AAKKKAEEKKKADEAKKKAEEDKKKADELKKAAAAKKKADEAKKKAEEKKKADEAKKKAE 1441

Query: 935  RRRRRRRRRRRRRRRRRRRRSGKEEEEEEKKKEEKKKEEEEKKKKEGKTKKEEKKKEEEE 994
              ++    +++    ++   + K+ EE +K  E KKK EE KK  E K K EE KK+ +E
Sbjct: 1442 EAKKADEAKKKAEEAKKAEEAKKKAEEAKKADEAKKKAEEAKKADEAKKKAEEAKKKADE 1501

Query: 995  -----EKKKKKKEEEKEEEEKKEEEEKEEEEKKRRRIRRK 1029
                 E KKK  E +K EE KK +E K+ EE K+    +K
Sbjct: 1502 AKKAAEAKKKADEAKKAEEAKKADEAKKAEEAKKADEAKK 1541

Length = 2084

>gnl|CDD|173412 PTZ00121, PTZ00121, MAEBL; Provisional

 Score = 84.4 bits (208), Expect = 2e-16
 Identities = 57/214 (26%), Positives = 98/214 (45%), Gaps = 8/214 (3%)

Query: 824  RKKKEEKKKW----KRRGGGRRRRRGKKEEEKKKKKEEEEEGGEKEEEEGGGGGGRRRRR 879
            +KK EE KK     K+    ++    KK+ E+ KKK +E +   + +++          +
Sbjct: 1463 KKKAEEAKKADEAKKKAEEAKKADEAKKKAEEAKKKADEAKKAAEAKKKADEAKKAEEAK 1522

Query: 880  RRRSGKEEEEKKKKEGGGGRRRRRRKKRRRSRRRRSRRRRRRRRRRRRRRRRRRRRRRRR 939
            +    K+ EE KK +       +++    +      +   +++    ++    +    R+
Sbjct: 1523 KADEAKKAEEAKKADEAKKAEEKKKADELKKAEELKKAEEKKKAEEAKKAEEDKNMALRK 1582

Query: 940  RRRRRRRRRRRRRRRSGKEEEEEEKKKEEKKKEEEEKKKKEGKTKKEEKKKEEEEEKKKK 999
                ++    R        EEE++ K EE KK EE K K E   K EE+KK+ E+ KKK+
Sbjct: 1583 AEEAKKAEEARIEEVMKLYEEEKKMKAEEAKKAEEAKIKAEELKKAEEEKKKVEQLKKKE 1642

Query: 1000 KKEEEKEEEEKKEEEE----KEEEEKKRRRIRRK 1029
             +E++K EE KK EEE      EE KK    ++K
Sbjct: 1643 AEEKKKAEELKKAEEENKIKAAEEAKKAEEDKKK 1676

Length = 2084

>gnl|CDD|237171 PRK12678, PRK12678, transcription termination factor Rho; Provisional

 Score = 83.0 bits (206), Expect = 3e-16
 Identities = 30/149 (20%), Positives = 43/149 (28%), Gaps = 1/149 (0%)

Query: 820 RRRRRKKKEEKKKWKRRGGGRRRRRGKKEEEKKKKKEEEEEGGEKEEEEGGGGGGRRRRR 879
              RR  +      +           K E     +        E            RR R
Sbjct: 75  AAARRAARAAAAARQAEQPAAEAAAAKAEAAPAARAAAAAAA-EAASAPEAAQARERRER 133

Query: 880 RRRSGKEEEEKKKKEGGGGRRRRRRKKRRRSRRRRSRRRRRRRRRRRRRRRRRRRRRRRR 939
              + +    K  + G       R     R+       RRRR  R  R+    R  R RR
Sbjct: 134 GEAARRGAARKAGEGGEQPATEARADAAERTEEEERDERRRRGDREDRQAEAERGERGRR 193

Query: 940 RRRRRRRRRRRRRRRSGKEEEEEEKKKEE 968
             R R    R RR R  + +  EE+ + +
Sbjct: 194 EERGRDGDDRDRRDRREQGDRREERGRRD 222

Length = 672

>gnl|CDD|173412 PTZ00121, PTZ00121, MAEBL; Provisional

 Score = 82.5 bits (203), Expect = 1e-15
 Identities = 65/226 (28%), Positives = 107/226 (47%), Gaps = 14/226 (6%)

Query: 819  RRRRRRKKKEEKKK--WKRRGGGRRRRRGKKEEEKKKKKEEEEEGGEKEEEEGGGGGGRR 876
            ++    KK EEKKK    ++    +    +K EE KK +E   E   K  EE        
Sbjct: 1552 KKAEELKKAEEKKKAEEAKKAEEDKNMALRKAEEAKKAEEARIEEVMKLYEEEKKMKAEE 1611

Query: 877  RRRRRRSGKEEEEKKKKEGGGGRRRRRRKKRRRSRRRRSRRRRRRRRRRRRRRRRRRRRR 936
             ++   +  + EE KK E    +  + +KK    +++    ++     + +     ++  
Sbjct: 1612 AKKAEEAKIKAEELKKAEEEKKKVEQLKKKEAEEKKKAEELKKAEEENKIKAAEEAKKAE 1671

Query: 937  RRRRR----RRRRRRRRRRRRRSGKEEEEEEKKKEEKKKEEEEKKKKE--------GKTK 984
              +++    ++     ++      KE EE +K +E KKKE EEKKK E         K K
Sbjct: 1672 EDKKKAEEAKKAEEDEKKAAEALKKEAEEAKKAEELKKKEAEEKKKAEELKKAEEENKIK 1731

Query: 985  KEEKKKEEEEEKKKKKKEEEKEEEEKKEEEEKEEEEKKRRRIRRKR 1030
             EE KKE EE+KKK ++ ++ EEE+KK    K+EEEKK   IR+++
Sbjct: 1732 AEEAKKEAEEDKKKAEEAKKDEEEKKKIAHLKKEEEKKAEEIRKEK 1777

Length = 2084

>gnl|CDD|173412 PTZ00121, PTZ00121, MAEBL; Provisional

 Score = 82.1 bits (202), Expect = 1e-15
 Identities = 52/213 (24%), Positives = 96/213 (45%), Gaps = 6/213 (2%)

Query: 823  RRKKKEEKKKWKRRGGGRRRRRGKKEEEKKKKKEEEEEGGE--KEEEEGGGGGGRRRRRR 880
             +K  E  K              +K E  +KKKEE ++  +  K++ E        +++ 
Sbjct: 1341 AKKAAEAAKAEAEAAADEAEAAEEKAEAAEKKKEEAKKKADAAKKKAEEKKKADEAKKKA 1400

Query: 881  RRSGKEEEEKKKKEGGGGRRRRRRKKRRRSRRRRSRRRRRRRRRRRRRRRRRRRRRRRRR 940
                K+ +E KK      +    +KK    ++    +++    ++    +++    ++  
Sbjct: 1401 EEDKKKADELKKAAAAKKKADEAKKKAEEKKKADEAKKKAEEAKKADEAKKKAEEAKKAE 1460

Query: 941  RRRRRRRRRRRRRRSGKEEEEEEKKKEEKKKEEEEKKKKEGKTKKEEKKKEEEE----EK 996
              +++    ++   + K+ EE +K  E KKK EE KKK +   K  E KK+ +E    E+
Sbjct: 1461 EAKKKAEEAKKADEAKKKAEEAKKADEAKKKAEEAKKKADEAKKAAEAKKKADEAKKAEE 1520

Query: 997  KKKKKEEEKEEEEKKEEEEKEEEEKKRRRIRRK 1029
             KK  E +K EE KK +E K+ EEKK+    +K
Sbjct: 1521 AKKADEAKKAEEAKKADEAKKAEEKKKADELKK 1553

Length = 2084

>gnl|CDD|237171 PRK12678, PRK12678, transcription termination factor Rho; Provisional

 Score = 80.3 bits (199), Expect = 2e-15
 Identities = 35/225 (15%), Positives = 74/225 (32%), Gaps = 8/225 (3%)

Query: 814  RNRRGRRRRRRKKKEEKKKWKRRGGGRRRRRGKKEE--------EKKKKKEEEEEGGEKE 865
            +  RG                 R   R     ++ E         K +            
Sbjct: 56   KEARGGGAAAAAATPAAPAAAARRAARAAAAARQAEQPAAEAAAAKAEAAPAARAAAAAA 115

Query: 866  EEEGGGGGGRRRRRRRRSGKEEEEKKKKEGGGGRRRRRRKKRRRSRRRRSRRRRRRRRRR 925
             E        + R RR  G+       ++ G G  +   + R  +  R     R  RRRR
Sbjct: 116  AEAASAPEAAQARERRERGEAARRGAARKAGEGGEQPATEARADAAERTEEEERDERRRR 175

Query: 926  RRRRRRRRRRRRRRRRRRRRRRRRRRRRRSGKEEEEEEKKKEEKKKEEEEKKKKEGKTKK 985
              R  R+    R  R RR  R R    R      E+ ++++E  +++  +++ +  +  +
Sbjct: 176  GDREDRQAEAERGERGRREERGRDGDDRDRRDRREQGDRREERGRRDGGDRRGRRRRRDR 235

Query: 986  EEKKKEEEEEKKKKKKEEEKEEEEKKEEEEKEEEEKKRRRIRRKR 1030
             + + ++  E +  +  ++ E    +      + +++ RR     
Sbjct: 236  RDARGDDNREDRGDRDGDDGEGRGGRRGRRFRDRDRRGRRGGDGG 280

Length = 672

>gnl|CDD|173412 PTZ00121, PTZ00121, MAEBL; Provisional

 Score = 81.7 bits (201), Expect = 2e-15
 Identities = 51/223 (22%), Positives = 109/223 (48%), Gaps = 4/223 (1%)

Query: 812  LSRNRRGRRRRRRKKKEEKKKWK--RRGGGRRRRRGKKEEEKKKKKEEEEEGGEKEEEEG 869
              +    ++    KK EE KK    ++   +++    K+ E+ KK EE+++  E ++ E 
Sbjct: 1515 AKKAEEAKKADEAKKAEEAKKADEAKKAEEKKKADELKKAEELKKAEEKKKAEEAKKAEE 1574

Query: 870  GGGGGRRRRRRRRSGKEEEEKKKKEGGGGRRRRRRKKRRRSRRRRSRRRRRRRRRRRRRR 929
                  R+    +  +E   ++  +     ++ + ++ +++   + +    ++    +++
Sbjct: 1575 DKNMALRKAEEAKKAEEARIEEVMKLYEEEKKMKAEEAKKAEEAKIKAEELKKAEEEKKK 1634

Query: 930  RRRRRRRRRRRRRRRRRRRRRRRRRSGKEEEEEEKKKEEKKKEEEEKKKKEGKTKKEEKK 989
              + +++    +++    ++       K  EE +K +E+KKK EE KK +E + K  E  
Sbjct: 1635 VEQLKKKEAEEKKKAEELKKAEEENKIKAAEEAKKAEEDKKKAEEAKKAEEDEKKAAEAL 1694

Query: 990  KEEEEEKKKKKKEEEKEEEEKKEEEE--KEEEEKKRRRIRRKR 1030
            K+E EE KK ++ ++KE EEKK+ EE  K EEE K +    K+
Sbjct: 1695 KKEAEEAKKAEELKKKEAEEKKKAEELKKAEEENKIKAEEAKK 1737

Length = 2084

>gnl|CDD|173412 PTZ00121, PTZ00121, MAEBL; Provisional

 Score = 81.3 bits (200), Expect = 2e-15
 Identities = 53/207 (25%), Positives = 103/207 (49%), Gaps = 2/207 (0%)

Query: 824  RKKKEEKKKWKRRGGGRRRRRGKKEEEKKKKKEEEEEGGEKEEEEGGGGGGRRRRRRRRS 883
             KKKEE KK       +   + K +E KKK +E++++  E ++           +++   
Sbjct: 1370 EKKKEEAKKKADAAKKKAEEKKKADEAKKKAEEDKKKADELKKAAAAKKKADEAKKKAEE 1429

Query: 884  GKEEEEKKKKEGGGGRRRRRRKKRRRSRRRRSRRRRRRRRRRRRRRRRRRRRRRRRRRRR 943
             K+ +E KKK     +    +KK   +++    +++    ++    +++    ++    +
Sbjct: 1430 KKKADEAKKKAEEAKKADEAKKKAEEAKKAEEAKKKAEEAKKADEAKKKAEEAKKADEAK 1489

Query: 944  RRRRRRRRRRRSGKEEEEEEKKKEEKKKEEEEKKKKEGKTKKEEKKKEEEEEKKKKKKEE 1003
            ++    +++    K+  E +KK +E KK EE KK  E K  +E KK +E ++ ++KKK +
Sbjct: 1490 KKAEEAKKKADEAKKAAEAKKKADEAKKAEEAKKADEAKKAEEAKKADEAKKAEEKKKAD 1549

Query: 1004 E--KEEEEKKEEEEKEEEEKKRRRIRR 1028
            E  K EE KK EE+K+ EE K+    +
Sbjct: 1550 ELKKAEELKKAEEKKKAEEAKKAEEDK 1576

Length = 2084

>gnl|CDD|173412 PTZ00121, PTZ00121, MAEBL; Provisional

 Score = 81.3 bits (200), Expect = 2e-15
 Identities = 52/213 (24%), Positives = 102/213 (47%), Gaps = 8/213 (3%)

Query: 825  KKKEEKKKWKRRGGGRRRRRGKKEEEKKKKKEEEEEGGEKEEEEGGGGGGRRRRRRRRS- 883
            KKK E+ K               E E  ++K E  E  ++E ++      ++   ++++ 
Sbjct: 1335 KKKAEEAKKAAEAAKAEAEAAADEAEAAEEKAEAAEKKKEEAKKKADAAKKKAEEKKKAD 1394

Query: 884  --GKEEEEKKKKEGGGGRRRRRRKKRRRSRRRRSRRRRRRRRRRRRRRRRRRRRRRRRRR 941
               K+ EE KKK     +    +KK   ++++   +++    +++    ++    +++  
Sbjct: 1395 EAKKKAEEDKKKADELKKAAAAKKKADEAKKKAEEKKKADEAKKKAEEAKKADEAKKKAE 1454

Query: 942  RRRRRRRRRRRRRSGKEEEEEEKKKEEKKKEEEEKKKKEGKTKKEEKKKEEEEEKKKK-- 999
              ++    +++    K+ +E +KK EE KK +E KKK E   KK ++ K+  E KKK   
Sbjct: 1455 EAKKAEEAKKKAEEAKKADEAKKKAEEAKKADEAKKKAEEAKKKADEAKKAAEAKKKADE 1514

Query: 1000 -KKEEEKE--EEEKKEEEEKEEEEKKRRRIRRK 1029
             KK EE +  +E KK EE K+ +E K+   ++K
Sbjct: 1515 AKKAEEAKKADEAKKAEEAKKADEAKKAEEKKK 1547

Length = 2084

>gnl|CDD|173412 PTZ00121, PTZ00121, MAEBL; Provisional

 Score = 81.0 bits (199), Expect = 2e-15
 Identities = 56/230 (24%), Positives = 112/230 (48%), Gaps = 17/230 (7%)

Query: 812  LSRNRRGRRRRRRKKKEEKKKWK--RRGGGRRRRRGKKEEEKKKKKEEEEEGGEKEEEEG 869
              +    ++    KK EEKKK    ++    ++   KK+ E+ KK EE++    ++ EE 
Sbjct: 1527 AKKAEEAKKADEAKKAEEKKKADELKKAEELKKAEEKKKAEEAKKAEEDKNMALRKAEEA 1586

Query: 870  GGGGGRRRRRRRRSGKEEEEKKKKEGGGGRRRRRRKKRRRSRRRRSRRRRRRRRRRRRRR 929
                  R     +  +EE++ K +E      ++  + + ++   +     +++  + +++
Sbjct: 1587 KKAEEARIEEVMKLYEEEKKMKAEEA-----KKAEEAKIKAEELKKAEEEKKKVEQLKKK 1641

Query: 930  RRRRRRRRRRRRRRRRRRRRRRRRRSGKEEEEEEKKKEEKKKEEEEKKKKEGKTKKEEKK 989
                +++    ++     + +    + K EE+++K +E KK EE+EKK  E   K+ E+ 
Sbjct: 1642 EAEEKKKAEELKKAEEENKIKAAEEAKKAEEDKKKAEEAKKAEEDEKKAAEALKKEAEEA 1701

Query: 990  KEEEEEKKKKKKEEEKEEEEKKEEEE----------KEEEEKKRRRIRRK 1029
            K+ EE KKK+ +E++K EE KK EEE          + EE+KK+    +K
Sbjct: 1702 KKAEELKKKEAEEKKKAEELKKAEEENKIKAEEAKKEAEEDKKKAEEAKK 1751

Length = 2084

>gnl|CDD|236766 PRK10811, rne, ribonuclease E; Reviewed

 Score = 81.2 bits (201), Expect = 2e-15
 Identities = 38/144 (26%), Positives = 82/144 (56%), Gaps = 4/144 (2%)

Query: 886  EEEEKKKKEGGGGRRRRRRKKRRRSRRRRSRRRRRRRRRRRRRRRRRRRRRRRRRRRRRR 945
            +E+   K E    R++ RRK R+ +RR R+ RR  R  R RR  R  R   RR    RR+
Sbjct: 589  QEQPAPKAEAKPERQQDRRKPRQNNRRDRNERRDTRDNRTRREGRENREENRR---NRRQ 645

Query: 946  RRRRRRRRRSGKEEEEEEKKKEEKKKEEEEKKKKEGKTKKEEKKKEEEEEKKKKKKEEEK 1005
             +++    R  ++ E  EK + + ++++  +++++ + + +EK++ ++E K    +E+  
Sbjct: 646  AQQQTAETRESQQAEVTEKARTQDEQQQAPRRERQ-RRRNDEKRQAQQEAKALNVEEQSV 704

Query: 1006 EEEEKKEEEEKEEEEKKRRRIRRK 1029
            +E E++E  ++ +  +K+R++ +K
Sbjct: 705  QETEQEERVQQVQPRRKQRQLNQK 728

Length = 1068

>gnl|CDD|173412 PTZ00121, PTZ00121, MAEBL; Provisional

 Score = 81.0 bits (199), Expect = 3e-15
 Identities = 54/217 (24%), Positives = 108/217 (49%), Gaps = 8/217 (3%)

Query: 819  RRRRRRKKKEEKKKWKRRGGGRRRRRGKKEEEKKKKKEEEEEGGE--KEEEEGGGGGGRR 876
            R+    KK EEKKK       ++    KK +E KKK EE ++  E  K+ EE        
Sbjct: 1278 RKADELKKAEEKKKADE---AKKAEEKKKADEAKKKAEEAKKADEAKKKAEEAKKKADAA 1334

Query: 877  RRRRRRSGKEEEEKKKKEGGGGRRRRRRKKRRRSRRRRSRRRRRRR---RRRRRRRRRRR 933
            +++   + K  E  K +           +++  +  ++    +++    +++   +++  
Sbjct: 1335 KKKAEEAKKAAEAAKAEAEAAADEAEAAEEKAEAAEKKKEEAKKKADAAKKKAEEKKKAD 1394

Query: 934  RRRRRRRRRRRRRRRRRRRRRSGKEEEEEEKKKEEKKKEEEEKKKKEGKTKKEEKKKEEE 993
              +++    +++    ++   + K+ +E +KK EEKKK +E KKK E   K +E KK+ E
Sbjct: 1395 EAKKKAEEDKKKADELKKAAAAKKKADEAKKKAEEKKKADEAKKKAEEAKKADEAKKKAE 1454

Query: 994  EEKKKKKKEEEKEEEEKKEEEEKEEEEKKRRRIRRKR 1030
            E KK ++ +++ EE +K +E +K+ EE K+    +K+
Sbjct: 1455 EAKKAEEAKKKAEEAKKADEAKKKAEEAKKADEAKKK 1491

Length = 2084

>gnl|CDD|236766 PRK10811, rne, ribonuclease E; Reviewed

 Score = 79.3 bits (196), Expect = 6e-15
 Identities = 35/148 (23%), Positives = 76/148 (51%), Gaps = 14/148 (9%)

Query: 885  KEEEEKKKKEGGGGRRRRRRKKRRRSRRRRSRRRRRRRRRRRRRRRRRRRRRRRRRRRRR 944
            K +E+   K           K  R+  RR+ R+  RR R  RR  R  R RR  R  R  
Sbjct: 587  KPQEQPAPKAE--------AKPERQQDRRKPRQNNRRDRNERRDTRDNRTRREGRENREE 638

Query: 945  RRRRRRRRRRSGKEEEEEEKKKEEKKKEEEEKKKKEGKTKKEEKKKEEEEEKKKKKKEEE 1004
             RR RR+ ++   E  E ++ +  +K   ++++++  + +++ ++ +E    K++ ++E 
Sbjct: 639  NRRNRRQAQQQTAETRESQQAEVTEKARTQDEQQQAPRRERQRRRNDE----KRQAQQEA 694

Query: 1005 KEEEEKKEEEEKEEEEKKRRRI--RRKR 1030
            K    +++  ++ E+E++ +++  RRK+
Sbjct: 695  KALNVEEQSVQETEQEERVQQVQPRRKQ 722

Length = 1068

>gnl|CDD|173412 PTZ00121, PTZ00121, MAEBL; Provisional

 Score = 79.8 bits (196), Expect = 7e-15
 Identities = 53/212 (25%), Positives = 104/212 (49%), Gaps = 3/212 (1%)

Query: 819  RRRRRRKKKEEKKKWKRRGGGRRRRRGKKEEEKKKKKEEEEEGGEKEEEEGGGGGGRRRR 878
            ++   +KK +  KK           + K EE+KKK  E ++    K++ +        ++
Sbjct: 1372 KKEEAKKKADAAKKKAEEKKKADEAKKKAEEDKKKADELKKAAAAKKKADEAKKKAEEKK 1431

Query: 879  RRRRSGKEEEEKKKKEGGGGRRRRRRKKRRRSRRRRSRRRRRRRRRRRRRRRRRRRRRRR 938
            +   + K+ EE KK +    ++    KK   ++++    ++    +++    ++    ++
Sbjct: 1432 KADEAKKKAEEAKKADEAK-KKAEEAKKAEEAKKKAEEAKKADEAKKKAEEAKKADEAKK 1490

Query: 939  RRRRRRRRRRRRRRRRSGKEEEEEEKKKEEKKKEEEEKKKKEGKTKKEEKKKEEEEEKKK 998
            +    +++    ++    K++ +E KK EE KK +E KK +E K   E KK EE+++  +
Sbjct: 1491 KAEEAKKKADEAKKAAEAKKKADEAKKAEEAKKADEAKKAEEAKKADEAKKAEEKKKADE 1550

Query: 999  KKKEEE--KEEEEKKEEEEKEEEEKKRRRIRR 1028
             KK EE  K EE+KK EE K+ EE K   +R+
Sbjct: 1551 LKKAEELKKAEEKKKAEEAKKAEEDKNMALRK 1582

Length = 2084

>gnl|CDD|99921 cd05538, POLBc_Pol_II_B, DNA polymerase type-II B subfamily catalytic domain

 Score = 76.8 bits (189), Expect = 8e-15
 Identities = 76/308 (24%), Positives = 112/308 (36%), Gaps = 45/308 (14%)

Query: 495 AYSGGLVLEPKKGFYDKFIILMDFNSLYPSIIQEYNICFTTIPVRMLQDSDITTLCEYLP 554
            + GG       G     I+  D  SLYPSI+  Y IC    P R   DS          
Sbjct: 2   KFEGGYAYVFITGVLGP-IVHADVASLYPSIMLAYRIC----PAR---DS---------- 43

Query: 555 EHQVDTGILPSEIKKLVESRRQVKALMKQPNLSSDLLMQYDIRQKALKLTANSMYGCLGF 614
                 GI  + +K LVE R   K   +     +     +  +Q A K+  NS YG LG 
Sbjct: 44  -----LGIFLALLKYLVELRLAAKESARAAARPA-ERDAFKAKQAAFKVLINSFYGYLGT 97

Query: 615 PNSRFFAQPLAALVTAKGREILLNTKSLVENLNYEVIYGDTDSLMISCNVNDYDSVFKIG 674
               F     AA VT  GRE+L      +       +  DTD +       +        
Sbjct: 98  GLHAFSDPEAAAEVTRLGRELLKLMIRWLRRRGATPVEVDTDGIYFI--PPNGVDTEDEE 155

Query: 675 NQIKSECNK-LYKQLELDIDGVYKYMLLLKKKKYAALSISKLSNGKMICSQEIKGVDVVR 733
            ++  E +  L K + ++ DG Y+ M   K K YA L      +GK+I    +KG     
Sbjct: 156 EELVRELSSTLPKGITVEFDGRYRAMFSYKIKNYALLD----YDGKLI----VKGSAFRS 207

Query: 734 RDWSQLASEAGKFVISQILDEQSYTDYSLDDRLQNIHEHMKKIRTDLDNGFVPLTLLEIT 793
           R       E   F+              L      +H+  +     L +  +P++ L  T
Sbjct: 208 RGIEPFLRE---FLR-------EAVRLLLQGDGAGVHDLYEDYLRRLRSHELPISDLART 257

Query: 794 KQLTKAPE 801
           + L ++PE
Sbjct: 258 ETLKESPE 265

Bacteria contain five DNA polymerases (I, II, III, IV and V). DNA polymerase II (Pol II) is a prototype for the B-family of polymerases. The role of Pol II in a variety of cellular activities, such as repair of DNA damaged by UV irradiation or oxidation has been proved by genetic studies. DNA polymerase III is the main enzyme responsible for replication of the bacterial chromosome; however, In vivo studies have also shown that Pol II is able to participate in chromosomal DNA replication with larger role in lagging-strand replication. Length = 347

>gnl|CDD|173412 PTZ00121, PTZ00121, MAEBL; Provisional

 Score = 79.0 bits (194), Expect = 1e-14
 Identities = 64/245 (26%), Positives = 112/245 (45%), Gaps = 8/245 (3%)

Query: 794  KQLTKAPEGGKVCITQIRLSRNRRGRRRRRRKKKEEKKKWKRRGGGRRRRRGKKEEEKKK 853
            ++L KA E  K    +          R+    KK E+ + +         +  K EE KK
Sbjct: 1555 EELKKAEEKKKAEEAKKAEEDKNMALRKAEEAKKAEEARIEEVMKLYEEEKKMKAEEAKK 1614

Query: 854  KKEEEEEGGE--KEEEEGGGGGGRRRRRRRRSGKEEEEKKKKEGGGGRRRRRRKKRRRSR 911
             +E + +  E  K EEE       +++      K EE KK +E    +     KK    +
Sbjct: 1615 AEEAKIKAEELKKAEEEKKKVEQLKKKEAEEKKKAEELKKAEEENKIKAAEEAKKAEEDK 1674

Query: 912  RRRSRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRS---GKEEEEEEKKKEE 968
            ++    ++     ++     ++     ++    +++    ++++    K EEE + K EE
Sbjct: 1675 KKAEEAKKAEEDEKKAAEALKKEAEEAKKAEELKKKEAEEKKKAEELKKAEEENKIKAEE 1734

Query: 969  KKKEEEEKKKKEGKTKKEEKKKEEEEEKKK---KKKEEEKEEEEKKEEEEKEEEEKKRRR 1025
             KKE EE KKK  + KK+E++K++    KK   KK EE ++E+E   EEE +EE++KRR 
Sbjct: 1735 AKKEAEEDKKKAEEAKKDEEEKKKIAHLKKEEEKKAEEIRKEKEAVIEEELDEEDEKRRM 1794

Query: 1026 IRRKR 1030
               K+
Sbjct: 1795 EVDKK 1799

Length = 2084

>gnl|CDD|173412 PTZ00121, PTZ00121, MAEBL; Provisional

 Score = 78.6 bits (193), Expect = 1e-14
 Identities = 54/211 (25%), Positives = 105/211 (49%), Gaps = 7/211 (3%)

Query: 819  RRRRRRKKKEEKKKWKRRGGGRRRRRGKKEEEKKKKKEEE----EEGGEKEEEEGGGGGG 874
            ++    KK EEKKK       ++    KK +E KKK EE     +   +K EE       
Sbjct: 1290 KKADEAKKAEEKKKADE--AKKKAEEAKKADEAKKKAEEAKKKADAAKKKAEEAKKAAEA 1347

Query: 875  RRRRRRRRSGKEEEEKKKKEGGGGRRRRRRKKRRRSRRRRSRRRRRRRRRRRRRRRRRRR 934
             +      + + E  ++K E    ++   +KK   ++++   +++    +++    +++ 
Sbjct: 1348 AKAEAEAAADEAEAAEEKAEAAEKKKEEAKKKADAAKKKAEEKKKADEAKKKAEEDKKKA 1407

Query: 935  RRRRRRRRRRRRRRRRRRRRSGKEEEEEEKKK-EEKKKEEEEKKKKEGKTKKEEKKKEEE 993
               ++    +++    +++   K++ +E KKK EE KK +E KKK E   K EE KK+ E
Sbjct: 1408 DELKKAAAAKKKADEAKKKAEEKKKADEAKKKAEEAKKADEAKKKAEEAKKAEEAKKKAE 1467

Query: 994  EEKKKKKKEEEKEEEEKKEEEEKEEEEKKRR 1024
            E KK  + +++ EE +K +E +K+ EE K++
Sbjct: 1468 EAKKADEAKKKAEEAKKADEAKKKAEEAKKK 1498

Length = 2084

>gnl|CDD|173412 PTZ00121, PTZ00121, MAEBL; Provisional

 Score = 77.5 bits (190), Expect = 3e-14
 Identities = 52/219 (23%), Positives = 93/219 (42%), Gaps = 6/219 (2%)

Query: 811  RLSRNRRGRRRRRRKKKEEKKKWKRRGGGRRRRRGKKEEEKKKKKEEEEEGGEKEEEEGG 870
            +    R+    +R +   + +  ++    R+    KK E  +K +E  +    ++ E+  
Sbjct: 1141 KAEEARKAEDAKRVEIARKAEDARKAEEARKAEDAKKAEAARKAEEVRKAEELRKAEDAR 1200

Query: 871  GGGGRRR----RRRRRSGKEEEEKKKKEGGGGRRRRRRKKRRRSRRRRSRRRRRRRRRRR 926
                 R+    R+   + K E+ KK +     +    +K    +++    R     R+  
Sbjct: 1201 KAEAARKAEEERKAEEARKAEDAKKAEAVK--KAEEAKKDAEEAKKAEEERNNEEIRKFE 1258

Query: 927  RRRRRRRRRRRRRRRRRRRRRRRRRRRRSGKEEEEEEKKKEEKKKEEEEKKKKEGKTKKE 986
              R     RR+   +    R+    ++   K++ +E KK EEKKK +E KKK E   K +
Sbjct: 1259 EARMAHFARRQAAIKAEEARKADELKKAEEKKKADEAKKAEEKKKADEAKKKAEEAKKAD 1318

Query: 987  EKKKEEEEEKKKKKKEEEKEEEEKKEEEEKEEEEKKRRR 1025
            E KK+ EE KKK    ++K EE KK  E  + E +    
Sbjct: 1319 EAKKKAEEAKKKADAAKKKAEEAKKAAEAAKAEAEAAAD 1357

Length = 2084

>gnl|CDD|173412 PTZ00121, PTZ00121, MAEBL; Provisional

 Score = 76.7 bits (188), Expect = 5e-14
 Identities = 57/199 (28%), Positives = 100/199 (50%), Gaps = 13/199 (6%)

Query: 826  KKEEKKKWKRRGGGRRRRRGKKEEEKKKKKEEEEEGGE---KEEEEGGGGGGRRRRRRRR 882
            KK E+ K K     +     KK E+ KKK+ EE++  E   K EEE       + +    
Sbjct: 1613 KKAEEAKIKAEELKKAEEEKKKVEQLKKKEAEEKKKAEELKKAEEEN------KIKAAEE 1666

Query: 883  SGKEEEEKKKKEGGGGRRRRRRKKRRRSRRRRSRRRRRRRRRRRRRRRRRRRRRRRRRRR 942
            + K EE+KKK E      ++  +  +++     +     ++    +++    +++    +
Sbjct: 1667 AKKAEEDKKKAE----EAKKAEEDEKKAAEALKKEAEEAKKAEELKKKEAEEKKKAEELK 1722

Query: 943  RRRRRRRRRRRRSGKEEEEEEKKKEEKKKEEEEKKKKEGKTKKEEKKKEEEEEKKKKKKE 1002
            +     + +   + KE EE++KK EE KK+EEEKKK     K+EEKK EE  ++K+   E
Sbjct: 1723 KAEEENKIKAEEAKKEAEEDKKKAEEAKKDEEEKKKIAHLKKEEEKKAEEIRKEKEAVIE 1782

Query: 1003 EEKEEEEKKEEEEKEEEEK 1021
            EE +EE++K   E +++ K
Sbjct: 1783 EELDEEDEKRRMEVDKKIK 1801

Length = 2084

>gnl|CDD|173412 PTZ00121, PTZ00121, MAEBL; Provisional

 Score = 76.7 bits (188), Expect = 6e-14
 Identities = 58/221 (26%), Positives = 104/221 (47%), Gaps = 15/221 (6%)

Query: 824  RKKKEEKKK---WKRRGGGRRRRRGKKEEEKKKKKEEEEEGGEKEEEEGGGGGGRRRRRR 880
            +K  E KKK    K+    ++    KK EE KK  E ++   +K+ +E       ++   
Sbjct: 1503 KKAAEAKKKADEAKKAEEAKKADEAKKAEEAKKADEAKKAEEKKKADELKKAEELKKAEE 1562

Query: 881  RRSGKEEEEKKKKEGGGGRRRRRRKKRRRSRRRRSRRRRRRRRRRRRRRRRRRRRRRRRR 940
            ++  +E ++ ++ +    R+    KK   +R     +     ++ +    ++    + + 
Sbjct: 1563 KKKAEEAKKAEEDKNMALRKAEEAKKAEEARIEEVMKLYEEEKKMKAEEAKKAEEAKIKA 1622

Query: 941  RRRRRRRRRRRRRRSGKEEEEEEKKKEEKKKEEEE----KKKKEGKTKKEEKKKEEE--- 993
               ++    +++    K++E EEKKK E+ K+ EE    K  +E K  +E+KKK EE   
Sbjct: 1623 EELKKAEEEKKKVEQLKKKEAEEKKKAEELKKAEEENKIKAAEEAKKAEEDKKKAEEAKK 1682

Query: 994  EEKKKKKKEEE--KEEEEKKEEEE---KEEEEKKRRRIRRK 1029
             E+ +KK  E   KE EE K+ EE   KE EEKK+    +K
Sbjct: 1683 AEEDEKKAAEALKKEAEEAKKAEELKKKEAEEKKKAEELKK 1723

Length = 2084

>gnl|CDD|173412 PTZ00121, PTZ00121, MAEBL; Provisional

 Score = 76.7 bits (188), Expect = 6e-14
 Identities = 40/205 (19%), Positives = 97/205 (47%), Gaps = 3/205 (1%)

Query: 823  RRKKKEEKKKWKRRGGGRRRRRGKKEEEKKKKKEEEEEGGEKEEEEGGGGGGRRRRRRRR 882
            R+ ++  K +  R+    R+   +++ E+ +K E+ ++    ++ E         ++   
Sbjct: 1188 RKAEELRKAEDARKAEAARKAEEERKAEEARKAEDAKKAEAVKKAEEAKKDAEEAKKAEE 1247

Query: 883  SGKEEEEKKKKEGGGGRRRRRRKKRRRSRRRRSRRRRRRRRRRRRRRRRRRRRRRRRRRR 942
                EE +K +E       RR+   +    R++   ++   +++    ++   +++    
Sbjct: 1248 ERNNEEIRKFEEARMAHFARRQAAIKAEEARKADELKKAEEKKKADEAKKAEEKKKADEA 1307

Query: 943  RRRRRRRRRRRRSGKEEEEEEKKKEEKKKEEEEKKKKEGKTKKEEKKKEEEEEKKKKKK- 1001
            +++    ++   + K+ EE +KK +  KK+ EE KK     K E +   +E E  ++K  
Sbjct: 1308 KKKAEEAKKADEAKKKAEEAKKKADAAKKKAEEAKKAAEAAKAEAEAAADEAEAAEEKAE 1367

Query: 1002 --EEEKEEEEKKEEEEKEEEEKKRR 1024
              E++KEE +KK +  K++ E+K++
Sbjct: 1368 AAEKKKEEAKKKADAAKKKAEEKKK 1392

Length = 2084

>gnl|CDD|173412 PTZ00121, PTZ00121, MAEBL; Provisional

 Score = 75.9 bits (186), Expect = 9e-14
 Identities = 45/222 (20%), Positives = 99/222 (44%), Gaps = 9/222 (4%)

Query: 811  RLSRNRRGRRRRRRKKKEEKKKWKRRGGGRRRRRGKKEEEKKKKKEEEEEGGEKEEEEGG 870
            +    R+    R+ ++  + +  ++    R+    +K EE +K ++ ++    K+ EE  
Sbjct: 1177 KAEAARKAEEVRKAEELRKAEDARKAEAARKAEEERKAEEARKAEDAKKAEAVKKAEEA- 1235

Query: 871  GGGGRRRRRRRRSGKEEEEKKKKEGGGGRRRRRRKKRRRSRRRRSRRRRRRRRRRRRRRR 930
                  ++    + K EEE+  +E       R     RR    ++   R+    ++   +
Sbjct: 1236 ------KKDAEEAKKAEEERNNEEIRKFEEARMAHFARRQAAIKAEEARKADELKKAEEK 1289

Query: 931  RRRRRRRRRRRRRRRRRRRRRRRRSGKEEEEEEKKKEEKKKEEEEKKKKEGKTKKEEKKK 990
            ++    ++   +++    +++   + K +E ++K +E KKK +  KKK E   K  E  K
Sbjct: 1290 KKADEAKKAEEKKKADEAKKKAEEAKKADEAKKKAEEAKKKADAAKKKAEEAKKAAEAAK 1349

Query: 991  EEEEEKKK--KKKEEEKEEEEKKEEEEKEEEEKKRRRIRRKR 1030
             E E      +  EE+ E  EKK+EE K++ +  +++   K+
Sbjct: 1350 AEAEAAADEAEAAEEKAEAAEKKKEEAKKKADAAKKKAEEKK 1391

Length = 2084

>gnl|CDD|173412 PTZ00121, PTZ00121, MAEBL; Provisional

 Score = 75.6 bits (185), Expect = 1e-13
 Identities = 52/241 (21%), Positives = 112/241 (46%), Gaps = 25/241 (10%)

Query: 809  QIRLSRNRRGRRRRRRKKKEEKKKWKRRGGGRRRRRGKKEEEKKKKKEEEEEGGEKEEEE 868
            ++R + + R     R+ ++E K +  R+    ++    K+ E+ KK  EE +  E+E   
Sbjct: 1192 ELRKAEDARKAEAARKAEEERKAEEARKAEDAKKAEAVKKAEEAKKDAEEAKKAEEERNN 1251

Query: 869  GGGGGGRRRR-----RRRRSGKEEEEKKKKEGGGGRRRRRRKKRRRSRRRRSRRRRRRRR 923
                     R     RR+ + K EE +K  E      +++  + +++  ++     +++ 
Sbjct: 1252 EEIRKFEEARMAHFARRQAAIKAEEARKADELKKAEEKKKADEAKKAEEKKKADEAKKKA 1311

Query: 924  RRRRRRRRRRRRRRRRRRR----RRRRRRRRRRRRSGKEEEE----------------EE 963
               ++    +++    +++    +++    ++   + K E E                E+
Sbjct: 1312 EEAKKADEAKKKAEEAKKKADAAKKKAEEAKKAAEAAKAEAEAAADEAEAAEEKAEAAEK 1371

Query: 964  KKKEEKKKEEEEKKKKEGKTKKEEKKKEEEEEKKKKKKEEEKEEEEKKEEEEKEEEEKKR 1023
            KK+E KKK +  KKK E K K +E KK+ EE+KKK  + ++    +KK +E K++ E+K+
Sbjct: 1372 KKEEAKKKADAAKKKAEEKKKADEAKKKAEEDKKKADELKKAAAAKKKADEAKKKAEEKK 1431

Query: 1024 R 1024
            +
Sbjct: 1432 K 1432

Length = 2084

>gnl|CDD|173412 PTZ00121, PTZ00121, MAEBL; Provisional

 Score = 75.6 bits (185), Expect = 1e-13
 Identities = 52/224 (23%), Positives = 105/224 (46%), Gaps = 12/224 (5%)

Query: 807  ITQIRLSRNRRGRRRRRRKKKEEKKKWKRRGGGRRRRRGKKEEEKKKKKEEEEEGGEKEE 866
            I +   +R     RR+   K EE +K              K+ E+KKK +E ++  EK++
Sbjct: 1254 IRKFEEARMAHFARRQAAIKAEEARKADEL----------KKAEEKKKADEAKKAEEKKK 1303

Query: 867  EEGGGGGGRRRRRRRRSGKEEEEKKKKEGGGGRRRRRRKKRRRSRRRRSRRRRRRRRRRR 926
             +         ++   + K+ EE KKK     ++    KK   + +  +           
Sbjct: 1304 ADEAKKKAEEAKKADEAKKKAEEAKKKADAAKKKAEEAKKAAEAAKAEAEAAADEAEAAE 1363

Query: 927  RRRRRRRRRRRRRRRRRRRRRRRRRRRRSGKEEEEEEKKKEEKKKEEEEKKKKEGKTKKE 986
             +     +++   +++    +++   ++  K +E ++K +E+KKK +E KK    K K +
Sbjct: 1364 EKAEAAEKKKEEAKKKADAAKKKAEEKK--KADEAKKKAEEDKKKADELKKAAAAKKKAD 1421

Query: 987  EKKKEEEEEKKKKKKEEEKEEEEKKEEEEKEEEEKKRRRIRRKR 1030
            E KK+ EE+KK  + +++ EE +K +E +K+ EE K+    +K+
Sbjct: 1422 EAKKKAEEKKKADEAKKKAEEAKKADEAKKKAEEAKKAEEAKKK 1465

Length = 2084

>gnl|CDD|173412 PTZ00121, PTZ00121, MAEBL; Provisional

 Score = 75.2 bits (184), Expect = 2e-13
 Identities = 62/231 (26%), Positives = 106/231 (45%), Gaps = 19/231 (8%)

Query: 819  RRRRRRKKKEEKKKWKRRGGGRRRRRGKKEEEKKKKKEEEEEGGEKEEEEGGGGGGRRRR 878
            ++    KKK ++ K K     +     KK EE KK  E +++  E ++ E         +
Sbjct: 1411 KKAAAAKKKADEAKKKAEEKKKADEAKKKAEEAKKADEAKKKAEEAKKAEEAKKKAEEAK 1470

Query: 879  RRRRSGKEEEEKKKKEGGGGRRRRRRKKRRRSRRRRSRRRRRRRRRRRRRRRRRRRRRRR 938
            +   + K+ EE KK +    +    +KK   +++    +++    ++    ++    ++ 
Sbjct: 1471 KADEAKKKAEEAKKADEAKKKAEEAKKKADEAKKAAEAKKKADEAKKAEEAKKADEAKKA 1530

Query: 939  RRRRRRRRRRRRRRRRSGKE--EEEEEKKKEEKKKEEEEKKKKEGKT----------KKE 986
               ++    ++   ++   E  + EE KK EEKKK EE KK +E K           K E
Sbjct: 1531 EEAKKADEAKKAEEKKKADELKKAEELKKAEEKKKAEEAKKAEEDKNMALRKAEEAKKAE 1590

Query: 987  EKKKEE-----EEEKKKKKKEEEKEEEEKKEEEE--KEEEEKKRRRIRRKR 1030
            E + EE     EEEKK K +E +K EE K + EE  K EEEKK+    +K+
Sbjct: 1591 EARIEEVMKLYEEEKKMKAEEAKKAEEAKIKAEELKKAEEEKKKVEQLKKK 1641

Length = 2084

>gnl|CDD|173412 PTZ00121, PTZ00121, MAEBL; Provisional

 Score = 74.8 bits (183), Expect = 2e-13
 Identities = 51/211 (24%), Positives = 99/211 (46%), Gaps = 4/211 (1%)

Query: 819  RRRRRRKKKEEKKKWKRRGGGRRRRRGKKEEEKKKKKEEEEEGGEKEEEEGGGGGGRRRR 878
            ++   +KK +E KK       +     K    KKK  E +++  EK++ +         +
Sbjct: 1385 KKAEEKKKADEAKKKAEEDKKKADELKKAAAAKKKADEAKKKAEEKKKADEAKKKAEEAK 1444

Query: 879  RRRRSGKEEEEKKKKEGGGGRRRRRRKKRRRSRRRRSRRRRRRRRRRRRRRRRRRRRRRR 938
            +   + K+ EE KK E    +++    K+    ++++   ++    +++    +++    
Sbjct: 1445 KADEAKKKAEEAKKAEEA--KKKAEEAKKADEAKKKAEEAKKADEAKKKAEEAKKKADEA 1502

Query: 939  RRRRRRRRRRRRRRRRSGKEEEEEEKKKEEKKKEEEEKKKKEGKTKKEEKKKEE--EEEK 996
            ++    +++    ++    ++ +E KK EE KK +E KK +E K   E KK EE  + E+
Sbjct: 1503 KKAAEAKKKADEAKKAEEAKKADEAKKAEEAKKADEAKKAEEKKKADELKKAEELKKAEE 1562

Query: 997  KKKKKEEEKEEEEKKEEEEKEEEEKKRRRIR 1027
            KKK +E +K EE+K     K EE KK    R
Sbjct: 1563 KKKAEEAKKAEEDKNMALRKAEEAKKAEEAR 1593

Length = 2084

>gnl|CDD|173412 PTZ00121, PTZ00121, MAEBL; Provisional

 Score = 73.6 bits (180), Expect = 5e-13
 Identities = 52/219 (23%), Positives = 101/219 (46%), Gaps = 12/219 (5%)

Query: 819  RRRRRRKKKEEKKKWKRRGGGRRRRRGKKEEEKKKKKEEEEEGGEKEEEEGGGGGGRRRR 878
            +    R  +E +K  + R     RR+   + E+ +K +E ++  EK++ +       +++
Sbjct: 1244 KAEEERNNEEIRKFEEARMAHFARRQAAIKAEEARKADELKKAEEKKKADEAKKAEEKKK 1303

Query: 879  RRRRSGKEEEEKKKKEGGGGRRRRRRKKRRRSRRRRSRRRRRRRRRRRRRRRRRRRRRRR 938
                  K EE KK  E     +++  + ++++   + +    ++     +          
Sbjct: 1304 ADEAKKKAEEAKKADEA----KKKAEEAKKKADAAKKKAEEAKKAAEAAKAEAEAAADEA 1359

Query: 939  RRRRRRRRRRRRRRRRSGKEEEEEEKKKEEKKKEEEEKKK-KEGKTKKEEKKKEEEEEKK 997
                 +     +++  + K+ +  +KK EEKKK +E KKK +E K K +E KK    +KK
Sbjct: 1360 EAAEEKAEAAEKKKEEAKKKADAAKKKAEEKKKADEAKKKAEEDKKKADELKKAAAAKKK 1419

Query: 998  ----KKKKEEEKEEEE---KKEEEEKEEEEKKRRRIRRK 1029
                KKK EE+K+ +E   K EE +K +E KK+    +K
Sbjct: 1420 ADEAKKKAEEKKKADEAKKKAEEAKKADEAKKKAEEAKK 1458

Length = 2084

>gnl|CDD|173412 PTZ00121, PTZ00121, MAEBL; Provisional

 Score = 72.9 bits (178), Expect = 8e-13
 Identities = 56/234 (23%), Positives = 101/234 (43%), Gaps = 14/234 (5%)

Query: 811  RLSRNRRGRRRRRRKKKEEKKKWKRRGGGRRRRRGKKEEEKKKKKEEEE-EGGEKEEEEG 869
            R+   R+    R+ ++  + +  K+    R+    +K EE +K ++  + E   K EEE 
Sbjct: 1153 RVEIARKAEDARKAEEARKAEDAKKAEAARKAEEVRKAEELRKAEDARKAEAARKAEEER 1212

Query: 870  GGGGGRRRRRRRRSG--KEEEEKKKKEGGGGRRRRRRKKRRRSRRRRSRRRRRRRRRRRR 927
                 R+    +++   K+ EE KK      +    R      +   +R     RR+   
Sbjct: 1213 KAEEARKAEDAKKAEAVKKAEEAKKDAEEAKKAEEERNNEEIRKFEEARMAHFARRQAAI 1272

Query: 928  RRRRRRRRRRRRRRRRRRRRRRRRRRRSGKEEEEEEKKKEEKKKEEEEKKKKEGKTKK-- 985
            +    R+    ++   +++    ++    K+ +E +KK EE KK +E KKK E   KK  
Sbjct: 1273 KAEEARKADELKKAEEKKKADEAKKAEEKKKADEAKKKAEEAKKADEAKKKAEEAKKKAD 1332

Query: 986  -------EEKKKEE--EEEKKKKKKEEEKEEEEKKEEEEKEEEEKKRRRIRRKR 1030
                   E KK  E  + E +    E E  EE+ +  E+K+EE KK+    +K+
Sbjct: 1333 AAKKKAEEAKKAAEAAKAEAEAAADEAEAAEEKAEAAEKKKEEAKKKADAAKKK 1386

Length = 2084

>gnl|CDD|233503 TIGR01642, U2AF_lg, U2 snRNP auxilliary factor, large subunit, splicing factor

 Score = 71.1 bits (174), Expect = 1e-12
 Identities = 36/117 (30%), Positives = 47/117 (40%), Gaps = 6/117 (5%)

Query: 875 RRRRRRRRSGKEEEEKKKKEGGGGRRRRRRKKRRRSRRRRSRRRRRRRRRRRRRRRRRRR 934
           R     R   K     + +     RRR R + R R R RRSR R  R   R R RRR   
Sbjct: 1   RDEEPDREREKSRGRDRDRSSERPRRRSRDRSRFRDRHRRSRERSYREDSRPRDRRRYDS 60

Query: 935 RRRR------RRRRRRRRRRRRRRRRSGKEEEEEEKKKEEKKKEEEEKKKKEGKTKK 985
           R  R       RR R R RRR R  RS ++     + +    +  ++ KK+     K
Sbjct: 61  RSPRSLRYSSVRRSRDRPRRRSRSVRSIEQHRRRLRDRSPSNQWRKDDKKRSLWDIK 117

These splicing factors consist of an N-terminal arginine-rich low complexity domain followed by three tandem RNA recognition motifs (pfam00076). The well-characterized members of this family are auxilliary components of the U2 small nuclear ribonuclearprotein splicing factor (U2AF). These proteins are closely related to the CC1-like subfamily of splicing factors (TIGR01622). Members of this subfamily are found in plants, metazoa and fungi. Length = 509

>gnl|CDD|173412 PTZ00121, PTZ00121, MAEBL; Provisional

 Score = 70.9 bits (173), Expect = 3e-12
 Identities = 56/238 (23%), Positives = 108/238 (45%), Gaps = 7/238 (2%)

Query: 797  TKAPEGGKVCITQIRLSRNRRGRRRRRRKKKEEKKKWKRRGGGRRRRRGKKEEEKKKKKE 856
             KA E  K      +    R+    R+ ++  + +  KR    R+    +K EE +K ++
Sbjct: 1115 RKAEEAKKKAEDARKAEEARKAEDARKAEEARKAEDAKRVEIARKAEDARKAEEARKAED 1174

Query: 857  EEEEGGEKEEEEGGGGGGRRR----RRRRRSGKEEEEKKKKEGGGGRRRRRRKKRRRSRR 912
             ++    ++ EE       R+    R+   + K EEE+K +E    R+    KK    ++
Sbjct: 1175 AKKAEAARKAEEVRKAEELRKAEDARKAEAARKAEEERKAEEA---RKAEDAKKAEAVKK 1231

Query: 913  RRSRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRSGKEEEEEEKKKEEKKKE 972
                ++     ++    R     R+    R     RR+   ++ +  + +E KK E+KK+
Sbjct: 1232 AEEAKKDAEEAKKAEEERNNEEIRKFEEARMAHFARRQAAIKAEEARKADELKKAEEKKK 1291

Query: 973  EEEKKKKEGKTKKEEKKKEEEEEKKKKKKEEEKEEEEKKEEEEKEEEEKKRRRIRRKR 1030
             +E KK E K K +E KK+ EE KK  + +++ EE +KK +  K++ E+ ++     +
Sbjct: 1292 ADEAKKAEEKKKADEAKKKAEEAKKADEAKKKAEEAKKKADAAKKKAEEAKKAAEAAK 1349

Length = 2084

>gnl|CDD|219953 pfam08648, DUF1777, Protein of unknown function (DUF1777)

 Score = 64.9 bits (158), Expect = 4e-12
 Identities = 46/113 (40%), Positives = 57/113 (50%), Gaps = 8/113 (7%)

Query: 896  GGGRRRRRRKKRRRSRRR-RSRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRR 954
            G  R R  R+ RRR R R R RR RRR R R R R RRRR R R   R RR R  RR R 
Sbjct: 2    GRSRSRSPRRSRRRGRSRSRDRRERRRERSRSRERDRRRRSRSRSPHRSRRSRSPRRHRS 61

Query: 955  SGKEEEEEEKKKEEKKKEEEEKKKKEGKTKKEEKKKEEEEEKKKKKKEEEKEE 1007
              +       +K E+ K+  E KK+       E++K  +EE  + K +EE E 
Sbjct: 62   RSRSPSRRRDRKRERDKDAREPKKR-------ERQKLIKEEDLEGKSDEEVEM 107

This is a family of eukaryotic proteins of unknown function. Some of the proteins in this family are putative nucleic acid binding proteins. Length = 158

>gnl|CDD|217301 pfam02956, TT_ORF1, TT viral orf 1

 Score = 69.2 bits (170), Expect = 5e-12
 Identities = 43/133 (32%), Positives = 46/133 (34%), Gaps = 78/133 (58%)

Query: 811 RLSRNRRGRRRRRRKKKEEKKKWKRRGGGRRRRRGKKEEEKKKKKEEEEEGGEKEEEEGG 870
           R  R  RGRRRRRR                                              
Sbjct: 8   RRRRRWRGRRRRRR---------------------------------------------- 21

Query: 871 GGGGRRRRRRRRSGKEEEEKKKKEGGGGRRRRRRKKRRRSRRRRSRRRRRRRRRRRRRRR 930
               RRR RRRR                            RRRR RRRRR RRRRRRRRR
Sbjct: 22  ----RRRARRRR----------------------------RRRRVRRRRRGRRRRRRRRR 49

Query: 931 RRRRRRRRRRRRR 943
           RRRRRRR+R++  
Sbjct: 50  RRRRRRRKRKKLI 62

TT virus (TTV), isolated initially from a Japanese patient with hepatitis of unknown aetiology, has since been found to infect both healthy and diseased individuals and numerous prevalence studies have raised questions about its role in unexplained hepatitis. ORF1 is a large 750 residue protein. The N-terminal half of this protein corresponds to the capsid protein. Length = 525

>gnl|CDD|221491 pfam12254, DNA_pol_alpha_N, DNA polymerase alpha subunit p180 N terminal

 Score = 61.1 bits (149), Expect = 7e-12
 Identities = 29/67 (43%), Positives = 43/67 (64%), Gaps = 3/67 (4%)

Query: 106 FQKLKDLKGQGVKHKYEFTADE--NVYEEVSEKEYTERVLKR-QEDDWIDDDGGDGYVED 162
             KL+  +  G K   E+  +E  ++Y+EV E+EY + V +R   DD+I DD G+GYV+D
Sbjct: 1   LAKLRAAREGGKKRLDEYEVEEEKDIYDEVDEEEYRKIVRQRLLNDDFIVDDDGEGYVDD 60

Query: 163 GREIFDD 169
           GRE +DD
Sbjct: 61  GREEWDD 67

This domain family is found in eukaryotes, and is approximately 70 amino acids in length. The family is found in association with pfam00136, pfam08996, pfam03104. This family is the N terminal of DNA polymerase alpha subunit p180 protein. The N terminal contains the catalytic region of the alpha subunit. Length = 67

>gnl|CDD|220648 pfam10243, MIP-T3, Microtubule-binding protein MIP-T3

 Score = 68.4 bits (167), Expect = 9e-12
 Identities = 37/186 (19%), Positives = 83/186 (44%), Gaps = 22/186 (11%)

Query: 845  GKKEEEKKKKKEEEEEGGEKEEEEGGGGGGRRRRRRRRSGKEEEEKKKKEGGGGRRRRRR 904
            G K    K K  +E +    +EEE                      K+KE     +++++
Sbjct: 84   GSKGPAAKTKPAKEPKNESGKEEE----------------------KEKEQVKEEKKKKK 121

Query: 905  KKRRRSRRRRSRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRSGKEEEEEEK 964
            +K +   + R  +   + +R  + + + + ++    R R   ++R R R   + ++  +K
Sbjct: 122  EKPKEEPKDRKPKEEAKEKRPPKEKEKEKEKKVEEPRDREEEKKRERVRAKSRPKKPPKK 181

Query: 965  KKEEKKKEEEEKKKKEGKTKKEEKKKEEEEEKKKKKKEEEKEEEEKKEEEEKEEEEKKRR 1024
            K   KKKE  E++K+    ++  K K EE +  +++++EE + ++++      EE++ R+
Sbjct: 182  KPPNKKKEPPEEEKQRQAAREAVKGKPEEPDVNEEREKEEDDGKDRETTTSPMEEDESRQ 241

Query: 1025 RIRRKR 1030
                 R
Sbjct: 242  SSEISR 247

This protein, which interacts with both microtubules and TRAF3 (tumour necrosis factor receptor-associated factor 3), is conserved from worms to humans. The N-terminal region is the microtubule binding domain and is well-conserved; the C-terminal 100 residues, also well-conserved, constitute the coiled-coil region which binds to TRAF3. The central region of the protein is rich in lysine and glutamic acid and carries KKE motifs which may also be necessary for tubulin-binding, but this region is the least well-conserved. Length = 506

>gnl|CDD|233503 TIGR01642, U2AF_lg, U2 snRNP auxilliary factor, large subunit, splicing factor

 Score = 68.0 bits (166), Expect = 1e-11
 Identities = 35/114 (30%), Positives = 47/114 (41%)

Query: 857 EEEEGGEKEEEEGGGGGGRRRRRRRRSGKEEEEKKKKEGGGGRRRRRRKKRRRSRRRRSR 916
           +EE   E+E+  G        R RRRS      + +      R  R   + R  RR  SR
Sbjct: 2   DEEPDREREKSRGRDRDRSSERPRRRSRDRSRFRDRHRRSRERSYREDSRPRDRRRYDSR 61

Query: 917 RRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRSGKEEEEEEKKKEEKK 970
             R  R    RR R R RRR R  R   + RRR R R    +  +++KK+    
Sbjct: 62  SPRSLRYSSVRRSRDRPRRRSRSVRSIEQHRRRLRDRSPSNQWRKDDKKRSLWD 115

These splicing factors consist of an N-terminal arginine-rich low complexity domain followed by three tandem RNA recognition motifs (pfam00076). The well-characterized members of this family are auxilliary components of the U2 small nuclear ribonuclearprotein splicing factor (U2AF). These proteins are closely related to the CC1-like subfamily of splicing factors (TIGR01622). Members of this subfamily are found in plants, metazoa and fungi. Length = 509

>gnl|CDD|217037 pfam02443, Circo_capsid, Circovirus capsid protein

 Score = 65.5 bits (160), Expect = 1e-11
 Identities = 26/41 (63%), Positives = 27/41 (65%)

Query: 916 RRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRSG 956
           R R RRR RR RRRRRRRR  RRR RRRR    RRR R + 
Sbjct: 1   RFRIRRRYRRPRRRRRRRRHWRRRYRRRRLHINRRRHRTNR 41

Circoviruses are small circular single stranded viruses. This family is the capsid protein from viruses such as porcine circovirus and beak and feather disease virus. These proteins are about 220 amino acids long. Length = 237

>gnl|CDD|233496 TIGR01622, SF-CC1, splicing factor, CC1-like family

 Score = 68.0 bits (166), Expect = 1e-11
 Identities = 34/86 (39%), Positives = 40/86 (46%)

Query: 877 RRRRRRSGKEEEEKKKKEGGGGRRRRRRKKRRRSRRRRSRRRRRRRRRRRRRRRRRRRRR 936
           R R R  G+   + ++ + G  R RRR + R RSRRRR R   R RR R R R   R  R
Sbjct: 1   RYRDRERGRLRNDTRRSDKGRERSRRRSRSRDRSRRRRDRDYYRGRRGRSRSRSPNRYYR 60

Query: 937 RRRRRRRRRRRRRRRRRRSGKEEEEE 962
            R  R  RR  RR  R       E E
Sbjct: 61  PRGDRSYRRDDRRSGRNTKEPLTEAE 86

This model represents a subfamily of RNA splicing factors including the Pad-1 protein (N. crassa), CAPER (M. musculus) and CC1.3 (H.sapiens). These proteins are characterized by an N-terminal arginine-rich, low complexity domain followed by three (or in the case of 4 H. sapiens paralogs, two) RNA recognition domains (rrm: pfam00706). These splicing factors are closely related to the U2AF splicing factor family (TIGR01642). A homologous gene from Plasmodium falciparum was identified in the course of the analysis of that genome at TIGR and was included in the seed. Length = 457

>gnl|CDD|219953 pfam08648, DUF1777, Protein of unknown function (DUF1777)

 Score = 63.0 bits (153), Expect = 2e-11
 Identities = 40/99 (40%), Positives = 53/99 (53%)

Query: 899 RRRRRRKKRRRSRRRRSRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRSGKE 958
           R RRR + R R RR R R R R R R RRRR R R   R RR R  RR R R R  S + 
Sbjct: 11  RSRRRGRSRSRDRRERRRERSRSRERDRRRRSRSRSPHRSRRSRSPRRHRSRSRSPSRRR 70

Query: 959 EEEEEKKKEEKKKEEEEKKKKEGKTKKEEKKKEEEEEKK 997
           + + E+ K+ ++ ++ E++K   +   E K  EE E  K
Sbjct: 71  DRKRERDKDAREPKKRERQKLIKEEDLEGKSDEEVEMMK 109

This is a family of eukaryotic proteins of unknown function. Some of the proteins in this family are putative nucleic acid binding proteins. Length = 158

>gnl|CDD|220648 pfam10243, MIP-T3, Microtubule-binding protein MIP-T3

 Score = 67.2 bits (164), Expect = 2e-11
 Identities = 37/203 (18%), Positives = 84/203 (41%), Gaps = 7/203 (3%)

Query: 825  KKKEEKKKWKRRGGGRRRRRGKKEEEKKKKKEEEEEGGEKEEEEGGGGGGRRRRRRRRSG 884
            K  +E K    +   + + + K+E++KKK+K +EE    K +EE        + +R    
Sbjct: 93   KPAKEPKNESGKEEEKEKEQVKEEKKKKKEKPKEEPKDRKPKEE-------AKEKRPPKE 145

Query: 885  KEEEEKKKKEGGGGRRRRRRKKRRRSRRRRSRRRRRRRRRRRRRRRRRRRRRRRRRRRRR 944
            KE+E++KK E    R   ++++R R++ R  +  +++   +++      ++R+  R   +
Sbjct: 146  KEKEKEKKVEEPRDREEEKKRERVRAKSRPKKPPKKKPPNKKKEPPEEEKQRQAAREAVK 205

Query: 945  RRRRRRRRRRSGKEEEEEEKKKEEKKKEEEEKKKKEGKTKKEEKKKEEEEEKKKKKKEEE 1004
             +          ++EE++ K +E      EE + ++            ++          
Sbjct: 206  GKPEEPDVNEEREKEEDDGKDRETTTSPMEEDESRQSSEISRRSSSSLKKPDPSPSMASP 265

Query: 1005 KEEEEKKEEEEKEEEEKKRRRIR 1027
            +  E  K  E +     +    R
Sbjct: 266  ETRESSKRTETRPRTSLRPPSAR 288

This protein, which interacts with both microtubules and TRAF3 (tumour necrosis factor receptor-associated factor 3), is conserved from worms to humans. The N-terminal region is the microtubule binding domain and is well-conserved; the C-terminal 100 residues, also well-conserved, constitute the coiled-coil region which binds to TRAF3. The central region of the protein is rich in lysine and glutamic acid and carries KKE motifs which may also be necessary for tubulin-binding, but this region is the least well-conserved. Length = 506

>gnl|CDD|217037 pfam02443, Circo_capsid, Circovirus capsid protein

 Score = 64.8 bits (158), Expect = 2e-11
 Identities = 27/41 (65%), Positives = 27/41 (65%)

Query: 912 RRRSRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRR 952
           R R RRR RR RRRRRRRR  RRR RRRR    RRR R  R
Sbjct: 1   RFRIRRRYRRPRRRRRRRRHWRRRYRRRRLHINRRRHRTNR 41

Circoviruses are small circular single stranded viruses. This family is the capsid protein from viruses such as porcine circovirus and beak and feather disease virus. These proteins are about 220 amino acids long. Length = 237

>gnl|CDD|217037 pfam02443, Circo_capsid, Circovirus capsid protein

 Score = 64.8 bits (158), Expect = 2e-11
 Identities = 27/41 (65%), Positives = 27/41 (65%)

Query: 914 RSRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRR 954
           R R RRR RR RRRRRRRR  RRR RRRR    RRR R  R
Sbjct: 1   RFRIRRRYRRPRRRRRRRRHWRRRYRRRRLHINRRRHRTNR 41

Circoviruses are small circular single stranded viruses. This family is the capsid protein from viruses such as porcine circovirus and beak and feather disease virus. These proteins are about 220 amino acids long. Length = 237

>gnl|CDD|235250 PRK04195, PRK04195, replication factor C large subunit; Provisional

 Score = 67.3 bits (165), Expect = 2e-11
 Identities = 38/70 (54%), Positives = 53/70 (75%)

Query: 953  RRSGKEEEEEEKKKEEKKKEEEEKKKKEGKTKKEEKKKEEEEEKKKKKKEEEKEEEEKKE 1012
              S K  ++ +K  E+ +K+ EE+KK++ K     KKKEEEEE++K+KKEEEKEEEE++ 
Sbjct: 403  TGSKKATKKIKKIVEKAEKKREEEKKEKKKKAFAGKKKEEEEEEEKEKKEEEKEEEEEEA 462

Query: 1013 EEEKEEEEKK 1022
            EEEKEEEE+K
Sbjct: 463  EEEKEEEEEK 472

Length = 482

>gnl|CDD|233503 TIGR01642, U2AF_lg, U2 snRNP auxilliary factor, large subunit, splicing factor

 Score = 66.1 bits (161), Expect = 4e-11
 Identities = 34/120 (28%), Positives = 50/120 (41%), Gaps = 5/120 (4%)

Query: 885 KEEEEKKKKEGGGGRRRRRRKKRRRSRRR-----RSRRRRRRRRRRRRRRRRRRRRRRRR 939
           ++EE  +++E   GR R R  +R R R R     R R RR R R  R   R R RRR   
Sbjct: 1   RDEEPDREREKSRGRDRDRSSERPRRRSRDRSRFRDRHRRSRERSYREDSRPRDRRRYDS 60

Query: 940 RRRRRRRRRRRRRRRSGKEEEEEEKKKEEKKKEEEEKKKKEGKTKKEEKKKEEEEEKKKK 999
           R  R  R    RR R          +  E+ +     +    + +K++KK+   + K   
Sbjct: 61  RSPRSLRYSSVRRSRDRPRRRSRSVRSIEQHRRRLRDRSPSNQWRKDDKKRSLWDIKPPG 120

These splicing factors consist of an N-terminal arginine-rich low complexity domain followed by three tandem RNA recognition motifs (pfam00076). The well-characterized members of this family are auxilliary components of the U2 small nuclear ribonuclearprotein splicing factor (U2AF). These proteins are closely related to the CC1-like subfamily of splicing factors (TIGR01622). Members of this subfamily are found in plants, metazoa and fungi. Length = 509

>gnl|CDD|233496 TIGR01622, SF-CC1, splicing factor, CC1-like family

 Score = 65.7 bits (160), Expect = 5e-11
 Identities = 35/92 (38%), Positives = 40/92 (43%), Gaps = 5/92 (5%)

Query: 874 GRRRRRRRRSGKEEEEKKKKEGGGGRRRRRRKKRRRSRRRRSRRRRRRRRRRRRRRRRRR 933
             R R R R   +     K     GR R RR+ R R R RR R R   R RR R R R  
Sbjct: 1   RYRDRERGRLRNDTRRSDK-----GRERSRRRSRSRDRSRRRRDRDYYRGRRGRSRSRSP 55

Query: 934 RRRRRRRRRRRRRRRRRRRRRSGKEEEEEEKK 965
            R  R R  R  RR  RR  R+ KE   E ++
Sbjct: 56  NRYYRPRGDRSYRRDDRRSGRNTKEPLTEAER 87

This model represents a subfamily of RNA splicing factors including the Pad-1 protein (N. crassa), CAPER (M. musculus) and CC1.3 (H.sapiens). These proteins are characterized by an N-terminal arginine-rich, low complexity domain followed by three (or in the case of 4 H. sapiens paralogs, two) RNA recognition domains (rrm: pfam00706). These splicing factors are closely related to the U2AF splicing factor family (TIGR01642). A homologous gene from Plasmodium falciparum was identified in the course of the analysis of that genome at TIGR and was included in the seed. Length = 457

>gnl|CDD|217037 pfam02443, Circo_capsid, Circovirus capsid protein

 Score = 63.2 bits (154), Expect = 6e-11
 Identities = 26/41 (63%), Positives = 26/41 (63%)

Query: 913 RRSRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRR 953
           R   RRR RR RRRRRRRR  RRR RRRR    RRR R  R
Sbjct: 1   RFRIRRRYRRPRRRRRRRRHWRRRYRRRRLHINRRRHRTNR 41

Circoviruses are small circular single stranded viruses. This family is the capsid protein from viruses such as porcine circovirus and beak and feather disease virus. These proteins are about 220 amino acids long. Length = 237

>gnl|CDD|234017 TIGR02794, tolA_full, TolA protein

 Score = 64.9 bits (158), Expect = 6e-11
 Identities = 31/115 (26%), Positives = 63/115 (54%), Gaps = 3/115 (2%)

Query: 916  RRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRSGKEEEEEEKKKEEKKKEEEE 975
            ++ + R+++  ++     ++R   + R++   +R    ++ K+ E+  K+ EEK+K+ EE
Sbjct: 64   KKEQERQKKLEQQAEEAEKQRAAEQARQKELEQRAAAEKAAKQAEQAAKQAEEKQKQAEE 123

Query: 976  KKKKEGKTKKEEKKKEEEEEKKKKKKEEEKEEEEKKEEEEKEEEEKKRRRIRRKR 1030
             K K+     E K K E E +KK K+E +K+ EE+ + +   E +KK    ++K 
Sbjct: 124  AKAKQ---AAEAKAKAEAEAEKKAKEEAKKQAEEEAKAKAAAEAKKKAAEAKKKA 175

TolA couples the inner membrane complex of itself with TolQ and TolR to the outer membrane complex of TolB and OprL (also called Pal). Most of the length of the protein consists of low-complexity sequence that may differ in both length and composition from one species to another, complicating efforts to discriminate TolA (the most divergent gene in the tol-pal system) from paralogs such as TonB. Selection of members of the seed alignment and criteria for setting scoring cutoffs are based largely conserved operon struction. //The Tol-Pal complex is required for maintaining outer membrane integrity. Also involved in transport (uptake) of colicins and filamentous DNA, and implicated in pathogenesis. Transport is energized by the proton motive force. TolA is an inner membrane protein that interacts with periplasmic TolB and with outer membrane porins ompC, phoE and lamB [Transport and binding proteins, Other, Cellular processes, Pathogenesis]. Length = 346

>gnl|CDD|173412 PTZ00121, PTZ00121, MAEBL; Provisional

 Score = 66.3 bits (161), Expect = 8e-11
 Identities = 55/234 (23%), Positives = 103/234 (44%), Gaps = 30/234 (12%)

Query: 814  RNRRGRRRRRRKKKEEKKKW---KRRGGGRRRRRGKKEEEKKKKKEEEEEGGEKEEEEGG 870
            +   G+    RK +E KKK    ++    R+    +K EE +K ++ +     ++ E+  
Sbjct: 1105 KTETGKAEEARKAEEAKKKAEDARKAEEARKAEDARKAEEARKAEDAKRVEIARKAEDA- 1163

Query: 871  GGGGRRRRRRRRSGKEEEEKKKKEGGGGRRRRRRKKRRRSRRRRSRRRRRRRRRRRRRRR 930
                   R+   + K E+ KK +        R+ ++ R++   R     R+    R+   
Sbjct: 1164 -------RKAEEARKAEDAKKAEAARKAEEVRKAEELRKAEDARKAEAARKAEEERKAEE 1216

Query: 931  RRRRRRRRRRRRRRRRRRRRRRRRSGKEEEEEEKKKEEKKKEE---------------EE 975
             R+    ++    ++    ++     K+ EEE   +E +K EE               EE
Sbjct: 1217 ARKAEDAKKAEAVKKAEEAKKDAEEAKKAEEERNNEEIRKFEEARMAHFARRQAAIKAEE 1276

Query: 976  KKKKEGKTKKEEKKKEEE----EEKKKKKKEEEKEEEEKKEEEEKEEEEKKRRR 1025
             +K +   K EEKKK +E    EEKKK  + ++K EE KK +E K++ E+ +++
Sbjct: 1277 ARKADELKKAEEKKKADEAKKAEEKKKADEAKKKAEEAKKADEAKKKAEEAKKK 1330

Length = 2084

>gnl|CDD|217037 pfam02443, Circo_capsid, Circovirus capsid protein

 Score = 62.8 bits (153), Expect = 9e-11
 Identities = 26/41 (63%), Positives = 26/41 (63%)

Query: 907 RRRSRRRRSRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRR 947
           R R RRR  R RRRRRRRR  RRR RRRR    RRR R  R
Sbjct: 1   RFRIRRRYRRPRRRRRRRRHWRRRYRRRRLHINRRRHRTNR 41

Circoviruses are small circular single stranded viruses. This family is the capsid protein from viruses such as porcine circovirus and beak and feather disease virus. These proteins are about 220 amino acids long. Length = 237

>gnl|CDD|233503 TIGR01642, U2AF_lg, U2 snRNP auxilliary factor, large subunit, splicing factor

 Score = 64.5 bits (157), Expect = 1e-10
 Identities = 32/118 (27%), Positives = 48/118 (40%)

Query: 854 KKEEEEEGGEKEEEEGGGGGGRRRRRRRRSGKEEEEKKKKEGGGGRRRRRRKKRRRSRRR 913
           + EE +   EK           R RRR R      ++ ++      R   R + RR    
Sbjct: 1   RDEEPDREREKSRGRDRDRSSERPRRRSRDRSRFRDRHRRSRERSYREDSRPRDRRRYDS 60

Query: 914 RSRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRSGKEEEEEEKKKEEKKK 971
           RS R  R    RR R R RRR R  R   + RRR R R   +   ++++++   + K 
Sbjct: 61  RSPRSLRYSSVRRSRDRPRRRSRSVRSIEQHRRRLRDRSPSNQWRKDDKKRSLWDIKP 118

These splicing factors consist of an N-terminal arginine-rich low complexity domain followed by three tandem RNA recognition motifs (pfam00076). The well-characterized members of this family are auxilliary components of the U2 small nuclear ribonuclearprotein splicing factor (U2AF). These proteins are closely related to the CC1-like subfamily of splicing factors (TIGR01622). Members of this subfamily are found in plants, metazoa and fungi. Length = 509

>gnl|CDD|233503 TIGR01642, U2AF_lg, U2 snRNP auxilliary factor, large subunit, splicing factor

 Score = 63.8 bits (155), Expect = 2e-10
 Identities = 32/106 (30%), Positives = 43/106 (40%), Gaps = 3/106 (2%)

Query: 899  RRRRRRKKRRRSRRRRSRRRRRRRRRRRRRRRRRRRRRRRRRR---RRRRRRRRRRRRRS 955
              R R K R R R R S R RRR R R R R R RR R R  R   R R RRR   R   
Sbjct: 5    PDREREKSRGRDRDRSSERPRRRSRDRSRFRDRHRRSRERSYREDSRPRDRRRYDSRSPR 64

Query: 956  GKEEEEEEKKKEEKKKEEEEKKKKEGKTKKEEKKKEEEEEKKKKKK 1001
                    + ++  ++     +  E   ++   +    + +K  KK
Sbjct: 65   SLRYSSVRRSRDRPRRRSRSVRSIEQHRRRLRDRSPSNQWRKDDKK 110

These splicing factors consist of an N-terminal arginine-rich low complexity domain followed by three tandem RNA recognition motifs (pfam00076). The well-characterized members of this family are auxilliary components of the U2 small nuclear ribonuclearprotein splicing factor (U2AF). These proteins are closely related to the CC1-like subfamily of splicing factors (TIGR01622). Members of this subfamily are found in plants, metazoa and fungi. Length = 509

>gnl|CDD|217037 pfam02443, Circo_capsid, Circovirus capsid protein

 Score = 62.1 bits (151), Expect = 2e-10
 Identities = 26/41 (63%), Positives = 26/41 (63%)

Query: 911 RRRRSRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRR 951
           R R  RR RR RRRRRRRR  RRR RRRR    RRR R  R
Sbjct: 1   RFRIRRRYRRPRRRRRRRRHWRRRYRRRRLHINRRRHRTNR 41

Circoviruses are small circular single stranded viruses. This family is the capsid protein from viruses such as porcine circovirus and beak and feather disease virus. These proteins are about 220 amino acids long. Length = 237

>gnl|CDD|217037 pfam02443, Circo_capsid, Circovirus capsid protein

 Score = 61.7 bits (150), Expect = 2e-10
 Identities = 26/41 (63%), Positives = 26/41 (63%)

Query: 909 RSRRRRSRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRR 949
           R R RR  RR RRRRRRRR  RRR RRRR    RRR R  R
Sbjct: 1   RFRIRRRYRRPRRRRRRRRHWRRRYRRRRLHINRRRHRTNR 41

Circoviruses are small circular single stranded viruses. This family is the capsid protein from viruses such as porcine circovirus and beak and feather disease virus. These proteins are about 220 amino acids long. Length = 237

>gnl|CDD|217037 pfam02443, Circo_capsid, Circovirus capsid protein

 Score = 61.7 bits (150), Expect = 2e-10
 Identities = 27/47 (57%), Positives = 27/47 (57%)

Query: 907 RRRSRRRRSRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRR 953
           R R R RR RRRRRRRR  RRR RRRR    RRR R  R    R  R
Sbjct: 3   RIRRRYRRPRRRRRRRRHWRRRYRRRRLHINRRRHRTNRIYTFRLTR 49

Circoviruses are small circular single stranded viruses. This family is the capsid protein from viruses such as porcine circovirus and beak and feather disease virus. These proteins are about 220 amino acids long. Length = 237

>gnl|CDD|235250 PRK04195, PRK04195, replication factor C large subunit; Provisional

 Score = 64.6 bits (158), Expect = 2e-10
 Identities = 33/73 (45%), Positives = 57/73 (78%)

Query: 951  RRRRSGKEEEEEEKKKEEKKKEEEEKKKKEGKTKKEEKKKEEEEEKKKKKKEEEKEEEEK 1010
               +   ++ ++  +K EKK+EEE+K+KK+     ++K++EEEEEK+KK++E+E+EEEE 
Sbjct: 403  TGSKKATKKIKKIVEKAEKKREEEKKEKKKKAFAGKKKEEEEEEEKEKKEEEKEEEEEEA 462

Query: 1011 KEEEEKEEEEKKR 1023
            +EE+E+EEE+KK+
Sbjct: 463  EEEKEEEEEKKKK 475

Length = 482

>gnl|CDD|217037 pfam02443, Circo_capsid, Circovirus capsid protein

 Score = 61.3 bits (149), Expect = 3e-10
 Identities = 26/41 (63%), Positives = 26/41 (63%)

Query: 908 RRSRRRRSRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRR 948
           R   RRR RR RRRRRRRR  RRR RRRR    RRR R  R
Sbjct: 1   RFRIRRRYRRPRRRRRRRRHWRRRYRRRRLHINRRRHRTNR 41

Circoviruses are small circular single stranded viruses. This family is the capsid protein from viruses such as porcine circovirus and beak and feather disease virus. These proteins are about 220 amino acids long. Length = 237

>gnl|CDD|219953 pfam08648, DUF1777, Protein of unknown function (DUF1777)

 Score = 59.1 bits (143), Expect = 4e-10
 Identities = 41/109 (37%), Positives = 56/109 (51%), Gaps = 8/109 (7%)

Query: 875 RRRRRRRRSGKEEEEKKKKEGGGGRRRRRRKKRRRSRRRRSRRRRRRRRRRRRRRRRRRR 934
           RR RRR RS   +  +++      R R R ++R R RR RSR   R RR R  RR R R 
Sbjct: 10  RRSRRRGRSRSRDRRERR------RERSRSRERDRRRRSRSRSPHRSRRSRSPRRHRSRS 63

Query: 935 R--RRRRRRRRRRRRRRRRRRRSGKEEEEEEKKKEEKKKEEEEKKKKEG 981
           R   RRR R+R R +  R  ++  +++  +E+  E K  EE E  K  G
Sbjct: 64  RSPSRRRDRKRERDKDAREPKKRERQKLIKEEDLEGKSDEEVEMMKMMG 112

This is a family of eukaryotic proteins of unknown function. Some of the proteins in this family are putative nucleic acid binding proteins. Length = 158

>gnl|CDD|235401 PRK05306, infB, translation initiation factor IF-2; Validated

 Score = 63.3 bits (155), Expect = 5e-10
 Identities = 25/145 (17%), Positives = 56/145 (38%), Gaps = 8/145 (5%)

Query: 848 EEEKKKKKEEEEEGGEKEEEEGGGGGGRRRRRRRRSGKEEEEKKKKEGGGGRRRRRRKKR 907
           EEE+ +K+E + E  E+ + E              +  EEE K +               
Sbjct: 39  EEEEARKEEAKREAEEEAKAE--------AEEAAAAEAEEEAKAEAAAAAPAEEAAEAAA 90

Query: 908 RRSRRRRSRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRSGKEEEEEEKKKE 967
                 R       R      RR + ++  ++++  + ++++ +R+ +   +  +  K  
Sbjct: 91  AAEAAARPAEDEAARPAEAAARRPKAKKAAKKKKGPKPKKKKPKRKAARGGKRGKGGKGR 150

Query: 968 EKKKEEEEKKKKEGKTKKEEKKKEE 992
            +++    ++KK+ K K  EK   E
Sbjct: 151 RRRRGRRRRRKKKKKQKPTEKIPRE 175

Length = 746

>gnl|CDD|219953 pfam08648, DUF1777, Protein of unknown function (DUF1777)

 Score = 58.7 bits (142), Expect = 6e-10
 Identities = 41/106 (38%), Positives = 56/106 (52%), Gaps = 5/106 (4%)

Query: 882 RSGKEEEEKKKKEGGGGRRRRRRKKRRRSR-RRRSRRRRRRRRRRRRRRRRRRRRRRRRR 940
           RS      + ++ G    R RR ++R RSR R R RRRR R R   R RR R  RR R R
Sbjct: 3   RSRSRSPRRSRRRGRSRSRDRRERRRERSRSRERDRRRRSRSRSPHRSRRSRSPRRHRSR 62

Query: 941 RRRRRRRRRRRRRRSGKEEEEEEKKKEEKKKEEEEKKKKEGKTKKE 986
            R   RRR R+R R     E +++++++  KEE      EGK+ +E
Sbjct: 63  SRSPSRRRDRKRERDKDAREPKKRERQKLIKEE----DLEGKSDEE 104

This is a family of eukaryotic proteins of unknown function. Some of the proteins in this family are putative nucleic acid binding proteins. Length = 158

>gnl|CDD|222447 pfam13904, DUF4207, Domain of unknown function (DUF4207)

 Score = 60.9 bits (148), Expect = 6e-10
 Identities = 28/123 (22%), Positives = 65/123 (52%), Gaps = 18/123 (14%)

Query: 921  RRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRSGKEEEEE--EKKKEEKKKEEEEKKK 978
             ++ +R+++ ++    ++++ R + R     R+R  KE+ EE   +K ++  K+   K K
Sbjct: 95   AKQAQRQKKLQKLLEEKQKQEREKEREEAELRQRLAKEKYEEWCRQKAQQAAKQRTPKHK 154

Query: 979  KEG----------------KTKKEEKKKEEEEEKKKKKKEEEKEEEEKKEEEEKEEEEKK 1022
            KE                    +EE KK  +E + KK K+++++ EE++ ++ K+++E++
Sbjct: 155  KEAAESASSSLSGSAKPERNVSQEEAKKRLQEWELKKLKQQQQKREEERRKQRKKQQEEE 214

Query: 1023 RRR 1025
             R+
Sbjct: 215  ERK 217

This family is found in eukaryotes; it has several conserved tryptophan residues. The function is not known. Length = 261

>gnl|CDD|217037 pfam02443, Circo_capsid, Circovirus capsid protein

 Score = 60.1 bits (146), Expect = 8e-10
 Identities = 26/49 (53%), Positives = 28/49 (57%)

Query: 900 RRRRRKKRRRSRRRRSRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRR 948
           R R R++ RR RRRR RRR  RRR RRRR    RRR R  R    R  R
Sbjct: 1   RFRIRRRYRRPRRRRRRRRHWRRRYRRRRLHINRRRHRTNRIYTFRLTR 49

Circoviruses are small circular single stranded viruses. This family is the capsid protein from viruses such as porcine circovirus and beak and feather disease virus. These proteins are about 220 amino acids long. Length = 237

>gnl|CDD|215824 pfam00260, Protamine_P1, Protamine P1

 Score = 54.9 bits (132), Expect = 9e-10
 Identities = 34/50 (68%), Positives = 34/50 (68%)

Query: 902 RRRKKRRRSRRRRSRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRR 951
           R R  R RSR R  RRRRRR RRRRRR  RRRRRR    RRR  RRRRRR
Sbjct: 2   RYRCCRSRSRSRCRRRRRRRCRRRRRRCCRRRRRRVGCCRRRYTRRRRRR 51

Length = 51

>gnl|CDD|173412 PTZ00121, PTZ00121, MAEBL; Provisional

 Score = 62.5 bits (151), Expect = 1e-09
 Identities = 52/206 (25%), Positives = 91/206 (44%), Gaps = 25/206 (12%)

Query: 844  RGKKEEEKKKKKEEEEEGGEKEEEEGGGGGGRRRRRRRRSGKEEEEKKKKEGGGGRRRRR 903
             GK EE KK +  + EE  + EE +      R+    R++   E+ +K +E       +R
Sbjct: 1097 FGKAEEAKKTETGKAEEARKAEEAKKKAEDARKAEEARKA---EDARKAEEARKAEDAKR 1153

Query: 904  RKKRRRSRRRRSRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRSGKEEEEEE 963
             +  R++    +R+    R+    ++    R+    R+    R+    R+     + EEE
Sbjct: 1154 VEIARKAED--ARKAEEARKAEDAKKAEAARKAEEVRKAEELRKAEDARKAEAARKAEEE 1211

Query: 964  KKKEEKKKEEEEKKKKEGKTKKEEKKKEEEEEKKKKKKEEE------------------- 1004
            +K EE +K E+ KK +  K  +E KK  EE +K ++++  E                   
Sbjct: 1212 RKAEEARKAEDAKKAEAVKKAEEAKKDAEEAKKAEEERNNEEIRKFEEARMAHFARRQAA 1271

Query: 1005 -KEEEEKKEEEEKEEEEKKRRRIRRK 1029
             K EE +K +E K+ EEKK+    +K
Sbjct: 1272 IKAEEARKADELKKAEEKKKADEAKK 1297

Length = 2084

>gnl|CDD|236766 PRK10811, rne, ribonuclease E; Reviewed

 Score = 62.4 bits (152), Expect = 1e-09
 Identities = 40/217 (18%), Positives = 82/217 (37%), Gaps = 37/217 (17%)

Query: 846  KKEEEKKKKKEEEEEGGEKEEEEGGGGGGRRRRRRRRSGKEEEEKKKKEGGGGRRRRRRK 905
             K +E+   K E +    +++        RR R  RR     + + ++EG   R   RR 
Sbjct: 586  TKPQEQPAPKAEAKPE-RQQDRRKPRQNNRRDRNERRD--TRDNRTRREGRENREENRRN 642

Query: 906  KRRR---------------SRRRRSRRRRRRRRRRRRRRRRRRRRRR------------- 937
            +R+                + + R++  +++  RR R+RRR   +R+             
Sbjct: 643  RRQAQQQTAETRESQQAEVTEKARTQDEQQQAPRRERQRRRNDEKRQAQQEAKALNVEEQ 702

Query: 938  ------RRRRRRRRRRRRRRRRRSGKEEEEEEKKKEEKKKEEEEKKKKEGKTKKEEKKKE 991
                  +  R ++ + RR++R+ + K   E+   +E      EE    E   ++    + 
Sbjct: 703  SVQETEQEERVQQVQPRRKQRQLNQKVRIEQSVAEEAVAPVVEETVAAEPVVQEVPAPRT 762

Query: 992  EEEEKKKKKKEEEKEEEEKKEEEEKEEEEKKRRRIRR 1028
            E  +       +   E++++   E  +     RR RR
Sbjct: 763  ELVKVPLPVVAQTAPEQDEENNAENRDNNGMPRRSRR 799

Length = 1068

>gnl|CDD|217037 pfam02443, Circo_capsid, Circovirus capsid protein

 Score = 59.4 bits (144), Expect = 1e-09
 Identities = 27/49 (55%), Positives = 28/49 (57%)

Query: 903 RRKKRRRSRRRRSRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRR 951
           R + RRR RR R RRRRRR  RRR RRRR    RRR R  R    R  R
Sbjct: 1   RFRIRRRYRRPRRRRRRRRHWRRRYRRRRLHINRRRHRTNRIYTFRLTR 49

Circoviruses are small circular single stranded viruses. This family is the capsid protein from viruses such as porcine circovirus and beak and feather disease virus. These proteins are about 220 amino acids long. Length = 237

>gnl|CDD|217037 pfam02443, Circo_capsid, Circovirus capsid protein

 Score = 59.4 bits (144), Expect = 1e-09
 Identities = 26/49 (53%), Positives = 27/49 (55%)

Query: 902 RRRKKRRRSRRRRSRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRR 950
           R R +RR  R RR RRRRR  RRR RRRR    RRR R  R    R  R
Sbjct: 1   RFRIRRRYRRPRRRRRRRRHWRRRYRRRRLHINRRRHRTNRIYTFRLTR 49

Circoviruses are small circular single stranded viruses. This family is the capsid protein from viruses such as porcine circovirus and beak and feather disease virus. These proteins are about 220 amino acids long. Length = 237

>gnl|CDD|206039 pfam13868, Trichoplein, Tumour suppressor, Mitostatin

 Score = 60.7 bits (148), Expect = 1e-09
 Identities = 54/229 (23%), Positives = 111/229 (48%), Gaps = 22/229 (9%)

Query: 816  RRGRRRRRRKKKEEKKKWKRRGGGRRRRRGKKEEEKKKKKEEEEEGGEKEEEEGGGGGGR 875
                + +R K+K+ +++          R  +KEEEK++++EEE +  E + E+       
Sbjct: 113  EAEAQEKREKQKKLREEIDE---FNEERIERKEEEKEREREEELKILEYQREKA-----E 164

Query: 876  RRRRRRRSGKEEEEKKKKEGGGGRRRRRRKKRRRSRRRRSRRRRRRRRRRRRRRRRRRRR 935
            R   R    +E +E+K++E    R ++   +  R      R    +    R+ R++ +  
Sbjct: 165  REEEREAERRERKEEKEREVARLRAQQEEAEDEREELDELRADLYQEEYERKERQKEKEE 224

Query: 936  RRRRRR--------RRRRRRRRRRRRRSGKEEEEEEKKKEEKKKEEEEKKKKEGKTKKEE 987
              +RRR        R  +   +  R +  + EEE E+++  +K+ E+E+ ++E   K+  
Sbjct: 225  AEKRRRQKQELQRAREEQIEEKEERLQEERAEEEAERERMLEKQAEDEELEQENAEKRRM 284

Query: 988  KKKEEEEE------KKKKKKEEEKEEEEKKEEEEKEEEEKKRRRIRRKR 1030
            K+ E   E      +K++++  E+EEE ++ E  +EEE +++ RI  +R
Sbjct: 285  KRLEHRRELEQQIEEKEERRAAEREEELEEGERLREEEAERQARIEEER 333

Trichoplein or mitostatin, was first defined as a meiosis-specific nuclear structural protein. It has since been linked with mitochondrial movement. It is associated with the mitochondrial outer membrane, and over-expression leads to reduction in mitochondrial motility whereas lack of it enhances mitochondrial movement. The activity appears to be mediated through binding the mitochondria to the actin intermediate filaments (IFs). Length = 349

>gnl|CDD|177369 PHA02528, 43, DNA polymerase; Provisional

 Score = 62.0 bits (151), Expect = 1e-09
 Identities = 59/246 (23%), Positives = 87/246 (35%), Gaps = 76/246 (30%)

Query: 487 KGKGRKKAAYSGGLVLEPKKGFYDKFIILMDFNSLYPSIIQEYNI-------CFTTIPV- 538
           + K  KK  Y+G  V EP  G Y  +++  D  SLYPSII++ NI        F   PV 
Sbjct: 368 ENKSHKKQKYAGAFVKEPVPGAYR-WVVSFDLTSLYPSIIRQVNISPETIAGTFHVAPVH 426

Query: 539 -----------------------------------------------RMLQDSDITTLCE 551
                                                          +ML       L +
Sbjct: 427 EYINKTAPRPSDEYSCSPNGWMYRKDIRGVIPTEIKKVFDQRKIYKKKMLAAERNAELIK 486

Query: 552 YLPEHQVDTGILPSEIKKLVESRRQVKALMKQPNLSSDLLM---------QYDIRQKALK 602
            + E   D+   P ++    +   + KA +K    SS   +           +  Q A K
Sbjct: 487 TILEDLNDSVDTPIDVDYYFDFSDEFKAELKTLTKSSLKALLEECEKEIALCNTIQMARK 546

Query: 603 LTANSMYGCLGFPNSRFFAQPLAALVTAKGR----------EILLNTKSLVENLNYEVIY 652
           +  NS+YG LG  + R++    A  +T  G+             LN     E+ +Y VIY
Sbjct: 547 ILINSLYGALGNEHFRYYDLRNAEAITLFGQLAIQWIERKMNEYLNKLCKTEDEDY-VIY 605

Query: 653 GDTDSL 658
           GDTDS+
Sbjct: 606 GDTDSI 611

Length = 881

>gnl|CDD|173412 PTZ00121, PTZ00121, MAEBL; Provisional

 Score = 61.7 bits (149), Expect = 2e-09
 Identities = 47/189 (24%), Positives = 89/189 (47%), Gaps = 6/189 (3%)

Query: 846  KKEEEKKKKKEEEEEGGEKEEEEGGGGGGRRRRRRRRSGKEEEEKKKKEGGGGRRRRRRK 905
             KE+ +  +  EE  G  +E ++   G     R+   + K+ E+ +K E    R+    +
Sbjct: 1083 AKEDNRADEATEEAFGKAEEAKKTETGKAEEARKAEEAKKKAEDARKAEEA--RKAEDAR 1140

Query: 906  KRRRSRRRRSRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRSGK-EEEEEEK 964
            K   +R+    +R    R+    R+    R+    ++    R+    R++ +  + E+ +
Sbjct: 1141 KAEEARKAEDAKRVEIARKAEDARKAEEARKAEDAKKAEAARKAEEVRKAEELRKAEDAR 1200

Query: 965  KKEEKKKEEEEKKKKEGKTKKEEKKKEE---EEEKKKKKKEEEKEEEEKKEEEEKEEEEK 1021
            K E  +K EEE+K +E +  ++ KK E     EE KK  +E +K EEE+  EE ++ EE 
Sbjct: 1201 KAEAARKAEEERKAEEARKAEDAKKAEAVKKAEEAKKDAEEAKKAEEERNNEEIRKFEEA 1260

Query: 1022 KRRRIRRKR 1030
            +     R++
Sbjct: 1261 RMAHFARRQ 1269

Length = 2084

>gnl|CDD|233503 TIGR01642, U2AF_lg, U2 snRNP auxilliary factor, large subunit, splicing factor

 Score = 61.1 bits (148), Expect = 2e-09
 Identities = 34/139 (24%), Positives = 49/139 (35%), Gaps = 21/139 (15%)

Query: 820 RRRRRKKKEEKKKWKRRGGGRRRRRGKKEEEKKKKKEEEEEGGEKEEEEGGGGGGRRRRR 879
             R R+K   + + +     RRR R +     + ++  E    E           R R R
Sbjct: 5   PDREREKSRGRDRDRSSERPRRRSRDRSRFRDRHRRSRERSYREDS---------RPRDR 55

Query: 880 RRRSGKEEEEKKKKEGGGGRRRRRRKKRRRSRRRRSRRRRRRRRRRRRRRRRRRRRRRRR 939
           RR   +              R  R    RRSR R  RR R  R   + RRR R R    +
Sbjct: 56  RRYDSRS------------PRSLRYSSVRRSRDRPRRRSRSVRSIEQHRRRLRDRSPSNQ 103

Query: 940 RRRRRRRRRRRRRRRSGKE 958
            R+  ++R     +  G E
Sbjct: 104 WRKDDKKRSLWDIKPPGYE 122

These splicing factors consist of an N-terminal arginine-rich low complexity domain followed by three tandem RNA recognition motifs (pfam00076). The well-characterized members of this family are auxilliary components of the U2 small nuclear ribonuclearprotein splicing factor (U2AF). These proteins are closely related to the CC1-like subfamily of splicing factors (TIGR01622). Members of this subfamily are found in plants, metazoa and fungi. Length = 509

>gnl|CDD|220648 pfam10243, MIP-T3, Microtubule-binding protein MIP-T3

 Score = 60.7 bits (147), Expect = 2e-09
 Identities = 39/209 (18%), Positives = 93/209 (44%), Gaps = 7/209 (3%)

Query: 822  RRRKKKEEKKKWKRRGGGRRRRRGKKEEEKKKKKEEEEEGGEKEEEEGGGGGGRRRRRRR 881
            +R +K   K    +    +  +    +EE+K+K++ +EE  +K+E+        +   + 
Sbjct: 78   KRVEKGGSKGPAAKTKPAKEPKNESGKEEEKEKEQVKEEKKKKKEKP-------KEEPKD 130

Query: 882  RSGKEEEEKKKKEGGGGRRRRRRKKRRRSRRRRSRRRRRRRRRRRRRRRRRRRRRRRRRR 941
            R  KEE ++K+      + + ++ +  R R    +R R R + R ++  +++   +++  
Sbjct: 131  RKPKEEAKEKRPPKEKEKEKEKKVEEPRDREEEKKRERVRAKSRPKKPPKKKPPNKKKEP 190

Query: 942  RRRRRRRRRRRRRSGKEEEEEEKKKEEKKKEEEEKKKKEGKTKKEEKKKEEEEEKKKKKK 1001
                ++R+  R     + EE +  +E +K+E++ K ++   +  EE +  +  E  ++  
Sbjct: 191  PEEEKQRQAAREAVKGKPEEPDVNEEREKEEDDGKDRETTTSPMEEDESRQSSEISRRSS 250

Query: 1002 EEEKEEEEKKEEEEKEEEEKKRRRIRRKR 1030
               K+ +        E  E  +R   R R
Sbjct: 251  SSLKKPDPSPSMASPETRESSKRTETRPR 279

This protein, which interacts with both microtubules and TRAF3 (tumour necrosis factor receptor-associated factor 3), is conserved from worms to humans. The N-terminal region is the microtubule binding domain and is well-conserved; the C-terminal 100 residues, also well-conserved, constitute the coiled-coil region which binds to TRAF3. The central region of the protein is rich in lysine and glutamic acid and carries KKE motifs which may also be necessary for tubulin-binding, but this region is the least well-conserved. Length = 506

>gnl|CDD|233496 TIGR01622, SF-CC1, splicing factor, CC1-like family

 Score = 60.3 bits (146), Expect = 2e-09
 Identities = 29/85 (34%), Positives = 40/85 (47%)

Query: 899 RRRRRRKKRRRSRRRRSRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRSGKE 958
           R R R   RR  + R   RRR R R R RRRR R   R RR R R R   R  R R  + 
Sbjct: 7   RGRLRNDTRRSDKGRERSRRRSRSRDRSRRRRDRDYYRGRRGRSRSRSPNRYYRPRGDRS 66

Query: 959 EEEEEKKKEEKKKEEEEKKKKEGKT 983
              ++++     KE   + +++ +T
Sbjct: 67  YRRDDRRSGRNTKEPLTEAERDDRT 91

This model represents a subfamily of RNA splicing factors including the Pad-1 protein (N. crassa), CAPER (M. musculus) and CC1.3 (H.sapiens). These proteins are characterized by an N-terminal arginine-rich, low complexity domain followed by three (or in the case of 4 H. sapiens paralogs, two) RNA recognition domains (rrm: pfam00706). These splicing factors are closely related to the U2AF splicing factor family (TIGR01642). A homologous gene from Plasmodium falciparum was identified in the course of the analysis of that genome at TIGR and was included in the seed. Length = 457

>gnl|CDD|215824 pfam00260, Protamine_P1, Protamine P1

 Score = 53.4 bits (128), Expect = 3e-09
 Identities = 33/48 (68%), Positives = 33/48 (68%)

Query: 907 RRRSRRRRSRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRR 954
           R    R RSR RRRRRRR RRRRRR  RRRRRR    RRR  RRRRRR
Sbjct: 4   RCCRSRSRSRCRRRRRRRCRRRRRRCCRRRRRRVGCCRRRYTRRRRRR 51

Length = 51

>gnl|CDD|233191 TIGR00927, 2A1904, K+-dependent Na+/Ca+ exchanger

 Score = 61.2 bits (148), Expect = 3e-09
 Identities = 45/223 (20%), Positives = 84/223 (37%), Gaps = 16/223 (7%)

Query: 816  RRGRRRRRRKKKEEKKKWKRRGGGRRRRRGKKEEEKKKKKEEEEEGGEKEEEEGGGGGGR 875
              G    +  + E K + +  G     R+G++E E + + +E +  GE E EE    G  
Sbjct: 662  ESGGEAEQEGETETKGENESEGEIPAERKGEQEGEGEIEAKEADHKGETEAEEVEHEGET 721

Query: 876  RRR--------RRRRSGKEEEEKKKKEGGGGRRRRRRKKRRRSRRRRSRRRRRRRRRRRR 927
                            G+E E++ + E  G         R+ +          +      
Sbjct: 722  EAEGTEDEGEIETGEEGEEVEDEGEGEAEGKHEVETEGDRKETEHEGETEAEGKEDEDEG 781

Query: 928  RRR-----RRRRRRRRRRRRRRRRRRRRRRRRSGKEEEEEEKKKEEKKKEEEEKK---KK 979
              +       +       +           +   + + E +    E K E  E++   + 
Sbjct: 782  EIQAGEDGEMKGDEGAEGKVEHEGETEAGEKDEHEGQSETQADDTEVKDETGEQELNAEN 841

Query: 980  EGKTKKEEKKKEEEEEKKKKKKEEEKEEEEKKEEEEKEEEEKK 1022
            +G+ K++EK  +          EEE+EEEE++EEEE+EEEE++
Sbjct: 842  QGEAKQDEKGVDGGGGSDGGDSEEEEEEEEEEEEEEEEEEEEE 884

[Transport and binding proteins, Cations and iron carrying compounds]. Length = 1096

>gnl|CDD|235250 PRK04195, PRK04195, replication factor C large subunit; Provisional

 Score = 59.9 bits (146), Expect = 4e-09
 Identities = 29/65 (44%), Positives = 55/65 (84%)

Query: 957  KEEEEEEKKKEEKKKEEEEKKKKEGKTKKEEKKKEEEEEKKKKKKEEEKEEEEKKEEEEK 1016
            K+  E+ +KK E++K+E++KK   GK K+EE+++E+E+++++K++EEE+ EEEK+EEEEK
Sbjct: 413  KKIVEKAEKKREEEKKEKKKKAFAGKKKEEEEEEEKEKKEEEKEEEEEEAEEEKEEEEEK 472

Query: 1017 EEEEK 1021
            ++++ 
Sbjct: 473  KKKQA 477

Length = 482

>gnl|CDD|215824 pfam00260, Protamine_P1, Protamine P1

 Score = 53.0 bits (127), Expect = 4e-09
 Identities = 33/50 (66%), Positives = 34/50 (68%)

Query: 900 RRRRRKKRRRSRRRRSRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRR 949
           R R  + R RSR RR RRRR RRRRRR  RRRRRR    RRR  RRRRRR
Sbjct: 2   RYRCCRSRSRSRCRRRRRRRCRRRRRRCCRRRRRRVGCCRRRYTRRRRRR 51

Length = 51

>gnl|CDD|215824 pfam00260, Protamine_P1, Protamine P1

 Score = 53.0 bits (127), Expect = 4e-09
 Identities = 33/50 (66%), Positives = 34/50 (68%)

Query: 904 RKKRRRSRRRRSRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRR 953
           R +  RSR R   RRRRRRR RRRRRR  RRRRRR    RRR  RRRRRR
Sbjct: 2   RYRCCRSRSRSRCRRRRRRRCRRRRRRCCRRRRRRVGCCRRRYTRRRRRR 51

Length = 51

>gnl|CDD|233037 TIGR00592, pol2, DNA polymerase (pol2)

 Score = 60.5 bits (146), Expect = 5e-09
 Identities = 31/90 (34%), Positives = 44/90 (48%), Gaps = 7/90 (7%)

Query: 129 VYEEVSEKEYTERVLKRQEDDWIDDDGGDGYVEDGREIFDDDI------EDVPQKKEKHD 182
           +YE+V E+EY++RV ++  DD    D G+GYVEDGRE F D+       +D     E   
Sbjct: 8   IYEDVDEEEYSKRVQEKPIDDIFVKDDGEGYVEDGREFFPDEDDILDLDKDDGSAAEAKK 67

Query: 183 KRKKN-KNIQNPNAKDDSLPLATDHENKKV 211
           K K+N K +  PN            + K  
Sbjct: 68  KDKENHKKVTKPNNIKAVRIACAPKKKKDR 97

All proteins in this superfamily for which functions are known are DNA polymerases.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University) [DNA metabolism, DNA replication, recombination, and repair]. Length = 1172

>gnl|CDD|173412 PTZ00121, PTZ00121, MAEBL; Provisional

 Score = 60.2 bits (145), Expect = 6e-09
 Identities = 46/205 (22%), Positives = 87/205 (42%), Gaps = 4/205 (1%)

Query: 828  EEKKKWKRRGGGRRRRRGKKEEEKKKKKEEEEEGGEKEEEEGGGGGGRRRRRRRRSGKEE 887
            E K + K   G     +   ++     KE+       EE  G     ++    +     +
Sbjct: 1057 EGKAEAKAHVGQDEGLKPSYKDFDFDAKEDNRADEATEEAFGKAEEAKKTETGKAEEARK 1116

Query: 888  EEKKKKEGGGGRRRRRRKKRRRSRRRRSRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRR 947
             E+ KK+    R+    +K   +R+    R+    +R    R+    R+    R+    +
Sbjct: 1117 AEEAKKKAEDARKAEEARKAEDARKAEEARKAEDAKRVEIARKAEDARKAEEARKAEDAK 1176

Query: 948  RRRRRRRSGKEEEEEEKKKEEKKKEEEEKKKKEGKTKKEEKKKEEEEEK----KKKKKEE 1003
            +    R++ +  + EE +K E  ++ E  +K E + K EE +K E+ +K    KK ++ +
Sbjct: 1177 KAEAARKAEEVRKAEELRKAEDARKAEAARKAEEERKAEEARKAEDAKKAEAVKKAEEAK 1236

Query: 1004 EKEEEEKKEEEEKEEEEKKRRRIRR 1028
            +  EE KK EEE+  EE ++    R
Sbjct: 1237 KDAEEAKKAEEERNNEEIRKFEEAR 1261

Length = 2084

>gnl|CDD|217037 pfam02443, Circo_capsid, Circovirus capsid protein

 Score = 57.1 bits (138), Expect = 8e-09
 Identities = 26/49 (53%), Positives = 27/49 (55%)

Query: 899 RRRRRRKKRRRSRRRRSRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRR 947
           R R RR+ RR  RRRR RR  RRR RRRR    RRR R  R    R  R
Sbjct: 1   RFRIRRRYRRPRRRRRRRRHWRRRYRRRRLHINRRRHRTNRIYTFRLTR 49

Circoviruses are small circular single stranded viruses. This family is the capsid protein from viruses such as porcine circovirus and beak and feather disease virus. These proteins are about 220 amino acids long. Length = 237

>gnl|CDD|233496 TIGR01622, SF-CC1, splicing factor, CC1-like family

 Score = 58.8 bits (142), Expect = 8e-09
 Identities = 33/85 (38%), Positives = 39/85 (45%), Gaps = 7/85 (8%)

Query: 890 KKKKEGGGGRRRRRRKKRRRSRRRRSRRRRRRRRRRR-------RRRRRRRRRRRRRRRR 942
            + +E G  R   RR  + R R RR  R R R RRRR       RR R R R   R  R 
Sbjct: 2   YRDRERGRLRNDTRRSDKGRERSRRRSRSRDRSRRRRDRDYYRGRRGRSRSRSPNRYYRP 61

Query: 943 RRRRRRRRRRRRSGKEEEEEEKKKE 967
           R  R  RR  RRSG+  +E   + E
Sbjct: 62  RGDRSYRRDDRRSGRNTKEPLTEAE 86

This model represents a subfamily of RNA splicing factors including the Pad-1 protein (N. crassa), CAPER (M. musculus) and CC1.3 (H.sapiens). These proteins are characterized by an N-terminal arginine-rich, low complexity domain followed by three (or in the case of 4 H. sapiens paralogs, two) RNA recognition domains (rrm: pfam00706). These splicing factors are closely related to the U2AF splicing factor family (TIGR01642). A homologous gene from Plasmodium falciparum was identified in the course of the analysis of that genome at TIGR and was included in the seed. Length = 457

>gnl|CDD|224117 COG1196, Smc, Chromosome segregation ATPases [Cell division and chromosome partitioning]

 Score = 59.7 bits (145), Expect = 8e-09
 Identities = 45/233 (19%), Positives = 95/233 (40%), Gaps = 9/233 (3%)

Query: 804  KVCITQIRLSRNRRGRRRRRRKKKEEKKKWKRRGGGRRRRRGKKEEEKKKKKEEEEEGGE 863
            K+      L    R       + + + ++ +R+    +R     EEE ++ +   EE   
Sbjct: 685  KLEEELKSLKNELRSLEDLLEELRRQLEELERQLEELKRELAALEEELEQLQSRLEE--- 741

Query: 864  KEEEEGGGGGGRRRRRRRRSGKEEEEKKKKEGGGGRRRRRRKKRRRSRRRRSRRRRRRRR 923
             EEE           + R    EEE +  +E     +    +   + +  +         
Sbjct: 742  LEEELEELEEELEELQERLEELEEELESLEEALAKLKEEIEELEEKRQALQEELEELEEE 801

Query: 924  RRRRRRRRRRRRRRRRRRRRRRRR------RRRRRRRSGKEEEEEEKKKEEKKKEEEEKK 977
                 RR     R      +RR R               +E+ +E +++ E+ ++E E+ 
Sbjct: 802  LEEAERRLDALERELESLEQRRERLEQEIEELEEEIEELEEKLDELEEELEELEKELEEL 861

Query: 978  KKEGKTKKEEKKKEEEEEKKKKKKEEEKEEEEKKEEEEKEEEEKKRRRIRRKR 1030
            K+E +  + EK++ E+E K+ ++++EE EEE ++ E E  E +++  ++R + 
Sbjct: 862  KEELEELEAEKEELEDELKELEEEKEELEEELRELESELAELKEEIEKLRERL 914

Length = 1163

>gnl|CDD|219924 pfam08597, eIF3_subunit, Translation initiation factor eIF3 subunit

 Score = 57.0 bits (138), Expect = 8e-09
 Identities = 26/75 (34%), Positives = 49/75 (65%), Gaps = 4/75 (5%)

Query: 958  EEEEEEKK----KEEKKKEEEEKKKKEGKTKKEEKKKEEEEEKKKKKKEEEKEEEEKKEE 1013
            E+E+++ K    +EE +++EEEK K   K K ++  K + EEK+K K+E+E++   + EE
Sbjct: 27   EDEDDDVKDSWDEEEDEEKEEEKAKVAAKAKAKKALKAKIEEKEKAKREKEEKGLRELEE 86

Query: 1014 EEKEEEEKKRRRIRR 1028
            +  E+E  ++ R+R+
Sbjct: 87   DTPEDELAEKLRLRK 101

This is a family of proteins which are subunits of the eukaryotic translation initiation factor 3 (eIF3). In yeast it is called Hcr1. The Saccharomyces cerevisiae protein eIF3j (HCR1) has been shown to be required for processing of 20S pre-rRNA and binds to 18S rRNA and eIF3 subunits Rpg1p and Prt1p. Length = 242

>gnl|CDD|220648 pfam10243, MIP-T3, Microtubule-binding protein MIP-T3

 Score = 58.7 bits (142), Expect = 9e-09
 Identities = 35/224 (15%), Positives = 94/224 (41%), Gaps = 21/224 (9%)

Query: 791  EITKQLTKAPEGGKVCITQIRLSRNRRGRRRRRRKKKEEKKKWKRRGGGRRRRRGKKEEE 850
            E  K++ K    G    T+          +   ++K++ K+              +K+++
Sbjct: 75   EAVKRVEKGGSKGPAAKTKPAKEPKNESGKEEEKEKEQVKE--------------EKKKK 120

Query: 851  KKKKKEEEEEGGEKEEEEGGGGGGRRRRRRRRSGKEEEEKKKKEGGGGRRRRRRKKRRRS 910
            K+K KEE ++   KEE +        +R  +   KE+E+K ++       ++R + R +S
Sbjct: 121  KEKPKEEPKDRKPKEEAK-------EKRPPKEKEKEKEKKVEEPRDREEEKKRERVRAKS 173

Query: 911  RRRRSRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRSGKEEEEEEKKKEEKK 970
            R ++  +++   +++      ++R+  R   + +         R  +E++ ++++     
Sbjct: 174  RPKKPPKKKPPNKKKEPPEEEKQRQAAREAVKGKPEEPDVNEEREKEEDDGKDRETTTSP 233

Query: 971  KEEEEKKKKEGKTKKEEKKKEEEEEKKKKKKEEEKEEEEKKEEE 1014
             EE+E ++    +++     ++ +        E +E  ++ E  
Sbjct: 234  MEEDESRQSSEISRRSSSSLKKPDPSPSMASPETRESSKRTETR 277

This protein, which interacts with both microtubules and TRAF3 (tumour necrosis factor receptor-associated factor 3), is conserved from worms to humans. The N-terminal region is the microtubule binding domain and is well-conserved; the C-terminal 100 residues, also well-conserved, constitute the coiled-coil region which binds to TRAF3. The central region of the protein is rich in lysine and glutamic acid and carries KKE motifs which may also be necessary for tubulin-binding, but this region is the least well-conserved. Length = 506

>gnl|CDD|221821 pfam12871, PRP38_assoc, Pre-mRNA-splicing factor 38-associated hydrophilic C-term

 Score = 53.2 bits (128), Expect = 9e-09
 Identities = 34/77 (44%), Positives = 42/77 (54%)

Query: 886 EEEEKKKKEGGGGRRRRRRKKRRRSRRRRSRRRRRRRRRRRRRRRRRRRRRRRRRRRRRR 945
           E EE++  E    +  R   + RRS RRR+RRR RRR+R R+RRRRRR R R R R R  
Sbjct: 15  ESEEEEDDEEIRRKAERDVDRGRRSPRRRTRRRSRRRKRSRKRRRRRRDRDRARYRDRDD 74

Query: 946 RRRRRRRRRSGKEEEEE 962
           R R R  R   +     
Sbjct: 75  RDRDRYDRSRSRSRSRS 91

This domain is a hydrophilic region found at the C-terminus of plant and metazoan pre-mRNA-splicing factor 38 proteins. The function is not known. Length = 97

>gnl|CDD|234017 TIGR02794, tolA_full, TolA protein

 Score = 57.9 bits (140), Expect = 1e-08
 Identities = 37/136 (27%), Positives = 69/136 (50%), Gaps = 9/136 (6%)

Query: 898  GRRRRRRKKRRRSRRRRSRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRSGK 957
             R ++++K   +  + R ++  ++     ++R   + R++   +R    +  ++  ++ K
Sbjct: 53   NRIQQQKKPAAKKEQERQKKLEQQAEEAEKQRAAEQARQKELEQRAAAEKAAKQAEQAAK 112

Query: 958  EEEEEEKKKEEKK-KEEEEKKKK-----EGKTKKEEKKKEEEEEKKKKKKEEEKEEEE-- 1009
            + EE++K+ EE K K+  E K K     E K K+E KK+ EEE K K   E +K+  E  
Sbjct: 113  QAEEKQKQAEEAKAKQAAEAKAKAEAEAEKKAKEEAKKQAEEEAKAKAAAEAKKKAAEAK 172

Query: 1010 -KKEEEEKEEEEKKRR 1024
             K E E K + E K +
Sbjct: 173  KKAEAEAKAKAEAKAK 188

TolA couples the inner membrane complex of itself with TolQ and TolR to the outer membrane complex of TolB and OprL (also called Pal). Most of the length of the protein consists of low-complexity sequence that may differ in both length and composition from one species to another, complicating efforts to discriminate TolA (the most divergent gene in the tol-pal system) from paralogs such as TonB. Selection of members of the seed alignment and criteria for setting scoring cutoffs are based largely conserved operon struction. //The Tol-Pal complex is required for maintaining outer membrane integrity. Also involved in transport (uptake) of colicins and filamentous DNA, and implicated in pathogenesis. Transport is energized by the proton motive force. TolA is an inner membrane protein that interacts with periplasmic TolB and with outer membrane porins ompC, phoE and lamB [Transport and binding proteins, Other, Cellular processes, Pathogenesis]. Length = 346

>gnl|CDD|206039 pfam13868, Trichoplein, Tumour suppressor, Mitostatin

 Score = 57.6 bits (140), Expect = 1e-08
 Identities = 64/254 (25%), Positives = 114/254 (44%), Gaps = 57/254 (22%)

Query: 820  RRRRRKKKEEKKKWKRRGGGRRRRRGKKE-----EEKKKKKEEEEEGGEKEEEEGGGGGG 874
              R +   EE+++ ++R     RR G+       EE++K+++EE E   +E E+      
Sbjct: 49   EERLKALAEEEERERKRK--EERREGRAVLQEQIEEREKRRQEEYEERLQEREQ------ 100

Query: 875  RRRRRRRRSGKEEEEKKKKEGGGGRRRRRRKKRR---RSRRRRSRRRRRRRRRRRR---- 927
                      +EE+E + +E    +R +++K R         R  R+   + R R     
Sbjct: 101  --MDEIIERIQEEDEAEAQE----KREKQKKLREEIDEFNEERIERKEEEKEREREEELK 154

Query: 928  -----RRRRRRRRRRRRRRRRRRRRRRRRRRRSGKEEEEEEKKKEEK-----KKEEEEKK 977
                 R +  R   R   RR R+  + R   R   ++EE E ++EE         +EE +
Sbjct: 155  ILEYQREKAEREEEREAERRERKEEKEREVARLRAQQEEAEDEREELDELRADLYQEEYE 214

Query: 978  KKEGKTKKEEKKK------------EEEEEKKKKKKEEEKEEEEK---------KEEEEK 1016
            +KE + +KEE +K            EE+ E+K+++ +EE+ EEE           E+EE 
Sbjct: 215  RKERQKEKEEAEKRRRQKQELQRAREEQIEEKEERLQEERAEEEAERERMLEKQAEDEEL 274

Query: 1017 EEEEKKRRRIRRKR 1030
            E+E  ++RR++R  
Sbjct: 275  EQENAEKRRMKRLE 288

Trichoplein or mitostatin, was first defined as a meiosis-specific nuclear structural protein. It has since been linked with mitochondrial movement. It is associated with the mitochondrial outer membrane, and over-expression leads to reduction in mitochondrial motility whereas lack of it enhances mitochondrial movement. The activity appears to be mediated through binding the mitochondria to the actin intermediate filaments (IFs). Length = 349

>gnl|CDD|221821 pfam12871, PRP38_assoc, Pre-mRNA-splicing factor 38-associated hydrophilic C-term

 Score = 52.9 bits (127), Expect = 1e-08
 Identities = 41/96 (42%), Positives = 46/96 (47%), Gaps = 9/96 (9%)

Query: 856 EEEEEGGEKEEEEGGGGGGRRRRRRRRSGKEEEEKKKKEGGGGRRRRRRKKRRRSRRRRS 915
           +EEEE  E+E++E       R   R R                RRR RR+KR R RRRR 
Sbjct: 11  DEEEESEEEEDDEEIRRKAERDVDRGRRSPRRRT---------RRRSRRRKRSRKRRRRR 61

Query: 916 RRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRR 951
           R R R R R R  R R R  R R R R R R RRRR
Sbjct: 62  RDRDRARYRDRDDRDRDRYDRSRSRSRSRSRDRRRR 97

This domain is a hydrophilic region found at the C-terminus of plant and metazoan pre-mRNA-splicing factor 38 proteins. The function is not known. Length = 97

>gnl|CDD|225606 COG3064, TolA, Membrane protein involved in colicin uptake [Cell envelope biogenesis, outer membrane]

 Score = 58.0 bits (140), Expect = 1e-08
 Identities = 39/159 (24%), Positives = 73/159 (45%), Gaps = 7/159 (4%)

Query: 874  GRRRRRRRRSGKEEEEKKKKEGGGGRRRRRRKKRRRSRRRRSRRRRRRRRRRRRRRRRRR 933
            GR + ++  + K E+++KKKE       + ++   + R ++  + R + + ++++     
Sbjct: 65   GRIQSQQSSAKKGEQQRKKKEEQVAEELKPKQAAEQERLKQLEKERLKAQEQQKQAEEAE 124

Query: 934  RRRRRRRRRRRRRRRRRRRRRSGKEEEEEEKKKEE--KKKEEEEKKKK--EGKTKKEEKK 989
            ++ +  ++++  + R+    +  K E  + K   E  K K   E KKK  E     EE K
Sbjct: 125  KQAQLEQKQQEEQARKAAAEQKKKAEAAKAKAAAEAAKLKAAAEAKKKAEEAAKAAEEAK 184

Query: 990  KEEEEEKKKKKKEEE---KEEEEKKEEEEKEEEEKKRRR 1025
             + E    KKK E E     E+ K E E K + EKK   
Sbjct: 185  AKAEAAAAKKKAEAEAKAAAEKAKAEAEAKAKAEKKAEA 223

Length = 387

>gnl|CDD|219838 pfam08432, DUF1742, Fungal protein of unknown function (DUF1742)

 Score = 55.5 bits (134), Expect = 1e-08
 Identities = 27/66 (40%), Positives = 50/66 (75%)

Query: 957  KEEEEEEKKKEEKKKEEEEKKKKEGKTKKEEKKKEEEEEKKKKKKEEEKEEEEKKEEEEK 1016
            K+++E  ++ E+ KKE EEK+K + K KK +KKK+++++KK  KK+++ E++++KE E+K
Sbjct: 62   KKKKELAEEIEKVKKEYEEKQKWKWKKKKSKKKKDKDKDKKDDKKDDKSEKKDEKEAEDK 121

Query: 1017 EEEEKK 1022
             E+  K
Sbjct: 122  LEDLTK 127

This is a family of fungal proteins of unknown function. Length = 182

>gnl|CDD|223046 PHA03328, PHA03328, nuclear egress lamina protein UL31; Provisional

 Score = 57.4 bits (139), Expect = 1e-08
 Identities = 23/60 (38%), Positives = 25/60 (41%)

Query: 894 EGGGGRRRRRRKKRRRSRRRRSRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRR 953
           +    RR     +R R   RRSRR  R   R R R R RRR  RR   RR       R R
Sbjct: 2   DDLALRRSSSSLRRSRRAARRSRRDGRVGSRGRSRYRSRRRSSRRSSTRRAELADTERDR 61

Length = 316

>gnl|CDD|233496 TIGR01622, SF-CC1, splicing factor, CC1-like family

 Score = 57.6 bits (139), Expect = 2e-08
 Identities = 25/87 (28%), Positives = 35/87 (40%)

Query: 912 RRRSRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRSGKEEEEEEKKKEEKKK 971
           R R R R R R   RR  + R R RRR R R R RRRR R    G+      +      +
Sbjct: 1   RYRDRERGRLRNDTRRSDKGRERSRRRSRSRDRSRRRRDRDYYRGRRGRSRSRSPNRYYR 60

Query: 972 EEEEKKKKEGKTKKEEKKKEEEEEKKK 998
              ++  +    +     KE   E ++
Sbjct: 61  PRGDRSYRRDDRRSGRNTKEPLTEAER 87

This model represents a subfamily of RNA splicing factors including the Pad-1 protein (N. crassa), CAPER (M. musculus) and CC1.3 (H.sapiens). These proteins are characterized by an N-terminal arginine-rich, low complexity domain followed by three (or in the case of 4 H. sapiens paralogs, two) RNA recognition domains (rrm: pfam00706). These splicing factors are closely related to the U2AF splicing factor family (TIGR01642). A homologous gene from Plasmodium falciparum was identified in the course of the analysis of that genome at TIGR and was included in the seed. Length = 457

>gnl|CDD|235401 PRK05306, infB, translation initiation factor IF-2; Validated

 Score = 57.9 bits (141), Expect = 2e-08
 Identities = 21/140 (15%), Positives = 54/140 (38%), Gaps = 3/140 (2%)

Query: 858 EEEGGEKEEEEGGGGGGRRRRRRRRSGKEEEEKKKKEGGGGRRRRRRKKRRRSRRRRSRR 917
           EEE   KEE +       +      +  E EE+ K E          ++   +       
Sbjct: 39  EEEEARKEEAKREAEEEAKAEAEEAAAAEAEEEAKAE---AAAAAPAEEAAEAAAAAEAA 95

Query: 918 RRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRSGKEEEEEEKKKEEKKKEEEEKK 977
            R       R      RR + ++  ++++  + ++++  ++     K+ +  K     + 
Sbjct: 96  ARPAEDEAARPAEAAARRPKAKKAAKKKKGPKPKKKKPKRKAARGGKRGKGGKGRRRRRG 155

Query: 978 KKEGKTKKEEKKKEEEEEKK 997
           ++  + KK+++K  E+  ++
Sbjct: 156 RRRRRKKKKKQKPTEKIPRE 175

Length = 746

>gnl|CDD|221821 pfam12871, PRP38_assoc, Pre-mRNA-splicing factor 38-associated hydrophilic C-term

 Score = 52.5 bits (126), Expect = 2e-08
 Identities = 33/71 (46%), Positives = 40/71 (56%)

Query: 886 EEEEKKKKEGGGGRRRRRRKKRRRSRRRRSRRRRRRRRRRRRRRRRRRRRRRRRRRRRRR 945
           EE E+++ +    R+  R   R R   RR  RRR RRR+R R+RRRRRR R R R R R 
Sbjct: 14  EESEEEEDDEEIRRKAERDVDRGRRSPRRRTRRRSRRRKRSRKRRRRRRDRDRARYRDRD 73

Query: 946 RRRRRRRRRSG 956
            R R R  RS 
Sbjct: 74  DRDRDRYDRSR 84

This domain is a hydrophilic region found at the C-terminus of plant and metazoan pre-mRNA-splicing factor 38 proteins. The function is not known. Length = 97

>gnl|CDD|219061 pfam06495, Transformer, Fruit fly transformer protein

 Score = 54.7 bits (131), Expect = 2e-08
 Identities = 28/84 (33%), Positives = 37/84 (44%)

Query: 874 GRRRRRRRRSGKEEEEKKKKEGGGGRRRRRRKKRRRSRRRRSRRRRRRRRRRRRRRRRRR 933
            R R R R   + + +  +       RR R + R +S  R S +RR R R R R R   R
Sbjct: 30  VRERDRVRNLRQRKTQSTRPTTSHRGRRTRSRSRSQSAERNSCQRRHRSRSRSRNRSDSR 89

Query: 934 RRRRRRRRRRRRRRRRRRRRRSGK 957
            R      RRRR R R R  R+ +
Sbjct: 90  HRSTSSTERRRRSRSRSRYSRTPR 113

This family consists of transformer proteins from several Drosophila species and also from Ceratitis capitata (Mediterranean fruit fly). The transformer locus (tra) produces an RNA processing protein that alternatively splices the doublesex pre-mRNA in the sex determination hierarchy of Drosophila melanogaster. Length = 182

>gnl|CDD|217037 pfam02443, Circo_capsid, Circovirus capsid protein

 Score = 55.1 bits (133), Expect = 3e-08
 Identities = 22/34 (64%), Positives = 23/34 (67%)

Query: 924 RRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRSGK 957
           R R RRR RR RRRRRRRR  RRR RRRR    +
Sbjct: 1   RFRIRRRYRRPRRRRRRRRHWRRRYRRRRLHINR 34

Circoviruses are small circular single stranded viruses. This family is the capsid protein from viruses such as porcine circovirus and beak and feather disease virus. These proteins are about 220 amino acids long. Length = 237

>gnl|CDD|233496 TIGR01622, SF-CC1, splicing factor, CC1-like family

 Score = 56.8 bits (137), Expect = 3e-08
 Identities = 29/86 (33%), Positives = 37/86 (43%)

Query: 901 RRRRKKRRRSRRRRSRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRSGKEEE 960
           R R ++R R R    R  + R R RRR R R R RRRR R   R RR R R R   +   
Sbjct: 1   RYRDRERGRLRNDTRRSDKGRERSRRRSRSRDRSRRRRDRDYYRGRRGRSRSRSPNRYYR 60

Query: 961 EEEKKKEEKKKEEEEKKKKEGKTKKE 986
               +   +      +  KE  T+ E
Sbjct: 61  PRGDRSYRRDDRRSGRNTKEPLTEAE 86

This model represents a subfamily of RNA splicing factors including the Pad-1 protein (N. crassa), CAPER (M. musculus) and CC1.3 (H.sapiens). These proteins are characterized by an N-terminal arginine-rich, low complexity domain followed by three (or in the case of 4 H. sapiens paralogs, two) RNA recognition domains (rrm: pfam00706). These splicing factors are closely related to the U2AF splicing factor family (TIGR01642). A homologous gene from Plasmodium falciparum was identified in the course of the analysis of that genome at TIGR and was included in the seed. Length = 457

>gnl|CDD|221821 pfam12871, PRP38_assoc, Pre-mRNA-splicing factor 38-associated hydrophilic C-term

 Score = 51.7 bits (124), Expect = 3e-08
 Identities = 35/97 (36%), Positives = 45/97 (46%)

Query: 853 KKKEEEEEGGEKEEEEGGGGGGRRRRRRRRSGKEEEEKKKKEGGGGRRRRRRKKRRRSRR 912
            +    EE  ++EEE          RR+     +   +  +     R RRR++ R+R RR
Sbjct: 1   PRVSALEEDLDEEEESEEEEDDEEIRRKAERDVDRGRRSPRRRTRRRSRRRKRSRKRRRR 60

Query: 913 RRSRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRR 949
           RR R R R R R  R R R  R R R R R R RRRR
Sbjct: 61  RRDRDRARYRDRDDRDRDRYDRSRSRSRSRSRDRRRR 97

This domain is a hydrophilic region found at the C-terminus of plant and metazoan pre-mRNA-splicing factor 38 proteins. The function is not known. Length = 97

>gnl|CDD|217051 pfam02463, SMC_N, RecF/RecN/SMC N terminal domain

 Score = 58.1 bits (140), Expect = 3e-08
 Identities = 43/192 (22%), Positives = 80/192 (41%), Gaps = 14/192 (7%)

Query: 846  KKEEEKKKKKEEEEEGGEKEEEEGGGGGGRRRRRRRRSGKEEEEKKKKEGGGGRRRRRRK 905
            KK+E  KK  EE E   E   +          + +    KE+ +K  +      +    +
Sbjct: 171  KKKERLKKLIEETENLAELIIDL------EELKLQELKLKEQAKKALEYYQLKEKLELEE 224

Query: 906  KRRRSRRRRSRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRSGKEEEEEEKK 965
            +             R    +   R  +      ++   +      +  +  KEEE+E+K 
Sbjct: 225  ENLLYLDYLKLNEERIDLLQELLRDEQEEIESSKQELEKEEEILAQVLKENKEEEKEKKL 284

Query: 966  KEEKKK--------EEEEKKKKEGKTKKEEKKKEEEEEKKKKKKEEEKEEEEKKEEEEKE 1017
            +EE+ K         + E  K E +   +E+K +E E++ KK ++E K+E+E+ EE EKE
Sbjct: 285  QEEELKLLAKEEEELKSELLKLERRKVDDEEKLKESEKELKKLEKELKKEKEEIEELEKE 344

Query: 1018 EEEKKRRRIRRK 1029
             +E + +R   +
Sbjct: 345  LKELEIKREAEE 356

This domain is found at the N terminus of SMC proteins. The SMC (structural maintenance of chromosomes) superfamily proteins have ATP-binding domains at the N- and C-termini, and two extended coiled-coil domains separated by a hinge in the middle. The eukaryotic SMC proteins form two kind of heterodimers: the SMC1/SMC3 and the SMC2/SMC4 types. These heterodimers constitute an essential part of higher order complexes, which are involved in chromatin and DNA dynamics. This family also includes the RecF and RecN proteins that are involved in DNA metabolism and recombination. Length = 1162

>gnl|CDD|217438 pfam03228, Adeno_VII, Adenoviral core protein VII

 Score = 52.5 bits (126), Expect = 3e-08
 Identities = 25/83 (30%), Positives = 29/83 (34%), Gaps = 8/83 (9%)

Query: 869 GGGGGGRRRRRRRRSGKEEEEKKKKEGGGGRRRRRRKKRRRSRRRRSRRRRRRRRRRRRR 928
            G   GR      R   ++  +K           R           S     R  RRRRR
Sbjct: 43  WGSLNGRTTVDDLRDNLKKYARKY--------TERTVASTVDPVADSVPAGARAYRRRRR 94

Query: 929 RRRRRRRRRRRRRRRRRRRRRRR 951
           R RR  RRR RR+  R RR  R 
Sbjct: 95  RLRRVARRRARRKSTRARRAARA 117

The function of this protein is unknown. It has a conserved amino terminus of 50 residues followed by a positively charged tail, suggesting it may interact with nucleic acid. The major core protein of the adenovirus, protein VII, was found to be associated with viral DNA throughout infection. The precursor to protein VII were shown to be in vivo and in vitro acceptors of ADP-ribose. The ADP-ribosylated core proteins were assembled into mature virus particles. ADP-ribosylation of adenovirus core proteins may have a role in virus decapsidation. Length = 117

>gnl|CDD|235401 PRK05306, infB, translation initiation factor IF-2; Validated

 Score = 57.2 bits (139), Expect = 4e-08
 Identities = 19/140 (13%), Positives = 49/140 (35%), Gaps = 4/140 (2%)

Query: 886  EEEEKKKKEGGGGRRRRRRKKRRRSRRRRSRRRRRRRRRRRRRRRRRRRRRRRRRRRRRR 945
            EEEE +K+E     +R   ++ +      +        +                     
Sbjct: 39   EEEEARKEE----AKREAEEEAKAEAEEAAAAEAEEEAKAEAAAAAPAEEAAEAAAAAEA 94

Query: 946  RRRRRRRRRSGKEEEEEEKKKEEKKKEEEEKKKKEGKTKKEEKKKEEEEEKKKKKKEEEK 1005
              R      +   E    + K +K  ++++  K + K  K +  +  +  K  K +   +
Sbjct: 95   AARPAEDEAARPAEAAARRPKAKKAAKKKKGPKPKKKKPKRKAARGGKRGKGGKGRRRRR 154

Query: 1006 EEEEKKEEEEKEEEEKKRRR 1025
                ++++++K++  +K  R
Sbjct: 155  GRRRRRKKKKKQKPTEKIPR 174

Length = 746

>gnl|CDD|215824 pfam00260, Protamine_P1, Protamine P1

 Score = 50.3 bits (120), Expect = 4e-08
 Identities = 31/50 (62%), Positives = 32/50 (64%)

Query: 899 RRRRRRKKRRRSRRRRSRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRR 948
           R R  R + R   RRR RRR RRRRRR  RRRRRR    RRR  RRRRRR
Sbjct: 2   RYRCCRSRSRSRCRRRRRRRCRRRRRRCCRRRRRRVGCCRRRYTRRRRRR 51

Length = 51

>gnl|CDD|233503 TIGR01642, U2AF_lg, U2 snRNP auxilliary factor, large subunit, splicing factor

 Score = 56.4 bits (136), Expect = 5e-08
 Identities = 25/112 (22%), Positives = 46/112 (41%), Gaps = 3/112 (2%)

Query: 903  RRKKRRRSR---RRRSRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRSGKEE 959
            R ++  R R   R R R R   R RRR R R R R R RR R R  R   R R R   + 
Sbjct: 1    RDEEPDREREKSRGRDRDRSSERPRRRSRDRSRFRDRHRRSRERSYREDSRPRDRRRYDS 60

Query: 960  EEEEKKKEEKKKEEEEKKKKEGKTKKEEKKKEEEEEKKKKKKEEEKEEEEKK 1011
                  +    +   ++ ++  ++ +  ++       +    +  K+++++ 
Sbjct: 61   RSPRSLRYSSVRRSRDRPRRRSRSVRSIEQHRRRLRDRSPSNQWRKDDKKRS 112

These splicing factors consist of an N-terminal arginine-rich low complexity domain followed by three tandem RNA recognition motifs (pfam00076). The well-characterized members of this family are auxilliary components of the U2 small nuclear ribonuclearprotein splicing factor (U2AF). These proteins are closely related to the CC1-like subfamily of splicing factors (TIGR01622). Members of this subfamily are found in plants, metazoa and fungi. Length = 509

>gnl|CDD|219953 pfam08648, DUF1777, Protein of unknown function (DUF1777)

 Score = 53.3 bits (128), Expect = 5e-08
 Identities = 30/102 (29%), Positives = 53/102 (51%)

Query: 919  RRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRSGKEEEEEEKKKEEKKKEEEEKKK 978
            R R R  RR RRR R R R RR RRR R R R R R  +       +    +     + +
Sbjct: 3    RSRSRSPRRSRRRGRSRSRDRRERRRERSRSRERDRRRRSRSRSPHRSRRSRSPRRHRSR 62

Query: 979  KEGKTKKEEKKKEEEEEKKKKKKEEEKEEEEKKEEEEKEEEE 1020
                +++ ++K+E +++ ++ KK E ++  ++++ E K +EE
Sbjct: 63   SRSPSRRRDRKRERDKDAREPKKRERQKLIKEEDLEGKSDEE 104

This is a family of eukaryotic proteins of unknown function. Some of the proteins in this family are putative nucleic acid binding proteins. Length = 158

>gnl|CDD|234017 TIGR02794, tolA_full, TolA protein

 Score = 56.0 bits (135), Expect = 5e-08
 Identities = 35/191 (18%), Positives = 83/191 (43%), Gaps = 14/191 (7%)

Query: 845  GKKEEEKKKKKEEEEEGGEKEEEEGGGGGGRRRRRRRRSGKEEEEKKKKEGGGGRRRRRR 904
            G   ++  + +++++   +KE+E        R+++  +  +E E+++  E    +   +R
Sbjct: 46   GAVAQQANRIQQQKKPAAKKEQE--------RQKKLEQQAEEAEKQRAAEQARQKELEQR 97

Query: 905  KKRRRSRRRRSRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRSGKEEEEEEK 964
                ++ ++  +  ++   ++++    + ++    + +      ++ +  + K+ EEE K
Sbjct: 98   AAAEKAAKQAEQAAKQAEEKQKQAEEAKAKQAAEAKAKAEAEAEKKAKEEAKKQAEEEAK 157

Query: 965  KKEE---KKKEEEEKKKKEGKTKKE---EKKKEEEEEKKKKKKEEEKEEEEKKEEEEKEE 1018
             K     KKK  E KKK E + K +   + K + EE K K +  + K   E   + E E 
Sbjct: 158  AKAAAEAKKKAAEAKKKAEAEAKAKAEAKAKAKAEEAKAKAEAAKAKAAAEAAAKAEAEA 217

Query: 1019 EEKKRRRIRRK 1029
                     RK
Sbjct: 218  AAAAAAEAERK 228

TolA couples the inner membrane complex of itself with TolQ and TolR to the outer membrane complex of TolB and OprL (also called Pal). Most of the length of the protein consists of low-complexity sequence that may differ in both length and composition from one species to another, complicating efforts to discriminate TolA (the most divergent gene in the tol-pal system) from paralogs such as TonB. Selection of members of the seed alignment and criteria for setting scoring cutoffs are based largely conserved operon struction. //The Tol-Pal complex is required for maintaining outer membrane integrity. Also involved in transport (uptake) of colicins and filamentous DNA, and implicated in pathogenesis. Transport is energized by the proton motive force. TolA is an inner membrane protein that interacts with periplasmic TolB and with outer membrane porins ompC, phoE and lamB [Transport and binding proteins, Other, Cellular processes, Pathogenesis]. Length = 346

>gnl|CDD|233758 TIGR02169, SMC_prok_A, chromosome segregation protein SMC, primarily archaeal type

 Score = 57.0 bits (138), Expect = 5e-08
 Identities = 50/239 (20%), Positives = 89/239 (37%), Gaps = 22/239 (9%)

Query: 810  IRLSRNRRGRRRRRRKKKEEKKKWKRRGGGRRRRRGKKEEEKKKKKEEEEEGGEKE---- 865
            I   R +  R RR R+K E  +   +    +R   G +  ++K+  E ++E  E++    
Sbjct: 193  IDEKRQQLERLRREREKAERYQALLKE---KREYEGYELLKEKEALERQKEAIERQLASL 249

Query: 866  EEEGGGGGGRRRRRRRRSG------KEEEEKKKKEGGGGRRRRRRK---------KRRRS 910
            EEE            +R        +E  +K K  G   + R + K            RS
Sbjct: 250  EEELEKLTEEISELEKRLEEIEQLLEELNKKIKDLGEEEQLRVKEKIGELEAEIASLERS 309

Query: 911  RRRRSRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRSGKEEEEEEKKKEEKK 970
               + R       R  +      +         R     R+RR    EE  E K++ E  
Sbjct: 310  IAEKERELEDAEERLAKLEAEIDKLLAEIEELEREIEEERKRRDKLTEEYAELKEELEDL 369

Query: 971  KEEEEKKKKEGKTKKEEKKKEEEEEKKKKKKEEEKEEEEKKEEEEKEEEEKKRRRIRRK 1029
            + E E+  KE    ++E K   E+ +K K++  E + E  + +EE +   ++   +   
Sbjct: 370  RAELEEVDKEFAETRDELKDYREKLEKLKREINELKRELDRLQEELQRLSEELADLNAA 428

SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]. Length = 1164

>gnl|CDD|206039 pfam13868, Trichoplein, Tumour suppressor, Mitostatin

 Score = 55.7 bits (135), Expect = 6e-08
 Identities = 39/158 (24%), Positives = 81/158 (51%), Gaps = 8/158 (5%)

Query: 880  RRRSGKEEEEKKKKEGGGGRRRRRRKKRRRSRRRRSRRRRRRRRRRRRRRRRRRRRRRRR 939
            ++R   EE+E++++        R +       R R R+  RR  R   + +   R +RR+
Sbjct: 29   KKRIKAEEKEEERRIDEMMEEERLKALAEEEERERKRKEERREGRAVLQEQIEEREKRRQ 88

Query: 940  RRRRRRRRRRRRRRRSGKEEEEEEKKKEEKKKEEEEKKKKE--------GKTKKEEKKKE 991
                 R + R +     +  +EE++ + ++K+E+++K ++E         + K+EEK++E
Sbjct: 89   EEYEERLQEREQMDEIIERIQEEDEAEAQEKREKQKKLREEIDEFNEERIERKEEEKERE 148

Query: 992  EEEEKKKKKKEEEKEEEEKKEEEEKEEEEKKRRRIRRK 1029
             EEE K  + + EK E E++ E E+ E ++++ R   +
Sbjct: 149  REEELKILEYQREKAEREEEREAERRERKEEKEREVAR 186

Trichoplein or mitostatin, was first defined as a meiosis-specific nuclear structural protein. It has since been linked with mitochondrial movement. It is associated with the mitochondrial outer membrane, and over-expression leads to reduction in mitochondrial motility whereas lack of it enhances mitochondrial movement. The activity appears to be mediated through binding the mitochondria to the actin intermediate filaments (IFs). Length = 349

>gnl|CDD|224117 COG1196, Smc, Chromosome segregation ATPases [Cell division and chromosome partitioning]

 Score = 56.6 bits (137), Expect = 6e-08
 Identities = 55/291 (18%), Positives = 110/291 (37%), Gaps = 20/291 (6%)

Query: 737  SQLASEAGKFVISQILDEQSYTDYSLDDRLQNIHEHMKKIRTDLDNGFVPLTLLEITKQL 796
            S LA +     + + L E       L++ L+++   ++ +   L+         E+ +QL
Sbjct: 661  SSLAQKRELKELEEELAELEAQLEKLEEELKSLKNELRSLEDLLE---------ELRRQL 711

Query: 797  TKAPEGGKVCITQIRLSRNRRGRRRRRRKKKEEKKKWKRRGGGRRRRRGKKEEEKKKKKE 856
             +     +    ++        + + R ++ EE+ +         + R ++ EE+ +  E
Sbjct: 712  EELERQLEELKRELAALEEELEQLQSRLEELEEELEELEEELEELQERLEELEEELESLE 771

Query: 857  EEEEGGEKEEEEGGGGGGRRRRRRRRSGKEEEEKKKKEGGGGRRRRRRKKRRRSRRRRSR 916
            E     ++E EE        +R+  +   EE E++           RR            
Sbjct: 772  EALAKLKEEIEE-----LEEKRQALQEELEELEEEL------EEAERRLDALERELESLE 820

Query: 917  RRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRSGKEEEEEEKKKEEKKKEEEEK 976
            +RR R  +              +            +     +EE EE + E+++ E+E K
Sbjct: 821  QRRERLEQEIEELEEEIEELEEKLDELEEELEELEKELEELKEELEELEAEKEELEDELK 880

Query: 977  KKKEGKTKKEEKKKEEEEEKKKKKKEEEKEEEEKKEEEEKEEEEKKRRRIR 1027
            + +E K + EE+ +E E E  + K+E EK  E  +E E K E  +      
Sbjct: 881  ELEEEKEELEEELRELESELAELKEEIEKLRERLEELEAKLERLEVELPEL 931

Length = 1163

>gnl|CDD|219408 pfam07423, DUF1510, Protein of unknown function (DUF1510)

 Score = 54.0 bits (130), Expect = 6e-08
 Identities = 26/70 (37%), Positives = 42/70 (60%), Gaps = 2/70 (2%)

Query: 955  SGKEEEEEEKKKEEKKKEEEEKKKKEGKTKK--EEKKKEEEEEKKKKKKEEEKEEEEKKE 1012
            + K +++E  + EE K+EE+E    E K  K   EK+ EE EE+ +++ EE  +E EK+ 
Sbjct: 51   AKKSDDQETAEIEEVKEEEKEAANSEDKEDKGDAEKEDEESEEENEEEDEESSDENEKET 110

Query: 1013 EEEKEEEEKK 1022
            EE+ E   +K
Sbjct: 111  EEKTESNVEK 120

This family consists of several hypothetical bacterial proteins of around 200 residues in length. The function of this family is unknown. Length = 214

>gnl|CDD|235401 PRK05306, infB, translation initiation factor IF-2; Validated

 Score = 56.4 bits (137), Expect = 7e-08
 Identities = 24/142 (16%), Positives = 45/142 (31%)

Query: 887  EEEKKKKEGGGGRRRRRRKKRRRSRRRRSRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRR 946
            EEE+ +KE          K               +                       R 
Sbjct: 39   EEEEARKEEAKREAEEEAKAEAEEAAAAEAEEEAKAEAAAAAPAEEAAEAAAAAEAAARP 98

Query: 947  RRRRRRRRSGKEEEEEEKKKEEKKKEEEEKKKKEGKTKKEEKKKEEEEEKKKKKKEEEKE 1006
                  R +       + KK  KKK+  + KKK+ K K     K  +  K ++++   + 
Sbjct: 99   AEDEAARPAEAAARRPKAKKAAKKKKGPKPKKKKPKRKAARGGKRGKGGKGRRRRRGRRR 158

Query: 1007 EEEKKEEEEKEEEEKKRRRIRR 1028
              +KK++++  E+  +   I  
Sbjct: 159  RRKKKKKQKPTEKIPREVVIPE 180

Length = 746

>gnl|CDD|224117 COG1196, Smc, Chromosome segregation ATPases [Cell division and chromosome partitioning]

 Score = 56.6 bits (137), Expect = 7e-08
 Identities = 41/219 (18%), Positives = 74/219 (33%), Gaps = 14/219 (6%)

Query: 815  NRRGRRRRRRKKKEEKKKWKRRGGGRRRRRGKKEEEKKKKKEEEEEGGEKEEEEGGGGGG 874
             R    +   ++ E      +    R+     +EE  + ++E EE   E EE E      
Sbjct: 213  ERYQELKAELRELELALLLAKLKELRKELEELEEELSRLEEELEELQEELEEAEKEIE-- 270

Query: 875  RRRRRRRRSGKEEEEKKKKEGGGGRRRRRRKKRRRSRRRRSRRRRRRRRRRRRRRRRRRR 934
               +      +EE E+ ++E          K+            R R             
Sbjct: 271  -ELKSELEELREELEELQEEL------LELKEEIEELEGEISLLRERLEELENELEELEE 323

Query: 935  RRRRRRRRRRRRRRRRRRRRSGKEEEEEEKKKEEKKKEEEEKKKKEGKTKKEEKKKEEEE 994
            R    + +    +     R +  EE E+   + E+ KEE E+K      + EE  +   E
Sbjct: 324  RLEELKEKIEALKEELEERETLLEELEQLLAELEEAKEELEEKLSALLEELEELFEALRE 383

Query: 995  E-----KKKKKKEEEKEEEEKKEEEEKEEEEKKRRRIRR 1028
            E      +  +   E EE +++ E  +E  E+   R+  
Sbjct: 384  ELAELEAELAEIRNELEELKREIESLEERLERLSERLED 422

Length = 1163

>gnl|CDD|219838 pfam08432, DUF1742, Fungal protein of unknown function (DUF1742)

 Score = 52.8 bits (127), Expect = 9e-08
 Identities = 21/70 (30%), Positives = 46/70 (65%)

Query: 957  KEEEEEEKKKEEKKKEEEEKKKKEGKTKKEEKKKEEEEEKKKKKKEEEKEEEEKKEEEEK 1016
            K++E  E+ ++ KK+ EE++K K  K K ++KK +++++K  KK ++ ++++EK+ E++ 
Sbjct: 63   KKKELAEEIEKVKKEYEEKQKWKWKKKKSKKKKDKDKDKKDDKKDDKSEKKDEKEAEDKL 122

Query: 1017 EEEEKKRRRI 1026
            E+  K     
Sbjct: 123  EDLTKSYSET 132

This is a family of fungal proteins of unknown function. Length = 182

>gnl|CDD|235250 PRK04195, PRK04195, replication factor C large subunit; Provisional

 Score = 55.3 bits (134), Expect = 1e-07
 Identities = 28/61 (45%), Positives = 50/61 (81%)

Query: 956  GKEEEEEEKKKEEKKKEEEEKKKKEGKTKKEEKKKEEEEEKKKKKKEEEKEEEEKKEEEE 1015
             K E++ E++K+EKKK+    KKKE + ++E++KKEEE+E+++++ EEEKEEEE+K++++
Sbjct: 417  EKAEKKREEEKKEKKKKAFAGKKKEEEEEEEKEKKEEEKEEEEEEAEEEKEEEEEKKKKQ 476

Query: 1016 K 1016
             
Sbjct: 477  A 477

Length = 482

>gnl|CDD|215824 pfam00260, Protamine_P1, Protamine P1

 Score = 48.7 bits (116), Expect = 1e-07
 Identities = 28/46 (60%), Positives = 29/46 (63%)

Query: 910 SRRRRSRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRS 955
           +R R  R R R R RRRRRRR RRRRRR  RRRRRR    RRR   
Sbjct: 1   ARYRCCRSRSRSRCRRRRRRRCRRRRRRCCRRRRRRVGCCRRRYTR 46

Length = 51

>gnl|CDD|206039 pfam13868, Trichoplein, Tumour suppressor, Mitostatin

 Score = 54.5 bits (132), Expect = 1e-07
 Identities = 52/227 (22%), Positives = 107/227 (47%), Gaps = 34/227 (14%)

Query: 823  RRKKKEEKKKWKRRGGGRRRRRGKKEEEKKKKKEEEEEGGEKEEEEGGGGGGRRRRRRRR 882
            R  + EEKK+ K       RR  +  EE++ K   EEE  E+E +         R+  RR
Sbjct: 22   RDAQIEEKKRIKAEEKEEERRIDEMMEEERLKALAEEE--ERERK---------RKEERR 70

Query: 883  SGKEEEEKKKKEGGGGRRRRRRKKRRRSRRRRSRRRRRRRRRRRRRRRRRRRRRRRRRRR 942
             G+   +++ +E    R +RR+++     + R +      R +       + +R ++++ 
Sbjct: 71   EGRAVLQEQIEE----REKRRQEEYEERLQEREQMDEIIERIQEEDEAEAQEKREKQKKL 126

Query: 943  RR------RRRRRRRRRRSGKEEEEEEK------KKEEKKKEEEEKKKKEGKTKKEEKKK 990
            R         R  R+     +E EEE K      +K E+++E E ++++  + K+ E  +
Sbjct: 127  REEIDEFNEERIERKEEEKEREREEELKILEYQREKAEREEEREAERRERKEEKEREVAR 186

Query: 991  EEEEEKKKKKKEEEKEE-------EEKKEEEEKEEEEKKRRRIRRKR 1030
               ++++ + + EE +E       EE + +E ++E+E+  +R R+K+
Sbjct: 187  LRAQQEEAEDEREELDELRADLYQEEYERKERQKEKEEAEKRRRQKQ 233

Trichoplein or mitostatin, was first defined as a meiosis-specific nuclear structural protein. It has since been linked with mitochondrial movement. It is associated with the mitochondrial outer membrane, and over-expression leads to reduction in mitochondrial motility whereas lack of it enhances mitochondrial movement. The activity appears to be mediated through binding the mitochondria to the actin intermediate filaments (IFs). Length = 349

>gnl|CDD|219838 pfam08432, DUF1742, Fungal protein of unknown function (DUF1742)

 Score = 52.8 bits (127), Expect = 1e-07
 Identities = 25/66 (37%), Positives = 43/66 (65%)

Query: 957  KEEEEEEKKKEEKKKEEEEKKKKEGKTKKEEKKKEEEEEKKKKKKEEEKEEEEKKEEEEK 1016
             EE E+ KK+ E+K++ + KKKK  K K ++K K+++++  K +K++EKE E+K E+  K
Sbjct: 68   AEEIEKVKKEYEEKQKWKWKKKKSKKKKDKDKDKKDDKKDDKSEKKDEKEAEDKLEDLTK 127

Query: 1017 EEEEKK 1022
               E  
Sbjct: 128  SYSETL 133

This is a family of fungal proteins of unknown function. Length = 182

>gnl|CDD|223046 PHA03328, PHA03328, nuclear egress lamina protein UL31; Provisional

 Score = 54.7 bits (132), Expect = 1e-07
 Identities = 22/56 (39%), Positives = 23/56 (41%)

Query: 900 RRRRRKKRRRSRRRRSRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRS 955
             RR     R  RR +RR RR  R   R R R R RRR  RR   RR       R 
Sbjct: 5   ALRRSSSSLRRSRRAARRSRRDGRVGSRGRSRYRSRRRSSRRSSTRRAELADTERD 60

Length = 316

>gnl|CDD|217438 pfam03228, Adeno_VII, Adenoviral core protein VII

 Score = 51.0 bits (122), Expect = 1e-07
 Identities = 22/62 (35%), Positives = 26/62 (41%), Gaps = 6/62 (9%)

Query: 900 RRRRRKKRRRSRRRRSRRRRR------RRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRR 953
           R   +K  R+   R                 R  RRRRRR RR  RRR RR+  R RR  
Sbjct: 56  RDNLKKYARKYTERTVASTVDPVADSVPAGARAYRRRRRRLRRVARRRARRKSTRARRAA 115

Query: 954 RS 955
           R+
Sbjct: 116 RA 117

The function of this protein is unknown. It has a conserved amino terminus of 50 residues followed by a positively charged tail, suggesting it may interact with nucleic acid. The major core protein of the adenovirus, protein VII, was found to be associated with viral DNA throughout infection. The precursor to protein VII were shown to be in vivo and in vitro acceptors of ADP-ribose. The ADP-ribosylated core proteins were assembled into mature virus particles. ADP-ribosylation of adenovirus core proteins may have a role in virus decapsidation. Length = 117

>gnl|CDD|218684 pfam05672, MAP7, MAP7 (E-MAP-115) family

 Score = 52.4 bits (125), Expect = 1e-07
 Identities = 34/117 (29%), Positives = 72/117 (61%)

Query: 911  RRRRSRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRSGKEEEEEEKKKEEKK 970
            +RR++R +R +  + RR +  + R  R   +RR    R RR   + ++EEE  ++KEEK 
Sbjct: 31   KRRQAREQREQEEQERREQEEQDRLEREELKRRAAEERLRREEEARRQEEERAREKEEKA 90

Query: 971  KEEEEKKKKEGKTKKEEKKKEEEEEKKKKKKEEEKEEEEKKEEEEKEEEEKKRRRIR 1027
            K + E+++K+ + ++E  +K++EE + + ++E E+   E+++  ++ E+E+  R+ R
Sbjct: 91   KRKAEEEEKQEQEEQERIQKQKEEAEARAREEAERMRLEREKHFQQIEQERLERKKR 147

The organisation of microtubules varies with the cell type and is presumably controlled by tissue-specific microtubule-associated proteins (MAPs). The 115-kDa epithelial MAP (E-MAP-115/MAP7) has been identified as a microtubule-stabilising protein predominantly expressed in cell lines of epithelial origin. The binding of this microtubule associated protein is nucleotide independent. Length = 171

>gnl|CDD|202096 pfam02029, Caldesmon, Caldesmon

 Score = 55.0 bits (132), Expect = 1e-07
 Identities = 52/219 (23%), Positives = 99/219 (45%), Gaps = 18/219 (8%)

Query: 816  RRGRRRRRRKKK-----EEKKKWKRRG------GGRRRRRGKKEEEKKKKKEEEEEGGEK 864
            R  RR  RR ++     E +K++K            RR +     E +  +EEE+E   +
Sbjct: 62   RLARREERRDERFSEALERQKEFKPTSTDQSLSEPSRRMQEDSGAENETVEEEEKEESRE 121

Query: 865  EEEEGGGGGGRRRRRRRRSGKEEEEKKKKEGGGGRRRRRRKKRRRSRRRRSRRRRRRRRR 924
            E EE     G  +  ++   ++ EE +K+E         + KR             + + 
Sbjct: 122  EREEVEETEGVTKSEQKNDWRDAEECQKEEKEPEPEEEEKPKRGSLEENNGEFMTHKLKH 181

Query: 925  RRRRRRRRRRRRRRRRRRRRRRRRRRRRRRSGKEEEEEEKKKEEKKK---EEEEKKKKEG 981
                  R      +    +   + +++++ +  E EE +KK+EE++K   EEE+++K+E 
Sbjct: 182  TENTFSRGGAEGAQVEAGKEFEKLKQKQQEAALELEELKKKREERRKVLEEEEQRRKQE- 240

Query: 982  KTKKEEKKKEEEEEKKKKKKEEEKEEEEKKEEEEKEEEE 1020
               + ++K  EEEEK++ K+E E+   E  E+ +K  E+
Sbjct: 241  ---EADRKSREEEEKRRLKEEIERRRAEAAEKRQKVPED 276

Length = 431

>gnl|CDD|233496 TIGR01622, SF-CC1, splicing factor, CC1-like family

 Score = 54.1 bits (130), Expect = 2e-07
 Identities = 27/90 (30%), Positives = 38/90 (42%)

Query: 907 RRRSRRRRSRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRSGKEEEEEEKKK 966
           R R R R   R   RR  + R R RRR R R R RRRR R   R RR   +        +
Sbjct: 1   RYRDRERGRLRNDTRRSDKGRERSRRRSRSRDRSRRRRDRDYYRGRRGRSRSRSPNRYYR 60

Query: 967 EEKKKEEEEKKKKEGKTKKEEKKKEEEEEK 996
               +      ++ G+  KE   + E +++
Sbjct: 61  PRGDRSYRRDDRRSGRNTKEPLTEAERDDR 90

This model represents a subfamily of RNA splicing factors including the Pad-1 protein (N. crassa), CAPER (M. musculus) and CC1.3 (H.sapiens). These proteins are characterized by an N-terminal arginine-rich, low complexity domain followed by three (or in the case of 4 H. sapiens paralogs, two) RNA recognition domains (rrm: pfam00706). These splicing factors are closely related to the U2AF splicing factor family (TIGR01642). A homologous gene from Plasmodium falciparum was identified in the course of the analysis of that genome at TIGR and was included in the seed. Length = 457

>gnl|CDD|235250 PRK04195, PRK04195, replication factor C large subunit; Provisional

 Score = 54.5 bits (132), Expect = 2e-07
 Identities = 28/66 (42%), Positives = 48/66 (72%)

Query: 957  KEEEEEEKKKEEKKKEEEEKKKKEGKTKKEEKKKEEEEEKKKKKKEEEKEEEEKKEEEEK 1016
            +EE E     ++  K+ ++  +K  K ++EEKK+++++    KKKEEE+EEE++K+EEEK
Sbjct: 396  EEEIEFLTGSKKATKKIKKIVEKAEKKREEEKKEKKKKAFAGKKKEEEEEEEKEKKEEEK 455

Query: 1017 EEEEKK 1022
            EEEE++
Sbjct: 456  EEEEEE 461

Length = 482

>gnl|CDD|235250 PRK04195, PRK04195, replication factor C large subunit; Provisional

 Score = 54.2 bits (131), Expect = 2e-07
 Identities = 23/66 (34%), Positives = 45/66 (68%)

Query: 960  EEEEKKKEEKKKEEEEKKKKEGKTKKEEKKKEEEEEKKKKKKEEEKEEEEKKEEEEKEEE 1019
             EEE +     K+  +K KK  +  ++++++E++E+KKK    ++KEEEE++E+E+KEEE
Sbjct: 395  TEEEIEFLTGSKKATKKIKKIVEKAEKKREEEKKEKKKKAFAGKKKEEEEEEEKEKKEEE 454

Query: 1020 EKKRRR 1025
            +++   
Sbjct: 455  KEEEEE 460

Length = 482

>gnl|CDD|224117 COG1196, Smc, Chromosome segregation ATPases [Cell division and chromosome partitioning]

 Score = 54.7 bits (132), Expect = 2e-07
 Identities = 37/225 (16%), Positives = 73/225 (32%), Gaps = 18/225 (8%)

Query: 814  RNRRGRRRRRRKKKEEKKKWKRRGGGRRRRRGKKEEEKKKKKEEEEEGGEKEEEEGGGGG 873
                 +  +  ++ E+ ++++      R         K K+  +E E  E+E        
Sbjct: 196  EELEKQLEKLERQAEKAERYQELKAELRELELALLLAKLKELRKELEELEEELSRL---- 251

Query: 874  GRRRRRRRRSGKEEEEKKKKEGGGGRRRRRRKKRRRSRRRRSRRRRRRRRRRRRRRRRRR 933
                       + +EE ++ E      +   ++ R             +           
Sbjct: 252  ------EEELEELQEELEEAEKEIEELKSELEELREELEELQEELLELKEEIEELEGEIS 305

Query: 934  RRRRRRRRRRRRRRRRRRRRRSGKEEEEEEKKK----EEKKKEEEEKKKKEGKTKKEEKK 989
              R R             R    KE+ E  K++    E   +E E+   +  + K+E ++
Sbjct: 306  LLRERLEELENELEELEERLEELKEKIEALKEELEERETLLEELEQLLAELEEAKEELEE 365

Query: 990  K----EEEEEKKKKKKEEEKEEEEKKEEEEKEEEEKKRRRIRRKR 1030
            K     EE E+  +   EE  E E +  E + E E+ +R I    
Sbjct: 366  KLSALLEELEELFEALREELAELEAELAEIRNELEELKREIESLE 410

Length = 1163

>gnl|CDD|221821 pfam12871, PRP38_assoc, Pre-mRNA-splicing factor 38-associated hydrophilic C-term

 Score = 49.8 bits (119), Expect = 2e-07
 Identities = 33/80 (41%), Positives = 43/80 (53%)

Query: 879 RRRRSGKEEEEKKKKEGGGGRRRRRRKKRRRSRRRRSRRRRRRRRRRRRRRRRRRRRRRR 938
               S +EE++++ +        R R+  RR  RRRSRRR+R R+RRRRRR R R R R 
Sbjct: 12  EEEESEEEEDDEEIRRKAERDVDRGRRSPRRRTRRRSRRRKRSRKRRRRRRDRDRARYRD 71

Query: 939 RRRRRRRRRRRRRRRRSGKE 958
           R  R R R  R R R   + 
Sbjct: 72  RDDRDRDRYDRSRSRSRSRS 91

This domain is a hydrophilic region found at the C-terminus of plant and metazoan pre-mRNA-splicing factor 38 proteins. The function is not known. Length = 97

>gnl|CDD|221821 pfam12871, PRP38_assoc, Pre-mRNA-splicing factor 38-associated hydrophilic C-term

 Score = 49.8 bits (119), Expect = 2e-07
 Identities = 35/82 (42%), Positives = 42/82 (51%)

Query: 875 RRRRRRRRSGKEEEEKKKKEGGGGRRRRRRKKRRRSRRRRSRRRRRRRRRRRRRRRRRRR 934
            R         EEEE +++E     RR+  +   R RR   RR RRR RRR+R R+RRRR
Sbjct: 1   PRVSALEEDLDEEEESEEEEDDEEIRRKAERDVDRGRRSPRRRTRRRSRRRKRSRKRRRR 60

Query: 935 RRRRRRRRRRRRRRRRRRRRSG 956
           RR R R R R R  R R R   
Sbjct: 61  RRDRDRARYRDRDDRDRDRYDR 82

This domain is a hydrophilic region found at the C-terminus of plant and metazoan pre-mRNA-splicing factor 38 proteins. The function is not known. Length = 97

>gnl|CDD|221821 pfam12871, PRP38_assoc, Pre-mRNA-splicing factor 38-associated hydrophilic C-term

 Score = 49.4 bits (118), Expect = 2e-07
 Identities = 32/72 (44%), Positives = 39/72 (54%)

Query: 887 EEEKKKKEGGGGRRRRRRKKRRRSRRRRSRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRR 946
             + ++    G R  RRR +RR  RR+RSR+RRRRRR R R R R R  R R R  R R 
Sbjct: 26  RRKAERDVDRGRRSPRRRTRRRSRRRKRSRKRRRRRRDRDRARYRDRDDRDRDRYDRSRS 85

Query: 947 RRRRRRRRSGKE 958
           R R R R   + 
Sbjct: 86  RSRSRSRDRRRR 97

This domain is a hydrophilic region found at the C-terminus of plant and metazoan pre-mRNA-splicing factor 38 proteins. The function is not known. Length = 97

>gnl|CDD|219838 pfam08432, DUF1742, Fungal protein of unknown function (DUF1742)

 Score = 52.0 bits (125), Expect = 2e-07
 Identities = 24/69 (34%), Positives = 48/69 (69%), Gaps = 4/69 (5%)

Query: 958  EEEEEEKKKEEKKKEEEEKKKKE----GKTKKEEKKKEEEEEKKKKKKEEEKEEEEKKEE 1013
             E  E KKK+++  EE EK KKE     K K ++KK +++++K K KK+++K+++ +K++
Sbjct: 55   AEYTEAKKKKKELAEEIEKVKKEYEEKQKWKWKKKKSKKKKDKDKDKKDDKKDDKSEKKD 114

Query: 1014 EEKEEEEKK 1022
            E++ E++ +
Sbjct: 115  EKEAEDKLE 123

This is a family of fungal proteins of unknown function. Length = 182

>gnl|CDD|223046 PHA03328, PHA03328, nuclear egress lamina protein UL31; Provisional

 Score = 53.9 bits (130), Expect = 2e-07
 Identities = 22/56 (39%), Positives = 24/56 (42%)

Query: 907 RRRSRRRRSRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRSGKEEEEE 962
             R      RR RR  RR RR  R   R R R R RRR  RR   RR    + E +
Sbjct: 5   ALRRSSSSLRRSRRAARRSRRDGRVGSRGRSRYRSRRRSSRRSSTRRAELADTERD 60

Length = 316

>gnl|CDD|217438 pfam03228, Adeno_VII, Adenoviral core protein VII

 Score = 50.2 bits (120), Expect = 2e-07
 Identities = 20/54 (37%), Positives = 22/54 (40%)

Query: 899 RRRRRRKKRRRSRRRRSRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRR 952
           R+   R                 R  RRRRRR RR  RRR RR+  R RR  R 
Sbjct: 64  RKYTERTVASTVDPVADSVPAGARAYRRRRRRLRRVARRRARRKSTRARRAARA 117

The function of this protein is unknown. It has a conserved amino terminus of 50 residues followed by a positively charged tail, suggesting it may interact with nucleic acid. The major core protein of the adenovirus, protein VII, was found to be associated with viral DNA throughout infection. The precursor to protein VII were shown to be in vivo and in vitro acceptors of ADP-ribose. The ADP-ribosylated core proteins were assembled into mature virus particles. ADP-ribosylation of adenovirus core proteins may have a role in virus decapsidation. Length = 117

>gnl|CDD|219408 pfam07423, DUF1510, Protein of unknown function (DUF1510)

 Score = 52.4 bits (126), Expect = 2e-07
 Identities = 23/73 (31%), Positives = 45/73 (61%), Gaps = 3/73 (4%)

Query: 953  RRSGKEEEEEEKKKEEKKKEEEEKKKKEGKTKKEEKKKEEEEEKKK---KKKEEEKEEEE 1009
             ++  +E+E +K  +++  E EE K++E +    E K+++ + +K+    ++E E+E+EE
Sbjct: 42   DQAAADEQEAKKSDDQETAEIEEVKEEEKEAANSEDKEDKGDAEKEDEESEEENEEEDEE 101

Query: 1010 KKEEEEKEEEEKK 1022
              +E EKE EEK 
Sbjct: 102  SSDENEKETEEKT 114

This family consists of several hypothetical bacterial proteins of around 200 residues in length. The function of this family is unknown. Length = 214

>gnl|CDD|223049 PHA03334, PHA03334, putative DNA polymerase catalytic subunit; Provisional

 Score = 55.2 bits (133), Expect = 2e-07
 Identities = 52/214 (24%), Positives = 75/214 (35%), Gaps = 46/214 (21%)

Query: 482 TGEANKGKGRKKAAYSGGLVLEPKKGF-----YDKFIILMDFNSLYPSIIQEYNIC---- 532
             E      R+K    GG V  P  G      Y    + +DF SLYPS + + NI     
Sbjct: 619 MPEKYARDCRQKIKLKGGYVFAPLTGLTFAGPYQGTELTLDFASLYPSNMCDANISPEAI 678

Query: 533 ----------------FTTIPVRMLQDSDITTLCEYLPE------HQVDTGILPSEIKKL 570
                           +  I     + + + T+    PE          T    S +   
Sbjct: 679 VDPDCTARVRGWVVFDWKKIDRGFGKATLMYTILRTKPEEPSWRRFTTYTT---SSLNHY 735

Query: 571 VESRRQVKALMKQPNLSSDLLMQYDIRQKALKLTANSMYGCLGFPNSRFFAQPLAA-LVT 629
           +  R + K  MKQ      L   ++  Q  +K+ ANS YG          A      L+T
Sbjct: 736 LSMRTEYKGAMKQAK-DPKLKSYHNQLQNEMKICANSHYGV---------APHACQHLIT 785

Query: 630 AKGR-EILLNTKSLVENLNYEVIYGDTDSLMISC 662
             GR +I L  + + +     V YGDTDS+M   
Sbjct: 786 TLGRHKIKLVEEFIKKEPGMTVNYGDTDSVMFQL 819

Length = 1545

>gnl|CDD|144437 pfam00841, Protamine_P2, Sperm histone P2

 Score = 49.6 bits (118), Expect = 2e-07
 Identities = 34/83 (40%), Positives = 39/83 (46%), Gaps = 2/83 (2%)

Query: 868 EGGGGGGRRRRRRRRSGKEEEEKKKKEGGGGRRRRRRKKRRRSRRRRSRRRRRRRRRRRR 927
           E    G  ++R     G+E+    +     GR  R     R   R  SRRR  R  RRRR
Sbjct: 11  ESPHQGYGQQREGEEQGQEQGLSPEDVEVYGRTHRGHYHYRH--RSCSRRRLYRIHRRRR 68

Query: 928 RRRRRRRRRRRRRRRRRRRRRRR 950
             RRRRRR  R RRR RR  RRR
Sbjct: 69  SCRRRRRRSCRHRRRHRRGCRRR 91

This protein also known as protamine P2 can substitute for histones in the chromatin of sperm. The alignment contains both the sequence of the mature P2 protein and its propeptide. Length = 91

>gnl|CDD|220383 pfam09756, DDRGK, DDRGK domain

 Score = 52.0 bits (125), Expect = 2e-07
 Identities = 30/95 (31%), Positives = 56/95 (58%)

Query: 927  RRRRRRRRRRRRRRRRRRRRRRRRRRRRSGKEEEEEEKKKEEKKKEEEEKKKKEGKTKKE 986
             ++R +   ++ RR++R      R  R+  +E+ E E+K+EE+ +EE EKKK+E + K+ 
Sbjct: 5    AKKRAKLEEKQARRQQREAEEEEREERKKLEEKREGERKEEEELEEEREKKKEEEERKER 64

Query: 987  EKKKEEEEEKKKKKKEEEKEEEEKKEEEEKEEEEK 1021
            E++  +E+E+ +K K     EEE  ++   +EE  
Sbjct: 65   EEQARKEQEEYEKLKSSFVVEEEGTDKLSADEESN 99

This is a family of proteins of approximately 300 residues, found in plants and vertebrates. They contain a highly conserved DDRGK motif. Length = 189

>gnl|CDD|235175 PRK03918, PRK03918, chromosome segregation protein; Provisional

 Score = 54.7 bits (132), Expect = 2e-07
 Identities = 45/216 (20%), Positives = 88/216 (40%), Gaps = 10/216 (4%)

Query: 810  IRLSRNRRGRRRRRRKKKEEKKKW--KRRGGGRRRRRGKKEEEKKKKKEEEEEGGEKEEE 867
              L        +  ++ +E K++     +         +K EEK ++ EE  E  +KE E
Sbjct: 217  PELREELEKLEKEVKELEELKEEIEELEKELESLEGSKRKLEEKIRELEERIEELKKEIE 276

Query: 868  EGGGGGGRRRRRRRRSGKEEEEKKKKEGGGGRRRRRRKKRRRSRRRRSRRRRRRRRRRRR 927
            E          + +   + +E+ ++             + R   +R SR          R
Sbjct: 277  E-------LEEKVKELKELKEKAEEYIKLSEFYEEYLDELREIEKRLSRLEEEINGIEER 329

Query: 928  RRRRRRRRRRRRRRRRRRRRRRRRRRRSGKEEEEEEKKKEEKKKEEEEKKKKEGKTKKEE 987
             +    +  R    +++ +   +R     +  E  E+ K +K++ E  KK+  G T ++ 
Sbjct: 330  IKELEEKEERLEELKKKLKELEKRLEELEERHELYEEAKAKKEELERLKKRLTGLTPEKL 389

Query: 988  KKKEEEEEKKKKKKEEEKEE-EEKKEEEEKEEEEKK 1022
            +K+ EE EK K++ EEE  +   +  E +KE +E K
Sbjct: 390  EKELEELEKAKEEIEEEISKITARIGELKKEIKELK 425

Length = 880

>gnl|CDD|219746 pfam08208, RNA_polI_A34, DNA-directed RNA polymerase I subunit RPA34

 Score = 52.0 bits (125), Expect = 2e-07
 Identities = 28/69 (40%), Positives = 46/69 (66%), Gaps = 2/69 (2%)

Query: 954  RSGKEEEEEEKKKEEKKKEEEEKKKKEGKTKKEEKKKEEEEEKKKKKKEEEKEEEEKKEE 1013
              G E E  EK+   K ++E E +++E K KK  KKKE ++EKK+KK ++EK  E K  +
Sbjct: 127  ELGSESETSEKETTAKVEKEAEVEEEEKKEKK--KKKEVKKEKKEKKDKKEKMVEPKGSK 184

Query: 1014 EEKEEEEKK 1022
            ++K++++KK
Sbjct: 185  KKKKKKKKK 193

5. This is a family of proteins conserved from yeasts to human. Subunit A34.5 of RNA polymerase I is a non-essential subunit which is thought to help Pol I overcome topological constraints imposed on ribosomal DNA during the process of transcription. Length = 193

>gnl|CDD|233503 TIGR01642, U2AF_lg, U2 snRNP auxilliary factor, large subunit, splicing factor

 Score = 53.7 bits (129), Expect = 3e-07
 Identities = 22/119 (18%), Positives = 46/119 (38%), Gaps = 7/119 (5%)

Query: 912  RRRSRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRSGKEEEEEEKKKEEKKK 971
              R R + R R R R   R RRR R R R R R RR R R  R  ++    ++++ + + 
Sbjct: 5    PDREREKSRGRDRDRSSERPRRRSRDRSRFRDRHRRSRERSYR--EDSRPRDRRRYDSRS 62

Query: 972  EEEEKKKKEGKTKKEEKKKEEEEEKKKKKKEEEKEEEEKKEEEEKEEEEKKRRRIRRKR 1030
                +     +++   +++      +  +  E+     +      +  +  ++R     
Sbjct: 63   PRSLRYSSVRRSRDRPRRRS-----RSVRSIEQHRRRLRDRSPSNQWRKDDKKRSLWDI 116

These splicing factors consist of an N-terminal arginine-rich low complexity domain followed by three tandem RNA recognition motifs (pfam00076). The well-characterized members of this family are auxilliary components of the U2 small nuclear ribonuclearprotein splicing factor (U2AF). These proteins are closely related to the CC1-like subfamily of splicing factors (TIGR01622). Members of this subfamily are found in plants, metazoa and fungi. Length = 509

>gnl|CDD|219953 pfam08648, DUF1777, Protein of unknown function (DUF1777)

 Score = 51.0 bits (122), Expect = 3e-07
 Identities = 31/102 (30%), Positives = 52/102 (50%)

Query: 918  RRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRSGKEEEEEEKKKEEKKKEEEEKK 977
            R R R  RR RRR R R R RR RRR R R R R RR         + +  +       +
Sbjct: 3    RSRSRSPRRSRRRGRSRSRDRRERRRERSRSRERDRRRRSRSRSPHRSRRSRSPRRHRSR 62

Query: 978  KKEGKTKKEEKKKEEEEEKKKKKKEEEKEEEEKKEEEEKEEE 1019
             +    +++ K++ +++ ++ KK+E +K  +E+  E + +EE
Sbjct: 63   SRSPSRRRDRKRERDKDAREPKKRERQKLIKEEDLEGKSDEE 104

This is a family of eukaryotic proteins of unknown function. Some of the proteins in this family are putative nucleic acid binding proteins. Length = 158

>gnl|CDD|225606 COG3064, TolA, Membrane protein involved in colicin uptake [Cell envelope biogenesis, outer membrane]

 Score = 53.8 bits (129), Expect = 3e-07
 Identities = 37/187 (19%), Positives = 83/187 (44%), Gaps = 15/187 (8%)

Query: 846  KKEEEKKKKKE---EEEEGGEKEEEEGGGGGGRRRRRRRRSGKEEEEKKKKEGGGGRRRR 902
            K E+++KKK+E   EE +  +  E+E      R ++  +   K +E++K+ E    + + 
Sbjct: 76   KGEQQRKKKEEQVAEELKPKQAAEQE------RLKQLEKERLKAQEQQKQAEEAEKQAQL 129

Query: 903  RRKKRRRSRRRRSRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRSG--KEEE 960
             +K++    R+ +  ++++    + +      + +     +++     +       K E 
Sbjct: 130  EQKQQEEQARKAAAEQKKKAEAAKAKAAAEAAKLKAAAEAKKKAEEAAKAAEEAKAKAEA 189

Query: 961  EEEKKKEE---KKKEEEEKKKKEGKTKKEEKKKEEEEEKKKKKKEEEKEEEEKKEEEEKE 1017
               KKK E   K   E+ K + E K K E+K +   EEK   +K ++   + K ++    
Sbjct: 190  AAAKKKAEAEAKAAAEKAKAEAEAKAKAEKKAEAAAEEKAAAEK-KKAAAKAKADKAAAA 248

Query: 1018 EEEKKRR 1024
             +  +R+
Sbjct: 249  AKAAERK 255

Length = 387

>gnl|CDD|217051 pfam02463, SMC_N, RecF/RecN/SMC N terminal domain

 Score = 54.2 bits (130), Expect = 3e-07
 Identities = 50/206 (24%), Positives = 92/206 (44%), Gaps = 2/206 (0%)

Query: 821  RRRRKKKEEKKKWKRRGGGRRRRRGKKEEEKKKKKEEEEEGGEKEEEEGGGGGGRRRRRR 880
            +   +  E+ K+ K   G  +     K  E  K KE     G   EE        +    
Sbjct: 611  KATLEADEDDKRAKVVEGILKDTELTKLLESAKAKESGLRKGVSLEEGLAEKSELKASLS 670

Query: 881  RRSGKEEEEKKKKEGGGGRRRRRRKKRRRSRRRRSRRRRRRRRRRRRRRRRRRRRRRRRR 940
              + +   E++ +E       +    RR+   ++  +R +   ++ +  +      + + 
Sbjct: 671  ELTKELLAEQELQEKAESELAKNEILRRQEEIKKKEQRIKEELKKLKLEKEELLADKVQE 730

Query: 941  RRRRRRRRRRRRRRSGKEEEEEEKKKEEKKKEEEEKKKKEGKTKKEEKKKEEEEEKKKKK 1000
             + +     +   +  KE+EEEE+K   KK+EEEE+K +   + KE++  EEEE+ +K K
Sbjct: 731  AQDKINEELKLLEQKIKEKEEEEEKSRLKKEEEEEEKSEL--SLKEKELAEEEEKTEKLK 788

Query: 1001 KEEEKEEEEKKEEEEKEEEEKKRRRI 1026
             EEEKEE+ K +EEE    E++ +  
Sbjct: 789  VEEEKEEKLKAQEEELRALEEELKEE 814

This domain is found at the N terminus of SMC proteins. The SMC (structural maintenance of chromosomes) superfamily proteins have ATP-binding domains at the N- and C-termini, and two extended coiled-coil domains separated by a hinge in the middle. The eukaryotic SMC proteins form two kind of heterodimers: the SMC1/SMC3 and the SMC2/SMC4 types. These heterodimers constitute an essential part of higher order complexes, which are involved in chromatin and DNA dynamics. This family also includes the RecF and RecN proteins that are involved in DNA metabolism and recombination. Length = 1162

>gnl|CDD|220648 pfam10243, MIP-T3, Microtubule-binding protein MIP-T3

 Score = 53.7 bits (129), Expect = 4e-07
 Identities = 43/231 (18%), Positives = 84/231 (36%), Gaps = 20/231 (8%)

Query: 819  RRRRRRKKKEEKKKWKRRGGGRRRRRGKKEEEKK----KKKEEEEEGGEKEEEEGGGGGG 874
             + +R  K++EK+K K+    R R   KK E  +     KK  +++   K++E       
Sbjct: 137  AKEKRPPKEKEKEKEKKVEEPRDREEEKKRERVRAKSRPKKPPKKKPPNKKKEPPEEEKQ 196

Query: 875  RRRRRRRRSGKEEEEKKKKEGGGGRRRRRRKKRRRSRRRRSRRRRRRRRRRRRRRRRRR- 933
            R+  R    GK EE    +E        + ++   S       R+     RR     ++ 
Sbjct: 197  RQAAREAVKGKPEEPDVNEEREKEEDDGKDRETTTSPMEEDESRQSSEISRRSSSSLKKP 256

Query: 934  -----------RRRRRRRRRRRRRRRRRRRRRSGKEEEEEEKKKEEKKKEEEEKKKKEGK 982
                       R   +R   R R   R    R         + K ++     +  +  GK
Sbjct: 257  DPSPSMASPETRESSKRTETRPRTSLRPPSARPASARPAPPRVKRKEIVTVLQDAQGVGK 316

Query: 983  T----KKEEKKKEEEEEKKKKKKEEEKEEEEKKEEEEKEEEEKKRRRIRRK 1029
                   E KK E+E+++    +   +  +     E++ E+ +++  + +K
Sbjct: 317  IVSNVILEGKKSEDEDDENFVVEAAAQAPDIVAGGEDEAEDGEQQGGLVQK 367

This protein, which interacts with both microtubules and TRAF3 (tumour necrosis factor receptor-associated factor 3), is conserved from worms to humans. The N-terminal region is the microtubule binding domain and is well-conserved; the C-terminal 100 residues, also well-conserved, constitute the coiled-coil region which binds to TRAF3. The central region of the protein is rich in lysine and glutamic acid and carries KKE motifs which may also be necessary for tubulin-binding, but this region is the least well-conserved. Length = 506

>gnl|CDD|223046 PHA03328, PHA03328, nuclear egress lamina protein UL31; Provisional

 Score = 52.8 bits (127), Expect = 4e-07
 Identities = 22/51 (43%), Positives = 22/51 (43%)

Query: 900 RRRRRKKRRRSRRRRSRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRR 950
           RR RR  RR  R  R   R R R R RRR  RR   RR       R R R 
Sbjct: 14  RRSRRAARRSRRDGRVGSRGRSRYRSRRRSSRRSSTRRAELADTERDRYRA 64

Length = 316

>gnl|CDD|223046 PHA03328, PHA03328, nuclear egress lamina protein UL31; Provisional

 Score = 52.8 bits (127), Expect = 4e-07
 Identities = 22/58 (37%), Positives = 22/58 (37%)

Query: 897 GGRRRRRRKKRRRSRRRRSRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRR 954
              RR     RR  R  R  RR  R   R R R R RRR  RR   RR       R R
Sbjct: 4   LALRRSSSSLRRSRRAARRSRRDGRVGSRGRSRYRSRRRSSRRSSTRRAELADTERDR 61

Length = 316

>gnl|CDD|235175 PRK03918, PRK03918, chromosome segregation protein; Provisional

 Score = 53.9 bits (130), Expect = 4e-07
 Identities = 35/206 (16%), Positives = 83/206 (40%), Gaps = 1/206 (0%)

Query: 820  RRRRRKKKEEKKKWKRRGGGRRRRRGKKEEEKKKKKEEEEEGGEKEEE-EGGGGGGRRRR 878
             +  +++ E  +K+ +R         +KE+E ++   E  E   +  E         +  
Sbjct: 171  IKEIKRRIERLEKFIKRTENIEELIKEKEKELEEVLREINEISSELPELREELEKLEKEV 230

Query: 879  RRRRSGKEEEEKKKKEGGGGRRRRRRKKRRRSRRRRSRRRRRRRRRRRRRRRRRRRRRRR 938
            +     KEE E+ +KE       +R+ + +           ++       + +  +  + 
Sbjct: 231  KELEELKEEIEELEKELESLEGSKRKLEEKIRELEERIEELKKEIEELEEKVKELKELKE 290

Query: 939  RRRRRRRRRRRRRRRRSGKEEEEEEKKKEEKKKEEEEKKKKEGKTKKEEKKKEEEEEKKK 998
            +     +             E E+   + E++    E++ KE + K+E  ++ +++ K+ 
Sbjct: 291  KAEEYIKLSEFYEEYLDELREIEKRLSRLEEEINGIEERIKELEEKEERLEELKKKLKEL 350

Query: 999  KKKEEEKEEEEKKEEEEKEEEEKKRR 1024
            +K+ EE EE  +  EE K ++E+  R
Sbjct: 351  EKRLEELEERHELYEEAKAKKEELER 376

Length = 880

>gnl|CDD|235175 PRK03918, PRK03918, chromosome segregation protein; Provisional

 Score = 53.9 bits (130), Expect = 4e-07
 Identities = 47/223 (21%), Positives = 91/223 (40%), Gaps = 24/223 (10%)

Query: 812  LSRNRRGRRRRRRKKKEEKKKWKRRGGGRRRRRGKKEEEKKKKKEEEEEGGEKEEEEGGG 871
            +S      R    K ++E K+ +           K+E E+ +K+ E  EG +++ EE   
Sbjct: 212  ISSELPELREELEKLEKEVKELEEL---------KEEIEELEKELESLEGSKRKLEEK-- 260

Query: 872  GGGRRRRRRRRSGKEEEEKKKKEGGGGRRRRRRKKRRRSRRRRSRRRRRRRRRRRRRRRR 931
                R    R    ++E ++ +E      + +  K  + +     +            R 
Sbjct: 261  ---IRELEERIEELKKEIEELEE------KVKELKELKEKAEEYIKLSEFYEEYLDELRE 311

Query: 932  RRRRRRRRRRRRRRRRRRRRRRRSGKEEEEEEKKKEEKKKEEEEKKKKEGKTKKEEKKKE 991
              +R  R          R +     +E  EE KKK ++ ++  E+ ++  +  +E K K+
Sbjct: 312  IEKRLSRLEEEINGIEERIKELEEKEERLEELKKKLKELEKRLEELEERHELYEEAKAKK 371

Query: 992  EEEEKKKKKKEEEKEEEEKKE----EEEKEEEEKKRRRIRRKR 1030
            EE E+ KK+      E+ +KE    E+ KEE E++  +I  + 
Sbjct: 372  EELERLKKRLTGLTPEKLEKELEELEKAKEEIEEEISKITARI 414

Length = 880

>gnl|CDD|217051 pfam02463, SMC_N, RecF/RecN/SMC N terminal domain

 Score = 53.4 bits (128), Expect = 5e-07
 Identities = 30/179 (16%), Positives = 75/179 (41%), Gaps = 9/179 (5%)

Query: 850  EKKKKKEEEEEGGEKEEEEGGGGGGRRRRRRRRSGKEEEEKKKKEGGGGRRRRRRKKRRR 909
             +++ + EEE  G +E+ +      + R ++     E   +   +    + +  + K + 
Sbjct: 153  PERRLEIEEEAAGSREKRKK-----KERLKKLIEETENLAELIIDLEELKLQELKLKEQA 207

Query: 910  SRRRRSRRRRRRRRRRRRR----RRRRRRRRRRRRRRRRRRRRRRRRRRSGKEEEEEEKK 965
             +     + + +              +    R    +   R  +     S +E E+EE+ 
Sbjct: 208  KKALEYYQLKEKLELEEENLLYLDYLKLNEERIDLLQELLRDEQEEIESSKQELEKEEEI 267

Query: 966  KEEKKKEEEEKKKKEGKTKKEEKKKEEEEEKKKKKKEEEKEEEEKKEEEEKEEEEKKRR 1024
              +  KE +E++K++   ++E K   +EEE+ K +  + +  +   EE+ KE E++ ++
Sbjct: 268  LAQVLKENKEEEKEKKLQEEELKLLAKEEEELKSELLKLERRKVDDEEKLKESEKELKK 326

This domain is found at the N terminus of SMC proteins. The SMC (structural maintenance of chromosomes) superfamily proteins have ATP-binding domains at the N- and C-termini, and two extended coiled-coil domains separated by a hinge in the middle. The eukaryotic SMC proteins form two kind of heterodimers: the SMC1/SMC3 and the SMC2/SMC4 types. These heterodimers constitute an essential part of higher order complexes, which are involved in chromatin and DNA dynamics. This family also includes the RecF and RecN proteins that are involved in DNA metabolism and recombination. Length = 1162

>gnl|CDD|219406 pfam07420, DUF1509, Protein of unknown function (DUF1509)

 Score = 52.7 bits (126), Expect = 5e-07
 Identities = 27/86 (31%), Positives = 33/86 (38%), Gaps = 2/86 (2%)

Query: 880 RRRSGKEEEEKKKKEGGGGRRRRRRKKRRRSRRRRSRRRRRRRRRRRRRRRRRRRRRRRR 939
           R  +  +     +   GG     RR     S  RR RRR R   R R R R   RR RRR
Sbjct: 292 RAGTPDDGSAISEDSAGGSHHTMRRPPHSTSGERRGRRRNRSESRSRSRSRSGSRRYRRR 351

Query: 940 RRRRRRRRRRRRRRRS--GKEEEEEE 963
           R R    RR   R+ +      E  +
Sbjct: 352 RGRGVPGRRSESRQDTVLVSSSEASD 377

This family consists of several uncharacterized viral proteins from the Marek's disease-like viruses. Members of this family are typically around 400 residues in length. The function of this family is unknown. Length = 377

>gnl|CDD|234017 TIGR02794, tolA_full, TolA protein

 Score = 52.5 bits (126), Expect = 6e-07
 Identities = 38/159 (23%), Positives = 70/159 (44%), Gaps = 17/159 (10%)

Query: 885  KEEEEKKKKEGGGGRRRRRRKKRRRSRRRRSRRRRRRRRRRRRRRR--RRRRRRRRRRRR 942
            KE+E +KK E    ++    +K+R + + R +   +R    +  ++  +  ++   ++++
Sbjct: 65   KEQERQKKLE----QQAEEAEKQRAAEQARQKELEQRAAAEKAAKQAEQAAKQAEEKQKQ 120

Query: 943  RRRRRRRRRRRRSGKEEEEEEKKKEE--KKKEEEEKKKK---EGKTKKEEKKKEEEEEKK 997
                + ++      K E E EKK +E  KK+ EEE K K   E K K  E KK+ E E K
Sbjct: 121  AEEAKAKQAAEAKAKAEAEAEKKAKEEAKKQAEEEAKAKAAAEAKKKAAEAKKKAEAEAK 180

Query: 998  ------KKKKEEEKEEEEKKEEEEKEEEEKKRRRIRRKR 1030
                   K K EE + + +  + +   E   +       
Sbjct: 181  AKAEAKAKAKAEEAKAKAEAAKAKAAAEAAAKAEAEAAA 219

TolA couples the inner membrane complex of itself with TolQ and TolR to the outer membrane complex of TolB and OprL (also called Pal). Most of the length of the protein consists of low-complexity sequence that may differ in both length and composition from one species to another, complicating efforts to discriminate TolA (the most divergent gene in the tol-pal system) from paralogs such as TonB. Selection of members of the seed alignment and criteria for setting scoring cutoffs are based largely conserved operon struction. //The Tol-Pal complex is required for maintaining outer membrane integrity. Also involved in transport (uptake) of colicins and filamentous DNA, and implicated in pathogenesis. Transport is energized by the proton motive force. TolA is an inner membrane protein that interacts with periplasmic TolB and with outer membrane porins ompC, phoE and lamB [Transport and binding proteins, Other, Cellular processes, Pathogenesis]. Length = 346

>gnl|CDD|219924 pfam08597, eIF3_subunit, Translation initiation factor eIF3 subunit

 Score = 51.6 bits (124), Expect = 6e-07
 Identities = 21/81 (25%), Positives = 47/81 (58%), Gaps = 3/81 (3%)

Query: 953  RRSGKEEEEEEKKKEEKKKEEEEKKKKEGKTKKEEKKKEEEEEKKKKKKEEEKEEEEKKE 1012
            +    +E+E++  K+   +EE+E+K++E      + K ++  + K ++KE+ K E+E+K 
Sbjct: 21   KDKWDDEDEDDDVKDSWDEEEDEEKEEEKAKVAAKAKAKKALKAKIEEKEKAKREKEEKG 80

Query: 1013 EEEKEE---EEKKRRRIRRKR 1030
              E EE   E++   ++R ++
Sbjct: 81   LRELEEDTPEDELAEKLRLRK 101

This is a family of proteins which are subunits of the eukaryotic translation initiation factor 3 (eIF3). In yeast it is called Hcr1. The Saccharomyces cerevisiae protein eIF3j (HCR1) has been shown to be required for processing of 20S pre-rRNA and binds to 18S rRNA and eIF3 subunits Rpg1p and Prt1p. Length = 242

>gnl|CDD|219838 pfam08432, DUF1742, Fungal protein of unknown function (DUF1742)

 Score = 50.5 bits (121), Expect = 6e-07
 Identities = 24/72 (33%), Positives = 48/72 (66%), Gaps = 1/72 (1%)

Query: 958  EEEEEEKKKEEKKKE-EEEKKKKEGKTKKEEKKKEEEEEKKKKKKEEEKEEEEKKEEEEK 1016
            E  E +KKK+E  +E E+ KK+ E K K + KKK+ +++K K K +++ ++++K E++++
Sbjct: 56   EYTEAKKKKKELAEEIEKVKKEYEEKQKWKWKKKKSKKKKDKDKDKKDDKKDDKSEKKDE 115

Query: 1017 EEEEKKRRRIRR 1028
            +E E K   + +
Sbjct: 116  KEAEDKLEDLTK 127

This is a family of fungal proteins of unknown function. Length = 182

>gnl|CDD|217787 pfam03910, Adeno_PV, Adenovirus minor core protein PV

 Score = 52.1 bits (125), Expect = 6e-07
 Identities = 26/43 (60%), Positives = 27/43 (62%)

Query: 904 RKKRRRSRRRRSRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRR 946
           R    RSR RR+ RRRR  RRRRRRRR    R RR R RR RR
Sbjct: 292 RGTTYRSRVRRATRRRRTTRRRRRRRRTAPARVRRVRTRRGRR 334

Length = 336

>gnl|CDD|233503 TIGR01642, U2AF_lg, U2 snRNP auxilliary factor, large subunit, splicing factor

 Score = 52.6 bits (126), Expect = 7e-07
 Identities = 26/113 (23%), Positives = 46/113 (40%), Gaps = 5/113 (4%)

Query: 902  RRRKKRRRSRRRRSRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRR---RRRRRRSGKE 958
            R  +  R   + R R R R   R RRR R R R R R RR R R  R   R R RR    
Sbjct: 1    RDEEPDREREKSRGRDRDRSSERPRRRSRDRSRFRDRHRRSRERSYREDSRPRDRRRYDS 60

Query: 959  EEEEEKKKEEKKKEEEEKKKKEGKTKKEEKKKEEEEEKKKKKKEEEKEEEEKK 1011
                  +    ++  +  +++    +  E  +     + +    + +++++K+
Sbjct: 61   RSPRSLRYSSVRRSRDRPRRRSRSVRSIE--QHRRRLRDRSPSNQWRKDDKKR 111

These splicing factors consist of an N-terminal arginine-rich low complexity domain followed by three tandem RNA recognition motifs (pfam00076). The well-characterized members of this family are auxilliary components of the U2 small nuclear ribonuclearprotein splicing factor (U2AF). These proteins are closely related to the CC1-like subfamily of splicing factors (TIGR01622). Members of this subfamily are found in plants, metazoa and fungi. Length = 509

>gnl|CDD|219408 pfam07423, DUF1510, Protein of unknown function (DUF1510)

 Score = 50.9 bits (122), Expect = 7e-07
 Identities = 21/68 (30%), Positives = 38/68 (55%)

Query: 955  SGKEEEEEEKKKEEKKKEEEEKKKKEGKTKKEEKKKEEEEEKKKKKKEEEKEEEEKKEEE 1014
               E EE +++++E    E+++ K + + + EE ++E EEE ++   E EKE EEK E  
Sbjct: 58   ETAEIEEVKEEEKEAANSEDKEDKGDAEKEDEESEEENEEEDEESSDENEKETEEKTESN 117

Query: 1015 EKEEEEKK 1022
             ++E    
Sbjct: 118  VEKEITNP 125

This family consists of several hypothetical bacterial proteins of around 200 residues in length. The function of this family is unknown. Length = 214

>gnl|CDD|219746 pfam08208, RNA_polI_A34, DNA-directed RNA polymerase I subunit RPA34

 Score = 50.5 bits (121), Expect = 7e-07
 Identities = 25/65 (38%), Positives = 45/65 (69%)

Query: 966  KEEKKKEEEEKKKKEGKTKKEEKKKEEEEEKKKKKKEEEKEEEEKKEEEEKEEEEKKRRR 1025
             E   + E  +K+   K +KE + +EEE+++KKKKKE +KE++EKK+++EK  E K  ++
Sbjct: 126  SELGSESETSEKETTAKVEKEAEVEEEEKKEKKKKKEVKKEKKEKKDKKEKMVEPKGSKK 185

Query: 1026 IRRKR 1030
             ++K+
Sbjct: 186  KKKKK 190

5. This is a family of proteins conserved from yeasts to human. Subunit A34.5 of RNA polymerase I is a non-essential subunit which is thought to help Pol I overcome topological constraints imposed on ribosomal DNA during the process of transcription. Length = 193

>gnl|CDD|178945 PRK00247, PRK00247, putative inner membrane protein translocase component YidC; Validated

 Score = 52.5 bits (126), Expect = 7e-07
 Identities = 18/114 (15%), Positives = 41/114 (35%)

Query: 906  KRRRSRRRRSRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRSGKEEEEEEKK 965
            ++R   R + + ++      RR R R      R           ++ R + K E +  KK
Sbjct: 289  EQRAQYREKQKEKKAFLWTLRRNRLRMIITPWRAPELHAENAEIKKTRTAEKNEAKARKK 348

Query: 966  KEEKKKEEEEKKKKEGKTKKEEKKKEEEEEKKKKKKEEEKEEEEKKEEEEKEEE 1019
            +  +K+   E++      ++          ++   K ++K   +    E+   E
Sbjct: 349  EIAQKRRAAEREINREARQERAAAMARARARRAAVKAKKKGLIDASPNEDTPSE 402

Length = 429

>gnl|CDD|223046 PHA03328, PHA03328, nuclear egress lamina protein UL31; Provisional

 Score = 52.0 bits (125), Expect = 8e-07
 Identities = 23/58 (39%), Positives = 23/58 (39%)

Query: 898 GRRRRRRKKRRRSRRRRSRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRS 955
              RR     RRSRR   R RR  R   R R R R RRR  RR   RR       R  
Sbjct: 4   LALRRSSSSLRRSRRAARRSRRDGRVGSRGRSRYRSRRRSSRRSSTRRAELADTERDR 61

Length = 316

>gnl|CDD|220383 pfam09756, DDRGK, DDRGK domain

 Score = 50.1 bits (120), Expect = 8e-07
 Identities = 30/109 (27%), Positives = 62/109 (56%), Gaps = 3/109 (2%)

Query: 925  RRRRRRRRRRRRRRRRRRRRRRRRRRRRRRSGKEEEEEEKKKEEKKKEEEEKKKKEGKTK 984
             ++R +   ++ RR++R      R  R++   K E E ++++E +++ E++K+++E K +
Sbjct: 5    AKKRAKLEEKQARRQQREAEEEEREERKKLEEKREGERKEEEELEEEREKKKEEEERKER 64

Query: 985  KEEKKKEEEEEKKKKKK---EEEKEEEEKKEEEEKEEEEKKRRRIRRKR 1030
            +E+ +KE+EE +K K     EEE  ++   +EE  E  E     I+ K+
Sbjct: 65   EEQARKEQEEYEKLKSSFVVEEEGTDKLSADEESNELLEDFINYIKLKK 113

This is a family of proteins of approximately 300 residues, found in plants and vertebrates. They contain a highly conserved DDRGK motif. Length = 189

>gnl|CDD|223496 COG0419, SbcC, ATPase involved in DNA repair [DNA replication, recombination, and repair]

 Score = 52.8 bits (127), Expect = 8e-07
 Identities = 46/226 (20%), Positives = 93/226 (41%), Gaps = 10/226 (4%)

Query: 798  KAPEGGKVCITQIRLSRNRRGRRRRRRKKKEEKKKWKRRGGGRRRRRGKKEEEKKKKKEE 857
            +  E  ++ + ++    +R       R++ EE +K  R          + EE  K++ EE
Sbjct: 474  ELLELYELELEELEEELSREKEEAELREEIEELEKELRELEEELIELLELEEALKEELEE 533

Query: 858  EEEGGEKEEEEGGGGGGRRRRRRRRSGKEEEEKKKKEGGGGRRRRRRKKRRRSRRRRSRR 917
            + E  E   EE         + + +  + +EE ++ E      R +  K      R  R 
Sbjct: 534  KLEKLENLLEEL-----EELKEKLQLQQLKEELRQLE-----DRLQELKELLEELRLLRT 583

Query: 918  RRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRSGKEEEEEEKKKEEKKKEEEEKK 977
            R+      R R +  +++ +    R  +     +     + E E E+ +EE + E E+  
Sbjct: 584  RKEELEELRERLKELKKKLKELEERLSQLEELLQSLELSEAENELEEAEEELESELEKLN 643

Query: 978  KKEGKTKKEEKKKEEEEEKKKKKKEEEKEEEEKKEEEEKEEEEKKR 1023
             +    +  +   EE EEK ++ + E + E ++ E EE+ EE+ + 
Sbjct: 644  LQAELEELLQAALEELEEKVEELEAEIRRELQRIENEEQLEEKLEE 689

Length = 908

>gnl|CDD|235250 PRK04195, PRK04195, replication factor C large subunit; Provisional

 Score = 51.8 bits (125), Expect = 1e-06
 Identities = 19/61 (31%), Positives = 46/61 (75%)

Query: 945  RRRRRRRRRRSGKEEEEEEKKKEEKKKEEEEKKKKEGKTKKEEKKKEEEEEKKKKKKEEE 1004
               +  ++R   K+E++++    +KK+EEEE++K++ + +KEE+++E EEEK++++++++
Sbjct: 415  IVEKAEKKREEEKKEKKKKAFAGKKKEEEEEEEKEKKEEEKEEEEEEAEEEKEEEEEKKK 474

Query: 1005 K 1005
            K
Sbjct: 475  K 475

Length = 482

>gnl|CDD|233191 TIGR00927, 2A1904, K+-dependent Na+/Ca+ exchanger

 Score = 52.7 bits (126), Expect = 1e-06
 Identities = 38/205 (18%), Positives = 80/205 (39%), Gaps = 1/205 (0%)

Query: 821  RRRRKKKEEKKKWKRRGGGRRRRRGKKEEEKKKKKEEEEEGGEKEEEEGGGGGGRRRRRR 880
            +    K E + +     G       + E E +  +E EE   E E E  G         R
Sbjct: 702  KEADHKGETEAEEVEHEGETEAEGTEDEGEIETGEEGEEVEDEGEGEAEGKHEVETEGDR 761

Query: 881  RRSGKEEEEKKKKEGGGGRRRRRRKKRRRSRRRRSRRRRRRRRRRRRRRRRRRRRRRRRR 940
            + +  E E + + +        +  +    +       +           +     +   
Sbjct: 762  KETEHEGETEAEGKEDEDEGEIQAGEDGEMKGDEGAEGKVEHEGETEAGEKDEHEGQSET 821

Query: 941  RRRRRRRRRRRRRRSGKEEEEEEKKKEEKKKEEEEKKKKEGKTKKEEKKKEEEEEKKKKK 1000
            +      +     +    E + E K++EK  +        G +++EE+++EEEEE+++++
Sbjct: 822  QADDTEVKDETGEQELNAENQGEAKQDEKGVDGGGGSDG-GDSEEEEEEEEEEEEEEEEE 880

Query: 1001 KEEEKEEEEKKEEEEKEEEEKKRRR 1025
            +EEE+EEEE +E    E  E ++++
Sbjct: 881  EEEEEEEEENEEPLSLEWPETRQKQ 905

[Transport and binding proteins, Cations and iron carrying compounds]. Length = 1096

>gnl|CDD|224117 COG1196, Smc, Chromosome segregation ATPases [Cell division and chromosome partitioning]

 Score = 52.8 bits (127), Expect = 1e-06
 Identities = 36/211 (17%), Positives = 74/211 (35%), Gaps = 15/211 (7%)

Query: 816  RRGRRRRRRKKKEEKKKWKRRGGGRRRRRGKKEEEKKKKKEEEEEGGEKEEEEGGGGGGR 875
               R R    + E ++  +R        + K E  K++ +E E    E E+        +
Sbjct: 305  SLLRERLEELENELEELEERL----EELKEKIEALKEELEERETLLEELEQLLAELEEAK 360

Query: 876  RRRRRRRSGKEEEEKKKKEGGGGRRRRRRKKRRRSRRRRSRRRRRRRRRRRRRRRRRRRR 935
                 + S   EE ++  E            R       +     R      +R      
Sbjct: 361  EELEEKLSALLEELEELFE----------ALREELAELEAELAEIRNELEELKREIESLE 410

Query: 936  RRRRRRRRRRRRRRRRRRRSGKEEEEEEKKKEEKKKEEEEKKKKEGKTKKE-EKKKEEEE 994
             R  R   R    +   +    E EE + + EE  +E EE +++  + +   ++ + E  
Sbjct: 411  ERLERLSERLEDLKEELKELEAELEELQTELEELNEELEELEEQLEELRDRLKELERELA 470

Query: 995  EKKKKKKEEEKEEEEKKEEEEKEEEEKKRRR 1025
            E +++ +  EKE    +   ++ E E++  +
Sbjct: 471  ELQEELQRLEKELSSLEARLDRLEAEQRASQ 501

Length = 1163

>gnl|CDD|223046 PHA03328, PHA03328, nuclear egress lamina protein UL31; Provisional

 Score = 51.6 bits (124), Expect = 1e-06
 Identities = 21/58 (36%), Positives = 24/58 (41%)

Query: 892 KKEGGGGRRRRRRKKRRRSRRRRSRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRR 949
           ++     RR RR  +R R   R   R R R R RRR  RR   RR       R R R 
Sbjct: 7   RRSSSSLRRSRRAARRSRRDGRVGSRGRSRYRSRRRSSRRSSTRRAELADTERDRYRA 64

Length = 316

>gnl|CDD|223046 PHA03328, PHA03328, nuclear egress lamina protein UL31; Provisional

 Score = 51.3 bits (123), Expect = 1e-06
 Identities = 21/58 (36%), Positives = 25/58 (43%)

Query: 891 KKKEGGGGRRRRRRKKRRRSRRRRSRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRR 948
           ++      R RR  ++ RR  R  SR R R R RRR  RR   RR       R R R 
Sbjct: 7   RRSSSSLRRSRRAARRSRRDGRVGSRGRSRYRSRRRSSRRSSTRRAELADTERDRYRA 64

Length = 316

>gnl|CDD|217051 pfam02463, SMC_N, RecF/RecN/SMC N terminal domain

 Score = 52.7 bits (126), Expect = 1e-06
 Identities = 31/215 (14%), Positives = 85/215 (39%)

Query: 808  TQIRLSRNRRGRRRRRRKKKEEKKKWKRRGGGRRRRRGKKEEEKKKKKEEEEEGGEKEEE 867
                      G R+    ++   +K + +       +    E++ ++K E E    +   
Sbjct: 638  LLESAKAKESGLRKGVSLEEGLAEKSELKASLSELTKELLAEQELQEKAESELAKNEILR 697

Query: 868  EGGGGGGRRRRRRRRSGKEEEEKKKKEGGGGRRRRRRKKRRRSRRRRSRRRRRRRRRRRR 927
                   + +R +    K + EK++      +  + +         +  + +     + R
Sbjct: 698  RQEEIKKKEQRIKEELKKLKLEKEELLADKVQEAQDKINEELKLLEQKIKEKEEEEEKSR 757

Query: 928  RRRRRRRRRRRRRRRRRRRRRRRRRRRSGKEEEEEEKKKEEKKKEEEEKKKKEGKTKKEE 987
             ++      +     + +       +    + EEE+++K + ++EE    ++E K + E 
Sbjct: 758  LKKEEEEEEKSELSLKEKELAEEEEKTEKLKVEEEKEEKLKAQEEELRALEEELKEEAEL 817

Query: 988  KKKEEEEEKKKKKKEEEKEEEEKKEEEEKEEEEKK 1022
             ++E+   ++++K +EE+ EE   E +E+++ EK 
Sbjct: 818  LEEEQLLIEQEEKIKEEELEELALELKEEQKLEKL 852

This domain is found at the N terminus of SMC proteins. The SMC (structural maintenance of chromosomes) superfamily proteins have ATP-binding domains at the N- and C-termini, and two extended coiled-coil domains separated by a hinge in the middle. The eukaryotic SMC proteins form two kind of heterodimers: the SMC1/SMC3 and the SMC2/SMC4 types. These heterodimers constitute an essential part of higher order complexes, which are involved in chromatin and DNA dynamics. This family also includes the RecF and RecN proteins that are involved in DNA metabolism and recombination. Length = 1162

>gnl|CDD|233758 TIGR02169, SMC_prok_A, chromosome segregation protein SMC, primarily archaeal type

 Score = 52.4 bits (126), Expect = 1e-06
 Identities = 37/182 (20%), Positives = 71/182 (39%), Gaps = 3/182 (1%)

Query: 847  KEEEKKKKKEEEEEGGEKEEEEGGGGGGRRRRRRRRSGKEEEEKKKKEGGGGRRR--RRR 904
            ++ E++  K E E      E E         R+RR    EE  + K+E    R       
Sbjct: 318  EDAEERLAKLEAEIDKLLAEIEELEREIEEERKRRDKLTEEYAELKEELEDLRAELEEVD 377

Query: 905  KKRRRSRRRRSRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRSGKEEEEEEK 964
            K+   +R      R +  + +R     +R   R +   +R          +    E +  
Sbjct: 378  KEFAETRDELKDYREKLEKLKREINELKRELDRLQEELQRLSEELADLNAAIAGIEAKIN 437

Query: 965  KKEEKKKE-EEEKKKKEGKTKKEEKKKEEEEEKKKKKKEEEKEEEEKKEEEEKEEEEKKR 1023
            + EE+K++   E KK+E K ++      + E++    KEE    E++  + ++E  E + 
Sbjct: 438  ELEEEKEDKALEIKKQEWKLEQLAADLSKYEQELYDLKEEYDRVEKELSKLQRELAEAEA 497

Query: 1024 RR 1025
            + 
Sbjct: 498  QA 499

SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]. Length = 1164

>gnl|CDD|202096 pfam02029, Caldesmon, Caldesmon

 Score = 52.0 bits (124), Expect = 1e-06
 Identities = 42/181 (23%), Positives = 79/181 (43%), Gaps = 20/181 (11%)

Query: 840  RRRRRGKKEEEKKKKKEEEEEGGEKEEEEGGGGGGRRRRRRRRSGKEEEEKKKKEGGGGR 899
            R RRR ++EE+ ++K+EE   G    + E            + S  +E    +       
Sbjct: 9    RERRRREREEQLRQKQEEGSLGQVTTQVEVNSQNSVPDEESKTSTDDEAALLE------- 61

Query: 900  RRRRRKKRRRSRRRRSRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRSGKEE 959
                         R +RR  RR  R      R++  +     +      RR +  SG E 
Sbjct: 62   -------------RLARREERRDERFSEALERQKEFKPTSTDQSLSEPSRRMQEDSGAEN 108

Query: 960  EEEEKKKEEKKKEEEEKKKKEGKTKKEEKKKEEEEEKKKKKKEEEKEEEEKKEEEEKEEE 1019
            E  E++++E+ +EE E+ ++     K E+K +  + ++ +K+E+E E EE+++ +    E
Sbjct: 109  ETVEEEEKEESREEREEVEETEGVTKSEQKNDWRDAEECQKEEKEPEPEEEEKPKRGSLE 168

Query: 1020 E 1020
            E
Sbjct: 169  E 169

Length = 431

>gnl|CDD|217787 pfam03910, Adeno_PV, Adenovirus minor core protein PV

 Score = 51.8 bits (124), Expect = 1e-06
 Identities = 26/43 (60%), Positives = 26/43 (60%)

Query: 909 RSRRRRSRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRR 951
           R    RSR RR  RRRR  RRRRRRRR    R RR R RR RR
Sbjct: 292 RGTTYRSRVRRATRRRRTTRRRRRRRRTAPARVRRVRTRRGRR 334

Length = 336

>gnl|CDD|218177 pfam04615, Utp14, Utp14 protein

 Score = 52.0 bits (125), Expect = 1e-06
 Identities = 42/192 (21%), Positives = 84/192 (43%), Gaps = 1/192 (0%)

Query: 840  RRRRRGKKEEEKKKKKEEEEEGGEKEEEEGGGGGGRRRRRRRRSGKEEEEKKKKEGGGGR 899
            RR+  GK   E+ + ++ + E  +++++E    G      R++ GK +E +  +E  G  
Sbjct: 315  RRKIEGKSVSEEDEDEDSDSEEEDEDDDEDDDDGENPWMLRKKLGKLKEGEDDEENSGLL 374

Query: 900  RRRRRKKRRRSRRRRSRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRSGKEE 959
              +  ++    ++  +       RR                 ++   RR+       KE 
Sbjct: 375  SMKFMQRAEARKKEENDAEIEELRRELEGEEESDEEENEEPSKKNVGRRKFGPENGEKEA 434

Query: 960  EEEEKKKEEKKKEEEEKKKKEGKTK-KEEKKKEEEEEKKKKKKEEEKEEEEKKEEEEKEE 1018
            E ++ KKE K + +E+K+  E +    EE+ K E+   K  K+ E+ ++EE++EE ++E 
Sbjct: 435  ESKKLKKENKNEFKEKKESDEEEELEDEEEAKVEKVANKLLKRSEKAQKEEEEEELDEEN 494

Query: 1019 EEKKRRRIRRKR 1030
               K      K 
Sbjct: 495  PWLKTTSSVGKS 506

This protein is found to be part of a large ribonucleoprotein complex containing the U3 snoRNA. Depletion of the Utp proteins impedes production of the 18S rRNA, indicating that they are part of the active pre-rRNA processing complex. This large RNP complex has been termed the small subunit (SSU) processome. Length = 728

>gnl|CDD|226894 COG4499, COG4499, Predicted membrane protein [Function unknown]

 Score = 51.7 bits (124), Expect = 1e-06
 Identities = 19/72 (26%), Positives = 45/72 (62%), Gaps = 4/72 (5%)

Query: 955  SGKEEEEEEKKKEEK----KKEEEEKKKKEGKTKKEEKKKEEEEEKKKKKKEEEKEEEEK 1010
            SG + +E  K+  +K     K+  E K +   +++ E K +EE+ K+++ ++++KE+ ++
Sbjct: 363  SGDKRQELLKEYNKKLQDYTKKLGEVKDETDASEEAEAKAKEEKLKQEENEKKQKEQADE 422

Query: 1011 KEEEEKEEEEKK 1022
             +E+ +++E KK
Sbjct: 423  DKEKRQKDERKK 434

Length = 434

>gnl|CDD|233503 TIGR01642, U2AF_lg, U2 snRNP auxilliary factor, large subunit, splicing factor

 Score = 51.0 bits (122), Expect = 2e-06
 Identities = 22/111 (19%), Positives = 45/111 (40%)

Query: 914  RSRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRSGKEEEEEEKKKEEKKKEE 973
            R     R R + R R R R   R RRR R R R R R RR   +   E+ + ++ ++ + 
Sbjct: 1    RDEEPDREREKSRGRDRDRSSERPRRRSRDRSRFRDRHRRSRERSYREDSRPRDRRRYDS 60

Query: 974  EEKKKKEGKTKKEEKKKEEEEEKKKKKKEEEKEEEEKKEEEEKEEEEKKRR 1024
               +     + +  + +     +  +  E+ +     +    +  ++ K+R
Sbjct: 61   RSPRSLRYSSVRRSRDRPRRRSRSVRSIEQHRRRLRDRSPSNQWRKDDKKR 111

These splicing factors consist of an N-terminal arginine-rich low complexity domain followed by three tandem RNA recognition motifs (pfam00076). The well-characterized members of this family are auxilliary components of the U2 small nuclear ribonuclearprotein splicing factor (U2AF). These proteins are closely related to the CC1-like subfamily of splicing factors (TIGR01622). Members of this subfamily are found in plants, metazoa and fungi. Length = 509

>gnl|CDD|225606 COG3064, TolA, Membrane protein involved in colicin uptake [Cell envelope biogenesis, outer membrane]

 Score = 50.7 bits (121), Expect = 2e-06
 Identities = 28/178 (15%), Positives = 80/178 (44%), Gaps = 15/178 (8%)

Query: 849  EEKKKKKEEEEEGGEKEEEEGGGGGGRRRRRRRRSGKEEEEKKKKEGGGGRRRRRRKKRR 908
            ++  + + ++    + E++           R+++  +  EE K K+     R ++ +K R
Sbjct: 62   QQYGRIQSQQSSAKKGEQQ-----------RKKKEEQVAEELKPKQAAEQERLKQLEKER 110

Query: 909  RSRRRRSRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRSGKEE----EEEEK 964
               + + ++     ++ +  ++++  + R+    ++++    + + + +        E K
Sbjct: 111  LKAQEQQKQAEEAEKQAQLEQKQQEEQARKAAAEQKKKAEAAKAKAAAEAAKLKAAAEAK 170

Query: 965  KKEEKKKEEEEKKKKEGKTKKEEKKKEEEEEKKKKKKEEEKEEEEKKEEEEKEEEEKK 1022
            KK E+  +  E+ K + +    +KK E E +   +K + E E + K E++ +   E+K
Sbjct: 171  KKAEEAAKAAEEAKAKAEAAAAKKKAEAEAKAAAEKAKAEAEAKAKAEKKAEAAAEEK 228

Length = 387

>gnl|CDD|219838 pfam08432, DUF1742, Fungal protein of unknown function (DUF1742)

 Score = 48.9 bits (117), Expect = 2e-06
 Identities = 20/81 (24%), Positives = 46/81 (56%), Gaps = 8/81 (9%)

Query: 958  EEEEEEKKKEEKKKEEEEKKKKEGKTKKEEKKKEEEEEKKKKKKEEEKEEEEKKEEEEKE 1017
            EE+++ K K++K K++++K K +   KK++K ++++E++ + K E+  +   +      E
Sbjct: 79   EEKQKWKWKKKKSKKKKDKDKDKKDDKKDDKSEKKDEKEAEDKLEDLTKSYSETLSTLSE 138

Query: 1018 EEEKK--------RRRIRRKR 1030
             + +K        + R+ RKR
Sbjct: 139  LKPRKYALHKDIYQSRLDRKR 159

This is a family of fungal proteins of unknown function. Length = 182

>gnl|CDD|219408 pfam07423, DUF1510, Protein of unknown function (DUF1510)

 Score = 49.3 bits (118), Expect = 2e-06
 Identities = 18/62 (29%), Positives = 35/62 (56%)

Query: 956  GKEEEEEEKKKEEKKKEEEEKKKKEGKTKKEEKKKEEEEEKKKKKKEEEKEEEEKKEEEE 1015
             KEEE+E    E+K+ + + +K+ E   ++ E++ EE  ++ +K+ EE+ E   +KE   
Sbjct: 65   VKEEEKEAANSEDKEDKGDAEKEDEESEEENEEEDEESSDENEKETEEKTESNVEKEITN 124

Query: 1016 KE 1017
              
Sbjct: 125  PS 126

This family consists of several hypothetical bacterial proteins of around 200 residues in length. The function of this family is unknown. Length = 214

>gnl|CDD|178945 PRK00247, PRK00247, putative inner membrane protein translocase component YidC; Validated

 Score = 51.0 bits (122), Expect = 2e-06
 Identities = 18/137 (13%), Positives = 48/137 (35%), Gaps = 13/137 (9%)

Query: 901  RRRRKKRRRSRRRRSRRRRRRRRRRR-------------RRRRRRRRRRRRRRRRRRRRR 947
             +R + R + + +++     RR R R                  ++ R   +   + R++
Sbjct: 289  EQRAQYREKQKEKKAFLWTLRRNRLRMIITPWRAPELHAENAEIKKTRTAEKNEAKARKK 348

Query: 948  RRRRRRRSGKEEEEEEKKKEEKKKEEEEKKKKEGKTKKEEKKKEEEEEKKKKKKEEEKEE 1007
               ++RR+ + E   E ++E        + ++     K++   +    +    + EE + 
Sbjct: 349  EIAQKRRAAEREINREARQERAAAMARARARRAAVKAKKKGLIDASPNEDTPSENEESKG 408

Query: 1008 EEKKEEEEKEEEEKKRR 1024
               + E     E  +  
Sbjct: 409  SPPQVEATTTAEPNREP 425

Length = 429

>gnl|CDD|217503 pfam03344, Daxx, Daxx Family

 Score = 51.8 bits (124), Expect = 2e-06
 Identities = 24/82 (29%), Positives = 48/82 (58%)

Query: 939  RRRRRRRRRRRRRRRRSGKEEEEEEKKKEEKKKEEEEKKKKEGKTKKEEKKKEEEEEKKK 998
            RR+R+ R R+    R S   +      +      +E ++++  + ++EE+++EEEEE++ 
Sbjct: 403  RRKRQERERQGTSSRSSDPSKASSTSGESPSMASQESEEEESVEEEEEEEEEEEEEEQES 462

Query: 999  KKKEEEKEEEEKKEEEEKEEEE 1020
            +++E E EEEE++ E +   EE
Sbjct: 463  EEEEGEDEEEEEEVEADNGSEE 484

The Daxx protein (also known as the Fas-binding protein) is thought to play a role in apoptosis, but precise role played by Daxx remains to be determined. Daxx forms a complex with Axin. Length = 715

>gnl|CDD|217503 pfam03344, Daxx, Daxx Family

 Score = 51.5 bits (123), Expect = 2e-06
 Identities = 31/104 (29%), Positives = 57/104 (54%), Gaps = 5/104 (4%)

Query: 925  RRRRRRRRRRRRRRRRRRRRRRRRRRRRRRSGKEEEEEEKKKEEKKKEEEEKKKKEGKTK 984
            RR+R+ R R+    R     +         S   +E EE++  E+++EEEE++++E +  
Sbjct: 403  RRKRQERERQGTSSRSSDPSKASSTSGESPSMASQESEEEESVEEEEEEEEEEEEEEQES 462

Query: 985  KEEKKKEEEEEKKKKKKEEEKEEEEKKEE-----EEKEEEEKKR 1023
            +EE+ ++EEEE++ +     +EE E   E     EE EE+ ++R
Sbjct: 463  EEEEGEDEEEEEEVEADNGSEEEMEGSSEGDGDGEEPEEDAERR 506

The Daxx protein (also known as the Fas-binding protein) is thought to play a role in apoptosis, but precise role played by Daxx remains to be determined. Daxx forms a complex with Axin. Length = 715

>gnl|CDD|240271 PTZ00108, PTZ00108, DNA topoisomerase 2-like protein; Provisional

 Score = 51.6 bits (124), Expect = 2e-06
 Identities = 63/367 (17%), Positives = 119/367 (32%), Gaps = 43/367 (11%)

Query: 689  ELDIDGVYKYMLL--LKKKKYAALSISKLSNGKMICSQEIKGVDVVRRDWSQLASEAGKF 746
            EL I    K  L+  LKK  Y  +    +   K       +         ++   EA   
Sbjct: 1025 ELVITNAKKKDLVKELKKLGY--VRFKDIIKKKSEKITAEEEEG------AEEDDEADDE 1076

Query: 747  VISQILDEQSYTDYSLDDRLQNI-HEHMKKIRTDLDNGFVPLTLLEITKQLTKAPEGGKV 805
               + L      DY L   + ++  E ++K+  +L+     L  L+ T       E    
Sbjct: 1077 DDEEELGAAVSYDYLLSMPIWSLTKEKVEKLNAELEKKEKELEKLKNTTPKDMWLEDLDK 1136

Query: 806  CITQIRLSRNRRGRRRRRRKKKEEKKKWKRRGGGRRRRRGKKEEEKKKKKEEEEEGGEKE 865
                +        +   + ++ + K K K      R+ + KK+E+KKKK   ++      
Sbjct: 1137 FEEALEEQEEVEEKEIAKEQRLKSKTKGKASK--LRKPKLKKKEKKKKKSSADKSKKASV 1194

Query: 866  EEEGGGGGGRRRRRRRR-------------SGKEEEEKKKKEGGGGRRRRRRKKRRRSRR 912
                       +R+                   +EE+K K +    +R + +K       
Sbjct: 1195 VGNSKRVDSDEKRKLDDKPDNKKSNSSGSDQEDDEEQKTKPKKSSVKRLKSKKNNSSKSS 1254

Query: 913  RRSRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRSGKEEEEEEKKKEEKKKE 972
              +         +  + +   +R    +       +R     +G  +     KK+ KK+ 
Sbjct: 1255 EDNDEFSSDDLSKEGKPKNAPKRVSAVQYSPPPPSKRPDGESNGGSKPSSPTKKKVKKRL 1314

Query: 973  EEEKKKKEGKTKKE----EKKKEEEEEKK-------------KKKKEEEKEEEEKKEEEE 1015
            E      + K K E     KKK +   K+             +KKK +   E++   E +
Sbjct: 1315 EGSLAALKKKKKSEKKTARKKKSKTRVKQASASQSSRLLRRPRKKKSDSSSEDDDDSEVD 1374

Query: 1016 KEEEEKK 1022
              E+E  
Sbjct: 1375 DSEDEDD 1381

Length = 1388

>gnl|CDD|235250 PRK04195, PRK04195, replication factor C large subunit; Provisional

 Score = 50.7 bits (122), Expect = 3e-06
 Identities = 20/66 (30%), Positives = 45/66 (68%)

Query: 959  EEEEEKKKEEKKKEEEEKKKKEGKTKKEEKKKEEEEEKKKKKKEEEKEEEEKKEEEEKEE 1018
             EEE +     KK  ++ KK   K +K+ +++++E++KK    ++++EEEE+++E+++EE
Sbjct: 395  TEEEIEFLTGSKKATKKIKKIVEKAEKKREEEKKEKKKKAFAGKKKEEEEEEEKEKKEEE 454

Query: 1019 EEKKRR 1024
            +E++  
Sbjct: 455  KEEEEE 460

Length = 482

>gnl|CDD|206039 pfam13868, Trichoplein, Tumour suppressor, Mitostatin

 Score = 50.3 bits (121), Expect = 3e-06
 Identities = 44/188 (23%), Positives = 87/188 (46%), Gaps = 11/188 (5%)

Query: 819  RRRRRRKKKEEKKKWKRRGGGRRRRRGKKEEEKKKKKEEEEEGGEKEEEEGGGGGGRRRR 878
            R   R  ++ E+K+ K R      R   ++EE + ++EE +E      +E         R
Sbjct: 165  REEEREAERRERKEEKER---EVARLRAQQEEAEDEREELDELRADLYQE------EYER 215

Query: 879  RRRRSGKEEEEKKKKEGGGGRRRRRRKKRRRSRRRRSRRRRRRRRRRRRRRRRRRRRRRR 938
            + R+  KEE EK++++    +R R  +   +  R +  R      R R   ++       
Sbjct: 216  KERQKEKEEAEKRRRQKQELQRAREEQIEEKEERLQEERAEEEAERERMLEKQAEDEELE 275

Query: 939  RRRRRRRRRRRRRRRRSGKE--EEEEEKKKEEKKKEEEEKKKKEGKTKKEEKKKEEEEEK 996
            +    +RR +R   RR  ++  EE+EE++  E+++E EE ++   +  + + + EEE ++
Sbjct: 276  QENAEKRRMKRLEHRRELEQQIEEKEERRAAEREEELEEGERLREEEAERQARIEEERQR 335

Query: 997  KKKKKEEE 1004
              K+  E 
Sbjct: 336  LLKEHAEA 343

Trichoplein or mitostatin, was first defined as a meiosis-specific nuclear structural protein. It has since been linked with mitochondrial movement. It is associated with the mitochondrial outer membrane, and over-expression leads to reduction in mitochondrial motility whereas lack of it enhances mitochondrial movement. The activity appears to be mediated through binding the mitochondria to the actin intermediate filaments (IFs). Length = 349

>gnl|CDD|224117 COG1196, Smc, Chromosome segregation ATPases [Cell division and chromosome partitioning]

 Score = 51.3 bits (123), Expect = 3e-06
 Identities = 28/135 (20%), Positives = 59/135 (43%)

Query: 896  GGGRRRRRRKKRRRSRRRRSRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRS 955
            GG R +R    ++R  +           +  +     +  +   R         RR+   
Sbjct: 654  GGSRNKRSSLAQKRELKELEEELAELEAQLEKLEEELKSLKNELRSLEDLLEELRRQLEE 713

Query: 956  GKEEEEEEKKKEEKKKEEEEKKKKEGKTKKEEKKKEEEEEKKKKKKEEEKEEEEKKEEEE 1015
             + + EE K++    +EE E+ +   +  +EE ++ EEE ++ +++ EE EEE +  EE 
Sbjct: 714  LERQLEELKRELAALEEELEQLQSRLEELEEELEELEEELEELQERLEELEEELESLEEA 773

Query: 1016 KEEEEKKRRRIRRKR 1030
              + +++   +  KR
Sbjct: 774  LAKLKEEIEELEEKR 788

Length = 1163

>gnl|CDD|217051 pfam02463, SMC_N, RecF/RecN/SMC N terminal domain

 Score = 51.5 bits (123), Expect = 3e-06
 Identities = 36/208 (17%), Positives = 82/208 (39%)

Query: 823  RRKKKEEKKKWKRRGGGRRRRRGKKEEEKKKKKEEEEEGGEKEEEEGGGGGGRRRRRRRR 882
              + K E  K +RR      +  + E+E KK ++E ++  E+ EE          +R   
Sbjct: 296  EEELKSELLKLERRKVDDEEKLKESEKELKKLEKELKKEKEEIEELEKELKELEIKREAE 355

Query: 883  SGKEEEEKKKKEGGGGRRRRRRKKRRRSRRRRSRRRRRRRRRRRRRRRRRRRRRRRRRRR 942
              +EE+ +K +E           K++    R S   + +      +    +  +      
Sbjct: 356  EEEEEQLEKLQEKLEQLEEELLAKKKLESERLSSAAKLKEEELELKNEEEKEAKLLLELS 415

Query: 943  RRRRRRRRRRRRSGKEEEEEEKKKEEKKKEEEEKKKKEGKTKKEEKKKEEEEEKKKKKKE 1002
             +     +  ++   +  EE ++  E K+ +  ++K+E + +  +  K++ E KK +   
Sbjct: 416  EQEEDLLKEEKKEELKIVEELEESLETKQGKLTEEKEELEKQALKLLKDKLELKKSEDLL 475

Query: 1003 EEKEEEEKKEEEEKEEEEKKRRRIRRKR 1030
            +E +  +  E+ E     +K     +K 
Sbjct: 476  KETKLVKLLEQLELLLLRQKLEEASQKE 503

This domain is found at the N terminus of SMC proteins. The SMC (structural maintenance of chromosomes) superfamily proteins have ATP-binding domains at the N- and C-termini, and two extended coiled-coil domains separated by a hinge in the middle. The eukaryotic SMC proteins form two kind of heterodimers: the SMC1/SMC3 and the SMC2/SMC4 types. These heterodimers constitute an essential part of higher order complexes, which are involved in chromatin and DNA dynamics. This family also includes the RecF and RecN proteins that are involved in DNA metabolism and recombination. Length = 1162

>gnl|CDD|217051 pfam02463, SMC_N, RecF/RecN/SMC N terminal domain

 Score = 51.1 bits (122), Expect = 3e-06
 Identities = 38/206 (18%), Positives = 92/206 (44%), Gaps = 1/206 (0%)

Query: 822  RRRKKKEEKKKWKRRGGGRRRRRGKKEEEKKKKKEEEEEGGEKEEEEGGGGGGRRRRRRR 881
             + + +  K +  RR    +++  + +EE KK K E+EE    + +E         +   
Sbjct: 684  EKAESELAKNEILRRQEEIKKKEQRIKEELKKLKLEKEELLADKVQEAQDKINEELKLLE 743

Query: 882  RSGKEEEEKKKKEGGGGRRRRRRKKRRRSRRRRSRRRRRRRRRRRRRRRRRRRRRRRRRR 941
                +E+E+++++    +     +K   S + +       +  + +    +  + + +  
Sbjct: 744  -QKIKEKEEEEEKSRLKKEEEEEEKSELSLKEKELAEEEEKTEKLKVEEEKEEKLKAQEE 802

Query: 942  RRRRRRRRRRRRRSGKEEEEEEKKKEEKKKEEEEKKKKEGKTKKEEKKKEEEEEKKKKKK 1001
              R      +      EEE+   ++EEK KEEE ++      ++++ +K  EEE ++ ++
Sbjct: 803  ELRALEEELKEEAELLEEEQLLIEQEEKIKEEELEELALELKEEQKLEKLAEEELERLEE 862

Query: 1002 EEEKEEEEKKEEEEKEEEEKKRRRIR 1027
            E  KEE  ++   ++EE E+++ +  
Sbjct: 863  EITKEELLQELLLKEEELEEQKLKDE 888

This domain is found at the N terminus of SMC proteins. The SMC (structural maintenance of chromosomes) superfamily proteins have ATP-binding domains at the N- and C-termini, and two extended coiled-coil domains separated by a hinge in the middle. The eukaryotic SMC proteins form two kind of heterodimers: the SMC1/SMC3 and the SMC2/SMC4 types. These heterodimers constitute an essential part of higher order complexes, which are involved in chromatin and DNA dynamics. This family also includes the RecF and RecN proteins that are involved in DNA metabolism and recombination. Length = 1162

>gnl|CDD|217787 pfam03910, Adeno_PV, Adenovirus minor core protein PV

 Score = 50.2 bits (120), Expect = 3e-06
 Identities = 25/44 (56%), Positives = 25/44 (56%)

Query: 910 SRRRRSRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRR 953
            R    R R RR  RRRR  RRRRRRRR    R RR R RR RR
Sbjct: 291 YRGTTYRSRVRRATRRRRTTRRRRRRRRTAPARVRRVRTRRGRR 334

Length = 336

>gnl|CDD|178945 PRK00247, PRK00247, putative inner membrane protein translocase component YidC; Validated

 Score = 50.2 bits (120), Expect = 3e-06
 Identities = 21/106 (19%), Positives = 39/106 (36%), Gaps = 10/106 (9%)

Query: 925  RRRRRRRRRRRRRRRRRRRRRRRRRRRRRRSGKEEEEEEKKKEEKKKEEEEKKKKEGKTK 984
             +R + R +++ ++      RR R R      +  E   +  E KK    E K +    K
Sbjct: 289  EQRAQYREKQKEKKAFLWTLRRNRLRMIITPWRAPELHAENAEIKKTRTAE-KNEAKARK 347

Query: 985  KEEKKKEEEEEKKKKKKEEEKEEEEKKEEEEKEEEEKKRRRIRRKR 1030
            KE           +K++  E+E   +  +E      + R R    +
Sbjct: 348  KEI---------AQKRRAAEREINREARQERAAAMARARARRAAVK 384

Length = 429

>gnl|CDD|219124 pfam06658, DUF1168, Protein of unknown function (DUF1168)

 Score = 47.7 bits (114), Expect = 3e-06
 Identities = 33/99 (33%), Positives = 57/99 (57%), Gaps = 2/99 (2%)

Query: 924  RRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRSGKEEEEEEKKKEEKKKEEEEKKKKEGKT 983
            R  RRR   R      + ++       +++R  K+ ++EEK    KK+ + +KKK++ K 
Sbjct: 42   RALRRREYERLELMDEKWKKETEDEEFQQKREEKKRKDEEKT--AKKRAKRQKKKQKKKK 99

Query: 984  KKEEKKKEEEEEKKKKKKEEEKEEEEKKEEEEKEEEEKK 1022
            KK+ KK  ++EEK+  K  EE  +EE++ EE+K+EE  +
Sbjct: 100  KKKAKKGNKKEEKEGSKSSEESSDEEEEGEEDKQEEPVE 138

This family consists of several hypothetical eukaryotic proteins of unknown function. Length = 142

>gnl|CDD|224117 COG1196, Smc, Chromosome segregation ATPases [Cell division and chromosome partitioning]

 Score = 50.5 bits (121), Expect = 4e-06
 Identities = 36/156 (23%), Positives = 69/156 (44%), Gaps = 1/156 (0%)

Query: 869  GGGGGGRRRRRRRRSGKEEEEKKKKEGGGGRRRRRRKKRRRSRRRRSRRRRRRRRRRRRR 928
            GG    R    ++R  KE EE+  +      +     K  ++  R         RR+   
Sbjct: 654  GGSRNKRSSLAQKRELKELEEELAELEAQLEKLEEELKSLKNELRSLEDLLEELRRQLEE 713

Query: 929  RRRRRRRRRRRRRRRRRRRRRRRRRRSGKEEEEEEKKKEEKKKEEEEKKKKEGKTKKEEK 988
              R+    +R          + + R    EEE EE + EE ++ +E  ++ E + +  E+
Sbjct: 714  LERQLEELKRELAALEEELEQLQSRLEELEEELEELE-EELEELQERLEELEEELESLEE 772

Query: 989  KKEEEEEKKKKKKEEEKEEEEKKEEEEKEEEEKKRR 1024
               + +E+ ++ +E+ +  +E+ EE E+E EE +RR
Sbjct: 773  ALAKLKEEIEELEEKRQALQEELEELEEELEEAERR 808

Length = 1163

>gnl|CDD|219924 pfam08597, eIF3_subunit, Translation initiation factor eIF3 subunit

 Score = 48.9 bits (117), Expect = 4e-06
 Identities = 26/66 (39%), Positives = 39/66 (59%), Gaps = 4/66 (6%)

Query: 957  KEEEEEEKKKEEKKKEEEEKKKKEGKTKKEEKKKEEEEEKKKKKKEEEKEEEEKKEEE-- 1014
             EE+EEEK K   K   + KK  + K +++EK K E+EEK  ++ EE+  E+E  E+   
Sbjct: 42   DEEKEEEKAKVAAKA--KAKKALKAKIEEKEKAKREKEEKGLRELEEDTPEDELAEKLRL 99

Query: 1015 EKEEEE 1020
             K +EE
Sbjct: 100  RKLQEE 105

This is a family of proteins which are subunits of the eukaryotic translation initiation factor 3 (eIF3). In yeast it is called Hcr1. The Saccharomyces cerevisiae protein eIF3j (HCR1) has been shown to be required for processing of 20S pre-rRNA and binds to 18S rRNA and eIF3 subunits Rpg1p and Prt1p. Length = 242

>gnl|CDD|217051 pfam02463, SMC_N, RecF/RecN/SMC N terminal domain

 Score = 50.7 bits (121), Expect = 4e-06
 Identities = 35/222 (15%), Positives = 91/222 (40%), Gaps = 4/222 (1%)

Query: 809  QIRLSRNRRGRRRRRRKKKEEKKKWKRRGGGRRRRRGKKEEEKKKKKEEEEEGGEKEEEE 868
              +           +    E++ + K      +    +++EE KKK++  +E  +K + E
Sbjct: 660  AEKSELKASLSELTKELLAEQELQEKAESELAKNEILRRQEEIKKKEQRIKEELKKLKLE 719

Query: 869  GGGGGGRRRRRRRRSGKEEEEKKKKEGGGGRRRRRRKKRRRSRRRRSRRRRRRRRRRRRR 928
                   + +  +    EE +  +++     + +  ++ +   ++      +     + +
Sbjct: 720  KEELLADKVQEAQDKINEELKLLEQK----IKEKEEEEEKSRLKKEEEEEEKSELSLKEK 775

Query: 929  RRRRRRRRRRRRRRRRRRRRRRRRRRSGKEEEEEEKKKEEKKKEEEEKKKKEGKTKKEEK 988
                   +  + +    +  + + +       EEE K+E +  EEE+   ++ +  KEE+
Sbjct: 776  ELAEEEEKTEKLKVEEEKEEKLKAQEEELRALEEELKEEAELLEEEQLLIEQEEKIKEEE 835

Query: 989  KKEEEEEKKKKKKEEEKEEEEKKEEEEKEEEEKKRRRIRRKR 1030
             +E   E K+++K E+  EEE +  EE+  +E+  + +  K 
Sbjct: 836  LEELALELKEEQKLEKLAEEELERLEEEITKEELLQELLLKE 877

This domain is found at the N terminus of SMC proteins. The SMC (structural maintenance of chromosomes) superfamily proteins have ATP-binding domains at the N- and C-termini, and two extended coiled-coil domains separated by a hinge in the middle. The eukaryotic SMC proteins form two kind of heterodimers: the SMC1/SMC3 and the SMC2/SMC4 types. These heterodimers constitute an essential part of higher order complexes, which are involved in chromatin and DNA dynamics. This family also includes the RecF and RecN proteins that are involved in DNA metabolism and recombination. Length = 1162

>gnl|CDD|233757 TIGR02168, SMC_prok_B, chromosome segregation protein SMC, common bacterial type

 Score = 50.8 bits (122), Expect = 4e-06
 Identities = 49/242 (20%), Positives = 84/242 (34%), Gaps = 26/242 (10%)

Query: 789  LLEITKQLTKAPEGGKVCITQIRLSRNRRGRRRRRRKKKEEKKKWKRRGGGRRRRRGKKE 848
            L E+ ++L +  +  +    QI   R    R     ++ EE          R  +  K+ 
Sbjct: 707  LEELEEELEQLRKELEELSRQISALRKDLARLEAEVEQLEE----------RIAQLSKEL 756

Query: 849  EEKKKKKEEEEEGGEKEEEEGGGGGGRRRRRRRRSGKEEEEKKKKEGGGGRRRRRRKKRR 908
             E + + EE EE  E+ EEE                 E E + ++      + +   K  
Sbjct: 757  TELEAEIEELEERLEEAEEEL---------------AEAEAEIEELEAQIEQLKEELKAL 801

Query: 909  RSRRRRSRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRSGKEEEEEEKKKE- 967
            R      R             R R     RR     RR      +     E+ E    E 
Sbjct: 802  REALDELRAELTLLNEEAANLRERLESLERRIAATERRLEDLEEQIEELSEDIESLAAEI 861

Query: 968  EKKKEEEEKKKKEGKTKKEEKKKEEEEEKKKKKKEEEKEEEEKKEEEEKEEEEKKRRRIR 1027
            E+ +E  E+ + E +    E+   EE     + + EE  EE ++ E ++ E  ++   +R
Sbjct: 862  EELEELIEELESELEALLNERASLEEALALLRSELEELSEELRELESKRSELRRELEELR 921

Query: 1028 RK 1029
             K
Sbjct: 922  EK 923

SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]. Length = 1179

>gnl|CDD|236545 PRK09510, tolA, cell envelope integrity inner membrane protein TolA; Provisional

 Score = 49.8 bits (119), Expect = 4e-06
 Identities = 26/137 (18%), Positives = 62/137 (45%), Gaps = 16/137 (11%)

Query: 903  RRKKRRRSRRRRSRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRSGKEEEEE 962
            R++++++S +R   +R+++ +++    ++++   + R ++  + R   + ++   EE  +
Sbjct: 66   RQQQQQKSAKRAEEQRKKKEQQQAEELQQKQAAEQERLKQLEKERLAAQEQKKQAEEAAK 125

Query: 963  EKKKEEKKKEEEEKKKKE----------------GKTKKEEKKKEEEEEKKKKKKEEEKE 1006
            +   ++K+ EE   K                    K    E KK+ E E  KK   E K+
Sbjct: 126  QAALKQKQAEEAAAKAAAAAKAKAEAEAKRAAAAAKKAAAEAKKKAEAEAAKKAAAEAKK 185

Query: 1007 EEEKKEEEEKEEEEKKR 1023
            + E +   +   E KK+
Sbjct: 186  KAEAEAAAKAAAEAKKK 202

Length = 387

>gnl|CDD|235250 PRK04195, PRK04195, replication factor C large subunit; Provisional

 Score = 49.9 bits (120), Expect = 5e-06
 Identities = 21/61 (34%), Positives = 47/61 (77%)

Query: 946  RRRRRRRRRSGKEEEEEEKKKEEKKKEEEEKKKKEGKTKKEEKKKEEEEEKKKKKKEEEK 1005
               +  ++R  +++E+++K    KKKEEEE+++KE K +++E+++EE EE+K++++E++K
Sbjct: 415  IVEKAEKKREEEKKEKKKKAFAGKKKEEEEEEEKEKKEEEKEEEEEEAEEEKEEEEEKKK 474

Query: 1006 E 1006
            +
Sbjct: 475  K 475

Length = 482

>gnl|CDD|235250 PRK04195, PRK04195, replication factor C large subunit; Provisional

 Score = 49.9 bits (120), Expect = 5e-06
 Identities = 23/63 (36%), Positives = 48/63 (76%)

Query: 948  RRRRRRRSGKEEEEEEKKKEEKKKEEEEKKKKEGKTKKEEKKKEEEEEKKKKKKEEEKEE 1007
               +  +  +EE++E+KKK    K++EE++++E + K+EEK++EEEE +++K++EEEK++
Sbjct: 415  IVEKAEKKREEEKKEKKKKAFAGKKKEEEEEEEKEKKEEEKEEEEEEAEEEKEEEEEKKK 474

Query: 1008 EEK 1010
            ++ 
Sbjct: 475  KQA 477

Length = 482

>gnl|CDD|222447 pfam13904, DUF4207, Domain of unknown function (DUF4207)

 Score = 49.0 bits (117), Expect = 5e-06
 Identities = 23/105 (21%), Positives = 55/105 (52%), Gaps = 7/105 (6%)

Query: 933  RRRRRRRRRRRRRRRRRRRRRRSGKEEEEEEKKKEEKKKEEE--EKKKKEGKTKKEEKKK 990
             ++ +R+++ ++    ++++ R  + EE E +++  K+K EE   +K ++   ++  K K
Sbjct: 95   AKQAQRQKKLQKLLEEKQKQEREKEREEAELRQRLAKEKYEEWCRQKAQQAAKQRTPKHK 154

Query: 991  EEEEEK-----KKKKKEEEKEEEEKKEEEEKEEEEKKRRRIRRKR 1030
            +E  E          K E    +E+ ++  +E E KK ++ ++KR
Sbjct: 155  KEAAESASSSLSGSAKPERNVSQEEAKKRLQEWELKKLKQQQQKR 199

This family is found in eukaryotes; it has several conserved tryptophan residues. The function is not known. Length = 261

>gnl|CDD|219746 pfam08208, RNA_polI_A34, DNA-directed RNA polymerase I subunit RPA34

 Score = 47.8 bits (114), Expect = 5e-06
 Identities = 21/71 (29%), Positives = 49/71 (69%), Gaps = 2/71 (2%)

Query: 957  KEEEEEEKKKEEKKKEEEEKKKKEGKTKKEEKKKEEEEEKKKKKKEEEKEEEEK--KEEE 1014
                E   + E  +KE   K +KE + ++EEKK+++++++ KK+K+E+K+++EK  + + 
Sbjct: 123  GPPSELGSESETSEKETTAKVEKEAEVEEEEKKEKKKKKEVKKEKKEKKDKKEKMVEPKG 182

Query: 1015 EKEEEEKKRRR 1025
             K++++KK+++
Sbjct: 183  SKKKKKKKKKK 193

5. This is a family of proteins conserved from yeasts to human. Subunit A34.5 of RNA polymerase I is a non-essential subunit which is thought to help Pol I overcome topological constraints imposed on ribosomal DNA during the process of transcription. Length = 193

>gnl|CDD|236545 PRK09510, tolA, cell envelope integrity inner membrane protein TolA; Provisional

 Score = 49.8 bits (119), Expect = 5e-06
 Identities = 37/183 (20%), Positives = 78/183 (42%), Gaps = 21/183 (11%)

Query: 863  EKEEEEGGGGGGR-----------------RRRRRRRSGKEEEEKKKKEGGGGRRRRRRK 905
            E  E  GGGGGG                  R++++++S K  EE++KK+        ++K
Sbjct: 36   ENIEASGGGGGGSVIDAVMVDPGAVVEQYNRQQQQQKSAKRAEEQRKKKEQQQAEELQQK 95

Query: 906  KRRRSRRRRSRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRSGKEEEEEEKK 965
            +     R +   + R   + ++++     ++   ++++      +    +  + E E K+
Sbjct: 96   QAAEQERLKQLEKERLAAQEQKKQAEEAAKQAALKQKQAEEAAAKAAAAAKAKAEAEAKR 155

Query: 966  KEE-KKKEEEEKKKK---EGKTKKEEKKKEEEEEKKKKKKEEEKEEEEKKEEEEKEEEEK 1021
                 KK   E KKK   E   K   + K++ E +   K   E +++ + E ++K   E 
Sbjct: 156  AAAAAKKAAAEAKKKAEAEAAKKAAAEAKKKAEAEAAAKAAAEAKKKAEAEAKKKAAAEA 215

Query: 1022 KRR 1024
            K++
Sbjct: 216  KKK 218

Length = 387

>gnl|CDD|219655 pfam07946, DUF1682, Protein of unknown function (DUF1682)

 Score = 49.2 bits (118), Expect = 5e-06
 Identities = 21/65 (32%), Positives = 45/65 (69%), Gaps = 2/65 (3%)

Query: 949  RRRRRRSGKEEEEEEKKKEEKKKEEEEKKKKEGKTKKEEKKKEEE--EEKKKKKKEEEKE 1006
             R+  ++ +EEEE+  K  E++++EE ++KKE K K+E + K  +   E+++K +E+E++
Sbjct: 258  LRKVDKTREEEEEKILKAAEEERQEEAQEKKEEKKKEEREAKLAKLSPEEQRKLEEKERK 317

Query: 1007 EEEKK 1011
            ++ +K
Sbjct: 318  KQARK 322

The members of this family are all hypothetical eukaryotic proteins of unknown function. One member is described as being an adipocyte-specific protein, but no evidence of this was found. Length = 322

>gnl|CDD|218752 pfam05793, TFIIF_alpha, Transcription initiation factor IIF, alpha subunit (TFIIF-alpha)

 Score = 50.0 bits (119), Expect = 5e-06
 Identities = 36/172 (20%), Positives = 74/172 (43%), Gaps = 2/172 (1%)

Query: 851  KKKKKEEEEEGGEKEEEEGGGGGGRRRRRRRRSGKEEEEKKKKEGGGGRRRRRRKKRRRS 910
            K       +E  E E E+GGGG G+  + +   G +E++  + + GG      + K+++ 
Sbjct: 187  KNGPAAFGDEDEETEGEKGGGGRGKDLKIKDLEGDDEDDGDESDKGGEDGDEEKSKKKKK 246

Query: 911  RRRRSRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRR--RRRRRRSGKEEEEEEKKKEE 968
            +  +++++    ++ +R                  R          SG + EE E K   
Sbjct: 247  KLAKNKKKLDDDKKGKRGGDDDADEYDSDDGDDEGREEDYISDSSASGNDPEEREDKLSP 306

Query: 969  KKKEEEEKKKKEGKTKKEEKKKEEEEEKKKKKKEEEKEEEEKKEEEEKEEEE 1020
            +   + E ++ E   + EE+K EEE    KK K+ +K + +K   ++ + + 
Sbjct: 307  EIPAKPEIEQDEDSEESEEEKNEEEGGLSKKGKKLKKLKGKKNGLDKDDSDS 358

Transcription initiation factor IIF, alpha subunit (TFIIF-alpha) or RNA polymerase II-associating protein 74 (RAP74) is the large subunit of transcription factor IIF (TFIIF), which is essential for accurate initiation and stimulates elongation by RNA polymerase II. Length = 528

>gnl|CDD|222581 pfam14181, YqfQ, YqfQ-like protein

 Score = 47.1 bits (112), Expect = 5e-06
 Identities = 23/61 (37%), Positives = 34/61 (55%), Gaps = 3/61 (4%)

Query: 953  RRSGKEEEEEEKKKEEKKKEEEEKKKKEGKTKKEEKKKEEEEEKKKKKKEEEKEEEEKKE 1012
            R     ++EEE+ +EE   E E++   E KT+ +EKKK    E  K K E+EK + E K+
Sbjct: 89   RELSSSDDEEEETEEESTDETEQEDPPETKTESKEKKK---REVPKPKTEKEKPKTEPKK 145

Query: 1013 E 1013
             
Sbjct: 146  P 146

The YqfQ-like protein family includes the B. subtilis YqfQ protein, also known as VrrA, which is functionally uncharacterized. This family of proteins is found in bacteria. Proteins in this family are typically between 146 and 237 amino acids in length. There are two conserved sequence motifs: QYGP and PKLY. Length = 155

>gnl|CDD|237178 PRK12705, PRK12705, hypothetical protein; Provisional

 Score = 49.7 bits (119), Expect = 6e-06
 Identities = 18/106 (16%), Positives = 48/106 (45%)

Query: 920  RRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRSGKEEEEEEKKKEEKKKEEEEKKKK 979
               ++R+R  +   R  +  ++    +              E  ++++E ++E EE +++
Sbjct: 23   VLLKKRQRLAKEAERILQEAQKEAEEKLEAALLEAKELLLRERNQQRQEARREREELQRE 82

Query: 980  EGKTKKEEKKKEEEEEKKKKKKEEEKEEEEKKEEEEKEEEEKKRRR 1025
            E +  ++E++ +   EK    + + +E E+     E E EE +++ 
Sbjct: 83   EERLVQKEEQLDARAEKLDNLENQLEEREKALSARELELEELEKQL 128

Length = 508

>gnl|CDD|220648 pfam10243, MIP-T3, Microtubule-binding protein MIP-T3

 Score = 49.5 bits (118), Expect = 7e-06
 Identities = 41/225 (18%), Positives = 80/225 (35%), Gaps = 23/225 (10%)

Query: 819  RRRRRRKKKEEKKKWKRRGGGRRRRRGKKEEEKKKKKEEEEEGGEKEE---EEGGGGGGR 875
            ++R R + K   KK  ++    +++   +EE++++   E  +G  +E    EE       
Sbjct: 164  KKRERVRAKSRPKKPPKKKPPNKKKEPPEEEKQRQAAREAVKGKPEEPDVNEEREKEEDD 223

Query: 876  RRRRRRRSGKEEEEKKKKEGGGGRRRRRRKKRRRSRRRRSRRRRRRRRRRRRRRRRRRRR 935
             + R   +   EE++ ++     RR     K+       +    R   +R   R R   R
Sbjct: 224  GKDRETTTSPMEEDESRQSSEISRRSSSSLKKPDPSPSMASPETRESSKRTETRPRTSLR 283

Query: 936  RRRRRRRRRRRRRRRRRRRSGKEEEEEEKK---------KEEKKKEEEEK-------KKK 979
                R    R    R +R+      ++ +           E KK E+E+          +
Sbjct: 284  PPSARPASARPAPPRVKRKEIVTVLQDAQGVGKIVSNVILEGKKSEDEDDENFVVEAAAQ 343

Query: 980  EGKTKKEEKKKEEEEEKK----KKKKEEEKEEEEKKEEEEKEEEE 1020
                    + + E+ E++    +K  E +KE E         E E
Sbjct: 344  APDIVAGGEDEAEDGEQQGGLVQKILETKKEYETGSGSASPGETE 388

This protein, which interacts with both microtubules and TRAF3 (tumour necrosis factor receptor-associated factor 3), is conserved from worms to humans. The N-terminal region is the microtubule binding domain and is well-conserved; the C-terminal 100 residues, also well-conserved, constitute the coiled-coil region which binds to TRAF3. The central region of the protein is rich in lysine and glutamic acid and carries KKE motifs which may also be necessary for tubulin-binding, but this region is the least well-conserved. Length = 506

>gnl|CDD|217037 pfam02443, Circo_capsid, Circovirus capsid protein

 Score = 48.2 bits (115), Expect = 7e-06
 Identities = 26/60 (43%), Positives = 26/60 (43%), Gaps = 13/60 (21%)

Query: 875 RRRRRRRRSGKEEEEKKKKEGGGGRRRRRRKKRRRSRRRRSRRRRRRRRRRRRRRRRRRR 934
           R RRR RR                RRRRRR  RRR RRRR    RRR R  R    R  R
Sbjct: 3   RIRRRYRR-------------PRRRRRRRRHWRRRYRRRRLHINRRRHRTNRIYTFRLTR 49

Circoviruses are small circular single stranded viruses. This family is the capsid protein from viruses such as porcine circovirus and beak and feather disease virus. These proteins are about 220 amino acids long. Length = 237

>gnl|CDD|217787 pfam03910, Adeno_PV, Adenovirus minor core protein PV

 Score = 49.1 bits (117), Expect = 7e-06
 Identities = 24/43 (55%), Positives = 25/43 (58%)

Query: 913 RRSRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRS 955
           R +  R R RR  RRRR  RRRRRRRR    R RR R RR R 
Sbjct: 292 RGTTYRSRVRRATRRRRTTRRRRRRRRTAPARVRRVRTRRGRR 334

Length = 336

>gnl|CDD|178945 PRK00247, PRK00247, putative inner membrane protein translocase component YidC; Validated

 Score = 49.5 bits (118), Expect = 7e-06
 Identities = 27/145 (18%), Positives = 51/145 (35%), Gaps = 9/145 (6%)

Query: 880  RRRSGKEEEEKKKKEGGGGRRRRRRKKRRRS-----RRRRSRRRRRRRRRRRRRRRRRRR 934
             +R+   E++K+KK          R+ R R      R           ++ R   +   +
Sbjct: 289  EQRAQYREKQKEKKA----FLWTLRRNRLRMIITPWRAPELHAENAEIKKTRTAEKNEAK 344

Query: 935  RRRRRRRRRRRRRRRRRRRRSGKEEEEEEKKKEEKKKEEEEKKKKEGKTKKEEKKKEEEE 994
             R++   ++RR   R   R + +E      +   ++   + KKK        E    E E
Sbjct: 345  ARKKEIAQKRRAAEREINREARQERAAAMARARARRAAVKAKKKGLIDASPNEDTPSENE 404

Query: 995  EKKKKKKEEEKEEEEKKEEEEKEEE 1019
            E K    + E     +   E  +E+
Sbjct: 405  ESKGSPPQVEATTTAEPNREPSQED 429

Length = 429

>gnl|CDD|223496 COG0419, SbcC, ATPase involved in DNA repair [DNA replication, recombination, and repair]

 Score = 49.8 bits (119), Expect = 7e-06
 Identities = 39/203 (19%), Positives = 72/203 (35%), Gaps = 12/203 (5%)

Query: 828  EEKKKWKRRGGGRRRRRGKKEEEKKKKKEEEEEGGEKEEEEGGGGGGRRRRRRRRSGKEE 887
            E+ +K         +    K EE + +  E  E  E   E                  +E
Sbjct: 167  EKYEKLSELLKEVIKEAKAKIEELEGQLSELLEDIEDLLE------------ALEEELKE 214

Query: 888  EEKKKKEGGGGRRRRRRKKRRRSRRRRSRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRR 947
             +K ++           ++      R +     + R    + R            + R  
Sbjct: 215  LKKLEEIQEEQEEEELEQEIEALEERLAELEEEKERLEELKARLLEIESLELEALKIREE 274

Query: 948  RRRRRRRSGKEEEEEEKKKEEKKKEEEEKKKKEGKTKKEEKKKEEEEEKKKKKKEEEKEE 1007
              R   R  +E EE+ ++ EE ++E EE +++    +   ++ EE  EK K  +E  ++ 
Sbjct: 275  ELRELERLLEELEEKIERLEELEREIEELEEELEGLRALLEELEELLEKLKSLEERLEKL 334

Query: 1008 EEKKEEEEKEEEEKKRRRIRRKR 1030
            EEK E+ E E EE    +    +
Sbjct: 335  EEKLEKLESELEELAEEKNELAK 357

Length = 908

>gnl|CDD|219124 pfam06658, DUF1168, Protein of unknown function (DUF1168)

 Score = 46.6 bits (111), Expect = 7e-06
 Identities = 38/101 (37%), Positives = 58/101 (57%), Gaps = 13/101 (12%)

Query: 938  RRRRRRRRRRRRRRRRRSGKEEEEEE--KKKEEKKKEEEEK---------KKKEGKTKKE 986
            R  RRR   R      +  KE E+EE  +K+EEKK+++EEK         KKK+ K KK+
Sbjct: 42   RALRRREYERLELMDEKWKKETEDEEFQQKREEKKRKDEEKTAKKRAKRQKKKQKKKKKK 101

Query: 987  EKKKEEEEEKK--KKKKEEEKEEEEKKEEEEKEEEEKKRRR 1025
            + KK  ++E+K   K  EE  +EEE+ EE+++EE  +   +
Sbjct: 102  KAKKGNKKEEKEGSKSSEESSDEEEEGEEDKQEEPVEIMEK 142

This family consists of several hypothetical eukaryotic proteins of unknown function. Length = 142

>gnl|CDD|219746 pfam08208, RNA_polI_A34, DNA-directed RNA polymerase I subunit RPA34

 Score = 47.4 bits (113), Expect = 8e-06
 Identities = 25/51 (49%), Positives = 38/51 (74%)

Query: 953  RRSGKEEEEEEKKKEEKKKEEEEKKKKEGKTKKEEKKKEEEEEKKKKKKEE 1003
            +   + E EEE+KKE+KKK+E +K+KKE K KKE+  + +  +KKKKKK++
Sbjct: 142  KVEKEAEVEEEEKKEKKKKKEVKKEKKEKKDKKEKMVEPKGSKKKKKKKKK 192

5. This is a family of proteins conserved from yeasts to human. Subunit A34.5 of RNA polymerase I is a non-essential subunit which is thought to help Pol I overcome topological constraints imposed on ribosomal DNA during the process of transcription. Length = 193

>gnl|CDD|217787 pfam03910, Adeno_PV, Adenovirus minor core protein PV

 Score = 48.7 bits (116), Expect = 8e-06
 Identities = 25/43 (58%), Positives = 26/43 (60%)

Query: 912 RRRSRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRR 954
           R  + R R RR  RRRR  RRRRRRRR    R RR R RR RR
Sbjct: 292 RGTTYRSRVRRATRRRRTTRRRRRRRRTAPARVRRVRTRRGRR 334

Length = 336

>gnl|CDD|226894 COG4499, COG4499, Predicted membrane protein [Function unknown]

 Score = 49.0 bits (117), Expect = 8e-06
 Identities = 20/68 (29%), Positives = 43/68 (63%)

Query: 958  EEEEEEKKKEEKKKEEEEKKKKEGKTKKEEKKKEEEEEKKKKKKEEEKEEEEKKEEEEKE 1017
            ++ +E  K+  KK ++  KK  E K + +  ++ E + K++K K+EE E+++K++ +E +
Sbjct: 365  DKRQELLKEYNKKLQDYTKKLGEVKDETDASEEAEAKAKEEKLKQEENEKKQKEQADEDK 424

Query: 1018 EEEKKRRR 1025
            E+ +K  R
Sbjct: 425  EKRQKDER 432

Length = 434

>gnl|CDD|114011 pfam05262, Borrelia_P83, Borrelia P83/100 protein

 Score = 49.2 bits (117), Expect = 8e-06
 Identities = 31/127 (24%), Positives = 61/127 (48%), Gaps = 8/127 (6%)

Query: 906  KRRRSRRRRSRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRSGKEEEEEEKK 965
            K R S+    R ++ +    +++    + +++    +    ++R   R+  +E +   K 
Sbjct: 204  KERESQEDAKRAQQLKEELDKKQIDADKAQQKADFAQDNADKQRDEVRQKQQEAKNLPKP 263

Query: 966  -----KEEKKKEEEEKKKKEGKTKKEEKKKEEEEEKKKKKKEEEKEEEEK---KEEEEKE 1017
                  +E K+  E +K++  K + E KK +EE  K K  K  + ++E K   KE E+KE
Sbjct: 264  ADTSSPKEDKQVAENQKREIEKAQIEIKKNDEEALKAKDHKAFDLKQESKASEKEAEDKE 323

Query: 1018 EEEKKRR 1024
             E +K+R
Sbjct: 324  LEAQKKR 330

This family consists of several Borrelia P83/P100 antigen proteins. Length = 489

>gnl|CDD|217438 pfam03228, Adeno_VII, Adenoviral core protein VII

 Score = 45.6 bits (108), Expect = 9e-06
 Identities = 18/58 (31%), Positives = 23/58 (39%)

Query: 899 RRRRRRKKRRRSRRRRSRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRSG 956
               R   ++ +R+   R                 R  RRRRRR RR  RRR RR+S 
Sbjct: 52  VDDLRDNLKKYARKYTERTVASTVDPVADSVPAGARAYRRRRRRLRRVARRRARRKST 109

The function of this protein is unknown. It has a conserved amino terminus of 50 residues followed by a positively charged tail, suggesting it may interact with nucleic acid. The major core protein of the adenovirus, protein VII, was found to be associated with viral DNA throughout infection. The precursor to protein VII were shown to be in vivo and in vitro acceptors of ADP-ribose. The ADP-ribosylated core proteins were assembled into mature virus particles. ADP-ribosylation of adenovirus core proteins may have a role in virus decapsidation. Length = 117

>gnl|CDD|235250 PRK04195, PRK04195, replication factor C large subunit; Provisional

 Score = 49.1 bits (118), Expect = 1e-05
 Identities = 18/61 (29%), Positives = 43/61 (70%)

Query: 940  RRRRRRRRRRRRRRRSGKEEEEEEKKKEEKKKEEEEKKKKEGKTKKEEKKKEEEEEKKKK 999
               +  ++R   ++   K+    +KK+EE+++E+E+K++++ + ++E ++++EEEE+KKK
Sbjct: 415  IVEKAEKKREEEKKEKKKKAFAGKKKEEEEEEEKEKKEEEKEEEEEEAEEEKEEEEEKKK 474

Query: 1000 K 1000
            K
Sbjct: 475  K 475

Length = 482

>gnl|CDD|235250 PRK04195, PRK04195, replication factor C large subunit; Provisional

 Score = 48.8 bits (117), Expect = 1e-05
 Identities = 18/61 (29%), Positives = 43/61 (70%)

Query: 938 RRRRRRRRRRRRRRRRRSGKEEEEEEKKKEEKKKEEEEKKKKEGKTKKEEKKKEEEEEKK 997
              +  ++R   ++ ++      ++++++EE++KE++E++K+E + + EE+K+EEEE+KK
Sbjct: 415 IVEKAEKKREEEKKEKKKKAFAGKKKEEEEEEEKEKKEEEKEEEEEEAEEEKEEEEEKKK 474

Query: 998 K 998
           K
Sbjct: 475 K 475

Length = 482

>gnl|CDD|235250 PRK04195, PRK04195, replication factor C large subunit; Provisional

 Score = 48.4 bits (116), Expect = 1e-05
 Identities = 22/51 (43%), Positives = 34/51 (66%)

Query: 976  KKKKEGKTKKEEKKKEEEEEKKKKKKEEEKEEEEKKEEEEKEEEEKKRRRI 1026
             KK   K KK  +K E++ E++KK+K+++    +KKEEEE+EE+EKK    
Sbjct: 405  SKKATKKIKKIVEKAEKKREEEKKEKKKKAFAGKKKEEEEEEEKEKKEEEK 455

Length = 482

>gnl|CDD|235401 PRK05306, infB, translation initiation factor IF-2; Validated

 Score = 49.1 bits (118), Expect = 1e-05
 Identities = 18/73 (24%), Positives = 31/73 (42%)

Query: 958  EEEEEEKKKEEKKKEEEEKKKKEGKTKKEEKKKEEEEEKKKKKKEEEKEEEEKKEEEEKE 1017
            EEEE  K++ +++ EEE K + E     E +++ + E       EE  E     E   + 
Sbjct: 39   EEEEARKEEAKREAEEEAKAEAEEAAAAEAEEEAKAEAAAAAPAEEAAEAAAAAEAAARP 98

Query: 1018 EEEKKRRRIRRKR 1030
             E++  R      
Sbjct: 99   AEDEAARPAEAAA 111

Length = 746

>gnl|CDD|206039 pfam13868, Trichoplein, Tumour suppressor, Mitostatin

 Score = 48.8 bits (117), Expect = 1e-05
 Identities = 41/216 (18%), Positives = 95/216 (43%), Gaps = 19/216 (8%)

Query: 806  CITQIRLSRNRRGRRRRRRKKKEEK--KKWKRRGGGRRRRRGKKEEEKKKKKEEEEEGGE 863
                      R+   + R +++E K  +  + +      R  ++ E K++K+ E      
Sbjct: 130  IDEFNEERIERKEEEKEREREEELKILEYQREKAEREEEREAERRERKEEKEREVARLRA 189

Query: 864  KEEEEGGGGGGRRRRRRR---RSGKEEEEKKKKEGGGGRRRRRRKKRRRSRRRRSRRRRR 920
            ++EE          R      R+   +EE ++KE    R++ + +  +R R+++  +R R
Sbjct: 190  QQEEA------EDEREELDELRADLYQEEYERKE----RQKEKEEAEKRRRQKQELQRAR 239

Query: 921  RRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRSGKEEEEEEKKKEEKKKEEEEKKKKE 980
              +   +  R +  R      R R   ++       +E  E+ + K  + + E E++ +E
Sbjct: 240  EEQIEEKEERLQEERAEEEAERERMLEKQAEDEELEQENAEKRRMKRLEHRRELEQQIEE 299

Query: 981  GKTKKEEKKKEEEEEKKKKKKEE----EKEEEEKKE 1012
             + ++  +++EE EE ++ ++EE     + EEE++ 
Sbjct: 300  KEERRAAEREEELEEGERLREEEAERQARIEEERQR 335

Trichoplein or mitostatin, was first defined as a meiosis-specific nuclear structural protein. It has since been linked with mitochondrial movement. It is associated with the mitochondrial outer membrane, and over-expression leads to reduction in mitochondrial motility whereas lack of it enhances mitochondrial movement. The activity appears to be mediated through binding the mitochondria to the actin intermediate filaments (IFs). Length = 349

>gnl|CDD|219408 pfam07423, DUF1510, Protein of unknown function (DUF1510)

 Score = 47.4 bits (113), Expect = 1e-05
 Identities = 20/58 (34%), Positives = 35/58 (60%)

Query: 964  KKKEEKKKEEEEKKKKEGKTKKEEKKKEEEEEKKKKKKEEEKEEEEKKEEEEKEEEEK 1021
               +    E+E KK  + +T + E+ KEEE+E    + +E+K + EK++EE +EE E+
Sbjct: 40   PSDQAAADEQEAKKSDDQETAEIEEVKEEEKEAANSEDKEDKGDAEKEDEESEEENEE 97

This family consists of several hypothetical bacterial proteins of around 200 residues in length. The function of this family is unknown. Length = 214

>gnl|CDD|219408 pfam07423, DUF1510, Protein of unknown function (DUF1510)

 Score = 47.0 bits (112), Expect = 1e-05
 Identities = 17/68 (25%), Positives = 42/68 (61%)

Query: 955  SGKEEEEEEKKKEEKKKEEEEKKKKEGKTKKEEKKKEEEEEKKKKKKEEEKEEEEKKEEE 1014
            S  ++   ++++ +K  ++E  + +E K +++E    E++E K   ++E++E EE+ EEE
Sbjct: 39   SPSDQAAADEQEAKKSDDQETAEIEEVKEEEKEAANSEDKEDKGDAEKEDEESEEENEEE 98

Query: 1015 EKEEEEKK 1022
            ++E  ++ 
Sbjct: 99   DEESSDEN 106

This family consists of several hypothetical bacterial proteins of around 200 residues in length. The function of this family is unknown. Length = 214

>gnl|CDD|144437 pfam00841, Protamine_P2, Sperm histone P2

 Score = 44.6 bits (105), Expect = 1e-05
 Identities = 27/76 (35%), Positives = 34/76 (44%)

Query: 878 RRRRRSGKEEEEKKKKEGGGGRRRRRRKKRRRSRRRRSRRRRRRRRRRRRRRRRRRRRRR 937
              +  G++ E +++ +  G          R  R     R R   RRR  R  RRRR  R
Sbjct: 12  SPHQGYGQQREGEEQGQEQGLSPEDVEVYGRTHRGHYHYRHRSCSRRRLYRIHRRRRSCR 71

Query: 938 RRRRRRRRRRRRRRRR 953
           RRRRR  R RRR RR 
Sbjct: 72  RRRRRSCRHRRRHRRG 87

This protein also known as protamine P2 can substitute for histones in the chromatin of sperm. The alignment contains both the sequence of the mature P2 protein and its propeptide. Length = 91

>gnl|CDD|217787 pfam03910, Adeno_PV, Adenovirus minor core protein PV

 Score = 48.3 bits (115), Expect = 1e-05
 Identities = 24/45 (53%), Positives = 26/45 (57%)

Query: 897 GGRRRRRRKKRRRSRRRRSRRRRRRRRRRRRRRRRRRRRRRRRRR 941
           G R    R + RR+ RRR   RRRRRRRR    R RR R RR RR
Sbjct: 290 GYRGTTYRSRVRRATRRRRTTRRRRRRRRTAPARVRRVRTRRGRR 334

Length = 336

>gnl|CDD|222581 pfam14181, YqfQ, YqfQ-like protein

 Score = 46.3 bits (110), Expect = 1e-05
 Identities = 18/43 (41%), Positives = 25/43 (58%)

Query: 958  EEEEEEKKKEEKKKEEEEKKKKEGKTKKEEKKKEEEEEKKKKK 1000
             +E E++   E K E +EKKK+E    K EK+K + E KK K 
Sbjct: 106  TDETEQEDPPETKTESKEKKKREVPKPKTEKEKPKTEPKKPKP 148

The YqfQ-like protein family includes the B. subtilis YqfQ protein, also known as VrrA, which is functionally uncharacterized. This family of proteins is found in bacteria. Proteins in this family are typically between 146 and 237 amino acids in length. There are two conserved sequence motifs: QYGP and PKLY. Length = 155

>gnl|CDD|237178 PRK12705, PRK12705, hypothetical protein; Provisional

 Score = 48.9 bits (117), Expect = 1e-05
 Identities = 26/123 (21%), Positives = 52/123 (42%), Gaps = 6/123 (4%)

Query: 896  GGGRRRRRRKKRRRSRRRRSRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRS 955
             G      +K++R ++      +  ++    +        +    R R ++R+  RR R 
Sbjct: 18   LGVLVVLLKKRQRLAKEAERILQEAQKEAEEKLEAALLEAKELLLRERNQQRQEARRER- 76

Query: 956  GKEEEEEEKKKEEKKKEEEEKKKKEGKTKKEEKKKEEEEEKKKKKKEEEKEEEEKKEEEE 1015
                 EE +++EE+  ++EE+     +     + + EE EK    +E E EE EK+ + E
Sbjct: 77   -----EELQREEERLVQKEEQLDARAEKLDNLENQLEEREKALSARELELEELEKQLDNE 131

Query: 1016 KEE 1018
               
Sbjct: 132  LYR 134

Length = 508

>gnl|CDD|222571 pfam14153, Spore_coat_CotO, Spore coat protein CotO

 Score = 47.1 bits (112), Expect = 1e-05
 Identities = 23/82 (28%), Positives = 49/82 (59%)

Query: 949  RRRRRRSGKEEEEEEKKKEEKKKEEEEKKKKEGKTKKEEKKKEEEEEKKKKKKEEEKEEE 1008
              ++    +EE+E   +  + K+EE++ + +E + +KE  + E E+  ++++KEE  +EE
Sbjct: 32   IIKKADEKEEEKENSDEHVKSKEEEQKIEYEEAEKEKEAGEPEREDIAEQQEKEEIAQEE 91

Query: 1009 EKKEEEEKEEEEKKRRRIRRKR 1030
            EK+EE E  ++++     R+K 
Sbjct: 92   EKEEEAEDVKQQEVFSFKRKKP 113

Bacillus spores are protected by a protein shell consisting of over 50 different polypeptides, known as the coat. This family of proteins has an important morphogenetic role in coat assembly, it is involved in the assembly of at least 5 different coat proteins including CotB, CotG, CotS, CotSA and CotW. It is likely to act at a late stage of coat assembly. Length = 185

>gnl|CDD|222636 pfam14265, DUF4355, Domain of unknown function (DUF4355)

 Score = 45.7 bits (109), Expect = 1e-05
 Identities = 24/72 (33%), Positives = 41/72 (56%)

Query: 958  EEEEEEKKKEEKKKEEEEKKKKEGKTKKEEKKKEEEEEKKKKKKEEEKEEEEKKEEEEKE 1017
            E EEE+   +++  +   K+K + + K+EEKK E E+  K   +E+ + E EK E+E +E
Sbjct: 1    EPEEEKTFTDKEVDKAIAKEKAKWEKKQEEKKSEAEKLAKMSAEEKAEYELEKLEKELEE 60

Query: 1018 EEEKKRRRIRRK 1029
             E +  RR  + 
Sbjct: 61   LEAELARRELKA 72

This family of proteins is found in bacteria and viruses. Proteins in this family are typically between 180 and 214 amino acids in length. Length = 125

>gnl|CDD|223003 PHA03169, PHA03169, hypothetical protein; Provisional

 Score = 48.8 bits (116), Expect = 1e-05
 Identities = 25/135 (18%), Positives = 38/135 (28%), Gaps = 12/135 (8%)

Query: 898  GRRRRRRKKRRRSRRRRSRRRRRRRRRRRRRRRRRRRRRRRRRR------------RRRR 945
              R+RR+ KR R   R S R   +R    R +  RRR    R              + R 
Sbjct: 1    MSRQRRKAKRSRHTLRSSCRGHCKRHGGTREQAGRRRGTAARAAKPAPPAPTTSGPQVRA 60

Query: 946  RRRRRRRRRSGKEEEEEEKKKEEKKKEEEEKKKKEGKTKKEEKKKEEEEEKKKKKKEEEK 1005
               +  R+     E  EE +  EK++  +      G               ++       
Sbjct: 61   VAEQGHRQTESDTETAEESRHGEKEERGQGGPSGSGSESVGSPTPSPSGSAEELASGLSP 120

Query: 1006 EEEEKKEEEEKEEEE 1020
            E       E      
Sbjct: 121  ENTSGSSPESPASHS 135

Length = 413

>gnl|CDD|179385 PRK02224, PRK02224, chromosome segregation protein; Provisional

 Score = 49.3 bits (118), Expect = 1e-05
 Identities = 47/210 (22%), Positives = 82/210 (39%), Gaps = 12/210 (5%)

Query: 816  RRGRRRRRRKKKEEKKKWKRRGGGRRRRRGKKEEEKKKKKEEEEEGGEKEEEEGGGGGGR 875
            R  R   RR+  EE    +R     +R R   EE +++  E E E  EK E         
Sbjct: 510  RIERLEERREDLEELIAERRETIEEKRER--AEELRERAAELEAEAEEKREAA------- 560

Query: 876  RRRRRRRSGKEEEEKKKKEGGGGRRRRRRKKRRRSRRRRSRRRRRRRRRRRRRRRRRRRR 935
                   + +  EE  +        + R +   R R   +          R R +R    
Sbjct: 561  -AEAEEEAEEAREEVAELNSKLAELKERIESLERIRTLLAAIADAEDEIERLREKREALA 619

Query: 936  RRRRRRRRRRRRRRRRRRRSGKEEEEE--EKKKEEKKKEEEEKKKKEGKTKKEEKKKEEE 993
                 RR R   +R R+R    E +E   E+ +E+K++ EE  ++ E K  +  +++++ 
Sbjct: 620  ELNDERRERLAEKRERKRELEAEFDEARIEEAREDKERAEEYLEQVEEKLDELREERDDL 679

Query: 994  EEKKKKKKEEEKEEEEKKEEEEKEEEEKKR 1023
            + +    + E +E EE +E  E  E   + 
Sbjct: 680  QAEIGAVENELEELEELRERREALENRVEA 709

Length = 880

>gnl|CDD|177283 PHA00451, PHA00451, protein kinase

 Score = 48.2 bits (115), Expect = 1e-05
 Identities = 15/56 (26%), Positives = 25/56 (44%), Gaps = 2/56 (3%)

Query: 900 RRRRRKKRR--RSRRRRSRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRR 953
           R + RK +R      + +R+   +RR+R R+ R R  +     R    + RR   R
Sbjct: 248 RCKNRKAKRDPNGTFQVARKAAMKRRKRNRKLRARNAKELAAMRMEANQIRRNEPR 303

Length = 362

>gnl|CDD|226082 COG3552, CoxE, Protein containing von Willebrand factor type A (vWA) domain [General function prediction only]

 Score = 48.2 bits (115), Expect = 1e-05
 Identities = 35/135 (25%), Positives = 47/135 (34%), Gaps = 12/135 (8%)

Query: 831 KKWKRRGGGRRRRRGKKEEEKKKKKEEEEEGGEKEEEEG---GGGGGRRRRRRRRSGKEE 887
           +  +      R R G+ E    + +  E  G   E          G     R   SG E 
Sbjct: 86  EAMRALILPGRARAGEDERRAMENRVSEALGTRSEAALTPMEASEGEPVAARLTPSGDEA 145

Query: 888 EEKKK-KEGGGGRRRRRRKKRRRSRRRRSRRRRRRRRRRRRRRRRRRRRRRRRRRR---- 942
              +   +      R   +  RR R   +RRR RR R  RRR+R   RR  R+       
Sbjct: 146 LADRDFAQLDTAELRALGEALRRLRAPLARRRSRRLRASRRRKRIDLRRTMRKSMSTGGE 205

Query: 943 ----RRRRRRRRRRR 953
                RRR RRR+  
Sbjct: 206 VILLVRRRPRRRKPP 220

Length = 395

>gnl|CDD|235250 PRK04195, PRK04195, replication factor C large subunit; Provisional

 Score = 48.4 bits (116), Expect = 2e-05
 Identities = 17/61 (27%), Positives = 44/61 (72%)

Query: 937 RRRRRRRRRRRRRRRRRRSGKEEEEEEKKKEEKKKEEEEKKKKEGKTKKEEKKKEEEEEK 996
              +  ++R   ++ +++     +++E+++EE+K+++EE+K++E +  +EEK++EEE++K
Sbjct: 415 IVEKAEKKREEEKKEKKKKAFAGKKKEEEEEEEKEKKEEEKEEEEEEAEEEKEEEEEKKK 474

Query: 997 K 997
           K
Sbjct: 475 K 475

Length = 482

>gnl|CDD|235250 PRK04195, PRK04195, replication factor C large subunit; Provisional

 Score = 48.0 bits (115), Expect = 2e-05
 Identities = 23/61 (37%), Positives = 44/61 (72%)

Query: 941  RRRRRRRRRRRRRRSGKEEEEEEKKKEEKKKEEEEKKKKEGKTKKEEKKKEEEEEKKKKK 1000
               +  ++R   ++  K++    KKKEE+++EE+EKK++E + ++EE ++E+EEE++KKK
Sbjct: 415  IVEKAEKKREEEKKEKKKKAFAGKKKEEEEEEEKEKKEEEKEEEEEEAEEEKEEEEEKKK 474

Query: 1001 K 1001
            K
Sbjct: 475  K 475

Length = 482

>gnl|CDD|235250 PRK04195, PRK04195, replication factor C large subunit; Provisional

 Score = 48.0 bits (115), Expect = 2e-05
 Identities = 21/61 (34%), Positives = 44/61 (72%)

Query: 942  RRRRRRRRRRRRRSGKEEEEEEKKKEEKKKEEEEKKKKEGKTKKEEKKKEEEEEKKKKKK 1001
               +  ++R   +  K+++    KK+E+++EEE++KK+E K ++EE+ +EE+EE+++KKK
Sbjct: 415  IVEKAEKKREEEKKEKKKKAFAGKKKEEEEEEEKEKKEEEKEEEEEEAEEEKEEEEEKKK 474

Query: 1002 E 1002
            +
Sbjct: 475  K 475

Length = 482

>gnl|CDD|224117 COG1196, Smc, Chromosome segregation ATPases [Cell division and chromosome partitioning]

 Score = 48.6 bits (116), Expect = 2e-05
 Identities = 25/132 (18%), Positives = 60/132 (45%)

Query: 899  RRRRRRKKRRRSRRRRSRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRSGKE 958
            R+    +K  R+     R         ++  +  R+  +  R +  +   R         
Sbjct: 173  RKEEAERKLERTEENLERLEDLLEELEKQLEKLERQAEKAERYQELKAELRELELALLLA 232

Query: 959  EEEEEKKKEEKKKEEEEKKKKEGKTKKEEKKKEEEEEKKKKKKEEEKEEEEKKEEEEKEE 1018
            + +E +K+ E+ +EE  + ++E +  +EE ++ E+E ++ K + EE  EE ++ +EE  E
Sbjct: 233  KLKELRKELEELEEELSRLEEELEELQEELEEAEKEIEELKSELEELREELEELQEELLE 292

Query: 1019 EEKKRRRIRRKR 1030
             +++   +  + 
Sbjct: 293  LKEEIEELEGEI 304

Length = 1163

>gnl|CDD|224117 COG1196, Smc, Chromosome segregation ATPases [Cell division and chromosome partitioning]

 Score = 48.2 bits (115), Expect = 2e-05
 Identities = 35/170 (20%), Positives = 71/170 (41%), Gaps = 6/170 (3%)

Query: 867  EEGGGGGGRRRRRRRRSGKEEEEKKKKEGGGGRRRRRRKKRRRSRRRRSRRRRRRRRRRR 926
            EE  G    + R+     K E  ++  E          K+  +  R+  +  R +  +  
Sbjct: 162  EEAAGVSKYKERKEEAERKLERTEENLERLEDLLEELEKQLEKLERQAEKAERYQELKAE 221

Query: 927  RRRRRRRRRRRRRRRRRRRRRRRRRRRRSGKEEEEEEKKKEEKKKEEEEKKKKEGKTKKE 986
             R         + +  R+            +EE EE +++ E+ ++E E+ K E +  +E
Sbjct: 222  LRELELALLLAKLKELRKELEELEEELSRLEEELEELQEELEEAEKEIEELKSELEELRE 281

Query: 987  EKKKEEEEEKKKKKKEEEKE------EEEKKEEEEKEEEEKKRRRIRRKR 1030
            E ++ +EE  + K++ EE E       E  +E E + EE ++R    +++
Sbjct: 282  ELEELQEELLELKEEIEELEGEISLLRERLEELENELEELEERLEELKEK 331

Length = 1163

>gnl|CDD|225606 COG3064, TolA, Membrane protein involved in colicin uptake [Cell envelope biogenesis, outer membrane]

 Score = 48.0 bits (114), Expect = 2e-05
 Identities = 32/205 (15%), Positives = 84/205 (40%), Gaps = 14/205 (6%)

Query: 817  RGRRRRRRKKKEEKKKWKRRGGGRRRRRGKKEEEKKKKKEEEEEGGEKEEEEGGGGGGRR 876
            + ++   +K ++++KK + +     + +   E+E+ K+ E+E    ++           +
Sbjct: 68   QSQQSSAKKGEQQRKKKEEQVAEELKPKQAAEQERLKQLEKERLKAQE-----------Q 116

Query: 877  RRRRRRSGKEEEEKKKKEGGGGRRRRRRKKRRRSRRRRSRRRRRRRRRRRRRRRRRRRRR 936
            +++   + K+ + ++K++    R+    +K++    +        + +     +++    
Sbjct: 117  QKQAEEAEKQAQLEQKQQEEQARKAAAEQKKKAEAAKAKAAAEAAKLKAAAEAKKKAEEA 176

Query: 937  RRRRRRRRRRRRRRRRRRSGKEEEEEEKKKEEKKKEEEEKKKKEGKTKKE-EKKKEEEEE 995
             +     + +      ++  K E E +   E+ K E E K K E K +   E+K   E++
Sbjct: 177  AKAAEEAKAKAEAAAAKK--KAEAEAKAAAEKAKAEAEAKAKAEKKAEAAAEEKAAAEKK 234

Query: 996  KKKKKKEEEKEEEEKKEEEEKEEEE 1020
            K   K + +K     K  E K    
Sbjct: 235  KAAAKAKADKAAAAAKAAERKAAAA 259

Length = 387

>gnl|CDD|219061 pfam06495, Transformer, Fruit fly transformer protein

 Score = 45.8 bits (108), Expect = 2e-05
 Identities = 26/92 (28%), Positives = 36/92 (39%)

Query: 876 RRRRRRRSGKEEEEKKKKEGGGGRRRRRRKKRRRSRRRRSRRRRRRRRRRRRRRRRRRRR 935
           R  RR    KE+      E     R R  ++R+    R +   R RR R R R +   R 
Sbjct: 11  RDTRRDSRKKEKIPYFADEVRERDRVRNLRQRKTQSTRPTTSHRGRRTRSRSRSQSAERN 70

Query: 936 RRRRRRRRRRRRRRRRRRRSGKEEEEEEKKKE 967
             +RR R R R R R   R       E +++ 
Sbjct: 71  SCQRRHRSRSRSRNRSDSRHRSTSSTERRRRS 102

This family consists of transformer proteins from several Drosophila species and also from Ceratitis capitata (Mediterranean fruit fly). The transformer locus (tra) produces an RNA processing protein that alternatively splices the doublesex pre-mRNA in the sex determination hierarchy of Drosophila melanogaster. Length = 182

>gnl|CDD|233758 TIGR02169, SMC_prok_A, chromosome segregation protein SMC, primarily archaeal type

 Score = 48.5 bits (116), Expect = 2e-05
 Identities = 37/173 (21%), Positives = 60/173 (34%), Gaps = 14/173 (8%)

Query: 862  GEKEEEEGGGGGGRRRRRRRRSGKEEEEKKKKEGGGGRRRRRRKKRRRSRRRRSRRRRRR 921
            GE  E+ G   GG R  R        E  + +     R R R +  +R         RR 
Sbjct: 646  GELFEKSGAMTGGSRAPRGGILFSRSEPAELQ-----RLRERLEGLKRELSSLQSELRRI 700

Query: 922  RRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRSGKEEEEEEKKKEEKKKEEEEKKKKEG 981
              R     +      R+     +   +  +     KE  EE ++     ++E E  K E 
Sbjct: 701  ENRLDELSQELSDASRKIGEIEKEIEQLEQEEEKLKERLEELEEDLSSLEQEIENVKSE- 759

Query: 982  KTKKEEKKKEEEEEKKKKKKEEEKE-------EEEKKEEEEKEEEEKKRRRIR 1027
              K+ E + EE EE   K +E   +           + + E  + E++  RI 
Sbjct: 760  -LKELEARIEELEEDLHKLEEALNDLEARLSHSRIPEIQAELSKLEEEVSRIE 811

SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]. Length = 1164

>gnl|CDD|218684 pfam05672, MAP7, MAP7 (E-MAP-115) family

 Score = 46.2 bits (109), Expect = 2e-05
 Identities = 35/130 (26%), Positives = 71/130 (54%), Gaps = 4/130 (3%)

Query: 899  RRRRRRKKRRRSRRRRSRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRSGKE 958
            RR+ R ++ +  + RR +  + R  R   +RR    R RR    RR+   R R +    +
Sbjct: 32   RRQAREQREQEEQERREQEEQDRLEREELKRRAAEERLRREEEARRQEEERAREKEEKAK 91

Query: 959  EEEEEKKKEEKKKEEEEKKKKEGKTKKEEKKKEEEEEKKKKKKEEEKEEEEKKEEEEKEE 1018
             + EE++K+E++++E  +K+KE    + E +  EE E+ + ++E+  ++ E++  E K+ 
Sbjct: 92   RKAEEEEKQEQEEQERIQKQKE----EAEARAREEAERMRLEREKHFQQIEQERLERKKR 147

Query: 1019 EEKKRRRIRR 1028
             E+  +R R+
Sbjct: 148  LEEIMKRTRK 157

The organisation of microtubules varies with the cell type and is presumably controlled by tissue-specific microtubule-associated proteins (MAPs). The 115-kDa epithelial MAP (E-MAP-115/MAP7) has been identified as a microtubule-stabilising protein predominantly expressed in cell lines of epithelial origin. The binding of this microtubule associated protein is nucleotide independent. Length = 171

>gnl|CDD|217787 pfam03910, Adeno_PV, Adenovirus minor core protein PV

 Score = 47.9 bits (114), Expect = 2e-05
 Identities = 23/43 (53%), Positives = 24/43 (55%)

Query: 915 SRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRSGK 957
            R    R R RR  RRRR  RRRRRRRR    R RR R R G+
Sbjct: 291 YRGTTYRSRVRRATRRRRTTRRRRRRRRTAPARVRRVRTRRGR 333

Length = 336

>gnl|CDD|223496 COG0419, SbcC, ATPase involved in DNA repair [DNA replication, recombination, and repair]

 Score = 48.2 bits (115), Expect = 2e-05
 Identities = 36/188 (19%), Positives = 71/188 (37%), Gaps = 3/188 (1%)

Query: 846  KKEEEKKKKKEEEEEGGEKEEEEGGGGGGRRRRRRRRSGKEEEEKKKKEGGGGRRRRRRK 905
            K+  ++ K K EE EG   E  E             +  K+ EE ++++      +    
Sbjct: 177  KEVIKEAKAKIEELEGQLSELLEDIEDLLEALEEELKELKKLEEIQEEQEEEELEQEIEA 236

Query: 906  KRRRSRRRRSRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRR---RRRRSGKEEEEE 962
               R       + R    + R            + R    R   R         +  EE 
Sbjct: 237  LEERLAELEEEKERLEELKARLLEIESLELEALKIREEELRELERLLEELEEKIERLEEL 296

Query: 963  EKKKEEKKKEEEEKKKKEGKTKKEEKKKEEEEEKKKKKKEEEKEEEEKKEEEEKEEEEKK 1022
            E++ EE ++E E  +    + ++  +K +  EE+ +K +E+ ++ E + EE  +E+ E  
Sbjct: 297  EREIEELEEELEGLRALLEELEELLEKLKSLEERLEKLEEKLEKLESELEELAEEKNELA 356

Query: 1023 RRRIRRKR 1030
            +    R +
Sbjct: 357  KLLEERLK 364

Length = 908

>gnl|CDD|217503 pfam03344, Daxx, Daxx Family

 Score = 48.4 bits (115), Expect = 2e-05
 Identities = 31/100 (31%), Positives = 54/100 (54%), Gaps = 2/100 (2%)

Query: 922  RRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRSGKEEEEEEKKKEEKKKEEEEKKKKEG 981
            RR+R+ R R+    R     +            S  +E EEE+  EE+++EEEE++++E 
Sbjct: 403  RRKRQERERQGTSSRSSDPSKASSTSGESPSMAS--QESEEEESVEEEEEEEEEEEEEEQ 460

Query: 982  KTKKEEKKKEEEEEKKKKKKEEEKEEEEKKEEEEKEEEEK 1021
            ++++EE + EEEEE+ +     E+E E   E +   EE +
Sbjct: 461  ESEEEEGEDEEEEEEVEADNGSEEEMEGSSEGDGDGEEPE 500

The Daxx protein (also known as the Fas-binding protein) is thought to play a role in apoptosis, but precise role played by Daxx remains to be determined. Daxx forms a complex with Axin. Length = 715

>gnl|CDD|236545 PRK09510, tolA, cell envelope integrity inner membrane protein TolA; Provisional

 Score = 47.9 bits (114), Expect = 2e-05
 Identities = 36/175 (20%), Positives = 74/175 (42%), Gaps = 10/175 (5%)

Query: 859  EEGGEKEEEEGGGGGGRRRRRRRRSGKEEEEKKKKEGGGGRRRRRRKKRRRSRRRRSRRR 918
            E+   +++++        +R+++   + EE ++K+     R ++  K+R  ++ ++ +  
Sbjct: 62   EQYNRQQQQQKSAKRAEEQRKKKEQQQAEELQQKQAAEQERLKQLEKERLAAQEQKKQAE 121

Query: 919  RRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRSGKEEEEEEKKKEE-----KKKEE 973
               ++   ++++      +     + +     +R  +  ++   E KK+      KK   
Sbjct: 122  EAAKQAALKQKQAEEAAAKAAAAAKAKAEAEAKRAAAAAKKAAAEAKKKAEAEAAKKAAA 181

Query: 974  EEKKKKE----GKTKKEEKKKEEEEEKKKKKKE-EEKEEEEKKEEEEKEEEEKKR 1023
            E KKK E     K   E KKK E E KKK   E ++K   E K    K   E K 
Sbjct: 182  EAKKKAEAEAAAKAAAEAKKKAEAEAKKKAAAEAKKKAAAEAKAAAAKAAAEAKA 236

Length = 387

>gnl|CDD|237178 PRK12705, PRK12705, hypothetical protein; Provisional

 Score = 47.8 bits (114), Expect = 2e-05
 Identities = 21/112 (18%), Positives = 50/112 (44%)

Query: 912  RRRSRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRSGKEEEEEEKKKEEKKK 971
                +R+R  +   R  +  ++    +        +    R R+ + +E   +++E +++
Sbjct: 23   VLLKKRQRLAKEAERILQEAQKEAEEKLEAALLEAKELLLRERNQQRQEARREREELQRE 82

Query: 972  EEEEKKKKEGKTKKEEKKKEEEEEKKKKKKEEEKEEEEKKEEEEKEEEEKKR 1023
            EE   +K+E    + EK    E + ++++K     E E +E E++ + E  R
Sbjct: 83   EERLVQKEEQLDARAEKLDNLENQLEEREKALSARELELEELEKQLDNELYR 134

Length = 508

>gnl|CDD|177283 PHA00451, PHA00451, protein kinase

 Score = 47.5 bits (113), Expect = 2e-05
 Identities = 12/63 (19%), Positives = 27/63 (42%)

Query: 902 RRRKKRRRSRRRRSRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRSGKEEEE 961
             ++   R + R+++R      +  R+   +RR+R R+ R R  +     R  + +    
Sbjct: 241 ANQRMIERCKNRKAKRDPNGTFQVARKAAMKRRKRNRKLRARNAKELAAMRMEANQIRRN 300

Query: 962 EEK 964
           E +
Sbjct: 301 EPR 303

Length = 362

>gnl|CDD|219563 pfam07767, Nop53, Nop53 (60S ribosomal biogenesis)

 Score = 48.2 bits (115), Expect = 2e-05
 Identities = 20/75 (26%), Positives = 43/75 (57%)

Query: 956  GKEEEEEEKKKEEKKKEEEEKKKKEGKTKKEEKKKEEEEEKKKKKKEEEKEEEEKKEEEE 1015
             + E E   K    K++ + ++ KE + K+ E++ +EE++ KKK  +  + +E  KE  +
Sbjct: 262  FESEYEPINKPVRPKRKTKAQRNKEKRRKELEREAKEEKQLKKKLAQLARLKEIAKEVAQ 321

Query: 1016 KEEEEKKRRRIRRKR 1030
            KE+   +++  R++R
Sbjct: 322  KEKARARKKEQRKER 336

This nucleolar family of proteins are involved in 60S ribosomal biogenesis. They are specifically involved in the processing beyond the 27S stage of 25S rRNA maturation. This family contains sequences that bear similarity to the glioma tumour suppressor candidate region gene 2 protein (p60). This protein has been found to interact with herpes simplex type 1 regulatory proteins. Length = 387

>gnl|CDD|219563 pfam07767, Nop53, Nop53 (60S ribosomal biogenesis)

 Score = 47.8 bits (114), Expect = 2e-05
 Identities = 20/112 (17%), Positives = 51/112 (45%)

Query: 918  RRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRSGKEEEEEEKKKEEKKKEEEEKK 977
             +  ++R+   R   ++  +      R             ++ EEE   E   +  E + 
Sbjct: 207  VKAEKKRQELERVEEKKLEKMAPEASRLDEMSEGLLEESDDDGEEESDDESAWEGFESEY 266

Query: 978  KKEGKTKKEEKKKEEEEEKKKKKKEEEKEEEEKKEEEEKEEEEKKRRRIRRK 1029
            +   K  + ++K + +  K+K++KE E+E +E+K+ ++K  +  + + I ++
Sbjct: 267  EPINKPVRPKRKTKAQRNKEKRRKELEREAKEEKQLKKKLAQLARLKEIAKE 318

This nucleolar family of proteins are involved in 60S ribosomal biogenesis. They are specifically involved in the processing beyond the 27S stage of 25S rRNA maturation. This family contains sequences that bear similarity to the glioma tumour suppressor candidate region gene 2 protein (p60). This protein has been found to interact with herpes simplex type 1 regulatory proteins. Length = 387

>gnl|CDD|237035 PRK12280, rplW, 50S ribosomal protein L23; Reviewed

 Score = 45.5 bits (108), Expect = 2e-05
 Identities = 23/64 (35%), Positives = 39/64 (60%)

Query: 959  EEEEEKKKEEKKKEEEEKKKKEGKTKKEEKKKEEEEEKKKKKKEEEKEEEEKKEEEEKEE 1018
             EE EK+++E  KE EEK+  + K +K+EKK+++  EK  KKK  +  +   K+  +K  
Sbjct: 92   PEESEKEQKEVSKETEEKEAIKAKKEKKEKKEKKVAEKLAKKKSTKTTKNTTKKATKKTT 151

Query: 1019 EEKK 1022
             +K+
Sbjct: 152  TKKE 155

Length = 158

>gnl|CDD|215774 pfam00183, HSP90, Hsp90 protein

 Score = 47.8 bits (114), Expect = 2e-05
 Identities = 28/57 (49%), Positives = 38/57 (66%), Gaps = 7/57 (12%)

Query: 959  EEEEEKKKEEKKKEEEEKKKKEGKTKKEEKKKEEEEEKKKKKKEEEKEEEEKKEEEE 1015
            +EEEE++KEEKK+EEE+   KE    +E  ++EE+EEKKKK K   K +E   E E 
Sbjct: 37   DEEEEEEKEEKKEEEEKTTDKE----EEVDEEEEKEEKKKKTK---KVKETTTEWEL 86

Length = 529

>gnl|CDD|146958 pfam04569, DUF591, Protein of unknown function

 Score = 43.6 bits (103), Expect = 2e-05
 Identities = 25/96 (26%), Positives = 31/96 (32%), Gaps = 14/96 (14%)

Query: 861 GGEKEEEEGGGGGGRRRRRRRRSGKEEEEKKKKEGGGGRRRRRRKKRRRSRRRRSRRRRR 920
            G +EE+E  G  GRR                   GG R     +     R RR+R    
Sbjct: 1   AGRREEDEAVGRNGRRTAAAS--------------GGARHGDTGEGEHTGRLRRTRGDEP 46

Query: 921 RRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRSG 956
             R RRR       RRR+   R+        R R  
Sbjct: 47  TARIRRRELDGGGLRRRQPAARKGGNGDGVTRGRFP 82

This family represents a conserved region in a number of uncharacterized plant proteins. Length = 89

>gnl|CDD|221641 pfam12569, NARP1, NMDA receptor-regulated protein 1

 Score = 48.0 bits (115), Expect = 2e-05
 Identities = 22/63 (34%), Positives = 32/63 (50%), Gaps = 1/63 (1%)

Query: 960  EEEEKKKEEKKKEEEEKKKKEGKTKKEEKKKEEEEEKKKKKKEEEKEEEEKKEEEEKEEE 1019
            E EE++ E       E+KK   K +K EKK E+EE +K   K ++ E   KK +    E 
Sbjct: 395  EGEEEEGENGNLSPAERKKLRKKQRKAEKKAEKEEAEKAAAK-KKAEAAAKKAKGPDGET 453

Query: 1020 EKK 1022
            +K 
Sbjct: 454  KKV 456

This domain family is found in eukaryotes, and is approximately 40 amino acids in length. The family is found in association with pfam07719, pfam00515. There is a single completely conserved residue L that may be functionally important. NARP1 is the mammalian homologue of a yeast N-terminal acetyltransferase that regulates entry into the G(0) phase of the cell cycle. Length = 516

>gnl|CDD|234750 PRK00409, PRK00409, recombination and DNA strand exchange inhibitor protein; Reviewed

 Score = 47.9 bits (115), Expect = 2e-05
 Identities = 24/72 (33%), Positives = 47/72 (65%), Gaps = 1/72 (1%)

Query: 960  EEEEKKKEEKKKEEEEKKKKEGKTKKE-EKKKEEEEEKKKKKKEEEKEEEEKKEEEEKEE 1018
            EE E++ E+K +E E   K+  K K+E E+KKE+ +E++ K  EE ++E ++  +E K+E
Sbjct: 526  EELERELEQKAEEAEALLKEAEKLKEELEEKKEKLQEEEDKLLEEAEKEAQQAIKEAKKE 585

Query: 1019 EEKKRRRIRRKR 1030
             ++  + +R+ +
Sbjct: 586  ADEIIKELRQLQ 597

Length = 782

>gnl|CDD|219838 pfam08432, DUF1742, Fungal protein of unknown function (DUF1742)

 Score = 45.5 bits (108), Expect = 3e-05
 Identities = 21/66 (31%), Positives = 36/66 (54%)

Query: 951  RRRRSGKEEEEEEKKKEEKKKEEEEKKKKEGKTKKEEKKKEEEEEKKKKKKEEEKEEEEK 1010
            ++    K++ + +KKK +KKK++++ KK + K  K EKK E+E E K +   +   E   
Sbjct: 75   KKEYEEKQKWKWKKKKSKKKKDKDKDKKDDKKDDKSEKKDEKEAEDKLEDLTKSYSETLS 134

Query: 1011 KEEEEK 1016
               E K
Sbjct: 135  TLSELK 140

This is a family of fungal proteins of unknown function. Length = 182

>gnl|CDD|219061 pfam06495, Transformer, Fruit fly transformer protein

 Score = 45.4 bits (107), Expect = 3e-05
 Identities = 26/95 (27%), Positives = 42/95 (44%)

Query: 877 RRRRRRSGKEEEEKKKKEGGGGRRRRRRKKRRRSRRRRSRRRRRRRRRRRRRRRRRRRRR 936
           R  RR S K+E+     +    R R R  ++R+++  R     R RR R R R +   R 
Sbjct: 11  RDTRRDSRKKEKIPYFADEVRERDRVRNLRQRKTQSTRPTTSHRGRRTRSRSRSQSAERN 70

Query: 937 RRRRRRRRRRRRRRRRRRSGKEEEEEEKKKEEKKK 971
             +RR R R R R R     +     E+++  + +
Sbjct: 71  SCQRRHRSRSRSRNRSDSRHRSTSSTERRRRSRSR 105

This family consists of transformer proteins from several Drosophila species and also from Ceratitis capitata (Mediterranean fruit fly). The transformer locus (tra) produces an RNA processing protein that alternatively splices the doublesex pre-mRNA in the sex determination hierarchy of Drosophila melanogaster. Length = 182

>gnl|CDD|202096 pfam02029, Caldesmon, Caldesmon

 Score = 47.3 bits (112), Expect = 3e-05
 Identities = 36/166 (21%), Positives = 72/166 (43%), Gaps = 4/166 (2%)

Query: 865  EEEEGGGGGGRRRRRRRRSGKEEEEKKKKEGGGGRRRRRRKKRRRSRRRRSRRRR----R 920
            ++EE      RRR R  +  +++EE    +         +        + S         
Sbjct: 2    DDEEEAARERRRREREEQLRQKQEEGSLGQVTTQVEVNSQNSVPDEESKTSTDDEAALLE 61

Query: 921  RRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRSGKEEEEEEKKKEEKKKEEEEKKKKE 980
            R  RR  RR  R      R++  +     +      +  +E+   + E  +EEE+++ +E
Sbjct: 62   RLARREERRDERFSEALERQKEFKPTSTDQSLSEPSRRMQEDSGAENETVEEEEKEESRE 121

Query: 981  GKTKKEEKKKEEEEEKKKKKKEEEKEEEEKKEEEEKEEEEKKRRRI 1026
             + + EE +   + E+K   ++ E+ ++E+KE E +EEE+ KR  +
Sbjct: 122  EREEVEETEGVTKSEQKNDWRDAEECQKEEKEPEPEEEEKPKRGSL 167

Length = 431

>gnl|CDD|218752 pfam05793, TFIIF_alpha, Transcription initiation factor IIF, alpha subunit (TFIIF-alpha)

 Score = 47.6 bits (113), Expect = 3e-05
 Identities = 27/147 (18%), Positives = 64/147 (43%), Gaps = 7/147 (4%)

Query: 884  GKEEEEKKKKEGGGGRRRRRRKKRRRSRRRRSRRRRRRRRRRRRRRRRRRRRRRRRRRRR 943
            G E+EE + ++GGGGR +  + K              +        + ++++++  + ++
Sbjct: 194  GDEDEETEGEKGGGGRGKDLKIKDLEGDDEDDGDESDKGGEDGDEEKSKKKKKKLAKNKK 253

Query: 944  RRRRRRRRRRRSGKEEEEEEKKKEEKKKEEE-----EKKKKEGKTKKEEKKKEEEEEKK- 997
            +    ++ +R    + +E +    + +  EE              ++E+K   E   K  
Sbjct: 254  KLDDDKKGKRGGDDDADEYDSDDGDDEGREEDYISDSSASGNDPEEREDKLSPEIPAKPE 313

Query: 998  -KKKKEEEKEEEEKKEEEEKEEEEKKR 1023
             ++ ++ E+ EEEK EEE    ++ K+
Sbjct: 314  IEQDEDSEESEEEKNEEEGGLSKKGKK 340

Transcription initiation factor IIF, alpha subunit (TFIIF-alpha) or RNA polymerase II-associating protein 74 (RAP74) is the large subunit of transcription factor IIF (TFIIF), which is essential for accurate initiation and stimulates elongation by RNA polymerase II. Length = 528

>gnl|CDD|215214 PLN02381, PLN02381, valyl-tRNA synthetase

 Score = 48.0 bits (114), Expect = 3e-05
 Identities = 28/76 (36%), Positives = 42/76 (55%), Gaps = 10/76 (13%)

Query: 958  EEEEEEKKKEEKKKEEEEKK----KKEGKTKKEEKKKEE------EEEKKKKKKEEEKEE 1007
            EE E +KKKEEK KE+E KK    +KE K K + ++  +      + EKK +K++ E E 
Sbjct: 16   EELERKKKKEEKAKEKELKKLKAAQKEAKAKLQAQQASDGTNVPKKSEKKSRKRDVEDEN 75

Query: 1008 EEKKEEEEKEEEEKKR 1023
             E   + +    +KKR
Sbjct: 76   PEDFIDPDTPFGQKKR 91

Length = 1066

>gnl|CDD|227594 COG5269, ZUO1, Ribosome-associated chaperone zuotin [Translation, ribosomal structure and biogenesis / Posttranslational modification, protein turnover, chaperones]

 Score = 47.3 bits (112), Expect = 3e-05
 Identities = 25/110 (22%), Positives = 54/110 (49%)

Query: 914  RSRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRSGKEEEEEEKKKEEKKKEE 973
            R R+R    + R +R + + +   R +R  +  ++R  R +S KE+E+E KK  + ++E 
Sbjct: 193  RDRKRYSEAKNREKRAKLKNQDNARLKRLVQIAKKRDPRIKSFKEQEKEMKKIRKWEREA 252

Query: 974  EEKKKKEGKTKKEEKKKEEEEEKKKKKKEEEKEEEEKKEEEEKEEEEKKR 1023
              + K     K + + K + E + +        +++ KE  +K  + +K+
Sbjct: 253  GARLKALAALKGKAEAKNKAEIEAEALASATAVKKKAKEVMKKALKMEKK 302

Length = 379

>gnl|CDD|220271 pfam09507, CDC27, DNA polymerase subunit Cdc27

 Score = 47.1 bits (112), Expect = 3e-05
 Identities = 27/77 (35%), Positives = 40/77 (51%), Gaps = 3/77 (3%)

Query: 954  RSGKEEEEEEKKK---EEKKKEEEEKKKKEGKTKKEEKKKEEEEEKKKKKKEEEKEEEEK 1010
            RS  EEE EEK+K   +  KK  E++ + E      E   EEEE ++ +     K+EEEK
Sbjct: 280  RSDSEEETEEKEKEKRKRLKKMMEDEDEDEEMEIVPESPVEEEESEEPEPPPLPKKEEEK 339

Query: 1011 KEEEEKEEEEKKRRRIR 1027
            +E     +  ++R R R
Sbjct: 340  EEVTVSPDGGRRRGRRR 356

This protein forms the C subunit of DNA polymerase delta. It carries the essential residues for binding to the Pol1 subunit of polymerase alpha, from residues 293-332, which are characterized by the motif D--G--VT, referred to as the DPIM motif. The first 160 residues of the protein form the minimal domain for binding to the B subunit, Cdc1, of polymerase delta, the final 10 C-terminal residues, 362-372, being the DNA sliding clamp, PCNA, binding motif. Length = 427

>gnl|CDD|219939 pfam08619, Nha1_C, Alkali metal cation/H+ antiporter Nha1 C terminus

 Score = 47.1 bits (112), Expect = 3e-05
 Identities = 26/115 (22%), Positives = 45/115 (39%)

Query: 891  KKKEGGGGRRRRRRKKRRRSRRRRSRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRR 950
              +  GG  RR R+KK+     RR+   RRRRR+RR+  +          +     +RR 
Sbjct: 47   PARPAGGMLRRVRKKKKGSRAGRRASSLRRRRRQRRKEPQAGTGALGPISQSAISPQRRS 106

Query: 951  RRRRSGKEEEEEEKKKEEKKKEEEEKKKKEGKTKKEEKKKEEEEEKKKKKKEEEK 1005
                +  E +       +  ++ E    +      E     EE  +  K +E+E+
Sbjct: 107  STGENSAESDNTSYGLSKLAEDSENIDVRPVYESDERSGISEEGSRPSKLREQEQ 161

The C terminus of the plasma membrane Nha1 antiporter plays an important role in the immediate cell response to hypo-osmotic shock which prevents an execessive loss of ions and water. This domain is found with pfam00999. Length = 430

>gnl|CDD|225288 COG2433, COG2433, Uncharacterized conserved protein [Function unknown]

 Score = 47.4 bits (113), Expect = 3e-05
 Identities = 21/109 (19%), Positives = 55/109 (50%)

Query: 921  RRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRSGKEEEEEEKKKEEKKKEEEEKKKKE 980
             + +   R R +       RR      +R ++     E  EEE  + +++ EE +++ ++
Sbjct: 395  SKVKEEERPREKEGTEEEERREITVYEKRIKKLEETVERLEEENSELKRELEELKREIEK 454

Query: 981  GKTKKEEKKKEEEEEKKKKKKEEEKEEEEKKEEEEKEEEEKKRRRIRRK 1029
             +++ E  ++E  ++ +K ++   ++   ++ E+E EE++K+   + RK
Sbjct: 455  LESELERFRREVRDKVRKDREIRARDRRIERLEKELEEKKKRVEELERK 503

Length = 652

>gnl|CDD|234017 TIGR02794, tolA_full, TolA protein

 Score = 46.8 bits (111), Expect = 4e-05
 Identities = 36/181 (19%), Positives = 73/181 (40%), Gaps = 18/181 (9%)

Query: 846  KKEEEKKKKKEEEEEGGEKE--EEEGGGGGGRRRRRRRRSGKEEEEKKKKEGGGGRRRRR 903
            KKE+E++KK E++ E  EK+   E+       R++   +    E+  K+ E      +  
Sbjct: 64   KKEQERQKKLEQQAEEAEKQRAAEQ------ARQKELEQRAAAEKAAKQAE------QAA 111

Query: 904  RKKRRRSRRRRSRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRSGKEEEEEE 963
            ++   + ++    + ++    + +      ++ +   +++     + +     K++  E 
Sbjct: 112  KQAEEKQKQAEEAKAKQAAEAKAKAEAEAEKKAKEEAKKQAEEEAKAKAAAEAKKKAAEA 171

Query: 964  KKKEE----KKKEEEEKKKKEGKTKKEEKKKEEEEEKKKKKKEEEKEEEEKKEEEEKEEE 1019
            KKK E     K E + K K E    K E  K +   +   K E E       E E K +E
Sbjct: 172  KKKAEAEAKAKAEAKAKAKAEEAKAKAEAAKAKAAAEAAAKAEAEAAAAAAAEAERKADE 231

Query: 1020 E 1020
             
Sbjct: 232  A 232

TolA couples the inner membrane complex of itself with TolQ and TolR to the outer membrane complex of TolB and OprL (also called Pal). Most of the length of the protein consists of low-complexity sequence that may differ in both length and composition from one species to another, complicating efforts to discriminate TolA (the most divergent gene in the tol-pal system) from paralogs such as TonB. Selection of members of the seed alignment and criteria for setting scoring cutoffs are based largely conserved operon struction. //The Tol-Pal complex is required for maintaining outer membrane integrity. Also involved in transport (uptake) of colicins and filamentous DNA, and implicated in pathogenesis. Transport is energized by the proton motive force. TolA is an inner membrane protein that interacts with periplasmic TolB and with outer membrane porins ompC, phoE and lamB [Transport and binding proteins, Other, Cellular processes, Pathogenesis]. Length = 346

>gnl|CDD|225606 COG3064, TolA, Membrane protein involved in colicin uptake [Cell envelope biogenesis, outer membrane]

 Score = 46.9 bits (111), Expect = 4e-05
 Identities = 18/99 (18%), Positives = 57/99 (57%), Gaps = 2/99 (2%)

Query: 933  RRRRRRRRRRRRRRRRRRRRRRSGKEEEEEEKKKEEKKKEEEEKKKKEGKTKK--EEKKK 990
            R + ++   ++  ++R+++  +  +E + ++  ++E+ K+ E+++ K  + +K  EE +K
Sbjct: 66   RIQSQQSSAKKGEQQRKKKEEQVAEELKPKQAAEQERLKQLEKERLKAQEQQKQAEEAEK 125

Query: 991  EEEEEKKKKKKEEEKEEEEKKEEEEKEEEEKKRRRIRRK 1029
            + + E+K+++++  K   E+K++ E  + +      + K
Sbjct: 126  QAQLEQKQQEEQARKAAAEQKKKAEAAKAKAAAEAAKLK 164

Length = 387

>gnl|CDD|218684 pfam05672, MAP7, MAP7 (E-MAP-115) family

 Score = 45.1 bits (106), Expect = 4e-05
 Identities = 34/127 (26%), Positives = 72/127 (56%), Gaps = 3/127 (2%)

Query: 907  RRRSRRRRSRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRSGKEEEEEEKKK 966
               + R  + +RR+ R +R +  + RR +  + R  R   +RR    R  +EEE   +++
Sbjct: 21   AEEATRLLAEKRRQAREQREQEEQERREQEEQDRLEREELKRRAAEERLRREEEARRQEE 80

Query: 967  EEKKKEEEEKKKKEGKTKKEEKKKEEEEEKKKKKKEEEKEEEEKKEEEEKEE---EEKKR 1023
            E  +++EE+ K+K  + +K+E++++E  +K+K++ E    EE ++   E+E+   + ++ 
Sbjct: 81   ERAREKEEKAKRKAEEEEKQEQEEQERIQKQKEEAEARAREEAERMRLEREKHFQQIEQE 140

Query: 1024 RRIRRKR 1030
            R  R+KR
Sbjct: 141  RLERKKR 147

The organisation of microtubules varies with the cell type and is presumably controlled by tissue-specific microtubule-associated proteins (MAPs). The 115-kDa epithelial MAP (E-MAP-115/MAP7) has been identified as a microtubule-stabilising protein predominantly expressed in cell lines of epithelial origin. The binding of this microtubule associated protein is nucleotide independent. Length = 171

>gnl|CDD|223496 COG0419, SbcC, ATPase involved in DNA repair [DNA replication, recombination, and repair]

 Score = 47.4 bits (113), Expect = 4e-05
 Identities = 39/226 (17%), Positives = 81/226 (35%), Gaps = 17/226 (7%)

Query: 814  RNRRGRRRRRRKKKEEKKKWKRRGGGRRRRRGKKEEEKKKKKEEEEEGGEKEEEEGGGGG 873
                 R ++  +  +E K+             ++ EE +K+ EE E   E+ EEE     
Sbjct: 378  EKALERLKQLEEAIQELKEELAELSAALEEIQEELEELEKELEELERELEELEEE----- 432

Query: 874  GRRRRRRRRSGKEEEEKKKKEGGGGR-------RRRRRKKRRRSRRRRSRRRRRRRRRRR 926
              ++   + +  E +E    E  G         +    +  +                  
Sbjct: 433  -IKKLEEQINQLESKELMIAELAGAGEKCPVCGQELPEEHEKELLELYELELEELEEELS 491

Query: 927  RRRRRRRRRRRRRRRRRRRRRRRRRRRRSGKEEEEEEKKKEEK----KKEEEEKKKKEGK 982
            R +     R       +  R          + EE  +++ EEK    +   EE ++ + K
Sbjct: 492  REKEEAELREEIEELEKELRELEEELIELLELEEALKEELEEKLEKLENLLEELEELKEK 551

Query: 983  TKKEEKKKEEEEEKKKKKKEEEKEEEEKKEEEEKEEEEKKRRRIRR 1028
             + ++ K+E  + + + ++ +E  EE +     KEE E+ R R++ 
Sbjct: 552  LQLQQLKEELRQLEDRLQELKELLEELRLLRTRKEELEELRERLKE 597

Length = 908

>gnl|CDD|237035 PRK12280, rplW, 50S ribosomal protein L23; Reviewed

 Score = 44.8 bits (106), Expect = 4e-05
 Identities = 21/65 (32%), Positives = 39/65 (60%)

Query: 958  EEEEEEKKKEEKKKEEEEKKKKEGKTKKEEKKKEEEEEKKKKKKEEEKEEEEKKEEEEKE 1017
             EE E+++KE  K+ EE++  K  K KKE+K+K+  E+  KKK  +  +   KK  ++  
Sbjct: 92   PEESEKEQKEVSKETEEKEAIKAKKEKKEKKEKKVAEKLAKKKSTKTTKNTTKKATKKTT 151

Query: 1018 EEEKK 1022
             ++++
Sbjct: 152  TKKEE 156

Length = 158

>gnl|CDD|215774 pfam00183, HSP90, Hsp90 protein

 Score = 47.1 bits (112), Expect = 4e-05
 Identities = 26/52 (50%), Positives = 36/52 (69%), Gaps = 2/52 (3%)

Query: 958  EEEEEEKKKEEKKKEEEEKKKKEGKTKKEEKKKEEEEEKKKKKKEEEKEEEE 1009
            +EEEEE+K+E  KKEEEEK   + +   EE++KEE+++K KK KE   E E 
Sbjct: 37   DEEEEEEKEE--KKEEEEKTTDKEEEVDEEEEKEEKKKKTKKVKETTTEWEL 86

Length = 529

>gnl|CDD|227278 COG4942, COG4942, Membrane-bound metallopeptidase [Cell division and chromosome partitioning]

 Score = 47.0 bits (112), Expect = 4e-05
 Identities = 16/112 (14%), Positives = 36/112 (32%)

Query: 917  RRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRSGKEEEEEEKKKEEKKKEEEEK 976
            R      +         +R ++ +  +    R++   +   E   ++KK EE +  E   
Sbjct: 177  RAEIAAEQAELTTLLSEQRAQQAKLAQLLEERKKTLAQLNSELSADQKKLEELRANESRL 236

Query: 977  KKKEGKTKKEEKKKEEEEEKKKKKKEEEKEEEEKKEEEEKEEEEKKRRRIRR 1028
            K +    +    K  E     +      +  E K+  E  +    ++  I  
Sbjct: 237  KNEIASAEAAAAKAREAAAAAEAAAARARAAEAKRTGETYKPTAPEKMLISS 288

Length = 420

>gnl|CDD|216147 pfam00844, Gemini_coat, Geminivirus coat protein/nuclear export factor BR1 family

 Score = 45.8 bits (109), Expect = 4e-05
 Identities = 17/44 (38%), Positives = 21/44 (47%)

Query: 900 RRRRRKKRRRSRRRRSRRRRRRRRRRRRRRRRRRRRRRRRRRRR 943
           RRR     RRSR R   RR   ++R   +R  RR+ R  R  R 
Sbjct: 1   RRRLNFDSRRSRARAPTRRSTNKKRGWSKRPMRRKGRSYRMYRS 44

It has been shown that the 104 N-terminal amino acids of the maize streak virus coat protein bind DNA non- specifically. This family also includes various geminivirus movement proteins that are nuclear export factors or shuttles. One member BR1 facilitates the export of both ds and ss DNA form the nucleus. Length = 244

>gnl|CDD|215824 pfam00260, Protamine_P1, Protamine P1

 Score = 41.4 bits (97), Expect = 5e-05
 Identities = 26/37 (70%), Positives = 26/37 (70%)

Query: 920 RRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRSG 956
           R R  R R R R RRRRRRR RRRRRR  RRRRRR G
Sbjct: 2   RYRCCRSRSRSRCRRRRRRRCRRRRRRCCRRRRRRVG 38

Length = 51

>gnl|CDD|222636 pfam14265, DUF4355, Domain of unknown function (DUF4355)

 Score = 43.4 bits (103), Expect = 5e-05
 Identities = 18/68 (26%), Positives = 37/68 (54%)

Query: 963  EKKKEEKKKEEEEKKKKEGKTKKEEKKKEEEEEKKKKKKEEEKEEEEKKEEEEKEEEEKK 1022
            E ++E+   ++E  K    +  K EKK+EE++ + +K  +   EE+ + E E+ E+E ++
Sbjct: 1    EPEEEKTFTDKEVDKAIAKEKAKWEKKQEEKKSEAEKLAKMSAEEKAEYELEKLEKELEE 60

Query: 1023 RRRIRRKR 1030
                  +R
Sbjct: 61   LEAELARR 68

This family of proteins is found in bacteria and viruses. Proteins in this family are typically between 180 and 214 amino acids in length. Length = 125

>gnl|CDD|237629 PRK14160, PRK14160, heat shock protein GrpE; Provisional

 Score = 45.5 bits (108), Expect = 5e-05
 Identities = 19/64 (29%), Positives = 38/64 (59%)

Query: 958  EEEEEEKKKEEKKKEEEEKKKKEGKTKKEEKKKEEEEEKKKKKKEEEKEEEEKKEEEEKE 1017
            E+E ++ K E  +++  ++ + + + K +E+  E EE +K++  E+ +E  E K EE K+
Sbjct: 2    EKECKDAKHENMEEDCCKENENKEEDKGKEEDLEFEEIEKEEIIEDSEESNEVKIEELKD 61

Query: 1018 EEEK 1021
            E  K
Sbjct: 62   ENNK 65

Length = 211

>gnl|CDD|188306 TIGR03319, RNase_Y, ribonuclease Y

 Score = 46.8 bits (112), Expect = 5e-05
 Identities = 44/168 (26%), Positives = 75/168 (44%), Gaps = 16/168 (9%)

Query: 875  RRRRRRRRSGKEEEEKKKKEGGGGRRRRRRKKRRRSRRRRSRRRRRRRRRRRRRRRRRRR 934
            +R   ++    EE  K+  E         +K+     +    + R    R  + RR   +
Sbjct: 20   KRIAEKKLGSAEELAKRIIEEAKKEAETLKKEALLEAKEEVHKLRAELERELKERRNELQ 79

Query: 935  RRRRRRRRRRRRRRRRRRRRSGKEEEEEEKKKE--EKKKEEEEKKKKEGKTKKEEKKKEE 992
            R  RR  +R     R+      KEE  E+K+KE   K+K  +EK+++  +   E++++ E
Sbjct: 80   RLERRLLQREETLDRKMESLDKKEENLEKKEKELSNKEKNLDEKEEELEELIAEQREELE 139

Query: 993  E------EEKKK---KKKEEEKEEE-----EKKEEEEKEEEEKKRRRI 1026
                   EE K+   ++ EEE   E     ++ EEE KEE +KK + I
Sbjct: 140  RISGLTQEEAKEILLEEVEEEARHEAAKLIKEIEEEAKEEADKKAKEI 187

Members of this family are RNase Y, an endoribonuclease. The member from Bacillus subtilis, YmdA, has been shown to be involved in turnover of yitJ riboswitch [Transcription, Degradation of RNA]. Length = 514

>gnl|CDD|237744 PRK14521, rpsP, 30S ribosomal protein S16; Provisional

 Score = 44.8 bits (106), Expect = 5e-05
 Identities = 24/67 (35%), Positives = 30/67 (44%), Gaps = 4/67 (5%)

Query: 959  EEEEEKK----KEEKKKEEEEKKKKEGKTKKEEKKKEEEEEKKKKKKEEEKEEEEKKEEE 1014
            E + E K    KEEK+ +   KK K  K KK  KK   E EKK  +   E   E+K  E 
Sbjct: 96   EAQAEAKFEAWKEEKEGKVNAKKDKLSKAKKAAKKAALEAEKKVNEARAEAVAEKKAAEA 155

Query: 1015 EKEEEEK 1021
                 E+
Sbjct: 156  AAVAAEE 162

Length = 186

>gnl|CDD|147747 pfam05762, VWA_CoxE, VWA domain containing CoxE-like protein

 Score = 45.4 bits (108), Expect = 5e-05
 Identities = 22/58 (37%), Positives = 24/58 (41%), Gaps = 3/58 (5%)

Query: 900 RRRRRKKRRRSRRRRSRRRRRRRRRR---RRRRRRRRRRRRRRRRRRRRRRRRRRRRR 954
            R          RRR RR+RRRR  R   RR  R   R      R  RR  R R+ RR
Sbjct: 2   ARALAALLLGLARRRRRRKRRRRGGRIDLRRTLRANLRHGGEPVRLVRREPRLRKPRR 59

This family is annotated by SMART as containing a VWA (von Willebrand factor type A) domain. The exact function of this family is unknown. It is found as part of a CO oxidising (Cox) system operon is several bacteria. Length = 223

>gnl|CDD|237177 PRK12704, PRK12704, phosphodiesterase; Provisional

 Score = 46.7 bits (112), Expect = 5e-05
 Identities = 41/126 (32%), Positives = 65/126 (51%), Gaps = 17/126 (13%)

Query: 918  RRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRSGKEEEEEEKKKE--EKKKEEEE 975
            + R    +  R RR   ++  +R  ++     R+     K EEE EKK++  E+K++E E
Sbjct: 68   KLRNEFEKELRERRNELQKLEKRLLQKEENLDRKLELLEKREEELEKKEKELEQKQQELE 127

Query: 976  KKKKEGKTKKEEKKKEEE-------EEKKK---KKKEEEKEEE-----EKKEEEEKEEEE 1020
            KK++E +   EE+ +E E       EE K+   +K EEE   E     ++ EEE KEE +
Sbjct: 128  KKEEELEELIEEQLQELERISGLTAEEAKEILLEKVEEEARHEAAVLIKEIEEEAKEEAD 187

Query: 1021 KKRRRI 1026
            KK + I
Sbjct: 188  KKAKEI 193

Length = 520

>gnl|CDD|217756 pfam03839, Sec62, Translocation protein Sec62

 Score = 45.2 bits (107), Expect = 5e-05
 Identities = 17/62 (27%), Positives = 32/62 (51%), Gaps = 1/62 (1%)

Query: 961  EEEKKKEEKKKEEEEKKKKEGKTKKEEKKKEEEEEKKKKKKEEEKEEEEKKEEEEKEEEE 1020
            E EK K  K K   E   K   ++ +  +K +   K +  +  +K   ++K+EE+K+ ++
Sbjct: 17   ESEKYKANKDKGNPEIYNKI-NSQDKAIEKFKLLIKAQMAERVKKLHSQEKKEEKKKPKK 75

Query: 1021 KK 1022
            KK
Sbjct: 76   KK 77

Length = 217

>gnl|CDD|217829 pfam03985, Paf1, Paf1

 Score = 46.7 bits (111), Expect = 5e-05
 Identities = 27/116 (23%), Positives = 51/116 (43%), Gaps = 7/116 (6%)

Query: 912  RRRSRRRRRRRRRRRRRRRRRRRRRRRRRRRR-------RRRRRRRRRRRSGKEEEEEEK 964
            R R   RRRR     R   R     +   + R       + R +RR R      EE +E 
Sbjct: 314  RSRVELRRRRVNDVIRPLVREHNNDQLNVKLRNPSTKESKMRDKRRARLDPIDFEEVDED 373

Query: 965  KKEEKKKEEEEKKKKEGKTKKEEKKKEEEEEKKKKKKEEEKEEEEKKEEEEKEEEE 1020
            + EE+++  +E +++EG+  +EE  +  E+   +   +   + E K ++E   + +
Sbjct: 374  EDEEEEQRSDEHEEEEGEDSEEEGSQSREDGSSESSSDVGSDSESKADKESASDSD 429

Members of this family are components of the RNA polymerase II associated Paf1 complex. The Paf1 complex functions during the elongation phase of transcription in conjunction with Spt4-Spt5 and Spt16-Pob3i. Length = 431

>gnl|CDD|218684 pfam05672, MAP7, MAP7 (E-MAP-115) family

 Score = 44.3 bits (104), Expect = 6e-05
 Identities = 37/141 (26%), Positives = 76/141 (53%), Gaps = 2/141 (1%)

Query: 877  RRRRRRSGKEEEEKKKKEGGGGRRRRRRKKRRRSRRRRSRRRRRRRRRRRRRRRRRRRRR 936
            +RR+ R  +E+EE++++E     R  R + +RR+   R RR    RR+   R R +  + 
Sbjct: 31   KRRQAREQREQEEQERREQEEQDRLEREELKRRAAEERLRREEEARRQEEERAREKEEKA 90

Query: 937  RRRRRRRRRRRRRRRRRRSGKEEEEEEKKKE--EKKKEEEEKKKKEGKTKKEEKKKEEEE 994
            +R+     ++ +  + R   ++EE E + +E  E+ + E EK  ++ + ++ E+KK  EE
Sbjct: 91   KRKAEEEEKQEQEEQERIQKQKEEAEARAREEAERMRLEREKHFQQIEQERLERKKRLEE 150

Query: 995  EKKKKKKEEEKEEEEKKEEEE 1015
              K+ +K E   + +K++ + 
Sbjct: 151  IMKRTRKSEVSPQVKKEDPKV 171

The organisation of microtubules varies with the cell type and is presumably controlled by tissue-specific microtubule-associated proteins (MAPs). The 115-kDa epithelial MAP (E-MAP-115/MAP7) has been identified as a microtubule-stabilising protein predominantly expressed in cell lines of epithelial origin. The binding of this microtubule associated protein is nucleotide independent. Length = 171

>gnl|CDD|219746 pfam08208, RNA_polI_A34, DNA-directed RNA polymerase I subunit RPA34

 Score = 44.7 bits (106), Expect = 6e-05
 Identities = 24/61 (39%), Positives = 43/61 (70%), Gaps = 3/61 (4%)

Query: 951  RRRRSGKEEEEEEKKKEEKKKEEEEKKKKEGKTKKEEKKKEEEEEKKKKKKEEEKEEEEK 1010
             +  + K E+E E ++EEKK   E+KKKKE K +K+EKK ++E+  + K  +++K++++K
Sbjct: 136  EKETTAKVEKEAEVEEEEKK---EKKKKKEVKKEKKEKKDKKEKMVEPKGSKKKKKKKKK 192

Query: 1011 K 1011
            K
Sbjct: 193  K 193

5. This is a family of proteins conserved from yeasts to human. Subunit A34.5 of RNA polymerase I is a non-essential subunit which is thought to help Pol I overcome topological constraints imposed on ribosomal DNA during the process of transcription. Length = 193

>gnl|CDD|233757 TIGR02168, SMC_prok_B, chromosome segregation protein SMC, common bacterial type

 Score = 47.0 bits (112), Expect = 6e-05
 Identities = 36/210 (17%), Positives = 81/210 (38%), Gaps = 16/210 (7%)

Query: 808  TQIRLSRNRRGRRRRRRKKKEEKKKWKRRGGGRRRRRGKKEEEKKKKKEEEEEGGEKEEE 867
                +SR  + ++  R +    +++ +           K +E  ++  E EE+  E +EE
Sbjct: 293  LANEISRLEQQKQILRERLANLERQLEELEAQLEELESKLDELAEELAELEEKLEELKEE 352

Query: 868  EGGGGGGRRRRRRRRSGKEEEEKKKKEGGGGRRRRRRKKRRRSRRRRSRRRRRRRRRRRR 927
                              E E ++ +        R  +   +    RS  +  +   +  
Sbjct: 353  --------------LESLEAELEELEAELEELESRLEELEEQLETLRS--KVAQLELQIA 396

Query: 928  RRRRRRRRRRRRRRRRRRRRRRRRRRRSGKEEEEEEKKKEEKKKEEEEKKKKEGKTKKEE 987
                   R   R  R   RR R ++      ++ EE + +E + E EE +++  + ++E 
Sbjct: 397  SLNNEIERLEARLERLEDRRERLQQEIEELLKKLEEAELKELQAELEELEEELEELQEEL 456

Query: 988  KKKEEEEEKKKKKKEEEKEEEEKKEEEEKE 1017
            ++ EE  E+ +++ EE ++  +  E E  +
Sbjct: 457  ERLEEALEELREELEEAEQALDAAERELAQ 486

SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]. Length = 1179

>gnl|CDD|114011 pfam05262, Borrelia_P83, Borrelia P83/100 protein

 Score = 46.5 bits (110), Expect = 6e-05
 Identities = 29/132 (21%), Positives = 66/132 (50%), Gaps = 5/132 (3%)

Query: 891  KKKEGGGGRRRRRRKKRRRSRRRRSRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRR 950
            K++E     +R ++ K    +++    + +++    +    ++R   R++++  +   + 
Sbjct: 204  KERESQEDAKRAQQLKEELDKKQIDADKAQQKADFAQDNADKQRDEVRQKQQEAKNLPKP 263

Query: 951  RRRRSGKEEEE--EEKKKEEKKKEEEEKKKKEGKTKKEEKKKEEEEEKKKKKKEEEKEEE 1008
                S KE+++  E +K+E +K + E KK  E   K ++ K     + K++ K  EKE E
Sbjct: 264  ADTSSPKEDKQVAENQKREIEKAQIEIKKNDEEALKAKDHKA---FDLKQESKASEKEAE 320

Query: 1009 EKKEEEEKEEEE 1020
            +K+ E +K+ E 
Sbjct: 321  DKELEAQKKREP 332

This family consists of several Borrelia P83/P100 antigen proteins. Length = 489

>gnl|CDD|237035 PRK12280, rplW, 50S ribosomal protein L23; Reviewed

 Score = 44.0 bits (104), Expect = 6e-05
 Identities = 21/59 (35%), Positives = 35/59 (59%)

Query: 957  KEEEEEEKKKEEKKKEEEEKKKKEGKTKKEEKKKEEEEEKKKKKKEEEKEEEEKKEEEE 1015
            KE  +E ++KE  K ++E+K+KKE K  ++  KK+  +  K   K+  K+   KKEE +
Sbjct: 100  KEVSKETEEKEAIKAKKEKKEKKEKKVAEKLAKKKSTKTTKNTTKKATKKTTTKKEEGK 158

Length = 158

>gnl|CDD|221641 pfam12569, NARP1, NMDA receptor-regulated protein 1

 Score = 46.5 bits (111), Expect = 6e-05
 Identities = 20/61 (32%), Positives = 30/61 (49%), Gaps = 4/61 (6%)

Query: 955  SGKEEEEEEKKKEEKKKEEEEKKKKEGKTKKEEKKKEEEEEKKKKKKEEEKEEEEKKEEE 1014
            +G     E KK  +K+++ E+K +KE   K   KKK E   KK K      + E KK + 
Sbjct: 403  NGNLSPAERKKLRKKQRKAEKKAEKEEAEKAAAKKKAEAAAKKAKG----PDGETKKVDP 458

Query: 1015 E 1015
            +
Sbjct: 459  D 459

This domain family is found in eukaryotes, and is approximately 40 amino acids in length. The family is found in association with pfam07719, pfam00515. There is a single completely conserved residue L that may be functionally important. NARP1 is the mammalian homologue of a yeast N-terminal acetyltransferase that regulates entry into the G(0) phase of the cell cycle. Length = 516

>gnl|CDD|237177 PRK12704, PRK12704, phosphodiesterase; Provisional

 Score = 46.7 bits (112), Expect = 6e-05
 Identities = 21/85 (24%), Positives = 45/85 (52%)

Query: 946  RRRRRRRRRSGKEEEEEEKKKEEKKKEEEEKKKKEGKTKKEEKKKEEEEEKKKKKKEEEK 1005
            R++    +    EEE +   +E KK+ E  KK+   + K+E  K   E EK+ +++  E 
Sbjct: 25   RKKIAEAKIKEAEEEAKRILEEAKKEAEAIKKEALLEAKEEIHKLRNEFEKELRERRNEL 84

Query: 1006 EEEEKKEEEEKEEEEKKRRRIRRKR 1030
            ++ EK+  +++E  ++K   + ++ 
Sbjct: 85   QKLEKRLLQKEENLDRKLELLEKRE 109

Length = 520

>gnl|CDD|221275 pfam11861, DUF3381, Domain of unknown function (DUF3381)

 Score = 43.8 bits (104), Expect = 6e-05
 Identities = 16/67 (23%), Positives = 40/67 (59%)

Query: 964  KKKEEKKKEEEEKKKKEGKTKKEEKKKEEEEEKKKKKKEEEKEEEEKKEEEEKEEEEKKR 1023
            +KK  K    ++K+K+E + ++ E ++ +EEE+  +  E+E  + ++++  E E ++K+ 
Sbjct: 87   RKKVRKLLGLDKKEKEEEEEEEVEVEELDEEEQIDELLEKELAKLKREKRRENERKQKEI 146

Query: 1024 RRIRRKR 1030
             + + K 
Sbjct: 147  LKEQMKM 153

This domain is functionally uncharacterized. This domain is found in eukaryotes. This presumed domain is typically between 156 to 174 amino acids in length. This domain is found associated with pfam07780, pfam01728. Length = 154

>gnl|CDD|215824 pfam00260, Protamine_P1, Protamine P1

 Score = 41.0 bits (96), Expect = 7e-05
 Identities = 25/38 (65%), Positives = 25/38 (65%)

Query: 919 RRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRSG 956
           R R  R R R R RRRRRRR RRRRRR  RRRRRR   
Sbjct: 2   RYRCCRSRSRSRCRRRRRRRCRRRRRRCCRRRRRRVGC 39

Length = 51

>gnl|CDD|146958 pfam04569, DUF591, Protein of unknown function

 Score = 42.0 bits (99), Expect = 7e-05
 Identities = 18/72 (25%), Positives = 21/72 (29%), Gaps = 6/72 (8%)

Query: 897 GGRRRRRRKKRRRSRRRRSRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRR------R 950
            GRR       R  RR  +     R           R RR R      R RRR       
Sbjct: 1   AGRREEDEAVGRNGRRTAAASGGARHGDTGEGEHTGRLRRTRGDEPTARIRRRELDGGGL 60

Query: 951 RRRRSGKEEEEE 962
           RRR+    +   
Sbjct: 61  RRRQPAARKGGN 72

This family represents a conserved region in a number of uncharacterized plant proteins. Length = 89

>gnl|CDD|235250 PRK04195, PRK04195, replication factor C large subunit; Provisional

 Score = 46.1 bits (110), Expect = 8e-05
 Identities = 18/63 (28%), Positives = 45/63 (71%)

Query: 943  RRRRRRRRRRRRSGKEEEEEEKKKEEKKKEEEEKKKKEGKTKKEEKKKEEEEEKKKKKKE 1002
               +  ++R     +++++    K+++++EEEEK+KKE + ++EE++ EEE+E++++KK+
Sbjct: 415  IVEKAEKKREEEKKEKKKKAFAGKKKEEEEEEEKEKKEEEKEEEEEEAEEEKEEEEEKKK 474

Query: 1003 EEK 1005
            ++ 
Sbjct: 475  KQA 477

Length = 482

>gnl|CDD|235401 PRK05306, infB, translation initiation factor IF-2; Validated

 Score = 46.4 bits (111), Expect = 8e-05
 Identities = 23/73 (31%), Positives = 31/73 (42%)

Query: 958  EEEEEEKKKEEKKKEEEEKKKKEGKTKKEEKKKEEEEEKKKKKKEEEKEEEEKKEEEEKE 1017
            +E   E K      EEEE +K+E K + EE+ K E EE    + EEE + E       +E
Sbjct: 25   KELGIEVKSHSSTVEEEEARKEEAKREAEEEAKAEAEEAAAAEAEEEAKAEAAAAAPAEE 84

Query: 1018 EEEKKRRRIRRKR 1030
              E         R
Sbjct: 85   AAEAAAAAEAAAR 97

Length = 746

>gnl|CDD|109943 pfam00906, Hepatitis_core, Hepatitis core antigen

 Score = 44.4 bits (105), Expect = 8e-05
 Identities = 16/34 (47%), Positives = 19/34 (55%)

Query: 925 RRRRRRRRRRRRRRRRRRRRRRRRRRRRRRSGKE 958
           RRR R  RRR    RRRR +  RRRR +  S + 
Sbjct: 149 RRRGRSPRRRTPSPRRRRSQSPRRRRSQSPSSQC 182

The core antigen of hepatitis viruses possesses a carboxyl terminus rich in arginine. On this basis it was predicted that the core antigen would bind DNA. There is some experimental evidence to support this. Length = 182

>gnl|CDD|223880 COG0810, TonB, Periplasmic protein TonB, links inner and outer membranes [Cell envelope biogenesis, outer membrane]

 Score = 45.2 bits (107), Expect = 8e-05
 Identities = 16/66 (24%), Positives = 32/66 (48%)

Query: 957  KEEEEEEKKKEEKKKEEEEKKKKEGKTKKEEKKKEEEEEKKKKKKEEEKEEEEKKEEEEK 1016
             + E E  +++ K   E E   +    K +EK K E++ KK K K + K + + K + + 
Sbjct: 56   PQPEPEPPEEQPKPPTEPETPPEPTPPKPKEKPKPEKKPKKPKPKPKPKPKPKPKVKPQP 115

Query: 1017 EEEEKK 1022
            + ++  
Sbjct: 116  KPKKPP 121

Length = 244

>gnl|CDD|223880 COG0810, TonB, Periplasmic protein TonB, links inner and outer membranes [Cell envelope biogenesis, outer membrane]

 Score = 45.2 bits (107), Expect = 8e-05
 Identities = 15/70 (21%), Positives = 32/70 (45%)

Query: 961  EEEKKKEEKKKEEEEKKKKEGKTKKEEKKKEEEEEKKKKKKEEEKEEEEKKEEEEKEEEE 1020
              E   EE + E E  +++     + E   E    K K+K + EK+ ++ K + + + + 
Sbjct: 48   VLEAPTEEPQPEPEPPEEQPKPPTEPETPPEPTPPKPKEKPKPEKKPKKPKPKPKPKPKP 107

Query: 1021 KKRRRIRRKR 1030
            K + + + K 
Sbjct: 108  KPKVKPQPKP 117

Length = 244

>gnl|CDD|223496 COG0419, SbcC, ATPase involved in DNA repair [DNA replication, recombination, and repair]

 Score = 46.3 bits (110), Expect = 9e-05
 Identities = 46/185 (24%), Positives = 71/185 (38%), Gaps = 4/185 (2%)

Query: 846  KKEEEKKKKKEEEEEGGEKEEEEGGGGGGRRRRRRRRSGKEEEEKKKKEGGGGRRRRRRK 905
            ++E ++ KK EE +E  E+EE E        R       KE  E+ K             
Sbjct: 209  EEELKELKKLEEIQEEQEEEELEQEIEALEERLAELEEEKERLEELKAR----LLEIESL 264

Query: 906  KRRRSRRRRSRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRSGKEEEEEEKK 965
            +    + R    R   R       +  R     R            R    + EE  EK 
Sbjct: 265  ELEALKIREEELRELERLLEELEEKIERLEELEREIEELEEELEGLRALLEELEELLEKL 324

Query: 966  KEEKKKEEEEKKKKEGKTKKEEKKKEEEEEKKKKKKEEEKEEEEKKEEEEKEEEEKKRRR 1025
            K  +++ E+ ++K E    + E+  EE+ E  K  +E  KE EE+ EE EKE E+   R 
Sbjct: 325  KSLEERLEKLEEKLEKLESELEELAEEKNELAKLLEERLKELEERLEELEKELEKALERL 384

Query: 1026 IRRKR 1030
             + + 
Sbjct: 385  KQLEE 389

Length = 908

>gnl|CDD|220271 pfam09507, CDC27, DNA polymerase subunit Cdc27

 Score = 46.0 bits (109), Expect = 9e-05
 Identities = 23/81 (28%), Positives = 48/81 (59%), Gaps = 7/81 (8%)

Query: 955  SGKEEEEEEKKKEEKKKEEEEKKKKEGKTKKEEKKKEEEEEKKKKKKEEEKEEEEKK--- 1011
            S  +++ +EKK++++  E   K++ E ++ K +   E+E  +     E+E E+E K    
Sbjct: 220  SFFKKKTKEKKEKKEASESTVKEESEEESGKRDVILEDESAEPTGLDEDEDEDEPKPSGE 279

Query: 1012 ----EEEEKEEEEKKRRRIRR 1028
                EEE +E+E++KR+R+++
Sbjct: 280  RSDSEEETEEKEKEKRKRLKK 300

This protein forms the C subunit of DNA polymerase delta. It carries the essential residues for binding to the Pol1 subunit of polymerase alpha, from residues 293-332, which are characterized by the motif D--G--VT, referred to as the DPIM motif. The first 160 residues of the protein form the minimal domain for binding to the B subunit, Cdc1, of polymerase delta, the final 10 C-terminal residues, 362-372, being the DNA sliding clamp, PCNA, binding motif. Length = 427

>gnl|CDD|233973 TIGR02680, TIGR02680, TIGR02680 family protein

 Score = 46.3 bits (110), Expect = 9e-05
 Identities = 27/165 (16%), Positives = 48/165 (29%), Gaps = 8/165 (4%)

Query: 811 RLSRNRRGRRRRRRKKKEEKKKWKRRGGGRRRRRGKKEEEKKKKKEEEEEGGEKEEEEGG 870
            L R R      +                 R    + EEE+++  EE     +  E E  
Sbjct: 334 ELERARADAEALQ-------AAAADARQAIREAESRLEEERRRLDEEAGRLDD-AERELR 385

Query: 871 GGGGRRRRRRRRSGKEEEEKKKKEGGGGRRRRRRKKRRRSRRRRSRRRRRRRRRRRRRRR 930
               +  R   R+G       + +     +  +      +RR+ + R   +R  +    R
Sbjct: 386 AAREQLARAAERAGLSPAHTAEPDAALAAQELQELGALDARRQDADRVIAQRSEQVALLR 445

Query: 931 RRRRRRRRRRRRRRRRRRRRRRRRSGKEEEEEEKKKEEKKKEEEE 975
           RR     R        R RR       E+     +  ++    E 
Sbjct: 446 RRDDVADRAEATHAAARARRDELDEEAEQAAARAELADEAVHREG 490

Members of this protein family belong to a conserved gene four-gene neighborhood found sporadically in a phylogenetically broad range of bacteria: Nocardia farcinica, Symbiobacterium thermophilum, and Streptomyces avermitilis (Actinobacteria), Geobacillus kaustophilus (Firmicutes), Azoarcus sp. EbN1 and Ralstonia solanacearum (Betaproteobacteria). Proteins in this family average over 1400 amino acids in length [Hypothetical proteins, Conserved]. Length = 1353

>gnl|CDD|173412 PTZ00121, PTZ00121, MAEBL; Provisional

 Score = 46.3 bits (109), Expect = 1e-04
 Identities = 55/252 (21%), Positives = 99/252 (39%), Gaps = 16/252 (6%)

Query: 794  KQLTKAPEGGKVCITQIRLSRNRRGRRRRRRKKKEEKKKWKRRGGGRRRRRGKKEEEKKK 853
            ++L KA E  K+   +         ++    KK EE +K       +     KK EE KK
Sbjct: 1650 EELKKAEEENKIKAAEEAKKAEEDKKKAEEAKKAEEDEKKAAEALKKEAEEAKKAEELKK 1709

Query: 854  KKEEEEEGGE--KEEEEGGGGGGRRRRRRRRSGKEEEEKKKKEGGGGRRRRRRKKRRRSR 911
            K+ EE++  E  K+ EE         ++     K++ E+ KK+    ++    KK    +
Sbjct: 1710 KEAEEKKKAEELKKAEEENKIKAEEAKKEAEEDKKKAEEAKKDEEEKKKIAHLKKEEEKK 1769

Query: 912  RRRSRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRSGKE---------EEEE 962
                R+ +             +RR    ++ +            GKE         E E+
Sbjct: 1770 AEEIRKEKEAVIEEELDEEDEKRRMEVDKKIKDIFDNFANIIEGGKEGNLVINDSKEMED 1829

Query: 963  EKKKE-----EKKKEEEEKKKKEGKTKKEEKKKEEEEEKKKKKKEEEKEEEEKKEEEEKE 1017
               KE       + EE +  +K    K  E  ++  +E    K+++ KE++E++ EE  E
Sbjct: 1830 SAIKEVADSKNMQLEEADAFEKHKFNKNNENGEDGNKEADFNKEKDLKEDDEEEIEEADE 1889

Query: 1018 EEEKKRRRIRRK 1029
             E+  +  I R+
Sbjct: 1890 IEKIDKDDIERE 1901

Length = 2084

>gnl|CDD|219953 pfam08648, DUF1777, Protein of unknown function (DUF1777)

 Score = 42.9 bits (101), Expect = 1e-04
 Identities = 23/96 (23%), Positives = 47/96 (48%), Gaps = 4/96 (4%)

Query: 927  RRRRRRRRRRRRRRRRRRRRRRRRRRRRSGKEEEEEEKKKEEKKKEEEEKKKKEGKTKKE 986
            R R R  RR RRR R R R RR RRR RS       E+ +  + +     + +  ++ + 
Sbjct: 3    RSRSRSPRRSRRRGRSRSRDRRERRRERS----RSRERDRRRRSRSRSPHRSRRSRSPRR 58

Query: 987  EKKKEEEEEKKKKKKEEEKEEEEKKEEEEKEEEEKK 1022
             + +     +++ +K E  ++  + ++ E+++  K+
Sbjct: 59   HRSRSRSPSRRRDRKRERDKDAREPKKRERQKLIKE 94

This is a family of eukaryotic proteins of unknown function. Some of the proteins in this family are putative nucleic acid binding proteins. Length = 158

>gnl|CDD|221821 pfam12871, PRP38_assoc, Pre-mRNA-splicing factor 38-associated hydrophilic C-term

 Score = 41.7 bits (98), Expect = 1e-04
 Identities = 26/78 (33%), Positives = 40/78 (51%)

Query: 892 KKEGGGGRRRRRRKKRRRSRRRRSRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRR 951
           +++          +     RR+  R   R RR  RRR RRR RRR+R R+RRRRRR R R
Sbjct: 7   EEDLDEEEESEEEEDDEEIRRKAERDVDRGRRSPRRRTRRRSRRRKRSRKRRRRRRDRDR 66

Query: 952 RRRSGKEEEEEEKKKEEK 969
            R   +++ + ++    +
Sbjct: 67  ARYRDRDDRDRDRYDRSR 84

This domain is a hydrophilic region found at the C-terminus of plant and metazoan pre-mRNA-splicing factor 38 proteins. The function is not known. Length = 97

>gnl|CDD|225606 COG3064, TolA, Membrane protein involved in colicin uptake [Cell envelope biogenesis, outer membrane]

 Score = 45.3 bits (107), Expect = 1e-04
 Identities = 19/113 (16%), Positives = 59/113 (52%)

Query: 916  RRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRSGKEEEEEEKKKEEKKKEEEE 975
            R + ++   ++  ++R+++  +     + ++   + R +  ++E  + ++++++ +E E+
Sbjct: 66   RIQSQQSSAKKGEQQRKKKEEQVAEELKPKQAAEQERLKQLEKERLKAQEQQKQAEEAEK 125

Query: 976  KKKKEGKTKKEEKKKEEEEEKKKKKKEEEKEEEEKKEEEEKEEEEKKRRRIRR 1028
            + + E K ++E+ +K   E+KKK +  + K   E  + +   E +KK     +
Sbjct: 126  QAQLEQKQQEEQARKAAAEQKKKAEAAKAKAAAEAAKLKAAAEAKKKAEEAAK 178

Length = 387

>gnl|CDD|217051 pfam02463, SMC_N, RecF/RecN/SMC N terminal domain

 Score = 45.7 bits (108), Expect = 1e-04
 Identities = 38/221 (17%), Positives = 87/221 (39%), Gaps = 17/221 (7%)

Query: 809  QIRLSRNRRGRRRRRRKKKEEKKKWKRRGGGRRRRRGKKEEEKKKKKEEEEEGGEKEEEE 868
               +      + +  + K++ KK                E  + K+K E EE      + 
Sbjct: 187  AELIIDLEELKLQELKLKEQAKK--------------ALEYYQLKEKLELEEENLLYLDY 232

Query: 869  GGGGGGRRRRRRRRSGKEEEEKKKKEGGGGRRRRRRKKRRRSRRRRSRRRRRRRRRRRRR 928
                     R         +E+++ E       +  +   +  +      + ++ +    
Sbjct: 233  ---LKLNEERIDLLQELLRDEQEEIESSKQELEKEEEILAQVLKENKEEEKEKKLQEEEL 289

Query: 929  RRRRRRRRRRRRRRRRRRRRRRRRRRSGKEEEEEEKKKEEKKKEEEEKKKKEGKTKKEEK 988
            +   +     +    +  RR+       KE E+E KK E++ K+E+E+ ++  K  KE +
Sbjct: 290  KLLAKEEEELKSELLKLERRKVDDEEKLKESEKELKKLEKELKKEKEEIEELEKELKELE 349

Query: 989  KKEEEEEKKKKKKEEEKEEEEKKEEEEKEEEEKKRRRIRRK 1029
             K E EE+++++ E+ +E+ E+ EEE   +++ +  R+   
Sbjct: 350  IKREAEEEEEEQLEKLQEKLEQLEEELLAKKKLESERLSSA 390

This domain is found at the N terminus of SMC proteins. The SMC (structural maintenance of chromosomes) superfamily proteins have ATP-binding domains at the N- and C-termini, and two extended coiled-coil domains separated by a hinge in the middle. The eukaryotic SMC proteins form two kind of heterodimers: the SMC1/SMC3 and the SMC2/SMC4 types. These heterodimers constitute an essential part of higher order complexes, which are involved in chromatin and DNA dynamics. This family also includes the RecF and RecN proteins that are involved in DNA metabolism and recombination. Length = 1162

>gnl|CDD|202096 pfam02029, Caldesmon, Caldesmon

 Score = 45.4 bits (107), Expect = 1e-04
 Identities = 47/226 (20%), Positives = 84/226 (37%), Gaps = 16/226 (7%)

Query: 814  RNRRGRRRRRRKKKEEKKKWKRRGGGRRRRRGKKEEEKKKKKEEEEEGGEKEEEEGGGGG 873
            R RR R  + R+K+EE    +         +    +E+ K   ++E    +         
Sbjct: 11   RRRREREEQLRQKQEEGSLGQVTTQVEVNSQNSVPDEESKTSTDDEAALLER-------L 63

Query: 874  GRRRRRRRRSGKEEEEKKKK------EGGGGRRRRRRKKRRRSRRRRSRRRRRRRRRRRR 927
             RR  RR     E  E++K+      +       RR ++   +         +   R  R
Sbjct: 64   ARREERRDERFSEALERQKEFKPTSTDQSLSEPSRRMQEDSGAENETVEEEEKEESREER 123

Query: 928  RRRRRRRRRRRRRRRRRRRRRRRRRRRSGKEEEEEEKKKEEKKKEEEEKKKKEGKTKKEE 987
                      +  ++   R     ++   + E EEE+K +    EE   +    K K  E
Sbjct: 124  EEVEETEGVTKSEQKNDWRDAEECQKEEKEPEPEEEEKPKRGSLEENNGEFMTHKLKHTE 183

Query: 988  K---KKEEEEEKKKKKKEEEKEEEEKKEEEEKEEEEKKRRRIRRKR 1030
                +   E  + +  KE EK +++++E   + EE KK+R  RRK 
Sbjct: 184  NTFSRGGAEGAQVEAGKEFEKLKQKQQEAALELEELKKKREERRKV 229

Length = 431

>gnl|CDD|235175 PRK03918, PRK03918, chromosome segregation protein; Provisional

 Score = 45.8 bits (109), Expect = 1e-04
 Identities = 25/105 (23%), Positives = 47/105 (44%)

Query: 924  RRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRSGKEEEEEEKKKEEKKKEEEEKKKKEGKT 983
            R            R    +  +  +     +   EE E+E +  E  K + E+K +E + 
Sbjct: 207  REINEISSELPELREELEKLEKEVKELEELKEEIEELEKELESLEGSKRKLEEKIRELEE 266

Query: 984  KKEEKKKEEEEEKKKKKKEEEKEEEEKKEEEEKEEEEKKRRRIRR 1028
            + EE KKE EE ++K K+ +E +E+ ++  +  E  E+    +R 
Sbjct: 267  RIEELKKEIEELEEKVKELKELKEKAEEYIKLSEFYEEYLDELRE 311

Length = 880

>gnl|CDD|235175 PRK03918, PRK03918, chromosome segregation protein; Provisional

 Score = 45.8 bits (109), Expect = 1e-04
 Identities = 51/224 (22%), Positives = 89/224 (39%), Gaps = 12/224 (5%)

Query: 817  RGRRRRRRKKKEEKKKWKRRGGGRRRRRGKKEEEKKKKKEEEEEGGEKEEEEGGGGGGRR 876
            R    R  + K+E ++ + +    +  + K EE  K  +  EE   E  E E        
Sbjct: 262  RELEERIEELKKEIEELEEKVKELKELKEKAEEYIKLSEFYEEYLDELREIEKRLSRLEE 321

Query: 877  RRRRRRSGKEEEEKKKKEGGGGRRRRRRKKRRRSRRRRSRRRRRRRRRRRRRRRRRRRRR 936
                     +E E+K++     +++ +  ++R              + ++    R ++R 
Sbjct: 322  EINGIEERIKELEEKEERLEELKKKLKELEKRLEELEERHELYEEAKAKKEELERLKKRL 381

Query: 937  RRRRRRRRRRRRRRRRRRSGKEEEEEEKKKEEKKKEEEEKKKKEGKTKKEEKKK------ 990
                  +  +      +   KEE EEE  K   +  E +K+ KE K   EE KK      
Sbjct: 382  TGLTPEKLEKELEELEKA--KEEIEEEISKITARIGELKKEIKELKKAIEELKKAKGKCP 439

Query: 991  ----EEEEEKKKKKKEEEKEEEEKKEEEEKEEEEKKRRRIRRKR 1030
                E  EE +K+  EE   E ++ E+E KE EEK+R+  +  R
Sbjct: 440  VCGRELTEEHRKELLEEYTAELKRIEKELKEIEEKERKLRKELR 483

Length = 880

>gnl|CDD|235175 PRK03918, PRK03918, chromosome segregation protein; Provisional

 Score = 45.8 bits (109), Expect = 1e-04
 Identities = 29/130 (22%), Positives = 58/130 (44%)

Query: 900  RRRRRKKRRRSRRRRSRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRSGKEE 959
             +  +++  R  +   R        + + +      R            R    +  KE 
Sbjct: 171  IKEIKRRIERLEKFIKRTENIEELIKEKEKELEEVLREINEISSELPELREELEKLEKEV 230

Query: 960  EEEEKKKEEKKKEEEEKKKKEGKTKKEEKKKEEEEEKKKKKKEEEKEEEEKKEEEEKEEE 1019
            +E E+ KEE ++ E+E +  EG  +K E+K  E EE+ ++ K+E +E EEK +E ++ +E
Sbjct: 231  KELEELKEEIEELEKELESLEGSKRKLEEKIRELEERIEELKKEIEELEEKVKELKELKE 290

Query: 1020 EKKRRRIRRK 1029
            + +      +
Sbjct: 291  KAEEYIKLSE 300

Length = 880

>gnl|CDD|235175 PRK03918, PRK03918, chromosome segregation protein; Provisional

 Score = 45.4 bits (108), Expect = 1e-04
 Identities = 53/282 (18%), Positives = 120/282 (42%), Gaps = 24/282 (8%)

Query: 761  SLDDRLQNIHEHMKKIRTDLDNGFVPLTLLEITKQLTKAPEGGKVCITQIRLSRNRRGRR 820
             L+++++ + E +++++ +++         E+ +++ +  E  +     I+LS       
Sbjct: 256  KLEEKIRELEERIEELKKEIE---------ELEEKVKELKELKEKAEEYIKLSEFYEEYL 306

Query: 821  RRRRKKKEEKKKWKRRGGGRRRRRGKKEEEKKKKKEEEEEGGEKEEEEGGGGGGRRRRRR 880
               R+ ++   + +    G   R  + EE++++ +E +++  E E+              
Sbjct: 307  DELREIEKRLSRLEEEINGIEERIKELEEKEERLEELKKKLKELEKRLEELEERHELYEE 366

Query: 881  RRSGKEEEEKKKKEGGGGRRRRRRKKRRRSRRRRSRRRRRRRRRRRRRRRRRRRRRRRRR 940
             ++ KEE E+ KK   G    +  K+     + +        +   R    ++  +  ++
Sbjct: 367  AKAKKEELERLKKRLTGLTPEKLEKELEELEKAKEEIEEEISKITARIGELKKEIKELKK 426

Query: 941  RRRRRRRRRRRRRRSGKEEEEEEKK--------------KEEKKKEEEEKKKKEGKTKKE 986
                 ++ + +    G+E  EE +K              KE K+ EE+E+K ++   + E
Sbjct: 427  AIEELKKAKGKCPVCGRELTEEHRKELLEEYTAELKRIEKELKEIEEKERKLRKELRELE 486

Query: 987  EKKKEEEEEKKKKKKEEE-KEEEEKKEEEEKEEEEKKRRRIR 1027
            +  K+E E  K K+  E+ KE EEK ++   EE EKK     
Sbjct: 487  KVLKKESELIKLKELAEQLKELEEKLKKYNLEELEKKAEEYE 528

Length = 880

>gnl|CDD|223496 COG0419, SbcC, ATPase involved in DNA repair [DNA replication, recombination, and repair]

 Score = 45.5 bits (108), Expect = 1e-04
 Identities = 37/220 (16%), Positives = 75/220 (34%), Gaps = 11/220 (5%)

Query: 811  RLSRNRRGRRRRRRKKKEEKKKWKRRGGGRRRRRGKKEEEKKKKKEEEEEGGEKEEEEGG 870
             L          + + +E K +              +EEE ++ +   EE  EK E    
Sbjct: 236  ALEERLAELEEEKERLEELKARLLEIESLELEALKIREEELRELERLLEELEEKIERLEE 295

Query: 871  GGGGRRRRRRRRSGKEEEEKKKKEGGGGRRRRRRKKRRRSRRRRSRRRRRRRRRRRRRRR 930
                         G     ++ +E         + K    R  +   +  +         
Sbjct: 296  LEREIEELEEELEGLRALLEELEE------LLEKLKSLEERLEKLEEKLEKLESELEELA 349

Query: 931  RRRRRRRRRRRRRRRRRRRRRRRRSGKEEEEEEKKKEEKKKEEEEKKKKEGKTKKEEKKK 990
              +    +    R +    R      + E+  E+ K+ ++  +E K++    +   E+ +
Sbjct: 350  EEKNELAKLLEERLKELEERLEELEKELEKALERLKQLEEAIQELKEELAELSAALEEIQ 409

Query: 991  EEEEEKKKKKKEEEKEEEEKKEEEEKEEEEKKRRRIRRKR 1030
            EE EE +K+ +E E+E EE +EE +K        +I +  
Sbjct: 410  EELEELEKELEELERELEELEEEIKK-----LEEQINQLE 444

Length = 908

>gnl|CDD|219655 pfam07946, DUF1682, Protein of unknown function (DUF1682)

 Score = 44.9 bits (107), Expect = 1e-04
 Identities = 22/67 (32%), Positives = 39/67 (58%), Gaps = 2/67 (2%)

Query: 935  RRRRRRRRRRRRRRRRRRRRSGKEEEEEEKKKEEKKKEEEEKKKKEGKTKKEEKKKEEEE 994
             R+  + R     +  +     ++EE +EKK+E+KK+E E K  K   + +E++K EE+E
Sbjct: 258  LRKVDKTREEEEEKILKAAEEERQEEAQEKKEEKKKEEREAKLAKL--SPEEQRKLEEKE 315

Query: 995  EKKKKKK 1001
             KK+ +K
Sbjct: 316  RKKQARK 322

The members of this family are all hypothetical eukaryotic proteins of unknown function. One member is described as being an adipocyte-specific protein, but no evidence of this was found. Length = 322

>gnl|CDD|222581 pfam14181, YqfQ, YqfQ-like protein

 Score = 43.6 bits (103), Expect = 1e-04
 Identities = 14/58 (24%), Positives = 36/58 (62%)

Query: 968  EKKKEEEEKKKKEGKTKKEEKKKEEEEEKKKKKKEEEKEEEEKKEEEEKEEEEKKRRR 1025
            E    ++E+++ E ++  E ++++  E K + K+++++E  + K E+EK + E K+ +
Sbjct: 90   ELSSSDDEEEETEEESTDETEQEDPPETKTESKEKKKREVPKPKTEKEKPKTEPKKPK 147

The YqfQ-like protein family includes the B. subtilis YqfQ protein, also known as VrrA, which is functionally uncharacterized. This family of proteins is found in bacteria. Proteins in this family are typically between 146 and 237 amino acids in length. There are two conserved sequence motifs: QYGP and PKLY. Length = 155

>gnl|CDD|237629 PRK14160, PRK14160, heat shock protein GrpE; Provisional

 Score = 44.0 bits (104), Expect = 1e-04
 Identities = 22/61 (36%), Positives = 37/61 (60%)

Query: 961  EEEKKKEEKKKEEEEKKKKEGKTKKEEKKKEEEEEKKKKKKEEEKEEEEKKEEEEKEEEE 1020
             E++ K+ K +  EE   KE + K+E+K KEE+ E ++ +KEE  E+ E+  E + EE +
Sbjct: 1    MEKECKDAKHENMEEDCCKENENKEEDKGKEEDLEFEEIEKEEIIEDSEESNEVKIEELK 60

Query: 1021 K 1021
             
Sbjct: 61   D 61

Length = 211

>gnl|CDD|147747 pfam05762, VWA_CoxE, VWA domain containing CoxE-like protein

 Score = 44.3 bits (105), Expect = 1e-04
 Identities = 20/54 (37%), Positives = 22/54 (40%)

Query: 899 RRRRRRKKRRRSRRRRSRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRR 952
                   RRR RR+R RR  R   RR  R   R      R  RR  R R+ RR
Sbjct: 6   AALLLGLARRRRRRKRRRRGGRIDLRRTLRANLRHGGEPVRLVRREPRLRKPRR 59

This family is annotated by SMART as containing a VWA (von Willebrand factor type A) domain. The exact function of this family is unknown. It is found as part of a CO oxidising (Cox) system operon is several bacteria. Length = 223

>gnl|CDD|109943 pfam00906, Hepatitis_core, Hepatitis core antigen

 Score = 43.6 bits (103), Expect = 1e-04
 Identities = 16/32 (50%), Positives = 18/32 (56%)

Query: 924 RRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRS 955
           RRR R  RRR    RRRR +  RRRR +   S
Sbjct: 149 RRRGRSPRRRTPSPRRRRSQSPRRRRSQSPSS 180

The core antigen of hepatitis viruses possesses a carboxyl terminus rich in arginine. On this basis it was predicted that the core antigen would bind DNA. There is some experimental evidence to support this. Length = 182

>gnl|CDD|233973 TIGR02680, TIGR02680, TIGR02680 family protein

 Score = 45.6 bits (108), Expect = 1e-04
 Identities = 36/232 (15%), Positives = 63/232 (27%), Gaps = 20/232 (8%)

Query: 811  RLSRNRRGRRRRRRKKKEEKKKWKRRGGGR-----RRRRGKKEEEKKKKKEEEEEGGEKE 865
             L+R  R    R+R   +E          R      RR  + E + +  + E      K 
Sbjct: 760  ELARELRALGARQRALADE---LAGAPSDRSLRAAHRRAAEAERQAESAERELARAARKA 816

Query: 866  EEEGGGGGGRRRRRRRRSG-----------KEEEEKKKKEGGGGRRRRRRKKRRRSRRRR 914
                      RR   R +            +      K+ G          +  R    R
Sbjct: 817  AAAAAAWKQARRELERDAADLDLPTDPDALEAVGLALKRFGDHLHTLEVAVRELRHAATR 876

Query: 915  SRRRRRRRRR-RRRRRRRRRRRRRRRRRRRRRRRRRRRRRRSGKEEEEEEKKKEEKKKEE 973
            +  +R R  R     R         R        R R    S     +E + +  + +  
Sbjct: 877  AAEQRARAARAESDAREAAEDAAEARAEAEEASLRLRTLEESVGAMVDEIRARLAETRAA 936

Query: 974  EEKKKKEGKTKKEEKKKEEEEEKKKKKKEEEKEEEEKKEEEEKEEEEKKRRR 1025
                 +E     E     EE   + ++K  E +    +  E ++    + R 
Sbjct: 937  LASGGRELPRLAEALATAEEARGRAEEKRAEADATLDERAEARDHAIGQLRE 988

Members of this protein family belong to a conserved gene four-gene neighborhood found sporadically in a phylogenetically broad range of bacteria: Nocardia farcinica, Symbiobacterium thermophilum, and Streptomyces avermitilis (Actinobacteria), Geobacillus kaustophilus (Firmicutes), Azoarcus sp. EbN1 and Ralstonia solanacearum (Betaproteobacteria). Proteins in this family average over 1400 amino acids in length [Hypothetical proteins, Conserved]. Length = 1353

>gnl|CDD|185616 PTZ00436, PTZ00436, 60S ribosomal protein L19-like protein; Provisional

 Score = 45.3 bits (106), Expect = 1e-04
 Identities = 36/145 (24%), Positives = 66/145 (45%), Gaps = 2/145 (1%)

Query: 878  RRRRRSGKEEEEKKKKEGGGGRRRRRRKKRRRSRRRRSRRRRRRRRRRRRRRRRRRRRRR 937
            R R R  KE +   + EG G  RR   ++ R   +    RR R  RR  R+ R  ++  R
Sbjct: 60   RSRWRHMKEAKSMGRHEGAG--RREGTREARMPSKELWMRRLRILRRLLRKYREEKKIDR 117

Query: 938  RRRRRRRRRRRRRRRRRSGKEEEEEEKKKEEKKKEEEEKKKKEGKTKKEEKKKEEEEEKK 997
               R    + +    R      E   K K EKKKE +  ++   K  K+E+ + +  +++
Sbjct: 118  HIYRELYVKAKGNVFRNKRNLMEHIHKVKNEKKKERQLAEQLAAKRLKDEQHRHKARKQE 177

Query: 998  KKKKEEEKEEEEKKEEEEKEEEEKK 1022
             +K+E+++E   +++       ++K
Sbjct: 178  LRKREKDRERARREDAAAAAAAKQK 202

Length = 357

>gnl|CDD|115057 pfam06375, BLVR, Bovine leukaemia virus receptor (BLVR)

 Score = 45.8 bits (108), Expect = 1e-04
 Identities = 42/231 (18%), Positives = 87/231 (37%), Gaps = 25/231 (10%)

Query: 810  IRLSRNRRGRRRRRRKKKEEKKKWKRRGGGRRRRRGKKEEEKKKK--------KEEEEEG 861
            ++L   RR R+R  + K+E+KK+ K + G RR      E ++            EE  E 
Sbjct: 82   VKLEEERRHRQRLEKDKREKKKREKEKRGRRRHHSLGTESDEDIAPAQMVDIVTEEMPEN 141

Query: 862  GEKEEEEGGGGGGRRRR-----------------RRRRSGKEEEEKKKKEGGGGRRRRRR 904
                +E+        R                  ++ R+ +  +  +K +     ++ ++
Sbjct: 142  ALPSDEDDKDPNDPYRALDIDLDKPLADSEKLPVQKHRNAETSKSPEKGDVPAVEKKSKK 201

Query: 905  KKRRRSRRRRSRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRSGKEEEEEEK 964
             K++  + +   R + +++     +                         +       + 
Sbjct: 202  PKKKEKKEKEKERDKDKKKEVEGFKSLLLALDDSPASAASVAEADEASLANTVSGTAPDS 261

Query: 965  KKEEKKKEEEEKKKKEGKTKKEEKKKEEEEEKKKKKKEEEKEEEEKKEEEE 1015
            + +E K  E E+ KK  K KK++++KE+EE+KKKKK    +        E+
Sbjct: 262  EPDEPKDAEAEETKKSPKHKKKKQRKEKEEKKKKKKHHHHRCHHSDGGAEQ 312

This family consists of several bovine specific leukaemia virus receptors which are thought to function as transmembrane proteins, although their exact function is unknown. Length = 561

>gnl|CDD|236779 PRK10864, PRK10864, putative methyltransferase; Provisional

 Score = 45.2 bits (107), Expect = 1e-04
 Identities = 15/62 (24%), Positives = 22/62 (35%)

Query: 906 KRRRSRRRRSRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRSGKEEEEEEKK 965
           KR  + R      R   + R    RR  R  R  + R R+      R  S    +E  +K
Sbjct: 25  KRTHNPRTGKGGGRPSGKSRADGGRRPARDDRNSQSRDRKWEDSPWRTVSRAPGDETPEK 84

Query: 966 KE 967
            +
Sbjct: 85  AD 86

Length = 346

>gnl|CDD|236779 PRK10864, PRK10864, putative methyltransferase; Provisional

 Score = 45.2 bits (107), Expect = 1e-04
 Identities = 13/64 (20%), Positives = 23/64 (35%)

Query: 882 RSGKEEEEKKKKEGGGGRRRRRRKKRRRSRRRRSRRRRRRRRRRRRRRRRRRRRRRRRRR 941
           +SGK +    + +    +R    +  +   R   + R    RR  R  R  + R R+   
Sbjct: 8   KSGKVKVMYVRSDDDSDKRTHNPRTGKGGGRPSGKSRADGGRRPARDDRNSQSRDRKWED 67

Query: 942 RRRR 945
              R
Sbjct: 68  SPWR 71

Length = 346

>gnl|CDD|235401 PRK05306, infB, translation initiation factor IF-2; Validated

 Score = 45.2 bits (108), Expect = 2e-04
 Identities = 14/104 (13%), Positives = 34/104 (32%)

Query: 815 NRRGRRRRRRKKKEEKKKWKRRGGGRRRRRGKKEEEKKKKKEEEEEGGEKEEEEGGGGGG 874
             +         +E  +         R    +     +      +     ++++G     
Sbjct: 71  EAKAEAAAAAPAEEAAEAAAAAEAAARPAEDEAARPAEAAARRPKAKKAAKKKKGPKPKK 130

Query: 875 RRRRRRRRSGKEEEEKKKKEGGGGRRRRRRKKRRRSRRRRSRRR 918
           ++ +R+   G +  +  K       RRRRRKK+++ +      R
Sbjct: 131 KKPKRKAARGGKRGKGGKGRRRRRGRRRRRKKKKKQKPTEKIPR 174

Length = 746

>gnl|CDD|223046 PHA03328, PHA03328, nuclear egress lamina protein UL31; Provisional

 Score = 43.9 bits (104), Expect = 2e-04
 Identities = 22/58 (37%), Positives = 23/58 (39%), Gaps = 10/58 (17%)

Query: 874 GRRRRRRRRSGKEEEEKKKKEGGGGRRRRRRKKRRRSRRRRSRRRRRRRRRRRRRRRR 931
            R  RR RR G            G R R R + RRRS RR S RR       R R R 
Sbjct: 17  RRAARRSRRDG----------RVGSRGRSRYRSRRRSSRRSSTRRAELADTERDRYRA 64

Length = 316

>gnl|CDD|217051 pfam02463, SMC_N, RecF/RecN/SMC N terminal domain

 Score = 45.0 bits (106), Expect = 2e-04
 Identities = 21/119 (17%), Positives = 55/119 (46%), Gaps = 10/119 (8%)

Query: 922  RRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRSGKEEEEEEKKKEEKKKEEEEKKK--- 978
            R+++ R ++                  + +  +  ++ ++  +  + K+K E E++    
Sbjct: 170  RKKKERLKKLIEETENLAELIIDLEELKLQELKLKEQAKKALEYYQLKEKLELEEENLLY 229

Query: 979  -------KEGKTKKEEKKKEEEEEKKKKKKEEEKEEEEKKEEEEKEEEEKKRRRIRRKR 1030
                   +E     +E  ++E+EE +  K+E EKEEE   +  ++ +EE+K ++++ + 
Sbjct: 230  LDYLKLNEERIDLLQELLRDEQEEIESSKQELEKEEEILAQVLKENKEEEKEKKLQEEE 288

This domain is found at the N terminus of SMC proteins. The SMC (structural maintenance of chromosomes) superfamily proteins have ATP-binding domains at the N- and C-termini, and two extended coiled-coil domains separated by a hinge in the middle. The eukaryotic SMC proteins form two kind of heterodimers: the SMC1/SMC3 and the SMC2/SMC4 types. These heterodimers constitute an essential part of higher order complexes, which are involved in chromatin and DNA dynamics. This family also includes the RecF and RecN proteins that are involved in DNA metabolism and recombination. Length = 1162

>gnl|CDD|178945 PRK00247, PRK00247, putative inner membrane protein translocase component YidC; Validated

 Score = 44.8 bits (106), Expect = 2e-04
 Identities = 27/115 (23%), Positives = 48/115 (41%), Gaps = 16/115 (13%)

Query: 819 RRRRRRKKKEEKKKWKRRGGGRRRRRGKKEEEKKKKKEEEEEGGEKEEEEGGGGGGRRRR 878
           +R + R+K++EKK +       RR R +      +  E   E                 +
Sbjct: 290 QRAQYREKQKEKKAFLW---TLRRNRLRMIITPWRAPELHAEN-------------AEIK 333

Query: 879 RRRRSGKEEEEKKKKEGGGGRRRRRRKKRRRSRRRRSRRRRRRRRRRRRRRRRRR 933
           + R + K E + +KKE    RR   R+  R +R+ R+    R R RR   + +++
Sbjct: 334 KTRTAEKNEAKARKKEIAQKRRAAEREINREARQERAAAMARARARRAAVKAKKK 388

Length = 429

>gnl|CDD|215774 pfam00183, HSP90, Hsp90 protein

 Score = 45.1 bits (107), Expect = 2e-04
 Identities = 24/62 (38%), Positives = 41/62 (66%), Gaps = 3/62 (4%)

Query: 959  EEEEEKKKEEKKKEEEEKKKKEGKTKKEEKKKEEEEEKKKKKKEEEKEEEEKKEEEEKEE 1018
            E+E EK   E   EEEE++K+E K ++E+   +EEE  ++++KEE+K++ +K +E   E 
Sbjct: 28   EKEVEK---EVPDEEEEEEKEEKKEEEEKTTDKEEEVDEEEEKEEKKKKTKKVKETTTEW 84

Query: 1019 EE 1020
            E 
Sbjct: 85   EL 86

Length = 529

>gnl|CDD|225288 COG2433, COG2433, Uncharacterized conserved protein [Function unknown]

 Score = 45.1 bits (107), Expect = 2e-04
 Identities = 28/127 (22%), Positives = 55/127 (43%), Gaps = 6/127 (4%)

Query: 902  RRRKKRRRSRRRRSRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRSGKEEEE 961
             + K+  R R +       RR      +R ++      R        +R      +E E+
Sbjct: 395  SKVKEEERPREKEGTEEEERREITVYEKRIKKLEETVERLEEENSELKRELEELKREIEK 454

Query: 962  EEKKKEEKKKEEEEKKKKEGKTKKEEKKKEEEEEKKKKKKEEEKEEEEKKEEEEKEEEEK 1021
             E + E  ++E  +K +K+    +E + ++   E+ +K+ EE+K+  E  E E K  E +
Sbjct: 455  LESELERFRREVRDKVRKD----REIRARDRRIERLEKELEEKKKRVE--ELERKLAELR 508

Query: 1022 KRRRIRR 1028
            K R++  
Sbjct: 509  KMRKLEL 515

Length = 652

>gnl|CDD|216147 pfam00844, Gemini_coat, Geminivirus coat protein/nuclear export factor BR1 family

 Score = 44.2 bits (105), Expect = 2e-04
 Identities = 16/44 (36%), Positives = 21/44 (47%)

Query: 911 RRRRSRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRR 954
           RRR +   RR R R   RR   ++R   +R  RR+ R  R  R 
Sbjct: 1   RRRLNFDSRRSRARAPTRRSTNKKRGWSKRPMRRKGRSYRMYRS 44

It has been shown that the 104 N-terminal amino acids of the maize streak virus coat protein bind DNA non- specifically. This family also includes various geminivirus movement proteins that are nuclear export factors or shuttles. One member BR1 facilitates the export of both ds and ss DNA form the nucleus. Length = 244

>gnl|CDD|216147 pfam00844, Gemini_coat, Geminivirus coat protein/nuclear export factor BR1 family

 Score = 44.2 bits (105), Expect = 2e-04
 Identities = 17/45 (37%), Positives = 21/45 (46%)

Query: 912 RRRSRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRSG 956
           RRR     RR R R   RR   ++R   +R  RR+ R  R  RS 
Sbjct: 1   RRRLNFDSRRSRARAPTRRSTNKKRGWSKRPMRRKGRSYRMYRSP 45

It has been shown that the 104 N-terminal amino acids of the maize streak virus coat protein bind DNA non- specifically. This family also includes various geminivirus movement proteins that are nuclear export factors or shuttles. One member BR1 facilitates the export of both ds and ss DNA form the nucleus. Length = 244

>gnl|CDD|216147 pfam00844, Gemini_coat, Geminivirus coat protein/nuclear export factor BR1 family

 Score = 44.2 bits (105), Expect = 2e-04
 Identities = 16/44 (36%), Positives = 22/44 (50%)

Query: 903 RRKKRRRSRRRRSRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRR 946
           RR+    SRR R+R   RR   ++R   +R  RR+ R  R  R 
Sbjct: 1   RRRLNFDSRRSRARAPTRRSTNKKRGWSKRPMRRKGRSYRMYRS 44

It has been shown that the 104 N-terminal amino acids of the maize streak virus coat protein bind DNA non- specifically. This family also includes various geminivirus movement proteins that are nuclear export factors or shuttles. One member BR1 facilitates the export of both ds and ss DNA form the nucleus. Length = 244

>gnl|CDD|216147 pfam00844, Gemini_coat, Geminivirus coat protein/nuclear export factor BR1 family

 Score = 43.8 bits (104), Expect = 2e-04
 Identities = 15/44 (34%), Positives = 20/44 (45%)

Query: 899 RRRRRRKKRRRSRRRRSRRRRRRRRRRRRRRRRRRRRRRRRRRR 942
           RRR     RR   R  +RR   ++R   +R  RR+ R  R  R 
Sbjct: 1   RRRLNFDSRRSRARAPTRRSTNKKRGWSKRPMRRKGRSYRMYRS 44

It has been shown that the 104 N-terminal amino acids of the maize streak virus coat protein bind DNA non- specifically. This family also includes various geminivirus movement proteins that are nuclear export factors or shuttles. One member BR1 facilitates the export of both ds and ss DNA form the nucleus. Length = 244

>gnl|CDD|109943 pfam00906, Hepatitis_core, Hepatitis core antigen

 Score = 42.9 bits (101), Expect = 2e-04
 Identities = 15/33 (45%), Positives = 18/33 (54%)

Query: 916 RRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRR 948
           RRR R  RRR    RRRR +  RRRR +    +
Sbjct: 149 RRRGRSPRRRTPSPRRRRSQSPRRRRSQSPSSQ 181

The core antigen of hepatitis viruses possesses a carboxyl terminus rich in arginine. On this basis it was predicted that the core antigen would bind DNA. There is some experimental evidence to support this. Length = 182

>gnl|CDD|109943 pfam00906, Hepatitis_core, Hepatitis core antigen

 Score = 42.9 bits (101), Expect = 2e-04
 Identities = 15/33 (45%), Positives = 18/33 (54%)

Query: 917 RRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRR 949
           RRR R  RRR    RRRR +  RRRR +    +
Sbjct: 149 RRRGRSPRRRTPSPRRRRSQSPRRRRSQSPSSQ 181

The core antigen of hepatitis viruses possesses a carboxyl terminus rich in arginine. On this basis it was predicted that the core antigen would bind DNA. There is some experimental evidence to support this. Length = 182

>gnl|CDD|109943 pfam00906, Hepatitis_core, Hepatitis core antigen

 Score = 42.9 bits (101), Expect = 2e-04
 Identities = 15/33 (45%), Positives = 18/33 (54%)

Query: 918 RRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRR 950
           RRR R  RRR    RRRR +  RRRR +    +
Sbjct: 149 RRRGRSPRRRTPSPRRRRSQSPRRRRSQSPSSQ 181

The core antigen of hepatitis viruses possesses a carboxyl terminus rich in arginine. On this basis it was predicted that the core antigen would bind DNA. There is some experimental evidence to support this. Length = 182

>gnl|CDD|109943 pfam00906, Hepatitis_core, Hepatitis core antigen

 Score = 42.9 bits (101), Expect = 2e-04
 Identities = 15/33 (45%), Positives = 18/33 (54%)

Query: 919 RRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRR 951
           RRR R  RRR    RRRR +  RRRR +    +
Sbjct: 149 RRRGRSPRRRTPSPRRRRSQSPRRRRSQSPSSQ 181

The core antigen of hepatitis viruses possesses a carboxyl terminus rich in arginine. On this basis it was predicted that the core antigen would bind DNA. There is some experimental evidence to support this. Length = 182

>gnl|CDD|109943 pfam00906, Hepatitis_core, Hepatitis core antigen

 Score = 42.9 bits (101), Expect = 2e-04
 Identities = 15/33 (45%), Positives = 18/33 (54%)

Query: 920 RRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRR 952
           RRR R  RRR    RRRR +  RRRR +    +
Sbjct: 149 RRRGRSPRRRTPSPRRRRSQSPRRRRSQSPSSQ 181

The core antigen of hepatitis viruses possesses a carboxyl terminus rich in arginine. On this basis it was predicted that the core antigen would bind DNA. There is some experimental evidence to support this. Length = 182

>gnl|CDD|109943 pfam00906, Hepatitis_core, Hepatitis core antigen

 Score = 42.9 bits (101), Expect = 2e-04
 Identities = 15/33 (45%), Positives = 18/33 (54%)

Query: 921 RRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRR 953
           RRR R  RRR    RRRR +  RRRR +    +
Sbjct: 149 RRRGRSPRRRTPSPRRRRSQSPRRRRSQSPSSQ 181

The core antigen of hepatitis viruses possesses a carboxyl terminus rich in arginine. On this basis it was predicted that the core antigen would bind DNA. There is some experimental evidence to support this. Length = 182

>gnl|CDD|109943 pfam00906, Hepatitis_core, Hepatitis core antigen

 Score = 42.9 bits (101), Expect = 2e-04
 Identities = 15/33 (45%), Positives = 18/33 (54%)

Query: 922 RRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRR 954
           RRR R  RRR    RRRR +  RRRR +    +
Sbjct: 149 RRRGRSPRRRTPSPRRRRSQSPRRRRSQSPSSQ 181

The core antigen of hepatitis viruses possesses a carboxyl terminus rich in arginine. On this basis it was predicted that the core antigen would bind DNA. There is some experimental evidence to support this. Length = 182

>gnl|CDD|109943 pfam00906, Hepatitis_core, Hepatitis core antigen

 Score = 42.9 bits (101), Expect = 2e-04
 Identities = 15/33 (45%), Positives = 18/33 (54%)

Query: 912 RRRSRRRRRRRRRRRRRRRRRRRRRRRRRRRRR 944
           RRR R  RRR    RRRR +  RRRR +    +
Sbjct: 149 RRRGRSPRRRTPSPRRRRSQSPRRRRSQSPSSQ 181

The core antigen of hepatitis viruses possesses a carboxyl terminus rich in arginine. On this basis it was predicted that the core antigen would bind DNA. There is some experimental evidence to support this. Length = 182

>gnl|CDD|223880 COG0810, TonB, Periplasmic protein TonB, links inner and outer membranes [Cell envelope biogenesis, outer membrane]

 Score = 43.6 bits (103), Expect = 2e-04
 Identities = 13/65 (20%), Positives = 32/65 (49%)

Query: 958  EEEEEEKKKEEKKKEEEEKKKKEGKTKKEEKKKEEEEEKKKKKKEEEKEEEEKKEEEEKE 1017
            E E  E++ +   + E   +    K K++ K +++ ++ K K K + K + + K + + +
Sbjct: 59   EPEPPEEQPKPPTEPETPPEPTPPKPKEKPKPEKKPKKPKPKPKPKPKPKPKVKPQPKPK 118

Query: 1018 EEEKK 1022
            +   K
Sbjct: 119  KPPSK 123

Length = 244

>gnl|CDD|223880 COG0810, TonB, Periplasmic protein TonB, links inner and outer membranes [Cell envelope biogenesis, outer membrane]

 Score = 43.6 bits (103), Expect = 2e-04
 Identities = 16/67 (23%), Positives = 30/67 (44%)

Query: 957  KEEEEEEKKKEEKKKEEEEKKKKEGKTKKEEKKKEEEEEKKKKKKEEEKEEEEKKEEEEK 1016
              EE+ +   E +   E    K + K K E+K K+ + + K K K + K + + K ++  
Sbjct: 62   PPEEQPKPPTEPETPPEPTPPKPKEKPKPEKKPKKPKPKPKPKPKPKPKVKPQPKPKKPP 121

Query: 1017 EEEEKKR 1023
             +   K 
Sbjct: 122  SKTAAKA 128

Length = 244

>gnl|CDD|115057 pfam06375, BLVR, Bovine leukaemia virus receptor (BLVR)

 Score = 45.1 bits (106), Expect = 2e-04
 Identities = 33/137 (24%), Positives = 63/137 (45%), Gaps = 41/137 (29%)

Query: 926  RRRRRRRRRRRRRRRRRRRRRRRRRRRRRSGKEEEE------------EEKKKEEKKKEE 973
            RR R+R  + +R +++R + +R RRR    G E +E            EE  +     +E
Sbjct: 88   RRHRQRLEKDKREKKKREKEKRGRRRHHSLGTESDEDIAPAQMVDIVTEEMPENALPSDE 147

Query: 974  EEK--------------------------KKKEGKTKKEEKKKEE---EEEKKKKKKEEE 1004
            ++K                          K +  +T K  +K +    E++ KK KK+E+
Sbjct: 148  DDKDPNDPYRALDIDLDKPLADSEKLPVQKHRNAETSKSPEKGDVPAVEKKSKKPKKKEK 207

Query: 1005 KEEEEKKEEEEKEEEEK 1021
            KE+E+++++++K+E E 
Sbjct: 208  KEKEKERDKDKKKEVEG 224

This family consists of several bovine specific leukaemia virus receptors which are thought to function as transmembrane proteins, although their exact function is unknown. Length = 561

>gnl|CDD|216553 pfam01528, Herpes_glycop, Herpesvirus glycoprotein M

 Score = 44.9 bits (107), Expect = 2e-04
 Identities = 14/49 (28%), Positives = 20/49 (40%)

Query: 914 RSRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRSGKEEEEE 962
           R+    RRR  R     R  R   +  +RRRR +  +    S   EE+ 
Sbjct: 326 RAYLYHRRRSTRYYALVRTVRETVKSYKRRRRSKLSQASESSILREEDS 374

The herpesvirus glycoprotein M (gM) is an integral membrane protein predicted to contain 8 transmembrane segments. Glycoprotein M is not essential for viral replication. Length = 374

>gnl|CDD|240388 PTZ00372, PTZ00372, endonuclease 4-like protein; Provisional

 Score = 44.7 bits (106), Expect = 2e-04
 Identities = 18/65 (27%), Positives = 38/65 (58%)

Query: 965  KKEEKKKEEEEKKKKEGKTKKEEKKKEEEEEKKKKKKEEEKEEEEKKEEEEKEEEEKKRR 1024
             KE      EE+ K    + K++KK+++  E KKK ++++K+++EKKE + + E +   +
Sbjct: 35   SKEILSTFSEEENKVATTSTKKDKKEDKNNESKKKSEKKKKKKKEKKEPKSEGETKLGFK 94

Query: 1025 RIRRK 1029
              ++ 
Sbjct: 95   TPKKS 99

Length = 413

>gnl|CDD|240388 PTZ00372, PTZ00372, endonuclease 4-like protein; Provisional

 Score = 44.7 bits (106), Expect = 2e-04
 Identities = 20/66 (30%), Positives = 35/66 (53%)

Query: 957  KEEEEEEKKKEEKKKEEEEKKKKEGKTKKEEKKKEEEEEKKKKKKEEEKEEEEKKEEEEK 1016
             +E      +EE K      KK + + K  E KK+ E++KKKKK+++E + E + +   K
Sbjct: 35   SKEILSTFSEEENKVATTSTKKDKKEDKNNESKKKSEKKKKKKKEKKEPKSEGETKLGFK 94

Query: 1017 EEEEKK 1022
              ++ K
Sbjct: 95   TPKKSK 100

Length = 413

>gnl|CDD|221175 pfam11705, RNA_pol_3_Rpc31, DNA-directed RNA polymerase III subunit Rpc31

 Score = 43.6 bits (103), Expect = 2e-04
 Identities = 21/71 (29%), Positives = 41/71 (57%), Gaps = 9/71 (12%)

Query: 950  RRRRRSGKEEEEEEKKKEEKKKEEEEKKKKEGKTKKEEKKKEEEEEKKKKKKEEEKEEEE 1009
            + +R+ G   EEEE   E+    E++ K+ E          E+ +E+ +K +EEE+EEEE
Sbjct: 134  KFKRKVGLFTEEEEDIDEKLSMLEKKLKELEA---------EDVDEEDEKDEEEEEEEEE 184

Query: 1010 KKEEEEKEEEE 1020
            + E+ + ++++
Sbjct: 185  EDEDFDDDDDD 195

RNA polymerase III contains seventeen subunits in yeasts and in human cells. Twelve of these are akin to RNA polymerase I or II and the other five are RNA pol III-specific, and form the functionally distinct groups (i) Rpc31-Rpc34-Rpc82, and (ii) Rpc37-Rpc53. Rpc31, Rpc34 and Rpc82 form a cluster of enzyme-specific subunits that contribute to transcription initiation in S.cerevisiae and H.sapiens. There is evidence that these subunits are anchored at or near the N-terminal Zn-fold of Rpc1, itself prolonged by a highly conserved but RNA polymerase III-specific domain. Length = 221

>gnl|CDD|233503 TIGR01642, U2AF_lg, U2 snRNP auxilliary factor, large subunit, splicing factor

 Score = 44.5 bits (105), Expect = 3e-04
 Identities = 21/109 (19%), Positives = 37/109 (33%), Gaps = 12/109 (11%)

Query: 813 SRNRRGRRRRRRKKKEEKKKWKRRGGGRR---RRRGKKEEEKKKKKEEEEEGGEKEEEEG 869
           SR R   R   R ++  + + + R   RR   R   +    + +++ +            
Sbjct: 12  SRGRDRDRSSERPRRRSRDRSRFRDRHRRSRERSYREDSRPRDRRRYDSRSPRSLRYSSV 71

Query: 870 GGGGGRRRRRRRRSGKEEEEKKKKEGGGGRRRRRRKKRRRSRRRRSRRR 918
                R RRR R     E+          RRR R +      R+  ++R
Sbjct: 72  RRSRDRPRRRSRSVRSIEQH---------RRRLRDRSPSNQWRKDDKKR 111

These splicing factors consist of an N-terminal arginine-rich low complexity domain followed by three tandem RNA recognition motifs (pfam00076). The well-characterized members of this family are auxilliary components of the U2 small nuclear ribonuclearprotein splicing factor (U2AF). These proteins are closely related to the CC1-like subfamily of splicing factors (TIGR01622). Members of this subfamily are found in plants, metazoa and fungi. Length = 509

>gnl|CDD|235250 PRK04195, PRK04195, replication factor C large subunit; Provisional

 Score = 44.1 bits (105), Expect = 3e-04
 Identities = 20/61 (32%), Positives = 43/61 (70%)

Query: 930 RRRRRRRRRRRRRRRRRRRRRRRRRSGKEEEEEEKKKEEKKKEEEEKKKKEGKTKKEEKK 989
              +  ++R   ++ ++++    ++  +EEEEE++KKEE+K+EEEE+ ++E + ++E+KK
Sbjct: 415 IVEKAEKKREEEKKEKKKKAFAGKKKEEEEEEEKEKKEEEKEEEEEEAEEEKEEEEEKKK 474

Query: 990 K 990
           K
Sbjct: 475 K 475

Length = 482

>gnl|CDD|224117 COG1196, Smc, Chromosome segregation ATPases [Cell division and chromosome partitioning]

 Score = 44.7 bits (106), Expect = 3e-04
 Identities = 43/213 (20%), Positives = 83/213 (38%), Gaps = 9/213 (4%)

Query: 813  SRNRRGRRRRRRKKKEEKKKWKRRGGGRRRRRGKKEEEKKKKKEEEEEGGEKEEEEGGGG 872
            SRN+R    ++R+ KE +++         +    +EE K  K E        EE      
Sbjct: 656  SRNKRSSLAQKRELKELEEE---LAELEAQLEKLEEELKSLKNELRSLEDLLEELRRQL- 711

Query: 873  GGRRRRRRRRSGKEEEEKKKKEGGGGRRRRRRKKRRRSRRRRSRRRRRRRRRRRRRRRRR 932
                  R+    K E    ++E    + R    +             + R          
Sbjct: 712  --EELERQLEELKRELAALEEELEQLQSRLEELEEELEELEEELEELQERLEELEEELES 769

Query: 933  RRRRRRRRRRRRRRRRRRRRRRSGKEEEEEEKKKEEKKKEEEEKKKKEGKTKKEEKKKEE 992
                  + +        +R+    + EE EE+ +E +++ +  +++ E   ++ E+ ++E
Sbjct: 770  LEEALAKLKEEIEELEEKRQALQEELEELEEELEEAERRLDALERELESLEQRRERLEQE 829

Query: 993  EEEKKKKK---KEEEKEEEEKKEEEEKEEEEKK 1022
             EE +++    +E+  E EE+ EE EKE EE K
Sbjct: 830  IEELEEEIEELEEKLDELEEELEELEKELEELK 862

Length = 1163

>gnl|CDD|217438 pfam03228, Adeno_VII, Adenoviral core protein VII

 Score = 41.0 bits (96), Expect = 3e-04
 Identities = 15/56 (26%), Positives = 19/56 (33%)

Query: 900 RRRRRKKRRRSRRRRSRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRS 955
           R      R   ++   +   R                 R  RRRRRR RR  RRR+
Sbjct: 49  RTTVDDLRDNLKKYARKYTERTVASTVDPVADSVPAGARAYRRRRRRLRRVARRRA 104

The function of this protein is unknown. It has a conserved amino terminus of 50 residues followed by a positively charged tail, suggesting it may interact with nucleic acid. The major core protein of the adenovirus, protein VII, was found to be associated with viral DNA throughout infection. The precursor to protein VII were shown to be in vivo and in vitro acceptors of ADP-ribose. The ADP-ribosylated core proteins were assembled into mature virus particles. ADP-ribosylation of adenovirus core proteins may have a role in virus decapsidation. Length = 117

>gnl|CDD|178945 PRK00247, PRK00247, putative inner membrane protein translocase component YidC; Validated

 Score = 44.1 bits (104), Expect = 3e-04
 Identities = 35/189 (18%), Positives = 60/189 (31%), Gaps = 48/189 (25%)

Query: 819  RRRRRRKKKEEKKKWKRRGGGRRRRRGKKEEEKKKKKEEEEEGGEKEEEEGGGGGGRRRR 878
             +R + ++K+++KK        RR R +      +  E   E                 +
Sbjct: 289  EQRAQYREKQKEKKAFLW--TLRRNRLRMIITPWRAPELHAE-------------NAEIK 333

Query: 879  RRRRSGKEEEEKKKKEGGGGRRRRRRKKRRRSRRRRSRRRRRRRRRRRRRRRRRRRRRRR 938
            + R + K E + +KKE          +KRR + R  +R  R+ R     R R RR   + 
Sbjct: 334  KTRTAEKNEAKARKKE--------IAQKRRAAEREINREARQERAAAMARARARRAAVK- 384

Query: 939  RRRRRRRRRRRRRRRRSGKEEEEEEKKKEEKKKEEEEKKKKEGKTKKEEKKKEEEEEKKK 998
                                     KKK        E    E +  K    + E     +
Sbjct: 385  ------------------------AKKKGLIDASPNEDTPSENEESKGSPPQVEATTTAE 420

Query: 999  KKKEEEKEE 1007
              +E  +E+
Sbjct: 421  PNREPSQED 429

Length = 429

>gnl|CDD|223496 COG0419, SbcC, ATPase involved in DNA repair [DNA replication, recombination, and repair]

 Score = 44.8 bits (106), Expect = 3e-04
 Identities = 36/212 (16%), Positives = 74/212 (34%)

Query: 816  RRGRRRRRRKKKEEKKKWKRRGGGRRRRRGKKEEEKKKKKEEEEEGGEKEEEEGGGGGGR 875
                     + KE KK  + +         ++ E  +++  E EE  E+ EE        
Sbjct: 202  EDLLEALEEELKELKKLEEIQEEQEEEELEQEIEALEERLAELEEEKERLEELKARLLEI 261

Query: 876  RRRRRRRSGKEEEEKKKKEGGGGRRRRRRKKRRRSRRRRSRRRRRRRRRRRRRRRRRRRR 935
                       EEE ++ E        + ++     R            R          
Sbjct: 262  ESLELEALKIREEELRELERLLEELEEKIERLEELEREIEELEEELEGLRALLEELEELL 321

Query: 936  RRRRRRRRRRRRRRRRRRRSGKEEEEEEKKKEEKKKEEEEKKKKEGKTKKEEKKKEEEEE 995
             + +    R  +   +  +   E EE  ++K E  K  EE+ K+  +  +E +K+ E+  
Sbjct: 322  EKLKSLEERLEKLEEKLEKLESELEELAEEKNELAKLLEERLKELEERLEELEKELEKAL 381

Query: 996  KKKKKKEEEKEEEEKKEEEEKEEEEKKRRRIR 1027
            ++ K+ EE  +E +++  E     E+ +  + 
Sbjct: 382  ERLKQLEEAIQELKEELAELSAALEEIQEELE 413

Length = 908

>gnl|CDD|222636 pfam14265, DUF4355, Domain of unknown function (DUF4355)

 Score = 41.5 bits (98), Expect = 3e-04
 Identities = 21/70 (30%), Positives = 39/70 (55%), Gaps = 3/70 (4%)

Query: 960  EEEEKKKEEKKKEEEEKKKKEGKTKKEEKKKEEEEEKKKKKKEEEKEEEEKKEEEEKEEE 1019
            ++E  K   K+K + EKK++E K++ E+  K   EEK +    E ++ E++ EE E E  
Sbjct: 10   DKEVDKAIAKEKAKWEKKQEEKKSEAEKLAKMSAEEKAEY---ELEKLEKELEELEAELA 66

Query: 1020 EKKRRRIRRK 1029
             ++ +   +K
Sbjct: 67   RRELKAEAKK 76

This family of proteins is found in bacteria and viruses. Proteins in this family are typically between 180 and 214 amino acids in length. Length = 125

>gnl|CDD|215214 PLN02381, PLN02381, valyl-tRNA synthetase

 Score = 44.5 bits (105), Expect = 3e-04
 Identities = 23/69 (33%), Positives = 40/69 (57%)

Query: 956  GKEEEEEEKKKEEKKKEEEEKKKKEGKTKKEEKKKEEEEEKKKKKKEEEKEEEEKKEEEE 1015
            G   E E +KK   ++E E KKKKE K K++E KK +  +K+ K K + ++  +     +
Sbjct: 1    GSRTESEAEKKILTEEELERKKKKEEKAKEKELKKLKAAQKEAKAKLQAQQASDGTNVPK 60

Query: 1016 KEEEEKKRR 1024
            K E++ ++R
Sbjct: 61   KSEKKSRKR 69

Length = 1066

>gnl|CDD|225288 COG2433, COG2433, Uncharacterized conserved protein [Function unknown]

 Score = 44.3 bits (105), Expect = 3e-04
 Identities = 30/147 (20%), Positives = 58/147 (39%)

Query: 876  RRRRRRRSGKEEEEKKKKEGGGGRRRRRRKKRRRSRRRRSRRRRRRRRRRRRRRRRRRRR 935
             + +     +E+E  +++E        +R K+      R        +R     +R   +
Sbjct: 395  SKVKEEERPREKEGTEEEERREITVYEKRIKKLEETVERLEEENSELKRELEELKREIEK 454

Query: 936  RRRRRRRRRRRRRRRRRRRSGKEEEEEEKKKEEKKKEEEEKKKKEGKTKKEEKKKEEEEE 995
                  R RR  R + R+       +   ++ EK+ EE++K+ +E + K  E +K  + E
Sbjct: 455  LESELERFRREVRDKVRKDREIRARDRRIERLEKELEEKKKRVEELERKLAELRKMRKLE 514

Query: 996  KKKKKKEEEKEEEEKKEEEEKEEEEKK 1022
               K    +  E+   E  E+ EEE  
Sbjct: 515  LSGKGTPVKVVEKLTLEAIEEAEEEYG 541

Length = 652

>gnl|CDD|237744 PRK14521, rpsP, 30S ribosomal protein S16; Provisional

 Score = 42.5 bits (100), Expect = 3e-04
 Identities = 19/66 (28%), Positives = 28/66 (42%)

Query: 955  SGKEEEEEEKKKEEKKKEEEEKKKKEGKTKKEEKKKEEEEEKKKKKKEEEKEEEEKKEEE 1014
              KE +   KK +  K ++  KK      KK  + + E   +KK  +      EE    E
Sbjct: 108  EEKEGKVNAKKDKLSKAKKAAKKAALEAEKKVNEARAEAVAEKKAAEAAAVAAEEAAAAE 167

Query: 1015 EKEEEE 1020
            E+E EE
Sbjct: 168  EEEAEE 173

Length = 186

>gnl|CDD|237744 PRK14521, rpsP, 30S ribosomal protein S16; Provisional

 Score = 42.5 bits (100), Expect = 3e-04
 Identities = 22/73 (30%), Positives = 34/73 (46%), Gaps = 4/73 (5%)

Query: 953  RRSGKEEEEEEKKKEEKKKE-EEEKKKKEGKTKKEEKKKEEEEEKKKKKK---EEEKEEE 1008
            + + K+++  + KK  KK   E EKK  E + +   +KK  E      ++    EE+E E
Sbjct: 113  KVNAKKDKLSKAKKAAKKAALEAEKKVNEARAEAVAEKKAAEAAAVAAEEAAAAEEEEAE 172

Query: 1009 EKKEEEEKEEEEK 1021
            E   EE   EE  
Sbjct: 173  EAPAEEAPAEESA 185

Length = 186

>gnl|CDD|147747 pfam05762, VWA_CoxE, VWA domain containing CoxE-like protein

 Score = 43.1 bits (102), Expect = 3e-04
 Identities = 22/47 (46%), Positives = 25/47 (53%), Gaps = 3/47 (6%)

Query: 898 GRRRRRRKKRRRSRR---RRSRRRRRRRRRRRRRRRRRRRRRRRRRR 941
            RRRRRRK+RRR  R   RR+ R   R      R  RR  R R+ RR
Sbjct: 13  ARRRRRRKRRRRGGRIDLRRTLRANLRHGGEPVRLVRREPRLRKPRR 59

This family is annotated by SMART as containing a VWA (von Willebrand factor type A) domain. The exact function of this family is unknown. It is found as part of a CO oxidising (Cox) system operon is several bacteria. Length = 223

>gnl|CDD|109943 pfam00906, Hepatitis_core, Hepatitis core antigen

 Score = 42.5 bits (100), Expect = 3e-04
 Identities = 15/32 (46%), Positives = 18/32 (56%)

Query: 911 RRRRSRRRRRRRRRRRRRRRRRRRRRRRRRRR 942
           RR RS RRR    RRRR +  RRRR +    +
Sbjct: 150 RRGRSPRRRTPSPRRRRSQSPRRRRSQSPSSQ 181

The core antigen of hepatitis viruses possesses a carboxyl terminus rich in arginine. On this basis it was predicted that the core antigen would bind DNA. There is some experimental evidence to support this. Length = 182

>gnl|CDD|236779 PRK10864, PRK10864, putative methyltransferase; Provisional

 Score = 44.0 bits (104), Expect = 3e-04
 Identities = 12/46 (26%), Positives = 17/46 (36%)

Query: 910 SRRRRSRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRS 955
           S +R    R  +   R   + R    RR  R  R  + R R+   S
Sbjct: 23  SDKRTHNPRTGKGGGRPSGKSRADGGRRPARDDRNSQSRDRKWEDS 68

Length = 346

>gnl|CDD|215521 PLN02967, PLN02967, kinase

 Score = 44.7 bits (105), Expect = 3e-04
 Identities = 20/83 (24%), Positives = 38/83 (45%), Gaps = 2/83 (2%)

Query: 941  RRRRRRRRRRRRRRSGKEEEEEEKKKEEKKKEEEEKKKKEGKTKKE--EKKKEEEEEKKK 998
            R  +R  ++     S   EE  E    E    ++E KK   +T+++      + EEEK +
Sbjct: 75   RSVKRATKKTVVEISEPLEEGSELVVNEDAALDKESKKTPRRTRRKAAAASSDVEEEKTE 134

Query: 999  KKKEEEKEEEEKKEEEEKEEEEK 1021
            KK  + ++ ++  E+ E +  E 
Sbjct: 135  KKVRKRRKVKKMDEDVEDQGSES 157

Length = 581

>gnl|CDD|217348 pfam03064, U79_P34, HSV U79 / HCMV P34

 Score = 43.3 bits (102), Expect = 3e-04
 Identities = 19/79 (24%), Positives = 44/79 (55%)

Query: 952  RRRSGKEEEEEEKKKEEKKKEEEEKKKKEGKTKKEEKKKEEEEEKKKKKKEEEKEEEEKK 1011
            R++S  E  +   K++EK++ E+ +K KE + KK+E+K+  +E+K+          +   
Sbjct: 152  RKKSDDEHRKRSGKQKEKRRVEDSQKHKEDRRKKQEEKRRNDEDKRPGGGGGSSGGQSGL 211

Query: 1012 EEEEKEEEEKKRRRIRRKR 1030
              +++  +EK+++    +R
Sbjct: 212  STKDEPPKEKRQKHHDPER 230

This family represents herpes virus protein U79 and cytomegalovirus early phosphoprotein P34 (UL112). Length = 238

>gnl|CDD|236941 PRK11634, PRK11634, ATP-dependent RNA helicase DeaD; Provisional

 Score = 44.1 bits (104), Expect = 3e-04
 Identities = 24/65 (36%), Positives = 29/65 (44%), Gaps = 6/65 (9%)

Query: 860 EGGEKEEEEGGGGGGRRRRRRRRSGKEEEEKKKKEGGGGRRRRRRKKRRRSRRRRSRRRR 919
            GGE+     G GG RR   R  SG+      ++EGG G  RR   +RR  R  R     
Sbjct: 567 TGGERRGGGRGFGGERREGGRNFSGE------RREGGRGDGRRFSGERREGRAPRRDDST 620

Query: 920 RRRRR 924
            RRR 
Sbjct: 621 GRRRF 625

Length = 629

>gnl|CDD|112952 pfam04162, Gyro_capsid, Gyrovirus capsid protein (VP1)

 Score = 44.0 bits (103), Expect = 3e-04
 Identities = 22/45 (48%), Positives = 27/45 (60%)

Query: 908 RRSRRRRSRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRR 952
           RR+RR R R    RR R    +R RRR + R RRR+R RRR  R+
Sbjct: 3   RRARRPRGRFYAFRRGRWHHLKRLRRRYKFRHRRRQRYRRRAFRK 47

Gyroviruses are small circular single stranded viruses. This family includes the VP1 protein from the chicken anaemia virus which is the viral capsid protein. Length = 449

>gnl|CDD|223747 COG0675, COG0675, Transposase and inactivated derivatives [DNA replication, recombination, and repair]

 Score = 43.9 bits (103), Expect = 3e-04
 Identities = 31/166 (18%), Positives = 58/166 (34%), Gaps = 22/166 (13%)

Query: 811 RLSRNRRGRRRRRRKKKEEKKKWKRRGGGRRRRRGKKEEEKKKKKEEEEEGGEKEEEEGG 870
              +  + +++R   K ++    KR G  +   R    +  K K          + +   
Sbjct: 84  NFFKGLKSKKKRGFPKFKKPSFKKRNGRLKLSLRKVIIKLPKFKGGIRILKLRLDPKGKK 143

Query: 871 GGGGRRRRRRRRS-------GKEEEEKKKKEG---------------GGGRRRRRRKKRR 908
           G    R R+ R           EEEE   K G                        +  R
Sbjct: 144 GKKVVRLRKSRGKYYLSVLVEVEEEEPVPKPGKVVGIDLGLKNLATVSDNGTVPIPRDGR 203

Query: 909 RSRRRRSRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRR 954
           +  +R  + ++R  R++ R +RR++ + +  R R R R RR+   +
Sbjct: 204 KLLKRLKKAQKRLSRKKSRSKRRKKAKLKLARLRERIRNRRKDFHK 249

Length = 364

>gnl|CDD|217051 pfam02463, SMC_N, RecF/RecN/SMC N terminal domain

 Score = 44.2 bits (104), Expect = 4e-04
 Identities = 26/149 (17%), Positives = 63/149 (42%), Gaps = 3/149 (2%)

Query: 885  KEEEEKKKKEGGGGRRRRRRKKRRRSRRRRSRRRRRRRRRRRRRRRRRRRRRRRRRRRRR 944
            K E   + +E   G R +R+KK R  +                  + +  + + + ++  
Sbjct: 152  KPERRLEIEEEAAGSREKRKKKERLKKLIEETENLAELIIDLEELKLQELKLKEQAKKAL 211

Query: 945  RRRRRRRRRRSGKEEE---EEEKKKEEKKKEEEEKKKKEGKTKKEEKKKEEEEEKKKKKK 1001
               + + +    +E     +  K  EE+    +E  + E +  +  K++ E+EE+   + 
Sbjct: 212  EYYQLKEKLELEEENLLYLDYLKLNEERIDLLQELLRDEQEEIESSKQELEKEEEILAQV 271

Query: 1002 EEEKEEEEKKEEEEKEEEEKKRRRIRRKR 1030
             +E +EEEK+++ ++EE +   +     +
Sbjct: 272  LKENKEEEKEKKLQEEELKLLAKEEEELK 300

This domain is found at the N terminus of SMC proteins. The SMC (structural maintenance of chromosomes) superfamily proteins have ATP-binding domains at the N- and C-termini, and two extended coiled-coil domains separated by a hinge in the middle. The eukaryotic SMC proteins form two kind of heterodimers: the SMC1/SMC3 and the SMC2/SMC4 types. These heterodimers constitute an essential part of higher order complexes, which are involved in chromatin and DNA dynamics. This family also includes the RecF and RecN proteins that are involved in DNA metabolism and recombination. Length = 1162

>gnl|CDD|217503 pfam03344, Daxx, Daxx Family

 Score = 43.7 bits (103), Expect = 4e-04
 Identities = 29/116 (25%), Positives = 53/116 (45%), Gaps = 17/116 (14%)

Query: 930  RRRRRRRRRRRRRRRRRRRRRRRRRSG-----------------KEEEEEEKKKEEKKKE 972
            RR+R+ R R+    R     +    SG                 +EEEEEE+++EE+++ 
Sbjct: 403  RRKRQERERQGTSSRSSDPSKASSTSGESPSMASQESEEEESVEEEEEEEEEEEEEEQES 462

Query: 973  EEEKKKKEGKTKKEEKKKEEEEEKKKKKKEEEKEEEEKKEEEEKEEEEKKRRRIRR 1028
            EEE+ + E + ++ E     EEE +   + +   EE +++ E +  E     R+  
Sbjct: 463  EEEEGEDEEEEEEVEADNGSEEEMEGSSEGDGDGEEPEEDAERRNSEMAGISRMSE 518

The Daxx protein (also known as the Fas-binding protein) is thought to play a role in apoptosis, but precise role played by Daxx remains to be determined. Daxx forms a complex with Axin. Length = 715

>gnl|CDD|233757 TIGR02168, SMC_prok_B, chromosome segregation protein SMC, common bacterial type

 Score = 44.3 bits (105), Expect = 4e-04
 Identities = 35/215 (16%), Positives = 77/215 (35%), Gaps = 5/215 (2%)

Query: 816  RRGRRRRRRKKKEEKKKWKRRGGGRRRRRGKKEEEKKKKKEEEEEGGEKEEEEGGGGGGR 875
            +  R R    +++ ++   +      +     EE  + +++ EE   E E  E       
Sbjct: 305  QILRERLANLERQLEELEAQLEELESKLDELAEELAELEEKLEELKEELESLEAELEELE 364

Query: 876  RRRRRRRSGKEEEEKKKKEGGGGRRRRRRKKRRRSRRRRSRRRRRRRRRRRRRRRRRRRR 935
                   S  EE E++  E    +  +   +         R   R  R   RR R ++  
Sbjct: 365  AELEELESRLEELEEQL-ETLRSKVAQLELQIASLNNEIERLEARLERLEDRRERLQQEI 423

Query: 936  RRRRRRRRRRRRRRRRRRRSGKEEEEEEKKKEEKKKEEEEKKKKEGKTKKEEK----KKE 991
                ++      +  +      EEE EE ++E ++ EE  ++ +E   + E+     ++E
Sbjct: 424  EELLKKLEEAELKELQAELEELEEELEELQEELERLEEALEELREELEEAEQALDAAERE 483

Query: 992  EEEEKKKKKKEEEKEEEEKKEEEEKEEEEKKRRRI 1026
              + + +    E  +E  +   E  +   K +  +
Sbjct: 484  LAQLQARLDSLERLQENLEGFSEGVKALLKNQSGL 518

SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]. Length = 1179

>gnl|CDD|177283 PHA00451, PHA00451, protein kinase

 Score = 43.6 bits (103), Expect = 4e-04
 Identities = 14/64 (21%), Positives = 22/64 (34%)

Query: 890 KKKKEGGGGRRRRRRKKRRRSRRRRSRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRR 949
           +K K    G  +  RK   + R+R  + R R  +     R    + RR   R R     +
Sbjct: 252 RKAKRDPNGTFQVARKAAMKRRKRNRKLRARNAKELAAMRMEANQIRRNEPRARMLMGDK 311

Query: 950 RRRR 953
               
Sbjct: 312 HWHN 315

Length = 362

>gnl|CDD|177283 PHA00451, PHA00451, protein kinase

 Score = 43.6 bits (103), Expect = 4e-04
 Identities = 12/56 (21%), Positives = 27/56 (48%)

Query: 914 RSRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRSGKEEEEEEKKKEEK 969
           R + R+ +R      +  R+   +RR+R R+ R R  +   + + E  + ++ E +
Sbjct: 248 RCKNRKAKRDPNGTFQVARKAAMKRRKRNRKLRARNAKELAAMRMEANQIRRNEPR 303

Length = 362

>gnl|CDD|109943 pfam00906, Hepatitis_core, Hepatitis core antigen

 Score = 42.1 bits (99), Expect = 4e-04
 Identities = 14/33 (42%), Positives = 18/33 (54%)

Query: 900 RRRRRKKRRRSRRRRSRRRRRRRRRRRRRRRRR 932
           RRR R  RRR+   R RR +  RRRR +    +
Sbjct: 149 RRRGRSPRRRTPSPRRRRSQSPRRRRSQSPSSQ 181

The core antigen of hepatitis viruses possesses a carboxyl terminus rich in arginine. On this basis it was predicted that the core antigen would bind DNA. There is some experimental evidence to support this. Length = 182

>gnl|CDD|109943 pfam00906, Hepatitis_core, Hepatitis core antigen

 Score = 42.1 bits (99), Expect = 4e-04
 Identities = 14/33 (42%), Positives = 17/33 (51%)

Query: 909 RSRRRRSRRRRRRRRRRRRRRRRRRRRRRRRRR 941
           R R R  RRR    RRRR +  RRRR +    +
Sbjct: 149 RRRGRSPRRRTPSPRRRRSQSPRRRRSQSPSSQ 181

The core antigen of hepatitis viruses possesses a carboxyl terminus rich in arginine. On this basis it was predicted that the core antigen would bind DNA. There is some experimental evidence to support this. Length = 182

>gnl|CDD|223880 COG0810, TonB, Periplasmic protein TonB, links inner and outer membranes [Cell envelope biogenesis, outer membrane]

 Score = 42.9 bits (101), Expect = 4e-04
 Identities = 15/68 (22%), Positives = 29/68 (42%), Gaps = 2/68 (2%)

Query: 956  GKEEEEEEKKKEEKKKE--EEEKKKKEGKTKKEEKKKEEEEEKKKKKKEEEKEEEEKKEE 1013
              EE+ +   + E   E    + K+K    KK +K K + + K K K + + + + KK  
Sbjct: 62   PPEEQPKPPTEPETPPEPTPPKPKEKPKPEKKPKKPKPKPKPKPKPKPKVKPQPKPKKPP 121

Query: 1014 EEKEEEEK 1021
             +   +  
Sbjct: 122  SKTAAKAP 129

Length = 244

>gnl|CDD|236779 PRK10864, PRK10864, putative methyltransferase; Provisional

 Score = 43.6 bits (103), Expect = 4e-04
 Identities = 13/62 (20%), Positives = 19/62 (30%)

Query: 901 RRRRKKRRRSRRRRSRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRSGKEEE 960
           +R    R      R   + R    RR  R  R  + R R+      R   R       E+
Sbjct: 25  KRTHNPRTGKGGGRPSGKSRADGGRRPARDDRNSQSRDRKWEDSPWRTVSRAPGDETPEK 84

Query: 961 EE 962
            +
Sbjct: 85  AD 86

Length = 346

>gnl|CDD|220102 pfam09073, BUD22, BUD22

 Score = 44.1 bits (104), Expect = 4e-04
 Identities = 22/61 (36%), Positives = 35/61 (57%)

Query: 961  EEEKKKEEKKKEEEEKKKKEGKTKKEEKKKEEEEEKKKKKKEEEKEEEEKKEEEEKEEEE 1020
            E + KK + KK+ ++ KKKE K   ++  +EE E + + K EE  E++   EEEE  + E
Sbjct: 143  ETKAKKGKAKKKTKKSKKKEAKESSDKDDEEESESEDESKSEESAEDDSDDEEEEDSDSE 202

Query: 1021 K 1021
             
Sbjct: 203  D 203

BUD22 has been shown in yeast to be a nuclear protein involved in bud-site selection. It plays a role in positioning the proximal bud pole signal. More recently it has been shown to be involved in ribosome biogenesis. Length = 424

>gnl|CDD|222665 pfam14303, NAM-associated, No apical meristem-associated C-terminal domain

 Score = 41.6 bits (98), Expect = 4e-04
 Identities = 26/92 (28%), Positives = 48/92 (52%)

Query: 938  RRRRRRRRRRRRRRRRRSGKEEEEEEKKKEEKKKEEEEKKKKEGKTKKEEKKKEEEEEKK 997
              +++++R         + + E+E+++   E K+ E  KK KE   + + K K+EE EK+
Sbjct: 28   ASKKKKKRSNSSPGSTSNEENEDEDDESTAESKRPEGRKKAKEKLRRDKLKAKKEEAEKE 87

Query: 998  KKKKEEEKEEEEKKEEEEKEEEEKKRRRIRRK 1029
            K+K+E   +   + E+E  E E+KK      K
Sbjct: 88   KEKEERFMKALAEAEKERAELEKKKAEAKLMK 119

This domain is found in a number of different types of plant proteins including NAM-like proteins. Length = 147

>gnl|CDD|218425 pfam05091, eIF-3_zeta, Eukaryotic translation initiation factor 3 subunit 7 (eIF-3)

 Score = 43.8 bits (104), Expect = 4e-04
 Identities = 22/65 (33%), Positives = 35/65 (53%)

Query: 890 KKKKEGGGGRRRRRRKKRRRSRRRRSRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRR 949
            K +    G+R+RR K+ R  RR +  + +R    RR +R  +R+++R +  R  RR  R
Sbjct: 86  LKARTTKHGKRKRRGKQTRTQRRGQGPQGKRGMTSRRAKRGGQRKQKRFQTGRGGRRGAR 145

Query: 950 RRRRR 954
            RR R
Sbjct: 146 HRRLR 150

This family is made up of eukaryotic translation initiation factor 3 subunit 7 (eIF-3 zeta/eIF3 p66/eIF3d). Eukaryotic initiation factor 3 is a multi-subunit complex that is required for binding of mRNA to 40 S ribosomal subunits, stabilisation of ternary complex binding to 40 S subunits, and dissociation of 40 and 60 S subunits. These functions and the complex nature of eIF3 suggest multiple interactions with many components of the translational machinery. The gene coding for the protein has been implicated in cancer in mammals. Length = 517

>gnl|CDD|223649 COG0576, GrpE, Molecular chaperone GrpE (heat shock protein) [Posttranslational modification, protein turnover, chaperones]

 Score = 42.3 bits (100), Expect = 4e-04
 Identities = 23/76 (30%), Positives = 45/76 (59%)

Query: 955  SGKEEEEEEKKKEEKKKEEEEKKKKEGKTKKEEKKKEEEEEKKKKKKEEEKEEEEKKEEE 1014
            S KE++ EE   EE ++ E+ ++++  + + EE+ + EEE+++  + E + EE + K   
Sbjct: 2    SDKEQKTEEPDAEETEEAEKSEEEEAEEEEPEEENELEEEQQEIAELEAQLEELKDKYLR 61

Query: 1015 EKEEEEKKRRRIRRKR 1030
             + E E  R+R  R+R
Sbjct: 62   AQAEFENLRKRTERER 77

Length = 193

>gnl|CDD|221937 pfam13148, DUF3987, Protein of unknown function (DUF3987)

 Score = 43.4 bits (103), Expect = 4e-04
 Identities = 22/70 (31%), Positives = 41/70 (58%)

Query: 957  KEEEEEEKKKEEKKKEEEEKKKKEGKTKKEEKKKEEEEEKKKKKKEEEKEEEEKKEEEEK 1016
            +E EEE +++ E++ +E E +K+  + +K+  +K+ ++  KK K EE   EE  + E E+
Sbjct: 64   EEIEEELREEYEEELKEYEAEKEIWEAEKKGLEKKAKKAIKKGKDEEALAEELLELEAEE 123

Query: 1017 EEEEKKRRRI 1026
             E   + R I
Sbjct: 124  PEPPLRPRLI 133

A family of uncharacterized proteins found by clustering human gut metagenomic sequences. Length = 379

>gnl|CDD|130141 TIGR01069, mutS2, MutS2 family protein

 Score = 44.0 bits (104), Expect = 4e-04
 Identities = 23/72 (31%), Positives = 44/72 (61%), Gaps = 1/72 (1%)

Query: 960  EEEEKKKEEKKKEEEEKKKKEGKTKKE-EKKKEEEEEKKKKKKEEEKEEEEKKEEEEKEE 1018
               EK+ E+K +  E+  K++ K KKE E++ EE +E+++ KK E ++E ++  +  K+E
Sbjct: 521  SALEKELEQKNEHLEKLLKEQEKLKKELEQEMEELKERERNKKLELEKEAQEALKALKKE 580

Query: 1019 EEKKRRRIRRKR 1030
             E   R ++ K+
Sbjct: 581  VESIIRELKEKK 592

Function of MutS2 is unknown. It should not be considered a DNA mismatch repair protein. It is likely a DNA mismatch binding protein of unknown cellular function [DNA metabolism, Other]. Length = 771

>gnl|CDD|235250 PRK04195, PRK04195, replication factor C large subunit; Provisional

 Score = 43.4 bits (103), Expect = 5e-04
 Identities = 22/61 (36%), Positives = 43/61 (70%)

Query: 931 RRRRRRRRRRRRRRRRRRRRRRRRSGKEEEEEEKKKEEKKKEEEEKKKKEGKTKKEEKKK 990
              +  ++R   ++ ++++    +  +EEEEEEK+K+E++KEEEE++ +E K ++EEKKK
Sbjct: 415 IVEKAEKKREEEKKEKKKKAFAGKKKEEEEEEEKEKKEEEKEEEEEEAEEEKEEEEEKKK 474

Query: 991 E 991
           +
Sbjct: 475 K 475

Length = 482

>gnl|CDD|224117 COG1196, Smc, Chromosome segregation ATPases [Cell division and chromosome partitioning]

 Score = 43.9 bits (104), Expect = 5e-04
 Identities = 37/195 (18%), Positives = 79/195 (40%), Gaps = 6/195 (3%)

Query: 838  GGRRRRRGKKEEEKKKKKEEEEEGGEKEEEEGGGGGGRRRRRRRRSGKEEEEKKKKEGGG 897
            GG R +R    ++++ K+ EEE    + + E      +  +   RS ++  E+ +++   
Sbjct: 654  GGSRNKRSSLAQKRELKELEEELAELEAQLEKLEEELKSLKNELRSLEDLLEELRRQ--- 710

Query: 898  GRRRRRRKKRRRSRRRRSRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRSGK 957
                  R+     R   +      + + R                  + R          
Sbjct: 711  -LEELERQLEELKRELAALEEELEQLQSRLEELEEELEELEEELEELQERLEELEEELES 769

Query: 958  EEEEEEKKKEEKKKEEEEKKKKEGKTKKEEKKKEEEEEKKKKKKEEEKEEEEKKE--EEE 1015
             EE   K KEE ++ EE+++  + + ++ E++ EE E +    + E +  E+++E  E+E
Sbjct: 770  LEEALAKLKEEIEELEEKRQALQEELEELEEELEEAERRLDALERELESLEQRRERLEQE 829

Query: 1016 KEEEEKKRRRIRRKR 1030
             EE E++   +  K 
Sbjct: 830  IEELEEEIEELEEKL 844

Length = 1163

>gnl|CDD|223046 PHA03328, PHA03328, nuclear egress lamina protein UL31; Provisional

 Score = 43.2 bits (102), Expect = 5e-04
 Identities = 21/63 (33%), Positives = 24/63 (38%), Gaps = 8/63 (12%)

Query: 870 GGGGGRRRRRRRRSGKEEEEKKKKEGGGGRRRRRRKKRRRSRRRRSRRRRRRRRRRRRRR 929
                R RR  RRS ++        G  G R R R + RR   RRS  RR       R R
Sbjct: 10  SSSLRRSRRAARRSRRD--------GRVGSRGRSRYRSRRRSSRRSSTRRAELADTERDR 61

Query: 930 RRR 932
            R 
Sbjct: 62  YRA 64

Length = 316

>gnl|CDD|235175 PRK03918, PRK03918, chromosome segregation protein; Provisional

 Score = 43.5 bits (103), Expect = 5e-04
 Identities = 48/207 (23%), Positives = 82/207 (39%), Gaps = 6/207 (2%)

Query: 824  RKKKEEKKKWKRRGGGRRRRRGKKEEEKKKKKEEEEEGGEKEEEEGGGGGGRRRRRRRRS 883
             K KE+  K K      ++   K EE KKK  E E++  E EEE          +     
Sbjct: 528  EKLKEKLIKLKGEIKSLKKELEKLEELKKKLAELEKKLDELEEELA-----ELLKELEEL 582

Query: 884  GKEEEEKKKKEGGGGRRRRRRKKRRRSRRRRSRRRRRRRRRRRRRRRRRRRRRRRRRRRR 943
            G E  E+ ++               +   +   R  +  ++      +         +R 
Sbjct: 583  GFESVEELEERLKELEPFYNEYLELKDAEKELEREEKELKKLEEELDKAFEELAETEKRL 642

Query: 944  RRRRRRRRRRRSGKEEEEEEKKKEEKKKEEEEKKKKEGKTKKEEKKKEEEEEKKKKKKEE 1003
               R+          EEE E+ +EE  +   E      + ++ EK++EE ++  +K KEE
Sbjct: 643  EELRKELEELEKKYSEEEYEELREEYLELSRELAGLRAELEELEKRREEIKKTLEKLKEE 702

Query: 1004 EKEEEEKKEEEEKEEEEKKR-RRIRRK 1029
             +E E+ K+E EK E+  +R   +R K
Sbjct: 703  LEEREKAKKELEKLEKALERVEELREK 729

Length = 880

>gnl|CDD|240271 PTZ00108, PTZ00108, DNA topoisomerase 2-like protein; Provisional

 Score = 43.9 bits (104), Expect = 5e-04
 Identities = 34/221 (15%), Positives = 82/221 (37%), Gaps = 16/221 (7%)

Query: 811  RLSRNRRGRRRRRRKKKEEKKKWKRRGGGRRRRRGKKE----EEKKKKKEEEEEGGEKEE 866
            +L + +  ++ +++KK    K  K    G  +R    E    ++K   K+    G ++E+
Sbjct: 1168 KLRKPKLKKKEKKKKKSSADKSKKASVVGNSKRVDSDEKRKLDDKPDNKKSNSSGSDQED 1227

Query: 867  EEGGGGGGRRRRRRRRSGKEEEEKKKKEGGGGRRRRRRKKRRRSRRRRSRRRRRRRRRRR 926
            +E      ++   +R   K+    K  E           K  + +    R    +     
Sbjct: 1228 DEEQKTKPKKSSVKRLKSKKNNSSKSSEDNDEFSSDDLSKEGKPKNAPKRVSAVQYSPPP 1287

Query: 927  RRRRRRRRRRRRRRRRRRRRRRRRRRRRSGKEEEEEEKKKE----EKKKEEEEKKKKEG- 981
              +R         +     +++ ++R        +++KK E     KKK +   K+    
Sbjct: 1288 PSKRPDGESNGGSKPSSPTKKKVKKRLEGSLAALKKKKKSEKKTARKKKSKTRVKQASAS 1347

Query: 982  -------KTKKEEKKKEEEEEKKKKKKEEEKEEEEKKEEEE 1015
                   + +K++     E++   +  + E E++E  E+++
Sbjct: 1348 QSSRLLRRPRKKKSDSSSEDDDDSEVDDSEDEDDEDDEDDD 1388

Length = 1388

>gnl|CDD|236545 PRK09510, tolA, cell envelope integrity inner membrane protein TolA; Provisional

 Score = 43.3 bits (102), Expect = 5e-04
 Identities = 34/199 (17%), Positives = 82/199 (41%), Gaps = 7/199 (3%)

Query: 831  KKWKRRGGGRRRRRGKKEEEKKKKKEEEEEGGEKEEEEGGGGGGRRRRRRRRSGKEEEEK 890
            +++ R+   ++  +  +E+ KKK++++ EE  +K+  E      R ++  +     +E+K
Sbjct: 62   EQYNRQQQQQKSAKRAEEQRKKKEQQQAEELQQKQAAEQE----RLKQLEKERLAAQEQK 117

Query: 891  KKKEGGGGRRRRRRKKRRRSRRRRSRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRR 950
            K+ E    +   ++K+   +  + +   + +     +R     ++     +++      +
Sbjct: 118  KQAEEAAKQAALKQKQAEEAAAKAAAAAKAKAEAEAKRAAAAAKKAAAEAKKKAEAEAAK 177

Query: 951  RRRRSGKEEEEEEKKKEEKKKEEEEKKKKEGKTKKEEKKKEEEEEKKKKKKEEEKEEEEK 1010
            +     K++ E E      K   E KKK E + KK+   + +++   + K    K   E 
Sbjct: 178  KAAAEAKKKAEAEAAA---KAAAEAKKKAEAEAKKKAAAEAKKKAAAEAKAAAAKAAAEA 234

Query: 1011 KEEEEKEEEEKKRRRIRRK 1029
            K   EK    K   +    
Sbjct: 235  KAAAEKAAAAKAAEKAAAA 253

Length = 387

>gnl|CDD|219655 pfam07946, DUF1682, Protein of unknown function (DUF1682)

 Score = 43.0 bits (102), Expect = 5e-04
 Identities = 24/49 (48%), Positives = 34/49 (69%), Gaps = 2/49 (4%)

Query: 984  KKEEKKKEEEEEKKKKKKEEEKEEE--EKKEEEEKEEEEKKRRRIRRKR 1030
            +K +K +EEEEEK  K  EEE++EE  EKKEE++KEE E K  ++  + 
Sbjct: 259  RKVDKTREEEEEKILKAAEEERQEEAQEKKEEKKKEEREAKLAKLSPEE 307

The members of this family are all hypothetical eukaryotic proteins of unknown function. One member is described as being an adipocyte-specific protein, but no evidence of this was found. Length = 322

>gnl|CDD|220271 pfam09507, CDC27, DNA polymerase subunit Cdc27

 Score = 43.7 bits (103), Expect = 5e-04
 Identities = 20/66 (30%), Positives = 36/66 (54%)

Query: 955  SGKEEEEEEKKKEEKKKEEEEKKKKEGKTKKEEKKKEEEEEKKKKKKEEEKEEEEKKEEE 1014
            SGK +   E +  E    +E++ + E K   E    EEE E+K+K+K +  ++  + E+E
Sbjct: 248  SGKRDVILEDESAEPTGLDEDEDEDEPKPSGERSDSEEETEEKEKEKRKRLKKMMEDEDE 307

Query: 1015 EKEEEE 1020
            ++E E 
Sbjct: 308  DEEMEI 313

This protein forms the C subunit of DNA polymerase delta. It carries the essential residues for binding to the Pol1 subunit of polymerase alpha, from residues 293-332, which are characterized by the motif D--G--VT, referred to as the DPIM motif. The first 160 residues of the protein form the minimal domain for binding to the B subunit, Cdc1, of polymerase delta, the final 10 C-terminal residues, 362-372, being the DNA sliding clamp, PCNA, binding motif. Length = 427

>gnl|CDD|217756 pfam03839, Sec62, Translocation protein Sec62

 Score = 42.1 bits (99), Expect = 5e-04
 Identities = 15/62 (24%), Positives = 29/62 (46%)

Query: 964  KKKEEKKKEEEEKKKKEGKTKKEEKKKEEEEEKKKKKKEEEKEEEEKKEEEEKEEEEKKR 1023
            +  E +K +  + K       K   + +  E+ K   K +  E  +K   +EK+EE+KK 
Sbjct: 14   RALESEKYKANKDKGNPEIYNKINSQDKAIEKFKLLIKAQMAERVKKLHSQEKKEEKKKP 73

Query: 1024 RR 1025
            ++
Sbjct: 74   KK 75

Length = 217

>gnl|CDD|109943 pfam00906, Hepatitis_core, Hepatitis core antigen

 Score = 41.7 bits (98), Expect = 5e-04
 Identities = 14/33 (42%), Positives = 20/33 (60%)

Query: 905 KKRRRSRRRRSRRRRRRRRRRRRRRRRRRRRRR 937
           ++R RS RRR+   RRRR +  RRRR +    +
Sbjct: 149 RRRGRSPRRRTPSPRRRRSQSPRRRRSQSPSSQ 181

The core antigen of hepatitis viruses possesses a carboxyl terminus rich in arginine. On this basis it was predicted that the core antigen would bind DNA. There is some experimental evidence to support this. Length = 182

>gnl|CDD|191249 pfam05279, Asp-B-Hydro_N, Aspartyl beta-hydroxylase N-terminal region

 Score = 42.6 bits (100), Expect = 5e-04
 Identities = 28/183 (15%), Positives = 70/183 (38%), Gaps = 40/183 (21%)

Query: 840  RRRRRGKKEEEKKKKKEEEEEGGEKEEEEGGGGGGRRRRRRRRSGKEEEEKKKKEGGGGR 899
            R+ ++  +EE K++ +   E+    ++EE G G   +    +    E+ + +++    G+
Sbjct: 95   RKTKQKVEEEVKEQLQSLLEKIVVSKQEEDGPGKEPQLDEDKFLLAEDSDDRQETLEAGK 154

Query: 900  RRRRRKKRRRSRRRRSRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRSGKEE 959
                 +         S +                                        ++
Sbjct: 155  VHEETEDSYHVEETASEQ---------------------------------------YKQ 175

Query: 960  EEEEKKKEEKKKEEEEKKKKEGKTKKEEKKKEEEE-EKKKKKKEEEKEEEEKKEEEEKEE 1018
            + +EK  E++ ++ +E  +K  +TK E     EE+ +++    E+ K  +E+  +E  EE
Sbjct: 176  DMKEKASEQENEDSKEPVEKAERTKAETDDVTEEDYDEEDNPVEDSKAIKEELAKEPVEE 235

Query: 1019 EEK 1021
            +++
Sbjct: 236  QQE 238

This family includes the N-terminal regions of the junctin, junctate and aspartyl beta-hydroxylase proteins. Junctate is an integral ER/SR membrane calcium binding protein, which comes from an alternatively spliced form of the same gene that generates aspartyl beta-hydroxylase and junctin. Aspartyl beta-hydroxylase catalyzes the post-translational hydroxylation of aspartic acid or asparagine residues contained within epidermal growth factor (EGF) domains of proteins. Length = 240

>gnl|CDD|221185 pfam11719, Drc1-Sld2, DNA replication and checkpoint protein

 Score = 43.6 bits (103), Expect = 5e-04
 Identities = 23/93 (24%), Positives = 42/93 (45%), Gaps = 4/93 (4%)

Query: 933  RRRRRRRRRRRRRRRRRRRRRRSGKEEEEEEKKKEEKKKEEEEKKKKEGKTKKEEKKKEE 992
            RR  +++ ++R  RR + R  R+   +E    + +     EE  K  E    +       
Sbjct: 281  RRVFKKKGQKRTTRRVKMRPVRAKPSDEPSLPESDI---HEEIPKLDEKSLSEFLGYMGG 337

Query: 993  EEEKKKK-KKEEEKEEEEKKEEEEKEEEEKKRR 1024
             +E  +    EE KEE EKK++ +K+  ++K  
Sbjct: 338  IDEDDEDEDDEESKEEVEKKQKVKKKPRKRKVN 370

Genome duplication is precisely regulated by cyclin-dependent kinases CDKs, which bring about the onset of S phase by activating replication origins and then prevent relicensing of origins until mitosis is completed. The optimum sequence motif for CDK phosphorylation is S/T-P-K/R-K/R, and Drc1-Sld2 is found to have at least 11 potential phosphorylation sites. Drc1 is required for DNA synthesis and S-M replication checkpoint control. Drc1 associates with Cdc2 and is phosphorylated at the onset of S phase when Cdc2 is activated. Thus Cdc2 promotes DNA replication by phosphorylating Drc1 and regulating its association with Cut5. Sld2 and Sld3 represent the minimal set of S-CDK substrates required for DNA replication. Length = 397

>gnl|CDD|217049 pfam02459, Adeno_terminal, Adenoviral DNA terminal protein

 Score = 43.5 bits (103), Expect = 5e-04
 Identities = 33/73 (45%), Positives = 43/73 (58%), Gaps = 6/73 (8%)

Query: 921 RRRRRRR------RRRRRRRRRRRRRRRRRRRRRRRRRRRSGKEEEEEEKKKEEKKKEEE 974
           R R   R      RRRR    RR   R   RRRRRRR   S  E EEEE+++EE  +EEE
Sbjct: 261 RPRENGRAVTESMRRRRGEMIRRFIDRLPLRRRRRRRPPPSPPEPEEEEEEEEEVPEEEE 320

Query: 975 EKKKKEGKTKKEE 987
           E++++E +T +EE
Sbjct: 321 EEEEEEERTFEEE 333

This protein is covalently attached to the terminii of replicating DNA in vivo. Length = 548

>gnl|CDD|219563 pfam07767, Nop53, Nop53 (60S ribosomal biogenesis)

 Score = 43.2 bits (102), Expect = 6e-04
 Identities = 19/76 (25%), Positives = 46/76 (60%), Gaps = 2/76 (2%)

Query: 957  KEEEEEEKKKEEKKKEEEEKKK-KEGKTKKEEKKKEEEEEKKKK-KKEEEKEEEEKKEEE 1014
            K    + K K ++ KE+  K+  +E K +K+ KKK  +  + K+  KE  ++E+ +  ++
Sbjct: 271  KPVRPKRKTKAQRNKEKRRKELEREAKEEKQLKKKLAQLARLKEIAKEVAQKEKARARKK 330

Query: 1015 EKEEEEKKRRRIRRKR 1030
            E+ +E  ++++++R++
Sbjct: 331  EQRKERGEKKKLKRRK 346

This nucleolar family of proteins are involved in 60S ribosomal biogenesis. They are specifically involved in the processing beyond the 27S stage of 25S rRNA maturation. This family contains sequences that bear similarity to the glioma tumour suppressor candidate region gene 2 protein (p60). This protein has been found to interact with herpes simplex type 1 regulatory proteins. Length = 387

>gnl|CDD|219939 pfam08619, Nha1_C, Alkali metal cation/H+ antiporter Nha1 C terminus

 Score = 42.9 bits (101), Expect = 6e-04
 Identities = 28/122 (22%), Positives = 50/122 (40%), Gaps = 14/122 (11%)

Query: 897  GGRRRRRRKKRRRSRRRRSRRRRRRRRRRRRRRRRRRRRRRRRR------RRRRRRRRRR 950
            GG  RR RKK++ SR  R        R    RRRRR+RR+  +          +     +
Sbjct: 52   GGMLRRVRKKKKGSRAGR--------RASSLRRRRRQRRKEPQAGTGALGPISQSAISPQ 103

Query: 951  RRRRSGKEEEEEEKKKEEKKKEEEEKKKKEGKTKKEEKKKEEEEEKKKKKKEEEKEEEEK 1010
            RR  +G+   E +       K  E+ +  + +   E  ++    E+  +  +  ++E+  
Sbjct: 104  RRSSTGENSAESDNTSYGLSKLAEDSENIDVRPVYESDERSGISEEGSRPSKLREQEQRP 163

Query: 1011 KE 1012
             E
Sbjct: 164  TE 165

The C terminus of the plasma membrane Nha1 antiporter plays an important role in the immediate cell response to hypo-osmotic shock which prevents an execessive loss of ions and water. This domain is found with pfam00999. Length = 430

>gnl|CDD|240388 PTZ00372, PTZ00372, endonuclease 4-like protein; Provisional

 Score = 43.2 bits (102), Expect = 6e-04
 Identities = 20/71 (28%), Positives = 35/71 (49%), Gaps = 3/71 (4%)

Query: 957  KEEEEEEKKKEEKKKEEEEKKKKEG---KTKKEEKKKEEEEEKKKKKKEEEKEEEEKKEE 1013
                    K+      EEE K       K KKE+K  E +++ +KKKK++++++E K E 
Sbjct: 28   YSNVLVLSKEILSTFSEEENKVATTSTKKDKKEDKNNESKKKSEKKKKKKKEKKEPKSEG 87

Query: 1014 EEKEEEEKKRR 1024
            E K   +  ++
Sbjct: 88   ETKLGFKTPKK 98

Length = 413

>gnl|CDD|236722 PRK10590, PRK10590, ATP-dependent RNA helicase RhlE; Provisional

 Score = 43.3 bits (102), Expect = 6e-04
 Identities = 14/61 (22%), Positives = 30/61 (49%)

Query: 891 KKKEGGGGRRRRRRKKRRRSRRRRSRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRR 950
           +++ GGGGR +   + +++ + RR     +    +   +  RR    +    ++RRRR R
Sbjct: 391 RQQRGGGGRGQGGGRGQQQGQPRRGEGGAKSASAKPAEKPSRRLGDAKPAGEQQRRRRPR 450

Query: 951 R 951
           +
Sbjct: 451 K 451

Length = 456

>gnl|CDD|220648 pfam10243, MIP-T3, Microtubule-binding protein MIP-T3

 Score = 43.0 bits (101), Expect = 7e-04
 Identities = 22/72 (30%), Positives = 42/72 (58%)

Query: 959  EEEEEKKKEEKKKEEEEKKKKEGKTKKEEKKKEEEEEKKKKKKEEEKEEEEKKEEEEKEE 1018
            E +    +  K+ E+   K    KTK  ++ K E  ++++K+KE+ KEE++KK+E+ KEE
Sbjct: 68   ESKLSSDEAVKRVEKGGSKGPAAKTKPAKEPKNESGKEEEKEKEQVKEEKKKKKEKPKEE 127

Query: 1019 EEKKRRRIRRKR 1030
             + ++ +   K 
Sbjct: 128  PKDRKPKEEAKE 139

This protein, which interacts with both microtubules and TRAF3 (tumour necrosis factor receptor-associated factor 3), is conserved from worms to humans. The N-terminal region is the microtubule binding domain and is well-conserved; the C-terminal 100 residues, also well-conserved, constitute the coiled-coil region which binds to TRAF3. The central region of the protein is rich in lysine and glutamic acid and carries KKE motifs which may also be necessary for tubulin-binding, but this region is the least well-conserved. Length = 506

>gnl|CDD|235401 PRK05306, infB, translation initiation factor IF-2; Validated

 Score = 43.3 bits (103), Expect = 7e-04
 Identities = 16/104 (15%), Positives = 37/104 (35%)

Query: 814 RNRRGRRRRRRKKKEEKKKWKRRGGGRRRRRGKKEEEKKKKKEEEEEGGEKEEEEGGGGG 873
             +         ++  +         R          +   +  + +   K+++      
Sbjct: 71  EAKAEAAAAAPAEEAAEAAAAAEAAARPAEDEAARPAEAAARRPKAKKAAKKKKGPKPKK 130

Query: 874 GRRRRRRRRSGKEEEEKKKKEGGGGRRRRRRKKRRRSRRRRSRR 917
            + +R+  R GK  +  K +    GRRRRR+KK+++    +  R
Sbjct: 131 KKPKRKAARGGKRGKGGKGRRRRRGRRRRRKKKKKQKPTEKIPR 174

Length = 746

>gnl|CDD|224117 COG1196, Smc, Chromosome segregation ATPases [Cell division and chromosome partitioning]

 Score = 43.2 bits (102), Expect = 7e-04
 Identities = 49/271 (18%), Positives = 107/271 (39%), Gaps = 18/271 (6%)

Query: 761  SLDDRLQNIHEHMKKIRTDLDNGFVPLTLLEITKQLTKAPEGGKVCITQIRLSRNRRGRR 820
             L++ L+ + E +++++  L+         E+ ++L    E       +I     +R   
Sbjct: 741  ELEEELEELEEELEELQERLE---------ELEEELESLEEALAKLKEEIEELEEKRQAL 791

Query: 821  RRRRKKKEEKKKWKRRGGGRRRRRGKKEEEKKKKKEEEEEGGEKEEEEGGGGGGRRRRRR 880
            +   ++ EE+ +   R      R  +  E+++++ E+E E  E+E EE        +   
Sbjct: 792  QEELEELEEELEEAERRLDALERELESLEQRRERLEQEIEELEEEIEEL-----EEKLDE 846

Query: 881  RRSGKEEEEKKKKEGGGGRRRRRRKKRRRSRRRRSRRRRRRRRRRRRRRRRRRRRRRRRR 940
                 EE EK+ +E          +K       +     +       R         +  
Sbjct: 847  LEEELEELEKELEELKEELEELEAEKEELEDELKELEEEKEELEEELRELESELAELKEE 906

Query: 941  RRRRRRRRRRRRRRSGKEEEEEEKKKEEKKKEEEEKKKKEGKTKKEEKKKEEEEEKK--K 998
              + R R      +  + E E  + +EE ++E E+  + E + + E  ++E E       
Sbjct: 907  IEKLRERLEELEAKLERLEVELPELEEELEEEYEDTLETELEREIERLEEEIEALGPVNL 966

Query: 999  KKKEEEKEEEEKKEE--EEKEEEEKKRRRIR 1027
            +  EE +E EE+ EE   ++E+ E+ + ++ 
Sbjct: 967  RAIEEYEEVEERYEELKSQREDLEEAKEKLL 997

Length = 1163

>gnl|CDD|237178 PRK12705, PRK12705, hypothetical protein; Provisional

 Score = 43.2 bits (102), Expect = 7e-04
 Identities = 32/165 (19%), Positives = 66/165 (40%), Gaps = 8/165 (4%)

Query: 869  GGGGGGRRRRRRRRSGKEEEEKKKKEGGGGRRRRRRKKRRRSRRRRSRRRRRRRRRRRRR 928
             G      ++R+R + + E   ++ +     +        +    R R ++R+  RR R 
Sbjct: 18   LGVLVVLLKKRQRLAKEAERILQEAQKEAEEKLEAALLEAKELLLRERNQQRQEARRERE 77

Query: 929  RRRRRRRRRRRRRRRRRRR-------RRRRRRRSGKEEEEEEKKKEEKKKEEEEKKKKEG 981
              +R   R  ++  +   R         +   R       E + +E +K+ + E  +  G
Sbjct: 78   ELQREEERLVQKEEQLDARAEKLDNLENQLEEREKALSARELELEELEKQLDNELYRVAG 137

Query: 982  KTKKEEKKKEEEEEKKKKKKEEEKEEEEKKEEEEKEEEEKKRRRI 1026
             T  E+ +K   +    + +EE+ +  +K EEE   E E+K + I
Sbjct: 138  LT-PEQARKLLLKLLDAELEEEKAQRVKKIEEEADLEAERKAQNI 181

Length = 508

>gnl|CDD|219563 pfam07767, Nop53, Nop53 (60S ribosomal biogenesis)

 Score = 42.8 bits (101), Expect = 7e-04
 Identities = 18/72 (25%), Positives = 44/72 (61%)

Query: 940  RRRRRRRRRRRRRRRSGKEEEEEEKKKEEKKKEEEEKKKKEGKTKKEEKKKEEEEEKKKK 999
            R +R+ + +R + +R  + E E +++K+ KKK  +  + KE   +  +K+K    +K+++
Sbjct: 274  RPKRKTKAQRNKEKRRKELEREAKEEKQLKKKLAQLARLKEIAKEVAQKEKARARKKEQR 333

Query: 1000 KKEEEKEEEEKK 1011
            K+  EK++ +++
Sbjct: 334  KERGEKKKLKRR 345

This nucleolar family of proteins are involved in 60S ribosomal biogenesis. They are specifically involved in the processing beyond the 27S stage of 25S rRNA maturation. This family contains sequences that bear similarity to the glioma tumour suppressor candidate region gene 2 protein (p60). This protein has been found to interact with herpes simplex type 1 regulatory proteins. Length = 387

>gnl|CDD|225288 COG2433, COG2433, Uncharacterized conserved protein [Function unknown]

 Score = 43.2 bits (102), Expect = 7e-04
 Identities = 32/145 (22%), Positives = 58/145 (40%)

Query: 849 EEKKKKKEEEEEGGEKEEEEGGGGGGRRRRRRRRSGKEEEEKKKKEGGGGRRRRRRKKRR 908
            + K+++   E+ G +EEE        +R ++     E  E++  E        +R+  +
Sbjct: 395 SKVKEEERPREKEGTEEEERREITVYEKRIKKLEETVERLEEENSELKRELEELKREIEK 454

Query: 909 RSRRRRSRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRSGKEEEEEEKKKEE 968
                   RR  R + R+ R  R R RR  R  +    +++R      K  E  + +K E
Sbjct: 455 LESELERFRREVRDKVRKDREIRARDRRIERLEKELEEKKKRVEELERKLAELRKMRKLE 514

Query: 969 KKKEEEEKKKKEGKTKKEEKKKEEE 993
              +    K  E  T +  ++ EEE
Sbjct: 515 LSGKGTPVKVVEKLTLEAIEEAEEE 539

Length = 652

>gnl|CDD|216147 pfam00844, Gemini_coat, Geminivirus coat protein/nuclear export factor BR1 family

 Score = 42.3 bits (100), Expect = 7e-04
 Identities = 15/44 (34%), Positives = 19/44 (43%)

Query: 909 RSRRRRSRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRR 952
           R R     RR R R   RR   ++R   +R  RR+ R  R  R 
Sbjct: 1   RRRLNFDSRRSRARAPTRRSTNKKRGWSKRPMRRKGRSYRMYRS 44

It has been shown that the 104 N-terminal amino acids of the maize streak virus coat protein bind DNA non- specifically. This family also includes various geminivirus movement proteins that are nuclear export factors or shuttles. One member BR1 facilitates the export of both ds and ss DNA form the nucleus. Length = 244

>gnl|CDD|216147 pfam00844, Gemini_coat, Geminivirus coat protein/nuclear export factor BR1 family

 Score = 42.3 bits (100), Expect = 7e-04
 Identities = 15/44 (34%), Positives = 19/44 (43%)

Query: 907 RRRSRRRRSRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRR 950
           RRR      R R R   RR   ++R   +R  RR+ R  R  R 
Sbjct: 1   RRRLNFDSRRSRARAPTRRSTNKKRGWSKRPMRRKGRSYRMYRS 44

It has been shown that the 104 N-terminal amino acids of the maize streak virus coat protein bind DNA non- specifically. This family also includes various geminivirus movement proteins that are nuclear export factors or shuttles. One member BR1 facilitates the export of both ds and ss DNA form the nucleus. Length = 244

>gnl|CDD|109943 pfam00906, Hepatitis_core, Hepatitis core antigen

 Score = 41.3 bits (97), Expect = 7e-04
 Identities = 13/33 (39%), Positives = 18/33 (54%)

Query: 904 RKKRRRSRRRRSRRRRRRRRRRRRRRRRRRRRR 936
           R++ R  RRR    RRRR +  RRRR +    +
Sbjct: 149 RRRGRSPRRRTPSPRRRRSQSPRRRRSQSPSSQ 181

The core antigen of hepatitis viruses possesses a carboxyl terminus rich in arginine. On this basis it was predicted that the core antigen would bind DNA. There is some experimental evidence to support this. Length = 182

>gnl|CDD|236779 PRK10864, PRK10864, putative methyltransferase; Provisional

 Score = 42.8 bits (101), Expect = 7e-04
 Identities = 12/50 (24%), Positives = 18/50 (36%)

Query: 909 RSRRRRSRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRSGKE 958
           RS     +R    R  +   R   + R    RR  R  R  + R R  ++
Sbjct: 18  RSDDDSDKRTHNPRTGKGGGRPSGKSRADGGRRPARDDRNSQSRDRKWED 67

Length = 346

>gnl|CDD|236941 PRK11634, PRK11634, ATP-dependent RNA helicase DeaD; Provisional

 Score = 43.3 bits (102), Expect = 7e-04
 Identities = 21/60 (35%), Positives = 22/60 (36%)

Query: 897 GGRRRRRRKKRRRSRRRRSRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRSG 956
           GG RR   +     RR   R     RR   R   RR    RR  R  RR     RRR  G
Sbjct: 568 GGERRGGGRGFGGERREGGRNFSGERREGGRGDGRRFSGERREGRAPRRDDSTGRRRFGG 627

Length = 629

>gnl|CDD|112890 pfam04094, DUF390, Protein of unknown function (DUF390)

 Score = 43.3 bits (101), Expect = 7e-04
 Identities = 48/214 (22%), Positives = 73/214 (34%), Gaps = 28/214 (13%)

Query: 837  GGGR---RRRRGKKEEEKKKKKEEEEEGGEKEEEEGGGGGGRRRRRRRRSG-----KEEE 888
            GGGR    R  G         + + ++ G        GGG  R   RR  G     + E 
Sbjct: 83   GGGRASGPRDGGPGGSRPADARGKRKQEGTPPPSPPRGGGAVRASSRRPEGAAPTSQPEG 142

Query: 889  EKKKK--------EGGGGRRRRRRKKRRRSRRRRSRRRRRRRRRRRRRRRRRRRRRRRRR 940
            E+KKK        E  GG   R    R       S  R  R        RR         
Sbjct: 143  ERKKKRFCKMGEPEHAGGNLIRLPGGRFADLPAGSSLRSPRPYSFSHLPRRVFTHPFLFV 202

Query: 941  RRRRRRR-----RRRRRRRSGKEEEEEEKKKEEKKKEEEEKKKKEGKTKKEEKKKEEEEE 995
                        R  R  +SG+ E E+    E +++E +   ++E   +  E ++  ++ 
Sbjct: 203  FWFFFCLSEIPSRPSRHSKSGQSEAEDPAAAEARRREAD---RREAADRLREAEEAAQDA 259

Query: 996  KKKKKKEEEKEEEEKK----EEEEKEEEEKKRRR 1025
             + ++ EE   EE  +    EE  +E E   R  
Sbjct: 260  ARARQAEEAAREEAARARQAEEAAREAEAAFRAD 293

This is a family of long proteins currently only found in the rice genome. They have no known function. However they may be some kind of transposable element. Length = 843

>gnl|CDD|220371 pfam09736, Bud13, Pre-mRNA-splicing factor of RES complex

 Score = 40.8 bits (96), Expect = 7e-04
 Identities = 26/73 (35%), Positives = 47/73 (64%)

Query: 950  RRRRRSGKEEEEEEKKKEEKKKEEEEKKKKEGKTKKEEKKKEEEEEKKKKKKEEEKEEEE 1009
            R      K EE+E +K+E+++KEE+EK+  +G  +KEE++K  EE +K K K   +  ++
Sbjct: 10   RIIDIEEKREEKEREKEEKERKEEKEKEWGKGLVQKEEREKRLEELEKAKNKPLARYADD 69

Query: 1010 KKEEEEKEEEEKK 1022
            +  +EE +E+E+ 
Sbjct: 70   EDYDEELKEQERW 82

This entry is characterized by proteins with alternating conserved and low-complexity regions. Bud13 together with Snu17p and a newly identified factor, Pml1p/Ylr016c, form a novel trimeric complex. called The RES complex, pre-mRNA retention and splicing complex. Subunits of this complex are not essential for viability of yeasts but they are required for efficient splicing in vitro and in vivo. Furthermore, inactivation of this complex causes pre-mRNA leakage from the nucleus. Bud13 contains a unique, phylogenetically conserved C-terminal region of unknown function. Length = 141

>gnl|CDD|219563 pfam07767, Nop53, Nop53 (60S ribosomal biogenesis)

 Score = 42.8 bits (101), Expect = 8e-04
 Identities = 28/174 (16%), Positives = 67/174 (38%), Gaps = 31/174 (17%)

Query: 827  KEEKKKWKRRGGGRRRRRGKKEEEKKKKKEEEEEGGEKEEEEGGGGGGRRRRRRRRSGKE 886
            ++E K  K+R         ++ E  ++KK E+        +E   G             +
Sbjct: 204  EKEVKAEKKR---------QELERVEEKKLEKMAPEASRLDEMSEGLLEESDDDGEEESD 254

Query: 887  EEEKKKKEGGGGRRRRRRKKRRRSRRRRSRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRR 946
            +E   +          +                        R +R+ + +R + +RR+  
Sbjct: 255  DESAWEGFESEYEPINKPV----------------------RPKRKTKAQRNKEKRRKEL 292

Query: 947  RRRRRRRRSGKEEEEEEKKKEEKKKEEEEKKKKEGKTKKEEKKKEEEEEKKKKK 1000
             R  +  +  K++  +  + +E  KE  +K+K   + K++ K++ E+++ K++K
Sbjct: 293  EREAKEEKQLKKKLAQLARLKEIAKEVAQKEKARARKKEQRKERGEKKKLKRRK 346

This nucleolar family of proteins are involved in 60S ribosomal biogenesis. They are specifically involved in the processing beyond the 27S stage of 25S rRNA maturation. This family contains sequences that bear similarity to the glioma tumour suppressor candidate region gene 2 protein (p60). This protein has been found to interact with herpes simplex type 1 regulatory proteins. Length = 387

>gnl|CDD|221275 pfam11861, DUF3381, Domain of unknown function (DUF3381)

 Score = 40.7 bits (96), Expect = 8e-04
 Identities = 17/51 (33%), Positives = 35/51 (68%)

Query: 957  KEEEEEEKKKEEKKKEEEEKKKKEGKTKKEEKKKEEEEEKKKKKKEEEKEE 1007
            ++EEEEE++ E ++ +EEE+  +  + +  + K+E+  E ++K+KE  KE+
Sbjct: 100  EKEEEEEEEVEVEELDEEEQIDELLEKELAKLKREKRRENERKQKEILKEQ 150

This domain is functionally uncharacterized. This domain is found in eukaryotes. This presumed domain is typically between 156 to 174 amino acids in length. This domain is found associated with pfam07780, pfam01728. Length = 154

>gnl|CDD|240388 PTZ00372, PTZ00372, endonuclease 4-like protein; Provisional

 Score = 42.8 bits (101), Expect = 8e-04
 Identities = 23/66 (34%), Positives = 35/66 (53%), Gaps = 4/66 (6%)

Query: 957  KEEEEEEKKKEEKKKEEEEKKKKEGKTKKEEKKKEEEEEKKKKKKEEEKEEEEKKEEEEK 1016
               EEE K      K    K KKE K  + +KK E++++KKK+KKE + E E K   +  
Sbjct: 41   TFSEEENKVATTSTK----KDKKEDKNNESKKKSEKKKKKKKEKKEPKSEGETKLGFKTP 96

Query: 1017 EEEEKK 1022
            ++ +K 
Sbjct: 97   KKSKKT 102

Length = 413

>gnl|CDD|221041 pfam11241, DUF3043, Protein of unknown function (DUF3043)

 Score = 41.1 bits (97), Expect = 8e-04
 Identities = 15/46 (32%), Positives = 20/46 (43%)

Query: 905 KKRRRSRRRRSRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRR 950
            K R + +RR     RRR      R+  ++  R  RR RR R R  
Sbjct: 1   GKGRPTPKRREAEAARRRPLVPEDRKAAKKAARAARRERRARARAA 46

Some members in this family of proteins with unknown function are annotated as membrane proteins. This cannot be confirmed. Length = 168

>gnl|CDD|113290 pfam04514, BTV_NS2, Bluetongue virus non-structural protein NS2

 Score = 42.6 bits (100), Expect = 8e-04
 Identities = 25/140 (17%), Positives = 47/140 (33%)

Query: 849 EEKKKKKEEEEEGGEKEEEEGGGGGGRRRRRRRRSGKEEEEKKKKEGGGGRRRRRRKKRR 908
           E ++K +EE E+  E++  +      R          E    ++         ++ +K  
Sbjct: 156 ELRQKIREEREKEKEEQPMKPAFKPERWMGGPDSDEDENPLDEEAPDMTPETSKQDQKEE 215

Query: 909 RSRRRRSRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRSGKEEEEEEKKKEE 968
           R      R              RRR  R+ +       R        G++ E+ E K E 
Sbjct: 216 RRAAVERRLAELVEMINWNLEERRRDLRKEQELEENVERDSDDEDEHGEDSEDGETKPES 275

Query: 969 KKKEEEEKKKKEGKTKKEEK 988
               E  ++  E +  K+E+
Sbjct: 276 YITSEYIERISEIRKMKDER 295

This family includes NS2 proteins from other members of the Orbivirus genus. NS2 is a non-specific single-stranded RNA-binding protein that forms large homomultimers and accumulates in viral inclusion bodies of infected cells. Three RNA binding regions have been identified in Bluetongue virus serotype 17 at residues 2-11, 153-166 and 274-286. NS2 multimers also possess nucleotidyl phosphatase activity. The precise function of NS2 is not known, but it may be involved in the transport and condensation of viral mRNAs. Length = 363

>gnl|CDD|220369 pfam09731, Mitofilin, Mitochondrial inner membrane protein

 Score = 42.7 bits (101), Expect = 8e-04
 Identities = 23/66 (34%), Positives = 39/66 (59%)

Query: 957  KEEEEEEKKKEEKKKEEEEKKKKEGKTKKEEKKKEEEEEKKKKKKEEEKEEEEKKEEEEK 1016
             EEEEE ++  ++K+EE   K +E    + E K+   E++ + + E EKEE  KK EE+ 
Sbjct: 184  AEEEEELERALKEKREELLSKLEEELLARLESKEAALEKQLRLEFEREKEELRKKYEEKL 243

Query: 1017 EEEEKK 1022
             +E ++
Sbjct: 244  RQELER 249

Mitofilin controls mitochondrial cristae morphology. Mitofilin is enriched in the narrow space between the inner boundary and the outer membranes, where it forms a homotypic interaction and assembles into a large multimeric protein complex. The first 78 amino acids contain a typical amino-terminal-cleavable mitochondrial presequence rich in positive-charged and hydroxylated residues and a membrane anchor domain. In addition, it has three centrally located coiled coil domains. Length = 493

>gnl|CDD|240402 PTZ00399, PTZ00399, cysteinyl-tRNA-synthetase; Provisional

 Score = 43.1 bits (102), Expect = 8e-04
 Identities = 18/45 (40%), Positives = 35/45 (77%)

Query: 957  KEEEEEEKKKEEKKKEEEEKKKKEGKTKKEEKKKEEEEEKKKKKK 1001
            K +++EE ++E+++KE  +++K+  K KK+E+KK++E EK +K K
Sbjct: 546  KLDDKEELQREKEEKEALKEQKRLRKLKKQEEKKKKELEKLEKAK 590

Length = 651

>gnl|CDD|223039 PHA03307, PHA03307, transcriptional regulator ICP4; Provisional

 Score = 43.2 bits (102), Expect = 8e-04
 Identities = 17/56 (30%), Positives = 18/56 (32%)

Query: 899 RRRRRRKKRRRSRRRRSRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRR 954
                 +KR R  R  S       R  RRR R     R RRR    R    R R  
Sbjct: 360 ADPSSPRKRPRPSRAPSSPAASAGRPTRRRARAAVAGRARRRDATGRFPAGRPRPS 415

Length = 1352

>gnl|CDD|218336 pfam04935, SURF6, Surfeit locus protein 6

 Score = 41.5 bits (98), Expect = 8e-04
 Identities = 32/114 (28%), Positives = 59/114 (51%), Gaps = 19/114 (16%)

Query: 923  RRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRSGKEEEEEEKKKEEKKKEEEE------- 975
            +RRR+R +R+ R++++R+  +++   ++      K EE + KKK    +  E        
Sbjct: 10   QRRRKREQRKARKKQKRKEAKKKEDAQKSEAEEVKNEENKSKKKAAPIENAEGNIVFSKV 69

Query: 976  --------KKKKEGKTKKEEKKKEEEEE----KKKKKKEEEKEEEEKKEEEEKE 1017
                    KK  + K KK++KK + ++     + +KKK EE +E++  E EEKE
Sbjct: 70   EFADGEQAKKDLKLKKKKKKKKTDYKQLLKKLEARKKKLEELDEDKAAEIEEKE 123

The surfeit locus protein SURF-6 is shown to be a component of the nucleolar matrix and has a strong binding capacity for nucleic acids. Length = 206

>gnl|CDD|235250 PRK04195, PRK04195, replication factor C large subunit; Provisional

 Score = 42.6 bits (101), Expect = 9e-04
 Identities = 17/60 (28%), Positives = 39/60 (65%)

Query: 971  KEEEEKKKKEGKTKKEEKKKEEEEEKKKKKKEEEKEEEEKKEEEEKEEEEKKRRRIRRKR 1030
            +EE E      K  K+ KK  E+ EKK++++++EK+++    ++++EEEE+++ +   ++
Sbjct: 396  EEEIEFLTGSKKATKKIKKIVEKAEKKREEEKKEKKKKAFAGKKKEEEEEEEKEKKEEEK 455

Length = 482

>gnl|CDD|225288 COG2433, COG2433, Uncharacterized conserved protein [Function unknown]

 Score = 42.8 bits (101), Expect = 9e-04
 Identities = 29/140 (20%), Positives = 56/140 (40%)

Query: 886  EEEEKKKKEGGGGRRRRRRKKRRRSRRRRSRRRRRRRRRRRRRRRRRRRRRRRRRRRRRR 945
            +EEE+ +++ G     RR       R ++      R        +R     +R   +   
Sbjct: 398  KEEERPREKEGTEEEERREITVYEKRIKKLEETVERLEEENSELKRELEELKREIEKLES 457

Query: 946  RRRRRRRRRSGKEEEEEEKKKEEKKKEEEEKKKKEGKTKKEEKKKEEEEEKKKKKKEEEK 1005
               R RR    K  ++ E +  +++ E  EK+ +E K + EE +++  E +K +K E   
Sbjct: 458  ELERFRREVRDKVRKDREIRARDRRIERLEKELEEKKKRVEELERKLAELRKMRKLELSG 517

Query: 1006 EEEEKKEEEEKEEEEKKRRR 1025
            +    K  E+   E  +   
Sbjct: 518  KGTPVKVVEKLTLEAIEEAE 537

Length = 652

>gnl|CDD|216147 pfam00844, Gemini_coat, Geminivirus coat protein/nuclear export factor BR1 family

 Score = 41.9 bits (99), Expect = 9e-04
 Identities = 16/44 (36%), Positives = 20/44 (45%)

Query: 908 RRSRRRRSRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRR 951
           RR     SRR R R   RR   ++R   +R  RR+ R  R  R 
Sbjct: 1   RRRLNFDSRRSRARAPTRRSTNKKRGWSKRPMRRKGRSYRMYRS 44

It has been shown that the 104 N-terminal amino acids of the maize streak virus coat protein bind DNA non- specifically. This family also includes various geminivirus movement proteins that are nuclear export factors or shuttles. One member BR1 facilitates the export of both ds and ss DNA form the nucleus. Length = 244

>gnl|CDD|240388 PTZ00372, PTZ00372, endonuclease 4-like protein; Provisional

 Score = 42.8 bits (101), Expect = 9e-04
 Identities = 21/72 (29%), Positives = 40/72 (55%), Gaps = 1/72 (1%)

Query: 956  GKEEEEEEKKKEEKKKEEEEKKKKEGKTKKEEKKKEEEEEKKKKK-KEEEKEEEEKKEEE 1014
               E +++ +K++KKK+E+++ K EG+TK   K  ++ ++ KKK  K +  E+ +    +
Sbjct: 62   KNNESKKKSEKKKKKKKEKKEPKSEGETKLGFKTPKKSKKTKKKPPKPKPNEDVDNAFNK 121

Query: 1015 EKEEEEKKRRRI 1026
              E  EK    I
Sbjct: 122  IAELAEKSNVYI 133

Length = 413

>gnl|CDD|221931 pfam13136, DUF3984, Protein of unknown function (DUF3984)

 Score = 42.4 bits (100), Expect = 9e-04
 Identities = 17/61 (27%), Positives = 20/61 (32%), Gaps = 5/61 (8%)

Query: 908 RRSRRRRSRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRR-----RRRRRSGKEEEEE 962
            R R   SRR  RR R           RR  R   RR  R          RR+  E+  +
Sbjct: 170 AREREHSSRRASRRGRSGYSTPSAALSRRGSRSASRRGSRADLSMTPLEARRADAEDSRD 229

Query: 963 E 963
            
Sbjct: 230 T 230

This family of proteins is functionally uncharacterized. This family of proteins is found in eukaryotes. Proteins in this family are typically between 393 and 442 amino acids in length. Length = 301

>gnl|CDD|114629 pfam05917, DUF874, Helicobacter pylori protein of unknown function (DUF874)

 Score = 42.6 bits (99), Expect = 9e-04
 Identities = 25/83 (30%), Positives = 51/83 (61%), Gaps = 1/83 (1%)

Query: 949  RRRRRRSGKE-EEEEEKKKEEKKKEEEEKKKKEGKTKKEEKKKEEEEEKKKKKKEEEKEE 1007
            R R  +SG E E+EE+K ++EK+K E+E  +      K E++K++ E++K+K ++E+++ 
Sbjct: 141  RDRANKSGIELEQEEQKTEQEKQKTEKEGIELANSQIKAEQEKQKTEQEKQKTEQEKQKT 200

Query: 1008 EEKKEEEEKEEEEKKRRRIRRKR 1030
                 +   E E++K++    K+
Sbjct: 201  SNIANKNAIELEQEKQKTENEKQ 223

This family consists of several hypothetical proteins specific to Helicobacter pylori. The function of this family is unknown. Length = 417

>gnl|CDD|235250 PRK04195, PRK04195, replication factor C large subunit; Provisional

 Score = 42.2 bits (100), Expect = 0.001
 Identities = 19/73 (26%), Positives = 38/73 (52%)

Query: 824 RKKKEEKKKWKRRGGGRRRRRGKKEEEKKKKKEEEEEGGEKEEEEGGGGGGRRRRRRRRS 883
              K+  KK K+      ++R ++++EKKKK    ++  E+EEEE       +      +
Sbjct: 403 TGSKKATKKIKKIVEKAEKKREEEKKEKKKKAFAGKKKEEEEEEEKEKKEEEKEEEEEEA 462

Query: 884 GKEEEEKKKKEGG 896
            +E+EE+++K+  
Sbjct: 463 EEEKEEEEEKKKK 475

Length = 482

>gnl|CDD|233758 TIGR02169, SMC_prok_A, chromosome segregation protein SMC, primarily archaeal type

 Score = 43.1 bits (102), Expect = 0.001
 Identities = 36/214 (16%), Positives = 72/214 (33%), Gaps = 16/214 (7%)

Query: 817  RGRRRRRRKKKEEKKKWKRRGGGRRRRRGKKEEEKKKKKEEEEEGGEKEEEEGGGGGGRR 876
                    +K  E +K   +      +  ++ EE ++     E+  E  + E      R 
Sbjct: 708  SQELSDASRKIGEIEKEIEQLEQEEEKLKERLEELEEDLSSLEQEIENVKSELKELEARI 767

Query: 877  RRRRRRSGKEEEEKKKKEGGGGRRRRRRKKRRRSRRRRSRRRRRRRRRRRRRRRRRRRRR 936
                    K EE     E              R    R    +    +      R   R 
Sbjct: 768  EELEEDLHKLEEALNDLE-------------ARLSHSRIPEIQAELSKLEEEVSRIEARL 814

Query: 937  RRRRRRRRRRRRRRRRRRSGKEEEEEEKKKEEKKKEEEEKKKKEGKTKKEEKKKEEEEEK 996
            R   ++  R    +       +E +E++   +++ +  EK+ +    KKEE +   EE +
Sbjct: 815  REIEQKLNRLTLEKEYLEKEIQELQEQRIDLKEQIKSIEKEIENLNGKKEELE---EELE 871

Query: 997  KKKKKEEEKEEEEKKEEEEKEEEEKKRRRIRRKR 1030
            + +    + E      ++E++E E + R + RK 
Sbjct: 872  ELEAALRDLESRLGDLKKERDELEAQLRELERKI 905

SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]. Length = 1164

>gnl|CDD|220383 pfam09756, DDRGK, DDRGK domain

 Score = 40.8 bits (96), Expect = 0.001
 Identities = 22/67 (32%), Positives = 48/67 (71%)

Query: 964  KKKEEKKKEEEEKKKKEGKTKKEEKKKEEEEEKKKKKKEEEKEEEEKKEEEEKEEEEKKR 1023
            KK   KK+ + E+K+   + ++ E+++ EE +K ++K+E E++EEE+ EEE ++++E++ 
Sbjct: 1    KKIGAKKRAKLEEKQARRQQREAEEEEREERKKLEEKREGERKEEEELEEEREKKKEEEE 60

Query: 1024 RRIRRKR 1030
            R+ R ++
Sbjct: 61   RKEREEQ 67

This is a family of proteins of approximately 300 residues, found in plants and vertebrates. They contain a highly conserved DDRGK motif. Length = 189

>gnl|CDD|235175 PRK03918, PRK03918, chromosome segregation protein; Provisional

 Score = 42.7 bits (101), Expect = 0.001
 Identities = 38/184 (20%), Positives = 72/184 (39%), Gaps = 1/184 (0%)

Query: 846  KKEEEKKKKKEEEEEGGEKEEEEGGGGGGRRRRRRRRSGKEEE-EKKKKEGGGGRRRRRR 904
            K ++   ++ E++ E  EK +E+     G  +  ++   K EE +KK  E          
Sbjct: 511  KLKKYNLEELEKKAEEYEKLKEKLIKLKGEIKSLKKELEKLEELKKKLAELEKKLDELEE 570

Query: 905  KKRRRSRRRRSRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRSGKEEEEEEK 964
            +     +               R +            +   +   R  +   K EEE +K
Sbjct: 571  ELAELLKELEELGFESVEELEERLKELEPFYNEYLELKDAEKELEREEKELKKLEEELDK 630

Query: 965  KKEEKKKEEEEKKKKEGKTKKEEKKKEEEEEKKKKKKEEEKEEEEKKEEEEKEEEEKKRR 1024
              EE  + E+  ++   + ++ EKK  EEE ++ +++  E   E      E EE EK+R 
Sbjct: 631  AFEELAETEKRLEELRKELEELEKKYSEEEYEELREEYLELSRELAGLRAELEELEKRRE 690

Query: 1025 RIRR 1028
             I++
Sbjct: 691  EIKK 694

Length = 880

>gnl|CDD|215774 pfam00183, HSP90, Hsp90 protein

 Score = 42.8 bits (101), Expect = 0.001
 Identities = 26/73 (35%), Positives = 47/73 (64%), Gaps = 10/73 (13%)

Query: 967  EEKKKEEEEKKKKE----------GKTKKEEKKKEEEEEKKKKKKEEEKEEEEKKEEEEK 1016
            EE++ +E  KK  E           K  ++E   EEEEE+K++KKEEE++  +K+EE ++
Sbjct: 4    EERRIKELVKKHSEFINYPIYLWVEKEVEKEVPDEEEEEEKEEKKEEEEKTTDKEEEVDE 63

Query: 1017 EEEEKKRRRIRRK 1029
            EEE++++++  +K
Sbjct: 64   EEEKEEKKKKTKK 76

Length = 529

>gnl|CDD|215774 pfam00183, HSP90, Hsp90 protein

 Score = 42.1 bits (99), Expect = 0.001
 Identities = 21/66 (31%), Positives = 45/66 (68%)

Query: 961  EEEKKKEEKKKEEEEKKKKEGKTKKEEKKKEEEEEKKKKKKEEEKEEEEKKEEEEKEEEE 1020
            E+E +KE   +EEEE+K+++ + +++   KEEE +++++K+E++K+ ++ KE   + E  
Sbjct: 28   EKEVEKEVPDEEEEEEKEEKKEEEEKTTDKEEEVDEEEEKEEKKKKTKKVKETTTEWELL 87

Query: 1021 KKRRRI 1026
             K + I
Sbjct: 88   NKTKPI 93

Length = 529

>gnl|CDD|215774 pfam00183, HSP90, Hsp90 protein

 Score = 42.1 bits (99), Expect = 0.001
 Identities = 24/62 (38%), Positives = 35/62 (56%)

Query: 956  GKEEEEEEKKKEEKKKEEEEKKKKEGKTKKEEKKKEEEEEKKKKKKEEEKEEEEKKEEEE 1015
             KEEEE+   KEE+  EEEEK++K+ KTKK ++   E E   K K    +  ++  +EE 
Sbjct: 47   KKEEEEKTTDKEEEVDEEEEKEEKKKKTKKVKETTTEWELLNKTKPIWTRNPKDVTKEEY 106

Query: 1016 KE 1017
              
Sbjct: 107  AA 108

Length = 529

>gnl|CDD|221641 pfam12569, NARP1, NMDA receptor-regulated protein 1

 Score = 42.2 bits (100), Expect = 0.001
 Identities = 16/56 (28%), Positives = 32/56 (57%)

Query: 970  KKEEEEKKKKEGKTKKEEKKKEEEEEKKKKKKEEEKEEEEKKEEEEKEEEEKKRRR 1025
              E EE++ + G     E+KK  ++++K +KK E++E E+   +++ E   KK + 
Sbjct: 393  LAEGEEEEGENGNLSPAERKKLRKKQRKAEKKAEKEEAEKAAAKKKAEAAAKKAKG 448

This domain family is found in eukaryotes, and is approximately 40 amino acids in length. The family is found in association with pfam07719, pfam00515. There is a single completely conserved residue L that may be functionally important. NARP1 is the mammalian homologue of a yeast N-terminal acetyltransferase that regulates entry into the G(0) phase of the cell cycle. Length = 516

>gnl|CDD|220271 pfam09507, CDC27, DNA polymerase subunit Cdc27

 Score = 42.1 bits (99), Expect = 0.001
 Identities = 34/175 (19%), Positives = 66/175 (37%), Gaps = 36/175 (20%)

Query: 845  GKKEEEKKKKKEEEEEGGEKEEEEGGGGGGRRRRRRRRSGKEEEEKKKKEGGGGRRRRRR 904
             KK +EKK+KKE  E   ++E EE  G             ++   + +     G      
Sbjct: 223  KKKTKEKKEKKEASESTVKEESEEESGK------------RDVILEDESAEPTGLDEDED 270

Query: 905  KKRRRSRRRRSRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRSGKEEEEEEK 964
            +   +    RS        + +                   +R+R ++    ++E+EE +
Sbjct: 271  EDEPKPSGERSDSEEETEEKEK------------------EKRKRLKKMMEDEDEDEEME 312

Query: 965  KKEEKKKEEEEKKKKEG------KTKKEEKKKEEEEEKKKKKKEEEKEEEEKKEE 1013
               E   EEEE ++ E       + +KEE     +  +++ ++   K++  K EE
Sbjct: 313  IVPESPVEEEESEEPEPPPLPKKEEEKEEVTVSPDGGRRRGRRRVMKKKTFKDEE 367

This protein forms the C subunit of DNA polymerase delta. It carries the essential residues for binding to the Pol1 subunit of polymerase alpha, from residues 293-332, which are characterized by the motif D--G--VT, referred to as the DPIM motif. The first 160 residues of the protein form the minimal domain for binding to the B subunit, Cdc1, of polymerase delta, the final 10 C-terminal residues, 362-372, being the DNA sliding clamp, PCNA, binding motif. Length = 427

>gnl|CDD|216147 pfam00844, Gemini_coat, Geminivirus coat protein/nuclear export factor BR1 family

 Score = 41.9 bits (99), Expect = 0.001
 Identities = 14/44 (31%), Positives = 20/44 (45%)

Query: 906 KRRRSRRRRSRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRR 949
           +RR +   R  R R   RR   ++R   +R  RR+ R  R  R 
Sbjct: 1   RRRLNFDSRRSRARAPTRRSTNKKRGWSKRPMRRKGRSYRMYRS 44

It has been shown that the 104 N-terminal amino acids of the maize streak virus coat protein bind DNA non- specifically. This family also includes various geminivirus movement proteins that are nuclear export factors or shuttles. One member BR1 facilitates the export of both ds and ss DNA form the nucleus. Length = 244

>gnl|CDD|237177 PRK12704, PRK12704, phosphodiesterase; Provisional

 Score = 42.5 bits (101), Expect = 0.001
 Identities = 22/69 (31%), Positives = 43/69 (62%), Gaps = 2/69 (2%)

Query: 957  KEEEEEEKKKEEKKKE--EEEKKKKEGKTKKEEKKKEEEEEKKKKKKEEEKEEEEKKEEE 1014
            KE   E K++  K +   E+E +++  + +K EK+  ++EE   +K E  ++ EE+ E++
Sbjct: 56   KEALLEAKEEIHKLRNEFEKELRERRNELQKLEKRLLQKEENLDRKLELLEKREEELEKK 115

Query: 1015 EKEEEEKKR 1023
            EKE E+K++
Sbjct: 116  EKELEQKQQ 124

Length = 520

>gnl|CDD|221275 pfam11861, DUF3381, Domain of unknown function (DUF3381)

 Score = 40.3 bits (95), Expect = 0.001
 Identities = 16/68 (23%), Positives = 38/68 (55%), Gaps = 4/68 (5%)

Query: 963  EKKKEEKKKEEEEKKKKEGKTKKEEKKKEEEEEKKKKKKEEEKEEEEKKEEEEKEEEEKK 1022
            +K ++    +++EK+++E +  + E+  EEE+      +  EKE  + K E+ +E E K+
Sbjct: 88   KKVRKLLGLDKKEKEEEEEEEVEVEELDEEEQI----DELLEKELAKLKREKRRENERKQ 143

Query: 1023 RRRIRRKR 1030
            +  ++ + 
Sbjct: 144  KEILKEQM 151

This domain is functionally uncharacterized. This domain is found in eukaryotes. This presumed domain is typically between 156 to 174 amino acids in length. This domain is found associated with pfam07780, pfam01728. Length = 154

>gnl|CDD|109943 pfam00906, Hepatitis_core, Hepatitis core antigen

 Score = 40.6 bits (95), Expect = 0.001
 Identities = 14/33 (42%), Positives = 17/33 (51%)

Query: 914 RSRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRR 946
           R R R  RRR    RRRR +  RRRR +    +
Sbjct: 149 RRRGRSPRRRTPSPRRRRSQSPRRRRSQSPSSQ 181

The core antigen of hepatitis viruses possesses a carboxyl terminus rich in arginine. On this basis it was predicted that the core antigen would bind DNA. There is some experimental evidence to support this. Length = 182

>gnl|CDD|236779 PRK10864, PRK10864, putative methyltransferase; Provisional

 Score = 42.1 bits (99), Expect = 0.001
 Identities = 13/62 (20%), Positives = 22/62 (35%)

Query: 907 RRRSRRRRSRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRSGKEEEEEEKKK 966
           +R    R  +   R   + R    RR  R  R  + R R+      R   +   +E  +K
Sbjct: 25  KRTHNPRTGKGGGRPSGKSRADGGRRPARDDRNSQSRDRKWEDSPWRTVSRAPGDETPEK 84

Query: 967 EE 968
            +
Sbjct: 85  AD 86

Length = 346

>gnl|CDD|236779 PRK10864, PRK10864, putative methyltransferase; Provisional

 Score = 42.1 bits (99), Expect = 0.001
 Identities = 11/45 (24%), Positives = 16/45 (35%)

Query: 915 SRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRSGKEE 959
           S +R    R  +   R   + R    RR  R  R  + R    E+
Sbjct: 23  SDKRTHNPRTGKGGGRPSGKSRADGGRRPARDDRNSQSRDRKWED 67

Length = 346

>gnl|CDD|236779 PRK10864, PRK10864, putative methyltransferase; Provisional

 Score = 42.1 bits (99), Expect = 0.001
 Identities = 11/47 (23%), Positives = 17/47 (36%)

Query: 900 RRRRRKKRRRSRRRRSRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRR 946
           +R    +  +   R S + R    RR  R  R  + R R+      R
Sbjct: 25  KRTHNPRTGKGGGRPSGKSRADGGRRPARDDRNSQSRDRKWEDSPWR 71

Length = 346

>gnl|CDD|216553 pfam01528, Herpes_glycop, Herpesvirus glycoprotein M

 Score = 41.9 bits (99), Expect = 0.001
 Identities = 13/49 (26%), Positives = 19/49 (38%)

Query: 913 RRSRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRSGKEEEE 961
           R     RRR  R     R  R   +  +RRRR +  +       +EE+ 
Sbjct: 326 RAYLYHRRRSTRYYALVRTVRETVKSYKRRRRSKLSQASESSILREEDS 374

The herpesvirus glycoprotein M (gM) is an integral membrane protein predicted to contain 8 transmembrane segments. Glycoprotein M is not essential for viral replication. Length = 374

>gnl|CDD|215521 PLN02967, PLN02967, kinase

 Score = 42.3 bits (99), Expect = 0.001
 Identities = 22/78 (28%), Positives = 37/78 (47%), Gaps = 8/78 (10%)

Query: 943  RRRRRRRRRRRRSGKEEEEEEKKKEEKKKEEEEKKKKEGKTKKEEKKKEEEEEKKKKKKE 1002
            ++  RR RR+  +   + EEEK         E+K +K  K KK ++  E++  + +    
Sbjct: 111  KKTPRRTRRKAAAASSDVEEEKT--------EKKVRKRRKVKKMDEDVEDQGSESEVSDV 162

Query: 1003 EEKEEEEKKEEEEKEEEE 1020
            EE E     E E +EE +
Sbjct: 163  EESEFVTSLENESEEELD 180

Length = 581

>gnl|CDD|236941 PRK11634, PRK11634, ATP-dependent RNA helicase DeaD; Provisional

 Score = 42.1 bits (99), Expect = 0.001
 Identities = 24/63 (38%), Positives = 27/63 (42%), Gaps = 5/63 (7%)

Query: 873 GGRRRRRRRRSGKEEEEKKKKEGGGGRRRRRRKKRRRSRRRRSRRRRRRRRRRRRRRRRR 932
           GG RR   R  G E     ++EGG      RR+  R   RR S  RR  R  RR     R
Sbjct: 568 GGERRGGGRGFGGE-----RREGGRNFSGERREGGRGDGRRFSGERREGRAPRRDDSTGR 622

Query: 933 RRR 935
           RR 
Sbjct: 623 RRF 625

Length = 629

>gnl|CDD|112952 pfam04162, Gyro_capsid, Gyrovirus capsid protein (VP1)

 Score = 42.1 bits (98), Expect = 0.001
 Identities = 21/45 (46%), Positives = 26/45 (57%)

Query: 900 RRRRRKKRRRSRRRRSRRRRRRRRRRRRRRRRRRRRRRRRRRRRR 944
           RR RR + R    RR R    +R RRR + R RRR+R RRR  R+
Sbjct: 3   RRARRPRGRFYAFRRGRWHHLKRLRRRYKFRHRRRQRYRRRAFRK 47

Gyroviruses are small circular single stranded viruses. This family includes the VP1 protein from the chicken anaemia virus which is the viral capsid protein. Length = 449

>gnl|CDD|112952 pfam04162, Gyro_capsid, Gyrovirus capsid protein (VP1)

 Score = 42.1 bits (98), Expect = 0.001
 Identities = 21/45 (46%), Positives = 26/45 (57%)

Query: 903 RRKKRRRSRRRRSRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRR 947
           RR +R R R    RR R    +R RRR + R RRR+R RRR  R+
Sbjct: 3   RRARRPRGRFYAFRRGRWHHLKRLRRRYKFRHRRRQRYRRRAFRK 47

Gyroviruses are small circular single stranded viruses. This family includes the VP1 protein from the chicken anaemia virus which is the viral capsid protein. Length = 449

>gnl|CDD|221185 pfam11719, Drc1-Sld2, DNA replication and checkpoint protein

 Score = 42.5 bits (100), Expect = 0.001
 Identities = 32/118 (27%), Positives = 53/118 (44%), Gaps = 5/118 (4%)

Query: 821 RRRRKKKEEKKKWKRRGGGRRRRRGKKEEEKKKKKEEEEEGGEKEEEEG----GGGGGRR 876
           RR  KKK +K+   RR   R  R    +E    + +  EE  + +E+      G  GG  
Sbjct: 281 RRVFKKKGQKRT-TRRVKMRPVRAKPSDEPSLPESDIHEEIPKLDEKSLSEFLGYMGGID 339

Query: 877 RRRRRRSGKEEEEKKKKEGGGGRRRRRRKKRRRSRRRRSRRRRRRRRRRRRRRRRRRR 934
                   +E +E+ +K+    ++ R+RK    S   R  + R +R++  + R RRRR
Sbjct: 340 EDDEDEDDEESKEEVEKKQKVKKKPRKRKVNPVSNNFRRLKLRNKRKKGFKGRFRRRR 397

Genome duplication is precisely regulated by cyclin-dependent kinases CDKs, which bring about the onset of S phase by activating replication origins and then prevent relicensing of origins until mitosis is completed. The optimum sequence motif for CDK phosphorylation is S/T-P-K/R-K/R, and Drc1-Sld2 is found to have at least 11 potential phosphorylation sites. Drc1 is required for DNA synthesis and S-M replication checkpoint control. Drc1 associates with Cdc2 and is phosphorylated at the onset of S phase when Cdc2 is activated. Thus Cdc2 promotes DNA replication by phosphorylating Drc1 and regulating its association with Cut5. Sld2 and Sld3 represent the minimal set of S-CDK substrates required for DNA replication. Length = 397

>gnl|CDD|217049 pfam02459, Adeno_terminal, Adenoviral DNA terminal protein

 Score = 42.3 bits (100), Expect = 0.001
 Identities = 33/88 (37%), Positives = 42/88 (47%), Gaps = 24/88 (27%)

Query: 926  RRRRRRR------RRRRRRRRRR---RRRRRRRRRRRRSGKEEEEEEKKKEEKKKEEEEK 976
            R R   R      RRRR    RR   R   RRRRRRR      E EE+++EE++  EEE 
Sbjct: 261  RPRENGRAVTESMRRRRGEMIRRFIDRLPLRRRRRRRPPPSPPEPEEEEEEEEEVPEEE- 319

Query: 977  KKKEGKTKKEEKKKEEEEEKKKKKKEEE 1004
                          EEEEE++++  EEE
Sbjct: 320  --------------EEEEEEEERTFEEE 333

This protein is covalently attached to the terminii of replicating DNA in vivo. Length = 548

>gnl|CDD|223039 PHA03307, PHA03307, transcriptional regulator ICP4; Provisional

 Score = 42.9 bits (101), Expect = 0.001
 Identities = 16/75 (21%), Positives = 18/75 (24%)

Query: 882 RSGKEEEEKKKKEGGGGRRRRRRKKRRRSRRRRSRRRRRRRRRRRRRRRRRRRRRRRRRR 941
             G                     ++R    R          R  RRR R     R RRR
Sbjct: 342 SPGPSPSRSPSPSRPPPPADPSSPRKRPRPSRAPSSPAASAGRPTRRRARAAVAGRARRR 401

Query: 942 RRRRRRRRRRRRRSG 956
               R    R R S 
Sbjct: 402 DATGRFPAGRPRPSP 416

Length = 1352

>gnl|CDD|221931 pfam13136, DUF3984, Protein of unknown function (DUF3984)

 Score = 41.6 bits (98), Expect = 0.001
 Identities = 19/53 (35%), Positives = 22/53 (41%), Gaps = 3/53 (5%)

Query: 886 EEEEKKKKEGGGGRRRRRRKKRRRSRRRRSRRRRRRRRRRRRRRRRRRRRRRR 938
           E+EE  ++E     R R    RR SRR RS          RR  R   RR  R
Sbjct: 160 EDEEDFEREA---AREREHSSRRASRRGRSGYSTPSAALSRRGSRSASRRGSR 209

This family of proteins is functionally uncharacterized. This family of proteins is found in eukaryotes. Proteins in this family are typically between 393 and 442 amino acids in length. Length = 301

>gnl|CDD|225361 COG2801, Tra5, Transposase and inactivated derivatives [DNA replication, recombination, and repair]

 Score = 41.9 bits (97), Expect = 0.001
 Identities = 13/56 (23%), Positives = 22/56 (39%)

Query: 899 RRRRRRKKRRRSRRRRSRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRR 954
            R ++  K  +   R  ++    RR      RR  R RR  R       +R +++R
Sbjct: 4   SRNQQIAKLSKEIVRIRKKLYGSRRLIETLYRRGIRVRRVARLLGVLGLKRLKKKR 59

Length = 232

>gnl|CDD|239286 cd02988, Phd_like_VIAF, Phosducin (Phd)-like family, Viral inhibitor of apoptosis (IAP)-associated factor (VIAF) subfamily; VIAF is a Phd-like protein that functions in caspase activation during apoptosis

 Score = 41.1 bits (97), Expect = 0.001
 Identities = 19/61 (31%), Positives = 31/61 (50%), Gaps = 7/61 (11%)

Query: 966  KEEKKKEEEEKKKKEGKTKKEEKKKEEEEEKKKKKKEEEKEEEEKKEEEEKEEEEKKRRR 1025
            K    KEEEE+  +    +  E   E       KK  +E +EE  +EE+++  EE +R+R
Sbjct: 16   KPPSPKEEEEEALELAIQEAHENALE-------KKLLDELDEELDEEEDDRFLEEYRRKR 68

Query: 1026 I 1026
            +
Sbjct: 69   L 69

It was identified as an IAP binding protein through a screen of a human B-cell library using a prototype IAP. VIAF lacks a consensus IAP binding motif and while it does not function as an IAP antagonist, it still plays a regulatory role in the complete activation of caspases. VIAF itself is a substrate for IAP-mediated ubiquitination, suggesting that it may be a target of IAPs in the prevention of cell death. The similarity of VIAF to Phd points to a potential role distinct from apoptosis regulation. Phd functions as a cytosolic regulator of G protein by specifically binding to G protein betagamma (Gbg)-subunits. The C-terminal domain of Phd adopts a thioredoxin fold, but it does not contain a CXXC motif. Phd interacts with G protein beta mostly through the N-terminal helical domain. Length = 192

>gnl|CDD|239286 cd02988, Phd_like_VIAF, Phosducin (Phd)-like family, Viral inhibitor of apoptosis (IAP)-associated factor (VIAF) subfamily; VIAF is a Phd-like protein that functions in caspase activation during apoptosis

 Score = 40.7 bits (96), Expect = 0.001
 Identities = 15/53 (28%), Positives = 28/53 (52%)

Query: 978  KKEGKTKKEEKKKEEEEEKKKKKKEEEKEEEEKKEEEEKEEEEKKRRRIRRKR 1030
            K     ++EE+  E   ++  +   E+K  +E  EE ++EE+++     RRKR
Sbjct: 16   KPPSPKEEEEEALELAIQEAHENALEKKLLDELDEELDEEEDDRFLEEYRRKR 68

It was identified as an IAP binding protein through a screen of a human B-cell library using a prototype IAP. VIAF lacks a consensus IAP binding motif and while it does not function as an IAP antagonist, it still plays a regulatory role in the complete activation of caspases. VIAF itself is a substrate for IAP-mediated ubiquitination, suggesting that it may be a target of IAPs in the prevention of cell death. The similarity of VIAF to Phd points to a potential role distinct from apoptosis regulation. Phd functions as a cytosolic regulator of G protein by specifically binding to G protein betagamma (Gbg)-subunits. The C-terminal domain of Phd adopts a thioredoxin fold, but it does not contain a CXXC motif. Phd interacts with G protein beta mostly through the N-terminal helical domain. Length = 192

>gnl|CDD|100110 cd05832, Ribosomal_L12p, Ribosomal protein L12p

 Score = 39.4 bits (92), Expect = 0.001
 Identities = 15/25 (60%), Positives = 21/25 (84%)

Query: 991  EEEEEKKKKKKEEEKEEEEKKEEEE 1015
               EEK ++K+EE+K+EEEK+EEEE
Sbjct: 72   AAAEEKAEEKEEEKKKEEEKEEEEE 96

This subfamily includes archaeal L12p, the protein that is functionally equivalent to L7/L12 in bacteria and the P1 and P2 proteins in eukaryotes. L12p is homologous to P1 and P2 but is not homologous to bacterial L7/L12. It is located in the L12 stalk, with proteins L10, L11, and 23S rRNA. L12p is the only protein in the ribosome to occur as multimers, always appearing as sets of dimers. Recent data indicate that most archaeal species contain six copies of L12p (three homodimers), while eukaryotes have four copies (two heterodimers), and bacteria may have four or six copies (two or three homodimers), depending on the species. The organization of proteins within the stalk has been characterized primarily in bacteria, where L7/L12 forms either two or three homodimers and each homodimer binds to the extended C-terminal helix of L10. L7/L12 is attached to the ribosome through L10 and is the only ribosomal protein that does not directly interact with rRNA. Archaeal L12p is believed to function in a similar fashion. However, hybrid ribosomes containing the large subunit from E. coli with an archaeal stalk are able to bind archaeal and eukaryotic elongation factors but not bacterial elongation factors. In several mesophilic and thermophilic archaeal species, the binding of 23S rRNA to protein L11 and to the L10/L12p pentameric complex was found to be temperature-dependent and cooperative. Length = 106

>gnl|CDD|218115 pfam04502, DUF572, Family of unknown function (DUF572)

 Score = 42.0 bits (99), Expect = 0.001
 Identities = 33/164 (20%), Positives = 52/164 (31%), Gaps = 6/164 (3%)

Query: 838  GGRRRRRGKKEEEKKKKKEEEEEGGEKEEEEGGGGGGRRRRRRRRSGKEEEEKKKKEGGG 897
            G  R     K +E+++++ E+E     EEE  G    +   R   S +E E  ++ E   
Sbjct: 103  GATRNYEADKLDEEQEERVEKER----EEELAGDAMKKLENRTADSKREMEVLERLEELK 158

Query: 898  GRRRRRRKKRRRSRRRRSRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRSGK 957
              + RR      S        RR ++             +           RRR      
Sbjct: 159  ELQSRRADVDVNSMLEA--LFRREKKEEEEEEEEDEALIKSLSFGPETEEDRRRADDEDS 216

Query: 958  EEEEEEKKKEEKKKEEEEKKKKEGKTKKEEKKKEEEEEKKKKKK 1001
            E++EE+       K       K     K+   K  E     K K
Sbjct: 217  EDDEEDNDNTPSPKSGSSSPAKPTSILKKSAAKRSEAPSSSKAK 260

Family of eukaryotic proteins with undetermined function. Length = 321

>gnl|CDD|220838 pfam10659, Trypan_glycop_C, Trypanosome variant surface glycoprotein C-terminal domain

 Score = 39.0 bits (91), Expect = 0.001
 Identities = 16/55 (29%), Positives = 27/55 (49%)

Query: 962  EEKKKEEKKKEEEEKKKKEGKTKKEEKKKEEEEEKKKKKKEEEKEEEEKKEEEEK 1016
            ++K+ + K K +E K KK G    +    E   EK K KK+++  ++  K E   
Sbjct: 19   DKKEDDGKCKPKEGKAKKNGAPVTQTAGTETTTEKCKGKKDKKDCKKGCKWEGNT 73

The trypanosome parasite expresses these proteins to evade the immune response. Length = 98

>gnl|CDD|218737 pfam05764, YL1, YL1 nuclear protein

 Score = 41.6 bits (98), Expect = 0.001
 Identities = 28/153 (18%), Positives = 72/153 (47%), Gaps = 10/153 (6%)

Query: 886  EEEEKKKKEGGGGRRRRRRKKRRRSRRRRSRRRRRRRRRRRRRRRRRRRRRRRRRRRRRR 945
            EEE +K+ +     ++++R K +  +    +++++     +  +    R +++  R    
Sbjct: 71   EEEGEKELQREERLKKKKRVKTKAYKEPTKKKKKKDPTAAKSPKAAAPRPKKKSERISWA 130

Query: 946  RRRRRRRRRSGKEEEEEEKKKEEKKKEEEEKKKKEGKTKKEEKKKEEEEEKKKKKKEEEK 1005
                   RR        + K+   ++ +E + +++ K + + +K++E++++K+  +EE  
Sbjct: 131  PTLLDSPRRKSSRSSTVQNKEATHERLKEREIRRK-KIQAKARKRKEKKKEKELTQEERL 189

Query: 1006 EEEEKKEE---------EEKEEEEKKRRRIRRK 1029
             E ++ E          EE+EEE+KK +    K
Sbjct: 190  AEAKETERINLKSLERYEEQEEEKKKAKIQALK 222

The proteins in this family are designated YL1. These proteins have been shown to be DNA-binding and may be a transcription factor. Length = 238

>gnl|CDD|234311 TIGR03685, L12P_arch, 50S ribosomal protein L12P

 Score = 39.3 bits (92), Expect = 0.001
 Identities = 12/28 (42%), Positives = 18/28 (64%)

Query: 845 GKKEEEKKKKKEEEEEGGEKEEEEGGGG 872
               EE+++++EEEEE  E+ EEE   G
Sbjct: 72  AAAAEEEEEEEEEEEEEEEESEEEAMAG 99

This model represents the L12P protein of the large (50S) subunit of the archaeal ribosome. Length = 105

>gnl|CDD|227352 COG5019, CDC3, Septin family protein [Cell division and chromosome partitioning / Cytoskeleton]

 Score = 41.9 bits (99), Expect = 0.001
 Identities = 18/77 (23%), Positives = 43/77 (55%)

Query: 945  RRRRRRRRRRSGKEEEEEEKKKEEKKKEEEEKKKKEGKTKKEEKKKEEEEEKKKKKKEEE 1004
            R  +    + SG+   +E  +    ++E E KKK   K +++EK+ EE E+   ++++E 
Sbjct: 288  RTEKLSGLKNSGEPSLKEIHEARLNEEERELKKKFTEKIREKEKRLEELEQNLIEERKEL 347

Query: 1005 KEEEEKKEEEEKEEEEK 1021
              + E+ +++ ++ E++
Sbjct: 348  NSKLEEIQKKLEDLEKR 364

Length = 373

>gnl|CDD|222389 pfam13801, Metal_resist, Heavy-metal resistance

 Score = 39.5 bits (93), Expect = 0.001
 Identities = 16/60 (26%), Positives = 17/60 (28%)

Query: 895 GGGGRRRRRRKKRRRSRRRRSRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRR 954
           G   R           RR             +RR  R   R  RR  R  RR  R  RR 
Sbjct: 15  GAALRGPGGPGPGGPRRRPGLGPAALALPPEQRRALRAALRAHRREVRPLRRALRAARRE 74

This is a metal-binding protein which is involved in resistance to heavy-metal ions. The protein forms a four-helix hooked hairpin, consisting of two long alpha helices each flanked by a shorter alpha helix. It binds a metal ion in a type-2 like centre. It contains two copies of an LTXXQ motif. Length = 125

>gnl|CDD|222389 pfam13801, Metal_resist, Heavy-metal resistance

 Score = 39.5 bits (93), Expect = 0.001
 Identities = 15/56 (26%), Positives = 18/56 (32%), Gaps = 3/56 (5%)

Query: 907 RRRSRRRRSRRRRRRRRRRRRR---RRRRRRRRRRRRRRRRRRRRRRRRRRSGKEE 959
           R          RRR             +RR  R   R  RR  R  RR  R+ + E
Sbjct: 19  RGPGGPGPGGPRRRPGLGPAALALPPEQRRALRAALRAHRREVRPLRRALRAARRE 74

This is a metal-binding protein which is involved in resistance to heavy-metal ions. The protein forms a four-helix hooked hairpin, consisting of two long alpha helices each flanked by a shorter alpha helix. It binds a metal ion in a type-2 like centre. It contains two copies of an LTXXQ motif. Length = 125

>gnl|CDD|222616 pfam14239, RRXRR, RRXRR protein

 Score = 40.2 bits (95), Expect = 0.001
 Identities = 17/40 (42%), Positives = 23/40 (57%)

Query: 918 RRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRSGK 957
           R ++ + R   RRR RRRRR R+ R R+ R   R+R  G 
Sbjct: 82  RGQQIKERLLSRRRLRRRRRNRKTRYRKPRFLNRKRPKGW 121

This domain is found in bacteria, eukaryotes and viruses, and is approximately 180 amino acids in length. It contains a conserved RRXRR motif. It is often found in association with pfam01844. Length = 174

>gnl|CDD|222977 PHA03089, PHA03089, late transcription factor VLTF-4; Provisional

 Score = 40.6 bits (95), Expect = 0.001
 Identities = 26/64 (40%), Positives = 38/64 (59%), Gaps = 2/64 (3%)

Query: 958  EEEEEEKKKEEKKKEEEEKKKKEGKTKKEEKKKEEEEEKKKKKKEEEKEEEEKKEEEEKE 1017
            E+ E   KK  KKK+   +KKK   TKK +KKK+E+EE  +   EE  + EE +E ++K 
Sbjct: 41   EDVEIPSKKTSKKKKTTPRKKK--TTKKTKKKKKEKEEVPELAAEELSDSEENEENDKKV 98

Query: 1018 EEEK 1021
            + E 
Sbjct: 99   DYEL 102

Length = 191

>gnl|CDD|202427 pfam02841, GBP_C, Guanylate-binding protein, C-terminal domain

 Score = 41.5 bits (98), Expect = 0.001
 Identities = 19/77 (24%), Positives = 40/77 (51%), Gaps = 5/77 (6%)

Query: 957  KEEEEEEKKKEEKKKEEEEKKKKEGKTKKEEKKKEEEEEKKKKKKEEEKEEEEKKEEEE- 1015
            KE  EE   + ++    +EK  +  + K E  + E+E  ++K+K+EE+  E +++  +E 
Sbjct: 185  KEAVEEAILQTDQALTAKEKAIEAERAKAEAAEAEQELLREKQKEEEQMMEAQERSYQEH 244

Query: 1016 ----KEEEEKKRRRIRR 1028
                 E+ E +R ++  
Sbjct: 245  VKQLIEKMEAEREKLLA 261

Transcription of the anti-viral guanylate-binding protein (GBP) is induced by interferon-gamma during macrophage induction. This family contains GBP1 and GPB2, both GTPases capable of binding GTP, GDP and GMP. Length = 297

>gnl|CDD|220648 pfam10243, MIP-T3, Microtubule-binding protein MIP-T3

 Score = 41.4 bits (97), Expect = 0.002
 Identities = 23/76 (30%), Positives = 43/76 (56%)

Query: 955  SGKEEEEEEKKKEEKKKEEEEKKKKEGKTKKEEKKKEEEEEKKKKKKEEEKEEEEKKEEE 1014
            S    +E  K+ E+   +    K K  K  K E  KEEE+EK++ K+E++K++E+ KEE 
Sbjct: 69   SKLSSDEAVKRVEKGGSKGPAAKTKPAKEPKNESGKEEEKEKEQVKEEKKKKKEKPKEEP 128

Query: 1015 EKEEEEKKRRRIRRKR 1030
            +  + +++ +  R  +
Sbjct: 129  KDRKPKEEAKEKRPPK 144

This protein, which interacts with both microtubules and TRAF3 (tumour necrosis factor receptor-associated factor 3), is conserved from worms to humans. The N-terminal region is the microtubule binding domain and is well-conserved; the C-terminal 100 residues, also well-conserved, constitute the coiled-coil region which binds to TRAF3. The central region of the protein is rich in lysine and glutamic acid and carries KKE motifs which may also be necessary for tubulin-binding, but this region is the least well-conserved. Length = 506

>gnl|CDD|234017 TIGR02794, tolA_full, TolA protein

 Score = 41.4 bits (97), Expect = 0.002
 Identities = 28/196 (14%), Positives = 79/196 (40%), Gaps = 18/196 (9%)

Query: 814  RNRRGRRRRRRKKKEEKKKWKRRGGGRRRRRGKKEEEKKKKKEEEEEGGEKEEEEGGGGG 873
            R ++ ++   +K++E +KK +++     ++R  ++  +K+ ++        ++ E     
Sbjct: 54   RIQQQKKPAAKKEQERQKKLEQQAEEAEKQRAAEQARQKELEQRAAAEKAAKQAE----- 108

Query: 874  GRRRRRRRRSGKEEEEKKKKEGGGGRRRRRRKKRRRSRRRRSRRRRRRRRRRRRRRRRRR 933
             +  ++     K+ EE K K+              +++      ++ +   +++     +
Sbjct: 109  -QAAKQAEEKQKQAEEAKAKQ----------AAEAKAKAEAEAEKKAKEEAKKQAEEEAK 157

Query: 934  RRRRRRRRRRRRRRRRRRRRRSGKEEEEEEKKKEEKKKEEEEKKKKEGKTKKEEKKKEEE 993
             +     +++    +++    +  + E + K K E+ K + E  K   K   E   K E 
Sbjct: 158  AKAAAEAKKKAAEAKKKAEAEAKAKAEAKAKAKAEEAKAKAEAAKA--KAAAEAAAKAEA 215

Query: 994  EEKKKKKKEEEKEEEE 1009
            E       E E++ +E
Sbjct: 216  EAAAAAAAEAERKADE 231

TolA couples the inner membrane complex of itself with TolQ and TolR to the outer membrane complex of TolB and OprL (also called Pal). Most of the length of the protein consists of low-complexity sequence that may differ in both length and composition from one species to another, complicating efforts to discriminate TolA (the most divergent gene in the tol-pal system) from paralogs such as TonB. Selection of members of the seed alignment and criteria for setting scoring cutoffs are based largely conserved operon struction. //The Tol-Pal complex is required for maintaining outer membrane integrity. Also involved in transport (uptake) of colicins and filamentous DNA, and implicated in pathogenesis. Transport is energized by the proton motive force. TolA is an inner membrane protein that interacts with periplasmic TolB and with outer membrane porins ompC, phoE and lamB [Transport and binding proteins, Other, Cellular processes, Pathogenesis]. Length = 346

>gnl|CDD|234017 TIGR02794, tolA_full, TolA protein

 Score = 41.4 bits (97), Expect = 0.002
 Identities = 14/70 (20%), Positives = 40/70 (57%), Gaps = 1/70 (1%)

Query: 962  EEKKKEEKKKEEEEKKKKEGKTKKEEKKKEEEEEKKKKKKEEEKE-EEEKKEEEEKEEEE 1020
             ++    +++++   KK++ + KK E++ EE E+++  ++  +KE E+    E+  ++ E
Sbjct: 49   AQQANRIQQQKKPAAKKEQERQKKLEQQAEEAEKQRAAEQARQKELEQRAAAEKAAKQAE 108

Query: 1021 KKRRRIRRKR 1030
            +  ++   K+
Sbjct: 109  QAAKQAEEKQ 118

TolA couples the inner membrane complex of itself with TolQ and TolR to the outer membrane complex of TolB and OprL (also called Pal). Most of the length of the protein consists of low-complexity sequence that may differ in both length and composition from one species to another, complicating efforts to discriminate TolA (the most divergent gene in the tol-pal system) from paralogs such as TonB. Selection of members of the seed alignment and criteria for setting scoring cutoffs are based largely conserved operon struction. //The Tol-Pal complex is required for maintaining outer membrane integrity. Also involved in transport (uptake) of colicins and filamentous DNA, and implicated in pathogenesis. Transport is energized by the proton motive force. TolA is an inner membrane protein that interacts with periplasmic TolB and with outer membrane porins ompC, phoE and lamB [Transport and binding proteins, Other, Cellular processes, Pathogenesis]. Length = 346

>gnl|CDD|224117 COG1196, Smc, Chromosome segregation ATPases [Cell division and chromosome partitioning]

 Score = 41.6 bits (98), Expect = 0.002
 Identities = 42/219 (19%), Positives = 86/219 (39%), Gaps = 15/219 (6%)

Query: 817  RGRRRRRRKKKEEKKKWKRRGGGRRRRRGKKEEEKKKKKEEEEEGGEKEEEEGGGGGGRR 876
                RR    + E +  ++R     +   + EEE ++ +E+ +E  E+ EE         
Sbjct: 803  EEAERRLDALERELESLEQRRERLEQEIEELEEEIEELEEKLDELEEELEEL-------- 854

Query: 877  RRRRRRSGKEEEEKKKKEGGGGRRRRRRKKRRRSRRRRSRRRRRRRRRRRRRRRRRRRRR 936
             +      +E EE + ++       +  ++ +       R         +    + R R 
Sbjct: 855  EKELEELKEELEELEAEKEELEDELKELEEEKEELEEELRELESELAELKEEIEKLRERL 914

Query: 937  RRRRRRRRRRRRRRRRRRSGKEEEEE---EKKKEEKKKEEEEKKKKEG----KTKKEEKK 989
                 +  R            EEE E   E + E + +  EE+ +  G    +  +E ++
Sbjct: 915  EELEAKLERLEVELPELEEELEEEYEDTLETELEREIERLEEEIEALGPVNLRAIEEYEE 974

Query: 990  KEEEEEKKKKKKEEEKEEEEKKEEEEKEEEEKKRRRIRR 1028
             EE  E+ K ++E+ +E +EK  E  +E +++KR R + 
Sbjct: 975  VEERYEELKSQREDLEEAKEKLLEVIEELDKEKRERFKE 1013

Length = 1163

>gnl|CDD|217051 pfam02463, SMC_N, RecF/RecN/SMC N terminal domain

 Score = 41.9 bits (98), Expect = 0.002
 Identities = 21/67 (31%), Positives = 36/67 (53%)

Query: 957  KEEEEEEKKKEEKKKEEEEKKKKEGKTKKEEKKKEEEEEKKKKKKEEEKEEEEKKEEEEK 1016
            KEEEEE  K+    KEE          + EEK++   +++ KK++ EE+++E  +E  E+
Sbjct: 956  KEEEEERNKRLLLAKEELGNVNLMAIAEFEEKEERYNKDELKKERLEEEKKELLREIIEE 1015

Query: 1017 EEEEKKR 1023
              +  K 
Sbjct: 1016 TCQRFKE 1022

This domain is found at the N terminus of SMC proteins. The SMC (structural maintenance of chromosomes) superfamily proteins have ATP-binding domains at the N- and C-termini, and two extended coiled-coil domains separated by a hinge in the middle. The eukaryotic SMC proteins form two kind of heterodimers: the SMC1/SMC3 and the SMC2/SMC4 types. These heterodimers constitute an essential part of higher order complexes, which are involved in chromatin and DNA dynamics. This family also includes the RecF and RecN proteins that are involved in DNA metabolism and recombination. Length = 1162

>gnl|CDD|202096 pfam02029, Caldesmon, Caldesmon

 Score = 41.6 bits (97), Expect = 0.002
 Identities = 40/174 (22%), Positives = 74/174 (42%), Gaps = 33/174 (18%)

Query: 840  RRRRRGKKEEEKKKKKEEEEEGGEKEEEEGGGGGGRRRRRRRRSGKEEEEKKKKEGGGGR 899
             R     ++EEK+ + EEEE+      EE  G     +       K  E    + G  G 
Sbjct: 141  WRDAEECQKEEKEPEPEEEEKPKRGSLEENNGEFMTHKL------KHTENTFSRGGAEGA 194

Query: 900  RRRRRKKRRRSRRRRSRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRSGKEE 959
            +    K+  + ++++          +++R  RR+                        EE
Sbjct: 195  QVEAGKEFEKLKQKQQEAALELEELKKKREERRKVL----------------------EE 232

Query: 960  EEEEKKKEE--KKKEEEEKKKKEGKTKKEEKKKEEEEEKKKKKKEEEKEEEEKK 1011
            EE+ +K+EE  +K  EEE+K++    K+E +++  E  +K++K  E+   E+KK
Sbjct: 233  EEQRRKQEEADRKSREEEEKRRL---KEEIERRRAEAAEKRQKVPEDGLSEDKK 283

Length = 431

>gnl|CDD|235175 PRK03918, PRK03918, chromosome segregation protein; Provisional

 Score = 41.6 bits (98), Expect = 0.002
 Identities = 54/211 (25%), Positives = 100/211 (47%), Gaps = 10/211 (4%)

Query: 824  RKKKEEKKKWKRRGGGRRRRRGKKEEEKKKKKEEEEEGGEKEEEEGGGGGGRRRRRRRRS 883
            + KKEE ++ K+R  G    + +KE E+ +K +EE E    +     G   +  +  +++
Sbjct: 368  KAKKEELERLKKRLTGLTPEKLEKELEELEKAKEEIEEEISKITARIGELKKEIKELKKA 427

Query: 884  GKEEEEKKKKEGGGGR-----RRRRRKKRRRSRRRRSRRRRRRRRRRRRRRRRRRRRRRR 938
             +E ++ K K    GR      R+   +   +  +R  +  +    + R+ R+  R   +
Sbjct: 428  IEELKKAKGKCPVCGRELTEEHRKELLEEYTAELKRIEKELKEIEEKERKLRKELRELEK 487

Query: 939  RRRRRRRRRRRRRRRRSGKEEEEEEKK---KEEKKKEEEEKKKKE--GKTKKEEKKKEEE 993
              ++     + +      KE EE+ KK   +E +KK EE +K KE   K K E K  ++E
Sbjct: 488  VLKKESELIKLKELAEQLKELEEKLKKYNLEELEKKAEEYEKLKEKLIKLKGEIKSLKKE 547

Query: 994  EEKKKKKKEEEKEEEEKKEEEEKEEEEKKRR 1024
             EK ++ K++  E E+K +E E+E  E  + 
Sbjct: 548  LEKLEELKKKLAELEKKLDELEEELAELLKE 578

Length = 880

>gnl|CDD|223496 COG0419, SbcC, ATPase involved in DNA repair [DNA replication, recombination, and repair]

 Score = 42.1 bits (99), Expect = 0.002
 Identities = 32/189 (16%), Positives = 75/189 (39%), Gaps = 7/189 (3%)

Query: 840  RRRRRGKKEEEKKKKKEEEEEGGEKEEEEGGGGGGRRRRRRRRSGKEEEEKKKKEGGGGR 899
             R  R +KEE ++ ++  +E   + +E E          +     + E E ++ E     
Sbjct: 578  LRLLRTRKEELEELRERLKELKKKLKELEERLSQLEELLQSLELSEAENELEEAE----- 632

Query: 900  RRRRRKKRRRSRRRRSRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRSGKEE 959
                 +        ++      +        +        RR  +R     +     +E 
Sbjct: 633  --EELESELEKLNLQAELEELLQAALEELEEKVEELEAEIRRELQRIENEEQLEEKLEEL 690

Query: 960  EEEEKKKEEKKKEEEEKKKKEGKTKKEEKKKEEEEEKKKKKKEEEKEEEEKKEEEEKEEE 1019
            E+ E++ E+ ++E EE  KK G+ ++  ++ E  + + ++ K+E ++ E+  E  E+  E
Sbjct: 691  EQLEEELEQLREELEELLKKLGEIEQLIEELESRKAELEELKKELEKLEKALELLEELRE 750

Query: 1020 EKKRRRIRR 1028
            +  +  +R 
Sbjct: 751  KLGKAGLRA 759

Length = 908

>gnl|CDD|219124 pfam06658, DUF1168, Protein of unknown function (DUF1168)

 Score = 39.3 bits (92), Expect = 0.002
 Identities = 27/115 (23%), Positives = 57/115 (49%), Gaps = 17/115 (14%)

Query: 901  RRRRKKRRRSRRRRSRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRSGKEEE 960
            RRR  +R      + ++       +++R  ++R+   +  ++R +R              
Sbjct: 45   RRREYERLELMDEKWKKETEDEEFQQKREEKKRKDEEKTAKKRAKR-------------- 90

Query: 961  EEEKKKEEKKKEEEEKKKKEGKTKKEEKKKEEEEEKKKKKKEEEKEEEEKKEEEE 1015
               +KK++KKK++++ KK   K +KE  K  EE   ++++ EE+K+EE  +  E+
Sbjct: 91   ---QKKKQKKKKKKKAKKGNKKEEKEGSKSSEESSDEEEEGEEDKQEEPVEIMEK 142

This family consists of several hypothetical eukaryotic proteins of unknown function. Length = 142

>gnl|CDD|233757 TIGR02168, SMC_prok_B, chromosome segregation protein SMC, common bacterial type

 Score = 41.6 bits (98), Expect = 0.002
 Identities = 22/92 (23%), Positives = 46/92 (50%), Gaps = 2/92 (2%)

Query: 941  RRRRRRRRRRRRRRSGKEEEEEEKKKEEKKKEEEEKKKKEGKTKKEEKKK--EEEEEKKK 998
            ++++  R R        EE E + ++ E K +E  ++  E + K EE K+  E  E + +
Sbjct: 302  QQKQILRERLANLERQLEELEAQLEELESKLDELAEELAELEEKLEELKEELESLEAELE 361

Query: 999  KKKEEEKEEEEKKEEEEKEEEEKKRRRIRRKR 1030
            + + E +E E + EE E++ E  + +  + + 
Sbjct: 362  ELEAELEELESRLEELEEQLETLRSKVAQLEL 393

SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]. Length = 1179

>gnl|CDD|222636 pfam14265, DUF4355, Domain of unknown function (DUF4355)

 Score = 38.8 bits (91), Expect = 0.002
 Identities = 21/62 (33%), Positives = 35/62 (56%), Gaps = 2/62 (3%)

Query: 953  RRSGKEEEEEEKKKEEKKKEEEEKKK--KEGKTKKEEKKKEEEEEKKKKKKEEEKEEEEK 1010
            +   KE+ + EKK+EEKK E E+  K   E K + E +K E+E E+ + +    + + E 
Sbjct: 15   KAIAKEKAKWEKKQEEKKSEAEKLAKMSAEEKAEYELEKLEKELEELEAELARRELKAEA 74

Query: 1011 KE 1012
            K+
Sbjct: 75   KK 76

This family of proteins is found in bacteria and viruses. Proteins in this family are typically between 180 and 214 amino acids in length. Length = 125

>gnl|CDD|177283 PHA00451, PHA00451, protein kinase

 Score = 40.9 bits (96), Expect = 0.002
 Identities = 14/82 (17%), Positives = 24/82 (29%), Gaps = 9/82 (10%)

Query: 876 RRRRRRRSGKEEEEKKKKEGGGGRRRRRRKKRRRSRRRRSRRRRRRRRRRRRRRRRRRRR 935
           + R+ +R            G     R+   KRR+  R+   R  +     R    + RR 
Sbjct: 250 KNRKAKRDPN---------GTFQVARKAAMKRRKRNRKLRARNAKELAAMRMEANQIRRN 300

Query: 936 RRRRRRRRRRRRRRRRRRRSGK 957
             R R     +        +  
Sbjct: 301 EPRARMLMGDKHWHNAWLHNNN 322

Length = 362

>gnl|CDD|215774 pfam00183, HSP90, Hsp90 protein

 Score = 42.1 bits (99), Expect = 0.002
 Identities = 27/53 (50%), Positives = 40/53 (75%), Gaps = 3/53 (5%)

Query: 980  EGKTKKEEKKKEEEEEKKKKKKEEEK---EEEEKKEEEEKEEEEKKRRRIRRK 1029
            E + +KE   +EEEEEK++KK+EEEK   +EEE  EEEEKEE++KK ++++  
Sbjct: 28   EKEVEKEVPDEEEEEEKEEKKEEEEKTTDKEEEVDEEEEKEEKKKKTKKVKET 80

Length = 529

>gnl|CDD|215214 PLN02381, PLN02381, valyl-tRNA synthetase

 Score = 42.2 bits (99), Expect = 0.002
 Identities = 28/76 (36%), Positives = 40/76 (52%), Gaps = 8/76 (10%)

Query: 955  SGKEEEEEEKKKEEKKKEEEEKKKKEGKTKKEEKKKEEEEEKKKKKKEEEKEEEEKKEEE 1014
            S  E E E+K   E   EE E+KK     KKEEK KE+E +K K  ++E K + + ++  
Sbjct: 2    SRTESEAEKKILTE---EELERKK-----KKEEKAKEKELKKLKAAQKEAKAKLQAQQAS 53

Query: 1015 EKEEEEKKRRRIRRKR 1030
            +     KK  +  RKR
Sbjct: 54   DGTNVPKKSEKKSRKR 69

Length = 1066

>gnl|CDD|216147 pfam00844, Gemini_coat, Geminivirus coat protein/nuclear export factor BR1 family

 Score = 40.7 bits (96), Expect = 0.002
 Identities = 13/44 (29%), Positives = 19/44 (43%)

Query: 904 RKKRRRSRRRRSRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRR 947
           R++     RR   R   RR   ++R   +R  RR+ R  R  R 
Sbjct: 1   RRRLNFDSRRSRARAPTRRSTNKKRGWSKRPMRRKGRSYRMYRS 44

It has been shown that the 104 N-terminal amino acids of the maize streak virus coat protein bind DNA non- specifically. This family also includes various geminivirus movement proteins that are nuclear export factors or shuttles. One member BR1 facilitates the export of both ds and ss DNA form the nucleus. Length = 244

>gnl|CDD|188306 TIGR03319, RNase_Y, ribonuclease Y

 Score = 41.4 bits (98), Expect = 0.002
 Identities = 30/98 (30%), Positives = 49/98 (50%), Gaps = 15/98 (15%)

Query: 947  RRRRRRRRSGKEEEEEEKKKEEKKKEEEEKKKK---EGKTKKEEKKKEEEEEKKKKKKEE 1003
            R+R   ++ G  EE  ++  EE KKE E  KK+   E K +  + + E E E K+++ E 
Sbjct: 19   RKRIAEKKLGSAEELAKRIIEEAKKEAETLKKEALLEAKEEVHKLRAELERELKERRNEL 78

Query: 1004 EKEE----------EEKKEEEEKEEE--EKKRRRIRRK 1029
            ++ E          + K E  +K+EE  EKK + +  K
Sbjct: 79   QRLERRLLQREETLDRKMESLDKKEENLEKKEKELSNK 116

Members of this family are RNase Y, an endoribonuclease. The member from Bacillus subtilis, YmdA, has been shown to be involved in turnover of yitJ riboswitch [Transcription, Degradation of RNA]. Length = 514

>gnl|CDD|147747 pfam05762, VWA_CoxE, VWA domain containing CoxE-like protein

 Score = 40.4 bits (95), Expect = 0.002
 Identities = 18/42 (42%), Positives = 19/42 (45%)

Query: 917 RRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRSGKE 958
            R          RRRRRR+RRRR  R   RR  R   R G E
Sbjct: 2   ARALAALLLGLARRRRRRKRRRRGGRIDLRRTLRANLRHGGE 43

This family is annotated by SMART as containing a VWA (von Willebrand factor type A) domain. The exact function of this family is unknown. It is found as part of a CO oxidising (Cox) system operon is several bacteria. Length = 223

>gnl|CDD|109943 pfam00906, Hepatitis_core, Hepatitis core antigen

 Score = 40.2 bits (94), Expect = 0.002
 Identities = 14/33 (42%), Positives = 17/33 (51%)

Query: 907 RRRSRRRRSRRRRRRRRRRRRRRRRRRRRRRRR 939
           RRR R  R R    RRRR +  RRRR +    +
Sbjct: 149 RRRGRSPRRRTPSPRRRRSQSPRRRRSQSPSSQ 181

The core antigen of hepatitis viruses possesses a carboxyl terminus rich in arginine. On this basis it was predicted that the core antigen would bind DNA. There is some experimental evidence to support this. Length = 182

>gnl|CDD|109943 pfam00906, Hepatitis_core, Hepatitis core antigen

 Score = 39.8 bits (93), Expect = 0.002
 Identities = 14/33 (42%), Positives = 17/33 (51%)

Query: 913 RRSRRRRRRRRRRRRRRRRRRRRRRRRRRRRRR 945
           RR  R  RRR    RRRR +  RRRR +    +
Sbjct: 149 RRRGRSPRRRTPSPRRRRSQSPRRRRSQSPSSQ 181

The core antigen of hepatitis viruses possesses a carboxyl terminus rich in arginine. On this basis it was predicted that the core antigen would bind DNA. There is some experimental evidence to support this. Length = 182

>gnl|CDD|112952 pfam04162, Gyro_capsid, Gyrovirus capsid protein (VP1)

 Score = 41.7 bits (97), Expect = 0.002
 Identities = 21/41 (51%), Positives = 25/41 (60%)

Query: 913 RRSRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRR 953
           RR+RR R R    RR R    +R RRR + R RRR+R RRR
Sbjct: 3   RRARRPRGRFYAFRRGRWHHLKRLRRRYKFRHRRRQRYRRR 43

Gyroviruses are small circular single stranded viruses. This family includes the VP1 protein from the chicken anaemia virus which is the viral capsid protein. Length = 449

>gnl|CDD|222665 pfam14303, NAM-associated, No apical meristem-associated C-terminal domain

 Score = 39.7 bits (93), Expect = 0.002
 Identities = 28/70 (40%), Positives = 42/70 (60%), Gaps = 6/70 (8%)

Query: 958  EEEEEEKKKEEKKKEEEEKKKKEGKTKKE--EKKKEEEEEKKKKKKEEEKE----EEEKK 1011
            E   E K+ E +KK +E+ ++ + K KKE  EK+KE+EE   K   E EKE    E++K 
Sbjct: 54   ESTAESKRPEGRKKAKEKLRRDKLKAKKEEAEKEKEKEERFMKALAEAEKERAELEKKKA 113

Query: 1012 EEEEKEEEEK 1021
            E +  +EE+K
Sbjct: 114  EAKLMKEEKK 123

This domain is found in a number of different types of plant proteins including NAM-like proteins. Length = 147

>gnl|CDD|217049 pfam02459, Adeno_terminal, Adenoviral DNA terminal protein

 Score = 41.9 bits (99), Expect = 0.002
 Identities = 37/110 (33%), Positives = 44/110 (40%), Gaps = 38/110 (34%)

Query: 923  RRRRRRR------RRRRRRRRRRRRRRRRRRRRRRRRRSGKEEEEEEKKKEEKKKEEEEK 976
            R R   R      RRRR    RR   R   RRRRRRR      E EE+            
Sbjct: 261  RPRENGRAVTESMRRRRGEMIRRFIDRLPLRRRRRRRPPPSPPEPEEE------------ 308

Query: 977  KKKEGKTKKEEKKKEEEEEKKKKKKEEEKEEEEKKEEEEKEEEEKKRRRI 1026
                          EEEEE      E  +EEEE++EEEE+  EE+ R  +
Sbjct: 309  --------------EEEEE------EVPEEEEEEEEEEERTFEEEVRATV 338

This protein is covalently attached to the terminii of replicating DNA in vivo. Length = 548

>gnl|CDD|236722 PRK10590, PRK10590, ATP-dependent RNA helicase RhlE; Provisional

 Score = 41.3 bits (97), Expect = 0.002
 Identities = 13/61 (21%), Positives = 28/61 (45%)

Query: 890 KKKKEGGGGRRRRRRKKRRRSRRRRSRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRR 949
           ++++ GGG  +   R +++   RR     +    +   +  RR    +    ++RRRR R
Sbjct: 391 RQQRGGGGRGQGGGRGQQQGQPRRGEGGAKSASAKPAEKPSRRLGDAKPAGEQQRRRRPR 450

Query: 950 R 950
           +
Sbjct: 451 K 451

Length = 456

>gnl|CDD|236722 PRK10590, PRK10590, ATP-dependent RNA helicase RhlE; Provisional

 Score = 41.3 bits (97), Expect = 0.002
 Identities = 18/66 (27%), Positives = 31/66 (46%), Gaps = 6/66 (9%)

Query: 866 EEEGGGGGGRRRRRRRRSGKEEEEKKKKEGGGGRRRRRRKKRRRSRRRRSRRRRRRRRRR 925
           ++ GGGG G+   R ++ G      + + G GG +    K   +  RR    +    ++R
Sbjct: 392 QQRGGGGRGQGGGRGQQQG------QPRRGEGGAKSASAKPAEKPSRRLGDAKPAGEQQR 445

Query: 926 RRRRRR 931
           RRR R+
Sbjct: 446 RRRPRK 451

Length = 456

>gnl|CDD|218115 pfam04502, DUF572, Family of unknown function (DUF572)

 Score = 40.9 bits (96), Expect = 0.002
 Identities = 26/101 (25%), Positives = 45/101 (44%), Gaps = 30/101 (29%)

Query: 957  KEEEEEEKKKEEKKKEEEEK---KKKEGKTKKEEKKKEEEE------------------- 994
            K +EE+E++ E++++EE      KK E +T   +++ E  E                   
Sbjct: 112  KLDEEQEERVEKEREEELAGDAMKKLENRTADSKREMEVLERLEELKELQSRRADVDVNS 171

Query: 995  --------EKKKKKKEEEKEEEEKKEEEEKEEEEKKRRRIR 1027
                    EKK++++EEE++E   K      E E+ RRR  
Sbjct: 172  MLEALFRREKKEEEEEEEEDEALIKSLSFGPETEEDRRRAD 212

Family of eukaryotic proteins with undetermined function. Length = 321

>gnl|CDD|220838 pfam10659, Trypan_glycop_C, Trypanosome variant surface glycoprotein C-terminal domain

 Score = 38.6 bits (90), Expect = 0.002
 Identities = 11/50 (22%), Positives = 24/50 (48%)

Query: 957  KEEEEEEKKKEEKKKEEEEKKKKEGKTKKEEKKKEEEEEKKKKKKEEEKE 1006
            K +++E+  K + K+ + +K           +   E+ + KK KK+ +K 
Sbjct: 17   KWDKKEDDGKCKPKEGKAKKNGAPVTQTAGTETTTEKCKGKKDKKDCKKG 66

The trypanosome parasite expresses these proteins to evade the immune response. Length = 98

>gnl|CDD|235334 PRK05035, PRK05035, electron transport complex protein RnfC; Provisional

 Score = 42.2 bits (100), Expect = 0.002
 Identities = 17/109 (15%), Positives = 39/109 (35%), Gaps = 5/109 (4%)

Query: 914  RSRRRRRRRRRRRRRR---RRRRRRRRRRRRRRRRRRRRRRRRRSGKE--EEEEEKKKEE 968
            R+  + +++    + R   R+ R  R +  R  R ++    R    K+       + K +
Sbjct: 439  RAIEQEKKKAEEAKARFEARQARLEREKAAREARHKKAAEARAAKDKDAVAAALARVKAK 498

Query: 969  KKKEEEEKKKKEGKTKKEEKKKEEEEEKKKKKKEEEKEEEEKKEEEEKE 1017
            K    +    K G            E +K + +  + E++     + K+
Sbjct: 499  KAAATQPIVIKAGARPDNSAVIAAREARKAQARARQAEKQAAAAADPKK 547

Length = 695

>gnl|CDD|227446 COG5116, RPN2, 26S proteasome regulatory complex component [Posttranslational modification, protein turnover, chaperones]

 Score = 42.2 bits (99), Expect = 0.002
 Identities = 13/65 (20%), Positives = 28/65 (43%), Gaps = 4/65 (6%)

Query: 943  RRRRRRRRRRRRSGKEEEEEEKKKEEKKKEEEEKKKKEGKTKKEEKKKEEEEEKKKKKKE 1002
            +   R +++ +  G  ++E + +    + E E    K+    +EEK  +       KKK+
Sbjct: 792  KAAARAKQKPKEKGPNDKEIKIESPSVETEGERCTIKQ----REEKGIDAPAILNVKKKK 847

Query: 1003 EEKEE 1007
              K +
Sbjct: 848  PYKVD 852

Length = 926

>gnl|CDD|215656 pfam00012, HSP70, Hsp70 protein

 Score = 41.8 bits (99), Expect = 0.002
 Identities = 26/80 (32%), Positives = 40/80 (50%), Gaps = 13/80 (16%)

Query: 957  KEEEEEEKKKEEKKKEEEEKKKKEGKTKKE--------EKKKEEEEEK-----KKKKKEE 1003
             +E E   K  E+   E++K+K+  + K E        EK  +EE +K     KKK +E 
Sbjct: 503  DDEIERMVKDAEEYAAEDKKRKERIEAKNEAEEYVYSLEKSLKEEGDKLPEADKKKVEEA 562

Query: 1004 EKEEEEKKEEEEKEEEEKKR 1023
             +  +E+ E E+KEE E K 
Sbjct: 563  IEWLKEELEGEDKEEIEAKT 582

Hsp70 chaperones help to fold many proteins. Hsp70 assisted folding involves repeated cycles of substrate binding and release. Hsp70 activity is ATP dependent. Hsp70 proteins are made up of two regions: the amino terminus is the ATPase domain and the carboxyl terminus is the substrate binding region. Length = 598

>gnl|CDD|217393 pfam03154, Atrophin-1, Atrophin-1 family

 Score = 42.0 bits (98), Expect = 0.002
 Identities = 17/41 (41%), Positives = 30/41 (73%)

Query: 985  KEEKKKEEEEEKKKKKKEEEKEEEEKKEEEEKEEEEKKRRR 1025
            K  KK+EE  EK K++ E++  EE ++E+E+++E E++R R
Sbjct: 576  KLAKKREEAVEKAKREAEQKAREEREREKEKEKERERERER 616

Atrophin-1 is the protein product of the dentatorubral-pallidoluysian atrophy (DRPLA) gene. DRPLA OMIM:125370 is a progressive neurodegenerative disorder. It is caused by the expansion of a CAG repeat in the DRPLA gene on chromosome 12p. This results in an extended polyglutamine region in atrophin-1, that is thought to confer toxicity to the protein, possibly through altering its interactions with other proteins. The expansion of a CAG repeat is also the underlying defect in six other neurodegenerative disorders, including Huntington's disease. One interaction of expanded polyglutamine repeats that is thought to be pathogenic is that with the short glutamine repeat in the transcriptional coactivator CREB binding protein, CBP. This interaction draws CBP away from its usual nuclear location to the expanded polyglutamine repeat protein aggregates that are characteristic of the polyglutamine neurodegenerative disorders. This interferes with CBP-mediated transcription and causes cytotoxicity. Length = 979

>gnl|CDD|148630 pfam07133, Merozoite_SPAM, Merozoite surface protein (SPAM)

 Score = 39.8 bits (93), Expect = 0.002
 Identities = 21/68 (30%), Positives = 43/68 (63%), Gaps = 6/68 (8%)

Query: 957  KEEEEEEKKKEEKKKEEEEKKKKEGKTKKEEKKKEEEEEKKKKKKEEEKEEEEKKEEEEK 1016
            KE E+ + +K+E  +EEEE+ ++E +  ++ + +EE  E      +EE+EEE++++  + 
Sbjct: 38   KENEDVKDEKQEDDEEEEEEDEEEIEEPEDIEDEEEIVE------DEEEEEEDEEDNVDL 91

Query: 1017 EEEEKKRR 1024
            ++ EKK  
Sbjct: 92   KDIEKKNI 99

This family consists of several Plasmodium falciparum SPAM (secreted polymorphic antigen associated with merozoites) proteins. Variation among SPAM alleles is the result of deletions and amino acid substitutions in non-repetitive sequences within and flanking the alanine heptad-repeat domain. Heptad repeats in which the a and d position contain hydrophobic residues generate amphipathic alpha-helices which give rise to helical bundles or coiled-coil structures in proteins. SPAM is an example of a P. falciparum antigen in which a repetitive sequence has features characteristic of a well-defined structural element. Length = 164

>gnl|CDD|220684 pfam10310, DUF2413, Protein of unknown function (DUF2413)

 Score = 41.7 bits (98), Expect = 0.002
 Identities = 13/62 (20%), Positives = 21/62 (33%)

Query: 957  KEEEEEEKKKEEKKKEEEEKKKKEGKTKKEEKKKEEEEEKKKKKKEEEKEEEEKKEEEEK 1016
            +       KK  K  E      +E   K  +  +       K K    + EEE++ EE  
Sbjct: 58   RPGTPRNPKKSSKPTESSAASSEEKPAKPRKSAESTRSSHPKSKAPSTESEEEEEPEETP 117

Query: 1017 EE 1018
            + 
Sbjct: 118  DP 119

This is a family of proteins conserved in fungi. The function is not known. Length = 436

>gnl|CDD|204414 pfam10211, Ax_dynein_light, Axonemal dynein light chain

 Score = 40.3 bits (95), Expect = 0.002
 Identities = 18/57 (31%), Positives = 35/57 (61%)

Query: 969  KKKEEEEKKKKEGKTKKEEKKKEEEEEKKKKKKEEEKEEEEKKEEEEKEEEEKKRRR 1025
            +K  + E+ K E + + ++ ++E+EE +K+  + E K E  +K EEE+ + E+KR  
Sbjct: 113  RKALQAEQGKSELEQEIKKLEEEKEELEKRVAELEAKLEAIEKREEEERQIEEKRHA 169

Axonemal dynein light chain proteins play a dynamic role in flagellar and cilia motility. Eukaryotic cilia and flagella are complex organelles consisting of a core structure, the axoneme, which is composed of nine microtubule doublets forming a cylinder that surrounds a pair of central singlet microtubules. This ultra-structural arrangement seems to be one of the most stable micro-tubular assemblies known and is responsible for the flagellar and ciliary movement of a large number of organisms ranging from protozoan to mammals. This light chain interacts directly with the N-terminal half of the heavy chains. Length = 189

>gnl|CDD|219913 pfam08576, DUF1764, Eukaryotic protein of unknown function (DUF1764)

 Score = 38.2 bits (89), Expect = 0.002
 Identities = 21/65 (32%), Positives = 39/65 (60%), Gaps = 4/65 (6%)

Query: 966  KEEKKKEEEEKKKKE----GKTKKEEKKKEEEEEKKKKKKEEEKEEEEKKEEEEKEEEEK 1021
            KEEKK E+ +K+  +       K+++KKK   +  + K  ++ +++++KK+E  +  EE 
Sbjct: 1    KEEKKNEKTDKRDIDDIFSNIKKRKKKKKRTAKTARPKATKKGQKKDKKKDEFPEFPEES 60

Query: 1022 KRRRI 1026
            KRRR 
Sbjct: 61   KRRRT 65

This is a family of eukaryotic proteins of unknown function. This family contains many hypothetical proteins. Length = 98

>gnl|CDD|220413 pfam09805, Nop25, Nucleolar protein 12 (25kDa)

 Score = 39.2 bits (92), Expect = 0.002
 Identities = 26/103 (25%), Positives = 51/103 (49%)

Query: 906  KRRRSRRRRSRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRSGKEEEEEEKK 965
            KR++ RR++++   + + R  R   R+R R  R++   ++ + R+   +  +EE ++E+ 
Sbjct: 29   KRKQQRRKKAQEEAKEKEREERIEERKRIREERKQELEKQLKERKEALKLLEEENDDEED 88

Query: 966  KEEKKKEEEEKKKKEGKTKKEEKKKEEEEEKKKKKKEEEKEEE 1008
             E +  E+ E  + EG  +      EEE   + K K     EE
Sbjct: 89   AETEDTEDVEDDEWEGFPEPTVTDYEEEYIDEDKYKTTVTVEE 131

Members of this family of proteins are part of the yeast nuclear pore complex-associated pre-60S ribosomal subunit. The family functions as a highly conserved exonuclease that is required for the 5'-end maturation of 5.8S and 25S rRNAs, demonstrating that 5'-end processing also has a redundant pathway. Nop25 binds late pre-60S ribosomes, accompanying them from the nucleolus to the nuclear periphery; and there is evidence for both physical and functional links between late 60S subunit processing and export. Length = 134

>gnl|CDD|225177 COG2268, COG2268, Uncharacterized protein conserved in bacteria [Function unknown]

 Score = 41.7 bits (98), Expect = 0.002
 Identities = 17/124 (13%), Positives = 44/124 (35%), Gaps = 2/124 (1%)

Query: 903  RRKKRRRSRRRRSRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRSGKEEEEE 962
             + +  +     +       +   RR   +      +  +  + +  +  + +   E  E
Sbjct: 262  EQTREVKIILAETEAEVAAWKAETRREAEQAEILAEQAIQEEKAQAEQEVQHAKALEARE 321

Query: 963  EKKKEEKKKEEEEKKKKEGKTKKEEKKKEEEEEKKKKKKEEEKE--EEEKKEEEEKEEEE 1020
             +    ++++E E + +E        +++ +EE K      E    + E   E  +E EE
Sbjct: 322  MRVGLIERQKETELEPQERSYFINAAQRQAQEEAKAAANIAEAIGAQAEAAVETARETEE 381

Query: 1021 KKRR 1024
             +R 
Sbjct: 382  AERA 385

Length = 548

>gnl|CDD|173502 PTZ00266, PTZ00266, NIMA-related protein kinase; Provisional

 Score = 41.6 bits (97), Expect = 0.002
 Identities = 28/120 (23%), Positives = 47/120 (39%)

Query: 852 KKKKEEEEEGGEKEEEEGGGGGGRRRRRRRRSGKEEEEKKKKEGGGGRRRRRRKKRRRSR 911
           K  ++  ++G        G  GGR  +      + E+E   ++    +   +++  R  R
Sbjct: 406 KDDRKYPQDGATHCHAVNGHYGGRVDKDHAERARIEKENAHRKALEMKILEKKRIERLER 465

Query: 912 RRRSRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRSGKEEEEEEKKKEEKKK 971
             R R  R R  R  R R  R R  R R  R R  R R  R    + +  E  + E+ ++
Sbjct: 466 EERERLERERMERIERERLERERLERERLERDRLERDRLDRLERERVDRLERDRLEKARR 525

Length = 1021

>gnl|CDD|236081 PRK07735, PRK07735, NADH dehydrogenase subunit C; Validated

 Score = 41.5 bits (97), Expect = 0.002
 Identities = 24/95 (25%), Positives = 42/95 (44%)

Query: 930  RRRRRRRRRRRRRRRRRRRRRRRRRSGKEEEEEEKKKEEKKKEEEEKKKKEGKTKKEEKK 989
             ++   RR +   R+R   +     S  EEE  EK+K   K ++   ++ + +     K 
Sbjct: 10   LKKEAARRAKEEARKRLVAKHGAEISKLEEENREKEKALPKNDDMTIEEAKRRAAAAAKA 69

Query: 990  KEEEEEKKKKKKEEEKEEEEKKEEEEKEEEEKKRR 1024
            K     K+K++  EE  EEEK + + K     K +
Sbjct: 70   KAAALAKQKREGTEEVTEEEKAKAKAKAAAAAKAK 104

Length = 430

>gnl|CDD|227466 COG5137, COG5137, Histone chaperone involved in gene silencing [Transcription / Chromatin structure and dynamics]

 Score = 40.7 bits (95), Expect = 0.002
 Identities = 27/74 (36%), Positives = 38/74 (51%), Gaps = 6/74 (8%)

Query: 956  GKEEEEEEKKKEEKKKE------EEEKKKKEGKTKKEEKKKEEEEEKKKKKKEEEKEEEE 1009
            G+EEEE+E+   +   E      EEE+++ EG    E+    E E   KK+ EEE+ EEE
Sbjct: 187  GREEEEDEEVGSDSYGEGNRELNEEEEEEAEGSDDGEDVVDYEGERIDKKQGEEEEMEEE 246

Query: 1010 KKEEEEKEEEEKKR 1023
                 E E EE+  
Sbjct: 247  VINLFEIEWEEESP 260

Length = 279

>gnl|CDD|218258 pfam04774, HABP4_PAI-RBP1, Hyaluronan / mRNA binding family

 Score = 38.2 bits (89), Expect = 0.002
 Identities = 33/99 (33%), Positives = 47/99 (47%), Gaps = 10/99 (10%)

Query: 929  RRRRRRRRRRRRRRRRRRRRRRRRRRSGKEEEEEEKKKEEKKKEEEEKKKKEGKTKKEEK 988
             RR   R     R    +R    R   G  ++E  +  EE+ +EEE+ + +E +  +EE 
Sbjct: 1    GRREFDRHSGSGRGGEDKREGAGRGNWGSVKDEIAELTEEQGEEEEKNEVEEKQAVEEEA 60

Query: 989  KKEEEEEKKKKKKEEEKEEEEKKE----EEEKEEEEKKR 1023
             KE   E      EEE EEEE KE    E EK  +EK++
Sbjct: 61   NKEGVVE------EEEVEEEEDKEMTLEEYEKALQEKRK 93

This family includes the HABP4 family of hyaluronan-binding proteins, and the PAI-1 mRNA-binding protein, PAI-RBP1. HABP4 has been observed to bind hyaluronan (a glucosaminoglycan), but it is not known whether this is its primary role in vivo. It has also been observed to bind RNA, but with a lower affinity than that for hyaluronan. PAI-1 mRNA-binding protein specifically binds the mRNA of type-1 plasminogen activator inhibitor (PAI-1), and is thought to be involved in regulation of mRNA stability. However, in both cases, the sequence motifs predicted to be important for ligand binding are not conserved throughout the family, so it is not known whether members of this family share a common function. Length = 106

>gnl|CDD|173412 PTZ00121, PTZ00121, MAEBL; Provisional

 Score = 41.3 bits (96), Expect = 0.003
 Identities = 27/101 (26%), Positives = 46/101 (45%), Gaps = 3/101 (2%)

Query: 932  RRRRRRRRRRRRRRRRRRRRRRRSGKEEEEEEKKKEEKKKEEEEKKKKEGKTKKEEKKKE 991
            +   +    +    +   +      KE+   ++  EE   + EE KK E    +E +K E
Sbjct: 1059 KAEAKAHVGQDEGLKPSYKDFDFDAKEDNRADEATEEAFGKAEEAKKTETGKAEEARKAE 1118

Query: 992  E---EEEKKKKKKEEEKEEEEKKEEEEKEEEEKKRRRIRRK 1029
            E   + E  +K +E  K E+ +K EE ++ E+ KR  I RK
Sbjct: 1119 EAKKKAEDARKAEEARKAEDARKAEEARKAEDAKRVEIARK 1159

Length = 2084

>gnl|CDD|233496 TIGR01622, SF-CC1, splicing factor, CC1-like family

 Score = 41.0 bits (96), Expect = 0.003
 Identities = 27/112 (24%), Positives = 35/112 (31%), Gaps = 22/112 (19%)

Query: 839 GRRRRRGKKEEEKKKKKEEEEEGGEKEEEEGGGGGGRRRRRRRRSGKEEEEKKKKEGGGG 898
             R R   +     ++ ++  E   +          R R RRRR                
Sbjct: 1   RYRDRERGRLRNDTRRSDKGRERSRRRSRS------RDRSRRRRD--------------- 39

Query: 899 RRRRRRKKRRRSRRRRSRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRR 950
            R   R +R RSR R   R  R R  R  RR  RR  R  +       R  R
Sbjct: 40  -RDYYRGRRGRSRSRSPNRYYRPRGDRSYRRDDRRSGRNTKEPLTEAERDDR 90

This model represents a subfamily of RNA splicing factors including the Pad-1 protein (N. crassa), CAPER (M. musculus) and CC1.3 (H.sapiens). These proteins are characterized by an N-terminal arginine-rich, low complexity domain followed by three (or in the case of 4 H. sapiens paralogs, two) RNA recognition domains (rrm: pfam00706). These splicing factors are closely related to the U2AF splicing factor family (TIGR01642). A homologous gene from Plasmodium falciparum was identified in the course of the analysis of that genome at TIGR and was included in the seed. Length = 457

>gnl|CDD|233496 TIGR01622, SF-CC1, splicing factor, CC1-like family

 Score = 41.0 bits (96), Expect = 0.003
 Identities = 14/90 (15%), Positives = 34/90 (37%)

Query: 934  RRRRRRRRRRRRRRRRRRRRRSGKEEEEEEKKKEEKKKEEEEKKKKEGKTKKEEKKKEEE 993
            R R R R R R   RR  + R         + +  ++++ +  + + G+++     +   
Sbjct: 1    RYRDRERGRLRNDTRRSDKGRERSRRRSRSRDRSRRRRDRDYYRGRRGRSRSRSPNRYYR 60

Query: 994  EEKKKKKKEEEKEEEEKKEEEEKEEEEKKR 1023
                +  + +++      +E   E E   R
Sbjct: 61   PRGDRSYRRDDRRSGRNTKEPLTEAERDDR 90

This model represents a subfamily of RNA splicing factors including the Pad-1 protein (N. crassa), CAPER (M. musculus) and CC1.3 (H.sapiens). These proteins are characterized by an N-terminal arginine-rich, low complexity domain followed by three (or in the case of 4 H. sapiens paralogs, two) RNA recognition domains (rrm: pfam00706). These splicing factors are closely related to the U2AF splicing factor family (TIGR01642). A homologous gene from Plasmodium falciparum was identified in the course of the analysis of that genome at TIGR and was included in the seed. Length = 457

>gnl|CDD|233191 TIGR00927, 2A1904, K+-dependent Na+/Ca+ exchanger

 Score = 41.5 bits (97), Expect = 0.003
 Identities = 32/176 (18%), Positives = 59/176 (33%)

Query: 845  GKKEEEKKKKKEEEEEGGEKEEEEGGGGGGRRRRRRRRSGKEEEEKKKKEGGGGRRRRRR 904
            G+  EE   + E+E E   K E E  G     R+  +    E E K+    G        
Sbjct: 657  GENGEESGGEAEQEGETETKGENESEGEIPAERKGEQEGEGEIEAKEADHKGETEAEEVE 716

Query: 905  KKRRRSRRRRSRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRSGKEEEEEEK 964
             +                                 +        R+     G+ E E ++
Sbjct: 717  HEGETEAEGTEDEGEIETGEEGEEVEDEGEGEAEGKHEVETEGDRKETEHEGETEAEGKE 776

Query: 965  KKEEKKKEEEEKKKKEGKTKKEEKKKEEEEEKKKKKKEEEKEEEEKKEEEEKEEEE 1020
             ++E + +  E  + +G    E K + E E +  +K E E + E + ++ E ++E 
Sbjct: 777  DEDEGEIQAGEDGEMKGDEGAEGKVEHEGETEAGEKDEHEGQSETQADDTEVKDET 832

[Transport and binding proteins, Cations and iron carrying compounds]. Length = 1096

>gnl|CDD|219061 pfam06495, Transformer, Fruit fly transformer protein

 Score = 39.3 bits (91), Expect = 0.003
 Identities = 25/100 (25%), Positives = 42/100 (42%)

Query: 879 RRRRSGKEEEEKKKKEGGGGRRRRRRKKRRRSRRRRSRRRRRRRRRRRRRRRRRRRRRRR 938
           R  R  + +  KK+K        R R + R  R+R+++  R     R RR R R R +  
Sbjct: 8   RSPRDTRRDSRKKEKIPYFADEVRERDRVRNLRQRKTQSTRPTTSHRGRRTRSRSRSQSA 67

Query: 939 RRRRRRRRRRRRRRRRSGKEEEEEEKKKEEKKKEEEEKKK 978
            R   +RR R R R R+  +         E+++    + +
Sbjct: 68  ERNSCQRRHRSRSRSRNRSDSRHRSTSSTERRRRSRSRSR 107

This family consists of transformer proteins from several Drosophila species and also from Ceratitis capitata (Mediterranean fruit fly). The transformer locus (tra) produces an RNA processing protein that alternatively splices the doublesex pre-mRNA in the sex determination hierarchy of Drosophila melanogaster. Length = 182

>gnl|CDD|233757 TIGR02168, SMC_prok_B, chromosome segregation protein SMC, common bacterial type

 Score = 41.6 bits (98), Expect = 0.003
 Identities = 31/149 (20%), Positives = 54/149 (36%), Gaps = 5/149 (3%)

Query: 876  RRRRRRRSGKEEEEKKKKEGGGGRRRRRRKKRRRSRRRRSRRRRRRRRRRRRRRRRRRRR 935
            RRR      ++ EE ++K     +     +K          + R+      R+    R+ 
Sbjct: 675  RRREIEELEEKIEELEEKIAELEKALAELRKELEELEEELEQLRKELEELSRQISALRKD 734

Query: 936  RRRRRRRRRRRRRRRRRRRSGKEEEEEEKKKEEKKKEEEEKKKKEGKTKKEEKKKEEEEE 995
              R      +   R  +      E E E ++ E++ EE E++  E      E + EE E 
Sbjct: 735  LARLEAEVEQLEERIAQLSKELTELEAEIEELEERLEEAEEELAEA-----EAEIEELEA 789

Query: 996  KKKKKKEEEKEEEEKKEEEEKEEEEKKRR 1024
            + ++ KEE K   E  +E   E       
Sbjct: 790  QIEQLKEELKALREALDELRAELTLLNEE 818

SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]. Length = 1179

>gnl|CDD|222571 pfam14153, Spore_coat_CotO, Spore coat protein CotO

 Score = 39.4 bits (92), Expect = 0.003
 Identities = 26/85 (30%), Positives = 47/85 (55%), Gaps = 6/85 (7%)

Query: 950  RRRRRSGKEEEEEEKKKEEKKKEEEEKKKKEGKTKKEEKKKEEEE------EKKKKKKEE 1003
              ++   KEEE+E   +  K KEEE+K + E   K++E  + E E      EK++  +EE
Sbjct: 32   IIKKADEKEEEKENSDEHVKSKEEEQKIEYEEAEKEKEAGEPEREDIAEQQEKEEIAQEE 91

Query: 1004 EKEEEEKKEEEEKEEEEKKRRRIRR 1028
            EKEEE +  ++++    K+++  + 
Sbjct: 92   EKEEEAEDVKQQEVFSFKRKKPFKE 116

Bacillus spores are protected by a protein shell consisting of over 50 different polypeptides, known as the coat. This family of proteins has an important morphogenetic role in coat assembly, it is involved in the assembly of at least 5 different coat proteins including CotB, CotG, CotS, CotSA and CotW. It is likely to act at a late stage of coat assembly. Length = 185

>gnl|CDD|219563 pfam07767, Nop53, Nop53 (60S ribosomal biogenesis)

 Score = 40.8 bits (96), Expect = 0.003
 Identities = 19/75 (25%), Positives = 37/75 (49%)

Query: 956  GKEEEEEEKKKEEKKKEEEEKKKKEGKTKKEEKKKEEEEEKKKKKKEEEKEEEEKKEEEE 1015
             ++E + EKK++E ++ EE+K +K         +  E   ++     EE+ ++E   E  
Sbjct: 203  YEKEVKAEKKRQELERVEEKKLEKMAPEASRLDEMSEGLLEESDDDGEEESDDESAWEGF 262

Query: 1016 KEEEEKKRRRIRRKR 1030
            + E E   + +R KR
Sbjct: 263  ESEYEPINKPVRPKR 277

This nucleolar family of proteins are involved in 60S ribosomal biogenesis. They are specifically involved in the processing beyond the 27S stage of 25S rRNA maturation. This family contains sequences that bear similarity to the glioma tumour suppressor candidate region gene 2 protein (p60). This protein has been found to interact with herpes simplex type 1 regulatory proteins. Length = 387

>gnl|CDD|220271 pfam09507, CDC27, DNA polymerase subunit Cdc27

 Score = 41.0 bits (96), Expect = 0.003
 Identities = 17/67 (25%), Positives = 35/67 (52%), Gaps = 1/67 (1%)

Query: 955  SGKEEEEEEKKKEEKKKEEEEKKKKEGKTKKEEKKKEEEEEKKKKKKEEEKEEEEKKEEE 1014
            S  +EE EE+  +     E+E  +  G   ++E + E +   ++   EEE EE+EK++ +
Sbjct: 238  STVKEESEEESGKRDVILEDESAEPTGL-DEDEDEDEPKPSGERSDSEEETEEKEKEKRK 296

Query: 1015 EKEEEEK 1021
              ++  +
Sbjct: 297  RLKKMME 303

This protein forms the C subunit of DNA polymerase delta. It carries the essential residues for binding to the Pol1 subunit of polymerase alpha, from residues 293-332, which are characterized by the motif D--G--VT, referred to as the DPIM motif. The first 160 residues of the protein form the minimal domain for binding to the B subunit, Cdc1, of polymerase delta, the final 10 C-terminal residues, 362-372, being the DNA sliding clamp, PCNA, binding motif. Length = 427

>gnl|CDD|109943 pfam00906, Hepatitis_core, Hepatitis core antigen

 Score = 39.8 bits (93), Expect = 0.003
 Identities = 14/33 (42%), Positives = 17/33 (51%)

Query: 911 RRRRSRRRRRRRRRRRRRRRRRRRRRRRRRRRR 943
           RRR    RRR    RRRR +  RRRR +    +
Sbjct: 149 RRRGRSPRRRTPSPRRRRSQSPRRRRSQSPSSQ 181

The core antigen of hepatitis viruses possesses a carboxyl terminus rich in arginine. On this basis it was predicted that the core antigen would bind DNA. There is some experimental evidence to support this. Length = 182

>gnl|CDD|115057 pfam06375, BLVR, Bovine leukaemia virus receptor (BLVR)

 Score = 41.2 bits (96), Expect = 0.003
 Identities = 17/123 (13%), Positives = 49/123 (39%), Gaps = 3/123 (2%)

Query: 842 RRRGKKEEEKKKKKEEEEEGGEKEEEEGGGGGGRRRRRRRRSGKEEEEKKKKEGGGGRRR 901
           ++  KKE+++K+K+ ++++  E E  +              S  E +E        G   
Sbjct: 200 KKPKKKEKKEKEKERDKDKKKEVEGFKSLLLALDDSPASAASVAEADEASLANTVSGTAP 259

Query: 902 RRRKKRRRSRRRRSRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRR---RSGKE 958
                  +       ++  + +++++R+ +  ++++++    R            ++G  
Sbjct: 260 DSEPDEPKDAEAEETKKSPKHKKKKQRKEKEEKKKKKKHHHHRCHHSDGGAEQPVQNGAV 319

Query: 959 EEE 961
           EEE
Sbjct: 320 EEE 322

This family consists of several bovine specific leukaemia virus receptors which are thought to function as transmembrane proteins, although their exact function is unknown. Length = 561

>gnl|CDD|240388 PTZ00372, PTZ00372, endonuclease 4-like protein; Provisional

 Score = 40.9 bits (96), Expect = 0.003
 Identities = 18/73 (24%), Positives = 40/73 (54%)

Query: 957  KEEEEEEKKKEEKKKEEEEKKKKEGKTKKEEKKKEEEEEKKKKKKEEEKEEEEKKEEEEK 1016
            KE++  E KK+ +KK++++K+KKE K++ E K   +  +K KK K++  + +  ++ +  
Sbjct: 59   KEDKNNESKKKSEKKKKKKKEKKEPKSEGETKLGFKTPKKSKKTKKKPPKPKPNEDVDNA 118

Query: 1017 EEEEKKRRRIRRK 1029
              +  +       
Sbjct: 119  FNKIAELAEKSNV 131

Length = 413

>gnl|CDD|215521 PLN02967, PLN02967, kinase

 Score = 41.2 bits (96), Expect = 0.003
 Identities = 24/98 (24%), Positives = 39/98 (39%), Gaps = 14/98 (14%)

Query: 947  RRRRRRRRSGKEEEEEEKKKEEKKKEEEEKKKKEGKTKKEEKKKEEE------------- 993
             R++       +EE +E     KKK     K+   KT  E  +  EE             
Sbjct: 48   SRKKIESALAVDEEPDENGAVSKKKPTRSVKRATKKTVVEISEPLEEGSELVVNEDAALD 107

Query: 994  -EEKKKKKKEEEKEEEEKKEEEEKEEEEKKRRRIRRKR 1030
             E KK  ++   K      + EE++ E+K R+R + K+
Sbjct: 108  KESKKTPRRTRRKAAAASSDVEEEKTEKKVRKRRKVKK 145

Length = 581

>gnl|CDD|217348 pfam03064, U79_P34, HSV U79 / HCMV P34

 Score = 39.9 bits (93), Expect = 0.003
 Identities = 21/80 (26%), Positives = 42/80 (52%), Gaps = 5/80 (6%)

Query: 939  RRRRRRRRRRRRRRRRSGKEEEEEEKKKEEKKKEEEEK---KKKEGKTKKEEKKKEEE-- 993
             R+R  +++ +RR   S K +E+  KK+EEK++ +E+K           +     ++E  
Sbjct: 159  HRKRSGKQKEKRRVEDSQKHKEDRRKKQEEKRRNDEDKRPGGGGGSSGGQSGLSTKDEPP 218

Query: 994  EEKKKKKKEEEKEEEEKKEE 1013
            +EK++K  + E+  E +  E
Sbjct: 219  KEKRQKHHDPERRLEPQSHE 238

This family represents herpes virus protein U79 and cytomegalovirus early phosphoprotein P34 (UL112). Length = 238

>gnl|CDD|112952 pfam04162, Gyro_capsid, Gyrovirus capsid protein (VP1)

 Score = 40.9 bits (95), Expect = 0.003
 Identities = 21/45 (46%), Positives = 26/45 (57%)

Query: 911 RRRRSRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRS 955
           R RR R R    RR R    +R RRR + R RRR+R RRR  R++
Sbjct: 4   RARRPRGRFYAFRRGRWHHLKRLRRRYKFRHRRRQRYRRRAFRKA 48

Gyroviruses are small circular single stranded viruses. This family includes the VP1 protein from the chicken anaemia virus which is the viral capsid protein. Length = 449

>gnl|CDD|221041 pfam11241, DUF3043, Protein of unknown function (DUF3043)

 Score = 39.5 bits (93), Expect = 0.003
 Identities = 15/49 (30%), Positives = 21/49 (42%)

Query: 914 RSRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRSGKEEEEE 962
           R   +RR     RRR      R+  ++  R  RR RR R R+     +E
Sbjct: 4   RPTPKRREAEAARRRPLVPEDRKAAKKAARAARRERRARARAAMMAGDE 52

Some members in this family of proteins with unknown function are annotated as membrane proteins. This cannot be confirmed. Length = 168

>gnl|CDD|225361 COG2801, Tra5, Transposase and inactivated derivatives [DNA replication, recombination, and repair]

 Score = 39.9 bits (92), Expect = 0.003
 Identities = 12/56 (21%), Positives = 21/56 (37%)

Query: 899 RRRRRRKKRRRSRRRRSRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRR 954
             R ++  +      R R++    RR      RR  R RR  R       +R +++
Sbjct: 3   VSRNQQIAKLSKEIVRIRKKLYGSRRLIETLYRRGIRVRRVARLLGVLGLKRLKKK 58

Length = 232

>gnl|CDD|225361 COG2801, Tra5, Transposase and inactivated derivatives [DNA replication, recombination, and repair]

 Score = 39.9 bits (92), Expect = 0.003
 Identities = 14/68 (20%), Positives = 25/68 (36%)

Query: 899 RRRRRRKKRRRSRRRRSRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRSGKE 958
           +  +  K+  R R++    RR      RR  R RR  R       +R +++RR+    + 
Sbjct: 8   QIAKLSKEIVRIRKKLYGSRRLIETLYRRGIRVRRVARLLGVLGLKRLKKKRRKYIRYEG 67

Query: 959 EEEEEKKK 966
                   
Sbjct: 68  LHSMWNLL 75

Length = 232

>gnl|CDD|100110 cd05832, Ribosomal_L12p, Ribosomal protein L12p

 Score = 37.9 bits (88), Expect = 0.003
 Identities = 16/24 (66%), Positives = 21/24 (87%)

Query: 997  KKKKKEEEKEEEEKKEEEEKEEEE 1020
              ++K EEKEEE+KKEEE++EEEE
Sbjct: 73   AAEEKAEEKEEEKKKEEEKEEEEE 96

This subfamily includes archaeal L12p, the protein that is functionally equivalent to L7/L12 in bacteria and the P1 and P2 proteins in eukaryotes. L12p is homologous to P1 and P2 but is not homologous to bacterial L7/L12. It is located in the L12 stalk, with proteins L10, L11, and 23S rRNA. L12p is the only protein in the ribosome to occur as multimers, always appearing as sets of dimers. Recent data indicate that most archaeal species contain six copies of L12p (three homodimers), while eukaryotes have four copies (two heterodimers), and bacteria may have four or six copies (two or three homodimers), depending on the species. The organization of proteins within the stalk has been characterized primarily in bacteria, where L7/L12 forms either two or three homodimers and each homodimer binds to the extended C-terminal helix of L10. L7/L12 is attached to the ribosome through L10 and is the only ribosomal protein that does not directly interact with rRNA. Archaeal L12p is believed to function in a similar fashion. However, hybrid ribosomes containing the large subunit from E. coli with an archaeal stalk are able to bind archaeal and eukaryotic elongation factors but not bacterial elongation factors. In several mesophilic and thermophilic archaeal species, the binding of 23S rRNA to protein L11 and to the L10/L12p pentameric complex was found to be temperature-dependent and cooperative. Length = 106

>gnl|CDD|222389 pfam13801, Metal_resist, Heavy-metal resistance

 Score = 38.8 bits (91), Expect = 0.003
 Identities = 17/60 (28%), Positives = 18/60 (30%)

Query: 895 GGGGRRRRRRKKRRRSRRRRSRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRR 954
            G   R          RRR             +RR  R   R  RR  R  RR  R  RR
Sbjct: 14  AGAALRGPGGPGPGGPRRRPGLGPAALALPPEQRRALRAALRAHRREVRPLRRALRAARR 73

This is a metal-binding protein which is involved in resistance to heavy-metal ions. The protein forms a four-helix hooked hairpin, consisting of two long alpha helices each flanked by a shorter alpha helix. It binds a metal ion in a type-2 like centre. It contains two copies of an LTXXQ motif. Length = 125

>gnl|CDD|202427 pfam02841, GBP_C, Guanylate-binding protein, C-terminal domain

 Score = 40.7 bits (96), Expect = 0.003
 Identities = 21/75 (28%), Positives = 42/75 (56%), Gaps = 4/75 (5%)

Query: 957  KEEEEEEKKKEEKKKEEEEKKKKEGKTKKEEKKKEEEE----EKKKKKKEEEKEEEEKKE 1012
            +E   E++K+EE+  E +E+  +E   +  EK + E E    E+++  + + +E+EE  +
Sbjct: 220  QELLREKQKEEEQMMEAQERSYQEHVKQLIEKMEAEREKLLAEQERMLEHKLQEQEELLK 279

Query: 1013 EEEKEEEEKKRRRIR 1027
            E  K E E  ++ I+
Sbjct: 280  EGFKTEAESLQKEIQ 294

Transcription of the anti-viral guanylate-binding protein (GBP) is induced by interferon-gamma during macrophage induction. This family contains GBP1 and GPB2, both GTPases capable of binding GTP, GDP and GMP. Length = 297

>gnl|CDD|217393 pfam03154, Atrophin-1, Atrophin-1 family

 Score = 41.2 bits (96), Expect = 0.003
 Identities = 21/52 (40%), Positives = 32/52 (61%), Gaps = 4/52 (7%)

Query: 965  KKEEKKKEEEEKKKKEGKTKKEEKKKEEEEEKKKKKKEEEKEEEEKKEEEEK 1016
            K  +K++E  EK K+E     E+K +EE E +K+K+KE E+E E + E   K
Sbjct: 576  KLAKKREEAVEKAKREA----EQKAREEREREKEKEKEREREREREAERAAK 623

Atrophin-1 is the protein product of the dentatorubral-pallidoluysian atrophy (DRPLA) gene. DRPLA OMIM:125370 is a progressive neurodegenerative disorder. It is caused by the expansion of a CAG repeat in the DRPLA gene on chromosome 12p. This results in an extended polyglutamine region in atrophin-1, that is thought to confer toxicity to the protein, possibly through altering its interactions with other proteins. The expansion of a CAG repeat is also the underlying defect in six other neurodegenerative disorders, including Huntington's disease. One interaction of expanded polyglutamine repeats that is thought to be pathogenic is that with the short glutamine repeat in the transcriptional coactivator CREB binding protein, CBP. This interaction draws CBP away from its usual nuclear location to the expanded polyglutamine repeat protein aggregates that are characteristic of the polyglutamine neurodegenerative disorders. This interferes with CBP-mediated transcription and causes cytotoxicity. Length = 979

>gnl|CDD|148630 pfam07133, Merozoite_SPAM, Merozoite surface protein (SPAM)

 Score = 39.5 bits (92), Expect = 0.003
 Identities = 17/58 (29%), Positives = 40/58 (68%)

Query: 957  KEEEEEEKKKEEKKKEEEEKKKKEGKTKKEEKKKEEEEEKKKKKKEEEKEEEEKKEEE 1014
            K+E++E+ ++EE++ EEE ++ ++ + ++E  + EEEEE+ ++   + K+ E+K   +
Sbjct: 44   KDEKQEDDEEEEEEDEEEIEEPEDIEDEEEIVEDEEEEEEDEEDNVDLKDIEKKNIND 101

This family consists of several Plasmodium falciparum SPAM (secreted polymorphic antigen associated with merozoites) proteins. Variation among SPAM alleles is the result of deletions and amino acid substitutions in non-repetitive sequences within and flanking the alanine heptad-repeat domain. Heptad repeats in which the a and d position contain hydrophobic residues generate amphipathic alpha-helices which give rise to helical bundles or coiled-coil structures in proteins. SPAM is an example of a P. falciparum antigen in which a repetitive sequence has features characteristic of a well-defined structural element. Length = 164

>gnl|CDD|236944 PRK11642, PRK11642, exoribonuclease R; Provisional

 Score = 41.3 bits (97), Expect = 0.003
 Identities = 19/88 (21%), Positives = 37/88 (42%)

Query: 915  SRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRSGKEEEEEEKKKEEKKKEEE 974
            S  R  R   +  R + ++    ++  +RR+  ++           E++ K +  KK+  
Sbjct: 726  SSERAPRNVGKTAREKAKKGDAGKKGGKRRQVGKKVNFEPDSAFRGEKKAKPKAAKKDAR 785

Query: 975  EKKKKEGKTKKEEKKKEEEEEKKKKKKE 1002
            + KK   KT+K     + +   KKK  E
Sbjct: 786  KAKKPSAKTQKIAAATKAKRAAKKKVAE 813

Length = 813

>gnl|CDD|221313 pfam11917, DUF3435, Protein of unknown function (DUF3435)

 Score = 41.2 bits (97), Expect = 0.003
 Identities = 20/108 (18%), Positives = 38/108 (35%), Gaps = 14/108 (12%)

Query: 876 RRRRRRRSGKEEEEKKKKEGGGGRRRRRRKKRRRSRRRRSRRRRRRRRRRRRRRRRRRRR 935
            RR R  + +++   ++        R+R   ++       +  + +      R  +RRR 
Sbjct: 270 PRRPRDLTDEQKASVEEDPELQELIRKRDHLKKEIIALYGQVAKAKGTPLYERLEKRRRE 329

Query: 936 RRRRRRRRRRRRRRRRRRR--------------SGKEEEEEEKKKEEK 969
            R  R+R RR  +++ R                SG    EE K+    
Sbjct: 330 VRNERQRLRRELKKKIREEFDEEQPVIDIERQLSGLAVSEEVKEDLPD 377

This family of proteins are functionally uncharacterized. This protein is found in eukaryotes. Proteins in this family are typically between 435 to 791 amino acids in length. This family is related to pfam00589 suggesting it may be an integrase enzyme. Length = 418

>gnl|CDD|218218 pfam04702, Vicilin_N, Vicilin N terminal region

 Score = 38.9 bits (90), Expect = 0.003
 Identities = 24/131 (18%), Positives = 72/131 (54%), Gaps = 2/131 (1%)

Query: 880  RRRSGKEEEEKKKKEGGGGRRRRRRKKRRRSRRRRSRRRRRRRRRRRRRRRRRRRRRRRR 939
            +RR  +E   +++++    R + + K+ ++ +R+R    +RR  + ++R ++   R R  
Sbjct: 17   QRRCEQETRGQREQQQCERRCKEQYKEEQQQQRQREEDPQRRYEQCQQRCQQHEPRHRPT 76

Query: 940  RRRRRRRRRRRRRRRSGKEEEEEEKKKEEKKKEEEEKKK--KEGKTKKEEKKKEEEEEKK 997
             ++R  RR  + +++  ++ +E +++ +++++    +++  +E + + +E  + E E   
Sbjct: 77   CQQRCERRYEKEQQQQQRQYQECQQRCQQQEQRPRRQQQCQRECREQYQEHGRGEGENIN 136

Query: 998  KKKKEEEKEEE 1008
            ++ +EE  EE 
Sbjct: 137  QEGEEERSEEG 147

This region is found in plant seed storage proteins, N-terminal to the Cupin domain (pfam00190). In Macadamia integrifolia, this region is processed into peptides of approximately 50 amino acids containing a C-X-X-X-C-(10-12)X-C-X-X-X-C motif. These peptides exhibit antimicrobial activity in vitro. Length = 147

>gnl|CDD|165026 PHA02644, PHA02644, hypothetical protein; Provisional

 Score = 38.4 bits (88), Expect = 0.003
 Identities = 25/64 (39%), Positives = 41/64 (64%)

Query: 960  EEEEKKKEEKKKEEEEKKKKEGKTKKEEKKKEEEEEKKKKKKEEEKEEEEKKEEEEKEEE 1019
            E+E K   E  K+E E +KK  K + E++KK E+ E + +KK E+ E E++KE E+ +  
Sbjct: 49   EDEMKTTHEHIKKENEDEKKPEKPENEDEKKPEKPENEDEKKPEKPENEDEKEFEDSDAS 108

Query: 1020 EKKR 1023
            +KK+
Sbjct: 109  DKKK 112

Length = 112

>gnl|CDD|225887 COG3351, FlaD, Putative archaeal flagellar protein D/E [Cell motility and secretion]

 Score = 39.8 bits (93), Expect = 0.003
 Identities = 17/63 (26%), Positives = 29/63 (46%)

Query: 961  EEEKKKEEKKKEEEEKKKKEGKTKKEEKKKEEEEEKKKKKKEEEKEEEEKKEEEEKEEEE 1020
               ++ +EK +E   + KK      EE  +  E+ K+    E+    EE+  E+EK   E
Sbjct: 18   FALEELKEKIEELPIQAKKSDDELVEELPERYEQTKENSLIEKVDSIEEEISEKEKVMSE 77

Query: 1021 KKR 1023
            K +
Sbjct: 78   KLK 80

Length = 214

>gnl|CDD|237496 PRK13766, PRK13766, Hef nuclease; Provisional

 Score = 41.4 bits (98), Expect = 0.003
 Identities = 25/73 (34%), Positives = 48/73 (65%)

Query: 950  RRRRRSGKEEEEEEKKKEEKKKEEEEKKKKEGKTKKEEKKKEEEEEKKKKKKEEEKEEEE 1009
            RR+ +  KEE +  K    KK +E ++++K  + +K+E+   ++  K K K+EEE+EE+E
Sbjct: 490  RRKEKKMKEELKNLKGILNKKLQELDEEQKGEEEEKDEQLSLDDFVKSKGKEEEEEEEKE 549

Query: 1010 KKEEEEKEEEEKK 1022
            +K++E +E+E + 
Sbjct: 550  EKDKETEEDEPEG 562

Length = 773

>gnl|CDD|214661 smart00435, TOPEUc, DNA Topoisomerase I (eukaryota)

 Score = 40.8 bits (96), Expect = 0.003
 Identities = 24/65 (36%), Positives = 41/65 (63%), Gaps = 1/65 (1%)

Query: 958  EEEEEEKKKEEKKKEEEEKKKKEGKTKKEEKKKEEEEEKKKKKKEEEKEEEEKKEEEEKE 1017
             E   + K++ K K E + +K + +  KE+KK++++EEKKKK+ E  +E  EK E +  +
Sbjct: 303  FEMISDLKRKLKSKFERDNEKLDAE-VKEKKKEKKKEEKKKKQIERLEERIEKLEVQATD 361

Query: 1018 EEEKK 1022
            +EE K
Sbjct: 362  KEENK 366

DNA Topoisomerase I (eukaryota), DNA topoisomerase V, Vaccina virus topoisomerase, Variola virus topoisomerase, Shope fibroma virus topoisomeras. Length = 391

>gnl|CDD|221821 pfam12871, PRP38_assoc, Pre-mRNA-splicing factor 38-associated hydrophilic C-term

 Score = 37.5 bits (87), Expect = 0.004
 Identities = 26/79 (32%), Positives = 40/79 (50%)

Query: 894 EGGGGRRRRRRKKRRRSRRRRSRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRR 953
           E          ++      RR   R   R RR  RRR RRR RRR+R R+RRRRRR R R
Sbjct: 7   EEDLDEEEESEEEEDDEEIRRKAERDVDRGRRSPRRRTRRRSRRRKRSRKRRRRRRDRDR 66

Query: 954 RSGKEEEEEEKKKEEKKKE 972
              ++ ++ ++ + ++ + 
Sbjct: 67  ARYRDRDDRDRDRYDRSRS 85

This domain is a hydrophilic region found at the C-terminus of plant and metazoan pre-mRNA-splicing factor 38 proteins. The function is not known. Length = 97

>gnl|CDD|219061 pfam06495, Transformer, Fruit fly transformer protein

 Score = 39.3 bits (91), Expect = 0.004
 Identities = 24/78 (30%), Positives = 33/78 (42%)

Query: 876 RRRRRRRSGKEEEEKKKKEGGGGRRRRRRKKRRRSRRRRSRRRRRRRRRRRRRRRRRRRR 935
           R  R  R    ++EK        R R R +  R+ + + +R     R RR R R R +  
Sbjct: 8   RSPRDTRRDSRKKEKIPYFADEVRERDRVRNLRQRKTQSTRPTTSHRGRRTRSRSRSQSA 67

Query: 936 RRRRRRRRRRRRRRRRRR 953
            R   +RR R R R R R
Sbjct: 68  ERNSCQRRHRSRSRSRNR 85

This family consists of transformer proteins from several Drosophila species and also from Ceratitis capitata (Mediterranean fruit fly). The transformer locus (tra) produces an RNA processing protein that alternatively splices the doublesex pre-mRNA in the sex determination hierarchy of Drosophila melanogaster. Length = 182

>gnl|CDD|178945 PRK00247, PRK00247, putative inner membrane protein translocase component YidC; Validated

 Score = 40.6 bits (95), Expect = 0.004
 Identities = 22/116 (18%), Positives = 40/116 (34%), Gaps = 36/116 (31%)

Query: 816 RRGRRRRRRKKKEEKKKWKRRGGGR-------------------RRRRGKKEEEKKKKKE 856
           +R + R ++K+K+      RR   R                   + R  +K E K +KKE
Sbjct: 290 QRAQYREKQKEKKAFLWTLRRNRLRMIITPWRAPELHAENAEIKKTRTAEKNEAKARKKE 349

Query: 857 EEEEGGEKEEEEGGGGGGRRRRRRRRSGKEEEEKKKKEGGGGRRRRRRKKRRRSRR 912
             ++               RR   R   +E  +++       R R RR   +  ++
Sbjct: 350 IAQK---------------RRAAEREINREARQERAAA--MARARARRAAVKAKKK 388

Length = 429

>gnl|CDD|226894 COG4499, COG4499, Predicted membrane protein [Function unknown]

 Score = 40.5 bits (95), Expect = 0.004
 Identities = 20/52 (38%), Positives = 33/52 (63%), Gaps = 1/52 (1%)

Query: 946 RRRRRRRRRSGKEEEEEEKKKEEK-KKEEEEKKKKEGKTKKEEKKKEEEEEK 996
           ++    +  +   EE E K KEEK K+EE EKK+KE   + +EK++++E +K
Sbjct: 383 KKLGEVKDETDASEEAEAKAKEEKLKQEENEKKQKEQADEDKEKRQKDERKK 434

Length = 434

>gnl|CDD|217503 pfam03344, Daxx, Daxx Family

 Score = 40.7 bits (95), Expect = 0.004
 Identities = 25/74 (33%), Positives = 43/74 (58%), Gaps = 15/74 (20%)

Query: 958  EEEEEEKKKEEKKKEEEEKKKKEGKTKKEEK-----------KKEEEEEKKKKKKEEEKE 1006
            + EEEE++    K++E E++    ++    K             +E EE++  ++EEE+E
Sbjct: 397  DTEEEERR----KRQERERQGTSSRSSDPSKASSTSGESPSMASQESEEEESVEEEEEEE 452

Query: 1007 EEEKKEEEEKEEEE 1020
            EEE++EE+E EEEE
Sbjct: 453  EEEEEEEQESEEEE 466

The Daxx protein (also known as the Fas-binding protein) is thought to play a role in apoptosis, but precise role played by Daxx remains to be determined. Daxx forms a complex with Axin. Length = 715

>gnl|CDD|237178 PRK12705, PRK12705, hypothetical protein; Provisional

 Score = 40.8 bits (96), Expect = 0.004
 Identities = 16/105 (15%), Positives = 49/105 (46%)

Query: 926  RRRRRRRRRRRRRRRRRRRRRRRRRRRRRSGKEEEEEEKKKEEKKKEEEEKKKKEGKTKK 985
               ++R+R  +   R  +  ++    +  +   E +E   +E  ++ +E ++++E   ++
Sbjct: 23   VLLKKRQRLAKEAERILQEAQKEAEEKLEAALLEAKELLLRERNQQRQEARREREELQRE 82

Query: 986  EEKKKEEEEEKKKKKKEEEKEEEEKKEEEEKEEEEKKRRRIRRKR 1030
            EE+  ++EE+   + ++ +  E + +E E+     +       K+
Sbjct: 83   EERLVQKEEQLDARAEKLDNLENQLEEREKALSARELELEELEKQ 127

Length = 508

>gnl|CDD|237035 PRK12280, rplW, 50S ribosomal protein L23; Reviewed

 Score = 38.6 bits (90), Expect = 0.004
 Identities = 17/53 (32%), Positives = 34/53 (64%)

Query: 972  EEEEKKKKEGKTKKEEKKKEEEEEKKKKKKEEEKEEEEKKEEEEKEEEEKKRR 1024
            EE EK++KE   + EEK+  + +++KK+KKE++  E+  K++  K  +   ++
Sbjct: 93   EESEKEQKEVSKETEEKEAIKAKKEKKEKKEKKVAEKLAKKKSTKTTKNTTKK 145

Length = 158

>gnl|CDD|237629 PRK14160, PRK14160, heat shock protein GrpE; Provisional

 Score = 39.4 bits (92), Expect = 0.004
 Identities = 24/68 (35%), Positives = 37/68 (54%), Gaps = 4/68 (5%)

Query: 957  KEEEEEEKKKEEKKKEEEEKKKKEGK----TKKEEKKKEEEEEKKKKKKEEEKEEEEKKE 1012
            K E  EE   +E + +EE+K K+E       +KEE  ++ EE  + K +E + E  + KE
Sbjct: 9    KHENMEEDCCKENENKEEDKGKEEDLEFEEIEKEEIIEDSEESNEVKIEELKDENNKLKE 68

Query: 1013 EEEKEEEE 1020
            E +K E E
Sbjct: 69   ENKKLENE 76

Length = 211

>gnl|CDD|188306 TIGR03319, RNase_Y, ribonuclease Y

 Score = 40.7 bits (96), Expect = 0.004
 Identities = 26/101 (25%), Positives = 48/101 (47%), Gaps = 11/101 (10%)

Query: 935  RRRRRRRRRRRRRRRRRRRRSGKEEEEEEKKKE---EKKKE--------EEEKKKKEGKT 983
            R+R   ++        +R     ++E E  KKE   E K+E        E E K++  + 
Sbjct: 19   RKRIAEKKLGSAEELAKRIIEEAKKEAETLKKEALLEAKEEVHKLRAELERELKERRNEL 78

Query: 984  KKEEKKKEEEEEKKKKKKEEEKEEEEKKEEEEKEEEEKKRR 1024
            ++ E++  + EE   +K E   ++EE  E++EKE   K++ 
Sbjct: 79   QRLERRLLQREETLDRKMESLDKKEENLEKKEKELSNKEKN 119

Members of this family are RNase Y, an endoribonuclease. The member from Bacillus subtilis, YmdA, has been shown to be involved in turnover of yitJ riboswitch [Transcription, Degradation of RNA]. Length = 514

>gnl|CDD|237744 PRK14521, rpsP, 30S ribosomal protein S16; Provisional

 Score = 39.4 bits (92), Expect = 0.004
 Identities = 16/65 (24%), Positives = 28/65 (43%)

Query: 956  GKEEEEEEKKKEEKKKEEEEKKKKEGKTKKEEKKKEEEEEKKKKKKEEEKEEEEKKEEEE 1015
             K ++  +K   E +K+  E + +    KK  +      E+    +EEE EE   +E   
Sbjct: 122  SKAKKAAKKAALEAEKKVNEARAEAVAEKKAAEAAAVAAEEAAAAEEEEAEEAPAEEAPA 181

Query: 1016 KEEEE 1020
            +E  E
Sbjct: 182  EESAE 186

Length = 186

>gnl|CDD|237177 PRK12704, PRK12704, phosphodiesterase; Provisional

 Score = 40.5 bits (96), Expect = 0.004
 Identities = 22/76 (28%), Positives = 44/76 (57%), Gaps = 2/76 (2%)

Query: 957  KEEEEEEKKKEEKKKEEEEKKKKEGKTKKEEKKKE-EEEEKKKKKKEEE-KEEEEKKEEE 1014
            KE E  +K+   + KEE  K + E + +  E++ E ++ EK+  +KEE    + E  E+ 
Sbjct: 49   KEAEAIKKEALLEAKEEIHKLRNEFEKELRERRNELQKLEKRLLQKEENLDRKLELLEKR 108

Query: 1015 EKEEEEKKRRRIRRKR 1030
            E+E E+K++   ++++
Sbjct: 109  EEELEKKEKELEQKQQ 124

Length = 520

>gnl|CDD|240388 PTZ00372, PTZ00372, endonuclease 4-like protein; Provisional

 Score = 40.5 bits (95), Expect = 0.004
 Identities = 23/74 (31%), Positives = 42/74 (56%), Gaps = 2/74 (2%)

Query: 957  KEEEEEEKKKEEKKKEEEEKKKKEGKTKKEEKKKEEEEEKKKKKKEEEKEEEEKKEEEEK 1016
            K++++E+K  E KKK E++KKKK  K KKE K + E +   K  K+ +K +++  + +  
Sbjct: 55   KKDKKEDKNNESKKKSEKKKKKK--KEKKEPKSEGETKLGFKTPKKSKKTKKKPPKPKPN 112

Query: 1017 EEEEKKRRRIRRKR 1030
            E+ +    +I    
Sbjct: 113  EDVDNAFNKIAELA 126

Length = 413

>gnl|CDD|221175 pfam11705, RNA_pol_3_Rpc31, DNA-directed RNA polymerase III subunit Rpc31

 Score = 39.7 bits (93), Expect = 0.004
 Identities = 23/63 (36%), Positives = 33/63 (52%), Gaps = 6/63 (9%)

Query: 964  KKKEEKKKEEEEKKKKEGKTKKE------EKKKEEEEEKKKKKKEEEKEEEEKKEEEEKE 1017
              K+  KK    K K++     E      EK    E++ K+ + E+  EE+EK EEEE+E
Sbjct: 122  INKKAGKKLALSKFKRKVGLFTEEEEDIDEKLSMLEKKLKELEAEDVDEEDEKDEEEEEE 181

Query: 1018 EEE 1020
            EEE
Sbjct: 182  EEE 184

RNA polymerase III contains seventeen subunits in yeasts and in human cells. Twelve of these are akin to RNA polymerase I or II and the other five are RNA pol III-specific, and form the functionally distinct groups (i) Rpc31-Rpc34-Rpc82, and (ii) Rpc37-Rpc53. Rpc31, Rpc34 and Rpc82 form a cluster of enzyme-specific subunits that contribute to transcription initiation in S.cerevisiae and H.sapiens. There is evidence that these subunits are anchored at or near the N-terminal Zn-fold of Rpc1, itself prolonged by a highly conserved but RNA polymerase III-specific domain. Length = 221

>gnl|CDD|217348 pfam03064, U79_P34, HSV U79 / HCMV P34

 Score = 39.9 bits (93), Expect = 0.004
 Identities = 24/89 (26%), Positives = 42/89 (47%), Gaps = 7/89 (7%)

Query: 812 LSRNRRGRRRRRRKKKEEKKKWKRRGGGRRRRRGKKEEEKKKKKEEEEEGGEKEEEEGGG 871
           LSR +     R+R  K+++K+       R     K +E+++KK+EE+    E +   GGG
Sbjct: 150 LSRKKSDDEHRKRSGKQKEKR-------RVEDSQKHKEDRRKKQEEKRRNDEDKRPGGGG 202

Query: 872 GGGRRRRRRRRSGKEEEEKKKKEGGGGRR 900
           G    +       +  +EK++K     RR
Sbjct: 203 GSSGGQSGLSTKDEPPKEKRQKHHDPERR 231

This family represents herpes virus protein U79 and cytomegalovirus early phosphoprotein P34 (UL112). Length = 238

>gnl|CDD|221185 pfam11719, Drc1-Sld2, DNA replication and checkpoint protein

 Score = 40.5 bits (95), Expect = 0.004
 Identities = 32/122 (26%), Positives = 54/122 (44%), Gaps = 9/122 (7%)

Query: 822 RRRKKKEEKKKWKRRGGGRRRRRGKKEEEKKKKKEEEEEGGEKEEEEG----GGGGGRRR 877
           RR  KK+ +K+  RR   R  R    +E    + +  EE  + +E+      G  GG   
Sbjct: 281 RRVFKKKGQKRTTRRVKMRPVRAKPSDEPSLPESDIHEEIPKLDEKSLSEFLGYMGGIDE 340

Query: 878 RRRRRSGKEEEEKKKKEGGGGRRRRRRKKRRRSRRRRSRRRRRRRRRRRRRRRRRRRRRR 937
                  +E +E+ +K+    ++ R+RK         S   RR + R +R++  + R RR
Sbjct: 341 DDEDEDDEESKEEVEKKQKVKKKPRKRK-----VNPVSNNFRRLKLRNKRKKGFKGRFRR 395

Query: 938 RR 939
           RR
Sbjct: 396 RR 397

Genome duplication is precisely regulated by cyclin-dependent kinases CDKs, which bring about the onset of S phase by activating replication origins and then prevent relicensing of origins until mitosis is completed. The optimum sequence motif for CDK phosphorylation is S/T-P-K/R-K/R, and Drc1-Sld2 is found to have at least 11 potential phosphorylation sites. Drc1 is required for DNA synthesis and S-M replication checkpoint control. Drc1 associates with Cdc2 and is phosphorylated at the onset of S phase when Cdc2 is activated. Thus Cdc2 promotes DNA replication by phosphorylating Drc1 and regulating its association with Cut5. Sld2 and Sld3 represent the minimal set of S-CDK substrates required for DNA replication. Length = 397

>gnl|CDD|220371 pfam09736, Bud13, Pre-mRNA-splicing factor of RES complex

 Score = 38.4 bits (90), Expect = 0.004
 Identities = 21/79 (26%), Positives = 50/79 (63%), Gaps = 2/79 (2%)

Query: 952  RRRSGKEEEEEEKKKEEKKKEEEEKKKKEGKTKKEEKKKEEEEEKKKKKKEEEKEEEEKK 1011
            R +SG+  + EEK++E+++++EE+++K+E   +KE  K   ++E+++K+ EE ++ + K 
Sbjct: 5    RDKSGRIIDIEEKREEKEREKEEKERKEE--KEKEWGKGLVQKEEREKRLEELEKAKNKP 62

Query: 1012 EEEEKEEEEKKRRRIRRKR 1030
                 ++E+       ++R
Sbjct: 63   LARYADDEDYDEELKEQER 81

This entry is characterized by proteins with alternating conserved and low-complexity regions. Bud13 together with Snu17p and a newly identified factor, Pml1p/Ylr016c, form a novel trimeric complex. called The RES complex, pre-mRNA retention and splicing complex. Subunits of this complex are not essential for viability of yeasts but they are required for efficient splicing in vitro and in vivo. Furthermore, inactivation of this complex causes pre-mRNA leakage from the nucleus. Bud13 contains a unique, phylogenetically conserved C-terminal region of unknown function. Length = 141

>gnl|CDD|221041 pfam11241, DUF3043, Protein of unknown function (DUF3043)

 Score = 39.2 bits (92), Expect = 0.004
 Identities = 15/49 (30%), Positives = 22/49 (44%)

Query: 913 RRSRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRSGKEEEE 961
           R + +RR     RRR      R+  ++  R  RR RR R R +    +E
Sbjct: 4   RPTPKRREAEAARRRPLVPEDRKAAKKAARAARRERRARARAAMMAGDE 52

Some members in this family of proteins with unknown function are annotated as membrane proteins. This cannot be confirmed. Length = 168

>gnl|CDD|100110 cd05832, Ribosomal_L12p, Ribosomal protein L12p

 Score = 37.5 bits (87), Expect = 0.004
 Identities = 15/27 (55%), Positives = 22/27 (81%)

Query: 991  EEEEEKKKKKKEEEKEEEEKKEEEEKE 1017
                E+K ++KEEEK++EE+KEEEE+E
Sbjct: 71   AAAAEEKAEEKEEEKKKEEEKEEEEEE 97

This subfamily includes archaeal L12p, the protein that is functionally equivalent to L7/L12 in bacteria and the P1 and P2 proteins in eukaryotes. L12p is homologous to P1 and P2 but is not homologous to bacterial L7/L12. It is located in the L12 stalk, with proteins L10, L11, and 23S rRNA. L12p is the only protein in the ribosome to occur as multimers, always appearing as sets of dimers. Recent data indicate that most archaeal species contain six copies of L12p (three homodimers), while eukaryotes have four copies (two heterodimers), and bacteria may have four or six copies (two or three homodimers), depending on the species. The organization of proteins within the stalk has been characterized primarily in bacteria, where L7/L12 forms either two or three homodimers and each homodimer binds to the extended C-terminal helix of L10. L7/L12 is attached to the ribosome through L10 and is the only ribosomal protein that does not directly interact with rRNA. Archaeal L12p is believed to function in a similar fashion. However, hybrid ribosomes containing the large subunit from E. coli with an archaeal stalk are able to bind archaeal and eukaryotic elongation factors but not bacterial elongation factors. In several mesophilic and thermophilic archaeal species, the binding of 23S rRNA to protein L11 and to the L10/L12p pentameric complex was found to be temperature-dependent and cooperative. Length = 106

>gnl|CDD|218737 pfam05764, YL1, YL1 nuclear protein

 Score = 39.7 bits (93), Expect = 0.004
 Identities = 12/106 (11%), Positives = 46/106 (43%)

Query: 925  RRRRRRRRRRRRRRRRRRRRRRRRRRRRRRSGKEEEEEEKKKEEKKKEEEEKKKKEGKTK 984
            +  +R  R ++++R + +  +   ++++++     +  +      KK+ E          
Sbjct: 76   KELQREERLKKKKRVKTKAYKEPTKKKKKKDPTAAKSPKAAAPRPKKKSERISWAPTLLD 135

Query: 985  KEEKKKEEEEEKKKKKKEEEKEEEEKKEEEEKEEEEKKRRRIRRKR 1030
               +K       + K+   E+ +E +   ++ + + +KR+  ++++
Sbjct: 136  SPRRKSSRSSTVQNKEATHERLKEREIRRKKIQAKARKRKEKKKEK 181

The proteins in this family are designated YL1. These proteins have been shown to be DNA-binding and may be a transcription factor. Length = 238

>gnl|CDD|217393 pfam03154, Atrophin-1, Atrophin-1 family

 Score = 40.8 bits (95), Expect = 0.004
 Identities = 18/48 (37%), Positives = 32/48 (66%), Gaps = 3/48 (6%)

Query: 977  KKKEGKTKKEEKKKEEEEEKKKKKKEEEKEEEEKKEEEEKEEEEKKRR 1024
            KK+E   +  EK K E E+K ++++E EKE+E+++E E + E E+  +
Sbjct: 579  KKRE---EAVEKAKREAEQKAREEREREKEKEKEREREREREAERAAK 623

Atrophin-1 is the protein product of the dentatorubral-pallidoluysian atrophy (DRPLA) gene. DRPLA OMIM:125370 is a progressive neurodegenerative disorder. It is caused by the expansion of a CAG repeat in the DRPLA gene on chromosome 12p. This results in an extended polyglutamine region in atrophin-1, that is thought to confer toxicity to the protein, possibly through altering its interactions with other proteins. The expansion of a CAG repeat is also the underlying defect in six other neurodegenerative disorders, including Huntington's disease. One interaction of expanded polyglutamine repeats that is thought to be pathogenic is that with the short glutamine repeat in the transcriptional coactivator CREB binding protein, CBP. This interaction draws CBP away from its usual nuclear location to the expanded polyglutamine repeat protein aggregates that are characteristic of the polyglutamine neurodegenerative disorders. This interferes with CBP-mediated transcription and causes cytotoxicity. Length = 979

>gnl|CDD|148630 pfam07133, Merozoite_SPAM, Merozoite surface protein (SPAM)

 Score = 38.7 bits (90), Expect = 0.004
 Identities = 23/67 (34%), Positives = 44/67 (65%), Gaps = 1/67 (1%)

Query: 964  KKKEEKKKEEEEKKKKEGKTKKEEKKKEEEEEKKKKKKEEEKE-EEEKKEEEEKEEEEKK 1022
              KE+  KE E+ K ++ +  +EE++++EEE ++ +  E+E+E  E+++EEEE EE+   
Sbjct: 31   WDKEDIIKENEDVKDEKQEDDEEEEEEDEEEIEEPEDIEDEEEIVEDEEEEEEDEEDNVD 90

Query: 1023 RRRIRRK 1029
             + I +K
Sbjct: 91   LKDIEKK 97

This family consists of several Plasmodium falciparum SPAM (secreted polymorphic antigen associated with merozoites) proteins. Variation among SPAM alleles is the result of deletions and amino acid substitutions in non-repetitive sequences within and flanking the alanine heptad-repeat domain. Heptad repeats in which the a and d position contain hydrophobic residues generate amphipathic alpha-helices which give rise to helical bundles or coiled-coil structures in proteins. SPAM is an example of a P. falciparum antigen in which a repetitive sequence has features characteristic of a well-defined structural element. Length = 164

>gnl|CDD|220623 pfam10186, Atg14, UV radiation resistance protein and autophagy-related subunit 14

 Score = 40.4 bits (95), Expect = 0.004
 Identities = 16/87 (18%), Positives = 35/87 (40%)

Query: 894 EGGGGRRRRRRKKRRRSRRRRSRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRR 953
           EG      +      +    R + R  + R R  + +    ++R R    +R   +RR  
Sbjct: 48  EGATNEDGKLAADLLKLEVARKKERLNQIRARISQLKEEIEQKRERIEELKRALAQRRSD 107

Query: 954 RSGKEEEEEEKKKEEKKKEEEEKKKKE 980
            S    + E+++  + +K ++E K+  
Sbjct: 108 LSSASYQLEKRRASQLEKLQDEIKRTR 134

The Atg14 or Apg14 proteins are hydrophilic proteins with a predicted molecular mass of 40.5 kDa, and have a coiled-coil motif at the N terminus region. Yeast cells with mutant Atg14 are defective not only in autophagy but also in sorting of carboxypeptidase Y (CPY), a vacuolar-soluble hydrolase, to the vacuole. Subcellular fractionation indicate that Apg14p and Apg6p are peripherally associated with a membrane structure(s). Apg14p was co-immunoprecipitated with Apg6p, suggesting that they form a stable protein complex. These results imply that Apg6/Vps30p has two distinct functions: in the autophagic process and in the vacuolar protein sorting pathway. Apg14p may be a component specifically required for the function of Apg6/Vps30p through the autophagic pathway. There are 17 auto-phagosomal component proteins which are categorized into six functional units, one of which is the AS-PI3K complex (Vps30/Atg6 and Atg14). The AS-PI3K complex and the Atg2-Atg18 complex are essential for nucleation, and the specific function of the AS-PI3K apparently is to produce phosphatidylinositol 3-phosphate (PtdIns(3)P) at the pre-autophagosomal structure (PAS). The localisation of this complex at the PAS is controlled by Atg14. Autophagy mediates the cellular response to nutrient deprivation, protein aggregation, and pathogen invasion in humans, and malfunction of autophagy has been implicated in multiple human diseases including cancer. This effect seems to be mediated through direct interaction of the human Atg14 with Beclin 1 in the human phosphatidylinositol 3-kinase class III complex. Length = 307

>gnl|CDD|233467 TIGR01554, major_cap_HK97, phage major capsid protein, HK97 family

 Score = 40.4 bits (95), Expect = 0.004
 Identities = 21/89 (23%), Positives = 37/89 (41%), Gaps = 9/89 (10%)

Query: 950  RRRRRSGKEEEEEEKKKEEKKKEEEEKKKKEGKTKKE---------EKKKEEEEEKKKKK 1000
             R   +   +E  +  ++EK  E EE+K +    K+E           ++  +E + K  
Sbjct: 4    LREALAELAKELRKLTEDEKLAEAEEEKAEYDALKEEIDKLDAEIDRLEELLDELEAKPA 63

Query: 1001 KEEEKEEEEKKEEEEKEEEEKKRRRIRRK 1029
               E    E++EEE K E  + R  +R  
Sbjct: 64   ASGEGGGGEEEEEEAKAEAAEFRAYLRGG 92

This model family represents the major capsid protein component of the heads (capsids) of bacteriophage HK97, phi-105, P27, and related phage. This model represents one of several analogous families lacking detectable sequence similarity. The gene encoding this component is typically located in an operon encoding the small and large terminase subunits, the portal protein and the prohead or maturation protease [Mobile and extrachromosomal element functions, Prophage functions]. Length = 384

>gnl|CDD|219256 pfam06991, Prp19_bind, Splicing factor, Prp19-binding domain

 Score = 39.9 bits (93), Expect = 0.004
 Identities = 29/88 (32%), Positives = 49/88 (55%), Gaps = 2/88 (2%)

Query: 945  RRRRRRRRRRSGKEEEEEEKKKEEKKKEEEEKKKKEGKTKKEEKKKEEEEEKKKKKKEEE 1004
            R++ R   +   +E  +E+  +EE K++ EE+K++  K  +EE KKE E +K+    E  
Sbjct: 43   RKKDRITIQEREREAAKEKALEEEAKRKAEERKRETLKIVEEEVKKELELKKRNTLLEAN 102

Query: 1005 KEEEEKKEEEEKEEEE--KKRRRIRRKR 1030
             ++ +  +E E+EE E  K R   R KR
Sbjct: 103  IDDVDTDDENEEEEYEAWKLRELKRIKR 130

This family represents the C-terminus (approximately 300 residues) of proteins that are involved as binding partners for Prp19 as part of the nuclear pore complex. The family in Drosophila is necessary for pre-mRNA splicing, and the human protein has been found in purifications of the spliceosome. In the past this family was thought, erroneously, to be associated with microfibrillin. Length = 277

>gnl|CDD|235795 PRK06402, rpl12p, 50S ribosomal protein L12P; Reviewed

 Score = 37.6 bits (88), Expect = 0.004
 Identities = 13/26 (50%), Positives = 17/26 (65%)

Query: 847 KEEEKKKKKEEEEEGGEKEEEEGGGG 872
              E+KK++EEEEE  E+ EEE   G
Sbjct: 75  AAAEEKKEEEEEEEEKEESEEEAAAG 100

Length = 106

>gnl|CDD|221668 pfam12619, MCM2_N, Mini-chromosome maintenance protein 2

 Score = 38.5 bits (90), Expect = 0.004
 Identities = 18/64 (28%), Positives = 21/64 (32%), Gaps = 11/64 (17%)

Query: 911 RRRRSRRRRRRRRRRRRRRRRR-----------RRRRRRRRRRRRRRRRRRRRRRSGKEE 959
           RR    R  RR R  RRRR                    + RRRRR+    R       +
Sbjct: 67  RRAAEARLNRRDRLLRRRRMPAAFLDDDDDDDGDFDLTAQPRRRRRQYDEDRDADDEDID 126

Query: 960 EEEE 963
             EE
Sbjct: 127 PLEE 130

This domain family is found in eukaryotes, and is typically between 138 and 153 amino acids in length. The family is found in association with pfam00493. Mini-chromosome maintenance (MCM) proteins are essential for DNA replication. These proteins use ATPase activity to perform this function. Length = 145

>gnl|CDD|219248 pfam06978, POP1, Ribonucleases P/MRP protein subunit POP1

 Score = 38.8 bits (91), Expect = 0.004
 Identities = 17/69 (24%), Positives = 31/69 (44%), Gaps = 12/69 (17%)

Query: 899 RRR------RRRKKRRRSRRRR------SRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRR 946
           RRR      +R  KR R R +R      +  +  R++  +R  R    R     R+ R+R
Sbjct: 36  RRRTASHNVKRVPKRLRKRAKREMAKDNTPTKLSRKKPSKRLLRLALARPPNLSRKYRKR 95

Query: 947 RRRRRRRRS 955
           ++R++   +
Sbjct: 96  QKRKKWLET 104

This family represents a conserved region approximately 150 residues long located towards the N-terminus of the POP1 subunit that is common to both the RNase MRP and RNase P ribonucleoproteins (EC:3.1.26.5). These RNA-containing enzymes generate mature tRNA molecules by cleaving their 5' ends. Length = 158

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	1030
KOG0970|consensus	1429		100.0
TIGR00592	1172	pol2 DNA polymerase (pol2). This family is based o	100.0
PTZ00166	1054	DNA polymerase delta catalytic subunit; Provisiona	100.0
KOG0969|consensus	1066		100.0
PHA03036	1004	DNA polymerase; Provisional	100.0
cd05534	451	POLBc_zeta DNA polymerase type-B zeta subfamily ca	100.0
PRK05761	787	DNA polymerase I; Reviewed	100.0
PRK05762	786	DNA polymerase II; Reviewed	100.0
COG0417	792	PolB DNA polymerase elongation subunit (family B)	100.0
cd05533	393	POLBc_delta DNA polymerase type-B delta subfamily	100.0
cd05532	400	POLBc_alpha DNA polymerase type-B alpha subfamily	100.0
PHA02528	881	43 DNA polymerase; Provisional	100.0
cd05536	371	POLBc_B3 DNA polymerase type-B B3 subfamily cataly	100.0
cd05530	372	POLBc_B1 DNA polymerase type-B B1 subfamily cataly	100.0
PF00136	466	DNA_pol_B: DNA polymerase family B Several related	100.0
cd05537	371	POLBc_Pol_II DNA polymerase type-II subfamily cata	100.0
cd05538	347	POLBc_Pol_II_B DNA polymerase type-II B subfamily	100.0
cd00145	323	POLBc DNA polymerase type-B family catalytic domai	100.0
KOG0968|consensus	1488		100.0
cd05531	352	POLBc_B2 DNA polymerase type-B B2 subfamily cataly	100.0
PHA03334	1545	putative DNA polymerase catalytic subunit; Provisi	100.0
cd05535	621	POLBc_epsilon DNA polymerase type-B epsilon subfam	100.0
smart00486	471	POLBc DNA polymerase type-B family. DNA polymerase	100.0
KOG1798|consensus	2173		99.98
KOG3236|consensus	225		99.98
PF09767	159	DUF2053: Predicted membrane protein (DUF2053); Int	99.97
PHA02523	391	43B DNA polymerase subunit B; Provisional	99.97
PHA02524	498	43A DNA polymerase subunit A; Provisional	99.95
PF12254	67	DNA_pol_alpha_N: DNA polymerase alpha subunit p180	99.87
PHA02563	630	DNA polymerase; Provisional	99.76
PF03104	325	DNA_pol_B_exo1: DNA polymerase family B, exonuclea	99.36
TIGR00592	1172	pol2 DNA polymerase (pol2). This family is based o	99.17
PF08490	396	DUF1744: Domain of unknown function (DUF1744); Int	98.46
PF03175	459	DNA_pol_B_2: DNA polymerase type B, organellar and	98.31
PHA02735	716	putative DNA polymerase type B; Provisional	98.11
PTZ00121	2084	MAEBL; Provisional	97.21
PTZ00121	2084	MAEBL; Provisional	96.97
KOG1798|consensus	2173		96.31
PTZ00266	1021	NIMA-related protein kinase; Provisional	95.39
PTZ00266	1021	NIMA-related protein kinase; Provisional	95.31
KOG4364|consensus	811		95.07
KOG4676|consensus	479		93.83
cd05776	234	DNA_polB_alpha_exo inactive DEDDy 3'-5' exonucleas	92.11
PHA03144	746	helicase-primase primase subunit; Provisional	89.06
KOG1029|consensus	1118		88.14
KOG1029|consensus	1118		87.48
KOG4676|consensus	479		86.21
PHA03181	764	helicase-primase primase subunit; Provisional	85.88
KOG0163|consensus	1259		85.85
KOG0334|consensus	997		85.76
KOG0151|consensus	877		84.9
KOG1847|consensus	878		81.61

>KOG0970|consensus

Probab=100.00  E-value=1.2e-187  Score=1640.31  Aligned_cols=718  Identities=49%  Similarity=0.818  Sum_probs=636.0

Q ss_pred             chhhhhhccHHHHHHHHHHHhhcCcceeeeeccccccccccChHHHHHHHHhhccCCeEEeCCCCccccccccccccccc
Q psy6283          93 NICLIDKTNKFAAFQKLKDLKGQGVKHKYEFTADENVYEEVSEKEYTERVLKRQEDDWIDDDGGDGYVEDGREIFDDDIE  172 (1030)
Q Consensus        93 n~slv~~~~~~~al~~l~~~~~~g~~~~~~v~~~~~vy~~vde~~y~~~v~~r~~dd~v~dd~g~gy~~~gre~~d~~~~  172 (1030)
                      ..+..+|++|++||++||+||  |.+.+|+|+++++|||+|||+||.+||++||+|||||||||.||||||+|+||.+.+
T Consensus        11 rR~~~~ks~r~~alerLk~ar--~s~~~Ye~e~~~~vYD~VDeeEY~k~v~~r~~DdfvVdDdG~GYvd~G~deeD~~~~   88 (1429)
T KOG0970|consen   11 RRSRGSKSSRLAALERLKAAR--TSGDKYEVEEVEDVYDTVDEEEYRKIVRQRLDDDFVVDDDGVGYVDNGVDEEDWSSP   88 (1429)
T ss_pred             hhhccCchhhHHHHHHHHHhh--ccCcccccccccccccccCHHHHHHHHHHHhcCCeEEeCCCccccccCcchhhccCC
Confidence            456668999999999999999  888999999999999999999999999999999999999999999999985553211


Q ss_pred             ---cchhhhhh-hh---hccc---------cCCCCCCc--------------------c-------C-------------
Q psy6283         173 ---DVPQKKEK-HD---KRKK---------NKNIQNPN--------------------A-------K-------------  196 (1030)
Q Consensus       173 ---~~~~~~~~-~~---~~~~---------~~~~~~~~--------------------~-------~-------------  196 (1030)
                         |....++| +|   +.|+         ..+|+++|                    |       +             
T Consensus        89 s~ed~~nek~k~gk~~kk~Kr~~k~~~~t~~~~~kk~~~~~~aka~~d~k~~~k~d~~~~diLg~~~e~~~e~~~~~~~i  168 (1429)
T KOG0970|consen   89 SDEDTGNEKKKGGKKPKKDKRKEKDHPVTQMLSTKKSNSALVAKATADQKKSVKIDNFMADILGSIDEEEAEEPEKLKKI  168 (1429)
T ss_pred             CccccccccccccccccchhhhhccccccccccccccchhhhhhhhccccccccchhhHHHHhhhccccccccccccccc
Confidence               21222211 11   1111         13344444                    0       0             


Q ss_pred             ------------------C---------------------------------------C---------------------
Q psy6283         197 ------------------D---------------------------------------D---------------------  198 (1030)
Q Consensus       197 ------------------~---------------------------------------~---------------------  198 (1030)
                                        |                                       |                     
T Consensus       169 ~~~~~s~~~rk~~~~a~n~~~~~~~~~~~~kki~~~~s~~ke~~s~Pvp~~~~~~~~~d~~~~~~e~e~~~~ate~e~~e  248 (1429)
T KOG0970|consen  169 RPATPSSPKRKFDSAAKNDSLVPVAIAKKKKKIAEDSSSDKERESSPVPTKRADFYIPDVQPEADEVENPVKATEFEDTE  248 (1429)
T ss_pred             cCCCCccccccccccccCCccCcccccccccccCCCCCcCCCCCCCCCCchhhhccCCCcccccccccCccccccccccc
Confidence                              0                                       0                     


Q ss_pred             ------------------------------------------C--CC--------------------------cccccC-
Q psy6283         199 ------------------------------------------S--LP--------------------------LATDHE-  207 (1030)
Q Consensus       199 ------------------------------------------~--~~--------------------------~~~~~~-  207 (1030)
                                                                +  +|                          ++...+ 
T Consensus       249 ~~~pl~~ee~~~dieet~~~~~~~~eeV~~~~~a~~~~~s~~s~~s~~~~~~di~~~~~~~~~~~~~~~s~~~~~~~~D~  328 (1429)
T KOG0970|consen  249 LENPLADEEDIEDIEETIAMKKLSMEEVTDTARANKDTISKLSPGSPPGEPEDIKGLGPSNSLQVDTDSSSGVLVKPEDV  328 (1429)
T ss_pred             cccccccccccccHHHHHHhhhHHHHHHhhhhhccccchhhcCCCCCCcChhhhhccCcccchhhccchhhccccccccc
Confidence                                                      0  00                          222223 


Q ss_pred             CCceEEEEEEeccccccCCCCEEEEEeeeeecCCCceeEEEEEEcceeeeEEEecCCCCCC--CC---CcccHHHHHHHH
Q psy6283         208 NKKVFRMFFLDAFEDIYKQPGTVYLFGKVFVKENNSHSSCCVIVQNIDRKIYLLPRSEHLK--TK---EPVSIAQVYSEF  282 (1030)
Q Consensus       208 ~~~~l~fy~~d~~e~~~~~~g~~~lfGkv~~~~~~~~~Sccv~v~~~~R~~~~lpr~~~~~--~~---~~~~~~~v~~e~  282 (1030)
                      .+++|+|||||||||+++.||+|||||||++ ++.+|+||||+|+||+|+||||||+..++  ++   .++++.|||+||
T Consensus       329 e~~~l~f~wlDaYee~~~~~g~l~LFGKVk~-~~~t~~Sccv~V~ni~R~lyflPR~~~l~~~~~e~~~~~s~~dv~~E~  407 (1429)
T KOG0970|consen  329 EDGSLRFFWLDAYEEVYKAPGTLYLFGKVKL-SGDTYVSCCVVVKNICRVLYFLPRPIKLSAAVGEDSIPESKRDVYKEV  407 (1429)
T ss_pred             ccceEEEEEehhhHHHhCCCceEEEEeeeec-cCCCceEEEEEEcCeeeEEEecccccccccccCCccchhhHHHHHHHH
Confidence            6899999999999999999999999999998 68899999999999999999999986652  32   567999999999


Q ss_pred             HH-HHHhcCCcceEEeeeeeccccCCCCCCCCccEEEEEeccCCCCCCCCCcCCceeeecccCchhhhhHHhhhhccCCe
Q psy6283         283 DQ-IATQYKILDFKSRKIEKKYAFNLPGVPDLSEYLEVRYSAKCPALPSDLSGDTFSHVFGTKTSFLENLLLERKIKGPS  361 (1030)
Q Consensus       283 ~~-~~~~~~i~~~~~k~v~~~yaf~~~~vp~~~~~lkv~y~~~~p~~~~~~~g~tfs~vfG~~~~~~E~f~l~~~i~Gp~  361 (1030)
                      .+ ++++++++.|++|||+++|||+.|+||..++||||.||+.+|.||+|++|.|||||||+||++||+|||.|+|||||
T Consensus       408 ~~~l~~k~~~~~fk~k~v~~~yafe~~dvp~~~dyLeV~y~~~~p~LP~Dlkgdsfshvfgt~tn~lE~fll~rKimGPC  487 (1429)
T KOG0970|consen  408 GSLLSNKLGLTEFKSKPVKKNYAFELPDVPMKSDYLEVLYSYETPKLPSDLKGDSFSHVFGTNTNPLERFLLSRKIMGPC  487 (1429)
T ss_pred             HHHHHhhhhhhHhhhhhhhhhhccccCCCCCCCcceEEeccccCCCCccccccchHHHHhccCccHHHHHHHhccccCce
Confidence            98 67789999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             EEEecCccCCCCcCccccceEeecchhhhc------------------------c---cCe-------------------
Q psy6283         362 WLEFPEAEKFPSRISWCKYEVQCNQMEKIR------------------------S---KQG-------------------  395 (1030)
Q Consensus       362 wl~i~~~~~~~~~~s~ck~e~~~~~~~~l~------------------------~---~~~-------------------  395 (1030)
                      ||+|.+++....++|||++||.+.+|+.|.                        +   +|.                   
T Consensus       488 Wlkv~~~s~~~~~~SwCk~Ev~v~sP~nI~~~~~~~a~~Ppl~llsL~i~T~~N~k~~~~Eiv~is~l~~~~~~id~p~p  567 (1429)
T KOG0970|consen  488 WLKVKGYSDPPRNASWCKVEVTVKSPQNITVVCSKKAPPPPLTLLSLNIRTSMNPKQNKNEIVMISMLCFHNFSIDKPAP  567 (1429)
T ss_pred             EEEeecCCCCCCCccceeeEEEecCCcceEEeecCCCCCCCeeEEEeeeeehhccccchhhhhhhhhhhcccccccCCCC
Confidence            999999997779999999999999987110                        0   000                   


Q ss_pred             ---------------------------------------------------------EEE--------------------
Q psy6283         396 ---------------------------------------------------------LIY--------------------  398 (1030)
Q Consensus       396 ---------------------------------------------------------viv--------------------  398 (1030)
                                                                               +||                    
T Consensus       568 ~~~~~~~~c~l~rP~~~~fP~g~~ela~~k~~~v~~~~sErALLs~fla~~~~~dpD~iVgHn~~~~~l~VLl~R~~~~K  647 (1429)
T KOG0970|consen  568 APAFPRHFCVLTRPPGTSFPLGLKELAKQKLSKVVLHNSERALLSHFLAMLNKEDPDVIVGHNIQGFYLDVLLSRLHALK  647 (1429)
T ss_pred             CCcccCcceeEecCCCCcCCchHHHHHHhccCceEEecCHHHHHHHHHHHhhccCCCEEEEeccccchHHHHHHHHHHhc
Confidence                                                                     222                    


Q ss_pred             -----Ecc------------------------------------------------------------------------
Q psy6283         399 -----LIG------------------------------------------------------------------------  401 (1030)
Q Consensus       399 -----r~G------------------------------------------------------------------------  401 (1030)
                           +||                                                                        
T Consensus       648 ip~WS~IgRLrrS~~~kfg~~s~~~e~~~~aGRl~CD~~~~a~~lik~~S~~LseL~q~~l~~eR~~i~~~~i~~~y~~s  727 (1429)
T KOG0970|consen  648 IPNWSSIGRLRRSWPPKFGRSSSFGEFFIIAGRLMCDLNLAARELIKAQSYSLSELSQQILKEERKEINANEIPKMYEDS  727 (1429)
T ss_pred             CcchhhhhhhhhccccccCCcccccccccccceEEeehHHHHHhhhccccccHHHHHHHHHhhhcccCCHhHhhhhccCh
Confidence                 111                                                                        


Q ss_pred             --HHHHHHHHHHHHHHHHHHHHHhcchHHHHHHHHHhCCcchhhccCchhHHHHHHHHHHHhhcCeeccCCccccCcCCC
Q psy6283         402 --IVEFIKFTMLHSSYIIKIMCELNVLPLAIQITNVCGNVLSRTLMGGRSERNEFLLLHAFHEKSYVLPDKQYGKNKKEG  479 (1030)
Q Consensus       402 --l~~lv~Y~~~Da~l~~~L~~kl~vlpl~~~lt~iaG~~~srtl~~gr~~r~E~lLL~~~~~~~yivPdk~~~kk~~~~  479 (1030)
                        |..++.+|+.|+.++++||+++|+|||++|||||+||.|++||+|||++||||+|||+||++|||+||+....+.+.+
T Consensus       728 ~~L~~ll~~~~~d~~~~l~i~~~l~~LpLs~qlTnIaGni~~RTL~G~RAeRnEylLLH~F~~~~fIvPDK~~ssk~~~d  807 (1429)
T KOG0970|consen  728 KSLTYLLEHTITDAELILQIMFRLNALPLSKQLTNIAGNIWARTLQGGRAERNEYLLLHEFYKNGFIVPDKQNSSKAQKD  807 (1429)
T ss_pred             HHHHHHHHHHhHHHHHHHHHHHHhccchHHHHHHHHHhHHHHHHhhccchhhhhHHHHHHHHHCCccCCCccchhhhhhh
Confidence              788999999999999999999999999999999999999999999999999999999999999999999855443332


Q ss_pred             ccc-ccc--ccCCCCCCccccCceeeccccccccceEEEeeccccChhHHHHhccccccccccCCCccccccccCCCCCc
Q psy6283         480 EET-GEA--NKGKGRKKAAYSGGLVLEPKKGFYDKFIILMDFNSLYPSIIQEYNICFTTIPVRMLQDSDITTLCEYLPEH  556 (1030)
Q Consensus       480 ~d~-~~~--~~~~~~~~~~Y~GGlVleP~~GlY~~~V~vLDFnSLYPSII~~~NIc~tTv~~~~~d~~~i~~~~p~~p~~  556 (1030)
                      .+. .++  ....++++++|+||+||+|+.|||+++|++||||||||||||+||||||||.+...|.+++    |.+|.+
T Consensus       808 ~d~~~eg~d~~~~~KKk~kYaGGLVlePkkGlYe~~VLllDFNSLYPSIIQEyNICFTTv~~~~~d~Dql----p~lP~s  883 (1429)
T KOG0970|consen  808 ADETEEGADEPSKGKKKAKYAGGLVLEPKKGLYEKYVLLLDFNSLYPSIIQEYNICFTTVDRFSVDSDQL----PRLPSS  883 (1429)
T ss_pred             hhhhhccccccccccccccccCceeeccccchhhheeEEEEccccchHHHHHhhheeeeccccccCcccC----CCCCCc
Confidence            222 111  1234566799999999999999999999999999999999999999999999854466677    899999


Q ss_pred             cccCCcchHHHHHHHHHHHHHHHHhcCCCCChHHHHhhHHHHHHhccccccccccCCCCCCCCCCHHHHHHHHHHhHHHH
Q psy6283         557 QVDTGILPSEIKKLVESRRQVKALMKQPNLSSDLLMQYDIRQKALKLTANSMYGCLGFPNSRFFAQPLAALVTAKGREIL  636 (1030)
Q Consensus       557 ~~~~GIlP~iL~~Ll~~R~~vKk~mk~~~~~~~~~~~~d~rQ~AlKl~aNS~YG~lG~~~srfy~~~lA~~IT~~GR~iL  636 (1030)
                      ...+||||.+|+.||++|++||++||+. .+|+++.||||||+|||||||||||||||.+||||+.|+|++||.+||+||
T Consensus       884 ~~~~GiLPr~l~~LVerRk~VK~lMK~~-~tp~~~~q~DIRQqALKLTANSMYGCLGf~~SRFyAkpLAaLVT~KGReiL  962 (1429)
T KOG0970|consen  884 SSEQGILPRLLENLVERRKEVKKLMKQE-LTPEKRKQLDIRQQALKLTANSMYGCLGFVNSRFYAKPLAALVTYKGREIL  962 (1429)
T ss_pred             cccCCccHHHHHHHHHHHHHHHHHHhcC-CCHHHHHhhhHHHHHHhhhhccchhhcccccchhhhhhHHHHHhhhhHHHH
Confidence            9999999999999999999999999995 999999999999999999999999999999999999999999999999999


Q ss_pred             HHHHHHhhhccceeEEecCcceeeecCCCCHHHHHHHHHHHHHHHhcccceeEEeecchhhhhhhcccccceEEeeeecC
Q psy6283         637 LNTKSLVENLNYEVIYGDTDSLMISCNVNDYDSVFKIGNQIKSECNKLYKQLELDIDGVYKYMLLLKKKKYAALSISKLS  716 (1030)
Q Consensus       637 ~~tkelve~~g~~VIYGDTDSI~V~~~~~d~eea~~ig~~i~~~Vn~~~~~leLe~E~vf~~llll~KKrYa~l~~~~~~  716 (1030)
                      ++|+++|++||++|||||||||||+++..|+++|++||++|++.||++|+.|+||+||||++|||++||+|||+.+.+++
T Consensus       963 m~Tk~Lve~mnl~VIYGDTDSvMInTn~td~~~a~kig~~~k~~VNkrYk~LEIDiDgVfkrlLLlkKKKYAAL~l~~dg 1042 (1429)
T KOG0970|consen  963 MNTKDLVEKMNLEVIYGDTDSVMINTNSTDYEEALKIGNEFKQAVNKRYKLLEIDIDGVFKRLLLLKKKKYAALTLNKDG 1042 (1429)
T ss_pred             HHHHHHHHhcCeEEEEcCCceEEeeCCCccHHHHHHHHHHHHHHHHHHhhhheeehhHHHHHHHHHhhhhheeEEecCCC
Confidence            99999999999999999999999999999999999999999999999999999999999999999999999999998766


Q ss_pred             CCceeeeceeeeeeeeeCChHHHHHHHHHHHHHHHhccCCCCCCChhHHHHHHHHHHHHHHHHhhCCCcChhhhHHhhcc
Q psy6283         717 NGKMICSQEIKGVDVVRRDWSQLASEAGKFVISQILDEQSYTDYSLDDRLQNIHEHMKKIRTDLDNGFVPLTLLEITKQL  796 (1030)
Q Consensus       717 dG~~~~~~e~KGle~vRRD~~~l~k~~~~~vL~~IL~~~~~~~~~~e~~v~~I~~~l~~~~~~l~~g~vpl~~lvItk~L  796 (1030)
                      +|  ++.+++|||||||||||+|+++++..||+.||++.     ++++++++||++|.++..+|.+|.||++.|+|+++|
T Consensus      1043 kg--~~~~E~KGLDmvRRDwc~Lake~g~~vLd~ILs~~-----~~ee~veaI~d~L~kI~~k~~~G~vpl~~fvI~k~L 1115 (1429)
T KOG0970|consen 1043 KG--VERIEVKGLDMVRRDWCQLAKEIGKAVLDKILSDK-----SREEIVEAIHDELRKISEKLENGNVPLEKFVITKTL 1115 (1429)
T ss_pred             CC--ceeeeecccchhHHHHHHHHHHHHHHHHHHHHcCC-----CHHHHHHHHHHHHHHHHHHHhcCccchhheeeehhc
Confidence            65  56889999999999999999999999999999999     999999999999999999999999999999999999


Q ss_pred             cCCCCC----CcchHHHHHHHHHHcCCccchhh
Q psy6283         797 TKAPEG----GKVCITQIRLSRNRRGRRRRRRK  825 (1030)
Q Consensus       797 sK~p~~----~~~pHV~vA~r~~~~g~~~~Kk~  825 (1030)
                      ||+|++    +++|||+||+||+++|+++.+..
T Consensus      1116 tK~Pe~Yp~~kslPhVqVALrm~~~G~~~~k~g 1148 (1429)
T KOG0970|consen 1116 TKNPEAYPDGKSLPHVQVALRMNKRGKRKVKAG 1148 (1429)
T ss_pred             cCChhhCCCcccCcHHHHHHHHHHhcCcccccC
Confidence            999998    88999999999999998777653

>TIGR00592 pol2 DNA polymerase (pol2)

Probab=100.00  E-value=1.4e-131  Score=1253.68  Aligned_cols=595  Identities=52%  Similarity=0.876  Sum_probs=529.0

Q ss_pred             CceEEEEEEeccccccCCCCEEEEEeeeeecCCCceeEEEEEEcceeeeEEEecCCCCC------CCCCcccHHHHHHHH
Q psy6283         209 KKVFRMFFLDAFEDIYKQPGTVYLFGKVFVKENNSHSSCCVIVQNIDRKIYLLPRSEHL------KTKEPVSIAQVYSEF  282 (1030)
Q Consensus       209 ~~~l~fy~~d~~e~~~~~~g~~~lfGkv~~~~~~~~~Sccv~v~~~~R~~~~lpr~~~~------~~~~~~~~~~v~~e~  282 (1030)
                      .+.+.||| |||+|+.+.+|++|||||.     ..++|||+.|.|++|++|+||++...      .+...+++++++.|+
T Consensus       305 ~~~~~~~~-da~~dr~~~~G~~~lfGr~-----~~~~s~~~~v~g~~R~~~~l~~~Grv~~D~~~~~~~~~~l~~y~le~  378 (1172)
T TIGR00592       305 RQVFQFYW-DAYEDPAEKLGVVLLFGRD-----VDHVSPCVQVKGINRDLFFLPREGKIDFDLGKVTRRTINLPDYYLEF  378 (1172)
T ss_pred             CceEEeeH-HhhhHHhhCCCeEEEeccc-----CCceeEEEEECCeeeeeEEeeccccccccccchhcccccHHHHHHHH
Confidence            34566777 9999988899999999993     23899999999999999999999765      345568999999998


Q ss_pred             HH-HHHhcCCcceEEeeeeeccccCCC--CCCCCccEEEEEec-----cCCCCCCCCCcCCceeeecccCchhhhhHHhh
Q psy6283         283 DQ-IATQYKILDFKSRKIEKKYAFNLP--GVPDLSEYLEVRYS-----AKCPALPSDLSGDTFSHVFGTKTSFLENLLLE  354 (1030)
Q Consensus       283 ~~-~~~~~~i~~~~~k~v~~~yaf~~~--~vp~~~~~lkv~y~-----~~~p~~~~~~~g~tfs~vfG~~~~~~E~f~l~  354 (1030)
                      .+ ++.+++++.|++|+|.++|||+.+  +||...+|++|.|+     +..|.+|.+++|.||+||||+|++.+|+|++.
T Consensus       379 vs~~~lg~~k~dv~~k~I~~~~~~~~~~~~v~y~~~~lkv~y~l~~~~~~l~~l~~~~~g~~~~~vf~~n~g~~erfll~  458 (1172)
T TIGR00592       379 VSELALGYKKEKFRAKPIAKKYEFEAPDIDAPYSSEYLEVTYELGKEFAPMEALPSDLKGQTFWHVFGSNTGNLERFLLL  458 (1172)
T ss_pred             HHHHHhhcCcCceeeEEehhhccCCCCccCCcCCcceEEEEEccCccchhhhhhhhhccCCcchheeccCHHHHHHHHhc
Confidence            77 788999999999999999999998  89999999999999     78889999999999999999999999999999


Q ss_pred             hhccCCeEEEecCccCCCCc-CccccceEeecchhh----------------hc-----c-----cC-------------
Q psy6283         355 RKIKGPSWLEFPEAEKFPSR-ISWCKYEVQCNQMEK----------------IR-----S-----KQ-------------  394 (1030)
Q Consensus       355 ~~i~Gp~wl~i~~~~~~~~~-~s~ck~e~~~~~~~~----------------l~-----~-----~~-------------  394 (1030)
                      ++|+|||||.+.++.....+ .|||++|+.+..+..                ++     +     .|             
T Consensus       459 rki~gp~WL~i~~p~~~~~~~~S~c~yEga~v~~p~v~~g~~~~~pPl~vLdFsi~SlyPsi~~~~nl~iS~~v~~~~~~  538 (1172)
T TIGR00592       459 RKIKGPCWLAVKGPDELEYPRRSWCKYEGGYVKPPNVEKGLDKTPPPLVVLDFSMKSLNPSIIRNEIVSIPDTLHREFAL  538 (1172)
T ss_pred             CCCCCCceEEeCCCcccCcCCccccceEEEEecCccccccccCCCCCeEEEEeeeEEecCccccCceEEEEEEEeecccc
Confidence            99999999999999887644 899999887754430                00     0     00             


Q ss_pred             ---------e----EEE---------------------------------------------------------------
Q psy6283         395 ---------G----LIY---------------------------------------------------------------  398 (1030)
Q Consensus       395 ---------~----viv---------------------------------------------------------------  398 (1030)
                               +    +++                                                               
T Consensus       539 d~~~~~~~~~~~~~~~~~~~~~~~p~~~~~~~~~~~~~~L~~~~sEr~lL~~fl~~~~~~DPDii~g~n~~qfdlkvl~n  618 (1172)
T TIGR00592       539 DKPPPEPPYDVHPCVGTRPKDCSFPLDLKGEFPGKKPSLVEDLATERALIKKFMAKVKKIDPDEIVGHDYQQRALKVLAN  618 (1172)
T ss_pred             cCCCCCCccceEEEEEEccCCCCCCchhhhhhhccCCcEEEEecCHHHHHHHHHHHHHhcCCCEEEEEcccCccHHHHHH
Confidence                     0    000                                                               


Q ss_pred             -----------Ecc------------------------------------------------------------------
Q psy6283         399 -----------LIG------------------------------------------------------------------  401 (1030)
Q Consensus       399 -----------r~G------------------------------------------------------------------  401 (1030)
                                 ++|                                                                  
T Consensus       619 R~~~l~i~~~~~~Gr~~~~~~~~~~~~~~~~Grl~~D~~~~~k~~~~~~sy~L~~v~~~~L~~~k~~~~~~~i~~~~~~~  698 (1172)
T TIGR00592       619 RINDLKIPTWSKIGRLRRSPKFGRRFGERTCGRMICDVEISAKELIRCKSYDLSELVQQILKTERKVIPIDNINNMYSES  698 (1172)
T ss_pred             HHHHcCCCcccccCccccCCCccccccceECCEEEEEHHHHHHHHhCcCCCCHHHHHHHHhCCCCcccCHHHHHHHHhCc
Confidence                       000                                                                  


Q ss_pred             --HHHHHHHHHHHHHHHHHHHHHhcchHHHHHHHHHhCCcchhhccCchhHHHHHHHHHHHhhcCeeccCCccccCcC--
Q psy6283         402 --IVEFIKFTMLHSSYIIKIMCELNVLPLAIQITNVCGNVLSRTLMGGRSERNEFLLLHAFHEKSYVLPDKQYGKNKK--  477 (1030)
Q Consensus       402 --l~~lv~Y~~~Da~l~~~L~~kl~vlpl~~~lt~iaG~~~srtl~~gr~~r~E~lLL~~~~~~~yivPdk~~~kk~~--  477 (1030)
                        +..++.||++||.++++|+.++++||++.+||+++|++|+++++|||++|||++|||+||++|||+|++....+.+  
T Consensus       699 ~~~~~~~~y~~~Da~l~~~L~~~l~~l~l~~~lt~i~G~~~~~~l~~~~~~r~e~lll~~~~~~~~i~P~~~~~~~~~~~  778 (1172)
T TIGR00592       699 SSLTYLLEHTWKDAMFILQIMCELNVLPLALQITNIAGNIMSRTLMGGRSERNEFLLLHAFYENNYIVPDKQIFRKQQKL  778 (1172)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHhhHHHHHHHHHHhCCcHHhccCCchHHHHHHHHHHHHHhCCEEccCcccccccccc
Confidence              3568899999999999999999999999999999999999999999999999999999999999999987543211  


Q ss_pred             CCccccccccCCCCCCccccCceeeccccccccceEEEeeccccChhHHHHhccccccccccCCCccccccccCCCCCcc
Q psy6283         478 EGEETGEANKGKGRKKAAYSGGLVLEPKKGFYDKFIILMDFNSLYPSIIQEYNICFTTIPVRMLQDSDITTLCEYLPEHQ  557 (1030)
Q Consensus       478 ~~~d~~~~~~~~~~~~~~Y~GGlVleP~~GlY~~~V~vLDFnSLYPSII~~~NIc~tTv~~~~~d~~~i~~~~p~~p~~~  557 (1030)
                      .+.+.. .+.....++.+|+||+|++|++|||++||++|||||||||||++||||||||++.. +.+++    |.+|.+.
T Consensus       779 ~~~~~~-~~~~~~~~~~~y~Gg~V~eP~~G~y~~~V~~lDF~SLYPSIi~~~Nic~~t~~~~~-~~~~~----~~~~~~~  852 (1172)
T TIGR00592       779 GDEDEE-IDGYKKGKKAAYAGGLVLEPKVGLYDKYVLLMDFNSLYPSIIQEFNICFTTVQQKV-DEDEL----PELPDSE  852 (1172)
T ss_pred             cccccc-ccccccccccCcCCCeEecCCCCcccCCEEEEEcCCccHHHHHHhCcCccccCCCC-cchhc----ccCCccc
Confidence            111110 01111224578999999999999999999999999999999999999999998754 33445    6777778


Q ss_pred             ccCCcchHHHHHHHHHHHHHHHHhcCCCCChHHHHhhHHHHHHhccccccccccCCCCCCCCCCHHHHHHHHHHhHHHHH
Q psy6283         558 VDTGILPSEIKKLVESRRQVKALMKQPNLSSDLLMQYDIRQKALKLTANSMYGCLGFPNSRFFAQPLAALVTAKGREILL  637 (1030)
Q Consensus       558 ~~~GIlP~iL~~Ll~~R~~vKk~mk~~~~~~~~~~~~d~rQ~AlKl~aNS~YG~lG~~~srfy~~~lA~~IT~~GR~iL~  637 (1030)
                      .+.||||.+|+.|++.|+++|++|++ +.+|.++.+||++|+|||++|||||||||+++|||||.++|++||++||++|+
T Consensus       853 ~~~Gilp~il~~L~~~R~~~K~~mk~-~~~~~~~~~~d~~Q~AlKi~aNS~YG~lG~~~~r~~~~~~A~~iT~~GR~~l~  931 (1172)
T TIGR00592       853 LEMGILPRELRKLVERRKEVKKLMKQ-DLNPDLRLQYDIRQKALKLTANSMYGCLGYSKSRFYAKPLAALVTAKGREILE  931 (1172)
T ss_pred             ccCcchHHHHHHHHHHHHHHHHHhhc-CCCHHHHHHHHHHHHHHHHhhhccccccccccccccChHHHHHHHHHHHHHHH
Confidence            89999999999999999999999999 88999999999999999999999999999999999999999999999999999


Q ss_pred             HHHHHhhhccceeEEecCcceeeecCCCCHHHHHHHHHHHHHHHhcccceeEEeecchhhhhhhcccccceEEeeeecCC
Q psy6283         638 NTKSLVENLNYEVIYGDTDSLMISCNVNDYDSVFKIGNQIKSECNKLYKQLELDIDGVYKYMLLLKKKKYAALSISKLSN  717 (1030)
Q Consensus       638 ~tkelve~~g~~VIYGDTDSI~V~~~~~d~eea~~ig~~i~~~Vn~~~~~leLe~E~vf~~llll~KKrYa~l~~~~~~d  717 (1030)
                      .|+++++++|++|||||||||||+++..+.++++++|.+|++.||+.|++|+|++|++|.++||++||||||+.++...+
T Consensus       932 ~~~~~~e~~g~~VIYGDTDSv~v~~~~~~~~e~~~~~~~~~~~in~~~~~l~le~e~vy~~~ll~~KKrYa~l~~~~~~~ 1011 (1172)
T TIGR00592       932 HTRQLVEEMNLEVIYGDTDSIMINTPGTKYEEVFKIGKEFKSEVNKLYKLLELDIDGVFKRLLLLKKKKYAAIKVEGDSD 1011 (1172)
T ss_pred             HHHHHHHHcCCEEEEecCCeEEEEcCCCCHHHHHHHHHHHHHHHhhcCCceEEeehhhhHhhHhhhccceEEEeeccCcC
Confidence            99999999999999999999999999999999999999999999999999999999999999999999999999876667


Q ss_pred             CceeeeceeeeeeeeeCChHHHHHHHHHHHHHHHhccCCCCCCChhHHHHHHHHHHHHHHHHhhCCCcChhhhHHhhccc
Q psy6283         718 GKMICSQEIKGVDVVRRDWSQLASEAGKFVISQILDEQSYTDYSLDDRLQNIHEHMKKIRTDLDNGFVPLTLLEITKQLT  797 (1030)
Q Consensus       718 G~~~~~~e~KGle~vRRD~~~l~k~~~~~vL~~IL~~~~~~~~~~e~~v~~I~~~l~~~~~~l~~g~vpl~~lvItk~Ls  797 (1030)
                      |...+++++||+++||||||+|+|+++..||+.||+++     +.+++++.|+++|.++..+|.+|.+|+++|+|+++|+
T Consensus      1012 g~~~~k~~~KGle~vRrD~~~l~k~~~~~vl~~il~~~-----~~~~~~~~i~~~l~~~~~~l~~g~~~~~~lvi~k~l~ 1086 (1172)
T TIGR00592      1012 GNYTTKQEVKGLDIVRRDWSPLAKETGKKVLDTILSDK-----DVEEAVEEVQEVLEKIGKNVLNGEVPLEKFVINKQLT 1086 (1172)
T ss_pred             CCcceeEEeecceEEECCcHHHHHHHHHHHHHHHHcCC-----CHHHHHHHHHHHHHHHHHHHhcCCCCHHHeeehhhcc
Confidence            87777899999999999999999999999999999999     8999999999999999999999999999999999999


Q ss_pred             CCCCC----CcchHHHHHHHHHHcCCcc
Q psy6283         798 KAPEG----GKVCITQIRLSRNRRGRRR  821 (1030)
Q Consensus       798 K~p~~----~~~pHV~vA~r~~~~g~~~  821 (1030)
                      |+|++    +++|||+||+||++++|..
T Consensus      1087 k~~~~Y~~~~~~phv~~A~~~~~~~g~~ 1114 (1172)
T TIGR00592      1087 RDPKDYPDGASLPHVHVALRINARGGRK 1114 (1172)
T ss_pred             CCHHHcCCCCCChHHHHHHHHHHhcCCC
Confidence            99877    6799999999999986544

This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).

>PTZ00166 DNA polymerase delta catalytic subunit; Provisional

Probab=100.00  E-value=4.3e-85  Score=819.07  Aligned_cols=388  Identities=29%  Similarity=0.455  Sum_probs=346.4

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHhcchHHHHHHHHHhCCcchhhccCchhHHHHHHHHHHHhhcCeeccCCccccCcCCCcc
Q psy6283         402 IVEFIKFTMLHSSYIIKIMCELNVLPLAIQITNVCGNVLSRTLMGGRSERNEFLLLHAFHEKSYVLPDKQYGKNKKEGEE  481 (1030)
Q Consensus       402 l~~lv~Y~~~Da~l~~~L~~kl~vlpl~~~lt~iaG~~~srtl~~gr~~r~E~lLL~~~~~~~yivPdk~~~kk~~~~~d  481 (1030)
                      +..++.||++||.|+++|+.++++++.+.++|+++|+++..++..|++.+++++|+|+++..||++|++....       
T Consensus       461 ~~~l~~Y~l~Da~L~~~L~~kl~~~~~~~e~arv~gip~~~v~~rG~q~kv~s~Llr~~~~~~~viP~~~~~~-------  533 (1054)
T PTZ00166        461 RRRIAVYCLKDAILPLRLLDKLLLIYNYVEMARVTGTPIGWLLTRGQQIKVTSQLLRKCKKLNYVIPTVKYSG-------  533 (1054)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHhHHHHHHHHhhccCCChHHhhcCCcchhHHHHHHHHHHhcCeeccCchhcc-------
Confidence            4579999999999999999999999999999999999999999999999999999999999999999875310       


Q ss_pred             ccccccCCCCCCccccCceeeccccccccceEEEeeccccChhHHHHhccccccccccCC----CccccccccCC---CC
Q psy6283         482 TGEANKGKGRKKAAYSGGLVLEPKKGFYDKFIILMDFNSLYPSIIQEYNICFTTIPVRML----QDSDITTLCEY---LP  554 (1030)
Q Consensus       482 ~~~~~~~~~~~~~~Y~GGlVleP~~GlY~~~V~vLDFnSLYPSII~~~NIc~tTv~~~~~----d~~~i~~~~p~---~p  554 (1030)
                              .....+|+||+|++|++|||++||++|||+|||||||++|||||||+++..+    .++.+ ...|.   |.
T Consensus       534 --------~~~~~~yeGg~VleP~~G~y~~pV~vLDF~SLYPSIiia~NlcysTl~~~~~~~~~~~~~~-~~~p~g~~Fv  604 (1054)
T PTZ00166        534 --------GGSEEKYEGATVLEPKKGFYDEPIATLDFASLYPSIMIAHNLCYSTLVPPNDANNYPEDTY-VTTPTGDKFV  604 (1054)
T ss_pred             --------ccccCCCCCceeecCCCCCeeCceEEeecCCcccHHHHhcCCCcceeecchhhccCCCcce-eecCCCceee
Confidence                    1234689999999999999999999999999999999999999999987642    01111 01121   44


Q ss_pred             CccccCCcchHHHHHHHHHHHHHHHHhcCCCCChHHHHhhHHHHHHhccccccccccCCCCC-CCCCCHHHHHHHHHHhH
Q psy6283         555 EHQVDTGILPSEIKKLVESRRQVKALMKQPNLSSDLLMQYDIRQKALKLTANSMYGCLGFPN-SRFFAQPLAALVTAKGR  633 (1030)
Q Consensus       555 ~~~~~~GIlP~iL~~Ll~~R~~vKk~mk~~~~~~~~~~~~d~rQ~AlKl~aNS~YG~lG~~~-srfy~~~lA~~IT~~GR  633 (1030)
                      .++.++||||.+|+.|++.|+++|+.|++. .||.++.+||.+|+|||++|||+|||+|+++ +||||.++|++||++||
T Consensus       605 ~~~~r~Gilp~iL~~Ll~~R~~~K~~mk~~-~d~~~~~~ld~rQ~AlKi~aNS~YG~~G~~~~gr~~c~~iA~sIT~~GR  683 (1054)
T PTZ00166        605 KKEVRKGILPLIVEELIAARKKAKKEMKDE-KDPLLKKVLNGRQLALKISANSVYGYTGAQVGGQLPCLEVSTSITSFGR  683 (1054)
T ss_pred             ecCCCCcccHHHHHHHHHHHHHHHHHHhhC-CCHHHHHHHHHHHHhhhhhccccccccccccCCccccHHHHHHHHHHHH
Confidence            445689999999999999999999999984 5999999999999999999999999999999 99999999999999999


Q ss_pred             HHHHHHHHHhhhc---------cceeEEecCcceeeecCCCCHHHHHHHHHHHHHHHhccc-ceeEEeecchhhhhhhcc
Q psy6283         634 EILLNTKSLVENL---------NYEVIYGDTDSLMISCNVNDYDSVFKIGNQIKSECNKLY-KQLELDIDGVYKYMLLLK  703 (1030)
Q Consensus       634 ~iL~~tkelve~~---------g~~VIYGDTDSI~V~~~~~d~eea~~ig~~i~~~Vn~~~-~~leLe~E~vf~~llll~  703 (1030)
                      ++|+.|++++++.         |++|||||||||||+++..+.++++++|.++++.||+.| ++|+||||+||.++||++
T Consensus       684 ~~i~~t~~~ie~~~~~~~g~~~g~~VIYGDTDSvfV~~~~~~~~ea~~~g~e~a~~Is~~~~~pi~LefEkvy~~~ll~~  763 (1054)
T PTZ00166        684 QMIDKTKELVEKHYTKANGYKHDATVIYGDTDSVMVKFGTDDIQEAMDLGKEAAERISKKFLKPIKLEFEKVYCPYLLMN  763 (1054)
T ss_pred             HHHHHHHHHHHHhccccccCcCCeEEEecCCCceEEEeCCccHHHHHHHHHHHHHHHHHhcCCCcEEEEeeeeeeeeecc
Confidence            9999999999986         999999999999999998899999999999999999987 589999999999999999


Q ss_pred             cccceEEeeeecCCCceeeeceeeeeeeeeCChHHHHHHHHHHHHHHHhccCCCCCCChhHHHHHHHHHHHHHHHHhhCC
Q psy6283         704 KKKYAALSISKLSNGKMICSQEIKGVDVVRRDWSQLASEAGKFVISQILDEQSYTDYSLDDRLQNIHEHMKKIRTDLDNG  783 (1030)
Q Consensus       704 KKrYa~l~~~~~~dG~~~~~~e~KGle~vRRD~~~l~k~~~~~vL~~IL~~~~~~~~~~e~~v~~I~~~l~~~~~~l~~g  783 (1030)
                      ||||||+.+++. ++  .+++++||+++||||||+|++++++.+|+.||.++     +.+.    +.+++.+.+.+|++|
T Consensus       764 KKrYag~~~~~~-~~--~~k~d~KGie~vRRD~c~~~k~~~~~vl~~il~~~-----d~~~----a~~~~~~~~~~l~~~  831 (1054)
T PTZ00166        764 KKRYAGLLYTNP-EK--YDKIDCKGIETVRRDNCLLVQQMVETVLNKILIEK-----DVES----AIEFTKGKISDLLQN  831 (1054)
T ss_pred             cceEEEEEEecC-CC--CceeeeeeeEEEeccchHHHHHHHHHHHHHHHccC-----CHHH----HHHHHHHHHHHHHcC
Confidence            999999988753 21  24679999999999999999999999999999987     6554    455666777889999


Q ss_pred             CcChhhhHHhhcccCCCCCCcchHHHHHHHHHHcC
Q psy6283         784 FVPLTLLEITKQLTKAPEGGKVCITQIRLSRNRRG  818 (1030)
Q Consensus       784 ~vpl~~lvItk~LsK~p~~~~~pHV~vA~r~~~~g  818 (1030)
                      ++|+++|+|+|+|+|.-+...+|||+||+||++++
T Consensus       832 ~v~i~~lvi~k~l~k~~Y~~~~phv~~A~rl~~rd  866 (1054)
T PTZ00166        832 RIDISLLVITKSLGKDDYEGRLAHVELAKKLRQRD  866 (1054)
T ss_pred             CCCHHHEEEEEEechhhCCCCCcHHHHHHHHHHhC
Confidence            99999999999999955557799999999999873

>KOG0969|consensus

Probab=100.00  E-value=1.4e-81  Score=722.19  Aligned_cols=492  Identities=28%  Similarity=0.432  Sum_probs=419.3

Q ss_pred             cHHHHHHHHHH-HHHhcCCcceEEeeeeeccccCCCCCCCCccEEEE---EeccCCCCCCCCCcCCce-eeecccCchhh
Q psy6283         274 SIAQVYSEFDQ-IATQYKILDFKSRKIEKKYAFNLPGVPDLSEYLEV---RYSAKCPALPSDLSGDTF-SHVFGTKTSFL  348 (1030)
Q Consensus       274 ~~~~v~~e~~~-~~~~~~i~~~~~k~v~~~yaf~~~~vp~~~~~lkv---~y~~~~p~~~~~~~g~tf-s~vfG~~~~~~  348 (1030)
                      .+..+..|+++ +...|+|.+|           +.|-+-.-+.-|+|   -|.++...+-+.++-.|| |+.||+.++- 
T Consensus       344 ~W~~firevDPDvI~GYNi~nF-----------DiPYll~RA~~L~Ie~Fp~LGRikn~~s~irDttfSSkq~GtRetK-  411 (1066)
T KOG0969|consen  344 SWRKFIREVDPDVIIGYNICNF-----------DIPYLLNRAKTLGIENFPYLGRIKNSRSVIRDSTFSSKQYGTRETK-  411 (1066)
T ss_pred             HHHHHHHhcCCCeEeccccccc-----------ccceecChHhhcCcccccccceecccceeeeccccchhhcCcccce-
Confidence            45667777776 6778888876           33333333444544   344555555667788999 5899999998 


Q ss_pred             hhHHhhhhccCCeEEEec----------CccCCCCcCccc---cceEeecchhhhcccCeEEEEccHHHHHHHHHHHHHH
Q psy6283         349 ENLLLERKIKGPSWLEFP----------EAEKFPSRISWC---KYEVQCNQMEKIRSKQGLIYLIGIVEFIKFTMLHSSY  415 (1030)
Q Consensus       349 E~f~l~~~i~Gp~wl~i~----------~~~~~~~~~s~c---k~e~~~~~~~~l~~~~~vivr~Gl~~lv~Y~~~Da~l  415 (1030)
                           ..+|.|.-.+++.          ++++|+.+..+.   |-+|..+.+.+|+++|.-    -..+|+.||++||+|
T Consensus       412 -----~v~I~GRlqfDllqvi~Rd~KLrSytLNaVs~hFL~EQKEDV~~siItdLQng~~~----TRRRlA~YCLkDAYL  482 (1066)
T KOG0969|consen  412 -----EVNIDGRLQFDLLQVILRDYKLRSYTLNAVSAHFLGEQKEDVHHSIITDLQNGNEQ----TRRRLAVYCLKDAYL  482 (1066)
T ss_pred             -----EEeecceeeehHHHHHHHhhhhhhcchhhhHHHhhhhhcccccccchhhhhcCcHH----HHHHHHHHHhhhhcc
Confidence                 6889999888773          444444443333   447777766677665420    178999999999999


Q ss_pred             HHHHHHHhcchHHHHHHHHHhCCcchhhccCchhHHHHHHHHHHHhhcCeeccCCccccCcCCCccccccccCCCCCCcc
Q psy6283         416 IIKIMCELNVLPLAIQITNVCGNVLSRTLMGGRSERNEFLLLHAFHEKSYVLPDKQYGKNKKEGEETGEANKGKGRKKAA  495 (1030)
Q Consensus       416 ~~~L~~kl~vlpl~~~lt~iaG~~~srtl~~gr~~r~E~lLL~~~~~~~yivPdk~~~kk~~~~~d~~~~~~~~~~~~~~  495 (1030)
                      .++|+.+|.+|-.+.+|++++|+|++..|+.|++.++-++||+.+...++++|+-...                +.....
T Consensus       483 PlRLlekLM~ivNy~EMARVTGVP~syLltRGqqIKVlSqLlRkakq~~~~~P~i~~~----------------~s~~e~  546 (1066)
T KOG0969|consen  483 PLRLLEKLMVIVNYTEMARVTGVPISYLLTRGQQIKVLSQLLRKAKQKDFVIPNIKSQ----------------GSDDEQ  546 (1066)
T ss_pred             hHHHHHHHHHHHhHHhhhhhhCCcHHHHHhCCcchHHHHHHHHHHhhcCeeeeeeccc----------------CCcccc
Confidence            9999999999999999999999999999999999999999999999999999986432                112357


Q ss_pred             ccCceeeccccccccceEEEeeccccChhHHHHhccccccccccCC-----CccccccccC---CCCCccccCCcchHHH
Q psy6283         496 YSGGLVLEPKKGFYDKFIILMDFNSLYPSIIQEYNICFTTIPVRML-----QDSDITTLCE---YLPEHQVDTGILPSEI  567 (1030)
Q Consensus       496 Y~GGlVleP~~GlY~~~V~vLDFnSLYPSII~~~NIc~tTv~~~~~-----d~~~i~~~~p---~~p~~~~~~GIlP~iL  567 (1030)
                      |+||.|++|..|||+.||+.|||+|||||||++||+||||++....     +++.+  ..|   +|.....++|+||.+|
T Consensus       547 yEGatVIEp~kGfY~~PIATLDFaSLYPSIMmahNLCYtTLl~~~t~~~l~~~~~~--~TP~g~yFv~~~~rkGlLP~IL  624 (1066)
T KOG0969|consen  547 YEGATVIEPRKGFYDKPIATLDFASLYPSIMMAHNLCYTTLLTKETVEKLGDEDYT--RTPTGDYFVKTEVRKGLLPEIL  624 (1066)
T ss_pred             ccccEEeecccccCCCCceeeehhhhhhHHHHHhhhhheeccccchhhhcCcccee--ECCCCCeeeehhhhccccHHHH
Confidence            9999999999999999999999999999999999999999987653     11121  123   3677788999999999


Q ss_pred             HHHHHHHHHHHHHhcCCCCChHHHHhhHHHHHHhccccccccccCCCCCCCCCCHHHHHHHHHHhHHHHHHHHHHhhh--
Q psy6283         568 KKLVESRRQVKALMKQPNLSSDLLMQYDIRQKALKLTANSMYGCLGFPNSRFFAQPLAALVTAKGREILLNTKSLVEN--  645 (1030)
Q Consensus       568 ~~Ll~~R~~vKk~mk~~~~~~~~~~~~d~rQ~AlKl~aNS~YG~lG~~~srfy~~~lA~~IT~~GR~iL~~tkelve~--  645 (1030)
                      .+||..|+.+|+.|+. ++||..++.||.||+|||+.|||.||++|++.+.++|.++..+||++||+||..|+.++|+  
T Consensus       625 e~ll~aRKraK~dlk~-ekDp~kr~vldGRQLAlKisANSvYGFTGAtvGkLPCleIS~SVT~yGR~MI~~TK~~Ve~~y  703 (1066)
T KOG0969|consen  625 EDLLTARKRAKADLKK-EKDPFKRAVLDGRQLALKISANSVYGFTGATVGKLPCLEISQSVTAYGRQMIEKTKKLVEEKY  703 (1066)
T ss_pred             HHHHHHHHHHHHHHHh-ccCHHHHhhhcchhhheeecccccccccccccCccceeeechhhHHHHHHHHHHHHHHHHHHh
Confidence            9999999999999999 7899999999999999999999999999999999999999999999999999999999996  


Q ss_pred             -------ccceeEEecCcceeeecCCCCHHHHHHHHHHHHHHHhccc-ceeEEeecchhhhhhhcccccceEEeeeecCC
Q psy6283         646 -------LNYEVIYGDTDSLMISCNVNDYDSVFKIGNQIKSECNKLY-KQLELDIDGVYKYMLLLKKKKYAALSISKLSN  717 (1030)
Q Consensus       646 -------~g~~VIYGDTDSI~V~~~~~d~eea~~ig~~i~~~Vn~~~-~~leLe~E~vf~~llll~KKrYa~l~~~~~~d  717 (1030)
                             .++.|||||||||||+++..+.++|+++|.++++.|+..| +||.||||+||.+.||+.||||||+.|.+...
T Consensus       704 ~~~ngy~~da~ViYGDTDSVMv~Fgv~~v~~am~lg~eaa~~vs~~F~~PIkLEFEKvY~PYLLInKKRYAGL~~t~pd~  783 (1066)
T KOG0969|consen  704 TIKNGYSHDAVVIYGDTDSVMVKFGVSDVEEAMKLGREAAEYVSSKFVKPIKLEFEKVYFPYLLINKKRYAGLLWTNPDV  783 (1066)
T ss_pred             hhccCCccccEEEecCCceEEEecCchhHHHHHHHhHHHHHHHHhcCCCCceeEeeeeecceEEeccceeeeeEeccCCc
Confidence                   3568999999999999999999999999999999999988 58999999999999999999999999985433


Q ss_pred             CceeeeceeeeeeeeeCChHHHHHHHHHHHHHHHhccCCCCCCChhHHHHHHHHHHHHHHHHhhCCCcChhhhHHhhccc
Q psy6283         718 GKMICSQEIKGVDVVRRDWSQLASEAGKFVISQILDEQSYTDYSLDDRLQNIHEHMKKIRTDLDNGFVPLTLLEITKQLT  797 (1030)
Q Consensus       718 G~~~~~~e~KGle~vRRD~~~l~k~~~~~vL~~IL~~~~~~~~~~e~~v~~I~~~l~~~~~~l~~g~vpl~~lvItk~Ls  797 (1030)
                         ..+++.||++.||||+|+|++++...+|+.||.+.     +++.+++.+++.    +.+|..+.++++.|||+|.|+
T Consensus       784 ---~DkmD~kGietVRRDnc~LV~~v~~~~L~kiLi~r-----dv~gA~~fvk~~----IsDlL~nriDiS~LVItK~Lt  851 (1066)
T KOG0969|consen  784 ---FDKMDCKGIETVRRDNCPLVANVVNTVLRKILIER-----DVEGALAFVKDT----ISDLLCNRIDISLLVITKELT  851 (1066)
T ss_pred             ---CccccccccchhccCCchHHHHHHHHHHHHHHhhc-----ChHHHHHHHHHH----HHHHHhcccceeeeeeeehhc
Confidence               24789999999999999999999999999999999     887777776654    567888999999999999999


Q ss_pred             CCCCC--CcchHHHHHHHHHHc
Q psy6283         798 KAPEG--GKVCITQIRLSRNRR  817 (1030)
Q Consensus       798 K~p~~--~~~pHV~vA~r~~~~  817 (1030)
                      |.-.+  ..++||++|.||+++
T Consensus       852 kagd~Y~~kqaHveLAermrkR  873 (1066)
T KOG0969|consen  852 KAGDDYAAKQAHVELAERMRKR  873 (1066)
T ss_pred             ccccchhhhhhhHHHHHHhhhc
Confidence            98666  789999999999887

>PHA03036 DNA polymerase; Provisional

Probab=100.00  E-value=5.4e-76  Score=716.00  Aligned_cols=398  Identities=23%  Similarity=0.328  Sum_probs=345.3

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHhcchHHHHHHHHHhCCcchhhccCchhHHHHHHHHHHHhhcCeeccCCccccCcCCCcc
Q psy6283         402 IVEFIKFTMLHSSYIIKIMCELNVLPLAIQITNVCGNVLSRTLMGGRSERNEFLLLHAFHEKSYVLPDKQYGKNKKEGEE  481 (1030)
Q Consensus       402 l~~lv~Y~~~Da~l~~~L~~kl~vlpl~~~lt~iaG~~~srtl~~gr~~r~E~lLL~~~~~~~yivPdk~~~kk~~~~~d  481 (1030)
                      ..+++.||++||.|+++|+.++.++.-..+++..+.+|..+++..+++.+++.+||+.+.+.|+++|....         
T Consensus       454 r~rla~YClkDa~L~l~L~~~l~~~~~v~~~a~~~~lp~~~~i~~~~s~~i~~qllr~~~~~~~i~p~~~~---------  524 (1004)
T PHA03036        454 ALEMARYCIHDACLCKYLWEYYGIETKIDAGASTYLLPQSMVFEYRASTLIKGPLLKLLLEEKTILVRSET---------  524 (1004)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCChhheEeeeeccccccHHHHHHHHCCcccccCCC---------
Confidence            68899999999999999999999988889999999999999999999999999999999999999983211         


Q ss_pred             ccccccCCCCCCccccCceeeccccccccceEEEeeccccChhHHHHhccccccccccCCCcc---------ccc-----
Q psy6283         482 TGEANKGKGRKKAAYSGGLVLEPKKGFYDKFIILMDFNSLYPSIIQEYNICFTTIPVRMLQDS---------DIT-----  547 (1030)
Q Consensus       482 ~~~~~~~~~~~~~~Y~GGlVleP~~GlY~~~V~vLDFnSLYPSII~~~NIc~tTv~~~~~d~~---------~i~-----  547 (1030)
                               ....+|+||+|++|++|+|++||++|||+|||||||++|||||+|+++..+..+         .+.     
T Consensus       525 ---------~~~~~YeGa~VlEP~~G~Y~~pV~vLDFaSLYPSIIia~NLcyeTlv~~~~~~~~~~~~i~~~~i~~~~p~  595 (1004)
T PHA03036        525 ---------KNKFPYEGGKVFAPKQKMFDNNVLIFDYNSLYPNVCIFGNLSPETLVGVVVNDNRLEAEINKQELRRKYPY  595 (1004)
T ss_pred             ---------CccCCcCceEEecCCCCcccCCEEEEEccccchHHHHHhCCCcCeEeeccccccccccccccccccccCCC
Confidence                     123479999999999999998999999999999999999999999986432000         000     


Q ss_pred             -c----cc-CC---C-----CCccccCCcchHHHHHHHHHHHHHHHHhcCCCCChHHHHhhHHHHHHhccccccccccCC
Q psy6283         548 -T----LC-EY---L-----PEHQVDTGILPSEIKKLVESRRQVKALMKQPNLSSDLLMQYDIRQKALKLTANSMYGCLG  613 (1030)
Q Consensus       548 -~----~~-p~---~-----p~~~~~~GIlP~iL~~Ll~~R~~vKk~mk~~~~~~~~~~~~d~rQ~AlKl~aNS~YG~lG  613 (1030)
                       +    .| |.   +     .....++||||++|+.|++.|+++|++|++ ..+|.++.+||.+|+|+|++|||+|||+|
T Consensus       596 ~dy~~v~~~~~~~~~v~~~~vf~~~rkGILP~iL~~Ll~~Rk~~Kk~mK~-~~d~~e~~~lD~rQlAlKI~aNS~YG~~G  674 (1004)
T PHA03036        596 PRYIYVHCEPRSPDLVSEIAVFDRRIEGIIPKLLKTFLEERARYKKLLKE-ATSSVEKAIYDSMQYTYKIVANSVYGLMG  674 (1004)
T ss_pred             ccceeeeccCCcccccccceeecCCCCcChHHHHHHHHHHHHHHHHHHhh-CCChHHHHHHHHHHHHHHHHHhccccccc
Confidence             0    01 21   1     112458999999999999999999999998 56888899999999999999999999999


Q ss_pred             CCCCCCCCHHHHHHHHHHhHHHHHHHHHHhhh--------------------------------------ccceeEEecC
Q psy6283         614 FPNSRFFAQPLAALVTAKGREILLNTKSLVEN--------------------------------------LNYEVIYGDT  655 (1030)
Q Consensus       614 ~~~srfy~~~lA~~IT~~GR~iL~~tkelve~--------------------------------------~g~~VIYGDT  655 (1030)
                      +++|+|||.++|++||++||++|+.|+++++.                                      +|++||||||
T Consensus       675 ~~~~rly~~~iA~sVTa~GR~mI~~tk~~Ve~~~~~~~~~~l~~~p~~~f~~~~r~~~~~~~~~l~~~~~~g~kVIYGDT  754 (1004)
T PHA03036        675 FRNSALYSYASAKSCTAIGRNMIKYLNSVLNGSKLINGKLILANCPINPFFKDDRSIDTNYDTNLPVEYNFTFRSVYGDT  754 (1004)
T ss_pred             ccCccccCHHHHHHHHHHHHHHHHHHHHHhhcccccchhhhhhhccccccccccccccccccccccccccCCcEEEEEec
Confidence            99999999999999999999999999876531                                      6899999999


Q ss_pred             cceeeecCCCCHHHHHHHHHHHHHHHhcc--cceeEEeecchhhhhhhcccccceEEeeeecCCCceeeeceeeeeeeee
Q psy6283         656 DSLMISCNVNDYDSVFKIGNQIKSECNKL--YKQLELDIDGVYKYMLLLKKKKYAALSISKLSNGKMICSQEIKGVDVVR  733 (1030)
Q Consensus       656 DSI~V~~~~~d~eea~~ig~~i~~~Vn~~--~~~leLe~E~vf~~llll~KKrYa~l~~~~~~dG~~~~~~e~KGle~vR  733 (1030)
                      |||||+++..+.++++++|.++++.||+.  +++++||||+||.++||++||||||+.+++..+|...+++++||+++||
T Consensus       755 DSVFV~~~~~d~eea~~ig~ela~~In~~lf~~pikLEfEKVY~~lLLl~KKRYAGl~~~~~~~~~~~~kid~KGie~VR  834 (1004)
T PHA03036        755 DSVFLEINTKDVDKSIKIAKELERIINEKVLFDNFKIEFEAVYKNLIMQSKKKYTTLKYIASSTDGSVPERVNKGTSETR  834 (1004)
T ss_pred             CeeEEEcCCCCHHHHHHHHHHHHHHHHHHhcCCCeEEEehhhHHHHHhhhhhheeeEeeccccCCCCceEEEEECceeEe
Confidence            99999999889999999999999999973  5799999999999999999999999998764323334678999999999


Q ss_pred             CChHHHHHHHHHHHHHHH---hccCCCCCCChhHHHHHHHHHHHHHHHHhhCCCcChhhhHHhhcccCCCCCCcchHHHH
Q psy6283         734 RDWSQLASEAGKFVISQI---LDEQSYTDYSLDDRLQNIHEHMKKIRTDLDNGFVPLTLLEITKQLTKAPEGGKVCITQI  810 (1030)
Q Consensus       734 RD~~~l~k~~~~~vL~~I---L~~~~~~~~~~e~~v~~I~~~l~~~~~~l~~g~vpl~~lvItk~LsK~p~~~~~pHV~v  810 (1030)
                      ||||+|++++++.+++.|   |++.+..  +.+.+++.+++.+.++...+++|.+|+++|+|+++|+++..+..+|||+|
T Consensus       835 RD~c~fvK~v~~~vi~~L~~iL~~~d~~--~~~~~i~~Lk~~i~dL~~n~~~~~vple~LviSk~l~~~Yk~~~~ph~~l  912 (1004)
T PHA03036        835 RDVSKFHKYMIKIYKTRLLDMLSEGNMN--SNQVCIDILRSLEKDLIIEFDSRSAPLEMFLLSRTHHCNYKSPDNPNMYL  912 (1004)
T ss_pred             CchHHHHHHHHHHHHHHHHHHhccCCch--hHHHHHHHHHHHHHHHHHHHhcCCCCHHHHhhhhcccccCCCCCCCHHHH
Confidence            999999999999977655   8776111  35678888888888888889999999999999999999977766999999


Q ss_pred             HHHHHHcCCc
Q psy6283         811 RLSRNRRGRR  820 (1030)
Q Consensus       811 A~r~~~~g~~  820 (1030)
                      |.||+++...
T Consensus       913 a~r~~~r~~~  922 (1004)
T PHA03036        913 VNEYNKNNPE  922 (1004)
T ss_pred             HHHHHhhCCC
Confidence            9999987654

>cd05534 POLBc_zeta DNA polymerase type-B zeta subfamily catalytic domain

Probab=100.00  E-value=1.1e-75  Score=680.18  Aligned_cols=347  Identities=27%  Similarity=0.419  Sum_probs=300.9

Q ss_pred             chhHHHHHHHHHHHhhcCeeccCCccccCcCCCccccccccCCCCCCccccCceeeccccccccceEEEeeccccChhHH
Q psy6283         447 GRSERNEFLLLHAFHEKSYVLPDKQYGKNKKEGEETGEANKGKGRKKAAYSGGLVLEPKKGFYDKFIILMDFNSLYPSII  526 (1030)
Q Consensus       447 gr~~r~E~lLL~~~~~~~yivPdk~~~kk~~~~~d~~~~~~~~~~~~~~Y~GGlVleP~~GlY~~~V~vLDFnSLYPSII  526 (1030)
                      |++.|+|++||+.+++.||++|+.....              .....+.|+||+|++|++|||++||++|||+|||||||
T Consensus         1 g~q~rve~~llr~~~~~g~~~p~~~~~~--------------~~~~~~~~~g~~V~eP~~G~y~~~V~vLDF~SLYPSIi   66 (451)
T cd05534           1 GSQFRVESMLLRLAKPENYILPSPSRQQ--------------VAQQRALECLPLVMEPESGFYSDPVIVLDFQSLYPSIM   66 (451)
T ss_pred             CCeEEeHHHHHHHHHHcCEEeecCchhc--------------cccccccccCcEeecCCcCcccCceEEEecccccHHHH
Confidence            5788999999999999999999764210              01124678999999999999999999999999999999


Q ss_pred             HHhccccccccccCCC----c----------------------cccccccCC---CCCccccCCcchHHHHHHHHHHHHH
Q psy6283         527 QEYNICFTTIPVRMLQ----D----------------------SDITTLCEY---LPEHQVDTGILPSEIKKLVESRRQV  577 (1030)
Q Consensus       527 ~~~NIc~tTv~~~~~d----~----------------------~~i~~~~p~---~p~~~~~~GIlP~iL~~Ll~~R~~v  577 (1030)
                      ++|||||||+++...+    .                      +.+. .+|.   |...+.+.||||.+|+.|++.|.++
T Consensus        67 ~~~Nic~sT~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~p~~~~f~~~~~~~Gilp~iL~~Ll~~R~~~  145 (451)
T cd05534          67 IAYNYCYSTCLGRVEELNGGGKFGFLGVKLYLPPPPLDLLLLKDDVT-ISPNGVMFVKKSVRKGILPKMLEEILDTRIMV  145 (451)
T ss_pred             HHhCcCcccccccccccccccccccccccccccccccccccCCCcEE-ECCCcceeecCCCCCCchHHHHHHHHHHHHHH
Confidence            9999999999864210    0                      0010 1121   3333458999999999999999999


Q ss_pred             HHHhcCCCCChHHHHhhHHHHHHhccccccccccCCCCC-CCCCCHHHHHHHHHHhHHHHHHHHHHhhh---ccceeEEe
Q psy6283         578 KALMKQPNLSSDLLMQYDIRQKALKLTANSMYGCLGFPN-SRFFAQPLAALVTAKGREILLNTKSLVEN---LNYEVIYG  653 (1030)
Q Consensus       578 Kk~mk~~~~~~~~~~~~d~rQ~AlKl~aNS~YG~lG~~~-srfy~~~lA~~IT~~GR~iL~~tkelve~---~g~~VIYG  653 (1030)
                      |++|++.+.++.++.+||.+|+|+||+|||+|||||+++ +||||.++|++||++||++|+.|++++++   +|++||||
T Consensus       146 K~~mk~~~~~~~~~~~ld~~Q~AlKi~~NS~YGy~G~~~~gr~~~~~iA~~IT~~GR~~l~~~~~~ie~~~~~g~~VIYG  225 (451)
T cd05534         146 KKAMKKYKDDKKLQRILDARQLALKLLANVTYGYTAASFSGRMPCVEIADSIVQTGRETLERAIELIESTPKWGAKVVYG  225 (451)
T ss_pred             HHHHhhCCCCHHHHHHHHHHHHHHHHHhhccccccccccccccccHHHHHHHHHHHHHHHHHHHHHHhhccccCceEEee
Confidence            999998666689999999999999999999999999997 59999999999999999999999999998   99999999


Q ss_pred             cCcceeeecCCCCHHHHHHHHHHHHHHHhcccc-eeEEeecchhhhhhhcccccceEEeeeecCCCceeeeceeeeeeee
Q psy6283         654 DTDSLMISCNVNDYDSVFKIGNQIKSECNKLYK-QLELDIDGVYKYMLLLKKKKYAALSISKLSNGKMICSQEIKGVDVV  732 (1030)
Q Consensus       654 DTDSI~V~~~~~d~eea~~ig~~i~~~Vn~~~~-~leLe~E~vf~~llll~KKrYa~l~~~~~~dG~~~~~~e~KGle~v  732 (1030)
                      |||||||++++.+.++++++|.+|++.||+.|+ +|+|++|++|.++||++||||||+.+++.+++  .+++++||+++|
T Consensus       226 DTDSvfv~~~~~~~~~~~~~~~~i~~~in~~~~~~i~le~E~vy~~~ll~~KKrYag~~~~~~~~~--~~ki~~KGle~v  303 (451)
T cd05534         226 DTDSLFVLLPGRTKEEAFKIGKEIAEAVTAANPSPIKLKFEKVYHPCVLVTKKRYVGYKYESPDQT--EPTFDAKGIETV  303 (451)
T ss_pred             cccceeEecCCCCHHHHHHHHHHHHHHHHHhCCCCceeeHHHHHHHHHHHhhhhEEEEEEecCCCC--CceEEeecceEE
Confidence            999999999988899999999999999999885 89999999999999999999999988764332  346799999999


Q ss_pred             eCChHHHHHHHHHHHHHHHhccCCCCCCChhHHHHHHHHHHHHHHHHhhCCCcChhhhHHhhcccCCCCC---CcchHHH
Q psy6283         733 RRDWSQLASEAGKFVISQILDEQSYTDYSLDDRLQNIHEHMKKIRTDLDNGFVPLTLLEITKQLTKAPEG---GKVCITQ  809 (1030)
Q Consensus       733 RRD~~~l~k~~~~~vL~~IL~~~~~~~~~~e~~v~~I~~~l~~~~~~l~~g~vpl~~lvItk~LsK~p~~---~~~pHV~  809 (1030)
                      |||||+|++++++.+|+.||.++     +.+    .+++++.+.+.+|++|.+|+++|+|+++|++.++.   ..+|||+
T Consensus       304 RrD~~~~~k~~~~~vl~~il~~~-----d~~----~~~~~l~~~~~~l~~g~~~~~dlii~k~l~~~~y~~~~~~p~hv~  374 (451)
T cd05534         304 RRDGCPAVQKILEKSLRILFETK-----DLS----TVKSYLQRQWSKLLQGRVSIQDFIFAKEVRLGTYKEGATLPAGAI  374 (451)
T ss_pred             ecccHHHHHHHHHHHHHHHhccC-----CHH----HHHHHHHHHHHHHHcCCCCHHHeEEEEEeeccccCccCCCChHHH
Confidence            99999999999999999999887     644    55667778888999999999999999999998743   4568999


Q ss_pred             HHHHHHHcCC
Q psy6283         810 IRLSRNRRGR  819 (1030)
Q Consensus       810 vA~r~~~~g~  819 (1030)
                      ||+++++++.
T Consensus       375 ~A~k~~~~~~  384 (451)
T cd05534         375 VALRRMEKDP  384 (451)
T ss_pred             HHHHHHHhCC
Confidence            9988887763

DNA polymerase (Pol) zeta is a member of the eukaryotic B-family of DNA polymerases and distantly related to DNA Pol delta. Pol zeta plays a major role in translesion replication and the production of either spontaneous or induced mutations. Apart from its role in translesion replication, Pol zeta also appears to be involved in somatic hypermutability in B lymphocytes, an important element for the production of high affinity antibodies in response to an antigen.

>PRK05761 DNA polymerase I; Reviewed

Probab=100.00  E-value=3.3e-74  Score=704.73  Aligned_cols=395  Identities=24%  Similarity=0.330  Sum_probs=333.8

Q ss_pred             EccHHHHHHHHHHHHHHHHHHH--HHhcchHHHHHHHHHhCCcchhhccCchhHHHHHHHHHHHhhcCeeccCCccccCc
Q psy6283         399 LIGIVEFIKFTMLHSSYIIKIM--CELNVLPLAIQITNVCGNVLSRTLMGGRSERNEFLLLHAFHEKSYVLPDKQYGKNK  476 (1030)
Q Consensus       399 r~Gl~~lv~Y~~~Da~l~~~L~--~kl~vlpl~~~lt~iaG~~~srtl~~gr~~r~E~lLL~~~~~~~yivPdk~~~kk~  476 (1030)
                      ++.+..|+.||++||.+|++|+  .+..+|++..+|++++|.|+.++..++.+.+++++|++++++.||++|++......
T Consensus       313 ~~~~~~l~~Y~l~Da~l~~~L~~f~~~~~l~~~~elarit~lpl~~v~r~~~g~~i~~~l~~~a~~~~~liP~~~~~~~~  392 (787)
T PRK05761        313 ELDLEELAEYNFRDAEITLKLTFFNNELVLKLILLLSRISKLPIEELSRATISTWISNLEYWEHRKRGWLIPWKEDILRL  392 (787)
T ss_pred             ccCHHHHHHHHHHHHHHHHHHHHhhhhhHHHHHHHHHHHHCcCHHHHhccCHHHHHHHHHHHHHHhCCEeCCCCcccccc
Confidence            3447899999999999999995  36789999999999999999999878888999999999999999999987641100


Q ss_pred             CCCccccccccCCCCCCccccCceeeccccccccceEEEeeccccChhHHHHhccccccccccCCCccccccccCCC--C
Q psy6283         477 KEGEETGEANKGKGRKKAAYSGGLVLEPKKGFYDKFIILMDFNSLYPSIIQEYNICFTTIPVRMLQDSDITTLCEYL--P  554 (1030)
Q Consensus       477 ~~~~d~~~~~~~~~~~~~~Y~GGlVleP~~GlY~~~V~vLDFnSLYPSII~~~NIc~tTv~~~~~d~~~i~~~~p~~--p  554 (1030)
                      ..  +   ..........+|.||+|++|.+|+|++ |++|||+|||||||++|||||+|+++..++.... ...+..  .
T Consensus       393 ~~--~---~~~~~~~~~~~y~Gg~V~~P~~G~y~~-V~vlDF~SLYPSIi~~~Ni~p~T~~~~~~~~~~~-~~~~~~~~~  465 (787)
T PRK05761        393 DH--E---VYKKAIIKGKKYRGGLVFQPPPGIFFN-VYVLDFASLYPSIIVKWNLSPETVRIPECKCHYD-DEVPELGHS  465 (787)
T ss_pred             cc--c---cccccccccCCcCCcEEeccCCCceee-EEEeeecccchHHHHHhCCChhhccCcccccccc-CCCCCCCce
Confidence            00  0   000112235689999999999999998 9999999999999999999999999776421110 000000  1


Q ss_pred             CccccCCcchHHHHHHHHHHHHHHHHhcCCC-CChHHHHhhHHHHHHhccccccccccCCCCCCCCCCHHHHHHHHHHhH
Q psy6283         555 EHQVDTGILPSEIKKLVESRRQVKALMKQPN-LSSDLLMQYDIRQKALKLTANSMYGCLGFPNSRFFAQPLAALVTAKGR  633 (1030)
Q Consensus       555 ~~~~~~GIlP~iL~~Ll~~R~~vKk~mk~~~-~~~~~~~~~d~rQ~AlKl~aNS~YG~lG~~~srfy~~~lA~~IT~~GR  633 (1030)
                      ....+.||+|.+|..|++.|+++|+.|++.. .+++++.+||.+|+|+||+|||+|||||++++||||+++|++||++||
T Consensus       466 ~~~~~~gl~~~il~~l~~~R~~~k~~~~~~~~~~~~~~~~ld~~Q~AlKi~~NS~YGy~G~~~~r~~~~~~A~~IT~~GR  545 (787)
T PRK05761        466 VCDDRPGLTSVLVGLLRDFRVKIYKKKAKDPNLDEERRAWYDVVQRALKVFLNASYGVFGAENFKLYRIEVAESITALGR  545 (787)
T ss_pred             eecCCCCchHHHHHHHHHHHHHHHHHhhccCCCCHHHHHHHHHHHHhheeeeecccccccccCCCCCCHHHHHHHHHHHH
Confidence            1235899999999999999999999998743 478899999999999999999999999999999999999999999999


Q ss_pred             HHHHHHHHHhhhccceeEEecCcceeeecCCCCHHHHHHHHHHHHHHHhcccceeEEeecchhhhhhhc-ccccceEEee
Q psy6283         634 EILLNTKSLVENLNYEVIYGDTDSLMISCNVNDYDSVFKIGNQIKSECNKLYKQLELDIDGVYKYMLLL-KKKKYAALSI  712 (1030)
Q Consensus       634 ~iL~~tkelve~~g~~VIYGDTDSI~V~~~~~d~eea~~ig~~i~~~Vn~~~~~leLe~E~vf~~llll-~KKrYa~l~~  712 (1030)
                      ++|+.|+++++++|++|||||||||||+.+.  .+.+.    ++.+.|++.+ +|+||+|++|.+++|. +||||||+. 
T Consensus       546 ~~l~~t~~~ie~~g~~VIYGDTDSvfv~~~~--~~~~~----~l~~~i~~~~-~i~LE~Ek~y~~~l~~~~KKrYag~~-  617 (787)
T PRK05761        546 EILLSTKKKAEELGLKVLYGDTDSLFVWGPT--KESLE----ELIKEIEERT-GIDLEVDKTYDWVAFSGLKKNYFGVL-  617 (787)
T ss_pred             HHHHHHHHHHHHcCCEEEEEeCceEEEECCC--HHHHH----HHHHHHHHhC-CCceEEEEEEEEEEEecccceEEEEe-
Confidence            9999999999999999999999999999764  23333    4556666666 4999999999999985 999999996 


Q ss_pred             eecCCCceeeeceeeeeeeeeCChHHHHHHHHHHHHHHHhccCCCCCCChh---HHHHHHHHHHHHHHHHhhCCCcChhh
Q psy6283         713 SKLSNGKMICSQEIKGVDVVRRDWSQLASEAGKFVISQILDEQSYTDYSLD---DRLQNIHEHMKKIRTDLDNGFVPLTL  789 (1030)
Q Consensus       713 ~~~~dG~~~~~~e~KGle~vRRD~~~l~k~~~~~vL~~IL~~~~~~~~~~e---~~v~~I~~~l~~~~~~l~~g~vpl~~  789 (1030)
                         .+|+    +++||++++|||||+|++++|..+|+.||.++     +++   .++..+++++.+.+.+|++|++|+++
T Consensus       618 ---~dgk----i~~KG~e~vRrD~~~~~k~~~~~vl~~ll~~~-----~~~~~~~~~~~~~~~v~~~~~~l~~g~~~~~~  685 (787)
T PRK05761        618 ---KDGK----VKIKGIVAKKRNTPEFVKELQREVLEVLKSIR-----SPEDVEKVKDEIEDVLKRYYEKLRAKDYPLDE  685 (787)
T ss_pred             ---cCCe----EEEEEEEEEeCCchHHHHHHHHHHHHHHhcCC-----ChhHHHHHHHHHHHHHHHHHHHHHcCCCCHHH
Confidence               3564    58999999999999999999999999999988     554   45668999999999999999999999


Q ss_pred             hHHhhcccCCCCC---CcchHHHHHHHHHHcCCc
Q psy6283         790 LEITKQLTKAPEG---GKVCITQIRLSRNRRGRR  820 (1030)
Q Consensus       790 lvItk~LsK~p~~---~~~pHV~vA~r~~~~g~~  820 (1030)
                      |+|+++|+|++++   +++|||+||++|.+.|..
T Consensus       686 lvi~k~l~k~~~~Y~~~~~~hv~aa~~~~~~g~~  719 (787)
T PRK05761        686 LAIRVRLSKPLDEYTKNTPQHVKAALQLRDYGVE  719 (787)
T ss_pred             EEEEeeecCCHHHhcCCCchHHHHHHHHHhCCCC
Confidence            9999999999887   467999999999887743

>PRK05762 DNA polymerase II; Reviewed

Probab=100.00  E-value=4.2e-74  Score=707.35  Aligned_cols=367  Identities=28%  Similarity=0.459  Sum_probs=326.4

Q ss_pred             cHHHHHHHHHHHHHHHHHHHHHhcchHHHHHHHHHhCCcchhhccCchhHHHHHHHHHHHhhcCeeccCCccccCcCCCc
Q psy6283         401 GIVEFIKFTMLHSSYIIKIMCELNVLPLAIQITNVCGNVLSRTLMGGRSERNEFLLLHAFHEKSYVLPDKQYGKNKKEGE  480 (1030)
Q Consensus       401 Gl~~lv~Y~~~Da~l~~~L~~kl~vlpl~~~lt~iaG~~~srtl~~gr~~r~E~lLL~~~~~~~yivPdk~~~kk~~~~~  480 (1030)
                      +...|+.||++||.+|+.|+.+++++|++.++|+++|++|++++  |++.++|++||+++|+.||++|++...       
T Consensus       326 ~~~~l~~Y~l~Da~lt~~L~~kl~ll~~~~ela~l~g~~~~~v~--~~~~~~e~lll~~~~~~g~v~P~~~~~-------  396 (786)
T PRK05762        326 DKPALARYNLKDCELVTRIFEKTKLLPFLLERATVTGLPLDRVG--GSVAAFEHLYLPRAHRAGYVAPNLGER-------  396 (786)
T ss_pred             hHHHHHHHHHHHHHHHHHHHHHhhHHHHHHHHHHHhCcCHHHhC--ccHHhHHHHHHHHHHHCCEeCCCcccc-------
Confidence            36889999999999999999999999999999999999999975  677788999999999999999986421       


Q ss_pred             cccccccCCCCCCccccCceeeccccccccceEEEeeccccChhHHHHhccccccccccCCCc--cccccccCC-CCCcc
Q psy6283         481 ETGEANKGKGRKKAAYSGGLVLEPKKGFYDKFIILMDFNSLYPSIIQEYNICFTTIPVRMLQD--SDITTLCEY-LPEHQ  557 (1030)
Q Consensus       481 d~~~~~~~~~~~~~~Y~GGlVleP~~GlY~~~V~vLDFnSLYPSII~~~NIc~tTv~~~~~d~--~~i~~~~p~-~p~~~  557 (1030)
                                 ....|.||+|++|+||||++ |++|||+|||||||++|||||+|++...+.+  +.+..  |. .-. .
T Consensus       397 -----------~~~~y~Gg~V~~p~~G~y~~-V~~lDF~SLYPSIi~~~Ni~p~T~~~~~~~~~~~~~~~--~~~~~f-~  461 (786)
T PRK05762        397 -----------PGEASPGGYVMDSKPGLYDS-VLVLDFKSLYPSIIRTFNIDPDGLVEGLAQPPEESVAG--FLGARF-S  461 (786)
T ss_pred             -----------cccccCccEEecCCCCCcCc-eEEEEchhhhHHHHHHhCcCccceecCCCCCCcccccC--CCCccc-c
Confidence                       23579999999999999997 9999999999999999999999998654311  11110  10 001 1


Q ss_pred             ccCCcchHHHHHHHHHHHHHHHHhcCCCCChHHHHhhHHHHHHhccccccccccCCCCCCCCCCHHHHHHHHHHhHHHHH
Q psy6283         558 VDTGILPSEIKKLVESRRQVKALMKQPNLSSDLLMQYDIRQKALKLTANSMYGCLGFPNSRFFAQPLAALVTAKGREILL  637 (1030)
Q Consensus       558 ~~~GIlP~iL~~Ll~~R~~vKk~mk~~~~~~~~~~~~d~rQ~AlKl~aNS~YG~lG~~~srfy~~~lA~~IT~~GR~iL~  637 (1030)
                      .+.||||.+|+.|++.|+++|+.|++            .+|+|+|++|||+|||||++++||||+++|++||+.||++|+
T Consensus       462 k~~gilp~~l~~l~~~R~~~K~~~~~------------~~q~a~Ki~~Ns~YG~~g~~~~r~~~~~~A~~it~~Gr~~l~  529 (786)
T PRK05762        462 REKHFLPEIVERLWEGRDEAKREMNK------------PLSQAIKIIMNAFYGVLGSSGCRFFDPRLASSITMRGHEIMK  529 (786)
T ss_pred             ccCcchHHHHHHHHHHHHHHHHHHHH------------HHHHHHHhhhhhcccccccccccccChHHHHHHHHhHHHHHH
Confidence            27999999999999999999999975            589999999999999999999999999999999999999999


Q ss_pred             HHHHHhhhccceeEEecCcceeeecC-CCCHHHHHHHHHHHHHHHhcccc-----------eeEEeecchhhhhhhc---
Q psy6283         638 NTKSLVENLNYEVIYGDTDSLMISCN-VNDYDSVFKIGNQIKSECNKLYK-----------QLELDIDGVYKYMLLL---  702 (1030)
Q Consensus       638 ~tkelve~~g~~VIYGDTDSI~V~~~-~~d~eea~~ig~~i~~~Vn~~~~-----------~leLe~E~vf~~llll---  702 (1030)
                      .|++++++.|++|||||||||||+++ ..+.+++.++|.+|.+.||+.|.           +|+||+|++|.+++|+   
T Consensus       530 ~~~~~~~~~g~~viYgDTDSifv~~~~~~~~~~~~~~~~~l~~~in~~~~~~l~~~~~~~~~l~le~E~vy~~~~l~~~r  609 (786)
T PRK05762        530 QTRELIEAQGYQVIYGDTDSTFVWLGGAHDEEDAAKIGRALVQEINQWWQEHLQQEFGLESALELEFEKHYRRFFMPTIR  609 (786)
T ss_pred             HHHHHHHHCCCEEEeecCCceEEEcCCCCCHHHHHHHHHHHHHHHHHHHHhhhhhhccCCCceEEEEeeeeehhcccccc
Confidence            99999999999999999999999998 57889999999999999998543           7999999999999995   


Q ss_pred             -----ccccceEEeeeecCCCceeeeceeeeeeeeeCChHHHHHHHHHHHHHHHhccCCCCCCChhHHHHHHHHHHHHHH
Q psy6283         703 -----KKKKYAALSISKLSNGKMICSQEIKGVDVVRRDWSQLASEAGKFVISQILDEQSYTDYSLDDRLQNIHEHMKKIR  777 (1030)
Q Consensus       703 -----~KKrYa~l~~~~~~dG~~~~~~e~KGle~vRRD~~~l~k~~~~~vL~~IL~~~~~~~~~~e~~v~~I~~~l~~~~  777 (1030)
                           +||||||+.+..+++|    ++++||+++||||||+|+|++|.++|+.||.++     +.       ++++.++.
T Consensus       610 g~~~~~KKrYag~~~~~~~~~----~~~~KGle~vRrD~~~~~k~~~~~vl~~il~~~-----~~-------~~~~~~~~  673 (786)
T PRK05762        610 GAEEGSKKRYAGLIQEGDGDG----RIVFKGLETVRTDWTPLAKEFQQELYERIFRGE-----PY-------VDYVREVI  673 (786)
T ss_pred             ccchhhhheEEEEEEccCCCc----eEEEEeeEEECCChHHHHHHHHHHHHHHHhcCC-----CH-------HHHHHHHH
Confidence                 9999999988544444    468999999999999999999999999999988     43       56777888


Q ss_pred             HHhhCCCcChhhhHHhhcccCCCCC---CcchHHHHHHHHHHcCCc
Q psy6283         778 TDLDNGFVPLTLLEITKQLTKAPEG---GKVCITQIRLSRNRRGRR  820 (1030)
Q Consensus       778 ~~l~~g~vpl~~lvItk~LsK~p~~---~~~pHV~vA~r~~~~g~~  820 (1030)
                      .+|++|++| ++|+|+++|+|++++   +++|||+||+++++.|..
T Consensus       674 ~~l~~~~~~-~~lv~~k~l~k~~~~Y~~~~~phv~aa~~~~~~~~~  718 (786)
T PRK05762        674 DKLRAGELD-EKLVYRKRLRRPLDEYQRNVPPHVRAARLADEMGYK  718 (786)
T ss_pred             HHHHcCCCc-hhEEEEehcCCCHHHcCCCCCHHHHHHHHHHhcCcc
Confidence            999999999 999999999999988   679999999999998865

>COG0417 PolB DNA polymerase elongation subunit (family B) [DNA replication, recombination, and repair]

Probab=100.00  E-value=5.9e-73  Score=696.56  Aligned_cols=385  Identities=34%  Similarity=0.552  Sum_probs=348.0

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHhcchHHHHHHHHHhCCcchhhccCchhHHHHHHHHHHHhhcCeeccCCccccCcCCCcc
Q psy6283         402 IVEFIKFTMLHSSYIIKIMCELNVLPLAIQITNVCGNVLSRTLMGGRSERNEFLLLHAFHEKSYVLPDKQYGKNKKEGEE  481 (1030)
Q Consensus       402 l~~lv~Y~~~Da~l~~~L~~kl~vlpl~~~lt~iaG~~~srtl~~gr~~r~E~lLL~~~~~~~yivPdk~~~kk~~~~~d  481 (1030)
                      ...++.||+.|+.++++++.+.++||+..++++++|+++.+++.+|++.+++++|++++++.|+++|++....       
T Consensus       329 ~~~~~~~~l~~~~l~~~~~~~~~~l~~~~e~s~vsg~~~~~~~~~~~~~~~~~~l~~~a~~~~~~iP~~~~~~-------  401 (792)
T COG0417         329 KLRLLLYNLSDADLVLRILLKNELLPLLIELSRVSGLPLDDVTRAGSGARVEGLLLREAKRRGELIPNKEERP-------  401 (792)
T ss_pred             hhHHHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHhCCCHHHHcccchhHHHHHHHHHHHhhcCEeccCccccc-------
Confidence            6889999999999999999999999999999999999999999999999999999999999999999876321       


Q ss_pred             ccccccCCCCCCccccCceeeccccccccceEEEeeccccChhHHHHhccccccccccCCCccccccccCCCCCccccCC
Q psy6283         482 TGEANKGKGRKKAAYSGGLVLEPKKGFYDKFIILMDFNSLYPSIIQEYNICFTTIPVRMLQDSDITTLCEYLPEHQVDTG  561 (1030)
Q Consensus       482 ~~~~~~~~~~~~~~Y~GGlVleP~~GlY~~~V~vLDFnSLYPSII~~~NIc~tTv~~~~~d~~~i~~~~p~~p~~~~~~G  561 (1030)
                                ....|.||+|++|.||||+| |++|||+|||||||++|||||+|+++.++...... ....+.....++|
T Consensus       402 ----------~~~~~~Gg~V~~P~~Gly~~-V~vLDF~SLYPSII~~~Ni~p~T~~~~~~~~~~~~-~~~~~~~~~~~~G  469 (792)
T COG0417         402 ----------ERKKYKGGLVLEPEPGLYEN-VLVLDFSSLYPSIIIKYNISPDTLVEEDCSDDYSP-PGVGHGFCKREKG  469 (792)
T ss_pred             ----------hhhhcCCCEEccCCccccCc-EEEEEccccChHHHHHhCCCcceecCCCccccccC-CCCcccccccCCC
Confidence                      11579999999999999999 99999999999999999999999998765211110 0011333457899


Q ss_pred             cchHHHHHHHHHHHHHHHHhcCCCCChHHHHhhHHHHHHhccccccccccCCCCCCCCCCHHHHHHHHHHhHHHHHHHHH
Q psy6283         562 ILPSEIKKLVESRRQVKALMKQPNLSSDLLMQYDIRQKALKLTANSMYGCLGFPNSRFFAQPLAALVTAKGREILLNTKS  641 (1030)
Q Consensus       562 IlP~iL~~Ll~~R~~vKk~mk~~~~~~~~~~~~d~rQ~AlKl~aNS~YG~lG~~~srfy~~~lA~~IT~~GR~iL~~tke  641 (1030)
                      ++|.+|..|++.|.++|+.|++ ..++.++.+||.+|+||||+|||+|||+|+++|||||.+||++||++||++|..|++
T Consensus       470 ~lp~il~~L~~~R~~~K~~~k~-~~~~~e~~~~d~rQ~AlKvl~NS~YGy~G~~~~rf~~~e~a~~VT~~gR~ii~~t~~  548 (792)
T COG0417         470 FLPEILEELLDRRDEIKKKMKK-EKDPSERKLLDGRQLALKVLANSFYGYLGYSNSRFYCIECAESVTAFGREILRETKE  548 (792)
T ss_pred             chHHHHHHHHHHHHHHHHHhcc-cCChHHHHHHHHHHHHHHHHHhhccccccccCCccCCHHHHHHHHHHHHHHHHHHHH
Confidence            9999999999999999999999 466779999999999999999999999999999999999999999999999999999


Q ss_pred             HhhhccceeEEecCcceeeecCCCCHHHHHHHHHHHHHHHhccc-ceeEEeecchhhhhhhcc-cccceEEeeeecCCCc
Q psy6283         642 LVENLNYEVIYGDTDSLMISCNVNDYDSVFKIGNQIKSECNKLY-KQLELDIDGVYKYMLLLK-KKKYAALSISKLSNGK  719 (1030)
Q Consensus       642 lve~~g~~VIYGDTDSI~V~~~~~d~eea~~ig~~i~~~Vn~~~-~~leLe~E~vf~~llll~-KKrYa~l~~~~~~dG~  719 (1030)
                      +++++|+.|||||||||||.++....+++++++.++.+.||..+ .+|+||+|++|+++||+. ||||||+.+    +|.
T Consensus       549 ~ae~~G~~ViyGDTDSlfv~~~~~~~~ea~~~~~~l~~~vn~~~~~~i~lE~e~~y~~~ll~~~KKRYag~~~----~g~  624 (792)
T COG0417         549 LAEEMGLRVIYGDTDSLFVTLPGATYEEAIKIGEELVEEVNERLPSGIELEVEKVYKRFLLPTAKKRYAGLLE----DGD  624 (792)
T ss_pred             HHHHcCCEEEEECCceeEEEcCCCchHHHHHHHHHHHHHHhhcCCCCeEEEeeehhhhhhccccccceEEEec----cCC
Confidence            99999999999999999999998779999999999999999975 489999999999999999 999999964    342


Q ss_pred             eeeeceeeeeeeeeCChHHHHHHHHHHHHHHHhccCCCCCCChhHHHHHHHHHHHHHHHHhhCCCcChhhhHHhhcccCC
Q psy6283         720 MICSQEIKGVDVVRRDWSQLASEAGKFVISQILDEQSYTDYSLDDRLQNIHEHMKKIRTDLDNGFVPLTLLEITKQLTKA  799 (1030)
Q Consensus       720 ~~~~~e~KGle~vRRD~~~l~k~~~~~vL~~IL~~~~~~~~~~e~~v~~I~~~l~~~~~~l~~g~vpl~~lvItk~LsK~  799 (1030)
                         .+++||++++|||||+|+|++|.+||+.||.+.     +++++.   ..++..+...+++|.+|+++|+|+++|++.
T Consensus       625 ---~~~vKG~e~~RrD~~~l~k~~q~~vl~~il~~~-----~~e~~~---~~~~~~v~~~l~~~~~~~~~lvi~k~l~k~  693 (792)
T COG0417         625 ---KIEVKGLETVRRDWPELVKEFQREVLEVLLSGR-----DVEEAL---AKYVRDVIEKLRNGEVPIEKLVISKRLTRP  693 (792)
T ss_pred             ---EEEEeeeEEEecCccHHHHHHHHHHHHHHHcCC-----CHHHHH---HHHHHHHHHHHHcCCcCHHHheeeeeeccC
Confidence               468999999999999999999999999999999     888774   666777888999999999999999999999


Q ss_pred             CCC--CcchHHHHHHHHHHcCCcc
Q psy6283         800 PEG--GKVCITQIRLSRNRRGRRR  821 (1030)
Q Consensus       800 p~~--~~~pHV~vA~r~~~~g~~~  821 (1030)
                      +.+  +++|||++|++++..|...
T Consensus       694 ~~ey~~~~p~~~~a~~~~~~g~~~  717 (792)
T COG0417         694 LSEYKANKPHVVVAARLRKRGINV  717 (792)
T ss_pred             hhhhcCCCcHHHHHHHHHhCCCCC
Confidence            877  8899999999999985544

>cd05533 POLBc_delta DNA polymerase type-B delta subfamily catalytic domain

Probab=100.00  E-value=5.7e-73  Score=648.41  Aligned_cols=310  Identities=33%  Similarity=0.504  Sum_probs=276.9

Q ss_pred             cccCceeeccccccccceEEEeeccccChhHHHHhccccccccccCCC----ccccccccCC---CCCccccCCcchHHH
Q psy6283         495 AYSGGLVLEPKKGFYDKFIILMDFNSLYPSIIQEYNICFTTIPVRMLQ----DSDITTLCEY---LPEHQVDTGILPSEI  567 (1030)
Q Consensus       495 ~Y~GGlVleP~~GlY~~~V~vLDFnSLYPSII~~~NIc~tTv~~~~~d----~~~i~~~~p~---~p~~~~~~GIlP~iL  567 (1030)
                      +|+||+|++|++|||++||++|||+|||||||++|||||+|+++..+.    ++++. ..|.   |...+.+.||||.+|
T Consensus         2 ~Y~Gg~V~eP~~G~y~~~V~~lDF~SLYPSIi~~~Nic~~T~~~~~~~~~~~~~~~~-~~p~~~~f~~~~~~~Gilp~iL   80 (393)
T cd05533           2 QYEGATVIEPIKGYYDVPIATLDFASLYPSIMMAHNLCYTTLLNKNTAKKLPPEDYI-KTPNGDYFVKSSVRKGLLPEIL   80 (393)
T ss_pred             CCCCeEeccCCCCCccCCeEEecCCCccHHHHHHhCcCccccccCcccccCCCcceE-ECCCCceeecCCCCCCchHHHH
Confidence            699999999999999999999999999999999999999999876530    11110 1121   333356899999999


Q ss_pred             HHHHHHHHHHHHHhcCCCCChHHHHhhHHHHHHhccccccccccCCCCCCCCCCHHHHHHHHHHhHHHHHHHHHHhhhc-
Q psy6283         568 KKLVESRRQVKALMKQPNLSSDLLMQYDIRQKALKLTANSMYGCLGFPNSRFFAQPLAALVTAKGREILLNTKSLVENL-  646 (1030)
Q Consensus       568 ~~Ll~~R~~vKk~mk~~~~~~~~~~~~d~rQ~AlKl~aNS~YG~lG~~~srfy~~~lA~~IT~~GR~iL~~tkelve~~-  646 (1030)
                      +.|++.|.++|+.|++ ..||.++.+||.+|+|+||+|||+|||||++++||||.++|++||++||.+|+.|++++++. 
T Consensus        81 ~~Ll~~R~~~K~~mk~-~~d~~~~~~ld~~Q~AlKi~~NS~YG~~G~~~~r~~~~~~A~~iT~~GR~~l~~~~~~ie~~~  159 (393)
T cd05533          81 EELLAARKRAKKDLKE-ETDPFKKAVLDGRQLALKISANSVYGFTGATVGKLPCLEISSSVTSFGRQMIEKTKKLVEEKY  159 (393)
T ss_pred             HHHHHHHHHHHHHHhh-CCCHHHHHHHHHHHHhhheeeeecccccccccCCccchHHHHHHHHhHHHHHHHHHHHHHHhh
Confidence            9999999999999998 56899999999999999999999999999999999999999999999999999999999975 


Q ss_pred             --------cceeEEecCcceeeecCCCCHHHHHHHHHHHHHHHhcccc-eeEEeecchhhhhhhcccccceEEeeeecCC
Q psy6283         647 --------NYEVIYGDTDSLMISCNVNDYDSVFKIGNQIKSECNKLYK-QLELDIDGVYKYMLLLKKKKYAALSISKLSN  717 (1030)
Q Consensus       647 --------g~~VIYGDTDSI~V~~~~~d~eea~~ig~~i~~~Vn~~~~-~leLe~E~vf~~llll~KKrYa~l~~~~~~d  717 (1030)
                              |++|||||||||||+++..+.++++++|.+|++.||+.|+ +|+||+|++|.++|+++||||||+.+++. +
T Consensus       160 ~~~~g~~~~~~VIYGDTDSvfv~~~~~~~~~~~~~~~ei~~~i~~~~~~~i~Le~E~vy~~~ll~~KKrYag~~~~~~-~  238 (393)
T cd05533         160 TKANGYSHDAKVIYGDTDSVMVKFGVSDVEEAMKLGKEAAEYVSKKFIKPIKLEFEKVYFPYLLINKKRYAGLLWTNP-D  238 (393)
T ss_pred             cccccCCCceEEEecCCCceEEEcCCCCHHHHHHHHHHHHHHHHhcCCCCeEEeeHHHHHHHHHHHHhhheEEEeecC-C
Confidence                    8899999999999999988999999999999999999985 89999999999999999999999987652 2


Q ss_pred             CceeeeceeeeeeeeeCChHHHHHHHHHHHHHHHhccCCCCCCChhHHHHHHHHHHHHHHHHhhCCCcChhhhHHhhccc
Q psy6283         718 GKMICSQEIKGVDVVRRDWSQLASEAGKFVISQILDEQSYTDYSLDDRLQNIHEHMKKIRTDLDNGFVPLTLLEITKQLT  797 (1030)
Q Consensus       718 G~~~~~~e~KGle~vRRD~~~l~k~~~~~vL~~IL~~~~~~~~~~e~~v~~I~~~l~~~~~~l~~g~vpl~~lvItk~Ls  797 (1030)
                      +  .+++++||++++|||||+|+|+++..+|+.||.++     +.+.    +++++.+++.+|.+|++|+++|+|+++|+
T Consensus       239 ~--~~ki~~KGle~vRRD~~~~~k~~~~~vl~~il~~~-----~~~~----~~~~~~~~~~~l~~~~~~~~~l~i~k~l~  307 (393)
T cd05533         239 K--HDKMDTKGIETVRRDNCLLVQNVVETCLNKILIER-----DVEG----AIEFVKGVISDLLQNKIDISLLVITKALT  307 (393)
T ss_pred             C--CceeEEeceEEEcccchHHHHHHHHHHHHHHHhcC-----CHHH----HHHHHHHHHHHHHcCCCCHHHEEEEeeec
Confidence            1  24678999999999999999999999999999887     6554    45566677788999999999999999999


Q ss_pred             CCCCC--CcchHHHHHHHHHHcC
Q psy6283         798 KAPEG--GKVCITQIRLSRNRRG  818 (1030)
Q Consensus       798 K~p~~--~~~pHV~vA~r~~~~g  818 (1030)
                      |+|++  ..+|||+||+||+++|
T Consensus       308 k~~~~Y~~~~phv~~A~rl~~~~  330 (393)
T cd05533         308 KTADDYAGKQAHVELAERMRKRD  330 (393)
T ss_pred             CChhhcCCCCchHHHHHHHHhcC
Confidence            99877  6699999999999986

Three DNA-dependent DNA polymerases type B (alpha, delta, and epsilon) have been identified as essential for nuclear DNA replication in eukaryotes. Presently, no direct data is available regarding the strand specificity of DNA polymerase during DNA replication in vivo. However, mutation analysis supports the hypothesis that DNA polymerase delta is the enzyme responsible for both elongation and maturation of Okazaki fragments on the lagging strand.

>cd05532 POLBc_alpha DNA polymerase type-B alpha subfamily catalytic domain

Probab=100.00  E-value=2.1e-72  Score=645.38  Aligned_cols=318  Identities=59%  Similarity=0.911  Sum_probs=291.1

Q ss_pred             CCCccccCceeeccccccccceEEEeeccccChhHHHHhccccccccccCCCccccccccCCCCCccccCCcchHHHHHH
Q psy6283         491 RKKAAYSGGLVLEPKKGFYDKFIILMDFNSLYPSIIQEYNICFTTIPVRMLQDSDITTLCEYLPEHQVDTGILPSEIKKL  570 (1030)
Q Consensus       491 ~~~~~Y~GGlVleP~~GlY~~~V~vLDFnSLYPSII~~~NIc~tTv~~~~~d~~~i~~~~p~~p~~~~~~GIlP~iL~~L  570 (1030)
                      ++..+|+||+|++|.+|||++||++|||+|||||||++|||||+|+++..+... ... ...++....+.||||.+|+.|
T Consensus         3 ~~~~~y~Gg~V~eP~~G~y~~~V~~lDF~SLYPSIi~~~Ni~~~Ti~~~~~~~~-~~~-~~~~~~~~~~~Gilp~~l~~l   80 (400)
T cd05532           3 KKKAKYAGGLVLEPKKGLYDKFILLLDFNSLYPSIIQEYNICFTTVDRADPDDE-DDE-EPPLPPSDQEKGILPRIIRKL   80 (400)
T ss_pred             CccCCcCCceeecCCCCcccCceEEEeccccchHHHHHhcCChhhccccccccc-CCc-cccccccccCCCchHHHHHHH
Confidence            456789999999999999999999999999999999999999999997654111 100 012444567899999999999


Q ss_pred             HHHHHHHHHHhcCCCCChHHHHhhHHHHHHhccccccccccCCCCCCCCCCHHHHHHHHHHhHHHHHHHHHHhhhcccee
Q psy6283         571 VESRRQVKALMKQPNLSSDLLMQYDIRQKALKLTANSMYGCLGFPNSRFFAQPLAALVTAKGREILLNTKSLVENLNYEV  650 (1030)
Q Consensus       571 l~~R~~vKk~mk~~~~~~~~~~~~d~rQ~AlKl~aNS~YG~lG~~~srfy~~~lA~~IT~~GR~iL~~tkelve~~g~~V  650 (1030)
                      ++.|.++|++|++ ..|+.++.+||.+|+|+|++|||+|||+|+++|||||.++|++||+.||.+|+.|++++++.|++|
T Consensus        81 ~~~R~~~K~~~k~-~~d~~~~~~~d~~Q~alKi~~NS~YG~~g~~~~r~~~~~~A~~iT~~GR~~l~~~~~~~e~~g~~V  159 (400)
T cd05532          81 VERRRQVKKLMKS-EKDPDKKAQLDIRQLALKLTANSMYGCLGFSYSRFYAKPLAALITSKGREILQKTKDLVEKMNLEV  159 (400)
T ss_pred             HHHHHHHHHHHhc-CCCHHHHHHHHHHHHHHHHHHhhcccccccccccccChHHHHHHHHHHHHHHHHHHHHHHHcCCEE
Confidence            9999999999999 458999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             EEecCcceeeecCCCCHHHHHHHHHHHHHHHhcccceeEEeecchhhhhhhcccccceEEeeeecCCCceeeeceeeeee
Q psy6283         651 IYGDTDSLMISCNVNDYDSVFKIGNQIKSECNKLYKQLELDIDGVYKYMLLLKKKKYAALSISKLSNGKMICSQEIKGVD  730 (1030)
Q Consensus       651 IYGDTDSI~V~~~~~d~eea~~ig~~i~~~Vn~~~~~leLe~E~vf~~llll~KKrYa~l~~~~~~dG~~~~~~e~KGle  730 (1030)
                      ||||||||||.++..+.+++++++.+|++.||+.|++|+|++|++|.+++|++|||||++.++.++  ...+++++||++
T Consensus       160 iYgDTDSifv~~~~~~~~~~~~~~~~i~~~in~~~~~i~le~e~iy~~~ll~~KKrYag~~~~~~~--~~~~k~~~KGie  237 (400)
T cd05532         160 IYGDTDSIMINTGTTDYEEAKKLGNKIKKEVNKSYKKLEIDIDGVFKRLLLLKKKKYAALKVVDDD--KGKLKKEVKGLD  237 (400)
T ss_pred             EEeCCCeEEEecCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhHHHHhhhhhcceEEEeecCC--ccceeeEEecee
Confidence            999999999999888899999999999999999999999999999999999999999999887543  223467999999


Q ss_pred             eeeCChHHHHHHHHHHHHHHHhccCCCCCCChhHHHHHHHHHHHHHHHHhhCCCcChhhhHHhhcccCCCCC--C--cch
Q psy6283         731 VVRRDWSQLASEAGKFVISQILDEQSYTDYSLDDRLQNIHEHMKKIRTDLDNGFVPLTLLEITKQLTKAPEG--G--KVC  806 (1030)
Q Consensus       731 ~vRRD~~~l~k~~~~~vL~~IL~~~~~~~~~~e~~v~~I~~~l~~~~~~l~~g~vpl~~lvItk~LsK~p~~--~--~~p  806 (1030)
                      ++|||||+|+++++..+|+.||.++     +.+++++.|++++.+++.+|.+|++|+++|+|+++|+|++++  .  ++|
T Consensus       238 ~~RrD~~~~~k~~~~~vl~~ll~~~-----~~~~~~~~i~~~~~~~~~~l~~~~~~~~~lii~k~l~k~~~~Y~~~~~~~  312 (400)
T cd05532         238 IVRRDWCPLSKEIGNYVLDQILSDK-----SREDIVENIHEYLRKINEDLRNGKIPLEKFIITKQLTKNPEEYPDKKSLP  312 (400)
T ss_pred             EEecccHHHHHHHHHHHHHHHHcCC-----ChHHHHHHHHHHHHHHHHHHHcCCCCHHHEEEeecccCChHHcCCCCCCc
Confidence            9999999999999999999999999     888999999999999999999999999999999999999877  2  689


Q ss_pred             HHHHHHHHHHcC
Q psy6283         807 ITQIRLSRNRRG  818 (1030)
Q Consensus       807 HV~vA~r~~~~g  818 (1030)
                      ||+||+||.+.|
T Consensus       313 hv~~A~rl~~~g  324 (400)
T cd05532         313 HVQVALRMNKRG  324 (400)
T ss_pred             HHHHHHHHHHcC
Confidence            999999999887

Three DNA-dependent DNA polymerases type B (alpha, delta, and epsilon) have been identified as essential for nuclear DNA replication in eukaryotes. DNA polymerase (Pol) alpha is almost exclusively required for the initiation of DNA replication and the priming of Okazaki fragments during elongation. In most organisms no specific repair role, other than check point control, has been assigned to this enzyme. Pol alpha contains both polymerase and exonuclease domains, but lacks exonuclease activity suggesting that the exonuclease domain may be for structural purposes only.

>PHA02528 43 DNA polymerase; Provisional

Probab=100.00  E-value=1.1e-68  Score=657.49  Aligned_cols=379  Identities=21%  Similarity=0.290  Sum_probs=303.4

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHhcchHHHHHHHHHhCCcchhhccCchhHHHHHHHHHHHhhcCeeccCCccccCcCCCcc
Q psy6283         402 IVEFIKFTMLHSSYIIKIMCELNVLPLAIQITNVCGNVLSRTLMGGRSERNEFLLLHAFHEKSYVLPDKQYGKNKKEGEE  481 (1030)
Q Consensus       402 l~~lv~Y~~~Da~l~~~L~~kl~vlpl~~~lt~iaG~~~srtl~~gr~~r~E~lLL~~~~~~~yivPdk~~~kk~~~~~d  481 (1030)
                      ...|+.||++||.|+++|+.++++|+++.++|+++|+++.+++  ++...+++++|+.+|+.|||+|++..         
T Consensus       303 ~~~l~~Ynl~Da~Lv~~L~~kl~ll~~~~e~ArltGi~l~~v~--sq~~~~~~lll~~~~r~g~viP~~~~---------  371 (881)
T PHA02528        303 HQKYIEYNIIDVELVDRLDDKRKLIELVLSMAYYAKINFEDVF--SPIKTWDAIIFNSLKEEKIVIPENKS---------  371 (881)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCcHHHhc--chHhHHHHHHHHHHHHcCcccCCccc---------
Confidence            6789999999999999999999999999999999999999995  34555689999999999999997642         


Q ss_pred             ccccccCCCCCCccccCceeeccccccccceEEEeeccccChhHHHHhccccccccccCCCc---cccccc---------
Q psy6283         482 TGEANKGKGRKKAAYSGGLVLEPKKGFYDKFIILMDFNSLYPSIIQEYNICFTTIPVRMLQD---SDITTL---------  549 (1030)
Q Consensus       482 ~~~~~~~~~~~~~~Y~GGlVleP~~GlY~~~V~vLDFnSLYPSII~~~NIc~tTv~~~~~d~---~~i~~~---------  549 (1030)
                               ....+|.||+|++|+||||+ +|++|||+|||||||++|||||+|+++..+..   ..+...         
T Consensus       372 ---------~~~~~y~Gg~V~eP~pGlY~-~VvVLDF~SLYPSIIiayNIcp~Tlv~~~~~~~~~~~~~~~~~~~~~~~~  441 (881)
T PHA02528        372 ---------HKKQKYAGAFVKEPVPGAYR-WVVSFDLTSLYPSIIRQVNISPETIAGTFHVAPVHEYINKTAPRPSDEYS  441 (881)
T ss_pred             ---------cCCCCCCCcEEecCCCCccc-ceEEEeccccChHHHHHhCCChhhccccccccccccccccccCCCCCcee
Confidence                     12357999999999999998 59999999999999999999999998753200   000001         


Q ss_pred             -cCC-CCCccccCCcchHHHHHHHHHHHHHHHHhcCCCCC----------------------------------------
Q psy6283         550 -CEY-LPEHQVDTGILPSEIKKLVESRRQVKALMKQPNLS----------------------------------------  587 (1030)
Q Consensus       550 -~p~-~p~~~~~~GIlP~iL~~Ll~~R~~vKk~mk~~~~~----------------------------------------  587 (1030)
                       +|. ......++||||.+|..|++.|.++|+.|++++.+                                        
T Consensus       442 ~~p~G~~F~k~~~GiLP~iL~~Ll~~R~~~Kk~Mk~~~~~~~~~k~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  521 (881)
T PHA02528        442 CSPNGWMYRKDIRGVIPTEIKKVFDQRKIYKKKMLAAERNAELIKTILEDLNDSVDTPIDVDYYFDFSDEFKAELKTLTK  521 (881)
T ss_pred             EcCCCCeEeCCCCeehHHHHHHHHHHHHHHHHHHHhccccccccccccccccccccccccccccccchhhhhhhhcccch
Confidence             111 00113469999999999999999999999764322                                        


Q ss_pred             ----------hHHHHhhHHHHHHhccccccccccCCCCCCCCCCHHHHHHHHHHhHHHHHHHHHHh----hh----cc-c
Q psy6283         588 ----------SDLLMQYDIRQKALKLTANSMYGCLGFPNSRFFAQPLAALVTAKGREILLNTKSLV----EN----LN-Y  648 (1030)
Q Consensus       588 ----------~~~~~~~d~rQ~AlKl~aNS~YG~lG~~~srfy~~~lA~~IT~~GR~iL~~tkelv----e~----~g-~  648 (1030)
                                ..++.+||.+|+|+|++|||+|||||+.++||||.++|++||++||.+|+.+...+    ++    .| +
T Consensus       522 ~~l~~~~~~~~~~~~~~d~~Q~A~KI~~NS~YG~lG~~~~r~y~~~~A~aiT~~Gr~~I~~i~~~~~e~l~~~~~~~g~~  601 (881)
T PHA02528        522 SSLKALLEECEKEIALCNTIQMARKILINSLYGALGNEHFRYYDLRNAEAITLFGQLAIQWIERKMNEYLNKLCKTEDED  601 (881)
T ss_pred             hhhhhhhhhhHHHHHHHHHHHHHHHHHHHhhhhhccCcCccCCCHHHHHHHHHHhHHHHHHHHHHHHHHHHHhhcccCCc
Confidence                      14678999999999999999999999999999999999999999999887665443    22    45 6


Q ss_pred             eeEEecCcceeeecCCC-CHH------HHH-------HHH------------HHHHHHHhcccceeEEeecchhhhhhhc
Q psy6283         649 EVIYGDTDSLMISCNVN-DYD------SVF-------KIG------------NQIKSECNKLYKQLELDIDGVYKYMLLL  702 (1030)
Q Consensus       649 ~VIYGDTDSI~V~~~~~-d~e------ea~-------~ig------------~~i~~~Vn~~~~~leLe~E~vf~~llll  702 (1030)
                      .|||||||||||+++.. +..      +..       +++            .++++.+|...+++.|++|++|.+++|+
T Consensus       602 ~VIYGDTDSvfV~~~~~~~~~~~~~~~~~~~lv~~~~~~~~~~l~~~~~~~~~el~e~~~~~~~~~~m~~ek~~~~~~~~  681 (881)
T PHA02528        602 YVIYGDTDSIYVNLDPLVEKVGEDKFKDTNHWVDFLDKFCKERMEPYIDSSYRELCEYMNNYEHLMFMDREAIAGPGFWT  681 (881)
T ss_pred             EEEEEcCCeeEEEeCCcchhhhhccchhHHHHHHHHHHHHHHhhhhhhhHHHHHHHHHHhhhccccchhHHHHhhHhhhh
Confidence            99999999999998642 110      001       111            1444556655556899999999999999


Q ss_pred             ccccceEEeeeecCCCce--eeeceeeeeeeeeCChHHHHHHHHHHHHHHHhccCCCCCCChhHHHHHHHHHHHHHHHHh
Q psy6283         703 KKKKYAALSISKLSNGKM--ICSQEIKGVDVVRRDWSQLASEAGKFVISQILDEQSYTDYSLDDRLQNIHEHMKKIRTDL  780 (1030)
Q Consensus       703 ~KKrYa~l~~~~~~dG~~--~~~~e~KGle~vRRD~~~l~k~~~~~vL~~IL~~~~~~~~~~e~~v~~I~~~l~~~~~~l  780 (1030)
                      +||||||+.|+.+  |..  .+++.+||+++||||||++++++|.++++.||.+.     . +    .+++++.++..++
T Consensus       682 sKKRYAgl~~~~~--g~~~~~~kl~~kGlEtvRsD~~~lak~~q~~vi~~Il~~~-----~-e----~~~~yvk~~i~~~  749 (881)
T PHA02528        682 AKKRYALNVWDSE--GTRYAEPKLKIMGIETQRSSTPKAVQKALKEAIRRILQEG-----E-E----SLQEYIKEFEKEF  749 (881)
T ss_pred             ccccEEEEeccCC--CcccCCCeEEEecceeeecchHHHHHHHHHHHHHHHHhCC-----c-H----hHHHHHHHHHHHH
Confidence            9999999976543  321  24678999999999999999999999999999986     3 3    4555666666777


Q ss_pred             hCCCcChhhhHHhhcccCCCCC----------CcchHHHHHH---HHHH
Q psy6283         781 DNGFVPLTLLEITKQLTKAPEG----------GKVCITQIRL---SRNR  816 (1030)
Q Consensus       781 ~~g~vpl~~lvItk~LsK~p~~----------~~~pHV~vA~---r~~~  816 (1030)
                      ++  +|+++++|+ ++.+++++          +.+|||.+|+   ++++
T Consensus       750 ~~--~d~~~i~~~-~~~~~l~~Y~~~~~~y~k~~pphV~aA~~~~~~~~  795 (881)
T PHA02528        750 RK--LDYEEIAFV-SSANNIAKYSDDKGIPGKGCPIHIRGALLYNRAVK  795 (881)
T ss_pred             Hc--CCHHHEEee-eccCCHHHhcccccccccCCCHHHHHHHHHHHHHh
Confidence            76  999999888 88887655          4589999999   7666

>cd05536 POLBc_B3 DNA polymerase type-B B3 subfamily catalytic domain

Probab=100.00  E-value=6.3e-69  Score=611.27  Aligned_cols=304  Identities=37%  Similarity=0.563  Sum_probs=268.4

Q ss_pred             ccccCceeeccccccccceEEEeeccccChhHHHHhccccccccccCCCccccccccCCCCCccccCCcchHHHHHHHHH
Q psy6283         494 AAYSGGLVLEPKKGFYDKFIILMDFNSLYPSIIQEYNICFTTIPVRMLQDSDITTLCEYLPEHQVDTGILPSEIKKLVES  573 (1030)
Q Consensus       494 ~~Y~GGlVleP~~GlY~~~V~vLDFnSLYPSII~~~NIc~tTv~~~~~d~~~i~~~~p~~p~~~~~~GIlP~iL~~Ll~~  573 (1030)
                      .+|+||+|++|.||||++ |++|||+|||||||++|||||||+++..+....+.. +........+.||+|.+|+.|++.
T Consensus         2 ~~y~Gg~V~~P~~G~y~~-V~~lDf~SLYPSii~~~Ni~~~Ti~~~~~~~~~~~~-~~~~~f~~~~~Gilp~il~~ll~~   79 (371)
T cd05536           2 ESYEGGIVLEPEKGLHEN-IVVLDFSSLYPSIMIKYNISPDTLVREGCEDCDVEP-QVGHKFRKDPPGFIPSVLEDLLEE   79 (371)
T ss_pred             CCCCceEEeCCCCCCcCC-EEEEEcccccHHHHHHHCcChhhcCCCCccccccCC-CCCcEEecCCCCchHHHHHHHHHH
Confidence            369999999999999997 999999999999999999999999876642222210 001111245799999999999999


Q ss_pred             HHHHHHHhcCCCCChHHHHhhHHHHHHhccccccccccCCCCCCCCCCHHHHHHHHHHhHHHHHHHHHHhhhccceeEEe
Q psy6283         574 RRQVKALMKQPNLSSDLLMQYDIRQKALKLTANSMYGCLGFPNSRFFAQPLAALVTAKGREILLNTKSLVENLNYEVIYG  653 (1030)
Q Consensus       574 R~~vKk~mk~~~~~~~~~~~~d~rQ~AlKl~aNS~YG~lG~~~srfy~~~lA~~IT~~GR~iL~~tkelve~~g~~VIYG  653 (1030)
                      |.++|++|++.+.++.++.+||.+|+|+||+|||+|||||+.+|||||.++|++||+.||.+|+.|++++++.|++||||
T Consensus        80 R~~~K~~mk~~~~~~~~~~~~d~~Q~AlKi~~NS~YG~~g~~~~r~~~~~~A~~iT~~GR~~l~~~~~~i~~~g~~VIYg  159 (371)
T cd05536          80 RRRIKEKMKKLDPESEEYKLLDERQRAIKILANSFYGYMGWANARWYCKECAEAVTAWGREYIKTTIKIAEEKGFKVIYG  159 (371)
T ss_pred             HHHHHHHHhhCCCcHHHHHHHHHHHHHHHHHHhccccccccccccCCCHHHHHHHHHHHHHHHHHHHHHHHHcCCEEEEE
Confidence            99999999997666689999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             cCcceeeecCCCCHHHHHHHHHHHHHHHhcccceeEEeecchhhhhhhcccccceEEeeeecCCCceeeeceeeeeeeee
Q psy6283         654 DTDSLMISCNVNDYDSVFKIGNQIKSECNKLYKQLELDIDGVYKYMLLLKKKKYAALSISKLSNGKMICSQEIKGVDVVR  733 (1030)
Q Consensus       654 DTDSI~V~~~~~d~eea~~ig~~i~~~Vn~~~~~leLe~E~vf~~llll~KKrYa~l~~~~~~dG~~~~~~e~KGle~vR  733 (1030)
                      |||||||+++..+.  +...+.++.+.||+.++ |+|++|++|.+|++++||||||+.    .+|+    +++||++++|
T Consensus       160 DTDSvfv~~~~~~~--~~~~~~~l~~~i~~~~~-i~le~E~vy~~~l~~~KKrY~g~~----~~g~----i~~KG~e~~R  228 (371)
T cd05536         160 DTDSLFVKIDGADA--VKKKVKKLLKYINEELP-LELEIEKFYKRGFFVTKKRYAGLT----EDGK----IDVVGLEVVR  228 (371)
T ss_pred             cCcccEEeecCchH--HHHHHHHHHHHHHhcCC-eeEEEeeeeHHHHHhhhceeEEEc----cCCe----EEEEeeeeEe
Confidence            99999999986542  55667788889999887 999999999999999999999984    3564    4799999999


Q ss_pred             CChHHHHHHHHHHHHHHHhccCCCCCCChhHHHHHHHHHHHHHHHHhhCCCcChhhhHHhhcccCCCCC--CcchHHHHH
Q psy6283         734 RDWSQLASEAGKFVISQILDEQSYTDYSLDDRLQNIHEHMKKIRTDLDNGFVPLTLLEITKQLTKAPEG--GKVCITQIR  811 (1030)
Q Consensus       734 RD~~~l~k~~~~~vL~~IL~~~~~~~~~~e~~v~~I~~~l~~~~~~l~~g~vpl~~lvItk~LsK~p~~--~~~pHV~vA  811 (1030)
                      ||||+|+++++.++|+.||.++     ++++++    .++.++.++|.+|++|+++|+|+++|+|+|++  ..+|||+||
T Consensus       229 rD~~~~~k~~~~~~l~~ll~~~-----~~~~~~----~~~~~~~~~l~~g~~~~~dlii~k~l~k~~~~Y~~~~~hv~~a  299 (371)
T cd05536         229 RDWSEIAKETQARVLEAILKEG-----DVEEAV----KIVKEVIEKLKRGEVPPEKLVIWKQLTKDLSEYKATGPHVAAA  299 (371)
T ss_pred             CccHHHHHHHHHHHHHHHHcCC-----CHHHHH----HHHHHHHHHHHcCCCCHHHeEEeHHhcCCHHHhCCCCcHHHHH
Confidence            9999999999999999999988     766654    55666778899999999999999999999988  779999999


Q ss_pred             HHHHHcCC
Q psy6283         812 LSRNRRGR  819 (1030)
Q Consensus       812 ~r~~~~g~  819 (1030)
                      ++|.++|.
T Consensus       300 ~~l~~~g~  307 (371)
T cd05536         300 KKLAKRGY  307 (371)
T ss_pred             HHHHhcCC
Confidence            99998864

Archaeal proteins that are involved in DNA replication are similar to those from eukaryotes. Some members of the archaea also possess multiple family B DNA polymerases (B1, B2 and B3). So far there is no specific function(s) has been assigned for different members of the archaea type B DNA polymerases. Phylogenetic analyses of eubacterial, archaeal, and eukaryotic family B DNA polymerases are support independent gene duplications during the evolution of archaeal and eukaryotic family B DNA polymerases. Structural comparison of the thermostable DNA polymerase type B to its mesostable homolog suggests several adaptations to high temperature such as shorter loops, disulfide bridges, and increasing electrostatic interaction at subdomain interfaces.

>cd05530 POLBc_B1 DNA polymerase type-B B1 subfamily catalytic domain

Probab=100.00  E-value=9.2e-68  Score=599.46  Aligned_cols=308  Identities=27%  Similarity=0.401  Sum_probs=263.4

Q ss_pred             CCccccCceeeccccccccceEEEeeccccChhHHHHhccccccccccCCCccccccccCCCCC--ccccCCcchHHHHH
Q psy6283         492 KKAAYSGGLVLEPKKGFYDKFIILMDFNSLYPSIIQEYNICFTTIPVRMLQDSDITTLCEYLPE--HQVDTGILPSEIKK  569 (1030)
Q Consensus       492 ~~~~Y~GGlVleP~~GlY~~~V~vLDFnSLYPSII~~~NIc~tTv~~~~~d~~~i~~~~p~~p~--~~~~~GIlP~iL~~  569 (1030)
                      +..+|+||+|++|++|||++ |++|||+|||||||++|||||+|+++..++....  ..|..+.  ...+.||+|.+|..
T Consensus         9 ~~~~y~Gg~V~~P~~G~y~~-V~~lDF~SLYPSIi~~~Ni~~~T~~~~~~~~~~~--~~p~~~~~~~~~~~Gilp~il~~   85 (372)
T cd05530           9 KGKKYRGAIVLEPPPGIFFN-VVVLDFASLYPSIIKVWNLSYETVNCPHCECKTN--EVPEVGHWVCKKRPGITSQIIGL   85 (372)
T ss_pred             cCCCCCCCEeecCCCCcccc-EEEEEcccccHHHHHHhCCChhhcccCcccccce--ecCCCCceEEecCCCccHHHHHH
Confidence            34689999999999999998 9999999999999999999999999765421111  1133221  14689999999999


Q ss_pred             HHHHHHHHH-HHhcCCCCChHHHHhhHHHHHHhccccccccccCCCCCCCCCCHHHHHHHHHHhHHHHHHHHHHhhhccc
Q psy6283         570 LVESRRQVK-ALMKQPNLSSDLLMQYDIRQKALKLTANSMYGCLGFPNSRFFAQPLAALVTAKGREILLNTKSLVENLNY  648 (1030)
Q Consensus       570 Ll~~R~~vK-k~mk~~~~~~~~~~~~d~rQ~AlKl~aNS~YG~lG~~~srfy~~~lA~~IT~~GR~iL~~tkelve~~g~  648 (1030)
                      |++.|.++| ++|+....+|.++.+||++|+|+||+|||+|||+|+.+++|||+++|++||++||.+|..|++++++.|+
T Consensus        86 L~~~R~~~~k~~~k~~~~d~~~~~~ld~~Q~alKi~~NS~YG~~g~~~~~~~~~~~A~~it~~GR~~l~~~~~~~~~~g~  165 (372)
T cd05530          86 LRDLRVKIYKKKAKDKSLDEEMRQWYDVVQSAMKVFINASYGVFGAENFPLYCPPVAESTTALGRYIITSTIKKARELGL  165 (372)
T ss_pred             HHHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHHHHHhccccccccccCCCCcHHHHHHHHHHHHHHHHHHHHHHHHCCc
Confidence            999999865 4555544489999999999999999999999999999999999999999999999999999999999999


Q ss_pred             eeEEecCcceeeecCCCCHHHHHHHHHHHHHHHhcccceeEEeecchhhhhhhc-ccccceEEeeeecCCCceeeeceee
Q psy6283         649 EVIYGDTDSLMISCNVNDYDSVFKIGNQIKSECNKLYKQLELDIDGVYKYMLLL-KKKKYAALSISKLSNGKMICSQEIK  727 (1030)
Q Consensus       649 ~VIYGDTDSI~V~~~~~d~eea~~ig~~i~~~Vn~~~~~leLe~E~vf~~llll-~KKrYa~l~~~~~~dG~~~~~~e~K  727 (1030)
                      +|||||||||||+++.  .+.+    .+|.+.|++.+ +++||+|++|++++|. +||||||+.    .+|+    +++|
T Consensus       166 ~VIYGDTDSvfv~~~~--~~~~----~~i~~~i~~~~-~i~le~E~~y~~~ll~~~KKrY~g~~----~~gk----i~~K  230 (372)
T cd05530         166 KVLYGDTDSLFLWNPP--QEQL----EDLVEWVEKEL-GLDLELDKEYRYVVFSGLKKNYLGVT----KDGS----VDIK  230 (372)
T ss_pred             EEEEEeccceEEecCC--hhHH----HHHHHHHhhcc-CceEEEEEEEeeeeeccccccEEEEe----cCCc----EEEE
Confidence            9999999999999764  2333    45566777766 4999999999988775 799999984    3564    5899


Q ss_pred             eeeeeeCChHHHHHHHHHHHHHHHhccCCCCCCChhHHHHHHHHHHHHHHHHhhCCCcChhhhHHhhcccCCCCC---Cc
Q psy6283         728 GVDVVRRDWSQLASEAGKFVISQILDEQSYTDYSLDDRLQNIHEHMKKIRTDLDNGFVPLTLLEITKQLTKAPEG---GK  804 (1030)
Q Consensus       728 Gle~vRRD~~~l~k~~~~~vL~~IL~~~~~~~~~~e~~v~~I~~~l~~~~~~l~~g~vpl~~lvItk~LsK~p~~---~~  804 (1030)
                      |++++|||||+|+++++.++|+.||.+++..  +.+.+++.+++++.+...+|.+|++|+++|+|+++|+|+|++   .+
T Consensus       231 Gie~~RrD~~~~~k~~~~~vl~~ll~~~~~~--~~~~~~~~i~~~~~~~~~~l~~g~~~~~~lvi~k~L~K~~~~Y~~~~  308 (372)
T cd05530         231 GLLGKKRNTPEFVKELFYEVIEILSAVNSPE--DFEKAREKIRDIVKGVYKRLKKKEYTLDQLAFKVMLSKPPEEYTKNT  308 (372)
T ss_pred             eEEEEeCCchHHHHHHHHHHHHHHHhcCChH--HHHHHHHHHHHHHHHHHHHHHcCCCCHHHheeehhccCCHHHhcCCC
Confidence            9999999999999999999999999987211  234567789999999999999999999999999999999988   56


Q ss_pred             chHHHHHHHHHHcCC
Q psy6283         805 VCITQIRLSRNRRGR  819 (1030)
Q Consensus       805 ~pHV~vA~r~~~~g~  819 (1030)
                      +|||+||++|.+.|.
T Consensus       309 ~phv~aa~~~~~~g~  323 (372)
T cd05530         309 PQHVKAARQLEKYGR  323 (372)
T ss_pred             CHHHHHHHHHHhcCC
Confidence            899999999988764

Archaeal proteins that are involved in DNA replication are similar to those from eukaryotes. Some archaeal members also possess multiple family B DNA polymerases (B1, B2 and B3). So far there is no specific function(s) has been assigned for different members of the archaea type B DNA polymerases. Phylogenetic analyses of eubacterial, archaeal, and eukaryotic family B DNA polymerases are support independent gene duplications during the evolution of archaeal and eukaryotic family B DNA polymerases.

>PF00136 DNA_pol_B: DNA polymerase family B Several related DNA polymerases were too dissimilar to be included

Probab=100.00  E-value=8.6e-69  Score=627.70  Aligned_cols=355  Identities=37%  Similarity=0.607  Sum_probs=297.5

Q ss_pred             chhHHHHHHHHHHHhhcCeeccCCccccCcCCCccccccccCCCCCCccccCceeeccccccccceEEEeeccccChhHH
Q psy6283         447 GRSERNEFLLLHAFHEKSYVLPDKQYGKNKKEGEETGEANKGKGRKKAAYSGGLVLEPKKGFYDKFIILMDFNSLYPSII  526 (1030)
Q Consensus       447 gr~~r~E~lLL~~~~~~~yivPdk~~~kk~~~~~d~~~~~~~~~~~~~~Y~GGlVleP~~GlY~~~V~vLDFnSLYPSII  526 (1030)
                      ||+.|+|++||+.+++.||++|++......         .........+|+||+|++|.+|||+++|.+|||+|||||||
T Consensus         1 gq~~~v~~~ll~~~~~~~~~~p~~~~~~~~---------~~~~~~~~~~y~Gg~V~~P~~G~~~~v~~~lDF~SLYPsii   71 (466)
T PF00136_consen    1 GQQIRVESLLLREAHRRNYIIPSKKERPEG---------FTSKSEQKEKYEGGYVLEPKPGLYENVVSVLDFASLYPSII   71 (466)
T ss_dssp             -CHHHHHHHHHHHHHHTTBE-B-HHHHHHT---------HHHHHHHCTCEEEC-BE--HSSEEEEEEEEEEETTHHHHHH
T ss_pred             CchhhHHHHHHHHHHHCCEEeeCCcccccc---------cccccccccccccceeeccccccccCceeeeecccccHHHH
Confidence            689999999999999999999987643100         00011235789999999999999999666899999999999


Q ss_pred             HHhccccccccccC-CCcccc---------cccc--C---CCCCccccCCcchHHHHHHHHHHHHHHHHhcCCCCChHH-
Q psy6283         527 QEYNICFTTIPVRM-LQDSDI---------TTLC--E---YLPEHQVDTGILPSEIKKLVESRRQVKALMKQPNLSSDL-  590 (1030)
Q Consensus       527 ~~~NIc~tTv~~~~-~d~~~i---------~~~~--p---~~p~~~~~~GIlP~iL~~Ll~~R~~vKk~mk~~~~~~~~-  590 (1030)
                      ++|||||+|+++.. +....+         ...+  +   .+.......||||.+|+.|++.|.++|+.|++. .++.+ 
T Consensus        72 ~~~Ni~~~T~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~gilp~~l~~~l~~R~~~K~~~~~~-~~~~~~  150 (466)
T PF00136_consen   72 IAYNICPETIVDDDECKDNEVSPDIKYDYGPFIVGSPVGVRFVKKGVRPGILPEILEELLEKRKEIKKLMKKA-KDPDEE  150 (466)
T ss_dssp             HHTTHSTTTBTCTTHCSSEEEHTTCCCCTCEEEECSCCSEEEESSTCSHHHHHHHHHHHHHHHHHHHHHHHHC-CHHHHH
T ss_pred             HhccCCcceEecchhhhcccccccccccccceeecCCceeeecccCcccccChHHHHHHHHHHHHHhhhhhhh-ccchhh
Confidence            99999999999875 211111         0000  1   122346789999999999999999999999984 45554 


Q ss_pred             HHhhHHHHHHhccccccccccCCCCCCCCCCHHHHHHHHHHhHHHHHHHHHHhhhc--cceeEEecCcceeeecCCCCHH
Q psy6283         591 LMQYDIRQKALKLTANSMYGCLGFPNSRFFAQPLAALVTAKGREILLNTKSLVENL--NYEVIYGDTDSLMISCNVNDYD  668 (1030)
Q Consensus       591 ~~~~d~rQ~AlKl~aNS~YG~lG~~~srfy~~~lA~~IT~~GR~iL~~tkelve~~--g~~VIYGDTDSI~V~~~~~d~e  668 (1030)
                      +..||++|+|+||+|||+|||||+.+||||++++|++||++||.+|+.|++++++.  |++|||||||||||.++..+.+
T Consensus       151 ~~~~d~~Q~a~Ki~~NS~YG~~g~~~~r~~~~~~a~~iT~~GR~~i~~~~~~~~~~~~g~~viYgDTDSv~v~~~~~~~~  230 (466)
T PF00136_consen  151 YAILDARQLALKIIANSFYGYLGAKNSRFYCKEIAEAITATGREIIKKAIEIIEEMEFGFEVIYGDTDSVFVQFPDSDKE  230 (466)
T ss_dssp             HHHHHHHHHHHHHHHTTHHHHHTSTTSTT--HHHHHHHHHHHHHHHHHHHHHHHHHSCTEEEEEEETTEEEEECTTCHHH
T ss_pred             HHHHHHHHHhhcccceeeEeecCccccchhhhhhhheehhhhHhhHHHHHHHHHhhcccceEEEEcccceEEecCCCcHH
Confidence            89999999999999999999999999999999999999999999999999999998  9999999999999999988888


Q ss_pred             HHHHHHHHHHHHHhcc--cceeEEeecchhhhhhhcccccceEEeeeecCCCceeeeceeeeeeeeeCChHHHHHHHHHH
Q psy6283         669 SVFKIGNQIKSECNKL--YKQLELDIDGVYKYMLLLKKKKYAALSISKLSNGKMICSQEIKGVDVVRRDWSQLASEAGKF  746 (1030)
Q Consensus       669 ea~~ig~~i~~~Vn~~--~~~leLe~E~vf~~llll~KKrYa~l~~~~~~dG~~~~~~e~KGle~vRRD~~~l~k~~~~~  746 (1030)
                      ++.+.+.++++.||..  +.+|+|++|++|.+++|++|||||++.+++.  |...+++++||++++|||||+|+++++..
T Consensus       231 ~~~~~~~~l~~~i~~~~~~~~i~le~E~~y~~~~l~~KKrY~~~~~~~~--~~~~~~~~~kG~e~~RrD~~~~~k~~~~~  308 (466)
T PF00136_consen  231 DAKKKGEELAKEINSELFPSPIKLEFEKVYRWFILLAKKRYAGLKYDNE--GKKKGKIKIKGLELVRRDWCPFVKDIQRE  308 (466)
T ss_dssp             HHHHHHHHHHHHHHHHSCSTTHEEEEEEEEEEEEEEETTEEEEEETCCC--EEETSEEEEESSSGGSSSSTHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHhhhhcCCCceeeecccEEEEEEEccCCccceeeeec--ccccceeEEeccccccCchhHHHHHHHHH
Confidence            8999999999999975  4689999999999999999999999988754  33335679999999999999999999999


Q ss_pred             HHHHHhccCCCCCCChhHHHHHHH----HHHHHHHHHhhCCCcChhhhHHhhcccCCCCC---CcchHHHHHHHHHHcC
Q psy6283         747 VISQILDEQSYTDYSLDDRLQNIH----EHMKKIRTDLDNGFVPLTLLEITKQLTKAPEG---GKVCITQIRLSRNRRG  818 (1030)
Q Consensus       747 vL~~IL~~~~~~~~~~e~~v~~I~----~~l~~~~~~l~~g~vpl~~lvItk~LsK~p~~---~~~pHV~vA~r~~~~g  818 (1030)
                      +|+.||.+.     +.+.+.+.|.    ++|..+..++.++.+|+++|+|++++++++++   ...|||.+|.+|+.+|
T Consensus       309 ~l~~il~~~-----~~~~~~~~i~~~~~e~l~~~~~~l~~~~~~~~~li~~k~l~k~~~~Y~~~~~~hv~~a~rl~~~~  382 (466)
T PF00136_consen  309 VLEIILKGK-----DPEEAVEKIKEVIIEYLKKYIEKLRNGEVPIEDLIISKRLSKDLEEYKKKTPPHVRAAKRLKKRG  382 (466)
T ss_dssp             HHHHHHTTC-----CHHHHHHHHHHHHHHHHHHHHHHHHTTCSHGGGGHEEEECCSCGGGCSSSHHHHHHHHHHHHCTT
T ss_pred             HHHHHhCCC-----CHHHHHHHHHHHHHHHHHHhhccccccchhHHHHHHhhhccCCcccccccCCcHHHHHHHHHhhh
Confidence            999999999     7777766554    77778888899999999999999999999988   4455999999999988

; InterPro: IPR006134 DNA is the biological information that instructs cells how to exist in an ordered fashion: accurate replication is thus one of the most important events in the life cycle of a cell. This function is performed by DNA- directed DNA-polymerases 2.7.7.7 from EC) by adding nucleotide triphosphate (dNTP) residues to the 5'-end of the growing chain of DNA, using a complementary DNA chain as a template. Small RNA molecules are generally used as primers for chain elongation, although terminal proteins may also be used for the de novo synthesis of a DNA chain. Even though there are 2 different methods of priming, these are mediated by 2 very similar polymerases classes, A and B, with similar methods of chain elongation. A number of DNA polymerases have been grouped under the designation of DNA polymerase family B. Six regions of similarity (numbered from I to VI) are found in all or a subset of the B family polymerases. The most conserved region (I) includes a conserved tetrapeptide with two aspartate residues. Its function is not yet known, however, it has been suggested that it may be involved in binding a magnesium ion. All sequences in the B family contain a characteristic DTDS motif, and possess many functional domains, including a 5'-3' elongation domain, a 3'-5' exonuclease domain [], a DNA binding domain, and binding domains for both dNTP's and pyrophosphate []. This domain of DNA polymerase B appears to consist of more than one activities, possibly including elongation, DNA-binding and dNTP binding [].; GO: 0000166 nucleotide binding, 0003677 DNA binding, 0003887 DNA-directed DNA polymerase activity, 0006260 DNA replication; PDB: 1QHT_A 1NOY_A 1NOZ_B 2CW7_A 2CW8_A 1WNS_A 2XHB_A 2VWK_A 2VWJ_A 1TGO_A ....

>cd05537 POLBc_Pol_II DNA polymerase type-II subfamily catalytic domain

Probab=100.00  E-value=5.9e-67  Score=593.91  Aligned_cols=293  Identities=28%  Similarity=0.454  Sum_probs=255.7

Q ss_pred             cccCceeeccccccccceEEEeeccccChhHHHHhccccccccccCCCc--cccccccCCCCC--ccccCCcchHHHHHH
Q psy6283         495 AYSGGLVLEPKKGFYDKFIILMDFNSLYPSIIQEYNICFTTIPVRMLQD--SDITTLCEYLPE--HQVDTGILPSEIKKL  570 (1030)
Q Consensus       495 ~Y~GGlVleP~~GlY~~~V~vLDFnSLYPSII~~~NIc~tTv~~~~~d~--~~i~~~~p~~p~--~~~~~GIlP~iL~~L  570 (1030)
                      .++||+|++|++|||++ |++|||+|||||||++|||||+|++...+.+  +..   .|....  -....||||.+|+.|
T Consensus         2 ~~~Gg~V~eP~~G~y~~-V~vlDF~SLYPSII~~~Ni~p~t~~~~~~~~~~~~~---~~~~~~~~f~~~~Gilp~~l~~l   77 (371)
T cd05537           2 SSPGGYVMDSKPGLYKN-VLVLDFKSLYPSIIRTFLIDPLGLIEGLKAPDPEDL---IPGFLGARFSREKHILPDLIARL   77 (371)
T ss_pred             CCCCcEEeCCCCCccCc-eEEEEcccccHHHHHHhCCCCceecCCCCCCCcccc---ccCCCCCeEecCCCchHHHHHHH
Confidence            46899999999999997 9999999999999999999999987654311  111   011111  023469999999999


Q ss_pred             HHHHHHHHHHhcCCCCChHHHHhhHHHHHHhccccccccccCCCCCCCCCCHHHHHHHHHHhHHHHHHHHHHhhhcccee
Q psy6283         571 VESRRQVKALMKQPNLSSDLLMQYDIRQKALKLTANSMYGCLGFPNSRFFAQPLAALVTAKGREILLNTKSLVENLNYEV  650 (1030)
Q Consensus       571 l~~R~~vKk~mk~~~~~~~~~~~~d~rQ~AlKl~aNS~YG~lG~~~srfy~~~lA~~IT~~GR~iL~~tkelve~~g~~V  650 (1030)
                      ++.|+++|+.|+.            .+|+|+||+|||+|||+|++++||||+++|++||++||.+|+.|+++++++|++|
T Consensus        78 ~~~R~~~K~~~~~------------~~q~AlKi~~Ns~YG~~g~~~~r~~~~~~A~~iT~~GR~~l~~~~~~~e~~g~~V  145 (371)
T cd05537          78 WAARDEAKREKNA------------PLSQAIKIIMNSFYGVLGSTGCRFFDPRLASSITLRGHEIMKQTRAWIEQQGYQV  145 (371)
T ss_pred             HHHHHHHHHhccH------------HHHHhHhhheecceeecccccccccChHHHHHHHHHHHHHHHHHHHHHHHcCCEE
Confidence            9999999998753            3799999999999999999999999999999999999999999999999999999


Q ss_pred             EEecCcceeeecCC-CCHHHHHHHHHHHHHHHhcccc-----------eeEEeecchhhhhhhc--------ccccceEE
Q psy6283         651 IYGDTDSLMISCNV-NDYDSVFKIGNQIKSECNKLYK-----------QLELDIDGVYKYMLLL--------KKKKYAAL  710 (1030)
Q Consensus       651 IYGDTDSI~V~~~~-~d~eea~~ig~~i~~~Vn~~~~-----------~leLe~E~vf~~llll--------~KKrYa~l  710 (1030)
                      ||||||||||+++. .+.+++.++|.+|++.||+.|+           +++|+||++|.++||+        +||||||+
T Consensus       146 iYgDTDSvfV~~~~~~~~~~~~~~~~~l~~~In~~~~~~~~~~~~~~~~l~Le~Ekvy~~~ll~~~~~~~~~~KKrYag~  225 (371)
T cd05537         146 IYGDTDSTFVWLGEELDAAEAQAIGKELASQINQWWAQKLKEEFGLESFLEIEFETHYSRFFMPTIRGSDEGSKKRYAGL  225 (371)
T ss_pred             EEecCCceEEecCCCCCHHHHHHHHHHHHHHHHHHHHHhhhhhhcCCCCceEEEeeeeeeeeeeccccccccccceEEEE
Confidence            99999999999986 6888999999999999998652           5899999999999986        79999999


Q ss_pred             eeeecCCCceeeeceeeeeeeeeCChHHHHHHHHHHHHHHHhccCCCCCCChhHHHHHHHHHHHHHHHHhhCCCcChhhh
Q psy6283         711 SISKLSNGKMICSQEIKGVDVVRRDWSQLASEAGKFVISQILDEQSYTDYSLDDRLQNIHEHMKKIRTDLDNGFVPLTLL  790 (1030)
Q Consensus       711 ~~~~~~dG~~~~~~e~KGle~vRRD~~~l~k~~~~~vL~~IL~~~~~~~~~~e~~v~~I~~~l~~~~~~l~~g~vpl~~l  790 (1030)
                      .++ +++|    ++++||++++|||||+|+++++.++|+.||.++     ++       ++++.++..+|++|.+| ++|
T Consensus       226 ~~~-~~~~----~i~~KGle~vRrD~~~l~k~~~~~vl~~il~~~-----~~-------~~~~~~~~~~l~~g~~~-~~l  287 (371)
T cd05537         226 KST-DGGD----ELVFKGLETVRSDWTPLARQFQKELYERVFNDE-----PY-------EGFIKETVEELLAGELD-ELL  287 (371)
T ss_pred             EEE-CCCc----EEEeecceeEecchHHHHHHHHHHHHHHHhcCC-----CH-------HHHHHHHHHHHHcCCCc-hHh
Confidence            875 3344    568999999999999999999999999999998     54       35566777899999999 999


Q ss_pred             HHhhcccCCCCC---CcchHHHHHHHHHHcCCcc
Q psy6283         791 EITKQLTKAPEG---GKVCITQIRLSRNRRGRRR  821 (1030)
Q Consensus       791 vItk~LsK~p~~---~~~pHV~vA~r~~~~g~~~  821 (1030)
                      +|+++|+|+|++   +++|||+||++|.+.|...
T Consensus       288 vi~k~L~k~~~~Y~~~~~phv~aa~~~~~~~~~~  321 (371)
T cd05537         288 VYRKRLRRPLSEYTKNVPPHVQAARLADQINREL  321 (371)
T ss_pred             EEehhcCCCHHHcCCCCCcHHHHHHHHHhcCCcc
Confidence            999999999987   5689999999999988643

Bacteria contain five DNA polymerases (I, II, III, IV and V). DNA polymerase II (Pol II) is a prototype for the B-family of polymerases. The role of Pol II in a variety of cellular activities, such as repair of DNA damaged by UV irradiation or oxidation has been proven by genetic studies. DNA polymerase III is the main enzyme responsible for replication of the bacterial chromosome; however, In vivo studies have also shown that Pol II is able to participate in chromosomal DNA replication with larger role in lagging-strand replication.

>cd05538 POLBc_Pol_II_B DNA polymerase type-II B subfamily catalytic domain

Probab=100.00  E-value=2.1e-64  Score=568.59  Aligned_cols=262  Identities=27%  Similarity=0.347  Sum_probs=237.5

Q ss_pred             cccCceeeccccccccceEEEeeccccChhHHHHhccccccccccCCCccccccccCCCCCccccCCcchHHHHHHHHHH
Q psy6283         495 AYSGGLVLEPKKGFYDKFIILMDFNSLYPSIIQEYNICFTTIPVRMLQDSDITTLCEYLPEHQVDTGILPSEIKKLVESR  574 (1030)
Q Consensus       495 ~Y~GGlVleP~~GlY~~~V~vLDFnSLYPSII~~~NIc~tTv~~~~~d~~~i~~~~p~~p~~~~~~GIlP~iL~~Ll~~R  574 (1030)
                      +|+||+|++|.||+|++ |++|||+|||||||++|||||+.                      ...||+|.+|+.|++.|
T Consensus         2 ~~~GG~v~~p~~Gl~~~-V~~lDf~SLYPSIi~~~ni~p~~----------------------~~~Gilp~il~~Ll~~R   58 (347)
T cd05538           2 KFEGGYAYVFITGVLGP-IVHADVASLYPSIMLAYRICPAR----------------------DSLGIFLALLKYLVELR   58 (347)
T ss_pred             CcCCceEcccCCcCcCc-eEEEEcccchHHHHHHhCCCCCC----------------------CCCcccHHHHHHHHHHH
Confidence            69999999999999997 99999999999999999999852                      25699999999999999


Q ss_pred             HHHHHHhcCCCCChHHHHhhHHHHHHhccccccccccCCCCCCCCCCHHHHHHHHHHhHHHHHHHHHHhhhccceeEEec
Q psy6283         575 RQVKALMKQPNLSSDLLMQYDIRQKALKLTANSMYGCLGFPNSRFFAQPLAALVTAKGREILLNTKSLVENLNYEVIYGD  654 (1030)
Q Consensus       575 ~~vKk~mk~~~~~~~~~~~~d~rQ~AlKl~aNS~YG~lG~~~srfy~~~lA~~IT~~GR~iL~~tkelve~~g~~VIYGD  654 (1030)
                      .++|+.|++ ..+|.++.+||.+|+|+||++||+|||||+.+++|||+++|++||++||.+|..|+++++++|++|||||
T Consensus        59 ~~~K~~~k~-~~~~~~~~~~d~~Q~AlKi~~NS~YG~lG~~~~r~~~~~~A~~iT~~GR~~L~~~~~~~e~~g~~VIygD  137 (347)
T cd05538          59 LAAKESARA-AARPAERDAFKAKQAAFKVLINSFYGYLGTGLHAFSDPEAAAEVTRLGRELLKLMIRWLRRRGATPVEVD  137 (347)
T ss_pred             HHHHHHHhc-CCChHHHHHHHHHHHHHhhhhhhchhhhcCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHCCCEEEEEc
Confidence            999999998 5688999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             CcceeeecCCC-C-HHHHHHHHHHHHHHHhccc-ceeEEeecchhhhhhhcccccceEEeeeecCCCceeeeceeeeeee
Q psy6283         655 TDSLMISCNVN-D-YDSVFKIGNQIKSECNKLY-KQLELDIDGVYKYMLLLKKKKYAALSISKLSNGKMICSQEIKGVDV  731 (1030)
Q Consensus       655 TDSI~V~~~~~-d-~eea~~ig~~i~~~Vn~~~-~~leLe~E~vf~~llll~KKrYa~l~~~~~~dG~~~~~~e~KGle~  731 (1030)
                      ||||||.++.. + .+++    .++.++|++.+ .+|+|++|++|.+||+++|||||++.    .+|+    +++||+++
T Consensus       138 TDSi~v~~~~~~~~~~~~----~~~~~~i~~~~~~~i~le~e~~y~~~l~~~KKrYa~~~----~~gk----i~~KG~e~  205 (347)
T cd05538         138 TDGIYFIPPNGVDTEDEE----EELVRELSSTLPKGITVEFDGRYRAMFSYKIKNYALLD----YDGK----LIVKGSAF  205 (347)
T ss_pred             CCeeEEEeCCCCChHHHH----HHHHHHHHHhCCCCeEEEEhHHHHHHHhhcCceEEEEe----cCCc----EEEECCCc
Confidence            99999987642 2 3333    45666676655 58999999999999999999999974    3565    47999999


Q ss_pred             eeCChHHHHHHHHHHHHHHHhccCCCCCCChhHHHHHHHHHHHHHHHHhhCCCcChhhhHHhhcccCCCCC
Q psy6283         732 VRRDWSQLASEAGKFVISQILDEQSYTDYSLDDRLQNIHEHMKKIRTDLDNGFVPLTLLEITKQLTKAPEG  802 (1030)
Q Consensus       732 vRRD~~~l~k~~~~~vL~~IL~~~~~~~~~~e~~v~~I~~~l~~~~~~l~~g~vpl~~lvItk~LsK~p~~  802 (1030)
                      ||||||+|+++++.++|+.||+++          .+.+++++.++..+|++|.+|+++|+|+++|+|+|++
T Consensus       206 vRrD~~~~~k~~~~~vl~~ll~~~----------~~~~~~~~~~~~~~l~~~~~~~~~l~i~k~l~k~~~~  266 (347)
T cd05538         206 RSRGIEPFLREFLREAVRLLLQGD----------GAGVHDLYEDYLRRLRSHELPISDLARTETLKESPEE  266 (347)
T ss_pred             ccCCchHHHHHHHHHHHHHHHcCC----------hHHHHHHHHHHHHHHHcCCCCHHHEEEEeecCCCHHH
Confidence            999999999999999999999875          2467888889999999999999999999999999987

Bacteria contain five DNA polymerases (I, II, III, IV and V). DNA polymerase II (Pol II) is a prototype for the B-family of polymerases. The role of Pol II in a variety of cellular activities, such as repair of DNA damaged by UV irradiation or oxidation has been proved by genetic studies. DNA polymerase III is the main enzyme responsible for replication of the bacterial chromosome; however, In vivo studies have also shown that Pol II is able to participate in chromosomal DNA replication with larger role in lagging-strand replication.

>cd00145 POLBc DNA polymerase type-B family catalytic domain

Probab=100.00  E-value=4.9e-63  Score=554.09  Aligned_cols=268  Identities=36%  Similarity=0.524  Sum_probs=236.3

Q ss_pred             cccCceeeccccccccceEEEeeccccChhHHHHhccccccccccCCCcccccc-ccCCCCCccccCCcchHHHHHHHHH
Q psy6283         495 AYSGGLVLEPKKGFYDKFIILMDFNSLYPSIIQEYNICFTTIPVRMLQDSDITT-LCEYLPEHQVDTGILPSEIKKLVES  573 (1030)
Q Consensus       495 ~Y~GGlVleP~~GlY~~~V~vLDFnSLYPSII~~~NIc~tTv~~~~~d~~~i~~-~~p~~p~~~~~~GIlP~iL~~Ll~~  573 (1030)
                      +|+||+|++|.+|+|+ +|++|||+|||||||++|||||+|++...+.. .... ....+.....++||+|.+|+.|++.
T Consensus         2 ~y~Gg~V~~P~~G~~~-~V~~lDf~SLYPSIi~~~Ni~~~T~~~~~~~~-~~~~~~~~~~~~~~~~~Gilp~iL~~Ll~~   79 (323)
T cd00145           2 PYEGGYVFDPIPGLYE-NVIVLDFKSLYPSIIITYNLSPTTLVGNGEIA-APEDYIGVGFRSPKDRKGLLPRILEELLNF   79 (323)
T ss_pred             CCCCcEEecCcccccC-ceEEeecCCccHHHHHHhCCCccccccccccc-CcccccCccccccCCCCCCCHHHHHHHHHH
Confidence            6999999999999998 59999999999999999999999998765311 0100 0012344567899999999999999


Q ss_pred             HHHHHHHhcCCCCChHHHHhhHHHHHHhccccccccccCCCCCCCCCCHHHHHHHHHHhHHHHHHHHHHhhhccceeEEe
Q psy6283         574 RRQVKALMKQPNLSSDLLMQYDIRQKALKLTANSMYGCLGFPNSRFFAQPLAALVTAKGREILLNTKSLVENLNYEVIYG  653 (1030)
Q Consensus       574 R~~vKk~mk~~~~~~~~~~~~d~rQ~AlKl~aNS~YG~lG~~~srfy~~~lA~~IT~~GR~iL~~tkelve~~g~~VIYG  653 (1030)
                      |.++|+.|++.+.++.++.+||.+|+|+||+|||+|||+|+++|||||.++|++||+.||.+|+.|+++++++|++||||
T Consensus        80 R~~~K~~mk~~~~~~~~~~~~d~~Q~AlKi~~NS~YG~~G~~~~r~~~~~~A~~IT~~GR~~l~~~~~~ie~~g~~VIYG  159 (323)
T cd00145          80 RDEAKKRMKAAKLAPEERVLYDNRQQALKVLANSFYGYLGAKFFRFYDPEVAASITSFGREIIQDTIALVEEHGARVIYG  159 (323)
T ss_pred             HHHHHHHHhhCcCCHHHHHHHHHHhhhhheeeecceeecccccccCCChHHHHHHHHHHHHHHHHHHHHHHHcCCEEEEE
Confidence            99999999997777999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             cCcceeeecCC-CCHHHHHHHHHHHHHHHhcccceeEEeecchhhhhhhcccccceEEeeeecCCCceeeeceeeeeeee
Q psy6283         654 DTDSLMISCNV-NDYDSVFKIGNQIKSECNKLYKQLELDIDGVYKYMLLLKKKKYAALSISKLSNGKMICSQEIKGVDVV  732 (1030)
Q Consensus       654 DTDSI~V~~~~-~d~eea~~ig~~i~~~Vn~~~~~leLe~E~vf~~llll~KKrYa~l~~~~~~dG~~~~~~e~KGle~v  732 (1030)
                      |||||||.++. .+.+++.++++++.+.| ..+.+|+||+|++|.++++++||||||+.+++.   ...+++++||++++
T Consensus       160 DTDSifv~~~~~~~~~~~~~~~~~~~~~i-~~~~~i~le~E~vy~~~ll~~KKrYag~~~~~~---~~~~~~~~KG~e~v  235 (323)
T cd00145         160 DTDSIFVSLPKMGTKEDAIKEGREILQEL-ADEHLLELEFEKVYLPFFLGKKKRYAGLDIWKG---QDEGKIDIKGLETR  235 (323)
T ss_pred             CCCceEEEeCCCCCHHHHHHHHHHHHHHh-CCCCCeEEEEchhhHHHHHhhhhhEEEEEEEcC---CCCceEEEEcceEE
Confidence            99999999998 78999999999999999 455689999999999999999999999988752   22346799999999


Q ss_pred             eCChHHHHHHHHHHHHHHHhccCCCCCCChhHHHHHHHHHHHHH
Q psy6283         733 RRDWSQLASEAGKFVISQILDEQSYTDYSLDDRLQNIHEHMKKI  776 (1030)
Q Consensus       733 RRD~~~l~k~~~~~vL~~IL~~~~~~~~~~e~~v~~I~~~l~~~  776 (1030)
                      |||||+|+++++.++|+.||.++        .+++.+++++.++
T Consensus       236 RrD~~~~~k~~~~~vl~~ll~~~--------~~~~~v~~~~~~l  271 (323)
T cd00145         236 RRDSPPLVKKFQKEVLELILEEE--------RKVEAVKEYIDEL  271 (323)
T ss_pred             ecCcHHHHHHHHHHHHHHHHcCC--------chHHHHHHHHHHh
Confidence            99999999999999999999953        2466677776655

DNA-directed DNA polymerases elongate DNA by adding nucleotide triphosphate (dNTP) residues to the 5'-end of the growing chain of DNA. DNA-directed DNA polymerases are multifunctional with both synthetic (polymerase) and degradative modes (exonucleases) and play roles in the processes of DNA replication, repair, and recombination. DNA-dependent DNA polymerases can be classified in six main groups based upon their phylogenetic relationships with E. coli polymerase I (class A), E. coli polymerase II (class B), E. coli polymerase III (class C), euryarchaeota polymerase II (class D), human polymerase beta (class x), E. coli UmuC/DinB, and eukaryotic RAP 30/Xeroderma pigmentosum variant (class Y). Family B DNA polymerases include E. coli DNA polymerase II, some eubacterial phage DNA polymerases, nuclear replicative DNA polymerases (alpha, delta, epsilon, and zeta), and eukaryotic viral and plasmid-borne enzymes. DNA polymerase is

>KOG0968|consensus

Probab=100.00  E-value=9.5e-63  Score=582.32  Aligned_cols=395  Identities=24%  Similarity=0.358  Sum_probs=347.2

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHhcchHHHHHHHHHhCCcchhhccCchhHHHHHHHHHHHhhcCeeccCCccccCcCCCcc
Q psy6283         402 IVEFIKFTMLHSSYIIKIMCELNVLPLAIQITNVCGNVLSRTLMGGRSERNEFLLLHAFHEKSYVLPDKQYGKNKKEGEE  481 (1030)
Q Consensus       402 l~~lv~Y~~~Da~l~~~L~~kl~vlpl~~~lt~iaG~~~srtl~~gr~~r~E~lLL~~~~~~~yivPdk~~~kk~~~~~d  481 (1030)
                      +..++.|-+.-|.+.++|+.+++++.-+.+++++.|+.+-.+++.|++.|+|++||+-+|..|||.|.+.....      
T Consensus       867 r~~~l~y~l~Ra~~NlelLsq~d~i~k~~E~ARv~GIdF~sV~tRGSQ~rVESmllRiAk~~Nyi~~SPs~kQv------  940 (1488)
T KOG0968|consen  867 RNDVLNYLLSRARLNLELLSQLDWILKNSEMARVIGIDFHSVLTRGSQFRVESMLLRIAKPMNYIAPSPSHKQV------  940 (1488)
T ss_pred             HHHHHHHHHHHhhhhHHHHHHHHHHHhhHHHHHhhcceeeEEeeccchhhHHHHHHHHhcccccccCCccHHHH------
Confidence            68889999999999999999999999999999999999999999999999999999999999999997653211      


Q ss_pred             ccccccCCCCCCccccCceeeccccccccceEEEeeccccChhHHHHhccccccccccCCC---ccccc-----------
Q psy6283         482 TGEANKGKGRKKAAYSGGLVLEPKKGFYDKFIILMDFNSLYPSIIQEYNICFTTIPVRMLQ---DSDIT-----------  547 (1030)
Q Consensus       482 ~~~~~~~~~~~~~~Y~GGlVleP~~GlY~~~V~vLDFnSLYPSII~~~NIc~tTv~~~~~d---~~~i~-----------  547 (1030)
                              ....+.-+=.+|++|+.-||.+||+||||.||||||||+||+||+|+.+....   .+++.           
T Consensus       941 --------~~q~A~EcvPLVMEPeS~fY~~PViVLDFQSLYPSivIAYNyCySTcLG~v~~l~~~~e~~LG~s~~s~~~d 1012 (1488)
T KOG0968|consen  941 --------AMQGAPECVPLVMEPESAFYFDPVIVLDFQSLYPSIVIAYNYCYSTCLGKVGNLNQMNEIKLGVSKYSLPPD 1012 (1488)
T ss_pred             --------hhcCCccccceeecchhhhccCceEEEEchhhcchHHHhHHHHHHHhhhHHHhhccccceeeeeeeccCCHH
Confidence                    11234556789999999999999999999999999999999999999875420   11110           


Q ss_pred             -------c--ccCC---CCCccccCCcchHHHHHHHHHHHHHHHHhcCCCCChHHHHhhHHHHHHhccccccccccCCCC
Q psy6283         548 -------T--LCEY---LPEHQVDTGILPSEIKKLVESRRQVKALMKQPNLSSDLLMQYDIRQKALKLTANSMYGCLGFP  615 (1030)
Q Consensus       548 -------~--~~p~---~p~~~~~~GIlP~iL~~Ll~~R~~vKk~mk~~~~~~~~~~~~d~rQ~AlKl~aNS~YG~lG~~  615 (1030)
                             +  ..|+   ++.+++++|+||.+|+++|+.|..||+.||..+.+......+|.||+||||+||..|||+.+.
T Consensus      1013 il~~~~ndV~isPNgv~yVK~sVRkgvLpkmLeEIL~tRiMVKkaMK~~~~~~~L~RiLnaRQLALKLiANVTYGYTsA~ 1092 (1488)
T KOG0968|consen 1013 ILVLAKNDVTISPNGVMYVKPSVRKGVLPKMLEEILATRIMVKKAMKRTKDNKKLKRILNARQLALKLIANVTYGYTSAN 1092 (1488)
T ss_pred             HHHHHhcceeeCCCceEEechhhhhhhHHHHHHHHHHHHHHHHHHHHHhcchHHHHHHhhhHHHHHHHHhhccccccccc
Confidence                   0  1232   445678999999999999999999999999965466677899999999999999999999998


Q ss_pred             CC-CCCCHHHHHHHHHHhHHHHHHHHHHhhh---ccceeEEecCcceeeecCCCCHHHHHHHHHHHHHHHhcccc-eeEE
Q psy6283         616 NS-RFFAQPLAALVTAKGREILLNTKSLVEN---LNYEVIYGDTDSLMISCNVNDYDSVFKIGNQIKSECNKLYK-QLEL  690 (1030)
Q Consensus       616 ~s-rfy~~~lA~~IT~~GR~iL~~tkelve~---~g~~VIYGDTDSI~V~~~~~d~eea~~ig~~i~~~Vn~~~~-~leL  690 (1030)
                      .| |++|.++|.+|..+||++|.+++++|+.   +|++||||||||+||.+++.+.++||.||.+|++.|+..+| |+.|
T Consensus      1093 FSGRMPCaElADsIV~~GRETLEraIe~Vn~~d~w~AkVVYGDTDSmFVlL~GaT~eeAF~IGq~iAe~VT~~NP~PV~L 1172 (1488)
T KOG0968|consen 1093 FSGRMPCAELADSIVQKGRETLERAIEMVNRGDYWGAKVVYGDTDSMFVLLPGATVEEAFEIGQEIAEAVTNSNPKPVVL 1172 (1488)
T ss_pred             cCCCCchHHHHHHHHHhhHHHHHHHHHHHhcCCcCCeEEEEcCCCceEEEecCccHHHHHHHHHHHHHHHHhcCCCCeEE
Confidence            87 9999999999999999999999999985   89999999999999999999999999999999999998875 8999


Q ss_pred             eecchhhhhhhcccccceEEeeeecCCCceeeeceeeeeeeeeCChHHHHHHHHHHHHHHHhccCCCCCCChhHHHHHHH
Q psy6283         691 DIDGVYKYMLLLKKKKYAALSISKLSNGKMICSQEIKGVDVVRRDWSQLASEAGKFVISQILDEQSYTDYSLDDRLQNIH  770 (1030)
Q Consensus       691 e~E~vf~~llll~KKrYa~l~~~~~~dG~~~~~~e~KGle~vRRD~~~l~k~~~~~vL~~IL~~~~~~~~~~e~~v~~I~  770 (1030)
                      .||+||.+++|++||||+|++|+.....  .+.++.||+++||||.||.+..+...+|..|++.+     +    +..|+
T Consensus      1173 KfEKVY~PCvL~tKKRYVG~~YEs~~Qk--~PiFDAKGIETVRRDtcPavakilEksL~LlFetk-----d----lS~IK 1241 (1488)
T KOG0968|consen 1173 KFEKVYHPCVLLTKKRYVGFMYESPNQK--EPIFDAKGIETVRRDTCPAVAKILEKSLRLLFETK-----D----LSKIK 1241 (1488)
T ss_pred             EeeeecccceeeeccceeeeeeccCccc--CCccccccceeeeccCcHHHHHHHHHHHHHHhhcc-----c----HHHHH
Confidence            9999999999999999999999865432  24679999999999999999999999999999987     4    67899


Q ss_pred             HHHHHHHHHhhCCCcChhhhHHhhcccC--CCCC-CcchHHHHHHHHHHcCCcc
Q psy6283         771 EHMKKIRTDLDNGFVPLTLLEITKQLTK--APEG-GKVCITQIRLSRNRRGRRR  821 (1030)
Q Consensus       771 ~~l~~~~~~l~~g~vpl~~lvItk~LsK--~p~~-~~~pHV~vA~r~~~~g~~~  821 (1030)
                      .|+...+.++..|++++.||++.|.+.-  .... ...|...||.|++....+.
T Consensus      1242 ~y~q~~~~ki~~Gkvs~qDF~FaKEvRl~~~~~~~~~pP~avva~r~i~~DpR~ 1295 (1488)
T KOG0968|consen 1242 KYLQNVCNKIQEGKVSFQDFCFAKEVRLEKYYSASAAPPGAVVARRRITKDPRH 1295 (1488)
T ss_pred             HHHHHHHHHHhhCCcchhhheeeeeecceeccccccCCchHHHHHHHhccCCcc
Confidence            9999999999999999999999998876  3333 5577888998888766543

>cd05531 POLBc_B2 DNA polymerase type-B B2 subfamily catalytic domain

Probab=100.00  E-value=2.6e-62  Score=552.80  Aligned_cols=290  Identities=28%  Similarity=0.456  Sum_probs=246.3

Q ss_pred             ccccCceeeccccccccceEEEeeccccChhHHHHhccccccccccCCCccccccccCCCC--CccccCCcchHHHHHHH
Q psy6283         494 AAYSGGLVLEPKKGFYDKFIILMDFNSLYPSIIQEYNICFTTIPVRMLQDSDITTLCEYLP--EHQVDTGILPSEIKKLV  571 (1030)
Q Consensus       494 ~~Y~GGlVleP~~GlY~~~V~vLDFnSLYPSII~~~NIc~tTv~~~~~d~~~i~~~~p~~p--~~~~~~GIlP~iL~~Ll  571 (1030)
                      .+|.||+|++|.+|||++ |++|||+|||||||++|||||+|+++.++.....    +...  ....+.||+|.+|+.|+
T Consensus         3 ~~~~Gg~V~~p~~G~~~~-V~~lDF~SLYPSii~~~ni~~~ti~~~~~~~~~~----~~~~~~~~~~~~gilp~~l~~l~   77 (352)
T cd05531           3 LADRGGLVFQPEPGLYEN-VAQIDFSSMYPSIIVKYNISPETINCRCCECRDH----VYLGHRICLKRRGFLPEVLEPLL   77 (352)
T ss_pred             cCCCCcEEecCCCCccCc-eEEEEccccchHHHHHhCCChhhccccCcccccC----CCCCceEecCCCCchHHHHHHHH
Confidence            479999999999999997 9999999999999999999999998765311111    1111  12468999999999999


Q ss_pred             HHHHHHHHHhcCCCCChHHHHhhHHHHHHhccccccccccCCCCCCCCCCHHHHHHHHHHhHHHHHHHHHHhhhccceeE
Q psy6283         572 ESRRQVKALMKQPNLSSDLLMQYDIRQKALKLTANSMYGCLGFPNSRFFAQPLAALVTAKGREILLNTKSLVENLNYEVI  651 (1030)
Q Consensus       572 ~~R~~vKk~mk~~~~~~~~~~~~d~rQ~AlKl~aNS~YG~lG~~~srfy~~~lA~~IT~~GR~iL~~tkelve~~g~~VI  651 (1030)
                      +.|.++|+.|++.+ +      +|.+|+|+||+|||+|||||+++|+||+.++|++||+.||.+|+.|+++++++|++||
T Consensus        78 ~~R~~~K~~~k~~~-~------~d~~q~AlKi~~NS~YGylG~~~~~f~~~~~A~~vT~~GR~~L~~~~~~~e~~g~~VI  150 (352)
T cd05531          78 ERRLEYKRLKKEED-P------YAGRQKALKWILVTSFGYLGYKNAKFGRIEVHEAITAYGRKILLRAKEIAEEMGFRVL  150 (352)
T ss_pred             HHHHHHHHHhhcCC-C------chHHHhhheeeeecccccccccccccCChHHHHHHHHHHHHHHHHHHHHHHHcCCEEE
Confidence            99999999999742 2      3999999999999999999999999999999999999999999999999999999999


Q ss_pred             EecCcceeeecCCCCHHHHHHHHHHHHHHHhcccceeEEeecchhhhhhhc-------ccccceEEeeeecCCCceeeec
Q psy6283         652 YGDTDSLMISCNVNDYDSVFKIGNQIKSECNKLYKQLELDIDGVYKYMLLL-------KKKKYAALSISKLSNGKMICSQ  724 (1030)
Q Consensus       652 YGDTDSI~V~~~~~d~eea~~ig~~i~~~Vn~~~~~leLe~E~vf~~llll-------~KKrYa~l~~~~~~dG~~~~~~  724 (1030)
                      |||||||||+++.    ...    +++.+|++.+ +++|++|++|.+++|+       .||||+|+..    +|+    +
T Consensus       151 ygDTDSvfv~~~~----~~~----~~~~~i~~~~-~i~l~le~~y~~~~~~~~~~~~~~kKrY~g~~~----~g~----i  213 (352)
T cd05531         151 HGIVDSLWIQGRG----DIE----ELAREIEERT-GIPLKLEGHYDWIVFLPERDGLGAPNRYFGRLS----DGE----M  213 (352)
T ss_pred             EEccccceeecCc----hHH----HHHHHHHHhc-CCceEEEEEEEEEEeeccccccCcceeEEEecC----CCc----E
Confidence            9999999999742    233    3444555555 4889999999998765       5899999852    564    4


Q ss_pred             eeeeeeeeeCChHHHHHHHHHHHHHHHhccCCCCCCChhHH---HHHHHHHHHHHHHHhhCCCcChhhhHHhhcccCCCC
Q psy6283         725 EIKGVDVVRRDWSQLASEAGKFVISQILDEQSYTDYSLDDR---LQNIHEHMKKIRTDLDNGFVPLTLLEITKQLTKAPE  801 (1030)
Q Consensus       725 e~KGle~vRRD~~~l~k~~~~~vL~~IL~~~~~~~~~~e~~---v~~I~~~l~~~~~~l~~g~vpl~~lvItk~LsK~p~  801 (1030)
                      ++||++++|||||+|++++|..+|+.||.++     +++++   ++.+++++.+...+|.+|.  +++|+|+++|+|+|+
T Consensus       214 ~~KG~e~vRrD~~~~~k~~~~~vl~~ll~~~-----~~~~~~~~~~~~~~~~~~~~~~l~~~~--~~~lvi~k~l~k~~~  286 (352)
T cd05531         214 KVRGIELRRRDTPPFVKKFQEEALDILASAK-----TPEELLKLREEALDLFRRYLQRLREGD--LEDLIIEKKISKRSS  286 (352)
T ss_pred             EEEeeEEEeCCchHHHHHHHHHHHHHHhcCC-----CHHHHHHHHHHHHHHHHHHHHHHhcCC--hHHEEEEEEecCCHH
Confidence            7999999999999999999999999999998     77653   5678889999999999997  999999999999998


Q ss_pred             C-CcchHHHHHHHHHHcCCc
Q psy6283         802 G-GKVCITQIRLSRNRRGRR  820 (1030)
Q Consensus       802 ~-~~~pHV~vA~r~~~~g~~  820 (1030)
                      + ...+|. ||++|++.|..
T Consensus       287 ~Y~~~~~~-~a~~l~~~g~~  305 (352)
T cd05531         287 EYKVLAST-ALKALRAKGVS  305 (352)
T ss_pred             HcCCchHH-HHHHHHhCCCC
Confidence            8 444444 89999888743

Archaeal proteins that are involved in DNA replication are similar to those from eukaryotes. Some archaeal members also possess multiple family B DNA polymerases (B1, B2 and B3). So far there is no specific function(s) has been assigned for different members of the archaea type B DNA polymerases. Phylogenetic analyses of eubacterial, archaeal, and eukaryotic family B DNA polymerases are support independent gene duplications during the evolution of archaeal and eukaryotic family B DNA polymerases.

>PHA03334 putative DNA polymerase catalytic subunit; Provisional

Probab=100.00  E-value=2.3e-50  Score=489.93  Aligned_cols=341  Identities=21%  Similarity=0.247  Sum_probs=253.8

Q ss_pred             cHHHHHHHHHHHHHHHHHHHHHhcchHHHHHHHHHhCCcchh------hccCc--hhHHHHHHHHHHHh-hcCeeccCCc
Q psy6283         401 GIVEFIKFTMLHSSYIIKIMCELNVLPLAIQITNVCGNVLSR------TLMGG--RSERNEFLLLHAFH-EKSYVLPDKQ  471 (1030)
Q Consensus       401 Gl~~lv~Y~~~Da~l~~~L~~kl~vlpl~~~lt~iaG~~~sr------tl~~g--r~~r~E~lLL~~~~-~~~yivPdk~  471 (1030)
                      |+.+++.||++||.|+++|+.++..+....++++++|++..-      ++..|  ||.|+-..+|..+. +.|+++|...
T Consensus       533 ~RaRla~YCLkDA~LvlrLlkkl~~h~e~~eraRvT~~id~~~l~RG~v~fdG~vQQIKV~s~lL~kA~~~~~~~ia~~~  612 (1545)
T PHA03334        533 ALARYLIYNLVDSELLIRIAKNLDPVIEFLNRLRATYNIDYVAHGRGVMNFCGFVQSTKSVEVPLLKARLRIGIFVATGR  612 (1545)
T ss_pred             hHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcccCCceeecccceecccCccchhhHHHHHHHHHHHhcCccccccc
Confidence            489999999999999999999999888888999998877532      34455  88887755555554 7888887322


Q ss_pred             cccCcCCCccccccccCCCCCCccccCceeecccccc-----ccceEEEeeccccChhHHHHhccccccccccCCCc--c
Q psy6283         472 YGKNKKEGEETGEANKGKGRKKAAYSGGLVLEPKKGF-----YDKFIILMDFNSLYPSIIQEYNICFTTIPVRMLQD--S  544 (1030)
Q Consensus       472 ~~kk~~~~~d~~~~~~~~~~~~~~Y~GGlVleP~~Gl-----Y~~~V~vLDFnSLYPSII~~~NIc~tTv~~~~~d~--~  544 (1030)
                      .... ...++. .  ....+...+|+||+|++|++||     |++||++|||+|||||||++|||||+|++...+..  .
T Consensus       613 i~~s-~ilP~~-~--~~~~~~~~~YeGAtVLEP~~Gf~~~~~Y~~PVaVLDFASLYPSIIiahNLCYeTLV~~~c~~~~~  688 (1545)
T PHA03334        613 IAES-LCMPEK-Y--ARDCRQKIKLKGGYVFAPLTGLTFAGPYQGTELTLDFASLYPSNMCDANISPEAIVDPDCTARVR  688 (1545)
T ss_pred             cccc-ccCCcc-c--ccccccccccCCeEeecCCCCccccccCCCcEEEEEccccchHHHHHhCCCcccccCccchhhhc
Confidence            1100 000000 0  0011335689999999999999     67799999999999999999999999999765411  0


Q ss_pred             --------cccc-c------------cCCCCCccccCCcchHHHHHHHHHHHHHHHHhcCCCCChHHHHhhHHHHHHhcc
Q psy6283         545 --------DITT-L------------CEYLPEHQVDTGILPSEIKKLVESRRQVKALMKQPNLSSDLLMQYDIRQKALKL  603 (1030)
Q Consensus       545 --------~i~~-~------------~p~~p~~~~~~GIlP~iL~~Ll~~R~~vKk~mk~~~~~~~~~~~~d~rQ~AlKl  603 (1030)
                              .++. .            .|..|......+++|.+|+.|++.|+++|+.||+ ..+|.++.+||.+|+|+|+
T Consensus       689 ~~~~~d~~k~p~gy~~~~~vy~V~~~~~~~P~~~rf~SiLp~LL~eLL~~RK~~Kk~MKk-~kDp~er~iLD~rQlALKV  767 (1545)
T PHA03334        689 GWVVFDWKKIDRGFGKATLMYTILRTKPEEPSWRRFTTYTTSSLNHYLSMRTEYKGAMKQ-AKDPKLKSYHNQLQNEMKI  767 (1545)
T ss_pred             cccccccccCCcccCccccceeeccccCcCCCcceecchHHHHHHHHHHHHHHHHHHHhh-CCCHHHHHHHHHHHHHHHH
Confidence                    0000 0            0113333345689999999999999999999998 5688899999999999999


Q ss_pred             ccccccccCCCCCCCCCCHHHHHHHHHHhHHHHHHHHHHhh-hccceeEEecCcceeeecCCCCH-----------HHHH
Q psy6283         604 TANSMYGCLGFPNSRFFAQPLAALVTAKGREILLNTKSLVE-NLNYEVIYGDTDSLMISCNVNDY-----------DSVF  671 (1030)
Q Consensus       604 ~aNS~YG~lG~~~srfy~~~lA~~IT~~GR~iL~~tkelve-~~g~~VIYGDTDSI~V~~~~~d~-----------eea~  671 (1030)
                      +|||+|||+|.        .+|++||++||++|+.|+++++ +.|++|||||||||||+++..+.           ++..
T Consensus       768 tANSvYGytG~--------~cA~lVTa~GRemI~~t~~~IE~e~G~~VIYGDTDSVfV~~p~~d~~~~~~d~v~~~~~~~  839 (1545)
T PHA03334        768 CANSHYGVAPH--------ACQHLITTLGRHKIKLVEEFIKKEPGMTVNYGDTDSVMFQLPPDDAETYLEDTVTLEDEER  839 (1545)
T ss_pred             HHHhhcCcchh--------HHHHHHHHHHHHHHHHHHHHHHHhCCCEEEEEeCCceEEEeCccccccccccccchhhhhh
Confidence            99999999875        4799999999999999999999 89999999999999999874321           0111


Q ss_pred             HHH------------HHHHH---------------HHhc-cc----------c------e---------------e----
Q psy6283         672 KIG------------NQIKS---------------ECNK-LY----------K------Q---------------L----  688 (1030)
Q Consensus       672 ~ig------------~~i~~---------------~Vn~-~~----------~------~---------------l----  688 (1030)
                      .++            +.+.+               -||. +|          .      |               +    
T Consensus       840 ~~~~~~~~~~s~~~~~~~~~~k~~~~~~~v~~~L~~l~~~l~d~m~~~l~~~~~~~~~~p~~~~~~~~~~d~~~g~~~~~  919 (1545)
T PHA03334        840 APLEYTLEEWSAEAVNHVTKAKTKREGETVQSILSDLNTVLYDDMIERLRYVDEGGSVEPFKDGEDWWVVDPLDGIWTYV  919 (1545)
T ss_pred             hhhhhhHHHHHHHHHHHHHhhhhhcccchHHHHHHHHHHHHHHHHHHhheEeCCCCcEeeccCCCceeeecCCCceEEEe
Confidence            111            11111               1111 00          0      1               1    


Q ss_pred             ----------EEeecchhhhhhhcccccceEEeeeecCCCce-eeeceeeeeeeeeCChHHHHHHHHHHHHHHHhccC
Q psy6283         689 ----------ELDIDGVYKYMLLLKKKKYAALSISKLSNGKM-ICSQEIKGVDVVRRDWSQLASEAGKFVISQILDEQ  755 (1030)
Q Consensus       689 ----------eLe~E~vf~~llll~KKrYa~l~~~~~~dG~~-~~~~e~KGle~vRRD~~~l~k~~~~~vL~~IL~~~  755 (1030)
                                +|++|..-.-.+.++||+|+..+|+.+ +|.+ .++++++|++.+++..+..++.+..++++.||.|.
T Consensus       920 ~~~f~~~~ItkL~yEn~stv~~~~aKK~Yi~~vhd~e-~~~~~~pKlK~~G~ea~KSStpga~r~~~~d~i~lI~~gg  996 (1545)
T PHA03334        920 RDPFSSELITKLCYENTSTVTCRLAKKMYIYTNHELN-NGPLGNTKIKMRGMQANKSSAAGATRRITNDFVNLIFKGG  996 (1545)
T ss_pred             ccchhHhHHHHHhhhcchhhhhhhhhhhhheeeeecC-CcccccceeeeccccccccCCcHHHHHHHHHHHHHHhcCC
Confidence                      233444444446679999999988854 5554 47899999999999999999999999999999987

>cd05535 POLBc_epsilon DNA polymerase type-B epsilon subfamily catalytic domain

Probab=100.00  E-value=4.5e-48  Score=449.17  Aligned_cols=251  Identities=23%  Similarity=0.284  Sum_probs=209.7

Q ss_pred             ccCCcchHHHHHHHHHHHHHHHHhcCCC---------CCh-------HHHHhhHHHHHHhccccccccccCCCCCCCCCC
Q psy6283         558 VDTGILPSEIKKLVESRRQVKALMKQPN---------LSS-------DLLMQYDIRQKALKLTANSMYGCLGFPNSRFFA  621 (1030)
Q Consensus       558 ~~~GIlP~iL~~Ll~~R~~vKk~mk~~~---------~~~-------~~~~~~d~rQ~AlKl~aNS~YG~lG~~~srfy~  621 (1030)
                      .+.+++...++.+.++|..+|.+.|...         .++       ..-.+||++|+|+|+++||||||+|+++||||+
T Consensus       219 rEn~Fyvdtvr~FrdrRy~yK~~~k~~k~~~~~~~~~~~~~~~~~a~~~~~lyDs~Q~A~KiIlNSfYGYlG~~gsRwYs  298 (621)
T cd05535         219 RENPFYVDTVRAFRDRRYEYKGLHKVWKKKLEAAKAAGDAAEIKEAKKMVVLYDSLQLAHKCILNSFYGYVMRKGSRWYS  298 (621)
T ss_pred             ccCCcHHhhHHHHHHHHHHHHHHHHHHHHHHhhhhccCChhHHHHHHHHHHHHHHHHHHHHHHHhhccCccCcCCcccCC
Confidence            5788999999999999999999887431         121       233689999999999999999999999999999


Q ss_pred             HHHHHHHHHHhHHHHHHHHHHhhhccceeEEecCcceeeecCCCCHHH---HHHHHHH---------HH-----HHHhcc
Q psy6283         622 QPLAALVTAKGREILLNTKSLVENLNYEVIYGDTDSLMISCNVNDYDS---VFKIGNQ---------IK-----SECNKL  684 (1030)
Q Consensus       622 ~~lA~~IT~~GR~iL~~tkelve~~g~~VIYGDTDSI~V~~~~~d~ee---a~~ig~~---------i~-----~~Vn~~  684 (1030)
                      .++|++||++||+||+.|+++++.+|+.| |||||||||.+|....++   +.+.|..         +.     ..+|..
T Consensus       299 ~emA~~VT~~GreIIk~tr~lvE~~G~~V-egDTDsI~~~lp~~~~e~~~~~~k~g~~~~~~~~~~~LN~~V~~~~tn~q  377 (621)
T cd05535         299 MEMAGIVCYTGANIIQMARELVEQIGRPL-ELDTDGIWCILPKSFPENFTFKTKNGKKVTISYPCVMLNHLVHKKFTNDQ  377 (621)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHhcCCEE-EEecCeeEEEcCCCChHHHHHHhhccchhhhhhhHHHHHHHHHHHHHHHH
Confidence            99999999999999999999999999988 799999999987654443   2222222         22     233332


Q ss_pred             c----------------ceeEEeecchhhhhhhc--------ccccceEEeeeecCCCceeeeceeeeeeeeeCChHHHH
Q psy6283         685 Y----------------KQLELDIDGVYKYMLLL--------KKKKYAALSISKLSNGKMICSQEIKGVDVVRRDWSQLA  740 (1030)
Q Consensus       685 ~----------------~~leLe~E~vf~~llll--------~KKrYa~l~~~~~~dG~~~~~~e~KGle~vRRD~~~l~  740 (1030)
                      |                .+|+||+||+|++|||+        .|||||++.    .||.+   .++||++++|||||+|+
T Consensus       378 y~~l~~p~~~~y~i~se~~IefEvDG~Yk~mllpask~~~~~~KKRYAv~~----~dG~i---~elKGfEikRRd~~~La  450 (621)
T cd05535         378 YQELVDPSTGTYETRSENSIFFEVDGPYKAMILPASKEEGKLLKKRYAVFN----EDGSL---AELKGFEVKRRGELQLI  450 (621)
T ss_pred             hhhccCcccccccccccceeEEEeccceeeeEcccccccccccccceEEEc----CCCCE---EEEeCceeeeCCHHHHH
Confidence            2                14999999999999995        699999873    46765   37999999999999999


Q ss_pred             HHHHHHHHHHHhccCCCCCCChhHHHHHHHHHHHHHHHHhhC--CCcC----hhhhHHhhcccCCCCC---CcchHHHHH
Q psy6283         741 SEAGKFVISQILDEQSYTDYSLDDRLQNIHEHMKKIRTDLDN--GFVP----LTLLEITKQLTKAPEG---GKVCITQIR  811 (1030)
Q Consensus       741 k~~~~~vL~~IL~~~~~~~~~~e~~v~~I~~~l~~~~~~l~~--g~vp----l~~lvItk~LsK~p~~---~~~pHV~vA  811 (1030)
                      |++|.+|++.||.|+     +.+++++.|++.+..+.+.|.+  +.++    ++.++++++|+|+|++   ...|||++|
T Consensus       451 K~fQ~eV~e~iL~g~-----~~Eea~~~V~~v~~~~ld~L~~~~~~~~d~eLi~li~~~k~LsK~l~eY~~~ks~~V~~A  525 (621)
T cd05535         451 KIFQSEVFDAFLKGS-----TLEECYAAVAAVANYWLDVLDSKGENLDDEELFELISENRSMSKKLEEYGNQKSTSITTA  525 (621)
T ss_pred             HHHHHHHHHHHHcCC-----CHHHHHHHHHHHHHHHHHHHHhccCCCChHHHHHHHHhhcccCCCHHHcCCCCCcHHHHH
Confidence            999999999999999     9999999999999998888888  5565    5557779999999998   368899999


Q ss_pred             HHHHHcCCcc
Q psy6283         812 LSRNRRGRRR  821 (1030)
Q Consensus       812 ~r~~~~g~~~  821 (1030)
                      +||++..|.-
T Consensus       526 kRl~e~lg~~  535 (621)
T cd05535         526 KRLAEFLGDQ  535 (621)
T ss_pred             HHHHHhhcCC
Confidence            9999865543

Three DNA-dependent DNA polymerases type B (alpha, delta, and epsilon) have been identified as essential for nuclear DNA replication in eukaryotes. DNA polymerase (Pol) epsilon has been proposed to play a role in elongation of the leading strand during DNA replication. Pol epsilon might also have a role in DNA repair. The structure of pol epsilon is characteristic of this family with the exception that it contains a large c-terminal domain with an unclear function. Phylogenetic analyses indicate that Pol epsilon is the ortholog to the archaeal Pol B3 rather than to Pol alpha, delta, or zeta. This might be because pol epsilon is ancestral to both archaea and eukaryotes DNA polymerases type B.

>smart00486 POLBc DNA polymerase type-B family

Probab=100.00  E-value=1e-45  Score=428.40  Aligned_cols=254  Identities=43%  Similarity=0.681  Sum_probs=217.4

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHhcchHHHHHHHHHhCCcchhhccCchhHHHHHHHHHHHhhcCeeccCCccccCcCCCcc
Q psy6283         402 IVEFIKFTMLHSSYIIKIMCELNVLPLAIQITNVCGNVLSRTLMGGRSERNEFLLLHAFHEKSYVLPDKQYGKNKKEGEE  481 (1030)
Q Consensus       402 l~~lv~Y~~~Da~l~~~L~~kl~vlpl~~~lt~iaG~~~srtl~~gr~~r~E~lLL~~~~~~~yivPdk~~~kk~~~~~d  481 (1030)
                      +..++.||++||.++++|+.+++++++..++++++|.++.+++.+|++.++++++++.++..|+++|++.......    
T Consensus       199 ~~~~~~Y~~~D~~l~~~l~~~l~~~~~~~~~s~~~~~~~~~~~~~g~~~~v~~~l~~~~~~~~~~~P~~~~~~~~~----  274 (471)
T smart00486      199 RDELLEYCIQDAVLTLKLFNKLNVIPLIIELARIAGIPQRRTLYYGSQIRVESLLLREAKKNNYILPSKSLIDFKG----  274 (471)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHCcCHHHHHhcCcHHHHHHHHHHHHhhCCEEeccchhccccc----
Confidence            6889999999999999999999999999999999999999999999999999999999999999999876421100    


Q ss_pred             ccccccCCCCCCccccCceeeccccccccceEEEeeccccChhHHHHhccccccccccCCCcccc----------ccccC
Q psy6283         482 TGEANKGKGRKKAAYSGGLVLEPKKGFYDKFIILMDFNSLYPSIIQEYNICFTTIPVRMLQDSDI----------TTLCE  551 (1030)
Q Consensus       482 ~~~~~~~~~~~~~~Y~GGlVleP~~GlY~~~V~vLDFnSLYPSII~~~NIc~tTv~~~~~d~~~i----------~~~~p  551 (1030)
                          .........+|.||+|++|.+|+|++||+++||+|||||||++|||||+|++.........          ....|
T Consensus       275 ----~~~~~~~~~~y~gg~v~~p~~g~~~~~v~~lDf~SlYPsii~~~nl~~~t~~~~~~~~~~~~~~~~~~~~~~~~~~  350 (471)
T smart00486      275 ----SEPELKKKAKYPGGKVLEPKKGFYDNPVLVLDFNSLYPSIIIAHNLCYSTLVGRGENSGELFLDVEDLLTIKYEKP  350 (471)
T ss_pred             ----ccccccccccccccEEecCCCCcccCceEEeehhhccHHHHHHhCCCCcccccccccccccCCChhhcceeeecCC
Confidence                0011234578999999999999999999999999999999999999999998755310000          00001


Q ss_pred             ---CCCCccccCCcchHHHHHHHHHHHHHHHHhcCCC-CChHHHHhhHHHHHHhccccccccccCCCCCCCCCCHHHHHH
Q psy6283         552 ---YLPEHQVDTGILPSEIKKLVESRRQVKALMKQPN-LSSDLLMQYDIRQKALKLTANSMYGCLGFPNSRFFAQPLAAL  627 (1030)
Q Consensus       552 ---~~p~~~~~~GIlP~iL~~Ll~~R~~vKk~mk~~~-~~~~~~~~~d~rQ~AlKl~aNS~YG~lG~~~srfy~~~lA~~  627 (1030)
                         .+.......||+|.+|..|+..|..+|+.|++.. .+..++..||.+|.|+|+++||+||++|+.+++||+.++|++
T Consensus       351 ~~~~~~~~~~~~gil~~~l~~l~~~R~~~K~~~~~~~~~~~~~~~~~d~~q~a~K~~~Ns~yG~~g~~~~~~~~~~~a~~  430 (471)
T smart00486      351 EGYHFVKKNIRKGILPKLLKKLLDKRKEIKKLMKKEKDESEELKKLLDSRQLALKLTANSVYGYLGFTNSRLYCKPLAAS  430 (471)
T ss_pred             CcceeecCCCCCeehHHHHHHHHHHHHHHHHHHhhCCCCcHHHHHHHHHHHHHHHhhhcccccccccccccCccHHHHHH
Confidence               1233344579999999999999999999998843 233489999999999999999999999999999999999999


Q ss_pred             HHHHhHHHHHHHHHHhhhcc----ceeEEecCcceeeecC
Q psy6283         628 VTAKGREILLNTKSLVENLN----YEVIYGDTDSLMISCN  663 (1030)
Q Consensus       628 IT~~GR~iL~~tkelve~~g----~~VIYGDTDSI~V~~~  663 (1030)
                      ||+.||.+|+.|+.++++.|    ++|||||||||||+++
T Consensus       431 iT~~gr~~l~~~~~~i~~~~~~~~~~viYgDTDSi~v~~~  470 (471)
T smart00486      431 VTALGREILEKTKELIEKNGYPPGFKVIYGDTDSIFVTKP  470 (471)
T ss_pred             HHHHHHHHHHHHHHHHHHhCCCCCeEEEEecCceEEEecC
Confidence            99999999999999999987    8999999999999875

DNA polymerase alpha, delta, epsilon and zeta chain (eukaryota), DNA polymerases in archaea, DNA polymerase II in e. coli, mitochondrial DNA polymerases and and virus DNA polymerases

>KOG1798|consensus

Probab=99.98  E-value=2.6e-32  Score=329.17  Aligned_cols=399  Identities=20%  Similarity=0.249  Sum_probs=304.7

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHhcchHHHHHHHHHhCCcchhhccCchhHHHHHHHHHHHhhcCeeccCCccccCcCCCcc
Q psy6283         402 IVEFIKFTMLHSSYIIKIMCELNVLPLAIQITNVCGNVLSRTLMGGRSERNEFLLLHAFHEKSYVLPDKQYGKNKKEGEE  481 (1030)
Q Consensus       402 l~~lv~Y~~~Da~l~~~L~~kl~vlpl~~~lt~iaG~~~srtl~~gr~~r~E~lLL~~~~~~~yivPdk~~~kk~~~~~d  481 (1030)
                      ++.|+.|+..||..|+-|.++- +.|+...|+.|.+.+.+.+|.-|++..+|+||+-++...|.|+|+|......+.   
T Consensus       429 PQ~lasYSVSDAVATYyLYMkY-VhPFIFsLctIIPl~PDevLRKGSGTLCE~LLmVeA~~~NIv~PNK~~e~~~~f---  504 (2173)
T KOG1798|consen  429 PQTLASYSVSDAVATYYLYMKY-VHPFIFSLCTIIPLNPDEVLRKGSGTLCEALLMVEAYHANIVFPNKHTEDPEKF---  504 (2173)
T ss_pred             chhhhhcchHHHHHHHHHHHHH-hhhHHhhhhhccccChHHHHhcCcchHHHHHHHHHHHhcCeecCCcCccchhhh---
Confidence            7899999999999999999884 899999999999999999999999999999999999999999999875211000   


Q ss_pred             ccccccCCCCCCccccCceeecccccccc---------------------------------------------------
Q psy6283         482 TGEANKGKGRKKAAYSGGLVLEPKKGFYD---------------------------------------------------  510 (1030)
Q Consensus       482 ~~~~~~~~~~~~~~Y~GGlVleP~~GlY~---------------------------------------------------  510 (1030)
                        +  .+.--....|-||.|=.-+.|++.                                                   
T Consensus       505 --~--dGhlleSETYVGGHVE~LesGVFRSDip~~F~~dp~a~~eLi~~l~~~L~~~l~vE~k~~vd~v~nfeEv~~~I~  580 (2173)
T KOG1798|consen  505 --Y--DGHLLESETYVGGHVECLESGVFRSDIPTEFRMDPSAYEELIDELGETLDFALTVENKVRVDEVTNFEEVKDEIL  580 (2173)
T ss_pred             --c--cCeeeeeeeeechhhhhHhcccccccCcccccCCHHHHHHHHHHHHHHHHHHHhhhcccchhhhcCHHHHHHHHH
Confidence              0  011123467899998878888764                                                   


Q ss_pred             --------------c-eEEEeeccccChhHHHHhccccccccccC----CCccc-----------------ccc------
Q psy6283         511 --------------K-FIILMDFNSLYPSIIQEYNICFTTIPVRM----LQDSD-----------------ITT------  548 (1030)
Q Consensus       511 --------------~-~V~vLDFnSLYPSII~~~NIc~tTv~~~~----~d~~~-----------------i~~------  548 (1030)
                                    + -|++||++||||+||....+.|.+|+...    ||.+.                 +++      
T Consensus       581 ~kL~~lrd~p~R~E~PlIYHLDVaaMYPNIilTNRLQP~siv~E~~C~~CDfN~P~ktC~Rkm~W~WRGe~~pa~r~EY~  660 (2173)
T KOG1798|consen  581 EKLEELRDVPIREEGPLIYHLDVAAMYPNIILTNRLQPDSIVDEEICAACDFNKPGKTCKRKMEWAWRGEYFPAKRSEYH  660 (2173)
T ss_pred             HHHHHhcCCCccccCCeEEEEehhhccCceeeecCCCCcccccHhhhccCCCCCCCcchhhhheeeeeeeEecCcchHHH
Confidence                          3 38999999999999999999999987542    22110                 000      


Q ss_pred             -------------ccCC--------CCC----------------------------------ccccCCcchHHHHHHHHH
Q psy6283         549 -------------LCEY--------LPE----------------------------------HQVDTGILPSEIKKLVES  573 (1030)
Q Consensus       549 -------------~~p~--------~p~----------------------------------~~~~~GIlP~iL~~Ll~~  573 (1030)
                                   ..|.        ++.                                  ...+..+.-..++.+.++
T Consensus       661 ~I~~qlesE~f~~~~~~~~~k~F~~L~~~eq~~~~kkRl~~Ysrk~Y~rv~~~~i~eRet~ICqRENpFYVdTVrsFRDR  740 (2173)
T KOG1798|consen  661 RIKKQLESESFPAGAPFSPSKSFHELSREEQAAKLKKRLKDYSRKVYHRVKDTEIEERETTICQRENPFYVDTVRSFRDR  740 (2173)
T ss_pred             HHHHHHHhccCCCCCCCCCCcccccCCHHHHHHHHHHHHHHHHHHHHhHhcccchhhhhcchhhccCchhhhhHHHhhhh
Confidence                         0000        000                                  024567888999999999


Q ss_pred             HHHHHHHhcCC---------CCChH-------HHHhhHHHHHHhccccccccccCCCCCCCCCCHHHHHHHHHHhHHHHH
Q psy6283         574 RRQVKALMKQP---------NLSSD-------LLMQYDIRQKALKLTANSMYGCLGFPNSRFFAQPLAALVTAKGREILL  637 (1030)
Q Consensus       574 R~~vKk~mk~~---------~~~~~-------~~~~~d~rQ~AlKl~aNS~YG~lG~~~srfy~~~lA~~IT~~GR~iL~  637 (1030)
                      |.++|.+.|..         ..+..       .-..||..|+|.|+++||+|||.-..+||||+.++|..||.+|..||+
T Consensus       741 RYeyK~L~K~wkg~ls~a~~sg~~a~i~eak~mvVlYdSLQLAHKcILNSFYGYVMRKGsRWYSMEMAGIvc~TGAnIIq  820 (2173)
T KOG1798|consen  741 RYEYKGLHKVWKGKLSAAKASGDLARIKEAKKMVVLYDSLQLAHKCILNSFYGYVMRKGSRWYSMEMAGIVCLTGANIIQ  820 (2173)
T ss_pred             hhHHHHHHHHHHHHHhhhhccCchhhHHhhhheEEehHhHHHHHHHHHhhhhhhhhccccchheeehhheeeccchHHHH
Confidence            99999987743         11111       124799999999999999999999999999999999999999999999


Q ss_pred             HHHHHhhhccceeEEecCcceeeecCCCCHHH-------HH--------H-HHHHHHH-HHhcc-----------c----
Q psy6283         638 NTKSLVENLNYEVIYGDTDSLMISCNVNDYDS-------VF--------K-IGNQIKS-ECNKL-----------Y----  685 (1030)
Q Consensus       638 ~tkelve~~g~~VIYGDTDSI~V~~~~~d~ee-------a~--------~-ig~~i~~-~Vn~~-----------~----  685 (1030)
                      .|++++|..|- ..--|||+||+-+|..-++.       ..        . +..-+.+ .-|.+           |    
T Consensus       821 ~AR~lVEriGr-PLELDTDGIWCilP~SFPEnf~Fk~~n~kkvtiSYPc~mLN~~V~e~fTN~QYq~L~dp~~~~Y~t~S  899 (2173)
T KOG1798|consen  821 MARELVERIGR-PLELDTDGIWCILPGSFPENFTFKLKNGKKVTISYPCVMLNHLVHEGFTNHQYQELVDPVRLTYVTRS  899 (2173)
T ss_pred             HHHHHHHHhCC-CeeccCCceEEeccCCCccceEEEecCCcEEEEechHHHHHHHHHhccchhhHHHhcCcccceeeecc
Confidence            99999999885 45689999999877542220       00        0 1111111 11222           2    


Q ss_pred             -ceeEEeecchhhhhhhcc--------cccceEEeeeecCCCceeeeceeeeeeeeeCChHHHHHHHHHHHHHHHhccCC
Q psy6283         686 -KQLELDIDGVYKYMLLLK--------KKKYAALSISKLSNGKMICSQEIKGVDVVRRDWSQLASEAGKFVISQILDEQS  756 (1030)
Q Consensus       686 -~~leLe~E~vf~~llll~--------KKrYa~l~~~~~~dG~~~~~~e~KGle~vRRD~~~l~k~~~~~vL~~IL~~~~  756 (1030)
                       ..|.+|+||.|+.|+|.+        |||||-+.    .||.+.   ++||+++.||.--+|+|.+|..+++.+|.|. 
T Consensus       900 EnSIfFEVDGPYkAMILPaSkEEGk~lKKRYAVFN----~DGsLA---ELKGFEiKRRGEL~lIK~FQs~lF~~FL~Gs-  971 (2173)
T KOG1798|consen  900 ENSIFFEVDGPYKAMILPASKEEGKLLKKRYAVFN----EDGSLA---ELKGFEIKRRGELKLIKVFQSELFKVFLKGS-  971 (2173)
T ss_pred             cceEEEEecCceeEEeeccchhhhhhhhheeEEec----CCCchh---hhcCceeeecchhhHHHHHHHHHHHHHhCCC-
Confidence             258899999999999974        89999883    588874   8999999999999999999999999999999 


Q ss_pred             CCCCChhHHHHHHHHHHHHHHHHhhCCC---cC----hhhhHHhhcccCCCCC---CcchHHHHHHHHHHcCCccc
Q psy6283         757 YTDYSLDDRLQNIHEHMKKIRTDLDNGF---VP----LTLLEITKQLTKAPEG---GKVCITQIRLSRNRRGRRRR  822 (1030)
Q Consensus       757 ~~~~~~e~~v~~I~~~l~~~~~~l~~g~---vp----l~~lvItk~LsK~p~~---~~~pHV~vA~r~~~~g~~~~  822 (1030)
                          +.|++.+.|..... .|-+|..+.   ++    ++.+.-+++++|...+   .....+..|+||...-|..+
T Consensus       972 ----tLEEcY~aVA~Vad-~WLDiL~s~G~~l~D~eL~elISEnrSMSk~L~dYg~QKStsitTAkRLaeFLGd~M 1042 (2173)
T KOG1798|consen  972 ----TLEECYSAVAAVAD-RWLDILDSHGADLTDSELLELISENRSMSKKLEDYGGQKSTSITTAKRLAEFLGDDM 1042 (2173)
T ss_pred             ----cHHHHHHHHHHHHH-HHHHHHHhccCCCCcHHHHHHHhhchhhhhhHHHhccccchHHHHHHHHHHHhchhh
Confidence                99999988876654 444454322   22    4455567888888877   44567889999988766544

>KOG3236|consensus

Probab=99.98  E-value=1.7e-33  Score=284.26  Aligned_cols=108  Identities=46%  Similarity=0.850  Sum_probs=100.7

Q ss_pred             CeEEeeeccCccCCCCccccHHHHHHHHHhHHHhhhhhhhhhcCCCCCceeeEEeecchhhHHHHHHhhhhHhhcCCCcc
Q psy6283           1 MLILATFVPTTDNFSGGVDVFGDLIKLSIDLIDYVGKYLVLSSIPGKGHAKILTAGVGWAGAEVILTRFLDLWVGARGAE   80 (1030)
Q Consensus         1 ml~latf~p~~~~~~~~~~~~~e~~k~~~~~~dl~g~y~~l~~~~~~~~~k~~~~glgW~~a~~~~~~~~~lw~garg~e   80 (1030)
                      ||+||||||+.+.  +.||+++|+|||++|++||+|++|+||+++|++|+|++++||||||||+|++|++||||||||+|
T Consensus        50 lL~lAtff~~~~s--~~f~~~~e~LK~s~di~dl~Gl~li~s~~~~~~~~k~~~~gLGWafA~sVlhRlipLWVGARG~e  127 (225)
T KOG3236|consen   50 MLILATFFPALES--GGFDFVPEFLKCSADIADLIGLHLIMSRFPGKGEVKFVVAGLGWAFAESVLHRLIPLWVGARGTE  127 (225)
T ss_pred             HHHHHHhhhcccc--cccchHHHHHHhhhhHHHHhhHHHHHhcCCCCCceeEEEeechHHHHHHHHHhhhHhhccccCce
Confidence            7899999999876  89999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             cchHHHHhhhccchhhhhhccHHHHHHHHHH
Q psy6283          81 FDWKYIQNSLDSNICLIDKTNKFAAFQKLKD  111 (1030)
Q Consensus        81 F~w~yi~~~~~sn~slv~~~~~~~al~~l~~  111 (1030)
                      |+|+|||+|||||++|+- .-+.+||--|-.
T Consensus       128 FtW~yVl~~LesN~~Lv~-~I~la~l~w~it  157 (225)
T KOG3236|consen  128 FTWDYVLQSLESNANLVQ-IISLAALGWMIT  157 (225)
T ss_pred             eEHHHHHHHhccCccHhh-hhHHHHHHHHhe
Confidence            999999999999999998 445666655533

>PF09767 DUF2053: Predicted membrane protein (DUF2053); InterPro: IPR019164 This family of proteins is conserved from plants to humans

Probab=99.97  E-value=2.3e-32  Score=275.58  Aligned_cols=96  Identities=61%  Similarity=1.068  Sum_probs=93.9

Q ss_pred             CeEEeeeccCccCCCCccccHHHHHHHHHhHHHhhhhhhhhhc--CCCCCceeeEEeecchhhHHHHHHhhhhHhhcCCC
Q psy6283           1 MLILATFVPTTDNFSGGVDVFGDLIKLSIDLIDYVGKYLVLSS--IPGKGHAKILTAGVGWAGAEVILTRFLDLWVGARG   78 (1030)
Q Consensus         1 ml~latf~p~~~~~~~~~~~~~e~~k~~~~~~dl~g~y~~l~~--~~~~~~~k~~~~glgW~~a~~~~~~~~~lw~garg   78 (1030)
                      ||+||||||+++.  ++||+++||+|+++|++||+||||+|++  .+|++|+||+++|||||+||+|+||++||||||||
T Consensus        49 ml~lATf~P~~~~--~~~~~~~eilk~~~d~~Dl~gi~~il~~~~~~~~~~~ril~~glGWa~ae~l~tr~~plwvgarg  126 (159)
T PF09767_consen   49 MLLLATFFPSSDS--STFDFIQEILKSSVDLIDLIGIYLILSSKANAGKGESRILAIGLGWAFAESLLTRFLPLWVGARG  126 (159)
T ss_pred             HHHHHHcCCcccc--ccchHHHHHHHHHHHHHHHHHHHHHHhCcccCCCcceeEEEEeeeeehHHHHHHHHHHHHhcccc
Confidence            7899999999887  6899999999999999999999999999  99999999999999999999999999999999999


Q ss_pred             cccchHHHHhhhccchhhhh
Q psy6283          79 AEFDWKYIQNSLDSNICLID   98 (1030)
Q Consensus        79 ~eF~w~yi~~~~~sn~slv~   98 (1030)
                      +||||+|||+|++||++++.
T Consensus       127 ~eF~wkyi~~sl~SNi~li~  146 (159)
T PF09767_consen  127 SEFDWKYIQMSLESNISLIQ  146 (159)
T ss_pred             ccccHHHHHHHHHHHHHHHH
Confidence            99999999999999999997

The function is unknown although some annotation suggests that it is a transmembrane protein.

>PHA02523 43B DNA polymerase subunit B; Provisional

Probab=99.97  E-value=2.5e-31  Score=292.42  Aligned_cols=217  Identities=19%  Similarity=0.238  Sum_probs=171.6

Q ss_pred             HhhHHHHHHhccccccccccCCCCCCCCCCHHHHHHHHHHhHHHHHHH--------HHHhhhccce-eEEecCcceeeec
Q psy6283         592 MQYDIRQKALKLTANSMYGCLGFPNSRFFAQPLAALVTAKGREILLNT--------KSLVENLNYE-VIYGDTDSLMISC  662 (1030)
Q Consensus       592 ~~~d~rQ~AlKl~aNS~YG~lG~~~srfy~~~lA~~IT~~GR~iL~~t--------kelve~~g~~-VIYGDTDSI~V~~  662 (1030)
                      +..+.+|.|+|+++||+|||||+.++|||++++|++||++||++|+.+        .++++..|+. |||||||||||++
T Consensus        37 a~~~~~q~AiKIlmNSfYGylG~~~~R~yd~e~A~aVT~~Gre~Ik~i~~~~ney~~~l~~t~G~~~VIYgDTDSifv~~  116 (391)
T PHA02523         37 QKRNTNQLNRKILINSLYGALGNNWFRYFDLRNAEAITTYGQLAIRWIERKLNEYINELVKTTGVDYVCYIDTDSVYLNM  116 (391)
T ss_pred             HHHhcchHHHHHHHHhhhhhhcCCCceecCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhcCcceEEEecCCeeEEEe
Confidence            456778999999999999999999999999999999999999999944        4466678996 9999999999998


Q ss_pred             CCCCHHHHH--------------H-HHHHHHHHHhccc-----------ceeEEeecchhhhh--------hhcccccce
Q psy6283         663 NVNDYDSVF--------------K-IGNQIKSECNKLY-----------KQLELDIDGVYKYM--------LLLKKKKYA  708 (1030)
Q Consensus       663 ~~~d~eea~--------------~-ig~~i~~~Vn~~~-----------~~leLe~E~vf~~l--------lll~KKrYa  708 (1030)
                      +...-....              + ...++...||..|           ..+.+++|++|.++        ++.+|||||
T Consensus       117 ~~~v~~~~~~~~~d~~~~vd~ldk~~~~~iE~~In~sY~el~eymna~~h~~~m~rE~ia~~f~~s~g~~gfw~~KKRYA  196 (391)
T PHA02523        117 EAVVNRVGIDKFRDTNHLIDFLDNLGSKKLEPFIDDSYKELEEYMNHDHHLLLMDREAIFGAPLGSDGIGGFWTGKKRYA  196 (391)
T ss_pred             cchHHHHhhhhhccchhhhHHHHHHHHHHhHHHHHHHHHHHHHHhcchhhhhhhhHHHhccccccccccchhhhhhhhhh
Confidence            642100000              0 1234445555443           36889999999996        778999999


Q ss_pred             EEeeeecCCCceeeeceeeeeeeeeCChHHHHHHHHHHHHHHHhccCCCCCCChhHHHHHHHHHHHHHHHHhhCCCcChh
Q psy6283         709 ALSISKLSNGKMICSQEIKGVDVVRRDWSQLASEAGKFVISQILDEQSYTDYSLDDRLQNIHEHMKKIRTDLDNGFVPLT  788 (1030)
Q Consensus       709 ~l~~~~~~dG~~~~~~e~KGle~vRRD~~~l~k~~~~~vL~~IL~~~~~~~~~~e~~v~~I~~~l~~~~~~l~~g~vpl~  788 (1030)
                      +.+|++++...-.+++++.|++.+|+|.|++++.++.++++.||.+.     .     +.|++|+.++....+  .+|++
T Consensus       197 ~~v~d~EG~r~~epklkI~G~E~qrSstp~~~~~~~ke~i~~Il~~~-----e-----e~iqeyi~~~~~ey~--~~~~~  264 (391)
T PHA02523        197 LNVYDMEGTRYAEPHLKIMGLETQRSSTPLACQKSLKESIRRLLQEG-----E-----SSLQDYFKEFKDEFK--NIPYQ  264 (391)
T ss_pred             heeeeccCccccCCccceeeeeecccCchHHHHHHHHHHHHHHHhCC-----h-----HHHHHHHHHHHHHHh--cCCHH
Confidence            99999764432236899999999999999999999999999999976     2     236777777777775  89999


Q ss_pred             hhHH---hhcccCCCCC------CcchHHHHHHHHHHcCCc
Q psy6283         789 LLEI---TKQLTKAPEG------GKVCITQIRLSRNRRGRR  820 (1030)
Q Consensus       789 ~lvI---tk~LsK~p~~------~~~pHV~vA~r~~~~g~~  820 (1030)
                      +..+   ...+.|..+.      ....||..|+-.|..-+.
T Consensus       265 ~Ia~~s~~~~I~K~~d~~~~~~kg~p~hvrGal~~N~~~~~  305 (391)
T PHA02523        265 DVAAVSSANNIGKNGDALGFPIKGTPYHVKGVLAYNRIAKT  305 (391)
T ss_pred             HhcccCCCCchhhcccccCCCCCCCchhhHHHHHHHHHhcc
Confidence            9998   4677777666      345799999877765444

>PHA02524 43A DNA polymerase subunit A; Provisional

Probab=99.95  E-value=2.2e-28  Score=284.19  Aligned_cols=220  Identities=19%  Similarity=0.281  Sum_probs=156.7

Q ss_pred             CceeeecccCchhhhhHHhhhhccCCeEEEecCccCC--CCcCccccceEeecchhhhcccCe----EEE---EccHHHH
Q psy6283         335 DTFSHVFGTKTSFLENLLLERKIKGPSWLEFPEAEKF--PSRISWCKYEVQCNQMEKIRSKQG----LIY---LIGIVEF  405 (1030)
Q Consensus       335 ~tfs~vfG~~~~~~E~f~l~~~i~Gp~wl~i~~~~~~--~~~~s~ck~e~~~~~~~~l~~~~~----viv---r~Gl~~l  405 (1030)
                      ...+..||.++        ...|.|..-|++-..-..  ..+++.++++-+..  ..++..+.    .|.   .-...+|
T Consensus       237 ~~s~~~~G~~~--------~~~I~GRv~iDl~~l~kk~s~~~l~sYsL~~Vs~--~~Lg~~K~d~~~~I~~l~~~d~~rl  306 (498)
T PHA02524        237 KTITNLYGEKI--------IYKIHGIALMDYMDVFKKFSFTPMPDYKLGNVGY--REVKADKLDYEGPINKFRKADHQRY  306 (498)
T ss_pred             ccceeecCcee--------EEEEeeEEEeEHHHHHHHhhhccCCCCCHHHHHH--HhcCCccccchhhHHHHhcCchHHH
Confidence            34456777643        137888887777433221  12444444433221  11211110    001   1126789


Q ss_pred             HHHHHHHHHHHHHHHHHhcchHHHHHHHHHhCCcchhhccCchhHHHHHHHHHHHhhcCeeccCCccccCcCCCcccccc
Q psy6283         406 IKFTMLHSSYIIKIMCELNVLPLAIQITNVCGNVLSRTLMGGRSERNEFLLLHAFHEKSYVLPDKQYGKNKKEGEETGEA  485 (1030)
Q Consensus       406 v~Y~~~Da~l~~~L~~kl~vlpl~~~lt~iaG~~~srtl~~gr~~r~E~lLL~~~~~~~yivPdk~~~kk~~~~~d~~~~  485 (1030)
                      +.||++||.|++.|+.++.+++++.++|+++|+++.+++  ++...++++|+++++++|+++|+....            
T Consensus       307 a~YclkDa~L~~~L~~~~~ll~~~~~larvtglpl~~v~--~qikv~~~lllr~~~~~g~viP~~~~~------------  372 (498)
T PHA02524        307 VDYCVRDTDIILLIDGRRCFIDLILSLSYYAKIRFDDVL--GTIKVWDSIIFNSLVESNVVIPAMKAS------------  372 (498)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCHHHhc--cHHHHHHHHHHHHHHHCCEecCCCCCC------------
Confidence            999999999999998889999999999999999999986  466678899999999999999975421            


Q ss_pred             ccCCCCCCccccCceeeccccccccceEEEeeccccChhHHHHhccccccccccCC--C-ccc---c---c----cccCC
Q psy6283         486 NKGKGRKKAAYSGGLVLEPKKGFYDKFIILMDFNSLYPSIIQEYNICFTTIPVRML--Q-DSD---I---T----TLCEY  552 (1030)
Q Consensus       486 ~~~~~~~~~~Y~GGlVleP~~GlY~~~V~vLDFnSLYPSII~~~NIc~tTv~~~~~--d-~~~---i---~----~~~p~  552 (1030)
                            ...+|+||+|++|.||+|++ |++|||+|||||||++|||||+|+++...  . ...   +   +    ...|.
T Consensus       373 ------~~~~Y~GA~V~eP~~GlY~~-VivLDFaSLYPSII~a~NIsPeTl~~~~~~~~~~~~~~~~~~~~~~~~~~~P~  445 (498)
T PHA02524        373 ------PKQSFPGAYVKEPVPGGYRY-GLSFDLTSLYPSILRLLNISPEMIAGMFSPARLEDYINKVAPKPSDQFSCAPN  445 (498)
T ss_pred             ------CCCccCCeEEecCCCccccC-eEEEEccccCHHHHHHhCCCHHHhhccccccchhhhccccCCCCCcceEECCC
Confidence                  13479999999999999998 57899999999999999999999975421  0 000   0   0    01121


Q ss_pred             -CCCccccCCcchHHHHHHHHHHHHHHHHhcCCC
Q psy6283         553 -LPEHQVDTGILPSEIKKLVESRRQVKALMKQPN  585 (1030)
Q Consensus       553 -~p~~~~~~GIlP~iL~~Ll~~R~~vKk~mk~~~  585 (1030)
                       .-..+..+||||.+|+.|++.|+++|+.|+++.
T Consensus       446 G~~F~K~~~GilP~iLe~Ll~~RK~~Kk~M~~a~  479 (498)
T PHA02524        446 GMMYKKGVVGVLPNETEKVFLQRKSEKKMMLAAI  479 (498)
T ss_pred             CCEEecCCCcccHHHHHHHHHHHHHHHHHHHHhH
Confidence             001236799999999999999999999999853

>PF12254 DNA_pol_alpha_N: DNA polymerase alpha subunit p180 N terminal; InterPro: IPR024647 This entry represents the N-terminal domain of DNA polymerase alpha catalytic subunit (the DNA polymerase alpha complex is composed of four subunits)

Probab=99.87  E-value=7.1e-23  Score=177.90  Aligned_cols=64  Identities=53%  Similarity=0.927  Sum_probs=60.0

Q ss_pred             HHHHHHHhhcCcce--eeeeccccccccccChHHHHHHHHhh-ccCCeEEeCCCCcccccccccccc
Q psy6283         106 FQKLKDLKGQGVKH--KYEFTADENVYEEVSEKEYTERVLKR-QEDDWIDDDGGDGYVEDGREIFDD  169 (1030)
Q Consensus       106 l~~l~~~~~~g~~~--~~~v~~~~~vy~~vde~~y~~~v~~r-~~dd~v~dd~g~gy~~~gre~~d~  169 (1030)
                      |++||+||++|.++  .|+|++.++|||+|||++|+++|++| |+|||||||||.||||||+|+|||
T Consensus         1 L~~Lk~~R~~g~~~~~~~ev~e~~~IYdeVdE~eY~~~v~~R~~~dDFIvDDdG~GYvD~G~e~wdd   67 (67)
T PF12254_consen    1 LEKLKAAREGGKKRTDEYEVEEEEDIYDEVDEEEYRKLVRKRLQEDDFIVDDDGEGYVDDGREEWDD   67 (67)
T ss_pred             CHHHHHHHhcCCccccchhhhcccccceeeCHHHHHHHHHHHHhcCCceEcCCCCcccccChhhccC
Confidence            68999999988776  68999999999999999999999999 589999999999999999999975

This domain is approximately 70 amino acids in length and it contains a specific labile site [].

>PHA02563 DNA polymerase; Provisional

Probab=99.76  E-value=2.1e-18  Score=206.22  Aligned_cols=206  Identities=23%  Similarity=0.305  Sum_probs=137.6

Q ss_pred             CccccCceee---ccccccccceEEEeeccccChhHHHHhccccccccccCCCcc----------cc-c------cccCC
Q psy6283         493 KAAYSGGLVL---EPKKGFYDKFIILMDFNSLYPSIIQEYNICFTTIPVRMLQDS----------DI-T------TLCEY  552 (1030)
Q Consensus       493 ~~~Y~GGlVl---eP~~GlY~~~V~vLDFnSLYPSII~~~NIc~tTv~~~~~d~~----------~i-~------~~~p~  552 (1030)
                      ..+|.||.|.   .+.+|++++ +.++|+||||||+|..+++|+.+-........          .+ .      ..+|.
T Consensus       235 r~sY~GGr~~~~~~~~~~~~~~-~~~yDvnSlYPsaM~~~~~P~g~p~~~~~k~~~~~~~~~~i~~~~~~f~~~ev~~p~  313 (630)
T PHA02563        235 RKFYRGGRTWYNPKYIGKLIEE-GYVYDVNSLYPYVMYNAKLPYGEPFYEKGKPAELKPDPLYIYNYGALFKLKKGYVPD  313 (630)
T ss_pred             HHheeCceeecccccccccccc-ccccccccccHHHHhhccCCCCCceeeccCcccccccccccccceEEEEEEEccCCC
Confidence            3689999998   888999987 67999999999999999998865211110000          00 0      00110


Q ss_pred             -----------------CCC-----------------------------------------ccccCCcchHHHHHHHHHH
Q psy6283         553 -----------------LPE-----------------------------------------HQVDTGILPSEIKKLVESR  574 (1030)
Q Consensus       553 -----------------~p~-----------------------------------------~~~~~GIlP~iL~~Ll~~R  574 (1030)
                                       +|.                                         -....+++.+.+..|.+.|
T Consensus       314 ~~~i~Ik~~~~~~~~~i~p~g~~~g~~~~~E~~~~~~~~i~le~~ik~y~~~~i~v~~Gy~fe~~~~~FkeyI~~lY~iK  393 (630)
T PHA02563        314 DMLIQIKSNLDFNGRLVLKVGIVKYVNSGNEYVDLNLNNLDLELEITHYDAFNEEVESGVVFECETGLFRDFIDHFYEIK  393 (630)
T ss_pred             ccccceeccccCCCceeeecccEeeEecCceEEEEEeceEEHHHhhhccceeEEEEEEEEEEcccCchHHHHHHHHHHHH
Confidence                             110                                         0012466777777777777


Q ss_pred             HHHHHHhcCCCCChHHHHhhHHHHHHhccccccccccCCCCCC---CC--------------------CC-HHHHHHHHH
Q psy6283         575 RQVKALMKQPNLSSDLLMQYDIRQKALKLTANSMYGCLGFPNS---RF--------------------FA-QPLAALVTA  630 (1030)
Q Consensus       575 ~~vKk~mk~~~~~~~~~~~~d~rQ~AlKl~aNS~YG~lG~~~s---rf--------------------y~-~~lA~~IT~  630 (1030)
                      .+.|+.-      +        .+...|+++||.||-+|..-.   .+                    +. +++|++||+
T Consensus       394 ~~~K~~~------~--------~~~i~KLlLNSLYGKfg~~p~~~~~~~~l~~~~~l~~~~~~~~~~~~~yv~iAa~ITa  459 (630)
T PHA02563        394 TNSKGAK------K--------QNMLAKLMLNSLYGKFALNPDNTGKVPYLDDNGRLDLISNGEENKEPNYIPIAAFITA  459 (630)
T ss_pred             hccccCc------c--------HHHHHHHHHhcccchhhcCccccCceeeecccceeeeecCCccccccccchHHHHHHH
Confidence            7755421      1        236899999999999986433   11                    11 679999999


Q ss_pred             HhHHHHHHHHHHhhhccceeEEecCcceeeecCCCCH-HHHHHHHHHHHHHHhcccceeEEeecchhhhhhhcccccceE
Q psy6283         631 KGREILLNTKSLVENLNYEVIYGDTDSLMISCNVNDY-DSVFKIGNQIKSECNKLYKQLELDIDGVYKYMLLLKKKKYAA  709 (1030)
Q Consensus       631 ~GR~iL~~tkelve~~g~~VIYGDTDSI~V~~~~~d~-eea~~ig~~i~~~Vn~~~~~leLe~E~vf~~llll~KKrYa~  709 (1030)
                      .||.+|..++..+++.   |+|||||||||....... .+-+-.+    .++.      .+++|.++...+++++|.|+.
T Consensus       460 ~aR~~m~~~~~~~~~~---v~Y~DTDSi~v~~~~~~~L~~~~i~~----~eLG------k~k~E~~~~~~~fl~~K~Y~l  526 (630)
T PHA02563        460 RARSNLLSALQYLYEK---FIYCDTDSIHLEGAETPKLPKDMIDP----KELG------KWDHEGEFIKAKYLRPKKYAL  526 (630)
T ss_pred             HHHHHHHHHHHHhhcc---EEEECCceEEEecCccccCchhhCCh----hHhc------ceeccceeeEEEEEeccEEEE
Confidence            9999999999988765   999999999998654321 1100001    1111      236788999999999999965


Q ss_pred             EeeeecCCCceeeeceeeeee
Q psy6283         710 LSISKLSNGKMICSQEIKGVD  730 (1030)
Q Consensus       710 l~~~~~~dG~~~~~~e~KGle  730 (1030)
                      +.  .+.+|.+  .+.+||+.
T Consensus       527 ~~--~d~~~~i--~ik~KGi~  543 (630)
T PHA02563        527 YA--EEVNGKL--KIKCAGMP  543 (630)
T ss_pred             Ee--cCCCceE--EEEeCCCC
Confidence            54  2345665  36789984

>PF03104 DNA_pol_B_exo1: DNA polymerase family B, exonuclease domain Several related DNA polymerases were too dissimilar to be included

Probab=99.36  E-value=8.5e-14  Score=155.26  Aligned_cols=136  Identities=27%  Similarity=0.516  Sum_probs=109.5

Q ss_pred             CceeEEEEEEcceeeeEEEecCCCCCCCCCcccHHHHHHHHHH-HHHhcCCcceEEeeeeeccccCCCCCCCCccEEEEE
Q psy6283         242 NSHSSCCVIVQNIDRKIYLLPRSEHLKTKEPVSIAQVYSEFDQ-IATQYKILDFKSRKIEKKYAFNLPGVPDLSEYLEVR  320 (1030)
Q Consensus       242 ~~~~Sccv~v~~~~R~~~~lpr~~~~~~~~~~~~~~v~~e~~~-~~~~~~i~~~~~k~v~~~yaf~~~~vp~~~~~lkv~  320 (1030)
                      ..+.||||+|.|+.+.+|++|++..       ...++.+.+.. +..+.++..+++++|+|+|+|+..+.|... ||+|.
T Consensus         3 ~~g~svcv~v~~f~pyfYv~~~~~~-------~~~~~~~~~~~~~~~~~~~~~~~~~~V~r~~~~~~y~~~~~~-~lkV~   74 (325)
T PF03104_consen    3 EDGKSVCVRVHGFRPYFYVLPPESD-------SPKDLEQFIEQLLRKKFKIDVFKIEKVKRKKSFYGYDGKEEP-FLKVY   74 (325)
T ss_dssp             CTSEEEEEEEST--EEEEEEESSGG-------GHHHHTTHEEHHEETTEEEEEEEEEEEEEEEESSEETTEEEE-EEEEE
T ss_pred             CCCCEEEEEEcCCCEEEEEECCCCc-------cHHHHHHHHHHHhhhccCCceEEEEEEEeeeeeccCCCCCce-EEEEE
Confidence            3579999999999999999999843       22233333222 566788999999999999999887777666 99999


Q ss_pred             eccCCC--CCCCCCcCCceeeecccCchhhhhHHhhhhccCCeEEEecCc-cCCCCcCccccceEeecc
Q psy6283         321 YSAKCP--ALPSDLSGDTFSHVFGTKTSFLENLLLERKIKGPSWLEFPEA-EKFPSRISWCKYEVQCNQ  386 (1030)
Q Consensus       321 y~~~~p--~~~~~~~g~tfs~vfG~~~~~~E~f~l~~~i~Gp~wl~i~~~-~~~~~~~s~ck~e~~~~~  386 (1030)
                      |+...+  .++..+.+ ++.++|+++.+.+++|+++++|+||||+.+.+. .......|||+.|+.+..
T Consensus        75 ~~~~~~~~~~~~~l~~-~~~~~~e~~i~~~~rfl~~~~i~~~~wi~i~~~~~~~~~~~s~~~~e~~~~~  142 (325)
T PF03104_consen   75 FSSPRDVRKLRDNLKK-TFFKVYEADIPPLERFLIDRNIRGPGWIKIKNPSKPVKDRVSWCDIEFSVDY  142 (325)
T ss_dssp             ESSTTHHHHHHHHHHH-TEEEEESTSS-HHHHHHHHTTHCTTEEEEEETTECHHHHHTCTCSCECECCH
T ss_pred             ECcHHHHHHHHHHHHh-ccchhhccCCCHHHheeeecCcccceeeeccccccccccccccccccccccc
Confidence            998877  66677777 999999999999999999999999999999998 344577899999998863

; InterPro: IPR006133 DNA is the biological information that instructs cells how to exist in an ordered fashion: accurate replication is thus one of the most important events in the life cycle of a cell. This function is performed by DNA- directed DNA-polymerases 2.7.7.7 from EC) by adding nucleotide triphosphate (dNTP) residues to the 5'-end of the growing chain of DNA, using a complementary DNA chain as a template. Small RNA molecules are generally used as primers for chain elongation, although terminal proteins may also be used for the de novo synthesis of a DNA chain. Even though there are 2 different methods of priming, these are mediated by 2 very similar polymerases classes, A and B, with similar methods of chain elongation. A number of DNA polymerases have been grouped under the designation of DNA polymerase family B. Six regions of similarity (numbered from I to VI) are found in all or a subset of the B family polymerases. The most conserved region (I) includes a conserved tetrapeptide with two aspartate residues. Its function is not yet known. However, it has been suggested that it may be involved in binding a magnesium ion. All sequences in the B family contain a characteristic DTDS motif, and possess many functional domains, including a 5'-3' elongation domain, a 3'-5' exonuclease domain [], a DNA binding domain, and binding domains for both dNTP's and pyrophosphate []. This domain has 3' to 5' exonuclease activity and adopts a ribonuclease H type fold [].; GO: 0003887 DNA-directed DNA polymerase activity, 0006260 DNA replication; PDB: 1QHT_A 4AHC_A 3A2F_A 2JGU_A 4AIL_C 1NOY_A 1NOZ_B 3IAY_A 1WNS_A 3K5O_A ....

>TIGR00592 pol2 DNA polymerase (pol2)

Probab=99.17  E-value=3.7e-13  Score=173.54  Aligned_cols=191  Identities=21%  Similarity=0.291  Sum_probs=144.2

Q ss_pred             HHHHHHHHHHHHHHHHHHHhcchHHHHHHHHHhCCcchhhccCchhHHHHHHHHHHHhhcCeeccCCccccCcCCCcccc
Q psy6283         404 EFIKFTMLHSSYIIKIMCELNVLPLAIQITNVCGNVLSRTLMGGRSERNEFLLLHAFHEKSYVLPDKQYGKNKKEGEETG  483 (1030)
Q Consensus       404 ~lv~Y~~~Da~l~~~L~~kl~vlpl~~~lt~iaG~~~srtl~~gr~~r~E~lLL~~~~~~~yivPdk~~~kk~~~~~d~~  483 (1030)
                      +++.||.+|+.+++.|+.++..++.  ..+.+.|.+++.+...+++..+.+++.+.+...+++.|..+....        
T Consensus       407 ~~v~y~~~~lkv~y~l~~~~~~l~~--l~~~~~g~~~~~vf~~n~g~~erfll~rki~gp~WL~i~~p~~~~--------  476 (1172)
T TIGR00592       407 IDAPYSSEYLEVTYELGKEFAPMEA--LPSDLKGQTFWHVFGSNTGNLERFLLLRKIKGPCWLAVKGPDELE--------  476 (1172)
T ss_pred             cCCcCCcceEEEEEccCccchhhhh--hhhhccCCcchheeccCHHHHHHHHhcCCCCCCceEEeCCCcccC--------
Confidence            4789999999999998877544443  345778999999888888888889998888888888876543210        


Q ss_pred             ccccCCCCCCccccCceeecc--ccccccc--eEEEeecc--ccChhHHHHhccccccccccCCC-----ccc-cc-ccc
Q psy6283         484 EANKGKGRKKAAYSGGLVLEP--KKGFYDK--FIILMDFN--SLYPSIIQEYNICFTTIPVRMLQ-----DSD-IT-TLC  550 (1030)
Q Consensus       484 ~~~~~~~~~~~~Y~GGlVleP--~~GlY~~--~V~vLDFn--SLYPSII~~~NIc~tTv~~~~~d-----~~~-i~-~~~  550 (1030)
                         . .......|+|+.|++|  .+|+|.+  ||++|||+  |||||||+++|||++|++.....     +.. .. ..|
T Consensus       477 ---~-~~~S~c~yEga~v~~p~v~~g~~~~~pPl~vLdFsi~SlyPsi~~~~nl~iS~~v~~~~~~d~~~~~~~~~~~~~  552 (1172)
T TIGR00592       477 ---Y-PRRSWCKYEGGYVKPPNVEKGLDKTPPPLVVLDFSMKSLNPSIIRNEIVSIPDTLHREFALDKPPPEPPYDVHPC  552 (1172)
T ss_pred             ---c-CCccccceEEEEecCccccccccCCCCCeEEEEeeeEEecCccccCceEEEEEEEeecccccCCCCCCccceEEE
Confidence               0 0122467999999999  9999998  89999999  99999999999997766543210     111 10 001


Q ss_pred             ----C---CCCC--ccccCCcchHHHHHHHHHHHHHHHHhcCC-CCChHHHHhhHHHHHHhccccccc
Q psy6283         551 ----E---YLPE--HQVDTGILPSEIKKLVESRRQVKALMKQP-NLSSDLLMQYDIRQKALKLTANSM  608 (1030)
Q Consensus       551 ----p---~~p~--~~~~~GIlP~iL~~Ll~~R~~vKk~mk~~-~~~~~~~~~~d~rQ~AlKl~aNS~  608 (1030)
                          |   .||.  .....|++|..|..+.+.|..+++.|+.. ..||+....||+.|.|||+++|=+
T Consensus       553 ~~~~~~~~~~p~~~~~~~~~~~~~~L~~~~sEr~lL~~fl~~~~~~DPDii~g~n~~qfdlkvl~nR~  620 (1172)
T TIGR00592       553 VGTRPKDCSFPLDLKGEFPGKKPSLVEDLATERALIKKFMAKVKKIDPDEIVGHDYQQRALKVLANRI  620 (1172)
T ss_pred             EEEccCCCCCCchhhhhhhccCCcEEEEecCHHHHHHHHHHHHHhcCCCEEEEEcccCccHHHHHHHH
Confidence                1   0121  12467999999999999999999999864 358999999999999999999933

This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).

>PF08490 DUF1744: Domain of unknown function (DUF1744); InterPro: IPR013697 This domain is found on the catalytic subunit of DNA polymerase epsilon

Probab=98.46  E-value=3.9e-06  Score=97.57  Aligned_cols=263  Identities=14%  Similarity=0.128  Sum_probs=170.5

Q ss_pred             hcchHHHHHHHHHhCCcchhhccCchhHHHHHHHHHHHhhcCeeccCCccccCcCC-CccccccccCCCCCCccccCcee
Q psy6283         423 LNVLPLAIQITNVCGNVLSRTLMGGRSERNEFLLLHAFHEKSYVLPDKQYGKNKKE-GEETGEANKGKGRKKAAYSGGLV  501 (1030)
Q Consensus       423 l~vlpl~~~lt~iaG~~~srtl~~gr~~r~E~lLL~~~~~~~yivPdk~~~kk~~~-~~d~~~~~~~~~~~~~~Y~GGlV  501 (1030)
                      ..+|...+++++.+++|+..+-......-..-+.-+.+++.|+|+=..+.. .|.. ..+.+  +.  ........-..+
T Consensus       119 ~~wl~~~i~laRY~~IPlgNl~~D~~~f~~Di~yAR~L~~~~~VLW~S~~~-~PDlGG~e~D--d~--~~~~~~~~~~~~  193 (396)
T PF08490_consen  119 GSWLSERIELARYAHIPLGNLPSDNPLFLIDIFYARRLRKNNHVLWWSPSP-RPDLGGKEED--DN--RLLWDMDELESP  193 (396)
T ss_pred             HHHHHHHHHHHHHcCCCcccCCcchHHHHHHHHHHHHHHHCCeEEeCCCCC-CCCCCcchhh--hh--cccccccccCce
Confidence            457778889999999998877555555567778888889999998443321 1110 00000  00  000011111223


Q ss_pred             eccccccccceEEEeecccc-ChhHHHHhccccccccccCC---Ccccc----cc---ccCCCCCccccCCcchHHHHHH
Q psy6283         502 LEPKKGFYDKFIILMDFNSL-YPSIIQEYNICFTTIPVRML---QDSDI----TT---LCEYLPEHQVDTGILPSEIKKL  570 (1030)
Q Consensus       502 leP~~GlY~~~V~vLDFnSL-YPSII~~~NIc~tTv~~~~~---d~~~i----~~---~~p~~p~~~~~~GIlP~iL~~L  570 (1030)
                      .--.||+|.+..+.||+..| .-+|.++.-|.=  +.+...   ..+..    .+   ....+    ....+-+..+.- 
T Consensus       194 ~in~pG~Y~~vcvEl~i~~LavnaiL~S~~i~e--~EG~~~~~~~~~~~~~~~~~~~~~~~~~----~e~~~~~~~f~i-  266 (396)
T PF08490_consen  194 EINNPGAYRSVCVELDISNLAVNAILQSSLINE--LEGSDSAGFNFDTASDASNGSANSSSSY----DESAFCSAAFRI-  266 (396)
T ss_pred             EEECCCccceEEEEEEecceeHHHHHHHhHHhh--hcCCcccccccccccccccccccccccc----ccccccHHHHHH-
Confidence            33578999998899999998 555555444321  000000   00000    00   00000    111222222222 


Q ss_pred             HHHHHHHHHHhcCCC-CChHHHHhhHHHHHHhccccccccccCCCCCCCCCCHHHHHHHHHHhHHHHHHHHHHhhhccce
Q psy6283         571 VESRRQVKALMKQPN-LSSDLLMQYDIRQKALKLTANSMYGCLGFPNSRFFAQPLAALVTAKGREILLNTKSLVENLNYE  649 (1030)
Q Consensus       571 l~~R~~vKk~mk~~~-~~~~~~~~~d~rQ~AlKl~aNS~YG~lG~~~srfy~~~lA~~IT~~GR~iL~~tkelve~~g~~  649 (1030)
                        .|..+|..+.... .++    ..|.       +++.+|-.+-.+.|.+|++.+...|-..=+..+.....-..++|.+
T Consensus       267 --Lr~mv~~w~~d~~~~n~----~AD~-------ll~~f~rWl~sp~S~LyDPaL~~~v~~LmkK~flqLl~Ef~rlG~~  333 (396)
T PF08490_consen  267 --LRSMVKSWLRDALKGNS----FADS-------LLQHFYRWLSSPSSLLYDPALHRMVHNLMKKVFLQLLAEFRRLGSK  333 (396)
T ss_pred             --HHHHHHHHHHHHhcCCc----cHHH-------HHHHHHHHHcCCcccccCHHHHHHHHHHHHHHHHHHHHHHHHcCCE
Confidence              2334444444310 111    1111       2577899999999999999999999999888888887777899999


Q ss_pred             eEEecCcceeeecCCCCHHHHHHHHHHHHHHHhc--ccceeEEeecchhhhhhhcccccceEE
Q psy6283         650 VIYGDTDSLMISCNVNDYDSVFKIGNQIKSECNK--LYKQLELDIDGVYKYMLLLKKKKYAAL  710 (1030)
Q Consensus       650 VIYGDTDSI~V~~~~~d~eea~~ig~~i~~~Vn~--~~~~leLe~E~vf~~llll~KKrYa~l  710 (1030)
                      |||+|-..|.|.++..+.++|..-++-|.+.|+.  +|..|.|++...|..++++.+-+|+|+
T Consensus       334 VVyA~~~riil~T~K~~~~~A~ay~~yi~~~i~~~~lF~~l~l~~~~~w~~LlwmD~~NygGi  396 (396)
T PF08490_consen  334 VVYADFNRIILCTGKTSLENAYAYVQYILKSIRSRELFSWLDLKPVRYWDSLLWMDPYNYGGI  396 (396)
T ss_pred             EEEEcCCEEEEECCCCCHHHHHHHHHHHHHHHhcccccccEEeEHHHHhhhheEecccccCCC
Confidence            9999999999999999999999999999998875  678899999999999999999999974

It is found C-terminal to IPR006133 from INTERPRO and IPR006134 from INTERPRO. ; GO: 0003887 DNA-directed DNA polymerase activity, 0008270 zinc ion binding, 0006260 DNA replication, 0005634 nucleus

>PF03175 DNA_pol_B_2: DNA polymerase type B, organellar and viral; InterPro: IPR004868 This entry is found in DNA polymerase type B proteins

Probab=98.31  E-value=6.8e-09  Score=122.67  Aligned_cols=34  Identities=38%  Similarity=0.564  Sum_probs=24.6

Q ss_pred             CccccCceeeccccccccceEEEeeccccChhHHH
Q psy6283         493 KAAYSGGLVLEPKKGFYDKFIILMDFNSLYPSIIQ  527 (1030)
Q Consensus       493 ~~~Y~GGlVleP~~GlY~~~V~vLDFnSLYPSII~  527 (1030)
                      ..+|-||.+-.-.+|.+. .|..+|++|||||+|.
T Consensus       203 r~s~~GGr~~~~~~~~~~-~i~~yDvnSLYP~~m~  236 (459)
T PF03175_consen  203 RKSYYGGRCEVFKPGIKN-KIYYYDVNSLYPSAMK  236 (459)
T ss_dssp             -EEE-GGGB-TEEEESE----EEEEETTHHHHHHH
T ss_pred             HhhcCCceeeeeeccccc-ceeeeeccCCcHHHHh
Confidence            468999998666667776 6999999999999998

Proteins in this entry are found in plant and fungal mitochondria, and in viruses.; GO: 0000166 nucleotide binding, 0003677 DNA binding, 0003887 DNA-directed DNA polymerase activity, 0008408 3'-5' exonuclease activity, 0006260 DNA replication; PDB: 1XI1_B 2EX3_G 1XHZ_D 1XHX_C 2PZS_B 2PY5_A 2PYL_A 2PYJ_A.

>PHA02735 putative DNA polymerase type B; Provisional

Probab=98.11  E-value=1.5e-05  Score=90.37  Aligned_cols=228  Identities=17%  Similarity=0.203  Sum_probs=111.4

Q ss_pred             cccHHHHHHHHHHHHHhcCCcceEEeeeeeccccCC----CCCCCCccEEEEEeccCCCCCCCCCcCCceeeecccCchh
Q psy6283         272 PVSIAQVYSEFDQIATQYKILDFKSRKIEKKYAFNL----PGVPDLSEYLEVRYSAKCPALPSDLSGDTFSHVFGTKTSF  347 (1030)
Q Consensus       272 ~~~~~~v~~e~~~~~~~~~i~~~~~k~v~~~yaf~~----~~vp~~~~~lkv~y~~~~p~~~~~~~g~tfs~vfG~~~~~  347 (1030)
                      +.+...|.+-+.+-....+|..|      -+.-|+.    .+|..+.+.-++..+++.-+ .   +..||...+.|.+.+
T Consensus        64 ~l~a~~i~~~ltd~k~rs~in~w------ynldfdan~il~~i~se~elaelvvs~ttla-n---sdrtyrqymdt~~~~  133 (716)
T PHA02735         64 ELDAEQIMDALTDHKARSNINIW------YNLDFDANAILNGICSEEELAELVVSGTTLA-N---SDRTYRQYMDTDKEL  133 (716)
T ss_pred             hhcHHHHHHHHhhhhhcccceee------EeccccHHHHHHhhcCHHHHhHHeecCcccc-c---cchhhhhhccccchh
Confidence            34445555544444445555554      2444543    35666666666666665443 2   336666666666655


Q ss_pred             hhhHHhhhhccCCeEEEecCccCCCCcCccccc-eEeecchh-----hhcccC---eEEE---------EccHHHHHHHH
Q psy6283         348 LENLLLERKIKGPSWLEFPEAEKFPSRISWCKY-EVQCNQME-----KIRSKQ---GLIY---------LIGIVEFIKFT  409 (1030)
Q Consensus       348 ~E~f~l~~~i~Gp~wl~i~~~~~~~~~~s~ck~-e~~~~~~~-----~l~~~~---~viv---------r~Gl~~lv~Y~  409 (1030)
                      ---=.+-.-|+| .+|.|.+-.-+-.  .++.. .+.+.+..     -|+..+   .|-.         .-....+++|+
T Consensus       134 ~~~ey~i~yik~-k~l~i~d~n~~i~--~hyd~aqffytsldna~~ewlge~ka~dgid~~~f~~k~yi~~n~~dilkya  210 (716)
T PHA02735        134 AGGEYEIFYIKG-KFLEIKDENGHIS--PHYDAAQFFYTSLDNAAEEWLGENKAKDGIDAGKFDAKEYIKDNFDDILKYA  210 (716)
T ss_pred             cCceEEEEEEec-eeEEEeccCCccc--ccccHHHHHHHHHHhHHHHHhccccccccccccccchHHHHhhhHHHHHHHH
Confidence            221112234566 5788864322110  11111 11111111     121111   0100         11277889999


Q ss_pred             HHHHHHHHHHHHHhcchHHHHHHHHHhCCcchhhccCchhHHHHHHHHHHHhhcCeeccCCccccCcCCCccccccccCC
Q psy6283         410 MLHSSYIIKIMCELNVLPLAIQITNVCGNVLSRTLMGGRSERNEFLLLHAFHEKSYVLPDKQYGKNKKEGEETGEANKGK  489 (1030)
Q Consensus       410 ~~Da~l~~~L~~kl~vlpl~~~lt~iaG~~~srtl~~gr~~r~E~lLL~~~~~~~yivPdk~~~kk~~~~~d~~~~~~~~  489 (1030)
                      -.||.|+..|...  ....+-+|    .+|+.|-.+.|-       |-.++...+  +-.++...     ....     +
T Consensus       211 k~da~l~~dl~~e--~~n~~e~l----dipmgrp~stgy-------la~~yl~~~--~~ekp~lg-----~~~m-----a  265 (716)
T PHA02735        211 KIDAELTQDLAIE--ATNEAEEL----DIPMGRPFSTGY-------LAAEYLDAN--LEEKPGLG-----NEAM-----A  265 (716)
T ss_pred             hhhHHHHHHHHHH--HhhhHhhc----CCccCCCcccch-------hhHHHHhcc--cccCCCCC-----hHHH-----H
Confidence            9999999987755  12222222    234433332221       111111111  11111100     0000     0


Q ss_pred             CCCCccccCceeeccccccccceEEEeeccccChhHHHHhcccccccccc
Q psy6283         490 GRKKAAYSGGLVLEPKKGFYDKFIILMDFNSLYPSIIQEYNICFTTIPVR  539 (1030)
Q Consensus       490 ~~~~~~Y~GGlVleP~~GlY~~~V~vLDFnSLYPSII~~~NIc~tTv~~~  539 (1030)
                      .---..|.||.+=--++|=+-. |+.-|.||+||+||+..- .|.|+...
T Consensus       266 ~~~wEsYyGGrfeV~KrgnvGE-v~~pDINSaYPaim~dlP-DpKTl~W~  313 (716)
T PHA02735        266 KLAWESYAGGRFEVFKRGNVGE-VAAPDINSAYPAILADLP-DPKTLNWK  313 (716)
T ss_pred             HHHHHhhcCCceEEeccCccce-eeeccccccchHHHHhCC-CCcccchh
Confidence            0113579999976667787765 999999999999999943 46776543

>PTZ00121 MAEBL; Provisional

Probab=97.21  E-value=0.0036  Score=79.96  Aligned_cols=8  Identities=38%  Similarity=0.580  Sum_probs=4.2

Q ss_pred             CCCCceee
Q psy6283          45 PGKGHAKI   52 (1030)
Q Consensus        45 ~~~~~~k~   52 (1030)
                      -|+|+.++
T Consensus        49 ~g~g~~ky   56 (2084)
T PTZ00121         49 HGEGDFKY   56 (2084)
T ss_pred             ccCCceee
Confidence            45555554

>PTZ00121 MAEBL; Provisional

Probab=96.97  E-value=0.014  Score=74.81  Aligned_cols=8  Identities=38%  Similarity=0.555  Sum_probs=4.9

Q ss_pred             cccceEEe
Q psy6283         704 KKKYAALS  711 (1030)
Q Consensus       704 KKrYa~l~  711 (1030)
                      +++|-|+.
T Consensus       966 r~k~WGvW  973 (2084)
T PTZ00121        966 RKKYWGIW  973 (2084)
T ss_pred             ccccceee
Confidence            56676663

>KOG1798|consensus

Probab=96.31  E-value=0.055  Score=70.00  Aligned_cols=267  Identities=12%  Similarity=0.157  Sum_probs=156.3

Q ss_pred             HHHHHHhcchHHHHHHHHHhCCcchhhccCchhHHHHHHHHHHHhhcCeeccCCccccCcC-C--CccccccccCCCCCC
Q psy6283         417 IKIMCELNVLPLAIQITNVCGNVLSRTLMGGRSERNEFLLLHAFHEKSYVLPDKQYGKNKK-E--GEETGEANKGKGRKK  493 (1030)
Q Consensus       417 ~~L~~kl~vlpl~~~lt~iaG~~~srtl~~gr~~r~E~lLL~~~~~~~yivPdk~~~kk~~-~--~~d~~~~~~~~~~~~  493 (1030)
                      ...+.-.++|....++++.+++|+...-..-...-+..++-+++.+.|.++=..... .+. +  +.|+....     ..
T Consensus      1583 ~h~~a~~~wl~~~i~~SRY~~VPigNl~~D~~~f~iD~~faR~Lrk~~~vLW~s~~~-~PDlGGie~d~~~~s-----~~ 1656 (2173)
T KOG1798|consen 1583 QHYLASGSWLSHRIKLSRYSHVPIGNLPEDWLTFIIDLFFARKLRKHNHVLWWSKNG-VPDLGGIENDEMLLS-----SE 1656 (2173)
T ss_pred             HHHHhHHHHHHHHHHHHHhcCCcccCCchHHHHHHHHHHHHHHHHhcCeeEEecCCC-CCCCCcccchhhhhh-----HH
Confidence            334444567888889999999988665433333457888889999988886221100 000 0  00000000     00


Q ss_pred             ccccCceeeccccccccceEEEeeccccChhHHHH-------hc-----cccccccccCCCccccccccCC-CCCccccC
Q psy6283         494 AAYSGGLVLEPKKGFYDKFIILMDFNSLYPSIIQE-------YN-----ICFTTIPVRMLQDSDITTLCEY-LPEHQVDT  560 (1030)
Q Consensus       494 ~~Y~GGlVleP~~GlY~~~V~vLDFnSLYPSII~~-------~N-----Ic~tTv~~~~~d~~~i~~~~p~-~p~~~~~~  560 (1030)
                      -.-....|.--.||+|++..+-|+..-|-=+-|..       -+     +.+....... ..+.+.+.|.. +.......
T Consensus      1657 ~~~~s~~~~ln~~G~Y~~v~vel~l~nlavntll~S~lvne~EG~d~~g~~~dv~~~~~-~~d~~~~~~~De~a~~~~~f 1735 (2173)
T KOG1798|consen 1657 LQTTSDTVELNRPGAYSTVCVELKLSNLAVNTLLQSALVNEMEGADFLGVTFDVNDRTA-AEDDLTGACYDETALCAQAF 1735 (2173)
T ss_pred             hcccccchhhccccccceeEEEEEehHHHHHHHHHHhhhhhhhccccccccccccccch-hhccccccccccccchHHHH
Confidence            00112455556789999977778764333222221       11     1110000000 01111111100 00000111


Q ss_pred             CcchHHHHHHHHHHHHHHHHhcCCCCChHHHHhhHHHHHHhccccccccccCCCCCCCCCCHHHHHHHHHHhHHHHHHHH
Q psy6283         561 GILPSEIKKLVESRRQVKALMKQPNLSSDLLMQYDIRQKALKLTANSMYGCLGFPNSRFFAQPLAALVTAKGREILLNTK  640 (1030)
Q Consensus       561 GIlP~iL~~Ll~~R~~vKk~mk~~~~~~~~~~~~d~rQ~AlKl~aNS~YG~lG~~~srfy~~~lA~~IT~~GR~iL~~tk  640 (1030)
                      -||-.+|..++..      ..+.    ...++         -++.++++-.+-...|.++++.+...+.-.=+.+++...
T Consensus      1736 ~VLk~llk~~~~d------~~~~----gN~~A---------D~iv~~l~~Wl~spss~L~dpaL~~~vh~lmkK~fl~L~ 1796 (2173)
T KOG1798|consen 1736 RVLKQLLKRWVLD------AAKS----GNIYA---------DLIVQHLSRWLRSPSSKLHDPALHRHVHVLMKKLFLQLL 1796 (2173)
T ss_pred             HHHHHHHHHHHHH------HHhh----cchhH---------HHHHHHHHHHHcCCcccccCHHHHHHHHHHHHHHHHHHH
Confidence            2333333333321      1111    01111         124456666677788999999999999988877777777


Q ss_pred             HHhhhccceeEEecCcceeeecCCCCHHHHHHHHHHHHHHHhc--ccceeEEeecchhhhhhhcccccceE
Q psy6283         641 SLVENLNYEVIYGDTDSLMISCNVNDYDSVFKIGNQIKSECNK--LYKQLELDIDGVYKYMLLLKKKKYAA  709 (1030)
Q Consensus       641 elve~~g~~VIYGDTDSI~V~~~~~d~eea~~ig~~i~~~Vn~--~~~~leLe~E~vf~~llll~KKrYa~  709 (1030)
                      .-+...|+.|||.|-+=|-|+++..+.+.|...++-+.+.|..  .|..|.|.+-..|..+++...-+|.|
T Consensus      1797 ~e~~rlGa~iIyA~~nkili~T~K~~~e~A~~y~e~l~ksi~t~~~f~~l~i~~~r~wd~llwmD~~n~~g 1867 (2173)
T KOG1798|consen 1797 AELRRLGAIIIYADFNKILINTGKFSVEAAKAYSEYLLKSISTLPVFHLLDINPVRYWDSLLWMDAHNYGG 1867 (2173)
T ss_pred             HHHHhcCCeEEEecCCEEEEecCCCCHHHHHHHHHHHHHhhhcccchhheeccHHHHHHHHhhhccccccc
Confidence            7778899999999999999999999999999999999888865  35678888888899999999888544

>PTZ00266 NIMA-related protein kinase; Provisional

Probab=95.39  E-value=0.059  Score=69.62  Aligned_cols=7  Identities=29%  Similarity=0.406  Sum_probs=4.1

Q ss_pred             EEEeecc
Q psy6283         513 IILMDFN  519 (1030)
Q Consensus       513 V~vLDFn  519 (1030)
                      |-+.||.
T Consensus       181 VKLsDFG  187 (1021)
T PTZ00266        181 AKIGDFG  187 (1021)
T ss_pred             eEEccCC
Confidence            4556664

>PTZ00266 NIMA-related protein kinase; Provisional

Probab=95.31  E-value=0.091  Score=67.98  Aligned_cols=6  Identities=33%  Similarity=0.296  Sum_probs=2.6

Q ss_pred             HHHHHH
Q psy6283         277 QVYSEF  282 (1030)
Q Consensus       277 ~v~~e~  282 (1030)
                      .+..|+
T Consensus        58 ~~~~EI   63 (1021)
T PTZ00266         58 QLVIEV   63 (1021)
T ss_pred             HHHHHH
Confidence            344444

>KOG4364|consensus

Probab=95.07  E-value=0.17  Score=61.35  Aligned_cols=11  Identities=18%  Similarity=0.280  Sum_probs=4.6

Q ss_pred             cchHHHHHHHH
Q psy6283         804 KVCITQIRLSR  814 (1030)
Q Consensus       804 ~~pHV~vA~r~  814 (1030)
                      +.+-|.++++.
T Consensus       162 ~s~~vVl~~~~  172 (811)
T KOG4364|consen  162 SSVRVVLKLRR  172 (811)
T ss_pred             CcchhHHhhhh
Confidence            34444444433

>KOG4676|consensus

Probab=93.83  E-value=0.017  Score=65.91  Aligned_cols=12  Identities=17%  Similarity=0.124  Sum_probs=6.9

Q ss_pred             cchHHHHHHHHH
Q psy6283         804 KVCITQIRLSRN  815 (1030)
Q Consensus       804 ~~pHV~vA~r~~  815 (1030)
                      .+..+.-|++|.
T Consensus       198 ~qts~~halr~~  209 (479)
T KOG4676|consen  198 KQTSSKHALRSH  209 (479)
T ss_pred             hhhhHHHHHHhc
Confidence            455556666663

>cd05776 DNA_polB_alpha_exo inactive DEDDy 3'-5' exonuclease domain of eukaryotic DNA polymerase alpha, a family-B DNA polymerase

Probab=92.11  E-value=0.075  Score=58.04  Aligned_cols=31  Identities=29%  Similarity=0.577  Sum_probs=28.8

Q ss_pred             cHHHHHHHHHHHHHHHHHHHHHhcchHHHHH
Q psy6283         401 GIVEFIKFTMLHSSYIIKIMCELNVLPLAIQ  431 (1030)
Q Consensus       401 Gl~~lv~Y~~~Da~l~~~L~~kl~vlpl~~~  431 (1030)
                      ++..++.||++||.++++|+.++++|||++|
T Consensus       204 ~l~~l~~y~~~Da~l~~~L~~kl~il~Ltkq  234 (234)
T cd05776         204 SLLKLLEHTEKDAYLILQLMFKLNILPLTKQ  234 (234)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHCCCcCCCC
Confidence            3889999999999999999999999999865

The 3'-5' exonuclease domain of eukaryotic DNA polymerase alpha. DNA polymerase alpha is a family-B DNA polymerase with a catalytic subunit that contains a DnaQ-like 3'-5' exonuclease domain. It is one of the three DNA-dependent type B DNA polymerases (delta and epsilon are the other two) that have been identified as essential for nuclear DNA replication in eukaryotes. DNA polymerase alpha is almost exclusively required for the initiation of DNA replication and the priming of Okazaki fragments during elongation. It associates with DNA primase and is the only enzyme able to start DNA synthesis de novo. The catalytic subunit contains both polymerase and 3'-5' exonuclease domains, but only exhibits polymerase activity. The 3'-5' exonuclease domain contains three sequence motifs termed ExoI, ExoII and ExoIII, without the four conserved acidic residues that are

>PHA03144 helicase-primase primase subunit; Provisional

Probab=89.06  E-value=11  Score=47.51  Aligned_cols=225  Identities=12%  Similarity=0.169  Sum_probs=139.3

Q ss_pred             eccccccccceEEEeeccccChhHHHHhccccccccccCCCccccccccCCCCCccccCCcchHHHHHHHHHHHHHHHHh
Q psy6283         502 LEPKKGFYDKFIILMDFNSLYPSIIQEYNICFTTIPVRMLQDSDITTLCEYLPEHQVDTGILPSEIKKLVESRRQVKALM  581 (1030)
Q Consensus       502 leP~~GlY~~~V~vLDFnSLYPSII~~~NIc~tTv~~~~~d~~~i~~~~p~~p~~~~~~GIlP~iL~~Ll~~R~~vKk~m  581 (1030)
                      ++|-.=+..-+++-|||+-++|++..+.  .|+     .                        .-|...+..|      +
T Consensus       402 l~~P~~i~~~wlAKFDFSaFfptLy~al--~p~-----h------------------------~RL~~~v~aR------~  444 (746)
T PHA03144        402 LDHPAVIGGVWLAKFDFSAFFPTLYLAL--FPG-----H------------------------ERLARAVRAR------A  444 (746)
T ss_pred             cCCCceecceeEEEeechhhHHHHHHHh--CCC-----c------------------------hhHHHHHHHH------h
Confidence            4443334444689999999999999887  232     0                        0133344444      2


Q ss_pred             cCCCCChHHHHhhHHHHHHhccccccccccCCCCCCCCCCHHHHHHHHHHhHHHHHHHHHHhhhccceeEEecCcceeee
Q psy6283         582 KQPNLSSDLLMQYDIRQKALKLTANSMYGCLGFPNSRFFAQPLAALVTAKGREILLNTKSLVENLNYEVIYGDTDSLMIS  661 (1030)
Q Consensus       582 k~~~~~~~~~~~~d~rQ~AlKl~aNS~YG~lG~~~srfy~~~lA~~IT~~GR~iL~~tkelve~~g~~VIYGDTDSI~V~  661 (1030)
                      +.  ..           -.||-.+-+++|-|-.     -++....+|-..+..|=......+...|+-|-=..-|+.|=-
T Consensus       445 r~--~~-----------pwlK~aLv~f~GgL~h-----~~p~~yr~ii~i~N~Is~~vE~~A~~~~FAiCtYvkDGfWG~  506 (746)
T PHA03144        445 RR--EK-----------PWLKAALVSFFGGLQH-----ICPAAYRALIALANAVSRALERAANAVGFAVCTYVKDGFWGV  506 (746)
T ss_pred             cc--cC-----------chHHHHHHHHhhhhhh-----cCHHHHHHHHHHHHHHHHHHHHHHhhcCeeEEeecCCceEEe
Confidence            22  11           1577788999997755     567888899998888877788888889998887888998755


Q ss_pred             cCCC-----C---HHHHHHHHHHHHHHHhc-------cc---ceeEEeecchhhhhhhcccccceEEeeeecCCCceeee
Q psy6283         662 CNVN-----D---YDSVFKIGNQIKSECNK-------LY---KQLELDIDGVYKYMLLLKKKKYAALSISKLSNGKMICS  723 (1030)
Q Consensus       662 ~~~~-----d---~eea~~ig~~i~~~Vn~-------~~---~~leLe~E~vf~~llll~KKrYa~l~~~~~~dG~~~~~  723 (1030)
                      ++..     .   ...+..+........++       .+   .++.|.+||||...++..-..|=..+-.   ++    .
T Consensus       507 f~~~~~~~~~~~a~~~ae~lR~ace~aA~~~L~~~GL~~~~~~~l~LRlEGvyThAvsW~~~~yWLwN~~---~~----~  579 (746)
T PHA03144        507 LGVDPQDAVSADALAAAERARAACQAAAEAVLADMGLLLPEGAPLHLRLEGLYTHAVSWSQHGYWLWNRR---TD----T  579 (746)
T ss_pred             ccCCcccccccchhhHHHHHHHHHHHHHHHHHHhcCCCCCCCCCceEEEeEEeeeeeeecCcceeeccCC---CC----c
Confidence            5432     1   12233332222222222       12   2578889999999999988888655421   21    1


Q ss_pred             ceeeeeeeeeCChHHHHHHHHHHHHHHHhccCCCCCCChhHHHHHHHHHHHHHHHHhhCCCcChhhhHHh
Q psy6283         724 QEIKGVDVVRRDWSQLASEAGKFVISQILDEQSYTDYSLDDRLQNIHEHMKKIRTDLDNGFVPLTLLEIT  793 (1030)
Q Consensus       724 ~e~KGle~vRRD~~~l~k~~~~~vL~~IL~~~~~~~~~~e~~v~~I~~~l~~~~~~l~~g~vpl~~lvIt  793 (1030)
                      -.+-|+-. |.-.+..+|+....+|.....+.    -+.+.+.+..++.+..+.........+.+-...+
T Consensus       580 ~~~vGFP~-Rs~~a~~ak~aL~~lL~~~~~~~----~~~~~~~~~a~~~cd~lv~~AF~~R~D~~fWs~~  644 (746)
T PHA03144        580 EDFVGFPL-RSAAARAAKAALRALLRAAVADS----ADAETLRQAAREACDRLVLEAFARRLDAEFWSVP  644 (746)
T ss_pred             cceeeccC-chHHHHHHHHHHHHHHHHhcCCh----hhHHHHHHHHHHHHHHHHHHHHhhcCCCCeeecC
Confidence            24579965 67777777777777775222221    1345566666666666666555555554443333

>KOG1029|consensus

Probab=88.14  E-value=4.7  Score=50.29  Aligned_cols=29  Identities=21%  Similarity=0.240  Sum_probs=16.0

Q ss_pred             hhccCchhHHHHHHHHHHH---hhcCeeccCC
Q psy6283         442 RTLMGGRSERNEFLLLHAF---HEKSYVLPDK  470 (1030)
Q Consensus       442 rtl~~gr~~r~E~lLL~~~---~~~~yivPdk  470 (1030)
                      ++-..|+...+||.+--.+   .-+|+-+|.-
T Consensus        59 DldkDGrmdi~EfSIAmkLi~lkLqG~~lP~~   90 (1118)
T KOG1029|consen   59 DLDKDGRMDIREFSIAMKLIKLKLQGIQLPPV   90 (1118)
T ss_pred             hcCccccchHHHHHHHHHHHHHHhcCCcCCCC
Confidence            3335566666776554332   3467766643

>KOG1029|consensus

Probab=87.48  E-value=2.7  Score=52.19  Aligned_cols=11  Identities=27%  Similarity=0.305  Sum_probs=5.0

Q ss_pred             HHhCCcchhhc
Q psy6283         434 NVCGNVLSRTL  444 (1030)
Q Consensus       434 ~iaG~~~srtl  444 (1030)
                      .+.|..+-.+|
T Consensus        81 kLqG~~lP~~L   91 (1118)
T KOG1029|consen   81 KLQGIQLPPVL   91 (1118)
T ss_pred             HhcCCcCCCCC
Confidence            34455544433

>KOG4676|consensus

Probab=86.21  E-value=0.041  Score=62.87  Aligned_cols=9  Identities=22%  Similarity=-0.016  Sum_probs=3.6

Q ss_pred             ccccccCCC
Q psy6283         606 NSMYGCLGF  614 (1030)
Q Consensus       606 NS~YG~lG~  614 (1030)
                      |+.-|.|.+
T Consensus       104 navprll~p  112 (479)
T KOG4676|consen  104 NAVPRLLPP  112 (479)
T ss_pred             cccccccCC
Confidence            344444433

>PHA03181 helicase-primase primase subunit; Provisional

Probab=85.88  E-value=18  Score=45.58  Aligned_cols=226  Identities=14%  Similarity=0.171  Sum_probs=143.5

Q ss_pred             eccccccccceEEEeeccccChhHHHHhccccccccccCCCccccccccCCCCCccccCCcchHHHHHHHHHHHHHHHHh
Q psy6283         502 LEPKKGFYDKFIILMDFNSLYPSIIQEYNICFTTIPVRMLQDSDITTLCEYLPEHQVDTGILPSEIKKLVESRRQVKALM  581 (1030)
Q Consensus       502 leP~~GlY~~~V~vLDFnSLYPSII~~~NIc~tTv~~~~~d~~~i~~~~p~~p~~~~~~GIlP~iL~~Ll~~R~~vKk~m  581 (1030)
                      ++|-.=+..-.++-|||+-++|+|..+.-  |+     .                        .-|...+..      .+
T Consensus       411 l~~P~~i~~~~~AkFDFSaFfptLylaLf--P~-----h------------------------~rL~~~v~a------R~  453 (764)
T PHA03181        411 FREPTLIENAAIAKFDFSAFFATLYLGLF--PC-----H------------------------SRLRDAVKA------RL  453 (764)
T ss_pred             cCCCceeccceEEEeechhhHHHHHHHHC--CC-----c------------------------HHHHHHHHH------Hh
Confidence            54444444456899999999999988743  32     0                        013333333      33


Q ss_pred             cCCCCChHHHHhhHHHHHHhccccccccccCCCCCCCCCCHHHHHHHHHHhHHHHHHHHHHhhhccceeEEecCcceeee
Q psy6283         582 KQPNLSSDLLMQYDIRQKALKLTANSMYGCLGFPNSRFFAQPLAALVTAKGREILLNTKSLVENLNYEVIYGDTDSLMIS  661 (1030)
Q Consensus       582 k~~~~~~~~~~~~d~rQ~AlKl~aNS~YG~lG~~~srfy~~~lA~~IT~~GR~iL~~tkelve~~g~~VIYGDTDSI~V~  661 (1030)
                      +..  .           --||..+-+++|-|-.     -++....+|-..+..|=...-..+...|+-|-=..-|+.|=-
T Consensus       454 rre--~-----------~wLK~aLv~f~G~Lkh-----~~p~~y~aii~i~N~Is~~vE~~A~~~~FAiCtYvkDGfWG~  515 (764)
T PHA03181        454 RRE--K-----------DWLKRPIVEFGGLLKH-----FREDVYKAIIGIGNHISLEVEATASTLMFAPCTYVKDGMWGT  515 (764)
T ss_pred             ccc--C-----------chHHHHHHHHhhhhhh-----cCHHHHHHHHHHHHHHHHHHHHHHhhcCeeEEeecCCceEEe
Confidence            321  1           1577788889987755     567888899999988888888888889998877888988755


Q ss_pred             cCCC-------C--HHHHH-HHHHHHHHHHhc-------ccc---eeEEeecchhhhhhhcccccceEEeeeecCCCcee
Q psy6283         662 CNVN-------D--YDSVF-KIGNQIKSECNK-------LYK---QLELDIDGVYKYMLLLKKKKYAALSISKLSNGKMI  721 (1030)
Q Consensus       662 ~~~~-------d--~eea~-~ig~~i~~~Vn~-------~~~---~leLe~E~vf~~llll~KKrYa~l~~~~~~dG~~~  721 (1030)
                      ++..       +  ...++ .+-.......++       .++   ++.|-+||||...++..-..|=..+.   .++.  
T Consensus       516 F~~~~~~~~~~~~~~~~a~~~lR~ac~~aA~~~l~~~GL~~p~~~~l~LRlEGvYThAvsW~~n~yWLwN~---~~~~--  590 (764)
T PHA03181        516 FIDKANNVIVSPEGNENIFETLRVACNESANRLATSIGLRFPDGINLQMRLEGVYTHAMSWNANCYWLWNR---NTRE--  590 (764)
T ss_pred             cccccccccccchhhHHHHHHHHHHHHHHHHHHHHhcCCCCCCCCCceEEEeEEeeeeeeecCcceeeccC---CCCC--
Confidence            4422       1  12232 222222222222       222   57788999999999988888765532   1211  


Q ss_pred             eeceeeeeeeeeCChHHHHHHHHHHHHHHHhccCCCCCCChhHHHHHHHHHHHHHHHHhhCCCcChhhhH
Q psy6283         722 CSQEIKGVDVVRRDWSQLASEAGKFVISQILDEQSYTDYSLDDRLQNIHEHMKKIRTDLDNGFVPLTLLE  791 (1030)
Q Consensus       722 ~~~e~KGle~vRRD~~~l~k~~~~~vL~~IL~~~~~~~~~~e~~v~~I~~~l~~~~~~l~~g~vpl~~lv  791 (1030)
                        -.+-|+- -|...+.-+|+....+|..|....+ +.-+.+.+++..++.+.++...-....-+.+-..
T Consensus       591 --~~~vGFP-~r~~~~~~ak~~Ls~lL~~i~~~~~-~~~~l~~~~~~a~~~cd~Lv~~AF~~R~D~~fWS  656 (764)
T PHA03181        591 --SDFVGFP-KQPEFATHAKEALSTLLEEICLCND-TDESLLTIQEKVQKVFEELLYMAFKKRGDASFWS  656 (764)
T ss_pred             --cceeecC-CCcHHHHHHHHHHHHHHHHHHhccC-CcccHHHHHHHHHHHHHHHHHHHHhhcCCCCeee
Confidence              1346884 5777888899999999988877652 1124555677777777766666655554444333

>KOG0163|consensus

Probab=85.85  E-value=3.3  Score=51.35  Aligned_cols=43  Identities=9%  Similarity=0.064  Sum_probs=24.0

Q ss_pred             HHHHHHHHHHHHHHHHHHHHhcchHHHHHHHHHhCCcchhhcc
Q psy6283         403 VEFIKFTMLHSSYIIKIMCELNVLPLAIQITNVCGNVLSRTLM  445 (1030)
Q Consensus       403 ~~lv~Y~~~Da~l~~~L~~kl~vlpl~~~lt~iaG~~~srtl~  445 (1030)
                      ..+-.+|+.=+.--++=|+.-.+|-.-.+|-.--|+....+-.
T Consensus       467 NSFEQFCINyCNEKLQ~FFNerILkeEQElYekEGLnv~ei~f  509 (1259)
T KOG0163|consen  467 NSFEQFCINYCNEKLQKFFNERILKEEQELYEKEGLNVPEIEF  509 (1259)
T ss_pred             ccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCCCceEe
Confidence            3444555555555555555555666666666666665554443

>KOG0334|consensus

Probab=85.76  E-value=0.88  Score=58.28  Aligned_cols=18  Identities=11%  Similarity=0.113  Sum_probs=10.8

Q ss_pred             HHHHHHHHHHHHHHHHHH
Q psy6283        1007 EEEKKEEEEKEEEEKKRR 1024 (1030)
Q Consensus      1007 ~ee~~~~eee~~~~re~~ 1024 (1030)
                      ...++.+.+++.+++++-
T Consensus       140 ~~~~~~l~e~l~~rr~~~  157 (997)
T KOG0334|consen  140 GSIQARLAEELRKRRERV  157 (997)
T ss_pred             chhhhhHHHHHHHHHHHH
Confidence            456666666666665544

>KOG0151|consensus

Probab=84.90  E-value=0.21  Score=60.94  Aligned_cols=11  Identities=36%  Similarity=0.232  Sum_probs=4.7

Q ss_pred             HHhCCcchhhc
Q psy6283         434 NVCGNVLSRTL  444 (1030)
Q Consensus       434 ~iaG~~~srtl  444 (1030)
                      .-.||++...|
T Consensus       345 re~~nplF~fl  355 (877)
T KOG0151|consen  345 RERGNPLFSFL  355 (877)
T ss_pred             hhccChhHHHH
Confidence            33445444433

>KOG1847|consensus

Probab=81.61  E-value=0.19  Score=60.55  Aligned_cols=23  Identities=13%  Similarity=0.088  Sum_probs=16.3

Q ss_pred             cceEEEeeccccChhHHHHhccc
Q psy6283         510 DKFIILMDFNSLYPSIIQEYNIC  532 (1030)
Q Consensus       510 ~~~V~vLDFnSLYPSII~~~NIc  532 (1030)
                      ++++.-+||.-+||..=+.-.|+
T Consensus       351 ~~~~p~~~~~~~~~tt~~~~~V~  373 (878)
T KOG1847|consen  351 DKSQPKLELQIVEPTTEMKRVVD  373 (878)
T ss_pred             CCCCccceeeeecccchhhhhhh
Confidence            34577788888888877665554

---

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

ID	Length	Definition	E-value
Query	1030
4fvm_A	910	Crystal Structure Of Yeast Dna Polymerase Alpha Len		3e-74
4fyd_A	910	Crystal Structure Of Yeast Dna Polymerase Alpha Bou		9e-74
4b08_A	910	Crystal Structure Of Yeast Dna Polymerase Alpha, Se		2e-70
4ahc_A	775	Crystal Structure Of An Evolved Replicating Dna Pol		3e-31
2jgu_A	775	Crystal Structure Of Dna-directed Dna Polymerase Le		3e-31
3a2f_A	775	Crystal Structure Of Pyrococcus Furiosus Dna Polyme		2e-30
1qht_A	775	Dna Polymerase From Thermococcus Sp. 9on-7 Archaeon		1e-29
2vwj_A	773	Uracil Recognition In Archaeal Dna Polymerases Capt		2e-28
2vwk_A	773	Uracil Recognition In Archaeal Dna Polymerases Capt		2e-28
2xhb_A	773	Crystal Structure Of Dna Polymerase From Thermococc		2e-28
1tgo_A	773	Thermostable B Type Dna Polymerase From Thermococcu		2e-28
1wn7_A	774	Crystal Structure Of Archaeal Family B Dna Polymera		3e-25
1wns_A	774	Crystal Structure Of Family B Dna Polymerase From H		4e-25
3iay_A	919	Ternary Complex Of Dna Polymerase Delta Length = 91		5e-23
4fm2_A	793	Pyrococcus Abyssi B Family Dna Polymerase (Triple M		4e-22
4flt_A	793	Pyrococcus Abyssi B Family Dna Polymerase Bound To		5e-22
1qqc_A	773	Crystal Structure Of An Archaebacterial Dna Polymer		2e-21
1d5a_A	733	Crystal Structure Of An Archaebacterial Dna Polymer		4e-21
2gv9_A	1193	Crystal Structure Of The Herpes Simplex Virus Type		2e-19
3k5l_A	786	Crystal Structure Of E.Coli Pol Ii-Abasic Dna-Datp		2e-18
1q8i_A	783	Crystal Structure Of Escherichia Coli Dna Polymeras		4e-18
1s5j_A	847	Insight In Dna Replication: The Crystal Structure O		1e-14
3kd1_E	913	Closed Binary Complex Of An Rb69 Gp43 Fingers Domai		4e-09
2dy4_A	903	Crystal Structure Of Rb69 Gp43 In Complex With Dna		2e-07
3l8b_A	906	Crystal Structure Of A Replicative Dna Polymerase B		5e-07
3lds_A	903	Crystal Structure Of Rb69 Gp43 With Dna And Datp Op		6e-07
3sq2_A	902	Rb69 Dna Polymerase Ternary Complex With Dttp Oppos		6e-07
3sq1_A	901	Rb69 Dna Polymerase Ternary Complex With Dupcpp Opp		6e-07
1waf_A	903	Dna Polymerase From Bacteriophage Rb69 Length = 903		6e-07
1ig9_A	903	Structure Of The Replicating Complex Of A Pol Alpha		6e-07
2dtu_A	896	Crystal Structure Of The Beta Hairpin Loop Deletion		6e-07
1q9y_A	906	Crystal Structure Of Enterobacteria Phage Rb69 Gp43		6e-07
3cq8_A	903	Ternary Complex Of The L415f Mutant Rb69 Exo(-)poly		2e-06
3suq_A	897	Rb69 Dna Polymerase (Y567a) Ternary Complex With Dc		6e-06
3lzi_A	903	Rb69 Dna Polymerase (Y567a) Ternary Complex With Da		6e-06
3rwu_A	901	Rb69 Dna Polymerase (Y567a) Ternary Complex With Da		6e-06
3suo_A	900	Rb69 Dna Polymerase (Y567a) Ternary Complex With Dt		6e-06
3sun_A	895	Rb69 Dna Polymerase (Y567a) Ternary Complex With Dt		6e-06
3qep_A	903	Rb69 Dna Polymerase (L561aS565GY567A) TERNARY COMPL		2e-05
4dtj_A	901	Rb69 Dna Polymerase Ternary Complex With Dttp Oppos		2e-05
3cfo_A	909	Triple Mutant Apo Structure Length = 909		2e-05
3ne6_A	903	Rb69 Dna Polymerase (S565gY567A) TERNARY COMPLEX WI		2e-05
3scx_A	903	Rb69 Dna Polymerase Triple Mutant(L561aS565GY567A)		2e-05
3spz_A	903	Dna Polymerase(L415aL561AS565GY567A) TERNARY COMPLE		6e-05
3spy_A	901	Rb69 Dna Polymerase(L415aL561AS565GY567A) TERNARY C		6e-05

>pdb|4FVM|A Chain A, Crystal Structure Of Yeast Dna Polymerase Alpha Length = 910

Iteration: 1
 Score =  277 bits (708), Expect = 3e-74,   Method: Compositional matrix adjust.
 Identities = 156/387 (40%), Positives = 226/387 (58%), Gaps = 15/387 (3%)
Query: 423 LNVLPLAIQITNVCGNVLSRTLMGGRSERNEFLLLHAFHEKSYVLPDKQ--YXXXXXXXX 480
           + +L L  Q+TN+ GN  ++TL G R+ RNE++LLH F    +++PDK+           
Sbjct: 420 IQLLTLTKQLTNLAGNAWAQTLGGTRAGRNEYILLHEFSRNGFIVPDKEGNRSRAQKQRQ 479
Query: 481 XXXXXXXXXXRKKAAYSGGLVLEPKKGFYDKFIILMDFNSLYPSIIQEYNICFTTIPVRM 540
                      KKA Y GGLV EP+KG +  ++++MDFNSLYPSIIQE+NICFTT+    
Sbjct: 480 NEENADAPVNSKKAKYQGGLVFEPEKGLHKNYVLVMDFNSLYPSIIQEFNICFTTVD--- 536
Query: 541 LQDSDITTLCEYLPEHQVDTGILPSEIKKLVESRRQVKALMKQPNLSSDLLMQYDIRQKA 600
               DI  L   +P  +VD G+LP  +  LV+ RR+VK +MK         +Q DIRQ+A
Sbjct: 537 RNKEDIDEL-PSVPPSEVDQGVLPRLLANLVDRRREVKKVMKT-ETDPHKRVQCDIRQQA 594
Query: 601 LKLTANSMYGCLGFPNSRFFAQPLAALVTAKGREILLNTKSLVENLNYEVIYGDTDSLMI 660
           LKLTANSMYGCLG+ NSRF+A+PLA LVT KGREIL+NT+ L E++N  V+YGDTDS+MI
Sbjct: 595 LKLTANSMYGCLGYVNSRFYAKPLAMLVTNKGREILMNTRQLAESMNLLVVYGDTDSVMI 654
Query: 661 SCNVNDYDSVFKIGNQIKSECNKLYKQLELDIDGVXXXXXXXXXXXXXXXXXXXXXNGKM 720
               ++Y    KIG   K   N+ Y+ LE+DID V                     NG  
Sbjct: 655 DTGCDNYADAIKIGLGFKRLVNERYRLLEIDIDNVFKKLLLHAKKKYAALTVNLDKNGNG 714
Query: 721 ICSQEIKGVDVVRRDWSQLASEAGKFVISQILDEQSYTDYSLDDRLQNIHEHMKKIRTDL 780
               E+KG+D+ RR++  L+ +    V++ IL     +D   ++ LQ ++++++ IR  +
Sbjct: 715 TTVLEVKGLDMKRREFCPLSRDVSIHVLNTIL-----SDKDPEEALQEVYDYLEDIRIKV 769
Query: 781 DNGFVPLTLLEITKQLTKAPE---GGK 804
           +   + +   +I  +L+K P+   GGK
Sbjct: 770 ETNNIRIDKYKINMKLSKDPKAYPGGK 796

>pdb|4FYD|A Chain A, Crystal Structure Of Yeast Dna Polymerase Alpha Bound To Dna/rna And Dgtp Length = 910

Iteration: 1
 Score =  275 bits (703), Expect = 9e-74,   Method: Compositional matrix adjust.
 Identities = 155/387 (40%), Positives = 226/387 (58%), Gaps = 15/387 (3%)
Query: 423 LNVLPLAIQITNVCGNVLSRTLMGGRSERNEFLLLHAFHEKSYVLPDKQ--YXXXXXXXX 480
           + +L L  Q+TN+ GN  ++TL G R+ RNE++LLH F    +++PDK+           
Sbjct: 420 IQLLTLTKQLTNLAGNAWAQTLGGTRAGRNEYILLHEFSRNGFIVPDKEGNRSRAQKQRQ 479
Query: 481 XXXXXXXXXXRKKAAYSGGLVLEPKKGFYDKFIILMDFNSLYPSIIQEYNICFTTIPVRM 540
                      KKA Y GGLV EP+KG +  ++++MDFNSLYPSIIQE+NICFTT+    
Sbjct: 480 NEENADAPVNSKKAKYQGGLVFEPEKGLHKNYVLVMDFNSLYPSIIQEFNICFTTVD--- 536
Query: 541 LQDSDITTLCEYLPEHQVDTGILPSEIKKLVESRRQVKALMKQPNLSSDLLMQYDIRQKA 600
               DI  L   +P  +VD G+LP  +  LV+ RR+VK +MK         +Q DIRQ+A
Sbjct: 537 RNKEDIDEL-PSVPPSEVDQGVLPRLLANLVDRRREVKKVMKT-ETDPHKRVQCDIRQQA 594
Query: 601 LKLTANSMYGCLGFPNSRFFAQPLAALVTAKGREILLNTKSLVENLNYEVIYGDTDSLMI 660
           LKLTANSMYGCLG+ NSRF+A+PLA LVT KGREIL+NT+ L E++N  V+YGDT+S+MI
Sbjct: 595 LKLTANSMYGCLGYVNSRFYAKPLAMLVTNKGREILMNTRQLAESMNLLVVYGDTNSVMI 654
Query: 661 SCNVNDYDSVFKIGNQIKSECNKLYKQLELDIDGVXXXXXXXXXXXXXXXXXXXXXNGKM 720
               ++Y    KIG   K   N+ Y+ LE+DID V                     NG  
Sbjct: 655 DTGCDNYADAIKIGLGFKRLVNERYRLLEIDIDNVFKKLLLHAKKKYAALTVNLDKNGNG 714
Query: 721 ICSQEIKGVDVVRRDWSQLASEAGKFVISQILDEQSYTDYSLDDRLQNIHEHMKKIRTDL 780
               E+KG+D+ RR++  L+ +    V++ IL     +D   ++ LQ ++++++ IR  +
Sbjct: 715 TTVLEVKGLDMKRREFCPLSRDVSIHVLNTIL-----SDKDPEEALQEVYDYLEDIRIKV 769
Query: 781 DNGFVPLTLLEITKQLTKAPE---GGK 804
           +   + +   +I  +L+K P+   GGK
Sbjct: 770 ETNNIRIDKYKINMKLSKDPKAYPGGK 796

>pdb|4B08|A Chain A, Crystal Structure Of Yeast Dna Polymerase Alpha, Selenomethionine Protein Length = 910

Iteration: 1
 Score =  264 bits (674), Expect = 2e-70,   Method: Compositional matrix adjust.
 Identities = 152/387 (39%), Positives = 219/387 (56%), Gaps = 15/387 (3%)
Query: 423 LNVLPLAIQITNVCGNVLSRTLMGGRSERNEFLLLHAFHEKSYVLPDKQ--YXXXXXXXX 480
           + +L L  Q+TN+ GN  ++TL G R+ RNE++LLH F    +++PDK+           
Sbjct: 420 IQLLTLTKQLTNLAGNAWAQTLGGTRAGRNEYILLHEFSRNGFIVPDKEGNRSRAQKQRQ 479
Query: 481 XXXXXXXXXXRKKAAYSGGLVLEPKKGFYDKFIILMDFNSLYPSIIQEYNICFTTIPVRM 540
                      KKA Y GGLV EP+KG +  ++++ DFNSLYPSIIQE+NICFTT+    
Sbjct: 480 NEENADAPVNSKKAKYQGGLVFEPEKGLHKNYVLVXDFNSLYPSIIQEFNICFTTVD--- 536
Query: 541 LQDSDITTLCEYLPEHQVDTGILPSEIKKLVESRRQVKALMKQPNLSSDLLMQYDIRQKA 600
               DI  L   +P  +VD G+LP  +  LV+ RR+VK + K         +Q DIRQ+A
Sbjct: 537 RNKEDIDEL-PSVPPSEVDQGVLPRLLANLVDRRREVKKVXKT-ETDPHKRVQCDIRQQA 594
Query: 601 LKLTANSMYGCLGFPNSRFFAQPLAALVTAKGREILLNTKSLVENLNYEVIYGDTDSLMI 660
           LKLTANS YGCLG+ NSRF+A+PLA LVT KGREIL NT+ L E+ N  V+YGDTDS+ I
Sbjct: 595 LKLTANSXYGCLGYVNSRFYAKPLAXLVTNKGREILXNTRQLAESXNLLVVYGDTDSVXI 654
Query: 661 SCNVNDYDSVFKIGNQIKSECNKLYKQLELDIDGVXXXXXXXXXXXXXXXXXXXXXNGKM 720
               ++Y    KIG   K   N+ Y+ LE+DID V                     NG  
Sbjct: 655 DTGCDNYADAIKIGLGFKRLVNERYRLLEIDIDNVFKKLLLHAKKKYAALTVNLDKNGNG 714
Query: 721 ICSQEIKGVDVVRRDWSQLASEAGKFVISQILDEQSYTDYSLDDRLQNIHEHMKKIRTDL 780
               E+KG+D  RR++  L+ +    V++ IL     +D   ++ LQ ++++++ IR  +
Sbjct: 715 TTVLEVKGLDXKRREFCPLSRDVSIHVLNTIL-----SDKDPEEALQEVYDYLEDIRIKV 769
Query: 781 DNGFVPLTLLEITKQLTKAPE---GGK 804
           +   + +   +I  +L+K P+   GGK
Sbjct: 770 ETNNIRIDKYKINXKLSKDPKAYPGGK 796

>pdb|4AHC|A Chain A, Crystal Structure Of An Evolved Replicating Dna Polymerase Length = 775

Iteration: 1
 Score =  134 bits (337), Expect = 3e-31,   Method: Compositional matrix adjust.
 Identities = 110/380 (28%), Positives = 184/380 (48%), Gaps = 44/380 (11%)
Query: 426 LPLAIQITNVCGNVLSRTLMGGRSERNEFLLLHAFHEKSYVLPDKQYXXXXXXXXXXXXX 485
           LP+ IQ++ + G  L            E+ LL   +E++ V P+K               
Sbjct: 327 LPMEIQLSRLIGQPLWDVSRSSTGNLVEWFLLRKAYERNEVAPNKP------------SE 374
Query: 486 XXXXXRKKAAYSGGLVLEPKKGFYDKFIILMDFNSLYPSIIQEYNICFTTIPVRMLQDSD 545
                R + +Y+GG V EP+KG +D  I+ +DF +LYPSII  +N+   T+ +   ++ D
Sbjct: 375 EEYQRRLRESYTGGFVKEPEKGLWDD-IVYLDFIALYPSIIITHNVSPDTLNLEGCKNYD 433
Query: 546 ITT-----LCEYLPEHQVDTGILPSEIKKLVESRRQVKALMKQPNLSSDLLMQYDIRQKA 600
           I        C+ +P      G +PS +  L+E R+++K  MK+     + ++  D RQKA
Sbjct: 434 IAPQVGHKFCKDIP------GFIPSLLGHLLEERQKIKTKMKETQDPIEKIL-LDYRQKA 486
Query: 601 LKLTANSMYGCLGFPNSRFFAQPLAALVTAKGRE-ILLNTKSLVENLNYEVIYGDTDSLM 659
           +KL ANS YG  G+  +R++ +  A  VTA GR+ I L  K L E   ++V+Y DTD L 
Sbjct: 487 IKLLANSFYGYYGYAKARWYCKECAESVTAWGRKYIELVWKELEEKFGFKVLYIDTDGLH 546
Query: 660 ISCNVNDYDSVFKIGNQ-IKSECNKLYKQLELDIDGVXXXXXXXXXXXXXXXXXXXXXNG 718
            +    + + + K   + +K   +KL   LEL+ +G                       G
Sbjct: 547 ATIPGGESEEIKKKALEFVKYINSKLPGLLELEYEGF----YKRGFFVTKKRYAVIDEEG 602
Query: 719 KMICSQEIKGVDVVRRDWSQLASEAGKFVISQILDEQSYTDYSLDDRLQNIHEHMKKIRT 778
           K+I     +G+++VRRDWS++A E    V+  IL         +++ ++ + E ++K   
Sbjct: 603 KVIT----RGLEIVRRDWSEIAKETQARVLETILKHG-----DVEEAVRIVKEVIQK--- 650
Query: 779 DLDNGFVPLTLLEITKQLTK 798
            L N  +P   L I +Q+T+
Sbjct: 651 -LANYEIPPEKLAIYEQITR 669

>pdb|2JGU|A Chain A, Crystal Structure Of Dna-directed Dna Polymerase Length = 775

Iteration: 1
 Score =  134 bits (337), Expect = 3e-31,   Method: Compositional matrix adjust.
 Identities = 109/380 (28%), Positives = 184/380 (48%), Gaps = 44/380 (11%)
Query: 426 LPLAIQITNVCGNVLSRTLMGGRSERNEFLLLHAFHEKSYVLPDKQYXXXXXXXXXXXXX 485
           LP+ IQ++ + G  L            E+ LL   +E++ V P+K               
Sbjct: 327 LPMEIQLSRLVGQPLWDVSRSSTGNLVEWFLLRKAYERNEVAPNKP------------SE 374
Query: 486 XXXXXRKKAAYSGGLVLEPKKGFYDKFIILMDFNSLYPSIIQEYNICFTTIPVRMLQDSD 545
                R + +Y+GG V EP+KG ++  I+ +D+ SLYPSII  +N+   T+ +   ++ D
Sbjct: 375 EEYQRRLRESYTGGFVKEPEKGLWEN-IVYLDYKSLYPSIIITHNVSPDTLNLEGCKNYD 433
Query: 546 IT-----TLCEYLPEHQVDTGILPSEIKKLVESRRQVKALMKQPNLSSDLLMQYDIRQKA 600
           I        C+ +P      G +PS +  L+E R+++K  MK+     + ++  D RQKA
Sbjct: 434 IAPQVGHKFCKDIP------GFIPSLLGHLLEERQKIKTKMKETQDPIEKIL-LDYRQKA 486
Query: 601 LKLTANSMYGCLGFPNSRFFAQPLAALVTAKGRE-ILLNTKSLVENLNYEVIYGDTDSLM 659
           +KL ANS YG  G+  +R++ +  A  VTA GR+ I L  K L E   ++V+Y DTD L 
Sbjct: 487 IKLLANSFYGYYGYAKARWYCKECAESVTAWGRKYIELVWKELEEKFGFKVLYIDTDGLY 546
Query: 660 ISCNVNDYDSVFKIGNQ-IKSECNKLYKQLELDIDGVXXXXXXXXXXXXXXXXXXXXXNG 718
            +    + + + K   + +K   +KL   LEL+ +G                       G
Sbjct: 547 ATIPGGESEEIKKKALEFVKYINSKLPGLLELEYEGF----YKRGFFVTKKRYAVIDEEG 602
Query: 719 KMICSQEIKGVDVVRRDWSQLASEAGKFVISQILDEQSYTDYSLDDRLQNIHEHMKKIRT 778
           K+I     +G+++VRRDWS++A E    V+  IL         +++ ++ + E ++K   
Sbjct: 603 KVIT----RGLEIVRRDWSEIAKETQARVLETILKHG-----DVEEAVRIVKEVIQK--- 650
Query: 779 DLDNGFVPLTLLEITKQLTK 798
            L N  +P   L I +Q+T+
Sbjct: 651 -LANYEIPPEKLAIYEQITR 669

>pdb|3A2F|A Chain A, Crystal Structure Of Pyrococcus Furiosus Dna PolymerasePCNA Monomer Mutant Complex Length = 775

Iteration: 1
 Score =  131 bits (329), Expect = 2e-30,   Method: Compositional matrix adjust.
 Identities = 108/380 (28%), Positives = 182/380 (47%), Gaps = 44/380 (11%)
Query: 426 LPLAIQITNVCGNVLSRTLMGGRSERNEFLLLHAFHEKSYVLPDKQYXXXXXXXXXXXXX 485
           LP  IQ++ + G  L            E+ LL   +E++ V P+K               
Sbjct: 327 LPXEIQLSRLVGQPLWDVSRSSTGNLVEWFLLRKAYERNEVAPNKP------------SE 374
Query: 486 XXXXXRKKAAYSGGLVLEPKKGFYDKFIILMDFNSLYPSIIQEYNICFTTIPVRMLQDSD 545
                R + +Y+GG V EP+KG ++  I+ +DF +LYPSII  +N+   T+ +   ++ D
Sbjct: 375 EEYQRRLRESYTGGFVKEPEKGLWEN-IVYLDFRALYPSIIITHNVSPDTLNLEGCKNYD 433
Query: 546 ITT-----LCEYLPEHQVDTGILPSEIKKLVESRRQVKALMKQPNLSSDLLMQYDIRQKA 600
           I        C+ +P      G +PS +  L+E R+++K   K+     + ++  D RQKA
Sbjct: 434 IAPQVGHKFCKDIP------GFIPSLLGHLLEERQKIKTKXKETQDPIEKIL-LDYRQKA 486
Query: 601 LKLTANSMYGCLGFPNSRFFAQPLAALVTAKGRE-ILLNTKSLVENLNYEVIYGDTDSLM 659
           +KL ANS YG  G+  +R++ +  A  VTA GR+ I L  K L E   ++V+Y DTD L 
Sbjct: 487 IKLLANSFYGYYGYAKARWYCKECAESVTAWGRKYIELVWKELEEKFGFKVLYIDTDGLY 546
Query: 660 ISCNVNDYDSVFKIGNQ-IKSECNKLYKQLELDIDGVXXXXXXXXXXXXXXXXXXXXXNG 718
            +    + + + K   + +K   +KL   LEL+ +G                       G
Sbjct: 547 ATIPGGESEEIKKKALEFVKYINSKLPGLLELEYEGF----YKRGFFVTKKRYAVIDEEG 602
Query: 719 KMICSQEIKGVDVVRRDWSQLASEAGKFVISQILDEQSYTDYSLDDRLQNIHEHMKKIRT 778
           K+I     +G+++VRRDWS++A E    V+  IL         +++ ++ + E ++K   
Sbjct: 603 KVIT----RGLEIVRRDWSEIAKETQARVLETILKHG-----DVEEAVRIVKEVIQK--- 650
Query: 779 DLDNGFVPLTLLEITKQLTK 798
            L N  +P   L I +Q+T+
Sbjct: 651 -LANYEIPPEKLAIYEQITR 669

>pdb|1QHT|A Chain A, Dna Polymerase From Thermococcus Sp. 9on-7 Archaeon Length = 775

Iteration: 1
 Score =  129 bits (323), Expect = 1e-29,   Method: Compositional matrix adjust.
 Identities = 100/346 (28%), Positives = 160/346 (46%), Gaps = 42/346 (12%)
Query: 418 KIMCELN--VLPLAIQITNVCGNVLSRTLMGGRSERNEFLLLHAFHEKSYVLPDKQYXXX 475
           K+  EL     P+  Q++ + G  L            E+ LL   ++++ + P+K     
Sbjct: 317 KVTYELGREFFPMEAQLSRLIGQSLWDVSRSSTGNLVEWFLLRKAYKRNELAPNKP---- 372
Query: 476 XXXXXXXXXXXXXXXRKKAAYSGGLVLEPKKGFYDKFIILMDFNSLYPSIIQEYNICFTT 535
                          R++  Y+GG V EP++G +D  I+ +DF SLYPSII  +N+   T
Sbjct: 373 ---------DERELARRRGGYAGGYVKEPERGLWDN-IVYLDFRSLYPSIIITHNVSPDT 422
Query: 536 IPVRMLQDSDIT-----TLCEYLPEHQVDTGILPSEIKKLVESRRQVKALMKQP--NLSS 588
           +     ++ D+        C+  P      G +PS +  L+E R+++K  MK     L  
Sbjct: 423 LNREGCKEYDVAPEVGHKFCKDFP------GFIPSLLGDLLEERQKIKRKMKATVDPLEK 476
Query: 589 DLLMQYDIRQKALKLTANSMYGCLGFPNSRFFAQPLAALVTAKGRE-ILLNTKSLVENLN 647
            LL   D RQ+A+K+ ANS YG  G+  +R++ +  A  VTA GRE I +  + L E   
Sbjct: 477 KLL---DYRQRAIKILANSFYGYYGYAKARWYCKECAESVTAWGREYIEMVIRELEEKFG 533
Query: 648 YEVIYGDTDSLMISCNVNDYDSVFKIGNQIKSECN-KLYKQLELDIDGVXXXXXXXXXXX 706
           ++V+Y DTD L  +    D ++V K   +     N KL   LEL+ +G            
Sbjct: 534 FKVLYADTDGLHATIPGADAETVKKKAKEFLKYINPKLPGLLELEYEGF----YVRGFFV 589
Query: 707 XXXXXXXXXXNGKMICSQEIKGVDVVRRDWSQLASEAGKFVISQIL 752
                      GK+      +G+++VRRDWS++A E    V+  IL
Sbjct: 590 TKKKYAVIDEEGKITT----RGLEIVRRDWSEIAKETQARVLEAIL 631

>pdb|2VWJ|A Chain A, Uracil Recognition In Archaeal Dna Polymerases Captured By X-Ray Crystallography Length = 773

Iteration: 1
 Score =  125 bits (313), Expect = 2e-28,   Method: Compositional matrix adjust.
 Identities = 95/346 (27%), Positives = 157/346 (45%), Gaps = 42/346 (12%)
Query: 418 KIMCELN--VLPLAIQITNVCGNVLSRTLMGGRSERNEFLLLHAFHEKSYVLPDKQYXXX 475
           K+  EL     P+  Q++ + G  L            E+ LL   +E++ + P+K     
Sbjct: 317 KVTYELGKEFFPMEAQLSRLVGQSLWDVSRSSTGNLVEWFLLRKAYERNELAPNKP---- 372
Query: 476 XXXXXXXXXXXXXXXRKKAAYSGGLVLEPKKGFYDKFIILMDFNSLYPSIIQEYNICFTT 535
                          R++ +Y+GG V EP++G ++  I+ +DF SLYPSII  +N+   T
Sbjct: 373 ---------DERELARRRESYAGGYVKEPERGLWEN-IVYLDFRSLYPSIIITHNVSPDT 422
Query: 536 IPVRMLQDSDIT-----TLCEYLPEHQVDTGILPSEIKKLVESRRQVKALMKQP--NLSS 588
           +     ++ D+        C+  P      G +PS +  L+E R++VK  MK     +  
Sbjct: 423 LNREGCEEYDVAPQVGHKFCKDFP------GFIPSLLGDLLEERQKVKKKMKATIDPIEK 476
Query: 589 DLLMQYDIRQKALKLTANSMYGCLGFPNSRFFAQPLAALVTAKGREILLNT-KSLVENLN 647
            LL   D RQ+A+K+ ANS YG  G+  +R++ +  A  VTA GR+ +  T + + E   
Sbjct: 477 KLL---DYRQRAIKILANSFYGYYGYAKARWYCKECAESVTAWGRQYIETTIREIEEKFG 533
Query: 648 YEVIYGDTDSLMISCNVNDYDSVFKIGNQIKSECN-KLYKQLELDIDGVXXXXXXXXXXX 706
           ++V+Y DTD    +    D ++V K   +     N KL   LEL+ +G            
Sbjct: 534 FKVLYADTDGFFATIPGADAETVKKKAKEFLDYINAKLPGLLELEYEGFYKRGFFVTKKK 593
Query: 707 XXXXXXXXXXNGKMICSQEIKGVDVVRRDWSQLASEAGKFVISQIL 752
                               +G+++VRRDWS++A E    V+  IL
Sbjct: 594 YAVIDEEDKIT--------TRGLEIVRRDWSEIAKETQARVLEAIL 631

>pdb|2VWK|A Chain A, Uracil Recognition In Archaeal Dna Polymerases Captured By X-Ray Crystallography. V93q Polymerase Variant Length = 773

Iteration: 1
 Score =  124 bits (312), Expect = 2e-28,   Method: Compositional matrix adjust.
 Identities = 95/346 (27%), Positives = 157/346 (45%), Gaps = 42/346 (12%)
Query: 418 KIMCELN--VLPLAIQITNVCGNVLSRTLMGGRSERNEFLLLHAFHEKSYVLPDKQYXXX 475
           K+  EL     P+  Q++ + G  L            E+ LL   +E++ + P+K     
Sbjct: 317 KVTYELGKEFFPMEAQLSRLVGQSLWDVSRSSTGNLVEWFLLRKAYERNELAPNKP---- 372
Query: 476 XXXXXXXXXXXXXXXRKKAAYSGGLVLEPKKGFYDKFIILMDFNSLYPSIIQEYNICFTT 535
                          R++ +Y+GG V EP++G ++  I+ +DF SLYPSII  +N+   T
Sbjct: 373 ---------DERELARRRESYAGGYVKEPERGLWEN-IVYLDFRSLYPSIIITHNVSPDT 422
Query: 536 IPVRMLQDSDIT-----TLCEYLPEHQVDTGILPSEIKKLVESRRQVKALMKQP--NLSS 588
           +     ++ D+        C+  P      G +PS +  L+E R++VK  MK     +  
Sbjct: 423 LNREGCEEYDVAPQVGHKFCKDFP------GFIPSLLGDLLEERQKVKKKMKATIDPIEK 476
Query: 589 DLLMQYDIRQKALKLTANSMYGCLGFPNSRFFAQPLAALVTAKGREILLNT-KSLVENLN 647
            LL   D RQ+A+K+ ANS YG  G+  +R++ +  A  VTA GR+ +  T + + E   
Sbjct: 477 KLL---DYRQRAIKILANSFYGYYGYAKARWYCKECAESVTAWGRQYIETTIREIEEKFG 533
Query: 648 YEVIYGDTDSLMISCNVNDYDSVFKIGNQIKSECN-KLYKQLELDIDGVXXXXXXXXXXX 706
           ++V+Y DTD    +    D ++V K   +     N KL   LEL+ +G            
Sbjct: 534 FKVLYADTDGFFATIPGADAETVKKKAKEFLDYINAKLPGLLELEYEGFYKRGFFVTKKK 593
Query: 707 XXXXXXXXXXNGKMICSQEIKGVDVVRRDWSQLASEAGKFVISQIL 752
                               +G+++VRRDWS++A E    V+  IL
Sbjct: 594 YAVIDEEDKIT--------TRGLEIVRRDWSEIAKETQARVLEAIL 631

>pdb|2XHB|A Chain A, Crystal Structure Of Dna Polymerase From Thermococcus Gorgonarius In Complex With Hypoxanthine-Containing Dna Length = 773

Iteration: 1
 Score =  124 bits (312), Expect = 2e-28,   Method: Compositional matrix adjust.
 Identities = 95/346 (27%), Positives = 157/346 (45%), Gaps = 42/346 (12%)
Query: 418 KIMCELN--VLPLAIQITNVCGNVLSRTLMGGRSERNEFLLLHAFHEKSYVLPDKQYXXX 475
           K+  EL     P+  Q++ + G  L            E+ LL   +E++ + P+K     
Sbjct: 317 KVTYELGKEFFPMEAQLSRLVGQSLWDVSRSSTGNLVEWFLLRKAYERNELAPNKP---- 372
Query: 476 XXXXXXXXXXXXXXXRKKAAYSGGLVLEPKKGFYDKFIILMDFNSLYPSIIQEYNICFTT 535
                          R++ +Y+GG V EP++G ++  I+ +DF SLYPSII  +N+   T
Sbjct: 373 ---------DERELARRRESYAGGYVKEPERGLWEN-IVYLDFRSLYPSIIITHNVSPDT 422
Query: 536 IPVRMLQDSDIT-----TLCEYLPEHQVDTGILPSEIKKLVESRRQVKALMKQP--NLSS 588
           +     ++ D+        C+  P      G +PS +  L+E R++VK  MK     +  
Sbjct: 423 LNREGCEEYDVAPQVGHKFCKDFP------GFIPSLLGDLLEERQKVKKKMKATIDPIEK 476
Query: 589 DLLMQYDIRQKALKLTANSMYGCLGFPNSRFFAQPLAALVTAKGREILLNT-KSLVENLN 647
            LL   D RQ+A+K+ ANS YG  G+  +R++ +  A  VTA GR+ +  T + + E   
Sbjct: 477 KLL---DYRQRAIKILANSFYGYYGYAKARWYCKECAESVTAWGRQYIETTIREIEEKFG 533
Query: 648 YEVIYGDTDSLMISCNVNDYDSVFKIGNQIKSECN-KLYKQLELDIDGVXXXXXXXXXXX 706
           ++V+Y DTD    +    D ++V K   +     N KL   LEL+ +G            
Sbjct: 534 FKVLYADTDGFFATIPGADAETVKKKAKEFLDYINAKLPGLLELEYEGFYKRGFFVTKKK 593
Query: 707 XXXXXXXXXXNGKMICSQEIKGVDVVRRDWSQLASEAGKFVISQIL 752
                               +G+++VRRDWS++A E    V+  IL
Sbjct: 594 YAVIDEEDKIT--------TRGLEIVRRDWSEIAKETQARVLEAIL 631

>pdb|1TGO|A Chain A, Thermostable B Type Dna Polymerase From Thermococcus Gorgonarius Length = 773

Iteration: 1
 Score =  124 bits (312), Expect = 2e-28,   Method: Compositional matrix adjust.
 Identities = 95/346 (27%), Positives = 157/346 (45%), Gaps = 42/346 (12%)
Query: 418 KIMCELN--VLPLAIQITNVCGNVLSRTLMGGRSERNEFLLLHAFHEKSYVLPDKQYXXX 475
           K+  EL     P+  Q++ + G  L            E+ LL   +E++ + P+K     
Sbjct: 317 KVTYELGKEFFPMEAQLSRLVGQSLWDVSRSSTGNLVEWFLLRKAYERNELAPNKP---- 372
Query: 476 XXXXXXXXXXXXXXXRKKAAYSGGLVLEPKKGFYDKFIILMDFNSLYPSIIQEYNICFTT 535
                          R++ +Y+GG V EP++G ++  I+ +DF SLYPSII  +N+   T
Sbjct: 373 ---------DERELARRRESYAGGYVKEPERGLWEN-IVYLDFRSLYPSIIITHNVSPDT 422
Query: 536 IPVRMLQDSDIT-----TLCEYLPEHQVDTGILPSEIKKLVESRRQVKALMKQP--NLSS 588
           +     ++ D+        C+  P      G +PS +  L+E R++VK  MK     +  
Sbjct: 423 LNREGCEEYDVAPQVGHKFCKDFP------GFIPSLLGDLLEERQKVKKKMKATIDPIEK 476
Query: 589 DLLMQYDIRQKALKLTANSMYGCLGFPNSRFFAQPLAALVTAKGREILLNT-KSLVENLN 647
            LL   D RQ+A+K+ ANS YG  G+  +R++ +  A  VTA GR+ +  T + + E   
Sbjct: 477 KLL---DYRQRAIKILANSFYGYYGYAKARWYCKECAESVTAWGRQYIETTIREIEEKFG 533
Query: 648 YEVIYGDTDSLMISCNVNDYDSVFKIGNQIKSECN-KLYKQLELDIDGVXXXXXXXXXXX 706
           ++V+Y DTD    +    D ++V K   +     N KL   LEL+ +G            
Sbjct: 534 FKVLYADTDGFFATIPGADAETVKKKAKEFLDYINAKLPGLLELEYEGFYKRGFFVTKKK 593
Query: 707 XXXXXXXXXXNGKMICSQEIKGVDVVRRDWSQLASEAGKFVISQIL 752
                               +G+++VRRDWS++A E    V+  IL
Sbjct: 594 YAVIDEEDKIT--------TRGLEIVRRDWSEIAKETQARVLEAIL 631

>pdb|1WN7|A Chain A, Crystal Structure Of Archaeal Family B Dna Polymerase Mutant Length = 774

Iteration: 1
 Score =  114 bits (284), Expect = 3e-25,   Method: Compositional matrix adjust.
 Identities = 108/392 (27%), Positives = 177/392 (45%), Gaps = 51/392 (13%)
Query: 418 KIMCELN--VLPLAIQITNVCGNVLSRTLMGGRSERNEFLLLHAFHEKSYVLPDKQYXXX 475
           K+  EL    LP+  Q++ + G  L            E+ LL   +E++ + P+K     
Sbjct: 317 KVTYELGKEFLPMEAQLSRLIGQSLWDVSRSSTGNLVEWFLLRKAYERNELAPNKP---- 372
Query: 476 XXXXXXXXXXXXXXXRKKAAYSGGLVLEPKKGFYDKFIILMDFNSLYPSIIQEYNICFTT 535
                          R++ +Y GG V EP++G ++  I+ +DF SLYPSII  +N+   T
Sbjct: 373 ---------DEKELARRRQSYEGGYVKEPERGLWEN-IVYLDFRSLYPSIIITHNVSPDT 422
Query: 536 IPVRMLQDSDITT-----LCEYLPEHQVDTGILPSEIKKLVESRRQVKALMKQP--NLSS 588
           +     ++ D+        C+  P      G +PS +  L+E R+++K  MK     +  
Sbjct: 423 LNREGCKEYDVAPQVGHRFCKDFP------GFIPSLLGDLLEERQKIKKKMKATIDPIER 476
Query: 589 DLLMQYDIRQKALKLTANSMYGCLGFPNSRFFAQPLAALVTAKGRE-ILLNTKSLVENLN 647
            LL   D RQ+A+K+ ANS YG  G+  +R++ +  A  VTA GRE I +  K + E   
Sbjct: 477 KLL---DYRQRAIKILANSYYGYYGYARARWYCKECAESVTAWGREYITMTIKEIEEKYG 533
Query: 648 YEVIYGDTDSLMISCNVNDYDSVFKIGNQIKSECN-KLYKQLELDIDGVXXXXXXXXXXX 706
           ++VIY DTD    +    D ++V K   +     N KL   LEL+ +G            
Sbjct: 534 FKVIYSDTDGFFATIPGADAETVKKKAMEFLKYINAKLPGALELEYEGF----YERGFFV 589
Query: 707 XXXXXXXXXXNGKMICSQEIKGVDVVRRDWSQLASEAGKFVISQILDEQSYTDYSLDDRL 766
                      GK+      +G+++VRRDWS++A E    V+  +L          D  +
Sbjct: 590 TKKKYAVIDEEGKITT----RGLEIVRRDWSEIAKETQARVLEALLK---------DGDV 636
Query: 767 QNIHEHMKKIRTDLDNGFVPLTLLEITKQLTK 798
           +     +K++   L    VP   L I +Q+T+
Sbjct: 637 EKAVRIVKEVTEKLSKYEVPPEKLVIHEQITR 668

>pdb|1WNS|A Chain A, Crystal Structure Of Family B Dna Polymerase From Hyperthermophilic Archaeon Pyrococcus Kodakaraensis Kod1 Length = 774

Iteration: 1
 Score =  114 bits (284), Expect = 4e-25,   Method: Compositional matrix adjust.
 Identities = 108/392 (27%), Positives = 177/392 (45%), Gaps = 51/392 (13%)
Query: 418 KIMCELN--VLPLAIQITNVCGNVLSRTLMGGRSERNEFLLLHAFHEKSYVLPDKQYXXX 475
           K+  EL    LP+  Q++ + G  L            E+ LL   +E++ + P+K     
Sbjct: 317 KVTYELGKEFLPMEAQLSRLIGQSLWDVSRSSTGNLVEWFLLRKAYERNELAPNKP---- 372
Query: 476 XXXXXXXXXXXXXXXRKKAAYSGGLVLEPKKGFYDKFIILMDFNSLYPSIIQEYNICFTT 535
                          R++ +Y GG V EP++G ++  I+ +DF SLYPSII  +N+   T
Sbjct: 373 ---------DEKELARRRQSYEGGYVKEPERGLWEN-IVYLDFRSLYPSIIITHNVSPDT 422
Query: 536 IPVRMLQDSDITT-----LCEYLPEHQVDTGILPSEIKKLVESRRQVKALMKQP--NLSS 588
           +     ++ D+        C+  P      G +PS +  L+E R+++K  MK     +  
Sbjct: 423 LNREGCKEYDVAPQVGHRFCKDFP------GFIPSLLGDLLEERQKIKKKMKATIDPIER 476
Query: 589 DLLMQYDIRQKALKLTANSMYGCLGFPNSRFFAQPLAALVTAKGRE-ILLNTKSLVENLN 647
            LL   D RQ+A+K+ ANS YG  G+  +R++ +  A  VTA GRE I +  K + E   
Sbjct: 477 KLL---DYRQRAIKILANSYYGYYGYARARWYCKECAESVTAWGREYITMTIKEIEEKYG 533
Query: 648 YEVIYGDTDSLMISCNVNDYDSVFKIGNQIKSECN-KLYKQLELDIDGVXXXXXXXXXXX 706
           ++VIY DTD    +    D ++V K   +     N KL   LEL+ +G            
Sbjct: 534 FKVIYSDTDGFFATIPGADAETVKKKAMEFLKYINAKLPGALELEYEGF----YKRGFFV 589
Query: 707 XXXXXXXXXXNGKMICSQEIKGVDVVRRDWSQLASEAGKFVISQILDEQSYTDYSLDDRL 766
                      GK+      +G+++VRRDWS++A E    V+  +L          D  +
Sbjct: 590 TKKKYAVIDEEGKITT----RGLEIVRRDWSEIAKETQARVLEALLK---------DGDV 636
Query: 767 QNIHEHMKKIRTDLDNGFVPLTLLEITKQLTK 798
           +     +K++   L    VP   L I +Q+T+
Sbjct: 637 EKAVRIVKEVTEKLSKYEVPPEKLVIHEQITR 668

>pdb|3IAY|A Chain A, Ternary Complex Of Dna Polymerase Delta Length = 919

Iteration: 1
 Score =  106 bits (265), Expect = 5e-23,   Method: Compositional matrix adjust.
 Identities = 67/212 (31%), Positives = 111/212 (52%), Gaps = 23/212 (10%)
Query: 496 YSGGLVLEPKKGFYDKFIILMDFNSLYPSIIQEYNICFTT---------IPVRMLQDSDI 546
           Y G  V+EP +G+YD  I  +DFNSLYPSI+  +N+C+TT         + +++ +D  I
Sbjct: 521 YEGATVIEPIRGYYDVPIATLDFNSLYPSIMMAHNLCYTTLCNKATVERLNLKIDEDYVI 580
Query: 547 TTLCEYLPEHQVDTGILPSEIKKLVESRRQVKALMKQPN--LSSDLLMQYDIRQKALKLT 604
           T   +Y    +   GILP  + +L+ +R++ K  ++        D+L   + RQ ALK++
Sbjct: 581 TPNGDYFVTTKRRRGILPIILDELISARKRAKKDLRDEKDPFKRDVL---NGRQLALKIS 637
Query: 605 ANSMYGCLGFPNSRFFAQPLAALVTAKGREILLNTKSLVE---------NLNYEVIYGDT 655
           ANS+YG  G    +     +++ VTA GR ++L TK+ V+           +  V+YGDT
Sbjct: 638 ANSVYGFTGATVGKLPCLAISSSVTAYGRTMILKTKTAVQEKYCIKNGYKHDAVVVYGDT 697
Query: 656 DSLMISCNVNDYDSVFKIGNQIKSECNKLYKQ 687
           DS+M+     D      +G +     + L+K 
Sbjct: 698 DSVMVKFGTTDLKEAMDLGTEAAKYVSTLFKH 729

>pdb|4FM2|A Chain A, Pyrococcus Abyssi B Family Dna Polymerase (Triple Mutant) Bound To A Dsdna, In Edition Mode Length = 793

Iteration: 1
 Score =  103 bits (257), Expect = 4e-22,   Method: Compositional matrix adjust.
 Identities = 103/406 (25%), Positives = 185/406 (45%), Gaps = 49/406 (12%)
Query: 401 GIVEFIKFTMLHSSYIIKIMCELNVLPLAIQITNVCGNVLSRTLMGGRSERNEFLLLHAF 460
           G+    K++M  +    ++  E    P+  Q+  + G  +            E+ LL   
Sbjct: 326 GLERVAKYSMEDAKVTFELGKEF--FPMEAQLARLVGQPVWAVSRSSTGNLVEWFLLRKA 383
Query: 461 HEKSYVLPDKQYXXXXXXXXXXXXXXXXXXRKKAAYSGGLVLEPKKGFYDKFIILMDFNS 520
           +E++ + P+K                    R + +Y GG V EP+KG ++  I+ +DF S
Sbjct: 384 YERNELAPNKP------------DEREYERRLRESYEGGYVKEPEKGLWEG-IVSLDFRS 430
Query: 521 LYPSIIQEYNICFTTIPVRMLQDSDITT-----LCEYLPEHQVDTGILPSEIKKLVESRR 575
           LYPSII  +N+   T+     ++ D+        C+  P      G +PS +  L+E R+
Sbjct: 431 LYPSIIITHNVSPDTLNRENCKEYDVAPQVGHRFCKDFP------GFIPSLLGNLLEERQ 484
Query: 576 QVKALMKQPN--LSSDLLMQYDIRQKALKLTANSMYGCLGFPNSRFFAQPLAALVTAKGR 633
           ++K  MK+    +   LL   D RQ+A+K+ ANS YG  G+  +R++ +  A  VTA GR
Sbjct: 485 KIKKRMKESKDPVEKKLL---DYRQRAIKILANSYYGYYGYAKARWYCKECAESVTAWGR 541
Query: 634 EILLNTKSLVENLNYEVIYGDTDSLMISCNVNDYDSVFKIGNQIKSECN-KLYKQLELDI 692
           + +   +  +E+  ++V+Y DTD L  +     ++ + +   +     N KL   LEL+ 
Sbjct: 542 QYIDLVRRELESRGFKVLYIDTDGLYATIPGAKHEEIKEKALKFVEYINSKLPGLLELEY 601
Query: 693 DGVXXXXXXXXXXXXXXXXXXXXXNGKMICSQEIKGVDVVRRDWSQLASEAGKFVISQIL 752
           +G                       GK++     +G+++VRRDWS++A E    V+  IL
Sbjct: 602 EGF----YARGFFVTKKKYALIDEEGKIVT----RGLEIVRRDWSEIAKETQAKVLEAIL 653
Query: 753 DEQSYTDYSLDDRLQNIHEHMKKIRTDLDNGFVPLTLLEITKQLTK 798
                   ++D+ ++ + E  +K    L    +P   L I +Q+T+
Sbjct: 654 KHG-----NVDEAVKIVKEVTEK----LSKYEIPPEKLVIYEQITR 690

>pdb|4FLT|A Chain A, Pyrococcus Abyssi B Family Dna Polymerase Bound To A Dsdna, In Edition Mode Length = 793

Iteration: 1
 Score =  103 bits (257), Expect = 5e-22,   Method: Compositional matrix adjust.
 Identities = 103/406 (25%), Positives = 185/406 (45%), Gaps = 49/406 (12%)
Query: 401 GIVEFIKFTMLHSSYIIKIMCELNVLPLAIQITNVCGNVLSRTLMGGRSERNEFLLLHAF 460
           G+    K++M  +    ++  E    P+  Q+  + G  +            E+ LL   
Sbjct: 326 GLERVAKYSMEDAKVTFELGKEF--FPMEAQLARLVGQPVWDVSRSSTGNLVEWFLLRKA 383
Query: 461 HEKSYVLPDKQYXXXXXXXXXXXXXXXXXXRKKAAYSGGLVLEPKKGFYDKFIILMDFNS 520
           +E++ + P+K                    R + +Y GG V EP+KG ++  I+ +DF S
Sbjct: 384 YERNELAPNKP------------DEREYERRLRESYEGGYVKEPEKGLWEG-IVSLDFRS 430
Query: 521 LYPSIIQEYNICFTTIPVRMLQDSDITT-----LCEYLPEHQVDTGILPSEIKKLVESRR 575
           LYPSII  +N+   T+     ++ D+        C+  P      G +PS +  L+E R+
Sbjct: 431 LYPSIIITHNVSPDTLNRENCKEYDVAPQVGHRFCKDFP------GFIPSLLGNLLEERQ 484
Query: 576 QVKALMKQPN--LSSDLLMQYDIRQKALKLTANSMYGCLGFPNSRFFAQPLAALVTAKGR 633
           ++K  MK+    +   LL   D RQ+A+K+ ANS YG  G+  +R++ +  A  VTA GR
Sbjct: 485 KIKKRMKESKDPVEKKLL---DYRQRAIKILANSYYGYYGYAKARWYCKECAESVTAWGR 541
Query: 634 EILLNTKSLVENLNYEVIYGDTDSLMISCNVNDYDSVFKIGNQIKSECN-KLYKQLELDI 692
           + +   +  +E+  ++V+Y DTD L  +     ++ + +   +     N KL   LEL+ 
Sbjct: 542 QYIDLVRRELESRGFKVLYIDTDGLYATIPGAKHEEIKEKALKFVEYINSKLPGLLELEY 601
Query: 693 DGVXXXXXXXXXXXXXXXXXXXXXNGKMICSQEIKGVDVVRRDWSQLASEAGKFVISQIL 752
           +G                       GK++     +G+++VRRDWS++A E    V+  IL
Sbjct: 602 EGF----YARGFFVTKKKYALIDEEGKIVT----RGLEIVRRDWSEIAKETQAKVLEAIL 653
Query: 753 DEQSYTDYSLDDRLQNIHEHMKKIRTDLDNGFVPLTLLEITKQLTK 798
                   ++D+ ++ + E  +K    L    +P   L I +Q+T+
Sbjct: 654 KHG-----NVDEAVKIVKEVTEK----LSKYEIPPEKLVIYEQITR 690

>pdb|1QQC|A Chain A, Crystal Structure Of An Archaebacterial Dna Polymerase D.Tok Length = 773

Iteration: 1
 Score =  101 bits (251), Expect = 2e-21,   Method: Compositional matrix adjust.
 Identities = 104/407 (25%), Positives = 180/407 (44%), Gaps = 51/407 (12%)
Query: 401 GIVEFIKFTMLHSSYIIKIMCELNVLPLAIQITNVCGNVLSRTLMGGRSERNEFLLLHAF 460
           G+    +++M  +    ++  E    P+  Q++ + G  L            E+ LL   
Sbjct: 304 GLERVARYSMEDAKATYELGKEF--FPMEAQLSRLVGQSLWDVSRSSTGNLVEWFLLRKA 361
Query: 461 HEKSYVLPDKQYXXXXXXXXXXXXXXXXXXRKKAAYSGGLVLEPKKGFYDKFIILMDFNS 520
           +E++ V P+K                    R+  +Y+GG V EP+KG ++  I+ +D+ S
Sbjct: 362 YERNDVAPNKP-------------DERELARRTESYAGGYVKEPEKGLWEN-IVYLDYKS 407
Query: 521 LYPSIIQEYNICFTTIPVRMLQDSDITT-----LCEYLPEHQVDTGILPSEIKKLVESRR 575
           LYPSII  +N+   T+     ++ D+        C+  P      G +PS +  L+E R+
Sbjct: 408 LYPSIIITHNVSPDTLNREGCREYDVAPQVGHRFCKDFP------GFIPSLLGDLLEERQ 461
Query: 576 QVKALMKQP--NLSSDLLMQYDIRQKALKLTANSMYGCLGFPNSRFFAQPLAALVTAKGR 633
           +VK  MK     +   LL   D RQ+A+K+ ANS YG   + N+R++ +  A  VTA GR
Sbjct: 462 KVKKKMKATVDPIERKLL---DYRQRAIKILANSYYGYYAYANARWYCRECAESVTAWGR 518
Query: 634 EILLNT-KSLVENLNYEVIYGDTDSLMISCNVNDYDSVFKIGNQIKSECN-KLYKQLELD 691
           + +  T + + E   ++V+Y DTD    +    D ++V     +  +  N +L   LEL+
Sbjct: 519 QYIETTMREIEEKFGFKVLYADTDGFFATIPGADAETVKNKAKEFLNYINPRLPGLLELE 578
Query: 692 IDGVXXXXXXXXXXXXXXXXXXXXXNGKMICSQEIKGVDVVRRDWSQLASEAGKFVISQI 751
            +G                                +G+++VRRDWS++A E    V+  I
Sbjct: 579 YEGFYRRGFFVTKKKYAVIDEEDKIT--------TRGLEIVRRDWSEIAKETQARVLEAI 630
Query: 752 LDEQSYTDYSLDDRLQNIHEHMKKIRTDLDNGFVPLTLLEITKQLTK 798
           L    + D     R+      +K++   L    VP   L I +Q+T+
Sbjct: 631 L---KHGDVEEAVRI------VKEVTEKLSRHEVPPEKLVIYEQITR 668

>pdb|1D5A|A Chain A, Crystal Structure Of An Archaebacterial Dna Polymerase D.Tok. Deposition Of Second Native Structure At 2.4 Angstrom Length = 733

Iteration: 1
 Score =  100 bits (249), Expect = 4e-21,   Method: Compositional matrix adjust.
 Identities = 91/336 (27%), Positives = 152/336 (45%), Gaps = 40/336 (11%)
Query: 426 LPLAIQITNVCGNVLSRTLMGGRSERNEFLLLHAFHEKSYVLPDKQYXXXXXXXXXXXXX 485
            P+  Q++ + G  L            E+ LL   +E++ V P+K               
Sbjct: 327 FPMEAQLSRLVGQSLWDVSRSSTGNLVEWFLLRKAYERNDVAPNKP-------------D 373
Query: 486 XXXXXRKKAAYSGGLVLEPKKGFYDKFIILMDFNSLYPSIIQEYNICFTTIPVRMLQDSD 545
                R+  +Y+GG V EP+KG ++  I+ +D+ SLYPSII  +N+   T+     ++ D
Sbjct: 374 ERELARRTESYAGGYVKEPEKGLWEN-IVYLDYKSLYPSIIITHNVSPDTLNREGCREYD 432
Query: 546 ITT-----LCEYLPEHQVDTGILPSEIKKLVESRRQVKALMKQP--NLSSDLLMQYDIRQ 598
           +        C+  P      G +PS +  L+E R++VK  MK     +   LL   D RQ
Sbjct: 433 VAPQVGHRFCKDFP------GFIPSLLGDLLEERQKVKKKMKATVDPIERKLL---DYRQ 483
Query: 599 KALKLTANSMYGCLGFPNSRFFAQPLAALVTAKGREILLNT-KSLVENLNYEVIYGDTDS 657
           +A+K+ ANS YG   + N+R++ +  A  VTA GR+ +  T + + E   ++V+Y DTD 
Sbjct: 484 RAIKILANSYYGYYAYANARWYCRECAESVTAWGRQYIETTMREIEEKFGFKVLYADTDG 543
Query: 658 LMISCNVNDYDSVFKIGNQIKSECN-KLYKQLELDIDGVXXXXXXXXXXXXXXXXXXXXX 716
              +    D ++V     +  +  N +L   LEL+ +G                      
Sbjct: 544 FFATIPGADAETVKNKAKEFLNYINPRLPGLLELEYEGFYRRGFFVTKKKYAVIDEEDKI 603
Query: 717 NGKMICSQEIKGVDVVRRDWSQLASEAGKFVISQIL 752
                     +G+++VRRDWS++A E    V+  IL
Sbjct: 604 T--------TRGLEIVRRDWSEIAKETQARVLEAIL 631

>pdb|2GV9|A Chain A, Crystal Structure Of The Herpes Simplex Virus Type 1 Dna Polymerase Length = 1193

Iteration: 1
 Score = 94.7 bits (234), Expect = 2e-19,   Method: Compositional matrix adjust.
 Identities = 76/291 (26%), Positives = 125/291 (42%), Gaps = 68/291 (23%)
Query: 492 KKAAYSGGLVLEPKKGFYDKFIILMDFNSLYPSIIQEYNICFTTIPVRMLQDSDITTLCE 551
           +   Y G  VL+P  GF+   +++ DF SLYPSIIQ +N+CF+T+ +R    + +    +
Sbjct: 650 RHVGYQGAKVLDPTSGFHVNPVVVFDFASLYPSIIQAHNLCFSTLSLRADAVAHLEAGKD 709
Query: 552 YLP-----------EHQVDTGILPSEIKKLVESRRQVKALMKQPNLSSDLLMQYDIRQKA 600
           YL            +  V   +L   ++  +  R+Q+++ + Q +    +L+  D +Q A
Sbjct: 710 YLEIEVGGRRLFFVKAHVRESLLSILLRDWLAMRKQIRSRIPQSSPEEAVLL--DKQQAA 767
Query: 601 LKLTANSMYGCLGFPNSRFFAQPLAALVTAKGREILLNTKSLVEN--------------- 645
           +K+  NS+YG  G  +       +AA VT  GRE+LL T+  V                 
Sbjct: 768 IKVVCNSVYGFTGVQHGLLPCLHVAATVTTIGREMLLATREYVHARWAAFEQLLADFPEA 827
Query: 646 --------LNYEVIYGDTDSLMISCNVNDYDSVFKIGNQ-------------IKSECNKL 684
                    +  +IYGDTDS+ + C       +  +G++             IK EC K 
Sbjct: 828 ADMRAPGPYSMRIIYGDTDSIFVLCRGLTAAGLTAMGDKMASHISRALFLPPIKLECEKT 887
Query: 685 YKQLELDIDGVXXXXXXXXXXXXXXXXXXXXXNGKMICSQEIKGVDVVRRD 735
           + +L L                           GKM+    IKGVD+VR++
Sbjct: 888 FTKLLL---------------IAKKKYIGVIYGGKML----IKGVDLVRKN 919

>pdb|3K5L|A Chain A, Crystal Structure Of E.Coli Pol Ii-Abasic Dna-Datp Lt(0, 3) Ternary Complex Length = 786

Iteration: 1
 Score = 91.3 bits (225), Expect = 2e-18,   Method: Compositional matrix adjust.
 Identities = 90/373 (24%), Positives = 146/373 (39%), Gaps = 74/373 (19%)
Query: 416 IIKIMCELNVLPLAIQITNVCGNVLSRTLMGGRSERNEFLLLHAFHEKSYVLPDKQYXXX 475
           + +I  +  ++P  ++   V G  + R   GG       L     H   YV P+      
Sbjct: 342 VTQIFHKTEIMPFLLERATVNGLPVDR--HGGSVAAFGHLYFPRMHRAGYVAPN------ 393
Query: 476 XXXXXXXXXXXXXXXRKKAAYSGGLVLEPKKGFYDKFIILMDFNSLYPSIIQEYNICFTT 535
                              A  GG V++ + G YD  ++L D+ SLYPSII+     F  
Sbjct: 394 ------------LGEVPPHASPGGYVMDSRPGLYDSVLVL-DYKSLYPSIIR----TFLI 436
Query: 536 IPVRMLQDSDITTLCEYLPEHQVDTGI----------LPSEIKKLVESRRQVKALMKQPN 585
            PV +++      + +  PEH  +  +          LP  +  +   R + K    +P 
Sbjct: 437 DPVGLVEG-----MAQPDPEHSTEGFLDAWFSREKHCLPEIVTNIWHGRDEAKRQGNKP- 490
Query: 586 LSSDLLMQYDIRQKALKLTANSMYGCLGFPNSRFFAQPLAALVTAKGREILLNTKSLVEN 645
           LS           +ALK+  N+ YG LG    RFF   LA+ +T +G +I+  TK+L+E 
Sbjct: 491 LS-----------QALKIIMNAFYGVLGTTACRFFDPRLASSITMRGHQIMRQTKALIEA 539
Query: 646 LNYEVIYGDTDSLMISC-NVNDYDSVFKIGNQIKSECN----------KLYKQLELDIDG 694
             Y+VIYGDTDS  +     +  +   KIG  +    N          +L   LEL+ + 
Sbjct: 540 QGYDVIYGDTDSTFVWLKGAHSEEEAAKIGRALVQHVNAWWAETLQKQRLTSALELEYET 599
Query: 695 -------VXXXXXXXXXXXXXXXXXXXXXNGKMICSQEIKGVDVVRRDWSQLASEAGKFV 747
                                          +M+     KG++ VR DW+ LA +  + +
Sbjct: 600 HFCRFLMPTIRGADTGSKKRYAGLIQEGDKQRMV----FKGLETVRTDWTPLAQQFQQEL 655
Query: 748 ISQILDEQSYTDY 760
             +I   + Y +Y
Sbjct: 656 YLRIFRNEPYQEY 668

>pdb|1Q8I|A Chain A, Crystal Structure Of Escherichia Coli Dna Polymerase Ii Length = 783

Iteration: 1
 Score = 90.5 bits (223), Expect = 4e-18,   Method: Compositional matrix adjust.
 Identities = 89/373 (23%), Positives = 146/373 (39%), Gaps = 74/373 (19%)
Query: 416 IIKIMCELNVLPLAIQITNVCGNVLSRTLMGGRSERNEFLLLHAFHEKSYVLPDKQYXXX 475
           + +I  +  ++P  ++   V G  + R   GG       L     H   YV P+      
Sbjct: 339 VTQIFHKTEIMPFLLERATVNGLPVDR--HGGSVAAFGHLYFPRMHRAGYVAPN------ 390
Query: 476 XXXXXXXXXXXXXXXRKKAAYSGGLVLEPKKGFYDKFIILMDFNSLYPSIIQEYNICFTT 535
                              A  GG V++ + G YD  ++L D+ SLYPSI++     F  
Sbjct: 391 ------------LGEVPPHASPGGYVMDSRPGLYDSVLVL-DYKSLYPSIVR----TFLI 433
Query: 536 IPVRMLQDSDITTLCEYLPEHQVDTGI----------LPSEIKKLVESRRQVKALMKQPN 585
            PV +++      + +  PEH  +  +          LP  +  +   R + K    +P 
Sbjct: 434 DPVGLVEG-----MAQPDPEHSTEGFLDAWFSREKHCLPEIVTNIWHGRDEAKRQGNKP- 487
Query: 586 LSSDLLMQYDIRQKALKLTANSMYGCLGFPNSRFFAQPLAALVTAKGREILLNTKSLVEN 645
           LS           +ALK+  N+ YG LG    RFF   LA+ +T +G +I+  TK+L+E 
Sbjct: 488 LS-----------QALKIIMNAFYGVLGTTACRFFDPRLASSITMRGHQIMRQTKALIEA 536
Query: 646 LNYEVIYGDTDSLMISC-NVNDYDSVFKIGNQIKSECN----------KLYKQLELDIDG 694
             Y+VIYGDTDS  +     +  +   KIG  +    N          +L   LEL+ + 
Sbjct: 537 QGYDVIYGDTDSTFVWLKGAHSEEEAAKIGRALVQHVNAWWAETLQKQRLTSALELEYET 596
Query: 695 -------VXXXXXXXXXXXXXXXXXXXXXNGKMICSQEIKGVDVVRRDWSQLASEAGKFV 747
                                          +M+     KG++ VR DW+ LA +  + +
Sbjct: 597 HFCRFLMPTIRGADTGSKKRYAGLIQEGDKQRMV----FKGLETVRTDWTPLAQQFQQEL 652
Query: 748 ISQILDEQSYTDY 760
             +I   + Y +Y
Sbjct: 653 YLRIFRNEPYQEY 665

>pdb|1S5J|A Chain A, Insight In Dna Replication: The Crystal Structure Of Dna Polymerase B1 From The Archaeon Sulfolobus Solfataricus Length = 847

Iteration: 1
 Score = 79.3 bits (194), Expect = 1e-14,   Method: Compositional matrix adjust.
 Identities = 55/179 (30%), Positives = 90/179 (50%), Gaps = 17/179 (9%)
Query: 492 KKAAYSGGLVLEPKKGFYDKFIILMDFNSLYPSIIQEYNICFTTIPVRM------LQDSD 545
           K   Y G +V++P  G +   I ++DF SLYPSII+ +N+ + T+ ++       ++D  
Sbjct: 455 KGKGYKGAVVIDPPAGIFFN-ITVLDFASLYPSIIRTWNLSYETVDIQQCKKPYEVKDET 513
Query: 546 ---ITTLCEYLPE-HQVDTGILPSEIKKLVESRRQVKALMKQPNLSSDLLMQYDIRQKAL 601
              +  +C   P    V TG+L     K+ + +       K PN S +  + YD+ Q+A+
Sbjct: 514 GEVLHIVCMDRPGITAVITGLLRDFRVKIYKKK------AKNPNNSEEQKLLYDVVQRAM 567
Query: 602 KLTANSMYGCLGFPNSRFFAQPLAALVTAKGREILLNTKSLVENLNYEVIYGDTDSLMI 660
           K+  N+ YG  G      +A  +A  VTA GR ++ +T          V+YGDTDSL +
Sbjct: 568 KVFINATYGVFGAETFPLYAPRVAESVTALGRYVITSTVKKAREEGLTVLYGDTDSLFL 626

>pdb|3KD1|E Chain E, Closed Binary Complex Of An Rb69 Gp43 Fingers Domain Mutant Complexed With An Acyclic Gmp Terminated Primer Template Pair. Length = 913

Iteration: 1
 Score = 60.8 bits (146), Expect = 4e-09,   Method: Compositional matrix adjust.
 Identities = 68/242 (28%), Positives = 93/242 (38%), Gaps = 76/242 (31%)
Query: 496 YSGGLVLEPKKGFYDKFIILMDFNSLYPSIIQEYNICFTTIP----VRMLQD-------- 543
           Y G  V EP    Y K+++  D  SLYPSII++ NI   TI     V  L D        
Sbjct: 391 YPGAFVKEPIPNRY-KYVMSFDLTSLYPSIIRQVNISPETIAGTFKVAPLHDYINAVAER 449
Query: 544 -SDITTLCEYLPEHQVDT-GILPSEIKKLVESRRQVKALM--------------KQPNLS 587
            SD+ +       +  D  G++P+EI K V  R++ K  M                PNLS
Sbjct: 450 PSDVYSCSPNGMMYYKDRDGVVPTEITKWVSQRKEHKGYMLAAQRNGEIIKEALHNPNLS 509
Query: 588 SDLLMQYDIR------------------------------------QKALKLTANSMYGC 611
            D  +  D R                                    Q ALK+T NS+YG 
Sbjct: 510 VDEPLDVDYRFDFSDEIKEKIKKLSAKSLNEMLFRAQRTEVAGMTAQMALKVTCNSLYGA 569
Query: 612 LGFPNSRFFAQPLAALVTAKGREIL----------LNTKSLVENLNYEVIYGDTDSLMIS 661
           LG    R++    A  +T  G+  L          LN     E   + V+YGDTDS+ +S
Sbjct: 570 LGNVWFRYYDLRNATAITTFGQMALQWIERKVNEYLNEVCGTEGEAF-VLYGDTDSIYVS 628
Query: 662 CN 663
            +
Sbjct: 629 AD 630

>pdb|2DY4|A Chain A, Crystal Structure Of Rb69 Gp43 In Complex With Dna Containing Thymine Glycol Length = 903

Iteration: 1
 Score = 55.1 bits (131), Expect = 2e-07,   Method: Compositional matrix adjust.
 Identities = 65/242 (26%), Positives = 94/242 (38%), Gaps = 76/242 (31%)
Query: 496 YSGGLVLEPKKGFYDKFIILMDFNSLYPSIIQEYNICFTTIP----VRMLQD-------- 543
           Y G  V EP    Y K++   D  SLYPSII++ NI   TI     V  L D        
Sbjct: 391 YPGAFVKEPIPNRY-KYVXSFDLTSLYPSIIRQVNISPETIAGTFKVAPLHDYINAVAER 449
Query: 544 -SDITTLCEYLPEHQVDT-GILPSEIKKLVESRRQ--------------VKALMKQPNLS 587
            SD+ +       +  D  G++P+EI K+   R++              +K  +  PNLS
Sbjct: 450 PSDVYSCSPNGXXYYKDRDGVVPTEITKVFNQRKEHKGYXLAAQRNGEIIKEALHNPNLS 509
Query: 588 SDLLMQYD--------IRQKALKLTA----------------------------NSMYGC 611
            D  +  D        I++K  KL+A                            NS+YG 
Sbjct: 510 VDEPLDVDYRFDFSDEIKEKIKKLSAKSLNEXLFRAQRTEVAGXTAQINRKLLINSLYGA 569
Query: 612 LGFPNSRFFAQPLAALVTAKGREIL----------LNTKSLVENLNYEVIYGDTDSLMIS 661
           LG    R++    A  +T  G+  L          LN     E   + V+YGDTDS+ +S
Sbjct: 570 LGNVWFRYYDLRNATAITTFGQXALQWIERKVNEYLNEVCGTEGEAF-VLYGDTDSIYVS 628
Query: 662 CN 663
            +
Sbjct: 629 AD 630

>pdb|3L8B|A Chain A, Crystal Structure Of A Replicative Dna Polymerase Bound To The Oxidized Guanine Lesion Guanidinohydantoin Length = 906

Iteration: 1
 Score = 53.5 bits (127), Expect = 5e-07,   Method: Compositional matrix adjust.
 Identities = 66/242 (27%), Positives = 94/242 (38%), Gaps = 76/242 (31%)
Query: 496 YSGGLVLEPKKGFYDKFIILMDFNSLYPSIIQEYNICFTTIP----VRMLQD-------- 543
           Y G  V EP    Y K+++  D  SLYPSII++ NI   TI     V  L D        
Sbjct: 391 YPGAFVKEPIPNRY-KYVMSFDLTSLYPSIIRQVNISPETIAGTFKVAPLHDYINAVAER 449
Query: 544 -SDITTLCEYLPEHQVDT-GILPSEIKKLVESRRQVKALM--------------KQPNLS 587
            SD+ +       +  D  G++P+EI K+   R++ K  M                PNLS
Sbjct: 450 PSDVYSCSPNGMMYYKDRDGVVPTEITKVFNQRKEHKGYMLAAQRNGEIIKEALHNPNLS 509
Query: 588 SDLLMQYD--------IRQKALKLTA----------------------------NSMYGC 611
            D  +  D        I++K  KL+A                            NS+YG 
Sbjct: 510 VDEPLDVDYRFDFSDEIKEKIKKLSAKSLNEMLFRAQRTEVAGMTAQINRKLLINSLYGA 569
Query: 612 LGFPNSRFFAQPLAALVTAKGREIL----------LNTKSLVENLNYEVIYGDTDSLMIS 661
           LG    R++    A  +T  G+  L          LN     E   + V+YGDTDS+ +S
Sbjct: 570 LGNVWFRYYDLRNATAITTFGQMALQWIERKVNEYLNEVCGTEGEAF-VLYGDTDSIYVS 628
Query: 662 CN 663
            +
Sbjct: 629 AD 630

>pdb|3LDS|A Chain A, Crystal Structure Of Rb69 Gp43 With Dna And Datp Opposite 8- Length = 903

Iteration: 1
 Score = 53.5 bits (127), Expect = 6e-07,   Method: Compositional matrix adjust.
 Identities = 66/242 (27%), Positives = 94/242 (38%), Gaps = 76/242 (31%)
Query: 496 YSGGLVLEPKKGFYDKFIILMDFNSLYPSIIQEYNICFTTIP----VRMLQD-------- 543
           Y G  V EP    Y K+++  D  SLYPSII++ NI   TI     V  L D        
Sbjct: 391 YPGAFVKEPIPNRY-KYVMSFDLTSLYPSIIRQVNISPETIAGTFKVAPLHDYINAVAER 449
Query: 544 -SDITTLCEYLPEHQVDT-GILPSEIKKLVESRRQVKALM--------------KQPNLS 587
            SD+ +       +  D  G++P+EI K+   R++ K  M                PNLS
Sbjct: 450 PSDVYSCSPNGMMYYKDRDGVVPTEITKVFNQRKEHKGYMLAAQRNGEIIKEALHNPNLS 509
Query: 588 SDLLMQYD--------IRQKALKLTA----------------------------NSMYGC 611
            D  +  D        I++K  KL+A                            NS+YG 
Sbjct: 510 VDEPLDVDYRFDFSDEIKEKIKKLSAKSLNEMLFRAQRTEVAGMTAQINRKALINSLYGA 569
Query: 612 LGFPNSRFFAQPLAALVTAKGREIL----------LNTKSLVENLNYEVIYGDTDSLMIS 661
           LG    R++    A  +T  G+  L          LN     E   + V+YGDTDS+ +S
Sbjct: 570 LGNVWFRYYDLRNATAITTFGQMALQWIERKVNEYLNEVCGTEGEAF-VLYGDTDSIYVS 628
Query: 662 CN 663
            +
Sbjct: 629 AD 630

>pdb|3SQ2|A Chain A, Rb69 Dna Polymerase Ternary Complex With Dttp Opposite 2ap (At Rich Sequence) Length = 902

Iteration: 1
 Score = 53.5 bits (127), Expect = 6e-07,   Method: Compositional matrix adjust.
 Identities = 66/242 (27%), Positives = 94/242 (38%), Gaps = 76/242 (31%)
Query: 496 YSGGLVLEPKKGFYDKFIILMDFNSLYPSIIQEYNICFTTIP----VRMLQD-------- 543
           Y G  V EP    Y K+++  D  SLYPSII++ NI   TI     V  L D        
Sbjct: 391 YPGAFVKEPIPNRY-KYVMSFDLTSLYPSIIRQVNISPETIAGTFKVAPLHDYINAVAER 449
Query: 544 -SDITTLCEYLPEHQVDT-GILPSEIKKLVESRRQVKALM--------------KQPNLS 587
            SD+ +       +  D  G++P+EI K+   R++ K  M                PNLS
Sbjct: 450 PSDVYSCSPNGMMYYKDRDGVVPTEITKVFNQRKEHKGYMLAAQRNGEIIKEALHNPNLS 509
Query: 588 SDLLMQYD--------IRQKALKLTA----------------------------NSMYGC 611
            D  +  D        I++K  KL+A                            NS+YG 
Sbjct: 510 VDEPLDVDYRFDFSDEIKEKIKKLSAKSLNEMLFRAQRTEVAGMTAQINRKLLINSLYGA 569
Query: 612 LGFPNSRFFAQPLAALVTAKGREIL----------LNTKSLVENLNYEVIYGDTDSLMIS 661
           LG    R++    A  +T  G+  L          LN     E   + V+YGDTDS+ +S
Sbjct: 570 LGNVWFRYYDLRNATAITTFGQMALQWIERKVNEYLNEVCGTEGEAF-VLYGDTDSIYVS 628
Query: 662 CN 663
            +
Sbjct: 629 AD 630

>pdb|3SQ1|A Chain A, Rb69 Dna Polymerase Ternary Complex With Dupcpp Opposite Da Length = 901

Iteration: 1
 Score = 53.5 bits (127), Expect = 6e-07,   Method: Compositional matrix adjust.
 Identities = 66/242 (27%), Positives = 94/242 (38%), Gaps = 76/242 (31%)
Query: 496 YSGGLVLEPKKGFYDKFIILMDFNSLYPSIIQEYNICFTTIP----VRMLQD-------- 543
           Y G  V EP    Y K+++  D  SLYPSII++ NI   TI     V  L D        
Sbjct: 391 YPGAFVKEPIPNRY-KYVMSFDLTSLYPSIIRQVNISPETIAGTFKVAPLHDYINAVAER 449
Query: 544 -SDITTLCEYLPEHQVDT-GILPSEIKKLVESRRQVKALM--------------KQPNLS 587
            SD+ +       +  D  G++P+EI K+   R++ K  M                PNLS
Sbjct: 450 PSDVYSCSPNGMMYYKDRDGVVPTEITKVFNQRKEHKGYMLAAQRNGEIIKEALHNPNLS 509
Query: 588 SDLLMQYD--------IRQKALKLTA----------------------------NSMYGC 611
            D  +  D        I++K  KL+A                            NS+YG 
Sbjct: 510 VDEPLDVDYRFDFSDEIKEKIKKLSAKSLNEMLFRAQRTEVAGMTAQINRKLLINSLYGA 569
Query: 612 LGFPNSRFFAQPLAALVTAKGREIL----------LNTKSLVENLNYEVIYGDTDSLMIS 661
           LG    R++    A  +T  G+  L          LN     E   + V+YGDTDS+ +S
Sbjct: 570 LGNVWFRYYDLRNATAITTFGQMALQWIERKVNEYLNEVCGTEGEAF-VLYGDTDSIYVS 628
Query: 662 CN 663
            +
Sbjct: 629 AD 630

>pdb|1WAF|A Chain A, Dna Polymerase From Bacteriophage Rb69 Length = 903

Iteration: 1
 Score = 53.5 bits (127), Expect = 6e-07,   Method: Compositional matrix adjust.
 Identities = 66/242 (27%), Positives = 94/242 (38%), Gaps = 76/242 (31%)
Query: 496 YSGGLVLEPKKGFYDKFIILMDFNSLYPSIIQEYNICFTTIP----VRMLQD-------- 543
           Y G  V EP    Y K+++  D  SLYPSII++ NI   TI     V  L D        
Sbjct: 391 YPGAFVKEPIPNRY-KYVMSFDLTSLYPSIIRQVNISPETIAGTFKVAPLHDYINAVAER 449
Query: 544 -SDITTLCEYLPEHQVDT-GILPSEIKKLVESRRQVKALM--------------KQPNLS 587
            SD+ +       +  D  G++P+EI K+   R++ K  M                PNLS
Sbjct: 450 PSDVYSCSPNGMMYYKDRDGVVPTEITKVFNQRKEHKGYMLAAQRNGEIIKEALHNPNLS 509
Query: 588 SDLLMQYD--------IRQKALKLTA----------------------------NSMYGC 611
            D  +  D        I++K  KL+A                            NS+YG 
Sbjct: 510 VDEPLDVDYRFDFSDEIKEKIKKLSAKSLNEMLFRAQRTEVAGMTAQINRKLLINSLYGA 569
Query: 612 LGFPNSRFFAQPLAALVTAKGREIL----------LNTKSLVENLNYEVIYGDTDSLMIS 661
           LG    R++    A  +T  G+  L          LN     E   + V+YGDTDS+ +S
Sbjct: 570 LGNVWFRYYDLRNATAITTFGQMALQWIERKVNEYLNEVCGTEGEAF-VLYGDTDSIYVS 628
Query: 662 CN 663
            +
Sbjct: 629 AD 630

>pdb|1IG9|A Chain A, Structure Of The Replicating Complex Of A Pol Alpha Family Dna Polymerase Length = 903

Iteration: 1
 Score = 53.5 bits (127), Expect = 6e-07,   Method: Compositional matrix adjust.
 Identities = 66/242 (27%), Positives = 94/242 (38%), Gaps = 76/242 (31%)
Query: 496 YSGGLVLEPKKGFYDKFIILMDFNSLYPSIIQEYNICFTTIP----VRMLQD-------- 543
           Y G  V EP    Y K+++  D  SLYPSII++ NI   TI     V  L D        
Sbjct: 391 YPGAFVKEPIPNRY-KYVMSFDLTSLYPSIIRQVNISPETIAGTFKVAPLHDYINAVAER 449
Query: 544 -SDITTLCEYLPEHQVDT-GILPSEIKKLVESRRQVKALM--------------KQPNLS 587
            SD+ +       +  D  G++P+EI K+   R++ K  M                PNLS
Sbjct: 450 PSDVYSCSPNGMMYYKDRDGVVPTEITKVFNQRKEHKGYMLAAQRNGEIIKEALHNPNLS 509
Query: 588 SDLLMQYD--------IRQKALKLTA----------------------------NSMYGC 611
            D  +  D        I++K  KL+A                            NS+YG 
Sbjct: 510 VDEPLDVDYRFDFSDEIKEKIKKLSAKSLNEMLFRAQRTEVAGMTAQINRKLLINSLYGA 569
Query: 612 LGFPNSRFFAQPLAALVTAKGREIL----------LNTKSLVENLNYEVIYGDTDSLMIS 661
           LG    R++    A  +T  G+  L          LN     E   + V+YGDTDS+ +S
Sbjct: 570 LGNVWFRYYDLRNATAITTFGQMALQWIERKVNEYLNEVCGTEGEAF-VLYGDTDSIYVS 628
Query: 662 CN 663
            +
Sbjct: 629 AD 630

>pdb|2DTU|A Chain A, Crystal Structure Of The Beta Hairpin Loop Deletion Variant Of Rb69 Gp43 In Complex With Dna Containing An Abasic Site Analog Length = 896

Iteration: 1
 Score = 53.5 bits (127), Expect = 6e-07,   Method: Compositional matrix adjust.
 Identities = 66/242 (27%), Positives = 94/242 (38%), Gaps = 76/242 (31%)
Query: 496 YSGGLVLEPKKGFYDKFIILMDFNSLYPSIIQEYNICFTTIP----VRMLQD-------- 543
           Y G  V EP    Y K+++  D  SLYPSII++ NI   TI     V  L D        
Sbjct: 384 YPGAFVKEPIPNRY-KYVMSFDLTSLYPSIIRQVNISPETIAGTFKVAPLHDYINAVAER 442
Query: 544 -SDITTLCEYLPEHQVDT-GILPSEIKKLVESRRQVKALM--------------KQPNLS 587
            SD+ +       +  D  G++P+EI K+   R++ K  M                PNLS
Sbjct: 443 PSDVYSCSPNGMMYYKDRDGVVPTEITKVFNQRKEHKGYMLAAQRNGEIIKEALHNPNLS 502
Query: 588 SDLLMQYD--------IRQKALKLTA----------------------------NSMYGC 611
            D  +  D        I++K  KL+A                            NS+YG 
Sbjct: 503 VDEPLDVDYRFDFSDEIKEKIKKLSAKSLNEMLFRAQRTEVAGMTAQINRKLLINSLYGA 562
Query: 612 LGFPNSRFFAQPLAALVTAKGREIL----------LNTKSLVENLNYEVIYGDTDSLMIS 661
           LG    R++    A  +T  G+  L          LN     E   + V+YGDTDS+ +S
Sbjct: 563 LGNVWFRYYDLRNATAITTFGQMALQWIERKVNEYLNEVCGTEGEAF-VLYGDTDSIYVS 621
Query: 662 CN 663
            +
Sbjct: 622 AD 623

>pdb|1Q9Y|A Chain A, Crystal Structure Of Enterobacteria Phage Rb69 Gp43 Dna Polymerase Complexed With 8-Oxoguanosine Containing Dna Length = 906

Iteration: 1
 Score = 53.5 bits (127), Expect = 6e-07,   Method: Compositional matrix adjust.
 Identities = 66/242 (27%), Positives = 94/242 (38%), Gaps = 76/242 (31%)
Query: 496 YSGGLVLEPKKGFYDKFIILMDFNSLYPSIIQEYNICFTTIP----VRMLQD-------- 543
           Y G  V EP    Y K+++  D  SLYPSII++ NI   TI     V  L D        
Sbjct: 394 YPGAFVKEPIPNRY-KYVMSFDLTSLYPSIIRQVNISPETIAGTFKVAPLHDYINAVAER 452
Query: 544 -SDITTLCEYLPEHQVDT-GILPSEIKKLVESRRQVKALM--------------KQPNLS 587
            SD+ +       +  D  G++P+EI K+   R++ K  M                PNLS
Sbjct: 453 PSDVYSCSPNGMMYYKDRDGVVPTEITKVFNQRKEHKGYMLAAQRNGEIIKEALHNPNLS 512
Query: 588 SDLLMQYD--------IRQKALKLTA----------------------------NSMYGC 611
            D  +  D        I++K  KL+A                            NS+YG 
Sbjct: 513 VDEPLDVDYRFDFSDEIKEKIKKLSAKSLNEMLFRAQRTEVAGMTAQINRKLLINSLYGA 572
Query: 612 LGFPNSRFFAQPLAALVTAKGREIL----------LNTKSLVENLNYEVIYGDTDSLMIS 661
           LG    R++    A  +T  G+  L          LN     E   + V+YGDTDS+ +S
Sbjct: 573 LGNVWFRYYDLRNATAITTFGQMALQWIERKVNEYLNEVCGTEGEAF-VLYGDTDSIYVS 631
Query: 662 CN 663
            +
Sbjct: 632 AD 633

>pdb|3CQ8|A Chain A, Ternary Complex Of The L415f Mutant Rb69 Exo(-)polymerase Length = 903

Iteration: 1
 Score = 52.0 bits (123), Expect = 2e-06,   Method: Compositional matrix adjust.
 Identities = 65/242 (26%), Positives = 93/242 (38%), Gaps = 76/242 (31%)
Query: 496 YSGGLVLEPKKGFYDKFIILMDFNSLYPSIIQEYNICFTTIP----VRMLQD-------- 543
           Y G  V EP    Y K+++  D  S YPSII++ NI   TI     V  L D        
Sbjct: 391 YPGAFVKEPIPNRY-KYVMSFDLTSFYPSIIRQVNISPETIAGTFKVAPLHDYINAVAER 449
Query: 544 -SDITTLCEYLPEHQVDT-GILPSEIKKLVESRRQVKALM--------------KQPNLS 587
            SD+ +       +  D  G++P+EI K+   R++ K  M                PNLS
Sbjct: 450 PSDVYSCSPNGMMYYKDRDGVVPTEITKVFNQRKEHKGYMLAAQRNGEIIKEALHNPNLS 509
Query: 588 SDLLMQYD--------IRQKALKLTA----------------------------NSMYGC 611
            D  +  D        I++K  KL+A                            NS+YG 
Sbjct: 510 VDEPLDVDYRFDFSDEIKEKIKKLSAKSLNEMLFRAQRTEVAGMTAQINRKLLINSLYGA 569
Query: 612 LGFPNSRFFAQPLAALVTAKGREIL----------LNTKSLVENLNYEVIYGDTDSLMIS 661
           LG    R++    A  +T  G+  L          LN     E   + V+YGDTDS+ +S
Sbjct: 570 LGNVWFRYYDLRNATAITTFGQMALQWIERKVNEYLNEVCGTEGEAF-VLYGDTDSIYVS 628
Query: 662 CN 663
            +
Sbjct: 629 AD 630

>pdb|3SUQ|A Chain A, Rb69 Dna Polymerase (Y567a) Ternary Complex With Dctp Opposite 2ap (At Rich Sequence) Length = 897

Iteration: 1
 Score = 50.4 bits (119), Expect = 6e-06,   Method: Compositional matrix adjust.
 Identities = 65/242 (26%), Positives = 93/242 (38%), Gaps = 76/242 (31%)
Query: 496 YSGGLVLEPKKGFYDKFIILMDFNSLYPSIIQEYNICFTTIP----VRMLQD-------- 543
           Y G  V EP    Y K+++  D  SLYPSII++ NI   TI     V  L D        
Sbjct: 391 YPGAFVKEPIPNRY-KYVMSFDLTSLYPSIIRQVNISPETIAGTFKVAPLHDYINAVAER 449
Query: 544 -SDITTLCEYLPEHQVDT-GILPSEIKKLVESRRQVKALM--------------KQPNLS 587
            SD+ +       +  D  G++P+EI K+   R++ K  M                PNLS
Sbjct: 450 PSDVYSCSPNGMMYYKDRDGVVPTEITKVFNQRKEHKGYMLAAQRNGEIIKEALHNPNLS 509
Query: 588 SDLLMQYD--------IRQKALKLTA----------------------------NSMYGC 611
            D  +  D        I++K  KL+A                            NS+ G 
Sbjct: 510 VDEPLDVDYRFDFSDEIKEKIKKLSAKSLNEMLFRAQRTEVAGMTAQINRKLLINSLAGA 569
Query: 612 LGFPNSRFFAQPLAALVTAKGREIL----------LNTKSLVENLNYEVIYGDTDSLMIS 661
           LG    R++    A  +T  G+  L          LN     E   + V+YGDTDS+ +S
Sbjct: 570 LGNVWFRYYDLRNATAITTFGQMALQWIERKVNEYLNEVCGTEGEAF-VLYGDTDSIYVS 628
Query: 662 CN 663
            +
Sbjct: 629 AD 630

>pdb|3LZI|A Chain A, Rb69 Dna Polymerase (Y567a) Ternary Complex With Datp Opposite 7,8- Dihydro-8-Oxoguanine Length = 903

Iteration: 1
 Score = 50.1 bits (118), Expect = 6e-06,   Method: Compositional matrix adjust.
 Identities = 65/242 (26%), Positives = 93/242 (38%), Gaps = 76/242 (31%)
Query: 496 YSGGLVLEPKKGFYDKFIILMDFNSLYPSIIQEYNICFTTIP----VRMLQD-------- 543
           Y G  V EP    Y K+++  D  SLYPSII++ NI   TI     V  L D        
Sbjct: 391 YPGAFVKEPIPNRY-KYVMSFDLTSLYPSIIRQVNISPETIAGTFKVAPLHDYINAVAER 449
Query: 544 -SDITTLCEYLPEHQVDT-GILPSEIKKLVESRRQVKALM--------------KQPNLS 587
            SD+ +       +  D  G++P+EI K+   R++ K  M                PNLS
Sbjct: 450 PSDVYSCSPNGMMYYKDRDGVVPTEITKVFNQRKEHKGYMLAAQRNGEIIKEALHNPNLS 509
Query: 588 SDLLMQYD--------IRQKALKLTA----------------------------NSMYGC 611
            D  +  D        I++K  KL+A                            NS+ G 
Sbjct: 510 VDEPLDVDYRFDFSDEIKEKIKKLSAKSLNEMLFRAQRTEVAGMTAQINRKLLINSLAGA 569
Query: 612 LGFPNSRFFAQPLAALVTAKGREIL----------LNTKSLVENLNYEVIYGDTDSLMIS 661
           LG    R++    A  +T  G+  L          LN     E   + V+YGDTDS+ +S
Sbjct: 570 LGNVWFRYYDLRNATAITTFGQMALQWIERKVNEYLNEVCGTEGEAF-VLYGDTDSIYVS 628
Query: 662 CN 663
            +
Sbjct: 629 AD 630

>pdb|3RWU|A Chain A, Rb69 Dna Polymerase (Y567a) Ternary Complex With Datp Opposite Difluorotoluene Nucleoside Length = 901

Iteration: 1
 Score = 50.1 bits (118), Expect = 6e-06,   Method: Compositional matrix adjust.
 Identities = 65/242 (26%), Positives = 93/242 (38%), Gaps = 76/242 (31%)
Query: 496 YSGGLVLEPKKGFYDKFIILMDFNSLYPSIIQEYNICFTTIP----VRMLQD-------- 543
           Y G  V EP    Y K+++  D  SLYPSII++ NI   TI     V  L D        
Sbjct: 391 YPGAFVKEPIPNRY-KYVMSFDLTSLYPSIIRQVNISPETIAGTFKVAPLHDYINAVAER 449
Query: 544 -SDITTLCEYLPEHQVDT-GILPSEIKKLVESRRQVKALM--------------KQPNLS 587
            SD+ +       +  D  G++P+EI K+   R++ K  M                PNLS
Sbjct: 450 PSDVYSCSPNGMMYYKDRDGVVPTEITKVFNQRKEHKGYMLAAQRNGEIIKEALHNPNLS 509
Query: 588 SDLLMQYD--------IRQKALKLTA----------------------------NSMYGC 611
            D  +  D        I++K  KL+A                            NS+ G 
Sbjct: 510 VDEPLDVDYRFDFSDEIKEKIKKLSAKSLNEMLFRAQRTEVAGMTAQINRKLLINSLAGA 569
Query: 612 LGFPNSRFFAQPLAALVTAKGREIL----------LNTKSLVENLNYEVIYGDTDSLMIS 661
           LG    R++    A  +T  G+  L          LN     E   + V+YGDTDS+ +S
Sbjct: 570 LGNVWFRYYDLRNATAITTFGQMALQWIERKVNEYLNEVCGTEGEAF-VLYGDTDSIYVS 628
Query: 662 CN 663
            +
Sbjct: 629 AD 630

>pdb|3SUO|A Chain A, Rb69 Dna Polymerase (Y567a) Ternary Complex With Dttp Opposite 2ap (Gc Rich Sequence) Length = 900

Iteration: 1
 Score = 50.1 bits (118), Expect = 6e-06,   Method: Compositional matrix adjust.
 Identities = 65/242 (26%), Positives = 93/242 (38%), Gaps = 76/242 (31%)
Query: 496 YSGGLVLEPKKGFYDKFIILMDFNSLYPSIIQEYNICFTTIP----VRMLQD-------- 543
           Y G  V EP    Y K+++  D  SLYPSII++ NI   TI     V  L D        
Sbjct: 391 YPGAFVKEPIPNRY-KYVMSFDLTSLYPSIIRQVNISPETIAGTFKVAPLHDYINAVAER 449
Query: 544 -SDITTLCEYLPEHQVDT-GILPSEIKKLVESRRQVKALM--------------KQPNLS 587
            SD+ +       +  D  G++P+EI K+   R++ K  M                PNLS
Sbjct: 450 PSDVYSCSPNGMMYYKDRDGVVPTEITKVFNQRKEHKGYMLAAQRNGEIIKEALHNPNLS 509
Query: 588 SDLLMQYD--------IRQKALKLTA----------------------------NSMYGC 611
            D  +  D        I++K  KL+A                            NS+ G 
Sbjct: 510 VDEPLDVDYRFDFSDEIKEKIKKLSAKSLNEMLFRAQRTEVAGMTAQINRKLLINSLAGA 569
Query: 612 LGFPNSRFFAQPLAALVTAKGREIL----------LNTKSLVENLNYEVIYGDTDSLMIS 661
           LG    R++    A  +T  G+  L          LN     E   + V+YGDTDS+ +S
Sbjct: 570 LGNVWFRYYDLRNATAITTFGQMALQWIERKVNEYLNEVCGTEGEAF-VLYGDTDSIYVS 628
Query: 662 CN 663
            +
Sbjct: 629 AD 630

>pdb|3SUN|A Chain A, Rb69 Dna Polymerase (Y567a) Ternary Complex With Dttp Opposite 2ap (At Rich Sequence) Length = 895

Iteration: 1
 Score = 50.1 bits (118), Expect = 6e-06,   Method: Compositional matrix adjust.
 Identities = 65/242 (26%), Positives = 93/242 (38%), Gaps = 76/242 (31%)
Query: 496 YSGGLVLEPKKGFYDKFIILMDFNSLYPSIIQEYNICFTTIP----VRMLQD-------- 543
           Y G  V EP    Y K+++  D  SLYPSII++ NI   TI     V  L D        
Sbjct: 391 YPGAFVKEPIPNRY-KYVMSFDLTSLYPSIIRQVNISPETIAGTFKVAPLHDYINAVAER 449
Query: 544 -SDITTLCEYLPEHQVDT-GILPSEIKKLVESRRQVKALM--------------KQPNLS 587
            SD+ +       +  D  G++P+EI K+   R++ K  M                PNLS
Sbjct: 450 PSDVYSCSPNGMMYYKDRDGVVPTEITKVFNQRKEHKGYMLAAQRNGEIIKEALHNPNLS 509
Query: 588 SDLLMQYD--------IRQKALKLTA----------------------------NSMYGC 611
            D  +  D        I++K  KL+A                            NS+ G 
Sbjct: 510 VDEPLDVDYRFDFSDEIKEKIKKLSAKSLNEMLFRAQRTEVAGMTAQINRKLLINSLAGA 569
Query: 612 LGFPNSRFFAQPLAALVTAKGREIL----------LNTKSLVENLNYEVIYGDTDSLMIS 661
           LG    R++    A  +T  G+  L          LN     E   + V+YGDTDS+ +S
Sbjct: 570 LGNVWFRYYDLRNATAITTFGQMALQWIERKVNEYLNEVCGTEGEAF-VLYGDTDSIYVS 628
Query: 662 CN 663
            +
Sbjct: 629 AD 630

>pdb|3QEP|A Chain A, Rb69 Dna Polymerase (L561aS565GY567A) TERNARY COMPLEX WITH DTTP Opposite Difluorotoluene Nucleoside Length = 903

Iteration: 1
 Score = 48.5 bits (114), Expect = 2e-05,   Method: Compositional matrix adjust.
 Identities = 64/242 (26%), Positives = 92/242 (38%), Gaps = 76/242 (31%)
Query: 496 YSGGLVLEPKKGFYDKFIILMDFNSLYPSIIQEYNICFTTIP----VRMLQD-------- 543
           Y G  V EP    Y K+++  D  SLYPSII++ NI   TI     V  L D        
Sbjct: 391 YPGAFVKEPIPNRY-KYVMSFDLTSLYPSIIRQVNISPETIAGTFKVAPLHDYINAVAER 449
Query: 544 -SDITTLCEYLPEHQVDT-GILPSEIKKLVESRRQVKALM--------------KQPNLS 587
            SD+ +       +  D  G++P+EI K+   R++ K  M                PNLS
Sbjct: 450 PSDVYSCSPNGMMYYKDRDGVVPTEITKVFNQRKEHKGYMLAAQRNGEIIKEALHNPNLS 509
Query: 588 SDLLMQYD--------IRQKALKLTA----------------------------NSMYGC 611
            D  +  D        I++K  KL+A                            N + G 
Sbjct: 510 VDEPLDVDYRFDFSDEIKEKIKKLSAKSLNEMLFRAQRTEVAGMTAQINRKALINGLAGA 569
Query: 612 LGFPNSRFFAQPLAALVTAKGREIL----------LNTKSLVENLNYEVIYGDTDSLMIS 661
           LG    R++    A  +T  G+  L          LN     E   + V+YGDTDS+ +S
Sbjct: 570 LGNVWFRYYDLRNATAITTFGQMALQWIERKVNEYLNEVCGTEGEAF-VLYGDTDSIYVS 628
Query: 662 CN 663
            +
Sbjct: 629 AD 630

>pdb|4DTJ|A Chain A, Rb69 Dna Polymerase Ternary Complex With Dttp Opposite An Abasic Site And DdtDA AS THE PENULTIMATE BASE-Pair Length = 901

Iteration: 1
 Score = 48.5 bits (114), Expect = 2e-05,   Method: Compositional matrix adjust.
 Identities = 64/242 (26%), Positives = 92/242 (38%), Gaps = 76/242 (31%)
Query: 496 YSGGLVLEPKKGFYDKFIILMDFNSLYPSIIQEYNICFTTIP----VRMLQD-------- 543
           Y G  V EP    Y K+++  D  SLYPSII++ NI   TI     V  L D        
Sbjct: 391 YPGAFVKEPIPNRY-KYVMSFDLTSLYPSIIRQVNISPETIAGTFKVAPLHDYINAVAER 449
Query: 544 -SDITTLCEYLPEHQVDT-GILPSEIKKLVESRRQVKALM--------------KQPNLS 587
            SD+ +       +  D  G++P+EI K+   R++ K  M                PNLS
Sbjct: 450 PSDVYSCSPNGMMYYKDRDGVVPTEITKVFNQRKEHKGYMLAAQRNGEIIKEALHNPNLS 509
Query: 588 SDLLMQYD--------IRQKALKLTA----------------------------NSMYGC 611
            D  +  D        I++K  KL+A                            N + G 
Sbjct: 510 VDEPLDVDYRFDFSDEIKEKIKKLSAKSLNEMLFRAQRTEVAGMTAQINRKALINGLAGA 569
Query: 612 LGFPNSRFFAQPLAALVTAKGREIL----------LNTKSLVENLNYEVIYGDTDSLMIS 661
           LG    R++    A  +T  G+  L          LN     E   + V+YGDTDS+ +S
Sbjct: 570 LGNVWFRYYDLRNATAITTFGQMALQWIERKVNEYLNEVCGTEGEAF-VLYGDTDSIYVS 628
Query: 662 CN 663
            +
Sbjct: 629 AD 630

>pdb|3CFO|A Chain A, Triple Mutant Apo Structure Length = 909

Iteration: 1
 Score = 48.5 bits (114), Expect = 2e-05,   Method: Compositional matrix adjust.
 Identities = 64/242 (26%), Positives = 92/242 (38%), Gaps = 76/242 (31%)
Query: 496 YSGGLVLEPKKGFYDKFIILMDFNSLYPSIIQEYNICFTTIP----VRMLQD-------- 543
           Y G  V EP    Y K+++  D  SLYPSII++ NI   TI     V  L D        
Sbjct: 391 YPGAFVKEPIPNRY-KYVMSFDLTSLYPSIIRQVNISPETIAGTFKVAPLHDYINAVAER 449
Query: 544 -SDITTLCEYLPEHQVDT-GILPSEIKKLVESRRQVKALM--------------KQPNLS 587
            SD+ +       +  D  G++P+EI K+   R++ K  M                PNLS
Sbjct: 450 PSDVYSCSPNGMMYYKDRDGVVPTEITKVFNQRKEHKGYMLAAQRNGEIIKEALHNPNLS 509
Query: 588 SDLLMQYD--------IRQKALKLTA----------------------------NSMYGC 611
            D  +  D        I++K  KL+A                            N + G 
Sbjct: 510 VDEPLDVDYRFDFSDEIKEKIKKLSAKSLNEMLFRAQRTEVAGMTAQINRKALINGLAGA 569
Query: 612 LGFPNSRFFAQPLAALVTAKGREIL----------LNTKSLVENLNYEVIYGDTDSLMIS 661
           LG    R++    A  +T  G+  L          LN     E   + V+YGDTDS+ +S
Sbjct: 570 LGNVWFRYYDLRNATAITTFGQMALQWIERKVNEYLNEVCGTEGEAF-VLYGDTDSIYVS 628
Query: 662 CN 663
            +
Sbjct: 629 AD 630

>pdb|3NE6|A Chain A, Rb69 Dna Polymerase (S565gY567A) TERNARY COMPLEX WITH DCTP OPPOSITE Dg Length = 903

Iteration: 1
 Score = 48.5 bits (114), Expect = 2e-05,   Method: Compositional matrix adjust.
 Identities = 64/242 (26%), Positives = 92/242 (38%), Gaps = 76/242 (31%)
Query: 496 YSGGLVLEPKKGFYDKFIILMDFNSLYPSIIQEYNICFTTIP----VRMLQD-------- 543
           Y G  V EP    Y K+++  D  SLYPSII++ NI   TI     V  L D        
Sbjct: 391 YPGAFVKEPIPNRY-KYVMSFDLTSLYPSIIRQVNISPETIAGTFKVAPLHDYINAVAER 449
Query: 544 -SDITTLCEYLPEHQVDT-GILPSEIKKLVESRRQVKALM--------------KQPNLS 587
            SD+ +       +  D  G++P+EI K+   R++ K  M                PNLS
Sbjct: 450 PSDVYSCSPNGMMYYKDRDGVVPTEITKVFNQRKEHKGYMLAAQRNGEIIKEALHNPNLS 509
Query: 588 SDLLMQYD--------IRQKALKLTA----------------------------NSMYGC 611
            D  +  D        I++K  KL+A                            N + G 
Sbjct: 510 VDEPLDVDYRFDFSDEIKEKIKKLSAKSLNEMLFRAQRTEVAGMTAQINRKLLINGLAGA 569
Query: 612 LGFPNSRFFAQPLAALVTAKGREIL----------LNTKSLVENLNYEVIYGDTDSLMIS 661
           LG    R++    A  +T  G+  L          LN     E   + V+YGDTDS+ +S
Sbjct: 570 LGNVWFRYYDLRNATAITTFGQMALQWIERKVNEYLNEVCGTEGEAF-VLYGDTDSIYVS 628
Query: 662 CN 663
            +
Sbjct: 629 AD 630

>pdb|3SCX|A Chain A, Rb69 Dna Polymerase Triple Mutant(L561aS565GY567A) TERNARY COMPLEX With Dupnpp And A Deoxy-Terminated Primer In The Presence Of Ca2+ Length = 903

Iteration: 1
 Score = 48.5 bits (114), Expect = 2e-05,   Method: Compositional matrix adjust.
 Identities = 64/242 (26%), Positives = 92/242 (38%), Gaps = 76/242 (31%)
Query: 496 YSGGLVLEPKKGFYDKFIILMDFNSLYPSIIQEYNICFTTIP----VRMLQD-------- 543
           Y G  V EP    Y K+++  D  SLYPSII++ NI   TI     V  L D        
Sbjct: 391 YPGAFVKEPIPNRY-KYVMSFDLTSLYPSIIRQVNISPETIAGTFKVAPLHDYINAVAER 449
Query: 544 -SDITTLCEYLPEHQVDT-GILPSEIKKLVESRRQVKALM--------------KQPNLS 587
            SD+ +       +  D  G++P+EI K+   R++ K  M                PNLS
Sbjct: 450 PSDVYSCSPNGMMYYKDRDGVVPTEITKVFNQRKEHKGYMLAAQRNGEIIKEALHNPNLS 509
Query: 588 SDLLMQYD--------IRQKALKLTA----------------------------NSMYGC 611
            D  +  D        I++K  KL+A                            N + G 
Sbjct: 510 VDEPLDVDYRFDFSDEIKEKIKKLSAKSLNEMLFRAQRTEVAGMTAQINRKALINGLAGA 569
Query: 612 LGFPNSRFFAQPLAALVTAKGREIL----------LNTKSLVENLNYEVIYGDTDSLMIS 661
           LG    R++    A  +T  G+  L          LN     E   + V+YGDTDS+ +S
Sbjct: 570 LGNVWFRYYDLRNATAITTFGQMALQWIERKVNEYLNEVCGTEGEAF-VLYGDTDSIYVS 628
Query: 662 CN 663
            +
Sbjct: 629 AD 630

>pdb|3SPZ|A Chain A, Dna Polymerase(L415aL561AS565GY567A) TERNARY COMPLEX WITH DUPCPP Opposite Da (Ca2+) Length = 903

Iteration: 1
 Score = 47.0 bits (110), Expect = 6e-05,   Method: Compositional matrix adjust.
 Identities = 63/242 (26%), Positives = 91/242 (37%), Gaps = 76/242 (31%)
Query: 496 YSGGLVLEPKKGFYDKFIILMDFNSLYPSIIQEYNICFTTIP----VRMLQD-------- 543
           Y G  V EP    Y K+++  D  S YPSII++ NI   TI     V  L D        
Sbjct: 391 YPGAFVKEPIPNRY-KYVMSFDLTSAYPSIIRQVNISPETIAGTFKVAPLHDYINAVAER 449
Query: 544 -SDITTLCEYLPEHQVDT-GILPSEIKKLVESRRQVKALM--------------KQPNLS 587
            SD+ +       +  D  G++P+EI K+   R++ K  M                PNLS
Sbjct: 450 PSDVYSCSPNGMMYYKDRDGVVPTEITKVFNQRKEHKGYMLAAQRNGEIIKEALHNPNLS 509
Query: 588 SDLLMQYD--------IRQKALKLTA----------------------------NSMYGC 611
            D  +  D        I++K  KL+A                            N + G 
Sbjct: 510 VDEPLDVDYRFDFSDEIKEKIKKLSAKSLNEMLFRAQRTEVAGMTAQINRKALINGLAGA 569
Query: 612 LGFPNSRFFAQPLAALVTAKGREIL----------LNTKSLVENLNYEVIYGDTDSLMIS 661
           LG    R++    A  +T  G+  L          LN     E   + V+YGDTDS+ +S
Sbjct: 570 LGNVWFRYYDLRNATAITTFGQMALQWIERKVNEYLNEVCGTEGEAF-VLYGDTDSIYVS 628
Query: 662 CN 663
            +
Sbjct: 629 AD 630

>pdb|3SPY|A Chain A, Rb69 Dna Polymerase(L415aL561AS565GY567A) TERNARY COMPLEX WITH Dupcpp Opposite Da Length = 901

Iteration: 1
 Score = 46.6 bits (109), Expect = 6e-05,   Method: Compositional matrix adjust.
 Identities = 63/242 (26%), Positives = 91/242 (37%), Gaps = 76/242 (31%)
Query: 496 YSGGLVLEPKKGFYDKFIILMDFNSLYPSIIQEYNICFTTIP----VRMLQD-------- 543
           Y G  V EP    Y K+++  D  S YPSII++ NI   TI     V  L D        
Sbjct: 391 YPGAFVKEPIPNRY-KYVMSFDLTSAYPSIIRQVNISPETIAGTFKVAPLHDYINAVAER 449
Query: 544 -SDITTLCEYLPEHQVDT-GILPSEIKKLVESRRQVKALM--------------KQPNLS 587
            SD+ +       +  D  G++P+EI K+   R++ K  M                PNLS
Sbjct: 450 PSDVYSCSPNGMMYYKDRDGVVPTEITKVFNQRKEHKGYMLAAQRNGEIIKEALHNPNLS 509
Query: 588 SDLLMQYD--------IRQKALKLTA----------------------------NSMYGC 611
            D  +  D        I++K  KL+A                            N + G 
Sbjct: 510 VDEPLDVDYRFDFSDEIKEKIKKLSAKSLNEMLFRAQRTEVAGMTAQINRKALINGLAGA 569
Query: 612 LGFPNSRFFAQPLAALVTAKGREIL----------LNTKSLVENLNYEVIYGDTDSLMIS 661
           LG    R++    A  +T  G+  L          LN     E   + V+YGDTDS+ +S
Sbjct: 570 LGNVWFRYYDLRNATAITTFGQMALQWIERKVNEYLNEVCGTEGEAF-VLYGDTDSIYVS 628
Query: 662 CN 663
            +
Sbjct: 629 AD 630

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	1030
3iay_A	919	DNA polymerase delta catalytic subunit; protein-DN	100.0
2gv9_A	1193	DNA polymerase; polymerase alpha fold, transferase	100.0
1qht_A	775	Protein (DNA polymerase); archaea, hyperthermostab	100.0
3k59_A	786	POL II, DNA polymerase II; protein-DNA complex, DN	100.0
1s5j_A	847	DNA polymerase I; replication, disulfide bonds, tr	100.0
3qex_A	903	DNA polymerase, GP43; difluorotoluene nucleoside;	100.0
2py5_A	575	DNA polymerase; protein-DNA complex, replication,	99.88
1noy_A	388	Protein (DNA polymerase (E.C.2.7.7.7)); exonucleas	98.67

>3iay_A DNA polymerase delta catalytic subunit; protein-DNA complex, DNA replication, DNA-BI DNA-directed DNA polymerase, exonuclease, hydrolase; HET: DNA DOC DCP; 2.00A {Saccharomyces cerevisiae}

Probab=100.00  E-value=1e-86  Score=827.10  Aligned_cols=388  Identities=27%  Similarity=0.395  Sum_probs=346.2

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHhcchHHHHHHHHHhCCcchhhccCchhHHHHHHHHHHHhhcCeeccCCccccCcCCCcc
Q psy6283         402 IVEFIKFTMLHSSYIIKIMCELNVLPLAIQITNVCGNVLSRTLMGGRSERNEFLLLHAFHEKSYVLPDKQYGKNKKEGEE  481 (1030)
Q Consensus       402 l~~lv~Y~~~Da~l~~~L~~kl~vlpl~~~lt~iaG~~~srtl~~gr~~r~E~lLL~~~~~~~yivPdk~~~kk~~~~~d  481 (1030)
                      +..|+.||++||.++++|+.++++++++.++|+++|++|+++++.|++.+++++|||++++.|||+|++...        
T Consensus       444 ~~~L~~Y~~~Da~l~~~L~~kl~~l~~~~elArl~Gi~~~~vl~rG~qi~ves~Llr~a~~~~~ilP~~~~~--------  515 (919)
T 3iay_A          444 RRRLAVYCLKDAYLPLRLMEKLMALVNYTEMARVTGVPFSYLLARGQQIKVVSQLFRKCLEIDTVIPNMQSQ--------  515 (919)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHTTHHHHHHHHHHHHCCCHHHHHHSCHHHHHHHHHHHHHHHTTEECBCCCCC--------
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHhhhHHHHHHHHHcCCCHHHhhcccchHHHHHHHHHHHhhCCeeCCCcccc--------
Confidence            458999999999999999999999999999999999999999999999999999999999999999987531        


Q ss_pred             ccccccCCCCCCccccCceeeccccccccceEEEeeccccChhHHHHhccccccccccCC------C-ccccccccCC--
Q psy6283         482 TGEANKGKGRKKAAYSGGLVLEPKKGFYDKFIILMDFNSLYPSIIQEYNICFTTIPVRML------Q-DSDITTLCEY--  552 (1030)
Q Consensus       482 ~~~~~~~~~~~~~~Y~GGlVleP~~GlY~~~V~vLDFnSLYPSII~~~NIc~tTv~~~~~------d-~~~i~~~~p~--  552 (1030)
                               ....+|+||+|++|++|+|++||++|||+|||||||++|||||||+++..+      . ++++. .+|.  
T Consensus       516 ---------~~~~~y~Gg~V~eP~~G~y~~pV~~lDF~SLYPSIi~~~Nlc~~Tl~~~~~~~~~~~~~~~~~~-~~p~g~  585 (919)
T 3iay_A          516 ---------ASDDQYEGATVIEPIRGYYDVPIATLDFNSLYPSIMMAHNLCYTTLCNKATVERLNLKIDEDYV-ITPNGD  585 (919)
T ss_dssp             ---------CCSSCCCCCCBCCCCCEEECSCEEEEEETTHHHHHHHHTTCSGGGEECHHHHHHTTCCBTTTEE-ECTTSC
T ss_pred             ---------cccccCCCCEEecCCCCceeccEEEEEecccchHHHHhcCcCcccccccchhhhcCCCCCccee-eCCCCc
Confidence                     124579999999999999999999999999999999999999999986431      0 01110 1221  


Q ss_pred             -CCCccccCCcchHHHHHHHHHHHHHHHHhcCCCCChHHHHhhHHHHHHhccccccccccCCCCCCCCCCHHHHHHHHHH
Q psy6283         553 -LPEHQVDTGILPSEIKKLVESRRQVKALMKQPNLSSDLLMQYDIRQKALKLTANSMYGCLGFPNSRFFAQPLAALVTAK  631 (1030)
Q Consensus       553 -~p~~~~~~GIlP~iL~~Ll~~R~~vKk~mk~~~~~~~~~~~~d~rQ~AlKl~aNS~YG~lG~~~srfy~~~lA~~IT~~  631 (1030)
                       |..++.+.||||.+|..|++.|+++|+.|++ +.+|.++.+||++|+|+|++|||+|||||++++||||.++|++||++
T Consensus       586 ~f~~~~~~~gilp~~l~~ll~~R~~~K~~mk~-~~d~~~~~~ld~~Q~AlKi~~NS~YG~~G~~~~r~~~~~iA~siT~~  664 (919)
T 3iay_A          586 YFVTTKRRRGILPIILDELISARKRAKKDLRD-EKDPFKRDVLNGRQLALKISANSVYGFTGATVGKLPCLAISSSVTAY  664 (919)
T ss_dssp             EEECTTTCCCHHHHHHHHHHHHHHHHHHHHHT-CCCHHHHHHHHHHHHHHHHHHHHHHHHHTCSSSSCCCHHHHHHHHHH
T ss_pred             EEeccCCCCCchHHHHHHHHHHHHHHHHHHhh-cCChHHHHHHHHHHHhhcccccccccccccccCccCCHHHHHHHHHH
Confidence             3334568999999999999999999999998 67999999999999999999999999999999999999999999999


Q ss_pred             hHHHHHHHHHHhhhc---------cceeEEecCcceeeecCCCCHHHHHHHHHHHHHHHhcccc-eeEEeecchhhhhhh
Q psy6283         632 GREILLNTKSLVENL---------NYEVIYGDTDSLMISCNVNDYDSVFKIGNQIKSECNKLYK-QLELDIDGVYKYMLL  701 (1030)
Q Consensus       632 GR~iL~~tkelve~~---------g~~VIYGDTDSI~V~~~~~d~eea~~ig~~i~~~Vn~~~~-~leLe~E~vf~~lll  701 (1030)
                      ||++|+.|++++++.         |++|||||||||||+++..+.++++++|+++++.||+.|+ +++||||++|.++||
T Consensus       665 GR~~l~~t~~~ie~~~~~~~g~~~~~~ViYGDTDSvfv~~~~~~~~~~~~~g~~~~~~v~~~~~~~i~le~E~vy~~~ll  744 (919)
T 3iay_A          665 GRTMILKTKTAVQEKYCIKNGYKHDAVVVYGDTDSVMVKFGTTDLKEAMDLGTEAAKYVSTLFKHPINLEFEKAYFPYLL  744 (919)
T ss_dssp             HHHHHHHHHHHHHHHSSGGGTCSSCCEEEECBSSEEEEECSCSCHHHHHHHHHHHHHHHHTTSCTTCCEEEEEEEEEEEE
T ss_pred             HHHHHHHHHHHHHHhhccccCCCCCeEEEEEcCCeeEEEcCCCCHHHHHHHHHHHHHHHHHhCCCCEEEEEeeeehhhhh
Confidence            999999999999986         8999999999999999999999999999999999999884 899999999999999


Q ss_pred             cccccceEEeeeecCCCceeeeceeeeeeeeeCChHHHHHHHHHHHHHHHhccCCCCCCChhHHHHHHHHHHHHHHHHhh
Q psy6283         702 LKKKKYAALSISKLSNGKMICSQEIKGVDVVRRDWSQLASEAGKFVISQILDEQSYTDYSLDDRLQNIHEHMKKIRTDLD  781 (1030)
Q Consensus       702 l~KKrYa~l~~~~~~dG~~~~~~e~KGle~vRRD~~~l~k~~~~~vL~~IL~~~~~~~~~~e~~v~~I~~~l~~~~~~l~  781 (1030)
                      ++||||||+.+++. ++  .+++++||+++||||||+|++++++.+|+.||.+.     +++.    +.+++.+++.+|+
T Consensus       745 ~~KKrYag~~~~~~-~~--~~~~~~KGie~vRrD~~~~~k~~~~~~l~~ll~~~-----~~~~----~~~~~~~~~~~l~  812 (919)
T 3iay_A          745 INKKRYAGLFWTNP-DK--FDKLDQKGLASVRRDSCSLVSIVMNKVLKKILIER-----NVDG----ALAFVRETINDIL  812 (919)
T ss_dssp             EETTEEEEEEESSS-SS--CCEEEEESSGGGCTTSCHHHHHHHHHHHHHHHTTC-----CHHH----HHHHHHHHHHHHH
T ss_pred             hcccceEEEEeccC-CC--CceEEEEeEEEEeCCchHHHHHHHHHHHHHHHcCC-----CHHH----HHHHHHHHHHHHH
Confidence            99999999987643 21  24679999999999999999999999999999988     7654    4566777788999


Q ss_pred             CCCcChhhhHHhhcccCCCCCCcchHHHHHHHHHHcCCcc
Q psy6283         782 NGFVPLTLLEITKQLTKAPEGGKVCITQIRLSRNRRGRRR  821 (1030)
Q Consensus       782 ~g~vpl~~lvItk~LsK~p~~~~~pHV~vA~r~~~~g~~~  821 (1030)
                      +|++|+++|+|+|+|+| -+...+|||+||+||++++|..
T Consensus       813 ~~~~~~~~lvi~k~l~k-~Y~~~~phv~~A~r~~~~~~~~  851 (919)
T 3iay_A          813 HNRVDISKLIISKTLAP-NYTNPQPHAVLAERMKRREGVG  851 (919)
T ss_dssp             TTCSCGGGGCEEEECCS-CCSSCCHHHHHHHHHHHHHSCC
T ss_pred             cCCCCHHHeEEeeeccc-CCCCCChHHHHHHHHHHhcCCC
Confidence            99999999999999999 3336799999999999986443

>2gv9_A DNA polymerase; polymerase alpha fold, transferase; HET: DNA; 2.68A {Human herpesvirus 1} PDB: 1dml_B*

Probab=100.00  E-value=3.2e-79  Score=773.48  Aligned_cols=401  Identities=24%  Similarity=0.419  Sum_probs=308.5

Q ss_pred             HHHHHHHHHHHHHHHHHHHHh-cchHHHHHHHHHhCCcchhhccCchhHHHHHHHHHHHhhcCeeccCCccccCcC----
Q psy6283         403 VEFIKFTMLHSSYIIKIMCEL-NVLPLAIQITNVCGNVLSRTLMGGRSERNEFLLLHAFHEKSYVLPDKQYGKNKK----  477 (1030)
Q Consensus       403 ~~lv~Y~~~Da~l~~~L~~kl-~vlpl~~~lt~iaG~~~srtl~~gr~~r~E~lLL~~~~~~~yivPdk~~~kk~~----  477 (1030)
                      ..|+.||++||.++++|+.++ .++.+ .+||+|+|++|++++++|++.|+|++|||++++.|||+|++......+    
T Consensus       530 ~~L~~Ycl~Da~lt~~L~~kl~~~lel-~elarl~gi~~~~vl~~G~~irves~Ll~~a~~~~~ilP~k~~~~~~~~~~~  608 (1193)
T 2gv9_A          530 GVIGEYCIQDSLLVGQLFFKFLPHLEL-SAVARLAGINITRTIYDGQQIRVFTCLLRLADQKGFILPDTQGRFRGAGGEA  608 (1193)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHCHHHHH-HHHHHHHTSCGGGTTSSCSTHHHHHHHHHHHHHHTEECBCCC----------
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHH-HHHHHHcCCCHHHHhcCccHHHHHHHHHHHHHHCCEeCCCcccccccccccc
Confidence            468899999999999999996 33444 589999999999999999999999999999999999999986321100    


Q ss_pred             -----C---Ccc-ccc-c-cc----------------CCCCCCccccCceeeccccccccceEEEeeccccChhHHHHhc
Q psy6283         478 -----E---GEE-TGE-A-NK----------------GKGRKKAAYSGGLVLEPKKGFYDKFIILMDFNSLYPSIIQEYN  530 (1030)
Q Consensus       478 -----~---~~d-~~~-~-~~----------------~~~~~~~~Y~GGlVleP~~GlY~~~V~vLDFnSLYPSII~~~N  530 (1030)
                           .   +.+ ..+ + ..                ...+...+|+||+|++|.+|||++||++|||+|||||||++||
T Consensus       609 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~Y~Gg~VleP~~Gly~~pV~vLDF~SLYPSII~a~N  688 (1193)
T 2gv9_A          609 PKRPAAAREDEERPEEEGEDEDEREEGGGEREPEGARETAGRHVGYQGAKVLDPTSGFHVNPVVVFDFASLYPSIIQAHN  688 (1193)
T ss_dssp             --------------------------------------------------CCCCCCEEECSCEEEEEEETHHHHHHHHTT
T ss_pred             cccccccccccccccccccccccccccccccccchhhhccccccccCCCEEeecCCCeeeCcEEEEeccccchHHHHHhc
Confidence                 0   000 000 0 00                0112345899999999999999999999999999999999999


Q ss_pred             cccccccccCCCc------cccccccC-----CCCCccccCCcchHHHHHHHHHHHHHHHHhcCCCCChHHHHhhHHHHH
Q psy6283         531 ICFTTIPVRMLQD------SDITTLCE-----YLPEHQVDTGILPSEIKKLVESRRQVKALMKQPNLSSDLLMQYDIRQK  599 (1030)
Q Consensus       531 Ic~tTv~~~~~d~------~~i~~~~p-----~~p~~~~~~GIlP~iL~~Ll~~R~~vKk~mk~~~~~~~~~~~~d~rQ~  599 (1030)
                      |||||++......      ++.....+     .|.....+.||||.+|+.|+++|+++|+.|++.  ++.++.+||++|+
T Consensus       689 lc~sTl~~~~~~~~~l~~~~dy~~~~~~~~~~~fvk~~~~~gilp~lL~~ll~~Rk~~K~~mk~~--~~~~~~llD~~Ql  766 (1193)
T 2gv9_A          689 LCFSTLSLRADAVAHLEAGKDYLEIEVGGRRLFFVKAHVRESLLSILLRDWLAMRKQIRSRIPQS--SPEEAVLLDKQQA  766 (1193)
T ss_dssp             CCTTTEESCSTTSTTCCTTTTEEEEECSSSEEEEECTTTSCCHHHHHHHHHHHHHHHHHHHGGGS--CHHHHHHHHHHHH
T ss_pred             CCcceeccCchhhccCCCccceeEecCCCCceeeccCccccchHHHHHHHHHHHHHHHHHhcccC--CHHHHHHHHHHHH
Confidence            9999998753210      01100000     133345678999999999999999999999984  7889999999999


Q ss_pred             HhccccccccccCCCCCCCCCCHHHHHHHHHHhHHHHHHHHHHhhh-----------------------ccceeEEecCc
Q psy6283         600 ALKLTANSMYGCLGFPNSRFFAQPLAALVTAKGREILLNTKSLVEN-----------------------LNYEVIYGDTD  656 (1030)
Q Consensus       600 AlKl~aNS~YG~lG~~~srfy~~~lA~~IT~~GR~iL~~tkelve~-----------------------~g~~VIYGDTD  656 (1030)
                      |+|++|||+|||+|+++++|||.++|++||++||+||+.|++++|+                       +|++|||||||
T Consensus       767 AlKi~aNS~YG~~G~~~grlpc~~iA~sVT~~GR~~L~~tk~~IE~~~~~~~~l~~~f~~~~~~~~~~~~g~~VIYGDTD  846 (1193)
T 2gv9_A          767 AIKVVCNSVYGFTGVQHGLLPCLHVAATVTTIGREMLLATREYVHARWAAFEQLLADFPEAADMRAPGPYSMRIIYGDTD  846 (1193)
T ss_dssp             HHHHHHHHHHHHHHCTTSSSCCHHHHHHHHHHHHHHHHHHHHHHHHHHSSHHHHHHHCGGGGGGBCSSCCEEEEEEECSS
T ss_pred             HHHHhhcceecccccccccccCHHHHHHHHHHHHHHHHHHHHHHHhhhcchhhhhhhcccccccccccccccceeeccCC
Confidence            9999999999999999999999999999999999999999999874                       48899999999


Q ss_pred             ceeeecCCCCHHHHHHHHHHHHHHHhcc-c-ceeEEeecchhhhhhhcccccceEEeeeecCCCceeeeceeeeeeeeeC
Q psy6283         657 SLMISCNVNDYDSVFKIGNQIKSECNKL-Y-KQLELDIDGVYKYMLLLKKKKYAALSISKLSNGKMICSQEIKGVDVVRR  734 (1030)
Q Consensus       657 SI~V~~~~~d~eea~~ig~~i~~~Vn~~-~-~~leLe~E~vf~~llll~KKrYa~l~~~~~~dG~~~~~~e~KGle~vRR  734 (1030)
                      ||||.++..+.++++++|++|++.||+. | .+|+||+|++|.+|||++||||||+.+    +|+    +++||+++|||
T Consensus       847 SvfV~~~~~~~~~~~~~g~~i~~~i~~~~~~~~i~LE~Ekvy~~~ll~~KKRYag~~~----~g~----l~~KG~e~vRR  918 (1193)
T 2gv9_A          847 SIFVLCRGLTAAGLTAMGDKMASHISRALFLPPIKLECEKTFTKLLLIAKKKYIGVIY----GGK----MLIKGVDLVRK  918 (1193)
T ss_dssp             EEEEEEETBCSTTHHHHHHHHHHHHHHHHCCTTCEEEEEEEEEEEEEEETTEEEEEET----TSC----EEEESCCSCCT
T ss_pred             ceEEecCCCCHHHHHHHHHHHHHHHHHhccCCCEEEEeceeeHHHhhhccceEEEEec----CCE----eEEECCeeecC
Confidence            9999998888899999999999999974 5 479999999999999999999999963    454    58999999999


Q ss_pred             ChHHHHHHHHHHHHHHHhccCCCCCCChhHHHH--------------------HHHHHHHHHHHHhhCCCcChhhhHHhh
Q psy6283         735 DWSQLASEAGKFVISQILDEQSYTDYSLDDRLQ--------------------NIHEHMKKIRTDLDNGFVPLTLLEITK  794 (1030)
Q Consensus       735 D~~~l~k~~~~~vL~~IL~~~~~~~~~~e~~v~--------------------~I~~~l~~~~~~l~~g~vpl~~lvItk  794 (1030)
                      |||+|++++++.+|+.||.++     +.+++++                    .|+++|.+.+.+|++|.+|+++|+|++
T Consensus       919 D~~~lvk~~~~~vl~~ll~~~-----d~~~a~~~v~~~~~~e~~~~~~~~~~~~i~~~l~~~~~~l~~~~v~i~~lvitk  993 (1193)
T 2gv9_A          919 NNCAFINRTSRALVDLLFYDD-----TVSGAAAALAERPAEEWLARPLPEGLQAFGAVLVDAHRRITDPERDIQDFVLTA  993 (1193)
T ss_dssp             TSCHHHHHHHHHHHHHHHHCH-----HHHHHHHHGGGSCHHHHHHSCCCGGGHHHHHHHHHHHHHHHSSCSCCGGGCBCC
T ss_pred             chHHHHHHHHHHHHHHHHcCC-----CHHHHHHHHhhcchhhhhhccchhHHHHHHHHHHHHHHHHHcCCCCHHHHHHHh
Confidence            999999999999999999998     6666543                    467789999999999999999999999


Q ss_pred             cccCCCCC---CcchHHHHHHHHHHcCC
Q psy6283         795 QLTKAPEG---GKVCITQIRLSRNRRGR  819 (1030)
Q Consensus       795 ~LsK~p~~---~~~pHV~vA~r~~~~g~  819 (1030)
                      +|+|+|++   +.+|||+||+||.++++
T Consensus       994 ~LsK~~~~Y~~~~~phv~vA~rl~~~~~ 1021 (1193)
T 2gv9_A          994 ELSRHPRAYTNKRLAHLTVYYKLMARRA 1021 (1193)
T ss_dssp             ----------------------------
T ss_pred             hcCCChhHhcccCCcHHHHHHHHHHhcC
Confidence            99999988   56999999999987764

>1qht_A Protein (DNA polymerase); archaea, hyperthermostable, family B polymer alpha family polymerase, transferase; 2.10A {Thermococcus SP} SCOP: c.55.3.5 e.8.1.1 PDB: 1tgo_A 2xhb_A* 2vwj_A* 2vwk_A* 1wns_A* 1wn7_A 1qqc_A* 4ahc_A* 4ail_C* 3a2f_A* 2jgu_A* 1d5a_A

Probab=100.00  E-value=1e-75  Score=720.59  Aligned_cols=383  Identities=28%  Similarity=0.454  Sum_probs=318.3

Q ss_pred             cHHHHHHHHHHHHHHHHHHHHHhcchHHHHHHHHHhCCcchhhccCchhHHHHHHHHHHHhhcCeeccCCccccCcCCCc
Q psy6283         401 GIVEFIKFTMLHSSYIIKIMCELNVLPLAIQITNVCGNVLSRTLMGGRSERNEFLLLHAFHEKSYVLPDKQYGKNKKEGE  480 (1030)
Q Consensus       401 Gl~~lv~Y~~~Da~l~~~L~~kl~vlpl~~~lt~iaG~~~srtl~~gr~~r~E~lLL~~~~~~~yivPdk~~~kk~~~~~  480 (1030)
                      ++..|+.||++||.+++.|+.+  ++|++.+||+++|+++..++.+|+++++|++|||++++.|||+|+++....     
T Consensus       304 ~l~~l~~Y~~~Da~lt~~L~~~--~~~~~~~la~i~g~~~~~v~r~~~~~~ve~~Ll~~~~~~~~i~P~~~~~~~-----  376 (775)
T 1qht_A          304 GLERVARYSMEDAKVTYELGRE--FFPMEAQLSRLIGQSLWDVSRSSTGNLVEWFLLRKAYKRNELAPNKPDERE-----  376 (775)
T ss_dssp             SHHHHHHHHHHHHHHHHHHHHH--HHHHHHHHHHHHTSCHHHHTTCCHHHHHHHHHHHHHHHTTBCCCCCCCHHH-----
T ss_pred             cHHHHHHHHHHHHHHHHHHHHh--hhHHHHHHHHHhCCCchhceecccHHHHHHHHhHHHHhCCEeCCCCCchhh-----
Confidence            3799999999999999999975  789999999999999999888888999999999999999999999753210     


Q ss_pred             cccccccCCCCCCccccCceeeccccccccceEEEeeccccChhHHHHhccccccccccCCCccccccccCCCC--Cccc
Q psy6283         481 ETGEANKGKGRKKAAYSGGLVLEPKKGFYDKFIILMDFNSLYPSIIQEYNICFTTIPVRMLQDSDITTLCEYLP--EHQV  558 (1030)
Q Consensus       481 d~~~~~~~~~~~~~~Y~GGlVleP~~GlY~~~V~vLDFnSLYPSII~~~NIc~tTv~~~~~d~~~i~~~~p~~p--~~~~  558 (1030)
                         .     .....+|+||+|++|++|+|++ |++|||+|||||||++|||||+|+++..++....   .|..+  ....
T Consensus       377 ---~-----~~~~~~y~Gg~V~eP~~G~y~~-v~~lDF~SLYPSIi~~~nl~~~t~~~~~~~~~~~---~~~~~~~f~~~  444 (775)
T 1qht_A          377 ---L-----ARRRGGYAGGYVKEPERGLWDN-IVYLDFRSLYPSIIITHNVSPDTLNREGCKEYDV---APEVGHKFCKD  444 (775)
T ss_dssp             ---H-----HHTTTCCCCCCBCCCCCSCEEE-EEEEECSSHHHHHHHHTTCSTTTBTCTTCSCEEE---CTTTCCEEECS
T ss_pred             ---h-----hccccccCCceEecccCCcccc-eeecchhcccHHHHHhcCCCcccccccccccccc---CCccCcccccc
Confidence               0     0115689999999999999997 9999999999999999999999998766532211   12111  1135


Q ss_pred             cCCcchHHHHHHHHHHHHHHHHhcCCCCChHHHHhhHHHHHHhccccccccccCCCCCCCCCCHHHHHHHHHHhHHHHHH
Q psy6283         559 DTGILPSEIKKLVESRRQVKALMKQPNLSSDLLMQYDIRQKALKLTANSMYGCLGFPNSRFFAQPLAALVTAKGREILLN  638 (1030)
Q Consensus       559 ~~GIlP~iL~~Ll~~R~~vKk~mk~~~~~~~~~~~~d~rQ~AlKl~aNS~YG~lG~~~srfy~~~lA~~IT~~GR~iL~~  638 (1030)
                      +.||+|.+|..|++.|+++|+.|++ ..+|.++.+||.+|+|+|++|||+|||+|++++||||+++|++||++||++|+.
T Consensus       445 ~~g~lp~~l~~l~~~R~~~K~~~k~-~~~~~~~~~~d~~Q~A~Ki~~NS~YG~~g~~~~r~~~~~~A~~vT~~Gr~~i~~  523 (775)
T 1qht_A          445 FPGFIPSLLGDLLEERQKIKRKMKA-TVDPLEKKLLDYRQRAIKILANSFYGYYGYAKARWYCKECAESVTAWGREYIEM  523 (775)
T ss_dssp             SCCHHHHHHHHHHHHHHHHHHHHHT-CCCHHHHHHHHHHHHHHHHHHTTHHHHHHCTTCSSCCHHHHHHHHHHHHHHHHH
T ss_pred             cCCCchHHHHHHHHHHHHHHHHhhc-CCCHHHHHHHHHHHHhhheeeccccccccccccCcCCHHHHHHHHHHHHHHHHH
Confidence            8999999999999999999999998 689999999999999999999999999999999999999999999999999999


Q ss_pred             HHHHh-hhccceeEEecCcceeeecCCCCHHHHHHHHHHHHHHHhccc-ceeEEeecchhhhhhhcccccceEEeeeecC
Q psy6283         639 TKSLV-ENLNYEVIYGDTDSLMISCNVNDYDSVFKIGNQIKSECNKLY-KQLELDIDGVYKYMLLLKKKKYAALSISKLS  716 (1030)
Q Consensus       639 tkelv-e~~g~~VIYGDTDSI~V~~~~~d~eea~~ig~~i~~~Vn~~~-~~leLe~E~vf~~llll~KKrYa~l~~~~~~  716 (1030)
                      |++.+ +++|++|||||||||||.++..+.+++.++|.++++.||+.+ .+++||+|++|.+++|++|||||++.    .
T Consensus       524 ~~~~i~~~~g~~ViygDTDSi~v~~~~~~~~~~~~~~~~~~~~i~~~~~~~~~le~e~~y~~~~l~~KKrYa~~~----~  599 (775)
T 1qht_A          524 VIRELEEKFGFKVLYADTDGLHATIPGADAETVKKKAKEFLKYINPKLPGLLELEYEGFYVRGFFVTKKKYAVID----E  599 (775)
T ss_dssp             HHHHHHHHHCCEEEEEETTEEEEECTTCCHHHHHHHHHHHHHHHC------CCCEEEEEEEEEEEEETTEEEEEC----T
T ss_pred             HHHHHHHhcCCeEEEeeccceEEEcCCCCHHHHHHHHHHHHHHHHhcCCCCeEEEEeEEeeeheecccCeEEEEc----c
Confidence            98764 567999999999999999999899999999999999999987 48999999999999999999999872    4


Q ss_pred             CCceeeeceeeeeeeeeCChHHHHHHHHHHHHHHHhccCCCCCCChhHHHHHHHHHHHHHHHHhhCCCcChhhhHHhhcc
Q psy6283         717 NGKMICSQEIKGVDVVRRDWSQLASEAGKFVISQILDEQSYTDYSLDDRLQNIHEHMKKIRTDLDNGFVPLTLLEITKQL  796 (1030)
Q Consensus       717 dG~~~~~~e~KGle~vRRD~~~l~k~~~~~vL~~IL~~~~~~~~~~e~~v~~I~~~l~~~~~~l~~g~vpl~~lvItk~L  796 (1030)
                      +|+    +++||+++||||||+|++++++.+|+.||.++     +++++++    ++.++..+|++|.+|+++|+|+++|
T Consensus       600 ~g~----l~~KG~e~vRrd~~~l~k~~~~~vl~~ll~~~-----d~~~~~~----~v~~~~~~l~~~~~~~~~lvi~k~l  666 (775)
T 1qht_A          600 EGK----ITTRGLEIVRRDWSEIAKETQARVLEAILKHG-----DVEEAVR----IVKEVTEKLSKYEVPPEKLVIHEQI  666 (775)
T ss_dssp             TCC----CEEESCSCCCSCCCHHHHHHHHHHHHHHHHHC-----CHHHHHH----HHHHTC------------CCBCCBC
T ss_pred             CCe----EEEEeeEEEeCCcHHHHHHHHHHHHHHHhcCC-----CHHHHHH----HHHHHHHHHHcCCCCHHHhhhhHHh
Confidence            564    47999999999999999999999999999998     7665554    5556667889999999999999999


Q ss_pred             cCCCCC--CcchHHHHHHHHHHcCCc
Q psy6283         797 TKAPEG--GKVCITQIRLSRNRRGRR  820 (1030)
Q Consensus       797 sK~p~~--~~~pHV~vA~r~~~~g~~  820 (1030)
                      +|++++  ..+|||+||++|+++|..
T Consensus       667 sk~~~~Y~~~~phv~~A~rl~~~g~~  692 (775)
T 1qht_A          667 TRDLRDYKATGPHVAVAKRLAARGVK  692 (775)
T ss_dssp             --------CCHHHHHHHHHHHTTTCC
T ss_pred             cCCHHHcCCCChHHHHHHHHHhcCCC
Confidence            999988  779999999999888753

>3k59_A POL II, DNA polymerase II; protein-DNA complex, DNA damage, DNA repair, DNA-binding; HET: DNA DOC DCP; 1.92A {Escherichia coli} PDB: 3k57_A* 3k58_A* 3k5l_A* 3k5m_A* 3k5n_A* 3k5o_A* 3maq_A* 1q8i_A*

Probab=100.00  E-value=4.5e-74  Score=703.03  Aligned_cols=364  Identities=25%  Similarity=0.403  Sum_probs=320.9

Q ss_pred             cHHHHHHHHHHHHHHHHHHHHHhcchHHHHHHHHHhCCcchhhccCchhHHHHHHHHHHHhhcCeeccCCccccCcCCCc
Q psy6283         401 GIVEFIKFTMLHSSYIIKIMCELNVLPLAIQITNVCGNVLSRTLMGGRSERNEFLLLHAFHEKSYVLPDKQYGKNKKEGE  480 (1030)
Q Consensus       401 Gl~~lv~Y~~~Da~l~~~L~~kl~vlpl~~~lt~iaG~~~srtl~~gr~~r~E~lLL~~~~~~~yivPdk~~~kk~~~~~  480 (1030)
                      +...|+.||++||.++++|+.+++++|++.++|+++|++|+++  ||++..+++++|+++|+.|||+|++...       
T Consensus       327 ~~~~L~~Y~l~Da~L~~~L~~kl~ll~~~~elarl~Gi~~~~~--ggs~~~~~~lll~~~~~~~~i~P~~~~~-------  397 (786)
T 3k59_A          327 DKPALATYNLKNCELVTQIFHKTEIMPFLLERATVNGLPVDRH--GGSVAAFGHLYFPRMHRAGYVAPNLGEV-------  397 (786)
T ss_dssp             CHHHHHHHHHHHHHHHHHHHHHHTHHHHHHHHHHHHCSCTTCC--CCHHHHHHHHHHHHHHHTTBCCCCTTSS-------
T ss_pred             CHHHHHHHHHHHHHHHHHHHHHhhHHHHHHHHHHHhCCCHHHc--ccHHHHHHHHHHHHHHHcCeeCCCcccc-------
Confidence            4678999999999999999999999999999999999999995  7888899999999999999999987531       


Q ss_pred             cccccccCCCCCCccccCceeeccccccccceEEEeeccccChhHHHHhccccccccccCC---CccccccccCCCCCcc
Q psy6283         481 ETGEANKGKGRKKAAYSGGLVLEPKKGFYDKFIILMDFNSLYPSIIQEYNICFTTIPVRML---QDSDITTLCEYLPEHQ  557 (1030)
Q Consensus       481 d~~~~~~~~~~~~~~Y~GGlVleP~~GlY~~~V~vLDFnSLYPSII~~~NIc~tTv~~~~~---d~~~i~~~~p~~p~~~  557 (1030)
                                 ...+|+||+|++|++|+|++ |++|||+|||||||++|||||+|++...+   +.+.+.+  |.-..-.
T Consensus       398 -----------~~~~y~Gg~V~eP~~G~y~~-V~~lDF~SLYPSIi~~~ni~~~t~~~~~~~~~~~~~~~~--~~g~~f~  463 (786)
T 3k59_A          398 -----------PPHASPGGYVMDSRPGLYDS-VLVLDYKSLYPSIIRTFLIDPVGLVEGMAQPDPEHSTEG--FLDAWFS  463 (786)
T ss_dssp             -----------CCCCCCCCCBCCCCCEEESC-EEEEEETTHHHHHHHHHCCCHHHHHHHHHSCSTTTEEEC--STTCEEE
T ss_pred             -----------ccccCCCcEEeeccCCceee-EEEEEhhhccHHHHHHhCCCccccccccCCccccccccC--CCCceEe
Confidence                       13579999999999999987 99999999999999999999999864321   1222211  1100012


Q ss_pred             ccCCcchHHHHHHHHHHHHHHHHhcCCCCChHHHHhhHHHHHHhccccccccccCCCCCCCCCCHHHHHHHHHHhHHHHH
Q psy6283         558 VDTGILPSEIKKLVESRRQVKALMKQPNLSSDLLMQYDIRQKALKLTANSMYGCLGFPNSRFFAQPLAALVTAKGREILL  637 (1030)
Q Consensus       558 ~~~GIlP~iL~~Ll~~R~~vKk~mk~~~~~~~~~~~~d~rQ~AlKl~aNS~YG~lG~~~srfy~~~lA~~IT~~GR~iL~  637 (1030)
                      .++||||.+|..|++.|+++|+.|++            .+|+|+|++|||+|||+|+++++|||+++|++||++||++|+
T Consensus       464 ~~~g~lp~~l~~l~~~R~~~K~~~~~------------~~q~AlKi~~Ns~YG~~G~~~~~~~~~~~A~~iT~~GR~~l~  531 (786)
T 3k59_A          464 REKHCLPEIVTNIWHGRDEAKRQGNK------------PLSQALKIIMNAFYGVLGTTACRFFDPRLASSITMRGHQIMR  531 (786)
T ss_dssp             SSCCSHHHHHHHHHHHHHHHHHTTCH------------HHHHHHHHHHHHHHHGGGSTTSTTCCHHHHHHHHHHHHHHHH
T ss_pred             ecCCchHHHHHHHHHHHHHHHHhcch------------HHHHhhheeeecccccccccCCCCCCHHHHHHHHHHHHHHHH
Confidence            37999999999999999999998753            479999999999999999999999999999999999999999


Q ss_pred             HHHHHhhhccceeEEecCcceeeecCC-CCHHHHHHHHHHHHHHHhccc----------ceeEEeecchhhhhhhc----
Q psy6283         638 NTKSLVENLNYEVIYGDTDSLMISCNV-NDYDSVFKIGNQIKSECNKLY----------KQLELDIDGVYKYMLLL----  702 (1030)
Q Consensus       638 ~tkelve~~g~~VIYGDTDSI~V~~~~-~d~eea~~ig~~i~~~Vn~~~----------~~leLe~E~vf~~llll----  702 (1030)
                      .|+++++++|++|||||||||||+++. .+.++++++|+++++.||+.|          .+|+||||++|.+|||+    
T Consensus       532 ~~~~~ie~~g~~ViYGDTDSvfv~~~~~~~~~~~~~~g~~l~~~vn~~~~~~~~~~~l~~~i~Le~Ekvy~~~ll~t~rg  611 (786)
T 3k59_A          532 QTKALIEAQGYDVIYGDTDSTFVWLKGAHSEEEAAKIGRALVQHVNAWWAETLQKQRLTSALELEYETHFCRFLMPTIRG  611 (786)
T ss_dssp             HHHHHHHHTTCEEEECBSSEEEEECCSCCCHHHHHHHHHHHHHHHHHHHHHHHHTTTCCCCCCEEEEEEESEEEECBCTT
T ss_pred             HHHHHHHHcCCEEEEEeccceEEEcCCCCCHHHHHHHHHHHHHHHHHHHHhhhhhhcCCCceEEEEEEeEhhheehhccC
Confidence            999999999999999999999999997 689999999999999999865          27999999999999986    


Q ss_pred             ----ccccceEEeeeecCCCceeeeceeeeeeeeeCChHHHHHHHHHHHHHHHhccCCCCCCChhHHHHHHHHHHHHHHH
Q psy6283         703 ----KKKKYAALSISKLSNGKMICSQEIKGVDVVRRDWSQLASEAGKFVISQILDEQSYTDYSLDDRLQNIHEHMKKIRT  778 (1030)
Q Consensus       703 ----~KKrYa~l~~~~~~dG~~~~~~e~KGle~vRRD~~~l~k~~~~~vL~~IL~~~~~~~~~~e~~v~~I~~~l~~~~~  778 (1030)
                          +||||||+.++.  +|   +++++||+++||||||+|++++++.+|+.||.++     ++       ++++.+++.
T Consensus       612 ~~~~~KKRYag~~~~~--~~---~~~~~KGle~vRrD~~~l~k~~~~~~l~~il~~~-----~v-------~~~~~~~~~  674 (786)
T 3k59_A          612 ADTGSKKRYAGLIQEG--DK---QRMVFKGLETVRTDWTPLAQQFQQELYLRIFRNE-----PY-------QEYVRETID  674 (786)
T ss_dssp             SSSBCSSCEEEEEEET--TE---EEEEEESSGGGCTTSCHHHHHHHHHHHHHHHTTC-----CC-------HHHHHHHHH
T ss_pred             CcccccceEEEEEecC--CC---CEEEEEeeEEEcCCccHHHHHHHHHHHHHHHcCC-----CH-------HHHHHHHHH
Confidence                599999998763  33   4678999999999999999999999999999988     43       467778889


Q ss_pred             HhhCCCcChhhhHHhhcccCCCCC---CcchHHHHHHHHHHc
Q psy6283         779 DLDNGFVPLTLLEITKQLTKAPEG---GKVCITQIRLSRNRR  817 (1030)
Q Consensus       779 ~l~~g~vpl~~lvItk~LsK~p~~---~~~pHV~vA~r~~~~  817 (1030)
                      +|++|++| ++|+|+|+|+|++++   +++|||+||++|.+.
T Consensus       675 ~l~~g~~~-~~lv~~k~l~k~~~~Y~~~~~phv~aa~~~~~~  715 (786)
T 3k59_A          675 KLMAGELD-ARLVYRKRLRRPLSEYQRNVPPHVRAARLADEE  715 (786)
T ss_dssp             HHHTTCCG-GGCCEEEEECSCGGGCCSCCCHHHHHHHHHHHH
T ss_pred             HHHcCCCC-hheEEEeeecCChHHcccCCcHHHHHHHHHHHh
Confidence            99999999 899999999999887   568999999998654

>1s5j_A DNA polymerase I; replication, disulfide bonds, transferase; HET: DNA; 2.40A {Sulfolobus solfataricus} SCOP: c.55.3.5 e.8.1.1

Probab=100.00  E-value=3.7e-71  Score=684.97  Aligned_cols=396  Identities=22%  Similarity=0.314  Sum_probs=279.1

Q ss_pred             cHHHHHHHHHHHHHHHHHHHH--HhcchHHHHHHHHHhCCcchhhccCchhHHHHHHHHHHHhhcCeeccCCccccCcCC
Q psy6283         401 GIVEFIKFTMLHSSYIIKIMC--ELNVLPLAIQITNVCGNVLSRTLMGGRSERNEFLLLHAFHEKSYVLPDKQYGKNKKE  478 (1030)
Q Consensus       401 Gl~~lv~Y~~~Da~l~~~L~~--kl~vlpl~~~lt~iaG~~~srtl~~gr~~r~E~lLL~~~~~~~yivPdk~~~kk~~~  478 (1030)
                      ++..++.||++||.++++|+.  +..+++++.+|++++|+++..++.+|.+.+++++||+++++.||++|++........
T Consensus       367 ~~~~l~~Ycl~Da~lt~~L~~~~~~~~~~~~~~la~i~~lp~~~l~r~~~~~~v~slll~~~~~~~~i~P~~~~~~~~~~  446 (847)
T 1s5j_A          367 DVEKLIEYNFRDAEITLQLTTFNNDLTMKLIVLFSRISRLGIEELTRTEISTWVKNLYYWEHRKRNWLIPLKEEILAKSS  446 (847)
T ss_dssp             CHHHHHHHHHHHHHHHHHTTTHHHHHHHHHHHHHHHHHCCCHHHHTTSCHHHHHHHHHHHHHHHHTBCCCCHHHHHHTTC
T ss_pred             cHHHHHHHHHHHHHHHHHHHHHHhHhHHHHHHHHHHHhCCCchhhcccchhhhhHHHHHHHHHhcCcccCCchhhhhhcc
Confidence            379999999999999999953  456899999999999999999887788889999999999999999999753211000


Q ss_pred             CccccccccCCCCCCccccCceeeccccccccceEEEeeccccChhHHHHhccccccccccCCCc-cccccccCCCCC--
Q psy6283         479 GEETGEANKGKGRKKAAYSGGLVLEPKKGFYDKFIILMDFNSLYPSIIQEYNICFTTIPVRMLQD-SDITTLCEYLPE--  555 (1030)
Q Consensus       479 ~~d~~~~~~~~~~~~~~Y~GGlVleP~~GlY~~~V~vLDFnSLYPSII~~~NIc~tTv~~~~~d~-~~i~~~~p~~p~--  555 (1030)
                      ..     ......+..+|+||+|++|++|+|++ |++|||+|||||||++|||||+|++...|.. .......|..+.  
T Consensus       447 ~~-----~~~~~~~~~~y~Gg~V~eP~~G~y~~-v~~lDf~SLYPSIi~~~Nl~~~T~~~~~~~~~~~~~~~~~~~~~~~  520 (847)
T 1s5j_A          447 NI-----RTSALIKGKGYKGAVVIDPPAGIFFN-ITVLDFASLYPSIIRTWNLSYETVDIQQCKKPYEVKDETGEVLHIV  520 (847)
T ss_dssp             C-------------------CCCCCCCSEEEEE-EEEEEETTHHHHHHHHTTCCTTTBSCSCCSSCCEECCSSSCCCEEB
T ss_pred             cc-----cchhccccccccCCcccCCCCCcccc-eeEeehhhhchHHHHHcCCCcceeccccccccccccccCCCCceeE
Confidence            00     00011234689999999999999997 9999999999999999999999998654311 100001132211  


Q ss_pred             ccccCCcchHHHHHHHHHHHHHHHHhcC-CCCChHHHHhhHHHHHHhccccccccccCCCCCCCCCCHHHHHHHHHHhHH
Q psy6283         556 HQVDTGILPSEIKKLVESRRQVKALMKQ-PNLSSDLLMQYDIRQKALKLTANSMYGCLGFPNSRFFAQPLAALVTAKGRE  634 (1030)
Q Consensus       556 ~~~~~GIlP~iL~~Ll~~R~~vKk~mk~-~~~~~~~~~~~d~rQ~AlKl~aNS~YG~lG~~~srfy~~~lA~~IT~~GR~  634 (1030)
                      ...+.||+|.+|..|++.|+.+|+.|++ ...+|.++.+||.+|+|+|++|||+|||+|+++++|||+++|++||++||+
T Consensus       521 ~~~~~g~~p~~l~~l~~~R~~~kk~~~k~~~~~~~~~~~~d~~Q~AlKi~~NS~YG~~g~~~~~~~~~~~A~~iT~~GR~  600 (847)
T 1s5j_A          521 CMDRPGITAVITGLLRDFRVKIYKKKAKNPNNSEEQKLLYDVVQRAMKVFINATYGVFGAETFPLYAPRVAESVTALGRY  600 (847)
T ss_dssp             CCSSCCHHHHHHHHHHHHHHHTHHHHHTCTTSCHHHHHHHHHHHHHHHHHHHHHHHHHHSTTSTTCCHHHHHHHHHHHHH
T ss_pred             eccCCcccHHHHHHHHHHHHHHHHHHHhccCCCHHHHHHHHHHHHHHHHHhhccccccccccccccCHHHHHHHHHHHHH
Confidence            1358999999999999999998877644 356888999999999999999999999999999999999999999999999


Q ss_pred             HHHHHHHHhhhccceeEEecCcceeeecCCCCHHHHHHHHHHHHHHHhcccceeEEeecchhhhhhhc-ccccceEEeee
Q psy6283         635 ILLNTKSLVENLNYEVIYGDTDSLMISCNVNDYDSVFKIGNQIKSECNKLYKQLELDIDGVYKYMLLL-KKKKYAALSIS  713 (1030)
Q Consensus       635 iL~~tkelve~~g~~VIYGDTDSI~V~~~~~d~eea~~ig~~i~~~Vn~~~~~leLe~E~vf~~llll-~KKrYa~l~~~  713 (1030)
                      +|+.|+++++++|++|||||||||||.++.  .+.+    .+|.+.|++.+ +++|++|++|.+|+|. +||||||+.  
T Consensus       601 ~l~~t~~~ve~~g~~ViYGDTDSi~v~~~~--~~~~----~~~~~~v~~~~-~i~le~e~vy~~~ll~~~KKrYag~~--  671 (847)
T 1s5j_A          601 VITSTVKKAREEGLTVLYGDTDSLFLLNPP--KNSL----ENIIKWVKTTF-NLDLEVDKTYKFVAFSGLKKNYFGVY--  671 (847)
T ss_dssp             HHHHHHHHHHTTTCCEEEEETTEEEEESCC--HHHH----HHHHHHHHHHS-SCCEEEEEEEEEEEEC----CEEEEC--
T ss_pred             HHHHHHHHHHhCCcEEecCCCcceEEecCc--HHHH----HHHHHHHHhhc-CccEEecchhHhHccchhhCcEEEEe--
Confidence            999999999999999999999999999764  2333    34556677666 5999999999998887 899999984  


Q ss_pred             ecCCCceeeeceeeeeeeeeCChHHHHHHHHHHHHHHHhccCCCCCCChhHHHHHHHHHHHHHHHHhhCCCcChhhhHHh
Q psy6283         714 KLSNGKMICSQEIKGVDVVRRDWSQLASEAGKFVISQILDEQSYTDYSLDDRLQNIHEHMKKIRTDLDNGFVPLTLLEIT  793 (1030)
Q Consensus       714 ~~~dG~~~~~~e~KGle~vRRD~~~l~k~~~~~vL~~IL~~~~~~~~~~e~~v~~I~~~l~~~~~~l~~g~vpl~~lvIt  793 (1030)
                        .+|+    +++||+++||||||+|++++++.+|+.||.+.+..  +.+.+++.|++++.++..+|++|.+|+++|+|+
T Consensus       672 --~~g~----~~~KG~e~vRrd~~~l~k~~~~~~l~~ll~~~~~~--~~~~~~~~i~~~~~~~~~~l~~~~~~~~~l~~~  743 (847)
T 1s5j_A          672 --QDGK----VDIKGMLVKKRNTPEFVKKVFNEVKELMISINSPN--DVKEIKRKIVDVVKGSYEKLKNKGYNLDELAFK  743 (847)
T ss_dssp             --SSSC----CCEESCCC--------CCSHHHHHHHHHHTTCCSC--CTTHHHHHHHHHHHHHHCTTC------------
T ss_pred             --cCCe----eeeeeeEEeeCCcHHHHHHHHHHHHHHHHhcCChh--hHHHHHHHHHHHHHHHHHHHHcCCCCHHHEEEE
Confidence              3554    58999999999999999999999999999976222  455688999999999999999999999999999


Q ss_pred             hcccCCCCC---CcchHHHHHHHHHHcCC
Q psy6283         794 KQLTKAPEG---GKVCITQIRLSRNRRGR  819 (1030)
Q Consensus       794 k~LsK~p~~---~~~pHV~vA~r~~~~g~  819 (1030)
                      ++|+|++++   +.+|||++|++|++.|.
T Consensus       744 k~l~k~~~~Y~~~~~~hv~~A~~~~~~g~  772 (847)
T 1s5j_A          744 VMLSKPLDAYKKNTPQHVKAALQLRPFGV  772 (847)
T ss_dssp             -----------------------------
T ss_pred             EEeccChhHhccCCCHHHHHHHHHHhcCC
Confidence            999999877   56899999999988763

>3qex_A DNA polymerase, GP43; difluorotoluene nucleoside; HET: DNA DOC DGT; 1.73A {Enterobacteria phage RB69} PDB: 3qei_A* 3qer_A* 3qes_A* 3qet_A* 3qep_A* 3qew_A* 3qev_A* 3s9h_A* 3sq0_A* 4dtn_A* 4dto_A* 4dtp_A* 4dtr_A* 4dts_A* 4dtu_A* 4dtx_A* 4e3s_A* 4fjm_A* 4fjl_A* 3spz_A* ...

Probab=100.00  E-value=9.8e-69  Score=659.40  Aligned_cols=383  Identities=19%  Similarity=0.234  Sum_probs=314.3

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHhcchHHHHHHHHHhCCcchhhccCchhHHHHHHHHHHHhhcCeeccCCccccCcCCCcc
Q psy6283         402 IVEFIKFTMLHSSYIIKIMCELNVLPLAIQITNVCGNVLSRTLMGGRSERNEFLLLHAFHEKSYVLPDKQYGKNKKEGEE  481 (1030)
Q Consensus       402 l~~lv~Y~~~Da~l~~~L~~kl~vlpl~~~lt~iaG~~~srtl~~gr~~r~E~lLL~~~~~~~yivPdk~~~kk~~~~~d  481 (1030)
                      +..|+.||++||.++++|+.+++++|++.++|+++|++|.++++  +...+|++|+|++++.||++|++..         
T Consensus       317 ~~~L~~Ycl~Da~Lt~~L~~Kl~li~~~~elArl~Gi~~~~vls--q~~v~e~LLlr~a~~~~~iiP~~~~---------  385 (903)
T 3qex_A          317 HQRYISYNIIAVYRVLQIDAKRQFINLSLDMGYYAKIQIQSVFS--PIKTWDAIIFNSLKEQNKVIPQGRS---------  385 (903)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHCHHHHHHHHHHHHTSCGGGGGC--HHHHHHHHHHHHHHTTTEECCCCCC---------
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHhhHHHHHHHHHHhCCCHHHhcc--hHHHHHHHHHHHHHHCCEeccCCcc---------
Confidence            68899999999999999999999999999999999999999984  4555699999999999999998752         


Q ss_pred             ccccccCCCCCCccccCceeeccccccccceEEEeeccccChhHHHHhccccccccccCCCcc---------cccc----
Q psy6283         482 TGEANKGKGRKKAAYSGGLVLEPKKGFYDKFIILMDFNSLYPSIIQEYNICFTTIPVRMLQDS---------DITT----  548 (1030)
Q Consensus       482 ~~~~~~~~~~~~~~Y~GGlVleP~~GlY~~~V~vLDFnSLYPSII~~~NIc~tTv~~~~~d~~---------~i~~----  548 (1030)
                               ....+|.||+|++|.+|+|++ |++|||+|||||||++|||||+|+++..+...         .++.    
T Consensus       386 ---------~~~~~y~Gg~V~~p~~G~y~~-v~~lDf~SLYPsIi~~~ni~~~T~~~~~~~~~~~~~i~~~~~~p~~~~~  455 (903)
T 3qex_A          386 ---------HPVQPYPGAFVKEPIPNRYKY-VMSFDLTSLYPSIIRQVNISPETIAGTFKVAPLHDYINAVAERPSDVYS  455 (903)
T ss_dssp             ---------CCCCCCCCCCBCCCCCEECSS-EEEEEETTHHHHHHHHHTCCGGGEEEECCCCCHHHHHTTCSCCSCSSSE
T ss_pred             ---------cccCCCCCCEEecccCCceEE-EEEEehhhhchHHHHHhCcChhhccccccccchhcccccccCCCCCcee
Confidence                     124679999999999999986 99999999999999999999999987643110         0000    


Q ss_pred             ccCC-CCCccccCCcchHHHHHHHHHHHHHHHHhcCCC-----------------CCh----------------------
Q psy6283         549 LCEY-LPEHQVDTGILPSEIKKLVESRRQVKALMKQPN-----------------LSS----------------------  588 (1030)
Q Consensus       549 ~~p~-~p~~~~~~GIlP~iL~~Ll~~R~~vKk~mk~~~-----------------~~~----------------------  588 (1030)
                      .+|. ......+.||||.+|+.|++.|+++|+.|++.+                 .||                      
T Consensus       456 ~~p~g~~F~k~~~GiLP~iL~~Ll~~R~~~K~~mk~~~~~~~~~k~~L~~~~~~~~dp~~~~~~~~~~~~~~~~~~~~~~  535 (903)
T 3qex_A          456 CSPNGMMYYKDRDGVVPTEITKVFNQRKEHKGYMLAAQRNGEIIKEALHNPNLSVDEPLDVDYRFDFSDEIKEKIKKLSA  535 (903)
T ss_dssp             ECTTSEEECCSSCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTSCCSSCCCCCCCCTTSCCCHHHHHHHTTCCH
T ss_pred             eCCCCceEecCCCcchHHHHHHHHHHHHHHHHHHhhccccchhhhhhcccccccccCccccccccccchhhhhhhhccch
Confidence            1111 001135899999999999999999999997531                 233                      


Q ss_pred             -----------HHHHhhHHHHHHhccccccccccCCCCCCCCCCHHHHHHHHHHhHHHHHHHHHHhhhc--------c-c
Q psy6283         589 -----------DLLMQYDIRQKALKLTANSMYGCLGFPNSRFFAQPLAALVTAKGREILLNTKSLVENL--------N-Y  648 (1030)
Q Consensus       589 -----------~~~~~~d~rQ~AlKl~aNS~YG~lG~~~srfy~~~lA~~IT~~GR~iL~~tkelve~~--------g-~  648 (1030)
                                 .++.+||++|+|+||+|||+|||||++++||||.++|++||++||++|+.|++.++++        | +
T Consensus       536 ~~L~~~l~~~~~~~~~~d~rQ~AlKi~~NS~YG~~G~~~~r~~~~~~A~sIT~~GR~~i~~~~~~v~~~~~~~~~~~~~~  615 (903)
T 3qex_A          536 KSLNEMLFRAQRTEVAGMTAQINRKALINGLAGALGNVWFRYYDLRNATAITTFGQMALQWIERKVNEYLNEVCGTEGEA  615 (903)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTSTTSTTCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTCSSCC
T ss_pred             hhhhhhhhhhhHHHHHHHHHHHHHHHHHHHHHHhhcCcccccCCHHHHHHHHHHhhHHHHHHHHHHHHHHHhhcCCCCCe
Confidence                       3577899999999999999999999999999999999999999999999999988863        4 5


Q ss_pred             eeEEecCcceeeecCCCC-H--HHHHHHHHHHHHHHhc----------------------cc-ceeEEeecchhhh----
Q psy6283         649 EVIYGDTDSLMISCNVND-Y--DSVFKIGNQIKSECNK----------------------LY-KQLELDIDGVYKY----  698 (1030)
Q Consensus       649 ~VIYGDTDSI~V~~~~~d-~--eea~~ig~~i~~~Vn~----------------------~~-~~leLe~E~vf~~----  698 (1030)
                      .|||||||||||+++... .  .+++++|+++.+.||+                      .| .++.|++|+||.+    
T Consensus       616 ~VIYGDTDSvfV~~~~~~~~~~~~~f~~g~~l~~~i~~~~~~~~~~~i~~~~~el~e~~~~~~~p~~l~~E~i~~~~~gs  695 (903)
T 3qex_A          616 FVLYGDTDSIYVSADKIIDKVGESKFRDTNHWVDFLDKFARERMEPAIDRGFREMCEYMNNKQHLMFMDREAIAGPPLGS  695 (903)
T ss_dssp             CEEEEETTEEEEECHHHHHHHCGGGCSSHHHHHHHHHHHHHHTHHHHHHHHHHHHHHHTTCSSCCCCEEEEEEECCCTTS
T ss_pred             EEEEEeCCceEEEeCCccchhhhhhhhHHHHHHHHHHHHHHHHHHHhhhhHHHHHHHHhccCCcceeeeeeeeecCcccc
Confidence            899999999999987531 1  1223334433333222                      23 4799999999999    


Q ss_pred             ----hhhcccccceEEeeeecCCCce--eeeceeeeeeeeeCChHHHHHHHHHHHHHHHhccCCCCCCChhHHHHHHHHH
Q psy6283         699 ----MLLLKKKKYAALSISKLSNGKM--ICSQEIKGVDVVRRDWSQLASEAGKFVISQILDEQSYTDYSLDDRLQNIHEH  772 (1030)
Q Consensus       699 ----llll~KKrYa~l~~~~~~dG~~--~~~~e~KGle~vRRD~~~l~k~~~~~vL~~IL~~~~~~~~~~e~~v~~I~~~  772 (1030)
                          ++|++||||||+.++.+  |+-  .+++++||+++||||||+++++++..+|+.||.+.     +     +.++++
T Consensus       696 ~~~~~~l~~KKRYag~~~~~~--g~~~~~~kl~~kGlE~vRrd~~~~~k~~~~~~l~~ll~~~-----~-----~~~~~y  763 (903)
T 3qex_A          696 KGIGGFWTGKKRYALNVWDME--GTRYAEPKLKIMGLETQKSSTPKAVQKALKECIRRMLQEG-----E-----ESLQEY  763 (903)
T ss_dssp             CCCCEEEEETTEEEEEEEEET--TEEEEEEEEEEESSGGGCTTSCHHHHHHHHHHHHHHHHTC-----H-----HHHHHH
T ss_pred             cccchheeeccceEEEEeecC--CcccCCCeeEEeceEEEeccchHHHHHHHHHHHHHHHhcC-----c-----HHHHHH
Confidence                99999999999998753  432  46789999999999999999999999999999986     2     567788


Q ss_pred             HHHHHHHhhCCCcChhhhHHhhcccCCCCC---------CcchHHHHHHHHHHcCCc
Q psy6283         773 MKKIRTDLDNGFVPLTLLEITKQLTKAPEG---------GKVCITQIRLSRNRRGRR  820 (1030)
Q Consensus       773 l~~~~~~l~~g~vpl~~lvItk~LsK~p~~---------~~~pHV~vA~r~~~~g~~  820 (1030)
                      +.++..++++  +++++|+|++++ ++++.         ...|||..|+..++..++
T Consensus       764 v~~~~~~~~~--~~~~di~~~~~~-~~l~~Y~~~~~~~~~~p~hv~ga~~~n~~~~~  817 (903)
T 3qex_A          764 FKEFEKEFRQ--LNYISIASVSSA-NNIAKYDVGGFPGPKCPFHIRGILTYNRAIKG  817 (903)
T ss_dssp             HHHHHHHGGG--SCGGGGCEEEEC-CCTGGGEETTEECTTCCHHHHHHHHHHHHTTT
T ss_pred             HHHHHHHHHc--CCHHHEEeeccc-CCHHHhCCCCCCCCCCchhHHHHHHHHHHhhc
Confidence            8888889988  678999999999 56665         245899999887776655

>2py5_A DNA polymerase; protein-DNA complex, replication, transferase/DNA complex; HET: DNA; 1.60A {Bacillus phage PHI29} SCOP: c.55.3.5 e.8.1.1 PDB: 1xhz_A* 1xhx_A* 2ex3_A* 1xi1_A* 2pyj_A* 2pyl_A* 2pzs_A*

Probab=99.88  E-value=1.5e-23  Score=250.14  Aligned_cols=142  Identities=25%  Similarity=0.311  Sum_probs=102.6

Q ss_pred             cCCcchHHHHHHHHHHHHHHHHhcCCCCChHHHHhhHHHHHHhccccccccccCCCCCC--------------CCC----
Q psy6283         559 DTGILPSEIKKLVESRRQVKALMKQPNLSSDLLMQYDIRQKALKLTANSMYGCLGFPNS--------------RFF----  620 (1030)
Q Consensus       559 ~~GIlP~iL~~Ll~~R~~vKk~mk~~~~~~~~~~~~d~rQ~AlKl~aNS~YG~lG~~~s--------------rfy----  620 (1030)
                      ..|+++..+..|++.|.+.+         +       ..++++|+++||+||.+|..-.              +|+    
T Consensus       356 ~~~~f~~~i~~l~~~k~~~~---------~-------~~~~~~Kl~lNS~YGk~g~~~~~~~~~~~~~~~~~~~f~~~e~  419 (575)
T 2py5_A          356 TTGLFKDFIDKWTYIKTTSE---------G-------AIKQLAKLMLNSLYGKFASNPDVTGKVPYLKENGALGFRLGEE  419 (575)
T ss_dssp             ESCTTHHHHHHHHHHHHHCC---------H-------HHHHHHHHHHHSSHHHHTCCSBCCBEEEEECTTSSEEEEECCC
T ss_pred             CCCchHHHHHHHHHHhhhCc---------H-------HHHHHHHHHHHhHhhhhccCccccceEEEecccceeeeecCcc
Confidence            47999999999999887622         1       2334779999999999998711              222    


Q ss_pred             ------CHHHHHHHHHHhHHHHHHHHHHhhhccceeEEecCcceeeec-CCCCHHHHHHHHHHHHHHH-hcccceeEEee
Q psy6283         621 ------AQPLAALVTAKGREILLNTKSLVENLNYEVIYGDTDSLMISC-NVNDYDSVFKIGNQIKSEC-NKLYKQLELDI  692 (1030)
Q Consensus       621 ------~~~lA~~IT~~GR~iL~~tkelve~~g~~VIYGDTDSI~V~~-~~~d~eea~~ig~~i~~~V-n~~~~~leLe~  692 (1030)
                            +.++|++||+.||.+|..+...+   |..|+||||||||+.. +..+   .      +.+.+ +....  .++.
T Consensus       420 ~~~~p~~v~ia~~iTa~aR~~m~~~~~~~---~~~v~Y~DTDSi~~~~~~~~~---~------l~~~~~~~~lG--~~~~  485 (575)
T 2py5_A          420 ETKDPVYTPMGVFITAWARYTTITAAQAC---YDRIIYCDTDSIHLTGTEIPD---V------IKDIVDPKKLG--YWAH  485 (575)
T ss_dssp             CBCCCCCHHHHHHHHHHHHHHHHHHHHHT---TTTEEEEETTEEEEESSSCCG---G------GGGGBCSSSTT--SEEE
T ss_pred             cccCcchhhHHHHHHHHHHHHHHHHHHHc---CCcEEEecCCcceeccccchh---h------hhhcccccchh--chhh
Confidence                  25699999999999998877655   9999999999999985 3221   1      11112 22222  3445


Q ss_pred             cchhhhhhhcccccceEEeeeecCCCce-----------eeeceeeeee
Q psy6283         693 DGVYKYMLLLKKKKYAALSISKLSNGKM-----------ICSQEIKGVD  730 (1030)
Q Consensus       693 E~vf~~llll~KKrYa~l~~~~~~dG~~-----------~~~~e~KGle  730 (1030)
                      |.++..++++++|+||+..+..+.+|++           ...+.+||+.
T Consensus       486 E~~~~~~~f~~~K~Y~~~~~~~~~~g~i~~~~~~~~~~~~~~~k~KGi~  534 (575)
T 2py5_A          486 ESTFKRAKYLRQKTYIQDIYMKEVDGKLVEGSPDDYTDIKFSVKCAGMT  534 (575)
T ss_dssp             EEEEEEEEEEETTEEEEEEEEEEETTEEEECBTTBCSEEEEEEEETTCC
T ss_pred             hhheeeEEEeeCceEeEeecccCCCCcEeecccccccCcceEEEcCCCC
Confidence            5688999999999999986544446776           4467889984

>1noy_A Protein (DNA polymerase (E.C.2.7.7.7)); exonuclease, DNA-binding, complex (nucleotidyltransferase/DNA); HET: DNA; 2.20A {Enterobacteria phage T4} SCOP: c.55.3.5 PDB: 1noz_A*

Probab=98.67  E-value=2.2e-08  Score=114.40  Aligned_cols=69  Identities=9%  Similarity=0.198  Sum_probs=54.9

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHhcchHHHHHHHHHhCCcchhhccCchhHHHHHHHHHHHhhcCeeccCCcc
Q psy6283         402 IVEFIKFTMLHSSYIIKIMCELNVLPLAIQITNVCGNVLSRTLMGGRSERNEFLLLHAFHEKSYVLPDKQY  472 (1030)
Q Consensus       402 l~~lv~Y~~~Da~l~~~L~~kl~vlpl~~~lt~iaG~~~srtl~~gr~~r~E~lLL~~~~~~~yivPdk~~  472 (1030)
                      +..++.||++||.++++|+.+++++|++.++|+++|++|++++ | +..-.|++|||++|++|||+|++..
T Consensus       314 ~~~l~~Y~~~D~~l~~~L~~kl~~l~~~~ela~i~g~~~~~vl-~-q~~~~~~lll~~~~~~~~i~P~~~~  382 (388)
T 1noy_A          314 HQRYISYNIIDVESVQAIDKIRGFIDLVLSMSYYAKMPFSGVM-S-PIKTWDAIIFNSLKGEHKVIPQQGS  382 (388)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHCHHHHHHHHHHHHTCCGGGGG-C-HHHHHHHHHHHHTTCC---------
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHChHHHHHHHhCccCCCHHHhC-c-cHHHHHHHHHHHHHhCCEEcccCCc
Confidence            6889999999999999999999999999999999999999999 3 3333488999999999999999864

---

Homologous Structure Domains

Structure Domains Detected by RPS-BLAST

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

ID	Length	Definition	E-value
Query	1030
d1tgoa2	426	e.8.1.1 (A:348-773) Family B DNA polymerase {Archa	1e-43
d1s5ja2	415	e.8.1.1 (A:450-864) Family B DNA polymerase {Sulfo	4e-42
d1q8ia2	394	e.8.1.1 (A:390-783) Family B DNA polymerase {Esche	2e-36
d1ih7a2	528	e.8.1.1 (A:376-903) Family B DNA polymerase {Bacte	4e-21
d2es4d1	280	a.137.15.1 (D:53-332) Lipase chaperone LifO (LipB)	1e-10
d2es4d1	280	a.137.15.1 (D:53-332) Lipase chaperone LifO (LipB)	1e-10
d2es4d1	280	a.137.15.1 (D:53-332) Lipase chaperone LifO (LipB)	6e-08
d2es4d1	280	a.137.15.1 (D:53-332) Lipase chaperone LifO (LipB)	2e-06
d2py5a2	388	e.8.1.1 (A:188-575) phi29 DNA polymerase {Bacterio	2e-10
d1q8ia1	388	c.55.3.5 (A:2-389) Exonuclease domain of family B	2e-09
d1sa0e_	138	a.137.10.1 (E:) Stathmin 4 {Rat (Rattus norvegicus	3e-08
d1sa0e_	138	a.137.10.1 (E:) Stathmin 4 {Rat (Rattus norvegicus	4e-08
d1sa0e_	138	a.137.10.1 (E:) Stathmin 4 {Rat (Rattus norvegicus	2e-07
d1sa0e_	138	a.137.10.1 (E:) Stathmin 4 {Rat (Rattus norvegicus	8e-07
d1sa0e_	138	a.137.10.1 (E:) Stathmin 4 {Rat (Rattus norvegicus	3e-05
d1sa0e_	138	a.137.10.1 (E:) Stathmin 4 {Rat (Rattus norvegicus	0.002
d1f5na1	300	a.114.1.1 (A:284-583) Interferon-induced guanylate	1e-07
d1f5na1	300	a.114.1.1 (A:284-583) Interferon-induced guanylate	3e-07
d1f5na1	300	a.114.1.1 (A:284-583) Interferon-induced guanylate	5e-06
d1f5na1	300	a.114.1.1 (A:284-583) Interferon-induced guanylate	0.003
d1xu6a_	80	g.16.3.1 (A:) Variant surface glycoprotein MITAT 1	0.001

>d1tgoa2 e.8.1.1 (A:348-773) Family B DNA polymerase {Archaeon Thermococcus gorgonarius [TaxId: 71997]} Length = 426

class: Multi-domain proteins (alpha and beta)
fold: DNA/RNA polymerases
superfamily: DNA/RNA polymerases
family: DNA polymerase I
domain: Family B DNA polymerase
species: Archaeon Thermococcus gorgonarius [TaxId: 71997]

 Score =  162 bits (411), Expect = 1e-43
 Identities = 101/380 (26%), Positives = 172/380 (45%), Gaps = 35/380 (9%)

Query: 448 RSERNEFLLLHAFHEKSYVLPDKQYGKNKKEGEETGEANKGKGRKKAAYSGGLVLEPKKG 507
                E+ LL   +E++ + P+K   +                R++ +Y+GG V EP++G
Sbjct: 2   TGNLVEWFLLRKAYERNELAPNKPDEREL-------------ARRRESYAGGYVKEPERG 48

Query: 508 FYDKFIILMDFNSLYPSIIQEYNICFTTIPVRMLQDSDITTLCEYLPEHQVDTGILPSEI 567
            ++  I+ +DF SLYPSII  +N+   T+     ++ D+     +        G +PS +
Sbjct: 49  LWEN-IVYLDFRSLYPSIIITHNVSPDTLNREGCEEYDVAPQVGHKFCKDFP-GFIPSLL 106

Query: 568 KKLVESRRQVKALMKQPNLSSDLLMQYDIRQKALKLTANSMYGCLGFPNSRFFAQPLAAL 627
             L+E R++VK  MK            D RQ+A+K+ ANS YG  G+  +R++ +  A  
Sbjct: 107 GDLLEERQKVKKKMKATI-DPIEKKLLDYRQRAIKILANSFYGYYGYAKARWYCKECAES 165

Query: 628 VTAKGREILLNTKSLVEN-LNYEVIYGDTDSLMISCNVNDYDSVFKIGNQIKSECNK-LY 685
           VTA GR+ +  T   +E    ++V+Y DTD    +    D ++V K   +     N  L 
Sbjct: 166 VTAWGRQYIETTIREIEEKFGFKVLYADTDGFFATIPGADAETVKKKAKEFLDYINAKLP 225

Query: 686 KQLELDIDGVYKYMLLLKKKKYAALSISKLSNGKMICSQEIKGVDVVRRDWSQLASEAGK 745
             LEL+ +G YK    + KKKYA                  +G+++VRRDWS++A E   
Sbjct: 226 GLLELEYEGFYKRGFFVTKKKYAV--------IDEEDKITTRGLEIVRRDWSEIAKETQA 277

Query: 746 FVISQILDEQSYTDYSLDDRLQNIHEHMKKIRTDLDNGFVPLTLLEITKQLTKAPEGGKV 805
            V+  IL             ++     +K++   L    VP   L I +Q+T+  +  K 
Sbjct: 278 RVLEAILK---------HGDVEEAVRIVKEVTEKLSKYEVPPEKLVIYEQITRDLKDYKA 328

Query: 806 CITQIRLSRNRRGRRRRRRK 825
               + +++    R  + R 
Sbjct: 329 TGPHVAVAKRLAARGIKIRP 348

>d1s5ja2 e.8.1.1 (A:450-864) Family B DNA polymerase {Sulfolobus solfataricus [TaxId: 2287]} Length = 415

class: Multi-domain proteins (alpha and beta)
fold: DNA/RNA polymerases
superfamily: DNA/RNA polymerases
family: DNA polymerase I
domain: Family B DNA polymerase
species: Sulfolobus solfataricus [TaxId: 2287]

 Score =  157 bits (398), Expect = 4e-42
 Identities = 90/384 (23%), Positives = 156/384 (40%), Gaps = 29/384 (7%)

Query: 455 LLLHAFHEKSYVLPDKQYGKNKKEGEETGEANKGKGRKKAAYSGGLVLEPKKGFYDKFII 514
           L      ++++++P K+    K     T    KGKG     Y G +V++P  G +   I 
Sbjct: 9   LYYWEHRKRNWLIPLKEEILAKSSNIRTSALIKGKG-----YKGAVVIDPPAGIFFN-IT 62

Query: 515 LMDFNSLYPSIIQEYNICFTTIPVRMLQDSDITTLCEYLPEHQVDT---GILPSEIKKLV 571
           ++DF SLYPSII+ +N+ + T+ ++  +             H V     GI       L 
Sbjct: 63  VLDFASLYPSIIRTWNLSYETVDIQQCKKPYEVKDETGEVLHIVCMDRPGITAVITGLLR 122

Query: 572 ESR-RQVKALMKQPNLSSDLLMQYDIRQKALKLTANSMYGCLGFPNSRFFAQPLAALVTA 630
           + R +  K   K PN S +  + YD+ Q+A+K+  N+ YG  G      +A  +A  VTA
Sbjct: 123 DFRVKIYKKKAKNPNNSEEQKLLYDVVQRAMKVFINATYGVFGAETFPLYAPRVAESVTA 182

Query: 631 KGREILLNTKSLVENLNYEVIYGDTDSLMISCNVNDYDSVFKIGNQIKSECNKLYKQLEL 690
            GR ++ +T          V+YGDTDSL +       +S+  I   +K+        L+L
Sbjct: 183 LGRYVITSTVKKAREEGLTVLYGDTDSLFLLN--PPKNSLENIIKWVKTTF-----NLDL 235

Query: 691 DIDGVYKYMLLLKKKKYAALSISKLSNGKMICSQEIKGVDVVRRDWSQLASEAGKFVISQ 750
           ++D  YK++     KK                  +IKG+ V +R+  +   +    V   
Sbjct: 236 EVDKTYKFVAFSGLKKNYFGVY-------QDGKVDIKGMLVKKRNTPEFVKKVFNEVKEL 288

Query: 751 ILDEQSYTDYSLDDRLQNIHEHMKKIRTDLDNGFVPLTLLEITKQLTKAPEG-GKVCITQ 809
           ++   S  D    +  + I + +K     L N    L  L     L+K  +   K     
Sbjct: 289 MISINSPNDV--KEIKRKIVDVVKGSYEKLKNKGYNLDELAFKVMLSKPLDAYKKNTPQH 346

Query: 810 IRLSRNRRGRRRRRRKKKEEKKKW 833
           ++ +   + R         +   +
Sbjct: 347 VKAA--LQLRPFGVNVLPRDIIYY 368

>d1q8ia2 e.8.1.1 (A:390-783) Family B DNA polymerase {Escherichia coli [TaxId: 562]} Length = 394

class: Multi-domain proteins (alpha and beta)
fold: DNA/RNA polymerases
superfamily: DNA/RNA polymerases
family: DNA polymerase I
domain: Family B DNA polymerase
species: Escherichia coli [TaxId: 562]

 Score =  140 bits (353), Expect = 2e-36
 Identities = 80/358 (22%), Positives = 146/358 (40%), Gaps = 38/358 (10%)

Query: 486 NKGKGRKKAAYSGGLVLEPKKGFYDKFIILMDFNSLYPSIIQEYNICFTTIPVRMLQDSD 545
           N G+     A  GG V++ + G YD  ++++D+ SLYPSI++ + I    +   M Q   
Sbjct: 1   NLGE-VPPHASPGGYVMDSRPGLYDS-VLVLDYKSLYPSIVRTFLIDPVGLVEGMAQPDP 58

Query: 546 ITTLCEYLPEH-QVDTGILPSEIKKLVESRRQVKALMKQPNLSSDLLMQYDIRQKALKLT 604
             +   +L      +   LP  +  +   R + K    +P              +ALK+ 
Sbjct: 59  EHSTEGFLDAWFSREKHCLPEIVTNIWHGRDEAKRQGNKPL------------SQALKII 106

Query: 605 ANSMYGCLGFPNSRFFAQPLAALVTAKGREILLNTKSLVENLNYEVIYGDTDSLMISC-N 663
            N+ YG LG    RFF   LA+ +T +G +I+  TK+L+E   Y+VIYGDTDS  +    
Sbjct: 107 MNAFYGVLGTTACRFFDPRLASSITMRGHQIMRQTKALIEAQGYDVIYGDTDSTFVWLKG 166

Query: 664 VNDYDSVFKIGNQIKSECN----------KLYKQLELDIDGVYKYMLLLKKKKYAALSIS 713
            +  +   KIG  +    N          +L   LEL+ +  +   L+   +     S  
Sbjct: 167 AHSEEEAAKIGRALVQHVNAWWAETLQKQRLTSALELEYETHFCRFLMPTIRGADTGSKK 226

Query: 714 KLSNGK---MICSQEIKGVDVVRRDWSQLASEAGKFVISQILDEQSYTDYSLDDRLQNIH 770
           + +             KG++ VR DW+ LA +  + +  +I   + Y      + ++   
Sbjct: 227 RYAGLIQEGDKQRMVFKGLETVRTDWTPLAQQFQQELYLRIFRNEPY-----QEYVRETI 281

Query: 771 EHMKKIRTDLDNGFVPLTLLEITKQLTKAPEGGKVCITQIRLSRNRRGRRRRRRKKKE 828
           + +     D    +       + + L++        +   RL+     +R R  + + 
Sbjct: 282 DKLMAGELDARLVYRK----RLRRPLSEYQRNVPPHVRAARLADEENQKRGRPLQYQN 335

>d1ih7a2 e.8.1.1 (A:376-903) Family B DNA polymerase {Bacteriophage RB69 [TaxId: 12353]} Length = 528

class: Multi-domain proteins (alpha and beta)
fold: DNA/RNA polymerases
superfamily: DNA/RNA polymerases
family: DNA polymerase I
domain: Family B DNA polymerase
species: Bacteriophage RB69 [TaxId: 12353]

 Score = 96.2 bits (238), Expect = 4e-21
 Identities = 66/377 (17%), Positives = 107/377 (28%), Gaps = 110/377 (29%)

Query: 487 KGKGRKKAAYSGGLVLEPKKGFYDKFIILMDFNSLYPSIIQEYNICFTTIPVRMLQDSDI 546
           +G+      Y G  V EP    Y  +++  D  SLYPSII++ NI   TI     + + +
Sbjct: 7   QGRSHPVQPYPGAFVKEPIPNRYK-YVMSFDLTSLYPSIIRQVNISPETI-AGTFKVAPL 64

Query: 547 TTLCEYLPEHQVDT---------------GILPSEIKKLVESRRQVKALM---------- 581
                 + E   D                G++P+EI K+   R++ K  M          
Sbjct: 65  HDYINAVAERPSDVYSCSPNGMMYYKDRDGVVPTEITKVFNQRKEHKGYMLAAQRNGEII 124

Query: 582 ----------------------------------------KQPNLSSDLLMQYDIRQKAL 601
                                                   +    +    +     Q   
Sbjct: 125 KEALHNPNLSVDEPLDVDYRFDFSDEIKEKIKKLSAKSLNEMLFRAQRTEVAGMTAQINR 184

Query: 602 KLTANSMYGCLGFPNSRFFAQPLAALVTAKGREILLNTKSLVENLNYE---------VIY 652
           KL  NS+YG LG    R++    A  +T  G+  L   +  V     E         V+Y
Sbjct: 185 KLLINSLYGALGNVWFRYYDLRNATAITTFGQMALQWIERKVNEYLNEVCGTEGEAFVLY 244

Query: 653 GDTDSLMISCNVNDYDSVFKIGNQIKSECNKLYKQLELDI-------------------- 692
           GDTDS+ +S +                  + L K     +                    
Sbjct: 245 GDTDSIYVSADKIIDKVGESKFRDTNHWVDFLDKFARERMEPAIDRGFREMCEYMNNKQH 304

Query: 693 --------------DGVYKYMLLLKKKKYAALSISKLSNGKMICSQEIKGVDVVRRDWSQ 738
                                    KK+YA                +I G++  +    +
Sbjct: 305 LMFMDREAIAGPPLGSKGIGGFWTGKKRYALNVWDMEGTRYAEPKLKIMGLETQKSSTPK 364

Query: 739 LASEAGKFVISQILDEQ 755
              +A K  I ++L E 
Sbjct: 365 AVQKALKECIRRMLQEG 381

>d2py5a2 e.8.1.1 (A:188-575) phi29 DNA polymerase {Bacteriophage phi-29 [TaxId: 10756]} Length = 388

class: Multi-domain proteins (alpha and beta)
fold: DNA/RNA polymerases
superfamily: DNA/RNA polymerases
family: DNA polymerase I
domain: phi29 DNA polymerase
species: Bacteriophage phi-29 [TaxId: 10756]

 Score = 61.8 bits (149), Expect = 2e-10
 Identities = 45/347 (12%), Positives = 94/347 (27%), Gaps = 96/347 (27%)

Query: 493 KAAYSGGLV--LEPKKGFYDKFIILMDFNSLYPSIIQEYNICFTTIPVRMLQDSDITTLC 550
           + AY GG     +  K       ++ D NSLYP+ +    + +    V   +        
Sbjct: 36  RYAYRGGFTWLNDRFKEKEIGEGMVFDVNSLYPAQMYSRLLPYGEPIVFEGKYVWDEDYP 95

Query: 551 EYL---------------------------------PEHQVDTGILPSEIKKLVESRRQV 577
            ++                                    ++    L +   +L++    +
Sbjct: 96  LHIQHIRCEFELKEGYIPTIQIKRSRFYKGNEYLKSSGGEIADLWLSNVDLELMKEHYDL 155

Query: 578 KALM--------KQPNLSSDLL--------MQYDIRQKALKLTANSMYGCLGFPNS---- 617
             +             L  D +              ++  KL  NS+YG           
Sbjct: 156 YNVEYISGLKFKATTGLFKDFIDKWTYIKTTSEGAIKQLAKLMLNSLYGKFASNPDVTGK 215

Query: 618 --------------------RFFAQPLAALVTAKGREILLNTKSLVENLNYEVIYGDTDS 657
                                    P+   +TA  R   +      +     +IY DTDS
Sbjct: 216 VPYLKENGALGFRLGEEETKDPVYTPMGVFITAWARYTTITAA---QACYDRIIYCDTDS 272

Query: 658 LMISCN-VNDYDSVFKIGNQIKSECNKLYKQLELDIDGVYKYMLLLKKKKYAALSISKLS 716
           + ++   + D         ++               +  +K    L++K Y      K  
Sbjct: 273 IHLTGTEIPDVIKDIVDPKKL----------GYWAHESTFKRAKYLRQKTYIQDIYMKEV 322

Query: 717 NGKMICSQEIKGVDVVRRDWSQLASEAGKFVISQILDEQSYTDYSLD 763
           +GK++   E    D     +S         +  +I  E ++ ++ + 
Sbjct: 323 DGKLV---EGSPDDYTDIKFSVKC----AGMTDKIKKEVTFENFKVG 362

>d1q8ia1 c.55.3.5 (A:2-389) Exonuclease domain of family B DNA polymerases {Escherichia coli [TaxId: 562]} Length = 388

class: Alpha and beta proteins (a/b)
fold: Ribonuclease H-like motif
superfamily: Ribonuclease H-like
family: DnaQ-like 3'-5' exonuclease
domain: Exonuclease domain of family B DNA polymerases
species: Escherichia coli [TaxId: 562]

 Score = 58.5 bits (141), Expect = 2e-09
 Identities = 12/65 (18%), Positives = 22/65 (33%), Gaps = 2/65 (3%)

Query: 404 EFIKFTMLHSSYIIKIMCELNVLPLAIQITNVCGNVLSRTLMGGRSERNEFLLLHAFHEK 463
               + +     + +I  +  ++P  ++   V G  + R   GG       L     H  
Sbjct: 326 ALATYNLKDCELVTQIFHKTEIMPFLLERATVNGLPVDRH--GGSVAAFGHLYFPRMHRA 383

Query: 464 SYVLP 468
            YV P
Sbjct: 384 GYVAP 388

>d1sa0e_ a.137.10.1 (E:) Stathmin 4 {Rat (Rattus norvegicus) [TaxId: 10116]} Length = 138

class: All alpha proteins
fold: Non-globular all-alpha subunits of globular proteins
superfamily: Stathmin
family: Stathmin
domain: Stathmin 4
species: Rat (Rattus norvegicus) [TaxId: 10116]

 Score = 51.4 bits (123), Expect = 3e-08
 Identities = 20/107 (18%), Positives = 42/107 (39%)

Query: 924  RRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRSGKEEEEEEKKKEEKKKEEEEKKKKEGKT 983
                      RRR       +++      RR  +E E  +   E+++ E E  +K   + 
Sbjct: 28   GVPEFNASLPRRRDPSLEEIQKKLEAAEERRKYQEAELLKHLAEKREHEREVIQKAIEEN 87

Query: 984  KKEEKKKEEEEEKKKKKKEEEKEEEEKKEEEEKEEEEKKRRRIRRKR 1030
                K  +E+  +K +  +E +E       E  +E++K    +R+ +
Sbjct: 88   NNFIKMAKEKLAQKMESNKENREAHLAAMLERLQEKDKHAEEVRKNK 134

>d1sa0e_ a.137.10.1 (E:) Stathmin 4 {Rat (Rattus norvegicus) [TaxId: 10116]} Length = 138

class: All alpha proteins
fold: Non-globular all-alpha subunits of globular proteins
superfamily: Stathmin
family: Stathmin
domain: Stathmin 4
species: Rat (Rattus norvegicus) [TaxId: 10116]

 Score = 51.0 bits (122), Expect = 4e-08
 Identities = 24/101 (23%), Positives = 41/101 (40%)

Query: 922  RRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRSGKEEEEEEKKKEEKKKEEEEKKKKEG 981
            RRR       +++      RR+ +     +     +E E E  +K  ++     K  KE 
Sbjct: 38   RRRDPSLEEIQKKLEAAEERRKYQEAELLKHLAEKREHEREVIQKAIEENNNFIKMAKEK 97

Query: 982  KTKKEEKKKEEEEEKKKKKKEEEKEEEEKKEEEEKEEEEKK 1022
              +K E  KE  E       E  +E+++  EE  K +E K+
Sbjct: 98   LAQKMESNKENREAHLAAMLERLQEKDKHAEEVRKNKELKE 138

>d1sa0e_ a.137.10.1 (E:) Stathmin 4 {Rat (Rattus norvegicus) [TaxId: 10116]} Length = 138

class: All alpha proteins
fold: Non-globular all-alpha subunits of globular proteins
superfamily: Stathmin
family: Stathmin
domain: Stathmin 4
species: Rat (Rattus norvegicus) [TaxId: 10116]

 Score = 49.1 bits (117), Expect = 2e-07
 Identities = 21/113 (18%), Positives = 43/113 (38%)

Query: 910  SRRRRSRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRSGKEEEEEEKKKEEK 969
            S            RRR       +++      RR+ +     +  + K E E E  ++  
Sbjct: 25   SFDGVPEFNASLPRRRDPSLEEIQKKLEAAEERRKYQEAELLKHLAEKREHEREVIQKAI 84

Query: 970  KKEEEEKKKKEGKTKKEEKKKEEEEEKKKKKKEEEKEEEEKKEEEEKEEEEKK 1022
            ++     K  + K  ++ +  +E  E       E  +E++K  EE ++ +E K
Sbjct: 85   EENNNFIKMAKEKLAQKMESNKENREAHLAAMLERLQEKDKHAEEVRKNKELK 137

>d1sa0e_ a.137.10.1 (E:) Stathmin 4 {Rat (Rattus norvegicus) [TaxId: 10116]} Length = 138

class: All alpha proteins
fold: Non-globular all-alpha subunits of globular proteins
superfamily: Stathmin
family: Stathmin
domain: Stathmin 4
species: Rat (Rattus norvegicus) [TaxId: 10116]

 Score = 47.2 bits (112), Expect = 8e-07
 Identities = 17/113 (15%), Positives = 45/113 (39%)

Query: 905  KKRRRSRRRRSRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRSGKEEEEEEK 964
                        RRR       +++      RR+ +     +    +R    +  ++  +
Sbjct: 26   FDGVPEFNASLPRRRDPSLEEIQKKLEAAEERRKYQEAELLKHLAEKREHEREVIQKAIE 85

Query: 965  KKEEKKKEEEEKKKKEGKTKKEEKKKEEEEEKKKKKKEEEKEEEEKKEEEEKE 1017
            +     K  +EK  ++ ++ KE ++       ++ +++++  EE +K +E KE
Sbjct: 86   ENNNFIKMAKEKLAQKMESNKENREAHLAAMLERLQEKDKHAEEVRKNKELKE 138

>d1sa0e_ a.137.10.1 (E:) Stathmin 4 {Rat (Rattus norvegicus) [TaxId: 10116]} Length = 138

class: All alpha proteins
fold: Non-globular all-alpha subunits of globular proteins
superfamily: Stathmin
family: Stathmin
domain: Stathmin 4
species: Rat (Rattus norvegicus) [TaxId: 10116]

 Score = 42.6 bits (100), Expect = 3e-05
 Identities = 14/91 (15%), Positives = 36/91 (39%)

Query: 899 RRRRRRKKRRRSRRRRSRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRSGKE 958
           +++    + RR  +     +    +R   R   ++         +  + +  ++  S KE
Sbjct: 48  QKKLEAAEERRKYQEAELLKHLAEKREHEREVIQKAIEENNNFIKMAKEKLAQKMESNKE 107

Query: 959 EEEEEKKKEEKKKEEEEKKKKEGKTKKEEKK 989
             E       ++ +E++K  +E +  KE K+
Sbjct: 108 NREAHLAAMLERLQEKDKHAEEVRKNKELKE 138

>d1sa0e_ a.137.10.1 (E:) Stathmin 4 {Rat (Rattus norvegicus) [TaxId: 10116]} Length = 138

class: All alpha proteins
fold: Non-globular all-alpha subunits of globular proteins
superfamily: Stathmin
family: Stathmin
domain: Stathmin 4
species: Rat (Rattus norvegicus) [TaxId: 10116]

 Score = 37.6 bits (87), Expect = 0.002
 Identities = 16/101 (15%), Positives = 40/101 (39%), Gaps = 3/101 (2%)

Query: 879 RRRRSGKEEEEKKKKEGGGGRRRRRRKKRRRSRRRRSRRRRRRRRRRRRRRRRRRRRRRR 938
           RRR    EE +KK +     R+ +  +  +    +R   R   ++         +  + +
Sbjct: 38  RRRDPSLEEIQKKLEAAEERRKYQEAELLKHLAEKREHEREVIQKAIEENNNFIKMAKEK 97

Query: 939 RRRRRRRRRRRRRRRRSGKEE---EEEEKKKEEKKKEEEEK 976
             ++    +  R    +   E   E+++  +E +K +E ++
Sbjct: 98  LAQKMESNKENREAHLAAMLERLQEKDKHAEEVRKNKELKE 138

>d1f5na1 a.114.1.1 (A:284-583) Interferon-induced guanylate-binding protein 1 (GBP1), C-terminal domain {Human (Homo sapiens) [TaxId: 9606]} Length = 300

class: All alpha proteins
fold: Interferon-induced guanylate-binding protein 1 (GBP1), C-terminal domain
superfamily: Interferon-induced guanylate-binding protein 1 (GBP1), C-terminal domain
family: Interferon-induced guanylate-binding protein 1 (GBP1), C-terminal domain
domain: Interferon-induced guanylate-binding protein 1 (GBP1), C-terminal domain
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 52.4 bits (125), Expect = 1e-07
 Identities = 14/152 (9%), Positives = 61/152 (40%)

Query: 873  GGRRRRRRRRSGKEEEEKKKKEGGGGRRRRRRKKRRRSRRRRSRRRRRRRRRRRRRRRRR 932
            GG R   ++    +++  ++   G       +   +          +  +    + +   
Sbjct: 148  GGYRLFVQKLQDLKKKYYEEPRKGIQAEEILQTYLKSKESMTDAILQTDQTLTEKEKEIE 207

Query: 933  RRRRRRRRRRRRRRRRRRRRRRSGKEEEEEEKKKEEKKKEEEEKKKKEGKTKKEEKKKEE 992
              R +    +   +     +R++ +  E++E+  +E  K+  EK + +     +E+++  
Sbjct: 208  VERVKAESAQASAKMLHEMQRKNEQMMEQKERSYQEHLKQLTEKMENDRVQLLKEQERTL 267

Query: 993  EEEKKKKKKEEEKEEEEKKEEEEKEEEEKKRR 1024
              + +++++  ++  +++    + E ++ + +
Sbjct: 268  ALKLQEQEQLLKEGFQKESRIMKNEIQDLQTK 299

>d1f5na1 a.114.1.1 (A:284-583) Interferon-induced guanylate-binding protein 1 (GBP1), C-terminal domain {Human (Homo sapiens) [TaxId: 9606]} Length = 300

class: All alpha proteins
fold: Interferon-induced guanylate-binding protein 1 (GBP1), C-terminal domain
superfamily: Interferon-induced guanylate-binding protein 1 (GBP1), C-terminal domain
family: Interferon-induced guanylate-binding protein 1 (GBP1), C-terminal domain
domain: Interferon-induced guanylate-binding protein 1 (GBP1), C-terminal domain
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 51.3 bits (122), Expect = 3e-07
 Identities = 25/214 (11%), Positives = 78/214 (36%), Gaps = 4/214 (1%)

Query: 821  RRRRKKKEEKKKWKRRGGGRRRRRGKKEEEKKKKKEEEEEGGEKEEEEGGGGGGRRRRRR 880
              R  ++E  + + R          +KE   + +K+ ++   + +E       G  +   
Sbjct: 73   LHRDSEREAIEVFIRSSFKDVDHLFQKELAAQLEKKRDDFCKQNQEASSDRCSGLLQVIF 132

Query: 881  RRSGKEEEEKKKKEGGGGRRRRRRKKRRRSRRRRSRRRRRR----RRRRRRRRRRRRRRR 936
                +E +     + GG R   ++ +  + +     R+  +     +   + +       
Sbjct: 133  SPLEEEVKAGIYSKPGGYRLFVQKLQDLKKKYYEEPRKGIQAEEILQTYLKSKESMTDAI 192

Query: 937  RRRRRRRRRRRRRRRRRRSGKEEEEEEKKKEEKKKEEEEKKKKEGKTKKEEKKKEEEEEK 996
             +  +    + +     R   E  +   K   + + + E+  ++ +   +E  K+  E+ 
Sbjct: 193  LQTDQTLTEKEKEIEVERVKAESAQASAKMLHEMQRKNEQMMEQKERSYQEHLKQLTEKM 252

Query: 997  KKKKKEEEKEEEEKKEEEEKEEEEKKRRRIRRKR 1030
            +  + +  KE+E     + +E+E+  +   +++ 
Sbjct: 253  ENDRVQLLKEQERTLALKLQEQEQLLKEGFQKES 286

>d1f5na1 a.114.1.1 (A:284-583) Interferon-induced guanylate-binding protein 1 (GBP1), C-terminal domain {Human (Homo sapiens) [TaxId: 9606]} Length = 300

class: All alpha proteins
fold: Interferon-induced guanylate-binding protein 1 (GBP1), C-terminal domain
superfamily: Interferon-induced guanylate-binding protein 1 (GBP1), C-terminal domain
family: Interferon-induced guanylate-binding protein 1 (GBP1), C-terminal domain
domain: Interferon-induced guanylate-binding protein 1 (GBP1), C-terminal domain
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 47.0 bits (111), Expect = 5e-06
 Identities = 22/153 (14%), Positives = 60/153 (39%), Gaps = 8/153 (5%)

Query: 846 KKEEEKKKKKEEEEEGGEKEEEEGGGGGGRRRRRRRRSGKEEEEKKKKEGGGGRRRRRRK 905
           +K ++ KKK  EE   G + EE          +   +S +   +   +       + +  
Sbjct: 155 QKLQDLKKKYYEEPRKGIQAEEI--------LQTYLKSKESMTDAILQTDQTLTEKEKEI 206

Query: 906 KRRRSRRRRSRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRSGKEEEEEEKK 965
           +  R +   ++   +     +R+  +   ++ R  +   ++   +      +  +E+E+ 
Sbjct: 207 EVERVKAESAQASAKMLHEMQRKNEQMMEQKERSYQEHLKQLTEKMENDRVQLLKEQERT 266

Query: 966 KEEKKKEEEEKKKKEGKTKKEEKKKEEEEEKKK 998
              K +E+E+  K+  + +    K E ++ + K
Sbjct: 267 LALKLQEQEQLLKEGFQKESRIMKNEIQDLQTK 299

>d1f5na1 a.114.1.1 (A:284-583) Interferon-induced guanylate-binding protein 1 (GBP1), C-terminal domain {Human (Homo sapiens) [TaxId: 9606]} Length = 300

class: All alpha proteins
fold: Interferon-induced guanylate-binding protein 1 (GBP1), C-terminal domain
superfamily: Interferon-induced guanylate-binding protein 1 (GBP1), C-terminal domain
family: Interferon-induced guanylate-binding protein 1 (GBP1), C-terminal domain
domain: Interferon-induced guanylate-binding protein 1 (GBP1), C-terminal domain
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 38.6 bits (89), Expect = 0.003
 Identities = 14/161 (8%), Positives = 51/161 (31%)

Query: 807 ITQIRLSRNRRGRRRRRRKKKEEKKKWKRRGGGRRRRRGKKEEEKKKKKEEEEEGGEKEE 866
           +     S+    R   ++ +  +KK ++    G +     +   K K+   +      + 
Sbjct: 139 VKAGIYSKPGGYRLFVQKLQDLKKKYYEEPRKGIQAEEILQTYLKSKESMTDAILQTDQT 198

Query: 867 EEGGGGGGRRRRRRRRSGKEEEEKKKKEGGGGRRRRRRKKRRRSRRRRSRRRRRRRRRRR 926
                      R +  S +   +   +      +   +K+R      +    +    R +
Sbjct: 199 LTEKEKEIEVERVKAESAQASAKMLHEMQRKNEQMMEQKERSYQEHLKQLTEKMENDRVQ 258

Query: 927 RRRRRRRRRRRRRRRRRRRRRRRRRRRRSGKEEEEEEKKKE 967
             + + R    + + + +  +   ++     + E ++ + +
Sbjct: 259 LLKEQERTLALKLQEQEQLLKEGFQKESRIMKNEIQDLQTK 299

Homologous Domains Detected by HHsearch

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

ID	Length	Definition	Probability
Query	1030
d1tgoa2	426	Family B DNA polymerase {Archaeon Thermococcus gor	100.0
d1s5ja2	415	Family B DNA polymerase {Sulfolobus solfataricus [	100.0
d1q8ia2	394	Family B DNA polymerase {Escherichia coli [TaxId:	100.0
d1ih7a2	528	Family B DNA polymerase {Bacteriophage RB69 [TaxId	100.0
d2py5a2	388	phi29 DNA polymerase {Bacteriophage phi-29 [TaxId:	99.9
d1q8ia1	388	Exonuclease domain of family B DNA polymerases {Es	99.1
d1noya_	372	Exonuclease domain of family B DNA polymerases {Ba	97.72
d1s5ja1	410	Exonuclease domain of family B DNA polymerases {Su	97.55
d1ih7a1	375	Exonuclease domain of family B DNA polymerases {Ba	97.5
d1tgoa1	347	Exonuclease domain of family B DNA polymerases {Ar	95.36

>d1tgoa2 e.8.1.1 (A:348-773) Family B DNA polymerase {Archaeon Thermococcus gorgonarius [TaxId: 71997]}

class: Multi-domain proteins (alpha and beta)
fold: DNA/RNA polymerases
superfamily: DNA/RNA polymerases
family: DNA polymerase I
domain: Family B DNA polymerase
species: Archaeon Thermococcus gorgonarius [TaxId: 71997]

Probab=100.00  E-value=1.6e-69  Score=623.00  Aligned_cols=338  Identities=29%  Similarity=0.473  Sum_probs=296.6

Q ss_pred             hhHHHHHHHHHHHhhcCeeccCCccccCcCCCccccccccCCCCCCccccCceeeccccccccceEEEeeccccChhHHH
Q psy6283         448 RSERNEFLLLHAFHEKSYVLPDKQYGKNKKEGEETGEANKGKGRKKAAYSGGLVLEPKKGFYDKFIILMDFNSLYPSIIQ  527 (1030)
Q Consensus       448 r~~r~E~lLL~~~~~~~yivPdk~~~kk~~~~~d~~~~~~~~~~~~~~Y~GGlVleP~~GlY~~~V~vLDFnSLYPSII~  527 (1030)
                      .+.++|++|+|+++++|+++|+++....             ......+|+||+|++|++|||+ +|++|||+|||||||+
T Consensus         2 ~g~~ve~~~~~~~~~~~~~~p~~~~~~~-------------~~~~~~~y~Gg~V~~p~~G~~~-~v~~lDf~SLYPsii~   67 (426)
T d1tgoa2           2 TGNLVEWFLLRKAYERNELAPNKPDERE-------------LARRRESYAGGYVKEPERGLWE-NIVYLDFRSLYPSIII   67 (426)
T ss_dssp             HHHHHHHHHHHHHHHTTBCCCCCCCHHH-------------HHHCCCCCCCCCEECCCCSEEE-EEEEEEESSHHHHHHH
T ss_pred             chHHHHHHHHHHHHHCCEEeccCCcccc-------------ccccccCcCCceEccCCCCcCC-CeEEEEccchhHHHHH
Confidence            3567999999999999999998753210             1123568999999999999997 5999999999999999


Q ss_pred             HhccccccccccCCCccccccccCCCCC--ccccCCcchHHHHHHHHHHHHHHHHhcCCCCChHHHHhhHHHHHHhcccc
Q psy6283         528 EYNICFTTIPVRMLQDSDITTLCEYLPE--HQVDTGILPSEIKKLVESRRQVKALMKQPNLSSDLLMQYDIRQKALKLTA  605 (1030)
Q Consensus       528 ~~NIc~tTv~~~~~d~~~i~~~~p~~p~--~~~~~GIlP~iL~~Ll~~R~~vKk~mk~~~~~~~~~~~~d~rQ~AlKl~a  605 (1030)
                      +|||||+|+++..++...+   .|....  .....||+|.+|+.|++.|.++|++|++ ..++.++..||.+|+|+||++
T Consensus        68 ~~Ni~p~T~~~~~~~~~~~---~~~~g~~~~~~~~Gilp~~l~~l~~~R~~~K~~~k~-~~~~~~~~~~d~~Q~a~Ki~~  143 (426)
T d1tgoa2          68 THNVSPDTLNREGCEEYDV---APQVGHKFCKDFPGFIPSLLGDLLEERQKVKKKMKA-TIDPIEKKLLDYRQRAIKILA  143 (426)
T ss_dssp             HTTCSTTTBTCTTCSSEEE---CTTTCCEEECSSCCHHHHHHHHHHHHHHHHHHHHHH-CCCHHHHHHHHHHHHHHHHHH
T ss_pred             HhCCChhhcCCCCcccccc---CCCCCceEeccCCCchHHHHHHHHHHHHHhhhhhhh-ccchHHHHHHHHHHHHHHHhh
Confidence            9999999999876533222   132221  2357899999999999999999999998 568999999999999999999


Q ss_pred             ccccccCCCCCCCCCCHHHHHHHHHHhHHHHHHHHHHhhh-ccceeEEecCcceeeecCCCCHHHHHHHHHHHHHHHhcc
Q psy6283         606 NSMYGCLGFPNSRFFAQPLAALVTAKGREILLNTKSLVEN-LNYEVIYGDTDSLMISCNVNDYDSVFKIGNQIKSECNKL  684 (1030)
Q Consensus       606 NS~YG~lG~~~srfy~~~lA~~IT~~GR~iL~~tkelve~-~g~~VIYGDTDSI~V~~~~~d~eea~~ig~~i~~~Vn~~  684 (1030)
                      ||+|||+|+++++|||.++|++||++||.+|..|+..+++ +|++|||||||||||.++..+.+++.+++.++.+.||..
T Consensus       144 NS~YG~~G~~~~~~~~~~~A~~iT~~GR~~i~~~~~~i~~~~g~~ViYgDTDSi~v~~~~~~~~~~~~~~~~~~~~i~~~  223 (426)
T d1tgoa2         144 NSFYGYYGYAKARWYCKECAESVTAWGRQYIETTIREIEEKFGFKVLYADTDGFFATIPGADAETVKKKAKEFLDYINAK  223 (426)
T ss_dssp             TTHHHHHHCTTCTTCCHHHHHHHHHHHHHHHHHHHHHHHHTTCCEEEEEESSEEEEECTTCCHHHHHHHHHHHHHHHHTT
T ss_pred             hHHHHHHhccchhhhhhhhhhhhHHHHHHHHHHHHHHHHHHcCCeeeeecccceEEecCCchhHHHHHHHHHHHHHHHHH
Confidence            9999999999999999999999999999999999887775 699999999999999999999999999999999999987


Q ss_pred             cc-eeEEeecchhhhhhhcccccceEEeeeecCCCceeeeceeeeeeeeeCChHHHHHHHHHHHHHHHhccCCCCCCChh
Q psy6283         685 YK-QLELDIDGVYKYMLLLKKKKYAALSISKLSNGKMICSQEIKGVDVVRRDWSQLASEAGKFVISQILDEQSYTDYSLD  763 (1030)
Q Consensus       685 ~~-~leLe~E~vf~~llll~KKrYa~l~~~~~~dG~~~~~~e~KGle~vRRD~~~l~k~~~~~vL~~IL~~~~~~~~~~e  763 (1030)
                      ++ +++|++|++|.+++|++||||+++.    .+|    ++++||++++|||||+++++++..+|+.||.+.     +.+
T Consensus       224 ~~~~i~le~E~iy~~~l~~~KKrY~~~~----~~~----k~~~kGie~~Rrd~~~~~k~~~~~vl~~il~~~-----d~~  290 (426)
T d1tgoa2         224 LPGLLELEYEGFYKRGFFVTKKKYAVID----EED----KITTRGLEIVRRDWSEIAKETQARVLEAILKHG-----DVE  290 (426)
T ss_dssp             SCTTCCEEEEEEEEEEEEEETTEEEEEC----TTC----CEEEESCSCCSSCBCHHHHHHHHHHHHHHHTTC-----CHH
T ss_pred             hcchhhhheeeeeeecceecccceeeee----cCC----CcccceeeecCCCCchhHHHHHHHHHHHHhccC-----ccc
Confidence            75 7999999999999999999999873    344    457999999999999999999999999999988     665


Q ss_pred             HHHHHHHHHHHHHHHHhhCCCcChhhhHHhhcccCCCCC--CcchHHHHHHHHHHcCCc
Q psy6283         764 DRLQNIHEHMKKIRTDLDNGFVPLTLLEITKQLTKAPEG--GKVCITQIRLSRNRRGRR  820 (1030)
Q Consensus       764 ~~v~~I~~~l~~~~~~l~~g~vpl~~lvItk~LsK~p~~--~~~pHV~vA~r~~~~g~~  820 (1030)
                      ++    .+++.+...+|.+|++|+++|+|+++|++++++  ..+|||++|.||.++|..
T Consensus       291 ~~----~~~i~~~~~~l~~~~~~~edl~i~~~l~k~~~~Yk~~~phv~~a~rl~~~g~~  345 (426)
T d1tgoa2         291 EA----VRIVKEVTEKLSKYEVPPEKLVIYEQITRDLKDYKATGPHVAVAKRLAARGIK  345 (426)
T ss_dssp             HH----HHHHHHHHHHHHTTCSCGGGSCEEEECSSCGGGSCSSSSHHHHHHHHHHHTCC
T ss_pred             hh----hHHHHHHHHHHhcCCCCHHHHhhhhhhccChhhccccCcHHHHHHHHHhcCCC
Confidence            54    455566677899999999999999999999988  678999999999988754

>d1s5ja2 e.8.1.1 (A:450-864) Family B DNA polymerase {Sulfolobus solfataricus [TaxId: 2287]}

class: Multi-domain proteins (alpha and beta)
fold: DNA/RNA polymerases
superfamily: DNA/RNA polymerases
family: DNA polymerase I
domain: Family B DNA polymerase
species: Sulfolobus solfataricus [TaxId: 2287]

Probab=100.00  E-value=7e-67  Score=599.07  Aligned_cols=346  Identities=24%  Similarity=0.344  Sum_probs=229.5

Q ss_pred             HHHHHHHHHhhcCeeccCCccccCcCCCccccccccCCCCCCccccCceeeccccccccceEEEeeccccChhHHHHhcc
Q psy6283         452 NEFLLLHAFHEKSYVLPDKQYGKNKKEGEETGEANKGKGRKKAAYSGGLVLEPKKGFYDKFIILMDFNSLYPSIIQEYNI  531 (1030)
Q Consensus       452 ~E~lLL~~~~~~~yivPdk~~~kk~~~~~d~~~~~~~~~~~~~~Y~GGlVleP~~GlY~~~V~vLDFnSLYPSII~~~NI  531 (1030)
                      +++||+|+++++||++|++.......   +.  .......+..+|+||+|++|++|+|++ |++|||+|||||||++|||
T Consensus         6 i~~~~~~~~~~~~~~iP~k~~~~~~~---~~--~~~~~~~~~~~y~Gg~V~~P~~G~~~~-V~~lDf~SLYPSii~~~Ni   79 (415)
T d1s5ja2           6 VKNLYYWEHRKRNWLIPLKEEILAKS---SN--IRTSALIKGKGYKGAVVIDPPAGIFFN-ITVLDFASLYPSIIRTWNL   79 (415)
T ss_dssp             HHHHHHHHHHHHTBCCCCHHHHHHTT---CC----------------CCCCCCCSEEEEE-EEEEEETTHHHHHHHHTTC
T ss_pred             HHHHHHHHHHHCCEeCCCCccccccc---cc--hhhhhccccCCcCCeEEcCCCCCccCc-eEEEEcccccHHHHHHhCC
Confidence            69999999999999999875321000   00  000112235689999999999999986 9999999999999999999


Q ss_pred             ccccccccCCC-ccccccccCCC--CCccccCCcchHHHHHHHHHHHHHHHH-hcCCCCChHHHHhhHHHHHHhcccccc
Q psy6283         532 CFTTIPVRMLQ-DSDITTLCEYL--PEHQVDTGILPSEIKKLVESRRQVKAL-MKQPNLSSDLLMQYDIRQKALKLTANS  607 (1030)
Q Consensus       532 c~tTv~~~~~d-~~~i~~~~p~~--p~~~~~~GIlP~iL~~Ll~~R~~vKk~-mk~~~~~~~~~~~~d~rQ~AlKl~aNS  607 (1030)
                      ||+|++...+. ...+.+..+.+  .....+.|++|.++..|++.|..+|+. ++....+++++.+||.+|+|+||++||
T Consensus        80 ~~~T~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~l~~~R~~~~~~~~k~~~~~~~~~~~~d~~Q~A~Ki~~NS  159 (415)
T d1s5ja2          80 SYETVDIQQCKKPYEVKDETGEVLHIVCMDRPGITAVITGLLRDFRVKIYKKKAKNPNNSEEQKLLYDVVQRAMKVFINA  159 (415)
T ss_dssp             CTTTBSCSCCSSCCEECCSSSCCCEEBCCSSCCHHHHHHHHHHHHHHHTHHHHHTCTTSCHHHHHHHHHHHHHHHHHHHH
T ss_pred             ChhhcCccccCCCcccccCCCCeeEEeeCCCCCccHHHHHHHHHHHHHhhhccccccccchhHHHHHHHHHHHHHHHHHH
Confidence            99999876642 11111111111  112457999999999999999987554 555566778899999999999999999


Q ss_pred             ccccCCCCCCCCCCHHHHHHHHHHhHHHHHHHHHHhhhccceeEEecCcceeeecCCCCHHHHHHHHHHHHHHHhcccce
Q psy6283         608 MYGCLGFPNSRFFAQPLAALVTAKGREILLNTKSLVENLNYEVIYGDTDSLMISCNVNDYDSVFKIGNQIKSECNKLYKQ  687 (1030)
Q Consensus       608 ~YG~lG~~~srfy~~~lA~~IT~~GR~iL~~tkelve~~g~~VIYGDTDSI~V~~~~~d~eea~~ig~~i~~~Vn~~~~~  687 (1030)
                      +|||||+++++|||+++|++||++||.+|+.|++++++.|++|||||||||||..+..+  .+.    ++.+.|+..+ +
T Consensus       160 ~YG~~G~~~~~~~~~~~A~~iT~~GR~~i~~~~~~~~~~g~~viygDTDSv~v~~~~~~--~~e----~~~~~i~~~~-~  232 (415)
T d1s5ja2         160 TYGVFGAETFPLYAPRVAESVTALGRYVITSTVKKAREEGLTVLYGDTDSLFLLNPPKN--SLE----NIIKWVKTTF-N  232 (415)
T ss_dssp             HHHHHHSTTSTTCCHHHHHHHHHHHHHHHHHHHHHHHTTTCCEEEEETTEEEEESCCHH--HHH----HHHHHHHHHS-S
T ss_pred             HHHHHhccccccccHHHHHHHHHHHHHHHHHHHHHhhhcCceeeeeecceeEEecCCCc--hHH----HHHHHHHhhc-c
Confidence            99999999999999999999999999999999999999999999999999999887532  232    3445555555 4


Q ss_pred             eEEeecchhhhhhhc-ccccceEEeeeecCCCceeeeceeeeeeeeeCChHHHHHHHHHHHHHHHhccCCCCCCChhHHH
Q psy6283         688 LELDIDGVYKYMLLL-KKKKYAALSISKLSNGKMICSQEIKGVDVVRRDWSQLASEAGKFVISQILDEQSYTDYSLDDRL  766 (1030)
Q Consensus       688 leLe~E~vf~~llll-~KKrYa~l~~~~~~dG~~~~~~e~KGle~vRRD~~~l~k~~~~~vL~~IL~~~~~~~~~~e~~v  766 (1030)
                      ++|++|++|.+++|+ +|||||++.    .+|+    +++||++++|||||++++.++..+|+.||.+.+..  +...++
T Consensus       233 ~~le~e~~~~~~~~~~~KKrY~g~~----~dgk----l~~kGie~vRrd~~~~~k~~~~~vl~~il~~~~~~--~~~~~~  302 (415)
T d1s5ja2         233 LDLEVDKTYKFVAFSGLKKNYFGVY----QDGK----VDIKGMLVKKRNTPEFVKKVFNEVKELMISINSPN--DVKEIK  302 (415)
T ss_dssp             CCEEEEEEEEEEEEC----CEEEEC----SSSC----CCEESCCC--------CCSHHHHHHHHHHTTCCSC--CTTHHH
T ss_pred             cccccceeeehhhhhhhhhhccccc----cccc----ceeeeeeccccccHHHHHHHHHHHHHHHHccCCHH--HHHHHH
Confidence            899999999988775 699999974    3554    57999999999999999999999999999987333  345577


Q ss_pred             HHHHHHHHHHHHHhhCCCcChhhhHHhhcccCCCCC---CcchHHHHHHHHHHcCCc
Q psy6283         767 QNIHEHMKKIRTDLDNGFVPLTLLEITKQLTKAPEG---GKVCITQIRLSRNRRGRR  820 (1030)
Q Consensus       767 ~~I~~~l~~~~~~l~~g~vpl~~lvItk~LsK~p~~---~~~pHV~vA~r~~~~g~~  820 (1030)
                      ..|.+++.+...+|.+|.+|+++|+|+++|+|++++   .++|||+||++|+++|..
T Consensus       303 ~~i~~~l~~~~~~l~~~~i~~~dl~~~k~l~k~~~~Y~~~~p~hv~~A~~l~~~g~~  359 (415)
T d1s5ja2         303 RKIVDVVKGSYEKLKNKGYNLDELAFKVMLSKPLDAYKKNTPQHVKAALQLRPFGVN  359 (415)
T ss_dssp             HHHHHHHHHHHCTTC------------------------------------------
T ss_pred             HHHHHHHHHHHHHHhcCCCChHHhccccccccChhhccCCCcHHHHHHHHHHhcCCC
Confidence            888999999999999999999999999999999877   567899999999988744

>d1q8ia2 e.8.1.1 (A:390-783) Family B DNA polymerase {Escherichia coli [TaxId: 562]}

class: Multi-domain proteins (alpha and beta)
fold: DNA/RNA polymerases
superfamily: DNA/RNA polymerases
family: DNA polymerase I
domain: Family B DNA polymerase
species: Escherichia coli [TaxId: 562]

Probab=100.00  E-value=5.4e-59  Score=528.87  Aligned_cols=295  Identities=27%  Similarity=0.408  Sum_probs=224.8

Q ss_pred             CCccccCceeeccccccccceEEEeeccccChhHHHHhccccccccccCCCccccccccCCCC--CccccCCcchHHHHH
Q psy6283         492 KKAAYSGGLVLEPKKGFYDKFIILMDFNSLYPSIIQEYNICFTTIPVRMLQDSDITTLCEYLP--EHQVDTGILPSEIKK  569 (1030)
Q Consensus       492 ~~~~Y~GGlVleP~~GlY~~~V~vLDFnSLYPSII~~~NIc~tTv~~~~~d~~~i~~~~p~~p--~~~~~~GIlP~iL~~  569 (1030)
                      +..+|+||+|++|++|+|+ +|++|||+|||||||++|||||+|++...+..+..... +.+.  ..+.+.||||.+|+.
T Consensus         6 ~~~~y~Gg~V~~p~~G~~~-~v~~lDf~SLYPsii~~~Ni~p~t~v~~~~~~~~~~~~-~~~~~~~~~~~~g~lp~~l~~   83 (394)
T d1q8ia2           6 PPHASPGGYVMDSRPGLYD-SVLVLDYKSLYPSIVRTFLIDPVGLVEGMAQPDPEHST-EGFLDAWFSREKHCLPEIVTN   83 (394)
T ss_dssp             CCCCCCCCCCBCCCCEEEE-EEEEEEETTHHHHHHHHHCCCHHHHHHHHHSCSTTTEE-ECSTTCEEESSSCSHHHHHHH
T ss_pred             CCCCCCCcEEcCCCCCcCC-CeeEEEccchHHHHHHHhCCChhhcCCCCcCCCCcccc-CCccceeeeechhHHHHHHHH
Confidence            3467999999999999996 59999999999999999999999998654311110000 1111  124578999999999


Q ss_pred             HHHHHHHHHHHhcCCCCChHHHHhhHHHHHHhccccccccccCCCCCCCCCCHHHHHHHHHHhHHHHHHHHHHhhhccce
Q psy6283         570 LVESRRQVKALMKQPNLSSDLLMQYDIRQKALKLTANSMYGCLGFPNSRFFAQPLAALVTAKGREILLNTKSLVENLNYE  649 (1030)
Q Consensus       570 Ll~~R~~vKk~mk~~~~~~~~~~~~d~rQ~AlKl~aNS~YG~lG~~~srfy~~~lA~~IT~~GR~iL~~tkelve~~g~~  649 (1030)
                      |++.|.++|+.|+            |.+|+|+||++||+||+||+++++|||.++|++||++||.+|+.|++++++.|++
T Consensus        84 l~~~R~~~K~~~~------------d~~Q~a~Ki~~NS~YG~~g~~~~~~~~~~~A~~iT~~Gr~~i~~~~~~~e~~g~~  151 (394)
T d1q8ia2          84 IWHGRDEAKRQGN------------KPLSQALKIIMNAFYGVLGTTACRFFDPRLASSITMRGHQIMRQTKALIEAQGYD  151 (394)
T ss_dssp             HHHHHHHHHHTTC------------HHHHHHHHHHHHHHHHHHTCTTSTTCCHHHHHHHHHHHHHHHHHHHHHHHHTTCE
T ss_pred             HHHhccccccccc------------cchhHHHHHhcchhhceecccccchhhhHHHHHHHHHhHHHHHHHHhhhhhhhhh
Confidence            9999999998764            5789999999999999999999999999999999999999999999999999999


Q ss_pred             eEEecCcceeeecCC-CCHHHHHHHHHHHHHHHhcc----------cceeEEeecchhhhhhhc--------ccccceEE
Q psy6283         650 VIYGDTDSLMISCNV-NDYDSVFKIGNQIKSECNKL----------YKQLELDIDGVYKYMLLL--------KKKKYAAL  710 (1030)
Q Consensus       650 VIYGDTDSI~V~~~~-~d~eea~~ig~~i~~~Vn~~----------~~~leLe~E~vf~~llll--------~KKrYa~l  710 (1030)
                      |||||||||||.++. .+.+++..++..+...+|..          ..+++|++|++|.+++++        +||+|+++
T Consensus       152 ViygDTDSi~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~le~E~~~~~~~~~~kk~~~~~~kkrY~g~  231 (394)
T d1q8ia2         152 VIYGDTDSTFVWLKGAHSEEEAAKIGRALVQHVNAWWAETLQKQRLTSALELEYETHFCRFLMPTIRGADTGSKKRYAGL  231 (394)
T ss_dssp             EEEECSSEEEEECSSCCCHHHHHHHHHHHHHHHHHHHHHHHHTTTCCCCCCEEEEEEEEEEEECCCCTTCTTCCSCEEEE
T ss_pred             hhhcccceEEEEeCCCchhhhHHHHHHHHHHHHHHhhhhHhhhhhccccccceeeeeeheeeehhhhhhhhhhhhhhhcc
Confidence            999999999999875 57888888888888777642          247999999999999974        68899998


Q ss_pred             eeeecCCCceeeeceeeeeeeeeCChHHHHHHHHHHHHHHHhccCCCCCCChhHHHHHHHHHHHHHHHHhhCCCcChhhh
Q psy6283         711 SISKLSNGKMICSQEIKGVDVVRRDWSQLASEAGKFVISQILDEQSYTDYSLDDRLQNIHEHMKKIRTDLDNGFVPLTLL  790 (1030)
Q Consensus       711 ~~~~~~dG~~~~~~e~KGle~vRRD~~~l~k~~~~~vL~~IL~~~~~~~~~~e~~v~~I~~~l~~~~~~l~~g~vpl~~l  790 (1030)
                      .++.  ++   ..+++||++++|||||+++|+++..+|+.||.+.     +.+       +++.++.++|++|.+| .++
T Consensus       232 ~~~~--~~---~~~~~KG~e~vRrd~~~~~k~~~~~vl~~i~~~~-----~~~-------e~vk~~~~~l~~~~i~-~~~  293 (394)
T d1q8ia2         232 IQEG--DK---QRMVFKGLETVRTDWTPLAQQFQQELYLRIFRNE-----PYQ-------EYVRETIDKLMAGELD-ARL  293 (394)
T ss_dssp             EEET--TE---EEEEEESSCC--CCCCHHHHHHHHHHHHHHHTTC-----CCH-------HHHHHHHHHHHTTTTG-GGG
T ss_pred             eeec--cc---ceEEEEeeeccccccchhHHHHHHHHHHHHhccc-----hHH-------HHHHHHHHHHhhcCCC-chh
Confidence            7652  21   2568999999999999999999999999999988     544       3455667889999999 569


Q ss_pred             HHhhcccCCCCC---CcchHHHHHHHHHHcC
Q psy6283         791 EITKQLTKAPEG---GKVCITQIRLSRNRRG  818 (1030)
Q Consensus       791 vItk~LsK~p~~---~~~pHV~vA~r~~~~g  818 (1030)
                      ++++++++++++   ..+|||.+|.+++...
T Consensus       294 i~~~~l~k~~~~y~~~~~~hV~~a~~~~~~~  324 (394)
T d1q8ia2         294 VYRKRLRRPLSEYQRNVPPHVRAARLADEEN  324 (394)
T ss_dssp             CC-----------------------------
T ss_pred             heeeeecccccccccCCChHHHHHHHHHHHh
Confidence            999999999888   5589999998876543

>d1ih7a2 e.8.1.1 (A:376-903) Family B DNA polymerase {Bacteriophage RB69 [TaxId: 12353]}

class: Multi-domain proteins (alpha and beta)
fold: DNA/RNA polymerases
superfamily: DNA/RNA polymerases
family: DNA polymerase I
domain: Family B DNA polymerase
species: Bacteriophage RB69 [TaxId: 12353]

Probab=100.00  E-value=4.6e-53  Score=497.60  Aligned_cols=311  Identities=23%  Similarity=0.254  Sum_probs=224.8

Q ss_pred             CccccCceeeccccccccceEEEeeccccChhHHHHhccccccccccCCCc---cccc----------cccCC-CCCccc
Q psy6283         493 KAAYSGGLVLEPKKGFYDKFIILMDFNSLYPSIIQEYNICFTTIPVRMLQD---SDIT----------TLCEY-LPEHQV  558 (1030)
Q Consensus       493 ~~~Y~GGlVleP~~GlY~~~V~vLDFnSLYPSII~~~NIc~tTv~~~~~d~---~~i~----------~~~p~-~p~~~~  558 (1030)
                      ..+|+||+|++|+||+|+ +|++|||+|||||||++|||||+|+++..+..   +.+.          ..+|. ......
T Consensus        13 ~~~Y~Ga~V~~P~~G~y~-~V~~lDf~SLYPSiIi~~NispeT~v~~~~~~~~~~~~~~~~~~~~~~~~~~~ng~~~~k~   91 (528)
T d1ih7a2          13 VQPYPGAFVKEPIPNRYK-YVMSFDLTSLYPSIIRQVNISPETIAGTFKVAPLHDYINAVAERPSDVYSCSPNGMMYYKD   91 (528)
T ss_dssp             CCCCCCCCBCCCCCEECS-SEEEEEESSHHHHHHHHHTCCTTCEEEECCCCCHHHHHTTCSCCSCSSSEECTTSEEECSS
T ss_pred             CCCcCCEEeCCCCCCCCC-CEeeeEccchhHHHHHHHCCCHhhcCCccccCchhhhhhcccccCCcceeecCCCceeecc
Confidence            468999999999999997 59999999999999999999999998754310   0010          01111 111245


Q ss_pred             cCCcchHHHHHHHHHHHHHHHHhcCCCC--------------------------------------------------Ch
Q psy6283         559 DTGILPSEIKKLVESRRQVKALMKQPNL--------------------------------------------------SS  588 (1030)
Q Consensus       559 ~~GIlP~iL~~Ll~~R~~vKk~mk~~~~--------------------------------------------------~~  588 (1030)
                      ..||+|.++..+++.|..+|+.|.....                                                  ..
T Consensus        92 ~~gi~p~~l~~~~~~R~~~K~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~k~~lk~~~~~~~~~~~~~~~  171 (528)
T d1ih7a2          92 RDGVVPTEITKVFNQRKEHKGYMLAAQRNGEIIKEALHNPNLSVDEPLDVDYRFDFSDEIKEKIKKLSAKSLNEMLFRAQ  171 (528)
T ss_dssp             SCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTSSCBCSCCCCCCCCTTSCCCHHHHHHHTTCBHHHHHHHHHHHH
T ss_pred             ccccCHHHHHHHHHHHHHHHHHHHHHhhhhhhhhhhhcccccccccccchhhhhhhhhHHHHHHhhhhhhhHHHHhhhhH
Confidence            7999999999999999999998843100                                                  01


Q ss_pred             HHHHhhHHHHHHhccccccccccCCCCCCCCCCHHHHHHHHHHhHHHHHHHHHHhhhccc---------eeEEecCccee
Q psy6283         589 DLLMQYDIRQKALKLTANSMYGCLGFPNSRFFAQPLAALVTAKGREILLNTKSLVENLNY---------EVIYGDTDSLM  659 (1030)
Q Consensus       589 ~~~~~~d~rQ~AlKl~aNS~YG~lG~~~srfy~~~lA~~IT~~GR~iL~~tkelve~~g~---------~VIYGDTDSI~  659 (1030)
                      .....||.+|+|+||+|||+||++|++++||||.++|++||+.||.+|+.|++++++.+.         .||||||||+|
T Consensus       172 ~~~~~~d~~Q~a~Ki~~NS~YG~~g~~~~r~~~~~~A~siT~~Gr~~I~~~~~~i~~~~~~~~~~~~~~~viYgDTDS~~  251 (528)
T d1ih7a2         172 RTEVAGMTAQINRKLLINSLYGALGNVWFRYYDLRNATAITTFGQMALQWIERKVNEYLNEVCGTEGEAFVLYGDTDSIY  251 (528)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHTCTTSTTCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTCSSCCCEEEEETTEEE
T ss_pred             HHHHHHHHHHHHHHHHHHHhhhHHhhccccccchhhhhhhhhhhHHHHHHHHHHHHHhhhcccCCcccceeecCCcccce
Confidence            123578999999999999999999999999999999999999999999999999997654         47999999999


Q ss_pred             eecCCC----------CHHHHHH----HH-HHHHHHHhcc-----------cceeEEeec--------chhhhhhhcccc
Q psy6283         660 ISCNVN----------DYDSVFK----IG-NQIKSECNKL-----------YKQLELDID--------GVYKYMLLLKKK  705 (1030)
Q Consensus       660 V~~~~~----------d~eea~~----ig-~~i~~~Vn~~-----------~~~leLe~E--------~vf~~llll~KK  705 (1030)
                      |+++..          ..+....    ++ ..+...+++.           ...+.++.|        +++.+++|++||
T Consensus       252 v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~k~E~i~~~~~~~~~~~~i~~aKK  331 (528)
T d1ih7a2         252 VSADKIIDKVGESKFRDTNHWVDFLDKFARERMEPAIDRGFREMCEYMNNKQHLMFMDREAIAGPPLGSKGIGGFWTGKK  331 (528)
T ss_dssp             EECHHHHHHHCGGGCSSHHHHHHHHHHHHHHTHHHHHHHHHHHHHHHTTCSSCCCCEEEEEEECCCTTSCCCCEEEEETT
T ss_pred             eecCcchhhhccchhhhhHHHHHHHHHHHHHHHHHHHHHHHHHHhhhhhcccchhhhccccccchhhccccccceecccc
Confidence            997421          1111111    11 1122222221           123444444        445577899999


Q ss_pred             cceEEeeeecCCCceeeeceeeeeeeeeCChHHHHHHHHHHHHHHHhccCCCCCCChhHHHHHHHHHHHHHHHHhhCCCc
Q psy6283         706 KYAALSISKLSNGKMICSQEIKGVDVVRRDWSQLASEAGKFVISQILDEQSYTDYSLDDRLQNIHEHMKKIRTDLDNGFV  785 (1030)
Q Consensus       706 rYa~l~~~~~~dG~~~~~~e~KGle~vRRD~~~l~k~~~~~vL~~IL~~~~~~~~~~e~~v~~I~~~l~~~~~~l~~g~v  785 (1030)
                      |||+.+++..+...-.+++++||++++|||||++++.++.++|+.||.+.      .+++.    +++.++...+.+  .
T Consensus       332 RYa~~v~~~~g~~~~~~Kl~~kGle~vRrd~~~~~k~~~~~vl~~Il~~~------~~~~~----~~i~~~~~~~~~--~  399 (528)
T d1ih7a2         332 RYALNVWDMEGTRYAEPKLKIMGLETQKSSTPKAVQKALKECIRRMLQEG------EESLQ----EYFKEFEKEFRQ--L  399 (528)
T ss_dssp             EEEEEEEEETTEEEEEEEEEEESSCSSCTTSCHHHHHHHHHHHHHHHHTC------HHHHH----HHHHHHHHHGGG--S
T ss_pred             ccceEEEeccccccccchhhhcccchhccccCHHHHHHHHHHHHHHHhcc------hHHHH----HHHHHHHHHHhc--C
Confidence            99999887543222345789999999999999999999999999999875      44444    445555666664  5


Q ss_pred             ChhhhHHhhccc---C----CCCC-CcchHHHHHHHHHH
Q psy6283         786 PLTLLEITKQLT---K----APEG-GKVCITQIRLSRNR  816 (1030)
Q Consensus       786 pl~~lvItk~Ls---K----~p~~-~~~pHV~vA~r~~~  816 (1030)
                      |++++.+++.+.   |    .... +.+|||.+|+-.+.
T Consensus       400 ~~~~i~~~~~~~~~~k~~~~~~~~k~~P~HVkaA~~yN~  438 (528)
T d1ih7a2         400 NYISIASVSSANNIAKYDVGGFPGPKCPFHIRGILTYNR  438 (528)
T ss_dssp             CHHHHCEEEECCSHHHHEETTEECTTCCHHHHHHHHHHH
T ss_pred             CHHHhhhHHHHHHHhhhccccccCCCCchhhHHHHHHHH
Confidence            677777765443   2    1122 44569999975443

>d2py5a2 e.8.1.1 (A:188-575) phi29 DNA polymerase {Bacteriophage phi-29 [TaxId: 10756]}

class: Multi-domain proteins (alpha and beta)
fold: DNA/RNA polymerases
superfamily: DNA/RNA polymerases
family: DNA polymerase I
domain: phi29 DNA polymerase
species: Bacteriophage phi-29 [TaxId: 10756]

Probab=99.90  E-value=3.4e-26  Score=257.64  Aligned_cols=247  Identities=17%  Similarity=0.091  Sum_probs=165.6

Q ss_pred             CccccCceee--ccccccccceEEEeeccccChhHHHHhccccccccccCC------Ccccc------c-----cccCCC
Q psy6283         493 KAAYSGGLVL--EPKKGFYDKFIILMDFNSLYPSIIQEYNICFTTIPVRML------QDSDI------T-----TLCEYL  553 (1030)
Q Consensus       493 ~~~Y~GGlVl--eP~~GlY~~~V~vLDFnSLYPSII~~~NIc~tTv~~~~~------d~~~i------~-----~~~p~~  553 (1030)
                      ..+|.||.|.  .+..|....+|.++||||||||+|++||+|+.|......      +....      .     ...|.+
T Consensus        36 r~~y~GG~~~~~~~~~~~~~~~i~~yD~nSLYPs~M~~~~~p~g~p~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~p~~  115 (388)
T d2py5a2          36 RYAYRGGFTWLNDRFKEKEIGEGMVFDVNSLYPAQMYSRLLPYGEPIVFEGKYVWDEDYPLHIQHIRCEFELKEGYIPTI  115 (388)
T ss_dssp             HTTCCCCCEEECGGGBTCEECSEEEEEETTHHHHHHHHSCEEEEEEEEEESSCCCCTTSCEEEEEEEEEEEECTTCCCCC
T ss_pred             HHhccCceeeccccccccccCceEEEeccCchHHHHhhCCCCCCcceeeecccccccccCCeeEEEEEEecCccccCCcc
Confidence            3689999874  333344444699999999999999999999766432111      00000      0     000111


Q ss_pred             C----------------CccccCCcchHHHHHHHHHHHHHHHHhc----------CC------CCChHHHHhhHHHHHHh
Q psy6283         554 P----------------EHQVDTGILPSEIKKLVESRRQVKALMK----------QP------NLSSDLLMQYDIRQKAL  601 (1030)
Q Consensus       554 p----------------~~~~~~GIlP~iL~~Ll~~R~~vKk~mk----------~~------~~~~~~~~~~d~rQ~Al  601 (1030)
                      |                .......+++..+..++..+..++..+.          ..      ..++...+..+.+|.++
T Consensus       116 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~f~~~~~~~k~~~~~~~~~kk~~~~~~q~~~  195 (388)
T d2py5a2         116 QIKRSRFYKGNEYLKSSGGEIADLWLSNVDLELMKEHYDLYNVEYISGLKFKATTGLFKDFIDKWTYIKTTSEGAIKQLA  195 (388)
T ss_dssp             CC-------CCSCCSBCTTSCEEEEEEHHHHHHHHHHEEEEEEEEEEEEEEEEESCTTHHHHHHHHHHHHHCCHHHHHHH
T ss_pred             cccccccCCCceEEeccCCceeeEEEcHHHHHHHHhcCCceEEEEEeeEEechhhHHHHHHHHhhhHHHHhccCHHHHHH
Confidence            1                1112333566666666655432211110          00      01122345678999999


Q ss_pred             ccccccccccCCCC------------------------CCCCCCHHHHHHHHHHhHHHHHHHHHHhhhccceeEEecCcc
Q psy6283         602 KLTANSMYGCLGFP------------------------NSRFFAQPLAALVTAKGREILLNTKSLVENLNYEVIYGDTDS  657 (1030)
Q Consensus       602 Kl~aNS~YG~lG~~------------------------~srfy~~~lA~~IT~~GR~iL~~tkelve~~g~~VIYGDTDS  657 (1030)
                      ||++||+||.+|..                        ...+++.++|++||+.||.+|..++   +..|..|+||||||
T Consensus       196 KLl~NSlYGk~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ia~~ita~~r~~~~~~~---~~~~~~v~Y~DTDS  272 (388)
T d2py5a2         196 KLMLNSLYGKFASNPDVTGKVPYLKENGALGFRLGEEETKDPVYTPMGVFITAWARYTTITAA---QACYDRIIYCDTDS  272 (388)
T ss_dssp             HHHHHSSHHHHTCCSBCCBEEEEECTTSSEEEEECCCCBCCCCCHHHHHHHHHHHHHHHHHHH---HHTTTTEEEEETTE
T ss_pred             HHhcchhhheeccccccccceeeccccceehhhhhccccccccchhHHHHHHHHHHHHHHHHh---hccCCcEEEEecce
Confidence            99999999999986                        4678899999999999999987765   45688999999999


Q ss_pred             eeeecCCCC-HHHHHHHHHHHHHHHhcccceeEEeecchhhhhhhcccccceEEeeeecCCCceeeeceeeeeeeeeCCh
Q psy6283         658 LMISCNVND-YDSVFKIGNQIKSECNKLYKQLELDIDGVYKYMLLLKKKKYAALSISKLSNGKMICSQEIKGVDVVRRDW  736 (1030)
Q Consensus       658 I~V~~~~~d-~eea~~ig~~i~~~Vn~~~~~leLe~E~vf~~llll~KKrYa~l~~~~~~dG~~~~~~e~KGle~vRRD~  736 (1030)
                      ||+..+..+ ......        ....  .-.+++|+++.+++++++|+||+..+..+..|.   ..+..|.+.++.++
T Consensus       273 i~~~~~~~~~~~~~~~--------~~~~--lg~~~~E~~~~~~~~~~~K~Y~~~~~~~~~~~~---~~~~~~~~~~~~~~  339 (388)
T d2py5a2         273 IHLTGTEIPDVIKDIV--------DPKK--LGYWAHESTFKRAKYLRQKTYIQDIYMKEVDGK---LVEGSPDDYTDIKF  339 (388)
T ss_dssp             EEEESSSCCGGGGGGB--------CSSS--TTSEEEEEEEEEEEEEETTEEEEEEEEEEETTE---EEECBTTBCSEEEE
T ss_pred             EEecCCcchhhHHhhh--------chhh--hcccccccccchhhccccchhhceEeccccccc---cccccceeecchhh
Confidence            999876533 111100        0111  124677899999999999999999887766664   34778889999999


Q ss_pred             HHHHHHHHHHHHHHHhccC
Q psy6283         737 SQLASEAGKFVISQILDEQ  755 (1030)
Q Consensus       737 ~~l~k~~~~~vL~~IL~~~  755 (1030)
                      |..++.+...++..|...+
T Consensus       340 ~~~~k~~~~~v~~~i~~~~  358 (388)
T d2py5a2         340 SVKCAGMTDKIKKEVTFEN  358 (388)
T ss_dssp             EEEETTCCHHHHTTCCTTT
T ss_pred             hhhhccchHHHHHHHHHhh
Confidence            9988888777777666544

>d1q8ia1 c.55.3.5 (A:2-389) Exonuclease domain of family B DNA polymerases {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: Ribonuclease H-like motif
superfamily: Ribonuclease H-like
family: DnaQ-like 3'-5' exonuclease
domain: Exonuclease domain of family B DNA polymerases
species: Escherichia coli [TaxId: 562]

Probab=99.10  E-value=1.8e-10  Score=128.95  Aligned_cols=65  Identities=18%  Similarity=0.403  Sum_probs=61.5

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHhcchHHHHHHHHHhCCcchhhccCchhHHHHHHHHHHHhhcCeecc
Q psy6283         402 IVEFIKFTMLHSSYIIKIMCELNVLPLAIQITNVCGNVLSRTLMGGRSERNEFLLLHAFHEKSYVLP  468 (1030)
Q Consensus       402 l~~lv~Y~~~Da~l~~~L~~kl~vlpl~~~lt~iaG~~~srtl~~gr~~r~E~lLL~~~~~~~yivP  468 (1030)
                      ...|+.||++||.|+++|+.+++++|++.+||+++|+++.++  ||++..+++|+||++|+.|||+|
T Consensus       324 ~~~l~~Y~~~D~~Lv~~L~~k~~~i~~~~ela~l~g~pl~~~--g~s~~~~~~lll~~~~r~g~v~P  388 (388)
T d1q8ia1         324 KPALATYNLKDCELVTQIFHKTEIMPFLLERATVNGLPVDRH--GGSVAAFGHLYFPRMHRAGYVAP  388 (388)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHTHHHHHHHHHHHHCSCTTTT--CCHHHHHHHHHHHHHHHTTBCCC
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCHHHC--CCcHHHHHHHHHHHHHHCCEeCC
Confidence            567999999999999999999999999999999999999984  78888899999999999999998

>d1noya_ c.55.3.5 (A:) Exonuclease domain of family B DNA polymerases {Bacteriophage T4 [TaxId: 10665]}

class: Alpha and beta proteins (a/b)
fold: Ribonuclease H-like motif
superfamily: Ribonuclease H-like
family: DnaQ-like 3'-5' exonuclease
domain: Exonuclease domain of family B DNA polymerases
species: Bacteriophage T4 [TaxId: 10665]

Probab=97.72  E-value=2e-05  Score=86.03  Aligned_cols=59  Identities=7%  Similarity=0.162  Sum_probs=54.3

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHhcchHHHHHHHHHhCCcchhhccCchhHHHHHHHHHHHhh
Q psy6283         402 IVEFIKFTMLHSSYIIKIMCELNVLPLAIQITNVCGNVLSRTLMGGRSERNEFLLLHAFHE  462 (1030)
Q Consensus       402 l~~lv~Y~~~Da~l~~~L~~kl~vlpl~~~lt~iaG~~~srtl~~gr~~r~E~lLL~~~~~  462 (1030)
                      +.+|++||++||.|+++|+.++++++++.+||+++|+++.+++  ++..-+++++++.+|.
T Consensus       313 ~~~l~~Yni~D~~L~~~L~~kl~~i~~~~~la~~~gvp~~~v~--~~~~~~~~~~~~~l~~  371 (372)
T d1noya_         313 HQRYISYNIIDVESVQAIDKIRGFIDLVLSMSYYAKMPFSGVM--SPIKTWDAIIFNSLKG  371 (372)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHCHHHHHHHHHHHHTCCGGGGG--CHHHHHHHHHHHHTTC
T ss_pred             hhHhheecHHHHHHHHHHHHHHhHHHHHHHHHHHHCcCHHHhC--cHHHHHHHHHHHHhhc
Confidence            7889999999999999999999999999999999999999996  4666689999998874

>d1s5ja1 c.55.3.5 (A:40-449) Exonuclease domain of family B DNA polymerases {Sulfolobus solfataricus [TaxId: 2287]}

class: Alpha and beta proteins (a/b)
fold: Ribonuclease H-like motif
superfamily: Ribonuclease H-like
family: DnaQ-like 3'-5' exonuclease
domain: Exonuclease domain of family B DNA polymerases
species: Sulfolobus solfataricus [TaxId: 2287]

Probab=97.55  E-value=0.00013  Score=81.12  Aligned_cols=133  Identities=9%  Similarity=0.036  Sum_probs=78.3

Q ss_pred             CCCceEEEEEEeccccccCCCCEEEEEeeeeecCCCceeEEEEEEcceeeeEEEecCCCCCCCCCcccHHHHHHHHHHHH
Q psy6283         207 ENKKVFRMFFLDAFEDIYKQPGTVYLFGKVFVKENNSHSSCCVIVQNIDRKIYLLPRSEHLKTKEPVSIAQVYSEFDQIA  286 (1030)
Q Consensus       207 ~~~~~l~fy~~d~~e~~~~~~g~~~lfGkv~~~~~~~~~Sccv~v~~~~R~~~~lpr~~~~~~~~~~~~~~v~~e~~~~~  286 (1030)
                      +..++..||.||+.-+.....=.|+|||+-     ..-.|.|+-+.+-.=-.|+.+.+            +-..++.++.
T Consensus         5 ~~~~~~~~~ll~~~Y~~~~~~~vi~~~g~~-----~~~~~v~~~~~gf~PYFyv~~~~------------~~~~~~~~~~   67 (410)
T d1s5ja1           5 EAQENKIYFLLQVDYDGKKGKAVCKLFDKE-----TQKIYALYDNTGHKPYFLVDLEP------------DKVGKIPKIV   67 (410)
T ss_dssp             BCCTTCEEEEEEEEEETTTTEEEEEEEETT-----TTEEEEEECCSCCCCEEEESSCH------------HHHTTCHHHH
T ss_pred             ccccCCcEEEEEeEEeeeCCEEEEEEEeec-----CCcEEEEEeCCCccceEEEECCc------------chHHHHHHHh
Confidence            345678999999998864333378899942     33578888777664444443221            1112222232


Q ss_pred             HhcCCcceEEeeeeeccccCCCCCCCCccEEEEEec--cCCCCCCCCCcCCceeeecccCchhhhhHHhhhhccCCeEEE
Q psy6283         287 TQYKILDFKSRKIEKKYAFNLPGVPDLSEYLEVRYS--AKCPALPSDLSGDTFSHVFGTKTSFLENLLLERKIKGPSWLE  364 (1030)
Q Consensus       287 ~~~~i~~~~~k~v~~~yaf~~~~vp~~~~~lkv~y~--~~~p~~~~~~~g~tfs~vfG~~~~~~E~f~l~~~i~Gp~wl~  364 (1030)
                      ..-++  ..+..|++.=.+..    .+..++||...  ...|.+-     ..+..+|-++-...-+|++.++|.|-+|+.
T Consensus        68 ~~~~~--~~~e~v~k~~~~~~----~~~~~~ki~~~~p~~v~~~r-----~~~~~~~EadI~~~~RfliD~~l~~~~w~~  136 (410)
T d1s5ja1          68 RDPSF--DHIETVSKIDPYTW----NKFKLTKIVVRDPLAVRRLR-----NDVPKAYEAHIKYFNNYMYDIGLIPGMPYV  136 (410)
T ss_dssp             TCTTE--EEEEEEEEECTTTC----CEEEEEEEEESSHHHHHHHT-----TSSSCEESCSSCHHHHHHHHHTCCTTSEEE
T ss_pred             hhccc--ceEEEEEEEeccCC----cceeEEEEEEcCHHHHHHHH-----HHhhhhcccccCchhcEEEEcCCccceEEE
Confidence            22222  34455555422221    23457777543  2223321     234568888889999999999999999988


Q ss_pred             ecC
Q psy6283         365 FPE  367 (1030)
Q Consensus       365 i~~  367 (1030)
                      +..
T Consensus       137 ~~~  139 (410)
T d1s5ja1         137 VKN  139 (410)
T ss_dssp             EET
T ss_pred             ecC
Confidence            753

>d1ih7a1 c.55.3.5 (A:1-375) Exonuclease domain of family B DNA polymerases {Bacteriophage RB69 [TaxId: 12353]}

class: Alpha and beta proteins (a/b)
fold: Ribonuclease H-like motif
superfamily: Ribonuclease H-like
family: DnaQ-like 3'-5' exonuclease
domain: Exonuclease domain of family B DNA polymerases
species: Bacteriophage RB69 [TaxId: 12353]

Probab=97.50  E-value=7.1e-05  Score=81.84  Aligned_cols=59  Identities=7%  Similarity=0.241  Sum_probs=52.7

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHhcchHHHHHHHHHhCCcchhhccCchhHHHHHHHHHHHhh
Q psy6283         402 IVEFIKFTMLHSSYIIKIMCELNVLPLAIQITNVCGNVLSRTLMGGRSERNEFLLLHAFHE  462 (1030)
Q Consensus       402 l~~lv~Y~~~Da~l~~~L~~kl~vlpl~~~lt~iaG~~~srtl~~gr~~r~E~lLL~~~~~  462 (1030)
                      +.+|+.||++||.|+++|+.++++++++.+||++||+++..++  ++..-++.|+++.+++
T Consensus       317 ~~~~~~Y~~~D~~L~~~L~~kl~~i~~~~~~a~~~~v~~~~v~--~q~~~~~~li~~~~~~  375 (375)
T d1ih7a1         317 HQRYISYNIIDVYRVLQIDAKRQFINLSLDMGYYAKIQIQSVF--SPIKTWDAIIFNSLKE  375 (375)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHCHHHHHHHHHHHHTSCGGGGG--CHHHHHHHHHHHHHHT
T ss_pred             hhHhhhhhHHHHHHHHHHHHHHhHHHHHHHHHHHHCcCHHHHh--HHHHHHHHHHHHHhhC
Confidence            7889999999999999999999999999999999999999986  3444468899988764

>d1tgoa1 c.55.3.5 (A:1-347) Exonuclease domain of family B DNA polymerases {Archaeon Thermococcus gorgonarius [TaxId: 71997]}

class: Alpha and beta proteins (a/b)
fold: Ribonuclease H-like motif
superfamily: Ribonuclease H-like
family: DnaQ-like 3'-5' exonuclease
domain: Exonuclease domain of family B DNA polymerases
species: Archaeon Thermococcus gorgonarius [TaxId: 71997]

Probab=95.36  E-value=0.0063  Score=65.37  Aligned_cols=41  Identities=15%  Similarity=0.305  Sum_probs=38.1

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHhcchHHHHHHHHHhCCcchhhc
Q psy6283         402 IVEFIKFTMLHSSYIIKIMCELNVLPLAIQITNVCGNVLSRTL  444 (1030)
Q Consensus       402 l~~lv~Y~~~Da~l~~~L~~kl~vlpl~~~lt~iaG~~~srtl  444 (1030)
                      +..++.||++||.++++|+.+  ++|++.+||+++|+++.+++
T Consensus       305 ~~~~~~Y~~~D~~l~~~L~~k--l~~~~~~~s~i~g~~~~~v~  345 (347)
T d1tgoa1         305 LERVARYSMEDAKVTYELGKE--FFPMEAQLSRLVGQSLWDVS  345 (347)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHH--HHHHHHHHHHHHTSCHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHH--HHHHHHHHHHHHCCCHHHhc
Confidence            788999999999999999998  58999999999999998764