Psyllid ID: psy17959

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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
Protein Sequence
LWSYRAEDYLREGSHDRGSPFKEILSSVPGYGHIAPKTTLGKVATIFYAIVGIPLMLLCLSNIGDIMAHSFRFLYWKDFDFFTEYYDTKGVGNAEQIKPVPIWLCVFLVISYIIGGAFLFSHWEPWGFPDSAYFCFITLTTIGFGDFVPAQKSTDVQTAEETAELRIALCSLYLLFGIALLAMSFNLVQEEVISNVKAIAKHLGIIKSSNGDSEYEDSDFDTSDEEYDSSEEEEEEEDEEEEEEEEEGEEEETETASSSTAKNDPQMVTVPITLCLMIMVGYIYGGAVLFSKWEDWNILDGSRSSSRSRSRQQTERSFTEKCKDYLRQFLAFLFSNIGIICLVIGYTIAGYGNVAPITFLGKITTIAYAIAGMPLFLLYLSNIGDILAKSFKWIYAKCCLCRGCPTRPRDLQKTIQDTTGAYNRRRSSAMNHNRRWNARNGDSEYEDSDFDTSDEEYDSSEEEEEEEEDEEEEEEEEEEEEEEEEEEGEEEETETASSSTAKNDPQMVTVPITLCLMIMVGYIYGGAVLFSKWEDWNILDGSYFCFISLSTIGFGDIVPGDKITGKNNDIGVQTLELSFILCAMYLMLGMALIAMCFNLMQEEVVHKMRTCSEVTQRKSKQQQQQQNSLPNIYSQFNHISTGKYDGKTTPYRGGYCTHASDFEPKAFRFRVPIAVSFLIIISFILLGSLIFNKLENWTFLDGTFFCFTSLGTIGFGELIPGESYDRTLRGNKNISVLVSSSYILVGMAVISMCFNLIQEEIIFMIKKFTLKLNKSGGSSGGVCDKNCDIS
Secondary Structure (PSIPRED)
ccccccccccccccccccccEEEEEEEccccccccccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHccccccccccccccccccccccHHHHHHHHHHHHHHHHHHHHHHccccccccEEEEEEEEEcccccccccccccccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHcccccccccccccccccccccccccccHHHHHHHHHHHHHHHHHccccccccccccccccccccccccHHHHHHHHHHHHHcccccccccccHHHHHHcccHHHHHHHHHHHHHHHHHHHHHHHccccccccccEEEEEEEEEEcccccccccccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHcHHHHHccccccccccccccEEHHHHHHHHHHHHHHHHHHHHHHccccccccccEEEEEEEEccccccccccccccccccccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHcccccccccccccccccccccccccccccccccccccccccEEEEHHHHHHHHHHHHHHHHHHHHHHHcccccccccEEEEEEEccccccccccccccccccccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHccccccccccccccc
Secondary Structure Prediction (SSPRO)
ccccccccccccccHHHHEEEEEEEEEEcccccccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHcccccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHccccHHHEEEEEEEEHHHcccccccccccccccccccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHcccHHHHHHccccccccccHHHccccccccHcHcHHccccccccccccccccccccccccEHHHHHHHHHHHHHHHHHHHHHHHHHcHHHHHHHHHHHHHccHHHHHHHHHHHHHHHHHcccEEcHHHHHHHHHHHHHHHcccccccccccHcHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHcccccccccHHHHHHHHHcccccHHHHHHHcHHHcccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccHHHHHHHHHHHHHHHHHHHHHHHccccHHHHEEEEHEEHHHcccccccccccccccccHHHHHccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHccccccccccccccccccccccccccccccccccccccccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHccccHHEEEEEEEEEHHHcccccccccccccHHHHcccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHccccccccccc
Coil and Loop (DISEMBL)
lwsyraedylregshdrgspfkeilssvpgyghiapkttlgKVATIFYAIVGIPLMLLCLSnigdimahSFRFLYWKDFDFFTeyydtkgvgnaeqikpvPIWLCVFLVISYIIGGAflfshwepwgfpdsayfcfitlttigfgdfvpaqkstdvQTAEETAELRIALCSLYLLFGIALLAMSFNLVQEEVISNVKAIAKHLGIikssngdseyedsdfdtsdeeydsseeeeeeedeeeeeeeeegeeeetetassstakndpqmvtVPITLCLMIMVGYIYGGAVLFskwedwnildgsrsssrsrsrqQTERSFTEKCKDYLRQFLAFLFSNIGIICLVIGYtiagygnvapitfLGKITTIAYAIAGMPLFLLYLSNIGDILAKSFKWIYAKcclcrgcptrprdlqKTIQDTTGAYNRRRSSamnhnrrwnarngdseyedsdfdtsdeeydsseeeeeeeedeeeeeeeeeeeeeeeeeegeeeetetassstakndpqmvtVPITLCLMIMVGYIYGGAVLFskwedwnildgsyfcfislstigfgdivpgdkitgknndigVQTLELSFILCAMYLMLGMALIAMCFNLMQEEVVHKMRTCSEVTQRKSKQQQQQQnslpniysqfnhistgkydgkttpyrggycthasdfepkafrfrvPIAVSFLIIISFILLGSLIfnklenwtfldgtffcftslgtigfgelipgesydrtlrgnknISVLVSSSYILVGMAVISMCFNLIQEEIIFMIKKFTLKLnksggssggvcdkncdis
Flexible Loop (DISEMBL)
lwsyraedylregshdrgspfKEILSSVPGYGHIAPKTTLGKVATIFYAIVGIPLMLLCLSNIGDIMAHSFRFLYWKDFDFFTEYYDTKGVGNAEQIKPVPIWLCVFLVISYIIGGAFLFSHWEPWGFPDSAYFCFITLTTIGFGDFVPAQKSTDVQTAEETAELRIALCSLYLLFGIALLAMSFNLVQEEVISNVKAIAKHLGiikssngdseyedsdfdtsdeeydsseeeeeeedeeeeeeeeegeeeetetassstakndpqmVTVPITLCLMIMVGYIYGGAVLFSKWEDWNILdgsrsssrsrsrqqtersfTEKCKDYLRQFLAFLFSNIGIICLVIGYTIAGYGNVAPITFLGKITTIAYAIAGMPLFLLYLSNIGDILAKSFKWIYAKCCLCRgcptrprdlqktiqdttgaynrrrssamnhnrrwnarngdseyedsdfdtsdeeydsseeeeeeeedeeeeeeeeeeeeeeeeeegeeeetetassstakndpqmVTVPITLCLMIMVGYIYGGAVLFSKWEDWNILDGSYFCFISLSTIGFGDIVPGDKITGKNNDIGVQTLELSFILCAMYLMLGMALIAMCFNLMQEEVVHKMRTCSEVTQRKSKQQQQQQNSLPNIYSQFNHISTGKYDGKTTPYRGGYCTHASDFEPKAFRFRVPIAVSFLIIISFILLGSLIFNKLENWTFLDGTFFCFTSLGTIGFGELIPGESYDRTLRGNKNISVLVSSSYILVGMAVISMCFNLIQEEIIFMIKKFTLKLnksggssggvcdkncdis
Low Complexity Region (SEG)
LWSYRAEDYLREGSHDRGSPFKEILSSVPGYGHIAPKTTLGKVATIFYAIVGIPLMLLCLSNIGDIMAHSFRFLYWKDFDFFTEYYDTKGVGNAEQIKPVPIWLCVFLVISYIIGGAFLFSHWEPWGFPDSAYFCFITLTTIGFGDFVPAQKSTDVQTAEETAELRIALCSLYLLFGIALLAMSFNLVQEEVISNVKAIAKHLGIIKSSNGdseyedsdfdtsdeeydsseeeeeeedeeeeeeeeegeeeetetassstAKNDPQMVTVPITLCLMIMVGYIYGGAVLFSKWEDWNILDGsrsssrsrsrQQTERSFTEKCKDYLRQFLAFLFSNIGIICLVIGYTIAGYGNVAPITFLGKITTIAYAIAGMPLFLLYLSNIGDILAKSFKWIYAKCCLCRGCPTRPRDLQKTIQDTTGAYNRRRSSAMNHNRRWNARNGdseyedsdfdtsdeeydsseeeeeeeedeeeeeeeeeeeeeeeeeegeeeeteTASSSTAKNDPQMVTVPITLCLMIMVGYIYGGAVLFSKWEDWNILDGSYFCFISLSTIGFGDIVPGDKITGKNNDIGVQTLELSFILCAMYLMLGMALIAMCFNLMQEEVVHKMRTCSEVTQRKSKqqqqqqNSLPNIYSQFNHISTGKYDGKTTPYRGGYCTHASDFEPKAFRFRVPIAVsfliiisfillgslifNKLENWTFLDGTFFCFTSLGTIGFGELIPGESYDRTLRGNKNisvlvsssyilvGMAVISMCFNLIQEEIIFMIKKFTLKLNKsggssggVCDKNCDIS
Disordered region (IsUnstruct)
***********************ILSSVPGYGHIAPKTTLGKVATIFYAIVGIPLMLLCLSNIGDIMAHSFRFLYWKDFDFFTEYYDTKGVGNAEQIKPVPIWLCVFLVISYIIGGAFLFSHWEPWGFPDSAYFCFITLTTIGFGDFVPAQKSTDVQTAEETAELRIALCSLYLLFGIALLAMSFNLVQEEVISNVKAIAKHLGII************************************************************MVTVPITLCLMIMVGYIYGGAVLFSKWEDWNIL********************EKCKDYLRQFLAFLFSNIGIICLVIGYTIAGYGNVAPITFLGKITTIAYAIAGMPLFLLYLSNIGDILAKSFKWIYAKCCLCRGCPTR***************************************************************************************************MVTVPITLCLMIMVGYIYGGAVLFSKWEDWNILDGSYFCFISLSTIGFGDIVPGDKITGKNNDIGVQTLELSFILCAMYLMLGMALIAMCFNLMQEEVVHKMRT*********************IYSQFNHISTGKYDGKTTPYRGGYCTHASDFEPKAFRFRVPIAVSFLIIISFILLGSLIFNKLENWTFLDGTFFCFTSLGTIGFGELIPGESYDRTLRGNKNISVLVSSSYILVGMAVISMCFNLIQEEIIFMIKKFTLKLN*****************
Disordered Region (DISOPRED)
********YLREGSHDRGSPFKEILSSVPGYGHIAPKTTLGKVATIFYAIVGIPLMLLCLSNIGDIMAHSFRFLYWKDFDFFTEYYDTKGVGNAEQIKPVPIWLCVFLVISYIIGGAFLFSHWEPWGFPDSAYFCFITLTTIGFGDFVPAQKSTDVQTAEETAELRIALCSLYLLFGIALLAMSFNLVQEEVISNVKAIAKHLGIIKSSNGDSEYEDSDFD**DE**DSSEEEEEEEDEEEEEEEEEGEEEETETASSSTAKNDPQMVTVPITLCLMIMVGYIYGGAVLFSKWEDWNILDGSRSSSRSRSRQQTERSFTEKCKDYLRQFLAFLFSNIGIICLVIGYTIAGYGNVAPITFLGKITTIAYAIAGMPLFLLYLSNIGDILAKSFKWIYAKCCLCRGCPTRPRDLQKTIQ******************************************************************************TASSSTAKNDPQMVTVPITLCLMIMVGYIYGGAVLFSKWEDWNILDGSYFCFISLSTIGFGDIVPGDKITGKNNDIGVQTLELSFILCAMYLMLGMALIAMCFNLMQEEVVHKMRTCSEVTQRKSKQQQQQQNSLPNIYSQF*******************CTHASDFEPKAFRFRVPIAVSFLIIISFILLGSLIFNKLENWTFLDGTFFCFTSLGTIGFGELIPGESYDRTLRGNKNISVLVSSSYILVGMAVISMCFNLIQEEIIFMIKKFTLKLNKSGGSSGGVCDKNCD**
Disordered Region (DISEMBL)
LWSYRAEDYLREGSHDRGSPFKEILSSVPGYGHIAPKTTLGKVATIFYAIVGIPLMLLCLSNIGDIMAHSFRFLYWKDFDFFTEYYDTKGVGNAEQIKPVPIWLCVFLVISYIIGGAFLFSHWEPWGFPDSAYFCFITLTTIGFGDFVPAQKSTDVQTAEETAELRIALCSLYLLFGIALLAMSFNLVQEEVISNVKAIAKHLGIIKSSN****************************************************NDPQMVTVPITLCLMIMVGYIYGGAVLFSKWEDWNILD******************TEKCKDYLRQFLAFLFSNIGIICLVIGYTIAGYGNVAPITFLGKITTIAYAIAGMPLFLLYLSNIGDILAKSFKWIYAKCCLCRGCPTRPRDLQKTIQDTTGAYNRRRSSAMNHNRRWNARN**************************************************************NDPQMVTVPITLCLMIMVGYIYGGAVLFSKWEDWNILDGSYFCFISLSTIGFGDIVPGDKITGKNNDIGVQTLELSFILCAMYLMLGMALIAMCFNLMQEEVVHKMR*******************LPNIYSQFNHISTGKYDGKTTPYRGGYCTHASDFEPKAFRFRVPIAVSFLIIISFILLGSLIFNKLENWTFLDGTFFCFTSLGTIGFGELIPGESYDRTLRGNKNISVLVSSSYILVGMAVISMCFNLIQEEIIFMIKKFTLKLNKSGGSSGGVCDKNCDIS
Disordered Region (DISPRO)
*WSYRAEDYLREGSHDRGSPFKEILSSVPGYGHIAPKTTLGKVATIFYAIVGIPLMLLCLSNIGDIMAHSFRFLYWKDFDFFTEYYDTKGVGNAEQIKPVPIWLCVFLVISYIIGGAFLFSHWEPWGFPDSAYFCFITLTTIGFGDFVPAQKSTDVQTAEETAELRIALCSLYLLFGIALLAMSFNLVQEEVISNVKAIAKHLGIIKSSN***********************************************SSTAKNDPQMVTVPITLCLMIMVGYIYGGAVLFSKWEDWNILDGSRSSSRSRSRQQTERSFTEKCKDYLRQFLAFLFSNIGIICLVIGYTIAGYGNVAPITFLGKITTIAYAIAGMPLFLLYLSNIGDILAKSFKWIYAKCCLCRGCPTRPRDLQKTIQDTTGAYNRRRSSAMNHNRRWNA*******************************************************************QMVTVPITLCLMIMVGYIYGGAVLFSKWEDWNILDGSYFCFISLSTIGFGDIVPGDKITGKNNDIGVQTLELSFILCAMYLMLGMALIAMCFNLMQEEVVHKMRTCSEVTQRKSKQQQQ***************************************PKAFRFRVPIAVSFLIIISFILLGSLIFNKLENWTFLDGTFFCFTSLGTIGFGELIPGESYDRTLRGNKNISVLVSSSYILVGMAVISMCFNLIQEEIIFMIKKFTLKLNKS***************
Transmembrane Helix (TMHMM)
ooooooooooooooooooooooooooooooooooooooooooooHHHHHHHHHHHHHHHHHHHHiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiHHHHHHHHHHHHHHHHHHHHHHHooooHHHHHHHHHHHHHHHHHHHHHHHiiiiiiiiiiiiiiiiiiiiHHHHHHHHHHHHHHHHHHHHoooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooHHHHHHHHHHHHHHHHHHHHHHHiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiHHHHHHHHHHHHHHHHHHHHHHHooooooooooooooHHHHHHHHHHHHHHHHHHHHHHHiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiHHHHHHHHHHHHHHHHHHHHHHHooooooooooooooooooooooooooooooooooooooooooooooHHHHHHHHHHHHHHHHHHHHHHHiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiHHHHHHHHHHHHHHHHHHHHHHHoooooooooooooooooooooooooooooooooooooooooooHHHHHHHHHHHHHHHHHHHHHHHiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
Transmembrane Helix (HMMTOP)
ooooooooooooooooooooooooooooooooooooooooooHHHHHHHHHHHHHHHHHHHHHHHHHiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiHHHHHHHHHHHHHHHHHHHHooooooooooooHHHHHHHHHHHHHHHHHHHiiiiiiiiiiiiiiiiHHHHHHHHHHHHHHHHHHHooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooHHHHHHHHHHHHHHHHHHHiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiHHHHHHHHHHHHHHHHHHHHooooooooooooHHHHHHHHHHHHHHHHHHHHHHiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiHHHHHHHHHHHHHHHHHHHHHHHHooooooooooooHHHHHHHHHHHHHHHHHHiiiiiiiiiiiiiiiiHHHHHHHHHHHHHHHHHHHHooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooHHHHHHHHHHHHHHHHHHHiiiiiiHHHHHHHHHHHHHHHHHHHHHHooooooooooooooHHHHHHHHHHHHHHHHHHHHHHHHiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
Transmembrane Helix (MEMSAT)
ooooooooooooooooooooooooooooooooooooooHHHHHHHHHHHHHHHHHHHHHHHHHiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiHHHHHHHHHHHHHHHHHHHHHHHHHooooooooooooooooooooooooooooooooooooooooooooooooooHHHHHHHHHHHHHHHHHHHHHHHHHiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiHHHHHHHHHHHHHHHHHHHHHHHHHooooooooooooooooooooooooooooooooooooooooooooooooHHHHHHHHHHHHHHHHHHHHiiiiiiiiHHHHHHHHHHHHHHHHHHHHHHHHoooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooHHHHHHHHHHHHHHHHHHHHHHHHHiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiHHHHHHHHHHHHHHHHHHHHHHHHHooooooooooooooooooooooooooooooooooooooooooooHHHHHHHHHHHHHHHHHHHHHHHHiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
TM Helix, Signal Peptide (MEMSAT_SVM)
oooooooooooooooooooooooooooooooooooooooHHHHHHHHHHHHHHHHHHHHHHHHHiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiHHHHHHHHHHHHHHHHHHHHHHHoooRRRRRRRRRRRRRRRRRRRooooooooooooooooooooooHHHHHHHHHHHHHHHHHHHHHiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiHHHHHHHHHHHHHHHHHHHHHHHoooooooooooooooooooooooooooooooooooooooHHHHHHHHHHHHHHHHHHHiiiiiiiiiiiHHHHHHHHHHHHHHHHHHHHHHHHoooHHHHHHHHHHHHHHHHiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiHHHHHHHHHHHHHHHHHHHHHHHHHoooRRRRRRRRRRRRRRRRRRRRooooooooooooooooooooooHHHHHHHHHHHHHHHHHHHHHHHiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiHHHHHHHHHHHHHHHHHHHHHHHHoooRRRRRRRRRRRRRRRRRRRRooooooooooooooooooHHHHHHHHHHHHHHHHHHHHHHiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
TM Helix, Signal Peptide (Phobius)
oooooooooooooooooooooooooooooooooooooooooooooHHHHHHHHHHHHHHHHHHHHHHHiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiHHHHHHHHHHHHHHHHHHHHoooooooooooHHHHHHHHHHHHHHHHHHiiiiiiiiiiiiiiiiiiiiHHHHHHHHHHHHHHHHHHHHoooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooHHHHHHHHHHHHHHHHHHHHHHHiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiHHHHHHHHHHHHHHHHHHHHHHHoooooHHHHHHHHHHHHHHHHHHHHHHHHiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiHHHHHHHHHHHHHHHHHHHHHHoooooooooooHHHHHHHHHHHHHHHHHHiiiiiiiiiiiiiiiiiiiiHHHHHHHHHHHHHHHHHHHHHHooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooHHHHHHHHHHHHHHHHHHHHHiiiiiiHHHHHHHHHHHHHHHHHHHoooooooooooooooooooHHHHHHHHHHHHHHHHHHHHHHiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
Signal Peptide (SignalP HMM Mode)
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Signal Peptide (SignalP NN Mode)
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Coiled Coils (COILS)
LWSYRAEDYLREGSHDRGSPFKEILSSVPGYGHIAPKTTLGKVATIFYAIVGIPLMLLCLSNIGDIMAHSFRFLYWKDFDFFTEYYDTKGVGNAEQIKPVPIWLCVFLVISYIIGGAFLFSHWEPWGFPDSAYFCFITLTTIGFGDFVPAQKSTDVQTAEETAELRIALCSLYLLFGIALLAMSFNLVQEEVISNVKAIAKHLGIIKSSNGDSEYEDSDFDTSDEExxxxxxxxxxxxxxxxxxxxxxxxxxxxxxSSSTAKNDPQMVTVPITLCLMIMVGYIYGGAVLFSKWEDWNILDGSRSSSRSRSRQQTERSFTEKCKDYLRQFLAFLFSNIGIICLVIGYTIAGYGNVAPITFLGKITTIAYAIAGMPLFLLYLSNIGDILAKSFKWIYAKCCLCRGCPTRPRDLQKTIQDTTGAYNRRRSSAMNHNRRWNARNGDSEYEDSDxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxSSSTAKNDPQMVTVPITLCLMIMVGYIYGGAVLFSKWEDWNILDGSYFCFISLSTIGFGDIVPGDKITGKNNDIGVQTLELSFILCAMYLMLGMALIAMCFNLMQEEVVHKMRTCSEVTQRKSKQQQQQQNSLPNIYSQFNHISTGKYDGKTTPYRGGYCTHASDFEPKAFRFRVPIAVSFLIIISFILLGSLIFNKLENWTFLDGTFFCFTSLGTIGFGELIPGESYDRTLRGNKNISVLVSSSYILVGMAVISMCFNLIQEEIIFMIKKFTLKLNKSGGSSGGVCDKNCDIS
Positional Conservation
no confident homologs detected

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Close Homologs for Annotation Transfer

Close Homologs in SWISS-PROT Database Detected by BLAST

Original result of BLAST against SWISS-PROT Database

ID	Length	Definition	RBH(Q2H)	RBH(H2Q)	Q cover	H cover	Identity	E-value
Query	790	2.2.26 [Sep-21-2011]
O14649	394	Potassium channel subfami	yes	N/A	0.184	0.370	0.378	1e-20
O17185	329	Two pore potassium channe	no	N/A	0.296	0.711	0.274	3e-19
O54912	411	Potassium channel subfami	yes	N/A	0.184	0.355	0.366	5e-19
O35111	409	Potassium channel subfami	yes	N/A	0.184	0.356	0.366	5e-19
Q63ZI0	374	Potassium channel subfami	N/A	N/A	0.187	0.395	0.345	7e-19
Q6Q1P3	405	Potassium channel subfami	no	N/A	0.369	0.720	0.248	3e-18
Q9NPC2	374	Potassium channel subfami	no	N/A	0.187	0.395	0.345	2e-17
Q3LS21	402	Potassium channel subfami	no	N/A	0.187	0.368	0.352	3e-17
Q9ES08	396	Potassium channel subfami	no	N/A	0.187	0.373	0.352	4e-17
Q9JL58	365	Potassium channel subfami	no	N/A	0.187	0.405	0.345	5e-17

>sp|O14649|KCNK3_HUMAN Potassium channel subfamily K member 3 OS=Homo sapiens GN=KCNK3 PE=1 SV=1

 Score =  102 bits (254), Expect = 1e-20,   Method: Compositional matrix adjust.
 Identities = 61/161 (37%), Positives = 88/161 (54%), Gaps = 15/161 (9%)

Query: 30  GYGHIAPKTTLGKVATIFYAIVGIPLMLLCLSNIGDIMAHSFRFLYWKDFDFFTEYYDTK 89
           GYGH AP T  GKV  +FYA++GIPL L+   ++G+ +    R+L  +           K
Sbjct: 95  GYGHAAPSTDGGKVFCMFYALLGIPLTLVMFQSLGERINTLVRYLLHRA---------KK 145

Query: 90  GVG--NAEQIKPVPIWLCVFLVISYIIGGAFLFSHWEPWGFPDSAYFCFITLTTIGFGDF 147
           G+G   A+      + +  F  IS +  GA  FSH+E W F  + Y+CFITLTTIGFGD+
Sbjct: 146 GLGMRRADVSMANMVLIGFFSCISTLCIGAAAFSHYEHWTFFQAYYYCFITLTTIGFGDY 205

Query: 148 VPAQKSTDVQTAEETAELRIALCSLYLLFGIALLAMSFNLV 188
           V  QK   +QT  +     +A   +Y+L G+ ++    NLV
Sbjct: 206 VALQKDQALQTQPQY----VAFSFVYILTGLTVIGAFLNLV 242

pH-dependent, voltage-insensitive, background potassium channel protein. Rectification direction results from potassium ion concentration on either side of the membrane. Acts as an outward rectifier when external potassium concentration is low. When external potassium concentration is high, current is inward.
Homo sapiens (taxid: 9606)

>sp|O17185|SUP9_CAEEL Two pore potassium channel protein sup-9 OS=Caenorhabditis elegans GN=sup-9 PE=1 SV=2

 Score = 97.4 bits (241), Expect = 3e-19,   Method: Compositional matrix adjust.
 Identities = 70/255 (27%), Positives = 117/255 (45%), Gaps = 21/255 (8%)

Query: 21  FKEILSSVPGYGHIAPKTTLGKVATIFYAIVGIPLMLLCLSNIGDIMAHSFRFLYWKDFD 80
           F   + +  GYGH  P T  GKV  + YA+ GIPL L+   +IG+ M ++F     K   
Sbjct: 86  FATTVITTIGYGHSTPMTDAGKVFCMLYALAGIPLGLIMFQSIGERM-NTFA---AKLLR 141

Query: 81  FFTEYYDTKGVGNAEQIKPVPIWLCVFLVISYIIGGAFLFSHWEPWGFPDSAYFCFITLT 140
           F       + +  +  +    I  C       I GGAF+FS +E W + D+ Y+CF+TLT
Sbjct: 142 FIRRAAGKQPIVTSSDL----IIFCTGWGGLLIFGGAFMFSSYENWTYFDAVYYCFVTLT 197

Query: 141 TIGFGDFVPAQKSTDVQTAEETAELRIALCSLYLLFGIALLAMSFNLV---------QEE 191
           TIGFGD+V  QK   +QT  E     +    +++LFG+ +++ + NL+         ++E
Sbjct: 198 TIGFGDYVALQKRGSLQTQPEYVFFSL----VFILFGLTVISAAMNLLVLRFLTMNTEDE 253

Query: 192 VISNVKAIAKHLGIIKSSNGDSEYEDSDFDTSDEEYDSSEEEEEEEDEEEEEEEEEGEEE 251
                +AI    G+++  +  ++ +      SD    +S    +  DE+      +  E 
Sbjct: 254 RRDEQEAILAAQGLVRVGDPTADDDFGRLPLSDNVSLASCSCYQLPDEKLRHRHRKHTEP 313

Query: 252 ETETASSSTAKNDPQ 266
                + S     P+
Sbjct: 314 HGGPPTFSGMTTRPK 328

Potassium channel involved in coordination of muscle contraction.

Caenorhabditis elegans (taxid: 6239)

>sp|O54912|KCNK3_RAT Potassium channel subfamily K member 3 OS=Rattus norvegicus GN=Kcnk3 PE=2 SV=1

 Score = 97.1 bits (240), Expect = 5e-19,   Method: Compositional matrix adjust.
 Identities = 59/161 (36%), Positives = 88/161 (54%), Gaps = 15/161 (9%)

Query: 30  GYGHIAPKTTLGKVATIFYAIVGIPLMLLCLSNIGDIMAHSFRFLYWKDFDFFTEYYDTK 89
           GYGH AP T  GKV  +FYA++GIPL L+   ++G+ +    R+L  +           +
Sbjct: 95  GYGHAAPSTDGGKVFCMFYALLGIPLTLVMFQSLGERINTFVRYLLHRA---------KR 145

Query: 90  GVG--NAEQIKPVPIWLCVFLVISYIIGGAFLFSHWEPWGFPDSAYFCFITLTTIGFGDF 147
           G+G  +AE      + +     IS +  GA  FS++E W F  + Y+CFITLTTIGFGD+
Sbjct: 146 GLGMRHAEVSMANMVLIGFVSCISTLCIGAAAFSYYERWTFFQAYYYCFITLTTIGFGDY 205

Query: 148 VPAQKSTDVQTAEETAELRIALCSLYLLFGIALLAMSFNLV 188
           V  QK   +QT  +     +A   +Y+L G+ ++    NLV
Sbjct: 206 VALQKDQALQTQPQY----VAFSFVYILTGLTVIGAFLNLV 242

pH-dependent, voltage-insensitive, background potassium channel protein. Rectification direction results from potassium ion concentration on either side of the membrane. Acts as an outward rectifier when external potassium concentration is low. When external potassium concentration is high, current is inward.

Rattus norvegicus (taxid: 10116)

>sp|O35111|KCNK3_MOUSE Potassium channel subfamily K member 3 OS=Mus musculus GN=Kcnk3 PE=2 SV=2

 Score = 97.1 bits (240), Expect = 5e-19,   Method: Compositional matrix adjust.
 Identities = 59/161 (36%), Positives = 88/161 (54%), Gaps = 15/161 (9%)

Query: 30  GYGHIAPKTTLGKVATIFYAIVGIPLMLLCLSNIGDIMAHSFRFLYWKDFDFFTEYYDTK 89
           GYGH AP T  GKV  +FYA++GIPL L+   ++G+ +    R+L  +           +
Sbjct: 95  GYGHAAPSTDGGKVFCMFYALLGIPLTLVMFQSLGERINTFVRYLLHRA---------KR 145

Query: 90  GVG--NAEQIKPVPIWLCVFLVISYIIGGAFLFSHWEPWGFPDSAYFCFITLTTIGFGDF 147
           G+G  +AE      + +     IS +  GA  FS++E W F  + Y+CFITLTTIGFGD+
Sbjct: 146 GLGMRHAEVSMANMVLIGFVSCISTLCIGAAAFSYYERWTFFQAYYYCFITLTTIGFGDY 205

Query: 148 VPAQKSTDVQTAEETAELRIALCSLYLLFGIALLAMSFNLV 188
           V  QK   +QT  +     +A   +Y+L G+ ++    NLV
Sbjct: 206 VALQKDQALQTQPQY----VAFSFVYILTGLTVIGAFLNLV 242

pH-dependent, voltage-insensitive, background potassium channel protein. Rectification direction results from potassium ion concentration on either side of the membrane. Acts as an outward rectifier when external potassium concentration is low. When external potassium concentration is high, current is inward.

Mus musculus (taxid: 10090)

>sp|Q63ZI0|KCNK9_XENLA Potassium channel subfamily K member 9 OS=Xenopus laevis GN=kcnk9 PE=2 SV=1

 Score = 96.7 bits (239), Expect = 7e-19,   Method: Compositional matrix adjust.
 Identities = 55/159 (34%), Positives = 83/159 (52%), Gaps = 11/159 (6%)

Query: 30  GYGHIAPKTTLGKVATIFYAIVGIPLMLLCLSNIGDIMAHSFRFLYWKDFDFFTEYYDTK 89
           GYGH AP T  GK   +FYA++GIPL L+   ++G+ M    ++L               
Sbjct: 95  GYGHAAPGTDAGKAFCMFYAVLGIPLTLVMFQSLGERMNTFVKYL-------LKRIKKCC 147

Query: 90  GVGNAEQIKPVPIWLCVFLVISYIIGGAFLFSHWEPWGFPDSAYFCFITLTTIGFGDFVP 149
           G+ + +      + +  F  +  +  GA  FSH+E W F  + Y+CFITLTTIGFGD+V 
Sbjct: 148 GMHSTDVSMENMVTVGFFSCMGTLCIGAAAFSHYEEWSFFQAYYYCFITLTTIGFGDYVA 207

Query: 150 AQKSTDVQTAEETAELRIALCSLYLLFGIALLAMSFNLV 188
            QK+  +Q       L +A   +Y+L G+ ++    NLV
Sbjct: 208 LQKNRALQ----KKPLYVAFSFMYILVGLTVIGAFLNLV 242

pH-dependent, voltage-insensitive, background potassium channel protein.

Xenopus laevis (taxid: 8355)

>sp|Q6Q1P3|KCNKI_RAT Potassium channel subfamily K member 18 OS=Rattus norvegicus GN=Kcnk18 PE=2 SV=1

 Score = 94.4 bits (233), Expect = 3e-18,   Method: Compositional matrix adjust.
 Identities = 80/322 (24%), Positives = 142/322 (44%), Gaps = 30/322 (9%)

Query: 295 DWNILDGSRSSSRSRSRQQTERSFTEKCKDYLRQFLAFLFSNIGIICLVIGYTIAGYGNV 354
           +  +++GSR        QQ +  + +  +D+   FL+ LF      C V  ++  GYG++
Sbjct: 94  NLTVVEGSRKD-LCEHLQQLKPQWFKAPEDW--SFLSALF----FCCTV--FSTVGYGHM 144

Query: 355 APITFLGKITTIAYAIAGMPLFLLYLSNIGDILA----KSFKWIYAKCCLCRGCPT-RPR 409
            P+T LGK   + YA+ G+PL  L L++IGDILA    +++    A  CL R     RP 
Sbjct: 145 YPVTRLGKFLCMLYALFGIPLMFLVLTDIGDILAAILSRAYSRFQALLCLPRDISKWRPL 204

Query: 410 DLQKTIQDTTGAYNRRRSSAMNHNRRWNARNGDSEYEDSDFDTSDEEYDSSEEEEEEEED 469
            L +   D+  A        ++        +     E +    + E ++     E++ E 
Sbjct: 205 LLCRKQTDSKPADEAIPQIVIDAGAD-ELLDPQPSREPASPSCNVELFERLVAREKQNEL 263

Query: 470 EEEEEEEEEEEEEEEEEEGEEEETETASSSTAKNDPQMVTVPITLCLMIMVGYIYGGAVL 529
           +      E      E   G    +  ++        + + +P+ +  +++  YI   A +
Sbjct: 264 QPPMRPVERSNSCPELVLGRLSCSILSNLDEVGQQVERLDIPLPVIALVIFAYISCAAAI 323

Query: 530 FSKWE-DWNILDGSYFCFISLSTIGFGDIVPGDKITGKNNDIGVQTLELSFILCAMYLML 588
              WE D    D  YFCF++L+TIGFGDI              V      F+  ++Y+++
Sbjct: 324 LPFWETDLGFEDAFYFCFVTLTTIGFGDI--------------VLVHPHFFLFFSIYIIV 369

Query: 589 GMALIAMCFNLMQEEVVHKMRT 610
           GM ++ + F LMQ  ++H  +T
Sbjct: 370 GMEILFIAFKLMQNRLLHTYKT 391

Outward rectifying potassium channel. Produces rapidly activating outward rectifier K(+) currents. May function as background potassium channel that sets the resting membrane potential. Channel activity is directly activated by calcium signal. Activated by the G(q)-protein coupled receptor pathway. The calcium signal robustly activates the channel via calcineurin, whereas the anchoring of 14-3-3/YWHAH interferes with the return of the current to the resting state after activation. Inhibited also by arachidonic acid and other naturally occurring unsaturated free fatty acids. Channel activity is also enhanced by volatile anesthetics, such as isoflurane. Appears to be the primary target of hydroxy-alpha-sanshool, an ingredient of Schezuan pepper. May be involved in the somatosensory function with special respect to pain sensation.

Rattus norvegicus (taxid: 10116)

>sp|Q9NPC2|KCNK9_HUMAN Potassium channel subfamily K member 9 OS=Homo sapiens GN=KCNK9 PE=1 SV=1

 Score = 91.7 bits (226), Expect = 2e-17,   Method: Compositional matrix adjust.
 Identities = 55/159 (34%), Positives = 80/159 (50%), Gaps = 11/159 (6%)

Query: 30  GYGHIAPKTTLGKVATIFYAIVGIPLMLLCLSNIGDIMAHSFRFLYWKDFDFFTEYYDTK 89
           GYGH AP T  GK   +FYA++GIPL L+   ++G+ M    R+L               
Sbjct: 95  GYGHAAPGTDAGKAFCMFYAVLGIPLTLVMFQSLGERMNTFVRYL-------LKRIKKCC 147

Query: 90  GVGNAEQIKPVPIWLCVFLVISYIIGGAFLFSHWEPWGFPDSAYFCFITLTTIGFGDFVP 149
           G+ N +      + +  F  +  +  GA  FS  E W F  + Y+CFITLTTIGFGD+V 
Sbjct: 148 GMRNTDVSMENMVTVGFFSCMGTLCIGAAAFSQCEEWSFFHAYYYCFITLTTIGFGDYVA 207

Query: 150 AQKSTDVQTAEETAELRIALCSLYLLFGIALLAMSFNLV 188
            Q     + A +   L +A   +Y+L G+ ++    NLV
Sbjct: 208 LQ----TKGALQKKPLYVAFSFMYILVGLTVIGAFLNLV 242

pH-dependent, voltage-insensitive, background potassium channel protein.

Homo sapiens (taxid: 9606)

>sp|Q3LS21|KCNK9_MOUSE Potassium channel subfamily K member 9 OS=Mus musculus GN=Kcnk9 PE=2 SV=1

 Score = 90.9 bits (224), Expect = 3e-17,   Method: Compositional matrix adjust.
 Identities = 56/159 (35%), Positives = 79/159 (49%), Gaps = 11/159 (6%)

Query: 30  GYGHIAPKTTLGKVATIFYAIVGIPLMLLCLSNIGDIMAHSFRFLYWKDFDFFTEYYDTK 89
           GYGH AP T  GK   +FYA++GIPL L+   ++G+ M    R+L               
Sbjct: 95  GYGHAAPGTDAGKAFCMFYAVLGIPLTLVMFQSLGERMNTFVRYL-------LKRIKKCC 147

Query: 90  GVGNAEQIKPVPIWLCVFLVISYIIGGAFLFSHWEPWGFPDSAYFCFITLTTIGFGDFVP 149
           G+ N E      + +  F  +  +  GA  FS  E W F  + Y+CFITLTTIGFGDFV 
Sbjct: 148 GMRNTEVSMENMVTVGFFSCMGTLCLGAAAFSQCEDWSFFHAYYYCFITLTTIGFGDFVA 207

Query: 150 AQKSTDVQTAEETAELRIALCSLYLLFGIALLAMSFNLV 188
            Q     + A +     +A   +Y+L G+ ++    NLV
Sbjct: 208 LQ----AKGALQRKPFYVAFSFMYILVGLTVIGAFLNLV 242

pH-dependent, voltage-insensitive, background potassium channel protein.

Mus musculus (taxid: 10090)

>sp|Q9ES08|KCNK9_RAT Potassium channel subfamily K member 9 OS=Rattus norvegicus GN=Kcnk9 PE=1 SV=2

 Score = 90.9 bits (224), Expect = 4e-17,   Method: Compositional matrix adjust.
 Identities = 56/159 (35%), Positives = 78/159 (49%), Gaps = 11/159 (6%)

Query: 30  GYGHIAPKTTLGKVATIFYAIVGIPLMLLCLSNIGDIMAHSFRFLYWKDFDFFTEYYDTK 89
           GYGH AP T  GK   +FYA++GIPL L+   ++G+ M    R+L               
Sbjct: 95  GYGHAAPGTDAGKAFCMFYAVLGIPLTLVMFQSLGERMNTFVRYL-------LKRIKKCC 147

Query: 90  GVGNAEQIKPVPIWLCVFLVISYIIGGAFLFSHWEPWGFPDSAYFCFITLTTIGFGDFVP 149
           G+ N E      + +  F  +  +  GA  FS  E W F  + Y+CFITLTTIGFGDFV 
Sbjct: 148 GMRNTEVSMENMVTVGFFSCMGTLCLGAAAFSQCEDWSFFHAYYYCFITLTTIGFGDFVA 207

Query: 150 AQKSTDVQTAEETAELRIALCSLYLLFGIALLAMSFNLV 188
            Q    +Q         +A   +Y+L G+ ++    NLV
Sbjct: 208 LQSKGALQ----RKPFYVAFSFMYILVGLTVIGAFLNLV 242

pH-dependent, voltage-insensitive, background potassium channel protein.

Rattus norvegicus (taxid: 10116)

>sp|Q9JL58|KCNK9_CAVPO Potassium channel subfamily K member 9 OS=Cavia porcellus GN=KCNK9 PE=1 SV=1

 Score = 90.1 bits (222), Expect = 5e-17,   Method: Compositional matrix adjust.
 Identities = 55/159 (34%), Positives = 78/159 (49%), Gaps = 11/159 (6%)

Query: 30  GYGHIAPKTTLGKVATIFYAIVGIPLMLLCLSNIGDIMAHSFRFLYWKDFDFFTEYYDTK 89
           GYGH AP T  GK   +FYA++GIPL L+   ++G+ M    R+L               
Sbjct: 95  GYGHAAPGTDAGKAFCMFYAVLGIPLTLVMFQSLGERMNTFVRYL-------LKRIKKCC 147

Query: 90  GVGNAEQIKPVPIWLCVFLVISYIIGGAFLFSHWEPWGFPDSAYFCFITLTTIGFGDFVP 149
           G+ N E      + +  F  +  +  GA  FS  E W F  + Y+CFITLTTIGFGD+V 
Sbjct: 148 GMRNTEVSMENMVTVGFFSCMGTLCIGAAAFSQCEEWSFFHAYYYCFITLTTIGFGDYVA 207

Query: 150 AQKSTDVQTAEETAELRIALCSLYLLFGIALLAMSFNLV 188
            Q    +Q         +A   +Y+L G+ ++    NLV
Sbjct: 208 LQSKGALQ----RKPFYVAFSFMYILVGLTVIGAFLNLV 242

pH-dependent, voltage-insensitive, background potassium channel protein.

Cavia porcellus (taxid: 10141)

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	790
242021264	423	conserved hypothetical protein [Pediculu	0.330	0.617	0.506	7e-67
328783862	390	PREDICTED: potassium channel subfamily K	0.360	0.730	0.442	1e-59
380018794	391	PREDICTED: TWiK family of potassium chan	0.362	0.731	0.437	2e-59
19921794	395	CG8713 [Drosophila melanogaster] gi|7304	0.316	0.632	0.460	7e-58
195455186	388	GK23078 [Drosophila willistoni] gi|19417	0.308	0.628	0.471	1e-57
194863596	395	GG23333 [Drosophila erecta] gi|190662385	0.316	0.632	0.460	1e-57
195120762	401	GI19352 [Drosophila mojavensis] gi|19390	0.324	0.638	0.457	1e-57
195474594	395	GE19175 [Drosophila yakuba] gi|194175677	0.316	0.632	0.460	1e-57
195332345	395	GM21006 [Drosophila sechellia] gi|194124	0.316	0.632	0.460	2e-57
332024510	268	Potassium channel subfamily K member 18	0.306	0.902	0.5	2e-57

>gi|242021264|ref|XP_002431065.1| conserved hypothetical protein [Pediculus humanus corporis] gi|212516299|gb|EEB18327.1| conserved hypothetical protein [Pediculus humanus corporis]

 Score =  261 bits (668), Expect = 7e-67,   Method: Compositional matrix adjust.
 Identities = 151/298 (50%), Positives = 186/298 (62%), Gaps = 37/298 (12%)

Query: 331 AFLFSNIGIICLVIGYTIAGYGNVAPITFLGKITTIAYAIAGMPLFLLYLSNIGDILAKS 390
           AFL+S   I       T  GYGNVAP T  GK+ TI YAI GMPLFLLYLSNIGDILAKS
Sbjct: 135 AFLYSLTVI-------TTIGYGNVAPRTEWGKLATIVYAIVGMPLFLLYLSNIGDILAKS 187

Query: 391 FKWIYAKCCLCRGCP-----TRPRDLQKTIQ-----DTTGAYNRRRSSAMNHNRRWNARN 440
           FKW Y K CLC+GCP      R + +++ I+      +   ++RRR    N    W    
Sbjct: 188 FKWSYTKVCLCKGCPGTESFRRRKRMKQNIKMSKMIKSQKDFSRRR----NRKTSWQPNV 243

Query: 441 GDSEYEDSDFDTSDEEYDSSEEEEEEEEDEEEEEEEEEEEEEEEEEEGEEEETETASSST 500
            D        D+ +E+    ++EE++ +DE                    +ETE + SS 
Sbjct: 244 HD--------DSRNEKRKKIDDEEDDSDDESSSSNSSSGSSSGGNTSDTNKETEISQSSL 295

Query: 501 AKND--PQMVTVPITLCLMIMVGYIYGGAVLFSKWEDWNILDGSYFCFISLSTIGFGDIV 558
           + +D  PQ VTVPITLCL IMVGY+ GGA+LF++WE+W  LDGSYFCFISLSTIGFGDIV
Sbjct: 296 SIDDYDPQTVTVPITLCLAIMVGYVCGGALLFARWENWGFLDGSYFCFISLSTIGFGDIV 355

Query: 559 PGDKITGKNNDIGVQTLELSFILCAMYLMLGMALIAMCFNLMQEEVVHKMRTCSEVTQ 616
           PGD I      I  Q +++SFIL A+YLMLGMALIAMCFNLMQEEV+HK R+C +  Q
Sbjct: 356 PGDSI------IQSQVIQISFILTAVYLMLGMALIAMCFNLMQEEVIHKTRSCIKCCQ 407

Source: Pediculus humanus corporis

Species: Pediculus humanus

Genus: Pediculus

Family: Pediculidae

Order: Phthiraptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|328783862|ref|XP_001120767.2| PREDICTED: potassium channel subfamily K member 18-like [Apis mellifera]

 Score =  238 bits (606), Expect = 1e-59,   Method: Compositional matrix adjust.
 Identities = 163/368 (44%), Positives = 200/368 (54%), Gaps = 83/368 (22%)

Query: 274 LCLMIMVGYIYGGAVLFSKWEDWNILDGSRSSSRSRSRQQ-------------TERSFTE 320
           +CL+  VGY   GA LF+  E  N LD      R R+                +ER +  
Sbjct: 62  VCLV--VGYTIAGAFLFTHIEGRNNLDIVGDVIRLRNVTAATLWELTSKENVFSERIWKA 119

Query: 321 KCKDYLRQFLAFL------------------FSNIGIICLVIGYTIAGYGNVAPITFLGK 362
           K K  L  +   +                  F+   +  L +  TI GYGN+ P T  GK
Sbjct: 120 KVKAILENYQKKMVTAIKNGYDGAEENKRWSFAGAFLYSLTVITTI-GYGNICPKTKWGK 178

Query: 363 ITTIAYAIAGMPLFLLYLSNIGDILAKSFKWIYAKCCLCRGCPTRPRDLQKTIQDTTGAY 422
           + TI YAI G+PLFLLYLSNIGDILAKSFKW YA+CCLC+ C  RP ++        GA 
Sbjct: 179 VVTIVYAIIGLPLFLLYLSNIGDILAKSFKWTYARCCLCK-CRRRPIEMAPRGSLENGAD 237

Query: 423 NRRRSSAMNHNRRWNARNGDSEYEDSDFDTSDEEYDSSEEEEEEEEDEEEEEEEEEEEEE 482
            RR     NH   W              D   +E DS   ++E   + +E +E++E    
Sbjct: 238 IRR-----NH---WQM-----------VDMHGKEIDSISIDKEVSIENDESKEDDESY-- 276

Query: 483 EEEEEGEEEETETASSSTAKNDPQMVTVPITLCLMIMVGYIYGGAVLFSKWEDWNILDGS 542
                                DPQ VTVP+TLC+ IMVGYI+GGA+LFS+WEDWN+LDGS
Sbjct: 277 ---------------------DPQRVTVPLTLCIAIMVGYIWGGAILFSEWEDWNMLDGS 315

Query: 543 YFCFISLSTIGFGDIVPGDKITGKNNDIGVQTLELSFILCAMYLMLGMALIAMCFNLMQE 602
           YFCF+SLSTIGFGDIVPGDKI         Q L+LSFI C+MYLMLGMALIAMCFNLMQE
Sbjct: 316 YFCFVSLSTIGFGDIVPGDKIY------AAQGLDLSFIFCSMYLMLGMALIAMCFNLMQE 369

Query: 603 EVVHKMRT 610
           EV+ K+R 
Sbjct: 370 EVIAKVRA 377

Source: Apis mellifera

Species: Apis mellifera

Genus: Apis

Family: Apidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|380018794|ref|XP_003693306.1| PREDICTED: TWiK family of potassium channels protein 18-like [Apis florea]

 Score =  237 bits (604), Expect = 2e-59,   Method: Compositional matrix adjust.
 Identities = 161/368 (43%), Positives = 200/368 (54%), Gaps = 82/368 (22%)

Query: 274 LCLMIMVGYIYGGAVLFSKWEDWNILDGSRSSSRSRSRQQ-------------TERSFTE 320
           +CL+  VGY   GA LF+  E  N LD      R R+                +ER +  
Sbjct: 62  VCLV--VGYTIAGAFLFTHIEGRNNLDIVGDVIRLRNVTAATLWELTSKENVFSERIWKA 119

Query: 321 KCKDYLRQFLAFL------------------FSNIGIICLVIGYTIAGYGNVAPITFLGK 362
           K K  L  +   +                  F+   +  L +  TI GYGN+ P T  GK
Sbjct: 120 KVKAILENYQKKMVTAIKNGYDGAEENKRWSFAGAFLYSLTVITTI-GYGNICPKTKWGK 178

Query: 363 ITTIAYAIAGMPLFLLYLSNIGDILAKSFKWIYAKCCLCRGCPTRPRDLQKTIQDTTGAY 422
           + TI YAI G+PLFLLYLSNIGDILAKSFKW YA+CCLC+ C  RP ++        G  
Sbjct: 179 VVTIVYAIIGLPLFLLYLSNIGDILAKSFKWTYARCCLCK-CRRRPIEMASRGSLKNGTN 237

Query: 423 NRRRSSAMNHNRRWNARNGDSEYEDSDFDTSDEEYDSSEEEEEEEEDEEEEEEEEEEEEE 482
            RR     NH   W              D   +E DS   ++E   + +E ++++E    
Sbjct: 238 IRR-----NH---WQM-----------VDMHGKEIDSVSVDKEVSIENDESKDDDE---- 274

Query: 483 EEEEEGEEEETETASSSTAKNDPQMVTVPITLCLMIMVGYIYGGAVLFSKWEDWNILDGS 542
                             +  DPQ VTVP+TLC+ IMVGYI+GGA+LFS+WEDWN+LDGS
Sbjct: 275 ------------------SSYDPQRVTVPLTLCIAIMVGYIWGGAILFSEWEDWNMLDGS 316

Query: 543 YFCFISLSTIGFGDIVPGDKITGKNNDIGVQTLELSFILCAMYLMLGMALIAMCFNLMQE 602
           YFCF+SLSTIGFGDIVPGDKI         Q L+LSFI C+MYLMLGMALIAMCFNLMQE
Sbjct: 317 YFCFVSLSTIGFGDIVPGDKIY------AAQGLDLSFIFCSMYLMLGMALIAMCFNLMQE 370

Query: 603 EVVHKMRT 610
           EV+ K+R 
Sbjct: 371 EVIAKVRA 378

Source: Apis florea

Species: Apis florea

Genus: Apis

Family: Apidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|19921794|ref|NP_610349.1| CG8713 [Drosophila melanogaster] gi|7304100|gb|AAF59138.1| CG8713 [Drosophila melanogaster] gi|17945478|gb|AAL48792.1| RE21922p [Drosophila melanogaster] gi|220948234|gb|ACL86660.1| CG8713-PA [synthetic construct] gi|220957472|gb|ACL91279.1| CG8713-PA [synthetic construct]

 Score =  232 bits (591), Expect = 7e-58,   Method: Compositional matrix adjust.
 Identities = 129/280 (46%), Positives = 167/280 (59%), Gaps = 30/280 (10%)

Query: 331 AFLFSNIGIICLVIGYTIAGYGNVAPITFLGKITTIAYAIAGMPLFLLYLSNIGDILAKS 390
           AFL+S   I       T  GYGN+ P +  GK+ TI YAI GMPLFLLYLSNIGD+LAKS
Sbjct: 132 AFLYSLTVI-------TTIGYGNITPHSECGKLVTILYAIIGMPLFLLYLSNIGDVLAKS 184

Query: 391 FKWIYAKCCLCRGCPTRPRDLQKTIQDTTGAYNRRRSSAMNHNRRWNARNGDSEYEDSDF 450
           FKWIY+K CLCR CP     + K          R+ + A+  +   NAR   S    S  
Sbjct: 185 FKWIYSKVCLCRICP----GVAKRRIIRERRKMRQLARALQMHDMENARGSSSYTSTSST 240

Query: 451 DTSDEEYDSSEEEEEEEEDEEEEEEEEEEEEEEEEEEGEEEETETASSSTAKNDPQMVTV 510
            +S+           +     + +  E + + E E  G  +E               +TV
Sbjct: 241 TSSNSSSSEYTRSSRQSSSLVDIQYTESDSDIEREIRGSTDE---------------ITV 285

Query: 511 PITLCLMIMVGYIYGGAVLFSKWEDWNILDGSYFCFISLSTIGFGDIVPGDKITGKNNDI 570
           P+T+C+ +MVGYI  GA+LF +WEDWN LDGSYFC ISLS+IGFGD+VPGD++   + D 
Sbjct: 286 PVTVCVFVMVGYILWGALLFGRWEDWNYLDGSYFCLISLSSIGFGDLVPGDRVITADRD- 344

Query: 571 GVQTLELSFILCAMYLMLGMALIAMCFNLMQEEVVHKMRT 610
               +E+SFILCA+YL+LGMA+IAMCFNLMQE+VVH +R 
Sbjct: 345 ---KVEVSFILCAIYLLLGMAVIAMCFNLMQEQVVHNIRA 381

Source: Drosophila melanogaster

Species: Drosophila melanogaster

Genus: Drosophila

Family: Drosophilidae

Order: Diptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|195455186|ref|XP_002074600.1| GK23078 [Drosophila willistoni] gi|194170685|gb|EDW85586.1| GK23078 [Drosophila willistoni]

 Score =  231 bits (589), Expect = 1e-57,   Method: Compositional matrix adjust.
 Identities = 132/280 (47%), Positives = 173/280 (61%), Gaps = 36/280 (12%)

Query: 331 AFLFSNIGIICLVIGYTIAGYGNVAPITFLGKITTIAYAIAGMPLFLLYLSNIGDILAKS 390
           AFL+S   I       T  GYGN+ P +  GK+ TI YAI GMPLFLLYLSNIGD+LAKS
Sbjct: 131 AFLYSLTVI-------TTIGYGNITPRSEWGKLVTILYAIIGMPLFLLYLSNIGDVLAKS 183

Query: 391 FKWIYAKCCLCRGCPTRPRDLQKTIQDTTGAYNRRRSSAMNHNRRWNARNGDSEYEDSDF 450
           FKWIY+K CLCR CP   +  ++ +++ +    RR + AM      N R+  S    S  
Sbjct: 184 FKWIYSKVCLCRICPGVAK--RRILRERSKM--RRLAKAMYDME--NVRSSYSTSTSSTT 237

Query: 451 DTSDEEYDSSEEEEEEEEDEEEEEEEEEEEEEEEEEEGEEEETETASSSTAKNDPQMVTV 510
           ++S +   +S +     +        E + + E E  G  +E               +TV
Sbjct: 238 NSSSDNTKNSLQTSSVVD----MPFSESDSDIEREIRGNTDE---------------ITV 278

Query: 511 PITLCLMIMVGYIYGGAVLFSKWEDWNILDGSYFCFISLSTIGFGDIVPGDKITGKNNDI 570
           P+T+C+ +MV YI  GA+LF +WE+WN LDGSYFCFISLS+IGFGD+VPGDK+   + D 
Sbjct: 279 PVTVCIFVMVSYILWGALLFGRWEEWNYLDGSYFCFISLSSIGFGDLVPGDKVITADKD- 337

Query: 571 GVQTLELSFILCAMYLMLGMALIAMCFNLMQEEVVHKMRT 610
               +E+SFILCA+YL+LGMALIAMCFNLMQEEVVH +R 
Sbjct: 338 ---KVEVSFILCAVYLLLGMALIAMCFNLMQEEVVHNIRA 374

Source: Drosophila willistoni

Species: Drosophila willistoni

Genus: Drosophila

Family: Drosophilidae

Order: Diptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|194863596|ref|XP_001970518.1| GG23333 [Drosophila erecta] gi|190662385|gb|EDV59577.1| GG23333 [Drosophila erecta]

 Score =  231 bits (589), Expect = 1e-57,   Method: Compositional matrix adjust.
 Identities = 129/280 (46%), Positives = 166/280 (59%), Gaps = 30/280 (10%)

Query: 331 AFLFSNIGIICLVIGYTIAGYGNVAPITFLGKITTIAYAIAGMPLFLLYLSNIGDILAKS 390
           AFL+S   I       T  GYGN+ P +  GK+ TI YAI GMPLFLLYLSNIGD+LAKS
Sbjct: 132 AFLYSLTVI-------TTIGYGNITPHSEWGKLVTILYAIIGMPLFLLYLSNIGDVLAKS 184

Query: 391 FKWIYAKCCLCRGCPTRPRDLQKTIQDTTGAYNRRRSSAMNHNRRWNARNGDSEYEDSDF 450
           FKWIY+K CLCR CP     + K          R+ + A+  +   NAR   S    S  
Sbjct: 185 FKWIYSKVCLCRICP----GVAKRRIIRERRKMRQLARALQMHDMENARGSSSYSSTSSA 240

Query: 451 DTSDEEYDSSEEEEEEEEDEEEEEEEEEEEEEEEEEEGEEEETETASSSTAKNDPQMVTV 510
            +S+           +     +    E + + E E  G  +E               +TV
Sbjct: 241 TSSNSSSSEYTRSSRQSSSLVDIPYTESDSDIEREIRGSTDE---------------ITV 285

Query: 511 PITLCLMIMVGYIYGGAVLFSKWEDWNILDGSYFCFISLSTIGFGDIVPGDKITGKNNDI 570
           P+T+C+ +MVGYI  GA+LF +WEDWN LDGSYFC ISLS+IGFGD+VPGD++   + D 
Sbjct: 286 PVTVCVFVMVGYILWGALLFGRWEDWNYLDGSYFCLISLSSIGFGDLVPGDRVITADRD- 344

Query: 571 GVQTLELSFILCAMYLMLGMALIAMCFNLMQEEVVHKMRT 610
               +E+SFILCA+YL+LGMA+IAMCFNLMQE+VVH +R 
Sbjct: 345 ---KVEVSFILCAIYLLLGMAVIAMCFNLMQEQVVHNIRA 381

Source: Drosophila erecta

Species: Drosophila erecta

Genus: Drosophila

Family: Drosophilidae

Order: Diptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|195120762|ref|XP_002004890.1| GI19352 [Drosophila mojavensis] gi|193909958|gb|EDW08825.1| GI19352 [Drosophila mojavensis]

 Score =  231 bits (589), Expect = 1e-57,   Method: Compositional matrix adjust.
 Identities = 128/280 (45%), Positives = 167/280 (59%), Gaps = 24/280 (8%)

Query: 331 AFLFSNIGIICLVIGYTIAGYGNVAPITFLGKITTIAYAIAGMPLFLLYLSNIGDILAKS 390
           AFL+S   I       T  GYGN+ P +  GK+ TI YAI GMPLFLLYLSNIGD+LAKS
Sbjct: 132 AFLYSLTVI-------TTIGYGNITPSSDWGKLVTILYAIIGMPLFLLYLSNIGDVLAKS 184

Query: 391 FKWIYAKCCLCRGCPTRPRDLQKTIQDTTGAYNRRRSSAMNHNRRWNARNGDSEYEDSDF 450
           FKWIY+K CLCR CP     + K          R+ + A+  +   +AR G S       
Sbjct: 185 FKWIYSKVCLCRICP----GVAKRRIIRERRKLRQLARALQLHNMESARGGSSSSNSYSS 240

Query: 451 DTSDEEYDSSEEEEEEEEDEEEEEEEEEEEEEEEEEEGEEEETETASSSTAKNDPQMVTV 510
           +++     SS       +   +     +    + + + E E          +     +TV
Sbjct: 241 NSNSSSISSSTSSSAYTKSSMQTSSVLDVPYSDSDSDIERE---------IRGSTDEITV 291

Query: 511 PITLCLMIMVGYIYGGAVLFSKWEDWNILDGSYFCFISLSTIGFGDIVPGDKITGKNNDI 570
           P+T+C+ +MV YI  GA+LF +WEDWN LDGSYFCFISLS+IGFGD+VPGD++   + D 
Sbjct: 292 PLTVCVFVMVSYILSGAILFGRWEDWNYLDGSYFCFISLSSIGFGDLVPGDRVITADKD- 350

Query: 571 GVQTLELSFILCAMYLMLGMALIAMCFNLMQEEVVHKMRT 610
               +ELSFILCA+YL+LGMALIAMCFNLMQE+V+H MR 
Sbjct: 351 ---KVELSFILCAVYLLLGMALIAMCFNLMQEQVIHNMRA 387

Source: Drosophila mojavensis

Species: Drosophila mojavensis

Genus: Drosophila

Family: Drosophilidae

Order: Diptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|195474594|ref|XP_002089576.1| GE19175 [Drosophila yakuba] gi|194175677|gb|EDW89288.1| GE19175 [Drosophila yakuba]

 Score =  231 bits (589), Expect = 1e-57,   Method: Compositional matrix adjust.
 Identities = 129/280 (46%), Positives = 165/280 (58%), Gaps = 30/280 (10%)

Query: 331 AFLFSNIGIICLVIGYTIAGYGNVAPITFLGKITTIAYAIAGMPLFLLYLSNIGDILAKS 390
           AFL+S   I       T  GYGN+ P +  GK+ TI YAI GMPLFLLYLSNIGD+LAKS
Sbjct: 132 AFLYSLTVI-------TTIGYGNITPHSEWGKLVTILYAIIGMPLFLLYLSNIGDVLAKS 184

Query: 391 FKWIYAKCCLCRGCPTRPRDLQKTIQDTTGAYNRRRSSAMNHNRRWNARNGDSEYEDSDF 450
           FKWIY+K CLCR CP     + K          R+ + A+  +   NAR   S    S  
Sbjct: 185 FKWIYSKVCLCRICP----GVAKRRIIRERRKMRQLARALQMHDMENARGSSSYTSTSST 240

Query: 451 DTSDEEYDSSEEEEEEEEDEEEEEEEEEEEEEEEEEEGEEEETETASSSTAKNDPQMVTV 510
            +S            +     +    E + + E E  G  +E               +TV
Sbjct: 241 TSSHSSSSEYTRSSRQSSSLMDIPYTESDSDIEREIRGSTDE---------------ITV 285

Query: 511 PITLCLMIMVGYIYGGAVLFSKWEDWNILDGSYFCFISLSTIGFGDIVPGDKITGKNNDI 570
           P+T+C+ +MVGYI  GA+LF +WEDWN LDGSYFC ISLS+IGFGD+VPGD++   + D 
Sbjct: 286 PVTVCVFVMVGYILWGALLFGRWEDWNYLDGSYFCLISLSSIGFGDLVPGDRVITADKD- 344

Query: 571 GVQTLELSFILCAMYLMLGMALIAMCFNLMQEEVVHKMRT 610
               +E+SFILCA+YL+LGMA+IAMCFNLMQE+VVH +R 
Sbjct: 345 ---KVEVSFILCAIYLLLGMAVIAMCFNLMQEQVVHNIRA 381

Source: Drosophila yakuba

Species: Drosophila yakuba

Genus: Drosophila

Family: Drosophilidae

Order: Diptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|195332345|ref|XP_002032859.1| GM21006 [Drosophila sechellia] gi|194124829|gb|EDW46872.1| GM21006 [Drosophila sechellia]

 Score =  231 bits (588), Expect = 2e-57,   Method: Compositional matrix adjust.
 Identities = 129/280 (46%), Positives = 166/280 (59%), Gaps = 30/280 (10%)

Query: 331 AFLFSNIGIICLVIGYTIAGYGNVAPITFLGKITTIAYAIAGMPLFLLYLSNIGDILAKS 390
           AFL+S   I       T  GYGN+ P +  GK+ TI YAI GMPLFLLYLSNIGD+LAKS
Sbjct: 132 AFLYSLTVI-------TTIGYGNITPHSEWGKLVTILYAIIGMPLFLLYLSNIGDVLAKS 184

Query: 391 FKWIYAKCCLCRGCPTRPRDLQKTIQDTTGAYNRRRSSAMNHNRRWNARNGDSEYEDSDF 450
           FKWIY+K CLCR CP     + K          R+ + A+  +   NAR   S    S  
Sbjct: 185 FKWIYSKVCLCRICP----GVAKRRIIRERRKMRQLARALQMHDMENARGSSSYTSTSST 240

Query: 451 DTSDEEYDSSEEEEEEEEDEEEEEEEEEEEEEEEEEEGEEEETETASSSTAKNDPQMVTV 510
            +S+           +     +    E + + E E  G  +E               +TV
Sbjct: 241 TSSNSSSSEYTRSSRQSSSLVDIPYTESDSDIEREIRGSTDE---------------ITV 285

Query: 511 PITLCLMIMVGYIYGGAVLFSKWEDWNILDGSYFCFISLSTIGFGDIVPGDKITGKNNDI 570
           P+T+C+ +MVGYI  GA+LF +WEDWN LDGSYFC ISLS+IGFGD+VPGD++   + D 
Sbjct: 286 PVTVCVFVMVGYILWGALLFGRWEDWNYLDGSYFCLISLSSIGFGDLVPGDRVITADRD- 344

Query: 571 GVQTLELSFILCAMYLMLGMALIAMCFNLMQEEVVHKMRT 610
               +E+SFILCA+YL+LGMA+IAMCFNLMQE+VVH +R 
Sbjct: 345 ---KVEVSFILCAIYLLLGMAVIAMCFNLMQEQVVHNIRA 381

Source: Drosophila sechellia

Species: Drosophila sechellia

Genus: Drosophila

Family: Drosophilidae

Order: Diptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|332024510|gb|EGI64708.1| Potassium channel subfamily K member 18 [Acromyrmex echinatior]

 Score =  231 bits (588), Expect = 2e-57,   Method: Compositional matrix adjust.
 Identities = 137/274 (50%), Positives = 165/274 (60%), Gaps = 32/274 (11%)

Query: 343 VIGYTIAGYGNVAPITFLGKITTIAYAIAGMPLFLLYLSNIGDILAKSFKWIYAKCCLCR 402
           V  +  AGYGN+ P T  GK+ TI YAI GMPLFLLYLSNIGDILA+SFKW YA+CCLC+
Sbjct: 20  VFSFNCAGYGNICPKTKWGKVATIVYAIIGMPLFLLYLSNIGDILARSFKWTYARCCLCK 79

Query: 403 GCPTRPRDLQKTIQDTTGAYNRRRSSAMNHNRRWNARNGDSEYEDSDFDTSDEEYDSSEE 462
               RP D          A N R S   N               D D      +   S  
Sbjct: 80  C-RRRPYD----------ATNARVSEISN---------------DPDAKRDRWQQIVSTY 113

Query: 463 EEEEEEDEEEEEEEEEEEEEEEEEEGEEEETETASSSTAKNDPQMVTVPITLCLMIMVGY 522
           +EE +      EE    +++  E  G + + E     +   DPQ VTVP+TLCL IMVGY
Sbjct: 114 DEEVDTSSLNVEETLPRDDDNGEVNGSDGDDEDDDDESDSYDPQHVTVPLTLCLAIMVGY 173

Query: 523 IYGGAVLFSKWEDWNILDGSYFCFISLSTIGFGDIVPGDKITGKNNDIGVQTLELSFILC 582
           I+GGA LFS WE W++LDGSYFCF+SLSTIGFGDIVPG+KI            +LSFI+C
Sbjct: 174 IWGGAFLFSTWESWDMLDGSYFCFVSLSTIGFGDIVPGEKIYSG------HAFDLSFIMC 227

Query: 583 AMYLMLGMALIAMCFNLMQEEVVHKMRTCSEVTQ 616
           +MYLMLGMALIAMCFNLMQEEV+ K+R    + +
Sbjct: 228 SMYLMLGMALIAMCFNLMQEEVIAKIRNLVRIVK 261

Source: Acromyrmex echinatior

Species: Acromyrmex echinatior

Genus: Acromyrmex

Family: Formicidae

Order: Hymenoptera

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	790
FB|FBgn0033257	395	CG8713 [Drosophila melanogaste	0.124	0.248	0.656	2.7e-61
FB|FBgn0035192	729	CG9194 [Drosophila melanogaste	0.135	0.146	0.699	4.3e-54
WB|WBGene00010784	372	twk-48 [Caenorhabditis elegans	0.143	0.303	0.436	9.2e-34
WB|WBGene00006690	676	twk-39 [Caenorhabditis elegans	0.116	0.136	0.54	1.3e-33
FB|FBgn0260971	1009	CG42594 [Drosophila melanogast	0.136	0.107	0.441	4.4e-29
FB|FBgn0027589	918	CG1688 [Drosophila melanogaste	0.121	0.104	0.407	2.2e-26
FB|FBgn0038621	389	CG10864 [Drosophila melanogast	0.167	0.339	0.387	1.1e-23
FB|FBgn0259242	484	CG42340 [Drosophila melanogast	0.125	0.204	0.370	6.2e-21
WB|WBGene00006318	329	sup-9 [Caenorhabditis elegans	0.192	0.462	0.345	7.6e-19
UNIPROTKB|O17185	329	sup-9 "Two pore potassium chan	0.192	0.462	0.345	7.6e-19

FB|FBgn0033257 CG8713 [Drosophila melanogaster (taxid:7227)]

 Score = 378 (138.1 bits), Expect = 2.7e-61, Sum P(3) = 2.7e-61
 Identities = 67/102 (65%), Positives = 86/102 (84%)

Query:   508 VTVPITLCLMIMVGYIYGGAVLFSKWEDWNILDGSYFCFISLSTIGFGDIVPGDKITGKN 567
             +TVP+T+C+ +MVGYI  GA+LF +WEDWN LDGSYFC ISLS+IGFGD+VPGD++   +
Sbjct:   283 ITVPVTVCVFVMVGYILWGALLFGRWEDWNYLDGSYFCLISLSSIGFGDLVPGDRVITAD 342

Query:   568 NDIGVQTLELSFILCAMYLMLGMALIAMCFNLMQEEVVHKMR 609
              D     +E+SFILCA+YL+LGMA+IAMCFNLMQE+VVH +R
Sbjct:   343 RD----KVEVSFILCAIYLLLGMAVIAMCFNLMQEQVVHNIR 380

GO:0005250 "A-type (transient outward) potassium channel activity" evidence=ISS

GO:0071805 "potassium ion transmembrane transport" evidence=IEA

GO:0016020 "membrane" evidence=IEA

FB|FBgn0035192 CG9194 [Drosophila melanogaster (taxid:7227)]

 Score = 405 (147.6 bits), Expect = 4.3e-54, Sum P(2) = 4.3e-54
 Identities = 79/113 (69%), Positives = 91/113 (80%)

Query:    98 KPVPIWLCVFLVISYIIGGAFLFSHWEPWGFPDSAYFCFITLTTIGFGDFVPAQKSTDVQ 157
             +PVPIWLCVFLV+SYI+GGA LF++WE W F DSAYFCFITLTTIGFGDFVPA+   D  
Sbjct:   617 RPVPIWLCVFLVVSYILGGAVLFAYWENWSFLDSAYFCFITLTTIGFGDFVPAKGVKD-- 674

Query:   158 TAEETAELRIALCSLYLLFGIALLAMSFNLVQEEVISNVKAIAKHLGIIKSSN 210
                  +E  IA CSLYLLFGIALLAMSFNLVQEE I+NVK +A+ LGI+K  +
Sbjct:   675 ----ESEQSIAYCSLYLLFGIALLAMSFNLVQEEFIANVKEVARRLGILKDDD 723

GO:0005252 "open rectifier potassium channel activity" evidence=ISS

GO:0071805 "potassium ion transmembrane transport" evidence=IEA

GO:0016020 "membrane" evidence=IEA

GO:0046331 "lateral inhibition" evidence=IMP

WB|WBGene00010784 twk-48 [Caenorhabditis elegans (taxid:6239)]

 Score = 253 (94.1 bits), Expect = 9.2e-34, Sum P(3) = 9.2e-34
 Identities = 52/119 (43%), Positives = 74/119 (62%)

Query:   500 TAKNDPQMVTVPITLCLMIMVGYIYGGAVLFSKWEDWNILDGSYFCFISLSTIGFGDIVP 559
             TA    + +TVPI+L +  M+GY+  G  +F  WE W  L+  YFCFISL+TIGFGD  P
Sbjct:   255 TAAAQLESMTVPISLVVFTMLGYLGVGTTIFKVWEGWTFLESFYFCFISLTTIGFGDKFP 314

Query:   560 GDKITGKNNDIGVQTLELSFILCAMYLMLGMALIAMCFNLMQEEVVHKMRTCSEVTQRK 618
                ++  N D   + L    ++ ++YL+ GMAL+AMCFNL QEEV +K R  ++  + K
Sbjct:   315 STSVS--NTDEAQEKL----VITSIYLLFGMALLAMCFNLAQEEVQNKTRWIADKFRSK 367

GO:0005267 "potassium channel activity" evidence=IEA

GO:0016020 "membrane" evidence=IEA

GO:0071805 "potassium ion transmembrane transport" evidence=IEA

GO:0005216 "ion channel activity" evidence=IEA

GO:0006811 "ion transport" evidence=IEA

GO:0055085 "transmembrane transport" evidence=IEA

GO:0016021 "integral to membrane" evidence=IEA

WB|WBGene00006690 twk-39 [Caenorhabditis elegans (taxid:6239)]

 Score = 275 (101.9 bits), Expect = 1.3e-33, Sum P(3) = 1.3e-33
 Identities = 54/100 (54%), Positives = 72/100 (72%)

Query:   510 VPITLCLMIMVGYIYGGAVLFSKWEDWNILDGSYFCFISLSTIGFGDIVPGDKITGKNND 569
             +P+++ + I+  +I GGA LFS WE+WN  DG+Y+CFI+LSTIGFGDIVPG  +     D
Sbjct:   492 MPVSVGICIVFAFISGGAWLFSWWENWNGFDGAYYCFITLSTIGFGDIVPGQAL-----D 546

Query:   570 IGVQTLELSFILCAMYLMLGMALIAMCFNLMQEEVVHKMR 609
              G Q      ++CA+YL+ GMALIAMCF LMQ++VV K R
Sbjct:   547 EGSQE---KLVVCALYLLFGMALIAMCFKLMQDDVVQKAR 583

GO:0005267 "potassium channel activity" evidence=IEA

GO:0016020 "membrane" evidence=IEA

GO:0071805 "potassium ion transmembrane transport" evidence=IEA

GO:0016021 "integral to membrane" evidence=IEA

FB|FBgn0260971 CG42594 [Drosophila melanogaster (taxid:7227)]

 Score = 241 (89.9 bits), Expect = 4.4e-29, Sum P(2) = 4.4e-29
 Identities = 53/120 (44%), Positives = 75/120 (62%)

Query:   495 TASSSTAKNDPQMVTVPITLCLMIMVGYI-YGGAVLFSKWEDWNILDGSYFCFISLSTIG 553
             +AS S        +  PI LC  +M+ YI +G AVL+ + E W ILDG YFCF+SLSTIG
Sbjct:   751 SASESRGSMHGLSILAPILLCFSMMIIYIVFGAAVLY-RLEKWPILDGIYFCFMSLSTIG 809

Query:   554 FGDIVPGDKITGKNNDIGVQTLELSFILCAMYLMLGMALIAMCFNLMQEEVVHKMRTCSE 613
             FGD++PG  +  ++N         +   C++Y+M GM L AMCFN++ EE+VH++R   E
Sbjct:   810 FGDMLPG--LRRESN--------ATTWFCSVYIMSGMTLTAMCFNVIHEEIVHRIRIVVE 859

GO:0005267 "potassium channel activity" evidence=ISS

GO:0006813 "potassium ion transport" evidence=ISS

GO:0016020 "membrane" evidence=IEA

GO:0071805 "potassium ion transmembrane transport" evidence=IEA

FB|FBgn0027589 CG1688 [Drosophila melanogaster (taxid:7227)]

 Score = 234 (87.4 bits), Expect = 2.2e-26, Sum P(3) = 2.2e-26
 Identities = 44/108 (40%), Positives = 68/108 (62%)

Query:   510 VPITLCLMIMVGYIYGGAVLFSKWEDWNILDGSYFCFISLSTIGFGDIVPGDKITGKNND 569
             VPI+L L+I+  YI  G V+F+ WE+W+++DG+YFCF++LSTIG+GD VP     G    
Sbjct:   815 VPISLVLLILASYICVGTVIFALWENWSLVDGAYFCFVTLSTIGYGDFVPARSFNGP--- 871

Query:   570 IGVQTLELSFILCAMYLMLGMALIAMCFNLMQEEVVHKMRTCSEVTQR 617
                   EL    C  YL+LG+ L+AM F++++ +++ K   C  +  R
Sbjct:   872 ------ELQLYACCAYLLLGLVLVAMSFSILETQLMWK---CKRIAVR 910

GO:0005267 "potassium channel activity" evidence=ISS

GO:0071805 "potassium ion transmembrane transport" evidence=IEA

GO:0016020 "membrane" evidence=IEA

FB|FBgn0038621 CG10864 [Drosophila melanogaster (taxid:7227)]

 Score = 252 (93.8 bits), Expect = 1.1e-23, Sum P(2) = 1.1e-23
 Identities = 55/142 (38%), Positives = 78/142 (54%)

Query:    30 GYGHIAPKTTLGKVATIFYAIVGIPLMLLCLSNIGDIMAHSFRFLYWKDFDFFTEY---- 85
             GYG++ P+T  GK  T+ YA  GIPL +L   N+G ++A SF+FLY    D   E+    
Sbjct:   158 GYGNMVPRTPWGKGFTVIYATFGIPLYILYFLNMGRVLARSFKFLYRSLHDCTQEHPRLD 217

Query:    86 -YDTK--GVGNAEQIKPVPIWLCVFLVISYIIGGAFLFSHWEPWGFPDSAYFCFITLTTI 142
               D    GVG   +   VP   C++++  Y++ G  +F++WE W   +S YFC  +L  I
Sbjct:   218 RMDALEGGVGMTRKKVIVPSTACLWVIFFYVLTGTVMFANWEKWSLLNSFYFCMTSLCKI 277

Query:   143 GFGDFVPAQK---STDVQTAEE 161
             GFGDFVP      S DV  A +
Sbjct:   278 GFGDFVPGASLTTSADVNAATQ 299

GO:0015271 "outward rectifier potassium channel activity" evidence=ISS

GO:0016020 "membrane" evidence=IEA

GO:0071805 "potassium ion transmembrane transport" evidence=IEA

FB|FBgn0259242 CG42340 [Drosophila melanogaster (taxid:7227)]

 Score = 210 (79.0 bits), Expect = 6.2e-21, Sum P(2) = 6.2e-21
 Identities = 43/116 (37%), Positives = 72/116 (62%)

Query:   497 SSSTAKNDPQMVTVPITLCLMIMVGYIYGGAVLFSKWEDWNILDGSYFCFISLSTIGFGD 556
             SS   +  P   +VPI++C+ +++ Y+  GA+LF K ++W++L+  YFCF SL TIGFG+
Sbjct:   362 SSGNRRGSP---SVPISICVCVLLCYVSSGAILFHKLQNWSVLESLYFCFTSLGTIGFGE 418

Query:   557 IVPGDKITGKNNDIGVQTLELSFILCAMYLMLGMALIAMCFNLMQEEVVHKMRTCS 612
             + P       N  + + T        + Y+++GMA++AMCF+L+Q E+V  +R  S
Sbjct:   419 MAP-------NGAVALYT-------ASAYILVGMAVVAMCFSLIQTEIVLWLRRFS 460

GO:0005267 "potassium channel activity" evidence=ISS

GO:0016020 "membrane" evidence=IEA

GO:0071805 "potassium ion transmembrane transport" evidence=IEA

WB|WBGene00006318 sup-9 [Caenorhabditis elegans (taxid:6239)]

 Score = 240 (89.5 bits), Expect = 7.6e-19, P = 7.6e-19
 Identities = 57/165 (34%), Positives = 91/165 (55%)

Query:    24 ILSSVPGYGHIAPKTTLGKVATIFYAIVGIPLMLLCLSNIGDIMAHSFRFLYWKDFDFFT 83
             +++++ GYGH  P T  GKV  + YA+ GIPL L+   +IG+ M ++F     K   F  
Sbjct:    90 VITTI-GYGHSTPMTDAGKVFCMLYALAGIPLGLIMFQSIGERM-NTFAA---KLLRFIR 144

Query:    84 EYYDTKGVGNAEQIKPVPIWLCVFLVISYIIGGAFLFSHWEPWGFPDSAYFCFITLTTIG 143
                  + +  +  +    I  C       I GGAF+FS +E W + D+ Y+CF+TLTTIG
Sbjct:   145 RAAGKQPIVTSSDL----IIFCTGWGGLLIFGGAFMFSSYENWTYFDAVYYCFVTLTTIG 200

Query:   144 FGDFVPAQKSTDVQTAEETAELRIALCSLYLLFGIALLAMSFNLV 188
             FGD+V  QK   +QT  E     +    +++LFG+ +++ + NL+
Sbjct:   201 FGDYVALQKRGSLQTQPEYVFFSL----VFILFGLTVISAAMNLL 241

GO:0005267 "potassium channel activity" evidence=IEA

GO:0016020 "membrane" evidence=IEA

GO:0071805 "potassium ion transmembrane transport" evidence=IEA

GO:0016021 "integral to membrane" evidence=IEA

GO:0005887 "integral to plasma membrane" evidence=IDA

GO:0055120 "striated muscle dense body" evidence=IDA

GO:0036195 "muscle cell projection membrane" evidence=IDA

UNIPROTKB|O17185 sup-9 "Two pore potassium channel protein sup-9" [Caenorhabditis elegans (taxid:6239)]

 Score = 240 (89.5 bits), Expect = 7.6e-19, P = 7.6e-19
 Identities = 57/165 (34%), Positives = 91/165 (55%)

Query:    24 ILSSVPGYGHIAPKTTLGKVATIFYAIVGIPLMLLCLSNIGDIMAHSFRFLYWKDFDFFT 83
             +++++ GYGH  P T  GKV  + YA+ GIPL L+   +IG+ M ++F     K   F  
Sbjct:    90 VITTI-GYGHSTPMTDAGKVFCMLYALAGIPLGLIMFQSIGERM-NTFAA---KLLRFIR 144

Query:    84 EYYDTKGVGNAEQIKPVPIWLCVFLVISYIIGGAFLFSHWEPWGFPDSAYFCFITLTTIG 143
                  + +  +  +    I  C       I GGAF+FS +E W + D+ Y+CF+TLTTIG
Sbjct:   145 RAAGKQPIVTSSDL----IIFCTGWGGLLIFGGAFMFSSYENWTYFDAVYYCFVTLTTIG 200

Query:   144 FGDFVPAQKSTDVQTAEETAELRIALCSLYLLFGIALLAMSFNLV 188
             FGD+V  QK   +QT  E     +    +++LFG+ +++ + NL+
Sbjct:   201 FGDYVALQKRGSLQTQPEYVFFSL----VFILFGLTVISAAMNLL 241

GO:0005887 "integral to plasma membrane" evidence=NAS

GO:0005267 "potassium channel activity" evidence=TAS

GO:0006813 "potassium ion transport" evidence=TAS

GO:0006937 "regulation of muscle contraction" evidence=IMP

---

Prediction of Enzyme Commission (EC) Number

EC Number Prediction by Annotation Transfer from SWISS-PROT Entries

Original result of BLAST against SWISS-PROT

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

EC Number Prediction by EFICAz Software

Prediction Level	EC number	Confidence of Prediction
3rd Layer	3.4.23	LOW CONFIDENCE prediction!

---

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	790
pfam07885	74	pfam07885, Ion_trans_2, Ion channel	1e-13
pfam07885	74	pfam07885, Ion_trans_2, Ion channel	3e-11
TIGR00927	1096	TIGR00927, 2A1904, K+-dependent Na+/Ca+ exchanger	4e-11
TIGR00927	1096	TIGR00927, 2A1904, K+-dependent Na+/Ca+ exchanger	5e-10
pfam04147	809	pfam04147, Nop14, Nop14-like family	6e-10
pfam07885	74	pfam07885, Ion_trans_2, Ion channel	2e-09
pfam11705	221	pfam11705, RNA_pol_3_Rpc31, DNA-directed RNA polym	9e-09
pfam05285	317	pfam05285, SDA1, SDA1	1e-08
pfam03344	715	pfam03344, Daxx, Daxx Family	1e-08
pfam07885	74	pfam07885, Ion_trans_2, Ion channel	3e-08
pfam03344	715	pfam03344, Daxx, Daxx Family	3e-08
pfam07133	164	pfam07133, Merozoite_SPAM, Merozoite surface prote	9e-08
pfam11081	172	pfam11081, DUF2890, Protein of unknown function (D	1e-07
pfam04889	241	pfam04889, Cwf_Cwc_15, Cwf15/Cwc15 cell cycle cont	1e-07
pfam03985	431	pfam03985, Paf1, Paf1	2e-07
PHA00435	306	PHA00435, PHA00435, capsid assembly protein	2e-07
pfam04147	809	pfam04147, Nop14, Nop14-like family	3e-07
pfam11081	172	pfam11081, DUF2890, Protein of unknown function (D	3e-07
pfam03247	106	pfam03247, Prothymosin, Prothymosin/parathymosin f	3e-07
pfam12253	76	pfam12253, CAF1A, Chromatin assembly factor 1 subu	3e-07
pfam03066	146	pfam03066, Nucleoplasmin, Nucleoplasmin	3e-07
pfam05285	317	pfam05285, SDA1, SDA1	4e-07
pfam05764	238	pfam05764, YL1, YL1 nuclear protein	4e-07
pfam04147	809	pfam04147, Nop14, Nop14-like family	5e-07
pfam05285	317	pfam05285, SDA1, SDA1	5e-07
pfam03344	715	pfam03344, Daxx, Daxx Family	5e-07
TIGR00927	1096	TIGR00927, 2A1904, K+-dependent Na+/Ca+ exchanger	6e-07
pfam07885	74	pfam07885, Ion_trans_2, Ion channel	7e-07
pfam08553	794	pfam08553, VID27, VID27 cytoplasmic protein	8e-07
pfam04712	481	pfam04712, Radial_spoke, Radial spokehead-like pro	9e-07
pfam04147	809	pfam04147, Nop14, Nop14-like family	1e-06
pfam05285	317	pfam05285, SDA1, SDA1	1e-06
pfam11081	172	pfam11081, DUF2890, Protein of unknown function (D	1e-06
pfam04889	241	pfam04889, Cwf_Cwc_15, Cwf15/Cwc15 cell cycle cont	1e-06
pfam03066	146	pfam03066, Nucleoplasmin, Nucleoplasmin	1e-06
pfam05793	528	pfam05793, TFIIF_alpha, Transcription initiation f	1e-06
TIGR00927	1096	TIGR00927, 2A1904, K+-dependent Na+/Ca+ exchanger	2e-06
pfam04147	809	pfam04147, Nop14, Nop14-like family	2e-06
pfam03066	146	pfam03066, Nucleoplasmin, Nucleoplasmin	2e-06
pfam14181	155	pfam14181, YqfQ, YqfQ-like protein	2e-06
pfam06213	282	pfam06213, CobT, Cobalamin biosynthesis protein Co	2e-06
PRK14160	211	PRK14160, PRK14160, heat shock protein GrpE; Provi	2e-06
pfam04050	171	pfam04050, Upf2, Up-frameshift suppressor 2	2e-06
pfam04147	809	pfam04147, Nop14, Nop14-like family	3e-06
pfam03066	146	pfam03066, Nucleoplasmin, Nucleoplasmin	3e-06
COG5406	1001	COG5406, COG5406, Nucleosome binding factor SPN, S	3e-06
PRK14891	131	PRK14891, PRK14891, 50S ribosomal protein L24e/unk	3e-06
TIGR00927	1096	TIGR00927, 2A1904, K+-dependent Na+/Ca+ exchanger	4e-06
pfam06213	282	pfam06213, CobT, Cobalamin biosynthesis protein Co	4e-06
pfam04050	171	pfam04050, Upf2, Up-frameshift suppressor 2	4e-06
pfam04050	171	pfam04050, Upf2, Up-frameshift suppressor 2	4e-06
PTZ00415	2849	PTZ00415, PTZ00415, transmission-blocking target a	4e-06
COG4547	620	COG4547, CobT, Cobalamin biosynthesis protein CobT	4e-06
pfam07423	214	pfam07423, DUF1510, Protein of unknown function (D	4e-06
pfam03344	715	pfam03344, Daxx, Daxx Family	5e-06
pfam07423	214	pfam07423, DUF1510, Protein of unknown function (D	5e-06
pfam03066	146	pfam03066, Nucleoplasmin, Nucleoplasmin	6e-06
PRK14891	131	PRK14891, PRK14891, 50S ribosomal protein L24e/unk	7e-06
TIGR03685	105	TIGR03685, L12P_arch, 50S ribosomal protein L12P	7e-06
pfam03066	146	pfam03066, Nucleoplasmin, Nucleoplasmin	8e-06
TIGR03685	105	TIGR03685, L12P_arch, 50S ribosomal protein L12P	8e-06
pfam04147	809	pfam04147, Nop14, Nop14-like family	9e-06
pfam03066	146	pfam03066, Nucleoplasmin, Nucleoplasmin	9e-06
PRK06402	106	PRK06402, rpl12p, 50S ribosomal protein L12P; Revi	9e-06
pfam04147	809	pfam04147, Nop14, Nop14-like family	1e-05
pfam04147	809	pfam04147, Nop14, Nop14-like family	1e-05
PRK06402	106	PRK06402, rpl12p, 50S ribosomal protein L12P; Revi	1e-05
PTZ00248	319	PTZ00248, PTZ00248, eukaryotic translation initiat	1e-05
PRK12329	449	PRK12329, nusA, transcription elongation factor Nu	1e-05
pfam00183	529	pfam00183, HSP90, Hsp90 protein	1e-05
pfam04546	211	pfam04546, Sigma70_ner, Sigma-70, non-essential re	1e-05
pfam09805	134	pfam09805, Nop25, Nucleolar protein 12 (25kDa)	1e-05
pfam04147	809	pfam04147, Nop14, Nop14-like family	2e-05
pfam03066	146	pfam03066, Nucleoplasmin, Nucleoplasmin	2e-05
pfam08553	794	pfam08553, VID27, VID27 cytoplasmic protein	2e-05
pfam04712	481	pfam04712, Radial_spoke, Radial spokehead-like pro	2e-05
pfam14181	155	pfam14181, YqfQ, YqfQ-like protein	2e-05
COG4547	620	COG4547, CobT, Cobalamin biosynthesis protein CobT	2e-05
PRK06402	106	PRK06402, rpl12p, 50S ribosomal protein L12P; Revi	2e-05
PTZ00248	319	PTZ00248, PTZ00248, eukaryotic translation initiat	2e-05
pfam09026	101	pfam09026, Cenp-B_dimeris, Centromere protein B di	2e-05
pfam09756	189	pfam09756, DDRGK, DDRGK domain	2e-05
TIGR00927	1096	TIGR00927, 2A1904, K+-dependent Na+/Ca+ exchanger	3e-05
pfam04147	809	pfam04147, Nop14, Nop14-like family	3e-05
pfam03066	146	pfam03066, Nucleoplasmin, Nucleoplasmin	3e-05
pfam03066	146	pfam03066, Nucleoplasmin, Nucleoplasmin	3e-05
PTZ00248	319	PTZ00248, PTZ00248, eukaryotic translation initiat	3e-05
pfam09026	101	pfam09026, Cenp-B_dimeris, Centromere protein B di	3e-05
pfam09026	101	pfam09026, Cenp-B_dimeris, Centromere protein B di	3e-05
pfam09184	285	pfam09184, PPP4R2, PPP4R2	3e-05
pfam09184	285	pfam09184, PPP4R2, PPP4R2	3e-05
pfam04931	784	pfam04931, DNA_pol_phi, DNA polymerase phi	3e-05
pfam04874	97	pfam04874, Mak16, Mak16 protein C-terminal region	3e-05
pfam04874	97	pfam04874, Mak16, Mak16 protein C-terminal region	3e-05
pfam09073	424	pfam09073, BUD22, BUD22	3e-05
pfam02459	548	pfam02459, Adeno_terminal, Adenoviral DNA terminal	3e-05
pfam04147	809	pfam04147, Nop14, Nop14-like family	4e-05
pfam03344	715	pfam03344, Daxx, Daxx Family	4e-05
pfam07133	164	pfam07133, Merozoite_SPAM, Merozoite surface prote	4e-05
pfam03066	146	pfam03066, Nucleoplasmin, Nucleoplasmin	4e-05
pfam04712	481	pfam04712, Radial_spoke, Radial spokehead-like pro	4e-05
pfam04712	481	pfam04712, Radial_spoke, Radial spokehead-like pro	4e-05
pfam02724	583	pfam02724, CDC45, CDC45-like protein	4e-05
pfam11861	154	pfam11861, DUF3381, Domain of unknown function (DU	4e-05
cd05832	106	cd05832, Ribosomal_L12p, Ribosomal protein L12p	4e-05
TIGR00927	1096	TIGR00927, 2A1904, K+-dependent Na+/Ca+ exchanger	5e-05
pfam04712	481	pfam04712, Radial_spoke, Radial spokehead-like pro	5e-05
pfam09026	101	pfam09026, Cenp-B_dimeris, Centromere protein B di	5e-05
pfam02459	548	pfam02459, Adeno_terminal, Adenoviral DNA terminal	5e-05
cd05832	106	cd05832, Ribosomal_L12p, Ribosomal protein L12p	5e-05
pfam05887	145	pfam05887, Trypan_PARP, Procyclic acidic repetitiv	5e-05
COG5137	279	COG5137, COG5137, Histone chaperone involved in ge	5e-05
pfam07423	214	pfam07423, DUF1510, Protein of unknown function (D	6e-05
pfam07423	214	pfam07423, DUF1510, Protein of unknown function (D	6e-05
pfam04874	97	pfam04874, Mak16, Mak16 protein C-terminal region	6e-05
pfam05432	291	pfam05432, BSP_II, Bone sialoprotein II (BSP-II)	6e-05
pfam04006	613	pfam04006, Mpp10, Mpp10 protein	6e-05
TIGR00927	1096	TIGR00927, 2A1904, K+-dependent Na+/Ca+ exchanger	7e-05
pfam07133	164	pfam07133, Merozoite_SPAM, Merozoite surface prote	7e-05
COG4547	620	COG4547, CobT, Cobalamin biosynthesis protein CobT	7e-05
pfam07423	214	pfam07423, DUF1510, Protein of unknown function (D	7e-05
PRK06402	106	PRK06402, rpl12p, 50S ribosomal protein L12P; Revi	7e-05
pfam04546	211	pfam04546, Sigma70_ner, Sigma-70, non-essential re	7e-05
PHA00435	306	PHA00435, PHA00435, capsid assembly protein	8e-05
pfam08553	794	pfam08553, VID27, VID27 cytoplasmic protein	8e-05
pfam05432	291	pfam05432, BSP_II, Bone sialoprotein II (BSP-II)	8e-05
PRK14140	191	PRK14140, PRK14140, heat shock protein GrpE; Provi	8e-05
COG2058	109	COG2058, RPP1A, Ribosomal protein L12E/L44/L45/RPP	8e-05
PRK04019	330	PRK04019, rplP0, acidic ribosomal protein P0; Vali	8e-05
pfam03066	146	pfam03066, Nucleoplasmin, Nucleoplasmin	9e-05
TIGR01651	600	TIGR01651, CobT, cobaltochelatase, CobT subunit	9e-05
PRK05901	509	PRK05901, PRK05901, RNA polymerase sigma factor; P	9e-05
pfam05285	317	pfam05285, SDA1, SDA1	1e-04
pfam03985	431	pfam03985, Paf1, Paf1	1e-04
pfam03247	106	pfam03247, Prothymosin, Prothymosin/parathymosin f	1e-04
pfam05764	238	pfam05764, YL1, YL1 nuclear protein	1e-04
pfam05764	238	pfam05764, YL1, YL1 nuclear protein	1e-04
pfam04712	481	pfam04712, Radial_spoke, Radial spokehead-like pro	1e-04
pfam06213	282	pfam06213, CobT, Cobalamin biosynthesis protein Co	1e-04
pfam06213	282	pfam06213, CobT, Cobalamin biosynthesis protein Co	1e-04
PTZ00415	2849	PTZ00415, PTZ00415, transmission-blocking target a	1e-04
TIGR03685	105	TIGR03685, L12P_arch, 50S ribosomal protein L12P	1e-04
pfam04546	211	pfam04546, Sigma70_ner, Sigma-70, non-essential re	1e-04
pfam04546	211	pfam04546, Sigma70_ner, Sigma-70, non-essential re	1e-04
pfam04546	211	pfam04546, Sigma70_ner, Sigma-70, non-essential re	1e-04
pfam04931	784	pfam04931, DNA_pol_phi, DNA polymerase phi	1e-04
pfam02459	548	pfam02459, Adeno_terminal, Adenoviral DNA terminal	1e-04
pfam02724	583	pfam02724, CDC45, CDC45-like protein	1e-04
cd05832	106	cd05832, Ribosomal_L12p, Ribosomal protein L12p	1e-04
pfam05432	291	pfam05432, BSP_II, Bone sialoprotein II (BSP-II)	1e-04
PRK04019	330	PRK04019, rplP0, acidic ribosomal protein P0; Vali	1e-04
PRK05901	509	PRK05901, PRK05901, RNA polymerase sigma factor; P	1e-04
pfam02029	431	pfam02029, Caldesmon, Caldesmon	1e-04
PRK05658	619	PRK05658, PRK05658, RNA polymerase sigma factor Rp	1e-04
PHA03169	413	PHA03169, PHA03169, hypothetical protein; Provisio	1e-04
pfam06390	261	pfam06390, NESP55, Neuroendocrine-specific golgi p	1e-04
pfam03344	715	pfam03344, Daxx, Daxx Family	2e-04
pfam03247	106	pfam03247, Prothymosin, Prothymosin/parathymosin f	2e-04
pfam12253	76	pfam12253, CAF1A, Chromatin assembly factor 1 subu	2e-04
pfam03066	146	pfam03066, Nucleoplasmin, Nucleoplasmin	2e-04
pfam04712	481	pfam04712, Radial_spoke, Radial spokehead-like pro	2e-04
pfam06213	282	pfam06213, CobT, Cobalamin biosynthesis protein Co	2e-04
pfam04050	171	pfam04050, Upf2, Up-frameshift suppressor 2	2e-04
pfam04050	171	pfam04050, Upf2, Up-frameshift suppressor 2	2e-04
PTZ00248	319	PTZ00248, PTZ00248, eukaryotic translation initiat	2e-04
PTZ00248	319	PTZ00248, PTZ00248, eukaryotic translation initiat	2e-04
pfam00183	529	pfam00183, HSP90, Hsp90 protein	2e-04
pfam04546	211	pfam04546, Sigma70_ner, Sigma-70, non-essential re	2e-04
pfam09026	101	pfam09026, Cenp-B_dimeris, Centromere protein B di	2e-04
pfam04874	97	pfam04874, Mak16, Mak16 protein C-terminal region	2e-04
pfam04874	97	pfam04874, Mak16, Mak16 protein C-terminal region	2e-04
pfam04874	97	pfam04874, Mak16, Mak16 protein C-terminal region	2e-04
pfam09073	424	pfam09073, BUD22, BUD22	2e-04
pfam04006	613	pfam04006, Mpp10, Mpp10 protein	2e-04
COG2058	109	COG2058, RPP1A, Ribosomal protein L12E/L44/L45/RPP	2e-04
PRK05901	509	PRK05901, PRK05901, RNA polymerase sigma factor; P	2e-04
PRK05901	509	PRK05901, PRK05901, RNA polymerase sigma factor; P	2e-04
pfam02029	431	pfam02029, Caldesmon, Caldesmon	2e-04
PHA03169	413	PHA03169, PHA03169, hypothetical protein; Provisio	2e-04
PHA03169	413	PHA03169, PHA03169, hypothetical protein; Provisio	2e-04
PRK04195	482	PRK04195, PRK04195, replication factor C large sub	2e-04
pfam12619	145	pfam12619, MCM2_N, Mini-chromosome maintenance pro	2e-04
pfam04774	106	pfam04774, HABP4_PAI-RBP1, Hyaluronan / mRNA bindi	2e-04
COG5414	392	COG5414, COG5414, TATA-binding protein-associated	2e-04
pfam05285	317	pfam05285, SDA1, SDA1	3e-04
pfam07133	164	pfam07133, Merozoite_SPAM, Merozoite surface prote	3e-04
pfam11081	172	pfam11081, DUF2890, Protein of unknown function (D	3e-04
pfam03985	431	pfam03985, Paf1, Paf1	3e-04
PHA00435	306	PHA00435, PHA00435, capsid assembly protein	3e-04
pfam08553	794	pfam08553, VID27, VID27 cytoplasmic protein	3e-04
PRK14160	211	PRK14160, PRK14160, heat shock protein GrpE; Provi	3e-04
PRK14160	211	PRK14160, PRK14160, heat shock protein GrpE; Provi	3e-04
PRK14160	211	PRK14160, PRK14160, heat shock protein GrpE; Provi	3e-04
pfam04050	171	pfam04050, Upf2, Up-frameshift suppressor 2	3e-04
PRK14891	131	PRK14891, PRK14891, 50S ribosomal protein L24e/unk	3e-04
pfam07423	214	pfam07423, DUF1510, Protein of unknown function (D	3e-04
TIGR03685	105	TIGR03685, L12P_arch, 50S ribosomal protein L12P	3e-04
TIGR03685	105	TIGR03685, L12P_arch, 50S ribosomal protein L12P	3e-04
PRK12329	449	PRK12329, nusA, transcription elongation factor Nu	3e-04
PRK12329	449	PRK12329, nusA, transcription elongation factor Nu	3e-04
pfam09026	101	pfam09026, Cenp-B_dimeris, Centromere protein B di	3e-04
pfam09184	285	pfam09184, PPP4R2, PPP4R2	3e-04
pfam04931	784	pfam04931, DNA_pol_phi, DNA polymerase phi	3e-04
pfam04874	97	pfam04874, Mak16, Mak16 protein C-terminal region	3e-04
pfam09073	424	pfam09073, BUD22, BUD22	3e-04
cd05832	106	cd05832, Ribosomal_L12p, Ribosomal protein L12p	3e-04
pfam05887	145	pfam05887, Trypan_PARP, Procyclic acidic repetitiv	3e-04
PRK14140	191	PRK14140, PRK14140, heat shock protein GrpE; Provi	3e-04
PRK14140	191	PRK14140, PRK14140, heat shock protein GrpE; Provi	3e-04
TIGR01651	600	TIGR01651, CobT, cobaltochelatase, CobT subunit	3e-04
COG5414	392	COG5414, COG5414, TATA-binding protein-associated	3e-04
pfam03154	979	pfam03154, Atrophin-1, Atrophin-1 family	3e-04
COG5167	776	COG5167, VID27, Protein involved in vacuole import	3e-04
COG5238	388	COG5238, RNA1, Ran GTPase-activating protein (RanG	3e-04
PLN00152	130	PLN00152, PLN00152, DNA-directed RNA polymerase; P	3e-04
pfam04147	809	pfam04147, Nop14, Nop14-like family	4e-04
pfam05285	317	pfam05285, SDA1, SDA1	4e-04
pfam03066	146	pfam03066, Nucleoplasmin, Nucleoplasmin	4e-04
pfam03066	146	pfam03066, Nucleoplasmin, Nucleoplasmin	4e-04
pfam05793	528	pfam05793, TFIIF_alpha, Transcription initiation f	4e-04
PRK14160	211	PRK14160, PRK14160, heat shock protein GrpE; Provi	4e-04
pfam04050	171	pfam04050, Upf2, Up-frameshift suppressor 2	4e-04
pfam04050	171	pfam04050, Upf2, Up-frameshift suppressor 2	4e-04
COG4547	620	COG4547, CobT, Cobalamin biosynthesis protein CobT	4e-04
PRK06402	106	PRK06402, rpl12p, 50S ribosomal protein L12P; Revi	4e-04
PTZ00248	319	PTZ00248, PTZ00248, eukaryotic translation initiat	4e-04
pfam09026	101	pfam09026, Cenp-B_dimeris, Centromere protein B di	4e-04
pfam04874	97	pfam04874, Mak16, Mak16 protein C-terminal region	4e-04
pfam09073	424	pfam09073, BUD22, BUD22	4e-04
cd05832	106	cd05832, Ribosomal_L12p, Ribosomal protein L12p	4e-04
cd05832	106	cd05832, Ribosomal_L12p, Ribosomal protein L12p	4e-04
pfam05432	291	pfam05432, BSP_II, Bone sialoprotein II (BSP-II)	4e-04
PHA03169	413	PHA03169, PHA03169, hypothetical protein; Provisio	4e-04
pfam04774	106	pfam04774, HABP4_PAI-RBP1, Hyaluronan / mRNA bindi	4e-04
PRK02363	129	PRK02363, PRK02363, DNA-directed RNA polymerase su	4e-04
pfam10446	449	pfam10446, DUF2457, Protein of unknown function (D	4e-04
pfam03896	281	pfam03896, TRAP_alpha, Translocon-associated prote	4e-04
COG3343	175	COG3343, RpoE, DNA-directed RNA polymerase, delta	4e-04
TIGR00927	1096	TIGR00927, 2A1904, K+-dependent Na+/Ca+ exchanger	5e-04
pfam03344	715	pfam03344, Daxx, Daxx Family	5e-04
pfam05793	528	pfam05793, TFIIF_alpha, Transcription initiation f	5e-04
pfam05793	528	pfam05793, TFIIF_alpha, Transcription initiation f	5e-04
PTZ00415	2849	PTZ00415, PTZ00415, transmission-blocking target a	5e-04
pfam07423	214	pfam07423, DUF1510, Protein of unknown function (D	5e-04
TIGR03685	105	TIGR03685, L12P_arch, 50S ribosomal protein L12P	5e-04
PRK06402	106	PRK06402, rpl12p, 50S ribosomal protein L12P; Revi	5e-04
pfam04874	97	pfam04874, Mak16, Mak16 protein C-terminal region	5e-04
cd05832	106	cd05832, Ribosomal_L12p, Ribosomal protein L12p	5e-04
COG5137	279	COG5137, COG5137, Histone chaperone involved in ge	5e-04
pfam04006	613	pfam04006, Mpp10, Mpp10 protein	5e-04
COG2058	109	COG2058, RPP1A, Ribosomal protein L12E/L44/L45/RPP	5e-04
pfam01056	329	pfam01056, Myc_N, Myc amino-terminal region	5e-04
pfam05285	317	pfam05285, SDA1, SDA1	6e-04
pfam03344	715	pfam03344, Daxx, Daxx Family	6e-04
pfam04889	241	pfam04889, Cwf_Cwc_15, Cwf15/Cwc15 cell cycle cont	6e-04
TIGR03685	105	TIGR03685, L12P_arch, 50S ribosomal protein L12P	6e-04
PTZ00248	319	PTZ00248, PTZ00248, eukaryotic translation initiat	6e-04
pfam00183	529	pfam00183, HSP90, Hsp90 protein	6e-04
pfam04546	211	pfam04546, Sigma70_ner, Sigma-70, non-essential re	6e-04
pfam09805	134	pfam09805, Nop25, Nucleolar protein 12 (25kDa)	6e-04
pfam09026	101	pfam09026, Cenp-B_dimeris, Centromere protein B di	6e-04
PRK14140	191	PRK14140, PRK14140, heat shock protein GrpE; Provi	6e-04
COG2058	109	COG2058, RPP1A, Ribosomal protein L12E/L44/L45/RPP	6e-04
pfam09747	178	pfam09747, DUF2052, Coiled-coil domain containing	6e-04
pfam06991	277	pfam06991, Prp19_bind, Splicing factor, Prp19-bind	6e-04
pfam11708	236	pfam11708, Slu7, Pre-mRNA splicing Prp18-interacti	6e-04
pfam05285	317	pfam05285, SDA1, SDA1	7e-04
pfam03066	146	pfam03066, Nucleoplasmin, Nucleoplasmin	7e-04
pfam06213	282	pfam06213, CobT, Cobalamin biosynthesis protein Co	7e-04
PRK14160	211	PRK14160, PRK14160, heat shock protein GrpE; Provi	7e-04
pfam04050	171	pfam04050, Upf2, Up-frameshift suppressor 2	7e-04
PRK14891	131	PRK14891, PRK14891, 50S ribosomal protein L24e/unk	7e-04
pfam04874	97	pfam04874, Mak16, Mak16 protein C-terminal region	7e-04
cd05832	106	cd05832, Ribosomal_L12p, Ribosomal protein L12p	7e-04
PRK14140	191	PRK14140, PRK14140, heat shock protein GrpE; Provi	7e-04
PRK14140	191	PRK14140, PRK14140, heat shock protein GrpE; Provi	7e-04
PRK14140	191	PRK14140, PRK14140, heat shock protein GrpE; Provi	7e-04
pfam04774	106	pfam04774, HABP4_PAI-RBP1, Hyaluronan / mRNA bindi	7e-04
smart00784	106	smart00784, SPT2, SPT2 chromatin protein	7e-04
pfam11942	92	pfam11942, Spt5_N, Spt5 transcription elongation f	7e-04
pfam04050	171	pfam04050, Upf2, Up-frameshift suppressor 2	8e-04
PRK12329	449	PRK12329, nusA, transcription elongation factor Nu	8e-04
pfam04006	613	pfam04006, Mpp10, Mpp10 protein	8e-04
PRK05901	509	PRK05901, PRK05901, RNA polymerase sigma factor; P	8e-04
pfam09026	101	pfam09026, Cenp-B_dimeris, Centromere protein B di	9e-04
pfam09747	178	pfam09747, DUF2052, Coiled-coil domain containing	9e-04
pfam05285	317	pfam05285, SDA1, SDA1	0.001
pfam05285	317	pfam05285, SDA1, SDA1	0.001
pfam03344	715	pfam03344, Daxx, Daxx Family	0.001
pfam07133	164	pfam07133, Merozoite_SPAM, Merozoite surface prote	0.001
pfam04889	241	pfam04889, Cwf_Cwc_15, Cwf15/Cwc15 cell cycle cont	0.001
pfam03066	146	pfam03066, Nucleoplasmin, Nucleoplasmin	0.001
pfam03066	146	pfam03066, Nucleoplasmin, Nucleoplasmin	0.001
pfam03066	146	pfam03066, Nucleoplasmin, Nucleoplasmin	0.001
pfam05764	238	pfam05764, YL1, YL1 nuclear protein	0.001
pfam06213	282	pfam06213, CobT, Cobalamin biosynthesis protein Co	0.001
COG5406	1001	COG5406, COG5406, Nucleosome binding factor SPN, S	0.001
COG5406	1001	COG5406, COG5406, Nucleosome binding factor SPN, S	0.001
TIGR03685	105	TIGR03685, L12P_arch, 50S ribosomal protein L12P	0.001
PRK06402	106	PRK06402, rpl12p, 50S ribosomal protein L12P; Revi	0.001
PRK06402	106	PRK06402, rpl12p, 50S ribosomal protein L12P; Revi	0.001
PRK06402	106	PRK06402, rpl12p, 50S ribosomal protein L12P; Revi	0.001
cd05832	106	cd05832, Ribosomal_L12p, Ribosomal protein L12p	0.001
cd05832	106	cd05832, Ribosomal_L12p, Ribosomal protein L12p	0.001
PRK14140	191	PRK14140, PRK14140, heat shock protein GrpE; Provi	0.001
PRK14140	191	PRK14140, PRK14140, heat shock protein GrpE; Provi	0.001
COG2058	109	COG2058, RPP1A, Ribosomal protein L12E/L44/L45/RPP	0.001
PRK05901	509	PRK05901, PRK05901, RNA polymerase sigma factor; P	0.001
PHA03169	413	PHA03169, PHA03169, hypothetical protein; Provisio	0.001
PRK04195	482	PRK04195, PRK04195, replication factor C large sub	0.001
COG5414	392	COG5414, COG5414, TATA-binding protein-associated	0.001
pfam03896	281	pfam03896, TRAP_alpha, Translocon-associated prote	0.001
pfam03896	281	pfam03896, TRAP_alpha, Translocon-associated prote	0.001
pfam06991	277	pfam06991, Prp19_bind, Splicing factor, Prp19-bind	0.001
pfam11942	92	pfam11942, Spt5_N, Spt5 transcription elongation f	0.001
pfam11942	92	pfam11942, Spt5_N, Spt5 transcription elongation f	0.001
pfam07767	387	pfam07767, Nop53, Nop53 (60S ribosomal biogenesis)	0.001
COG1614	470	COG1614, CdhC, CO dehydrogenase/acetyl-CoA synthas	0.001
pfam05178	99	pfam05178, Kri1, KRI1-like family	0.001
pfam05320	167	pfam05320, Pox_RNA_Pol_19, Poxvirus DNA-directed R	0.001
PRK13108	460	PRK13108, PRK13108, prolipoprotein diacylglyceryl	0.001
pfam00428	88	pfam00428, Ribosomal_60s, 60s Acidic ribosomal pro	0.001
COG5271	4600	COG5271, MDN1, AAA ATPase containing von Willebran	0.001
pfam03032	46	pfam03032, Brevenin, Brevenin/esculentin/gaegurin/	0.001
pfam07133	164	pfam07133, Merozoite_SPAM, Merozoite surface prote	0.002
pfam11081	172	pfam11081, DUF2890, Protein of unknown function (D	0.002
pfam04712	481	pfam04712, Radial_spoke, Radial spokehead-like pro	0.002
pfam04712	481	pfam04712, Radial_spoke, Radial spokehead-like pro	0.002
pfam04050	171	pfam04050, Upf2, Up-frameshift suppressor 2	0.002
COG5406	1001	COG5406, COG5406, Nucleosome binding factor SPN, S	0.002
PRK14891	131	PRK14891, PRK14891, 50S ribosomal protein L24e/unk	0.002
PTZ00248	319	PTZ00248, PTZ00248, eukaryotic translation initiat	0.002
PRK12329	449	PRK12329, nusA, transcription elongation factor Nu	0.002
PRK12329	449	PRK12329, nusA, transcription elongation factor Nu	0.002
pfam00183	529	pfam00183, HSP90, Hsp90 protein	0.002
pfam00183	529	pfam00183, HSP90, Hsp90 protein	0.002
pfam04546	211	pfam04546, Sigma70_ner, Sigma-70, non-essential re	0.002
pfam09805	134	pfam09805, Nop25, Nucleolar protein 12 (25kDa)	0.002
pfam09026	101	pfam09026, Cenp-B_dimeris, Centromere protein B di	0.002
pfam09026	101	pfam09026, Cenp-B_dimeris, Centromere protein B di	0.002
pfam02459	548	pfam02459, Adeno_terminal, Adenoviral DNA terminal	0.002
pfam02459	548	pfam02459, Adeno_terminal, Adenoviral DNA terminal	0.002
pfam02724	583	pfam02724, CDC45, CDC45-like protein	0.002
cd05832	106	cd05832, Ribosomal_L12p, Ribosomal protein L12p	0.002
pfam05887	145	pfam05887, Trypan_PARP, Procyclic acidic repetitiv	0.002
pfam04006	613	pfam04006, Mpp10, Mpp10 protein	0.002
PRK14140	191	PRK14140, PRK14140, heat shock protein GrpE; Provi	0.002
COG2058	109	COG2058, RPP1A, Ribosomal protein L12E/L44/L45/RPP	0.002
PRK04019	330	PRK04019, rplP0, acidic ribosomal protein P0; Vali	0.002
TIGR01651	600	TIGR01651, CobT, cobaltochelatase, CobT subunit	0.002
pfam02029	431	pfam02029, Caldesmon, Caldesmon	0.002
PRK05658	619	PRK05658, PRK05658, RNA polymerase sigma factor Rp	0.002
PRK05658	619	PRK05658, PRK05658, RNA polymerase sigma factor Rp	0.002
PHA03169	413	PHA03169, PHA03169, hypothetical protein; Provisio	0.002
PHA03169	413	PHA03169, PHA03169, hypothetical protein; Provisio	0.002
PRK04195	482	PRK04195, PRK04195, replication factor C large sub	0.002
PRK04195	482	PRK04195, PRK04195, replication factor C large sub	0.002
PRK04195	482	PRK04195, PRK04195, replication factor C large sub	0.002
COG5238	388	COG5238, RNA1, Ran GTPase-activating protein (RanG	0.002
pfam09747	178	pfam09747, DUF2052, Coiled-coil domain containing	0.002
PRK13108	460	PRK13108, PRK13108, prolipoprotein diacylglyceryl	0.002
pfam03153	332	pfam03153, TFIIA, Transcription factor IIA, alpha/	0.002
pfam03153	332	pfam03153, TFIIA, Transcription factor IIA, alpha/	0.002
pfam09507	427	pfam09507, CDC27, DNA polymerase subunit Cdc27	0.002
PRK05657	325	PRK05657, PRK05657, RNA polymerase sigma factor Rp	0.002
pfam07222	243	pfam07222, PBP_sp32, Proacrosin binding protein sp	0.002
COG4499	434	COG4499, COG4499, Predicted membrane protein [Func	0.002
pfam06524	314	pfam06524, NOA36, NOA36 protein	0.002
pfam09538	104	pfam09538, FYDLN_acid, Protein of unknown function	0.002
pfam11748	115	pfam11748, DUF3306, Protein of unknown function (D	0.002
pfam03286	198	pfam03286, Pox_Ag35, Pox virus Ag35 surface protei	0.002
pfam05285	317	pfam05285, SDA1, SDA1	0.003
pfam04889	241	pfam04889, Cwf_Cwc_15, Cwf15/Cwc15 cell cycle cont	0.003
pfam08553	794	pfam08553, VID27, VID27 cytoplasmic protein	0.003
pfam04712	481	pfam04712, Radial_spoke, Radial spokehead-like pro	0.003
COG4547	620	COG4547, CobT, Cobalamin biosynthesis protein CobT	0.003
pfam07423	214	pfam07423, DUF1510, Protein of unknown function (D	0.003
pfam09805	134	pfam09805, Nop25, Nucleolar protein 12 (25kDa)	0.003
pfam04931	784	pfam04931, DNA_pol_phi, DNA polymerase phi	0.003
pfam04874	97	pfam04874, Mak16, Mak16 protein C-terminal region	0.003
pfam09073	424	pfam09073, BUD22, BUD22	0.003
pfam02459	548	pfam02459, Adeno_terminal, Adenoviral DNA terminal	0.003
pfam05432	291	pfam05432, BSP_II, Bone sialoprotein II (BSP-II)	0.003
PRK14140	191	PRK14140, PRK14140, heat shock protein GrpE; Provi	0.003
TIGR01651	600	TIGR01651, CobT, cobaltochelatase, CobT subunit	0.003
PRK05658	619	PRK05658, PRK05658, RNA polymerase sigma factor Rp	0.003
PHA03169	413	PHA03169, PHA03169, hypothetical protein; Provisio	0.003
PHA03169	413	PHA03169, PHA03169, hypothetical protein; Provisio	0.003
PHA03169	413	PHA03169, PHA03169, hypothetical protein; Provisio	0.003
pfam06390	261	pfam06390, NESP55, Neuroendocrine-specific golgi p	0.003
PRK04195	482	PRK04195, PRK04195, replication factor C large sub	0.003
pfam12619	145	pfam12619, MCM2_N, Mini-chromosome maintenance pro	0.003
COG5414	392	COG5414, COG5414, TATA-binding protein-associated	0.003
COG3343	175	COG3343, RpoE, DNA-directed RNA polymerase, delta	0.003
pfam07767	387	pfam07767, Nop53, Nop53 (60S ribosomal biogenesis)	0.003
COG1614	470	COG1614, CdhC, CO dehydrogenase/acetyl-CoA synthas	0.003
pfam03032	46	pfam03032, Brevenin, Brevenin/esculentin/gaegurin/	0.003
pfam03153	332	pfam03153, TFIIA, Transcription factor IIA, alpha/	0.003
pfam05395	170	pfam05395, DARPP-32, Protein phosphatase inhibitor	0.003
PLN03142	1033	PLN03142, PLN03142, Probable chromatin-remodeling	0.003
TIGR02907	338	TIGR02907, spore_VI_D, stage VI sporulation protei	0.003
PRK05299	258	PRK05299, rpsB, 30S ribosomal protein S2; Provisio	0.003
pfam13422	99	pfam13422, DUF4110, Domain of unknown function (DU	0.003
pfam05285	317	pfam05285, SDA1, SDA1	0.004
pfam04889	241	pfam04889, Cwf_Cwc_15, Cwf15/Cwc15 cell cycle cont	0.004
pfam03066	146	pfam03066, Nucleoplasmin, Nucleoplasmin	0.004
pfam06213	282	pfam06213, CobT, Cobalamin biosynthesis protein Co	0.004
PRK14160	211	PRK14160, PRK14160, heat shock protein GrpE; Provi	0.004
PRK14891	131	PRK14891, PRK14891, 50S ribosomal protein L24e/unk	0.004
PRK14891	131	PRK14891, PRK14891, 50S ribosomal protein L24e/unk	0.004
pfam07423	214	pfam07423, DUF1510, Protein of unknown function (D	0.004
PRK12329	449	PRK12329, nusA, transcription elongation factor Nu	0.004
pfam09805	134	pfam09805, Nop25, Nucleolar protein 12 (25kDa)	0.004
pfam09805	134	pfam09805, Nop25, Nucleolar protein 12 (25kDa)	0.004
pfam04931	784	pfam04931, DNA_pol_phi, DNA polymerase phi	0.004
pfam02459	548	pfam02459, Adeno_terminal, Adenoviral DNA terminal	0.004
pfam11861	154	pfam11861, DUF3381, Domain of unknown function (DU	0.004
pfam05887	145	pfam05887, Trypan_PARP, Procyclic acidic repetitiv	0.004
COG5137	279	COG5137, COG5137, Histone chaperone involved in ge	0.004
PRK14140	191	PRK14140, PRK14140, heat shock protein GrpE; Provi	0.004
PRK14140	191	PRK14140, PRK14140, heat shock protein GrpE; Provi	0.004
PRK04019	330	PRK04019, rplP0, acidic ribosomal protein P0; Vali	0.004
PRK05901	509	PRK05901, PRK05901, RNA polymerase sigma factor; P	0.004
pfam02029	431	pfam02029, Caldesmon, Caldesmon	0.004
PHA03169	413	PHA03169, PHA03169, hypothetical protein; Provisio	0.004
PHA03169	413	PHA03169, PHA03169, hypothetical protein; Provisio	0.004
COG5414	392	COG5414, COG5414, TATA-binding protein-associated	0.004
PRK02363	129	PRK02363, PRK02363, DNA-directed RNA polymerase su	0.004
COG3343	175	COG3343, RpoE, DNA-directed RNA polymerase, delta	0.004
pfam05320	167	pfam05320, Pox_RNA_Pol_19, Poxvirus DNA-directed R	0.004
PRK13108	460	PRK13108, PRK13108, prolipoprotein diacylglyceryl	0.004
COG5271	4600	COG5271, MDN1, AAA ATPase containing von Willebran	0.004
pfam03032	46	pfam03032, Brevenin, Brevenin/esculentin/gaegurin/	0.004
pfam03032	46	pfam03032, Brevenin, Brevenin/esculentin/gaegurin/	0.004
PRK05657	325	PRK05657, PRK05657, RNA polymerase sigma factor Rp	0.004
PRK05299	258	PRK05299, rpsB, 30S ribosomal protein S2; Provisio	0.004
COG0576	193	COG0576, GrpE, Molecular chaperone GrpE (heat shoc	0.004
pfam08597	242	pfam08597, eIF3_subunit, Translation initiation fa	0.004
pfam14153	185	pfam14153, Spore_coat_CotO, Spore coat protein Cot	0.004

>gnl|CDD|219619 pfam07885, Ion_trans_2, Ion channel

 Score = 66.5 bits (163), Expect = 1e-13
 Identities = 28/86 (32%), Positives = 41/86 (47%), Gaps = 15/86 (17%)

Query: 107 FLVISYIIGGAFLFSHWE---PWGFPDSAYFCFITLTTIGFGDFVPAQKSTDVQTAEETA 163
            L++  +I G   +S  E    W F D+ YF F+TLTTIG+GD VP            T 
Sbjct: 1   ILLLLVLIFGTVYYSLEEEGWGWDFLDALYFSFVTLTTIGYGDIVP-----------LTD 49

Query: 164 ELRIALCSLYLLFGIALLAMSFNLVQ 189
             R+    +Y+L GI L  +   ++ 
Sbjct: 50  AGRL-FTIIYILIGIPLFLLFLAVLG 74

This family includes the two membrane helix type ion channels found in bacteria. Length = 74

>gnl|CDD|219619 pfam07885, Ion_trans_2, Ion channel

 Score = 59.5 bits (145), Expect = 3e-11
 Identities = 23/88 (26%), Positives = 45/88 (51%), Gaps = 17/88 (19%)

Query: 517 MIMVGYIYGGAVLFSKWED---WNILDGSYFCFISLSTIGFGDIVPGDKITGKNNDIGVQ 573
           ++++  +  G V +S  E+   W+ LD  YF F++L+TIG+GDIVP     G+       
Sbjct: 1   ILLLLVLIFGTVYYSLEEEGWGWDFLDALYFSFVTLTTIGYGDIVPLT-DAGR------- 52

Query: 574 TLELSFILCAMYLMLGMALIAMCFNLMQ 601
                 +   +Y+++G+ L  +   ++ 
Sbjct: 53  ------LFTIIYILIGIPLFLLFLAVLG 74

This family includes the two membrane helix type ion channels found in bacteria. Length = 74

>gnl|CDD|233191 TIGR00927, 2A1904, K+-dependent Na+/Ca+ exchanger

 Score = 66.6 bits (162), Expect = 4e-11
 Identities = 31/55 (56%), Positives = 34/55 (61%)

Query: 437 NARNGDSEYEDSDFDTSDEEYDSSEEEEEEEEDEEEEEEEEEEEEEEEEEEGEEE 491
           NA N     +D          D  + EEEEEE+EEEEEEEEEEEEEEEEEE  EE
Sbjct: 838 NAENQGEAKQDEKGVDGGGGSDGGDSEEEEEEEEEEEEEEEEEEEEEEEEEENEE 892

[Transport and binding proteins, Cations and iron carrying compounds]. Length = 1096

>gnl|CDD|233191 TIGR00927, 2A1904, K+-dependent Na+/Ca+ exchanger

 Score = 62.7 bits (152), Expect = 5e-10
 Identities = 37/87 (42%), Positives = 46/87 (52%), Gaps = 7/87 (8%)

Query: 412 QKTIQDTTGAYNRRRSSAMNHNRRWNARNGDSEYED---SDFDTSDEEYDSSEEEEEEEE 468
            +T  D T   +      +N   +  A+  +   +    SD   S+EE    EEEEEEEE
Sbjct: 819 SETQADDTEVKDETGEQELNAENQGEAKQDEKGVDGGGGSDGGDSEEE----EEEEEEEE 874

Query: 469 DEEEEEEEEEEEEEEEEEEGEEEETET 495
           +EEEEEEEEEEEEEE EE    E  ET
Sbjct: 875 EEEEEEEEEEEEEEENEEPLSLEWPET 901

[Transport and binding proteins, Cations and iron carrying compounds]. Length = 1096

>gnl|CDD|217927 pfam04147, Nop14, Nop14-like family

 Score = 62.7 bits (153), Expect = 6e-10
 Identities = 20/73 (27%), Positives = 45/73 (61%), Gaps = 1/73 (1%)

Query: 442 DSEYEDSDFDTSDEEYDSSEEEEEEEEDEEEEEEEEEEEEEEEEEEGEEEETETASSSTA 501
           D   ++ + D  D+  +  E+ +  +E+E+EE+E+ ++E++EEEEE E+E+ +  S+ + 
Sbjct: 328 DGVDDEDEEDDDDDLEEEEEDVDLSDEEEDEEDEDSDDEDDEEEEEEEKEKKKKKSAEST 387

Query: 502 KND-PQMVTVPIT 513
           +++ P     P +
Sbjct: 388 RSELPFTFPCPKS 400

Emg1 and Nop14 are novel proteins whose interaction is required for the maturation of the 18S rRNA and for 40S ribosome production. Length = 809

>gnl|CDD|219619 pfam07885, Ion_trans_2, Ion channel

 Score = 54.5 bits (132), Expect = 2e-09
 Identities = 20/84 (23%), Positives = 43/84 (51%), Gaps = 13/84 (15%)

Query: 678 LIIISFILLGSLIFNKLEN---WTFLDGTFFCFTSLGTIGFGELIPGESYDRTLRGNKNI 734
           ++++  ++ G++ ++  E    W FLD  +F F +L TIG+G+++P     R        
Sbjct: 1   ILLLLVLIFGTVYYSLEEEGWGWDFLDALYFSFVTLTTIGYGDIVPLTDAGR-------- 52

Query: 735 SVLVSSSYILVGMAVISMCFNLIQ 758
             L +  YIL+G+ +  +   ++ 
Sbjct: 53  --LFTIIYILIGIPLFLLFLAVLG 74

This family includes the two membrane helix type ion channels found in bacteria. Length = 74

>gnl|CDD|221175 pfam11705, RNA_pol_3_Rpc31, DNA-directed RNA polymerase III subunit Rpc31

 Score = 56.3 bits (136), Expect = 9e-09
 Identities = 24/88 (27%), Positives = 45/88 (51%), Gaps = 2/88 (2%)

Query: 408 PRDLQKTIQDTTGAYNRRRSSAMNHNRRWNARNGDSEYEDSDFDTSDEEYDSSEEEEEEE 467
           P++L   +     A  +   S     R+      + E  D      +++    E E+ +E
Sbjct: 113 PKELYSVMGINKKAGKKLALSK--FKRKVGLFTEEEEDIDEKLSMLEKKLKELEAEDVDE 170

Query: 468 EDEEEEEEEEEEEEEEEEEEGEEEETET 495
           EDE++EEEEEEEEEE+E+ + ++++ + 
Sbjct: 171 EDEKDEEEEEEEEEEDEDFDDDDDDDDD 198

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|218538 pfam05285, SDA1, SDA1

 Score = 57.4 bits (139), Expect = 1e-08
 Identities = 20/69 (28%), Positives = 39/69 (56%), Gaps = 2/69 (2%)

Query: 436 WNARNGDSEYEDSDF--DTSDEEYDSSEEEEEEEEDEEEEEEEEEEEEEEEEEEGEEEET 493
           W     +   ++ ++    SD+E +SS+ E+EEE+DE  ++ +E+ +EE  EE+ EE   
Sbjct: 104 WEVEEDEDSDDEGEWIDVESDKEIESSDSEDEEEKDEAAKKAKEDSDEELSEEDEEEAAE 163

Query: 494 ETASSSTAK 502
           E  + +  +
Sbjct: 164 EEEAEAEKE 172

This family consists of several SDA1 protein homologues. SDA1 is a Saccharomyces cerevisiae protein which is involved in the control of the actin cytoskeleton. The protein is essential for cell viability and is localised in the nucleus. Length = 317

>gnl|CDD|217503 pfam03344, Daxx, Daxx Family

 Score = 58.0 bits (140), Expect = 1e-08
 Identities = 32/86 (37%), Positives = 44/86 (51%), Gaps = 4/86 (4%)

Query: 424 RRRSSAMNHNRRWNARNGDS----EYEDSDFDTSDEEYDSSEEEEEEEEDEEEEEEEEEE 479
           R+ +S+ + +    +           ++S+ + S EE +  EEEEEEEE E EEEE E+E
Sbjct: 411 RQGTSSRSSDPSKASSTSGESPSMASQESEEEESVEEEEEEEEEEEEEEQESEEEEGEDE 470

Query: 480 EEEEEEEEGEEEETETASSSTAKNDP 505
           EEEEE E     E E   SS    D 
Sbjct: 471 EEEEEVEADNGSEEEMEGSSEGDGDG 496

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|219619 pfam07885, Ion_trans_2, Ion channel

 Score = 50.7 bits (122), Expect = 3e-08
 Identities = 18/35 (51%), Positives = 24/35 (68%)

Query: 30 GYGHIAPKTTLGKVATIFYAIVGIPLMLLCLSNIG 64
          GYG I P T  G++ TI Y ++GIPL LL L+ +G
Sbjct: 40 GYGDIVPLTDAGRLFTIIYILIGIPLFLLFLAVLG 74

This family includes the two membrane helix type ion channels found in bacteria. Length = 74

>gnl|CDD|217503 pfam03344, Daxx, Daxx Family

 Score = 56.8 bits (137), Expect = 3e-08
 Identities = 38/93 (40%), Positives = 50/93 (53%), Gaps = 2/93 (2%)

Query: 416 QDTTGAYNRRRSSAMNHNRRWNARNGDSEYEDSDFDTS-DEEYDSSEEEEEEEEDEEEEE 474
           QD T    RR+       +  ++R+ D     S    S       SEEEE  EE+EEEEE
Sbjct: 395 QDDTEEEERRKRQE-RERQGTSSRSSDPSKASSTSGESPSMASQESEEEESVEEEEEEEE 453

Query: 475 EEEEEEEEEEEEEGEEEETETASSSTAKNDPQM 507
           EEEEEE+E EEEEGE+EE E    +   ++ +M
Sbjct: 454 EEEEEEQESEEEEGEDEEEEEEVEADNGSEEEM 486

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|148630 pfam07133, Merozoite_SPAM, Merozoite surface protein (SPAM)

 Score = 52.2 bits (125), Expect = 9e-08
 Identities = 23/60 (38%), Positives = 35/60 (58%)

Query: 447 DSDFDTSDEEYDSSEEEEEEEEDEEEEEEEEEEEEEEEEEEGEEEETETASSSTAKNDPQ 506
             D +  +EE +   EE E+ EDEEE  E+EEEEEE+EE+  + ++ E  + +   N  Q
Sbjct: 48  QEDDEEEEEEDEEEIEEPEDIEDEEEIVEDEEEEEEDEEDNVDLKDIEKKNINDIFNSTQ 107

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|220972 pfam11081, DUF2890, Protein of unknown function (DUF2890)

 Score = 52.2 bits (125), Expect = 1e-07
 Identities = 25/49 (51%), Positives = 30/49 (61%)

Query: 452 TSDEEYDSSEEEEEEEEDEEEEEEEEEEEEEEEEEEGEEEETETASSST 500
           T DEE D   + EE EEDEEE E+ E+  +EE+EE  E EE   ASS  
Sbjct: 17  TKDEEEDWDSQAEEVEEDEEEMEDWEDSLDEEDEEAEEVEEETAASSKA 65

This family is conserved in dsDNA adenoviruses of vertebrates. The function is not known. Length = 172

>gnl|CDD|218312 pfam04889, Cwf_Cwc_15, Cwf15/Cwc15 cell cycle control protein

 Score = 53.2 bits (128), Expect = 1e-07
 Identities = 20/82 (24%), Positives = 35/82 (42%), Gaps = 12/82 (14%)

Query: 438 ARNGDSEYEDSDFDTSDEEYDSSEEEEEEEEDEEEEEEEE------------EEEEEEEE 485
            +  + +  +SD D SD   DS   +++ ++D+ E+E                EE+E EE
Sbjct: 107 RKRIEEDARNSDADDSDSSSDSDSSDDDSDDDDSEDETAALLRELEKIKKERAEEKEREE 166

Query: 486 EEGEEEETETASSSTAKNDPQM 507
           EE   EE +         +P +
Sbjct: 167 EEKAAEEEKAREEEILTGNPLL 188

This family represents Cwf15/Cwc15 (from Schizosaccharomyces pombe and Saccharomyces cerevisiae respectively) and their homologues. The function of these proteins is unknown, but they form part of the spliceosome and are thus thought to be involved in mRNA splicing. Length = 241

>gnl|CDD|217829 pfam03985, Paf1, Paf1

 Score = 54.0 bits (130), Expect = 2e-07
 Identities = 25/83 (30%), Positives = 42/83 (50%), Gaps = 7/83 (8%)

Query: 424 RRRSSAMNHNRRWNARNGDSEYEDSDFDTSDEEYDSSEEEEEEEEDEEEEEEEEEEEEEE 483
            R  S      R   R   +  +  DF+  DE+    E+EEEE+  +E EEEE E+ EEE
Sbjct: 344 LRNPSTKESKMRDKRR---ARLDPIDFEEVDED----EDEEEEQRSDEHEEEEGEDSEEE 396

Query: 484 EEEEGEEEETETASSSTAKNDPQ 506
             +  E+  +E++S   + ++ +
Sbjct: 397 GSQSREDGSSESSSDVGSDSESK 419

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|222792 PHA00435, PHA00435, capsid assembly protein

 Score = 52.9 bits (127), Expect = 2e-07
 Identities = 29/66 (43%), Positives = 39/66 (59%), Gaps = 9/66 (13%)

Query: 438 ARNGDSEYEDSDFDTSDEEYDSSEEEEEEEE---------DEEEEEEEEEEEEEEEEEEG 488
           AR+GD   E ++ +TSD+ Y + +   E++E         D EEEE EE EE+EEEE E 
Sbjct: 38  ARDGDDAIELAEPETSDDPYGNPDPFGEDDEGRIEVRISEDGEEEEVEEGEEDEEEEGEE 97

Query: 489 EEEETE 494
           E EE E
Sbjct: 98  ESEEFE 103

Length = 306

>gnl|CDD|217927 pfam04147, Nop14, Nop14-like family

 Score = 53.9 bits (130), Expect = 3e-07
 Identities = 17/62 (27%), Positives = 37/62 (59%)

Query: 445 YEDSDFDTSDEEYDSSEEEEEEEEDEEEEEEEEEEEEEEEEEEGEEEETETASSSTAKND 504
                 +  +EE D  ++E+EE++D++ EEEEE+ +  +EEE+ E+E+++       + +
Sbjct: 315 GLGQGEEDEEEEEDGVDDEDEEDDDDDLEEEEEDVDLSDEEEDEEDEDSDDEDDEEEEEE 374

Query: 505 PQ 506
            +
Sbjct: 375 EK 376

Emg1 and Nop14 are novel proteins whose interaction is required for the maturation of the 18S rRNA and for 40S ribosome production. Length = 809

>gnl|CDD|220972 pfam11081, DUF2890, Protein of unknown function (DUF2890)

 Score = 50.7 bits (121), Expect = 3e-07
 Identities = 24/50 (48%), Positives = 35/50 (70%), Gaps = 2/50 (4%)

Query: 455 EEYDSSEEEEEEEEDEEEEEEEEEEEEEEEEEEGEEEETET--ASSSTAK 502
           E++DS  EE EE+E+E E+ E+  +EE+EE EE EEE   +  A SS++K
Sbjct: 22  EDWDSQAEEVEEDEEEMEDWEDSLDEEDEEAEEVEEETAASSKAPSSSSK 71

This family is conserved in dsDNA adenoviruses of vertebrates. The function is not known. Length = 172

>gnl|CDD|217450 pfam03247, Prothymosin, Prothymosin/parathymosin family

 Score = 49.2 bits (117), Expect = 3e-07
 Identities = 27/70 (38%), Positives = 36/70 (51%), Gaps = 2/70 (2%)

Query: 437 NARNGDSEYEDSDFDTSDEEYDSSEEEEEEEEDEEEEEEEEEEEEEEEEEEGEEEETETA 496
           NA    +E E++     D+E +  EEEE +E+DEEEE E EEEE EEEEE         A
Sbjct: 31  NAPANGNENEENGAQEGDDEME--EEEEVDEDDEEEEGEGEEEEGEEEEETEGATGKRAA 88

Query: 497 SSSTAKNDPQ 506
                  + +
Sbjct: 89  EDEEDDAETK 98

Prothymosin alpha and parathymosin are two ubiquitous small acidic nuclear proteins that are thought to be involved in cell cycle progression, proliferation, and cell differentiation. Length = 106

>gnl|CDD|221490 pfam12253, CAF1A, Chromatin assembly factor 1 subunit A

 Score = 48.0 bits (115), Expect = 3e-07
 Identities = 18/34 (52%), Positives = 27/34 (79%)

Query: 454 DEEYDSSEEEEEEEEDEEEEEEEEEEEEEEEEEE 487
           D +YDS  E EEEEE E+ E E+EE+EEE+++++
Sbjct: 39  DYDYDSDAEWEEEEEGEDLESEDEEDEEEDDDDD 72

The CAF-1 or chromatin assembly factor-1 consists of three subunits, and this is the first, or A. The A domain is uniquely required for the progression of S phase in mouse cells, independent of its ability to promote histone deposition but dependent on its ability to interact with HP1 - heterochromatin protein 1-rich heterochromatin domains next to centromeres that are crucial for chromosome segregation during mitosis. This HP1-CAF-1 interaction module functions as a built-in replication control for heterochromatin, which, like a control barrier, has an impact on S-phase progression in addition to DNA-based checkpoints. Length = 76

>gnl|CDD|145949 pfam03066, Nucleoplasmin, Nucleoplasmin

 Score = 50.0 bits (120), Expect = 3e-07
 Identities = 18/32 (56%), Positives = 29/32 (90%)

Query: 462 EEEEEEEDEEEEEEEEEEEEEEEEEEGEEEET 493
            EE+E +D+EE+EEEE++EE+++E+E EEEE+
Sbjct: 109 SEEDESDDDEEDEEEEDDEEDDDEDESEEEES 140

Nucleoplasmins are also known as chromatin decondensation proteins. They bind to core histones and transfer DNA to them in a reaction that requires ATP. This is thought to play a role in the assembly of regular nucleosomal arrays. Length = 146

>gnl|CDD|218538 pfam05285, SDA1, SDA1

 Score = 52.4 bits (126), Expect = 4e-07
 Identities = 20/72 (27%), Positives = 36/72 (50%), Gaps = 6/72 (8%)

Query: 441 GDSEYEDSDFDTSDEE------YDSSEEEEEEEEDEEEEEEEEEEEEEEEEEEGEEEETE 494
            + E+E  + + SD+E          E E  + EDEEE++E  ++ +E+ +EE  EE+ E
Sbjct: 100 EEEEWEVEEDEDSDDEGEWIDVESDKEIESSDSEDEEEKDEAAKKAKEDSDEELSEEDEE 159

Query: 495 TASSSTAKNDPQ 506
            A+        +
Sbjct: 160 EAAEEEEAEAEK 171

This family consists of several SDA1 protein homologues. SDA1 is a Saccharomyces cerevisiae protein which is involved in the control of the actin cytoskeleton. The protein is essential for cell viability and is localised in the nucleus. Length = 317

>gnl|CDD|218737 pfam05764, YL1, YL1 nuclear protein

 Score = 51.6 bits (124), Expect = 4e-07
 Identities = 22/46 (47%), Positives = 33/46 (71%), Gaps = 4/46 (8%)

Query: 446 EDSDFDTSDEEYDSSEEEEEEEEDEEEEEEEEEEEEEEEEEEGEEE 491
           E+ D    DEE++  EEEEEEE D + ++ E++E E ++EEEGE+E
Sbjct: 36  EEED----DEEFEIEEEEEEEEVDSDFDDSEDDEPESDDEEEGEKE 77

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|217927 pfam04147, Nop14, Nop14-like family

 Score = 53.1 bits (128), Expect = 5e-07
 Identities = 22/66 (33%), Positives = 40/66 (60%), Gaps = 1/66 (1%)

Query: 440 NGDSEYEDSD-FDTSDEEYDSSEEEEEEEEDEEEEEEEEEEEEEEEEEEGEEEETETASS 498
           + + E +D D F     E D  EEE+  ++++EE+++++ EEEEE+ +  +EEE E    
Sbjct: 303 DDEFEPDDDDNFGLGQGEEDEEEEEDGVDDEDEEDDDDDLEEEEEDVDLSDEEEDEEDED 362

Query: 499 STAKND 504
           S  ++D
Sbjct: 363 SDDEDD 368

Emg1 and Nop14 are novel proteins whose interaction is required for the maturation of the 18S rRNA and for 40S ribosome production. Length = 809

>gnl|CDD|218538 pfam05285, SDA1, SDA1

 Score = 52.0 bits (125), Expect = 5e-07
 Identities = 21/57 (36%), Positives = 39/57 (68%)

Query: 442 DSEYEDSDFDTSDEEYDSSEEEEEEEEDEEEEEEEEEEEEEEEEEEGEEEETETASS 498
           D E E SD +  +E+ +++++ +E+ ++E  EE+EEE  EEEE E  +E+ +E A++
Sbjct: 124 DKEIESSDSEDEEEKDEAAKKAKEDSDEELSEEDEEEAAEEEEAEAEKEKASELATT 180

This family consists of several SDA1 protein homologues. SDA1 is a Saccharomyces cerevisiae protein which is involved in the control of the actin cytoskeleton. The protein is essential for cell viability and is localised in the nucleus. Length = 317

>gnl|CDD|217503 pfam03344, Daxx, Daxx Family

 Score = 53.0 bits (127), Expect = 5e-07
 Identities = 22/66 (33%), Positives = 33/66 (50%)

Query: 441 GDSEYEDSDFDTSDEEYDSSEEEEEEEEDEEEEEEEEEEEEEEEEEEGEEEETETASSST 500
                E+   +  +EE +  EEEE+E E+EE E+EEEEEE E +    EE E  +     
Sbjct: 436 SQESEEEESVEEEEEEEEEEEEEEQESEEEEGEDEEEEEEVEADNGSEEEMEGSSEGDGD 495

Query: 501 AKNDPQ 506
            +   +
Sbjct: 496 GEEPEE 501

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|233191 TIGR00927, 2A1904, K+-dependent Na+/Ca+ exchanger

 Score = 53.1 bits (127), Expect = 6e-07
 Identities = 24/37 (64%), Positives = 27/37 (72%)

Query: 216 EDSDFDTSDEEYDSSEEEEEEEDEEEEEEEEEGEEEE 252
             SD   S+EE +  EEEEEEE+EEEEEEEEE E EE
Sbjct: 856 GGSDGGDSEEEEEEEEEEEEEEEEEEEEEEEEEENEE 892

[Transport and binding proteins, Cations and iron carrying compounds]. Length = 1096

>gnl|CDD|219619 pfam07885, Ion_trans_2, Ion channel

 Score = 47.2 bits (113), Expect = 7e-07
 Identities = 19/38 (50%), Positives = 29/38 (76%), Gaps = 1/38 (2%)

Query: 347 TIAGYGNVAPITFLGKITTIAYAIAGMPLFLLYLSNIG 384
           TI GYG++ P+T  G++ TI Y + G+PLFLL+L+ +G
Sbjct: 38  TI-GYGDIVPLTDAGRLFTIIYILIGIPLFLLFLAVLG 74

This family includes the two membrane helix type ion channels found in bacteria. Length = 74

>gnl|CDD|219900 pfam08553, VID27, VID27 cytoplasmic protein

 Score = 52.4 bits (126), Expect = 8e-07
 Identities = 21/59 (35%), Positives = 37/59 (62%), Gaps = 1/59 (1%)

Query: 445 YEDSDFDTSDEEYDSSEEEEEEEEDEEEEEEEEEEEEEEEEEEGEEEETETASSSTAKN 503
           +   + + ++ E D  EEEE+EEE+EEE+E+E   +E  ++EE EE++ E+    +  N
Sbjct: 376 FSALEIEDANTERDD-EEEEDEEEEEEEDEDEGPSKEHSDDEEFEEDDVESKYEDSDGN 433

This is a family of fungal and plant proteins and contains many hypothetical proteins. VID27 is a cytoplasmic protein that plays a potential role in vacuolar protein degradation. Length = 794

>gnl|CDD|218223 pfam04712, Radial_spoke, Radial spokehead-like protein

 Score = 52.0 bits (125), Expect = 9e-07
 Identities = 19/34 (55%), Positives = 26/34 (76%)

Query: 457 YDSSEEEEEEEEDEEEEEEEEEEEEEEEEEEGEE 490
            +  +++EEEE+++EEEEEEEEE EE E EEG  
Sbjct: 342 VNPEQKDEEEEQEDEEEEEEEEEPEEPEPEEGPP 375

This family includes the radial spoke head proteins RSP4 and RSP6 from Chlamydomonas reinhardtii, and several eukaryotic homologues, including mammalian RSHL1, the protein product of a familial ciliary dyskinesia candidate gene. Length = 481

>gnl|CDD|217927 pfam04147, Nop14, Nop14-like family

 Score = 51.9 bits (125), Expect = 1e-06
 Identities = 24/63 (38%), Positives = 40/63 (63%), Gaps = 4/63 (6%)

Query: 212 DSEYEDSDFDTSDEEYDSSEEEEEEEDEEEEEEEEEGEEEETETASSSTAKND-PQMVTV 270
           D E E+ D D SDEE    +EE+E+ D+E++EEEEE E+E+ +  S+ + +++ P     
Sbjct: 341 DLEEEEEDVDLSDEE---EDEEDEDSDDEDDEEEEEEEKEKKKKKSAESTRSELPFTFPC 397

Query: 271 PIT 273
           P +
Sbjct: 398 PKS 400

Emg1 and Nop14 are novel proteins whose interaction is required for the maturation of the 18S rRNA and for 40S ribosome production. Length = 809

>gnl|CDD|218538 pfam05285, SDA1, SDA1

 Score = 51.2 bits (123), Expect = 1e-06
 Identities = 19/80 (23%), Positives = 29/80 (36%), Gaps = 7/80 (8%)

Query: 433 NRRWNARNGDSEYEDSDFDT-------SDEEYDSSEEEEEEEEDEEEEEEEEEEEEEEEE 485
             R           D D D         DE+ D   E  + E D+E E  + E+EEE++E
Sbjct: 81  EERKKKEAEQGLESDDDDDEEEEWEVEEDEDSDDEGEWIDVESDKEIESSDSEDEEEKDE 140

Query: 486 EEGEEEETETASSSTAKNDP 505
              + +E      S    + 
Sbjct: 141 AAKKAKEDSDEELSEEDEEE 160

This family consists of several SDA1 protein homologues. SDA1 is a Saccharomyces cerevisiae protein which is involved in the control of the actin cytoskeleton. The protein is essential for cell viability and is localised in the nucleus. Length = 317

>gnl|CDD|220972 pfam11081, DUF2890, Protein of unknown function (DUF2890)

 Score = 49.1 bits (117), Expect = 1e-06
 Identities = 24/81 (29%), Positives = 38/81 (46%), Gaps = 2/81 (2%)

Query: 433 NRRWNARNGDSEYEDSDFDTSDEEYDSSEEEEEEEEDEEEEEEEEEEEEEEEE--EEGEE 490
            ++   R   ++ E+ D+D+  EE +  EEE E+ ED  +EE+EE EE EEE        
Sbjct: 7   AKKLKVRPPPTKDEEEDWDSQAEEVEEDEEEMEDWEDSLDEEDEEAEEVEEETAASSKAP 66

Query: 491 EETETASSSTAKNDPQMVTVP 511
             +  +SS    + P      
Sbjct: 67  SSSSKSSSQETISIPPTPPAR 87

This family is conserved in dsDNA adenoviruses of vertebrates. The function is not known. Length = 172

>gnl|CDD|218312 pfam04889, Cwf_Cwc_15, Cwf15/Cwc15 cell cycle control protein

 Score = 50.1 bits (120), Expect = 1e-06
 Identities = 21/67 (31%), Positives = 33/67 (49%), Gaps = 12/67 (17%)

Query: 437 NARNGDSEYEDSDFDTSDEEYDSSEEEEEEEEDEEEE---------EEEEEEEEEEEEEE 487
           +ARN D+   D    +SD +    + ++++ EDE            +E  EE+E EEEE+
Sbjct: 113 DARNSDA---DDSDSSSDSDSSDDDSDDDDSEDETAALLRELEKIKKERAEEKEREEEEK 169

Query: 488 GEEEETE 494
             EEE  
Sbjct: 170 AAEEEKA 176

This family represents Cwf15/Cwc15 (from Schizosaccharomyces pombe and Saccharomyces cerevisiae respectively) and their homologues. The function of these proteins is unknown, but they form part of the spliceosome and are thus thought to be involved in mRNA splicing. Length = 241

>gnl|CDD|145949 pfam03066, Nucleoplasmin, Nucleoplasmin

 Score = 48.1 bits (115), Expect = 1e-06
 Identities = 17/31 (54%), Positives = 27/31 (87%)

Query: 461 EEEEEEEEDEEEEEEEEEEEEEEEEEEGEEE 491
            EE+E ++DEE+EEEE++EE+++E+E  EEE
Sbjct: 109 SEEDESDDDEEDEEEEDDEEDDDEDESEEEE 139

Nucleoplasmins are also known as chromatin decondensation proteins. They bind to core histones and transfer DNA to them in a reaction that requires ATP. This is thought to play a role in the assembly of regular nucleosomal arrays. Length = 146

>gnl|CDD|218752 pfam05793, TFIIF_alpha, Transcription initiation factor IIF, alpha subunit (TFIIF-alpha)

 Score = 51.5 bits (123), Expect = 1e-06
 Identities = 22/69 (31%), Positives = 32/69 (46%), Gaps = 6/69 (8%)

Query: 441 GDSEYEDSDFDTSDEEYDSSEEEEEE-----EEDEEEEEEEEEEEEEEEEEEGEEEETET 495
           GD E  + D+  SD     ++ EE E     E   + E E++E+ EE EEE+ EEE   +
Sbjct: 277 GDDEGREEDY-ISDSSASGNDPEEREDKLSPEIPAKPEIEQDEDSEESEEEKNEEEGGLS 335

Query: 496 ASSSTAKND 504
                 K  
Sbjct: 336 KKGKKLKKL 344

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|233191 TIGR00927, 2A1904, K+-dependent Na+/Ca+ exchanger

 Score = 51.5 bits (123), Expect = 2e-06
 Identities = 24/37 (64%), Positives = 26/37 (70%)

Query: 221 DTSDEEYDSSEEEEEEEDEEEEEEEEEGEEEETETAS 257
           D  D E +  EEEEEEE+EEEEEEEEE EEE  E  S
Sbjct: 859 DGGDSEEEEEEEEEEEEEEEEEEEEEEEEEENEEPLS 895

[Transport and binding proteins, Cations and iron carrying compounds]. Length = 1096

>gnl|CDD|217927 pfam04147, Nop14, Nop14-like family

 Score = 51.2 bits (123), Expect = 2e-06
 Identities = 20/55 (36%), Positives = 34/55 (61%)

Query: 212 DSEYEDSDFDTSDEEYDSSEEEEEEEDEEEEEEEEEGEEEETETASSSTAKNDPQ 266
           D E +D D +  +E+ D S+EEE+EEDE+ ++E++E EEEE +      +    +
Sbjct: 334 DEEDDDDDLEEEEEDVDLSDEEEDEEDEDSDDEDDEEEEEEEKEKKKKKSAESTR 388

Emg1 and Nop14 are novel proteins whose interaction is required for the maturation of the 18S rRNA and for 40S ribosome production. Length = 809

>gnl|CDD|145949 pfam03066, Nucleoplasmin, Nucleoplasmin

 Score = 47.7 bits (114), Expect = 2e-06
 Identities = 16/31 (51%), Positives = 27/31 (87%)

Query: 455 EEYDSSEEEEEEEEDEEEEEEEEEEEEEEEE 485
            E D S+++EE+EE+E++EE+++E+E EEEE
Sbjct: 109 SEEDESDDDEEDEEEEDDEEDDDEDESEEEE 139

Nucleoplasmins are also known as chromatin decondensation proteins. They bind to core histones and transfer DNA to them in a reaction that requires ATP. This is thought to play a role in the assembly of regular nucleosomal arrays. Length = 146

>gnl|CDD|222581 pfam14181, YqfQ, YqfQ-like protein

 Score = 48.2 bits (115), Expect = 2e-06
 Identities = 19/58 (32%), Positives = 30/58 (51%)

Query: 456 EYDSSEEEEEEEEDEEEEEEEEEEEEEEEEEEGEEEETETASSSTAKNDPQMVTVPIT 513
           E  SS++EEEE E+E  +E E+E+  E + E  E+++ E     T K  P+       
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|148051 pfam06213, CobT, Cobalamin biosynthesis protein CobT

 Score = 50.2 bits (120), Expect = 2e-06
 Identities = 24/64 (37%), Positives = 30/64 (46%), Gaps = 4/64 (6%)

Query: 442 DSE-YEDSDFDTSDEEYDSSEEEEEEEEDEEEEEEEEEEEEEEEEEEGEEEETETASSST 500
           DSE  ED D    DE+ D  EEEE    D   E+ +   EE E    GE E  E ++  T
Sbjct: 220 DSEDNEDEDDPKEDEDDDQGEEEESGSSDSLSEDSDASSEEME---SGEMEAAEASADDT 276

Query: 501 AKND 504
             +D
Sbjct: 277 PDSD 280

This family consists of several bacterial cobalamin biosynthesis (CobT) proteins. CobT is involved in the transformation of precorrin-3 into cobyrinic acid. Length = 282

>gnl|CDD|237629 PRK14160, PRK14160, heat shock protein GrpE; Provisional

 Score = 49.0 bits (117), Expect = 2e-06
 Identities = 21/60 (35%), Positives = 31/60 (51%)

Query: 444 EYEDSDFDTSDEEYDSSEEEEEEEEDEEEEEEEEEEEEEEEEEEGEEEETETASSSTAKN 503
           E E  D    + E D  +E E +EED+ +EE+ E EE E+EE   + EE+        K+
Sbjct: 2   EKECKDAKHENMEEDCCKENENKEEDKGKEEDLEFEEIEKEEIIEDSEESNEVKIEELKD 61

Length = 211

>gnl|CDD|217861 pfam04050, Upf2, Up-frameshift suppressor 2

 Score = 48.1 bits (115), Expect = 2e-06
 Identities = 21/57 (36%), Positives = 32/57 (56%), Gaps = 4/57 (7%)

Query: 439 RNGDSE----YEDSDFDTSDEEYDSSEEEEEEEEDEEEEEEEEEEEEEEEEEEGEEE 491
              +SE     ED +    DE+ +SS+EEE +  D+E++EE + EEE+      EEE
Sbjct: 1   SGSESESDDGEEDEELPEEDEDDESSDEEEVDLPDDEQDEESDSEEEQIFVTRQEEE 57

Transcripts harbouring premature signals for translation termination are recognised and rapidly degraded by eukaryotic cells through a pathway known as nonsense-mediated mRNA decay. In Saccharomyces cerevisiae, three trans-acting factors (Upf1 to Upf3) are required for nonsense-mediated mRNA decay. Length = 171

>gnl|CDD|217927 pfam04147, Nop14, Nop14-like family

 Score = 50.4 bits (121), Expect = 3e-06
 Identities = 18/56 (32%), Positives = 38/56 (67%)

Query: 440 NGDSEYEDSDFDTSDEEYDSSEEEEEEEEDEEEEEEEEEEEEEEEEEEGEEEETET 495
           + + + +D + +  D +    EE+EE+E+ ++E++EEEEEEE+E++++   E T +
Sbjct: 334 DEEDDDDDLEEEEEDVDLSDEEEDEEDEDSDDEDDEEEEEEEKEKKKKKSAESTRS 389

Emg1 and Nop14 are novel proteins whose interaction is required for the maturation of the 18S rRNA and for 40S ribosome production. Length = 809

>gnl|CDD|145949 pfam03066, Nucleoplasmin, Nucleoplasmin

 Score = 46.9 bits (112), Expect = 3e-06
 Identities = 17/31 (54%), Positives = 26/31 (83%)

Query: 453 SDEEYDSSEEEEEEEEDEEEEEEEEEEEEEE 483
           S+E+    +EE+EEEED+EE+++E+E EEEE
Sbjct: 109 SEEDESDDDEEDEEEEDDEEDDDEDESEEEE 139

Nucleoplasmins are also known as chromatin decondensation proteins. They bind to core histones and transfer DNA to them in a reaction that requires ATP. This is thought to play a role in the assembly of regular nucleosomal arrays. Length = 146

>gnl|CDD|227693 COG5406, COG5406, Nucleosome binding factor SPN, SPT16 subunit [Transcription / DNA replication, recombination, and repair / Chromatin structure and dynamics]

 Score = 50.8 bits (121), Expect = 3e-06
 Identities = 25/57 (43%), Positives = 34/57 (59%), Gaps = 1/57 (1%)

Query: 443 SEYEDSDFDTSDEEYDSSEEEEEEEEDEEEEEEEEEEEEEEEEEEGEEEETETASSS 499
           SEYE S  D SDE  D  EE +E  ED  E+E E +  +EE+ E+ +E E++ A  S
Sbjct: 939 SEYEASSDDESDET-DEDEESDESSEDLSEDESENDSSDEEDGEDWDELESKAAYDS 994

Length = 1001

>gnl|CDD|184885 PRK14891, PRK14891, 50S ribosomal protein L24e/unknown domain fusion protein; Provisional

 Score = 46.9 bits (111), Expect = 3e-06
 Identities = 19/64 (29%), Positives = 32/64 (50%)

Query: 441 GDSEYEDSDFDTSDEEYDSSEEEEEEEEDEEEEEEEEEEEEEEEEEEGEEEETETASSST 500
           G +E   +   T+  E     E  + +ED +E  E +  +E +EEEE +E   ETA  + 
Sbjct: 56  GRAEKGPAAAATAAAEAAEEAEAADADEDADEAAEADAADEADEEEETDEAVDETADEAD 115

Query: 501 AKND 504
           A+ +
Sbjct: 116 AEAE 119

Length = 131

>gnl|CDD|233191 TIGR00927, 2A1904, K+-dependent Na+/Ca+ exchanger

 Score = 50.4 bits (120), Expect = 4e-06
 Identities = 22/40 (55%), Positives = 26/40 (65%)

Query: 212 DSEYEDSDFDTSDEEYDSSEEEEEEEDEEEEEEEEEGEEE 251
           D        D+ +EE +  EEEEEEE+EEEEEEEEE  EE
Sbjct: 853 DGGGGSDGGDSEEEEEEEEEEEEEEEEEEEEEEEEEENEE 892

[Transport and binding proteins, Cations and iron carrying compounds]. Length = 1096

>gnl|CDD|148051 pfam06213, CobT, Cobalamin biosynthesis protein CobT

 Score = 48.7 bits (116), Expect = 4e-06
 Identities = 17/61 (27%), Positives = 28/61 (45%), Gaps = 1/61 (1%)

Query: 441 GDSEYEDSDFDTSDEEYDSSEEEEEEEEDEEE-EEEEEEEEEEEEEEEGEEEETETASSS 499
           GD        D  DE+    +E++++ E+EE    +   E+ +   EE E  E E A +S
Sbjct: 213 GDEPESADSEDNEDEDDPKEDEDDDQGEEEESGSSDSLSEDSDASSEEMESGEMEAAEAS 272

Query: 500 T 500
            
Sbjct: 273 A 273

This family consists of several bacterial cobalamin biosynthesis (CobT) proteins. CobT is involved in the transformation of precorrin-3 into cobyrinic acid. Length = 282

>gnl|CDD|217861 pfam04050, Upf2, Up-frameshift suppressor 2

 Score = 47.8 bits (114), Expect = 4e-06
 Identities = 17/51 (33%), Positives = 31/51 (60%), Gaps = 3/51 (5%)

Query: 444 EYEDSDFDTSDEEYDSSEEEEEEEEDEEEEEEEEEEEEEEEEEEGEEEETE 494
              +S+   SD+  +  E  EE+E+DE  +EEE +  ++E++EE + EE +
Sbjct: 1   SGSESE---SDDGEEDEELPEEDEDDESSDEEEVDLPDDEQDEESDSEEEQ 48

Transcripts harbouring premature signals for translation termination are recognised and rapidly degraded by eukaryotic cells through a pathway known as nonsense-mediated mRNA decay. In Saccharomyces cerevisiae, three trans-acting factors (Upf1 to Upf3) are required for nonsense-mediated mRNA decay. Length = 171

>gnl|CDD|217861 pfam04050, Upf2, Up-frameshift suppressor 2

 Score = 47.8 bits (114), Expect = 4e-06
 Identities = 15/44 (34%), Positives = 27/44 (61%)

Query: 456 EYDSSEEEEEEEEDEEEEEEEEEEEEEEEEEEGEEEETETASSS 499
               SE ++ EE++E  EE+E++E  +EEE +  ++E +  S S
Sbjct: 1   SGSESESDDGEEDEELPEEDEDDESSDEEEVDLPDDEQDEESDS 44

Transcripts harbouring premature signals for translation termination are recognised and rapidly degraded by eukaryotic cells through a pathway known as nonsense-mediated mRNA decay. In Saccharomyces cerevisiae, three trans-acting factors (Upf1 to Upf3) are required for nonsense-mediated mRNA decay. Length = 171

>gnl|CDD|185603 PTZ00415, PTZ00415, transmission-blocking target antigen s230; Provisional

 Score = 50.4 bits (120), Expect = 4e-06
 Identities = 28/82 (34%), Positives = 41/82 (50%), Gaps = 9/82 (10%)

Query: 424 RRRSSAMNHNRRWNARNGDSEYEDSDFDTSDEEYDSSEEEEEEEEDEEEEEEEEEEEEEE 483
                 M   +R  AR+     E+      +   D  +E+E+E++D+EE++EEEEEEEEE
Sbjct: 123 EIGDLDMIIIKRRRARHLA---EEDMSPRDNFVIDDDDEDEDEDDDDEEDDEEEEEEEEE 179

Query: 484 ------EEEEGEEEETETASSS 499
                 E+EE E  E  T   S
Sbjct: 180 IKGFDDEDEEDEGGEDFTYEKS 201

Length = 2849

>gnl|CDD|226920 COG4547, CobT, Cobalamin biosynthesis protein CobT (nicotinate-mononucleotide:5, 6-dimethylbenzimidazole phosphoribosyltransferase) [Coenzyme metabolism]

 Score = 49.8 bits (119), Expect = 4e-06
 Identities = 23/60 (38%), Positives = 35/60 (58%), Gaps = 1/60 (1%)

Query: 441 GDSEYEDSD-FDTSDEEYDSSEEEEEEEEDEEEEEEEEEEEEEEEEEEGEEEETETASSS 499
            D   ED+D  D  D++ D++E+ E   E+ E  +E EE+E E  + EGEE E + A +S
Sbjct: 224 DDGIEEDADEEDGDDDQPDNNEDSEAGREESEGSDESEEDEAEATDGEGEEGEMDAAEAS 283

Length = 620

>gnl|CDD|219408 pfam07423, DUF1510, Protein of unknown function (DUF1510)

 Score = 48.2 bits (115), Expect = 4e-06
 Identities = 18/61 (29%), Positives = 30/61 (49%)

Query: 437 NARNGDSEYEDSDFDTSDEEYDSSEEEEEEEEDEEEEEEEEEEEEEEEEEEGEEEETETA 496
                  E +++      E+   +E+E+EE E+E EEE+EE  +E E+E E + E     
Sbjct: 61  EIEEVKEEEKEAANSEDKEDKGDAEKEDEESEEENEEEDEESSDENEKETEEKTESNVEK 120

Query: 497 S 497
            
Sbjct: 121 E 121

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|217503 pfam03344, Daxx, Daxx Family

 Score = 49.9 bits (119), Expect = 5e-06
 Identities = 25/67 (37%), Positives = 33/67 (49%), Gaps = 9/67 (13%)

Query: 442 DSEYEDSDFDTSDEEYDSSEEEEEEEEDEEEEEEEEEEEEEEEE---------EEGEEEE 492
             E E+ + +  +EE   SEEEE E+E+EEEE E +   EEE E         EE EE+ 
Sbjct: 444 SVEEEEEEEEEEEEEEQESEEEEGEDEEEEEEVEADNGSEEEMEGSSEGDGDGEEPEEDA 503

Query: 493 TETASSS 499
               S  
Sbjct: 504 ERRNSEM 510

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|219408 pfam07423, DUF1510, Protein of unknown function (DUF1510)

 Score = 47.8 bits (114), Expect = 5e-06
 Identities = 21/61 (34%), Positives = 36/61 (59%)

Query: 442 DSEYEDSDFDTSDEEYDSSEEEEEEEEDEEEEEEEEEEEEEEEEEEGEEEETETASSSTA 501
               E  +    ++E  +SE++E++ + E+E+EE EEE EEE+EE  +E E ET   + +
Sbjct: 57  QETAEIEEVKEEEKEAANSEDKEDKGDAEKEDEESEEENEEEDEESSDENEKETEEKTES 116

Query: 502 K 502
            
Sbjct: 117 N 117

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|145949 pfam03066, Nucleoplasmin, Nucleoplasmin

 Score = 46.2 bits (110), Expect = 6e-06
 Identities = 15/28 (53%), Positives = 25/28 (89%)

Query: 460 SEEEEEEEEDEEEEEEEEEEEEEEEEEE 487
            +E +++EEDEEEE++EE+++E+E EEE
Sbjct: 111 EDESDDDEEDEEEEDDEEDDDEDESEEE 138

Nucleoplasmins are also known as chromatin decondensation proteins. They bind to core histones and transfer DNA to them in a reaction that requires ATP. This is thought to play a role in the assembly of regular nucleosomal arrays. Length = 146

>gnl|CDD|184885 PRK14891, PRK14891, 50S ribosomal protein L24e/unknown domain fusion protein; Provisional

 Score = 45.7 bits (108), Expect = 7e-06
 Identities = 26/89 (29%), Positives = 39/89 (43%), Gaps = 4/89 (4%)

Query: 408 PRDLQKTIQDTTGAYNRRRSSAMNHNRRWNARNGDSEYEDSDFDTSDEEYDSSEEEEEEE 467
            RDL+ T            ++A        A   ++   D D D + E   + E +EEEE
Sbjct: 47  ARDLEWTEAGRAEKGPAAAATAAAEA----AEEAEAADADEDADEAAEADAADEADEEEE 102

Query: 468 EDEEEEEEEEEEEEEEEEEEGEEEETETA 496
            DE  +E  +E + E EE + EE+E   A
Sbjct: 103 TDEAVDETADEADAEAEEADEEEDEEAEA 131

Length = 131

>gnl|CDD|234311 TIGR03685, L12P_arch, 50S ribosomal protein L12P

 Score = 45.0 bits (107), Expect = 7e-06
 Identities = 19/30 (63%), Positives = 22/30 (73%)

Query: 459 SSEEEEEEEEDEEEEEEEEEEEEEEEEEEG 488
           ++    EEEE+EEEEEEEEEEE EEE   G
Sbjct: 70  AAAAAAEEEEEEEEEEEEEEEESEEEAMAG 99

This model represents the L12P protein of the large (50S) subunit of the archaeal ribosome. Length = 105

>gnl|CDD|145949 pfam03066, Nucleoplasmin, Nucleoplasmin

 Score = 45.8 bits (109), Expect = 8e-06
 Identities = 15/31 (48%), Positives = 27/31 (87%)

Query: 459 SSEEEEEEEEDEEEEEEEEEEEEEEEEEEGE 489
           S E+E +++E++EEEE++EE+++E+E EE E
Sbjct: 109 SEEDESDDDEEDEEEEDDEEDDDEDESEEEE 139

Nucleoplasmins are also known as chromatin decondensation proteins. They bind to core histones and transfer DNA to them in a reaction that requires ATP. This is thought to play a role in the assembly of regular nucleosomal arrays. Length = 146

>gnl|CDD|234311 TIGR03685, L12P_arch, 50S ribosomal protein L12P

 Score = 45.0 bits (107), Expect = 8e-06
 Identities = 18/31 (58%), Positives = 21/31 (67%)

Query: 459 SSEEEEEEEEDEEEEEEEEEEEEEEEEEEGE 489
           ++      EE+EEEEEEEEEEEEE EEE   
Sbjct: 68  AAAAAAAAEEEEEEEEEEEEEEEESEEEAMA 98

This model represents the L12P protein of the large (50S) subunit of the archaeal ribosome. Length = 105

>gnl|CDD|217927 pfam04147, Nop14, Nop14-like family

 Score = 48.8 bits (117), Expect = 9e-06
 Identities = 18/62 (29%), Positives = 34/62 (54%), Gaps = 1/62 (1%)

Query: 441 GDSEYEDSDFDTSDEEYDSSEEEEEEEEDEEEEEEEEEEEEEEEEEEGEEEETETASSST 500
                ED + +  D   D  EE+++++ +EEEE+ +  +EEE+EE+E  ++E +      
Sbjct: 316 LGQGEEDEE-EEEDGVDDEDEEDDDDDLEEEEEDVDLSDEEEDEEDEDSDDEDDEEEEEE 374

Query: 501 AK 502
            K
Sbjct: 375 EK 376

Emg1 and Nop14 are novel proteins whose interaction is required for the maturation of the 18S rRNA and for 40S ribosome production. Length = 809

>gnl|CDD|145949 pfam03066, Nucleoplasmin, Nucleoplasmin

 Score = 45.8 bits (109), Expect = 9e-06
 Identities = 17/38 (44%), Positives = 31/38 (81%)

Query: 453 SDEEYDSSEEEEEEEEDEEEEEEEEEEEEEEEEEEGEE 490
           S +   +SEE+E ++++E+EEEE++EE+++E+E E EE
Sbjct: 102 SGQHLVASEEDESDDDEEDEEEEDDEEDDDEDESEEEE 139

Nucleoplasmins are also known as chromatin decondensation proteins. They bind to core histones and transfer DNA to them in a reaction that requires ATP. This is thought to play a role in the assembly of regular nucleosomal arrays. Length = 146

>gnl|CDD|235795 PRK06402, rpl12p, 50S ribosomal protein L12P; Reviewed

 Score = 44.9 bits (107), Expect = 9e-06
 Identities = 16/28 (57%), Positives = 18/28 (64%)

Query: 461 EEEEEEEEDEEEEEEEEEEEEEEEEEEG 488
                EE+ EEEEEEEE+EE EEE   G
Sbjct: 73  AAAAAEEKKEEEEEEEEKEESEEEAAAG 100

Length = 106

>gnl|CDD|217927 pfam04147, Nop14, Nop14-like family

 Score = 48.8 bits (117), Expect = 1e-05
 Identities = 25/78 (32%), Positives = 43/78 (55%), Gaps = 7/78 (8%)

Query: 434 RRWNARNGDSEYEDSDFDTSDEEYDSSEEEEEE-------EEDEEEEEEEEEEEEEEEEE 486
           RR      D E E+   +++D+  D  E ++++       EEDEEEEE+  ++E+EE+++
Sbjct: 280 RRMRGEEEDDEEEEDSKESADDLDDEFEPDDDDNFGLGQGEEDEEEEEDGVDDEDEEDDD 339

Query: 487 EGEEEETETASSSTAKND 504
           +  EEE E    S  + D
Sbjct: 340 DDLEEEEEDVDLSDEEED 357

Emg1 and Nop14 are novel proteins whose interaction is required for the maturation of the 18S rRNA and for 40S ribosome production. Length = 809

>gnl|CDD|217927 pfam04147, Nop14, Nop14-like family

 Score = 48.5 bits (116), Expect = 1e-05
 Identities = 17/66 (25%), Positives = 34/66 (51%)

Query: 439 RNGDSEYEDSDFDTSDEEYDSSEEEEEEEEDEEEEEEEEEEEEEEEEEEGEEEETETASS 498
            + D   ++ + D  D       EE+EEEE++  ++E+EE+++++ EEE E+ +      
Sbjct: 297 ESADDLDDEFEPDDDDNFGLGQGEEDEEEEEDGVDDEDEEDDDDDLEEEEEDVDLSDEEE 356

Query: 499 STAKND 504
                D
Sbjct: 357 DEEDED 362

Emg1 and Nop14 are novel proteins whose interaction is required for the maturation of the 18S rRNA and for 40S ribosome production. Length = 809

>gnl|CDD|235795 PRK06402, rpl12p, 50S ribosomal protein L12P; Reviewed

 Score = 44.6 bits (106), Expect = 1e-05
 Identities = 14/29 (48%), Positives = 18/29 (62%)

Query: 462 EEEEEEEDEEEEEEEEEEEEEEEEEEGEE 490
                  +E++EEEEEEEE+EE EEE   
Sbjct: 71  AAAAAAAEEKKEEEEEEEEKEESEEEAAA 99

Length = 106

>gnl|CDD|240329 PTZ00248, PTZ00248, eukaryotic translation initiation factor 2 subunit 1; Provisional

 Score = 48.1 bits (115), Expect = 1e-05
 Identities = 18/45 (40%), Positives = 34/45 (75%)

Query: 446 EDSDFDTSDEEYDSSEEEEEEEEDEEEEEEEEEEEEEEEEEEGEE 490
           ++ D +   E+ +  EEE++  E E+E+EE+E+EEEEE+++EG++
Sbjct: 275 DEEDLEELLEKAEEEEEEDDYSESEDEDEEDEDEEEEEDDDEGDK 319

Length = 319

>gnl|CDD|237063 PRK12329, nusA, transcription elongation factor NusA; Provisional

 Score = 48.2 bits (115), Expect = 1e-05
 Identities = 14/65 (21%), Positives = 23/65 (35%)

Query: 442 DSEYEDSDFDTSDEEYDSSEEEEEEEEDEEEEEEEEEEEEEEEEEEGEEEETETASSSTA 501
           D E ED+       + +  E  + E E+  E E+ E  EE+    E      +       
Sbjct: 377 DQEAEDAKVAELISQREEEEALQREAEERLEAEQAERAEEDARLRELYPLPEDEFEDEDE 436

Query: 502 KNDPQ 506
             + Q
Sbjct: 437 LEEAQ 441

Length = 449

>gnl|CDD|215774 pfam00183, HSP90, Hsp90 protein

 Score = 48.6 bits (116), Expect = 1e-05
 Identities = 20/52 (38%), Positives = 34/52 (65%)

Query: 452 TSDEEYDSSEEEEEEEEDEEEEEEEEEEEEEEEEEEGEEEETETASSSTAKN 503
             + E +  +EEEEEE++E++EEEE+  ++EEE +E EE+E +   +   K 
Sbjct: 28  EKEVEKEVPDEEEEEEKEEKKEEEEKTTDKEEEVDEEEEKEEKKKKTKKVKE 79

Length = 529

>gnl|CDD|203043 pfam04546, Sigma70_ner, Sigma-70, non-essential region

 Score = 46.4 bits (111), Expect = 1e-05
 Identities = 14/46 (30%), Positives = 30/46 (65%)

Query: 447 DSDFDTSDEEYDSSEEEEEEEEDEEEEEEEEEEEEEEEEEEGEEEE 492
           ++    +      SE +EE+ ED+++++E+E+E++EEE + G + E
Sbjct: 33  NAAAAAATAAAIESELDEEDLEDDDDDDEDEDEDDEEEADLGPDPE 78

The domain is found in the primary vegetative sigma factor. The function of this domain is unclear and can be removed without loss of function. Length = 211

>gnl|CDD|220413 pfam09805, Nop25, Nucleolar protein 12 (25kDa)

 Score = 45.0 bits (107), Expect = 1e-05
 Identities = 19/53 (35%), Positives = 28/53 (52%), Gaps = 1/53 (1%)

Query: 461 EEEEEEEEDEEEEEEEEEEEEEEEEEEGEEEETETASSSTAKN-DPQMVTVPI 512
           +  EEE +DEE+ E E+ E+ E++E EG  E T T       + D    TV +
Sbjct: 77  KLLEEENDDEEDAETEDTEDVEDDEWEGFPEPTVTDYEEEYIDEDKYKTTVTV 129

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|217927 pfam04147, Nop14, Nop14-like family

 Score = 48.1 bits (115), Expect = 2e-05
 Identities = 15/62 (24%), Positives = 30/62 (48%)

Query: 202 HLGIIKSSNGDSEYEDSDFDTSDEEYDSSEEEEEEEDEEEEEEEEEGEEEETETASSSTA 261
             G       +   +D D +  D++ +  EE+ +  DEEE+EE+E+ ++E+ E       
Sbjct: 317 GQGEEDEEEEEDGVDDEDEEDDDDDLEEEEEDVDLSDEEEDEEDEDSDDEDDEEEEEEEK 376

Query: 262 KN 263
           + 
Sbjct: 377 EK 378

Emg1 and Nop14 are novel proteins whose interaction is required for the maturation of the 18S rRNA and for 40S ribosome production. Length = 809

>gnl|CDD|145949 pfam03066, Nucleoplasmin, Nucleoplasmin

 Score = 45.4 bits (108), Expect = 2e-05
 Identities = 16/32 (50%), Positives = 27/32 (84%)

Query: 464 EEEEEDEEEEEEEEEEEEEEEEEEGEEEETET 495
            EE+E +++EE+EEEE++EE+++E E EE E+
Sbjct: 109 SEEDESDDDEEDEEEEDDEEDDDEDESEEEES 140

Nucleoplasmins are also known as chromatin decondensation proteins. They bind to core histones and transfer DNA to them in a reaction that requires ATP. This is thought to play a role in the assembly of regular nucleosomal arrays. Length = 146

>gnl|CDD|219900 pfam08553, VID27, VID27 cytoplasmic protein

 Score = 47.8 bits (114), Expect = 2e-05
 Identities = 28/72 (38%), Positives = 40/72 (55%), Gaps = 3/72 (4%)

Query: 441 GDSEYEDSDFDTSDEEYDSSEEEEEEEEDEEEEEEEEEEEEEEEEEEGEEEETETASSST 500
              E ED++ +  DEE +  EEEEEE+EDE   +E  ++EE EE++   + E    +SS 
Sbjct: 377 SALEIEDANTERDDEEEEDEEEEEEEDEDEGPSKEHSDDEEFEEDDVESKYEDSDGNSSL 436

Query: 501 A---KNDPQMVT 509
           A   KND   V 
Sbjct: 437 AVGYKNDRSYVV 448

This is a family of fungal and plant proteins and contains many hypothetical proteins. VID27 is a cytoplasmic protein that plays a potential role in vacuolar protein degradation. Length = 794

>gnl|CDD|218223 pfam04712, Radial_spoke, Radial spokehead-like protein

 Score = 47.4 bits (113), Expect = 2e-05
 Identities = 19/31 (61%), Positives = 25/31 (80%)

Query: 461 EEEEEEEEDEEEEEEEEEEEEEEEEEEGEEE 491
             E+++EE+E+E+EEEEEEEEE EE E EE 
Sbjct: 343 NPEQKDEEEEQEDEEEEEEEEEPEEPEPEEG 373

This family includes the radial spoke head proteins RSP4 and RSP6 from Chlamydomonas reinhardtii, and several eukaryotic homologues, including mammalian RSHL1, the protein product of a familial ciliary dyskinesia candidate gene. Length = 481

>gnl|CDD|222581 pfam14181, YqfQ, YqfQ-like protein

 Score = 45.1 bits (107), Expect = 2e-05
 Identities = 16/56 (28%), Positives = 32/56 (57%)

Query: 451 DTSDEEYDSSEEEEEEEEDEEEEEEEEEEEEEEEEEEGEEEETETASSSTAKNDPQ 506
            +SD+E + +EEE  +E ++E+  E + E +E+++ E  + +TE     T    P+
Sbjct: 92  SSSDDEEEETEEESTDETEQEDPPETKTESKEKKKREVPKPKTEKEKPKTEPKKPK 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|226920 COG4547, CobT, Cobalamin biosynthesis protein CobT (nicotinate-mononucleotide:5, 6-dimethylbenzimidazole phosphoribosyltransferase) [Coenzyme metabolism]

 Score = 47.9 bits (114), Expect = 2e-05
 Identities = 22/107 (20%), Positives = 40/107 (37%), Gaps = 9/107 (8%)

Query: 411 LQKTIQDTTGAYNRRRSSAMNHNRRWNARNGDSEYEDSDFDTSDEEYDSSEEEEEEEEDE 470
            +  I+D  G      ++ ++  +   A            D ++E  D   EE+ +EED 
Sbjct: 180 WRDEIEDKAGEDLDGLAAEIDDQQ---AFARVVRDMLGSMDMAEETGDDGIEEDADEEDG 236

Query: 471 EE------EEEEEEEEEEEEEEEGEEEETETASSSTAKNDPQMVTVP 511
           ++      E+ E   EE E  +E EE+E E       + +       
Sbjct: 237 DDDQPDNNEDSEAGREESEGSDESEEDEAEATDGEGEEGEMDAAEAS 283

Length = 620

>gnl|CDD|235795 PRK06402, rpl12p, 50S ribosomal protein L12P; Reviewed

 Score = 43.8 bits (104), Expect = 2e-05
 Identities = 14/29 (48%), Positives = 18/29 (62%)

Query: 461 EEEEEEEEDEEEEEEEEEEEEEEEEEEGE 489
                  E+++EEEEEEEE+EE EEE   
Sbjct: 71  AAAAAAAEEKKEEEEEEEEKEESEEEAAA 99

Length = 106

>gnl|CDD|240329 PTZ00248, PTZ00248, eukaryotic translation initiation factor 2 subunit 1; Provisional

 Score = 47.0 bits (112), Expect = 2e-05
 Identities = 21/44 (47%), Positives = 31/44 (70%)

Query: 451 DTSDEEYDSSEEEEEEEEDEEEEEEEEEEEEEEEEEEGEEEETE 494
           D  D E    + EEEEEED+  E E+E+EE+E+EEEE +++E +
Sbjct: 275 DEEDLEELLEKAEEEEEEDDYSESEDEDEEDEDEEEEEDDDEGD 318

Length = 319

>gnl|CDD|117592 pfam09026, Cenp-B_dimeris, Centromere protein B dimerisation domain

 Score = 44.0 bits (103), Expect = 2e-05
 Identities = 13/30 (43%), Positives = 27/30 (90%)

Query: 454 DEEYDSSEEEEEEEEDEEEEEEEEEEEEEE 483
           D + DS EEE++++EDEE+++E+++E+++E
Sbjct: 11  DSDSDSDEEEDDDDEDEEDDDEDDDEDDDE 40

The centromere protein B (CENP-B) dimerisation domain is composed of two alpha-helices, which are folded into an antiparallel configuration. Dimerisation of CENP-B is mediated by this domain, in which monomers dimerise to form a symmetrical, antiparallel, four-helix bundle structure with a large hydrophobic patch in which 23 residues of one monomer form van der Waals contacts with the other monomer. This CENP-B dimer configuration may be suitable for capturing two distant CENP-B boxes during centromeric heterochromatin formation. Length = 101

>gnl|CDD|220383 pfam09756, DDRGK, DDRGK domain

 Score = 45.5 bits (108), Expect = 2e-05
 Identities = 23/66 (34%), Positives = 35/66 (53%)

Query: 434 RRWNARNGDSEYEDSDFDTSDEEYDSSEEEEEEEEDEEEEEEEEEEEEEEEEEEGEEEET 493
            R   R  + E  +      ++     +EEEE EE+ E+++EEEE +E EE+   E+EE 
Sbjct: 16  ARRQQREAEEEEREERKKLEEKREGERKEEEELEEEREKKKEEEERKEREEQARKEQEEY 75

Query: 494 ETASSS 499
           E   SS
Sbjct: 76  EKLKSS 81

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|233191 TIGR00927, 2A1904, K+-dependent Na+/Ca+ exchanger

 Score = 47.3 bits (112), Expect = 3e-05
 Identities = 24/42 (57%), Positives = 27/42 (64%), Gaps = 7/42 (16%)

Query: 208 SSNGDSEYEDSDFDTSDEEYDSSEEEEEEEDEEEEEEEEEGE 249
           S  GDSE E+       EE +  EEEEEEE+EEEEEEEE  E
Sbjct: 858 SDGGDSEEEE-------EEEEEEEEEEEEEEEEEEEEEENEE 892

[Transport and binding proteins, Cations and iron carrying compounds]. Length = 1096

>gnl|CDD|217927 pfam04147, Nop14, Nop14-like family

 Score = 47.3 bits (113), Expect = 3e-05
 Identities = 19/55 (34%), Positives = 31/55 (56%)

Query: 212 DSEYEDSDFDTSDEEYDSSEEEEEEEDEEEEEEEEEGEEEETETASSSTAKNDPQ 266
           D E E+   D  DEE D  + EEEEED +  +EEE+ E+E+++       + + +
Sbjct: 322 DEEEEEDGVDDEDEEDDDDDLEEEEEDVDLSDEEEDEEDEDSDDEDDEEEEEEEK 376

Emg1 and Nop14 are novel proteins whose interaction is required for the maturation of the 18S rRNA and for 40S ribosome production. Length = 809

>gnl|CDD|145949 pfam03066, Nucleoplasmin, Nucleoplasmin

 Score = 44.6 bits (106), Expect = 3e-05
 Identities = 17/30 (56%), Positives = 26/30 (86%)

Query: 224 DEEYDSSEEEEEEEDEEEEEEEEEGEEEET 253
           ++E D  EE+EEEED+EE+++E+E EEEE+
Sbjct: 111 EDESDDDEEDEEEEDDEEDDDEDESEEEES 140

Nucleoplasmins are also known as chromatin decondensation proteins. They bind to core histones and transfer DNA to them in a reaction that requires ATP. This is thought to play a role in the assembly of regular nucleosomal arrays. Length = 146

>gnl|CDD|145949 pfam03066, Nucleoplasmin, Nucleoplasmin

 Score = 44.2 bits (105), Expect = 3e-05
 Identities = 15/30 (50%), Positives = 23/30 (76%)

Query: 452 TSDEEYDSSEEEEEEEEDEEEEEEEEEEEE 481
             DE  D  E+EEEE+++E+++E+E EEEE
Sbjct: 110 EEDESDDDEEDEEEEDDEEDDDEDESEEEE 139

Nucleoplasmins are also known as chromatin decondensation proteins. They bind to core histones and transfer DNA to them in a reaction that requires ATP. This is thought to play a role in the assembly of regular nucleosomal arrays. Length = 146

>gnl|CDD|240329 PTZ00248, PTZ00248, eukaryotic translation initiation factor 2 subunit 1; Provisional

 Score = 46.6 bits (111), Expect = 3e-05
 Identities = 20/44 (45%), Positives = 33/44 (75%)

Query: 449 DFDTSDEEYDSSEEEEEEEEDEEEEEEEEEEEEEEEEEEGEEEE 492
           D +  +E  + +EEEEEE++  E E+E+EE+E+EEEEE+ +E +
Sbjct: 275 DEEDLEELLEKAEEEEEEDDYSESEDEDEEDEDEEEEEDDDEGD 318

Length = 319

>gnl|CDD|117592 pfam09026, Cenp-B_dimeris, Centromere protein B dimerisation domain

 Score = 43.2 bits (101), Expect = 3e-05
 Identities = 14/39 (35%), Positives = 29/39 (74%)

Query: 461 EEEEEEEEDEEEEEEEEEEEEEEEEEEGEEEETETASSS 499
           E EE+ + D +EEE++++E+EE+++E+ +E++ E    S
Sbjct: 7   EGEEDSDSDSDEEEDDDDEDEEDDDEDDDEDDDEVPVPS 45

The centromere protein B (CENP-B) dimerisation domain is composed of two alpha-helices, which are folded into an antiparallel configuration. Dimerisation of CENP-B is mediated by this domain, in which monomers dimerise to form a symmetrical, antiparallel, four-helix bundle structure with a large hydrophobic patch in which 23 residues of one monomer form van der Waals contacts with the other monomer. This CENP-B dimer configuration may be suitable for capturing two distant CENP-B boxes during centromeric heterochromatin formation. Length = 101

>gnl|CDD|117592 pfam09026, Cenp-B_dimeris, Centromere protein B dimerisation domain

 Score = 43.2 bits (101), Expect = 3e-05
 Identities = 13/32 (40%), Positives = 28/32 (87%)

Query: 456 EYDSSEEEEEEEEDEEEEEEEEEEEEEEEEEE 487
           E DS  + +EEE+D++E+EE+++E+++E+++E
Sbjct: 9   EEDSDSDSDEEEDDDDEDEEDDDEDDDEDDDE 40

The centromere protein B (CENP-B) dimerisation domain is composed of two alpha-helices, which are folded into an antiparallel configuration. Dimerisation of CENP-B is mediated by this domain, in which monomers dimerise to form a symmetrical, antiparallel, four-helix bundle structure with a large hydrophobic patch in which 23 residues of one monomer form van der Waals contacts with the other monomer. This CENP-B dimer configuration may be suitable for capturing two distant CENP-B boxes during centromeric heterochromatin formation. Length = 101

>gnl|CDD|220135 pfam09184, PPP4R2, PPP4R2

 Score = 46.4 bits (110), Expect = 3e-05
 Identities = 26/57 (45%), Positives = 35/57 (61%), Gaps = 2/57 (3%)

Query: 437 NARNGDSEYEDSDF--DTSDEEYDSSEEEEEEEEDEEEEEEEEEEEEEEEEEEGEEE 491
            A + D   + SD     SD+E D  ++ +  EE E +E+EEEEE EEEEEEE E+E
Sbjct: 229 AAASQDDGPKGSDVKNKKSDDEEDDDQDGDYVEEKELKEDEEEEETEEEEEEEDEDE 285

PPP4R2 (protein phosphatase 4 core regulatory subunit R2) is the regulatory subunit of the histone H2A phosphatase complex. It has been shown to confer resistance to the anticancer drug cisplatin in yeast, and may confer resistance in higher eukaryotes. Length = 285

>gnl|CDD|220135 pfam09184, PPP4R2, PPP4R2

 Score = 46.4 bits (110), Expect = 3e-05
 Identities = 22/66 (33%), Positives = 35/66 (53%), Gaps = 10/66 (15%)

Query: 442 DSEYEDSDFDTSDEEYDS----------SEEEEEEEEDEEEEEEEEEEEEEEEEEEGEEE 491
           +  YE    D +  + D           S++EE++++D +  EE+E +E+EEEEE  EEE
Sbjct: 219 EEYYEKESSDAAASQDDGPKGSDVKNKKSDDEEDDDQDGDYVEEKELKEDEEEEETEEEE 278

Query: 492 ETETAS 497
           E E   
Sbjct: 279 EEEDED 284

PPP4R2 (protein phosphatase 4 core regulatory subunit R2) is the regulatory subunit of the histone H2A phosphatase complex. It has been shown to confer resistance to the anticancer drug cisplatin in yeast, and may confer resistance in higher eukaryotes. Length = 285

>gnl|CDD|218333 pfam04931, DNA_pol_phi, DNA polymerase phi

 Score = 47.2 bits (112), Expect = 3e-05
 Identities = 17/71 (23%), Positives = 35/71 (49%), Gaps = 1/71 (1%)

Query: 437 NARNGDSEYEDSDFDTSDEEYDSSEEEEEEEEDEEEEEEEEEEEEEEEEEEGEEEETETA 496
            A    S ++   F+  +E+ D  EE +++E++ E  E+ E E E + E+  E+E+ + A
Sbjct: 633 KADENKSRHQQL-FEGEEEDEDDLEETDDDEDECEAIEDSESESESDGEDGEEDEQEDDA 691

Query: 497 SSSTAKNDPQM 507
            ++        
Sbjct: 692 EANEGVVPIDK 702

This family includes the fifth essential DNA polymerase in yeast EC:2.7.7.7. Pol5p is localised exclusively to the nucleolus and binds near or at the enhancer region of rRNA-encoding DNA repeating units. Length = 784

>gnl|CDD|218303 pfam04874, Mak16, Mak16 protein C-terminal region

 Score = 42.9 bits (101), Expect = 3e-05
 Identities = 20/34 (58%), Positives = 24/34 (70%)

Query: 461 EEEEEEEEDEEEEEEEEEEEEEEEEEEGEEEETE 494
           EE EE +E+EEEEEEEE+E E E   + EE E E
Sbjct: 58  EESEENDEEEEEEEEEEDEGEIEYVSDDEELEEE 91

The precise function of this eukaryotic protein family is unknown. The yeast orthologues have been implicated in cell cycle progression and biogenesis of 60S ribosomal subunits. The Schistosoma mansoni Mak16 has been shown to target protein transport to the nucleolus. Length = 97

>gnl|CDD|218303 pfam04874, Mak16, Mak16 protein C-terminal region

 Score = 42.9 bits (101), Expect = 3e-05
 Identities = 22/34 (64%), Positives = 25/34 (73%)

Query: 461 EEEEEEEEDEEEEEEEEEEEEEEEEEEGEEEETE 494
           E EE EE DEEEEEEEEEE+E E E   ++EE E
Sbjct: 56  EAEESEENDEEEEEEEEEEDEGEIEYVSDDEELE 89

The precise function of this eukaryotic protein family is unknown. The yeast orthologues have been implicated in cell cycle progression and biogenesis of 60S ribosomal subunits. The Schistosoma mansoni Mak16 has been shown to target protein transport to the nucleolus. Length = 97

>gnl|CDD|220102 pfam09073, BUD22, BUD22

 Score = 46.8 bits (111), Expect = 3e-05
 Identities = 22/76 (28%), Positives = 29/76 (38%), Gaps = 13/76 (17%)

Query: 443 SEYEDSDFDTSDEEYDSSEEEEEEEEDE-------------EEEEEEEEEEEEEEEEEGE 489
           SE ED        E DS +EEEE+ + E             +EEE EE       E+  E
Sbjct: 175 SESEDESKSEESAEDDSDDEEEEDSDSEDYSQYDGMLVDSSDEEEGEEAPSINYNEDTSE 234

Query: 490 EEETETASSSTAKNDP 505
            E  E+ S  +     
Sbjct: 235 SESDESDSEISESRSV 250

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|217049 pfam02459, Adeno_terminal, Adenoviral DNA terminal protein

 Score = 47.0 bits (112), Expect = 3e-05
 Identities = 24/33 (72%), Positives = 25/33 (75%)

Query: 460 SEEEEEEEEDEEEEEEEEEEEEEEEEEEGEEEE 492
           S  E EEEE+EEEE  EEEEEEEEEEE   EEE
Sbjct: 301 SPPEPEEEEEEEEEVPEEEEEEEEEEERTFEEE 333

This protein is covalently attached to the terminii of replicating DNA in vivo. Length = 548

>gnl|CDD|217927 pfam04147, Nop14, Nop14-like family

 Score = 46.9 bits (112), Expect = 4e-05
 Identities = 20/59 (33%), Positives = 32/59 (54%)

Query: 211 GDSEYEDSDFDTSDEEYDSSEEEEEEEDEEEEEEEEEGEEEETETASSSTAKNDPQMVT 269
            D + ED D D  +EE D    +EEE++E+E+ ++E+ EEEE E       K+     +
Sbjct: 331 DDEDEEDDDDDLEEEEEDVDLSDEEEDEEDEDSDDEDDEEEEEEEKEKKKKKSAESTRS 389

Emg1 and Nop14 are novel proteins whose interaction is required for the maturation of the 18S rRNA and for 40S ribosome production. Length = 809

>gnl|CDD|217503 pfam03344, Daxx, Daxx Family

 Score = 46.8 bits (111), Expect = 4e-05
 Identities = 20/59 (33%), Positives = 30/59 (50%)

Query: 208 SSNGDSEYEDSDFDTSDEEYDSSEEEEEEEDEEEEEEEEEGEEEETETASSSTAKNDPQ 266
           S       E+   +  +EE +  EEEE+E +EEE E+EEE EE E +  S    +   +
Sbjct: 433 SMASQESEEEESVEEEEEEEEEEEEEEQESEEEEGEDEEEEEEVEADNGSEEEMEGSSE 491

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|148630 pfam07133, Merozoite_SPAM, Merozoite surface protein (SPAM)

 Score = 44.1 bits (104), Expect = 4e-05
 Identities = 26/68 (38%), Positives = 35/68 (51%), Gaps = 11/68 (16%)

Query: 451 DTSDEEYDSSEE--EEEEEEDEEEEEEEEEEE---------EEEEEEEGEEEETETASSS 499
           D   E  D  +E  E++EEE+EE+EEE EE E         E+EEEEE +EE+       
Sbjct: 35  DIIKENEDVKDEKQEDDEEEEEEDEEEIEEPEDIEDEEEIVEDEEEEEEDEEDNVDLKDI 94

Query: 500 TAKNDPQM 507
             KN   +
Sbjct: 95  EKKNINDI 102

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|145949 pfam03066, Nucleoplasmin, Nucleoplasmin

 Score = 44.2 bits (105), Expect = 4e-05
 Identities = 16/32 (50%), Positives = 25/32 (78%)

Query: 466 EEEDEEEEEEEEEEEEEEEEEEGEEEETETAS 497
            EEDE +++EE+EEEE++EE++ E+E  E  S
Sbjct: 109 SEEDESDDDEEDEEEEDDEEDDDEDESEEEES 140

Nucleoplasmins are also known as chromatin decondensation proteins. They bind to core histones and transfer DNA to them in a reaction that requires ATP. This is thought to play a role in the assembly of regular nucleosomal arrays. Length = 146

>gnl|CDD|218223 pfam04712, Radial_spoke, Radial spokehead-like protein

 Score = 46.6 bits (111), Expect = 4e-05
 Identities = 19/31 (61%), Positives = 23/31 (74%)

Query: 464 EEEEEDEEEEEEEEEEEEEEEEEEGEEEETE 494
             E++DEEEE+E+EEEEEEEEE E  E E  
Sbjct: 343 NPEQKDEEEEQEDEEEEEEEEEPEEPEPEEG 373

This family includes the radial spoke head proteins RSP4 and RSP6 from Chlamydomonas reinhardtii, and several eukaryotic homologues, including mammalian RSHL1, the protein product of a familial ciliary dyskinesia candidate gene. Length = 481

>gnl|CDD|218223 pfam04712, Radial_spoke, Radial spokehead-like protein

 Score = 46.6 bits (111), Expect = 4e-05
 Identities = 18/33 (54%), Positives = 24/33 (72%)

Query: 462 EEEEEEEDEEEEEEEEEEEEEEEEEEGEEEETE 494
             E+++E+EE+E+EEEEEEEEE EE   EE   
Sbjct: 343 NPEQKDEEEEQEDEEEEEEEEEPEEPEPEEGPP 375

This family includes the radial spoke head proteins RSP4 and RSP6 from Chlamydomonas reinhardtii, and several eukaryotic homologues, including mammalian RSHL1, the protein product of a familial ciliary dyskinesia candidate gene. Length = 481

>gnl|CDD|217203 pfam02724, CDC45, CDC45-like protein

 Score = 46.9 bits (112), Expect = 4e-05
 Identities = 17/58 (29%), Positives = 39/58 (67%)

Query: 440 NGDSEYEDSDFDTSDEEYDSSEEEEEEEEDEEEEEEEEEEEEEEEEEEGEEEETETAS 497
           +GD E E  D    D+ Y   EE+++++E+ +EE+EE  + E++E+++ ++++ + A+
Sbjct: 103 DGDIEEELQDEPRYDDAYRDLEEDDDDDEESDEEDEESSKSEDDEDDDDDDDDDDIAT 160

CDC45 is an essential gene required for initiation of DNA replication in S. cerevisiae, forming a complex with MCM5/CDC46. Homologues of CDC45 have been identified in human, mouse and smut fungus among others. Length = 583

>gnl|CDD|221275 pfam11861, DUF3381, Domain of unknown function (DUF3381)

 Score = 44.2 bits (105), Expect = 4e-05
 Identities = 18/59 (30%), Positives = 29/59 (49%)

Query: 450 FDTSDEEYDSSEEEEEEEEDEEEEEEEEEEEEEEEEEEGEEEETETASSSTAKNDPQMV 508
            D  ++E +  EE E EE DEEE+ +E  E+E  + +  +  E E       K   +M+
Sbjct: 96  LDKKEKEEEEEEEVEVEELDEEEQIDELLEKELAKLKREKRRENERKQKEILKEQMKML 154

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|100110 cd05832, Ribosomal_L12p, Ribosomal protein L12p

 Score = 42.9 bits (101), Expect = 4e-05
 Identities = 16/29 (55%), Positives = 24/29 (82%)

Query: 460 SEEEEEEEEDEEEEEEEEEEEEEEEEEEG 488
           + EE+ EE++EE+++EEE+EEEEEE   G
Sbjct: 73  AAEEKAEEKEEEKKKEEEKEEEEEEALAG 101

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|233191 TIGR00927, 2A1904, K+-dependent Na+/Ca+ exchanger

 Score = 46.5 bits (110), Expect = 5e-05
 Identities = 24/79 (30%), Positives = 39/79 (49%), Gaps = 3/79 (3%)

Query: 438 ARNGDSEYEDSDFDTSDEEYDSSEEEEEEEEDEEEE---EEEEEEEEEEEEEEGEEEETE 494
           A + + + E  + + + E    ++++E+  +        + EEEEEEEEEEEE EEEE E
Sbjct: 823 ADDTEVKDETGEQELNAENQGEAKQDEKGVDGGGGSDGGDSEEEEEEEEEEEEEEEEEEE 882

Query: 495 TASSSTAKNDPQMVTVPIT 513
                    +P  +  P T
Sbjct: 883 EEEEEEENEEPLSLEWPET 901

[Transport and binding proteins, Cations and iron carrying compounds]. Length = 1096

>gnl|CDD|218223 pfam04712, Radial_spoke, Radial spokehead-like protein

 Score = 46.2 bits (110), Expect = 5e-05
 Identities = 18/32 (56%), Positives = 24/32 (75%)

Query: 461 EEEEEEEEDEEEEEEEEEEEEEEEEEEGEEEE 492
            E+++EEE++E+EEEEEEEEE EE E  E   
Sbjct: 344 PEQKDEEEEQEDEEEEEEEEEPEEPEPEEGPP 375

This family includes the radial spoke head proteins RSP4 and RSP6 from Chlamydomonas reinhardtii, and several eukaryotic homologues, including mammalian RSHL1, the protein product of a familial ciliary dyskinesia candidate gene. Length = 481

>gnl|CDD|117592 pfam09026, Cenp-B_dimeris, Centromere protein B dimerisation domain

 Score = 42.8 bits (100), Expect = 5e-05
 Identities = 14/36 (38%), Positives = 30/36 (83%)

Query: 450 FDTSDEEYDSSEEEEEEEEDEEEEEEEEEEEEEEEE 485
           F   +E+ DS  +EEE+++DE+EE+++E+++E+++E
Sbjct: 5   FLEGEEDSDSDSDEEEDDDDEDEEDDDEDDDEDDDE 40

The centromere protein B (CENP-B) dimerisation domain is composed of two alpha-helices, which are folded into an antiparallel configuration. Dimerisation of CENP-B is mediated by this domain, in which monomers dimerise to form a symmetrical, antiparallel, four-helix bundle structure with a large hydrophobic patch in which 23 residues of one monomer form van der Waals contacts with the other monomer. This CENP-B dimer configuration may be suitable for capturing two distant CENP-B boxes during centromeric heterochromatin formation. Length = 101

>gnl|CDD|217049 pfam02459, Adeno_terminal, Adenoviral DNA terminal protein

 Score = 46.2 bits (110), Expect = 5e-05
 Identities = 24/33 (72%), Positives = 25/33 (75%)

Query: 459 SSEEEEEEEEDEEEEEEEEEEEEEEEEEEGEEE 491
           S  E EEEEE+EEE  EEEEEEEEEEE   EEE
Sbjct: 301 SPPEPEEEEEEEEEVPEEEEEEEEEEERTFEEE 333

This protein is covalently attached to the terminii of replicating DNA in vivo. Length = 548

>gnl|CDD|100110 cd05832, Ribosomal_L12p, Ribosomal protein L12p

 Score = 42.9 bits (101), Expect = 5e-05
 Identities = 15/29 (51%), Positives = 22/29 (75%)

Query: 461 EEEEEEEEDEEEEEEEEEEEEEEEEEEGE 489
              EE+ E++EEE+++EEE+EEEEEE   
Sbjct: 72  AAAEEKAEEKEEEKKKEEEKEEEEEEALA 100

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|114603 pfam05887, Trypan_PARP, Procyclic acidic repetitive protein (PARP)

 Score = 43.8 bits (102), Expect = 5e-05
 Identities = 27/66 (40%), Positives = 34/66 (51%)

Query: 441 GDSEYEDSDFDTSDEEYDSSEEEEEEEEDEEEEEEEEEEEEEEEEEEGEEEETETASSST 500
           G+   +    DT+  + D   EEEEE E EEE EEE E EEE EEE   EE  E      
Sbjct: 44  GEKGTKVGADDTNGTDPDDEPEEEEEPEPEEEGEEEPEPEEEGEEEPEPEETGEEEPEPE 103

Query: 501 AKNDPQ 506
            + +P+
Sbjct: 104 PEPEPE 109

This family consists of several Trypanosoma brucei procyclic acidic repetitive protein (PARP) like sequences. The procyclic acidic repetitive protein (parp) genes of Trypanosoma brucei encode a small family of abundant surface proteins whose expression is restricted to the procyclic form of the parasite. They are found at two unlinked loci, parpA and parpB; transcription of both loci is developmentally regulated. Length = 145

>gnl|CDD|227466 COG5137, COG5137, Histone chaperone involved in gene silencing [Transcription / Chromatin structure and dynamics]

 Score = 45.4 bits (107), Expect = 5e-05
 Identities = 21/63 (33%), Positives = 30/63 (47%), Gaps = 3/63 (4%)

Query: 433 NRRWNARNGDSEYEDSDFDTSDEEYDSSEEEEEEEEDEEEE---EEEEEEEEEEEEEEGE 489
           N  W+    + E   +  D  +EE +  EE +  EE+E+EE   +   E   E  EEE E
Sbjct: 155 NIVWDNDEDNDEAPPAQPDVDNEEEERLEESDGREEEEDEEVGSDSYGEGNRELNEEEEE 214

Query: 490 EEE 492
           E E
Sbjct: 215 EAE 217

Length = 279

>gnl|CDD|219408 pfam07423, DUF1510, Protein of unknown function (DUF1510)

 Score = 44.7 bits (106), Expect = 6e-05
 Identities = 19/61 (31%), Positives = 36/61 (59%), Gaps = 2/61 (3%)

Query: 442 DSEYEDSDFDTSDEEYDSSEEEEEEEEDEEEEEEEEEEEEEEEEEEGEEEETETASSSTA 501
             E ++ + + ++   +  E++ + E+++EE EEE EEE+EE  +E E+E  E   S+  
Sbjct: 62  IEEVKEEEKEAANS--EDKEDKGDAEKEDEESEEENEEEDEESSDENEKETEEKTESNVE 119

Query: 502 K 502
           K
Sbjct: 120 K 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|219408 pfam07423, DUF1510, Protein of unknown function (DUF1510)

 Score = 44.7 bits (106), Expect = 6e-05
 Identities = 20/66 (30%), Positives = 37/66 (56%), Gaps = 4/66 (6%)

Query: 441 GDSEYEDSDFDTSDEEYDSSEEEEEEEEDEEEEEEEEEEEEEEEEEEGEEE----ETETA 496
            D +      +  +EE +++  E++E++ + E+E+EE EEE EEE+E   +    ETE  
Sbjct: 54  SDDQETAEIEEVKEEEKEAANSEDKEDKGDAEKEDEESEEENEEEDEESSDENEKETEEK 113

Query: 497 SSSTAK 502
           + S  +
Sbjct: 114 TESNVE 119

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|218303 pfam04874, Mak16, Mak16 protein C-terminal region

 Score = 42.2 bits (99), Expect = 6e-05
 Identities = 22/50 (44%), Positives = 31/50 (62%)

Query: 445 YEDSDFDTSDEEYDSSEEEEEEEEDEEEEEEEEEEEEEEEEEEGEEEETE 494
           Y D  ++ S   +  + E EE EE++EEEEEEEEEE+E E E   ++E  
Sbjct: 39  YGDEPYNISQSAFKKALEAEESEENDEEEEEEEEEEDEGEIEYVSDDEEL 88

The precise function of this eukaryotic protein family is unknown. The yeast orthologues have been implicated in cell cycle progression and biogenesis of 60S ribosomal subunits. The Schistosoma mansoni Mak16 has been shown to target protein transport to the nucleolus. Length = 97

>gnl|CDD|114172 pfam05432, BSP_II, Bone sialoprotein II (BSP-II)

 Score = 45.5 bits (107), Expect = 6e-05
 Identities = 22/37 (59%), Positives = 29/37 (78%)

Query: 464 EEEEEDEEEEEEEEEEEEEEEEEEGEEEETETASSST 500
           +E+E DE+EEEEEEEEEEE E EE E+    T+++ST
Sbjct: 131 KEDESDEDEEEEEEEEEEEAEVEENEQGTNGTSTNST 167

Bone sialoprotein (BSP) is a major structural protein of the bone matrix that is specifically expressed by fully-differentiated osteoblasts. The expression of bone sialoprotein (BSP) is normally restricted to mineralised connective tissues of bones and teeth where it has been associated with mineral crystal formation. However, it has been found that ectopic expression of BSP occurs in various lesions, including oral and extraoral carcinomas, in which it has been associated with the formation of microcrystalline deposits and the metastasis of cancer cells to bone. Length = 291

>gnl|CDD|217840 pfam04006, Mpp10, Mpp10 protein

 Score = 46.1 bits (109), Expect = 6e-05
 Identities = 17/53 (32%), Positives = 29/53 (54%)

Query: 442 DSEYEDSDFDTSDEEYDSSEEEEEEEEDEEEEEEEEEEEEEEEEEEGEEEETE 494
           + E  + +    ++E D   E E   ED  ++E E++EE++ EEEE  EE+  
Sbjct: 123 EDESLEDEMIDDEDEADLFNESESSLEDLSDDETEDDEEKKMEEEEAGEEKES 175

This family includes proteins related to Mpp10 (M phase phosphoprotein 10). The U3 small nucleolar ribonucleoprotein (snoRNP) is required for three cleavage events that generate the mature 18S rRNA from the pre-rRNA. In Saccharomyces cerevisiae, depletion of Mpp10, a U3 snoRNP-specific protein, halts 18S rRNA production and impairs cleavage at the three U3 snoRNP-dependent sites. Length = 613

>gnl|CDD|233191 TIGR00927, 2A1904, K+-dependent Na+/Ca+ exchanger

 Score = 46.1 bits (109), Expect = 7e-05
 Identities = 20/30 (66%), Positives = 22/30 (73%)

Query: 225 EEYDSSEEEEEEEDEEEEEEEEEGEEEETE 254
              D  + EEEEE+EEEEEEEEE EEEE E
Sbjct: 856 GGSDGGDSEEEEEEEEEEEEEEEEEEEEEE 885

[Transport and binding proteins, Cations and iron carrying compounds]. Length = 1096

>gnl|CDD|148630 pfam07133, Merozoite_SPAM, Merozoite surface protein (SPAM)

 Score = 43.7 bits (103), Expect = 7e-05
 Identities = 20/47 (42%), Positives = 33/47 (70%)

Query: 452 TSDEEYDSSEEEEEEEEDEEEEEEEEEEEEEEEEEEGEEEETETASS 498
           TS ++ D  +E E+ +++++E++EEEEEE+EEE EE E+ E E    
Sbjct: 29  TSWDKEDIIKENEDVKDEKQEDDEEEEEEDEEEIEEPEDIEDEEEIV 75

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|226920 COG4547, CobT, Cobalamin biosynthesis protein CobT (nicotinate-mononucleotide:5, 6-dimethylbenzimidazole phosphoribosyltransferase) [Coenzyme metabolism]

 Score = 46.0 bits (109), Expect = 7e-05
 Identities = 23/77 (29%), Positives = 31/77 (40%), Gaps = 18/77 (23%)

Query: 442 DSEYEDSDFDTSDEEYDSSEEEEEEE-------------EDEEEEEEEE-----EEEEEE 483
           D++ ED D D  D   DS    EE E             + E EE E +     E+ E +
Sbjct: 230 DADEEDGDDDQPDNNEDSEAGREESEGSDESEEDEAEATDGEGEEGEMDAAEASEDSESD 289

Query: 484 EEEEGEEEETETASSST 500
           E +E  E   E A  +T
Sbjct: 290 ESDEDTETPGEDARPAT 306

Length = 620

>gnl|CDD|219408 pfam07423, DUF1510, Protein of unknown function (DUF1510)

 Score = 44.3 bits (105), Expect = 7e-05
 Identities = 19/49 (38%), Positives = 27/49 (55%)

Query: 446 EDSDFDTSDEEYDSSEEEEEEEEDEEEEEEEEEEEEEEEEEEGEEEETE 494
            +   D  D E +  E EEE EE++EE  +E E+E EE+ E   E+E  
Sbjct: 75  SEDKEDKGDAEKEDEESEEENEEEDEESSDENEKETEEKTESNVEKEIT 123

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|235795 PRK06402, rpl12p, 50S ribosomal protein L12P; Reviewed

 Score = 42.2 bits (100), Expect = 7e-05
 Identities = 15/29 (51%), Positives = 18/29 (62%)

Query: 466 EEEDEEEEEEEEEEEEEEEEEEGEEEETE 494
                  EE++EEEEEEEE+EE EEE   
Sbjct: 71  AAAAAAAEEKKEEEEEEEEKEESEEEAAA 99

Length = 106

>gnl|CDD|203043 pfam04546, Sigma70_ner, Sigma-70, non-essential region

 Score = 44.5 bits (106), Expect = 7e-05
 Identities = 12/44 (27%), Positives = 27/44 (61%)

Query: 451 DTSDEEYDSSEEEEEEEEDEEEEEEEEEEEEEEEEEEGEEEETE 494
           D +     ++    E E DEE+ E++++++E+E+E++ EE +  
Sbjct: 31  DPNAAAAAATAAAIESELDEEDLEDDDDDDEDEDEDDEEEADLG 74

The domain is found in the primary vegetative sigma factor. The function of this domain is unclear and can be removed without loss of function. Length = 211

>gnl|CDD|222792 PHA00435, PHA00435, capsid assembly protein

 Score = 45.2 bits (107), Expect = 8e-05
 Identities = 25/60 (41%), Positives = 31/60 (51%), Gaps = 1/60 (1%)

Query: 440 NGDSEYEDSDFDTSDEEYDSSEEEEEEEEDEEEEEEEEEEEEE-EEEEEGEEEETETASS 498
           N D   ED +        +  EEEE EE +E+EEEE EEE EE E   +  EE TE +  
Sbjct: 59  NPDPFGEDDEGRIEVRISEDGEEEEVEEGEEDEEEEGEEESEEFEPLGDTPEELTEASEQ 118

Length = 306

>gnl|CDD|219900 pfam08553, VID27, VID27 cytoplasmic protein

 Score = 45.9 bits (109), Expect = 8e-05
 Identities = 20/70 (28%), Positives = 33/70 (47%), Gaps = 1/70 (1%)

Query: 436 WNARNGDSEYEDSDFDTSDEEYDSSEEEEEEEEDEEEEEEEEEEEEEEEEEEGEEEETET 495
           W   N    +  +     D   D+    E E+ + E ++EEEE+EEEEEEE+ +E  ++ 
Sbjct: 353 WETLNKQK-WTKAKETEQDYILDAFSALEIEDANTERDDEEEEDEEEEEEEDEDEGPSKE 411

Query: 496 ASSSTAKNDP 505
            S      + 
Sbjct: 412 HSDDEEFEED 421

This is a family of fungal and plant proteins and contains many hypothetical proteins. VID27 is a cytoplasmic protein that plays a potential role in vacuolar protein degradation. Length = 794

>gnl|CDD|114172 pfam05432, BSP_II, Bone sialoprotein II (BSP-II)

 Score = 45.1 bits (106), Expect = 8e-05
 Identities = 27/96 (28%), Positives = 39/96 (40%), Gaps = 23/96 (23%)

Query: 439 RNGDSEYEDSDFDTSDEEYDSSEEEEEEEEDEEEEEE----------------------- 475
           + G++  + +  D SDE+ +  EEEEEEE + EE E+                       
Sbjct: 121 KAGNAGKKATKEDESDEDEEEEEEEEEEEAEVEENEQGTNGTSTNSTEVDHGNGSSGGDN 180

Query: 476 EEEEEEEEEEEEGEEEETETASSSTAKNDPQMVTVP 511
            EE EEE   E   E  T    ++T+ N     T P
Sbjct: 181 GEEGEEESVTEAEAEGTTVAGPTTTSPNGGFQPTTP 216

Bone sialoprotein (BSP) is a major structural protein of the bone matrix that is specifically expressed by fully-differentiated osteoblasts. The expression of bone sialoprotein (BSP) is normally restricted to mineralised connective tissues of bones and teeth where it has been associated with mineral crystal formation. However, it has been found that ectopic expression of BSP occurs in various lesions, including oral and extraoral carcinomas, in which it has been associated with the formation of microcrystalline deposits and the metastasis of cancer cells to bone. Length = 291

>gnl|CDD|237622 PRK14140, PRK14140, heat shock protein GrpE; Provisional

 Score = 43.8 bits (104), Expect = 8e-05
 Identities = 21/42 (50%), Positives = 25/42 (59%)

Query: 455 EEYDSSEEEEEEEEDEEEEEEEEEEEEEEEEEEGEEEETETA 496
           E+ +  EEE EE E EE  E+E EEE  EEE E E  + E A
Sbjct: 3   EKNEQVEEEVEETEVEEAVEDEVEEETVEEESEAELLDEEQA 44

Length = 191

>gnl|CDD|224969 COG2058, RPP1A, Ribosomal protein L12E/L44/L45/RPP1/RPP2 [Translation, ribosomal structure and biogenesis]

 Score = 42.4 bits (100), Expect = 8e-05
 Identities = 14/31 (45%), Positives = 20/31 (64%)

Query: 458 DSSEEEEEEEEDEEEEEEEEEEEEEEEEEEG 488
            ++  E   E DE EEEE+EEE EEE +++ 
Sbjct: 73  AAAGAEAAAEADEAEEEEKEEEAEEESDDDM 103

Length = 109

>gnl|CDD|179712 PRK04019, rplP0, acidic ribosomal protein P0; Validated

 Score = 45.2 bits (108), Expect = 8e-05
 Identities = 18/46 (39%), Positives = 26/46 (56%)

Query: 443 SEYEDSDFDTSDEEYDSSEEEEEEEEDEEEEEEEEEEEEEEEEEEG 488
           ++ +  D +  +     ++    EEE+EEEEEEEEEE  EEE   G
Sbjct: 279 ADKDALDEELKEVLSAQAQAAAAEEEEEEEEEEEEEEPSEEEAAAG 324

Length = 330

>gnl|CDD|145949 pfam03066, Nucleoplasmin, Nucleoplasmin

 Score = 43.1 bits (102), Expect = 9e-05
 Identities = 16/30 (53%), Positives = 22/30 (73%)

Query: 222 TSDEEYDSSEEEEEEEDEEEEEEEEEGEEE 251
             DE  D  E+EEEE+DEE+++E+E  EEE
Sbjct: 110 EEDESDDDEEDEEEEDDEEDDDEDESEEEE 139

Nucleoplasmins are also known as chromatin decondensation proteins. They bind to core histones and transfer DNA to them in a reaction that requires ATP. This is thought to play a role in the assembly of regular nucleosomal arrays. Length = 146

>gnl|CDD|130712 TIGR01651, CobT, cobaltochelatase, CobT subunit

 Score = 45.7 bits (108), Expect = 9e-05
 Identities = 20/65 (30%), Positives = 37/65 (56%), Gaps = 4/65 (6%)

Query: 448 SDFDTSDEEYDSSEEEEEEEEDEEEEEEEEEEEEEEEEEEGEE----EETETASSSTAKN 503
              + ++E  D +E E+EE+ D+++  E E+EE+ E E EG+E    +E+E     +   
Sbjct: 195 RSMELAEEMGDDTESEDEEDGDDDQPTENEQEEQGEGEGEGQEGSAPQESEATDRESESG 254

Query: 504 DPQMV 508
           + +MV
Sbjct: 255 EEEMV 259

This model describes Pseudomonas denitrificans CobT gene product, which is a cobalt chelatase subunit that functions in cobalamin biosynthesis. Cobalamin (vitamin B12) can be synthesized via several pathways, including an aerobic pathway (found in Pseudomonas denitrificans) and an anaerobic pathway (found in P. shermanii and Salmonella typhimurium). These pathways differ in the point of cobalt insertion during corrin ring formation. There are apparently a number of variations on these two pathways, where the major differences seem to be concerned with the process of ring contraction. Confusion regarding the functions of enzymes found in the aerobic vs. anaerobic pathways has arisen because nonhomologous genes in these different pathways were given the same gene symbols. Thus, cobT in the aerobic pathway (P. denitrificans) is not a homolog of cobT in the anaerobic pathway (S. typhimurium). It should be noted that E. coli synthesizes cobalamin only when it is supplied with the precursor cobinamide, which is a complex intermediate. Additionally, all E. coli cobalamin synthesis genes (cobU, cobS and cobT) were named after their Salmonella typhimurium homologs which function in the anaerobic cobalamin synthesis pathway. This model describes the aerobic cobalamin pathway Pseudomonas denitrificans CobT gene product, which is a cobalt chelatase subunit, with a MW ~70 kDa. The aerobic pathway cobalt chelatase is a heterotrimeric, ATP-dependent enzyme that catalyzes cobalt insertion during cobalamin biosynthesis. The other two subunits are the P. denitrificans CobS (TIGR01650) and CobN (pfam02514 CobN/Magnesium Chelatase) proteins. To avoid potential confusion with the nonhomologous Salmonella typhimurium/E.coli cobT gene product, the P. denitrificans gene symbol is not used in the name of this model [Biosynthesis of cofactors, prosthetic groups, and carriers, Heme, porphyrin, and cobalamin]. Length = 600

>gnl|CDD|235640 PRK05901, PRK05901, RNA polymerase sigma factor; Provisional

 Score = 45.4 bits (108), Expect = 9e-05
 Identities = 16/58 (27%), Positives = 38/58 (65%)

Query: 437 NARNGDSEYEDSDFDTSDEEYDSSEEEEEEEEDEEEEEEEEEEEEEEEEEEGEEEETE 494
            A + D + +D D D  D + D  +E+++E++D+++ ++E+EE++E +E E   ++ +
Sbjct: 129 QADDDDDDDDDDDLDDDDIDDDDDDEDDDEDDDDDDVDDEDEEKKEAKELEKLSDDDD 186

Length = 509

>gnl|CDD|218538 pfam05285, SDA1, SDA1

 Score = 44.3 bits (105), Expect = 1e-04
 Identities = 16/55 (29%), Positives = 28/55 (50%)

Query: 444 EYEDSDFDTSDEEYDSSEEEEEEEEDEEEEEEEEEEEEEEEEEEGEEEETETASS 498
           E    +     E     E +++++E+EE E EE+E+ ++E E    E + E  SS
Sbjct: 76  EKWKEEERKKKEAEQGLESDDDDDEEEEWEVEEDEDSDDEGEWIDVESDKEIESS 130

This family consists of several SDA1 protein homologues. SDA1 is a Saccharomyces cerevisiae protein which is involved in the control of the actin cytoskeleton. The protein is essential for cell viability and is localised in the nucleus. Length = 317

>gnl|CDD|217829 pfam03985, Paf1, Paf1

 Score = 45.1 bits (107), Expect = 1e-04
 Identities = 18/48 (37%), Positives = 25/48 (52%)

Query: 218 SDFDTSDEEYDSSEEEEEEEDEEEEEEEEEGEEEETETASSSTAKNDP 265
           +  D  D E    +E+EEEE   +E EEEEGE+ E E + S    +  
Sbjct: 360 ARLDPIDFEEVDEDEDEEEEQRSDEHEEEEGEDSEEEGSQSREDGSSE 407

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|217450 pfam03247, Prothymosin, Prothymosin/parathymosin family

 Score = 41.9 bits (98), Expect = 1e-04
 Identities = 24/67 (35%), Positives = 39/67 (58%), Gaps = 3/67 (4%)

Query: 431 NHNRRWNARNGDSEYEDSDFDTSDEEYDSSEEEEEEEEDEEEEEEEEEE---EEEEEEEE 487
           N N    A+ GD E E+ +    D+E +  E EEEE E+EEE E    +   E+EE++ E
Sbjct: 37  NENEENGAQEGDDEMEEEEEVDEDDEEEEGEGEEEEGEEEEETEGATGKRAAEDEEDDAE 96

Query: 488 GEEEETE 494
            ++++T+
Sbjct: 97  TKKQKTD 103

Prothymosin alpha and parathymosin are two ubiquitous small acidic nuclear proteins that are thought to be involved in cell cycle progression, proliferation, and cell differentiation. Length = 106

>gnl|CDD|218737 pfam05764, YL1, YL1 nuclear protein

 Score = 43.9 bits (104), Expect = 1e-04
 Identities = 16/53 (30%), Positives = 31/53 (58%), Gaps = 2/53 (3%)

Query: 436 WNARNGDSEYEDSDFDTSDEEYDS-SEEEEEEEEDEEEEEEEEEEEEEEEEEE 487
           +     D E+E  + +  +EE DS  ++ E++E + ++EEE E+E + EE  +
Sbjct: 34  FEEEEDDEEFEIEE-EEEEEEVDSDFDDSEDDEPESDDEEEGEKELQREERLK 85

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|218737 pfam05764, YL1, YL1 nuclear protein

 Score = 43.9 bits (104), Expect = 1e-04
 Identities = 17/47 (36%), Positives = 27/47 (57%), Gaps = 3/47 (6%)

Query: 211 GDSEYEDSDFDTSDEE---YDSSEEEEEEEDEEEEEEEEEGEEEETE 254
            D E+E  + +  +E    +D SE++E E D+EEE E+E   EE  +
Sbjct: 39  DDEEFEIEEEEEEEEVDSDFDDSEDDEPESDDEEEGEKELQREERLK 85

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|218223 pfam04712, Radial_spoke, Radial spokehead-like protein

 Score = 45.1 bits (107), Expect = 1e-04
 Identities = 18/33 (54%), Positives = 22/33 (66%)

Query: 454 DEEYDSSEEEEEEEEDEEEEEEEEEEEEEEEEE 486
           + E    EEE+E+EE+EEEEEE EE E EE   
Sbjct: 343 NPEQKDEEEEQEDEEEEEEEEEPEEPEPEEGPP 375

This family includes the radial spoke head proteins RSP4 and RSP6 from Chlamydomonas reinhardtii, and several eukaryotic homologues, including mammalian RSHL1, the protein product of a familial ciliary dyskinesia candidate gene. Length = 481

>gnl|CDD|148051 pfam06213, CobT, Cobalamin biosynthesis protein CobT

 Score = 44.4 bits (105), Expect = 1e-04
 Identities = 18/49 (36%), Positives = 35/49 (71%), Gaps = 2/49 (4%)

Query: 458 DSSEE--EEEEEEDEEEEEEEEEEEEEEEEEEGEEEETETASSSTAKND 504
           D +EE  +E E  D E+ E+E++ +E+E++++GEEEE+ ++ S +  +D
Sbjct: 207 DMAEELGDEPESADSEDNEDEDDPKEDEDDDQGEEEESGSSDSLSEDSD 255

This family consists of several bacterial cobalamin biosynthesis (CobT) proteins. CobT is involved in the transformation of precorrin-3 into cobyrinic acid. Length = 282

>gnl|CDD|148051 pfam06213, CobT, Cobalamin biosynthesis protein CobT

 Score = 44.0 bits (104), Expect = 1e-04
 Identities = 24/72 (33%), Positives = 32/72 (44%), Gaps = 7/72 (9%)

Query: 200 AKHLGIIKSSNGDSEYEDSDFDTSDEEYDSSEEEEE-------EEDEEEEEEEEEGEEEE 252
           A+ LG    S    + ED D    DE+ D  EEEE        E+ +   EE E GE E 
Sbjct: 209 AEELGDEPESADSEDNEDEDDPKEDEDDDQGEEEESGSSDSLSEDSDASSEEMESGEMEA 268

Query: 253 TETASSSTAKND 264
            E ++  T  +D
Sbjct: 269 AEASADDTPDSD 280

This family consists of several bacterial cobalamin biosynthesis (CobT) proteins. CobT is involved in the transformation of precorrin-3 into cobyrinic acid. Length = 282

>gnl|CDD|185603 PTZ00415, PTZ00415, transmission-blocking target antigen s230; Provisional

 Score = 45.8 bits (108), Expect = 1e-04
 Identities = 17/52 (32%), Positives = 33/52 (63%)

Query: 454 DEEYDSSEEEEEEEEDEEEEEEEEEEEEEEEEEEGEEEETETASSSTAKNDP 505
            EE  S  +    ++D+E+E+E++++EE++EEEE EEEE +       +++ 
Sbjct: 141 AEEDMSPRDNFVIDDDDEDEDEDDDDEEDDEEEEEEEEEIKGFDDEDEEDEG 192

Length = 2849

>gnl|CDD|234311 TIGR03685, L12P_arch, 50S ribosomal protein L12P

 Score = 41.6 bits (98), Expect = 1e-04
 Identities = 18/25 (72%), Positives = 18/25 (72%)

Query: 468 EDEEEEEEEEEEEEEEEEEEGEEEE 492
                EEEEEEEEEEEEEEE  EEE
Sbjct: 71  AAAAAEEEEEEEEEEEEEEEESEEE 95

This model represents the L12P protein of the large (50S) subunit of the archaeal ribosome. Length = 105

>gnl|CDD|203043 pfam04546, Sigma70_ner, Sigma-70, non-essential region

 Score = 43.7 bits (104), Expect = 1e-04
 Identities = 10/39 (25%), Positives = 25/39 (64%)

Query: 458 DSSEEEEEEEEDEEEEEEEEEEEEEEEEEEGEEEETETA 496
            ++      E + +EE+ E++++++E+E+E +EEE +  
Sbjct: 36  AAAATAAAIESELDEEDLEDDDDDDEDEDEDDEEEADLG 74

The domain is found in the primary vegetative sigma factor. The function of this domain is unclear and can be removed without loss of function. Length = 211

>gnl|CDD|203043 pfam04546, Sigma70_ner, Sigma-70, non-essential region

 Score = 43.7 bits (104), Expect = 1e-04
 Identities = 11/49 (22%), Positives = 24/49 (48%), Gaps = 2/49 (4%)

Query: 460 SEEEEEEEEDEEEEEEEEEEEEEEEEEEGEEEETETASSSTAKNDPQMV 508
           +          E E +EE+ E++++++E E+E+ E  +      DP+  
Sbjct: 34  AAAAAATAAAIESELDEEDLEDDDDDDEDEDEDDEEEADLGP--DPEEA 80

The domain is found in the primary vegetative sigma factor. The function of this domain is unclear and can be removed without loss of function. Length = 211

>gnl|CDD|203043 pfam04546, Sigma70_ner, Sigma-70, non-essential region

 Score = 43.7 bits (104), Expect = 1e-04
 Identities = 10/44 (22%), Positives = 28/44 (63%)

Query: 449 DFDTSDEEYDSSEEEEEEEEDEEEEEEEEEEEEEEEEEEGEEEE 492
           D + +     ++  E E +E++ E++++++E+E+E++EE  +  
Sbjct: 31  DPNAAAAAATAAAIESELDEEDLEDDDDDDEDEDEDDEEEADLG 74

The domain is found in the primary vegetative sigma factor. The function of this domain is unclear and can be removed without loss of function. Length = 211

>gnl|CDD|218333 pfam04931, DNA_pol_phi, DNA polymerase phi

 Score = 45.6 bits (108), Expect = 1e-04
 Identities = 18/61 (29%), Positives = 30/61 (49%)

Query: 430 MNHNRRWNARNGDSEYEDSDFDTSDEEYDSSEEEEEEEEDEEEEEEEEEEEEEEEEEEGE 489
           +  +   +      E E+ D D  +E  D  +E E  E+ E E E + E+ EE+E+E+  
Sbjct: 632 LKADENKSRHQQLFEGEEEDEDDLEETDDDEDECEAIEDSESESESDGEDGEEDEQEDDA 691

Query: 490 E 490
           E
Sbjct: 692 E 692

This family includes the fifth essential DNA polymerase in yeast EC:2.7.7.7. Pol5p is localised exclusively to the nucleolus and binds near or at the enhancer region of rRNA-encoding DNA repeating units. Length = 784

>gnl|CDD|217049 pfam02459, Adeno_terminal, Adenoviral DNA terminal protein

 Score = 45.0 bits (107), Expect = 1e-04
 Identities = 21/35 (60%), Positives = 22/35 (62%)

Query: 460 SEEEEEEEEDEEEEEEEEEEEEEEEEEEGEEEETE 494
                E EE+EEEEEE  EEEEEEEEEE    E E
Sbjct: 299 PPSPPEPEEEEEEEEEVPEEEEEEEEEEERTFEEE 333

This protein is covalently attached to the terminii of replicating DNA in vivo. Length = 548

>gnl|CDD|217203 pfam02724, CDC45, CDC45-like protein

 Score = 45.0 bits (107), Expect = 1e-04
 Identities = 17/57 (29%), Positives = 30/57 (52%)

Query: 210 NGDSEYEDSDFDTSDEEYDSSEEEEEEEDEEEEEEEEEGEEEETETASSSTAKNDPQ 266
           +GD E E  D    D+ Y   EE++++++E +EE+EE  + E+ E        +D  
Sbjct: 103 DGDIEEELQDEPRYDDAYRDLEEDDDDDEESDEEDEESSKSEDDEDDDDDDDDDDIA 159

CDC45 is an essential gene required for initiation of DNA replication in S. cerevisiae, forming a complex with MCM5/CDC46. Homologues of CDC45 have been identified in human, mouse and smut fungus among others. Length = 583

>gnl|CDD|100110 cd05832, Ribosomal_L12p, Ribosomal protein L12p

 Score = 41.7 bits (98), Expect = 1e-04
 Identities = 15/28 (53%), Positives = 22/28 (78%)

Query: 461 EEEEEEEEDEEEEEEEEEEEEEEEEEEG 488
               EE+ +E+EEE+++EEE+EEEEEE 
Sbjct: 71  AAAAEEKAEEKEEEKKKEEEKEEEEEEA 98

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|114172 pfam05432, BSP_II, Bone sialoprotein II (BSP-II)

 Score = 44.7 bits (105), Expect = 1e-04
 Identities = 19/51 (37%), Positives = 28/51 (54%)

Query: 451 DTSDEEYDSSEEEEEEEEDEEEEEEEEEEEEEEEEEEGEEEETETASSSTA 501
           D+S+E  D    EEE EE+   EEE  E+ +  E+EE E E T  ++ +  
Sbjct: 49  DSSEENGDGDSSEEEGEEETSNEEENNEDSDGNEDEEAEAENTTLSTVTLG 99

Bone sialoprotein (BSP) is a major structural protein of the bone matrix that is specifically expressed by fully-differentiated osteoblasts. The expression of bone sialoprotein (BSP) is normally restricted to mineralised connective tissues of bones and teeth where it has been associated with mineral crystal formation. However, it has been found that ectopic expression of BSP occurs in various lesions, including oral and extraoral carcinomas, in which it has been associated with the formation of microcrystalline deposits and the metastasis of cancer cells to bone. Length = 291

>gnl|CDD|179712 PRK04019, rplP0, acidic ribosomal protein P0; Validated

 Score = 44.5 bits (106), Expect = 1e-04
 Identities = 22/45 (48%), Positives = 27/45 (60%), Gaps = 3/45 (6%)

Query: 448 SDFDTSDEEY---DSSEEEEEEEEDEEEEEEEEEEEEEEEEEEGE 489
           +D D  DEE     S++ +    E+EEEEEEEEEEEE  EEE   
Sbjct: 279 ADKDALDEELKEVLSAQAQAAAAEEEEEEEEEEEEEEPSEEEAAA 323

Length = 330

>gnl|CDD|235640 PRK05901, PRK05901, RNA polymerase sigma factor; Provisional

 Score = 45.4 bits (108), Expect = 1e-04
 Identities = 17/65 (26%), Positives = 41/65 (63%), Gaps = 2/65 (3%)

Query: 442 DSEYEDSDFDTSDEEYDSSEEEEEEEEDEEEEEEEEEEEEE--EEEEEGEEEETETASSS 499
           D + +D D D  D++ D  E++++++ D+E+EE++E +E E   ++++   +E ++ +  
Sbjct: 139 DDDLDDDDIDDDDDDEDDDEDDDDDDVDDEDEEKKEAKELEKLSDDDDFVWDEDDSEALR 198

Query: 500 TAKND 504
            A+ D
Sbjct: 199 QARKD 203

Length = 509

>gnl|CDD|202096 pfam02029, Caldesmon, Caldesmon

 Score = 45.0 bits (106), Expect = 1e-04
 Identities = 21/61 (34%), Positives = 31/61 (50%)

Query: 446 EDSDFDTSDEEYDSSEEEEEEEEDEEEEEEEEEEEEEEEEEEGEEEETETASSSTAKNDP 505
           ++    ++D+         +E+   E E  EEEE+EE  EE  E EETE  + S  KND 
Sbjct: 82  KEFKPTSTDQSLSEPSRRMQEDSGAENETVEEEEKEESREEREEVEETEGVTKSEQKNDW 141

Query: 506 Q 506
           +
Sbjct: 142 R 142

Length = 431

>gnl|CDD|235549 PRK05658, PRK05658, RNA polymerase sigma factor RpoD; Validated

 Score = 45.2 bits (108), Expect = 1e-04
 Identities = 15/47 (31%), Positives = 20/47 (42%), Gaps = 2/47 (4%)

Query: 459 SSEEEEEEEEDEEEEEEEEEEEEEEEEEEGEEEETETASSSTAKNDP 505
               +   EED      E EE +++E+E  EEEE E   S  A    
Sbjct: 171 DGFVDPNAEEDPAHVGSELEELDDDEDE--EEEEDENDDSLAADESE 215

Length = 619

>gnl|CDD|223003 PHA03169, PHA03169, hypothetical protein; Provisional

 Score = 45.0 bits (106), Expect = 1e-04
 Identities = 12/59 (20%), Positives = 22/59 (37%), Gaps = 4/59 (6%)

Query: 451 DTSDEEYDSSEEEEEEEEDEEEEEEEEEE----EEEEEEEEGEEEETETASSSTAKNDP 505
               E ++ S  ++     +   E+  EE      E E +     ++ET +SS     P
Sbjct: 149 PAPPESHNPSPNQQPSSFLQPSHEDSPEEPEPPTSEPEPDSPGPPQSETPTSSPPPQSP 207

Length = 413

>gnl|CDD|115071 pfam06390, NESP55, Neuroendocrine-specific golgi protein P55 (NESP55)

 Score = 44.1 bits (103), Expect = 1e-04
 Identities = 34/136 (25%), Positives = 56/136 (41%), Gaps = 18/136 (13%)

Query: 383 IGDILAKSFKWIYAKCCLCRGCPTRPRDLQKTIQDTTGAYNRRRSSAMNHNRRWNARNG- 441
           IG   A +  W+     L R   +     Q+       A  +RRS    H+R   A    
Sbjct: 24  IGRRAATALLWLSCSIALLRALASSNARAQQR------AAAQRRSFLNAHHRSAAAAAAA 77

Query: 442 ---------DSEYEDSDFDTS--DEEYDSSEEEEEEEEDEEEEEEEEEEEEEEEEEEGEE 490
                    +S++ED DF+      E    +E++ + E + E E E + E E E E   E
Sbjct: 78  QVFPEPSEPESDHEDEDFEPELARPECLEYDEDDFDTETDSETEPESDIESETEFETEPE 137

Query: 491 EETETASSSTAKNDPQ 506
            E +TA ++  + +P+
Sbjct: 138 TEPDTAPTTEPETEPE 153

This family consists of several mammalian neuroendocrine-specific golgi protein P55 (NESP55) sequences. NESP55 is a novel member of the chromogranin family and is a soluble, acidic, heat-stable secretory protein that is expressed exclusively in endocrine and nervous tissues, although less widely than chromogranins. Length = 261

>gnl|CDD|217503 pfam03344, Daxx, Daxx Family

 Score = 44.9 bits (106), Expect = 2e-04
 Identities = 22/66 (33%), Positives = 31/66 (46%)

Query: 442 DSEYEDSDFDTSDEEYDSSEEEEEEEEDEEEEEEEEEEEEEEEEEEGEEEETETASSSTA 501
           + E E+ +   S+EE    EEEEEE E +   EEE E   E + +  E EE     +S  
Sbjct: 451 EEEEEEEEEQESEEEEGEDEEEEEEVEADNGSEEEMEGSSEGDGDGEEPEEDAERRNSEM 510

Query: 502 KNDPQM 507
               +M
Sbjct: 511 AGISRM 516

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|217450 pfam03247, Prothymosin, Prothymosin/parathymosin family

 Score = 40.7 bits (95), Expect = 2e-04
 Identities = 25/59 (42%), Positives = 35/59 (59%), Gaps = 1/59 (1%)

Query: 207 KSSNGDSEYEDSDFDTSDEEYDSSEEEEEEEDEEEEEEEEEG-EEEETETASSSTAKND 264
             +NG+   E+   +  DE  +  E +E++E+EE E EEEEG EEEETE A+   A  D
Sbjct: 32  APANGNENEENGAQEGDDEMEEEEEVDEDDEEEEGEGEEEEGEEEEETEGATGKRAAED 90

Prothymosin alpha and parathymosin are two ubiquitous small acidic nuclear proteins that are thought to be involved in cell cycle progression, proliferation, and cell differentiation. Length = 106

>gnl|CDD|221490 pfam12253, CAF1A, Chromatin assembly factor 1 subunit A

 Score = 39.9 bits (94), Expect = 2e-04
 Identities = 16/36 (44%), Positives = 26/36 (72%), Gaps = 1/36 (2%)

Query: 217 DSDFDTSDEEYDSSEEEEEEEDEEEEEEEEEGEEEE 252
           D D+D SD E++  EE E+ E E+EE+EEE+ +++ 
Sbjct: 39  DYDYD-SDAEWEEEEEGEDLESEDEEDEEEDDDDDM 73

The CAF-1 or chromatin assembly factor-1 consists of three subunits, and this is the first, or A. The A domain is uniquely required for the progression of S phase in mouse cells, independent of its ability to promote histone deposition but dependent on its ability to interact with HP1 - heterochromatin protein 1-rich heterochromatin domains next to centromeres that are crucial for chromosome segregation during mitosis. This HP1-CAF-1 interaction module functions as a built-in replication control for heterochromatin, which, like a control barrier, has an impact on S-phase progression in addition to DNA-based checkpoints. Length = 76

>gnl|CDD|145949 pfam03066, Nucleoplasmin, Nucleoplasmin

 Score = 41.9 bits (99), Expect = 2e-04
 Identities = 14/38 (36%), Positives = 27/38 (71%)

Query: 465 EEEEDEEEEEEEEEEEEEEEEEEGEEEETETASSSTAK 502
            EE++ +++EE+EEEE++EE+++ +E E E +     K
Sbjct: 109 SEEDESDDDEEDEEEEDDEEDDDEDESEEEESPVKKVK 146

Nucleoplasmins are also known as chromatin decondensation proteins. They bind to core histones and transfer DNA to them in a reaction that requires ATP. This is thought to play a role in the assembly of regular nucleosomal arrays. Length = 146

>gnl|CDD|218223 pfam04712, Radial_spoke, Radial spokehead-like protein

 Score = 44.3 bits (105), Expect = 2e-04
 Identities = 19/30 (63%), Positives = 23/30 (76%)

Query: 466 EEEDEEEEEEEEEEEEEEEEEEGEEEETET 495
             E ++EEEE+E+EEEEEEEEE EE E E 
Sbjct: 343 NPEQKDEEEEQEDEEEEEEEEEPEEPEPEE 372

This family includes the radial spoke head proteins RSP4 and RSP6 from Chlamydomonas reinhardtii, and several eukaryotic homologues, including mammalian RSHL1, the protein product of a familial ciliary dyskinesia candidate gene. Length = 481

>gnl|CDD|148051 pfam06213, CobT, Cobalamin biosynthesis protein CobT

 Score = 44.0 bits (104), Expect = 2e-04
 Identities = 13/57 (22%), Positives = 31/57 (54%)

Query: 454 DEEYDSSEEEEEEEEDEEEEEEEEEEEEEEEEEEGEEEETETASSSTAKNDPQMVTV 510
           + E   SE+ E+E++ +E+E++++ EEEE    +   E+++ +S      + +    
Sbjct: 215 EPESADSEDNEDEDDPKEDEDDDQGEEEESGSSDSLSEDSDASSEEMESGEMEAAEA 271

This family consists of several bacterial cobalamin biosynthesis (CobT) proteins. CobT is involved in the transformation of precorrin-3 into cobyrinic acid. Length = 282

>gnl|CDD|217861 pfam04050, Upf2, Up-frameshift suppressor 2

 Score = 42.4 bits (100), Expect = 2e-04
 Identities = 17/54 (31%), Positives = 30/54 (55%)

Query: 458 DSSEEEEEEEEDEEEEEEEEEEEEEEEEEEGEEEETETASSSTAKNDPQMVTVP 511
             SE E ++ E++EE  EE+E++E  +EEE +  + E    S ++ +   VT  
Sbjct: 1   SGSESESDDGEEDEELPEEDEDDESSDEEEVDLPDDEQDEESDSEEEQIFVTRQ 54

Transcripts harbouring premature signals for translation termination are recognised and rapidly degraded by eukaryotic cells through a pathway known as nonsense-mediated mRNA decay. In Saccharomyces cerevisiae, three trans-acting factors (Upf1 to Upf3) are required for nonsense-mediated mRNA decay. Length = 171

>gnl|CDD|217861 pfam04050, Upf2, Up-frameshift suppressor 2

 Score = 42.4 bits (100), Expect = 2e-04
 Identities = 20/62 (32%), Positives = 35/62 (56%), Gaps = 5/62 (8%)

Query: 451 DTSDEEYDSSEEEEE--EEEDEEEEEEEEEEEEEEEEEEGE---EEETETASSSTAKNDP 505
             S+ E D  EE+EE  EE++++E  +EEE +  ++E++ E   EEE    +    + DP
Sbjct: 1   SGSESESDDGEEDEELPEEDEDDESSDEEEVDLPDDEQDEESDSEEEQIFVTRQEEEVDP 60

Query: 506 QM 507
           + 
Sbjct: 61  EA 62

Transcripts harbouring premature signals for translation termination are recognised and rapidly degraded by eukaryotic cells through a pathway known as nonsense-mediated mRNA decay. In Saccharomyces cerevisiae, three trans-acting factors (Upf1 to Upf3) are required for nonsense-mediated mRNA decay. Length = 171

>gnl|CDD|240329 PTZ00248, PTZ00248, eukaryotic translation initiation factor 2 subunit 1; Provisional

 Score = 43.9 bits (104), Expect = 2e-04
 Identities = 21/40 (52%), Positives = 29/40 (72%)

Query: 455 EEYDSSEEEEEEEEDEEEEEEEEEEEEEEEEEEGEEEETE 494
           EE     EEEEEE+D  E E+E+EE+E+EEEEE ++E  +
Sbjct: 280 EELLEKAEEEEEEDDYSESEDEDEEDEDEEEEEDDDEGDK 319

Length = 319

>gnl|CDD|240329 PTZ00248, PTZ00248, eukaryotic translation initiation factor 2 subunit 1; Provisional

 Score = 43.5 bits (103), Expect = 2e-04
 Identities = 15/47 (31%), Positives = 30/47 (63%)

Query: 441 GDSEYEDSDFDTSDEEYDSSEEEEEEEEDEEEEEEEEEEEEEEEEEE 487
           G  E +  +     EE +  ++  E E+++EE+E+EEEEE+++E ++
Sbjct: 273 GGDEEDLEELLEKAEEEEEEDDYSESEDEDEEDEDEEEEEDDDEGDK 319

Length = 319

>gnl|CDD|215774 pfam00183, HSP90, Hsp90 protein

 Score = 44.4 bits (105), Expect = 2e-04
 Identities = 19/37 (51%), Positives = 27/37 (72%)

Query: 459 SSEEEEEEEEDEEEEEEEEEEEEEEEEEEGEEEETET 495
             +E E+E  DEEEEEE+EE++EEEE+   +EEE + 
Sbjct: 27  VEKEVEKEVPDEEEEEEKEEKKEEEEKTTDKEEEVDE 63

Length = 529

>gnl|CDD|203043 pfam04546, Sigma70_ner, Sigma-70, non-essential region

 Score = 42.9 bits (102), Expect = 2e-04
 Identities = 14/49 (28%), Positives = 29/49 (59%)

Query: 442 DSEYEDSDFDTSDEEYDSSEEEEEEEEDEEEEEEEEEEEEEEEEEEGEE 490
           D     +    +  E +  EE+ E+++D++E+E+E++EEE +   + EE
Sbjct: 31  DPNAAAAAATAAAIESELDEEDLEDDDDDDEDEDEDDEEEADLGPDPEE 79

The domain is found in the primary vegetative sigma factor. The function of this domain is unclear and can be removed without loss of function. Length = 211

>gnl|CDD|117592 pfam09026, Cenp-B_dimeris, Centromere protein B dimerisation domain

 Score = 40.9 bits (95), Expect = 2e-04
 Identities = 13/32 (40%), Positives = 28/32 (87%)

Query: 455 EEYDSSEEEEEEEEDEEEEEEEEEEEEEEEEE 486
           EE   S+ +EEE++D+E+EE+++E+++E+++E
Sbjct: 9   EEDSDSDSDEEEDDDDEDEEDDDEDDDEDDDE 40

The centromere protein B (CENP-B) dimerisation domain is composed of two alpha-helices, which are folded into an antiparallel configuration. Dimerisation of CENP-B is mediated by this domain, in which monomers dimerise to form a symmetrical, antiparallel, four-helix bundle structure with a large hydrophobic patch in which 23 residues of one monomer form van der Waals contacts with the other monomer. This CENP-B dimer configuration may be suitable for capturing two distant CENP-B boxes during centromeric heterochromatin formation. Length = 101

>gnl|CDD|218303 pfam04874, Mak16, Mak16 protein C-terminal region

 Score = 41.0 bits (96), Expect = 2e-04
 Identities = 19/39 (48%), Positives = 27/39 (69%)

Query: 454 DEEYDSSEEEEEEEEDEEEEEEEEEEEEEEEEEEGEEEE 492
            EE + ++EEEEEEE+EE+E E E   ++EE EE  E+ 
Sbjct: 57  AEESEENDEEEEEEEEEEDEGEIEYVSDDEELEEEIEDL 95

The precise function of this eukaryotic protein family is unknown. The yeast orthologues have been implicated in cell cycle progression and biogenesis of 60S ribosomal subunits. The Schistosoma mansoni Mak16 has been shown to target protein transport to the nucleolus. Length = 97

>gnl|CDD|218303 pfam04874, Mak16, Mak16 protein C-terminal region

 Score = 41.0 bits (96), Expect = 2e-04
 Identities = 22/46 (47%), Positives = 29/46 (63%)

Query: 447 DSDFDTSDEEYDSSEEEEEEEEDEEEEEEEEEEEEEEEEEEGEEEE 492
            S F  + E  +S E +EEEEE+EEEE+E E E   ++EE  EE E
Sbjct: 48  QSAFKKALEAEESEENDEEEEEEEEEEDEGEIEYVSDDEELEEEIE 93

The precise function of this eukaryotic protein family is unknown. The yeast orthologues have been implicated in cell cycle progression and biogenesis of 60S ribosomal subunits. The Schistosoma mansoni Mak16 has been shown to target protein transport to the nucleolus. Length = 97

>gnl|CDD|218303 pfam04874, Mak16, Mak16 protein C-terminal region

 Score = 41.0 bits (96), Expect = 2e-04
 Identities = 18/38 (47%), Positives = 25/38 (65%)

Query: 454 DEEYDSSEEEEEEEEDEEEEEEEEEEEEEEEEEEGEEE 491
           + E +  EEEEEEEE++E E E   ++EE EEE  + E
Sbjct: 59  ESEENDEEEEEEEEEEDEGEIEYVSDDEELEEEIEDLE 96

The precise function of this eukaryotic protein family is unknown. The yeast orthologues have been implicated in cell cycle progression and biogenesis of 60S ribosomal subunits. The Schistosoma mansoni Mak16 has been shown to target protein transport to the nucleolus. Length = 97

>gnl|CDD|220102 pfam09073, BUD22, BUD22

 Score = 44.4 bits (105), Expect = 2e-04
 Identities = 20/93 (21%), Positives = 33/93 (35%), Gaps = 13/93 (13%)

Query: 434 RRWNARNGDSEYEDSDFDTSDEEYDSSEEEEEEEEDEEEEEEEEEEEEEEEEEEGEEEET 493
            +++    DS  E+   +     Y+    E E +E + E  E     + EE     ++  
Sbjct: 205 SQYDGMLVDSSDEEEGEEAPSINYNEDTSESESDESDSEISESRSVSDSEESSPPSKKPK 264

Query: 494 ETASSSTAKNDPQMVTVPITLCLMIMVGYIYGG 526
           E  +SST    P +           M GY  G 
Sbjct: 265 EKKTSST--FLPSL-----------MGGYFSGS 284

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|217840 pfam04006, Mpp10, Mpp10 protein

 Score = 44.6 bits (105), Expect = 2e-04
 Identities = 24/67 (35%), Positives = 36/67 (53%)

Query: 442 DSEYEDSDFDTSDEEYDSSEEEEEEEEDEEEEEEEEEEEEEEEEEEGEEEETETASSSTA 501
           D   ED   D  DE    +E E   E+  ++E E++EE++ EEEE GEE+E+   ++   
Sbjct: 124 DESLEDEMIDDEDEADLFNESESSLEDLSDDETEDDEEKKMEEEEAGEEKESVEQATREK 183

Query: 502 KNDPQMV 508
           K D   V
Sbjct: 184 KFDKSGV 190

This family includes proteins related to Mpp10 (M phase phosphoprotein 10). The U3 small nucleolar ribonucleoprotein (snoRNP) is required for three cleavage events that generate the mature 18S rRNA from the pre-rRNA. In Saccharomyces cerevisiae, depletion of Mpp10, a U3 snoRNP-specific protein, halts 18S rRNA production and impairs cleavage at the three U3 snoRNP-dependent sites. Length = 613

>gnl|CDD|224969 COG2058, RPP1A, Ribosomal protein L12E/L44/L45/RPP1/RPP2 [Translation, ribosomal structure and biogenesis]

 Score = 40.8 bits (96), Expect = 2e-04
 Identities = 13/31 (41%), Positives = 19/31 (61%)

Query: 458 DSSEEEEEEEEDEEEEEEEEEEEEEEEEEEG 488
            ++   E   E +E EEEE+EEE EEE ++ 
Sbjct: 72  AAAAGAEAAAEADEAEEEEKEEEAEEESDDD 102

Length = 109

>gnl|CDD|235640 PRK05901, PRK05901, RNA polymerase sigma factor; Provisional

 Score = 44.6 bits (106), Expect = 2e-04
 Identities = 15/69 (21%), Positives = 37/69 (53%)

Query: 442 DSEYEDSDFDTSDEEYDSSEEEEEEEEDEEEEEEEEEEEEEEEEEEGEEEETETASSSTA 501
           D + +  D D  D++ D  ++E+++++D ++E+EE++E +E E+   +++       S A
Sbjct: 137 DDDDDLDDDDIDDDDDDEDDDEDDDDDDVDDEDEEKKEAKELEKLSDDDDFVWDEDDSEA 196

Query: 502 KNDPQMVTV 510
               +    
Sbjct: 197 LRQARKDAK 205

Length = 509

>gnl|CDD|235640 PRK05901, PRK05901, RNA polymerase sigma factor; Provisional

 Score = 44.2 bits (105), Expect = 2e-04
 Identities = 15/69 (21%), Positives = 39/69 (56%)

Query: 436 WNARNGDSEYEDSDFDTSDEEYDSSEEEEEEEEDEEEEEEEEEEEEEEEEEEGEEEETET 495
            +  N   + +D D D   ++ D  +++++E++DE++++++ ++E+EE++E  E E+   
Sbjct: 124 IDVLNQADDDDDDDDDDDLDDDDIDDDDDDEDDDEDDDDDDVDDEDEEKKEAKELEKLSD 183

Query: 496 ASSSTAKND 504
                   D
Sbjct: 184 DDDFVWDED 192

Length = 509

>gnl|CDD|202096 pfam02029, Caldesmon, Caldesmon

 Score = 43.9 bits (103), Expect = 2e-04
 Identities = 17/86 (19%), Positives = 34/86 (39%), Gaps = 2/86 (2%)

Query: 409 RDLQKTIQDTTGAYNRRRSSAMNHNRRWNARNGDSEYEDSDFDTSDEEYDSSEEEEEEEE 468
                T Q  +     RR    +          + E    + +  +E    ++ E++ + 
Sbjct: 84  FKPTSTDQSLSEP--SRRMQEDSGAENETVEEEEKEESREEREEVEETEGVTKSEQKNDW 141

Query: 469 DEEEEEEEEEEEEEEEEEEGEEEETE 494
            + EE ++EE+E E EEEE  +  + 
Sbjct: 142 RDAEECQKEEKEPEPEEEEKPKRGSL 167

Length = 431

>gnl|CDD|223003 PHA03169, PHA03169, hypothetical protein; Provisional

 Score = 44.6 bits (105), Expect = 2e-04
 Identities = 10/67 (14%), Positives = 19/67 (28%), Gaps = 1/67 (1%)

Query: 441 GDSEYEDSDFDTSDEEYDSSEEEEEEEEDEEEEEEEEEEEEEEEEEEGEE-EETETASSS 499
             SE E         E  +S    +   DE  E +    ++       +  E  +  +  
Sbjct: 181 PTSEPEPDSPGPPQSETPTSSPPPQSPPDEPGEPQSPTPQQAPSPNTQQAVEHEDEPTEP 240

Query: 500 TAKNDPQ 506
             +  P 
Sbjct: 241 EREGPPF 247

Length = 413

>gnl|CDD|223003 PHA03169, PHA03169, hypothetical protein; Provisional

 Score = 44.2 bits (104), Expect = 2e-04
 Identities = 14/60 (23%), Positives = 20/60 (33%)

Query: 438 ARNGDSEYEDSDFDTSDEEYDSSEEEEEEEEDEEEEEEEEEEEEEEEEEEGEEEETETAS 497
           +  G  E    +          S   +   ED  EE E    E E +     + ET T+S
Sbjct: 142 SHPGPHEPAPPESHNPSPNQQPSSFLQPSHEDSPEEPEPPTSEPEPDSPGPPQSETPTSS 201

Length = 413

>gnl|CDD|235250 PRK04195, PRK04195, replication factor C large subunit; Provisional

 Score = 44.5 bits (106), Expect = 2e-04
 Identities = 24/50 (48%), Positives = 36/50 (72%)

Query: 451 DTSDEEYDSSEEEEEEEEDEEEEEEEEEEEEEEEEEEGEEEETETASSST 500
           +   + +   ++EEEEEE++E++EEE+EEEEEE EEE EEEE +    +T
Sbjct: 429 EKKKKAFAGKKKEEEEEEEKEKKEEEKEEEEEEAEEEKEEEEEKKKKQAT 478

Length = 482

>gnl|CDD|221668 pfam12619, MCM2_N, Mini-chromosome maintenance protein 2

 Score = 42.3 bits (100), Expect = 2e-04
 Identities = 14/29 (48%), Positives = 24/29 (82%)

Query: 462 EEEEEEEDEEEEEEEEEEEEEEEEEEGEE 490
           E+E +EE+E E++ ++ +EE EEEE+GE+
Sbjct: 1   EDEPDEEEELEDDIDDLDEEAEEEEDGED 29

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|218258 pfam04774, HABP4_PAI-RBP1, Hyaluronan / mRNA binding family

 Score = 40.9 bits (96), Expect = 2e-04
 Identities = 19/45 (42%), Positives = 24/45 (53%)

Query: 451 DTSDEEYDSSEEEEEEEEDEEEEEEEEEEEEEEEEEEGEEEETET 495
           D   E  +   EEEE+ E EE++  EEE  +E   EE E EE E 
Sbjct: 32  DEIAELTEEQGEEEEKNEVEEKQAVEEEANKEGVVEEEEVEEEED 76

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|227701 COG5414, COG5414, TATA-binding protein-associated factor [Transcription]

 Score = 44.3 bits (104), Expect = 2e-04
 Identities = 19/54 (35%), Positives = 28/54 (51%)

Query: 441 GDSEYEDSDFDTSDEEYDSSEEEEEEEEDEEEEEEEEEEEEEEEEEEGEEEETE 494
           G +E E+ +    D+E    E E  E   EE + +  +E  EE+EE+ E EE E
Sbjct: 280 GAAEIENKEVSEGDKEQQQEEVENAEAHKEEVQSDRPDEIGEEKEEDDENEENE 333

Length = 392

>gnl|CDD|218538 pfam05285, SDA1, SDA1

 Score = 43.1 bits (102), Expect = 3e-04
 Identities = 16/61 (26%), Positives = 32/61 (52%), Gaps = 4/61 (6%)

Query: 208 SSNGDSEYEDSDFDTSDEEY----DSSEEEEEEEDEEEEEEEEEGEEEETETASSSTAKN 263
             + + E+E  + + SD+E       S++E E  D E+EEE++E  ++  E +    ++ 
Sbjct: 97  DDDEEEEWEVEEDEDSDDEGEWIDVESDKEIESSDSEDEEEKDEAAKKAKEDSDEELSEE 156

Query: 264 D 264
           D
Sbjct: 157 D 157

This family consists of several SDA1 protein homologues. SDA1 is a Saccharomyces cerevisiae protein which is involved in the control of the actin cytoskeleton. The protein is essential for cell viability and is localised in the nucleus. Length = 317

>gnl|CDD|148630 pfam07133, Merozoite_SPAM, Merozoite surface protein (SPAM)

 Score = 41.8 bits (98), Expect = 3e-04
 Identities = 17/62 (27%), Positives = 34/62 (54%)

Query: 442 DSEYEDSDFDTSDEEYDSSEEEEEEEEDEEEEEEEEEEEEEEEEEEGEEEETETASSSTA 501
           + E E+ + +  + E    EEE  E+E+EEEE+EE+  + ++ E++   +   +     A
Sbjct: 52  EEEEEEDEEEIEEPEDIEDEEEIVEDEEEEEEDEEDNVDLKDIEKKNINDIFNSTQDDNA 111

Query: 502 KN 503
           +N
Sbjct: 112 QN 113

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|220972 pfam11081, DUF2890, Protein of unknown function (DUF2890)

 Score = 42.2 bits (99), Expect = 3e-04
 Identities = 22/48 (45%), Positives = 33/48 (68%)

Query: 214 EYEDSDFDTSDEEYDSSEEEEEEEDEEEEEEEEEGEEEETETASSSTA 261
           + E+ D+D+  EE +  EEE E+ ++  +EE+EE EE E ETA+SS A
Sbjct: 18  KDEEEDWDSQAEEVEEDEEEMEDWEDSLDEEDEEAEEVEEETAASSKA 65

This family is conserved in dsDNA adenoviruses of vertebrates. The function is not known. Length = 172

>gnl|CDD|217829 pfam03985, Paf1, Paf1

 Score = 43.6 bits (103), Expect = 3e-04
 Identities = 18/52 (34%), Positives = 29/52 (55%)

Query: 213 SEYEDSDFDTSDEEYDSSEEEEEEEDEEEEEEEEEGEEEETETASSSTAKND 264
           +  +  DF+  DE+ D  EE+  +E EEEE E+ E E  ++    SS + +D
Sbjct: 360 ARLDPIDFEEVDEDEDEEEEQRSDEHEEEEGEDSEEEGSQSREDGSSESSSD 411

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|222792 PHA00435, PHA00435, capsid assembly protein

 Score = 43.3 bits (102), Expect = 3e-04
 Identities = 21/45 (46%), Positives = 24/45 (53%)

Query: 210 NGDSEYEDSDFDTSDEEYDSSEEEEEEEDEEEEEEEEEGEEEETE 254
           N D   ED +        +  EEEE EE EE+EEEE E E EE E
Sbjct: 59  NPDPFGEDDEGRIEVRISEDGEEEEVEEGEEDEEEEGEEESEEFE 103

Length = 306

>gnl|CDD|219900 pfam08553, VID27, VID27 cytoplasmic protein

 Score = 44.0 bits (104), Expect = 3e-04
 Identities = 19/58 (32%), Positives = 32/58 (55%), Gaps = 9/58 (15%)

Query: 215 YEDSDFDTSDEEYDSSEEEEEEEDEEEEEEE---------EEGEEEETETASSSTAKN 263
           +   + + ++ E D  EEE+EEE+EEE+E+E         EE EE++ E+    +  N
Sbjct: 376 FSALEIEDANTERDDEEEEDEEEEEEEDEDEGPSKEHSDDEEFEEDDVESKYEDSDGN 433

This is a family of fungal and plant proteins and contains many hypothetical proteins. VID27 is a cytoplasmic protein that plays a potential role in vacuolar protein degradation. Length = 794

>gnl|CDD|237629 PRK14160, PRK14160, heat shock protein GrpE; Provisional

 Score = 42.8 bits (101), Expect = 3e-04
 Identities = 15/51 (29%), Positives = 27/51 (52%)

Query: 444 EYEDSDFDTSDEEYDSSEEEEEEEEDEEEEEEEEEEEEEEEEEEGEEEETE 494
           E    + +  +E+    E+ E EE ++EE  E+ EE  E + EE ++E  +
Sbjct: 15  EDCCKENENKEEDKGKEEDLEFEEIEKEEIIEDSEESNEVKIEELKDENNK 65

Length = 211

>gnl|CDD|237629 PRK14160, PRK14160, heat shock protein GrpE; Provisional

 Score = 42.4 bits (100), Expect = 3e-04
 Identities = 19/65 (29%), Positives = 31/65 (47%)

Query: 438 ARNGDSEYEDSDFDTSDEEYDSSEEEEEEEEDEEEEEEEEEEEEEEEEEEGEEEETETAS 497
           A++ + E +    + + EE    EE+ E EE E+EE  E+ EE  E + E  ++E     
Sbjct: 8   AKHENMEEDCCKENENKEEDKGKEEDLEFEEIEKEEIIEDSEESNEVKIEELKDENNKLK 67

Query: 498 SSTAK 502
               K
Sbjct: 68  EENKK 72

Length = 211

>gnl|CDD|237629 PRK14160, PRK14160, heat shock protein GrpE; Provisional

 Score = 42.4 bits (100), Expect = 3e-04
 Identities = 13/50 (26%), Positives = 25/50 (50%)

Query: 455 EEYDSSEEEEEEEEDEEEEEEEEEEEEEEEEEEGEEEETETASSSTAKND 504
            E +  + + E  E++  +E E +EE++ +EE+ E EE E         +
Sbjct: 1   MEKECKDAKHENMEEDCCKENENKEEDKGKEEDLEFEEIEKEEIIEDSEE 50

Length = 211

>gnl|CDD|217861 pfam04050, Upf2, Up-frameshift suppressor 2

 Score = 42.0 bits (99), Expect = 3e-04
 Identities = 15/52 (28%), Positives = 28/52 (53%)

Query: 442 DSEYEDSDFDTSDEEYDSSEEEEEEEEDEEEEEEEEEEEEEEEEEEGEEEET 493
                +SD    DEE    +E++E  ++EE +  ++E++EE + EE +   T
Sbjct: 1   SGSESESDDGEEDEELPEEDEDDESSDEEEVDLPDDEQDEESDSEEEQIFVT 52

Transcripts harbouring premature signals for translation termination are recognised and rapidly degraded by eukaryotic cells through a pathway known as nonsense-mediated mRNA decay. In Saccharomyces cerevisiae, three trans-acting factors (Upf1 to Upf3) are required for nonsense-mediated mRNA decay. Length = 171

>gnl|CDD|184885 PRK14891, PRK14891, 50S ribosomal protein L24e/unknown domain fusion protein; Provisional

 Score = 41.1 bits (96), Expect = 3e-04
 Identities = 15/61 (24%), Positives = 30/61 (49%), Gaps = 5/61 (8%)

Query: 446 EDSDFDTSDEEYDSSEEEEEEEEDEEEEEEEE-----EEEEEEEEEEGEEEETETASSST 500
           E ++   + +  + ++E  E +  +E +EEEE     +E  +E + E EE + E    + 
Sbjct: 71  EAAEEAEAADADEDADEAAEADAADEADEEEETDEAVDETADEADAEAEEADEEEDEEAE 130

Query: 501 A 501
           A
Sbjct: 131 A 131

Length = 131

>gnl|CDD|219408 pfam07423, DUF1510, Protein of unknown function (DUF1510)

 Score = 42.8 bits (101), Expect = 3e-04
 Identities = 23/73 (31%), Positives = 35/73 (47%), Gaps = 3/73 (4%)

Query: 437 NARNGDSEYEDSDFDTSDEEYDSSEEE---EEEEEDEEEEEEEEEEEEEEEEEEGEEEET 493
            A   +++  D       EE    E+E    E++ED+ + E+E+EE EEE EEE EE   
Sbjct: 45  AADEQEAKKSDDQETAEIEEVKEEEKEAANSEDKEDKGDAEKEDEESEEENEEEDEESSD 104

Query: 494 ETASSSTAKNDPQ 506
           E    +  K +  
Sbjct: 105 ENEKETEEKTESN 117

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|234311 TIGR03685, L12P_arch, 50S ribosomal protein L12P

 Score = 40.4 bits (95), Expect = 3e-04
 Identities = 19/25 (76%), Positives = 19/25 (76%)

Query: 467 EEDEEEEEEEEEEEEEEEEEEGEEE 491
                EEEEEEEEEEEEEEEE EEE
Sbjct: 71  AAAAAEEEEEEEEEEEEEEEESEEE 95

This model represents the L12P protein of the large (50S) subunit of the archaeal ribosome. Length = 105

>gnl|CDD|234311 TIGR03685, L12P_arch, 50S ribosomal protein L12P

 Score = 40.4 bits (95), Expect = 3e-04
 Identities = 17/29 (58%), Positives = 18/29 (62%)

Query: 470 EEEEEEEEEEEEEEEEEEGEEEETETASS 498
                EEEEEEEEEEEEE EE E E  + 
Sbjct: 71  AAAAAEEEEEEEEEEEEEEEESEEEAMAG 99

This model represents the L12P protein of the large (50S) subunit of the archaeal ribosome. Length = 105

>gnl|CDD|237063 PRK12329, nusA, transcription elongation factor NusA; Provisional

 Score = 43.6 bits (103), Expect = 3e-04
 Identities = 14/57 (24%), Positives = 24/57 (42%), Gaps = 3/57 (5%)

Query: 443 SEYEDSDFDTSDEEYDSSEEEEEEEEDEEEEEEEEEEEEEEEEEEGEEEETETASSS 499
           S+ E+ +   + +       E E+ E  EE+    E     E+E  +E+E E A   
Sbjct: 390 SQREEEE---ALQREAEERLEAEQAERAEEDARLRELYPLPEDEFEDEDELEEAQPE 443

Length = 449

>gnl|CDD|237063 PRK12329, nusA, transcription elongation factor NusA; Provisional

 Score = 43.6 bits (103), Expect = 3e-04
 Identities = 19/63 (30%), Positives = 24/63 (38%)

Query: 443 SEYEDSDFDTSDEEYDSSEEEEEEEEDEEEEEEEEEEEEEEEEEEGEEEETETASSSTAK 502
           +EY+    D    E  S  EEEE  + E EE  E E+ E  EE+    E           
Sbjct: 374 AEYDQEAEDAKVAELISQREEEEALQREAEERLEAEQAERAEEDARLRELYPLPEDEFED 433

Query: 503 NDP 505
            D 
Sbjct: 434 EDE 436

Length = 449

>gnl|CDD|117592 pfam09026, Cenp-B_dimeris, Centromere protein B dimerisation domain

 Score = 40.5 bits (94), Expect = 3e-04
 Identities = 13/41 (31%), Positives = 30/41 (73%)

Query: 461 EEEEEEEEDEEEEEEEEEEEEEEEEEEGEEEETETASSSTA 501
           EE+ + + DEEE++++E+EE+++E+++ +++E    S   A
Sbjct: 9   EEDSDSDSDEEEDDDDEDEEDDDEDDDEDDDEVPVPSFGEA 49

The centromere protein B (CENP-B) dimerisation domain is composed of two alpha-helices, which are folded into an antiparallel configuration. Dimerisation of CENP-B is mediated by this domain, in which monomers dimerise to form a symmetrical, antiparallel, four-helix bundle structure with a large hydrophobic patch in which 23 residues of one monomer form van der Waals contacts with the other monomer. This CENP-B dimer configuration may be suitable for capturing two distant CENP-B boxes during centromeric heterochromatin formation. Length = 101

>gnl|CDD|220135 pfam09184, PPP4R2, PPP4R2

 Score = 42.9 bits (101), Expect = 3e-04
 Identities = 15/64 (23%), Positives = 35/64 (54%)

Query: 441 GDSEYEDSDFDTSDEEYDSSEEEEEEEEDEEEEEEEEEEEEEEEEEEGEEEETETASSST 500
            + E  D+     D    S  + ++ +++E+++++ +  EE+E +E+ EEEETE      
Sbjct: 222 YEKESSDAAASQDDGPKGSDVKNKKSDDEEDDDQDGDYVEEKELKEDEEEEETEEEEEEE 281

Query: 501 AKND 504
            +++
Sbjct: 282 DEDE 285

PPP4R2 (protein phosphatase 4 core regulatory subunit R2) is the regulatory subunit of the histone H2A phosphatase complex. It has been shown to confer resistance to the anticancer drug cisplatin in yeast, and may confer resistance in higher eukaryotes. Length = 285

>gnl|CDD|218333 pfam04931, DNA_pol_phi, DNA polymerase phi

 Score = 44.1 bits (104), Expect = 3e-04
 Identities = 20/78 (25%), Positives = 38/78 (48%), Gaps = 4/78 (5%)

Query: 430 MNHNRRWNARNGDSEYEDSDF----DTSDEEYDSSEEEEEEEEDEEEEEEEEEEEEEEEE 485
            + N+  + +  + E ED D     D  ++E ++ E+ E E E + E+ EE+E+E++ E 
Sbjct: 634 ADENKSRHQQLFEGEEEDEDDLEETDDDEDECEAIEDSESESESDGEDGEEDEQEDDAEA 693

Query: 486 EEGEEEETETASSSTAKN 503
            EG     +    +  K 
Sbjct: 694 NEGVVPIDKAVRRALPKV 711

This family includes the fifth essential DNA polymerase in yeast EC:2.7.7.7. Pol5p is localised exclusively to the nucleolus and binds near or at the enhancer region of rRNA-encoding DNA repeating units. Length = 784

>gnl|CDD|218303 pfam04874, Mak16, Mak16 protein C-terminal region

 Score = 40.2 bits (94), Expect = 3e-04
 Identities = 18/35 (51%), Positives = 24/35 (68%)

Query: 460 SEEEEEEEEDEEEEEEEEEEEEEEEEEEGEEEETE 494
             +EEEEEE+EEE+E E E   ++EE E E E+ E
Sbjct: 62  ENDEEEEEEEEEEDEGEIEYVSDDEELEEEIEDLE 96

The precise function of this eukaryotic protein family is unknown. The yeast orthologues have been implicated in cell cycle progression and biogenesis of 60S ribosomal subunits. The Schistosoma mansoni Mak16 has been shown to target protein transport to the nucleolus. Length = 97

>gnl|CDD|220102 pfam09073, BUD22, BUD22

 Score = 43.7 bits (103), Expect = 3e-04
 Identities = 17/40 (42%), Positives = 24/40 (60%)

Query: 454 DEEYDSSEEEEEEEEDEEEEEEEEEEEEEEEEEEGEEEET 493
            E  D  +EEE E EDE + EE  E++ ++EEEE  + E 
Sbjct: 164 KESSDKDDEEESESEDESKSEESAEDDSDDEEEEDSDSED 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|100110 cd05832, Ribosomal_L12p, Ribosomal protein L12p

 Score = 40.6 bits (95), Expect = 3e-04
 Identities = 15/28 (53%), Positives = 21/28 (75%)

Query: 466 EEEDEEEEEEEEEEEEEEEEEEGEEEET 493
               EE+ EE+EEE+++EEE+E EEEE 
Sbjct: 71  AAAAEEKAEEKEEEKKKEEEKEEEEEEA 98

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|114603 pfam05887, Trypan_PARP, Procyclic acidic repetitive protein (PARP)

 Score = 41.5 bits (96), Expect = 3e-04
 Identities = 28/66 (42%), Positives = 36/66 (54%)

Query: 446 EDSDFDTSDEEYDSSEEEEEEEEDEEEEEEEEEEEEEEEEEEGEEEETETASSSTAKNDP 505
           +D++    D+E +  EE E EEE EEE E EEE EEE E EE  EEE E       + +P
Sbjct: 53  DDTNGTDPDDEPEEEEEPEPEEEGEEEPEPEEEGEEEPEPEETGEEEPEPEPEPEPEPEP 112

Query: 506 QMVTVP 511
           +    P
Sbjct: 113 EPEPEP 118

This family consists of several Trypanosoma brucei procyclic acidic repetitive protein (PARP) like sequences. The procyclic acidic repetitive protein (parp) genes of Trypanosoma brucei encode a small family of abundant surface proteins whose expression is restricted to the procyclic form of the parasite. They are found at two unlinked loci, parpA and parpB; transcription of both loci is developmentally regulated. Length = 145

>gnl|CDD|237622 PRK14140, PRK14140, heat shock protein GrpE; Provisional

 Score = 42.3 bits (100), Expect = 3e-04
 Identities = 19/43 (44%), Positives = 26/43 (60%)

Query: 454 DEEYDSSEEEEEEEEDEEEEEEEEEEEEEEEEEEGEEEETETA 496
           +E+ +   EE E EE  E+E EEE  EEE E E  +EE+ + A
Sbjct: 5   NEQVEEEVEETEVEEAVEDEVEEETVEEESEAELLDEEQAKIA 47

Length = 191

>gnl|CDD|237622 PRK14140, PRK14140, heat shock protein GrpE; Provisional

 Score = 41.9 bits (99), Expect = 3e-04
 Identities = 19/40 (47%), Positives = 22/40 (55%)

Query: 455 EEYDSSEEEEEEEEDEEEEEEEEEEEEEEEEEEGEEEETE 494
           EE +   EEE EE + EE  E+E EEE  EEE   E   E
Sbjct: 2   EEKNEQVEEEVEETEVEEAVEDEVEEETVEEESEAELLDE 41

Length = 191

>gnl|CDD|130712 TIGR01651, CobT, cobaltochelatase, CobT subunit

 Score = 43.8 bits (103), Expect = 3e-04
 Identities = 18/66 (27%), Positives = 28/66 (42%), Gaps = 1/66 (1%)

Query: 441 GDSEYEDSDFDTSDEEYDSSEEEEEEEEDEEEEEEEEEEEEEEEEEEGEEEETETASSST 500
           GD   E  D +  D++  +  E+EE+ E E E +E    +E E  +   E   E    S 
Sbjct: 204 GDDT-ESEDEEDGDDDQPTENEQEEQGEGEGEGQEGSAPQESEATDRESESGEEEMVQSD 262

Query: 501 AKNDPQ 506
             + P 
Sbjct: 263 QDDLPD 268

This model describes Pseudomonas denitrificans CobT gene product, which is a cobalt chelatase subunit that functions in cobalamin biosynthesis. Cobalamin (vitamin B12) can be synthesized via several pathways, including an aerobic pathway (found in Pseudomonas denitrificans) and an anaerobic pathway (found in P. shermanii and Salmonella typhimurium). These pathways differ in the point of cobalt insertion during corrin ring formation. There are apparently a number of variations on these two pathways, where the major differences seem to be concerned with the process of ring contraction. Confusion regarding the functions of enzymes found in the aerobic vs. anaerobic pathways has arisen because nonhomologous genes in these different pathways were given the same gene symbols. Thus, cobT in the aerobic pathway (P. denitrificans) is not a homolog of cobT in the anaerobic pathway (S. typhimurium). It should be noted that E. coli synthesizes cobalamin only when it is supplied with the precursor cobinamide, which is a complex intermediate. Additionally, all E. coli cobalamin synthesis genes (cobU, cobS and cobT) were named after their Salmonella typhimurium homologs which function in the anaerobic cobalamin synthesis pathway. This model describes the aerobic cobalamin pathway Pseudomonas denitrificans CobT gene product, which is a cobalt chelatase subunit, with a MW ~70 kDa. The aerobic pathway cobalt chelatase is a heterotrimeric, ATP-dependent enzyme that catalyzes cobalt insertion during cobalamin biosynthesis. The other two subunits are the P. denitrificans CobS (TIGR01650) and CobN (pfam02514 CobN/Magnesium Chelatase) proteins. To avoid potential confusion with the nonhomologous Salmonella typhimurium/E.coli cobT gene product, the P. denitrificans gene symbol is not used in the name of this model [Biosynthesis of cofactors, prosthetic groups, and carriers, Heme, porphyrin, and cobalamin]. Length = 600

>gnl|CDD|227701 COG5414, COG5414, TATA-binding protein-associated factor [Transcription]

 Score = 43.5 bits (102), Expect = 3e-04
 Identities = 17/54 (31%), Positives = 30/54 (55%)

Query: 438 ARNGDSEYEDSDFDTSDEEYDSSEEEEEEEEDEEEEEEEEEEEEEEEEEEGEEE 491
           A   + E  + D +   EE +++E  +EE + +  +E  EE+EE++E EE E  
Sbjct: 282 AEIENKEVSEGDKEQQQEEVENAEAHKEEVQSDRPDEIGEEKEEDDENEENERH 335

Length = 392

>gnl|CDD|217393 pfam03154, Atrophin-1, Atrophin-1 family

 Score = 44.3 bits (104), Expect = 3e-04
 Identities = 20/54 (37%), Positives = 33/54 (61%), Gaps = 2/54 (3%)

Query: 454 DEEYDSSEEEEEEEEDEEEEEEEEEEEEEEEEEEGEEEETETASSSTAKNDPQM 507
           +E  + ++ E E++  EE E E+E+E+E E E E E E    ASSS+  ++ +M
Sbjct: 582 EEAVEKAKREAEQKAREEREREKEKEKEREREREREAERAAKASSSS--HESRM 633

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|227496 COG5167, VID27, Protein involved in vacuole import and degradation [Intracellular trafficking and secretion]

 Score = 43.8 bits (103), Expect = 3e-04
 Identities = 19/68 (27%), Positives = 29/68 (42%)

Query: 437 NARNGDSEYEDSDFDTSDEEYDSSEEEEEEEEDEEEEEEEEEEEEEEEEEEGEEEETETA 496
           N + G+ E E  D+          ++ ++    E+ E E    EE E EEE E+ E E  
Sbjct: 338 NEKWGNEEAERKDYILDSSSVPLEKQFDDILYFEKMEIENRNPEESEHEEEVEDYEDEND 397

Query: 497 SSSTAKND 504
            S    +D
Sbjct: 398 HSKRICDD 405

Length = 776

>gnl|CDD|227563 COG5238, RNA1, Ran GTPase-activating protein (RanGAP) involved in mRNA processing and transport [Signal transduction mechanisms / RNA processing and modification]

 Score = 43.4 bits (102), Expect = 3e-04
 Identities = 20/61 (32%), Positives = 28/61 (45%)

Query: 439 RNGDSEYEDSDFDTSDEEYDSSEEEEEEEEDEEEEEEEEEEEEEEEEEEGEEEETETASS 498
           RNG+   E +DF    E+     E  E++E +   EE  +EE E+E E  E    E A  
Sbjct: 310 RNGNRIKELADFGDYYEDIFEVVEVVEKQEGDVVTEESTDEESEDEVEIDESVIEEVAEM 369

Query: 499 S 499
            
Sbjct: 370 E 370

Length = 388

>gnl|CDD|177755 PLN00152, PLN00152, DNA-directed RNA polymerase; Provisional

 Score = 41.0 bits (96), Expect = 3e-04
 Identities = 14/47 (29%), Positives = 23/47 (48%)

Query: 446 EDSDFDTSDEEYDSSEEEEEEEEDEEEEEEEEEEEEEEEEEEGEEEE 492
           + +D D   E+  S  E EE  E++ E    +E +    E E +EE+
Sbjct: 1   DYNDMDMGYEDEPSEPEIEEGAEEDSESNNNDEVKGSIGENEDKEEQ 47

Length = 130

>gnl|CDD|217927 pfam04147, Nop14, Nop14-like family

 Score = 43.4 bits (103), Expect = 4e-04
 Identities = 18/59 (30%), Positives = 33/59 (55%), Gaps = 1/59 (1%)

Query: 209 SNGDSEYEDSD-FDTSDEEYDSSEEEEEEEDEEEEEEEEEGEEEETETASSSTAKNDPQ 266
            + + E +D D F     E D  EEE+  +DE+EE+++++ EEEE +   S   +++  
Sbjct: 302 LDDEFEPDDDDNFGLGQGEEDEEEEEDGVDDEDEEDDDDDLEEEEEDVDLSDEEEDEED 360

Emg1 and Nop14 are novel proteins whose interaction is required for the maturation of the 18S rRNA and for 40S ribosome production. Length = 809

>gnl|CDD|218538 pfam05285, SDA1, SDA1

 Score = 43.1 bits (102), Expect = 4e-04
 Identities = 19/59 (32%), Positives = 30/59 (50%), Gaps = 6/59 (10%)

Query: 212 DSEYEDSDFDT------SDEEYDSSEEEEEEEDEEEEEEEEEGEEEETETASSSTAKND 264
             E EDSD +       SD+E +SS+ E+EEE +E  ++ +E  +EE        A  +
Sbjct: 106 VEEDEDSDDEGEWIDVESDKEIESSDSEDEEEKDEAAKKAKEDSDEELSEEDEEEAAEE 164

This family consists of several SDA1 protein homologues. SDA1 is a Saccharomyces cerevisiae protein which is involved in the control of the actin cytoskeleton. The protein is essential for cell viability and is localised in the nucleus. Length = 317

>gnl|CDD|145949 pfam03066, Nucleoplasmin, Nucleoplasmin

 Score = 41.2 bits (97), Expect = 4e-04
 Identities = 13/31 (41%), Positives = 24/31 (77%)

Query: 223 SDEEYDSSEEEEEEEDEEEEEEEEEGEEEET 253
           S+E+    +EE+EEE+++EE+++E+  EEE 
Sbjct: 109 SEEDESDDDEEDEEEEDDEEDDDEDESEEEE 139

Nucleoplasmins are also known as chromatin decondensation proteins. They bind to core histones and transfer DNA to them in a reaction that requires ATP. This is thought to play a role in the assembly of regular nucleosomal arrays. Length = 146

>gnl|CDD|145949 pfam03066, Nucleoplasmin, Nucleoplasmin

 Score = 41.2 bits (97), Expect = 4e-04
 Identities = 15/31 (48%), Positives = 26/31 (83%)

Query: 225 EEYDSSEEEEEEEDEEEEEEEEEGEEEETET 255
           EE +S ++EE+EE+E++EE+++E E EE E+
Sbjct: 110 EEDESDDDEEDEEEEDDEEDDDEDESEEEES 140

Nucleoplasmins are also known as chromatin decondensation proteins. They bind to core histones and transfer DNA to them in a reaction that requires ATP. This is thought to play a role in the assembly of regular nucleosomal arrays. Length = 146

>gnl|CDD|218752 pfam05793, TFIIF_alpha, Transcription initiation factor IIF, alpha subunit (TFIIF-alpha)

 Score = 43.4 bits (102), Expect = 4e-04
 Identities = 19/72 (26%), Positives = 29/72 (40%), Gaps = 16/72 (22%)

Query: 208 SSNGDSEYEDSDFDTSDEEYDSSEEEEEEE---------------DEEEEEEEEEGEEEE 252
           S +GD E  + D+  SD     ++ EE E+               ++ EE EEE+ EEE 
Sbjct: 274 SDDGDDEGREEDY-ISDSSASGNDPEEREDKLSPEIPAKPEIEQDEDSEESEEEKNEEEG 332

Query: 253 TETASSSTAKND 264
             +      K  
Sbjct: 333 GLSKKGKKLKKL 344

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|237629 PRK14160, PRK14160, heat shock protein GrpE; Provisional

 Score = 42.0 bits (99), Expect = 4e-04
 Identities = 16/52 (30%), Positives = 27/52 (51%), Gaps = 1/52 (1%)

Query: 454 DEEYDSSEEEEEEEEDEEEEEEEEEEE-EEEEEEEGEEEETETASSSTAKND 504
            E+     + E  EED  +E E +EE+  +EE+ E EE E E     + +++
Sbjct: 1   MEKECKDAKHENMEEDCCKENENKEEDKGKEEDLEFEEIEKEEIIEDSEESN 52

Length = 211

>gnl|CDD|217861 pfam04050, Upf2, Up-frameshift suppressor 2

 Score = 41.6 bits (98), Expect = 4e-04
 Identities = 17/45 (37%), Positives = 28/45 (62%)

Query: 208 SSNGDSEYEDSDFDTSDEEYDSSEEEEEEEDEEEEEEEEEGEEEE 252
            S  D   ED +    DE+ +SS+EEE +  ++E++EE + EEE+
Sbjct: 4   ESESDDGEEDEELPEEDEDDESSDEEEVDLPDDEQDEESDSEEEQ 48

Transcripts harbouring premature signals for translation termination are recognised and rapidly degraded by eukaryotic cells through a pathway known as nonsense-mediated mRNA decay. In Saccharomyces cerevisiae, three trans-acting factors (Upf1 to Upf3) are required for nonsense-mediated mRNA decay. Length = 171

>gnl|CDD|217861 pfam04050, Upf2, Up-frameshift suppressor 2

 Score = 41.6 bits (98), Expect = 4e-04
 Identities = 18/47 (38%), Positives = 28/47 (59%)

Query: 446 EDSDFDTSDEEYDSSEEEEEEEEDEEEEEEEEEEEEEEEEEEGEEEE 492
           ED D ++SDEE     ++E++EE + EEE+     +EEE +   E E
Sbjct: 19  EDEDDESSDEEEVDLPDDEQDEESDSEEEQIFVTRQEEEVDPEAEAE 65

Transcripts harbouring premature signals for translation termination are recognised and rapidly degraded by eukaryotic cells through a pathway known as nonsense-mediated mRNA decay. In Saccharomyces cerevisiae, three trans-acting factors (Upf1 to Upf3) are required for nonsense-mediated mRNA decay. Length = 171

>gnl|CDD|226920 COG4547, CobT, Cobalamin biosynthesis protein CobT (nicotinate-mononucleotide:5, 6-dimethylbenzimidazole phosphoribosyltransferase) [Coenzyme metabolism]

 Score = 43.3 bits (102), Expect = 4e-04
 Identities = 13/61 (21%), Positives = 22/61 (36%)

Query: 211 GDSEYEDSDFDTSDEEYDSSEEEEEEEDEEEEEEEEEGEEEETETASSSTAKNDPQMVTV 270
           GD   E+   +   ++      E+ E   EE E  +E EE+E E       + +      
Sbjct: 223 GDDGIEEDADEEDGDDDQPDNNEDSEAGREESEGSDESEEDEAEATDGEGEEGEMDAAEA 282

Query: 271 P 271
            
Sbjct: 283 S 283

Length = 620

>gnl|CDD|235795 PRK06402, rpl12p, 50S ribosomal protein L12P; Reviewed

 Score = 40.3 bits (95), Expect = 4e-04
 Identities = 14/29 (48%), Positives = 17/29 (58%)

Query: 464 EEEEEDEEEEEEEEEEEEEEEEEEGEEEE 492
                  EE++EEEEEEEE+EE E E   
Sbjct: 71  AAAAAAAEEKKEEEEEEEEKEESEEEAAA 99

Length = 106

>gnl|CDD|240329 PTZ00248, PTZ00248, eukaryotic translation initiation factor 2 subunit 1; Provisional

 Score = 43.1 bits (102), Expect = 4e-04
 Identities = 18/47 (38%), Positives = 32/47 (68%)

Query: 440 NGDSEYEDSDFDTSDEEYDSSEEEEEEEEDEEEEEEEEEEEEEEEEE 486
            GD E  +   + ++EE +  +  E E+EDEE+E+EEEEE+++E ++
Sbjct: 273 GGDEEDLEELLEKAEEEEEEDDYSESEDEDEEDEDEEEEEDDDEGDK 319

Length = 319

>gnl|CDD|117592 pfam09026, Cenp-B_dimeris, Centromere protein B dimerisation domain

 Score = 40.1 bits (93), Expect = 4e-04
 Identities = 17/32 (53%), Positives = 27/32 (84%), Gaps = 1/32 (3%)

Query: 216 EDSDFDTSDEEYDSSEEEEEEEDEEEEEEEEE 247
           EDSD D SDEE D  +E+EE++DE+++E+++E
Sbjct: 10  EDSDSD-SDEEEDDDDEDEEDDDEDDDEDDDE 40

The centromere protein B (CENP-B) dimerisation domain is composed of two alpha-helices, which are folded into an antiparallel configuration. Dimerisation of CENP-B is mediated by this domain, in which monomers dimerise to form a symmetrical, antiparallel, four-helix bundle structure with a large hydrophobic patch in which 23 residues of one monomer form van der Waals contacts with the other monomer. This CENP-B dimer configuration may be suitable for capturing two distant CENP-B boxes during centromeric heterochromatin formation. Length = 101

>gnl|CDD|218303 pfam04874, Mak16, Mak16 protein C-terminal region

 Score = 39.9 bits (93), Expect = 4e-04
 Identities = 20/38 (52%), Positives = 27/38 (71%)

Query: 455 EEYDSSEEEEEEEEDEEEEEEEEEEEEEEEEEEGEEEE 492
           E  ++ EEEEEEEE+E+E E E   ++EE EEE E+ E
Sbjct: 59  ESEENDEEEEEEEEEEDEGEIEYVSDDEELEEEIEDLE 96

The precise function of this eukaryotic protein family is unknown. The yeast orthologues have been implicated in cell cycle progression and biogenesis of 60S ribosomal subunits. The Schistosoma mansoni Mak16 has been shown to target protein transport to the nucleolus. Length = 97

>gnl|CDD|220102 pfam09073, BUD22, BUD22

 Score = 43.3 bits (102), Expect = 4e-04
 Identities = 21/84 (25%), Positives = 33/84 (39%), Gaps = 14/84 (16%)

Query: 437 NARNGDSEYEDSDFDTSD-EEYDSSEEEEEEEEDEEEEEEEEEE-------------EEE 482
             +      +  D + S+ E+   SEE  E++ D+EEEE+ + E             +EE
Sbjct: 159 KKKEAKESSDKDDEEESESEDESKSEESAEDDSDDEEEEDSDSEDYSQYDGMLVDSSDEE 218

Query: 483 EEEEEGEEEETETASSSTAKNDPQ 506
           E EE       E  S S +     
Sbjct: 219 EGEEAPSINYNEDTSESESDESDS 242

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|100110 cd05832, Ribosomal_L12p, Ribosomal protein L12p

 Score = 40.2 bits (94), Expect = 4e-04
 Identities = 14/34 (41%), Positives = 22/34 (64%)

Query: 465 EEEEDEEEEEEEEEEEEEEEEEEGEEEETETASS 498
               +E+ EE+EEE+++EEE+EE EEE      +
Sbjct: 71  AAAAEEKAEEKEEEKKKEEEKEEEEEEALAGLGA 104

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|100110 cd05832, Ribosomal_L12p, Ribosomal protein L12p

 Score = 40.2 bits (94), Expect = 4e-04
 Identities = 14/30 (46%), Positives = 21/30 (70%)

Query: 470 EEEEEEEEEEEEEEEEEEGEEEETETASSS 499
              EE+ EE+EEE+++EE +EEE E A + 
Sbjct: 72  AAAEEKAEEKEEEKKKEEEKEEEEEEALAG 101

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|114172 pfam05432, BSP_II, Bone sialoprotein II (BSP-II)

 Score = 42.8 bits (100), Expect = 4e-04
 Identities = 24/60 (40%), Positives = 27/60 (45%), Gaps = 4/60 (6%)

Query: 458 DSSEEE----EEEEEDEEEEEEEEEEEEEEEEEEGEEEETETASSSTAKNDPQMVTVPIT 513
           DSSEE       EEE EEE   EEE  E+ +  E EE E E  + ST          P T
Sbjct: 49  DSSEENGDGDSSEEEGEEETSNEEENNEDSDGNEDEEAEAENTTLSTVTLGYGGDATPGT 108

Bone sialoprotein (BSP) is a major structural protein of the bone matrix that is specifically expressed by fully-differentiated osteoblasts. The expression of bone sialoprotein (BSP) is normally restricted to mineralised connective tissues of bones and teeth where it has been associated with mineral crystal formation. However, it has been found that ectopic expression of BSP occurs in various lesions, including oral and extraoral carcinomas, in which it has been associated with the formation of microcrystalline deposits and the metastasis of cancer cells to bone. Length = 291

>gnl|CDD|223003 PHA03169, PHA03169, hypothetical protein; Provisional

 Score = 43.4 bits (102), Expect = 4e-04
 Identities = 10/67 (14%), Positives = 18/67 (26%)

Query: 440 NGDSEYEDSDFDTSDEEYDSSEEEEEEEEDEEEEEEEEEEEEEEEEEEGEEEETETASSS 499
           N      +S    S      S     E    E       ++     +   E+  E     
Sbjct: 122 NTSGSSPESPASHSPPPSPPSHPGPHEPAPPESHNPSPNQQPSSFLQPSHEDSPEEPEPP 181

Query: 500 TAKNDPQ 506
           T++ +P 
Sbjct: 182 TSEPEPD 188

Length = 413

>gnl|CDD|218258 pfam04774, HABP4_PAI-RBP1, Hyaluronan / mRNA binding family

 Score = 40.1 bits (94), Expect = 4e-04
 Identities = 19/49 (38%), Positives = 24/49 (48%)

Query: 446 EDSDFDTSDEEYDSSEEEEEEEEDEEEEEEEEEEEEEEEEEEGEEEETE 494
              +     EE    EE+ E EE +  EEE  +E   EEEE  EEE+ E
Sbjct: 30  VKDEIAELTEEQGEEEEKNEVEEKQAVEEEANKEGVVEEEEVEEEEDKE 78

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|235033 PRK02363, PRK02363, DNA-directed RNA polymerase subunit delta; Reviewed

 Score = 40.8 bits (96), Expect = 4e-04
 Identities = 12/44 (27%), Positives = 25/44 (56%)

Query: 444 EYEDSDFDTSDEEYDSSEEEEEEEEDEEEEEEEEEEEEEEEEEE 487
           E  D       +  D   +++   +D+ +EE+ +EE++E+EE+E
Sbjct: 85  EKFDKKKKKFMDGDDDIIDDDILPDDDFDEEDLDEEDDEDEEDE 128

Length = 129

>gnl|CDD|220759 pfam10446, DUF2457, Protein of unknown function (DUF2457)

 Score = 43.4 bits (102), Expect = 4e-04
 Identities = 13/50 (26%), Positives = 37/50 (74%)

Query: 455 EEYDSSEEEEEEEEDEEEEEEEEEEEEEEEEEEGEEEETETASSSTAKND 504
           +E +    EEE++++E+++++++E+E+++++++ E++E E    ST  +D
Sbjct: 43  KEAEEEAMEEEDDDEEDDDDDDDEDEDDDDDDDDEDDEDEDDDDSTLHDD 92

This is a family of uncharacterized proteins. Length = 449

>gnl|CDD|217783 pfam03896, TRAP_alpha, Translocon-associated protein (TRAP), alpha subunit

 Score = 42.8 bits (101), Expect = 4e-04
 Identities = 19/38 (50%), Positives = 26/38 (68%)

Query: 452 TSDEEYDSSEEEEEEEEDEEEEEEEEEEEEEEEEEEGE 489
           T DEE +    +E+EE++   EE+E E  EEEE+EEGE
Sbjct: 35  TEDEEAEDDVVDEDEEDEAVVEEDENELTEEEEDEEGE 72

The alpha-subunit of the TRAP complex (TRAP alpha) is a single-spanning membrane protein of the endoplasmic reticulum (ER) which is found in proximity of nascent polypeptide chains translocating across the membrane. Length = 281

>gnl|CDD|225880 COG3343, RpoE, DNA-directed RNA polymerase, delta subunit [Transcription]

 Score = 41.7 bits (98), Expect = 4e-04
 Identities = 13/48 (27%), Positives = 30/48 (62%)

Query: 443 SEYEDSDFDTSDEEYDSSEEEEEEEEDEEEEEEEEEEEEEEEEEEGEE 490
            + E    D  +++ D  ++E  E   E++E +E+E+++E+EE+E ++
Sbjct: 128 EDDEVDSLDDENDDEDEDDDEIVEILIEDDEVDEDEDDDEDEEDEEDK 175

Length = 175

>gnl|CDD|233191 TIGR00927, 2A1904, K+-dependent Na+/Ca+ exchanger

 Score = 43.4 bits (102), Expect = 5e-04
 Identities = 19/41 (46%), Positives = 23/41 (56%)

Query: 214 EYEDSDFDTSDEEYDSSEEEEEEEDEEEEEEEEEGEEEETE 254
           E +  +            + EEEE+EEEEEEEEE EEEE E
Sbjct: 844 EAKQDEKGVDGGGGSDGGDSEEEEEEEEEEEEEEEEEEEEE 884

[Transport and binding proteins, Cations and iron carrying compounds]. Length = 1096

>gnl|CDD|217503 pfam03344, Daxx, Daxx Family

 Score = 43.4 bits (102), Expect = 5e-04
 Identities = 23/62 (37%), Positives = 28/62 (45%), Gaps = 3/62 (4%)

Query: 207 KSSNGDSEYEDSDFDTSDEEYDSSE---EEEEEEDEEEEEEEEEGEEEETETASSSTAKN 263
            S   + E    + +  +EE +  E   EEEE EDEEEEEE E     E E   SS    
Sbjct: 435 ASQESEEEESVEEEEEEEEEEEEEEQESEEEEGEDEEEEEEVEADNGSEEEMEGSSEGDG 494

Query: 264 DP 265
           D 
Sbjct: 495 DG 496

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|218752 pfam05793, TFIIF_alpha, Transcription initiation factor IIF, alpha subunit (TFIIF-alpha)

 Score = 43.0 bits (101), Expect = 5e-04
 Identities = 12/53 (22%), Positives = 25/53 (47%)

Query: 442 DSEYEDSDFDTSDEEYDSSEEEEEEEEDEEEEEEEEEEEEEEEEEEGEEEETE 494
           + + +D D +  +E+Y S       + +E E++   E   + E E+ E+ E  
Sbjct: 271 EYDSDDGDDEGREEDYISDSSASGNDPEEREDKLSPEIPAKPEIEQDEDSEES 323

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|218752 pfam05793, TFIIF_alpha, Transcription initiation factor IIF, alpha subunit (TFIIF-alpha)

 Score = 43.0 bits (101), Expect = 5e-04
 Identities = 17/78 (21%), Positives = 28/78 (35%), Gaps = 10/78 (12%)

Query: 437 NARNGDSEYEDS----DFDTSDEEYDSSEEEEEEEE------DEEEEEEEEEEEEEEEEE 486
            A+N     +D       D   +EYDS + ++E  E            + EE E++   E
Sbjct: 248 LAKNKKKLDDDKKGKRGGDDDADEYDSDDGDDEGREEDYISDSSASGNDPEEREDKLSPE 307

Query: 487 EGEEEETETASSSTAKND 504
              + E E    S    +
Sbjct: 308 IPAKPEIEQDEDSEESEE 325

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|185603 PTZ00415, PTZ00415, transmission-blocking target antigen s230; Provisional

 Score = 43.5 bits (102), Expect = 5e-04
 Identities = 15/39 (38%), Positives = 25/39 (64%)

Query: 216 EDSDFDTSDEEYDSSEEEEEEEDEEEEEEEEEGEEEETE 254
            + D    D      ++E+E+ED+++EE++EE EEEE E
Sbjct: 141 AEEDMSPRDNFVIDDDDEDEDEDDDDEEDDEEEEEEEEE 179

Length = 2849

>gnl|CDD|219408 pfam07423, DUF1510, Protein of unknown function (DUF1510)

 Score = 42.0 bits (99), Expect = 5e-04
 Identities = 20/59 (33%), Positives = 32/59 (54%)

Query: 446 EDSDFDTSDEEYDSSEEEEEEEEDEEEEEEEEEEEEEEEEEEGEEEETETASSSTAKND 504
           E+ +   S+++ D  + E+E+EE EEE EEE+EE  +E E+E EE+             
Sbjct: 68  EEKEAANSEDKEDKGDAEKEDEESEEENEEEDEESSDENEKETEEKTESNVEKEITNPS 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|234311 TIGR03685, L12P_arch, 50S ribosomal protein L12P

 Score = 40.0 bits (94), Expect = 5e-04
 Identities = 16/22 (72%), Positives = 17/22 (77%)

Query: 231 EEEEEEEDEEEEEEEEEGEEEE 252
              EEEE+EEEEEEEEE E EE
Sbjct: 73  AAAEEEEEEEEEEEEEEEESEE 94

This model represents the L12P protein of the large (50S) subunit of the archaeal ribosome. Length = 105

>gnl|CDD|235795 PRK06402, rpl12p, 50S ribosomal protein L12P; Reviewed

 Score = 39.9 bits (94), Expect = 5e-04
 Identities = 15/29 (51%), Positives = 18/29 (62%)

Query: 470 EEEEEEEEEEEEEEEEEEGEEEETETASS 498
                 EE++EEEEEEEE EE E E A+ 
Sbjct: 72  AAAAAAEEKKEEEEEEEEKEESEEEAAAG 100

Length = 106

>gnl|CDD|218303 pfam04874, Mak16, Mak16 protein C-terminal region

 Score = 39.9 bits (93), Expect = 5e-04
 Identities = 21/39 (53%), Positives = 28/39 (71%)

Query: 456 EYDSSEEEEEEEEDEEEEEEEEEEEEEEEEEEGEEEETE 494
           E + SEE +EEEE+EEEEE+E E E   ++EE EEE  +
Sbjct: 56  EAEESEENDEEEEEEEEEEDEGEIEYVSDDEELEEEIED 94

The precise function of this eukaryotic protein family is unknown. The yeast orthologues have been implicated in cell cycle progression and biogenesis of 60S ribosomal subunits. The Schistosoma mansoni Mak16 has been shown to target protein transport to the nucleolus. Length = 97

>gnl|CDD|100110 cd05832, Ribosomal_L12p, Ribosomal protein L12p

 Score = 39.8 bits (93), Expect = 5e-04
 Identities = 15/27 (55%), Positives = 20/27 (74%)

Query: 463 EEEEEEDEEEEEEEEEEEEEEEEEEGE 489
               EE  EE+EEE+++EEE+EEEE 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|227466 COG5137, COG5137, Histone chaperone involved in gene silencing [Transcription / Chromatin structure and dynamics]

 Score = 42.7 bits (100), Expect = 5e-04
 Identities = 18/70 (25%), Positives = 31/70 (44%), Gaps = 1/70 (1%)

Query: 442 DSEYEDSDFDTSDEEYDSSEEEE-EEEEDEEEEEEEEEEEEEEEEEEGEEEETETASSST 500
             E  D   +  DEE  S    E   E +EEEEEE E  ++ E+  + E E  +      
Sbjct: 181 RLEESDGREEEEDEEVGSDSYGEGNRELNEEEEEEAEGSDDGEDVVDYEGERIDKKQGEE 240

Query: 501 AKNDPQMVTV 510
            + + +++ +
Sbjct: 241 EEMEEEVINL 250

Length = 279

>gnl|CDD|217840 pfam04006, Mpp10, Mpp10 protein

 Score = 43.4 bits (102), Expect = 5e-04
 Identities = 23/78 (29%), Positives = 34/78 (43%), Gaps = 11/78 (14%)

Query: 440 NGDSEYEDSDFDTSDEEYDSSEEEE-----------EEEEDEEEEEEEEEEEEEEEEEEG 488
             D + EDS  D  +EE D S E+E            E E   E+  ++E E++EE++  
Sbjct: 106 GSDMDSEDSADDEEEEEEDESLEDEMIDDEDEADLFNESESSLEDLSDDETEDDEEKKME 165

Query: 489 EEEETETASSSTAKNDPQ 506
           EEE  E   S       +
Sbjct: 166 EEEAGEEKESVEQATREK 183

This family includes proteins related to Mpp10 (M phase phosphoprotein 10). The U3 small nucleolar ribonucleoprotein (snoRNP) is required for three cleavage events that generate the mature 18S rRNA from the pre-rRNA. In Saccharomyces cerevisiae, depletion of Mpp10, a U3 snoRNP-specific protein, halts 18S rRNA production and impairs cleavage at the three U3 snoRNP-dependent sites. Length = 613

>gnl|CDD|224969 COG2058, RPP1A, Ribosomal protein L12E/L44/L45/RPP1/RPP2 [Translation, ribosomal structure and biogenesis]

 Score = 40.1 bits (94), Expect = 5e-04
 Identities = 13/32 (40%), Positives = 19/32 (59%)

Query: 459 SSEEEEEEEEDEEEEEEEEEEEEEEEEEEGEE 490
           ++     E   E +E EEEE+EEE EEE  ++
Sbjct: 71  AAAAAGAEAAAEADEAEEEEKEEEAEEESDDD 102

Length = 109

>gnl|CDD|216269 pfam01056, Myc_N, Myc amino-terminal region

 Score = 43.0 bits (101), Expect = 5e-04
 Identities = 23/61 (37%), Positives = 28/61 (45%), Gaps = 5/61 (8%)

Query: 451 DTSDEEYDSSEEEEEEEEDEEEEEEEEEEEE-----EEEEEEGEEEETETASSSTAKNDP 505
            T      SS  + E EEDEEEEEEEEEEEE      E+       +  T+ S T  +  
Sbjct: 213 RTPPNSSSSSGSDSESEEDEEEEEEEEEEEEIDVVTVEKRRSSSNRKASTSESITVPSRR 272

Query: 506 Q 506
            
Sbjct: 273 H 273

The myc family belongs to the basic helix-loop-helix leucine zipper class of transcription factors, see pfam00010. Myc forms a heterodimer with Max, and this complex regulates cell growth through direct activation of genes involved in cell replication. Mutations in the C-terminal 20 residues of this domain cause unique changes in the induction of apoptosis, transformation, and G2 arrest. Length = 329

>gnl|CDD|218538 pfam05285, SDA1, SDA1

 Score = 42.3 bits (100), Expect = 6e-04
 Identities = 16/46 (34%), Positives = 26/46 (56%)

Query: 454 DEEYDSSEEEEEEEEDEEEEEEEEEEEEEEEEEEGEEEETETASSS 499
            EE    +E E+  E +++++EEEE E EE+E+  +E E     S 
Sbjct: 79  KEEERKKKEAEQGLESDDDDDEEEEWEVEEDEDSDDEGEWIDVESD 124

This family consists of several SDA1 protein homologues. SDA1 is a Saccharomyces cerevisiae protein which is involved in the control of the actin cytoskeleton. The protein is essential for cell viability and is localised in the nucleus. Length = 317

>gnl|CDD|217503 pfam03344, Daxx, Daxx Family

 Score = 43.0 bits (101), Expect = 6e-04
 Identities = 24/52 (46%), Positives = 36/52 (69%), Gaps = 2/52 (3%)

Query: 216 EDSDFDTSDEEYDSSEEEEEEEDEEEEEEEEEGEEEETETASSSTAKNDPQM 267
           ++S+ + S EE +  EEEEEEE+EE+E EEEEGE+EE E    +   ++ +M
Sbjct: 437 QESEEEESVEEEE--EEEEEEEEEEQESEEEEGEDEEEEEEVEADNGSEEEM 486

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|218312 pfam04889, Cwf_Cwc_15, Cwf15/Cwc15 cell cycle control protein

 Score = 42.0 bits (99), Expect = 6e-04
 Identities = 12/43 (27%), Positives = 22/43 (51%)

Query: 205 IIKSSNGDSEYEDSDFDTSDEEYDSSEEEEEEEDEEEEEEEEE 247
            IK    + +  +SD D SD   DS   +++ +D++ E+E   
Sbjct: 104 EIKRKRIEEDARNSDADDSDSSSDSDSSDDDSDDDDSEDETAA 146

This family represents Cwf15/Cwc15 (from Schizosaccharomyces pombe and Saccharomyces cerevisiae respectively) and their homologues. The function of these proteins is unknown, but they form part of the spliceosome and are thus thought to be involved in mRNA splicing. Length = 241

>gnl|CDD|234311 TIGR03685, L12P_arch, 50S ribosomal protein L12P

 Score = 39.6 bits (93), Expect = 6e-04
 Identities = 18/25 (72%), Positives = 18/25 (72%)

Query: 466 EEEDEEEEEEEEEEEEEEEEEEGEE 490
                EEEEEEEEEEEEEEEE  EE
Sbjct: 71  AAAAAEEEEEEEEEEEEEEEESEEE 95

This model represents the L12P protein of the large (50S) subunit of the archaeal ribosome. Length = 105

>gnl|CDD|240329 PTZ00248, PTZ00248, eukaryotic translation initiation factor 2 subunit 1; Provisional

 Score = 42.3 bits (100), Expect = 6e-04
 Identities = 19/40 (47%), Positives = 28/40 (70%)

Query: 453 SDEEYDSSEEEEEEEEDEEEEEEEEEEEEEEEEEEGEEEE 492
             +E D  E  E+ EE+EEE++  E E+E+EE+E+ EEEE
Sbjct: 273 GGDEEDLEELLEKAEEEEEEDDYSESEDEDEEDEDEEEEE 312

Length = 319

>gnl|CDD|215774 pfam00183, HSP90, Hsp90 protein

 Score = 42.8 bits (101), Expect = 6e-04
 Identities = 23/60 (38%), Positives = 41/60 (68%), Gaps = 2/60 (3%)

Query: 453 SDEEYDSSEEEEEEEEDEEEEEEEEEEEEEEEEEEGEEEETETASSSTAKNDPQMVTVPI 512
            DEE +  EE+EE++E+EE+  ++EEE +EEEE+E ++++T+    +T + +    T PI
Sbjct: 36  PDEEEE--EEKEEKKEEEEKTTDKEEEVDEEEEKEEKKKKTKKVKETTTEWELLNKTKPI 93

Length = 529

>gnl|CDD|203043 pfam04546, Sigma70_ner, Sigma-70, non-essential region

 Score = 41.4 bits (98), Expect = 6e-04
 Identities = 12/43 (27%), Positives = 28/43 (65%)

Query: 445 YEDSDFDTSDEEYDSSEEEEEEEEDEEEEEEEEEEEEEEEEEE 487
           + D +   +     + E E +EE+ E++++++E+E+E++EEE 
Sbjct: 29  FIDPNAAAAAATAAAIESELDEEDLEDDDDDDEDEDEDDEEEA 71

The domain is found in the primary vegetative sigma factor. The function of this domain is unclear and can be removed without loss of function. Length = 211

>gnl|CDD|220413 pfam09805, Nop25, Nucleolar protein 12 (25kDa)

 Score = 40.4 bits (95), Expect = 6e-04
 Identities = 15/51 (29%), Positives = 21/51 (41%)

Query: 460 SEEEEEEEEDEEEEEEEEEEEEEEEEEEGEEEETETASSSTAKNDPQMVTV 510
            EEE ++EED E E+ E+ E++E E                       VTV
Sbjct: 79  LEEENDDEEDAETEDTEDVEDDEWEGFPEPTVTDYEEEYIDEDKYKTTVTV 129

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|117592 pfam09026, Cenp-B_dimeris, Centromere protein B dimerisation domain

 Score = 39.8 bits (92), Expect = 6e-04
 Identities = 15/31 (48%), Positives = 26/31 (83%)

Query: 446 EDSDFDTSDEEYDSSEEEEEEEEDEEEEEEE 476
           EDSD D+ +EE D  E+EE+++ED++E+++E
Sbjct: 10  EDSDSDSDEEEDDDDEDEEDDDEDDDEDDDE 40

The centromere protein B (CENP-B) dimerisation domain is composed of two alpha-helices, which are folded into an antiparallel configuration. Dimerisation of CENP-B is mediated by this domain, in which monomers dimerise to form a symmetrical, antiparallel, four-helix bundle structure with a large hydrophobic patch in which 23 residues of one monomer form van der Waals contacts with the other monomer. This CENP-B dimer configuration may be suitable for capturing two distant CENP-B boxes during centromeric heterochromatin formation. Length = 101

>gnl|CDD|237622 PRK14140, PRK14140, heat shock protein GrpE; Provisional

 Score = 41.5 bits (98), Expect = 6e-04
 Identities = 18/43 (41%), Positives = 25/43 (58%)

Query: 464 EEEEEDEEEEEEEEEEEEEEEEEEGEEEETETASSSTAKNDPQ 506
            EE+ ++ EEE EE E EE  E+E EEE  E  S +   ++ Q
Sbjct: 1   MEEKNEQVEEEVEETEVEEAVEDEVEEETVEEESEAELLDEEQ 43

Length = 191

>gnl|CDD|224969 COG2058, RPP1A, Ribosomal protein L12E/L44/L45/RPP1/RPP2 [Translation, ribosomal structure and biogenesis]

 Score = 39.7 bits (93), Expect = 6e-04
 Identities = 12/29 (41%), Positives = 18/29 (62%)

Query: 460 SEEEEEEEEDEEEEEEEEEEEEEEEEEEG 488
             E   E ++ EEEE+EEE EEE +++  
Sbjct: 76  GAEAAAEADEAEEEEKEEEAEEESDDDML 104

Length = 109

>gnl|CDD|220377 pfam09747, DUF2052, Coiled-coil domain containing protein (DUF2052)

 Score = 41.3 bits (97), Expect = 6e-04
 Identities = 22/47 (46%), Positives = 26/47 (55%)

Query: 455 EEYDSSEEEEEEEEDEEEEEEEEEEEEEEEEEEGEEEETETASSSTA 501
            E    EE  EEEE++ EEE EEEEEE +    GEEEE +  S    
Sbjct: 74  LEQQEEEESAEEEEEDPEEENEEEEEEYQRGPFGEEEEEDGDSYDEL 120

This entry is of sequences of two conserved domains separated by a region of low complexity, spanning some 200 residues. The function is unknown. Length = 178

>gnl|CDD|219256 pfam06991, Prp19_bind, Splicing factor, Prp19-binding domain

 Score = 42.2 bits (99), Expect = 6e-04
 Identities = 19/34 (55%), Positives = 24/34 (70%)

Query: 456 EYDSSEEEEEEEEDEEEEEEEEEEEEEEEEEEGE 489
           E +  E EEE+E  EEEEEE EEEEE + E++ E
Sbjct: 1   ETEVLELEEEDESGEEEEEESEEEEETDSEDDME 34

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|221177 pfam11708, Slu7, Pre-mRNA splicing Prp18-interacting factor

 Score = 41.6 bits (98), Expect = 6e-04
 Identities = 18/69 (26%), Positives = 36/69 (52%), Gaps = 6/69 (8%)

Query: 435 RWNARNGDSEYEDSDFDTSDEEYDSSEEEEEEEEDEEEEEEEEEEEEEEEEEEGEEEETE 494
           RWN       Y+ S++    EEY+  EE  ++ + ++E++ ++ + E+E+EE   +E   
Sbjct: 10  RWNG------YDPSEYKEVVEEYEKLEELRKKLKAKKEDDSDDTDYEDEDEELYLDESDM 63

Query: 495 TASSSTAKN 503
             S S  + 
Sbjct: 64  GDSDSKTRT 72

The spliceosome, an assembly of snRNAs (U1, U2, U4/U6, and U5) and proteins, catalyzes the excision of introns from pre-mRNAs in two successive trans-esterification reactions. Step 2 depends upon integral spliceosome constituents such as U5 snRNA and Prp8 and non-spliceosomal proteins Prp16, Slu7, Prp18, and Prp22. ATP hydrolysis by the DEAH-box enzyme Prp16 promotes a conformational change in the spliceosome that leads to protection of the 3'ss from targeted RNase H cleavage. This change, which probably reflects binding of the 3'ss PyAG in the catalytic centre of the spliceosome, requires the ordered recruitment of Slu7, Prp18, and Prp22 to the spliceosome. There is a close functional relationship between Prp8, Prp18, and Slu7, and Prp18 interacts with Slu7, so that together they recruit Prp22 to the spliceosome. Most members of the family carry a zinc-finger of the CCHC-type upstream of this domain. Length = 236

>gnl|CDD|218538 pfam05285, SDA1, SDA1

 Score = 41.9 bits (99), Expect = 7e-04
 Identities = 15/53 (28%), Positives = 27/53 (50%)

Query: 210 NGDSEYEDSDFDTSDEEYDSSEEEEEEEDEEEEEEEEEGEEEETETASSSTAK 262
           + +S+ E    D+ DEE      ++ +ED +EE  EE+ EE   E  + +  +
Sbjct: 120 DVESDKEIESSDSEDEEEKDEAAKKAKEDSDEELSEEDEEEAAEEEEAEAEKE 172

This family consists of several SDA1 protein homologues. SDA1 is a Saccharomyces cerevisiae protein which is involved in the control of the actin cytoskeleton. The protein is essential for cell viability and is localised in the nucleus. Length = 317

>gnl|CDD|145949 pfam03066, Nucleoplasmin, Nucleoplasmin

 Score = 40.4 bits (95), Expect = 7e-04
 Identities = 14/38 (36%), Positives = 26/38 (68%)

Query: 225 EEYDSSEEEEEEEDEEEEEEEEEGEEEETETASSSTAK 262
            E D S+++EE+E+EE++EE+++ +E E E +     K
Sbjct: 109 SEEDESDDDEEDEEEEDDEEDDDEDESEEEESPVKKVK 146

Nucleoplasmins are also known as chromatin decondensation proteins. They bind to core histones and transfer DNA to them in a reaction that requires ATP. This is thought to play a role in the assembly of regular nucleosomal arrays. Length = 146

>gnl|CDD|148051 pfam06213, CobT, Cobalamin biosynthesis protein CobT

 Score = 42.1 bits (99), Expect = 7e-04
 Identities = 13/50 (26%), Positives = 28/50 (56%)

Query: 455 EEYDSSEEEEEEEEDEEEEEEEEEEEEEEEEEEGEEEETETASSSTAKND 504
           EE     E  + E++E+E++ +E+E++++ EEE        +  S A ++
Sbjct: 210 EELGDEPESADSEDNEDEDDPKEDEDDDQGEEEESGSSDSLSEDSDASSE 259

This family consists of several bacterial cobalamin biosynthesis (CobT) proteins. CobT is involved in the transformation of precorrin-3 into cobyrinic acid. Length = 282

>gnl|CDD|237629 PRK14160, PRK14160, heat shock protein GrpE; Provisional

 Score = 41.7 bits (98), Expect = 7e-04
 Identities = 14/51 (27%), Positives = 24/51 (47%)

Query: 454 DEEYDSSEEEEEEEEDEEEEEEEEEEEEEEEEEEGEEEETETASSSTAKND 504
           + +    E  EE+   E E +EE++ +EE+ E E  E+E     S  +   
Sbjct: 4   ECKDAKHENMEEDCCKENENKEEDKGKEEDLEFEEIEKEEIIEDSEESNEV 54

Length = 211

>gnl|CDD|217861 pfam04050, Upf2, Up-frameshift suppressor 2

 Score = 40.8 bits (96), Expect = 7e-04
 Identities = 14/47 (29%), Positives = 25/47 (53%)

Query: 440 NGDSEYEDSDFDTSDEEYDSSEEEEEEEEDEEEEEEEEEEEEEEEEE 486
           +  S+ E+ D    +++ +S  EEE+     +EEE + E E E + E
Sbjct: 23  DESSDEEEVDLPDDEQDEESDSEEEQIFVTRQEEEVDPEAEAEFDRE 69

Transcripts harbouring premature signals for translation termination are recognised and rapidly degraded by eukaryotic cells through a pathway known as nonsense-mediated mRNA decay. In Saccharomyces cerevisiae, three trans-acting factors (Upf1 to Upf3) are required for nonsense-mediated mRNA decay. Length = 171

>gnl|CDD|184885 PRK14891, PRK14891, 50S ribosomal protein L24e/unknown domain fusion protein; Provisional

 Score = 39.9 bits (93), Expect = 7e-04
 Identities = 13/66 (19%), Positives = 31/66 (46%)

Query: 439 RNGDSEYEDSDFDTSDEEYDSSEEEEEEEEDEEEEEEEEEEEEEEEEEEGEEEETETASS 498
                    +    + EE ++++ +E+ +E  E +  +E +EEEE +E  +E   E  + 
Sbjct: 58  AEKGPAAAATAAAEAAEEAEAADADEDADEAAEADAADEADEEEETDEAVDETADEADAE 117

Query: 499 STAKND 504
           +   ++
Sbjct: 118 AEEADE 123

Length = 131

>gnl|CDD|218303 pfam04874, Mak16, Mak16 protein C-terminal region

 Score = 39.1 bits (91), Expect = 7e-04
 Identities = 22/52 (42%), Positives = 29/52 (55%), Gaps = 6/52 (11%)

Query: 453 SDEEYDSSEE------EEEEEEDEEEEEEEEEEEEEEEEEEGEEEETETASS 498
            DE Y+ S+       E EE E+ +EEEEEEEEEE+E E E   ++ E    
Sbjct: 40  GDEPYNISQSAFKKALEAEESEENDEEEEEEEEEEDEGEIEYVSDDEELEEE 91

The precise function of this eukaryotic protein family is unknown. The yeast orthologues have been implicated in cell cycle progression and biogenesis of 60S ribosomal subunits. The Schistosoma mansoni Mak16 has been shown to target protein transport to the nucleolus. Length = 97

>gnl|CDD|100110 cd05832, Ribosomal_L12p, Ribosomal protein L12p

 Score = 39.4 bits (92), Expect = 7e-04
 Identities = 14/27 (51%), Positives = 21/27 (77%)

Query: 464 EEEEEDEEEEEEEEEEEEEEEEEEGEE 490
               E++ EE+EEE+++EEE+EEE EE
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|237622 PRK14140, PRK14140, heat shock protein GrpE; Provisional

 Score = 41.1 bits (97), Expect = 7e-04
 Identities = 18/44 (40%), Positives = 22/44 (50%)

Query: 451 DTSDEEYDSSEEEEEEEEDEEEEEEEEEEEEEEEEEEGEEEETE 494
           +   EE     E EE  EDE EEE  EEE E E  +E + +  E
Sbjct: 5   NEQVEEEVEETEVEEAVEDEVEEETVEEESEAELLDEEQAKIAE 48

Length = 191

>gnl|CDD|237622 PRK14140, PRK14140, heat shock protein GrpE; Provisional

 Score = 41.1 bits (97), Expect = 7e-04
 Identities = 19/35 (54%), Positives = 24/35 (68%)

Query: 461 EEEEEEEEDEEEEEEEEEEEEEEEEEEGEEEETET 495
           EE+ E+ E+E EE E EE  E+E EEE  EEE+E 
Sbjct: 2   EEKNEQVEEEVEETEVEEAVEDEVEEETVEEESEA 36

Length = 191

>gnl|CDD|237622 PRK14140, PRK14140, heat shock protein GrpE; Provisional

 Score = 41.1 bits (97), Expect = 7e-04
 Identities = 18/36 (50%), Positives = 21/36 (58%)

Query: 463 EEEEEEDEEEEEEEEEEEEEEEEEEGEEEETETASS 498
           EEE EE E EE  E+E EEE  EEE E E  +   +
Sbjct: 9   EEEVEETEVEEAVEDEVEEETVEEESEAELLDEEQA 44

Length = 191

>gnl|CDD|218258 pfam04774, HABP4_PAI-RBP1, Hyaluronan / mRNA binding family

 Score = 39.3 bits (92), Expect = 7e-04
 Identities = 19/56 (33%), Positives = 29/56 (51%)

Query: 434 RRWNARNGDSEYEDSDFDTSDEEYDSSEEEEEEEEDEEEEEEEEEEEEEEEEEEGE 489
            R N  +   E  +   +  +EE  +  EE++  E+E  +E   EEEE EEEE+ E
Sbjct: 23  GRGNWGSVKDEIAELTEEQGEEEEKNEVEEKQAVEEEANKEGVVEEEEVEEEEDKE 78

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|214818 smart00784, SPT2, SPT2 chromatin protein

 Score = 39.3 bits (92), Expect = 7e-04
 Identities = 18/52 (34%), Positives = 23/52 (44%), Gaps = 3/52 (5%)

Query: 442 DSEYEDSDFDTSDEEYDSSEEEEEEEEDE---EEEEEEEEEEEEEEEEEGEE 490
              Y D D D  D E   ++ +EEE         E+ EEE  E+EEE E   
Sbjct: 51  RYAYRDDDDDDDDMEAGGADIQEEERRSARLARLEDREEERLEKEEEREKRA 102

This entry includes the Saccharomyces cerevisiae protein SPT2 which is a chromatin protein involved in transcriptional regulation. Length = 106

>gnl|CDD|221333 pfam11942, Spt5_N, Spt5 transcription elongation factor, acidic N-terminal

 Score = 39.0 bits (91), Expect = 7e-04
 Identities = 19/42 (45%), Positives = 25/42 (59%), Gaps = 1/42 (2%)

Query: 450 FDTSDEEYDSSEEEEEEEEDEEEEEEEEEEEEEEEEEEGEEE 491
            DT  E  D  EEEEEEEED+ E+  +E+E  +E E E +  
Sbjct: 2   LDTEAEV-DDEEEEEEEEEDDLEDLSDEDEFIDEAEAEDDRR 42

This is the very acidic N-terminal region of the early transcription elongation factor Spt5. The Spt5-Spt4 complex regulates early transcription elongation by RNA polymerase II and has an imputed role in pre-mRNA processing via its physical association with mRNA capping enzymes. The actual function of this N-terminal domain is not known although it is dispensable for binding to Spt4. Length = 92

>gnl|CDD|217861 pfam04050, Upf2, Up-frameshift suppressor 2

 Score = 40.4 bits (95), Expect = 8e-04
 Identities = 17/53 (32%), Positives = 26/53 (49%), Gaps = 3/53 (5%)

Query: 442 DSEYEDSDFDTSDEEYDSSEEEEEEEEDEEEEEEEEEEEEE---EEEEEGEEE 491
             E ED +    +E     +E++EE + EEE+     +EEE   E E E + E
Sbjct: 17  PEEDEDDESSDEEEVDLPDDEQDEESDSEEEQIFVTRQEEEVDPEAEAEFDRE 69

Transcripts harbouring premature signals for translation termination are recognised and rapidly degraded by eukaryotic cells through a pathway known as nonsense-mediated mRNA decay. In Saccharomyces cerevisiae, three trans-acting factors (Upf1 to Upf3) are required for nonsense-mediated mRNA decay. Length = 171

>gnl|CDD|237063 PRK12329, nusA, transcription elongation factor NusA; Provisional

 Score = 42.5 bits (100), Expect = 8e-04
 Identities = 15/58 (25%), Positives = 24/58 (41%)

Query: 438 ARNGDSEYEDSDFDTSDEEYDSSEEEEEEEEDEEEEEEEEEEEEEEEEEEGEEEETET 495
            R  +   +    +  + E     EE+    +     E+E E+E+E EE   EEE E 
Sbjct: 391 QREEEEALQREAEERLEAEQAERAEEDARLRELYPLPEDEFEDEDELEEAQPEEEEEA 448

Length = 449

>gnl|CDD|217840 pfam04006, Mpp10, Mpp10 protein

 Score = 42.7 bits (100), Expect = 8e-04
 Identities = 23/64 (35%), Positives = 31/64 (48%), Gaps = 11/64 (17%)

Query: 442 DSEYEDSDFDTSDE-EYDSSEEEEEEEEDEEEEEE----------EEEEEEEEEEEEGEE 490
           DSE  +   D SD    DS+++EEEEEEDE  E+E            E E   E+   +E
Sbjct: 96  DSESHEDGSDGSDMDSEDSADDEEEEEEDESLEDEMIDDEDEADLFNESESSLEDLSDDE 155

Query: 491 EETE 494
            E +
Sbjct: 156 TEDD 159

This family includes proteins related to Mpp10 (M phase phosphoprotein 10). The U3 small nucleolar ribonucleoprotein (snoRNP) is required for three cleavage events that generate the mature 18S rRNA from the pre-rRNA. In Saccharomyces cerevisiae, depletion of Mpp10, a U3 snoRNP-specific protein, halts 18S rRNA production and impairs cleavage at the three U3 snoRNP-dependent sites. Length = 613

>gnl|CDD|235640 PRK05901, PRK05901, RNA polymerase sigma factor; Provisional

 Score = 42.3 bits (100), Expect = 8e-04
 Identities = 14/66 (21%), Positives = 38/66 (57%)

Query: 442 DSEYEDSDFDTSDEEYDSSEEEEEEEEDEEEEEEEEEEEEEEEEEEGEEEETETASSSTA 501
           D + +D D D  D++ D  +++E++++D+ ++E+EE++E +E E+  ++++       + 
Sbjct: 136 DDDDDDLDDDDIDDDDDDEDDDEDDDDDDVDDEDEEKKEAKELEKLSDDDDFVWDEDDSE 195

Query: 502 KNDPQM 507
                 
Sbjct: 196 ALRQAR 201

Length = 509

>gnl|CDD|117592 pfam09026, Cenp-B_dimeris, Centromere protein B dimerisation domain

 Score = 39.0 bits (90), Expect = 9e-04
 Identities = 11/33 (33%), Positives = 28/33 (84%)

Query: 455 EEYDSSEEEEEEEEDEEEEEEEEEEEEEEEEEE 487
           E  + S+ + +EEED+++E+EE+++E+++E+++
Sbjct: 7   EGEEDSDSDSDEEEDDDDEDEEDDDEDDDEDDD 39

The centromere protein B (CENP-B) dimerisation domain is composed of two alpha-helices, which are folded into an antiparallel configuration. Dimerisation of CENP-B is mediated by this domain, in which monomers dimerise to form a symmetrical, antiparallel, four-helix bundle structure with a large hydrophobic patch in which 23 residues of one monomer form van der Waals contacts with the other monomer. This CENP-B dimer configuration may be suitable for capturing two distant CENP-B boxes during centromeric heterochromatin formation. Length = 101

>gnl|CDD|220377 pfam09747, DUF2052, Coiled-coil domain containing protein (DUF2052)

 Score = 40.5 bits (95), Expect = 9e-04
 Identities = 23/57 (40%), Positives = 28/57 (49%)

Query: 448 SDFDTSDEEYDSSEEEEEEEEDEEEEEEEEEEEEEEEEEEGEEEETETASSSTAKND 504
           S  D  +   +  E++EEEE  EEEEE+ EEE EEEEEE       E         D
Sbjct: 62  SSLDREEARLELLEQQEEEESAEEEEEDPEEENEEEEEEYQRGPFGEEEEEDGDSYD 118

This entry is of sequences of two conserved domains separated by a region of low complexity, spanning some 200 residues. The function is unknown. Length = 178

>gnl|CDD|218538 pfam05285, SDA1, SDA1

 Score = 41.6 bits (98), Expect = 0.001
 Identities = 20/51 (39%), Positives = 31/51 (60%)

Query: 212 DSEYEDSDFDTSDEEYDSSEEEEEEEDEEEEEEEEEGEEEETETASSSTAK 262
           DSE E+   + + +  + S+EE  EEDEEE  EEEE E E+ + +  +T +
Sbjct: 131 DSEDEEEKDEAAKKAKEDSDEELSEEDEEEAAEEEEAEAEKEKASELATTR 181

This family consists of several SDA1 protein homologues. SDA1 is a Saccharomyces cerevisiae protein which is involved in the control of the actin cytoskeleton. The protein is essential for cell viability and is localised in the nucleus. Length = 317

>gnl|CDD|218538 pfam05285, SDA1, SDA1

 Score = 41.6 bits (98), Expect = 0.001
 Identities = 19/51 (37%), Positives = 29/51 (56%), Gaps = 1/51 (1%)

Query: 212 DSEYEDSDFDTSDEEYDSSEEEEEEEDEEEEEEEEEGEEEETETASSSTAK 262
           D E E SD +  +EE D + ++ +E+ +EE  EE+E E  E E A +   K
Sbjct: 124 DKEIESSDSE-DEEEKDEAAKKAKEDSDEELSEEDEEEAAEEEEAEAEKEK 173

This family consists of several SDA1 protein homologues. SDA1 is a Saccharomyces cerevisiae protein which is involved in the control of the actin cytoskeleton. The protein is essential for cell viability and is localised in the nucleus. Length = 317

>gnl|CDD|217503 pfam03344, Daxx, Daxx Family

 Score = 42.2 bits (99), Expect = 0.001
 Identities = 23/90 (25%), Positives = 39/90 (43%)

Query: 405 PTRPRDLQKTIQDTTGAYNRRRSSAMNHNRRWNARNGDSEYEDSDFDTSDEEYDSSEEEE 464
            T  R    +   +T   +   +S  +          + E E+ + +   EE +  +EEE
Sbjct: 413 GTSSRSSDPSKASSTSGESPSMASQESEEEESVEEEEEEEEEEEEEEQESEEEEGEDEEE 472

Query: 465 EEEEDEEEEEEEEEEEEEEEEEEGEEEETE 494
           EEE + +   EEE E   E + +GEE E +
Sbjct: 473 EEEVEADNGSEEEMEGSSEGDGDGEEPEED 502

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|148630 pfam07133, Merozoite_SPAM, Merozoite surface protein (SPAM)

 Score = 40.2 bits (94), Expect = 0.001
 Identities = 27/84 (32%), Positives = 39/84 (46%), Gaps = 5/84 (5%)

Query: 189 QEEVISNVKAIAKHLGIIKSSNGDSEYEDSDFDTSDEEYDSSEEEEEEEDEEEEE----- 243
            E ++ +VK  +     I   N D + E  + D  +EE D  E EE E+ E+EEE     
Sbjct: 19  DENLLEHVKITSWDKEDIIKENEDVKDEKQEDDEEEEEEDEEEIEEPEDIEDEEEIVEDE 78

Query: 244 EEEEGEEEETETASSSTAKNDPQM 267
           EEEE +EE+         KN   +
Sbjct: 79  EEEEEDEEDNVDLKDIEKKNINDI 102

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|218312 pfam04889, Cwf_Cwc_15, Cwf15/Cwc15 cell cycle control protein

 Score = 41.2 bits (97), Expect = 0.001
 Identities = 20/62 (32%), Positives = 28/62 (45%), Gaps = 11/62 (17%)

Query: 208 SSNGDSEYEDSDFDTSDEEYDS-----------SEEEEEEEDEEEEEEEEEGEEEETETA 256
            S+ DS+  D D D  D E ++            E  EE+E EEEE+  EE +  E E  
Sbjct: 123 DSSSDSDSSDDDSDDDDSEDETAALLRELEKIKKERAEEKEREEEEKAAEEEKAREEEIL 182

Query: 257 SS 258
           + 
Sbjct: 183 TG 184

This family represents Cwf15/Cwc15 (from Schizosaccharomyces pombe and Saccharomyces cerevisiae respectively) and their homologues. The function of these proteins is unknown, but they form part of the spliceosome and are thus thought to be involved in mRNA splicing. Length = 241

>gnl|CDD|145949 pfam03066, Nucleoplasmin, Nucleoplasmin

 Score = 40.0 bits (94), Expect = 0.001
 Identities = 14/29 (48%), Positives = 23/29 (79%)

Query: 449 DFDTSDEEYDSSEEEEEEEEDEEEEEEEE 477
           + ++ D+E D  EE++EE++DE+E EEEE
Sbjct: 111 EDESDDDEEDEEEEDDEEDDDEDESEEEE 139

Nucleoplasmins are also known as chromatin decondensation proteins. They bind to core histones and transfer DNA to them in a reaction that requires ATP. This is thought to play a role in the assembly of regular nucleosomal arrays. Length = 146

>gnl|CDD|145949 pfam03066, Nucleoplasmin, Nucleoplasmin

 Score = 40.0 bits (94), Expect = 0.001
 Identities = 14/29 (48%), Positives = 23/29 (79%)

Query: 219 DFDTSDEEYDSSEEEEEEEDEEEEEEEEE 247
           + ++ D+E D  EE++EE+D+E+E EEEE
Sbjct: 111 EDESDDDEEDEEEEDDEEDDDEDESEEEE 139

Nucleoplasmins are also known as chromatin decondensation proteins. They bind to core histones and transfer DNA to them in a reaction that requires ATP. This is thought to play a role in the assembly of regular nucleosomal arrays. Length = 146

>gnl|CDD|145949 pfam03066, Nucleoplasmin, Nucleoplasmin

 Score = 39.6 bits (93), Expect = 0.001
 Identities = 15/28 (53%), Positives = 23/28 (82%)

Query: 451 DTSDEEYDSSEEEEEEEEDEEEEEEEEE 478
           D SD++ +  EEE++EE+D+E+E EEEE
Sbjct: 112 DESDDDEEDEEEEDDEEDDDEDESEEEE 139

Nucleoplasmins are also known as chromatin decondensation proteins. They bind to core histones and transfer DNA to them in a reaction that requires ATP. This is thought to play a role in the assembly of regular nucleosomal arrays. Length = 146

>gnl|CDD|218737 pfam05764, YL1, YL1 nuclear protein

 Score = 41.2 bits (97), Expect = 0.001
 Identities = 21/51 (41%), Positives = 29/51 (56%), Gaps = 5/51 (9%)

Query: 461 EEEEEEEEDEE-----EEEEEEEEEEEEEEEEGEEEETETASSSTAKNDPQ 506
           EEE EE+E        EEEE++EE E EEEEE EE +++   S   + +  
Sbjct: 19  EEELEEDEFFWTYLLFEEEEDDEEFEIEEEEEEEEVDSDFDDSEDDEPESD 69

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|148051 pfam06213, CobT, Cobalamin biosynthesis protein CobT

 Score = 41.3 bits (97), Expect = 0.001
 Identities = 11/48 (22%), Positives = 28/48 (58%)

Query: 451 DTSDEEYDSSEEEEEEEEDEEEEEEEEEEEEEEEEEEGEEEETETASS 498
            + D   +  +E E  + ++ E+E++ +E+E++++ E EE  +  + S
Sbjct: 204 SSMDMAEELGDEPESADSEDNEDEDDPKEDEDDDQGEEEESGSSDSLS 251

This family consists of several bacterial cobalamin biosynthesis (CobT) proteins. CobT is involved in the transformation of precorrin-3 into cobyrinic acid. Length = 282

>gnl|CDD|227693 COG5406, COG5406, Nucleosome binding factor SPN, SPT16 subunit [Transcription / DNA replication, recombination, and repair / Chromatin structure and dynamics]

 Score = 42.3 bits (99), Expect = 0.001
 Identities = 20/62 (32%), Positives = 35/62 (56%), Gaps = 3/62 (4%)

Query: 436 WNARNGDSEYEDSDFDTSDEEYDSSEEEEEEEEDEEEEEEEEEEEEEEEEEE---GEEEE 492
           W+     S+ E  + +    EY++S ++E +E DE+EE +E  E+  E+E E    +EE+
Sbjct: 920 WSFLMVGSDDESDESEEEVSEYEASSDDESDETDEDEESDESSEDLSEDESENDSSDEED 979

Query: 493 TE 494
            E
Sbjct: 980 GE 981

Length = 1001

>gnl|CDD|227693 COG5406, COG5406, Nucleosome binding factor SPN, SPT16 subunit [Transcription / DNA replication, recombination, and repair / Chromatin structure and dynamics]

 Score = 41.9 bits (98), Expect = 0.001
 Identities = 18/40 (45%), Positives = 23/40 (57%)

Query: 213 SEYEDSDFDTSDEEYDSSEEEEEEEDEEEEEEEEEGEEEE 252
           SEYE S  D SDE  +  E +E  ED  E+E E +  +EE
Sbjct: 939 SEYEASSDDESDETDEDEESDESSEDLSEDESENDSSDEE 978

Length = 1001

>gnl|CDD|234311 TIGR03685, L12P_arch, 50S ribosomal protein L12P

 Score = 38.9 bits (91), Expect = 0.001
 Identities = 16/30 (53%), Positives = 20/30 (66%)

Query: 229 SSEEEEEEEDEEEEEEEEEGEEEETETASS 258
           ++    EEE+EEEEEEEEE EE E E  + 
Sbjct: 70  AAAAAAEEEEEEEEEEEEEEEESEEEAMAG 99

This model represents the L12P protein of the large (50S) subunit of the archaeal ribosome. Length = 105

>gnl|CDD|235795 PRK06402, rpl12p, 50S ribosomal protein L12P; Reviewed

 Score = 38.8 bits (91), Expect = 0.001
 Identities = 13/30 (43%), Positives = 18/30 (60%)

Query: 470 EEEEEEEEEEEEEEEEEEGEEEETETASSS 499
                  EE++EEEEEEE +EE  E A++ 
Sbjct: 71  AAAAAAAEEKKEEEEEEEEKEESEEEAAAG 100

Length = 106

>gnl|CDD|235795 PRK06402, rpl12p, 50S ribosomal protein L12P; Reviewed

 Score = 38.8 bits (91), Expect = 0.001
 Identities = 13/22 (59%), Positives = 15/22 (68%)

Query: 231 EEEEEEEDEEEEEEEEEGEEEE 252
               EE+ EEEEEEEE+ E EE
Sbjct: 74  AAAAEEKKEEEEEEEEKEESEE 95

Length = 106

>gnl|CDD|235795 PRK06402, rpl12p, 50S ribosomal protein L12P; Reviewed

 Score = 38.4 bits (90), Expect = 0.001
 Identities = 15/28 (53%), Positives = 17/28 (60%)

Query: 231 EEEEEEEDEEEEEEEEEGEEEETETASS 258
                EE +EEEEEEEE EE E E A+ 
Sbjct: 73  AAAAAEEKKEEEEEEEEKEESEEEAAAG 100

Length = 106

>gnl|CDD|100110 cd05832, Ribosomal_L12p, Ribosomal protein L12p

 Score = 39.0 bits (91), Expect = 0.001
 Identities = 15/25 (60%), Positives = 24/25 (96%)

Query: 459 SSEEEEEEEEDEEEEEEEEEEEEEE 483
           ++EE+ EE+E+E+++EEE+EEEEEE
Sbjct: 73  AAEEKAEEKEEEKKKEEEKEEEEEE 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|100110 cd05832, Ribosomal_L12p, Ribosomal protein L12p

 Score = 39.0 bits (91), Expect = 0.001
 Identities = 13/29 (44%), Positives = 21/29 (72%)

Query: 231 EEEEEEEDEEEEEEEEEGEEEETETASSS 259
             EE+ E++EEE+++EE +EEE E A + 
Sbjct: 73  AAEEKAEEKEEEKKKEEEKEEEEEEALAG 101

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|237622 PRK14140, PRK14140, heat shock protein GrpE; Provisional

 Score = 40.8 bits (96), Expect = 0.001
 Identities = 17/37 (45%), Positives = 21/37 (56%)

Query: 460 SEEEEEEEEDEEEEEEEEEEEEEEEEEEGEEEETETA 496
            E+ E+ EE+ EE E EE  E+E EEE  EEE     
Sbjct: 2   EEKNEQVEEEVEETEVEEAVEDEVEEETVEEESEAEL 38

Length = 191

>gnl|CDD|237622 PRK14140, PRK14140, heat shock protein GrpE; Provisional

 Score = 40.4 bits (95), Expect = 0.001
 Identities = 20/44 (45%), Positives = 23/44 (52%)

Query: 459 SSEEEEEEEEDEEEEEEEEEEEEEEEEEEGEEEETETASSSTAK 502
             + E+ EEE EE E EE  E+E EEE   EE E E      AK
Sbjct: 2   EEKNEQVEEEVEETEVEEAVEDEVEEETVEEESEAELLDEEQAK 45

Length = 191

>gnl|CDD|224969 COG2058, RPP1A, Ribosomal protein L12E/L44/L45/RPP1/RPP2 [Translation, ribosomal structure and biogenesis]

 Score = 38.5 bits (90), Expect = 0.001
 Identities = 13/33 (39%), Positives = 20/33 (60%)

Query: 459 SSEEEEEEEEDEEEEEEEEEEEEEEEEEEGEEE 491
           ++      E   E +E EEEE+EEE EEE +++
Sbjct: 70  AAAAAAGAEAAAEADEAEEEEKEEEAEEESDDD 102

Length = 109

>gnl|CDD|235640 PRK05901, PRK05901, RNA polymerase sigma factor; Provisional

 Score = 41.5 bits (98), Expect = 0.001
 Identities = 14/65 (21%), Positives = 38/65 (58%)

Query: 442 DSEYEDSDFDTSDEEYDSSEEEEEEEEDEEEEEEEEEEEEEEEEEEGEEEETETASSSTA 501
           D + +D   D   ++ D  E+++E+++D++ ++E+EE++E +E E+  +++        +
Sbjct: 135 DDDDDDDLDDDDIDDDDDDEDDDEDDDDDDVDDEDEEKKEAKELEKLSDDDDFVWDEDDS 194

Query: 502 KNDPQ 506
           +   Q
Sbjct: 195 EALRQ 199

Length = 509

>gnl|CDD|223003 PHA03169, PHA03169, hypothetical protein; Provisional

 Score = 41.5 bits (97), Expect = 0.001
 Identities = 14/95 (14%), Positives = 23/95 (24%), Gaps = 2/95 (2%)

Query: 412 QKTIQDTTGAYNRRRSSAMNHNRRWNARNGDSEYEDSD-FDTSDEEYDSSEEEEEEEEDE 470
           ++T  DT  A   R        +   + +G           +   E  +S    E     
Sbjct: 67  RQTESDTETAEESRHGEKEERGQGGPSGSGSESVGSPTPSPSGSAEELASGLSPENTSGS 126

Query: 471 EEE-EEEEEEEEEEEEEEGEEEETETASSSTAKND 504
             E               G  E     S + + N 
Sbjct: 127 SPESPASHSPPPSPPSHPGPHEPAPPESHNPSPNQ 161

Length = 413

>gnl|CDD|235250 PRK04195, PRK04195, replication factor C large subunit; Provisional

 Score = 41.8 bits (99), Expect = 0.001
 Identities = 18/46 (39%), Positives = 28/46 (60%)

Query: 458 DSSEEEEEEEEDEEEEEEEEEEEEEEEEEEGEEEETETASSSTAKN 503
              +    ++++EEEEEE+E++EEE+EEEE E EE +       K 
Sbjct: 430 KKKKAFAGKKKEEEEEEEKEKKEEEKEEEEEEAEEEKEEEEEKKKK 475

Length = 482

>gnl|CDD|227701 COG5414, COG5414, TATA-binding protein-associated factor [Transcription]

 Score = 42.0 bits (98), Expect = 0.001
 Identities = 17/61 (27%), Positives = 26/61 (42%), Gaps = 2/61 (3%)

Query: 454 DEEYDSSEEEEEEEEDEEEEEEEEEEEEEEEEEEGEEEETETASSSTAKNDPQM--VTVP 511
            E +    + +  +E  EE+EE++E EE E   E   +E         +   QM   T P
Sbjct: 304 AEAHKEEVQSDRPDEIGEEKEEDDENEENERHTELLADELNELEKGIEEKRRQMESATNP 363

Query: 512 I 512
           I
Sbjct: 364 I 364

Length = 392

>gnl|CDD|217783 pfam03896, TRAP_alpha, Translocon-associated protein (TRAP), alpha subunit

 Score = 41.7 bits (98), Expect = 0.001
 Identities = 18/54 (33%), Positives = 31/54 (57%)

Query: 448 SDFDTSDEEYDSSEEEEEEEEDEEEEEEEEEEEEEEEEEEGEEEETETASSSTA 501
             F ++ +  +  E E++  +++EE+E   EE+E E  EE E+EE E  +S  A
Sbjct: 26  GPFASAQDLTEDEEAEDDVVDEDEEDEAVVEEDENELTEEEEDEEGEVKASPDA 79

The alpha-subunit of the TRAP complex (TRAP alpha) is a single-spanning membrane protein of the endoplasmic reticulum (ER) which is found in proximity of nascent polypeptide chains translocating across the membrane. Length = 281

>gnl|CDD|217783 pfam03896, TRAP_alpha, Translocon-associated protein (TRAP), alpha subunit

 Score = 40.9 bits (96), Expect = 0.001
 Identities = 18/48 (37%), Positives = 28/48 (58%)

Query: 456 EYDSSEEEEEEEEDEEEEEEEEEEEEEEEEEEGEEEETETASSSTAKN 503
             D +E+EE E++  +E+EE+E   EE+E E  EEEE E      + +
Sbjct: 31  AQDLTEDEEAEDDVVDEDEEDEAVVEEDENELTEEEEDEEGEVKASPD 78

The alpha-subunit of the TRAP complex (TRAP alpha) is a single-spanning membrane protein of the endoplasmic reticulum (ER) which is found in proximity of nascent polypeptide chains translocating across the membrane. Length = 281

>gnl|CDD|219256 pfam06991, Prp19_bind, Splicing factor, Prp19-binding domain

 Score = 41.4 bits (97), Expect = 0.001
 Identities = 19/34 (55%), Positives = 23/34 (67%)

Query: 461 EEEEEEEEDEEEEEEEEEEEEEEEEEEGEEEETE 494
           E E  E E+E+E  EEEEEE EEEEE   E++ E
Sbjct: 1   ETEVLELEEEDESGEEEEEESEEEEETDSEDDME 34

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|221333 pfam11942, Spt5_N, Spt5 transcription elongation factor, acidic N-terminal

 Score = 38.6 bits (90), Expect = 0.001
 Identities = 16/39 (41%), Positives = 27/39 (69%)

Query: 454 DEEYDSSEEEEEEEEDEEEEEEEEEEEEEEEEEEGEEEE 492
           D E +  +EEEEEEE+E++ E+  +E+E  +E E E++ 
Sbjct: 3   DTEAEVDDEEEEEEEEEDDLEDLSDEDEFIDEAEAEDDR 41

This is the very acidic N-terminal region of the early transcription elongation factor Spt5. The Spt5-Spt4 complex regulates early transcription elongation by RNA polymerase II and has an imputed role in pre-mRNA processing via its physical association with mRNA capping enzymes. The actual function of this N-terminal domain is not known although it is dispensable for binding to Spt4. Length = 92

>gnl|CDD|221333 pfam11942, Spt5_N, Spt5 transcription elongation factor, acidic N-terminal

 Score = 38.6 bits (90), Expect = 0.001
 Identities = 14/36 (38%), Positives = 24/36 (66%)

Query: 461 EEEEEEEEDEEEEEEEEEEEEEEEEEEGEEEETETA 496
           + E E +++EEEEEEEE++ E+  +E+   +E E  
Sbjct: 3   DTEAEVDDEEEEEEEEEDDLEDLSDEDEFIDEAEAE 38

This is the very acidic N-terminal region of the early transcription elongation factor Spt5. The Spt5-Spt4 complex regulates early transcription elongation by RNA polymerase II and has an imputed role in pre-mRNA processing via its physical association with mRNA capping enzymes. The actual function of this N-terminal domain is not known although it is dispensable for binding to Spt4. Length = 92

>gnl|CDD|219563 pfam07767, Nop53, Nop53 (60S ribosomal biogenesis)

 Score = 42.0 bits (99), Expect = 0.001
 Identities = 13/33 (39%), Positives = 18/33 (54%)

Query: 458 DSSEEEEEEEEDEEEEEEEEEEEEEEEEEEGEE 490
           + SE   EE +D+ EEE ++E   E  E E E 
Sbjct: 236 EMSEGLLEESDDDGEEESDDESAWEGFESEYEP 268

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|224530 COG1614, CdhC, CO dehydrogenase/acetyl-CoA synthase beta subunit [Energy production and conversion]

 Score = 42.1 bits (99), Expect = 0.001
 Identities = 19/48 (39%), Positives = 24/48 (50%)

Query: 461 EEEEEEEEDEEEEEEEEEEEEEEEEEEGEEEETETASSSTAKNDPQMV 508
            EEEEEEE+EEEEE  E E   EE   G E       ++      ++V
Sbjct: 402 AEEEEEEEEEEEEEAAEAEAPMEEPVPGFEVPEMPMPAAGGGGGIKIV 449

Length = 470

>gnl|CDD|218482 pfam05178, Kri1, KRI1-like family

 Score = 38.8 bits (91), Expect = 0.001
 Identities = 21/80 (26%), Positives = 38/80 (47%), Gaps = 13/80 (16%)

Query: 186 NLVQEEVISNVKAIAKHLGIIKSSNGDSEYEDSDFDTS----------DEEYDSSEEEEE 235
           NL +EE+   ++ I K  G+  +   + +  D DFD             ++Y   E+EEE
Sbjct: 20  NLKREEIEEKLEKIKKVAGLRGADLSEEDLADGDFDPEKWDEEMAKLFGDDYYEEEDEEE 79

Query: 236 E---EDEEEEEEEEEGEEEE 252
           +   +D+E+  +    E+EE
Sbjct: 80  KPTWDDDEDIGDLVPDEDEE 99

The yeast member of this family (Kri1p) is found to be required for 40S ribosome biogenesis in the nucleolus. Length = 99

>gnl|CDD|218555 pfam05320, Pox_RNA_Pol_19, Poxvirus DNA-directed RNA polymerase 19 kDa subunit

 Score = 40.1 bits (94), Expect = 0.001
 Identities = 17/43 (39%), Positives = 25/43 (58%)

Query: 221 DTSDEEYDSSEEEEEEEDEEEEEEEEEGEEEETETASSSTAKN 263
           D+ D     S++++ EE EEEEE+EE+ E  E+   SS    N
Sbjct: 3   DSDDIIDYESDDDDSEEYEEEEEDEEDAESLESSDVSSLKQSN 45

This family contains several DNA-directed RNA polymerase 19 kDa polypeptides. The Poxvirus DNA-directed RNA polymerase (EC: 2.7.7.6) catalyzes DNA-template-directed extension of the 3'-end of an RNA strand by one nucleotide at a time. Length = 167

>gnl|CDD|237284 PRK13108, PRK13108, prolipoprotein diacylglyceryl transferase; Reviewed

 Score = 41.9 bits (98), Expect = 0.001
 Identities = 20/108 (18%), Positives = 35/108 (32%), Gaps = 7/108 (6%)

Query: 403 GCPTRPRDLQKTIQDTTGAYNRRRSSAMNHNRRWNARNGDSEYEDSDFDTSDEEYDSSEE 462
           G P +P D+ + ++            A     +   R+G+S     +   +D E +   +
Sbjct: 321 GEPNQPDDVAEAVKAE--VAEVTDEVAAESVVQVADRDGESTPAVEETSEADIEREQPGD 378

Query: 463 -----EEEEEEDEEEEEEEEEEEEEEEEEEGEEEETETASSSTAKNDP 505
                    + D E      EE      E  +E E E    +    DP
Sbjct: 379 LAGQAPAAHQVDAEAASAAPEEPAALASEAHDETEPEVPEKAAPIPDP 426

Length = 460

>gnl|CDD|215914 pfam00428, Ribosomal_60s, 60s Acidic ribosomal protein

 Score = 38.4 bits (90), Expect = 0.001
 Identities = 12/24 (50%), Positives = 17/24 (70%)

Query: 465 EEEEDEEEEEEEEEEEEEEEEEEG 488
                 EEE++EEEEEEEE+++ G
Sbjct: 61  AAAAAAEEEKKEEEEEEEEDDDMG 84

This family includes archaebacterial L12, eukaryotic P0, P1 and P2. Length = 88

>gnl|CDD|227596 COG5271, MDN1, AAA ATPase containing von Willebrand factor type A (vWA) domain [General function prediction only]

 Score = 42.3 bits (99), Expect = 0.001
 Identities = 16/71 (22%), Positives = 36/71 (50%), Gaps = 6/71 (8%)

Query: 440  NGDSEYEDS--DFDTSDEEYDSSEEEEEEEEDEEEEEEEEEEEEEEE----EEEGEEEET 493
              D +  D   D D  D + ++++E +EE + E++E  ++E+  EE     E+  +++ +
Sbjct: 3994 KLDEKEGDVSKDSDLEDMDMEAADENKEEADAEKDEPMQDEDPLEENNTLDEDIQQDDFS 4053

Query: 494  ETASSSTAKND 504
            + A      N+
Sbjct: 4054 DLAEDDEKMNE 4064

Length = 4600

>gnl|CDD|111875 pfam03032, Brevenin, Brevenin/esculentin/gaegurin/rugosin family

 Score = 36.9 bits (86), Expect = 0.001
 Identities = 15/24 (62%), Positives = 19/24 (79%)

Query: 463 EEEEEEDEEEEEEEEEEEEEEEEE 486
           EEE+ EDEEE E+EEE EE+ E +
Sbjct: 22  EEEKREDEEENEDEEEGEEQSEVK 45

This family contains a number of defence peptides secreted from the skin of amphibians, including the opiate-like dermorphins and deltorphins, and the antimicrobial dermoseptins and temporins. The alignment for this family includes the signal peptide. Length = 46

>gnl|CDD|148630 pfam07133, Merozoite_SPAM, Merozoite surface protein (SPAM)

 Score = 39.1 bits (91), Expect = 0.002
 Identities = 18/64 (28%), Positives = 34/64 (53%), Gaps = 2/64 (3%)

Query: 442 DSEYEDSDFDTSDEEYDS--SEEEEEEEEDEEEEEEEEEEEEEEEEEEGEEEETETASSS 499
           + E E+   +  D E +    E+EEEEEEDEE+  + ++ E++   +     + + A + 
Sbjct: 55  EEEDEEEIEEPEDIEDEEEIVEDEEEEEEDEEDNVDLKDIEKKNINDIFNSTQDDNAQNL 114

Query: 500 TAKN 503
            +KN
Sbjct: 115 ISKN 118

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|220972 pfam11081, DUF2890, Protein of unknown function (DUF2890)

 Score = 39.9 bits (93), Expect = 0.002
 Identities = 18/59 (30%), Positives = 30/59 (50%)

Query: 214 EYEDSDFDTSDEEYDSSEEEEEEEDEEEEEEEEEGEEEETETASSSTAKNDPQMVTVPI 272
           E  DS  +  +E+ +  E+ E+  DEE+EE EE  EE    + + S++       T+ I
Sbjct: 22  EDWDSQAEEVEEDEEEMEDWEDSLDEEDEEAEEVEEETAASSKAPSSSSKSSSQETISI 80

This family is conserved in dsDNA adenoviruses of vertebrates. The function is not known. Length = 172

>gnl|CDD|218223 pfam04712, Radial_spoke, Radial spokehead-like protein

 Score = 41.6 bits (98), Expect = 0.002
 Identities = 16/28 (57%), Positives = 21/28 (75%)

Query: 227 YDSSEEEEEEEDEEEEEEEEEGEEEETE 254
            +  +++EEEE E+EEEEEEE E EE E
Sbjct: 342 VNPEQKDEEEEQEDEEEEEEEEEPEEPE 369

This family includes the radial spoke head proteins RSP4 and RSP6 from Chlamydomonas reinhardtii, and several eukaryotic homologues, including mammalian RSHL1, the protein product of a familial ciliary dyskinesia candidate gene. Length = 481

>gnl|CDD|218223 pfam04712, Radial_spoke, Radial spokehead-like protein

 Score = 41.2 bits (97), Expect = 0.002
 Identities = 19/25 (76%), Positives = 21/25 (84%)

Query: 231 EEEEEEEDEEEEEEEEEGEEEETET 255
           +EEEE+EDEEEEEEEEE EE E E 
Sbjct: 348 DEEEEQEDEEEEEEEEEPEEPEPEE 372

This family includes the radial spoke head proteins RSP4 and RSP6 from Chlamydomonas reinhardtii, and several eukaryotic homologues, including mammalian RSHL1, the protein product of a familial ciliary dyskinesia candidate gene. Length = 481

>gnl|CDD|217861 pfam04050, Upf2, Up-frameshift suppressor 2

 Score = 39.7 bits (93), Expect = 0.002
 Identities = 13/44 (29%), Positives = 27/44 (61%)

Query: 214 EYEDSDFDTSDEEYDSSEEEEEEEDEEEEEEEEEGEEEETETAS 257
              +S+ D  +E+ +  EE+E++E  +EEE +   +E++ E+ S
Sbjct: 1   SGSESESDDGEEDEELPEEDEDDESSDEEEVDLPDDEQDEESDS 44

Transcripts harbouring premature signals for translation termination are recognised and rapidly degraded by eukaryotic cells through a pathway known as nonsense-mediated mRNA decay. In Saccharomyces cerevisiae, three trans-acting factors (Upf1 to Upf3) are required for nonsense-mediated mRNA decay. Length = 171

>gnl|CDD|227693 COG5406, COG5406, Nucleosome binding factor SPN, SPT16 subunit [Transcription / DNA replication, recombination, and repair / Chromatin structure and dynamics]

 Score = 41.2 bits (96), Expect = 0.002
 Identities = 23/49 (46%), Positives = 32/49 (65%), Gaps = 3/49 (6%)

Query: 453 SDEEYDSSEEEEEEEE---DEEEEEEEEEEEEEEEEEEGEEEETETASS 498
           SD+E D SEEE  E E   D+E +E +E+EE +E  E+  E+E+E  SS
Sbjct: 927 SDDESDESEEEVSEYEASSDDESDETDEDEESDESSEDLSEDESENDSS 975

Length = 1001

>gnl|CDD|184885 PRK14891, PRK14891, 50S ribosomal protein L24e/unknown domain fusion protein; Provisional

 Score = 38.8 bits (90), Expect = 0.002
 Identities = 10/66 (15%), Positives = 29/66 (43%)

Query: 441 GDSEYEDSDFDTSDEEYDSSEEEEEEEEDEEEEEEEEEEEEEEEEEEGEEEETETASSST 500
             +    +     + E   ++E+ +E  + +  +E +EEEE +E  +   +E +  +   
Sbjct: 62  PAAAATAAAEAAEEAEAADADEDADEAAEADAADEADEEEETDEAVDETADEADAEAEEA 121

Query: 501 AKNDPQ 506
            + + +
Sbjct: 122 DEEEDE 127

Length = 131

>gnl|CDD|240329 PTZ00248, PTZ00248, eukaryotic translation initiation factor 2 subunit 1; Provisional

 Score = 40.8 bits (96), Expect = 0.002
 Identities = 15/35 (42%), Positives = 24/35 (68%)

Query: 460 SEEEEEEEEDEEEEEEEEEEEEEEEEEEGEEEETE 494
             +EE+ EE  E+ EEEEEE++  E E+ +EE+ +
Sbjct: 273 GGDEEDLEELLEKAEEEEEEDDYSESEDEDEEDED 307

Length = 319

>gnl|CDD|237063 PRK12329, nusA, transcription elongation factor NusA; Provisional

 Score = 41.3 bits (97), Expect = 0.002
 Identities = 15/55 (27%), Positives = 21/55 (38%)

Query: 446 EDSDFDTSDEEYDSSEEEEEEEEDEEEEEEEEEEEEEEEEEEGEEEETETASSST 500
           E+       EE   +E+ E  EED    E     E+E E+E+  EE         
Sbjct: 394 EEEALQREAEERLEAEQAERAEEDARLRELYPLPEDEFEDEDELEEAQPEEEEEA 448

Length = 449

>gnl|CDD|237063 PRK12329, nusA, transcription elongation factor NusA; Provisional

 Score = 40.9 bits (96), Expect = 0.002
 Identities = 13/40 (32%), Positives = 20/40 (50%)

Query: 455 EEYDSSEEEEEEEEDEEEEEEEEEEEEEEEEEEGEEEETE 494
           +   + E+    E     E+E E+E+E EE +  EEEE  
Sbjct: 410 QAERAEEDARLRELYPLPEDEFEDEDELEEAQPEEEEEAR 449

Length = 449

>gnl|CDD|215774 pfam00183, HSP90, Hsp90 protein

 Score = 41.3 bits (97), Expect = 0.002
 Identities = 17/41 (41%), Positives = 25/41 (60%)

Query: 222 TSDEEYDSSEEEEEEEDEEEEEEEEEGEEEETETASSSTAK 262
             +EE +  EE++EEE++  ++EEE  EEEE E     T K
Sbjct: 36  PDEEEEEEKEEKKEEEEKTTDKEEEVDEEEEKEEKKKKTKK 76

Length = 529

>gnl|CDD|215774 pfam00183, HSP90, Hsp90 protein

 Score = 41.3 bits (97), Expect = 0.002
 Identities = 22/60 (36%), Positives = 37/60 (61%), Gaps = 3/60 (5%)

Query: 436 WNARNGDSEYEDSDFDTSDEEYDSSEEEEEEEEDEEEEEEEEEEEEEEEEEEGEEEETET 495
           W  +  + E  D + +   EE    +EEEE+  D+EEE +EEEE+EE++++  + +ET T
Sbjct: 26  WVEKEVEKEVPDEEEEEEKEE---KKEEEEKTTDKEEEVDEEEEKEEKKKKTKKVKETTT 82

Length = 529

>gnl|CDD|203043 pfam04546, Sigma70_ner, Sigma-70, non-essential region

 Score = 39.9 bits (94), Expect = 0.002
 Identities = 12/41 (29%), Positives = 24/41 (58%)

Query: 212 DSEYEDSDFDTSDEEYDSSEEEEEEEDEEEEEEEEEGEEEE 252
           D     +    +  E +  EE+ E++D+++E+E+E+ EEE 
Sbjct: 31  DPNAAAAAATAAAIESELDEEDLEDDDDDDEDEDEDDEEEA 71

The domain is found in the primary vegetative sigma factor. The function of this domain is unclear and can be removed without loss of function. Length = 211

>gnl|CDD|220413 pfam09805, Nop25, Nucleolar protein 12 (25kDa)

 Score = 38.5 bits (90), Expect = 0.002
 Identities = 14/39 (35%), Positives = 21/39 (53%)

Query: 454 DEEYDSSEEEEEEEEDEEEEEEEEEEEEEEEEEEGEEEE 492
             E ++ +EE+ E ED E+ E++E E   E      EEE
Sbjct: 78  LLEEENDDEEDAETEDTEDVEDDEWEGFPEPTVTDYEEE 116

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|117592 pfam09026, Cenp-B_dimeris, Centromere protein B dimerisation domain

 Score = 37.8 bits (87), Expect = 0.002
 Identities = 13/35 (37%), Positives = 27/35 (77%)

Query: 220 FDTSDEEYDSSEEEEEEEDEEEEEEEEEGEEEETE 254
           F   +E+ DS  +EEE++D+E+EE+++E ++E+ +
Sbjct: 5   FLEGEEDSDSDSDEEEDDDDEDEEDDDEDDDEDDD 39

The centromere protein B (CENP-B) dimerisation domain is composed of two alpha-helices, which are folded into an antiparallel configuration. Dimerisation of CENP-B is mediated by this domain, in which monomers dimerise to form a symmetrical, antiparallel, four-helix bundle structure with a large hydrophobic patch in which 23 residues of one monomer form van der Waals contacts with the other monomer. This CENP-B dimer configuration may be suitable for capturing two distant CENP-B boxes during centromeric heterochromatin formation. Length = 101

>gnl|CDD|117592 pfam09026, Cenp-B_dimeris, Centromere protein B dimerisation domain

 Score = 37.8 bits (87), Expect = 0.002
 Identities = 9/34 (26%), Positives = 28/34 (82%)

Query: 458 DSSEEEEEEEEDEEEEEEEEEEEEEEEEEEGEEE 491
           +  E+ + + ++EE++++E+EE+++E+++E ++E
Sbjct: 7   EGEEDSDSDSDEEEDDDDEDEEDDDEDDDEDDDE 40

The centromere protein B (CENP-B) dimerisation domain is composed of two alpha-helices, which are folded into an antiparallel configuration. Dimerisation of CENP-B is mediated by this domain, in which monomers dimerise to form a symmetrical, antiparallel, four-helix bundle structure with a large hydrophobic patch in which 23 residues of one monomer form van der Waals contacts with the other monomer. This CENP-B dimer configuration may be suitable for capturing two distant CENP-B boxes during centromeric heterochromatin formation. Length = 101

>gnl|CDD|217049 pfam02459, Adeno_terminal, Adenoviral DNA terminal protein

 Score = 41.6 bits (98), Expect = 0.002
 Identities = 20/30 (66%), Positives = 20/30 (66%)

Query: 466 EEEDEEEEEEEEEEEEEEEEEEGEEEETET 495
               E EEEEEEEEE  EEEEE EEEE  T
Sbjct: 300 PSPPEPEEEEEEEEEVPEEEEEEEEEEERT 329

This protein is covalently attached to the terminii of replicating DNA in vivo. Length = 548

>gnl|CDD|217049 pfam02459, Adeno_terminal, Adenoviral DNA terminal protein

 Score = 41.2 bits (97), Expect = 0.002
 Identities = 24/48 (50%), Positives = 27/48 (56%), Gaps = 6/48 (12%)

Query: 455 EEYDSSEEEEEEEEDEEEEEEEEEEEEE------EEEEEGEEEETETA 496
           EE +  EEE  EEE+EEEEEEE   EEE      E     EEE T +A
Sbjct: 306 EEEEEEEEEVPEEEEEEEEEEERTFEEEVRATVAEAIRLLEEELTVSA 353

This protein is covalently attached to the terminii of replicating DNA in vivo. Length = 548

>gnl|CDD|217203 pfam02724, CDC45, CDC45-like protein

 Score = 41.5 bits (98), Expect = 0.002
 Identities = 15/58 (25%), Positives = 28/58 (48%)

Query: 449 DFDTSDEEYDSSEEEEEEEEDEEEEEEEEEEEEEEEEEEGEEEETETASSSTAKNDPQ 506
           D    +EE       ++   D EE+++++EE +EE+EE  + E+ E        +D  
Sbjct: 102 DDGDIEEELQDEPRYDDAYRDLEEDDDDDEESDEEDEESSKSEDDEDDDDDDDDDDIA 159

CDC45 is an essential gene required for initiation of DNA replication in S. cerevisiae, forming a complex with MCM5/CDC46. Homologues of CDC45 have been identified in human, mouse and smut fungus among others. Length = 583

>gnl|CDD|100110 cd05832, Ribosomal_L12p, Ribosomal protein L12p

 Score = 38.2 bits (89), Expect = 0.002
 Identities = 15/29 (51%), Positives = 21/29 (72%)

Query: 230 SEEEEEEEDEEEEEEEEEGEEEETETASS 258
           + EE+ EE EEE+++EEE EEEE E  + 
Sbjct: 73  AAEEKAEEKEEEKKKEEEKEEEEEEALAG 101

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|114603 pfam05887, Trypan_PARP, Procyclic acidic repetitive protein (PARP)

 Score = 38.8 bits (89), Expect = 0.002
 Identities = 26/61 (42%), Positives = 31/61 (50%)

Query: 451 DTSDEEYDSSEEEEEEEEDEEEEEEEEEEEEEEEEEEGEEEETETASSSTAKNDPQMVTV 510
           D  +EE +   EEE EEE E EEE EEE E EE  EE  E E E       + +P+    
Sbjct: 62  DEPEEEEEPEPEEEGEEEPEPEEEGEEEPEPEETGEEEPEPEPEPEPEPEPEPEPEPEPE 121

Query: 511 P 511
           P
Sbjct: 122 P 122

This family consists of several Trypanosoma brucei procyclic acidic repetitive protein (PARP) like sequences. The procyclic acidic repetitive protein (parp) genes of Trypanosoma brucei encode a small family of abundant surface proteins whose expression is restricted to the procyclic form of the parasite. They are found at two unlinked loci, parpA and parpB; transcription of both loci is developmentally regulated. Length = 145

>gnl|CDD|217840 pfam04006, Mpp10, Mpp10 protein

 Score = 41.5 bits (97), Expect = 0.002
 Identities = 18/62 (29%), Positives = 33/62 (53%)

Query: 441 GDSEYEDSDFDTSDEEYDSSEEEEEEEEDEEEEEEEEEEEEEEEEEEGEEEETETASSST 500
              +  +S  D SD     SE+  ++EE+EEE+E  E+E  ++E+E     E+E++    
Sbjct: 92  AKLQDSESHEDGSDGSDMDSEDSADDEEEEEEDESLEDEMIDDEDEADLFNESESSLEDL 151

Query: 501 AK 502
           + 
Sbjct: 152 SD 153

This family includes proteins related to Mpp10 (M phase phosphoprotein 10). The U3 small nucleolar ribonucleoprotein (snoRNP) is required for three cleavage events that generate the mature 18S rRNA from the pre-rRNA. In Saccharomyces cerevisiae, depletion of Mpp10, a U3 snoRNP-specific protein, halts 18S rRNA production and impairs cleavage at the three U3 snoRNP-dependent sites. Length = 613

>gnl|CDD|237622 PRK14140, PRK14140, heat shock protein GrpE; Provisional

 Score = 39.6 bits (93), Expect = 0.002
 Identities = 17/43 (39%), Positives = 24/43 (55%)

Query: 452 TSDEEYDSSEEEEEEEEDEEEEEEEEEEEEEEEEEEGEEEETE 494
             +E  ++  EE  E+E EEE  EEE E E  +EE+ +  E E
Sbjct: 8   VEEEVEETEVEEAVEDEVEEETVEEESEAELLDEEQAKIAELE 50

Length = 191

>gnl|CDD|224969 COG2058, RPP1A, Ribosomal protein L12E/L44/L45/RPP1/RPP2 [Translation, ribosomal structure and biogenesis]

 Score = 38.2 bits (89), Expect = 0.002
 Identities = 12/34 (35%), Positives = 19/34 (55%)

Query: 459 SSEEEEEEEEDEEEEEEEEEEEEEEEEEEGEEEE 492
           ++       E   E +E EEEE+EEE EE  +++
Sbjct: 69  AAAAAAAGAEAAAEADEAEEEEKEEEAEEESDDD 102

Length = 109

>gnl|CDD|179712 PRK04019, rplP0, acidic ribosomal protein P0; Validated

 Score = 40.6 bits (96), Expect = 0.002
 Identities = 26/74 (35%), Positives = 39/74 (52%), Gaps = 3/74 (4%)

Query: 181 LAMSFNLVQEEVISNV--KAIAKHLGIIKSSNGDSEYEDSDFDTSDEEYDSSEEEEEEED 238
           LA+   +V  E   ++  KA+A+ L  + ++  D +  D +          +   EEEE+
Sbjct: 248 LAVEAGIVTPETADDILSKAVAQAL-ALAAALADKDALDEELKEVLSAQAQAAAAEEEEE 306

Query: 239 EEEEEEEEEGEEEE 252
           EEEEEEEEE  EEE
Sbjct: 307 EEEEEEEEEPSEEE 320

Length = 330

>gnl|CDD|130712 TIGR01651, CobT, cobaltochelatase, CobT subunit

 Score = 41.1 bits (96), Expect = 0.002
 Identities = 17/67 (25%), Positives = 28/67 (41%), Gaps = 1/67 (1%)

Query: 442 DSEYEDSDFDTSDEEYDSSEEEEE-EEEDEEEEEEEEEEEEEEEEEEGEEEETETASSST 500
           D E  D D  T +E+ +  E E E +E    +E E  + E E  EEE  + + +     +
Sbjct: 211 DEEDGDDDQPTENEQEEQGEGEGEGQEGSAPQESEATDRESESGEEEMVQSDQDDLPDES 270

Query: 501 AKNDPQM 507
             +    
Sbjct: 271 DDDSETP 277

This model describes Pseudomonas denitrificans CobT gene product, which is a cobalt chelatase subunit that functions in cobalamin biosynthesis. Cobalamin (vitamin B12) can be synthesized via several pathways, including an aerobic pathway (found in Pseudomonas denitrificans) and an anaerobic pathway (found in P. shermanii and Salmonella typhimurium). These pathways differ in the point of cobalt insertion during corrin ring formation. There are apparently a number of variations on these two pathways, where the major differences seem to be concerned with the process of ring contraction. Confusion regarding the functions of enzymes found in the aerobic vs. anaerobic pathways has arisen because nonhomologous genes in these different pathways were given the same gene symbols. Thus, cobT in the aerobic pathway (P. denitrificans) is not a homolog of cobT in the anaerobic pathway (S. typhimurium). It should be noted that E. coli synthesizes cobalamin only when it is supplied with the precursor cobinamide, which is a complex intermediate. Additionally, all E. coli cobalamin synthesis genes (cobU, cobS and cobT) were named after their Salmonella typhimurium homologs which function in the anaerobic cobalamin synthesis pathway. This model describes the aerobic cobalamin pathway Pseudomonas denitrificans CobT gene product, which is a cobalt chelatase subunit, with a MW ~70 kDa. The aerobic pathway cobalt chelatase is a heterotrimeric, ATP-dependent enzyme that catalyzes cobalt insertion during cobalamin biosynthesis. The other two subunits are the P. denitrificans CobS (TIGR01650) and CobN (pfam02514 CobN/Magnesium Chelatase) proteins. To avoid potential confusion with the nonhomologous Salmonella typhimurium/E.coli cobT gene product, the P. denitrificans gene symbol is not used in the name of this model [Biosynthesis of cofactors, prosthetic groups, and carriers, Heme, porphyrin, and cobalamin]. Length = 600

>gnl|CDD|202096 pfam02029, Caldesmon, Caldesmon

 Score = 41.2 bits (96), Expect = 0.002
 Identities = 22/99 (22%), Positives = 36/99 (36%), Gaps = 3/99 (3%)

Query: 409 RDLQKTIQDTTGAYNRRRSSAMNHNRRWNARNGDSEYEDSDFDTSDEEYDSSEEEEEEEE 468
           R  +     T  + +         +    A N   E E+ +    + E     E   + E
Sbjct: 80  RQKEFKPTSTDQSLSEPSRRMQEDS---GAENETVEEEEKEESREEREEVEETEGVTKSE 136

Query: 469 DEEEEEEEEEEEEEEEEEEGEEEETETASSSTAKNDPQM 507
            + +  + EE ++EE+E E EEEE     S    N   M
Sbjct: 137 QKNDWRDAEECQKEEKEPEPEEEEKPKRGSLEENNGEFM 175

Length = 431

>gnl|CDD|235549 PRK05658, PRK05658, RNA polymerase sigma factor RpoD; Validated

 Score = 40.9 bits (97), Expect = 0.002
 Identities = 12/41 (29%), Positives = 23/41 (56%)

Query: 454 DEEYDSSEEEEEEEEDEEEEEEEEEEEEEEEEEEGEEEETE 494
           D   +        E +E +++E+EEEEE+E ++    +E+E
Sbjct: 175 DPNAEEDPAHVGSELEELDDDEDEEEEEDENDDSLAADESE 215

Length = 619

>gnl|CDD|235549 PRK05658, PRK05658, RNA polymerase sigma factor RpoD; Validated

 Score = 40.9 bits (97), Expect = 0.002
 Identities = 11/48 (22%), Positives = 24/48 (50%)

Query: 448 SDFDTSDEEYDSSEEEEEEEEDEEEEEEEEEEEEEEEEEEGEEEETET 495
            +      + ++ E+      + EE +++E+EEEEE+E +      E+
Sbjct: 167 RELIDGFVDPNAEEDPAHVGSELEELDDDEDEEEEEDENDDSLAADES 214

Length = 619

>gnl|CDD|223003 PHA03169, PHA03169, hypothetical protein; Provisional

 Score = 41.5 bits (97), Expect = 0.002
 Identities = 14/60 (23%), Positives = 20/60 (33%), Gaps = 2/60 (3%)

Query: 441 GDSEYEDSDFDTSDEEYDSSEEEEEEEEDEEEEEEEEEEEEEEEEEEGEEEETETASSST 500
             S    S  D   E    S   ++      ++  E E+E  E E EG       + S T
Sbjct: 199 TSSPPPQSPPDEPGE--PQSPTPQQAPSPNTQQAVEHEDEPTEPEREGPPFPGHRSHSYT 256

Length = 413

>gnl|CDD|223003 PHA03169, PHA03169, hypothetical protein; Provisional

 Score = 40.7 bits (95), Expect = 0.002
 Identities = 9/61 (14%), Positives = 13/61 (21%)

Query: 438 ARNGDSEYEDSDFDTSDEEYDSSEEEEEEEEDEEEEEEEEEEEEEEEEEEGEEEETETAS 497
                S  E +   + +    SS E                  E    E       +  S
Sbjct: 105 PSPSGSAEELASGLSPENTSGSSPESPASHSPPPSPPSHPGPHEPAPPESHNPSPNQQPS 164

Query: 498 S 498
           S
Sbjct: 165 S 165

Length = 413

>gnl|CDD|235250 PRK04195, PRK04195, replication factor C large subunit; Provisional

 Score = 41.4 bits (98), Expect = 0.002
 Identities = 21/54 (38%), Positives = 31/54 (57%)

Query: 454 DEEYDSSEEEEEEEEDEEEEEEEEEEEEEEEEEEGEEEETETASSSTAKNDPQM 507
           +EE    +++    + +EEEEEEE+E++EEE+EE EEE  E       K   Q 
Sbjct: 424 EEEKKEKKKKAFAGKKKEEEEEEEKEKKEEEKEEEEEEAEEEKEEEEEKKKKQA 477

Length = 482

>gnl|CDD|235250 PRK04195, PRK04195, replication factor C large subunit; Provisional

 Score = 41.4 bits (98), Expect = 0.002
 Identities = 20/55 (36%), Positives = 32/55 (58%)

Query: 455 EEYDSSEEEEEEEEDEEEEEEEEEEEEEEEEEEGEEEETETASSSTAKNDPQMVT 509
           EE    ++++     ++EEEEEEE+E++EEE+E EEEE E       +   +  T
Sbjct: 424 EEEKKEKKKKAFAGKKKEEEEEEEKEKKEEEKEEEEEEAEEEKEEEEEKKKKQAT 478

Length = 482

>gnl|CDD|235250 PRK04195, PRK04195, replication factor C large subunit; Provisional

 Score = 41.1 bits (97), Expect = 0.002
 Identities = 20/43 (46%), Positives = 33/43 (76%)

Query: 452 TSDEEYDSSEEEEEEEEDEEEEEEEEEEEEEEEEEEGEEEETE 494
             +++  +   +++EEE+EEE+E++EEE+EEEEEE  EE+E E
Sbjct: 427 KKEKKKKAFAGKKKEEEEEEEKEKKEEEKEEEEEEAEEEKEEE 469

Length = 482

>gnl|CDD|227563 COG5238, RNA1, Ran GTPase-activating protein (RanGAP) involved in mRNA processing and transport [Signal transduction mechanisms / RNA processing and modification]

 Score = 41.1 bits (96), Expect = 0.002
 Identities = 15/54 (27%), Positives = 24/54 (44%)

Query: 446 EDSDFDTSDEEYDSSEEEEEEEEDEEEEEEEEEEEEEEEEEEGEEEETETASSS 499
           E  +    D   + S +EE E+E E +E   EE  E E  E   ++  E  + +
Sbjct: 333 EVVEKQEGDVVTEESTDEESEDEVEIDESVIEEVAEMELLEVQVDDLAERLAET 386

Length = 388

>gnl|CDD|220377 pfam09747, DUF2052, Coiled-coil domain containing protein (DUF2052)

 Score = 39.3 bits (92), Expect = 0.002
 Identities = 20/57 (35%), Positives = 27/57 (47%)

Query: 455 EEYDSSEEEEEEEEDEEEEEEEEEEEEEEEEEEGEEEETETASSSTAKNDPQMVTVP 511
           EE      E++EEE+  EEEEE+ EEE EEEEE  +            +    +  P
Sbjct: 67  EEARLELLEQQEEEESAEEEEEDPEEENEEEEEEYQRGPFGEEEEEDGDSYDELPTP 123

This entry is of sequences of two conserved domains separated by a region of low complexity, spanning some 200 residues. The function is unknown. Length = 178

>gnl|CDD|237284 PRK13108, PRK13108, prolipoprotein diacylglyceryl transferase; Reviewed

 Score = 41.1 bits (96), Expect = 0.002
 Identities = 14/69 (20%), Positives = 25/69 (36%)

Query: 438 ARNGDSEYEDSDFDTSDEEYDSSEEEEEEEEDEEEEEEEEEEEEEEEEEEGEEEETETAS 497
            + GD   +       D E  S+  EE      E  +E E E  E+     +  + +  +
Sbjct: 374 EQPGDLAGQAPAAHQVDAEAASAAPEEPAALASEAHDETEPEVPEKAAPIPDPAKPDELA 433

Query: 498 SSTAKNDPQ 506
            +   +DP 
Sbjct: 434 VAGPGDDPA 442

Length = 460

>gnl|CDD|217392 pfam03153, TFIIA, Transcription factor IIA, alpha/beta subunit

 Score = 41.3 bits (97), Expect = 0.002
 Identities = 11/53 (20%), Positives = 25/53 (47%), Gaps = 2/53 (3%)

Query: 433 NRRWNARNGDSEYEDSDFDTSDEEYDSSEEEEE--EEEDEEEEEEEEEEEEEE 483
           ++R      D    D + D SD++ D    E +  + +D+  +E+ E+  + +
Sbjct: 236 SKRRTIAQIDGIDSDDEGDGSDDDDDEDAIESDLDDSDDDVSDEDGEDLFDTD 288

Transcription initiation factor IIA (TFIIA) is a heterotrimer, the three subunits being known as alpha, beta, and gamma, in order of molecular weight. The N and C-terminal domains of the gamma subunit are represented in pfam02268 and pfam02751, respectively. This family represents the precursor that yields both the alpha and beta subunits. The TFIIA heterotrimer is an essential general transcription initiation factor for the expression of genes transcribed by RNA polymerase II. Together with TFIID, TFIIA binds to the promoter region; this is the first step in the formation of a pre-initiation complex (PIC). Binding of the rest of the transcription machinery follows this step. After initiation, the PIC does not completely dissociate from the promoter. Some components, including TFIIA, remain attached and re-initiate a subsequent round of transcription. Length = 332

>gnl|CDD|217392 pfam03153, TFIIA, Transcription factor IIA, alpha/beta subunit

 Score = 40.9 bits (96), Expect = 0.002
 Identities = 15/61 (24%), Positives = 29/61 (47%)

Query: 191 EVISNVKAIAKHLGIIKSSNGDSEYEDSDFDTSDEEYDSSEEEEEEEDEEEEEEEEEGEE 250
           +V+   K  AK       +  D    D + D SD++ D    E + +D +++  +E+GE+
Sbjct: 224 KVLKQPKKQAKSSKRRTIAQIDGIDSDDEGDGSDDDDDEDAIESDLDDSDDDVSDEDGED 283

Query: 251 E 251
            
Sbjct: 284 L 284

Transcription initiation factor IIA (TFIIA) is a heterotrimer, the three subunits being known as alpha, beta, and gamma, in order of molecular weight. The N and C-terminal domains of the gamma subunit are represented in pfam02268 and pfam02751, respectively. This family represents the precursor that yields both the alpha and beta subunits. The TFIIA heterotrimer is an essential general transcription initiation factor for the expression of genes transcribed by RNA polymerase II. Together with TFIID, TFIIA binds to the promoter region; this is the first step in the formation of a pre-initiation complex (PIC). Binding of the rest of the transcription machinery follows this step. After initiation, the PIC does not completely dissociate from the promoter. Some components, including TFIIA, remain attached and re-initiate a subsequent round of transcription. Length = 332

>gnl|CDD|220271 pfam09507, CDC27, DNA polymerase subunit Cdc27

 Score = 41.0 bits (96), Expect = 0.002
 Identities = 26/82 (31%), Positives = 37/82 (45%), Gaps = 9/82 (10%)

Query: 438 ARNGDSEYEDSDFDTSDEEYDSSEEEEEEEEDEEEEEEEEEEEEEEEEEE--------GE 489
              G  E ED D      E   SEEE EE+E E+ +  ++  E+E+E+EE         E
Sbjct: 261 EPTGLDEDEDEDEPKPSGERSDSEEETEEKEKEKRKRLKKMMEDEDEDEEMEIVPESPVE 320

Query: 490 EEETETASSSTA-KNDPQMVTV 510
           EEE+E        K + +   V
Sbjct: 321 EEESEEPEPPPLPKKEEEKEEV 342

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|235548 PRK05657, PRK05657, RNA polymerase sigma factor RpoS; Validated

 Score = 40.7 bits (96), Expect = 0.002
 Identities = 12/50 (24%), Positives = 22/50 (44%)

Query: 451 DTSDEEYDSSEEEEEEEEDEEEEEEEEEEEEEEEEEEGEEEETETASSST 500
              +E+ D  E   E  +++   EEE  + +  EEE   +  T+    +T
Sbjct: 6   HDLNEDADFDENGVEVFDEKALVEEEPSDNDLAEEELLSQGATQRVLDAT 55

Length = 325

>gnl|CDD|148682 pfam07222, PBP_sp32, Proacrosin binding protein sp32

 Score = 40.4 bits (94), Expect = 0.002
 Identities = 16/37 (43%), Positives = 26/37 (70%)

Query: 455 EEYDSSEEEEEEEEDEEEEEEEEEEEEEEEEEEGEEE 491
           +EY    + EE++  EE+EEEE EEE ++EE +G ++
Sbjct: 207 QEYLQEHKTEEKQPQEEQEEEEVEEEAKQEEGQGTDD 243

This family consists of several mammalian specific proacrosin binding protein sp32 sequences. sp32 is a sperm specific protein which is known to bind with with 55- and 53-kDa proacrosins and the 49-kDa acrosin intermediate. The exact function of sp32 is unclear, it is thought however that the binding of sp32 to proacrosin may be involved in packaging the acrosin zymogen into the acrosomal matrix. Length = 243

>gnl|CDD|226894 COG4499, COG4499, Predicted membrane protein [Function unknown]

 Score = 40.9 bits (96), Expect = 0.002
 Identities = 14/42 (33%), Positives = 26/42 (61%)

Query: 455 EEYDSSEEEEEEEEDEEEEEEEEEEEEEEEEEEGEEEETETA 496
           ++Y     E ++E D  EE E + +EE+ ++EE E+++ E A
Sbjct: 379 QDYTKKLGEVKDETDASEEAEAKAKEEKLKQEENEKKQKEQA 420

Length = 434

>gnl|CDD|115196 pfam06524, NOA36, NOA36 protein

 Score = 40.7 bits (95), Expect = 0.002
 Identities = 13/59 (22%), Positives = 27/59 (45%), Gaps = 1/59 (1%)

Query: 439 RNGDSEYEDSDFDTSDEEYDSSEEEEEEEEDEEEEEEEEEEEEEEEEEEGEEEETETAS 497
           +N  S     DF   +  Y+S ++E     D +EEE+ ++++ E+ ++       E   
Sbjct: 254 QNLSSNK-YGDFKGVNYGYESDDDEGSSSNDYDEEEDGDDDDNEDNDDTNTNHGDEDCD 311

This family consists of several NOA36 proteins which contain 29 highly conserved cysteine residues. The function of this protein is unknown. Length = 314

>gnl|CDD|220284 pfam09538, FYDLN_acid, Protein of unknown function (FYDLN_acid)

 Score = 38.1 bits (89), Expect = 0.002
 Identities = 5/55 (9%), Positives = 28/55 (50%)

Query: 444 EYEDSDFDTSDEEYDSSEEEEEEEEDEEEEEEEEEEEEEEEEEEGEEEETETASS 498
           E       +     D+ +  +++E++E+E++   ++++++++++   +  +    
Sbjct: 35  EVPPEVAKSRAPAADAEDAAKKDEDEEDEDDVVLDDDDDDDDDDDLPDLDDDDVD 89

Members of this family are bacterial proteins with a conserved motif [KR]FYDLN, sometimes flanked by a pair of CXXC motifs, followed by a long region of low complexity sequence in which roughly half the residues are Asp and Glu, including multiple runs of five or more acidic residues. The function of members of this family is unknown. Length = 104

>gnl|CDD|221203 pfam11748, DUF3306, Protein of unknown function (DUF3306)

 Score = 38.1 bits (89), Expect = 0.002
 Identities = 17/50 (34%), Positives = 19/50 (38%)

Query: 460 SEEEEEEEEDEEEEEEEEEEEEEEEEEEGEEEETETASSSTAKNDPQMVT 509
           +EE  E  E  EEE          EEEE  E E E         DP  +T
Sbjct: 15  AEEPAEPAETAEEEAAAAAPAPAPEEEEEAELEDEELLEELDLPDPDTLT 64

This family of proteobacterial species proteins has no known function. Length = 115

>gnl|CDD|217476 pfam03286, Pox_Ag35, Pox virus Ag35 surface protein

 Score = 39.7 bits (93), Expect = 0.002
 Identities = 11/53 (20%), Positives = 29/53 (54%)

Query: 458 DSSEEEEEEEEDEEEEEEEEEEEEEEEEEEGEEEETETASSSTAKNDPQMVTV 510
              ++E+  EE+++ E ++++ EE E + +  EE  ++  S++A +   +   
Sbjct: 69  KKKDKEKLTEEEKKPESDDDKTEENENDPDNNEESGDSQESASANSLSDIDNE 121

Length = 198

>gnl|CDD|218538 pfam05285, SDA1, SDA1

 Score = 40.0 bits (94), Expect = 0.003
 Identities = 14/39 (35%), Positives = 25/39 (64%)

Query: 461 EEEEEEEEDEEEEEEEEEEEEEEEEEEGEEEETETASSS 499
           + +EEE + +E E+  E +++++EEEE E EE E +   
Sbjct: 77  KWKEEERKKKEAEQGLESDDDDDEEEEWEVEEDEDSDDE 115

This family consists of several SDA1 protein homologues. SDA1 is a Saccharomyces cerevisiae protein which is involved in the control of the actin cytoskeleton. The protein is essential for cell viability and is localised in the nucleus. Length = 317

>gnl|CDD|218312 pfam04889, Cwf_Cwc_15, Cwf15/Cwc15 cell cycle control protein

 Score = 39.7 bits (93), Expect = 0.003
 Identities = 23/91 (25%), Positives = 33/91 (36%), Gaps = 13/91 (14%)

Query: 188 VQEEVISNVKAIAKHLGIIKSSNGDSEYEDSDFDTSDEEYDSSEEEEE-----------E 236
            +E+ I   +            +  S   DS  D SD+  D SE+E             E
Sbjct: 100 DEEDEIKRKRIEEDARNSDADDSDSSSDSDSSDDDSDD--DDSEDETAALLRELEKIKKE 157

Query: 237 EDEEEEEEEEEGEEEETETASSSTAKNDPQM 267
             EE+E EEEE   EE +         +P +
Sbjct: 158 RAEEKEREEEEKAAEEEKAREEEILTGNPLL 188

This family represents Cwf15/Cwc15 (from Schizosaccharomyces pombe and Saccharomyces cerevisiae respectively) and their homologues. The function of these proteins is unknown, but they form part of the spliceosome and are thus thought to be involved in mRNA splicing. Length = 241

>gnl|CDD|219900 pfam08553, VID27, VID27 cytoplasmic protein

 Score = 40.9 bits (96), Expect = 0.003
 Identities = 20/59 (33%), Positives = 32/59 (54%), Gaps = 1/59 (1%)

Query: 207 KSSNGDSEY-EDSDFDTSDEEYDSSEEEEEEEDEEEEEEEEEGEEEETETASSSTAKND 264
           K+   + +Y  D+      E+ ++  ++EEEEDEEEEEEE+E E    E +     + D
Sbjct: 363 KAKETEQDYILDAFSALEIEDANTERDDEEEEDEEEEEEEDEDEGPSKEHSDDEEFEED 421

This is a family of fungal and plant proteins and contains many hypothetical proteins. VID27 is a cytoplasmic protein that plays a potential role in vacuolar protein degradation. Length = 794

>gnl|CDD|218223 pfam04712, Radial_spoke, Radial spokehead-like protein

 Score = 40.4 bits (95), Expect = 0.003
 Identities = 18/29 (62%), Positives = 22/29 (75%)

Query: 224 DEEYDSSEEEEEEEDEEEEEEEEEGEEEE 252
            E+ D  EE+E+EE+EEEEEE EE E EE
Sbjct: 344 PEQKDEEEEQEDEEEEEEEEEPEEPEPEE 372

This family includes the radial spoke head proteins RSP4 and RSP6 from Chlamydomonas reinhardtii, and several eukaryotic homologues, including mammalian RSHL1, the protein product of a familial ciliary dyskinesia candidate gene. Length = 481

>gnl|CDD|226920 COG4547, CobT, Cobalamin biosynthesis protein CobT (nicotinate-mononucleotide:5, 6-dimethylbenzimidazole phosphoribosyltransferase) [Coenzyme metabolism]

 Score = 41.0 bits (96), Expect = 0.003
 Identities = 19/60 (31%), Positives = 25/60 (41%), Gaps = 7/60 (11%)

Query: 208 SSNGDSEYEDSDFDTSDEEYDSSEEEEEEE-------DEEEEEEEEEGEEEETETASSST 260
           S  G  E E SD    DE   +  E EE E       ++ E +E +E  E   E A  +T
Sbjct: 247 SEAGREESEGSDESEEDEAEATDGEGEEGEMDAAEASEDSESDESDEDTETPGEDARPAT 306

Length = 620

>gnl|CDD|219408 pfam07423, DUF1510, Protein of unknown function (DUF1510)

 Score = 39.7 bits (93), Expect = 0.003
 Identities = 17/61 (27%), Positives = 34/61 (55%), Gaps = 1/61 (1%)

Query: 447 DSDFDTSDEEYDSSEEEEEEEEDEEEEEEEEEE-EEEEEEEEGEEEETETASSSTAKNDP 505
            SD   +DE+     +++E  E EE +EEE+E    E++E++G+ E+ +  S    + + 
Sbjct: 40  PSDQAAADEQEAKKSDDQETAEIEEVKEEEKEAANSEDKEDKGDAEKEDEESEEENEEED 99

Query: 506 Q 506
           +
Sbjct: 100 E 100

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|220413 pfam09805, Nop25, Nucleolar protein 12 (25kDa)

 Score = 38.5 bits (90), Expect = 0.003
 Identities = 10/40 (25%), Positives = 23/40 (57%)

Query: 453 SDEEYDSSEEEEEEEEDEEEEEEEEEEEEEEEEEEGEEEE 492
            +++ + +E E+ E+ +++E E   E    + EEE  +E+
Sbjct: 82  ENDDEEDAETEDTEDVEDDEWEGFPEPTVTDYEEEYIDED 121

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|218333 pfam04931, DNA_pol_phi, DNA polymerase phi

 Score = 40.6 bits (95), Expect = 0.003
 Identities = 16/61 (26%), Positives = 30/61 (49%)

Query: 449 DFDTSDEEYDSSEEEEEEEEDEEEEEEEEEEEEEEEEEEGEEEETETASSSTAKNDPQMV 508
           D + S  +     EEE+E++ EE +++E+E E  E+ E   E + E       ++D +  
Sbjct: 635 DENKSRHQQLFEGEEEDEDDLEETDDDEDECEAIEDSESESESDGEDGEEDEQEDDAEAN 694

Query: 509 T 509
            
Sbjct: 695 E 695

This family includes the fifth essential DNA polymerase in yeast EC:2.7.7.7. Pol5p is localised exclusively to the nucleolus and binds near or at the enhancer region of rRNA-encoding DNA repeating units. Length = 784

>gnl|CDD|218303 pfam04874, Mak16, Mak16 protein C-terminal region

 Score = 37.5 bits (87), Expect = 0.003
 Identities = 18/41 (43%), Positives = 27/41 (65%)

Query: 449 DFDTSDEEYDSSEEEEEEEEDEEEEEEEEEEEEEEEEEEGE 489
           + + S+E  +  EEEEEEE++ E E   ++EE EEE E+ E
Sbjct: 56  EAEESEENDEEEEEEEEEEDEGEIEYVSDDEELEEEIEDLE 96

The precise function of this eukaryotic protein family is unknown. The yeast orthologues have been implicated in cell cycle progression and biogenesis of 60S ribosomal subunits. The Schistosoma mansoni Mak16 has been shown to target protein transport to the nucleolus. Length = 97

>gnl|CDD|220102 pfam09073, BUD22, BUD22

 Score = 40.6 bits (95), Expect = 0.003
 Identities = 22/75 (29%), Positives = 26/75 (34%), Gaps = 14/75 (18%)

Query: 206 IKSSNGDSEYEDSDFDTSDEEYDSSEEEEEEEDEE--------------EEEEEEEGEEE 251
            K    +SE ED        E DS +EEEE+ D E              EEE EE     
Sbjct: 168 DKDDEEESESEDESKSEESAEDDSDDEEEEDSDSEDYSQYDGMLVDSSDEEEGEEAPSIN 227

Query: 252 ETETASSSTAKNDPQ 266
             E  S S +     
Sbjct: 228 YNEDTSESESDESDS 242

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|217049 pfam02459, Adeno_terminal, Adenoviral DNA terminal protein

 Score = 40.8 bits (96), Expect = 0.003
 Identities = 18/30 (60%), Positives = 19/30 (63%)

Query: 468 EDEEEEEEEEEEEEEEEEEEGEEEETETAS 497
               E EEEEEEEEE  EEE EEEE E  +
Sbjct: 300 PSPPEPEEEEEEEEEVPEEEEEEEEEEERT 329

This protein is covalently attached to the terminii of replicating DNA in vivo. Length = 548

>gnl|CDD|114172 pfam05432, BSP_II, Bone sialoprotein II (BSP-II)

 Score = 40.1 bits (93), Expect = 0.003
 Identities = 18/33 (54%), Positives = 25/33 (75%)

Query: 231 EEEEEEEDEEEEEEEEEGEEEETETASSSTAKN 263
           +E +E+E+EEEEEEEEE E EE E  ++ T+ N
Sbjct: 133 DESDEDEEEEEEEEEEEAEVEENEQGTNGTSTN 165

Bone sialoprotein (BSP) is a major structural protein of the bone matrix that is specifically expressed by fully-differentiated osteoblasts. The expression of bone sialoprotein (BSP) is normally restricted to mineralised connective tissues of bones and teeth where it has been associated with mineral crystal formation. However, it has been found that ectopic expression of BSP occurs in various lesions, including oral and extraoral carcinomas, in which it has been associated with the formation of microcrystalline deposits and the metastasis of cancer cells to bone. Length = 291

>gnl|CDD|237622 PRK14140, PRK14140, heat shock protein GrpE; Provisional

 Score = 39.2 bits (92), Expect = 0.003
 Identities = 17/37 (45%), Positives = 21/37 (56%)

Query: 461 EEEEEEEEDEEEEEEEEEEEEEEEEEEGEEEETETAS 497
            EE+ E+ +EE EE E EE  E+E EE   EE   A 
Sbjct: 1   MEEKNEQVEEEVEETEVEEAVEDEVEEETVEEESEAE 37

Length = 191

>gnl|CDD|130712 TIGR01651, CobT, cobaltochelatase, CobT subunit

 Score = 40.7 bits (95), Expect = 0.003
 Identities = 16/61 (26%), Positives = 29/61 (47%)

Query: 444 EYEDSDFDTSDEEYDSSEEEEEEEEDEEEEEEEEEEEEEEEEEEGEEEETETASSSTAKN 503
           E  D      +E+ D  +  E E+E++ E E E +E    +E E  + E+E+      ++
Sbjct: 202 EMGDDTESEDEEDGDDDQPTENEQEEQGEGEGEGQEGSAPQESEATDRESESGEEEMVQS 261

Query: 504 D 504
           D
Sbjct: 262 D 262

This model describes Pseudomonas denitrificans CobT gene product, which is a cobalt chelatase subunit that functions in cobalamin biosynthesis. Cobalamin (vitamin B12) can be synthesized via several pathways, including an aerobic pathway (found in Pseudomonas denitrificans) and an anaerobic pathway (found in P. shermanii and Salmonella typhimurium). These pathways differ in the point of cobalt insertion during corrin ring formation. There are apparently a number of variations on these two pathways, where the major differences seem to be concerned with the process of ring contraction. Confusion regarding the functions of enzymes found in the aerobic vs. anaerobic pathways has arisen because nonhomologous genes in these different pathways were given the same gene symbols. Thus, cobT in the aerobic pathway (P. denitrificans) is not a homolog of cobT in the anaerobic pathway (S. typhimurium). It should be noted that E. coli synthesizes cobalamin only when it is supplied with the precursor cobinamide, which is a complex intermediate. Additionally, all E. coli cobalamin synthesis genes (cobU, cobS and cobT) were named after their Salmonella typhimurium homologs which function in the anaerobic cobalamin synthesis pathway. This model describes the aerobic cobalamin pathway Pseudomonas denitrificans CobT gene product, which is a cobalt chelatase subunit, with a MW ~70 kDa. The aerobic pathway cobalt chelatase is a heterotrimeric, ATP-dependent enzyme that catalyzes cobalt insertion during cobalamin biosynthesis. The other two subunits are the P. denitrificans CobS (TIGR01650) and CobN (pfam02514 CobN/Magnesium Chelatase) proteins. To avoid potential confusion with the nonhomologous Salmonella typhimurium/E.coli cobT gene product, the P. denitrificans gene symbol is not used in the name of this model [Biosynthesis of cofactors, prosthetic groups, and carriers, Heme, porphyrin, and cobalamin]. Length = 600

>gnl|CDD|235549 PRK05658, PRK05658, RNA polymerase sigma factor RpoD; Validated

 Score = 40.5 bits (96), Expect = 0.003
 Identities = 18/49 (36%), Positives = 26/49 (53%)

Query: 443 SEYEDSDFDTSDEEYDSSEEEEEEEEDEEEEEEEEEEEEEEEEEEGEEE 491
            E  D   D + EE  +    E EE D++E+EEEEE+E ++     E E
Sbjct: 167 RELIDGFVDPNAEEDPAHVGSELEELDDDEDEEEEEDENDDSLAADESE 215

Length = 619

>gnl|CDD|223003 PHA03169, PHA03169, hypothetical protein; Provisional

 Score = 40.7 bits (95), Expect = 0.003
 Identities = 13/94 (13%), Positives = 20/94 (21%), Gaps = 1/94 (1%)

Query: 405 PTRPRDLQKTIQDTTGAYNRRRSSAMNHNRRWNARNGDSEYEDSDFDTSDEEYDSSEEEE 464
           P  P       Q    A    R +  +      +R+G+ E       +            
Sbjct: 46  PAPPAPTTSGPQVRAVAEQGHRQTESDTETAEESRHGEKEERGQGGPSGSGSESVGSPTP 105

Query: 465 EEEEDEEEEEEEEEEEEEEEE-EEGEEEETETAS 497
                 EE       E       E     +   S
Sbjct: 106 SPSGSAEELASGLSPENTSGSSPESPASHSPPPS 139

Length = 413

>gnl|CDD|223003 PHA03169, PHA03169, hypothetical protein; Provisional

 Score = 40.3 bits (94), Expect = 0.003
 Identities = 8/53 (15%), Positives = 13/53 (24%)

Query: 442 DSEYEDSDFDTSDEEYDSSEEEEEEEEDEEEEEEEEEEEEEEEEEEGEEEETE 494
              +  S           S E+  EE +    E E +     + E        
Sbjct: 152 PESHNPSPNQQPSSFLQPSHEDSPEEPEPPTSEPEPDSPGPPQSETPTSSPPP 204

Length = 413

>gnl|CDD|223003 PHA03169, PHA03169, hypothetical protein; Provisional

 Score = 40.3 bits (94), Expect = 0.003
 Identities = 10/65 (15%), Positives = 19/65 (29%)

Query: 441 GDSEYEDSDFDTSDEEYDSSEEEEEEEEDEEEEEEEEEEEEEEEEEEGEEEETETASSST 500
                     + +  E  +    ++     +   E+  EE E    E E +      S T
Sbjct: 138 PSPPSHPGPHEPAPPESHNPSPNQQPSSFLQPSHEDSPEEPEPPTSEPEPDSPGPPQSET 197

Query: 501 AKNDP 505
             + P
Sbjct: 198 PTSSP 202

Length = 413

>gnl|CDD|115071 pfam06390, NESP55, Neuroendocrine-specific golgi protein P55 (NESP55)

 Score = 39.8 bits (92), Expect = 0.003
 Identities = 21/72 (29%), Positives = 34/72 (47%), Gaps = 12/72 (16%)

Query: 207 KSSNGDSEYEDSDF------------DTSDEEYDSSEEEEEEEDEEEEEEEEEGEEEETE 254
           + S  +S++ED DF            D  D + ++  E E E D E E E E   E E +
Sbjct: 82  EPSEPESDHEDEDFEPELARPECLEYDEDDFDTETDSETEPESDIESETEFETEPETEPD 141

Query: 255 TASSSTAKNDPQ 266
           TA ++  + +P+
Sbjct: 142 TAPTTEPETEPE 153

This family consists of several mammalian neuroendocrine-specific golgi protein P55 (NESP55) sequences. NESP55 is a novel member of the chromogranin family and is a soluble, acidic, heat-stable secretory protein that is expressed exclusively in endocrine and nervous tissues, although less widely than chromogranins. Length = 261

>gnl|CDD|235250 PRK04195, PRK04195, replication factor C large subunit; Provisional

 Score = 40.7 bits (96), Expect = 0.003
 Identities = 16/51 (31%), Positives = 34/51 (66%)

Query: 455 EEYDSSEEEEEEEEDEEEEEEEEEEEEEEEEEEGEEEETETASSSTAKNDP 505
           ++ +  ++E++++    +++EEEEEEE+E++EE +EEE E A     + + 
Sbjct: 421 KKREEEKKEKKKKAFAGKKKEEEEEEEKEKKEEEKEEEEEEAEEEKEEEEE 471

Length = 482

>gnl|CDD|221668 pfam12619, MCM2_N, Mini-chromosome maintenance protein 2

 Score = 38.5 bits (90), Expect = 0.003
 Identities = 12/29 (41%), Positives = 22/29 (75%)

Query: 464 EEEEEDEEEEEEEEEEEEEEEEEEGEEEE 492
           E+E ++EEE E++ ++ +EE EEE + E+
Sbjct: 1   EDEPDEEEELEDDIDDLDEEAEEEEDGED 29

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|227701 COG5414, COG5414, TATA-binding protein-associated factor [Transcription]

 Score = 40.5 bits (94), Expect = 0.003
 Identities = 14/52 (26%), Positives = 28/52 (53%)

Query: 444 EYEDSDFDTSDEEYDSSEEEEEEEEDEEEEEEEEEEEEEEEEEEGEEEETET 495
           E ++      +++ +  E  E  +E+ + +  +E  EE+EE++E EE E  T
Sbjct: 285 ENKEVSEGDKEQQQEEVENAEAHKEEVQSDRPDEIGEEKEEDDENEENERHT 336

Length = 392

>gnl|CDD|225880 COG3343, RpoE, DNA-directed RNA polymerase, delta subunit [Transcription]

 Score = 39.0 bits (91), Expect = 0.003
 Identities = 15/49 (30%), Positives = 30/49 (61%)

Query: 447 DSDFDTSDEEYDSSEEEEEEEEDEEEEEEEEEEEEEEEEEEGEEEETET 495
           + + D   +  D   ++E+E++DE  E   E++E +E+E++ E+EE E 
Sbjct: 125 EEEEDDEVDSLDDENDDEDEDDDEIVEILIEDDEVDEDEDDDEDEEDEE 173

Length = 175

>gnl|CDD|219563 pfam07767, Nop53, Nop53 (60S ribosomal biogenesis)

 Score = 40.5 bits (95), Expect = 0.003
 Identities = 14/41 (34%), Positives = 20/41 (48%)

Query: 455 EEYDSSEEEEEEEEDEEEEEEEEEEEEEEEEEEGEEEETET 495
               S  +E  E   EE +++ EEE ++E   EG E E E 
Sbjct: 228 APEASRLDEMSEGLLEESDDDGEEESDDESAWEGFESEYEP 268

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|224530 COG1614, CdhC, CO dehydrogenase/acetyl-CoA synthase beta subunit [Energy production and conversion]

 Score = 40.6 bits (95), Expect = 0.003
 Identities = 17/30 (56%), Positives = 18/30 (60%)

Query: 461 EEEEEEEEDEEEEEEEEEEEEEEEEEEGEE 490
           E   EEEE+EEEEEEEE  E E   EE   
Sbjct: 399 ERWAEEEEEEEEEEEEEAAEAEAPMEEPVP 428

Length = 470

>gnl|CDD|111875 pfam03032, Brevenin, Brevenin/esculentin/gaegurin/rugosin family

 Score = 35.8 bits (83), Expect = 0.003
 Identities = 13/24 (54%), Positives = 19/24 (79%)

Query: 461 EEEEEEEEDEEEEEEEEEEEEEEE 484
           EEE+ E+E+E E+EEE EE+ E +
Sbjct: 22  EEEKREDEEENEDEEEGEEQSEVK 45

This family contains a number of defence peptides secreted from the skin of amphibians, including the opiate-like dermorphins and deltorphins, and the antimicrobial dermoseptins and temporins. The alignment for this family includes the signal peptide. Length = 46

>gnl|CDD|217392 pfam03153, TFIIA, Transcription factor IIA, alpha/beta subunit

 Score = 40.1 bits (94), Expect = 0.003
 Identities = 7/46 (15%), Positives = 23/46 (50%), Gaps = 3/46 (6%)

Query: 449 DFDTSDEEYDSSEEEEEEEEDEEEEE---EEEEEEEEEEEEEGEEE 491
             D  D + +    +++++ED  E +    +++  +E+ E+  + +
Sbjct: 243 QIDGIDSDDEGDGSDDDDDEDAIESDLDDSDDDVSDEDGEDLFDTD 288

Transcription initiation factor IIA (TFIIA) is a heterotrimer, the three subunits being known as alpha, beta, and gamma, in order of molecular weight. The N and C-terminal domains of the gamma subunit are represented in pfam02268 and pfam02751, respectively. This family represents the precursor that yields both the alpha and beta subunits. The TFIIA heterotrimer is an essential general transcription initiation factor for the expression of genes transcribed by RNA polymerase II. Together with TFIID, TFIIA binds to the promoter region; this is the first step in the formation of a pre-initiation complex (PIC). Binding of the rest of the transcription machinery follows this step. After initiation, the PIC does not completely dissociate from the promoter. Some components, including TFIIA, remain attached and re-initiate a subsequent round of transcription. Length = 332

>gnl|CDD|218576 pfam05395, DARPP-32, Protein phosphatase inhibitor 1/DARPP-32

 Score = 39.1 bits (91), Expect = 0.003
 Identities = 14/61 (22%), Positives = 24/61 (39%), Gaps = 7/61 (11%)

Query: 453 SDEEYDSSEEEEEEEE-------DEEEEEEEEEEEEEEEEEEGEEEETETASSSTAKNDP 505
           S EE  +SEEE+E +          E E  E ++ EE      ++ ++E           
Sbjct: 96  SLEENQASEEEDELDSPDELGYPTGETESTEAQDSEEPGSCPTQDAQSEVGLEGPWHRTA 155

Query: 506 Q 506
           +
Sbjct: 156 E 156

This family consists of several mammalian protein phosphatase inhibitor 1 (IPP-1) and dopamine- and cAMP-regulated neuronal phosphoprotein (DARPP-32) proteins. Protein phosphatase inhibitor-1 is involved in signal transduction and is an endogenous inhibitor of protein phosphatase-1. It has been demonstrated that DARPP-32, if phosphorylated, can inhibit protein-phosphatase-1. DARPP-32 has a key role in many neurotransmitter pathways throughout the brain and has been shown to be involved in controlling receptors, ion channels and other physiological factors including the brain's response to drugs of abuse, such as cocaine, opiates and nicotine. DARPP-32 is reciprocally regulated by the two neurotransmitters that are most often implicated in schizophrenia - dopamine and glutamate. Dopamine activates DARPP-32 through the D1 receptor pathway and disables DARPP-32 through the D2 receptor. Glutamate, acting through the N-methyl-d-aspartate receptor, renders DARPP-32 inactive. A mutant form of DARPP-32 has been linked with gastric cancers. Length = 170

>gnl|CDD|215601 PLN03142, PLN03142, Probable chromatin-remodeling complex ATPase chain; Provisional

 Score = 40.9 bits (96), Expect = 0.003
 Identities = 17/55 (30%), Positives = 31/55 (56%), Gaps = 5/55 (9%)

Query: 455 EEYDSSEEEEEEEEDEEE-----EEEEEEEEEEEEEEEGEEEETETASSSTAKND 504
           EE  +++  EEE+E+E E        + +++E   E+E E+EE +  + S AK +
Sbjct: 2   EEQVNTQANEEEDEEELEAVARSAGSDSDDDEVPAEDEDEDEEDDEEAESPAKAE 56

Length = 1033

>gnl|CDD|234055 TIGR02907, spore_VI_D, stage VI sporulation protein D

 Score = 40.3 bits (94), Expect = 0.003
 Identities = 20/55 (36%), Positives = 25/55 (45%)

Query: 446 EDSDFDTSDEEYDSSEEEEEEEEDEEEEEEEEEEEEEEEEEEGEEEETETASSST 500
           E    D  DE   S+ E  + E + E   EEE  EE E+E E E E+ E A    
Sbjct: 190 EQPADDDPDEWKISASEPFQLESEVEASPEEENYEEYEDETELEVEDEEKALDEQ 244

SpoVID, the stage VI sporulation protein D, is restricted to endospore-forming members of the bacteria, all of which are found among the Firmicutes. It is widely distributed but not quite universal in this group. Between well-conserved N-terminal and C-terminal domains is a poorly conserved, low-complexity region of variable length, rich enough in glutamic acid to cause spurious BLAST search results unless a filter is used. The seed alignment for this model was trimmed, in effect, by choosing member sequences in which these regions are relatively short. SpoVID is involved in spore coat assembly by the mother cell compartment late in the process of sporulation [Cellular processes, Sporulation and germination]. Length = 338

>gnl|CDD|235396 PRK05299, rpsB, 30S ribosomal protein S2; Provisional

 Score = 39.8 bits (94), Expect = 0.003
 Identities = 20/33 (60%), Positives = 21/33 (63%)

Query: 460 SEEEEEEEEDEEEEEEEEEEEEEEEEEEGEEEE 492
                E  E+EEEE EEEEEEEEEEE E  E E
Sbjct: 226 QGRLAEAAEEEEEEAEEEEEEEEEEEAEEAEAE 258

Length = 258

>gnl|CDD|222117 pfam13422, DUF4110, Domain of unknown function (DUF4110)

 Score = 37.3 bits (87), Expect = 0.003
 Identities = 15/45 (33%), Positives = 20/45 (44%)

Query: 450 FDTSDEEYDSSEEEEEEEEDEEEEEEEEEEEEEEEEEEGEEEETE 494
           FD ++E Y    EE    EDEEEE+   EE     +E+       
Sbjct: 52  FDLAEERYWELREELRALEDEEEEQAGIEEVVSLAKEKDWGGGEG 96

This is a family that is found predominantly at the C-terminus of Kelch-containing proteins. However, the exact function of this region is not known. Length = 99

>gnl|CDD|218538 pfam05285, SDA1, SDA1

 Score = 39.6 bits (93), Expect = 0.004
 Identities = 14/55 (25%), Positives = 30/55 (54%)

Query: 208 SSNGDSEYEDSDFDTSDEEYDSSEEEEEEEDEEEEEEEEEGEEEETETASSSTAK 262
            S+ + E+ D + D   E  DS +EEE++E  ++ +E+ + E  E +   ++  +
Sbjct: 111 DSDDEGEWIDVESDKEIESSDSEDEEEKDEAAKKAKEDSDEELSEEDEEEAAEEE 165

This family consists of several SDA1 protein homologues. SDA1 is a Saccharomyces cerevisiae protein which is involved in the control of the actin cytoskeleton. The protein is essential for cell viability and is localised in the nucleus. Length = 317

>gnl|CDD|218312 pfam04889, Cwf_Cwc_15, Cwf15/Cwc15 cell cycle control protein

 Score = 39.3 bits (92), Expect = 0.004
 Identities = 18/91 (19%), Positives = 41/91 (45%), Gaps = 5/91 (5%)

Query: 409 RDLQKTIQDTTGAYNRRR---SSAMNHNRRWNARNGDSEYEDSDFDTSDEEYDSSEEEEE 465
           RDL+  +++   A+  ++    +  + ++  N     S   D D D  DE      EE+ 
Sbjct: 57  RDLRAELEEAERAHKSKKENKLAIEDADKSTNLD--ASNEGDEDDDEEDEIKRKRIEEDA 114

Query: 466 EEEDEEEEEEEEEEEEEEEEEEGEEEETETA 496
              D ++ +   + +  +++ + ++ E ETA
Sbjct: 115 RNSDADDSDSSSDSDSSDDDSDDDDSEDETA 145

This family represents Cwf15/Cwc15 (from Schizosaccharomyces pombe and Saccharomyces cerevisiae respectively) and their homologues. The function of these proteins is unknown, but they form part of the spliceosome and are thus thought to be involved in mRNA splicing. Length = 241

>gnl|CDD|145949 pfam03066, Nucleoplasmin, Nucleoplasmin

 Score = 38.5 bits (90), Expect = 0.004
 Identities = 13/34 (38%), Positives = 23/34 (67%)

Query: 470 EEEEEEEEEEEEEEEEEEGEEEETETASSSTAKN 503
           E+E +++EE+EEEE++EE ++E+      S  K 
Sbjct: 111 EDESDDDEEDEEEEDDEEDDDEDESEEEESPVKK 144

Nucleoplasmins are also known as chromatin decondensation proteins. They bind to core histones and transfer DNA to them in a reaction that requires ATP. This is thought to play a role in the assembly of regular nucleosomal arrays. Length = 146

>gnl|CDD|148051 pfam06213, CobT, Cobalamin biosynthesis protein CobT

 Score = 39.8 bits (93), Expect = 0.004
 Identities = 15/57 (26%), Positives = 24/57 (42%), Gaps = 3/57 (5%)

Query: 439 RNGDSEYEDSDFDTSDEE---YDSSEEEEEEEEDEEEEEEEEEEEEEEEEEEGEEEE 492
            + D   ED D D  +EE      S  E+ +   EE E  E E  E   ++  + ++
Sbjct: 225 EDEDDPKEDEDDDQGEEEESGSSDSLSEDSDASSEEMESGEMEAAEASADDTPDSDD 281

This family consists of several bacterial cobalamin biosynthesis (CobT) proteins. CobT is involved in the transformation of precorrin-3 into cobyrinic acid. Length = 282

>gnl|CDD|237629 PRK14160, PRK14160, heat shock protein GrpE; Provisional

 Score = 39.4 bits (92), Expect = 0.004
 Identities = 15/51 (29%), Positives = 27/51 (52%)

Query: 214 EYEDSDFDTSDEEYDSSEEEEEEEDEEEEEEEEEGEEEETETASSSTAKND 264
           E E  D    + E D  +E E +E+++ +EE+ E EE E E     + +++
Sbjct: 2   EKECKDAKHENMEEDCCKENENKEEDKGKEEDLEFEEIEKEEIIEDSEESN 52

Length = 211

>gnl|CDD|184885 PRK14891, PRK14891, 50S ribosomal protein L24e/unknown domain fusion protein; Provisional

 Score = 38.0 bits (88), Expect = 0.004
 Identities = 13/49 (26%), Positives = 27/49 (55%)

Query: 216 EDSDFDTSDEEYDSSEEEEEEEDEEEEEEEEEGEEEETETASSSTAKND 264
           E ++   + +  + ++E  E +  +E +EEEE +E   ETA  + A+ +
Sbjct: 71  EAAEEAEAADADEDADEAAEADAADEADEEEETDEAVDETADEADAEAE 119

Length = 131

>gnl|CDD|184885 PRK14891, PRK14891, 50S ribosomal protein L24e/unknown domain fusion protein; Provisional

 Score = 38.0 bits (88), Expect = 0.004
 Identities = 17/45 (37%), Positives = 23/45 (51%)

Query: 211 GDSEYEDSDFDTSDEEYDSSEEEEEEEDEEEEEEEEEGEEEETET 255
            D   E    D +DEE ++ E  +E  DE + E EE  EEE+ E 
Sbjct: 85  ADEAAEADAADEADEEEETDEAVDETADEADAEAEEADEEEDEEA 129

Length = 131

>gnl|CDD|219408 pfam07423, DUF1510, Protein of unknown function (DUF1510)

 Score = 38.9 bits (91), Expect = 0.004
 Identities = 17/70 (24%), Positives = 33/70 (47%), Gaps = 5/70 (7%)

Query: 440 NGDSEYEDSDFDTSDEEYDSSEEEEEEEEDEEEEE-----EEEEEEEEEEEEEGEEEETE 494
                 + +  +   ++ D  E  E EE  EEE+E     ++E++ + E+E+E  EEE E
Sbjct: 37  PSSPSDQAAADEQEAKKSDDQETAEIEEVKEEEKEAANSEDKEDKGDAEKEDEESEEENE 96

Query: 495 TASSSTAKND 504
                ++  +
Sbjct: 97  EEDEESSDEN 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|237063 PRK12329, nusA, transcription elongation factor NusA; Provisional

 Score = 40.2 bits (94), Expect = 0.004
 Identities = 13/38 (34%), Positives = 19/38 (50%)

Query: 453 SDEEYDSSEEEEEEEEDEEEEEEEEEEEEEEEEEEGEE 490
              E D+   E     ++E E+E+E EE + EEEE   
Sbjct: 412 ERAEEDARLRELYPLPEDEFEDEDELEEAQPEEEEEAR 449

Length = 449

>gnl|CDD|220413 pfam09805, Nop25, Nucleolar protein 12 (25kDa)

 Score = 38.1 bits (89), Expect = 0.004
 Identities = 14/44 (31%), Positives = 25/44 (56%)

Query: 461 EEEEEEEEDEEEEEEEEEEEEEEEEEEGEEEETETASSSTAKND 504
           +E +E  +  EEE ++EE+ E E+ E+ E++E E     T  + 
Sbjct: 70  KERKEALKLLEEENDDEEDAETEDTEDVEDDEWEGFPEPTVTDY 113

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|220413 pfam09805, Nop25, Nucleolar protein 12 (25kDa)

 Score = 38.1 bits (89), Expect = 0.004
 Identities = 15/42 (35%), Positives = 25/42 (59%)

Query: 454 DEEYDSSEEEEEEEEDEEEEEEEEEEEEEEEEEEGEEEETET 495
           D+E D+  E+ E+ ED+E E   E    + EEE  +E++ +T
Sbjct: 84  DDEEDAETEDTEDVEDDEWEGFPEPTVTDYEEEYIDEDKYKT 125

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|218333 pfam04931, DNA_pol_phi, DNA polymerase phi

 Score = 40.2 bits (94), Expect = 0.004
 Identities = 15/63 (23%), Positives = 30/63 (47%)

Query: 207 KSSNGDSEYEDSDFDTSDEEYDSSEEEEEEEDEEEEEEEEEGEEEETETASSSTAKNDPQ 266
           +   G+ E ED   +T D+E +    E+ E + E + E+ E +E+E +  ++       +
Sbjct: 643 QLFEGEEEDEDDLEETDDDEDECEAIEDSESESESDGEDGEEDEQEDDAEANEGVVPIDK 702

Query: 267 MVT 269
            V 
Sbjct: 703 AVR 705

This family includes the fifth essential DNA polymerase in yeast EC:2.7.7.7. Pol5p is localised exclusively to the nucleolus and binds near or at the enhancer region of rRNA-encoding DNA repeating units. Length = 784

>gnl|CDD|217049 pfam02459, Adeno_terminal, Adenoviral DNA terminal protein

 Score = 40.4 bits (95), Expect = 0.004
 Identities = 19/30 (63%), Positives = 19/30 (63%)

Query: 467 EEDEEEEEEEEEEEEEEEEEEGEEEETETA 496
               E EEEEEEEEE  EEEE EEEE E  
Sbjct: 300 PSPPEPEEEEEEEEEVPEEEEEEEEEEERT 329

This protein is covalently attached to the terminii of replicating DNA in vivo. Length = 548

>gnl|CDD|221275 pfam11861, DUF3381, Domain of unknown function (DUF3381)

 Score = 38.4 bits (90), Expect = 0.004
 Identities = 15/38 (39%), Positives = 24/38 (63%)

Query: 461 EEEEEEEEDEEEEEEEEEEEEEEEEEEGEEEETETASS 498
           +    +++++EEEEEEE E EE +EEE  +E  E   +
Sbjct: 92  KLLGLDKKEKEEEEEEEVEVEELDEEEQIDELLEKELA 129

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|114603 pfam05887, Trypan_PARP, Procyclic acidic repetitive protein (PARP)

 Score = 38.0 bits (87), Expect = 0.004
 Identities = 24/68 (35%), Positives = 35/68 (51%)

Query: 439 RNGDSEYEDSDFDTSDEEYDSSEEEEEEEEDEEEEEEEEEEEEEEEEEEGEEEETETASS 498
           + G  + E      +D+   +  ++E EEE+E E EEE EEE E EEE  EE E E    
Sbjct: 38  KGGKGKGEKGTKVGADDTNGTDPDDEPEEEEEPEPEEEGEEEPEPEEEGEEEPEPEETGE 97

Query: 499 STAKNDPQ 506
              + +P+
Sbjct: 98  EEPEPEPE 105

This family consists of several Trypanosoma brucei procyclic acidic repetitive protein (PARP) like sequences. The procyclic acidic repetitive protein (parp) genes of Trypanosoma brucei encode a small family of abundant surface proteins whose expression is restricted to the procyclic form of the parasite. They are found at two unlinked loci, parpA and parpB; transcription of both loci is developmentally regulated. Length = 145

>gnl|CDD|227466 COG5137, COG5137, Histone chaperone involved in gene silencing [Transcription / Chromatin structure and dynamics]

 Score = 39.6 bits (92), Expect = 0.004
 Identities = 18/61 (29%), Positives = 30/61 (49%)

Query: 444 EYEDSDFDTSDEEYDSSEEEEEEEEDEEEEEEEEEEEEEEEEEEGEEEETETASSSTAKN 503
           E   SD         + EEEEE E  ++ E+  + E E  ++++GEEEE E    +  + 
Sbjct: 194 EEVGSDSYGEGNRELNEEEEEEAEGSDDGEDVVDYEGERIDKKQGEEEEMEEEVINLFEI 253

Query: 504 D 504
           +
Sbjct: 254 E 254

Length = 279

>gnl|CDD|237622 PRK14140, PRK14140, heat shock protein GrpE; Provisional

 Score = 38.8 bits (91), Expect = 0.004
 Identities = 17/44 (38%), Positives = 24/44 (54%)

Query: 451 DTSDEEYDSSEEEEEEEEDEEEEEEEEEEEEEEEEEEGEEEETE 494
           +T  EE    E EEE  E+E E E  +EE+ +  E E + +E E
Sbjct: 14  ETEVEEAVEDEVEEETVEEESEAELLDEEQAKIAELEAKLDELE 57

Length = 191

>gnl|CDD|237622 PRK14140, PRK14140, heat shock protein GrpE; Provisional

 Score = 38.8 bits (91), Expect = 0.004
 Identities = 18/42 (42%), Positives = 23/42 (54%)

Query: 225 EEYDSSEEEEEEEDEEEEEEEEEGEEEETETASSSTAKNDPQ 266
           EE +   EEE EE E EE  E+E EEE  E  S +   ++ Q
Sbjct: 2   EEKNEQVEEEVEETEVEEAVEDEVEEETVEEESEAELLDEEQ 43

Length = 191

>gnl|CDD|179712 PRK04019, rplP0, acidic ribosomal protein P0; Validated

 Score = 39.8 bits (94), Expect = 0.004
 Identities = 18/39 (46%), Positives = 23/39 (58%)

Query: 461 EEEEEEEEDEEEEEEEEEEEEEEEEEEGEEEETETASSS 499
           EE +E    + +    EEEEEEEEEEE EE   E A++ 
Sbjct: 286 EELKEVLSAQAQAAAAEEEEEEEEEEEEEEPSEEEAAAG 324

Length = 330

>gnl|CDD|235640 PRK05901, PRK05901, RNA polymerase sigma factor; Provisional

 Score = 40.0 bits (94), Expect = 0.004
 Identities = 12/60 (20%), Positives = 36/60 (60%), Gaps = 3/60 (5%)

Query: 442 DSEYEDSDFDTSDEEYDSSEEEEEEEEDEEEEEEEE---EEEEEEEEEEGEEEETETASS 498
           D +  +   D  D++ D   ++++ ++D+++E+++E   +++ ++E+EE +E +     S
Sbjct: 123 DIDVLNQADDDDDDDDDDDLDDDDIDDDDDDEDDDEDDDDDDVDDEDEEKKEAKELEKLS 182

Length = 509

>gnl|CDD|202096 pfam02029, Caldesmon, Caldesmon

 Score = 40.0 bits (93), Expect = 0.004
 Identities = 19/75 (25%), Positives = 32/75 (42%), Gaps = 4/75 (5%)

Query: 424 RRRSSAMNHNRRWNARNGDSEYEDSDFDTSDEEYDSSEEEEEEEEDEEEEEEEEEEEEE- 482
            R S A+   + +   + D    +      ++    +E  EEEE++E  EE EE EE E 
Sbjct: 72  ERFSEALERQKEFKPTSTDQSLSEPSRRMQEDSGAENETVEEEEKEESREEREEVEETEG 131

Query: 483 ---EEEEEGEEEETE 494
               E++    +  E
Sbjct: 132 VTKSEQKNDWRDAEE 146

Length = 431

>gnl|CDD|223003 PHA03169, PHA03169, hypothetical protein; Provisional

 Score = 40.3 bits (94), Expect = 0.004
 Identities = 14/89 (15%), Positives = 26/89 (29%), Gaps = 2/89 (2%)

Query: 417 DTTGAYNRRRSSAMNHNRRWNARNGDSEYEDSDFDTSDEEYDSSEEEEEEEEDEEEEEEE 476
             T +  + R+ A   +R+  +       E+S     +E           E         
Sbjct: 50  APTTSGPQVRAVAEQGHRQTESDTE--TAEESRHGEKEERGQGGPSGSGSESVGSPTPSP 107

Query: 477 EEEEEEEEEEEGEEEETETASSSTAKNDP 505
               EE       E  + ++  S A + P
Sbjct: 108 SGSAEELASGLSPENTSGSSPESPASHSP 136

Length = 413

>gnl|CDD|223003 PHA03169, PHA03169, hypothetical protein; Provisional

 Score = 40.3 bits (94), Expect = 0.004
 Identities = 5/54 (9%), Positives = 10/54 (18%)

Query: 441 GDSEYEDSDFDTSDEEYDSSEEEEEEEEDEEEEEEEEEEEEEEEEEEGEEEETE 494
                 ++   +S E   S              E    E       +      +
Sbjct: 115 ASGLSPENTSGSSPESPASHSPPPSPPSHPGPHEPAPPESHNPSPNQQPSSFLQ 168

Length = 413

>gnl|CDD|227701 COG5414, COG5414, TATA-binding protein-associated factor [Transcription]

 Score = 40.1 bits (93), Expect = 0.004
 Identities = 14/48 (29%), Positives = 22/48 (45%)

Query: 447 DSDFDTSDEEYDSSEEEEEEEEDEEEEEEEEEEEEEEEEEEGEEEETE 494
                   +E   + E  +EE   +  +E  EE+EE++E E  E  TE
Sbjct: 290 SEGDKEQQQEEVENAEAHKEEVQSDRPDEIGEEKEEDDENEENERHTE 337

Length = 392

>gnl|CDD|235033 PRK02363, PRK02363, DNA-directed RNA polymerase subunit delta; Reviewed

 Score = 38.1 bits (89), Expect = 0.004
 Identities = 14/36 (38%), Positives = 25/36 (69%)

Query: 445 YEDSDFDTSDEEYDSSEEEEEEEEDEEEEEEEEEEE 480
           + D D D  D++    ++ +EE+ DEE++E+EE+EE
Sbjct: 94  FMDGDDDIIDDDILPDDDFDEEDLDEEDDEDEEDEE 129

Length = 129

>gnl|CDD|225880 COG3343, RpoE, DNA-directed RNA polymerase, delta subunit [Transcription]

 Score = 38.6 bits (90), Expect = 0.004
 Identities = 18/50 (36%), Positives = 32/50 (64%)

Query: 445 YEDSDFDTSDEEYDSSEEEEEEEEDEEEEEEEEEEEEEEEEEEGEEEETE 494
            E  D    D+E D+ EE +E+E D +E++EEEE++E +  ++  ++E E
Sbjct: 95  TEKKDIKAKDKEVDAFEEGDEDELDYDEDKEEEEDDEVDSLDDENDDEDE 144

Length = 175

>gnl|CDD|218555 pfam05320, Pox_RNA_Pol_19, Poxvirus DNA-directed RNA polymerase 19 kDa subunit

 Score = 38.5 bits (90), Expect = 0.004
 Identities = 15/41 (36%), Positives = 27/41 (65%)

Query: 462 EEEEEEEDEEEEEEEEEEEEEEEEEEGEEEETETASSSTAK 502
           E+ ++  D E ++++ EE EEEEE+E + E  E++  S+ K
Sbjct: 2   EDSDDIIDYESDDDDSEEYEEEEEDEEDAESLESSDVSSLK 42

This family contains several DNA-directed RNA polymerase 19 kDa polypeptides. The Poxvirus DNA-directed RNA polymerase (EC: 2.7.7.6) catalyzes DNA-template-directed extension of the 3'-end of an RNA strand by one nucleotide at a time. Length = 167

>gnl|CDD|237284 PRK13108, PRK13108, prolipoprotein diacylglyceryl transferase; Reviewed

 Score = 40.3 bits (94), Expect = 0.004
 Identities = 18/67 (26%), Positives = 22/67 (32%)

Query: 205 IIKSSNGDSEYEDSDFDTSDEEYDSSEEEEEEEDEEEEEEEEEGEEEETETASSSTAKND 264
           I +   GD   +       D E  S+  EE      E  +E E E  E        AK D
Sbjct: 371 IEREQPGDLAGQAPAAHQVDAEAASAAPEEPAALASEAHDETEPEVPEKAAPIPDPAKPD 430

Query: 265 PQMVTVP 271
              V  P
Sbjct: 431 ELAVAGP 437

Length = 460

>gnl|CDD|227596 COG5271, MDN1, AAA ATPase containing von Willebrand factor type A (vWA) domain [General function prediction only]

 Score = 40.8 bits (95), Expect = 0.004
 Identities = 15/53 (28%), Positives = 28/53 (52%)

Query: 442  DSEYEDSDFDTSDEEYDSSEEEEEEEEDEEEEEEEEEEEEEEEEEEGEEEETE 494
            +   +D   D ++++   +E+  EE   E EE  E+  + +EE E+GE  E +
Sbjct: 4045 EDIQQDDFSDLAEDDEKMNEDGFEENVQENEESTEDGVKSDEELEQGEVPEDQ 4097

Length = 4600

>gnl|CDD|111875 pfam03032, Brevenin, Brevenin/esculentin/gaegurin/rugosin family

 Score = 35.4 bits (82), Expect = 0.004
 Identities = 13/24 (54%), Positives = 19/24 (79%)

Query: 464 EEEEEDEEEEEEEEEEEEEEEEEE 487
           EEE+ ++EEE E+EEE EE+ E +
Sbjct: 22  EEEKREDEEENEDEEEGEEQSEVK 45

This family contains a number of defence peptides secreted from the skin of amphibians, including the opiate-like dermorphins and deltorphins, and the antimicrobial dermoseptins and temporins. The alignment for this family includes the signal peptide. Length = 46

>gnl|CDD|111875 pfam03032, Brevenin, Brevenin/esculentin/gaegurin/rugosin family

 Score = 35.4 bits (82), Expect = 0.004
 Identities = 13/24 (54%), Positives = 19/24 (79%)

Query: 462 EEEEEEEDEEEEEEEEEEEEEEEE 485
           EEE+ E++EE E+EEE EE+ E +
Sbjct: 22  EEEKREDEEENEDEEEGEEQSEVK 45

This family contains a number of defence peptides secreted from the skin of amphibians, including the opiate-like dermorphins and deltorphins, and the antimicrobial dermoseptins and temporins. The alignment for this family includes the signal peptide. Length = 46

>gnl|CDD|235548 PRK05657, PRK05657, RNA polymerase sigma factor RpoS; Validated

 Score = 39.9 bits (94), Expect = 0.004
 Identities = 8/42 (19%), Positives = 18/42 (42%)

Query: 446 EDSDFDTSDEEYDSSEEEEEEEEDEEEEEEEEEEEEEEEEEE 487
            + D D  +   +  +E+   EE+  + +  EEE   +   +
Sbjct: 8   LNEDADFDENGVEVFDEKALVEEEPSDNDLAEEELLSQGATQ 49

Length = 325

>gnl|CDD|235396 PRK05299, rpsB, 30S ribosomal protein S2; Provisional

 Score = 39.8 bits (94), Expect = 0.004
 Identities = 21/33 (63%), Positives = 22/33 (66%)

Query: 459 SSEEEEEEEEDEEEEEEEEEEEEEEEEEEGEEE 491
                E  EE+EEE EEEEEEEEEEE EE E E
Sbjct: 226 QGRLAEAAEEEEEEAEEEEEEEEEEEAEEAEAE 258

Length = 258

>gnl|CDD|223649 COG0576, GrpE, Molecular chaperone GrpE (heat shock protein) [Posttranslational modification, protein turnover, chaperones]

 Score = 38.9 bits (91), Expect = 0.004
 Identities = 22/42 (52%), Positives = 28/42 (66%)

Query: 453 SDEEYDSSEEEEEEEEDEEEEEEEEEEEEEEEEEEGEEEETE 494
           SD+E  + E + EE E+ E+ EEEE EEEE EEE   EEE +
Sbjct: 2   SDKEQKTEEPDAEETEEAEKSEEEEAEEEEPEEENELEEEQQ 43

Length = 193

>gnl|CDD|219924 pfam08597, eIF3_subunit, Translation initiation factor eIF3 subunit

 Score = 39.3 bits (92), Expect = 0.004
 Identities = 14/35 (40%), Positives = 27/35 (77%)

Query: 468 EDEEEEEEEEEEEEEEEEEEGEEEETETASSSTAK 502
           +DE+E+++ ++  +EEE+EE EEE+ + A+ + AK
Sbjct: 25  DDEDEDDDVKDSWDEEEDEEKEEEKAKVAAKAKAK 59

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|222571 pfam14153, Spore_coat_CotO, Spore coat protein CotO

 Score = 38.7 bits (90), Expect = 0.004
 Identities = 21/84 (25%), Positives = 35/84 (41%), Gaps = 3/84 (3%)

Query: 411 LQKTIQDTTGAYNRRRSSAMNHNRRWNARNGDSEYEDSDFDTSDEEYDSSEEEEEEEEDE 470
           +QKT                + + +        EYE       ++E    E E+  E+ E
Sbjct: 27  MQKTFIIKKADEKEEEKENSDEHVKSKEEEQKIEYE---EAEKEKEAGEPEREDIAEQQE 83

Query: 471 EEEEEEEEEEEEEEEEEGEEEETE 494
           +EE  +EEE+EEE E+  ++E   
Sbjct: 84  KEEIAQEEEKEEEAEDVKQQEVFS 107

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

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	790
KOG4404|consensus	350		100.0
KOG4404|consensus	350		100.0
KOG1418|consensus	433		99.94
KOG1418|consensus	433		99.93
PF07885	79	Ion_trans_2: Ion channel; InterPro: IPR013099 This	99.47
PF07885	79	Ion_trans_2: Ion channel; InterPro: IPR013099 This	99.38
KOG3713|consensus	477		99.21
PRK10537	393	voltage-gated potassium channel; Provisional	99.09
KOG3713|consensus	477		99.02
KOG1419|consensus	654		98.82
PRK10537	393	voltage-gated potassium channel; Provisional	98.76
KOG1420|consensus	1103		98.74
KOG1545|consensus	507		98.71
PLN03192	823	Voltage-dependent potassium channel; Provisional	98.65
KOG1545|consensus	507		98.62
KOG1419|consensus	654		98.59
PLN03192	823	Voltage-dependent potassium channel; Provisional	98.48
KOG4390|consensus	632		98.26
KOG3193|consensus	1087		98.16
KOG1420|consensus	1103		98.14
KOG4390|consensus	632		97.98
KOG0498|consensus	727		97.92
KOG3684|consensus	489		97.77
KOG3684|consensus	489		97.72
KOG0498|consensus	727		97.67
PF01007	336	IRK: Inward rectifier potassium channel; InterPro:	97.36
KOG0501|consensus	971		97.09
KOG3193|consensus	1087		96.55
KOG0501|consensus	971		96.5
PF01007	336	IRK: Inward rectifier potassium channel; InterPro:	95.95
TIGR00933	390	2a38 potassium uptake protein, TrkH family. The pr	91.8
PF00520	200	Ion_trans: Ion transport protein calcium channel s	91.61
KOG0500|consensus	536		91.49
KOG0500|consensus	536		89.8
KOG3827|consensus	400		89.47
PF00520	200	Ion_trans: Ion transport protein calcium channel s	88.51
PRK10750	483	potassium transporter; Provisional	84.44
KOG0499|consensus	815		82.31
KOG3827|consensus	400		81.62

>KOG4404|consensus

Probab=100.00  E-value=2.9e-37  Score=315.55  Aligned_cols=239  Identities=27%  Similarity=0.437  Sum_probs=175.6

Q ss_pred             HHHHHHHHHHHhhccceeeeccccccccCCCCCccccchhhc-----hhchHHHHHHHHHhh-----hhhhccccceeee
Q psy17959        273 TLCLMIMVGYIYGGAVLFSKWEDWNILDGSRSSSRSRSRQQT-----ERSFTEKCKDYLRQF-----LAFLFSNIGIICL  342 (790)
Q Consensus       273 ~~~~~~~v~y~~~Ga~iF~~~E~~~~~~~~~~~~~~~~~~~~-----~~~~~e~~~~~~~~~-----~~~~f~~~~~~~~  342 (790)
                      ..+++..+.|+++||+||.++|.++|.++++.-..+..+...     +.++.+..--+.+.-     ..|.|..+++|..
T Consensus        10 l~Livct~tYLLvGAaVFdaLEse~E~~~r~~l~~~~~~~~~kyn~s~~d~r~~er~i~~s~ph~ag~qWkF~GaFYFa~   89 (350)
T KOG4404|consen   10 LLLIVCTFTYLLVGAAVFDALESENEARERERLERRLANLKRKYNLSEEDYRELERVILKSEPHKAGPQWKFAGAFYFAT   89 (350)
T ss_pred             HHHHHHHHHHHHHHHHHHHHhcCcchHHHHHHHHHHHHHHHHhhCCCHHHHHHHHHHHHhcCccccccccccCcceEEEE
Confidence            344455677999999999999999888875433333332222     222222211111111     2399998887765


Q ss_pred             EEEEEeecccccccccCCcceehhhHHHHhHHHHHHHHHHhhHHHHHHhHHHHhhccccccCCCCCccccchhccccccc
Q psy17959        343 VIGYTIAGYGNVAPITFLGKITTIAYAIAGMPLFLLYLSNIGDILAKSFKWIYAKCCLCRGCPTRPRDLQKTIQDTTGAY  422 (790)
Q Consensus       343 ~~~~ttiGyg~~~p~t~~g~~~~i~y~~~gipl~~~~~~~~g~~l~~~~~~~~~~~~~~~~~~~~~~~~~k~i~~~~~~~  422 (790)
                       |++||||||+.+|.|.+||+|||+||++|||+.++.+..+|+.+...+..+.+++.++.+                   
T Consensus        90 -TVItTIGyGhstP~T~~GK~Fcm~Yal~Gipl~lvmFqs~gERlnt~~ayil~~~r~~~~-------------------  149 (350)
T KOG4404|consen   90 -TVITTIGYGHSTPSTDGGKAFCMFYALVGIPLTLVMFQSIGERLNTFVAYILRRCRRRLG-------------------  149 (350)
T ss_pred             -EEEeeeccCCCCCCCcCceehhhhHHHhcCchHHHHHHHHHHHHHHHHHHHHHHHHHHhc-------------------
Confidence             777999999999999999999999999999999999999999999999887655332211                   


Q ss_pred             cccccccccccccccccCCCCCccCCCCCCCccccCCchhhhhhhchhhhhhhhhhhhhhHhhhhcccccccccCCCCCC
Q psy17959        423 NRRRSSAMNHNRRWNARNGDSEYEDSDFDTSDEEYDSSEEEEEEEEDEEEEEEEEEEEEEEEEEEGEEEETETASSSTAK  502 (790)
Q Consensus       423 ~~~r~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~s~ee~~~~~e~e~e~~~e~ee~~e~e~e~~ee~~~~~~~s~~~~  502 (790)
                                .+.+..    +                                                           
T Consensus       150 ----------~r~~~~----S-----------------------------------------------------------  156 (350)
T KOG4404|consen  150 ----------RRRWDV----S-----------------------------------------------------------  156 (350)
T ss_pred             ----------cccCCC----c-----------------------------------------------------------
Confidence                      000100    0                                                           


Q ss_pred             CCCceeeehHHHHHHHHHHhhhhhceeeecccccCcccceeEEEEeecccccCCCccCCCcCCCCCCcccchhhhHHHHH
Q psy17959        503 NDPQMVTVPITLCLMIMVGYIYGGAVLFSKWEDWNILDGSYFCFISLSTIGFGDIVPGDKITGKNNDIGVQTLELSFILC  582 (790)
Q Consensus       503 ~~~~~~~~~~~~~l~~~~~~i~~ga~~f~~~e~w~~~da~Yf~~itltTIGfGD~~P~~~~~~~~~~~~~~~~~~~~~~~  582 (790)
                           ..-.+.+.+...++.++.||++|+..|+|+|+||+||||||+|||||||+|+.++...      -+..+.|..+.
T Consensus       157 -----~~~l~~i~~~~~~~~i~~gaa~fs~~E~Wsyfds~YyCFITltTIGFGDyValQ~~~a------lq~qplYv~~s  225 (350)
T KOG4404|consen  157 -----VYNLVLILFTACILLICCGAAMFSSVEGWSYFDSYYYCFITLTTIGFGDYVALQQDAA------LQSQPLYVFFS  225 (350)
T ss_pred             -----HHHHHHHHHHHHHHHHHhhHHHhhcccCcchhhhhheeeeeeeeccccchhhhcchhh------hhCCCceehHh
Confidence                 0013455556667789999999999999999999999999999999999999866322      24556788999


Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHhHHHH
Q psy17959        583 AMYLMLGMALIAMCFNLMQEEVVHKMRTCSEVT  615 (790)
Q Consensus       583 ~~~il~Gl~~~~~~~~~~~~~~~~~~~~~~~~~  615 (790)
                      ++||++|+++++.++|++.-.+.....+..++.
T Consensus       226 f~fIL~Gl~vi~a~~NllvLrf~t~~~~~~rr~  258 (350)
T KOG4404|consen  226 FVFILLGLCVIYALLNLLVLRFMTMNAEDERRD  258 (350)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHhhhHHHHHH
Confidence            999999999999999998877666544444433

>KOG4404|consensus

Probab=100.00  E-value=1.1e-34  Score=296.76  Aligned_cols=177  Identities=28%  Similarity=0.486  Sum_probs=137.5

Q ss_pred             CCCCCCCCeEEEEEeccccccccccCCCcceehhhHHHHhhHHHHHHHHHHHHHHHHHHHHHHHHhcccccccccccCCC
Q psy17959         13 GSHDRGSPFKEILSSVPGYGHIAPKTTLGKVATIFYAIVGIPLMLLCLSNIGDIMAHSFRFLYWKDFDFFTEYYDTKGVG   92 (790)
Q Consensus        13 ~~~~~~~~f~~t~~tTiGYG~i~P~T~~Gr~f~i~yaliGIPl~l~~l~~~g~~l~~~~~~l~~~~~~~~~~~~~~~~~~   92 (790)
                      |-|.++.+|+.||+|||||||.+|.|++||+|||+||++|||+.++++..+|+.+...++++..+-..+.    ..+.  
T Consensus        79 WkF~GaFYFa~TVItTIGyGhstP~T~~GK~Fcm~Yal~Gipl~lvmFqs~gERlnt~~ayil~~~r~~~----~~r~--  152 (350)
T KOG4404|consen   79 WKFAGAFYFATTVITTIGYGHSTPSTDGGKAFCMFYALVGIPLTLVMFQSIGERLNTFVAYILRRCRRRL----GRRR--  152 (350)
T ss_pred             cccCcceEEEEEEEeeeccCCCCCCCcCceehhhhHHHhcCchHHHHHHHHHHHHHHHHHHHHHHHHHHh----cccc--
Confidence            3444445599999999999999999999999999999999999999999999999888776554321111    0000  


Q ss_pred             Ccccccchhhh-HHHHHHHHHHHHHhHHhhcccCCCCccceeeeeeecccccccccccCCCCcchhhhhhhhhhhHHHHH
Q psy17959         93 NAEQIKPVPIW-LCVFLVISYIIGGAFLFSHWEPWGFPDSAYFCFITLTTIGFGDFVPAQKSTDVQTAEETAELRIALCS  171 (790)
Q Consensus        93 ~~~~~~~~~~~-~~~~~~~~~i~~ga~~~~~~e~wsf~da~Yf~~iTltTIGfGDi~P~~~~~~~~~~~~~~~~~~~~~~  171 (790)
                        .......++ +.+.+.++.++.||++|+..|+|+|+||+||||||+|||||||+|+.++...    ..+.++++.+.+
T Consensus       153 --~~~S~~~l~~i~~~~~~~~i~~gaa~fs~~E~Wsyfds~YyCFITltTIGFGDyValQ~~~a----lq~qplYv~~sf  226 (350)
T KOG4404|consen  153 --WDVSVYNLVLILFTACILLICCGAAMFSSVEGWSYFDSYYYCFITLTTIGFGDYVALQQDAA----LQSQPLYVFFSF  226 (350)
T ss_pred             --CCCcHHHHHHHHHHHHHHHHHhhHHHhhcccCcchhhhhheeeeeeeeccccchhhhcchhh----hhCCCceehHhH
Confidence              011112222 3344456778999999999999999999999999999999999999876422    224567899999


Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q psy17959        172 LYLLFGIALLAMSFNLVQEEVISNVKAIAK  201 (790)
Q Consensus       172 ~~~l~Gl~~~~~~i~~i~~~~~~~~~~~~~  201 (790)
                      +||++|+++++.++|++.-.+........|
T Consensus       227 ~fIL~Gl~vi~a~~NllvLrf~t~~~~~~r  256 (350)
T KOG4404|consen  227 VFILLGLCVIYALLNLLVLRFMTMNAEDER  256 (350)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHhhhHHHH
Confidence            999999999999999999887765544433

>KOG1418|consensus

Probab=99.94  E-value=1.8e-27  Score=269.34  Aligned_cols=257  Identities=30%  Similarity=0.434  Sum_probs=170.9

Q ss_pred             eeEehhHHHHHHHHHHHhhccceeeeccccccccCC-CCCccccch-------hhchhchHHHHHHHHH-----------
Q psy17959        267 MVTVPITLCLMIMVGYIYGGAVLFSKWEDWNILDGS-RSSSRSRSR-------QQTERSFTEKCKDYLR-----------  327 (790)
Q Consensus       267 ~~~l~~~~~~~~~v~y~~~Ga~iF~~~E~~~~~~~~-~~~~~~~~~-------~~~~~~~~e~~~~~~~-----------  327 (790)
                      +....|..+++.++.|.+.||.+|.++|.+++.+.. ........+       +..+............           
T Consensus        14 ~~~~~~~~l~~~~~~y~~~ga~~f~~~e~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~   93 (433)
T KOG1418|consen   14 RFGIRHVLLLLLVLLYLVLGAFIFQALERPKELELKQRELGLLLSNFILRIWRCIDELVLEEESRTKAHKQKASVLLALL   93 (433)
T ss_pred             hhhcchhhHHHHHHHHHhhHHHHHHHhcchHHHHHhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhh
Confidence            445667778888999999999999999998877762 111111110       0001110111111000           


Q ss_pred             ----------------hhhhhhccccceeeeEEEEEeecccccccccCCcceehhhHHHHhHHHHHHHHHHhhHHHHHHh
Q psy17959        328 ----------------QFLAFLFSNIGIICLVIGYTIAGYGNVAPITFLGKITTIAYAIAGMPLFLLYLSNIGDILAKSF  391 (790)
Q Consensus       328 ----------------~~~~~~f~~~~~~~~~~~~ttiGyg~~~p~t~~g~~~~i~y~~~gipl~~~~~~~~g~~l~~~~  391 (790)
                                      ....|+|.++.+|+. |++|||||||++|.|.+||++||+||++|||+++++++++|+++.+.+
T Consensus        94 ~~~~~~~~~~~~~~~~~~~~W~f~~al~fs~-tv~TTIGYG~i~P~T~~Gr~~~i~YaliGIPl~li~l~~~g~~l~~~~  172 (433)
T KOG1418|consen   94 LGVANSALSLEGDESPDTQQWSFSSALLFSI-TVITTIGYGNIAPRTDAGRLFTILYALVGIPLMLLILADIGKFLADSL  172 (433)
T ss_pred             hhcchhhcccccccCCCCcceecchhHhhhh-heeeeccCCcccCCcCcchhHHHHHHHHhhHHHHHHHHHHHHHHHHHH
Confidence                            011399999998887 667999999999999999999999999999999999999999999999


Q ss_pred             HHHHhhccccccCCCCCccccchhccccccccccccccccccccccccCCCCCccCCCCCCCccccCCchhhhhhhchhh
Q psy17959        392 KWIYAKCCLCRGCPTRPRDLQKTIQDTTGAYNRRRSSAMNHNRRWNARNGDSEYEDSDFDTSDEEYDSSEEEEEEEEDEE  471 (790)
Q Consensus       392 ~~~~~~~~~~~~~~~~~~~~~k~i~~~~~~~~~~r~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~s~ee~~~~~e~e~  471 (790)
                      ++++.+....                      +++..     ......   .+.++              +..    +  
T Consensus       173 ~~~~~~~~~~----------------------~~~~~-----~~~~~~---~~~~~--------------~~~----~--  202 (433)
T KOG1418|consen  173 RKLYRRRHVE----------------------LQRDR-----IRSNLR---RSIGL--------------RNR----S--  202 (433)
T ss_pred             HHHHHHhhhh----------------------hhhhh-----hhhhhh---ccccc--------------hhc----c--
Confidence            9888530000                      00000     000000   00000              000    0  


Q ss_pred             hhhhhhhhhhhHhhhhcccccccccCCCCCCCCCceeeehHHHHHHHHHHhhhhhceeeecccccCcccceeEEEEeecc
Q psy17959        472 EEEEEEEEEEEEEEEEGEEEETETASSSTAKNDPQMVTVPITLCLMIMVGYIYGGAVLFSKWEDWNILDGSYFCFISLST  551 (790)
Q Consensus       472 e~~~e~ee~~e~e~e~~ee~~~~~~~s~~~~~~~~~~~~~~~~~l~~~~~~i~~ga~~f~~~e~w~~~da~Yf~~itltT  551 (790)
                                   .+.+.+            .... .+.++.+++.++++|+..|+.++..+|+|+|++|+||||+|+||
T Consensus       203 -------------~~~~~~------------~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~e~w~f~~~~Yf~fisltT  256 (433)
T KOG1418|consen  203 -------------VELGIE------------LLDE-LRFILLLLLGISLVYLSPGSLLFSLQEQWSFIEAFYFSFISLTT  256 (433)
T ss_pred             -------------cccchh------------hccC-cceehhhhheeeEEEecccceeeeceeceeeEeeeeEEEEEeee
Confidence                         000000            0001 45678888888999999999999999999999999999999999


Q ss_pred             cccCCCccCCCcCCCCCCcccchhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q psy17959        552 IGFGDIVPGDKITGKNNDIGVQTLELSFILCAMYLMLGMALIAMCFNLMQEEVVH  606 (790)
Q Consensus       552 IGfGD~~P~~~~~~~~~~~~~~~~~~~~~~~~~~il~Gl~~~~~~~~~~~~~~~~  606 (790)
                      |||||++|.+..++.      .....+..+..+++++|++.++++.......+..
T Consensus       257 IG~GD~vp~~~~~~~------~~~~~~~~~~~~~~~~g~~~~~~~~~~~~~~~~~  305 (433)
T KOG1418|consen  257 IGFGDIVPRTLLGRF------RREELVDPLASVWILSGLALLALVLLGPDRRLEN  305 (433)
T ss_pred             ecCCccccCCCccee------eccccccchhHHHHHhhhhHHHHHhhccccchhh
Confidence            999999999876541      0111123678889999999999998654444433

>KOG1418|consensus

Probab=99.93  E-value=1.8e-27  Score=269.35  Aligned_cols=178  Identities=36%  Similarity=0.565  Sum_probs=132.3

Q ss_pred             CCCCCCCCeEEEEEeccccccccccCCCcceehhhHHHHhhHHHHHHHHHHHHHHHHHHHHHHHH---hcccc-cccccc
Q psy17959         13 GSHDRGSPFKEILSSVPGYGHIAPKTTLGKVATIFYAIVGIPLMLLCLSNIGDIMAHSFRFLYWK---DFDFF-TEYYDT   88 (790)
Q Consensus        13 ~~~~~~~~f~~t~~tTiGYG~i~P~T~~Gr~f~i~yaliGIPl~l~~l~~~g~~l~~~~~~l~~~---~~~~~-~~~~~~   88 (790)
                      |+|-.+++|++|++|||||||++|.|+.||+|||+||++||||++++++++|+++...++.++.+   ...+. .+....
T Consensus       114 W~f~~al~fs~tv~TTIGYG~i~P~T~~Gr~~~i~YaliGIPl~li~l~~~g~~l~~~~~~~~~~~~~~~~~~~~~~~~~  193 (433)
T KOG1418|consen  114 WSFSSALLFSITVITTIGYGNIAPRTDAGRLFTILYALVGIPLMLLILADIGKFLADSLRKLYRRRHVELQRDRIRSNLR  193 (433)
T ss_pred             eecchhHhhhhheeeeccCCcccCCcCcchhHHHHHHHHhhHHHHHHHHHHHHHHHHHHHHHHHHhhhhhhhhhhhhhhh
Confidence            45555555999999999999999999999999999999999999999999999999999887752   10000 000000


Q ss_pred             c-------CCCCcccc---cchhhhHHHHHHHHHHHHHhHHhhcccCCCCccceeeeeeecccccccccccCCCCcchhh
Q psy17959         89 K-------GVGNAEQI---KPVPIWLCVFLVISYIIGGAFLFSHWEPWGFPDSAYFCFITLTTIGFGDFVPAQKSTDVQT  158 (790)
Q Consensus        89 ~-------~~~~~~~~---~~~~~~~~~~~~~~~i~~ga~~~~~~e~wsf~da~Yf~~iTltTIGfGDi~P~~~~~~~~~  158 (790)
                      .       ........   .+.++...+..+++|+..|+.++..+|+|+|++|+||||+|+|||||||++|.+...... 
T Consensus       194 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~e~w~f~~~~Yf~fisltTIG~GD~vp~~~~~~~~-  272 (433)
T KOG1418|consen  194 RSIGLRNRSVELGIELLDELRFILLLLLGISLVYLSPGSLLFSLQEQWSFIEAFYFSFISLTTIGFGDIVPRTLLGRFR-  272 (433)
T ss_pred             ccccchhcccccchhhccCcceehhhhheeeEEEecccceeeeceeceeeEeeeeEEEEEeeeecCCccccCCCcceee-
Confidence            0       00001111   245566666677789999999999999999999999999999999999999998652100 


Q ss_pred             hhhhhhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q psy17959        159 AEETAELRIALCSLYLLFGIALLAMSFNLVQEEVIS  194 (790)
Q Consensus       159 ~~~~~~~~~~~~~~~~l~Gl~~~~~~i~~i~~~~~~  194 (790)
                         .......+..+++++|+..++++.......+.+
T Consensus       273 ---~~~~~~~~~~~~~~~g~~~~~~~~~~~~~~~~~  305 (433)
T KOG1418|consen  273 ---REELVDPLASVWILSGLALLALVLLGPDRRLEN  305 (433)
T ss_pred             ---ccccccchhHHHHHhhhhHHHHHhhccccchhh
Confidence               000123577889999999999998655554444

>PF07885 Ion_trans_2: Ion channel; InterPro: IPR013099 This entry includes the two membrane helix type ion channels found in bacteria []

Probab=99.47  E-value=4.8e-14  Score=121.32  Aligned_cols=75  Identities=23%  Similarity=0.704  Sum_probs=62.8

Q ss_pred             HHHHHHHHHHHhhhh---hcCCCccchhhheeeeeeccccCCcccCCCcccccccccchhhHHHHHHHHHHHHHHHHHHH
Q psy17959        679 IIISFILLGSLIFNK---LENWTFLDGTFFCFTSLGTIGFGELIPGESYDRTLRGNKNISVLVSSSYILVGMAVISMCFN  755 (790)
Q Consensus       679 ~~~~~~~~g~~~~~~---~e~~s~~da~Y~~~vt~tTVGyGD~~p~t~~gr~~~~~~~~~~~~~~~~~~~g~~~~~~~~~  755 (790)
                      +++++++.|++.++.   .|+|++.||+||+++|+|||||||+.|.++.||          +++++++++|+.++++.++
T Consensus         2 ~~~~~l~~~~~~~~~~~~~~~~~~~da~yfs~~t~tTvGyGDi~p~t~~gr----------~~~~~~~~~G~~~~~~~~~   71 (79)
T PF07885_consen    2 ILLLVLAFGAIFFYISEGSEKWSFIDALYFSFVTITTVGYGDIVPQTPAGR----------IFTIIYMLIGIFLFALFLS   71 (79)
T ss_dssp             HHHHHHHHHHHHHHHTTSSSTTSHHHHHHHHHHHHTT---SSSSTSSHHHH----------HHHHHHHHHHHHHHHHHHH
T ss_pred             EEEeeeHHHHHHHHHHHhcccCCHHHHHHHHHHHHhcccCCCccCCccchH----------HHHHHHHHHHHHHHHHHHH
Confidence            345556677777777   678999999999999999999999999999999          8899999999999999999


Q ss_pred             HHHHHHHH
Q psy17959        756 LIQEEIIF  763 (790)
Q Consensus       756 ~i~~~~~~  763 (790)
                      .+++.+.+
T Consensus        72 ~~~~~l~~   79 (79)
T PF07885_consen   72 VLASVLTQ   79 (79)
T ss_dssp             HHHHHHH-
T ss_pred             HHHHHhcC
Confidence            99987653

; PDB: 1KKD_A 2A0L_A 1ORQ_C 3UKM_C 1LNQ_E 3OUS_A 3LDC_A 3LDD_A 3RBZ_A 3LDE_A ....

>PF07885 Ion_trans_2: Ion channel; InterPro: IPR013099 This entry includes the two membrane helix type ion channels found in bacteria []

Probab=99.38  E-value=3.2e-13  Score=116.19  Aligned_cols=73  Identities=33%  Similarity=0.669  Sum_probs=60.3

Q ss_pred             HHHHHHHHhHHhhc---ccCCCCccceeeeeeecccccccccccCCCCcchhhhhhhhhhhHHHHHHHHHHHHHHHHHHH
Q psy17959        109 VISYIIGGAFLFSH---WEPWGFPDSAYFCFITLTTIGFGDFVPAQKSTDVQTAEETAELRIALCSLYLLFGIALLAMSF  185 (790)
Q Consensus       109 ~~~~i~~ga~~~~~---~e~wsf~da~Yf~~iTltTIGfGDi~P~~~~~~~~~~~~~~~~~~~~~~~~~l~Gl~~~~~~i  185 (790)
                      ++.+++.+++.+..   .|+|+|.||+||+++|+|||||||++|.++.            +|+++++++++|+.++++++
T Consensus         3 ~~~~l~~~~~~~~~~~~~~~~~~~da~yfs~~t~tTvGyGDi~p~t~~------------gr~~~~~~~~~G~~~~~~~~   70 (79)
T PF07885_consen    3 LLLVLAFGAIFFYISEGSEKWSFIDALYFSFVTITTVGYGDIVPQTPA------------GRIFTIIYMLIGIFLFALFL   70 (79)
T ss_dssp             HHHHHHHHHHHHHHTTSSSTTSHHHHHHHHHHHHTT---SSSSTSSHH------------HHHHHHHHHHHHHHHHHHHH
T ss_pred             EEeeeHHHHHHHHHHHhcccCCHHHHHHHHHHHHhcccCCCccCCccc------------hHHHHHHHHHHHHHHHHHHH
Confidence            34556667777776   6789999999999999999999999999654            89999999999999999999


Q ss_pred             HHHHHHHH
Q psy17959        186 NLVQEEVI  193 (790)
Q Consensus       186 ~~i~~~~~  193 (790)
                      +.+.+.+.
T Consensus        71 ~~~~~~l~   78 (79)
T PF07885_consen   71 SVLASVLT   78 (79)
T ss_dssp             HHHHHHHH
T ss_pred             HHHHHHhc
Confidence            99888765

; PDB: 1KKD_A 2A0L_A 1ORQ_C 3UKM_C 1LNQ_E 3OUS_A 3LDC_A 3LDD_A 3RBZ_A 3LDE_A ....

>KOG3713|consensus

Probab=99.21  E-value=3.7e-11  Score=131.78  Aligned_cols=66  Identities=23%  Similarity=0.476  Sum_probs=58.4

Q ss_pred             CCccceeeeeeecccccccccccCCCCcchhhhhhhhhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhc
Q psy17959        127 GFPDSAYFCFITLTTIGFGDFVPAQKSTDVQTAEETAELRIALCSLYLLFGIALLAMSFNLVQEEVISNVKAIAKHLG  204 (790)
Q Consensus       127 sf~da~Yf~~iTltTIGfGDi~P~~~~~~~~~~~~~~~~~~~~~~~~~l~Gl~~~~~~i~~i~~~~~~~~~~~~~~~~  204 (790)
                      |..-++|||+||+|||||||++|.|..            |++++..-++.|+.++|+.+.+|.+.+.+.+++.+.+-.
T Consensus       377 SIPa~~WWaiVTMTTVGYGDm~P~T~~------------Gklvas~cil~GVLvlAlPItiIv~nF~~~y~~~k~~~~  442 (477)
T KOG3713|consen  377 SIPAGFWWAVVTMTTVGYGDMVPVTVL------------GKLVASLCILCGVLVLALPITIIVNNFSMYYSELKAREK  442 (477)
T ss_pred             cccchhheeeEEEeeecccCccccccc------------hHHHHHHHHHHhHHHhhcchHhHhhhHHHHHHHHHHHHH
Confidence            478899999999999999999999876            899999999999999999999999999987765554433

>PRK10537 voltage-gated potassium channel; Provisional

Probab=99.09  E-value=2.3e-10  Score=127.27  Aligned_cols=83  Identities=20%  Similarity=0.413  Sum_probs=68.3

Q ss_pred             HHHHHHHHHHHHHHHhhhhhcC------CCccchhhheeeeeeccccCCcccCCCcccccccccchhhHHHHHHHHHHHH
Q psy17959        675 VSFLIIISFILLGSLIFNKLEN------WTFLDGTFFCFTSLGTIGFGELIPGESYDRTLRGNKNISVLVSSSYILVGMA  748 (790)
Q Consensus       675 ~~~~~~~~~~~~g~~~~~~~e~------~s~~da~Y~~~vt~tTVGyGD~~p~t~~gr~~~~~~~~~~~~~~~~~~~g~~  748 (790)
                      ..+..+..+++.|+++++++|+      +++.||+||+++|+|||||||+.|.|+.||          +|+++++++|++
T Consensus       139 ~~~~~~~~l~~~~~~g~~~~~~~f~~~~~s~~dA~y~svvt~tTvGyGdi~p~t~~gr----------l~~i~~ii~Gi~  208 (393)
T PRK10537        139 FAVISITSLLFYSTFGALYLGDGFSPPIESLSTAFYFSIVTMSTVGYGDIVPVSESAR----------LFTISVIILGIT  208 (393)
T ss_pred             HHHHHHHHHHHHHHHHHHHHccccCcCCCCHHHHHHhhheeeecccCCCCCCCCHHHH----------HHHHHHHHHHHH
Confidence            4444555566777887777774      899999999999999999999999999999          999999999999


Q ss_pred             HHHHHHHHHHHHHH-HHHHH
Q psy17959        749 VISMCFNLIQEEII-FMIKK  767 (790)
Q Consensus       749 ~~~~~~~~i~~~~~-~~~~~  767 (790)
                      ++++.++.+...++ .++++
T Consensus       209 vf~~~is~i~~p~i~~~l~~  228 (393)
T PRK10537        209 VFATSISAIFGPVIRGNLKR  228 (393)
T ss_pred             HHHHHHHHHHHHHHHHHHHH
Confidence            99999988876444 34443

>KOG3713|consensus

Probab=99.02  E-value=7.4e-10  Score=121.65  Aligned_cols=85  Identities=20%  Similarity=0.400  Sum_probs=66.7

Q ss_pred             HHHHHHHHHHHHHHHHHhhhhhcC-------CCccchhhheeeeeeccccCCcccCCCcccccccccchhhHHHHHHHHH
Q psy17959        673 IAVSFLIIISFILLGSLIFNKLEN-------WTFLDGTFFCFTSLGTIGFGELIPGESYDRTLRGNKNISVLVSSSYILV  745 (790)
Q Consensus       673 ~~~~~~~~~~~~~~g~~~~~~~e~-------~s~~da~Y~~~vt~tTVGyGD~~p~t~~gr~~~~~~~~~~~~~~~~~~~  745 (790)
                      +.+.++.+++-+++.+...|+.|.       -|..-|+|||+||+|||||||++|.|..||          +++..=++.
T Consensus       345 lglLllfL~~GI~iFStlvY~~Ek~~~~~~FtSIPa~~WWaiVTMTTVGYGDm~P~T~~Gk----------lvas~cil~  414 (477)
T KOG3713|consen  345 LGLLLLFLAVGIVIFSTLVYFAEKDEPDTKFTSIPAGFWWAVVTMTTVGYGDMVPVTVLGK----------LVASLCILC  414 (477)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHhhhcCCCCCCccccchhheeeEEEeeecccCccccccchH----------HHHHHHHHH
Confidence            443333333334444455555663       488999999999999999999999999999          889999999


Q ss_pred             HHHHHHHHHHHHHHHHHHHHHH
Q psy17959        746 GMAVISMCFNLIQEEIIFMIKK  767 (790)
Q Consensus       746 g~~~~~~~~~~i~~~~~~~~~~  767 (790)
                      |+.++++.+..|..-|.+-.++
T Consensus       415 GVLvlAlPItiIv~nF~~~y~~  436 (477)
T KOG3713|consen  415 GVLVLALPITIIVNNFSMYYSE  436 (477)
T ss_pred             hHHHhhcchHhHhhhHHHHHHH
Confidence            9999999999999888875544

>KOG1419|consensus

Probab=98.82  E-value=5.4e-09  Score=115.04  Aligned_cols=81  Identities=19%  Similarity=0.423  Sum_probs=66.7

Q ss_pred             HHHHHHHHHHHHHHHHHhhhhhcC-----------CCccchhhheeeeeeccccCCcccCCCcccccccccchhhHHHHH
Q psy17959        673 IAVSFLIIISFILLGSLIFNKLEN-----------WTFLDGTFFCFTSLGTIGFGELIPGESYDRTLRGNKNISVLVSSS  741 (790)
Q Consensus       673 ~~~~~~~~~~~~~~g~~~~~~~e~-----------~s~~da~Y~~~vt~tTVGyGD~~p~t~~gr~~~~~~~~~~~~~~~  741 (790)
                      ++...-+-++.+++.+.+.|..|.           -||-||+||.+||+|||||||.+|.|..||          +++..
T Consensus       233 LiTt~YIGFL~LIfsSflVYLaEKd~~~e~~n~~F~TyADALWWG~ITltTIGYGDk~P~TWlGr----------~laa~  302 (654)
T KOG1419|consen  233 LITTWYIGFLVLIFSSFLVYLAEKDAQGEGTNDEFPTYADALWWGVITLTTIGYGDKTPQTWLGR----------LLAAC  302 (654)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHhhcccccccccccchhHHHHHHhhheeEEeeccCCcCcccchhH----------HHHHH
Confidence            444444444455566777777773           389999999999999999999999999999          88999


Q ss_pred             HHHHHHHHHHHHHHHHHHHHHH
Q psy17959        742 YILVGMAVISMCFNLIQEEIIF  763 (790)
Q Consensus       742 ~~~~g~~~~~~~~~~i~~~~~~  763 (790)
                      +.++|+.++++..+.++.-|.-
T Consensus       303 fsligiSFFALPAGILGSGfAL  324 (654)
T KOG1419|consen  303 FSLIGISFFALPAGILGSGFAL  324 (654)
T ss_pred             HHHHHHHHHhcccccccchhhh
Confidence            9999999999999999866653

>PRK10537 voltage-gated potassium channel; Provisional

Probab=98.76  E-value=4.8e-08  Score=108.93  Aligned_cols=62  Identities=29%  Similarity=0.562  Sum_probs=53.2

Q ss_pred             CCCccceeeeeeecccccccccccCCCCcchhhhhhhhhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHH-HHHHH
Q psy17959        126 WGFPDSAYFCFITLTTIGFGDFVPAQKSTDVQTAEETAELRIALCSLYLLFGIALLAMSFNLVQEEVIS-NVKAI  199 (790)
Q Consensus       126 wsf~da~Yf~~iTltTIGfGDi~P~~~~~~~~~~~~~~~~~~~~~~~~~l~Gl~~~~~~i~~i~~~~~~-~~~~~  199 (790)
                      |++.||+||+++|+|||||||++|.+..            +|+++.+++++|++++++.++.+...+++ +.++.
T Consensus       167 ~s~~dA~y~svvt~tTvGyGdi~p~t~~------------grl~~i~~ii~Gi~vf~~~is~i~~p~i~~~l~~~  229 (393)
T PRK10537        167 ESLSTAFYFSIVTMSTVGYGDIVPVSES------------ARLFTISVIILGITVFATSISAIFGPVIRGNLKRL  229 (393)
T ss_pred             CCHHHHHHhhheeeecccCCCCCCCCHH------------HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            7999999999999999999999998765            89999999999999999988877765554 34433

>KOG1420|consensus

Probab=98.74  E-value=7.5e-09  Score=113.39  Aligned_cols=104  Identities=24%  Similarity=0.306  Sum_probs=82.3

Q ss_pred             HHHHHHHHHHHHHHHHHHhhhhhcC-------------CCccchhhheeeeeeccccCCcccCCCcccccccccchhhHH
Q psy17959        672 PIAVSFLIIISFILLGSLIFNKLEN-------------WTFLDGTFFCFTSLGTIGFGELIPGESYDRTLRGNKNISVLV  738 (790)
Q Consensus       672 ~~~~~~~~~~~~~~~g~~~~~~~e~-------------~s~~da~Y~~~vt~tTVGyGD~~p~t~~gr~~~~~~~~~~~~  738 (790)
                      ++.-.+.+++.+|+.+|...+++|+             .+|+|++||-+||++||||||+.-.|..||          +|
T Consensus       249 rl~qlvsifisvwltaag~ihllensgdp~~~f~n~hrltyw~cvyfl~vtmstvgygdvyc~t~lgr----------lf  318 (1103)
T KOG1420|consen  249 RLVQLVSIFISVWLTAAGFIHLLENSGDPWENFQNNHRLTYWECVYFLMVTMSTVGYGDVYCKTTLGR----------LF  318 (1103)
T ss_pred             hHHHHHHHHHHHHHhhcceeehhhcCCChhHhccCcccchhhheeeeeEEEeeeccccceeehhhhhH----------HH
Confidence            3455566788888999999999884             589999999999999999999999999999          88


Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhccCCCCCCcccCC
Q psy17959        739 SSSYILVGMAVISMCFNLIQEEIIFMIKKFTLKLNKSGGSSGGVCDKN  786 (790)
Q Consensus       739 ~~~~~~~g~~~~~~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  786 (790)
                      .+++++.|+++++..+..|.+.+-. ++|++...+.--|-++-++||.
T Consensus       319 mvffil~glamfasyvpeiielign-r~kyggeyk~ehgkkhivvcgh  365 (1103)
T KOG1420|consen  319 MVFFILGGLAMFASYVPEIIELIGN-RKKYGGEYKAEHGKKHIVVCGH  365 (1103)
T ss_pred             HHHHHHHHHHHHHhhhHHHHHHHcc-ccccCceeehhcCCeeEEEecc
Confidence            9999999999999999888876655 4444443333334444466653

>KOG1545|consensus

Probab=98.71  E-value=1.8e-09  Score=112.97  Aligned_cols=59  Identities=24%  Similarity=0.474  Sum_probs=51.3

Q ss_pred             CCccceeeeeeecccccccccccCCCCcchhhhhhhhhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q psy17959        127 GFPDSAYFCFITLTTIGFGDFVPAQKSTDVQTAEETAELRIALCSLYLLFGIALLAMSFNLVQEEVISNVK  197 (790)
Q Consensus       127 sf~da~Yf~~iTltTIGfGDi~P~~~~~~~~~~~~~~~~~~~~~~~~~l~Gl~~~~~~i~~i~~~~~~~~~  197 (790)
                      |..||+||++||+|||||||++|.+..            |+++..+..+.|+..+|+.+-+|.+.+..-+|
T Consensus       393 SIPdaFWwavVTMTTVGYGDm~P~Tvg------------GKIVGslCAiaGVLTiALPVPVIVsNFnyFYh  451 (507)
T KOG1545|consen  393 SIPDAFWWAVVTMTTVGYGDMVPVTVG------------GKIVGSLCAIAGVLTIALPVPVIVSNFNYFYH  451 (507)
T ss_pred             cCcccceEEEEEEEeeccccceecccC------------ceehhhHHhhhhheEecccccEEEecccceee
Confidence            489999999999999999999999876            78888899999999999998888776655443

>PLN03192 Voltage-dependent potassium channel; Provisional

Probab=98.65  E-value=4e-08  Score=120.79  Aligned_cols=53  Identities=13%  Similarity=0.382  Sum_probs=49.9

Q ss_pred             chhhheeeeeeccccCCcccCCCcccccccccchhhHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q psy17959        701 DGTFFCFTSLGTIGFGELIPGESYDRTLRGNKNISVLVSSSYILVGMAVISMCFNLIQEEIIF  763 (790)
Q Consensus       701 da~Y~~~vt~tTVGyGD~~p~t~~gr~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~i~~~~~~  763 (790)
                      .|+||+++|+|||||||++|.+..+|          +|+++++++|++++++.++.++..+..
T Consensus       253 ~slYwai~TmtTVGYGDi~p~t~~E~----------i~~i~~ml~g~~~~a~~ig~i~~li~~  305 (823)
T PLN03192        253 SAIYWSITTMTTVGYGDLHAVNTIEM----------IFIIFYMLFNLGLTAYLIGNMTNLVVE  305 (823)
T ss_pred             HHHHHHHHHHhhccCCCcCCCccchH----------HHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            37999999999999999999999999          999999999999999999999987764

>KOG1545|consensus

Probab=98.62  E-value=2e-08  Score=105.12  Aligned_cols=56  Identities=18%  Similarity=0.408  Sum_probs=50.0

Q ss_pred             CCccchhhheeeeeeccccCCcccCCCcccccccccchhhHHHHHHHHHHHHHHHHHHHHHHHHHH
Q psy17959        697 WTFLDGTFFCFTSLGTIGFGELIPGESYDRTLRGNKNISVLVSSSYILVGMAVISMCFNLIQEEII  762 (790)
Q Consensus       697 ~s~~da~Y~~~vt~tTVGyGD~~p~t~~gr~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~i~~~~~  762 (790)
                      -|..||+||++||+|||||||.+|.|..||          ++..+-.+.|+..+++..-+|...+.
T Consensus       392 ~SIPdaFWwavVTMTTVGYGDm~P~TvgGK----------IVGslCAiaGVLTiALPVPVIVsNFn  447 (507)
T KOG1545|consen  392 SSIPDAFWWAVVTMTTVGYGDMVPVTVGGK----------IVGSLCAIAGVLTIALPVPVIVSNFN  447 (507)
T ss_pred             CcCcccceEEEEEEEeeccccceecccCce----------ehhhHHhhhhheEecccccEEEeccc
Confidence            589999999999999999999999999999          77888888999999888888775554

>KOG1419|consensus

Probab=98.59  E-value=5.4e-08  Score=107.31  Aligned_cols=58  Identities=29%  Similarity=0.501  Sum_probs=51.4

Q ss_pred             CCccceeeeeeecccccccccccCCCCcchhhhhhhhhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q psy17959        127 GFPDSAYFCFITLTTIGFGDFVPAQKSTDVQTAEETAELRIALCSLYLLFGIALLAMSFNLVQEEVISNV  196 (790)
Q Consensus       127 sf~da~Yf~~iTltTIGfGDi~P~~~~~~~~~~~~~~~~~~~~~~~~~l~Gl~~~~~~i~~i~~~~~~~~  196 (790)
                      +|.||+||..||+|||||||.+|.+-.            +++++.++.++|++++++.-+++.+-+.-++
T Consensus       269 TyADALWWG~ITltTIGYGDk~P~TWl------------Gr~laa~fsligiSFFALPAGILGSGfALKV  326 (654)
T KOG1419|consen  269 TYADALWWGVITLTTIGYGDKTPQTWL------------GRLLAACFSLIGISFFALPAGILGSGFALKV  326 (654)
T ss_pred             hHHHHHHhhheeEEeeccCCcCcccch------------hHHHHHHHHHHHHHHHhcccccccchhhhhh
Confidence            599999999999999999999998644            9999999999999999999998877655433

>PLN03192 Voltage-dependent potassium channel; Provisional

Probab=98.48  E-value=1.1e-07  Score=116.84  Aligned_cols=55  Identities=24%  Similarity=0.529  Sum_probs=50.1

Q ss_pred             CccceeeeeeecccccccccccCCCCcchhhhhhhhhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q psy17959        128 FPDSAYFCFITLTTIGFGDFVPAQKSTDVQTAEETAELRIALCSLYLLFGIALLAMSFNLVQEEVIS  194 (790)
Q Consensus       128 f~da~Yf~~iTltTIGfGDi~P~~~~~~~~~~~~~~~~~~~~~~~~~l~Gl~~~~~~i~~i~~~~~~  194 (790)
                      |+.|+||+++|+|||||||++|.+..            .++++++++++|+++.+++++.+...+.+
T Consensus       251 Yi~slYwai~TmtTVGYGDi~p~t~~------------E~i~~i~~ml~g~~~~a~~ig~i~~li~~  305 (823)
T PLN03192        251 YISAIYWSITTMTTVGYGDLHAVNTI------------EMIFIIFYMLFNLGLTAYLIGNMTNLVVE  305 (823)
T ss_pred             HHHHHHHHHHHHhhccCCCcCCCccc------------hHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            45589999999999999999999876            88999999999999999999999987765

>KOG4390|consensus

Probab=98.26  E-value=1.4e-07  Score=99.50  Aligned_cols=80  Identities=15%  Similarity=0.319  Sum_probs=63.4

Q ss_pred             HHHHHHHHHHHHHhhhhhcC-------CCccchhhheeeeeeccccCCcccCCCcccccccccchhhHHHHHHHHHHHHH
Q psy17959        677 FLIIISFILLGSLIFNKLEN-------WTFLDGTFFCFTSLGTIGFGELIPGESYDRTLRGNKNISVLVSSSYILVGMAV  749 (790)
Q Consensus       677 ~~~~~~~~~~g~~~~~~~e~-------~s~~da~Y~~~vt~tTVGyGD~~p~t~~gr~~~~~~~~~~~~~~~~~~~g~~~  749 (790)
                      ++.+..-|++.|-++++.|.       -|..-|+|+++||+||.||||.+|.|.+||          +|..+-.+.|+.+
T Consensus       328 lFSLtMAIIIFATvMfYAEKg~~at~FTsIPaaFWYTIVTmTTLGYGDMVp~TIaGK----------IfGsiCSLSGVLV  397 (632)
T KOG4390|consen  328 LFSLTMAIIIFATVMFYAEKGSSATKFTSIPAAFWYTIVTMTTLGYGDMVPSTIAGK----------IFGSICSLSGVLV  397 (632)
T ss_pred             HHHHHHHHHHHHHHHHhhhccccccccccCcHhHhhheeeeeeccccccchHHHHHH----------HhhhhhcccceEE
Confidence            33344444555666666673       478899999999999999999999999999          8999999999999


Q ss_pred             HHHHHHHHHHHHHHHHH
Q psy17959        750 ISMCFNLIQEEIIFMIK  766 (790)
Q Consensus       750 ~~~~~~~i~~~~~~~~~  766 (790)
                      +++..-+|...+.+..+
T Consensus       398 IALPVPvIVSNFSRIYH  414 (632)
T KOG4390|consen  398 IALPVPVIVSNFSRIYH  414 (632)
T ss_pred             EeccccEEEechhHHHh
Confidence            99988877766665443

>KOG3193|consensus

Probab=98.16  E-value=3.3e-06  Score=92.58  Aligned_cols=84  Identities=15%  Similarity=0.309  Sum_probs=67.7

Q ss_pred             HHHHHHHHHHHHHHHHHHHHhhhhhc-----CCCccchhhheeeeeeccccCCcccCCCcccccccccchhhHHHHHHHH
Q psy17959        670 RVPIAVSFLIIISFILLGSLIFNKLE-----NWTFLDGTFFCFTSLGTIGFGELIPGESYDRTLRGNKNISVLVSSSYIL  744 (790)
Q Consensus       670 ~~~~~~~~~~~~~~~~~g~~~~~~~e-----~~s~~da~Y~~~vt~tTVGyGD~~p~t~~gr~~~~~~~~~~~~~~~~~~  744 (790)
                      .+.+.+.+..++++++.|....-+++     +.+.+.++||.+||++||||||.+|--.+.+          +..+++|.
T Consensus       184 ~~ql~ll~s~l~clift~~c~i~h~qra~~k~i~lf~s~y~v~vtfstvgygd~~pd~w~sq----------l~~vi~ic  253 (1087)
T KOG3193|consen  184 FRQLLLLFSVLACLIFTGMCSIEHLQRARGKRIDLFTSFYFVMVTFSTVGYGDWYPDYWASQ----------LCVVILIC  253 (1087)
T ss_pred             HHHHHHHHHHHHHHHHhhhhhHHHHHHccCceeeeeeeEEEEEEEEeeccccccccccchhh----------HHHHHHHH
Confidence            34566677778888888888887776     4799999999999999999999999966665          77888888


Q ss_pred             HHHHHHHHHHHHHHHHHHH
Q psy17959        745 VGMAVISMCFNLIQEEIIF  763 (790)
Q Consensus       745 ~g~~~~~~~~~~i~~~~~~  763 (790)
                      ++++++.--+..++....+
T Consensus       254 val~~ip~q~~~l~~tw~e  272 (1087)
T KOG3193|consen  254 VALGLIPKQLDELGQTWSE  272 (1087)
T ss_pred             HHHhccHHHHHHHHHHHHH
Confidence            8888888877777754433

>KOG1420|consensus

Probab=98.14  E-value=3.1e-06  Score=93.35  Aligned_cols=82  Identities=18%  Similarity=0.413  Sum_probs=67.1

Q ss_pred             hHHHHHHHHHHhhhhhceeeecccc----c---------CcccceeEEEEeecccccCCCccCCCcCCCCCCcccchhhh
Q psy17959        511 PITLCLMIMVGYIYGGAVLFSKWED----W---------NILDGSYFCFISLSTIGFGDIVPGDKITGKNNDIGVQTLEL  577 (790)
Q Consensus       511 ~~~~~l~~~~~~i~~ga~~f~~~e~----w---------~~~da~Yf~~itltTIGfGD~~P~~~~~~~~~~~~~~~~~~  577 (790)
                      .+.-.+.+++..++.+|.+.+.+|+    |         +|.+++||.++|++||||||+.-.+..||            
T Consensus       249 rl~qlvsifisvwltaag~ihllensgdp~~~f~n~hrltyw~cvyfl~vtmstvgygdvyc~t~lgr------------  316 (1103)
T KOG1420|consen  249 RLVQLVSIFISVWLTAAGFIHLLENSGDPWENFQNNHRLTYWECVYFLMVTMSTVGYGDVYCKTTLGR------------  316 (1103)
T ss_pred             hHHHHHHHHHHHHHhhcceeehhhcCCChhHhccCcccchhhheeeeeEEEeeeccccceeehhhhhH------------
Confidence            4455556666777788888887765    4         79999999999999999999999998887            


Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q psy17959        578 SFILCAMYLMLGMALIAMCFNLMQEEVVH  606 (790)
Q Consensus       578 ~~~~~~~~il~Gl~~~~~~~~~~~~~~~~  606 (790)
                        +|.++|++.|+++++-.+.-+.+.+-+
T Consensus       317 --lfmvffil~glamfasyvpeiielign  343 (1103)
T KOG1420|consen  317 --LFMVFFILGGLAMFASYVPEIIELIGN  343 (1103)
T ss_pred             --HHHHHHHHHHHHHHHhhhHHHHHHHcc
Confidence              899999999999998877666665543

>KOG4390|consensus

Probab=97.98  E-value=7.5e-07  Score=94.19  Aligned_cols=86  Identities=17%  Similarity=0.349  Sum_probs=66.7

Q ss_pred             HHHHhhhhhceeeecccc------cCcccceeEEEEeecccccCCCccCCCcCCCCCCcccchhhhHHHHHHHHHHHHHH
Q psy17959        518 IMVGYIYGGAVLFSKWED------WNILDGSYFCFISLSTIGFGDIVPGDKITGKNNDIGVQTLELSFILCAMYLMLGMA  591 (790)
Q Consensus       518 ~~~~~i~~ga~~f~~~e~------w~~~da~Yf~~itltTIGfGD~~P~~~~~~~~~~~~~~~~~~~~~~~~~~il~Gl~  591 (790)
                      +.+..|++..++|..-.+      -+..-||||+++||||.||||+||.+-.|+              +|..+.-+.|+.
T Consensus       331 LtMAIIIFATvMfYAEKg~~at~FTsIPaaFWYTIVTmTTLGYGDMVp~TIaGK--------------IfGsiCSLSGVL  396 (632)
T KOG4390|consen  331 LTMAIIIFATVMFYAEKGSSATKFTSIPAAFWYTIVTMTTLGYGDMVPSTIAGK--------------IFGSICSLSGVL  396 (632)
T ss_pred             HHHHHHHHHHHHHhhhccccccccccCcHhHhhheeeeeeccccccchHHHHHH--------------HhhhhhcccceE
Confidence            344556666666654322      356788999999999999999999988877              899999999999


Q ss_pred             HHHHHHHHHHHHHHHHHHHhHHHHHH
Q psy17959        592 LIAMCFNLMQEEVVHKMRTCSEVTQR  617 (790)
Q Consensus       592 ~~~~~~~~~~~~~~~~~~~~~~~~~~  617 (790)
                      ++++.+.++.+.+.+.++...+.-+|
T Consensus       397 VIALPVPvIVSNFSRIYHQNQRADKR  422 (632)
T KOG4390|consen  397 VIALPVPVIVSNFSRIYHQNQRADKR  422 (632)
T ss_pred             EEeccccEEEechhHHHhhhhhhhHH
Confidence            99999998888887777665544333

>KOG0498|consensus

Probab=97.92  E-value=7.1e-06  Score=96.55  Aligned_cols=55  Identities=13%  Similarity=0.333  Sum_probs=50.5

Q ss_pred             ccchhhheeeeeeccccCCcccCCCcccccccccchhhHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q psy17959        699 FLDGTFFCFTSLGTIGFGELIPGESYDRTLRGNKNISVLVSSSYILVGMAVISMCFNLIQEEIIF  763 (790)
Q Consensus       699 ~~da~Y~~~vt~tTVGyGD~~p~t~~gr~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~i~~~~~~  763 (790)
                      |.-|+||++.|+|||||||.+|.+..-+          +|+++++++|+++.+++||+++..+++
T Consensus       295 Y~~aLyw~l~tLstvG~g~~~s~~~~E~----------iFsi~~mi~GllL~A~lIGNmt~~iqs  349 (727)
T KOG0498|consen  295 YVYALYWGLSTLSTVGYGLVHANNMGEK----------IFSIFIMLFGLLLFAYLIGNMTALLQS  349 (727)
T ss_pred             HHHHHHHHhhHhhhccCCccCCCCcHHH----------HHHHHHHHHhHHHHHHHHhhHHHhHHH
Confidence            4458999999999999999999987666          999999999999999999999988886

>KOG3684|consensus

Probab=97.77  E-value=0.00013  Score=79.98  Aligned_cols=82  Identities=18%  Similarity=0.317  Sum_probs=64.7

Q ss_pred             hhhHHHHHHHHHHHHHhHHhhccc--C------CCCccceeeeeeecccccccccccCCCCcchhhhhhhhhhhHHHHHH
Q psy17959        101 PIWLCVFLVISYIIGGAFLFSHWE--P------WGFPDSAYFCFITLTTIGFGDFVPAQKSTDVQTAEETAELRIALCSL  172 (790)
Q Consensus       101 ~~~~~~~~~~~~i~~ga~~~~~~e--~------wsf~da~Yf~~iTltTIGfGDi~P~~~~~~~~~~~~~~~~~~~~~~~  172 (790)
                      |..+.+.+.+.+.++.+.++..-|  .      -.|.+++|+-.||+.+|||||++|.+.-            |+.++++
T Consensus       253 Pg~vL~vftl~~Wii~sW~~~~cER~~~~~~~~~~~~nsmWli~iTFlsiGYGDiVP~Tyc------------Gr~v~l~  320 (489)
T KOG3684|consen  253 PGTVLLVFTLSLWIIASWMLRQCERYHDSQDVTINYLNSMWLIAITFLSIGYGDIVPNTYC------------GRGVALL  320 (489)
T ss_pred             chHHHHHHHHHHHHHHHHHHHHHHHHhcchhhHHHHHhhHHHHHHHHhhcccCcccCCccc------------cchHHHH
Confidence            444444445556667777777665  2      2389999999999999999999999876            8889888


Q ss_pred             HHHHHHHHHHHHHHHHHHHHHH
Q psy17959        173 YLLFGIALLAMSFNLVQEEVIS  194 (790)
Q Consensus       173 ~~l~Gl~~~~~~i~~i~~~~~~  194 (790)
                      --++|.++.|+++.++...+..
T Consensus       321 tGivGa~~sallvAvisRKLeL  342 (489)
T KOG3684|consen  321 TGIVGAGCSSLLVAVIARKLEL  342 (489)
T ss_pred             hhhhhhhHHHHHHHHHHHHHHH
Confidence            8999999999999988876553

>KOG3684|consensus

Probab=97.72  E-value=4.1e-05  Score=83.67  Aligned_cols=82  Identities=20%  Similarity=0.390  Sum_probs=70.3

Q ss_pred             HHHHHHHHHHHHHHHHHHHhhhhhc--C------CCccchhhheeeeeeccccCCcccCCCcccccccccchhhHHHHHH
Q psy17959        671 VPIAVSFLIIISFILLGSLIFNKLE--N------WTFLDGTFFCFTSLGTIGFGELIPGESYDRTLRGNKNISVLVSSSY  742 (790)
Q Consensus       671 ~~~~~~~~~~~~~~~~g~~~~~~~e--~------~s~~da~Y~~~vt~tTVGyGD~~p~t~~gr~~~~~~~~~~~~~~~~  742 (790)
                      ++....++..+.+|++.+..+...|  +      -++++++|+..+|+-+|||||++|.|-.||          ..+++-
T Consensus       252 ~Pg~vL~vftl~~Wii~sW~~~~cER~~~~~~~~~~~~nsmWli~iTFlsiGYGDiVP~TycGr----------~v~l~t  321 (489)
T KOG3684|consen  252 CPGTVLLVFTLSLWIIASWMLRQCERYHDSQDVTINYLNSMWLIAITFLSIGYGDIVPNTYCGR----------GVALLT  321 (489)
T ss_pred             CchHHHHHHHHHHHHHHHHHHHHHHHHhcchhhHHHHHhhHHHHHHHHhhcccCcccCCccccc----------hHHHHh
Confidence            3455666777888888898888877  2      359999999999999999999999999999          778888


Q ss_pred             HHHHHHHHHHHHHHHHHHHH
Q psy17959        743 ILVGMAVISMCFNLIQEEII  762 (790)
Q Consensus       743 ~~~g~~~~~~~~~~i~~~~~  762 (790)
                      .++|.++.+.++.++++-+.
T Consensus       322 GivGa~~sallvAvisRKLe  341 (489)
T KOG3684|consen  322 GIVGAGCSSLLVAVIARKLE  341 (489)
T ss_pred             hhhhhhHHHHHHHHHHHHHH
Confidence            89999999999999986654

>KOG0498|consensus

Probab=97.67  E-value=2.3e-05  Score=92.40  Aligned_cols=65  Identities=18%  Similarity=0.314  Sum_probs=56.2

Q ss_pred             CcccceeEEEEeecccccCCCccCCCcCCCCCCcccchhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhHHHH
Q psy17959        537 NILDGSYFCFISLSTIGFGDIVPGDKITGKNNDIGVQTLELSFILCAMYLMLGMALIAMCFNLMQEEVVHKMRTCSEVT  615 (790)
Q Consensus       537 ~~~da~Yf~~itltTIGfGD~~P~~~~~~~~~~~~~~~~~~~~~~~~~~il~Gl~~~~~~~~~~~~~~~~~~~~~~~~~  615 (790)
                      -|.-|+||++.||||+||||..|.+..-.              +|+++++++|+.++|++++-|+..+++...+..++.
T Consensus       294 kY~~aLyw~l~tLstvG~g~~~s~~~~E~--------------iFsi~~mi~GllL~A~lIGNmt~~iqs~tsR~~~~r  358 (727)
T KOG0498|consen  294 KYVYALYWGLSTLSTVGYGLVHANNMGEK--------------IFSIFIMLFGLLLFAYLIGNMTALLQSLTSRTEEMR  358 (727)
T ss_pred             HHHHHHHHHhhHhhhccCCccCCCCcHHH--------------HHHHHHHHHhHHHHHHHHhhHHHhHHHHhHHHHHHH
Confidence            57889999999999999999999866433              999999999999999999999999988766554443

>PF01007 IRK: Inward rectifier potassium channel; InterPro: IPR013521 Potassium channels are the most diverse group of the ion channel family [, ]

Probab=97.36  E-value=0.00026  Score=77.43  Aligned_cols=81  Identities=20%  Similarity=0.287  Sum_probs=56.7

Q ss_pred             HHHHHHHHHHHHHHHHHhhhhh-------cC--------------CCccchhhheeeeeeccccCC--cccCCCcccccc
Q psy17959        673 IAVSFLIIISFILLGSLIFNKL-------EN--------------WTFLDGTFFCFTSLGTIGFGE--LIPGESYDRTLR  729 (790)
Q Consensus       673 ~~~~~~~~~~~~~~g~~~~~~~-------e~--------------~s~~da~Y~~~vt~tTVGyGD--~~p~t~~gr~~~  729 (790)
                      +.+.++..++.+++.|++|+.+       +.              -+|.+|++|++-|.||||||.  +.|..+.+-   
T Consensus        38 l~~f~~~y~~~~~~Fa~~y~~i~~~~gdl~~~~~~~~~~~Cv~~~~~f~~aF~FSveT~tTIGYG~~~~~~~c~~a~---  114 (336)
T PF01007_consen   38 LLLFVLSYLLSWLFFALLYYLIAYSHGDLEPIHADSNWTPCVSNVNSFTSAFLFSVETQTTIGYGSRYPTPECPYAI---  114 (336)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHTSCCTTTSBTTS-TSECT-TTHHHHHHHHHHHHTT---SSSEB-CSHHHHH---
T ss_pred             eehhHHHHHHHHHHHHHHHHHHhhhcccchhcccccCCCCceecccchhhheeEEEEEEEEeccCCcccCCCcchhH---
Confidence            3344456677777778777652       11              489999999999999999999  455544443   


Q ss_pred             cccchhhHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q psy17959        730 GNKNISVLVSSSYILVGMAVISMCFNLIQEEIIF  763 (790)
Q Consensus       730 ~~~~~~~~~~~~~~~~g~~~~~~~~~~i~~~~~~  763 (790)
                             ++.++..++|+.+.+.++|.+-.-+.+
T Consensus       115 -------~l~~~q~~~g~l~~a~~~Glvfar~sr  141 (336)
T PF01007_consen  115 -------FLVTIQSLVGLLLDAFMTGLVFARFSR  141 (336)
T ss_dssp             -------HHHHHHHHHHHHHHHHHHHHHHHHHTS
T ss_pred             -------HHHHHHHHHHHHHHHHHHHHHHHHhcC
Confidence                   667889999999999999888655443

They are important in shaping the action potential, and in neuronal excitability and plasticity []. The potassium channel family is composed of several functionally distinct isoforms, which can be broadly separated into 2 groups []: the practically non-inactivating 'delayed' group and the rapidly inactivating 'transient' group. These are all highly similar proteins, with only small amino acid changes causing the diversity of the voltage-dependent gating mechanism, channel conductance and toxin binding properties. Each type of K+ channel is activated by different signals and conditions depending on their type of regulation: some open in response to depolarisation of the plasma membrane; others in response to hyperpolarisation or an increase in intracellular calcium concentration; some can be regulated by binding of a transmitter, together with intracellular kinases; while others are regulated by GTP-binding proteins or other second messengers []. In eukaryotic cells, K+ channels are involved in neural signalling and generation of the cardiac rhythm, act as effectors in signal transduction pathways involving G protein-coupled receptors (GPCRs) and may have a role in target cell lysis by cytotoxic T-lymphocytes []. In prokaryotic cells, they play a role in the maintenance of ionic homeostasis []. All K+ channels discovered so far possess a core of alpha subunits, each comprising either one or two copies of a highly conserved pore loop domain (P-domain). The P-domain contains the sequence (T/SxxTxGxG), which has been termed the K+ selectivity sequence. In families that contain one P-domain, four subunits assemble to form a selective pathway for K+ across the membrane. However, it remains unclear how the 2 P-domain subunits assemble to form a selective pore. The functional diversity of these families can arise through homo- or hetero-associations of alpha subunits or association with auxiliary cytoplasmic beta subunits. K+ channel subunits containing one pore domain can be assigned into one of two superfamilies: those that possess six transmembrane (TM) domains and those that possess only two TM domains. The six TM domain superfamily can be further subdivided into conserved gene families: the voltage-gated (Kv) channels; the KCNQ channels (originally known as KvLQT channels); the EAG-like K+ channels; and three types of calcium (Ca)-activated K+ channels (BK, IK and SK) []. The 2TM domain family comprises inward-rectifying K+ channels. In addition, there are K+ channel alpha-subunits that possess two P-domains. These are usually highly regulated K+ selective leak channels. Inwardly-rectifying potassium channels (Kir) are the principal class of two-TM domain potassium channels. They are characterised by the property of inward-rectification, which is described as the ability to allow large inward currents and smaller outward currents. Inwardly rectifying potassium channels (Kir) are responsible for regulating diverse processes including: cellular excitability, vascular tone, heart rate, renal salt flow, and insulin release []. To date, around twenty members of this superfamily have been cloned, which can be grouped into six families by sequence similarity, and these are designated Kir1.x-6.x [, ]. Cloned Kir channel cDNAs encode proteins of between ~370-500 residues, both N- and C-termini are thought to be cytoplasmic, and the N terminus lacks a signal sequence. Kir channel alpha subunits possess only 2TM domains linked with a P-domain. Thus, Kir channels share similarity with the fifth and sixth domains, and P-domain of the other families. It is thought that four Kir subunits assemble to form a tetrameric channel complex, which may be hetero- or homomeric [].; PDB: 3AT9_A 3AUW_D 3SYA_A 3ATE_A 3SYQ_A 3SYO_A 3ATB_A 3SYC_A 3AT8_A 3ATA_A ....

>KOG0501|consensus

Probab=97.09  E-value=0.00057  Score=76.35  Aligned_cols=56  Identities=18%  Similarity=0.523  Sum_probs=51.7

Q ss_pred             CccchhhheeeeeeccccCCcccCCCcccccccccchhhHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q psy17959        698 TFLDGTFFCFTSLGTIGFGELIPGESYDRTLRGNKNISVLVSSSYILVGMAVISMCFNLIQEEIIF  763 (790)
Q Consensus       698 s~~da~Y~~~vt~tTVGyGD~~p~t~~gr~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~i~~~~~~  763 (790)
                      -|..++||+++++||||||.+.|.|..-|          +|++..+++|-.+-+..++.++..|+.
T Consensus       423 ~YissLYfTMt~mttvGFGNiA~~TD~EK----------iF~v~mMii~aLLYAtIFG~vTTI~QQ  478 (971)
T KOG0501|consen  423 AYISSLYFTMTCMTTVGFGNIAPNTDNEK----------IFGVCMMIIGALLYATIFGHVTTIIQQ  478 (971)
T ss_pred             eehhhhhhhhhhhhcccccccCCCccHHH----------HHHHHHHHHHHHHHHHHHhhHHHHHHH
Confidence            37789999999999999999999999999          999999999999999999999877775

>KOG3193|consensus

Probab=96.55  E-value=0.0047  Score=68.56  Aligned_cols=30  Identities=27%  Similarity=0.609  Sum_probs=26.3

Q ss_pred             cCcccceeEEEEeecccccCCCccCCCcCC
Q psy17959        536 WNILDGSYFCFISLSTIGFGDIVPGDKITG  565 (790)
Q Consensus       536 w~~~da~Yf~~itltTIGfGD~~P~~~~~~  565 (790)
                      .+.+.++||.++|++||||||.+|.--+++
T Consensus       216 i~lf~s~y~v~vtfstvgygd~~pd~w~sq  245 (1087)
T KOG3193|consen  216 IDLFTSFYFVMVTFSTVGYGDWYPDYWASQ  245 (1087)
T ss_pred             eeeeeeEEEEEEEEeeccccccccccchhh
Confidence            688999999999999999999999755443

>KOG0501|consensus

Probab=96.50  E-value=0.0031  Score=70.62  Aligned_cols=55  Identities=25%  Similarity=0.482  Sum_probs=46.6

Q ss_pred             CccceeeeeeecccccccccccCCCCcchhhhhhhhhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q psy17959        128 FPDSAYFCFITLTTIGFGDFVPAQKSTDVQTAEETAELRIALCSLYLLFGIALLAMSFNLVQEEVIS  194 (790)
Q Consensus       128 f~da~Yf~~iTltTIGfGDi~P~~~~~~~~~~~~~~~~~~~~~~~~~l~Gl~~~~~~i~~i~~~~~~  194 (790)
                      |+.++||+..++||||||.+.|.++.            .++|.+..+++|-.+-|.+++-+..-+.+
T Consensus       424 YissLYfTMt~mttvGFGNiA~~TD~------------EKiF~v~mMii~aLLYAtIFG~vTTI~QQ  478 (971)
T KOG0501|consen  424 YISSLYFTMTCMTTVGFGNIAPNTDN------------EKIFGVCMMIIGALLYATIFGHVTTIIQQ  478 (971)
T ss_pred             ehhhhhhhhhhhhcccccccCCCccH------------HHHHHHHHHHHHHHHHHHHHhhHHHHHHH
Confidence            88999999999999999999999876            67888889999988888887766554444

>PF01007 IRK: Inward rectifier potassium channel; InterPro: IPR013521 Potassium channels are the most diverse group of the ion channel family [, ]

Probab=95.95  E-value=0.0073  Score=66.17  Aligned_cols=58  Identities=29%  Similarity=0.386  Sum_probs=42.1

Q ss_pred             CCccceeeeeeecccccccccccCCCCcchhhhhhhhhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q psy17959        127 GFPDSAYFCFITLTTIGFGDFVPAQKSTDVQTAEETAELRIALCSLYLLFGIALLAMSFNLVQEEVIS  194 (790)
Q Consensus       127 sf~da~Yf~~iTltTIGfGDi~P~~~~~~~~~~~~~~~~~~~~~~~~~l~Gl~~~~~~i~~i~~~~~~  194 (790)
                      +|.+|++||+-|+||||||...|...          ..++.+++.+=.++|+.+.+.+++++-.++.+
T Consensus        84 ~f~~aF~FSveT~tTIGYG~~~~~~~----------c~~a~~l~~~q~~~g~l~~a~~~Glvfar~sr  141 (336)
T PF01007_consen   84 SFTSAFLFSVETQTTIGYGSRYPTPE----------CPYAIFLVTIQSLVGLLLDAFMTGLVFARFSR  141 (336)
T ss_dssp             THHHHHHHHHHHHTT---SSSEB-CS----------HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTS
T ss_pred             chhhheeEEEEEEEEeccCCcccCCC----------cchhHHHHHHHHHHHHHHHHHHHHHHHHHhcC
Confidence            69999999999999999998544321          23466677778899999999998887776554

They are important in shaping the action potential, and in neuronal excitability and plasticity []. The potassium channel family is composed of several functionally distinct isoforms, which can be broadly separated into 2 groups []: the practically non-inactivating 'delayed' group and the rapidly inactivating 'transient' group. These are all highly similar proteins, with only small amino acid changes causing the diversity of the voltage-dependent gating mechanism, channel conductance and toxin binding properties. Each type of K+ channel is activated by different signals and conditions depending on their type of regulation: some open in response to depolarisation of the plasma membrane; others in response to hyperpolarisation or an increase in intracellular calcium concentration; some can be regulated by binding of a transmitter, together with intracellular kinases; while others are regulated by GTP-binding proteins or other second messengers []. In eukaryotic cells, K+ channels are involved in neural signalling and generation of the cardiac rhythm, act as effectors in signal transduction pathways involving G protein-coupled receptors (GPCRs) and may have a role in target cell lysis by cytotoxic T-lymphocytes []. In prokaryotic cells, they play a role in the maintenance of ionic homeostasis []. All K+ channels discovered so far possess a core of alpha subunits, each comprising either one or two copies of a highly conserved pore loop domain (P-domain). The P-domain contains the sequence (T/SxxTxGxG), which has been termed the K+ selectivity sequence. In families that contain one P-domain, four subunits assemble to form a selective pathway for K+ across the membrane. However, it remains unclear how the 2 P-domain subunits assemble to form a selective pore. The functional diversity of these families can arise through homo- or hetero-associations of alpha subunits or association with auxiliary cytoplasmic beta subunits. K+ channel subunits containing one pore domain can be assigned into one of two superfamilies: those that possess six transmembrane (TM) domains and those that possess only two TM domains. The six TM domain superfamily can be further subdivided into conserved gene families: the voltage-gated (Kv) channels; the KCNQ channels (originally known as KvLQT channels); the EAG-like K+ channels; and three types of calcium (Ca)-activated K+ channels (BK, IK and SK) []. The 2TM domain family comprises inward-rectifying K+ channels. In addition, there are K+ channel alpha-subunits that possess two P-domains. These are usually highly regulated K+ selective leak channels. Inwardly-rectifying potassium channels (Kir) are the principal class of two-TM domain potassium channels. They are characterised by the property of inward-rectification, which is described as the ability to allow large inward currents and smaller outward currents. Inwardly rectifying potassium channels (Kir) are responsible for regulating diverse processes including: cellular excitability, vascular tone, heart rate, renal salt flow, and insulin release []. To date, around twenty members of this superfamily have been cloned, which can be grouped into six families by sequence similarity, and these are designated Kir1.x-6.x [, ]. Cloned Kir channel cDNAs encode proteins of between ~370-500 residues, both N- and C-termini are thought to be cytoplasmic, and the N terminus lacks a signal sequence. Kir channel alpha subunits possess only 2TM domains linked with a P-domain. Thus, Kir channels share similarity with the fifth and sixth domains, and P-domain of the other families. It is thought that four Kir subunits assemble to form a tetrameric channel complex, which may be hetero- or homomeric [].; PDB: 3AT9_A 3AUW_D 3SYA_A 3ATE_A 3SYQ_A 3SYO_A 3ATB_A 3SYC_A 3AT8_A 3ATA_A ....

>TIGR00933 2a38 potassium uptake protein, TrkH family

Probab=91.80  E-value=0.083  Score=59.58  Aligned_cols=42  Identities=19%  Similarity=0.403  Sum_probs=30.5

Q ss_pred             cCCCccchhhheeeeeeccccC--C-cccCCCcccccccccchhhHHHHHHHHHH
Q psy17959        695 ENWTFLDGTFFCFTSLGTIGFG--E-LIPGESYDRTLRGNKNISVLVSSSYILVG  746 (790)
Q Consensus       695 e~~s~~da~Y~~~vt~tTVGyG--D-~~p~t~~gr~~~~~~~~~~~~~~~~~~~g  746 (790)
                      .+.++.|+++=++-+++|||.+  . ....++.+|          +..++.|++|
T Consensus       345 ~~~~~~~~~fe~~Sa~~tvGls~g~~~~~l~~~~k----------~il~~~M~~G  389 (390)
T TIGR00933       345 SGYDFLTSLFEVVSAFGTVGLSVGLTTANLPDAGK----------LILIVLMFIG  389 (390)
T ss_pred             cCCCHHHHHHHHHHHhcCcCCCCCCCcccCCHHHH----------HHHHHHHHcC
Confidence            3789999999999999999964  2 334556677          5555555544

The proteins of the Trk family are derived from Gram-negative and Gram-positive bacteria, yeast and wheat. The proteins of E. coli K12 TrkH and TrkG as well as several yeast proteins have been functionally characterized.The E. coli TrkH and TrkG proteins are complexed to two peripheral membrane proteins, TrkA, an NAD-binding protein, and TrkE, an ATP-binding protein. This complex forms the potassium uptake system.

>PF00520 Ion_trans: Ion transport protein calcium channel signature potassium channel signature sodium channel signature; InterPro: IPR005821 This group of proteins is found in sodium, potassium, and calcium ion channels proteins

Probab=91.61  E-value=0.33  Score=48.07  Aligned_cols=56  Identities=20%  Similarity=0.430  Sum_probs=39.7

Q ss_pred             CCccchhhheeeeeeccccCCcccCCCcccccccccchhhHHH-HHHHHHHHHHHHHHHHHH
Q psy17959        697 WTFLDGTFFCFTSLGTIGFGELIPGESYDRTLRGNKNISVLVS-SSYILVGMAVISMCFNLI  757 (790)
Q Consensus       697 ~s~~da~Y~~~vt~tTVGyGD~~p~t~~gr~~~~~~~~~~~~~-~~~~~~g~~~~~~~~~~i  757 (790)
                      -++..|+|+.+.++||.|+||..|.....+     .....++. ++.++.++.++.++++.+
T Consensus       144 ~~~~~s~~~~~~~~t~~~~~~~~~~~~~~~-----~~~~~~~~~~~~~i~~~~l~nlliavi  200 (200)
T PF00520_consen  144 DSFGESLYWLFQTMTGEGWGDVMPSCMSAR-----SWLAVIFFISFIIIVSILLLNLLIAVI  200 (200)
T ss_dssp             SSHHHHHHHHHHHHTTTTCCCCHHHHHHTT-----STTHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             ccccccccccccccccCCcccccccccccc-----chhHhHHhhhhhhhHHHHHHHHHHhcC
Confidence            479999999999999999999999721000     12223555 666677777777777654

The proteins have 6 transmembrane helices in which the last two helices flank a loop which determines ion selectivity. In some Na channels proteins the domain is repeated four times, whereas in others (e.g. K channels) the protein forms a tetramer in the membrane. A bacterial structure of the protein is known for the last two helices but is not included in the Pfam family due to it lacking the first four helices. ; GO: 0005216 ion channel activity, 0006811 ion transport, 0055085 transmembrane transport, 0016020 membrane; PDB: 3VMX_B 1QG9_A 1UJL_A 2LE7_A 2LCM_A 3A2A_A 3RW0_A 4EKW_A 3RVY_B 3RVZ_B ....

>KOG0500|consensus

Probab=91.49  E-value=0.54  Score=52.78  Aligned_cols=65  Identities=17%  Similarity=0.113  Sum_probs=47.8

Q ss_pred             chhhheeeeeeccccCCcccCCCcccccccccchhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhccC
Q psy17959        701 DGTFFCFTSLGTIGFGELIPGESYDRTLRGNKNISVLVSSSYILVGMAVISMCFNLIQEEIIFMIKKFTLKLNKSG  776 (790)
Q Consensus       701 da~Y~~~vt~tTVGyGD~~p~t~~gr~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~i~~~~~~~~~~~~~~~~~~~  776 (790)
                      =++|||.-|+||+| --..|.+..-          ..|.++=.++|+.++|..+|.++..+..+-.......++..
T Consensus       186 ~S~YWStLTlTTiG-e~P~P~t~~e----------y~F~I~d~LiGvliFAtIvG~VGsmVtnmna~r~EFq~~mD  250 (536)
T KOG0500|consen  186 YSLYWSTLTLTTIG-EQPPPVTSSE----------YAFVIVDTLIGVLIFATIVGNVGSMVTNMNAARTEFQAKMD  250 (536)
T ss_pred             HHHHHHhhhhhhcc-CCCCCCcCch----------hhHHHHHHHHHHHHHhhhhccHhHHHHhhhHHHHHHHHHHH
Confidence            38999999999998 4456665433          37889999999999999999998877764444444333333

>KOG0500|consensus

Probab=89.80  E-value=0.71  Score=51.89  Aligned_cols=52  Identities=31%  Similarity=0.335  Sum_probs=38.3

Q ss_pred             cceeeeeeecccccccccccCCCCcchhhhhhhhhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q psy17959        130 DSAYFCFITLTTIGFGDFVPAQKSTDVQTAEETAELRIALCSLYLLFGIALLAMSFNLVQEEVIS  194 (790)
Q Consensus       130 da~Yf~~iTltTIGfGDi~P~~~~~~~~~~~~~~~~~~~~~~~~~l~Gl~~~~~~i~~i~~~~~~  194 (790)
                      -++|||-.|+||||=- -.|.++.            .-+|.++=.++|+.++|.+++-+.+.+.+
T Consensus       186 ~S~YWStLTlTTiGe~-P~P~t~~------------ey~F~I~d~LiGvliFAtIvG~VGsmVtn  237 (536)
T KOG0500|consen  186 YSLYWSTLTLTTIGEQ-PPPVTSS------------EYAFVIVDTLIGVLIFATIVGNVGSMVTN  237 (536)
T ss_pred             HHHHHHhhhhhhccCC-CCCCcCc------------hhhHHHHHHHHHHHHHhhhhccHhHHHHh
Confidence            3799999999999831 1222222            34577778899999999999988887665

>KOG3827|consensus

Probab=89.47  E-value=1.3  Score=48.34  Aligned_cols=88  Identities=17%  Similarity=0.231  Sum_probs=62.7

Q ss_pred             hhHHHHHHHHHHHHHHHHHHHHhhhhhc-------------C--------CCccchhhheeeeeeccccCCcccCCCccc
Q psy17959        668 RFRVPIAVSFLIIISFILLGSLIFNKLE-------------N--------WTFLDGTFFCFTSLGTIGFGELIPGESYDR  726 (790)
Q Consensus       668 ~~~~~~~~~~~~~~~~~~~g~~~~~~~e-------------~--------~s~~da~Y~~~vt~tTVGyGD~~p~t~~gr  726 (790)
                      +.+..+.+..+.+++-|++.+++++.+-             +        -||.-||=|++-|=||||||-=.++..=- 
T Consensus        61 kWR~~lliF~~sf~~SWl~Fg~iwwlIA~~hGDL~~~~~~~~~tpCV~nV~sf~sAFLFSiETQtTIGYG~R~vTeeCP-  139 (400)
T KOG3827|consen   61 KWRWMLLIFSLSFVLSWLFFGVIWWLIAYAHGDLEPDPPGENHTPCVMNVHSFTSAFLFSIETQTTIGYGFRYVTEECP-  139 (400)
T ss_pred             hhHHHHHHHHHHHHHHHHHHHHHHHHHHHhhCCcccCCCCcCCCcceeeccchhhhheeeeeeeeeeeccccccCccCh-
Confidence            3445555556667777888888888631             1        27899999999999999999877765322 


Q ss_pred             ccccccchhhHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q psy17959        727 TLRGNKNISVLVSSSYILVGMAVISMCFNLIQEEIIF  763 (790)
Q Consensus       727 ~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~i~~~~~~  763 (790)
                             .+++..++..++|+.+=+..+|.+-.-+.+
T Consensus       140 -------~aI~ll~~Q~I~g~ii~afm~G~i~aKiar  169 (400)
T KOG3827|consen  140 -------EAIFLLVLQSILGVIINAFMVGAIFAKIAR  169 (400)
T ss_pred             -------HHHHHHHHHHHHHHHHHHHHHHHHHHHhcC
Confidence                   233666778888888888877776544443

>PF00520 Ion_trans: Ion transport protein calcium channel signature potassium channel signature sodium channel signature; InterPro: IPR005821 This group of proteins is found in sodium, potassium, and calcium ion channels proteins

Probab=88.51  E-value=0.52  Score=46.65  Aligned_cols=55  Identities=29%  Similarity=0.538  Sum_probs=38.4

Q ss_pred             CCccceeeeeeecccccccccccCCCCcchhhhhhhhhhhHHHH-HHHHHHHHHHHHHHHHHH
Q psy17959        127 GFPDSAYFCFITLTTIGFGDFVPAQKSTDVQTAEETAELRIALC-SLYLLFGIALLAMSFNLV  188 (790)
Q Consensus       127 sf~da~Yf~~iTltTIGfGDi~P~~~~~~~~~~~~~~~~~~~~~-~~~~l~Gl~~~~~~i~~i  188 (790)
                      +|..|+|+.+.++||.|+||..|....       .......++. .+.++.++.+++++++.+
T Consensus       145 ~~~~s~~~~~~~~t~~~~~~~~~~~~~-------~~~~~~~~~~~~~~~i~~~~l~nlliavi  200 (200)
T PF00520_consen  145 SFGESLYWLFQTMTGEGWGDVMPSCMS-------ARSWLAVIFFISFIIIVSILLLNLLIAVI  200 (200)
T ss_dssp             SHHHHHHHHHHHHTTTTCCCCHHHHHH-------TTSTTHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             cccccccccccccccCCcccccccccc-------ccchhHhHHhhhhhhhHHHHHHHHHHhcC
Confidence            488999999999999999999996210       0011244444 566667778888887754

The proteins have 6 transmembrane helices in which the last two helices flank a loop which determines ion selectivity. In some Na channels proteins the domain is repeated four times, whereas in others (e.g. K channels) the protein forms a tetramer in the membrane. A bacterial structure of the protein is known for the last two helices but is not included in the Pfam family due to it lacking the first four helices. ; GO: 0005216 ion channel activity, 0006811 ion transport, 0055085 transmembrane transport, 0016020 membrane; PDB: 3VMX_B 1QG9_A 1UJL_A 2LE7_A 2LCM_A 3A2A_A 3RW0_A 4EKW_A 3RVY_B 3RVZ_B ....

>PRK10750 potassium transporter; Provisional

Probab=84.44  E-value=1.8  Score=50.17  Aligned_cols=65  Identities=11%  Similarity=0.086  Sum_probs=42.3

Q ss_pred             HHHHHHHHHHHHHHHHHHHhhhhhcCCCccchhhheeeeeecccc--CCc----ccCCCcccccccccchhhHHHHHHHH
Q psy17959        671 VPIAVSFLIIISFILLGSLIFNKLENWTFLDGTFFCFTSLGTIGF--GEL----IPGESYDRTLRGNKNISVLVSSSYIL  744 (790)
Q Consensus       671 ~~~~~~~~~~~~~~~~g~~~~~~~e~~s~~da~Y~~~vt~tTVGy--GD~----~p~t~~gr~~~~~~~~~~~~~~~~~~  744 (790)
                      .++...+++.++++++++++. ..++.+..+|+--+..++++||.  |..    ...++.+|          ++.++.|+
T Consensus       395 ~~v~~~~~ly~~~~~~~~~~l-~~~g~~~~sA~~~v~s~l~nvG~s~G~~~~~f~~l~~~~K----------~il~~~Ml  463 (483)
T PRK10750        395 EAVWGFFSAYALVFIVSMLAI-IATGVDDFSAFASVVATLNNLGPGLGVVADNFTSMNPVAK----------WILIANML  463 (483)
T ss_pred             HHHHHHHHHHHHHHHHHHHHH-HHcCCcHHHHHHHHHHHhcCCCCCchhhccccccCCHHHH----------HHHHHHHH
Confidence            344444555555556666655 56788999999888889998885  433    23455666          55666666


Q ss_pred             HH
Q psy17959        745 VG  746 (790)
Q Consensus       745 ~g  746 (790)
                      +|
T Consensus       464 lG  465 (483)
T PRK10750        464 FG  465 (483)
T ss_pred             HH
Confidence            55

>KOG0499|consensus

Probab=82.31  E-value=2.3  Score=48.90  Aligned_cols=80  Identities=15%  Similarity=0.240  Sum_probs=55.5

Q ss_pred             HHHHHHHHHHHHHHHHHhhhhh---------------cCCCccchhhheeeeeeccccCCcccCCCcccccccccchhhH
Q psy17959        673 IAVSFLIIISFILLGSLIFNKL---------------ENWTFLDGTFFCFTSLGTIGFGELIPGESYDRTLRGNKNISVL  737 (790)
Q Consensus       673 ~~~~~~~~~~~~~~g~~~~~~~---------------e~~s~~da~Y~~~vt~tTVGyGD~~p~t~~gr~~~~~~~~~~~  737 (790)
                      ++..+.-++.++=+-+.+|+..               +|-.|.-|+||++-|++||| |...|.+.          +-++
T Consensus       363 V~rT~~YmlyilHinacvYY~~SayqglG~~rWVydg~Gn~YiRCyyfa~kt~~tiG-~~P~P~~~----------~E~V  431 (815)
T KOG0499|consen  363 VIRTTGYLLYILHINACVYYWASAYQGLGTTRWVYDGEGNEYIRCYYFAVKTLITIG-GLPEPQTL----------FEIV  431 (815)
T ss_pred             hHHHHHHHHHHHhhhHHHHHHHHhhcccccceeEEcCCCCceeeehhhHHHHHHHhc-CCCCcchH----------HHHH
Confidence            3333444444445566666642               23489999999999999999 99999852          2234


Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHH
Q psy17959        738 VSSSYILVGMAVISMCFNLIQEEIIF  763 (790)
Q Consensus       738 ~~~~~~~~g~~~~~~~~~~i~~~~~~  763 (790)
                      |-.+=-+.|+-+++.++|.+-+.+-.
T Consensus       432 f~~~~w~mGVFvFslliGQmRDvi~a  457 (815)
T KOG0499|consen  432 FQLLNWFMGVFVFSLLIGQMRDVIGA  457 (815)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHhh
Confidence            55555567999999999988766653

>KOG3827|consensus

Probab=81.62  E-value=5.4  Score=43.83  Aligned_cols=58  Identities=22%  Similarity=0.301  Sum_probs=43.0

Q ss_pred             CCccceeeeeeecccccccccccCCCCcchhhhhhhhhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q psy17959        127 GFPDSAYFCFITLTTIGFGDFVPAQKSTDVQTAEETAELRIALCSLYLLFGIALLAMSFNLVQEEVIS  194 (790)
Q Consensus       127 sf~da~Yf~~iTltTIGfGDi~P~~~~~~~~~~~~~~~~~~~~~~~~~l~Gl~~~~~~i~~i~~~~~~  194 (790)
                      +|.-||-|++=|=||||||--.++..=          +.++++.++=.++|+.+-+.+++.+-..+.+
T Consensus       112 sf~sAFLFSiETQtTIGYG~R~vTeeC----------P~aI~ll~~Q~I~g~ii~afm~G~i~aKiar  169 (400)
T KOG3827|consen  112 SFTSAFLFSIETQTTIGYGFRYVTEEC----------PEAIFLLVLQSILGVIINAFMVGAIFAKIAR  169 (400)
T ss_pred             chhhhheeeeeeeeeeeccccccCccC----------hHHHHHHHHHHHHHHHHHHHHHHHHHHHhcC
Confidence            477889999999999999988877532          2355566666788888777777776665544

---

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

ID	Length	Definition	E-value
Query	790
3um7_A	309	Crystal Structure Of The Human Two Pore Domain K+ I		1e-11
3ukm_A	280	Crystal Structure Of The Human Two Pore Domain Pota		6e-10
3ukm_A	280	Crystal Structure Of The Human Two Pore Domain Pota		3e-07
3ukm_A	280	Crystal Structure Of The Human Two Pore Domain Pota		5e-05
4h33_A	137	Crystal Structure Of A Voltage-gated K+ Channel Por		7e-04

>pdb|3UM7|A Chain A, Crystal Structure Of The Human Two Pore Domain K+ Ion Channel Traak (K2p4.1) Length = 309

Iteration: 1
 Score = 68.6 bits (166), Expect = 1e-11,   Method: Compositional matrix adjust.
 Identities = 65/216 (30%), Positives = 101/216 (46%), Gaps = 49/216 (22%)
Query: 16  DRGSPF---KEILSSVPGYGHIAPKTTLGKVATIFYAIVGIPLMLLCLSNIGDIMAHSFR 72
           D GS F     I++++ GYG++A +T  G++  IFYA+VGIPL  + L+ +GD +  S R
Sbjct: 115 DLGSAFFFSGTIITTI-GYGNVALRTDAGRLFCIFYALVGIPLFGILLAGVGDRLGSSLR 173
Query: 73  FLYWKDFDFFTEYYDTKGVGNAEQI---KPVPIWLC------VFLVIS---YIIGGAFLF 120
                            G+G+ E I     VP  L       +FL+I    +++   F+F
Sbjct: 174 ----------------HGIGHIEAIFLKWHVPPELVRVLSAMLFLLIGCLLFVLTPTFVF 217
Query: 121 SHWEPWGFPDSAYFCFITLTTIGFGDFV----PAQKSTDVQTAEETAELRIALCSLYLLF 176
            + E W   ++ YF  +TLTT+GFGD+V    P Q S   Q           L   ++L 
Sbjct: 218 CYMEDWSKLEAIYFVIVTLTTVGFGDYVAGADPRQDSPAYQP----------LVWFWILL 267
Query: 177 GIALLAMSFNLVQE--EVISNVKAIAKHLGIIKSSN 210
           G+A  A     +     V+S  +  A+  G+   SN
Sbjct: 268 GLAYFASVLTTIGNWLRVVSR-RTRAEMGGLTAQSN 302

>pdb|3UKM|A Chain A, Crystal Structure Of The Human Two Pore Domain Potassium Ion Channel K2p1 (Twik-1) Length = 280

Iteration: 1
 Score = 63.2 bits (152), Expect = 6e-10,   Method: Compositional matrix adjust.
 Identities = 53/167 (31%), Positives = 79/167 (47%), Gaps = 17/167 (10%)
Query: 21  FKEILSSVPGYGHIAPKTTLGKVATIFYAIVGIPLMLLCLSNI-GDIMAHSFRFLYWKDF 79
           F   + S  GYGH  P +  GK   I Y+++GIP  LL L+ +   I  H  R       
Sbjct: 100 FASTVLSTTGYGHTVPLSDGGKAFCIIYSVIGIPFTLLFLTAVVQRITVHVTRRP----- 154
Query: 80  DFFTEYYDTKGVGNAEQIKPVPIWLCVFLVIS--YIIGGAFLFSHWEPWGFPDSAYFCFI 137
                Y+  +   + + +  V   L  F+ +S  + I  A      + W F +S YFCFI
Sbjct: 155 ---VLYFHIRWGFSKQVVAIVHAVLLGFVTVSCFFFIPAAVFSVLEDDWNFLESFYFCFI 211
Query: 138 TLTTIGFGDFVPAQKSTDVQTAEETAELRIALCSLYLLFG-IALLAM 183
           +L+TIG GD+VP +     Q   E  ++ I   + YLL G IA+L +
Sbjct: 212 SLSTIGLGDYVPGEGYN--QKFRELYKIGI---TCYLLLGLIAMLVV 253

>pdb|3UKM|A Chain A, Crystal Structure Of The Human Two Pore Domain Potassium Ion Channel K2p1 (Twik-1) Length = 280

Iteration: 1
 Score = 53.9 bits (128), Expect = 3e-07,   Method: Compositional matrix adjust.
 Identities = 38/84 (45%), Positives = 46/84 (54%), Gaps = 10/84 (11%)
Query: 527 AVLFSKWED-WNILDGSYFCFISLSTIGFGDIVPGDKITGKNNDIGVQTLELSFILCAMY 585
           A +FS  ED WN L+  YFCFISLSTIG GD VPG+    K         EL  I    Y
Sbjct: 190 AAVFSVLEDDWNFLESFYFCFISLSTIGLGDYVPGEGYNQKFR-------ELYKIGITCY 242
Query: 586 LMLGMALIAMCFNLMQEEVVHKMR 609
           L+LG  LIAM   L     +H+++
Sbjct: 243 LLLG--LIAMLVVLETFCELHELK 264

>pdb|3UKM|A Chain A, Crystal Structure Of The Human Two Pore Domain Potassium Ion Channel K2p1 (Twik-1) Length = 280

Iteration: 1
 Score = 47.0 bits (110), Expect = 5e-05,   Method: Compositional matrix adjust.
 Identities = 17/35 (48%), Positives = 25/35 (71%)
Query: 695 ENWTFLDGTFFCFTSLGTIGFGELIPGESYDRTLR 729
           ++W FL+  +FCF SL TIG G+ +PGE Y++  R
Sbjct: 198 DDWNFLESFYFCFISLSTIGLGDYVPGEGYNQKFR 232

>pdb|4H33|A Chain A, Crystal Structure Of A Voltage-gated K+ Channel Pore Module In A Closed State In Lipid Membranes, Tetragonal Crystal Form Length = 137

Iteration: 1
 Score = 43.1 bits (100), Expect = 7e-04,   Method: Compositional matrix adjust.
 Identities = 24/81 (29%), Positives = 41/81 (50%), Gaps = 12/81 (14%)
Query: 103 WLCVFLVISYIIGGAFLFSHWEPWGFPDSAYFCFITLTTIGFGDFVPAQKSTDVQTAEET 162
           +L +F+++  II    +F   E   +PD+ ++  +T TT+G+GD VP      +      
Sbjct: 19  FLMIFVLLVIIIPVPMVFIEPEINNYPDALWWAIVTATTVGYGDIVPVTPIGRI------ 72
Query: 163 AELRIALCSLYLLFGIALLAM 183
                 L S+ +LFGIA + M
Sbjct: 73  ------LASIMMLFGIAFIGM 87

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	790
3um7_A	309	Potassium channel subfamily K member 4; potassium	99.97
3ukm_A	280	Potassium channel subfamily K member 1; membrane p	99.97
3um7_A	309	Potassium channel subfamily K member 4; potassium	99.96
3ukm_A	280	Potassium channel subfamily K member 1; membrane p	99.96
2k1e_A	103	Water soluble analogue of potassium channel, KCSA;	99.67
3ldc_A	82	Calcium-gated potassium channel MTHK; transmembran	99.66
3ouf_A	97	Potassium channel protein; ION channel, membrane,	99.63
3eff_K	139	Voltage-gated potassium channel; FULL length KCSA,	99.62
2q67_A	114	Potassium channel protein; inverted teepee, helix	99.61
2ih3_C	122	Voltage-gated potassium channel; ION channel D-ami	99.57
3ldc_A	82	Calcium-gated potassium channel MTHK; transmembran	99.57
3vou_A	148	ION transport 2 domain protein, voltage-gated SOD	99.56
3ouf_A	97	Potassium channel protein; ION channel, membrane,	99.56
2a9h_A	155	Voltage-gated potassium channel; potassium channel	99.55
3eff_K	139	Voltage-gated potassium channel; FULL length KCSA,	99.55
2q67_A	114	Potassium channel protein; inverted teepee, helix	99.53
2k1e_A	103	Water soluble analogue of potassium channel, KCSA;	99.53
3vou_A	148	ION transport 2 domain protein, voltage-gated SOD	99.51
4h33_A	137	LMO2059 protein; bilayers, KVLM, lipidic cubic pha	99.5
2ih3_C	122	Voltage-gated potassium channel; ION channel D-ami	99.47
2a9h_A	155	Voltage-gated potassium channel; potassium channel	99.45
4h33_A	137	LMO2059 protein; bilayers, KVLM, lipidic cubic pha	99.43
3pjs_K	166	KCSA, voltage-gated potassium channel; ION channel	99.42
3pjs_K	166	KCSA, voltage-gated potassium channel; ION channel	99.33
1orq_C	223	Potassium channel; voltage-dependent, KVAP, FAB co	99.33
1orq_C	223	Potassium channel; voltage-dependent, KVAP, FAB co	99.25
1lnq_A	336	MTHK channels, potassium channel related protein;	99.23
4gx0_A	565	TRKA domain protein; membrane protein, ION channel	99.17
3beh_A	355	MLL3241 protein; transmembrane protein, membrane p	99.17
1xl4_A	301	Inward rectifier potassium channel; integral membr	99.13
1lnq_A	336	MTHK channels, potassium channel related protein;	99.07
1p7b_A	333	Integral membrane channel and cytosolic domains; t	99.05
2qks_A	321	KIR3.1-prokaryotic KIR channel chimera; G-protein	99.04
2r9r_B	514	Paddle chimera voltage gated potassium channel KV;	98.93
3beh_A	355	MLL3241 protein; transmembrane protein, membrane p	98.91
4gx0_A	565	TRKA domain protein; membrane protein, ION channel	98.91
2r9r_B	514	Paddle chimera voltage gated potassium channel KV;	98.87
1xl4_A	301	Inward rectifier potassium channel; integral membr	98.85
1p7b_A	333	Integral membrane channel and cytosolic domains; t	98.83
2qks_A	321	KIR3.1-prokaryotic KIR channel chimera; G-protein	98.8
3sya_A	340	G protein-activated inward rectifier potassium CH;	98.69
3spc_A	343	Inward-rectifier K+ channel KIR2.2; PIP, membrane	98.6
3sya_A	340	G protein-activated inward rectifier potassium CH;	98.3
3spc_A	343	Inward-rectifier K+ channel KIR2.2; PIP, membrane	98.07
3rvy_A	285	ION transport protein; tetrameric ION channel, vol	97.95
3rvy_A	285	ION transport protein; tetrameric ION channel, vol	97.68
4dxw_A	229	Navrh, ION transport protein; tetrameric, voltage-	91.62
3kg2_A	823	Glutamate receptor 2; ION channel, membrane protei	86.91
4dxw_A	229	Navrh, ION transport protein; tetrameric, voltage-	80.94

>3um7_A Potassium channel subfamily K member 4; potassium ION channel, metal transport; 3.31A {Homo sapiens}

Probab=99.97  E-value=8.2e-33  Score=293.20  Aligned_cols=229  Identities=23%  Similarity=0.323  Sum_probs=164.7

Q ss_pred             HHHHHHHHHHhhccceeeeccccccccCCCCCccc------cchhhchhchHHHHHHHHHh----------------hhh
Q psy17959        274 LCLMIMVGYIYGGAVLFSKWEDWNILDGSRSSSRS------RSRQQTERSFTEKCKDYLRQ----------------FLA  331 (790)
Q Consensus       274 ~~~~~~v~y~~~Ga~iF~~~E~~~~~~~~~~~~~~------~~~~~~~~~~~e~~~~~~~~----------------~~~  331 (790)
                      .+++.+++|+++||++|+++|+++|.+.+++-...      +..+.++.++.+-.+.....                ...
T Consensus        34 ~Ll~~~~~YL~~GA~vF~~LE~~~E~~~~~~l~~~~~~fl~~~~~~~~~~l~~l~~~v~~A~~~Gv~~~~~~~~~~~~~~  113 (309)
T 3um7_A           34 ALLALVLLYLVSGALVFRALEQPHEQQAQRELGEVREKFLRAHPCVSDQELGLLIKEVADALGGGADPETQSTSQSSHSA  113 (309)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHTTTCCCHHHHHHHHHGGGTSSCCCSCSHHHHHHHHHHHHHHHTTCCCSSCCCC-----C
T ss_pred             HHHHHHHHHHHHHHHHHHHHhCCcHHHHHHHHHHHHHHHHHhcccccHHHHHHHHHHHHHHHhcCCCccccccCCCCCCC
Confidence            35666788999999999999999987764221111      11112233333222222211                134


Q ss_pred             hhccccceeeeEEEEEeecccccccccCCcceehhhHHHHhHHHHHHHHHHhhHHHHHHhHHHHhhccccccCCCCCccc
Q psy17959        332 FLFSNIGIICLVIGYTIAGYGNVAPITFLGKITTIAYAIAGMPLFLLYLSNIGDILAKSFKWIYAKCCLCRGCPTRPRDL  411 (790)
Q Consensus       332 ~~f~~~~~~~~~~~~ttiGyg~~~p~t~~g~~~~i~y~~~gipl~~~~~~~~g~~l~~~~~~~~~~~~~~~~~~~~~~~~  411 (790)
                      |+|.++++|+.+ .+|||||||++|.|..||+||++|+++|||++.++++.+++.+.+.+++...+...+..        
T Consensus       114 w~~~~a~yf~~~-t~tTvGYGdi~P~T~~gk~~~i~~~l~Gi~~~~~~~~~i~~~l~~~~~~~i~~le~~~~--------  184 (309)
T 3um7_A          114 WDLGSAFFFSGT-IITTIGYGNVALRTDAGRLFCIFYALVGIPLFGILLAGVGDRLGSSLRHGIGHIEAIFL--------  184 (309)
T ss_dssp             CSHHHHHHHHHH-HHTSCCCCSSCCCSHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTHHHHHHHT--------
T ss_pred             CChhhhhHhhhe-eeeecccCCCCCCCccchhHHHHHHHHHHHHHHHHHHHHHHHHHHhhhhhHHHHHHHHh--------
Confidence            999999988775 45999999999999999999999999999999999999999998877655433211100        


Q ss_pred             cchhccccccccccccccccccccccccCCCCCccCCCCCCCccccCCchhhhhhhchhhhhhhhhhhhhhHhhhhcccc
Q psy17959        412 QKTIQDTTGAYNRRRSSAMNHNRRWNARNGDSEYEDSDFDTSDEEYDSSEEEEEEEEDEEEEEEEEEEEEEEEEEEGEEE  491 (790)
Q Consensus       412 ~k~i~~~~~~~~~~r~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~s~ee~~~~~e~e~e~~~e~ee~~e~e~e~~ee~  491 (790)
                                  +++..                                                               
T Consensus       185 ------------~~~~~---------------------------------------------------------------  189 (309)
T 3um7_A          185 ------------KWHVP---------------------------------------------------------------  189 (309)
T ss_dssp             ------------TTC-----------------------------------------------------------------
T ss_pred             ------------ccccc---------------------------------------------------------------
Confidence                        00000                                                               


Q ss_pred             cccccCCCCCCCCCceeeehHHHHHHHHHHhhhhhceeeecccccCcccceeEEEEeecccccCCCccCCCcCCCCCCcc
Q psy17959        492 ETETASSSTAKNDPQMVTVPITLCLMIMVGYIYGGAVLFSKWEDWNILDGSYFCFISLSTIGFGDIVPGDKITGKNNDIG  571 (790)
Q Consensus       492 ~~~~~~s~~~~~~~~~~~~~~~~~l~~~~~~i~~ga~~f~~~e~w~~~da~Yf~~itltTIGfGD~~P~~~~~~~~~~~~  571 (790)
                                 .........+.+.++.+++++++|+++|+..|+|+|.||+|||++|+|||||||++|.++.++      
T Consensus       190 -----------~~~~~~~~~~l~~~~~~~~~l~~ga~~~~~~E~~~~~da~y~~~vTltTvGyGd~~p~t~~g~------  252 (309)
T 3um7_A          190 -----------PELVRVLSAMLFLLIGCLLFVLTPTFVFCYMEDWSKLEAIYFVIVTLTTVGFGDYVAGADPRQ------  252 (309)
T ss_dssp             -----------CCHHHHHHHHHHHHHHHHHHTHHHHHHHHHHHCCCHHHHHHHHHHHHTTCCCSSCCTTCCTTC------
T ss_pred             -----------hhHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCHHHHHHHHHhheeccccCCCCCCCcccc------
Confidence                       000001112334455667889999999999999999999999999999999999999988776      


Q ss_pred             cchhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q psy17959        572 VQTLELSFILCAMYLMLGMALIAMCFNLMQEEVV  605 (790)
Q Consensus       572 ~~~~~~~~~~~~~~il~Gl~~~~~~~~~~~~~~~  605 (790)
                        ..+.|++++++|+++|+++++++++.+.+.+.
T Consensus       253 --~~~~y~~~~~~~il~Gl~~~a~~~~~i~~~~~  284 (309)
T 3um7_A          253 --DSPAYQPLVWFWILLGLAYFASVLTTIGNWLR  284 (309)
T ss_dssp             --CCSTHHHHHHHHHHHHHHHHHHHHHHHHHHTT
T ss_pred             --ccchHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence              23468899999999999999999998766544

>3ukm_A Potassium channel subfamily K member 1; membrane protein, eukaryotic, two-pore DO potassium channel, K2P channel, membrane; HET: UND; 3.40A {Homo sapiens}

Probab=99.97  E-value=3.4e-33  Score=291.84  Aligned_cols=235  Identities=26%  Similarity=0.374  Sum_probs=167.2

Q ss_pred             EehhHHHHHHHHHHHhhccceeeeccccccccCCCCCccccc------hhhchhchHHHHHHHHH-------------hh
Q psy17959        269 TVPITLCLMIMVGYIYGGAVLFSKWEDWNILDGSRSSSRSRS------RQQTERSFTEKCKDYLR-------------QF  329 (790)
Q Consensus       269 ~l~~~~~~~~~v~y~~~Ga~iF~~~E~~~~~~~~~~~~~~~~------~~~~~~~~~e~~~~~~~-------------~~  329 (790)
                      ...+..+++.+++|+++||++|+++|+++|.+.+++-...+.      .+.+++++.+-.++..+             ..
T Consensus        10 ~~~l~lLil~~~~Yl~~GA~vF~~LE~p~E~~~r~~~~~~~~~fl~~~~~~s~~~l~~~~~~~~~a~~~g~~~~~~~~~~   89 (280)
T 3ukm_A           10 ATMFGFLVLGYLLYLVFGAVVFSSVELPYEDLLRQELRKLKRRFLEEHECLSEQQLEQFLGRVLEASNYGVSVLSQASGN   89 (280)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCTTCCHHHHHHHHHHHHHHHTTTCCCC------
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHhCccHHHHHHHHHHHHHHHHHhcccccHHHHHHHHHHHHHHHhcCCccccCCCCC
Confidence            344666777788999999999999999998876422211111      11222333333332221             22


Q ss_pred             hhhhccccceeeeEEEEEeecccccccccCCcceehhhHHHHhHHHHHHHHHHhhHHHHHHhHHHHhhccccccCCCCCc
Q psy17959        330 LAFLFSNIGIICLVIGYTIAGYGNVAPITFLGKITTIAYAIAGMPLFLLYLSNIGDILAKSFKWIYAKCCLCRGCPTRPR  409 (790)
Q Consensus       330 ~~~~f~~~~~~~~~~~~ttiGyg~~~p~t~~g~~~~i~y~~~gipl~~~~~~~~g~~l~~~~~~~~~~~~~~~~~~~~~~  409 (790)
                      ..|+|.++.+|+.++ +|||||||++|.|..||+++++|+++|||++.++++.+++.+.....+.   ..  +.      
T Consensus        90 ~~w~~~~a~yf~~~t-~tTvGyGd~~P~T~~Gk~f~~~~~l~Gi~~~~~~~~~~~~~l~~~~~~~---~~--~~------  157 (280)
T 3ukm_A           90 WNWDFTSALFFASTV-LSTTGYGHTVPLSDGGKAFCIIYSVIGIPFTLLFLTAVVQRITVHVTRR---PV--LY------  157 (280)
T ss_dssp             CCSSHHHHHHHHHHH-HTTCCCCSSCCCSHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHSST---TT--TT------
T ss_pred             CCCChhcchhheeee-eeccccCCcCCCCchhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH---HH--HH------
Confidence            359999999888754 5999999999999999999999999999999999999998775543110   00  00      


Q ss_pred             cccchhccccccccccccccccccccccccCCCCCccCCCCCCCccccCCchhhhhhhchhhhhhhhhhhhhhHhhhhcc
Q psy17959        410 DLQKTIQDTTGAYNRRRSSAMNHNRRWNARNGDSEYEDSDFDTSDEEYDSSEEEEEEEEDEEEEEEEEEEEEEEEEEEGE  489 (790)
Q Consensus       410 ~~~k~i~~~~~~~~~~r~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~s~ee~~~~~e~e~e~~~e~ee~~e~e~e~~e  489 (790)
                           .        +++         +..    +       .           ..                         
T Consensus       158 -----~--------~~~---------~~~----~-------~-----------~~-------------------------  168 (280)
T 3ukm_A          158 -----F--------HIR---------WGF----S-------K-----------QV-------------------------  168 (280)
T ss_dssp             -----C---------------------------C-------C-----------HH-------------------------
T ss_pred             -----H--------HHH---------hcC----C-------h-----------hH-------------------------
Confidence                 0        000         000    0       0           00                         


Q ss_pred             cccccccCCCCCCCCCceeeehHHHHHHHHHHhhhhhceeeeccc-ccCcccceeEEEEeecccccCCCccCCCcCCCCC
Q psy17959        490 EEETETASSSTAKNDPQMVTVPITLCLMIMVGYIYGGAVLFSKWE-DWNILDGSYFCFISLSTIGFGDIVPGDKITGKNN  568 (790)
Q Consensus       490 e~~~~~~~s~~~~~~~~~~~~~~~~~l~~~~~~i~~ga~~f~~~e-~w~~~da~Yf~~itltTIGfGD~~P~~~~~~~~~  568 (790)
                                      ......+.+.++++++++++|+++|+..| +|+|.||+|||++|+|||||||++|.++.++   
T Consensus       169 ----------------~~~~~~~~l~~~~~~~~~~~ga~~~~~~E~~~s~~da~y~~~iTltTvGyGD~~p~t~~~~---  229 (280)
T 3ukm_A          169 ----------------VAIVHAVLLGFVTVSCFFFIPAAVFSVLEDDWNFLESFYFCFISLSTIGLGDYVPGEGYNQ---  229 (280)
T ss_dssp             ----------------HHHHHHHHHHHHHHHHHTHHHHHHHHHHSSSCCHHHHHHHHHHHHTTCCCCSCCSSCSSSC---
T ss_pred             ----------------HHHHHHHHHHHHHHHHHHhHHHHHHHHHhcCCchhhhhhheeeeeecccCCCCCCCCCccc---
Confidence                            00011234556677789999999999999 8999999999999999999999999988764   


Q ss_pred             CcccchhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q psy17959        569 DIGVQTLELSFILCAMYLMLGMALIAMCFNLMQEEVVHK  607 (790)
Q Consensus       569 ~~~~~~~~~~~~~~~~~il~Gl~~~~~~~~~~~~~~~~~  607 (790)
                          +...++++++++|+++|+++++++++.+.+....+
T Consensus       230 ----~~~~l~r~~~~~~il~Gl~~~~~~~~~i~~~~~~~  264 (280)
T 3ukm_A          230 ----KFRELYKIGITCYLLLGLIAMLVVLETFCELHELK  264 (280)
T ss_dssp             ----TTHHHHHHHHHHHHHHHHHHHHHHHHHHHTSHHHH
T ss_pred             ----ccchhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence                35567889999999999999999999988766544

>3um7_A Potassium channel subfamily K member 4; potassium ION channel, metal transport; 3.31A {Homo sapiens}

Probab=99.96  E-value=8e-31  Score=277.98  Aligned_cols=173  Identities=18%  Similarity=0.414  Sum_probs=136.6

Q ss_pred             ccCcccceeEEEEeecccccCCCccCCCcCCCCCCcccchhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhHHH
Q psy17959        535 DWNILDGSYFCFISLSTIGFGDIVPGDKITGKNNDIGVQTLELSFILCAMYLMLGMALIAMCFNLMQEEVVHKMRTCSEV  614 (790)
Q Consensus       535 ~w~~~da~Yf~~itltTIGfGD~~P~~~~~~~~~~~~~~~~~~~~~~~~~~il~Gl~~~~~~~~~~~~~~~~~~~~~~~~  614 (790)
                      +|+|.||+||+++|+|||||||++|.+..||              +++++|+++|+++++++++.+.+.+.+..++...+
T Consensus       113 ~w~~~~a~yf~~~t~tTvGYGdi~P~T~~gk--------------~~~i~~~l~Gi~~~~~~~~~i~~~l~~~~~~~i~~  178 (309)
T 3um7_A          113 AWDLGSAFFFSGTIITTIGYGNVALRTDAGR--------------LFCIFYALVGIPLFGILLAGVGDRLGSSLRHGIGH  178 (309)
T ss_dssp             CCSHHHHHHHHHHHHTSCCCCSSCCCSHHHH--------------HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTHH
T ss_pred             CCChhhhhHhhheeeeecccCCCCCCCccch--------------hHHHHHHHHHHHHHHHHHHHHHHHHHHhhhhhHHH
Confidence            4999999999999999999999999998876              99999999999999999999988887765443322


Q ss_pred             HHHHHHHHHhhhcccccccccccccccCCCCCCCCCCCCCcccccccccccchhhHHHHHHHHHHHHHHHHHHHHhhhhh
Q psy17959        615 TQRKSKQQQQQQNSLPNIYSQFNHISTGKYDGKTTPYRGGYCTHASDFEPKAFRFRVPIAVSFLIIISFILLGSLIFNKL  694 (790)
Q Consensus       615 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~~~~~~  694 (790)
                      .++..          ...                         +   ..+...+....+...++.+++++++|+++|+..
T Consensus       179 le~~~----------~~~-------------------------~---~~~~~~~~~~~~l~~~~~~~~~l~~ga~~~~~~  220 (309)
T 3um7_A          179 IEAIF----------LKW-------------------------H---VPPELVRVLSAMLFLLIGCLLFVLTPTFVFCYM  220 (309)
T ss_dssp             HHHHH----------TTT-------------------------C-----CCHHHHHHHHHHHHHHHHHHTHHHHHHHHHH
T ss_pred             HHHHH----------hcc-------------------------c---cchhHHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence            22110          000                         0   000111222233444556677889999999999


Q ss_pred             cCCCccchhhheeeeeeccccCCcccCCCcccccccccchhhHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q psy17959        695 ENWTFLDGTFFCFTSLGTIGFGELIPGESYDRTLRGNKNISVLVSSSYILVGMAVISMCFNLIQEEIIF  763 (790)
Q Consensus       695 e~~s~~da~Y~~~vt~tTVGyGD~~p~t~~gr~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~i~~~~~~  763 (790)
                      |+|+|+||+|||++|+|||||||++|.+..||.    ....++++++++++|++++++.++.+++.+..
T Consensus       221 E~~~~~da~y~~~vTltTvGyGd~~p~t~~g~~----~~~y~~~~~~~il~Gl~~~a~~~~~i~~~~~~  285 (309)
T 3um7_A          221 EDWSKLEAIYFVIVTLTTVGFGDYVAGADPRQD----SPAYQPLVWFWILLGLAYFASVLTTIGNWLRV  285 (309)
T ss_dssp             HCCCHHHHHHHHHHHHTTCCCSSCCTTCCTTCC----CSTHHHHHHHHHHHHHHHHHHHHHHHHHHTTT
T ss_pred             cCCCHHHHHHHHHhheeccccCCCCCCCccccc----cchHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            999999999999999999999999999999983    23566799999999999999999998876654

>3ukm_A Potassium channel subfamily K member 1; membrane protein, eukaryotic, two-pore DO potassium channel, K2P channel, membrane; HET: UND; 3.40A {Homo sapiens}

Probab=99.96  E-value=5e-30  Score=267.93  Aligned_cols=172  Identities=23%  Similarity=0.544  Sum_probs=134.8

Q ss_pred             cccCcccceeEEEEeecccccCCCccCCCcCCCCCCcccchhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHh-H
Q psy17959        534 EDWNILDGSYFCFISLSTIGFGDIVPGDKITGKNNDIGVQTLELSFILCAMYLMLGMALIAMCFNLMQEEVVHKMRTC-S  612 (790)
Q Consensus       534 e~w~~~da~Yf~~itltTIGfGD~~P~~~~~~~~~~~~~~~~~~~~~~~~~~il~Gl~~~~~~~~~~~~~~~~~~~~~-~  612 (790)
                      |+|+|.||+||+++|+|||||||++|.++.||              +++++|+++|++++++.++.+.+.+.....+. .
T Consensus        90 ~~w~~~~a~yf~~~t~tTvGyGd~~P~T~~Gk--------------~f~~~~~l~Gi~~~~~~~~~~~~~l~~~~~~~~~  155 (280)
T 3ukm_A           90 WNWDFTSALFFASTVLSTTGYGHTVPLSDGGK--------------AFCIIYSVIGIPFTLLFLTAVVQRITVHVTRRPV  155 (280)
T ss_dssp             CCSSHHHHHHHHHHHHTTCCCCSSCCCSHHHH--------------HHHHHHHHHHHHHHHHHHHHHHHHHHHHHSSTTT
T ss_pred             CCCChhcchhheeeeeeccccCCcCCCCchhH--------------HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            35999999999999999999999999998877              99999999999999999988887665543110 0


Q ss_pred             HHHHHHHHHHHhhhcccccccccccccccCCCCCCCCCCCCCcccccccccccchhhHHHHHHHHHHHHHHHHHHHHhhh
Q psy17959        613 EVTQRKSKQQQQQQNSLPNIYSQFNHISTGKYDGKTTPYRGGYCTHASDFEPKAFRFRVPIAVSFLIIISFILLGSLIFN  692 (790)
Q Consensus       613 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~~~~  692 (790)
                      +.+++                                  +       ....+.+......+.+.++++++++++|+++|+
T Consensus       156 ~~~~~----------------------------------~-------~~~~~~~~~~~~~~~l~~~~~~~~~~~ga~~~~  194 (280)
T 3ukm_A          156 LYFHI----------------------------------R-------WGFSKQVVAIVHAVLLGFVTVSCFFFIPAAVFS  194 (280)
T ss_dssp             TTC-----------------------------------------------CCHHHHHHHHHHHHHHHHHHHTHHHHHHHH
T ss_pred             HHHHH----------------------------------H-------hcCChhHHHHHHHHHHHHHHHHHHHhHHHHHHH
Confidence            00000                                  0       000111112233445566777888899999999


Q ss_pred             hhc-CCCccchhhheeeeeeccccCCcccCCCcccccccccchhhHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q psy17959        693 KLE-NWTFLDGTFFCFTSLGTIGFGELIPGESYDRTLRGNKNISVLVSSSYILVGMAVISMCFNLIQEEIIF  763 (790)
Q Consensus       693 ~~e-~~s~~da~Y~~~vt~tTVGyGD~~p~t~~gr~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~i~~~~~~  763 (790)
                      ..| +|+|+||+|||++|+|||||||++|.++.||.+   ....+++++++|++|++++++.++.+++.+..
T Consensus       195 ~~E~~~s~~da~y~~~iTltTvGyGD~~p~t~~~~~~---~~l~r~~~~~~il~Gl~~~~~~~~~i~~~~~~  263 (280)
T 3ukm_A          195 VLEDDWNFLESFYFCFISLSTIGLGDYVPGEGYNQKF---RELYKIGITCYLLLGLIAMLVVLETFCELHEL  263 (280)
T ss_dssp             HHSSSCCHHHHHHHHHHHHTTCCCCSCCSSCSSSCTT---HHHHHHHHHHHHHHHHHHHHHHHHHHHTSHHH
T ss_pred             HHhcCCchhhhhhheeeeeecccCCCCCCCCCccccc---chhHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            999 999999999999999999999999999988532   23456999999999999999999999987664

>2k1e_A Water soluble analogue of potassium channel, KCSA; homotetramer, ION transport, ionic channel, membrane, transmembrane, transport; NMR {Escherichia coli} PDB: 2kb1_A

Probab=99.67  E-value=5.2e-17  Score=145.79  Aligned_cols=89  Identities=12%  Similarity=0.155  Sum_probs=80.0

Q ss_pred             HHHHHHHHHHHHHHHHHHHhhhhhcCC-------CccchhhheeeeeeccccCCcccCCCcccccccccchhhHHHHHHH
Q psy17959        671 VPIAVSFLIIISFILLGSLIFNKLENW-------TFLDGTFFCFTSLGTIGFGELIPGESYDRTLRGNKNISVLVSSSYI  743 (790)
Q Consensus       671 ~~~~~~~~~~~~~~~~g~~~~~~~e~~-------s~~da~Y~~~vt~tTVGyGD~~p~t~~gr~~~~~~~~~~~~~~~~~  743 (790)
                      +.+..+++++++++++++.+|+..|+|       +|.||+||+++|+|||||||++|.++.||          +++++++
T Consensus         6 r~~l~~~~~~~~~~~~~a~~~~~~E~~~~~~~~~~~~~a~y~~~~T~tTvGyGDi~P~t~~gr----------~~~~~~~   75 (103)
T 2k1e_A            6 REAQKAEEELQKVLEEASKKAVEAERGAPGAALISYPDAIWWSVETATTVGYGDRYPVTEEGR----------KVAEQVM   75 (103)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHTTSTTCCCCCGGGTTTTTTGGGGCCSCCSSCCCSSSCT----------HHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHhhhhhccCCCCcccccHHHHHHHHHHHHhcccCCCCCCCChhHH----------HHHHHHH
Confidence            345566777888889999999999987       99999999999999999999999999999          8999999


Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHH
Q psy17959        744 LVGMAVISMCFNLIQEEIIFMIKKFT  769 (790)
Q Consensus       744 ~~g~~~~~~~~~~i~~~~~~~~~~~~  769 (790)
                      ++|++++++.++.++..+.++.++..
T Consensus        76 l~G~~~~~~~~~~i~~~~~~~~~~~~  101 (103)
T 2k1e_A           76 KAGIEVFALVTAALATDFVRREEERR  101 (103)
T ss_dssp             HHHHHHHHHTHHHHHTTGGGHHHHTT
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHhc
Confidence            99999999999999998888666543

>3ldc_A Calcium-gated potassium channel MTHK; transmembrane, ION channel, open conformation, IO transport; 1.45A {Methanothermobacter thermautotrophicusorganism_taxid} PDB: 3lde_A 4hyo_A 4hz3_D 3r65_A 3ous_A 3ldd_A

Probab=99.66  E-value=4.8e-17  Score=139.61  Aligned_cols=78  Identities=17%  Similarity=0.454  Sum_probs=72.2

Q ss_pred             HHHHHHHHHHHHHHHHhhhhhcCCCccchhhheeeeeeccccCCcccCCCcccccccccchhhHHHHHHHHHHHHHHHHH
Q psy17959        674 AVSFLIIISFILLGSLIFNKLENWTFLDGTFFCFTSLGTIGFGELIPGESYDRTLRGNKNISVLVSSSYILVGMAVISMC  753 (790)
Q Consensus       674 ~~~~~~~~~~~~~g~~~~~~~e~~s~~da~Y~~~vt~tTVGyGD~~p~t~~gr~~~~~~~~~~~~~~~~~~~g~~~~~~~  753 (790)
                      ...++++++++++|+++|+..|+|++.||+||+++|+|||||||++|.|+.||          ++++++++.|++++++.
T Consensus         4 ~~~~~l~~~~~~~g~~~~~~~e~~~~~~a~yf~~~T~tTvGyGdi~P~t~~~r----------~~~~~~~~~G~~~~~~~   73 (82)
T 3ldc_A            4 TRILLLVLAVIIYGTAGFHFIEGESWTVSLYWTFVTIATVGYGDYSPHTPLGM----------YFTCTLIVLGIGTFAVA   73 (82)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHTTCCCCSSCCCSHHHH----------HHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHHhcccCCCCCCCCCccHH----------HHHHHHHHHHHHHHHHH
Confidence            44566677788899999999999999999999999999999999999999999          89999999999999999


Q ss_pred             HHHHHHHH
Q psy17959        754 FNLIQEEI  761 (790)
Q Consensus       754 ~~~i~~~~  761 (790)
                      ++.+++.+
T Consensus        74 ~~~i~~~l   81 (82)
T 3ldc_A           74 VERLLEFL   81 (82)
T ss_dssp             HHHHHHHH
T ss_pred             HHHHHHHH
Confidence            99998765

>3ouf_A Potassium channel protein; ION channel, membrane, membrane protein; 1.55A {Bacillus cereus} PDB: 3t4z_A 3tcu_A 3t1c_A 3tet_A 3t4d_A 3t2m_A 3e86_A 3e83_A 3e89_A 3e8b_A 3e8f_A 3e8g_A 3e8h_A 3k0d_A 3k0g_A 3k06_A 3k08_A 3k04_A 3k03_A

Probab=99.63  E-value=2e-16  Score=140.18  Aligned_cols=82  Identities=18%  Similarity=0.528  Sum_probs=75.3

Q ss_pred             HHHHHHHHHHHHHHHHHHhhhhhcCCCccchhhheeeeeeccccCCcccCCCcccccccccchhhHHHHHHHHHHHHHHH
Q psy17959        672 PIAVSFLIIISFILLGSLIFNKLENWTFLDGTFFCFTSLGTIGFGELIPGESYDRTLRGNKNISVLVSSSYILVGMAVIS  751 (790)
Q Consensus       672 ~~~~~~~~~~~~~~~g~~~~~~~e~~s~~da~Y~~~vt~tTVGyGD~~p~t~~gr~~~~~~~~~~~~~~~~~~~g~~~~~  751 (790)
                      .+...++++++++++|+++|+..|+|++.||+||+++|+|||||||++|.++.||          +++++++++|+++++
T Consensus         6 ~~~~~~~~~~~~~~~g~~~~~~~e~~~~~~a~yf~~~T~tTvGyGdi~P~t~~gr----------~~~~~~~~~G~~~~~   75 (97)
T 3ouf_A            6 EFQVLFVLTILTLISGTIFYSTVEGLRPIDALYFSVVTLTTVGYGDFSPQTDFGK----------IFTILYIFIGIGLVF   75 (97)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHSCCCHHHHHHHHHHHHTTCCCCSSCCCSHHHH----------HHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHhcCCCHHHHHHHHHHHHHccCCCCCCCCCccHH----------HHHHHHHHHHHHHHH
Confidence            4556677777888899999999999999999999999999999999999999999          899999999999999


Q ss_pred             HHHHHHHHHHHH
Q psy17959        752 MCFNLIQEEIIF  763 (790)
Q Consensus       752 ~~~~~i~~~~~~  763 (790)
                      +.++.+++.+..
T Consensus        76 ~~i~~i~~~~~~   87 (97)
T 3ouf_A           76 GFIHKLAVNVQL   87 (97)
T ss_dssp             HHHHHHHHHTHH
T ss_pred             HHHHHHHHHHhH
Confidence            999999987764

>3eff_K Voltage-gated potassium channel; FULL length KCSA, bulge helix, cell membrane, ION transport, ionic channel, membrane, transmembrane; 3.80A {Streptomyces lividans}

Probab=99.62  E-value=2.1e-16  Score=149.96  Aligned_cols=88  Identities=16%  Similarity=0.311  Sum_probs=78.7

Q ss_pred             HHHHHHHHHHHHHHHHHHHHhhhhhcC-------CCccchhhheeeeeeccccCCcccCCCcccccccccchhhHHHHHH
Q psy17959        670 RVPIAVSFLIIISFILLGSLIFNKLEN-------WTFLDGTFFCFTSLGTIGFGELIPGESYDRTLRGNKNISVLVSSSY  742 (790)
Q Consensus       670 ~~~~~~~~~~~~~~~~~g~~~~~~~e~-------~s~~da~Y~~~vt~tTVGyGD~~p~t~~gr~~~~~~~~~~~~~~~~  742 (790)
                      .+.+..+++++++++++++.+++..|+       |+|+||+||+++|+|||||||++|.|+.||          ++++++
T Consensus         5 ~r~~~~~~~~~~~~~~~~a~~~~~~e~~~~~~~~~~~~~a~yf~~~T~tTvGyGd~~P~t~~~r----------~~~~~~   74 (139)
T 3eff_K            5 WRAAGAATVLLVIVLLAGSYLAVLAERGAPGAQLITYPRALWWSVETATTVGYGDLYPVTLWGR----------LVAVVV   74 (139)
T ss_dssp             HHTHHHHHHHHHHHHHHHHHHHHHTTSSCTTCCCCCHHHHHHHHHHHHTTCCCSSSCCCSSHHH----------HHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHhcCCCCcccCCHHHHHHHHheeeecccCCCCcCCCcCHH----------HHHHHH
Confidence            345667777888889999999999998       999999999999999999999999999999          899999


Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHH
Q psy17959        743 ILVGMAVISMCFNLIQEEIIFMIKK  767 (790)
Q Consensus       743 ~~~g~~~~~~~~~~i~~~~~~~~~~  767 (790)
                      +++|++++++.++.++..+.+..++
T Consensus        75 ~~~G~~~~~~~~~~i~~~~~~~~~~   99 (139)
T 3eff_K           75 MVAGITSFGLVTAALATWFVGREQE   99 (139)
T ss_dssp             HHHHHHHHHHHHHHHTTTTTHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            9999999999999998776654443

>2q67_A Potassium channel protein; inverted teepee, helix bundle, tetramer, central cavity, ION metal transport, membrane protein; 2.30A {Bacillus cereus} PDB: 2q68_A 2q6a_A 2q69_A 2ahy_A 2ahz_A

Probab=99.61  E-value=2.8e-16  Score=143.52  Aligned_cols=80  Identities=19%  Similarity=0.497  Sum_probs=72.7

Q ss_pred             HHHHHHHHHHHHHHHHHhhhhhcCCCccchhhheeeeeeccccCCcccCCCcccccccccchhhHHHHHHHHHHHHHHHH
Q psy17959        673 IAVSFLIIISFILLGSLIFNKLENWTFLDGTFFCFTSLGTIGFGELIPGESYDRTLRGNKNISVLVSSSYILVGMAVISM  752 (790)
Q Consensus       673 ~~~~~~~~~~~~~~g~~~~~~~e~~s~~da~Y~~~vt~tTVGyGD~~p~t~~gr~~~~~~~~~~~~~~~~~~~g~~~~~~  752 (790)
                      +...++++++++++|+++|+..|+|++.||+||+++|+|||||||++|.|+.||          +++++++++|++++++
T Consensus        24 ~~~~~~~~~~~~~~g~~~~~~~e~~~~~~a~y~~~~T~tTvGyGdi~P~t~~gr----------~~~~~~~~~G~~~~~~   93 (114)
T 2q67_A           24 FQVLFVLTILTLISGTIFYSTVEGLRPIDALYFSVVTLTTVGAGNFSPQTDFGK----------IFTILYIFIGIGLVFG   93 (114)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHSCCCHHHHHHHHHHHHTSCCCSSCCCCSHHHH----------HHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHhcCCCHHHHHHHHHHHhcceeCCCCccCCHhHH----------HHHHHHHHHHHHHHHH
Confidence            345566677778889999999999999999999999999999999999999999          8999999999999999


Q ss_pred             HHHHHHHHHH
Q psy17959        753 CFNLIQEEII  762 (790)
Q Consensus       753 ~~~~i~~~~~  762 (790)
                      .++.+++.+.
T Consensus        94 ~~~~l~~~~~  103 (114)
T 2q67_A           94 FIHKLAVNVQ  103 (114)
T ss_dssp             HHHHHHHHHC
T ss_pred             HHHHHHHHHH
Confidence            9999997763

>2ih3_C Voltage-gated potassium channel; ION channel D-amino acid semi-synthetic, membrane protein; HET: 1EM; 1.72A {Streptomyces lividans} PDB: 2ih1_C* 1r3j_C* 1k4d_C* 1r3i_C* 1k4c_C* 1r3k_C* 1r3l_C* 2bob_C* 2boc_C* 2hvj_C* 2hvk_C* 2itc_C 2itd_C 3gb7_C* 3iga_C* 1jvm_A 1s5h_C* 3ifx_A* 1j95_A 2jk5_C* ...

Probab=99.57  E-value=2e-15  Score=139.70  Aligned_cols=84  Identities=15%  Similarity=0.316  Sum_probs=75.6

Q ss_pred             HHHHHHHHHHHHHHHHhhhhhcC-------CCccchhhheeeeeeccccCCcccCCCcccccccccchhhHHHHHHHHHH
Q psy17959        674 AVSFLIIISFILLGSLIFNKLEN-------WTFLDGTFFCFTSLGTIGFGELIPGESYDRTLRGNKNISVLVSSSYILVG  746 (790)
Q Consensus       674 ~~~~~~~~~~~~~g~~~~~~~e~-------~s~~da~Y~~~vt~tTVGyGD~~p~t~~gr~~~~~~~~~~~~~~~~~~~g  746 (790)
                      ..++..+++++++++.+++..|+       |++.||+||+++|+|||||||++|.|+.||          +++++++++|
T Consensus        30 ~~~~~~~~~~~~~~a~~~~~~E~~~~~~~~~~~~~a~y~~~~T~tTvGyGDi~P~t~~gr----------~~~~~~~~~G   99 (122)
T 2ih3_C           30 GAATVLLVIVLLAGSYLAVLAERGAPGAQLITYPRALWWACETATTVAYGDLYPVTLWGR----------LVAVVVMVAG   99 (122)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHTTSTTCCCCSHHHHHHHHHHHHTTCCCSSSCCCSHHHH----------HHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHhhheeeecCCCCccCccccchhheeeeeeeeecCCCCCCCccHH----------HHHHHHHHHH
Confidence            34455666777889999999997       999999999999999999999999999999          8999999999


Q ss_pred             HHHHHHHHHHHHHHHHHHHHH
Q psy17959        747 MAVISMCFNLIQEEIIFMIKK  767 (790)
Q Consensus       747 ~~~~~~~~~~i~~~~~~~~~~  767 (790)
                      ++++++.++.+++.+.+..++
T Consensus       100 i~~~~~~~~~i~~~~~~~~~~  120 (122)
T 2ih3_C          100 ITSFGLVTAALATWFVGREQE  120 (122)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHh
Confidence            999999999999999886654

>3ldc_A Calcium-gated potassium channel MTHK; transmembrane, ION channel, open conformation, IO transport; 1.45A {Methanothermobacter thermautotrophicusorganism_taxid} PDB: 3lde_A 4hyo_A 4hz3_D 3r65_A 3ous_A 3ldd_A

Probab=99.57  E-value=9.2e-16  Score=131.57  Aligned_cols=79  Identities=25%  Similarity=0.436  Sum_probs=70.7

Q ss_pred             hhHHHHHHHHHHHHHhHHhhcccCCCCccceeeeeeecccccccccccCCCCcchhhhhhhhhhhHHHHHHHHHHHHHHH
Q psy17959        102 IWLCVFLVISYIIGGAFLFSHWEPWGFPDSAYFCFITLTTIGFGDFVPAQKSTDVQTAEETAELRIALCSLYLLFGIALL  181 (790)
Q Consensus       102 ~~~~~~~~~~~i~~ga~~~~~~e~wsf~da~Yf~~iTltTIGfGDi~P~~~~~~~~~~~~~~~~~~~~~~~~~l~Gl~~~  181 (790)
                      ....+.+++.+++.|+++|+..|+|+|.||+||+++|+|||||||++|.++.            +|.++.+++++|+.++
T Consensus         3 ~~~~~~l~~~~~~~g~~~~~~~e~~~~~~a~yf~~~T~tTvGyGdi~P~t~~------------~r~~~~~~~~~G~~~~   70 (82)
T 3ldc_A            3 ATRILLLVLAVIIYGTAGFHFIEGESWTVSLYWTFVTIATVGYGDYSPHTPL------------GMYFTCTLIVLGIGTF   70 (82)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHTTCCCCSSCCCSHH------------HHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHHhcccCCCCCCCCCcc------------HHHHHHHHHHHHHHHH
Confidence            3455666677889999999999999999999999999999999999998764            8999999999999999


Q ss_pred             HHHHHHHHHHH
Q psy17959        182 AMSFNLVQEEV  192 (790)
Q Consensus       182 ~~~i~~i~~~~  192 (790)
                      +++++.+.+.+
T Consensus        71 ~~~~~~i~~~l   81 (82)
T 3ldc_A           71 AVAVERLLEFL   81 (82)
T ss_dssp             HHHHHHHHHHH
T ss_pred             HHHHHHHHHHH
Confidence            99999888754

>3vou_A ION transport 2 domain protein, voltage-gated SOD channel; 4-helical bundle, ION channel, membrane, transport protein; 3.20A {Bacillus weihenstephanensis}

Probab=99.56  E-value=3.1e-15  Score=143.40  Aligned_cols=77  Identities=19%  Similarity=0.468  Sum_probs=71.0

Q ss_pred             HHHHHHHHHHHHHHHHHhhhhhcCCCccchhhheeeeeeccccCCcccCCCcccccccccchhhHHHHHHHHHHHHHHHH
Q psy17959        673 IAVSFLIIISFILLGSLIFNKLENWTFLDGTFFCFTSLGTIGFGELIPGESYDRTLRGNKNISVLVSSSYILVGMAVISM  752 (790)
Q Consensus       673 ~~~~~~~~~~~~~~g~~~~~~~e~~s~~da~Y~~~vt~tTVGyGD~~p~t~~gr~~~~~~~~~~~~~~~~~~~g~~~~~~  752 (790)
                      +...++++++++++|+++|+..|+|+|.||+|||++|+|||||||++|.|+.||          +++++++++|++++++
T Consensus        27 ~~~~~~~~~~~~~~g~~~~~~~e~~~~~~a~y~~~~t~tTvGyGd~~p~t~~~r----------~~~~~~~~~g~~~~~~   96 (148)
T 3vou_A           27 FQVLFVLTFLTLTSGTIFYSTVEGLRPLDALYFSVVTLTTVGDGNFSPQTDFGK----------VFTILYIFIGIGLVFG   96 (148)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHTSCCCHHHHHHHHHHHHTTCCCSSCCCCSHHHH----------HHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHhcCCCHHHHHHHHHHHHHccCCCCCCCCCccHH----------HHHHHHHHHHHHHHHH
Confidence            455666777788899999999999999999999999999999999999999999          8999999999999999


Q ss_pred             HHHHHHH
Q psy17959        753 CFNLIQE  759 (790)
Q Consensus       753 ~~~~i~~  759 (790)
                      .++.++.
T Consensus        97 ~~~~~~~  103 (148)
T 3vou_A           97 FIHKLAV  103 (148)
T ss_dssp             HHHHHHC
T ss_pred             HHHHHHH
Confidence            9999875

>3ouf_A Potassium channel protein; ION channel, membrane, membrane protein; 1.55A {Bacillus cereus} PDB: 3t4z_A 3tcu_A 3t1c_A 3tet_A 3t4d_A 3t2m_A 3e86_A 3e83_A 3e89_A 3e8b_A 3e8f_A 3e8g_A 3e8h_A 3k0d_A 3k0g_A 3k06_A 3k08_A 3k04_A 3k03_A

Probab=99.56  E-value=1.8e-15  Score=133.98  Aligned_cols=82  Identities=29%  Similarity=0.455  Sum_probs=73.3

Q ss_pred             hhhhHHHHHHHHHHHHHhHHhhcccCCCCccceeeeeeecccccccccccCCCCcchhhhhhhhhhhHHHHHHHHHHHHH
Q psy17959        100 VPIWLCVFLVISYIIGGAFLFSHWEPWGFPDSAYFCFITLTTIGFGDFVPAQKSTDVQTAEETAELRIALCSLYLLFGIA  179 (790)
Q Consensus       100 ~~~~~~~~~~~~~i~~ga~~~~~~e~wsf~da~Yf~~iTltTIGfGDi~P~~~~~~~~~~~~~~~~~~~~~~~~~l~Gl~  179 (790)
                      .++...+++++++++.|+++|+..|+|+|.||+||+++|+|||||||++|.+..            +|+++.+++++|++
T Consensus         5 ~~~~~~~~~~~~~~~~g~~~~~~~e~~~~~~a~yf~~~T~tTvGyGdi~P~t~~------------gr~~~~~~~~~G~~   72 (97)
T 3ouf_A            5 KEFQVLFVLTILTLISGTIFYSTVEGLRPIDALYFSVVTLTTVGYGDFSPQTDF------------GKIFTILYIFIGIG   72 (97)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHSCCCHHHHHHHHHHHHTTCCCCSSCCCSHH------------HHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHhcCCCHHHHHHHHHHHHHccCCCCCCCCCcc------------HHHHHHHHHHHHHH
Confidence            455566677778889999999999999999999999999999999999998764            89999999999999


Q ss_pred             HHHHHHHHHHHHHH
Q psy17959        180 LLAMSFNLVQEEVI  193 (790)
Q Consensus       180 ~~~~~i~~i~~~~~  193 (790)
                      +++++++.+...+.
T Consensus        73 ~~~~~i~~i~~~~~   86 (97)
T 3ouf_A           73 LVFGFIHKLAVNVQ   86 (97)
T ss_dssp             HHHHHHHHHHHHTH
T ss_pred             HHHHHHHHHHHHHh
Confidence            99999998887665

>2a9h_A Voltage-gated potassium channel; potassium channel, KCSA, structure, membrane protein, metal transport; HET: PCA; NMR {Streptomyces lividans} SCOP: f.14.1.1

Probab=99.55  E-value=1.4e-15  Score=146.34  Aligned_cols=83  Identities=17%  Similarity=0.358  Sum_probs=74.2

Q ss_pred             HHHHHHHHHHHHHHHHhhhhhcCC-------CccchhhheeeeeeccccCCcccCCCcccccccccchhhHHHHHHHHHH
Q psy17959        674 AVSFLIIISFILLGSLIFNKLENW-------TFLDGTFFCFTSLGTIGFGELIPGESYDRTLRGNKNISVLVSSSYILVG  746 (790)
Q Consensus       674 ~~~~~~~~~~~~~g~~~~~~~e~~-------s~~da~Y~~~vt~tTVGyGD~~p~t~~gr~~~~~~~~~~~~~~~~~~~g  746 (790)
                      ...++++++++++++++|+..|+|       ++.||+||+++|+|||||||++|.|+.||          +++++++++|
T Consensus        53 ~~~~~~~~~~i~~~a~~~~~~E~~~~~~~~~s~~~a~y~s~vTltTVGYGDi~P~t~~gr----------~~~~~~~l~G  122 (155)
T 2a9h_A           53 GAATVLLVIVLLAGSYLAVLAERGAPGAALISYPDALWWSVETATTVGYGDLYPVTLWGR----------CVAVVVMVAG  122 (155)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHTTSSCSSTTSHHHHHHHHHHHHTTCCCSSSCCCSHHHH----------HHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHhccCCCCccCcccceeheeeeeeecccCCCCCCCChhHH----------HHHHHHHHHH
Confidence            344555667778899999999987       89999999999999999999999999999          8999999999


Q ss_pred             HHHHHHHHHHHHHHHHHHHH
Q psy17959        747 MAVISMCFNLIQEEIIFMIK  766 (790)
Q Consensus       747 ~~~~~~~~~~i~~~~~~~~~  766 (790)
                      ++++++.++.++..+.++.+
T Consensus       123 v~~~a~~~~~i~~~~~~~~~  142 (155)
T 2a9h_A          123 ITSYGLVFAAVATWFVGREQ  142 (155)
T ss_dssp             HHHHHHHHHHHHHHHHSCCC
T ss_pred             HHHHHHHHHHHHHHHHHHHH
Confidence            99999999999998886443

>3eff_K Voltage-gated potassium channel; FULL length KCSA, bulge helix, cell membrane, ION transport, ionic channel, membrane, transmembrane; 3.80A {Streptomyces lividans}

Probab=99.55  E-value=2.5e-15  Score=142.52  Aligned_cols=86  Identities=16%  Similarity=0.293  Sum_probs=75.4

Q ss_pred             hhHHHHHHHHHHHHHhHHhhcccC-------CCCccceeeeeeecccccccccccCCCCcchhhhhhhhhhhHHHHHHHH
Q psy17959        102 IWLCVFLVISYIIGGAFLFSHWEP-------WGFPDSAYFCFITLTTIGFGDFVPAQKSTDVQTAEETAELRIALCSLYL  174 (790)
Q Consensus       102 ~~~~~~~~~~~i~~ga~~~~~~e~-------wsf~da~Yf~~iTltTIGfGDi~P~~~~~~~~~~~~~~~~~~~~~~~~~  174 (790)
                      +...+++++++++++++++...|+       |+|.||+||+++|+|||||||++|.+..            +++++++++
T Consensus         8 ~~~~~~~~~~~~~~~a~~~~~~e~~~~~~~~~~~~~a~yf~~~T~tTvGyGd~~P~t~~------------~r~~~~~~~   75 (139)
T 3eff_K            8 AGAATVLLVIVLLAGSYLAVLAERGAPGAQLITYPRALWWSVETATTVGYGDLYPVTLW------------GRLVAVVVM   75 (139)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHTTSSCTTCCCCCHHHHHHHHHHHHTTCCCSSSCCCSSH------------HHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHhcCCCCcccCCHHHHHHHHheeeecccCCCCcCCCcC------------HHHHHHHHH
Confidence            344566677788899999999997       9999999999999999999999998765            899999999


Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHH
Q psy17959        175 LFGIALLAMSFNLVQEEVISNVKAI  199 (790)
Q Consensus       175 l~Gl~~~~~~i~~i~~~~~~~~~~~  199 (790)
                      ++|+++++++++.+.+.+.+..++.
T Consensus        76 ~~G~~~~~~~~~~i~~~~~~~~~~~  100 (139)
T 3eff_K           76 VAGITSFGLVTAALATWFVGREQER  100 (139)
T ss_dssp             HHHHHHHHHHHHHHTTTTTHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            9999999999999998877765543

>2q67_A Potassium channel protein; inverted teepee, helix bundle, tetramer, central cavity, ION metal transport, membrane protein; 2.30A {Bacillus cereus} PDB: 2q68_A 2q6a_A 2q69_A 2ahy_A 2ahz_A

Probab=99.53  E-value=2.7e-15  Score=136.98  Aligned_cols=80  Identities=29%  Similarity=0.440  Sum_probs=71.0

Q ss_pred             hhhHHHHHHHHHHHHHhHHhhcccCCCCccceeeeeeecccccccccccCCCCcchhhhhhhhhhhHHHHHHHHHHHHHH
Q psy17959        101 PIWLCVFLVISYIIGGAFLFSHWEPWGFPDSAYFCFITLTTIGFGDFVPAQKSTDVQTAEETAELRIALCSLYLLFGIAL  180 (790)
Q Consensus       101 ~~~~~~~~~~~~i~~ga~~~~~~e~wsf~da~Yf~~iTltTIGfGDi~P~~~~~~~~~~~~~~~~~~~~~~~~~l~Gl~~  180 (790)
                      ++...+++++++++.|+++|+..|+|+|.||+||+++|+|||||||++|.++.            +++++.+++++|+++
T Consensus        23 ~~~~~~~~~~~~~~~g~~~~~~~e~~~~~~a~y~~~~T~tTvGyGdi~P~t~~------------gr~~~~~~~~~G~~~   90 (114)
T 2q67_A           23 EFQVLFVLTILTLISGTIFYSTVEGLRPIDALYFSVVTLTTVGAGNFSPQTDF------------GKIFTILYIFIGIGL   90 (114)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHSCCCHHHHHHHHHHHHTSCCCSSCCCCSHH------------HHHHHHHHHHHHHHH
T ss_pred             hHHHHHHHHHHHHHHHHHHHHHhcCCCHHHHHHHHHHHhcceeCCCCccCCHh------------HHHHHHHHHHHHHHH
Confidence            34455666677888999999999999999999999999999999999998765            899999999999999


Q ss_pred             HHHHHHHHHHHH
Q psy17959        181 LAMSFNLVQEEV  192 (790)
Q Consensus       181 ~~~~i~~i~~~~  192 (790)
                      ++++++.+.+.+
T Consensus        91 ~~~~~~~l~~~~  102 (114)
T 2q67_A           91 VFGFIHKLAVNV  102 (114)
T ss_dssp             HHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHH
Confidence            999999888765

>2k1e_A Water soluble analogue of potassium channel, KCSA; homotetramer, ION transport, ionic channel, membrane, transmembrane, transport; NMR {Escherichia coli} PDB: 2kb1_A

Probab=99.53  E-value=2.7e-15  Score=134.59  Aligned_cols=85  Identities=15%  Similarity=0.194  Sum_probs=74.6

Q ss_pred             hhhHHHHHHHHHHHHHhHHhhcccCC-------CCccceeeeeeecccccccccccCCCCcchhhhhhhhhhhHHHHHHH
Q psy17959        101 PIWLCVFLVISYIIGGAFLFSHWEPW-------GFPDSAYFCFITLTTIGFGDFVPAQKSTDVQTAEETAELRIALCSLY  173 (790)
Q Consensus       101 ~~~~~~~~~~~~i~~ga~~~~~~e~w-------sf~da~Yf~~iTltTIGfGDi~P~~~~~~~~~~~~~~~~~~~~~~~~  173 (790)
                      ++...++++++++++++.+|+..|+|       +|.||+||+++|+|||||||++|.+..            +|++++++
T Consensus         7 ~~l~~~~~~~~~~~~~a~~~~~~E~~~~~~~~~~~~~a~y~~~~T~tTvGyGDi~P~t~~------------gr~~~~~~   74 (103)
T 2k1e_A            7 EAQKAEEELQKVLEEASKKAVEAERGAPGAALISYPDAIWWSVETATTVGYGDRYPVTEE------------GRKVAEQV   74 (103)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHTTSTTCCCCCGGGTTTTTTGGGGCCSCCSSCCCSSS------------CTHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHhhhhhccCCCCcccccHHHHHHHHHHHHhcccCCCCCCCChh------------HHHHHHHH
Confidence            44455666777888999999999987       899999999999999999999999876            88999999


Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHH
Q psy17959        174 LLFGIALLAMSFNLVQEEVISNVK  197 (790)
Q Consensus       174 ~l~Gl~~~~~~i~~i~~~~~~~~~  197 (790)
                      +++|+.+++++++.+.+.+.++.+
T Consensus        75 ~l~G~~~~~~~~~~i~~~~~~~~~   98 (103)
T 2k1e_A           75 MKAGIEVFALVTAALATDFVRREE   98 (103)
T ss_dssp             HHHHHHHHHHTHHHHHTTGGGHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHH
Confidence            999999999999999887776544

>3vou_A ION transport 2 domain protein, voltage-gated SOD channel; 4-helical bundle, ION channel, membrane, transport protein; 3.20A {Bacillus weihenstephanensis}

Probab=99.51  E-value=5.8e-15  Score=141.49  Aligned_cols=78  Identities=26%  Similarity=0.396  Sum_probs=69.7

Q ss_pred             hhhHHHHHHHHHHHHHhHHhhcccCCCCccceeeeeeecccccccccccCCCCcchhhhhhhhhhhHHHHHHHHHHHHHH
Q psy17959        101 PIWLCVFLVISYIIGGAFLFSHWEPWGFPDSAYFCFITLTTIGFGDFVPAQKSTDVQTAEETAELRIALCSLYLLFGIAL  180 (790)
Q Consensus       101 ~~~~~~~~~~~~i~~ga~~~~~~e~wsf~da~Yf~~iTltTIGfGDi~P~~~~~~~~~~~~~~~~~~~~~~~~~l~Gl~~  180 (790)
                      ++.+.+++++++++.|+++|...|+|+|.||+|||++|+|||||||++|.++.            +++++++++++|+++
T Consensus        26 ~~~~~~~~~~~~~~~g~~~~~~~e~~~~~~a~y~~~~t~tTvGyGd~~p~t~~------------~r~~~~~~~~~g~~~   93 (148)
T 3vou_A           26 EFQVLFVLTFLTLTSGTIFYSTVEGLRPLDALYFSVVTLTTVGDGNFSPQTDF------------GKVFTILYIFIGIGL   93 (148)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHTSCCCHHHHHHHHHHHHTTCCCSSCCCCSHH------------HHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHhcCCCHHHHHHHHHHHHHccCCCCCCCCCcc------------HHHHHHHHHHHHHHH
Confidence            44555666777889999999999999999999999999999999999998754            899999999999999


Q ss_pred             HHHHHHHHHH
Q psy17959        181 LAMSFNLVQE  190 (790)
Q Consensus       181 ~~~~i~~i~~  190 (790)
                      ++++++.+..
T Consensus        94 ~~~~~~~~~~  103 (148)
T 3vou_A           94 VFGFIHKLAV  103 (148)
T ss_dssp             HHHHHHHHHC
T ss_pred             HHHHHHHHHH
Confidence            9999988775

>4h33_A LMO2059 protein; bilayers, KVLM, lipidic cubic phase (LCP), pore module, ION membrane protein; HET: OLC; 3.10A {Listeria monocytogenes} PDB: 4h37_A

Probab=99.50  E-value=3.8e-15  Score=140.57  Aligned_cols=76  Identities=20%  Similarity=0.430  Sum_probs=63.4

Q ss_pred             HHHHHHHHHHHHHhhhhhc--CCCccchhhheeeeeeccccCCcccCCCcccccccccchhhHHHHHHHHHHHHHHHHHH
Q psy17959        677 FLIIISFILLGSLIFNKLE--NWTFLDGTFFCFTSLGTIGFGELIPGESYDRTLRGNKNISVLVSSSYILVGMAVISMCF  754 (790)
Q Consensus       677 ~~~~~~~~~~g~~~~~~~e--~~s~~da~Y~~~vt~tTVGyGD~~p~t~~gr~~~~~~~~~~~~~~~~~~~g~~~~~~~~  754 (790)
                      ++++++++++++..+++.|  .|+|+||+|||++|+|||||||++|.|+.||          +++++++++|++++++.+
T Consensus        20 l~~~~~~~~~~~~~~~~~e~~~~~~~~a~y~~~~T~tTvGyGDi~P~t~~gr----------~~~~~~~~~g~~~~~~~~   89 (137)
T 4h33_A           20 LMIFVLLVIIIPVPMVFIEPEINNYPDALWWAIVTATTVGYGDIVPVTPIGR----------ILASIMMLFGIAFIGMIT   89 (137)
T ss_dssp             HHHHHHHHHHTHHHHHHHCSSCCSHHHHHHHHHHHHTTCCCSSSCCCSHHHH----------HHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHcCCCCHHHHHHHHHHHHHcccCCCCCCCCHhHH----------HHHHHHHHHHHHHHHHHH
Confidence            3333444444555555555  5999999999999999999999999999999          899999999999999999


Q ss_pred             HHHHHHHH
Q psy17959        755 NLIQEEII  762 (790)
Q Consensus       755 ~~i~~~~~  762 (790)
                      +.++..+.
T Consensus        90 ~~i~~~~~   97 (137)
T 4h33_A           90 STITNFFR   97 (137)
T ss_dssp             HHHHTTTT
T ss_pred             HHHHHHHH
Confidence            99997765

>2ih3_C Voltage-gated potassium channel; ION channel D-amino acid semi-synthetic, membrane protein; HET: 1EM; 1.72A {Streptomyces lividans} PDB: 2ih1_C* 1r3j_C* 1k4d_C* 1r3i_C* 1k4c_C* 1r3k_C* 1r3l_C* 2bob_C* 2boc_C* 2hvj_C* 2hvk_C* 2itc_C 2itd_C 3gb7_C* 3iga_C* 1jvm_A 1s5h_C* 3ifx_A* 1j95_A 2jk5_C* ...

Probab=99.47  E-value=2.4e-14  Score=132.34  Aligned_cols=82  Identities=16%  Similarity=0.310  Sum_probs=71.6

Q ss_pred             HHHHHHHHHHHHHhHHhhcccC-------CCCccceeeeeeecccccccccccCCCCcchhhhhhhhhhhHHHHHHHHHH
Q psy17959        104 LCVFLVISYIIGGAFLFSHWEP-------WGFPDSAYFCFITLTTIGFGDFVPAQKSTDVQTAEETAELRIALCSLYLLF  176 (790)
Q Consensus       104 ~~~~~~~~~i~~ga~~~~~~e~-------wsf~da~Yf~~iTltTIGfGDi~P~~~~~~~~~~~~~~~~~~~~~~~~~l~  176 (790)
                      ..++.+++++++++.+++..|+       |+|.||+||+++|+|||||||++|.++.            +++++.+++++
T Consensus        31 ~~~~~~~~~~~~~a~~~~~~E~~~~~~~~~~~~~a~y~~~~T~tTvGyGDi~P~t~~------------gr~~~~~~~~~   98 (122)
T 2ih3_C           31 AATVLLVIVLLAGSYLAVLAERGAPGAQLITYPRALWWACETATTVAYGDLYPVTLW------------GRLVAVVVMVA   98 (122)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHTTSTTCCCCSHHHHHHHHHHHHTTCCCSSSCCCSHH------------HHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHhhheeeecCCCCccCccccchhheeeeeeeeecCCCCCCCcc------------HHHHHHHHHHH
Confidence            3444555677888898988886       9999999999999999999999998765            89999999999


Q ss_pred             HHHHHHHHHHHHHHHHHHHHH
Q psy17959        177 GIALLAMSFNLVQEEVISNVK  197 (790)
Q Consensus       177 Gl~~~~~~i~~i~~~~~~~~~  197 (790)
                      |+.+++++++.+.+.+.+..+
T Consensus        99 Gi~~~~~~~~~i~~~~~~~~~  119 (122)
T 2ih3_C           99 GITSFGLVTAALATWFVGREQ  119 (122)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHH
Confidence            999999999999998887654

>2a9h_A Voltage-gated potassium channel; potassium channel, KCSA, structure, membrane protein, metal transport; HET: PCA; NMR {Streptomyces lividans} SCOP: f.14.1.1

Probab=99.45  E-value=1.3e-14  Score=139.43  Aligned_cols=82  Identities=21%  Similarity=0.379  Sum_probs=71.9

Q ss_pred             hhHHHHHHHHHHHHHhHHhhcccCC-------CCccceeeeeeecccccccccccCCCCcchhhhhhhhhhhHHHHHHHH
Q psy17959        102 IWLCVFLVISYIIGGAFLFSHWEPW-------GFPDSAYFCFITLTTIGFGDFVPAQKSTDVQTAEETAELRIALCSLYL  174 (790)
Q Consensus       102 ~~~~~~~~~~~i~~ga~~~~~~e~w-------sf~da~Yf~~iTltTIGfGDi~P~~~~~~~~~~~~~~~~~~~~~~~~~  174 (790)
                      ....+++++++++++|++++..|+|       +|.||+||+++|+|||||||++|.+..            +++++++++
T Consensus        52 ~~~~~~~~~~~i~~~a~~~~~~E~~~~~~~~~s~~~a~y~s~vTltTVGYGDi~P~t~~------------gr~~~~~~~  119 (155)
T 2a9h_A           52 AGAATVLLVIVLLAGSYLAVLAERGAPGAALISYPDALWWSVETATTVGYGDLYPVTLW------------GRCVAVVVM  119 (155)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHTTSSCSSTTSHHHHHHHHHHHHTTCCCSSSCCCSHH------------HHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHhccCCCCccCcccceeheeeeeeecccCCCCCCCChh------------HHHHHHHHH
Confidence            3344555667788999999999987       899999999999999999999998765            899999999


Q ss_pred             HHHHHHHHHHHHHHHHHHHHH
Q psy17959        175 LFGIALLAMSFNLVQEEVISN  195 (790)
Q Consensus       175 l~Gl~~~~~~i~~i~~~~~~~  195 (790)
                      ++|+++++++++.+.+.+.+.
T Consensus       120 l~Gv~~~a~~~~~i~~~~~~~  140 (155)
T 2a9h_A          120 VAGITSYGLVFAAVATWFVGR  140 (155)
T ss_dssp             HHHHHHHHHHHHHHHHHHHSC
T ss_pred             HHHHHHHHHHHHHHHHHHHHH
Confidence            999999999999999887764

>4h33_A LMO2059 protein; bilayers, KVLM, lipidic cubic phase (LCP), pore module, ION membrane protein; HET: OLC; 3.10A {Listeria monocytogenes} PDB: 4h37_A

Probab=99.43  E-value=1.4e-14  Score=136.70  Aligned_cols=75  Identities=29%  Similarity=0.519  Sum_probs=61.3

Q ss_pred             HHHHHHHHHhHHhhcccCCCCccceeeeeeecccccccccccCCCCcchhhhhhhhhhhHHHHHHHHHHHHHHHHHHHHH
Q psy17959        108 LVISYIIGGAFLFSHWEPWGFPDSAYFCFITLTTIGFGDFVPAQKSTDVQTAEETAELRIALCSLYLLFGIALLAMSFNL  187 (790)
Q Consensus       108 ~~~~~i~~ga~~~~~~e~wsf~da~Yf~~iTltTIGfGDi~P~~~~~~~~~~~~~~~~~~~~~~~~~l~Gl~~~~~~i~~  187 (790)
                      +++++++.++..+...|.|+|.||+||+++|+|||||||++|.+..            +++++++++++|+++++++++.
T Consensus        24 ~~~~~~~~~~~~~~e~~~~~~~~a~y~~~~T~tTvGyGDi~P~t~~------------gr~~~~~~~~~g~~~~~~~~~~   91 (137)
T 4h33_A           24 VLLVIIIPVPMVFIEPEINNYPDALWWAIVTATTVGYGDIVPVTPI------------GRILASIMMLFGIAFIGMITST   91 (137)
T ss_dssp             HHHHHHTHHHHHHHCSSCCSHHHHHHHHHHHHTTCCCSSSCCCSHH------------HHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHcCCCCHHHHHHHHHHHHHcccCCCCCCCCHh------------HHHHHHHHHHHHHHHHHHHHHH
Confidence            3334444445555555679999999999999999999999998765            8999999999999999999998


Q ss_pred             HHHHHHH
Q psy17959        188 VQEEVIS  194 (790)
Q Consensus       188 i~~~~~~  194 (790)
                      +.+.+.+
T Consensus        92 i~~~~~~   98 (137)
T 4h33_A           92 ITNFFRC   98 (137)
T ss_dssp             HHTTTTT
T ss_pred             HHHHHHH
Confidence            8876543

>3pjs_K KCSA, voltage-gated potassium channel; ION channel, conducts K+ IONS, cell membrane, transport PROT; 3.80A {Streptomyces lividans} PDB: 1f6g_A

Probab=99.42  E-value=1.1e-15  Score=149.32  Aligned_cols=78  Identities=18%  Similarity=0.395  Sum_probs=69.6

Q ss_pred             HHHHHHHHHHHHHHHhhhhhcC-------CCccchhhheeeeeeccccCCcccCCCcccccccccchhhHHHHHHHHHHH
Q psy17959        675 VSFLIIISFILLGSLIFNKLEN-------WTFLDGTFFCFTSLGTIGFGELIPGESYDRTLRGNKNISVLVSSSYILVGM  747 (790)
Q Consensus       675 ~~~~~~~~~~~~g~~~~~~~e~-------~s~~da~Y~~~vt~tTVGyGD~~p~t~~gr~~~~~~~~~~~~~~~~~~~g~  747 (790)
                      ..++++++++++++++++..|+       |+|+||+|||++|+|||||||++|.|+.||          +++++++++|+
T Consensus        37 ~~~~~~~~~~~~~a~~~~~~e~~~~~~~~~~~~~a~yf~~~T~tTvGyGDi~P~t~~~r----------~~~~~~~l~G~  106 (166)
T 3pjs_K           37 AATVLLVIVLLAGSYLAVLAERGAPGAQLITYPRALWWSVETATTVGYGDLYPVTLWGR----------LVAVVVMVAGI  106 (166)
T ss_dssp             TTSSSSTTTTTTTSSSSSSTTSSSTTCCCCSTTTTTTTTHHHHSCCCCSSSCCCSSTTT----------TTTHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHhcCCCCcccCCHHHHHHHHHHHhccccCCCCCCCCHhHH----------HHHHHHHHHHH
Confidence            3444566777889999999998       999999999999999999999999999999          88999999999


Q ss_pred             HHHHHHHHHHHHHHH
Q psy17959        748 AVISMCFNLIQEEII  762 (790)
Q Consensus       748 ~~~~~~~~~i~~~~~  762 (790)
                      +++++.++.++..+.
T Consensus       107 ~~~~~~~~~i~~~~~  121 (166)
T 3pjs_K          107 TSFGLVTAALATWFV  121 (166)
T ss_dssp             HHHHHHHTTSSSSSS
T ss_pred             HHHHHHHHHHHHHHH
Confidence            999999999975544

>3pjs_K KCSA, voltage-gated potassium channel; ION channel, conducts K+ IONS, cell membrane, transport PROT; 3.80A {Streptomyces lividans} PDB: 1f6g_A

Probab=99.33  E-value=2.3e-14  Score=139.89  Aligned_cols=80  Identities=14%  Similarity=0.250  Sum_probs=69.6

Q ss_pred             HHHHHHHHhhhhhceeeecccc-------cCcccceeEEEEeecccccCCCccCCCcCCCCCCcccchhhhHHHHHHHHH
Q psy17959        514 LCLMIMVGYIYGGAVLFSKWED-------WNILDGSYFCFISLSTIGFGDIVPGDKITGKNNDIGVQTLELSFILCAMYL  586 (790)
Q Consensus       514 ~~l~~~~~~i~~ga~~f~~~e~-------w~~~da~Yf~~itltTIGfGD~~P~~~~~~~~~~~~~~~~~~~~~~~~~~i  586 (790)
                      ..++++++++++++.+|...|+       |+|.||+||+++|+|||||||++|.+..++              +++++++
T Consensus        37 ~~~~~~~~~~~~~a~~~~~~e~~~~~~~~~~~~~a~yf~~~T~tTvGyGDi~P~t~~~r--------------~~~~~~~  102 (166)
T 3pjs_K           37 AATVLLVIVLLAGSYLAVLAERGAPGAQLITYPRALWWSVETATTVGYGDLYPVTLWGR--------------LVAVVVM  102 (166)
T ss_dssp             TTSSSSTTTTTTTSSSSSSTTSSSTTCCCCSTTTTTTTTHHHHSCCCCSSSCCCSSTTT--------------TTTHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHhcCCCCcccCCHHHHHHHHHHHhccccCCCCCCCCHhHH--------------HHHHHHH
Confidence            3344556788889999999998       999999999999999999999999998887              8999999


Q ss_pred             HHHHHHHHHHHHHHHHHHHHH
Q psy17959        587 MLGMALIAMCFNLMQEEVVHK  607 (790)
Q Consensus       587 l~Gl~~~~~~~~~~~~~~~~~  607 (790)
                      ++|+++++++++.+.+.+.+.
T Consensus       103 l~G~~~~~~~~~~i~~~~~~~  123 (166)
T 3pjs_K          103 VAGITSFGLVTAALATWFVGQ  123 (166)
T ss_dssp             HHHHHHHHHHHTTSSSSSSSS
T ss_pred             HHHHHHHHHHHHHHHHHHHHH
Confidence            999999999998876665543

>1orq_C Potassium channel; voltage-dependent, KVAP, FAB complex, MEM protein; 3.20A {Aeropyrum pernix} SCOP: f.14.1.1 PDB: 2a0l_A

Probab=99.33  E-value=8.7e-13  Score=135.15  Aligned_cols=83  Identities=13%  Similarity=0.393  Sum_probs=74.6

Q ss_pred             HHHHHHHHHHHHHHHHHhhhhhcC-------CCccchhhheeeeeeccccCCcccCCCcccccccccchhhHHHHHHHHH
Q psy17959        673 IAVSFLIIISFILLGSLIFNKLEN-------WTFLDGTFFCFTSLGTIGFGELIPGESYDRTLRGNKNISVLVSSSYILV  745 (790)
Q Consensus       673 ~~~~~~~~~~~~~~g~~~~~~~e~-------~s~~da~Y~~~vt~tTVGyGD~~p~t~~gr~~~~~~~~~~~~~~~~~~~  745 (790)
                      +...+..+++++.+++.+++..|+       |++.||+||+++|+|||||||++|.|+.||          ++++++++.
T Consensus       133 l~~~~~~~~~~~~~~~~~~~~~e~~~~~~~~~~~~~s~y~~~~t~tTvGyGdi~P~t~~~~----------~~~~~~~~~  202 (223)
T 1orq_C          133 FYHLFGAVMLTVLYGAFAIYIVEYPDPNSSIKSVFDALWWAVVTATTVGYGDVVPATPIGK----------VIGIAVMLT  202 (223)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHTTSSSTTCSCCSHHHHHHHHHHHHTTCCCCSSCCCSHHHH----------HHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHhCCcCCCcCcchhHHHhHHhHHhccCCCCCCCCCHhHH----------HHHHHHHHH
Confidence            444555666777889999999998       999999999999999999999999999999          899999999


Q ss_pred             HHHHHHHHHHHHHHHHHHHH
Q psy17959        746 GMAVISMCFNLIQEEIIFMI  765 (790)
Q Consensus       746 g~~~~~~~~~~i~~~~~~~~  765 (790)
                      |++++++.++.+++.+.++.
T Consensus       203 G~~~~~~~i~~i~~~~~~~~  222 (223)
T 1orq_C          203 GISALTLLIGTVSNMFQKIL  222 (223)
T ss_dssp             HHHHHHHHHHHHHHHHHHHT
T ss_pred             HHHHHHHHHHHHHHHHHHhh
Confidence            99999999999999888754

>1orq_C Potassium channel; voltage-dependent, KVAP, FAB complex, MEM protein; 3.20A {Aeropyrum pernix} SCOP: f.14.1.1 PDB: 2a0l_A

Probab=99.25  E-value=2.4e-12  Score=131.88  Aligned_cols=79  Identities=25%  Similarity=0.299  Sum_probs=69.2

Q ss_pred             HHHHHHHHHHHHhHHhhcccC-------CCCccceeeeeeecccccccccccCCCCcchhhhhhhhhhhHHHHHHHHHHH
Q psy17959        105 CVFLVISYIIGGAFLFSHWEP-------WGFPDSAYFCFITLTTIGFGDFVPAQKSTDVQTAEETAELRIALCSLYLLFG  177 (790)
Q Consensus       105 ~~~~~~~~i~~ga~~~~~~e~-------wsf~da~Yf~~iTltTIGfGDi~P~~~~~~~~~~~~~~~~~~~~~~~~~l~G  177 (790)
                      .+.++++++.++|.+++..|+       |+|.||+||+++|+|||||||++|.++.            +++++.+++++|
T Consensus       136 ~~~~~~~~~~~~~~~~~~~e~~~~~~~~~~~~~s~y~~~~t~tTvGyGdi~P~t~~------------~~~~~~~~~~~G  203 (223)
T 1orq_C          136 LFGAVMLTVLYGAFAIYIVEYPDPNSSIKSVFDALWWAVVTATTVGYGDVVPATPI------------GKVIGIAVMLTG  203 (223)
T ss_dssp             HHHHHHHHHHHHHHHHHHTTSSSTTCSCCSHHHHHHHHHHHHTTCCCCSSCCCSHH------------HHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHhCCcCCCcCcchhHHHhHHhHHhccCCCCCCCCCHh------------HHHHHHHHHHHH
Confidence            444455667778888888887       9999999999999999999999998654            899999999999


Q ss_pred             HHHHHHHHHHHHHHHHHH
Q psy17959        178 IALLAMSFNLVQEEVISN  195 (790)
Q Consensus       178 l~~~~~~i~~i~~~~~~~  195 (790)
                      +++++++++.+.+.+.++
T Consensus       204 ~~~~~~~i~~i~~~~~~~  221 (223)
T 1orq_C          204 ISALTLLIGTVSNMFQKI  221 (223)
T ss_dssp             HHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHh
Confidence            999999999999887764

>1lnq_A MTHK channels, potassium channel related protein; rossman fold, helix bundle, membrane protein; 3.30A {Methanothermobacter thermautotrophicusorganism_taxid} SCOP: c.2.1.9 d.286.1.1 f.14.1.1 PDB: 3rbz_A

Probab=99.23  E-value=8.4e-14  Score=151.71  Aligned_cols=80  Identities=18%  Similarity=0.440  Sum_probs=70.4

Q ss_pred             HHHHHHHHHHHHHHHhhhhhcCCCccchhhheeeeeeccccCCcccCCCcccccccccchhhHHHHHHHHHHHHHHHHHH
Q psy17959        675 VSFLIIISFILLGSLIFNKLENWTFLDGTFFCFTSLGTIGFGELIPGESYDRTLRGNKNISVLVSSSYILVGMAVISMCF  754 (790)
Q Consensus       675 ~~~~~~~~~~~~g~~~~~~~e~~s~~da~Y~~~vt~tTVGyGD~~p~t~~gr~~~~~~~~~~~~~~~~~~~g~~~~~~~~  754 (790)
                      ..++++++++++|+++|+..|+|+|+||+||+++|+|||||||++|.|+.||          +|+++++++|++++++.+
T Consensus        22 ~~~~~~~~~~~~~~~~~~~~e~~~~~~a~y~~~~t~tTvGyGd~~p~t~~~r----------~~~~~~~~~g~~~~~~~~   91 (336)
T 1lnq_A           22 RILLLVLAVIIYGTAGFHFIEGESWTVSLYWTFVTIATVGYGDYSPSTPLGM----------YFTVTLIVLGIGTFAVAV   91 (336)
T ss_dssp             SSTTTTTTSHHHHTTTTTTSSSCCSSTTHHHHHHHHTTCCCSSCCCCCSSHH----------HHHTHHHHTTSTTTTTHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHhCCCHHHHHHHHHHHhhcccCCCCCCCCcCHH----------HHHHHHHHHHHHHHHHHH
Confidence            3444556677889999999999999999999999999999999999999999          889999999999999999


Q ss_pred             HHHHHHHHHH
Q psy17959        755 NLIQEEIIFM  764 (790)
Q Consensus       755 ~~i~~~~~~~  764 (790)
                      +.+++.+..+
T Consensus        92 ~~~~~~~~~~  101 (336)
T 1lnq_A           92 ERLLEFLINR  101 (336)
T ss_dssp             HHHTTTC---
T ss_pred             HHHHHHHHHH
Confidence            9998877763

>4gx0_A TRKA domain protein; membrane protein, ION channel, ADP binding, NAD binding, MEM transport protein; HET: MAL GLC; 2.60A {Geobacter sulfurreducens} PDB: 4gx1_A* 4gx2_A* 4gx5_A 4gvl_A*

Probab=99.17  E-value=1.8e-11  Score=142.75  Aligned_cols=86  Identities=17%  Similarity=0.360  Sum_probs=71.3

Q ss_pred             hhHHHHHHHHHHHHHHHHHHHHhhhh----hcC--CCccchhhheeeeeeccccCCcccCCCcccccccccchhhHHHHH
Q psy17959        668 RFRVPIAVSFLIIISFILLGSLIFNK----LEN--WTFLDGTFFCFTSLGTIGFGELIPGESYDRTLRGNKNISVLVSSS  741 (790)
Q Consensus       668 ~~~~~~~~~~~~~~~~~~~g~~~~~~----~e~--~s~~da~Y~~~vt~tTVGyGD~~p~t~~gr~~~~~~~~~~~~~~~  741 (790)
                      +.++.+...++++++++++++++|+.    .|+  |+|+||+||+++|+|||||||++|.|+.||          +|+++
T Consensus        15 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~e~~~~~~~~~~y~~~~t~tTvGygd~~p~~~~~~----------~~~~~   84 (565)
T 4gx0_A           15 QNLKVLLLYCAFLLVMLLAYASIFRYLMWHLEGRAYSFMAGIYWTITVMTTLGFGDITFESDAGY----------LFASI   84 (565)
T ss_dssp             CCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHTTCCCCSSCCCSHHHH----------HHHHH
T ss_pred             hhHHHHHHHHHHHHHHHHHHHHHHHHHHHhhcCCCCchhhhhheeeeeeeeecCCCcCCCCccHH----------HHHHH
Confidence            33445566666677777778887776    566  999999999999999999999999999999          89999


Q ss_pred             HHHHHHHHHHHHHHH-HHHHHHH
Q psy17959        742 YILVGMAVISMCFNL-IQEEIIF  763 (790)
Q Consensus       742 ~~~~g~~~~~~~~~~-i~~~~~~  763 (790)
                      ++++|++++++.++. +.+.+..
T Consensus        85 ~~~~g~~~~~~~~~~~~~~~~~~  107 (565)
T 4gx0_A           85 VTVSGVIFLDIILPFGFVSMFLA  107 (565)
T ss_dssp             HHHHHHHHHHTHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHH
Confidence            999999999999988 5554443

>3beh_A MLL3241 protein; transmembrane protein, membrane protein; HET: LDA; 3.10A {Mesorhizobium loti} PDB: 2zd9_A*

Probab=99.17  E-value=2.7e-11  Score=132.83  Aligned_cols=87  Identities=11%  Similarity=0.268  Sum_probs=76.9

Q ss_pred             HHHHHHHHHHHHHHHHHHHhhhhhcCC-------CccchhhheeeeeeccccCCcccCCCcccccccccchhhHHHHHHH
Q psy17959        671 VPIAVSFLIIISFILLGSLIFNKLENW-------TFLDGTFFCFTSLGTIGFGELIPGESYDRTLRGNKNISVLVSSSYI  743 (790)
Q Consensus       671 ~~~~~~~~~~~~~~~~g~~~~~~~e~~-------s~~da~Y~~~vt~tTVGyGD~~p~t~~gr~~~~~~~~~~~~~~~~~  743 (790)
                      ..+...++++++++.++|.+++..|++       ++.||+||+++|+|||||||++|.|+.||          +++++++
T Consensus       127 ~~l~~~~~~~~~~~~~~a~~~~~~e~~~~~~~f~~~~~s~y~~~~t~ttvGygd~~p~t~~~~----------~~~~~~~  196 (355)
T 3beh_A          127 RNLIGVTTLFGVVLFAVALAAYVIERDIQPEKFGSIPQAMWWAVVTLSTTGYGDTIPQSFAGR----------VLAGAVM  196 (355)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHTTTCHHHHSSHHHHHHHHHHHHTTCCCSSSCCCSHHHH----------HHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHhhcCCCCcccccHHHHHHHHHhheeecCCCCCCCCChhHH----------HHHHHHH
Confidence            345555666677788899999999986       89999999999999999999999999999          8899999


Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHH
Q psy17959        744 LVGMAVISMCFNLIQEEIIFMIKK  767 (790)
Q Consensus       744 ~~g~~~~~~~~~~i~~~~~~~~~~  767 (790)
                      ++|++++++.++.+++.+.+..++
T Consensus       197 ~~g~~~~~~~~~~i~~~~~~~~~~  220 (355)
T 3beh_A          197 MSGIGIFGLWAGILATGFYQEVRR  220 (355)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHH
Confidence            999999999999999988876554

>1xl4_A Inward rectifier potassium channel; integral membrane protein, ION channel, inwardly rectifying channel, metal transport; 2.60A {Magnetospirillum magnetotacticum} SCOP: b.1.18.16 f.14.1.1 PDB: 1xl6_A* 2wlh_A 2wli_B 2wlj_A* 2wlk_A* 2wlm_A 2wlo_A 2wln_A 3zrs_A 2wli_A 2x6c_A* 2x6b_A* 2x6a_A*

Probab=99.13  E-value=3e-11  Score=128.59  Aligned_cols=76  Identities=24%  Similarity=0.327  Sum_probs=64.1

Q ss_pred             HHHHHHHHHHHHhhhhhcC-------CCccchhhheeeeeeccccCCcccCCCcccccccccchhhHHHHHHHHHHHHHH
Q psy17959        678 LIIISFILLGSLIFNKLEN-------WTFLDGTFFCFTSLGTIGFGELIPGESYDRTLRGNKNISVLVSSSYILVGMAVI  750 (790)
Q Consensus       678 ~~~~~~~~~g~~~~~~~e~-------~s~~da~Y~~~vt~tTVGyGD~~p~t~~gr~~~~~~~~~~~~~~~~~~~g~~~~  750 (790)
                      ++.++.+++.|.+|+..++       ++|.||+||+++|+|||||||++|.++.||          +++++++++|++++
T Consensus        55 ~~~~~~~l~fa~ly~~~~~~~~~~~~~s~~~a~yfs~vT~tTvGYGDi~P~t~~gr----------~~~~~~~l~G~~~~  124 (301)
T 1xl4_A           55 GLYLVTNALFALAYLACGDVIENARPGSFTDAFFFSVQTMATIGYGKLIPIGPLAN----------TLVTLEALCGMLGL  124 (301)
T ss_dssp             HHHHHHHHHHHHHHHHTCSCSTTSCTTCHHHHHHHHHHHHTTCCCSSSCCCHHHHH----------HHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHhhccccCCCCcCCHHHHHHHhhhheeccCCCCCcCCCHHHH----------HHHHHHHHHHHHHH
Confidence            3334454566666776652       899999999999999999999999999999          88999999999999


Q ss_pred             HHHHHHHHHHHHH
Q psy17959        751 SMCFNLIQEEIIF  763 (790)
Q Consensus       751 ~~~~~~i~~~~~~  763 (790)
                      ++.++.+...+.+
T Consensus       125 a~~~g~v~~~~~~  137 (301)
T 1xl4_A          125 AVAASLIYARFTR  137 (301)
T ss_dssp             HHHHHHHHHHHTC
T ss_pred             HHHHHHHHHHHHh
Confidence            9999988877654

>1lnq_A MTHK channels, potassium channel related protein; rossman fold, helix bundle, membrane protein; 3.30A {Methanothermobacter thermautotrophicusorganism_taxid} SCOP: c.2.1.9 d.286.1.1 f.14.1.1 PDB: 3rbz_A

Probab=99.07  E-value=3.1e-12  Score=139.27  Aligned_cols=79  Identities=27%  Similarity=0.488  Sum_probs=68.1

Q ss_pred             HHHHHHHHHHHHhHHhhcccCCCCccceeeeeeecccccccccccCCCCcchhhhhhhhhhhHHHHHHHHHHHHHHHHHH
Q psy17959        105 CVFLVISYIIGGAFLFSHWEPWGFPDSAYFCFITLTTIGFGDFVPAQKSTDVQTAEETAELRIALCSLYLLFGIALLAMS  184 (790)
Q Consensus       105 ~~~~~~~~i~~ga~~~~~~e~wsf~da~Yf~~iTltTIGfGDi~P~~~~~~~~~~~~~~~~~~~~~~~~~l~Gl~~~~~~  184 (790)
                      .++++++++++|+++|+..|+|+|.||+||+++|+|||||||++|.+..            +++++++++++|+++++++
T Consensus        23 ~~~~~~~~~~~~~~~~~~~e~~~~~~a~y~~~~t~tTvGyGd~~p~t~~------------~r~~~~~~~~~g~~~~~~~   90 (336)
T 1lnq_A           23 ILLLVLAVIIYGTAGFHFIEGESWTVSLYWTFVTIATVGYGDYSPSTPL------------GMYFTVTLIVLGIGTFAVA   90 (336)
T ss_dssp             STTTTTTSHHHHTTTTTTSSSCCSSTTHHHHHHHHTTCCCSSCCCCCSS------------HHHHHTHHHHTTSTTTTTH
T ss_pred             HHHHHHHHHHHHHHHHHHHhCCCHHHHHHHHHHHhhcccCCCCCCCCcC------------HHHHHHHHHHHHHHHHHHH
Confidence            3444455678899999999999999999999999999999999999776            8999999999999999999


Q ss_pred             HHHHHHHHHHH
Q psy17959        185 FNLVQEEVISN  195 (790)
Q Consensus       185 i~~i~~~~~~~  195 (790)
                      ++.+.+.+.+.
T Consensus        91 ~~~~~~~~~~~  101 (336)
T 1lnq_A           91 VERLLEFLINR  101 (336)
T ss_dssp             HHHHTTTC---
T ss_pred             HHHHHHHHHHH
Confidence            99988876664

>1p7b_A Integral membrane channel and cytosolic domains; transmembrane helices, ION conduction, immunoglobulin fold, assembly; 3.65A {Burkholderia pseudomallei} SCOP: b.1.18.16 f.14.1.1 PDB: 2wll_B* 2wll_A*

Probab=99.05  E-value=1.4e-10  Score=124.72  Aligned_cols=78  Identities=22%  Similarity=0.381  Sum_probs=65.0

Q ss_pred             HHHHHHHHHHHHHHhhhhhc-------CCCccchhhheeeeeeccccCCcccCCCcccccccccchhhHHHHHHHHHHHH
Q psy17959        676 SFLIIISFILLGSLIFNKLE-------NWTFLDGTFFCFTSLGTIGFGELIPGESYDRTLRGNKNISVLVSSSYILVGMA  748 (790)
Q Consensus       676 ~~~~~~~~~~~g~~~~~~~e-------~~s~~da~Y~~~vt~tTVGyGD~~p~t~~gr~~~~~~~~~~~~~~~~~~~g~~  748 (790)
                      .++++++++++++++|+...       .++|.||+||+++|+|||||||++|.++.||          +++++++++|++
T Consensus        67 ~~~~~l~~~l~fally~~e~~~~~~~~~~s~~~a~yfs~vT~tTVGYGDi~P~t~~gr----------~~~~~~~l~G~~  136 (333)
T 1p7b_A           67 LAALFVVNNTLFALLYQLGDAPIANQSPPGFVGAFFFSVETLATVGYGDMHPQTVYAH----------AIATLEIFVGMS  136 (333)
T ss_dssp             HHHHHHHHHHHHHTTTSSSSSCCCCSSSSSTHHHHHHHTTTTTTCCCSCCCCCSHHHH----------HHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHhcccccCCCCCcHHHhHhhhheeeeecCCCCCcCCCHHHH----------HHHHHHHHHHHH
Confidence            33444556677777765421       2589999999999999999999999999999          889999999999


Q ss_pred             HHHHHHHHHHHHHHH
Q psy17959        749 VISMCFNLIQEEIIF  763 (790)
Q Consensus       749 ~~~~~~~~i~~~~~~  763 (790)
                      ++++.++.+...+.+
T Consensus       137 ~~a~~ig~i~~~~~~  151 (333)
T 1p7b_A          137 GIALSTGLVFARFAR  151 (333)
T ss_dssp             HHHHHHHHHHHHHTS
T ss_pred             HHHHHHHHHHHHHHH
Confidence            999999999877664

>2qks_A KIR3.1-prokaryotic KIR channel chimera; G-protein gated inward rectifier, potassium channel selectivity filter, metal transport; HET: BNG; 2.20A {Burkholderia xenovorans}

Probab=99.04  E-value=1.4e-10  Score=124.38  Aligned_cols=58  Identities=24%  Similarity=0.433  Sum_probs=54.3

Q ss_pred             CCCccchhhheeeeeeccccCCcccCCCcccccccccchhhHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q psy17959        696 NWTFLDGTFFCFTSLGTIGFGELIPGESYDRTLRGNKNISVLVSSSYILVGMAVISMCFNLIQEEIIF  763 (790)
Q Consensus       696 ~~s~~da~Y~~~vt~tTVGyGD~~p~t~~gr~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~i~~~~~~  763 (790)
                      +|+|.||+||+++|+|||||||++|.+..||          +++++++++|++++++.++.+...+.+
T Consensus        76 ~~s~~~a~y~s~vT~tTVGYGDi~P~t~~gr----------~~~~~~~l~G~~~~a~~~g~i~~~~~~  133 (321)
T 2qks_A           76 PAGFGGAFFFSVETLATVGYGDMHPQTVYAH----------WIATLEIFVGMSSIALATGCAFIKMSQ  133 (321)
T ss_dssp             STTHHHHHHHHHHHHTTCCCCSSCBCSHHHH----------HHHHHHHHHHHHHHHHHHHHHHHHHHS
T ss_pred             CcchhheeeeeeEEeccccCCCcCcccHHHH----------HHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            4699999999999999999999999999999          889999999999999999999977765

>2r9r_B Paddle chimera voltage gated potassium channel KV; voltage sensor, voltage dependent, ION CH shaker, membrane protein, eukaryotic; HET: NAP PGW; 2.40A {Rattus norvegicus} PDB: 3lnm_B* 3lut_B* 2a79_B*

Probab=98.93  E-value=4.5e-10  Score=128.69  Aligned_cols=73  Identities=21%  Similarity=0.387  Sum_probs=59.5

Q ss_pred             HHHHHhHHhhcccCC-------CCccceeeeeeecccccccccccCCCCcchhhhhhhhhhhHHHHHHHHHHHHHHHHHH
Q psy17959        112 YIIGGAFLFSHWEPW-------GFPDSAYFCFITLTTIGFGDFVPAQKSTDVQTAEETAELRIALCSLYLLFGIALLAMS  184 (790)
Q Consensus       112 ~i~~ga~~~~~~e~w-------sf~da~Yf~~iTltTIGfGDi~P~~~~~~~~~~~~~~~~~~~~~~~~~l~Gl~~~~~~  184 (790)
                      .++.|+++| ..|++       +|.+|+||+++|+|||||||++|.+..            +++++++++++|+++++++
T Consensus       354 ~~if~~~~~-~~e~~~~~~~F~s~~~a~y~~~vT~TTvGYGDi~P~t~~------------gr~f~~~~~l~G~~~l~l~  420 (514)
T 2r9r_B          354 VILFSSAVY-FAEADERDSQFPSIPDAFWWAVVSMTTVGYGDMVPTTIG------------GKIVGSLCAIAGVLTIALP  420 (514)
T ss_dssp             HHHHHHHHH-HHHTTCTTCSCSSHHHHHHHHHHHHTTCCCSSSCCCSHH------------HHHHHHHHHHHHHHHHHTT
T ss_pred             HHHHHhhhh-eeeccCCCccccchhhhhheeeeEEEecccCCCCCCCcc------------hHhhehhHHHHHHHHHHHH
Confidence            334444444 44543       799999999999999999999998654            7899999999999999999


Q ss_pred             HHHHHHHHHHHHH
Q psy17959        185 FNLVQEEVISNVK  197 (790)
Q Consensus       185 i~~i~~~~~~~~~  197 (790)
                      ++++.+.+.+..+
T Consensus       421 iavI~~~f~~~~~  433 (514)
T 2r9r_B          421 VPVIVSNFNYFYH  433 (514)
T ss_dssp             HHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHH
Confidence            9999987776544

>3beh_A MLL3241 protein; transmembrane protein, membrane protein; HET: LDA; 3.10A {Mesorhizobium loti} PDB: 2zd9_A*

Probab=98.91  E-value=6.8e-10  Score=121.64  Aligned_cols=81  Identities=19%  Similarity=0.315  Sum_probs=69.2

Q ss_pred             HHHHHHHHHHHHhHHhhcccCC-------CCccceeeeeeecccccccccccCCCCcchhhhhhhhhhhHHHHHHHHHHH
Q psy17959        105 CVFLVISYIIGGAFLFSHWEPW-------GFPDSAYFCFITLTTIGFGDFVPAQKSTDVQTAEETAELRIALCSLYLLFG  177 (790)
Q Consensus       105 ~~~~~~~~i~~ga~~~~~~e~w-------sf~da~Yf~~iTltTIGfGDi~P~~~~~~~~~~~~~~~~~~~~~~~~~l~G  177 (790)
                      .+.++++.++++|++++..|+|       +|.||+||+++|+|||||||++|.+..            +++++.+++++|
T Consensus       132 ~~~~~~~~~~~~a~~~~~~e~~~~~~~f~~~~~s~y~~~~t~ttvGygd~~p~t~~------------~~~~~~~~~~~g  199 (355)
T 3beh_A          132 VTTLFGVVLFAVALAAYVIERDIQPEKFGSIPQAMWWAVVTLSTTGYGDTIPQSFA------------GRVLAGAVMMSG  199 (355)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHTTTCHHHHSSHHHHHHHHHHHHTTCCCSSSCCCSHH------------HHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHhhcCCCCcccccHHHHHHHHHhheeecCCCCCCCCChh------------HHHHHHHHHHHH
Confidence            3444455677788888888876       799999999999999999999998754            899999999999


Q ss_pred             HHHHHHHHHHHHHHHHHHHH
Q psy17959        178 IALLAMSFNLVQEEVISNVK  197 (790)
Q Consensus       178 l~~~~~~i~~i~~~~~~~~~  197 (790)
                      +++++++++.+.+.+.+..+
T Consensus       200 ~~~~~~~~~~i~~~~~~~~~  219 (355)
T 3beh_A          200 IGIFGLWAGILATGFYQEVR  219 (355)
T ss_dssp             HHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHH
Confidence            99999999999988877544

>4gx0_A TRKA domain protein; membrane protein, ION channel, ADP binding, NAD binding, MEM transport protein; HET: MAL GLC; 2.60A {Geobacter sulfurreducens} PDB: 4gx1_A* 4gx2_A* 4gx5_A 4gvl_A*

Probab=98.91  E-value=7e-10  Score=129.21  Aligned_cols=78  Identities=18%  Similarity=0.376  Sum_probs=61.9

Q ss_pred             HHHHHHHHHHHHhHHhhc----ccC--CCCccceeeeeeecccccccccccCCCCcchhhhhhhhhhhHHHHHHHHHHHH
Q psy17959        105 CVFLVISYIIGGAFLFSH----WEP--WGFPDSAYFCFITLTTIGFGDFVPAQKSTDVQTAEETAELRIALCSLYLLFGI  178 (790)
Q Consensus       105 ~~~~~~~~i~~ga~~~~~----~e~--wsf~da~Yf~~iTltTIGfGDi~P~~~~~~~~~~~~~~~~~~~~~~~~~l~Gl  178 (790)
                      .++++++++++++++|+.    +|+  |+|+||+||+++|+|||||||++|.+..            +++++++++++|+
T Consensus        23 ~~~~~~~~~~~~~~~~~~~~~~~e~~~~~~~~~~y~~~~t~tTvGygd~~p~~~~------------~~~~~~~~~~~g~   90 (565)
T 4gx0_A           23 YCAFLLVMLLAYASIFRYLMWHLEGRAYSFMAGIYWTITVMTTLGFGDITFESDA------------GYLFASIVTVSGV   90 (565)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHTTCCCCSSCCCSHH------------HHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHhhcCCCCchhhhhheeeeeeeeecCCCcCCCCcc------------HHHHHHHHHHHHH
Confidence            334444455566665554    566  9999999999999999999999998764            8999999999999


Q ss_pred             HHHHHHHHH-HHHHHHH
Q psy17959        179 ALLAMSFNL-VQEEVIS  194 (790)
Q Consensus       179 ~~~~~~i~~-i~~~~~~  194 (790)
                      ++++++++. +.+.+..
T Consensus        91 ~~~~~~~~~~~~~~~~~  107 (565)
T 4gx0_A           91 IFLDIILPFGFVSMFLA  107 (565)
T ss_dssp             HHHHTHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHH
Confidence            999999987 5554444

>2r9r_B Paddle chimera voltage gated potassium channel KV; voltage sensor, voltage dependent, ION CH shaker, membrane protein, eukaryotic; HET: NAP PGW; 2.40A {Rattus norvegicus} PDB: 3lnm_B* 3lut_B* 2a79_B*

Probab=98.87  E-value=1.3e-09  Score=124.76  Aligned_cols=74  Identities=20%  Similarity=0.395  Sum_probs=62.4

Q ss_pred             HHHHHHHHhhhhhcCC-------CccchhhheeeeeeccccCCcccCCCcccccccccchhhHHHHHHHHHHHHHHHHHH
Q psy17959        682 SFILLGSLIFNKLENW-------TFLDGTFFCFTSLGTIGFGELIPGESYDRTLRGNKNISVLVSSSYILVGMAVISMCF  754 (790)
Q Consensus       682 ~~~~~g~~~~~~~e~~-------s~~da~Y~~~vt~tTVGyGD~~p~t~~gr~~~~~~~~~~~~~~~~~~~g~~~~~~~~  754 (790)
                      ++++.|+++ +..|++       ++.||+||+++|+|||||||+.|.+..||          +|+++++++|++++++.+
T Consensus       353 ~~~if~~~~-~~~e~~~~~~~F~s~~~a~y~~~vT~TTvGYGDi~P~t~~gr----------~f~~~~~l~G~~~l~l~i  421 (514)
T 2r9r_B          353 GVILFSSAV-YFAEADERDSQFPSIPDAFWWAVVSMTTVGYGDMVPTTIGGK----------IVGSLCAIAGVLTIALPV  421 (514)
T ss_dssp             HHHHHHHHH-HHHHTTCTTCSCSSHHHHHHHHHHHHTTCCCSSSCCCSHHHH----------HHHHHHHHHHHHHHHTTH
T ss_pred             HHHHHHhhh-heeeccCCCccccchhhhhheeeeEEEecccCCCCCCCcchH----------hhehhHHHHHHHHHHHHH
Confidence            334444444 456764       89999999999999999999999999998          889999999999999999


Q ss_pred             HHHHHHHHHHHH
Q psy17959        755 NLIQEEIIFMIK  766 (790)
Q Consensus       755 ~~i~~~~~~~~~  766 (790)
                      +.+.+.+....+
T Consensus       422 avI~~~f~~~~~  433 (514)
T 2r9r_B          422 PVIVSNFNYFYH  433 (514)
T ss_dssp             HHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHH
Confidence            999988776544

>1xl4_A Inward rectifier potassium channel; integral membrane protein, ION channel, inwardly rectifying channel, metal transport; 2.60A {Magnetospirillum magnetotacticum} SCOP: b.1.18.16 f.14.1.1 PDB: 1xl6_A* 2wlh_A 2wli_B 2wlj_A* 2wlk_A* 2wlm_A 2wlo_A 2wln_A 3zrs_A 2wli_A 2x6c_A* 2x6b_A* 2x6a_A*

Probab=98.85  E-value=1.1e-09  Score=116.40  Aligned_cols=66  Identities=27%  Similarity=0.432  Sum_probs=56.0

Q ss_pred             HhHHhhccc-------CCCCccceeeeeeecccccccccccCCCCcchhhhhhhhhhhHHHHHHHHHHHHHHHHHHHHHH
Q psy17959        116 GAFLFSHWE-------PWGFPDSAYFCFITLTTIGFGDFVPAQKSTDVQTAEETAELRIALCSLYLLFGIALLAMSFNLV  188 (790)
Q Consensus       116 ga~~~~~~e-------~wsf~da~Yf~~iTltTIGfGDi~P~~~~~~~~~~~~~~~~~~~~~~~~~l~Gl~~~~~~i~~i  188 (790)
                      .|.+|...+       .++|.||+||+++|+|||||||++|.+..            +++++.+.+++|+.+++++++.+
T Consensus        64 fa~ly~~~~~~~~~~~~~s~~~a~yfs~vT~tTvGYGDi~P~t~~------------gr~~~~~~~l~G~~~~a~~~g~v  131 (301)
T 1xl4_A           64 FALAYLACGDVIENARPGSFTDAFFFSVQTMATIGYGKLIPIGPL------------ANTLVTLEALCGMLGLAVAASLI  131 (301)
T ss_dssp             HHHHHHHTCSCSTTSCTTCHHHHHHHHHHHHTTCCCSSSCCCHHH------------HHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHhhccccCCCCcCCHHHHHHHhhhheeccCCCCCcCCCHH------------HHHHHHHHHHHHHHHHHHHHHHH
Confidence            344465554       28899999999999999999999997654            89999999999999999999988


Q ss_pred             HHHHH
Q psy17959        189 QEEVI  193 (790)
Q Consensus       189 ~~~~~  193 (790)
                      ...+.
T Consensus       132 ~~~~~  136 (301)
T 1xl4_A          132 YARFT  136 (301)
T ss_dssp             HHHHT
T ss_pred             HHHHH
Confidence            77664

>1p7b_A Integral membrane channel and cytosolic domains; transmembrane helices, ION conduction, immunoglobulin fold, assembly; 3.65A {Burkholderia pseudomallei} SCOP: b.1.18.16 f.14.1.1 PDB: 2wll_B* 2wll_A*

Probab=98.83  E-value=1.9e-09  Score=115.88  Aligned_cols=71  Identities=28%  Similarity=0.413  Sum_probs=58.6

Q ss_pred             HHHHhHHhhccc-------CCCCccceeeeeeecccccccccccCCCCcchhhhhhhhhhhHHHHHHHHHHHHHHHHHHH
Q psy17959        113 IIGGAFLFSHWE-------PWGFPDSAYFCFITLTTIGFGDFVPAQKSTDVQTAEETAELRIALCSLYLLFGIALLAMSF  185 (790)
Q Consensus       113 i~~ga~~~~~~e-------~wsf~da~Yf~~iTltTIGfGDi~P~~~~~~~~~~~~~~~~~~~~~~~~~l~Gl~~~~~~i  185 (790)
                      ++++|++|....       .++|.||+||+++|+|||||||++|.+..            +++++.+++++|+.++++++
T Consensus        75 ~l~fally~~e~~~~~~~~~~s~~~a~yfs~vT~tTVGYGDi~P~t~~------------gr~~~~~~~l~G~~~~a~~i  142 (333)
T 1p7b_A           75 NTLFALLYQLGDAPIANQSPPGFVGAFFFSVETLATVGYGDMHPQTVY------------AHAIATLEIFVGMSGIALST  142 (333)
T ss_dssp             HHHHHTTTSSSSSCCCCSSSSSTHHHHHHHTTTTTTCCCSCCCCCSHH------------HHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHhcccccCCCCCcHHHhHhhhheeeeecCCCCCcCCCHH------------HHHHHHHHHHHHHHHHHHHH
Confidence            345566654322       35899999999999999999999998654            89999999999999999999


Q ss_pred             HHHHHHHHHH
Q psy17959        186 NLVQEEVISN  195 (790)
Q Consensus       186 ~~i~~~~~~~  195 (790)
                      +.+...+.+.
T Consensus       143 g~i~~~~~~~  152 (333)
T 1p7b_A          143 GLVFARFARP  152 (333)
T ss_dssp             HHHHHHHTSC
T ss_pred             HHHHHHHHHH
Confidence            9988877643

>2qks_A KIR3.1-prokaryotic KIR channel chimera; G-protein gated inward rectifier, potassium channel selectivity filter, metal transport; HET: BNG; 2.20A {Burkholderia xenovorans}

Probab=98.80  E-value=2.3e-09  Score=114.91  Aligned_cols=58  Identities=24%  Similarity=0.450  Sum_probs=52.8

Q ss_pred             CCCCccceeeeeeecccccccccccCCCCcchhhhhhhhhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q psy17959        125 PWGFPDSAYFCFITLTTIGFGDFVPAQKSTDVQTAEETAELRIALCSLYLLFGIALLAMSFNLVQEEVIS  194 (790)
Q Consensus       125 ~wsf~da~Yf~~iTltTIGfGDi~P~~~~~~~~~~~~~~~~~~~~~~~~~l~Gl~~~~~~i~~i~~~~~~  194 (790)
                      +|+|.||+||+++|+|||||||++|.+..            +++++.+++++|+++++++++.+...+.+
T Consensus        76 ~~s~~~a~y~s~vT~tTVGYGDi~P~t~~------------gr~~~~~~~l~G~~~~a~~~g~i~~~~~~  133 (321)
T 2qks_A           76 PAGFGGAFFFSVETLATVGYGDMHPQTVY------------AHWIATLEIFVGMSSIALATGCAFIKMSQ  133 (321)
T ss_dssp             STTHHHHHHHHHHHHTTCCCCSSCBCSHH------------HHHHHHHHHHHHHHHHHHHHHHHHHHHHS
T ss_pred             CcchhheeeeeeEEeccccCCCcCcccHH------------HHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            57999999999999999999999998654            89999999999999999999998877664

>3sya_A G protein-activated inward rectifier potassium CH; ION channel, potassium channel, inward rectification, sodium PIP2 binding, G protein binding; HET: PIO; 2.98A {Mus musculus} PDB: 3syo_A 3syc_A 3syp_A 3syq_A*

Probab=98.69  E-value=1.1e-08  Score=109.67  Aligned_cols=80  Identities=14%  Similarity=0.138  Sum_probs=64.8

Q ss_pred             HHHHHHHHHHHHHHHHhhhhh-----c---------------CCCccchhhheeeeeeccccCCcccC--CCcccccccc
Q psy17959        674 AVSFLIIISFILLGSLIFNKL-----E---------------NWTFLDGTFFCFTSLGTIGFGELIPG--ESYDRTLRGN  731 (790)
Q Consensus       674 ~~~~~~~~~~~~~g~~~~~~~-----e---------------~~s~~da~Y~~~vt~tTVGyGD~~p~--t~~gr~~~~~  731 (790)
                      .+.++..++.+++.|++|+.+     +               .-++.||+||+++|+|||||||+.|.  ++.|+     
T Consensus        47 lif~~~y~~swl~Fa~ly~~ia~~~Gdl~~~~~~~~~~Cv~~~~sf~~af~fSv~T~TTvGYGd~~p~~~~~~g~-----  121 (340)
T 3sya_A           47 LIFVMVYTVTWLFFGMIWWLIAYIRGDMDHIEDPSWTPCVTNLNGFVSAFLFSIETETTIGYGYRVITDKCPEGI-----  121 (340)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHTTTTCSSCSSCCCSBSCCCSTTHHHHHHHHHHSCCCCSSSCBCTTCHHHH-----
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHhhcccccccccccccchhccccCHHHHHhhhheeeeeecCCCccCcCcCHHHH-----
Confidence            344444666677778777652     1               13899999999999999999999997  57788     


Q ss_pred             cchhhHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q psy17959        732 KNISVLVSSSYILVGMAVISMCFNLIQEEIIF  763 (790)
Q Consensus       732 ~~~~~~~~~~~~~~g~~~~~~~~~~i~~~~~~  763 (790)
                           +++++.+++|+.+++..++.+...+.+
T Consensus       122 -----~l~~~~~l~G~~l~a~~~giv~ak~sr  148 (340)
T 3sya_A          122 -----ILLLIQSVLGSIVNAFMVGCMFVKISQ  148 (340)
T ss_dssp             -----HHHHHHHHHHHHHHHHHHHHHHHHHHC
T ss_pred             -----HHHHHHHHHHHHHHHHHHHHHHHHHhH
Confidence                 889999999999999999998876665

>3spc_A Inward-rectifier K+ channel KIR2.2; PIP, membrane protein, lipid, receptor, metal transport; HET: P8P; 2.45A {Gallus gallus} PDB: 3jyc_A* 3spi_A* 3sph_A* 3spj_A 3spg_A*

Probab=98.60  E-value=3.1e-08  Score=106.44  Aligned_cols=80  Identities=20%  Similarity=0.185  Sum_probs=64.8

Q ss_pred             HHHHHHHHHHHHHHHHhhhhh---c------------------CCCccchhhheeeeeeccccCCcccC--CCccccccc
Q psy17959        674 AVSFLIIISFILLGSLIFNKL---E------------------NWTFLDGTFFCFTSLGTIGFGELIPG--ESYDRTLRG  730 (790)
Q Consensus       674 ~~~~~~~~~~~~~g~~~~~~~---e------------------~~s~~da~Y~~~vt~tTVGyGD~~p~--t~~gr~~~~  730 (790)
                      .+.++..++.+++.|++|+.+   +                  .-+|.||+||+++|+|||||||+.|.  ++.|+    
T Consensus        49 l~f~~~y~~swl~Fally~~ia~~~gdl~~~~~~~~~~~Cv~~~~sf~~af~fSv~T~TTvGYGd~~p~~~~~~~~----  124 (343)
T 3spc_A           49 LLFSLAFLVSWLLFGLIFWLIALIHGDLENPGGDDTFKPCVLQVNGFVAAFLFSIETQTTIGYGFRCVTEECPLAV----  124 (343)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHTGGGCTTCCSSCCCSEETCCSHHHHHHHHHHHHSCCCCSSSEECSSCHHHH----
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHhcCCccccccccccccccccccCCHHHHhheeeeeeEeecCCCccCCCCCHHHH----
Confidence            344455677778888887652   1                  14899999999999999999999975  78888    


Q ss_pred             ccchhhHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q psy17959        731 NKNISVLVSSSYILVGMAVISMCFNLIQEEIIF  763 (790)
Q Consensus       731 ~~~~~~~~~~~~~~~g~~~~~~~~~~i~~~~~~  763 (790)
                            +++++.+++|+.+++..++.+...+.+
T Consensus       125 ------~l~~~~~l~G~~l~a~~~giv~ak~sr  151 (343)
T 3spc_A          125 ------FMVVVQSIVGCIIDSFMIGAIMAKMAR  151 (343)
T ss_dssp             ------HHHHHHHHHHHHHHHHHHHHHHHHHHS
T ss_pred             ------HHHHHHHHHHHHHHHHHHHHHHHHHhh
Confidence                  789999999999999999988866554

>3sya_A G protein-activated inward rectifier potassium CH; ION channel, potassium channel, inward rectification, sodium PIP2 binding, G protein binding; HET: PIO; 2.98A {Mus musculus} PDB: 3syo_A 3syc_A 3syp_A 3syq_A*

Probab=98.30  E-value=7.2e-07  Score=95.70  Aligned_cols=59  Identities=25%  Similarity=0.278  Sum_probs=51.4

Q ss_pred             CCccceeeeeeecccccccccccCCCCcchhhhhhhhhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q psy17959        127 GFPDSAYFCFITLTTIGFGDFVPAQKSTDVQTAEETAELRIALCSLYLLFGIALLAMSFNLVQEEVISN  195 (790)
Q Consensus       127 sf~da~Yf~~iTltTIGfGDi~P~~~~~~~~~~~~~~~~~~~~~~~~~l~Gl~~~~~~i~~i~~~~~~~  195 (790)
                      +|.||+||+++|+|||||||+.|...          ...+++++.+-+++|+.++|++++++...+.+-
T Consensus        91 sf~~af~fSv~T~TTvGYGd~~p~~~----------~~~g~~l~~~~~l~G~~l~a~~~giv~ak~srp  149 (340)
T 3sya_A           91 GFVSAFLFSIETETTIGYGYRVITDK----------CPEGIILLLIQSVLGSIVNAFMVGCMFVKISQP  149 (340)
T ss_dssp             STTHHHHHHHHHHSCCCCSSSCBCTT----------CHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCG
T ss_pred             CHHHHHhhhheeeeeecCCCccCcCc----------CHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhHH
Confidence            68999999999999999999999742          235889999999999999999999888776653

>3spc_A Inward-rectifier K+ channel KIR2.2; PIP, membrane protein, lipid, receptor, metal transport; HET: P8P; 2.45A {Gallus gallus} PDB: 3jyc_A* 3spi_A* 3sph_A* 3spj_A 3spg_A*

Probab=98.07  E-value=2.7e-06  Score=91.32  Aligned_cols=58  Identities=19%  Similarity=0.310  Sum_probs=49.8

Q ss_pred             CCccceeeeeeecccccccccccCCCCcchhhhhhhhhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q psy17959        127 GFPDSAYFCFITLTTIGFGDFVPAQKSTDVQTAEETAELRIALCSLYLLFGIALLAMSFNLVQEEVIS  194 (790)
Q Consensus       127 sf~da~Yf~~iTltTIGfGDi~P~~~~~~~~~~~~~~~~~~~~~~~~~l~Gl~~~~~~i~~i~~~~~~  194 (790)
                      +|.||+||+++|+|||||||+.|...          ...+++++.+-+++|+.++|.+++++..++.+
T Consensus        94 sf~~af~fSv~T~TTvGYGd~~p~~~----------~~~~~~l~~~~~l~G~~l~a~~~giv~ak~sr  151 (343)
T 3spc_A           94 GFVAAFLFSIETQTTIGYGFRCVTEE----------CPLAVFMVVVQSIVGCIIDSFMIGAIMAKMAR  151 (343)
T ss_dssp             SHHHHHHHHHHHHSCCCCSSSEECSS----------CHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHS
T ss_pred             CHHHHhheeeeeeEeecCCCccCCCC----------CHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhh
Confidence            68999999999999999999998632          23478899999999999999999988877654

>3rvy_A ION transport protein; tetrameric ION channel, voltage-gated sodium-selective ION C membrane, metal transport; HET: PX4; 2.70A {Arcobacter butzleri} PDB: 3rvz_A* 4ekw_A* 3rw0_A*

Probab=97.95  E-value=5.2e-06  Score=87.79  Aligned_cols=65  Identities=11%  Similarity=0.153  Sum_probs=51.9

Q ss_pred             CCccchhhheeeeeeccccC-Ccc-cCCCcccccccccchhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q psy17959        697 WTFLDGTFFCFTSLGTIGFG-ELI-PGESYDRTLRGNKNISVLVSSSYILVGMAVISMCFNLIQEEIIFMIKK  767 (790)
Q Consensus       697 ~s~~da~Y~~~vt~tTVGyG-D~~-p~t~~gr~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~i~~~~~~~~~~  767 (790)
                      -|+.||+||+++|+||+||| |+. |.+..|+      .....|+++.++.|++++.+.++.+.+.+.+..++
T Consensus       179 ~s~~~a~~~~~~~~T~~g~~~di~~p~~~~~~------~~~~~f~~~~~i~~~~~lnl~~aii~~~f~~~~~~  245 (285)
T 3rvy_A          179 GTLGESFYTLFQVMTLESWSMGIVRPLMEVYP------YAWVFFIPFIFVVTFVMINLVVAICVDAMAILNQK  245 (285)
T ss_dssp             SSHHHHHHHHHHHHTTTTCCCCCHHHHHTTCT------TTHHHHHHHHHHHHHHHHHHHHHHHHHHC------
T ss_pred             CCHHHHHHHHHHHHHhCCCcHHHHHHHHHcCC------hHHhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            48899999999999999999 996 9887764      23457888999999999999999999988865443

>3rvy_A ION transport protein; tetrameric ION channel, voltage-gated sodium-selective ION C membrane, metal transport; HET: PX4; 2.70A {Arcobacter butzleri} PDB: 3rvz_A* 4ekw_A* 3rw0_A*

Probab=97.68  E-value=6.8e-06  Score=86.89  Aligned_cols=63  Identities=10%  Similarity=0.178  Sum_probs=49.1

Q ss_pred             CCccceeeeeeeccccccc-ccc-cCCCCcchhhhhhhhhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q psy17959        127 GFPDSAYFCFITLTTIGFG-DFV-PAQKSTDVQTAEETAELRIALCSLYLLFGIALLAMSFNLVQEEVISNVK  197 (790)
Q Consensus       127 sf~da~Yf~~iTltTIGfG-Di~-P~~~~~~~~~~~~~~~~~~~~~~~~~l~Gl~~~~~~i~~i~~~~~~~~~  197 (790)
                      ++.+|+||+|+++||+||| |+. |.+..+        ...++.++.+.++.|+.+++++++++.+.+.+..+
T Consensus       180 s~~~a~~~~~~~~T~~g~~~di~~p~~~~~--------~~~~~~f~~~~~i~~~~~lnl~~aii~~~f~~~~~  244 (285)
T 3rvy_A          180 TLGESFYTLFQVMTLESWSMGIVRPLMEVY--------PYAWVFFIPFIFVVTFVMINLVVAICVDAMAILNQ  244 (285)
T ss_dssp             SHHHHHHHHHHHHTTTTCCCCCHHHHHTTC--------TTTHHHHHHHHHHHHHHHHHHHHHHHHHHC-----
T ss_pred             CHHHHHHHHHHHHHhCCCcHHHHHHHHHcC--------ChHHhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            5889999999999999999 997 876541        12357788888899999999999999998876544

>4dxw_A Navrh, ION transport protein; tetrameric, voltage-gated sodium channel, sodium selective, gated ION channel; HET: BNG PX4; 3.05A {Alpha proteobacterium HIMB114}

Probab=91.62  E-value=0.15  Score=51.31  Aligned_cols=62  Identities=10%  Similarity=0.016  Sum_probs=45.6

Q ss_pred             CCccchhhheeeeeeccccCCcccCCCcccccccccchhhHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q psy17959        697 WTFLDGTFFCFTSLGTIGFGELIPGESYDRTLRGNKNISVLVSSSYILVGMAVISMCFNLIQEEIIF  763 (790)
Q Consensus       697 ~s~~da~Y~~~vt~tTVGyGD~~p~t~~gr~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~i~~~~~~  763 (790)
                      -|+.+|+|+.+.++||.|++|+-..+-.+.     ......|..++++.+..++.+.++.+.+.+.+
T Consensus       164 ~~~~~a~~~lf~~~t~~~w~~i~~~~~~~~-----~~~~~~f~~~~~i~~~i~lNlfiavi~~~f~~  225 (229)
T 4dxw_A          164 GDLGISLITLFQVLTLSSWETVMLPMQEIY-----WWSWVYFFSFIIICSITILNLVIAILVDVVIQ  225 (229)
T ss_dssp             SSHHHHHHHHHHHHTTSSTHHHHHHHHTTC-----TTHHHHHHHHHHHHHHHHHHHHHHHHHHHHHT
T ss_pred             cCHHHHHHHHHHHHccCCHHHHHHHHHHhC-----CcHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            378999999999999999999844322111     12334556667777788999999998887764

>3kg2_A Glutamate receptor 2; ION channel, membrane protein, cell membrane, glycoprotein, transport, membrane, postsynaptic cell membrane, editing; HET: ZK1 NAG BMA; 3.60A {Rattus norvegicus}

Probab=86.91  E-value=0.53  Score=56.43  Aligned_cols=54  Identities=13%  Similarity=0.287  Sum_probs=43.9

Q ss_pred             ccchhhheeeeeeccccCCcccCCCcccccccccchhhHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q psy17959        699 FLDGTFFCFTSLGTIGFGELIPGESYDRTLRGNKNISVLVSSSYILVGMAVISMCFNLIQEEIIF  763 (790)
Q Consensus       699 ~~da~Y~~~vt~tTVGyGD~~p~t~~gr~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~i~~~~~~  763 (790)
                      +.+++|+++.+++..| ++..|.+..+|          ++.++|+++++.+++...+.++..+..
T Consensus       564 ~~~~~~~~~~~l~~~g-~~~~p~~~~~R----------~~~~~w~~~~lil~~~Yta~L~s~Lt~  617 (823)
T 3kg2_A          564 IFNSLWFSLGAFMQQG-ADISPRSLSGR----------IVGGVWWFFTLIIISSYTANLAAFLTV  617 (823)
T ss_dssp             HHHHHHHTTTTSCC-------CCCHHHH----------HHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHhcC-CCcCCcchhhh----------hHHHHHHHHHHHHHHHHHHHHHHHhcc
Confidence            6689999999999999 78899988888          889999999999999999999988775

>4dxw_A Navrh, ION transport protein; tetrameric, voltage-gated sodium channel, sodium selective, gated ION channel; HET: BNG PX4; 3.05A {Alpha proteobacterium HIMB114}

Probab=80.94  E-value=0.72  Score=46.26  Aligned_cols=63  Identities=17%  Similarity=0.250  Sum_probs=43.7

Q ss_pred             CCC-CccceeeeeeecccccccccccCCCCcchhhhhhhhhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q psy17959        125 PWG-FPDSAYFCFITLTTIGFGDFVPAQKSTDVQTAEETAELRIALCSLYLLFGIALLAMSFNLVQEEVIS  194 (790)
Q Consensus       125 ~ws-f~da~Yf~~iTltTIGfGDi~P~~~~~~~~~~~~~~~~~~~~~~~~~l~Gl~~~~~~i~~i~~~~~~  194 (790)
                      +++ +.+|+|+.|.++||.|++|+.......       .......+...+++.+..++.++++++.+.+.+
T Consensus       162 ~F~~~~~a~~~lf~~~t~~~w~~i~~~~~~~-------~~~~~~~f~~~~~i~~~i~lNlfiavi~~~f~~  225 (229)
T 4dxw_A          162 RWGDLGISLITLFQVLTLSSWETVMLPMQEI-------YWWSWVYFFSFIIICSITILNLVIAILVDVVIQ  225 (229)
T ss_dssp             TTSSHHHHHHHHHHHHTTSSTHHHHHHHHTT-------CTTHHHHHHHHHHHHHHHHHHHHHHHHHHHHHT
T ss_pred             cccCHHHHHHHHHHHHccCCHHHHHHHHHHh-------CCcHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            343 899999999999999999985432110       011234455556666688889999888877664

---

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	790
d1lnqa2	80	f.14.1.1 (A:19-98) Potassium channel-related prote	5e-18
d1lnqa2	80	f.14.1.1 (A:19-98) Potassium channel-related prote	2e-16
d1lnqa2	80	f.14.1.1 (A:19-98) Potassium channel-related prote	2e-14
d1lnqa2	80	f.14.1.1 (A:19-98) Potassium channel-related prote	1e-10
d1lnqa2	80	f.14.1.1 (A:19-98) Potassium channel-related prote	2e-06
d1p7ba2	116	f.14.1.1 (A:36-151) Inward rectifier potassium cha	2e-07
d1p7ba2	116	f.14.1.1 (A:36-151) Inward rectifier potassium cha	8e-04
d1xl4a2	116	f.14.1.1 (A:23-138) Inward rectifier potassium cha	3e-06
d1xl4a2	116	f.14.1.1 (A:23-138) Inward rectifier potassium cha	5e-04
d1r3jc_	103	f.14.1.1 (C:) Potassium channel protein {Streptomy	1e-05
d1r3jc_	103	f.14.1.1 (C:) Potassium channel protein {Streptomy	1e-04
d1qkla_	127	a.143.1.2 (A:) RPB6 {Human (Homo sapiens) [TaxId:	3e-04
d1qkla_	127	a.143.1.2 (A:) RPB6 {Human (Homo sapiens) [TaxId:	4e-04
d2ayua1	301	d.305.1.1 (A:70-370) Nucleosome assembly protein,	4e-04
d1ofcx3	102	a.187.1.1 (X:697-798) HAND domain of the nucleosom	7e-04

>d1lnqa2 f.14.1.1 (A:19-98) Potassium channel-related protein MthK {Archaeon Methanothermobacter thermautotrophicus [TaxId: 145262]} Length = 80

class: Membrane and cell surface proteins and peptides
fold: Voltage-gated potassium channels
superfamily: Voltage-gated potassium channels
family: Voltage-gated potassium channels
domain: Potassium channel-related protein MthK
species: Archaeon Methanothermobacter thermautotrophicus [TaxId: 145262]

 Score = 77.1 bits (190), Expect = 5e-18
 Identities = 22/90 (24%), Positives = 37/90 (41%), Gaps = 12/90 (13%)

Query: 101 PIWLCVFLVISYIIGGAFLFSHWEPWGFPDSAYFCFITLTTIGFGDFVPAQKSTDVQTAE 160
           P    + LV++ II G   F   E   +  S Y+ F+T+ T+G+GD+ P           
Sbjct: 1   PATRILLLVLAVIIYGTAGFHFIEGESWTVSLYWTFVTIATVGYGDYSP----------- 49

Query: 161 ETAELRIALCSLYLLFGIALLAMSFNLVQE 190
            T           ++ GI   A++   + E
Sbjct: 50  STPLGMY-FTVTLIVLGIGTFAVAVERLLE 78

>d1lnqa2 f.14.1.1 (A:19-98) Potassium channel-related protein MthK {Archaeon Methanothermobacter thermautotrophicus [TaxId: 145262]} Length = 80

class: Membrane and cell surface proteins and peptides
fold: Voltage-gated potassium channels
superfamily: Voltage-gated potassium channels
family: Voltage-gated potassium channels
domain: Potassium channel-related protein MthK
species: Archaeon Methanothermobacter thermautotrophicus [TaxId: 145262]

 Score = 72.0 bits (177), Expect = 2e-16
 Identities = 19/92 (20%), Positives = 36/92 (39%), Gaps = 14/92 (15%)

Query: 511 PITLCLMIMVGYIYGGAVLFSKWEDWNILDGSYFCFISLSTIGFGDIVPGDKITGKNNDI 570
           P T  L++++  I  G   F   E  +     Y+ F++++T+G+GD  P           
Sbjct: 1   PATRILLLVLAVIIYGTAGFHFIEGESWTVSLYWTFVTIATVGYGDYSPST--------- 51

Query: 571 GVQTLELSFILCAMYLMLGMALIAMCFNLMQE 602
                 L        ++LG+   A+    + E
Sbjct: 52  -----PLGMYFTVTLIVLGIGTFAVAVERLLE 78

>d1lnqa2 f.14.1.1 (A:19-98) Potassium channel-related protein MthK {Archaeon Methanothermobacter thermautotrophicus [TaxId: 145262]} Length = 80

class: Membrane and cell surface proteins and peptides
fold: Voltage-gated potassium channels
superfamily: Voltage-gated potassium channels
family: Voltage-gated potassium channels
domain: Potassium channel-related protein MthK
species: Archaeon Methanothermobacter thermautotrophicus [TaxId: 145262]

 Score = 67.0 bits (164), Expect = 2e-14
 Identities = 14/90 (15%), Positives = 40/90 (44%), Gaps = 10/90 (11%)

Query: 672 PIAVSFLIIISFILLGSLIFNKLENWTFLDGTFFCFTSLGTIGFGELIPGESYDRTLRGN 731
           P     L++++ I+ G+  F+ +E  ++    ++ F ++ T+G+G+  P           
Sbjct: 1   PATRILLLVLAVIIYGTAGFHFIEGESWTVSLYWTFVTIATVGYGDYSPSTPLGM----- 55

Query: 732 KNISVLVSSSYILVGMAVISMCFNLIQEEI 761
                  + + I++G+   ++    + E +
Sbjct: 56  -----YFTVTLIVLGIGTFAVAVERLLEFL 80

>d1lnqa2 f.14.1.1 (A:19-98) Potassium channel-related protein MthK {Archaeon Methanothermobacter thermautotrophicus [TaxId: 145262]} Length = 80

class: Membrane and cell surface proteins and peptides
fold: Voltage-gated potassium channels
superfamily: Voltage-gated potassium channels
family: Voltage-gated potassium channels
domain: Potassium channel-related protein MthK
species: Archaeon Methanothermobacter thermautotrophicus [TaxId: 145262]

 Score = 55.9 bits (135), Expect = 1e-10
 Identities = 18/117 (15%), Positives = 36/117 (30%), Gaps = 37/117 (31%)

Query: 271 PITLCLMIMVGYIYGGAVLFSKWEDWNILDGSRSSSRSRSRQQTERSFTEKCKDYLRQFL 330
           P T  L++++  I  G   F   E  +                                 
Sbjct: 1   PATRILLLVLAVIIYGTAGFHFIEGESWTV------------------------------ 30

Query: 331 AFLFSNIGIICLVIGYTIAGYGNVAPITFLGKITTIAYAIAGMPLFLLYLSNIGDIL 387
           +  ++        +     GYG+ +P T LG   T+   + G+  F + +  + + L
Sbjct: 31  SLYWT-------FVTIATVGYGDYSPSTPLGMYFTVTLIVLGIGTFAVAVERLLEFL 80

>d1lnqa2 f.14.1.1 (A:19-98) Potassium channel-related protein MthK {Archaeon Methanothermobacter thermautotrophicus [TaxId: 145262]} Length = 80

class: Membrane and cell surface proteins and peptides
fold: Voltage-gated potassium channels
superfamily: Voltage-gated potassium channels
family: Voltage-gated potassium channels
domain: Potassium channel-related protein MthK
species: Archaeon Methanothermobacter thermautotrophicus [TaxId: 145262]

 Score = 44.3 bits (105), Expect = 2e-06
 Identities = 10/38 (26%), Positives = 19/38 (50%)

Query: 30 GYGHIAPKTTLGKVATIFYAIVGIPLMLLCLSNIGDIM 67
          GYG  +P T LG   T+   ++GI    + +  + + +
Sbjct: 43 GYGDYSPSTPLGMYFTVTLIVLGIGTFAVAVERLLEFL 80

>d1p7ba2 f.14.1.1 (A:36-151) Inward rectifier potassium channel Kirbac1.1 {Burkholderia pseudomallei [TaxId: 28450]} Length = 116

class: Membrane and cell surface proteins and peptides
fold: Voltage-gated potassium channels
superfamily: Voltage-gated potassium channels
family: Voltage-gated potassium channels
domain: Inward rectifier potassium channel Kirbac1.1
species: Burkholderia pseudomallei [TaxId: 28450]

 Score = 47.7 bits (113), Expect = 2e-07
 Identities = 26/130 (20%), Positives = 46/130 (35%), Gaps = 29/130 (22%)

Query: 66  IMAHSFRFLYWKDFDFFTEYYDTKGVGNAEQIKPVPIWLCVFLVISYIIGGAFLFSHW-- 123
           ++A+      W+D  ++            +   PV       L +      A L+     
Sbjct: 3   VIAYGMPASVWRDLYYWA----------LKVSWPVFFASLAALFVVNNTLFALLYQLGDA 52

Query: 124 -----EPWGFPDSAYFCFITLTTIGFGDFVPAQKSTDVQTAEETAELRIALCSLYLLFGI 178
                 P GF  + +F   TL T+G+GD  P                  A+ +L +  G+
Sbjct: 53  PIANQSPPGFVGAFFFSVETLATVGYGDMHP------------QTVYAHAIATLEIFVGM 100

Query: 179 ALLAMSFNLV 188
           + +A+S  LV
Sbjct: 101 SGIALSTGLV 110

>d1p7ba2 f.14.1.1 (A:36-151) Inward rectifier potassium channel Kirbac1.1 {Burkholderia pseudomallei [TaxId: 28450]} Length = 116

class: Membrane and cell surface proteins and peptides
fold: Voltage-gated potassium channels
superfamily: Voltage-gated potassium channels
family: Voltage-gated potassium channels
domain: Inward rectifier potassium channel Kirbac1.1
species: Burkholderia pseudomallei [TaxId: 28450]

 Score = 37.7 bits (87), Expect = 8e-04
 Identities = 19/101 (18%), Positives = 38/101 (37%), Gaps = 17/101 (16%)

Query: 668 RFRVPIAVSFLIIISFILLGSLIFNK-------LENWTFLDGTFFCFTSLGTIGFGELIP 720
            + V  A    + +    L +L++              F+   FF   +L T+G+G++ P
Sbjct: 24  SWPVFFASLAALFVVNNTLFALLYQLGDAPIANQSPPGFVGAFFFSVETLATVGYGDMHP 83

Query: 721 GESYDRTLRGNKNISVLVSSSYILVGMAVISMCFNLIQEEI 761
              Y             +++  I VGM+ I++   L+    
Sbjct: 84  QTVYAH----------AIATLEIFVGMSGIALSTGLVFARF 114

>d1xl4a2 f.14.1.1 (A:23-138) Inward rectifier potassium channel kirbac3.1 {Magnetospirillum magnetotacticum [TaxId: 188]} Length = 116

class: Membrane and cell surface proteins and peptides
fold: Voltage-gated potassium channels
superfamily: Voltage-gated potassium channels
family: Voltage-gated potassium channels
domain: Inward rectifier potassium channel kirbac3.1
species: Magnetospirillum magnetotacticum [TaxId: 188]

 Score = 45.0 bits (106), Expect = 3e-06
 Identities = 22/92 (23%), Positives = 39/92 (42%), Gaps = 17/92 (18%)

Query: 102 IWLCVFLVISYIIGGAFLFSHW-----EPWGFPDSAYFCFITLTTIGFGDFVPAQKSTDV 156
           +   ++LV + +   A+L          P  F D+ +F   T+ TIG+G  +P       
Sbjct: 30  LITGLYLVTNALFALAYLACGDVIENARPGSFTDAFFFSVQTMATIGYGKLIP------- 82

Query: 157 QTAEETAELRIALCSLYLLFGIALLAMSFNLV 188
                   L   L +L  L G+  LA++ +L+
Sbjct: 83  -----IGPLANTLVTLEALCGMLGLAVAASLI 109

>d1xl4a2 f.14.1.1 (A:23-138) Inward rectifier potassium channel kirbac3.1 {Magnetospirillum magnetotacticum [TaxId: 188]} Length = 116

class: Membrane and cell surface proteins and peptides
fold: Voltage-gated potassium channels
superfamily: Voltage-gated potassium channels
family: Voltage-gated potassium channels
domain: Inward rectifier potassium channel kirbac3.1
species: Magnetospirillum magnetotacticum [TaxId: 188]

 Score = 38.4 bits (89), Expect = 5e-04
 Identities = 20/101 (19%), Positives = 38/101 (37%), Gaps = 17/101 (16%)

Query: 668 RFRVPIAVSFLIIISFILLGSLIFNKLEN-------WTFLDGTFFCFTSLGTIGFGELIP 720
            + V I +   + +    L +L +    +        +F D  FF   ++ TIG+G+LIP
Sbjct: 23  SWPVFITLITGLYLVTNALFALAYLACGDVIENARPGSFTDAFFFSVQTMATIGYGKLIP 82

Query: 721 GESYDRTLRGNKNISVLVSSSYILVGMAVISMCFNLIQEEI 761
                            + +   L GM  +++  +LI    
Sbjct: 83  IGPLAN----------TLVTLEALCGMLGLAVAASLIYARF 113

>d1r3jc_ f.14.1.1 (C:) Potassium channel protein {Streptomyces coelicolor [TaxId: 1902]} Length = 103

class: Membrane and cell surface proteins and peptides
fold: Voltage-gated potassium channels
superfamily: Voltage-gated potassium channels
family: Voltage-gated potassium channels
domain: Potassium channel protein
species: Streptomyces coelicolor [TaxId: 1902]

 Score = 42.6 bits (100), Expect = 1e-05
 Identities = 17/108 (15%), Positives = 37/108 (34%), Gaps = 19/108 (17%)

Query: 102 IWLCVFLVISYIIGGAFLFSHWEPWG-------FPDSAYFCFITLTTIGFGDFVPAQKST 154
                 L++  ++ G++L    E          +P + ++   T TT+G+GD  P     
Sbjct: 8   AGAATVLLVIVLLAGSYLAVLAERGAPGAQLITYPRALWWSVETATTVGYGDLYP----- 62

Query: 155 DVQTAEETAELRIALCSLYLLFGIALLAMSFNLVQEEVISNVKAIAKH 202
                  T   R  +  + ++ GI    +    +    +   +    H
Sbjct: 63  ------VTLWGRC-VAVVVMVAGITSFGLVTAALATWFVGREQERRGH 103

>d1r3jc_ f.14.1.1 (C:) Potassium channel protein {Streptomyces coelicolor [TaxId: 1902]} Length = 103

class: Membrane and cell surface proteins and peptides
fold: Voltage-gated potassium channels
superfamily: Voltage-gated potassium channels
family: Voltage-gated potassium channels
domain: Potassium channel protein
species: Streptomyces coelicolor [TaxId: 1902]

 Score = 39.5 bits (92), Expect = 1e-04
 Identities = 15/108 (13%), Positives = 38/108 (35%), Gaps = 16/108 (14%)

Query: 666 AFRFRVPIAVSFLIIISFILLGSLIF------NKLENWTFLDGTFFCFTSLGTIGFGELI 719
           A  +R   A + L++I  +    L           +  T+    ++   +  T+G+G+L 
Sbjct: 2   ALHWRAAGAATVLLVIVLLAGSYLAVLAERGAPGAQLITYPRALWWSVETATTVGYGDLY 61

Query: 720 PGESYDRTLRGNKNISVLVSSSYILVGMAVISMCFNLIQEEIIFMIKK 767
           P   + R           V+   ++ G+    +    +    +   ++
Sbjct: 62  PVTLWGR----------CVAVVVMVAGITSFGLVTAALATWFVGREQE 99

>d1qkla_ a.143.1.2 (A:) RPB6 {Human (Homo sapiens) [TaxId: 9606]} Length = 127

class: All alpha proteins
fold: RPB6/omega subunit-like
superfamily: RPB6/omega subunit-like
family: RPB6
domain: RPB6
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 39.4 bits (92), Expect = 3e-04
 Identities = 15/55 (27%), Positives = 27/55 (49%)

Query: 218 SDFDTSDEEYDSSEEEEEEEDEEEEEEEEEGEEEETETASSSTAKNDPQMVTVPI 272
           SD + + +  D  + EE+E  ++ E  EEEG+E      S    + + + +T P 
Sbjct: 2   SDNEDNFDGDDFDDVEEDEGLDDLENAEEEGQENVEILPSGERPQANQKRITTPY 56

>d1qkla_ a.143.1.2 (A:) RPB6 {Human (Homo sapiens) [TaxId: 9606]} Length = 127

class: All alpha proteins
fold: RPB6/omega subunit-like
superfamily: RPB6/omega subunit-like
family: RPB6
domain: RPB6
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 39.0 bits (91), Expect = 4e-04
 Identities = 13/52 (25%), Positives = 27/52 (51%)

Query: 461 EEEEEEEEDEEEEEEEEEEEEEEEEEEGEEEETETASSSTAKNDPQMVTVPI 512
           E+  + ++ ++ EE+E  ++ E  EEEG+E      S    + + + +T P 
Sbjct: 5   EDNFDGDDFDDVEEDEGLDDLENAEEEGQENVEILPSGERPQANQKRITTPY 56

>d2ayua1 d.305.1.1 (A:70-370) Nucleosome assembly protein, NAP {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]} Length = 301

class: Alpha and beta proteins (a+b)
fold: NAP-like
superfamily: NAP-like
family: NAP-like
domain: Nucleosome assembly protein, NAP
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

 Score = 40.8 bits (95), Expect = 4e-04
 Identities = 25/176 (14%), Positives = 50/176 (28%), Gaps = 23/176 (13%)

Query: 456 EYDSSEEEEEEEEDEEEEEEEEEEEEEEEEEEGEEEETETASSSTAKNDPQMVTVPITLC 515
           +     E+  + ++  E   E E   +EEE+   + E E      +     +  +PI +C
Sbjct: 73  QEQPKPEQIAKGQEIVESLNETELLVDEEEKAQNDSEEEQVKGIPSFWLTALENLPI-VC 131

Query: 516 LMIMVGYIYGGAVLFSKWEDWNILDGSYFCFISLSTIGFGDIVPGDKIT-----GKNNDI 570
             I                D  +L+        +      D  PG K+        N   
Sbjct: 132 DTI-------------TDRDAEVLE----YLQDIGLEYLTDGRPGFKLLFRFDSSANPFF 174

Query: 571 GVQTLELSFILCAMYLMLGMALIAMCFNLMQEEVVHKMRTCSEVTQRKSKQQQQQQ 626
               L  ++         G  +             +      ++  RK + +  +Q
Sbjct: 175 TNDILCKTYFYQKELGYSGDFIYDHAEGCEISWKDNAHNVTVDLEMRKQRNKTTKQ 230

>d1ofcx3 a.187.1.1 (X:697-798) HAND domain of the nucleosome remodeling ATPase ISWI {Fruit fly (Drosophila melanogaster) [TaxId: 7227]} Length = 102

class: All alpha proteins
fold: HAND domain of the nucleosome remodeling ATPase ISWI
superfamily: HAND domain of the nucleosome remodeling ATPase ISWI
family: HAND domain of the nucleosome remodeling ATPase ISWI
domain: HAND domain of the nucleosome remodeling ATPase ISWI
species: Fruit fly (Drosophila melanogaster) [TaxId: 7227]

 Score = 37.5 bits (87), Expect = 7e-04
 Identities = 12/67 (17%), Positives = 26/67 (38%), Gaps = 1/67 (1%)

Query: 422 YNRRRSSAMNHNRRWNARNGDSEYEDSDFDTSDEEYDSSEEEEEEEEDEEEEEEEEEEEE 481
           +  R    ++    +  +    +   +    SD       EE+ + ++ E   EEE +E+
Sbjct: 35  FPPRLFELLDQEIYYFRKTVGYKVPKNTELGSDAT-KVQREEQRKIDEAEPLTEEEIQEK 93

Query: 482 EEEEEEG 488
           E    +G
Sbjct: 94  ENLLSQG 100

Homologous Domains Detected by HHsearch

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

ID	Length	Definition	Probability
Query	790
d1r3jc_	103	Potassium channel protein {Streptomyces coelicolor	99.62
d1lnqa2	80	Potassium channel-related protein MthK {Archaeon M	99.54
d1lnqa2	80	Potassium channel-related protein MthK {Archaeon M	99.46
d1r3jc_	103	Potassium channel protein {Streptomyces coelicolor	99.46
d1p7ba2	116	Inward rectifier potassium channel Kirbac1.1 {Burk	99.3
d1xl4a2	116	Inward rectifier potassium channel kirbac3.1 {Magn	99.27
d1p7ba2	116	Inward rectifier potassium channel Kirbac1.1 {Burk	99.08
d1xl4a2	116	Inward rectifier potassium channel kirbac3.1 {Magn	99.03
d2h8pc1	57	Potassium channel protein {Streptomyces coelicolor	98.25
d2h8pc1	57	Potassium channel protein {Streptomyces coelicolor	97.22

>d1r3jc_ f.14.1.1 (C:) Potassium channel protein {Streptomyces coelicolor [TaxId: 1902]}

class: Membrane and cell surface proteins and peptides
fold: Voltage-gated potassium channels
superfamily: Voltage-gated potassium channels
family: Voltage-gated potassium channels
domain: Potassium channel protein
species: Streptomyces coelicolor [TaxId: 1902]

Probab=99.62  E-value=2.1e-16  Score=139.64  Aligned_cols=88  Identities=15%  Similarity=0.290  Sum_probs=77.5

Q ss_pred             HHHHHHHHHHHHHHHHHHHHhhhhhcC-------CCccchhhheeeeeeccccCCcccCCCcccccccccchhhHHHHHH
Q psy17959        670 RVPIAVSFLIIISFILLGSLIFNKLEN-------WTFLDGTFFCFTSLGTIGFGELIPGESYDRTLRGNKNISVLVSSSY  742 (790)
Q Consensus       670 ~~~~~~~~~~~~~~~~~g~~~~~~~e~-------~s~~da~Y~~~vt~tTVGyGD~~p~t~~gr~~~~~~~~~~~~~~~~  742 (790)
                      ++.+..+++++++++++++..++..|+       .++.||+||+++|+|||||||++|.|+.||          ++++++
T Consensus         5 ~r~~~~~~~~~~~~~~~~s~~~~~~e~~~~~~~~~s~~~aly~~~vT~tTvGYGDi~P~t~~gr----------~~~~~~   74 (103)
T d1r3jc_           5 WRAAGAATVLLVIVLLAGSYLAVLAERGAPGAQLITYPRALWWSVETATTVGYGDLYPVTLWGR----------CVAVVV   74 (103)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHTTSTTCCCCSHHHHHHHHHHHHTTCCCSSSCCCSHHHH----------HHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHhccCCCcccCchhhhhhhheeeecccccCccccCChhHH----------HHHHHH
Confidence            445556666777778889999999885       489999999999999999999999999999          899999


Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHH
Q psy17959        743 ILVGMAVISMCFNLIQEEIIFMIKK  767 (790)
Q Consensus       743 ~~~g~~~~~~~~~~i~~~~~~~~~~  767 (790)
                      ++.|++++++.++.+++.+..+.++
T Consensus        75 ~~~Gi~~~~~~~~~i~~~~~~~~~~   99 (103)
T d1r3jc_          75 MVAGITSFGLVTAALATWFVGREQE   99 (103)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            9999999999999999998876554

>d1lnqa2 f.14.1.1 (A:19-98) Potassium channel-related protein MthK {Archaeon Methanothermobacter thermautotrophicus [TaxId: 145262]}

class: Membrane and cell surface proteins and peptides
fold: Voltage-gated potassium channels
superfamily: Voltage-gated potassium channels
family: Voltage-gated potassium channels
domain: Potassium channel-related protein MthK
species: Archaeon Methanothermobacter thermautotrophicus [TaxId: 145262]

Probab=99.54  E-value=3.8e-17  Score=137.43  Aligned_cols=71  Identities=17%  Similarity=0.494  Sum_probs=65.9

Q ss_pred             HHHHHHHHHHHhhhhhcCCCccchhhheeeeeeccccCCcccCCCcccccccccchhhHHHHHHHHHHHHHHHHHHHHHH
Q psy17959        679 IIISFILLGSLIFNKLENWTFLDGTFFCFTSLGTIGFGELIPGESYDRTLRGNKNISVLVSSSYILVGMAVISMCFNLIQ  758 (790)
Q Consensus       679 ~~~~~~~~g~~~~~~~e~~s~~da~Y~~~vt~tTVGyGD~~p~t~~gr~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~i~  758 (790)
                      +++.++++|+.+|+..|+|||+||+||+++|+|||||||++|.|+.||          ++++++++.|++++++.++.++
T Consensus         8 ~~~~~~~~g~~~~~~~e~~s~~dalyf~~~T~tTiGyGD~~P~t~~~r----------~~~~~~~l~g~~~~~~~i~~i~   77 (80)
T d1lnqa2           8 LVLAVIIYGTAGFHFIEGESWTVSLYWTFVTIATVGYGDYSPSTPLGM----------YFTVTLIVLGIGTFAVAVERLL   77 (80)
T ss_dssp             TTTTSHHHHTTTTTTSSSCCSSTTHHHHHHHHTTCCCSSCCCCCSSHH----------HHHTHHHHTTSTTTTTHHHHHT
T ss_pred             HHHHHHHHHHHHHHHHhCCCHHHHHHHHhhheeeccCCCCCCCCcchH----------HHHHHHHHHHHHHHHHHHHHHH
Confidence            455567789999999999999999999999999999999999999999          8999999999999999999887


Q ss_pred             H
Q psy17959        759 E  759 (790)
Q Consensus       759 ~  759 (790)
                      +
T Consensus        78 ~   78 (80)
T d1lnqa2          78 E   78 (80)
T ss_dssp             T
T ss_pred             H
Confidence            5

>d1lnqa2 f.14.1.1 (A:19-98) Potassium channel-related protein MthK {Archaeon Methanothermobacter thermautotrophicus [TaxId: 145262]}

class: Membrane and cell surface proteins and peptides
fold: Voltage-gated potassium channels
superfamily: Voltage-gated potassium channels
family: Voltage-gated potassium channels
domain: Potassium channel-related protein MthK
species: Archaeon Methanothermobacter thermautotrophicus [TaxId: 145262]

Probab=99.46  E-value=4.5e-16  Score=130.77  Aligned_cols=71  Identities=28%  Similarity=0.516  Sum_probs=64.3

Q ss_pred             HHHHHHHHHhHHhhcccCCCCccceeeeeeecccccccccccCCCCcchhhhhhhhhhhHHHHHHHHHHHHHHHHHHHHH
Q psy17959        108 LVISYIIGGAFLFSHWEPWGFPDSAYFCFITLTTIGFGDFVPAQKSTDVQTAEETAELRIALCSLYLLFGIALLAMSFNL  187 (790)
Q Consensus       108 ~~~~~i~~ga~~~~~~e~wsf~da~Yf~~iTltTIGfGDi~P~~~~~~~~~~~~~~~~~~~~~~~~~l~Gl~~~~~~i~~  187 (790)
                      +++.++++|+..|+..|+|+|.||+||+++|+|||||||++|.++.            +|+++++++++|+.+++++++.
T Consensus         8 ~~~~~~~~g~~~~~~~e~~s~~dalyf~~~T~tTiGyGD~~P~t~~------------~r~~~~~~~l~g~~~~~~~i~~   75 (80)
T d1lnqa2           8 LVLAVIIYGTAGFHFIEGESWTVSLYWTFVTIATVGYGDYSPSTPL------------GMYFTVTLIVLGIGTFAVAVER   75 (80)
T ss_dssp             TTTTSHHHHTTTTTTSSSCCSSTTHHHHHHHHTTCCCSSCCCCCSS------------HHHHHTHHHHTTSTTTTTHHHH
T ss_pred             HHHHHHHHHHHHHHHHhCCCHHHHHHHHhhheeeccCCCCCCCCcc------------hHHHHHHHHHHHHHHHHHHHHH
Confidence            3445678899999999999999999999999999999999999876            8999999999999999999887


Q ss_pred             HHH
Q psy17959        188 VQE  190 (790)
Q Consensus       188 i~~  190 (790)
                      +.+
T Consensus        76 i~~   78 (80)
T d1lnqa2          76 LLE   78 (80)
T ss_dssp             HTT
T ss_pred             HHH
Confidence            654

>d1r3jc_ f.14.1.1 (C:) Potassium channel protein {Streptomyces coelicolor [TaxId: 1902]}

class: Membrane and cell surface proteins and peptides
fold: Voltage-gated potassium channels
superfamily: Voltage-gated potassium channels
family: Voltage-gated potassium channels
domain: Potassium channel protein
species: Streptomyces coelicolor [TaxId: 1902]

Probab=99.46  E-value=1.5e-14  Score=127.44  Aligned_cols=83  Identities=17%  Similarity=0.339  Sum_probs=69.1

Q ss_pred             HHHHHHHHHHHHHhHHhhcccC-------CCCccceeeeeeecccccccccccCCCCcchhhhhhhhhhhHHHHHHHHHH
Q psy17959        104 LCVFLVISYIIGGAFLFSHWEP-------WGFPDSAYFCFITLTTIGFGDFVPAQKSTDVQTAEETAELRIALCSLYLLF  176 (790)
Q Consensus       104 ~~~~~~~~~i~~ga~~~~~~e~-------wsf~da~Yf~~iTltTIGfGDi~P~~~~~~~~~~~~~~~~~~~~~~~~~l~  176 (790)
                      ..++++++.+++++.++...|+       .+|.||+||+++|+|||||||++|.+..            +|+++.+++++
T Consensus        10 ~~~~~~~~~~~~~s~~~~~~e~~~~~~~~~s~~~aly~~~vT~tTvGYGDi~P~t~~------------gr~~~~~~~~~   77 (103)
T d1r3jc_          10 AATVLLVIVLLAGSYLAVLAERGAPGAQLITYPRALWWSVETATTVGYGDLYPVTLW------------GRCVAVVVMVA   77 (103)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHTTSTTCCCCSHHHHHHHHHHHHTTCCCSSSCCCSHH------------HHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHhccCCCcccCchhhhhhhheeeecccccCccccCChh------------HHHHHHHHHHH
Confidence            3444455566777777777764       4689999999999999999999999765            89999999999


Q ss_pred             HHHHHHHHHHHHHHHHHHHHHH
Q psy17959        177 GIALLAMSFNLVQEEVISNVKA  198 (790)
Q Consensus       177 Gl~~~~~~i~~i~~~~~~~~~~  198 (790)
                      |+.+++++++.+.+.+.++.++
T Consensus        78 Gi~~~~~~~~~i~~~~~~~~~~   99 (103)
T d1r3jc_          78 GITSFGLVTAALATWFVGREQE   99 (103)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHH
Confidence            9999999999999988876543

>d1p7ba2 f.14.1.1 (A:36-151) Inward rectifier potassium channel Kirbac1.1 {Burkholderia pseudomallei [TaxId: 28450]}

class: Membrane and cell surface proteins and peptides
fold: Voltage-gated potassium channels
superfamily: Voltage-gated potassium channels
family: Voltage-gated potassium channels
domain: Inward rectifier potassium channel Kirbac1.1
species: Burkholderia pseudomallei [TaxId: 28450]

Probab=99.30  E-value=7.5e-13  Score=119.09  Aligned_cols=76  Identities=22%  Similarity=0.408  Sum_probs=62.9

Q ss_pred             HHHHHHHHHHHHHHhhhhhc-------CCCccchhhheeeeeeccccCCcccCCCcccccccccchhhHHHHHHHHHHHH
Q psy17959        676 SFLIIISFILLGSLIFNKLE-------NWTFLDGTFFCFTSLGTIGFGELIPGESYDRTLRGNKNISVLVSSSYILVGMA  748 (790)
Q Consensus       676 ~~~~~~~~~~~g~~~~~~~e-------~~s~~da~Y~~~vt~tTVGyGD~~p~t~~gr~~~~~~~~~~~~~~~~~~~g~~  748 (790)
                      .++..+++++++++.|+..+       .++|.||+||+++|+|||||||++|.++.||          +++++++++|++
T Consensus        32 ~~~~~~~~~~~fa~~y~~~~~~~~~~~~~~~~~a~yfs~~T~tTvGYGDi~P~t~~~~----------~~~~~~~~~g~~  101 (116)
T d1p7ba2          32 LAALFVVNNTLFALLYQLGDAPIANQSPPGFVGAFFFSVETLATVGYGDMHPQTVYAH----------AIATLEIFVGMS  101 (116)
T ss_dssp             HHHHHHHHHHHHHTTTSSSSSCCCCSSSSSTHHHHHHHTTTTTTCCCSCCCCCSHHHH----------HHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHhhcccCCCCCCCHHHHHHHHHHHHHhccccccccCCcHHH----------HHHHHHHHHHHH
Confidence            33345555566677765532       4799999999999999999999999999999          889999999999


Q ss_pred             HHHHHHHHHHHHH
Q psy17959        749 VISMCFNLIQEEI  761 (790)
Q Consensus       749 ~~~~~~~~i~~~~  761 (790)
                      ++++.++.+...+
T Consensus       102 ~~a~~~g~i~~~~  114 (116)
T d1p7ba2         102 GIALSTGLVFARF  114 (116)
T ss_dssp             HHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHH
Confidence            9999999887554

>d1xl4a2 f.14.1.1 (A:23-138) Inward rectifier potassium channel kirbac3.1 {Magnetospirillum magnetotacticum [TaxId: 188]}

class: Membrane and cell surface proteins and peptides
fold: Voltage-gated potassium channels
superfamily: Voltage-gated potassium channels
family: Voltage-gated potassium channels
domain: Inward rectifier potassium channel kirbac3.1
species: Magnetospirillum magnetotacticum [TaxId: 188]

Probab=99.27  E-value=1.2e-12  Score=117.78  Aligned_cols=75  Identities=24%  Similarity=0.324  Sum_probs=62.1

Q ss_pred             HHHHHHHHHHHHHhhhhhc-------CCCccchhhheeeeeeccccCCcccCCCcccccccccchhhHHHHHHHHHHHHH
Q psy17959        677 FLIIISFILLGSLIFNKLE-------NWTFLDGTFFCFTSLGTIGFGELIPGESYDRTLRGNKNISVLVSSSYILVGMAV  749 (790)
Q Consensus       677 ~~~~~~~~~~g~~~~~~~e-------~~s~~da~Y~~~vt~tTVGyGD~~p~t~~gr~~~~~~~~~~~~~~~~~~~g~~~  749 (790)
                      ++..++.+++.++++...+       .++|.||+||+++|+|||||||++|.++.||          ++++++++.|+.+
T Consensus        32 ~~~~~~~~~~fa~~y~~~~~~~~~~~~~~~~~a~yfs~~T~tTvGYGDi~P~t~~~r----------~~~~~~~~~G~~~  101 (116)
T d1xl4a2          32 TGLYLVTNALFALAYLACGDVIENARPGSFTDAFFFSVQTMATIGYGKLIPIGPLAN----------TLVTLEALCGMLG  101 (116)
T ss_dssp             HHHHHHHHHHHHHHHHHTCSCSTTSCTTCHHHHHHHHHHHHTTCCCSSSCCCHHHHH----------HHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHhhcCCCCCCCCHHHHHHHHHHHHccCCCCccccCCcHHH----------HHHHHHHHHHHHH
Confidence            3334455556666665543       3799999999999999999999999999999          8999999999999


Q ss_pred             HHHHHHHHHHHH
Q psy17959        750 ISMCFNLIQEEI  761 (790)
Q Consensus       750 ~~~~~~~i~~~~  761 (790)
                      +++.++.+...+
T Consensus       102 ~a~~~g~i~~~f  113 (116)
T d1xl4a2         102 LAVAASLIYARF  113 (116)
T ss_dssp             HHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHh
Confidence            999999887654

>d1p7ba2 f.14.1.1 (A:36-151) Inward rectifier potassium channel Kirbac1.1 {Burkholderia pseudomallei [TaxId: 28450]}

class: Membrane and cell surface proteins and peptides
fold: Voltage-gated potassium channels
superfamily: Voltage-gated potassium channels
family: Voltage-gated potassium channels
domain: Inward rectifier potassium channel Kirbac1.1
species: Burkholderia pseudomallei [TaxId: 28450]

Probab=99.08  E-value=3.6e-11  Score=107.86  Aligned_cols=56  Identities=32%  Similarity=0.549  Sum_probs=51.1

Q ss_pred             CCCCccceeeeeeecccccccccccCCCCcchhhhhhhhhhhHHHHHHHHHHHHHHHHHHHHHHHHHH
Q psy17959        125 PWGFPDSAYFCFITLTTIGFGDFVPAQKSTDVQTAEETAELRIALCSLYLLFGIALLAMSFNLVQEEV  192 (790)
Q Consensus       125 ~wsf~da~Yf~~iTltTIGfGDi~P~~~~~~~~~~~~~~~~~~~~~~~~~l~Gl~~~~~~i~~i~~~~  192 (790)
                      .++|.||+||+++|+|||||||++|.+..            +++++.+.+++|+.+++++++.+..++
T Consensus        59 ~~~~~~a~yfs~~T~tTvGYGDi~P~t~~------------~~~~~~~~~~~g~~~~a~~~g~i~~~~  114 (116)
T d1p7ba2          59 PPGFVGAFFFSVETLATVGYGDMHPQTVY------------AHAIATLEIFVGMSGIALSTGLVFARF  114 (116)
T ss_dssp             SSSTHHHHHHHTTTTTTCCCSCCCCCSHH------------HHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             CCCHHHHHHHHHHHHHhccccccccCCcH------------HHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            57899999999999999999999998654            889999999999999999999887765

>d1xl4a2 f.14.1.1 (A:23-138) Inward rectifier potassium channel kirbac3.1 {Magnetospirillum magnetotacticum [TaxId: 188]}

class: Membrane and cell surface proteins and peptides
fold: Voltage-gated potassium channels
superfamily: Voltage-gated potassium channels
family: Voltage-gated potassium channels
domain: Inward rectifier potassium channel kirbac3.1
species: Magnetospirillum magnetotacticum [TaxId: 188]

Probab=99.03  E-value=5.9e-11  Score=106.45  Aligned_cols=56  Identities=30%  Similarity=0.521  Sum_probs=50.7

Q ss_pred             CCCCccceeeeeeecccccccccccCCCCcchhhhhhhhhhhHHHHHHHHHHHHHHHHHHHHHHHHHH
Q psy17959        125 PWGFPDSAYFCFITLTTIGFGDFVPAQKSTDVQTAEETAELRIALCSLYLLFGIALLAMSFNLVQEEV  192 (790)
Q Consensus       125 ~wsf~da~Yf~~iTltTIGfGDi~P~~~~~~~~~~~~~~~~~~~~~~~~~l~Gl~~~~~~i~~i~~~~  192 (790)
                      .++|.||+||+++|+|||||||++|.+..            +++++.++++.|+.+.++.++.+...+
T Consensus        58 ~~~~~~a~yfs~~T~tTvGYGDi~P~t~~------------~r~~~~~~~~~G~~~~a~~~g~i~~~f  113 (116)
T d1xl4a2          58 PGSFTDAFFFSVQTMATIGYGKLIPIGPL------------ANTLVTLEALCGMLGLAVAASLIYARF  113 (116)
T ss_dssp             TTCHHHHHHHHHHHHTTCCCSSSCCCHHH------------HHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             CCCHHHHHHHHHHHHccCCCCccccCCcH------------HHHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence            46899999999999999999999998654            899999999999999999999887765

>d2h8pc1 f.14.1.1 (C:22-78) Potassium channel protein {Streptomyces coelicolor [TaxId: 1902]}

class: Membrane and cell surface proteins and peptides
fold: Voltage-gated potassium channels
superfamily: Voltage-gated potassium channels
family: Voltage-gated potassium channels
domain: Potassium channel protein
species: Streptomyces coelicolor [TaxId: 1902]

Probab=98.25  E-value=1.7e-07  Score=71.11  Aligned_cols=46  Identities=15%  Similarity=0.315  Sum_probs=38.2

Q ss_pred             HHHHHHHHHHHHHHHHHHHHhhhhhcC-------CCccchhhheeeeeecccc
Q psy17959        670 RVPIAVSFLIIISFILLGSLIFNKLEN-------WTFLDGTFFCFTSLGTIGF  715 (790)
Q Consensus       670 ~~~~~~~~~~~~~~~~~g~~~~~~~e~-------~s~~da~Y~~~vt~tTVGy  715 (790)
                      ++.+..+++++++++++++.++++.|+       -|+.||+||+++|+|||||
T Consensus         5 ~R~~~~~~~~~~i~i~~~s~~~y~~E~~~~~~~f~sip~a~WWaivT~TTVGY   57 (57)
T d2h8pc1           5 WRAAGAATVLLVIVLLAGSYLAVLAERGAPGAQLITYPRALWWACETATTVGY   57 (57)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHTTSTTCCCCSHHHHHHHHHHHHTTCCC
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHhcCCCCccccccchhhhhheeeeecccC
Confidence            345666777777777888888888884       4899999999999999998

>d2h8pc1 f.14.1.1 (C:22-78) Potassium channel protein {Streptomyces coelicolor [TaxId: 1902]}

class: Membrane and cell surface proteins and peptides
fold: Voltage-gated potassium channels
superfamily: Voltage-gated potassium channels
family: Voltage-gated potassium channels
domain: Potassium channel protein
species: Streptomyces coelicolor [TaxId: 1902]

Probab=97.22  E-value=2.6e-05  Score=58.89  Aligned_cols=39  Identities=23%  Similarity=0.513  Sum_probs=26.0

Q ss_pred             HHHHHHHHHHHhHHhhccc------CC-CCccceeeeeeecccccc
Q psy17959        106 VFLVISYIIGGAFLFSHWE------PW-GFPDSAYFCFITLTTIGF  144 (790)
Q Consensus       106 ~~~~~~~i~~ga~~~~~~e------~w-sf~da~Yf~~iTltTIGf  144 (790)
                      ++++++.+++++.+....|      +. |+.||+||+++|+|||||
T Consensus        12 ~~~~~i~i~~~s~~~y~~E~~~~~~~f~sip~a~WWaivT~TTVGY   57 (57)
T d2h8pc1          12 TVLLVIVLLAGSYLAVLAERGAPGAQLITYPRALWWACETATTVGY   57 (57)
T ss_dssp             HHHHHHHHHHHHHHHHHHHTTSTTCCCCSHHHHHHHHHHHHTTCCC
T ss_pred             HHHHHHHHHHHHHHHHHHhcCCCCccccccchhhhhheeeeecccC
Confidence            3333344444444444445      23 589999999999999998