Citrus Sinensis ID: 040027

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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-----
Protein Sequence
MGLESCCNRSFSFASAPISAFRSNFSSLLVHFRDLTTREGDINVITPNEAFCIFDYMLRMHPSPPPVSSFNILLASLAKNKHYDTRLNATGLFPNLYTYNILINCFCKIGRVSLGFIAFGRILRSCFTPNAATFNSLIKGLHAESRIMEAAALFTKLKAFGCEPNVITYNTLINGLCRTGHTMIALNLFEEMANGNGEIGVVCKPNTVTYSTIIDGLCKEGFVDKAKALFLQMKDENINPDVVTYNSLIHGLCHANDWNEAKRLFIEMMDQGVQPSVVTFNVIMDELCKNRKMDEASRLLDLMVQRGVRPNACTYNTLMDGFCLMGKINRAEELFGSMESMGCKHDDVSYNILINGYCKNKEVEEALSLYREMVSKGIKPTVVTYNTLFLGLFEIHQVEHALKLFDEMQRDGVAADTRTYTTFIDGLCKNGYIIEAVELFRTLRILKCELDIQAYNCLIDGLCKSGRLKFAWELFCSLPHGVLVPNVVTYNIMIQGLCNDGQMDKARDLFLDMEENAAAPDVITFDMLIHGFIRINEPSKVNELLHKMKEKKVMPDASIVSIVVDLLVKNEISLKSLPSFLVQERQGEVGESNVK
Secondary Structure (PSIPRED)
cccccccccccccccccccccccccccHHHHHHHHHHHccccccccHHHHHHHHHHHHHcccccccHHHHHHHHHHHHHcccHHHHHHHccccccHHHHHHHHHHHHHcccHHHHHHHHHHHHHccccccHHHHHHHHHHHHHcccHHHHHHHHHHHHHcccccccccHHHHHHHHHHcccHHHHHHHHHHHHHcccccccccccccEEHHHHHHHHHccccHHHHHHHHHHHHHcccccccccHHHHHHHHHccccHHHHHHHHHHHHHccccccHHHHHHHHHHHHHcccHHHHHHHHHHHHHccccccHHHHHHHHHHHHccccHHHHHHHHHHHHHccccccHHHHHHHHHHHHHcccHHHHHHHHHHHHHccccccHHHHHHHHHHHHHcccHHHHHHHHHHHHHccccccHHHHHHHHHHHHHcccHHHHHHHHHHHHHccccccHHHHHHHHHHHHHcccHHHHHHHHHHcccccccccHHHHHHHHHHHHHcccHHHHHHHHHHHHHccccccHHHHHHHHHHHHHcccHHHHHHHHHHHHHccccccHHHHHHHHHHHHHcccHHHHHHHHHHHHHcccccccccc
Secondary Structure Prediction (SSPRO)
cccccccccHHHHHHHHHHHHHcccccccHHHHHHHHHHHHHccccHHHHHHHHHHHHHHcccccccHHHHHHHHHHHHcccHHHHHHHcccccccHHHHHHHHHHHHcccHHHHHHHHHHHHHccccccEEEHHHHHHHHHHcccHHHHHHHHHHHHHccccccEEEHHHHHHHHHHcccHHHHHHHHHHHHHccccccccccccEEEHHHHHHHHHHcccHHHHHHHHHHHHHccccccEEEHHHHHHHHHHcccHHHHHHHHHHHHHccccccEEEHHHHHHHHHHcccHHHHHHHHHHHHHccccccEEEHHHHHHHHHHcccHHHHHHHHHHHHHccccccEEEHHHHHHHHHHcccHHHHHHHHHHHHHccccccEEEHHHHHHHHHHcccHHHHHHHHHHHHHccccccEEEHHHHHHHHHHcccHHHHHHHHHHHHHccccccEEEHHHHHHHHHHcccHHHHHHHHHHHHHccccccEHHHHHHHHHHHHcccHHHHHHHHHHHHHcccccccHHHHHHHHHHHHcccHHHHHHHHHHHHHccccccHHHHHHHHHHHHHcccHHHHHHHHHHHHHcccccccccc
Coil and Loop (DISEMBL)
mglesccnrsfsfasapisAFRSNFSSLLVHFRdlttregdinvitpneafCIFDymlrmhpspppvssFNILLASLAknkhydtrlnatglfpnlytyNILINCFCKIGRVSLGFIAFGRIlrscftpnaaTFNSLIKGLHAESRIMEAAALFTKLkafgcepnvitYNTLINGLCRTGHTMIALNLFEEmangngeigvvckpntvtYSTIIDGLCKEGFVDKAKALFLQMkdeninpdvvtyNSLIHGLCHANDWNEAKRLFIEMMdqgvqpsvVTFNVIMDELCKNRKMDEASRLLDLMVQrgvrpnactyntlmdgFCLMGKINRAEELFgsmesmgckhddvsyNILINGYCKNKEVEEALSLYREMVSKGIKPTVVTYNTLFLGLFEIHQVEHALKLFDEMQRDGVAADTRTYTTFIDGLCKNGYIIEAVELFRTLRILKCELDIQAYNCLIDGLCKSGRLKFAWELFCslphgvlvpnvVTYNIMIQGLCNDGQMDKARDLFLDMeenaaapdvitfdMLIHGFIRINEPSKVNELLHKMKekkvmpdasIVSIVVDLLVKNEISLKSLPSflvqerqgevgesnvk
Flexible Loop (DISEMBL)
MGLESCCNRSFSFASAPISAFRSNFSSLLVHFRDLTtregdinvitpNEAFCIFDYMLRMHPSPPPVSSFNILLASLAKNKHYDTRLNATGLFPNLYTYNILINCFCKIGRVSLGFIAFGRILRSCFTPNAATFNSLIKGLHAESRIMEAAALFTKLKAFGCEPNVITYNTLINGLCRTGHTMIALNLFEEMANGNGEIGVVCKPNTVTYSTIIDGLCKEGFVDKAKALFLQMKDENINPDVVTYNSLIHGLCHANDWNEAKRLFIEMMDQGVQPSVVTFNVIMDELCKNRKMDEASRLLDLMVQRGVRPNACTYNTLMDGFCLMGKINRAEELFGSMESMGCKHDDVSYNILINGYCKNKEVEEALSLYREMVSKGIKPTVVTYNTLFLGLFEIHQVEHALKLFDEMQRDGVAADTRTYTTFIDGLCKNGYIIEAVELFRTLRILKCELDIQAYNCLIDGLCKSGRLKFAWELFCSLPHGVLVPNVVTYNIMIQGLCNDGQMDKARDLFLDMEENAAAPDVITFDMLIHGFIRINEPSKVNELLHKMKekkvmpdaSIVSIVVDLLVKNEislkslpsflvqerqgevgesnvk
Low Complexity Region (SEG)
MGLESCCNRsfsfasapisafrsNFSSLLVHFRDLTTREGDINVITPNEAFCIFDYMLRMHPSPPPVSSFNILLASLAKNKHYDTRLNATGLFPNLYTYNILINCFCKIGRVSLGFIAFGRILRSCFTPNAATFNSLIKGLHAESRIMEAAALFTKLKAFGCEPNVITYNTLINGLCRTGHTMIALNLFEEMANGNGEIGVVCKPNTVTYSTIIDGLCKEGFVDKAKALFLQMKDENINPDVVTYNSLIHGLCHANDWNEAKRLFIEMMDQGVQPSVVTFNVIMDELCKNRKMDEASRLLDLMVQRGVRPNACTYNTLMDGFCLMGKINRAEELFGSMESMGCKHDDVSYNILINGYCKNKEVEEALSLYREMVSKGIKPTVVTYNTLFLGLFEIHQVEHALKLFDEMQRDGVAADTRTYTTFIDGLCKNGYIIEAVELFRTLRILKCELDIQAYNCLIDGLCKSGRLKFAWELFCSLPHGVLVPNVVTYNIMIQGLCNDGQMDKARDLFLDMEENAAAPDVITFDMLIHGFIRINEPSKVNELLHKMKEKKVMPDASIVSIVVDLLVKNEISLKSLPSFLVQERQGEVGESNVK
Disordered region (IsUnstruct)
*****CCNRSFSFASAPISAFRSNFSSLLVHFRDLTTREGDINVITPNEAFCIFDYML***********FNILLASLAKNKHYDTRLNATGLFPNLYTYNILINCFCKIGRVSLGFIAFGRILRSCFTPNAATFNSLIKGLHAESRIMEAAALFTKLKAFGCEPNVITYNTLINGLCRTGHTMIALNLFEEMANGNGEIGVVCKPNTVTYSTIIDGLCKEGFVDKAKALFLQMKDENINPDVVTYNSLIHGLCHANDWNEAKRLFIEMMDQGVQPSVVTFNVIMDELCKNRKMDEASRLLDLMVQRGVRPNACTYNTLMDGFCLMGKINRAEELFGSMESMGCKHDDVSYNILINGYCKNKEVEEALSLYREMVSKGIKPTVVTYNTLFLGLFEIHQVEHALKLFDEMQRDGVAADTRTYTTFIDGLCKNGYIIEAVELFRTLRILKCELDIQAYNCLIDGLCKSGRLKFAWELFCSLPHGVLVPNVVTYNIMIQGLCNDGQMDKARDLFLDMEENAAAPDVITFDMLIHGFIRINEPSKVNELLHKMKEKKVMPDASIVSIVVDLLVKNEISLKSLPSFL**************
Disordered Region (DISOPRED)
************************FSSLLVHFRDLTTREGDINVITPNEAFCIFDYMLRMHPSPPPVSSFNILLASLAKNKHYDTRLNATGLFPNLYTYNILINCFCKIGRVSLGFIAFGRILRSCFTPNAATFNSLIKGLHAESRIMEAAALFTKLKAFGCEPNVITYNTLINGLCRTGHTMIALNLFEEMANGNGEIGVVCKPNTVTYSTIIDGLCKEGFVDKAKALFLQMKDENINPDVVTYNSLIHGLCHANDWNEAKRLFIEMMDQGVQPSVVTFNVIMDELCKNRKMDEASRLLDLMVQRGVRPNACTYNTLMDGFCLMGKINRAEELFGSMESMGCKHDDVSYNILINGYCKNKEVEEALSLYREMVSKGIKPTVVTYNTLFLGLFEIHQVEHALKLFDEMQRDGVAADTRTYTTFIDGLCKNGYIIEAVELFRTLRILKCELDIQAYNCLIDGLCKSGRLKFAWELFCSLPHGVLVPNVVTYNIMIQGLCNDGQMDKARDLFLDMEENAAAPDVITFDMLIHGFIRINEPSKVNELLHKMKEKKVMPDASIVSIVVDLLVKNEISLKSLPSFLVQERQGEVGE****
Disordered Region (DISEMBL)
MGLESCCNRSFSFASAPISAFRSNFSSLLVHFRDLTTREGDINVITPNEAFCIFDYMLRMHPSPPPVSSFNILLASLAKNKHYDTRLNATGLFPNLYTYNILINCFCKIGRVSLGFIAFGRILRSCFTPNAATFNSLIKGLHAESRIMEAAALFTKLKAFGCEPNVITYNTLINGLCRTGHTMIALNLFEEMANGNGEIGVVCKPNTVTYSTIIDGLCKEGFVDKAKALFLQMKDENINPDVVTYNSLIHGLCHANDWNEAKRLFIEMMDQGVQPSVVTFNVIMDELCKNRKMDEASRLLDLMVQRGVRPNACTYNTLMDGFCLMGKINRAEELFGSMESMGCKHDDVSYNILINGYCKNKEVEEALSLYREMVSKGIKPTVVTYNTLFLGLFEIHQVEHALKLFDEMQRDGVAADTRTYTTFIDGLCKNGYIIEAVELFRTLRILKCELDIQAYNCLIDGLCKSGRLKFAWELFCSLPHGVLVPNVVTYNIMIQGLCNDGQMDKARDLFLDMEENAAAPDVITFDMLIHGFIRINEPSKVNELLHKMKEKKVMPDASIVSIVVDLLVKNEISLKSLPSFLVQ************
Disordered Region (DISPRO)
****SCCNRSFSFASAPISAFRSNFSSLLVHFRDLTTREGDINVITPNEAFCIFDYMLRMHPSPPPVSSFNILLASLAKNKHYDTRLNATGLFPNLYTYNILINCFCKIGRVSLGFIAFGRILRSCFTPNAATFNSLIKGLHAESRIMEAAALFTKLKAFGCEPNVITYNTLINGLCRTGHTMIALNLFEEMANGNGEIGVVCKPNTVTYSTIIDGLCKEGFVDKAKALFLQMKDENINPDVVTYNSLIHGLCHANDWNEAKRLFIEMMDQGVQPSVVTFNVIMDELCKNRKMDEASRLLDLMVQRGVRPNACTYNTLMDGFCLMGKINRAEELFGSMESMGCKHDDVSYNILINGYCKNKEVEEALSLYREMVSKGIKPTVVTYNTLFLGLFEIHQVEHALKLFDEMQRDGVAADTRTYTTFIDGLCKNGYIIEAVELFRTLRILKCELDIQAYNCLIDGLCKSGRLKFAWELFCSLPHGVLVPNVVTYNIMIQGLCNDGQMDKARDLFLDMEENAAAPDVITFDMLIHGFIRINEPSKVNELLHKMKEKKVMPDASIVSIVVDLLVKNEISLKSLPSFLVQERQGEV******
Transmembrane Helix (TMHMM)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (MEMSAT)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooohhhhhhhhhhhhhhhhhhhhhiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
TM Helix, Signal Peptide (MEMSAT_SVM)
SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (Phobius)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
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Signal Peptide (SignalP NN Mode)
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Coiled Coils (COILS)
MGLESCCNRSFSFASAPISAFRSNFSSLLVHFRDLTTREGDINVITPNEAFCIFDYMLRMHPSPPPVSSFNILLASLAKNKHYDTRLNATGLFPNLYTYNILINCFCKIGRVSLGFIAFGRILRSCFTPNAATFNSLIKGLHAESRIMEAAALFTKLKAFGCEPNVITYNTLINGLCRTGHTMIALNLFEEMANGNGEIGVVCKPNTVTYSTIIDGLCKEGFVDKAKALFLQMKDENINPDVVTYNSLIHGLCHANDWNEAKRLFIEMMDQGVQPSVVTFNVIMDELCKNRKMDEASRLLDLMVQRGVRPNACTYNTLMDGFCLMGKINRAEELFGSMESMGCKHDDVSYNILINGYCKNKEVEEALSLYREMVSKGIKPTVVTYNTLFLGLFEIHQVEHALKLFDEMQRDGVAADTRTYTTFIDGLCKNGYIIEAVELFRTLRILKCELDIQAYNCLIDGLCKSGRLKFAWELFCSLPHGVLVPNVVTYNIMIQGLCNDGQMDKARDLFLDMEENAAAPDVITFDMLIHGFIRINEPSKVNELLHKMKEKKVMPDASIVSIVVDLLVKNEISLKSLPSFLVQERQGEVGESNVK
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	595	2.2.26 [Sep-21-2011]
P0C7Q7	602	Putative pentatricopeptid	yes	no	0.921	0.910	0.367	1e-115
Q9CAN5	614	Pentatricopeptide repeat-	no	no	0.912	0.884	0.352	1e-108
Q0WKV3	637	Pentatricopeptide repeat-	no	no	0.915	0.855	0.364	1e-107
Q9LPX2	644	Pentatricopeptide repeat-	no	no	0.949	0.877	0.356	1e-106
Q9LQ14	629	Pentatricopeptide repeat-	no	no	0.915	0.866	0.356	1e-106
Q9SXD1	630	Pentatricopeptide repeat-	no	no	0.914	0.863	0.35	1e-105
Q9CAN0	630	Pentatricopeptide repeat-	no	no	0.934	0.882	0.345	1e-105
Q9SXD8	634	Pentatricopeptide repeat-	no	no	0.897	0.842	0.357	1e-105
Q6NQ83	619	Pentatricopeptide repeat-	no	no	0.912	0.877	0.347	1e-104
Q9C8T7	559	Pentatricopeptide repeat-	no	no	0.847	0.901	0.364	1e-103

>sp|P0C7Q7|PPR38_ARATH Putative pentatricopeptide repeat-containing protein At1g12700, mitochondrial OS=Arabidopsis thaliana GN=At1g12700 PE=3 SV=1

 Score =  415 bits (1066), Expect = e-115,   Method: Compositional matrix adjust.
 Identities = 211/574 (36%), Positives = 330/574 (57%), Gaps = 26/574 (4%)

Query: 5   SCCNRSFSFASAPISAFRSNFSSLLVHFRDLTTREGDINVITPNEAFCIFDYMLRMHPSP 64
           S C R FS  S     FR    S +V              I  ++A  +F  M+R  P P
Sbjct: 40  SSCERDFSSISNGNVCFRERLRSGIVD-------------IKKDDAIALFQEMIRSRPLP 86

Query: 65  PPVSSFNILLASLAKNKHYD------TRLNATGLFPNLYTYNILINCFCKIGRVSLGFIA 118
             V  F+   +++A+ K ++       +L   G+  N+YT NI+INCFC+  +    +  
Sbjct: 87  SLVD-FSRFFSAIARTKQFNLVLDFCKQLELNGIAHNIYTLNIMINCFCRCCKTCFAYSV 145

Query: 119 FGRILRSCFTPNAATFNSLIKGLHAESRIMEAAALFTKLKAFGCEPNVITYNTLINGLCR 178
            G++++  + P+  TFN+LIKGL  E ++ EA  L  ++   GC+P+V+TYN+++NG+CR
Sbjct: 146 LGKVMKLGYEPDTTTFNTLIKGLFLEGKVSEAVVLVDRMVENGCQPDVVTYNSIVNGICR 205

Query: 179 TGHTMIALNLFEEMANGNGEIGVVCKPNTVTYSTIIDGLCKEGFVDKAKALFLQMKDENI 238
           +G T +AL+L  +M   N       K +  TYSTIID LC++G +D A +LF +M+ + I
Sbjct: 206 SGDTSLALDLLRKMEERN------VKADVFTYSTIIDSLCRDGCIDAAISLFKEMETKGI 259

Query: 239 NPDVVTYNSLIHGLCHANDWNEAKRLFIEMMDQGVQPSVVTFNVIMDELCKNRKMDEASR 298
              VVTYNSL+ GLC A  WN+   L  +M+ + + P+V+TFNV++D   K  K+ EA+ 
Sbjct: 260 KSSVVTYNSLVRGLCKAGKWNDGALLLKDMVSREIVPNVITFNVLLDVFVKEGKLQEANE 319

Query: 299 LLDLMVQRGVRPNACTYNTLMDGFCLMGKINRAEELFGSMESMGCKHDDVSYNILINGYC 358
           L   M+ RG+ PN  TYNTLMDG+C+  +++ A  +   M    C  D V++  LI GYC
Sbjct: 320 LYKEMITRGISPNIITYNTLMDGYCMQNRLSEANNMLDLMVRNKCSPDIVTFTSLIKGYC 379

Query: 359 KNKEVEEALSLYREMVSKGIKPTVVTYNTLFLGLFEIHQVEHALKLFDEMQRDGVAADTR 418
             K V++ + ++R +  +G+    VTY+ L  G  +  +++ A +LF EM   GV  D  
Sbjct: 380 MVKRVDDGMKVFRNISKRGLVANAVTYSILVQGFCQSGKIKLAEELFQEMVSHGVLPDVM 439

Query: 419 TYTTFIDGLCKNGYIIEAVELFRTLRILKCELDIQAYNCLIDGLCKSGRLKFAWELFCSL 478
           TY   +DGLC NG + +A+E+F  L+  K +L I  Y  +I+G+CK G+++ AW LFCSL
Sbjct: 440 TYGILLDGLCDNGKLEKALEIFEDLQKSKMDLGIVMYTTIIEGMCKGGKVEDAWNLFCSL 499

Query: 479 PHGVLVPNVVTYNIMIQGLCNDGQMDKARDLFLDMEENAAAPDVITFDMLIHGFIRINEP 538
           P   + PNV+TY +MI GLC  G + +A  L   MEE+  AP+  T++ LI   +R  + 
Sbjct: 500 PCKGVKPNVMTYTVMISGLCKKGSLSEANILLRKMEEDGNAPNDCTYNTLIRAHLRDGDL 559

Query: 539 SKVNELLHKMKEKKVMPDASIVSIVVDLLVKNEI 572
           +   +L+ +MK      DAS + +V+D+L+  E+
Sbjct: 560 TASAKLIEEMKSCGFSADASSIKMVIDMLLSGEL 593

Arabidopsis thaliana (taxid: 3702)

>sp|Q9CAN5|PPR98_ARATH Pentatricopeptide repeat-containing protein At1g63080, mitochondrial OS=Arabidopsis thaliana GN=At1g63080 PE=2 SV=1

 Score =  394 bits (1011), Expect = e-108,   Method: Compositional matrix adjust.
 Identities = 213/605 (35%), Positives = 332/605 (54%), Gaps = 62/605 (10%)

Query: 5   SCCNRSFSFASAPISAFRSNFS-SLLVHFRDLTTREGDINVITPNEAFCIFDYMLRMHPS 63
           S C R   F+      +R   S + L+H +              +EA  +F  M++  P 
Sbjct: 16  SFCLRGIYFSGLSYDGYREKLSRNALLHLK-------------LDEAVDLFGEMVKSRPF 62

Query: 64  PPPVSSFNILLASLAKNKHYD------TRLNATGLFPNLYTYNILINCFCKIGRVSLGFI 117
           P  V  F+ LL+++AK K +D       ++   G+  NLYTYNI+INC C+  ++S    
Sbjct: 63  PSIVE-FSKLLSAIAKMKKFDLVISFGEKMEILGVSHNLYTYNIMINCLCRRSQLSFALA 121

Query: 118 AFGRILR-----------------------------------SCFTPNAATFNSLIKGLH 142
             G++++                                     + P+  TF +L+ GL 
Sbjct: 122 ILGKMMKLGYGPSIVTLNSLLNGFCHGNRISEAVALVDQMVEMGYQPDTVTFTTLVHGLF 181

Query: 143 AESRIMEAAALFTKLKAFGCEPNVITYNTLINGLCRTGHTMIALNLFEEMANGNGEIGVV 202
             ++  EA AL  ++   GC+P+++TY  +INGLC+ G   +ALNL  +M  G  E  VV
Sbjct: 182 QHNKASEAVALVERMVVKGCQPDLVTYGAVINGLCKRGEPDLALNLLNKMEKGKIEADVV 241

Query: 203 CKPNTVTYSTIIDGLCKEGFVDKAKALFLQMKDENINPDVVTYNSLIHGLCHANDWNEAK 262
                  YST+ID LCK   VD A  LF +M ++ I PDV TY+SLI  LC+   W++A 
Sbjct: 242 ------IYSTVIDSLCKYRHVDDALNLFTEMDNKGIRPDVFTYSSLISCLCNYGRWSDAS 295

Query: 263 RLFIEMMDQGVQPSVVTFNVIMDELCKNRKMDEASRLLDLMVQRGVRPNACTYNTLMDGF 322
           RL  +M+++ + P+VVTFN ++D   K  K+ EA +L D M+QR + PN  TYN+L++GF
Sbjct: 296 RLLSDMLERKINPNVVTFNSLIDAFAKEGKLIEAEKLFDEMIQRSIDPNIVTYNSLINGF 355

Query: 323 CLMGKINRAEELFGSMESMGCKHDDVSYNILINGYCKNKEVEEALSLYREMVSKGIKPTV 382
           C+  +++ A+++F  M S  C  D V+YN LING+CK K+V + + L+R+M  +G+    
Sbjct: 356 CMHDRLDEAQQIFTLMVSKDCLPDVVTYNTLINGFCKAKKVVDGMELFRDMSRRGLVGNT 415

Query: 383 VTYNTLFLGLFEIHQVEHALKLFDEMQRDGVAADTRTYTTFIDGLCKNGYIIEAVELFRT 442
           VTY TL  G F+    ++A  +F +M  DGV  +  TY T +DGLCKNG + +A+ +F  
Sbjct: 416 VTYTTLIHGFFQASDCDNAQMVFKQMVSDGVHPNIMTYNTLLDGLCKNGKLEKAMVVFEY 475

Query: 443 LRILKCELDIQAYNCLIDGLCKSGRLKFAWELFCSLPHGVLVPNVVTYNIMIQGLCNDGQ 502
           L+  K E DI  YN + +G+CK+G+++  W+LFCSL    + P+V+ YN MI G C  G 
Sbjct: 476 LQKSKMEPDIYTYNIMSEGMCKAGKVEDGWDLFCSLSLKGVKPDVIAYNTMISGFCKKGL 535

Query: 503 MDKARDLFLDMEENAAAPDVITFDMLIHGFIRINEPSKVNELLHKMKEKKVMPDASIVSI 562
            ++A  LF+ M+E+   PD  T++ LI   +R  + +   EL+ +M+  +   DAS   +
Sbjct: 536 KEEAYTLFIKMKEDGPLPDSGTYNTLIRAHLRDGDKAASAELIKEMRSCRFAGDASTYGL 595

Query: 563 VVDLL 567
           V D+L
Sbjct: 596 VTDML 600

Arabidopsis thaliana (taxid: 3702)

>sp|Q0WKV3|PPR36_ARATH Pentatricopeptide repeat-containing protein At1g12300, mitochondrial OS=Arabidopsis thaliana GN=At1g12300 PE=2 SV=1

 Score =  388 bits (997), Expect = e-107,   Method: Compositional matrix adjust.
 Identities = 221/606 (36%), Positives = 331/606 (54%), Gaps = 61/606 (10%)

Query: 3   LESCCNRSFSFASAPISAFRSNFSSLLVHFRDLTTREGDINVITPNEAFCIFDYMLRMHP 62
           L  CC R FS  S    ++R    S LV              I  ++A  +F  M+   P
Sbjct: 38  LSFCCERGFSAFSDRNLSYRERLRSGLVD-------------IKADDAIDLFRDMIHSRP 84

Query: 63  SPPPVSSFNILLASLAKNKHYD------TRLNATGLFPNLYTYNILINCFCKIGRVSLGF 116
             P V  F+ L +++AK K YD       ++   G+  NLYT +I+INCFC+  ++ L F
Sbjct: 85  -LPTVIDFSRLFSAIAKTKQYDLVLALCKQMELKGIAHNLYTLSIMINCFCRCRKLCLAF 143

Query: 117 IAFGRILRSCFTPNAATFNSLIKGLHAESRIMEAAALFTKLKAFGCEPNVITYNTLINGL 176
            A G+I++  + PN  TF++LI GL  E R+ EA  L  ++   G +P++IT NTL+NGL
Sbjct: 144 SAMGKIIKLGYEPNTITFSTLINGLCLEGRVSEALELVDRMVEMGHKPDLITINTLVNGL 203

Query: 177 CRTGHTMIALNLFEEMANGNGEIGVVCKPNTVTY-------------------------- 210
           C +G    A+ L ++M     E G  C+PN VTY                          
Sbjct: 204 CLSGKEAEAMLLIDKMV----EYG--CQPNAVTYGPVLNVMCKSGQTALAMELLRKMEER 257

Query: 211 ---------STIIDGLCKEGFVDKAKALFLQMKDENINPDVVTYNSLIHGLCHANDWNEA 261
                    S IIDGLCK G +D A  LF +M+ + I  +++TYN LI G C+A  W++ 
Sbjct: 258 NIKLDAVKYSIIIDGLCKHGSLDNAFNLFNEMEMKGITTNIITYNILIGGFCNAGRWDDG 317

Query: 262 KRLFIEMMDQGVQPSVVTFNVIMDELCKNRKMDEASRLLDLMVQRGVRPNACTYNTLMDG 321
            +L  +M+ + + P+VVTF+V++D   K  K+ EA  L   M+ RG+ P+  TY +L+DG
Sbjct: 318 AKLLRDMIKRKINPNVVTFSVLIDSFVKEGKLREAEELHKEMIHRGIAPDTITYTSLIDG 377

Query: 322 FCLMGKINRAEELFGSMESMGCKHDDVSYNILINGYCKNKEVEEALSLYREMVSKGIKPT 381
           FC    +++A ++   M S GC  +  ++NILINGYCK   +++ L L+R+M  +G+   
Sbjct: 378 FCKENHLDKANQMVDLMVSKGCDPNIRTFNILINGYCKANRIDDGLELFRKMSLRGVVAD 437

Query: 382 VVTYNTLFLGLFEIHQVEHALKLFDEMQRDGVAADTRTYTTFIDGLCKNGYIIEAVELFR 441
            VTYNTL  G  E+ ++  A +LF EM    V  +  TY   +DGLC NG   +A+E+F 
Sbjct: 438 TVTYNTLIQGFCELGKLNVAKELFQEMVSRKVPPNIVTYKILLDGLCDNGESEKALEIFE 497

Query: 442 TLRILKCELDIQAYNCLIDGLCKSGRLKFAWELFCSLPHGVLVPNVVTYNIMIQGLCNDG 501
            +   K ELDI  YN +I G+C + ++  AW+LFCSLP   + P V TYNIMI GLC  G
Sbjct: 498 KIEKSKMELDIGIYNIIIHGMCNASKVDDAWDLFCSLPLKGVKPGVKTYNIMIGGLCKKG 557

Query: 502 QMDKARDLFLDMEENAAAPDVITFDMLIHGFIRINEPSKVNELLHKMKEKKVMPDASIVS 561
            + +A  LF  MEE+  APD  T+++LI   +   + +K  +L+ ++K      DAS + 
Sbjct: 558 PLSEAELLFRKMEEDGHAPDGWTYNILIRAHLGDGDATKSVKLIEELKRCGFSVDASTIK 617

Query: 562 IVVDLL 567
           +V+D+L
Sbjct: 618 MVIDML 623

Arabidopsis thaliana (taxid: 3702)

>sp|Q9LPX2|PPR39_ARATH Pentatricopeptide repeat-containing protein At1g12775, mitochondrial OS=Arabidopsis thaliana GN=At1g12775 PE=2 SV=1

 Score =  387 bits (994), Expect = e-106,   Method: Compositional matrix adjust.
 Identities = 219/615 (35%), Positives = 333/615 (54%), Gaps = 50/615 (8%)

Query: 6   CCNRSFSFASAPISAFRSNFSSLLVHFRDLTTREGDINVITPNEAFCIFDYMLRMHPSPP 65
           CC R FS  S    ++R   SS LV              I  ++A  +F  M++  P  P
Sbjct: 41  CCERGFSTFSDRNLSYRDKLSSGLVG-------------IKADDAVDLFRDMIQSRP-LP 86

Query: 66  PVSSFNILLASLAKNKHYD------TRLNATGLFPNLYTYNILINCFCKIGRVSLGFIAF 119
            V  FN L +++AK K Y+       ++ + G+  ++YT +I+INCFC+  ++S  F   
Sbjct: 87  TVIDFNRLFSAIAKTKQYELVLALCKQMESKGIAHSIYTLSIMINCFCRCRKLSYAFSTM 146

Query: 120 GRILRSCFTPNAATFNSLIKGLHAESRIMEAAALFTKLKAFGCEPNVITYNTLINGLCRT 179
           G+I++  + P+   FN+L+ GL  E R+ EA  L  ++   G +P +IT NTL+NGLC  
Sbjct: 147 GKIMKLGYEPDTVIFNTLLNGLCLECRVSEALELVDRMVEMGHKPTLITLNTLVNGLCLN 206

Query: 180 GHTMIALNLFEEMANGNGE---------IGVVCKP--------------------NTVTY 210
           G    A+ L + M     +         + V+CK                     + V Y
Sbjct: 207 GKVSDAVVLIDRMVETGFQPNEVTYGPVLNVMCKSGQTALAMELLRKMEERNIKLDAVKY 266

Query: 211 STIIDGLCKEGFVDKAKALFLQMKDENINPDVVTYNSLIHGLCHANDWNEAKRLFIEMMD 270
           S IIDGLCK+G +D A  LF +M+ +    D++TYN+LI G C+A  W++  +L  +M+ 
Sbjct: 267 SIIIDGLCKDGSLDNAFNLFNEMEIKGFKADIITYNTLIGGFCNAGRWDDGAKLLRDMIK 326

Query: 271 QGVQPSVVTFNVIMDELCKNRKMDEASRLLDLMVQRGVRPNACTYNTLMDGFCLMGKINR 330
           + + P+VVTF+V++D   K  K+ EA +LL  M+QRG+ PN  TYN+L+DGFC   ++  
Sbjct: 327 RKISPNVVTFSVLIDSFVKEGKLREADQLLKEMMQRGIAPNTITYNSLIDGFCKENRLEE 386

Query: 331 AEELFGSMESMGCKHDDVSYNILINGYCKNKEVEEALSLYREMVSKGIKPTVVTYNTLFL 390
           A ++   M S GC  D +++NILINGYCK   +++ L L+REM  +G+    VTYNTL  
Sbjct: 387 AIQMVDLMISKGCDPDIMTFNILINGYCKANRIDDGLELFREMSLRGVIANTVTYNTLVQ 446

Query: 391 GLFEIHQVEHALKLFDEMQRDGVAADTRTYTTFIDGLCKNGYIIEAVELFRTLRILKCEL 450
           G  +  ++E A KLF EM    V  D  +Y   +DGLC NG + +A+E+F  +   K EL
Sbjct: 447 GFCQSGKLEVAKKLFQEMVSRRVRPDIVSYKILLDGLCDNGELEKALEIFGKIEKSKMEL 506

Query: 451 DIQAYNCLIDGLCKSGRLKFAWELFCSLPHGVLVPNVVTYNIMIQGLCNDGQMDKARDLF 510
           DI  Y  +I G+C + ++  AW+LFCSLP   +  +   YNIMI  LC    + KA  LF
Sbjct: 507 DIGIYMIIIHGMCNASKVDDAWDLFCSLPLKGVKLDARAYNIMISELCRKDSLSKADILF 566

Query: 511 LDMEENAAAPDVITFDMLIHGFIRINEPSKVNELLHKMKEKKVMPDASIVSIVVDLLVKN 570
             M E   APD +T+++LI   +  ++ +   EL+ +MK      D S V +V+++L   
Sbjct: 567 RKMTEEGHAPDELTYNILIRAHLGDDDATTAAELIEEMKSSGFPADVSTVKMVINMLSSG 626

Query: 571 EISLKSLPSFLVQER 585
           E+  KS    L   R
Sbjct: 627 ELD-KSFLDMLSTTR 640

Arabidopsis thaliana (taxid: 3702)

>sp|Q9LQ14|PPR96_ARATH Pentatricopeptide repeat-containing protein At1g62930, chloroplastic OS=Arabidopsis thaliana GN=At1g62930 PE=2 SV=2

 Score =  385 bits (990), Expect = e-106,   Method: Compositional matrix adjust.
 Identities = 212/595 (35%), Positives = 341/595 (57%), Gaps = 50/595 (8%)

Query: 15  SAPISAFRS-NFSSLLVHFRDLTTREGDINVITPNEAFCIFDYMLRMHPSPPPVSSFNIL 73
           ++P+ + R   FS+    +R+  +R   ++ +  ++A  +F  M++  P P  V  FN L
Sbjct: 29  ASPLFSLRGVYFSAASYDYREKLSRNVLLD-LKLDDAVDLFGEMVQSRPLPSIVE-FNKL 86

Query: 74  LASLAKNKHYD------TRLNATGLFPNLYTYNILINCFCKIGRVSLGFIAFGRILR--- 124
           L+++AK   +D       R+    +  +LY+YNILINCFC+  ++ L     G++++   
Sbjct: 87  LSAIAKMNKFDLVISLGERMQNLRISYDLYSYNILINCFCRRSQLPLALAVLGKMMKLGY 146

Query: 125 -------------SC-------------------FTPNAATFNSLIKGLHAESRIMEAAA 152
                         C                   + PN  TFN+LI GL   ++  EA A
Sbjct: 147 EPDIVTLSSLLNGYCHGKRISEAVALVDQMFVMEYQPNTVTFNTLIHGLFLHNKASEAVA 206

Query: 153 LFTKLKAFGCEPNVITYNTLINGLCRTGHTMIALNLFEEMANGNGEIGVVCKPNTVTYST 212
           L  ++ A GC+P++ TY T++NGLC+ G   +AL+L ++M  G  E  VV       Y+T
Sbjct: 207 LIDRMVARGCQPDLFTYGTVVNGLCKRGDIDLALSLLKKMEKGKIEADVV------IYTT 260

Query: 213 IIDGLCKEGFVDKAKALFLQMKDENINPDVVTYNSLIHGLCHANDWNEAKRLFIEMMDQG 272
           IID LC    V+ A  LF +M ++ I P+VVTYNSLI  LC+   W++A RL  +M+++ 
Sbjct: 261 IIDALCNYKNVNDALNLFTEMDNKGIRPNVVTYNSLIRCLCNYGRWSDASRLLSDMIERK 320

Query: 273 VQPSVVTFNVIMDELCKNRKMDEASRLLDLMVQRGVRPNACTYNTLMDGFCLMGKINRAE 332
           + P+VVTF+ ++D   K  K+ EA +L D M++R + P+  TY++L++GFC+  +++ A+
Sbjct: 321 INPNVVTFSALIDAFVKEGKLVEAEKLYDEMIKRSIDPDIFTYSSLINGFCMHDRLDEAK 380

Query: 333 ELFGSMESMGCKHDDVSYNILINGYCKNKEVEEALSLYREMVSKGIKPTVVTYNTLFLGL 392
            +F  M S  C  + V+YN LI G+CK K VEE + L+REM  +G+    VTYNTL  GL
Sbjct: 381 HMFELMISKDCFPNVVTYNTLIKGFCKAKRVEEGMELFREMSQRGLVGNTVTYNTLIQGL 440

Query: 393 FEIHQVEHALKLFDEMQRDGVAADTRTYTTFIDGLCKNGYIIEAVELFRTLRILKCELDI 452
           F+    + A K+F +M  DGV  D  TY+  +DGLCK G + +A+ +F  L+  K E DI
Sbjct: 441 FQAGDCDMAQKIFKKMVSDGVPPDIITYSILLDGLCKYGKLEKALVVFEYLQKSKMEPDI 500

Query: 453 QAYNCLIDGLCKSGRLKFAWELFCSLPHGVLVPNVVTYNIMIQGLCNDGQMDKARDLFLD 512
             YN +I+G+CK+G+++  W+LFCSL    + PNV+ Y  MI G C  G  ++A  LF +
Sbjct: 501 YTYNIMIEGMCKAGKVEDGWDLFCSLSLKGVKPNVIIYTTMISGFCRKGLKEEADALFRE 560

Query: 513 MEENAAAPDVITFDMLIHGFIRINEPSKVNELLHKMKEKKVMPDASIVSIVVDLL 567
           M+E+   P+  T++ LI   +R  + +   EL+ +M+    + DAS +S+V+++L
Sbjct: 561 MKEDGTLPNSGTYNTLIRARLRDGDKAASAELIKEMRSCGFVGDASTISMVINML 615

Arabidopsis thaliana (taxid: 3702)

>sp|Q9SXD1|PPR91_ARATH Pentatricopeptide repeat-containing protein At1g62670, mitochondrial OS=Arabidopsis thaliana GN=At1g62670 PE=2 SV=2

 Score =  384 bits (986), Expect = e-105,   Method: Compositional matrix adjust.
 Identities = 210/600 (35%), Positives = 337/600 (56%), Gaps = 56/600 (9%)

Query: 10  SFSFASAPISAFRSNFSSLLVH-FRDLTTREGDINVITPNEAFCIFDYMLRMHPSPPPVS 68
           SFSF       +R  FS    + +R+  +R G ++ +  ++A  +F  M++  P P  + 
Sbjct: 31  SFSFF------WRRAFSGKTSYDYREKLSRNG-LSELKLDDAVALFGEMVKSRPFPSIIE 83

Query: 69  SFNILLASLAKNKHYDT------RLNATGLFPNLYTYNILINCFCKIGRVSLGFIAFGRI 122
            F+ LL+++AK   +D       ++   G+  N YTY+ILINCFC+  ++ L     G++
Sbjct: 84  -FSKLLSAIAKMNKFDVVISLGEQMQNLGIPHNHYTYSILINCFCRRSQLPLALAVLGKM 142

Query: 123 LR-----------------------------------SCFTPNAATFNSLIKGLHAESRI 147
           ++                                   + + PN  TFN+LI GL   ++ 
Sbjct: 143 MKLGYEPNIVTLSSLLNGYCHSKRISEAVALVDQMFVTGYQPNTVTFNTLIHGLFLHNKA 202

Query: 148 MEAAALFTKLKAFGCEPNVITYNTLINGLCRTGHTMIALNLFEEMANGNGEIGVVCKPNT 207
            EA AL  ++ A GC+P+++TY  ++NGLC+ G T +A NL  +M  G  E      P  
Sbjct: 203 SEAMALIDRMVAKGCQPDLVTYGVVVNGLCKRGDTDLAFNLLNKMEQGKLE------PGV 256

Query: 208 VTYSTIIDGLCKEGFVDKAKALFLQMKDENINPDVVTYNSLIHGLCHANDWNEAKRLFIE 267
           + Y+TIIDGLCK   +D A  LF +M+ + I P+VVTY+SLI  LC+   W++A RL  +
Sbjct: 257 LIYNTIIDGLCKYKHMDDALNLFKEMETKGIRPNVVTYSSLISCLCNYGRWSDASRLLSD 316

Query: 268 MMDQGVQPSVVTFNVIMDELCKNRKMDEASRLLDLMVQRGVRPNACTYNTLMDGFCLMGK 327
           M+++ + P V TF+ ++D   K  K+ EA +L D MV+R + P+  TY++L++GFC+  +
Sbjct: 317 MIERKINPDVFTFSALIDAFVKEGKLVEAEKLYDEMVKRSIDPSIVTYSSLINGFCMHDR 376

Query: 328 INRAEELFGSMESMGCKHDDVSYNILINGYCKNKEVEEALSLYREMVSKGIKPTVVTYNT 387
           ++ A+++F  M S  C  D V+YN LI G+CK K VEE + ++REM  +G+    VTYN 
Sbjct: 377 LDEAKQMFEFMVSKHCFPDVVTYNTLIKGFCKYKRVEEGMEVFREMSQRGLVGNTVTYNI 436

Query: 388 LFLGLFEIHQVEHALKLFDEMQRDGVAADTRTYTTFIDGLCKNGYIIEAVELFRTLRILK 447
           L  GLF+    + A ++F EM  DGV  +  TY T +DGLCKNG + +A+ +F  L+  K
Sbjct: 437 LIQGLFQAGDCDMAQEIFKEMVSDGVPPNIMTYNTLLDGLCKNGKLEKAMVVFEYLQRSK 496

Query: 448 CELDIQAYNCLIDGLCKSGRLKFAWELFCSLPHGVLVPNVVTYNIMIQGLCNDGQMDKAR 507
            E  I  YN +I+G+CK+G+++  W+LFC+L    + P+VV YN MI G C  G  ++A 
Sbjct: 497 MEPTIYTYNIMIEGMCKAGKVEDGWDLFCNLSLKGVKPDVVAYNTMISGFCRKGSKEEAD 556

Query: 508 DLFLDMEENAAAPDVITFDMLIHGFIRINEPSKVNELLHKMKEKKVMPDASIVSIVVDLL 567
            LF +M+E+   P+   ++ LI   +R  +     EL+ +M+      DAS + +V ++L
Sbjct: 557 ALFKEMKEDGTLPNSGCYNTLIRARLRDGDREASAELIKEMRSCGFAGDASTIGLVTNML 616

Arabidopsis thaliana (taxid: 3702)

>sp|Q9CAN0|PPR99_ARATH Pentatricopeptide repeat-containing protein At1g63130, mitochondrial OS=Arabidopsis thaliana GN=At1g63130 PE=2 SV=1

 Score =  383 bits (984), Expect = e-105,   Method: Compositional matrix adjust.
 Identities = 210/608 (34%), Positives = 340/608 (55%), Gaps = 52/608 (8%)

Query: 1   MGLESCCNRSFSFASAPISAFRSNFSSLLVHFRDLTTREGDINVITPNEAFCIFDYMLRM 60
           +G   C     SF+    S +  +FS +   +R ++     +N +  ++A  +F  M++ 
Sbjct: 20  LGKGKCGTAPPSFSHC--SFWVRDFSGVRYDYRKISINR--LNDLKLDDAVNLFGDMVKS 75

Query: 61  HPSPPPVSSFNILLASLAKNKHYD------TRLNATGLFPNLYTYNILINCFCKIGRVSL 114
            P P  V  F+ LL+++AK   +D       ++   G+  NLYTY+ILINCFC+  ++SL
Sbjct: 76  RPFPSIVE-FSKLLSAIAKMNKFDLVISLGEQMQNLGISHNLYTYSILINCFCRRSQLSL 134

Query: 115 GFIAF-----------------------------------GRILRSCFTPNAATFNSLIK 139
                                                   G+++   + P++ TFN+LI 
Sbjct: 135 ALAVLAKMMKLGYEPDIVTLNSLLNGFCHGNRISDAVSLVGQMVEMGYQPDSFTFNTLIH 194

Query: 140 GLHAESRIMEAAALFTKLKAFGCEPNVITYNTLINGLCRTGHTMIALNLFEEMANGNGEI 199
           GL   +R  EA AL  ++   GC+P+++TY  ++NGLC+ G   +AL+L ++M  G  E 
Sbjct: 195 GLFRHNRASEAVALVDRMVVKGCQPDLVTYGIVVNGLCKRGDIDLALSLLKKMEQGKIE- 253

Query: 200 GVVCKPNTVTYSTIIDGLCKEGFVDKAKALFLQMKDENINPDVVTYNSLIHGLCHANDWN 259
                P  V Y+TIID LC    V+ A  LF +M ++ I P+VVTYNSLI  LC+   W+
Sbjct: 254 -----PGVVIYNTIIDALCNYKNVNDALNLFTEMDNKGIRPNVVTYNSLIRCLCNYGRWS 308

Query: 260 EAKRLFIEMMDQGVQPSVVTFNVIMDELCKNRKMDEASRLLDLMVQRGVRPNACTYNTLM 319
           +A RL  +M+++ + P+VVTF+ ++D   K  K+ EA +L D M++R + P+  TY++L+
Sbjct: 309 DASRLLSDMIERKINPNVVTFSALIDAFVKEGKLVEAEKLYDEMIKRSIDPDIFTYSSLI 368

Query: 320 DGFCLMGKINRAEELFGSMESMGCKHDDVSYNILINGYCKNKEVEEALSLYREMVSKGIK 379
           +GFC+  +++ A+ +F  M S  C  + V+YN LI G+CK K V+E + L+REM  +G+ 
Sbjct: 369 NGFCMHDRLDEAKHMFELMISKDCFPNVVTYNTLIKGFCKAKRVDEGMELFREMSQRGLV 428

Query: 380 PTVVTYNTLFLGLFEIHQVEHALKLFDEMQRDGVAADTRTYTTFIDGLCKNGYIIEAVEL 439
              VTY TL  G F+  + ++A  +F +M  DGV  D  TY+  +DGLC NG +  A+ +
Sbjct: 429 GNTVTYTTLIHGFFQARECDNAQIVFKQMVSDGVLPDIMTYSILLDGLCNNGKVETALVV 488

Query: 440 FRTLRILKCELDIQAYNCLIDGLCKSGRLKFAWELFCSLPHGVLVPNVVTYNIMIQGLCN 499
           F  L+  K E DI  YN +I+G+CK+G+++  W+LFCSL    + PNVVTY  M+ G C 
Sbjct: 489 FEYLQRSKMEPDIYTYNIMIEGMCKAGKVEDGWDLFCSLSLKGVKPNVVTYTTMMSGFCR 548

Query: 500 DGQMDKARDLFLDMEENAAAPDVITFDMLIHGFIRINEPSKVNELLHKMKEKKVMPDASI 559
            G  ++A  LF +M+E    PD  T++ LI   +R  + +   EL+ +M+  + + DAS 
Sbjct: 549 KGLKEEADALFREMKEEGPLPDSGTYNTLIRAHLRDGDKAASAELIREMRSCRFVGDAST 608

Query: 560 VSIVVDLL 567
           + +V ++L
Sbjct: 609 IGLVTNML 616

Arabidopsis thaliana (taxid: 3702)

>sp|Q9SXD8|PPR90_ARATH Pentatricopeptide repeat-containing protein At1g62590 OS=Arabidopsis thaliana GN=At1g62590 PE=2 SV=1

 Score =  381 bits (978), Expect = e-105,   Method: Compositional matrix adjust.
 Identities = 209/584 (35%), Positives = 333/584 (57%), Gaps = 50/584 (8%)

Query: 25  FSSLLVHFRDLTTREGDINVITPNEAFCIFDYMLRMHPSPPPVSSFNILLASLAKNKHYD 84
           FSS    +R++  R G ++ +  ++A  +F  M++  P P  V  FN LL+++AK K +D
Sbjct: 46  FSSGSGDYREIL-RNG-LHDMKLDDAIGLFGGMVKSRPLPSIVE-FNKLLSAIAKMKKFD 102

Query: 85  T------RLNATGLFPNLYTYNILINCFCKIGRVSLGFIAFGRILR-------------- 124
                  ++    +   LYTYNILINCFC+  ++SL     G++++              
Sbjct: 103 VVISLGEKMQRLEIVHGLYTYNILINCFCRRSQISLALALLGKMMKLGYEPSIVTLSSLL 162

Query: 125 ---------------------SCFTPNAATFNSLIKGLHAESRIMEAAALFTKLKAFGCE 163
                                  + P+  TF +LI GL   ++  EA AL  ++   GC+
Sbjct: 163 NGYCHGKRISDAVALVDQMVEMGYRPDTITFTTLIHGLFLHNKASEAVALVDRMVQRGCQ 222

Query: 164 PNVITYNTLINGLCRTGHTMIALNLFEEMANGNGEIGVVCKPNTVTYSTIIDGLCKEGFV 223
           PN++TY  ++NGLC+ G T +ALNL  +M     E  VV       ++TIID LCK   V
Sbjct: 223 PNLVTYGVVVNGLCKRGDTDLALNLLNKMEAAKIEADVV------IFNTIIDSLCKYRHV 276

Query: 224 DKAKALFLQMKDENINPDVVTYNSLIHGLCHANDWNEAKRLFIEMMDQGVQPSVVTFNVI 283
           D A  LF +M+ + I P+VVTY+SLI  LC    W++A +L  +M+++ + P++VTFN +
Sbjct: 277 DDALNLFKEMETKGIRPNVVTYSSLISCLCSYGRWSDASQLLSDMIEKKINPNLVTFNAL 336

Query: 284 MDELCKNRKMDEASRLLDLMVQRGVRPNACTYNTLMDGFCLMGKINRAEELFGSMESMGC 343
           +D   K  K  EA +L D M++R + P+  TYN+L++GFC+  ++++A+++F  M S  C
Sbjct: 337 IDAFVKEGKFVEAEKLYDDMIKRSIDPDIFTYNSLVNGFCMHDRLDKAKQMFEFMVSKDC 396

Query: 344 KHDDVSYNILINGYCKNKEVEEALSLYREMVSKGIKPTVVTYNTLFLGLFEIHQVEHALK 403
             D V+YN LI G+CK+K VE+   L+REM  +G+    VTY TL  GLF     ++A K
Sbjct: 397 FPDVVTYNTLIKGFCKSKRVEDGTELFREMSHRGLVGDTVTYTTLIQGLFHDGDCDNAQK 456

Query: 404 LFDEMQRDGVAADTRTYTTFIDGLCKNGYIIEAVELFRTLRILKCELDIQAYNCLIDGLC 463
           +F +M  DGV  D  TY+  +DGLC NG + +A+E+F  ++  + +LDI  Y  +I+G+C
Sbjct: 457 VFKQMVSDGVPPDIMTYSILLDGLCNNGKLEKALEVFDYMQKSEIKLDIYIYTTMIEGMC 516

Query: 464 KSGRLKFAWELFCSLPHGVLVPNVVTYNIMIQGLCNDGQMDKARDLFLDMEENAAAPDVI 523
           K+G++   W+LFCSL    + PNVVTYN MI GLC+   + +A  L   M+E+   P+  
Sbjct: 517 KAGKVDDGWDLFCSLSLKGVKPNVVTYNTMISGLCSKRLLQEAYALLKKMKEDGPLPNSG 576

Query: 524 TFDMLIHGFIRINEPSKVNELLHKMKEKKVMPDASIVSIVVDLL 567
           T++ LI   +R  + +   EL+ +M+  + + DAS + +V ++L
Sbjct: 577 TYNTLIRAHLRDGDKAASAELIREMRSCRFVGDASTIGLVANML 620

Arabidopsis thaliana (taxid: 3702)

>sp|Q6NQ83|PP247_ARATH Pentatricopeptide repeat-containing protein At3g22470, mitochondrial OS=Arabidopsis thaliana GN=At3g22470 PE=2 SV=1

 Score =  379 bits (973), Expect = e-104,   Method: Compositional matrix adjust.
 Identities = 211/607 (34%), Positives = 334/607 (55%), Gaps = 64/607 (10%)

Query: 17  PISAFRSNFSSLL------VHFRDLTT---------REGDINVITPNEAFCIFDYMLRMH 61
           P++   SNF+ +L      +H+  +T          R G ++ I  N+A  +F+ M++  
Sbjct: 7   PLNRKASNFTQILEKGTSLLHYSSITEAKLSYKERLRNGIVD-IKVNDAIDLFESMIQSR 65

Query: 62  PSPPPVSSFNILLASLAKNKHYDTRLN------ATGLFPNLYTYNILINCFCKIGRVSLG 115
           P P P+  FN L +++A+ K YD  L         G+  ++YT  I+INC+C+  ++   
Sbjct: 66  PLPTPID-FNRLCSAVARTKQYDLVLGFCKGMELNGIEHDMYTMTIMINCYCRKKKLLFA 124

Query: 116 FIAFGRILRSCFTPNAATFNSLIKGLHAESRIMEAAALFTKLKAFGCEPNVITYNTLING 175
           F   GR  +  + P+  TF++L+ G   E R+ EA AL  ++      P+++T +TLING
Sbjct: 125 FSVLGRAWKLGYEPDTITFSTLVNGFCLEGRVSEAVALVDRMVEMKQRPDLVTVSTLING 184

Query: 176 LC-----------------------------------RTGHTMIALNLFEEMANGNGEIG 200
           LC                                   ++G++ +AL+LF +M   N    
Sbjct: 185 LCLKGRVSEALVLIDRMVEYGFQPDEVTYGPVLNRLCKSGNSALALDLFRKMEERN---- 240

Query: 201 VVCKPNTVTYSTIIDGLCKEGFVDKAKALFLQMKDENINPDVVTYNSLIHGLCHANDWNE 260
              K + V YS +ID LCK+G  D A +LF +M+ + I  DVVTY+SLI GLC+   W++
Sbjct: 241 --IKASVVQYSIVIDSLCKDGSFDDALSLFNEMEMKGIKADVVTYSSLIGGLCNDGKWDD 298

Query: 261 AKRLFIEMMDQGVQPSVVTFNVIMDELCKNRKMDEASRLLDLMVQRGVRPNACTYNTLMD 320
             ++  EM+ + + P VVTF+ ++D   K  K+ EA  L + M+ RG+ P+  TYN+L+D
Sbjct: 299 GAKMLREMIGRNIIPDVVTFSALIDVFVKEGKLLEAKELYNEMITRGIAPDTITYNSLID 358

Query: 321 GFCLMGKINRAEELFGSMESMGCKHDDVSYNILINGYCKNKEVEEALSLYREMVSKGIKP 380
           GFC    ++ A ++F  M S GC+ D V+Y+ILIN YCK K V++ + L+RE+ SKG+ P
Sbjct: 359 GFCKENCLHEANQMFDLMVSKGCEPDIVTYSILINSYCKAKRVDDGMRLFREISSKGLIP 418

Query: 381 TVVTYNTLFLGLFEIHQVEHALKLFDEMQRDGVAADTRTYTTFIDGLCKNGYIIEAVELF 440
             +TYNTL LG  +  ++  A +LF EM   GV     TY   +DGLC NG + +A+E+F
Sbjct: 419 NTITYNTLVLGFCQSGKLNAAKELFQEMVSRGVPPSVVTYGILLDGLCDNGELNKALEIF 478

Query: 441 RTLRILKCELDIQAYNCLIDGLCKSGRLKFAWELFCSLPHGVLVPNVVTYNIMIQGLCND 500
             ++  +  L I  YN +I G+C + ++  AW LFCSL    + P+VVTYN+MI GLC  
Sbjct: 479 EKMQKSRMTLGIGIYNIIIHGMCNASKVDDAWSLFCSLSDKGVKPDVVTYNVMIGGLCKK 538

Query: 501 GQMDKARDLFLDMEENAAAPDVITFDMLIHGFIRINEPSKVNELLHKMKEKKVMPDASIV 560
           G + +A  LF  M+E+   PD  T+++LI   +  +      EL+ +MK      D+S +
Sbjct: 539 GSLSEADMLFRKMKEDGCTPDDFTYNILIRAHLGGSGLISSVELIEEMKVCGFSADSSTI 598

Query: 561 SIVVDLL 567
            +V+D+L
Sbjct: 599 KMVIDML 605

Arabidopsis thaliana (taxid: 3702)

>sp|Q9C8T7|PP101_ARATH Pentatricopeptide repeat-containing protein At1g63330 OS=Arabidopsis thaliana GN=At1g63330 PE=2 SV=2

 Score =  377 bits (967), Expect = e-103,   Method: Compositional matrix adjust.
 Identities = 201/552 (36%), Positives = 316/552 (57%), Gaps = 48/552 (8%)

Query: 57  MLRMHPSPPPVSSFNILLASLAKNKHYD------TRLNATGLFPNLYTYNILINCFCKIG 110
           M++  P  P +  FN LL+++AK K +D       ++   G+  NLYTYNILINCFC+  
Sbjct: 1   MVKSRP-LPSIFEFNKLLSAIAKMKKFDLVISLGEKMQRLGISHNLYTYNILINCFCRRS 59

Query: 111 RVSLGFIAFGRILR----------------SC-------------------FTPNAATFN 135
           ++SL     G++++                 C                   + P+  TF 
Sbjct: 60  QISLALALLGKMMKLGYEPSIVTLSSLLNGYCHGKRISDAVALVDQMVEMGYRPDTITFT 119

Query: 136 SLIKGLHAESRIMEAAALFTKLKAFGCEPNVITYNTLINGLCRTGHTMIALNLFEEMANG 195
           +LI GL   ++  EA AL  ++   GC+PN++TY  ++NGLC+ G   +A NL  +M   
Sbjct: 120 TLIHGLFLHNKASEAVALVDRMVQRGCQPNLVTYGVVVNGLCKRGDIDLAFNLLNKMEAA 179

Query: 196 NGEIGVVCKPNTVTYSTIIDGLCKEGFVDKAKALFLQMKDENINPDVVTYNSLIHGLCHA 255
             E  VV       ++TIID LCK   VD A  LF +M+ + I P+VVTY+SLI  LC  
Sbjct: 180 KIEADVV------IFNTIIDSLCKYRHVDDALNLFKEMETKGIRPNVVTYSSLISCLCSY 233

Query: 256 NDWNEAKRLFIEMMDQGVQPSVVTFNVIMDELCKNRKMDEASRLLDLMVQRGVRPNACTY 315
             W++A +L  +M+++ + P++VTFN ++D   K  K  EA +L D M++R + P+  TY
Sbjct: 234 GRWSDASQLLSDMIEKKINPNLVTFNALIDAFVKEGKFVEAEKLHDDMIKRSIDPDIFTY 293

Query: 316 NTLMDGFCLMGKINRAEELFGSMESMGCKHDDVSYNILINGYCKNKEVEEALSLYREMVS 375
           N+L++GFC+  ++++A+++F  M S  C  D  +YN LI G+CK+K VE+   L+REM  
Sbjct: 294 NSLINGFCMHDRLDKAKQMFEFMVSKDCFPDLDTYNTLIKGFCKSKRVEDGTELFREMSH 353

Query: 376 KGIKPTVVTYNTLFLGLFEIHQVEHALKLFDEMQRDGVAADTRTYTTFIDGLCKNGYIIE 435
           +G+    VTY TL  GLF     ++A K+F +M  DGV  D  TY+  +DGLC NG + +
Sbjct: 354 RGLVGDTVTYTTLIQGLFHDGDCDNAQKVFKQMVSDGVPPDIMTYSILLDGLCNNGKLEK 413

Query: 436 AVELFRTLRILKCELDIQAYNCLIDGLCKSGRLKFAWELFCSLPHGVLVPNVVTYNIMIQ 495
           A+E+F  ++  + +LDI  Y  +I+G+CK+G++   W+LFCSL    + PNVVTYN MI 
Sbjct: 414 ALEVFDYMQKSEIKLDIYIYTTMIEGMCKAGKVDDGWDLFCSLSLKGVKPNVVTYNTMIS 473

Query: 496 GLCNDGQMDKARDLFLDMEENAAAPDVITFDMLIHGFIRINEPSKVNELLHKMKEKKVMP 555
           GLC+   + +A  L   M+E+   PD  T++ LI   +R  + +   EL+ +M+  + + 
Sbjct: 474 GLCSKRLLQEAYALLKKMKEDGPLPDSGTYNTLIRAHLRDGDKAASAELIREMRSCRFVG 533

Query: 556 DASIVSIVVDLL 567
           DAS + +V ++L
Sbjct: 534 DASTIGLVANML 545

Arabidopsis thaliana (taxid: 3702)

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	595
359479583	627	PREDICTED: pentatricopeptide repeat-cont	0.910	0.864	0.525	1e-159
449529622	618	PREDICTED: pentatricopeptide repeat-cont	0.931	0.896	0.5	1e-153
449520325	605	PREDICTED: pentatricopeptide repeat-cont	0.942	0.927	0.474	1e-148
255559961	628	pentatricopeptide repeat-containing prot	0.910	0.863	0.471	1e-142
449520323	605	PREDICTED: pentatricopeptide repeat-cont	0.865	0.851	0.494	1e-140
449462477	597	PREDICTED: pentatricopeptide repeat-cont	0.852	0.849	0.486	1e-135
225451354	744	PREDICTED: putative pentatricopeptide re	0.912	0.729	0.397	1e-116
359488009	579	PREDICTED: putative pentatricopeptide re	0.924	0.949	0.404	1e-116
225452994	588	PREDICTED: putative pentatricopeptide re	0.892	0.903	0.402	1e-116
147768816	653	hypothetical protein VITISV_031897 [Viti	0.892	0.813	0.402	1e-115

>gi|359479583|ref|XP_002275680.2| PREDICTED: pentatricopeptide repeat-containing protein At3g22470, mitochondrial-like [Vitis vinifera] gi|297735515|emb|CBI17955.3| unnamed protein product [Vitis vinifera]

 Score =  569 bits (1467), Expect = e-159,   Method: Compositional matrix adjust.
 Identities = 290/552 (52%), Positives = 373/552 (67%), Gaps = 10/552 (1%)

Query: 45  ITPNEAFCIFDYMLRMHPSPPPVSSFNILLASLAKNKHY------DTRLNATGLFPNLYT 98
           I  +EAF +F++++ M P+PP +SSFN LL ++AK K Y        R++  GL P+  T
Sbjct: 71  IKRSEAFSVFNHLIDMQPTPP-ISSFNTLLGAVAKIKRYFDVISLYKRMSLIGLAPDFIT 129

Query: 99  YNILINCFCKIGRVSLGFIAFGRILRSCFTPNAATFNSLIKGLHAESRIMEAAALFTKLK 158
            NILINC+C + +V  G    G +LR   +PN  TF SL+KGL   SRI EA  L  K+ 
Sbjct: 130 LNILINCYCNLNKVDFGLAVLGEMLRRGHSPNTVTFTSLVKGLCLGSRISEATGLLRKMV 189

Query: 159 AFGCEPNVITYNTLINGLCRTGHTMIALNLFEEMANGNGEIGVVCKPNTVTYSTIIDGLC 218
             G  PNV+TY TL+NGLC TG+TM+A+ L EEM NGNG  GV  KPN V Y TIID LC
Sbjct: 190 RMGYRPNVVTYGTLLNGLCMTGNTMLAVKLHEEMLNGNGGFGVTIKPNLVCYCTIIDSLC 249

Query: 219 KEGFVDKAKALFLQMKDENINPDVVTYNSLIHGLCHANDWNEAKRLFIEMMDQGVQPSVV 278
           K+G +DK K LFL+MK   I+PDVV Y+S+IHG+CH   W  AK LF EM+D+GV P+VV
Sbjct: 250 KDGLIDKGKELFLEMKGRGISPDVVAYSSIIHGMCHTGRWEGAKGLFNEMVDEGVHPNVV 309

Query: 279 TFNVIMDELCKNRKMDEASRLLDLMVQRGVRPNACTYNTLMDGFCLMGKINRAEELFGSM 338
           TFNV++D LCK  KM+EA+ LL LM+QRG  P+  TYNTL+DGFCL G+I+ A +LF SM
Sbjct: 310 TFNVLIDALCKAGKMEEANHLLKLMIQRGESPDTFTYNTLIDGFCLEGRIDDARDLFVSM 369

Query: 339 ESMGCKHDDVSYNILINGYCKNKEVEEALSLYREMVSKGIKPTVVTYNTLFLGLFEIHQV 398
           ES G + D VSYN+LINGYCK+  + EA  LYREM+ K I PTV+TYNTL  GLF   +V
Sbjct: 370 ESKGIETDAVSYNVLINGYCKSGRMVEAKKLYREMMCKEIMPTVITYNTLLTGLFREGKV 429

Query: 399 EHALKLFDEMQRDGVAADTRTYTTFIDGLCKNGYIIEAVELFRTLRILKCELDIQAYNCL 458
             A  LF EM+   +  ++ TY   +DGLCKN ++ EA+ELF  L     +  IQ +NCL
Sbjct: 430 RDAWNLFGEMKVHDLTPESCTYNILLDGLCKNNHLSEAMELFHYLENHDFQPSIQIFNCL 489

Query: 459 IDGLCKSGRLKFAWELFCSLPHGVLVPNVVTYNIMIQGLCNDGQMDKARDLFLDMEENAA 518
           IDGLCK+ +++ A ELF  L H  L PNV+TY +MI GLC  GQ++ A+DLFL MEE   
Sbjct: 490 IDGLCKARKIEIARELFNRLSHEGLEPNVITYTVMIHGLCKSGQLENAKDLFLGMEEKGC 549

Query: 519 APDVITFDMLIHGFIRINEPSKVNELLHKMKEKKVMPDASIVSIVVDLLVKNEI---SLK 575
           AP+++TF+ L+ GF + +E  KV ELL +M EK   PDAS +SIVVDLL K+E     L 
Sbjct: 550 APNLVTFNTLMRGFCQNDEMQKVVELLQEMAEKDFSPDASTISIVVDLLSKDEKYREYLH 609

Query: 576 SLPSFLVQERQG 587
            LP+F  Q + G
Sbjct: 610 LLPTFPAQGQTG 621

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|449529622|ref|XP_004171797.1| PREDICTED: pentatricopeptide repeat-containing protein At3g22470, mitochondrial-like [Cucumis sativus]

 Score =  547 bits (1409), Expect = e-153,   Method: Compositional matrix adjust.
 Identities = 282/564 (50%), Positives = 370/564 (65%), Gaps = 10/564 (1%)

Query: 31  HFRDLTTREGDINVITPNEAFCIFDYMLRMHPSPPPVSSFNILLASLAKNKHYD------ 84
           H   L  R      IT  +AF  FD M+R HP PP +SSFN LL  LAK  HY       
Sbjct: 56  HPLSLFLRNCKTGNITAIQAFHFFDLMMRSHPIPP-ISSFNRLLGGLAKINHYSQLFSLY 114

Query: 85  TRLNATGLFPNLYTYNILINCFCKIGRVSLGFIAFGRILRSCFTPNAATFNSLIKGLHAE 144
             +   GL P+L+T +IL NC C + RVS    A   ILR  + PN  T+ +LIKGL  E
Sbjct: 115 NEMRLAGLSPDLFTLSILANCLCNVNRVSEALAAMAGILRRGYIPNVVTYTTLIKGLCME 174

Query: 145 SRIMEAAALFTKLKAFGCEPNVITYNTLINGLCRTGHTMIALNLFEEMANGNGEIGVVCK 204
            RI EA  LF +++  GC PN +TY TLI GLC+TG+  IAL L +EM N   + GV CK
Sbjct: 175 HRISEATRLFLRMQKLGCTPNAVTYGTLIKGLCQTGNVNIALKLHKEMLNDASQYGVNCK 234

Query: 205 PNTVTYSTIIDGLCKEGFVDKAKALFLQMKDENINPDVVTYNSLIHGLCHANDWNEAKRL 264
           P  +TYS IIDGLCK G  D+AK LF +MK + + PDV++Y++LIHG C A  W+++K L
Sbjct: 235 PGVITYSIIIDGLCKVGREDEAKELFEEMKAQGMIPDVISYSTLIHGFCCAGKWDQSKHL 294

Query: 265 FIEMMDQGVQPSVVTFNVIMDELCKNRKMDEASRLLDLMVQRGVRPNACTYNTLMDGFCL 324
           F EM+DQGVQP +VTF+V++D LCK  K+ EA +LL++M+QRG+ PN  TYN+L+DGFC+
Sbjct: 295 FDEMVDQGVQPDMVTFSVLIDTLCKEGKVTEAKKLLEVMIQRGIVPNLITYNSLIDGFCM 354

Query: 325 MGKINRAEELFGSMESMGCKHDDVSYNILINGYCKNKEVEEALSLYREMVSKGIKPTVVT 384
           +G +N A ELF SM S G + D++SY  LINGYCK  +V+EA++LY EM+  G  P V T
Sbjct: 355 VGDLNSARELFLSMPSKGLEPDEISYTTLINGYCKTWKVKEAMNLYNEMLQVGKSPNVTT 414

Query: 385 YNTLFLGLFEIHQVEHALKLFDEMQRDGVAADTRTYTTFIDGLCKNGYIIEAVELFRTLR 444
           Y TL  GLF+  +V  A KLF  M+  GV+A+++ Y  F+DGLCKN  + EA+ELF  L+
Sbjct: 415 YGTLLKGLFQKGKVGDAKKLFGVMKTYGVSANSQIYGIFLDGLCKNDCLFEAMELFNELK 474

Query: 445 ILKCELDIQAYNCLIDGLCKSGRLKFAWELFCSLPHGVLVPNVVTYNIMIQGLCNDGQMD 504
               +L+I+ Y+CLIDGLCK+G+L+ AWELF  L    L P+VVTYNIMI G C  GQ+D
Sbjct: 475 SYNFKLNIENYSCLIDGLCKAGKLETAWELFEKLSQEGLQPDVVTYNIMIHGFCKVGQVD 534

Query: 505 KARDLFLDMEENAAAPDVITFDMLIHGFIRINEPSKVNELLHKMKEKKVMPDASIVSIVV 564
            A  LF  MEEN   PD+I ++ L+ GF   N+  +V +LLHKM +K V P+A+  +IVV
Sbjct: 535 NANILFEKMEENGCTPDIIAYNTLLCGFCEGNKLEEVIKLLHKMVQKDVSPNAASCTIVV 594

Query: 565 DLLVKNEISLKS---LPSFLVQER 585
           D+L K+E   K    LP F VQ  
Sbjct: 595 DMLCKDEKYKKFVDLLPKFPVQRH 618

Source: Cucumis sativus

Species: Cucumis sativus

Genus: Cucumis

Family: Cucurbitaceae

Order: Cucurbitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|449520325|ref|XP_004167184.1| PREDICTED: pentatricopeptide repeat-containing protein At3g22470, mitochondrial-like [Cucumis sativus]

 Score =  532 bits (1371), Expect = e-148,   Method: Compositional matrix adjust.
 Identities = 275/580 (47%), Positives = 374/580 (64%), Gaps = 19/580 (3%)

Query: 23  SNFSSLLVHFRDLTT---------REGDINVITPNEAFCIFDYMLRMHPSPPPVSSFNIL 73
           SN SSL  H   + +         R      +T   A   F  M+R  P+P  +SSFN L
Sbjct: 17  SNLSSLFTHSSAIPSPNPQIAFFLRHCKTGNVTATHALHFFHLMMRSTPTPS-LSSFNHL 75

Query: 74  LASLAKNKHYD------TRLNATGLFPNLYTYNILINCFCKIGRVSLGFIAFGRILRSCF 127
           L+ LAK KHY        ++  +GL  +  T NIL+NC C + R+  GF AF  ILR  +
Sbjct: 76  LSGLAKIKHYSQVFSLYNQMRLSGLSSDRCTLNILLNCLCNVNRLREGFAAFAGILRRGY 135

Query: 128 TPNAATFNSLIKGLHAESRIMEAAALFTKLKAFGCEPNVITYNTLINGLCRTGHTMIALN 187
           +PN  T+N+LIKGL  E RI EA  LF +++  GC P+V+TY TLI GLC TG+  IAL 
Sbjct: 136 SPNIVTYNTLIKGLCMEHRISEATRLFLRMQKLGCTPDVVTYGTLIKGLCGTGNINIALK 195

Query: 188 LFEEMANGNGEIGVVCKPNTVTYSTIIDGLCKEGFVDKAKALFLQMKDENINPDVVTYNS 247
           L +EM N      + CKPN +TY+ I+DGLCK G  D+AK LF +MK + + P +++YNS
Sbjct: 196 LHQEMLNDISRYEINCKPNVITYNIIVDGLCKVGREDEAKQLFEEMKTQGMIPSIISYNS 255

Query: 248 LIHGLCHANDWNEAKRLFIEMMDQGVQPSVVTFNVIMDELCKNRKMDEASRLLDLMVQRG 307
           LIHG C A  W E+KRL  EM+DQG+QP +VTFNV++D LCK  K+ EA +LL +M++ G
Sbjct: 256 LIHGFCCAGKWEESKRLLDEMLDQGLQPDMVTFNVLIDTLCKEGKVIEAKKLLGVMIESG 315

Query: 308 VRPNACTYNTLMDGFCLMGKINRAEELFGSMESMGCKHDDVSYNILINGYCKNKEVEEAL 367
           + P+  TYN+L++GFC++G +N A ELF SM S GC+ D +SYN+LINGY K  +VEEA+
Sbjct: 316 IVPDLVTYNSLIEGFCMVGDLNSARELFVSMPSKGCEPDVISYNVLINGYSKTLKVEEAM 375

Query: 368 SLYREMVSKGIKPTVVTYNTLFLGLFEIHQVEHALKLFDEMQRDGVAADTRTYTTFIDGL 427
            LY EM+  G +P V+TY++L  G+F   +V+ A KLF  M+  G+A ++ TY  F+DGL
Sbjct: 376 KLYNEMLLVGKRPNVITYDSLLKGIFLAGKVDDAKKLFSVMKAHGIAENSYTYGIFLDGL 435

Query: 428 CKNGYIIEAVELFRTLRILKCELDIQAYNCLIDGLCKSGRLKFAWELFCSLPHGVLVPNV 487
           CKN  + EA++LF  L+    +L+I+  NCLIDGLCK+G+L+ AWELF  L +    PNV
Sbjct: 436 CKNDCLFEAMKLFTELKSSNFKLEIENLNCLIDGLCKAGKLETAWELFEKLSNEGHEPNV 495

Query: 488 VTYNIMIQGLCNDGQMDKARDLFLDMEENAAAPDVITFDMLIHGFIRINEPSKVNELLHK 547
           VTY IMI G C +GQ+DKA  L   ME N   PD+IT++ L+ GF   N+  +V +LLH+
Sbjct: 496 VTYTIMIHGFCREGQVDKANVLIQKMEANGCTPDIITYNTLMRGFYESNKLEEVVQLLHR 555

Query: 548 MKEKKVMPDASIVSIVVDLLVKNEI---SLKSLPSFLVQE 584
           M +K V PDA   SIVVD+L K+E     L  LP F +Q+
Sbjct: 556 MAQKDVSPDAITCSIVVDMLSKDEKYQECLHLLPRFPIQK 595

Source: Cucumis sativus

Species: Cucumis sativus

Genus: Cucumis

Family: Cucurbitaceae

Order: Cucurbitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|255559961|ref|XP_002520999.1| pentatricopeptide repeat-containing protein, putative [Ricinus communis] gi|223539836|gb|EEF41416.1| pentatricopeptide repeat-containing protein, putative [Ricinus communis]

 Score =  510 bits (1314), Expect = e-142,   Method: Compositional matrix adjust.
 Identities = 268/568 (47%), Positives = 369/568 (64%), Gaps = 26/568 (4%)

Query: 29  LVHFRDLTTREGDINVITPNEAFCIFDYMLRMHPSPPPVSSFNILLASLAKNKHY----- 83
           L  F ++  + GD    T +EA   F+ M+ M  +P  +S FN L  +LAK K Y     
Sbjct: 73  LEQFLEINCKSGDF---TLHEALHFFNQMIHMQTTPA-LSRFNNLFGALAKKKQYLHVIS 128

Query: 84  -DTRLNATGLFPNLYTYNILINCFCKIGRVSLGFIAFGRILRSCFTPNAATFNSLIKGLH 142
              R+N+ GL  N  + NIL+NC C + RV  GF+ FG ILR  + PN  TF +L+KGL 
Sbjct: 129 MCGRMNSIGLLKNFISLNILLNCLCSVKRVFEGFVVFGMILRKGYRPNTRTFTNLVKGLC 188

Query: 143 AESRIMEAAALFTKLKAFGCEPNVITYNTLINGLCRTGHTMIALNLFEEMANGNGEIGVV 202
            E +I EA  +F  +  F C P+ IT   LI+GLCRTG+T  AL L E M NGN + G+ 
Sbjct: 189 LEGKIGEAVRVFKIMGVFDCRPSAITCGVLISGLCRTGNTCNALKLHEAMINGNSDFGIN 248

Query: 203 CKPNTVTYSTIIDGLCKEGFVDKAKALFLQMKDENINPDVVTYNSLIHGLCHANDWNEAK 262
           CKP  V+YS IID LCK+G V++AK  F++MK++ I P+VVTY SL+HGLC A++W EAK
Sbjct: 249 CKPTVVSYSCIIDSLCKDGLVERAKEFFVEMKEKGIFPNVVTYTSLLHGLCSASEWEEAK 308

Query: 263 RLFIEMMDQGVQPSVVTFNVIMDELCKNRKMDEASRLLDLMVQRGVRPNACTYNTLMDGF 322
           RLFIEM+D G+ P VVTF+V++  LCK  K+ EAS L DLMVQR V P+  TYN L++G+
Sbjct: 309 RLFIEMVDHGLLPDVVTFSVLIGALCKVGKVKEASGLFDLMVQRYVEPSTRTYNILIEGY 368

Query: 323 CLMGKINRAEELFGSMESMGCKHDDVSYNILINGYCKNKEVEEALSLYREMVSKGIKPTV 382
           CL G ++  +++F SM +  C+HD  SY+IL+  YCK+ EV  A+ LYREM+ +GI+PTV
Sbjct: 369 CLAGMVDEGKKIFLSMVNKRCQHDAGSYSILMKAYCKDSEVHGAMILYREMMDRGIQPTV 428

Query: 383 VTYNTLFLGLFEIHQVEHALKLFDEMQRDGVAADTRTYT---TFIDGLCKNGYIIEAVEL 439
           +TY+          +V  A KLF E+Q   +  D+ +Y+    ++DGLCKNG + EA+++
Sbjct: 429 ITYS----------KVGDARKLFGEIQFQDMVLDSISYSIYNVYLDGLCKNGCVSEALDV 478

Query: 440 FRTLRILKCELDIQAYNCLIDGLCKSGRLKFAWELFCSLPHGVLVPNVVTYNIMIQGLCN 499
           F  L   K   ++  +N LI+G+C+S +L+ AWELF  L +  L P+VVTY IMI GLC 
Sbjct: 479 FYGLENCKFASNVAIFNSLINGMCRSEKLEIAWELFNRLCNEALQPDVVTYTIMIYGLCK 538

Query: 500 DGQMDKARDLFLDMEENAAAPDVITFDMLIHGFIRINEPSKVNELLHKMKEKKVMPDASI 559
            GQ  KA DLFL+MEE   AP+V+TF+ L+ G    +E  K+ ELLHKM  +K+ PDAS 
Sbjct: 539 VGQPQKAYDLFLEMEEKGCAPNVVTFNTLMRGLCLNSERPKIVELLHKMAARKLSPDAST 598

Query: 560 VSIVVDLLVKNE---ISLKSLPSFLVQE 584
           + IV+D+L+K+E     L  LP+F VQE
Sbjct: 599 LLIVMDILLKDENYHECLNLLPTFPVQE 626

Source: Ricinus communis

Species: Ricinus communis

Genus: Ricinus

Family: Euphorbiaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|449520323|ref|XP_004167183.1| PREDICTED: pentatricopeptide repeat-containing protein At3g22470, mitochondrial-like [Cucumis sativus]

 Score =  506 bits (1304), Expect = e-140,   Method: Compositional matrix adjust.
 Identities = 258/522 (49%), Positives = 340/522 (65%), Gaps = 7/522 (1%)

Query: 45  ITPNEAFCIFDYMLRMHPSPPPVSSFNILLASLAKNKHYD------TRLNATGLFPNLYT 98
           IT  +AF  F  M+  +P+PP +SSF  LL+ LAK KHY        ++  +G+ P+  T
Sbjct: 75  ITATQAFQFFHLMMYSNPTPP-LSSFTHLLSGLAKIKHYSQVFYLYNQMRLSGISPDCCT 133

Query: 99  YNILINCFCKIGRVSLGFIAFGRILRSCFTPNAATFNSLIKGLHAESRIMEAAALFTKLK 158
            NIL+NC C + RV  G      ILR  + P+  T+ +LIKGL  E RI +AA LFT+++
Sbjct: 134 LNILLNCLCNVNRVGEGLAVMAGILRRGYIPDIVTYTTLIKGLCMEHRISKAALLFTRMQ 193

Query: 159 AFGCEPNVITYNTLINGLCRTGHTMIALNLFEEMANGNGEIGVVCKPNTVTYSTIIDGLC 218
             GC PN ITY TL+ GLCRTG+  IAL L +EM N +   G+  KP  ++YS IID LC
Sbjct: 194 KLGCTPNAITYGTLMKGLCRTGNISIALKLHQEMLNDSSLYGINFKPVVISYSIIIDALC 253

Query: 219 KEGFVDKAKALFLQMKDENINPDVVTYNSLIHGLCHANDWNEAKRLFIEMMDQGVQPSVV 278
           K+   D+A+ LF +MK + + P V++Y SLIHG C    W EAKRLF EM++QGVQP+VV
Sbjct: 254 KDRREDEARDLFEEMKVQGMTPTVISYTSLIHGFCCGGKWEEAKRLFNEMVNQGVQPNVV 313

Query: 279 TFNVIMDELCKNRKMDEASRLLDLMVQRGVRPNACTYNTLMDGFCLMGKINRAEELFGSM 338
           TFNV++D LCK  K+ EA  LL++M+QRG+ PN  TYN+L++GFCL+G +N A ELF SM
Sbjct: 314 TFNVLIDVLCKEGKVIEAKDLLEVMIQRGIVPNLLTYNSLIEGFCLVGDLNSARELFVSM 373

Query: 339 ESMGCKHDDVSYNILINGYCKNKEVEEALSLYREMVSKGIKPTVVTYNTLFLGLFEIHQV 398
            S GC+ D + Y +LINGYCK  +VEEA+ LY  M+  G +P V TY  L  GLF+  +V
Sbjct: 374 PSKGCEPDVICYTVLINGYCKTSKVEEAMKLYNGMLQVGKRPDVKTYGALLTGLFQGGKV 433

Query: 399 EHALKLFDEMQRDGVAADTRTYTTFIDGLCKNGYIIEAVELFRTLRILKCELDIQAYNCL 458
             A KLF  M+  G+  D   Y  F++GLCKNG + EA+ELF  L+    +LDI+ +NCL
Sbjct: 434 GDAKKLFGVMKVYGIPGDLYIYGIFLNGLCKNGCLFEAMELFNKLKSYNIKLDIECFNCL 493

Query: 459 IDGLCKSGRLKFAWELFCSLPHGVLVPNVVTYNIMIQGLCNDGQMDKARDLFLDMEENAA 518
           IDGLCK+G+L+ AWELF  LP   L P+VVTYNIMI   C  GQ+ KA  LF  ME+N  
Sbjct: 494 IDGLCKAGKLETAWELFEKLPQEELQPDVVTYNIMIHEFCRGGQVVKANILFQKMEKNGC 553

Query: 519 APDVITFDMLIHGFIRINEPSKVNELLHKMKEKKVMPDASIV 560
            PD IT+  LI GF    +  KV ELLH M ++ V  D +I+
Sbjct: 554 TPDKITYATLIRGFFESKKLEKVVELLHMMVQRDVSLDVNIL 595

Source: Cucumis sativus

Species: Cucumis sativus

Genus: Cucumis

Family: Cucurbitaceae

Order: Cucurbitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|449462477|ref|XP_004148967.1| PREDICTED: pentatricopeptide repeat-containing protein At3g22470, mitochondrial-like [Cucumis sativus]

 Score =  490 bits (1261), Expect = e-135,   Method: Compositional matrix adjust.
 Identities = 254/522 (48%), Positives = 337/522 (64%), Gaps = 15/522 (2%)

Query: 45  ITPNEAFCIFDYMLRMHPSPPPVSSFNILLASLAKNKHYD------TRLNATGLFPNLYT 98
           IT  +AF  F  M+  +P+PP +SSF  LL+ LAK KHY        ++  +G+ P+  T
Sbjct: 75  ITAIQAFQFFHLMMYSNPTPP-LSSFTHLLSGLAKIKHYSQVFYLYNQMRLSGISPDCCT 133

Query: 99  YNILINCFCKIGRVSLGFIAFGRILRSCFTPNAATFNSLIKGLHAESRIMEAAALFTKLK 158
            NIL+NC C + RV  G      ILR  + P+  T+ +LIKGL  E RI +AA LFT+++
Sbjct: 134 LNILLNCLCNVNRVGEGLAVMAGILRRGYIPDIVTYTTLIKGLCMEHRISKAALLFTRMQ 193

Query: 159 AFGCEPNVITYNTLINGLCRTGHTMIALNLFEEMANGNGEIGVVCKPNTVTYSTIIDGLC 218
             GC PN ITY TL+ GLCRTG+  IAL L +EM N +   G+  KP  ++YS IID LC
Sbjct: 194 KLGCTPNAITYGTLMKGLCRTGNISIALKLHQEMLNDSSLYGINFKPVVISYSIIIDALC 253

Query: 219 KEGFVDKAKALFLQMKDENINPDVVTYNSLIHGLCHANDWNEAKRLFIEMMDQGVQPSVV 278
           K+   D+A+ LF +MK + + P V++Y SL+        W EAKRLF EM++QGVQP+VV
Sbjct: 254 KDRREDEARDLFEEMKVQGMTPTVISYTSLM--------WEEAKRLFNEMVNQGVQPNVV 305

Query: 279 TFNVIMDELCKNRKMDEASRLLDLMVQRGVRPNACTYNTLMDGFCLMGKINRAEELFGSM 338
           TFNV++D LCK  K+ EA  LL++M+QRG+ PN  TYN+L++GFCL+G +N A ELF SM
Sbjct: 306 TFNVLIDVLCKEGKVIEAKDLLEVMIQRGIVPNLLTYNSLIEGFCLVGDLNSARELFVSM 365

Query: 339 ESMGCKHDDVSYNILINGYCKNKEVEEALSLYREMVSKGIKPTVVTYNTLFLGLFEIHQV 398
            S GC+ D + Y +LINGYCK  +VEEA+ LY  M+  G +P V TY  L  GLF+  +V
Sbjct: 366 PSKGCEPDVICYTVLINGYCKTSKVEEAMKLYNGMLQVGKRPDVKTYGALLTGLFQGGKV 425

Query: 399 EHALKLFDEMQRDGVAADTRTYTTFIDGLCKNGYIIEAVELFRTLRILKCELDIQAYNCL 458
             A KLF  M+  G+  D   Y  F++GLCKNG + EA+ELF  L+    +LDI+ +NCL
Sbjct: 426 GDAKKLFGVMKVYGIPGDLYIYGIFLNGLCKNGCLFEAMELFNKLKSYNIKLDIECFNCL 485

Query: 459 IDGLCKSGRLKFAWELFCSLPHGVLVPNVVTYNIMIQGLCNDGQMDKARDLFLDMEENAA 518
           IDGLCK+G+L+ AWELF  LP   L P+VVTYNIMI   C  GQ+ KA  LF  ME+N  
Sbjct: 486 IDGLCKAGKLETAWELFEKLPQEELQPDVVTYNIMIHEFCRGGQVVKANILFQKMEKNGC 545

Query: 519 APDVITFDMLIHGFIRINEPSKVNELLHKMKEKKVMPDASIV 560
            PD IT+  LI GF    +  KV ELLH M ++ V  D +I+
Sbjct: 546 TPDKITYATLIRGFFESKKLEKVVELLHMMVQRDVSLDVNIL 587

Source: Cucumis sativus

Species: Cucumis sativus

Genus: Cucumis

Family: Cucurbitaceae

Order: Cucurbitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|225451354|ref|XP_002275019.1| PREDICTED: putative pentatricopeptide repeat-containing protein At1g12700, mitochondrial-like [Vitis vinifera]

 Score =  426 bits (1096), Expect = e-116,   Method: Compositional matrix adjust.
 Identities = 227/571 (39%), Positives = 334/571 (58%), Gaps = 28/571 (4%)

Query: 15  SAPISAFRS---NFSSLLVHFRDLTTREGDINVITPNEAFCIFDYMLRMHPSPPPVSSFN 71
           S P+  F S   NF S  +HF  L            ++A   F+ +L MHP PP +  F 
Sbjct: 14  SPPLPFFSSSQNNFHSKSLHFNTL------------DDALSSFNRLLHMHP-PPSIVDFA 60

Query: 72  ILLASLAKNKHYDT------RLNATGLFPNLYTYNILINCFCKIGRVSLGFIAFGRILRS 125
            LL S+AK KHY T      ++++ G+ PN+YT NILIN FC + RV   F    +IL+ 
Sbjct: 61  KLLTSIAKMKHYSTVLSLSTQMDSFGVPPNVYTLNILINSFCHLNRVGFAFSVLAKILKL 120

Query: 126 CFTPNAATFNSLIKGLHAESRIMEAAALFTKLKAFGCEPNVITYNTLINGLCRTGHTMIA 185
              P+  TF +LI+GL  E +I EA  LF K+   G +PNV+TY TLINGLC+ G+T  A
Sbjct: 121 GHQPDPTTFTTLIRGLCVEGKIGEALHLFDKMIDEGFQPNVVTYGTLINGLCKVGNTSAA 180

Query: 186 LNLFEEMANGNGEIGVVCKPNTVTYSTIIDGLCKEGFVDKAKALFLQMKDENINPDVVTY 245
           + L   M  GN      C+P+ V Y++IID LCK+  V +A  LF QM  + I+PD+ TY
Sbjct: 181 IRLLRSMEQGN------CQPDVVIYTSIIDSLCKDRQVTEAFNLFSQMVGQGISPDIFTY 234

Query: 246 NSLIHGLCHANDWNEAKRLFIEMMDQGVQPSVVTFNVIMDELCKNRKMDEASRLLDLMVQ 305
            SL+H LC+  +W     L  +M++  + P VV F+ ++D LCK  K+ EA  ++D+M+Q
Sbjct: 235 TSLVHALCNLCEWKHVTTLLNQMVNSKILPDVVIFSTVVDALCKEGKVTEAHEIVDMMIQ 294

Query: 306 RGVRPNACTYNTLMDGFCLMGKINRAEELFGSMESMGCKHDDVSYNILINGYCKNKEVEE 365
           RGV P+  TY TLMDG CL  +++ A ++F  M   G   D +SY  LINGYCK  ++++
Sbjct: 295 RGVEPDVVTYTTLMDGHCLQSEMDEAVKVFDMMVRKGFAPDVISYTTLINGYCKIHKIDK 354

Query: 366 ALSLYREMVSKGIKPTVVTYNTLFLGLFEIHQVEHALKLFDEMQRDGVAADTRTYTTFID 425
           A+ L+ EM  K   P   TYNTL  GL  + +++ A+ LF EM   G   D  TY+  +D
Sbjct: 355 AMYLFEEMCRKEWIPDTKTYNTLMHGLCHVGRLQDAIALFHEMVARGQMPDLVTYSILLD 414

Query: 426 GLCKNGYIIEAVELFRTLRILKCELDIQAYNCLIDGLCKSGRLKFAWELFCSLPHGVLVP 485
            LCKN ++ EA+ L + +       DIQ YN +IDG+C++G L+ A +LF +L    L P
Sbjct: 415 SLCKNCHLEEAMALLKAIEASNLNPDIQVYNIIIDGMCRAGELEAARDLFSNLSSKGLHP 474

Query: 486 NVVTYNIMIQGLCNDGQMDKARDLFLDMEENAAAPDVITFDMLIHGFIRINEPSKVNELL 545
           +V TYNIMI GLC  G +++A  LF++M+ N  +PD  T++ +  GF++ NE  +  +LL
Sbjct: 475 SVWTYNIMIHGLCKRGLLNEANKLFMEMDGNDCSPDGCTYNTIARGFLQNNETLRAIQLL 534

Query: 546 HKMKEKKVMPDASIVSIVVDLLVKNEISLKS 576
            +M  +    D S  +++V++L  + +   S
Sbjct: 535 EEMLARGFSADVSTTTLLVEMLSDDGLDQSS 565

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|359488009|ref|XP_003633686.1| PREDICTED: putative pentatricopeptide repeat-containing protein At1g12700, mitochondrial-like [Vitis vinifera]

 Score =  426 bits (1094), Expect = e-116,   Method: Compositional matrix adjust.
 Identities = 230/568 (40%), Positives = 336/568 (59%), Gaps = 18/568 (3%)

Query: 27  SLLVHFRDLTT---REGDINVITPNEAFCIFDYMLRMHPSPPPVSSFNILLASLAKNKHY 83
           SLL HF  L+        ++  T + A   F+ MLRM P PP    FN LL S+AK KH+
Sbjct: 19  SLLAHFLSLSHNRFHSKSLHFNTIDGAISSFNRMLRMQP-PPSTVDFNKLLTSIAKMKHH 77

Query: 84  DT------RLNATGLFPNLYTYNILINCFCKIGRVSLGFIAFGRILRSCFTPNAATFNSL 137
            T      ++++ G+ PN+YT +ILIN FC + RV   F    +IL+    P+ ATF +L
Sbjct: 78  STLLSLSHQMDSFGIPPNIYTLHILINSFCHLNRVGFAFSVLAKILKLGHQPDTATFTTL 137

Query: 138 IKGLHAESRIMEAAALFTKLKAFGCEPNVITYNTLINGLCRTGHTMIALNLFEEMANGNG 197
           I+G++ E +I EA  LF K+   G  P+V+TY TLINGLC+ G+T  A+ L   M   N 
Sbjct: 138 IRGIYVEGKIGEALHLFDKMIGEGFRPDVVTYGTLINGLCKVGNTSAAIRLLGSMVQKN- 196

Query: 198 EIGVVCKPNTVTYSTIIDGLCKEGFVDKAKALFLQMKDENINPDVVTYNSLIHGLCHAND 257
                C+PN   Y+TIID LCK+  V +A  LF +M  + I+PD+ TYNSLIH LC+  +
Sbjct: 197 -----CQPNVFAYNTIIDSLCKDRQVTEAFNLFSEMVTKGISPDIFTYNSLIHALCNLCE 251

Query: 258 WNEAKRLFIEMMDQGVQPSVVTFNVIMDELCKNRKMDEASRLLDLMVQRGVRPNACTYNT 317
           W     L  EM+D  + P VV+FN ++D LCK  K+ EA  ++D M+QRGV PN  TY  
Sbjct: 252 WKHVATLLNEMVDSKIMPDVVSFNTVVDALCKEGKVTEAHDVVDKMIQRGVEPNVVTYTA 311

Query: 318 LMDGFCLMGKINRAEELFGSMESMGCKHDDVSYNILINGYCKNKEVEEALSLYREMVSKG 377
           LMDG CL+ +++ A ++F +M   GC  + +SYN LINGYCK + +++A+ L+ EM  + 
Sbjct: 312 LMDGHCLLSEMDEAVKVFDTMVCKGCMPNVISYNTLINGYCKIQRIDKAMYLFGEMCRQE 371

Query: 378 IKPTVVTYNTLFLGLFEIHQVEHALKLFDEMQRDGVAADTRTYTTFIDGLCKNGYIIEAV 437
           + P  VTY+TL  GL  + +++ A+ LF EM       +  TY   +D LCKN Y+ EA+
Sbjct: 372 LIPDTVTYSTLIHGLCHVERLQDAIALFHEMVACSQIPNLVTYRILLDYLCKNRYLAEAM 431

Query: 438 ELFRTLRILKCELDIQAYNCLIDGLCKSGRLKFAWELFCSLPHGVLVPNVVTYNIMIQGL 497
            L + +     + DIQ  N  IDG+C++G L+ A +LF +L    L P+V TY+IMI GL
Sbjct: 432 ALLKAIEGSNLDPDIQVNNIAIDGMCRAGELEAARDLFSNLSSKGLQPDVWTYSIMINGL 491

Query: 498 CNDGQMDKARDLFLDMEENAAAPDVITFDMLIHGFIRINEPSKVNELLHKMKEKKVMPDA 557
           C  G +D+A  LF +M+EN    +   ++ +  GF+R NE S+  +LL +M  +    DA
Sbjct: 492 CRRGLLDEASKLFREMDENGCTLNGCIYNTITRGFLRNNETSRAIQLLQEMVARGFSADA 551

Query: 558 SIVSIVVDLLVKNEI--SLKSLPSFLVQ 583
           S +++ V +L  + +  SLK +    VQ
Sbjct: 552 STMTLFVKMLSDDGLDQSLKQILREFVQ 579

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|225452994|ref|XP_002263091.1| PREDICTED: putative pentatricopeptide repeat-containing protein At1g12700, mitochondrial-like [Vitis vinifera]

 Score =  424 bits (1090), Expect = e-116,   Method: Compositional matrix adjust.
 Identities = 224/556 (40%), Positives = 327/556 (58%), Gaps = 25/556 (4%)

Query: 18  ISAFRSNFSSLLVHFRDLTTREGDINVITPNEAFCIFDYMLRMHPSPPPVSSFNILLASL 77
           +S+  + F S  +HF  L            +EA   F+ ML   P PP    FN LL S+
Sbjct: 34  LSSSHNTFHSKPLHFNTL------------DEALSTFNRMLHKQP-PPSTVDFNRLLTSI 80

Query: 78  AKNKHYDT------RLNATGLFPNLYTYNILINCFCKIGRVSLGFIAFGRILRSCFTPNA 131
           AK KH+ T      ++++ G+ P++YT  I+IN  C + RV   F A  +IL+    P+A
Sbjct: 81  AKTKHHSTLLSLSRQMDSFGIPPDVYTLAIVINSLCHLNRVDFAFSALAKILKLGHQPDA 140

Query: 132 ATFNSLIKGLHAESRIMEAAALFTKLKAFGCEPNVITYNTLINGLCRTGHTMIALNLFEE 191
            TF +LI+GL  E +I EA  LF K+   G +PNV+TY TLINGLC+ G+T  A+ L   
Sbjct: 141 TTFTTLIRGLCVEGKIGEALHLFDKMIGEGFQPNVVTYGTLINGLCKVGNTSAAIRLLRS 200

Query: 192 MANGNGEIGVVCKPNTVTYSTIIDGLCKEGFVDKAKALFLQMKDENINPDVVTYNSLIHG 251
           M  GN      C+PN V +ST+ID LCK+  V +A  +F +M  + I+P++VTYNSLIHG
Sbjct: 201 MEQGN------CQPNVVVFSTLIDSLCKDRQVTEAFNIFSEMITKGISPNIVTYNSLIHG 254

Query: 252 LCHANDWNEAKRLFIEMMDQGVQPSVVTFNVIMDELCKNRKMDEASRLLDLMVQRGVRPN 311
           LC   +W     L  EM+D  + P V T N ++D LCK   + EA  ++D+M+ RGV PN
Sbjct: 255 LCKLCEWKHVTTLMNEMVDSKIMPDVFTLNTVVDALCKEGMVAEAHDVVDMMIHRGVEPN 314

Query: 312 ACTYNTLMDGFCLMGKINRAEELFGSMESMGCKHDDVSYNILINGYCKNKEVEEALSLYR 371
             TYN LMDG CL  +++ A ++F +M    C  + +SYN LINGYCK + V++A+ L+ 
Sbjct: 315 VVTYNALMDGHCLRNEVDVAVKVFDTMVHKDCVANVISYNTLINGYCKIQSVDKAMYLFE 374

Query: 372 EMVSKGIKPTVVTYNTLFLGLFEIHQVEHALKLFDEMQRDGVAADTRTYTTFIDGLCKNG 431
           EM  + + P  VTYNTL  GL  + +++ A+ LF EM   G   D  TY T  D LCKN 
Sbjct: 375 EMSRQELTPNTVTYNTLIHGLCHVGRLQDAISLFHEMVARGQIPDLVTYRTLSDYLCKNR 434

Query: 432 YIIEAVELFRTLRILKCELDIQAYNCLIDGLCKSGRLKFAWELFCSLPHGVLVPNVVTYN 491
           ++ +A+ L + +     + DIQ Y  ++DG+C++G L+ A +LF +L    L PNV TYN
Sbjct: 435 HLDKAMALLKAIEGSNWDPDIQIYTTILDGMCRAGELEDARDLFSNLSSKGLQPNVWTYN 494

Query: 492 IMIQGLCNDGQMDKARDLFLDMEENAAAPDVITFDMLIHGFIRINEPSKVNELLHKMKEK 551
           IMI GLC  G + +A  LF +M +N  +P+  T++++  GF+R NE  +  ELL +M  +
Sbjct: 495 IMIHGLCKQGLLAEASKLFSEMNKNGCSPNDCTYNLITRGFLRNNEALRTIELLEEMLAR 554

Query: 552 KVMPDASIVSIVVDLL 567
               D S  +++V +L
Sbjct: 555 GFSVDVSTTTLLVGML 570

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|147768816|emb|CAN62673.1| hypothetical protein VITISV_031897 [Vitis vinifera]

 Score =  423 bits (1088), Expect = e-115,   Method: Compositional matrix adjust.
 Identities = 224/556 (40%), Positives = 327/556 (58%), Gaps = 25/556 (4%)

Query: 18  ISAFRSNFSSLLVHFRDLTTREGDINVITPNEAFCIFDYMLRMHPSPPPVSSFNILLASL 77
           +S+  + F S  +HF  L            +EA   F+ ML   P PP    FN LL S+
Sbjct: 34  LSSSHNTFHSKPLHFNTL------------DEALSTFNRMLHKQP-PPSTVDFNRLLTSI 80

Query: 78  AKNKHYDT------RLNATGLFPNLYTYNILINCFCKIGRVSLGFIAFGRILRSCFTPNA 131
           AK KH+ T      ++++ G+ P++YT  I+IN  C + RV   F A  +IL+    P+A
Sbjct: 81  AKTKHHSTLLSLSRQMDSFGIPPDVYTLAIVINSLCHLNRVDFAFSALAKILKLGHQPDA 140

Query: 132 ATFNSLIKGLHAESRIMEAAALFTKLKAFGCEPNVITYNTLINGLCRTGHTMIALNLFEE 191
            TF +LI+GL  E +I EA  LF K+   G +PNV+TY TLINGLC+ G+T  A+ L   
Sbjct: 141 TTFTTLIRGLCVEGKIGEALHLFDKMIGEGFQPNVVTYGTLINGLCKVGNTSAAIRLLRS 200

Query: 192 MANGNGEIGVVCKPNTVTYSTIIDGLCKEGFVDKAKALFLQMKDENINPDVVTYNSLIHG 251
           M  GN      C+PN V +ST+ID LCK+  V +A  +F +M  + I+P++VTYNSLIHG
Sbjct: 201 MEQGN------CQPNVVVFSTLIDSLCKDRQVTEAFNIFSEMITKGISPNIVTYNSLIHG 254

Query: 252 LCHANDWNEAKRLFIEMMDQGVQPSVVTFNVIMDELCKNRKMDEASRLLDLMVQRGVRPN 311
           LC   +W     L  EM+D  + P V T N ++D LCK   + EA  ++D+M+ RGV PN
Sbjct: 255 LCKLCEWKHVTTLMNEMVDSKIMPDVFTLNTVVDALCKEGMVAEAHDVVDMMIHRGVEPN 314

Query: 312 ACTYNTLMDGFCLMGKINRAEELFGSMESMGCKHDDVSYNILINGYCKNKEVEEALSLYR 371
             TYN LMDG CL  +++ A ++F +M    C  + +SYN LINGYCK + V++A+ L+ 
Sbjct: 315 VVTYNALMDGHCLRNEVDVAVKVFDTMVHKDCVANVISYNTLINGYCKIQSVDKAMYLFE 374

Query: 372 EMVSKGIKPTVVTYNTLFLGLFEIHQVEHALKLFDEMQRDGVAADTRTYTTFIDGLCKNG 431
           EM  + + P  VTYNTL  GL  + +++ A+ LF EM   G   D  TY T  D LCKN 
Sbjct: 375 EMSRQELTPNTVTYNTLIHGLCHVGRLQDAISLFHEMVARGQIPDLVTYRTLSDYLCKNR 434

Query: 432 YIIEAVELFRTLRILKCELDIQAYNCLIDGLCKSGRLKFAWELFCSLPHGVLVPNVVTYN 491
           ++ +A+ L + +     + DIQ Y  ++DG+C++G L+ A +LF +L    L PNV TYN
Sbjct: 435 HLDKAMALLKAIEGSNWDPDIQIYTTILDGMCRAGELEDARDLFSNLSSKGLQPNVWTYN 494

Query: 492 IMIQGLCNDGQMDKARDLFLDMEENAAAPDVITFDMLIHGFIRINEPSKVNELLHKMKEK 551
           IMI GLC  G + +A  LF +M +N  +P+  T++++  GF+R NE  +  ELL +M  +
Sbjct: 495 IMIHGLCKQGLLAEASKLFSEMNKNGCSPNDCTYNLITRGFLRNNEALRTIELLEEMLAR 554

Query: 552 KVMPDASIVSIVVDLL 567
               D S  +++V +L
Sbjct: 555 GFSVDVSTTTLLVGML 570

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

---

Prediction of Gene Ontology (GO) Terms

Close Homologs with Gene Ontology terms Detected by BLAST

Original result of BLAST against Gene Ontology (AMIGO)

ID	Length	Definition	Q cover	H cover	Identity	E-value
Query	595
TAIR|locus:2015228	614	AT1G63080 [Arabidopsis thalian	0.791	0.767	0.392	4.7e-96
TAIR|locus:2015208	630	AT1G63130 [Arabidopsis thalian	0.818	0.773	0.382	3.8e-94
TAIR|locus:2026192	630	RPF2 "rna processing factor 2"	0.791	0.747	0.387	2.1e-93
TAIR|locus:2015494	629	RPF3 "RNA processing factor 3"	0.828	0.783	0.378	5.5e-93
TAIR|locus:2077061	619	AT3G22470 "AT3G22470" [Arabido	0.791	0.760	0.385	1.3e-91
TAIR|locus:2203916	634	AT1G62590 [Arabidopsis thalian	0.791	0.742	0.381	1.7e-91
TAIR|locus:2034760	637	AT1G12300 [Arabidopsis thalian	0.791	0.739	0.385	5.7e-91
TAIR|locus:2015213	629	AT1G63150 [Arabidopsis thalian	0.813	0.769	0.372	3.6e-89
TAIR|locus:1009023134	644	AT1G12775 [Arabidopsis thalian	0.818	0.756	0.375	9.6e-89
TAIR|locus:2015218	590	AT1G63070 [Arabidopsis thalian	0.862	0.869	0.358	1.1e-87

TAIR|locus:2015228 AT1G63080 [Arabidopsis thaliana (taxid:3702)]

 Score = 955 (341.2 bits), Expect = 4.7e-96, P = 4.7e-96
 Identities = 187/477 (39%), Positives = 288/477 (60%)

Query:    91 GLFPNLYTYNILINCFCKIGRVSLGFIAFGRILRSCFTPNAATFNSLIKGLHAESRIMEA 150
             G  P++ T N L+N FC   R+S       +++   + P+  TF +L+ GL   ++  EA
Sbjct:   130 GYGPSIVTLNSLLNGFCHGNRISEAVALVDQMVEMGYQPDTVTFTTLVHGLFQHNKASEA 189

Query:   151 AALFTKLKAFGCEPNVITYNTLINGLCRTGHTMIALNLFEEMANGNGEIGVVCKPNTVTY 210
              AL  ++   GC+P+++TY  +INGLC+ G   +ALNL  +M  G  E  VV       Y
Sbjct:   190 VALVERMVVKGCQPDLVTYGAVINGLCKRGEPDLALNLLNKMEKGKIEADVVI------Y 243

Query:   211 STIIDGLCKEGFVDKAKALFLQMKDENINPDVVTYNSLIHGLCHANDWNEAKRLFIEMMD 270
             ST+ID LCK   VD A  LF +M ++ I PDV TY+SLI  LC+   W++A RL  +M++
Sbjct:   244 STVIDSLCKYRHVDDALNLFTEMDNKGIRPDVFTYSSLISCLCNYGRWSDASRLLSDMLE 303

Query:   271 QGVQPSVVTFNVIMDELCKNRKMDEASRLLDLMVQRGVRPNACTYNTLMDGFCLMGKINR 330
             + + P+VVTFN ++D   K  K+ EA +L D M+QR + PN  TYN+L++GFC+  +++ 
Sbjct:   304 RKINPNVVTFNSLIDAFAKEGKLIEAEKLFDEMIQRSIDPNIVTYNSLINGFCMHDRLDE 363

Query:   331 AEELFGSMESMGCKHDDVSYNILINGYCKNKEVEEALSLYREMVSKGIKPTVVTYNTLFL 390
             A+++F  M S  C  D V+YN LING+CK K+V + + L+R+M  +G+    VTY TL  
Sbjct:   364 AQQIFTLMVSKDCLPDVVTYNTLINGFCKAKKVVDGMELFRDMSRRGLVGNTVTYTTLIH 423

Query:   391 GLFEIHQVEHALKLFDEMQRDGVAADTRTYTTFIDGLCKNGYIIEAVELFRTLRILKCEL 450
             G F+    ++A  +F +M  DGV  +  TY T +DGLCKNG + +A+ +F  L+  K E 
Sbjct:   424 GFFQASDCDNAQMVFKQMVSDGVHPNIMTYNTLLDGLCKNGKLEKAMVVFEYLQKSKMEP 483

Query:   451 DIQAYNCLIDGLCKSGRLKFAWELFCSLPHGVLVPNVVTYNIMIQGLCNDGQMDKARDLF 510
             DI  YN + +G+CK+G+++  W+LFCSL    + P+V+ YN MI G C  G  ++A  LF
Sbjct:   484 DIYTYNIMSEGMCKAGKVEDGWDLFCSLSLKGVKPDVIAYNTMISGFCKKGLKEEAYTLF 543

Query:   511 LDMEENAAAPDVITFDMLIHGFIRINEPSKVNELLHKMKEKKVMPDASIVSIVVDLL 567
             + M+E+   PD  T++ LI   +R  + +   EL+ +M+  +   DAS   +V D+L
Sbjct:   544 IKMKEDGPLPDSGTYNTLIRAHLRDGDKAASAELIKEMRSCRFAGDASTYGLVTDML 600

GO:0005739 "mitochondrion" evidence=ISM

GO:0008150 "biological_process" evidence=ND

TAIR|locus:2015208 AT1G63130 [Arabidopsis thaliana (taxid:3702)]

 Score = 937 (334.9 bits), Expect = 3.8e-94, P = 3.8e-94
 Identities = 191/500 (38%), Positives = 301/500 (60%)

Query:    68 SSFNILLASLAKNKHYDTRLNATGLFPNLYTYNILINCFCKIGRVSLGFIAFGRILRSCF 127
             S  ++ LA LAK       +   G  P++ T N L+N FC   R+S      G+++   +
Sbjct:   130 SQLSLALAVLAK-------MMKLGYEPDIVTLNSLLNGFCHGNRISDAVSLVGQMVEMGY 182

Query:   128 TPNAATFNSLIKGLHAESRIMEAAALFTKLKAFGCEPNVITYNTLINGLCRTGHTMIALN 187
              P++ TFN+LI GL   +R  EA AL  ++   GC+P+++TY  ++NGLC+ G   +AL+
Sbjct:   183 QPDSFTFNTLIHGLFRHNRASEAVALVDRMVVKGCQPDLVTYGIVVNGLCKRGDIDLALS 242

Query:   188 LFEEMANGNGEIGVVCKPNTVTYSTIIDGLCKEGFVDKAKALFLQMKDENINPDVVTYNS 247
             L ++M  G  E GVV       Y+TIID LC    V+ A  LF +M ++ I P+VVTYNS
Sbjct:   243 LLKKMEQGKIEPGVVI------YNTIIDALCNYKNVNDALNLFTEMDNKGIRPNVVTYNS 296

Query:   248 LIHGLCHANDWNEAKRLFIEMMDQGVQPSVVTFNVIMDELCKNRKMDEASRLLDLMVQRG 307
             LI  LC+   W++A RL  +M+++ + P+VVTF+ ++D   K  K+ EA +L D M++R 
Sbjct:   297 LIRCLCNYGRWSDASRLLSDMIERKINPNVVTFSALIDAFVKEGKLVEAEKLYDEMIKRS 356

Query:   308 VRPNACTYNTLMDGFCLMGKINRAEELFGSMESMGCKHDDVSYNILINGYCKNKEVEEAL 367
             + P+  TY++L++GFC+  +++ A+ +F  M S  C  + V+YN LI G+CK K V+E +
Sbjct:   357 IDPDIFTYSSLINGFCMHDRLDEAKHMFELMISKDCFPNVVTYNTLIKGFCKAKRVDEGM 416

Query:   368 SLYREMVSKGIKPTVVTYNTLFLGLFEIHQVEHALKLFDEMQRDGVAADTRTYTTFIDGL 427
              L+REM  +G+    VTY TL  G F+  + ++A  +F +M  DGV  D  TY+  +DGL
Sbjct:   417 ELFREMSQRGLVGNTVTYTTLIHGFFQARECDNAQIVFKQMVSDGVLPDIMTYSILLDGL 476

Query:   428 CKNGYIIEAVELFRTLRILKCELDIQAYNCLIDGLCKSGRLKFAWELFCSLPHGVLVPNV 487
             C NG +  A+ +F  L+  K E DI  YN +I+G+CK+G+++  W+LFCSL    + PNV
Sbjct:   477 CNNGKVETALVVFEYLQRSKMEPDIYTYNIMIEGMCKAGKVEDGWDLFCSLSLKGVKPNV 536

Query:   488 VTYNIMIQGLCNDGQMDKARDLFLDMEENAAAPDVITFDMLIHGFIRINEPSKVNELLHK 547
             VTY  M+ G C  G  ++A  LF +M+E    PD  T++ LI   +R  + +   EL+ +
Sbjct:   537 VTYTTMMSGFCRKGLKEEADALFREMKEEGPLPDSGTYNTLIRAHLRDGDKAASAELIRE 596

Query:   548 MKEKKVMPDASIVSIVVDLL 567
             M+  + + DAS + +V ++L
Sbjct:   597 MRSCRFVGDASTIGLVTNML 616

GO:0005739 "mitochondrion" evidence=ISM

GO:0008150 "biological_process" evidence=ND

TAIR|locus:2026192 RPF2 "rna processing factor 2" [Arabidopsis thaliana (taxid:3702)]

 Score = 930 (332.4 bits), Expect = 2.1e-93, P = 2.1e-93
 Identities = 185/477 (38%), Positives = 289/477 (60%)

Query:    91 GLFPNLYTYNILINCFCKIGRVSLGFIAFGRILRSCFTPNAATFNSLIKGLHAESRIMEA 150
             G  PN+ T + L+N +C   R+S       ++  + + PN  TFN+LI GL   ++  EA
Sbjct:   146 GYEPNIVTLSSLLNGYCHSKRISEAVALVDQMFVTGYQPNTVTFNTLIHGLFLHNKASEA 205

Query:   151 AALFTKLKAFGCEPNVITYNTLINGLCRTGHTMIALNLFEEMANGNGEIGVVCKPNTVTY 210
              AL  ++ A GC+P+++TY  ++NGLC+ G T +A NL  +M  G  E GV+       Y
Sbjct:   206 MALIDRMVAKGCQPDLVTYGVVVNGLCKRGDTDLAFNLLNKMEQGKLEPGVLI------Y 259

Query:   211 STIIDGLCKEGFVDKAKALFLQMKDENINPDVVTYNSLIHGLCHANDWNEAKRLFIEMMD 270
             +TIIDGLCK   +D A  LF +M+ + I P+VVTY+SLI  LC+   W++A RL  +M++
Sbjct:   260 NTIIDGLCKYKHMDDALNLFKEMETKGIRPNVVTYSSLISCLCNYGRWSDASRLLSDMIE 319

Query:   271 QGVQPSVVTFNVIMDELCKNRKMDEASRLLDLMVQRGVRPNACTYNTLMDGFCLMGKINR 330
             + + P V TF+ ++D   K  K+ EA +L D MV+R + P+  TY++L++GFC+  +++ 
Sbjct:   320 RKINPDVFTFSALIDAFVKEGKLVEAEKLYDEMVKRSIDPSIVTYSSLINGFCMHDRLDE 379

Query:   331 AEELFGSMESMGCKHDDVSYNILINGYCKNKEVEEALSLYREMVSKGIKPTVVTYNTLFL 390
             A+++F  M S  C  D V+YN LI G+CK K VEE + ++REM  +G+    VTYN L  
Sbjct:   380 AKQMFEFMVSKHCFPDVVTYNTLIKGFCKYKRVEEGMEVFREMSQRGLVGNTVTYNILIQ 439

Query:   391 GLFEIHQVEHALKLFDEMQRDGVAADTRTYTTFIDGLCKNGYIIEAVELFRTLRILKCEL 450
             GLF+    + A ++F EM  DGV  +  TY T +DGLCKNG + +A+ +F  L+  K E 
Sbjct:   440 GLFQAGDCDMAQEIFKEMVSDGVPPNIMTYNTLLDGLCKNGKLEKAMVVFEYLQRSKMEP 499

Query:   451 DIQAYNCLIDGLCKSGRLKFAWELFCSLPHGVLVPNVVTYNIMIQGLCNDGQMDKARDLF 510
              I  YN +I+G+CK+G+++  W+LFC+L    + P+VV YN MI G C  G  ++A  LF
Sbjct:   500 TIYTYNIMIEGMCKAGKVEDGWDLFCNLSLKGVKPDVVAYNTMISGFCRKGSKEEADALF 559

Query:   511 LDMEENAAAPDVITFDMLIHGFIRINEPSKVNELLHKMKEKKVMPDASIVSIVVDLL 567
              +M+E+   P+   ++ LI   +R  +     EL+ +M+      DAS + +V ++L
Sbjct:   560 KEMKEDGTLPNSGCYNTLIRARLRDGDREASAELIKEMRSCGFAGDASTIGLVTNML 616

GO:0005739 "mitochondrion" evidence=ISM;IDA

GO:0000966 "RNA 5'-end processing" evidence=IMP

GO:0003723 "RNA binding" evidence=IDA

TAIR|locus:2015494 RPF3 "RNA processing factor 3" [Arabidopsis thaliana (taxid:3702)]

 Score = 926 (331.0 bits), Expect = 5.5e-93, P = 5.5e-93
 Identities = 191/505 (37%), Positives = 300/505 (59%)

Query:    69 SFNILLASLAKNKHYDTRLNATGLF------PNLYTYNILINCFCKIGRVSLGFIAFGRI 122
             S+NIL+    +       L   G        P++ T + L+N +C   R+S       ++
Sbjct:   117 SYNILINCFCRRSQLPLALAVLGKMMKLGYEPDIVTLSSLLNGYCHGKRISEAVALVDQM 176

Query:   123 LRSCFTPNAATFNSLIKGLHAESRIMEAAALFTKLKAFGCEPNVITYNTLINGLCRTGHT 182
                 + PN  TFN+LI GL   ++  EA AL  ++ A GC+P++ TY T++NGLC+ G  
Sbjct:   177 FVMEYQPNTVTFNTLIHGLFLHNKASEAVALIDRMVARGCQPDLFTYGTVVNGLCKRGDI 236

Query:   183 MIALNLFEEMANGNGEIGVVCKPNTVTYSTIIDGLCKEGFVDKAKALFLQMKDENINPDV 242
              +AL+L ++M  G  E  VV       Y+TIID LC    V+ A  LF +M ++ I P+V
Sbjct:   237 DLALSLLKKMEKGKIEADVVI------YTTIIDALCNYKNVNDALNLFTEMDNKGIRPNV 290

Query:   243 VTYNSLIHGLCHANDWNEAKRLFIEMMDQGVQPSVVTFNVIMDELCKNRKMDEASRLLDL 302
             VTYNSLI  LC+   W++A RL  +M+++ + P+VVTF+ ++D   K  K+ EA +L D 
Sbjct:   291 VTYNSLIRCLCNYGRWSDASRLLSDMIERKINPNVVTFSALIDAFVKEGKLVEAEKLYDE 350

Query:   303 MVQRGVRPNACTYNTLMDGFCLMGKINRAEELFGSMESMGCKHDDVSYNILINGYCKNKE 362
             M++R + P+  TY++L++GFC+  +++ A+ +F  M S  C  + V+YN LI G+CK K 
Sbjct:   351 MIKRSIDPDIFTYSSLINGFCMHDRLDEAKHMFELMISKDCFPNVVTYNTLIKGFCKAKR 410

Query:   363 VEEALSLYREMVSKGIKPTVVTYNTLFLGLFEIHQVEHALKLFDEMQRDGVAADTRTYTT 422
             VEE + L+REM  +G+    VTYNTL  GLF+    + A K+F +M  DGV  D  TY+ 
Sbjct:   411 VEEGMELFREMSQRGLVGNTVTYNTLIQGLFQAGDCDMAQKIFKKMVSDGVPPDIITYSI 470

Query:   423 FIDGLCKNGYIIEAVELFRTLRILKCELDIQAYNCLIDGLCKSGRLKFAWELFCSLPHGV 482
              +DGLCK G + +A+ +F  L+  K E DI  YN +I+G+CK+G+++  W+LFCSL    
Sbjct:   471 LLDGLCKYGKLEKALVVFEYLQKSKMEPDIYTYNIMIEGMCKAGKVEDGWDLFCSLSLKG 530

Query:   483 LVPNVVTYNIMIQGLCNDGQMDKARDLFLDMEENAAAPDVITFDMLIHGFIRINEPSKVN 542
             + PNV+ Y  MI G C  G  ++A  LF +M+E+   P+  T++ LI   +R  + +   
Sbjct:   531 VKPNVIIYTTMISGFCRKGLKEEADALFREMKEDGTLPNSGTYNTLIRARLRDGDKAASA 590

Query:   543 ELLHKMKEKKVMPDASIVSIVVDLL 567
             EL+ +M+    + DAS +S+V+++L
Sbjct:   591 ELIKEMRSCGFVGDASTISMVINML 615

GO:0005739 "mitochondrion" evidence=ISM;IDA

GO:0006397 "mRNA processing" evidence=IMP

TAIR|locus:2077061 AT3G22470 "AT3G22470" [Arabidopsis thaliana (taxid:3702)]

 Score = 913 (326.5 bits), Expect = 1.3e-91, P = 1.3e-91
 Identities = 184/477 (38%), Positives = 286/477 (59%)

Query:    91 GLFPNLYTYNILINCFCKIGRVSLGFIAFGRILRSCFTPNAATFNSLIKGLHAESRIMEA 150
             G  P+  T++ L+N FC  GRVS       R++     P+  T ++LI GL  + R+ EA
Sbjct:   135 GYEPDTITFSTLVNGFCLEGRVSEAVALVDRMVEMKQRPDLVTVSTLINGLCLKGRVSEA 194

Query:   151 AALFTKLKAFGCEPNVITYNTLINGLCRTGHTMIALNLFEEMANGNGEIGVVCKPNTVTY 210
               L  ++  +G +P+ +TY  ++N LC++G++ +AL+LF +M   N       K + V Y
Sbjct:   195 LVLIDRMVEYGFQPDEVTYGPVLNRLCKSGNSALALDLFRKMEERN------IKASVVQY 248

Query:   211 STIIDGLCKEGFVDKAKALFLQMKDENINPDVVTYNSLIHGLCHANDWNEAKRLFIEMMD 270
             S +ID LCK+G  D A +LF +M+ + I  DVVTY+SLI GLC+   W++  ++  EM+ 
Sbjct:   249 SIVIDSLCKDGSFDDALSLFNEMEMKGIKADVVTYSSLIGGLCNDGKWDDGAKMLREMIG 308

Query:   271 QGVQPSVVTFNVIMDELCKNRKMDEASRLLDLMVQRGVRPNACTYNTLMDGFCLMGKINR 330
             + + P VVTF+ ++D   K  K+ EA  L + M+ RG+ P+  TYN+L+DGFC    ++ 
Sbjct:   309 RNIIPDVVTFSALIDVFVKEGKLLEAKELYNEMITRGIAPDTITYNSLIDGFCKENCLHE 368

Query:   331 AEELFGSMESMGCKHDDVSYNILINGYCKNKEVEEALSLYREMVSKGIKPTVVTYNTLFL 390
             A ++F  M S GC+ D V+Y+ILIN YCK K V++ + L+RE+ SKG+ P  +TYNTL L
Sbjct:   369 ANQMFDLMVSKGCEPDIVTYSILINSYCKAKRVDDGMRLFREISSKGLIPNTITYNTLVL 428

Query:   391 GLFEIHQVEHALKLFDEMQRDGVAADTRTYTTFIDGLCKNGYIIEAVELFRTLRILKCEL 450
             G  +  ++  A +LF EM   GV     TY   +DGLC NG + +A+E+F  ++  +  L
Sbjct:   429 GFCQSGKLNAAKELFQEMVSRGVPPSVVTYGILLDGLCDNGELNKALEIFEKMQKSRMTL 488

Query:   451 DIQAYNCLIDGLCKSGRLKFAWELFCSLPHGVLVPNVVTYNIMIQGLCNDGQMDKARDLF 510
              I  YN +I G+C + ++  AW LFCSL    + P+VVTYN+MI GLC  G + +A  LF
Sbjct:   489 GIGIYNIIIHGMCNASKVDDAWSLFCSLSDKGVKPDVVTYNVMIGGLCKKGSLSEADMLF 548

Query:   511 LDMEENAAAPDVITFDMLIHGFIRINEPSKVNELLHKMKEKKVMPDASIVSIVVDLL 567
               M+E+   PD  T+++LI   +  +      EL+ +MK      D+S + +V+D+L
Sbjct:   549 RKMKEDGCTPDDFTYNILIRAHLGGSGLISSVELIEEMKVCGFSADSSTIKMVIDML 605

GO:0003674 "molecular_function" evidence=ND

GO:0005739 "mitochondrion" evidence=ISM

GO:0008150 "biological_process" evidence=ND

TAIR|locus:2203916 AT1G62590 [Arabidopsis thaliana (taxid:3702)]

 Score = 912 (326.1 bits), Expect = 1.7e-91, P = 1.7e-91
 Identities = 182/477 (38%), Positives = 290/477 (60%)

Query:    91 GLFPNLYTYNILINCFCKIGRVSLGFIAFGRILRSCFTPNAATFNSLIKGLHAESRIMEA 150
             G  P++ T + L+N +C   R+S       +++   + P+  TF +LI GL   ++  EA
Sbjct:   150 GYEPSIVTLSSLLNGYCHGKRISDAVALVDQMVEMGYRPDTITFTTLIHGLFLHNKASEA 209

Query:   151 AALFTKLKAFGCEPNVITYNTLINGLCRTGHTMIALNLFEEMANGNGEIGVVCKPNTVTY 210
              AL  ++   GC+PN++TY  ++NGLC+ G T +ALNL  +M     E  VV       +
Sbjct:   210 VALVDRMVQRGCQPNLVTYGVVVNGLCKRGDTDLALNLLNKMEAAKIEADVVI------F 263

Query:   211 STIIDGLCKEGFVDKAKALFLQMKDENINPDVVTYNSLIHGLCHANDWNEAKRLFIEMMD 270
             +TIID LCK   VD A  LF +M+ + I P+VVTY+SLI  LC    W++A +L  +M++
Sbjct:   264 NTIIDSLCKYRHVDDALNLFKEMETKGIRPNVVTYSSLISCLCSYGRWSDASQLLSDMIE 323

Query:   271 QGVQPSVVTFNVIMDELCKNRKMDEASRLLDLMVQRGVRPNACTYNTLMDGFCLMGKINR 330
             + + P++VTFN ++D   K  K  EA +L D M++R + P+  TYN+L++GFC+  ++++
Sbjct:   324 KKINPNLVTFNALIDAFVKEGKFVEAEKLYDDMIKRSIDPDIFTYNSLVNGFCMHDRLDK 383

Query:   331 AEELFGSMESMGCKHDDVSYNILINGYCKNKEVEEALSLYREMVSKGIKPTVVTYNTLFL 390
             A+++F  M S  C  D V+YN LI G+CK+K VE+   L+REM  +G+    VTY TL  
Sbjct:   384 AKQMFEFMVSKDCFPDVVTYNTLIKGFCKSKRVEDGTELFREMSHRGLVGDTVTYTTLIQ 443

Query:   391 GLFEIHQVEHALKLFDEMQRDGVAADTRTYTTFIDGLCKNGYIIEAVELFRTLRILKCEL 450
             GLF     ++A K+F +M  DGV  D  TY+  +DGLC NG + +A+E+F  ++  + +L
Sbjct:   444 GLFHDGDCDNAQKVFKQMVSDGVPPDIMTYSILLDGLCNNGKLEKALEVFDYMQKSEIKL 503

Query:   451 DIQAYNCLIDGLCKSGRLKFAWELFCSLPHGVLVPNVVTYNIMIQGLCNDGQMDKARDLF 510
             DI  Y  +I+G+CK+G++   W+LFCSL    + PNVVTYN MI GLC+   + +A  L 
Sbjct:   504 DIYIYTTMIEGMCKAGKVDDGWDLFCSLSLKGVKPNVVTYNTMISGLCSKRLLQEAYALL 563

Query:   511 LDMEENAAAPDVITFDMLIHGFIRINEPSKVNELLHKMKEKKVMPDASIVSIVVDLL 567
               M+E+   P+  T++ LI   +R  + +   EL+ +M+  + + DAS + +V ++L
Sbjct:   564 KKMKEDGPLPNSGTYNTLIRAHLRDGDKAASAELIREMRSCRFVGDASTIGLVANML 620

GO:0005739 "mitochondrion" evidence=ISM

GO:0008150 "biological_process" evidence=ND

TAIR|locus:2034760 AT1G12300 [Arabidopsis thaliana (taxid:3702)]

 Score = 907 (324.3 bits), Expect = 5.7e-91, P = 5.7e-91
 Identities = 184/477 (38%), Positives = 279/477 (58%)

Query:    91 GLFPNLYTYNILINCFCKIGRVSLGFIAFGRILRSCFTPNAATFNSLIKGLHAESRIMEA 150
             G  PN  T++ LIN  C  GRVS       R++     P+  T N+L+ GL    +  EA
Sbjct:   153 GYEPNTITFSTLINGLCLEGRVSEALELVDRMVEMGHKPDLITINTLVNGLCLSGKEAEA 212

Query:   151 AALFTKLKAFGCEPNVITYNTLINGLCRTGHTMIALNLFEEMANGNGEIGVVCKPNTVTY 210
               L  K+  +GC+PN +TY  ++N +C++G T +A+ L  +M   N       K + V Y
Sbjct:   213 MLLIDKMVEYGCQPNAVTYGPVLNVMCKSGQTALAMELLRKMEERN------IKLDAVKY 266

Query:   211 STIIDGLCKEGFVDKAKALFLQMKDENINPDVVTYNSLIHGLCHANDWNEAKRLFIEMMD 270
             S IIDGLCK G +D A  LF +M+ + I  +++TYN LI G C+A  W++  +L  +M+ 
Sbjct:   267 SIIIDGLCKHGSLDNAFNLFNEMEMKGITTNIITYNILIGGFCNAGRWDDGAKLLRDMIK 326

Query:   271 QGVQPSVVTFNVIMDELCKNRKMDEASRLLDLMVQRGVRPNACTYNTLMDGFCLMGKINR 330
             + + P+VVTF+V++D   K  K+ EA  L   M+ RG+ P+  TY +L+DGFC    +++
Sbjct:   327 RKINPNVVTFSVLIDSFVKEGKLREAEELHKEMIHRGIAPDTITYTSLIDGFCKENHLDK 386

Query:   331 AEELFGSMESMGCKHDDVSYNILINGYCKNKEVEEALSLYREMVSKGIKPTVVTYNTLFL 390
             A ++   M S GC  +  ++NILINGYCK   +++ L L+R+M  +G+    VTYNTL  
Sbjct:   387 ANQMVDLMVSKGCDPNIRTFNILINGYCKANRIDDGLELFRKMSLRGVVADTVTYNTLIQ 446

Query:   391 GLFEIHQVEHALKLFDEMQRDGVAADTRTYTTFIDGLCKNGYIIEAVELFRTLRILKCEL 450
             G  E+ ++  A +LF EM    V  +  TY   +DGLC NG   +A+E+F  +   K EL
Sbjct:   447 GFCELGKLNVAKELFQEMVSRKVPPNIVTYKILLDGLCDNGESEKALEIFEKIEKSKMEL 506

Query:   451 DIQAYNCLIDGLCKSGRLKFAWELFCSLPHGVLVPNVVTYNIMIQGLCNDGQMDKARDLF 510
             DI  YN +I G+C + ++  AW+LFCSLP   + P V TYNIMI GLC  G + +A  LF
Sbjct:   507 DIGIYNIIIHGMCNASKVDDAWDLFCSLPLKGVKPGVKTYNIMIGGLCKKGPLSEAELLF 566

Query:   511 LDMEENAAAPDVITFDMLIHGFIRINEPSKVNELLHKMKEKKVMPDASIVSIVVDLL 567
               MEE+  APD  T+++LI   +   + +K  +L+ ++K      DAS + +V+D+L
Sbjct:   567 RKMEEDGHAPDGWTYNILIRAHLGDGDATKSVKLIEELKRCGFSVDASTIKMVIDML 623

GO:0005739 "mitochondrion" evidence=ISM

GO:0008150 "biological_process" evidence=ND

TAIR|locus:2015213 AT1G63150 [Arabidopsis thaliana (taxid:3702)]

 Score = 890 (318.4 bits), Expect = 3.6e-89, P = 3.6e-89
 Identities = 186/500 (37%), Positives = 299/500 (59%)

Query:    68 SSFNILLASLAKNKHYDTRLNATGLFPNLYTYNILINCFCKIGRVSLGFIAFGRILRSCF 127
             S  ++ LA LAK       +   G  P++ T + L+N +C   R+S       +++   +
Sbjct:   132 SQLSLALAVLAK-------MMKLGYEPDIVTLSSLLNGYCHSKRISDAVALVDQMVEMGY 184

Query:   128 TPNAATFNSLIKGLHAESRIMEAAALFTKLKAFGCEPNVITYNTLINGLCRTGHTMIALN 187
              P+  TF +LI GL   ++  EA AL  ++   GC+P+++TY T++NGLC+ G   +ALN
Sbjct:   185 KPDTFTFTTLIHGLFLHNKASEAVALVDQMVQRGCQPDLVTYGTVVNGLCKRGDIDLALN 244

Query:   188 LFEEMANGNGEIGVVCKPNTVTYSTIIDGLCKEGFVDKAKALFLQMKDENINPDVVTYNS 247
             L  +M     E   + K N V ++TIID LCK   V+ A  LF +M+ + I P+VVTYNS
Sbjct:   245 LLNKM-----EAARI-KANVVIFNTIIDSLCKYRHVEVAVDLFTEMETKGIRPNVVTYNS 298

Query:   248 LIHGLCHANDWNEAKRLFIEMMDQGVQPSVVTFNVIMDELCKNRKMDEASRLLDLMVQRG 307
             LI+ LC+   W++A RL   M+++ + P+VVTFN ++D   K  K+ EA +L + M+QR 
Sbjct:   299 LINCLCNYGRWSDASRLLSNMLEKKINPNVVTFNALIDAFFKEGKLVEAEKLHEEMIQRS 358

Query:   308 VRPNACTYNTLMDGFCLMGKINRAEELFGSMESMGCKHDDVSYNILINGYCKNKEVEEAL 367
             + P+  TYN L++GFC+  +++ A+++F  M S  C  +  +YN LING+CK K VE+ +
Sbjct:   359 IDPDTITYNLLINGFCMHNRLDEAKQMFKFMVSKDCLPNIQTYNTLINGFCKCKRVEDGV 418

Query:   368 SLYREMVSKGIKPTVVTYNTLFLGLFEIHQVEHALKLFDEMQRDGVAADTRTYTTFIDGL 427
              L+REM  +G+    VTY T+  G F+    + A  +F +M  + V  D  TY+  + GL
Sbjct:   419 ELFREMSQRGLVGNTVTYTTIIQGFFQAGDCDSAQMVFKQMVSNRVPTDIMTYSILLHGL 478

Query:   428 CKNGYIIEAVELFRTLRILKCELDIQAYNCLIDGLCKSGRLKFAWELFCSLPHGVLVPNV 487
             C  G +  A+ +F+ L+  + EL+I  YN +I+G+CK+G++  AW+LFCSL    + P+V
Sbjct:   479 CSYGKLDTALVIFKYLQKSEMELNIFIYNTMIEGMCKAGKVGEAWDLFCSLS---IKPDV 535

Query:   488 VTYNIMIQGLCNDGQMDKARDLFLDMEENAAAPDVITFDMLIHGFIRINEPSKVNELLHK 547
             VTYN MI GLC+   + +A DLF  M+E+   P+  T++ LI   +R  + +   EL+ +
Sbjct:   536 VTYNTMISGLCSKRLLQEADDLFRKMKEDGTLPNSGTYNTLIRANLRDCDRAASAELIKE 595

Query:   548 MKEKKVMPDASIVSIVVDLL 567
             M+    + DAS +S+V ++L
Sbjct:   596 MRSSGFVGDASTISLVTNML 615

GO:0005739 "mitochondrion" evidence=ISM

TAIR|locus:1009023134 AT1G12775 [Arabidopsis thaliana (taxid:3702)]

 Score = 886 (316.9 bits), Expect = 9.6e-89, P = 9.6e-89
 Identities = 186/496 (37%), Positives = 282/496 (56%)

Query:    91 GLFPNLYTYNILINCFCKIGRVSLGFIAFGRILRSCFTPNAATFNSLIKGLHAESRIMEA 150
             G  P+   +N L+N  C   RVS       R++     P   T N+L+ GL    ++ +A
Sbjct:   153 GYEPDTVIFNTLLNGLCLECRVSEALELVDRMVEMGHKPTLITLNTLVNGLCLNGKVSDA 212

Query:   151 AALFTKLKAFGCEPNVITYNTLINGLCRTGHTMIALNLFEEMANGNGEIGVVCKPNTVTY 210
               L  ++   G +PN +TY  ++N +C++G T +A+ L  +M   N       K + V Y
Sbjct:   213 VVLIDRMVETGFQPNEVTYGPVLNVMCKSGQTALAMELLRKMEERN------IKLDAVKY 266

Query:   211 STIIDGLCKEGFVDKAKALFLQMKDENINPDVVTYNSLIHGLCHANDWNEAKRLFIEMMD 270
             S IIDGLCK+G +D A  LF +M+ +    D++TYN+LI G C+A  W++  +L  +M+ 
Sbjct:   267 SIIIDGLCKDGSLDNAFNLFNEMEIKGFKADIITYNTLIGGFCNAGRWDDGAKLLRDMIK 326

Query:   271 QGVQPSVVTFNVIMDELCKNRKMDEASRLLDLMVQRGVRPNACTYNTLMDGFCLMGKINR 330
             + + P+VVTF+V++D   K  K+ EA +LL  M+QRG+ PN  TYN+L+DGFC   ++  
Sbjct:   327 RKISPNVVTFSVLIDSFVKEGKLREADQLLKEMMQRGIAPNTITYNSLIDGFCKENRLEE 386

Query:   331 AEELFGSMESMGCKHDDVSYNILINGYCKNKEVEEALSLYREMVSKGIKPTVVTYNTLFL 390
             A ++   M S GC  D +++NILINGYCK   +++ L L+REM  +G+    VTYNTL  
Sbjct:   387 AIQMVDLMISKGCDPDIMTFNILINGYCKANRIDDGLELFREMSLRGVIANTVTYNTLVQ 446

Query:   391 GLFEIHQVEHALKLFDEMQRDGVAADTRTYTTFIDGLCKNGYIIEAVELFRTLRILKCEL 450
             G  +  ++E A KLF EM    V  D  +Y   +DGLC NG + +A+E+F  +   K EL
Sbjct:   447 GFCQSGKLEVAKKLFQEMVSRRVRPDIVSYKILLDGLCDNGELEKALEIFGKIEKSKMEL 506

Query:   451 DIQAYNCLIDGLCKSGRLKFAWELFCSLP-HGVLVPNVVTYNIMIQGLCNDGQMDKARDL 509
             DI  Y  +I G+C + ++  AW+LFCSLP  GV + +   YNIMI  LC    + KA  L
Sbjct:   507 DIGIYMIIIHGMCNASKVDDAWDLFCSLPLKGVKL-DARAYNIMISELCRKDSLSKADIL 565

Query:   510 FLDMEENAAAPDVITFDMLIHGFIRINEPSKVNELLHKMKEKKVMPDASIVSIVVDLLVK 569
             F  M E   APD +T+++LI   +  ++ +   EL+ +MK      D S V +V+++L  
Sbjct:   566 FRKMTEEGHAPDELTYNILIRAHLGDDDATTAAELIEEMKSSGFPADVSTVKMVINMLSS 625

Query:   570 NEISLKSLPSFLVQER 585
              E+  KS    L   R
Sbjct:   626 GELD-KSFLDMLSTTR 640

GO:0005739 "mitochondrion" evidence=ISM

TAIR|locus:2015218 AT1G63070 [Arabidopsis thaliana (taxid:3702)]

 Score = 876 (313.4 bits), Expect = 1.1e-87, P = 1.1e-87
 Identities = 189/527 (35%), Positives = 300/527 (56%)

Query:    48 NEAFCIFDYMLRMHPSPPPVSSFNILLASLAKNKHYDT------RLNATGLFPNLYTYNI 101
             ++A  +F  M++  P P  V  F+ LL+++AK   +D       ++   G+  NLYTY+I
Sbjct:    57 DDAIGLFGDMVKSRPFPSIVE-FSKLLSAIAKMNKFDLVISLGEQMQNLGISHNLYTYSI 115

Query:   102 LINCFCKIGRVSLGFIAFGRILRSCFTPNAATFNSLIKGLHAESRIMEAAALFTKLKAFG 161
              IN FC+  ++SL     G++++  + P+  T NSL+ G    +RI EA AL  ++   G
Sbjct:   116 FINYFCRRSQLSLALAILGKMMKLGYGPSIVTLNSLLNGFCHGNRISEAVALVDQMVEMG 175

Query:   162 CEPNVITYNTLINGLCRTGHTMIALNLFEEMANGNGEIGVVCKPNTVTYSTIIDGLCKEG 221
              +P+ +T+ TL++GL +      A+ L E M    G     C+P+ VTY  +I+GLCK G
Sbjct:   176 YQPDTVTFTTLVHGLFQHNKASEAVALVERMVV-KG-----CQPDLVTYGAVINGLCKRG 229

Query:   222 FVDKAKALFLQMKDENINPDVVTYNSLIHGLCHANDWNEAKRLFIEMMDQGVQPSVVTFN 281
               D A  L  +M+   I  DVV YN++I GLC     ++A  LF +M  +G++P V T+N
Sbjct:   230 EPDLALNLLNKMEKGKIEADVVIYNTIIDGLCKYKHMDDAFDLFNKMETKGIKPDVFTYN 289

Query:   282 VIMDELCKNRKMDEASRLLDLMVQRGVRPNACTYNTLMDGFCLMGKINRAEELFGSM-ES 340
              ++  LC   +  +ASRLL  M+++ + P+   +N L+D F   GK+  AE+L+  M +S
Sbjct:   290 PLISCLCNYGRWSDASRLLSDMLEKNINPDLVFFNALIDAFVKEGKLVEAEKLYDEMVKS 349

Query:   341 MGCKHDDVSYNILINGYCKNKEVEEALSLYREMVSKGIKPTVVTYNTLFLGLFEIHQVEH 400
               C  D V+YN LI G+CK K VEE + ++REM  +G+    VTY TL  G F+    ++
Sbjct:   350 KHCFPDVVAYNTLIKGFCKYKRVEEGMEVFREMSQRGLVGNTVTYTTLIHGFFQARDCDN 409

Query:   401 ALKLFDEMQRDGVAADTRTYTTFIDGLCKNGYIIEAVELFRTLRILKCELDIQAYNCLID 460
             A  +F +M  DGV  D  TY   +DGLC NG +  A+ +F  ++    +LDI  Y  +I+
Sbjct:   410 AQMVFKQMVSDGVHPDIMTYNILLDGLCNNGNVETALVVFEYMQKRDMKLDIVTYTTMIE 469

Query:   461 GLCKSGRLKFAWELFCSLPHGVLVPNVVTYNIMIQGLCNDGQMDKARDLFLDMEENAAAP 520
              LCK+G+++  W+LFCSL    + PNVVTY  M+ G C  G  ++A  LF++M+E+   P
Sbjct:   470 ALCKAGKVEDGWDLFCSLSLKGVKPNVVTYTTMMSGFCRKGLKEEADALFVEMKEDGPLP 529

Query:   521 DVITFDMLIHGFIRINEPSKVNELLHKMKEKKVMPDASIVSIVVDLL 567
             +  T++ LI   +R  + +   EL+ +M+      DAS   +V ++L
Sbjct:   530 NSGTYNTLIRARLRDGDEAASAELIKEMRSCGFAGDASTFGLVTNML 576

GO:0005739 "mitochondrion" evidence=ISM

GO:0008150 "biological_process" evidence=ND

---

Prediction of Enzyme Commission (EC) Number

EC Number Prediction by Annotation Transfer from SWISS-PROT Entries

Original result of BLAST against SWISS-PROT

ID	Name	Annotated EC number	Identity	Query coverage	Hit coverage	RBH(Q2H)	RBH(H2Q)
P0C7Q7	PPR38_ARATH	No assigned EC number	0.3675	0.9210	0.9102	yes	no

EC Number Prediction by Ezypred Server

Original result from Ezypred Server

Fail to connect to Ezypred Server

EC Number Prediction by EFICAz Software

No EC number assignment, probably not an enzyme!

---

Prediction of Functionally Associated Proteins

Functionally Associated Proteins Detected by STRING

Original result from the STRING server

Fail to connect to STRING server

---

Conserved Domains and Related Protein Families

Conserved Domains Detected by RPS-BLAST

Original result of RPS-BLAST against CDD database part I

ID	Length	Definition	E-value
Query	595
PLN03218	1060	PLN03218, PLN03218, maturation of RBCL 1; Provisio	7e-35
PLN03218	1060	PLN03218, PLN03218, maturation of RBCL 1; Provisio	1e-26
PLN03077	857	PLN03077, PLN03077, Protein ECB2; Provisional	2e-26
PLN03218	1060	PLN03218, PLN03218, maturation of RBCL 1; Provisio	1e-25
PLN03218	1060	PLN03218, PLN03218, maturation of RBCL 1; Provisio	8e-24
PLN03081	697	PLN03081, PLN03081, pentatricopeptide (PPR) repeat	3e-21
PLN03077	857	PLN03077, PLN03077, Protein ECB2; Provisional	1e-19
pfam13041	50	pfam13041, PPR_2, PPR repeat family	3e-19
pfam13041	50	pfam13041, PPR_2, PPR repeat family	9e-18
pfam13041	50	pfam13041, PPR_2, PPR repeat family	2e-17
pfam13041	50	pfam13041, PPR_2, PPR repeat family	2e-17
pfam13041	50	pfam13041, PPR_2, PPR repeat family	6e-17
PLN03077	857	PLN03077, PLN03077, Protein ECB2; Provisional	1e-16
pfam13041	50	pfam13041, PPR_2, PPR repeat family	2e-16
pfam13041	50	pfam13041, PPR_2, PPR repeat family	1e-15
pfam13041	50	pfam13041, PPR_2, PPR repeat family	1e-15
pfam13041	50	pfam13041, PPR_2, PPR repeat family	2e-13
pfam13041	50	pfam13041, PPR_2, PPR repeat family	2e-12
PLN03077	857	PLN03077, PLN03077, Protein ECB2; Provisional	2e-11
pfam12854	34	pfam12854, PPR_1, PPR repeat	5e-11
pfam12854	34	pfam12854, PPR_1, PPR repeat	3e-10
pfam13041	50	pfam13041, PPR_2, PPR repeat family	5e-10
pfam12854	34	pfam12854, PPR_1, PPR repeat	7e-10
TIGR00756	35	TIGR00756, PPR, pentatricopeptide repeat domain (P	7e-10
pfam12854	34	pfam12854, PPR_1, PPR repeat	1e-09
PLN03081	697	PLN03081, PLN03081, pentatricopeptide (PPR) repeat	3e-09
pfam12854	34	pfam12854, PPR_1, PPR repeat	3e-09
pfam01535	31	pfam01535, PPR, PPR repeat	4e-09
pfam12854	34	pfam12854, PPR_1, PPR repeat	7e-09
TIGR00756	35	TIGR00756, PPR, pentatricopeptide repeat domain (P	6e-08
pfam12854	34	pfam12854, PPR_1, PPR repeat	2e-07
TIGR00756	35	TIGR00756, PPR, pentatricopeptide repeat domain (P	3e-07
pfam12854	34	pfam12854, PPR_1, PPR repeat	6e-07
TIGR00756	35	TIGR00756, PPR, pentatricopeptide repeat domain (P	2e-06
pfam01535	31	pfam01535, PPR, PPR repeat	2e-06
pfam13041	50	pfam13041, PPR_2, PPR repeat family	3e-06
pfam01535	31	pfam01535, PPR, PPR repeat	3e-06
pfam01535	31	pfam01535, PPR, PPR repeat	5e-06
pfam13812	34	pfam13812, PPR_3, Pentatricopeptide repeat domain	5e-06
pfam13041	50	pfam13041, PPR_2, PPR repeat family	6e-06
pfam12854	34	pfam12854, PPR_1, PPR repeat	7e-06
TIGR00756	35	TIGR00756, PPR, pentatricopeptide repeat domain (P	7e-06
pfam12854	34	pfam12854, PPR_1, PPR repeat	8e-06
pfam01535	31	pfam01535, PPR, PPR repeat	9e-06
pfam13812	34	pfam13812, PPR_3, Pentatricopeptide repeat domain	9e-06
TIGR00756	35	TIGR00756, PPR, pentatricopeptide repeat domain (P	2e-05
pfam12854	34	pfam12854, PPR_1, PPR repeat	3e-05
pfam01535	31	pfam01535, PPR, PPR repeat	1e-04
pfam01535	31	pfam01535, PPR, PPR repeat	2e-04
TIGR00756	35	TIGR00756, PPR, pentatricopeptide repeat domain (P	5e-04
pfam01535	31	pfam01535, PPR, PPR repeat	8e-04
TIGR00756	35	TIGR00756, PPR, pentatricopeptide repeat domain (P	0.001
TIGR00756	35	TIGR00756, PPR, pentatricopeptide repeat domain (P	0.002
pfam01535	31	pfam01535, PPR, PPR repeat	0.002
TIGR00756	35	TIGR00756, PPR, pentatricopeptide repeat domain (P	0.004
pfam13812	34	pfam13812, PPR_3, Pentatricopeptide repeat domain	0.004

>gnl|CDD|215636 PLN03218, PLN03218, maturation of RBCL 1; Provisional

 Score =  140 bits (355), Expect = 7e-35
 Identities = 86/371 (23%), Positives = 167/371 (45%), Gaps = 11/371 (2%)

Query: 65  PPVSSFNILLASLAKNKHYDTRL------NATGLFPNLYTYNILINCFCKIGRVSLGFIA 118
           P +S+FN+L++  A ++  D  L         GL  +   Y  LI+   K G+V   F  
Sbjct: 435 PTLSTFNMLMSVCASSQDIDGALRVLRLVQEAGLKADCKLYTTLISTCAKSGKVDAMFEV 494

Query: 119 FGRILRSCFTPNAATFNSLIKGLHAESRIMEAAALFTKLKAFGCEPNVITYNTLINGLCR 178
           F  ++ +    N  TF +LI G     ++ +A   +  +++   +P+ + +N LI+   +
Sbjct: 495 FHEMVNAGVEANVHTFGALIDGCARAGQVAKAFGAYGIMRSKNVKPDRVVFNALISACGQ 554

Query: 179 TGHTMIALNLFEEMANGNGEIGVVCKPNTVTYSTIIDGLCKEGFVDKAKALFLQMKDENI 238
           +G    A ++  EM      I     P+ +T   ++      G VD+AK ++  + + NI
Sbjct: 555 SGAVDRAFDVLAEMKAETHPI----DPDHITVGALMKACANAGQVDRAKEVYQMIHEYNI 610

Query: 239 NPDVVTYNSLIHGLCHANDWNEAKRLFIEMMDQGVQPSVVTFNVIMDELCKNRKMDEASR 298
                 Y   ++      DW+ A  ++ +M  +GV+P  V F+ ++D       +D+A  
Sbjct: 611 KGTPEVYTIAVNSCSQKGDWDFALSIYDDMKKKGVKPDEVFFSALVDVAGHAGDLDKAFE 670

Query: 299 LLDLMVQRGVRPNACTYNTLMDGFCLMGKINRAEELFGSMESMGCKHDDVSYNILINGYC 358
           +L    ++G++    +Y++LM          +A EL+  ++S+  +    + N LI   C
Sbjct: 671 ILQDARKQGIKLGTVSYSSLMGACSNAKNWKKALELYEDIKSIKLRPTVSTMNALITALC 730

Query: 359 KNKEVEEALSLYREMVSKGIKPTVVTYNTLFLGLFEIHQVEHALKLFDEMQRDGVAADTR 418
           +  ++ +AL +  EM   G+ P  +TY+ L +        +  L L  + + DG+  +  
Sbjct: 731 EGNQLPKALEVLSEMKRLGLCPNTITYSILLVASERKDDADVGLDLLSQAKEDGIKPNLV 790

Query: 419 TYTTFIDGLCK 429
                I GLC 
Sbjct: 791 MCRC-ITGLCL 800

Length = 1060

>gnl|CDD|215636 PLN03218, PLN03218, maturation of RBCL 1; Provisional

 Score =  114 bits (288), Expect = 1e-26
 Identities = 95/423 (22%), Positives = 176/423 (41%), Gaps = 42/423 (9%)

Query: 107 CKIGRVSLGFIAFGRILRSCFTPNAATFNSLIKGLHAESRIMEAAALFTKLKAFGCEPNV 166
           CK  R       F +++R    P  +TFN L+    +   I  A  +   ++  G + + 
Sbjct: 416 CKKQRAVKEAFRFAKLIR---NPTLSTFNMLMSVCASSQDIDGALRVLRLVQEAGLKADC 472

Query: 167 ITYNTLINGLCRTGHTMIALNLFEEMANGNGEIGVVCKPNTVTYSTIIDGLCKEGFVDKA 226
             Y TLI+   ++G       +F EM N   E       N  T+  +IDG  + G V KA
Sbjct: 473 KLYTTLISTCAKSGKVDAMFEVFHEMVNAGVE------ANVHTFGALIDGCARAGQVAKA 526

Query: 227 KALFLQMKDENINPDVVTYNSLIHGLCHANDWNEAKRLFIEMMDQGVQPSVVTFNVIMDE 286
              +  M+ +N+ PD V +N+LI     +   + A                  F+V+ + 
Sbjct: 527 FGAYGIMRSKNVKPDRVVFNALISACGQSGAVDRA------------------FDVLAE- 567

Query: 287 LCKNRKMDEASRLLDLMVQRGVRPNACTYNTLMDGFCLMGKINRAEELFGSMESMGCKHD 346
                 M   +  +D        P+  T   LM      G+++RA+E++  +     K  
Sbjct: 568 ------MKAETHPID--------PDHITVGALMKACANAGQVDRAKEVYQMIHEYNIKGT 613

Query: 347 DVSYNILINGYCKNKEVEEALSLYREMVSKGIKPTVVTYNTLFLGLFEIHQVEHALKLFD 406
              Y I +N   +  + + ALS+Y +M  KG+KP  V ++ L         ++ A ++  
Sbjct: 614 PEVYTIAVNSCSQKGDWDFALSIYDDMKKKGVKPDEVFFSALVDVAGHAGDLDKAFEILQ 673

Query: 407 EMQRDGVAADTRTYTTFIDGLCKNGYIIEAVELFRTLRILKCELDIQAYNCLIDGLCKSG 466
           + ++ G+   T +Y++ +          +A+EL+  ++ +K    +   N LI  LC+  
Sbjct: 674 DARKQGIKLGTVSYSSLMGACSNAKNWKKALELYEDIKSIKLRPTVSTMNALITALCEGN 733

Query: 467 RLKFAWELFCSLPHGVLVPNVVTYNIMIQGLCNDGQMDKARDLFLDMEENAAAPDVITFD 526
           +L  A E+   +    L PN +TY+I++         D   DL    +E+   P+++   
Sbjct: 734 QLPKALEVLSEMKRLGLCPNTITYSILLVASERKDDADVGLDLLSQAKEDGIKPNLVMCR 793

Query: 527 MLI 529
            + 
Sbjct: 794 CIT 796

Length = 1060

>gnl|CDD|215561 PLN03077, PLN03077, Protein ECB2; Provisional

 Score =  114 bits (286), Expect = 2e-26
 Identities = 119/513 (23%), Positives = 219/513 (42%), Gaps = 41/513 (7%)

Query: 67  VSSFNILLASLAKNKHYDTRLNA------TGLFPNLYTYNILINCFCKIGRVSLGFIAFG 120
           + S+N+L+   AK  ++D  L         G+ P++YT+  ++     I  ++ G     
Sbjct: 152 LFSWNVLVGGYAKAGYFDEALCLYHRMLWAGVRPDVYTFPCVLRTCGGIPDLARGREVHA 211

Query: 121 RILRSCFTPNAATFNSLIKGLHAESRIMEAAALFTKLKAFGCEPNVITYNTLINGLCRTG 180
            ++R  F  +    N+LI        ++ A  +F ++    C    I++N +I+G    G
Sbjct: 212 HVVRFGFELDVDVVNALITMYVKCGDVVSARLVFDRMPRRDC----ISWNAMISGYFENG 267

Query: 181 HTMIALNLFEEMANGNGEIGVVCKPNTVTYSTIIDG---LCKEGFVDKAKALFLQMKDEN 237
             +  L LF  M        +   P+ +T +++I     L  E    +     ++     
Sbjct: 268 ECLEGLELFFTM------RELSVDPDLMTITSVISACELLGDERLGREMHGYVVK---TG 318

Query: 238 INPDVVTYNSLIHGLCHANDWNEAKRLFIEMMDQGVQPSVVTFNVIMDELCKNRKMDEAS 297
              DV   NSLI        W EA+++F  M  +      V++  ++    KN   D+A 
Sbjct: 319 FAVDVSVCNSLIQMYLSLGSWGEAEKVFSRMETK----DAVSWTAMISGYEKNGLPDKAL 374

Query: 298 RLLDLMVQRGVRPNACTYNTLMDGFCLMGKINRAEELFGSMESMGCKHDDVSYNILINGY 357
               LM Q  V P+  T  +++     +G ++   +L    E  G     V  N LI  Y
Sbjct: 375 ETYALMEQDNVSPDEITIASVLSACACLGDLDVGVKLHELAERKGLISYVVVANALIEMY 434

Query: 358 CKNKEVEEALSLYREMVSKGIKPTVVTYNTLFLGLFEIHQVEHALKLFDEMQRDGVAADT 417
            K K +++AL ++  +  K     V+++ ++  GL   ++   AL  F +M    +  ++
Sbjct: 435 SKCKCIDKALEVFHNIPEK----DVISWTSIIAGLRLNNRCFEALIFFRQMLLT-LKPNS 489

Query: 418 RTYTTFIDGLCKNGYIIEAVELFRTLRILKCELDIQAY--NCLIDGLCKSGRLKFAWELF 475
            T    +    + G ++   E+     +L+  +    +  N L+D   + GR+ +AW  F
Sbjct: 490 VTLIAALSACARIGALMCGKEIHA--HVLRTGIGFDGFLPNALLDLYVRCGRMNYAWNQF 547

Query: 476 CSLPHGVLVPNVVTYNIMIQGLCNDGQMDKARDLFLDMEENAAAPDVITFDMLIHGFIRI 535
            S        +VV++NI++ G    G+   A +LF  M E+   PD +TF  L+    R 
Sbjct: 548 NSHEK-----DVVSWNILLTGYVAHGKGSMAVELFNRMVESGVNPDEVTFISLLCACSRS 602

Query: 536 NEPSKVNELLHKMKEK-KVMPDASIVSIVVDLL 567
              ++  E  H M+EK  + P+    + VVDLL
Sbjct: 603 GMVTQGLEYFHSMEEKYSITPNLKHYACVVDLL 635

Length = 857

>gnl|CDD|215636 PLN03218, PLN03218, maturation of RBCL 1; Provisional

 Score =  112 bits (281), Expect = 1e-25
 Identities = 86/386 (22%), Positives = 156/386 (40%), Gaps = 69/386 (17%)

Query: 91  GLFPNLYTYNILINCFCKIGRVSLGFIAFGRILRS-CFTPNAATFNSLIKGLHAESRIME 149
           G+  N++T+  LI+   + G+V+  F A+G I+RS    P+   FN+LI        +  
Sbjct: 502 GVEANVHTFGALIDGCARAGQVAKAFGAYG-IMRSKNVKPDRVVFNALISACGQSGAVDR 560

Query: 150 AAALFTKLKAFG--CEPNVITYNTLINGLCRTGHTMIALNLFEEMANGN----------- 196
           A  +  ++KA     +P+ IT   L+      G    A  +++ +   N           
Sbjct: 561 AFDVLAEMKAETHPIDPDHITVGALMKACANAGQVDRAKEVYQMIHEYNIKGTPEVYTIA 620

Query: 197 -------GEIGVVC-----------KPNTVTYSTIIDGLCKEGFVDKAKALFLQMKDENI 238
                  G+                KP+ V +S ++D     G +DKA  +    + + I
Sbjct: 621 VNSCSQKGDWDFALSIYDDMKKKGVKPDEVFFSALVDVAGHAGDLDKAFEILQDARKQGI 680

Query: 239 NPDVVTYNSLIHGLCHANDWNEAKRLFIEMMDQGVQPSVVTFNVIMDELCKNRKMDEASR 298
               V+Y+SL+    +A +W +A  L+ ++    ++P+V T N ++  LC+  ++ +A  
Sbjct: 681 KLGTVSYSSLMGACSNAKNWKKALELYEDIKSIKLRPTVSTMNALITALCEGNQLPKALE 740

Query: 299 LLDLMVQRGVRPNACTYNTLMDGFCLMGKINRAEELFGSMESMGCKHDDVSYNIL----I 354
           +L  M + G+ PN  TY+ L+         +   +L         K D +  N++    I
Sbjct: 741 VLSEMKRLGLCPNTITYSILLVASERKDDADVGLDLL-----SQAKEDGIKPNLVMCRCI 795

Query: 355 NGYCK------------------------NKEVEEALSLYREMVSKGIKPTVVTYNTLFL 390
            G C                         NK    AL +YRE +S G  PT+   + +  
Sbjct: 796 TGLCLRRFEKACALGEPVVSFDSGRPQIENKWTSWALMVYRETISAGTLPTMEVLSQVLG 855

Query: 391 GLFEIHQVEHALKLFDEMQRDGVAAD 416
            L   H      +L + +   G++AD
Sbjct: 856 CLQLPHDATLRNRLIENL---GISAD 878

Length = 1060

>gnl|CDD|215636 PLN03218, PLN03218, maturation of RBCL 1; Provisional

 Score =  106 bits (266), Expect = 8e-24
 Identities = 83/365 (22%), Positives = 151/365 (41%), Gaps = 37/365 (10%)

Query: 239 NPDVVTYNSLIHGLCHANDWNEAKRLFIEMMDQGVQPSVVTFNVIMDELCKNRKMDEASR 298
           NP + T+N L+     + D + A R+   + + G++     +  ++    K+ K+D    
Sbjct: 434 NPTLSTFNMLMSVCASSQDIDGALRVLRLVQEAGLKADCKLYTTLISTCAKSGKVDAMFE 493

Query: 299 LLDLMVQRGVRPNACTYNTLMDGFCLMGKINRAEELFGSMESMGCKHDDVSYNILINGYC 358
           +   MV  GV  N  T+  L+DG    G++ +A   +G M S   K D V +N LI+   
Sbjct: 494 VFHEMVNAGVEANVHTFGALIDGCARAGQVAKAFGAYGIMRSKNVKPDRVVFNALISACG 553

Query: 359 KNKEVEEALSLYREMV--SKGIKPTVVTYNTLFLGLFEIHQVEHAL-------------- 402
           ++  V+ A  +  EM   +  I P  +T   L        QV+ A               
Sbjct: 554 QSGAVDRAFDVLAEMKAETHPIDPDHITVGALMKACANAGQVDRAKEVYQMIHEYNIKGT 613

Query: 403 ---------------------KLFDEMQRDGVAADTRTYTTFIDGLCKNGYIIEAVELFR 441
                                 ++D+M++ GV  D   ++  +D     G + +A E+ +
Sbjct: 614 PEVYTIAVNSCSQKGDWDFALSIYDDMKKKGVKPDEVFFSALVDVAGHAGDLDKAFEILQ 673

Query: 442 TLRILKCELDIQAYNCLIDGLCKSGRLKFAWELFCSLPHGVLVPNVVTYNIMIQGLCNDG 501
             R    +L   +Y+ L+     +   K A EL+  +    L P V T N +I  LC   
Sbjct: 674 DARKQGIKLGTVSYSSLMGACSNAKNWKKALELYEDIKSIKLRPTVSTMNALITALCEGN 733

Query: 502 QMDKARDLFLDMEENAAAPDVITFDMLIHGFIRINEPSKVNELLHKMKEKKVMPDASIVS 561
           Q+ KA ++  +M+     P+ IT+ +L+    R ++     +LL + KE  + P+  +  
Sbjct: 734 QLPKALEVLSEMKRLGLCPNTITYSILLVASERKDDADVGLDLLSQAKEDGIKPNLVMCR 793

Query: 562 IVVDL 566
            +  L
Sbjct: 794 CITGL 798

Length = 1060

>gnl|CDD|215563 PLN03081, PLN03081, pentatricopeptide (PPR) repeat-containing protein; Provisional

 Score = 97.6 bits (243), Expect = 3e-21
 Identities = 91/386 (23%), Positives = 159/386 (41%), Gaps = 19/386 (4%)

Query: 132 ATFNSLIKGLHAESRIMEAAALFTKLKA-FGCEPNVITYNTLINGLCRTGHTMIALNLFE 190
            +  S I+ L A  R  EA  LF  L+A         TY+ L+              ++ 
Sbjct: 88  VSLCSQIEKLVACGRHREALELFEILEAGCPFTLPASTYDALVEACIALKSIRCVKAVYW 147

Query: 191 EMANGNGEIGVVCKPNTVTYSTIIDGLCKEGFVDKAKALFLQMKDENINPDVVTYNSLIH 250
            + +   E      P+    + ++    K G +  A+ LF +M + N+     ++ ++I 
Sbjct: 148 HVESSGFE------PDQYMMNRVLLMHVKCGMLIDARRLFDEMPERNL----ASWGTIIG 197

Query: 251 GLCHANDWNEAKRLFIEMMDQGVQPSVVTFNVIMDELCKNRKMDEASRLLDLMVQRGVRP 310
           GL  A ++ EA  LF EM + G      TF V++             +L   +++ GV  
Sbjct: 198 GLVDAGNYREAFALFREMWEDGSDAEPRTFVVMLRASAGLGSARAGQQLHCCVLKTGVVG 257

Query: 311 NACTYNTLMDGFCLMGKINRAEELFGSMESMGCKHDDVSYNILINGYCKNKEVEEALSLY 370
           +      L+D +   G I  A  +F  M     +   V++N ++ GY  +   EEAL LY
Sbjct: 258 DTFVSCALIDMYSKCGDIEDARCVFDGMP----EKTTVAWNSMLAGYALHGYSEEALCLY 313

Query: 371 REMVSKGIKPTVVTYNTLFLGLFEIHQVEHALKLFDEMQRDGVAADTRTYTTFIDGLCKN 430
            EM   G+     T++ +      +  +EHA +    + R G   D    T  +D   K 
Sbjct: 314 YEMRDSGVSIDQFTFSIMIRIFSRLALLEHAKQAHAGLIRTGFPLDIVANTALVDLYSKW 373

Query: 431 GYIIEAVELFRTLRILKCELDIQAYNCLIDGLCKSGRLKFAWELFCSLPHGVLVPNVVTY 490
           G + +A  +F  +       ++ ++N LI G    GR   A E+F  +    + PN VT+
Sbjct: 374 GRMEDARNVFDRMPRK----NLISWNALIAGYGNHGRGTKAVEMFERMIAEGVAPNHVTF 429

Query: 491 NIMIQGLCNDGQMDKARDLFLDMEEN 516
             ++      G  ++  ++F  M EN
Sbjct: 430 LAVLSACRYSGLSEQGWEIFQSMSEN 455

Length = 697

>gnl|CDD|215561 PLN03077, PLN03077, Protein ECB2; Provisional

 Score = 93.0 bits (231), Expect = 1e-19
 Identities = 91/365 (24%), Positives = 143/365 (39%), Gaps = 71/365 (19%)

Query: 246 NSLIHGLCHANDWNEAKRLFIEMMDQGVQPSVVTFNVIMDELCKNRKMDEA-----SRLL 300
           NS +  LC      +A +L   M +  V      + V +  LC+ ++  E      SR L
Sbjct: 55  NSQLRALCSHGQLEQALKLLESMQELRVPVDEDAY-VALFRLCEWKRAVEEGSRVCSRAL 113

Query: 301 DLMVQRGVRPNACTYNTLMDGFCLMGKINRAEELFGSMESMGCKHDDVSYNILINGYCKN 360
                 GVR      N ++  F   G++  A  +FG M     + D  S+N+L+ GY K 
Sbjct: 114 SSHPSLGVRLG----NAMLSMFVRFGELVHAWYVFGKMP----ERDLFSWNVLVGGYAKA 165

Query: 361 KEVEEALSLYREMVSKGIKPTVVTY----------------------------------- 385
              +EAL LY  M+  G++P V T+                                   
Sbjct: 166 GYFDEALCLYHRMLWAGVRPDVYTFPCVLRTCGGIPDLARGREVHAHVVRFGFELDVDVV 225

Query: 386 NTLFLGLFEIHQVEHALKLFDEMQRDGVAADTRTYTTFIDGLCKNGYIIEAVELFRTLRI 445
           N L     +   V  A  +FD M R     D  ++   I G  +NG  +E +ELF T+R 
Sbjct: 226 NALITMYVKCGDVVSARLVFDRMPR----RDCISWNAMISGYFENGECLEGLELFFTMRE 281

Query: 446 LKCELDIQAYNCLIDGLCKSGRLKFAWELFCSLPHGVLVP-----NVVTYNIMIQGLCND 500
           L  + D+     +I      G  +   E+     HG +V      +V   N +IQ   + 
Sbjct: 282 LSVDPDLMTITSVISACELLGDERLGREM-----HGYVVKTGFAVDVSVCNSLIQMYLSL 336

Query: 501 GQMDKARDLFLDMEENAAAPDVITFDMLIHGFIRINEPSKVNELLHKMKEKKVMPD---- 556
           G   +A  +F  ME      D +++  +I G+ +   P K  E    M++  V PD    
Sbjct: 337 GSWGEAEKVFSRMETK----DAVSWTAMISGYEKNGLPDKALETYALMEQDNVSPDEITI 392

Query: 557 ASIVS 561
           AS++S
Sbjct: 393 ASVLS 397

Length = 857

>gnl|CDD|205222 pfam13041, PPR_2, PPR repeat family

 Score = 80.9 bits (201), Expect = 3e-19
 Identities = 27/50 (54%), Positives = 36/50 (72%)

Query: 205 PNTVTYSTIIDGLCKEGFVDKAKALFLQMKDENINPDVVTYNSLIHGLCH 254
           P+ VTY+T+IDG CK+G V++A  LF +MK   I P+V TY+ LI GLC 
Sbjct: 1   PDVVTYNTLIDGYCKKGKVEEALKLFNEMKKRGIKPNVYTYSILIDGLCK 50

This repeat has no known function. It is about 35 amino acids long and is found in up to 18 copies in some proteins. The family appears to be greatly expanded in plants and fungi. The repeat has been called PPR. Length = 50

>gnl|CDD|205222 pfam13041, PPR_2, PPR repeat family

 Score = 76.7 bits (190), Expect = 9e-18
 Identities = 25/50 (50%), Positives = 36/50 (72%)

Query: 240 PDVVTYNSLIHGLCHANDWNEAKRLFIEMMDQGVQPSVVTFNVIMDELCK 289
           PDVVTYN+LI G C      EA +LF EM  +G++P+V T+++++D LCK
Sbjct: 1   PDVVTYNTLIDGYCKKGKVEEALKLFNEMKKRGIKPNVYTYSILIDGLCK 50

This repeat has no known function. It is about 35 amino acids long and is found in up to 18 copies in some proteins. The family appears to be greatly expanded in plants and fungi. The repeat has been called PPR. Length = 50

>gnl|CDD|205222 pfam13041, PPR_2, PPR repeat family

 Score = 75.9 bits (188), Expect = 2e-17
 Identities = 23/49 (46%), Positives = 35/49 (71%)

Query: 275 PSVVTFNVIMDELCKNRKMDEASRLLDLMVQRGVRPNACTYNTLMDGFC 323
           P VVT+N ++D  CK  K++EA +L + M +RG++PN  TY+ L+DG C
Sbjct: 1   PDVVTYNTLIDGYCKKGKVEEALKLFNEMKKRGIKPNVYTYSILIDGLC 49

This repeat has no known function. It is about 35 amino acids long and is found in up to 18 copies in some proteins. The family appears to be greatly expanded in plants and fungi. The repeat has been called PPR. Length = 50

>gnl|CDD|205222 pfam13041, PPR_2, PPR repeat family

 Score = 75.5 bits (187), Expect = 2e-17
 Identities = 28/47 (59%), Positives = 34/47 (72%)

Query: 346 DDVSYNILINGYCKNKEVEEALSLYREMVSKGIKPTVVTYNTLFLGL 392
           D V+YN LI+GYCK  +VEEAL L+ EM  +GIKP V TY+ L  GL
Sbjct: 2   DVVTYNTLIDGYCKKGKVEEALKLFNEMKKRGIKPNVYTYSILIDGL 48

This repeat has no known function. It is about 35 amino acids long and is found in up to 18 copies in some proteins. The family appears to be greatly expanded in plants and fungi. The repeat has been called PPR. Length = 50

>gnl|CDD|205222 pfam13041, PPR_2, PPR repeat family

 Score = 74.4 bits (184), Expect = 6e-17
 Identities = 24/50 (48%), Positives = 34/50 (68%)

Query: 310 PNACTYNTLMDGFCLMGKINRAEELFGSMESMGCKHDDVSYNILINGYCK 359
           P+  TYNTL+DG+C  GK+  A +LF  M+  G K +  +Y+ILI+G CK
Sbjct: 1   PDVVTYNTLIDGYCKKGKVEEALKLFNEMKKRGIKPNVYTYSILIDGLCK 50

This repeat has no known function. It is about 35 amino acids long and is found in up to 18 copies in some proteins. The family appears to be greatly expanded in plants and fungi. The repeat has been called PPR. Length = 50

>gnl|CDD|215561 PLN03077, PLN03077, Protein ECB2; Provisional

 Score = 83.7 bits (207), Expect = 1e-16
 Identities = 82/388 (21%), Positives = 158/388 (40%), Gaps = 56/388 (14%)

Query: 94  PNLYTYNILINCFCKIGRVSLGFIAFGRILRSCFTPNAATFNSLIKGLHAESRIMEAAAL 153
           P+L T   +I+    +G   LG    G ++++ F  + +  NSLI+   +     EA  +
Sbjct: 286 PDLMTITSVISACELLGDERLGREMHGYVVKTGFAVDVSVCNSLIQMYLSLGSWGEAEKV 345

Query: 154 FTKLKAFGCEPNVITYNTLINGLCRTGHTMIALNLFEEMANGNGEIGVVCKPNTVTYSTI 213
           F++++      + +++  +I+G  + G    AL  +  M   N        P+ +T +++
Sbjct: 346 FSRMET----KDAVSWTAMISGYEKNGLPDKALETYALMEQDN------VSPDEITIASV 395

Query: 214 -----------------------------------IDGLCKEGFVDKAKALFLQMKDENI 238
                                              I+   K   +DKA  +F  + ++  
Sbjct: 396 LSACACLGDLDVGVKLHELAERKGLISYVVVANALIEMYSKCKCIDKALEVFHNIPEK-- 453

Query: 239 NPDVVTYNSLIHGLCHANDWNEAKRLFIEMMDQGVQPSVVTFNVIMDELCKNRKMDEASR 298
             DV+++ S+I GL   N   EA  +F   M   ++P+ VT    +    +   +     
Sbjct: 454 --DVISWTSIIAGLRLNNRCFEA-LIFFRQMLLTLKPNSVTLIAALSACARIGALMCGKE 510

Query: 299 LLDLMVQRGVRPNACTYNTLMDGFCLMGKINRAEELFGSMESMGCKHDDVSYNILINGYC 358
           +   +++ G+  +    N L+D +   G++N A   F S      + D VS+NIL+ GY 
Sbjct: 511 IHAHVLRTGIGFDGFLPNALLDLYVRCGRMNYAWNQFNS-----HEKDVVSWNILLTGYV 565

Query: 359 KNKEVEEALSLYREMVSKGIKPTVVTYNTLFLGLFEIHQVEHALKLFDEMQRD-GVAADT 417
            + +   A+ L+  MV  G+ P  VT+ +L         V   L+ F  M+    +  + 
Sbjct: 566 AHGKGSMAVELFNRMVESGVNPDEVTFISLLCACSRSGMVTQGLEYFHSMEEKYSITPNL 625

Query: 418 RTYTTFIDGLCKNGYIIEAVELFRTLRI 445
           + Y   +D L + G + EA      + I
Sbjct: 626 KHYACVVDLLGRAGKLTEAYNFINKMPI 653

Length = 857

>gnl|CDD|205222 pfam13041, PPR_2, PPR repeat family

 Score = 72.8 bits (180), Expect = 2e-16
 Identities = 29/56 (51%), Positives = 34/56 (60%), Gaps = 6/56 (10%)

Query: 164 PNVITYNTLINGLCRTGHTMIALNLFEEMANGNGEIGVVCKPNTVTYSTIIDGLCK 219
           P+V+TYNTLI+G C+ G    AL LF EM           KPN  TYS +IDGLCK
Sbjct: 1   PDVVTYNTLIDGYCKKGKVEEALKLFNEMKKRG------IKPNVYTYSILIDGLCK 50

This repeat has no known function. It is about 35 amino acids long and is found in up to 18 copies in some proteins. The family appears to be greatly expanded in plants and fungi. The repeat has been called PPR. Length = 50

>gnl|CDD|205222 pfam13041, PPR_2, PPR repeat family

 Score = 70.9 bits (175), Expect = 1e-15
 Identities = 20/48 (41%), Positives = 32/48 (66%)

Query: 485 PNVVTYNIMIQGLCNDGQMDKARDLFLDMEENAAAPDVITFDMLIHGF 532
           P+VVTYN +I G C  G++++A  LF +M++    P+V T+ +LI G 
Sbjct: 1   PDVVTYNTLIDGYCKKGKVEEALKLFNEMKKRGIKPNVYTYSILIDGL 48

This repeat has no known function. It is about 35 amino acids long and is found in up to 18 copies in some proteins. The family appears to be greatly expanded in plants and fungi. The repeat has been called PPR. Length = 50

>gnl|CDD|205222 pfam13041, PPR_2, PPR repeat family

 Score = 70.5 bits (174), Expect = 1e-15
 Identities = 27/50 (54%), Positives = 35/50 (70%)

Query: 380 PTVVTYNTLFLGLFEIHQVEHALKLFDEMQRDGVAADTRTYTTFIDGLCK 429
           P VVTYNTL  G  +  +VE ALKLF+EM++ G+  +  TY+  IDGLCK
Sbjct: 1   PDVVTYNTLIDGYCKKGKVEEALKLFNEMKKRGIKPNVYTYSILIDGLCK 50

This repeat has no known function. It is about 35 amino acids long and is found in up to 18 copies in some proteins. The family appears to be greatly expanded in plants and fungi. The repeat has been called PPR. Length = 50

>gnl|CDD|205222 pfam13041, PPR_2, PPR repeat family

 Score = 64.3 bits (158), Expect = 2e-13
 Identities = 23/49 (46%), Positives = 32/49 (65%)

Query: 451 DIQAYNCLIDGLCKSGRLKFAWELFCSLPHGVLVPNVVTYNIMIQGLCN 499
           D+  YN LIDG CK G+++ A +LF  +    + PNV TY+I+I GLC 
Sbjct: 2   DVVTYNTLIDGYCKKGKVEEALKLFNEMKKRGIKPNVYTYSILIDGLCK 50

This repeat has no known function. It is about 35 amino acids long and is found in up to 18 copies in some proteins. The family appears to be greatly expanded in plants and fungi. The repeat has been called PPR. Length = 50

>gnl|CDD|205222 pfam13041, PPR_2, PPR repeat family

 Score = 61.7 bits (151), Expect = 2e-12
 Identities = 22/50 (44%), Positives = 34/50 (68%)

Query: 129 PNAATFNSLIKGLHAESRIMEAAALFTKLKAFGCEPNVITYNTLINGLCR 178
           P+  T+N+LI G   + ++ EA  LF ++K  G +PNV TY+ LI+GLC+
Sbjct: 1   PDVVTYNTLIDGYCKKGKVEEALKLFNEMKKRGIKPNVYTYSILIDGLCK 50

This repeat has no known function. It is about 35 amino acids long and is found in up to 18 copies in some proteins. The family appears to be greatly expanded in plants and fungi. The repeat has been called PPR. Length = 50

>gnl|CDD|215561 PLN03077, PLN03077, Protein ECB2; Provisional

 Score = 66.8 bits (163), Expect = 2e-11
 Identities = 76/392 (19%), Positives = 149/392 (38%), Gaps = 53/392 (13%)

Query: 170 NTLINGLCRTGHTMIALNLFEEMANGNGEIGVVCKPNTVTYSTIIDGLCKEGFVDKAKAL 229
           N +++   R G  + A  +F +M           + +  +++ ++ G  K G+ D+A  L
Sbjct: 125 NAMLSMFVRFGELVHAWYVFGKMP----------ERDLFSWNVLVGGYAKAGYFDEALCL 174

Query: 230 FLQMKDENINPDVVTYNSLIHGLCHANDWNEAKRLFIEMMDQGVQPSVVTFNVIMDELCK 289
           + +M    + PDV T+  ++       D             + V   VV F   +D    
Sbjct: 175 YHRMLWAGVRPDVYTFPCVLRTCGGIPDL---------ARGREVHAHVVRFGFELD---- 221

Query: 290 NRKMDEASRLLDLMVQRGVRPNACTYNTLMDGFCLMGKINRAEELFGSMESMGCKHDDVS 349
                     +D++            N L+  +   G +  A  +F  M    C    +S
Sbjct: 222 ----------VDVV------------NALITMYVKCGDVVSARLVFDRMPRRDC----IS 255

Query: 350 YNILINGYCKNKEVEEALSLYREMVSKGIKPTVVTYNTLFLGLFEIHQVEHALKLFDEMQ 409
           +N +I+GY +N E  E L L+  M    + P ++T  ++      +       ++   + 
Sbjct: 256 WNAMISGYFENGECLEGLELFFTMRELSVDPDLMTITSVISACELLGDERLGREMHGYVV 315

Query: 410 RDGVAADTRTYTTFIDGLCKNGYIIEAVELFRTLRILKCELDIQAYNCLIDGLCKSGRLK 469
           + G A D     + I      G   EA ++F     ++ + D  ++  +I G  K+G   
Sbjct: 316 KTGFAVDVSVCNSLIQMYLSLGSWGEAEKVFSR---METK-DAVSWTAMISGYEKNGLPD 371

Query: 470 FAWELFCSLPHGVLVPNVVTYNIMIQGLCNDGQMDKARDLFLDMEENAAAPDVITFDMLI 529
            A E +  +    + P+ +T   ++      G +D    L    E       V+  + LI
Sbjct: 372 KALETYALMEQDNVSPDEITIASVLSACACLGDLDVGVKLHELAERKGLISYVVVANALI 431

Query: 530 HGFIRINEPSKVNELLHKMKEKKVMPDASIVS 561
             + +     K  E+ H + EK V+   SI++
Sbjct: 432 EMYSKCKCIDKALEVFHNIPEKDVISWTSIIA 463

Length = 857

>gnl|CDD|205109 pfam12854, PPR_1, PPR repeat

 Score = 57.4 bits (140), Expect = 5e-11
 Identities = 18/33 (54%), Positives = 24/33 (72%)

Query: 160 FGCEPNVITYNTLINGLCRTGHTMIALNLFEEM 192
            G +P+V+TYNTLI+GLCR G    A+ L +EM
Sbjct: 1   KGLKPDVVTYNTLIDGLCRAGRVDEAVELLDEM 33

This family matches additional variants of the PPR repeat that were not captured by the model for pfam01535. The exact function is not known. Length = 34

>gnl|CDD|205109 pfam12854, PPR_1, PPR repeat

 Score = 55.0 bits (134), Expect = 3e-10
 Identities = 17/32 (53%), Positives = 24/32 (75%)

Query: 203 CKPNTVTYSTIIDGLCKEGFVDKAKALFLQMK 234
            KP+ VTY+T+IDGLC+ G VD+A  L  +M+
Sbjct: 3   LKPDVVTYNTLIDGLCRAGRVDEAVELLDEME 34

This family matches additional variants of the PPR repeat that were not captured by the model for pfam01535. The exact function is not known. Length = 34

>gnl|CDD|205222 pfam13041, PPR_2, PPR repeat family

 Score = 54.7 bits (133), Expect = 5e-10
 Identities = 22/49 (44%), Positives = 31/49 (63%)

Query: 416 DTRTYTTFIDGLCKNGYIIEAVELFRTLRILKCELDIQAYNCLIDGLCK 464
           D  TY T IDG CK G + EA++LF  ++    + ++  Y+ LIDGLCK
Sbjct: 2   DVVTYNTLIDGYCKKGKVEEALKLFNEMKKRGIKPNVYTYSILIDGLCK 50

This repeat has no known function. It is about 35 amino acids long and is found in up to 18 copies in some proteins. The family appears to be greatly expanded in plants and fungi. The repeat has been called PPR. Length = 50

>gnl|CDD|205109 pfam12854, PPR_1, PPR repeat

 Score = 53.9 bits (131), Expect = 7e-10
 Identities = 16/34 (47%), Positives = 21/34 (61%)

Query: 341 MGCKHDDVSYNILINGYCKNKEVEEALSLYREMV 374
            G K D V+YN LI+G C+   V+EA+ L  EM 
Sbjct: 1   KGLKPDVVTYNTLIDGLCRAGRVDEAVELLDEME 34

This family matches additional variants of the PPR repeat that were not captured by the model for pfam01535. The exact function is not known. Length = 34

>gnl|CDD|213555 TIGR00756, PPR, pentatricopeptide repeat domain (PPR motif)

 Score = 54.0 bits (131), Expect = 7e-10
 Identities = 20/35 (57%), Positives = 26/35 (74%)

Query: 348 VSYNILINGYCKNKEVEEALSLYREMVSKGIKPTV 382
           V+YN LI+G CK   VEEAL L++EM  +GI+P V
Sbjct: 1   VTYNTLIDGLCKAGRVEEALELFKEMKERGIEPDV 35

This model describes a domain called the PPR motif, or pentatricopeptide repeat. Its consensus sequence is 35 positions long and typically is found in four or more tandem copies. This family is strongly represented in plant proteins, particularly those sorted to chloroplasts or mitochondria. The pfam model pfam01535, domain of unknown function DUF17, consists of 6 copies of this repeat. This family has a similar consensus to the TPR domain (tetratricopeptide), pfam pfam00515, a 33-residue repeat. It is predicted to form a pair of antiparallel helices similar to that of TPR. Length = 35

>gnl|CDD|205109 pfam12854, PPR_1, PPR repeat

 Score = 53.5 bits (130), Expect = 1e-09
 Identities = 16/34 (47%), Positives = 24/34 (70%)

Query: 306 RGVRPNACTYNTLMDGFCLMGKINRAEELFGSME 339
           +G++P+  TYNTL+DG C  G+++ A EL   ME
Sbjct: 1   KGLKPDVVTYNTLIDGLCRAGRVDEAVELLDEME 34

This family matches additional variants of the PPR repeat that were not captured by the model for pfam01535. The exact function is not known. Length = 34

>gnl|CDD|215563 PLN03081, PLN03081, pentatricopeptide (PPR) repeat-containing protein; Provisional

 Score = 59.5 bits (144), Expect = 3e-09
 Identities = 58/249 (23%), Positives = 115/249 (46%), Gaps = 16/249 (6%)

Query: 74  LASLAKNKHYDTRLNATGLFPNLYTYNILINCFCKIGRVSLGFIAFGRILRSCFTPNAAT 133
           LA L   K     L  TG   ++     L++ + K GR+      F R+ R     N  +
Sbjct: 338 LALLEHAKQAHAGLIRTGFPLDIVANTALVDLYSKWGRMEDARNVFDRMPRK----NLIS 393

Query: 134 FNSLIKGLHAESRIMEAAALFTKLKAFGCEPNVITYNTLINGLCRTGHTMIALNLFEEMA 193
           +N+LI G     R  +A  +F ++ A G  PN +T+  +++    +G +     +F+ M+
Sbjct: 394 WNALIAGYGNHGRGTKAVEMFERMIAEGVAPNHVTFLAVLSACRYSGLSEQGWEIFQSMS 453

Query: 194 NGNGEIGVVCKPNTVTYSTIIDGLCKEGFVDKAKALFLQMKDENINPDVVTYNSLIHGLC 253
             +       KP  + Y+ +I+ L +EG +D+A A+   ++     P V  + +L+   C
Sbjct: 454 ENHR-----IKPRAMHYACMIELLGREGLLDEAYAM---IRRAPFKPTVNMWAALLTA-C 504

Query: 254 HANDWNEAKRLFIEMMDQGVQPSVVTFNVIMDELCKNR-KMDEASRLLDLMVQRGVR-PN 311
             +   E  RL  E +  G+ P  +   V++  L  +  +  EA+++++ + ++G+    
Sbjct: 505 RIHKNLELGRLAAEKL-YGMGPEKLNNYVVLLNLYNSSGRQAEAAKVVETLKRKGLSMHP 563

Query: 312 ACTYNTLMD 320
           ACT+  +  
Sbjct: 564 ACTWIEVKK 572

Length = 697

>gnl|CDD|205109 pfam12854, PPR_1, PPR repeat

 Score = 52.4 bits (127), Expect = 3e-09
 Identities = 17/32 (53%), Positives = 24/32 (75%)

Query: 483 LVPNVVTYNIMIQGLCNDGQMDKARDLFLDME 514
           L P+VVTYN +I GLC  G++D+A +L  +ME
Sbjct: 3   LKPDVVTYNTLIDGLCRAGRVDEAVELLDEME 34

This family matches additional variants of the PPR repeat that were not captured by the model for pfam01535. The exact function is not known. Length = 34

>gnl|CDD|144943 pfam01535, PPR, PPR repeat

 Score = 51.7 bits (125), Expect = 4e-09
 Identities = 18/31 (58%), Positives = 25/31 (80%)

Query: 348 VSYNILINGYCKNKEVEEALSLYREMVSKGI 378
           V+YN LI+GYCK  ++EEAL L++EM  KG+
Sbjct: 1   VTYNSLISGYCKAGKLEEALELFKEMKEKGV 31

This repeat has no known function. It is about 35 amino acids long and found in up to 18 copies in some proteins. This family appears to be greatly expanded in plants. This repeat occurs in PET309, which may be involved in RNA stabilisation. This domain occurs in crp1 that is involved in RNA processing. This repeat is associated with a predicted plant protein that has a domain organisation similar to the human BRCA1 protein. The repeat has been called PPR. Length = 31

>gnl|CDD|205109 pfam12854, PPR_1, PPR repeat

 Score = 51.2 bits (124), Expect = 7e-09
 Identities = 18/32 (56%), Positives = 21/32 (65%)

Query: 237 NINPDVVTYNSLIHGLCHANDWNEAKRLFIEM 268
            + PDVVTYN+LI GLC A   +EA  L  EM
Sbjct: 2   GLKPDVVTYNTLIDGLCRAGRVDEAVELLDEM 33

This family matches additional variants of the PPR repeat that were not captured by the model for pfam01535. The exact function is not known. Length = 34

>gnl|CDD|213555 TIGR00756, PPR, pentatricopeptide repeat domain (PPR motif)

 Score = 48.6 bits (117), Expect = 6e-08
 Identities = 19/35 (54%), Positives = 24/35 (68%)

Query: 243 VTYNSLIHGLCHANDWNEAKRLFIEMMDQGVQPSV 277
           VTYN+LI GLC A    EA  LF EM ++G++P V
Sbjct: 1   VTYNTLIDGLCKAGRVEEALELFKEMKERGIEPDV 35

This model describes a domain called the PPR motif, or pentatricopeptide repeat. Its consensus sequence is 35 positions long and typically is found in four or more tandem copies. This family is strongly represented in plant proteins, particularly those sorted to chloroplasts or mitochondria. The pfam model pfam01535, domain of unknown function DUF17, consists of 6 copies of this repeat. This family has a similar consensus to the TPR domain (tetratricopeptide), pfam pfam00515, a 33-residue repeat. It is predicted to form a pair of antiparallel helices similar to that of TPR. Length = 35

>gnl|CDD|205109 pfam12854, PPR_1, PPR repeat

 Score = 47.0 bits (113), Expect = 2e-07
 Identities = 16/34 (47%), Positives = 25/34 (73%)

Query: 271 QGVQPSVVTFNVIMDELCKNRKMDEASRLLDLMV 304
           +G++P VVT+N ++D LC+  ++DEA  LLD M 
Sbjct: 1   KGLKPDVVTYNTLIDGLCRAGRVDEAVELLDEME 34

This family matches additional variants of the PPR repeat that were not captured by the model for pfam01535. The exact function is not known. Length = 34

>gnl|CDD|213555 TIGR00756, PPR, pentatricopeptide repeat domain (PPR motif)

 Score = 46.7 bits (112), Expect = 3e-07
 Identities = 21/35 (60%), Positives = 27/35 (77%)

Query: 208 VTYSTIIDGLCKEGFVDKAKALFLQMKDENINPDV 242
           VTY+T+IDGLCK G V++A  LF +MK+  I PDV
Sbjct: 1   VTYNTLIDGLCKAGRVEEALELFKEMKERGIEPDV 35

This model describes a domain called the PPR motif, or pentatricopeptide repeat. Its consensus sequence is 35 positions long and typically is found in four or more tandem copies. This family is strongly represented in plant proteins, particularly those sorted to chloroplasts or mitochondria. The pfam model pfam01535, domain of unknown function DUF17, consists of 6 copies of this repeat. This family has a similar consensus to the TPR domain (tetratricopeptide), pfam pfam00515, a 33-residue repeat. It is predicted to form a pair of antiparallel helices similar to that of TPR. Length = 35

>gnl|CDD|205109 pfam12854, PPR_1, PPR repeat

 Score = 45.8 bits (110), Expect = 6e-07
 Identities = 16/31 (51%), Positives = 19/31 (61%)

Query: 411 DGVAADTRTYTTFIDGLCKNGYIIEAVELFR 441
            G+  D  TY T IDGLC+ G + EAVEL  
Sbjct: 1   KGLKPDVVTYNTLIDGLCRAGRVDEAVELLD 31

This family matches additional variants of the PPR repeat that were not captured by the model for pfam01535. The exact function is not known. Length = 34

>gnl|CDD|213555 TIGR00756, PPR, pentatricopeptide repeat domain (PPR motif)

 Score = 44.4 bits (106), Expect = 2e-06
 Identities = 16/35 (45%), Positives = 21/35 (60%)

Query: 313 CTYNTLMDGFCLMGKINRAEELFGSMESMGCKHDD 347
            TYNTL+DG C  G++  A ELF  M+  G + D 
Sbjct: 1   VTYNTLIDGLCKAGRVEEALELFKEMKERGIEPDV 35

This model describes a domain called the PPR motif, or pentatricopeptide repeat. Its consensus sequence is 35 positions long and typically is found in four or more tandem copies. This family is strongly represented in plant proteins, particularly those sorted to chloroplasts or mitochondria. The pfam model pfam01535, domain of unknown function DUF17, consists of 6 copies of this repeat. This family has a similar consensus to the TPR domain (tetratricopeptide), pfam pfam00515, a 33-residue repeat. It is predicted to form a pair of antiparallel helices similar to that of TPR. Length = 35

>gnl|CDD|144943 pfam01535, PPR, PPR repeat

 Score = 44.0 bits (105), Expect = 2e-06
 Identities = 18/31 (58%), Positives = 20/31 (64%)

Query: 243 VTYNSLIHGLCHANDWNEAKRLFIEMMDQGV 273
           VTYNSLI G C A    EA  LF EM ++GV
Sbjct: 1   VTYNSLISGYCKAGKLEEALELFKEMKEKGV 31

This repeat has no known function. It is about 35 amino acids long and found in up to 18 copies in some proteins. This family appears to be greatly expanded in plants. This repeat occurs in PET309, which may be involved in RNA stabilisation. This domain occurs in crp1 that is involved in RNA processing. This repeat is associated with a predicted plant protein that has a domain organisation similar to the human BRCA1 protein. The repeat has been called PPR. Length = 31

>gnl|CDD|205222 pfam13041, PPR_2, PPR repeat family

 Score = 44.3 bits (106), Expect = 3e-06
 Identities = 18/53 (33%), Positives = 25/53 (47%), Gaps = 12/53 (22%)

Query: 65  PPVSSFNILLASLAKNKHYDTRLNATGLF---------PNLYTYNILINCFCK 108
           P V ++N L+    K    +    A  LF         PN+YTY+ILI+  CK
Sbjct: 1   PDVVTYNTLIDGYCKKGKVE---EALKLFNEMKKRGIKPNVYTYSILIDGLCK 50

This repeat has no known function. It is about 35 amino acids long and is found in up to 18 copies in some proteins. The family appears to be greatly expanded in plants and fungi. The repeat has been called PPR. Length = 50

>gnl|CDD|144943 pfam01535, PPR, PPR repeat

 Score = 43.6 bits (104), Expect = 3e-06
 Identities = 13/31 (41%), Positives = 23/31 (74%)

Query: 208 VTYSTIIDGLCKEGFVDKAKALFLQMKDENI 238
           VTY+++I G CK G +++A  LF +MK++ +
Sbjct: 1   VTYNSLISGYCKAGKLEEALELFKEMKEKGV 31

This repeat has no known function. It is about 35 amino acids long and found in up to 18 copies in some proteins. This family appears to be greatly expanded in plants. This repeat occurs in PET309, which may be involved in RNA stabilisation. This domain occurs in crp1 that is involved in RNA processing. This repeat is associated with a predicted plant protein that has a domain organisation similar to the human BRCA1 protein. The repeat has been called PPR. Length = 31

>gnl|CDD|144943 pfam01535, PPR, PPR repeat

 Score = 43.2 bits (103), Expect = 5e-06
 Identities = 13/29 (44%), Positives = 21/29 (72%)

Query: 488 VTYNIMIQGLCNDGQMDKARDLFLDMEEN 516
           VTYN +I G C  G++++A +LF +M+E 
Sbjct: 1   VTYNSLISGYCKAGKLEEALELFKEMKEK 29

This repeat has no known function. It is about 35 amino acids long and found in up to 18 copies in some proteins. This family appears to be greatly expanded in plants. This repeat occurs in PET309, which may be involved in RNA stabilisation. This domain occurs in crp1 that is involved in RNA processing. This repeat is associated with a predicted plant protein that has a domain organisation similar to the human BRCA1 protein. The repeat has been called PPR. Length = 31

>gnl|CDD|205985 pfam13812, PPR_3, Pentatricopeptide repeat domain

 Score = 42.9 bits (102), Expect = 5e-06
 Identities = 11/33 (33%), Positives = 19/33 (57%)

Query: 348 VSYNILINGYCKNKEVEEALSLYREMVSKGIKP 380
            +YN L+    K  + + AL++  EM + G+KP
Sbjct: 2   ETYNALLLALAKAGDPDLALAVLEEMKASGLKP 34

This family matches additional variants of the PPR repeat that were not captured by the model for pfam01535. The exact function is not known. Length = 34

>gnl|CDD|205222 pfam13041, PPR_2, PPR repeat family

 Score = 43.2 bits (103), Expect = 6e-06
 Identities = 16/50 (32%), Positives = 32/50 (64%)

Query: 520 PDVITFDMLIHGFIRINEPSKVNELLHKMKEKKVMPDASIVSIVVDLLVK 569
           PDV+T++ LI G+ +  +  +  +L ++MK++ + P+    SI++D L K
Sbjct: 1   PDVVTYNTLIDGYCKKGKVEEALKLFNEMKKRGIKPNVYTYSILIDGLCK 50

This repeat has no known function. It is about 35 amino acids long and is found in up to 18 copies in some proteins. The family appears to be greatly expanded in plants and fungi. The repeat has been called PPR. Length = 50

>gnl|CDD|205109 pfam12854, PPR_1, PPR repeat

 Score = 42.7 bits (102), Expect = 7e-06
 Identities = 14/28 (50%), Positives = 19/28 (67%)

Query: 448 CELDIQAYNCLIDGLCKSGRLKFAWELF 475
            + D+  YN LIDGLC++GR+  A EL 
Sbjct: 3   LKPDVVTYNTLIDGLCRAGRVDEAVELL 30

This family matches additional variants of the PPR repeat that were not captured by the model for pfam01535. The exact function is not known. Length = 34

>gnl|CDD|213555 TIGR00756, PPR, pentatricopeptide repeat domain (PPR motif)

 Score = 42.4 bits (101), Expect = 7e-06
 Identities = 14/35 (40%), Positives = 23/35 (65%)

Query: 278 VTFNVIMDELCKNRKMDEASRLLDLMVQRGVRPNA 312
           VT+N ++D LCK  +++EA  L   M +RG+ P+ 
Sbjct: 1   VTYNTLIDGLCKAGRVEEALELFKEMKERGIEPDV 35

This model describes a domain called the PPR motif, or pentatricopeptide repeat. Its consensus sequence is 35 positions long and typically is found in four or more tandem copies. This family is strongly represented in plant proteins, particularly those sorted to chloroplasts or mitochondria. The pfam model pfam01535, domain of unknown function DUF17, consists of 6 copies of this repeat. This family has a similar consensus to the TPR domain (tetratricopeptide), pfam pfam00515, a 33-residue repeat. It is predicted to form a pair of antiparallel helices similar to that of TPR. Length = 35

>gnl|CDD|205109 pfam12854, PPR_1, PPR repeat

 Score = 42.3 bits (101), Expect = 8e-06
 Identities = 12/22 (54%), Positives = 16/22 (72%)

Query: 91  GLFPNLYTYNILINCFCKIGRV 112
           GL P++ TYN LI+  C+ GRV
Sbjct: 2   GLKPDVVTYNTLIDGLCRAGRV 23

This family matches additional variants of the PPR repeat that were not captured by the model for pfam01535. The exact function is not known. Length = 34

>gnl|CDD|144943 pfam01535, PPR, PPR repeat

 Score = 42.1 bits (100), Expect = 9e-06
 Identities = 14/30 (46%), Positives = 19/30 (63%)

Query: 314 TYNTLMDGFCLMGKINRAEELFGSMESMGC 343
           TYN+L+ G+C  GK+  A ELF  M+  G 
Sbjct: 2   TYNSLISGYCKAGKLEEALELFKEMKEKGV 31

This repeat has no known function. It is about 35 amino acids long and found in up to 18 copies in some proteins. This family appears to be greatly expanded in plants. This repeat occurs in PET309, which may be involved in RNA stabilisation. This domain occurs in crp1 that is involved in RNA processing. This repeat is associated with a predicted plant protein that has a domain organisation similar to the human BRCA1 protein. The repeat has been called PPR. Length = 31

>gnl|CDD|205985 pfam13812, PPR_3, Pentatricopeptide repeat domain

 Score = 42.2 bits (100), Expect = 9e-06
 Identities = 12/34 (35%), Positives = 19/34 (55%)

Query: 242 VVTYNSLIHGLCHANDWNEAKRLFIEMMDQGVQP 275
           + TYN+L+  L  A D + A  +  EM   G++P
Sbjct: 1   LETYNALLLALAKAGDPDLALAVLEEMKASGLKP 34

This family matches additional variants of the PPR repeat that were not captured by the model for pfam01535. The exact function is not known. Length = 34

>gnl|CDD|213555 TIGR00756, PPR, pentatricopeptide repeat domain (PPR motif)

 Score = 41.7 bits (99), Expect = 2e-05
 Identities = 17/35 (48%), Positives = 25/35 (71%)

Query: 488 VTYNIMIQGLCNDGQMDKARDLFLDMEENAAAPDV 522
           VTYN +I GLC  G++++A +LF +M+E    PDV
Sbjct: 1   VTYNTLIDGLCKAGRVEEALELFKEMKERGIEPDV 35

This model describes a domain called the PPR motif, or pentatricopeptide repeat. Its consensus sequence is 35 positions long and typically is found in four or more tandem copies. This family is strongly represented in plant proteins, particularly those sorted to chloroplasts or mitochondria. The pfam model pfam01535, domain of unknown function DUF17, consists of 6 copies of this repeat. This family has a similar consensus to the TPR domain (tetratricopeptide), pfam pfam00515, a 33-residue repeat. It is predicted to form a pair of antiparallel helices similar to that of TPR. Length = 35

>gnl|CDD|205109 pfam12854, PPR_1, PPR repeat

 Score = 40.8 bits (97), Expect = 3e-05
 Identities = 19/34 (55%), Positives = 25/34 (73%)

Query: 376 KGIKPTVVTYNTLFLGLFEIHQVEHALKLFDEMQ 409
           KG+KP VVTYNTL  GL    +V+ A++L DEM+
Sbjct: 1   KGLKPDVVTYNTLIDGLCRAGRVDEAVELLDEME 34

This family matches additional variants of the PPR repeat that were not captured by the model for pfam01535. The exact function is not known. Length = 34

>gnl|CDD|144943 pfam01535, PPR, PPR repeat

 Score = 39.0 bits (92), Expect = 1e-04
 Identities = 12/31 (38%), Positives = 19/31 (61%)

Query: 278 VTFNVIMDELCKNRKMDEASRLLDLMVQRGV 308
           VT+N ++   CK  K++EA  L   M ++GV
Sbjct: 1   VTYNSLISGYCKAGKLEEALELFKEMKEKGV 31

This repeat has no known function. It is about 35 amino acids long and found in up to 18 copies in some proteins. This family appears to be greatly expanded in plants. This repeat occurs in PET309, which may be involved in RNA stabilisation. This domain occurs in crp1 that is involved in RNA processing. This repeat is associated with a predicted plant protein that has a domain organisation similar to the human BRCA1 protein. The repeat has been called PPR. Length = 31

>gnl|CDD|144943 pfam01535, PPR, PPR repeat

 Score = 38.2 bits (90), Expect = 2e-04
 Identities = 14/26 (53%), Positives = 19/26 (73%)

Query: 167 ITYNTLINGLCRTGHTMIALNLFEEM 192
           +TYN+LI+G C+ G    AL LF+EM
Sbjct: 1   VTYNSLISGYCKAGKLEEALELFKEM 26

This repeat has no known function. It is about 35 amino acids long and found in up to 18 copies in some proteins. This family appears to be greatly expanded in plants. This repeat occurs in PET309, which may be involved in RNA stabilisation. This domain occurs in crp1 that is involved in RNA processing. This repeat is associated with a predicted plant protein that has a domain organisation similar to the human BRCA1 protein. The repeat has been called PPR. Length = 31

>gnl|CDD|213555 TIGR00756, PPR, pentatricopeptide repeat domain (PPR motif)

 Score = 37.4 bits (88), Expect = 5e-04
 Identities = 18/35 (51%), Positives = 23/35 (65%)

Query: 383 VTYNTLFLGLFEIHQVEHALKLFDEMQRDGVAADT 417
           VTYNTL  GL +  +VE AL+LF EM+  G+  D 
Sbjct: 1   VTYNTLIDGLCKAGRVEEALELFKEMKERGIEPDV 35

This model describes a domain called the PPR motif, or pentatricopeptide repeat. Its consensus sequence is 35 positions long and typically is found in four or more tandem copies. This family is strongly represented in plant proteins, particularly those sorted to chloroplasts or mitochondria. The pfam model pfam01535, domain of unknown function DUF17, consists of 6 copies of this repeat. This family has a similar consensus to the TPR domain (tetratricopeptide), pfam pfam00515, a 33-residue repeat. It is predicted to form a pair of antiparallel helices similar to that of TPR. Length = 35

>gnl|CDD|144943 pfam01535, PPR, PPR repeat

 Score = 36.7 bits (86), Expect = 8e-04
 Identities = 15/31 (48%), Positives = 21/31 (67%)

Query: 383 VTYNTLFLGLFEIHQVEHALKLFDEMQRDGV 413
           VTYN+L  G  +  ++E AL+LF EM+  GV
Sbjct: 1   VTYNSLISGYCKAGKLEEALELFKEMKEKGV 31

This repeat has no known function. It is about 35 amino acids long and found in up to 18 copies in some proteins. This family appears to be greatly expanded in plants. This repeat occurs in PET309, which may be involved in RNA stabilisation. This domain occurs in crp1 that is involved in RNA processing. This repeat is associated with a predicted plant protein that has a domain organisation similar to the human BRCA1 protein. The repeat has been called PPR. Length = 31

>gnl|CDD|213555 TIGR00756, PPR, pentatricopeptide repeat domain (PPR motif)

 Score = 36.3 bits (85), Expect = 0.001
 Identities = 17/35 (48%), Positives = 23/35 (65%)

Query: 418 RTYTTFIDGLCKNGYIIEAVELFRTLRILKCELDI 452
            TY T IDGLCK G + EA+ELF+ ++    E D+
Sbjct: 1   VTYNTLIDGLCKAGRVEEALELFKEMKERGIEPDV 35

This model describes a domain called the PPR motif, or pentatricopeptide repeat. Its consensus sequence is 35 positions long and typically is found in four or more tandem copies. This family is strongly represented in plant proteins, particularly those sorted to chloroplasts or mitochondria. The pfam model pfam01535, domain of unknown function DUF17, consists of 6 copies of this repeat. This family has a similar consensus to the TPR domain (tetratricopeptide), pfam pfam00515, a 33-residue repeat. It is predicted to form a pair of antiparallel helices similar to that of TPR. Length = 35

>gnl|CDD|213555 TIGR00756, PPR, pentatricopeptide repeat domain (PPR motif)

 Score = 35.9 bits (84), Expect = 0.002
 Identities = 17/34 (50%), Positives = 23/34 (67%)

Query: 454 AYNCLIDGLCKSGRLKFAWELFCSLPHGVLVPNV 487
            YN LIDGLCK+GR++ A ELF  +    + P+V
Sbjct: 2   TYNTLIDGLCKAGRVEEALELFKEMKERGIEPDV 35

This model describes a domain called the PPR motif, or pentatricopeptide repeat. Its consensus sequence is 35 positions long and typically is found in four or more tandem copies. This family is strongly represented in plant proteins, particularly those sorted to chloroplasts or mitochondria. The pfam model pfam01535, domain of unknown function DUF17, consists of 6 copies of this repeat. This family has a similar consensus to the TPR domain (tetratricopeptide), pfam pfam00515, a 33-residue repeat. It is predicted to form a pair of antiparallel helices similar to that of TPR. Length = 35

>gnl|CDD|144943 pfam01535, PPR, PPR repeat

 Score = 35.9 bits (84), Expect = 0.002
 Identities = 12/23 (52%), Positives = 16/23 (69%)

Query: 419 TYTTFIDGLCKNGYIIEAVELFR 441
           TY + I G CK G + EA+ELF+
Sbjct: 2   TYNSLISGYCKAGKLEEALELFK 24

This repeat has no known function. It is about 35 amino acids long and found in up to 18 copies in some proteins. This family appears to be greatly expanded in plants. This repeat occurs in PET309, which may be involved in RNA stabilisation. This domain occurs in crp1 that is involved in RNA processing. This repeat is associated with a predicted plant protein that has a domain organisation similar to the human BRCA1 protein. The repeat has been called PPR. Length = 31

>gnl|CDD|213555 TIGR00756, PPR, pentatricopeptide repeat domain (PPR motif)

 Score = 34.7 bits (81), Expect = 0.004
 Identities = 16/26 (61%), Positives = 20/26 (76%)

Query: 167 ITYNTLINGLCRTGHTMIALNLFEEM 192
           +TYNTLI+GLC+ G    AL LF+EM
Sbjct: 1   VTYNTLIDGLCKAGRVEEALELFKEM 26

This model describes a domain called the PPR motif, or pentatricopeptide repeat. Its consensus sequence is 35 positions long and typically is found in four or more tandem copies. This family is strongly represented in plant proteins, particularly those sorted to chloroplasts or mitochondria. The pfam model pfam01535, domain of unknown function DUF17, consists of 6 copies of this repeat. This family has a similar consensus to the TPR domain (tetratricopeptide), pfam pfam00515, a 33-residue repeat. It is predicted to form a pair of antiparallel helices similar to that of TPR. Length = 35

>gnl|CDD|205985 pfam13812, PPR_3, Pentatricopeptide repeat domain

 Score = 34.8 bits (81), Expect = 0.004
 Identities = 10/34 (29%), Positives = 18/34 (52%)

Query: 277 VVTFNVIMDELCKNRKMDEASRLLDLMVQRGVRP 310
           + T+N ++  L K    D A  +L+ M   G++P
Sbjct: 1   LETYNALLLALAKAGDPDLALAVLEEMKASGLKP 34

This family matches additional variants of the PPR repeat that were not captured by the model for pfam01535. The exact function is not known. Length = 34

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	595
PLN03218	1060	maturation of RBCL 1; Provisional	100.0
PLN03077	857	Protein ECB2; Provisional	100.0
PLN03218	1060	maturation of RBCL 1; Provisional	100.0
PLN03077	857	Protein ECB2; Provisional	100.0
PLN03081	697	pentatricopeptide (PPR) repeat-containing protein;	100.0
PLN03081	697	pentatricopeptide (PPR) repeat-containing protein;	100.0
TIGR02917	899	PEP_TPR_lipo putative PEP-CTERM system TPR-repeat	100.0
TIGR02917	899	PEP_TPR_lipo putative PEP-CTERM system TPR-repeat	100.0
PRK11447	1157	cellulose synthase subunit BcsC; Provisional	99.98
PRK11447	1157	cellulose synthase subunit BcsC; Provisional	99.97
KOG4626	966	consensus O-linked N-acetylglucosamine transferase	99.97
PRK09782	987	bacteriophage N4 receptor, outer membrane subunit;	99.96
KOG4626	966	consensus O-linked N-acetylglucosamine transferase	99.96
KOG2002	1018	consensus TPR-containing nuclear phosphoprotein th	99.96
PRK09782	987	bacteriophage N4 receptor, outer membrane subunit;	99.94
TIGR00990	615	3a0801s09 mitochondrial precursor proteins import	99.94
KOG2002	1018	consensus TPR-containing nuclear phosphoprotein th	99.93
TIGR00990	615	3a0801s09 mitochondrial precursor proteins import	99.92
PRK11788	389	tetratricopeptide repeat protein; Provisional	99.91
PRK15174	656	Vi polysaccharide export protein VexE; Provisional	99.91
PRK10049	765	pgaA outer membrane protein PgaA; Provisional	99.91
PRK15174	656	Vi polysaccharide export protein VexE; Provisional	99.91
PRK10049	765	pgaA outer membrane protein PgaA; Provisional	99.91
PRK11788	389	tetratricopeptide repeat protein; Provisional	99.9
PRK14574	822	hmsH outer membrane protein; Provisional	99.89
PRK14574	822	hmsH outer membrane protein; Provisional	99.89
KOG0495	913	consensus HAT repeat protein [RNA processing and m	99.89
KOG2076	895	consensus RNA polymerase III transcription factor	99.88
KOG1915	677	consensus Cell cycle control protein (crooked neck	99.88
KOG2003	840	consensus TPR repeat-containing protein [General f	99.87
KOG0495	913	consensus HAT repeat protein [RNA processing and m	99.86
KOG1915	677	consensus Cell cycle control protein (crooked neck	99.85
KOG2003	840	consensus TPR repeat-containing protein [General f	99.82
KOG2076	895	consensus RNA polymerase III transcription factor	99.79
KOG4422	625	consensus Uncharacterized conserved protein [Funct	99.77
KOG4422	625	consensus Uncharacterized conserved protein [Funct	99.77
KOG0547	606	consensus Translocase of outer mitochondrial membr	99.74
KOG0547	606	consensus Translocase of outer mitochondrial membr	99.74
KOG1155	559	consensus Anaphase-promoting complex (APC), Cdc23	99.71
KOG1155	559	consensus Anaphase-promoting complex (APC), Cdc23	99.71
KOG2047	835	consensus mRNA splicing factor [RNA processing and	99.71
PF13429	280	TPR_15: Tetratricopeptide repeat; PDB: 2VQ2_A 2PL2	99.7
PRK10747	398	putative protoheme IX biogenesis protein; Provisio	99.69
KOG1173	611	consensus Anaphase-promoting complex (APC), Cdc16	99.69
PRK10747	398	putative protoheme IX biogenesis protein; Provisio	99.69
TIGR00540	409	hemY_coli hemY protein. This is an uncharacterized	99.68
TIGR00540	409	hemY_coli hemY protein. This is an uncharacterized	99.67
PF13429	280	TPR_15: Tetratricopeptide repeat; PDB: 2VQ2_A 2PL2	99.67
KOG1126	638	consensus DNA-binding cell division cycle control	99.66
COG3071	400	HemY Uncharacterized enzyme of heme biosynthesis [	99.66
KOG1173	611	consensus Anaphase-promoting complex (APC), Cdc16	99.65
KOG3785	557	consensus Uncharacterized conserved protein [Funct	99.65
KOG1126	638	consensus DNA-binding cell division cycle control	99.65
KOG2047	835	consensus mRNA splicing factor [RNA processing and	99.63
COG2956	389	Predicted N-acetylglucosaminyl transferase [Carboh	99.63
COG2956	389	Predicted N-acetylglucosaminyl transferase [Carboh	99.62
COG3071	400	HemY Uncharacterized enzyme of heme biosynthesis [	99.62
KOG3785	557	consensus Uncharacterized conserved protein [Funct	99.6
KOG1156	700	consensus N-terminal acetyltransferase [Chromatin	99.59
KOG4162	799	consensus Predicted calmodulin-binding protein [Si	99.58
KOG1156	700	consensus N-terminal acetyltransferase [Chromatin	99.55
KOG1174	564	consensus Anaphase-promoting complex (APC), subuni	99.54
PRK12370	553	invasion protein regulator; Provisional	99.52
KOG1129	478	consensus TPR repeat-containing protein [General f	99.51
KOG1129	478	consensus TPR repeat-containing protein [General f	99.51
KOG1174	564	consensus Anaphase-promoting complex (APC), subuni	99.5
TIGR02521	234	type_IV_pilW type IV pilus biogenesis/stability pr	99.5
KOG4162	799	consensus Predicted calmodulin-binding protein [Si	99.5
PRK12370	553	invasion protein regulator; Provisional	99.48
KOG2376	652	consensus Signal recognition particle, subunit Srp	99.47
TIGR02521	234	type_IV_pilW type IV pilus biogenesis/stability pr	99.43
KOG2376	652	consensus Signal recognition particle, subunit Srp	99.43
KOG4318	1088	consensus Bicoid mRNA stability factor [RNA proces	99.42
COG3063	250	PilF Tfp pilus assembly protein PilF [Cell motilit	99.4
KOG0548	539	consensus Molecular co-chaperone STI1 [Posttransla	99.4
PF12569	517	NARP1: NMDA receptor-regulated protein 1 ; InterPr	99.39
KOG0548	539	consensus Molecular co-chaperone STI1 [Posttransla	99.37
PF12569	517	NARP1: NMDA receptor-regulated protein 1 ; InterPr	99.35
KOG1127	1238	consensus TPR repeat-containing protein [RNA proce	99.35
COG3063	250	PilF Tfp pilus assembly protein PilF [Cell motilit	99.33
KOG1840	508	consensus Kinesin light chain [Cytoskeleton]	99.32
KOG0985	1666	consensus Vesicle coat protein clathrin, heavy cha	99.31
PRK11189	296	lipoprotein NlpI; Provisional	99.28
PRK11189	296	lipoprotein NlpI; Provisional	99.28
KOG1840	508	consensus Kinesin light chain [Cytoskeleton]	99.28
KOG4340	459	consensus Uncharacterized conserved protein [Funct	99.26
KOG4318	1088	consensus Bicoid mRNA stability factor [RNA proces	99.25
KOG0624	504	consensus dsRNA-activated protein kinase inhibitor	99.22
KOG1127	1238	consensus TPR repeat-containing protein [RNA proce	99.22
KOG1914	656	consensus mRNA cleavage and polyadenylation factor	99.21
KOG3617	1416	consensus WD40 and TPR repeat-containing protein [	99.21
cd05804	355	StaR_like StaR_like; a well-conserved protein foun	99.2
cd05804	355	StaR_like StaR_like; a well-conserved protein foun	99.18
KOG1125	579	consensus TPR repeat-containing protein [General f	99.18
KOG4340	459	consensus Uncharacterized conserved protein [Funct	99.15
KOG1125	579	consensus TPR repeat-containing protein [General f	99.15
KOG2053	932	consensus Mitochondrial inheritance and actin cyto	99.13
KOG3616	1636	consensus Selective LIM binding factor [Transcript	99.11
PRK04841	903	transcriptional regulator MalT; Provisional	99.11
KOG3617	1416	consensus WD40 and TPR repeat-containing protein [	99.1
PRK04841	903	transcriptional regulator MalT; Provisional	99.1
PF13041	50	PPR_2: PPR repeat family	99.08
PF04733	290	Coatomer_E: Coatomer epsilon subunit; InterPro: IP	99.08
KOG0624	504	consensus dsRNA-activated protein kinase inhibitor	99.07
KOG1914	656	consensus mRNA cleavage and polyadenylation factor	99.04
PF13041	50	PPR_2: PPR repeat family	99.04
KOG0985	1666	consensus Vesicle coat protein clathrin, heavy cha	99.0
PF04733	290	Coatomer_E: Coatomer epsilon subunit; InterPro: IP	98.97
KOG1128	777	consensus Uncharacterized conserved protein, conta	98.95
KOG1070	1710	consensus rRNA processing protein Rrp5 [RNA proces	98.9
PLN02789	320	farnesyltranstransferase	98.88
PLN02789	320	farnesyltranstransferase	98.87
KOG3616	1636	consensus Selective LIM binding factor [Transcript	98.86
COG5010	257	TadD Flp pilus assembly protein TadD, contains TPR	98.86
PRK10370	198	formate-dependent nitrite reductase complex subuni	98.83
KOG3060	289	consensus Uncharacterized conserved protein [Funct	98.83
KOG1070	1710	consensus rRNA processing protein Rrp5 [RNA proces	98.83
COG5010	257	TadD Flp pilus assembly protein TadD, contains TPR	98.82
KOG2053	932	consensus Mitochondrial inheritance and actin cyto	98.82
TIGR03302	235	OM_YfiO outer membrane assembly lipoprotein YfiO.	98.81
KOG1128	777	consensus Uncharacterized conserved protein, conta	98.81
TIGR03302	235	OM_YfiO outer membrane assembly lipoprotein YfiO.	98.73
PRK14720	906	transcript cleavage factor/unknown domain fusion p	98.73
PRK10370	198	formate-dependent nitrite reductase complex subuni	98.73
PRK15359	144	type III secretion system chaperone protein SscB;	98.69
PRK14720	906	transcript cleavage factor/unknown domain fusion p	98.67
PRK15359	144	type III secretion system chaperone protein SscB;	98.65
KOG3081	299	consensus Vesicle coat complex COPI, epsilon subun	98.64
PRK15179	694	Vi polysaccharide biosynthesis protein TviE; Provi	98.63
KOG3081	299	consensus Vesicle coat complex COPI, epsilon subun	98.62
PRK15179	694	Vi polysaccharide biosynthesis protein TviE; Provi	98.59
TIGR02552	135	LcrH_SycD type III secretion low calcium response	98.56
KOG3060	289	consensus Uncharacterized conserved protein [Funct	98.54
COG4783	484	Putative Zn-dependent protease, contains TPR repea	98.46
TIGR02552	135	LcrH_SycD type III secretion low calcium response	98.42
PF12854	34	PPR_1: PPR repeat	98.39
COG4783	484	Putative Zn-dependent protease, contains TPR repea	98.38
KOG0550	486	consensus Molecular chaperone (DnaJ superfamily) [	98.31
PF12854	34	PPR_1: PPR repeat	98.31
PF09976	145	TPR_21: Tetratricopeptide repeat; InterPro: IPR018	98.3
PF09976	145	TPR_21: Tetratricopeptide repeat; InterPro: IPR018	98.3
KOG2041	1189	consensus WD40 repeat protein [General function pr	98.22
PF09295	395	ChAPs: ChAPs (Chs5p-Arf1p-binding proteins); Inter	98.16
PF09295	395	ChAPs: ChAPs (Chs5p-Arf1p-binding proteins); Inter	98.15
KOG0550	486	consensus Molecular chaperone (DnaJ superfamily) [	98.13
PRK15363	157	pathogenicity island 2 chaperone protein SscA; Pro	98.03
KOG0553	304	consensus TPR repeat-containing protein [General f	98.02
COG4235	287	Cytochrome c biogenesis factor [Posttranslational	98.02
TIGR02795	119	tol_pal_ybgF tol-pal system protein YbgF. Members	98.0
PF07079	549	DUF1347: Protein of unknown function (DUF1347); In	97.99
TIGR02795	119	tol_pal_ybgF tol-pal system protein YbgF. Members	97.98
PF12895	84	Apc3: Anaphase-promoting complex, cyclosome, subun	97.98
PRK10866	243	outer membrane biogenesis protein BamD; Provisiona	97.97
PRK15363	157	pathogenicity island 2 chaperone protein SscA; Pro	97.97
cd00189	100	TPR Tetratricopeptide repeat domain; typically con	97.93
CHL00033	168	ycf3 photosystem I assembly protein Ycf3	97.92
KOG2041	1189	consensus WD40 repeat protein [General function pr	97.92
KOG0553	304	consensus TPR repeat-containing protein [General f	97.9
COG4700	251	Uncharacterized protein conserved in bacteria cont	97.89
PRK10866	243	outer membrane biogenesis protein BamD; Provisiona	97.88
PLN03088	356	SGT1, suppressor of G2 allele of SKP1; Provisional	97.88
COG4700	251	Uncharacterized protein conserved in bacteria cont	97.87
PRK02603	172	photosystem I assembly protein Ycf3; Provisional	97.87
PF12895	84	Apc3: Anaphase-promoting complex, cyclosome, subun	97.85
cd00189	100	TPR Tetratricopeptide repeat domain; typically con	97.84
PLN03088	356	SGT1, suppressor of G2 allele of SKP1; Provisional	97.83
PF10037	429	MRP-S27: Mitochondrial 28S ribosomal protein S27;	97.81
COG4235	287	Cytochrome c biogenesis factor [Posttranslational	97.78
TIGR00756	35	PPR pentatricopeptide repeat domain (PPR motif). T	97.77
COG5107	660	RNA14 Pre-mRNA 3'-end processing (cleavage and pol	97.76
PRK10153	517	DNA-binding transcriptional activator CadC; Provis	97.75
PF05843	280	Suf: Suppressor of forked protein (Suf); InterPro:	97.75
COG3898	531	Uncharacterized membrane-bound protein [Function u	97.74
TIGR00756	35	PPR pentatricopeptide repeat domain (PPR motif). T	97.73
PRK02603	172	photosystem I assembly protein Ycf3; Provisional	97.73
CHL00033	168	ycf3 photosystem I assembly protein Ycf3	97.72
KOG1130	639	consensus Predicted G-alpha GTPase interaction pro	97.71
PF13812	34	PPR_3: Pentatricopeptide repeat domain	97.7
PRK10153	517	DNA-binding transcriptional activator CadC; Provis	97.69
PF13812	34	PPR_3: Pentatricopeptide repeat domain	97.69
PF13414	69	TPR_11: TPR repeat; PDB: 2HO1_B 2FI7_B 2DBA_A 3Q4A	97.68
PF05843	280	Suf: Suppressor of forked protein (Suf); InterPro:	97.68
PF14938	282	SNAP: Soluble NSF attachment protein, SNAP; PDB: 1	97.66
PF12688	120	TPR_5: Tetratrico peptide repeat	97.65
PF14938	282	SNAP: Soluble NSF attachment protein, SNAP; PDB: 1	97.65
PF14559	68	TPR_19: Tetratricopeptide repeat; PDB: 2R5S_A 3QDN	97.63
PF12688	120	TPR_5: Tetratrico peptide repeat	97.63
PF13432	65	TPR_16: Tetratricopeptide repeat; PDB: 3CVP_A 3CVL	97.61
PF13525	203	YfiO: Outer membrane lipoprotein; PDB: 3TGO_A 3Q5M	97.6
PF10037	429	MRP-S27: Mitochondrial 28S ribosomal protein S27;	97.6
KOG1130	639	consensus Predicted G-alpha GTPase interaction pro	97.59
KOG2114	933	consensus Vacuolar assembly/sorting protein PEP5/V	97.58
PF14559	68	TPR_19: Tetratricopeptide repeat; PDB: 2R5S_A 3QDN	97.52
KOG1258	577	consensus mRNA processing protein [RNA processing	97.51
PF13525	203	YfiO: Outer membrane lipoprotein; PDB: 3TGO_A 3Q5M	97.48
PF13414	69	TPR_11: TPR repeat; PDB: 2HO1_B 2FI7_B 2DBA_A 3Q4A	97.48
PF13432	65	TPR_16: Tetratricopeptide repeat; PDB: 3CVP_A 3CVL	97.45
PF08579	120	RPM2: Mitochondrial ribonuclease P subunit (RPM2);	97.44
PF08579	120	RPM2: Mitochondrial ribonuclease P subunit (RPM2);	97.42
COG5107	660	RNA14 Pre-mRNA 3'-end processing (cleavage and pol	97.41
COG3898	531	Uncharacterized membrane-bound protein [Function u	97.41
KOG2796	366	consensus Uncharacterized conserved protein [Funct	97.39
PRK10803	263	tol-pal system protein YbgF; Provisional	97.31
PF01535	31	PPR: PPR repeat; InterPro: IPR002885 This entry re	97.29
KOG1538	1081	consensus Uncharacterized conserved protein WDR10,	97.27
KOG1258	577	consensus mRNA processing protein [RNA processing	97.27
PF13371	73	TPR_9: Tetratricopeptide repeat	97.26
PF03704	146	BTAD: Bacterial transcriptional activator domain;	97.25
PRK10803	263	tol-pal system protein YbgF; Provisional	97.22
PF01535	31	PPR: PPR repeat; InterPro: IPR002885 This entry re	97.19
PF06239	228	ECSIT: Evolutionarily conserved signalling interme	97.14
PF04840	319	Vps16_C: Vps16, C-terminal region; InterPro: IPR00	97.12
KOG2796	366	consensus Uncharacterized conserved protein [Funct	97.1
COG4105	254	ComL DNA uptake lipoprotein [General function pred	97.09
PF13281	374	DUF4071: Domain of unknown function (DUF4071)	97.08
PF06239	228	ECSIT: Evolutionarily conserved signalling interme	97.06
PF07079	549	DUF1347: Protein of unknown function (DUF1347); In	97.05
PF03704	146	BTAD: Bacterial transcriptional activator domain;	97.02
PRK15331	165	chaperone protein SicA; Provisional	96.97
PF13371	73	TPR_9: Tetratricopeptide repeat	96.95
PRK15331	165	chaperone protein SicA; Provisional	96.93
PF13424	78	TPR_12: Tetratricopeptide repeat; PDB: 3RO2_A 3Q15	96.85
COG3118	304	Thioredoxin domain-containing protein [Posttransla	96.83
PF13281	374	DUF4071: Domain of unknown function (DUF4071)	96.82
PF13424	78	TPR_12: Tetratricopeptide repeat; PDB: 3RO2_A 3Q15	96.82
KOG1538	1081	consensus Uncharacterized conserved protein WDR10,	96.8
PRK11906	458	transcriptional regulator; Provisional	96.78
PLN03098	453	LPA1 LOW PSII ACCUMULATION1; Provisional	96.63
KOG1585	308	consensus Protein required for fusion of vesicles	96.63
KOG2114	933	consensus Vacuolar assembly/sorting protein PEP5/V	96.59
KOG1585	308	consensus Protein required for fusion of vesicles	96.55
PLN03098	453	LPA1 LOW PSII ACCUMULATION1; Provisional	96.54
PRK11906	458	transcriptional regulator; Provisional	96.52
COG3118	304	Thioredoxin domain-containing protein [Posttransla	96.48
PF04840	319	Vps16_C: Vps16, C-terminal region; InterPro: IPR00	96.48
PF10300	468	DUF3808: Protein of unknown function (DUF3808); In	96.48
KOG0543	397	consensus FKBP-type peptidyl-prolyl cis-trans isom	96.47
KOG0543	397	consensus FKBP-type peptidyl-prolyl cis-trans isom	96.43
PF10300	468	DUF3808: Protein of unknown function (DUF3808); In	96.36
COG1729	262	Uncharacterized protein conserved in bacteria [Fun	96.25
PF08631	278	SPO22: Meiosis protein SPO22/ZIP4 like; InterPro:	96.2
KOG2280	829	consensus Vacuolar assembly/sorting protein VPS16	96.17
KOG2610	491	consensus Uncharacterized conserved protein [Funct	96.17
KOG2610	491	consensus Uncharacterized conserved protein [Funct	96.14
PF13512	142	TPR_18: Tetratricopeptide repeat	96.12
PF12921	126	ATP13: Mitochondrial ATPase expression; InterPro:	95.99
PF12921	126	ATP13: Mitochondrial ATPase expression; InterPro:	95.94
PF13428	44	TPR_14: Tetratricopeptide repeat	95.93
COG4105	254	ComL DNA uptake lipoprotein [General function pred	95.93
PF04053	443	Coatomer_WDAD: Coatomer WD associated region ; Int	95.74
PF13428	44	TPR_14: Tetratricopeptide repeat	95.68
PF04053	443	Coatomer_WDAD: Coatomer WD associated region ; Int	95.67
KOG4555	175	consensus TPR repeat-containing protein [Function	95.66
COG4649	221	Uncharacterized protein conserved in bacteria [Fun	95.66
COG0457	291	NrfG FOG: TPR repeat [General function prediction	95.58
KOG1941	518	consensus Acetylcholine receptor-associated protei	95.55
PF04184	539	ST7: ST7 protein; InterPro: IPR007311 The ST7 (for	95.54
KOG1941	518	consensus Acetylcholine receptor-associated protei	95.53
COG1729	262	Uncharacterized protein conserved in bacteria [Fun	95.43
COG4649	221	Uncharacterized protein conserved in bacteria [Fun	95.42
PF09613	160	HrpB1_HrpK: Bacterial type III secretion protein (	95.41
PF13512	142	TPR_18: Tetratricopeptide repeat	95.3
KOG2280	829	consensus Vacuolar assembly/sorting protein VPS16	95.3
COG0457	291	NrfG FOG: TPR repeat [General function prediction	95.27
COG4785	297	NlpI Lipoprotein NlpI, contains TPR repeats [Gener	95.21
PF04184	539	ST7: ST7 protein; InterPro: IPR007311 The ST7 (for	95.21
smart00299	140	CLH Clathrin heavy chain repeat homology.	95.19
COG3629	280	DnrI DNA-binding transcriptional activator of the	95.12
KOG4555	175	consensus TPR repeat-containing protein [Function	94.97
PF08631	278	SPO22: Meiosis protein SPO22/ZIP4 like; InterPro:	94.89
KOG1920	1265	consensus IkappaB kinase complex, IKAP component [	94.71
smart00299	140	CLH Clathrin heavy chain repeat homology.	94.66
COG4785	297	NlpI Lipoprotein NlpI, contains TPR repeats [Gener	94.61
PF13431	34	TPR_17: Tetratricopeptide repeat	94.5
COG3629	280	DnrI DNA-binding transcriptional activator of the	94.48
PRK09687	280	putative lyase; Provisional	94.36
PRK15180	831	Vi polysaccharide biosynthesis protein TviD; Provi	94.34
KOG3941	406	consensus Intermediate in Toll signal transduction	93.97
KOG1920	1265	consensus IkappaB kinase complex, IKAP component [	93.72
PF13431	34	TPR_17: Tetratricopeptide repeat	93.68
PF10602	177	RPN7: 26S proteasome subunit RPN7; InterPro: IPR01	93.49
PF10602	177	RPN7: 26S proteasome subunit RPN7; InterPro: IPR01	93.27
PF13176	36	TPR_7: Tetratricopeptide repeat; PDB: 3SF4_C 3RO3_	93.14
KOG4648	536	consensus Uncharacterized conserved protein, conta	93.11
PF09205	161	DUF1955: Domain of unknown function (DUF1955); Int	93.05
PF13176	36	TPR_7: Tetratricopeptide repeat; PDB: 3SF4_C 3RO3_	92.99
KOG1550	552	consensus Extracellular protein SEL-1 and related	92.74
PF00515	34	TPR_1: Tetratricopeptide repeat; InterPro: IPR0014	92.46
PF13170	297	DUF4003: Protein of unknown function (DUF4003)	92.42
KOG1550	552	consensus Extracellular protein SEL-1 and related	92.41
PF06552	186	TOM20_plant: Plant specific mitochondrial import r	92.17
PF07719	34	TPR_2: Tetratricopeptide repeat; InterPro: IPR0131	92.16
KOG2396	568	consensus HAT (Half-A-TPR) repeat-containing prote	92.03
PF09205	161	DUF1955: Domain of unknown function (DUF1955); Int	91.93
KOG3941	406	consensus Intermediate in Toll signal transduction	91.79
KOG4234	271	consensus TPR repeat-containing protein [General f	91.74
COG3947	361	Response regulator containing CheY-like receiver a	91.72
KOG4234	271	consensus TPR repeat-containing protein [General f	91.19
PF07719	34	TPR_2: Tetratricopeptide repeat; InterPro: IPR0131	90.59
COG1747	711	Uncharacterized N-terminal domain of the transcrip	90.39
PF13170	297	DUF4003: Protein of unknown function (DUF4003)	90.36
PF00515	34	TPR_1: Tetratricopeptide repeat; InterPro: IPR0014	90.32
PF08424	321	NRDE-2: NRDE-2, necessary for RNA interference; In	90.3
TIGR02561	153	HrpB1_HrpK type III secretion protein HrpB1/HrpK.	90.18
KOG2471	696	consensus TPR repeat-containing protein [General f	90.15
PF07035	167	Mic1: Colon cancer-associated protein Mic1-like; I	90.07
PRK11619	644	lytic murein transglycosylase; Provisional	89.9
PF07575	566	Nucleopor_Nup85: Nup85 Nucleoporin; InterPro: IPR0	89.61
PF09613	160	HrpB1_HrpK: Bacterial type III secretion protein (	89.46
PF02259	352	FAT: FAT domain; InterPro: IPR003151 The FAT domai	89.22
PF02284	108	COX5A: Cytochrome c oxidase subunit Va; InterPro:	89.19
PF02284	108	COX5A: Cytochrome c oxidase subunit Va; InterPro:	88.97
COG2976	207	Uncharacterized protein conserved in bacteria [Fun	88.9
PF00637	143	Clathrin: Region in Clathrin and VPS; InterPro: IP	88.84
cd00923	103	Cyt_c_Oxidase_Va Cytochrome c oxidase subunit Va.	88.75
PF04097	613	Nic96: Nup93/Nic96; InterPro: IPR007231 Nup93/Nic9	88.66
KOG2396	568	consensus HAT (Half-A-TPR) repeat-containing prote	88.63
PRK09687	280	putative lyase; Provisional	88.59
PF02259	352	FAT: FAT domain; InterPro: IPR003151 The FAT domai	88.49
PF11207	203	DUF2989: Protein of unknown function (DUF2989); In	88.4
KOG2471	696	consensus TPR repeat-containing protein [General f	88.38
KOG0890	2382	consensus Protein kinase of the PI-3 kinase family	88.3
COG2976	207	Uncharacterized protein conserved in bacteria [Fun	88.28
KOG1464	440	consensus COP9 signalosome, subunit CSN2 [Posttran	88.27
PF06552	186	TOM20_plant: Plant specific mitochondrial import r	88.19
PF13374	42	TPR_10: Tetratricopeptide repeat; PDB: 3CEQ_B 3EDT	87.23
PF11207	203	DUF2989: Protein of unknown function (DUF2989); In	87.17
KOG4642	284	consensus Chaperone-dependent E3 ubiquitin protein	87.01
PF10345	608	Cohesin_load: Cohesin loading factor; InterPro: IP	86.98
PF13374	42	TPR_10: Tetratricopeptide repeat; PDB: 3CEQ_B 3EDT	86.94
KOG4648	536	consensus Uncharacterized conserved protein, conta	86.7
KOG4642	284	consensus Chaperone-dependent E3 ubiquitin protein	86.64
PRK15180	831	Vi polysaccharide biosynthesis protein TviD; Provi	86.62
KOG1586	288	consensus Protein required for fusion of vesicles	86.54
KOG2300	629	consensus Uncharacterized conserved protein [Funct	86.4
KOG2066	846	consensus Vacuolar assembly/sorting protein VPS41	86.11
KOG0276	794	consensus Vesicle coat complex COPI, beta' subunit	85.9
KOG0276	794	consensus Vesicle coat complex COPI, beta' subunit	85.72
smart00386	33	HAT HAT (Half-A-TPR) repeats. Present in several R	85.64
KOG4521	1480	consensus Nuclear pore complex, Nup160 component [	85.35
PF07035	167	Mic1: Colon cancer-associated protein Mic1-like; I	85.22
COG4455	273	ImpE Protein of avirulence locus involved in tempe	84.76
COG4455	273	ImpE Protein of avirulence locus involved in tempe	84.57
KOG2066	846	consensus Vacuolar assembly/sorting protein VPS41	84.15
COG1747	711	Uncharacterized N-terminal domain of the transcrip	84.14
PF13181	34	TPR_8: Tetratricopeptide repeat; PDB: 3GW4_B 3MA5_	83.99
PF04097	613	Nic96: Nup93/Nic96; InterPro: IPR007231 Nup93/Nic9	83.96
PF13181	34	TPR_8: Tetratricopeptide repeat; PDB: 3GW4_B 3MA5_	83.84
COG2909	894	MalT ATP-dependent transcriptional regulator [Tran	83.46
TIGR02561	153	HrpB1_HrpK type III secretion protein HrpB1/HrpK.	83.35
KOG4570	418	consensus Uncharacterized conserved protein [Funct	82.96
cd00923	103	Cyt_c_Oxidase_Va Cytochrome c oxidase subunit Va.	82.92
PF07721	26	TPR_4: Tetratricopeptide repeat; InterPro: IPR0117	82.7
PF13174	33	TPR_6: Tetratricopeptide repeat; PDB: 3QKY_A 2XEV_	82.52
PF08424	321	NRDE-2: NRDE-2, necessary for RNA interference; In	82.3
PF13174	33	TPR_6: Tetratricopeptide repeat; PDB: 3QKY_A 2XEV_	82.11
TIGR03504	44	FimV_Cterm FimV C-terminal domain. This protein is	80.89
COG2909	894	MalT ATP-dependent transcriptional regulator [Tran	80.39
COG3947	361	Response regulator containing CheY-like receiver a	80.09
PF10345	608	Cohesin_load: Cohesin loading factor; InterPro: IP	80.03

>PLN03218 maturation of RBCL 1; Provisional

Probab=100.00  E-value=2.4e-65  Score=534.53  Aligned_cols=512  Identities=19%  Similarity=0.295  Sum_probs=481.5

Q ss_pred             ccccCCCChHHHHHHHHHHHHhCCCCCCHhhHHHHHHHHHcCCCchh--HHhhCCCCCCHHHHHHHHHHHHhcCChhHHH
Q 040027           39 EGDINVITPNEAFCIFDYMLRMHPSPPPVSSFNILLASLAKNKHYDT--RLNATGLFPNLYTYNILINCFCKIGRVSLGF  116 (595)
Q Consensus        39 ~~~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~--~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~  116 (595)
                      ..+++.|++++|+++|++|.+.+..+++...++.++.+|.+.|...+  .+......||..+|+.++.+|++.|+++.|.
T Consensus       378 ~~l~r~G~l~eAl~Lfd~M~~~gvv~~~~v~~~~li~~~~~~g~~~eAl~lf~~M~~pd~~Tyn~LL~a~~k~g~~e~A~  457 (1060)
T PLN03218        378 NRLLRDGRIKDCIDLLEDMEKRGLLDMDKIYHAKFFKACKKQRAVKEAFRFAKLIRNPTLSTFNMLMSVCASSQDIDGAL  457 (1060)
T ss_pred             HHHHHCcCHHHHHHHHHHHHhCCCCCchHHHHHHHHHHHHHCCCHHHHHHHHHHcCCCCHHHHHHHHHHHHhCcCHHHHH
Confidence            34577899999999999999988765678888999999999999887  3444444599999999999999999999999


Q ss_pred             HHHHHHHhCCCCCCHHHHHHHHHHHHhcCCHhHHHHHHHHHHhcCCCCCHhhHHHHHHHHHhcCChhHHHHHHHHHHhcC
Q 040027          117 IAFGRILRSCFTPNAATFNSLIKGLHAESRIMEAAALFTKLKAFGCEPNVITYNTLINGLCRTGHTMIALNLFEEMANGN  196 (595)
Q Consensus       117 ~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~  196 (595)
                      .+|++|.+.|+.||..+|+.++.+|++.|++++|.++|++|.+.|+.||..+|+.+|.+|++.|++++|.++|++|...+
T Consensus       458 ~lf~~M~~~Gl~pD~~tynsLI~~y~k~G~vd~A~~vf~eM~~~Gv~PdvvTynaLI~gy~k~G~~eeAl~lf~~M~~~G  537 (1060)
T PLN03218        458 RVLRLVQEAGLKADCKLYTTLISTCAKSGKVDAMFEVFHEMVNAGVEANVHTFGALIDGCARAGQVAKAFGAYGIMRSKN  537 (1060)
T ss_pred             HHHHHHHHcCCCCCHHHHHHHHHHHHhCcCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHHCcCHHHHHHHHHHHHHcC
Confidence            99999999999999999999999999999999999999999999999999999999999999999999999999999988


Q ss_pred             CCCCccccCcHHHHHHHHHHHHHcCCHhHHHHHHHHHhh--CCCCCCHhHHHHHHHHHHhcCCHHHHHHHHHHHHHCCCC
Q 040027          197 GEIGVVCKPNTVTYSTIIDGLCKEGFVDKAKALFLQMKD--ENINPDVVTYNSLIHGLCHANDWNEAKRLFIEMMDQGVQ  274 (595)
Q Consensus       197 ~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~--~~~~~~~~~~~~ll~~~~~~~~~~~A~~~~~~~~~~~~~  274 (595)
                            +.||..+|+.++.+|++.|++++|.++|++|..  .++.||..+|+.|+.+|++.|++++|.++|+.|.+.|+.
T Consensus       538 ------v~PD~vTYnsLI~a~~k~G~~deA~~lf~eM~~~~~gi~PD~vTynaLI~ay~k~G~ldeA~elf~~M~e~gi~  611 (1060)
T PLN03218        538 ------VKPDRVVFNALISACGQSGAVDRAFDVLAEMKAETHPIDPDHITVGALMKACANAGQVDRAKEVYQMIHEYNIK  611 (1060)
T ss_pred             ------CCCCHHHHHHHHHHHHHCCCHHHHHHHHHHHHHhcCCCCCcHHHHHHHHHHHHHCCCHHHHHHHHHHHHHcCCC
Confidence                  889999999999999999999999999999986  578999999999999999999999999999999999999


Q ss_pred             CCHhhHHHHHHHHHhcCChHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHhcCCCCCHHHHHHHH
Q 040027          275 PSVVTFNVIMDELCKNRKMDEASRLLDLMVQRGVRPNACTYNTLMDGFCLMGKINRAEELFGSMESMGCKHDDVSYNILI  354 (595)
Q Consensus       275 ~~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~  354 (595)
                      |+..+|+.++.+|++.|++++|.++|++|.+.|+.||..+|+.++.+|++.|++++|.++++.|.+.|+.|+..+|+.++
T Consensus       612 p~~~tynsLI~ay~k~G~~deAl~lf~eM~~~Gv~PD~~TynsLI~a~~k~G~~eeA~~l~~eM~k~G~~pd~~tynsLI  691 (1060)
T PLN03218        612 GTPEVYTIAVNSCSQKGDWDFALSIYDDMKKKGVKPDEVFFSALVDVAGHAGDLDKAFEILQDARKQGIKLGTVSYSSLM  691 (1060)
T ss_pred             CChHHHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhCCCHHHHHHHHHHHHHcCCCCCHHHHHHHH
Confidence            99999999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             HHHHhCCCHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHccCCHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHhcCCHH
Q 040027          355 NGYCKNKEVEEALSLYREMVSKGIKPTVVTYNTLFLGLFEIHQVEHALKLFDEMQRDGVAADTRTYTTFIDGLCKNGYII  434 (595)
Q Consensus       355 ~~~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~  434 (595)
                      .+|++.|++++|.++|++|.+.|+.|+..+|+.++.+|++.|++++|.++|++|.+.|+.||..+|+.++.+|++.|+++
T Consensus       692 ~ay~k~G~~eeA~~lf~eM~~~g~~PdvvtyN~LI~gy~k~G~~eeAlelf~eM~~~Gi~Pd~~Ty~sLL~a~~k~G~le  771 (1060)
T PLN03218        692 GACSNAKNWKKALELYEDIKSIKLRPTVSTMNALITALCEGNQLPKALEVLSEMKRLGLCPNTITYSILLVASERKDDAD  771 (1060)
T ss_pred             HHHHhCCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHHCCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHHCCCHH
Confidence            99999999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             HHHHHHHHHHHcCCCcCHHHHHHHHHHHHh----c-------------------CChHHHHHHHHhcccCCCCCCHHHHH
Q 040027          435 EAVELFRTLRILKCELDIQAYNCLIDGLCK----S-------------------GRLKFAWELFCSLPHGVLVPNVVTYN  491 (595)
Q Consensus       435 ~A~~~~~~~~~~~~~~~~~~~~~l~~~~~~----~-------------------g~~~~A~~~~~~~~~~~~~p~~~~~~  491 (595)
                      +|.+++++|.+.|+.||..+|+.++..|.+    .                   +..+.|..+|++|.+.|+.||..||+
T Consensus       772 ~A~~l~~~M~k~Gi~pd~~tynsLIglc~~~y~ka~~l~~~v~~f~~g~~~~~n~w~~~Al~lf~eM~~~Gi~Pd~~T~~  851 (1060)
T PLN03218        772 VGLDLLSQAKEDGIKPNLVMCRCITGLCLRRFEKACALGEPVVSFDSGRPQIENKWTSWALMVYRETISAGTLPTMEVLS  851 (1060)
T ss_pred             HHHHHHHHHHHcCCCCCHHHHHHHHHHHHHHHHHHhhhhhhhhhhhccccccccchHHHHHHHHHHHHHCCCCCCHHHHH
Confidence            999999999999999999999999876432    1                   12467999999999999999999999


Q ss_pred             HHHHHHHhcCChhHHHHHHHHHHHcCCCCCHHHHHHHHHHHHHcCChhHHHHHHHHHHHCCCCCCHH
Q 040027          492 IMIQGLCNDGQMDKARDLFLDMEENAAAPDVITFDMLIHGFIRINEPSKVNELLHKMKEKKVMPDAS  558 (595)
Q Consensus       492 ~l~~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~p~~~  558 (595)
                      .++.+++..+....+..+++.|...+..|+..+|+.+++++.+.  .++|..++++|...|+.|+..
T Consensus       852 ~vL~cl~~~~~~~~~~~m~~~m~~~~~~~~~~~y~~Li~g~~~~--~~~A~~l~~em~~~Gi~p~~~  916 (1060)
T PLN03218        852 QVLGCLQLPHDATLRNRLIENLGISADSQKQSNLSTLVDGFGEY--DPRAFSLLEEAASLGVVPSVS  916 (1060)
T ss_pred             HHHHHhcccccHHHHHHHHHHhccCCCCcchhhhHHHHHhhccC--hHHHHHHHHHHHHcCCCCCcc
Confidence            99988888899999999999998888889999999999988332  368999999999999999864

>PLN03077 Protein ECB2; Provisional

Probab=100.00  E-value=4.2e-66  Score=552.05  Aligned_cols=517  Identities=23%  Similarity=0.334  Sum_probs=453.5

Q ss_pred             ccccCCCChHHHHHHHHHHHHhCCCCCCHhhHHHHHHHHHcCCCchh------HHhhCCCCCCHHHHHHHHHHHHhcCCh
Q 040027           39 EGDINVITPNEAFCIFDYMLRMHPSPPPVSSFNILLASLAKNKHYDT------RLNATGLFPNLYTYNILINCFCKIGRV  112 (595)
Q Consensus        39 ~~~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~------~~~~~~~~~~~~~~~~l~~~~~~~g~~  112 (595)
                      ..|.+.|+++.|+++|+++.    . ++..+|+.++.+|.+.|++++      +|...|+.||..+|+.++.+|...+++
T Consensus       129 ~~~~~~g~~~~A~~~f~~m~----~-~d~~~~n~li~~~~~~g~~~~A~~~f~~M~~~g~~Pd~~t~~~ll~~~~~~~~~  203 (857)
T PLN03077        129 SMFVRFGELVHAWYVFGKMP----E-RDLFSWNVLVGGYAKAGYFDEALCLYHRMLWAGVRPDVYTFPCVLRTCGGIPDL  203 (857)
T ss_pred             HHHHhCCChHHHHHHHhcCC----C-CCeeEHHHHHHHHHhCCCHHHHHHHHHHHHHcCCCCChhHHHHHHHHhCCccch
Confidence            34567788888888888772    2 577788888888888888776      566778888888888888888888888


Q ss_pred             hHHHHHHHHHHhCCCCCCHHHHHHHHHHHHhcCCHhHHHHHHHHHHhcCCCCCHhhHHHHHHHHHhcCChhHHHHHHHHH
Q 040027          113 SLGFIAFGRILRSCFTPNAATFNSLIKGLHAESRIMEAAALFTKLKAFGCEPNVITYNTLINGLCRTGHTMIALNLFEEM  192 (595)
Q Consensus       113 ~~A~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~  192 (595)
                      ..+.+++..+.+.|+.||..+++.++.+|.+.|++++|.++|++|.    .+|..+|+.++.+|++.|++++|+++|++|
T Consensus       204 ~~~~~~~~~~~~~g~~~~~~~~n~Li~~y~k~g~~~~A~~lf~~m~----~~d~~s~n~li~~~~~~g~~~eAl~lf~~M  279 (857)
T PLN03077        204 ARGREVHAHVVRFGFELDVDVVNALITMYVKCGDVVSARLVFDRMP----RRDCISWNAMISGYFENGECLEGLELFFTM  279 (857)
T ss_pred             hhHHHHHHHHHHcCCCcccchHhHHHHHHhcCCCHHHHHHHHhcCC----CCCcchhHHHHHHHHhCCCHHHHHHHHHHH
Confidence            8888888888888888888888888888888888888888888886    457788888888888888888888888888


Q ss_pred             HhcCCCCCccccCcHHHHHHHHHHHHHcCCHhHHHHHHHHHhhCCCCCCHhHHHHHHHHHHhcCCHHHHHHHHHHHHHCC
Q 040027          193 ANGNGEIGVVCKPNTVTYSTIIDGLCKEGFVDKAKALFLQMKDENINPDVVTYNSLIHGLCHANDWNEAKRLFIEMMDQG  272 (595)
Q Consensus       193 ~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~~ll~~~~~~~~~~~A~~~~~~~~~~~  272 (595)
                      ...+      +.||..+|+.++.++.+.|+.+.|.+++..+.+.|+.||..+|+.|+.+|.+.|++++|.++|++|.   
T Consensus       280 ~~~g------~~Pd~~ty~~ll~a~~~~g~~~~a~~l~~~~~~~g~~~d~~~~n~Li~~y~k~g~~~~A~~vf~~m~---  350 (857)
T PLN03077        280 RELS------VDPDLMTITSVISACELLGDERLGREMHGYVVKTGFAVDVSVCNSLIQMYLSLGSWGEAEKVFSRME---  350 (857)
T ss_pred             HHcC------CCCChhHHHHHHHHHHhcCChHHHHHHHHHHHHhCCccchHHHHHHHHHHHhcCCHHHHHHHHhhCC---
Confidence            8877      7888888888888888888888888888888888888888889999999999999999999988885   


Q ss_pred             CCCCHhhHHHHHHHHHhcCChHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHhcCCCCCHHHHHH
Q 040027          273 VQPSVVTFNVIMDELCKNRKMDEASRLLDLMVQRGVRPNACTYNTLMDGFCLMGKINRAEELFGSMESMGCKHDDVSYNI  352 (595)
Q Consensus       273 ~~~~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~  352 (595)
                       .||..+|+.++.+|.+.|++++|.++|++|.+.|+.||..+|+.++.+|++.|+++.+.++++.+.+.|+.++..+++.
T Consensus       351 -~~d~~s~n~li~~~~~~g~~~~A~~lf~~M~~~g~~Pd~~t~~~ll~a~~~~g~~~~a~~l~~~~~~~g~~~~~~~~n~  429 (857)
T PLN03077        351 -TKDAVSWTAMISGYEKNGLPDKALETYALMEQDNVSPDEITIASVLSACACLGDLDVGVKLHELAERKGLISYVVVANA  429 (857)
T ss_pred             -CCCeeeHHHHHHHHHhCCCHHHHHHHHHHHHHhCCCCCceeHHHHHHHHhccchHHHHHHHHHHHHHhCCCcchHHHHH
Confidence             3688889999999999999999999999998888889999999999999999999999999999988888888889999


Q ss_pred             HHHHHHhCCCHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHccCCHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHhcCC
Q 040027          353 LINGYCKNKEVEEALSLYREMVSKGIKPTVVTYNTLFLGLFEIHQVEHALKLFDEMQRDGVAADTRTYTTFIDGLCKNGY  432 (595)
Q Consensus       353 l~~~~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~  432 (595)
                      ++.+|.+.|++++|.++|++|.+    ++..+|+.++.+|.+.|+.++|..+|++|.. ++.||..+|..++.+|++.|+
T Consensus       430 Li~~y~k~g~~~~A~~vf~~m~~----~d~vs~~~mi~~~~~~g~~~eA~~lf~~m~~-~~~pd~~t~~~lL~a~~~~g~  504 (857)
T PLN03077        430 LIEMYSKCKCIDKALEVFHNIPE----KDVISWTSIIAGLRLNNRCFEALIFFRQMLL-TLKPNSVTLIAALSACARIGA  504 (857)
T ss_pred             HHHHHHHcCCHHHHHHHHHhCCC----CCeeeHHHHHHHHHHCCCHHHHHHHHHHHHh-CCCCCHhHHHHHHHHHhhhch
Confidence            99999999999999999988864    4778899999999999999999999999976 488999999999999999999


Q ss_pred             HHHHHHHHHHHHHcCCCcCHHHHHHHHHHHHhcCChHHHHHHHHhcccCCCCCCHHHHHHHHHHHHhcCChhHHHHHHHH
Q 040027          433 IIEAVELFRTLRILKCELDIQAYNCLIDGLCKSGRLKFAWELFCSLPHGVLVPNVVTYNIMIQGLCNDGQMDKARDLFLD  512 (595)
Q Consensus       433 ~~~A~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~p~~~~~~~l~~~~~~~g~~~~A~~~~~~  512 (595)
                      ++.+.+++..+.+.|+.++..+++.++.+|.+.|++++|..+|+.+     .||..+|+.++.+|++.|+.++|+++|++
T Consensus       505 l~~~~~i~~~~~~~g~~~~~~~~naLi~~y~k~G~~~~A~~~f~~~-----~~d~~s~n~lI~~~~~~G~~~~A~~lf~~  579 (857)
T PLN03077        505 LMCGKEIHAHVLRTGIGFDGFLPNALLDLYVRCGRMNYAWNQFNSH-----EKDVVSWNILLTGYVAHGKGSMAVELFNR  579 (857)
T ss_pred             HHHhHHHHHHHHHhCCCccceechHHHHHHHHcCCHHHHHHHHHhc-----CCChhhHHHHHHHHHHcCCHHHHHHHHHH
Confidence            9999999999999999999999999999999999999999999887     47999999999999999999999999999


Q ss_pred             HHHcCCCCCHHHHHHHHHHHHHcCChhHHHHHHHHHH-HCCCCCCHHHHHHHHHHHHhcCccc---ccchHHHHhh
Q 040027          513 MEENAAAPDVITFDMLIHGFIRINEPSKVNELLHKMK-EKKVMPDASIVSIVVDLLVKNEISL---KSLPSFLVQE  584 (595)
Q Consensus       513 ~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~-~~~~~p~~~~~~~l~~~~~~~g~~~---~~i~~~~~~~  584 (595)
                      |.+.|+.||..||..++.+|.+.|++++|.++|+.|. +.|+.|+..+|..++++|.++|+++   +++++||.+|
T Consensus       580 M~~~g~~Pd~~T~~~ll~a~~~~g~v~ea~~~f~~M~~~~gi~P~~~~y~~lv~~l~r~G~~~eA~~~~~~m~~~p  655 (857)
T PLN03077        580 MVESGVNPDEVTFISLLCACSRSGMVTQGLEYFHSMEEKYSITPNLKHYACVVDLLGRAGKLTEAYNFINKMPITP  655 (857)
T ss_pred             HHHcCCCCCcccHHHHHHHHhhcChHHHHHHHHHHHHHHhCCCCchHHHHHHHHHHHhCCCHHHHHHHHHHCCCCC
Confidence            9999999999999999999999999999999999999 6799999999999999999999999   7777776443

>PLN03218 maturation of RBCL 1; Provisional

Probab=100.00  E-value=5.1e-63  Score=517.08  Aligned_cols=510  Identities=17%  Similarity=0.267  Sum_probs=472.9

Q ss_pred             hHHHHHHHHHHHHhCCCCCCHhhHHHHHHHHHcCCCchh------HHhhCCC-CCCHHHHHHHHHHHHhcCChhHHHHHH
Q 040027           47 PNEAFCIFDYMLRMHPSPPPVSSFNILLASLAKNKHYDT------RLNATGL-FPNLYTYNILINCFCKIGRVSLGFIAF  119 (595)
Q Consensus        47 ~~~A~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~------~~~~~~~-~~~~~~~~~l~~~~~~~g~~~~A~~~~  119 (595)
                      ...++...++....   .++...+..++..+.+.|++.+      .|...++ .++...++.++..|.+.|..++|..+|
T Consensus       353 ~~~~~~~~~~~~~~---~~~~~~~~~~y~~l~r~G~l~eAl~Lfd~M~~~gvv~~~~v~~~~li~~~~~~g~~~eAl~lf  429 (1060)
T PLN03218        353 EENSLAAYNGGVSG---KRKSPEYIDAYNRLLRDGRIKDCIDLLEDMEKRGLLDMDKIYHAKFFKACKKQRAVKEAFRFA  429 (1060)
T ss_pred             hhhhHHHhccccCC---CCCchHHHHHHHHHHHCcCHHHHHHHHHHHHhCCCCCchHHHHHHHHHHHHHCCCHHHHHHHH
Confidence            33444444444333   2467788888899999999887      6777775 468888899999999999999999999


Q ss_pred             HHHHhCCCCCCHHHHHHHHHHHHhcCCHhHHHHHHHHHHhcCCCCCHhhHHHHHHHHHhcCChhHHHHHHHHHHhcCCCC
Q 040027          120 GRILRSCFTPNAATFNSLIKGLHAESRIMEAAALFTKLKAFGCEPNVITYNTLINGLCRTGHTMIALNLFEEMANGNGEI  199 (595)
Q Consensus       120 ~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~  199 (595)
                      +.|..    |+..+|+.++.+|++.|++++|.++|+.|.+.|+.||..+|+.++.+|++.|+.++|.++|++|...+   
T Consensus       430 ~~M~~----pd~~Tyn~LL~a~~k~g~~e~A~~lf~~M~~~Gl~pD~~tynsLI~~y~k~G~vd~A~~vf~eM~~~G---  502 (1060)
T PLN03218        430 KLIRN----PTLSTFNMLMSVCASSQDIDGALRVLRLVQEAGLKADCKLYTTLISTCAKSGKVDAMFEVFHEMVNAG---  502 (1060)
T ss_pred             HHcCC----CCHHHHHHHHHHHHhCcCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhCcCHHHHHHHHHHHHHcC---
Confidence            98874    89999999999999999999999999999999999999999999999999999999999999999988   


Q ss_pred             CccccCcHHHHHHHHHHHHHcCCHhHHHHHHHHHhhCCCCCCHhHHHHHHHHHHhcCCHHHHHHHHHHHHH--CCCCCCH
Q 040027          200 GVVCKPNTVTYSTIIDGLCKEGFVDKAKALFLQMKDENINPDVVTYNSLIHGLCHANDWNEAKRLFIEMMD--QGVQPSV  277 (595)
Q Consensus       200 ~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~~ll~~~~~~~~~~~A~~~~~~~~~--~~~~~~~  277 (595)
                         +.||..+|+.+|.+|++.|++++|.++|++|.+.|+.||..+|+.|+.+|++.|++++|.++|++|..  .|+.||.
T Consensus       503 ---v~PdvvTynaLI~gy~k~G~~eeAl~lf~~M~~~Gv~PD~vTYnsLI~a~~k~G~~deA~~lf~eM~~~~~gi~PD~  579 (1060)
T PLN03218        503 ---VEANVHTFGALIDGCARAGQVAKAFGAYGIMRSKNVKPDRVVFNALISACGQSGAVDRAFDVLAEMKAETHPIDPDH  579 (1060)
T ss_pred             ---CCCCHHHHHHHHHHHHHCcCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHHCCCHHHHHHHHHHHHHhcCCCCCcH
Confidence               78999999999999999999999999999999999999999999999999999999999999999986  5789999


Q ss_pred             hhHHHHHHHHHhcCChHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHhcCCCCCHHHHHHHHHHH
Q 040027          278 VTFNVIMDELCKNRKMDEASRLLDLMVQRGVRPNACTYNTLMDGFCLMGKINRAEELFGSMESMGCKHDDVSYNILINGY  357 (595)
Q Consensus       278 ~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~  357 (595)
                      .+|+.++.+|++.|++++|.++|+.|.+.|+.|+..+|+.++.+|++.|++++|.++|++|.+.|+.||..+|+.++.+|
T Consensus       580 vTynaLI~ay~k~G~ldeA~elf~~M~e~gi~p~~~tynsLI~ay~k~G~~deAl~lf~eM~~~Gv~PD~~TynsLI~a~  659 (1060)
T PLN03218        580 ITVGALMKACANAGQVDRAKEVYQMIHEYNIKGTPEVYTIAVNSCSQKGDWDFALSIYDDMKKKGVKPDEVFFSALVDVA  659 (1060)
T ss_pred             HHHHHHHHHHHHCCCHHHHHHHHHHHHHcCCCCChHHHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHH
Confidence            99999999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             HhCCCHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHccCCHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHhcCCHHHHH
Q 040027          358 CKNKEVEEALSLYREMVSKGIKPTVVTYNTLFLGLFEIHQVEHALKLFDEMQRDGVAADTRTYTTFIDGLCKNGYIIEAV  437 (595)
Q Consensus       358 ~~~~~~~~A~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~  437 (595)
                      .+.|++++|.+++++|.+.|+.|+..+|+.++.+|++.|++++|.++|++|.+.|+.|+..+|+.+|.+|++.|++++|.
T Consensus       660 ~k~G~~eeA~~l~~eM~k~G~~pd~~tynsLI~ay~k~G~~eeA~~lf~eM~~~g~~PdvvtyN~LI~gy~k~G~~eeAl  739 (1060)
T PLN03218        660 GHAGDLDKAFEILQDARKQGIKLGTVSYSSLMGACSNAKNWKKALELYEDIKSIKLRPTVSTMNALITALCEGNQLPKAL  739 (1060)
T ss_pred             HhCCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhCCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHHCCCHHHHH
Confidence            99999999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             HHHHHHHHcCCCcCHHHHHHHHHHHHhcCChHHHHHHHHhcccCCCCCCHHHHHHHHHHHHh----c-------------
Q 040027          438 ELFRTLRILKCELDIQAYNCLIDGLCKSGRLKFAWELFCSLPHGVLVPNVVTYNIMIQGLCN----D-------------  500 (595)
Q Consensus       438 ~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~p~~~~~~~l~~~~~~----~-------------  500 (595)
                      ++|++|...|+.||..+|+.++.+|.+.|++++|.+++++|.+.|+.||..+|+.++..|.+    .             
T Consensus       740 elf~eM~~~Gi~Pd~~Ty~sLL~a~~k~G~le~A~~l~~~M~k~Gi~pd~~tynsLIglc~~~y~ka~~l~~~v~~f~~g  819 (1060)
T PLN03218        740 EVLSEMKRLGLCPNTITYSILLVASERKDDADVGLDLLSQAKEDGIKPNLVMCRCITGLCLRRFEKACALGEPVVSFDSG  819 (1060)
T ss_pred             HHHHHHHHcCCCCCHHHHHHHHHHHHHCCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHHHHHHHhhhhhhhhhhhcc
Confidence            99999999999999999999999999999999999999999999999999999999865432    1             


Q ss_pred             ------CChhHHHHHHHHHHHcCCCCCHHHHHHHHHHHHHcCChhHHHHHHHHHHHCCCCCCHHHHHHHHHHHHh
Q 040027          501 ------GQMDKARDLFLDMEENAAAPDVITFDMLIHGFIRINEPSKVNELLHKMKEKKVMPDASIVSIVVDLLVK  569 (595)
Q Consensus       501 ------g~~~~A~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~p~~~~~~~l~~~~~~  569 (595)
                            +..++|..+|++|.+.|+.||..+|..++.+++..+..+.+..+++.|...+..|+..+|..+++.+.+
T Consensus       820 ~~~~~n~w~~~Al~lf~eM~~~Gi~Pd~~T~~~vL~cl~~~~~~~~~~~m~~~m~~~~~~~~~~~y~~Li~g~~~  894 (1060)
T PLN03218        820 RPQIENKWTSWALMVYRETISAGTLPTMEVLSQVLGCLQLPHDATLRNRLIENLGISADSQKQSNLSTLVDGFGE  894 (1060)
T ss_pred             ccccccchHHHHHHHHHHHHHCCCCCCHHHHHHHHHHhcccccHHHHHHHHHHhccCCCCcchhhhHHHHHhhcc
Confidence                  224679999999999999999999999998888889999999999999888888999999999998854

>PLN03077 Protein ECB2; Provisional

Probab=100.00  E-value=3.6e-64  Score=537.28  Aligned_cols=510  Identities=19%  Similarity=0.310  Sum_probs=486.2

Q ss_pred             ccccccCCCChHHHHHHHHHHHHhCCCCCCHhhHHHHHHHHHcCCCchh------HHhhCCCCCCHHHHHHHHHHHHhcC
Q 040027           37 TREGDINVITPNEAFCIFDYMLRMHPSPPPVSSFNILLASLAKNKHYDT------RLNATGLFPNLYTYNILINCFCKIG  110 (595)
Q Consensus        37 ~~~~~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~------~~~~~~~~~~~~~~~~l~~~~~~~g  110 (595)
                      ...+|.+.|++++|+++|++|.+.+.. |+..+|+.++.++.+.+....      .+...|+.||+.+++.++..|.+.|
T Consensus       158 li~~~~~~g~~~~A~~~f~~M~~~g~~-Pd~~t~~~ll~~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~n~Li~~y~k~g  236 (857)
T PLN03077        158 LVGGYAKAGYFDEALCLYHRMLWAGVR-PDVYTFPCVLRTCGGIPDLARGREVHAHVVRFGFELDVDVVNALITMYVKCG  236 (857)
T ss_pred             HHHHHHhCCCHHHHHHHHHHHHHcCCC-CChhHHHHHHHHhCCccchhhHHHHHHHHHHcCCCcccchHhHHHHHHhcCC
Confidence            345668899999999999999998877 899999999999999888765      6788999999999999999999999


Q ss_pred             ChhHHHHHHHHHHhCCCCCCHHHHHHHHHHHHhcCCHhHHHHHHHHHHhcCCCCCHhhHHHHHHHHHhcCChhHHHHHHH
Q 040027          111 RVSLGFIAFGRILRSCFTPNAATFNSLIKGLHAESRIMEAAALFTKLKAFGCEPNVITYNTLINGLCRTGHTMIALNLFE  190 (595)
Q Consensus       111 ~~~~A~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~  190 (595)
                      +++.|..+|++|.    .+|..+|+.++.+|.+.|++++|.++|++|...|+.||..+|+.++.++.+.|+.+.+.+++.
T Consensus       237 ~~~~A~~lf~~m~----~~d~~s~n~li~~~~~~g~~~eAl~lf~~M~~~g~~Pd~~ty~~ll~a~~~~g~~~~a~~l~~  312 (857)
T PLN03077        237 DVVSARLVFDRMP----RRDCISWNAMISGYFENGECLEGLELFFTMRELSVDPDLMTITSVISACELLGDERLGREMHG  312 (857)
T ss_pred             CHHHHHHHHhcCC----CCCcchhHHHHHHHHhCCCHHHHHHHHHHHHHcCCCCChhHHHHHHHHHHhcCChHHHHHHHH
Confidence            9999999999986    568899999999999999999999999999999999999999999999999999999999999


Q ss_pred             HHHhcCCCCCccccCcHHHHHHHHHHHHHcCCHhHHHHHHHHHhhCCCCCCHhHHHHHHHHHHhcCCHHHHHHHHHHHHH
Q 040027          191 EMANGNGEIGVVCKPNTVTYSTIIDGLCKEGFVDKAKALFLQMKDENINPDVVTYNSLIHGLCHANDWNEAKRLFIEMMD  270 (595)
Q Consensus       191 ~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~~ll~~~~~~~~~~~A~~~~~~~~~  270 (595)
                      .+.+.+      ..||..+|+.++.+|++.|++++|.++|++|..    ||..+|+.++.+|.+.|++++|+++|++|.+
T Consensus       313 ~~~~~g------~~~d~~~~n~Li~~y~k~g~~~~A~~vf~~m~~----~d~~s~n~li~~~~~~g~~~~A~~lf~~M~~  382 (857)
T PLN03077        313 YVVKTG------FAVDVSVCNSLIQMYLSLGSWGEAEKVFSRMET----KDAVSWTAMISGYEKNGLPDKALETYALMEQ  382 (857)
T ss_pred             HHHHhC------CccchHHHHHHHHHHHhcCCHHHHHHHHhhCCC----CCeeeHHHHHHHHHhCCCHHHHHHHHHHHHH
Confidence            999988      889999999999999999999999999999964    6889999999999999999999999999999


Q ss_pred             CCCCCCHhhHHHHHHHHHhcCChHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHhcCCCCCHHHH
Q 040027          271 QGVQPSVVTFNVIMDELCKNRKMDEASRLLDLMVQRGVRPNACTYNTLMDGFCLMGKINRAEELFGSMESMGCKHDDVSY  350 (595)
Q Consensus       271 ~~~~~~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~  350 (595)
                      .|+.||..+|+.++.+|++.|+++.+.++++.+.+.|+.++..+++.++.+|++.|++++|.++|++|.+    +|..+|
T Consensus       383 ~g~~Pd~~t~~~ll~a~~~~g~~~~a~~l~~~~~~~g~~~~~~~~n~Li~~y~k~g~~~~A~~vf~~m~~----~d~vs~  458 (857)
T PLN03077        383 DNVSPDEITIASVLSACACLGDLDVGVKLHELAERKGLISYVVVANALIEMYSKCKCIDKALEVFHNIPE----KDVISW  458 (857)
T ss_pred             hCCCCCceeHHHHHHHHhccchHHHHHHHHHHHHHhCCCcchHHHHHHHHHHHHcCCHHHHHHHHHhCCC----CCeeeH
Confidence            9999999999999999999999999999999999999999999999999999999999999999999874    578899


Q ss_pred             HHHHHHHHhCCCHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHccCCHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHhc
Q 040027          351 NILINGYCKNKEVEEALSLYREMVSKGIKPTVVTYNTLFLGLFEIHQVEHALKLFDEMQRDGVAADTRTYTTFIDGLCKN  430 (595)
Q Consensus       351 ~~l~~~~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~  430 (595)
                      +.++.+|.+.|+.++|+.+|++|.. ++.||..||..++.+|.+.|+.+.+.+++..+.+.|+.++..+++.++.+|++.
T Consensus       459 ~~mi~~~~~~g~~~eA~~lf~~m~~-~~~pd~~t~~~lL~a~~~~g~l~~~~~i~~~~~~~g~~~~~~~~naLi~~y~k~  537 (857)
T PLN03077        459 TSIIAGLRLNNRCFEALIFFRQMLL-TLKPNSVTLIAALSACARIGALMCGKEIHAHVLRTGIGFDGFLPNALLDLYVRC  537 (857)
T ss_pred             HHHHHHHHHCCCHHHHHHHHHHHHh-CCCCCHhHHHHHHHHHhhhchHHHhHHHHHHHHHhCCCccceechHHHHHHHHc
Confidence            9999999999999999999999986 589999999999999999999999999999999999999999999999999999


Q ss_pred             CCHHHHHHHHHHHHHcCCCcCHHHHHHHHHHHHhcCChHHHHHHHHhcccCCCCCCHHHHHHHHHHHHhcCChhHHHHHH
Q 040027          431 GYIIEAVELFRTLRILKCELDIQAYNCLIDGLCKSGRLKFAWELFCSLPHGVLVPNVVTYNIMIQGLCNDGQMDKARDLF  510 (595)
Q Consensus       431 g~~~~A~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~p~~~~~~~l~~~~~~~g~~~~A~~~~  510 (595)
                      |++++|..+|+.+     .+|..+|+.++.+|++.|+.++|.++|++|.+.|+.||..||+.++.+|.+.|++++|.++|
T Consensus       538 G~~~~A~~~f~~~-----~~d~~s~n~lI~~~~~~G~~~~A~~lf~~M~~~g~~Pd~~T~~~ll~a~~~~g~v~ea~~~f  612 (857)
T PLN03077        538 GRMNYAWNQFNSH-----EKDVVSWNILLTGYVAHGKGSMAVELFNRMVESGVNPDEVTFISLLCACSRSGMVTQGLEYF  612 (857)
T ss_pred             CCHHHHHHHHHhc-----CCChhhHHHHHHHHHHcCCHHHHHHHHHHHHHcCCCCCcccHHHHHHHHhhcChHHHHHHHH
Confidence            9999999999886     67999999999999999999999999999999999999999999999999999999999999


Q ss_pred             HHHH-HcCCCCCHHHHHHHHHHHHHcCChhHHHHHHHHHHHCCCCCCHHHHHHHHHHHHhcCccc
Q 040027          511 LDME-ENAAAPDVITFDMLIHGFIRINEPSKVNELLHKMKEKKVMPDASIVSIVVDLLVKNEISL  574 (595)
Q Consensus       511 ~~~~-~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~p~~~~~~~l~~~~~~~g~~~  574 (595)
                      ++|. +.|+.|+..+|..++.+|.+.|++++|.+++++|.   +.||..+|.+++.+|...|+.+
T Consensus       613 ~~M~~~~gi~P~~~~y~~lv~~l~r~G~~~eA~~~~~~m~---~~pd~~~~~aLl~ac~~~~~~e  674 (857)
T PLN03077        613 HSMEEKYSITPNLKHYACVVDLLGRAGKLTEAYNFINKMP---ITPDPAVWGALLNACRIHRHVE  674 (857)
T ss_pred             HHHHHHhCCCCchHHHHHHHHHHHhCCCHHHHHHHHHHCC---CCCCHHHHHHHHHHHHHcCChH
Confidence            9999 67999999999999999999999999999999984   7899999999999888877776

>PLN03081 pentatricopeptide (PPR) repeat-containing protein; Provisional

Probab=100.00  E-value=6e-59  Score=485.30  Aligned_cols=469  Identities=18%  Similarity=0.264  Sum_probs=444.5

Q ss_pred             CCHhhHHHHHHHHHcCCCchh------HHhhC-CCCCCHHHHHHHHHHHHhcCChhHHHHHHHHHHhCCCCCCHHHHHHH
Q 040027           65 PPVSSFNILLASLAKNKHYDT------RLNAT-GLFPNLYTYNILINCFCKIGRVSLGFIAFGRILRSCFTPNAATFNSL  137 (595)
Q Consensus        65 ~~~~~~~~l~~~~~~~~~~~~------~~~~~-~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~~l  137 (595)
                      .+..+|+.++.++.+.|++.+      .|... +..||..+|+.++.+|.+.++++.+.+++..+.+.|+.||..+|+.+
T Consensus        85 ~~~~~~~~~i~~l~~~g~~~~Al~~f~~m~~~~~~~~~~~t~~~ll~a~~~~~~~~~a~~l~~~m~~~g~~~~~~~~n~L  164 (697)
T PLN03081         85 KSGVSLCSQIEKLVACGRHREALELFEILEAGCPFTLPASTYDALVEACIALKSIRCVKAVYWHVESSGFEPDQYMMNRV  164 (697)
T ss_pred             CCceeHHHHHHHHHcCCCHHHHHHHHHHHHhcCCCCCCHHHHHHHHHHHHhCCCHHHHHHHHHHHHHhCCCcchHHHHHH
Confidence            456799999999999999888      44444 36799999999999999999999999999999999999999999999


Q ss_pred             HHHHHhcCCHhHHHHHHHHHHhcCCCCCHhhHHHHHHHHHhcCChhHHHHHHHHHHhcCCCCCccccCcHHHHHHHHHHH
Q 040027          138 IKGLHAESRIMEAAALFTKLKAFGCEPNVITYNTLINGLCRTGHTMIALNLFEEMANGNGEIGVVCKPNTVTYSTIIDGL  217 (595)
Q Consensus       138 ~~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~  217 (595)
                      +.+|.+.|++++|.++|++|.    .||..+|+.++.+|++.|++++|+++|++|.+.+      ..|+..+|..++.++
T Consensus       165 i~~y~k~g~~~~A~~lf~~m~----~~~~~t~n~li~~~~~~g~~~~A~~lf~~M~~~g------~~p~~~t~~~ll~a~  234 (697)
T PLN03081        165 LLMHVKCGMLIDARRLFDEMP----ERNLASWGTIIGGLVDAGNYREAFALFREMWEDG------SDAEPRTFVVMLRAS  234 (697)
T ss_pred             HHHHhcCCCHHHHHHHHhcCC----CCCeeeHHHHHHHHHHCcCHHHHHHHHHHHHHhC------CCCChhhHHHHHHHH
Confidence            999999999999999999996    4799999999999999999999999999999887      789999999999999


Q ss_pred             HHcCCHhHHHHHHHHHhhCCCCCCHhHHHHHHHHHHhcCCHHHHHHHHHHHHHCCCCCCHhhHHHHHHHHHhcCChHHHH
Q 040027          218 CKEGFVDKAKALFLQMKDENINPDVVTYNSLIHGLCHANDWNEAKRLFIEMMDQGVQPSVVTFNVIMDELCKNRKMDEAS  297 (595)
Q Consensus       218 ~~~g~~~~A~~~~~~~~~~~~~~~~~~~~~ll~~~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~a~  297 (595)
                      .+.|..+.+.+++..+.+.|+.||..+|+.|+.+|.+.|++++|.++|+.|..    +|..+|+.++.+|.+.|++++|.
T Consensus       235 ~~~~~~~~~~~l~~~~~~~g~~~d~~~~n~Li~~y~k~g~~~~A~~vf~~m~~----~~~vt~n~li~~y~~~g~~~eA~  310 (697)
T PLN03081        235 AGLGSARAGQQLHCCVLKTGVVGDTFVSCALIDMYSKCGDIEDARCVFDGMPE----KTTVAWNSMLAGYALHGYSEEAL  310 (697)
T ss_pred             hcCCcHHHHHHHHHHHHHhCCCccceeHHHHHHHHHHCCCHHHHHHHHHhCCC----CChhHHHHHHHHHHhCCCHHHHH
Confidence            99999999999999999999999999999999999999999999999999854    68999999999999999999999


Q ss_pred             HHHHHHHHCCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHhcCCCCCHHHHHHHHHHHHhCCCHHHHHHHHHHHHHCC
Q 040027          298 RLLDLMVQRGVRPNACTYNTLMDGFCLMGKINRAEELFGSMESMGCKHDDVSYNILINGYCKNKEVEEALSLYREMVSKG  377 (595)
Q Consensus       298 ~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~~~  377 (595)
                      ++|++|.+.|+.||..+|+.++.+|++.|++++|.+++..+.+.|++++..+++.++.+|++.|++++|.++|++|.+  
T Consensus       311 ~lf~~M~~~g~~pd~~t~~~ll~a~~~~g~~~~a~~i~~~m~~~g~~~d~~~~~~Li~~y~k~G~~~~A~~vf~~m~~--  388 (697)
T PLN03081        311 CLYYEMRDSGVSIDQFTFSIMIRIFSRLALLEHAKQAHAGLIRTGFPLDIVANTALVDLYSKWGRMEDARNVFDRMPR--  388 (697)
T ss_pred             HHHHHHHHcCCCCCHHHHHHHHHHHHhccchHHHHHHHHHHHHhCCCCCeeehHHHHHHHHHCCCHHHHHHHHHhCCC--
Confidence            999999999999999999999999999999999999999999999999999999999999999999999999999864  


Q ss_pred             CCCCHHHHHHHHHHHHccCCHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHH-cCCCcCHHHHH
Q 040027          378 IKPTVVTYNTLFLGLFEIHQVEHALKLFDEMQRDGVAADTRTYTTFIDGLCKNGYIIEAVELFRTLRI-LKCELDIQAYN  456 (595)
Q Consensus       378 ~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~-~~~~~~~~~~~  456 (595)
                        ||..+|+.++.+|.+.|+.++|.++|++|.+.|+.||..||+.++.+|.+.|..++|.++|+.|.+ .++.|+..+|+
T Consensus       389 --~d~~t~n~lI~~y~~~G~~~~A~~lf~~M~~~g~~Pd~~T~~~ll~a~~~~g~~~~a~~~f~~m~~~~g~~p~~~~y~  466 (697)
T PLN03081        389 --KNLISWNALIAGYGNHGRGTKAVEMFERMIAEGVAPNHVTFLAVLSACRYSGLSEQGWEIFQSMSENHRIKPRAMHYA  466 (697)
T ss_pred             --CCeeeHHHHHHHHHHcCCHHHHHHHHHHHHHhCCCCCHHHHHHHHHHHhcCCcHHHHHHHHHHHHHhcCCCCCccchH
Confidence              689999999999999999999999999999999999999999999999999999999999999986 68899999999


Q ss_pred             HHHHHHHhcCChHHHHHHHHhcccCCCCCCHHHHHHHHHHHHhcCChhHHHHHHHHHHHcCCCCCHHHHHHHHHHHHHcC
Q 040027          457 CLIDGLCKSGRLKFAWELFCSLPHGVLVPNVVTYNIMIQGLCNDGQMDKARDLFLDMEENAAAPDVITFDMLIHGFIRIN  536 (595)
Q Consensus       457 ~l~~~~~~~g~~~~A~~~~~~~~~~~~~p~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g  536 (595)
                      .++.+|.+.|++++|.++++++.   +.|+..+|+.++.+|...|+++.|..+++++.+.+ +.+..+|..++..|++.|
T Consensus       467 ~li~~l~r~G~~~eA~~~~~~~~---~~p~~~~~~~Ll~a~~~~g~~~~a~~~~~~l~~~~-p~~~~~y~~L~~~y~~~G  542 (697)
T PLN03081        467 CMIELLGREGLLDEAYAMIRRAP---FKPTVNMWAALLTACRIHKNLELGRLAAEKLYGMG-PEKLNNYVVLLNLYNSSG  542 (697)
T ss_pred             hHHHHHHhcCCHHHHHHHHHHCC---CCCCHHHHHHHHHHHHHcCCcHHHHHHHHHHhCCC-CCCCcchHHHHHHHHhCC
Confidence            99999999999999999999875   68999999999999999999999999999998754 335679999999999999


Q ss_pred             ChhHHHHHHHHHHHCCCCC
Q 040027          537 EPSKVNELLHKMKEKKVMP  555 (595)
Q Consensus       537 ~~~~A~~~~~~~~~~~~~p  555 (595)
                      ++++|.+++++|.+.|+..
T Consensus       543 ~~~~A~~v~~~m~~~g~~k  561 (697)
T PLN03081        543 RQAEAAKVVETLKRKGLSM  561 (697)
T ss_pred             CHHHHHHHHHHHHHcCCcc
Confidence            9999999999999998753

>PLN03081 pentatricopeptide (PPR) repeat-containing protein; Provisional

Probab=100.00  E-value=9.5e-58  Score=476.33  Aligned_cols=476  Identities=20%  Similarity=0.277  Sum_probs=448.6

Q ss_pred             CCCCHHHHHHHHHHHHhcCChhHHHHHHHHHHhCC-CCCCHHHHHHHHHHHHhcCCHhHHHHHHHHHHhcCCCCCHhhHH
Q 040027           92 LFPNLYTYNILINCFCKIGRVSLGFIAFGRILRSC-FTPNAATFNSLIKGLHAESRIMEAAALFTKLKAFGCEPNVITYN  170 (595)
Q Consensus        92 ~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~-~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~  170 (595)
                      ...+..+|+.++..+.+.|++++|+.+|+.|...+ +.||..+|+.++.++.+.++++.|.+++..|.+.|+.||..+++
T Consensus        83 ~~~~~~~~~~~i~~l~~~g~~~~Al~~f~~m~~~~~~~~~~~t~~~ll~a~~~~~~~~~a~~l~~~m~~~g~~~~~~~~n  162 (697)
T PLN03081         83 IRKSGVSLCSQIEKLVACGRHREALELFEILEAGCPFTLPASTYDALVEACIALKSIRCVKAVYWHVESSGFEPDQYMMN  162 (697)
T ss_pred             CCCCceeHHHHHHHHHcCCCHHHHHHHHHHHHhcCCCCCCHHHHHHHHHHHHhCCCHHHHHHHHHHHHHhCCCcchHHHH
Confidence            34566789999999999999999999999998764 67999999999999999999999999999999999999999999


Q ss_pred             HHHHHHHhcCChhHHHHHHHHHHhcCCCCCccccCcHHHHHHHHHHHHHcCCHhHHHHHHHHHhhCCCCCCHhHHHHHHH
Q 040027          171 TLINGLCRTGHTMIALNLFEEMANGNGEIGVVCKPNTVTYSTIIDGLCKEGFVDKAKALFLQMKDENINPDVVTYNSLIH  250 (595)
Q Consensus       171 ~l~~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~~ll~  250 (595)
                      .++..|++.|+++.|.++|++|.+          ||..+|+.++.+|++.|++++|.++|++|.+.|+.|+..+|+.++.
T Consensus       163 ~Li~~y~k~g~~~~A~~lf~~m~~----------~~~~t~n~li~~~~~~g~~~~A~~lf~~M~~~g~~p~~~t~~~ll~  232 (697)
T PLN03081        163 RVLLMHVKCGMLIDARRLFDEMPE----------RNLASWGTIIGGLVDAGNYREAFALFREMWEDGSDAEPRTFVVMLR  232 (697)
T ss_pred             HHHHHHhcCCCHHHHHHHHhcCCC----------CCeeeHHHHHHHHHHCcCHHHHHHHHHHHHHhCCCCChhhHHHHHH
Confidence            999999999999999999999963          6789999999999999999999999999999999999999999999


Q ss_pred             HHHhcCCHHHHHHHHHHHHHCCCCCCHhhHHHHHHHHHhcCChHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHhcCCHHH
Q 040027          251 GLCHANDWNEAKRLFIEMMDQGVQPSVVTFNVIMDELCKNRKMDEASRLLDLMVQRGVRPNACTYNTLMDGFCLMGKINR  330 (595)
Q Consensus       251 ~~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~  330 (595)
                      +|...|..+.+.+++..+.+.|+.||..+++.++.+|++.|++++|.++|+.|..    +|..+|+.++.+|++.|+.++
T Consensus       233 a~~~~~~~~~~~~l~~~~~~~g~~~d~~~~n~Li~~y~k~g~~~~A~~vf~~m~~----~~~vt~n~li~~y~~~g~~~e  308 (697)
T PLN03081        233 ASAGLGSARAGQQLHCCVLKTGVVGDTFVSCALIDMYSKCGDIEDARCVFDGMPE----KTTVAWNSMLAGYALHGYSEE  308 (697)
T ss_pred             HHhcCCcHHHHHHHHHHHHHhCCCccceeHHHHHHHHHHCCCHHHHHHHHHhCCC----CChhHHHHHHHHHHhCCCHHH
Confidence            9999999999999999999999999999999999999999999999999999964    588999999999999999999


Q ss_pred             HHHHHHHHHhcCCCCCHHHHHHHHHHHHhCCCHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHccCCHHHHHHHHHHHHH
Q 040027          331 AEELFGSMESMGCKHDDVSYNILINGYCKNKEVEEALSLYREMVSKGIKPTVVTYNTLFLGLFEIHQVEHALKLFDEMQR  410 (595)
Q Consensus       331 a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~  410 (595)
                      |.++|++|.+.|+.||..+|+.++.+|++.|++++|.+++..|.+.|+.|+..+++.++.+|++.|++++|.++|++|. 
T Consensus       309 A~~lf~~M~~~g~~pd~~t~~~ll~a~~~~g~~~~a~~i~~~m~~~g~~~d~~~~~~Li~~y~k~G~~~~A~~vf~~m~-  387 (697)
T PLN03081        309 ALCLYYEMRDSGVSIDQFTFSIMIRIFSRLALLEHAKQAHAGLIRTGFPLDIVANTALVDLYSKWGRMEDARNVFDRMP-  387 (697)
T ss_pred             HHHHHHHHHHcCCCCCHHHHHHHHHHHHhccchHHHHHHHHHHHHhCCCCCeeehHHHHHHHHHCCCHHHHHHHHHhCC-
Confidence            9999999999999999999999999999999999999999999999999999999999999999999999999999986 


Q ss_pred             CCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCcCHHHHHHHHHHHHhcCChHHHHHHHHhccc-CCCCCCHHH
Q 040027          411 DGVAADTRTYTTFIDGLCKNGYIIEAVELFRTLRILKCELDIQAYNCLIDGLCKSGRLKFAWELFCSLPH-GVLVPNVVT  489 (595)
Q Consensus       411 ~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~-~~~~p~~~~  489 (595)
                         .||..+|+.+|.+|++.|+.++|.++|++|.+.|+.||..+|+.++.+|.+.|.+++|.++|+.|.+ .++.|+..+
T Consensus       388 ---~~d~~t~n~lI~~y~~~G~~~~A~~lf~~M~~~g~~Pd~~T~~~ll~a~~~~g~~~~a~~~f~~m~~~~g~~p~~~~  464 (697)
T PLN03081        388 ---RKNLISWNALIAGYGNHGRGTKAVEMFERMIAEGVAPNHVTFLAVLSACRYSGLSEQGWEIFQSMSENHRIKPRAMH  464 (697)
T ss_pred             ---CCCeeeHHHHHHHHHHcCCHHHHHHHHHHHHHhCCCCCHHHHHHHHHHHhcCCcHHHHHHHHHHHHHhcCCCCCccc
Confidence               4688999999999999999999999999999999999999999999999999999999999999986 689999999


Q ss_pred             HHHHHHHHHhcCChhHHHHHHHHHHHcCCCCCHHHHHHHHHHHHHcCChhHHHHHHHHHHHCCCCC-CHHHHHHHHHHHH
Q 040027          490 YNIMIQGLCNDGQMDKARDLFLDMEENAAAPDVITFDMLIHGFIRINEPSKVNELLHKMKEKKVMP-DASIVSIVVDLLV  568 (595)
Q Consensus       490 ~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~p-~~~~~~~l~~~~~  568 (595)
                      |+.++.+|++.|++++|.+++++|   +..|+..+|..++.+|...|+++.|..+++++.+  +.| +..+|..++++|.
T Consensus       465 y~~li~~l~r~G~~~eA~~~~~~~---~~~p~~~~~~~Ll~a~~~~g~~~~a~~~~~~l~~--~~p~~~~~y~~L~~~y~  539 (697)
T PLN03081        465 YACMIELLGREGLLDEAYAMIRRA---PFKPTVNMWAALLTACRIHKNLELGRLAAEKLYG--MGPEKLNNYVVLLNLYN  539 (697)
T ss_pred             hHhHHHHHHhcCCHHHHHHHHHHC---CCCCCHHHHHHHHHHHHHcCCcHHHHHHHHHHhC--CCCCCCcchHHHHHHHH
Confidence            999999999999999999998876   5689999999999999999999999999999985  456 4789999999999


Q ss_pred             hcCccc---ccchHHHHhhhhcccc
Q 040027          569 KNEISL---KSLPSFLVQERQGEVG  590 (595)
Q Consensus       569 ~~g~~~---~~i~~~~~~~~~~~~~  590 (595)
                      +.|+++   ++.+.|....-+++++
T Consensus       540 ~~G~~~~A~~v~~~m~~~g~~k~~g  564 (697)
T PLN03081        540 SSGRQAEAAKVVETLKRKGLSMHPA  564 (697)
T ss_pred             hCCCHHHHHHHHHHHHHcCCccCCC
Confidence            999999   6667776554444444

>TIGR02917 PEP_TPR_lipo putative PEP-CTERM system TPR-repeat lipoprotein

Probab=100.00  E-value=3.2e-34  Score=314.87  Aligned_cols=515  Identities=12%  Similarity=0.038  Sum_probs=375.5

Q ss_pred             cCCCChHHHHHHHHHHHHhCCCCCCHhhHHHHHHHHHcCCCchh------HHhhCCCCCCHHHHHHHHHHHHhcCChhHH
Q 040027           42 INVITPNEAFCIFDYMLRMHPSPPPVSSFNILLASLAKNKHYDT------RLNATGLFPNLYTYNILINCFCKIGRVSLG  115 (595)
Q Consensus        42 ~~~~~~~~A~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~------~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A  115 (595)
                      .+.|++++|.+.|+++++.+|.  ++..|..+...+...|++.+      ...... +.+...+..++..+.+.|++++|
T Consensus       374 ~~~g~~~~A~~~~~~~~~~~~~--~~~~~~~l~~~~~~~~~~~~A~~~~~~a~~~~-~~~~~~~~~l~~~~~~~~~~~~A  450 (899)
T TIGR02917       374 LALGDFEKAAEYLAKATELDPE--NAAARTQLGISKLSQGDPSEAIADLETAAQLD-PELGRADLLLILSYLRSGQFDKA  450 (899)
T ss_pred             HHCCCHHHHHHHHHHHHhcCCC--CHHHHHHHHHHHHhCCChHHHHHHHHHHHhhC-CcchhhHHHHHHHHHhcCCHHHH
Confidence            4445555555555555555444  44444455555555555443      111111 11223344455555556666666


Q ss_pred             HHHHHHHHhCCCCCCHHHHHHHHHHHHhcCCHhHHHHHHHHHHhcCCCCCHhhHHHHHHHHHhcCChhHHHHHHHHHHhc
Q 040027          116 FIAFGRILRSCFTPNAATFNSLIKGLHAESRIMEAAALFTKLKAFGCEPNVITYNTLINGLCRTGHTMIALNLFEEMANG  195 (595)
Q Consensus       116 ~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~  195 (595)
                      ..+++++.... +.+..+|..+...+...|++++|.+.|+++.+.. +.+...+..++..+...|++++|.+.|+++...
T Consensus       451 ~~~~~~~~~~~-~~~~~~~~~l~~~~~~~~~~~~A~~~~~~a~~~~-~~~~~~~~~la~~~~~~g~~~~A~~~~~~~~~~  528 (899)
T TIGR02917       451 LAAAKKLEKKQ-PDNASLHNLLGAIYLGKGDLAKAREAFEKALSIE-PDFFPAAANLARIDIQEGNPDDAIQRFEKVLTI  528 (899)
T ss_pred             HHHHHHHHHhC-CCCcHHHHHHHHHHHhCCCHHHHHHHHHHHHhhC-CCcHHHHHHHHHHHHHCCCHHHHHHHHHHHHHh
Confidence            66666655542 4456667777777777777777777777776653 335556666777777777777777777777765


Q ss_pred             CCCCCccccCcHHHHHHHHHHHHHcCCHhHHHHHHHHHhhCCCCCCHhHHHHHHHHHHhcCCHHHHHHHHHHHHHCCCCC
Q 040027          196 NGEIGVVCKPNTVTYSTIIDGLCKEGFVDKAKALFLQMKDENINPDVVTYNSLIHGLCHANDWNEAKRLFIEMMDQGVQP  275 (595)
Q Consensus       196 ~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~~ll~~~~~~~~~~~A~~~~~~~~~~~~~~  275 (595)
                      .       +.+..++..+...+.+.|+.++|..+++++...+ +.+...+..++..+...|++++|..+++.+.+. .+.
T Consensus       529 ~-------~~~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~~~-~~~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~~-~~~  599 (899)
T TIGR02917       529 D-------PKNLRAILALAGLYLRTGNEEEAVAWLEKAAELN-PQEIEPALALAQYYLGKGQLKKALAILNEAADA-APD  599 (899)
T ss_pred             C-------cCcHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhC-ccchhHHHHHHHHHHHCCCHHHHHHHHHHHHHc-CCC
Confidence            4       4556677777777777788888888877776653 335666777777888888888888888887764 344


Q ss_pred             CHhhHHHHHHHHHhcCChHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHhcCCCCCHHHHHHHHH
Q 040027          276 SVVTFNVIMDELCKNRKMDEASRLLDLMVQRGVRPNACTYNTLMDGFCLMGKINRAEELFGSMESMGCKHDDVSYNILIN  355 (595)
Q Consensus       276 ~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~  355 (595)
                      +...|..++.++...|++++|...|+.+.+.. +.+...+..++.++...|++++|..+++++.+.. +.+..++..++.
T Consensus       600 ~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~~~-~~~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~~~-~~~~~~~~~l~~  677 (899)
T TIGR02917       600 SPEAWLMLGRAQLAAGDLNKAVSSFKKLLALQ-PDSALALLLLADAYAVMKNYAKAITSLKRALELK-PDNTEAQIGLAQ  677 (899)
T ss_pred             CHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhC-CCChHHHHHHHHHHHHcCCHHHHHHHHHHHHhcC-CCCHHHHHHHHH
Confidence            66778888888888888888888888887753 3356667778888888888888888888887764 455677888888


Q ss_pred             HHHhCCCHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHccCCHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHhcCCHHH
Q 040027          356 GYCKNKEVEEALSLYREMVSKGIKPTVVTYNTLFLGLFEIHQVEHALKLFDEMQRDGVAADTRTYTTFIDGLCKNGYIIE  435 (595)
Q Consensus       356 ~~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~  435 (595)
                      .+...|++++|..+++.+.+..+ .+...+..+...+...|++++|.+.++.+...+  |+..++..++.++.+.|++++
T Consensus       678 ~~~~~~~~~~A~~~~~~~~~~~~-~~~~~~~~~~~~~~~~g~~~~A~~~~~~~~~~~--~~~~~~~~l~~~~~~~g~~~~  754 (899)
T TIGR02917       678 LLLAAKRTESAKKIAKSLQKQHP-KAALGFELEGDLYLRQKDYPAAIQAYRKALKRA--PSSQNAIKLHRALLASGNTAE  754 (899)
T ss_pred             HHHHcCCHHHHHHHHHHHHhhCc-CChHHHHHHHHHHHHCCCHHHHHHHHHHHHhhC--CCchHHHHHHHHHHHCCCHHH
Confidence            88888888888888888877653 366677778888888899999999998888763  444677778888888999999


Q ss_pred             HHHHHHHHHHcCCCcCHHHHHHHHHHHHhcCChHHHHHHHHhcccCCCCCCHHHHHHHHHHHHhcCChhHHHHHHHHHHH
Q 040027          436 AVELFRTLRILKCELDIQAYNCLIDGLCKSGRLKFAWELFCSLPHGVLVPNVVTYNIMIQGLCNDGQMDKARDLFLDMEE  515 (595)
Q Consensus       436 A~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~p~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~  515 (595)
                      |...++++.+.. +.+...+..++..|...|++++|...|+++.+.. +++..+++.++..+...|+ .+|+.+++++.+
T Consensus       755 A~~~~~~~l~~~-~~~~~~~~~la~~~~~~g~~~~A~~~~~~~~~~~-p~~~~~~~~l~~~~~~~~~-~~A~~~~~~~~~  831 (899)
T TIGR02917       755 AVKTLEAWLKTH-PNDAVLRTALAELYLAQKDYDKAIKHYRTVVKKA-PDNAVVLNNLAWLYLELKD-PRALEYAEKALK  831 (899)
T ss_pred             HHHHHHHHHHhC-CCCHHHHHHHHHHHHHCcCHHHHHHHHHHHHHhC-CCCHHHHHHHHHHHHhcCc-HHHHHHHHHHHh
Confidence            999999888765 6678888889999999999999999999988752 3467788888999999999 889999999988


Q ss_pred             cCCCCCHHHHHHHHHHHHHcCChhHHHHHHHHHHHCCCCCCHHHHHHHHHHHHhcCcccccchHH
Q 040027          516 NAAAPDVITFDMLIHGFIRINEPSKVNELLHKMKEKKVMPDASIVSIVVDLLVKNEISLKSLPSF  580 (595)
Q Consensus       516 ~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~p~~~~~~~l~~~~~~~g~~~~~i~~~  580 (595)
                      .. +.+..++..++.++...|++++|.++++++.+.+ +.++.++..++.+|.+.|+.+++++.+
T Consensus       832 ~~-~~~~~~~~~~~~~~~~~g~~~~A~~~~~~a~~~~-~~~~~~~~~l~~~~~~~g~~~~A~~~~  894 (899)
T TIGR02917       832 LA-PNIPAILDTLGWLLVEKGEADRALPLLRKAVNIA-PEAAAIRYHLALALLATGRKAEARKEL  894 (899)
T ss_pred             hC-CCCcHHHHHHHHHHHHcCCHHHHHHHHHHHHhhC-CCChHHHHHHHHHHHHcCCHHHHHHHH
Confidence            63 4566777888899999999999999999999865 338899999999999999998655543

This protein family occurs in strictly within a subset of Gram-negative bacterial species with the proposed PEP-CTERM/exosortase system, analogous to the LPXTG/sortase system common in Gram-positive bacteria. This protein occurs in a species if and only if a transmembrane histidine kinase (TIGR02916) and a DNA-binding response regulator (TIGR02915) also occur. The present of tetratricopeptide repeats (TPR) suggests protein-protein interaction, possibly for the regulation of PEP-CTERM protein expression, since many PEP-CTERM proteins in these genomes are preceded by a proposed DNA binding site for the response regulator.

>TIGR02917 PEP_TPR_lipo putative PEP-CTERM system TPR-repeat lipoprotein

Probab=100.00  E-value=3.3e-33  Score=306.91  Aligned_cols=518  Identities=12%  Similarity=0.057  Sum_probs=267.4

Q ss_pred             ccCCCChHHHHHHHHHHHHhCCCCCCHhhHHHHHHHHHcCCCchh--H---HhhCCCCCCHHHHHHHHHHHHhcCChhHH
Q 040027           41 DINVITPNEAFCIFDYMLRMHPSPPPVSSFNILLASLAKNKHYDT--R---LNATGLFPNLYTYNILINCFCKIGRVSLG  115 (595)
Q Consensus        41 ~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~--~---~~~~~~~~~~~~~~~l~~~~~~~g~~~~A  115 (595)
                      +...|++++|...|+++++..|.  ++..+..+...+.+.|++++  .   -.....+.++..+..+...+.+.|++++|
T Consensus       305 ~~~~g~~~~A~~~~~~~~~~~p~--~~~~~~~la~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A  382 (899)
T TIGR02917       305 EYQLGNLEQAYQYLNQILKYAPN--SHQARRLLASIQLRLGRVDEAIATLSPALGLDPDDPAALSLLGEAYLALGDFEKA  382 (899)
T ss_pred             HHHcCCHHHHHHHHHHHHHhCCC--ChHHHHHHHHHHHHCCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHHHHCCCHHHH
Confidence            45667777777777777777766  66666777777777777766  1   11112234566777777777777777777


Q ss_pred             HHHHHHHHhCCCCCCHHHHHHHHHHHHhcCCHhHHHHHHHHHHhcCCCCCHhhHHHHHHHHHhcCChhHHHHHHHHHHhc
Q 040027          116 FIAFGRILRSCFTPNAATFNSLIKGLHAESRIMEAAALFTKLKAFGCEPNVITYNTLINGLCRTGHTMIALNLFEEMANG  195 (595)
Q Consensus       116 ~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~  195 (595)
                      ..+|+++.+.. +.+...+..+...+...|++++|++.++.+...... .......++..+.+.|++++|..+++.+...
T Consensus       383 ~~~~~~~~~~~-~~~~~~~~~l~~~~~~~~~~~~A~~~~~~a~~~~~~-~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~~  460 (899)
T TIGR02917       383 AEYLAKATELD-PENAAARTQLGISKLSQGDPSEAIADLETAAQLDPE-LGRADLLLILSYLRSGQFDKALAAAKKLEKK  460 (899)
T ss_pred             HHHHHHHHhcC-CCCHHHHHHHHHHHHhCCChHHHHHHHHHHHhhCCc-chhhHHHHHHHHHhcCCHHHHHHHHHHHHHh
Confidence            77777777653 335556666666666677777777777666654321 2333344455555555555555555555543


Q ss_pred             CCCCCccccCcHHHHHHHHHHHHHcCCHhHHHHHHHHHhhCCCCCCHhHHHHHHHHHHhcCCHHHHHHHHHHHHHCCCCC
Q 040027          196 NGEIGVVCKPNTVTYSTIIDGLCKEGFVDKAKALFLQMKDENINPDVVTYNSLIHGLCHANDWNEAKRLFIEMMDQGVQP  275 (595)
Q Consensus       196 ~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~~ll~~~~~~~~~~~A~~~~~~~~~~~~~~  275 (595)
                      .       +.++.++..+..++...|++++|.+.|+++.+.. +.+...+..++..+...|++++|.+.|+++.... +.
T Consensus       461 ~-------~~~~~~~~~l~~~~~~~~~~~~A~~~~~~a~~~~-~~~~~~~~~la~~~~~~g~~~~A~~~~~~~~~~~-~~  531 (899)
T TIGR02917       461 Q-------PDNASLHNLLGAIYLGKGDLAKAREAFEKALSIE-PDFFPAAANLARIDIQEGNPDDAIQRFEKVLTID-PK  531 (899)
T ss_pred             C-------CCCcHHHHHHHHHHHhCCCHHHHHHHHHHHHhhC-CCcHHHHHHHHHHHHHCCCHHHHHHHHHHHHHhC-cC
Confidence            2       3344555555555555555555555555555432 2234444445555555555555555555555432 12


Q ss_pred             CHhhHHHHHHHHHhcCChHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHhcCCCCCHHHHHHHHH
Q 040027          276 SVVTFNVIMDELCKNRKMDEASRLLDLMVQRGVRPNACTYNTLMDGFCLMGKINRAEELFGSMESMGCKHDDVSYNILIN  355 (595)
Q Consensus       276 ~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~  355 (595)
                      +..++..+...+...|++++|..+++++...+ +.+...+..++..+...|++++|..+++.+.+.. +.+...|..++.
T Consensus       532 ~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~~~-~~~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~~~-~~~~~~~~~l~~  609 (899)
T TIGR02917       532 NLRAILALAGLYLRTGNEEEAVAWLEKAAELN-PQEIEPALALAQYYLGKGQLKKALAILNEAADAA-PDSPEAWLMLGR  609 (899)
T ss_pred             cHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhC-ccchhHHHHHHHHHHHCCCHHHHHHHHHHHHHcC-CCCHHHHHHHHH
Confidence            34444445555555555555555555554432 1233344444444455555555555555444332 333444444455


Q ss_pred             HHHhCCCHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHccCCHHHHHHHHHHHHHCC-----------------------
Q 040027          356 GYCKNKEVEEALSLYREMVSKGIKPTVVTYNTLFLGLFEIHQVEHALKLFDEMQRDG-----------------------  412 (595)
Q Consensus       356 ~~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~-----------------------  412 (595)
                      ++...|++++|+..|+++.+... .+...+..+...+...|++++|...++++.+..                       
T Consensus       610 ~~~~~~~~~~A~~~~~~~~~~~~-~~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~A  688 (899)
T TIGR02917       610 AQLAAGDLNKAVSSFKKLLALQP-DSALALLLLADAYAVMKNYAKAITSLKRALELKPDNTEAQIGLAQLLLAAKRTESA  688 (899)
T ss_pred             HHHHcCCHHHHHHHHHHHHHhCC-CChHHHHHHHHHHHHcCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHHHHcCCHHHH
Confidence            55555555555555554444321 133344444444444445555555444444431                       


Q ss_pred             ----------CCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCcCHHHHHHHHHHHHhcCChHHHHHHHHhcccCC
Q 040027          413 ----------VAADTRTYTTFIDGLCKNGYIIEAVELFRTLRILKCELDIQAYNCLIDGLCKSGRLKFAWELFCSLPHGV  482 (595)
Q Consensus       413 ----------~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~  482 (595)
                                .+.+...+..+...+...|++++|...++++....  |+..++..++.++...|++++|...++++.+. 
T Consensus       689 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~~~A~~~~~~~~~~~--~~~~~~~~l~~~~~~~g~~~~A~~~~~~~l~~-  765 (899)
T TIGR02917       689 KKIAKSLQKQHPKAALGFELEGDLYLRQKDYPAAIQAYRKALKRA--PSSQNAIKLHRALLASGNTAEAVKTLEAWLKT-  765 (899)
T ss_pred             HHHHHHHHhhCcCChHHHHHHHHHHHHCCCHHHHHHHHHHHHhhC--CCchHHHHHHHHHHHCCCHHHHHHHHHHHHHh-
Confidence                      13333444444444444455555555554444432  22234444444455555555555555544442 


Q ss_pred             CCCCHHHHHHHHHHHHhcCChhHHHHHHHHHHHcCCCCCHHHHHHHHHHHHHcCChhHHHHHHHHHHHCCCCCCHHHHHH
Q 040027          483 LVPNVVTYNIMIQGLCNDGQMDKARDLFLDMEENAAAPDVITFDMLIHGFIRINEPSKVNELLHKMKEKKVMPDASIVSI  562 (595)
Q Consensus       483 ~~p~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~p~~~~~~~  562 (595)
                      .+.+...+..++..|...|++++|...|+++.+.. +++..++..++..+...|+ .+|..+++++.+.. +-++.++..
T Consensus       766 ~~~~~~~~~~la~~~~~~g~~~~A~~~~~~~~~~~-p~~~~~~~~l~~~~~~~~~-~~A~~~~~~~~~~~-~~~~~~~~~  842 (899)
T TIGR02917       766 HPNDAVLRTALAELYLAQKDYDKAIKHYRTVVKKA-PDNAVVLNNLAWLYLELKD-PRALEYAEKALKLA-PNIPAILDT  842 (899)
T ss_pred             CCCCHHHHHHHHHHHHHCcCHHHHHHHHHHHHHhC-CCCHHHHHHHHHHHHhcCc-HHHHHHHHHHHhhC-CCCcHHHHH
Confidence            12234444445555555555555555555555443 3344445555555555555 44555555555421 123444555


Q ss_pred             HHHHHHhcCcccccchHH
Q 040027          563 VVDLLVKNEISLKSLPSF  580 (595)
Q Consensus       563 l~~~~~~~g~~~~~i~~~  580 (595)
                      ++.++.+.|++++++..+
T Consensus       843 ~~~~~~~~g~~~~A~~~~  860 (899)
T TIGR02917       843 LGWLLVEKGEADRALPLL  860 (899)
T ss_pred             HHHHHHHcCCHHHHHHHH
Confidence            555555555555444443

This protein family occurs in strictly within a subset of Gram-negative bacterial species with the proposed PEP-CTERM/exosortase system, analogous to the LPXTG/sortase system common in Gram-positive bacteria. This protein occurs in a species if and only if a transmembrane histidine kinase (TIGR02916) and a DNA-binding response regulator (TIGR02915) also occur. The present of tetratricopeptide repeats (TPR) suggests protein-protein interaction, possibly for the regulation of PEP-CTERM protein expression, since many PEP-CTERM proteins in these genomes are preceded by a proposed DNA binding site for the response regulator.

>PRK11447 cellulose synthase subunit BcsC; Provisional

Probab=99.98  E-value=3.1e-26  Score=251.32  Aligned_cols=527  Identities=14%  Similarity=0.058  Sum_probs=370.4

Q ss_pred             cCCCChHHHHHHHHHHHHhCCCCCCHhhHHHHHHHHHcCCCchh------HHhhCCCCCCHHH----------------H
Q 040027           42 INVITPNEAFCIFDYMLRMHPSPPPVSSFNILLASLAKNKHYDT------RLNATGLFPNLYT----------------Y   99 (595)
Q Consensus        42 ~~~~~~~~A~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~------~~~~~~~~~~~~~----------------~   99 (595)
                      ...++.+.|.+.+++++..+|+  ++..+..++..+...|+.++      ++.... +.++..                .
T Consensus        39 ~~~~~~d~a~~~l~kl~~~~p~--~p~~~~~~~~~~l~~g~~~~A~~~l~~l~~~~-P~~~~~~~~~~~~~~~~~~~~~~  115 (1157)
T PRK11447         39 EATHREDLVRQSLYRLELIDPN--NPDVIAARFRLLLRQGDSDGAQKLLDRLSQLA-PDSNAYRSSRTTMLLSTPEGRQA  115 (1157)
T ss_pred             HhhCChHHHHHHHHHHHccCCC--CHHHHHHHHHHHHhCCCHHHHHHHHHHHHhhC-CCChHHHHHHHHHHhcCCchhhH
Confidence            5679999999999999999999  89999999999999999888      222222 223333                2


Q ss_pred             HHHHHHHHhcCChhHHHHHHHHHHhCCCCCCHHHHHHH-HHHHHhcCCHhHHHHHHHHHHhcCCCCCHhhHHHHHHHHHh
Q 040027          100 NILINCFCKIGRVSLGFIAFGRILRSCFTPNAATFNSL-IKGLHAESRIMEAAALFTKLKAFGCEPNVITYNTLINGLCR  178 (595)
Q Consensus       100 ~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~~l-~~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~~l~~~~~~  178 (595)
                      ..+++.+.+.|++++|+..|+++.+.. +++...-... .......|+.++|++.++++.+.. +.+...+..+...+..
T Consensus       116 l~~A~ll~~~g~~~eA~~~~~~~l~~~-p~~~~la~~y~~~~~~~~g~~~~A~~~L~~ll~~~-P~~~~~~~~LA~ll~~  193 (1157)
T PRK11447        116 LQQARLLATTGRTEEALASYDKLFNGA-PPELDLAVEYWRLVAKLPAQRPEAINQLQRLNADY-PGNTGLRNTLALLLFS  193 (1157)
T ss_pred             HHHHHHHHhCCCHHHHHHHHHHHccCC-CCChHHHHHHHHHHhhCCccHHHHHHHHHHHHHhC-CCCHHHHHHHHHHHHc
Confidence            445567889999999999999999874 3343321112 222234699999999999999875 4477788899999999


Q ss_pred             cCChhHHHHHHHHHHhcCCCCC------------cccc--------------CcHH----H-----------------HH
Q 040027          179 TGHTMIALNLFEEMANGNGEIG------------VVCK--------------PNTV----T-----------------YS  211 (595)
Q Consensus       179 ~g~~~~A~~~~~~~~~~~~~~~------------~~~~--------------~~~~----~-----------------~~  211 (595)
                      .|+.++|+..++++........            ....              |+..    .                 ..
T Consensus       194 ~g~~~eAl~~l~~~~~~~~~~~~aa~~~~~~l~~~~~~~~~~~~l~~~l~~~p~~~~~~~A~~~L~~~~~~~~dp~~~~~  273 (1157)
T PRK11447        194 SGRRDEGFAVLEQMAKSPAGRDAAAQLWYGQIKDMPVSDASVAALQKYLQVFSDGDSVAAARSQLAEQQKQLADPAFRAR  273 (1157)
T ss_pred             cCCHHHHHHHHHHHhhCCCchHHHHHHHHHHHhccCCChhhHHHHHHHHHHCCCchHHHHHHHHHHHHHHhccCcchHHH
Confidence            9999999999999865321000            0000              0000    0                 01


Q ss_pred             HHHHHHHHcCCHhHHHHHHHHHhhCCCCCCHhHHHHHHHHHHhcCCHHHHHHHHHHHHHCCCCC-CHhhH----------
Q 040027          212 TIIDGLCKEGFVDKAKALFLQMKDENINPDVVTYNSLIHGLCHANDWNEAKRLFIEMMDQGVQP-SVVTF----------  280 (595)
Q Consensus       212 ~l~~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~~ll~~~~~~~~~~~A~~~~~~~~~~~~~~-~~~~~----------  280 (595)
                      .....+...|++++|+..|++..+.. +.+...+..|...+.+.|++++|+..|++.++..... ....+          
T Consensus       274 ~~G~~~~~~g~~~~A~~~l~~aL~~~-P~~~~a~~~Lg~~~~~~g~~~eA~~~l~~Al~~~p~~~~~~~~~~ll~~~~~~  352 (1157)
T PRK11447        274 AQGLAAVDSGQGGKAIPELQQAVRAN-PKDSEALGALGQAYSQQGDRARAVAQFEKALALDPHSSNRDKWESLLKVNRYW  352 (1157)
T ss_pred             HHHHHHHHCCCHHHHHHHHHHHHHhC-CCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCCCccchhHHHHHHHhhhHH
Confidence            12445677899999999999998864 3378889999999999999999999999998753221 11111          


Q ss_pred             --HHHHHHHHhcCChHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHhcCCCCCHHHHHHHH----
Q 040027          281 --NVIMDELCKNRKMDEASRLLDLMVQRGVRPNACTYNTLMDGFCLMGKINRAEELFGSMESMGCKHDDVSYNILI----  354 (595)
Q Consensus       281 --~~l~~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~----  354 (595)
                        ......+.+.|++++|...|+++.+.. +.+...+..+..++...|++++|++.|+++.+.. +.+...+..+.    
T Consensus       353 ~~~~~g~~~~~~g~~~eA~~~~~~Al~~~-P~~~~a~~~Lg~~~~~~g~~~eA~~~y~~aL~~~-p~~~~a~~~L~~l~~  430 (1157)
T PRK11447        353 LLIQQGDAALKANNLAQAERLYQQARQVD-NTDSYAVLGLGDVAMARKDYAAAERYYQQALRMD-PGNTNAVRGLANLYR  430 (1157)
T ss_pred             HHHHHHHHHHHCCCHHHHHHHHHHHHHhC-CCCHHHHHHHHHHHHHCCCHHHHHHHHHHHHHhC-CCCHHHHHHHHHHHH
Confidence              123456778999999999999999874 3356677788999999999999999999998764 23333333332    


Q ss_pred             --------------------------------------HHHHhCCCHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHccC
Q 040027          355 --------------------------------------NGYCKNKEVEEALSLYREMVSKGIKPTVVTYNTLFLGLFEIH  396 (595)
Q Consensus       355 --------------------------------------~~~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~  396 (595)
                                                            ..+...|++++|++.|+++++..+. +...+..+...+...|
T Consensus       431 ~~~~~~A~~~l~~l~~~~~~~~~~~~~~l~~~~~~~~a~~~~~~g~~~eA~~~~~~Al~~~P~-~~~~~~~LA~~~~~~G  509 (1157)
T PRK11447        431 QQSPEKALAFIASLSASQRRSIDDIERSLQNDRLAQQAEALENQGKWAQAAELQRQRLALDPG-SVWLTYRLAQDLRQAG  509 (1157)
T ss_pred             hcCHHHHHHHHHhCCHHHHHHHHHHHHHhhhhHHHHHHHHHHHCCCHHHHHHHHHHHHHhCCC-CHHHHHHHHHHHHHcC
Confidence                                                  3344578888888888888876443 5566777778888888


Q ss_pred             CHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHHc------------------------------
Q 040027          397 QVEHALKLFDEMQRDGVAADTRTYTTFIDGLCKNGYIIEAVELFRTLRIL------------------------------  446 (595)
Q Consensus       397 ~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~------------------------------  446 (595)
                      ++++|...++++.+.. +.+...+..+...+...++.++|...++.+...                              
T Consensus       510 ~~~~A~~~l~~al~~~-P~~~~~~~a~al~l~~~~~~~~Al~~l~~l~~~~~~~~~~~l~~~l~~~~~l~~a~~l~~~G~  588 (1157)
T PRK11447        510 QRSQADALMRRLAQQK-PNDPEQVYAYGLYLSGSDRDRAALAHLNTLPRAQWNSNIQELAQRLQSDQVLETANRLRDSGK  588 (1157)
T ss_pred             CHHHHHHHHHHHHHcC-CCCHHHHHHHHHHHHhCCCHHHHHHHHHhCCchhcChhHHHHHHHHhhhHHHHHHHHHHHCCC
Confidence            8888888888887652 334433333333333444444444443332100                              


Q ss_pred             ---------CCCcCHHHHHHHHHHHHhcCChHHHHHHHHhcccCCCCC-CHHHHHHHHHHHHhcCChhHHHHHHHHHHHc
Q 040027          447 ---------KCELDIQAYNCLIDGLCKSGRLKFAWELFCSLPHGVLVP-NVVTYNIMIQGLCNDGQMDKARDLFLDMEEN  516 (595)
Q Consensus       447 ---------~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~p-~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~  516 (595)
                               ..+.+...+..+...+.+.|++++|+..|+++.+.  .| +...+..++..|...|++++|++.++.+.+.
T Consensus       589 ~~eA~~~l~~~p~~~~~~~~La~~~~~~g~~~~A~~~y~~al~~--~P~~~~a~~~la~~~~~~g~~~eA~~~l~~ll~~  666 (1157)
T PRK11447        589 EAEAEALLRQQPPSTRIDLTLADWAQQRGDYAAARAAYQRVLTR--EPGNADARLGLIEVDIAQGDLAAARAQLAKLPAT  666 (1157)
T ss_pred             HHHHHHHHHhCCCCchHHHHHHHHHHHcCCHHHHHHHHHHHHHh--CCCCHHHHHHHHHHHHHCCCHHHHHHHHHHHhcc
Confidence                     11445556677777888888888888888888873  44 4677888888888888888888888887765


Q ss_pred             CCCCCHHHHHHHHHHHHHcCChhHHHHHHHHHHHCCC--CC---CHHHHHHHHHHHHhcCcccccchHHH
Q 040027          517 AAAPDVITFDMLIHGFIRINEPSKVNELLHKMKEKKV--MP---DASIVSIVVDLLVKNEISLKSLPSFL  581 (595)
Q Consensus       517 ~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~--~p---~~~~~~~l~~~~~~~g~~~~~i~~~~  581 (595)
                      . +.+..++..+..++...|++++|.++++++....-  .|   +..++..+..++.+.|+.++++..+.
T Consensus       667 ~-p~~~~~~~~la~~~~~~g~~~eA~~~~~~al~~~~~~~~~~~~a~~~~~~a~~~~~~G~~~~A~~~y~  735 (1157)
T PRK11447        667 A-NDSLNTQRRVALAWAALGDTAAAQRTFNRLIPQAKSQPPSMESALVLRDAARFEAQTGQPQQALETYK  735 (1157)
T ss_pred             C-CCChHHHHHHHHHHHhCCCHHHHHHHHHHHhhhCccCCcchhhHHHHHHHHHHHHHcCCHHHHHHHHH
Confidence            3 34456667777888888888888888888876421  12   23466667888888888886665544

>PRK11447 cellulose synthase subunit BcsC; Provisional

Probab=99.97  E-value=4.1e-25  Score=242.54  Aligned_cols=500  Identities=14%  Similarity=0.058  Sum_probs=368.8

Q ss_pred             ccccCCCChHHHHHHHHHHHHhCCCCCCHhhH----------------HHHHHHHHcCCCchh-----HHhhCCCCCCHH
Q 040027           39 EGDINVITPNEAFCIFDYMLRMHPSPPPVSSF----------------NILLASLAKNKHYDT-----RLNATGLFPNLY   97 (595)
Q Consensus        39 ~~~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~----------------~~l~~~~~~~~~~~~-----~~~~~~~~~~~~   97 (595)
                      ..+++.|++++|.+.++++++.+|+  ++..+                ..+...+...|++++     .....+.+|+..
T Consensus        70 ~~~l~~g~~~~A~~~l~~l~~~~P~--~~~~~~~~~~~~~~~~~~~~~l~~A~ll~~~g~~~eA~~~~~~~l~~~p~~~~  147 (1157)
T PRK11447         70 RLLLRQGDSDGAQKLLDRLSQLAPD--SNAYRSSRTTMLLSTPEGRQALQQARLLATTGRTEEALASYDKLFNGAPPELD  147 (1157)
T ss_pred             HHHHhCCCHHHHHHHHHHHHhhCCC--ChHHHHHHHHHHhcCCchhhHHHHHHHHHhCCCHHHHHHHHHHHccCCCCChH
Confidence            3447889999999999999999998  55443                334557888999888     122233344433


Q ss_pred             HHH-HHHHHHHhcCChhHHHHHHHHHHhCCCCCCHHHHHHHHHHHHhcCCHhHHHHHHHHHHhcCC--------------
Q 040027           98 TYN-ILINCFCKIGRVSLGFIAFGRILRSCFTPNAATFNSLIKGLHAESRIMEAAALFTKLKAFGC--------------  162 (595)
Q Consensus        98 ~~~-~l~~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~--------------  162 (595)
                      .-. .........|++++|+..++++.+.. +.+...+..+...+...|++++|++.++++.....              
T Consensus       148 la~~y~~~~~~~~g~~~~A~~~L~~ll~~~-P~~~~~~~~LA~ll~~~g~~~eAl~~l~~~~~~~~~~~~aa~~~~~~l~  226 (1157)
T PRK11447        148 LAVEYWRLVAKLPAQRPEAINQLQRLNADY-PGNTGLRNTLALLLFSSGRRDEGFAVLEQMAKSPAGRDAAAQLWYGQIK  226 (1157)
T ss_pred             HHHHHHHHHhhCCccHHHHHHHHHHHHHhC-CCCHHHHHHHHHHHHccCCHHHHHHHHHHHhhCCCchHHHHHHHHHHHh
Confidence            211 12222334699999999999999985 55777888999999999999999999998754311              


Q ss_pred             ----C--------------CCHhhH---------------------HHHHHHHHhcCChhHHHHHHHHHHhcCCCCCccc
Q 040027          163 ----E--------------PNVITY---------------------NTLINGLCRTGHTMIALNLFEEMANGNGEIGVVC  203 (595)
Q Consensus       163 ----~--------------~~~~~~---------------------~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~  203 (595)
                          .              |+....                     ......+...|++++|+..|++..+.+       
T Consensus       227 ~~~~~~~~~~~l~~~l~~~p~~~~~~~A~~~L~~~~~~~~dp~~~~~~~G~~~~~~g~~~~A~~~l~~aL~~~-------  299 (1157)
T PRK11447        227 DMPVSDASVAALQKYLQVFSDGDSVAAARSQLAEQQKQLADPAFRARAQGLAAVDSGQGGKAIPELQQAVRAN-------  299 (1157)
T ss_pred             ccCCChhhHHHHHHHHHHCCCchHHHHHHHHHHHHHHhccCcchHHHHHHHHHHHCCCHHHHHHHHHHHHHhC-------
Confidence                0              000000                     012445667899999999999999875       


Q ss_pred             cCcHHHHHHHHHHHHHcCCHhHHHHHHHHHhhCCCCC-CHhHH------------HHHHHHHHhcCCHHHHHHHHHHHHH
Q 040027          204 KPNTVTYSTIIDGLCKEGFVDKAKALFLQMKDENINP-DVVTY------------NSLIHGLCHANDWNEAKRLFIEMMD  270 (595)
Q Consensus       204 ~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~-~~~~~------------~~ll~~~~~~~~~~~A~~~~~~~~~  270 (595)
                      |.+..++..+..++.+.|++++|+..|++..+..... ....|            ..+...+.+.|++++|...|+++++
T Consensus       300 P~~~~a~~~Lg~~~~~~g~~~eA~~~l~~Al~~~p~~~~~~~~~~ll~~~~~~~~~~~g~~~~~~g~~~eA~~~~~~Al~  379 (1157)
T PRK11447        300 PKDSEALGALGQAYSQQGDRARAVAQFEKALALDPHSSNRDKWESLLKVNRYWLLIQQGDAALKANNLAQAERLYQQARQ  379 (1157)
T ss_pred             CCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCCCccchhHHHHHHHhhhHHHHHHHHHHHHHCCCHHHHHHHHHHHHH
Confidence            5678899999999999999999999999988764221 11112            1234567889999999999999998


Q ss_pred             CCCCCCHhhHHHHHHHHHhcCChHHHHHHHHHHHHCCCCCCHHHHHH---------------------------------
Q 040027          271 QGVQPSVVTFNVIMDELCKNRKMDEASRLLDLMVQRGVRPNACTYNT---------------------------------  317 (595)
Q Consensus       271 ~~~~~~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~---------------------------------  317 (595)
                      .. +.+...+..+..++...|++++|.+.|+++.+.... +...+..                                 
T Consensus       380 ~~-P~~~~a~~~Lg~~~~~~g~~~eA~~~y~~aL~~~p~-~~~a~~~L~~l~~~~~~~~A~~~l~~l~~~~~~~~~~~~~  457 (1157)
T PRK11447        380 VD-NTDSYAVLGLGDVAMARKDYAAAERYYQQALRMDPG-NTNAVRGLANLYRQQSPEKALAFIASLSASQRRSIDDIER  457 (1157)
T ss_pred             hC-CCCHHHHHHHHHHHHHCCCHHHHHHHHHHHHHhCCC-CHHHHHHHHHHHHhcCHHHHHHHHHhCCHHHHHHHHHHHH
Confidence            63 335667788899999999999999999999876322 2222222                                 


Q ss_pred             ---------HHHHHHhcCCHHHHHHHHHHHHhcCCCCCHHHHHHHHHHHHhCCCHHHHHHHHHHHHHCCCCCCHHHHHHH
Q 040027          318 ---------LMDGFCLMGKINRAEELFGSMESMGCKHDDVSYNILINGYCKNKEVEEALSLYREMVSKGIKPTVVTYNTL  388 (595)
Q Consensus       318 ---------l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~~l  388 (595)
                               +...+...|++++|+..|++..+.. +.+...+..+...|.+.|++++|...++++.+..+. +...+..+
T Consensus       458 ~l~~~~~~~~a~~~~~~g~~~eA~~~~~~Al~~~-P~~~~~~~~LA~~~~~~G~~~~A~~~l~~al~~~P~-~~~~~~a~  535 (1157)
T PRK11447        458 SLQNDRLAQQAEALENQGKWAQAAELQRQRLALD-PGSVWLTYRLAQDLRQAGQRSQADALMRRLAQQKPN-DPEQVYAY  535 (1157)
T ss_pred             HhhhhHHHHHHHHHHHCCCHHHHHHHHHHHHHhC-CCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHcCCC-CHHHHHHH
Confidence                     2334556799999999999998874 456778888999999999999999999999875432 33333333


Q ss_pred             HHHHHccCCHHHHHHHHHHHHHC---------------------------------------CCCCCHHHHHHHHHHHHh
Q 040027          389 FLGLFEIHQVEHALKLFDEMQRD---------------------------------------GVAADTRTYTTFIDGLCK  429 (595)
Q Consensus       389 ~~~~~~~~~~~~a~~~~~~~~~~---------------------------------------~~~~~~~~~~~l~~~~~~  429 (595)
                      ...+...++.++|...++.+...                                       ..+.+...+..+...+.+
T Consensus       536 al~l~~~~~~~~Al~~l~~l~~~~~~~~~~~l~~~l~~~~~l~~a~~l~~~G~~~eA~~~l~~~p~~~~~~~~La~~~~~  615 (1157)
T PRK11447        536 GLYLSGSDRDRAALAHLNTLPRAQWNSNIQELAQRLQSDQVLETANRLRDSGKEAEAEALLRQQPPSTRIDLTLADWAQQ  615 (1157)
T ss_pred             HHHHHhCCCHHHHHHHHHhCCchhcChhHHHHHHHHhhhHHHHHHHHHHHCCCHHHHHHHHHhCCCCchHHHHHHHHHHH
Confidence            33333444444444443322100                                       124566677788889999


Q ss_pred             cCCHHHHHHHHHHHHHcCCCcCHHHHHHHHHHHHhcCChHHHHHHHHhcccCCCCC-CHHHHHHHHHHHHhcCChhHHHH
Q 040027          430 NGYIIEAVELFRTLRILKCELDIQAYNCLIDGLCKSGRLKFAWELFCSLPHGVLVP-NVVTYNIMIQGLCNDGQMDKARD  508 (595)
Q Consensus       430 ~g~~~~A~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~p-~~~~~~~l~~~~~~~g~~~~A~~  508 (595)
                      .|++++|+..|+++++.. +.+...+..++.++...|++++|+..++.+..  ..| +...+..+..++...|++++|.+
T Consensus       616 ~g~~~~A~~~y~~al~~~-P~~~~a~~~la~~~~~~g~~~eA~~~l~~ll~--~~p~~~~~~~~la~~~~~~g~~~eA~~  692 (1157)
T PRK11447        616 RGDYAAARAAYQRVLTRE-PGNADARLGLIEVDIAQGDLAAARAQLAKLPA--TANDSLNTQRRVALAWAALGDTAAAQR  692 (1157)
T ss_pred             cCCHHHHHHHHHHHHHhC-CCCHHHHHHHHHHHHHCCCHHHHHHHHHHHhc--cCCCChHHHHHHHHHHHhCCCHHHHHH
Confidence            999999999999999876 67889999999999999999999999999887  344 45667778899999999999999


Q ss_pred             HHHHHHHcCC--CC---CHHHHHHHHHHHHHcCChhHHHHHHHHHHH-CCCCC
Q 040027          509 LFLDMEENAA--AP---DVITFDMLIHGFIRINEPSKVNELLHKMKE-KKVMP  555 (595)
Q Consensus       509 ~~~~~~~~~~--~~---~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~-~~~~p  555 (595)
                      ++++++....  +|   +...+..+...+...|++++|...|+++.. .|+.|
T Consensus       693 ~~~~al~~~~~~~~~~~~a~~~~~~a~~~~~~G~~~~A~~~y~~Al~~~~~~~  745 (1157)
T PRK11447        693 TFNRLIPQAKSQPPSMESALVLRDAARFEAQTGQPQQALETYKDAMVASGITP  745 (1157)
T ss_pred             HHHHHhhhCccCCcchhhHHHHHHHHHHHHHcCCHHHHHHHHHHHHhhcCCCC
Confidence            9999987531  12   224566678889999999999999999974 34443

>KOG4626 consensus O-linked N-acetylglucosamine transferase OGT [Carbohydrate transport and metabolism; Posttranslational modification, protein turnover, chaperones; Signal transduction mechanisms]

Probab=99.97  E-value=1.1e-26  Score=215.54  Aligned_cols=444  Identities=14%  Similarity=0.099  Sum_probs=363.6

Q ss_pred             hcccccccccccCCCChHHHHHHHHHHHHhCCCCCCHhhHHHHHHHHHcCCCchh-----HHhhCCCCCCHHHHHHHHHH
Q 040027           31 HFRDLTTREGDINVITPNEAFCIFDYMLRMHPSPPPVSSFNILLASLAKNKHYDT-----RLNATGLFPNLYTYNILINC  105 (595)
Q Consensus        31 ~~~~~~~~~~~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~-----~~~~~~~~~~~~~~~~l~~~  105 (595)
                      ...++.+++++-+.|+++.|.+...-+-+.+|.  +......+-..+.+..+.+.     ..-..-.+.-.++|+-+...
T Consensus        48 ~~~~l~lah~~yq~gd~~~a~~h~nmv~~~d~t--~~~~llll~ai~~q~~r~d~s~a~~~~a~r~~~q~ae~ysn~aN~  125 (966)
T KOG4626|consen   48 SDDRLELAHRLYQGGDYKQAEKHCNMVGQEDPT--NTERLLLLSAIFFQGSRLDKSSAGSLLAIRKNPQGAEAYSNLANI  125 (966)
T ss_pred             chhHHHHHHHHHhccCHHHHHHHHhHhhccCCC--cccceeeehhhhhcccchhhhhhhhhhhhhccchHHHHHHHHHHH
Confidence            344556778888999999999999999999987  55555566667777777776     11122233456888889999


Q ss_pred             HHhcCChhHHHHHHHHHHhCCCCCCHHHHHHHHHHHHhcCCHhHHHHHHHHHHhcCCCCCH-hhHHHHHHHHHhcCChhH
Q 040027          106 FCKIGRVSLGFIAFGRILRSCFTPNAATFNSLIKGLHAESRIMEAAALFTKLKAFGCEPNV-ITYNTLINGLCRTGHTMI  184 (595)
Q Consensus       106 ~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~~~-~~~~~l~~~~~~~g~~~~  184 (595)
                      +-..|++++|+.+++.+++.. +.....|..+..++...|+.+.|.+.|...++.  .|+. .....+...+-..|+..+
T Consensus       126 ~kerg~~~~al~~y~~aiel~-p~fida~inla~al~~~~~~~~a~~~~~~alql--nP~l~ca~s~lgnLlka~Grl~e  202 (966)
T KOG4626|consen  126 LKERGQLQDALALYRAAIELK-PKFIDAYINLAAALVTQGDLELAVQCFFEALQL--NPDLYCARSDLGNLLKAEGRLEE  202 (966)
T ss_pred             HHHhchHHHHHHHHHHHHhcC-chhhHHHhhHHHHHHhcCCCcccHHHHHHHHhc--CcchhhhhcchhHHHHhhcccch
Confidence            999999999999999999985 447889999999999999999999999999887  4443 344556666677899999


Q ss_pred             HHHHHHHHHhcCCCCCccccCcHHHHHHHHHHHHHcCCHhHHHHHHHHHhhCCCCCC-HhHHHHHHHHHHhcCCHHHHHH
Q 040027          185 ALNLFEEMANGNGEIGVVCKPNTVTYSTIIDGLCKEGFVDKAKALFLQMKDENINPD-VVTYNSLIHGLCHANDWNEAKR  263 (595)
Q Consensus       185 A~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~~-~~~~~~ll~~~~~~~~~~~A~~  263 (595)
                      |...+.+.....       +.-..+|..|...+...|+...|++.|++.++.+  |+ ...|..|...|...+.+++|..
T Consensus       203 a~~cYlkAi~~q-------p~fAiawsnLg~~f~~~Gei~~aiq~y~eAvkld--P~f~dAYiNLGnV~ke~~~~d~Avs  273 (966)
T KOG4626|consen  203 AKACYLKAIETQ-------PCFAIAWSNLGCVFNAQGEIWLAIQHYEEAVKLD--PNFLDAYINLGNVYKEARIFDRAVS  273 (966)
T ss_pred             hHHHHHHHHhhC-------CceeeeehhcchHHhhcchHHHHHHHHHHhhcCC--CcchHHHhhHHHHHHHHhcchHHHH
Confidence            999999988864       3336789999999999999999999999998863  43 5678899999999999999999


Q ss_pred             HHHHHHHCCCCC-CHhhHHHHHHHHHhcCChHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHhcC
Q 040027          264 LFIEMMDQGVQP-SVVTFNVIMDELCKNRKMDEASRLLDLMVQRGVRPNACTYNTLMDGFCLMGKINRAEELFGSMESMG  342 (595)
Q Consensus       264 ~~~~~~~~~~~~-~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~  342 (595)
                      .|......  .| ....+..+.-.|..+|.++-|++.|++.++.... -+..|+.+..++...|+..+|.+.|.+.+...
T Consensus       274 ~Y~rAl~l--rpn~A~a~gNla~iYyeqG~ldlAI~~Ykral~~~P~-F~~Ay~NlanALkd~G~V~ea~~cYnkaL~l~  350 (966)
T KOG4626|consen  274 CYLRALNL--RPNHAVAHGNLACIYYEQGLLDLAIDTYKRALELQPN-FPDAYNNLANALKDKGSVTEAVDCYNKALRLC  350 (966)
T ss_pred             HHHHHHhc--CCcchhhccceEEEEeccccHHHHHHHHHHHHhcCCC-chHHHhHHHHHHHhccchHHHHHHHHHHHHhC
Confidence            99988775  34 4567888888899999999999999999986322 36789999999999999999999999998874


Q ss_pred             CCCCHHHHHHHHHHHHhCCCHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHccCCHHHHHHHHHHHHHCCCCCC-HHHHH
Q 040027          343 CKHDDVSYNILINGYCKNKEVEEALSLYREMVSKGIKPTVVTYNTLFLGLFEIHQVEHALKLFDEMQRDGVAAD-TRTYT  421 (595)
Q Consensus       343 ~~~~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~-~~~~~  421 (595)
                       +....+.+.|...|...|.+++|..+|....+-.+. -....+.+...|-..|++++|+..|++.++-  .|+ ...++
T Consensus       351 -p~hadam~NLgni~~E~~~~e~A~~ly~~al~v~p~-~aaa~nNLa~i~kqqgnl~~Ai~~YkealrI--~P~fAda~~  426 (966)
T KOG4626|consen  351 -PNHADAMNNLGNIYREQGKIEEATRLYLKALEVFPE-FAAAHNNLASIYKQQGNLDDAIMCYKEALRI--KPTFADALS  426 (966)
T ss_pred             -CccHHHHHHHHHHHHHhccchHHHHHHHHHHhhChh-hhhhhhhHHHHHHhcccHHHHHHHHHHHHhc--CchHHHHHH
Confidence             556778899999999999999999999998875322 3456788888999999999999999999874  454 46788


Q ss_pred             HHHHHHHhcCCHHHHHHHHHHHHHcCCCcCHHHHHHHHHHHHhcCChHHHHHHHHhcccCCCCCC-HHHHHHHHHHHH
Q 040027          422 TFIDGLCKNGYIIEAVELFRTLRILKCELDIQAYNCLIDGLCKSGRLKFAWELFCSLPHGVLVPN-VVTYNIMIQGLC  498 (595)
Q Consensus       422 ~l~~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~p~-~~~~~~l~~~~~  498 (595)
                      .+...|...|+...|.+.+.+++..+ +.-...++.|...|...|+..+|+.-|++.+.  ++|| +..+..++.++-
T Consensus       427 NmGnt~ke~g~v~~A~q~y~rAI~~n-Pt~AeAhsNLasi~kDsGni~~AI~sY~~aLk--lkPDfpdA~cNllh~lq  501 (966)
T KOG4626|consen  427 NMGNTYKEMGDVSAAIQCYTRAIQIN-PTFAEAHSNLASIYKDSGNIPEAIQSYRTALK--LKPDFPDAYCNLLHCLQ  501 (966)
T ss_pred             hcchHHHHhhhHHHHHHHHHHHHhcC-cHHHHHHhhHHHHhhccCCcHHHHHHHHHHHc--cCCCCchhhhHHHHHHH
Confidence            89999999999999999999999765 55577889999999999999999999999988  7887 567777776554

>PRK09782 bacteriophage N4 receptor, outer membrane subunit; Provisional

Probab=99.96  E-value=2.6e-23  Score=217.84  Aligned_cols=504  Identities=13%  Similarity=0.043  Sum_probs=331.1

Q ss_pred             cCCCChHHHHHHHHHHHHhCCCCCCHhhHHHHHHHHHcCCCchh--HHhhC--CCCC-CHHHHHHHHHHHHhcCChhHHH
Q 040027           42 INVITPNEAFCIFDYMLRMHPSPPPVSSFNILLASLAKNKHYDT--RLNAT--GLFP-NLYTYNILINCFCKIGRVSLGF  116 (595)
Q Consensus        42 ~~~~~~~~A~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~--~~~~~--~~~~-~~~~~~~l~~~~~~~g~~~~A~  116 (595)
                      ...|++++|+..|+.+++.+|+  ++.++..+..+|...|+.++  .....  ...| |...+..+ ...   +++++|.
T Consensus        55 ~~~Gd~~~A~~~l~~Al~~dP~--n~~~~~~LA~~yl~~g~~~~A~~~~~kAv~ldP~n~~~~~~L-a~i---~~~~kA~  128 (987)
T PRK09782         55 QKNNDEATAIREFEYIHQQVPD--NIPLTLYLAEAYRHFGHDDRARLLLEDQLKRHPGDARLERSL-AAI---PVEVKSV  128 (987)
T ss_pred             HhCCCHHHHHHHHHHHHHhCCC--CHHHHHHHHHHHHHCCCHHHHHHHHHHHHhcCcccHHHHHHH-HHh---ccChhHH
Confidence            4459999999999999999999  79999999999999999998  22222  2233 44444444 222   8999999


Q ss_pred             HHHHHHHhCCCCCCHHHHHHHHHH--------HHhcCCHhHHHHHHHHHHhcCCCCCHhhHHHH-HHHHHhcCChhHHHH
Q 040027          117 IAFGRILRSCFTPNAATFNSLIKG--------LHAESRIMEAAALFTKLKAFGCEPNVITYNTL-INGLCRTGHTMIALN  187 (595)
Q Consensus       117 ~~~~~~~~~~~~~~~~~~~~l~~~--------~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~~l-~~~~~~~g~~~~A~~  187 (595)
                      .+++++.... +-+..++..+...        |.+.   ++|.+.++ .......|+..+.... ...|.+.|++++|+.
T Consensus       129 ~~ye~l~~~~-P~n~~~~~~la~~~~~~~~l~y~q~---eqAl~AL~-lr~~~~~~~~~vL~L~~~rlY~~l~dw~~Ai~  203 (987)
T PRK09782        129 TTVEELLAQQ-KACDAVPTLRCRSEVGQNALRLAQL---PVARAQLN-DATFAASPEGKTLRTDLLQRAIYLKQWSQADT  203 (987)
T ss_pred             HHHHHHHHhC-CCChhHHHHHHHHhhccchhhhhhH---HHHHHHHH-HhhhCCCCCcHHHHHHHHHHHHHHhCHHHHHH
Confidence            9999999884 3345555555544        4444   44444444 3333233344444444 778888888888888


Q ss_pred             HHHHHHhcCCCCCccccCcHHHHHHHHHHHHH-cCCHhHHHHHHHHHhhCCCCCCHhHHHHHHHHHHhcCCHHHHHHHHH
Q 040027          188 LFEEMANGNGEIGVVCKPNTVTYSTIIDGLCK-EGFVDKAKALFLQMKDENINPDVVTYNSLIHGLCHANDWNEAKRLFI  266 (595)
Q Consensus       188 ~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~-~g~~~~A~~~~~~~~~~~~~~~~~~~~~ll~~~~~~~~~~~A~~~~~  266 (595)
                      ++.++.+.+       +.+......+..+|.. .++ +++..+++..    .+.+...+..++..|.+.|+.++|.+++.
T Consensus       204 lL~~L~k~~-------pl~~~~~~~L~~ay~q~l~~-~~a~al~~~~----lk~d~~l~~ala~~yi~~G~~~~A~~~L~  271 (987)
T PRK09782        204 LYNEARQQN-------TLSAAERRQWFDVLLAGQLD-DRLLALQSQG----IFTDPQSRITYATALAYRGEKARLQHYLI  271 (987)
T ss_pred             HHHHHHhcC-------CCCHHHHHHHHHHHHHhhCH-HHHHHHhchh----cccCHHHHHHHHHHHHHCCCHHHHHHHHH
Confidence            888887765       3334444445455554 244 4444443321    11245555555555555555555555554


Q ss_pred             HHHHCCCC-C----------------------------------------------------------------------
Q 040027          267 EMMDQGVQ-P----------------------------------------------------------------------  275 (595)
Q Consensus       267 ~~~~~~~~-~----------------------------------------------------------------------  275 (595)
                      ++...-.. |                                                                      
T Consensus       272 ~~~~~~~~~~~~~~~~~~l~r~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~r~~~  351 (987)
T PRK09782        272 ENKPLFTTDAQEKSWLYLLSKYSANPVQALANYTVQFADNRQYVVGATLPVLLKEGQYDAAQKLLATLPANEMLEERYAV  351 (987)
T ss_pred             hCcccccCCCccHHHHHHHHhccCchhhhccchhhhhHHHHHHHHHHHHHHHHhccHHHHHHHHhcCCCcchHHHHHHhh
Confidence            44321000 0                                                                      


Q ss_pred             -----------------------CHhhHHHHHHHHHhcCChHHHHHHHHHHHHC--CCCCCHHHHHHHHHHHHhcCC---
Q 040027          276 -----------------------SVVTFNVIMDELCKNRKMDEASRLLDLMVQR--GVRPNACTYNTLMDGFCLMGK---  327 (595)
Q Consensus       276 -----------------------~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~--~~~~~~~~~~~l~~~~~~~~~---  327 (595)
                                             +......+.....+.|+.++|.++++.....  +...+......++..|.+.+.   
T Consensus       352 ~~~~~~~~~~~~~~~~~y~~~~~~~~~l~q~~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~l~~~l~~~~~~~~~~~~  431 (987)
T PRK09782        352 SVATRNKAEALRLARLLYQQEPANLTRLDQLTWQLMQNGQSREAADLLLQRYPFQGDARLSQTLMARLASLLESHPYLAT  431 (987)
T ss_pred             ccccCchhHHHHHHHHHHhcCCCCHHHHHHHHHHHHHcccHHHHHHHHHHhcCCCcccccCHHHHHHHHHHHHhCCcccc
Confidence                                   1111111222233455666666666655542  112233344456666666544   


Q ss_pred             HHHHHHH-------------------------HHHHHhcCCCC--CHHHHHHHHHHHHhCCCHHHHHHHHHHHHHCCCCC
Q 040027          328 INRAEEL-------------------------FGSMESMGCKH--DDVSYNILINGYCKNKEVEEALSLYREMVSKGIKP  380 (595)
Q Consensus       328 ~~~a~~~-------------------------~~~~~~~~~~~--~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~~~~~~  380 (595)
                      ..++..+                         +..+... .++  +...|..+..++.. ++.++|+..+.+.....  |
T Consensus       432 ~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~al~~-~p~~~~~~a~~~LG~~l~~-~~~~eAi~a~~~Al~~~--P  507 (987)
T PRK09782        432 PAKVAILSKPLPLAEQRQWQSQLPGIADNCPAIVRLLGD-MSPSYDAAAWNRLAKCYRD-TLPGVALYAWLQAEQRQ--P  507 (987)
T ss_pred             hHHHHHhccccccchhHHHHhhhhhhhhhHHHHHHhccc-CCCCCCHHHHHHHHHHHHh-CCcHHHHHHHHHHHHhC--C
Confidence            2222222                         1111111 133  56677777777776 78888999888877663  4


Q ss_pred             CHHHHHHHHHHHHccCCHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCcCHHHHHHHHH
Q 040027          381 TVVTYNTLFLGLFEIHQVEHALKLFDEMQRDGVAADTRTYTTFIDGLCKNGYIIEAVELFRTLRILKCELDIQAYNCLID  460 (595)
Q Consensus       381 ~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~~l~~  460 (595)
                      +......+...+...|++++|...|+++...  +|+...+..+..++.+.|++++|...++++++.. +.+...+..+..
T Consensus       508 d~~~~L~lA~al~~~Gr~eeAi~~~rka~~~--~p~~~a~~~la~all~~Gd~~eA~~~l~qAL~l~-P~~~~l~~~La~  584 (987)
T PRK09782        508 DAWQHRAVAYQAYQVEDYATALAAWQKISLH--DMSNEDLLAAANTAQAAGNGAARDRWLQQAEQRG-LGDNALYWWLHA  584 (987)
T ss_pred             chHHHHHHHHHHHHCCCHHHHHHHHHHHhcc--CCCcHHHHHHHHHHHHCCCHHHHHHHHHHHHhcC-CccHHHHHHHHH
Confidence            5444444455556899999999999987654  4555556677778888999999999999998765 444444445555


Q ss_pred             HHHhcCChHHHHHHHHhcccCCCCCCHHHHHHHHHHHHhcCChhHHHHHHHHHHHcCCCCCHHHHHHHHHHHHHcCChhH
Q 040027          461 GLCKSGRLKFAWELFCSLPHGVLVPNVVTYNIMIQGLCNDGQMDKARDLFLDMEENAAAPDVITFDMLIHGFIRINEPSK  540 (595)
Q Consensus       461 ~~~~~g~~~~A~~~~~~~~~~~~~p~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~  540 (595)
                      .....|++++|...+++..+  +.|+...+..+..++.+.|++++|+..++++++.. +.+...+..+..++...|++++
T Consensus       585 ~l~~~Gr~~eAl~~~~~AL~--l~P~~~a~~~LA~~l~~lG~~deA~~~l~~AL~l~-Pd~~~a~~nLG~aL~~~G~~ee  661 (987)
T PRK09782        585 QRYIPGQPELALNDLTRSLN--IAPSANAYVARATIYRQRHNVPAAVSDLRAALELE-PNNSNYQAALGYALWDSGDIAQ  661 (987)
T ss_pred             HHHhCCCHHHHHHHHHHHHH--hCCCHHHHHHHHHHHHHCCCHHHHHHHHHHHHHhC-CCCHHHHHHHHHHHHHCCCHHH
Confidence            55566999999999999988  56788888899999999999999999999999875 5567788888889999999999


Q ss_pred             HHHHHHHHHHCCCCC-CHHHHHHHHHHHHhcCcccccchHH
Q 040027          541 VNELLHKMKEKKVMP-DASIVSIVVDLLVKNEISLKSLPSF  580 (595)
Q Consensus       541 A~~~~~~~~~~~~~p-~~~~~~~l~~~~~~~g~~~~~i~~~  580 (595)
                      |...++++.+.  .| ++..+..++.++...|++++++..+
T Consensus       662 Ai~~l~~AL~l--~P~~~~a~~nLA~al~~lGd~~eA~~~l  700 (987)
T PRK09782        662 SREMLERAHKG--LPDDPALIRQLAYVNQRLDDMAATQHYA  700 (987)
T ss_pred             HHHHHHHHHHh--CCCCHHHHHHHHHHHHHCCCHHHHHHHH
Confidence            99999999974  35 6788999999999999999555544

>KOG4626 consensus O-linked N-acetylglucosamine transferase OGT [Carbohydrate transport and metabolism; Posttranslational modification, protein turnover, chaperones; Signal transduction mechanisms]

Probab=99.96  E-value=2.8e-25  Score=206.45  Aligned_cols=479  Identities=15%  Similarity=0.086  Sum_probs=381.6

Q ss_pred             HHHHHHHHhCCCCCCHhhHHHHHHHHHcCCCchhHHhhCCCCCCHHHHHHHHHHHHhcCChhHHHHHHHHHHhCCCCCCH
Q 040027           52 CIFDYMLRMHPSPPPVSSFNILLASLAKNKHYDTRLNATGLFPNLYTYNILINCFCKIGRVSLGFIAFGRILRSCFTPNA  131 (595)
Q Consensus        52 ~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~~~  131 (595)
                      +.|...+..+++   ...-+.++.-+.+....            ......+..-..+.|++.+|++.-..+-+.+ +.+.
T Consensus        19 ~~~~~~ld~~~~---s~~s~~v~qq~~~t~~~------------~~~~l~lah~~yq~gd~~~a~~h~nmv~~~d-~t~~   82 (966)
T KOG4626|consen   19 EAFSRKLDQSVS---SSGSSSVLQQFNKTHEG------------SDDRLELAHRLYQGGDYKQAEKHCNMVGQED-PTNT   82 (966)
T ss_pred             HHHHHHhccCcc---cccchHHHHHhccCCcc------------chhHHHHHHHHHhccCHHHHHHHHhHhhccC-CCcc
Confidence            666777766664   22233444433333221            1124567777888999999999887776664 3333


Q ss_pred             HHHHHHHHHHHhcCCHhHHHHHHHHHHhcCCCCCHhhHHHHHHHHHhcCChhHHHHHHHHHHhcCCCCCccccCcHHHHH
Q 040027          132 ATFNSLIKGLHAESRIMEAAALFTKLKAFGCEPNVITYNTLINGLCRTGHTMIALNLFEEMANGNGEIGVVCKPNTVTYS  211 (595)
Q Consensus       132 ~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~~~~~~~  211 (595)
                      .....+-..+.+..+.+....--....+.. +.-.++|..+...+-..|++++|+..++.+.+..       +.....|.
T Consensus        83 ~~llll~ai~~q~~r~d~s~a~~~~a~r~~-~q~ae~ysn~aN~~kerg~~~~al~~y~~aiel~-------p~fida~i  154 (966)
T KOG4626|consen   83 ERLLLLSAIFFQGSRLDKSSAGSLLAIRKN-PQGAEAYSNLANILKERGQLQDALALYRAAIELK-------PKFIDAYI  154 (966)
T ss_pred             cceeeehhhhhcccchhhhhhhhhhhhhcc-chHHHHHHHHHHHHHHhchHHHHHHHHHHHHhcC-------chhhHHHh
Confidence            443444455677777776665544444442 4467899999999999999999999999999875       45688999


Q ss_pred             HHHHHHHHcCCHhHHHHHHHHHhhCCCCCCHhHH-HHHHHHHHhcCCHHHHHHHHHHHHHCCCCCC-HhhHHHHHHHHHh
Q 040027          212 TIIDGLCKEGFVDKAKALFLQMKDENINPDVVTY-NSLIHGLCHANDWNEAKRLFIEMMDQGVQPS-VVTFNVIMDELCK  289 (595)
Q Consensus       212 ~l~~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~-~~ll~~~~~~~~~~~A~~~~~~~~~~~~~~~-~~~~~~l~~~~~~  289 (595)
                      .+..++...|+.+.|.+.|.+..+.  .|+.... ..+...+...|+.++|...|.+.+..  .|. ...|..+.-.+..
T Consensus       155 nla~al~~~~~~~~a~~~~~~alql--nP~l~ca~s~lgnLlka~Grl~ea~~cYlkAi~~--qp~fAiawsnLg~~f~~  230 (966)
T KOG4626|consen  155 NLAAALVTQGDLELAVQCFFEALQL--NPDLYCARSDLGNLLKAEGRLEEAKACYLKAIET--QPCFAIAWSNLGCVFNA  230 (966)
T ss_pred             hHHHHHHhcCCCcccHHHHHHHHhc--CcchhhhhcchhHHHHhhcccchhHHHHHHHHhh--CCceeeeehhcchHHhh
Confidence            9999999999999999999998885  4554443 34556666789999999999998875  333 5678899999999


Q ss_pred             cCChHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHhcCCCCCHHHHHHHHHHHHhCCCHHHHHHH
Q 040027          290 NRKMDEASRLLDLMVQRGVRPNACTYNTLMDGFCLMGKINRAEELFGSMESMGCKHDDVSYNILINGYCKNKEVEEALSL  369 (595)
Q Consensus       290 ~g~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~A~~~  369 (595)
                      +|+...|+..|++.++.+.. -...|..|...|...+.++.|...|.+..... +.....+..+...|...|..+-|+..
T Consensus       231 ~Gei~~aiq~y~eAvkldP~-f~dAYiNLGnV~ke~~~~d~Avs~Y~rAl~lr-pn~A~a~gNla~iYyeqG~ldlAI~~  308 (966)
T KOG4626|consen  231 QGEIWLAIQHYEEAVKLDPN-FLDAYINLGNVYKEARIFDRAVSCYLRALNLR-PNHAVAHGNLACIYYEQGLLDLAIDT  308 (966)
T ss_pred             cchHHHHHHHHHHhhcCCCc-chHHHhhHHHHHHHHhcchHHHHHHHHHHhcC-CcchhhccceEEEEeccccHHHHHHH
Confidence            99999999999999986322 35678889999999999999999999988763 45566888888999999999999999


Q ss_pred             HHHHHHCCCCCCHHHHHHHHHHHHccCCHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHHcCCC
Q 040027          370 YREMVSKGIKPTVVTYNTLFLGLFEIHQVEHALKLFDEMQRDGVAADTRTYTTFIDGLCKNGYIIEAVELFRTLRILKCE  449 (595)
Q Consensus       370 ~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~  449 (595)
                      |++.++..+. -...|+.+..++-..|++.+|...|.+.+... +......+.+...|...|.+++|..+|....+.. +
T Consensus       309 Ykral~~~P~-F~~Ay~NlanALkd~G~V~ea~~cYnkaL~l~-p~hadam~NLgni~~E~~~~e~A~~ly~~al~v~-p  385 (966)
T KOG4626|consen  309 YKRALELQPN-FPDAYNNLANALKDKGSVTEAVDCYNKALRLC-PNHADAMNNLGNIYREQGKIEEATRLYLKALEVF-P  385 (966)
T ss_pred             HHHHHhcCCC-chHHHhHHHHHHHhccchHHHHHHHHHHHHhC-CccHHHHHHHHHHHHHhccchHHHHHHHHHHhhC-h
Confidence            9999987443 46789999999999999999999999999873 5566788899999999999999999999998764 4


Q ss_pred             cCHHHHHHHHHHHHhcCChHHHHHHHHhcccCCCCCC-HHHHHHHHHHHHhcCChhHHHHHHHHHHHcCCCCC-HHHHHH
Q 040027          450 LDIQAYNCLIDGLCKSGRLKFAWELFCSLPHGVLVPN-VVTYNIMIQGLCNDGQMDKARDLFLDMEENAAAPD-VITFDM  527 (595)
Q Consensus       450 ~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~p~-~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~~-~~~~~~  527 (595)
                      .-...++.|...|-.+|++++|+..|++.++  +.|+ ...++.+...|-..|+.+.|+..+.+++..  .|. ...++.
T Consensus       386 ~~aaa~nNLa~i~kqqgnl~~Ai~~Ykealr--I~P~fAda~~NmGnt~ke~g~v~~A~q~y~rAI~~--nPt~AeAhsN  461 (966)
T KOG4626|consen  386 EFAAAHNNLASIYKQQGNLDDAIMCYKEALR--IKPTFADALSNMGNTYKEMGDVSAAIQCYTRAIQI--NPTFAEAHSN  461 (966)
T ss_pred             hhhhhhhhHHHHHHhcccHHHHHHHHHHHHh--cCchHHHHHHhcchHHHHhhhHHHHHHHHHHHHhc--CcHHHHHHhh
Confidence            4467889999999999999999999999998  8888 578999999999999999999999999985  455 578899


Q ss_pred             HHHHHHHcCChhHHHHHHHHHHHCCCCCC-HHHHHHHHHHHHh
Q 040027          528 LIHGFIRINEPSKVNELLHKMKEKKVMPD-ASIVSIVVDLLVK  569 (595)
Q Consensus       528 l~~~~~~~g~~~~A~~~~~~~~~~~~~p~-~~~~~~l~~~~~~  569 (595)
                      |...|-.+|+..+|++-|++.++  ++|| +..+.-++.++.=
T Consensus       462 Lasi~kDsGni~~AI~sY~~aLk--lkPDfpdA~cNllh~lq~  502 (966)
T KOG4626|consen  462 LASIYKDSGNIPEAIQSYRTALK--LKPDFPDAYCNLLHCLQI  502 (966)
T ss_pred             HHHHhhccCCcHHHHHHHHHHHc--cCCCCchhhhHHHHHHHH
Confidence            99999999999999999999997  5676 4555555555443

>KOG2002 consensus TPR-containing nuclear phosphoprotein that regulates K(+) uptake [Inorganic ion transport and metabolism]

Probab=99.96  E-value=9.6e-24  Score=206.53  Aligned_cols=508  Identities=14%  Similarity=0.071  Sum_probs=397.4

Q ss_pred             hhhcccccccccccCCCChHHHHHHHHHHHHhCCCCCCHhhHHHHHHHHHcCCCchh-----HHhhCC---CCCCHHHHH
Q 040027           29 LVHFRDLTTREGDINVITPNEAFCIFDYMLRMHPSPPPVSSFNILLASLAKNKHYDT-----RLNATG---LFPNLYTYN  100 (595)
Q Consensus        29 ~~~~~~~~~~~~~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~-----~~~~~~---~~~~~~~~~  100 (595)
                      ...-.+.++++++.+.|+.+.|+..|.++++++|.  ++.++-.|...-....+.+.     .+....   -.-+|.+.+
T Consensus       197 ~~aD~rIgig~Cf~kl~~~~~a~~a~~ralqLdp~--~v~alv~L~~~~l~~~d~~s~~~~~~ll~~ay~~n~~nP~~l~  274 (1018)
T KOG2002|consen  197 CKADVRIGIGHCFWKLGMSEKALLAFERALQLDPT--CVSALVALGEVDLNFNDSDSYKKGVQLLQRAYKENNENPVALN  274 (1018)
T ss_pred             cCCCccchhhhHHHhccchhhHHHHHHHHHhcChh--hHHHHHHHHHHHHHccchHHHHHHHHHHHHHHhhcCCCcHHHH
Confidence            34445567889999999999999999999999997  66666555555555554443     111111   235888899


Q ss_pred             HHHHHHHhcCChhHHHHHHHHHHhCCCC--CCHHHHHHHHHHHHhcCCHhHHHHHHHHHHhcCCCCCHhhHHHHHHHHHh
Q 040027          101 ILINCFCKIGRVSLGFIAFGRILRSCFT--PNAATFNSLIKGLHAESRIMEAAALFTKLKAFGCEPNVITYNTLINGLCR  178 (595)
Q Consensus       101 ~l~~~~~~~g~~~~A~~~~~~~~~~~~~--~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~~l~~~~~~  178 (595)
                      .|...|...|++..+..+...+......  .-...|..+.++|...|++++|...|-+..+....-....+..++..+..
T Consensus       275 ~LAn~fyfK~dy~~v~~la~~ai~~t~~~~~~aes~Y~~gRs~Ha~Gd~ekA~~yY~~s~k~~~d~~~l~~~GlgQm~i~  354 (1018)
T KOG2002|consen  275 HLANHFYFKKDYERVWHLAEHAIKNTENKSIKAESFYQLGRSYHAQGDFEKAFKYYMESLKADNDNFVLPLVGLGQMYIK  354 (1018)
T ss_pred             HHHHHHhhcccHHHHHHHHHHHHHhhhhhHHHHHHHHHHHHHHHhhccHHHHHHHHHHHHccCCCCccccccchhHHHHH
Confidence            9999999999999999999999886311  22445888999999999999999999998877432224456678899999


Q ss_pred             cCChhHHHHHHHHHHhcCCCCCccccCcHHHHHHHHHHHHHcC----CHhHHHHHHHHHhhCCCCCCHhHHHHHHHHHHh
Q 040027          179 TGHTMIALNLFEEMANGNGEIGVVCKPNTVTYSTIIDGLCKEG----FVDKAKALFLQMKDENINPDVVTYNSLIHGLCH  254 (595)
Q Consensus       179 ~g~~~~A~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g----~~~~A~~~~~~~~~~~~~~~~~~~~~ll~~~~~  254 (595)
                      .|+.+.+...|+.+....       |.+..+...|...|...+    ..+.|..++.+..+.. +.|...|..+...+..
T Consensus       355 ~~dle~s~~~fEkv~k~~-------p~~~etm~iLG~Lya~~~~~~~~~d~a~~~l~K~~~~~-~~d~~a~l~laql~e~  426 (1018)
T KOG2002|consen  355 RGDLEESKFCFEKVLKQL-------PNNYETMKILGCLYAHSAKKQEKRDKASNVLGKVLEQT-PVDSEAWLELAQLLEQ  426 (1018)
T ss_pred             hchHHHHHHHHHHHHHhC-------cchHHHHHHHHhHHHhhhhhhHHHHHHHHHHHHHHhcc-cccHHHHHHHHHHHHh
Confidence            999999999999999875       667888888888888875    5677888888877763 4578889888888777


Q ss_pred             cCCHHHHHHHHHHHH----HCCCCCCHhhHHHHHHHHHhcCChHHHHHHHHHHHHC---CCCC------CHHHHHHHHHH
Q 040027          255 ANDWNEAKRLFIEMM----DQGVQPSVVTFNVIMDELCKNRKMDEASRLLDLMVQR---GVRP------NACTYNTLMDG  321 (595)
Q Consensus       255 ~~~~~~A~~~~~~~~----~~~~~~~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~---~~~~------~~~~~~~l~~~  321 (595)
                      .+-+.. +..|..+.    ..+.++.+...|.+...+...|+++.|...|......   ...+      +..+-..+.++
T Consensus       427 ~d~~~s-L~~~~~A~d~L~~~~~~ip~E~LNNvaslhf~~g~~~~A~~~f~~A~~~~~~~~n~de~~~~~lt~~YNlarl  505 (1018)
T KOG2002|consen  427 TDPWAS-LDAYGNALDILESKGKQIPPEVLNNVASLHFRLGNIEKALEHFKSALGKLLEVANKDEGKSTNLTLKYNLARL  505 (1018)
T ss_pred             cChHHH-HHHHHHHHHHHHHcCCCCCHHHHHhHHHHHHHhcChHHHHHHHHHHhhhhhhhcCccccccchhHHHHHHHHH
Confidence            665555 77776554    3455577889999999999999999999999988765   1122      22344557777


Q ss_pred             HHhcCCHHHHHHHHHHHHhcCCCCCHHHHHHHHHHHHhCCCHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHccCCHHHH
Q 040027          322 FCLMGKINRAEELFGSMESMGCKHDDVSYNILINGYCKNKEVEEALSLYREMVSKGIKPTVVTYNTLFLGLFEIHQVEHA  401 (595)
Q Consensus       322 ~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a  401 (595)
                      .-..++.+.|.+.|..+.+.. |.-+..|..++.+....++..+|...+.+.....- .++..+..+...+.....+..|
T Consensus       506 ~E~l~~~~~A~e~Yk~Ilkeh-p~YId~ylRl~~ma~~k~~~~ea~~~lk~~l~~d~-~np~arsl~G~~~l~k~~~~~a  583 (1018)
T KOG2002|consen  506 LEELHDTEVAEEMYKSILKEH-PGYIDAYLRLGCMARDKNNLYEASLLLKDALNIDS-SNPNARSLLGNLHLKKSEWKPA  583 (1018)
T ss_pred             HHhhhhhhHHHHHHHHHHHHC-chhHHHHHHhhHHHHhccCcHHHHHHHHHHHhccc-CCcHHHHHHHHHHHhhhhhccc
Confidence            888899999999999998863 22334555555444556788999999999887543 3667777777788888889888


Q ss_pred             HHHHHHHHHC-CCCCCHHHHHHHHHHHHh------------cCCHHHHHHHHHHHHHcCCCcCHHHHHHHHHHHHhcCCh
Q 040027          402 LKLFDEMQRD-GVAADTRTYTTFIDGLCK------------NGYIIEAVELFRTLRILKCELDIQAYNCLIDGLCKSGRL  468 (595)
Q Consensus       402 ~~~~~~~~~~-~~~~~~~~~~~l~~~~~~------------~g~~~~A~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~  468 (595)
                      .+-|..+.+. ...+|......|...|.+            .+..++|+++|.++++.. |.|..+-+.++-+++..|++
T Consensus       584 ~k~f~~i~~~~~~~~D~YsliaLGN~~~~~l~~~~rn~ek~kk~~~KAlq~y~kvL~~d-pkN~yAANGIgiVLA~kg~~  662 (1018)
T KOG2002|consen  584 KKKFETILKKTSTKTDAYSLIALGNVYIQALHNPSRNPEKEKKHQEKALQLYGKVLRND-PKNMYAANGIGIVLAEKGRF  662 (1018)
T ss_pred             ccHHHHHHhhhccCCchhHHHHhhHHHHHHhcccccChHHHHHHHHHHHHHHHHHHhcC-cchhhhccchhhhhhhccCc
Confidence            8877777654 234677777777776653            345788999999999877 77889999999999999999


Q ss_pred             HHHHHHHHhcccCCCCCCHHHHHHHHHHHHhcCChhHHHHHHHHHHHc-CCCCCHHHHHHHHHHHHHcCChhHHHHHHHH
Q 040027          469 KFAWELFCSLPHGVLVPNVVTYNIMIQGLCNDGQMDKARDLFLDMEEN-AAAPDVITFDMLIHGFIRINEPSKVNELLHK  547 (595)
Q Consensus       469 ~~A~~~~~~~~~~~~~p~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~-~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~  547 (595)
                      .+|..+|.+..+.. ..+..+|..++.+|...|+|..|+++|+..... ....+......|..++.+.|.+.+|.+.+..
T Consensus       663 ~~A~dIFsqVrEa~-~~~~dv~lNlah~~~e~~qy~~AIqmYe~~lkkf~~~~~~~vl~~Lara~y~~~~~~eak~~ll~  741 (1018)
T KOG2002|consen  663 SEARDIFSQVREAT-SDFEDVWLNLAHCYVEQGQYRLAIQMYENCLKKFYKKNRSEVLHYLARAWYEAGKLQEAKEALLK  741 (1018)
T ss_pred             hHHHHHHHHHHHHH-hhCCceeeeHHHHHHHHHHHHHHHHHHHHHHHHhcccCCHHHHHHHHHHHHHhhhHHHHHHHHHH
Confidence            99999999998853 235678999999999999999999999998875 3345678889999999999999999999999


Q ss_pred             HHHC
Q 040027          548 MKEK  551 (595)
Q Consensus       548 ~~~~  551 (595)
                      +...
T Consensus       742 a~~~  745 (1018)
T KOG2002|consen  742 ARHL  745 (1018)
T ss_pred             HHHh
Confidence            8864

>PRK09782 bacteriophage N4 receptor, outer membrane subunit; Provisional

Probab=99.94  E-value=5.1e-21  Score=200.71  Aligned_cols=314  Identities=12%  Similarity=0.046  Sum_probs=234.4

Q ss_pred             HHhcCCHHHHHHHHHHHHHC-C-CCCCHhhHHHHHHHHHhcCC---hHHH----------------------HHHHHHHH
Q 040027          252 LCHANDWNEAKRLFIEMMDQ-G-VQPSVVTFNVIMDELCKNRK---MDEA----------------------SRLLDLMV  304 (595)
Q Consensus       252 ~~~~~~~~~A~~~~~~~~~~-~-~~~~~~~~~~l~~~~~~~g~---~~~a----------------------~~~~~~~~  304 (595)
                      ..+.|+.++|.++|...... + -.++......++..|...+.   ...+                      ...++...
T Consensus       386 ~~~~~~~~~a~~~~~~~~~~~~~~~~~~~l~~~l~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~  465 (987)
T PRK09782        386 LMQNGQSREAADLLLQRYPFQGDARLSQTLMARLASLLESHPYLATPAKVAILSKPLPLAEQRQWQSQLPGIADNCPAIV  465 (987)
T ss_pred             HHHcccHHHHHHHHHHhcCCCcccccCHHHHHHHHHHHHhCCcccchHHHHHhccccccchhHHHHhhhhhhhhhHHHHH
Confidence            34566777777777776652 1 12233344466777776655   2222                      22222222


Q ss_pred             HC-C-CCC--CHHHHHHHHHHHHhcCCHHHHHHHHHHHHhcCCCCCHHHHHHHHHHHHhCCCHHHHHHHHHHHHHCCCCC
Q 040027          305 QR-G-VRP--NACTYNTLMDGFCLMGKINRAEELFGSMESMGCKHDDVSYNILINGYCKNKEVEEALSLYREMVSKGIKP  380 (595)
Q Consensus       305 ~~-~-~~~--~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~~~~~~  380 (595)
                      .. + .++  +...+..+..++.. ++.++|+..+.+....  .|+......+...+...|++++|...|+++...  +|
T Consensus       466 ~al~~~p~~~~~~a~~~LG~~l~~-~~~~eAi~a~~~Al~~--~Pd~~~~L~lA~al~~~Gr~eeAi~~~rka~~~--~p  540 (987)
T PRK09782        466 RLLGDMSPSYDAAAWNRLAKCYRD-TLPGVALYAWLQAEQR--QPDAWQHRAVAYQAYQVEDYATALAAWQKISLH--DM  540 (987)
T ss_pred             HhcccCCCCCCHHHHHHHHHHHHh-CCcHHHHHHHHHHHHh--CCchHHHHHHHHHHHHCCCHHHHHHHHHHHhcc--CC
Confidence            21 1 133  56677888888776 8888999988888766  355544444556667899999999999998665  34


Q ss_pred             CHHHHHHHHHHHHccCCHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCcCHHHHHHHHH
Q 040027          381 TVVTYNTLFLGLFEIHQVEHALKLFDEMQRDGVAADTRTYTTFIDGLCKNGYIIEAVELFRTLRILKCELDIQAYNCLID  460 (595)
Q Consensus       381 ~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~~l~~  460 (595)
                      ....+..+...+...|+.++|...+++..+.+ +.....+..+...+...|++++|...++++++..  |+...+..+..
T Consensus       541 ~~~a~~~la~all~~Gd~~eA~~~l~qAL~l~-P~~~~l~~~La~~l~~~Gr~~eAl~~~~~AL~l~--P~~~a~~~LA~  617 (987)
T PRK09782        541 SNEDLLAAANTAQAAGNGAARDRWLQQAEQRG-LGDNALYWWLHAQRYIPGQPELALNDLTRSLNIA--PSANAYVARAT  617 (987)
T ss_pred             CcHHHHHHHHHHHHCCCHHHHHHHHHHHHhcC-CccHHHHHHHHHHHHhCCCHHHHHHHHHHHHHhC--CCHHHHHHHHH
Confidence            55556777788899999999999999999864 3344444444445556799999999999999874  56889999999


Q ss_pred             HHHhcCChHHHHHHHHhcccCCCCCC-HHHHHHHHHHHHhcCChhHHHHHHHHHHHcCCCCCHHHHHHHHHHHHHcCChh
Q 040027          461 GLCKSGRLKFAWELFCSLPHGVLVPN-VVTYNIMIQGLCNDGQMDKARDLFLDMEENAAAPDVITFDMLIHGFIRINEPS  539 (595)
Q Consensus       461 ~~~~~g~~~~A~~~~~~~~~~~~~p~-~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~  539 (595)
                      ++.+.|++++|+..+++...  ..|+ ...++.+..++...|++++|+..++++++.. +.+...+..+..++...|+++
T Consensus       618 ~l~~lG~~deA~~~l~~AL~--l~Pd~~~a~~nLG~aL~~~G~~eeAi~~l~~AL~l~-P~~~~a~~nLA~al~~lGd~~  694 (987)
T PRK09782        618 IYRQRHNVPAAVSDLRAALE--LEPNNSNYQAALGYALWDSGDIAQSREMLERAHKGL-PDDPALIRQLAYVNQRLDDMA  694 (987)
T ss_pred             HHHHCCCHHHHHHHHHHHHH--hCCCCHHHHHHHHHHHHHCCCHHHHHHHHHHHHHhC-CCCHHHHHHHHHHHHHCCCHH
Confidence            99999999999999999998  4565 6788889999999999999999999999974 557788999999999999999


Q ss_pred             HHHHHHHHHHHCCCCCC-HHHHHHHHHHHHhcCcccccch
Q 040027          540 KVNELLHKMKEKKVMPD-ASIVSIVVDLLVKNEISLKSLP  578 (595)
Q Consensus       540 ~A~~~~~~~~~~~~~p~-~~~~~~l~~~~~~~g~~~~~i~  578 (595)
                      +|...++++.+.  .|+ ..+....++.+.+..+++.+.+
T Consensus       695 eA~~~l~~Al~l--~P~~a~i~~~~g~~~~~~~~~~~a~~  732 (987)
T PRK09782        695 ATQHYARLVIDD--IDNQALITPLTPEQNQQRFNFRRLHE  732 (987)
T ss_pred             HHHHHHHHHHhc--CCCCchhhhhhhHHHHHHHHHHHHHH
Confidence            999999999974  464 4677777777777776664433

>TIGR00990 3a0801s09 mitochondrial precursor proteins import receptor (72 kDa mitochondrial outermembrane protein) (mitochondrial import receptor for the ADP/ATP carrier) (translocase of outermembrane tom70)

Probab=99.94  E-value=2.1e-21  Score=200.52  Aligned_cols=428  Identities=11%  Similarity=-0.013  Sum_probs=306.9

Q ss_pred             HHHHHHHHHhcCChhHHHHHHHHHHhCCCCCCHHHHHHHHHHHHhcCCHhHHHHHHHHHHhcCCCCCHhhHHHHHHHHHh
Q 040027           99 YNILINCFCKIGRVSLGFIAFGRILRSCFTPNAATFNSLIKGLHAESRIMEAAALFTKLKAFGCEPNVITYNTLINGLCR  178 (595)
Q Consensus        99 ~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~~l~~~~~~  178 (595)
                      +...+..+.+.|++++|+..|++++..  .|+...|..+..+|.+.|++++|++.+++.++.. +.+..++..+..+|..
T Consensus       130 ~k~~G~~~~~~~~~~~Ai~~y~~al~~--~p~~~~~~n~a~~~~~l~~~~~Ai~~~~~al~l~-p~~~~a~~~~a~a~~~  206 (615)
T TIGR00990       130 LKEKGNKAYRNKDFNKAIKLYSKAIEC--KPDPVYYSNRAACHNALGDWEKVVEDTTAALELD-PDYSKALNRRANAYDG  206 (615)
T ss_pred             HHHHHHHHHHcCCHHHHHHHHHHHHhc--CCchHHHHHHHHHHHHhCCHHHHHHHHHHHHHcC-CCCHHHHHHHHHHHHH
Confidence            445677888899999999999999887  5677888888899999999999999999998874 3367788889999999


Q ss_pred             cCChhHHHHHHHHHHhcCCCCCccccCcHHHHHHHHHHHHHcCCHhHHHHHHHHHhhCCCCCCHhHHHHHHHHHHhcCCH
Q 040027          179 TGHTMIALNLFEEMANGNGEIGVVCKPNTVTYSTIIDGLCKEGFVDKAKALFLQMKDENINPDVVTYNSLIHGLCHANDW  258 (595)
Q Consensus       179 ~g~~~~A~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~~ll~~~~~~~~~  258 (595)
                      .|++++|+..|..+...+       +.+......++..+..    ..+........... +++...+..+...+ .....
T Consensus       207 lg~~~eA~~~~~~~~~~~-------~~~~~~~~~~~~~~l~----~~a~~~~~~~l~~~-~~~~~~~~~~~~~~-~~~~~  273 (615)
T TIGR00990       207 LGKYADALLDLTASCIID-------GFRNEQSAQAVERLLK----KFAESKAKEILETK-PENLPSVTFVGNYL-QSFRP  273 (615)
T ss_pred             cCCHHHHHHHHHHHHHhC-------CCccHHHHHHHHHHHH----HHHHHHHHHHHhcC-CCCCCCHHHHHHHH-HHccC
Confidence            999999998887766543       1122222222222211    12233333333321 22222333333222 21111


Q ss_pred             HHHHHHHHHHHHCCCCCC-HhhHHHHHHH---HHhcCChHHHHHHHHHHHHCC--CCCCHHHHHHHHHHHHhcCCHHHHH
Q 040027          259 NEAKRLFIEMMDQGVQPS-VVTFNVIMDE---LCKNRKMDEASRLLDLMVQRG--VRPNACTYNTLMDGFCLMGKINRAE  332 (595)
Q Consensus       259 ~~A~~~~~~~~~~~~~~~-~~~~~~l~~~---~~~~g~~~~a~~~~~~~~~~~--~~~~~~~~~~l~~~~~~~~~~~~a~  332 (595)
                      .....-+....+  ..+. ...+..+...   ....+++++|.+.|+.+...+  .+.....+..+..++...|++++|+
T Consensus       274 ~~~~~~~~~~~~--~~~~~~~~~~~l~~~~~e~~~~~~y~~A~~~~~~al~~~~~~~~~a~a~~~lg~~~~~~g~~~eA~  351 (615)
T TIGR00990       274 KPRPAGLEDSNE--LDEETGNGQLQLGLKSPESKADESYEEAARAFEKALDLGKLGEKEAIALNLRGTFKCLKGKHLEAL  351 (615)
T ss_pred             Ccchhhhhcccc--cccccccchHHHHHHHHHhhhhhhHHHHHHHHHHHHhcCCCChhhHHHHHHHHHHHHHcCCHHHHH
Confidence            111111211111  1111 1111111111   123478999999999998764  2234566788888899999999999


Q ss_pred             HHHHHHHhcCCCCCHHHHHHHHHHHHhCCCHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHccCCHHHHHHHHHHHHHCC
Q 040027          333 ELFGSMESMGCKHDDVSYNILINGYCKNKEVEEALSLYREMVSKGIKPTVVTYNTLFLGLFEIHQVEHALKLFDEMQRDG  412 (595)
Q Consensus       333 ~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~  412 (595)
                      ..+++..+.. +.....|..+...+...|++++|+..|+++++..+. +...+..+...+...|++++|...|++.++..
T Consensus       352 ~~~~kal~l~-P~~~~~~~~la~~~~~~g~~~eA~~~~~~al~~~p~-~~~~~~~lg~~~~~~g~~~~A~~~~~kal~l~  429 (615)
T TIGR00990       352 ADLSKSIELD-PRVTQSYIKRASMNLELGDPDKAEEDFDKALKLNSE-DPDIYYHRAQLHFIKGEFAQAGKDYQKSIDLD  429 (615)
T ss_pred             HHHHHHHHcC-CCcHHHHHHHHHHHHHCCCHHHHHHHHHHHHHhCCC-CHHHHHHHHHHHHHcCCHHHHHHHHHHHHHcC
Confidence            9999998874 344668888999999999999999999999887433 67788889999999999999999999999874


Q ss_pred             CCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCcCHHHHHHHHHHHHhcCChHHHHHHHHhcccCCCCCCH-H---
Q 040027          413 VAADTRTYTTFIDGLCKNGYIIEAVELFRTLRILKCELDIQAYNCLIDGLCKSGRLKFAWELFCSLPHGVLVPNV-V---  488 (595)
Q Consensus       413 ~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~p~~-~---  488 (595)
                       +.+...+..+..++.+.|++++|+..+++.++.. +.+...++.+..++...|++++|+..|++...  +.|+. .   
T Consensus       430 -P~~~~~~~~la~~~~~~g~~~eA~~~~~~al~~~-P~~~~~~~~lg~~~~~~g~~~~A~~~~~~Al~--l~p~~~~~~~  505 (615)
T TIGR00990       430 -PDFIFSHIQLGVTQYKEGSIASSMATFRRCKKNF-PEAPDVYNYYGELLLDQNKFDEAIEKFDTAIE--LEKETKPMYM  505 (615)
T ss_pred             -ccCHHHHHHHHHHHHHCCCHHHHHHHHHHHHHhC-CCChHHHHHHHHHHHHccCHHHHHHHHHHHHh--cCCccccccc
Confidence             5567778888889999999999999999998765 66788999999999999999999999999887  33321 1   


Q ss_pred             ----HHHHHHHHHHhcCChhHHHHHHHHHHHcCCCCCHHHHHHHHHHHHHcCChhHHHHHHHHHHHC
Q 040027          489 ----TYNIMIQGLCNDGQMDKARDLFLDMEENAAAPDVITFDMLIHGFIRINEPSKVNELLHKMKEK  551 (595)
Q Consensus       489 ----~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~  551 (595)
                          .++..+..+...|++++|..+++++++.. +.+...+..++.++...|++++|.++|+++.+.
T Consensus       506 ~~~~l~~~a~~~~~~~~~~~eA~~~~~kAl~l~-p~~~~a~~~la~~~~~~g~~~eAi~~~e~A~~l  571 (615)
T TIGR00990       506 NVLPLINKALALFQWKQDFIEAENLCEKALIID-PECDIAVATMAQLLLQQGDVDEALKLFERAAEL  571 (615)
T ss_pred             cHHHHHHHHHHHHHHhhhHHHHHHHHHHHHhcC-CCcHHHHHHHHHHHHHccCHHHHHHHHHHHHHH
Confidence                12222233445699999999999998864 445667888999999999999999999999875

>KOG2002 consensus TPR-containing nuclear phosphoprotein that regulates K(+) uptake [Inorganic ion transport and metabolism]

Probab=99.93  E-value=4.2e-21  Score=188.23  Aligned_cols=520  Identities=13%  Similarity=0.057  Sum_probs=344.1

Q ss_pred             cCCCChHHHHHHHHHHHHhCCCCCCHhhHHHHHHHHHcCCCchh--HHhhC--CCCC-CHHHHHHHHHHHHh---cCChh
Q 040027           42 INVITPNEAFCIFDYMLRMHPSPPPVSSFNILLASLAKNKHYDT--RLNAT--GLFP-NLYTYNILINCFCK---IGRVS  113 (595)
Q Consensus        42 ~~~~~~~~A~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~--~~~~~--~~~~-~~~~~~~l~~~~~~---~g~~~  113 (595)
                      -+.|+|..|+.+|..++..+|. ..+...-.+..++++.|....  ..+..  .+.| ++..+..|...-..   ...+.
T Consensus       175 ynkkdY~~al~yyk~al~inp~-~~aD~rIgig~Cf~kl~~~~~a~~a~~ralqLdp~~v~alv~L~~~~l~~~d~~s~~  253 (1018)
T KOG2002|consen  175 YNKKDYRGALKYYKKALRINPA-CKADVRIGIGHCFWKLGMSEKALLAFERALQLDPTCVSALVALGEVDLNFNDSDSYK  253 (1018)
T ss_pred             hccccHHHHHHHHHHHHhcCcc-cCCCccchhhhHHHhccchhhHHHHHHHHHhcChhhHHHHHHHHHHHHHccchHHHH
Confidence            4556777777777777766665 223333334455566665554  11111  1222 22222222222111   23345


Q ss_pred             HHHHHHHHHHhCCCCCCHHHHHHHHHHHHhcCCHhHHHHHHHHHHhcCCC--CCHhhHHHHHHHHHhcCChhHHHHHHHH
Q 040027          114 LGFIAFGRILRSCFTPNAATFNSLIKGLHAESRIMEAAALFTKLKAFGCE--PNVITYNTLINGLCRTGHTMIALNLFEE  191 (595)
Q Consensus       114 ~A~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~--~~~~~~~~l~~~~~~~g~~~~A~~~~~~  191 (595)
                      .++.++.++.... +.++.+.+.|...+...|++..+..+...+......  .-...|..+.++|...|++++|...|.+
T Consensus       254 ~~~~ll~~ay~~n-~~nP~~l~~LAn~fyfK~dy~~v~~la~~ai~~t~~~~~~aes~Y~~gRs~Ha~Gd~ekA~~yY~~  332 (1018)
T KOG2002|consen  254 KGVQLLQRAYKEN-NENPVALNHLANHFYFKKDYERVWHLAEHAIKNTENKSIKAESFYQLGRSYHAQGDFEKAFKYYME  332 (1018)
T ss_pred             HHHHHHHHHHhhc-CCCcHHHHHHHHHHhhcccHHHHHHHHHHHHHhhhhhHHHHHHHHHHHHHHHhhccHHHHHHHHHH
Confidence            5666666666553 446677777777777778888888777777654211  1234467777888888888888888877


Q ss_pred             HHhcCCCCCccccCc-HHHHHHHHHHHHHcCCHhHHHHHHHHHhhCCCCCCHhHHHHHHHHHHhcC----CHHHHHHHHH
Q 040027          192 MANGNGEIGVVCKPN-TVTYSTIIDGLCKEGFVDKAKALFLQMKDENINPDVVTYNSLIHGLCHAN----DWNEAKRLFI  266 (595)
Q Consensus       192 ~~~~~~~~~~~~~~~-~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~~ll~~~~~~~----~~~~A~~~~~  266 (595)
                      ..+.+       +.+ ...+..+...+.+.|+++.+...|+.+.+.. +.+..+...|...|...+    ..+.|..++.
T Consensus       333 s~k~~-------~d~~~l~~~GlgQm~i~~~dle~s~~~fEkv~k~~-p~~~etm~iLG~Lya~~~~~~~~~d~a~~~l~  404 (1018)
T KOG2002|consen  333 SLKAD-------NDNFVLPLVGLGQMYIKRGDLEESKFCFEKVLKQL-PNNYETMKILGCLYAHSAKKQEKRDKASNVLG  404 (1018)
T ss_pred             HHccC-------CCCccccccchhHHHHHhchHHHHHHHHHHHHHhC-cchHHHHHHHHhHHHhhhhhhHHHHHHHHHHH
Confidence            77654       122 3445567777888888888888888777653 335666666666666654    4456666666


Q ss_pred             HHHHCCCCCCHhhHHHHHHHHHhcCChHHHHHHHHHHH----HCCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHhc-
Q 040027          267 EMMDQGVQPSVVTFNVIMDELCKNRKMDEASRLLDLMV----QRGVRPNACTYNTLMDGFCLMGKINRAEELFGSMESM-  341 (595)
Q Consensus       267 ~~~~~~~~~~~~~~~~l~~~~~~~g~~~~a~~~~~~~~----~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~-  341 (595)
                      +..+.- +.|...|..+...+....- ..++.+|..+.    ..+..+.+...+.++..+...|++..|...|...... 
T Consensus       405 K~~~~~-~~d~~a~l~laql~e~~d~-~~sL~~~~~A~d~L~~~~~~ip~E~LNNvaslhf~~g~~~~A~~~f~~A~~~~  482 (1018)
T KOG2002|consen  405 KVLEQT-PVDSEAWLELAQLLEQTDP-WASLDAYGNALDILESKGKQIPPEVLNNVASLHFRLGNIEKALEHFKSALGKL  482 (1018)
T ss_pred             HHHhcc-cccHHHHHHHHHHHHhcCh-HHHHHHHHHHHHHHHHcCCCCCHHHHHhHHHHHHHhcChHHHHHHHHHHhhhh
Confidence            665542 3356666666665554433 33366665444    3444466777888888888888888888888877644 


Q ss_pred             --CCCCCH------HHHHHHHHHHHhCCCHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHccCCHHHHHHHHHHHHHCCC
Q 040027          342 --GCKHDD------VSYNILINGYCKNKEVEEALSLYREMVSKGIKPTVVTYNTLFLGLFEIHQVEHALKLFDEMQRDGV  413 (595)
Q Consensus       342 --~~~~~~------~~~~~l~~~~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~  413 (595)
                        ...++.      .+-..+..++-..++.+.|.+.|..+.+..+. -+..|..++......+...+|...++.+...+ 
T Consensus       483 ~~~~n~de~~~~~lt~~YNlarl~E~l~~~~~A~e~Yk~Ilkehp~-YId~ylRl~~ma~~k~~~~ea~~~lk~~l~~d-  560 (1018)
T KOG2002|consen  483 LEVANKDEGKSTNLTLKYNLARLLEELHDTEVAEEMYKSILKEHPG-YIDAYLRLGCMARDKNNLYEASLLLKDALNID-  560 (1018)
T ss_pred             hhhcCccccccchhHHHHHHHHHHHhhhhhhHHHHHHHHHHHHCch-hHHHHHHhhHHHHhccCcHHHHHHHHHHHhcc-
Confidence              112222      23445666677777888888888888776322 33445555434444577788888888887653 


Q ss_pred             CCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHHcC-CCcCHHHHHHHHHHHHh------------cCChHHHHHHHHhccc
Q 040027          414 AADTRTYTTFIDGLCKNGYIIEAVELFRTLRILK-CELDIQAYNCLIDGLCK------------SGRLKFAWELFCSLPH  480 (595)
Q Consensus       414 ~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~-~~~~~~~~~~l~~~~~~------------~g~~~~A~~~~~~~~~  480 (595)
                      ..++..++.+...+.+...+..|..-|+.+.+.. ..+|+.+...|++.|..            .+..++|+++|.++++
T Consensus       561 ~~np~arsl~G~~~l~k~~~~~a~k~f~~i~~~~~~~~D~YsliaLGN~~~~~l~~~~rn~ek~kk~~~KAlq~y~kvL~  640 (1018)
T KOG2002|consen  561 SSNPNARSLLGNLHLKKSEWKPAKKKFETILKKTSTKTDAYSLIALGNVYIQALHNPSRNPEKEKKHQEKALQLYGKVLR  640 (1018)
T ss_pred             cCCcHHHHHHHHHHHhhhhhcccccHHHHHHhhhccCCchhHHHHhhHHHHHHhcccccChHHHHHHHHHHHHHHHHHHh
Confidence            5566677777778888888888888777666432 13577777788876653            3457789999999888


Q ss_pred             CCCCCCHHHHHHHHHHHHhcCChhHHHHHHHHHHHcCCCCCHHHHHHHHHHHHHcCChhHHHHHHHHHHHCCC-CCCHHH
Q 040027          481 GVLVPNVVTYNIMIQGLCNDGQMDKARDLFLDMEENAAAPDVITFDMLIHGFIRINEPSKVNELLHKMKEKKV-MPDASI  559 (595)
Q Consensus       481 ~~~~p~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~-~p~~~~  559 (595)
                      . -+-|...-|.+..+++..|++.+|..+|.+..+.. .....+|..++++|..+|+|..|.++|+...+.-. .-+..+
T Consensus       641 ~-dpkN~yAANGIgiVLA~kg~~~~A~dIFsqVrEa~-~~~~dv~lNlah~~~e~~qy~~AIqmYe~~lkkf~~~~~~~v  718 (1018)
T KOG2002|consen  641 N-DPKNMYAANGIGIVLAEKGRFSEARDIFSQVREAT-SDFEDVWLNLAHCYVEQGQYRLAIQMYENCLKKFYKKNRSEV  718 (1018)
T ss_pred             c-CcchhhhccchhhhhhhccCchHHHHHHHHHHHHH-hhCCceeeeHHHHHHHHHHHHHHHHHHHHHHHHhcccCCHHH
Confidence            4 23366777888899999999999999999999874 34667899999999999999999999999986533 347899


Q ss_pred             HHHHHHHHHhcCcccccc
Q 040027          560 VSIVVDLLVKNEISLKSL  577 (595)
Q Consensus       560 ~~~l~~~~~~~g~~~~~i  577 (595)
                      ...|.+++.+.|++.+..
T Consensus       719 l~~Lara~y~~~~~~eak  736 (1018)
T KOG2002|consen  719 LHYLARAWYEAGKLQEAK  736 (1018)
T ss_pred             HHHHHHHHHHhhhHHHHH
Confidence            999999999999988333

>TIGR00990 3a0801s09 mitochondrial precursor proteins import receptor (72 kDa mitochondrial outermembrane protein) (mitochondrial import receptor for the ADP/ATP carrier) (translocase of outermembrane tom70)

Probab=99.92  E-value=8.4e-20  Score=188.62  Aligned_cols=424  Identities=13%  Similarity=0.021  Sum_probs=306.4

Q ss_pred             HHHHHHHHHHhcCCHhHHHHHHHHHHhcCCCCCHhhHHHHHHHHHhcCChhHHHHHHHHHHhcCCCCCccccCcHHHHHH
Q 040027          133 TFNSLIKGLHAESRIMEAAALFTKLKAFGCEPNVITYNTLINGLCRTGHTMIALNLFEEMANGNGEIGVVCKPNTVTYST  212 (595)
Q Consensus       133 ~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~~~~~~~~  212 (595)
                      .+......+.+.|++++|+..|++.+..  .|+...|..+..+|...|++++|+..++...+.+       +.+..++..
T Consensus       129 ~~k~~G~~~~~~~~~~~Ai~~y~~al~~--~p~~~~~~n~a~~~~~l~~~~~Ai~~~~~al~l~-------p~~~~a~~~  199 (615)
T TIGR00990       129 KLKEKGNKAYRNKDFNKAIKLYSKAIEC--KPDPVYYSNRAACHNALGDWEKVVEDTTAALELD-------PDYSKALNR  199 (615)
T ss_pred             HHHHHHHHHHHcCCHHHHHHHHHHHHhc--CCchHHHHHHHHHHHHhCCHHHHHHHHHHHHHcC-------CCCHHHHHH
Confidence            3456677889999999999999999876  5678889999999999999999999999999876       556889999


Q ss_pred             HHHHHHHcCCHhHHHHHHHHHhhCCCCCCHhHHHHHHHHHHhcCCHHHHHHHHHHHHHCCCCCCHhhHHHHHHHHHhcCC
Q 040027          213 IIDGLCKEGFVDKAKALFLQMKDENINPDVVTYNSLIHGLCHANDWNEAKRLFIEMMDQGVQPSVVTFNVIMDELCKNRK  292 (595)
Q Consensus       213 l~~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~~ll~~~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~  292 (595)
                      +..+|...|++++|...|..+...+.. +......++..+..    ..+........+.. +++...+..+...+ ....
T Consensus       200 ~a~a~~~lg~~~eA~~~~~~~~~~~~~-~~~~~~~~~~~~l~----~~a~~~~~~~l~~~-~~~~~~~~~~~~~~-~~~~  272 (615)
T TIGR00990       200 RANAYDGLGKYADALLDLTASCIIDGF-RNEQSAQAVERLLK----KFAESKAKEILETK-PENLPSVTFVGNYL-QSFR  272 (615)
T ss_pred             HHHHHHHcCCHHHHHHHHHHHHHhCCC-ccHHHHHHHHHHHH----HHHHHHHHHHHhcC-CCCCCCHHHHHHHH-HHcc
Confidence            999999999999999988776554211 22212222222221    22233333333321 22333333333322 2212


Q ss_pred             hHHHHHHHHHHHHCCCCCC-HHHHHHHHHHH---HhcCCHHHHHHHHHHHHhcC--CCCCHHHHHHHHHHHHhCCCHHHH
Q 040027          293 MDEASRLLDLMVQRGVRPN-ACTYNTLMDGF---CLMGKINRAEELFGSMESMG--CKHDDVSYNILINGYCKNKEVEEA  366 (595)
Q Consensus       293 ~~~a~~~~~~~~~~~~~~~-~~~~~~l~~~~---~~~~~~~~a~~~~~~~~~~~--~~~~~~~~~~l~~~~~~~~~~~~A  366 (595)
                      ......-+......  .+. ...+..+...+   ...+++++|...|+...+.+  .+.....+..+..++...|++++|
T Consensus       273 ~~~~~~~~~~~~~~--~~~~~~~~~~l~~~~~e~~~~~~y~~A~~~~~~al~~~~~~~~~a~a~~~lg~~~~~~g~~~eA  350 (615)
T TIGR00990       273 PKPRPAGLEDSNEL--DEETGNGQLQLGLKSPESKADESYEEAARAFEKALDLGKLGEKEAIALNLRGTFKCLKGKHLEA  350 (615)
T ss_pred             CCcchhhhhccccc--ccccccchHHHHHHHHHhhhhhhHHHHHHHHHHHHhcCCCChhhHHHHHHHHHHHHHcCCHHHH
Confidence            22222222221111  111 11111111111   23478999999999998764  133445788888999999999999


Q ss_pred             HHHHHHHHHCCCCCCHHHHHHHHHHHHccCCHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHHc
Q 040027          367 LSLYREMVSKGIKPTVVTYNTLFLGLFEIHQVEHALKLFDEMQRDGVAADTRTYTTFIDGLCKNGYIIEAVELFRTLRIL  446 (595)
Q Consensus       367 ~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~  446 (595)
                      +..+++.++..+. ....|..+...+...|++++|...++++++.. +.+..++..+...+...|++++|...|++.++.
T Consensus       351 ~~~~~kal~l~P~-~~~~~~~la~~~~~~g~~~eA~~~~~~al~~~-p~~~~~~~~lg~~~~~~g~~~~A~~~~~kal~l  428 (615)
T TIGR00990       351 LADLSKSIELDPR-VTQSYIKRASMNLELGDPDKAEEDFDKALKLN-SEDPDIYYHRAQLHFIKGEFAQAGKDYQKSIDL  428 (615)
T ss_pred             HHHHHHHHHcCCC-cHHHHHHHHHHHHHCCCHHHHHHHHHHHHHhC-CCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHc
Confidence            9999999986432 46678888889999999999999999998874 566888999999999999999999999999987


Q ss_pred             CCCcCHHHHHHHHHHHHhcCChHHHHHHHHhcccCCCCC-CHHHHHHHHHHHHhcCChhHHHHHHHHHHHcCCCCCHH--
Q 040027          447 KCELDIQAYNCLIDGLCKSGRLKFAWELFCSLPHGVLVP-NVVTYNIMIQGLCNDGQMDKARDLFLDMEENAAAPDVI--  523 (595)
Q Consensus       447 ~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~p-~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~~~~--  523 (595)
                      . +.+...+..+..++.+.|++++|+..|++....  .| +...++.+..++...|++++|++.|+++++.....+..  
T Consensus       429 ~-P~~~~~~~~la~~~~~~g~~~eA~~~~~~al~~--~P~~~~~~~~lg~~~~~~g~~~~A~~~~~~Al~l~p~~~~~~~  505 (615)
T TIGR00990       429 D-PDFIFSHIQLGVTQYKEGSIASSMATFRRCKKN--FPEAPDVYNYYGELLLDQNKFDEAIEKFDTAIELEKETKPMYM  505 (615)
T ss_pred             C-ccCHHHHHHHHHHHHHCCCHHHHHHHHHHHHHh--CCCChHHHHHHHHHHHHccCHHHHHHHHHHHHhcCCccccccc
Confidence            6 667888889999999999999999999999873  45 47889999999999999999999999999863211111  


Q ss_pred             ----HHHHHHHHHHHcCChhHHHHHHHHHHHCCCCC-CHHHHHHHHHHHHhcCcccccchHHH
Q 040027          524 ----TFDMLIHGFIRINEPSKVNELLHKMKEKKVMP-DASIVSIVVDLLVKNEISLKSLPSFL  581 (595)
Q Consensus       524 ----~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~p-~~~~~~~l~~~~~~~g~~~~~i~~~~  581 (595)
                          .+...+..+...|++++|.++++++++.  .| +...+..++.++.+.|+++++++.+.
T Consensus       506 ~~~~l~~~a~~~~~~~~~~~eA~~~~~kAl~l--~p~~~~a~~~la~~~~~~g~~~eAi~~~e  566 (615)
T TIGR00990       506 NVLPLINKALALFQWKQDFIEAENLCEKALII--DPECDIAVATMAQLLLQQGDVDEALKLFE  566 (615)
T ss_pred             cHHHHHHHHHHHHHHhhhHHHHHHHHHHHHhc--CCCcHHHHHHHHHHHHHccCHHHHHHHHH
Confidence                1122222334469999999999999875  35 45678899999999999997666554

>PRK11788 tetratricopeptide repeat protein; Provisional

Probab=99.91  E-value=1.7e-21  Score=191.33  Aligned_cols=312  Identities=15%  Similarity=0.129  Sum_probs=215.9

Q ss_pred             HHHHhcCCHHHHHHHHHHHHHCCCCCCHhhHHHHHHHHHhcCChHHHHHHHHHHHHCCCCCC---HHHHHHHHHHHHhcC
Q 040027          250 HGLCHANDWNEAKRLFIEMMDQGVQPSVVTFNVIMDELCKNRKMDEASRLLDLMVQRGVRPN---ACTYNTLMDGFCLMG  326 (595)
Q Consensus       250 ~~~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~~~~~---~~~~~~l~~~~~~~~  326 (595)
                      ..+...|++++|...|.++.+.+ +.+..++..+...+...|++++|..+++.+...+..++   ...+..++..|...|
T Consensus        43 ~~~~~~~~~~~A~~~~~~al~~~-p~~~~~~~~la~~~~~~g~~~~A~~~~~~~l~~~~~~~~~~~~~~~~La~~~~~~g  121 (389)
T PRK11788         43 LNFLLNEQPDKAIDLFIEMLKVD-PETVELHLALGNLFRRRGEVDRAIRIHQNLLSRPDLTREQRLLALQELGQDYLKAG  121 (389)
T ss_pred             HHHHhcCChHHHHHHHHHHHhcC-cccHHHHHHHHHHHHHcCcHHHHHHHHHHHhcCCCCCHHHHHHHHHHHHHHHHHCC
Confidence            34455666666666666666542 22344566666666666666666666666665422111   234566677777777


Q ss_pred             CHHHHHHHHHHHHhcCCCCCHHHHHHHHHHHHhCCCHHHHHHHHHHHHHCCCCCCH----HHHHHHHHHHHccCCHHHHH
Q 040027          327 KINRAEELFGSMESMGCKHDDVSYNILINGYCKNKEVEEALSLYREMVSKGIKPTV----VTYNTLFLGLFEIHQVEHAL  402 (595)
Q Consensus       327 ~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~~~~~~~~----~~~~~l~~~~~~~~~~~~a~  402 (595)
                      ++++|..+|+++.+.. +.+..++..++..+.+.|++++|.+.++.+.+.+..+..    ..+..+...+...|++++|.
T Consensus       122 ~~~~A~~~~~~~l~~~-~~~~~~~~~la~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~~~~~~la~~~~~~~~~~~A~  200 (389)
T PRK11788        122 LLDRAEELFLQLVDEG-DFAEGALQQLLEIYQQEKDWQKAIDVAERLEKLGGDSLRVEIAHFYCELAQQALARGDLDAAR  200 (389)
T ss_pred             CHHHHHHHHHHHHcCC-cchHHHHHHHHHHHHHhchHHHHHHHHHHHHHhcCCcchHHHHHHHHHHHHHHHhCCCHHHHH
Confidence            7777777777776642 345566777777777777777777777777765433221    13445566677788888888


Q ss_pred             HHHHHHHHCCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCcCHHHHHHHHHHHHhcCChHHHHHHHHhcccCC
Q 040027          403 KLFDEMQRDGVAADTRTYTTFIDGLCKNGYIIEAVELFRTLRILKCELDIQAYNCLIDGLCKSGRLKFAWELFCSLPHGV  482 (595)
Q Consensus       403 ~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~  482 (595)
                      ..++++.+.. +.+...+..+...+.+.|++++|.++++++...+......++..++.+|...|++++|...++++.+  
T Consensus       201 ~~~~~al~~~-p~~~~~~~~la~~~~~~g~~~~A~~~~~~~~~~~p~~~~~~~~~l~~~~~~~g~~~~A~~~l~~~~~--  277 (389)
T PRK11788        201 ALLKKALAAD-PQCVRASILLGDLALAQGDYAAAIEALERVEEQDPEYLSEVLPKLMECYQALGDEAEGLEFLRRALE--  277 (389)
T ss_pred             HHHHHHHhHC-cCCHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHChhhHHHHHHHHHHHHHHcCCHHHHHHHHHHHHH--
Confidence            8888887653 3445667777788888888888888888888654222245677888888888999999999888887  


Q ss_pred             CCCCHHHHHHHHHHHHhcCChhHHHHHHHHHHHcCCCCCHHHHHHHHHHHHH---cCChhHHHHHHHHHHHCCCCCCHHH
Q 040027          483 LVPNVVTYNIMIQGLCNDGQMDKARDLFLDMEENAAAPDVITFDMLIHGFIR---INEPSKVNELLHKMKEKKVMPDASI  559 (595)
Q Consensus       483 ~~p~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~~l~~~~~~---~g~~~~A~~~~~~~~~~~~~p~~~~  559 (595)
                      ..|+...+..++..+.+.|++++|..+++++.+.  .|+...+..++..+..   .|+.+++..++++|.+.++.|++. 
T Consensus       278 ~~p~~~~~~~la~~~~~~g~~~~A~~~l~~~l~~--~P~~~~~~~l~~~~~~~~~~g~~~~a~~~~~~~~~~~~~~~p~-  354 (389)
T PRK11788        278 EYPGADLLLALAQLLEEQEGPEAAQALLREQLRR--HPSLRGFHRLLDYHLAEAEEGRAKESLLLLRDLVGEQLKRKPR-  354 (389)
T ss_pred             hCCCchHHHHHHHHHHHhCCHHHHHHHHHHHHHh--CcCHHHHHHHHHHhhhccCCccchhHHHHHHHHHHHHHhCCCC-
Confidence            4567666778888888899999999999888875  5777777777776664   458888999999888877777766 


Q ss_pred             HHHHHHHHHhcCccc
Q 040027          560 VSIVVDLLVKNEISL  574 (595)
Q Consensus       560 ~~~l~~~~~~~g~~~  574 (595)
                           .+|..+|...
T Consensus       355 -----~~c~~cg~~~  364 (389)
T PRK11788        355 -----YRCRNCGFTA  364 (389)
T ss_pred             -----EECCCCCCCC
Confidence                 3355555543

>PRK15174 Vi polysaccharide export protein VexE; Provisional

Probab=99.91  E-value=7.5e-20  Score=188.06  Aligned_cols=356  Identities=12%  Similarity=0.044  Sum_probs=245.9

Q ss_pred             HHHHHHHHHHHhcCChhHHHHHHHHHHhCCCCCCHHHHHHHHHHHHhcCCHhHHHHHHHHHHhcCCCCCHhhHHHHHHHH
Q 040027           97 YTYNILINCFCKIGRVSLGFIAFGRILRSCFTPNAATFNSLIKGLHAESRIMEAAALFTKLKAFGCEPNVITYNTLINGL  176 (595)
Q Consensus        97 ~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~~l~~~~  176 (595)
                      .....++..+.+.|++++|..+++..+... +.+...+..++.+....|++++|+..|+++.... +.+...+..+...+
T Consensus        43 ~~~~~~~~~~~~~g~~~~A~~l~~~~l~~~-p~~~~~l~~l~~~~l~~g~~~~A~~~l~~~l~~~-P~~~~a~~~la~~l  120 (656)
T PRK15174         43 QNIILFAIACLRKDETDVGLTLLSDRVLTA-KNGRDLLRRWVISPLASSQPDAVLQVVNKLLAVN-VCQPEDVLLVASVL  120 (656)
T ss_pred             cCHHHHHHHHHhcCCcchhHHHhHHHHHhC-CCchhHHHHHhhhHhhcCCHHHHHHHHHHHHHhC-CCChHHHHHHHHHH
Confidence            334456667778888888888888887774 3345556666667777888888888888888764 33566777778888


Q ss_pred             HhcCChhHHHHHHHHHHhcCCCCCccccCcHHHHHHHHHHHHHcCCHhHHHHHHHHHhhCCCCCCHhHHHHHHHHHHhcC
Q 040027          177 CRTGHTMIALNLFEEMANGNGEIGVVCKPNTVTYSTIIDGLCKEGFVDKAKALFLQMKDENINPDVVTYNSLIHGLCHAN  256 (595)
Q Consensus       177 ~~~g~~~~A~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~~ll~~~~~~~  256 (595)
                      ...|++++|+..++++....       |.+...+..++.++...|++++|...++.+...... +...+..+ ..+...|
T Consensus       121 ~~~g~~~~Ai~~l~~Al~l~-------P~~~~a~~~la~~l~~~g~~~eA~~~~~~~~~~~P~-~~~a~~~~-~~l~~~g  191 (656)
T PRK15174        121 LKSKQYATVADLAEQAWLAF-------SGNSQIFALHLRTLVLMDKELQAISLARTQAQEVPP-RGDMIATC-LSFLNKS  191 (656)
T ss_pred             HHcCCHHHHHHHHHHHHHhC-------CCcHHHHHHHHHHHHHCCChHHHHHHHHHHHHhCCC-CHHHHHHH-HHHHHcC
Confidence            88888888888888888764       455777777888888888888888888877655322 33333333 3467778


Q ss_pred             CHHHHHHHHHHHHHCCCCCCHhhHHHHHHHHHhcCChHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHhcCCHHH----HH
Q 040027          257 DWNEAKRLFIEMMDQGVQPSVVTFNVIMDELCKNRKMDEASRLLDLMVQRGVRPNACTYNTLMDGFCLMGKINR----AE  332 (595)
Q Consensus       257 ~~~~A~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~----a~  332 (595)
                      ++++|...++.+++....++......++..+...|++++|...++++...+ +.+...+..+..++...|++++    |.
T Consensus       192 ~~~eA~~~~~~~l~~~~~~~~~~~~~l~~~l~~~g~~~eA~~~~~~al~~~-p~~~~~~~~Lg~~l~~~G~~~eA~~~A~  270 (656)
T PRK15174        192 RLPEDHDLARALLPFFALERQESAGLAVDTLCAVGKYQEAIQTGESALARG-LDGAALRRSLGLAYYQSGRSREAKLQAA  270 (656)
T ss_pred             CHHHHHHHHHHHHhcCCCcchhHHHHHHHHHHHCCCHHHHHHHHHHHHhcC-CCCHHHHHHHHHHHHHcCCchhhHHHHH
Confidence            888888888887765333334444555667778888888888888887764 3356667777788888888775    67


Q ss_pred             HHHHHHHhcCCCCCHHHHHHHHHHHHhCCCHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHccCCHHHHHHHHHHHHHCC
Q 040027          333 ELFGSMESMGCKHDDVSYNILINGYCKNKEVEEALSLYREMVSKGIKPTVVTYNTLFLGLFEIHQVEHALKLFDEMQRDG  412 (595)
Q Consensus       333 ~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~  412 (595)
                      ..++++.+.. |.+...+..+...+...|++++|+..++++....+. +...+..+...+...|++++|...++.+.+.+
T Consensus       271 ~~~~~Al~l~-P~~~~a~~~lg~~l~~~g~~~eA~~~l~~al~l~P~-~~~a~~~La~~l~~~G~~~eA~~~l~~al~~~  348 (656)
T PRK15174        271 EHWRHALQFN-SDNVRIVTLYADALIRTGQNEKAIPLLQQSLATHPD-LPYVRAMYARALRQVGQYTAASDEFVQLAREK  348 (656)
T ss_pred             HHHHHHHhhC-CCCHHHHHHHHHHHHHCCCHHHHHHHHHHHHHhCCC-CHHHHHHHHHHHHHCCCHHHHHHHHHHHHHhC
Confidence            7888777664 445667777788888888888888888887776433 45566667777778888888888888777652


Q ss_pred             CCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCcCHHHHHHHHHHHHhcCChHHHHHHHHhccc
Q 040027          413 VAADTRTYTTFIDGLCKNGYIIEAVELFRTLRILKCELDIQAYNCLIDGLCKSGRLKFAWELFCSLPH  480 (595)
Q Consensus       413 ~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~  480 (595)
                       +.+...+..+..++...|+.++|...|+++.+..  |+..           ...+++|...+.+..+
T Consensus       349 -P~~~~~~~~~a~al~~~G~~deA~~~l~~al~~~--P~~~-----------~~~~~ea~~~~~~~~~  402 (656)
T PRK15174        349 -GVTSKWNRYAAAALLQAGKTSEAESVFEHYIQAR--ASHL-----------PQSFEEGLLALDGQIS  402 (656)
T ss_pred             -ccchHHHHHHHHHHHHCCCHHHHHHHHHHHHHhC--hhhc-----------hhhHHHHHHHHHHHHH
Confidence             2222333344566777888888888888877653  2211           2344556666665555

>PRK10049 pgaA outer membrane protein PgaA; Provisional

Probab=99.91  E-value=3.7e-19  Score=187.09  Aligned_cols=419  Identities=12%  Similarity=0.014  Sum_probs=215.0

Q ss_pred             HHHHHHHhcCChhHHHHHHHHHHhCCCCCCHHHHHHHHHHHHhcCCHhHHHHHHHHHHhcCCCCCHhhHHHHHHHHHhcC
Q 040027          101 ILINCFCKIGRVSLGFIAFGRILRSCFTPNAATFNSLIKGLHAESRIMEAAALFTKLKAFGCEPNVITYNTLINGLCRTG  180 (595)
Q Consensus       101 ~l~~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g  180 (595)
                      -.+.+....|+.++|+.+|.++.... +.+...+..+...+...|++++|.++|+++.... +.+...+..++..+...|
T Consensus        20 d~~~ia~~~g~~~~A~~~~~~~~~~~-~~~a~~~~~lA~~~~~~g~~~~A~~~~~~al~~~-P~~~~a~~~la~~l~~~g   97 (765)
T PRK10049         20 DWLQIALWAGQDAEVITVYNRYRVHM-QLPARGYAAVAVAYRNLKQWQNSLTLWQKALSLE-PQNDDYQRGLILTLADAG   97 (765)
T ss_pred             HHHHHHHHcCCHHHHHHHHHHHHhhC-CCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhC-CCCHHHHHHHHHHHHHCC
Confidence            33444444555555555555554321 2333344455555555555555555555544442 223444444444555555


Q ss_pred             ChhHHHHHHHHHHhcCCCCCccccCcHHHHHHHHHHHHHcCCHhHHHHHHHHHhhCCCCCCHhHHHHHHHHHHhcCCHHH
Q 040027          181 HTMIALNLFEEMANGNGEIGVVCKPNTVTYSTIIDGLCKEGFVDKAKALFLQMKDENINPDVVTYNSLIHGLCHANDWNE  260 (595)
Q Consensus       181 ~~~~A~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~~ll~~~~~~~~~~~  260 (595)
                      ++++|+..++++....       |.+.. +..+..++...|+.++|...++++.+.. +.+...+..+..++...+..++
T Consensus        98 ~~~eA~~~l~~~l~~~-------P~~~~-~~~la~~l~~~g~~~~Al~~l~~al~~~-P~~~~~~~~la~~l~~~~~~e~  168 (765)
T PRK10049         98 QYDEALVKAKQLVSGA-------PDKAN-LLALAYVYKRAGRHWDELRAMTQALPRA-PQTQQYPTEYVQALRNNRLSAP  168 (765)
T ss_pred             CHHHHHHHHHHHHHhC-------CCCHH-HHHHHHHHHHCCCHHHHHHHHHHHHHhC-CCCHHHHHHHHHHHHHCCChHH
Confidence            5555555555554443       23333 4444445555555555555555554432 1133333344444444455555


Q ss_pred             HHHHHHHHHHCCCCCCHhhHHHHHHHHHhcCChHHHHHHHHHHHHCCCCCCHHHHHHHHHHHH-----hcCCH---HHHH
Q 040027          261 AKRLFIEMMDQGVQPSVVTFNVIMDELCKNRKMDEASRLLDLMVQRGVRPNACTYNTLMDGFC-----LMGKI---NRAE  332 (595)
Q Consensus       261 A~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~-----~~~~~---~~a~  332 (595)
                      |+..++.+..   .|+...                           +.  .......+++...     ..+++   ++|+
T Consensus       169 Al~~l~~~~~---~p~~~~---------------------------~l--~~~~~~~~~r~~~~~~~~~~~r~~~ad~Al  216 (765)
T PRK10049        169 ALGAIDDANL---TPAEKR---------------------------DL--EADAAAELVRLSFMPTRSEKERYAIADRAL  216 (765)
T ss_pred             HHHHHHhCCC---CHHHHH---------------------------HH--HHHHHHHHHHhhcccccChhHHHHHHHHHH
Confidence            5544443332   111000                           00  0000111111111     11122   5566


Q ss_pred             HHHHHHHhc-CCCCCHH-HH----HHHHHHHHhCCCHHHHHHHHHHHHHCCCC-CCHHHHHHHHHHHHccCCHHHHHHHH
Q 040027          333 ELFGSMESM-GCKHDDV-SY----NILINGYCKNKEVEEALSLYREMVSKGIK-PTVVTYNTLFLGLFEIHQVEHALKLF  405 (595)
Q Consensus       333 ~~~~~~~~~-~~~~~~~-~~----~~l~~~~~~~~~~~~A~~~~~~~~~~~~~-~~~~~~~~l~~~~~~~~~~~~a~~~~  405 (595)
                      ..++.+.+. ...|+.. .+    ...+..+...+++++|+..|+.+.+.+.+ |+. ....+...+...|++++|+..|
T Consensus       217 ~~~~~ll~~~~~~p~~~~~~~~a~~d~l~~Ll~~g~~~eA~~~~~~ll~~~~~~P~~-a~~~la~~yl~~g~~e~A~~~l  295 (765)
T PRK10049        217 AQYDALEALWHDNPDATADYQRARIDRLGALLARDRYKDVISEYQRLKAEGQIIPPW-AQRWVASAYLKLHQPEKAQSIL  295 (765)
T ss_pred             HHHHHHHhhcccCCccchHHHHHHHHHHHHHHHhhhHHHHHHHHHHhhccCCCCCHH-HHHHHHHHHHhcCCcHHHHHHH
Confidence            666665533 1111111 11    11122334556777777777776665422 221 1222355666677777777777


Q ss_pred             HHHHHCCCCC---CHHHHHHHHHHHHhcCCHHHHHHHHHHHHHcCC-----------CcC---HHHHHHHHHHHHhcCCh
Q 040027          406 DEMQRDGVAA---DTRTYTTFIDGLCKNGYIIEAVELFRTLRILKC-----------ELD---IQAYNCLIDGLCKSGRL  468 (595)
Q Consensus       406 ~~~~~~~~~~---~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~-----------~~~---~~~~~~l~~~~~~~g~~  468 (595)
                      +++.+.....   .......+..++...|++++|..+++.+.....           .|+   ...+..++..+...|++
T Consensus       296 ~~~l~~~p~~~~~~~~~~~~L~~a~~~~g~~~eA~~~l~~~~~~~P~~~~~~~~~~~~p~~~~~~a~~~~a~~l~~~g~~  375 (765)
T PRK10049        296 TELFYHPETIADLSDEELADLFYSLLESENYPGALTVTAHTINNSPPFLRLYGSPTSIPNDDWLQGQSLLSQVAKYSNDL  375 (765)
T ss_pred             HHHhhcCCCCCCCChHHHHHHHHHHHhcccHHHHHHHHHHHhhcCCceEeecCCCCCCCCchHHHHHHHHHHHHHHcCCH
Confidence            7666532110   123344455556677777777777776665420           112   23445566677778888


Q ss_pred             HHHHHHHHhcccCCCCCCHHHHHHHHHHHHhcCChhHHHHHHHHHHHcCCCCCHHHHHHHHHHHHHcCChhHHHHHHHHH
Q 040027          469 KFAWELFCSLPHGVLVPNVVTYNIMIQGLCNDGQMDKARDLFLDMEENAAAPDVITFDMLIHGFIRINEPSKVNELLHKM  548 (595)
Q Consensus       469 ~~A~~~~~~~~~~~~~p~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~  548 (595)
                      ++|+.+++++... .+.+...+..++..+...|++++|++.++++++.. |.+...+...+..+...|++++|..+++++
T Consensus       376 ~eA~~~l~~al~~-~P~n~~l~~~lA~l~~~~g~~~~A~~~l~~al~l~-Pd~~~l~~~~a~~al~~~~~~~A~~~~~~l  453 (765)
T PRK10049        376 PQAEMRARELAYN-APGNQGLRIDYASVLQARGWPRAAENELKKAEVLE-PRNINLEVEQAWTALDLQEWRQMDVLTDDV  453 (765)
T ss_pred             HHHHHHHHHHHHh-CCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHhhC-CCChHHHHHHHHHHHHhCCHHHHHHHHHHH
Confidence            8888888887763 22245677777777778888888888888887754 444566666677777788888888888888


Q ss_pred             HHCCCCCCHHHHHHHHHHH
Q 040027          549 KEKKVMPDASIVSIVVDLL  567 (595)
Q Consensus       549 ~~~~~~p~~~~~~~l~~~~  567 (595)
                      ++.  .|+......+-..+
T Consensus       454 l~~--~Pd~~~~~~~~~~~  470 (765)
T PRK10049        454 VAR--EPQDPGVQRLARAR  470 (765)
T ss_pred             HHh--CCCCHHHHHHHHHH
Confidence            863  46655555555544

>PRK15174 Vi polysaccharide export protein VexE; Provisional

Probab=99.91  E-value=1.5e-19  Score=185.80  Aligned_cols=357  Identities=9%  Similarity=-0.020  Sum_probs=283.2

Q ss_pred             ccCCCChHHHHHHHHHHHHhCCCCC-CHhhHHHHHHHHHcCCCchh-----HHhhCCCCCCHHHHHHHHHHHHhcCChhH
Q 040027           41 DINVITPNEAFCIFDYMLRMHPSPP-PVSSFNILLASLAKNKHYDT-----RLNATGLFPNLYTYNILINCFCKIGRVSL  114 (595)
Q Consensus        41 ~~~~~~~~~A~~~~~~~~~~~~~~~-~~~~~~~l~~~~~~~~~~~~-----~~~~~~~~~~~~~~~~l~~~~~~~g~~~~  114 (595)
                      ++++.+++.---+|...-+.+.... +..-....+..+.+.|++.+     .......+.++..+..++......|++++
T Consensus        15 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~~~A~~l~~~~l~~~p~~~~~l~~l~~~~l~~g~~~~   94 (656)
T PRK15174         15 LLKQEDWEGLCLYFSQHPEKVRDSAGNEQNIILFAIACLRKDETDVGLTLLSDRVLTAKNGRDLLRRWVISPLASSQPDA   94 (656)
T ss_pred             hhhhhchhhHhHHhhcccHhhhhhcccccCHHHHHHHHHhcCCcchhHHHhHHHHHhCCCchhHHHHHhhhHhhcCCHHH
Confidence            4566777776666665544433211 23445567788899999887     22333344456667777788888999999


Q ss_pred             HHHHHHHHHhCCCCCCHHHHHHHHHHHHhcCCHhHHHHHHHHHHhcCCCCCHhhHHHHHHHHHhcCChhHHHHHHHHHHh
Q 040027          115 GFIAFGRILRSCFTPNAATFNSLIKGLHAESRIMEAAALFTKLKAFGCEPNVITYNTLINGLCRTGHTMIALNLFEEMAN  194 (595)
Q Consensus       115 A~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~  194 (595)
                      |+..++++.... |.+...+..+...+...|++++|+..++++.... +.+...+..++..+...|++++|...++.+..
T Consensus        95 A~~~l~~~l~~~-P~~~~a~~~la~~l~~~g~~~~Ai~~l~~Al~l~-P~~~~a~~~la~~l~~~g~~~eA~~~~~~~~~  172 (656)
T PRK15174         95 VLQVVNKLLAVN-VCQPEDVLLVASVLLKSKQYATVADLAEQAWLAF-SGNSQIFALHLRTLVLMDKELQAISLARTQAQ  172 (656)
T ss_pred             HHHHHHHHHHhC-CCChHHHHHHHHHHHHcCCHHHHHHHHHHHHHhC-CCcHHHHHHHHHHHHHCCChHHHHHHHHHHHH
Confidence            999999999985 5577888899999999999999999999999874 44677888999999999999999999998877


Q ss_pred             cCCCCCccccCcHHHHHHHHHHHHHcCCHhHHHHHHHHHhhCCCCCCHhHHHHHHHHHHhcCCHHHHHHHHHHHHHCCCC
Q 040027          195 GNGEIGVVCKPNTVTYSTIIDGLCKEGFVDKAKALFLQMKDENINPDVVTYNSLIHGLCHANDWNEAKRLFIEMMDQGVQ  274 (595)
Q Consensus       195 ~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~~ll~~~~~~~~~~~A~~~~~~~~~~~~~  274 (595)
                      ..       +.+...+..+ ..+...|++++|...++.+......++...+..++..+...|++++|...++++.... +
T Consensus       173 ~~-------P~~~~a~~~~-~~l~~~g~~~eA~~~~~~~l~~~~~~~~~~~~~l~~~l~~~g~~~eA~~~~~~al~~~-p  243 (656)
T PRK15174        173 EV-------PPRGDMIATC-LSFLNKSRLPEDHDLARALLPFFALERQESAGLAVDTLCAVGKYQEAIQTGESALARG-L  243 (656)
T ss_pred             hC-------CCCHHHHHHH-HHHHHcCCHHHHHHHHHHHHhcCCCcchhHHHHHHHHHHHCCCHHHHHHHHHHHHhcC-C
Confidence            64       3344455444 3478899999999999998876433445555666788999999999999999999864 3


Q ss_pred             CCHhhHHHHHHHHHhcCChHH----HHHHHHHHHHCCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHhcCCCCCHHHH
Q 040027          275 PSVVTFNVIMDELCKNRKMDE----ASRLLDLMVQRGVRPNACTYNTLMDGFCLMGKINRAEELFGSMESMGCKHDDVSY  350 (595)
Q Consensus       275 ~~~~~~~~l~~~~~~~g~~~~----a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~  350 (595)
                      .+...+..+...+...|++++    |...|+++.+.. +.+...+..+...+...|++++|+..++++.... +.+...+
T Consensus       244 ~~~~~~~~Lg~~l~~~G~~~eA~~~A~~~~~~Al~l~-P~~~~a~~~lg~~l~~~g~~~eA~~~l~~al~l~-P~~~~a~  321 (656)
T PRK15174        244 DGAALRRSLGLAYYQSGRSREAKLQAAEHWRHALQFN-SDNVRIVTLYADALIRTGQNEKAIPLLQQSLATH-PDLPYVR  321 (656)
T ss_pred             CCHHHHHHHHHHHHHcCCchhhHHHHHHHHHHHHhhC-CCCHHHHHHHHHHHHHCCCHHHHHHHHHHHHHhC-CCCHHHH
Confidence            367788889999999999986    899999999874 3367788899999999999999999999999874 4566778


Q ss_pred             HHHHHHHHhCCCHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHccCCHHHHHHHHHHHHHC
Q 040027          351 NILINGYCKNKEVEEALSLYREMVSKGIKPTVVTYNTLFLGLFEIHQVEHALKLFDEMQRD  411 (595)
Q Consensus       351 ~~l~~~~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~  411 (595)
                      ..+..++.+.|++++|+..|+++...++. +...+..+..++...|++++|...|+++.+.
T Consensus       322 ~~La~~l~~~G~~~eA~~~l~~al~~~P~-~~~~~~~~a~al~~~G~~deA~~~l~~al~~  381 (656)
T PRK15174        322 AMYARALRQVGQYTAASDEFVQLAREKGV-TSKWNRYAAAALLQAGKTSEAESVFEHYIQA  381 (656)
T ss_pred             HHHHHHHHHCCCHHHHHHHHHHHHHhCcc-chHHHHHHHHHHHHCCCHHHHHHHHHHHHHh
Confidence            88999999999999999999999886432 2233444567788999999999999999876

>PRK10049 pgaA outer membrane protein PgaA; Provisional

Probab=99.91  E-value=5.8e-19  Score=185.60  Aligned_cols=432  Identities=9%  Similarity=-0.016  Sum_probs=262.9

Q ss_pred             HHHHHHHHhCCCCCCHhhHHHHHHHHHcCCCchh---HHhhC--CCCCCHHHHHHHHHHHHhcCChhHHHHHHHHHHhCC
Q 040027           52 CIFDYMLRMHPSPPPVSSFNILLASLAKNKHYDT---RLNAT--GLFPNLYTYNILINCFCKIGRVSLGFIAFGRILRSC  126 (595)
Q Consensus        52 ~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~---~~~~~--~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~  126 (595)
                      ..++. -+.+|.  ++.-..-.+.+..-.|+.++   .....  .-+.+...+..+...+...|++++|..+|+++++..
T Consensus         3 ~~~~~-~~~~~~--~~~~~~d~~~ia~~~g~~~~A~~~~~~~~~~~~~~a~~~~~lA~~~~~~g~~~~A~~~~~~al~~~   79 (765)
T PRK10049          3 SWLRQ-ALKSAL--SNNQIADWLQIALWAGQDAEVITVYNRYRVHMQLPARGYAAVAVAYRNLKQWQNSLTLWQKALSLE   79 (765)
T ss_pred             hhhhh-hhccCC--CHHHHHHHHHHHHHcCCHHHHHHHHHHHHhhCCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhC
Confidence            34444 344444  55555555666777888777   11111  123455678999999999999999999999999884


Q ss_pred             CCCCHHHHHHHHHHHHhcCCHhHHHHHHHHHHhcCCCCCHhhHHHHHHHHHhcCChhHHHHHHHHHHhcCCCCCccccCc
Q 040027          127 FTPNAATFNSLIKGLHAESRIMEAAALFTKLKAFGCEPNVITYNTLINGLCRTGHTMIALNLFEEMANGNGEIGVVCKPN  206 (595)
Q Consensus       127 ~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~~  206 (595)
                       +.+...+..++..+...|++++|+..++++.+.. +.+.. +..+..++...|+.++|+..++++.+..       |.+
T Consensus        80 -P~~~~a~~~la~~l~~~g~~~eA~~~l~~~l~~~-P~~~~-~~~la~~l~~~g~~~~Al~~l~~al~~~-------P~~  149 (765)
T PRK10049         80 -PQNDDYQRGLILTLADAGQYDEALVKAKQLVSGA-PDKAN-LLALAYVYKRAGRHWDELRAMTQALPRA-------PQT  149 (765)
T ss_pred             -CCCHHHHHHHHHHHHHCCCHHHHHHHHHHHHHhC-CCCHH-HHHHHHHHHHCCCHHHHHHHHHHHHHhC-------CCC
Confidence             5567788888899999999999999999999874 34566 8889999999999999999999999976       566


Q ss_pred             HHHHHHHHHHHHHcCCHhHHHHHHHHHhhCCCCCCHh------HHHHHHHHHHh-----cCCH---HHHHHHHHHHHHC-
Q 040027          207 TVTYSTIIDGLCKEGFVDKAKALFLQMKDENINPDVV------TYNSLIHGLCH-----ANDW---NEAKRLFIEMMDQ-  271 (595)
Q Consensus       207 ~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~~~~------~~~~ll~~~~~-----~~~~---~~A~~~~~~~~~~-  271 (595)
                      ...+..+..++...+..++|.+.++.+..   .|+..      ....++.....     .+++   ++|+..++.+.+. 
T Consensus       150 ~~~~~~la~~l~~~~~~e~Al~~l~~~~~---~p~~~~~l~~~~~~~~~r~~~~~~~~~~~r~~~ad~Al~~~~~ll~~~  226 (765)
T PRK10049        150 QQYPTEYVQALRNNRLSAPALGAIDDANL---TPAEKRDLEADAAAELVRLSFMPTRSEKERYAIADRALAQYDALEALW  226 (765)
T ss_pred             HHHHHHHHHHHHHCCChHHHHHHHHhCCC---CHHHHHHHHHHHHHHHHHhhcccccChhHHHHHHHHHHHHHHHHHhhc
Confidence            77778888889899999999999987764   23310      11111111111     1122   4455555555432 


Q ss_pred             CCCCCHh-hHH----HHHHHHHhcCChHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHhcCCCC-
Q 040027          272 GVQPSVV-TFN----VIMDELCKNRKMDEASRLLDLMVQRGVRPNACTYNTLMDGFCLMGKINRAEELFGSMESMGCKH-  345 (595)
Q Consensus       272 ~~~~~~~-~~~----~l~~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~-  345 (595)
                      ...|+.. .+.    ..+..+...|++++|+..|+.+.+.+.+........+..+|...|++++|+.+|+++.+..... 
T Consensus       227 ~~~p~~~~~~~~a~~d~l~~Ll~~g~~~eA~~~~~~ll~~~~~~P~~a~~~la~~yl~~g~~e~A~~~l~~~l~~~p~~~  306 (765)
T PRK10049        227 HDNPDATADYQRARIDRLGALLARDRYKDVISEYQRLKAEGQIIPPWAQRWVASAYLKLHQPEKAQSILTELFYHPETIA  306 (765)
T ss_pred             ccCCccchHHHHHHHHHHHHHHHhhhHHHHHHHHHHhhccCCCCCHHHHHHHHHHHHhcCCcHHHHHHHHHHhhcCCCCC
Confidence            1111111 110    0122233445555555555555444321011111123444555555555555555544331000 


Q ss_pred             --CHHHHHHHHHHHHhCCCHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHccCCHHHHHHHHHHHHHCCCCCC---HHHH
Q 040027          346 --DDVSYNILINGYCKNKEVEEALSLYREMVSKGIKPTVVTYNTLFLGLFEIHQVEHALKLFDEMQRDGVAAD---TRTY  420 (595)
Q Consensus       346 --~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~---~~~~  420 (595)
                        .......+..++...|++++|...++.+....+. ....+.                     ..  ...|+   ...+
T Consensus       307 ~~~~~~~~~L~~a~~~~g~~~eA~~~l~~~~~~~P~-~~~~~~---------------------~~--~~~p~~~~~~a~  362 (765)
T PRK10049        307 DLSDEELADLFYSLLESENYPGALTVTAHTINNSPP-FLRLYG---------------------SP--TSIPNDDWLQGQ  362 (765)
T ss_pred             CCChHHHHHHHHHHHhcccHHHHHHHHHHHhhcCCc-eEeecC---------------------CC--CCCCCchHHHHH
Confidence              0122333344444555555555555544443110 000000                     00  00122   1244


Q ss_pred             HHHHHHHHhcCCHHHHHHHHHHHHHcCCCcCHHHHHHHHHHHHhcCChHHHHHHHHhcccCCCCCC-HHHHHHHHHHHHh
Q 040027          421 TTFIDGLCKNGYIIEAVELFRTLRILKCELDIQAYNCLIDGLCKSGRLKFAWELFCSLPHGVLVPN-VVTYNIMIQGLCN  499 (595)
Q Consensus       421 ~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~p~-~~~~~~l~~~~~~  499 (595)
                      ..+...+...|++++|+.+++++.... |.+...+..++..+...|++++|++.++++..  +.|+ ...+..++..+..
T Consensus       363 ~~~a~~l~~~g~~~eA~~~l~~al~~~-P~n~~l~~~lA~l~~~~g~~~~A~~~l~~al~--l~Pd~~~l~~~~a~~al~  439 (765)
T PRK10049        363 SLLSQVAKYSNDLPQAEMRARELAYNA-PGNQGLRIDYASVLQARGWPRAAENELKKAEV--LEPRNINLEVEQAWTALD  439 (765)
T ss_pred             HHHHHHHHHcCCHHHHHHHHHHHHHhC-CCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHh--hCCCChHHHHHHHHHHHH
Confidence            556667777888888888888887765 66677888888888888888888888888877  4565 5566667777778


Q ss_pred             cCChhHHHHHHHHHHHcCCCCCHHHHHHH
Q 040027          500 DGQMDKARDLFLDMEENAAAPDVITFDML  528 (595)
Q Consensus       500 ~g~~~~A~~~~~~~~~~~~~~~~~~~~~l  528 (595)
                      .|++++|+.+++++++.  .|+......+
T Consensus       440 ~~~~~~A~~~~~~ll~~--~Pd~~~~~~~  466 (765)
T PRK10049        440 LQEWRQMDVLTDDVVAR--EPQDPGVQRL  466 (765)
T ss_pred             hCCHHHHHHHHHHHHHh--CCCCHHHHHH
Confidence            88888888888888875  3444433333

>PRK11788 tetratricopeptide repeat protein; Provisional

Probab=99.90  E-value=1.3e-20  Score=185.19  Aligned_cols=304  Identities=15%  Similarity=0.061  Sum_probs=145.5

Q ss_pred             HHHhcCChhHHHHHHHHHHhCCCCCCHHHHHHHHHHHHhcCCHhHHHHHHHHHHhcCCCCC---HhhHHHHHHHHHhcCC
Q 040027          105 CFCKIGRVSLGFIAFGRILRSCFTPNAATFNSLIKGLHAESRIMEAAALFTKLKAFGCEPN---VITYNTLINGLCRTGH  181 (595)
Q Consensus       105 ~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~~---~~~~~~l~~~~~~~g~  181 (595)
                      .+...|++++|+..|+++.+.+ +.+..++..+...+...|++++|..+++.+...+..++   ..++..++..|...|+
T Consensus        44 ~~~~~~~~~~A~~~~~~al~~~-p~~~~~~~~la~~~~~~g~~~~A~~~~~~~l~~~~~~~~~~~~~~~~La~~~~~~g~  122 (389)
T PRK11788         44 NFLLNEQPDKAIDLFIEMLKVD-PETVELHLALGNLFRRRGEVDRAIRIHQNLLSRPDLTREQRLLALQELGQDYLKAGL  122 (389)
T ss_pred             HHHhcCChHHHHHHHHHHHhcC-cccHHHHHHHHHHHHHcCcHHHHHHHHHHHhcCCCCCHHHHHHHHHHHHHHHHHCCC
Confidence            3445556666666666665553 23344555555555555666666655555554321111   1234444555555555


Q ss_pred             hhHHHHHHHHHHhcCCCCCccccCcHHHHHHHHHHHHHcCCHhHHHHHHHHHhhCCCCCCHhHHHHHHHHHHhcCCHHHH
Q 040027          182 TMIALNLFEEMANGNGEIGVVCKPNTVTYSTIIDGLCKEGFVDKAKALFLQMKDENINPDVVTYNSLIHGLCHANDWNEA  261 (595)
Q Consensus       182 ~~~A~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~~ll~~~~~~~~~~~A  261 (595)
                      +++|..+|+++.+..       +.+..++..++.++...|++++|.+.++.+.+.+..+....                 
T Consensus       123 ~~~A~~~~~~~l~~~-------~~~~~~~~~la~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~-----------------  178 (389)
T PRK11788        123 LDRAEELFLQLVDEG-------DFAEGALQQLLEIYQQEKDWQKAIDVAERLEKLGGDSLRVE-----------------  178 (389)
T ss_pred             HHHHHHHHHHHHcCC-------cchHHHHHHHHHHHHHhchHHHHHHHHHHHHHhcCCcchHH-----------------
Confidence            555555555555432       23344455555555555555555555555544321111000                 


Q ss_pred             HHHHHHHHHCCCCCCHhhHHHHHHHHHhcCChHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHhc
Q 040027          262 KRLFIEMMDQGVQPSVVTFNVIMDELCKNRKMDEASRLLDLMVQRGVRPNACTYNTLMDGFCLMGKINRAEELFGSMESM  341 (595)
Q Consensus       262 ~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~  341 (595)
                                    ....+..++..+.+.|++++|...++++.+.. +.+...+..++..+...|++++|.++++++.+.
T Consensus       179 --------------~~~~~~~la~~~~~~~~~~~A~~~~~~al~~~-p~~~~~~~~la~~~~~~g~~~~A~~~~~~~~~~  243 (389)
T PRK11788        179 --------------IAHFYCELAQQALARGDLDAARALLKKALAAD-PQCVRASILLGDLALAQGDYAAAIEALERVEEQ  243 (389)
T ss_pred             --------------HHHHHHHHHHHHHhCCCHHHHHHHHHHHHhHC-cCCHHHHHHHHHHHHHCCCHHHHHHHHHHHHHH
Confidence                          00122333444444555555555555544432 112334444455555555555555555555543


Q ss_pred             CCCCCHHHHHHHHHHHHhCCCHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHccCCHHHHHHHHHHHHHCCCCCCHHHHH
Q 040027          342 GCKHDDVSYNILINGYCKNKEVEEALSLYREMVSKGIKPTVVTYNTLFLGLFEIHQVEHALKLFDEMQRDGVAADTRTYT  421 (595)
Q Consensus       342 ~~~~~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~  421 (595)
                      +.......+..++.+|...|++++|...++++.+.  .|+...+..++..+.+.|++++|..+++++.+.  .|+...+.
T Consensus       244 ~p~~~~~~~~~l~~~~~~~g~~~~A~~~l~~~~~~--~p~~~~~~~la~~~~~~g~~~~A~~~l~~~l~~--~P~~~~~~  319 (389)
T PRK11788        244 DPEYLSEVLPKLMECYQALGDEAEGLEFLRRALEE--YPGADLLLALAQLLEEQEGPEAAQALLREQLRR--HPSLRGFH  319 (389)
T ss_pred             ChhhHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHh--CCCchHHHHHHHHHHHhCCHHHHHHHHHHHHHh--CcCHHHHH
Confidence            21111233445555555555555555555555544  233333455555555555555555555555543  34555555


Q ss_pred             HHHHHHHh---cCCHHHHHHHHHHHHHcCCCcCH
Q 040027          422 TFIDGLCK---NGYIIEAVELFRTLRILKCELDI  452 (595)
Q Consensus       422 ~l~~~~~~---~g~~~~A~~~~~~~~~~~~~~~~  452 (595)
                      .++..+..   .|+.+++..+++++.+.++.|++
T Consensus       320 ~l~~~~~~~~~~g~~~~a~~~~~~~~~~~~~~~p  353 (389)
T PRK11788        320 RLLDYHLAEAEEGRAKESLLLLRDLVGEQLKRKP  353 (389)
T ss_pred             HHHHHhhhccCCccchhHHHHHHHHHHHHHhCCC
Confidence            44444432   33555555555555544433333

>PRK14574 hmsH outer membrane protein; Provisional

Probab=99.89  E-value=1.1e-17  Score=172.24  Aligned_cols=423  Identities=10%  Similarity=0.017  Sum_probs=226.9

Q ss_pred             cCCCChHHHHHHHHHHHHhCCCCCCH-hhHHHHHHHHHcCCCchh--HHhhCCCCCC---HHHHHHHHHHHHhcCChhHH
Q 040027           42 INVITPNEAFCIFDYMLRMHPSPPPV-SSFNILLASLAKNKHYDT--RLNATGLFPN---LYTYNILINCFCKIGRVSLG  115 (595)
Q Consensus        42 ~~~~~~~~A~~~~~~~~~~~~~~~~~-~~~~~l~~~~~~~~~~~~--~~~~~~~~~~---~~~~~~l~~~~~~~g~~~~A  115 (595)
                      .+.|+++.|+..|+++++.+|.  ++ ..+ -++..+...|+..+  ......+.|+   ......++..+...|++++|
T Consensus        45 ~r~Gd~~~Al~~L~qaL~~~P~--~~~av~-dll~l~~~~G~~~~A~~~~eka~~p~n~~~~~llalA~ly~~~gdyd~A  121 (822)
T PRK14574         45 ARAGDTAPVLDYLQEESKAGPL--QSGQVD-DWLQIAGWAGRDQEVIDVYERYQSSMNISSRGLASAARAYRNEKRWDQA  121 (822)
T ss_pred             HhCCCHHHHHHHHHHHHhhCcc--chhhHH-HHHHHHHHcCCcHHHHHHHHHhccCCCCCHHHHHHHHHHHHHcCCHHHH
Confidence            7889999999999999999998  43 333 66667777777776  2222222332   22223335567777888888


Q ss_pred             HHHHHHHHhCCCCCCHHHHHHHHHHHHhcCCHhHHHHHHHHHHhcCCCCCHhhHHHHHHHHHhcCChhHHHHHHHHHHhc
Q 040027          116 FIAFGRILRSCFTPNAATFNSLIKGLHAESRIMEAAALFTKLKAFGCEPNVITYNTLINGLCRTGHTMIALNLFEEMANG  195 (595)
Q Consensus       116 ~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~  195 (595)
                      +.+|+++++.. +.++..+..++..+...++.++|++.++++...  .|+...+..++..+...++..+|++.++++.+.
T Consensus       122 iely~kaL~~d-P~n~~~l~gLa~~y~~~~q~~eAl~~l~~l~~~--dp~~~~~l~layL~~~~~~~~~AL~~~ekll~~  198 (822)
T PRK14574        122 LALWQSSLKKD-PTNPDLISGMIMTQADAGRGGVVLKQATELAER--DPTVQNYMTLSYLNRATDRNYDALQASSEAVRL  198 (822)
T ss_pred             HHHHHHHHhhC-CCCHHHHHHHHHHHhhcCCHHHHHHHHHHhccc--CcchHHHHHHHHHHHhcchHHHHHHHHHHHHHh
Confidence            88888888775 335666667777777788888888888887765  444444444444444455665688888888776


Q ss_pred             CCCCCccccCcHHHHHHHHHHHHHcCCHhHHHHHHHHHhhCCCCCCHhHH------HHHHHHH---H--hcCC---HHHH
Q 040027          196 NGEIGVVCKPNTVTYSTIIDGLCKEGFVDKAKALFLQMKDENINPDVVTY------NSLIHGL---C--HAND---WNEA  261 (595)
Q Consensus       196 ~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~------~~ll~~~---~--~~~~---~~~A  261 (595)
                      +       |.+...+..+..++.+.|-...|.++..+-... +.+....+      ..+++.-   .  ...+   .+.|
T Consensus       199 ~-------P~n~e~~~~~~~~l~~~~~~~~a~~l~~~~p~~-f~~~~~~~l~~~~~a~~vr~a~~~~~~~~~r~~~~d~a  270 (822)
T PRK14574        199 A-------PTSEEVLKNHLEILQRNRIVEPALRLAKENPNL-VSAEHYRQLERDAAAEQVRMAVLPTRSETERFDIADKA  270 (822)
T ss_pred             C-------CCCHHHHHHHHHHHHHcCCcHHHHHHHHhCccc-cCHHHHHHHHHHHHHHHHhhcccccccchhhHHHHHHH
Confidence            5       456777777777777777777777666554322 11111111      0001000   0  0111   2334


Q ss_pred             HHHHHHHHHC-CCCCCH-h----hHHHHHHHHHhcCChHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHhcCCHHHHHHHH
Q 040027          262 KRLFIEMMDQ-GVQPSV-V----TFNVIMDELCKNRKMDEASRLLDLMVQRGVRPNACTYNTLMDGFCLMGKINRAEELF  335 (595)
Q Consensus       262 ~~~~~~~~~~-~~~~~~-~----~~~~l~~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~  335 (595)
                      +.-++.+... +..|.. .    .....+-++...|++.++++.|+.+...+.+....+-..++.+|...+++++|+.+|
T Consensus       271 la~~~~l~~~~~~~p~~~~~~~~~~~Drl~aL~~r~r~~~vi~~y~~l~~~~~~~P~y~~~a~adayl~~~~P~kA~~l~  350 (822)
T PRK14574        271 LADYQNLLTRWGKDPEAQADYQRARIDRLGALLVRHQTADLIKEYEAMEAEGYKMPDYARRWAASAYIDRRLPEKAAPIL  350 (822)
T ss_pred             HHHHHHHHhhccCCCccchHHHHHHHHHHHHHHHhhhHHHHHHHHHHhhhcCCCCCHHHHHHHHHHHHhcCCcHHHHHHH
Confidence            4444444332 111211 1    111233455556666666666666665554444445555666666666666666666


Q ss_pred             HHHHhcCC-----CCCHHHHHHHHHHHHhCCCHHHHHHHHHHHHHCCC-----------CC--CH-HHHHHHHHHHHccC
Q 040027          336 GSMESMGC-----KHDDVSYNILINGYCKNKEVEEALSLYREMVSKGI-----------KP--TV-VTYNTLFLGLFEIH  396 (595)
Q Consensus       336 ~~~~~~~~-----~~~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~~~~-----------~~--~~-~~~~~l~~~~~~~~  396 (595)
                      +.+.....     +++......|..+|...+++++|..+++++.+..+           .|  +- .....++..+...|
T Consensus       351 ~~~~~~~~~~~~~~~~~~~~~~L~yA~ld~e~~~~A~~~l~~~~~~~p~~~~~~~~~~~~pn~d~~~~~~l~a~~~~~~g  430 (822)
T PRK14574        351 SSLYYSDGKTFRNSDDLLDADDLYYSLNESEQLDKAYQFAVNYSEQTPYQVGVYGLPGKEPNDDWIEGQTLLVQSLVALN  430 (822)
T ss_pred             HHHhhccccccCCCcchHHHHHHHHHHHhcccHHHHHHHHHHHHhcCCcEEeccCCCCCCCCccHHHHHHHHHHHHHHcC
Confidence            66544320     11222234555666666666666666666655211           01  11 11222333344445


Q ss_pred             CHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCcCHHHHHHHHHHHHhcCChHHHHHHHH
Q 040027          397 QVEHALKLFDEMQRDGVAADTRTYTTFIDGLCKNGYIIEAVELFRTLRILKCELDIQAYNCLIDGLCKSGRLKFAWELFC  476 (595)
Q Consensus       397 ~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~  476 (595)
                      +..+|++.++.+... .|-+......+...+...|.+.+|...++.+.... +.+..+....+.++...+++++|..+.+
T Consensus       431 dl~~Ae~~le~l~~~-aP~n~~l~~~~A~v~~~Rg~p~~A~~~~k~a~~l~-P~~~~~~~~~~~~al~l~e~~~A~~~~~  508 (822)
T PRK14574        431 DLPTAQKKLEDLSST-APANQNLRIALASIYLARDLPRKAEQELKAVESLA-PRSLILERAQAETAMALQEWHQMELLTD  508 (822)
T ss_pred             CHHHHHHHHHHHHHh-CCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHhhhC-CccHHHHHHHHHHHHhhhhHHHHHHHHH
Confidence            555555555554443 24444444444444455555555555554444332 3334444444444444455555544444


Q ss_pred             hccc
Q 040027          477 SLPH  480 (595)
Q Consensus       477 ~~~~  480 (595)
                      .+.+
T Consensus       509 ~l~~  512 (822)
T PRK14574        509 DVIS  512 (822)
T ss_pred             HHHh
Confidence            4444

>PRK14574 hmsH outer membrane protein; Provisional

Probab=99.89  E-value=2.6e-17  Score=169.51  Aligned_cols=449  Identities=12%  Similarity=0.029  Sum_probs=326.8

Q ss_pred             HHHHHHHHHHHHhcCChhHHHHHHHHHHhCCCCCCH--HHHHHHHHHHHhcCCHhHHHHHHHHHHhcCCCCCHhhHHHHH
Q 040027           96 LYTYNILINCFCKIGRVSLGFIAFGRILRSCFTPNA--ATFNSLIKGLHAESRIMEAAALFTKLKAFGCEPNVITYNTLI  173 (595)
Q Consensus        96 ~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~~~--~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~~l~  173 (595)
                      +.+.-.-+-...+.|+++.|+..|+++++..  |+.  .++ .++..+...|+.++|+..+++..... +........++
T Consensus        34 ~~~~y~~aii~~r~Gd~~~Al~~L~qaL~~~--P~~~~av~-dll~l~~~~G~~~~A~~~~eka~~p~-n~~~~~llalA  109 (822)
T PRK14574         34 ADTQYDSLIIRARAGDTAPVLDYLQEESKAG--PLQSGQVD-DWLQIAGWAGRDQEVIDVYERYQSSM-NISSRGLASAA  109 (822)
T ss_pred             hhHHHHHHHHHHhCCCHHHHHHHHHHHHhhC--ccchhhHH-HHHHHHHHcCCcHHHHHHHHHhccCC-CCCHHHHHHHH
Confidence            3333344445778999999999999999884  443  344 88888888999999999999998321 22333344446


Q ss_pred             HHHHhcCChhHHHHHHHHHHhcCCCCCccccCcHHHHHHHHHHHHHcCCHhHHHHHHHHHhhCCCCCCHhHHHHHHHHHH
Q 040027          174 NGLCRTGHTMIALNLFEEMANGNGEIGVVCKPNTVTYSTIIDGLCKEGFVDKAKALFLQMKDENINPDVVTYNSLIHGLC  253 (595)
Q Consensus       174 ~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~~ll~~~~  253 (595)
                      ..+...|++++|+++|+++.+.+       |.++..+..++..+...++.++|++.++++...  .|+...+..++..+.
T Consensus       110 ~ly~~~gdyd~Aiely~kaL~~d-------P~n~~~l~gLa~~y~~~~q~~eAl~~l~~l~~~--dp~~~~~l~layL~~  180 (822)
T PRK14574        110 RAYRNEKRWDQALALWQSSLKKD-------PTNPDLISGMIMTQADAGRGGVVLKQATELAER--DPTVQNYMTLSYLNR  180 (822)
T ss_pred             HHHHHcCCHHHHHHHHHHHHhhC-------CCCHHHHHHHHHHHhhcCCHHHHHHHHHHhccc--CcchHHHHHHHHHHH
Confidence            68888999999999999999986       566788888889999999999999999999886  455555655555555


Q ss_pred             hcCCHHHHHHHHHHHHHCCCCCCHhhHHHHHHHHHhcCChHHHHHHHHHHHHCCCCCCHHH------HHHHHHHH---H-
Q 040027          254 HANDWNEAKRLFIEMMDQGVQPSVVTFNVIMDELCKNRKMDEASRLLDLMVQRGVRPNACT------YNTLMDGF---C-  323 (595)
Q Consensus       254 ~~~~~~~A~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~------~~~l~~~~---~-  323 (595)
                      ..++..+|++.++++.+.. +.+...+..+..++.+.|-...|.++..+-... +.+....      ....++.-   . 
T Consensus       181 ~~~~~~~AL~~~ekll~~~-P~n~e~~~~~~~~l~~~~~~~~a~~l~~~~p~~-f~~~~~~~l~~~~~a~~vr~a~~~~~  258 (822)
T PRK14574        181 ATDRNYDALQASSEAVRLA-PTSEEVLKNHLEILQRNRIVEPALRLAKENPNL-VSAEHYRQLERDAAAEQVRMAVLPTR  258 (822)
T ss_pred             hcchHHHHHHHHHHHHHhC-CCCHHHHHHHHHHHHHcCCcHHHHHHHHhCccc-cCHHHHHHHHHHHHHHHHhhcccccc
Confidence            5677767999999999873 336777788889999999999888777653321 1111100      11111110   0 


Q ss_pred             -hcCC---HHHHHHHHHHHHhc-CCCCCH-H----HHHHHHHHHHhCCCHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHH
Q 040027          324 -LMGK---INRAEELFGSMESM-GCKHDD-V----SYNILINGYCKNKEVEEALSLYREMVSKGIKPTVVTYNTLFLGLF  393 (595)
Q Consensus       324 -~~~~---~~~a~~~~~~~~~~-~~~~~~-~----~~~~l~~~~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~~l~~~~~  393 (595)
                       ...+   .+.|..-++.+... +..|.. .    ...-.+.++...+++.++++.|+.+...+.+....+...+..+|.
T Consensus       259 ~~~~r~~~~d~ala~~~~l~~~~~~~p~~~~~~~~~~~Drl~aL~~r~r~~~vi~~y~~l~~~~~~~P~y~~~a~adayl  338 (822)
T PRK14574        259 SETERFDIADKALADYQNLLTRWGKDPEAQADYQRARIDRLGALLVRHQTADLIKEYEAMEAEGYKMPDYARRWAASAYI  338 (822)
T ss_pred             cchhhHHHHHHHHHHHHHHHhhccCCCccchHHHHHHHHHHHHHHHhhhHHHHHHHHHHhhhcCCCCCHHHHHHHHHHHH
Confidence             1122   34455555555542 111221 1    223446677889999999999999998876655567888999999


Q ss_pred             ccCCHHHHHHHHHHHHHCC-----CCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHHcCC-----------CcC---HHH
Q 040027          394 EIHQVEHALKLFDEMQRDG-----VAADTRTYTTFIDGLCKNGYIIEAVELFRTLRILKC-----------ELD---IQA  454 (595)
Q Consensus       394 ~~~~~~~a~~~~~~~~~~~-----~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~-----------~~~---~~~  454 (595)
                      ..+++++|..+|..+....     .+++......|.-+|...+++++|..+++++.+...           .|+   ...
T Consensus       339 ~~~~P~kA~~l~~~~~~~~~~~~~~~~~~~~~~~L~yA~ld~e~~~~A~~~l~~~~~~~p~~~~~~~~~~~~pn~d~~~~  418 (822)
T PRK14574        339 DRRLPEKAAPILSSLYYSDGKTFRNSDDLLDADDLYYSLNESEQLDKAYQFAVNYSEQTPYQVGVYGLPGKEPNDDWIEG  418 (822)
T ss_pred             hcCCcHHHHHHHHHHhhccccccCCCcchHHHHHHHHHHHhcccHHHHHHHHHHHHhcCCcEEeccCCCCCCCCccHHHH
Confidence            9999999999999987642     123444457788889999999999999999987321           112   223


Q ss_pred             HHHHHHHHHhcCChHHHHHHHHhcccCCCCC-CHHHHHHHHHHHHhcCChhHHHHHHHHHHHcCCCCCHHHHHHHHHHHH
Q 040027          455 YNCLIDGLCKSGRLKFAWELFCSLPHGVLVP-NVVTYNIMIQGLCNDGQMDKARDLFLDMEENAAAPDVITFDMLIHGFI  533 (595)
Q Consensus       455 ~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~p-~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~~l~~~~~  533 (595)
                      +..++..+...|++.+|++.++++...  .| |......+...+...|.+.+|...++.+.... +.+..+....+.++.
T Consensus       419 ~~l~a~~~~~~gdl~~Ae~~le~l~~~--aP~n~~l~~~~A~v~~~Rg~p~~A~~~~k~a~~l~-P~~~~~~~~~~~~al  495 (822)
T PRK14574        419 QTLLVQSLVALNDLPTAQKKLEDLSST--APANQNLRIALASIYLARDLPRKAEQELKAVESLA-PRSLILERAQAETAM  495 (822)
T ss_pred             HHHHHHHHHHcCCHHHHHHHHHHHHHh--CCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHhhhC-CccHHHHHHHHHHHH
Confidence            455677788999999999999999874  44 67888999999999999999999997777763 555677788889999


Q ss_pred             HcCChhHHHHHHHHHHHCCCCCCHHHHHHHH
Q 040027          534 RINEPSKVNELLHKMKEKKVMPDASIVSIVV  564 (595)
Q Consensus       534 ~~g~~~~A~~~~~~~~~~~~~p~~~~~~~l~  564 (595)
                      ..|++.+|..+.+.+.+.  .|+......+-
T Consensus       496 ~l~e~~~A~~~~~~l~~~--~Pe~~~~~~l~  524 (822)
T PRK14574        496 ALQEWHQMELLTDDVISR--SPEDIPSQELD  524 (822)
T ss_pred             hhhhHHHHHHHHHHHHhh--CCCchhHHHHH
Confidence            999999999999999874  46554444433

>KOG0495 consensus HAT repeat protein [RNA processing and modification]

Probab=99.89  E-value=1.5e-17  Score=156.37  Aligned_cols=515  Identities=12%  Similarity=0.054  Sum_probs=413.7

Q ss_pred             ChHHHHHHHHHHHHhCCCCCCHhhHHHHHHHHHcCCCchhHHhhCC---CCCCHHHHHHHHHHHHhcCChhHHHHHHHHH
Q 040027           46 TPNEAFCIFDYMLRMHPSPPPVSSFNILLASLAKNKHYDTRLNATG---LFPNLYTYNILINCFCKIGRVSLGFIAFGRI  122 (595)
Q Consensus        46 ~~~~A~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~---~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~  122 (595)
                      +...=.++++++++..|.  ++..|......  .......-|....   .+.+...|.+    +.+..-|+.|..++..+
T Consensus       361 ~~~~K~RVlRKALe~iP~--sv~LWKaAVel--E~~~darilL~rAveccp~s~dLwlA----larLetYenAkkvLNka  432 (913)
T KOG0495|consen  361 DTKNKKRVLRKALEHIPR--SVRLWKAAVEL--EEPEDARILLERAVECCPQSMDLWLA----LARLETYENAKKVLNKA  432 (913)
T ss_pred             HHHHHHHHHHHHHHhCCc--hHHHHHHHHhc--cChHHHHHHHHHHHHhccchHHHHHH----HHHHHHHHHHHHHHHHH
Confidence            345556899999999998  88999876642  1111111333333   2345666664    45567789999999999


Q ss_pred             HhCCCCCCHHHHHHHHHHHHhcCCHhHHHHHHHH----HHhcCCCCCHhhHHHHHHHHHhcCChhHHHHHHHHHHhcCCC
Q 040027          123 LRSCFTPNAATFNSLIKGLHAESRIMEAAALFTK----LKAFGCEPNVITYNTLINGLCRTGHTMIALNLFEEMANGNGE  198 (595)
Q Consensus       123 ~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~----~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~  198 (595)
                      .+. ++.+..+|......--.+|+.+...++.++    +...|+..+...|..=...+-..|..-.+..++...+..+.+
T Consensus       433 Re~-iptd~~IWitaa~LEE~ngn~~mv~kii~rgl~~L~~ngv~i~rdqWl~eAe~~e~agsv~TcQAIi~avigigvE  511 (913)
T KOG0495|consen  433 REI-IPTDREIWITAAKLEEANGNVDMVEKIIDRGLSELQANGVEINRDQWLKEAEACEDAGSVITCQAIIRAVIGIGVE  511 (913)
T ss_pred             Hhh-CCCChhHHHHHHHHHHhcCCHHHHHHHHHHHHHHHhhcceeecHHHHHHHHHHHhhcCChhhHHHHHHHHHhhccc
Confidence            887 577899998888877889999999988776    445688889999999999999999999999999988876622


Q ss_pred             CCccccCcHHHHHHHHHHHHHcCCHhHHHHHHHHHhhCCCCCCHhHHHHHHHHHHhcCCHHHHHHHHHHHHHCCCCCCHh
Q 040027          199 IGVVCKPNTVTYSTIIDGLCKEGFVDKAKALFLQMKDENINPDVVTYNSLIHGLCHANDWNEAKRLFIEMMDQGVQPSVV  278 (595)
Q Consensus       199 ~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~~ll~~~~~~~~~~~A~~~~~~~~~~~~~~~~~  278 (595)
                          -.....+|..-...|.+.+.++-|..+|....+. ++-+...|......--..|..++...++++.... .+....
T Consensus       512 ----eed~~~tw~~da~~~~k~~~~~carAVya~alqv-fp~k~slWlra~~~ek~hgt~Esl~Allqkav~~-~pkae~  585 (913)
T KOG0495|consen  512 ----EEDRKSTWLDDAQSCEKRPAIECARAVYAHALQV-FPCKKSLWLRAAMFEKSHGTRESLEALLQKAVEQ-CPKAEI  585 (913)
T ss_pred             ----cchhHhHHhhhHHHHHhcchHHHHHHHHHHHHhh-ccchhHHHHHHHHHHHhcCcHHHHHHHHHHHHHh-CCcchh
Confidence                1233678999999999999999999999999886 3457778888888888889999999999999987 344666


Q ss_pred             hHHHHHHHHHhcCChHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHhcCCCCCHHHHHHHHHHHH
Q 040027          279 TFNVIMDELCKNRKMDEASRLLDLMVQRGVRPNACTYNTLMDGFCLMGKINRAEELFGSMESMGCKHDDVSYNILINGYC  358 (595)
Q Consensus       279 ~~~~l~~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~  358 (595)
                      .|......+...|+...|..++..+.+.+. .+...+...+..-....+++.|..+|.+....  .++...|..-+..--
T Consensus       586 lwlM~ake~w~agdv~~ar~il~~af~~~p-nseeiwlaavKle~en~e~eraR~llakar~~--sgTeRv~mKs~~~er  662 (913)
T KOG0495|consen  586 LWLMYAKEKWKAGDVPAARVILDQAFEANP-NSEEIWLAAVKLEFENDELERARDLLAKARSI--SGTERVWMKSANLER  662 (913)
T ss_pred             HHHHHHHHHHhcCCcHHHHHHHHHHHHhCC-CcHHHHHHHHHHhhccccHHHHHHHHHHHhcc--CCcchhhHHHhHHHH
Confidence            788888888999999999999999998753 37888888899999999999999999998876  577778887787777


Q ss_pred             hCCCHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHccCCHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHhcCCHHHHHH
Q 040027          359 KNKEVEEALSLYREMVSKGIKPTVVTYNTLFLGLFEIHQVEHALKLFDEMQRDGVAADTRTYTTFIDGLCKNGYIIEAVE  438 (595)
Q Consensus       359 ~~~~~~~A~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~  438 (595)
                      -.++.++|++++++.++.- +.-...|..+.+.+.+.++.+.|...|..-.+. ++.....|..+...--+.|.+-+|..
T Consensus       663 ~ld~~eeA~rllEe~lk~f-p~f~Kl~lmlGQi~e~~~~ie~aR~aY~~G~k~-cP~~ipLWllLakleEk~~~~~rAR~  740 (913)
T KOG0495|consen  663 YLDNVEEALRLLEEALKSF-PDFHKLWLMLGQIEEQMENIEMAREAYLQGTKK-CPNSIPLWLLLAKLEEKDGQLVRARS  740 (913)
T ss_pred             HhhhHHHHHHHHHHHHHhC-CchHHHHHHHhHHHHHHHHHHHHHHHHHhcccc-CCCCchHHHHHHHHHHHhcchhhHHH
Confidence            8899999999999998862 324567888889999999999999999887776 46666777777777788899999999


Q ss_pred             HHHHHHHcCCCcCHHHHHHHHHHHHhcCChHHHHHHHHhcccCCCCCCHHHHHHHHHHHHhcCChhHHHHHHHHHHHcCC
Q 040027          439 LFRTLRILKCELDIQAYNCLIDGLCKSGRLKFAWELFCSLPHGVLVPNVVTYNIMIQGLCNDGQMDKARDLFLDMEENAA  518 (595)
Q Consensus       439 ~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~p~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~  518 (595)
                      ++++....+ |.+...|...+++-.+.|+.+.|..+..++++. .+.+...|..-|....+.++-....+.+++.     
T Consensus       741 ildrarlkN-Pk~~~lwle~Ir~ElR~gn~~~a~~lmakALQe-cp~sg~LWaEaI~le~~~~rkTks~DALkkc-----  813 (913)
T KOG0495|consen  741 ILDRARLKN-PKNALLWLESIRMELRAGNKEQAELLMAKALQE-CPSSGLLWAEAIWLEPRPQRKTKSIDALKKC-----  813 (913)
T ss_pred             HHHHHHhcC-CCcchhHHHHHHHHHHcCCHHHHHHHHHHHHHh-CCccchhHHHHHHhccCcccchHHHHHHHhc-----
Confidence            999999877 788999999999999999999999999998875 4445678888888888887766666655544     


Q ss_pred             CCCHHHHHHHHHHHHHcCChhHHHHHHHHHHHCCCCCC-HHHHHHHHHHHHhcCccc---ccchHH-HHhhhhccc
Q 040027          519 APDVITFDMLIHGFIRINEPSKVNELLHKMKEKKVMPD-ASIVSIVVDLLVKNEISL---KSLPSF-LVQERQGEV  589 (595)
Q Consensus       519 ~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~p~-~~~~~~l~~~~~~~g~~~---~~i~~~-~~~~~~~~~  589 (595)
                      ..|+.....+...|....++++|.++|++.++.+  || -.+|..+...+.+.|.-+   ++++++ ..+|+.|+.
T Consensus       814 e~dphVllaia~lfw~e~k~~kar~Wf~Ravk~d--~d~GD~wa~fykfel~hG~eed~kev~~~c~~~EP~hG~~  887 (913)
T KOG0495|consen  814 EHDPHVLLAIAKLFWSEKKIEKAREWFERAVKKD--PDNGDAWAWFYKFELRHGTEEDQKEVLKKCETAEPTHGEL  887 (913)
T ss_pred             cCCchhHHHHHHHHHHHHHHHHHHHHHHHHHccC--CccchHHHHHHHHHHHhCCHHHHHHHHHHHhccCCCCCcH
Confidence            3466777788888899999999999999999754  64 588888899999999665   555554 355555543

>KOG2076 consensus RNA polymerase III transcription factor TFIIIC [Transcription]

Probab=99.88  E-value=2.7e-17  Score=160.82  Aligned_cols=361  Identities=14%  Similarity=0.127  Sum_probs=268.5

Q ss_pred             ccccccCCCChHHHHHHHHHHHHhCCCCCCHhhHHHHHHHHHcCCCchh----HHhhCCCC-CCHHHHHHHHHHHHhcCC
Q 040027           37 TREGDINVITPNEAFCIFDYMLRMHPSPPPVSSFNILLASLAKNKHYDT----RLNATGLF-PNLYTYNILINCFCKIGR  111 (595)
Q Consensus        37 ~~~~~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~----~~~~~~~~-~~~~~~~~l~~~~~~~g~  111 (595)
                      .+.-+-.+|++++|.+++.++++.+|.  ++..|..|..+|-..|+...    .+....+. .|...|..+.....+.|+
T Consensus       145 eAN~lfarg~~eeA~~i~~EvIkqdp~--~~~ay~tL~~IyEqrGd~eK~l~~~llAAHL~p~d~e~W~~ladls~~~~~  222 (895)
T KOG2076|consen  145 EANNLFARGDLEEAEEILMEVIKQDPR--NPIAYYTLGEIYEQRGDIEKALNFWLLAAHLNPKDYELWKRLADLSEQLGN  222 (895)
T ss_pred             HHHHHHHhCCHHHHHHHHHHHHHhCcc--chhhHHHHHHHHHHcccHHHHHHHHHHHHhcCCCChHHHHHHHHHHHhccc
Confidence            333444559999999999999999998  99999999999999998887    44445544 488999999999999999


Q ss_pred             hhHHHHHHHHHHhCCCCCCHHHHHHHHHHHHhcCCHhHHHHHHHHHHhcCCCCCHhhHH----HHHHHHHhcCChhHHHH
Q 040027          112 VSLGFIAFGRILRSCFTPNAATFNSLIKGLHAESRIMEAAALFTKLKAFGCEPNVITYN----TLINGLCRTGHTMIALN  187 (595)
Q Consensus       112 ~~~A~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~----~l~~~~~~~g~~~~A~~  187 (595)
                      +++|+-.|.++++.. +++....-.-...|-+.|+...|.+.|.++.....+.|..-..    ..+..+...++-+.|.+
T Consensus       223 i~qA~~cy~rAI~~~-p~n~~~~~ers~L~~~~G~~~~Am~~f~~l~~~~p~~d~er~~d~i~~~~~~~~~~~~~e~a~~  301 (895)
T KOG2076|consen  223 INQARYCYSRAIQAN-PSNWELIYERSSLYQKTGDLKRAMETFLQLLQLDPPVDIERIEDLIRRVAHYFITHNERERAAK  301 (895)
T ss_pred             HHHHHHHHHHHHhcC-CcchHHHHHHHHHHHHhChHHHHHHHHHHHHhhCCchhHHHHHHHHHHHHHHHHHhhHHHHHHH
Confidence            999999999999996 4555555566778899999999999999999885433333333    34556677888899999


Q ss_pred             HHHHHHhcCCCCCccccCcHHHHHHHHHHHHHcCCHhHHHHHHHHHhhCC---------------------------CCC
Q 040027          188 LFEEMANGNGEIGVVCKPNTVTYSTIIDGLCKEGFVDKAKALFLQMKDEN---------------------------INP  240 (595)
Q Consensus       188 ~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~---------------------------~~~  240 (595)
                      .++.......     -..+...++.++..+.+...++.+...........                           ..+
T Consensus       302 ~le~~~s~~~-----~~~~~ed~ni~ael~l~~~q~d~~~~~i~~~~~r~~e~d~~e~~~~~~~~~~~~~~~~~~~~~s~  376 (895)
T KOG2076|consen  302 ALEGALSKEK-----DEASLEDLNILAELFLKNKQSDKALMKIVDDRNRESEKDDSEWDTDERRREEPNALCEVGKELSY  376 (895)
T ss_pred             HHHHHHhhcc-----ccccccHHHHHHHHHHHhHHHHHhhHHHHHHhccccCCChhhhhhhhhccccccccccCCCCCCc
Confidence            9999887432     13445678889999999999999988887776621                           122


Q ss_pred             CHhHHHHHHHHHHhcCCHHHHHHHHHHHHHCC--CCCCHhhHHHHHHHHHhcCChHHHHHHHHHHHHCCCCCCHHHHHHH
Q 040027          241 DVVTYNSLIHGLCHANDWNEAKRLFIEMMDQG--VQPSVVTFNVIMDELCKNRKMDEASRLLDLMVQRGVRPNACTYNTL  318 (595)
Q Consensus       241 ~~~~~~~ll~~~~~~~~~~~A~~~~~~~~~~~--~~~~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~l  318 (595)
                      +... ..++-++.+.+..+....+...+....  +..+...|..+..++...|++.+|+++|..+......-+..+|..+
T Consensus       377 ~l~v-~rl~icL~~L~~~e~~e~ll~~l~~~n~~~~d~~dL~~d~a~al~~~~~~~~Al~~l~~i~~~~~~~~~~vw~~~  455 (895)
T KOG2076|consen  377 DLRV-IRLMICLVHLKERELLEALLHFLVEDNVWVSDDVDLYLDLADALTNIGKYKEALRLLSPITNREGYQNAFVWYKL  455 (895)
T ss_pred             cchh-HhHhhhhhcccccchHHHHHHHHHHhcCChhhhHHHHHHHHHHHHhcccHHHHHHHHHHHhcCccccchhhhHHH
Confidence            2222 122334444444444444444444444  3345667888999999999999999999999987655678899999


Q ss_pred             HHHHHhcCCHHHHHHHHHHHHhcCCCCCHHHHHHHHHHHHhCCCHHHHHHHHHHHHHC--------CCCCCHHHHHHHHH
Q 040027          319 MDGFCLMGKINRAEELFGSMESMGCKHDDVSYNILINGYCKNKEVEEALSLYREMVSK--------GIKPTVVTYNTLFL  390 (595)
Q Consensus       319 ~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~~--------~~~~~~~~~~~l~~  390 (595)
                      +.+|...|.++.|++.|+.++... |.+...-..|...+.+.|+.++|.+.+..+...        +..|+.........
T Consensus       456 a~c~~~l~e~e~A~e~y~kvl~~~-p~~~D~Ri~Lasl~~~~g~~EkalEtL~~~~~~D~~~~e~~a~~~e~ri~~~r~d  534 (895)
T KOG2076|consen  456 ARCYMELGEYEEAIEFYEKVLILA-PDNLDARITLASLYQQLGNHEKALETLEQIINPDGRNAEACAWEPERRILAHRCD  534 (895)
T ss_pred             HHHHHHHhhHHHHHHHHHHHHhcC-CCchhhhhhHHHHHHhcCCHHHHHHHHhcccCCCccchhhccccHHHHHHHHHHH
Confidence            999999999999999999998874 556667788888999999999999999886532        22333334444445


Q ss_pred             HHHccCCHHHHHHHHHH
Q 040027          391 GLFEIHQVEHALKLFDE  407 (595)
Q Consensus       391 ~~~~~~~~~~a~~~~~~  407 (595)
                      .+...|+.++-..+...
T Consensus       535 ~l~~~gk~E~fi~t~~~  551 (895)
T KOG2076|consen  535 ILFQVGKREEFINTAST  551 (895)
T ss_pred             HHHHhhhHHHHHHHHHH
Confidence            55666666554444333

>KOG1915 consensus Cell cycle control protein (crooked neck) [Cell cycle control, cell division, chromosome partitioning]

Probab=99.88  E-value=7.8e-17  Score=146.06  Aligned_cols=438  Identities=11%  Similarity=0.090  Sum_probs=325.1

Q ss_pred             CCHHHHHHHHHHHHhcCChhHHHHHHHHHHhCCCCCCHHHHHHHHHHHHhcCCHhHHHHHHHHHHhcCCCCCHhhHHHHH
Q 040027           94 PNLYTYNILINCFCKIGRVSLGFIAFGRILRSCFTPNAATFNSLIKGLHAESRIMEAAALFTKLKAFGCEPNVITYNTLI  173 (595)
Q Consensus        94 ~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~~l~  173 (595)
                      .+...|...+.+-.+....+.|+.+|++++..- |.-...|-..+-+--..|++..|.++|++....  .|+..+|.+.+
T Consensus       105 r~itLWlkYae~Emknk~vNhARNv~dRAvt~l-PRVdqlWyKY~ymEE~LgNi~gaRqiferW~~w--~P~eqaW~sfI  181 (677)
T KOG1915|consen  105 RNITLWLKYAEFEMKNKQVNHARNVWDRAVTIL-PRVDQLWYKYIYMEEMLGNIAGARQIFERWMEW--EPDEQAWLSFI  181 (677)
T ss_pred             ccchHHHHHHHHHHhhhhHhHHHHHHHHHHHhc-chHHHHHHHHHHHHHHhcccHHHHHHHHHHHcC--CCcHHHHHHHH
Confidence            466778888888888899999999999998873 333345555555556679999999999998876  78999999999


Q ss_pred             HHHHhcCChhHHHHHHHHHHhcCCCCCccccCcHHHHHHHHHHHHHcCCHhHHHHHHHHHhhC-CC-CCCHhHHHHHHHH
Q 040027          174 NGLCRTGHTMIALNLFEEMANGNGEIGVVCKPNTVTYSTIIDGLCKEGFVDKAKALFLQMKDE-NI-NPDVVTYNSLIHG  251 (595)
Q Consensus       174 ~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~-~~-~~~~~~~~~ll~~  251 (595)
                      ..-.+...++.|..++++.+-        +.|+...|......-.++|...-|..+|+...+. |- ..+...+.+....
T Consensus       182 ~fElRykeieraR~IYerfV~--------~HP~v~~wikyarFE~k~g~~~~aR~VyerAie~~~~d~~~e~lfvaFA~f  253 (677)
T KOG1915|consen  182 KFELRYKEIERARSIYERFVL--------VHPKVSNWIKYARFEEKHGNVALARSVYERAIEFLGDDEEAEILFVAFAEF  253 (677)
T ss_pred             HHHHHhhHHHHHHHHHHHHhe--------ecccHHHHHHHHHHHHhcCcHHHHHHHHHHHHHHhhhHHHHHHHHHHHHHH
Confidence            999999999999999999876        5688999988888888999999999999887764 10 1123345555555


Q ss_pred             HHhcCCHHHHHHHHHHHHHCCCCCC--HhhHHHHHHHHHhcCChHHHHHH--------HHHHHHCCCCCCHHHHHHHHHH
Q 040027          252 LCHANDWNEAKRLFIEMMDQGVQPS--VVTFNVIMDELCKNRKMDEASRL--------LDLMVQRGVRPNACTYNTLMDG  321 (595)
Q Consensus       252 ~~~~~~~~~A~~~~~~~~~~~~~~~--~~~~~~l~~~~~~~g~~~~a~~~--------~~~~~~~~~~~~~~~~~~l~~~  321 (595)
                      -..+..++.|.-+|+-.+++ ++.+  ...|..+...--+-|+.....+.        |+.+++.+ +.|-.+|...++.
T Consensus       254 Ee~qkE~ERar~iykyAld~-~pk~raeeL~k~~~~fEKqfGd~~gIEd~Iv~KRk~qYE~~v~~n-p~nYDsWfdylrL  331 (677)
T KOG1915|consen  254 EERQKEYERARFIYKYALDH-IPKGRAEELYKKYTAFEKQFGDKEGIEDAIVGKRKFQYEKEVSKN-PYNYDSWFDYLRL  331 (677)
T ss_pred             HHHHHHHHHHHHHHHHHHHh-cCcccHHHHHHHHHHHHHHhcchhhhHHHHhhhhhhHHHHHHHhC-CCCchHHHHHHHH
Confidence            56678889999999888876 3323  33455555444455665544333        44555543 4477788888888


Q ss_pred             HHhcCCHHHHHHHHHHHHhcCCCCCHH--HHHHHHHH--------HHhCCCHHHHHHHHHHHHHCCCCCCHHHHHHHHHH
Q 040027          322 FCLMGKINRAEELFGSMESMGCKHDDV--SYNILING--------YCKNKEVEEALSLYREMVSKGIKPTVVTYNTLFLG  391 (595)
Q Consensus       322 ~~~~~~~~~a~~~~~~~~~~~~~~~~~--~~~~l~~~--------~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~~l~~~  391 (595)
                      -...|+.+...++|++++.. ++|-..  .|...|..        -....+.+.+.++|+..++. ++....||..+--.
T Consensus       332 ~e~~g~~~~Ire~yErAIan-vpp~~ekr~W~RYIYLWinYalyeEle~ed~ertr~vyq~~l~l-IPHkkFtFaKiWlm  409 (677)
T KOG1915|consen  332 EESVGDKDRIRETYERAIAN-VPPASEKRYWRRYIYLWINYALYEELEAEDVERTRQVYQACLDL-IPHKKFTFAKIWLM  409 (677)
T ss_pred             HHhcCCHHHHHHHHHHHHcc-CCchhHHHHHHHHHHHHHHHHHHHHHHhhhHHHHHHHHHHHHhh-cCcccchHHHHHHH
Confidence            88889999999999998875 344221  23222221        23478899999999998884 55566666555444


Q ss_pred             H----HccCCHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCcCHHHHHHHHHHHHhcCC
Q 040027          392 L----FEIHQVEHALKLFDEMQRDGVAADTRTYTTFIDGLCKNGYIIEAVELFRTLRILKCELDIQAYNCLIDGLCKSGR  467 (595)
Q Consensus       392 ~----~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~  467 (595)
                      |    .++.++..|.+++...+.  .-|...++...|..-.+.++++.+..+|++.++.+ |.+..+|......-...|+
T Consensus       410 yA~feIRq~~l~~ARkiLG~AIG--~cPK~KlFk~YIelElqL~efDRcRkLYEkfle~~-Pe~c~~W~kyaElE~~Lgd  486 (677)
T KOG1915|consen  410 YAQFEIRQLNLTGARKILGNAIG--KCPKDKLFKGYIELELQLREFDRCRKLYEKFLEFS-PENCYAWSKYAELETSLGD  486 (677)
T ss_pred             HHHHHHHHcccHHHHHHHHHHhc--cCCchhHHHHHHHHHHHHhhHHHHHHHHHHHHhcC-hHhhHHHHHHHHHHHHhhh
Confidence            4    467889999999988875  47888999999999999999999999999999887 7788999999988889999


Q ss_pred             hHHHHHHHHhcccCC-CCCCHHHHHHHHHHHHhcCChhHHHHHHHHHHHcCCCCCHHHHHHHHHHHH-----HcC-----
Q 040027          468 LKFAWELFCSLPHGV-LVPNVVTYNIMIQGLCNDGQMDKARDLFLDMEENAAAPDVITFDMLIHGFI-----RIN-----  536 (595)
Q Consensus       468 ~~~A~~~~~~~~~~~-~~p~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~~l~~~~~-----~~g-----  536 (595)
                      .+.|..+|.-+++.. +......|-+.|..-...|.++.|..+++++++.  .+....|.....--.     ..+     
T Consensus       487 tdRaRaifelAi~qp~ldmpellwkaYIdFEi~~~E~ekaR~LYerlL~r--t~h~kvWisFA~fe~s~~~~~~~~~~~~  564 (677)
T KOG1915|consen  487 TDRARAIFELAISQPALDMPELLWKAYIDFEIEEGEFEKARALYERLLDR--TQHVKVWISFAKFEASASEGQEDEDLAE  564 (677)
T ss_pred             HHHHHHHHHHHhcCcccccHHHHHHHhhhhhhhcchHHHHHHHHHHHHHh--cccchHHHhHHHHhccccccccccchhh
Confidence            999999999988742 1223456777777777899999999999999986  344455655543222     233     


Q ss_pred             ------ChhHHHHHHHHHHHC
Q 040027          537 ------EPSKVNELLHKMKEK  551 (595)
Q Consensus       537 ------~~~~A~~~~~~~~~~  551 (595)
                            ....|.++|+++...
T Consensus       565 ~e~~~~~~~~AR~iferAn~~  585 (677)
T KOG1915|consen  565 LEITDENIKRARKIFERANTY  585 (677)
T ss_pred             hhcchhHHHHHHHHHHHHHHH
Confidence                  467888999988743

>KOG2003 consensus TPR repeat-containing protein [General function prediction only]

Probab=99.87  E-value=1.2e-18  Score=156.86  Aligned_cols=473  Identities=15%  Similarity=0.118  Sum_probs=337.8

Q ss_pred             HHHHHHHHHHHHhcCChhHHHHHHHHHHhCCCCCCHHHHH-HHHHHHHhcCCHhHHHHHHHHHHhcCCCCC----HhhHH
Q 040027           96 LYTYNILINCFCKIGRVSLGFIAFGRILRSCFTPNAATFN-SLIKGLHAESRIMEAAALFTKLKAFGCEPN----VITYN  170 (595)
Q Consensus        96 ~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~-~l~~~~~~~g~~~~A~~~~~~~~~~~~~~~----~~~~~  170 (595)
                      -.+...|...|.......+|+..|+-+++...-|+..... .+...+.+..++..|++.|+..+..-+..+    ..+.+
T Consensus       201 fsvl~nlaqqy~~ndm~~ealntyeiivknkmf~nag~lkmnigni~~kkr~fskaikfyrmaldqvpsink~~rikil~  280 (840)
T KOG2003|consen  201 FSVLFNLAQQYEANDMTAEALNTYEIIVKNKMFPNAGILKMNIGNIHFKKREFSKAIKFYRMALDQVPSINKDMRIKILN  280 (840)
T ss_pred             HHHHHHHHHHhhhhHHHHHHhhhhhhhhcccccCCCceeeeeecceeeehhhHHHHHHHHHHHHhhccccchhhHHHHHh
Confidence            3444556677777888999999999999887777766553 455778899999999999998887632222    23455


Q ss_pred             HHHHHHHhcCChhHHHHHHHHHHhcCCCCCccccCcHHHHHHHHHHHHHcCCHhHHHHHHHHHhhCCCC-----------
Q 040027          171 TLINGLCRTGHTMIALNLFEEMANGNGEIGVVCKPNTVTYSTIIDGLCKEGFVDKAKALFLQMKDENIN-----------  239 (595)
Q Consensus       171 ~l~~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~-----------  239 (595)
                      .+...+.+.|+++.|+..|+...+..        |+..+-..|+-++..-|+.++..+.|.+|...-..           
T Consensus       281 nigvtfiq~gqy~dainsfdh~m~~~--------pn~~a~~nl~i~~f~i~d~ekmkeaf~kli~ip~~~dddkyi~~~d  352 (840)
T KOG2003|consen  281 NIGVTFIQAGQYDDAINSFDHCMEEA--------PNFIAALNLIICAFAIGDAEKMKEAFQKLIDIPGEIDDDKYIKEKD  352 (840)
T ss_pred             hcCeeEEecccchhhHhhHHHHHHhC--------ccHHhhhhhhhhheecCcHHHHHHHHHHHhcCCCCCCcccccCCcC
Confidence            66667889999999999999998865        77666666777777889999999999999764222           


Q ss_pred             -CCHhHHHHHH-----HHHHhc--CCHHHHHHHHHHHHHCCCCCCHhh---HH------------------HHHHHHHhc
Q 040027          240 -PDVVTYNSLI-----HGLCHA--NDWNEAKRLFIEMMDQGVQPSVVT---FN------------------VIMDELCKN  290 (595)
Q Consensus       240 -~~~~~~~~ll-----~~~~~~--~~~~~A~~~~~~~~~~~~~~~~~~---~~------------------~l~~~~~~~  290 (595)
                       |+....+.-+     ...-+.  .+-++++-.-.+++.--+.|+-..   |.                  .-...+.+.
T Consensus       353 dp~~~ll~eai~nd~lk~~ek~~ka~aek~i~ta~kiiapvi~~~fa~g~dwcle~lk~s~~~~la~dlei~ka~~~lk~  432 (840)
T KOG2003|consen  353 DPDDNLLNEAIKNDHLKNMEKENKADAEKAIITAAKIIAPVIAPDFAAGCDWCLESLKASQHAELAIDLEINKAGELLKN  432 (840)
T ss_pred             CcchHHHHHHHhhHHHHHHHHhhhhhHHHHHHHHHHHhccccccchhcccHHHHHHHHHhhhhhhhhhhhhhHHHHHHhc
Confidence             2222222222     111111  122233322222322222233110   10                  112346789


Q ss_pred             CChHHHHHHHHHHHHCCCCCCHHHHHHHHHHH-Hh-cCCHHHHHHHHHHHHhcCCCCCHHHHHHHHHHHHhCCCHHHHHH
Q 040027          291 RKMDEASRLLDLMVQRGVRPNACTYNTLMDGF-CL-MGKINRAEELFGSMESMGCKHDDVSYNILINGYCKNKEVEEALS  368 (595)
Q Consensus       291 g~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~-~~-~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~A~~  368 (595)
                      |+++.|.+++.-..+.+-+.-....+.+...+ .+ ..++..|.++-+..+..+ ..+......-...-..+|++++|.+
T Consensus       433 ~d~~~aieilkv~~~kdnk~~saaa~nl~~l~flqggk~~~~aqqyad~aln~d-ryn~~a~~nkgn~~f~ngd~dka~~  511 (840)
T KOG2003|consen  433 GDIEGAIEILKVFEKKDNKTASAAANNLCALRFLQGGKDFADAQQYADIALNID-RYNAAALTNKGNIAFANGDLDKAAE  511 (840)
T ss_pred             cCHHHHHHHHHHHHhccchhhHHHhhhhHHHHHHhcccchhHHHHHHHHHhccc-ccCHHHhhcCCceeeecCcHHHHHH
Confidence            99999999999887764333333333333332 22 346788888777776543 3444444444455566899999999


Q ss_pred             HHHHHHHCCCCCCHHHHHHHHHHHHccCCHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHHcCC
Q 040027          369 LYREMVSKGIKPTVVTYNTLFLGLFEIHQVEHALKLFDEMQRDGVAADTRTYTTFIDGLCKNGYIIEAVELFRTLRILKC  448 (595)
Q Consensus       369 ~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~  448 (595)
                      .|++.+..+.. -...+..+...+...|+.++|+..|-++..- +..+..++..+...|-...+...|++++.+.... +
T Consensus       512 ~ykeal~ndas-c~ealfniglt~e~~~~ldeald~f~klh~i-l~nn~evl~qianiye~led~aqaie~~~q~~sl-i  588 (840)
T KOG2003|consen  512 FYKEALNNDAS-CTEALFNIGLTAEALGNLDEALDCFLKLHAI-LLNNAEVLVQIANIYELLEDPAQAIELLMQANSL-I  588 (840)
T ss_pred             HHHHHHcCchH-HHHHHHHhcccHHHhcCHHHHHHHHHHHHHH-HHhhHHHHHHHHHHHHHhhCHHHHHHHHHHhccc-C
Confidence            99999986332 2233334445677899999999999887653 3456778888889999999999999999998765 3


Q ss_pred             CcCHHHHHHHHHHHHhcCChHHHHHHHHhcccCCCCCCHHHHHHHHHHHHhcCChhHHHHHHHHHHHcCCCCCHHHHHHH
Q 040027          449 ELDIQAYNCLIDGLCKSGRLKFAWELFCSLPHGVLVPNVVTYNIMIQGLCNDGQMDKARDLFLDMEENAAAPDVITFDML  528 (595)
Q Consensus       449 ~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~p~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~~l  528 (595)
                      +.|+.+...|...|-+.|+-.+|.+.+-.--+. ++.|..+...|...|....-+++|+.+|+++.-  +.|+..-|..+
T Consensus       589 p~dp~ilskl~dlydqegdksqafq~~ydsyry-fp~nie~iewl~ayyidtqf~ekai~y~ekaal--iqp~~~kwqlm  665 (840)
T KOG2003|consen  589 PNDPAILSKLADLYDQEGDKSQAFQCHYDSYRY-FPCNIETIEWLAAYYIDTQFSEKAINYFEKAAL--IQPNQSKWQLM  665 (840)
T ss_pred             CCCHHHHHHHHHHhhcccchhhhhhhhhhcccc-cCcchHHHHHHHHHHHhhHHHHHHHHHHHHHHh--cCccHHHHHHH
Confidence            889999999999999999999999987666553 566889999999999999999999999999876  68999999877


Q ss_pred             HHH-HHHcCChhHHHHHHHHHHHCCCCCCHHHHHHHHHHHHhcCccc--ccchHHHHhh
Q 040027          529 IHG-FIRINEPSKVNELLHKMKEKKVMPDASIVSIVVDLLVKNEISL--KSLPSFLVQE  584 (595)
Q Consensus       529 ~~~-~~~~g~~~~A~~~~~~~~~~~~~p~~~~~~~l~~~~~~~g~~~--~~i~~~~~~~  584 (595)
                      +.. +.+.|++++|..+|+....+ ++.|..++..+++++..-|..+  +..+++.+..
T Consensus       666 iasc~rrsgnyqka~d~yk~~hrk-fpedldclkflvri~~dlgl~d~key~~klek~e  723 (840)
T KOG2003|consen  666 IASCFRRSGNYQKAFDLYKDIHRK-FPEDLDCLKFLVRIAGDLGLKDAKEYADKLEKAE  723 (840)
T ss_pred             HHHHHHhcccHHHHHHHHHHHHHh-CccchHHHHHHHHHhccccchhHHHHHHHHHHHH
Confidence            654 45789999999999999874 6779999999999999999887  5555444333

>KOG0495 consensus HAT repeat protein [RNA processing and modification]

Probab=99.86  E-value=1.5e-16  Score=149.87  Aligned_cols=507  Identities=11%  Similarity=0.023  Sum_probs=398.4

Q ss_pred             hhhhcccccccccccCCCChHHHHHHHHHHHHhCCCCCCHhhHHHHHHHHHcCCCchh-----HHhhCCCCCCHHHHHHH
Q 040027           28 LLVHFRDLTTREGDINVITPNEAFCIFDYMLRMHPSPPPVSSFNILLASLAKNKHYDT-----RLNATGLFPNLYTYNIL  102 (595)
Q Consensus        28 ~~~~~~~~~~~~~~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~-----~~~~~~~~~~~~~~~~l  102 (595)
                      +--.+.+..++-.-+..-+.++|+.++.++.+.-|.  +...|.++.+    ...+..     --....++-++..|.+.
T Consensus       373 Le~iP~sv~LWKaAVelE~~~darilL~rAveccp~--s~dLwlAlar----LetYenAkkvLNkaRe~iptd~~IWita  446 (913)
T KOG0495|consen  373 LEHIPRSVRLWKAAVELEEPEDARILLERAVECCPQ--SMDLWLALAR----LETYENAKKVLNKAREIIPTDREIWITA  446 (913)
T ss_pred             HHhCCchHHHHHHHHhccChHHHHHHHHHHHHhccc--hHHHHHHHHH----HHHHHHHHHHHHHHHhhCCCChhHHHHH
Confidence            333444555566666777888899999999999887  7777765543    222222     11234566789999998


Q ss_pred             HHHHHhcCChhHHHHHHHHHH----hCCCCCCHHHHHHHHHHHHhcCCHhHHHHHHHHHHhcCCCC--CHhhHHHHHHHH
Q 040027          103 INCFCKIGRVSLGFIAFGRIL----RSCFTPNAATFNSLIKGLHAESRIMEAAALFTKLKAFGCEP--NVITYNTLINGL  176 (595)
Q Consensus       103 ~~~~~~~g~~~~A~~~~~~~~----~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~--~~~~~~~l~~~~  176 (595)
                      ...--+.|+.+...++..+.+    ..|+.-+...|..=...|-..|..-.+..+....+..|++-  -..+|..-...|
T Consensus       447 a~LEE~ngn~~mv~kii~rgl~~L~~ngv~i~rdqWl~eAe~~e~agsv~TcQAIi~avigigvEeed~~~tw~~da~~~  526 (913)
T KOG0495|consen  447 AKLEEANGNVDMVEKIIDRGLSELQANGVEINRDQWLKEAEACEDAGSVITCQAIIRAVIGIGVEEEDRKSTWLDDAQSC  526 (913)
T ss_pred             HHHHHhcCCHHHHHHHHHHHHHHHhhcceeecHHHHHHHHHHHhhcCChhhHHHHHHHHHhhccccchhHhHHhhhHHHH
Confidence            888888999999988888754    35778888999888888988999999999999888887663  246788888899


Q ss_pred             HhcCChhHHHHHHHHHHhcCCCCCccccCcHHHHHHHHHHHHHcCCHhHHHHHHHHHhhCCCCCCHhHHHHHHHHHHhcC
Q 040027          177 CRTGHTMIALNLFEEMANGNGEIGVVCKPNTVTYSTIIDGLCKEGFVDKAKALFLQMKDENINPDVVTYNSLIHGLCHAN  256 (595)
Q Consensus       177 ~~~g~~~~A~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~~ll~~~~~~~  256 (595)
                      .+.+.++-|..+|...++..       +.+...|...+..--..|..+.-..+|+++... ++-....|......+-..|
T Consensus       527 ~k~~~~~carAVya~alqvf-------p~k~slWlra~~~ek~hgt~Esl~Allqkav~~-~pkae~lwlM~ake~w~ag  598 (913)
T KOG0495|consen  527 EKRPAIECARAVYAHALQVF-------PCKKSLWLRAAMFEKSHGTRESLEALLQKAVEQ-CPKAEILWLMYAKEKWKAG  598 (913)
T ss_pred             HhcchHHHHHHHHHHHHhhc-------cchhHHHHHHHHHHHhcCcHHHHHHHHHHHHHh-CCcchhHHHHHHHHHHhcC
Confidence            99999999999999998874       566788888888888889999999999998876 3445666777778888889


Q ss_pred             CHHHHHHHHHHHHHCCCCCCHhhHHHHHHHHHhcCChHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHhcCCHHHHHHHHH
Q 040027          257 DWNEAKRLFIEMMDQGVQPSVVTFNVIMDELCKNRKMDEASRLLDLMVQRGVRPNACTYNTLMDGFCLMGKINRAEELFG  336 (595)
Q Consensus       257 ~~~~A~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~  336 (595)
                      +...|..++....+... .+...|...+.......+++.|..+|.+....  .++..+|..-+..-.-.+..++|+++++
T Consensus       599 dv~~ar~il~~af~~~p-nseeiwlaavKle~en~e~eraR~llakar~~--sgTeRv~mKs~~~er~ld~~eeA~rllE  675 (913)
T KOG0495|consen  599 DVPAARVILDQAFEANP-NSEEIWLAAVKLEFENDELERARDLLAKARSI--SGTERVWMKSANLERYLDNVEEALRLLE  675 (913)
T ss_pred             CcHHHHHHHHHHHHhCC-CcHHHHHHHHHHhhccccHHHHHHHHHHHhcc--CCcchhhHHHhHHHHHhhhHHHHHHHHH
Confidence            99999999999888633 36778888888889999999999999988764  5677788777777777889999999999


Q ss_pred             HHHhcCCCCCHHHHHHHHHHHHhCCCHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHccCCHHHHHHHHHHHHHCCCCCC
Q 040027          337 SMESMGCKHDDVSYNILINGYCKNKEVEEALSLYREMVSKGIKPTVVTYNTLFLGLFEIHQVEHALKLFDEMQRDGVAAD  416 (595)
Q Consensus       337 ~~~~~~~~~~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~  416 (595)
                      +.++. ++.-...|-.+...+.+.++.+.|.+.|..-.+. ++.....|..+...-.+.|++-.|..+++...-.+ +.+
T Consensus       676 e~lk~-fp~f~Kl~lmlGQi~e~~~~ie~aR~aY~~G~k~-cP~~ipLWllLakleEk~~~~~rAR~ildrarlkN-Pk~  752 (913)
T KOG0495|consen  676 EALKS-FPDFHKLWLMLGQIEEQMENIEMAREAYLQGTKK-CPNSIPLWLLLAKLEEKDGQLVRARSILDRARLKN-PKN  752 (913)
T ss_pred             HHHHh-CCchHHHHHHHhHHHHHHHHHHHHHHHHHhcccc-CCCCchHHHHHHHHHHHhcchhhHHHHHHHHHhcC-CCc
Confidence            88876 2334457888888999999999999988876654 44456677777777778889999999999887764 667


Q ss_pred             HHHHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCcCHHHHHHHHHHHHhcCChHHHHHHHHhcccCCCCCCHHHHHHHHHH
Q 040027          417 TRTYTTFIDGLCKNGYIIEAVELFRTLRILKCELDIQAYNCLIDGLCKSGRLKFAWELFCSLPHGVLVPNVVTYNIMIQG  496 (595)
Q Consensus       417 ~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~p~~~~~~~l~~~  496 (595)
                      ...|...|++-.+.|..+.|..+..++++.- +.+...|..-|....+.++-......+++..     -|+++...+...
T Consensus       753 ~~lwle~Ir~ElR~gn~~~a~~lmakALQec-p~sg~LWaEaI~le~~~~rkTks~DALkkce-----~dphVllaia~l  826 (913)
T KOG0495|consen  753 ALLWLESIRMELRAGNKEQAELLMAKALQEC-PSSGLLWAEAIWLEPRPQRKTKSIDALKKCE-----HDPHVLLAIAKL  826 (913)
T ss_pred             chhHHHHHHHHHHcCCHHHHHHHHHHHHHhC-CccchhHHHHHHhccCcccchHHHHHHHhcc-----CCchhHHHHHHH
Confidence            8889999999999999999999999888754 6677788888888777777666666666554     377777788888


Q ss_pred             HHhcCChhHHHHHHHHHHHcCCCCCHHHHHHHHHHHHHcCChhHHHHHHHHHHHCCCCCC-HHHHHHH
Q 040027          497 LCNDGQMDKARDLFLDMEENAAAPDVITFDMLIHGFIRINEPSKVNELLHKMKEKKVMPD-ASIVSIV  563 (595)
Q Consensus       497 ~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~p~-~~~~~~l  563 (595)
                      +....++++|.+.|.+.++.+ +.+-.+|..+...+...|.-++-.+++.+....  .|. -..|.++
T Consensus       827 fw~e~k~~kar~Wf~Ravk~d-~d~GD~wa~fykfel~hG~eed~kev~~~c~~~--EP~hG~~W~av  891 (913)
T KOG0495|consen  827 FWSEKKIEKAREWFERAVKKD-PDNGDAWAWFYKFELRHGTEEDQKEVLKKCETA--EPTHGELWQAV  891 (913)
T ss_pred             HHHHHHHHHHHHHHHHHHccC-CccchHHHHHHHHHHHhCCHHHHHHHHHHHhcc--CCCCCcHHHHH
Confidence            888899999999999999875 455678888888889999888888888888753  453 2444443

>KOG1915 consensus Cell cycle control protein (crooked neck) [Cell cycle control, cell division, chromosome partitioning]

Probab=99.85  E-value=7.7e-16  Score=139.74  Aligned_cols=449  Identities=10%  Similarity=0.071  Sum_probs=350.7

Q ss_pred             CHHHHHHHHHHHHhcCChhHHHHHHHHHHhCCCCCCHHHHHHHHHHHHhcCCHhHHHHHHHHHHhcCCCCCHhhHHHHHH
Q 040027           95 NLYTYNILINCFCKIGRVSLGFIAFGRILRSCFTPNAATFNSLIKGLHAESRIMEAAALFTKLKAFGCEPNVITYNTLIN  174 (595)
Q Consensus        95 ~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~~l~~  174 (595)
                      +...|...++--..++++..|+.+|++++... ..+...|...+.+-.+++.+..|..++++.... .+.-...|...+.
T Consensus        72 ~~~~WikYaqwEesq~e~~RARSv~ERALdvd-~r~itLWlkYae~Emknk~vNhARNv~dRAvt~-lPRVdqlWyKY~y  149 (677)
T KOG1915|consen   72 NMQVWIKYAQWEESQKEIQRARSVFERALDVD-YRNITLWLKYAEFEMKNKQVNHARNVWDRAVTI-LPRVDQLWYKYIY  149 (677)
T ss_pred             HHHHHHHHHHHHHhHHHHHHHHHHHHHHHhcc-cccchHHHHHHHHHHhhhhHhHHHHHHHHHHHh-cchHHHHHHHHHH
Confidence            66778888888888999999999999999876 568889999999999999999999999999886 2334456677777


Q ss_pred             HHHhcCChhHHHHHHHHHHhcCCCCCccccCcHHHHHHHHHHHHHcCCHhHHHHHHHHHhhCCCCCCHhHHHHHHHHHHh
Q 040027          175 GLCRTGHTMIALNLFEEMANGNGEIGVVCKPNTVTYSTIIDGLCKEGFVDKAKALFLQMKDENINPDVVTYNSLIHGLCH  254 (595)
Q Consensus       175 ~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~~ll~~~~~  254 (595)
                      .--..|+...|.++|++....        .|+..+|...|..-.+-+.++.|..+|++.+-.  .|+..+|......-.+
T Consensus       150 mEE~LgNi~gaRqiferW~~w--------~P~eqaW~sfI~fElRykeieraR~IYerfV~~--HP~v~~wikyarFE~k  219 (677)
T KOG1915|consen  150 MEEMLGNIAGARQIFERWMEW--------EPDEQAWLSFIKFELRYKEIERARSIYERFVLV--HPKVSNWIKYARFEEK  219 (677)
T ss_pred             HHHHhcccHHHHHHHHHHHcC--------CCcHHHHHHHHHHHHHhhHHHHHHHHHHHHhee--cccHHHHHHHHHHHHh
Confidence            777899999999999999985        599999999999999999999999999998874  6899999999999999


Q ss_pred             cCCHHHHHHHHHHHHHC-CC-CCCHhhHHHHHHHHHhcCChHHHHHHHHHHHHCCCCCC--HHHHHHHHHHHHhcCCHHH
Q 040027          255 ANDWNEAKRLFIEMMDQ-GV-QPSVVTFNVIMDELCKNRKMDEASRLLDLMVQRGVRPN--ACTYNTLMDGFCLMGKINR  330 (595)
Q Consensus       255 ~~~~~~A~~~~~~~~~~-~~-~~~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~~~~~--~~~~~~l~~~~~~~~~~~~  330 (595)
                      .|....+..+|...++. |- ..+...+.+....-..+..++.|.-+|.-.++. ++.+  ...|......--+.|+...
T Consensus       220 ~g~~~~aR~VyerAie~~~~d~~~e~lfvaFA~fEe~qkE~ERar~iykyAld~-~pk~raeeL~k~~~~fEKqfGd~~g  298 (677)
T KOG1915|consen  220 HGNVALARSVYERAIEFLGDDEEAEILFVAFAEFEERQKEYERARFIYKYALDH-IPKGRAEELYKKYTAFEKQFGDKEG  298 (677)
T ss_pred             cCcHHHHHHHHHHHHHHhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHh-cCcccHHHHHHHHHHHHHHhcchhh
Confidence            99999999999988764 21 112334555555666788899999999998886 3333  4455555555556677544


Q ss_pred             HHHH--------HHHHHhcCCCCCHHHHHHHHHHHHhCCCHHHHHHHHHHHHHCCCCCCHH--HHHHHH--------HHH
Q 040027          331 AEEL--------FGSMESMGCKHDDVSYNILINGYCKNKEVEEALSLYREMVSKGIKPTVV--TYNTLF--------LGL  392 (595)
Q Consensus       331 a~~~--------~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~~~~~~~~~--~~~~l~--------~~~  392 (595)
                      ..+.        ++.+++.+ +.|..+|-..++.-...|+.+...++|++++.. ++|-..  .|...+        -.-
T Consensus       299 IEd~Iv~KRk~qYE~~v~~n-p~nYDsWfdylrL~e~~g~~~~Ire~yErAIan-vpp~~ekr~W~RYIYLWinYalyeE  376 (677)
T KOG1915|consen  299 IEDAIVGKRKFQYEKEVSKN-PYNYDSWFDYLRLEESVGDKDRIRETYERAIAN-VPPASEKRYWRRYIYLWINYALYEE  376 (677)
T ss_pred             hHHHHhhhhhhHHHHHHHhC-CCCchHHHHHHHHHHhcCCHHHHHHHHHHHHcc-CCchhHHHHHHHHHHHHHHHHHHHH
Confidence            4433        34444443 678889999999999999999999999999986 444221  222222        112


Q ss_pred             HccCCHHHHHHHHHHHHHCCCCCCHHHHHHHHH----HHHhcCCHHHHHHHHHHHHHcCCCcCHHHHHHHHHHHHhcCCh
Q 040027          393 FEIHQVEHALKLFDEMQRDGVAADTRTYTTFID----GLCKNGYIIEAVELFRTLRILKCELDIQAYNCLIDGLCKSGRL  468 (595)
Q Consensus       393 ~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~----~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~  468 (595)
                      ....+.+.+.++|+..++. +|....|+..+--    .-.++.++..|.+++..++  |.-|...+|...+..-.+.+++
T Consensus       377 le~ed~ertr~vyq~~l~l-IPHkkFtFaKiWlmyA~feIRq~~l~~ARkiLG~AI--G~cPK~KlFk~YIelElqL~ef  453 (677)
T KOG1915|consen  377 LEAEDVERTRQVYQACLDL-IPHKKFTFAKIWLMYAQFEIRQLNLTGARKILGNAI--GKCPKDKLFKGYIELELQLREF  453 (677)
T ss_pred             HHhhhHHHHHHHHHHHHhh-cCcccchHHHHHHHHHHHHHHHcccHHHHHHHHHHh--ccCCchhHHHHHHHHHHHHhhH
Confidence            3578999999999999985 5555555554433    3457889999999999988  4478899999999999999999


Q ss_pred             HHHHHHHHhcccCCCCC-CHHHHHHHHHHHHhcCChhHHHHHHHHHHHcCC-CCCHHHHHHHHHHHHHcCChhHHHHHHH
Q 040027          469 KFAWELFCSLPHGVLVP-NVVTYNIMIQGLCNDGQMDKARDLFLDMEENAA-APDVITFDMLIHGFIRINEPSKVNELLH  546 (595)
Q Consensus       469 ~~A~~~~~~~~~~~~~p-~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~-~~~~~~~~~l~~~~~~~g~~~~A~~~~~  546 (595)
                      +.+..++++.++.  .| |-.+|...+..-...|+.+.|..+|.-+++... ......|...++.=...|.++.|..+|+
T Consensus       454 DRcRkLYEkfle~--~Pe~c~~W~kyaElE~~LgdtdRaRaifelAi~qp~ldmpellwkaYIdFEi~~~E~ekaR~LYe  531 (677)
T KOG1915|consen  454 DRCRKLYEKFLEF--SPENCYAWSKYAELETSLGDTDRARAIFELAISQPALDMPELLWKAYIDFEIEEGEFEKARALYE  531 (677)
T ss_pred             HHHHHHHHHHHhc--ChHhhHHHHHHHHHHHHhhhHHHHHHHHHHHhcCcccccHHHHHHHhhhhhhhcchHHHHHHHHH
Confidence            9999999999984  45 568898888888899999999999999988531 1123455666666678999999999999


Q ss_pred             HHHHCCCCCCHHHHHHHHH
Q 040027          547 KMKEKKVMPDASIVSIVVD  565 (595)
Q Consensus       547 ~~~~~~~~p~~~~~~~l~~  565 (595)
                      ++++..  +...+|-.+..
T Consensus       532 rlL~rt--~h~kvWisFA~  548 (677)
T KOG1915|consen  532 RLLDRT--QHVKVWISFAK  548 (677)
T ss_pred             HHHHhc--ccchHHHhHHH
Confidence            999753  44445555444

>KOG2003 consensus TPR repeat-containing protein [General function prediction only]

Probab=99.82  E-value=5.3e-17  Score=146.37  Aligned_cols=426  Identities=15%  Similarity=0.107  Sum_probs=304.1

Q ss_pred             HHHHHHhcCChhHHHHHHHHHHhCCCCCC----HHHHHHHHHHHHhcCCHhHHHHHHHHHHhcCCCCCHhhHHHHHHHHH
Q 040027          102 LINCFCKIGRVSLGFIAFGRILRSCFTPN----AATFNSLIKGLHAESRIMEAAALFTKLKAFGCEPNVITYNTLINGLC  177 (595)
Q Consensus       102 l~~~~~~~g~~~~A~~~~~~~~~~~~~~~----~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~~l~~~~~  177 (595)
                      +...+.+..++.+|++.|+-++..-+..+    ....+.+...+.+.|+++.|+..|+...+.  .|+..+-..|+..+.
T Consensus       243 igni~~kkr~fskaikfyrmaldqvpsink~~rikil~nigvtfiq~gqy~dainsfdh~m~~--~pn~~a~~nl~i~~f  320 (840)
T KOG2003|consen  243 IGNIHFKKREFSKAIKFYRMALDQVPSINKDMRIKILNNIGVTFIQAGQYDDAINSFDHCMEE--APNFIAALNLIICAF  320 (840)
T ss_pred             ecceeeehhhHHHHHHHHHHHHhhccccchhhHHHHHhhcCeeEEecccchhhHhhHHHHHHh--CccHHhhhhhhhhhe
Confidence            55677888899999999999887632222    234555666688999999999999998876  678888778888888


Q ss_pred             hcCChhHHHHHHHHHHhcCCCCCcc--c----cCcHHHHHHH-----HHHHHHcC--CHhHHHHHHHHHhhCCCCCCHhH
Q 040027          178 RTGHTMIALNLFEEMANGNGEIGVV--C----KPNTVTYSTI-----IDGLCKEG--FVDKAKALFLQMKDENINPDVVT  244 (595)
Q Consensus       178 ~~g~~~~A~~~~~~~~~~~~~~~~~--~----~~~~~~~~~l-----~~~~~~~g--~~~~A~~~~~~~~~~~~~~~~~~  244 (595)
                      ..|+.++..+.|.++....+.....  .    .|+....+..     +.-+-+.+  +.++++-.--++...-+.|+...
T Consensus       321 ~i~d~ekmkeaf~kli~ip~~~dddkyi~~~ddp~~~ll~eai~nd~lk~~ek~~ka~aek~i~ta~kiiapvi~~~fa~  400 (840)
T KOG2003|consen  321 AIGDAEKMKEAFQKLIDIPGEIDDDKYIKEKDDPDDNLLNEAIKNDHLKNMEKENKADAEKAIITAAKIIAPVIAPDFAA  400 (840)
T ss_pred             ecCcHHHHHHHHHHHhcCCCCCCcccccCCcCCcchHHHHHHHhhHHHHHHHHhhhhhHHHHHHHHHHHhccccccchhc
Confidence            8999999999999998765432211  1    1222222222     22222221  22333322223332222233110


Q ss_pred             -------------HHH--------HHHHHHhcCCHHHHHHHHHHHHHCCCCCCHhhHHHHHHHHHh--cCChHHHHHHHH
Q 040027          245 -------------YNS--------LIHGLCHANDWNEAKRLFIEMMDQGVQPSVVTFNVIMDELCK--NRKMDEASRLLD  301 (595)
Q Consensus       245 -------------~~~--------ll~~~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~~l~~~~~~--~g~~~~a~~~~~  301 (595)
                                   +..        -..-+.++|+++.|.++++-..+..-+.-...-+.+-..+..  -+++..|..+-+
T Consensus       401 g~dwcle~lk~s~~~~la~dlei~ka~~~lk~~d~~~aieilkv~~~kdnk~~saaa~nl~~l~flqggk~~~~aqqyad  480 (840)
T KOG2003|consen  401 GCDWCLESLKASQHAELAIDLEINKAGELLKNGDIEGAIEILKVFEKKDNKTASAAANNLCALRFLQGGKDFADAQQYAD  480 (840)
T ss_pred             ccHHHHHHHHHhhhhhhhhhhhhhHHHHHHhccCHHHHHHHHHHHHhccchhhHHHhhhhHHHHHHhcccchhHHHHHHH
Confidence                         111        123477899999999999888765333223333333333333  457888888887


Q ss_pred             HHHHCCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHhcCCCCCHHHHHHHHHHHHhCCCHHHHHHHHHHHHHCCCCCC
Q 040027          302 LMVQRGVRPNACTYNTLMDGFCLMGKINRAEELFGSMESMGCKHDDVSYNILINGYCKNKEVEEALSLYREMVSKGIKPT  381 (595)
Q Consensus       302 ~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~~~~~~~  381 (595)
                      ..+..+ .-++.....-.+.....|++++|.+.|++.+..+. ........+.-.+...|+.++|++.|-++... +..+
T Consensus       481 ~aln~d-ryn~~a~~nkgn~~f~ngd~dka~~~ykeal~nda-sc~ealfniglt~e~~~~ldeald~f~klh~i-l~nn  557 (840)
T KOG2003|consen  481 IALNID-RYNAAALTNKGNIAFANGDLDKAAEFYKEALNNDA-SCTEALFNIGLTAEALGNLDEALDCFLKLHAI-LLNN  557 (840)
T ss_pred             HHhccc-ccCHHHhhcCCceeeecCcHHHHHHHHHHHHcCch-HHHHHHHHhcccHHHhcCHHHHHHHHHHHHHH-HHhh
Confidence            776642 33444444445555678999999999999987531 12223334455677899999999999877653 2237


Q ss_pred             HHHHHHHHHHHHccCCHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCcCHHHHHHHHHH
Q 040027          382 VVTYNTLFLGLFEIHQVEHALKLFDEMQRDGVAADTRTYTTFIDGLCKNGYIIEAVELFRTLRILKCELDIQAYNCLIDG  461 (595)
Q Consensus       382 ~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~~l~~~  461 (595)
                      ...+..+...|....+...|++++-+.... ++.|+.+++.+...|-+.|+-..|.+.+-.--+ -++.+..+...|...
T Consensus       558 ~evl~qianiye~led~aqaie~~~q~~sl-ip~dp~ilskl~dlydqegdksqafq~~ydsyr-yfp~nie~iewl~ay  635 (840)
T KOG2003|consen  558 AEVLVQIANIYELLEDPAQAIELLMQANSL-IPNDPAILSKLADLYDQEGDKSQAFQCHYDSYR-YFPCNIETIEWLAAY  635 (840)
T ss_pred             HHHHHHHHHHHHHhhCHHHHHHHHHHhccc-CCCCHHHHHHHHHHhhcccchhhhhhhhhhccc-ccCcchHHHHHHHHH
Confidence            778888888999999999999999888876 788999999999999999999999988765443 347788999999999


Q ss_pred             HHhcCChHHHHHHHHhcccCCCCCCHHHHHHHHHHH-HhcCChhHHHHHHHHHHHcCCCCCHHHHHHHHHHHHHcCC
Q 040027          462 LCKSGRLKFAWELFCSLPHGVLVPNVVTYNIMIQGL-CNDGQMDKARDLFLDMEENAAAPDVITFDMLIHGFIRINE  537 (595)
Q Consensus       462 ~~~~g~~~~A~~~~~~~~~~~~~p~~~~~~~l~~~~-~~~g~~~~A~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~  537 (595)
                      |....-+++++.+|++..-  +.|+..-|..++..| .+.|++.+|.++++....+ ++-|...+..|++.+...|-
T Consensus       636 yidtqf~ekai~y~ekaal--iqp~~~kwqlmiasc~rrsgnyqka~d~yk~~hrk-fpedldclkflvri~~dlgl  709 (840)
T KOG2003|consen  636 YIDTQFSEKAINYFEKAAL--IQPNQSKWQLMIASCFRRSGNYQKAFDLYKDIHRK-FPEDLDCLKFLVRIAGDLGL  709 (840)
T ss_pred             HHhhHHHHHHHHHHHHHHh--cCccHHHHHHHHHHHHHhcccHHHHHHHHHHHHHh-CccchHHHHHHHHHhccccc
Confidence            9999999999999999876  789999999888555 5789999999999999876 57788999999998887773

>KOG2076 consensus RNA polymerase III transcription factor TFIIIC [Transcription]

Probab=99.79  E-value=4e-15  Score=145.88  Aligned_cols=362  Identities=15%  Similarity=0.132  Sum_probs=277.5

Q ss_pred             HHHHHHHcCCHhHHHHHHHHHhhCCCCCCHhHHHHHHHHHHhcCCHHHHHHHHHHHHHCCCCCCHhhHHHHHHHHHhcCC
Q 040027          213 IIDGLCKEGFVDKAKALFLQMKDENINPDVVTYNSLIHGLCHANDWNEAKRLFIEMMDQGVQPSVVTFNVIMDELCKNRK  292 (595)
Q Consensus       213 l~~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~~ll~~~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~  292 (595)
                      ........|++++|.+++.++++.. +.+...|.+|...|-..|+.+++...+-.+-.. .+.|...|..+.....+.|+
T Consensus       145 eAN~lfarg~~eeA~~i~~EvIkqd-p~~~~ay~tL~~IyEqrGd~eK~l~~~llAAHL-~p~d~e~W~~ladls~~~~~  222 (895)
T KOG2076|consen  145 EANNLFARGDLEEAEEILMEVIKQD-PRNPIAYYTLGEIYEQRGDIEKALNFWLLAAHL-NPKDYELWKRLADLSEQLGN  222 (895)
T ss_pred             HHHHHHHhCCHHHHHHHHHHHHHhC-ccchhhHHHHHHHHHHcccHHHHHHHHHHHHhc-CCCChHHHHHHHHHHHhccc
Confidence            3344455699999999999999875 447889999999999999999999988666544 34477889999999999999


Q ss_pred             hHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHhcCCCCCHH----HHHHHHHHHHhCCCHHHHHH
Q 040027          293 MDEASRLLDLMVQRGVRPNACTYNTLMDGFCLMGKINRAEELFGSMESMGCKHDDV----SYNILINGYCKNKEVEEALS  368 (595)
Q Consensus       293 ~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~----~~~~l~~~~~~~~~~~~A~~  368 (595)
                      +++|.-+|.++++... ++...+..-...|-+.|+...|...|.++.....+.+..    .....+..+...++.+.|.+
T Consensus       223 i~qA~~cy~rAI~~~p-~n~~~~~ers~L~~~~G~~~~Am~~f~~l~~~~p~~d~er~~d~i~~~~~~~~~~~~~e~a~~  301 (895)
T KOG2076|consen  223 INQARYCYSRAIQANP-SNWELIYERSSLYQKTGDLKRAMETFLQLLQLDPPVDIERIEDLIRRVAHYFITHNERERAAK  301 (895)
T ss_pred             HHHHHHHHHHHHhcCC-cchHHHHHHHHHHHHhChHHHHHHHHHHHHhhCCchhHHHHHHHHHHHHHHHHHhhHHHHHHH
Confidence            9999999999999853 355555666788999999999999999999875322222    23344666777888899999


Q ss_pred             HHHHHHHCC-CCCCHHHHHHHHHHHHccCCHHHHHHHHHHHHHCC---------------------------CCCCHHHH
Q 040027          369 LYREMVSKG-IKPTVVTYNTLFLGLFEIHQVEHALKLFDEMQRDG---------------------------VAADTRTY  420 (595)
Q Consensus       369 ~~~~~~~~~-~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~---------------------------~~~~~~~~  420 (595)
                      .+......+ -..+...++.++..+.+..+++.+...........                           ..++..++
T Consensus       302 ~le~~~s~~~~~~~~ed~ni~ael~l~~~q~d~~~~~i~~~~~r~~e~d~~e~~~~~~~~~~~~~~~~~~~~~s~~l~v~  381 (895)
T KOG2076|consen  302 ALEGALSKEKDEASLEDLNILAELFLKNKQSDKALMKIVDDRNRESEKDDSEWDTDERRREEPNALCEVGKELSYDLRVI  381 (895)
T ss_pred             HHHHHHhhccccccccHHHHHHHHHHHhHHHHHhhHHHHHHhccccCCChhhhhhhhhccccccccccCCCCCCccchhH
Confidence            998887732 22355667888888999999999998887776511                           12222221


Q ss_pred             HHHHHHHH--hcCCHHHHHHHHHHHHHcCCCcCHHHHHHHHHHHHhcCChHHHHHHHHhcccCCCCCCHHHHHHHHHHHH
Q 040027          421 TTFIDGLC--KNGYIIEAVELFRTLRILKCELDIQAYNCLIDGLCKSGRLKFAWELFCSLPHGVLVPNVVTYNIMIQGLC  498 (595)
Q Consensus       421 ~~l~~~~~--~~g~~~~A~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~p~~~~~~~l~~~~~  498 (595)
                      . +.-++.  +.+...+++..+-......+..+...|..+..+|...|++.+|+.+|..+......-+...|..++.+|.
T Consensus       382 r-l~icL~~L~~~e~~e~ll~~l~~~n~~~~d~~dL~~d~a~al~~~~~~~~Al~~l~~i~~~~~~~~~~vw~~~a~c~~  460 (895)
T KOG2076|consen  382 R-LMICLVHLKERELLEALLHFLVEDNVWVSDDVDLYLDLADALTNIGKYKEALRLLSPITNREGYQNAFVWYKLARCYM  460 (895)
T ss_pred             h-HhhhhhcccccchHHHHHHHHHHhcCChhhhHHHHHHHHHHHHhcccHHHHHHHHHHHhcCccccchhhhHHHHHHHH
Confidence            1 111222  3344444444433333322445678899999999999999999999999998544446789999999999


Q ss_pred             hcCChhHHHHHHHHHHHcCCCCCHHHHHHHHHHHHHcCChhHHHHHHHHHH--------HCCCCCCHHHHHHHHHHHHhc
Q 040027          499 NDGQMDKARDLFLDMEENAAAPDVITFDMLIHGFIRINEPSKVNELLHKMK--------EKKVMPDASIVSIVVDLLVKN  570 (595)
Q Consensus       499 ~~g~~~~A~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~--------~~~~~p~~~~~~~l~~~~~~~  570 (595)
                      ..|.+++|++.|+..+... +.+...-..|...+...|+.++|.+.++.+.        ..+..|+..+.....+.|...
T Consensus       461 ~l~e~e~A~e~y~kvl~~~-p~~~D~Ri~Lasl~~~~g~~EkalEtL~~~~~~D~~~~e~~a~~~e~ri~~~r~d~l~~~  539 (895)
T KOG2076|consen  461 ELGEYEEAIEFYEKVLILA-PDNLDARITLASLYQQLGNHEKALETLEQIINPDGRNAEACAWEPERRILAHRCDILFQV  539 (895)
T ss_pred             HHhhHHHHHHHHHHHHhcC-CCchhhhhhHHHHHHhcCCHHHHHHHHhcccCCCccchhhccccHHHHHHHHHHHHHHHh
Confidence            9999999999999999974 5566777889999999999999999999953        335677888899999999999


Q ss_pred             CcccccchH
Q 040027          571 EISLKSLPS  579 (595)
Q Consensus       571 g~~~~~i~~  579 (595)
                      |+.|++|+.
T Consensus       540 gk~E~fi~t  548 (895)
T KOG2076|consen  540 GKREEFINT  548 (895)
T ss_pred             hhHHHHHHH
Confidence            999966554

>KOG4422 consensus Uncharacterized conserved protein [Function unknown]

Probab=99.77  E-value=1.6e-13  Score=123.40  Aligned_cols=306  Identities=18%  Similarity=0.277  Sum_probs=137.1

Q ss_pred             HHHHHHHHHHHHhcCChhHHHHHHHHHHhCCCCCCHHHHHHHHHH--HHhcCCHhHH-HHHHHHHHhcCC----------
Q 040027           96 LYTYNILINCFCKIGRVSLGFIAFGRILRSCFTPNAATFNSLIKG--LHAESRIMEA-AALFTKLKAFGC----------  162 (595)
Q Consensus        96 ~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~~l~~~--~~~~g~~~~A-~~~~~~~~~~~~----------  162 (595)
                      +++=+.|+. ....|...++.-+|++|...|++.+...-..+++.  |....++--| .+.|-.|...|-          
T Consensus       116 V~~E~nL~k-mIS~~EvKDs~ilY~~m~~e~~~vS~kvq~~L~~LV~~~Ns~~~~~~E~~~Fv~~~~~~E~S~~sWK~G~  194 (625)
T KOG4422|consen  116 VETENNLLK-MISSREVKDSCILYERMRSENVDVSEKVQLELFRLVTYYNSSNVPFAEWEEFVGMRNFGEDSTSSWKSGA  194 (625)
T ss_pred             hcchhHHHH-HHhhcccchhHHHHHHHHhcCCCCCHHHHHHHHHHHHhhcCCCCcchhHHHHhhcccccccccccccccc
Confidence            344444444 45678999999999999999888887776666543  3333332211 122333333221          


Q ss_pred             ---------CCCHhhHHHHHHHHHhcCChhHHHHHHHHHHhcCCCCCccccCcHHHHHHHHHHHHHcCCHhHHHHHHHHH
Q 040027          163 ---------EPNVITYNTLINGLCRTGHTMIALNLFEEMANGNGEIGVVCKPNTVTYSTIIDGLCKEGFVDKAKALFLQM  233 (595)
Q Consensus       163 ---------~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~  233 (595)
                               +-...++..+|.++++--..+.|.+++++.....      .+.+..++|.+|.+-.-..+    .++..+|
T Consensus       195 vAdL~~E~~PKT~et~s~mI~Gl~K~~~~ERA~~L~kE~~~~k------~kv~~~aFN~lI~~~S~~~~----K~Lv~EM  264 (625)
T KOG4422|consen  195 VADLLFETLPKTDETVSIMIAGLCKFSSLERARELYKEHRAAK------GKVYREAFNGLIGASSYSVG----KKLVAEM  264 (625)
T ss_pred             HHHHHHhhcCCCchhHHHHHHHHHHHHhHHHHHHHHHHHHHhh------heeeHHhhhhhhhHHHhhcc----HHHHHHH
Confidence                     1233444445555554444455555554444333      23344444444443222111    3444444


Q ss_pred             hhCCCCCCHhHHHHHHHHHHhcCCHHH----HHHHHHHHHHCCCCCCHhhHHHHHHHHHhcCChHH-HHHHHHHHHHC--
Q 040027          234 KDENINPDVVTYNSLIHGLCHANDWNE----AKRLFIEMMDQGVQPSVVTFNVIMDELCKNRKMDE-ASRLLDLMVQR--  306 (595)
Q Consensus       234 ~~~~~~~~~~~~~~ll~~~~~~~~~~~----A~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~-a~~~~~~~~~~--  306 (595)
                      ....+.||..|+|+++.+..+.|+++.    |.+++.+|.+.|+.|...+|..++..+.+.++..+ +..+..++...  
T Consensus       265 isqkm~Pnl~TfNalL~c~akfg~F~~ar~aalqil~EmKeiGVePsLsSyh~iik~f~re~dp~k~as~~i~dI~N~lt  344 (625)
T KOG4422|consen  265 ISQKMTPNLFTFNALLSCAAKFGKFEDARKAALQILGEMKEIGVEPSLSSYHLIIKNFKRESDPQKVASSWINDIQNSLT  344 (625)
T ss_pred             HHhhcCCchHhHHHHHHHHHHhcchHHHHHHHHHHHHHHHHhCCCcchhhHHHHHHHhcccCCchhhhHHHHHHHHHhhc
Confidence            444444555555555555555554432    23344444444555555555554444444443322 22222222211  


Q ss_pred             --CCC---C-CHHHHHHHHHHHHhcCCHHHHHHHHHHHHhcC----CCCCH---HHHHHHHHHHHhCCCHHHHHHHHHHH
Q 040027          307 --GVR---P-NACTYNTLMDGFCLMGKINRAEELFGSMESMG----CKHDD---VSYNILINGYCKNKEVEEALSLYREM  373 (595)
Q Consensus       307 --~~~---~-~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~----~~~~~---~~~~~l~~~~~~~~~~~~A~~~~~~~  373 (595)
                        ..+   | +...|...+..|.+..+.+.|.++..-+....    +.++.   .-|..+....++....+.-...|+.|
T Consensus       345 GK~fkp~~p~d~~FF~~AM~Ic~~l~d~~LA~~v~~ll~tg~N~~~ig~~~~~~fYyr~~~~licq~es~~~~~~~Y~~l  424 (625)
T KOG4422|consen  345 GKTFKPITPTDNKFFQSAMSICSSLRDLELAYQVHGLLKTGDNWKFIGPDQHRNFYYRKFFDLICQMESIDVTLKWYEDL  424 (625)
T ss_pred             cCcccCCCCchhHHHHHHHHHHHHhhhHHHHHHHHHHHHcCCchhhcChHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence              111   1 12223333444444444444444433322110    11111   12233333344444444444444444


Q ss_pred             HHCCCCCCHHHHHHHHHHHHccCCHHHHHHHHHHHHHCC
Q 040027          374 VSKGIKPTVVTYNTLFLGLFEIHQVEHALKLFDEMQRDG  412 (595)
Q Consensus       374 ~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~  412 (595)
                      +-.-.-|+..+...++++....+.++-.-++|.+++..|
T Consensus       425 VP~~y~p~~~~m~~~lrA~~v~~~~e~ipRiw~D~~~~g  463 (625)
T KOG4422|consen  425 VPSAYFPHSQTMIHLLRALDVANRLEVIPRIWKDSKEYG  463 (625)
T ss_pred             ccceecCCchhHHHHHHHHhhcCcchhHHHHHHHHHHhh
Confidence            444344444444444454444455555555554444443

>KOG4422 consensus Uncharacterized conserved protein [Function unknown]

Probab=99.77  E-value=9.6e-14  Score=124.78  Aligned_cols=442  Identities=15%  Similarity=0.136  Sum_probs=229.8

Q ss_pred             cccccCCCChHHHHHHHHHHHHhCCCCCCHhhHHHHHHH--HHcCCCch--h-----HHhhCCCCCCHHHHHHHHHHHHh
Q 040027           38 REGDINVITPNEAFCIFDYMLRMHPSPPPVSSFNILLAS--LAKNKHYD--T-----RLNATGLFPNLYTYNILINCFCK  108 (595)
Q Consensus        38 ~~~~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~~~l~~~--~~~~~~~~--~-----~~~~~~~~~~~~~~~~l~~~~~~  108 (595)
                      ...++.+|.++++.-+|++|.+.+.. .++..-..+++.  |..+.+..  +     .|...| ..+..+|        +
T Consensus       122 L~kmIS~~EvKDs~ilY~~m~~e~~~-vS~kvq~~L~~LV~~~Ns~~~~~~E~~~Fv~~~~~~-E~S~~sW--------K  191 (625)
T KOG4422|consen  122 LLKMISSREVKDSCILYERMRSENVD-VSEKVQLELFRLVTYYNSSNVPFAEWEEFVGMRNFG-EDSTSSW--------K  191 (625)
T ss_pred             HHHHHhhcccchhHHHHHHHHhcCCC-CCHHHHHHHHHHHHhhcCCCCcchhHHHHhhccccc-ccccccc--------c
Confidence            45668889999999999999998876 566554444432  22222211  1     111111 0111222        1


Q ss_pred             cCChhHHHHHHHHHHhCCCCCCHHHHHHHHHHHHhcCCHhHHHHHHHHHHhcCCCCCHhhHHHHHHHHHhcCChhHHHHH
Q 040027          109 IGRVSLGFIAFGRILRSCFTPNAATFNSLIKGLHAESRIMEAAALFTKLKAFGCEPNVITYNTLINGLCRTGHTMIALNL  188 (595)
Q Consensus       109 ~g~~~~A~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~  188 (595)
                      .|...  .-+|+. .    +....++..+|.++++--..++|.++|++........+..+++.+|.+-.-...    .++
T Consensus       192 ~G~vA--dL~~E~-~----PKT~et~s~mI~Gl~K~~~~ERA~~L~kE~~~~k~kv~~~aFN~lI~~~S~~~~----K~L  260 (625)
T KOG4422|consen  192 SGAVA--DLLFET-L----PKTDETVSIMIAGLCKFSSLERARELYKEHRAAKGKVYREAFNGLIGASSYSVG----KKL  260 (625)
T ss_pred             cccHH--HHHHhh-c----CCCchhHHHHHHHHHHHHhHHHHHHHHHHHHHhhheeeHHhhhhhhhHHHhhcc----HHH
Confidence            12221  122221 1    234455556666666666666666666665555555566666666554432222    455


Q ss_pred             HHHHHhcCCCCCccccCcHHHHHHHHHHHHHcCCHhHH----HHHHHHHhhCCCCCCHhHHHHHHHHHHhcCCHHH-HHH
Q 040027          189 FEEMANGNGEIGVVCKPNTVTYSTIIDGLCKEGFVDKA----KALFLQMKDENINPDVVTYNSLIHGLCHANDWNE-AKR  263 (595)
Q Consensus       189 ~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A----~~~~~~~~~~~~~~~~~~~~~ll~~~~~~~~~~~-A~~  263 (595)
                      +.+|.+..      ..||..++|+++.+..+.|+++.|    .+++.+|++.|+.|...+|..++..+.+.++..+ +..
T Consensus       261 v~EMisqk------m~Pnl~TfNalL~c~akfg~F~~ar~aalqil~EmKeiGVePsLsSyh~iik~f~re~dp~k~as~  334 (625)
T KOG4422|consen  261 VAEMISQK------MTPNLFTFNALLSCAAKFGKFEDARKAALQILGEMKEIGVEPSLSSYHLIIKNFKRESDPQKVASS  334 (625)
T ss_pred             HHHHHHhh------cCCchHhHHHHHHHHHHhcchHHHHHHHHHHHHHHHHhCCCcchhhHHHHHHHhcccCCchhhhHH
Confidence            55555554      456666666666666666655433    3445555556666666666666665555555433 333


Q ss_pred             HHHHHHHC--C--CC----CCHhhHHHHHHHHHhcCChHHHHHHHHHHHHCC----CCCC---HHHHHHHHHHHHhcCCH
Q 040027          264 LFIEMMDQ--G--VQ----PSVVTFNVIMDELCKNRKMDEASRLLDLMVQRG----VRPN---ACTYNTLMDGFCLMGKI  328 (595)
Q Consensus       264 ~~~~~~~~--~--~~----~~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~----~~~~---~~~~~~l~~~~~~~~~~  328 (595)
                      ++.++...  |  ++    .|...|...+..|....+.+-|.++...+....    +.|+   ...|..+..+.++....
T Consensus       335 ~i~dI~N~ltGK~fkp~~p~d~~FF~~AM~Ic~~l~d~~LA~~v~~ll~tg~N~~~ig~~~~~~fYyr~~~~licq~es~  414 (625)
T KOG4422|consen  335 WINDIQNSLTGKTFKPITPTDNKFFQSAMSICSSLRDLELAYQVHGLLKTGDNWKFIGPDQHRNFYYRKFFDLICQMESI  414 (625)
T ss_pred             HHHHHHHhhccCcccCCCCchhHHHHHHHHHHHHhhhHHHHHHHHHHHHcCCchhhcChHHHHHHHHHHHHHHHHHHHHH
Confidence            33443322  1  11    133344555555555566555555544443211    1111   12334444455555555


Q ss_pred             HHHHHHHHHHHhcCCCCCHHHHHHHHHHHHhCCCHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHccC------------
Q 040027          329 NRAEELFGSMESMGCKHDDVSYNILINGYCKNKEVEEALSLYREMVSKGIKPTVVTYNTLFLGLFEIH------------  396 (595)
Q Consensus       329 ~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~------------  396 (595)
                      +.....|+.++-.-.-|+..+...++++..-.+.++-.-+++.+++..|..........++..+++..            
T Consensus       415 ~~~~~~Y~~lVP~~y~p~~~~m~~~lrA~~v~~~~e~ipRiw~D~~~~ght~r~~l~eeil~~L~~~k~hp~tp~r~Ql~  494 (625)
T KOG4422|consen  415 DVTLKWYEDLVPSAYFPHSQTMIHLLRALDVANRLEVIPRIWKDSKEYGHTFRSDLREEILMLLARDKLHPLTPEREQLQ  494 (625)
T ss_pred             HHHHHHHHHhccceecCCchhHHHHHHHHhhcCcchhHHHHHHHHHHhhhhhhHHHHHHHHHHHhcCCCCCCChHHHHHH
Confidence            66666666665444445555555555555556666555555555555443322222222222222211            


Q ss_pred             --------CH-HHHHHHHHHHHHCCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHHcCC----CcCHHHHHHHHHHHH
Q 040027          397 --------QV-EHALKLFDEMQRDGVAADTRTYTTFIDGLCKNGYIIEAVELFRTLRILKC----ELDIQAYNCLIDGLC  463 (595)
Q Consensus       397 --------~~-~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~----~~~~~~~~~l~~~~~  463 (595)
                              ++ +.....-.++.+.  .......+.++-.+.+.|+.++|.+++..+.+.+-    .|...+...+++.-.
T Consensus       495 ~~~ak~aad~~e~~e~~~~R~r~~--~~~~t~l~~ia~Ll~R~G~~qkA~e~l~l~~~~~~~ip~~p~lnAm~El~d~a~  572 (625)
T KOG4422|consen  495 VAFAKCAADIKEAYESQPIRQRAQ--DWPATSLNCIAILLLRAGRTQKAWEMLGLFLRKHNKIPRSPLLNAMAELMDSAK  572 (625)
T ss_pred             HHHHHHHHHHHHHHHhhHHHHHhc--cCChhHHHHHHHHHHHcchHHHHHHHHHHHHhcCCcCCCCcchhhHHHHHHHHH
Confidence                    01 1111111223333  44556677777788899999999999998865432    233444446667777


Q ss_pred             hcCChHHHHHHHHhcccCCCCCCHHHHHHHHHHHHhcCChhHHHH
Q 040027          464 KSGRLKFAWELFCSLPHGVLVPNVVTYNIMIQGLCNDGQMDKARD  508 (595)
Q Consensus       464 ~~g~~~~A~~~~~~~~~~~~~p~~~~~~~l~~~~~~~g~~~~A~~  508 (595)
                      ..++...|...++-+...+...-...-+.+...|.-+..-.+|+.
T Consensus       573 ~~~spsqA~~~lQ~a~~~n~~~~E~La~RI~e~f~iNqeq~~~ls  617 (625)
T KOG4422|consen  573 VSNSPSQAIEVLQLASAFNLPICEGLAQRIMEDFAINQEQKEALS  617 (625)
T ss_pred             hcCCHHHHHHHHHHHHHcCchhhhHHHHHHHHhcCcCHHHHHHHh
Confidence            788899999999988775433222233444455544433334433

>KOG0547 consensus Translocase of outer mitochondrial membrane complex, subunit TOM70/TOM72 [Intracellular trafficking, secretion, and vesicular transport]

Probab=99.74  E-value=2.4e-14  Score=130.74  Aligned_cols=87  Identities=10%  Similarity=-0.031  Sum_probs=67.8

Q ss_pred             HHHHHHHHHhcCChhHHHHHHHHHHhCCCCCC-HHHHHHHHHHHHhcCCHhHHHHHHHHHHhcCCCCCHhhHHHHHHHHH
Q 040027           99 YNILINCFCKIGRVSLGFIAFGRILRSCFTPN-AATFNSLIKGLHAESRIMEAAALFTKLKAFGCEPNVITYNTLINGLC  177 (595)
Q Consensus        99 ~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~~-~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~~l~~~~~  177 (595)
                      +-...+.|.+.|.+++|++.|..++..  .|+ +..|.....+|...|+++++++--.+.++.+. .-+.++..-..++-
T Consensus       118 lK~~GN~~f~~kkY~eAIkyY~~AI~l--~p~epiFYsNraAcY~~lgd~~~Vied~TkALEl~P-~Y~KAl~RRA~A~E  194 (606)
T KOG0547|consen  118 LKTKGNKFFRNKKYDEAIKYYTQAIEL--CPDEPIFYSNRAACYESLGDWEKVIEDCTKALELNP-DYVKALLRRASAHE  194 (606)
T ss_pred             HHhhhhhhhhcccHHHHHHHHHHHHhc--CCCCchhhhhHHHHHHHHhhHHHHHHHHHHHhhcCc-HHHHHHHHHHHHHH
Confidence            344566788899999999999999987  566 77788888899999999999998888887642 23556666677778


Q ss_pred             hcCChhHHHHH
Q 040027          178 RTGHTMIALNL  188 (595)
Q Consensus       178 ~~g~~~~A~~~  188 (595)
                      +.|++++|+.-
T Consensus       195 ~lg~~~eal~D  205 (606)
T KOG0547|consen  195 QLGKFDEALFD  205 (606)
T ss_pred             hhccHHHHHHh
Confidence            88888887653

>KOG0547 consensus Translocase of outer mitochondrial membrane complex, subunit TOM70/TOM72 [Intracellular trafficking, secretion, and vesicular transport]

Probab=99.74  E-value=3e-14  Score=130.15  Aligned_cols=226  Identities=15%  Similarity=0.129  Sum_probs=173.0

Q ss_pred             HHHHHhcCChHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHhcCCCCCHHHHHHHHHHHHhCCCH
Q 040027          284 MDELCKNRKMDEASRLLDLMVQRGVRPNACTYNTLMDGFCLMGKINRAEELFGSMESMGCKHDDVSYNILINGYCKNKEV  363 (595)
Q Consensus       284 ~~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~  363 (595)
                      ...+.-.|+...+..-|+..+.....+ ...|..+..+|....+.++....|......+ +.++.+|..-..++.-.+++
T Consensus       333 gtF~fL~g~~~~a~~d~~~~I~l~~~~-~~lyI~~a~~y~d~~~~~~~~~~F~~A~~ld-p~n~dvYyHRgQm~flL~q~  410 (606)
T KOG0547|consen  333 GTFHFLKGDSLGAQEDFDAAIKLDPAF-NSLYIKRAAAYADENQSEKMWKDFNKAEDLD-PENPDVYYHRGQMRFLLQQY  410 (606)
T ss_pred             hhhhhhcCCchhhhhhHHHHHhcCccc-chHHHHHHHHHhhhhccHHHHHHHHHHHhcC-CCCCchhHhHHHHHHHHHHH
Confidence            334556788888999999888875443 3337777888889999999999999988876 56777888888888888999


Q ss_pred             HHHHHHHHHHHHCCCCCCHHHHHHHHHHHHccCCHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHH
Q 040027          364 EEALSLYREMVSKGIKPTVVTYNTLFLGLFEIHQVEHALKLFDEMQRDGVAADTRTYTTFIDGLCKNGYIIEAVELFRTL  443 (595)
Q Consensus       364 ~~A~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~  443 (595)
                      ++|..-|++.++..+. +...|..+.-+..+.++++++...|++.++. +|..+..|+...+.+..++++++|.+.|+..
T Consensus       411 e~A~aDF~Kai~L~pe-~~~~~iQl~~a~Yr~~k~~~~m~~Fee~kkk-FP~~~Evy~~fAeiLtDqqqFd~A~k~YD~a  488 (606)
T KOG0547|consen  411 EEAIADFQKAISLDPE-NAYAYIQLCCALYRQHKIAESMKTFEEAKKK-FPNCPEVYNLFAEILTDQQQFDKAVKQYDKA  488 (606)
T ss_pred             HHHHHHHHHHhhcChh-hhHHHHHHHHHHHHHHHHHHHHHHHHHHHHh-CCCCchHHHHHHHHHhhHHhHHHHHHHHHHH
Confidence            9999999998887443 5566777777777888999999999998887 6778889999999999999999999999988


Q ss_pred             HHcCCCc-----C--HHHHHHHHHHHHhcCChHHHHHHHHhcccCCCCCC-HHHHHHHHHHHHhcCChhHHHHHHHHHHH
Q 040027          444 RILKCEL-----D--IQAYNCLIDGLCKSGRLKFAWELFCSLPHGVLVPN-VVTYNIMIQGLCNDGQMDKARDLFLDMEE  515 (595)
Q Consensus       444 ~~~~~~~-----~--~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~p~-~~~~~~l~~~~~~~g~~~~A~~~~~~~~~  515 (595)
                      +......     +  +.+...++..- -.+++..|..+++++.+  +.|- ...+..|...-.+.|+.++|+++|++...
T Consensus       489 i~LE~~~~~~~v~~~plV~Ka~l~~q-wk~d~~~a~~Ll~KA~e--~Dpkce~A~~tlaq~~lQ~~~i~eAielFEksa~  565 (606)
T KOG0547|consen  489 IELEPREHLIIVNAAPLVHKALLVLQ-WKEDINQAENLLRKAIE--LDPKCEQAYETLAQFELQRGKIDEAIELFEKSAQ  565 (606)
T ss_pred             HhhccccccccccchhhhhhhHhhhc-hhhhHHHHHHHHHHHHc--cCchHHHHHHHHHHHHHHHhhHHHHHHHHHHHHH
Confidence            8653110     1  11112222222 23888889999988887  5554 46788888888888999999999988766


Q ss_pred             c
Q 040027          516 N  516 (595)
Q Consensus       516 ~  516 (595)
                      .
T Consensus       566 l  566 (606)
T KOG0547|consen  566 L  566 (606)
T ss_pred             H
Confidence            3

>KOG1155 consensus Anaphase-promoting complex (APC), Cdc23 subunit [Cell cycle control, cell division, chromosome partitioning; Posttranslational modification, protein turnover, chaperones]

Probab=99.71  E-value=6.6e-12  Score=114.40  Aligned_cols=256  Identities=13%  Similarity=0.082  Sum_probs=115.4

Q ss_pred             HHHhcCCHHHHHHHHHHHHHCCCCCCHhhHHHHHHHHHhcCChHHHHHHHHHHHHCCCC--CCHHHHHHHHHHHHhcCCH
Q 040027          251 GLCHANDWNEAKRLFIEMMDQGVQPSVVTFNVIMDELCKNRKMDEASRLLDLMVQRGVR--PNACTYNTLMDGFCLMGKI  328 (595)
Q Consensus       251 ~~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~~~--~~~~~~~~l~~~~~~~~~~  328 (595)
                      ++....+.++++.-.......|++-+...-+....+.....++++|+.+|+++.+.++-  -|..+|..++.+-......
T Consensus       236 a~~el~q~~e~~~k~e~l~~~gf~~~~~i~~~~A~~~y~~rDfD~a~s~Feei~knDPYRl~dmdlySN~LYv~~~~skL  315 (559)
T KOG1155|consen  236 AYQELHQHEEALQKKERLSSVGFPNSMYIKTQIAAASYNQRDFDQAESVFEEIRKNDPYRLDDMDLYSNVLYVKNDKSKL  315 (559)
T ss_pred             HHHHHHHHHHHHHHHHHHHhccCCccHHHHHHHHHHHhhhhhHHHHHHHHHHHHhcCCCcchhHHHHhHHHHHHhhhHHH
Confidence            33334444555555545544444444433344444444555555555555555554210  1233333332221111111


Q ss_pred             HHHHHHHHH-HHhcCCCCCHHHHHHHHHHHHhCCCHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHccCCHHHHHHHHHH
Q 040027          329 NRAEELFGS-MESMGCKHDDVSYNILINGYCKNKEVEEALSLYREMVSKGIKPTVVTYNTLFLGLFEIHQVEHALKLFDE  407 (595)
Q Consensus       329 ~~a~~~~~~-~~~~~~~~~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~  407 (595)
                          ..+.. ....+ +.-+.+...+.+-|.-.++.++|+..|++.++.++. ....|+.+..-|...++...|...|+.
T Consensus       316 ----s~LA~~v~~id-KyR~ETCCiIaNYYSlr~eHEKAv~YFkRALkLNp~-~~~aWTLmGHEyvEmKNt~AAi~sYRr  389 (559)
T KOG1155|consen  316 ----SYLAQNVSNID-KYRPETCCIIANYYSLRSEHEKAVMYFKRALKLNPK-YLSAWTLMGHEYVEMKNTHAAIESYRR  389 (559)
T ss_pred             ----HHHHHHHHHhc-cCCccceeeehhHHHHHHhHHHHHHHHHHHHhcCcc-hhHHHHHhhHHHHHhcccHHHHHHHHH
Confidence                11111 00000 122234444444455555555555555555554322 333444444455555555555555555


Q ss_pred             HHHCCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCcCHHHHHHHHHHHHhcCChHHHHHHHHhcccCCCCCCH
Q 040027          408 MQRDGVAADTRTYTTFIDGLCKNGYIIEAVELFRTLRILKCELDIQAYNCLIDGLCKSGRLKFAWELFCSLPHGVLVPNV  487 (595)
Q Consensus       408 ~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~p~~  487 (595)
                      +++-+ |.|-..|-.+.++|.-.+...-|+-.|+++.... |.|...|.+|+.+|.+.++.++|+..|......|- .+.
T Consensus       390 Avdi~-p~DyRAWYGLGQaYeim~Mh~YaLyYfqkA~~~k-PnDsRlw~aLG~CY~kl~~~~eAiKCykrai~~~d-te~  466 (559)
T KOG1155|consen  390 AVDIN-PRDYRAWYGLGQAYEIMKMHFYALYYFQKALELK-PNDSRLWVALGECYEKLNRLEEAIKCYKRAILLGD-TEG  466 (559)
T ss_pred             HHhcC-chhHHHHhhhhHHHHHhcchHHHHHHHHHHHhcC-CCchHHHHHHHHHHHHhccHHHHHHHHHHHHhccc-cch
Confidence            55442 3444555555555555555555555555555443 44555555555555555555555555555544321 133


Q ss_pred             HHHHHHHHHHHhcCChhHHHHHHHHHHH
Q 040027          488 VTYNIMIQGLCNDGQMDKARDLFLDMEE  515 (595)
Q Consensus       488 ~~~~~l~~~~~~~g~~~~A~~~~~~~~~  515 (595)
                      ..+..++..|-+.++.++|...|++.++
T Consensus       467 ~~l~~LakLye~l~d~~eAa~~yek~v~  494 (559)
T KOG1155|consen  467 SALVRLAKLYEELKDLNEAAQYYEKYVE  494 (559)
T ss_pred             HHHHHHHHHHHHHHhHHHHHHHHHHHHH
Confidence            4445555555555555555555554443

>KOG1155 consensus Anaphase-promoting complex (APC), Cdc23 subunit [Cell cycle control, cell division, chromosome partitioning; Posttranslational modification, protein turnover, chaperones]

Probab=99.71  E-value=1.9e-12  Score=117.85  Aligned_cols=365  Identities=11%  Similarity=0.040  Sum_probs=263.0

Q ss_pred             CCCHHHHHHHHHHHHhcCCHhHHHHHHHHHHhcCCCCCHhhHHHHHHHHHhcCChhHHHHHHHHHHhcCCCCCccccCcH
Q 040027          128 TPNAATFNSLIKGLHAESRIMEAAALFTKLKAFGCEPNVITYNTLINGLCRTGHTMIALNLFEEMANGNGEIGVVCKPNT  207 (595)
Q Consensus       128 ~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~~~  207 (595)
                      .-|...+-.....+.+.|....|++.|......- +-...+|..|.....   +    ++.........       +.+.
T Consensus       161 ~~D~fllYL~Gvv~k~~~~~s~A~~sfv~~v~~~-P~~W~AWleL~~lit---~----~e~~~~l~~~l-------~~~~  225 (559)
T KOG1155|consen  161 EKDEFLLYLYGVVLKELGLLSLAIDSFVEVVNRY-PWFWSAWLELSELIT---D----IEILSILVVGL-------PSDM  225 (559)
T ss_pred             cchhHHHHHHHHHHHhhchHHHHHHHHHHHHhcC-CcchHHHHHHHHhhc---h----HHHHHHHHhcC-------cccc
Confidence            4444444444455667889999999998887652 445566665554432   2    22222222211       1111


Q ss_pred             --HHHHHHHHHHHHcCCHhHHHHHHHHHhhCCCCCCHhHHHHHHHHHHhcCCHHHHHHHHHHHHHCCCC--CCHhhHHHH
Q 040027          208 --VTYSTIIDGLCKEGFVDKAKALFLQMKDENINPDVVTYNSLIHGLCHANDWNEAKRLFIEMMDQGVQ--PSVVTFNVI  283 (595)
Q Consensus       208 --~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~~ll~~~~~~~~~~~A~~~~~~~~~~~~~--~~~~~~~~l  283 (595)
                        ..-.-+..++....+.+++..-.+.....|++.+...-+....+.....|++.|+.+|+++.+...-  .|..+|..+
T Consensus       226 h~M~~~F~~~a~~el~q~~e~~~k~e~l~~~gf~~~~~i~~~~A~~~y~~rDfD~a~s~Feei~knDPYRl~dmdlySN~  305 (559)
T KOG1155|consen  226 HWMKKFFLKKAYQELHQHEEALQKKERLSSVGFPNSMYIKTQIAAASYNQRDFDQAESVFEEIRKNDPYRLDDMDLYSNV  305 (559)
T ss_pred             hHHHHHHHHHHHHHHHHHHHHHHHHHHHHhccCCccHHHHHHHHHHHhhhhhHHHHHHHHHHHHhcCCCcchhHHHHhHH
Confidence              1112244566666788888888888888888766666666667788899999999999999987311  155667666


Q ss_pred             HHHHHhcCChHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHhcCCCCCHHHHHHHHHHHHhCCCH
Q 040027          284 MDELCKNRKMDEASRLLDLMVQRGVRPNACTYNTLMDGFCLMGKINRAEELFGSMESMGCKHDDVSYNILINGYCKNKEV  363 (595)
Q Consensus       284 ~~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~  363 (595)
                      +-.  +..+..  +.++..-...-.+.-+.|...+++-|.-.++.++|...|++.++.+ +....+|+.+..-|....+.
T Consensus       306 LYv--~~~~sk--Ls~LA~~v~~idKyR~ETCCiIaNYYSlr~eHEKAv~YFkRALkLN-p~~~~aWTLmGHEyvEmKNt  380 (559)
T KOG1155|consen  306 LYV--KNDKSK--LSYLAQNVSNIDKYRPETCCIIANYYSLRSEHEKAVMYFKRALKLN-PKYLSAWTLMGHEYVEMKNT  380 (559)
T ss_pred             HHH--HhhhHH--HHHHHHHHHHhccCCccceeeehhHHHHHHhHHHHHHHHHHHHhcC-cchhHHHHHhhHHHHHhccc
Confidence            543  322221  1112111111123345677788899999999999999999999986 44566899999999999999


Q ss_pred             HHHHHHHHHHHHCCCCCCHHHHHHHHHHHHccCCHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHH
Q 040027          364 EEALSLYREMVSKGIKPTVVTYNTLFLGLFEIHQVEHALKLFDEMQRDGVAADTRTYTTFIDGLCKNGYIIEAVELFRTL  443 (595)
Q Consensus       364 ~~A~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~  443 (595)
                      ..|++.|+.+++-.+. |...|..+.++|.-.+.+.=|+-.|++.... .|.|+..|.++.++|.+.++.++|+..|+++
T Consensus       381 ~AAi~sYRrAvdi~p~-DyRAWYGLGQaYeim~Mh~YaLyYfqkA~~~-kPnDsRlw~aLG~CY~kl~~~~eAiKCykra  458 (559)
T KOG1155|consen  381 HAAIESYRRAVDINPR-DYRAWYGLGQAYEIMKMHFYALYYFQKALEL-KPNDSRLWVALGECYEKLNRLEEAIKCYKRA  458 (559)
T ss_pred             HHHHHHHHHHHhcCch-hHHHHhhhhHHHHHhcchHHHHHHHHHHHhc-CCCchHHHHHHHHHHHHhccHHHHHHHHHHH
Confidence            9999999999997555 8899999999999999999999999999987 3789999999999999999999999999999


Q ss_pred             HHcCCCcCHHHHHHHHHHHHhcCChHHHHHHHHhccc----CC-CCCC-HHHHHHHHHHHHhcCChhHHHHHHHHHHH
Q 040027          444 RILKCELDIQAYNCLIDGLCKSGRLKFAWELFCSLPH----GV-LVPN-VVTYNIMIQGLCNDGQMDKARDLFLDMEE  515 (595)
Q Consensus       444 ~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~----~~-~~p~-~~~~~~l~~~~~~~g~~~~A~~~~~~~~~  515 (595)
                      ...+ ..+...+..|++.|-+.++..+|...|.+.++    .| +.|. .....-|...+.+.+++++|..+......
T Consensus       459 i~~~-dte~~~l~~LakLye~l~d~~eAa~~yek~v~~~~~eg~~~~~t~ka~~fLA~~f~k~~~~~~As~Ya~~~~~  535 (559)
T KOG1155|consen  459 ILLG-DTEGSALVRLAKLYEELKDLNEAAQYYEKYVEVSELEGEIDDETIKARLFLAEYFKKMKDFDEASYYATLVLK  535 (559)
T ss_pred             Hhcc-ccchHHHHHHHHHHHHHHhHHHHHHHHHHHHHHHHhhcccchHHHHHHHHHHHHHHhhcchHHHHHHHHHHhc
Confidence            9987 66779999999999999999999999988766    22 2221 22223355666677888877665555443

>KOG2047 consensus mRNA splicing factor [RNA processing and modification]

Probab=99.71  E-value=1.9e-11  Score=115.81  Aligned_cols=524  Identities=12%  Similarity=0.097  Sum_probs=341.4

Q ss_pred             HHHHHHHHHHHHhCCCCCCHhhHHHHHHHHHcCCC---chh-------HHhhCCC---CCCHHHHHHHHHHHHhcCChhH
Q 040027           48 NEAFCIFDYMLRMHPSPPPVSSFNILLASLAKNKH---YDT-------RLNATGL---FPNLYTYNILINCFCKIGRVSL  114 (595)
Q Consensus        48 ~~A~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~---~~~-------~~~~~~~---~~~~~~~~~l~~~~~~~g~~~~  114 (595)
                      +.-.-+|+++++.-|.  +--.|..-+..=...-+   ...       .....++   .--+..|...++.+..+|+...
T Consensus        43 k~~~~lYERal~~lp~--sykiW~~YL~~R~~~vk~~~~T~~~~~~vn~c~er~lv~mHkmpRIwl~Ylq~l~~Q~~iT~  120 (835)
T KOG2047|consen   43 KQRNLLYERALKELPG--SYKIWYDYLKARRAQVKHLCPTDPAYESVNNCFERCLVFMHKMPRIWLDYLQFLIKQGLITR  120 (835)
T ss_pred             HHHHHHHHHHHHHCCC--chHHHHHHHHHHHHHhhccCCCChHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHHhcchHHH
Confidence            4456788999999887  77788777643222111   111       1111111   1356788889999999999999


Q ss_pred             HHHHHHHHHhC-CCCCCHHHHHHHHHHHHhcCCHhHHHHHHHHHHhcCCCCCHhhHHHHHHHHHhcCChhHHHHHHHHHH
Q 040027          115 GFIAFGRILRS-CFTPNAATFNSLIKGLHAESRIMEAAALFTKLKAFGCEPNVITYNTLINGLCRTGHTMIALNLFEEMA  193 (595)
Q Consensus       115 A~~~~~~~~~~-~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~  193 (595)
                      .+..|++++.. .+.....+|...+......+-++-++.+|++.++.    ++......+..++..+++++|.+.+..++
T Consensus       121 tR~tfdrALraLpvtqH~rIW~lyl~Fv~~~~lPets~rvyrRYLk~----~P~~~eeyie~L~~~d~~~eaa~~la~vl  196 (835)
T KOG2047|consen  121 TRRTFDRALRALPVTQHDRIWDLYLKFVESHGLPETSIRVYRRYLKV----APEAREEYIEYLAKSDRLDEAAQRLATVL  196 (835)
T ss_pred             HHHHHHHHHHhCchHhhccchHHHHHHHHhCCChHHHHHHHHHHHhc----CHHHHHHHHHHHHhccchHHHHHHHHHhc
Confidence            99999999876 33445668999999888999999999999999976    45557888999999999999999999988


Q ss_pred             hcCCCCCccccCcHHHHHHHHHHHHHcCCHh---HHHHHHHHHhhCCCCCCHhHHHHHHHHHHhcCCHHHHHHHHHHHHH
Q 040027          194 NGNGEIGVVCKPNTVTYSTIIDGLCKEGFVD---KAKALFLQMKDENINPDVVTYNSLIHGLCHANDWNEAKRLFIEMMD  270 (595)
Q Consensus       194 ~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~---~A~~~~~~~~~~~~~~~~~~~~~ll~~~~~~~~~~~A~~~~~~~~~  270 (595)
                      ..+.-.+.-.+.+...|..+-....+.-+.-   ...++++.+..+-..--...|.+|...|.+.|.+++|.++|++.+.
T Consensus       197 n~d~f~sk~gkSn~qlw~elcdlis~~p~~~~slnvdaiiR~gi~rftDq~g~Lw~SLAdYYIr~g~~ekarDvyeeai~  276 (835)
T KOG2047|consen  197 NQDEFVSKKGKSNHQLWLELCDLISQNPDKVQSLNVDAIIRGGIRRFTDQLGFLWCSLADYYIRSGLFEKARDVYEEAIQ  276 (835)
T ss_pred             CchhhhhhcccchhhHHHHHHHHHHhCcchhcccCHHHHHHhhcccCcHHHHHHHHHHHHHHHHhhhhHHHHHHHHHHHH
Confidence            6553333223556667777777666654432   3344455544431111245689999999999999999999998877


Q ss_pred             CCCCCCHhhHHHHHHHHHh----------------cC------ChHHHHHHHHHHHHCCC-----------CCCHHHHHH
Q 040027          271 QGVQPSVVTFNVIMDELCK----------------NR------KMDEASRLLDLMVQRGV-----------RPNACTYNT  317 (595)
Q Consensus       271 ~~~~~~~~~~~~l~~~~~~----------------~g------~~~~a~~~~~~~~~~~~-----------~~~~~~~~~  317 (595)
                      .-  ....-|..+..+|..                .+      +++-....|+.+.....           +.+...|..
T Consensus       277 ~v--~tvrDFt~ifd~Ya~FEE~~~~~~me~a~~~~~n~ed~~dl~~~~a~~e~lm~rr~~~lNsVlLRQn~~nV~eW~k  354 (835)
T KOG2047|consen  277 TV--MTVRDFTQIFDAYAQFEESCVAAKMELADEESGNEEDDVDLELHMARFESLMNRRPLLLNSVLLRQNPHNVEEWHK  354 (835)
T ss_pred             hh--eehhhHHHHHHHHHHHHHHHHHHHHhhhhhcccChhhhhhHHHHHHHHHHHHhccchHHHHHHHhcCCccHHHHHh
Confidence            52  122223333333321                11      12233344444443211           122333333


Q ss_pred             HHHHHHhcCCHHHHHHHHHHHHhcCCCC------CHHHHHHHHHHHHhCCCHHHHHHHHHHHHHCCCCCC---HHHHHHH
Q 040027          318 LMDGFCLMGKINRAEELFGSMESMGCKH------DDVSYNILINGYCKNKEVEEALSLYREMVSKGIKPT---VVTYNTL  388 (595)
Q Consensus       318 l~~~~~~~~~~~~a~~~~~~~~~~~~~~------~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~~~~~~~---~~~~~~l  388 (595)
                      -..  ...|+..+-...|.++.+. +.|      -...|..+...|-..|+.+.|..+|++..+-..+--   ..+|...
T Consensus       355 RV~--l~e~~~~~~i~tyteAv~~-vdP~ka~Gs~~~Lw~~faklYe~~~~l~~aRvifeka~~V~y~~v~dLa~vw~~w  431 (835)
T KOG2047|consen  355 RVK--LYEGNAAEQINTYTEAVKT-VDPKKAVGSPGTLWVEFAKLYENNGDLDDARVIFEKATKVPYKTVEDLAEVWCAW  431 (835)
T ss_pred             hhh--hhcCChHHHHHHHHHHHHc-cCcccCCCChhhHHHHHHHHHHhcCcHHHHHHHHHHhhcCCccchHHHHHHHHHH
Confidence            222  2356677777788877654 122      224688889999999999999999999887543311   2345555


Q ss_pred             HHHHHccCCHHHHHHHHHHHHHCCCCC-----------------CHHHHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCcC
Q 040027          389 FLGLFEIHQVEHALKLFDEMQRDGVAA-----------------DTRTYTTFIDGLCKNGYIIEAVELFRTLRILKCELD  451 (595)
Q Consensus       389 ~~~~~~~~~~~~a~~~~~~~~~~~~~~-----------------~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~~  451 (595)
                      ...-.++.+++.|+++++........|                 +..+|...+..--..|-++....+|++++...+ .+
T Consensus       432 aemElrh~~~~~Al~lm~~A~~vP~~~~~~~yd~~~pvQ~rlhrSlkiWs~y~DleEs~gtfestk~vYdriidLri-aT  510 (835)
T KOG2047|consen  432 AEMELRHENFEAALKLMRRATHVPTNPELEYYDNSEPVQARLHRSLKIWSMYADLEESLGTFESTKAVYDRIIDLRI-AT  510 (835)
T ss_pred             HHHHHhhhhHHHHHHHHHhhhcCCCchhhhhhcCCCcHHHHHHHhHHHHHHHHHHHHHhccHHHHHHHHHHHHHHhc-CC
Confidence            566677888999999888776431111                 234556666666678899999999999998774 35


Q ss_pred             HHHHHHHHHHHHhcCChHHHHHHHHhcccCCCCCCH-HHHHHHHHHHHh---cCChhHHHHHHHHHHHcCCCCCH-HHHH
Q 040027          452 IQAYNCLIDGLCKSGRLKFAWELFCSLPHGVLVPNV-VTYNIMIQGLCN---DGQMDKARDLFLDMEENAAAPDV-ITFD  526 (595)
Q Consensus       452 ~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~p~~-~~~~~l~~~~~~---~g~~~~A~~~~~~~~~~~~~~~~-~~~~  526 (595)
                      +.+.......+-...-++++.+++++-+..--.|++ ..|+..+.-+.+   ...++.|..+|+++++ |-+|.. .++.
T Consensus       511 Pqii~NyAmfLEeh~yfeesFk~YErgI~LFk~p~v~diW~tYLtkfi~rygg~klEraRdLFEqaL~-~Cpp~~aKtiy  589 (835)
T KOG2047|consen  511 PQIIINYAMFLEEHKYFEESFKAYERGISLFKWPNVYDIWNTYLTKFIKRYGGTKLERARDLFEQALD-GCPPEHAKTIY  589 (835)
T ss_pred             HHHHHHHHHHHHhhHHHHHHHHHHHcCCccCCCccHHHHHHHHHHHHHHHhcCCCHHHHHHHHHHHHh-cCCHHHHHHHH
Confidence            666666666677778899999999987775344664 678887766653   2378999999999999 445543 2222


Q ss_pred             HH-HHHHHHcCChhHHHHHHHHHHHCCCCCC--HHHHHHHHHHHHh-c------CcccccchHHHHhhh
Q 040027          527 ML-IHGFIRINEPSKVNELLHKMKEKKVMPD--ASIVSIVVDLLVK-N------EISLKSLPSFLVQER  585 (595)
Q Consensus       527 ~l-~~~~~~~g~~~~A~~~~~~~~~~~~~p~--~~~~~~l~~~~~~-~------g~~~~~i~~~~~~~~  585 (595)
                      .+ ...=-+-|....|..+++++... +++.  -..|+..+.--.. -      +-++++|+++|....
T Consensus       590 LlYA~lEEe~GLar~amsiyerat~~-v~~a~~l~myni~I~kaae~yGv~~TR~iYekaIe~Lp~~~~  657 (835)
T KOG2047|consen  590 LLYAKLEEEHGLARHAMSIYERATSA-VKEAQRLDMYNIYIKKAAEIYGVPRTREIYEKAIESLPDSKA  657 (835)
T ss_pred             HHHHHHHHHhhHHHHHHHHHHHHHhc-CCHHHHHHHHHHHHHHHHHHhCCcccHHHHHHHHHhCChHHH
Confidence            22 22223458888999999998753 3432  2444444432211 2      234478887775543

>PF13429 TPR_15: Tetratricopeptide repeat; PDB: 2VQ2_A 2PL2_B

Probab=99.70  E-value=9.8e-17  Score=148.95  Aligned_cols=262  Identities=15%  Similarity=0.112  Sum_probs=94.2

Q ss_pred             HHHHHHHhcCChHHHHHHHHHHHHCC-CCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHhcCCCCCHHHHHHHHHHHHhC
Q 040027          282 VIMDELCKNRKMDEASRLLDLMVQRG-VRPNACTYNTLMDGFCLMGKINRAEELFGSMESMGCKHDDVSYNILINGYCKN  360 (595)
Q Consensus       282 ~l~~~~~~~g~~~~a~~~~~~~~~~~-~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~  360 (595)
                      .+...+...|++++|+++++...... .+.+...+..+.......++++.|+..++++...+ +.++..+..++.. ...
T Consensus        13 ~~A~~~~~~~~~~~Al~~L~~~~~~~~~~~~~~~~~~~a~La~~~~~~~~A~~ay~~l~~~~-~~~~~~~~~l~~l-~~~   90 (280)
T PF13429_consen   13 RLARLLYQRGDYEKALEVLKKAAQKIAPPDDPEYWRLLADLAWSLGDYDEAIEAYEKLLASD-KANPQDYERLIQL-LQD   90 (280)
T ss_dssp             --------------------------------------------------------------------------------
T ss_pred             cccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccc-ccccccccccccc-ccc
Confidence            34556667777777777775544332 23344445555556666777777777777776654 2244455555555 567


Q ss_pred             CCHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHccCCHHHHHHHHHHHHHCC-CCCCHHHHHHHHHHHHhcCCHHHHHHH
Q 040027          361 KEVEEALSLYREMVSKGIKPTVVTYNTLFLGLFEIHQVEHALKLFDEMQRDG-VAADTRTYTTFIDGLCKNGYIIEAVEL  439 (595)
Q Consensus       361 ~~~~~A~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~-~~~~~~~~~~l~~~~~~~g~~~~A~~~  439 (595)
                      +++++|.+++....+..  ++...+..++..+...++++++..+++.+.... .+.+...|..+...+.+.|+.++|...
T Consensus        91 ~~~~~A~~~~~~~~~~~--~~~~~l~~~l~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~a~~~~~~G~~~~A~~~  168 (280)
T PF13429_consen   91 GDPEEALKLAEKAYERD--GDPRYLLSALQLYYRLGDYDEAEELLEKLEELPAAPDSARFWLALAEIYEQLGDPDKALRD  168 (280)
T ss_dssp             -----------------------------H-HHHTT-HHHHHHHHHHHHH-T---T-HHHHHHHHHHHHHCCHHHHHHHH
T ss_pred             ccccccccccccccccc--cccchhhHHHHHHHHHhHHHHHHHHHHHHHhccCCCCCHHHHHHHHHHHHHcCCHHHHHHH
Confidence            77777777776655542  345556666667777777777777777766432 345666677777777777888888888


Q ss_pred             HHHHHHcCCCcCHHHHHHHHHHHHhcCChHHHHHHHHhcccCCCCCCHHHHHHHHHHHHhcCChhHHHHHHHHHHHcCCC
Q 040027          440 FRTLRILKCELDIQAYNCLIDGLCKSGRLKFAWELFCSLPHGVLVPNVVTYNIMIQGLCNDGQMDKARDLFLDMEENAAA  519 (595)
Q Consensus       440 ~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~p~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~  519 (595)
                      ++++++.. |.+......++..+...|+.+++.+++....... +.|+..|..+..+|...|+.++|+..|++..... +
T Consensus       169 ~~~al~~~-P~~~~~~~~l~~~li~~~~~~~~~~~l~~~~~~~-~~~~~~~~~la~~~~~lg~~~~Al~~~~~~~~~~-p  245 (280)
T PF13429_consen  169 YRKALELD-PDDPDARNALAWLLIDMGDYDEAREALKRLLKAA-PDDPDLWDALAAAYLQLGRYEEALEYLEKALKLN-P  245 (280)
T ss_dssp             HHHHHHH--TT-HHHHHHHHHHHCTTCHHHHHHHHHHHHHHH--HTSCCHCHHHHHHHHHHT-HHHHHHHHHHHHHHS-T
T ss_pred             HHHHHHcC-CCCHHHHHHHHHHHHHCCChHHHHHHHHHHHHHC-cCHHHHHHHHHHHhcccccccccccccccccccc-c
Confidence            88777765 4567777777777777777777777777666531 3345566777777778888888888888877754 5


Q ss_pred             CCHHHHHHHHHHHHHcCChhHHHHHHHHHHH
Q 040027          520 PDVITFDMLIHGFIRINEPSKVNELLHKMKE  550 (595)
Q Consensus       520 ~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~  550 (595)
                      .|+.....++.++...|+.++|.++.+++..
T Consensus       246 ~d~~~~~~~a~~l~~~g~~~~A~~~~~~~~~  276 (280)
T PF13429_consen  246 DDPLWLLAYADALEQAGRKDEALRLRRQALR  276 (280)
T ss_dssp             T-HHHHHHHHHHHT-----------------
T ss_pred             ccccccccccccccccccccccccccccccc
Confidence            5677777777788888888888777776653

>PRK10747 putative protoheme IX biogenesis protein; Provisional

Probab=99.69  E-value=3.8e-13  Score=130.66  Aligned_cols=221  Identities=10%  Similarity=0.033  Sum_probs=109.2

Q ss_pred             HHHHhcCCHHHHHHHHHHHHhcCCCCCHHHHHHHHHHHHhCCCHHHHHHHHHHHHHCCCCCCH-------HHHHHHHHHH
Q 040027          320 DGFCLMGKINRAEELFGSMESMGCKHDDVSYNILINGYCKNKEVEEALSLYREMVSKGIKPTV-------VTYNTLFLGL  392 (595)
Q Consensus       320 ~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~~~~~~~~-------~~~~~l~~~~  392 (595)
                      ..+...|+++.|...++++.+.. |.++.....+...|.+.|++++|.+++..+.+.+..++.       .++..++...
T Consensus       161 ~l~l~~g~~~~Al~~l~~~~~~~-P~~~~al~ll~~~~~~~gdw~~a~~~l~~l~k~~~~~~~~~~~l~~~a~~~l~~~~  239 (398)
T PRK10747        161 RIQLARNENHAARHGVDKLLEVA-PRHPEVLRLAEQAYIRTGAWSSLLDILPSMAKAHVGDEEHRAMLEQQAWIGLMDQA  239 (398)
T ss_pred             HHHHHCCCHHHHHHHHHHHHhcC-CCCHHHHHHHHHHHHHHHhHHHHHHHHHHHHHcCCCCHHHHHHHHHHHHHHHHHHH
Confidence            33444444444444444444332 223334444444444444444444444444443222111       1112222222


Q ss_pred             HccCCHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCcCHHHHHHHHHHHHhcCChHHHH
Q 040027          393 FEIHQVEHALKLFDEMQRDGVAADTRTYTTFIDGLCKNGYIIEAVELFRTLRILKCELDIQAYNCLIDGLCKSGRLKFAW  472 (595)
Q Consensus       393 ~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~  472 (595)
                      ....+.+...++|+.+.+. .+.++.....+...+...|+.++|..++++..+.  +++.....  +.+....++.+++.
T Consensus       240 ~~~~~~~~l~~~w~~lp~~-~~~~~~~~~~~A~~l~~~g~~~~A~~~L~~~l~~--~~~~~l~~--l~~~l~~~~~~~al  314 (398)
T PRK10747        240 MADQGSEGLKRWWKNQSRK-TRHQVALQVAMAEHLIECDDHDTAQQIILDGLKR--QYDERLVL--LIPRLKTNNPEQLE  314 (398)
T ss_pred             HHhcCHHHHHHHHHhCCHH-HhCCHHHHHHHHHHHHHCCCHHHHHHHHHHHHhc--CCCHHHHH--HHhhccCCChHHHH
Confidence            2233344444444444332 2345555556666666666666666666666552  33432221  22223446666666


Q ss_pred             HHHHhcccCCCCC-CHHHHHHHHHHHHhcCChhHHHHHHHHHHHcCCCCCHHHHHHHHHHHHHcCChhHHHHHHHHHHH
Q 040027          473 ELFCSLPHGVLVP-NVVTYNIMIQGLCNDGQMDKARDLFLDMEENAAAPDVITFDMLIHGFIRINEPSKVNELLHKMKE  550 (595)
Q Consensus       473 ~~~~~~~~~~~~p-~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~  550 (595)
                      +..+...+.  .| |+..+..+...+.+.+++++|.+.|+.+.+.  .|+...+..+..++.+.|+.++|.+++++...
T Consensus       315 ~~~e~~lk~--~P~~~~l~l~lgrl~~~~~~~~~A~~~le~al~~--~P~~~~~~~La~~~~~~g~~~~A~~~~~~~l~  389 (398)
T PRK10747        315 KVLRQQIKQ--HGDTPLLWSTLGQLLMKHGEWQEASLAFRAALKQ--RPDAYDYAWLADALDRLHKPEEAAAMRRDGLM  389 (398)
T ss_pred             HHHHHHHhh--CCCCHHHHHHHHHHHHHCCCHHHHHHHHHHHHhc--CCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHh
Confidence            666666553  23 3445556666666666666666666666663  46666666666666666666666666666543

>KOG1173 consensus Anaphase-promoting complex (APC), Cdc16 subunit [Cell cycle control, cell division, chromosome partitioning; Posttranslational modification, protein turnover, chaperones]

Probab=99.69  E-value=1.4e-12  Score=121.79  Aligned_cols=462  Identities=11%  Similarity=0.021  Sum_probs=320.8

Q ss_pred             CHHHHHHHHHHHHhcCChhHHHHHHHHHHhCCCCCCHHHHHHHHHHHHhcCCHhHHHHHHHHHHhcCCCCCHhhHHHHHH
Q 040027           95 NLYTYNILINCFCKIGRVSLGFIAFGRILRSCFTPNAATFNSLIKGLHAESRIMEAAALFTKLKAFGCEPNVITYNTLIN  174 (595)
Q Consensus        95 ~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~~l~~  174 (595)
                      +..-+..+.+-+..+.++..|..+-+++...+  .|+.....+++++.-.|++.+|..+...-.-.  ..|..+......
T Consensus        15 s~~~~~~~~r~~l~q~~y~~a~f~adkV~~l~--~dp~d~~~~aq~l~~~~~y~ra~~lit~~~le--~~d~~cryL~~~   90 (611)
T KOG1173|consen   15 SLEKYRRLVRDALMQHRYKTALFWADKVAGLT--NDPADIYWLAQVLYLGRQYERAAHLITTYKLE--KRDIACRYLAAK   90 (611)
T ss_pred             cHHHHHHHHHHHHHHHhhhHHHHHHHHHHhcc--CChHHHHHHHHHHHhhhHHHHHHHHHHHhhhh--hhhHHHHHHHHH
Confidence            55566677777777888888888888887774  45555556777788888888887776654332  346777777778


Q ss_pred             HHHhcCChhHHHHHHHHHHhcCCCC-------CccccCc-----------HHHHHHHHHHHHHcCCHhHHHHHHHHHhhC
Q 040027          175 GLCRTGHTMIALNLFEEMANGNGEI-------GVVCKPN-----------TVTYSTIIDGLCKEGFVDKAKALFLQMKDE  236 (595)
Q Consensus       175 ~~~~~g~~~~A~~~~~~~~~~~~~~-------~~~~~~~-----------~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~  236 (595)
                      .+.+..++++|..++..........       +....++           ...+-.-...|......++|...|.+....
T Consensus        91 ~l~~lk~~~~al~vl~~~~~~~~~f~yy~~~~~~~l~~n~~~~~~~~~~essic~lRgk~y~al~n~~~ar~~Y~~Al~~  170 (611)
T KOG1173|consen   91 CLVKLKEWDQALLVLGRGHVETNPFSYYEKDAANTLELNSAGEDLMINLESSICYLRGKVYVALDNREEARDKYKEALLA  170 (611)
T ss_pred             HHHHHHHHHHHHHHhcccchhhcchhhcchhhhceeccCcccccccccchhceeeeeeehhhhhccHHHHHHHHHHHHhc
Confidence            8888888888888877221100000       0000011           111111123455566777888888777654


Q ss_pred             CCCCCHhHHHHHHHHHHh-----------------cCCHHHHHHHHHHHHH-----------------CCCCCCHhhHHH
Q 040027          237 NINPDVVTYNSLIHGLCH-----------------ANDWNEAKRLFIEMMD-----------------QGVQPSVVTFNV  282 (595)
Q Consensus       237 ~~~~~~~~~~~ll~~~~~-----------------~~~~~~A~~~~~~~~~-----------------~~~~~~~~~~~~  282 (595)
                      .+. ....+..|+....-                 .+...+-++.+-++..                 .+...+......
T Consensus       171 D~~-c~Ea~~~lvs~~mlt~~Ee~~ll~~l~~a~~~~ed~e~l~~lyel~~~k~~n~~~~~r~~~~sl~~l~~~~dll~~  249 (611)
T KOG1173|consen  171 DAK-CFEAFEKLVSAHMLTAQEEFELLESLDLAMLTKEDVERLEILYELKLCKNRNEESLTRNEDESLIGLAENLDLLAE  249 (611)
T ss_pred             chh-hHHHHHHHHHHHhcchhHHHHHHhcccHHhhhhhHHHHHHHHHHhhhhhhccccccccCchhhhhhhhhcHHHHHH
Confidence            222 22222222222111                 1111111222111110                 011223344445


Q ss_pred             HHHHHHhcCChHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHhcCCCCCHHHHHHHHHHHHhCCC
Q 040027          283 IMDELCKNRKMDEASRLLDLMVQRGVRPNACTYNTLMDGFCLMGKINRAEELFGSMESMGCKHDDVSYNILINGYCKNKE  362 (595)
Q Consensus       283 l~~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~  362 (595)
                      ...-+...+++.+..++.+.+.+.. ++....+..-+.++...|+..+-..+=.++++.- |..+.+|..+.--|...|+
T Consensus       250 ~ad~~y~~c~f~~c~kit~~lle~d-pfh~~~~~~~ia~l~el~~~n~Lf~lsh~LV~~y-P~~a~sW~aVg~YYl~i~k  327 (611)
T KOG1173|consen  250 KADRLYYGCRFKECLKITEELLEKD-PFHLPCLPLHIACLYELGKSNKLFLLSHKLVDLY-PSKALSWFAVGCYYLMIGK  327 (611)
T ss_pred             HHHHHHHcChHHHHHHHhHHHHhhC-CCCcchHHHHHHHHHHhcccchHHHHHHHHHHhC-CCCCcchhhHHHHHHHhcC
Confidence            5666778899999999999998873 4455566666778888898888777777777763 6667799999999999999


Q ss_pred             HHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHccCCHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHH
Q 040027          363 VEEALSLYREMVSKGIKPTVVTYNTLFLGLFEIHQVEHALKLFDEMQRDGVAADTRTYTTFIDGLCKNGYIIEAVELFRT  442 (595)
Q Consensus       363 ~~~A~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~  442 (595)
                      ..+|.+.|.+....+.. -...|..+..++.-.+..++|...|..+.+. ++....-+.-+.--|.+.++++.|.+.|.+
T Consensus       328 ~seARry~SKat~lD~~-fgpaWl~fghsfa~e~EhdQAmaaY~tAarl-~~G~hlP~LYlgmey~~t~n~kLAe~Ff~~  405 (611)
T KOG1173|consen  328 YSEARRYFSKATTLDPT-FGPAWLAFGHSFAGEGEHDQAMAAYFTAARL-MPGCHLPSLYLGMEYMRTNNLKLAEKFFKQ  405 (611)
T ss_pred             cHHHHHHHHHHhhcCcc-ccHHHHHHhHHhhhcchHHHHHHHHHHHHHh-ccCCcchHHHHHHHHHHhccHHHHHHHHHH
Confidence            99999999998776433 3467888999999999999999999888875 222333333445568889999999999999


Q ss_pred             HHHcCCCcCHHHHHHHHHHHHhcCChHHHHHHHHhcccC--CCC---C-CHHHHHHHHHHHHhcCChhHHHHHHHHHHHc
Q 040027          443 LRILKCELDIQAYNCLIDGLCKSGRLKFAWELFCSLPHG--VLV---P-NVVTYNIMIQGLCNDGQMDKARDLFLDMEEN  516 (595)
Q Consensus       443 ~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~--~~~---p-~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~  516 (595)
                      +.... |.|+...+.+.-.....+.+.+|...|+..+..  ...   + -..+++.|+.+|.+.+.+++|+..+++.+..
T Consensus       406 A~ai~-P~Dplv~~Elgvvay~~~~y~~A~~~f~~~l~~ik~~~~e~~~w~p~~~NLGH~~Rkl~~~~eAI~~~q~aL~l  484 (611)
T KOG1173|consen  406 ALAIA-PSDPLVLHELGVVAYTYEEYPEALKYFQKALEVIKSVLNEKIFWEPTLNNLGHAYRKLNKYEEAIDYYQKALLL  484 (611)
T ss_pred             HHhcC-CCcchhhhhhhheeehHhhhHHHHHHHHHHHHHhhhccccccchhHHHHhHHHHHHHHhhHHHHHHHHHHHHHc
Confidence            99766 778899999988888899999999999987731  011   1 2356889999999999999999999999997


Q ss_pred             CCCCCHHHHHHHHHHHHHcCChhHHHHHHHHHHHCCCCCCHHHHHHHHHHHHh
Q 040027          517 AAAPDVITFDMLIHGFIRINEPSKVNELLHKMKEKKVMPDASIVSIVVDLLVK  569 (595)
Q Consensus       517 ~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~p~~~~~~~l~~~~~~  569 (595)
                      . +.+..++..++-.|...|+++.|.+.|.+.+.  +.|+..+...++..+..
T Consensus       485 ~-~k~~~~~asig~iy~llgnld~Aid~fhKaL~--l~p~n~~~~~lL~~aie  534 (611)
T KOG1173|consen  485 S-PKDASTHASIGYIYHLLGNLDKAIDHFHKALA--LKPDNIFISELLKLAIE  534 (611)
T ss_pred             C-CCchhHHHHHHHHHHHhcChHHHHHHHHHHHh--cCCccHHHHHHHHHHHH
Confidence            4 77899999999999999999999999999996  67887666666554444

>PRK10747 putative protoheme IX biogenesis protein; Provisional

Probab=99.69  E-value=4e-13  Score=130.55  Aligned_cols=283  Identities=13%  Similarity=0.067  Sum_probs=156.2

Q ss_pred             cCCHhHHHHHHHHHHhcCCCCCHhhHHHH-HHHHHhcCChhHHHHHHHHHHhcCCCCCccccCcHHHH--HHHHHHHHHc
Q 040027          144 ESRIMEAAALFTKLKAFGCEPNVITYNTL-INGLCRTGHTMIALNLFEEMANGNGEIGVVCKPNTVTY--STIIDGLCKE  220 (595)
Q Consensus       144 ~g~~~~A~~~~~~~~~~~~~~~~~~~~~l-~~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~~~~~~--~~l~~~~~~~  220 (595)
                      .|+++.|.+.+....+..  +++..+..+ ..+..+.|+++.|...++++.+..        |+....  ......+...
T Consensus        97 eGd~~~A~k~l~~~~~~~--~~p~l~~llaA~aA~~~g~~~~A~~~l~~A~~~~--------~~~~~~~~l~~a~l~l~~  166 (398)
T PRK10747         97 EGDYQQVEKLMTRNADHA--EQPVVNYLLAAEAAQQRGDEARANQHLERAAELA--------DNDQLPVEITRVRIQLAR  166 (398)
T ss_pred             CCCHHHHHHHHHHHHhcc--cchHHHHHHHHHHHHHCCCHHHHHHHHHHHHhcC--------CcchHHHHHHHHHHHHHC
Confidence            466666665555544431  122222222 233355666666666666665532        232211  1224555666


Q ss_pred             CCHhHHHHHHHHHhhCCCCCCHhHHHHHHHHHHhcCCHHHHHHHHHHHHHCCCCCCH-------hhHHHHHHHHHhcCCh
Q 040027          221 GFVDKAKALFLQMKDENINPDVVTYNSLIHGLCHANDWNEAKRLFIEMMDQGVQPSV-------VTFNVIMDELCKNRKM  293 (595)
Q Consensus       221 g~~~~A~~~~~~~~~~~~~~~~~~~~~ll~~~~~~~~~~~A~~~~~~~~~~~~~~~~-------~~~~~l~~~~~~~g~~  293 (595)
                      |++++|.+.++++.+.. +-+......+...|.+.|+|++|.+++..+.+.+..++.       .+|..++.......+.
T Consensus       167 g~~~~Al~~l~~~~~~~-P~~~~al~ll~~~~~~~gdw~~a~~~l~~l~k~~~~~~~~~~~l~~~a~~~l~~~~~~~~~~  245 (398)
T PRK10747        167 NENHAARHGVDKLLEVA-PRHPEVLRLAEQAYIRTGAWSSLLDILPSMAKAHVGDEEHRAMLEQQAWIGLMDQAMADQGS  245 (398)
T ss_pred             CCHHHHHHHHHHHHhcC-CCCHHHHHHHHHHHHHHHhHHHHHHHHHHHHHcCCCCHHHHHHHHHHHHHHHHHHHHHhcCH
Confidence            66666666666665553 224555555666666666666666666666655433211       1222233333333444


Q ss_pred             HHHHHHHHHHHHCCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHhcCCCCCHHHHHHHHHHHHhCCCHHHHHHHHHHH
Q 040027          294 DEASRLLDLMVQRGVRPNACTYNTLMDGFCLMGKINRAEELFGSMESMGCKHDDVSYNILINGYCKNKEVEEALSLYREM  373 (595)
Q Consensus       294 ~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~A~~~~~~~  373 (595)
                      +...++++.+.+. .+.++.....+...+...|+.++|..++++..+.  +++....  ++.+....++.+++++..+..
T Consensus       246 ~~l~~~w~~lp~~-~~~~~~~~~~~A~~l~~~g~~~~A~~~L~~~l~~--~~~~~l~--~l~~~l~~~~~~~al~~~e~~  320 (398)
T PRK10747        246 EGLKRWWKNQSRK-TRHQVALQVAMAEHLIECDDHDTAQQIILDGLKR--QYDERLV--LLIPRLKTNNPEQLEKVLRQQ  320 (398)
T ss_pred             HHHHHHHHhCCHH-HhCCHHHHHHHHHHHHHCCCHHHHHHHHHHHHhc--CCCHHHH--HHHhhccCCChHHHHHHHHHH
Confidence            5555555554332 2335556666666777777777777777666653  3443221  223333446677777777766


Q ss_pred             HHCCCCCCHHHHHHHHHHHHccCCHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHH
Q 040027          374 VSKGIKPTVVTYNTLFLGLFEIHQVEHALKLFDEMQRDGVAADTRTYTTFIDGLCKNGYIIEAVELFRTLRI  445 (595)
Q Consensus       374 ~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~  445 (595)
                      .+..+. |...+..+...+.+.+++++|.+.|+.+.+.  .|+...+..+...+.+.|+.++|.+++++...
T Consensus       321 lk~~P~-~~~l~l~lgrl~~~~~~~~~A~~~le~al~~--~P~~~~~~~La~~~~~~g~~~~A~~~~~~~l~  389 (398)
T PRK10747        321 IKQHGD-TPLLWSTLGQLLMKHGEWQEASLAFRAALKQ--RPDAYDYAWLADALDRLHKPEEAAAMRRDGLM  389 (398)
T ss_pred             HhhCCC-CHHHHHHHHHHHHHCCCHHHHHHHHHHHHhc--CCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHh
Confidence            665333 5555666666777777777777777777664  56666666677777777777777777776654

>TIGR00540 hemY_coli hemY protein

Probab=99.68  E-value=4.8e-13  Score=130.76  Aligned_cols=290  Identities=11%  Similarity=0.062  Sum_probs=170.5

Q ss_pred             HhcCCHHHHHHHHHHHHHCCCCCC-HhhHHHHHHHHHhcCChHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHhcCCHHHH
Q 040027          253 CHANDWNEAKRLFIEMMDQGVQPS-VVTFNVIMDELCKNRKMDEASRLLDLMVQRGVRPNACTYNTLMDGFCLMGKINRA  331 (595)
Q Consensus       253 ~~~~~~~~A~~~~~~~~~~~~~~~-~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a  331 (595)
                      ...|+++.|.+.+.+..+..  |+ ...+-....++...|+++.+.+++.+..+....+...........+...|+++.|
T Consensus        95 ~~~g~~~~A~~~l~~~~~~~--~~~~~~~llaA~aa~~~g~~~~A~~~l~~a~~~~p~~~l~~~~~~a~l~l~~~~~~~A  172 (409)
T TIGR00540        95 LAEGDYAKAEKLIAKNADHA--AEPVLNLIKAAEAAQQRGDEARANQHLEEAAELAGNDNILVEIARTRILLAQNELHAA  172 (409)
T ss_pred             HhCCCHHHHHHHHHHHhhcC--CCCHHHHHHHHHHHHHCCCHHHHHHHHHHHHHhCCcCchHHHHHHHHHHHHCCCHHHH
Confidence            34566666666666655532  22 2233344555666677777777776665542222222333345666667777777


Q ss_pred             HHHHHHHHhcCCCCCHHHHHHHHHHHHhCCCHHHHHHHHHHHHHCCCCCCHHHHH----HHHHHHHccCCHHHHHHHHHH
Q 040027          332 EELFGSMESMGCKHDDVSYNILINGYCKNKEVEEALSLYREMVSKGIKPTVVTYN----TLFLGLFEIHQVEHALKLFDE  407 (595)
Q Consensus       332 ~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~----~l~~~~~~~~~~~~a~~~~~~  407 (595)
                      ...++.+.+.. |.+...+..+...+.+.|++++|.+.+..+.+.++. +...+.    .........+..+.....+..
T Consensus       173 l~~l~~l~~~~-P~~~~~l~ll~~~~~~~~d~~~a~~~l~~l~k~~~~-~~~~~~~l~~~a~~~~l~~~~~~~~~~~L~~  250 (409)
T TIGR00540       173 RHGVDKLLEMA-PRHKEVLKLAEEAYIRSGAWQALDDIIDNMAKAGLF-DDEEFADLEQKAEIGLLDEAMADEGIDGLLN  250 (409)
T ss_pred             HHHHHHHHHhC-CCCHHHHHHHHHHHHHHhhHHHHHHHHHHHHHcCCC-CHHHHHHHHHHHHHHHHHHHHHhcCHHHHHH
Confidence            77777766654 445556666667777777777777777777666443 222221    111111222222222333333


Q ss_pred             HHHCC---CCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCcCHHH--HHHHHHHHHhcCChHHHHHHHHhcccCC
Q 040027          408 MQRDG---VAADTRTYTTFIDGLCKNGYIIEAVELFRTLRILKCELDIQA--YNCLIDGLCKSGRLKFAWELFCSLPHGV  482 (595)
Q Consensus       408 ~~~~~---~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~--~~~l~~~~~~~g~~~~A~~~~~~~~~~~  482 (595)
                      +.+..   .+.+...+..+...+...|+.++|..++++..+.. +.+...  ...........++.+.+.+.+++..+. 
T Consensus       251 ~~~~~p~~~~~~~~l~~~~a~~l~~~g~~~~A~~~l~~~l~~~-pd~~~~~~~~l~~~~~l~~~~~~~~~~~~e~~lk~-  328 (409)
T TIGR00540       251 WWKNQPRHRRHNIALKIALAEHLIDCDDHDSAQEIIFDGLKKL-GDDRAISLPLCLPIPRLKPEDNEKLEKLIEKQAKN-  328 (409)
T ss_pred             HHHHCCHHHhCCHHHHHHHHHHHHHCCChHHHHHHHHHHHhhC-CCcccchhHHHHHhhhcCCCChHHHHHHHHHHHHh-
Confidence            33321   12366777777778888888888888888887754 222211  111111223346777788888777763 


Q ss_pred             CCCC-H--HHHHHHHHHHHhcCChhHHHHHHHHHHHcCCCCCHHHHHHHHHHHHHcCChhHHHHHHHHHH
Q 040027          483 LVPN-V--VTYNIMIQGLCNDGQMDKARDLFLDMEENAAAPDVITFDMLIHGFIRINEPSKVNELLHKMK  549 (595)
Q Consensus       483 ~~p~-~--~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~  549 (595)
                       .|+ +  ....++.+.+.+.|++++|.+.|+........|+...+..++..+.+.|+.++|.+++++..
T Consensus       329 -~p~~~~~~ll~sLg~l~~~~~~~~~A~~~le~a~a~~~~p~~~~~~~La~ll~~~g~~~~A~~~~~~~l  397 (409)
T TIGR00540       329 -VDDKPKCCINRALGQLLMKHGEFIEAADAFKNVAACKEQLDANDLAMAADAFDQAGDKAEAAAMRQDSL  397 (409)
T ss_pred             -CCCChhHHHHHHHHHHHHHcccHHHHHHHHHHhHHhhcCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHH
Confidence             444 3  45567788888888888888888853333346777777788888888888888888888765

This is an uncharacterized protein encoded next to a heme-biosynthetic enzyme in two gamma division proteobacteria (E. coli and H. influenzae). It is known in no other species. The gene symbol hemY is unfortunate in that an unrelated protein, protoporphyrinogen oxidase, is designated as HemG in E. coli but as HemY in Bacillus subtilis.

>TIGR00540 hemY_coli hemY protein

Probab=99.67  E-value=6.8e-13  Score=129.72  Aligned_cols=295  Identities=9%  Similarity=-0.015  Sum_probs=138.9

Q ss_pred             hcCChhHHHHHHHHHHhcCCCCCccccCcHHHHHHHHHHHHHcCCHhHHHHHHHHHhhCCCCCCHhHHHHHHHHHHhcCC
Q 040027          178 RTGHTMIALNLFEEMANGNGEIGVVCKPNTVTYSTIIDGLCKEGFVDKAKALFLQMKDENINPDVVTYNSLIHGLCHAND  257 (595)
Q Consensus       178 ~~g~~~~A~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~~ll~~~~~~~~  257 (595)
                      ..|+++.|.+.+.+..+..       +.....+-....++...|+.+.|.+.+.+..+....+...........+...|+
T Consensus        96 ~~g~~~~A~~~l~~~~~~~-------~~~~~~~llaA~aa~~~g~~~~A~~~l~~a~~~~p~~~l~~~~~~a~l~l~~~~  168 (409)
T TIGR00540        96 AEGDYAKAEKLIAKNADHA-------AEPVLNLIKAAEAAQQRGDEARANQHLEEAAELAGNDNILVEIARTRILLAQNE  168 (409)
T ss_pred             hCCCHHHHHHHHHHHhhcC-------CCCHHHHHHHHHHHHHCCCHHHHHHHHHHHHHhCCcCchHHHHHHHHHHHHCCC
Confidence            4566666666666555432       111223333445555566666666666665543211111223333555566666


Q ss_pred             HHHHHHHHHHHHHCCCCCCHhhHHHHHHHHHhcCChHHHHHHHHHHHHCCCCCCHHHHHHHHHHH---HhcCCHHHHHHH
Q 040027          258 WNEAKRLFIEMMDQGVQPSVVTFNVIMDELCKNRKMDEASRLLDLMVQRGVRPNACTYNTLMDGF---CLMGKINRAEEL  334 (595)
Q Consensus       258 ~~~A~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~---~~~~~~~~a~~~  334 (595)
                      ++.|...++.+.+.. +-+...+..+...+...|+++++.+.+..+.+.+..++.........++   ...+..+...+.
T Consensus       169 ~~~Al~~l~~l~~~~-P~~~~~l~ll~~~~~~~~d~~~a~~~l~~l~k~~~~~~~~~~~l~~~a~~~~l~~~~~~~~~~~  247 (409)
T TIGR00540       169 LHAARHGVDKLLEMA-PRHKEVLKLAEEAYIRSGAWQALDDIIDNMAKAGLFDDEEFADLEQKAEIGLLDEAMADEGIDG  247 (409)
T ss_pred             HHHHHHHHHHHHHhC-CCCHHHHHHHHHHHHHHhhHHHHHHHHHHHHHcCCCCHHHHHHHHHHHHHHHHHHHHHhcCHHH
Confidence            666666666666543 2244455566666666666666666666666654332211111111111   111111212222


Q ss_pred             HHHHHhcCC---CCCHHHHHHHHHHHHhCCCHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHccCCHHHHHHHHHHHHHC
Q 040027          335 FGSMESMGC---KHDDVSYNILINGYCKNKEVEEALSLYREMVSKGIKPTVVTYNTLFLGLFEIHQVEHALKLFDEMQRD  411 (595)
Q Consensus       335 ~~~~~~~~~---~~~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~  411 (595)
                      +..+.+...   +.+...+..++..+...|+.++|.+++++..+..+......+.                         
T Consensus       248 L~~~~~~~p~~~~~~~~l~~~~a~~l~~~g~~~~A~~~l~~~l~~~pd~~~~~~~-------------------------  302 (409)
T TIGR00540       248 LLNWWKNQPRHRRHNIALKIALAEHLIDCDDHDSAQEIIFDGLKKLGDDRAISLP-------------------------  302 (409)
T ss_pred             HHHHHHHCCHHHhCCHHHHHHHHHHHHHCCChHHHHHHHHHHHhhCCCcccchhH-------------------------
Confidence            222222210   1244444445555555555555555555554432211100000                         


Q ss_pred             CCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCcCH--HHHHHHHHHHHhcCChHHHHHHHHhcccCCCCCCHHH
Q 040027          412 GVAADTRTYTTFIDGLCKNGYIIEAVELFRTLRILKCELDI--QAYNCLIDGLCKSGRLKFAWELFCSLPHGVLVPNVVT  489 (595)
Q Consensus       412 ~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~~~--~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~p~~~~  489 (595)
                             .+  ........++.+.+.+.+++..+.. +.|+  ....+++..+.+.|++++|.+.|+........|+...
T Consensus       303 -------~l--~~~~~l~~~~~~~~~~~~e~~lk~~-p~~~~~~ll~sLg~l~~~~~~~~~A~~~le~a~a~~~~p~~~~  372 (409)
T TIGR00540       303 -------LC--LPIPRLKPEDNEKLEKLIEKQAKNV-DDKPKCCINRALGQLLMKHGEFIEAADAFKNVAACKEQLDAND  372 (409)
T ss_pred             -------HH--HHhhhcCCCChHHHHHHHHHHHHhC-CCChhHHHHHHHHHHHHHcccHHHHHHHHHHhHHhhcCCCHHH
Confidence                   00  0011122344555555565555543 3344  4555666666666666666666663222214566655


Q ss_pred             HHHHHHHHHhcCChhHHHHHHHHHHH
Q 040027          490 YNIMIQGLCNDGQMDKARDLFLDMEE  515 (595)
Q Consensus       490 ~~~l~~~~~~~g~~~~A~~~~~~~~~  515 (595)
                      +..+...+.+.|+.++|.+++++...
T Consensus       373 ~~~La~ll~~~g~~~~A~~~~~~~l~  398 (409)
T TIGR00540       373 LAMAADAFDQAGDKAEAAAMRQDSLG  398 (409)
T ss_pred             HHHHHHHHHHcCCHHHHHHHHHHHHH
Confidence            66666666666666666666666543

This is an uncharacterized protein encoded next to a heme-biosynthetic enzyme in two gamma division proteobacteria (E. coli and H. influenzae). It is known in no other species. The gene symbol hemY is unfortunate in that an unrelated protein, protoporphyrinogen oxidase, is designated as HemG in E. coli but as HemY in Bacillus subtilis.

>PF13429 TPR_15: Tetratricopeptide repeat; PDB: 2VQ2_A 2PL2_B

Probab=99.67  E-value=5.1e-16  Score=144.16  Aligned_cols=261  Identities=16%  Similarity=0.135  Sum_probs=73.0

Q ss_pred             HHHHHHHhcCChhHHHHHHHHHHhCC-CCCCHHHHHHHHHHHHhcCCHhHHHHHHHHHHhcCCCCCHhhHHHHHHHHHhc
Q 040027          101 ILINCFCKIGRVSLGFIAFGRILRSC-FTPNAATFNSLIKGLHAESRIMEAAALFTKLKAFGCEPNVITYNTLINGLCRT  179 (595)
Q Consensus       101 ~l~~~~~~~g~~~~A~~~~~~~~~~~-~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~~l~~~~~~~  179 (595)
                      .+...+.+.|++++|..++++..... .+.+...|..+.......++++.|++.++++...+.. +...+..++.. ...
T Consensus        13 ~~A~~~~~~~~~~~Al~~L~~~~~~~~~~~~~~~~~~~a~La~~~~~~~~A~~ay~~l~~~~~~-~~~~~~~l~~l-~~~   90 (280)
T PF13429_consen   13 RLARLLYQRGDYEKALEVLKKAAQKIAPPDDPEYWRLLADLAWSLGDYDEAIEAYEKLLASDKA-NPQDYERLIQL-LQD   90 (280)
T ss_dssp             --------------------------------------------------------------------------------
T ss_pred             cccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccc-ccccccccccc-ccc
Confidence            44555666666666666665444332 2333444444444555566666666666666655322 34444445444 456


Q ss_pred             CChhHHHHHHHHHHhcCCCCCccccCcHHHHHHHHHHHHHcCCHhHHHHHHHHHhhCC-CCCCHhHHHHHHHHHHhcCCH
Q 040027          180 GHTMIALNLFEEMANGNGEIGVVCKPNTVTYSTIIDGLCKEGFVDKAKALFLQMKDEN-INPDVVTYNSLIHGLCHANDW  258 (595)
Q Consensus       180 g~~~~A~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~-~~~~~~~~~~ll~~~~~~~~~  258 (595)
                      +++++|.++++...+..        +++..+...+..+...++++++.++++.+.... .+.+...|..+...+.+.|+.
T Consensus        91 ~~~~~A~~~~~~~~~~~--------~~~~~l~~~l~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~a~~~~~~G~~  162 (280)
T PF13429_consen   91 GDPEEALKLAEKAYERD--------GDPRYLLSALQLYYRLGDYDEAEELLEKLEELPAAPDSARFWLALAEIYEQLGDP  162 (280)
T ss_dssp             -----------------------------------H-HHHTT-HHHHHHHHHHHHH-T---T-HHHHHHHHHHHHHCCHH
T ss_pred             ccccccccccccccccc--------cccchhhHHHHHHHHHhHHHHHHHHHHHHHhccCCCCCHHHHHHHHHHHHHcCCH
Confidence            66666666665554332        334445555555666666666666666654321 223455555555666666666


Q ss_pred             HHHHHHHHHHHHCCCCCCHhhHHHHHHHHHhcCChHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHH
Q 040027          259 NEAKRLFIEMMDQGVQPSVVTFNVIMDELCKNRKMDEASRLLDLMVQRGVRPNACTYNTLMDGFCLMGKINRAEELFGSM  338 (595)
Q Consensus       259 ~~A~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~  338 (595)
                      ++|++.|++.++.. +.|......++..+...|+.+++..++....+.. +.++..+..+..++...|+.++|...+++.
T Consensus       163 ~~A~~~~~~al~~~-P~~~~~~~~l~~~li~~~~~~~~~~~l~~~~~~~-~~~~~~~~~la~~~~~lg~~~~Al~~~~~~  240 (280)
T PF13429_consen  163 DKALRDYRKALELD-PDDPDARNALAWLLIDMGDYDEAREALKRLLKAA-PDDPDLWDALAAAYLQLGRYEEALEYLEKA  240 (280)
T ss_dssp             HHHHHHHHHHHHH--TT-HHHHHHHHHHHCTTCHHHHHHHHHHHHHHH--HTSCCHCHHHHHHHHHHT-HHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHcC-CCCHHHHHHHHHHHHHCCChHHHHHHHHHHHHHC-cCHHHHHHHHHHHhcccccccccccccccc
Confidence            66666666665542 1134455555556666666666555555554442 233444555556666666666666666665


Q ss_pred             HhcCCCCCHHHHHHHHHHHHhCCCHHHHHHHHHHHH
Q 040027          339 ESMGCKHDDVSYNILINGYCKNKEVEEALSLYREMV  374 (595)
Q Consensus       339 ~~~~~~~~~~~~~~l~~~~~~~~~~~~A~~~~~~~~  374 (595)
                      .+.. +.|+.....+..++...|+.++|..+.+++.
T Consensus       241 ~~~~-p~d~~~~~~~a~~l~~~g~~~~A~~~~~~~~  275 (280)
T PF13429_consen  241 LKLN-PDDPLWLLAYADALEQAGRKDEALRLRRQAL  275 (280)
T ss_dssp             HHHS-TT-HHHHHHHHHHHT----------------
T ss_pred             cccc-ccccccccccccccccccccccccccccccc
Confidence            5542 3355555555666666666666665555443

>KOG1126 consensus DNA-binding cell division cycle control protein [Cell cycle control, cell division, chromosome partitioning]

Probab=99.66  E-value=2.8e-14  Score=135.76  Aligned_cols=282  Identities=13%  Similarity=0.060  Sum_probs=122.6

Q ss_pred             CHHHHHHHHHHHHHCCCCCCHhhHHHHHHHHHhcCChHHHHHHHHHHHHCCC--CCCHHHHHHHHHHHHhcCCHHHHHHH
Q 040027          257 DWNEAKRLFIEMMDQGVQPSVVTFNVIMDELCKNRKMDEASRLLDLMVQRGV--RPNACTYNTLMDGFCLMGKINRAEEL  334 (595)
Q Consensus       257 ~~~~A~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~~--~~~~~~~~~l~~~~~~~~~~~~a~~~  334 (595)
                      +..+|+..|.++..+ +.-.......+.++|...+++++|.++|+.+.+...  ..+..+|...+..+-+    +-+...
T Consensus       334 ~~~~A~~~~~klp~h-~~nt~wvl~q~GrayFEl~~Y~~a~~~F~~~r~~~p~rv~~meiyST~LWHLq~----~v~Ls~  408 (638)
T KOG1126|consen  334 NCREALNLFEKLPSH-HYNTGWVLSQLGRAYFELIEYDQAERIFSLVRRIEPYRVKGMEIYSTTLWHLQD----EVALSY  408 (638)
T ss_pred             HHHHHHHHHHhhHHh-cCCchHHHHHHHHHHHHHHHHHHHHHHHHHHHhhccccccchhHHHHHHHHHHh----hHHHHH
Confidence            345555555553332 221223344455555555555555555555544310  1133334333332211    111222


Q ss_pred             HHH-HHhcCCCCCHHHHHHHHHHHHhCCCHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHccCCHHHHHHHHHHHHHCCC
Q 040027          335 FGS-MESMGCKHDDVSYNILINGYCKNKEVEEALSLYREMVSKGIKPTVVTYNTLFLGLFEIHQVEHALKLFDEMQRDGV  413 (595)
Q Consensus       335 ~~~-~~~~~~~~~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~  413 (595)
                      +.+ +.+. -+..+.+|..+..+|.-+++.+.|++.|++.++.+.. ...+|+.+..-+.....+|.|...|+..+..+ 
T Consensus       409 Laq~Li~~-~~~sPesWca~GNcfSLQkdh~~Aik~f~RAiQldp~-faYayTLlGhE~~~~ee~d~a~~~fr~Al~~~-  485 (638)
T KOG1126|consen  409 LAQDLIDT-DPNSPESWCALGNCFSLQKDHDTAIKCFKRAIQLDPR-FAYAYTLLGHESIATEEFDKAMKSFRKALGVD-  485 (638)
T ss_pred             HHHHHHhh-CCCCcHHHHHhcchhhhhhHHHHHHHHHHHhhccCCc-cchhhhhcCChhhhhHHHHhHHHHHHhhhcCC-
Confidence            211 1111 1334445555555555555555555555555543221 33444444444444445555555555444321 


Q ss_pred             CCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCcCHHHHHHHHHHHHhcCChHHHHHHHHhcccCCCCC-CHHHHHH
Q 040027          414 AADTRTYTTFIDGLCKNGYIIEAVELFRTLRILKCELDIQAYNCLIDGLCKSGRLKFAWELFCSLPHGVLVP-NVVTYNI  492 (595)
Q Consensus       414 ~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~p-~~~~~~~  492 (595)
                      +-+-..|..+...|.+.++++.|.-.|+++.+.+ |.+......++..+.+.|+.++|+.+++++...  .| |+..-..
T Consensus       486 ~rhYnAwYGlG~vy~Kqek~e~Ae~~fqkA~~IN-P~nsvi~~~~g~~~~~~k~~d~AL~~~~~A~~l--d~kn~l~~~~  562 (638)
T KOG1126|consen  486 PRHYNAWYGLGTVYLKQEKLEFAEFHFQKAVEIN-PSNSVILCHIGRIQHQLKRKDKALQLYEKAIHL--DPKNPLCKYH  562 (638)
T ss_pred             chhhHHHHhhhhheeccchhhHHHHHHHhhhcCC-ccchhHHhhhhHHHHHhhhhhHHHHHHHHHHhc--CCCCchhHHH
Confidence            1122233344444555555555555555555443 334444444444455555555555555554442  22 2333333


Q ss_pred             HHHHHHhcCChhHHHHHHHHHHHcCCCCCHHHHHHHHHHHHHcCChhHHHHHHHHHHH
Q 040027          493 MIQGLCNDGQMDKARDLFLDMEENAAAPDVITFDMLIHGFIRINEPSKVNELLHKMKE  550 (595)
Q Consensus       493 l~~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~  550 (595)
                      .+..+...+++++|+..++++.+. ++.+...|..++..|.+.|+.+.|+.-|--|.+
T Consensus       563 ~~~il~~~~~~~eal~~LEeLk~~-vP~es~v~~llgki~k~~~~~~~Al~~f~~A~~  619 (638)
T KOG1126|consen  563 RASILFSLGRYVEALQELEELKEL-VPQESSVFALLGKIYKRLGNTDLALLHFSWALD  619 (638)
T ss_pred             HHHHHHhhcchHHHHHHHHHHHHh-CcchHHHHHHHHHHHHHHccchHHHHhhHHHhc
Confidence            334444445555555555554443 222334444444555555555555544444443

>COG3071 HemY Uncharacterized enzyme of heme biosynthesis [Coenzyme metabolism]

Probab=99.66  E-value=1.9e-12  Score=116.05  Aligned_cols=287  Identities=12%  Similarity=0.108  Sum_probs=201.8

Q ss_pred             cCCHHHHHHHHHHHHHCCCCCCHhhHHHHHHHHHhcCChHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHhcCCHHHHHHH
Q 040027          255 ANDWNEAKRLFIEMMDQGVQPSVVTFNVIMDELCKNRKMDEASRLLDLMVQRGVRPNACTYNTLMDGFCLMGKINRAEEL  334 (595)
Q Consensus       255 ~~~~~~A~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~  334 (595)
                      .|+|..|.+...+-.+.+.. ....|..-.++.-..|+.+.+-+++.++.+....++........+.....|+++.|..-
T Consensus        97 eG~~~qAEkl~~rnae~~e~-p~l~~l~aA~AA~qrgd~~~an~yL~eaae~~~~~~l~v~ltrarlll~~~d~~aA~~~  175 (400)
T COG3071          97 EGDFQQAEKLLRRNAEHGEQ-PVLAYLLAAEAAQQRGDEDRANRYLAEAAELAGDDTLAVELTRARLLLNRRDYPAAREN  175 (400)
T ss_pred             cCcHHHHHHHHHHhhhcCcc-hHHHHHHHHHHHHhcccHHHHHHHHHHHhccCCCchHHHHHHHHHHHHhCCCchhHHHH
Confidence            57777777777776665544 23445556666777777777777777777654445555666666777777777777777


Q ss_pred             HHHHHhcCCCCCHHHHHHHHHHHHhCCCHHHHHHHHHHHHHCCCCCCH-------HHHHHHHHHHHccCCHHHHHHHHHH
Q 040027          335 FGSMESMGCKHDDVSYNILINGYCKNKEVEEALSLYREMVSKGIKPTV-------VTYNTLFLGLFEIHQVEHALKLFDE  407 (595)
Q Consensus       335 ~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~~~~~~~~-------~~~~~l~~~~~~~~~~~~a~~~~~~  407 (595)
                      +.++.+.+ +.++........+|.+.|++.+...++..+.+.+.-.+.       .++..+++-....+..+.-...|+.
T Consensus       176 v~~ll~~~-pr~~~vlrLa~r~y~~~g~~~~ll~~l~~L~ka~~l~~~e~~~le~~a~~glL~q~~~~~~~~gL~~~W~~  254 (400)
T COG3071         176 VDQLLEMT-PRHPEVLRLALRAYIRLGAWQALLAILPKLRKAGLLSDEEAARLEQQAWEGLLQQARDDNGSEGLKTWWKN  254 (400)
T ss_pred             HHHHHHhC-cCChHHHHHHHHHHHHhccHHHHHHHHHHHHHccCCChHHHHHHHHHHHHHHHHHHhccccchHHHHHHHh
Confidence            77777665 456667777777888888888888888887777655443       2455555555555555555566666


Q ss_pred             HHHCCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCcCHHHHHHHHHHHHhcCChHHHHHHHHhcccCCCCCCH
Q 040027          408 MQRDGVAADTRTYTTFIDGLCKNGYIIEAVELFRTLRILKCELDIQAYNCLIDGLCKSGRLKFAWELFCSLPHGVLVPNV  487 (595)
Q Consensus       408 ~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~p~~  487 (595)
                      ..+. ...++..-..++.-+.+.|+.++|.++.++..+.+.++..    ...-.+.+-++.+.-++..++.... .+.++
T Consensus       255 ~pr~-lr~~p~l~~~~a~~li~l~~~~~A~~~i~~~Lk~~~D~~L----~~~~~~l~~~d~~~l~k~~e~~l~~-h~~~p  328 (400)
T COG3071         255 QPRK-LRNDPELVVAYAERLIRLGDHDEAQEIIEDALKRQWDPRL----CRLIPRLRPGDPEPLIKAAEKWLKQ-HPEDP  328 (400)
T ss_pred             ccHH-hhcChhHHHHHHHHHHHcCChHHHHHHHHHHHHhccChhH----HHHHhhcCCCCchHHHHHHHHHHHh-CCCCh
Confidence            6554 3556677777888888888888888888888887655551    1222345667777766666666553 23345


Q ss_pred             HHHHHHHHHHHhcCChhHHHHHHHHHHHcCCCCCHHHHHHHHHHHHHcCChhHHHHHHHHHHHC
Q 040027          488 VTYNIMIQGLCNDGQMDKARDLFLDMEENAAAPDVITFDMLIHGFIRINEPSKVNELLHKMKEK  551 (595)
Q Consensus       488 ~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~  551 (595)
                      ..+.+|...|.+++.|.+|...|+..++.  .|+..+|..+.+++.+.|+..+|.++.++.+..
T Consensus       329 ~L~~tLG~L~~k~~~w~kA~~~leaAl~~--~~s~~~~~~la~~~~~~g~~~~A~~~r~e~L~~  390 (400)
T COG3071         329 LLLSTLGRLALKNKLWGKASEALEAALKL--RPSASDYAELADALDQLGEPEEAEQVRREALLL  390 (400)
T ss_pred             hHHHHHHHHHHHhhHHHHHHHHHHHHHhc--CCChhhHHHHHHHHHHcCChHHHHHHHHHHHHH
Confidence            77788888888888999998888887774  688888888888888889888888888887743

>KOG1173 consensus Anaphase-promoting complex (APC), Cdc16 subunit [Cell cycle control, cell division, chromosome partitioning; Posttranslational modification, protein turnover, chaperones]

Probab=99.65  E-value=2.9e-12  Score=119.73  Aligned_cols=474  Identities=12%  Similarity=0.046  Sum_probs=306.0

Q ss_pred             cccCCCChHHHHHHHHHHHHhCCCCCCHhhHHHHHHHHHcCCCchh---HHhhCC-CCCCHHHHHHHHHHHHhcCChhHH
Q 040027           40 GDINVITPNEAFCIFDYMLRMHPSPPPVSSFNILLASLAKNKHYDT---RLNATG-LFPNLYTYNILINCFCKIGRVSLG  115 (595)
Q Consensus        40 ~~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~---~~~~~~-~~~~~~~~~~l~~~~~~~g~~~~A  115 (595)
                      ..+.+.++..|.-+-+++.... .  +|..-..+..++.-.|.+..   .+.... ...|..+...+...+.+..++++|
T Consensus        25 ~~l~q~~y~~a~f~adkV~~l~-~--dp~d~~~~aq~l~~~~~y~ra~~lit~~~le~~d~~cryL~~~~l~~lk~~~~a  101 (611)
T KOG1173|consen   25 DALMQHRYKTALFWADKVAGLT-N--DPADIYWLAQVLYLGRQYERAAHLITTYKLEKRDIACRYLAAKCLVKLKEWDQA  101 (611)
T ss_pred             HHHHHHhhhHHHHHHHHHHhcc-C--ChHHHHHHHHHHHhhhHHHHHHHHHHHhhhhhhhHHHHHHHHHHHHHHHHHHHH
Confidence            5566788888888888888777 3  44444456777777777666   222222 235777777788888888899999


Q ss_pred             HHHHHHHHhC--CC-----------CCCHHH-----------HHHHHHHHHhcCCHhHHHHHHHHHHhcCCCCCHhhHHH
Q 040027          116 FIAFGRILRS--CF-----------TPNAAT-----------FNSLIKGLHAESRIMEAAALFTKLKAFGCEPNVITYNT  171 (595)
Q Consensus       116 ~~~~~~~~~~--~~-----------~~~~~~-----------~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~~  171 (595)
                      ..++.+....  ++           .+|..-           +-.-...|....++++|...|.+.....+. ..+.+..
T Consensus       102 l~vl~~~~~~~~~f~yy~~~~~~~l~~n~~~~~~~~~~essic~lRgk~y~al~n~~~ar~~Y~~Al~~D~~-c~Ea~~~  180 (611)
T KOG1173|consen  102 LLVLGRGHVETNPFSYYEKDAANTLELNSAGEDLMINLESSICYLRGKVYVALDNREEARDKYKEALLADAK-CFEAFEK  180 (611)
T ss_pred             HHHhcccchhhcchhhcchhhhceeccCcccccccccchhceeeeeeehhhhhccHHHHHHHHHHHHhcchh-hHHHHHH
Confidence            8888833110  00           000000           000012233445666677677666654221 1222222


Q ss_pred             HHHHHHhcCChhHHHHHHHHHHhcCCCCCccccCcHHHHHHHHHHHHHcCCHhHHHHHHHHHhhCCCCCCHhHHHHHHHH
Q 040027          172 LINGLCRTGHTMIALNLFEEMANGNGEIGVVCKPNTVTYSTIIDGLCKEGFVDKAKALFLQMKDENINPDVVTYNSLIHG  251 (595)
Q Consensus       172 l~~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~~ll~~  251 (595)
                      ++....-     .+.+.++.+...+-.  .....+......+.....-...-+.....-++..-.+..-+......-..-
T Consensus       181 lvs~~ml-----t~~Ee~~ll~~l~~a--~~~~ed~e~l~~lyel~~~k~~n~~~~~r~~~~sl~~l~~~~dll~~~ad~  253 (611)
T KOG1173|consen  181 LVSAHML-----TAQEEFELLESLDLA--MLTKEDVERLEILYELKLCKNRNEESLTRNEDESLIGLAENLDLLAEKADR  253 (611)
T ss_pred             HHHHHhc-----chhHHHHHHhcccHH--hhhhhHHHHHHHHHHhhhhhhccccccccCchhhhhhhhhcHHHHHHHHHH
Confidence            2222211     121222222221100  000111111111111110000000000000000011223345555566677


Q ss_pred             HHhcCCHHHHHHHHHHHHHCCCCCCHhhHHHHHHHHHhcCChHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHhcCCHHHH
Q 040027          252 LCHANDWNEAKRLFIEMMDQGVQPSVVTFNVIMDELCKNRKMDEASRLLDLMVQRGVRPNACTYNTLMDGFCLMGKINRA  331 (595)
Q Consensus       252 ~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a  331 (595)
                      +...+++.+..++.+.+.+. .++....+..-+.++.+.|+..+-..+=.++++. .+..+.+|..++--|...|+.++|
T Consensus       254 ~y~~c~f~~c~kit~~lle~-dpfh~~~~~~~ia~l~el~~~n~Lf~lsh~LV~~-yP~~a~sW~aVg~YYl~i~k~seA  331 (611)
T KOG1173|consen  254 LYYGCRFKECLKITEELLEK-DPFHLPCLPLHIACLYELGKSNKLFLLSHKLVDL-YPSKALSWFAVGCYYLMIGKYSEA  331 (611)
T ss_pred             HHHcChHHHHHHHhHHHHhh-CCCCcchHHHHHHHHHHhcccchHHHHHHHHHHh-CCCCCcchhhHHHHHHHhcCcHHH
Confidence            88899999999999999886 3456666777777899999998888888888886 455778899999889899999999


Q ss_pred             HHHHHHHHhcCCCCCHHHHHHHHHHHHhCCCHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHccCCHHHHHHHHHHHHHC
Q 040027          332 EELFGSMESMGCKHDDVSYNILINGYCKNKEVEEALSLYREMVSKGIKPTVVTYNTLFLGLFEIHQVEHALKLFDEMQRD  411 (595)
Q Consensus       332 ~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~  411 (595)
                      .+.|.+....+ +.=...|-.+...|.-.+..++|+..|..+-+.-.. ....+..+..-|.+.++.+.|.+.|.+....
T Consensus       332 Rry~SKat~lD-~~fgpaWl~fghsfa~e~EhdQAmaaY~tAarl~~G-~hlP~LYlgmey~~t~n~kLAe~Ff~~A~ai  409 (611)
T KOG1173|consen  332 RRYFSKATTLD-PTFGPAWLAFGHSFAGEGEHDQAMAAYFTAARLMPG-CHLPSLYLGMEYMRTNNLKLAEKFFKQALAI  409 (611)
T ss_pred             HHHHHHHhhcC-ccccHHHHHHhHHhhhcchHHHHHHHHHHHHHhccC-CcchHHHHHHHHHHhccHHHHHHHHHHHHhc
Confidence            99999987664 223457889999999999999999999888765222 3333444556688899999999999998876


Q ss_pred             CCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHHc----C--CCcCHHHHHHHHHHHHhcCChHHHHHHHHhcccCCCCC
Q 040027          412 GVAADTRTYTTFIDGLCKNGYIIEAVELFRTLRIL----K--CELDIQAYNCLIDGLCKSGRLKFAWELFCSLPHGVLVP  485 (595)
Q Consensus       412 ~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~----~--~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~p  485 (595)
                       .|.|+...+.+.-.....+.+.+|..+|+..+..    .  ......+++.|+.+|.+.+.+++|+..+++.+.. .+.
T Consensus       410 -~P~Dplv~~Elgvvay~~~~y~~A~~~f~~~l~~ik~~~~e~~~w~p~~~NLGH~~Rkl~~~~eAI~~~q~aL~l-~~k  487 (611)
T KOG1173|consen  410 -APSDPLVLHELGVVAYTYEEYPEALKYFQKALEVIKSVLNEKIFWEPTLNNLGHAYRKLNKYEEAIDYYQKALLL-SPK  487 (611)
T ss_pred             -CCCcchhhhhhhheeehHhhhHHHHHHHHHHHHHhhhccccccchhHHHHhHHHHHHHHhhHHHHHHHHHHHHHc-CCC
Confidence             4677888888887777889999999999987721    1  0124567899999999999999999999998874 244


Q ss_pred             CHHHHHHHHHHHHhcCChhHHHHHHHHHHHcCCCCCHHHHHHHHHHH
Q 040027          486 NVVTYNIMIQGLCNDGQMDKARDLFLDMEENAAAPDVITFDMLIHGF  532 (595)
Q Consensus       486 ~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~~l~~~~  532 (595)
                      +..++.+++-.|...|+++.|++.|.+.+..  .|+..+...++..+
T Consensus       488 ~~~~~asig~iy~llgnld~Aid~fhKaL~l--~p~n~~~~~lL~~a  532 (611)
T KOG1173|consen  488 DASTHASIGYIYHLLGNLDKAIDHFHKALAL--KPDNIFISELLKLA  532 (611)
T ss_pred             chhHHHHHHHHHHHhcChHHHHHHHHHHHhc--CCccHHHHHHHHHH
Confidence            7889999999999999999999999999884  67765555555433

>KOG3785 consensus Uncharacterized conserved protein [Function unknown]

Probab=99.65  E-value=5.6e-12  Score=110.81  Aligned_cols=422  Identities=14%  Similarity=0.090  Sum_probs=223.6

Q ss_pred             HHHhcCChhHHHHHHHHHHhCCCCCCHHHHHHHHHHHHhcCCHhHHHHHHHHHHhcCCCCCHhhHHHHHHHHHhcCChhH
Q 040027          105 CFCKIGRVSLGFIAFGRILRSCFTPNAATFNSLIKGLHAESRIMEAAALFTKLKAFGCEPNVITYNTLINGLCRTGHTMI  184 (595)
Q Consensus       105 ~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~  184 (595)
                      -+....++..|+.+++-....+-.....+-..+..++...|++++|...|..+.... .++...+..|.-.+.-.|.+.+
T Consensus        31 dfls~rDytGAislLefk~~~~~EEE~~~~lWia~C~fhLgdY~~Al~~Y~~~~~~~-~~~~el~vnLAcc~FyLg~Y~e  109 (557)
T KOG3785|consen   31 DFLSNRDYTGAISLLEFKLNLDREEEDSLQLWIAHCYFHLGDYEEALNVYTFLMNKD-DAPAELGVNLACCKFYLGQYIE  109 (557)
T ss_pred             HHHhcccchhHHHHHHHhhccchhhhHHHHHHHHHHHHhhccHHHHHHHHHHHhccC-CCCcccchhHHHHHHHHHHHHH
Confidence            344455666666666655544322222233334445555666666666666655532 4455555555555555666666


Q ss_pred             HHHHHHHHHhcCCCCCccccCcHHHHHHHHHHHHHcCCHhHHHHHHHHHhhCCCCCCHhHHHHHHHHHHhcCCHHHHHHH
Q 040027          185 ALNLFEEMANGNGEIGVVCKPNTVTYSTIIDGLCKEGFVDKAKALFLQMKDENINPDVVTYNSLIHGLCHANDWNEAKRL  264 (595)
Q Consensus       185 A~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~~ll~~~~~~~~~~~A~~~  264 (595)
                      |..+-.+.           +.++..-..+.....+.++-++-..+.+.+..     +...-.+|.......-.+++|+++
T Consensus       110 A~~~~~ka-----------~k~pL~~RLlfhlahklndEk~~~~fh~~LqD-----~~EdqLSLAsvhYmR~HYQeAIdv  173 (557)
T KOG3785|consen  110 AKSIAEKA-----------PKTPLCIRLLFHLAHKLNDEKRILTFHSSLQD-----TLEDQLSLASVHYMRMHYQEAIDV  173 (557)
T ss_pred             HHHHHhhC-----------CCChHHHHHHHHHHHHhCcHHHHHHHHHHHhh-----hHHHHHhHHHHHHHHHHHHHHHHH
Confidence            65554443           22333334444445555555554444444432     223333444445555556666666


Q ss_pred             HHHHHHCCCCCCHhhHHHHH-HHHHhcCChHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHhc--C---------------
Q 040027          265 FIEMMDQGVQPSVVTFNVIM-DELCKNRKMDEASRLLDLMVQRGVRPNACTYNTLMDGFCLM--G---------------  326 (595)
Q Consensus       265 ~~~~~~~~~~~~~~~~~~l~-~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~--~---------------  326 (595)
                      |...+..  .|.-...+..+ -+|.+..-++-+.++++--++. ++.++...+..+....+.  |               
T Consensus       174 YkrvL~d--n~ey~alNVy~ALCyyKlDYydvsqevl~vYL~q-~pdStiA~NLkacn~fRl~ngr~ae~E~k~ladN~~  250 (557)
T KOG3785|consen  174 YKRVLQD--NPEYIALNVYMALCYYKLDYYDVSQEVLKVYLRQ-FPDSTIAKNLKACNLFRLINGRTAEDEKKELADNID  250 (557)
T ss_pred             HHHHHhc--ChhhhhhHHHHHHHHHhcchhhhHHHHHHHHHHh-CCCcHHHHHHHHHHHhhhhccchhHHHHHHHHhccc
Confidence            6665543  12333333322 2444555555555555544443 222222222222211111  1               


Q ss_pred             ------------------CHHHHHHHHHHHHhcCCCCCHHHHHHHHHHHHhCCCHHHHHHHHHHHHHCCCCCCHHHHHHH
Q 040027          327 ------------------KINRAEELFGSMESMGCKHDDVSYNILINGYCKNKEVEEALSLYREMVSKGIKPTVVTYNTL  388 (595)
Q Consensus       327 ------------------~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~~l  388 (595)
                                        .-+.|.+++-.+.+.    -+.+-..++--|.+.+++.+|..+.+++.-.    ++.-|..-
T Consensus       251 ~~~~f~~~l~rHNLVvFrngEgALqVLP~L~~~----IPEARlNL~iYyL~q~dVqeA~~L~Kdl~Pt----tP~EyilK  322 (557)
T KOG3785|consen  251 QEYPFIEYLCRHNLVVFRNGEGALQVLPSLMKH----IPEARLNLIIYYLNQNDVQEAISLCKDLDPT----TPYEYILK  322 (557)
T ss_pred             ccchhHHHHHHcCeEEEeCCccHHHhchHHHhh----ChHhhhhheeeecccccHHHHHHHHhhcCCC----ChHHHHHH
Confidence                              123333333333322    1233445566678888888888887765321    33333322


Q ss_pred             HHHHHccCC-------HHHHHHHHHHHHHCCCCCCH-HHHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCcCHHHHHHHHH
Q 040027          389 FLGLFEIHQ-------VEHALKLFDEMQRDGVAADT-RTYTTFIDGLCKNGYIIEAVELFRTLRILKCELDIQAYNCLID  460 (595)
Q Consensus       389 ~~~~~~~~~-------~~~a~~~~~~~~~~~~~~~~-~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~~l~~  460 (595)
                      .-.+...|+       ..-|.+.|...-..+..-|. ..-..+..++.-...+++.+-.++.+..--.. |...-..+.+
T Consensus       323 gvv~aalGQe~gSreHlKiAqqffqlVG~Sa~ecDTIpGRQsmAs~fFL~~qFddVl~YlnSi~sYF~N-dD~Fn~N~AQ  401 (557)
T KOG3785|consen  323 GVVFAALGQETGSREHLKIAQQFFQLVGESALECDTIPGRQSMASYFFLSFQFDDVLTYLNSIESYFTN-DDDFNLNLAQ  401 (557)
T ss_pred             HHHHHHhhhhcCcHHHHHHHHHHHHHhcccccccccccchHHHHHHHHHHHHHHHHHHHHHHHHHHhcC-cchhhhHHHH
Confidence            233344443       23344444333333322222 12234445555566788888888777764423 3333345788


Q ss_pred             HHHhcCChHHHHHHHHhcccCCCCCCHHHHH-HHHHHHHhcCChhHHHHHHHHHHHcCCCCCH-HHHHHHHHHHHHcCCh
Q 040027          461 GLCKSGRLKFAWELFCSLPHGVLVPNVVTYN-IMIQGLCNDGQMDKARDLFLDMEENAAAPDV-ITFDMLIHGFIRINEP  538 (595)
Q Consensus       461 ~~~~~g~~~~A~~~~~~~~~~~~~p~~~~~~-~l~~~~~~~g~~~~A~~~~~~~~~~~~~~~~-~~~~~l~~~~~~~g~~  538 (595)
                      +++..|++.+|+++|-++....++ |..+|. .|.++|.+++.++-|.+++-++-.   +.+. .....+...|.+.+.+
T Consensus       402 Ak~atgny~eaEelf~~is~~~ik-n~~~Y~s~LArCyi~nkkP~lAW~~~lk~~t---~~e~fsLLqlIAn~CYk~~eF  477 (557)
T KOG3785|consen  402 AKLATGNYVEAEELFIRISGPEIK-NKILYKSMLARCYIRNKKPQLAWDMMLKTNT---PSERFSLLQLIANDCYKANEF  477 (557)
T ss_pred             HHHHhcChHHHHHHHhhhcChhhh-hhHHHHHHHHHHHHhcCCchHHHHHHHhcCC---chhHHHHHHHHHHHHHHHHHH
Confidence            888999999999999888764343 445554 556888899999988776655432   2222 3345566788889988


Q ss_pred             hHHHHHHHHHHHCCCCCCHHHHH
Q 040027          539 SKVNELLHKMKEKKVMPDASIVS  561 (595)
Q Consensus       539 ~~A~~~~~~~~~~~~~p~~~~~~  561 (595)
                      --|.+.|+.+..  ..|+++-|.
T Consensus       478 yyaaKAFd~lE~--lDP~pEnWe  498 (557)
T KOG3785|consen  478 YYAAKAFDELEI--LDPTPENWE  498 (557)
T ss_pred             HHHHHhhhHHHc--cCCCccccC
Confidence            888888888775  457777765

>KOG1126 consensus DNA-binding cell division cycle control protein [Cell cycle control, cell division, chromosome partitioning]

Probab=99.65  E-value=1.1e-13  Score=131.82  Aligned_cols=279  Identities=15%  Similarity=0.094  Sum_probs=161.5

Q ss_pred             ChHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHhcCC--CCCHHHHHHHHHHHHhCCCHHHHHHH
Q 040027          292 KMDEASRLLDLMVQRGVRPNACTYNTLMDGFCLMGKINRAEELFGSMESMGC--KHDDVSYNILINGYCKNKEVEEALSL  369 (595)
Q Consensus       292 ~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~--~~~~~~~~~l~~~~~~~~~~~~A~~~  369 (595)
                      +..+|...|..+... +.-+..+...++++|...+++++|+.+|+.+.+...  -.+...|...+..+.+    +-++..
T Consensus       334 ~~~~A~~~~~klp~h-~~nt~wvl~q~GrayFEl~~Y~~a~~~F~~~r~~~p~rv~~meiyST~LWHLq~----~v~Ls~  408 (638)
T KOG1126|consen  334 NCREALNLFEKLPSH-HYNTGWVLSQLGRAYFELIEYDQAERIFSLVRRIEPYRVKGMEIYSTTLWHLQD----EVALSY  408 (638)
T ss_pred             HHHHHHHHHHhhHHh-cCCchHHHHHHHHHHHHHHHHHHHHHHHHHHHhhccccccchhHHHHHHHHHHh----hHHHHH
Confidence            345666666664443 333445555666677777777777777776655420  1133344444433321    112222


Q ss_pred             H-HHHHHCCCCCCHHHHHHHHHHHHccCCHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHHcCC
Q 040027          370 Y-REMVSKGIKPTVVTYNTLFLGLFEIHQVEHALKLFDEMQRDGVAADTRTYTTFIDGLCKNGYIIEAVELFRTLRILKC  448 (595)
Q Consensus       370 ~-~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~  448 (595)
                      + +.++... +-.+.+|..+...|.-.++++.|++.|++.++.+ +-...+|+.+..-+....++|+|...|+.++... 
T Consensus       409 Laq~Li~~~-~~sPesWca~GNcfSLQkdh~~Aik~f~RAiQld-p~faYayTLlGhE~~~~ee~d~a~~~fr~Al~~~-  485 (638)
T KOG1126|consen  409 LAQDLIDTD-PNSPESWCALGNCFSLQKDHDTAIKCFKRAIQLD-PRFAYAYTLLGHESIATEEFDKAMKSFRKALGVD-  485 (638)
T ss_pred             HHHHHHhhC-CCCcHHHHHhcchhhhhhHHHHHHHHHHHhhccC-CccchhhhhcCChhhhhHHHHhHHHHHHhhhcCC-
Confidence            2 2333322 2255667777777777777777777777766652 2255666666666666667777777777666433 


Q ss_pred             CcCHHHHHHHHHHHHhcCChHHHHHHHHhcccCCCCCC-HHHHHHHHHHHHhcCChhHHHHHHHHHHHcCCCCCHHHHHH
Q 040027          449 ELDIQAYNCLIDGLCKSGRLKFAWELFCSLPHGVLVPN-VVTYNIMIQGLCNDGQMDKARDLFLDMEENAAAPDVITFDM  527 (595)
Q Consensus       449 ~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~p~-~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~~  527 (595)
                      +.+-.+|-.++..|.++++++.|+-.|+++.+  +.|. ......+...+-+.|+.++|+++++++...+ +.|+..-..
T Consensus       486 ~rhYnAwYGlG~vy~Kqek~e~Ae~~fqkA~~--INP~nsvi~~~~g~~~~~~k~~d~AL~~~~~A~~ld-~kn~l~~~~  562 (638)
T KOG1126|consen  486 PRHYNAWYGLGTVYLKQEKLEFAEFHFQKAVE--INPSNSVILCHIGRIQHQLKRKDKALQLYEKAIHLD-PKNPLCKYH  562 (638)
T ss_pred             chhhHHHHhhhhheeccchhhHHHHHHHhhhc--CCccchhHHhhhhHHHHHhhhhhHHHHHHHHHHhcC-CCCchhHHH
Confidence            33344455566666777777777777777666  4443 3444555566666677777777777776654 334444444


Q ss_pred             HHHHHHHcCChhHHHHHHHHHHHCCCCC-CHHHHHHHHHHHHhcCcccccchHHHHh
Q 040027          528 LIHGFIRINEPSKVNELLHKMKEKKVMP-DASIVSIVVDLLVKNEISLKSLPSFLVQ  583 (595)
Q Consensus       528 l~~~~~~~g~~~~A~~~~~~~~~~~~~p-~~~~~~~l~~~~~~~g~~~~~i~~~~~~  583 (595)
                      -+..+...+++++|+..++++++.  .| +..++..++.+|.+.|+.+.++.++...
T Consensus       563 ~~~il~~~~~~~eal~~LEeLk~~--vP~es~v~~llgki~k~~~~~~~Al~~f~~A  617 (638)
T KOG1126|consen  563 RASILFSLGRYVEALQELEELKEL--VPQESSVFALLGKIYKRLGNTDLALLHFSWA  617 (638)
T ss_pred             HHHHHHhhcchHHHHHHHHHHHHh--CcchHHHHHHHHHHHHHHccchHHHHhhHHH
Confidence            555666667777777777777663  34 4566666677777777776555555433

>KOG2047 consensus mRNA splicing factor [RNA processing and modification]

Probab=99.63  E-value=1.2e-09  Score=103.92  Aligned_cols=509  Identities=12%  Similarity=0.096  Sum_probs=315.7

Q ss_pred             hHHHHHHHHHHHHhCCCCCCHhhHHHHHHHHHcCCCchh-------HHhhCCCCCCHHHHHHHHHHHHhcCChhHHHHHH
Q 040027           47 PNEAFCIFDYMLRMHPSPPPVSSFNILLASLAKNKHYDT-------RLNATGLFPNLYTYNILINCFCKIGRVSLGFIAF  119 (595)
Q Consensus        47 ~~~A~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~-------~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~  119 (595)
                      ++..-..|++++..-..  -|..|..-+..+.++|+...       .+...-+......|...+......|-++-+..++
T Consensus        84 ~~~vn~c~er~lv~mHk--mpRIwl~Ylq~l~~Q~~iT~tR~tfdrALraLpvtqH~rIW~lyl~Fv~~~~lPets~rvy  161 (835)
T KOG2047|consen   84 YESVNNCFERCLVFMHK--MPRIWLDYLQFLIKQGLITRTRRTFDRALRALPVTQHDRIWDLYLKFVESHGLPETSIRVY  161 (835)
T ss_pred             HHHHHHHHHHHHHHHhc--CCHHHHHHHHHHHhcchHHHHHHHHHHHHHhCchHhhccchHHHHHHHHhCCChHHHHHHH
Confidence            33444445555542222  45688888888888888776       3444445556778999999999999999999999


Q ss_pred             HHHHhCCCCCCHHHHHHHHHHHHhcCCHhHHHHHHHHHHhcC------CCCCHhhHHHHHHHHHhcC---ChhHHHHHHH
Q 040027          120 GRILRSCFTPNAATFNSLIKGLHAESRIMEAAALFTKLKAFG------CEPNVITYNTLINGLCRTG---HTMIALNLFE  190 (595)
Q Consensus       120 ~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~------~~~~~~~~~~l~~~~~~~g---~~~~A~~~~~  190 (595)
                      ++.++.    ++..-...+..+...++.++|.+.+..+....      .+.+-..|..+....++.-   ..-....+++
T Consensus       162 rRYLk~----~P~~~eeyie~L~~~d~~~eaa~~la~vln~d~f~sk~gkSn~qlw~elcdlis~~p~~~~slnvdaiiR  237 (835)
T KOG2047|consen  162 RRYLKV----APEAREEYIEYLAKSDRLDEAAQRLATVLNQDEFVSKKGKSNHQLWLELCDLISQNPDKVQSLNVDAIIR  237 (835)
T ss_pred             HHHHhc----CHHHHHHHHHHHHhccchHHHHHHHHHhcCchhhhhhcccchhhHHHHHHHHHHhCcchhcccCHHHHHH
Confidence            999976    45557888899999999999999998876531      1224455666666555533   2233445555


Q ss_pred             HHHhcCCCCCccccCcHHHHHHHHHHHHHcCCHhHHHHHHHHHhhCCCCCCHhHHHHHHHHHHhc---------------
Q 040027          191 EMANGNGEIGVVCKPNTVTYSTIIDGLCKEGFVDKAKALFLQMKDENINPDVVTYNSLIHGLCHA---------------  255 (595)
Q Consensus       191 ~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~~ll~~~~~~---------------  255 (595)
                      .+...-      ...-...|+.|...|.+.|.+++|..+|++....-  .+..-|+.+.+.|..-               
T Consensus       238 ~gi~rf------tDq~g~Lw~SLAdYYIr~g~~ekarDvyeeai~~v--~tvrDFt~ifd~Ya~FEE~~~~~~me~a~~~  309 (835)
T KOG2047|consen  238 GGIRRF------TDQLGFLWCSLADYYIRSGLFEKARDVYEEAIQTV--MTVRDFTQIFDAYAQFEESCVAAKMELADEE  309 (835)
T ss_pred             hhcccC------cHHHHHHHHHHHHHHHHhhhhHHHHHHHHHHHHhh--eehhhHHHHHHHHHHHHHHHHHHHHhhhhhc
Confidence            555543      11125679999999999999999999999987641  2333344444443321               


Q ss_pred             -C------CHHHHHHHHHHHHHCCC-----------CCCHhhHHHHHHHHHhcCChHHHHHHHHHHHHCCCCCC------
Q 040027          256 -N------DWNEAKRLFIEMMDQGV-----------QPSVVTFNVIMDELCKNRKMDEASRLLDLMVQRGVRPN------  311 (595)
Q Consensus       256 -~------~~~~A~~~~~~~~~~~~-----------~~~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~~~~~------  311 (595)
                       +      +++-.+..|+.+...+.           +.+...|..-+.  ...|+..+....|.++++. +.|.      
T Consensus       310 ~~n~ed~~dl~~~~a~~e~lm~rr~~~lNsVlLRQn~~nV~eW~kRV~--l~e~~~~~~i~tyteAv~~-vdP~ka~Gs~  386 (835)
T KOG2047|consen  310 SGNEEDDVDLELHMARFESLMNRRPLLLNSVLLRQNPHNVEEWHKRVK--LYEGNAAEQINTYTEAVKT-VDPKKAVGSP  386 (835)
T ss_pred             ccChhhhhhHHHHHHHHHHHHhccchHHHHHHHhcCCccHHHHHhhhh--hhcCChHHHHHHHHHHHHc-cCcccCCCCh
Confidence             1      23333444555444321           112333433332  3456777888888888775 3322      


Q ss_pred             HHHHHHHHHHHHhcCCHHHHHHHHHHHHhcCCCCC---HHHHHHHHHHHHhCCCHHHHHHHHHHHHHCCCCC--------
Q 040027          312 ACTYNTLMDGFCLMGKINRAEELFGSMESMGCKHD---DVSYNILINGYCKNKEVEEALSLYREMVSKGIKP--------  380 (595)
Q Consensus       312 ~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~---~~~~~~l~~~~~~~~~~~~A~~~~~~~~~~~~~~--------  380 (595)
                      ...|..+...|-..|+++.|..+|++..+...+.-   ..+|.....+-.+..+++.|+++.++.....-.|        
T Consensus       387 ~~Lw~~faklYe~~~~l~~aRvifeka~~V~y~~v~dLa~vw~~waemElrh~~~~~Al~lm~~A~~vP~~~~~~~yd~~  466 (835)
T KOG2047|consen  387 GTLWVEFAKLYENNGDLDDARVIFEKATKVPYKTVEDLAEVWCAWAEMELRHENFEAALKLMRRATHVPTNPELEYYDNS  466 (835)
T ss_pred             hhHHHHHHHHHHhcCcHHHHHHHHHHhhcCCccchHHHHHHHHHHHHHHHhhhhHHHHHHHHHhhhcCCCchhhhhhcCC
Confidence            34677888999999999999999999887643322   2356666677778889999999988876431111        


Q ss_pred             ---------CHHHHHHHHHHHHccCCHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCcC
Q 040027          381 ---------TVVTYNTLFLGLFEIHQVEHALKLFDEMQRDGVAADTRTYTTFIDGLCKNGYIIEAVELFRTLRILKCELD  451 (595)
Q Consensus       381 ---------~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~~  451 (595)
                               +...|...+......|-++....+|+.+++..+. ++.+.......+-.+.-++++.++|++-+..--.|+
T Consensus       467 ~pvQ~rlhrSlkiWs~y~DleEs~gtfestk~vYdriidLria-TPqii~NyAmfLEeh~yfeesFk~YErgI~LFk~p~  545 (835)
T KOG2047|consen  467 EPVQARLHRSLKIWSMYADLEESLGTFESTKAVYDRIIDLRIA-TPQIIINYAMFLEEHKYFEESFKAYERGISLFKWPN  545 (835)
T ss_pred             CcHHHHHHHhHHHHHHHHHHHHHhccHHHHHHHHHHHHHHhcC-CHHHHHHHHHHHHhhHHHHHHHHHHHcCCccCCCcc
Confidence                     2334555566666678888888888888876432 333333333334455567777777776665433344


Q ss_pred             -HHHHHHHHHHHHhc---CChHHHHHHHHhcccCCCCCCHHHHHHHH--HHHHhcCChhHHHHHHHHHHHc---------
Q 040027          452 -IQAYNCLIDGLCKS---GRLKFAWELFCSLPHGVLVPNVVTYNIMI--QGLCNDGQMDKARDLFLDMEEN---------  516 (595)
Q Consensus       452 -~~~~~~l~~~~~~~---g~~~~A~~~~~~~~~~~~~p~~~~~~~l~--~~~~~~g~~~~A~~~~~~~~~~---------  516 (595)
                       ...|+..+.-+.+.   ..++.|..+|+++++ +.+|...-+-.|+  ..--..|-...|+.+++++...         
T Consensus       546 v~diW~tYLtkfi~rygg~klEraRdLFEqaL~-~Cpp~~aKtiyLlYA~lEEe~GLar~amsiyerat~~v~~a~~l~m  624 (835)
T KOG2047|consen  546 VYDIWNTYLTKFIKRYGGTKLERARDLFEQALD-GCPPEHAKTIYLLYAKLEEEHGLARHAMSIYERATSAVKEAQRLDM  624 (835)
T ss_pred             HHHHHHHHHHHHHHHhcCCCHHHHHHHHHHHHh-cCCHHHHHHHHHHHHHHHHHhhHHHHHHHHHHHHHhcCCHHHHHHH
Confidence             34566655555432   346777777777776 3444322111111  1111335555555555543221         


Q ss_pred             ------------CCCCCHHHHHHHH----------------HHHHHcCChhHHHHHHHHHHHC-CCCCCHHHHHHHHHHH
Q 040027          517 ------------AAAPDVITFDMLI----------------HGFIRINEPSKVNELLHKMKEK-KVMPDASIVSIVVDLL  567 (595)
Q Consensus       517 ------------~~~~~~~~~~~l~----------------~~~~~~g~~~~A~~~~~~~~~~-~~~p~~~~~~~l~~~~  567 (595)
                                  |++..-..|...|                ..=.+.|..+.|..++.-..+. .-+.+...|..+-..=
T Consensus       625 yni~I~kaae~yGv~~TR~iYekaIe~Lp~~~~r~mclrFAdlEtklGEidRARaIya~~sq~~dPr~~~~fW~twk~FE  704 (835)
T KOG2047|consen  625 YNIYIKKAAEIYGVPRTREIYEKAIESLPDSKAREMCLRFADLETKLGEIDRARAIYAHGSQICDPRVTTEFWDTWKEFE  704 (835)
T ss_pred             HHHHHHHHHHHhCCcccHHHHHHHHHhCChHHHHHHHHHHHHHhhhhhhHHHHHHHHHhhhhcCCCcCChHHHHHHHHHH
Confidence                        2222222222222                2224678888888888877764 2233678899998888


Q ss_pred             HhcCccc
Q 040027          568 VKNEISL  574 (595)
Q Consensus       568 ~~~g~~~  574 (595)
                      .+.|+-+
T Consensus       705 vrHGned  711 (835)
T KOG2047|consen  705 VRHGNED  711 (835)
T ss_pred             HhcCCHH
Confidence            8999854

>COG2956 Predicted N-acetylglucosaminyl transferase [Carbohydrate transport and metabolism]

Probab=99.63  E-value=2.5e-12  Score=111.71  Aligned_cols=286  Identities=14%  Similarity=0.156  Sum_probs=166.2

Q ss_pred             cCCHhHHHHHHHHHhhCCCCCCHhHHHHHHHHHHhcCCHHHHHHHHHHHHHCCCCCCH------hhHHHHHHHHHhcCCh
Q 040027          220 EGFVDKAKALFLQMKDENINPDVVTYNSLIHGLCHANDWNEAKRLFIEMMDQGVQPSV------VTFNVIMDELCKNRKM  293 (595)
Q Consensus       220 ~g~~~~A~~~~~~~~~~~~~~~~~~~~~ll~~~~~~~~~~~A~~~~~~~~~~~~~~~~------~~~~~l~~~~~~~g~~  293 (595)
                      .++.++|.++|-+|.+.. +.+..+..+|.+.|.+.|..+.|+++.+.+.+.   ||.      .....+..-|...|-+
T Consensus        48 s~Q~dKAvdlF~e~l~~d-~~t~e~~ltLGnLfRsRGEvDRAIRiHQ~L~~s---pdlT~~qr~lAl~qL~~Dym~aGl~  123 (389)
T COG2956          48 SNQPDKAVDLFLEMLQED-PETFEAHLTLGNLFRSRGEVDRAIRIHQTLLES---PDLTFEQRLLALQQLGRDYMAAGLL  123 (389)
T ss_pred             hcCcchHHHHHHHHHhcC-chhhHHHHHHHHHHHhcchHHHHHHHHHHHhcC---CCCchHHHHHHHHHHHHHHHHhhhh
Confidence            467788888888887753 235556667778888888888888888877765   332      2233455566667777


Q ss_pred             HHHHHHHHHHHHCCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHhcCCCCCH----HHHHHHHHHHHhCCCHHHHHHH
Q 040027          294 DEASRLLDLMVQRGVRPNACTYNTLMDGFCLMGKINRAEELFGSMESMGCKHDD----VSYNILINGYCKNKEVEEALSL  369 (595)
Q Consensus       294 ~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~----~~~~~l~~~~~~~~~~~~A~~~  369 (595)
                      +.|.++|..+.+.+ ..-......++..|-...+|++|+++-+++.+.+-.+..    ..|.-+...+....+.+.|..+
T Consensus       124 DRAE~~f~~L~de~-efa~~AlqqLl~IYQ~treW~KAId~A~~L~k~~~q~~~~eIAqfyCELAq~~~~~~~~d~A~~~  202 (389)
T COG2956         124 DRAEDIFNQLVDEG-EFAEGALQQLLNIYQATREWEKAIDVAERLVKLGGQTYRVEIAQFYCELAQQALASSDVDRAREL  202 (389)
T ss_pred             hHHHHHHHHHhcch-hhhHHHHHHHHHHHHHhhHHHHHHHHHHHHHHcCCccchhHHHHHHHHHHHHHhhhhhHHHHHHH
Confidence            77777777776643 223445666677777777777777777766665433221    1344445555556666666766


Q ss_pred             HHHHHHCCCCCCHHHHHHHHHHHHccCCHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHHcCCC
Q 040027          370 YREMVSKGIKPTVVTYNTLFLGLFEIHQVEHALKLFDEMQRDGVAADTRTYTTFIDGLCKNGYIIEAVELFRTLRILKCE  449 (595)
Q Consensus       370 ~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~  449 (595)
                      +.+..+.+.+ .+..-..+.......|+++.|.+.|+.+.+.+..--+.+...+..+|.+.|+.++....+.++.+..  
T Consensus       203 l~kAlqa~~~-cvRAsi~lG~v~~~~g~y~~AV~~~e~v~eQn~~yl~evl~~L~~~Y~~lg~~~~~~~fL~~~~~~~--  279 (389)
T COG2956         203 LKKALQADKK-CVRASIILGRVELAKGDYQKAVEALERVLEQNPEYLSEVLEMLYECYAQLGKPAEGLNFLRRAMETN--  279 (389)
T ss_pred             HHHHHhhCcc-ceehhhhhhHHHHhccchHHHHHHHHHHHHhChHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHcc--
Confidence            6666665433 3344444555666666666666666666666444444556666666666666666666666666543  


Q ss_pred             cCHHHHHHHHHHHHhcCChHHHHHHHHhcccCCCCCCHHHHHHHHHHHHh---cCChhHHHHHHHHHHH
Q 040027          450 LDIQAYNCLIDGLCKSGRLKFAWELFCSLPHGVLVPNVVTYNIMIQGLCN---DGQMDKARDLFLDMEE  515 (595)
Q Consensus       450 ~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~p~~~~~~~l~~~~~~---~g~~~~A~~~~~~~~~  515 (595)
                      +....-..+...-....-.+.|...+.+-+.  -.|+...+..++.....   .|...+-...++.|+.
T Consensus       280 ~g~~~~l~l~~lie~~~G~~~Aq~~l~~Ql~--r~Pt~~gf~rl~~~~l~daeeg~~k~sL~~lr~mvg  346 (389)
T COG2956         280 TGADAELMLADLIELQEGIDAAQAYLTRQLR--RKPTMRGFHRLMDYHLADAEEGRAKESLDLLRDMVG  346 (389)
T ss_pred             CCccHHHHHHHHHHHhhChHHHHHHHHHHHh--hCCcHHHHHHHHHhhhccccccchhhhHHHHHHHHH
Confidence            2222333333333333334444444444333  25666666666554442   2334444445555543

>COG2956 Predicted N-acetylglucosaminyl transferase [Carbohydrate transport and metabolism]

Probab=99.62  E-value=3.4e-12  Score=110.94  Aligned_cols=291  Identities=15%  Similarity=0.136  Sum_probs=186.7

Q ss_pred             cCCHhHHHHHHHHHHhcCCCCCHhhHHHHHHHHHhcCChhHHHHHHHHHHhcCCCCCccccCcHHHHHHHHHHHHHcCCH
Q 040027          144 ESRIMEAAALFTKLKAFGCEPNVITYNTLINGLCRTGHTMIALNLFEEMANGNGEIGVVCKPNTVTYSTIIDGLCKEGFV  223 (595)
Q Consensus       144 ~g~~~~A~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~  223 (595)
                      ..+.++|+++|-+|.+.. +.+..+...|.+.|-+.|..+.|+.+-+.+..+.+   .+......+...|..-|...|-+
T Consensus        48 s~Q~dKAvdlF~e~l~~d-~~t~e~~ltLGnLfRsRGEvDRAIRiHQ~L~~spd---lT~~qr~lAl~qL~~Dym~aGl~  123 (389)
T COG2956          48 SNQPDKAVDLFLEMLQED-PETFEAHLTLGNLFRSRGEVDRAIRIHQTLLESPD---LTFEQRLLALQQLGRDYMAAGLL  123 (389)
T ss_pred             hcCcchHHHHHHHHHhcC-chhhHHHHHHHHHHHhcchHHHHHHHHHHHhcCCC---CchHHHHHHHHHHHHHHHHhhhh
Confidence            466788888888888753 22455667788888888888888888888776531   00111233455667778888888


Q ss_pred             hHHHHHHHHHhhCCCCCCHhHHHHHHHHHHhcCCHHHHHHHHHHHHHCCCCCCH----hhHHHHHHHHHhcCChHHHHHH
Q 040027          224 DKAKALFLQMKDENINPDVVTYNSLIHGLCHANDWNEAKRLFIEMMDQGVQPSV----VTFNVIMDELCKNRKMDEASRL  299 (595)
Q Consensus       224 ~~A~~~~~~~~~~~~~~~~~~~~~ll~~~~~~~~~~~A~~~~~~~~~~~~~~~~----~~~~~l~~~~~~~g~~~~a~~~  299 (595)
                      |.|+++|..+.+.+. --......|+..|-...+|++|+++-.++.+.+-++..    ..|.-+...+....+++.|...
T Consensus       124 DRAE~~f~~L~de~e-fa~~AlqqLl~IYQ~treW~KAId~A~~L~k~~~q~~~~eIAqfyCELAq~~~~~~~~d~A~~~  202 (389)
T COG2956         124 DRAEDIFNQLVDEGE-FAEGALQQLLNIYQATREWEKAIDVAERLVKLGGQTYRVEIAQFYCELAQQALASSDVDRAREL  202 (389)
T ss_pred             hHHHHHHHHHhcchh-hhHHHHHHHHHHHHHhhHHHHHHHHHHHHHHcCCccchhHHHHHHHHHHHHHhhhhhHHHHHHH
Confidence            888888888877532 24556777888888888888888888877776544322    2345555556666777777888


Q ss_pred             HHHHHHCCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHhcCCCCCHHHHHHHHHHHHhCCCHHHHHHHHHHHHHCCCC
Q 040027          300 LDLMVQRGVRPNACTYNTLMDGFCLMGKINRAEELFGSMESMGCKHDDVSYNILINGYCKNKEVEEALSLYREMVSKGIK  379 (595)
Q Consensus       300 ~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~~~~~  379 (595)
                      +.+..+.+.+ .+..-..+.+.+...|+++.|.+.++.+.+.+...-+.+...|..+|.+.|+.++....+..+.+... 
T Consensus       203 l~kAlqa~~~-cvRAsi~lG~v~~~~g~y~~AV~~~e~v~eQn~~yl~evl~~L~~~Y~~lg~~~~~~~fL~~~~~~~~-  280 (389)
T COG2956         203 LKKALQADKK-CVRASIILGRVELAKGDYQKAVEALERVLEQNPEYLSEVLEMLYECYAQLGKPAEGLNFLRRAMETNT-  280 (389)
T ss_pred             HHHHHhhCcc-ceehhhhhhHHHHhccchHHHHHHHHHHHHhChHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHccC-
Confidence            7777776422 44445556777777888888888888877765444445667777788888888888877777776532 


Q ss_pred             CCHHHHHHHHHHHHccCCHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHh---cCCHHHHHHHHHHHH
Q 040027          380 PTVVTYNTLFLGLFEIHQVEHALKLFDEMQRDGVAADTRTYTTFIDGLCK---NGYIIEAVELFRTLR  444 (595)
Q Consensus       380 ~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~---~g~~~~A~~~~~~~~  444 (595)
                       ....-..+........-.+.|...+.+-++.  .|+...+..++.....   .|...+-..+++.|.
T Consensus       281 -g~~~~l~l~~lie~~~G~~~Aq~~l~~Ql~r--~Pt~~gf~rl~~~~l~daeeg~~k~sL~~lr~mv  345 (389)
T COG2956         281 -GADAELMLADLIELQEGIDAAQAYLTRQLRR--KPTMRGFHRLMDYHLADAEEGRAKESLDLLRDMV  345 (389)
T ss_pred             -CccHHHHHHHHHHHhhChHHHHHHHHHHHhh--CCcHHHHHHHHHhhhccccccchhhhHHHHHHHH
Confidence             3333333444334444445555554444443  5677777777665443   233444444555544

>COG3071 HemY Uncharacterized enzyme of heme biosynthesis [Coenzyme metabolism]

Probab=99.62  E-value=8.8e-12  Score=111.89  Aligned_cols=287  Identities=11%  Similarity=0.070  Sum_probs=156.9

Q ss_pred             cCCHhHHHHHHHHHHhcCCCCCHhhHHHHHHHHHhcCChhHHHHHHHHHHhcCCCCCccccCcHHHHHHHHHHHHHcCCH
Q 040027          144 ESRIMEAAALFTKLKAFGCEPNVITYNTLINGLCRTGHTMIALNLFEEMANGNGEIGVVCKPNTVTYSTIIDGLCKEGFV  223 (595)
Q Consensus       144 ~g~~~~A~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~  223 (595)
                      .|++.+|.++..+..+.+-. ....|..-+++-.+.|+.+.+-.++.++.+..      -.++....-.........|++
T Consensus        97 eG~~~qAEkl~~rnae~~e~-p~l~~l~aA~AA~qrgd~~~an~yL~eaae~~------~~~~l~v~ltrarlll~~~d~  169 (400)
T COG3071          97 EGDFQQAEKLLRRNAEHGEQ-PVLAYLLAAEAAQQRGDEDRANRYLAEAAELA------GDDTLAVELTRARLLLNRRDY  169 (400)
T ss_pred             cCcHHHHHHHHHHhhhcCcc-hHHHHHHHHHHHHhcccHHHHHHHHHHHhccC------CCchHHHHHHHHHHHHhCCCc
Confidence            46666666666665554322 22333334444555666666666666665542      123344444455555566666


Q ss_pred             hHHHHHHHHHhhCCCCCCHhHHHHHHHHHHhcCCHHHHHHHHHHHHHCCCCCCH-------hhHHHHHHHHHhcCChHHH
Q 040027          224 DKAKALFLQMKDENINPDVVTYNSLIHGLCHANDWNEAKRLFIEMMDQGVQPSV-------VTFNVIMDELCKNRKMDEA  296 (595)
Q Consensus       224 ~~A~~~~~~~~~~~~~~~~~~~~~ll~~~~~~~~~~~A~~~~~~~~~~~~~~~~-------~~~~~l~~~~~~~g~~~~a  296 (595)
                      +.|..-.+.+.+.+ +-++........+|.+.|++.+...++.++.+.+.-.+.       .+|..++.-....+..+.-
T Consensus       170 ~aA~~~v~~ll~~~-pr~~~vlrLa~r~y~~~g~~~~ll~~l~~L~ka~~l~~~e~~~le~~a~~glL~q~~~~~~~~gL  248 (400)
T COG3071         170 PAARENVDQLLEMT-PRHPEVLRLALRAYIRLGAWQALLAILPKLRKAGLLSDEEAARLEQQAWEGLLQQARDDNGSEGL  248 (400)
T ss_pred             hhHHHHHHHHHHhC-cCChHHHHHHHHHHHHhccHHHHHHHHHHHHHccCCChHHHHHHHHHHHHHHHHHHhccccchHH
Confidence            66666666555543 224455555556666666666666666666665543332       2344455555555555554


Q ss_pred             HHHHHHHHHCCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHhcCCCCCHHHHHHHHHHHHhCCCHHHHHHHHHHHHHC
Q 040027          297 SRLLDLMVQRGVRPNACTYNTLMDGFCLMGKINRAEELFGSMESMGCKHDDVSYNILINGYCKNKEVEEALSLYREMVSK  376 (595)
Q Consensus       297 ~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~~  376 (595)
                      ...++..... .+.++.....++.-+.++|+.++|.++..+..+.+..+.    -.....+.+.++...-++..++..+.
T Consensus       249 ~~~W~~~pr~-lr~~p~l~~~~a~~li~l~~~~~A~~~i~~~Lk~~~D~~----L~~~~~~l~~~d~~~l~k~~e~~l~~  323 (400)
T COG3071         249 KTWWKNQPRK-LRNDPELVVAYAERLIRLGDHDEAQEIIEDALKRQWDPR----LCRLIPRLRPGDPEPLIKAAEKWLKQ  323 (400)
T ss_pred             HHHHHhccHH-hhcChhHHHHHHHHHHHcCChHHHHHHHHHHHHhccChh----HHHHHhhcCCCCchHHHHHHHHHHHh
Confidence            4555554443 333455555566666666666666666666666543333    11122234455555555555555444


Q ss_pred             CCCCCHHHHHHHHHHHHccCCHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHHc
Q 040027          377 GIKPTVVTYNTLFLGLFEIHQVEHALKLFDEMQRDGVAADTRTYTTFIDGLCKNGYIIEAVELFRTLRIL  446 (595)
Q Consensus       377 ~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~  446 (595)
                      .+. ++..+..+...|.+.+.|.+|...|+...+.  .|+..+|..+..++.+.|+..+|.++.++....
T Consensus       324 h~~-~p~L~~tLG~L~~k~~~w~kA~~~leaAl~~--~~s~~~~~~la~~~~~~g~~~~A~~~r~e~L~~  390 (400)
T COG3071         324 HPE-DPLLLSTLGRLALKNKLWGKASEALEAALKL--RPSASDYAELADALDQLGEPEEAEQVRREALLL  390 (400)
T ss_pred             CCC-ChhHHHHHHHHHHHhhHHHHHHHHHHHHHhc--CCChhhHHHHHHHHHHcCChHHHHHHHHHHHHH
Confidence            222 4455666666666666666666666665554  566666666666666677777666666665543

>KOG3785 consensus Uncharacterized conserved protein [Function unknown]

Probab=99.60  E-value=1.6e-10  Score=101.93  Aligned_cols=430  Identities=12%  Similarity=0.139  Sum_probs=239.4

Q ss_pred             HHHHHHhcCChhHHHHHHHHHHhCCCCCCHHHHHHHHHHHHhcCCHhHHHHHHHHHHhcCCCCCHhhHHHHHHHHHhcCC
Q 040027          102 LINCFCKIGRVSLGFIAFGRILRSCFTPNAATFNSLIKGLHAESRIMEAAALFTKLKAFGCEPNVITYNTLINGLCRTGH  181 (595)
Q Consensus       102 l~~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~  181 (595)
                      +..++...|++++|..++..+.+.. .++...+..+..++.-.|.+.+|..+-.+..+     ++-....++..-.+.|+
T Consensus        63 ia~C~fhLgdY~~Al~~Y~~~~~~~-~~~~el~vnLAcc~FyLg~Y~eA~~~~~ka~k-----~pL~~RLlfhlahklnd  136 (557)
T KOG3785|consen   63 IAHCYFHLGDYEEALNVYTFLMNKD-DAPAELGVNLACCKFYLGQYIEAKSIAEKAPK-----TPLCIRLLFHLAHKLND  136 (557)
T ss_pred             HHHHHHhhccHHHHHHHHHHHhccC-CCCcccchhHHHHHHHHHHHHHHHHHHhhCCC-----ChHHHHHHHHHHHHhCc
Confidence            4555666677777777776666543 55566666666666666666666665544322     22222333344444454


Q ss_pred             hhHHHHHHHHHHhcCCCCCccccCcHHHHHHHHHHHHHcCCHhHHHHHHHHHhhCCCCCCHhHHHH-HHHHHHhcCCHHH
Q 040027          182 TMIALNLFEEMANGNGEIGVVCKPNTVTYSTIIDGLCKEGFVDKAKALFLQMKDENINPDVVTYNS-LIHGLCHANDWNE  260 (595)
Q Consensus       182 ~~~A~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~~-ll~~~~~~~~~~~  260 (595)
                      -++-...-+.+..           ...--..|.+.....-.+++|++++.++...+  |+....+. +.-+|.+..-++-
T Consensus       137 Ek~~~~fh~~LqD-----------~~EdqLSLAsvhYmR~HYQeAIdvYkrvL~dn--~ey~alNVy~ALCyyKlDYydv  203 (557)
T KOG3785|consen  137 EKRILTFHSSLQD-----------TLEDQLSLASVHYMRMHYQEAIDVYKRVLQDN--PEYIALNVYMALCYYKLDYYDV  203 (557)
T ss_pred             HHHHHHHHHHHhh-----------hHHHHHhHHHHHHHHHHHHHHHHHHHHHHhcC--hhhhhhHHHHHHHHHhcchhhh
Confidence            4444333333221           11222233333333334566666666655532  23333332 2234455555555


Q ss_pred             HHHHHHHHHHCCCCCCHhhHHHHHHHHHhc-----------------------------------CChHHHHHHHHHHHH
Q 040027          261 AKRLFIEMMDQGVQPSVVTFNVIMDELCKN-----------------------------------RKMDEASRLLDLMVQ  305 (595)
Q Consensus       261 A~~~~~~~~~~~~~~~~~~~~~l~~~~~~~-----------------------------------g~~~~a~~~~~~~~~  305 (595)
                      +.++++-.+++ ++.+....+..+....+.                                   ++-+.|++++--+.+
T Consensus       204 sqevl~vYL~q-~pdStiA~NLkacn~fRl~ngr~ae~E~k~ladN~~~~~~f~~~l~rHNLVvFrngEgALqVLP~L~~  282 (557)
T KOG3785|consen  204 SQEVLKVYLRQ-FPDSTIAKNLKACNLFRLINGRTAEDEKKELADNIDQEYPFIEYLCRHNLVVFRNGEGALQVLPSLMK  282 (557)
T ss_pred             HHHHHHHHHHh-CCCcHHHHHHHHHHHhhhhccchhHHHHHHHHhcccccchhHHHHHHcCeEEEeCCccHHHhchHHHh
Confidence            55555555443 222222333222221111                                   122333333333332


Q ss_pred             CCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHhcCCCCCHHHHHHHHHHHHhCCC-------HHHHHHHHHHHHHCCC
Q 040027          306 RGVRPNACTYNTLMDGFCLMGKINRAEELFGSMESMGCKHDDVSYNILINGYCKNKE-------VEEALSLYREMVSKGI  378 (595)
Q Consensus       306 ~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~-------~~~A~~~~~~~~~~~~  378 (595)
                      .  .  +..-..++--|.+.++.++|..+.+++.    |.++.-|-.-.-.+...|+       ..-|.+.|+-.-+.+.
T Consensus       283 ~--I--PEARlNL~iYyL~q~dVqeA~~L~Kdl~----PttP~EyilKgvv~aalGQe~gSreHlKiAqqffqlVG~Sa~  354 (557)
T KOG3785|consen  283 H--I--PEARLNLIIYYLNQNDVQEAISLCKDLD----PTTPYEYILKGVVFAALGQETGSREHLKIAQQFFQLVGESAL  354 (557)
T ss_pred             h--C--hHhhhhheeeecccccHHHHHHHHhhcC----CCChHHHHHHHHHHHHhhhhcCcHHHHHHHHHHHHHhccccc
Confidence            1  1  1223345556788999999998887764    3344444333333333333       4455555554444433


Q ss_pred             CCCH-HHHHHHHHHHHccCCHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCcCHHHHHH
Q 040027          379 KPTV-VTYNTLFLGLFEIHQVEHALKLFDEMQRDGVAADTRTYTTFIDGLCKNGYIIEAVELFRTLRILKCELDIQAYNC  457 (595)
Q Consensus       379 ~~~~-~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~~  457 (595)
                      .-|. .....+...+.-..++++++..++.+... +..|......+.++++..|++.+|.++|-++....++.+..-...
T Consensus       355 ecDTIpGRQsmAs~fFL~~qFddVl~YlnSi~sY-F~NdD~Fn~N~AQAk~atgny~eaEelf~~is~~~ikn~~~Y~s~  433 (557)
T KOG3785|consen  355 ECDTIPGRQSMASYFFLSFQFDDVLTYLNSIESY-FTNDDDFNLNLAQAKLATGNYVEAEELFIRISGPEIKNKILYKSM  433 (557)
T ss_pred             ccccccchHHHHHHHHHHHHHHHHHHHHHHHHHH-hcCcchhhhHHHHHHHHhcChHHHHHHHhhhcChhhhhhHHHHHH
Confidence            2222 22344555566667889999888888876 344555555678899999999999999988875544434444456


Q ss_pred             HHHHHHhcCChHHHHHHHHhcccCCCCCCHHHHHH-HHHHHHhcCChhHHHHHHHHHHHcCCCCCHHHHHHHHHHHHHcC
Q 040027          458 LIDGLCKSGRLKFAWELFCSLPHGVLVPNVVTYNI-MIQGLCNDGQMDKARDLFLDMEENAAAPDVITFDMLIHGFIRIN  536 (595)
Q Consensus       458 l~~~~~~~g~~~~A~~~~~~~~~~~~~p~~~~~~~-l~~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g  536 (595)
                      +.++|.+.+.++.|+.++-++..   +.+..+... +..-|.+.+.+--|.+.|..+...  .|++..|.         |
T Consensus       434 LArCyi~nkkP~lAW~~~lk~~t---~~e~fsLLqlIAn~CYk~~eFyyaaKAFd~lE~l--DP~pEnWe---------G  499 (557)
T KOG3785|consen  434 LARCYIRNKKPQLAWDMMLKTNT---PSERFSLLQLIANDCYKANEFYYAAKAFDELEIL--DPTPENWE---------G  499 (557)
T ss_pred             HHHHHHhcCCchHHHHHHHhcCC---chhHHHHHHHHHHHHHHHHHHHHHHHhhhHHHcc--CCCccccC---------C
Confidence            77889999999999988776653   223344433 346778889998899999888775  56766664         3


Q ss_pred             ChhHHHHHHHHHHHCCCCC-CHHHHHHHHHHHHhcCccc
Q 040027          537 EPSKVNELLHKMKEKKVMP-DASIVSIVVDLLVKNEISL  574 (595)
Q Consensus       537 ~~~~A~~~~~~~~~~~~~p-~~~~~~~l~~~~~~~g~~~  574 (595)
                      +-.....+|..+....-.| .....+-++..+...+..+
T Consensus       500 KRGACaG~f~~l~~~~~~~~p~~~~rEVvhllr~~~nsq  538 (557)
T KOG3785|consen  500 KRGACAGLFRQLANHKTDPIPISQMREVVHLLRMKPNSQ  538 (557)
T ss_pred             ccchHHHHHHHHHcCCCCCCchhHHHHHHHHHHhCCCch
Confidence            3344455666666443334 3466777777777777665

>KOG1156 consensus N-terminal acetyltransferase [Chromatin structure and dynamics]

Probab=99.59  E-value=5.1e-10  Score=106.70  Aligned_cols=451  Identities=14%  Similarity=0.106  Sum_probs=298.8

Q ss_pred             CChHHHHHHHHHHHHhCCCCCCHhhHHHHHHHHHcCCCchh--HHhhCCC---CCCHHHHHHHHHHHHhcCChhHHHHHH
Q 040027           45 ITPNEAFCIFDYMLRMHPSPPPVSSFNILLASLAKNKHYDT--RLNATGL---FPNLYTYNILINCFCKIGRVSLGFIAF  119 (595)
Q Consensus        45 ~~~~~A~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~--~~~~~~~---~~~~~~~~~l~~~~~~~g~~~~A~~~~  119 (595)
                      ++|...++..+.+++..|.  ++.+.......+...|+-.+  ..+..|+   ..+.+.|..++-.+....++++|+..|
T Consensus        21 kQYkkgLK~~~~iL~k~~e--HgeslAmkGL~L~~lg~~~ea~~~vr~glr~d~~S~vCwHv~gl~~R~dK~Y~eaiKcy   98 (700)
T KOG1156|consen   21 KQYKKGLKLIKQILKKFPE--HGESLAMKGLTLNCLGKKEEAYELVRLGLRNDLKSHVCWHVLGLLQRSDKKYDEAIKCY   98 (700)
T ss_pred             HHHHhHHHHHHHHHHhCCc--cchhHHhccchhhcccchHHHHHHHHHHhccCcccchhHHHHHHHHhhhhhHHHHHHHH
Confidence            6788888999999999998  55555555555666777666  4444444   357888998888888899999999999


Q ss_pred             HHHHhCCCCCCHHHHHHHHHHHHhcCCHhHHHHHHHHHHhcCCCCCHhhHHHHHHHHHhcCChhHHHHHHHHHHhcCCCC
Q 040027          120 GRILRSCFTPNAATFNSLIKGLHAESRIMEAAALFTKLKAFGCEPNVITYNTLINGLCRTGHTMIALNLFEEMANGNGEI  199 (595)
Q Consensus       120 ~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~  199 (595)
                      +.++..+ +.|...|.-+.-.-.+.|+++........+.+.. +.....|..++.++.-.|+...|..+++...+...  
T Consensus        99 ~nAl~~~-~dN~qilrDlslLQ~QmRd~~~~~~tr~~LLql~-~~~ra~w~~~Avs~~L~g~y~~A~~il~ef~~t~~--  174 (700)
T KOG1156|consen   99 RNALKIE-KDNLQILRDLSLLQIQMRDYEGYLETRNQLLQLR-PSQRASWIGFAVAQHLLGEYKMALEILEEFEKTQN--  174 (700)
T ss_pred             HHHHhcC-CCcHHHHHHHHHHHHHHHhhhhHHHHHHHHHHhh-hhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhc--
Confidence            9999986 5578888888777788899998888888887763 33566788888999999999999999999887652  


Q ss_pred             CccccCcHHHHHHH------HHHHHHcCCHhHHHHHHHHHhhCCCCCCHhHHHHHHHHHHhcCCHHHHHHHHHHHHHCCC
Q 040027          200 GVVCKPNTVTYSTI------IDGLCKEGFVDKAKALFLQMKDENINPDVVTYNSLIHGLCHANDWNEAKRLFIEMMDQGV  273 (595)
Q Consensus       200 ~~~~~~~~~~~~~l------~~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~~ll~~~~~~~~~~~A~~~~~~~~~~~~  273 (595)
                         ..++...+...      .......|..++|.+.+...... +......-..-...+.+.++.++|..+|..++..  
T Consensus       175 ---~~~s~~~~e~se~~Ly~n~i~~E~g~~q~ale~L~~~e~~-i~Dkla~~e~ka~l~~kl~~lEeA~~~y~~Ll~r--  248 (700)
T KOG1156|consen  175 ---TSPSKEDYEHSELLLYQNQILIEAGSLQKALEHLLDNEKQ-IVDKLAFEETKADLLMKLGQLEEAVKVYRRLLER--  248 (700)
T ss_pred             ---cCCCHHHHHHHHHHHHHHHHHHHcccHHHHHHHHHhhhhH-HHHHHHHhhhHHHHHHHHhhHHhHHHHHHHHHhh--
Confidence               13444444332      24456678888888877665443 1112223334557788999999999999999986  


Q ss_pred             CCCHhhHHHH-HHHHHhcCChHHHH-HHHHHHHHCCCCCCHHHHHHH-HHHHHhcCCHHHHHHHHHHHHhcCCCCCHHHH
Q 040027          274 QPSVVTFNVI-MDELCKNRKMDEAS-RLLDLMVQRGVRPNACTYNTL-MDGFCLMGKINRAEELFGSMESMGCKHDDVSY  350 (595)
Q Consensus       274 ~~~~~~~~~l-~~~~~~~g~~~~a~-~~~~~~~~~~~~~~~~~~~~l-~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~  350 (595)
                      .||...|... ..++.+-.+..++. .+|....+. ++ .......+ +.......-.+..-.++....+.|+++   ++
T Consensus       249 nPdn~~Yy~~l~~~lgk~~d~~~~lk~ly~~ls~~-y~-r~e~p~Rlplsvl~~eel~~~vdkyL~~~l~Kg~p~---vf  323 (700)
T KOG1156|consen  249 NPDNLDYYEGLEKALGKIKDMLEALKALYAILSEK-YP-RHECPRRLPLSVLNGEELKEIVDKYLRPLLSKGVPS---VF  323 (700)
T ss_pred             CchhHHHHHHHHHHHHHHhhhHHHHHHHHHHHhhc-Cc-ccccchhccHHHhCcchhHHHHHHHHHHHhhcCCCc---hh
Confidence            3565555544 44444333333444 666666553 11 11111111 111111222334445666667777544   34


Q ss_pred             HHHHHHHHhCCCHHHHHHHHHHHHH----CC----------CCCCHHHH--HHHHHHHHccCCHHHHHHHHHHHHHCCCC
Q 040027          351 NILINGYCKNKEVEEALSLYREMVS----KG----------IKPTVVTY--NTLFLGLFEIHQVEHALKLFDEMQRDGVA  414 (595)
Q Consensus       351 ~~l~~~~~~~~~~~~A~~~~~~~~~----~~----------~~~~~~~~--~~l~~~~~~~~~~~~a~~~~~~~~~~~~~  414 (595)
                      ..+...|-.....+-..++...+..    .|          -+|+...|  ..+.+.+-..|+++.|...++..+.+  .
T Consensus       324 ~dl~SLyk~p~k~~~le~Lvt~y~~~L~~~~~f~~~D~~~~E~PttllWt~y~laqh~D~~g~~~~A~~yId~AIdH--T  401 (700)
T KOG1156|consen  324 KDLRSLYKDPEKVAFLEKLVTSYQHSLSGTGMFNFLDDGKQEPPTTLLWTLYFLAQHYDKLGDYEVALEYIDLAIDH--T  401 (700)
T ss_pred             hhhHHHHhchhHhHHHHHHHHHHHhhcccccCCCcccccccCCchHHHHHHHHHHHHHHHcccHHHHHHHHHHHhcc--C
Confidence            4444444332222211111111111    11          14455444  45667788999999999999999876  4


Q ss_pred             CC-HHHHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCcCHHHHHHHHHHHHhcCChHHHHHHHHhcccCCCC--CC----H
Q 040027          415 AD-TRTYTTFIDGLCKNGYIIEAVELFRTLRILKCELDIQAYNCLIDGLCKSGRLKFAWELFCSLPHGVLV--PN----V  487 (595)
Q Consensus       415 ~~-~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~--p~----~  487 (595)
                      |+ ...|..-.+.+...|++++|..++++..+.+ .+|..+-..-+.-..++.+.++|.++.....+.|..  -|    .
T Consensus       402 PTliEly~~KaRI~kH~G~l~eAa~~l~ea~elD-~aDR~INsKcAKYmLrAn~i~eA~~~~skFTr~~~~~~~~L~~mq  480 (700)
T KOG1156|consen  402 PTLIELYLVKARIFKHAGLLDEAAAWLDEAQELD-TADRAINSKCAKYMLRANEIEEAEEVLSKFTREGFGAVNNLAEMQ  480 (700)
T ss_pred             chHHHHHHHHHHHHHhcCChHHHHHHHHHHHhcc-chhHHHHHHHHHHHHHccccHHHHHHHHHhhhcccchhhhHHHhh
Confidence            44 3556666678889999999999999999887 666666557777788999999999999988876531  11    1


Q ss_pred             HHHHHH--HHHHHhcCChhHHHHHHHHHHH
Q 040027          488 VTYNIM--IQGLCNDGQMDKARDLFLDMEE  515 (595)
Q Consensus       488 ~~~~~l--~~~~~~~g~~~~A~~~~~~~~~  515 (595)
                      -+|..+  +.+|.+.|++..|++-|..+..
T Consensus       481 cmWf~~E~g~ay~r~~k~g~ALKkfh~i~k  510 (700)
T KOG1156|consen  481 CMWFQLEDGEAYLRQNKLGLALKKFHEIEK  510 (700)
T ss_pred             hHHHhHhhhHHHHHHHHHHHHHHHHhhHHH
Confidence            133332  3567888888888877666544

>KOG4162 consensus Predicted calmodulin-binding protein [Signal transduction mechanisms]

Probab=99.58  E-value=5.7e-10  Score=108.56  Aligned_cols=434  Identities=13%  Similarity=0.040  Sum_probs=284.7

Q ss_pred             HHhcCChhHHHHHH----HHHHhCCCCCCHHHHHHHHHHHHhcCCHhHHHHHHHHHHhcCCCCCHhhHHHHHHHHHhcCC
Q 040027          106 FCKIGRVSLGFIAF----GRILRSCFTPNAATFNSLIKGLHAESRIMEAAALFTKLKAFGCEPNVITYNTLINGLCRTGH  181 (595)
Q Consensus       106 ~~~~g~~~~A~~~~----~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~  181 (595)
                      +.-..+.+++....    .++....+..|+..|..+.-++...|+++.+.+.|++....-+. ..+.|..+...|...|.
T Consensus       294 ~i~Re~~~d~ilslm~~~~k~r~~~~qnd~ai~d~Lt~al~~~g~f~~lae~fE~~~~~~~~-~~e~w~~~als~saag~  372 (799)
T KOG4162|consen  294 LIPRENIEDAILSLMLLLRKLRLKKFQNDAAIFDHLTFALSRCGQFEVLAEQFEQALPFSFG-EHERWYQLALSYSAAGS  372 (799)
T ss_pred             ccccccHHHHHHHHHHHHHHHHHhhhcchHHHHHHHHHHHHHHHHHHHHHHHHHHHhHhhhh-hHHHHHHHHHHHHHhcc
Confidence            34444555554333    33333345678889999999999999999999999998765333 67789999999999999


Q ss_pred             hhHHHHHHHHHHhcCCCCCccccCcHHHHHHHHHHHHH-cCCHhHHHHHHHHHhhC--CC--CCCHhHHHHHHHHHHhc-
Q 040027          182 TMIALNLFEEMANGNGEIGVVCKPNTVTYSTIIDGLCK-EGFVDKAKALFLQMKDE--NI--NPDVVTYNSLIHGLCHA-  255 (595)
Q Consensus       182 ~~~A~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~-~g~~~~A~~~~~~~~~~--~~--~~~~~~~~~ll~~~~~~-  255 (595)
                      ...|..+++.......     .++++..+...-..|.. .+..++++++..++...  +.  ......|..+.-+|... 
T Consensus       373 ~s~Av~ll~~~~~~~~-----~ps~~s~~Lmasklc~e~l~~~eegldYA~kai~~~~~~~~~l~~~~~l~lGi~y~~~A  447 (799)
T KOG4162|consen  373 DSKAVNLLRESLKKSE-----QPSDISVLLMASKLCIERLKLVEEGLDYAQKAISLLGGQRSHLKPRGYLFLGIAYGFQA  447 (799)
T ss_pred             chHHHHHHHhhccccc-----CCCcchHHHHHHHHHHhchhhhhhHHHHHHHHHHHhhhhhhhhhhhHHHHHHHHHHhHh
Confidence            9999999988776541     13445555444454544 46777777777776652  11  11344455555444432 


Q ss_pred             ----------CCHHHHHHHHHHHHHCCCCCCHhhHHHHHHHHHhcCChHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHhc
Q 040027          256 ----------NDWNEAKRLFIEMMDQGVQPSVVTFNVIMDELCKNRKMDEASRLLDLMVQRGVRPNACTYNTLMDGFCLM  325 (595)
Q Consensus       256 ----------~~~~~A~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~  325 (595)
                                ....++++.+++..+.+.. |+.....+.--|...++++.|.+...+..+.+...+...|..+...+...
T Consensus       448 ~~a~~~seR~~~h~kslqale~av~~d~~-dp~~if~lalq~A~~R~l~sAl~~~~eaL~l~~~~~~~~whLLALvlSa~  526 (799)
T KOG4162|consen  448 RQANLKSERDALHKKSLQALEEAVQFDPT-DPLVIFYLALQYAEQRQLTSALDYAREALALNRGDSAKAWHLLALVLSAQ  526 (799)
T ss_pred             hcCCChHHHHHHHHHHHHHHHHHHhcCCC-CchHHHHHHHHHHHHHhHHHHHHHHHHHHHhcCCccHHHHHHHHHHHhhh
Confidence                      1245677888888776432 33333444456788899999999999999986677888999999999999


Q ss_pred             CCHHHHHHHHHHHHhcCCCCCHHHHHHHHHHHHhCCCHHHHHHHHHHHHHC--CCCCCHHH------HHHHHHHHHccCC
Q 040027          326 GKINRAEELFGSMESMGCKHDDVSYNILINGYCKNKEVEEALSLYREMVSK--GIKPTVVT------YNTLFLGLFEIHQ  397 (595)
Q Consensus       326 ~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~~--~~~~~~~~------~~~l~~~~~~~~~  397 (595)
                      +++.+|+.+.+.....- +.|-.....-+..-...++.++++.....+...  ...+-..+      ...-.......++
T Consensus       527 kr~~~Al~vvd~al~E~-~~N~~l~~~~~~i~~~~~~~e~~l~t~~~~L~~we~~~~~q~~~~~g~~~~lk~~l~la~~q  605 (799)
T KOG4162|consen  527 KRLKEALDVVDAALEEF-GDNHVLMDGKIHIELTFNDREEALDTCIHKLALWEAEYGVQQTLDEGKLLRLKAGLHLALSQ  605 (799)
T ss_pred             hhhHHHHHHHHHHHHHh-hhhhhhchhhhhhhhhcccHHHHHHHHHHHHHHHHhhhhHhhhhhhhhhhhhhcccccCccc
Confidence            99999999998876541 122222222233334466666666655544321  00000000      0000000000111


Q ss_pred             HHHHHHHHHHH-----------------HHCCCC--CC------HHHHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCcCH
Q 040027          398 VEHALKLFDEM-----------------QRDGVA--AD------TRTYTTFIDGLCKNGYIIEAVELFRTLRILKCELDI  452 (595)
Q Consensus       398 ~~~a~~~~~~~-----------------~~~~~~--~~------~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~~~  452 (595)
                      ..++.+....+                 ......  |+      ...|......+.+.+..++|...+.++.+.. +...
T Consensus       606 ~~~a~s~sr~ls~l~a~~~~~~~se~~Lp~s~~~~~~~~~~~~~~~lwllaa~~~~~~~~~~~a~~CL~Ea~~~~-~l~~  684 (799)
T KOG4162|consen  606 PTDAISTSRYLSSLVASQLKSAGSELKLPSSTVLPGPDSLWYLLQKLWLLAADLFLLSGNDDEARSCLLEASKID-PLSA  684 (799)
T ss_pred             ccccchhhHHHHHHHHhhhhhcccccccCcccccCCCCchHHHHHHHHHHHHHHHHhcCCchHHHHHHHHHHhcc-hhhH
Confidence            11111111111                 000011  12      1344556667788888999998888887765 6667


Q ss_pred             HHHHHHHHHHHhcCChHHHHHHHHhcccCCCCCC-HHHHHHHHHHHHhcCChhHHHH--HHHHHHHcCCCCCHHHHHHHH
Q 040027          453 QAYNCLIDGLCKSGRLKFAWELFCSLPHGVLVPN-VVTYNIMIQGLCNDGQMDKARD--LFLDMEENAAAPDVITFDMLI  529 (595)
Q Consensus       453 ~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~p~-~~~~~~l~~~~~~~g~~~~A~~--~~~~~~~~~~~~~~~~~~~l~  529 (595)
                      ..|...+..+...|.+++|.+.|.....  +.|+ +....+++.++...|+..-|..  ++..+++.+ +.+...|..++
T Consensus       685 ~~~~~~G~~~~~~~~~~EA~~af~~Al~--ldP~hv~s~~Ala~~lle~G~~~la~~~~~L~dalr~d-p~n~eaW~~LG  761 (799)
T KOG4162|consen  685 SVYYLRGLLLEVKGQLEEAKEAFLVALA--LDPDHVPSMTALAELLLELGSPRLAEKRSLLSDALRLD-PLNHEAWYYLG  761 (799)
T ss_pred             HHHHHhhHHHHHHHhhHHHHHHHHHHHh--cCCCCcHHHHHHHHHHHHhCCcchHHHHHHHHHHHhhC-CCCHHHHHHHH
Confidence            7788888888889999999999998887  6776 5678888999999998887777  899999876 66789999999


Q ss_pred             HHHHHcCChhHHHHHHHHHHHC
Q 040027          530 HGFIRINEPSKVNELLHKMKEK  551 (595)
Q Consensus       530 ~~~~~~g~~~~A~~~~~~~~~~  551 (595)
                      ..+.+.|+.++|.+.|....+.
T Consensus       762 ~v~k~~Gd~~~Aaecf~aa~qL  783 (799)
T KOG4162|consen  762 EVFKKLGDSKQAAECFQAALQL  783 (799)
T ss_pred             HHHHHccchHHHHHHHHHHHhh
Confidence            9999999999999999988863

>KOG1156 consensus N-terminal acetyltransferase [Chromatin structure and dynamics]

Probab=99.55  E-value=2e-09  Score=102.74  Aligned_cols=450  Identities=14%  Similarity=0.072  Sum_probs=276.0

Q ss_pred             HHhcCChhHHHHHHHHHHhCCCCCCHHHHHHHHHHHHhcCCHhHHHHHHHHHHhcCCCCCHhhHHHHHHHHHhcCChhHH
Q 040027          106 FCKIGRVSLGFIAFGRILRSCFTPNAATFNSLIKGLHAESRIMEAAALFTKLKAFGCEPNVITYNTLINGLCRTGHTMIA  185 (595)
Q Consensus       106 ~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A  185 (595)
                      +...+++...+...+.+++. .+-...+.....-.+...|+.++|....+...+..+ .+...|+.+...+-...++++|
T Consensus        17 ~yE~kQYkkgLK~~~~iL~k-~~eHgeslAmkGL~L~~lg~~~ea~~~vr~glr~d~-~S~vCwHv~gl~~R~dK~Y~ea   94 (700)
T KOG1156|consen   17 CYETKQYKKGLKLIKQILKK-FPEHGESLAMKGLTLNCLGKKEEAYELVRLGLRNDL-KSHVCWHVLGLLQRSDKKYDEA   94 (700)
T ss_pred             HHHHHHHHhHHHHHHHHHHh-CCccchhHHhccchhhcccchHHHHHHHHHHhccCc-ccchhHHHHHHHHhhhhhHHHH
Confidence            44567888888888888774 333444443333345566888888887777776543 3667777777777778888888


Q ss_pred             HHHHHHHHhcCCCCCccccCcHHHHHHHHHHHHHcCCHhHHHHHHHHHhhCCCCCCHhHHHHHHHHHHhcCCHHHHHHHH
Q 040027          186 LNLFEEMANGNGEIGVVCKPNTVTYSTIIDGLCKEGFVDKAKALFLQMKDENINPDVVTYNSLIHGLCHANDWNEAKRLF  265 (595)
Q Consensus       186 ~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~~ll~~~~~~~~~~~A~~~~  265 (595)
                      ++.|..+...+       +.|...|.-+.-.-++.|+++........+.+.. +.....|..+..++.-.|+...|..+.
T Consensus        95 iKcy~nAl~~~-------~dN~qilrDlslLQ~QmRd~~~~~~tr~~LLql~-~~~ra~w~~~Avs~~L~g~y~~A~~il  166 (700)
T KOG1156|consen   95 IKCYRNALKIE-------KDNLQILRDLSLLQIQMRDYEGYLETRNQLLQLR-PSQRASWIGFAVAQHLLGEYKMALEIL  166 (700)
T ss_pred             HHHHHHHHhcC-------CCcHHHHHHHHHHHHHHHhhhhHHHHHHHHHHhh-hhhHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            88888888775       5667777777777777788877777776666642 224566777777777888888888888


Q ss_pred             HHHHHCC-CCCCHhhHHHH------HHHHHhcCChHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHH
Q 040027          266 IEMMDQG-VQPSVVTFNVI------MDELCKNRKMDEASRLLDLMVQRGVRPNACTYNTLMDGFCLMGKINRAEELFGSM  338 (595)
Q Consensus       266 ~~~~~~~-~~~~~~~~~~l------~~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~  338 (595)
                      +...+.. ..|+...+...      .....+.|..+.|++.+...... +......-..-...+.+.+++++|..++..+
T Consensus       167 ~ef~~t~~~~~s~~~~e~se~~Ly~n~i~~E~g~~q~ale~L~~~e~~-i~Dkla~~e~ka~l~~kl~~lEeA~~~y~~L  245 (700)
T KOG1156|consen  167 EEFEKTQNTSPSKEDYEHSELLLYQNQILIEAGSLQKALEHLLDNEKQ-IVDKLAFEETKADLLMKLGQLEEAVKVYRRL  245 (700)
T ss_pred             HHHHHhhccCCCHHHHHHHHHHHHHHHHHHHcccHHHHHHHHHhhhhH-HHHHHHHhhhHHHHHHHHhhHHhHHHHHHHH
Confidence            8777653 23444433321      23455677777777776655443 2212223334456677888888888888888


Q ss_pred             HhcCCCCCHHHHHHH-HHHHHhCCCHHHHH-HHHHHHHHCCCCCCHHHHHHHHHHHHc-cCCHHHHHHHHHHHHHCCCCC
Q 040027          339 ESMGCKHDDVSYNIL-INGYCKNKEVEEAL-SLYREMVSKGIKPTVVTYNTLFLGLFE-IHQVEHALKLFDEMQRDGVAA  415 (595)
Q Consensus       339 ~~~~~~~~~~~~~~l-~~~~~~~~~~~~A~-~~~~~~~~~~~~~~~~~~~~l~~~~~~-~~~~~~a~~~~~~~~~~~~~~  415 (595)
                      +..  .||...|... ..++.+-.+.-+++ .+|....+.  .|.......+-..... ..-.+...+++....+.|+++
T Consensus       246 l~r--nPdn~~Yy~~l~~~lgk~~d~~~~lk~ly~~ls~~--y~r~e~p~Rlplsvl~~eel~~~vdkyL~~~l~Kg~p~  321 (700)
T KOG1156|consen  246 LER--NPDNLDYYEGLEKALGKIKDMLEALKALYAILSEK--YPRHECPRRLPLSVLNGEELKEIVDKYLRPLLSKGVPS  321 (700)
T ss_pred             Hhh--CchhHHHHHHHHHHHHHHhhhHHHHHHHHHHHhhc--CcccccchhccHHHhCcchhHHHHHHHHHHHhhcCCCc
Confidence            876  3555554443 34443333333444 556655543  1222211111111111 222344455566666777654


Q ss_pred             CHHHHHHHHHHHHhcCCHHHHHHHHHHHH----H----cC----------CCcCHHHHH--HHHHHHHhcCChHHHHHHH
Q 040027          416 DTRTYTTFIDGLCKNGYIIEAVELFRTLR----I----LK----------CELDIQAYN--CLIDGLCKSGRLKFAWELF  475 (595)
Q Consensus       416 ~~~~~~~l~~~~~~~g~~~~A~~~~~~~~----~----~~----------~~~~~~~~~--~l~~~~~~~g~~~~A~~~~  475 (595)
                      -.   ..+...|-.-...+    +++++.    .    .+          -+|....|.  .++..+-..|+++.|...+
T Consensus       322 vf---~dl~SLyk~p~k~~----~le~Lvt~y~~~L~~~~~f~~~D~~~~E~PttllWt~y~laqh~D~~g~~~~A~~yI  394 (700)
T KOG1156|consen  322 VF---KDLRSLYKDPEKVA----FLEKLVTSYQHSLSGTGMFNFLDDGKQEPPTTLLWTLYFLAQHYDKLGDYEVALEYI  394 (700)
T ss_pred             hh---hhhHHHHhchhHhH----HHHHHHHHHHhhcccccCCCcccccccCCchHHHHHHHHHHHHHHHcccHHHHHHHH
Confidence            32   22322222211111    222221    0    00          145544443  4566678899999999999


Q ss_pred             HhcccCCCCCC-HHHHHHHHHHHHhcCChhHHHHHHHHHHHcCCCCCHHHHHHHHHHHHHcCChhHHHHHHHHHHHCCCC
Q 040027          476 CSLPHGVLVPN-VVTYNIMIQGLCNDGQMDKARDLFLDMEENAAAPDVITFDMLIHGFIRINEPSKVNELLHKMKEKKVM  554 (595)
Q Consensus       476 ~~~~~~~~~p~-~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~  554 (595)
                      +.+++  ..|+ +..|..-.+.+.+.|++++|..++++..+.+ .+|...-..-+.-..++++.++|.++.......|..
T Consensus       395 d~AId--HTPTliEly~~KaRI~kH~G~l~eAa~~l~ea~elD-~aDR~INsKcAKYmLrAn~i~eA~~~~skFTr~~~~  471 (700)
T KOG1156|consen  395 DLAID--HTPTLIELYLVKARIFKHAGLLDEAAAWLDEAQELD-TADRAINSKCAKYMLRANEIEEAEEVLSKFTREGFG  471 (700)
T ss_pred             HHHhc--cCchHHHHHHHHHHHHHhcCChHHHHHHHHHHHhcc-chhHHHHHHHHHHHHHccccHHHHHHHHHhhhcccc
Confidence            99988  4666 4566666788899999999999999998875 455544445666777889999999999888876642


Q ss_pred             C--CHH----HHHH--HHHHHHhcCcccccchHH
Q 040027          555 P--DAS----IVSI--VVDLLVKNEISLKSLPSF  580 (595)
Q Consensus       555 p--~~~----~~~~--l~~~~~~~g~~~~~i~~~  580 (595)
                      .  +-.    .|..  -+.+|.|.|++-.+++++
T Consensus       472 ~~~~L~~mqcmWf~~E~g~ay~r~~k~g~ALKkf  505 (700)
T KOG1156|consen  472 AVNNLAEMQCMWFQLEDGEAYLRQNKLGLALKKF  505 (700)
T ss_pred             hhhhHHHhhhHHHhHhhhHHHHHHHHHHHHHHHH
Confidence            1  111    1111  255677777766555544

>KOG1174 consensus Anaphase-promoting complex (APC), subunit 7 [Cell cycle control, cell division, chromosome partitioning; Posttranslational modification, protein turnover, chaperones]

Probab=99.54  E-value=5.3e-09  Score=94.42  Aligned_cols=301  Identities=13%  Similarity=0.028  Sum_probs=224.5

Q ss_pred             HHhcCCHHHHHHHHHHHHHC-CCCCCHhhHHHHHHHHHhcCChHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHhcCCHHH
Q 040027          252 LCHANDWNEAKRLFIEMMDQ-GVQPSVVTFNVIMDELCKNRKMDEASRLLDLMVQRGVRPNACTYNTLMDGFCLMGKINR  330 (595)
Q Consensus       252 ~~~~~~~~~A~~~~~~~~~~-~~~~~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~  330 (595)
                      .+..++...+...+-.+... .++.|......+...+...|+..+|...|+.....+.. +..........+.+.|+.+.
T Consensus       206 q~~~~~hs~a~~t~l~le~~~~lr~NvhLl~~lak~~~~~Gdn~~a~~~Fe~~~~~dpy-~i~~MD~Ya~LL~~eg~~e~  284 (564)
T KOG1174|consen  206 QMFNFKHSDASQTFLMLHDNTTLRCNEHLMMALGKCLYYNGDYFQAEDIFSSTLCANPD-NVEAMDLYAVLLGQEGGCEQ  284 (564)
T ss_pred             HHHhcccchhhhHHHHHHhhccCCccHHHHHHHhhhhhhhcCchHHHHHHHHHhhCChh-hhhhHHHHHHHHHhccCHhh
Confidence            33445555555554444333 35667788889999999999999999999998775311 22333333445567888888


Q ss_pred             HHHHHHHHHhcCCCCCHHHHHHHHHHHHhCCCHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHccCCHHHHHHHHHHHHH
Q 040027          331 AEELFGSMESMGCKHDDVSYNILINGYCKNKEVEEALSLYREMVSKGIKPTVVTYNTLFLGLFEIHQVEHALKLFDEMQR  410 (595)
Q Consensus       331 a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~  410 (595)
                      ...+...+.... +.....|..-+......+++..|+.+-++.++.+.. +...+..-...+...+++++|.-.|+....
T Consensus       285 ~~~L~~~Lf~~~-~~ta~~wfV~~~~l~~~K~~~rAL~~~eK~I~~~~r-~~~alilKG~lL~~~~R~~~A~IaFR~Aq~  362 (564)
T KOG1174|consen  285 DSALMDYLFAKV-KYTASHWFVHAQLLYDEKKFERALNFVEKCIDSEPR-NHEALILKGRLLIALERHTQAVIAFRTAQM  362 (564)
T ss_pred             HHHHHHHHHhhh-hcchhhhhhhhhhhhhhhhHHHHHHHHHHHhccCcc-cchHHHhccHHHHhccchHHHHHHHHHHHh
Confidence            888888876542 234445555556666788999999999998886444 556666666788899999999999999887


Q ss_pred             CCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCcCHHHHHHHH-HHHHhc-CChHHHHHHHHhcccCCCCCC-H
Q 040027          411 DGVAADTRTYTTFIDGLCKNGYIIEAVELFRTLRILKCELDIQAYNCLI-DGLCKS-GRLKFAWELFCSLPHGVLVPN-V  487 (595)
Q Consensus       411 ~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~~l~-~~~~~~-g~~~~A~~~~~~~~~~~~~p~-~  487 (595)
                      .. |-+..+|..++..|...|++.+|..+-+...+.- +.+..+...++ ..+.-. .--++|..++++...  +.|+ .
T Consensus       363 La-p~rL~~Y~GL~hsYLA~~~~kEA~~~An~~~~~~-~~sA~~LtL~g~~V~~~dp~~rEKAKkf~ek~L~--~~P~Y~  438 (564)
T KOG1174|consen  363 LA-PYRLEIYRGLFHSYLAQKRFKEANALANWTIRLF-QNSARSLTLFGTLVLFPDPRMREKAKKFAEKSLK--INPIYT  438 (564)
T ss_pred             cc-hhhHHHHHHHHHHHHhhchHHHHHHHHHHHHHHh-hcchhhhhhhcceeeccCchhHHHHHHHHHhhhc--cCCccH
Confidence            62 5678999999999999999999998888776542 55666666553 333322 335789999999887  6787 4


Q ss_pred             HHHHHHHHHHHhcCChhHHHHHHHHHHHcCCCCCHHHHHHHHHHHHHcCChhHHHHHHHHHHHCCCCCC-HHHHHHH
Q 040027          488 VTYNIMIQGLCNDGQMDKARDLFLDMEENAAAPDVITFDMLIHGFIRINEPSKVNELLHKMKEKKVMPD-ASIVSIV  563 (595)
Q Consensus       488 ~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~p~-~~~~~~l  563 (595)
                      ...+.+...+...|..+.++.++++.+..  .||....+.|++.+...+.+++|...|..++..  .|. ..+..-+
T Consensus       439 ~AV~~~AEL~~~Eg~~~D~i~LLe~~L~~--~~D~~LH~~Lgd~~~A~Ne~Q~am~~y~~ALr~--dP~~~~sl~Gl  511 (564)
T KOG1174|consen  439 PAVNLIAELCQVEGPTKDIIKLLEKHLII--FPDVNLHNHLGDIMRAQNEPQKAMEYYYKALRQ--DPKSKRTLRGL  511 (564)
T ss_pred             HHHHHHHHHHHhhCccchHHHHHHHHHhh--ccccHHHHHHHHHHHHhhhHHHHHHHHHHHHhc--CccchHHHHHH
Confidence            56778888999999999999999999884  688899999999999999999999999999974  464 4444443

>PRK12370 invasion protein regulator; Provisional

Probab=99.52  E-value=1e-11  Score=126.18  Aligned_cols=261  Identities=13%  Similarity=0.071  Sum_probs=169.8

Q ss_pred             CChHHHHHHHHHHHHhCCCCCCHhhHHHHHHHHHcCCCchhHHhhCCCCCCHHHHHHHHHHHHhcCChhHHHHHHHHHHh
Q 040027           45 ITPNEAFCIFDYMLRMHPSPPPVSSFNILLASLAKNKHYDTRLNATGLFPNLYTYNILINCFCKIGRVSLGFIAFGRILR  124 (595)
Q Consensus        45 ~~~~~A~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~  124 (595)
                      +++++|...|+++++.+|+  ++..|..+..++...+..       |             .+...+++++|...++++++
T Consensus       275 ~~~~~A~~~~~~Al~ldP~--~a~a~~~La~~~~~~~~~-------g-------------~~~~~~~~~~A~~~~~~Al~  332 (553)
T PRK12370        275 YSLQQALKLLTQCVNMSPN--SIAPYCALAECYLSMAQM-------G-------------IFDKQNAMIKAKEHAIKATE  332 (553)
T ss_pred             HHHHHHHHHHHHHHhcCCc--cHHHHHHHHHHHHHHHHc-------C-------------CcccchHHHHHHHHHHHHHh
Confidence            4466788888888888877  666665555443322110       0             01134567889999999988


Q ss_pred             CCCCCCHHHHHHHHHHHHhcCCHhHHHHHHHHHHhcCCCCCHhhHHHHHHHHHhcCChhHHHHHHHHHHhcCCCCCcccc
Q 040027          125 SCFTPNAATFNSLIKGLHAESRIMEAAALFTKLKAFGCEPNVITYNTLINGLCRTGHTMIALNLFEEMANGNGEIGVVCK  204 (595)
Q Consensus       125 ~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~  204 (595)
                      .. +.+..++..+...+...|++++|...|+++.+.+ +.+...+..+...+...|++++|+..++++.+.+       |
T Consensus       333 ld-P~~~~a~~~lg~~~~~~g~~~~A~~~~~~Al~l~-P~~~~a~~~lg~~l~~~G~~~eAi~~~~~Al~l~-------P  403 (553)
T PRK12370        333 LD-HNNPQALGLLGLINTIHSEYIVGSLLFKQANLLS-PISADIKYYYGWNLFMAGQLEEALQTINECLKLD-------P  403 (553)
T ss_pred             cC-CCCHHHHHHHHHHHHHccCHHHHHHHHHHHHHhC-CCCHHHHHHHHHHHHHCCCHHHHHHHHHHHHhcC-------C
Confidence            85 5577788888888888899999999999988875 3367778888888889999999999999988876       3


Q ss_pred             CcHHHHHHHHHHHHHcCCHhHHHHHHHHHhhCCCCCCHhHHHHHHHHHHhcCCHHHHHHHHHHHHHCCCCCCHhhHHHHH
Q 040027          205 PNTVTYSTIIDGLCKEGFVDKAKALFLQMKDENINPDVVTYNSLIHGLCHANDWNEAKRLFIEMMDQGVQPSVVTFNVIM  284 (595)
Q Consensus       205 ~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~~ll~~~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~~l~  284 (595)
                      .+...+..++..+...|++++|...++++.....+.+...+..+..++...|++++|...+.++... .+.+....+.+.
T Consensus       404 ~~~~~~~~~~~~~~~~g~~eeA~~~~~~~l~~~~p~~~~~~~~la~~l~~~G~~~eA~~~~~~~~~~-~~~~~~~~~~l~  482 (553)
T PRK12370        404 TRAAAGITKLWITYYHTGIDDAIRLGDELRSQHLQDNPILLSMQVMFLSLKGKHELARKLTKEISTQ-EITGLIAVNLLY  482 (553)
T ss_pred             CChhhHHHHHHHHHhccCHHHHHHHHHHHHHhccccCHHHHHHHHHHHHhCCCHHHHHHHHHHhhhc-cchhHHHHHHHH
Confidence            3333444445556667888889888888776532224555677777888888888888888877654 111233444555


Q ss_pred             HHHHhcCChHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHhc
Q 040027          285 DELCKNRKMDEASRLLDLMVQRGVRPNACTYNTLMDGFCLMGKINRAEELFGSMESM  341 (595)
Q Consensus       285 ~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~  341 (595)
                      ..+...|  +.+...++.+.+..-. ...........|.-.|+-+.+..+ +++.+.
T Consensus       483 ~~~~~~g--~~a~~~l~~ll~~~~~-~~~~~~~~~~~~~~~g~~~~~~~~-~~~~~~  535 (553)
T PRK12370        483 AEYCQNS--ERALPTIREFLESEQR-IDNNPGLLPLVLVAHGEAIAEKMW-NKFKNE  535 (553)
T ss_pred             HHHhccH--HHHHHHHHHHHHHhhH-hhcCchHHHHHHHHHhhhHHHHHH-HHhhcc
Confidence            5566666  4666666665553110 111111133444455665555554 555543

>KOG1129 consensus TPR repeat-containing protein [General function prediction only]

Probab=99.51  E-value=2.1e-12  Score=112.15  Aligned_cols=233  Identities=15%  Similarity=0.073  Sum_probs=196.3

Q ss_pred             HHHHHHHHhcCCHHHHHHHHHHHHhcCCCCCHHHHHHHHHHHHhCCCHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHcc
Q 040027          316 NTLMDGFCLMGKINRAEELFGSMESMGCKHDDVSYNILINGYCKNKEVEEALSLYREMVSKGIKPTVVTYNTLFLGLFEI  395 (595)
Q Consensus       316 ~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~~l~~~~~~~  395 (595)
                      +.+.++|.+.|-+.+|...++..++.  .|-+.+|..|..+|.+..++..|+.++.+-++. .+.++.......+.+...
T Consensus       227 ~Q~gkCylrLgm~r~AekqlqssL~q--~~~~dTfllLskvY~ridQP~~AL~~~~~gld~-fP~~VT~l~g~ARi~eam  303 (478)
T KOG1129|consen  227 QQMGKCYLRLGMPRRAEKQLQSSLTQ--FPHPDTFLLLSKVYQRIDQPERALLVIGEGLDS-FPFDVTYLLGQARIHEAM  303 (478)
T ss_pred             HHHHHHHHHhcChhhhHHHHHHHhhc--CCchhHHHHHHHHHHHhccHHHHHHHHhhhhhc-CCchhhhhhhhHHHHHHH
Confidence            56788999999999999999988876  677889999999999999999999999988876 333555566677788889


Q ss_pred             CCHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCcCHHHHHHHHHHHHhcCChHHHHHHH
Q 040027          396 HQVEHALKLFDEMQRDGVAADTRTYTTFIDGLCKNGYIIEAVELFRTLRILKCELDIQAYNCLIDGLCKSGRLKFAWELF  475 (595)
Q Consensus       396 ~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~  475 (595)
                      ++.+++.++|+...+.. +.+.+....+...|.-.++++-|+..|++++..| ..++..|+.+.-+|.-.+++|-++.-|
T Consensus       304 ~~~~~a~~lYk~vlk~~-~~nvEaiAcia~~yfY~~~PE~AlryYRRiLqmG-~~speLf~NigLCC~yaqQ~D~~L~sf  381 (478)
T KOG1129|consen  304 EQQEDALQLYKLVLKLH-PINVEAIACIAVGYFYDNNPEMALRYYRRILQMG-AQSPELFCNIGLCCLYAQQIDLVLPSF  381 (478)
T ss_pred             HhHHHHHHHHHHHHhcC-CccceeeeeeeeccccCCChHHHHHHHHHHHHhc-CCChHHHhhHHHHHHhhcchhhhHHHH
Confidence            99999999999998873 5666777777778888999999999999999998 568999999999999999999999999


Q ss_pred             HhcccCCCCCC--HHHHHHHHHHHHhcCChhHHHHHHHHHHHcCCCCCHHHHHHHHHHHHHcCChhHHHHHHHHHHHCCC
Q 040027          476 CSLPHGVLVPN--VVTYNIMIQGLCNDGQMDKARDLFLDMEENAAAPDVITFDMLIHGFIRINEPSKVNELLHKMKEKKV  553 (595)
Q Consensus       476 ~~~~~~~~~p~--~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~  553 (595)
                      +++...--.|+  ..+|..+.......||+.-|.+.|+-.+..+ +.+...++.|.-.-.+.|+.++|..++..+...  
T Consensus       382 ~RAlstat~~~~aaDvWYNlg~vaV~iGD~nlA~rcfrlaL~~d-~~h~ealnNLavL~~r~G~i~~Arsll~~A~s~--  458 (478)
T KOG1129|consen  382 QRALSTATQPGQAADVWYNLGFVAVTIGDFNLAKRCFRLALTSD-AQHGEALNNLAVLAARSGDILGARSLLNAAKSV--  458 (478)
T ss_pred             HHHHhhccCcchhhhhhhccceeEEeccchHHHHHHHHHHhccC-cchHHHHHhHHHHHhhcCchHHHHHHHHHhhhh--
Confidence            98877433344  5789999988889999999999999998875 556788888888888999999999999998863  


Q ss_pred             CCC
Q 040027          554 MPD  556 (595)
Q Consensus       554 ~p~  556 (595)
                      .|+
T Consensus       459 ~P~  461 (478)
T KOG1129|consen  459 MPD  461 (478)
T ss_pred             Ccc
Confidence            455

>KOG1129 consensus TPR repeat-containing protein [General function prediction only]

Probab=99.51  E-value=8.6e-12  Score=108.48  Aligned_cols=230  Identities=15%  Similarity=0.019  Sum_probs=172.4

Q ss_pred             HHHHHHHHhcCCHhHHHHHHHHHHhcCCCCCHhhHHHHHHHHHhcCChhHHHHHHHHHHhcCCCCCccccCcHHHHHHHH
Q 040027          135 NSLIKGLHAESRIMEAAALFTKLKAFGCEPNVITYNTLINGLCRTGHTMIALNLFEEMANGNGEIGVVCKPNTVTYSTII  214 (595)
Q Consensus       135 ~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~~~~~~~~l~  214 (595)
                      +.+..+|.+.|.+.+|.+.++..++.  .|-+.+|..|...|.+..+...|+.+|.+.++..       |.++.......
T Consensus       227 ~Q~gkCylrLgm~r~AekqlqssL~q--~~~~dTfllLskvY~ridQP~~AL~~~~~gld~f-------P~~VT~l~g~A  297 (478)
T KOG1129|consen  227 QQMGKCYLRLGMPRRAEKQLQSSLTQ--FPHPDTFLLLSKVYQRIDQPERALLVIGEGLDSF-------PFDVTYLLGQA  297 (478)
T ss_pred             HHHHHHHHHhcChhhhHHHHHHHhhc--CCchhHHHHHHHHHHHhccHHHHHHHHhhhhhcC-------CchhhhhhhhH
Confidence            46778888888888888888887776  5566777888888888888888888888877753       55555566677


Q ss_pred             HHHHHcCCHhHHHHHHHHHhhCCCCCCHhHHHHHHHHHHhcCCHHHHHHHHHHHHHCCCCCCHhhHHHHHHHHHhcCChH
Q 040027          215 DGLCKEGFVDKAKALFLQMKDENINPDVVTYNSLIHGLCHANDWNEAKRLFIEMMDQGVQPSVVTFNVIMDELCKNRKMD  294 (595)
Q Consensus       215 ~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~~ll~~~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~  294 (595)
                      +++-..++.++|.++|+...+.. +.+++....+...|.-.++++-|+.+|+.+++.|+. ++..|+.+.-+|.-.++++
T Consensus       298 Ri~eam~~~~~a~~lYk~vlk~~-~~nvEaiAcia~~yfY~~~PE~AlryYRRiLqmG~~-speLf~NigLCC~yaqQ~D  375 (478)
T KOG1129|consen  298 RIHEAMEQQEDALQLYKLVLKLH-PINVEAIACIAVGYFYDNNPEMALRYYRRILQMGAQ-SPELFCNIGLCCLYAQQID  375 (478)
T ss_pred             HHHHHHHhHHHHHHHHHHHHhcC-CccceeeeeeeeccccCCChHHHHHHHHHHHHhcCC-ChHHHhhHHHHHHhhcchh
Confidence            77778888888888888877653 335666666666777778888888888888888776 7777888888888888888


Q ss_pred             HHHHHHHHHHHCCCCC--CHHHHHHHHHHHHhcCCHHHHHHHHHHHHhcCCCCCHHHHHHHHHHHHhCCCHHHHHHHHHH
Q 040027          295 EASRLLDLMVQRGVRP--NACTYNTLMDGFCLMGKINRAEELFGSMESMGCKHDDVSYNILINGYCKNKEVEEALSLYRE  372 (595)
Q Consensus       295 ~a~~~~~~~~~~~~~~--~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~A~~~~~~  372 (595)
                      -++..|.+....--.|  -..+|..+.......||+..|.+.|+..+..+ +.....++.|.-.-.+.|++++|..++..
T Consensus       376 ~~L~sf~RAlstat~~~~aaDvWYNlg~vaV~iGD~nlA~rcfrlaL~~d-~~h~ealnNLavL~~r~G~i~~Arsll~~  454 (478)
T KOG1129|consen  376 LVLPSFQRALSTATQPGQAADVWYNLGFVAVTIGDFNLAKRCFRLALTSD-AQHGEALNNLAVLAARSGDILGARSLLNA  454 (478)
T ss_pred             hhHHHHHHHHhhccCcchhhhhhhccceeEEeccchHHHHHHHHHHhccC-cchHHHHHhHHHHHhhcCchHHHHHHHHH
Confidence            8888888777653222  24567777777777888888888888877664 34556778887777888888888888877


Q ss_pred             HHHC
Q 040027          373 MVSK  376 (595)
Q Consensus       373 ~~~~  376 (595)
                      ....
T Consensus       455 A~s~  458 (478)
T KOG1129|consen  455 AKSV  458 (478)
T ss_pred             hhhh
Confidence            7654

>KOG1174 consensus Anaphase-promoting complex (APC), subunit 7 [Cell cycle control, cell division, chromosome partitioning; Posttranslational modification, protein turnover, chaperones]

Probab=99.50  E-value=2.4e-09  Score=96.56  Aligned_cols=400  Identities=14%  Similarity=0.092  Sum_probs=259.9

Q ss_pred             CHhhHHHHHHHHHhcCChhHHHHHHHHHHhcCCCCCccccCcHHHHHHHHHHHHHc-CCHhHHHHHHHHHhhCCCCCCHh
Q 040027          165 NVITYNTLINGLCRTGHTMIALNLFEEMANGNGEIGVVCKPNTVTYSTIIDGLCKE-GFVDKAKALFLQMKDENINPDVV  243 (595)
Q Consensus       165 ~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~-g~~~~A~~~~~~~~~~~~~~~~~  243 (595)
                      +.......+..|...++.+.|+.++.+.+...        ..+. .+.++..+.+. ++-.++.--+.+.+.. .+.-..
T Consensus        96 ~~e~~r~~aecy~~~~n~~~Ai~~l~~~p~t~--------r~p~-inlMla~l~~~g~r~~~~vl~ykevvre-cp~aL~  165 (564)
T KOG1174|consen   96 DAEQRRRAAECYRQIGNTDMAIETLLQVPPTL--------RSPR-INLMLARLQHHGSRHKEAVLAYKEVIRE-CPMALQ  165 (564)
T ss_pred             cHHHHHHHHHHHHHHccchHHHHHHhcCCccc--------cchh-HHHHHHHHHhccccccHHHHhhhHHHHh-cchHHH
Confidence            44455667778888888888888877765432        1122 23333333332 2222232223333222 111111


Q ss_pred             HHHHHHHHHHhcCCHHHHHHHHHHHHHCCCCCCHhhHHHHHHHH--HhcCChHHHHHHHHHHHHC-CCCCCHHHHHHHHH
Q 040027          244 TYNSLIHGLCHANDWNEAKRLFIEMMDQGVQPSVVTFNVIMDEL--CKNRKMDEASRLLDLMVQR-GVRPNACTYNTLMD  320 (595)
Q Consensus       244 ~~~~ll~~~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~~l~~~~--~~~g~~~~a~~~~~~~~~~-~~~~~~~~~~~l~~  320 (595)
                      ....++..-.+ | .+.+   -..|-...++|........+.++  +..++...+...+-.+... -.+-|......+..
T Consensus       166 ~i~~ll~l~v~-g-~e~~---S~~m~~~~~~~~~dwls~wika~Aq~~~~~hs~a~~t~l~le~~~~lr~NvhLl~~lak  240 (564)
T KOG1174|consen  166 VIEALLELGVN-G-NEIN---SLVMHAATVPDHFDWLSKWIKALAQMFNFKHSDASQTFLMLHDNTTLRCNEHLMMALGK  240 (564)
T ss_pred             HHHHHHHHhhc-c-hhhh---hhhhhheecCCCccHHHHHHHHHHHHHhcccchhhhHHHHHHhhccCCccHHHHHHHhh
Confidence            11111111111 1 1111   11122222344444444444433  3444444444444333332 36678889999999


Q ss_pred             HHHhcCCHHHHHHHHHHHHhcCCCCCHHHHHHHHHHHHhCCCHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHccCCHHH
Q 040027          321 GFCLMGKINRAEELFGSMESMGCKHDDVSYNILINGYCKNKEVEEALSLYREMVSKGIKPTVVTYNTLFLGLFEIHQVEH  400 (595)
Q Consensus       321 ~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~  400 (595)
                      ++...|+.++|+..|++..-.+ +.+..........+.+.|+++....+...+.... +-+...|..-+......++++.
T Consensus       241 ~~~~~Gdn~~a~~~Fe~~~~~d-py~i~~MD~Ya~LL~~eg~~e~~~~L~~~Lf~~~-~~ta~~wfV~~~~l~~~K~~~r  318 (564)
T KOG1174|consen  241 CLYYNGDYFQAEDIFSSTLCAN-PDNVEAMDLYAVLLGQEGGCEQDSALMDYLFAKV-KYTASHWFVHAQLLYDEKKFER  318 (564)
T ss_pred             hhhhhcCchHHHHHHHHHhhCC-hhhhhhHHHHHHHHHhccCHhhHHHHHHHHHhhh-hcchhhhhhhhhhhhhhhhHHH
Confidence            9999999999999999988663 2333344445556678899999988888887642 1234445555566677889999


Q ss_pred             HHHHHHHHHHCCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCcCHHHHHHHHHHHHhcCChHHHHHHHHhccc
Q 040027          401 ALKLFDEMQRDGVAADTRTYTTFIDGLCKNGYIIEAVELFRTLRILKCELDIQAYNCLIDGLCKSGRLKFAWELFCSLPH  480 (595)
Q Consensus       401 a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~  480 (595)
                      |+.+-++.++.+ +-+...+..-...+...|+.++|.-.|+.+.... |-+...|..|+..|...|++.+|.-.-+....
T Consensus       319 AL~~~eK~I~~~-~r~~~alilKG~lL~~~~R~~~A~IaFR~Aq~La-p~rL~~Y~GL~hsYLA~~~~kEA~~~An~~~~  396 (564)
T KOG1174|consen  319 ALNFVEKCIDSE-PRNHEALILKGRLLIALERHTQAVIAFRTAQMLA-PYRLEIYRGLFHSYLAQKRFKEANALANWTIR  396 (564)
T ss_pred             HHHHHHHHhccC-cccchHHHhccHHHHhccchHHHHHHHHHHHhcc-hhhHHHHHHHHHHHHhhchHHHHHHHHHHHHH
Confidence            999999888764 4455666666778889999999999999998775 67899999999999999999999888776655


Q ss_pred             CCCCCCHHHHHHHH-HHHH-hcCChhHHHHHHHHHHHcCCCCC-HHHHHHHHHHHHHcCChhHHHHHHHHHHHCCCCCCH
Q 040027          481 GVLVPNVVTYNIMI-QGLC-NDGQMDKARDLFLDMEENAAAPD-VITFDMLIHGFIRINEPSKVNELLHKMKEKKVMPDA  557 (595)
Q Consensus       481 ~~~~p~~~~~~~l~-~~~~-~~g~~~~A~~~~~~~~~~~~~~~-~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~p~~  557 (595)
                      . +..+..+...+. ..+. .-.--++|.+++++.+..  .|+ ......+...+...|+++++..++++.+.  ..||.
T Consensus       397 ~-~~~sA~~LtL~g~~V~~~dp~~rEKAKkf~ek~L~~--~P~Y~~AV~~~AEL~~~Eg~~~D~i~LLe~~L~--~~~D~  471 (564)
T KOG1174|consen  397 L-FQNSARSLTLFGTLVLFPDPRMREKAKKFAEKSLKI--NPIYTPAVNLIAELCQVEGPTKDIIKLLEKHLI--IFPDV  471 (564)
T ss_pred             H-hhcchhhhhhhcceeeccCchhHHHHHHHHHhhhcc--CCccHHHHHHHHHHHHhhCccchHHHHHHHHHh--hcccc
Confidence            2 233455554442 3333 233457899999988875  465 45667788889999999999999999996  67999


Q ss_pred             HHHHHHHHHHHhcCcccccchHHHHhhhhcc
Q 040027          558 SIVSIVVDLLVKNEISLKSLPSFLVQERQGE  588 (595)
Q Consensus       558 ~~~~~l~~~~~~~g~~~~~i~~~~~~~~~~~  588 (595)
                      .....+++++...+.+++..+.+...-+..+
T Consensus       472 ~LH~~Lgd~~~A~Ne~Q~am~~y~~ALr~dP  502 (564)
T KOG1174|consen  472 NLHNHLGDIMRAQNEPQKAMEYYYKALRQDP  502 (564)
T ss_pred             HHHHHHHHHHHHhhhHHHHHHHHHHHHhcCc
Confidence            9999999999999999977777665554443

>TIGR02521 type_IV_pilW type IV pilus biogenesis/stability protein PilW

Probab=99.50  E-value=4.6e-11  Score=108.41  Aligned_cols=203  Identities=11%  Similarity=0.045  Sum_probs=131.9

Q ss_pred             CCHHHHHHHHHHHHhcCChhHHHHHHHHHHhCCCCCCHHHHHHHHHHHHhcCCHhHHHHHHHHHHhcCCCCCHhhHHHHH
Q 040027           94 PNLYTYNILINCFCKIGRVSLGFIAFGRILRSCFTPNAATFNSLIKGLHAESRIMEAAALFTKLKAFGCEPNVITYNTLI  173 (595)
Q Consensus        94 ~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~~l~  173 (595)
                      .....+..+...+...|++++|...++++.+.. +.+...+..+...+...|++++|.+.+++..... +.+...+..+.
T Consensus        29 ~~~~~~~~la~~~~~~~~~~~A~~~~~~~l~~~-p~~~~~~~~la~~~~~~~~~~~A~~~~~~al~~~-~~~~~~~~~~~  106 (234)
T TIGR02521        29 KAAKIRVQLALGYLEQGDLEVAKENLDKALEHD-PDDYLAYLALALYYQQLGELEKAEDSFRRALTLN-PNNGDVLNNYG  106 (234)
T ss_pred             cHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHhC-cccHHHHHHHHHHHHHcCCHHHHHHHHHHHHhhC-CCCHHHHHHHH
Confidence            345667777777777888888888888777663 3456666677777777777777777777777654 23556666677


Q ss_pred             HHHHhcCChhHHHHHHHHHHhcCCCCCccccCcHHHHHHHHHHHHHcCCHhHHHHHHHHHhhCCCCCCHhHHHHHHHHHH
Q 040027          174 NGLCRTGHTMIALNLFEEMANGNGEIGVVCKPNTVTYSTIIDGLCKEGFVDKAKALFLQMKDENINPDVVTYNSLIHGLC  253 (595)
Q Consensus       174 ~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~~ll~~~~  253 (595)
                      ..+...|++++|.+.++++.....     .+.....+..+..++...|++++|...+++..... +.+...+..+...+.
T Consensus       107 ~~~~~~g~~~~A~~~~~~~~~~~~-----~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~-~~~~~~~~~la~~~~  180 (234)
T TIGR02521       107 TFLCQQGKYEQAMQQFEQAIEDPL-----YPQPARSLENAGLCALKAGDFDKAEKYLTRALQID-PQRPESLLELAELYY  180 (234)
T ss_pred             HHHHHcccHHHHHHHHHHHHhccc-----cccchHHHHHHHHHHHHcCCHHHHHHHHHHHHHhC-cCChHHHHHHHHHHH
Confidence            777777777777777777765321     12234455666666777777777777777766543 224455666666677


Q ss_pred             hcCCHHHHHHHHHHHHHCCCCCCHhhHHHHHHHHHhcCChHHHHHHHHHHHH
Q 040027          254 HANDWNEAKRLFIEMMDQGVQPSVVTFNVIMDELCKNRKMDEASRLLDLMVQ  305 (595)
Q Consensus       254 ~~~~~~~A~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~  305 (595)
                      ..|++++|...+++.... .+.+...+..+...+...|+.++|..+.+.+..
T Consensus       181 ~~~~~~~A~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~a~~~~~~~~~  231 (234)
T TIGR02521       181 LRGQYKDARAYLERYQQT-YNQTAESLWLGIRIARALGDVAAAQRYGAQLQK  231 (234)
T ss_pred             HcCCHHHHHHHHHHHHHh-CCCCHHHHHHHHHHHHHHhhHHHHHHHHHHHHh
Confidence            777777777777766654 233444555555666666666666666655543

Members of this family are designated PilF in ref (PubMed:8973346) and PilW in ref (PubMed:15612916). This outer membrane protein is required both for pilus stability and for pilus function such as adherence to human cells. Members of this family contain copies of the TPR (tetratricopeptide repeat) domain.

>KOG4162 consensus Predicted calmodulin-binding protein [Signal transduction mechanisms]

Probab=99.50  E-value=2.4e-09  Score=104.30  Aligned_cols=416  Identities=12%  Similarity=0.013  Sum_probs=281.8

Q ss_pred             CCCCHHHHHHHHHHHHhcCChhHHHHHHHHHHhCCCCCCHHHHHHHHHHHHhcCCHhHHHHHHHHHHhcCCCCC-HhhHH
Q 040027           92 LFPNLYTYNILINCFCKIGRVSLGFIAFGRILRSCFTPNAATFNSLIKGLHAESRIMEAAALFTKLKAFGCEPN-VITYN  170 (595)
Q Consensus        92 ~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~~-~~~~~  170 (595)
                      +.-++..|..+.-+...+|++..+.+.|++..... .-....|..+.-.|...|.-..|+.+++........|+ ...+.
T Consensus       319 ~qnd~ai~d~Lt~al~~~g~f~~lae~fE~~~~~~-~~~~e~w~~~als~saag~~s~Av~ll~~~~~~~~~ps~~s~~L  397 (799)
T KOG4162|consen  319 FQNDAAIFDHLTFALSRCGQFEVLAEQFEQALPFS-FGEHERWYQLALSYSAAGSDSKAVNLLRESLKKSEQPSDISVLL  397 (799)
T ss_pred             hcchHHHHHHHHHHHHHHHHHHHHHHHHHHHhHhh-hhhHHHHHHHHHHHHHhccchHHHHHHHhhcccccCCCcchHHH
Confidence            34688999999999999999999999999998764 33677889999999999999999999998776643343 33333


Q ss_pred             HHHHHHH-hcCChhHHHHHHHHHHhcCCCCCccccCcHHHHHHHHHHHHHc-----------CCHhHHHHHHHHHhhCCC
Q 040027          171 TLINGLC-RTGHTMIALNLFEEMANGNGEIGVVCKPNTVTYSTIIDGLCKE-----------GFVDKAKALFLQMKDENI  238 (595)
Q Consensus       171 ~l~~~~~-~~g~~~~A~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~-----------g~~~~A~~~~~~~~~~~~  238 (595)
                      .....|. +.+..++++....++....+.-.  -...+..+..+.-+|...           ....++.+.+++..+.+.
T Consensus       398 masklc~e~l~~~eegldYA~kai~~~~~~~--~~l~~~~~l~lGi~y~~~A~~a~~~seR~~~h~kslqale~av~~d~  475 (799)
T KOG4162|consen  398 MASKLCIERLKLVEEGLDYAQKAISLLGGQR--SHLKPRGYLFLGIAYGFQARQANLKSERDALHKKSLQALEEAVQFDP  475 (799)
T ss_pred             HHHHHHHhchhhhhhHHHHHHHHHHHhhhhh--hhhhhhHHHHHHHHHHhHhhcCCChHHHHHHHHHHHHHHHHHHhcCC
Confidence            3333333 46788888888777776321100  122345555555555432           124577888888887643


Q ss_pred             CCCHhHHHHHHHHHHhcCCHHHHHHHHHHHHHCCCCCCHhhHHHHHHHHHhcCChHHHHHHHHHHHHCCCCCCHHHHHHH
Q 040027          239 NPDVVTYNSLIHGLCHANDWNEAKRLFIEMMDQGVQPSVVTFNVIMDELCKNRKMDEASRLLDLMVQRGVRPNACTYNTL  318 (595)
Q Consensus       239 ~~~~~~~~~ll~~~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~l  318 (595)
                      . |+.....+.--|+..++...|.+...+.++.+-..+...|..+...+...+++.+|+.+.+.....- ..|......-
T Consensus       476 ~-dp~~if~lalq~A~~R~l~sAl~~~~eaL~l~~~~~~~~whLLALvlSa~kr~~~Al~vvd~al~E~-~~N~~l~~~~  553 (799)
T KOG4162|consen  476 T-DPLVIFYLALQYAEQRQLTSALDYAREALALNRGDSAKAWHLLALVLSAQKRLKEALDVVDAALEEF-GDNHVLMDGK  553 (799)
T ss_pred             C-CchHHHHHHHHHHHHHhHHHHHHHHHHHHHhcCCccHHHHHHHHHHHhhhhhhHHHHHHHHHHHHHh-hhhhhhchhh
Confidence            2 3444444555678889999999999999998666789999999999999999999999999887641 1122222222


Q ss_pred             HHHHHhcCCHHHHHHHHHHHHhcCC-CCCHH-------HHHHHHHHHHhCCCHHHHHHHHHH-----------------H
Q 040027          319 MDGFCLMGKINRAEELFGSMESMGC-KHDDV-------SYNILINGYCKNKEVEEALSLYRE-----------------M  373 (595)
Q Consensus       319 ~~~~~~~~~~~~a~~~~~~~~~~~~-~~~~~-------~~~~l~~~~~~~~~~~~A~~~~~~-----------------~  373 (595)
                      +..-...++.+++......+...=- .+...       ....-.......++..++.+..+.                 +
T Consensus       554 ~~i~~~~~~~e~~l~t~~~~L~~we~~~~~q~~~~~g~~~~lk~~l~la~~q~~~a~s~sr~ls~l~a~~~~~~~se~~L  633 (799)
T KOG4162|consen  554 IHIELTFNDREEALDTCIHKLALWEAEYGVQQTLDEGKLLRLKAGLHLALSQPTDAISTSRYLSSLVASQLKSAGSELKL  633 (799)
T ss_pred             hhhhhhcccHHHHHHHHHHHHHHHHhhhhHhhhhhhhhhhhhhcccccCcccccccchhhHHHHHHHHhhhhhccccccc
Confidence            2333335565555544443321100 00000       000000000001111111111111                 1


Q ss_pred             HHCCCCCCH--------HHHHHHHHHHHccCCHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHH
Q 040027          374 VSKGIKPTV--------VTYNTLFLGLFEIHQVEHALKLFDEMQRDGVAADTRTYTTFIDGLCKNGYIIEAVELFRTLRI  445 (595)
Q Consensus       374 ~~~~~~~~~--------~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~  445 (595)
                      ....+.|..        ..|......+...+..+++...+.+..+. .+.....|......+...|...+|.+.|.....
T Consensus       634 p~s~~~~~~~~~~~~~~~lwllaa~~~~~~~~~~~a~~CL~Ea~~~-~~l~~~~~~~~G~~~~~~~~~~EA~~af~~Al~  712 (799)
T KOG4162|consen  634 PSSTVLPGPDSLWYLLQKLWLLAADLFLLSGNDDEARSCLLEASKI-DPLSASVYYLRGLLLEVKGQLEEAKEAFLVALA  712 (799)
T ss_pred             CcccccCCCCchHHHHHHHHHHHHHHHHhcCCchHHHHHHHHHHhc-chhhHHHHHHhhHHHHHHHhhHHHHHHHHHHHh
Confidence            111111111        23445556677888899999888888776 366677788888888999999999999999998


Q ss_pred             cCCCcCHHHHHHHHHHHHhcCChHHHHH--HHHhcccCCCCC-CHHHHHHHHHHHHhcCChhHHHHHHHHHHHc
Q 040027          446 LKCELDIQAYNCLIDGLCKSGRLKFAWE--LFCSLPHGVLVP-NVVTYNIMIQGLCNDGQMDKARDLFLDMEEN  516 (595)
Q Consensus       446 ~~~~~~~~~~~~l~~~~~~~g~~~~A~~--~~~~~~~~~~~p-~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~  516 (595)
                      .+ |.++....++..++.+.|+...|..  ++..+.+  +.| +...|..+...+.+.|+.++|.+.|..+.+.
T Consensus       713 ld-P~hv~s~~Ala~~lle~G~~~la~~~~~L~dalr--~dp~n~eaW~~LG~v~k~~Gd~~~Aaecf~aa~qL  783 (799)
T KOG4162|consen  713 LD-PDHVPSMTALAELLLELGSPRLAEKRSLLSDALR--LDPLNHEAWYYLGEVFKKLGDSKQAAECFQAALQL  783 (799)
T ss_pred             cC-CCCcHHHHHHHHHHHHhCCcchHHHHHHHHHHHh--hCCCCHHHHHHHHHHHHHccchHHHHHHHHHHHhh
Confidence            76 6678899999999999999888888  9999998  455 5899999999999999999999999999875

>PRK12370 invasion protein regulator; Provisional

Probab=99.48  E-value=9e-11  Score=119.38  Aligned_cols=269  Identities=15%  Similarity=0.070  Sum_probs=189.3

Q ss_pred             CCCHHHHHHHHHHHHh-----cCCHhHHHHHHHHHHhcCCCCCHhhHHHHHHHHHh---------cCChhHHHHHHHHHH
Q 040027          128 TPNAATFNSLIKGLHA-----ESRIMEAAALFTKLKAFGCEPNVITYNTLINGLCR---------TGHTMIALNLFEEMA  193 (595)
Q Consensus       128 ~~~~~~~~~l~~~~~~-----~g~~~~A~~~~~~~~~~~~~~~~~~~~~l~~~~~~---------~g~~~~A~~~~~~~~  193 (595)
                      +.+...|...+.+...     .+.+++|++.|++..+... -+...+..+..++..         .+++++|...++++.
T Consensus       253 ~~~~da~~~~lrg~~~~~~~~~~~~~~A~~~~~~Al~ldP-~~a~a~~~La~~~~~~~~~g~~~~~~~~~~A~~~~~~Al  331 (553)
T PRK12370        253 LNSIDSTMVYLRGKHELNQYTPYSLQQALKLLTQCVNMSP-NSIAPYCALAECYLSMAQMGIFDKQNAMIKAKEHAIKAT  331 (553)
T ss_pred             CCChHHHHHHHHhHHHHHccCHHHHHHHHHHHHHHHhcCC-ccHHHHHHHHHHHHHHHHcCCcccchHHHHHHHHHHHHH
Confidence            5567766666655322     2456789999999998742 245566666655442         345789999999999


Q ss_pred             hcCCCCCccccCcHHHHHHHHHHHHHcCCHhHHHHHHHHHhhCCCCCCHhHHHHHHHHHHhcCCHHHHHHHHHHHHHCCC
Q 040027          194 NGNGEIGVVCKPNTVTYSTIIDGLCKEGFVDKAKALFLQMKDENINPDVVTYNSLIHGLCHANDWNEAKRLFIEMMDQGV  273 (595)
Q Consensus       194 ~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~~ll~~~~~~~~~~~A~~~~~~~~~~~~  273 (595)
                      +.+       |.+..++..+..++...|++++|...|+++.+.+ +.+...+..+...+...|++++|...+++.++...
T Consensus       332 ~ld-------P~~~~a~~~lg~~~~~~g~~~~A~~~~~~Al~l~-P~~~~a~~~lg~~l~~~G~~~eAi~~~~~Al~l~P  403 (553)
T PRK12370        332 ELD-------HNNPQALGLLGLINTIHSEYIVGSLLFKQANLLS-PISADIKYYYGWNLFMAGQLEEALQTINECLKLDP  403 (553)
T ss_pred             hcC-------CCCHHHHHHHHHHHHHccCHHHHHHHHHHHHHhC-CCCHHHHHHHHHHHHHCCCHHHHHHHHHHHHhcCC
Confidence            876       5678888888889999999999999999998875 33567788888999999999999999999988643


Q ss_pred             CCCHhhHHHHHHHHHhcCChHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHhcCCCCCHHHHHHH
Q 040027          274 QPSVVTFNVIMDELCKNRKMDEASRLLDLMVQRGVRPNACTYNTLMDGFCLMGKINRAEELFGSMESMGCKHDDVSYNIL  353 (595)
Q Consensus       274 ~~~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l  353 (595)
                      . +...+..++..+...|++++|...++++.....+.++..+..+..++...|++++|...+.++.... +.+....+.+
T Consensus       404 ~-~~~~~~~~~~~~~~~g~~eeA~~~~~~~l~~~~p~~~~~~~~la~~l~~~G~~~eA~~~~~~~~~~~-~~~~~~~~~l  481 (553)
T PRK12370        404 T-RAAAGITKLWITYYHTGIDDAIRLGDELRSQHLQDNPILLSMQVMFLSLKGKHELARKLTKEISTQE-ITGLIAVNLL  481 (553)
T ss_pred             C-ChhhHHHHHHHHHhccCHHHHHHHHHHHHHhccccCHHHHHHHHHHHHhCCCHHHHHHHHHHhhhcc-chhHHHHHHH
Confidence            2 2233334455567789999999999998876433355567778888899999999999998876552 2334455666


Q ss_pred             HHHHHhCCCHHHHHHHHHHHHHCC-CCCCHHHHHHHHHHHHccCCHHHHHHHHHHHHHCC
Q 040027          354 INGYCKNKEVEEALSLYREMVSKG-IKPTVVTYNTLFLGLFEIHQVEHALKLFDEMQRDG  412 (595)
Q Consensus       354 ~~~~~~~~~~~~A~~~~~~~~~~~-~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~  412 (595)
                      ...|...|  +.|...++.+.+.. ..+....+  +...+.-.|+.+.+... +++.+.+
T Consensus       482 ~~~~~~~g--~~a~~~l~~ll~~~~~~~~~~~~--~~~~~~~~g~~~~~~~~-~~~~~~~  536 (553)
T PRK12370        482 YAEYCQNS--ERALPTIREFLESEQRIDNNPGL--LPLVLVAHGEAIAEKMW-NKFKNED  536 (553)
T ss_pred             HHHHhccH--HHHHHHHHHHHHHhhHhhcCchH--HHHHHHHHhhhHHHHHH-HHhhccc
Confidence            66777777  47777777766531 11222222  33445556666666655 7776653

>KOG2376 consensus Signal recognition particle, subunit Srp72 [Intracellular trafficking, secretion, and vesicular transport]

Probab=99.47  E-value=1.3e-08  Score=96.29  Aligned_cols=222  Identities=14%  Similarity=0.071  Sum_probs=136.1

Q ss_pred             HHHHHHHHHhcCChhHHHHHHHHHHhCCCCCCHHHHHHHHHHHHhcCCHhHHHHHHHHHHhcCCCCCHhhHHHHHHHHHh
Q 040027           99 YNILINCFCKIGRVSLGFIAFGRILRSCFTPNAATFNSLIKGLHAESRIMEAAALFTKLKAFGCEPNVITYNTLINGLCR  178 (595)
Q Consensus        99 ~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~~l~~~~~~  178 (595)
                      ..+=++.+...|++++|.+...+++..+ +.+..++..=+.++.+.+++++|+.+.+.-...  ..+..-+..-+-+..+
T Consensus        15 l~t~ln~~~~~~e~e~a~k~~~Kil~~~-pdd~~a~~cKvValIq~~ky~~ALk~ikk~~~~--~~~~~~~fEKAYc~Yr   91 (652)
T KOG2376|consen   15 LLTDLNRHGKNGEYEEAVKTANKILSIV-PDDEDAIRCKVVALIQLDKYEDALKLIKKNGAL--LVINSFFFEKAYCEYR   91 (652)
T ss_pred             HHHHHHHhccchHHHHHHHHHHHHHhcC-CCcHhhHhhhHhhhhhhhHHHHHHHHHHhcchh--hhcchhhHHHHHHHHH
Confidence            3345566778899999999999999876 567777777788899999999999665543321  1111111222334447


Q ss_pred             cCChhHHHHHHHHHHhcCCCCCccccCcHHHHHHHHHHHHHcCCHhHHHHHHHHHhhCCCCCCHhHHHHHHHH-HHhcCC
Q 040027          179 TGHTMIALNLFEEMANGNGEIGVVCKPNTVTYSTIIDGLCKEGFVDKAKALFLQMKDENINPDVVTYNSLIHG-LCHAND  257 (595)
Q Consensus       179 ~g~~~~A~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~~ll~~-~~~~~~  257 (595)
                      .+..++|+..++...          +.+..+...-...+.+.|++++|.++|+.+.+.+.+ +   +...+.+ +...+-
T Consensus        92 lnk~Dealk~~~~~~----------~~~~~ll~L~AQvlYrl~~ydealdiY~~L~kn~~d-d---~d~~~r~nl~a~~a  157 (652)
T KOG2376|consen   92 LNKLDEALKTLKGLD----------RLDDKLLELRAQVLYRLERYDEALDIYQHLAKNNSD-D---QDEERRANLLAVAA  157 (652)
T ss_pred             cccHHHHHHHHhccc----------ccchHHHHHHHHHHHHHhhHHHHHHHHHHHHhcCCc-h---HHHHHHHHHHHHHH
Confidence            899999999988332          233456666778888999999999999999876432 2   2211111 111111


Q ss_pred             HHHHHHHHHHHHHCCCCCCHhhHHH---HHHHHHhcCChHHHHHHHHHHHHCC-------CCCC------H-HHHHHHHH
Q 040027          258 WNEAKRLFIEMMDQGVQPSVVTFNV---IMDELCKNRKMDEASRLLDLMVQRG-------VRPN------A-CTYNTLMD  320 (595)
Q Consensus       258 ~~~A~~~~~~~~~~~~~~~~~~~~~---l~~~~~~~g~~~~a~~~~~~~~~~~-------~~~~------~-~~~~~l~~  320 (595)
                      -..+. +   +......| ..+|..   ..-.+...|++.+|+++++...+.+       -.-+      . ..-..+..
T Consensus       158 ~l~~~-~---~q~v~~v~-e~syel~yN~Ac~~i~~gky~qA~elL~kA~~~~~e~l~~~d~~eEeie~el~~IrvQlay  232 (652)
T KOG2376|consen  158 ALQVQ-L---LQSVPEVP-EDSYELLYNTACILIENGKYNQAIELLEKALRICREKLEDEDTNEEEIEEELNPIRVQLAY  232 (652)
T ss_pred             hhhHH-H---HHhccCCC-cchHHHHHHHHHHHHhcccHHHHHHHHHHHHHHHHHhhcccccchhhHHHHHHHHHHHHHH
Confidence            11111 1   22222222 223333   3345678899999999998883211       1101      1 12233455


Q ss_pred             HHHhcCCHHHHHHHHHHHHhcC
Q 040027          321 GFCLMGKINRAEELFGSMESMG  342 (595)
Q Consensus       321 ~~~~~~~~~~a~~~~~~~~~~~  342 (595)
                      ++-..|+.++|..++..+++..
T Consensus       233 VlQ~~Gqt~ea~~iy~~~i~~~  254 (652)
T KOG2376|consen  233 VLQLQGQTAEASSIYVDIIKRN  254 (652)
T ss_pred             HHHHhcchHHHHHHHHHHHHhc
Confidence            6677899999999999888775

>TIGR02521 type_IV_pilW type IV pilus biogenesis/stability protein PilW

Probab=99.43  E-value=1.9e-10  Score=104.32  Aligned_cols=199  Identities=13%  Similarity=0.060  Sum_probs=127.6

Q ss_pred             HHHHHHHHHHHHhCCCHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHccCCHHHHHHHHHHHHHCCCCCCHHHHHHHHHH
Q 040027          347 DVSYNILINGYCKNKEVEEALSLYREMVSKGIKPTVVTYNTLFLGLFEIHQVEHALKLFDEMQRDGVAADTRTYTTFIDG  426 (595)
Q Consensus       347 ~~~~~~l~~~~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~  426 (595)
                      ...+..+...+...|++++|...++++.+..+. +...+..+...+...|++++|.+.+++..+.. +.+...+..+...
T Consensus        31 ~~~~~~la~~~~~~~~~~~A~~~~~~~l~~~p~-~~~~~~~la~~~~~~~~~~~A~~~~~~al~~~-~~~~~~~~~~~~~  108 (234)
T TIGR02521        31 AKIRVQLALGYLEQGDLEVAKENLDKALEHDPD-DYLAYLALALYYQQLGELEKAEDSFRRALTLN-PNNGDVLNNYGTF  108 (234)
T ss_pred             HHHHHHHHHHHHHCCCHHHHHHHHHHHHHhCcc-cHHHHHHHHHHHHHcCCHHHHHHHHHHHHhhC-CCCHHHHHHHHHH
Confidence            344555566666666666666666666554322 34455556666666666666666666666543 3344555666666


Q ss_pred             HHhcCCHHHHHHHHHHHHHcCC-CcCHHHHHHHHHHHHhcCChHHHHHHHHhcccCCCCC-CHHHHHHHHHHHHhcCChh
Q 040027          427 LCKNGYIIEAVELFRTLRILKC-ELDIQAYNCLIDGLCKSGRLKFAWELFCSLPHGVLVP-NVVTYNIMIQGLCNDGQMD  504 (595)
Q Consensus       427 ~~~~g~~~~A~~~~~~~~~~~~-~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~p-~~~~~~~l~~~~~~~g~~~  504 (595)
                      +...|++++|...++++..... +.....+..+..++...|++++|...+++....  .| +...+..+...+...|+++
T Consensus       109 ~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~--~~~~~~~~~~la~~~~~~~~~~  186 (234)
T TIGR02521       109 LCQQGKYEQAMQQFEQAIEDPLYPQPARSLENAGLCALKAGDFDKAEKYLTRALQI--DPQRPESLLELAELYYLRGQYK  186 (234)
T ss_pred             HHHcccHHHHHHHHHHHHhccccccchHHHHHHHHHHHHcCCHHHHHHHHHHHHHh--CcCChHHHHHHHHHHHHcCCHH
Confidence            6677777777777777665321 223445666677777777777777777777663  33 3556667777777788888


Q ss_pred             HHHHHHHHHHHcCCCCCHHHHHHHHHHHHHcCChhHHHHHHHHHHH
Q 040027          505 KARDLFLDMEENAAAPDVITFDMLIHGFIRINEPSKVNELLHKMKE  550 (595)
Q Consensus       505 ~A~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~  550 (595)
                      +|...++++.+.. +.+...+..++..+...|+.++|..+.+.+..
T Consensus       187 ~A~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~a~~~~~~~~~  231 (234)
T TIGR02521       187 DARAYLERYQQTY-NQTAESLWLGIRIARALGDVAAAQRYGAQLQK  231 (234)
T ss_pred             HHHHHHHHHHHhC-CCCHHHHHHHHHHHHHHhhHHHHHHHHHHHHh
Confidence            8888888777652 44556666667777777888888777777654

Members of this family are designated PilF in ref (PubMed:8973346) and PilW in ref (PubMed:15612916). This outer membrane protein is required both for pilus stability and for pilus function such as adherence to human cells. Members of this family contain copies of the TPR (tetratricopeptide repeat) domain.

>KOG2376 consensus Signal recognition particle, subunit Srp72 [Intracellular trafficking, secretion, and vesicular transport]

Probab=99.43  E-value=2.4e-08  Score=94.60  Aligned_cols=457  Identities=12%  Similarity=0.072  Sum_probs=246.1

Q ss_pred             cccCCCChHHHHHHHHHHHHhCCCCCCHhhHHHHHHHHHcCCCchhH--HhhCCC--CCCHHHHHHHHHHHHhcCChhHH
Q 040027           40 GDINVITPNEAFCIFDYMLRMHPSPPPVSSFNILLASLAKNKHYDTR--LNATGL--FPNLYTYNILINCFCKIGRVSLG  115 (595)
Q Consensus        40 ~~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~--~~~~~~--~~~~~~~~~l~~~~~~~g~~~~A  115 (595)
                      .....|++++|.+.-++++...|+  +...+..-+-++.+.++|++.  .+....  .-+...+..-+.++.+.+..++|
T Consensus        21 ~~~~~~e~e~a~k~~~Kil~~~pd--d~~a~~cKvValIq~~ky~~ALk~ikk~~~~~~~~~~~fEKAYc~Yrlnk~Dea   98 (652)
T KOG2376|consen   21 RHGKNGEYEEAVKTANKILSIVPD--DEDAIRCKVVALIQLDKYEDALKLIKKNGALLVINSFFFEKAYCEYRLNKLDEA   98 (652)
T ss_pred             HhccchHHHHHHHHHHHHHhcCCC--cHhhHhhhHhhhhhhhHHHHHHHHHHhcchhhhcchhhHHHHHHHHHcccHHHH
Confidence            445679999999999999999998  888888888889999998882  222111  11222222345566788999999


Q ss_pred             HHHHHHHHhCCCCCCHHHHHHHHHHHHhcCCHhHHHHHHHHHHhcCCCC-CHhhHHHHHHHHHhcCChhHHHHHHHHHHh
Q 040027          116 FIAFGRILRSCFTPNAATFNSLIKGLHAESRIMEAAALFTKLKAFGCEP-NVITYNTLINGLCRTGHTMIALNLFEEMAN  194 (595)
Q Consensus       116 ~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~-~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~  194 (595)
                      +..++-+.    +.+..+...-...+.+.|++++|.++|+.+.+.+.+. +......++..-.    ...+. +.+....
T Consensus        99 lk~~~~~~----~~~~~ll~L~AQvlYrl~~ydealdiY~~L~kn~~dd~d~~~r~nl~a~~a----~l~~~-~~q~v~~  169 (652)
T KOG2376|consen   99 LKTLKGLD----RLDDKLLELRAQVLYRLERYDEALDIYQHLAKNNSDDQDEERRANLLAVAA----ALQVQ-LLQSVPE  169 (652)
T ss_pred             HHHHhccc----ccchHHHHHHHHHHHHHhhHHHHHHHHHHHHhcCCchHHHHHHHHHHHHHH----hhhHH-HHHhccC
Confidence            99888322    2233355556677888899999999999997764321 1122222222111    11111 2222221


Q ss_pred             cCCCCCccccC-cHHHHHHHHHHHHHcCCHhHHHHHHHHHhhCC-------CCCCH-------hHHHHHHHHHHhcCCHH
Q 040027          195 GNGEIGVVCKP-NTVTYSTIIDGLCKEGFVDKAKALFLQMKDEN-------INPDV-------VTYNSLIHGLCHANDWN  259 (595)
Q Consensus       195 ~~~~~~~~~~~-~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~-------~~~~~-------~~~~~ll~~~~~~~~~~  259 (595)
                              ++. +-..+......++..|++.+|+++++...+.+       -.-+.       ..-..|...+...|+.+
T Consensus       170 --------v~e~syel~yN~Ac~~i~~gky~qA~elL~kA~~~~~e~l~~~d~~eEeie~el~~IrvQlayVlQ~~Gqt~  241 (652)
T KOG2376|consen  170 --------VPEDSYELLYNTACILIENGKYNQAIELLEKALRICREKLEDEDTNEEEIEEELNPIRVQLAYVLQLQGQTA  241 (652)
T ss_pred             --------CCcchHHHHHHHHHHHHhcccHHHHHHHHHHHHHHHHHhhcccccchhhHHHHHHHHHHHHHHHHHHhcchH
Confidence                    111 23334445566777899999999988873321       00000       01222334455667777


Q ss_pred             HHHHHHHHHHHCCCCCCHhhH----HHHHHHHHhcCChHH-HHHHHHHHHHCCCCCCHHHHHHHHHHHHhcCCHHHHHHH
Q 040027          260 EAKRLFIEMMDQGVQPSVVTF----NVIMDELCKNRKMDE-ASRLLDLMVQRGVRPNACTYNTLMDGFCLMGKINRAEEL  334 (595)
Q Consensus       260 ~A~~~~~~~~~~~~~~~~~~~----~~l~~~~~~~g~~~~-a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~  334 (595)
                      +|..+|...++... +|....    |.++..-....-++. ++..++...                       ...+...
T Consensus       242 ea~~iy~~~i~~~~-~D~~~~Av~~NNLva~~~d~~~~d~~~l~~k~~~~-----------------------~~l~~~~  297 (652)
T KOG2376|consen  242 EASSIYVDIIKRNP-ADEPSLAVAVNNLVALSKDQNYFDGDLLKSKKSQV-----------------------FKLAEFL  297 (652)
T ss_pred             HHHHHHHHHHHhcC-CCchHHHHHhcchhhhccccccCchHHHHHHHHHH-----------------------HHhHHHH
Confidence            77777766666532 233221    111111100000110 000111000                       0001111


Q ss_pred             HHHHHhcCCCCCHHHHHHHHHHHHhCCCHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHH--ccCCHHHHHHHHHHHHHCC
Q 040027          335 FGSMESMGCKHDDVSYNILINGYCKNKEVEEALSLYREMVSKGIKPTVVTYNTLFLGLF--EIHQVEHALKLFDEMQRDG  412 (595)
Q Consensus       335 ~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~~l~~~~~--~~~~~~~a~~~~~~~~~~~  412 (595)
                      +..+.... ......-+.++..|  .+..+.+.++......  ..|.. .+..++..+.  +...+..+..++...-+..
T Consensus       298 l~~Ls~~q-k~~i~~N~~lL~l~--tnk~~q~r~~~a~lp~--~~p~~-~~~~ll~~~t~~~~~~~~ka~e~L~~~~~~~  371 (652)
T KOG2376|consen  298 LSKLSKKQ-KQAIYRNNALLALF--TNKMDQVRELSASLPG--MSPES-LFPILLQEATKVREKKHKKAIELLLQFADGH  371 (652)
T ss_pred             HHHHHHHH-HHHHHHHHHHHHHH--hhhHHHHHHHHHhCCc--cCchH-HHHHHHHHHHHHHHHHHhhhHHHHHHHhccC
Confidence            11111100 00111112222223  2333344443333222  12222 2233333222  2224667777777666653


Q ss_pred             CCCCHHHHHHHHHHHHhcCCHHHHHHHHH--------HHHHcCCCcCHHHHHHHHHHHHhcCChHHHHHHHHhcccCC--
Q 040027          413 VAADTRTYTTFIDGLCKNGYIIEAVELFR--------TLRILKCELDIQAYNCLIDGLCKSGRLKFAWELFCSLPHGV--  482 (595)
Q Consensus       413 ~~~~~~~~~~l~~~~~~~g~~~~A~~~~~--------~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~--  482 (595)
                      ......+....++.....|+++.|.+++.        .+.+.+  -.+.+...++..+.+.++.+.|..++.+.+..-  
T Consensus       372 p~~s~~v~L~~aQl~is~gn~~~A~~il~~~~~~~~ss~~~~~--~~P~~V~aiv~l~~~~~~~~~a~~vl~~Ai~~~~~  449 (652)
T KOG2376|consen  372 PEKSKVVLLLRAQLKISQGNPEVALEILSLFLESWKSSILEAK--HLPGTVGAIVALYYKIKDNDSASAVLDSAIKWWRK  449 (652)
T ss_pred             CchhHHHHHHHHHHHHhcCCHHHHHHHHHHHhhhhhhhhhhhc--cChhHHHHHHHHHHhccCCccHHHHHHHHHHHHHH
Confidence            22334556666677778888888888888        444433  334556667777777777777777777665410  


Q ss_pred             CCCC----HHHHHHHHHHHHhcCChhHHHHHHHHHHHcCCCCCHHHHHHHHHHHHHcCChhHHHHHHHHHH
Q 040027          483 LVPN----VVTYNIMIQGLCNDGQMDKARDLFLDMEENAAAPDVITFDMLIHGFIRINEPSKVNELLHKMK  549 (595)
Q Consensus       483 ~~p~----~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~  549 (595)
                      ..+.    ..+|..++..-.+.|+-++|..+++++.+.+ ++|..+...++.+|++. +.+.|..+-+.+.
T Consensus       450 ~~t~s~~l~~~~~~aa~f~lr~G~~~ea~s~leel~k~n-~~d~~~l~~lV~a~~~~-d~eka~~l~k~L~  518 (652)
T KOG2376|consen  450 QQTGSIALLSLMREAAEFKLRHGNEEEASSLLEELVKFN-PNDTDLLVQLVTAYARL-DPEKAESLSKKLP  518 (652)
T ss_pred             hcccchHHHhHHHHHhHHHHhcCchHHHHHHHHHHHHhC-CchHHHHHHHHHHHHhc-CHHHHHHHhhcCC
Confidence            1111    2233344444557799999999999999975 77888888899888776 4788877766654

>KOG4318 consensus Bicoid mRNA stability factor [RNA processing and modification]

Probab=99.42  E-value=1.9e-09  Score=106.32  Aligned_cols=101  Identities=12%  Similarity=0.102  Sum_probs=56.2

Q ss_pred             HHHHHHHHHHHhcCChHHHHHHHHhcccCC--CCCCHHHHHHHHHHHHhcCChhHHHHHHHHHHHcCC-CCC-HHHHHHH
Q 040027          453 QAYNCLIDGLCKSGRLKFAWELFCSLPHGV--LVPNVVTYNIMIQGLCNDGQMDKARDLFLDMEENAA-APD-VITFDML  528 (595)
Q Consensus       453 ~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~--~~p~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~-~~~-~~~~~~l  528 (595)
                      ..|..+++.+......+.|..+.+++....  +.-|..-+..+.....+.+....+..++.++.+.-. .|+ ..++..+
T Consensus       492 g~ya~Li~l~~~hdkle~Al~~~~e~d~~d~s~~Ld~~~m~~l~dLL~r~~~l~dl~tiL~e~ks~a~n~~~~a~~~f~~  571 (1088)
T KOG4318|consen  492 GLYALLIKLMDLHDKLEYALSFVDEIDTRDESIHLDLPLMTSLQDLLQRLAILYDLSTILYEDKSSAENEPLVAIILFPL  571 (1088)
T ss_pred             hHHHHHhhhHHHHHHHHHHHhchhhhcccchhhhcccHhHHHHHHHHHHhHHHHHHHHHHhhhhHHhhCCchHHHHHHHH
Confidence            345555666666666666666666654421  222344555666666777777777777777665311 221 3344455


Q ss_pred             HHHHHHcCChhHHHHHHHHHHHCCC
Q 040027          529 IHGFIRINEPSKVNELLHKMKEKKV  553 (595)
Q Consensus       529 ~~~~~~~g~~~~A~~~~~~~~~~~~  553 (595)
                      +......|+.+...++.+-+...|+
T Consensus       572 lns~a~agqqe~Lkkl~d~lvslgl  596 (1088)
T KOG4318|consen  572 LNSGAPAGQQEKLKKLADILVSLGL  596 (1088)
T ss_pred             HhhhhhccCHHHHHHHHHHHHHhhh
Confidence            5555566666666666555554443

>COG3063 PilF Tfp pilus assembly protein PilF [Cell motility and secretion / Intracellular trafficking and secretion]

Probab=99.40  E-value=1.7e-10  Score=95.97  Aligned_cols=200  Identities=15%  Similarity=0.031  Sum_probs=143.1

Q ss_pred             hcccccccccccCCCChHHHHHHHHHHHHhCCCCCCHhhHHHHHHHHHcCCCchhHHhhCCCCCCHHHHHHHHHHHHhcC
Q 040027           31 HFRDLTTREGDINVITPNEAFCIFDYMLRMHPSPPPVSSFNILLASLAKNKHYDTRLNATGLFPNLYTYNILINCFCKIG  110 (595)
Q Consensus        31 ~~~~~~~~~~~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g  110 (595)
                      ...++..+.+|+++|++..|.+.++++++.+|+                               +..+|..+...|.+.|
T Consensus        35 a~arlqLal~YL~~gd~~~A~~nlekAL~~DPs-------------------------------~~~a~~~~A~~Yq~~G   83 (250)
T COG3063          35 AKARLQLALGYLQQGDYAQAKKNLEKALEHDPS-------------------------------YYLAHLVRAHYYQKLG   83 (250)
T ss_pred             HHHHHHHHHHHHHCCCHHHHHHHHHHHHHhCcc-------------------------------cHHHHHHHHHHHHHcC
Confidence            334556777888888888888888888888887                               3444556666677778


Q ss_pred             ChhHHHHHHHHHHhCCCCCCHHHHHHHHHHHHhcCCHhHHHHHHHHHHhcC-CCCCHhhHHHHHHHHHhcCChhHHHHHH
Q 040027          111 RVSLGFIAFGRILRSCFTPNAATFNSLIKGLHAESRIMEAAALFTKLKAFG-CEPNVITYNTLINGLCRTGHTMIALNLF  189 (595)
Q Consensus       111 ~~~~A~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~-~~~~~~~~~~l~~~~~~~g~~~~A~~~~  189 (595)
                      +.+.|.+.|++++... +.+..+.|.....++.+|++++|...|++....- ...-..+|..+..+..+.|+++.|...|
T Consensus        84 e~~~A~e~YrkAlsl~-p~~GdVLNNYG~FLC~qg~~~eA~q~F~~Al~~P~Y~~~s~t~eN~G~Cal~~gq~~~A~~~l  162 (250)
T COG3063          84 ENDLADESYRKALSLA-PNNGDVLNNYGAFLCAQGRPEEAMQQFERALADPAYGEPSDTLENLGLCALKAGQFDQAEEYL  162 (250)
T ss_pred             ChhhHHHHHHHHHhcC-CCccchhhhhhHHHHhCCChHHHHHHHHHHHhCCCCCCcchhhhhhHHHHhhcCCchhHHHHH
Confidence            8888888888888774 4466777777777888888888888888776641 1123456777777777778888888888


Q ss_pred             HHHHhcCCCCCccccCcHHHHHHHHHHHHHcCCHhHHHHHHHHHhhCCCCCCHhHHHHHHHHHHhcCCHHHHHHHHHHHH
Q 040027          190 EEMANGNGEIGVVCKPNTVTYSTIIDGLCKEGFVDKAKALFLQMKDENINPDVVTYNSLIHGLCHANDWNEAKRLFIEMM  269 (595)
Q Consensus       190 ~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~~ll~~~~~~~~~~~A~~~~~~~~  269 (595)
                      ++.+..+       +..+.+...+.......|++-.|...++.....+. ++..+.-..+..-...|+.+.+.++=..+.
T Consensus       163 ~raL~~d-------p~~~~~~l~~a~~~~~~~~y~~Ar~~~~~~~~~~~-~~A~sL~L~iriak~~gd~~~a~~Y~~qL~  234 (250)
T COG3063         163 KRALELD-------PQFPPALLELARLHYKAGDYAPARLYLERYQQRGG-AQAESLLLGIRIAKRLGDRAAAQRYQAQLQ  234 (250)
T ss_pred             HHHHHhC-------cCCChHHHHHHHHHHhcccchHHHHHHHHHHhccc-ccHHHHHHHHHHHHHhccHHHHHHHHHHHH
Confidence            8777765       34456666677777777777777777777776654 666666666777777777777666655554


Q ss_pred             H
Q 040027          270 D  270 (595)
Q Consensus       270 ~  270 (595)
                      +
T Consensus       235 r  235 (250)
T COG3063         235 R  235 (250)
T ss_pred             H
Confidence            4

>KOG0548 consensus Molecular co-chaperone STI1 [Posttranslational modification, protein turnover, chaperones]

Probab=99.40  E-value=6.7e-09  Score=97.29  Aligned_cols=99  Identities=14%  Similarity=0.149  Sum_probs=81.0

Q ss_pred             cccCCCChHHHHHHHHHHHHhCCCCCCHhhHHHHHHHHHcCCCchh----HHhhCCCCCC-HHHHHHHHHHHHhcCChhH
Q 040027           40 GDINVITPNEAFCIFDYMLRMHPSPPPVSSFNILLASLAKNKHYDT----RLNATGLFPN-LYTYNILINCFCKIGRVSL  114 (595)
Q Consensus        40 ~~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~----~~~~~~~~~~-~~~~~~l~~~~~~~g~~~~  114 (595)
                      +....|+++.|+..|-.++.++|.  +...|..-..+|+..|++.+    ......+.|+ +.-|+....++.-.|++++
T Consensus        11 aa~s~~d~~~ai~~~t~ai~l~p~--nhvlySnrsaa~a~~~~~~~al~da~k~~~l~p~w~kgy~r~Gaa~~~lg~~~e   88 (539)
T KOG0548|consen   11 AAFSSGDFETAIRLFTEAIMLSPT--NHVLYSNRSAAYASLGSYEKALKDATKTRRLNPDWAKGYSRKGAALFGLGDYEE   88 (539)
T ss_pred             hhcccccHHHHHHHHHHHHccCCC--ccchhcchHHHHHHHhhHHHHHHHHHHHHhcCCchhhHHHHhHHHHHhcccHHH
Confidence            346679999999999999999997  88999999999999999998    2333445554 5778999999999999999


Q ss_pred             HHHHHHHHHhCCCCCCHHHHHHHHHHH
Q 040027          115 GFIAFGRILRSCFTPNAATFNSLIKGL  141 (595)
Q Consensus       115 A~~~~~~~~~~~~~~~~~~~~~l~~~~  141 (595)
                      |+..|.+-++.. +.+...++.+..++
T Consensus        89 A~~ay~~GL~~d-~~n~~L~~gl~~a~  114 (539)
T KOG0548|consen   89 AILAYSEGLEKD-PSNKQLKTGLAQAY  114 (539)
T ss_pred             HHHHHHHHhhcC-CchHHHHHhHHHhh
Confidence            999999999874 44555667777666

>PF12569 NARP1: NMDA receptor-regulated protein 1 ; InterPro: IPR021183 This group represents N-terminal acetyltransferase A (NatA) auxiliary subunit and represents a non-catalytic component of the NatA N-terminal acetyltransferase, which catalyzes acetylation of proteins beginning with Met-Ser, Met-Gly and Met-Ala

Probab=99.39  E-value=2.6e-08  Score=97.95  Aligned_cols=297  Identities=13%  Similarity=0.078  Sum_probs=191.3

Q ss_pred             HHHHHHHHHHhcCChhHHHHHHHHHHhCCCCCCHH-HHHHHHHHHHhcCCHhHHHHHHHHHHhcCCCCCHhhHHHHHHHH
Q 040027           98 TYNILINCFCKIGRVSLGFIAFGRILRSCFTPNAA-TFNSLIKGLHAESRIMEAAALFTKLKAFGCEPNVITYNTLINGL  176 (595)
Q Consensus        98 ~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~~~~-~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~~l~~~~  176 (595)
                      ........+...|++++|+..++.....  -+|.. ........+.+.|+.++|..+|..++..++ .+..-|..+..+.
T Consensus         6 ~lLY~~~il~e~g~~~~AL~~L~~~~~~--I~Dk~~~~E~rA~ll~kLg~~~eA~~~y~~Li~rNP-dn~~Yy~~L~~~~   82 (517)
T PF12569_consen    6 LLLYKNSILEEAGDYEEALEHLEKNEKQ--ILDKLAVLEKRAELLLKLGRKEEAEKIYRELIDRNP-DNYDYYRGLEEAL   82 (517)
T ss_pred             HHHHHHHHHHHCCCHHHHHHHHHhhhhh--CCCHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHCC-CcHHHHHHHHHHH
Confidence            3344455677889999999988876655  33444 445667778888999999999999988853 2444555555554


Q ss_pred             Hhc-----CChhHHHHHHHHHHhcCCCCCccccCcHHHHHHHHHHHHHcCCHh-HHHHHHHHHhhCCCCCCHhHHHHHHH
Q 040027          177 CRT-----GHTMIALNLFEEMANGNGEIGVVCKPNTVTYSTIIDGLCKEGFVD-KAKALFLQMKDENINPDVVTYNSLIH  250 (595)
Q Consensus       177 ~~~-----g~~~~A~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~-~A~~~~~~~~~~~~~~~~~~~~~ll~  250 (595)
                      ...     .+.+...++++++....        |...+...+.-.+.....+. .+..++..+...|++   .+|..|-.
T Consensus        83 g~~~~~~~~~~~~~~~~y~~l~~~y--------p~s~~~~rl~L~~~~g~~F~~~~~~yl~~~l~KgvP---slF~~lk~  151 (517)
T PF12569_consen   83 GLQLQLSDEDVEKLLELYDELAEKY--------PRSDAPRRLPLDFLEGDEFKERLDEYLRPQLRKGVP---SLFSNLKP  151 (517)
T ss_pred             hhhcccccccHHHHHHHHHHHHHhC--------ccccchhHhhcccCCHHHHHHHHHHHHHHHHhcCCc---hHHHHHHH
Confidence            222     24667778888777654        22222222222222212232 344556666677754   34555555


Q ss_pred             HHHhcCCHHHHHHHHHHHHHC----C----------CCCCHh--hHHHHHHHHHhcCChHHHHHHHHHHHHCCCCCCHHH
Q 040027          251 GLCHANDWNEAKRLFIEMMDQ----G----------VQPSVV--TFNVIMDELCKNRKMDEASRLLDLMVQRGVRPNACT  314 (595)
Q Consensus       251 ~~~~~~~~~~A~~~~~~~~~~----~----------~~~~~~--~~~~l~~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~  314 (595)
                      .|.......-..+++......    +          -+|+..  ++..+...|...|++++|+.+.++.+... +..+..
T Consensus       152 Ly~d~~K~~~i~~l~~~~~~~l~~~~~~~~~~~~~~~~p~~~lw~~~~lAqhyd~~g~~~~Al~~Id~aI~ht-Pt~~el  230 (517)
T PF12569_consen  152 LYKDPEKAAIIESLVEEYVNSLESNGSFSNGDDEEKEPPSTLLWTLYFLAQHYDYLGDYEKALEYIDKAIEHT-PTLVEL  230 (517)
T ss_pred             HHcChhHHHHHHHHHHHHHHhhcccCCCCCccccccCCchHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHhcC-CCcHHH
Confidence            565554444445555554432    1          123332  34556677888899999999999888873 224677


Q ss_pred             HHHHHHHHHhcCCHHHHHHHHHHHHhcCCCCCHHHHHHHHHHHHhCCCHHHHHHHHHHHHHCCCCCCHHH--------HH
Q 040027          315 YNTLMDGFCLMGKINRAEELFGSMESMGCKHDDVSYNILINGYCKNKEVEEALSLYREMVSKGIKPTVVT--------YN  386 (595)
Q Consensus       315 ~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~~~~~~~~~~--------~~  386 (595)
                      |..-++++-..|++.+|.+.++.....+ .-|...-+..+..+.+.|+.++|.+++....+.+..|....        ..
T Consensus       231 y~~KarilKh~G~~~~Aa~~~~~Ar~LD-~~DRyiNsK~aKy~LRa~~~e~A~~~~~~Ftr~~~~~~~~L~~mQc~Wf~~  309 (517)
T PF12569_consen  231 YMTKARILKHAGDLKEAAEAMDEARELD-LADRYINSKCAKYLLRAGRIEEAEKTASLFTREDVDPLSNLNDMQCMWFET  309 (517)
T ss_pred             HHHHHHHHHHCCCHHHHHHHHHHHHhCC-hhhHHHHHHHHHHHHHCCCHHHHHHHHHhhcCCCCCcccCHHHHHHHHHHH
Confidence            7888888889999999999998888775 34666667777888889999999998888877654332221        13


Q ss_pred             HHHHHHHccCCHHHHHHHHHHHHH
Q 040027          387 TLFLGLFEIHQVEHALKLFDEMQR  410 (595)
Q Consensus       387 ~l~~~~~~~~~~~~a~~~~~~~~~  410 (595)
                      ....+|.+.|++..|++.|..+.+
T Consensus       310 e~a~a~~r~~~~~~ALk~~~~v~k  333 (517)
T PF12569_consen  310 ECAEAYLRQGDYGLALKRFHAVLK  333 (517)
T ss_pred             HHHHHHHHHhhHHHHHHHHHHHHH
Confidence            445678888888888887776654

N-terminal acetylation plays a role in normal eukaryotic translation and processing, protect against proteolytic degradation and protein turnover. NAT1 anchors ARD1 and NAT5 to the ribosome and may present the N- terminal of nascent polypeptides for acetylation [], [].

>KOG0548 consensus Molecular co-chaperone STI1 [Posttranslational modification, protein turnover, chaperones]

Probab=99.37  E-value=1.7e-08  Score=94.71  Aligned_cols=434  Identities=12%  Similarity=0.042  Sum_probs=248.1

Q ss_pred             HHHHhcCChhHHHHHHHHHHhCCCCCCHHHHHHHHHHHHhcCCHhHHHHHHHHHHhcCCCCC-HhhHHHHHHHHHhcCCh
Q 040027          104 NCFCKIGRVSLGFIAFGRILRSCFTPNAATFNSLIKGLHAESRIMEAAALFTKLKAFGCEPN-VITYNTLINGLCRTGHT  182 (595)
Q Consensus       104 ~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~~-~~~~~~l~~~~~~~g~~  182 (595)
                      .+.+..|+++.|+..|-+++... +++...|..-..+|...|++++|.+=-.+-.+.  .|+ ...|.....++.-.|++
T Consensus        10 naa~s~~d~~~ai~~~t~ai~l~-p~nhvlySnrsaa~a~~~~~~~al~da~k~~~l--~p~w~kgy~r~Gaa~~~lg~~   86 (539)
T KOG0548|consen   10 NAAFSSGDFETAIRLFTEAIMLS-PTNHVLYSNRSAAYASLGSYEKALKDATKTRRL--NPDWAKGYSRKGAALFGLGDY   86 (539)
T ss_pred             HhhcccccHHHHHHHHHHHHccC-CCccchhcchHHHHHHHhhHHHHHHHHHHHHhc--CCchhhHHHHhHHHHHhcccH
Confidence            45567899999999999999986 558888998999999999999999877776665  445 45788889999999999


Q ss_pred             hHHHHHHHHHHhcCCCCCccccCcHHHHHHHHHHHHHcCCHhHH---HHHHHHHhhC---CCCCCHhHHHHHHHHHHhcC
Q 040027          183 MIALNLFEEMANGNGEIGVVCKPNTVTYSTIIDGLCKEGFVDKA---KALFLQMKDE---NINPDVVTYNSLIHGLCHAN  256 (595)
Q Consensus       183 ~~A~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A---~~~~~~~~~~---~~~~~~~~~~~ll~~~~~~~  256 (595)
                      ++|+..|.+-++.+       +.+...+..+..++.......+.   -.++..+...   ........|..++..+-+.-
T Consensus        87 ~eA~~ay~~GL~~d-------~~n~~L~~gl~~a~~~~~~~~~~~~~p~~~~~l~~~p~t~~~~~~~~~~~~l~~~~~~p  159 (539)
T KOG0548|consen   87 EEAILAYSEGLEKD-------PSNKQLKTGLAQAYLEDYAADQLFTKPYFHEKLANLPLTNYSLSDPAYVKILEIIQKNP  159 (539)
T ss_pred             HHHHHHHHHHhhcC-------CchHHHHHhHHHhhhHHHHhhhhccCcHHHHHhhcChhhhhhhccHHHHHHHHHhhcCc
Confidence            99999999999876       56677777777776211100000   0111111110   00001112222222221110


Q ss_pred             -------CHHHHHHHHHHHHHCCCCCCHhhHHHHHHHHHh-cCChH----HHHHHHHHHHH-CCCCCCHHHHHHHHHHHH
Q 040027          257 -------DWNEAKRLFIEMMDQGVQPSVVTFNVIMDELCK-NRKMD----EASRLLDLMVQ-RGVRPNACTYNTLMDGFC  323 (595)
Q Consensus       257 -------~~~~A~~~~~~~~~~~~~~~~~~~~~l~~~~~~-~g~~~----~a~~~~~~~~~-~~~~~~~~~~~~l~~~~~  323 (595)
                             .........-.+...+.    ..+......... .....    .......+..+ .....-..-...++++..
T Consensus       160 ~~l~~~l~d~r~m~a~~~l~~~~~----~~~~~~~~~~~~~~~~p~~~~~~~~~~~~d~~ee~~~k~~a~~ek~lgnaay  235 (539)
T KOG0548|consen  160 TSLKLYLNDPRLMKADGQLKGVDE----LLFYASGIEILASMAEPCKQEHNGFPIIEDNTEERRVKEKAHKEKELGNAAY  235 (539)
T ss_pred             HhhhcccccHHHHHHHHHHhcCcc----ccccccccccCCCCCCcccccCCCCCccchhHHHHHHHHhhhHHHHHHHHHH
Confidence                   00000000000000000    000000000000 00000    00000000000 000001123445677777


Q ss_pred             hcCCHHHHHHHHHHHHhcCCCCCHHHHHHHHHHHHhCCCHHHHHHHHHHHHHCCCCCCHHHHHH-------HHHHHHccC
Q 040027          324 LMGKINRAEELFGSMESMGCKHDDVSYNILINGYCKNKEVEEALSLYREMVSKGIKPTVVTYNT-------LFLGLFEIH  396 (595)
Q Consensus       324 ~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~~-------l~~~~~~~~  396 (595)
                      +..+++.+++.+....+..  .+..-++....+|...|.+........+.++.|.. ...-++.       +..++.+.+
T Consensus       236 kkk~f~~a~q~y~~a~el~--~~it~~~n~aA~~~e~~~~~~c~~~c~~a~E~gre-~rad~klIak~~~r~g~a~~k~~  312 (539)
T KOG0548|consen  236 KKKDFETAIQHYAKALELA--TDITYLNNIAAVYLERGKYAECIELCEKAVEVGRE-LRADYKLIAKALARLGNAYTKRE  312 (539)
T ss_pred             HhhhHHHHHHHHHHHHhHh--hhhHHHHHHHHHHHhccHHHHhhcchHHHHHHhHH-HHHHHHHHHHHHHHhhhhhhhHH
Confidence            7788888888888887764  45566677777888888888777777776665432 2222332       333555667


Q ss_pred             CHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCcCHHHHHHHHHHHHhcCChHHHHHHHH
Q 040027          397 QVEHALKLFDEMQRDGVAADTRTYTTFIDGLCKNGYIIEAVELFRTLRILKCELDIQAYNCLIDGLCKSGRLKFAWELFC  476 (595)
Q Consensus       397 ~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~  476 (595)
                      +++.++..|.+.+.....|+.         ..+....+++....+...-.+... ..-...-+..+.+.|++..|+..|.
T Consensus       313 ~~~~ai~~~~kaLte~Rt~~~---------ls~lk~~Ek~~k~~e~~a~~~pe~-A~e~r~kGne~Fk~gdy~~Av~~Yt  382 (539)
T KOG0548|consen  313 DYEGAIKYYQKALTEHRTPDL---------LSKLKEAEKALKEAERKAYINPEK-AEEEREKGNEAFKKGDYPEAVKHYT  382 (539)
T ss_pred             hHHHHHHHHHHHhhhhcCHHH---------HHHHHHHHHHHHHHHHHHhhChhH-HHHHHHHHHHHHhccCHHHHHHHHH
Confidence            788888888776654333221         122333444444444443332111 2222233566778888888888888


Q ss_pred             hcccCCCCCCHHHHHHHHHHHHhcCChhHHHHHHHHHHHcCCCCCHHHHHHHHHHHHHcCChhHHHHHHHHHHHCCCCCC
Q 040027          477 SLPHGVLVPNVVTYNIMIQGLCNDGQMDKARDLFLDMEENAAAPDVITFDMLIHGFIRINEPSKVNELLHKMKEKKVMPD  556 (595)
Q Consensus       477 ~~~~~~~~p~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~p~  556 (595)
                      +++... +-|...|.....+|.+.|.+..|+.-.+..++.+ ++....|..-+.++....+|++|.+.|++.++.+  |+
T Consensus       383 eAIkr~-P~Da~lYsNRAac~~kL~~~~~aL~Da~~~ieL~-p~~~kgy~RKg~al~~mk~ydkAleay~eale~d--p~  458 (539)
T KOG0548|consen  383 EAIKRD-PEDARLYSNRAACYLKLGEYPEALKDAKKCIELD-PNFIKAYLRKGAALRAMKEYDKALEAYQEALELD--PS  458 (539)
T ss_pred             HHHhcC-CchhHHHHHHHHHHHHHhhHHHHHHHHHHHHhcC-chHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcC--ch
Confidence            888753 2246778888888888888888888888887764 4456667777777777788888888888888754  54


Q ss_pred             -HHHHHHHHHHHH
Q 040027          557 -ASIVSIVVDLLV  568 (595)
Q Consensus       557 -~~~~~~l~~~~~  568 (595)
                       ......+.+++.
T Consensus       459 ~~e~~~~~~rc~~  471 (539)
T KOG0548|consen  459 NAEAIDGYRRCVE  471 (539)
T ss_pred             hHHHHHHHHHHHH
Confidence             444455555444

>PF12569 NARP1: NMDA receptor-regulated protein 1 ; InterPro: IPR021183 This group represents N-terminal acetyltransferase A (NatA) auxiliary subunit and represents a non-catalytic component of the NatA N-terminal acetyltransferase, which catalyzes acetylation of proteins beginning with Met-Ser, Met-Gly and Met-Ala

Probab=99.35  E-value=6.7e-09  Score=102.00  Aligned_cols=296  Identities=17%  Similarity=0.137  Sum_probs=208.9

Q ss_pred             HHHHHHHHHHcCCHhHHHHHHHHHhhCCCCCCHhHHHHHHHHHHhcCCHHHHHHHHHHHHHCCCCCCHhh-HHHHHHHHH
Q 040027          210 YSTIIDGLCKEGFVDKAKALFLQMKDENINPDVVTYNSLIHGLCHANDWNEAKRLFIEMMDQGVQPSVVT-FNVIMDELC  288 (595)
Q Consensus       210 ~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~~ll~~~~~~~~~~~A~~~~~~~~~~~~~~~~~~-~~~l~~~~~  288 (595)
                      ..-...++...|++++|.+.++.-... +.............+.+.|+.++|..+|..+++.+  |+... |..+..+..
T Consensus         7 lLY~~~il~e~g~~~~AL~~L~~~~~~-I~Dk~~~~E~rA~ll~kLg~~~eA~~~y~~Li~rN--Pdn~~Yy~~L~~~~g   83 (517)
T PF12569_consen    7 LLYKNSILEEAGDYEEALEHLEKNEKQ-ILDKLAVLEKRAELLLKLGRKEEAEKIYRELIDRN--PDNYDYYRGLEEALG   83 (517)
T ss_pred             HHHHHHHHHHCCCHHHHHHHHHhhhhh-CCCHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHC--CCcHHHHHHHHHHHh
Confidence            334456678899999999999886654 33345566677899999999999999999999975  44444 444444442


Q ss_pred             h-----cCChHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHhcCCH-HHHHHHHHHHHhcCCCCCHHHHHHHHHHHHhCCC
Q 040027          289 K-----NRKMDEASRLLDLMVQRGVRPNACTYNTLMDGFCLMGKI-NRAEELFGSMESMGCKHDDVSYNILINGYCKNKE  362 (595)
Q Consensus       289 ~-----~g~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~-~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~  362 (595)
                      -     ..+.+....+|+++...-  |.......+.-.+.....+ ..+..++......|+|   .+|..+-..|.....
T Consensus        84 ~~~~~~~~~~~~~~~~y~~l~~~y--p~s~~~~rl~L~~~~g~~F~~~~~~yl~~~l~KgvP---slF~~lk~Ly~d~~K  158 (517)
T PF12569_consen   84 LQLQLSDEDVEKLLELYDELAEKY--PRSDAPRRLPLDFLEGDEFKERLDEYLRPQLRKGVP---SLFSNLKPLYKDPEK  158 (517)
T ss_pred             hhcccccccHHHHHHHHHHHHHhC--ccccchhHhhcccCCHHHHHHHHHHHHHHHHhcCCc---hHHHHHHHHHcChhH
Confidence            2     235678888999887753  2222222222222221222 3455666677777754   356666666765555


Q ss_pred             HHHHHHHHHHHHHC----C----------CCCCHH--HHHHHHHHHHccCCHHHHHHHHHHHHHCCCCCCHHHHHHHHHH
Q 040027          363 VEEALSLYREMVSK----G----------IKPTVV--TYNTLFLGLFEIHQVEHALKLFDEMQRDGVAADTRTYTTFIDG  426 (595)
Q Consensus       363 ~~~A~~~~~~~~~~----~----------~~~~~~--~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~  426 (595)
                      .+-...++......    +          -+|+..  ++..+.+.|...|++++|+..+++.++.. |..+..|..-...
T Consensus       159 ~~~i~~l~~~~~~~l~~~~~~~~~~~~~~~~p~~~lw~~~~lAqhyd~~g~~~~Al~~Id~aI~ht-Pt~~ely~~Kari  237 (517)
T PF12569_consen  159 AAIIESLVEEYVNSLESNGSFSNGDDEEKEPPSTLLWTLYFLAQHYDYLGDYEKALEYIDKAIEHT-PTLVELYMTKARI  237 (517)
T ss_pred             HHHHHHHHHHHHHhhcccCCCCCccccccCCchHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHhcC-CCcHHHHHHHHHH
Confidence            55555565555432    1          123332  44666788889999999999999999873 4447788888999


Q ss_pred             HHhcCCHHHHHHHHHHHHHcCCCcCHHHHHHHHHHHHhcCChHHHHHHHHhcccCCCCCCH--H----HH--HHHHHHHH
Q 040027          427 LCKNGYIIEAVELFRTLRILKCELDIQAYNCLIDGLCKSGRLKFAWELFCSLPHGVLVPNV--V----TY--NIMIQGLC  498 (595)
Q Consensus       427 ~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~p~~--~----~~--~~l~~~~~  498 (595)
                      +-..|++.+|...++.+...+ .-|..+-+..+..+.+.|+.++|..++......+..|-.  .    .|  ...+.+|.
T Consensus       238 lKh~G~~~~Aa~~~~~Ar~LD-~~DRyiNsK~aKy~LRa~~~e~A~~~~~~Ftr~~~~~~~~L~~mQc~Wf~~e~a~a~~  316 (517)
T PF12569_consen  238 LKHAGDLKEAAEAMDEARELD-LADRYINSKCAKYLLRAGRIEEAEKTASLFTREDVDPLSNLNDMQCMWFETECAEAYL  316 (517)
T ss_pred             HHHCCCHHHHHHHHHHHHhCC-hhhHHHHHHHHHHHHHCCCHHHHHHHHHhhcCCCCCcccCHHHHHHHHHHHHHHHHHH
Confidence            999999999999999999887 667788888889999999999999999998876543322  1    33  34457888


Q ss_pred             hcCChhHHHHHHHHHHH
Q 040027          499 NDGQMDKARDLFLDMEE  515 (595)
Q Consensus       499 ~~g~~~~A~~~~~~~~~  515 (595)
                      +.|++..|++.|....+
T Consensus       317 r~~~~~~ALk~~~~v~k  333 (517)
T PF12569_consen  317 RQGDYGLALKRFHAVLK  333 (517)
T ss_pred             HHhhHHHHHHHHHHHHH
Confidence            99999999998877765

N-terminal acetylation plays a role in normal eukaryotic translation and processing, protect against proteolytic degradation and protein turnover. NAT1 anchors ARD1 and NAT5 to the ribosome and may present the N- terminal of nascent polypeptides for acetylation [], [].

>KOG1127 consensus TPR repeat-containing protein [RNA processing and modification]

Probab=99.35  E-value=6.2e-09  Score=104.08  Aligned_cols=154  Identities=13%  Similarity=0.053  Sum_probs=120.2

Q ss_pred             cccccCCCChHHHHHHHHHHHHhCCCCCCHhhHHHHHHHHHcCCCchh----HHhhCCCCC---CHHHHHHHHHHHHhcC
Q 040027           38 REGDINVITPNEAFCIFDYMLRMHPSPPPVSSFNILLASLAKNKHYDT----RLNATGLFP---NLYTYNILINCFCKIG  110 (595)
Q Consensus        38 ~~~~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~----~~~~~~~~~---~~~~~~~l~~~~~~~g  110 (595)
                      ++-|+...+...|.+.|+.+.+.++.  +..++..+...|++..+++.    .+......|   -...|..+.-.|...+
T Consensus       499 G~iYrd~~Dm~RA~kCf~KAFeLDat--daeaaaa~adtyae~~~we~a~~I~l~~~qka~a~~~k~nW~~rG~yyLea~  576 (1238)
T KOG1127|consen  499 GQIYRDSDDMKRAKKCFDKAFELDAT--DAEAAAASADTYAEESTWEEAFEICLRAAQKAPAFACKENWVQRGPYYLEAH  576 (1238)
T ss_pred             HHHHHHHHHHHHHHHHHHHHhcCCch--hhhhHHHHHHHhhccccHHHHHHHHHHHhhhchHHHHHhhhhhccccccCcc
Confidence            34445556889999999999999998  99999999999999999988    111111111   2334555555678889


Q ss_pred             ChhHHHHHHHHHHhCCCCCCHHHHHHHHHHHHhcCCHhHHHHHHHHHHhcCCCCCHhhHHHHHHHHHhcCChhHHHHHHH
Q 040027          111 RVSLGFIAFGRILRSCFTPNAATFNSLIKGLHAESRIMEAAALFTKLKAFGCEPNVITYNTLINGLCRTGHTMIALNLFE  190 (595)
Q Consensus       111 ~~~~A~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~  190 (595)
                      +..+|+..|+.+.+.. |.|...|..+..+|...|++..|.++|.++.... +.+...........+..|++.+|+..+.
T Consensus       577 n~h~aV~~fQsALR~d-PkD~n~W~gLGeAY~~sGry~~AlKvF~kAs~Lr-P~s~y~~fk~A~~ecd~GkYkeald~l~  654 (1238)
T KOG1127|consen  577 NLHGAVCEFQSALRTD-PKDYNLWLGLGEAYPESGRYSHALKVFTKASLLR-PLSKYGRFKEAVMECDNGKYKEALDALG  654 (1238)
T ss_pred             chhhHHHHHHHHhcCC-chhHHHHHHHHHHHHhcCceehHHHhhhhhHhcC-cHhHHHHHHHHHHHHHhhhHHHHHHHHH
Confidence            9999999999999885 6689999999999999999999999999998763 2233344445556678999999999998


Q ss_pred             HHHhc
Q 040027          191 EMANG  195 (595)
Q Consensus       191 ~~~~~  195 (595)
                      .+...
T Consensus       655 ~ii~~  659 (1238)
T KOG1127|consen  655 LIIYA  659 (1238)
T ss_pred             HHHHH
Confidence            88753

>COG3063 PilF Tfp pilus assembly protein PilF [Cell motility and secretion / Intracellular trafficking and secretion]

Probab=99.33  E-value=3.2e-09  Score=88.55  Aligned_cols=200  Identities=13%  Similarity=0.014  Sum_probs=135.7

Q ss_pred             HHHHHHHHHHhcCChhHHHHHHHHHHhCCCCCCHHHHHHHHHHHHhcCCHhHHHHHHHHHHhcCCCCCHhhHHHHHHHHH
Q 040027           98 TYNILINCFCKIGRVSLGFIAFGRILRSCFTPNAATFNSLIKGLHAESRIMEAAALFTKLKAFGCEPNVITYNTLINGLC  177 (595)
Q Consensus        98 ~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~~l~~~~~  177 (595)
                      ....|.-.|.+.|++..|..-++++++.. +.+..+|..+...|.+.|..+.|.+.|++..... +-+..+.+.....+|
T Consensus        37 arlqLal~YL~~gd~~~A~~nlekAL~~D-Ps~~~a~~~~A~~Yq~~Ge~~~A~e~YrkAlsl~-p~~GdVLNNYG~FLC  114 (250)
T COG3063          37 ARLQLALGYLQQGDYAQAKKNLEKALEHD-PSYYLAHLVRAHYYQKLGENDLADESYRKALSLA-PNNGDVLNNYGAFLC  114 (250)
T ss_pred             HHHHHHHHHHHCCCHHHHHHHHHHHHHhC-cccHHHHHHHHHHHHHcCChhhHHHHHHHHHhcC-CCccchhhhhhHHHH
Confidence            44556667777777777777777777764 4456677777777777777777777777777764 335667777777777


Q ss_pred             hcCChhHHHHHHHHHHhcCCCCCccccCcHHHHHHHHHHHHHcCCHhHHHHHHHHHhhCCCCCCHhHHHHHHHHHHhcCC
Q 040027          178 RTGHTMIALNLFEEMANGNGEIGVVCKPNTVTYSTIIDGLCKEGFVDKAKALFLQMKDENINPDVVTYNSLIHGLCHAND  257 (595)
Q Consensus       178 ~~g~~~~A~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~~ll~~~~~~~~  257 (595)
                      ..|++++|...|++......     ...-..+|..+.-+..+.|+++.|.+.|++..+.. +-...+...+.....+.|+
T Consensus       115 ~qg~~~eA~q~F~~Al~~P~-----Y~~~s~t~eN~G~Cal~~gq~~~A~~~l~raL~~d-p~~~~~~l~~a~~~~~~~~  188 (250)
T COG3063         115 AQGRPEEAMQQFERALADPA-----YGEPSDTLENLGLCALKAGQFDQAEEYLKRALELD-PQFPPALLELARLHYKAGD  188 (250)
T ss_pred             hCCChHHHHHHHHHHHhCCC-----CCCcchhhhhhHHHHhhcCCchhHHHHHHHHHHhC-cCCChHHHHHHHHHHhccc
Confidence            77777777777777766431     23335667777777777777777777777776653 2244556666677777777


Q ss_pred             HHHHHHHHHHHHHCCCCCCHhhHHHHHHHHHhcCChHHHHHHHHHHHHC
Q 040027          258 WNEAKRLFIEMMDQGVQPSVVTFNVIMDELCKNRKMDEASRLLDLMVQR  306 (595)
Q Consensus       258 ~~~A~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~  306 (595)
                      +-.|...++.....+. ++..+....++.....|+.+.+.++=..+.+.
T Consensus       189 y~~Ar~~~~~~~~~~~-~~A~sL~L~iriak~~gd~~~a~~Y~~qL~r~  236 (250)
T COG3063         189 YAPARLYLERYQQRGG-AQAESLLLGIRIAKRLGDRAAAQRYQAQLQRL  236 (250)
T ss_pred             chHHHHHHHHHHhccc-ccHHHHHHHHHHHHHhccHHHHHHHHHHHHHh
Confidence            7777777777666544 56666666677777777776666655555443

>KOG1840 consensus Kinesin light chain [Cytoskeleton]

Probab=99.32  E-value=6.2e-10  Score=107.72  Aligned_cols=243  Identities=18%  Similarity=0.127  Sum_probs=156.9

Q ss_pred             HHHHHHHHHHHhcCChhHHHHHHHHHHhC-----CC-CCCHH-HHHHHHHHHHhcCCHhHHHHHHHHHHhc-----CCC-
Q 040027           97 YTYNILINCFCKIGRVSLGFIAFGRILRS-----CF-TPNAA-TFNSLIKGLHAESRIMEAAALFTKLKAF-----GCE-  163 (595)
Q Consensus        97 ~~~~~l~~~~~~~g~~~~A~~~~~~~~~~-----~~-~~~~~-~~~~l~~~~~~~g~~~~A~~~~~~~~~~-----~~~-  163 (595)
                      .+...+...|...|+++.|..+++.+++.     |. -|... ..+.+...|...+++++|+.+|+++...     |-. 
T Consensus       200 ~~~~~La~~y~~~g~~e~A~~l~k~Al~~l~k~~G~~hl~va~~l~~~a~~y~~~~k~~eAv~ly~~AL~i~e~~~G~~h  279 (508)
T KOG1840|consen  200 RTLRNLAEMYAVQGRLEKAEPLCKQALRILEKTSGLKHLVVASMLNILALVYRSLGKYDEAVNLYEEALTIREEVFGEDH  279 (508)
T ss_pred             HHHHHHHHHHHHhccHHHHHHHHHHHHHHHHHccCccCHHHHHHHHHHHHHHHHhccHHHHHHHHHHHHHHHHHhcCCCC
Confidence            45556899999999999999999999876     11 22233 3445778899999999999999998753     211 


Q ss_pred             -CCHhhHHHHHHHHHhcCChhHHHHHHHHHHhcCCCCCccccCc-HHHHHHHHHHHHHcCCHhHHHHHHHHHhhC---CC
Q 040027          164 -PNVITYNTLINGLCRTGHTMIALNLFEEMANGNGEIGVVCKPN-TVTYSTIIDGLCKEGFVDKAKALFLQMKDE---NI  238 (595)
Q Consensus       164 -~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~~-~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~---~~  238 (595)
                       .-..++..|..+|...|++++|...++++...-........+. ...++.++..+...+++++|..++....+.   -+
T Consensus       280 ~~va~~l~nLa~ly~~~GKf~EA~~~~e~Al~I~~~~~~~~~~~v~~~l~~~~~~~~~~~~~Eea~~l~q~al~i~~~~~  359 (508)
T KOG1840|consen  280 PAVAATLNNLAVLYYKQGKFAEAEEYCERALEIYEKLLGASHPEVAAQLSELAAILQSMNEYEEAKKLLQKALKIYLDAP  359 (508)
T ss_pred             HHHHHHHHHHHHHHhccCChHHHHHHHHHHHHHHHHhhccChHHHHHHHHHHHHHHHHhcchhHHHHHHHHHHHHHHhhc
Confidence             1245678888899999999999998888765432111011222 334666777788888888888888765542   01


Q ss_pred             CC----CHhHHHHHHHHHHhcCCHHHHHHHHHHHHHCC----C--CC-CHhhHHHHHHHHHhcCChHHHHHHHHHHHHC-
Q 040027          239 NP----DVVTYNSLIHGLCHANDWNEAKRLFIEMMDQG----V--QP-SVVTFNVIMDELCKNRKMDEASRLLDLMVQR-  306 (595)
Q Consensus       239 ~~----~~~~~~~ll~~~~~~~~~~~A~~~~~~~~~~~----~--~~-~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~-  306 (595)
                      .+    -..+++.|...|.+.|++++|.++|++++...    -  .+ ....++.+...|.+.+.+.+|.++|.+.... 
T Consensus       360 g~~~~~~a~~~~nl~~l~~~~gk~~ea~~~~k~ai~~~~~~~~~~~~~~~~~l~~la~~~~~~k~~~~a~~l~~~~~~i~  439 (508)
T KOG1840|consen  360 GEDNVNLAKIYANLAELYLKMGKYKEAEELYKKAIQILRELLGKKDYGVGKPLNQLAEAYEELKKYEEAEQLFEEAKDIM  439 (508)
T ss_pred             cccchHHHHHHHHHHHHHHHhcchhHHHHHHHHHHHHHHhcccCcChhhhHHHHHHHHHHHHhcccchHHHHHHHHHHHH
Confidence            11    23467777777777777777777777765431    1  11 1234556666666666666666666554321 


Q ss_pred             ---C--CCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHH
Q 040027          307 ---G--VRPNACTYNTLMDGFCLMGKINRAEELFGSME  339 (595)
Q Consensus       307 ---~--~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~  339 (595)
                         |  .+-...+|..|+..|.+.|+++.|+++.+.+.
T Consensus       440 ~~~g~~~~~~~~~~~nL~~~Y~~~g~~e~a~~~~~~~~  477 (508)
T KOG1840|consen  440 KLCGPDHPDVTYTYLNLAALYRAQGNYEAAEELEEKVL  477 (508)
T ss_pred             HHhCCCCCchHHHHHHHHHHHHHcccHHHHHHHHHHHH
Confidence               1  11123455566666666666666666655543

>KOG0985 consensus Vesicle coat protein clathrin, heavy chain [Intracellular trafficking, secretion, and vesicular transport]

Probab=99.31  E-value=5.9e-08  Score=97.29  Aligned_cols=441  Identities=12%  Similarity=0.094  Sum_probs=266.5

Q ss_pred             cCCCChHHHHHHHHHHHHhCCCCCCHhhHHHHHHHHHcCCCchhHHhhCCCCCCHHHHHHHHHHHHhcCChhHHHHHHHH
Q 040027           42 INVITPNEAFCIFDYMLRMHPSPPPVSSFNILLASLAKNKHYDTRLNATGLFPNLYTYNILINCFCKIGRVSLGFIAFGR  121 (595)
Q Consensus        42 ~~~~~~~~A~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~  121 (595)
                      -++++++--...++..++.+..  ++.+++++...|...++-.++......--|    +..+..|+...++.-|.-.|++
T Consensus       849 EkRNRLklLlp~LE~~i~eG~~--d~a~hnAlaKIyIDSNNnPE~fLkeN~yYD----s~vVGkYCEKRDP~lA~vaYer  922 (1666)
T KOG0985|consen  849 EKRNRLKLLLPWLESLIQEGSQ--DPATHNALAKIYIDSNNNPERFLKENPYYD----SKVVGKYCEKRDPHLACVAYER  922 (1666)
T ss_pred             HhhhhHHHHHHHHHHHHhccCc--chHHHhhhhheeecCCCChHHhcccCCcch----hhHHhhhhcccCCceEEEeecc
Confidence            4678888888899999999877  999999999999999987775544432222    2344455555555444433332


Q ss_pred             HHhC----CCCCCHHHHHHHHHHHHhcCCHhH-----------HHHHHHHHHhcCCC--CCHhhHHHHHHHHHhcCChhH
Q 040027          122 ILRS----CFTPNAATFNSLIKGLHAESRIME-----------AAALFTKLKAFGCE--PNVITYNTLINGLCRTGHTMI  184 (595)
Q Consensus       122 ~~~~----~~~~~~~~~~~l~~~~~~~g~~~~-----------A~~~~~~~~~~~~~--~~~~~~~~l~~~~~~~g~~~~  184 (595)
                      -...    ++....+.|....+.+.+..+.+-           -.++.+...+.+++  .|+......+.++...+-..+
T Consensus       923 GqcD~elI~vcNeNSlfK~~aRYlv~R~D~~LW~~VL~e~n~~rRqLiDqVv~tal~E~~dPe~vS~tVkAfMtadLp~e 1002 (1666)
T KOG0985|consen  923 GQCDLELINVCNENSLFKSQARYLVERSDPDLWAKVLNEENPYRRQLIDQVVQTALPETQDPEEVSVTVKAFMTADLPNE 1002 (1666)
T ss_pred             cCCcHHHHHhcCchhHHHHHHHHHHhccChHHHHHHHhccChHHHHHHHHHHHhcCCccCChHHHHHHHHHHHhcCCcHH
Confidence            1100    012223334444444444333321           12344555444332  356667777888888888888


Q ss_pred             HHHHHHHHHhcCCCCCccccCcHHHHHHHHHHHHHcCCHhHHHHHHHHHhhCCCCCCHhHHHHHHHHHHhcCCHHHHHHH
Q 040027          185 ALNLFEEMANGNGEIGVVCKPNTVTYSTIIDGLCKEGFVDKAKALFLQMKDENINPDVVTYNSLIHGLCHANDWNEAKRL  264 (595)
Q Consensus       185 A~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~~ll~~~~~~~~~~~A~~~  264 (595)
                      -+++++++.-.+..    +..+...-+.|+-...+ -+..+..++.+++-.-+. |+      +...+...+-+++|..+
T Consensus      1003 LIELLEKIvL~~S~----Fse~~nLQnLLiLtAik-ad~trVm~YI~rLdnyDa-~~------ia~iai~~~LyEEAF~i 1070 (1666)
T KOG0985|consen 1003 LIELLEKIVLDNSV----FSENRNLQNLLILTAIK-ADRTRVMEYINRLDNYDA-PD------IAEIAIENQLYEEAFAI 1070 (1666)
T ss_pred             HHHHHHHHhcCCcc----cccchhhhhhHHHHHhh-cChHHHHHHHHHhccCCc-hh------HHHHHhhhhHHHHHHHH
Confidence            88888888765422    12233334444444444 345566677766654321 12      34456667778888888


Q ss_pred             HHHHHHCCCCCCHhhHHHHHHHHHhcCChHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHhcCCC
Q 040027          265 FIEMMDQGVQPSVVTFNVIMDELCKNRKMDEASRLLDLMVQRGVRPNACTYNTLMDGFCLMGKINRAEELFGSMESMGCK  344 (595)
Q Consensus       265 ~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~  344 (595)
                      |++.-     .+....+.++.   .-+..+.|.++-++.-      .+.+|..+..+-.+.|...+|++-|-+.      
T Consensus      1071 fkkf~-----~n~~A~~VLie---~i~~ldRA~efAe~~n------~p~vWsqlakAQL~~~~v~dAieSyika------ 1130 (1666)
T KOG0985|consen 1071 FKKFD-----MNVSAIQVLIE---NIGSLDRAYEFAERCN------EPAVWSQLAKAQLQGGLVKDAIESYIKA------ 1130 (1666)
T ss_pred             HHHhc-----ccHHHHHHHHH---HhhhHHHHHHHHHhhC------ChHHHHHHHHHHHhcCchHHHHHHHHhc------
Confidence            87643     24445555543   3455666666555432      4567888888888888888887766442      


Q ss_pred             CCHHHHHHHHHHHHhCCCHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHccCCHHHHHHHHHHHHHCCCCCCHHHHHHHH
Q 040027          345 HDDVSYNILINGYCKNKEVEEALSLYREMVSKGIKPTVVTYNTLFLGLFEIHQVEHALKLFDEMQRDGVAADTRTYTTFI  424 (595)
Q Consensus       345 ~~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~  424 (595)
                      .|+..|...+....+.|.|++-.+.+....+..-.|...  ..++-+|++.++..+.++.+       ..|+......+.
T Consensus      1131 dDps~y~eVi~~a~~~~~~edLv~yL~MaRkk~~E~~id--~eLi~AyAkt~rl~elE~fi-------~gpN~A~i~~vG 1201 (1666)
T KOG0985|consen 1131 DDPSNYLEVIDVASRTGKYEDLVKYLLMARKKVREPYID--SELIFAYAKTNRLTELEEFI-------AGPNVANIQQVG 1201 (1666)
T ss_pred             CCcHHHHHHHHHHHhcCcHHHHHHHHHHHHHhhcCccch--HHHHHHHHHhchHHHHHHHh-------cCCCchhHHHHh
Confidence            366678888888888888888888777766654444443  55677788877776655443       246666667777


Q ss_pred             HHHHhcCCHHHHHHHHHHHHHcCCCcCHHHHHHHHHHHHhcCChHHHHHHHHhcccCCCCCCHHHHHHHHHHHHhcCChh
Q 040027          425 DGLCKNGYIIEAVELFRTLRILKCELDIQAYNCLIDGLCKSGRLKFAWELFCSLPHGVLVPNVVTYNIMIQGLCNDGQMD  504 (595)
Q Consensus       425 ~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~p~~~~~~~l~~~~~~~g~~~  504 (595)
                      .-|...|.++.|.-+|..         ...|..+...+...|++..|...-+++.      +..+|-.+-.+|...+.+.
T Consensus      1202 drcf~~~~y~aAkl~y~~---------vSN~a~La~TLV~LgeyQ~AVD~aRKAn------s~ktWK~VcfaCvd~~EFr 1266 (1666)
T KOG0985|consen 1202 DRCFEEKMYEAAKLLYSN---------VSNFAKLASTLVYLGEYQGAVDAARKAN------STKTWKEVCFACVDKEEFR 1266 (1666)
T ss_pred             HHHhhhhhhHHHHHHHHH---------hhhHHHHHHHHHHHHHHHHHHHHhhhcc------chhHHHHHHHHHhchhhhh
Confidence            777777777777766653         3345566666666777777666555443      3456666666666555443


Q ss_pred             HHHHHHHHHHHcCCCCCHHHHHHHHHHHHHcCChhHHHHHHHHHH
Q 040027          505 KARDLFLDMEENAAAPDVITFDMLIHGFIRINEPSKVNELLHKMK  549 (595)
Q Consensus       505 ~A~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~  549 (595)
                      -|     +|...++-....-...++..|...|-+++-..+++..+
T Consensus      1267 lA-----QiCGL~iivhadeLeeli~~Yq~rGyFeElIsl~Ea~L 1306 (1666)
T KOG0985|consen 1267 LA-----QICGLNIIVHADELEELIEYYQDRGYFEELISLLEAGL 1306 (1666)
T ss_pred             HH-----HhcCceEEEehHhHHHHHHHHHhcCcHHHHHHHHHhhh
Confidence            33     23333333344445556666666666666666655544

>PRK11189 lipoprotein NlpI; Provisional

Probab=99.28  E-value=4.4e-09  Score=97.87  Aligned_cols=94  Identities=12%  Similarity=-0.014  Sum_probs=45.1

Q ss_pred             HHHHHHHHHhcCCHHHHHHHHHHHHhcCCCCCHHHHHHHHHHHHhCCCHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHc
Q 040027          315 YNTLMDGFCLMGKINRAEELFGSMESMGCKHDDVSYNILINGYCKNKEVEEALSLYREMVSKGIKPTVVTYNTLFLGLFE  394 (595)
Q Consensus       315 ~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~~l~~~~~~  394 (595)
                      +..+...|...|++++|...|++..+.. +.+...|+.+...+...|++++|...|++.++..+. +..++..+...+..
T Consensus        67 ~~~~g~~~~~~g~~~~A~~~~~~Al~l~-P~~~~a~~~lg~~~~~~g~~~~A~~~~~~Al~l~P~-~~~a~~~lg~~l~~  144 (296)
T PRK11189         67 HYERGVLYDSLGLRALARNDFSQALALR-PDMADAYNYLGIYLTQAGNFDAAYEAFDSVLELDPT-YNYAYLNRGIALYY  144 (296)
T ss_pred             HHHHHHHHHHCCCHHHHHHHHHHHHHcC-CCCHHHHHHHHHHHHHCCCHHHHHHHHHHHHHhCCC-CHHHHHHHHHHHHH
Confidence            4444445555555555555555554442 233445555555555555555555555555443222 23344444444444


Q ss_pred             cCCHHHHHHHHHHHHH
Q 040027          395 IHQVEHALKLFDEMQR  410 (595)
Q Consensus       395 ~~~~~~a~~~~~~~~~  410 (595)
                      .|++++|.+.++...+
T Consensus       145 ~g~~~eA~~~~~~al~  160 (296)
T PRK11189        145 GGRYELAQDDLLAFYQ  160 (296)
T ss_pred             CCCHHHHHHHHHHHHH
Confidence            4555555555554444

>PRK11189 lipoprotein NlpI; Provisional

Probab=99.28  E-value=7.4e-09  Score=96.36  Aligned_cols=94  Identities=14%  Similarity=-0.049  Sum_probs=42.6

Q ss_pred             HHHHHHHHHhCCCHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHccCCHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHh
Q 040027          350 YNILINGYCKNKEVEEALSLYREMVSKGIKPTVVTYNTLFLGLFEIHQVEHALKLFDEMQRDGVAADTRTYTTFIDGLCK  429 (595)
Q Consensus       350 ~~~l~~~~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~  429 (595)
                      |..+...|...|++++|...|++.++..+. +...|..+...+...|++++|...|+..++.. +.+...+..+..++..
T Consensus        67 ~~~~g~~~~~~g~~~~A~~~~~~Al~l~P~-~~~a~~~lg~~~~~~g~~~~A~~~~~~Al~l~-P~~~~a~~~lg~~l~~  144 (296)
T PRK11189         67 HYERGVLYDSLGLRALARNDFSQALALRPD-MADAYNYLGIYLTQAGNFDAAYEAFDSVLELD-PTYNYAYLNRGIALYY  144 (296)
T ss_pred             HHHHHHHHHHCCCHHHHHHHHHHHHHcCCC-CHHHHHHHHHHHHHCCCHHHHHHHHHHHHHhC-CCCHHHHHHHHHHHHH
Confidence            444444444444555554444444443222 33444444444444455555554444444432 2223344444444444


Q ss_pred             cCCHHHHHHHHHHHHH
Q 040027          430 NGYIIEAVELFRTLRI  445 (595)
Q Consensus       430 ~g~~~~A~~~~~~~~~  445 (595)
                      .|++++|.+.+++..+
T Consensus       145 ~g~~~eA~~~~~~al~  160 (296)
T PRK11189        145 GGRYELAQDDLLAFYQ  160 (296)
T ss_pred             CCCHHHHHHHHHHHHH
Confidence            4455555555444444

>KOG1840 consensus Kinesin light chain [Cytoskeleton]

Probab=99.28  E-value=1.6e-09  Score=104.90  Aligned_cols=247  Identities=20%  Similarity=0.187  Sum_probs=164.0

Q ss_pred             CCCHHHHHHHHHHHHhcCCHhHHHHHHHHHHhc-----C-CCCCHhhH-HHHHHHHHhcCChhHHHHHHHHHHhcCCC-C
Q 040027          128 TPNAATFNSLIKGLHAESRIMEAAALFTKLKAF-----G-CEPNVITY-NTLINGLCRTGHTMIALNLFEEMANGNGE-I  199 (595)
Q Consensus       128 ~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~-----~-~~~~~~~~-~~l~~~~~~~g~~~~A~~~~~~~~~~~~~-~  199 (595)
                      |.-..+...+...|..+|+++.|..+++...+.     | ..|...+. ..+...|...+++.+|..+|+++...... .
T Consensus       196 P~~~~~~~~La~~y~~~g~~e~A~~l~k~Al~~l~k~~G~~hl~va~~l~~~a~~y~~~~k~~eAv~ly~~AL~i~e~~~  275 (508)
T KOG1840|consen  196 PERLRTLRNLAEMYAVQGRLEKAEPLCKQALRILEKTSGLKHLVVASMLNILALVYRSLGKYDEAVNLYEEALTIREEVF  275 (508)
T ss_pred             chHHHHHHHHHHHHHHhccHHHHHHHHHHHHHHHHHccCccCHHHHHHHHHHHHHHHHhccHHHHHHHHHHHHHHHHHhc
Confidence            333445666889999999999999999988764     2 12333333 34778899999999999999998864321 1


Q ss_pred             CccccCcHHHHHHHHHHHHHcCCHhHHHHHHHHHhhC-----CC-CCC-HhHHHHHHHHHHhcCCHHHHHHHHHHHHHC-
Q 040027          200 GVVCKPNTVTYSTIIDGLCKEGFVDKAKALFLQMKDE-----NI-NPD-VVTYNSLIHGLCHANDWNEAKRLFIEMMDQ-  271 (595)
Q Consensus       200 ~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~-----~~-~~~-~~~~~~ll~~~~~~~~~~~A~~~~~~~~~~-  271 (595)
                      |...+.-..+++.|..+|.+.|++++|...+++..+.     +. .|. ...++.+...+...+++++|..++....+. 
T Consensus       276 G~~h~~va~~l~nLa~ly~~~GKf~EA~~~~e~Al~I~~~~~~~~~~~v~~~l~~~~~~~~~~~~~Eea~~l~q~al~i~  355 (508)
T KOG1840|consen  276 GEDHPAVAATLNNLAVLYYKQGKFAEAEEYCERALEIYEKLLGASHPEVAAQLSELAAILQSMNEYEEAKKLLQKALKIY  355 (508)
T ss_pred             CCCCHHHHHHHHHHHHHHhccCChHHHHHHHHHHHHHHHHhhccChHHHHHHHHHHHHHHHHhcchhHHHHHHHHHHHHH
Confidence            2222334667888999999999999999888876542     11 112 223555667788888888888888766542 


Q ss_pred             --CCCCC----HhhHHHHHHHHHhcCChHHHHHHHHHHHHCC----C---CCCHHHHHHHHHHHHhcCCHHHHHHHHHHH
Q 040027          272 --GVQPS----VVTFNVIMDELCKNRKMDEASRLLDLMVQRG----V---RPNACTYNTLMDGFCLMGKINRAEELFGSM  338 (595)
Q Consensus       272 --~~~~~----~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~----~---~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~  338 (595)
                        -+.++    ..+++.+...|...|++++|.++++.++...    .   .-....++.+...|.+.+++..|.++|.+.
T Consensus       356 ~~~~g~~~~~~a~~~~nl~~l~~~~gk~~ea~~~~k~ai~~~~~~~~~~~~~~~~~l~~la~~~~~~k~~~~a~~l~~~~  435 (508)
T KOG1840|consen  356 LDAPGEDNVNLAKIYANLAELYLKMGKYKEAEELYKKAIQILRELLGKKDYGVGKPLNQLAEAYEELKKYEEAEQLFEEA  435 (508)
T ss_pred             HhhccccchHHHHHHHHHHHHHHHhcchhHHHHHHHHHHHHHHhcccCcChhhhHHHHHHHHHHHHhcccchHHHHHHHH
Confidence              11111    3467778888888888888888887776531    1   112345566677777777777777776654


Q ss_pred             Hhc----C--CCCCHHHHHHHHHHHHhCCCHHHHHHHHHHHH
Q 040027          339 ESM----G--CKHDDVSYNILINGYCKNKEVEEALSLYREMV  374 (595)
Q Consensus       339 ~~~----~--~~~~~~~~~~l~~~~~~~~~~~~A~~~~~~~~  374 (595)
                      ...    |  .+....+|..|...|...|+++.|.++.+.+.
T Consensus       436 ~~i~~~~g~~~~~~~~~~~nL~~~Y~~~g~~e~a~~~~~~~~  477 (508)
T KOG1840|consen  436 KDIMKLCGPDHPDVTYTYLNLAALYRAQGNYEAAEELEEKVL  477 (508)
T ss_pred             HHHHHHhCCCCCchHHHHHHHHHHHHHcccHHHHHHHHHHHH
Confidence            321    1  12223466677777777777777777666554

>KOG4340 consensus Uncharacterized conserved protein [Function unknown]

Probab=99.26  E-value=1.6e-08  Score=87.40  Aligned_cols=420  Identities=15%  Similarity=0.120  Sum_probs=244.6

Q ss_pred             HHHHHHHHHhcCChhHHHHHHHHHHhCCCCCCHHHHHHHHHHHHhcCCHhHHHHHHHHHHhcCCCCCHhhHH-HHHHHHH
Q 040027           99 YNILINCFCKIGRVSLGFIAFGRILRSCFTPNAATFNSLIKGLHAESRIMEAAALFTKLKAFGCEPNVITYN-TLINGLC  177 (595)
Q Consensus        99 ~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~-~l~~~~~  177 (595)
                      +.+++..+.+..++++|++++..-.++. +.+......+..+|....++..|.+.|+++...  .|...-|. .-...+.
T Consensus        13 ftaviy~lI~d~ry~DaI~~l~s~~Er~-p~~rAgLSlLgyCYY~~Q~f~~AA~CYeQL~ql--~P~~~qYrlY~AQSLY   89 (459)
T KOG4340|consen   13 FTAVVYRLIRDARYADAIQLLGSELERS-PRSRAGLSLLGYCYYRLQEFALAAECYEQLGQL--HPELEQYRLYQAQSLY   89 (459)
T ss_pred             hHHHHHHHHHHhhHHHHHHHHHHHHhcC-ccchHHHHHHHHHHHHHHHHHHHHHHHHHHHhh--ChHHHHHHHHHHHHHH
Confidence            4466667788899999999999988884 336666777778888899999999999999876  44444443 3456677


Q ss_pred             hcCChhHHHHHHHHHHhcCCCCCccccCcHHHHHHHHHHHHHcCCHhHHHHHHHHHhhCCCCCCHhHHHHHHHHHHhcCC
Q 040027          178 RTGHTMIALNLFEEMANGNGEIGVVCKPNTVTYSTIIDGLCKEGFVDKAKALFLQMKDENINPDVVTYNSLIHGLCHAND  257 (595)
Q Consensus       178 ~~g~~~~A~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~~ll~~~~~~~~  257 (595)
                      +.+.+..|+.+...|....       .....+...-..+....+|+..+..+.++....|   +..+.+...-...+.|+
T Consensus        90 ~A~i~ADALrV~~~~~D~~-------~L~~~~lqLqaAIkYse~Dl~g~rsLveQlp~en---~Ad~~in~gCllykegq  159 (459)
T KOG4340|consen   90 KACIYADALRVAFLLLDNP-------ALHSRVLQLQAAIKYSEGDLPGSRSLVEQLPSEN---EADGQINLGCLLYKEGQ  159 (459)
T ss_pred             HhcccHHHHHHHHHhcCCH-------HHHHHHHHHHHHHhcccccCcchHHHHHhccCCC---ccchhccchheeecccc
Confidence            8899999999988876421       0111222222334456789999999998887543   45555566666788999


Q ss_pred             HHHHHHHHHHHHHC-CCCCCHhhHHHHHHHHHhcCChHHHHHHHHHHHHCCCCCCHHHH----HHHHHHHHhcCCHHHHH
Q 040027          258 WNEAKRLFIEMMDQ-GVQPSVVTFNVIMDELCKNRKMDEASRLLDLMVQRGVRPNACTY----NTLMDGFCLMGKINRAE  332 (595)
Q Consensus       258 ~~~A~~~~~~~~~~-~~~~~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~----~~l~~~~~~~~~~~~a~  332 (595)
                      ++.|.+-|+...+. |.. ....|+..+ ++.+.|++..|++...+++.+|++..+..-    .-.+.+ ...|+.   .
T Consensus       160 yEaAvqkFqaAlqvsGyq-pllAYniAL-aHy~~~qyasALk~iSEIieRG~r~HPElgIGm~tegiDv-rsvgNt---~  233 (459)
T KOG4340|consen  160 YEAAVQKFQAALQVSGYQ-PLLAYNLAL-AHYSSRQYASALKHISEIIERGIRQHPELGIGMTTEGIDV-RSVGNT---L  233 (459)
T ss_pred             HHHHHHHHHHHHhhcCCC-chhHHHHHH-HHHhhhhHHHHHHHHHHHHHhhhhcCCccCccceeccCch-hcccch---H
Confidence            99999999998876 454 345566444 677889999999999999998865322210    000000 000110   0


Q ss_pred             HHHHHHHhcCCCCCHHHHHHHHHHHHhCCCHHHHHHHHHHHHHC-CCCCCHHHHHHHHHHHHccCCHHHHHHHHHHHHHC
Q 040027          333 ELFGSMESMGCKHDDVSYNILINGYCKNKEVEEALSLYREMVSK-GIKPTVVTYNTLFLGLFEIHQVEHALKLFDEMQRD  411 (595)
Q Consensus       333 ~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~~-~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~  411 (595)
                      .+....       -...+|.-...+.+.++++.|.+.+.+|.-+ .-..|+.|...+.-.- ..+++....+-+.-++..
T Consensus       234 ~lh~Sa-------l~eAfNLKaAIeyq~~n~eAA~eaLtDmPPRaE~elDPvTLHN~Al~n-~~~~p~~g~~KLqFLL~~  305 (459)
T KOG4340|consen  234 VLHQSA-------LVEAFNLKAAIEYQLRNYEAAQEALTDMPPRAEEELDPVTLHNQALMN-MDARPTEGFEKLQFLLQQ  305 (459)
T ss_pred             HHHHHH-------HHHHhhhhhhhhhhcccHHHHHHHhhcCCCcccccCCchhhhHHHHhc-ccCCccccHHHHHHHHhc
Confidence            000000       1224455555677788888888887777533 1233555555443222 234444445555555554


Q ss_pred             CCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHHcCC-CcCHHHHHHHHHHHHhcCChHHHHHHHHhcccCCCCCCHHHH
Q 040027          412 GVAADTRTYTTFIDGLCKNGYIIEAVELFRTLRILKC-ELDIQAYNCLIDGLCKSGRLKFAWELFCSLPHGVLVPNVVTY  490 (595)
Q Consensus       412 ~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~-~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~p~~~~~  490 (595)
                      + |-...|+..++-.||+..-++-|-.++.+-..... -.+...|+.+=..-......++|.+-++.+... +.-.....
T Consensus       306 n-PfP~ETFANlLllyCKNeyf~lAADvLAEn~~lTyk~L~~Yly~LLdaLIt~qT~pEea~KKL~~La~~-l~~kLRkl  383 (459)
T KOG4340|consen  306 N-PFPPETFANLLLLYCKNEYFDLAADVLAENAHLTYKFLTPYLYDLLDALITCQTAPEEAFKKLDGLAGM-LTEKLRKL  383 (459)
T ss_pred             C-CCChHHHHHHHHHHhhhHHHhHHHHHHhhCcchhHHHhhHHHHHHHHHHHhCCCCHHHHHHHHHHHHHH-HHHHHHHH
Confidence            3 34557777788888888888888777754332111 122333333222222345566666665554331 00000011


Q ss_pred             HHHHHHHHhcCCh---hHHHHHHHHHHHcCCCCCHHHHHHHHHHHHHcCChhHHHHHHHHHHHC
Q 040027          491 NIMIQGLCNDGQM---DKARDLFLDMEENAAAPDVITFDMLIHGFIRINEPSKVNELLHKMKEK  551 (595)
Q Consensus       491 ~~l~~~~~~~g~~---~~A~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~  551 (595)
                      ..-+.--...++-   ..|++-+++.++.    -......-.+.|++..++..+.+.|+.-.+.
T Consensus       384 Ai~vQe~r~~~dd~a~R~ai~~Yd~~LE~----YLPVlMa~AkiyW~~~Dy~~vEk~Fr~Svef  443 (459)
T KOG4340|consen  384 AIQVQEARHNRDDEAIRKAVNEYDETLEK----YLPVLMAQAKIYWNLEDYPMVEKIFRKSVEF  443 (459)
T ss_pred             HHHHHHHHhcccHHHHHHHHHHHHHHHHH----HHHHHHHHHHhhccccccHHHHHHHHHHHhh
Confidence            1111111111111   1222333333332    1122334456677888888888888877753

>KOG4318 consensus Bicoid mRNA stability factor [RNA processing and modification]

Probab=99.25  E-value=9e-09  Score=101.79  Aligned_cols=86  Identities=21%  Similarity=0.259  Sum_probs=56.4

Q ss_pred             CCCHHHHHHHHHHHHhCCCHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHccCCHHHHHHHHHHHHHCCCCCCHHHHHHH
Q 040027          344 KHDDVSYNILINGYCKNKEVEEALSLYREMVSKGIKPTVVTYNTLFLGLFEIHQVEHALKLFDEMQRDGVAADTRTYTTF  423 (595)
Q Consensus       344 ~~~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l  423 (595)
                      .+++.++...+.+-...|+.+.|..++.+|.+.|++.+..-|..++-+   .++...+..+++-|...|+.|+..|+...
T Consensus       201 ~~~s~~l~a~l~~alaag~~d~Ak~ll~emke~gfpir~HyFwpLl~g---~~~~q~~e~vlrgmqe~gv~p~seT~ady  277 (1088)
T KOG4318|consen  201 APTSETLHAVLKRALAAGDVDGAKNLLYEMKEKGFPIRAHYFWPLLLG---INAAQVFEFVLRGMQEKGVQPGSETQADY  277 (1088)
T ss_pred             CCChHHHHHHHHHHHhcCchhhHHHHHHHHHHcCCCcccccchhhhhc---CccchHHHHHHHHHHHhcCCCCcchhHHH
Confidence            366667777777777777777777777777777766666655555544   56666666666666677777777776666


Q ss_pred             HHHHHhcCC
Q 040027          424 IDGLCKNGY  432 (595)
Q Consensus       424 ~~~~~~~g~  432 (595)
                      +..+...|.
T Consensus       278 vip~l~N~~  286 (1088)
T KOG4318|consen  278 VIPQLSNGQ  286 (1088)
T ss_pred             HHhhhcchh
Confidence            655555443

>KOG0624 consensus dsRNA-activated protein kinase inhibitor P58, contains TPR and DnaJ domains [Defense mechanisms]

Probab=99.22  E-value=5.2e-07  Score=79.88  Aligned_cols=192  Identities=8%  Similarity=0.048  Sum_probs=94.5

Q ss_pred             HHHHHhcCChHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHhcCCCCCHHHHHHHHHHHHhCCCH
Q 040027          284 MDELCKNRKMDEASRLLDLMVQRGVRPNACTYNTLMDGFCLMGKINRAEELFGSMESMGCKHDDVSYNILINGYCKNKEV  363 (595)
Q Consensus       284 ~~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~  363 (595)
                      +..+...|+...++.....+++.. +-+...+..-..+|...|++..|+.-++...+.. ..+...+..+-..+...|+.
T Consensus       162 l~s~~~~GD~~~ai~~i~~llEi~-~Wda~l~~~Rakc~i~~~e~k~AI~Dlk~askLs-~DnTe~~ykis~L~Y~vgd~  239 (504)
T KOG0624|consen  162 LKSASGSGDCQNAIEMITHLLEIQ-PWDASLRQARAKCYIAEGEPKKAIHDLKQASKLS-QDNTEGHYKISQLLYTVGDA  239 (504)
T ss_pred             HHHHhcCCchhhHHHHHHHHHhcC-cchhHHHHHHHHHHHhcCcHHHHHHHHHHHHhcc-ccchHHHHHHHHHHHhhhhH
Confidence            334455666666666666666642 2255555556666666777776666666655543 33444555556666666777


Q ss_pred             HHHHHHHHHHHHCCCCCCHHH-H---HH---H------HHHHHccCCHHHHHHHHHHHHHCCCCCCH---HHHHHHHHHH
Q 040027          364 EEALSLYREMVSKGIKPTVVT-Y---NT---L------FLGLFEIHQVEHALKLFDEMQRDGVAADT---RTYTTFIDGL  427 (595)
Q Consensus       364 ~~A~~~~~~~~~~~~~~~~~~-~---~~---l------~~~~~~~~~~~~a~~~~~~~~~~~~~~~~---~~~~~l~~~~  427 (595)
                      +.++...++.++.  .|+... |   ..   +      +......++|.+++...+...+.......   ..+..+-.++
T Consensus       240 ~~sL~~iRECLKl--dpdHK~Cf~~YKklkKv~K~les~e~~ie~~~~t~cle~ge~vlk~ep~~~~ir~~~~r~~c~C~  317 (504)
T KOG0624|consen  240 ENSLKEIRECLKL--DPDHKLCFPFYKKLKKVVKSLESAEQAIEEKHWTECLEAGEKVLKNEPEETMIRYNGFRVLCTCY  317 (504)
T ss_pred             HHHHHHHHHHHcc--CcchhhHHHHHHHHHHHHHHHHHHHHHHhhhhHHHHHHHHHHHHhcCCcccceeeeeeheeeecc
Confidence            7666666666654  233211 1   00   0      01112233444444444444443211111   1122222333


Q ss_pred             HhcCCHHHHHHHHHHHHHcCCCcCHHHHHHHHHHHHhcCChHHHHHHHHhccc
Q 040027          428 CKNGYIIEAVELFRTLRILKCELDIQAYNCLIDGLCKSGRLKFAWELFCSLPH  480 (595)
Q Consensus       428 ~~~g~~~~A~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~  480 (595)
                      ...|.+.+|++...+++... +.|..++..-..+|.-...++.|+.-|+.+.+
T Consensus       318 ~~d~~~~eAiqqC~evL~~d-~~dv~~l~dRAeA~l~dE~YD~AI~dye~A~e  369 (504)
T KOG0624|consen  318 REDEQFGEAIQQCKEVLDID-PDDVQVLCDRAEAYLGDEMYDDAIHDYEKALE  369 (504)
T ss_pred             cccCCHHHHHHHHHHHHhcC-chHHHHHHHHHHHHhhhHHHHHHHHHHHHHHh
Confidence            44455555555555555432 22344555555555555555555555555554

>KOG1127 consensus TPR repeat-containing protein [RNA processing and modification]

Probab=99.22  E-value=2.1e-07  Score=93.51  Aligned_cols=501  Identities=12%  Similarity=-0.015  Sum_probs=246.1

Q ss_pred             CChHHHHHHHHHHHHhCCCCCCHhhHHHHHHHHHcCCCchh--HHh--hCCCC-CCHHHHHHHHHHHHhcCChhHHHHHH
Q 040027           45 ITPNEAFCIFDYMLRMHPSPPPVSSFNILLASLAKNKHYDT--RLN--ATGLF-PNLYTYNILINCFCKIGRVSLGFIAF  119 (595)
Q Consensus        45 ~~~~~A~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~--~~~--~~~~~-~~~~~~~~l~~~~~~~g~~~~A~~~~  119 (595)
                      .+...|+..|-++++.++.  =...|..+...|...-+-..  ...  .-.+. .+...+..+...|.+..+++.|..+.
T Consensus       472 K~~~~al~ali~alrld~~--~apaf~~LG~iYrd~~Dm~RA~kCf~KAFeLDatdaeaaaa~adtyae~~~we~a~~I~  549 (1238)
T KOG1127|consen  472 KNSALALHALIRALRLDVS--LAPAFAFLGQIYRDSDDMKRAKKCFDKAFELDATDAEAAAASADTYAEESTWEEAFEIC  549 (1238)
T ss_pred             hhHHHHHHHHHHHHhcccc--hhHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCchhhhhHHHHHHHhhccccHHHHHHHH
Confidence            4466666777777777665  44455555555444331111  111  11111 24555666666666666666666663


Q ss_pred             HHHHhCCCCCC--HHHHHHHHHHHHhcCCHhHHHHHHHHHHhcCCCCCHhhHHHHHHHHHhcCChhHHHHHHHHHHhcCC
Q 040027          120 GRILRSCFTPN--AATFNSLIKGLHAESRIMEAAALFTKLKAFGCEPNVITYNTLINGLCRTGHTMIALNLFEEMANGNG  197 (595)
Q Consensus       120 ~~~~~~~~~~~--~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~  197 (595)
                      -+.-+.. +.-  ...|-...-.|.+.++...|+..|+...+.. +-|...|..++.+|...|++..|+++|.++...+ 
T Consensus       550 l~~~qka-~a~~~k~nW~~rG~yyLea~n~h~aV~~fQsALR~d-PkD~n~W~gLGeAY~~sGry~~AlKvF~kAs~Lr-  626 (1238)
T KOG1127|consen  550 LRAAQKA-PAFACKENWVQRGPYYLEAHNLHGAVCEFQSALRTD-PKDYNLWLGLGEAYPESGRYSHALKVFTKASLLR-  626 (1238)
T ss_pred             HHHhhhc-hHHHHHhhhhhccccccCccchhhHHHHHHHHhcCC-chhHHHHHHHHHHHHhcCceehHHHhhhhhHhcC-
Confidence            3333221 111  1122223334556666666666666666654 2366666677777777777777777776666543 


Q ss_pred             CCCccccCcHHHHHHHHHHHHHcCCHhHHHHHHHHHhhC------CCCCCHhHHHHHHHHHHhcCCHHHHHHHHHH----
Q 040027          198 EIGVVCKPNTVTYSTIIDGLCKEGFVDKAKALFLQMKDE------NINPDVVTYNSLIHGLCHANDWNEAKRLFIE----  267 (595)
Q Consensus       198 ~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~------~~~~~~~~~~~ll~~~~~~~~~~~A~~~~~~----  267 (595)
                            |.+...-.-.....+..|.+.+|...+..+...      +...-..++..+...+...|-..++.+++++    
T Consensus       627 ------P~s~y~~fk~A~~ecd~GkYkeald~l~~ii~~~s~e~~~q~gLaE~~ir~akd~~~~gf~~kavd~~eksie~  700 (1238)
T KOG1127|consen  627 ------PLSKYGRFKEAVMECDNGKYKEALDALGLIIYAFSLERTGQNGLAESVIRDAKDSAITGFQKKAVDFFEKSIES  700 (1238)
T ss_pred             ------cHhHHHHHHHHHHHHHhhhHHHHHHHHHHHHHHHHHHHHhhhhHHHHHHHHHHHHHHHHHhhhhhHHHHHHHHH
Confidence                  112222222233344556666666666655432      0111122333333333333333333333322    


Q ss_pred             ---HHHCCCCCCHhhHHHHHHHHHhcCChHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHhcCCH---H---HHHHHHHHH
Q 040027          268 ---MMDQGVQPSVVTFNVIMDELCKNRKMDEASRLLDLMVQRGVRPNACTYNTLMDGFCLMGKI---N---RAEELFGSM  338 (595)
Q Consensus       268 ---~~~~~~~~~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~---~---~a~~~~~~~  338 (595)
                         ...+....+...|-.+..          +..+|-... .+ .|+......+..-....+..   +   -+.+.+-.-
T Consensus       701 f~~~l~h~~~~~~~~Wi~asd----------ac~~f~q~e-~~-~vn~h~l~il~~q~e~~~~l~~~d~l~Lg~~c~~~h  768 (1238)
T KOG1127|consen  701 FIVSLIHSLQSDRLQWIVASD----------ACYIFSQEE-PS-IVNMHYLIILSKQLEKTGALKKNDLLFLGYECGIAH  768 (1238)
T ss_pred             HHHHHHHhhhhhHHHHHHHhH----------HHHHHHHhc-cc-chHHHHHHHHHHHHHhcccCcchhHHHHHHHHhhHH
Confidence               222211112222222221          111222211 00 11222222111111111111   1   011111111


Q ss_pred             HhcCCCCCHHHHHHHHHHHHh--------CCCHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHccCCHHHHHHHHHHHHH
Q 040027          339 ESMGCKHDDVSYNILINGYCK--------NKEVEEALSLYREMVSKGIKPTVVTYNTLFLGLFEIHQVEHALKLFDEMQR  410 (595)
Q Consensus       339 ~~~~~~~~~~~~~~l~~~~~~--------~~~~~~A~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~  410 (595)
                      .+.  ..+..+|..++..|.+        ..+...|+..+.+.++..-. +..+|+.+.-. ...|++.-+...|-+-..
T Consensus       769 lsl--~~~~~~WyNLGinylr~f~~l~et~~~~~~Ai~c~KkaV~L~an-n~~~WnaLGVl-sg~gnva~aQHCfIks~~  844 (1238)
T KOG1127|consen  769 LSL--AIHMYPWYNLGINYLRYFLLLGETMKDACTAIRCCKKAVSLCAN-NEGLWNALGVL-SGIGNVACAQHCFIKSRF  844 (1238)
T ss_pred             HHH--hhccchHHHHhHHHHHHHHHcCCcchhHHHHHHHHHHHHHHhhc-cHHHHHHHHHh-hccchhhhhhhhhhhhhh
Confidence            111  1123344444444433        12234677777777664222 45555555443 666777777777666554


Q ss_pred             CCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCcCHHHHHHHHHHHHhcCChHHHHHHHHhccc----CCCCCC
Q 040027          411 DGVAADTRTYTTFIDGLCKNGYIIEAVELFRTLRILKCELDIQAYNCLIDGLCKSGRLKFAWELFCSLPH----GVLVPN  486 (595)
Q Consensus       411 ~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~----~~~~p~  486 (595)
                      . .+....+|..+...+.+..+++-|...|....... |.+...|..........|+.-++..+|..-..    .|-.|+
T Consensus       845 s-ep~~~~~W~NlgvL~l~n~d~E~A~~af~~~qSLd-P~nl~~WlG~Ali~eavG~ii~~~~lfaHs~el~~~~gka~~  922 (1238)
T KOG1127|consen  845 S-EPTCHCQWLNLGVLVLENQDFEHAEPAFSSVQSLD-PLNLVQWLGEALIPEAVGRIIERLILFAHSDELCSKEGKAKK  922 (1238)
T ss_pred             c-cccchhheeccceeEEecccHHHhhHHHHhhhhcC-chhhHHHHHHHHhHHHHHHHHHHHHHHHhhHHhhccccccch
Confidence            4 25556677777777888888888888888888765 55666666666666677887777777776221    223344


Q ss_pred             HHHHHHHHHHHHhcCChhHHHHHHHHHHH---------cCCCCCHHHHHHHHHHHHHcCChhHHHHHHHHHHHC-CCCCC
Q 040027          487 VVTYNIMIQGLCNDGQMDKARDLFLDMEE---------NAAAPDVITFDMLIHGFIRINEPSKVNELLHKMKEK-KVMPD  556 (595)
Q Consensus       487 ~~~~~~l~~~~~~~g~~~~A~~~~~~~~~---------~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~-~~~p~  556 (595)
                      ..-|.........+|+.++-+...+.+..         .+.+.....|...+...-+.+.+..|.....++... -...|
T Consensus       923 f~Yw~c~te~h~~Ng~~e~~I~t~~ki~sAs~al~~yf~~~p~~~fAy~~~gstlEhL~ey~~a~ela~RliglLe~k~d 1002 (1238)
T KOG1127|consen  923 FQYWLCATEIHLQNGNIEESINTARKISSASLALSYYFLGHPQLCFAYAANGSTLEHLEEYRAALELATRLIGLLELKLD 1002 (1238)
T ss_pred             hhHHHHHHHHHHhccchHHHHHHhhhhhhhHHHHHHHHhcCcchhHHHHHHHhHHHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence            44554444555566666654443333221         133445567777777777778887777777766511 01123


Q ss_pred             HHH----HHHHHHHHHhcCccc
Q 040027          557 ASI----VSIVVDLLVKNEISL  574 (595)
Q Consensus       557 ~~~----~~~l~~~~~~~g~~~  574 (595)
                      ...    -...+..+...|.+|
T Consensus      1003 ~sqynvak~~~gRL~lslgefe 1024 (1238)
T KOG1127|consen 1003 ESQYNVAKPDAGRLELSLGEFE 1024 (1238)
T ss_pred             hhhhhhhhhhhhhhhhhhcchh
Confidence            333    334555666677776

>KOG1914 consensus mRNA cleavage and polyadenylation factor I complex, subunit RNA14 [RNA processing and modification]

Probab=99.21  E-value=3.2e-06  Score=79.75  Aligned_cols=434  Identities=10%  Similarity=0.075  Sum_probs=234.1

Q ss_pred             CHHHHHHHHHHHHhcCChhHHHHHHHHHHhCCCCCCHHHHHHHHHHHHhcCCHhHHHHHHHHHHhcCCCCCHhhHHHHHH
Q 040027           95 NLYTYNILINCFCKIGRVSLGFIAFGRILRSCFTPNAATFNSLIKGLHAESRIMEAAALFTKLKAFGCEPNVITYNTLIN  174 (595)
Q Consensus        95 ~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~~l~~  174 (595)
                      |..+|+.|++-+..+ -.++++..++++... ++..+..|..-+..-...++++...++|.+.+..  ..+...|...+.
T Consensus        19 di~sw~~lire~qt~-~~~~~R~~YEq~~~~-FP~s~r~W~~yi~~El~skdfe~VEkLF~RCLvk--vLnlDLW~lYl~   94 (656)
T KOG1914|consen   19 DIDSWSQLIREAQTQ-PIDKVRETYEQLVNV-FPSSPRAWKLYIERELASKDFESVEKLFSRCLVK--VLNLDLWKLYLS   94 (656)
T ss_pred             cHHHHHHHHHHHccC-CHHHHHHHHHHHhcc-CCCCcHHHHHHHHHHHHhhhHHHHHHHHHHHHHH--HhhHhHHHHHHH
Confidence            555566666555444 667777777777655 3555666777777777777777777777776654  234444444433


Q ss_pred             HHHh-cCChh----HHHHHHHHHHhcCCCCCccccCcHHHHHHHHH---------HHHHcCCHhHHHHHHHHHhhCCCCC
Q 040027          175 GLCR-TGHTM----IALNLFEEMANGNGEIGVVCKPNTVTYSTIID---------GLCKEGFVDKAKALFLQMKDENINP  240 (595)
Q Consensus       175 ~~~~-~g~~~----~A~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~---------~~~~~g~~~~A~~~~~~~~~~~~~~  240 (595)
                      ---+ .|+..    .-.+.|+-.....+   + -..+...|+..+.         -|....+++...++|+++...-+..
T Consensus        95 YVR~~~~~~~~~r~~m~qAy~f~l~kig---~-di~s~siW~eYi~FL~~vea~gk~ee~QRI~~vRriYqral~tPm~n  170 (656)
T KOG1914|consen   95 YVRETKGKLFGYREKMVQAYDFALEKIG---M-DIKSYSIWDEYINFLEGVEAVGKYEENQRITAVRRIYQRALVTPMHN  170 (656)
T ss_pred             HHHHHccCcchHHHHHHHHHHHHHHHhc---c-CcccchhHHHHHHHHHcccccccHHHHHHHHHHHHHHHHHhcCcccc
Confidence            2211 22222    22233443333221   0 0112233333332         2333446667777777776542111


Q ss_pred             CHhHHH------HHHHH-------HHhcCCHHHHHHHHHHHHHC--CCCCCHh---------------hHHHHHHHHHhc
Q 040027          241 DVVTYN------SLIHG-------LCHANDWNEAKRLFIEMMDQ--GVQPSVV---------------TFNVIMDELCKN  290 (595)
Q Consensus       241 ~~~~~~------~ll~~-------~~~~~~~~~A~~~~~~~~~~--~~~~~~~---------------~~~~l~~~~~~~  290 (595)
                      =...|+      .=++.       --+...+..|.++++++...  |......               .|..+|..-...
T Consensus       171 lEkLW~DY~~fE~~IN~~tarK~i~e~s~~Ym~AR~~~qel~~lt~GL~r~~~~vp~~~T~~e~~qv~~W~n~I~wEksN  250 (656)
T KOG1914|consen  171 LEKLWKDYEAFEQEINIITARKFIGERSPEYMNARRVYQELQNLTRGLNRNAPAVPPKGTKDEIQQVELWKNWIKWEKSN  250 (656)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHhhCHHHHHHHHHHHHHHHHHhhhcccCCCCCCCCChHHHHHHHHHHHHHHHHhcC
Confidence            111221      11111       11234577788887777542  3221111               133333221111


Q ss_pred             CC--------hHHHHHHHHHHHHC-CCCCCHHHH-----HHHHHHHHhcCC-------HHHHHHHHHHHHhcCCCCCHHH
Q 040027          291 RK--------MDEASRLLDLMVQR-GVRPNACTY-----NTLMDGFCLMGK-------INRAEELFGSMESMGCKHDDVS  349 (595)
Q Consensus       291 g~--------~~~a~~~~~~~~~~-~~~~~~~~~-----~~l~~~~~~~~~-------~~~a~~~~~~~~~~~~~~~~~~  349 (595)
                      +-        -....-++++.+.. +..|+....     ......+...|+       -+++..++++....-...+...
T Consensus       251 pL~t~~~~~~~~Rv~yayeQ~ll~l~~~peiWy~~s~yl~~~s~l~~~~~d~~~a~~~t~e~~~~yEr~I~~l~~~~~~L  330 (656)
T KOG1914|consen  251 PLRTLDGTMLTRRVMYAYEQCLLYLGYHPEIWYDYSMYLIEISDLLTEKGDVPDAKSLTDEAASIYERAIEGLLKENKLL  330 (656)
T ss_pred             CcccccccHHHHHHHHHHHHHHHHHhcCHHHHHHHHHHHHHhhHHHHHhcccccchhhHHHHHHHHHHHHHHHHHHHHHH
Confidence            10        01122223332221 222222110     111223333343       3556666666554322223334


Q ss_pred             HHHHHHHHHhC---CCHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHccCCHHHHHHHHHHHHHCCCCC-CHHHHHHHHH
Q 040027          350 YNILINGYCKN---KEVEEALSLYREMVSKGIKPTVVTYNTLFLGLFEIHQVEHALKLFDEMQRDGVAA-DTRTYTTFID  425 (595)
Q Consensus       350 ~~~l~~~~~~~---~~~~~A~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~-~~~~~~~l~~  425 (595)
                      |..+...--..   +..+.....++++......--..+|..++....+..-++.|..+|.++.+.+..+ +..+..+++.
T Consensus       331 y~~~a~~eE~~~~~n~~~~~~~~~~~ll~~~~~~~tLv~~~~mn~irR~eGlkaaR~iF~kaR~~~r~~hhVfVa~A~mE  410 (656)
T KOG1914|consen  331 YFALADYEESRYDDNKEKKVHEIYNKLLKIEDIDLTLVYCQYMNFIRRAEGLKAARKIFKKAREDKRTRHHVFVAAALME  410 (656)
T ss_pred             HHHHHhhHHHhcccchhhhhHHHHHHHHhhhccCCceehhHHHHHHHHhhhHHHHHHHHHHHhhccCCcchhhHHHHHHH
Confidence            43333321111   2356666777776654322233567777777778888899999999988876555 6667777777


Q ss_pred             HHHhcCCHHHHHHHHHHHHHcCCCcCHHHHHHHHHHHHhcCChHHHHHHHHhcccCCCCCC--HHHHHHHHHHHHhcCCh
Q 040027          426 GLCKNGYIIEAVELFRTLRILKCELDIQAYNCLIDGLCKSGRLKFAWELFCSLPHGVLVPN--VVTYNIMIQGLCNDGQM  503 (595)
Q Consensus       426 ~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~p~--~~~~~~l~~~~~~~g~~  503 (595)
                      .|| .++.+-|.++|+--++.- ..++.-....+..+...++-..+..+|++....++.|+  ...|..++..-..-|++
T Consensus       411 y~c-skD~~~AfrIFeLGLkkf-~d~p~yv~~YldfL~~lNdd~N~R~LFEr~l~s~l~~~ks~~Iw~r~l~yES~vGdL  488 (656)
T KOG1914|consen  411 YYC-SKDKETAFRIFELGLKKF-GDSPEYVLKYLDFLSHLNDDNNARALFERVLTSVLSADKSKEIWDRMLEYESNVGDL  488 (656)
T ss_pred             HHh-cCChhHHHHHHHHHHHhc-CCChHHHHHHHHHHHHhCcchhHHHHHHHHHhccCChhhhHHHHHHHHHHHHhcccH
Confidence            666 578888999998766543 45566667778888888999999999999888766665  57899999888889999


Q ss_pred             hHHHHHHHHHHHcC---CCCCHHHHHHHHHHHHHcCCh
Q 040027          504 DKARDLFLDMEENA---AAPDVITFDMLIHGFIRINEP  538 (595)
Q Consensus       504 ~~A~~~~~~~~~~~---~~~~~~~~~~l~~~~~~~g~~  538 (595)
                      ..+.++-+++...-   ..+....-..+++-|.-.+.+
T Consensus       489 ~si~~lekR~~~af~~~qe~~~~~~~~~v~RY~~~d~~  526 (656)
T KOG1914|consen  489 NSILKLEKRRFTAFPADQEYEGNETALFVDRYGILDLY  526 (656)
T ss_pred             HHHHHHHHHHHHhcchhhcCCCChHHHHHHHHhhcccc
Confidence            99888887776531   111112233445555555554

>KOG3617 consensus WD40 and TPR repeat-containing protein [General function prediction only]

Probab=99.21  E-value=2.1e-07  Score=91.58  Aligned_cols=479  Identities=14%  Similarity=0.073  Sum_probs=246.4

Q ss_pred             cccccccccccCCCChHHHHHHHHHHHHhCCCCCCHhhHHHHHHHHHcCCCchhHHhhCC--------------C-CCCH
Q 040027           32 FRDLTTREGDINVITPNEAFCIFDYMLRMHPSPPPVSSFNILLASLAKNKHYDTRLNATG--------------L-FPNL   96 (595)
Q Consensus        32 ~~~~~~~~~~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~--------------~-~~~~   96 (595)
                      ....=..+.|+--|+.|.|.+--...       .+...|..+.+.+.+..+.+-.++..|              . .|+ 
T Consensus       729 Rkaml~FSfyvtiG~MD~AfksI~~I-------kS~~vW~nmA~McVkT~RLDVAkVClGhm~~aRgaRAlR~a~q~~~-  800 (1416)
T KOG3617|consen  729 RKAMLDFSFYVTIGSMDAAFKSIQFI-------KSDSVWDNMASMCVKTRRLDVAKVCLGHMKNARGARALRRAQQNGE-  800 (1416)
T ss_pred             HHhhhceeEEEEeccHHHHHHHHHHH-------hhhHHHHHHHHHhhhhccccHHHHhhhhhhhhhhHHHHHHHHhCCc-
Confidence            33333566778889999998766655       255789999999999999886222222              1 122 


Q ss_pred             HHHHHHHHHHHhcCChhHHHHHHHHHHhCCCCCCHHHHHHHHHHHHhcCCHhHHHHHHHHHHhcCCCCCHhhHHHHHHHH
Q 040027           97 YTYNILINCFCKIGRVSLGFIAFGRILRSCFTPNAATFNSLIKGLHAESRIMEAAALFTKLKAFGCEPNVITYNTLINGL  176 (595)
Q Consensus        97 ~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~~l~~~~  176 (595)
                      +.--.+.......|.+++|..+|++....         ..|=..|...|.+++|.++-+.-.+..   =..+|......+
T Consensus       801 e~eakvAvLAieLgMlEeA~~lYr~ckR~---------DLlNKlyQs~g~w~eA~eiAE~~DRiH---Lr~Tyy~yA~~L  868 (1416)
T KOG3617|consen  801 EDEAKVAVLAIELGMLEEALILYRQCKRY---------DLLNKLYQSQGMWSEAFEIAETKDRIH---LRNTYYNYAKYL  868 (1416)
T ss_pred             chhhHHHHHHHHHhhHHHHHHHHHHHHHH---------HHHHHHHHhcccHHHHHHHHhhcccee---hhhhHHHHHHHH
Confidence            22233444456779999999999988753         334455677899999998876644332   235677777777


Q ss_pred             HhcCChhHHHHHHHHHHhcCCCCC-------------ccccCcHHHHHHHHHHHHHcCCHhHHHHHHHHHhhC-------
Q 040027          177 CRTGHTMIALNLFEEMANGNGEIG-------------VVCKPNTVTYSTIIDGLCKEGFVDKAKALFLQMKDE-------  236 (595)
Q Consensus       177 ~~~g~~~~A~~~~~~~~~~~~~~~-------------~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~-------  236 (595)
                      ...++.+.|++.|++.-....+..             .-...+...|.-....+-..|+.+.|+.+|......       
T Consensus       869 ear~Di~~AleyyEK~~~hafev~rmL~e~p~~~e~Yv~~~~d~~L~~WWgqYlES~GemdaAl~~Y~~A~D~fs~VrI~  948 (1416)
T KOG3617|consen  869 EARRDIEAALEYYEKAGVHAFEVFRMLKEYPKQIEQYVRRKRDESLYSWWGQYLESVGEMDAALSFYSSAKDYFSMVRIK  948 (1416)
T ss_pred             HhhccHHHHHHHHHhcCChHHHHHHHHHhChHHHHHHHHhccchHHHHHHHHHHhcccchHHHHHHHHHhhhhhhheeeE
Confidence            778889888888876522110000             000123333444444555567777777777665431       


Q ss_pred             ---C----------CCCCHhHHHHHHHHHHhcCCHHHHHHHHHHHHHCCCCCCHhhHHHHHHHHHh--------------
Q 040027          237 ---N----------INPDVVTYNSLIHGLCHANDWNEAKRLFIEMMDQGVQPSVVTFNVIMDELCK--------------  289 (595)
Q Consensus       237 ---~----------~~~~~~~~~~ll~~~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~~l~~~~~~--------------  289 (595)
                         |          -.-|....-.|.+.|-..|++.+|...|.+....         ...|+.|-.              
T Consensus       949 C~qGk~~kAa~iA~esgd~AAcYhlaR~YEn~g~v~~Av~FfTrAqaf---------snAIRlcKEnd~~d~L~nlal~s 1019 (1416)
T KOG3617|consen  949 CIQGKTDKAARIAEESGDKAACYHLARMYENDGDVVKAVKFFTRAQAF---------SNAIRLCKENDMKDRLANLALMS 1019 (1416)
T ss_pred             eeccCchHHHHHHHhcccHHHHHHHHHHhhhhHHHHHHHHHHHHHHHH---------HHHHHHHHhcCHHHHHHHHHhhc
Confidence               0          0112223333455555555555555555443221         111111111              


Q ss_pred             -cCChHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHH--------HHh--cCCCCCHHHHHHHHHHHH
Q 040027          290 -NRKMDEASRLLDLMVQRGVRPNACTYNTLMDGFCLMGKINRAEELFGS--------MES--MGCKHDDVSYNILINGYC  358 (595)
Q Consensus       290 -~g~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~--------~~~--~~~~~~~~~~~~l~~~~~  358 (595)
                       ..+.-.|.++|++.--        -+......|-+.|.+.+|+++--+        ++.  .....|+...+.....+.
T Consensus      1020 ~~~d~v~aArYyEe~g~--------~~~~AVmLYHkAGm~~kALelAF~tqQf~aL~lIa~DLd~~sDp~ll~RcadFF~ 1091 (1416)
T KOG3617|consen 1020 GGSDLVSAARYYEELGG--------YAHKAVMLYHKAGMIGKALELAFRTQQFSALDLIAKDLDAGSDPKLLRRCADFFE 1091 (1416)
T ss_pred             CchhHHHHHHHHHHcch--------hhhHHHHHHHhhcchHHHHHHHHhhcccHHHHHHHHhcCCCCCHHHHHHHHHHHH
Confidence             1111122222222110        011122334455555554443111        111  122345566666667777


Q ss_pred             hCCCHHHHHHHHHHHHH----------CC----------------CCCCH----HHHHHHHHHHHccCCHHHHHHHHHHH
Q 040027          359 KNKEVEEALSLYREMVS----------KG----------------IKPTV----VTYNTLFLGLFEIHQVEHALKLFDEM  408 (595)
Q Consensus       359 ~~~~~~~A~~~~~~~~~----------~~----------------~~~~~----~~~~~l~~~~~~~~~~~~a~~~~~~~  408 (595)
                      ...++++|..++-...+          ++                -.|+.    ..+..+...|.+.|.+..|.+-|-+.
T Consensus      1092 ~~~qyekAV~lL~~ar~~~~AlqlC~~~nv~vtee~aE~mTp~Kd~~~~e~~R~~vLeqvae~c~qQG~Yh~AtKKfTQA 1171 (1416)
T KOG3617|consen 1092 NNQQYEKAVNLLCLAREFSGALQLCKNRNVRVTEEFAELMTPTKDDMPNEQERKQVLEQVAELCLQQGAYHAATKKFTQA 1171 (1416)
T ss_pred             hHHHHHHHHHHHHHHHHHHHHHHHHhcCCCchhHHHHHhcCcCcCCCccHHHHHHHHHHHHHHHHhccchHHHHHHHhhh
Confidence            77777777665543322          11                12222    23455566777888877776655332


Q ss_pred             ----------HHCCCC----------CCHHHHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCcCHHHHHHHHHHHHh----
Q 040027          409 ----------QRDGVA----------ADTRTYTTFIDGLCKNGYIIEAVELFRTLRILKCELDIQAYNCLIDGLCK----  464 (595)
Q Consensus       409 ----------~~~~~~----------~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~~l~~~~~~----  464 (595)
                                ++.|-.          -...+| ++..-|.+.-++.+--++++.+...  -.....+..|...|..    
T Consensus      1172 GdKl~AMraLLKSGdt~KI~FFAn~sRqkEiY-ImAANyLQtlDWq~~pq~mK~I~tF--YTKgqafd~LanFY~~cAqi 1248 (1416)
T KOG3617|consen 1172 GDKLSAMRALLKSGDTQKIRFFANTSRQKEIY-IMAANYLQTLDWQDNPQTMKDIETF--YTKGQAFDHLANFYKSCAQI 1248 (1416)
T ss_pred             hhHHHHHHHHHhcCCcceEEEEeeccccceee-eehhhhhhhcccccChHHHhhhHhh--hhcchhHHHHHHHHHHHHHh
Confidence                      222210          011112 2223344444444444444444321  1122233333333221    


Q ss_pred             -----------cCChHHHHHHHHhcccCCCCCCHHHHHHHHHHHH-----------hcCChhHHHHHHHHHHHcCCCC--
Q 040027          465 -----------SGRLKFAWELFCSLPHGVLVPNVVTYNIMIQGLC-----------NDGQMDKARDLFLDMEENAAAP--  520 (595)
Q Consensus       465 -----------~g~~~~A~~~~~~~~~~~~~p~~~~~~~l~~~~~-----------~~g~~~~A~~~~~~~~~~~~~~--  520 (595)
                                 .|-.++|-..+.++..++  .....++.|-.-..           -..|....++-...|++...-|  
T Consensus      1249 Eiee~q~ydKa~gAl~eA~kCl~ka~~k~--~~~t~l~~Lq~~~a~vk~~l~~~q~~~eD~~~~i~qc~~lleep~ld~~ 1326 (1416)
T KOG3617|consen 1249 EIEELQTYDKAMGALEEAAKCLLKAEQKN--MSTTGLDALQEDLAKVKVQLRKLQIMKEDAADGIRQCTTLLEEPILDDI 1326 (1416)
T ss_pred             hHHHHhhhhHHhHHHHHHHHHHHHHHhhc--chHHHHHHHHHHHHHHHHHHHHHHHhhhhHHHHHHHHHHHhhCcCCCCc
Confidence                       233444444444444332  11222322222111           1225555666666666653333  


Q ss_pred             --CHHHHHHHHHHHHHcCChhHHHHHHHHHHHCC
Q 040027          521 --DVITFDMLIHGFIRINEPSKVNELLHKMKEKK  552 (595)
Q Consensus       521 --~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~  552 (595)
                        -...|..++..+....+|+.|.+.+++|..+-
T Consensus      1327 Ir~~~~~a~lie~~v~~k~y~~AyRal~el~~k~ 1360 (1416)
T KOG3617|consen 1327 IRCTRLFALLIEDHVSRKNYKPAYRALTELQKKV 1360 (1416)
T ss_pred             chhHHHHHHHHHHHHhhhhccHHHHHHHHHhhcC
Confidence              24678899999999999999999999999753

>cd05804 StaR_like StaR_like; a well-conserved protein found in bacteria, plants, and animals

Probab=99.20  E-value=2.5e-07  Score=89.80  Aligned_cols=202  Identities=10%  Similarity=-0.024  Sum_probs=129.4

Q ss_pred             CHHHHHHHHHHHHhcCChhHHHHHHHHHHhCCC-CCCHH-HHHHHHHHHHhcCCHhHHHHHHHHHHhcCCCCCHhhHHHH
Q 040027           95 NLYTYNILINCFCKIGRVSLGFIAFGRILRSCF-TPNAA-TFNSLIKGLHAESRIMEAAALFTKLKAFGCEPNVITYNTL  172 (595)
Q Consensus        95 ~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~-~~~~~-~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~~l  172 (595)
                      .+..|..+...+...|+.+.+...+.+..+... ..+.. ........+...|++++|.+.++++.... +.+...+.. 
T Consensus         5 ~~~a~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~e~~~~~a~~~~~~g~~~~A~~~~~~~l~~~-P~~~~a~~~-   82 (355)
T cd05804           5 FALGHAAAALLLLLGGERPAAAAKAAAAAQALAARATERERAHVEALSAWIAGDLPKALALLEQLLDDY-PRDLLALKL-   82 (355)
T ss_pred             cHHHHHHHHHHHHhcCCcchHHHHHHHHHHHhccCCCHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHC-CCcHHHHHH-
Confidence            455566677777777888887777777666532 11221 22222344567889999999988888763 334434432 


Q ss_pred             HHHHH----hcCChhHHHHHHHHHHhcCCCCCccccCcHHHHHHHHHHHHHcCCHhHHHHHHHHHhhCCCCCCHhHHHHH
Q 040027          173 INGLC----RTGHTMIALNLFEEMANGNGEIGVVCKPNTVTYSTIIDGLCKEGFVDKAKALFLQMKDENINPDVVTYNSL  248 (595)
Q Consensus       173 ~~~~~----~~g~~~~A~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~~l  248 (595)
                      ...+.    ..+....+.+.++.....       .+........+...+...|++++|.+.+++..+.. +.+...+..+
T Consensus        83 ~~~~~~~~~~~~~~~~~~~~l~~~~~~-------~~~~~~~~~~~a~~~~~~G~~~~A~~~~~~al~~~-p~~~~~~~~l  154 (355)
T cd05804          83 HLGAFGLGDFSGMRDHVARVLPLWAPE-------NPDYWYLLGMLAFGLEEAGQYDRAEEAARRALELN-PDDAWAVHAV  154 (355)
T ss_pred             hHHHHHhcccccCchhHHHHHhccCcC-------CCCcHHHHHHHHHHHHHcCCHHHHHHHHHHHHhhC-CCCcHHHHHH
Confidence            22222    244455555555442111       23334455566677888899999999998888764 3356677778


Q ss_pred             HHHHHhcCCHHHHHHHHHHHHHCCCC-CCH--hhHHHHHHHHHhcCChHHHHHHHHHHHHC
Q 040027          249 IHGLCHANDWNEAKRLFIEMMDQGVQ-PSV--VTFNVIMDELCKNRKMDEASRLLDLMVQR  306 (595)
Q Consensus       249 l~~~~~~~~~~~A~~~~~~~~~~~~~-~~~--~~~~~l~~~~~~~g~~~~a~~~~~~~~~~  306 (595)
                      ...+...|++++|..++++....... ++.  ..|..+...+...|++++|..+++++...
T Consensus       155 a~i~~~~g~~~eA~~~l~~~l~~~~~~~~~~~~~~~~la~~~~~~G~~~~A~~~~~~~~~~  215 (355)
T cd05804         155 AHVLEMQGRFKEGIAFMESWRDTWDCSSMLRGHNWWHLALFYLERGDYEAALAIYDTHIAP  215 (355)
T ss_pred             HHHHHHcCCHHHHHHHHHhhhhccCCCcchhHHHHHHHHHHHHHCCCHHHHHHHHHHHhcc
Confidence            88888899999999888887765321 222  23446777888888888888888887543

A family member from Streptomyces toyocaensis, StaR is part of a gene cluster involved in the biosynthesis of glycopeptide antibiotics (GPAs), specifically A47934. It has been speculated that StaR could be a flavoprotein hydroxylating a tyrosine sidechain. Some family members have been annotated as proteins containing tetratricopeptide (TPR) repeats, which may at least indicate mostly alpha-helical secondary structure.

>cd05804 StaR_like StaR_like; a well-conserved protein found in bacteria, plants, and animals

Probab=99.18  E-value=2.4e-07  Score=89.88  Aligned_cols=264  Identities=11%  Similarity=0.016  Sum_probs=158.2

Q ss_pred             HHHHHHhcCChhHHHHHHHHHHhCCCCCCHHHHHHHHHHHH----hcCCHhHHHHHHHHHHhcCCCCCHhhHHHHHHHHH
Q 040027          102 LINCFCKIGRVSLGFIAFGRILRSCFTPNAATFNSLIKGLH----AESRIMEAAALFTKLKAFGCEPNVITYNTLINGLC  177 (595)
Q Consensus       102 l~~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~~l~~~~~----~~g~~~~A~~~~~~~~~~~~~~~~~~~~~l~~~~~  177 (595)
                      ....+...|++++|...++++.+.. |.+...+.. ...+.    ..+..+.+.+.++.... ..+........+...+.
T Consensus        49 ~a~~~~~~g~~~~A~~~~~~~l~~~-P~~~~a~~~-~~~~~~~~~~~~~~~~~~~~l~~~~~-~~~~~~~~~~~~a~~~~  125 (355)
T cd05804          49 EALSAWIAGDLPKALALLEQLLDDY-PRDLLALKL-HLGAFGLGDFSGMRDHVARVLPLWAP-ENPDYWYLLGMLAFGLE  125 (355)
T ss_pred             HHHHHHHcCCHHHHHHHHHHHHHHC-CCcHHHHHH-hHHHHHhcccccCchhHHHHHhccCc-CCCCcHHHHHHHHHHHH
Confidence            3445677899999999999999874 445545442 22222    24555555555554211 11223344456677888


Q ss_pred             hcCChhHHHHHHHHHHhcCCCCCccccCcHHHHHHHHHHHHHcCCHhHHHHHHHHHhhCCC-CCCH--hHHHHHHHHHHh
Q 040027          178 RTGHTMIALNLFEEMANGNGEIGVVCKPNTVTYSTIIDGLCKEGFVDKAKALFLQMKDENI-NPDV--VTYNSLIHGLCH  254 (595)
Q Consensus       178 ~~g~~~~A~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~-~~~~--~~~~~ll~~~~~  254 (595)
                      ..|++++|...+++..+..       +.+...+..+..++...|++++|...+++...... .++.  ..|..+...+..
T Consensus       126 ~~G~~~~A~~~~~~al~~~-------p~~~~~~~~la~i~~~~g~~~eA~~~l~~~l~~~~~~~~~~~~~~~~la~~~~~  198 (355)
T cd05804         126 EAGQYDRAEEAARRALELN-------PDDAWAVHAVAHVLEMQGRFKEGIAFMESWRDTWDCSSMLRGHNWWHLALFYLE  198 (355)
T ss_pred             HcCCHHHHHHHHHHHHhhC-------CCCcHHHHHHHHHHHHcCCHHHHHHHHHhhhhccCCCcchhHHHHHHHHHHHHH
Confidence            9999999999999999976       56677888999999999999999999999877532 1222  345578889999


Q ss_pred             cCCHHHHHHHHHHHHHCCC-CCCHhhH-H--HHHHHHHhcCChHHHHHH--H-HHHHHCCC-CCCHHHHHHHHHHHHhcC
Q 040027          255 ANDWNEAKRLFIEMMDQGV-QPSVVTF-N--VIMDELCKNRKMDEASRL--L-DLMVQRGV-RPNACTYNTLMDGFCLMG  326 (595)
Q Consensus       255 ~~~~~~A~~~~~~~~~~~~-~~~~~~~-~--~l~~~~~~~g~~~~a~~~--~-~~~~~~~~-~~~~~~~~~l~~~~~~~~  326 (595)
                      .|++++|..++++...... .+..... +  .++..+...|....+.++  + ........ ............++...|
T Consensus       199 ~G~~~~A~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~g~~~~~~~w~~~~~~~~~~~~~~~~~~~~~~~a~~~~~~~  278 (355)
T cd05804         199 RGDYEAALAIYDTHIAPSAESDPALDLLDAASLLWRLELAGHVDVGDRWEDLADYAAWHFPDHGLAFNDLHAALALAGAG  278 (355)
T ss_pred             CCCHHHHHHHHHHHhccccCCChHHHHhhHHHHHHHHHhcCCCChHHHHHHHHHHHHhhcCcccchHHHHHHHHHHhcCC
Confidence            9999999999999864322 1111111 1  223333344433333332  1 11111100 111111224555666777


Q ss_pred             CHHHHHHHHHHHHhcCCC---C-----CHHHHHHHHHHHHhCCCHHHHHHHHHHHHH
Q 040027          327 KINRAEELFGSMESMGCK---H-----DDVSYNILINGYCKNKEVEEALSLYREMVS  375 (595)
Q Consensus       327 ~~~~a~~~~~~~~~~~~~---~-----~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~  375 (595)
                      +.+.|...++.+......   .     .........-.+...|++++|.+.+.....
T Consensus       279 ~~~~a~~~L~~l~~~~~~~~~~~~~~~~~~~~~l~A~~~~~~g~~~~A~~~L~~al~  335 (355)
T cd05804         279 DKDALDKLLAALKGRASSADDNKQPARDVGLPLAEALYAFAEGNYATALELLGPVRD  335 (355)
T ss_pred             CHHHHHHHHHHHHHHHhccCchhhhHHhhhHHHHHHHHHHHcCCHHHHHHHHHHHHH
Confidence            788888877776543211   0     011112223334556677777666666554

A family member from Streptomyces toyocaensis, StaR is part of a gene cluster involved in the biosynthesis of glycopeptide antibiotics (GPAs), specifically A47934. It has been speculated that StaR could be a flavoprotein hydroxylating a tyrosine sidechain. Some family members have been annotated as proteins containing tetratricopeptide (TPR) repeats, which may at least indicate mostly alpha-helical secondary structure.

>KOG1125 consensus TPR repeat-containing protein [General function prediction only]

Probab=99.18  E-value=5.4e-09  Score=98.76  Aligned_cols=250  Identities=17%  Similarity=0.104  Sum_probs=161.8

Q ss_pred             HHHHhcCChHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHhcCCCCCHHHHHHHHHHHHhCCCHH
Q 040027          285 DELCKNRKMDEASRLLDLMVQRGVRPNACTYNTLMDGFCLMGKINRAEELFGSMESMGCKHDDVSYNILINGYCKNKEVE  364 (595)
Q Consensus       285 ~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~  364 (595)
                      .-+.+.|++.+|.-.|+..++.+.. +...|..|.......++-..|+..+++.++.. +.+..+.-.|.-.|...|.-.
T Consensus       293 ~~lm~nG~L~~A~LafEAAVkqdP~-haeAW~~LG~~qaENE~E~~ai~AL~rcl~Ld-P~NleaLmaLAVSytNeg~q~  370 (579)
T KOG1125|consen  293 CNLMKNGDLSEAALAFEAAVKQDPQ-HAEAWQKLGITQAENENEQNAISALRRCLELD-PTNLEALMALAVSYTNEGLQN  370 (579)
T ss_pred             HHHHhcCCchHHHHHHHHHHhhChH-HHHHHHHhhhHhhhccchHHHHHHHHHHHhcC-CccHHHHHHHHHHHhhhhhHH
Confidence            3456777788888888877776433 66777777777777777778888888887774 445667777777788888777


Q ss_pred             HHHHHHHHHHHCCCCCCHHHHH----HHH---HHHHccCCHHHHHHHHHHHHH-CCCCCCHHHHHHHHHHHHhcCCHHHH
Q 040027          365 EALSLYREMVSKGIKPTVVTYN----TLF---LGLFEIHQVEHALKLFDEMQR-DGVAADTRTYTTFIDGLCKNGYIIEA  436 (595)
Q Consensus       365 ~A~~~~~~~~~~~~~~~~~~~~----~l~---~~~~~~~~~~~a~~~~~~~~~-~~~~~~~~~~~~l~~~~~~~g~~~~A  436 (595)
                      .|+..+++-+...++ -.....    ...   ..+.....+....++|-++.. .+..+|+.+...|.-.|.-.|++++|
T Consensus       371 ~Al~~L~~Wi~~~p~-y~~l~~a~~~~~~~~~~s~~~~~~l~~i~~~fLeaa~~~~~~~DpdvQ~~LGVLy~ls~efdra  449 (579)
T KOG1125|consen  371 QALKMLDKWIRNKPK-YVHLVSAGENEDFENTKSFLDSSHLAHIQELFLEAARQLPTKIDPDVQSGLGVLYNLSGEFDRA  449 (579)
T ss_pred             HHHHHHHHHHHhCcc-chhccccCccccccCCcCCCCHHHHHHHHHHHHHHHHhCCCCCChhHHhhhHHHHhcchHHHHH
Confidence            888887777654211 000000    000   011112223344444444443 33346777777777777777888888


Q ss_pred             HHHHHHHHHcCCCcCHHHHHHHHHHHHhcCChHHHHHHHHhcccCCCCCC-HHHHHHHHHHHHhcCChhHHHHHHHHHHH
Q 040027          437 VELFRTLRILKCELDIQAYNCLIDGLCKSGRLKFAWELFCSLPHGVLVPN-VVTYNIMIQGLCNDGQMDKARDLFLDMEE  515 (595)
Q Consensus       437 ~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~p~-~~~~~~l~~~~~~~g~~~~A~~~~~~~~~  515 (595)
                      ...|+.++... |.|..+||.|+..++...+.++|+..|+++++  +.|+ +.+...|...|...|.+.+|.+.|-.++.
T Consensus       450 iDcf~~AL~v~-Pnd~~lWNRLGAtLAN~~~s~EAIsAY~rALq--LqP~yVR~RyNlgIS~mNlG~ykEA~~hlL~AL~  526 (579)
T KOG1125|consen  450 VDCFEAALQVK-PNDYLLWNRLGATLANGNRSEEAISAYNRALQ--LQPGYVRVRYNLGISCMNLGAYKEAVKHLLEALS  526 (579)
T ss_pred             HHHHHHHHhcC-CchHHHHHHhhHHhcCCcccHHHHHHHHHHHh--cCCCeeeeehhhhhhhhhhhhHHHHHHHHHHHHH
Confidence            88888887765 66777888888888888888888888888877  6776 45677777788888888888887776654


Q ss_pred             cC---------CCCCHHHHHHHHHHHHHcCChhH
Q 040027          516 NA---------AAPDVITFDMLIHGFIRINEPSK  540 (595)
Q Consensus       516 ~~---------~~~~~~~~~~l~~~~~~~g~~~~  540 (595)
                      ..         ..++..+|..|=.++...++.+-
T Consensus       527 mq~ks~~~~~~~~~se~iw~tLR~als~~~~~D~  560 (579)
T KOG1125|consen  527 MQRKSRNHNKAPMASENIWQTLRLALSAMNRSDL  560 (579)
T ss_pred             hhhcccccccCCcchHHHHHHHHHHHHHcCCchH
Confidence            21         01123455555555555555543

>KOG4340 consensus Uncharacterized conserved protein [Function unknown]

Probab=99.15  E-value=9.9e-08  Score=82.63  Aligned_cols=262  Identities=15%  Similarity=0.127  Sum_probs=140.5

Q ss_pred             HHHHHHHHHHHHhcCChhHHHHHHHHHHhCCCCCCHHHHH-HHHHHHHhcCCHhHHHHHHHHHHhcCCCCCHhhHHHHHH
Q 040027           96 LYTYNILINCFCKIGRVSLGFIAFGRILRSCFTPNAATFN-SLIKGLHAESRIMEAAALFTKLKAFGCEPNVITYNTLIN  174 (595)
Q Consensus        96 ~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~-~l~~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~~l~~  174 (595)
                      ....+.+..+|....++..|...++++...  -|...-|. .-...+.+.+.+..|+.+...|.... ..-......-..
T Consensus        44 rAgLSlLgyCYY~~Q~f~~AA~CYeQL~ql--~P~~~qYrlY~AQSLY~A~i~ADALrV~~~~~D~~-~L~~~~lqLqaA  120 (459)
T KOG4340|consen   44 RAGLSLLGYCYYRLQEFALAAECYEQLGQL--HPELEQYRLYQAQSLYKACIYADALRVAFLLLDNP-ALHSRVLQLQAA  120 (459)
T ss_pred             hHHHHHHHHHHHHHHHHHHHHHHHHHHHhh--ChHHHHHHHHHHHHHHHhcccHHHHHHHHHhcCCH-HHHHHHHHHHHH
Confidence            334445555666666666666777666655  33344343 23455566667777777666665420 001111111222


Q ss_pred             HHHhcCChhHHHHHHHHHHhcCCCCCccccCcHHHHHHHHHHHHHcCCHhHHHHHHHHHhhCCCCCCHhHHHHHHHHHHh
Q 040027          175 GLCRTGHTMIALNLFEEMANGNGEIGVVCKPNTVTYSTIIDGLCKEGFVDKAKALFLQMKDENINPDVVTYNSLIHGLCH  254 (595)
Q Consensus       175 ~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~~ll~~~~~  254 (595)
                      ...+.+++..+..++++....+         +..+.+...-...+.|+++.|.+-|+...+.+--.....|+.. -++.+
T Consensus       121 IkYse~Dl~g~rsLveQlp~en---------~Ad~~in~gCllykegqyEaAvqkFqaAlqvsGyqpllAYniA-LaHy~  190 (459)
T KOG4340|consen  121 IKYSEGDLPGSRSLVEQLPSEN---------EADGQINLGCLLYKEGQYEAAVQKFQAALQVSGYQPLLAYNLA-LAHYS  190 (459)
T ss_pred             HhcccccCcchHHHHHhccCCC---------ccchhccchheeeccccHHHHHHHHHHHHhhcCCCchhHHHHH-HHHHh
Confidence            3335666666666666655322         3444444555556677777777777766654322234445433 34556


Q ss_pred             cCCHHHHHHHHHHHHHCCCCC-------------C---------------HhhHHHHHHHHHhcCChHHHHHHHHHHHHC
Q 040027          255 ANDWNEAKRLFIEMMDQGVQP-------------S---------------VVTFNVIMDELCKNRKMDEASRLLDLMVQR  306 (595)
Q Consensus       255 ~~~~~~A~~~~~~~~~~~~~~-------------~---------------~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~  306 (595)
                      .+++..|++...+++++|++.             |               ...+|.-...+.+.|+++.|.+.+-+|.-+
T Consensus       191 ~~qyasALk~iSEIieRG~r~HPElgIGm~tegiDvrsvgNt~~lh~Sal~eAfNLKaAIeyq~~n~eAA~eaLtDmPPR  270 (459)
T KOG4340|consen  191 SRQYASALKHISEIIERGIRQHPELGIGMTTEGIDVRSVGNTLVLHQSALVEAFNLKAAIEYQLRNYEAAQEALTDMPPR  270 (459)
T ss_pred             hhhHHHHHHHHHHHHHhhhhcCCccCccceeccCchhcccchHHHHHHHHHHHhhhhhhhhhhcccHHHHHHHhhcCCCc
Confidence            667777777777776665431             1               122334444556677777777777666543


Q ss_pred             C-CCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHhcCCCCCHHHHHHHHHHHHhCCCHHHHHHHHHH
Q 040027          307 G-VRPNACTYNTLMDGFCLMGKINRAEELFGSMESMGCKHDDVSYNILINGYCKNKEVEEALSLYRE  372 (595)
Q Consensus       307 ~-~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~A~~~~~~  372 (595)
                      . ...|+.|...+.-.- ..+++....+-+.-+...+ |....+|..++-.|+++.-++-|..++.+
T Consensus       271 aE~elDPvTLHN~Al~n-~~~~p~~g~~KLqFLL~~n-PfP~ETFANlLllyCKNeyf~lAADvLAE  335 (459)
T KOG4340|consen  271 AEEELDPVTLHNQALMN-MDARPTEGFEKLQFLLQQN-PFPPETFANLLLLYCKNEYFDLAADVLAE  335 (459)
T ss_pred             ccccCCchhhhHHHHhc-ccCCccccHHHHHHHHhcC-CCChHHHHHHHHHHhhhHHHhHHHHHHhh
Confidence            2 234555554433221 1233444444444444443 34556777777777777777777666543

>KOG1125 consensus TPR repeat-containing protein [General function prediction only]

Probab=99.15  E-value=6.3e-09  Score=98.32  Aligned_cols=236  Identities=16%  Similarity=0.041  Sum_probs=149.1

Q ss_pred             hhhhhhcccccccccccCCCChHHHHHHHHHHHHhCCCCCCHhhHHHHHHHHHcCCCchhHHhhCCCCCCHHHHHHHHHH
Q 040027           26 SSLLVHFRDLTTREGDINVITPNEAFCIFDYMLRMHPSPPPVSSFNILLASLAKNKHYDTRLNATGLFPNLYTYNILINC  105 (595)
Q Consensus        26 ~~~~~~~~~~~~~~~~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~  105 (595)
                      ++-.-++.+.-.+..+++-|++.+|.-.|+.+++.+|.  +                             .+.|..|..+
T Consensus       280 Np~~~~pdPf~eG~~lm~nG~L~~A~LafEAAVkqdP~--h-----------------------------aeAW~~LG~~  328 (579)
T KOG1125|consen  280 NPYIDHPDPFKEGCNLMKNGDLSEAALAFEAAVKQDPQ--H-----------------------------AEAWQKLGIT  328 (579)
T ss_pred             CcccCCCChHHHHHHHHhcCCchHHHHHHHHHHhhChH--H-----------------------------HHHHHHhhhH
Confidence            45555666666777778889999999999999999887  4                             4445556666


Q ss_pred             HHhcCChhHHHHHHHHHHhCCCCCCHHHHHHHHHHHHhcCCHhHHHHHHHHHHhcCCCCCHhhHHHHH---------HHH
Q 040027          106 FCKIGRVSLGFIAFGRILRSCFTPNAATFNSLIKGLHAESRIMEAAALFTKLKAFGCEPNVITYNTLI---------NGL  176 (595)
Q Consensus       106 ~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~~l~---------~~~  176 (595)
                      ....++-..|+..++++++.. +.+..+.-.|...|...|.-.+|.+.++..+...++ -  .|....         ..+
T Consensus       329 qaENE~E~~ai~AL~rcl~Ld-P~NleaLmaLAVSytNeg~q~~Al~~L~~Wi~~~p~-y--~~l~~a~~~~~~~~~~s~  404 (579)
T KOG1125|consen  329 QAENENEQNAISALRRCLELD-PTNLEALMALAVSYTNEGLQNQALKMLDKWIRNKPK-Y--VHLVSAGENEDFENTKSF  404 (579)
T ss_pred             hhhccchHHHHHHHHHHHhcC-CccHHHHHHHHHHHhhhhhHHHHHHHHHHHHHhCcc-c--hhccccCccccccCCcCC
Confidence            667777778888888888885 456777788888888888888888888887665321 0  000000         001


Q ss_pred             HhcCChhHHHHHHHHHHhcCCCCCccccCcHHHHHHHHHHHHHcCCHhHHHHHHHHHhhCCCCCCHhHHHHHHHHHHhcC
Q 040027          177 CRTGHTMIALNLFEEMANGNGEIGVVCKPNTVTYSTIIDGLCKEGFVDKAKALFLQMKDENINPDVVTYNSLIHGLCHAN  256 (595)
Q Consensus       177 ~~~g~~~~A~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~~ll~~~~~~~  256 (595)
                      .....+....++|-++....+     ...|+.....|...|.-.|++++|.+.|+.+.... +-|...||.|...+....
T Consensus       405 ~~~~~l~~i~~~fLeaa~~~~-----~~~DpdvQ~~LGVLy~ls~efdraiDcf~~AL~v~-Pnd~~lWNRLGAtLAN~~  478 (579)
T KOG1125|consen  405 LDSSHLAHIQELFLEAARQLP-----TKIDPDVQSGLGVLYNLSGEFDRAVDCFEAALQVK-PNDYLLWNRLGATLANGN  478 (579)
T ss_pred             CCHHHHHHHHHHHHHHHHhCC-----CCCChhHHhhhHHHHhcchHHHHHHHHHHHHHhcC-CchHHHHHHhhHHhcCCc
Confidence            111122233444444443331     23566666666666666777777777777666643 225566777777777767


Q ss_pred             CHHHHHHHHHHHHHCCCCCC-HhhHHHHHHHHHhcCChHHHHHHHHHHH
Q 040027          257 DWNEAKRLFIEMMDQGVQPS-VVTFNVIMDELCKNRKMDEASRLLDLMV  304 (595)
Q Consensus       257 ~~~~A~~~~~~~~~~~~~~~-~~~~~~l~~~~~~~g~~~~a~~~~~~~~  304 (595)
                      +.++|+..|.+.++.  +|+ +.+...+.-.|...|.+++|...|-.++
T Consensus       479 ~s~EAIsAY~rALqL--qP~yVR~RyNlgIS~mNlG~ykEA~~hlL~AL  525 (579)
T KOG1125|consen  479 RSEEAISAYNRALQL--QPGYVRVRYNLGISCMNLGAYKEAVKHLLEAL  525 (579)
T ss_pred             ccHHHHHHHHHHHhc--CCCeeeeehhhhhhhhhhhhHHHHHHHHHHHH
Confidence            777777777766653  443 2244445556666677776666665544

>KOG2053 consensus Mitochondrial inheritance and actin cytoskeleton organization protein [Cytoskeleton]

Probab=99.13  E-value=1.5e-05  Score=80.03  Aligned_cols=526  Identities=14%  Similarity=0.137  Sum_probs=293.8

Q ss_pred             ccCCCChHHHHHHHHHHHHhCCCCCCHhhHHHHHHHHHcCCCchhH-----HhhCCCCCCHHHHHHHHHHHHhcCChhHH
Q 040027           41 DINVITPNEAFCIFDYMLRMHPSPPPVSSFNILLASLAKNKHYDTR-----LNATGLFPNLYTYNILINCFCKIGRVSLG  115 (595)
Q Consensus        41 ~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~-----~~~~~~~~~~~~~~~l~~~~~~~g~~~~A  115 (595)
                      .+..++++.|....+++++.+|+.+..-++.++  .+.+.|+.++.     ....-..-|..+...+-.+|.+.|++++|
T Consensus        19 ~ld~~qfkkal~~~~kllkk~Pn~~~a~vLkaL--sl~r~gk~~ea~~~Le~~~~~~~~D~~tLq~l~~~y~d~~~~d~~   96 (932)
T KOG2053|consen   19 LLDSSQFKKALAKLGKLLKKHPNALYAKVLKAL--SLFRLGKGDEALKLLEALYGLKGTDDLTLQFLQNVYRDLGKLDEA   96 (932)
T ss_pred             HhhhHHHHHHHHHHHHHHHHCCCcHHHHHHHHH--HHHHhcCchhHHHHHhhhccCCCCchHHHHHHHHHHHHHhhhhHH
Confidence            356789999999999999999994444444444  46788887771     11111223778888888899999999999


Q ss_pred             HHHHHHHHhCCCCCCHHHHHHHHHHHHhcCCHhHHHHHHHHHHhcCCCCCHhhHHHHHHHHHhcCC----------hhHH
Q 040027          116 FIAFGRILRSCFTPNAATFNSLIKGLHAESRIMEAAALFTKLKAFGCEPNVITYNTLINGLCRTGH----------TMIA  185 (595)
Q Consensus       116 ~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~----------~~~A  185 (595)
                      ..+|+++.+.  .|+......+..+|.+.+++.+-.++--++.+. ++-++..+-+++..+.+.-.          ..-|
T Consensus        97 ~~~Ye~~~~~--~P~eell~~lFmayvR~~~yk~qQkaa~~LyK~-~pk~~yyfWsV~Slilqs~~~~~~~~~~i~l~LA  173 (932)
T KOG2053|consen   97 VHLYERANQK--YPSEELLYHLFMAYVREKSYKKQQKAALQLYKN-FPKRAYYFWSVISLILQSIFSENELLDPILLALA  173 (932)
T ss_pred             HHHHHHHHhh--CCcHHHHHHHHHHHHHHHHHHHHHHHHHHHHHh-CCcccchHHHHHHHHHHhccCCcccccchhHHHH
Confidence            9999999988  566777788888899888876655444444432 34466666677776655321          2235


Q ss_pred             HHHHHHHHhcCCCCCccccCcHHHHHHHHHHHHHcCCHhHHHHHHH-HHhhCCCCCCHhHHHHHHHHHHhcCCHHHHHHH
Q 040027          186 LNLFEEMANGNGEIGVVCKPNTVTYSTIIDGLCKEGFVDKAKALFL-QMKDENINPDVVTYNSLIHGLCHANDWNEAKRL  264 (595)
Q Consensus       186 ~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~-~~~~~~~~~~~~~~~~ll~~~~~~~~~~~A~~~  264 (595)
                      .+.++.+....|.     -.+..-...-...+-..|.+++|.+++. ...+.-.+.+...-+.-+..+...++|.+..++
T Consensus       174 ~~m~~~~l~~~gk-----~~s~aE~~Lyl~iL~~~~k~~eal~~l~~~la~~l~~~~~~l~~~~~dllk~l~~w~~l~~l  248 (932)
T KOG2053|consen  174 EKMVQKLLEKKGK-----IESEAEIILYLLILELQGKYQEALEFLAITLAEKLTSANLYLENKKLDLLKLLNRWQELFEL  248 (932)
T ss_pred             HHHHHHHhccCCc-----cchHHHHHHHHHHHHhcccHHHHHHHHHHHHHHhccccchHHHHHHHHHHHHhcChHHHHHH
Confidence            6667777665421     1122223334455667889999999984 444443333444555667888889999999999


Q ss_pred             HHHHHHCCCCCCHhhHHHHHHH----------------HHhcCChHHHHHHHHHHHHCCCCCCHHHHHHHHHHHH---hc
Q 040027          265 FIEMMDQGVQPSVVTFNVIMDE----------------LCKNRKMDEASRLLDLMVQRGVRPNACTYNTLMDGFC---LM  325 (595)
Q Consensus       265 ~~~~~~~~~~~~~~~~~~l~~~----------------~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~---~~  325 (595)
                      -.++...|.. |   |...+..                +...+..+...+...+......   -..|.+-+.++.   ..
T Consensus       249 ~~~Ll~k~~D-d---y~~~~~sv~klLe~~~~~~a~~~~s~~~~l~~~~ek~~~~i~~~~---Rgp~LA~lel~kr~~~~  321 (932)
T KOG2053|consen  249 SSRLLEKGND-D---YKIYTDSVFKLLELLNKEPAEAAHSLSKSLDECIEKAQKNIGSKS---RGPYLARLELDKRYKLI  321 (932)
T ss_pred             HHHHHHhCCc-c---hHHHHHHHHHHHHhcccccchhhhhhhhhHHHHHHHHHHhhcccc---cCcHHHHHHHHHHhccc
Confidence            8888887533 2   2222211                1112223333333333332211   122333333333   45


Q ss_pred             CCHHHHHHHHHHHHhcCCCCCHHHHHHHHHHHHhCCCHHHHHHHHHHHHHCCCCCC--HHH---HHHHHHHHHccC----
Q 040027          326 GKINRAEELFGSMESMGCKHDDVSYNILINGYCKNKEVEEALSLYREMVSKGIKPT--VVT---YNTLFLGLFEIH----  396 (595)
Q Consensus       326 ~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~~~~~~~--~~~---~~~l~~~~~~~~----  396 (595)
                      |+.+++...|-+-.  |-.|   .+..=+..|...=..+.-..++...........  ...   +...+..-...|    
T Consensus       322 gd~ee~~~~y~~kf--g~kp---cc~~Dl~~yl~~l~~~q~~~l~~~l~~~~~~~s~~~k~l~~h~c~l~~~rl~G~~~~  396 (932)
T KOG2053|consen  322 GDSEEMLSYYFKKF--GDKP---CCAIDLNHYLGHLNIDQLKSLMSKLVLADDDSSGDEKVLQQHLCVLLLLRLLGLYEK  396 (932)
T ss_pred             CChHHHHHHHHHHh--CCCc---HhHhhHHHhhccCCHHHHHHHHHHhhccCCcchhhHHHHHHHHHHHHHHHHhhcccc
Confidence            77777655443322  2112   222223333333333333444444333211100  000   011111111112    


Q ss_pred             -CHHHHHHHHHHHH---HCC------CCCCH---------HHHHHHHHHHHhcCCHH---HHHHHHHHHHHcCCCcCHHH
Q 040027          397 -QVEHALKLFDEMQ---RDG------VAADT---------RTYTTFIDGLCKNGYII---EAVELFRTLRILKCELDIQA  454 (595)
Q Consensus       397 -~~~~a~~~~~~~~---~~~------~~~~~---------~~~~~l~~~~~~~g~~~---~A~~~~~~~~~~~~~~~~~~  454 (595)
                       .-+....++.+..   +.|      .-|+.         -+.+.++..+.+.++..   +|+-+++...... +.|..+
T Consensus       397 l~ad~i~a~~~kl~~~ye~gls~~K~ll~TE~~~g~~~llLav~~Lid~~rktnd~~~l~eaI~LLE~glt~s-~hnf~~  475 (932)
T KOG2053|consen  397 LPADSILAYVRKLKLTYEKGLSLSKDLLPTEYSFGDELLLLAVNHLIDLWRKTNDLTDLFEAITLLENGLTKS-PHNFQT  475 (932)
T ss_pred             CChHHHHHHHHHHHHHHhccccccccccccccccHHHHHHHHHHHHHHHHHhcCcHHHHHHHHHHHHHHhhcC-CccHHH
Confidence             1122222222221   111      12222         23456677788877765   4555555555544 556777


Q ss_pred             HHHHHHHHHhcCChHHHHHHHHhcccCCCCCCHHHHHHHHHHHHhcCChhHHHHHHHHHHHcCCCCCH-HHHHHHHHHHH
Q 040027          455 YNCLIDGLCKSGRLKFAWELFCSLPHGVLVPNVVTYNIMIQGLCNDGQMDKARDLFLDMEENAAAPDV-ITFDMLIHGFI  533 (595)
Q Consensus       455 ~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~p~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~~~-~~~~~l~~~~~  533 (595)
                      --.++..|.-.|-+..|.++|..+.-+.+..|...| .+..-+...|++..+...+......- ..+. .+-.....+ .
T Consensus       476 KLlLiriY~~lGa~p~a~~~y~tLdIK~IQ~DTlgh-~~~~~~~t~g~~~~~s~~~~~~lkfy-~~~~kE~~eyI~~A-Y  552 (932)
T KOG2053|consen  476 KLLLIRIYSYLGAFPDAYELYKTLDIKNIQTDTLGH-LIFRRAETSGRSSFASNTFNEHLKFY-DSSLKETPEYIALA-Y  552 (932)
T ss_pred             HHHHHHHHHHhcCChhHHHHHHhcchHHhhhccchH-HHHHHHHhcccchhHHHHHHHHHHHH-hhhhhhhHHHHHHH-H
Confidence            778899999999999999999988765555444333 23345566788888888887776531 1111 222223333 4


Q ss_pred             HcCChhHHHHHH---HHHHHCCCCCCHHHHHHHHHHHHhcCccc---ccchHHHHhhhhcccccc
Q 040027          534 RINEPSKVNELL---HKMKEKKVMPDASIVSIVVDLLVKNEISL---KSLPSFLVQERQGEVGES  592 (595)
Q Consensus       534 ~~g~~~~A~~~~---~~~~~~~~~p~~~~~~~l~~~~~~~g~~~---~~i~~~~~~~~~~~~~~~  592 (595)
                      +.|.+++..++.   +++....-.--..+-+..++.+...++.+   +.+..|..++.-+++++.
T Consensus       553 r~g~ySkI~em~~fr~rL~~S~q~~a~~VE~~~l~ll~~~~~~~q~~~~~~~~~l~~~e~~I~w~  617 (932)
T KOG2053|consen  553 RRGAYSKIPEMLAFRDRLMHSLQKWACRVENLQLSLLCNADRGTQLLKLLESMKLPPSEDRIQWV  617 (932)
T ss_pred             HcCchhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCcHHHHHHHHhccccCcchhhcccc
Confidence            667776655443   23321111122445566777788888877   556666666666666653

>KOG3616 consensus Selective LIM binding factor [Transcription]

Probab=99.11  E-value=1.1e-06  Score=85.66  Aligned_cols=167  Identities=20%  Similarity=0.197  Sum_probs=87.2

Q ss_pred             HHHHHhcCCHHHHHHHHHHHHhcCCCCCHHHHHHHHHHHHhCCCHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHccCCH
Q 040027          319 MDGFCLMGKINRAEELFGSMESMGCKHDDVSYNILINGYCKNKEVEEALSLYREMVSKGIKPTVVTYNTLFLGLFEIHQV  398 (595)
Q Consensus       319 ~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~  398 (595)
                      +.+.....+|.+|+.+++.+...  +.-..-|..+...|...|+++.|.++|.+.-         .++..+..|.+.|+|
T Consensus       739 ieaai~akew~kai~ildniqdq--k~~s~yy~~iadhyan~~dfe~ae~lf~e~~---------~~~dai~my~k~~kw  807 (1636)
T KOG3616|consen  739 IEAAIGAKEWKKAISILDNIQDQ--KTASGYYGEIADHYANKGDFEIAEELFTEAD---------LFKDAIDMYGKAGKW  807 (1636)
T ss_pred             HHHHhhhhhhhhhHhHHHHhhhh--ccccccchHHHHHhccchhHHHHHHHHHhcc---------hhHHHHHHHhccccH
Confidence            44445556667777777666654  2233345556666677777777776665431         234455666677777


Q ss_pred             HHHHHHHHHHHHCCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCcCHHHHHHHHHHHHhcCChHHHHHHHHhc
Q 040027          399 EHALKLFDEMQRDGVAADTRTYTTFIDGLCKNGYIIEAVELFRTLRILKCELDIQAYNCLIDGLCKSGRLKFAWELFCSL  478 (595)
Q Consensus       399 ~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~  478 (595)
                      +.|.++-.+...  .......|..-..-+-++|++.+|.++|-.+-    .|+.     .+.+|-+.|..+..+++..+-
T Consensus       808 ~da~kla~e~~~--~e~t~~~yiakaedldehgkf~eaeqlyiti~----~p~~-----aiqmydk~~~~ddmirlv~k~  876 (1636)
T KOG3616|consen  808 EDAFKLAEECHG--PEATISLYIAKAEDLDEHGKFAEAEQLYITIG----EPDK-----AIQMYDKHGLDDDMIRLVEKH  876 (1636)
T ss_pred             HHHHHHHHHhcC--chhHHHHHHHhHHhHHhhcchhhhhheeEEcc----CchH-----HHHHHHhhCcchHHHHHHHHh
Confidence            776666555432  23333444444444556666666666554332    2332     244555555555555554442


Q ss_pred             ccCCCCCC--HHHHHHHHHHHHhcCChhHHHHHHHH
Q 040027          479 PHGVLVPN--VVTYNIMIQGLCNDGQMDKARDLFLD  512 (595)
Q Consensus       479 ~~~~~~p~--~~~~~~l~~~~~~~g~~~~A~~~~~~  512 (595)
                      -     |+  ..|...+..-|-..|+...|...|-+
T Consensus       877 h-----~d~l~dt~~~f~~e~e~~g~lkaae~~fle  907 (1636)
T KOG3616|consen  877 H-----GDHLHDTHKHFAKELEAEGDLKAAEEHFLE  907 (1636)
T ss_pred             C-----hhhhhHHHHHHHHHHHhccChhHHHHHHHh
Confidence            2     12  23333444444455555555544433

>PRK04841 transcriptional regulator MalT; Provisional

Probab=99.11  E-value=1.8e-06  Score=95.00  Aligned_cols=338  Identities=12%  Similarity=0.014  Sum_probs=216.1

Q ss_pred             HHHHHcCCHhHHHHHHHHHhhCCCCCCHhHHHHHHHHHHhcCCHHHHHHHHHHHHHCCC------CCC--HhhHHHHHHH
Q 040027          215 DGLCKEGFVDKAKALFLQMKDENINPDVVTYNSLIHGLCHANDWNEAKRLFIEMMDQGV------QPS--VVTFNVIMDE  286 (595)
Q Consensus       215 ~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~~ll~~~~~~~~~~~A~~~~~~~~~~~~------~~~--~~~~~~l~~~  286 (595)
                      ......|+++.+..+++.+.......+..........+...|+++++..++......--      .+.  ......+...
T Consensus       382 ~~l~~~g~~~~l~~~l~~lp~~~~~~~~~l~~~~a~~~~~~g~~~~a~~~l~~a~~~~~~~~~~~~~~~~~~~~~~~a~~  461 (903)
T PRK04841        382 WSLFNQGELSLLEECLNALPWEVLLENPRLVLLQAWLAQSQHRYSEVNTLLARAEQELKDRNIELDGTLQAEFNALRAQV  461 (903)
T ss_pred             HHHHhcCChHHHHHHHHhCCHHHHhcCcchHHHHHHHHHHCCCHHHHHHHHHHHHHhccccCcccchhHHHHHHHHHHHH
Confidence            34455677777777776653211111222333445566788999999999987754311      111  1122233456


Q ss_pred             HHhcCChHHHHHHHHHHHHCCCCCCH----HHHHHHHHHHHhcCCHHHHHHHHHHHHhcCC---CCC--HHHHHHHHHHH
Q 040027          287 LCKNRKMDEASRLLDLMVQRGVRPNA----CTYNTLMDGFCLMGKINRAEELFGSMESMGC---KHD--DVSYNILINGY  357 (595)
Q Consensus       287 ~~~~g~~~~a~~~~~~~~~~~~~~~~----~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~---~~~--~~~~~~l~~~~  357 (595)
                      +...|++++|...++.........+.    .....+...+...|+++.|...+.+......   .+.  ...+..+...+
T Consensus       462 ~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~a~~~lg~~~~~~G~~~~A~~~~~~al~~~~~~g~~~~~~~~~~~la~~~  541 (903)
T PRK04841        462 AINDGDPEEAERLAELALAELPLTWYYSRIVATSVLGEVHHCKGELARALAMMQQTEQMARQHDVYHYALWSLLQQSEIL  541 (903)
T ss_pred             HHhCCCHHHHHHHHHHHHhcCCCccHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHhhhcchHHHHHHHHHHHHHH
Confidence            67899999999999988763111121    2345566677889999999999988764311   111  23455667788


Q ss_pred             HhCCCHHHHHHHHHHHHHC----CCC--C-CHHHHHHHHHHHHccCCHHHHHHHHHHHHHC--CCCC--CHHHHHHHHHH
Q 040027          358 CKNKEVEEALSLYREMVSK----GIK--P-TVVTYNTLFLGLFEIHQVEHALKLFDEMQRD--GVAA--DTRTYTTFIDG  426 (595)
Q Consensus       358 ~~~~~~~~A~~~~~~~~~~----~~~--~-~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~--~~~~--~~~~~~~l~~~  426 (595)
                      ...|++++|...+++....    +..  + ....+..+...+...|++++|...+.+....  ...+  ....+..+...
T Consensus       542 ~~~G~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~~~la~~~~~~G~~~~A~~~~~~al~~~~~~~~~~~~~~~~~la~~  621 (903)
T PRK04841        542 FAQGFLQAAYETQEKAFQLIEEQHLEQLPMHEFLLRIRAQLLWEWARLDEAEQCARKGLEVLSNYQPQQQLQCLAMLAKI  621 (903)
T ss_pred             HHCCCHHHHHHHHHHHHHHHHHhccccccHHHHHHHHHHHHHHHhcCHHHHHHHHHHhHHhhhccCchHHHHHHHHHHHH
Confidence            8999999999998886652    211  1 1223445556677789999999999887653  1112  12334445667


Q ss_pred             HHhcCCHHHHHHHHHHHHHcCCCc-CHHHH-----HHHHHHHHhcCChHHHHHHHHhcccCCCCCC---HHHHHHHHHHH
Q 040027          427 LCKNGYIIEAVELFRTLRILKCEL-DIQAY-----NCLIDGLCKSGRLKFAWELFCSLPHGVLVPN---VVTYNIMIQGL  497 (595)
Q Consensus       427 ~~~~g~~~~A~~~~~~~~~~~~~~-~~~~~-----~~l~~~~~~~g~~~~A~~~~~~~~~~~~~p~---~~~~~~l~~~~  497 (595)
                      +...|++++|...+.++....... ....+     ...+..+...|+.+.|...+...........   ...+..+..++
T Consensus       622 ~~~~G~~~~A~~~l~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~~~A~~~l~~~~~~~~~~~~~~~~~~~~~a~~~  701 (903)
T PRK04841        622 SLARGDLDNARRYLNRLENLLGNGRYHSDWIANADKVRLIYWQMTGDKEAAANWLRQAPKPEFANNHFLQGQWRNIARAQ  701 (903)
T ss_pred             HHHcCCHHHHHHHHHHHHHHHhcccccHhHhhHHHHHHHHHHHHCCCHHHHHHHHHhcCCCCCccchhHHHHHHHHHHHH
Confidence            788999999999998886431111 11111     1122444568999999999887665211111   11235667788


Q ss_pred             HhcCChhHHHHHHHHHHHc----CCCCC-HHHHHHHHHHHHHcCChhHHHHHHHHHHHCC
Q 040027          498 CNDGQMDKARDLFLDMEEN----AAAPD-VITFDMLIHGFIRINEPSKVNELLHKMKEKK  552 (595)
Q Consensus       498 ~~~g~~~~A~~~~~~~~~~----~~~~~-~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~  552 (595)
                      ...|++++|...++++...    |...+ ..+...+..++...|+.++|...+.++.+..
T Consensus       702 ~~~g~~~~A~~~l~~al~~~~~~g~~~~~a~~~~~la~a~~~~G~~~~A~~~L~~Al~la  761 (903)
T PRK04841        702 ILLGQFDEAEIILEELNENARSLRLMSDLNRNLILLNQLYWQQGRKSEAQRVLLEALKLA  761 (903)
T ss_pred             HHcCCHHHHHHHHHHHHHHHHHhCchHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHh
Confidence            8999999999999998763    32222 2456677888999999999999999998653

>KOG3617 consensus WD40 and TPR repeat-containing protein [General function prediction only]

Probab=99.10  E-value=3.9e-06  Score=82.96  Aligned_cols=239  Identities=13%  Similarity=0.104  Sum_probs=143.9

Q ss_pred             CHhhHHHHHH--HHHcCCCchhHHhhCCCCCCHHHHHHHHHHHHhcCChhHHHHHHHHHHhCC---------CCCCHHHH
Q 040027           66 PVSSFNILLA--SLAKNKHYDTRLNATGLFPNLYTYNILINCFCKIGRVSLGFIAFGRILRSC---------FTPNAATF  134 (595)
Q Consensus        66 ~~~~~~~l~~--~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~---------~~~~~~~~  134 (595)
                      |+.+-..++.  .|..-|+-+.....-.+--+-.+|..+...|.+..+++-|.-.+..|....         -.++ ..-
T Consensus       725 d~~TRkaml~FSfyvtiG~MD~AfksI~~IkS~~vW~nmA~McVkT~RLDVAkVClGhm~~aRgaRAlR~a~q~~~-e~e  803 (1416)
T KOG3617|consen  725 DESTRKAMLDFSFYVTIGSMDAAFKSIQFIKSDSVWDNMASMCVKTRRLDVAKVCLGHMKNARGARALRRAQQNGE-EDE  803 (1416)
T ss_pred             CHHHHHhhhceeEEEEeccHHHHHHHHHHHhhhHHHHHHHHHhhhhccccHHHHhhhhhhhhhhHHHHHHHHhCCc-chh
Confidence            4444444432  344445544422222233467889999999999998888877766554321         0111 222


Q ss_pred             HHHHHHHHhcCCHhHHHHHHHHHHhcCCCCCHhhHHHHHHHHHhcCChhHHHHHHHHHHhcCCCCCccccCcHHHHHHHH
Q 040027          135 NSLIKGLHAESRIMEAAALFTKLKAFGCEPNVITYNTLINGLCRTGHTMIALNLFEEMANGNGEIGVVCKPNTVTYSTII  214 (595)
Q Consensus       135 ~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~~~~~~~~l~  214 (595)
                      ..+.......|.+++|..+|++..+.         ..|-..|...|.|++|+++-+.--+..         -..+|....
T Consensus       804 akvAvLAieLgMlEeA~~lYr~ckR~---------DLlNKlyQs~g~w~eA~eiAE~~DRiH---------Lr~Tyy~yA  865 (1416)
T KOG3617|consen  804 AKVAVLAIELGMLEEALILYRQCKRY---------DLLNKLYQSQGMWSEAFEIAETKDRIH---------LRNTYYNYA  865 (1416)
T ss_pred             hHHHHHHHHHhhHHHHHHHHHHHHHH---------HHHHHHHHhcccHHHHHHHHhhcccee---------hhhhHHHHH
Confidence            23334456779999999999998864         345567778999999998866543321         235666677


Q ss_pred             HHHHHcCCHhHHHHHHHHHhhC----------C---------CCCCHhHHHHHHHHHHhcCCHHHHHHHHHHHHHCCCCC
Q 040027          215 DGLCKEGFVDKAKALFLQMKDE----------N---------INPDVVTYNSLIHGLCHANDWNEAKRLFIEMMDQGVQP  275 (595)
Q Consensus       215 ~~~~~~g~~~~A~~~~~~~~~~----------~---------~~~~~~~~~~ll~~~~~~~~~~~A~~~~~~~~~~~~~~  275 (595)
                      .-+-..+|.+.|++.|++....          .         -..+...|.-....+-..|+.+.|+.+|....+     
T Consensus       866 ~~Lear~Di~~AleyyEK~~~hafev~rmL~e~p~~~e~Yv~~~~d~~L~~WWgqYlES~GemdaAl~~Y~~A~D-----  940 (1416)
T KOG3617|consen  866 KYLEARRDIEAALEYYEKAGVHAFEVFRMLKEYPKQIEQYVRRKRDESLYSWWGQYLESVGEMDAALSFYSSAKD-----  940 (1416)
T ss_pred             HHHHhhccHHHHHHHHHhcCChHHHHHHHHHhChHHHHHHHHhccchHHHHHHHHHHhcccchHHHHHHHHHhhh-----
Confidence            7777788999999888765321          0         011333444445555566777777777765543     


Q ss_pred             CHhhHHHHHHHHHhcCChHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHH
Q 040027          276 SVVTFNVIMDELCKNRKMDEASRLLDLMVQRGVRPNACTYNTLMDGFCLMGKINRAEELFGSM  338 (595)
Q Consensus       276 ~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~  338 (595)
                          |..+++..+-+|+.++|.++-++-      -|......+.+.|...|++.+|..+|.+.
T Consensus       941 ----~fs~VrI~C~qGk~~kAa~iA~es------gd~AAcYhlaR~YEn~g~v~~Av~FfTrA  993 (1416)
T KOG3617|consen  941 ----YFSMVRIKCIQGKTDKAARIAEES------GDKAACYHLARMYENDGDVVKAVKFFTRA  993 (1416)
T ss_pred             ----hhhheeeEeeccCchHHHHHHHhc------ccHHHHHHHHHHhhhhHHHHHHHHHHHHH
Confidence                334445555566666666554432      14445555666666667766666666554

>PRK04841 transcriptional regulator MalT; Provisional

Probab=99.10  E-value=1.1e-06  Score=96.57  Aligned_cols=337  Identities=11%  Similarity=-0.011  Sum_probs=214.5

Q ss_pred             HHHhcCChhHHHHHHHHHHhcCCCCCccccCcHHHHHHHHHHHHHcCCHhHHHHHHHHHhhCCC------CCC--HhHHH
Q 040027          175 GLCRTGHTMIALNLFEEMANGNGEIGVVCKPNTVTYSTIIDGLCKEGFVDKAKALFLQMKDENI------NPD--VVTYN  246 (595)
Q Consensus       175 ~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~------~~~--~~~~~  246 (595)
                      .+...|++..+...++.+....      ...++.........+...|+++++..+++.....--      .+.  .....
T Consensus       383 ~l~~~g~~~~l~~~l~~lp~~~------~~~~~~l~~~~a~~~~~~g~~~~a~~~l~~a~~~~~~~~~~~~~~~~~~~~~  456 (903)
T PRK04841        383 SLFNQGELSLLEECLNALPWEV------LLENPRLVLLQAWLAQSQHRYSEVNTLLARAEQELKDRNIELDGTLQAEFNA  456 (903)
T ss_pred             HHHhcCChHHHHHHHHhCCHHH------HhcCcchHHHHHHHHHHCCCHHHHHHHHHHHHHhccccCcccchhHHHHHHH
Confidence            3445677777666666542211      011222334445556678999999999987754310      111  11222


Q ss_pred             HHHHHHHhcCCHHHHHHHHHHHHHCCCCCCH----hhHHHHHHHHHhcCChHHHHHHHHHHHHC----CCC-CCHHHHHH
Q 040027          247 SLIHGLCHANDWNEAKRLFIEMMDQGVQPSV----VTFNVIMDELCKNRKMDEASRLLDLMVQR----GVR-PNACTYNT  317 (595)
Q Consensus       247 ~ll~~~~~~~~~~~A~~~~~~~~~~~~~~~~----~~~~~l~~~~~~~g~~~~a~~~~~~~~~~----~~~-~~~~~~~~  317 (595)
                      .+...+...|++++|...++.....-...+.    ...+.+...+...|++++|...+++....    |.. ....+...
T Consensus       457 ~~a~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~a~~~lg~~~~~~G~~~~A~~~~~~al~~~~~~g~~~~~~~~~~~  536 (903)
T PRK04841        457 LRAQVAINDGDPEEAERLAELALAELPLTWYYSRIVATSVLGEVHHCKGELARALAMMQQTEQMARQHDVYHYALWSLLQ  536 (903)
T ss_pred             HHHHHHHhCCCHHHHHHHHHHHHhcCCCccHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHhhhcchHHHHHHHHH
Confidence            3345667899999999999988763111121    23455666788899999999999888753    111 11234556


Q ss_pred             HHHHHHhcCCHHHHHHHHHHHHhc----CCCC---CHHHHHHHHHHHHhCCCHHHHHHHHHHHHHCC--CCC--CHHHHH
Q 040027          318 LMDGFCLMGKINRAEELFGSMESM----GCKH---DDVSYNILINGYCKNKEVEEALSLYREMVSKG--IKP--TVVTYN  386 (595)
Q Consensus       318 l~~~~~~~~~~~~a~~~~~~~~~~----~~~~---~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~~~--~~~--~~~~~~  386 (595)
                      +...+...|+++.|...+++....    +...   ....+..+...+...|++++|...+++.....  ..+  ....+.
T Consensus       537 la~~~~~~G~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~~~la~~~~~~G~~~~A~~~~~~al~~~~~~~~~~~~~~~~  616 (903)
T PRK04841        537 QSEILFAQGFLQAAYETQEKAFQLIEEQHLEQLPMHEFLLRIRAQLLWEWARLDEAEQCARKGLEVLSNYQPQQQLQCLA  616 (903)
T ss_pred             HHHHHHHCCCHHHHHHHHHHHHHHHHHhccccccHHHHHHHHHHHHHHHhcCHHHHHHHHHHhHHhhhccCchHHHHHHH
Confidence            677888999999999998886542    2111   12234456667778899999999998876531  111  233444


Q ss_pred             HHHHHHHccCCHHHHHHHHHHHHHCC--CCCCHH--H--HHHHHHHHHhcCCHHHHHHHHHHHHHcCCCcC---HHHHHH
Q 040027          387 TLFLGLFEIHQVEHALKLFDEMQRDG--VAADTR--T--YTTFIDGLCKNGYIIEAVELFRTLRILKCELD---IQAYNC  457 (595)
Q Consensus       387 ~l~~~~~~~~~~~~a~~~~~~~~~~~--~~~~~~--~--~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~~---~~~~~~  457 (595)
                      .+...+...|+++.|...+.......  ......  .  ....+..+...|+.+.|..++...........   ...+..
T Consensus       617 ~la~~~~~~G~~~~A~~~l~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~~~A~~~l~~~~~~~~~~~~~~~~~~~~  696 (903)
T PRK04841        617 MLAKISLARGDLDNARRYLNRLENLLGNGRYHSDWIANADKVRLIYWQMTGDKEAAANWLRQAPKPEFANNHFLQGQWRN  696 (903)
T ss_pred             HHHHHHHHcCCHHHHHHHHHHHHHHHhcccccHhHhhHHHHHHHHHHHHCCCHHHHHHHHHhcCCCCCccchhHHHHHHH
Confidence            56667788999999999998875421  111111  1  11122445568999999999877654221111   112356


Q ss_pred             HHHHHHhcCChHHHHHHHHhcccC----CCCCC-HHHHHHHHHHHHhcCChhHHHHHHHHHHHcC
Q 040027          458 LIDGLCKSGRLKFAWELFCSLPHG----VLVPN-VVTYNIMIQGLCNDGQMDKARDLFLDMEENA  517 (595)
Q Consensus       458 l~~~~~~~g~~~~A~~~~~~~~~~----~~~p~-~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~  517 (595)
                      +..++...|++++|...++++...    +..++ ..+...+..++...|+.++|...+.++.+..
T Consensus       697 ~a~~~~~~g~~~~A~~~l~~al~~~~~~g~~~~~a~~~~~la~a~~~~G~~~~A~~~L~~Al~la  761 (903)
T PRK04841        697 IARAQILLGQFDEAEIILEELNENARSLRLMSDLNRNLILLNQLYWQQGRKSEAQRVLLEALKLA  761 (903)
T ss_pred             HHHHHHHcCCHHHHHHHHHHHHHHHHHhCchHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHh
Confidence            777888999999999999987652    22222 3456677788899999999999999998864

>PF13041 PPR_2: PPR repeat family

Probab=99.08  E-value=4e-10  Score=72.78  Aligned_cols=49  Identities=41%  Similarity=0.867  Sum_probs=25.9

Q ss_pred             CCHHHHHHHHHHHHhcCChhHHHHHHHHHHHcCCCCCHHHHHHHHHHHH
Q 040027          485 PNVVTYNIMIQGLCNDGQMDKARDLFLDMEENAAAPDVITFDMLIHGFI  533 (595)
Q Consensus       485 p~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~~l~~~~~  533 (595)
                      ||..+|+.++.+|++.|++++|.++|++|.+.|+.||..||+.++.+|+
T Consensus         1 P~~~~yn~li~~~~~~~~~~~a~~l~~~M~~~g~~P~~~Ty~~li~~~~   49 (50)
T PF13041_consen    1 PDVVTYNTLISGYCKAGKFEEALKLFKEMKKRGIKPDSYTYNILINGLC   49 (50)
T ss_pred             CchHHHHHHHHHHHHCcCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHc
Confidence            4455555555555555555555555555555555555555555555543

>PF04733 Coatomer_E: Coatomer epsilon subunit; InterPro: IPR006822 Proteins synthesised on the ribosome and processed in the endoplasmic reticulum are transported from the Golgi apparatus to the trans-Golgi network (TGN), and from there via small carrier vesicles to their final destination compartment

Probab=99.08  E-value=9.9e-09  Score=93.88  Aligned_cols=149  Identities=18%  Similarity=0.173  Sum_probs=75.4

Q ss_pred             HHHccCCHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCcCHHHHHHHHHHHH----hcC
Q 040027          391 GLFEIHQVEHALKLFDEMQRDGVAADTRTYTTFIDGLCKNGYIIEAVELFRTLRILKCELDIQAYNCLIDGLC----KSG  466 (595)
Q Consensus       391 ~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~~l~~~~~----~~g  466 (595)
                      .+...|++++|++++...      .+.......+..|.+.++++.|.+.++.+.+.+  .| .+...+..++.    ...
T Consensus       111 i~~~~~~~~~AL~~l~~~------~~lE~~al~Vqi~L~~~R~dlA~k~l~~~~~~~--eD-~~l~qLa~awv~l~~g~e  181 (290)
T PF04733_consen  111 ILFHEGDYEEALKLLHKG------GSLELLALAVQILLKMNRPDLAEKELKNMQQID--ED-SILTQLAEAWVNLATGGE  181 (290)
T ss_dssp             HHCCCCHHHHHHCCCTTT------TCHHHHHHHHHHHHHTT-HHHHHHHHHHHHCCS--CC-HHHHHHHHHHHHHHHTTT
T ss_pred             HHHHcCCHHHHHHHHHcc------CcccHHHHHHHHHHHcCCHHHHHHHHHHHHhcC--Cc-HHHHHHHHHHHHHHhCch
Confidence            344455666555554321      234445555556666666666666666665432  22 22222332222    122


Q ss_pred             ChHHHHHHHHhcccCCCCCCHHHHHHHHHHHHhcCChhHHHHHHHHHHHcCCCCCHHHHHHHHHHHHHcCCh-hHHHHHH
Q 040027          467 RLKFAWELFCSLPHGVLVPNVVTYNIMIQGLCNDGQMDKARDLFLDMEENAAAPDVITFDMLIHGFIRINEP-SKVNELL  545 (595)
Q Consensus       467 ~~~~A~~~~~~~~~~~~~p~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~-~~A~~~~  545 (595)
                      .+.+|.-+|+++.+. ..+++.+.+.++.++...|++++|.+++.++.+.+ +.++.++..++.+....|+. +.+.+++
T Consensus       182 ~~~~A~y~f~El~~~-~~~t~~~lng~A~~~l~~~~~~eAe~~L~~al~~~-~~~~d~LaNliv~~~~~gk~~~~~~~~l  259 (290)
T PF04733_consen  182 KYQDAFYIFEELSDK-FGSTPKLLNGLAVCHLQLGHYEEAEELLEEALEKD-PNDPDTLANLIVCSLHLGKPTEAAERYL  259 (290)
T ss_dssp             CCCHHHHHHHHHHCC-S--SHHHHHHHHHHHHHCT-HHHHHHHHHHHCCC--CCHHHHHHHHHHHHHHTT-TCHHHHHHH
T ss_pred             hHHHHHHHHHHHHhc-cCCCHHHHHHHHHHHHHhCCHHHHHHHHHHHHHhc-cCCHHHHHHHHHHHHHhCCChhHHHHHH
Confidence            466666666665543 34555666666666666666666666666665543 33455555555555566655 4455566


Q ss_pred             HHHHH
Q 040027          546 HKMKE  550 (595)
Q Consensus       546 ~~~~~  550 (595)
                      .++..
T Consensus       260 ~qL~~  264 (290)
T PF04733_consen  260 SQLKQ  264 (290)
T ss_dssp             HHCHH
T ss_pred             HHHHH
Confidence            65554

This traffic is bidirectional, to ensure that proteins required to form vesicles are recycled. Vesicles have specific coat proteins (such as clathrin or coatomer) that are important for cargo selection and direction of transfer []. While clathrin mediates endocytic protein transport, and transport from ER to Golgi, coatomers primarily mediate intra-Golgi transport, as well as the reverse Golgi to ER transport of dilysine-tagged proteins []. For example, the coatomer COP1 (coat protein complex 1) is responsible for reverse transport of recycled proteins from Golgi and pre-Golgi compartments back to the ER, while COPII buds vesicles from the ER to the Golgi []. Coatomers reversibly associate with Golgi (non-clathrin-coated) vesicles to mediate protein transport and for budding from Golgi membranes []. Activated small guanine triphosphatases (GTPases) attract coat proteins to specific membrane export sites, thereby linking coatomers to export cargos. As coat proteins polymerise, vesicles are formed and budded from membrane-bound organelles. Coatomer complexes also influence Golgi structural integrity, as well as the processing, activity, and endocytic recycling of LDL receptors. In mammals, coatomer complexes can only be recruited by membranes associated to ADP-ribosylation factors (ARFs), which are small GTP-binding proteins. Coatomer complexes are hetero-oligomers composed of at least an alpha, beta, beta', gamma, delta, epsilon and zeta subunits. This entry represents the epsilon subunit of the coatomer complex, which is involved in the regulation of intracellular protein trafficking between the endoplasmic reticulum and the Golgi complex []. More information about these proteins can be found at Protein of the Month: Clathrin [].; GO: 0005198 structural molecule activity, 0006890 retrograde vesicle-mediated transport, Golgi to ER, 0030126 COPI vesicle coat; PDB: 3MV2_B 3MV3_F 3MKR_A.

>KOG0624 consensus dsRNA-activated protein kinase inhibitor P58, contains TPR and DnaJ domains [Defense mechanisms]

Probab=99.07  E-value=2.8e-06  Score=75.40  Aligned_cols=320  Identities=10%  Similarity=0.023  Sum_probs=184.3

Q ss_pred             CCHHHHHHHHHHHHhcCChhHHHHHHHHHHhCCCCCCHHHHHHHHHHHHhcCCHhHHHHHHHHHHhcCCCCCHh-hHHHH
Q 040027           94 PNLYTYNILINCFCKIGRVSLGFIAFGRILRSCFTPNAATFNSLIKGLHAESRIMEAAALFTKLKAFGCEPNVI-TYNTL  172 (595)
Q Consensus        94 ~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~~~~-~~~~l  172 (595)
                      .++.-...+...+...|++.+|+.-|-.+++.. +.+-.++..-...|...|+..-|+.=+++.++.  .||-. +...-
T Consensus        36 advekhlElGk~lla~~Q~sDALt~yHaAve~d-p~~Y~aifrRaT~yLAmGksk~al~Dl~rVlel--KpDF~~ARiQR  112 (504)
T KOG0624|consen   36 ADVEKHLELGKELLARGQLSDALTHYHAAVEGD-PNNYQAIFRRATVYLAMGKSKAALQDLSRVLEL--KPDFMAARIQR  112 (504)
T ss_pred             HHHHHHHHHHHHHHHhhhHHHHHHHHHHHHcCC-chhHHHHHHHHHHHhhhcCCccchhhHHHHHhc--CccHHHHHHHh
Confidence            356667778888888899999999998888763 222233344456688888888888888888876  55533 23344


Q ss_pred             HHHHHhcCChhHHHHHHHHHHhcCCCCCccccCcHHHHH------------HHHHHHHHcCCHhHHHHHHHHHhhCCCCC
Q 040027          173 INGLCRTGHTMIALNLFEEMANGNGEIGVVCKPNTVTYS------------TIIDGLCKEGFVDKAKALFLQMKDENINP  240 (595)
Q Consensus       173 ~~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~~~~~~~------------~l~~~~~~~g~~~~A~~~~~~~~~~~~~~  240 (595)
                      ...+.++|++++|..-|+.+++.+...+    .....+.            ..+..+...||...|++....+.+.. +.
T Consensus       113 g~vllK~Gele~A~~DF~~vl~~~~s~~----~~~eaqskl~~~~e~~~l~~ql~s~~~~GD~~~ai~~i~~llEi~-~W  187 (504)
T KOG0624|consen  113 GVVLLKQGELEQAEADFDQVLQHEPSNG----LVLEAQSKLALIQEHWVLVQQLKSASGSGDCQNAIEMITHLLEIQ-PW  187 (504)
T ss_pred             chhhhhcccHHHHHHHHHHHHhcCCCcc----hhHHHHHHHHhHHHHHHHHHHHHHHhcCCchhhHHHHHHHHHhcC-cc
Confidence            5667788999999999988887652111    0111111            11222333455555555555555432 33


Q ss_pred             CHhHHHHHHHHHHhcCCHHHHHHHHHHHHHCCCCCCHhhHHHHHHHHHhcCChHHHHHHHHHHHHCCCCCCHHHHHHHHH
Q 040027          241 DVVTYNSLIHGLCHANDWNEAKRLFIEMMDQGVQPSVVTFNVIMDELCKNRKMDEASRLLDLMVQRGVRPNACTYNTLMD  320 (595)
Q Consensus       241 ~~~~~~~ll~~~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~l~~  320 (595)
                      +...|..-..+|...|++..|+.-++...+... .+...+..+...+...|+.+.++...++.++.  .||......   
T Consensus       188 da~l~~~Rakc~i~~~e~k~AI~Dlk~askLs~-DnTe~~ykis~L~Y~vgd~~~sL~~iRECLKl--dpdHK~Cf~---  261 (504)
T KOG0624|consen  188 DASLRQARAKCYIAEGEPKKAIHDLKQASKLSQ-DNTEGHYKISQLLYTVGDAENSLKEIRECLKL--DPDHKLCFP---  261 (504)
T ss_pred             hhHHHHHHHHHHHhcCcHHHHHHHHHHHHhccc-cchHHHHHHHHHHHhhhhHHHHHHHHHHHHcc--CcchhhHHH---
Confidence            455555555555555555555555444443321 23344444444555555555555555555543  233221110   


Q ss_pred             HHHhcCCHHHHHHHHHHHHhcCCCCCHHHHHHHHHHHHhCCCHHHHHHHHHHHHHCCCCCCH---HHHHHHHHHHHccCC
Q 040027          321 GFCLMGKINRAEELFGSMESMGCKHDDVSYNILINGYCKNKEVEEALSLYREMVSKGIKPTV---VTYNTLFLGLFEIHQ  397 (595)
Q Consensus       321 ~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~~~~~~~~---~~~~~l~~~~~~~~~  397 (595)
                      .|-+   +.+....++.                +......++|-++++..+...+..+....   ..+..+-.++...++
T Consensus       262 ~YKk---lkKv~K~les----------------~e~~ie~~~~t~cle~ge~vlk~ep~~~~ir~~~~r~~c~C~~~d~~  322 (504)
T KOG0624|consen  262 FYKK---LKKVVKSLES----------------AEQAIEEKHWTECLEAGEKVLKNEPEETMIRYNGFRVLCTCYREDEQ  322 (504)
T ss_pred             HHHH---HHHHHHHHHH----------------HHHHHhhhhHHHHHHHHHHHHhcCCcccceeeeeeheeeecccccCC
Confidence            0000   0111111111                12234456677777777777765433112   233445556667788


Q ss_pred             HHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHHcC
Q 040027          398 VEHALKLFDEMQRDGVAADTRTYTTFIDGLCKNGYIIEAVELFRTLRILK  447 (595)
Q Consensus       398 ~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~  447 (595)
                      +.+|++...+++... +.|..++..-..+|.-...++.|+.-|+.+.+.+
T Consensus       323 ~~eAiqqC~evL~~d-~~dv~~l~dRAeA~l~dE~YD~AI~dye~A~e~n  371 (504)
T KOG0624|consen  323 FGEAIQQCKEVLDID-PDDVQVLCDRAEAYLGDEMYDDAIHDYEKALELN  371 (504)
T ss_pred             HHHHHHHHHHHHhcC-chHHHHHHHHHHHHhhhHHHHHHHHHHHHHHhcC
Confidence            888888888887652 3447778778888888888888888888888765

>KOG1914 consensus mRNA cleavage and polyadenylation factor I complex, subunit RNA14 [RNA processing and modification]

Probab=99.04  E-value=1.9e-05  Score=74.67  Aligned_cols=432  Identities=11%  Similarity=0.089  Sum_probs=261.0

Q ss_pred             CCCHHHHHHHHHHHHhcCCHhHHHHHHHHHHhcCCCCCHhhHHHHHHHHHhcCChhHHHHHHHHHHhcCCCCCccccCcH
Q 040027          128 TPNAATFNSLIKGLHAESRIMEAAALFTKLKAFGCEPNVITYNTLINGLCRTGHTMIALNLFEEMANGNGEIGVVCKPNT  207 (595)
Q Consensus       128 ~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~~~  207 (595)
                      +-|..+|+.|++-+..+ .++++.+.++++... ++-....|...+.......+++....+|.+-+..-        .+.
T Consensus        17 P~di~sw~~lire~qt~-~~~~~R~~YEq~~~~-FP~s~r~W~~yi~~El~skdfe~VEkLF~RCLvkv--------Lnl   86 (656)
T KOG1914|consen   17 PYDIDSWSQLIREAQTQ-PIDKVRETYEQLVNV-FPSSPRAWKLYIERELASKDFESVEKLFSRCLVKV--------LNL   86 (656)
T ss_pred             CccHHHHHHHHHHHccC-CHHHHHHHHHHHhcc-CCCCcHHHHHHHHHHHHhhhHHHHHHHHHHHHHHH--------hhH
Confidence            77999999999987766 999999999999876 35567889999999999999999999999988643        557


Q ss_pred             HHHHHHHHHHHH-cCCHhH----HHHHHHHHhh-CCCCC-CHhHHHHHHHH---------HHhcCCHHHHHHHHHHHHHC
Q 040027          208 VTYSTIIDGLCK-EGFVDK----AKALFLQMKD-ENINP-DVVTYNSLIHG---------LCHANDWNEAKRLFIEMMDQ  271 (595)
Q Consensus       208 ~~~~~l~~~~~~-~g~~~~----A~~~~~~~~~-~~~~~-~~~~~~~ll~~---------~~~~~~~~~A~~~~~~~~~~  271 (595)
                      ..|..-++.-.+ .|+...    ..+.|+-... .|+.+ +...|+..+..         +..+.+.+...++|++++..
T Consensus        87 DLW~lYl~YVR~~~~~~~~~r~~m~qAy~f~l~kig~di~s~siW~eYi~FL~~vea~gk~ee~QRI~~vRriYqral~t  166 (656)
T KOG1914|consen   87 DLWKLYLSYVRETKGKLFGYREKMVQAYDFALEKIGMDIKSYSIWDEYINFLEGVEAVGKYEENQRITAVRRIYQRALVT  166 (656)
T ss_pred             hHHHHHHHHHHHHccCcchHHHHHHHHHHHHHHHhccCcccchhHHHHHHHHHcccccccHHHHHHHHHHHHHHHHHhcC
Confidence            777776654333 233333    2334444333 34322 23345444432         33445677788888888764


Q ss_pred             CCCCCHhhHHH------HHHHH-------HhcCChHHHHHHHHHHHH--CCCCCC------HHH---------HHHHHHH
Q 040027          272 GVQPSVVTFNV------IMDEL-------CKNRKMDEASRLLDLMVQ--RGVRPN------ACT---------YNTLMDG  321 (595)
Q Consensus       272 ~~~~~~~~~~~------l~~~~-------~~~g~~~~a~~~~~~~~~--~~~~~~------~~~---------~~~l~~~  321 (595)
                      .+.-=...|+.      -++..       -+...+..|.++++++..  .|....      ..|         |..+|.-
T Consensus       167 Pm~nlEkLW~DY~~fE~~IN~~tarK~i~e~s~~Ym~AR~~~qel~~lt~GL~r~~~~vp~~~T~~e~~qv~~W~n~I~w  246 (656)
T KOG1914|consen  167 PMHNLEKLWKDYEAFEQEINIITARKFIGERSPEYMNARRVYQELQNLTRGLNRNAPAVPPKGTKDEIQQVELWKNWIKW  246 (656)
T ss_pred             ccccHHHHHHHHHHHHHHHHHHHHHHHHHhhCHHHHHHHHHHHHHHHHHhhhcccCCCCCCCCChHHHHHHHHHHHHHHH
Confidence            22211112221      12111       133456677777777754  232211      111         2222221


Q ss_pred             HHhcCCHH---------HHHHHHHHHH-hcCCCCCHHHHHHHH-------HHHHhCCC-------HHHHHHHHHHHHHCC
Q 040027          322 FCLMGKIN---------RAEELFGSME-SMGCKHDDVSYNILI-------NGYCKNKE-------VEEALSLYREMVSKG  377 (595)
Q Consensus       322 ~~~~~~~~---------~a~~~~~~~~-~~~~~~~~~~~~~l~-------~~~~~~~~-------~~~A~~~~~~~~~~~  377 (595)
                       -+.+-..         ...-++++.. -.+.  .+..|....       ..+...|+       -+++..+++..+..-
T Consensus       247 -EksNpL~t~~~~~~~~Rv~yayeQ~ll~l~~--~peiWy~~s~yl~~~s~l~~~~~d~~~a~~~t~e~~~~yEr~I~~l  323 (656)
T KOG1914|consen  247 -EKSNPLRTLDGTMLTRRVMYAYEQCLLYLGY--HPEIWYDYSMYLIEISDLLTEKGDVPDAKSLTDEAASIYERAIEGL  323 (656)
T ss_pred             -HhcCCcccccccHHHHHHHHHHHHHHHHHhc--CHHHHHHHHHHHHHhhHHHHHhcccccchhhHHHHHHHHHHHHHHH
Confidence             1111111         1111222221 1222  222222211       12333333       456666666665532


Q ss_pred             CCCCHHHHHHHHHHHHcc---CCHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCc-CHH
Q 040027          378 IKPTVVTYNTLFLGLFEI---HQVEHALKLFDEMQRDGVAADTRTYTTFIDGLCKNGYIIEAVELFRTLRILKCEL-DIQ  453 (595)
Q Consensus       378 ~~~~~~~~~~l~~~~~~~---~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~-~~~  453 (595)
                      ..-+..+|..+...-...   ...+.....+++++......-.-+|..++..-.+...+..|..+|.++.+.+..+ ++.
T Consensus       324 ~~~~~~Ly~~~a~~eE~~~~~n~~~~~~~~~~~ll~~~~~~~tLv~~~~mn~irR~eGlkaaR~iF~kaR~~~r~~hhVf  403 (656)
T KOG1914|consen  324 LKENKLLYFALADYEESRYDDNKEKKVHEIYNKLLKIEDIDLTLVYCQYMNFIRRAEGLKAARKIFKKAREDKRTRHHVF  403 (656)
T ss_pred             HHHHHHHHHHHHhhHHHhcccchhhhhHHHHHHHHhhhccCCceehhHHHHHHHHhhhHHHHHHHHHHHhhccCCcchhh
Confidence            222333333333221111   1356666677776654222223456777777778888999999999999876665 677


Q ss_pred             HHHHHHHHHHhcCChHHHHHHHHhcccCCCCCCHHHHHHHHHHHHhcCChhHHHHHHHHHHHcCCCCC--HHHHHHHHHH
Q 040027          454 AYNCLIDGLCKSGRLKFAWELFCSLPHGVLVPNVVTYNIMIQGLCNDGQMDKARDLFLDMEENAAAPD--VITFDMLIHG  531 (595)
Q Consensus       454 ~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~p~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~~--~~~~~~l~~~  531 (595)
                      +..+++..|+ .++.+.|.++|+-=... ...++.-....+..+...++-..|..+|++.+..+++++  ..+|..++.-
T Consensus       404 Va~A~mEy~c-skD~~~AfrIFeLGLkk-f~d~p~yv~~YldfL~~lNdd~N~R~LFEr~l~s~l~~~ks~~Iw~r~l~y  481 (656)
T KOG1914|consen  404 VAAALMEYYC-SKDKETAFRIFELGLKK-FGDSPEYVLKYLDFLSHLNDDNNARALFERVLTSVLSADKSKEIWDRMLEY  481 (656)
T ss_pred             HHHHHHHHHh-cCChhHHHHHHHHHHHh-cCCChHHHHHHHHHHHHhCcchhHHHHHHHHHhccCChhhhHHHHHHHHHH
Confidence            7777777665 68889999999875553 233445556777888889999999999999998866665  4688988888


Q ss_pred             HHHcCChhHHHHHHHHHHHC-C--CCCCHHHHHHHHHHHHhcCccc
Q 040027          532 FIRINEPSKVNELLHKMKEK-K--VMPDASIVSIVVDLLVKNEISL  574 (595)
Q Consensus       532 ~~~~g~~~~A~~~~~~~~~~-~--~~p~~~~~~~l~~~~~~~g~~~  574 (595)
                      =..-|+...+.++-+++... .  ..+.......+++-|.=.|.+.
T Consensus       482 ES~vGdL~si~~lekR~~~af~~~qe~~~~~~~~~v~RY~~~d~~~  527 (656)
T KOG1914|consen  482 ESNVGDLNSILKLEKRRFTAFPADQEYEGNETALFVDRYGILDLYP  527 (656)
T ss_pred             HHhcccHHHHHHHHHHHHHhcchhhcCCCChHHHHHHHHhhccccc
Confidence            88889999999998888753 1  2233445566677676666665

>PF13041 PPR_2: PPR repeat family

Probab=99.04  E-value=8.9e-10  Score=71.14  Aligned_cols=50  Identities=30%  Similarity=0.602  Sum_probs=48.4

Q ss_pred             CCHHHHHHHHHHHHHcCChhHHHHHHHHHHHCCCCCCHHHHHHHHHHHHh
Q 040027          520 PDVITFDMLIHGFIRINEPSKVNELLHKMKEKKVMPDASIVSIVVDLLVK  569 (595)
Q Consensus       520 ~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~p~~~~~~~l~~~~~~  569 (595)
                      ||..+|+.++.+|++.|++++|.++|++|.+.|+.||..||..++++|++
T Consensus         1 P~~~~yn~li~~~~~~~~~~~a~~l~~~M~~~g~~P~~~Ty~~li~~~~k   50 (50)
T PF13041_consen    1 PDVVTYNTLISGYCKAGKFEEALKLFKEMKKRGIKPDSYTYNILINGLCK   50 (50)
T ss_pred             CchHHHHHHHHHHHHCcCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHcC
Confidence            78999999999999999999999999999999999999999999999875

>KOG0985 consensus Vesicle coat protein clathrin, heavy chain [Intracellular trafficking, secretion, and vesicular transport]

Probab=99.00  E-value=2.3e-05  Score=79.42  Aligned_cols=325  Identities=14%  Similarity=0.154  Sum_probs=186.4

Q ss_pred             HhhCCCC--CCHHHHHHHHHHHHhcCChhHHHHHHHHHHhCC--CCCCHHHHHHHHHHHHhcCCHhHHHHHHHHHHhcCC
Q 040027           87 LNATGLF--PNLYTYNILINCFCKIGRVSLGFIAFGRILRSC--FTPNAATFNSLIKGLHAESRIMEAAALFTKLKAFGC  162 (595)
Q Consensus        87 ~~~~~~~--~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~--~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~  162 (595)
                      .+..+++  .||+.-+..+.++...+-..+.++++++++-.+  +.-+...-+.++-...+ -+..+..+..+++...+.
T Consensus       973 Vv~tal~E~~dPe~vS~tVkAfMtadLp~eLIELLEKIvL~~S~Fse~~nLQnLLiLtAik-ad~trVm~YI~rLdnyDa 1051 (1666)
T KOG0985|consen  973 VVQTALPETQDPEEVSVTVKAFMTADLPNELIELLEKIVLDNSVFSENRNLQNLLILTAIK-ADRTRVMEYINRLDNYDA 1051 (1666)
T ss_pred             HHHhcCCccCChHHHHHHHHHHHhcCCcHHHHHHHHHHhcCCcccccchhhhhhHHHHHhh-cChHHHHHHHHHhccCCc
Confidence            3344443  577777788888888888888888888877542  11222333444433333 334556666666655431


Q ss_pred             CCCHhhHHHHHHHHHhcCChhHHHHHHHHHHhcCCCCCccccCcHHHHHHHHHHHHHcCCHhHHHHHHHHHhhCCCCCCH
Q 040027          163 EPNVITYNTLINGLCRTGHTMIALNLFEEMANGNGEIGVVCKPNTVTYSTIIDGLCKEGFVDKAKALFLQMKDENINPDV  242 (595)
Q Consensus       163 ~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~~~  242 (595)
                      +       .+.......+-+++|+.+|++..           .+..+.+.|+.-   -+..+.|.+.-++.-      .+
T Consensus      1052 ~-------~ia~iai~~~LyEEAF~ifkkf~-----------~n~~A~~VLie~---i~~ldRA~efAe~~n------~p 1104 (1666)
T KOG0985|consen 1052 P-------DIAEIAIENQLYEEAFAIFKKFD-----------MNVSAIQVLIEN---IGSLDRAYEFAERCN------EP 1104 (1666)
T ss_pred             h-------hHHHHHhhhhHHHHHHHHHHHhc-----------ccHHHHHHHHHH---hhhHHHHHHHHHhhC------Ch
Confidence            1       23445556677778888877653           344555555443   355666666555442      45


Q ss_pred             hHHHHHHHHHHhcCCHHHHHHHHHHHHHCCCCCCHhhHHHHHHHHHhcCChHHHHHHHHHHHHCCCCCCHHHHHHHHHHH
Q 040027          243 VTYNSLIHGLCHANDWNEAKRLFIEMMDQGVQPSVVTFNVIMDELCKNRKMDEASRLLDLMVQRGVRPNACTYNTLMDGF  322 (595)
Q Consensus       243 ~~~~~ll~~~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~  322 (595)
                      ..|..+..+-.+.|...+|++-|-+.      .|+..|..++....+.|.+++-.+++....+..-.|...  ..++-+|
T Consensus      1105 ~vWsqlakAQL~~~~v~dAieSyika------dDps~y~eVi~~a~~~~~~edLv~yL~MaRkk~~E~~id--~eLi~Ay 1176 (1666)
T KOG0985|consen 1105 AVWSQLAKAQLQGGLVKDAIESYIKA------DDPSNYLEVIDVASRTGKYEDLVKYLLMARKKVREPYID--SELIFAY 1176 (1666)
T ss_pred             HHHHHHHHHHHhcCchHHHHHHHHhc------CCcHHHHHHHHHHHhcCcHHHHHHHHHHHHHhhcCccch--HHHHHHH
Confidence            67888888888888888887776443      366677888888888888888888887777765555443  3567777


Q ss_pred             HhcCCHHHHHHHHHHHHhcCCCCCHHHHHHHHHHHHhCCCHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHccCCHHHHH
Q 040027          323 CLMGKINRAEELFGSMESMGCKHDDVSYNILINGYCKNKEVEEALSLYREMVSKGIKPTVVTYNTLFLGLFEIHQVEHAL  402 (595)
Q Consensus       323 ~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~  402 (595)
                      ++.++..+.++++.       .|+......+..-|...+.++.|.-+|..         +..|..+...+...|++..|.
T Consensus      1177 Akt~rl~elE~fi~-------gpN~A~i~~vGdrcf~~~~y~aAkl~y~~---------vSN~a~La~TLV~LgeyQ~AV 1240 (1666)
T KOG0985|consen 1177 AKTNRLTELEEFIA-------GPNVANIQQVGDRCFEEKMYEAAKLLYSN---------VSNFAKLASTLVYLGEYQGAV 1240 (1666)
T ss_pred             HHhchHHHHHHHhc-------CCCchhHHHHhHHHhhhhhhHHHHHHHHH---------hhhHHHHHHHHHHHHHHHHHH
Confidence            77777666554431       24444444445555555555555444432         222333444444444444433


Q ss_pred             HHHHH------------------------HHHCCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCcCHHHHHHH
Q 040027          403 KLFDE------------------------MQRDGVAADTRTYTTFIDGLCKNGYIIEAVELFRTLRILKCELDIQAYNCL  458 (595)
Q Consensus       403 ~~~~~------------------------~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~~l  458 (595)
                      ..-++                        |-..++-....-...++..|...|-+++.+.+++..+... ......|+.+
T Consensus      1241 D~aRKAns~ktWK~VcfaCvd~~EFrlAQiCGL~iivhadeLeeli~~Yq~rGyFeElIsl~Ea~LGLE-RAHMgmfTEL 1319 (1666)
T KOG0985|consen 1241 DAARKANSTKTWKEVCFACVDKEEFRLAQICGLNIIVHADELEELIEYYQDRGYFEELISLLEAGLGLE-RAHMGMFTEL 1319 (1666)
T ss_pred             HHhhhccchhHHHHHHHHHhchhhhhHHHhcCceEEEehHhHHHHHHHHHhcCcHHHHHHHHHhhhchh-HHHHHHHHHH
Confidence            32221                        2222223334445556666666666666666666655332 2334455555


Q ss_pred             HHHHHh
Q 040027          459 IDGLCK  464 (595)
Q Consensus       459 ~~~~~~  464 (595)
                      .-.|.+
T Consensus      1320 aiLYsk 1325 (1666)
T KOG0985|consen 1320 AILYSK 1325 (1666)
T ss_pred             HHHHHh
Confidence            555544

>PF04733 Coatomer_E: Coatomer epsilon subunit; InterPro: IPR006822 Proteins synthesised on the ribosome and processed in the endoplasmic reticulum are transported from the Golgi apparatus to the trans-Golgi network (TGN), and from there via small carrier vesicles to their final destination compartment

Probab=98.97  E-value=3e-08  Score=90.75  Aligned_cols=252  Identities=13%  Similarity=0.068  Sum_probs=137.1

Q ss_pred             HHHHHhcCChhHHHHHHHHHHhCCCCCCHHHHHHHHHHHHhcCCHhHHHHHHHHHHhcCCCCCHhhHHHHHHHHHhcCCh
Q 040027          103 INCFCKIGRVSLGFIAFGRILRSCFTPNAATFNSLIKGLHAESRIMEAAALFTKLKAFGCEPNVITYNTLINGLCRTGHT  182 (595)
Q Consensus       103 ~~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~  182 (595)
                      ++.+.-.|++..++.-.+ ......+.+......+.+++...|+++.++   .++.... .|.......+...+...++-
T Consensus         8 vrn~fy~G~Y~~~i~e~~-~~~~~~~~~~e~~~~~~Rs~iAlg~~~~vl---~ei~~~~-~~~l~av~~la~y~~~~~~~   82 (290)
T PF04733_consen    8 VRNQFYLGNYQQCINEAS-LKSFSPENKLERDFYQYRSYIALGQYDSVL---SEIKKSS-SPELQAVRLLAEYLSSPSDK   82 (290)
T ss_dssp             HHHHHCTT-HHHHCHHHH-CHTSTCHHHHHHHHHHHHHHHHTT-HHHHH---HHS-TTS-SCCCHHHHHHHHHHCTSTTH
T ss_pred             HHHHHHhhhHHHHHHHhh-ccCCCchhHHHHHHHHHHHHHHcCChhHHH---HHhccCC-ChhHHHHHHHHHHHhCccch
Confidence            344555678887776666 222221223334455667777777766543   3332222 45555554444444333444


Q ss_pred             hHHHHHHHHHHhcCCCCCcccc-CcHHHHHHHHHHHHHcCCHhHHHHHHHHHhhCCCCCCHhHHHHHHHHHHhcCCHHHH
Q 040027          183 MIALNLFEEMANGNGEIGVVCK-PNTVTYSTIIDGLCKEGFVDKAKALFLQMKDENINPDVVTYNSLIHGLCHANDWNEA  261 (595)
Q Consensus       183 ~~A~~~~~~~~~~~~~~~~~~~-~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~~ll~~~~~~~~~~~A  261 (595)
                      +.++.-+++.....      .. .+.........++...|++++|.+++...      .+.......+..|.+.++++.|
T Consensus        83 e~~l~~l~~~~~~~------~~~~~~~~~~~~A~i~~~~~~~~~AL~~l~~~------~~lE~~al~Vqi~L~~~R~dlA  150 (290)
T PF04733_consen   83 ESALEELKELLADQ------AGESNEIVQLLAATILFHEGDYEEALKLLHKG------GSLELLALAVQILLKMNRPDLA  150 (290)
T ss_dssp             HCHHHHHHHCCCTS---------CHHHHHHHHHHHHCCCCHHHHHHCCCTTT------TCHHHHHHHHHHHHHTT-HHHH
T ss_pred             HHHHHHHHHHHHhc------cccccHHHHHHHHHHHHHcCCHHHHHHHHHcc------CcccHHHHHHHHHHHcCCHHHH
Confidence            45555444433322      11 22222223334455567777777766543      2566666667777778888888


Q ss_pred             HHHHHHHHHCCCCCCHhhHHHHHHHHH----hcCChHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHH
Q 040027          262 KRLFIEMMDQGVQPSVVTFNVIMDELC----KNRKMDEASRLLDLMVQRGVRPNACTYNTLMDGFCLMGKINRAEELFGS  337 (595)
Q Consensus       262 ~~~~~~~~~~~~~~~~~~~~~l~~~~~----~~g~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~  337 (595)
                      .+.++.|.+.  ..| .+...+..++.    ....+.+|..+|+++.+. ..+++.+.+.++.++...|++++|.+++.+
T Consensus       151 ~k~l~~~~~~--~eD-~~l~qLa~awv~l~~g~e~~~~A~y~f~El~~~-~~~t~~~lng~A~~~l~~~~~~eAe~~L~~  226 (290)
T PF04733_consen  151 EKELKNMQQI--DED-SILTQLAEAWVNLATGGEKYQDAFYIFEELSDK-FGSTPKLLNGLAVCHLQLGHYEEAEELLEE  226 (290)
T ss_dssp             HHHHHHHHCC--SCC-HHHHHHHHHHHHHHHTTTCCCHHHHHHHHHHCC-S--SHHHHHHHHHHHHHCT-HHHHHHHHHH
T ss_pred             HHHHHHHHhc--CCc-HHHHHHHHHHHHHHhCchhHHHHHHHHHHHHhc-cCCCHHHHHHHHHHHHHhCCHHHHHHHHHH
Confidence            8887777664  222 33333433332    233577777777776654 455667777777777777777777777777


Q ss_pred             HHhcCCCCCHHHHHHHHHHHHhCCCH-HHHHHHHHHHHHC
Q 040027          338 MESMGCKHDDVSYNILINGYCKNKEV-EEALSLYREMVSK  376 (595)
Q Consensus       338 ~~~~~~~~~~~~~~~l~~~~~~~~~~-~~A~~~~~~~~~~  376 (595)
                      ....+ +.++.+...++.+....|+. +.+.+.+.++...
T Consensus       227 al~~~-~~~~d~LaNliv~~~~~gk~~~~~~~~l~qL~~~  265 (290)
T PF04733_consen  227 ALEKD-PNDPDTLANLIVCSLHLGKPTEAAERYLSQLKQS  265 (290)
T ss_dssp             HCCC--CCHHHHHHHHHHHHHHTT-TCHHHHHHHHHCHHH
T ss_pred             HHHhc-cCCHHHHHHHHHHHHHhCCChhHHHHHHHHHHHh
Confidence            76554 34555666666666666665 4555666666553

This traffic is bidirectional, to ensure that proteins required to form vesicles are recycled. Vesicles have specific coat proteins (such as clathrin or coatomer) that are important for cargo selection and direction of transfer []. While clathrin mediates endocytic protein transport, and transport from ER to Golgi, coatomers primarily mediate intra-Golgi transport, as well as the reverse Golgi to ER transport of dilysine-tagged proteins []. For example, the coatomer COP1 (coat protein complex 1) is responsible for reverse transport of recycled proteins from Golgi and pre-Golgi compartments back to the ER, while COPII buds vesicles from the ER to the Golgi []. Coatomers reversibly associate with Golgi (non-clathrin-coated) vesicles to mediate protein transport and for budding from Golgi membranes []. Activated small guanine triphosphatases (GTPases) attract coat proteins to specific membrane export sites, thereby linking coatomers to export cargos. As coat proteins polymerise, vesicles are formed and budded from membrane-bound organelles. Coatomer complexes also influence Golgi structural integrity, as well as the processing, activity, and endocytic recycling of LDL receptors. In mammals, coatomer complexes can only be recruited by membranes associated to ADP-ribosylation factors (ARFs), which are small GTP-binding proteins. Coatomer complexes are hetero-oligomers composed of at least an alpha, beta, beta', gamma, delta, epsilon and zeta subunits. This entry represents the epsilon subunit of the coatomer complex, which is involved in the regulation of intracellular protein trafficking between the endoplasmic reticulum and the Golgi complex []. More information about these proteins can be found at Protein of the Month: Clathrin [].; GO: 0005198 structural molecule activity, 0006890 retrograde vesicle-mediated transport, Golgi to ER, 0030126 COPI vesicle coat; PDB: 3MV2_B 3MV3_F 3MKR_A.

>KOG1128 consensus Uncharacterized conserved protein, contains TPR repeats [General function prediction only]

Probab=98.95  E-value=4.7e-07  Score=88.32  Aligned_cols=233  Identities=14%  Similarity=0.102  Sum_probs=181.6

Q ss_pred             HHHHHHHHHHhcCCHHHHHHHHHHHHhcCCCCCHHHHHHHHHHHHhCCCHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHH
Q 040027          314 TYNTLMDGFCLMGKINRAEELFGSMESMGCKHDDVSYNILINGYCKNKEVEEALSLYREMVSKGIKPTVVTYNTLFLGLF  393 (595)
Q Consensus       314 ~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~~l~~~~~  393 (595)
                      .-..+...+...|-...|..+++++.         .|...+.+|...|+..+|..+..+..++  +|++..|..+.....
T Consensus       400 ~q~~laell~slGitksAl~I~Erle---------mw~~vi~CY~~lg~~~kaeei~~q~lek--~~d~~lyc~LGDv~~  468 (777)
T KOG1128|consen  400 LQRLLAELLLSLGITKSALVIFERLE---------MWDPVILCYLLLGQHGKAEEINRQELEK--DPDPRLYCLLGDVLH  468 (777)
T ss_pred             HHHHHHHHHHHcchHHHHHHHHHhHH---------HHHHHHHHHHHhcccchHHHHHHHHhcC--CCcchhHHHhhhhcc
Confidence            34556777888888899998887754         5777889999999999999998888874  678888888888777


Q ss_pred             ccCCHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCcCHHHHHHHHHHHHhcCChHHHHH
Q 040027          394 EIHQVEHALKLFDEMQRDGVAADTRTYTTFIDGLCKNGYIIEAVELFRTLRILKCELDIQAYNCLIDGLCKSGRLKFAWE  473 (595)
Q Consensus       394 ~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~  473 (595)
                      ...-+++|.++.+.....       .-..+.......++++++.+.|+.-.+.+ +....+|-.+..+..+.+++..|..
T Consensus       469 d~s~yEkawElsn~~sar-------A~r~~~~~~~~~~~fs~~~~hle~sl~~n-plq~~~wf~~G~~ALqlek~q~av~  540 (777)
T KOG1128|consen  469 DPSLYEKAWELSNYISAR-------AQRSLALLILSNKDFSEADKHLERSLEIN-PLQLGTWFGLGCAALQLEKEQAAVK  540 (777)
T ss_pred             ChHHHHHHHHHhhhhhHH-------HHHhhccccccchhHHHHHHHHHHHhhcC-ccchhHHHhccHHHHHHhhhHHHHH
Confidence            777778888887765432       11122222334789999999999988876 7778899999999999999999999


Q ss_pred             HHHhcccCCCCCC-HHHHHHHHHHHHhcCChhHHHHHHHHHHHcCCCCCHHHHHHHHHHHHHcCChhHHHHHHHHHHHCC
Q 040027          474 LFCSLPHGVLVPN-VVTYNIMIQGLCNDGQMDKARDLFLDMEENAAAPDVITFDMLIHGFIRINEPSKVNELLHKMKEKK  552 (595)
Q Consensus       474 ~~~~~~~~~~~p~-~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~  552 (595)
                      .|.....  +.|| ...||++..+|.+.|+..+|...+.++.+-+ ..+...|........+.|.+++|.+.+.++.+..
T Consensus       541 aF~rcvt--L~Pd~~eaWnNls~ayi~~~~k~ra~~~l~EAlKcn-~~~w~iWENymlvsvdvge~eda~~A~~rll~~~  617 (777)
T KOG1128|consen  541 AFHRCVT--LEPDNAEAWNNLSTAYIRLKKKKRAFRKLKEALKCN-YQHWQIWENYMLVSVDVGEFEDAIKAYHRLLDLR  617 (777)
T ss_pred             HHHHHhh--cCCCchhhhhhhhHHHHHHhhhHHHHHHHHHHhhcC-CCCCeeeechhhhhhhcccHHHHHHHHHHHHHhh
Confidence            9999988  6776 5799999999999999999999999999876 5566677777777889999999999999998532


Q ss_pred             C-CCCHHHHHHHHHHHH
Q 040027          553 V-MPDASIVSIVVDLLV  568 (595)
Q Consensus       553 ~-~p~~~~~~~l~~~~~  568 (595)
                      . ..|..+...++....
T Consensus       618 ~~~~d~~vl~~iv~~~~  634 (777)
T KOG1128|consen  618 KKYKDDEVLLIIVRTVL  634 (777)
T ss_pred             hhcccchhhHHHHHHHH
Confidence            1 125555555544443

>KOG1070 consensus rRNA processing protein Rrp5 [RNA processing and modification]

Probab=98.90  E-value=1.8e-06  Score=90.18  Aligned_cols=214  Identities=10%  Similarity=0.041  Sum_probs=148.2

Q ss_pred             HhhCCCCCCHHHHHHHHHHHHhcCChhHHHHHHHHHHhCC-CCC---CHHHHHHHHHHHHhcCCHhHHHHHHHHHHhcCC
Q 040027           87 LNATGLFPNLYTYNILINCFCKIGRVSLGFIAFGRILRSC-FTP---NAATFNSLIKGLHAESRIMEAAALFTKLKAFGC  162 (595)
Q Consensus        87 ~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~-~~~---~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~  162 (595)
                      +.-.+-+-+...|...+..+...++.+.|+.++++++..- +.-   -...|.++++.-..-|.-+...++|+++.+.  
T Consensus      1449 rlvrssPNSSi~WI~YMaf~LelsEiekAR~iaerAL~tIN~REeeEKLNiWiA~lNlEn~yG~eesl~kVFeRAcqy-- 1526 (1710)
T KOG1070|consen 1449 RLVRSSPNSSILWIRYMAFHLELSEIEKARKIAERALKTINFREEEEKLNIWIAYLNLENAYGTEESLKKVFERACQY-- 1526 (1710)
T ss_pred             HHHhcCCCcchHHHHHHHHHhhhhhhHHHHHHHHHHhhhCCcchhHHHHHHHHHHHhHHHhhCcHHHHHHHHHHHHHh--
Confidence            3334445577888888888888999999999999888752 111   2335666666666667777777888887765  


Q ss_pred             CCCHhhHHHHHHHHHhcCChhHHHHHHHHHHhcCCCCCccccCcHHHHHHHHHHHHHcCCHhHHHHHHHHHhhCCCC-CC
Q 040027          163 EPNVITYNTLINGLCRTGHTMIALNLFEEMANGNGEIGVVCKPNTVTYSTIIDGLCKEGFVDKAKALFLQMKDENIN-PD  241 (595)
Q Consensus       163 ~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~-~~  241 (595)
                      --.-.+|..|...|.+.+++++|.++|+.|.+.-       ......|...+..+.++++.+.|..++.+..+.-.+ -.
T Consensus      1527 cd~~~V~~~L~~iy~k~ek~~~A~ell~~m~KKF-------~q~~~vW~~y~~fLl~~ne~~aa~~lL~rAL~~lPk~eH 1599 (1710)
T KOG1070|consen 1527 CDAYTVHLKLLGIYEKSEKNDEADELLRLMLKKF-------GQTRKVWIMYADFLLRQNEAEAARELLKRALKSLPKQEH 1599 (1710)
T ss_pred             cchHHHHHHHHHHHHHhhcchhHHHHHHHHHHHh-------cchhhHHHHHHHHHhcccHHHHHHHHHHHHHhhcchhhh
Confidence            2234556777778888888888888888887763       345677888888888888888888888777664111 02


Q ss_pred             HhHHHHHHHHHHhcCCHHHHHHHHHHHHHCCCCCCHhhHHHHHHHHHhcCChHHHHHHHHHHHHCCCCC
Q 040027          242 VVTYNSLIHGLCHANDWNEAKRLFIEMMDQGVQPSVVTFNVIMDELCKNRKMDEASRLLDLMVQRGVRP  310 (595)
Q Consensus       242 ~~~~~~ll~~~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~~~~  310 (595)
                      .......+..-.+.|+.+.+..+|+..+.. .+--...|+.++..-.+.|+.+.+..+|+++...++.+
T Consensus      1600 v~~IskfAqLEFk~GDaeRGRtlfEgll~a-yPKRtDlW~VYid~eik~~~~~~vR~lfeRvi~l~l~~ 1667 (1710)
T KOG1070|consen 1600 VEFISKFAQLEFKYGDAERGRTLFEGLLSA-YPKRTDLWSVYIDMEIKHGDIKYVRDLFERVIELKLSI 1667 (1710)
T ss_pred             HHHHHHHHHHHhhcCCchhhHHHHHHHHhh-CccchhHHHHHHHHHHccCCHHHHHHHHHHHHhcCCCh
Confidence            333344455566778888888888777765 22345677778887788888888888888877766554

>PLN02789 farnesyltranstransferase

Probab=98.88  E-value=7.4e-06  Score=76.21  Aligned_cols=216  Identities=10%  Similarity=0.045  Sum_probs=142.1

Q ss_pred             HHHHHHHHHHHhcCChhHHHHHHHHHHhCCCCCCHHHHHHHHHHHHhcC-CHhHHHHHHHHHHhcCCCCCHhhHHHHHHH
Q 040027           97 YTYNILINCFCKIGRVSLGFIAFGRILRSCFTPNAATFNSLIKGLHAES-RIMEAAALFTKLKAFGCEPNVITYNTLING  175 (595)
Q Consensus        97 ~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g-~~~~A~~~~~~~~~~~~~~~~~~~~~l~~~  175 (595)
                      .++..+-..+...++.++|+.+.+++++.. +-+..+|+.-...+...| ++++++..++++..... -+..+|+.....
T Consensus        38 ~a~~~~ra~l~~~e~serAL~lt~~aI~ln-P~~ytaW~~R~~iL~~L~~~l~eeL~~~~~~i~~np-knyqaW~~R~~~  115 (320)
T PLN02789         38 EAMDYFRAVYASDERSPRALDLTADVIRLN-PGNYTVWHFRRLCLEALDADLEEELDFAEDVAEDNP-KNYQIWHHRRWL  115 (320)
T ss_pred             HHHHHHHHHHHcCCCCHHHHHHHHHHHHHC-chhHHHHHHHHHHHHHcchhHHHHHHHHHHHHHHCC-cchHHhHHHHHH
Confidence            344555556666788888999988888874 445667776666666666 57888888888887643 355667766555


Q ss_pred             HHhcCCh--hHHHHHHHHHHhcCCCCCccccCcHHHHHHHHHHHHHcCCHhHHHHHHHHHhhCCCCCCHhHHHHHHHHHH
Q 040027          176 LCRTGHT--MIALNLFEEMANGNGEIGVVCKPNTVTYSTIIDGLCKEGFVDKAKALFLQMKDENINPDVVTYNSLIHGLC  253 (595)
Q Consensus       176 ~~~~g~~--~~A~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~~ll~~~~  253 (595)
                      +.+.|+.  ++++..++++.+.+       +.+..+|....-++...|+++++++.++++++.++. +...|+.....+.
T Consensus       116 l~~l~~~~~~~el~~~~kal~~d-------pkNy~AW~~R~w~l~~l~~~~eeL~~~~~~I~~d~~-N~sAW~~R~~vl~  187 (320)
T PLN02789        116 AEKLGPDAANKELEFTRKILSLD-------AKNYHAWSHRQWVLRTLGGWEDELEYCHQLLEEDVR-NNSAWNQRYFVIT  187 (320)
T ss_pred             HHHcCchhhHHHHHHHHHHHHhC-------cccHHHHHHHHHHHHHhhhHHHHHHHHHHHHHHCCC-chhHHHHHHHHHH
Confidence            5566653  66788888888776       567788888888888888888888888888877543 6666766655554


Q ss_pred             hc---CC----HHHHHHHHHHHHHCCCCCCHhhHHHHHHHHHhc----CChHHHHHHHHHHHHCCCCCCHHHHHHHHHHH
Q 040027          254 HA---ND----WNEAKRLFIEMMDQGVQPSVVTFNVIMDELCKN----RKMDEASRLLDLMVQRGVRPNACTYNTLMDGF  322 (595)
Q Consensus       254 ~~---~~----~~~A~~~~~~~~~~~~~~~~~~~~~l~~~~~~~----g~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~  322 (595)
                      +.   |.    .++.+....+++... +-+...|+.+...+...    +...++...+.+..+.++ .+...+..++..|
T Consensus       188 ~~~~l~~~~~~~e~el~y~~~aI~~~-P~N~SaW~Yl~~ll~~~~~~l~~~~~~~~~~~~~~~~~~-~s~~al~~l~d~~  265 (320)
T PLN02789        188 RSPLLGGLEAMRDSELKYTIDAILAN-PRNESPWRYLRGLFKDDKEALVSDPEVSSVCLEVLSKDS-NHVFALSDLLDLL  265 (320)
T ss_pred             hccccccccccHHHHHHHHHHHHHhC-CCCcCHHHHHHHHHhcCCcccccchhHHHHHHHhhcccC-CcHHHHHHHHHHH
Confidence            43   22    245666665666542 23566676666666552    334556666666655432 2455566666666


Q ss_pred             Hh
Q 040027          323 CL  324 (595)
Q Consensus       323 ~~  324 (595)
                      +.
T Consensus       266 ~~  267 (320)
T PLN02789        266 CE  267 (320)
T ss_pred             Hh
Confidence            54

>PLN02789 farnesyltranstransferase

Probab=98.87  E-value=4.1e-06  Score=77.88  Aligned_cols=218  Identities=11%  Similarity=0.043  Sum_probs=121.0

Q ss_pred             cCCHHHHHHHHHHHHhcCCCCCHHHHHHHHHHHHhCC-CHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHccCCH--HHH
Q 040027          325 MGKINRAEELFGSMESMGCKHDDVSYNILINGYCKNK-EVEEALSLYREMVSKGIKPTVVTYNTLFLGLFEIHQV--EHA  401 (595)
Q Consensus       325 ~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~-~~~~A~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~--~~a  401 (595)
                      .+..++|+..+.++++.+ +.+..+|+....++...+ ++++++..++++.+..++ +..+|..-...+.+.++.  +++
T Consensus        50 ~e~serAL~lt~~aI~ln-P~~ytaW~~R~~iL~~L~~~l~eeL~~~~~~i~~npk-nyqaW~~R~~~l~~l~~~~~~~e  127 (320)
T PLN02789         50 DERSPRALDLTADVIRLN-PGNYTVWHFRRLCLEALDADLEEELDFAEDVAEDNPK-NYQIWHHRRWLAEKLGPDAANKE  127 (320)
T ss_pred             CCCCHHHHHHHHHHHHHC-chhHHHHHHHHHHHHHcchhHHHHHHHHHHHHHHCCc-chHHhHHHHHHHHHcCchhhHHH
Confidence            344555555555555543 233344554444455555 456666666666655433 334444444344444432  455


Q ss_pred             HHHHHHHHHCCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCcCHHHHHHHHHHHHhc---CCh----HHHHHH
Q 040027          402 LKLFDEMQRDGVAADTRTYTTFIDGLCKNGYIIEAVELFRTLRILKCELDIQAYNCLIDGLCKS---GRL----KFAWEL  474 (595)
Q Consensus       402 ~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~~l~~~~~~~---g~~----~~A~~~  474 (595)
                      ...++.+++.+ +-+..+|.....++...|+++++++.++++++.+ +.+..+|+....++.+.   |..    ++++.+
T Consensus       128 l~~~~kal~~d-pkNy~AW~~R~w~l~~l~~~~eeL~~~~~~I~~d-~~N~sAW~~R~~vl~~~~~l~~~~~~~e~el~y  205 (320)
T PLN02789        128 LEFTRKILSLD-AKNYHAWSHRQWVLRTLGGWEDELEYCHQLLEED-VRNNSAWNQRYFVITRSPLLGGLEAMRDSELKY  205 (320)
T ss_pred             HHHHHHHHHhC-cccHHHHHHHHHHHHHhhhHHHHHHHHHHHHHHC-CCchhHHHHHHHHHHhccccccccccHHHHHHH
Confidence            66666666543 4455666666666666666777777777766655 44555666555554443   222    345666


Q ss_pred             HHhcccCCCCC-CHHHHHHHHHHHHhc----CChhHHHHHHHHHHHcCCCCCHHHHHHHHHHHHHcC-------------
Q 040027          475 FCSLPHGVLVP-NVVTYNIMIQGLCND----GQMDKARDLFLDMEENAAAPDVITFDMLIHGFIRIN-------------  536 (595)
Q Consensus       475 ~~~~~~~~~~p-~~~~~~~l~~~~~~~----g~~~~A~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g-------------  536 (595)
                      ..+++.  ..| |...|+.+...+...    ++..+|.+.+.+..+.+ +.+......|++.|+...             
T Consensus       206 ~~~aI~--~~P~N~SaW~Yl~~ll~~~~~~l~~~~~~~~~~~~~~~~~-~~s~~al~~l~d~~~~~~~~~~~~~~~~~~~  282 (320)
T PLN02789        206 TIDAIL--ANPRNESPWRYLRGLFKDDKEALVSDPEVSSVCLEVLSKD-SNHVFALSDLLDLLCEGLQPTAEFRDTVDTL  282 (320)
T ss_pred             HHHHHH--hCCCCcCHHHHHHHHHhcCCcccccchhHHHHHHHhhccc-CCcHHHHHHHHHHHHhhhccchhhhhhhhcc
Confidence            655555  234 456677666666652    33456777777766643 345566677777776532             


Q ss_pred             -----ChhHHHHHHHHHH
Q 040027          537 -----EPSKVNELLHKMK  549 (595)
Q Consensus       537 -----~~~~A~~~~~~~~  549 (595)
                           ..++|.++++.+.
T Consensus       283 ~~~~~~~~~a~~~~~~l~  300 (320)
T PLN02789        283 AEELSDSTLAQAVCSELE  300 (320)
T ss_pred             ccccccHHHHHHHHHHHH
Confidence                 2356777777774

>KOG3616 consensus Selective LIM binding factor [Transcription]

Probab=98.86  E-value=2.5e-05  Score=76.56  Aligned_cols=316  Identities=17%  Similarity=0.155  Sum_probs=168.4

Q ss_pred             hHHHHHHHHHcCCCchh--HHhhCCCCCCHHHHHHHHHHHHhcCChhHHHHHHHHHHhCCCCCCHHHHHHHHHHHHhcCC
Q 040027           69 SFNILLASLAKNKHYDT--RLNATGLFPNLYTYNILINCFCKIGRVSLGFIAFGRILRSCFTPNAATFNSLIKGLHAESR  146 (595)
Q Consensus        69 ~~~~l~~~~~~~~~~~~--~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~  146 (595)
                      .-++.++++...|....  ++....  .|   -.+.|+.|.+.|.+..|.+....=...  ..|......+..++.+..-
T Consensus       591 lk~sy~q~l~dt~qd~ka~elk~sd--gd---~laaiqlyika~~p~~a~~~a~n~~~l--~~de~il~~ia~alik~el  663 (1636)
T KOG3616|consen  591 LKRSYLQALMDTGQDEKAAELKESD--GD---GLAAIQLYIKAGKPAKAARAALNDEEL--LADEEILEHIAAALIKGEL  663 (1636)
T ss_pred             HHHHHHHHHHhcCchhhhhhhcccc--Cc---cHHHHHHHHHcCCchHHHHhhcCHHHh--hccHHHHHHHHHHHHhhHH
Confidence            45567778888887665  222111  11   235678899999988887665432222  3456666666666666555


Q ss_pred             HhHHHHHHHHHHhc----------------------CCCCCHhhH-HHHHHHHHhcCChhHHHHHHHHHHhcCCCCCccc
Q 040027          147 IMEAAALFTKLKAF----------------------GCEPNVITY-NTLINGLCRTGHTMIALNLFEEMANGNGEIGVVC  203 (595)
Q Consensus       147 ~~~A~~~~~~~~~~----------------------~~~~~~~~~-~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~  203 (595)
                      ++.|-.+|+++...                      .++...... ......+.+.|+++.|+.-|-+..          
T Consensus       664 ydkagdlfeki~d~dkale~fkkgdaf~kaielarfafp~evv~lee~wg~hl~~~~q~daainhfiea~----------  733 (1636)
T KOG3616|consen  664 YDKAGDLFEKIHDFDKALECFKKGDAFGKAIELARFAFPEEVVKLEEAWGDHLEQIGQLDAAINHFIEAN----------  733 (1636)
T ss_pred             HHhhhhHHHHhhCHHHHHHHHHcccHHHHHHHHHHhhCcHHHhhHHHHHhHHHHHHHhHHHHHHHHHHhh----------
Confidence            66666666655431                      001000000 111222233333333333332221          


Q ss_pred             cCcHHHHHHHHHHHHHcCCHhHHHHHHHHHhhCCCCCCHhHHHHHHHHHHhcCCHHHHHHHHHHHHHCCCCCCHhhHHHH
Q 040027          204 KPNTVTYSTIIDGLCKEGFVDKAKALFLQMKDENINPDVVTYNSLIHGLCHANDWNEAKRLFIEMMDQGVQPSVVTFNVI  283 (595)
Q Consensus       204 ~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~~ll~~~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~~l  283 (595)
                           .....+.+......+.+|+.+++.+.....  -..-|..+...|...|+++.|.++|.+.         ..++..
T Consensus       734 -----~~~kaieaai~akew~kai~ildniqdqk~--~s~yy~~iadhyan~~dfe~ae~lf~e~---------~~~~da  797 (1636)
T KOG3616|consen  734 -----CLIKAIEAAIGAKEWKKAISILDNIQDQKT--ASGYYGEIADHYANKGDFEIAEELFTEA---------DLFKDA  797 (1636)
T ss_pred             -----hHHHHHHHHhhhhhhhhhHhHHHHhhhhcc--ccccchHHHHHhccchhHHHHHHHHHhc---------chhHHH
Confidence                 122234445555667777777776665432  2334555666777777777777776442         234555


Q ss_pred             HHHHHhcCChHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHhcCCCCCHHHHHHHHHHHHhCCCH
Q 040027          284 MDELCKNRKMDEASRLLDLMVQRGVRPNACTYNTLMDGFCLMGKINRAEELFGSMESMGCKHDDVSYNILINGYCKNKEV  363 (595)
Q Consensus       284 ~~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~  363 (595)
                      +.+|.+.|++++|.++-.+..  |.......|..-..-.-..|++.+|.++|-.+.    .|+     ..|.+|-+.|..
T Consensus       798 i~my~k~~kw~da~kla~e~~--~~e~t~~~yiakaedldehgkf~eaeqlyiti~----~p~-----~aiqmydk~~~~  866 (1636)
T KOG3616|consen  798 IDMYGKAGKWEDAFKLAEECH--GPEATISLYIAKAEDLDEHGKFAEAEQLYITIG----EPD-----KAIQMYDKHGLD  866 (1636)
T ss_pred             HHHHhccccHHHHHHHHHHhc--CchhHHHHHHHhHHhHHhhcchhhhhheeEEcc----Cch-----HHHHHHHhhCcc
Confidence            667777777777777665543  223344445444555556677777766653332    222     235667777777


Q ss_pred             HHHHHHHHHHHHCCCCCCHHHHHHHHHHHHccCCHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHhcCCHHHHHHHH
Q 040027          364 EEALSLYREMVSKGIKPTVVTYNTLFLGLFEIHQVEHALKLFDEMQRDGVAADTRTYTTFIDGLCKNGYIIEAVELF  440 (595)
Q Consensus       364 ~~A~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~  440 (595)
                      +..+++..+-...   .-..|...+..-+...|+...|...|-+..+         |...+.+|...+-+++|.++-
T Consensus       867 ddmirlv~k~h~d---~l~dt~~~f~~e~e~~g~lkaae~~flea~d---------~kaavnmyk~s~lw~dayria  931 (1636)
T KOG3616|consen  867 DDMIRLVEKHHGD---HLHDTHKHFAKELEAEGDLKAAEEHFLEAGD---------FKAAVNMYKASELWEDAYRIA  931 (1636)
T ss_pred             hHHHHHHHHhChh---hhhHHHHHHHHHHHhccChhHHHHHHHhhhh---------HHHHHHHhhhhhhHHHHHHHH
Confidence            7766666553321   1234455556666667777777666544322         334444555555555555443

>COG5010 TadD Flp pilus assembly protein TadD, contains TPR repeats [Intracellular trafficking and secretion]

Probab=98.86  E-value=3.7e-07  Score=78.28  Aligned_cols=178  Identities=14%  Similarity=0.030  Sum_probs=116.3

Q ss_pred             CChHHHHHHHHHHHHhCCCCCCHhhHHHHHHHHHcCCCchh---HHh--hCCCCCCHHHHHHHHHHHHhcCChhHHHHHH
Q 040027           45 ITPNEAFCIFDYMLRMHPSPPPVSSFNILLASLAKNKHYDT---RLN--ATGLFPNLYTYNILINCFCKIGRVSLGFIAF  119 (595)
Q Consensus        45 ~~~~~A~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~---~~~--~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~  119 (595)
                      .+...+...+-+....+|.  +... ..+...+.-.|+.+.   .+.  ....+.|.......+....+.|++..|+..+
T Consensus        47 ~q~~~a~~al~~~~~~~p~--d~~i-~~~a~a~~~~G~a~~~l~~~~~~~~~~~~d~~ll~~~gk~~~~~g~~~~A~~~~  123 (257)
T COG5010          47 RQTQGAAAALGAAVLRNPE--DLSI-AKLATALYLRGDADSSLAVLQKSAIAYPKDRELLAAQGKNQIRNGNFGEAVSVL  123 (257)
T ss_pred             HhhhHHHHHHHHHHhcCcc--hHHH-HHHHHHHHhcccccchHHHHhhhhccCcccHHHHHHHHHHHHHhcchHHHHHHH
Confidence            3344466666666666676  4444 555666666666555   111  1223345556666777777777777777777


Q ss_pred             HHHHhCCCCCCHHHHHHHHHHHHhcCCHhHHHHHHHHHHhcCCCCCHhhHHHHHHHHHhcCChhHHHHHHHHHHhcCCCC
Q 040027          120 GRILRSCFTPNAATFNSLIKGLHAESRIMEAAALFTKLKAFGCEPNVITYNTLINGLCRTGHTMIALNLFEEMANGNGEI  199 (595)
Q Consensus       120 ~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~  199 (595)
                      +++.... ++|...|+.+..+|.+.|++++|...|.+..+.. .-++...+.+.-.+.-.|+.+.|..++.......   
T Consensus       124 rkA~~l~-p~d~~~~~~lgaaldq~Gr~~~Ar~ay~qAl~L~-~~~p~~~nNlgms~~L~gd~~~A~~lll~a~l~~---  198 (257)
T COG5010         124 RKAARLA-PTDWEAWNLLGAALDQLGRFDEARRAYRQALELA-PNEPSIANNLGMSLLLRGDLEDAETLLLPAYLSP---  198 (257)
T ss_pred             HHHhccC-CCChhhhhHHHHHHHHccChhHHHHHHHHHHHhc-cCCchhhhhHHHHHHHcCCHHHHHHHHHHHHhCC---
Confidence            7777664 6677777777777777777777777777777663 3356666777777777777777777777776654   


Q ss_pred             CccccCcHHHHHHHHHHHHHcCCHhHHHHHHHHHh
Q 040027          200 GVVCKPNTVTYSTIIDGLCKEGFVDKAKALFLQMK  234 (595)
Q Consensus       200 ~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~  234 (595)
                          +.+...-..+.......|+++.|..+...-.
T Consensus       199 ----~ad~~v~~NLAl~~~~~g~~~~A~~i~~~e~  229 (257)
T COG5010         199 ----AADSRVRQNLALVVGLQGDFREAEDIAVQEL  229 (257)
T ss_pred             ----CCchHHHHHHHHHHhhcCChHHHHhhccccc
Confidence                3356666677777777777777776665443

>PRK10370 formate-dependent nitrite reductase complex subunit NrfG; Provisional

Probab=98.83  E-value=8.2e-07  Score=76.75  Aligned_cols=123  Identities=13%  Similarity=0.079  Sum_probs=83.5

Q ss_pred             cCCHHHHHHHHHHHHHcCCCcCHHHHHHHHHHHHhcCChHHHHHHHHhcccCCCCC-CHHHHHHHHHHH-HhcCC--hhH
Q 040027          430 NGYIIEAVELFRTLRILKCELDIQAYNCLIDGLCKSGRLKFAWELFCSLPHGVLVP-NVVTYNIMIQGL-CNDGQ--MDK  505 (595)
Q Consensus       430 ~g~~~~A~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~p-~~~~~~~l~~~~-~~~g~--~~~  505 (595)
                      .++.+++...+++.++.+ +.+...|..++..|...|++++|...|++...  +.| +...+..+..++ ...|+  .++
T Consensus        52 ~~~~~~~i~~l~~~L~~~-P~~~~~w~~Lg~~~~~~g~~~~A~~a~~~Al~--l~P~~~~~~~~lA~aL~~~~g~~~~~~  128 (198)
T PRK10370         52 QQTPEAQLQALQDKIRAN-PQNSEQWALLGEYYLWRNDYDNALLAYRQALQ--LRGENAELYAALATVLYYQAGQHMTPQ  128 (198)
T ss_pred             chhHHHHHHHHHHHHHHC-CCCHHHHHHHHHHHHHCCCHHHHHHHHHHHHH--hCCCCHHHHHHHHHHHHHhcCCCCcHH
Confidence            455666666677666655 66777777777777777777777777777776  344 456666666653 55565  477


Q ss_pred             HHHHHHHHHHcCCCCCHHHHHHHHHHHHHcCChhHHHHHHHHHHHCCCCCCH
Q 040027          506 ARDLFLDMEENAAAPDVITFDMLIHGFIRINEPSKVNELLHKMKEKKVMPDA  557 (595)
Q Consensus       506 A~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~p~~  557 (595)
                      |.++++++++.+ +.+...+..++..+...|++++|...|+++++.. +|+.
T Consensus       129 A~~~l~~al~~d-P~~~~al~~LA~~~~~~g~~~~Ai~~~~~aL~l~-~~~~  178 (198)
T PRK10370        129 TREMIDKALALD-ANEVTALMLLASDAFMQADYAQAIELWQKVLDLN-SPRV  178 (198)
T ss_pred             HHHHHHHHHHhC-CCChhHHHHHHHHHHHcCCHHHHHHHHHHHHhhC-CCCc
Confidence            777777777764 4456677777777777777777777777777643 3443

>KOG3060 consensus Uncharacterized conserved protein [Function unknown]

Probab=98.83  E-value=3.4e-06  Score=71.76  Aligned_cols=187  Identities=13%  Similarity=0.127  Sum_probs=107.5

Q ss_pred             CCHHHHHHHHHHHHHC---C-CCCCHH-HHHHHHHHHHccCCHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHhcCCHHH
Q 040027          361 KEVEEALSLYREMVSK---G-IKPTVV-TYNTLFLGLFEIHQVEHALKLFDEMQRDGVAADTRTYTTFIDGLCKNGYIIE  435 (595)
Q Consensus       361 ~~~~~A~~~~~~~~~~---~-~~~~~~-~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~  435 (595)
                      .+.++.++++..+...   | ..++.. .+..++-+....|+.+.|..+++.+... ++.+..+...-...+-..|++++
T Consensus        26 rnseevv~l~~~~~~~~k~~~~g~e~w~l~EqV~IAAld~~~~~lAq~C~~~L~~~-fp~S~RV~~lkam~lEa~~~~~~  104 (289)
T KOG3060|consen   26 RNSEEVVQLGSEVLNYSKSGALGDEIWTLYEQVFIAALDTGRDDLAQKCINQLRDR-FPGSKRVGKLKAMLLEATGNYKE  104 (289)
T ss_pred             cCHHHHHHHHHHHHHHhhhcccCchHHHHHHHHHHHHHHhcchHHHHHHHHHHHHh-CCCChhHHHHHHHHHHHhhchhh
Confidence            3455555555555432   2 222322 3344445555666666666666666655 34344333333333445666777


Q ss_pred             HHHHHHHHHHcCCCcCHHHHHHHHHHHHhcCChHHHHHHHHhcccCCCCCCHHHHHHHHHHHHhcCChhHHHHHHHHHHH
Q 040027          436 AVELFRTLRILKCELDIQAYNCLIDGLCKSGRLKFAWELFCSLPHGVLVPNVVTYNIMIQGLCNDGQMDKARDLFLDMEE  515 (595)
Q Consensus       436 A~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~p~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~  515 (595)
                      |.++++.+++.+ |.|..++..=+...-..|+.-+|++-+....+. +.-|...|..+...|...|++++|.-.+++++-
T Consensus       105 A~e~y~~lL~dd-pt~~v~~KRKlAilka~GK~l~aIk~ln~YL~~-F~~D~EAW~eLaeiY~~~~~f~kA~fClEE~ll  182 (289)
T KOG3060|consen  105 AIEYYESLLEDD-PTDTVIRKRKLAILKAQGKNLEAIKELNEYLDK-FMNDQEAWHELAEIYLSEGDFEKAAFCLEELLL  182 (289)
T ss_pred             HHHHHHHHhccC-cchhHHHHHHHHHHHHcCCcHHHHHHHHHHHHH-hcCcHHHHHHHHHHHHhHhHHHHHHHHHHHHHH
Confidence            777777666655 555566655555555666666666666666554 344666777777777777777777777777666


Q ss_pred             cCCCCCHHHHHHHHHHHHHcC---ChhHHHHHHHHHHHC
Q 040027          516 NAAAPDVITFDMLIHGFIRIN---EPSKVNELLHKMKEK  551 (595)
Q Consensus       516 ~~~~~~~~~~~~l~~~~~~~g---~~~~A~~~~~~~~~~  551 (595)
                      .. |-++..|..+...+.-.|   +++-+.++|.+.++.
T Consensus       183 ~~-P~n~l~f~rlae~~Yt~gg~eN~~~arkyy~~alkl  220 (289)
T KOG3060|consen  183 IQ-PFNPLYFQRLAEVLYTQGGAENLELARKYYERALKL  220 (289)
T ss_pred             cC-CCcHHHHHHHHHHHHHHhhHHHHHHHHHHHHHHHHh
Confidence            43 445555566666655544   445666666666653

>KOG1070 consensus rRNA processing protein Rrp5 [RNA processing and modification]

Probab=98.83  E-value=3.6e-06  Score=87.97  Aligned_cols=198  Identities=16%  Similarity=0.122  Sum_probs=83.0

Q ss_pred             hHHHHHHHHHhcCChHHHHHHHHHHHHC-CCCC---CHHHHHHHHHHHHhcCCHHHHHHHHHHHHhcCCCCCHHHHHHHH
Q 040027          279 TFNVIMDELCKNRKMDEASRLLDLMVQR-GVRP---NACTYNTLMDGFCLMGKINRAEELFGSMESMGCKHDDVSYNILI  354 (595)
Q Consensus       279 ~~~~l~~~~~~~g~~~~a~~~~~~~~~~-~~~~---~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~  354 (595)
                      .|-..|......++.+.|.++.++++.. ++.-   -...|.++++.-...|.-+...++|+++.+..  .....|..|.
T Consensus      1460 ~WI~YMaf~LelsEiekAR~iaerAL~tIN~REeeEKLNiWiA~lNlEn~yG~eesl~kVFeRAcqyc--d~~~V~~~L~ 1537 (1710)
T KOG1070|consen 1460 LWIRYMAFHLELSEIEKARKIAERALKTINFREEEEKLNIWIAYLNLENAYGTEESLKKVFERACQYC--DAYTVHLKLL 1537 (1710)
T ss_pred             HHHHHHHHHhhhhhhHHHHHHHHHHhhhCCcchhHHHHHHHHHHHhHHHhhCcHHHHHHHHHHHHHhc--chHHHHHHHH
Confidence            4444444455555555555555554432 1100   11233344444334444444444555444431  1223444444


Q ss_pred             HHHHhCCCHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHccCCHHHHHHHHHHHHHCCCCC--CHHHHHHHHHHHHhcCC
Q 040027          355 NGYCKNKEVEEALSLYREMVSKGIKPTVVTYNTLFLGLFEIHQVEHALKLFDEMQRDGVAA--DTRTYTTFIDGLCKNGY  432 (595)
Q Consensus       355 ~~~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~--~~~~~~~l~~~~~~~g~  432 (595)
                      ..|.+.+.+++|.++++.|.+.- .-....|...+..+.+..+-+.|..++.++++. .+.  ........+..-.+.|+
T Consensus      1538 ~iy~k~ek~~~A~ell~~m~KKF-~q~~~vW~~y~~fLl~~ne~~aa~~lL~rAL~~-lPk~eHv~~IskfAqLEFk~GD 1615 (1710)
T KOG1070|consen 1538 GIYEKSEKNDEADELLRLMLKKF-GQTRKVWIMYADFLLRQNEAEAARELLKRALKS-LPKQEHVEFISKFAQLEFKYGD 1615 (1710)
T ss_pred             HHHHHhhcchhHHHHHHHHHHHh-cchhhHHHHHHHHHhcccHHHHHHHHHHHHHhh-cchhhhHHHHHHHHHHHhhcCC
Confidence            44555555555555555544431 123344444444444444444444444444432 111  11222233333334444


Q ss_pred             HHHHHHHHHHHHHcCCCcCHHHHHHHHHHHHhcCChHHHHHHHHhcccC
Q 040027          433 IIEAVELFRTLRILKCELDIQAYNCLIDGLCKSGRLKFAWELFCSLPHG  481 (595)
Q Consensus       433 ~~~A~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~  481 (595)
                      .+.+..+|+..+... |.....|+.+++.-.++|+.+.++.+|+++...
T Consensus      1616 aeRGRtlfEgll~ay-PKRtDlW~VYid~eik~~~~~~vR~lfeRvi~l 1663 (1710)
T KOG1070|consen 1616 AERGRTLFEGLLSAY-PKRTDLWSVYIDMEIKHGDIKYVRDLFERVIEL 1663 (1710)
T ss_pred             chhhHHHHHHHHhhC-ccchhHHHHHHHHHHccCCHHHHHHHHHHHHhc
Confidence            444444444444332 333344444444444444444444444444443

>COG5010 TadD Flp pilus assembly protein TadD, contains TPR repeats [Intracellular trafficking and secretion]

Probab=98.82  E-value=1.2e-06  Score=75.21  Aligned_cols=159  Identities=19%  Similarity=0.156  Sum_probs=107.9

Q ss_pred             HHHHHHHHccCCHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCcCHHHHHHHHHHHHhc
Q 040027          386 NTLFLGLFEIHQVEHALKLFDEMQRDGVAADTRTYTTFIDGLCKNGYIIEAVELFRTLRILKCELDIQAYNCLIDGLCKS  465 (595)
Q Consensus       386 ~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~~l~~~~~~~  465 (595)
                      ..+...+...|+-+....+....... .+.+.......+....+.|++..|...++++.... ++|...|+.+.-+|.+.
T Consensus        70 ~~~a~a~~~~G~a~~~l~~~~~~~~~-~~~d~~ll~~~gk~~~~~g~~~~A~~~~rkA~~l~-p~d~~~~~~lgaaldq~  147 (257)
T COG5010          70 AKLATALYLRGDADSSLAVLQKSAIA-YPKDRELLAAQGKNQIRNGNFGEAVSVLRKAARLA-PTDWEAWNLLGAALDQL  147 (257)
T ss_pred             HHHHHHHHhcccccchHHHHhhhhcc-CcccHHHHHHHHHHHHHhcchHHHHHHHHHHhccC-CCChhhhhHHHHHHHHc
Confidence            44555566666666666665554432 24455556666777777777777777777777665 67777777777777777


Q ss_pred             CChHHHHHHHHhcccCCCCCC-HHHHHHHHHHHHhcCChhHHHHHHHHHHHcCCCCCHHHHHHHHHHHHHcCChhHHHHH
Q 040027          466 GRLKFAWELFCSLPHGVLVPN-VVTYNIMIQGLCNDGQMDKARDLFLDMEENAAAPDVITFDMLIHGFIRINEPSKVNEL  544 (595)
Q Consensus       466 g~~~~A~~~~~~~~~~~~~p~-~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~  544 (595)
                      |+++.|..-|.+..+  +.|+ +..++.+...+.-.|+++.|..++......+ .-|..+-..+..+....|++++|.++
T Consensus       148 Gr~~~Ar~ay~qAl~--L~~~~p~~~nNlgms~~L~gd~~~A~~lll~a~l~~-~ad~~v~~NLAl~~~~~g~~~~A~~i  224 (257)
T COG5010         148 GRFDEARRAYRQALE--LAPNEPSIANNLGMSLLLRGDLEDAETLLLPAYLSP-AADSRVRQNLALVVGLQGDFREAEDI  224 (257)
T ss_pred             cChhHHHHHHHHHHH--hccCCchhhhhHHHHHHHcCCHHHHHHHHHHHHhCC-CCchHHHHHHHHHHhhcCChHHHHhh
Confidence            777777777777776  4443 5666777777777777777777777777654 33555666677777777777777776


Q ss_pred             HHHHH
Q 040027          545 LHKMK  549 (595)
Q Consensus       545 ~~~~~  549 (595)
                      ...-.
T Consensus       225 ~~~e~  229 (257)
T COG5010         225 AVQEL  229 (257)
T ss_pred             ccccc
Confidence            55544

>KOG2053 consensus Mitochondrial inheritance and actin cytoskeleton organization protein [Cytoskeleton]

Probab=98.82  E-value=0.00024  Score=71.76  Aligned_cols=122  Identities=15%  Similarity=0.034  Sum_probs=82.1

Q ss_pred             HHHHHHHHHhcCChH---HHHHHHHhcccCCCCCCHHHHHHHHHHHHhcCChhHHHHHHHHHHHcCCCCCHHHHHHHHHH
Q 040027          455 YNCLIDGLCKSGRLK---FAWELFCSLPHGVLVPNVVTYNIMIQGLCNDGQMDKARDLFLDMEENAAAPDVITFDMLIHG  531 (595)
Q Consensus       455 ~~~l~~~~~~~g~~~---~A~~~~~~~~~~~~~p~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~~l~~~  531 (595)
                      .+.+++.+.+.++..   +|+-+++.-... -+-|..+-..+++.|.-.|-+..|.++|..+--+++.-|...|. +...
T Consensus       439 v~~Lid~~rktnd~~~l~eaI~LLE~glt~-s~hnf~~KLlLiriY~~lGa~p~a~~~y~tLdIK~IQ~DTlgh~-~~~~  516 (932)
T KOG2053|consen  439 VNHLIDLWRKTNDLTDLFEAITLLENGLTK-SPHNFQTKLLLIRIYSYLGAFPDAYELYKTLDIKNIQTDTLGHL-IFRR  516 (932)
T ss_pred             HHHHHHHHHhcCcHHHHHHHHHHHHHHhhc-CCccHHHHHHHHHHHHHhcCChhHHHHHHhcchHHhhhccchHH-HHHH
Confidence            456778888888865   455555555542 12245556678899999999999999999987666666654443 3455


Q ss_pred             HHHcCChhHHHHHHHHHHHCCCCCCHHHHHHHHHHHHhcCcccccchH
Q 040027          532 FIRINEPSKVNELLHKMKEKKVMPDASIVSIVVDLLVKNEISLKSLPS  579 (595)
Q Consensus       532 ~~~~g~~~~A~~~~~~~~~~~~~p~~~~~~~l~~~~~~~g~~~~~i~~  579 (595)
                      +...|++..+...+...... +..+-.-..-++..-.+.|.++++.+-
T Consensus       517 ~~t~g~~~~~s~~~~~~lkf-y~~~~kE~~eyI~~AYr~g~ySkI~em  563 (932)
T KOG2053|consen  517 AETSGRSSFASNTFNEHLKF-YDSSLKETPEYIALAYRRGAYSKIPEM  563 (932)
T ss_pred             HHhcccchhHHHHHHHHHHH-HhhhhhhhHHHHHHHHHcCchhhhHHH
Confidence            66788999999888888763 223333344455556677888854443

>TIGR03302 OM_YfiO outer membrane assembly lipoprotein YfiO

Probab=98.81  E-value=2.3e-06  Score=77.43  Aligned_cols=187  Identities=8%  Similarity=-0.085  Sum_probs=133.7

Q ss_pred             CCCHHHHHHHHHHHHhcCChhHHHHHHHHHHhCCCCCCH---HHHHHHHHHHHhcCCHhHHHHHHHHHHhcCCCCCHh--
Q 040027           93 FPNLYTYNILINCFCKIGRVSLGFIAFGRILRSCFTPNA---ATFNSLIKGLHAESRIMEAAALFTKLKAFGCEPNVI--  167 (595)
Q Consensus        93 ~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~~~---~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~~~~--  167 (595)
                      ...+..+..++..+...|+++.|...|+++.... +.+.   .++..+..++.+.|++++|+..++++.+.... +..  
T Consensus        30 ~~~~~~~~~~g~~~~~~~~~~~A~~~~~~~~~~~-p~~~~~~~a~~~la~~~~~~~~~~~A~~~~~~~l~~~p~-~~~~~  107 (235)
T TIGR03302        30 EWPAEELYEEAKEALDSGDYTEAIKYFEALESRY-PFSPYAEQAQLDLAYAYYKSGDYAEAIAAADRFIRLHPN-HPDAD  107 (235)
T ss_pred             cCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhC-CCchhHHHHHHHHHHHHHhcCCHHHHHHHHHHHHHHCcC-CCchH
Confidence            4577888889999999999999999999998874 2222   46778889999999999999999999987432 222  


Q ss_pred             -hHHHHHHHHHhc--------CChhHHHHHHHHHHhcCCCCCccccCcHHHHHHHHHHHHHcCCHhHHHHHHHHHhhCCC
Q 040027          168 -TYNTLINGLCRT--------GHTMIALNLFEEMANGNGEIGVVCKPNTVTYSTIIDGLCKEGFVDKAKALFLQMKDENI  238 (595)
Q Consensus       168 -~~~~l~~~~~~~--------g~~~~A~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~  238 (595)
                       ++..+..++...        |++++|.+.|+++....       |.+...+..+......    ..      ..     
T Consensus       108 ~a~~~~g~~~~~~~~~~~~~~~~~~~A~~~~~~~~~~~-------p~~~~~~~a~~~~~~~----~~------~~-----  165 (235)
T TIGR03302       108 YAYYLRGLSNYNQIDRVDRDQTAAREAFEAFQELIRRY-------PNSEYAPDAKKRMDYL----RN------RL-----  165 (235)
T ss_pred             HHHHHHHHHHHHhcccccCCHHHHHHHHHHHHHHHHHC-------CCChhHHHHHHHHHHH----HH------HH-----
Confidence             456666666654        78899999999998865       3333333222211110    00      00     


Q ss_pred             CCCHhHHHHHHHHHHhcCCHHHHHHHHHHHHHCCC--CCCHhhHHHHHHHHHhcCChHHHHHHHHHHHHC
Q 040027          239 NPDVVTYNSLIHGLCHANDWNEAKRLFIEMMDQGV--QPSVVTFNVIMDELCKNRKMDEASRLLDLMVQR  306 (595)
Q Consensus       239 ~~~~~~~~~ll~~~~~~~~~~~A~~~~~~~~~~~~--~~~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~  306 (595)
                         ......+...+.+.|++++|...+...++...  +.....+..+..++...|++++|..+++.+...
T Consensus       166 ---~~~~~~~a~~~~~~g~~~~A~~~~~~al~~~p~~~~~~~a~~~l~~~~~~lg~~~~A~~~~~~l~~~  232 (235)
T TIGR03302       166 ---AGKELYVARFYLKRGAYVAAINRFETVVENYPDTPATEEALARLVEAYLKLGLKDLAQDAAAVLGAN  232 (235)
T ss_pred             ---HHHHHHHHHHHHHcCChHHHHHHHHHHHHHCCCCcchHHHHHHHHHHHHHcCCHHHHHHHHHHHHhh
Confidence               01122456678888999999999988887521  123467788888999999999999988887765

Members of this protein family include YfiO, a near-essential protein of the outer membrane, part of a complex involved in protein insertion into the bacterial outer membrane. Many proteins in this family are annotated as ComL, based on the involvement of this protein in natural transformation with exogenous DNA in Neisseria gonorrhoeae. This protein family shows sequence similarity to, but is distinct from, the tol-pal system protein YbgF (TIGR02795).

>KOG1128 consensus Uncharacterized conserved protein, contains TPR repeats [General function prediction only]

Probab=98.81  E-value=4.7e-07  Score=88.30  Aligned_cols=216  Identities=13%  Similarity=0.091  Sum_probs=179.6

Q ss_pred             HHHHHHHHHhcCChHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHhcCCCCCHHHHHHHHHHHHh
Q 040027          280 FNVIMDELCKNRKMDEASRLLDLMVQRGVRPNACTYNTLMDGFCLMGKINRAEELFGSMESMGCKHDDVSYNILINGYCK  359 (595)
Q Consensus       280 ~~~l~~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~  359 (595)
                      -..+...+...|-...|..+++++.         .+...+.+|...|+..+|..+..+..+.  +|++..|..+......
T Consensus       401 q~~laell~slGitksAl~I~Erle---------mw~~vi~CY~~lg~~~kaeei~~q~lek--~~d~~lyc~LGDv~~d  469 (777)
T KOG1128|consen  401 QRLLAELLLSLGITKSALVIFERLE---------MWDPVILCYLLLGQHGKAEEINRQELEK--DPDPRLYCLLGDVLHD  469 (777)
T ss_pred             HHHHHHHHHHcchHHHHHHHHHhHH---------HHHHHHHHHHHhcccchHHHHHHHHhcC--CCcchhHHHhhhhccC
Confidence            3456778889999999999998764         4566788999999999999999988875  7899999999888877


Q ss_pred             CCCHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHccCCHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHhcCCHHHHHHH
Q 040027          360 NKEVEEALSLYREMVSKGIKPTVVTYNTLFLGLFEIHQVEHALKLFDEMQRDGVAADTRTYTTFIDGLCKNGYIIEAVEL  439 (595)
Q Consensus       360 ~~~~~~A~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~  439 (595)
                      ..-+++|.++.+.....       .-..+.....+.++++++.+.|+.-.+.+ +....+|....-+..+.++++.|.+.
T Consensus       470 ~s~yEkawElsn~~sar-------A~r~~~~~~~~~~~fs~~~~hle~sl~~n-plq~~~wf~~G~~ALqlek~q~av~a  541 (777)
T KOG1128|consen  470 PSLYEKAWELSNYISAR-------AQRSLALLILSNKDFSEADKHLERSLEIN-PLQLGTWFGLGCAALQLEKEQAAVKA  541 (777)
T ss_pred             hHHHHHHHHHhhhhhHH-------HHHhhccccccchhHHHHHHHHHHHhhcC-ccchhHHHhccHHHHHHhhhHHHHHH
Confidence            77789999888765332       22233333455789999999999888764 56778888888889999999999999


Q ss_pred             HHHHHHcCCCcCHHHHHHHHHHHHhcCChHHHHHHHHhcccCCCCCCHHHHHHHHHHHHhcCChhHHHHHHHHHHHc
Q 040027          440 FRTLRILKCELDIQAYNCLIDGLCKSGRLKFAWELFCSLPHGVLVPNVVTYNIMIQGLCNDGQMDKARDLFLDMEEN  516 (595)
Q Consensus       440 ~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~p~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~  516 (595)
                      |....... +.+...||++-.+|.+.++-.+|...+.++.+.+ .-+...|.+.+....+.|.+++|++.+.++.+.
T Consensus       542 F~rcvtL~-Pd~~eaWnNls~ayi~~~~k~ra~~~l~EAlKcn-~~~w~iWENymlvsvdvge~eda~~A~~rll~~  616 (777)
T KOG1128|consen  542 FHRCVTLE-PDNAEAWNNLSTAYIRLKKKKRAFRKLKEALKCN-YQHWQIWENYMLVSVDVGEFEDAIKAYHRLLDL  616 (777)
T ss_pred             HHHHhhcC-CCchhhhhhhhHHHHHHhhhHHHHHHHHHHhhcC-CCCCeeeechhhhhhhcccHHHHHHHHHHHHHh
Confidence            99998875 6678899999999999999999999999999876 446678888888899999999999999998763

>TIGR03302 OM_YfiO outer membrane assembly lipoprotein YfiO

Probab=98.73  E-value=2.2e-06  Score=77.45  Aligned_cols=187  Identities=10%  Similarity=-0.019  Sum_probs=134.9

Q ss_pred             CCCHHHHHHHHHHHHhcCCHhHHHHHHHHHHhcCCCCC---HhhHHHHHHHHHhcCChhHHHHHHHHHHhcCCCCCcccc
Q 040027          128 TPNAATFNSLIKGLHAESRIMEAAALFTKLKAFGCEPN---VITYNTLINGLCRTGHTMIALNLFEEMANGNGEIGVVCK  204 (595)
Q Consensus       128 ~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~~---~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~  204 (595)
                      +.....+..+...+...|++++|...|+++...... +   ..++..+..++...|++++|+..++++.+..       |
T Consensus        30 ~~~~~~~~~~g~~~~~~~~~~~A~~~~~~~~~~~p~-~~~~~~a~~~la~~~~~~~~~~~A~~~~~~~l~~~-------p  101 (235)
T TIGR03302        30 EWPAEELYEEAKEALDSGDYTEAIKYFEALESRYPF-SPYAEQAQLDLAYAYYKSGDYAEAIAAADRFIRLH-------P  101 (235)
T ss_pred             cCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCCC-chhHHHHHHHHHHHHHhcCCHHHHHHHHHHHHHHC-------c
Confidence            345667888888999999999999999999886322 2   2467888999999999999999999999865       2


Q ss_pred             CcH---HHHHHHHHHHHHc--------CCHhHHHHHHHHHhhCCCCCCHhHHHHHHHHHHhcCCHHHHHHHHHHHHHCCC
Q 040027          205 PNT---VTYSTIIDGLCKE--------GFVDKAKALFLQMKDENINPDVVTYNSLIHGLCHANDWNEAKRLFIEMMDQGV  273 (595)
Q Consensus       205 ~~~---~~~~~l~~~~~~~--------g~~~~A~~~~~~~~~~~~~~~~~~~~~ll~~~~~~~~~~~A~~~~~~~~~~~~  273 (595)
                      .+.   .++..+..++...        |+.++|.+.|+.+...... +...+..+.....    ...      ..     
T Consensus       102 ~~~~~~~a~~~~g~~~~~~~~~~~~~~~~~~~A~~~~~~~~~~~p~-~~~~~~a~~~~~~----~~~------~~-----  165 (235)
T TIGR03302       102 NHPDADYAYYLRGLSNYNQIDRVDRDQTAAREAFEAFQELIRRYPN-SEYAPDAKKRMDY----LRN------RL-----  165 (235)
T ss_pred             CCCchHHHHHHHHHHHHHhcccccCCHHHHHHHHHHHHHHHHHCCC-ChhHHHHHHHHHH----HHH------HH-----
Confidence            222   2466666666654        7788999999998876321 2223322221111    000      00     


Q ss_pred             CCCHhhHHHHHHHHHhcCChHHHHHHHHHHHHCCC--CCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHhc
Q 040027          274 QPSVVTFNVIMDELCKNRKMDEASRLLDLMVQRGV--RPNACTYNTLMDGFCLMGKINRAEELFGSMESM  341 (595)
Q Consensus       274 ~~~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~~--~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~  341 (595)
                         ......+...+.+.|++.+|...++.+.+...  +.....+..++.++...|++++|..+++.+...
T Consensus       166 ---~~~~~~~a~~~~~~g~~~~A~~~~~~al~~~p~~~~~~~a~~~l~~~~~~lg~~~~A~~~~~~l~~~  232 (235)
T TIGR03302       166 ---AGKELYVARFYLKRGAYVAAINRFETVVENYPDTPATEEALARLVEAYLKLGLKDLAQDAAAVLGAN  232 (235)
T ss_pred             ---HHHHHHHHHHHHHcCChHHHHHHHHHHHHHCCCCcchHHHHHHHHHHHHHcCCHHHHHHHHHHHHhh
Confidence               01122566778999999999999999988632  224568889999999999999999999988765

Members of this protein family include YfiO, a near-essential protein of the outer membrane, part of a complex involved in protein insertion into the bacterial outer membrane. Many proteins in this family are annotated as ComL, based on the involvement of this protein in natural transformation with exogenous DNA in Neisseria gonorrhoeae. This protein family shows sequence similarity to, but is distinct from, the tol-pal system protein YbgF (TIGR02795).

>PRK14720 transcript cleavage factor/unknown domain fusion protein; Provisional

Probab=98.73  E-value=7.9e-06  Score=84.75  Aligned_cols=220  Identities=9%  Similarity=0.069  Sum_probs=124.0

Q ss_pred             CCHHHHHHHHHHHHhcCChhHHHHHHHHHHhCCCCCCHHHHHHHHHHHHhcCCHhHHHHHHHHHHhcCCCC---------
Q 040027           94 PNLYTYNILINCFCKIGRVSLGFIAFGRILRSCFTPNAATFNSLIKGLHAESRIMEAAALFTKLKAFGCEP---------  164 (595)
Q Consensus        94 ~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~---------  164 (595)
                      .+...|..|+..+...|++++|..+.+...+.. +.....|-.+...+.+.++.+.+.-+  .+... +..         
T Consensus        29 ~n~~a~~~Li~~~~~~~~~deai~i~~~~l~~~-P~~i~~yy~~G~l~~q~~~~~~~~lv--~~l~~-~~~~~~~~~ve~  104 (906)
T PRK14720         29 SKFKELDDLIDAYKSENLTDEAKDICEEHLKEH-KKSISALYISGILSLSRRPLNDSNLL--NLIDS-FSQNLKWAIVEH  104 (906)
T ss_pred             chHHHHHHHHHHHHhcCCHHHHHHHHHHHHHhC-CcceehHHHHHHHHHhhcchhhhhhh--hhhhh-cccccchhHHHH
Confidence            467788888888888899999999988777763 22333343343456666666655544  22221 011         


Q ss_pred             ----------CHhhHHHHHHHHHhcCChhHHHHHHHHHHhcCCCCCccccCcHHHHHHHHHHHHHcCCHhHHHHHHHHHh
Q 040027          165 ----------NVITYNTLINGLCRTGHTMIALNLFEEMANGNGEIGVVCKPNTVTYSTIIDGLCKEGFVDKAKALFLQMK  234 (595)
Q Consensus       165 ----------~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~  234 (595)
                                +..++..++.+|-+.|+.++|..+++++.+.+       +.|+.+.|.+...|... ++++|.+++.+.+
T Consensus       105 ~~~~i~~~~~~k~Al~~LA~~Ydk~g~~~ka~~~yer~L~~D-------~~n~~aLNn~AY~~ae~-dL~KA~~m~~KAV  176 (906)
T PRK14720        105 ICDKILLYGENKLALRTLAEAYAKLNENKKLKGVWERLVKAD-------RDNPEIVKKLATSYEEE-DKEKAITYLKKAI  176 (906)
T ss_pred             HHHHHHhhhhhhHHHHHHHHHHHHcCChHHHHHHHHHHHhcC-------cccHHHHHHHHHHHHHh-hHHHHHHHHHHHH
Confidence                      12344555555555566666666666666554       34555556665555555 5666665555554


Q ss_pred             hCCCCCCHhHHHHHHHHHHhcCCHHHHHHHHHHHHHCCCCCCHhhHHHHHHHHHhcCChHHHHHHHHHHHHC-CCCCCHH
Q 040027          235 DENINPDVVTYNSLIHGLCHANDWNEAKRLFIEMMDQGVQPSVVTFNVIMDELCKNRKMDEASRLLDLMVQR-GVRPNAC  313 (595)
Q Consensus       235 ~~~~~~~~~~~~~ll~~~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~-~~~~~~~  313 (595)
                      ..               +...+++..+.++|.++.....                 .+++.-..+.+.+... |..--..
T Consensus       177 ~~---------------~i~~kq~~~~~e~W~k~~~~~~-----------------~d~d~f~~i~~ki~~~~~~~~~~~  224 (906)
T PRK14720        177 YR---------------FIKKKQYVGIEEIWSKLVHYNS-----------------DDFDFFLRIERKVLGHREFTRLVG  224 (906)
T ss_pred             HH---------------HHhhhcchHHHHHHHHHHhcCc-----------------ccchHHHHHHHHHHhhhccchhHH
Confidence            42               3444455555555555544311                 1122222223333222 2222334


Q ss_pred             HHHHHHHHHHhcCCHHHHHHHHHHHHhcCCCCCHHHHHHHHHHHH
Q 040027          314 TYNTLMDGFCLMGKINRAEELFGSMESMGCKHDDVSYNILINGYC  358 (595)
Q Consensus       314 ~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~  358 (595)
                      ++..+-..|...++++++..+++.+.+.. +.|..+...++.+|.
T Consensus       225 ~~~~l~~~y~~~~~~~~~i~iLK~iL~~~-~~n~~a~~~l~~~y~  268 (906)
T PRK14720        225 LLEDLYEPYKALEDWDEVIYILKKILEHD-NKNNKAREELIRFYK  268 (906)
T ss_pred             HHHHHHHHHhhhhhhhHHHHHHHHHHhcC-CcchhhHHHHHHHHH
Confidence            45555566777778888888888888775 445566777777765

>PRK10370 formate-dependent nitrite reductase complex subunit NrfG; Provisional

Probab=98.73  E-value=1e-06  Score=76.14  Aligned_cols=100  Identities=15%  Similarity=0.171  Sum_probs=84.8

Q ss_pred             CHHHHHHHHHHHHhcCChhHHHHHHHHHHhCCCCCCHHHHHHHHHHH-HhcCC--HhHHHHHHHHHHhcCCCCCHhhHHH
Q 040027           95 NLYTYNILINCFCKIGRVSLGFIAFGRILRSCFTPNAATFNSLIKGL-HAESR--IMEAAALFTKLKAFGCEPNVITYNT  171 (595)
Q Consensus        95 ~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~~l~~~~-~~~g~--~~~A~~~~~~~~~~~~~~~~~~~~~  171 (595)
                      |+..|..+...|...|++++|...|+++.+.. +.+...+..+..++ ...|+  .++|.+++++..+.+.. +..++..
T Consensus        72 ~~~~w~~Lg~~~~~~g~~~~A~~a~~~Al~l~-P~~~~~~~~lA~aL~~~~g~~~~~~A~~~l~~al~~dP~-~~~al~~  149 (198)
T PRK10370         72 NSEQWALLGEYYLWRNDYDNALLAYRQALQLR-GENAELYAALATVLYYQAGQHMTPQTREMIDKALALDAN-EVTALML  149 (198)
T ss_pred             CHHHHHHHHHHHHHCCCHHHHHHHHHHHHHhC-CCCHHHHHHHHHHHHHhcCCCCcHHHHHHHHHHHHhCCC-ChhHHHH
Confidence            67777788888889999999999999999986 55788888888764 66677  58999999999988633 7888899


Q ss_pred             HHHHHHhcCChhHHHHHHHHHHhcC
Q 040027          172 LINGLCRTGHTMIALNLFEEMANGN  196 (595)
Q Consensus       172 l~~~~~~~g~~~~A~~~~~~~~~~~  196 (595)
                      +...+...|++++|+..++++.+..
T Consensus       150 LA~~~~~~g~~~~Ai~~~~~aL~l~  174 (198)
T PRK10370        150 LASDAFMQADYAQAIELWQKVLDLN  174 (198)
T ss_pred             HHHHHHHcCCHHHHHHHHHHHHhhC
Confidence            9999999999999999999998876

>PRK15359 type III secretion system chaperone protein SscB; Provisional

Probab=98.69  E-value=1.1e-06  Score=71.75  Aligned_cols=112  Identities=10%  Similarity=-0.059  Sum_probs=94.2

Q ss_pred             CHHHHHHHHHHHHhcCChhHHHHHHHHHHhCCCCCCHHHHHHHHHHHHhcCCHhHHHHHHHHHHhcCCCCCHhhHHHHHH
Q 040027           95 NLYTYNILINCFCKIGRVSLGFIAFGRILRSCFTPNAATFNSLIKGLHAESRIMEAAALFTKLKAFGCEPNVITYNTLIN  174 (595)
Q Consensus        95 ~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~~l~~  174 (595)
                      ++..+..+...+...|++++|...|++++... +.+...|..+..++...|++++|+..|++..... +.+...+..+..
T Consensus        23 ~p~~~~~~g~~~~~~g~~~~A~~~~~~al~~~-P~~~~a~~~lg~~~~~~g~~~~A~~~y~~Al~l~-p~~~~a~~~lg~  100 (144)
T PRK15359         23 DPETVYASGYASWQEGDYSRAVIDFSWLVMAQ-PWSWRAHIALAGTWMMLKEYTTAINFYGHALMLD-ASHPEPVYQTGV  100 (144)
T ss_pred             CHHHHHHHHHHHHHcCCHHHHHHHHHHHHHcC-CCcHHHHHHHHHHHHHHhhHHHHHHHHHHHHhcC-CCCcHHHHHHHH
Confidence            34345567778899999999999999999885 5688899999999999999999999999999875 458889999999


Q ss_pred             HHHhcCChhHHHHHHHHHHhcCCCCCccccCcHHHHHHHHH
Q 040027          175 GLCRTGHTMIALNLFEEMANGNGEIGVVCKPNTVTYSTIID  215 (595)
Q Consensus       175 ~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~  215 (595)
                      ++...|++++|+..|+......       +.++..+.....
T Consensus       101 ~l~~~g~~~eAi~~~~~Al~~~-------p~~~~~~~~~~~  134 (144)
T PRK15359        101 CLKMMGEPGLAREAFQTAIKMS-------YADASWSEIRQN  134 (144)
T ss_pred             HHHHcCCHHHHHHHHHHHHHhC-------CCChHHHHHHHH
Confidence            9999999999999999999875       445555544433

>PRK14720 transcript cleavage factor/unknown domain fusion protein; Provisional

Probab=98.67  E-value=2e-05  Score=81.81  Aligned_cols=239  Identities=10%  Similarity=0.098  Sum_probs=127.3

Q ss_pred             cCcHHHHHHHHHHHHHcCCHhHHHHHHHHHhhCCCCCCHhHHHHHHHHHHhcCCHHHHHHHHHHHHHCCCCCCHhhHHHH
Q 040027          204 KPNTVTYSTIIDGLCKEGFVDKAKALFLQMKDENINPDVVTYNSLIHGLCHANDWNEAKRLFIEMMDQGVQPSVVTFNVI  283 (595)
Q Consensus       204 ~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~~ll~~~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~~l  283 (595)
                      +.+...+..|+..+...+++++|.++.+...... +-....|-.++..+.+.++.+++..+  .               +
T Consensus        28 p~n~~a~~~Li~~~~~~~~~deai~i~~~~l~~~-P~~i~~yy~~G~l~~q~~~~~~~~lv--~---------------~   89 (906)
T PRK14720         28 LSKFKELDDLIDAYKSENLTDEAKDICEEHLKEH-KKSISALYISGILSLSRRPLNDSNLL--N---------------L   89 (906)
T ss_pred             cchHHHHHHHHHHHHhcCCHHHHHHHHHHHHHhC-CcceehHHHHHHHHHhhcchhhhhhh--h---------------h
Confidence            4446667777777777777777777777555542 11233333333455555554443333  1               2


Q ss_pred             HHHHHhcCChHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHhcCCCCCHHHHHHHHHHHHhCCCH
Q 040027          284 MDELCKNRKMDEASRLLDLMVQRGVRPNACTYNTLMDGFCLMGKINRAEELFGSMESMGCKHDDVSYNILINGYCKNKEV  363 (595)
Q Consensus       284 ~~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~  363 (595)
                      +.......++..+..++..+...  ..+...+..++.+|-+.|+.+++..+++++++.+ +.++.+.+.+...|... +.
T Consensus        90 l~~~~~~~~~~~ve~~~~~i~~~--~~~k~Al~~LA~~Ydk~g~~~ka~~~yer~L~~D-~~n~~aLNn~AY~~ae~-dL  165 (906)
T PRK14720         90 IDSFSQNLKWAIVEHICDKILLY--GENKLALRTLAEAYAKLNENKKLKGVWERLVKAD-RDNPEIVKKLATSYEEE-DK  165 (906)
T ss_pred             hhhcccccchhHHHHHHHHHHhh--hhhhHHHHHHHHHHHHcCChHHHHHHHHHHHhcC-cccHHHHHHHHHHHHHh-hH
Confidence            22222233333333333344432  2233456666777777777777777777777665 55666777777777766 77


Q ss_pred             HHHHHHHHHHHHCCCCCCHHHHHHHHHHHHccCCHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHH
Q 040027          364 EEALSLYREMVSKGIKPTVVTYNTLFLGLFEIHQVEHALKLFDEMQRDGVAADTRTYTTFIDGLCKNGYIIEAVELFRTL  443 (595)
Q Consensus       364 ~~A~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~  443 (595)
                      ++|.+++.+++..               +...+++..+..+|.++.... +.+...+..+.+                .+
T Consensus       166 ~KA~~m~~KAV~~---------------~i~~kq~~~~~e~W~k~~~~~-~~d~d~f~~i~~----------------ki  213 (906)
T PRK14720        166 EKAITYLKKAIYR---------------FIKKKQYVGIEEIWSKLVHYN-SDDFDFFLRIER----------------KV  213 (906)
T ss_pred             HHHHHHHHHHHHH---------------HHhhhcchHHHHHHHHHHhcC-cccchHHHHHHH----------------HH
Confidence            7777776665543               445556667777777766652 222222222221                12


Q ss_pred             HHc-CCCcCHHHHHHHHHHHHhcCChHHHHHHHHhcccCCCCC-CHHHHHHHHHHHH
Q 040027          444 RIL-KCELDIQAYNCLIDGLCKSGRLKFAWELFCSLPHGVLVP-NVVTYNIMIQGLC  498 (595)
Q Consensus       444 ~~~-~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~p-~~~~~~~l~~~~~  498 (595)
                      ... +...-..++..+...|...++++++..+++.+++.  .| |.....-++.+|.
T Consensus       214 ~~~~~~~~~~~~~~~l~~~y~~~~~~~~~i~iLK~iL~~--~~~n~~a~~~l~~~y~  268 (906)
T PRK14720        214 LGHREFTRLVGLLEDLYEPYKALEDWDEVIYILKKILEH--DNKNNKAREELIRFYK  268 (906)
T ss_pred             HhhhccchhHHHHHHHHHHHhhhhhhhHHHHHHHHHHhc--CCcchhhHHHHHHHHH
Confidence            111 11222344445555566666677777777777663  33 3444555555554

>PRK15359 type III secretion system chaperone protein SscB; Provisional

Probab=98.65  E-value=2.4e-06  Score=69.82  Aligned_cols=93  Identities=11%  Similarity=-0.090  Sum_probs=55.0

Q ss_pred             HHHHHHHHHhcCChHHHHHHHHhcccCCCCC-CHHHHHHHHHHHHhcCChhHHHHHHHHHHHcCCCCCHHHHHHHHHHHH
Q 040027          455 YNCLIDGLCKSGRLKFAWELFCSLPHGVLVP-NVVTYNIMIQGLCNDGQMDKARDLFLDMEENAAAPDVITFDMLIHGFI  533 (595)
Q Consensus       455 ~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~p-~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~~l~~~~~  533 (595)
                      +..+...+...|++++|...|+.+..  +.| +...|..+..++...|++++|+..|+++.+.+ +.+...+..++.++.
T Consensus        27 ~~~~g~~~~~~g~~~~A~~~~~~al~--~~P~~~~a~~~lg~~~~~~g~~~~A~~~y~~Al~l~-p~~~~a~~~lg~~l~  103 (144)
T PRK15359         27 VYASGYASWQEGDYSRAVIDFSWLVM--AQPWSWRAHIALAGTWMMLKEYTTAINFYGHALMLD-ASHPEPVYQTGVCLK  103 (144)
T ss_pred             HHHHHHHHHHcCCHHHHHHHHHHHHH--cCCCcHHHHHHHHHHHHHHhhHHHHHHHHHHHHhcC-CCCcHHHHHHHHHHH
Confidence            33445555566666666666666655  233 34555666666666666666666666666543 445555666666666


Q ss_pred             HcCChhHHHHHHHHHHH
Q 040027          534 RINEPSKVNELLHKMKE  550 (595)
Q Consensus       534 ~~g~~~~A~~~~~~~~~  550 (595)
                      ..|++++|...|++..+
T Consensus       104 ~~g~~~eAi~~~~~Al~  120 (144)
T PRK15359        104 MMGEPGLAREAFQTAIK  120 (144)
T ss_pred             HcCCHHHHHHHHHHHHH
Confidence            66666666666666665

>KOG3081 consensus Vesicle coat complex COPI, epsilon subunit [Intracellular trafficking, secretion, and vesicular transport]

Probab=98.64  E-value=4.7e-05  Score=65.60  Aligned_cols=87  Identities=15%  Similarity=0.194  Sum_probs=38.3

Q ss_pred             HHHhcCCHHHHHHHHHHHHHCCCCCCHhhHHHHHHHHHh----cCChHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHhcC
Q 040027          251 GLCHANDWNEAKRLFIEMMDQGVQPSVVTFNVIMDELCK----NRKMDEASRLLDLMVQRGVRPNACTYNTLMDGFCLMG  326 (595)
Q Consensus       251 ~~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~~l~~~~~~----~g~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~  326 (595)
                      .+.+..+++-|.+.+++|.+.   .+..+.+.+..++.+    .+.+.+|.-+|+++-+. .+|+..+.+..+.++...|
T Consensus       146 I~lk~~r~d~A~~~lk~mq~i---ded~tLtQLA~awv~la~ggek~qdAfyifeE~s~k-~~~T~~llnG~Av~~l~~~  221 (299)
T KOG3081|consen  146 ILLKMHRFDLAEKELKKMQQI---DEDATLTQLAQAWVKLATGGEKIQDAFYIFEELSEK-TPPTPLLLNGQAVCHLQLG  221 (299)
T ss_pred             HHHHHHHHHHHHHHHHHHHcc---chHHHHHHHHHHHHHHhccchhhhhHHHHHHHHhcc-cCCChHHHccHHHHHHHhc
Confidence            344444455555555555442   133333333333322    22344444444444443 3344444444444444445


Q ss_pred             CHHHHHHHHHHHHhc
Q 040027          327 KINRAEELFGSMESM  341 (595)
Q Consensus       327 ~~~~a~~~~~~~~~~  341 (595)
                      ++++|..+++.....
T Consensus       222 ~~eeAe~lL~eaL~k  236 (299)
T KOG3081|consen  222 RYEEAESLLEEALDK  236 (299)
T ss_pred             CHHHHHHHHHHHHhc
Confidence            555555555444443

>PRK15179 Vi polysaccharide biosynthesis protein TviE; Provisional

Probab=98.63  E-value=2e-05  Score=81.09  Aligned_cols=141  Identities=13%  Similarity=0.060  Sum_probs=90.3

Q ss_pred             CHHHHHHHHHHHHccCCHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCcCHHHHHHHHH
Q 040027          381 TVVTYNTLFLGLFEIHQVEHALKLFDEMQRDGVAADTRTYTTFIDGLCKNGYIIEAVELFRTLRILKCELDIQAYNCLID  460 (595)
Q Consensus       381 ~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~~l~~  460 (595)
                      +...+..|.....+.|.+++|..+++.+.+.. |-+......++..+.+.+++++|...+++..... +.+......+..
T Consensus        85 ~~~~~~~La~i~~~~g~~~ea~~~l~~~~~~~-Pd~~~a~~~~a~~L~~~~~~eeA~~~~~~~l~~~-p~~~~~~~~~a~  162 (694)
T PRK15179         85 TELFQVLVARALEAAHRSDEGLAVWRGIHQRF-PDSSEAFILMLRGVKRQQGIEAGRAEIELYFSGG-SSSAREILLEAK  162 (694)
T ss_pred             cHHHHHHHHHHHHHcCCcHHHHHHHHHHHhhC-CCcHHHHHHHHHHHHHhccHHHHHHHHHHHhhcC-CCCHHHHHHHHH
Confidence            56666666667777777777777777776652 3334455556666667777777777777776655 555666666666


Q ss_pred             HHHhcCChHHHHHHHHhcccCCCCC-CHHHHHHHHHHHHhcCChhHHHHHHHHHHHcCCCCCHHHHH
Q 040027          461 GLCKSGRLKFAWELFCSLPHGVLVP-NVVTYNIMIQGLCNDGQMDKARDLFLDMEENAAAPDVITFD  526 (595)
Q Consensus       461 ~~~~~g~~~~A~~~~~~~~~~~~~p-~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~  526 (595)
                      ++...|++++|..+|+++...  .| +..++..+..++...|+.++|...|+++.+.. .+....|+
T Consensus       163 ~l~~~g~~~~A~~~y~~~~~~--~p~~~~~~~~~a~~l~~~G~~~~A~~~~~~a~~~~-~~~~~~~~  226 (694)
T PRK15179        163 SWDEIGQSEQADACFERLSRQ--HPEFENGYVGWAQSLTRRGALWRARDVLQAGLDAI-GDGARKLT  226 (694)
T ss_pred             HHHHhcchHHHHHHHHHHHhc--CCCcHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhh-CcchHHHH
Confidence            777777777777777777652  23 35666666677777777777777777776652 33444444

>KOG3081 consensus Vesicle coat complex COPI, epsilon subunit [Intracellular trafficking, secretion, and vesicular transport]

Probab=98.62  E-value=9.5e-05  Score=63.76  Aligned_cols=88  Identities=18%  Similarity=0.194  Sum_probs=41.9

Q ss_pred             HHHHHcCCHhHHHHHHHHHhhCCCCCCHhHHHHHHHHHHh----cCCHHHHHHHHHHHHHCCCCCCHhhHHHHHHHHHhc
Q 040027          215 DGLCKEGFVDKAKALFLQMKDENINPDVVTYNSLIHGLCH----ANDWNEAKRLFIEMMDQGVQPSVVTFNVIMDELCKN  290 (595)
Q Consensus       215 ~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~~ll~~~~~----~~~~~~A~~~~~~~~~~~~~~~~~~~~~l~~~~~~~  290 (595)
                      .++.+..+++-|.+.+++|.+..   +..+.+.|..++.+    .+...+|.-+|++|-+. .+|+..+.+-...++...
T Consensus       145 qI~lk~~r~d~A~~~lk~mq~id---ed~tLtQLA~awv~la~ggek~qdAfyifeE~s~k-~~~T~~llnG~Av~~l~~  220 (299)
T KOG3081|consen  145 QILLKMHRFDLAEKELKKMQQID---EDATLTQLAQAWVKLATGGEKIQDAFYIFEELSEK-TPPTPLLLNGQAVCHLQL  220 (299)
T ss_pred             HHHHHHHHHHHHHHHHHHHHccc---hHHHHHHHHHHHHHHhccchhhhhHHHHHHHHhcc-cCCChHHHccHHHHHHHh
Confidence            33444445555555555555432   33344444443332    23345555555555432 344444555555555555


Q ss_pred             CChHHHHHHHHHHHHC
Q 040027          291 RKMDEASRLLDLMVQR  306 (595)
Q Consensus       291 g~~~~a~~~~~~~~~~  306 (595)
                      |++++|..+++.++..
T Consensus       221 ~~~eeAe~lL~eaL~k  236 (299)
T KOG3081|consen  221 GRYEEAESLLEEALDK  236 (299)
T ss_pred             cCHHHHHHHHHHHHhc
Confidence            5555555555555544

>PRK15179 Vi polysaccharide biosynthesis protein TviE; Provisional

Probab=98.59  E-value=1.9e-05  Score=81.29  Aligned_cols=133  Identities=13%  Similarity=0.113  Sum_probs=60.4

Q ss_pred             CCHHHHHHHHHHHHhcCChhHHHHHHHHHHhCCCCCCHHHHHHHHHHHHhcCCHhHHHHHHHHHHhcCCCCCHhhHHHHH
Q 040027           94 PNLYTYNILINCFCKIGRVSLGFIAFGRILRSCFTPNAATFNSLIKGLHAESRIMEAAALFTKLKAFGCEPNVITYNTLI  173 (595)
Q Consensus        94 ~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~~l~  173 (595)
                      .++..+..|.+...+.|++++|..+++.+.+.. |-+...+..++..+.+.+++++|...+++..... +-+......+.
T Consensus        84 ~~~~~~~~La~i~~~~g~~~ea~~~l~~~~~~~-Pd~~~a~~~~a~~L~~~~~~eeA~~~~~~~l~~~-p~~~~~~~~~a  161 (694)
T PRK15179         84 HTELFQVLVARALEAAHRSDEGLAVWRGIHQRF-PDSSEAFILMLRGVKRQQGIEAGRAEIELYFSGG-SSSAREILLEA  161 (694)
T ss_pred             ccHHHHHHHHHHHHHcCCcHHHHHHHHHHHhhC-CCcHHHHHHHHHHHHHhccHHHHHHHHHHHhhcC-CCCHHHHHHHH
Confidence            344444444444444555555555555544442 2223333444444444455555555544444442 11333444444


Q ss_pred             HHHHhcCChhHHHHHHHHHHhcCCCCCccccCcHHHHHHHHHHHHHcCCHhHHHHHHHHHhh
Q 040027          174 NGLCRTGHTMIALNLFEEMANGNGEIGVVCKPNTVTYSTIIDGLCKEGFVDKAKALFLQMKD  235 (595)
Q Consensus       174 ~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~  235 (595)
                      .++.+.|++++|..+|+++...+       +.+..++..+..++...|+.++|...|++...
T Consensus       162 ~~l~~~g~~~~A~~~y~~~~~~~-------p~~~~~~~~~a~~l~~~G~~~~A~~~~~~a~~  216 (694)
T PRK15179        162 KSWDEIGQSEQADACFERLSRQH-------PEFENGYVGWAQSLTRRGALWRARDVLQAGLD  216 (694)
T ss_pred             HHHHHhcchHHHHHHHHHHHhcC-------CCcHHHHHHHHHHHHHcCCHHHHHHHHHHHHH
Confidence            44444455555555555444422       22344444444444444555555554444443

>TIGR02552 LcrH_SycD type III secretion low calcium response chaperone LcrH/SycD

Probab=98.56  E-value=3e-06  Score=68.96  Aligned_cols=99  Identities=16%  Similarity=0.071  Sum_probs=60.3

Q ss_pred             CHHHHHHHHHHHHhcCChHHHHHHHHhcccCCCCCCHHHHHHHHHHHHhcCChhHHHHHHHHHHHcCCCCCHHHHHHHHH
Q 040027          451 DIQAYNCLIDGLCKSGRLKFAWELFCSLPHGVLVPNVVTYNIMIQGLCNDGQMDKARDLFLDMEENAAAPDVITFDMLIH  530 (595)
Q Consensus       451 ~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~p~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~~l~~  530 (595)
                      +......++..+...|++++|...|+.+...+ +.+...|..+..++...|++++|...+++..+.+ +.+...+..+..
T Consensus        16 ~~~~~~~~a~~~~~~~~~~~A~~~~~~~~~~~-p~~~~~~~~la~~~~~~~~~~~A~~~~~~~~~~~-p~~~~~~~~la~   93 (135)
T TIGR02552        16 QLEQIYALAYNLYQQGRYDEALKLFQLLAAYD-PYNSRYWLGLAACCQMLKEYEEAIDAYALAAALD-PDDPRPYFHAAE   93 (135)
T ss_pred             hHHHHHHHHHHHHHcccHHHHHHHHHHHHHhC-CCcHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcC-CCChHHHHHHHH
Confidence            34445555566666666666666666665521 2245566666666666666666666666666553 444556666666


Q ss_pred             HHHHcCChhHHHHHHHHHHHC
Q 040027          531 GFIRINEPSKVNELLHKMKEK  551 (595)
Q Consensus       531 ~~~~~g~~~~A~~~~~~~~~~  551 (595)
                      +|...|++++|...+++..+.
T Consensus        94 ~~~~~g~~~~A~~~~~~al~~  114 (135)
T TIGR02552        94 CLLALGEPESALKALDLAIEI  114 (135)
T ss_pred             HHHHcCCHHHHHHHHHHHHHh
Confidence            666666666666666666653

ScyD/LcrH contains three central tetratricopeptide-like repeats that are predicted to fold into an all-alpha-helical array.

>KOG3060 consensus Uncharacterized conserved protein [Function unknown]

Probab=98.54  E-value=0.00014  Score=62.26  Aligned_cols=187  Identities=13%  Similarity=0.070  Sum_probs=98.1

Q ss_pred             CHHHHHHHHHHHHHC---C-CCCCHh-hHHHHHHHHHhcCChHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHhcCCHHHH
Q 040027          257 DWNEAKRLFIEMMDQ---G-VQPSVV-TFNVIMDELCKNRKMDEASRLLDLMVQRGVRPNACTYNTLMDGFCLMGKINRA  331 (595)
Q Consensus       257 ~~~~A~~~~~~~~~~---~-~~~~~~-~~~~l~~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a  331 (595)
                      +.++..+++.+++..   | ..++.. .|..++-+....|+.+.|...++.+... ++-+..+...-...+-..|.+++|
T Consensus        27 nseevv~l~~~~~~~~k~~~~g~e~w~l~EqV~IAAld~~~~~lAq~C~~~L~~~-fp~S~RV~~lkam~lEa~~~~~~A  105 (289)
T KOG3060|consen   27 NSEEVVQLGSEVLNYSKSGALGDEIWTLYEQVFIAALDTGRDDLAQKCINQLRDR-FPGSKRVGKLKAMLLEATGNYKEA  105 (289)
T ss_pred             CHHHHHHHHHHHHHHhhhcccCchHHHHHHHHHHHHHHhcchHHHHHHHHHHHHh-CCCChhHHHHHHHHHHHhhchhhH
Confidence            445555555554432   2 223332 2334444555666666666666666655 232333333333344456666666


Q ss_pred             HHHHHHHHhcCCCCCHHHHHHHHHHHHhCCCHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHccCCHHHHHHHHHHHHHC
Q 040027          332 EELFGSMESMGCKHDDVSYNILINGYCKNKEVEEALSLYREMVSKGIKPTVVTYNTLFLGLFEIHQVEHALKLFDEMQRD  411 (595)
Q Consensus       332 ~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~  411 (595)
                      +++++.+++.+ |.|..++..-+...-..|+.-+|++-+.+..+.. ..|...|..+...|...|++++|.-.++++.-.
T Consensus       106 ~e~y~~lL~dd-pt~~v~~KRKlAilka~GK~l~aIk~ln~YL~~F-~~D~EAW~eLaeiY~~~~~f~kA~fClEE~ll~  183 (289)
T KOG3060|consen  106 IEYYESLLEDD-PTDTVIRKRKLAILKAQGKNLEAIKELNEYLDKF-MNDQEAWHELAEIYLSEGDFEKAAFCLEELLLI  183 (289)
T ss_pred             HHHHHHHhccC-cchhHHHHHHHHHHHHcCCcHHHHHHHHHHHHHh-cCcHHHHHHHHHHHHhHhHHHHHHHHHHHHHHc
Confidence            66666666654 4444455544444455555556666666655542 336666666666666666666666666666543


Q ss_pred             CCCCCHHHHHHHHHHHHhcC---CHHHHHHHHHHHHHcC
Q 040027          412 GVAADTRTYTTFIDGLCKNG---YIIEAVELFRTLRILK  447 (595)
Q Consensus       412 ~~~~~~~~~~~l~~~~~~~g---~~~~A~~~~~~~~~~~  447 (595)
                      . |.++..+..+...+.-.|   +.+-+.+.|.+.++..
T Consensus       184 ~-P~n~l~f~rlae~~Yt~gg~eN~~~arkyy~~alkl~  221 (289)
T KOG3060|consen  184 Q-PFNPLYFQRLAEVLYTQGGAENLELARKYYERALKLN  221 (289)
T ss_pred             C-CCcHHHHHHHHHHHHHHhhHHHHHHHHHHHHHHHHhC
Confidence            2 333333444444433222   4455566666666543

>COG4783 Putative Zn-dependent protease, contains TPR repeats [General function prediction only]

Probab=98.46  E-value=0.0001  Score=69.27  Aligned_cols=142  Identities=15%  Similarity=0.093  Sum_probs=98.4

Q ss_pred             HHHHHccCCHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCcCHHHHHHHHHHHHhcCCh
Q 040027          389 FLGLFEIHQVEHALKLFDEMQRDGVAADTRTYTTFIDGLCKNGYIIEAVELFRTLRILKCELDIQAYNCLIDGLCKSGRL  468 (595)
Q Consensus       389 ~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~  468 (595)
                      ...+...|+++.|+..+..+++. .+.++.......+.+.+.++.++|.+.++++.... +........+..+|.+.|++
T Consensus       313 A~~~~~~~~~d~A~~~l~~L~~~-~P~N~~~~~~~~~i~~~~nk~~~A~e~~~kal~l~-P~~~~l~~~~a~all~~g~~  390 (484)
T COG4783         313 ALQTYLAGQYDEALKLLQPLIAA-QPDNPYYLELAGDILLEANKAKEAIERLKKALALD-PNSPLLQLNLAQALLKGGKP  390 (484)
T ss_pred             HHHHHHhcccchHHHHHHHHHHh-CCCCHHHHHHHHHHHHHcCChHHHHHHHHHHHhcC-CCccHHHHHHHHHHHhcCCh
Confidence            33455667777888888777765 35566666666777778888888888888877664 33366667777778888888


Q ss_pred             HHHHHHHHhcccCCCCCCHHHHHHHHHHHHhcCChhHHHHHHHHHHHcCCCCCHHHHHHHHHHHHHcCChhHHHHHHHHH
Q 040027          469 KFAWELFCSLPHGVLVPNVVTYNIMIQGLCNDGQMDKARDLFLDMEENAAAPDVITFDMLIHGFIRINEPSKVNELLHKM  548 (595)
Q Consensus       469 ~~A~~~~~~~~~~~~~p~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~  548 (595)
                      .+|+.+++..... .+-|+..|..|..+|...|+..+|.....                  ..|...|++++|...+..+
T Consensus       391 ~eai~~L~~~~~~-~p~dp~~w~~LAqay~~~g~~~~a~~A~A------------------E~~~~~G~~~~A~~~l~~A  451 (484)
T COG4783         391 QEAIRILNRYLFN-DPEDPNGWDLLAQAYAELGNRAEALLARA------------------EGYALAGRLEQAIIFLMRA  451 (484)
T ss_pred             HHHHHHHHHHhhc-CCCCchHHHHHHHHHHHhCchHHHHHHHH------------------HHHHhCCCHHHHHHHHHHH
Confidence            8888888777664 33457778888888887777776654333                  3345667777777777777


Q ss_pred             HHC
Q 040027          549 KEK  551 (595)
Q Consensus       549 ~~~  551 (595)
                      .+.
T Consensus       452 ~~~  454 (484)
T COG4783         452 SQQ  454 (484)
T ss_pred             HHh
Confidence            654

>TIGR02552 LcrH_SycD type III secretion low calcium response chaperone LcrH/SycD

Probab=98.42  E-value=1.4e-05  Score=65.08  Aligned_cols=111  Identities=13%  Similarity=0.025  Sum_probs=82.1

Q ss_pred             HHHHHHHCCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCcCHHHHHHHHHHHHhcCChHHHHHHHHhcccCCC
Q 040027          404 LFDEMQRDGVAADTRTYTTFIDGLCKNGYIIEAVELFRTLRILKCELDIQAYNCLIDGLCKSGRLKFAWELFCSLPHGVL  483 (595)
Q Consensus       404 ~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~  483 (595)
                      .++.+.... +.+......+...+...|++++|...++.+...+ +.+...+..+..++...|++++|...+++....+ 
T Consensus         5 ~~~~~l~~~-p~~~~~~~~~a~~~~~~~~~~~A~~~~~~~~~~~-p~~~~~~~~la~~~~~~~~~~~A~~~~~~~~~~~-   81 (135)
T TIGR02552         5 TLKDLLGLD-SEQLEQIYALAYNLYQQGRYDEALKLFQLLAAYD-PYNSRYWLGLAACCQMLKEYEEAIDAYALAAALD-   81 (135)
T ss_pred             hHHHHHcCC-hhhHHHHHHHHHHHHHcccHHHHHHHHHHHHHhC-CCcHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcC-
Confidence            344555442 2244555666677788888888888888887765 5677888888888888888888888888877642 


Q ss_pred             CCCHHHHHHHHHHHHhcCChhHHHHHHHHHHHcC
Q 040027          484 VPNVVTYNIMIQGLCNDGQMDKARDLFLDMEENA  517 (595)
Q Consensus       484 ~p~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~  517 (595)
                      +.+...+..+..+|...|++++|+..|++.++..
T Consensus        82 p~~~~~~~~la~~~~~~g~~~~A~~~~~~al~~~  115 (135)
T TIGR02552        82 PDDPRPYFHAAECLLALGEPESALKALDLAIEIC  115 (135)
T ss_pred             CCChHHHHHHHHHHHHcCCHHHHHHHHHHHHHhc
Confidence            3346777778888888888888888888888853

ScyD/LcrH contains three central tetratricopeptide-like repeats that are predicted to fold into an all-alpha-helical array.

>PF12854 PPR_1: PPR repeat

Probab=98.39  E-value=5.3e-07  Score=52.00  Aligned_cols=32  Identities=47%  Similarity=0.845  Sum_probs=17.5

Q ss_pred             CCCCCHHHHHHHHHHHHhcCChhHHHHHHHHH
Q 040027          482 VLVPNVVTYNIMIQGLCNDGQMDKARDLFLDM  513 (595)
Q Consensus       482 ~~~p~~~~~~~l~~~~~~~g~~~~A~~~~~~~  513 (595)
                      |+.||..+|+.++.+|++.|++++|.++|++|
T Consensus         2 G~~Pd~~ty~~lI~~~Ck~G~~~~A~~l~~~M   33 (34)
T PF12854_consen    2 GCEPDVVTYNTLIDGYCKAGRVDEAFELFDEM   33 (34)
T ss_pred             CCCCcHhHHHHHHHHHHHCCCHHHHHHHHHhC
Confidence            34555555555555555555555555555554

>COG4783 Putative Zn-dependent protease, contains TPR repeats [General function prediction only]

Probab=98.38  E-value=0.00027  Score=66.62  Aligned_cols=146  Identities=13%  Similarity=0.087  Sum_probs=88.0

Q ss_pred             HHHHHHHHHhCCCHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHccCCHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHh
Q 040027          350 YNILINGYCKNKEVEEALSLYREMVSKGIKPTVVTYNTLFLGLFEIHQVEHALKLFDEMQRDGVAADTRTYTTFIDGLCK  429 (595)
Q Consensus       350 ~~~l~~~~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~  429 (595)
                      .......+...|++++|+..++.++...+ -|+..+......+...++.++|.+.++.+.... +........+..+|.+
T Consensus       309 ~YG~A~~~~~~~~~d~A~~~l~~L~~~~P-~N~~~~~~~~~i~~~~nk~~~A~e~~~kal~l~-P~~~~l~~~~a~all~  386 (484)
T COG4783         309 QYGRALQTYLAGQYDEALKLLQPLIAAQP-DNPYYLELAGDILLEANKAKEAIERLKKALALD-PNSPLLQLNLAQALLK  386 (484)
T ss_pred             HHHHHHHHHHhcccchHHHHHHHHHHhCC-CCHHHHHHHHHHHHHcCChHHHHHHHHHHHhcC-CCccHHHHHHHHHHHh
Confidence            33334445556666666666666665522 244444555556666667777777666666652 2224445556666677


Q ss_pred             cCCHHHHHHHHHHHHHcCCCcCHHHHHHHHHHHHhcCChHHHHHHHHhcccCCCCCCHHHHHHHHHHHHhcCChhHHHHH
Q 040027          430 NGYIIEAVELFRTLRILKCELDIQAYNCLIDGLCKSGRLKFAWELFCSLPHGVLVPNVVTYNIMIQGLCNDGQMDKARDL  509 (595)
Q Consensus       430 ~g~~~~A~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~p~~~~~~~l~~~~~~~g~~~~A~~~  509 (595)
                      .|++.+|+..++...... +.|+..|..|..+|...|+..++....                  ...|...|++++|+..
T Consensus       387 ~g~~~eai~~L~~~~~~~-p~dp~~w~~LAqay~~~g~~~~a~~A~------------------AE~~~~~G~~~~A~~~  447 (484)
T COG4783         387 GGKPQEAIRILNRYLFND-PEDPNGWDLLAQAYAELGNRAEALLAR------------------AEGYALAGRLEQAIIF  447 (484)
T ss_pred             cCChHHHHHHHHHHhhcC-CCCchHHHHHHHHHHHhCchHHHHHHH------------------HHHHHhCCCHHHHHHH
Confidence            777777777777666554 566677777777777777666554432                  2344556777777777


Q ss_pred             HHHHHHc
Q 040027          510 FLDMEEN  516 (595)
Q Consensus       510 ~~~~~~~  516 (595)
                      +..+.+.
T Consensus       448 l~~A~~~  454 (484)
T COG4783         448 LMRASQQ  454 (484)
T ss_pred             HHHHHHh
Confidence            7666665

>KOG0550 consensus Molecular chaperone (DnaJ superfamily) [Posttranslational modification, protein turnover, chaperones]

Probab=98.31  E-value=0.00044  Score=63.62  Aligned_cols=274  Identities=13%  Similarity=0.041  Sum_probs=146.4

Q ss_pred             cccccccCCCChHHHHHHHHHHHHhCCCCCCHhhHHHHHHHHHcCCCchhHH----hhCCCCC-CHHHHHHHHHHHHhcC
Q 040027           36 TTREGDINVITPNEAFCIFDYMLRMHPSPPPVSSFNILLASLAKNKHYDTRL----NATGLFP-NLYTYNILINCFCKIG  110 (595)
Q Consensus        36 ~~~~~~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~----~~~~~~~-~~~~~~~l~~~~~~~g  110 (595)
                      .....+.+..+|.+|+..+..+++..|.  ++..|..-+..+.--|++++..    ....+.| .+.......+++...+
T Consensus        54 ~~gn~~yk~k~Y~nal~~yt~Ai~~~pd--~a~yy~nRAa~~m~~~~~~~a~~dar~~~r~kd~~~k~~~r~~~c~~a~~  131 (486)
T KOG0550|consen   54 EEGNAFYKQKTYGNALKNYTFAIDMCPD--NASYYSNRAATLMMLGRFEEALGDARQSVRLKDGFSKGQLREGQCHLALS  131 (486)
T ss_pred             hhcchHHHHhhHHHHHHHHHHHHHhCcc--chhhhchhHHHHHHHHhHhhcccchhhheecCCCccccccchhhhhhhhH
Confidence            5667788889999999999999999998  7888888888888888888711    1111222 2233444445555555


Q ss_pred             ChhHHHHHHHHHHhCCCCCCHHHHHHHHHHHHhcCCHhHHHHHHHHHHhcCC-CCCHhhHHHH-HHHHHhcCChhHHHHH
Q 040027          111 RVSLGFIAFGRILRSCFTPNAATFNSLIKGLHAESRIMEAAALFTKLKAFGC-EPNVITYNTL-INGLCRTGHTMIALNL  188 (595)
Q Consensus       111 ~~~~A~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~-~~~~~~~~~l-~~~~~~~g~~~~A~~~  188 (595)
                      +..+|...++.         ...+           ....++..++.+..... +|.-..+..+ ...+.-.|+.++|.++
T Consensus       132 ~~i~A~~~~~~---------~~~~-----------~~anal~~~~~~~~s~s~~pac~~a~~lka~cl~~~~~~~~a~~e  191 (486)
T KOG0550|consen  132 DLIEAEEKLKS---------KQAY-----------KAANALPTLEKLAPSHSREPACFKAKLLKAECLAFLGDYDEAQSE  191 (486)
T ss_pred             HHHHHHHHhhh---------hhhh-----------HHhhhhhhhhcccccccCCchhhHHHHhhhhhhhhcccchhHHHH
Confidence            55555554441         1111           11112222222222111 1222233322 2233445666666666


Q ss_pred             HHHHHhcCCCCCccccCcHHHHHHHHHHHHHcCCHhHHHHHHHHHhhCCCCCCHhH-------------HHHHHHHHHhc
Q 040027          189 FEEMANGNGEIGVVCKPNTVTYSTIIDGLCKEGFVDKAKALFLQMKDENINPDVVT-------------YNSLIHGLCHA  255 (595)
Q Consensus       189 ~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~-------------~~~ll~~~~~~  255 (595)
                      --.+.+.+       +.+......-..++...++.+.+..-|++.+..+  |+...             +..=.+-..+.
T Consensus       192 a~~ilkld-------~~n~~al~vrg~~~yy~~~~~ka~~hf~qal~ld--pdh~~sk~~~~~~k~le~~k~~gN~~fk~  262 (486)
T KOG0550|consen  192 AIDILKLD-------ATNAEALYVRGLCLYYNDNADKAINHFQQALRLD--PDHQKSKSASMMPKKLEVKKERGNDAFKN  262 (486)
T ss_pred             HHHHHhcc-------cchhHHHHhcccccccccchHHHHHHHhhhhccC--hhhhhHHhHhhhHHHHHHHHhhhhhHhhc
Confidence            55555543       2233333222334444556666666666655542  22211             11122345566


Q ss_pred             CCHHHHHHHHHHHHHC---CCCCCHhhHHHHHHHHHhcCChHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHhcCCHHHHH
Q 040027          256 NDWNEAKRLFIEMMDQ---GVQPSVVTFNVIMDELCKNRKMDEASRLLDLMVQRGVRPNACTYNTLMDGFCLMGKINRAE  332 (595)
Q Consensus       256 ~~~~~A~~~~~~~~~~---~~~~~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~  332 (595)
                      |.+..|.+.|.+.+..   .+.++...|........+.|+..+|+.-.+...+.+.. -...+..-.+++...++|++|.
T Consensus       263 G~y~~A~E~Yteal~idP~n~~~naklY~nra~v~~rLgrl~eaisdc~~Al~iD~s-yikall~ra~c~l~le~~e~AV  341 (486)
T KOG0550|consen  263 GNYRKAYECYTEALNIDPSNKKTNAKLYGNRALVNIRLGRLREAISDCNEALKIDSS-YIKALLRRANCHLALEKWEEAV  341 (486)
T ss_pred             cchhHHHHHHHHhhcCCccccchhHHHHHHhHhhhcccCCchhhhhhhhhhhhcCHH-HHHHHHHHHHHHHHHHHHHHHH
Confidence            7777777777776653   23334445555566666677777777766666654110 1122333344555666677777


Q ss_pred             HHHHHHHhc
Q 040027          333 ELFGSMESM  341 (595)
Q Consensus       333 ~~~~~~~~~  341 (595)
                      +-++...+.
T Consensus       342 ~d~~~a~q~  350 (486)
T KOG0550|consen  342 EDYEKAMQL  350 (486)
T ss_pred             HHHHHHHhh
Confidence            776666554

>PF12854 PPR_1: PPR repeat

Probab=98.31  E-value=9.8e-07  Score=50.87  Aligned_cols=34  Identities=32%  Similarity=0.653  Sum_probs=31.6

Q ss_pred             cCCCCCHHHHHHHHHHHHHcCChhHHHHHHHHHH
Q 040027          516 NAAAPDVITFDMLIHGFIRINEPSKVNELLHKMK  549 (595)
Q Consensus       516 ~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~  549 (595)
                      .|+.||..+|+.++.+|++.|++++|.++|++|.
T Consensus         1 ~G~~Pd~~ty~~lI~~~Ck~G~~~~A~~l~~~M~   34 (34)
T PF12854_consen    1 RGCEPDVVTYNTLIDGYCKAGRVDEAFELFDEMK   34 (34)
T ss_pred             CCCCCcHhHHHHHHHHHHHCCCHHHHHHHHHhCc
Confidence            3789999999999999999999999999999984

>PF09976 TPR_21: Tetratricopeptide repeat; InterPro: IPR018704 This domain, found in various hypothetical prokaryotic proteins, has no known function

Probab=98.30  E-value=5.3e-05  Score=62.22  Aligned_cols=127  Identities=17%  Similarity=0.148  Sum_probs=94.3

Q ss_pred             HHHHHHHHHHHhcCChhHHHHHHHHHHhCCCCCC---HHHHHHHHHHHHhcCCHhHHHHHHHHHHhcCCCCC--HhhHHH
Q 040027           97 YTYNILINCFCKIGRVSLGFIAFGRILRSCFTPN---AATFNSLIKGLHAESRIMEAAALFTKLKAFGCEPN--VITYNT  171 (595)
Q Consensus        97 ~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~~---~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~~--~~~~~~  171 (595)
                      ..|..++..+ ..++...+...++.+.... +.+   ......+...+...|++++|...|+.+......++  ......
T Consensus        13 ~~y~~~~~~~-~~~~~~~~~~~~~~l~~~~-~~s~ya~~A~l~lA~~~~~~g~~~~A~~~l~~~~~~~~d~~l~~~a~l~   90 (145)
T PF09976_consen   13 ALYEQALQAL-QAGDPAKAEAAAEQLAKDY-PSSPYAALAALQLAKAAYEQGDYDEAKAALEKALANAPDPELKPLARLR   90 (145)
T ss_pred             HHHHHHHHHH-HCCCHHHHHHHHHHHHHHC-CCChHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHhhCCCHHHHHHHHHH
Confidence            4455666655 4788999999999998874 223   23344566778889999999999999998753332  234566


Q ss_pred             HHHHHHhcCChhHHHHHHHHHHhcCCCCCccccCcHHHHHHHHHHHHHcCCHhHHHHHHHHH
Q 040027          172 LINGLCRTGHTMIALNLFEEMANGNGEIGVVCKPNTVTYSTIIDGLCKEGFVDKAKALFLQM  233 (595)
Q Consensus       172 l~~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~  233 (595)
                      +...+...|++++|+..++.....        ...+..+.....++.+.|+.++|...|+..
T Consensus        91 LA~~~~~~~~~d~Al~~L~~~~~~--------~~~~~~~~~~Gdi~~~~g~~~~A~~~y~~A  144 (145)
T PF09976_consen   91 LARILLQQGQYDEALATLQQIPDE--------AFKALAAELLGDIYLAQGDYDEARAAYQKA  144 (145)
T ss_pred             HHHHHHHcCCHHHHHHHHHhccCc--------chHHHHHHHHHHHHHHCCCHHHHHHHHHHh
Confidence            788888999999999999775432        345667778889999999999999998764

>PF09976 TPR_21: Tetratricopeptide repeat; InterPro: IPR018704 This domain, found in various hypothetical prokaryotic proteins, has no known function

Probab=98.30  E-value=3.9e-05  Score=63.02  Aligned_cols=117  Identities=14%  Similarity=0.051  Sum_probs=69.8

Q ss_pred             hcCCHHHHHHHHHHHHHcCCCcC---HHHHHHHHHHHHhcCChHHHHHHHHhcccCCCCCC--HHHHHHHHHHHHhcCCh
Q 040027          429 KNGYIIEAVELFRTLRILKCELD---IQAYNCLIDGLCKSGRLKFAWELFCSLPHGVLVPN--VVTYNIMIQGLCNDGQM  503 (595)
Q Consensus       429 ~~g~~~~A~~~~~~~~~~~~~~~---~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~p~--~~~~~~l~~~~~~~g~~  503 (595)
                      ..++...+...++.+.+.. +.+   ......+...+...|++++|...|+.+......|+  ......+...+...|++
T Consensus        23 ~~~~~~~~~~~~~~l~~~~-~~s~ya~~A~l~lA~~~~~~g~~~~A~~~l~~~~~~~~d~~l~~~a~l~LA~~~~~~~~~  101 (145)
T PF09976_consen   23 QAGDPAKAEAAAEQLAKDY-PSSPYAALAALQLAKAAYEQGDYDEAKAALEKALANAPDPELKPLARLRLARILLQQGQY  101 (145)
T ss_pred             HCCCHHHHHHHHHHHHHHC-CCChHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHhhCCCHHHHHHHHHHHHHHHHHcCCH
Confidence            3566666666666666543 323   22333455666677777777777777776432222  12334456666677777


Q ss_pred             hHHHHHHHHHHHcCCCCCHHHHHHHHHHHHHcCChhHHHHHHHHH
Q 040027          504 DKARDLFLDMEENAAAPDVITFDMLIHGFIRINEPSKVNELLHKM  548 (595)
Q Consensus       504 ~~A~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~  548 (595)
                      ++|+..++.....  ......+...+.+|.+.|++++|...|++.
T Consensus       102 d~Al~~L~~~~~~--~~~~~~~~~~Gdi~~~~g~~~~A~~~y~~A  144 (145)
T PF09976_consen  102 DEALATLQQIPDE--AFKALAAELLGDIYLAQGDYDEARAAYQKA  144 (145)
T ss_pred             HHHHHHHHhccCc--chHHHHHHHHHHHHHHCCCHHHHHHHHHHh
Confidence            7777777553322  233445566677777777777777777654

>KOG2041 consensus WD40 repeat protein [General function prediction only]

Probab=98.22  E-value=0.0053  Score=60.52  Aligned_cols=61  Identities=16%  Similarity=0.256  Sum_probs=29.4

Q ss_pred             HHHHHHHHHHHhcCChHHHHHHHHhccc-CCCCCCHHHHHHHHHHHHhcCChhHHHHHHHHH
Q 040027          453 QAYNCLIDGLCKSGRLKFAWELFCSLPH-GVLVPNVVTYNIMIQGLCNDGQMDKARDLFLDM  513 (595)
Q Consensus       453 ~~~~~l~~~~~~~g~~~~A~~~~~~~~~-~~~~p~~~~~~~l~~~~~~~g~~~~A~~~~~~~  513 (595)
                      ..|..+.+--...|..+.|+..--.+.+ ..+-|....|..++.+-+....+...-+.|-++
T Consensus      1022 yHFmilAQrql~eg~v~~Al~Tal~L~DYEd~lpP~eiySllALaaca~raFGtCSKAfmkL 1083 (1189)
T KOG2041|consen 1022 YHFMILAQRQLFEGRVKDALQTALILSDYEDFLPPAEIYSLLALAACAVRAFGTCSKAFMKL 1083 (1189)
T ss_pred             HHHHHHHHHHHHhchHHHHHHHHhhhccHhhcCCHHHHHHHHHHHHhhhhhhhhhHHHHHHH
Confidence            3444444445556666666655444433 123455555555554444444444444433333

>PF09295 ChAPs: ChAPs (Chs5p-Arf1p-binding proteins); InterPro: IPR015374 ChAPs (Chs5p-Arf1p-binding proteins) are required for the export of specialised cargo from the Golgi

Probab=98.16  E-value=9.4e-05  Score=70.35  Aligned_cols=125  Identities=11%  Similarity=0.032  Sum_probs=80.1

Q ss_pred             HHHHHHHHHhcCChhHHHHHHHHHHhCCCCCCHHHHHHHHHHHHhcCCHhHHHHHHHHHHhcCCCCCHhhHHHHHHHHHh
Q 040027           99 YNILINCFCKIGRVSLGFIAFGRILRSCFTPNAATFNSLIKGLHAESRIMEAAALFTKLKAFGCEPNVITYNTLINGLCR  178 (595)
Q Consensus        99 ~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~~l~~~~~~  178 (595)
                      -..++..+...++++.|+.+++++.+..  |+  ....++..+...++-.+|++++.+..... +.+...+......+.+
T Consensus       172 v~~Ll~~l~~t~~~~~ai~lle~L~~~~--pe--v~~~LA~v~l~~~~E~~AI~ll~~aL~~~-p~d~~LL~~Qa~fLl~  246 (395)
T PF09295_consen  172 VDTLLKYLSLTQRYDEAIELLEKLRERD--PE--VAVLLARVYLLMNEEVEAIRLLNEALKEN-PQDSELLNLQAEFLLS  246 (395)
T ss_pred             HHHHHHHHhhcccHHHHHHHHHHHHhcC--Cc--HHHHHHHHHHhcCcHHHHHHHHHHHHHhC-CCCHHHHHHHHHHHHh
Confidence            3445556666677777777777777652  33  33446666666666677777777766542 3355555666666667


Q ss_pred             cCChhHHHHHHHHHHhcCCCCCccccCcHHHHHHHHHHHHHcCCHhHHHHHHHHHhh
Q 040027          179 TGHTMIALNLFEEMANGNGEIGVVCKPNTVTYSTIIDGLCKEGFVDKAKALFLQMKD  235 (595)
Q Consensus       179 ~g~~~~A~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~  235 (595)
                      .++++.|+++.+++....       |.+..+|..|..+|...|+++.|.-.++.+..
T Consensus       247 k~~~~lAL~iAk~av~ls-------P~~f~~W~~La~~Yi~~~d~e~ALlaLNs~Pm  296 (395)
T PF09295_consen  247 KKKYELALEIAKKAVELS-------PSEFETWYQLAECYIQLGDFENALLALNSCPM  296 (395)
T ss_pred             cCCHHHHHHHHHHHHHhC-------chhHHHHHHHHHHHHhcCCHHHHHHHHhcCcC
Confidence            777777777777777653       44556777777777777777777766666543

They physically interact with Chs3, Chs5 and the small GTPase Arf1, and they also form interactions with each other [].

>PF09295 ChAPs: ChAPs (Chs5p-Arf1p-binding proteins); InterPro: IPR015374 ChAPs (Chs5p-Arf1p-binding proteins) are required for the export of specialised cargo from the Golgi

Probab=98.15  E-value=0.00013  Score=69.32  Aligned_cols=126  Identities=15%  Similarity=0.164  Sum_probs=86.1

Q ss_pred             HHHHHHHHHHhCCCHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHccCCHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHH
Q 040027          349 SYNILINGYCKNKEVEEALSLYREMVSKGIKPTVVTYNTLFLGLFEIHQVEHALKLFDEMQRDGVAADTRTYTTFIDGLC  428 (595)
Q Consensus       349 ~~~~l~~~~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~  428 (595)
                      ....++..+...++++.|+.+++++.+..  |+  ....++..+...++..+|.+++.+.++. .+.+...+..-...+.
T Consensus       171 Lv~~Ll~~l~~t~~~~~ai~lle~L~~~~--pe--v~~~LA~v~l~~~~E~~AI~ll~~aL~~-~p~d~~LL~~Qa~fLl  245 (395)
T PF09295_consen  171 LVDTLLKYLSLTQRYDEAIELLEKLRERD--PE--VAVLLARVYLLMNEEVEAIRLLNEALKE-NPQDSELLNLQAEFLL  245 (395)
T ss_pred             HHHHHHHHHhhcccHHHHHHHHHHHHhcC--Cc--HHHHHHHHHHhcCcHHHHHHHHHHHHHh-CCCCHHHHHHHHHHHH
Confidence            33445555666677777777777777663  33  3344666666667777777777777754 2445666666666677


Q ss_pred             hcCCHHHHHHHHHHHHHcCCCcCHHHHHHHHHHHHhcCChHHHHHHHHhccc
Q 040027          429 KNGYIIEAVELFRTLRILKCELDIQAYNCLIDGLCKSGRLKFAWELFCSLPH  480 (595)
Q Consensus       429 ~~g~~~~A~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~  480 (595)
                      +.++++.|..+.+++.... |.+..+|..|+.+|...|+++.|+..++.+.-
T Consensus       246 ~k~~~~lAL~iAk~av~ls-P~~f~~W~~La~~Yi~~~d~e~ALlaLNs~Pm  296 (395)
T PF09295_consen  246 SKKKYELALEIAKKAVELS-PSEFETWYQLAECYIQLGDFENALLALNSCPM  296 (395)
T ss_pred             hcCCHHHHHHHHHHHHHhC-chhHHHHHHHHHHHHhcCCHHHHHHHHhcCcC
Confidence            7788888888888877764 55566788888888888888888877777653

They physically interact with Chs3, Chs5 and the small GTPase Arf1, and they also form interactions with each other [].

>KOG0550 consensus Molecular chaperone (DnaJ superfamily) [Posttranslational modification, protein turnover, chaperones]

Probab=98.13  E-value=0.0022  Score=59.15  Aligned_cols=90  Identities=17%  Similarity=0.090  Sum_probs=53.0

Q ss_pred             HHHhCCCHHHHHHHHHHHHHCC---CCCCHHHHHHHHHHHHccCCHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHhcCC
Q 040027          356 GYCKNKEVEEALSLYREMVSKG---IKPTVVTYNTLFLGLFEIHQVEHALKLFDEMQRDGVAADTRTYTTFIDGLCKNGY  432 (595)
Q Consensus       356 ~~~~~~~~~~A~~~~~~~~~~~---~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~  432 (595)
                      -..+.|++..|.+.|.+.+...   ..++...|.....+..+.|+..+|+.--+...+.+ +.=...+..-..++...++
T Consensus       258 ~~fk~G~y~~A~E~Yteal~idP~n~~~naklY~nra~v~~rLgrl~eaisdc~~Al~iD-~syikall~ra~c~l~le~  336 (486)
T KOG0550|consen  258 DAFKNGNYRKAYECYTEALNIDPSNKKTNAKLYGNRALVNIRLGRLREAISDCNEALKID-SSYIKALLRRANCHLALEK  336 (486)
T ss_pred             hHhhccchhHHHHHHHHhhcCCccccchhHHHHHHhHhhhcccCCchhhhhhhhhhhhcC-HHHHHHHHHHHHHHHHHHH
Confidence            3456677777777777776642   33444555555666677777777777766666431 0011222233344555677


Q ss_pred             HHHHHHHHHHHHHc
Q 040027          433 IIEAVELFRTLRIL  446 (595)
Q Consensus       433 ~~~A~~~~~~~~~~  446 (595)
                      +++|.+-++...+.
T Consensus       337 ~e~AV~d~~~a~q~  350 (486)
T KOG0550|consen  337 WEEAVEDYEKAMQL  350 (486)
T ss_pred             HHHHHHHHHHHHhh
Confidence            77777777777654

>PRK15363 pathogenicity island 2 chaperone protein SscA; Provisional

Probab=98.03  E-value=0.00028  Score=56.68  Aligned_cols=95  Identities=7%  Similarity=-0.112  Sum_probs=64.8

Q ss_pred             HHHHHHHHHHhcCChHHHHHHHHhcccCCCCC-CHHHHHHHHHHHHhcCChhHHHHHHHHHHHcCCCCCHHHHHHHHHHH
Q 040027          454 AYNCLIDGLCKSGRLKFAWELFCSLPHGVLVP-NVVTYNIMIQGLCNDGQMDKARDLFLDMEENAAAPDVITFDMLIHGF  532 (595)
Q Consensus       454 ~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~p-~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~~l~~~~  532 (595)
                      ..-.+...+...|++++|..+|+.+..  +.| +..-|..|..++-..|++++|+..|..+...+ +.|+..+..+..++
T Consensus        37 ~lY~~A~~ly~~G~l~~A~~~f~~L~~--~Dp~~~~y~~gLG~~~Q~~g~~~~AI~aY~~A~~L~-~ddp~~~~~ag~c~  113 (157)
T PRK15363         37 TLYRYAMQLMEVKEFAGAARLFQLLTI--YDAWSFDYWFRLGECCQAQKHWGEAIYAYGRAAQIK-IDAPQAPWAAAECY  113 (157)
T ss_pred             HHHHHHHHHHHCCCHHHHHHHHHHHHH--hCcccHHHHHHHHHHHHHHhhHHHHHHHHHHHHhcC-CCCchHHHHHHHHH
Confidence            334445555667777777777777766  344 35566677777777777777777777777765 45666777777777


Q ss_pred             HHcCChhHHHHHHHHHHHC
Q 040027          533 IRINEPSKVNELLHKMKEK  551 (595)
Q Consensus       533 ~~~g~~~~A~~~~~~~~~~  551 (595)
                      ...|+.+.|.+.|+..+..
T Consensus       114 L~lG~~~~A~~aF~~Ai~~  132 (157)
T PRK15363        114 LACDNVCYAIKALKAVVRI  132 (157)
T ss_pred             HHcCCHHHHHHHHHHHHHH
Confidence            7777777777777777653

>KOG0553 consensus TPR repeat-containing protein [General function prediction only]

Probab=98.02  E-value=5.6e-05  Score=66.55  Aligned_cols=98  Identities=19%  Similarity=0.145  Sum_probs=74.5

Q ss_pred             HHHHhcCCHHHHHHHHHHHHHcCCCcCHHHHHHHHHHHHhcCChHHHHHHHHhcccCCCCCC-HHHHHHHHHHHHhcCCh
Q 040027          425 DGLCKNGYIIEAVELFRTLRILKCELDIQAYNCLIDGLCKSGRLKFAWELFCSLPHGVLVPN-VVTYNIMIQGLCNDGQM  503 (595)
Q Consensus       425 ~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~p~-~~~~~~l~~~~~~~g~~  503 (595)
                      .-+.+.+++.+|+..|.++++.. +.|+..|..-..+|.+.|.++.|++-.+..+.  +.|+ ..+|..|..+|...|++
T Consensus        89 N~~m~~~~Y~eAv~kY~~AI~l~-P~nAVyycNRAAAy~~Lg~~~~AVkDce~Al~--iDp~yskay~RLG~A~~~~gk~  165 (304)
T KOG0553|consen   89 NKLMKNKDYQEAVDKYTEAIELD-PTNAVYYCNRAAAYSKLGEYEDAVKDCESALS--IDPHYSKAYGRLGLAYLALGKY  165 (304)
T ss_pred             HHHHHhhhHHHHHHHHHHHHhcC-CCcchHHHHHHHHHHHhcchHHHHHHHHHHHh--cChHHHHHHHHHHHHHHccCcH
Confidence            34567788888888888888776 66777777778888888888888888888777  5665 46788888888888888


Q ss_pred             hHHHHHHHHHHHcCCCCCHHHHHH
Q 040027          504 DKARDLFLDMEENAAAPDVITFDM  527 (595)
Q Consensus       504 ~~A~~~~~~~~~~~~~~~~~~~~~  527 (595)
                      ++|++.|++.++.  .|+..+|..
T Consensus       166 ~~A~~aykKaLel--dP~Ne~~K~  187 (304)
T KOG0553|consen  166 EEAIEAYKKALEL--DPDNESYKS  187 (304)
T ss_pred             HHHHHHHHhhhcc--CCCcHHHHH
Confidence            8888888888874  566555543

>COG4235 Cytochrome c biogenesis factor [Posttranslational modification, protein turnover, chaperones]

Probab=98.02  E-value=0.00047  Score=61.29  Aligned_cols=100  Identities=18%  Similarity=0.216  Sum_probs=81.7

Q ss_pred             CHHHHHHHHHHHHhcCChhHHHHHHHHHHhCCCCCCHHHHHHHHHHHHhc---CCHhHHHHHHHHHHhcCCCCCHhhHHH
Q 040027           95 NLYTYNILINCFCKIGRVSLGFIAFGRILRSCFTPNAATFNSLIKGLHAE---SRIMEAAALFTKLKAFGCEPNVITYNT  171 (595)
Q Consensus        95 ~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~~l~~~~~~~---g~~~~A~~~~~~~~~~~~~~~~~~~~~  171 (595)
                      |+..|-.|..+|...|++..|...|.++.+.. ++++..+..+..++...   ....++..+|+++...+ +-|..+...
T Consensus       155 d~egW~~Lg~~ym~~~~~~~A~~AY~~A~rL~-g~n~~~~~g~aeaL~~~a~~~~ta~a~~ll~~al~~D-~~~iral~l  232 (287)
T COG4235         155 DAEGWDLLGRAYMALGRASDALLAYRNALRLA-GDNPEILLGLAEALYYQAGQQMTAKARALLRQALALD-PANIRALSL  232 (287)
T ss_pred             CchhHHHHHHHHHHhcchhHHHHHHHHHHHhC-CCCHHHHHHHHHHHHHhcCCcccHHHHHHHHHHHhcC-CccHHHHHH
Confidence            77778888888999999999999999999885 56777777777776543   34467889999999875 337788888


Q ss_pred             HHHHHHhcCChhHHHHHHHHHHhcC
Q 040027          172 LINGLCRTGHTMIALNLFEEMANGN  196 (595)
Q Consensus       172 l~~~~~~~g~~~~A~~~~~~~~~~~  196 (595)
                      |...+...|++.+|...++.|.+..
T Consensus       233 LA~~afe~g~~~~A~~~Wq~lL~~l  257 (287)
T COG4235         233 LAFAAFEQGDYAEAAAAWQMLLDLL  257 (287)
T ss_pred             HHHHHHHcccHHHHHHHHHHHHhcC
Confidence            8888999999999999999999875

>TIGR02795 tol_pal_ybgF tol-pal system protein YbgF

Probab=98.00  E-value=0.00025  Score=56.04  Aligned_cols=100  Identities=15%  Similarity=0.013  Sum_probs=82.3

Q ss_pred             HHHHHHHHHHHhcCChhHHHHHHHHHHhCCCC--CCHHHHHHHHHHHHhcCCHhHHHHHHHHHHhcCCC--CCHhhHHHH
Q 040027           97 YTYNILINCFCKIGRVSLGFIAFGRILRSCFT--PNAATFNSLIKGLHAESRIMEAAALFTKLKAFGCE--PNVITYNTL  172 (595)
Q Consensus        97 ~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~--~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~--~~~~~~~~l  172 (595)
                      .++..++..+.+.|++++|...|+.+......  .....+..+...+.+.|++++|.+.|+.+......  ....++..+
T Consensus         3 ~~~~~~~~~~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~~~p~~~~~~~~~~~~   82 (119)
T TIGR02795         3 EAYYDAALLVLKAGDYADAIQAFQAFLKKYPKSTYAPNAHYWLGEAYYAQGKYADAAKAFLAVVKKYPKSPKAPDALLKL   82 (119)
T ss_pred             HHHHHHHHHHHHcCCHHHHHHHHHHHHHHCCCccccHHHHHHHHHHHHhhccHHHHHHHHHHHHHHCCCCCcccHHHHHH
Confidence            45677888899999999999999999986421  12456777889999999999999999999876322  125668888


Q ss_pred             HHHHHhcCChhHHHHHHHHHHhcC
Q 040027          173 INGLCRTGHTMIALNLFEEMANGN  196 (595)
Q Consensus       173 ~~~~~~~g~~~~A~~~~~~~~~~~  196 (595)
                      ..++...|++++|...++++....
T Consensus        83 ~~~~~~~~~~~~A~~~~~~~~~~~  106 (119)
T TIGR02795        83 GMSLQELGDKEKAKATLQQVIKRY  106 (119)
T ss_pred             HHHHHHhCChHHHHHHHHHHHHHC
Confidence            899999999999999999999875

Members of this protein family are the product of one of seven genes regularly clustered in operons to encode the proteins of the tol-pal system, which is critical for maintaining the integrity of the bacterial outer membrane. The gene for this periplasmic protein has been designated orf2 and ybgF. All members of the seed alignment were from unique tol-pal gene regions from completed bacterial genomes. The architecture of this protein is a signal sequence, a low-complexity region usually rich in Asn and Gln, a well-conserved region with tandem repeats that resemble the tetratricopeptide (TPR) repeat, involved in protein-protein interaction.

>PF07079 DUF1347: Protein of unknown function (DUF1347); InterPro: IPR010764 This family consists of several hypothetical bacterial proteins of around 610 residues in length

Probab=97.99  E-value=0.015  Score=54.63  Aligned_cols=128  Identities=16%  Similarity=0.145  Sum_probs=76.8

Q ss_pred             HHhcCC-HHHHHHHHHHHHHcCCCcCHHHHHHHHH----HHHh---cCChHHHHHHHHhcccCCCCCC----HHHHHHHH
Q 040027          427 LCKNGY-IIEAVELFRTLRILKCELDIQAYNCLID----GLCK---SGRLKFAWELFCSLPHGVLVPN----VVTYNIMI  494 (595)
Q Consensus       427 ~~~~g~-~~~A~~~~~~~~~~~~~~~~~~~~~l~~----~~~~---~g~~~~A~~~~~~~~~~~~~p~----~~~~~~l~  494 (595)
                      +-+.|. -++|..+++.+++.. +-|...-+.+..    +|..   ...+..-..+-+-+.+.|+.|-    ...-|-|.
T Consensus       389 lW~~g~~dekalnLLk~il~ft-~yD~ec~n~v~~fvKq~Y~qaLs~~~~~rLlkLe~fi~e~gl~~i~i~e~eian~La  467 (549)
T PF07079_consen  389 LWEIGQCDEKALNLLKLILQFT-NYDIECENIVFLFVKQAYKQALSMHAIPRLLKLEDFITEVGLTPITISEEEIANFLA  467 (549)
T ss_pred             HHhcCCccHHHHHHHHHHHHhc-cccHHHHHHHHHHHHHHHHHHHhhhhHHHHHHHHHHHHhcCCCcccccHHHHHHHHH
Confidence            344454 677777777777643 334443333222    2221   1223333344344445556552    33444444


Q ss_pred             HH--HHhcCChhHHHHHHHHHHHcCCCCCHHHHHHHHHHHHHcCChhHHHHHHHHHHHCCCCCCHHHHHH
Q 040027          495 QG--LCNDGQMDKARDLFLDMEENAAAPDVITFDMLIHGFIRINEPSKVNELLHKMKEKKVMPDASIVSI  562 (595)
Q Consensus       495 ~~--~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~p~~~~~~~  562 (595)
                      .+  +..+|++.++.-.-.-..+  +.|++.+|..++-++....+|++|..++..+     +|+..+++.
T Consensus       468 DAEyLysqgey~kc~~ys~WL~~--iaPS~~~~RLlGl~l~e~k~Y~eA~~~l~~L-----P~n~~~~ds  530 (549)
T PF07079_consen  468 DAEYLYSQGEYHKCYLYSSWLTK--IAPSPQAYRLLGLCLMENKRYQEAWEYLQKL-----PPNERMRDS  530 (549)
T ss_pred             HHHHHHhcccHHHHHHHHHHHHH--hCCcHHHHHHHHHHHHHHhhHHHHHHHHHhC-----CCchhhHHH
Confidence            33  4468888888776666655  5788899998888888899999999988765     456555554

Members of this family are highly conserved and seem to be specific to Chlamydia species. The function of this family is unknown.

>TIGR02795 tol_pal_ybgF tol-pal system protein YbgF

Probab=97.98  E-value=0.00027  Score=55.82  Aligned_cols=95  Identities=14%  Similarity=0.112  Sum_probs=47.9

Q ss_pred             HHHHHHHHHhcCChHHHHHHHHhcccCCCCCC----HHHHHHHHHHHHhcCChhHHHHHHHHHHHcCCC--CCHHHHHHH
Q 040027          455 YNCLIDGLCKSGRLKFAWELFCSLPHGVLVPN----VVTYNIMIQGLCNDGQMDKARDLFLDMEENAAA--PDVITFDML  528 (595)
Q Consensus       455 ~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~p~----~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~--~~~~~~~~l  528 (595)
                      +..++..+.+.|++++|...|+.+...  .|+    ...+..++.++...|++++|...|+++......  ....++..+
T Consensus         5 ~~~~~~~~~~~~~~~~A~~~~~~~~~~--~~~~~~~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~~~p~~~~~~~~~~~~   82 (119)
T TIGR02795         5 YYDAALLVLKAGDYADAIQAFQAFLKK--YPKSTYAPNAHYWLGEAYYAQGKYADAAKAFLAVVKKYPKSPKAPDALLKL   82 (119)
T ss_pred             HHHHHHHHHHcCCHHHHHHHHHHHHHH--CCCccccHHHHHHHHHHHHhhccHHHHHHHHHHHHHHCCCCCcccHHHHHH
Confidence            344444555555555555555555442  121    233444555555556666666666655543211  113344555


Q ss_pred             HHHHHHcCChhHHHHHHHHHHHC
Q 040027          529 IHGFIRINEPSKVNELLHKMKEK  551 (595)
Q Consensus       529 ~~~~~~~g~~~~A~~~~~~~~~~  551 (595)
                      +.++...|++++|.+.++++.+.
T Consensus        83 ~~~~~~~~~~~~A~~~~~~~~~~  105 (119)
T TIGR02795        83 GMSLQELGDKEKAKATLQQVIKR  105 (119)
T ss_pred             HHHHHHhCChHHHHHHHHHHHHH
Confidence            55555566666666666665553

Members of this protein family are the product of one of seven genes regularly clustered in operons to encode the proteins of the tol-pal system, which is critical for maintaining the integrity of the bacterial outer membrane. The gene for this periplasmic protein has been designated orf2 and ybgF. All members of the seed alignment were from unique tol-pal gene regions from completed bacterial genomes. The architecture of this protein is a signal sequence, a low-complexity region usually rich in Asn and Gln, a well-conserved region with tandem repeats that resemble the tetratricopeptide (TPR) repeat, involved in protein-protein interaction.

>PF12895 Apc3: Anaphase-promoting complex, cyclosome, subunit 3; PDB: 3KAE_D 3Q4A_B 2C2L_D 3Q47_B 3Q49_B 2XPI_A 3ULQ_A

Probab=97.98  E-value=1.1e-05  Score=58.95  Aligned_cols=81  Identities=15%  Similarity=0.148  Sum_probs=40.7

Q ss_pred             cCChHHHHHHHHhcccCCC-CCCHHHHHHHHHHHHhcCChhHHHHHHHHHHHcCCCCCHHHHHHHHHHHHHcCChhHHHH
Q 040027          465 SGRLKFAWELFCSLPHGVL-VPNVVTYNIMIQGLCNDGQMDKARDLFLDMEENAAAPDVITFDMLIHGFIRINEPSKVNE  543 (595)
Q Consensus       465 ~g~~~~A~~~~~~~~~~~~-~p~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~  543 (595)
                      .|+++.|+.+++++.+... .++...+..++.+|.+.|++++|..++++ .+.+ +.+......++.+|...|++++|++
T Consensus         2 ~~~y~~Ai~~~~k~~~~~~~~~~~~~~~~la~~~~~~~~y~~A~~~~~~-~~~~-~~~~~~~~l~a~~~~~l~~y~eAi~   79 (84)
T PF12895_consen    2 QGNYENAIKYYEKLLELDPTNPNSAYLYNLAQCYFQQGKYEEAIELLQK-LKLD-PSNPDIHYLLARCLLKLGKYEEAIK   79 (84)
T ss_dssp             TT-HHHHHHHHHHHHHHHCGTHHHHHHHHHHHHHHHTTHHHHHHHHHHC-HTHH-HCHHHHHHHHHHHHHHTT-HHHHHH
T ss_pred             CccHHHHHHHHHHHHHHCCCChhHHHHHHHHHHHHHCCCHHHHHHHHHH-hCCC-CCCHHHHHHHHHHHHHhCCHHHHHH
Confidence            3556666666666655211 01233444456666666666666666655 2221 1122333444666666666666666


Q ss_pred             HHHH
Q 040027          544 LLHK  547 (595)
Q Consensus       544 ~~~~  547 (595)
                      ++++
T Consensus        80 ~l~~   83 (84)
T PF12895_consen   80 ALEK   83 (84)
T ss_dssp             HHHH
T ss_pred             HHhc
Confidence            6654

>PRK10866 outer membrane biogenesis protein BamD; Provisional

Probab=97.97  E-value=0.0011  Score=59.54  Aligned_cols=179  Identities=15%  Similarity=0.035  Sum_probs=103.8

Q ss_pred             ccccccCCCChHHHHHHHHHHHHhCCCCCCHhhHHHHHHHHHcCCCchhHHhhCCCCCCHHHHHHHHHHHHhcCChhHHH
Q 040027           37 TREGDINVITPNEAFCIFDYMLRMHPSPPPVSSFNILLASLAKNKHYDTRLNATGLFPNLYTYNILINCFCKIGRVSLGF  116 (595)
Q Consensus        37 ~~~~~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~  116 (595)
                      .+..+...|++++|++.|+.++...|.  ++..-..                          ...++.++.+.++++.|+
T Consensus        38 ~A~~~~~~g~y~~Ai~~f~~l~~~yP~--s~~a~~a--------------------------~l~la~ayy~~~~y~~A~   89 (243)
T PRK10866         38 TAQQKLQDGNWKQAITQLEALDNRYPF--GPYSQQV--------------------------QLDLIYAYYKNADLPLAQ   89 (243)
T ss_pred             HHHHHHHCCCHHHHHHHHHHHHHhCCC--ChHHHHH--------------------------HHHHHHHHHhcCCHHHHH
Confidence            345557789999999999999999998  4433322                          225777888999999999


Q ss_pred             HHHHHHHhCCCCCCHHHHHHHHHHHHh--c---------------CC---HhHHHHHHHHHHhcCCCCCHhhHHHHHHHH
Q 040027          117 IAFGRILRSCFTPNAATFNSLIKGLHA--E---------------SR---IMEAAALFTKLKAFGCEPNVITYNTLINGL  176 (595)
Q Consensus       117 ~~~~~~~~~~~~~~~~~~~~l~~~~~~--~---------------g~---~~~A~~~~~~~~~~~~~~~~~~~~~l~~~~  176 (595)
                      ..+++.++..+......+...+.+++.  .               .+   ...|++.|+.+++.  -|+.          
T Consensus        90 ~~~e~fi~~~P~~~~~~~a~Y~~g~~~~~~~~~~~~~~~~~~~~~rD~~~~~~A~~~~~~li~~--yP~S----------  157 (243)
T PRK10866         90 AAIDRFIRLNPTHPNIDYVLYMRGLTNMALDDSALQGFFGVDRSDRDPQHARAAFRDFSKLVRG--YPNS----------  157 (243)
T ss_pred             HHHHHHHHhCcCCCchHHHHHHHHHhhhhcchhhhhhccCCCccccCHHHHHHHHHHHHHHHHH--CcCC----------
Confidence            999999988543323333333333221  1               11   23455566666654  2332          


Q ss_pred             HhcCChhHHHHHHHHHHhcCCCCCccccCcHHHHHHHHHHHHHcCCHhHHHHHHHHHhhC--CCCCCHhHHHHHHHHHHh
Q 040027          177 CRTGHTMIALNLFEEMANGNGEIGVVCKPNTVTYSTIIDGLCKEGFVDKAKALFLQMKDE--NINPDVVTYNSLIHGLCH  254 (595)
Q Consensus       177 ~~~g~~~~A~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~--~~~~~~~~~~~ll~~~~~  254 (595)
                         .-..+|...+..+...-          ...-..+...|.+.|.+..|..-++.+.+.  +.+........+..+|..
T Consensus       158 ---~ya~~A~~rl~~l~~~l----------a~~e~~ia~~Y~~~~~y~AA~~r~~~v~~~Yp~t~~~~eal~~l~~ay~~  224 (243)
T PRK10866        158 ---QYTTDATKRLVFLKDRL----------AKYELSVAEYYTKRGAYVAVVNRVEQMLRDYPDTQATRDALPLMENAYRQ  224 (243)
T ss_pred             ---hhHHHHHHHHHHHHHHH----------HHHHHHHHHHHHHcCchHHHHHHHHHHHHHCCCCchHHHHHHHHHHHHHH
Confidence               22233333333332210          111124455566666666666666666553  444455566666666777


Q ss_pred             cCCHHHHHHHHHHH
Q 040027          255 ANDWNEAKRLFIEM  268 (595)
Q Consensus       255 ~~~~~~A~~~~~~~  268 (595)
                      .|..++|..+...+
T Consensus       225 lg~~~~a~~~~~~l  238 (243)
T PRK10866        225 LQLNAQADKVAKII  238 (243)
T ss_pred             cCChHHHHHHHHHH
Confidence            77766666655444

>PRK15363 pathogenicity island 2 chaperone protein SscA; Provisional

Probab=97.97  E-value=0.00046  Score=55.47  Aligned_cols=101  Identities=8%  Similarity=-0.090  Sum_probs=87.7

Q ss_pred             CCHHHHHHHHHHHHhcCChhHHHHHHHHHHhCCCCCCHHHHHHHHHHHHhcCCHhHHHHHHHHHHhcCCCCCHhhHHHHH
Q 040027           94 PNLYTYNILINCFCKIGRVSLGFIAFGRILRSCFTPNAATFNSLIKGLHAESRIMEAAALFTKLKAFGCEPNVITYNTLI  173 (595)
Q Consensus        94 ~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~~l~  173 (595)
                      .+....-.+...+...|++++|..+|+.+.... +.+..-|..|..++-..|++++|+..|.......+ -|+..+..+.
T Consensus        33 ~~l~~lY~~A~~ly~~G~l~~A~~~f~~L~~~D-p~~~~y~~gLG~~~Q~~g~~~~AI~aY~~A~~L~~-ddp~~~~~ag  110 (157)
T PRK15363         33 QPLNTLYRYAMQLMEVKEFAGAARLFQLLTIYD-AWSFDYWFRLGECCQAQKHWGEAIYAYGRAAQIKI-DAPQAPWAAA  110 (157)
T ss_pred             HHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHhC-cccHHHHHHHHHHHHHHhhHHHHHHHHHHHHhcCC-CCchHHHHHH
Confidence            344556667778889999999999999999885 44677788888889999999999999999999874 4889999999


Q ss_pred             HHHHhcCChhHHHHHHHHHHhcC
Q 040027          174 NGLCRTGHTMIALNLFEEMANGN  196 (595)
Q Consensus       174 ~~~~~~g~~~~A~~~~~~~~~~~  196 (595)
                      .++...|+.+.|.+.|+..+..-
T Consensus       111 ~c~L~lG~~~~A~~aF~~Ai~~~  133 (157)
T PRK15363        111 ECYLACDNVCYAIKALKAVVRIC  133 (157)
T ss_pred             HHHHHcCCHHHHHHHHHHHHHHh
Confidence            99999999999999999988754

>cd00189 TPR Tetratricopeptide repeat domain; typically contains 34 amino acids [WLF]-X(2)-[LIM]-[GAS]-X(2)-[YLF]-X(8)-[ASE]-X(3)-[FYL]-X(2)-[ASL]-X(4)-[PKE] is the consensus sequence; found in a variety of organisms including bacteria, cyanobacteria, yeast, fungi, plants, and humans in various subcellular locations; involved in a variety of functions including protein-protein interactions, but common features in the interaction partners have not been defined; involved in chaperone, cell-cycle, transciption, and protein transport complexes; the number of TPR motifs varies among proteins (1,3-11,13 15,16,19); 5-6 tandem repeats generate a right-handed helical structure with an amphipathic channel that is thought to accomodate an alpha-helix of a target protein; it has been proposed that TPR proteins preferably interact with WD-40 repeat proteins, but in many instances several TPR-proteins seem to aggregate to multi-protein complexes; examples of TPR-proteins include, Cdc16p, Cdc23p and C

Probab=97.93  E-value=0.00018  Score=54.13  Aligned_cols=93  Identities=16%  Similarity=0.099  Sum_probs=58.7

Q ss_pred             HHHHHHHHHhcCChHHHHHHHHhcccCCCCC-CHHHHHHHHHHHHhcCChhHHHHHHHHHHHcCCCCCHHHHHHHHHHHH
Q 040027          455 YNCLIDGLCKSGRLKFAWELFCSLPHGVLVP-NVVTYNIMIQGLCNDGQMDKARDLFLDMEENAAAPDVITFDMLIHGFI  533 (595)
Q Consensus       455 ~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~p-~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~~l~~~~~  533 (595)
                      +..++..+...|++++|...++++.+.  .| +...+..+...+...|++++|.+.+++..+.. +.+..++..++..+.
T Consensus         3 ~~~~a~~~~~~~~~~~A~~~~~~~~~~--~~~~~~~~~~~~~~~~~~~~~~~a~~~~~~~~~~~-~~~~~~~~~~~~~~~   79 (100)
T cd00189           3 LLNLGNLYYKLGDYDEALEYYEKALEL--DPDNADAYYNLAAAYYKLGKYEEALEDYEKALELD-PDNAKAYYNLGLAYY   79 (100)
T ss_pred             HHHHHHHHHHHhcHHHHHHHHHHHHhc--CCccHHHHHHHHHHHHHHHHHHHHHHHHHHHHhCC-CcchhHHHHHHHHHH
Confidence            344555566667777777777666552  23 23556666666667777777777777766653 334456666666777


Q ss_pred             HcCChhHHHHHHHHHHH
Q 040027          534 RINEPSKVNELLHKMKE  550 (595)
Q Consensus       534 ~~g~~~~A~~~~~~~~~  550 (595)
                      ..|++++|...+++..+
T Consensus        80 ~~~~~~~a~~~~~~~~~   96 (100)
T cd00189          80 KLGKYEEALEAYEKALE   96 (100)
T ss_pred             HHHhHHHHHHHHHHHHc
Confidence            77777777777776654

>CHL00033 ycf3 photosystem I assembly protein Ycf3

Probab=97.92  E-value=0.00021  Score=60.48  Aligned_cols=121  Identities=8%  Similarity=-0.065  Sum_probs=72.1

Q ss_pred             HHHHHHHHHHHHhcCChHHHHHHHHhcccCCCCC--CHHHHHHHHHHHHhcCChhHHHHHHHHHHHcCCCCCHHHHHHHH
Q 040027          452 IQAYNCLIDGLCKSGRLKFAWELFCSLPHGVLVP--NVVTYNIMIQGLCNDGQMDKARDLFLDMEENAAAPDVITFDMLI  529 (595)
Q Consensus       452 ~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~p--~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~~l~  529 (595)
                      ...+..++..+...|++++|+..|++.......|  ...+|..+..++...|++++|+..++++.... +.....+..+.
T Consensus        35 a~~~~~~g~~~~~~g~~~~A~~~~~~al~l~~~~~~~~~~~~~lg~~~~~~g~~~eA~~~~~~Al~~~-~~~~~~~~~la  113 (168)
T CHL00033         35 AFTYYRDGMSAQSEGEYAEALQNYYEAMRLEIDPYDRSYILYNIGLIHTSNGEHTKALEYYFQALERN-PFLPQALNNMA  113 (168)
T ss_pred             HHHHHHHHHHHHHcCCHHHHHHHHHHHHhccccchhhHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhC-cCcHHHHHHHH
Confidence            4455666666777777777777777776532121  13467777777888888888888888877653 33345555566


Q ss_pred             HHHH-------HcCChhHHHHHHHHHHHC---CCCCCHHHHHHHHHHHHhcCcc
Q 040027          530 HGFI-------RINEPSKVNELLHKMKEK---KVMPDASIVSIVVDLLVKNEIS  573 (595)
Q Consensus       530 ~~~~-------~~g~~~~A~~~~~~~~~~---~~~p~~~~~~~l~~~~~~~g~~  573 (595)
                      ..+.       ..|++++|...+++....   .+..++..+..+...+...|++
T Consensus       114 ~i~~~~~~~~~~~g~~~~A~~~~~~a~~~~~~a~~~~p~~~~~~~~~~~~~~~~  167 (168)
T CHL00033        114 VICHYRGEQAIEQGDSEIAEAWFDQAAEYWKQAIALAPGNYIEAQNWLKITGRF  167 (168)
T ss_pred             HHHHHhhHHHHHcccHHHHHHHHHHHHHHHHHHHHhCcccHHHHHHHHHHhcCC
Confidence            6665       677777555555544311   1223443344444555555554

>KOG2041 consensus WD40 repeat protein [General function prediction only]

Probab=97.92  E-value=0.029  Score=55.61  Aligned_cols=205  Identities=13%  Similarity=0.105  Sum_probs=120.9

Q ss_pred             CCCHHHHHHHHHHHHhcCCHhHHHHHHHHHHhcCCCCCHhhHHHHHH----------HHHhcCChhHHHHHHHHHHhcCC
Q 040027          128 TPNAATFNSLIKGLHAESRIMEAAALFTKLKAFGCEPNVITYNTLIN----------GLCRTGHTMIALNLFEEMANGNG  197 (595)
Q Consensus       128 ~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~~l~~----------~~~~~g~~~~A~~~~~~~~~~~~  197 (595)
                      .|.+..|..+.....+.-.++-|...|-+....   +.......|-.          .-.--|++++|.+++-.+-+++ 
T Consensus       689 nPHprLWrllAe~Al~Kl~l~tAE~AFVrc~dY---~Gik~vkrl~~i~s~~~q~aei~~~~g~feeaek~yld~drrD-  764 (1189)
T KOG2041|consen  689 NPHPRLWRLLAEYALFKLALDTAEHAFVRCGDY---AGIKLVKRLRTIHSKEQQRAEISAFYGEFEEAEKLYLDADRRD-  764 (1189)
T ss_pred             CCchHHHHHHHHHHHHHHhhhhHhhhhhhhccc---cchhHHHHhhhhhhHHHHhHhHhhhhcchhHhhhhhhccchhh-
Confidence            678889998888887777888888777665432   12211111111          1122477777777776665432 


Q ss_pred             CCCccccCcHHHHHHHHHHHHHcCCHhHHHHHHHHHhhC-CCCCCHhHHHHHHHHHHhcCCHHHHHHHHHHHHHCCCCCC
Q 040027          198 EIGVVCKPNTVTYSTIIDGLCKEGFVDKAKALFLQMKDE-NINPDVVTYNSLIHGLCHANDWNEAKRLFIEMMDQGVQPS  276 (595)
Q Consensus       198 ~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~-~~~~~~~~~~~ll~~~~~~~~~~~A~~~~~~~~~~~~~~~  276 (595)
                                    ..+..+.+.||+-...++++.--.. .-..-...|+.+...+.....|++|.+.|..-..      
T Consensus       765 --------------LAielr~klgDwfrV~qL~r~g~~d~dD~~~e~A~r~ig~~fa~~~~We~A~~yY~~~~~------  824 (1189)
T KOG2041|consen  765 --------------LAIELRKKLGDWFRVYQLIRNGGSDDDDEGKEDAFRNIGETFAEMMEWEEAAKYYSYCGD------  824 (1189)
T ss_pred             --------------hhHHHHHhhhhHHHHHHHHHccCCCcchHHHHHHHHHHHHHHHHHHHHHHHHHHHHhccc------
Confidence                          3456666777777776666542211 0011245677788888888888888887765422      


Q ss_pred             HhhHHHHHHHHHhcCChHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHhcCCCCCHHHHHHHHHH
Q 040027          277 VVTFNVIMDELCKNRKMDEASRLLDLMVQRGVRPNACTYNTLMDGFCLMGKINRAEELFGSMESMGCKHDDVSYNILING  356 (595)
Q Consensus       277 ~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~  356 (595)
                         ....+.++.+..++++-..+...+     +.+....-.+..++.+.|.-++|.+.+-+..    .|     ...+..
T Consensus       825 ---~e~~~ecly~le~f~~LE~la~~L-----pe~s~llp~~a~mf~svGMC~qAV~a~Lr~s----~p-----kaAv~t  887 (1189)
T KOG2041|consen  825 ---TENQIECLYRLELFGELEVLARTL-----PEDSELLPVMADMFTSVGMCDQAVEAYLRRS----LP-----KAAVHT  887 (1189)
T ss_pred             ---hHhHHHHHHHHHhhhhHHHHHHhc-----CcccchHHHHHHHHHhhchHHHHHHHHHhcc----Cc-----HHHHHH
Confidence               123455666666666555444433     3345556667777777787777776654321    11     123455


Q ss_pred             HHhCCCHHHHHHHHHHH
Q 040027          357 YCKNKEVEEALSLYREM  373 (595)
Q Consensus       357 ~~~~~~~~~A~~~~~~~  373 (595)
                      |...++|.+|.++-++.
T Consensus       888 Cv~LnQW~~avelaq~~  904 (1189)
T KOG2041|consen  888 CVELNQWGEAVELAQRF  904 (1189)
T ss_pred             HHHHHHHHHHHHHHHhc
Confidence            66677777777766543

>KOG0553 consensus TPR repeat-containing protein [General function prediction only]

Probab=97.90  E-value=0.00042  Score=61.20  Aligned_cols=153  Identities=16%  Similarity=0.067  Sum_probs=110.6

Q ss_pred             HHHHHccCCHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCcCHHHHHHHHHHHHhcCCh
Q 040027          389 FLGLFEIHQVEHALKLFDEMQRDGVAADTRTYTTFIDGLCKNGYIIEAVELFRTLRILKCELDIQAYNCLIDGLCKSGRL  468 (595)
Q Consensus       389 ~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~  468 (595)
                      ..-+.+.+++.+|+..|.++++.. +.+...|..-..+|.+.|.++.|++-.+..+..+ +-...+|..|..+|...|++
T Consensus        88 GN~~m~~~~Y~eAv~kY~~AI~l~-P~nAVyycNRAAAy~~Lg~~~~AVkDce~Al~iD-p~yskay~RLG~A~~~~gk~  165 (304)
T KOG0553|consen   88 GNKLMKNKDYQEAVDKYTEAIELD-PTNAVYYCNRAAAYSKLGEYEDAVKDCESALSID-PHYSKAYGRLGLAYLALGKY  165 (304)
T ss_pred             HHHHHHhhhHHHHHHHHHHHHhcC-CCcchHHHHHHHHHHHhcchHHHHHHHHHHHhcC-hHHHHHHHHHHHHHHccCcH
Confidence            344678899999999999999974 6677888889999999999999999999999875 55678999999999999999


Q ss_pred             HHHHHHHHhcccCCCCCCHHHHHHHH-HHHHhcCChh---HHHHHHHHHHHcCCCCCHHHHHHHHHHHHHcCChhHHHHH
Q 040027          469 KFAWELFCSLPHGVLVPNVVTYNIMI-QGLCNDGQMD---KARDLFLDMEENAAAPDVITFDMLIHGFIRINEPSKVNEL  544 (595)
Q Consensus       469 ~~A~~~~~~~~~~~~~p~~~~~~~l~-~~~~~~g~~~---~A~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~  544 (595)
                      ++|++.|++.++  +.|+..+|-.=+ .+-.+.+...   .+..-++.....|..|+......     ...-.......+
T Consensus       166 ~~A~~aykKaLe--ldP~Ne~~K~nL~~Ae~~l~e~~~~~~~~~~~d~~~~ig~~Pd~~s~~~-----~~l~nnp~l~~~  238 (304)
T KOG0553|consen  166 EEAIEAYKKALE--LDPDNESYKSNLKIAEQKLNEPKSSAQASGSFDMAGLIGAFPDSRSMFN-----GDLMNNPQLMQL  238 (304)
T ss_pred             HHHHHHHHhhhc--cCCCcHHHHHHHHHHHHHhcCCCcccccccchhhhhhccCCccchhhhc-----cccccCHHHHHH
Confidence            999999999999  889877664433 3333344433   44444555445554455433221     122233444555


Q ss_pred             HHHHHH
Q 040027          545 LHKMKE  550 (595)
Q Consensus       545 ~~~~~~  550 (595)
                      ...|..
T Consensus       239 ~~~m~~  244 (304)
T KOG0553|consen  239 ASQMMK  244 (304)
T ss_pred             HHHHhh
Confidence            555654

>COG4700 Uncharacterized protein conserved in bacteria containing a divergent form of TPR repeats [Function unknown]

Probab=97.89  E-value=0.0056  Score=50.06  Aligned_cols=128  Identities=14%  Similarity=0.033  Sum_probs=65.3

Q ss_pred             CCHHHHHHHHHHHHhcCCHhHHHHHHHHHHhcCCCCCHhhHHHHHHHHHhcCChhHHHHHHHHHHhcCCCCCccccCcHH
Q 040027          129 PNAATFNSLIKGLHAESRIMEAAALFTKLKAFGCEPNVITYNTLINGLCRTGHTMIALNLFEEMANGNGEIGVVCKPNTV  208 (595)
Q Consensus       129 ~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~~~~  208 (595)
                      |.+..-..+..++...|+..+|...|++...--+.-|......+..+....+++..|...++++.+.+.     ...++.
T Consensus        87 pTvqnr~rLa~al~elGr~~EA~~hy~qalsG~fA~d~a~lLglA~Aqfa~~~~A~a~~tLe~l~e~~p-----a~r~pd  161 (251)
T COG4700          87 PTVQNRYRLANALAELGRYHEAVPHYQQALSGIFAHDAAMLLGLAQAQFAIQEFAAAQQTLEDLMEYNP-----AFRSPD  161 (251)
T ss_pred             hhHHHHHHHHHHHHHhhhhhhhHHHHHHHhccccCCCHHHHHHHHHHHHhhccHHHHHHHHHHHhhcCC-----ccCCCC
Confidence            344444455555666666666666666655433334555555555666666666666666666555431     111233


Q ss_pred             HHHHHHHHHHHcCCHhHHHHHHHHHhhCCCCCCHhHHHHHHHHHHhcCCHHHHHH
Q 040027          209 TYSTIIDGLCKEGFVDKAKALFLQMKDENINPDVVTYNSLIHGLCHANDWNEAKR  263 (595)
Q Consensus       209 ~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~~ll~~~~~~~~~~~A~~  263 (595)
                      ....+.+.+...|...+|+..|+.....  -|+...-..-...+.++|+.+++..
T Consensus       162 ~~Ll~aR~laa~g~~a~Aesafe~a~~~--ypg~~ar~~Y~e~La~qgr~~ea~a  214 (251)
T COG4700         162 GHLLFARTLAAQGKYADAESAFEVAISY--YPGPQARIYYAEMLAKQGRLREANA  214 (251)
T ss_pred             chHHHHHHHHhcCCchhHHHHHHHHHHh--CCCHHHHHHHHHHHHHhcchhHHHH
Confidence            3444555556666666666666655553  2333333333334445554444433

>PRK10866 outer membrane biogenesis protein BamD; Provisional

Probab=97.88  E-value=0.0042  Score=55.75  Aligned_cols=66  Identities=8%  Similarity=-0.077  Sum_probs=41.4

Q ss_pred             CHHHHHHHHHHHHhcCChhHHHHHHHHHHhCCCCCCHHH---HHHHHHHHHhcCCHhHHHHHHHHHHhcC
Q 040027           95 NLYTYNILINCFCKIGRVSLGFIAFGRILRSCFTPNAAT---FNSLIKGLHAESRIMEAAALFTKLKAFG  161 (595)
Q Consensus        95 ~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~---~~~l~~~~~~~g~~~~A~~~~~~~~~~~  161 (595)
                      ++..+-.....+...|++++|+..|+.+...-+. +...   ...++.++.+.+++++|+..+++..+..
T Consensus        31 ~~~~~Y~~A~~~~~~g~y~~Ai~~f~~l~~~yP~-s~~a~~a~l~la~ayy~~~~y~~A~~~~e~fi~~~   99 (243)
T PRK10866         31 PPSEIYATAQQKLQDGNWKQAITQLEALDNRYPF-GPYSQQVQLDLIYAYYKNADLPLAQAAIDRFIRLN   99 (243)
T ss_pred             CHHHHHHHHHHHHHCCCHHHHHHHHHHHHHhCCC-ChHHHHHHHHHHHHHHhcCCHHHHHHHHHHHHHhC
Confidence            4444444555666677888888888877776321 2222   2345566677777777777777777663

>PLN03088 SGT1, suppressor of G2 allele of SKP1; Provisional

Probab=97.88  E-value=0.00036  Score=66.79  Aligned_cols=90  Identities=13%  Similarity=-0.023  Sum_probs=55.8

Q ss_pred             HHHHHhcCCHHHHHHHHHHHHHcCCCcCHHHHHHHHHHHHhcCChHHHHHHHHhcccCCCCC-CHHHHHHHHHHHHhcCC
Q 040027          424 IDGLCKNGYIIEAVELFRTLRILKCELDIQAYNCLIDGLCKSGRLKFAWELFCSLPHGVLVP-NVVTYNIMIQGLCNDGQ  502 (595)
Q Consensus       424 ~~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~p-~~~~~~~l~~~~~~~g~  502 (595)
                      ...+...|++++|+..|+++++.. +.+...+..+..+|...|++++|+..+++++.  +.| +...|..+..+|...|+
T Consensus         9 a~~a~~~~~~~~Ai~~~~~Al~~~-P~~~~a~~~~a~~~~~~g~~~eAl~~~~~Al~--l~P~~~~a~~~lg~~~~~lg~   85 (356)
T PLN03088          9 AKEAFVDDDFALAVDLYTQAIDLD-PNNAELYADRAQANIKLGNFTEAVADANKAIE--LDPSLAKAYLRKGTACMKLEE   85 (356)
T ss_pred             HHHHHHcCCHHHHHHHHHHHHHhC-CCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHH--hCcCCHHHHHHHHHHHHHhCC
Confidence            344455666666666666666654 44566666666666666666666666666665  334 34556666666666666


Q ss_pred             hhHHHHHHHHHHHc
Q 040027          503 MDKARDLFLDMEEN  516 (595)
Q Consensus       503 ~~~A~~~~~~~~~~  516 (595)
                      +++|+..|+++++.
T Consensus        86 ~~eA~~~~~~al~l   99 (356)
T PLN03088         86 YQTAKAALEKGASL   99 (356)
T ss_pred             HHHHHHHHHHHHHh
Confidence            66666666666664

>COG4700 Uncharacterized protein conserved in bacteria containing a divergent form of TPR repeats [Function unknown]

Probab=97.87  E-value=0.0037  Score=51.07  Aligned_cols=137  Identities=18%  Similarity=0.184  Sum_probs=111.1

Q ss_pred             hCCCCCCHHHHHHHHHHHHhcCChhHHHHHHHHHHhCCCCCCHHHHHHHHHHHHhcCCHhHHHHHHHHHHhcCCC-CCHh
Q 040027           89 ATGLFPNLYTYNILINCFCKIGRVSLGFIAFGRILRSCFTPNAATFNSLIKGLHAESRIMEAAALFTKLKAFGCE-PNVI  167 (595)
Q Consensus        89 ~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~-~~~~  167 (595)
                      .....|++.....|..+....|++.+|...|++...--+..|......+.++....+++..|...++++-+.... .++.
T Consensus        82 ~~~~ApTvqnr~rLa~al~elGr~~EA~~hy~qalsG~fA~d~a~lLglA~Aqfa~~~~A~a~~tLe~l~e~~pa~r~pd  161 (251)
T COG4700          82 ELAIAPTVQNRYRLANALAELGRYHEAVPHYQQALSGIFAHDAAMLLGLAQAQFAIQEFAAAQQTLEDLMEYNPAFRSPD  161 (251)
T ss_pred             HHhhchhHHHHHHHHHHHHHhhhhhhhHHHHHHHhccccCCCHHHHHHHHHHHHhhccHHHHHHHHHHHhhcCCccCCCC
Confidence            344568888889999999999999999999999998767788999999999999999999999999998876321 2345


Q ss_pred             hHHHHHHHHHhcCChhHHHHHHHHHHhcCCCCCccccCcHHHHHHHHHHHHHcCCHhHHHHHHHHH
Q 040027          168 TYNTLINGLCRTGHTMIALNLFEEMANGNGEIGVVCKPNTVTYSTIIDGLCKEGFVDKAKALFLQM  233 (595)
Q Consensus       168 ~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~  233 (595)
                      ....+.+.+...|+.+.|...|+.....-        |+..........+.++|+.+++..-+..+
T Consensus       162 ~~Ll~aR~laa~g~~a~Aesafe~a~~~y--------pg~~ar~~Y~e~La~qgr~~ea~aq~~~v  219 (251)
T COG4700         162 GHLLFARTLAAQGKYADAESAFEVAISYY--------PGPQARIYYAEMLAKQGRLREANAQYVAV  219 (251)
T ss_pred             chHHHHHHHHhcCCchhHHHHHHHHHHhC--------CCHHHHHHHHHHHHHhcchhHHHHHHHHH
Confidence            56778899999999999999999999854        66666566667778888777665544443

>PRK02603 photosystem I assembly protein Ycf3; Provisional

Probab=97.87  E-value=0.00076  Score=57.28  Aligned_cols=83  Identities=16%  Similarity=0.045  Sum_probs=39.4

Q ss_pred             HHHHHHHHHhcCCHHHHHHHHHHHHHcCCCcC--HHHHHHHHHHHHhcCChHHHHHHHHhcccCCCCC-CHHHHHHHHHH
Q 040027          420 YTTFIDGLCKNGYIIEAVELFRTLRILKCELD--IQAYNCLIDGLCKSGRLKFAWELFCSLPHGVLVP-NVVTYNIMIQG  496 (595)
Q Consensus       420 ~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~~--~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~p-~~~~~~~l~~~  496 (595)
                      +..+...+...|++++|...++++.+....+.  ...+..++.++.+.|++++|...+++..+  ..| +...+..+..+
T Consensus        38 ~~~lg~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~la~~~~~~g~~~~A~~~~~~al~--~~p~~~~~~~~lg~~  115 (172)
T PRK02603         38 YYRDGMSAQADGEYAEALENYEEALKLEEDPNDRSYILYNMGIIYASNGEHDKALEYYHQALE--LNPKQPSALNNIAVI  115 (172)
T ss_pred             HHHHHHHHHHcCCHHHHHHHHHHHHHHhhccchHHHHHHHHHHHHHHcCCHHHHHHHHHHHHH--hCcccHHHHHHHHHH
Confidence            44444455555555555555555554321111  23445555555555555555555555554  222 23344444444


Q ss_pred             HHhcCChh
Q 040027          497 LCNDGQMD  504 (595)
Q Consensus       497 ~~~~g~~~  504 (595)
                      +...|+..
T Consensus       116 ~~~~g~~~  123 (172)
T PRK02603        116 YHKRGEKA  123 (172)
T ss_pred             HHHcCChH
Confidence            44444433

>PF12895 Apc3: Anaphase-promoting complex, cyclosome, subunit 3; PDB: 3KAE_D 3Q4A_B 2C2L_D 3Q47_B 3Q49_B 2XPI_A 3ULQ_A

Probab=97.85  E-value=5e-05  Score=55.46  Aligned_cols=47  Identities=19%  Similarity=0.244  Sum_probs=20.1

Q ss_pred             CCHhHHHHHHHHHHhcCCC-CCHhhHHHHHHHHHhcCChhHHHHHHHH
Q 040027          145 SRIMEAAALFTKLKAFGCE-PNVITYNTLINGLCRTGHTMIALNLFEE  191 (595)
Q Consensus       145 g~~~~A~~~~~~~~~~~~~-~~~~~~~~l~~~~~~~g~~~~A~~~~~~  191 (595)
                      |+++.|+.+++++...... ++...+..+..++.+.|++++|+.++++
T Consensus         3 ~~y~~Ai~~~~k~~~~~~~~~~~~~~~~la~~~~~~~~y~~A~~~~~~   50 (84)
T PF12895_consen    3 GNYENAIKYYEKLLELDPTNPNSAYLYNLAQCYFQQGKYEEAIELLQK   50 (84)
T ss_dssp             T-HHHHHHHHHHHHHHHCGTHHHHHHHHHHHHHHHTTHHHHHHHHHHC
T ss_pred             ccHHHHHHHHHHHHHHCCCChhHHHHHHHHHHHHHCCCHHHHHHHHHH
Confidence            4444455555444444211 1223333344445555555555555544

>cd00189 TPR Tetratricopeptide repeat domain; typically contains 34 amino acids [WLF]-X(2)-[LIM]-[GAS]-X(2)-[YLF]-X(8)-[ASE]-X(3)-[FYL]-X(2)-[ASL]-X(4)-[PKE] is the consensus sequence; found in a variety of organisms including bacteria, cyanobacteria, yeast, fungi, plants, and humans in various subcellular locations; involved in a variety of functions including protein-protein interactions, but common features in the interaction partners have not been defined; involved in chaperone, cell-cycle, transciption, and protein transport complexes; the number of TPR motifs varies among proteins (1,3-11,13 15,16,19); 5-6 tandem repeats generate a right-handed helical structure with an amphipathic channel that is thought to accomodate an alpha-helix of a target protein; it has been proposed that TPR proteins preferably interact with WD-40 repeat proteins, but in many instances several TPR-proteins seem to aggregate to multi-protein complexes; examples of TPR-proteins include, Cdc16p, Cdc23p and C

Probab=97.84  E-value=0.00032  Score=52.68  Aligned_cols=97  Identities=19%  Similarity=0.170  Sum_probs=81.7

Q ss_pred             HHHHHHHHHHhcCChhHHHHHHHHHHhCCCCCCHHHHHHHHHHHHhcCCHhHHHHHHHHHHhcCCCCCHhhHHHHHHHHH
Q 040027           98 TYNILINCFCKIGRVSLGFIAFGRILRSCFTPNAATFNSLIKGLHAESRIMEAAALFTKLKAFGCEPNVITYNTLINGLC  177 (595)
Q Consensus        98 ~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~~l~~~~~  177 (595)
                      .+..++..+...|++++|...++++.+.. +.+...+..+...+...|++++|.+.++...... +.+..++..+...+.
T Consensus         2 ~~~~~a~~~~~~~~~~~A~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~a~~~~~~~~~~~-~~~~~~~~~~~~~~~   79 (100)
T cd00189           2 ALLNLGNLYYKLGDYDEALEYYEKALELD-PDNADAYYNLAAAYYKLGKYEEALEDYEKALELD-PDNAKAYYNLGLAYY   79 (100)
T ss_pred             HHHHHHHHHHHHhcHHHHHHHHHHHHhcC-CccHHHHHHHHHHHHHHHHHHHHHHHHHHHHhCC-CcchhHHHHHHHHHH
Confidence            35667788889999999999999998874 4455778888899999999999999999998875 335578888899999


Q ss_pred             hcCChhHHHHHHHHHHhcC
Q 040027          178 RTGHTMIALNLFEEMANGN  196 (595)
Q Consensus       178 ~~g~~~~A~~~~~~~~~~~  196 (595)
                      ..|+++.|...++......
T Consensus        80 ~~~~~~~a~~~~~~~~~~~   98 (100)
T cd00189          80 KLGKYEEALEAYEKALELD   98 (100)
T ss_pred             HHHhHHHHHHHHHHHHccC
Confidence            9999999999999887643

>PLN03088 SGT1, suppressor of G2 allele of SKP1; Provisional

Probab=97.83  E-value=0.00068  Score=64.89  Aligned_cols=94  Identities=12%  Similarity=-0.064  Sum_probs=83.5

Q ss_pred             HHHHHHHhcCChhHHHHHHHHHHhCCCCCCHHHHHHHHHHHHhcCCHhHHHHHHHHHHhcCCCCCHhhHHHHHHHHHhcC
Q 040027          101 ILINCFCKIGRVSLGFIAFGRILRSCFTPNAATFNSLIKGLHAESRIMEAAALFTKLKAFGCEPNVITYNTLINGLCRTG  180 (595)
Q Consensus       101 ~l~~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g  180 (595)
                      .-+..+...|++++|+..|+++++.. +.+...|..+..+|...|++++|+..+++++... +.+...|..+..+|...|
T Consensus         7 ~~a~~a~~~~~~~~Ai~~~~~Al~~~-P~~~~a~~~~a~~~~~~g~~~eAl~~~~~Al~l~-P~~~~a~~~lg~~~~~lg   84 (356)
T PLN03088          7 DKAKEAFVDDDFALAVDLYTQAIDLD-PNNAELYADRAQANIKLGNFTEAVADANKAIELD-PSLAKAYLRKGTACMKLE   84 (356)
T ss_pred             HHHHHHHHcCCHHHHHHHHHHHHHhC-CCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhC-cCCHHHHHHHHHHHHHhC
Confidence            34566778899999999999999985 5578889999999999999999999999999885 347788999999999999


Q ss_pred             ChhHHHHHHHHHHhcC
Q 040027          181 HTMIALNLFEEMANGN  196 (595)
Q Consensus       181 ~~~~A~~~~~~~~~~~  196 (595)
                      ++++|+..|++....+
T Consensus        85 ~~~eA~~~~~~al~l~  100 (356)
T PLN03088         85 EYQTAKAALEKGASLA  100 (356)
T ss_pred             CHHHHHHHHHHHHHhC
Confidence            9999999999999875

>PF10037 MRP-S27: Mitochondrial 28S ribosomal protein S27; InterPro: IPR019266 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms

Probab=97.81  E-value=0.00038  Score=66.62  Aligned_cols=120  Identities=13%  Similarity=0.058  Sum_probs=66.3

Q ss_pred             CCCHHHHHHHHHHHHccCCHHHHHHHHHHHHHC--CCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCcCHHHHH
Q 040027          379 KPTVVTYNTLFLGLFEIHQVEHALKLFDEMQRD--GVAADTRTYTTFIDGLCKNGYIIEAVELFRTLRILKCELDIQAYN  456 (595)
Q Consensus       379 ~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~--~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~  456 (595)
                      +.+......++..+....+.+.+..++-+....  ....-+.+..++++.|...|..+.++.+++.=...|+-||..+++
T Consensus        63 ~vS~~dld~fvn~~~~~~~~d~~~~~L~k~R~s~~~~~~~~~t~ha~vR~~l~~~~~~~~l~~L~n~~~yGiF~D~~s~n  142 (429)
T PF10037_consen   63 PVSSLDLDIFVNNVESKDDLDEVEDVLYKFRHSPNCSYLLPSTHHALVRQCLELGAEDELLELLKNRLQYGIFPDNFSFN  142 (429)
T ss_pred             CCcHHHHHHHHhhcCCHhHHHHHHHHHHHHHcCcccccccCccHHHHHHHHHhcCCHHHHHHHHhChhhcccCCChhhHH
Confidence            334555555556555556666666666555543  111112233466666666666666666666666666666666666


Q ss_pred             HHHHHHHhcCChHHHHHHHHhcccCCCCCCHHHHHHHHHHHH
Q 040027          457 CLIDGLCKSGRLKFAWELFCSLPHGVLVPNVVTYNIMIQGLC  498 (595)
Q Consensus       457 ~l~~~~~~~g~~~~A~~~~~~~~~~~~~p~~~~~~~l~~~~~  498 (595)
                      .+++.+.+.|++..|.++...|...+...+..|+.-.+.+|.
T Consensus       143 ~Lmd~fl~~~~~~~A~~V~~~~~lQe~~~~~~t~~L~l~~~~  184 (429)
T PF10037_consen  143 LLMDHFLKKGNYKSAAKVATEMMLQEEFDNPSTQALALYSCY  184 (429)
T ss_pred             HHHHHHhhcccHHHHHHHHHHHHHhhccCCchHHHHHHHHHH
Confidence            666666666666666666665554443344444433333333

The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites [, ]. About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits. Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome [, ]. This entry represents a family of small ribosomal proteins possessing one of three conserved sequence blocks found in proteins that stimulate the dissociation of guanine nucleotides from G-proteins. This leaves open the possibility that they may be functional partners of GTP-binding ribosomal proteins [].

>COG4235 Cytochrome c biogenesis factor [Posttranslational modification, protein turnover, chaperones]

Probab=97.78  E-value=0.0014  Score=58.48  Aligned_cols=102  Identities=12%  Similarity=0.037  Sum_probs=74.6

Q ss_pred             CcCHHHHHHHHHHHHhcCChHHHHHHHHhcccCCCCCCHHHHHHHHHHHHhc---CChhHHHHHHHHHHHcCCCCCHHHH
Q 040027          449 ELDIQAYNCLIDGLCKSGRLKFAWELFCSLPHGVLVPNVVTYNIMIQGLCND---GQMDKARDLFLDMEENAAAPDVITF  525 (595)
Q Consensus       449 ~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~p~~~~~~~l~~~~~~~---g~~~~A~~~~~~~~~~~~~~~~~~~  525 (595)
                      +.|...|..|..+|...|+++.|...|.+..+. ..+|+..+..+..++...   .+..++..+|++++..+ +-|..+.
T Consensus       153 P~d~egW~~Lg~~ym~~~~~~~A~~AY~~A~rL-~g~n~~~~~g~aeaL~~~a~~~~ta~a~~ll~~al~~D-~~~iral  230 (287)
T COG4235         153 PGDAEGWDLLGRAYMALGRASDALLAYRNALRL-AGDNPEILLGLAEALYYQAGQQMTAKARALLRQALALD-PANIRAL  230 (287)
T ss_pred             CCCchhHHHHHHHHHHhcchhHHHHHHHHHHHh-CCCCHHHHHHHHHHHHHhcCCcccHHHHHHHHHHHhcC-CccHHHH
Confidence            667888888888888888888888888888773 223466666666665532   24557788888888765 5566777


Q ss_pred             HHHHHHHHHcCChhHHHHHHHHHHHCC
Q 040027          526 DMLIHGFIRINEPSKVNELLHKMKEKK  552 (595)
Q Consensus       526 ~~l~~~~~~~g~~~~A~~~~~~~~~~~  552 (595)
                      ..|...+...|++.+|...|+.|++..
T Consensus       231 ~lLA~~afe~g~~~~A~~~Wq~lL~~l  257 (287)
T COG4235         231 SLLAFAAFEQGDYAEAAAAWQMLLDLL  257 (287)
T ss_pred             HHHHHHHHHcccHHHHHHHHHHHHhcC
Confidence            777888888888888888888888753

>TIGR00756 PPR pentatricopeptide repeat domain (PPR motif)

Probab=97.77  E-value=5.4e-05  Score=44.34  Aligned_cols=33  Identities=45%  Similarity=0.902  Sum_probs=18.3

Q ss_pred             HHHHHHHHHHhcCChhHHHHHHHHHHHcCCCCC
Q 040027          489 TYNIMIQGLCNDGQMDKARDLFLDMEENAAAPD  521 (595)
Q Consensus       489 ~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~~  521 (595)
                      +|+.++.+|++.|++++|.++|++|.+.|+.||
T Consensus         2 ~~n~li~~~~~~~~~~~a~~~~~~M~~~g~~p~   34 (35)
T TIGR00756         2 TYNTLIDGLCKAGRVEEALELFKEMLERGIEPD   34 (35)
T ss_pred             cHHHHHHHHHHCCCHHHHHHHHHHHHHcCCCCC
Confidence            455555555555555555555555555555554

This family has a similar consensus to the TPR domain (tetratricopeptide), pfam pfam00515, a 33-residue repeat. It is predicted to form a pair of antiparallel helices similar to that of TPR.

>COG5107 RNA14 Pre-mRNA 3'-end processing (cleavage and polyadenylation) factor [RNA processing and modification]

Probab=97.76  E-value=0.038  Score=51.95  Aligned_cols=129  Identities=17%  Similarity=0.162  Sum_probs=83.1

Q ss_pred             HHHHHHHHHHHhcCCHHHHHHHHHHHHHcC-CCcCHHHHHHHHHHHHhcCChHHHHHHHHhcccCCCCCCHHH-HHHHHH
Q 040027          418 RTYTTFIDGLCKNGYIIEAVELFRTLRILK-CELDIQAYNCLIDGLCKSGRLKFAWELFCSLPHGVLVPNVVT-YNIMIQ  495 (595)
Q Consensus       418 ~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~-~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~p~~~~-~~~l~~  495 (595)
                      ..|...+.+..+...++.|..+|.++.+.+ +.+++.++++++..+ ..|+...|..+|+-=...  -||... .+..+.
T Consensus       398 ~v~C~~~N~v~r~~Gl~aaR~~F~k~rk~~~~~h~vyi~~A~~E~~-~~~d~~ta~~ifelGl~~--f~d~~~y~~kyl~  474 (660)
T COG5107         398 FVFCVHLNYVLRKRGLEAARKLFIKLRKEGIVGHHVYIYCAFIEYY-ATGDRATAYNIFELGLLK--FPDSTLYKEKYLL  474 (660)
T ss_pred             hHHHHHHHHHHHHhhHHHHHHHHHHHhccCCCCcceeeeHHHHHHH-hcCCcchHHHHHHHHHHh--CCCchHHHHHHHH
Confidence            344555565566666777788887777766 456666777777654 367777777777764442  344433 345555


Q ss_pred             HHHhcCChhHHHHHHHHHHHcCCCCC--HHHHHHHHHHHHHcCChhHHHHHHHHHHH
Q 040027          496 GLCNDGQMDKARDLFLDMEENAAAPD--VITFDMLIHGFIRINEPSKVNELLHKMKE  550 (595)
Q Consensus       496 ~~~~~g~~~~A~~~~~~~~~~~~~~~--~~~~~~l~~~~~~~g~~~~A~~~~~~~~~  550 (595)
                      .+...++-+.|..+|+..+.. +..+  ..+|..++.-=..-|+...+..+=++|.+
T Consensus       475 fLi~inde~naraLFetsv~r-~~~~q~k~iy~kmi~YEs~~G~lN~v~sLe~rf~e  530 (660)
T COG5107         475 FLIRINDEENARALFETSVER-LEKTQLKRIYDKMIEYESMVGSLNNVYSLEERFRE  530 (660)
T ss_pred             HHHHhCcHHHHHHHHHHhHHH-HHHhhhhHHHHHHHHHHHhhcchHHHHhHHHHHHH
Confidence            666777777777777766553 2223  45677777766677777777777777765

>PRK10153 DNA-binding transcriptional activator CadC; Provisional

Probab=97.75  E-value=0.0025  Score=63.84  Aligned_cols=142  Identities=10%  Similarity=-0.039  Sum_probs=78.5

Q ss_pred             CCCHHHHHHHHHHHHh--c---CCHHHHHHHHHHHHHcCCCcCHHHHHHHHHHHHhc--------CChHHHHHHHHhccc
Q 040027          414 AADTRTYTTFIDGLCK--N---GYIIEAVELFRTLRILKCELDIQAYNCLIDGLCKS--------GRLKFAWELFCSLPH  480 (595)
Q Consensus       414 ~~~~~~~~~l~~~~~~--~---g~~~~A~~~~~~~~~~~~~~~~~~~~~l~~~~~~~--------g~~~~A~~~~~~~~~  480 (595)
                      +.+...|..++++...  .   +....|..+|+++++.. |.....+..+..++...        .+...+.+...+...
T Consensus       334 ~~~~~Ay~~~lrg~~~~~~~~~~~~~~A~~lle~Ai~ld-P~~a~a~A~la~~~~~~~~~~~~~~~~l~~a~~~~~~a~a  412 (517)
T PRK10153        334 PHQGAALTLFYQAHHYLNSGDAKSLNKASDLLEEILKSE-PDFTYAQAEKALADIVRHSQQPLDEKQLAALSTELDNIVA  412 (517)
T ss_pred             CCCHHHHHHHHHHHHHHhcCCHHHHHHHHHHHHHHHHhC-CCcHHHHHHHHHHHHHHHhcCCccHHHHHHHHHHHHHhhh
Confidence            4455555555554322  1   22556666666666553 33344444433333221        112333444444333


Q ss_pred             CC-CCCCHHHHHHHHHHHHhcCChhHHHHHHHHHHHcCCCCCHHHHHHHHHHHHHcCChhHHHHHHHHHHHCCCCCCHHH
Q 040027          481 GV-LVPNVVTYNIMIQGLCNDGQMDKARDLFLDMEENAAAPDVITFDMLIHGFIRINEPSKVNELLHKMKEKKVMPDASI  559 (595)
Q Consensus       481 ~~-~~p~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~p~~~~  559 (595)
                      .. ...+...+..+.......|++++|...++++++.+  |+...|..++.++...|+.++|...++++...  .|...+
T Consensus       413 l~~~~~~~~~~~ala~~~~~~g~~~~A~~~l~rAl~L~--ps~~a~~~lG~~~~~~G~~~eA~~~~~~A~~L--~P~~pt  488 (517)
T PRK10153        413 LPELNVLPRIYEILAVQALVKGKTDEAYQAINKAIDLE--MSWLNYVLLGKVYELKGDNRLAADAYSTAFNL--RPGENT  488 (517)
T ss_pred             cccCcCChHHHHHHHHHHHhcCCHHHHHHHHHHHHHcC--CCHHHHHHHHHHHHHcCCHHHHHHHHHHHHhc--CCCCch
Confidence            11 12234566666666666777788888777777754  56677777777777778888887777777763  354334


Q ss_pred             H
Q 040027          560 V  560 (595)
Q Consensus       560 ~  560 (595)
                      |
T Consensus       489 ~  489 (517)
T PRK10153        489 L  489 (517)
T ss_pred             H
Confidence            3

>PF05843 Suf: Suppressor of forked protein (Suf); InterPro: IPR008847 This domain consists of several eukaryotic suppressor of forked (Suf) like proteins

Probab=97.75  E-value=0.0013  Score=60.52  Aligned_cols=129  Identities=12%  Similarity=0.097  Sum_probs=62.1

Q ss_pred             HHHHHHHHHHhcCCHhHHHHHHHHHHhcCCCCCHhhHHHHHHHHHh-cCChhHHHHHHHHHHhcCCCCCccccCcHHHHH
Q 040027          133 TFNSLIKGLHAESRIMEAAALFTKLKAFGCEPNVITYNTLINGLCR-TGHTMIALNLFEEMANGNGEIGVVCKPNTVTYS  211 (595)
Q Consensus       133 ~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~~l~~~~~~-~g~~~~A~~~~~~~~~~~~~~~~~~~~~~~~~~  211 (595)
                      +|..++....+.+..+.|.++|.+..+.+ ..+..+|...+..-.. .++.+.|.++|+...+.       ++.+...|.
T Consensus         3 v~i~~m~~~~r~~g~~~aR~vF~~a~~~~-~~~~~vy~~~A~~E~~~~~d~~~A~~Ife~glk~-------f~~~~~~~~   74 (280)
T PF05843_consen    3 VWIQYMRFMRRTEGIEAARKVFKRARKDK-RCTYHVYVAYALMEYYCNKDPKRARKIFERGLKK-------FPSDPDFWL   74 (280)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHCCC-CS-THHHHHHHHHHHHTCS-HHHHHHHHHHHHHH-------HTT-HHHHH
T ss_pred             HHHHHHHHHHHhCChHHHHHHHHHHHcCC-CCCHHHHHHHHHHHHHhCCCHHHHHHHHHHHHHH-------CCCCHHHHH
Confidence            34445555555555555555555554321 2233334433333222 34444466666655554       244555555


Q ss_pred             HHHHHHHHcCCHhHHHHHHHHHhhCCCCCC---HhHHHHHHHHHHhcCCHHHHHHHHHHHHH
Q 040027          212 TIIDGLCKEGFVDKAKALFLQMKDENINPD---VVTYNSLIHGLCHANDWNEAKRLFIEMMD  270 (595)
Q Consensus       212 ~l~~~~~~~g~~~~A~~~~~~~~~~~~~~~---~~~~~~ll~~~~~~~~~~~A~~~~~~~~~  270 (595)
                      ..+..+...|+.+.|..+|++.... +.++   ...|...+..-.+.|+.+.+..+.+.+.+
T Consensus        75 ~Y~~~l~~~~d~~~aR~lfer~i~~-l~~~~~~~~iw~~~i~fE~~~Gdl~~v~~v~~R~~~  135 (280)
T PF05843_consen   75 EYLDFLIKLNDINNARALFERAISS-LPKEKQSKKIWKKFIEFESKYGDLESVRKVEKRAEE  135 (280)
T ss_dssp             HHHHHHHHTT-HHHHHHHHHHHCCT-SSCHHHCHHHHHHHHHHHHHHS-HHHHHHHHHHHHH
T ss_pred             HHHHHHHHhCcHHHHHHHHHHHHHh-cCchhHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHH
Confidence            5555555666666666666665543 1111   12555555555555666655555555554

The Drosophila melanogaster suppressor of forked [Su(f)] protein shares homology with the Saccharomyces cerevisiae RNA14 protein and the 77 kDa subunit of Homo sapiens cleavage stimulation factor, which are proteins involved in mRNA 3' end formation. This suggests a role for Su(f) in mRNA 3' end formation in Drosophila. The su(f) gene produces three transcripts; two of them are polyadenylated at the end of the transcription unit, and one is a truncated transcript, polyadenylated in intron 4. It is thought that su(f) plays a role in the regulation of poly(A) site utilisation and the GU-rich sequence is important for this regulation to occur [].; GO: 0006397 mRNA processing, 0005634 nucleus; PDB: 2L9B_B 2OND_B 2OOE_A 4E85_B 4EBA_C 4E6H_A 2UY1_B.

>COG3898 Uncharacterized membrane-bound protein [Function unknown]

Probab=97.74  E-value=0.036  Score=51.14  Aligned_cols=254  Identities=15%  Similarity=0.093  Sum_probs=148.9

Q ss_pred             HhcCChHHHHHHHHHHHHCCCCCCHHH--HHHHHHHHHhcCCHHHHHHHHHHHHhcCCCCCHHHHHHHHHHHHhCCCHHH
Q 040027          288 CKNRKMDEASRLLDLMVQRGVRPNACT--YNTLMDGFCLMGKINRAEELFGSMESMGCKHDDVSYNILINGYCKNKEVEE  365 (595)
Q Consensus       288 ~~~g~~~~a~~~~~~~~~~~~~~~~~~--~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~  365 (595)
                      .-.|+++.|.+-|+.|...   |....  +..|.-...+.|+.+.|..+-+.....- +.-...+...+...+..|+|+.
T Consensus       131 l~eG~~~~Ar~kfeAMl~d---PEtRllGLRgLyleAqr~GareaAr~yAe~Aa~~A-p~l~WA~~AtLe~r~~~gdWd~  206 (531)
T COG3898         131 LLEGDYEDARKKFEAMLDD---PETRLLGLRGLYLEAQRLGAREAARHYAERAAEKA-PQLPWAARATLEARCAAGDWDG  206 (531)
T ss_pred             HhcCchHHHHHHHHHHhcC---hHHHHHhHHHHHHHHHhcccHHHHHHHHHHHHhhc-cCCchHHHHHHHHHHhcCChHH
Confidence            3456666666666666642   11111  1112222235666777776666665542 3334566667777777777777


Q ss_pred             HHHHHHHHHHCC-CCCCHHH--HHHHHHHH---HccCCHHHHHHHHHHHHHCCCCCCHH-HHHHHHHHHHhcCCHHHHHH
Q 040027          366 ALSLYREMVSKG-IKPTVVT--YNTLFLGL---FEIHQVEHALKLFDEMQRDGVAADTR-TYTTFIDGLCKNGYIIEAVE  438 (595)
Q Consensus       366 A~~~~~~~~~~~-~~~~~~~--~~~l~~~~---~~~~~~~~a~~~~~~~~~~~~~~~~~-~~~~l~~~~~~~g~~~~A~~  438 (595)
                      |+++++.-.... +.++..-  -..|+.+-   .-..+...|...-.+..+.  .|+.. .-.....++.+.|+..++-.
T Consensus       207 AlkLvd~~~~~~vie~~~aeR~rAvLLtAkA~s~ldadp~~Ar~~A~~a~KL--~pdlvPaav~AAralf~d~~~rKg~~  284 (531)
T COG3898         207 ALKLVDAQRAAKVIEKDVAERSRAVLLTAKAMSLLDADPASARDDALEANKL--APDLVPAAVVAARALFRDGNLRKGSK  284 (531)
T ss_pred             HHHHHHHHHHHHhhchhhHHHHHHHHHHHHHHHHhcCChHHHHHHHHHHhhc--CCccchHHHHHHHHHHhccchhhhhh
Confidence            777776655432 2222211  11121111   1123455565555555543  44432 22334567889999999999


Q ss_pred             HHHHHHHcCCCcCHHHHHHHHHHHHhcCChHHHHHHHHhccc-CCCCCC-HHHHHHHHHHHHhcCChhHHHHHHHHHHHc
Q 040027          439 LFRTLRILKCELDIQAYNCLIDGLCKSGRLKFAWELFCSLPH-GVLVPN-VVTYNIMIQGLCNDGQMDKARDLFLDMEEN  516 (595)
Q Consensus       439 ~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~-~~~~p~-~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~  516 (595)
                      +++.+-+.  .|.+.++..+  .+.+.|+  .+..-+++... ..++|| ..+...+..+-...|++..|..--+.... 
T Consensus       285 ilE~aWK~--ePHP~ia~lY--~~ar~gd--ta~dRlkRa~~L~slk~nnaes~~~va~aAlda~e~~~ARa~Aeaa~r-  357 (531)
T COG3898         285 ILETAWKA--EPHPDIALLY--VRARSGD--TALDRLKRAKKLESLKPNNAESSLAVAEAALDAGEFSAARAKAEAAAR-  357 (531)
T ss_pred             HHHHHHhc--CCChHHHHHH--HHhcCCC--cHHHHHHHHHHHHhcCccchHHHHHHHHHHHhccchHHHHHHHHHHhh-
Confidence            99999876  4555544332  2334454  33333333322 114555 56667777888889999988887777766 


Q ss_pred             CCCCCHHHHHHHHHHHHHc-CChhHHHHHHHHHHHCCCCC
Q 040027          517 AAAPDVITFDMLIHGFIRI-NEPSKVNELLHKMKEKKVMP  555 (595)
Q Consensus       517 ~~~~~~~~~~~l~~~~~~~-g~~~~A~~~~~~~~~~~~~p  555 (595)
                       ..|....|..+.+.-... |+-.++..++-+.++..-.|
T Consensus       358 -~~pres~~lLlAdIeeAetGDqg~vR~wlAqav~APrdP  396 (531)
T COG3898         358 -EAPRESAYLLLADIEEAETGDQGKVRQWLAQAVKAPRDP  396 (531)
T ss_pred             -hCchhhHHHHHHHHHhhccCchHHHHHHHHHHhcCCCCC
Confidence             368888888887776554 99999999999998654344

>TIGR00756 PPR pentatricopeptide repeat domain (PPR motif)

Probab=97.73  E-value=6.8e-05  Score=43.91  Aligned_cols=33  Identities=30%  Similarity=0.573  Sum_probs=31.8

Q ss_pred             HHHHHHHHHHHcCChhHHHHHHHHHHHCCCCCC
Q 040027          524 TFDMLIHGFIRINEPSKVNELLHKMKEKKVMPD  556 (595)
Q Consensus       524 ~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~p~  556 (595)
                      +|+.++.+|++.|++++|.++|++|.+.|+.||
T Consensus         2 ~~n~li~~~~~~~~~~~a~~~~~~M~~~g~~p~   34 (35)
T TIGR00756         2 TYNTLIDGLCKAGRVEEALELFKEMLERGIEPD   34 (35)
T ss_pred             cHHHHHHHHHHCCCHHHHHHHHHHHHHcCCCCC
Confidence            689999999999999999999999999999997

This family has a similar consensus to the TPR domain (tetratricopeptide), pfam pfam00515, a 33-residue repeat. It is predicted to form a pair of antiparallel helices similar to that of TPR.

>PRK02603 photosystem I assembly protein Ycf3; Provisional

Probab=97.73  E-value=0.0022  Score=54.43  Aligned_cols=91  Identities=14%  Similarity=0.072  Sum_probs=60.5

Q ss_pred             HHHHHHHHHHHHhcCCHhHHHHHHHHHHhcCCCCC--HhhHHHHHHHHHhcCChhHHHHHHHHHHhcCCCCCccccCcHH
Q 040027          131 AATFNSLIKGLHAESRIMEAAALFTKLKAFGCEPN--VITYNTLINGLCRTGHTMIALNLFEEMANGNGEIGVVCKPNTV  208 (595)
Q Consensus       131 ~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~~--~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~~~~  208 (595)
                      ...+..+...+...|++++|...|++..+....+.  ...+..+...+...|++++|+..+++..+..       +.+..
T Consensus        35 a~~~~~lg~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~la~~~~~~g~~~~A~~~~~~al~~~-------p~~~~  107 (172)
T PRK02603         35 AFVYYRDGMSAQADGEYAEALENYEEALKLEEDPNDRSYILYNMGIIYASNGEHDKALEYYHQALELN-------PKQPS  107 (172)
T ss_pred             HHHHHHHHHHHHHcCCHHHHHHHHHHHHHHhhccchHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhC-------cccHH
Confidence            33455666667777888888887777776532222  3567777777788888888888888877754       34566


Q ss_pred             HHHHHHHHHHHcCCHhHHHH
Q 040027          209 TYSTIIDGLCKEGFVDKAKA  228 (595)
Q Consensus       209 ~~~~l~~~~~~~g~~~~A~~  228 (595)
                      .+..+..++...|+...+..
T Consensus       108 ~~~~lg~~~~~~g~~~~a~~  127 (172)
T PRK02603        108 ALNNIAVIYHKRGEKAEEAG  127 (172)
T ss_pred             HHHHHHHHHHHcCChHhHhh
Confidence            66667777777666544443

>CHL00033 ycf3 photosystem I assembly protein Ycf3

Probab=97.72  E-value=0.0012  Score=55.91  Aligned_cols=114  Identities=16%  Similarity=0.050  Sum_probs=75.0

Q ss_pred             hhHHHHHHHHHHh-CCCCCCHHHHHHHHHHHHhcCCHhHHHHHHHHHHhcCCCC--CHhhHHHHHHHHHhcCChhHHHHH
Q 040027          112 VSLGFIAFGRILR-SCFTPNAATFNSLIKGLHAESRIMEAAALFTKLKAFGCEP--NVITYNTLINGLCRTGHTMIALNL  188 (595)
Q Consensus       112 ~~~A~~~~~~~~~-~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~--~~~~~~~l~~~~~~~g~~~~A~~~  188 (595)
                      +..+...+..+.+ .+.......|..+...+...|++++|...|++.......+  ...++..+..++...|++++|+..
T Consensus        15 ~~~~~~~l~~~~~~~~~~~~a~~~~~~g~~~~~~g~~~~A~~~~~~al~l~~~~~~~~~~~~~lg~~~~~~g~~~eA~~~   94 (168)
T CHL00033         15 FTIVADILLRILPTTSGEKEAFTYYRDGMSAQSEGEYAEALQNYYEAMRLEIDPYDRSYILYNIGLIHTSNGEHTKALEY   94 (168)
T ss_pred             cccchhhhhHhccCCchhHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHhccccchhhHHHHHHHHHHHHHcCCHHHHHHH
Confidence            4444444544432 2222234556777777888899999999999887653222  234788888889999999999999


Q ss_pred             HHHHHhcCCCCCccccCcHHHHHHHHHHHH-------HcCCHhHHHHHHHH
Q 040027          189 FEEMANGNGEIGVVCKPNTVTYSTIIDGLC-------KEGFVDKAKALFLQ  232 (595)
Q Consensus       189 ~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~-------~~g~~~~A~~~~~~  232 (595)
                      +++.....       +.....+..+...+.       ..|+++.|...+++
T Consensus        95 ~~~Al~~~-------~~~~~~~~~la~i~~~~~~~~~~~g~~~~A~~~~~~  138 (168)
T CHL00033         95 YFQALERN-------PFLPQALNNMAVICHYRGEQAIEQGDSEIAEAWFDQ  138 (168)
T ss_pred             HHHHHHhC-------cCcHHHHHHHHHHHHHhhHHHHHcccHHHHHHHHHH
Confidence            99988764       344556666666666       56666654444433

>KOG1130 consensus Predicted G-alpha GTPase interaction protein, contains GoLoco domain [Signal transduction mechanisms]

Probab=97.71  E-value=0.00042  Score=63.58  Aligned_cols=285  Identities=14%  Similarity=0.078  Sum_probs=143.7

Q ss_pred             HHHHhcCCHHHHHHHHHHHHHCCCCCCH----hhHHHHHHHHHhcCChHHHHHHHHH--HHHC--CCC-CCHHHHHHHHH
Q 040027          250 HGLCHANDWNEAKRLFIEMMDQGVQPSV----VTFNVIMDELCKNRKMDEASRLLDL--MVQR--GVR-PNACTYNTLMD  320 (595)
Q Consensus       250 ~~~~~~~~~~~A~~~~~~~~~~~~~~~~----~~~~~l~~~~~~~g~~~~a~~~~~~--~~~~--~~~-~~~~~~~~l~~  320 (595)
                      .-+++.|+......+|+..++.|.. |.    ..|..+..+|.-.+++++|+++...  .+.+  |-+ -.......+.+
T Consensus        25 ERLck~gdcraGv~ff~aA~qvGTe-Dl~tLSAIYsQLGNAyfyL~DY~kAl~yH~hDltlar~lgdklGEAKssgNLGN  103 (639)
T KOG1130|consen   25 ERLCKMGDCRAGVDFFKAALQVGTE-DLSTLSAIYSQLGNAYFYLKDYEKALKYHTHDLTLARLLGDKLGEAKSSGNLGN  103 (639)
T ss_pred             HHHHhccchhhhHHHHHHHHHhcch-HHHHHHHHHHHhcchhhhHhhHHHHHhhhhhhHHHHHHhcchhccccccccccc
Confidence            4577888888888888888887654 33    3455666777777778877776532  1111  111 01222334455


Q ss_pred             HHHhcCCHHHHHHHHHHH----HhcCCC-CCHHHHHHHHHHHHhCCCHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHcc
Q 040027          321 GFCLMGKINRAEELFGSM----ESMGCK-HDDVSYNILINGYCKNKEVEEALSLYREMVSKGIKPTVVTYNTLFLGLFEI  395 (595)
Q Consensus       321 ~~~~~~~~~~a~~~~~~~----~~~~~~-~~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~~l~~~~~~~  395 (595)
                      .+--.|.+++|.-...+-    .+.|-. .....+..+...|...|+.-....    -.+.|-.+... -          
T Consensus       104 tlKv~G~fdeA~~cc~rhLd~areLgDrv~e~RAlYNlgnvYhakGk~~g~~~----pee~g~f~~ev-~----------  168 (639)
T KOG1130|consen  104 TLKVKGAFDEALTCCFRHLDFARELGDRVLESRALYNLGNVYHAKGKCTGLEA----PEEKGAFNAEV-T----------  168 (639)
T ss_pred             hhhhhcccchHHHHHHHHhHHHHHHhHHHhhhHHHhhhhhhhhhcccccCCCC----hhhcccccHHH-H----------
Confidence            555566666665543332    222211 112244445555554443100000    00000000000 0          


Q ss_pred             CCHHHHHHHHHHHHH----CCC-CCCHHHHHHHHHHHHhcCCHHHHHHHHHHHH----HcCC-CcCHHHHHHHHHHHHhc
Q 040027          396 HQVEHALKLFDEMQR----DGV-AADTRTYTTFIDGLCKNGYIIEAVELFRTLR----ILKC-ELDIQAYNCLIDGLCKS  465 (595)
Q Consensus       396 ~~~~~a~~~~~~~~~----~~~-~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~----~~~~-~~~~~~~~~l~~~~~~~  465 (595)
                      ..++.|.+.|.+-++    .|- ......|..+...|.-.|+++.|+...+.-+    +.|- .....++..+..+++-.
T Consensus       169 ~al~~Av~fy~eNL~l~~~lgDr~aqGRa~GnLGNTyYlLGdf~~ai~~H~~RL~ia~efGDrAaeRRA~sNlgN~hifl  248 (639)
T KOG1130|consen  169 SALENAVKFYMENLELSEKLGDRLAQGRAYGNLGNTYYLLGDFDQAIHFHKLRLEIAQEFGDRAAERRAHSNLGNCHIFL  248 (639)
T ss_pred             HHHHHHHHHHHHHHHHHHHhhhHHhhcchhcccCceeeeeccHHHHHHHHHHHHHHHHHhhhHHHHHHhhcccchhhhhh
Confidence            011223333322111    110 0112344455555556677777776655432    2221 11234566677777777


Q ss_pred             CChHHHHHHHHhccc----CC-CCCCHHHHHHHHHHHHhcCChhHHHHHHHHHHHc-----CCCCCHHHHHHHHHHHHHc
Q 040027          466 GRLKFAWELFCSLPH----GV-LVPNVVTYNIMIQGLCNDGQMDKARDLFLDMEEN-----AAAPDVITFDMLIHGFIRI  535 (595)
Q Consensus       466 g~~~~A~~~~~~~~~----~~-~~p~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~-----~~~~~~~~~~~l~~~~~~~  535 (595)
                      |+++.|.+.|+....    .| -.....+..+|..+|.-..++++|+.++.+-+.-     +..-....+..|..+|...
T Consensus       249 g~fe~A~ehYK~tl~LAielg~r~vEAQscYSLgNtytll~e~~kAI~Yh~rHLaIAqeL~DriGe~RacwSLgna~~al  328 (639)
T KOG1130|consen  249 GNFELAIEHYKLTLNLAIELGNRTVEAQSCYSLGNTYTLLKEVQKAITYHQRHLAIAQELEDRIGELRACWSLGNAFNAL  328 (639)
T ss_pred             cccHhHHHHHHHHHHHHHHhcchhHHHHHHHHhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhhHHHHHHHHHHHHhh
Confidence            777777777765432    11 1122345556777777777778888777665431     1122345667777888888


Q ss_pred             CChhHHHHHHHHHHH
Q 040027          536 NEPSKVNELLHKMKE  550 (595)
Q Consensus       536 g~~~~A~~~~~~~~~  550 (595)
                      |..++|+.+.+..++
T Consensus       329 g~h~kAl~fae~hl~  343 (639)
T KOG1130|consen  329 GEHRKALYFAELHLR  343 (639)
T ss_pred             hhHHHHHHHHHHHHH
Confidence            888888777766653

>PF13812 PPR_3: Pentatricopeptide repeat domain

Probab=97.70  E-value=8.4e-05  Score=43.14  Aligned_cols=32  Identities=34%  Similarity=0.607  Sum_probs=15.5

Q ss_pred             HHHHHHHHHHhcCChhHHHHHHHHHHHcCCCC
Q 040027          489 TYNIMIQGLCNDGQMDKARDLFLDMEENAAAP  520 (595)
Q Consensus       489 ~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~  520 (595)
                      +|+.++.+|.+.|+++.|.++|++|.+.|+.|
T Consensus         3 ty~~ll~a~~~~g~~~~a~~~~~~M~~~gv~P   34 (34)
T PF13812_consen    3 TYNALLRACAKAGDPDAALQLFDEMKEQGVKP   34 (34)
T ss_pred             HHHHHHHHHHHCCCHHHHHHHHHHHHHhCCCC
Confidence            44444444555555555555555544444443

>PRK10153 DNA-binding transcriptional activator CadC; Provisional

Probab=97.69  E-value=0.0056  Score=61.40  Aligned_cols=62  Identities=15%  Similarity=0.035  Sum_probs=33.7

Q ss_pred             HHHHHHHHHHHHHcCCHhHHHHHHHHHhhCCCCCCHhHHHHHHHHHHhcCCHHHHHHHHHHHHH
Q 040027          207 TVTYSTIIDGLCKEGFVDKAKALFLQMKDENINPDVVTYNSLIHGLCHANDWNEAKRLFIEMMD  270 (595)
Q Consensus       207 ~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~~ll~~~~~~~~~~~A~~~~~~~~~  270 (595)
                      +..+..+.......|++++|...++++...+  |+...|..+...+...|+.++|.+.|.+...
T Consensus       420 ~~~~~ala~~~~~~g~~~~A~~~l~rAl~L~--ps~~a~~~lG~~~~~~G~~~eA~~~~~~A~~  481 (517)
T PRK10153        420 PRIYEILAVQALVKGKTDEAYQAINKAIDLE--MSWLNYVLLGKVYELKGDNRLAADAYSTAFN  481 (517)
T ss_pred             hHHHHHHHHHHHhcCCHHHHHHHHHHHHHcC--CCHHHHHHHHHHHHHcCCHHHHHHHHHHHHh
Confidence            3444444444444555555555555555543  3455555555555555666665555555554

>PF13812 PPR_3: Pentatricopeptide repeat domain

Probab=97.69  E-value=8.4e-05  Score=43.14  Aligned_cols=33  Identities=27%  Similarity=0.540  Sum_probs=31.4

Q ss_pred             HHHHHHHHHHHHcCChhHHHHHHHHHHHCCCCC
Q 040027          523 ITFDMLIHGFIRINEPSKVNELLHKMKEKKVMP  555 (595)
Q Consensus       523 ~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~p  555 (595)
                      .+|+.++.+|.+.|+++.|.+++++|.+.|++|
T Consensus         2 ~ty~~ll~a~~~~g~~~~a~~~~~~M~~~gv~P   34 (34)
T PF13812_consen    2 HTYNALLRACAKAGDPDAALQLFDEMKEQGVKP   34 (34)
T ss_pred             cHHHHHHHHHHHCCCHHHHHHHHHHHHHhCCCC
Confidence            479999999999999999999999999999987

>PF13414 TPR_11: TPR repeat; PDB: 2HO1_B 2FI7_B 2DBA_A 3Q4A_B 2C2L_D 3Q47_B 3Q49_B 2PL2_B 3IEG_B 2FBN_A

Probab=97.68  E-value=0.00019  Score=50.05  Aligned_cols=64  Identities=14%  Similarity=0.150  Sum_probs=48.0

Q ss_pred             CHHHHHHHHHHHHhcCChhHHHHHHHHHHHcCCCCCHHHHHHHHHHHHHcC-ChhHHHHHHHHHHH
Q 040027          486 NVVTYNIMIQGLCNDGQMDKARDLFLDMEENAAAPDVITFDMLIHGFIRIN-EPSKVNELLHKMKE  550 (595)
Q Consensus       486 ~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g-~~~~A~~~~~~~~~  550 (595)
                      +..+|..++..+...|++++|+..|+++++.+ +.+...|..++.+|...| ++++|.+.+++.++
T Consensus         2 ~a~~~~~~g~~~~~~~~~~~A~~~~~~ai~~~-p~~~~~~~~~g~~~~~~~~~~~~A~~~~~~al~   66 (69)
T PF13414_consen    2 NAEAWYNLGQIYFQQGDYEEAIEYFEKAIELD-PNNAEAYYNLGLAYMKLGKDYEEAIEDFEKALK   66 (69)
T ss_dssp             SHHHHHHHHHHHHHTTHHHHHHHHHHHHHHHS-TTHHHHHHHHHHHHHHTTTHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHcCCHHHHHHHHHHHHHcC-CCCHHHHHHHHHHHHHhCccHHHHHHHHHHHHH
Confidence            45667777777788888888888888887764 445667777777888887 67888888877765

...

>PF05843 Suf: Suppressor of forked protein (Suf); InterPro: IPR008847 This domain consists of several eukaryotic suppressor of forked (Suf) like proteins

Probab=97.68  E-value=0.0016  Score=60.10  Aligned_cols=130  Identities=17%  Similarity=0.095  Sum_probs=75.5

Q ss_pred             HHHHHHHHHHccCCHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHh-cCCHHHHHHHHHHHHHcCCCcCHHHHHHHHHHH
Q 040027          384 TYNTLFLGLFEIHQVEHALKLFDEMQRDGVAADTRTYTTFIDGLCK-NGYIIEAVELFRTLRILKCELDIQAYNCLIDGL  462 (595)
Q Consensus       384 ~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~-~g~~~~A~~~~~~~~~~~~~~~~~~~~~l~~~~  462 (595)
                      +|..++....+.+..+.|..+|.++.+.+ ..+..+|......-.. .++.+.|..+|+...+.- +.+...|...+..+
T Consensus         3 v~i~~m~~~~r~~g~~~aR~vF~~a~~~~-~~~~~vy~~~A~~E~~~~~d~~~A~~Ife~glk~f-~~~~~~~~~Y~~~l   80 (280)
T PF05843_consen    3 VWIQYMRFMRRTEGIEAARKVFKRARKDK-RCTYHVYVAYALMEYYCNKDPKRARKIFERGLKKF-PSDPDFWLEYLDFL   80 (280)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHCCC-CS-THHHHHHHHHHHHTCS-HHHHHHHHHHHHHHH-TT-HHHHHHHHHHH
T ss_pred             HHHHHHHHHHHhCChHHHHHHHHHHHcCC-CCCHHHHHHHHHHHHHhCCCHHHHHHHHHHHHHHC-CCCHHHHHHHHHHH
Confidence            45555666666666677777776666432 2233444443333222 455555777777766543 55666677777777


Q ss_pred             HhcCChHHHHHHHHhcccCCCCCCH---HHHHHHHHHHHhcCChhHHHHHHHHHHHc
Q 040027          463 CKSGRLKFAWELFCSLPHGVLVPNV---VTYNIMIQGLCNDGQMDKARDLFLDMEEN  516 (595)
Q Consensus       463 ~~~g~~~~A~~~~~~~~~~~~~p~~---~~~~~l~~~~~~~g~~~~A~~~~~~~~~~  516 (595)
                      ...++.+.|..+|++.+.. +.++.   ..|...+..-.+.|+.+.+.++.+++.+.
T Consensus        81 ~~~~d~~~aR~lfer~i~~-l~~~~~~~~iw~~~i~fE~~~Gdl~~v~~v~~R~~~~  136 (280)
T PF05843_consen   81 IKLNDINNARALFERAISS-LPKEKQSKKIWKKFIEFESKYGDLESVRKVEKRAEEL  136 (280)
T ss_dssp             HHTT-HHHHHHHHHHHCCT-SSCHHHCHHHHHHHHHHHHHHS-HHHHHHHHHHHHHH
T ss_pred             HHhCcHHHHHHHHHHHHHh-cCchhHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHH
Confidence            7777777777777777664 22222   36667776666777777777777777664

The Drosophila melanogaster suppressor of forked [Su(f)] protein shares homology with the Saccharomyces cerevisiae RNA14 protein and the 77 kDa subunit of Homo sapiens cleavage stimulation factor, which are proteins involved in mRNA 3' end formation. This suggests a role for Su(f) in mRNA 3' end formation in Drosophila. The su(f) gene produces three transcripts; two of them are polyadenylated at the end of the transcription unit, and one is a truncated transcript, polyadenylated in intron 4. It is thought that su(f) plays a role in the regulation of poly(A) site utilisation and the GU-rich sequence is important for this regulation to occur [].; GO: 0006397 mRNA processing, 0005634 nucleus; PDB: 2L9B_B 2OND_B 2OOE_A 4E85_B 4EBA_C 4E6H_A 2UY1_B.

>PF14938 SNAP: Soluble NSF attachment protein, SNAP; PDB: 1QQE_A 2IFU_A

Probab=97.66  E-value=0.0064  Score=56.34  Aligned_cols=90  Identities=12%  Similarity=0.115  Sum_probs=36.8

Q ss_pred             HHHhc-CCHHHHHHHHHHHHHC----CCCC-CHhhHHHHHHHHHhcCChHHHHHHHHHHHHCCCCC-----CHH-HHHHH
Q 040027          251 GLCHA-NDWNEAKRLFIEMMDQ----GVQP-SVVTFNVIMDELCKNRKMDEASRLLDLMVQRGVRP-----NAC-TYNTL  318 (595)
Q Consensus       251 ~~~~~-~~~~~A~~~~~~~~~~----~~~~-~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~~~~-----~~~-~~~~l  318 (595)
                      .|... |++++|++.|.+..+.    +.+. -..++..+...+.+.|++++|..+|+++.......     +.. .+...
T Consensus       123 ~ye~~~~d~e~Ai~~Y~~A~~~y~~e~~~~~a~~~~~~~A~l~~~l~~y~~A~~~~e~~~~~~l~~~l~~~~~~~~~l~a  202 (282)
T PF14938_consen  123 IYEEQLGDYEKAIEYYQKAAELYEQEGSPHSAAECLLKAADLYARLGRYEEAIEIYEEVAKKCLENNLLKYSAKEYFLKA  202 (282)
T ss_dssp             HHCCTT--HHHHHHHHHHHHHHHHHTT-HHHHHHHHHHHHHHHHHTT-HHHHHHHHHHHHHTCCCHCTTGHHHHHHHHHH
T ss_pred             HHHHHcCCHHHHHHHHHHHHHHHHHCCChhhHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHhhcccccchhHHHHHHHH
Confidence            34444 5555555555554332    1000 01233444455555555555555555554432111     111 11222


Q ss_pred             HHHHHhcCCHHHHHHHHHHHHh
Q 040027          319 MDGFCLMGKINRAEELFGSMES  340 (595)
Q Consensus       319 ~~~~~~~~~~~~a~~~~~~~~~  340 (595)
                      +-++...||...|...+++...
T Consensus       203 ~l~~L~~~D~v~A~~~~~~~~~  224 (282)
T PF14938_consen  203 ILCHLAMGDYVAARKALERYCS  224 (282)
T ss_dssp             HHHHHHTT-HHHHHHHHHHHGT
T ss_pred             HHHHHHcCCHHHHHHHHHHHHh
Confidence            3344445555555555555543

>PF12688 TPR_5: Tetratrico peptide repeat

Probab=97.65  E-value=0.0029  Score=49.07  Aligned_cols=56  Identities=21%  Similarity=0.057  Sum_probs=25.9

Q ss_pred             HHHHhcCChHHHHHHHHhcccCCCCCC--HHHHHHHHHHHHhcCChhHHHHHHHHHHH
Q 040027          460 DGLCKSGRLKFAWELFCSLPHGVLVPN--VVTYNIMIQGLCNDGQMDKARDLFLDMEE  515 (595)
Q Consensus       460 ~~~~~~g~~~~A~~~~~~~~~~~~~p~--~~~~~~l~~~~~~~g~~~~A~~~~~~~~~  515 (595)
                      .++-..|+.++|+.+|++....|+...  ...+-.+...+...|++++|..++++...
T Consensus         9 ~a~d~~G~~~~Ai~~Y~~Al~~gL~~~~~~~a~i~lastlr~LG~~deA~~~L~~~~~   66 (120)
T PF12688_consen    9 WAHDSLGREEEAIPLYRRALAAGLSGADRRRALIQLASTLRNLGRYDEALALLEEALE   66 (120)
T ss_pred             HHHHhcCCHHHHHHHHHHHHHcCCCchHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHH
Confidence            334444555555555555544443322  22333444445555555555555555444

>PF14938 SNAP: Soluble NSF attachment protein, SNAP; PDB: 1QQE_A 2IFU_A

Probab=97.65  E-value=0.0027  Score=58.81  Aligned_cols=137  Identities=13%  Similarity=0.088  Sum_probs=69.5

Q ss_pred             HHHHHHHHHHHhcCChhHHHHHHHHHHhCCC---CCC--HHHHHHHHHHHHhcCCHhHHHHHHHHHHhc----CCC-CCH
Q 040027           97 YTYNILINCFCKIGRVSLGFIAFGRILRSCF---TPN--AATFNSLIKGLHAESRIMEAAALFTKLKAF----GCE-PNV  166 (595)
Q Consensus        97 ~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~---~~~--~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~----~~~-~~~  166 (595)
                      ..|......|...|++++|...|.++.....   .+.  ...|......| +..++++|++.+++....    |-. .-.
T Consensus        36 ~~y~~Aa~~fk~~~~~~~A~~ay~kAa~~~~~~~~~~~Aa~~~~~Aa~~~-k~~~~~~Ai~~~~~A~~~y~~~G~~~~aA  114 (282)
T PF14938_consen   36 DLYEKAANCFKLAKDWEKAAEAYEKAADCYEKLGDKFEAAKAYEEAANCY-KKGDPDEAIECYEKAIEIYREAGRFSQAA  114 (282)
T ss_dssp             HHHHHHHHHHHHTT-CHHHHHHHHHHHHHHHHTT-HHHHHHHHHHHHHHH-HHTTHHHHHHHHHHHHHHHHHCT-HHHHH
T ss_pred             HHHHHHHHHHHHHhccchhHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHH-HhhCHHHHHHHHHHHHHHHHhcCcHHHHH
Confidence            5677888888888999999999888755311   111  11233333333 344777777777766542    210 012


Q ss_pred             hhHHHHHHHHHhc-CChhHHHHHHHHHHhcCCCCCccccCcHHHHHHHHHHHHHcCCHhHHHHHHHHHhh
Q 040027          167 ITYNTLINGLCRT-GHTMIALNLFEEMANGNGEIGVVCKPNTVTYSTIIDGLCKEGFVDKAKALFLQMKD  235 (595)
Q Consensus       167 ~~~~~l~~~~~~~-g~~~~A~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~  235 (595)
                      ..+..+...|... |++++|++.|++....-...+. ...-..++..++..+.+.|++++|.++|+++..
T Consensus       115 ~~~~~lA~~ye~~~~d~e~Ai~~Y~~A~~~y~~e~~-~~~a~~~~~~~A~l~~~l~~y~~A~~~~e~~~~  183 (282)
T PF14938_consen  115 KCLKELAEIYEEQLGDYEKAIEYYQKAAELYEQEGS-PHSAAECLLKAADLYARLGRYEEAIEIYEEVAK  183 (282)
T ss_dssp             HHHHHHHHHHCCTT--HHHHHHHHHHHHHHHHHTT--HHHHHHHHHHHHHHHHHTT-HHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHCCC-hhhHHHHHHHHHHHHHHhCCHHHHHHHHHHHHH
Confidence            2344555555555 6666666666655432100000 000123344455555556666666666655544

>PF14559 TPR_19: Tetratricopeptide repeat; PDB: 2R5S_A 3QDN_B 3QOU_A 3ASG_A 3ASD_A 3AS5_A 3AS4_A 3ASH_B 3FP3_A 3LCA_A

Probab=97.63  E-value=0.00013  Score=50.67  Aligned_cols=52  Identities=17%  Similarity=0.118  Sum_probs=26.9

Q ss_pred             hcCChhHHHHHHHHHHhCCCCCCHHHHHHHHHHHHhcCCHhHHHHHHHHHHhc
Q 040027          108 KIGRVSLGFIAFGRILRSCFTPNAATFNSLIKGLHAESRIMEAAALFTKLKAF  160 (595)
Q Consensus       108 ~~g~~~~A~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~  160 (595)
                      +.|++++|+..|+++.... +.+..++..++.+|.+.|++++|.++++++...
T Consensus         3 ~~~~~~~A~~~~~~~l~~~-p~~~~~~~~la~~~~~~g~~~~A~~~l~~~~~~   54 (68)
T PF14559_consen    3 KQGDYDEAIELLEKALQRN-PDNPEARLLLAQCYLKQGQYDEAEELLERLLKQ   54 (68)
T ss_dssp             HTTHHHHHHHHHHHHHHHT-TTSHHHHHHHHHHHHHTT-HHHHHHHHHCCHGG
T ss_pred             hccCHHHHHHHHHHHHHHC-CCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHH
Confidence            3455555555555555543 234445555555555555555555555555544

...

>PF12688 TPR_5: Tetratrico peptide repeat

Probab=97.63  E-value=0.0043  Score=48.18  Aligned_cols=20  Identities=20%  Similarity=0.278  Sum_probs=8.4

Q ss_pred             HHhcCChhHHHHHHHHHHhC
Q 040027          106 FCKIGRVSLGFIAFGRILRS  125 (595)
Q Consensus       106 ~~~~g~~~~A~~~~~~~~~~  125 (595)
                      +-..|+.++|+.+|+++...
T Consensus        11 ~d~~G~~~~Ai~~Y~~Al~~   30 (120)
T PF12688_consen   11 HDSLGREEEAIPLYRRALAA   30 (120)
T ss_pred             HHhcCCHHHHHHHHHHHHHc
Confidence            33344444444444444443

>PF13432 TPR_16: Tetratricopeptide repeat; PDB: 3CVP_A 3CVL_A 3CVQ_A 3CV0_A 2GW1_B 3CVN_A 3QKY_A 2PL2_B

Probab=97.61  E-value=0.00025  Score=48.76  Aligned_cols=57  Identities=12%  Similarity=0.133  Sum_probs=35.3

Q ss_pred             HHHHHHhcCChhHHHHHHHHHHHcCCCCCHHHHHHHHHHHHHcCChhHHHHHHHHHHH
Q 040027          493 MIQGLCNDGQMDKARDLFLDMEENAAAPDVITFDMLIHGFIRINEPSKVNELLHKMKE  550 (595)
Q Consensus       493 l~~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~  550 (595)
                      ++..+...|++++|++.|+++++.. +.+...+..++.++...|++++|..+|+++++
T Consensus         3 ~a~~~~~~g~~~~A~~~~~~~l~~~-P~~~~a~~~lg~~~~~~g~~~~A~~~~~~a~~   59 (65)
T PF13432_consen    3 LARALYQQGDYDEAIAAFEQALKQD-PDNPEAWYLLGRILYQQGRYDEALAYYERALE   59 (65)
T ss_dssp             HHHHHHHCTHHHHHHHHHHHHHCCS-TTHHHHHHHHHHHHHHTT-HHHHHHHHHHHHH
T ss_pred             HHHHHHHcCCHHHHHHHHHHHHHHC-CCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHH
Confidence            3455566666666666666666653 33455666666666666666666666666665

>PF13525 YfiO: Outer membrane lipoprotein; PDB: 3TGO_A 3Q5M_A 2YHC_A

Probab=97.60  E-value=0.0084  Score=52.39  Aligned_cols=64  Identities=9%  Similarity=-0.018  Sum_probs=38.2

Q ss_pred             HHHHHHHHHHHhcCChhHHHHHHHHHHhCCC--CCCHHHHHHHHHHHHhcCCHhHHHHHHHHHHhc
Q 040027           97 YTYNILINCFCKIGRVSLGFIAFGRILRSCF--TPNAATFNSLIKGLHAESRIMEAAALFTKLKAF  160 (595)
Q Consensus        97 ~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~--~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~  160 (595)
                      ..+-..+..+...|++.+|+..|+.+...-+  +--..+...++.++.+.|+++.|...++++.+.
T Consensus         6 ~~lY~~a~~~~~~g~y~~Ai~~f~~l~~~~P~s~~a~~A~l~la~a~y~~~~y~~A~~~~~~fi~~   71 (203)
T PF13525_consen    6 EALYQKALEALQQGDYEEAIKLFEKLIDRYPNSPYAPQAQLMLAYAYYKQGDYEEAIAAYERFIKL   71 (203)
T ss_dssp             HHHHHHHHHHHHCT-HHHHHHHHHHHHHH-TTSTTHHHHHHHHHHHHHHTT-HHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHCCCHHHHHHHHHHHHHHCCCChHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHH
Confidence            3344455566667777777777777776521  112334555666677777777777777776665

>PF10037 MRP-S27: Mitochondrial 28S ribosomal protein S27; InterPro: IPR019266 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms

Probab=97.60  E-value=0.0013  Score=63.11  Aligned_cols=124  Identities=11%  Similarity=0.119  Sum_probs=93.5

Q ss_pred             CCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHHc--CCCcCHHHHHHHHHHHHhcCChHHHHHHHHhcccCCCCCCHHH
Q 040027          412 GVAADTRTYTTFIDGLCKNGYIIEAVELFRTLRIL--KCELDIQAYNCLIDGLCKSGRLKFAWELFCSLPHGVLVPNVVT  489 (595)
Q Consensus       412 ~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~--~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~p~~~~  489 (595)
                      +.+.+...+..++..+....+.+.+..++.+....  ....-+.+..++++.|...|..+.++.+++.=...|+-||..+
T Consensus        61 ~~~vS~~dld~fvn~~~~~~~~d~~~~~L~k~R~s~~~~~~~~~t~ha~vR~~l~~~~~~~~l~~L~n~~~yGiF~D~~s  140 (429)
T PF10037_consen   61 KKPVSSLDLDIFVNNVESKDDLDEVEDVLYKFRHSPNCSYLLPSTHHALVRQCLELGAEDELLELLKNRLQYGIFPDNFS  140 (429)
T ss_pred             CCCCcHHHHHHHHhhcCCHhHHHHHHHHHHHHHcCcccccccCccHHHHHHHHHhcCCHHHHHHHHhChhhcccCCChhh
Confidence            44667777777787777777788888888877754  2222344556888888888888888888888888888888888


Q ss_pred             HHHHHHHHHhcCChhHHHHHHHHHHHcCCCCCHHHHHHHHHHHHHc
Q 040027          490 YNIMIQGLCNDGQMDKARDLFLDMEENAAAPDVITFDMLIHGFIRI  535 (595)
Q Consensus       490 ~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~~l~~~~~~~  535 (595)
                      ++.|+..+.+.|++..|.++...|...+...+..++...+.+|.+-
T Consensus       141 ~n~Lmd~fl~~~~~~~A~~V~~~~~lQe~~~~~~t~~L~l~~~~~~  186 (429)
T PF10037_consen  141 FNLLMDHFLKKGNYKSAAKVATEMMLQEEFDNPSTQALALYSCYKY  186 (429)
T ss_pred             HHHHHHHHhhcccHHHHHHHHHHHHHhhccCCchHHHHHHHHHHHh
Confidence            8888888888888888888888887766666667776666666555

The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites [, ]. About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits. Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome [, ]. This entry represents a family of small ribosomal proteins possessing one of three conserved sequence blocks found in proteins that stimulate the dissociation of guanine nucleotides from G-proteins. This leaves open the possibility that they may be functional partners of GTP-binding ribosomal proteins [].

>KOG1130 consensus Predicted G-alpha GTPase interaction protein, contains GoLoco domain [Signal transduction mechanisms]

Probab=97.59  E-value=0.0017  Score=59.83  Aligned_cols=288  Identities=16%  Similarity=0.097  Sum_probs=146.6

Q ss_pred             HHHHHcCCHhHHHHHHHHHhhCCCCCC----HhHHHHHHHHHHhcCCHHHHHHHHHHH--HHC--CCC-CCHhhHHHHHH
Q 040027          215 DGLCKEGFVDKAKALFLQMKDENINPD----VVTYNSLIHGLCHANDWNEAKRLFIEM--MDQ--GVQ-PSVVTFNVIMD  285 (595)
Q Consensus       215 ~~~~~~g~~~~A~~~~~~~~~~~~~~~----~~~~~~ll~~~~~~~~~~~A~~~~~~~--~~~--~~~-~~~~~~~~l~~  285 (595)
                      .-+++.|+......+|+..++.|.. |    ...|..|..+|.-.+++++|+++...=  +..  |-+ -...+...+..
T Consensus        25 ERLck~gdcraGv~ff~aA~qvGTe-Dl~tLSAIYsQLGNAyfyL~DY~kAl~yH~hDltlar~lgdklGEAKssgNLGN  103 (639)
T KOG1130|consen   25 ERLCKMGDCRAGVDFFKAALQVGTE-DLSTLSAIYSQLGNAYFYLKDYEKALKYHTHDLTLARLLGDKLGEAKSSGNLGN  103 (639)
T ss_pred             HHHHhccchhhhHHHHHHHHHhcch-HHHHHHHHHHHhcchhhhHhhHHHHHhhhhhhHHHHHHhcchhccccccccccc
Confidence            4588999999999999999998743 3    345777888888899999999875321  111  111 11223344566


Q ss_pred             HHHhcCChHHHHHHHHHHH----HCCCC-CCHHHHHHHHHHHHhcCCHHHHHHHHHHHHhcCCCCCHH--HHHHHHHHHH
Q 040027          286 ELCKNRKMDEASRLLDLMV----QRGVR-PNACTYNTLMDGFCLMGKINRAEELFGSMESMGCKHDDV--SYNILINGYC  358 (595)
Q Consensus       286 ~~~~~g~~~~a~~~~~~~~----~~~~~-~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~--~~~~l~~~~~  358 (595)
                      .+-..|.+++|+-...+-+    +.|-+ .....+..+...|...|+--....-    .+.|-.+...  .+...+..|.
T Consensus       104 tlKv~G~fdeA~~cc~rhLd~areLgDrv~e~RAlYNlgnvYhakGk~~g~~~p----ee~g~f~~ev~~al~~Av~fy~  179 (639)
T KOG1130|consen  104 TLKVKGAFDEALTCCFRHLDFARELGDRVLESRALYNLGNVYHAKGKCTGLEAP----EEKGAFNAEVTSALENAVKFYM  179 (639)
T ss_pred             hhhhhcccchHHHHHHHHhHHHHHHhHHHhhhHHHhhhhhhhhhcccccCCCCh----hhcccccHHHHHHHHHHHHHHH
Confidence            6667788888776554332    22211 1234555567777665542110000    0001001000  1111111111


Q ss_pred             hCCCHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHccCCHHHHHHHHHHHHH----CCC-CCCHHHHHHHHHHHHhcCCH
Q 040027          359 KNKEVEEALSLYREMVSKGIKPTVVTYNTLFLGLFEIHQVEHALKLFDEMQR----DGV-AADTRTYTTFIDGLCKNGYI  433 (595)
Q Consensus       359 ~~~~~~~A~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~----~~~-~~~~~~~~~l~~~~~~~g~~  433 (595)
                            +-+++.+++-..  ..--..|..+...|.-.|+++.|+...+.-+.    .|- ......+..+..++.-.|++
T Consensus       180 ------eNL~l~~~lgDr--~aqGRa~GnLGNTyYlLGdf~~ai~~H~~RL~ia~efGDrAaeRRA~sNlgN~hiflg~f  251 (639)
T KOG1130|consen  180 ------ENLELSEKLGDR--LAQGRAYGNLGNTYYLLGDFDQAIHFHKLRLEIAQEFGDRAAERRAHSNLGNCHIFLGNF  251 (639)
T ss_pred             ------HHHHHHHHhhhH--HhhcchhcccCceeeeeccHHHHHHHHHHHHHHHHHhhhHHHHHHhhcccchhhhhhccc
Confidence                  111111111110  00123344555555566666666655443221    111 11234455666666667777


Q ss_pred             HHHHHHHHHHHHc----C-CCcCHHHHHHHHHHHHhcCChHHHHHHHHhccc----CC-CCCCHHHHHHHHHHHHhcCCh
Q 040027          434 IEAVELFRTLRIL----K-CELDIQAYNCLIDGLCKSGRLKFAWELFCSLPH----GV-LVPNVVTYNIMIQGLCNDGQM  503 (595)
Q Consensus       434 ~~A~~~~~~~~~~----~-~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~----~~-~~p~~~~~~~l~~~~~~~g~~  503 (595)
                      +.|.+.|+.....    + .........+|..+|.-..++++|+.++.+-+.    .+ ..-....+.+|..+|...|..
T Consensus       252 e~A~ehYK~tl~LAielg~r~vEAQscYSLgNtytll~e~~kAI~Yh~rHLaIAqeL~DriGe~RacwSLgna~~alg~h  331 (639)
T KOG1130|consen  252 ELAIEHYKLTLNLAIELGNRTVEAQSCYSLGNTYTLLKEVQKAITYHQRHLAIAQELEDRIGELRACWSLGNAFNALGEH  331 (639)
T ss_pred             HhHHHHHHHHHHHHHHhcchhHHHHHHHHhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhhHHHHHHHHHHHHhhhhH
Confidence            7777776654322    2 122334445566666666677777776665322    00 111234555667777777777


Q ss_pred             hHHHHHHHHHHH
Q 040027          504 DKARDLFLDMEE  515 (595)
Q Consensus       504 ~~A~~~~~~~~~  515 (595)
                      ++|+.+.+..++
T Consensus       332 ~kAl~fae~hl~  343 (639)
T KOG1130|consen  332 RKALYFAELHLR  343 (639)
T ss_pred             HHHHHHHHHHHH
Confidence            777766655543

>KOG2114 consensus Vacuolar assembly/sorting protein PEP5/VPS11 [Intracellular trafficking, secretion, and vesicular transport]

Probab=97.58  E-value=0.075  Score=54.14  Aligned_cols=180  Identities=13%  Similarity=0.082  Sum_probs=116.8

Q ss_pred             HHHHHHHHHHHhcCChhHHHHHHHHHHhCCCCCC--HHHHHHHHHHHHhcCCHhHHHHHHHHHHhcCCCCCHhhHHHHHH
Q 040027           97 YTYNILINCFCKIGRVSLGFIAFGRILRSCFTPN--AATFNSLIKGLHAESRIMEAAALFTKLKAFGCEPNVITYNTLIN  174 (595)
Q Consensus        97 ~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~~--~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~~l~~  174 (595)
                      .....-+..+.+...++-|+.+.+.-..   +++  ..........+.+.|++++|...|-+.+.. ++|     ..++.
T Consensus       335 k~le~kL~iL~kK~ly~~Ai~LAk~~~~---d~d~~~~i~~kYgd~Ly~Kgdf~~A~~qYI~tI~~-le~-----s~Vi~  405 (933)
T KOG2114|consen  335 KDLETKLDILFKKNLYKVAINLAKSQHL---DEDTLAEIHRKYGDYLYGKGDFDEATDQYIETIGF-LEP-----SEVIK  405 (933)
T ss_pred             ccHHHHHHHHHHhhhHHHHHHHHHhcCC---CHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHHccc-CCh-----HHHHH
Confidence            3444566777788888888887765331   222  223344455567889999999988887653 232     24556


Q ss_pred             HHHhcCChhHHHHHHHHHHhcCCCCCccccCcHHHHHHHHHHHHHcCCHhHHHHHHHHHhhCCCCCCHhHHHHHHHHHHh
Q 040027          175 GLCRTGHTMIALNLFEEMANGNGEIGVVCKPNTVTYSTIIDGLCKEGFVDKAKALFLQMKDENINPDVVTYNSLIHGLCH  254 (595)
Q Consensus       175 ~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~~ll~~~~~  254 (595)
                      -|....+..+-..+++.+.+.+       -.+...-..|+.+|.+.++.++-.+..+... .|.-  ..-....+..+.+
T Consensus       406 kfLdaq~IknLt~YLe~L~~~g-------la~~dhttlLLncYiKlkd~~kL~efI~~~~-~g~~--~fd~e~al~Ilr~  475 (933)
T KOG2114|consen  406 KFLDAQRIKNLTSYLEALHKKG-------LANSDHTTLLLNCYIKLKDVEKLTEFISKCD-KGEW--FFDVETALEILRK  475 (933)
T ss_pred             HhcCHHHHHHHHHHHHHHHHcc-------cccchhHHHHHHHHHHhcchHHHHHHHhcCC-Ccce--eeeHHHHHHHHHH
Confidence            6666667777778888888776       3445566789999999999998887776654 2211  1123456677777


Q ss_pred             cCCHHHHHHHHHHHHHCCCCCCHhhHHHHHHHHHhcCChHHHHHHHHHH
Q 040027          255 ANDWNEAKRLFIEMMDQGVQPSVVTFNVIMDELCKNRKMDEASRLLDLM  303 (595)
Q Consensus       255 ~~~~~~A~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~a~~~~~~~  303 (595)
                      .+-.++|..+-.....     ......   -.+-..+++++|+++++.+
T Consensus       476 snyl~~a~~LA~k~~~-----he~vl~---ille~~~ny~eAl~yi~sl  516 (933)
T KOG2114|consen  476 SNYLDEAELLATKFKK-----HEWVLD---ILLEDLHNYEEALRYISSL  516 (933)
T ss_pred             hChHHHHHHHHHHhcc-----CHHHHH---HHHHHhcCHHHHHHHHhcC
Confidence            7777777766554432     222222   3345678899999888765

>PF14559 TPR_19: Tetratricopeptide repeat; PDB: 2R5S_A 3QDN_B 3QOU_A 3ASG_A 3ASD_A 3AS5_A 3AS4_A 3ASH_B 3FP3_A 3LCA_A

Probab=97.52  E-value=0.00057  Score=47.45  Aligned_cols=59  Identities=27%  Similarity=0.189  Sum_probs=35.5

Q ss_pred             hcCCHHHHHHHHHHHHHcCCCcCHHHHHHHHHHHHhcCChHHHHHHHHhcccCCCCCCHHHH
Q 040027          429 KNGYIIEAVELFRTLRILKCELDIQAYNCLIDGLCKSGRLKFAWELFCSLPHGVLVPNVVTY  490 (595)
Q Consensus       429 ~~g~~~~A~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~p~~~~~  490 (595)
                      +.|++++|...|+++.... |.+...+..++.+|.+.|++++|..+++++..  ..|+...|
T Consensus         3 ~~~~~~~A~~~~~~~l~~~-p~~~~~~~~la~~~~~~g~~~~A~~~l~~~~~--~~~~~~~~   61 (68)
T PF14559_consen    3 KQGDYDEAIELLEKALQRN-PDNPEARLLLAQCYLKQGQYDEAEELLERLLK--QDPDNPEY   61 (68)
T ss_dssp             HTTHHHHHHHHHHHHHHHT-TTSHHHHHHHHHHHHHTT-HHHHHHHHHCCHG--GGTTHHHH
T ss_pred             hccCHHHHHHHHHHHHHHC-CCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHH--HCcCHHHH
Confidence            4566666666666666554 44666666666666666666666666666665  34453333

...

>KOG1258 consensus mRNA processing protein [RNA processing and modification]

Probab=97.51  E-value=0.12  Score=50.93  Aligned_cols=183  Identities=8%  Similarity=0.028  Sum_probs=78.6

Q ss_pred             HHHHHHHHHHHccCCHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCcCHHHHHHHHHHH
Q 040027          383 VTYNTLFLGLFEIHQVEHALKLFDEMQRDGVAADTRTYTTFIDGLCKNGYIIEAVELFRTLRILKCELDIQAYNCLIDGL  462 (595)
Q Consensus       383 ~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~~l~~~~  462 (595)
                      .+|...+.--...|+.+.+.-+++...-. +..=...|-..+.-....|+.+-|..++.+..+...+..+.+...-....
T Consensus       298 ~nw~~yLdf~i~~g~~~~~~~l~ercli~-cA~Y~efWiky~~~m~~~~~~~~~~~~~~~~~~i~~k~~~~i~L~~a~f~  376 (577)
T KOG1258|consen  298 KNWRYYLDFEITLGDFSRVFILFERCLIP-CALYDEFWIKYARWMESSGDVSLANNVLARACKIHVKKTPIIHLLEARFE  376 (577)
T ss_pred             HHHHHHhhhhhhcccHHHHHHHHHHHHhH-HhhhHHHHHHHHHHHHHcCchhHHHHHHHhhhhhcCCCCcHHHHHHHHHH
Confidence            34555555555556666655555554421 11112333333333344466666665555555433332222222222223


Q ss_pred             HhcCChHHHHHHHHhcccCCCCCCH-HHHHHHHHHHHhcCChhHHH---HHHHHHHHcCCCCCHHHHHHHH----H-HHH
Q 040027          463 CKSGRLKFAWELFCSLPHGVLVPNV-VTYNIMIQGLCNDGQMDKAR---DLFLDMEENAAAPDVITFDMLI----H-GFI  533 (595)
Q Consensus       463 ~~~g~~~~A~~~~~~~~~~~~~p~~-~~~~~l~~~~~~~g~~~~A~---~~~~~~~~~~~~~~~~~~~~l~----~-~~~  533 (595)
                      -..|+++.|..+++.+.+. . |+. ..-..-+....+.|+.+.+.   .++......  .-+..+...+.    + .+.
T Consensus       377 e~~~n~~~A~~~lq~i~~e-~-pg~v~~~l~~~~~e~r~~~~~~~~~~~~l~s~~~~~--~~~~~i~~~l~~~~~r~~~~  452 (577)
T KOG1258|consen  377 ESNGNFDDAKVILQRIESE-Y-PGLVEVVLRKINWERRKGNLEDANYKNELYSSIYEG--KENNGILEKLYVKFARLRYK  452 (577)
T ss_pred             HhhccHHHHHHHHHHHHhh-C-CchhhhHHHHHhHHHHhcchhhhhHHHHHHHHhccc--ccCcchhHHHHHHHHHHHHH
Confidence            3445666666666666553 2 432 12122223333455555554   222222211  11111111111    1 122


Q ss_pred             HcCChhHHHHHHHHHHHCCCCCCHHHHHHHHHHHHhcC
Q 040027          534 RINEPSKVNELLHKMKEKKVMPDASIVSIVVDLLVKNE  571 (595)
Q Consensus       534 ~~g~~~~A~~~~~~~~~~~~~p~~~~~~~l~~~~~~~g  571 (595)
                      -.++.+.|..++.++.+. ++++...|..+++...-.+
T Consensus       453 i~~d~~~a~~~l~~~~~~-~~~~k~~~~~~~~~~~~~~  489 (577)
T KOG1258|consen  453 IREDADLARIILLEANDI-LPDCKVLYLELIRFELIQP  489 (577)
T ss_pred             HhcCHHHHHHHHHHhhhc-CCccHHHHHHHHHHHHhCC
Confidence            345556666666666653 3444555555555444443

>PF13525 YfiO: Outer membrane lipoprotein; PDB: 3TGO_A 3Q5M_A 2YHC_A

Probab=97.48  E-value=0.032  Score=48.78  Aligned_cols=63  Identities=14%  Similarity=0.089  Sum_probs=30.9

Q ss_pred             HHHHHHHHhcCChhHHHHHHHHHHhcCCCCCccccCcHHHHHHHHHHHHHcCCHhHHHHHHHHHhhC
Q 040027          170 NTLINGLCRTGHTMIALNLFEEMANGNGEIGVVCKPNTVTYSTIIDGLCKEGFVDKAKALFLQMKDE  236 (595)
Q Consensus       170 ~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~  236 (595)
                      ...+..+...|++.+|++.|+.+....+.    .+.-..+...++.++.+.|+++.|...+++..+.
T Consensus         9 Y~~a~~~~~~g~y~~Ai~~f~~l~~~~P~----s~~a~~A~l~la~a~y~~~~y~~A~~~~~~fi~~   71 (203)
T PF13525_consen    9 YQKALEALQQGDYEEAIKLFEKLIDRYPN----SPYAPQAQLMLAYAYYKQGDYEEAIAAYERFIKL   71 (203)
T ss_dssp             HHHHHHHHHCT-HHHHHHHHHHHHHH-TT----STTHHHHHHHHHHHHHHTT-HHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHCCCHHHHHHHHHHHHHHCCC----ChHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHH
Confidence            33444455566666666666666554310    1112334445555566666666666666665543

>PF13414 TPR_11: TPR repeat; PDB: 2HO1_B 2FI7_B 2DBA_A 3Q4A_B 2C2L_D 3Q47_B 3Q49_B 2PL2_B 3IEG_B 2FBN_A

Probab=97.48  E-value=0.00055  Score=47.71  Aligned_cols=65  Identities=17%  Similarity=0.103  Sum_probs=47.9

Q ss_pred             CHHHHHHHHHHHHhcCChhHHHHHHHHHHhCCCCCCHHHHHHHHHHHHhcC-CHhHHHHHHHHHHhc
Q 040027           95 NLYTYNILINCFCKIGRVSLGFIAFGRILRSCFTPNAATFNSLIKGLHAES-RIMEAAALFTKLKAF  160 (595)
Q Consensus        95 ~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g-~~~~A~~~~~~~~~~  160 (595)
                      ++..|..++..+...|++++|+..|+++++.. +.+..+|..+..++...| ++++|++.+++.++.
T Consensus         2 ~a~~~~~~g~~~~~~~~~~~A~~~~~~ai~~~-p~~~~~~~~~g~~~~~~~~~~~~A~~~~~~al~l   67 (69)
T PF13414_consen    2 NAEAWYNLGQIYFQQGDYEEAIEYFEKAIELD-PNNAEAYYNLGLAYMKLGKDYEEAIEDFEKALKL   67 (69)
T ss_dssp             SHHHHHHHHHHHHHTTHHHHHHHHHHHHHHHS-TTHHHHHHHHHHHHHHTTTHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHcCCHHHHHHHHHHHHHcC-CCCHHHHHHHHHHHHHhCccHHHHHHHHHHHHHc
Confidence            45677777777778888888888888877774 445667777777777777 677777777777654

...

>PF13432 TPR_16: Tetratricopeptide repeat; PDB: 3CVP_A 3CVL_A 3CVQ_A 3CV0_A 2GW1_B 3CVN_A 3QKY_A 2PL2_B

Probab=97.45  E-value=0.00069  Score=46.49  Aligned_cols=58  Identities=21%  Similarity=0.242  Sum_probs=39.0

Q ss_pred             HHHHHHhcCChhHHHHHHHHHHhCCCCCCHHHHHHHHHHHHhcCCHhHHHHHHHHHHhc
Q 040027          102 LINCFCKIGRVSLGFIAFGRILRSCFTPNAATFNSLIKGLHAESRIMEAAALFTKLKAF  160 (595)
Q Consensus       102 l~~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~  160 (595)
                      ++..+.+.|++++|+..|+++++.. +-+...+..+..++...|++++|...|+++.+.
T Consensus         3 ~a~~~~~~g~~~~A~~~~~~~l~~~-P~~~~a~~~lg~~~~~~g~~~~A~~~~~~a~~~   60 (65)
T PF13432_consen    3 LARALYQQGDYDEAIAAFEQALKQD-PDNPEAWYLLGRILYQQGRYDEALAYYERALEL   60 (65)
T ss_dssp             HHHHHHHCTHHHHHHHHHHHHHCCS-TTHHHHHHHHHHHHHHTT-HHHHHHHHHHHHHH
T ss_pred             HHHHHHHcCCHHHHHHHHHHHHHHC-CCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHH
Confidence            4556667777777777777777664 335666667777777777777777777777655

>PF08579 RPM2: Mitochondrial ribonuclease P subunit (RPM2); InterPro: IPR013888 Ribonuclease P (RNase P) generates mature tRNA molecules by cleaving their 5' ends

Probab=97.44  E-value=0.0032  Score=46.90  Aligned_cols=69  Identities=22%  Similarity=0.471  Sum_probs=31.4

Q ss_pred             hcCCHHHHHHHHHHHHHCCC-CCCHhhHHHHHHHHHhcC--------ChHHHHHHHHHHHHCCCCCCHHHHHHHHHHH
Q 040027          254 HANDWNEAKRLFIEMMDQGV-QPSVVTFNVIMDELCKNR--------KMDEASRLLDLMVQRGVRPNACTYNTLMDGF  322 (595)
Q Consensus       254 ~~~~~~~A~~~~~~~~~~~~-~~~~~~~~~l~~~~~~~g--------~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~  322 (595)
                      ..+++.....+|+.+++.|+ .|+..+|+.++.+..+..        ..-..+.+|++|+..+++|+..+|+.++..+
T Consensus        37 ~~~d~N~I~~lYqslkRN~i~lPsv~~Yn~VL~Si~~R~lD~~~ie~kl~~LLtvYqDiL~~~lKP~~etYnivl~~L  114 (120)
T PF08579_consen   37 ENEDYNIINPLYQSLKRNGITLPSVELYNKVLKSIAKRELDSEDIENKLTNLLTVYQDILSNKLKPNDETYNIVLGSL  114 (120)
T ss_pred             hhcchHHHHHHHHHHHhcCCCCCcHHHHHHHHHHHHHccccchhHHHHHHHHHHHHHHHHHhccCCcHHHHHHHHHHH
Confidence            33444444444444444444 444444444444333321        1223444555555555555555555554443

Rpm2 is a protein subunit of the yeast mitochondrial RNase P. It has the ability to act as a transcriptional activator in the nucleus, where it plays a role in defining the steady-state levels of mRNAs for some nucleus-encoded mitochondrial components. Rpm2p is also involved in maturation of Rpm1 and in translation of mitochondrial mRNAs [, , ].

>PF08579 RPM2: Mitochondrial ribonuclease P subunit (RPM2); InterPro: IPR013888 Ribonuclease P (RNase P) generates mature tRNA molecules by cleaving their 5' ends

Probab=97.42  E-value=0.0036  Score=46.67  Aligned_cols=79  Identities=16%  Similarity=0.343  Sum_probs=66.6

Q ss_pred             HHHHHHHHHcCCHhHHHHHHHHHhhCCC-CCCHhHHHHHHHHHHhcCC--------HHHHHHHHHHHHHCCCCCCHhhHH
Q 040027          211 STIIDGLCKEGFVDKAKALFLQMKDENI-NPDVVTYNSLIHGLCHAND--------WNEAKRLFIEMMDQGVQPSVVTFN  281 (595)
Q Consensus       211 ~~l~~~~~~~g~~~~A~~~~~~~~~~~~-~~~~~~~~~ll~~~~~~~~--------~~~A~~~~~~~~~~~~~~~~~~~~  281 (595)
                      ...|.-+...+++...-.+|+.+++.|+ .|+..+|+.++....+..-        .-..+.+|+.|+..+++|+..+|+
T Consensus        29 i~~I~~~~~~~d~N~I~~lYqslkRN~i~lPsv~~Yn~VL~Si~~R~lD~~~ie~kl~~LLtvYqDiL~~~lKP~~etYn  108 (120)
T PF08579_consen   29 IDNINSCFENEDYNIINPLYQSLKRNGITLPSVELYNKVLKSIAKRELDSEDIENKLTNLLTVYQDILSNKLKPNDETYN  108 (120)
T ss_pred             HHHHHHHHhhcchHHHHHHHHHHHhcCCCCCcHHHHHHHHHHHHHccccchhHHHHHHHHHHHHHHHHHhccCCcHHHHH
Confidence            3455566667999999999999999999 8999999999988776532        345678999999999999999999


Q ss_pred             HHHHHHHh
Q 040027          282 VIMDELCK  289 (595)
Q Consensus       282 ~l~~~~~~  289 (595)
                      .++..+.+
T Consensus       109 ivl~~Llk  116 (120)
T PF08579_consen  109 IVLGSLLK  116 (120)
T ss_pred             HHHHHHHH
Confidence            99987764

Rpm2 is a protein subunit of the yeast mitochondrial RNase P. It has the ability to act as a transcriptional activator in the nucleus, where it plays a role in defining the steady-state levels of mRNAs for some nucleus-encoded mitochondrial components. Rpm2p is also involved in maturation of Rpm1 and in translation of mitochondrial mRNAs [, , ].

>COG5107 RNA14 Pre-mRNA 3'-end processing (cleavage and polyadenylation) factor [RNA processing and modification]

Probab=97.41  E-value=0.12  Score=48.82  Aligned_cols=119  Identities=17%  Similarity=0.171  Sum_probs=92.7

Q ss_pred             HHHHHHHHHHHHhcCChHHHHHHHHhcccCC-CCCCHHHHHHHHHHHHhcCChhHHHHHHHHHHHcCCCCCHHHH-HHHH
Q 040027          452 IQAYNCLIDGLCKSGRLKFAWELFCSLPHGV-LVPNVVTYNIMIQGLCNDGQMDKARDLFLDMEENAAAPDVITF-DMLI  529 (595)
Q Consensus       452 ~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~-~~p~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~-~~l~  529 (595)
                      ..+|..++..-.+..-++.|..+|-++.+.+ ..+++..+++++..++ .|+...|-.+|+--+..  -||...| ...+
T Consensus       397 t~v~C~~~N~v~r~~Gl~aaR~~F~k~rk~~~~~h~vyi~~A~~E~~~-~~d~~ta~~ifelGl~~--f~d~~~y~~kyl  473 (660)
T COG5107         397 TFVFCVHLNYVLRKRGLEAARKLFIKLRKEGIVGHHVYIYCAFIEYYA-TGDRATAYNIFELGLLK--FPDSTLYKEKYL  473 (660)
T ss_pred             hhHHHHHHHHHHHHhhHHHHHHHHHHHhccCCCCcceeeeHHHHHHHh-cCCcchHHHHHHHHHHh--CCCchHHHHHHH
Confidence            4567777777778888999999999999877 5567788888887665 68899999999987765  3454444 5667


Q ss_pred             HHHHHcCChhHHHHHHHHHHHCCCCCC--HHHHHHHHHHHHhcCccc
Q 040027          530 HGFIRINEPSKVNELLHKMKEKKVMPD--ASIVSIVVDLLVKNEISL  574 (595)
Q Consensus       530 ~~~~~~g~~~~A~~~~~~~~~~~~~p~--~~~~~~l~~~~~~~g~~~  574 (595)
                      .-+...|+-+.|..+|++.+++ +..+  ..+|..+++-=+.-|.+.
T Consensus       474 ~fLi~inde~naraLFetsv~r-~~~~q~k~iy~kmi~YEs~~G~lN  519 (660)
T COG5107         474 LFLIRINDEENARALFETSVER-LEKTQLKRIYDKMIEYESMVGSLN  519 (660)
T ss_pred             HHHHHhCcHHHHHHHHHHhHHH-HHHhhhhHHHHHHHHHHHhhcchH
Confidence            7778899999999999988754 3344  678899988888888875

>COG3898 Uncharacterized membrane-bound protein [Function unknown]

Probab=97.41  E-value=0.11  Score=48.21  Aligned_cols=286  Identities=11%  Similarity=0.070  Sum_probs=148.5

Q ss_pred             cCCHhHHHHHHHHHHhcCCCCCHhhHHHHHHH--HHhcCChhHHHHHHHHHHhcCCCCCccccCcHHH--HHHHHHHHHH
Q 040027          144 ESRIMEAAALFTKLKAFGCEPNVITYNTLING--LCRTGHTMIALNLFEEMANGNGEIGVVCKPNTVT--YSTIIDGLCK  219 (595)
Q Consensus       144 ~g~~~~A~~~~~~~~~~~~~~~~~~~~~l~~~--~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~~~~~--~~~l~~~~~~  219 (595)
                      .|+-..|.++-.+..+. +..|......++.+  -.-.|+++.|.+-|+.|...         |....  ...|.-..-+
T Consensus        97 AGda~lARkmt~~~~~l-lssDqepLIhlLeAQaal~eG~~~~Ar~kfeAMl~d---------PEtRllGLRgLyleAqr  166 (531)
T COG3898          97 AGDASLARKMTARASKL-LSSDQEPLIHLLEAQAALLEGDYEDARKKFEAMLDD---------PETRLLGLRGLYLEAQR  166 (531)
T ss_pred             cCchHHHHHHHHHHHhh-hhccchHHHHHHHHHHHHhcCchHHHHHHHHHHhcC---------hHHHHHhHHHHHHHHHh
Confidence            45666666655554322 12233333333332  23467777777777777642         11111  1222222335


Q ss_pred             cCCHhHHHHHHHHHhhCCCCCCHhHHHHHHHHHHhcCCHHHHHHHHHHHHHCC-CCCCHhhH--HHHHHH--H-HhcCCh
Q 040027          220 EGFVDKAKALFLQMKDENINPDVVTYNSLIHGLCHANDWNEAKRLFIEMMDQG-VQPSVVTF--NVIMDE--L-CKNRKM  293 (595)
Q Consensus       220 ~g~~~~A~~~~~~~~~~~~~~~~~~~~~ll~~~~~~~~~~~A~~~~~~~~~~~-~~~~~~~~--~~l~~~--~-~~~g~~  293 (595)
                      .|+.+.|..+-+..-..- +--...+...+...+..|+|+.|+++.+.-.... +.++..--  -.++.+  . .-.-+.
T Consensus       167 ~GareaAr~yAe~Aa~~A-p~l~WA~~AtLe~r~~~gdWd~AlkLvd~~~~~~vie~~~aeR~rAvLLtAkA~s~ldadp  245 (531)
T COG3898         167 LGAREAARHYAERAAEKA-PQLPWAARATLEARCAAGDWDGALKLVDAQRAAKVIEKDVAERSRAVLLTAKAMSLLDADP  245 (531)
T ss_pred             cccHHHHHHHHHHHHhhc-cCCchHHHHHHHHHHhcCChHHHHHHHHHHHHHHhhchhhHHHHHHHHHHHHHHHHhcCCh
Confidence            677777777666655432 2234556666777777777777777776654432 22332211  111111  1 112244


Q ss_pred             HHHHHHHHHHHHCCCCCCHHH-HHHHHHHHHhcCCHHHHHHHHHHHHhcCCCCCHHHHHHHHHHHHhCCCHHHHHHHHHH
Q 040027          294 DEASRLLDLMVQRGVRPNACT-YNTLMDGFCLMGKINRAEELFGSMESMGCKHDDVSYNILINGYCKNKEVEEALSLYRE  372 (595)
Q Consensus       294 ~~a~~~~~~~~~~~~~~~~~~-~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~A~~~~~~  372 (595)
                      ..|.+.-.+..+.  .|+... .....+++.+.|+..++-.+++.+-+..  |.+..+.  +..+.+.|+  .++.-+++
T Consensus       246 ~~Ar~~A~~a~KL--~pdlvPaav~AAralf~d~~~rKg~~ilE~aWK~e--PHP~ia~--lY~~ar~gd--ta~dRlkR  317 (531)
T COG3898         246 ASARDDALEANKL--APDLVPAAVVAARALFRDGNLRKGSKILETAWKAE--PHPDIAL--LYVRARSGD--TALDRLKR  317 (531)
T ss_pred             HHHHHHHHHHhhc--CCccchHHHHHHHHHHhccchhhhhhHHHHHHhcC--CChHHHH--HHHHhcCCC--cHHHHHHH
Confidence            5555555544443  333222 2233566777778888878877777663  3333332  222334443  33333332


Q ss_pred             HHHC-CCCC-CHHHHHHHHHHHHccCCHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHH-hcCCHHHHHHHHHHHHHcCCC
Q 040027          373 MVSK-GIKP-TVVTYNTLFLGLFEIHQVEHALKLFDEMQRDGVAADTRTYTTFIDGLC-KNGYIIEAVELFRTLRILKCE  449 (595)
Q Consensus       373 ~~~~-~~~~-~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~-~~g~~~~A~~~~~~~~~~~~~  449 (595)
                      .... ..+| +..+...+..+-...|++..|..--+...+.  .|....|..+...-. ..|+-.++..++.+..+...+
T Consensus       318 a~~L~slk~nnaes~~~va~aAlda~e~~~ARa~Aeaa~r~--~pres~~lLlAdIeeAetGDqg~vR~wlAqav~APrd  395 (531)
T COG3898         318 AKKLESLKPNNAESSLAVAEAALDAGEFSAARAKAEAAARE--APRESAYLLLADIEEAETGDQGKVRQWLAQAVKAPRD  395 (531)
T ss_pred             HHHHHhcCccchHHHHHHHHHHHhccchHHHHHHHHHHhhh--CchhhHHHHHHHHHhhccCchHHHHHHHHHHhcCCCC
Confidence            2211 1222 4455566666777777777777666666553  566666666666543 348888888888877765433


Q ss_pred             c
Q 040027          450 L  450 (595)
Q Consensus       450 ~  450 (595)
                      |
T Consensus       396 P  396 (531)
T COG3898         396 P  396 (531)
T ss_pred             C
Confidence            3

>KOG2796 consensus Uncharacterized conserved protein [Function unknown]

Probab=97.39  E-value=0.079  Score=46.21  Aligned_cols=130  Identities=12%  Similarity=0.022  Sum_probs=75.1

Q ss_pred             HHHHHHHHccCCHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCcCHHH-----HHHHHH
Q 040027          386 NTLFLGLFEIHQVEHALKLFDEMQRDGVAADTRTYTTFIDGLCKNGYIIEAVELFRTLRILKCELDIQA-----YNCLID  460 (595)
Q Consensus       386 ~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~-----~~~l~~  460 (595)
                      +.++..+.-.+.+.-....+.+.++...+.++...+.++..-.+.|+.+.|...|++..+..-..+...     ......
T Consensus       181 y~~~~~llG~kEy~iS~d~~~~vi~~~~e~~p~L~s~Lgr~~MQ~GD~k~a~~yf~~vek~~~kL~~~q~~~~V~~n~a~  260 (366)
T KOG2796|consen  181 YSMANCLLGMKEYVLSVDAYHSVIKYYPEQEPQLLSGLGRISMQIGDIKTAEKYFQDVEKVTQKLDGLQGKIMVLMNSAF  260 (366)
T ss_pred             HHHHHHHhcchhhhhhHHHHHHHHHhCCcccHHHHHHHHHHHHhcccHHHHHHHHHHHHHHHhhhhccchhHHHHhhhhh
Confidence            444555556666666666777776665556666667777777777777777777776554322222222     222233


Q ss_pred             HHHhcCChHHHHHHHHhcccCCCCCCHHHHHHHHHHHHhcCChhHHHHHHHHHHHc
Q 040027          461 GLCKSGRLKFAWELFCSLPHGVLVPNVVTYNIMIQGLCNDGQMDKARDLFLDMEEN  516 (595)
Q Consensus       461 ~~~~~g~~~~A~~~~~~~~~~~~~p~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~  516 (595)
                      .|.-++++..|...++++...+ +.|+...|.-+.+..-.|+...|++.++.|.+.
T Consensus       261 i~lg~nn~a~a~r~~~~i~~~D-~~~~~a~NnKALcllYlg~l~DAiK~~e~~~~~  315 (366)
T KOG2796|consen  261 LHLGQNNFAEAHRFFTEILRMD-PRNAVANNNKALCLLYLGKLKDALKQLEAMVQQ  315 (366)
T ss_pred             heecccchHHHHHHHhhccccC-CCchhhhchHHHHHHHHHHHHHHHHHHHHHhcc
Confidence            4445566666666666666531 123444455455555566667777777766664

>PRK10803 tol-pal system protein YbgF; Provisional

Probab=97.31  E-value=0.0065  Score=54.97  Aligned_cols=94  Identities=16%  Similarity=0.094  Sum_probs=56.2

Q ss_pred             HHHHHHHHHhcCChHHHHHHHHhcccCCCCCCH----HHHHHHHHHHHhcCChhHHHHHHHHHHHcC--CCCCHHHHHHH
Q 040027          455 YNCLIDGLCKSGRLKFAWELFCSLPHGVLVPNV----VTYNIMIQGLCNDGQMDKARDLFLDMEENA--AAPDVITFDML  528 (595)
Q Consensus       455 ~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~p~~----~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~--~~~~~~~~~~l  528 (595)
                      |...+....+.|++++|+..|+.++..  .|+.    ..+..++.+|...|++++|...|+.+++..  -+.....+..+
T Consensus       146 Y~~A~~l~~~~~~y~~Ai~af~~fl~~--yP~s~~a~~A~y~LG~~y~~~g~~~~A~~~f~~vv~~yP~s~~~~dAl~kl  223 (263)
T PRK10803        146 YNAAIALVQDKSRQDDAIVAFQNFVKK--YPDSTYQPNANYWLGQLNYNKGKKDDAAYYFASVVKNYPKSPKAADAMFKV  223 (263)
T ss_pred             HHHHHHHHHhcCCHHHHHHHHHHHHHH--CcCCcchHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHCCCCcchhHHHHHH
Confidence            344333344556677777777666652  3332    355566667777777777777777776541  11124445555


Q ss_pred             HHHHHHcCChhHHHHHHHHHHH
Q 040027          529 IHGFIRINEPSKVNELLHKMKE  550 (595)
Q Consensus       529 ~~~~~~~g~~~~A~~~~~~~~~  550 (595)
                      +.++...|++++|.++|+++.+
T Consensus       224 g~~~~~~g~~~~A~~~~~~vi~  245 (263)
T PRK10803        224 GVIMQDKGDTAKAKAVYQQVIK  245 (263)
T ss_pred             HHHHHHcCCHHHHHHHHHHHHH
Confidence            6666677777777777777765

>PF01535 PPR: PPR repeat; InterPro: IPR002885 This entry represents the PPR repeat

Probab=97.29  E-value=0.00039  Score=39.21  Aligned_cols=29  Identities=41%  Similarity=0.799  Sum_probs=16.4

Q ss_pred             HHHHHHHHHHhcCChhHHHHHHHHHHHcC
Q 040027          489 TYNIMIQGLCNDGQMDKARDLFLDMEENA  517 (595)
Q Consensus       489 ~~~~l~~~~~~~g~~~~A~~~~~~~~~~~  517 (595)
                      +|+.++.+|++.|++++|.++|++|.+.|
T Consensus         2 ~y~~li~~~~~~~~~~~a~~~~~~M~~~g   30 (31)
T PF01535_consen    2 TYNSLISGYCKMGQFEEALEVFDEMRERG   30 (31)
T ss_pred             cHHHHHHHHHccchHHHHHHHHHHHhHCc
Confidence            45555555555555555555555555543

Pentatricopeptide repeat (PPR) proteins are characterised by tandem repeats of a degenerate 35 amino acid motif []. Most of PPR proteins have roles in mitochondria or plastid []. PPR repeats were discovered while screening Arabidopsis proteins for those predicted to be targeted to mitochondria or chloroplast [, ]. Some of these proteins have been shown to play a role in post-transcriptional processes within organelles and they are thought to be sequence-specific RNA-binding proteins [, , ]. Plant genomes have between one hundred to five hundred PPR genes per genome whereas non-plant genomes encode two to six PPR proteins. Although no PPR structures are yet known, the motif is predicted to fold into a helix-turn-helix structure similar to those found in the tetratricopeptide repeat (TPR) family (see PDOC50005 from PROSITEDOC) []. The plant PPR protein family has been divided in two subfamilies on the basis of their motif content and organisation [, ]. Examples of PPR repeat-containing proteins include PET309 P32522 from SWISSPROT, which may be involved in RNA stabilisation [], and crp1, which is involved in RNA processing []. The repeat is associated with a predicted plant protein O49549 from SWISSPROT that has a domain organisation similar to the human BRCA1 protein.

>KOG1538 consensus Uncharacterized conserved protein WDR10, contains WD40 repeats [General function prediction only]

Probab=97.27  E-value=0.04  Score=54.19  Aligned_cols=53  Identities=15%  Similarity=0.110  Sum_probs=29.2

Q ss_pred             HHHHHHHHHHhcCCHHHHHHHHHHHHhcCCCCCHHHHHHHHHHHHhCCCHHHHHHHHHHHHH
Q 040027          314 TYNTLMDGFCLMGKINRAEELFGSMESMGCKHDDVSYNILINGYCKNKEVEEALSLYREMVS  375 (595)
Q Consensus       314 ~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~  375 (595)
                      +...+..-+.+...+..|.++|..|-..         ..++..+...++|++|..+-+...+
T Consensus       749 ~l~~~a~ylk~l~~~gLAaeIF~k~gD~---------ksiVqlHve~~~W~eAFalAe~hPe  801 (1081)
T KOG1538|consen  749 PLLLCATYLKKLDSPGLAAEIFLKMGDL---------KSLVQLHVETQRWDEAFALAEKHPE  801 (1081)
T ss_pred             HHHHHHHHHhhccccchHHHHHHHhccH---------HHHhhheeecccchHhHhhhhhCcc
Confidence            3444444444555566666666655321         2345556666777777766655443

>KOG1258 consensus mRNA processing protein [RNA processing and modification]

Probab=97.27  E-value=0.23  Score=49.00  Aligned_cols=400  Identities=10%  Similarity=-0.004  Sum_probs=185.1

Q ss_pred             ChhHHHHHHHHHHhCCCCCCHHHHHHHHHHHHhcCCHhHHHHHHHHHHhcCCCCCHhhHHHHHHHHH-hcCChhHHHHHH
Q 040027          111 RVSLGFIAFGRILRSCFTPNAATFNSLIKGLHAESRIMEAAALFTKLKAFGCEPNVITYNTLINGLC-RTGHTMIALNLF  189 (595)
Q Consensus       111 ~~~~A~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~~l~~~~~-~~g~~~~A~~~~  189 (595)
                      ..+.+..++..++.. .|.--.-|......=.+.|..+.+.++|++.+. +++.+...|......+. ..|+.+.....|
T Consensus        60 ~~~~~r~~y~~fL~k-yPl~~gyW~kfA~~E~klg~~~~s~~Vfergv~-aip~SvdlW~~Y~~f~~n~~~d~~~lr~~f  137 (577)
T KOG1258|consen   60 DVDALREVYDIFLSK-YPLCYGYWKKFADYEYKLGNAENSVKVFERGVQ-AIPLSVDLWLSYLAFLKNNNGDPETLRDLF  137 (577)
T ss_pred             HHHHHHHHHHHHHhh-CccHHHHHHHHHHHHHHhhhHHHHHHHHHHHHH-hhhhHHHHHHHHHHHHhccCCCHHHHHHHH
Confidence            335555566666543 122223445555555566777788888887765 35666666665555443 356666777777


Q ss_pred             HHHHhcCCCCCccccCcHHHHHHHHHHHHHcCCHhHHHHHHHHHhhCCCCCCHhHHHHHHHHHH---hc------CCHHH
Q 040027          190 EEMANGNGEIGVVCKPNTVTYSTIIDGLCKEGFVDKAKALFLQMKDENINPDVVTYNSLIHGLC---HA------NDWNE  260 (595)
Q Consensus       190 ~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~~ll~~~~---~~------~~~~~  260 (595)
                      +.+....|.    --.....|...|..-...+++.....+++++.+.    ....++....-|.   +.      ...++
T Consensus       138 e~A~~~vG~----dF~S~~lWdkyie~en~qks~k~v~~iyeRilei----P~~~~~~~f~~f~~~l~~~~~~~l~~~d~  209 (577)
T KOG1258|consen  138 ERAKSYVGL----DFLSDPLWDKYIEFENGQKSWKRVANIYERILEI----PLHQLNRHFDRFKQLLNQNEEKILLSIDE  209 (577)
T ss_pred             HHHHHhccc----chhccHHHHHHHHHHhccccHHHHHHHHHHHHhh----hhhHhHHHHHHHHHHHhcCChhhhcCHHH
Confidence            777665321    1123456777777777777788888888877763    1222222222221   11      12222


Q ss_pred             HHHHHHHHHHC---C-CCCCHhhHHHHHHHHH-hcCChHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHhcCCHHHHHHHH
Q 040027          261 AKRLFIEMMDQ---G-VQPSVVTFNVIMDELC-KNRKMDEASRLLDLMVQRGVRPNACTYNTLMDGFCLMGKINRAEELF  335 (595)
Q Consensus       261 A~~~~~~~~~~---~-~~~~~~~~~~l~~~~~-~~g~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~  335 (595)
                      +.++-......   + ..+....+...+.-.. ..+..+++...+.+...           ..-.++-..-.....+..+
T Consensus       210 ~~~l~~~~~~~~~~~~~~~~~e~~~~~v~~~~~~s~~l~~~~~~l~~~~~-----------~~~~~~~~s~~~~~kr~~f  278 (577)
T KOG1258|consen  210 LIQLRSDVAERSKITHSQEPLEELEIGVKDSTDPSKSLTEEKTILKRIVS-----------IHEKVYQKSEEEEEKRWGF  278 (577)
T ss_pred             HHHHhhhHHhhhhcccccChhHHHHHHHhhccCccchhhHHHHHHHHHHH-----------HHHHHHHhhHhHHHHHHhh
Confidence            22222221110   0 0000000000000000 00011111111111100           0001111112222222233


Q ss_pred             HHHHhcC-------CCCCHHHHHHHHHHHHhCCCHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHccCCHHHHHHHHHHH
Q 040027          336 GSMESMG-------CKHDDVSYNILINGYCKNKEVEEALSLYREMVSKGIKPTVVTYNTLFLGLFEIHQVEHALKLFDEM  408 (595)
Q Consensus       336 ~~~~~~~-------~~~~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~  408 (595)
                      +.-.+.-       .+.....|...+..-...|+++.+.-+|++..-. +..-...|-..+.-....|+.+-+..++...
T Consensus       279 E~~IkrpYfhvkpl~~aql~nw~~yLdf~i~~g~~~~~~~l~ercli~-cA~Y~efWiky~~~m~~~~~~~~~~~~~~~~  357 (577)
T KOG1258|consen  279 EEGIKRPYFHVKPLDQAQLKNWRYYLDFEITLGDFSRVFILFERCLIP-CALYDEFWIKYARWMESSGDVSLANNVLARA  357 (577)
T ss_pred             hhhccccccccCcccHHHHHHHHHHhhhhhhcccHHHHHHHHHHHHhH-HhhhHHHHHHHHHHHHHcCchhHHHHHHHhh
Confidence            3222210       0123345666666677777777777777766531 1112233444444444457777777666655


Q ss_pred             HHCCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCcCHHHHHHHHHHHHhcCChHHHH---HHHHhcccCCCCC
Q 040027          409 QRDGVAADTRTYTTFIDGLCKNGYIIEAVELFRTLRILKCELDIQAYNCLIDGLCKSGRLKFAW---ELFCSLPHGVLVP  485 (595)
Q Consensus       409 ~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~---~~~~~~~~~~~~p  485 (595)
                      .+-..+..+.+-..-....-..|++..|..+++.+...- +--...-..-+....+.|+.+.+.   .++........  
T Consensus       358 ~~i~~k~~~~i~L~~a~f~e~~~n~~~A~~~lq~i~~e~-pg~v~~~l~~~~~e~r~~~~~~~~~~~~l~s~~~~~~~--  434 (577)
T KOG1258|consen  358 CKIHVKKTPIIHLLEARFEESNGNFDDAKVILQRIESEY-PGLVEVVLRKINWERRKGNLEDANYKNELYSSIYEGKE--  434 (577)
T ss_pred             hhhcCCCCcHHHHHHHHHHHhhccHHHHHHHHHHHHhhC-CchhhhHHHHHhHHHHhcchhhhhHHHHHHHHhccccc--
Confidence            554322222222111122234567777777777777643 222222233344455666766666   44443333211  


Q ss_pred             CHHHHHHHHH-----HHHhcCChhHHHHHHHHHHHcCCCCCHHHHHHHHHHHHHcC
Q 040027          486 NVVTYNIMIQ-----GLCNDGQMDKARDLFLDMEENAAAPDVITFDMLIHGFIRIN  536 (595)
Q Consensus       486 ~~~~~~~l~~-----~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g  536 (595)
                      +......+..     .+.-.++.+.|..++.++.+. ++++...|..+++.+...+
T Consensus       435 ~~~i~~~l~~~~~r~~~~i~~d~~~a~~~l~~~~~~-~~~~k~~~~~~~~~~~~~~  489 (577)
T KOG1258|consen  435 NNGILEKLYVKFARLRYKIREDADLARIILLEANDI-LPDCKVLYLELIRFELIQP  489 (577)
T ss_pred             CcchhHHHHHHHHHHHHHHhcCHHHHHHHHHHhhhc-CCccHHHHHHHHHHHHhCC
Confidence            1111211111     122356777777777777775 3556666666666555444

>PF13371 TPR_9: Tetratricopeptide repeat

Probab=97.26  E-value=0.0021  Score=45.35  Aligned_cols=56  Identities=13%  Similarity=0.027  Sum_probs=38.8

Q ss_pred             HHHHhcCChhHHHHHHHHHHHcCCCCCHHHHHHHHHHHHHcCChhHHHHHHHHHHHC
Q 040027          495 QGLCNDGQMDKARDLFLDMEENAAAPDVITFDMLIHGFIRINEPSKVNELLHKMKEK  551 (595)
Q Consensus       495 ~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~  551 (595)
                      ..|.+.+++++|.+++++++..+ |.+...+...+.++...|++++|.+.+++..+.
T Consensus         3 ~~~~~~~~~~~A~~~~~~~l~~~-p~~~~~~~~~a~~~~~~g~~~~A~~~l~~~l~~   58 (73)
T PF13371_consen    3 QIYLQQEDYEEALEVLERALELD-PDDPELWLQRARCLFQLGRYEEALEDLERALEL   58 (73)
T ss_pred             HHHHhCCCHHHHHHHHHHHHHhC-cccchhhHHHHHHHHHhccHHHHHHHHHHHHHH
Confidence            45666777777777777777764 445566666777777777777777777777764

>PF03704 BTAD: Bacterial transcriptional activator domain; InterPro: IPR005158 Found in the DNRI/REDD/AFSR family of regulators, this region of AFSR (P25941 from SWISSPROT) along with the C-terminal region is capable of independently directing actinorhodin production

Probab=97.25  E-value=0.0034  Score=51.63  Aligned_cols=75  Identities=11%  Similarity=0.189  Sum_probs=53.2

Q ss_pred             HHHHHHHHHHhcCChhHHHHHHHHHHHcCCCCCHHHHHHHHHHHHHcCChhHHHHHHHHHH-----HCCCCCCHHHHHHH
Q 040027          489 TYNIMIQGLCNDGQMDKARDLFLDMEENAAAPDVITFDMLIHGFIRINEPSKVNELLHKMK-----EKKVMPDASIVSIV  563 (595)
Q Consensus       489 ~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~-----~~~~~p~~~~~~~l  563 (595)
                      ....++..+...|++++|+.+.++++... |-+...|..++.+|...|+..+|.++|+++.     +.|+.|++.+-...
T Consensus        64 ~~~~l~~~~~~~~~~~~a~~~~~~~l~~d-P~~E~~~~~lm~~~~~~g~~~~A~~~Y~~~~~~l~~elg~~Ps~~~~~l~  142 (146)
T PF03704_consen   64 ALERLAEALLEAGDYEEALRLLQRALALD-PYDEEAYRLLMRALAAQGRRAEALRVYERYRRRLREELGIEPSPETRALY  142 (146)
T ss_dssp             HHHHHHHHHHHTT-HHHHHHHHHHHHHHS-TT-HHHHHHHHHHHHHTT-HHHHHHHHHHHHHHHHHHHS----HHHHHHH
T ss_pred             HHHHHHHHHHhccCHHHHHHHHHHHHhcC-CCCHHHHHHHHHHHHHCcCHHHHHHHHHHHHHHHHHHhCcCcCHHHHHHH
Confidence            44556667778889999999998888875 6677888888999999999999988888875     45888888776554


Q ss_pred             H
Q 040027          564 V  564 (595)
Q Consensus       564 ~  564 (595)
                      -
T Consensus       143 ~  143 (146)
T PF03704_consen  143 R  143 (146)
T ss_dssp             H
T ss_pred             H
Confidence            3

It is important for the formation of secondary metabolites.; PDB: 2FF4_B 2FEZ_A.

>PRK10803 tol-pal system protein YbgF; Provisional

Probab=97.22  E-value=0.0071  Score=54.72  Aligned_cols=100  Identities=13%  Similarity=0.024  Sum_probs=78.8

Q ss_pred             HHHHHHHHHHHhcCChhHHHHHHHHHHhCCCCCC--HHHHHHHHHHHHhcCCHhHHHHHHHHHHhcCC--CCCHhhHHHH
Q 040027           97 YTYNILINCFCKIGRVSLGFIAFGRILRSCFTPN--AATFNSLIKGLHAESRIMEAAALFTKLKAFGC--EPNVITYNTL  172 (595)
Q Consensus        97 ~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~~--~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~--~~~~~~~~~l  172 (595)
                      ..|...+....+.|++++|+..|+.+++.-+...  +.++..+...|...|++++|+..|+.+...-.  +....++..+
T Consensus       144 ~~Y~~A~~l~~~~~~y~~Ai~af~~fl~~yP~s~~a~~A~y~LG~~y~~~g~~~~A~~~f~~vv~~yP~s~~~~dAl~kl  223 (263)
T PRK10803        144 TDYNAAIALVQDKSRQDDAIVAFQNFVKKYPDSTYQPNANYWLGQLNYNKGKKDDAAYYFASVVKNYPKSPKAADAMFKV  223 (263)
T ss_pred             HHHHHHHHHHHhcCCHHHHHHHHHHHHHHCcCCcchHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHCCCCcchhHHHHHH
Confidence            4455555555778999999999999999832211  35788899999999999999999999987621  1235566677


Q ss_pred             HHHHHhcCChhHHHHHHHHHHhcC
Q 040027          173 INGLCRTGHTMIALNLFEEMANGN  196 (595)
Q Consensus       173 ~~~~~~~g~~~~A~~~~~~~~~~~  196 (595)
                      +.++...|+.++|..+|+.+.+..
T Consensus       224 g~~~~~~g~~~~A~~~~~~vi~~y  247 (263)
T PRK10803        224 GVIMQDKGDTAKAKAVYQQVIKKY  247 (263)
T ss_pred             HHHHHHcCCHHHHHHHHHHHHHHC
Confidence            888889999999999999999865

>PF01535 PPR: PPR repeat; InterPro: IPR002885 This entry represents the PPR repeat

Probab=97.19  E-value=0.00054  Score=38.61  Aligned_cols=30  Identities=23%  Similarity=0.591  Sum_probs=28.2

Q ss_pred             HHHHHHHHHHHcCChhHHHHHHHHHHHCCC
Q 040027          524 TFDMLIHGFIRINEPSKVNELLHKMKEKKV  553 (595)
Q Consensus       524 ~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~  553 (595)
                      +|+.++.+|++.|++++|.+++++|.+.|+
T Consensus         2 ~y~~li~~~~~~~~~~~a~~~~~~M~~~g~   31 (31)
T PF01535_consen    2 TYNSLISGYCKMGQFEEALEVFDEMRERGI   31 (31)
T ss_pred             cHHHHHHHHHccchHHHHHHHHHHHhHCcC
Confidence            689999999999999999999999998774

Pentatricopeptide repeat (PPR) proteins are characterised by tandem repeats of a degenerate 35 amino acid motif []. Most of PPR proteins have roles in mitochondria or plastid []. PPR repeats were discovered while screening Arabidopsis proteins for those predicted to be targeted to mitochondria or chloroplast [, ]. Some of these proteins have been shown to play a role in post-transcriptional processes within organelles and they are thought to be sequence-specific RNA-binding proteins [, , ]. Plant genomes have between one hundred to five hundred PPR genes per genome whereas non-plant genomes encode two to six PPR proteins. Although no PPR structures are yet known, the motif is predicted to fold into a helix-turn-helix structure similar to those found in the tetratricopeptide repeat (TPR) family (see PDOC50005 from PROSITEDOC) []. The plant PPR protein family has been divided in two subfamilies on the basis of their motif content and organisation [, ]. Examples of PPR repeat-containing proteins include PET309 P32522 from SWISSPROT, which may be involved in RNA stabilisation [], and crp1, which is involved in RNA processing []. The repeat is associated with a predicted plant protein O49549 from SWISSPROT that has a domain organisation similar to the human BRCA1 protein.

>PF06239 ECSIT: Evolutionarily conserved signalling intermediate in Toll pathway; InterPro: IPR010418 Activation of NF-kappaB as a consequence of signalling through the Toll and IL-1 receptors is a major element of innate immune responses

Probab=97.14  E-value=0.0065  Score=51.48  Aligned_cols=105  Identities=14%  Similarity=0.273  Sum_probs=54.4

Q ss_pred             CcCHHHHHHHHHHHHh-----cCChHHHHHHHHhcccCCCCCCHHHHHHHHHHHHhcCChhHHHHHHHHHHHcCCCCCHH
Q 040027          449 ELDIQAYNCLIDGLCK-----SGRLKFAWELFCSLPHGVLVPNVVTYNIMIQGLCNDGQMDKARDLFLDMEENAAAPDVI  523 (595)
Q Consensus       449 ~~~~~~~~~l~~~~~~-----~g~~~~A~~~~~~~~~~~~~p~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~~~~  523 (595)
                      ..+..+|..+++.|.+     .|..+=....+..|.+.|+.-|..+|+.|+..+=+ |.+-               |. .
T Consensus        44 ~k~K~~F~~~V~~f~~~~~~RRGHVeFI~aAL~~M~efgv~kDL~~Y~~LLDvFPK-g~fv---------------p~-n  106 (228)
T PF06239_consen   44 AKDKATFLEAVDIFKQRDVRRRGHVEFIYAALKKMDEFGVEKDLEVYKALLDVFPK-GKFV---------------PR-N  106 (228)
T ss_pred             cccHHHHHHHHHHHHhcCCCCcChHHHHHHHHHHHHHcCCcccHHHHHHHHHhCCC-CCcc---------------cc-c
Confidence            3456666666666653     24555555556666666666666666666665553 2211               00 0


Q ss_pred             HHHHHHHHHHHcCChhHHHHHHHHHHHCCCCCCHHHHHHHHHHHHhcCc
Q 040027          524 TFDMLIHGFIRINEPSKVNELLHKMKEKKVMPDASIVSIVVDLLVKNEI  572 (595)
Q Consensus       524 ~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~p~~~~~~~l~~~~~~~g~  572 (595)
                      .+.....-|  -.+.+-|++++++|...|+-||.+++..+++++++.+.
T Consensus       107 ~fQ~~F~hy--p~Qq~c~i~lL~qME~~gV~Pd~Et~~~ll~iFG~~s~  153 (228)
T PF06239_consen  107 FFQAEFMHY--PRQQECAIDLLEQMENNGVMPDKETEQMLLNIFGRKSH  153 (228)
T ss_pred             HHHHHhccC--cHHHHHHHHHHHHHHHcCCCCcHHHHHHHHHHhccccH
Confidence            000000000  01224566666666666666666666666666666554

ECSIT plays an important role in signalling to NF-kappaB, functioning as the intermediate in the signalling pathways between TRAF-6 and MEKK-1 [].

>PF04840 Vps16_C: Vps16, C-terminal region; InterPro: IPR006925 This protein forms part of the Class C vacuolar protein sorting (Vps) complex

Probab=97.12  E-value=0.24  Score=46.41  Aligned_cols=107  Identities=17%  Similarity=0.091  Sum_probs=52.9

Q ss_pred             HHHHHHhCCCHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHccCCHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHhcCC
Q 040027          353 LINGYCKNKEVEEALSLYREMVSKGIKPTVVTYNTLFLGLFEIHQVEHALKLFDEMQRDGVAADTRTYTTFIDGLCKNGY  432 (595)
Q Consensus       353 l~~~~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~  432 (595)
                      -+.-+...|+...|.++-.+..    .|+..-|...+.+++..++|++..+....      .-++..|..++.+|.+.|.
T Consensus       183 Ti~~li~~~~~k~A~kl~k~Fk----v~dkrfw~lki~aLa~~~~w~eL~~fa~s------kKsPIGyepFv~~~~~~~~  252 (319)
T PF04840_consen  183 TIRKLIEMGQEKQAEKLKKEFK----VPDKRFWWLKIKALAENKDWDELEKFAKS------KKSPIGYEPFVEACLKYGN  252 (319)
T ss_pred             HHHHHHHCCCHHHHHHHHHHcC----CcHHHHHHHHHHHHHhcCCHHHHHHHHhC------CCCCCChHHHHHHHHHCCC
Confidence            3444445555555555544432    23555555556666666666555443221      1123445555666666666


Q ss_pred             HHHHHHHHHHHHHcCCCcCHHHHHHHHHHHHhcCChHHHHHHHHhcc
Q 040027          433 IIEAVELFRTLRILKCELDIQAYNCLIDGLCKSGRLKFAWELFCSLP  479 (595)
Q Consensus       433 ~~~A~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~  479 (595)
                      ..+|..++.++     +.     ..-+..|.+.|++.+|.+.--+..
T Consensus       253 ~~eA~~yI~k~-----~~-----~~rv~~y~~~~~~~~A~~~A~~~k  289 (319)
T PF04840_consen  253 KKEASKYIPKI-----PD-----EERVEMYLKCGDYKEAAQEAFKEK  289 (319)
T ss_pred             HHHHHHHHHhC-----Ch-----HHHHHHHHHCCCHHHHHHHHHHcC
Confidence            66665555541     11     223445555566655555544433

Vps16 is essential for vacuolar protein sorting, which is essential for viability in plants, but not yeast []. The Class C Vps complex is required for SNARE-mediated membrane fusion at the lysosome-like yeast vacuole. It is thought to play essential roles in membrane docking and fusion at the Golgi-to-endosome and endosome-to-vacuole stages of transport []. The role of VPS16 in this complex is not known.; GO: 0006886 intracellular protein transport, 0005737 cytoplasm

>KOG2796 consensus Uncharacterized conserved protein [Function unknown]

Probab=97.10  E-value=0.17  Score=44.27  Aligned_cols=141  Identities=14%  Similarity=0.041  Sum_probs=92.3

Q ss_pred             HHHHHHHHHhCCCHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHccCCHHHHHHHHHHHHHCC-----CCCCHHHHHHHH
Q 040027          350 YNILINGYCKNKEVEEALSLYREMVSKGIKPTVVTYNTLFLGLFEIHQVEHALKLFDEMQRDG-----VAADTRTYTTFI  424 (595)
Q Consensus       350 ~~~l~~~~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~-----~~~~~~~~~~l~  424 (595)
                      .+.++.++.-.+.+.-....+.+.++...+-++.....+++.-.+.|+.+.|...|++..+..     ............
T Consensus       180 my~~~~~llG~kEy~iS~d~~~~vi~~~~e~~p~L~s~Lgr~~MQ~GD~k~a~~yf~~vek~~~kL~~~q~~~~V~~n~a  259 (366)
T KOG2796|consen  180 MYSMANCLLGMKEYVLSVDAYHSVIKYYPEQEPQLLSGLGRISMQIGDIKTAEKYFQDVEKVTQKLDGLQGKIMVLMNSA  259 (366)
T ss_pred             HHHHHHHHhcchhhhhhHHHHHHHHHhCCcccHHHHHHHHHHHHhcccHHHHHHHHHHHHHHHhhhhccchhHHHHhhhh
Confidence            344555666666777777777777776555566666777777777777777777777665431     222222233333


Q ss_pred             HHHHhcCCHHHHHHHHHHHHHcCCCcCHHHHHHHHHHHHhcCChHHHHHHHHhcccCCCCCCHHHHHHH
Q 040027          425 DGLCKNGYIIEAVELFRTLRILKCELDIQAYNCLIDGLCKSGRLKFAWELFCSLPHGVLVPNVVTYNIM  493 (595)
Q Consensus       425 ~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~p~~~~~~~l  493 (595)
                      ..|.-.+++..|...+.++...+ +.++...|.-.-+..-.|+...|++.++.+.+  ..|.+.+-+++
T Consensus       260 ~i~lg~nn~a~a~r~~~~i~~~D-~~~~~a~NnKALcllYlg~l~DAiK~~e~~~~--~~P~~~l~es~  325 (366)
T KOG2796|consen  260 FLHLGQNNFAEAHRFFTEILRMD-PRNAVANNNKALCLLYLGKLKDALKQLEAMVQ--QDPRHYLHESV  325 (366)
T ss_pred             hheecccchHHHHHHHhhccccC-CCchhhhchHHHHHHHHHHHHHHHHHHHHHhc--cCCccchhhhH
Confidence            44566778888888888887765 55666666666666667889999999998888  45655544433

>COG4105 ComL DNA uptake lipoprotein [General function prediction only]

Probab=97.09  E-value=0.17  Score=44.55  Aligned_cols=77  Identities=22%  Similarity=0.199  Sum_probs=56.4

Q ss_pred             cccccCCCChHHHHHHHHHHHHhCCCCCCHhhHHHHHHHHHcCCCchhHHhhCCCCCCHHHHHHHHHHHHhcCChhHHHH
Q 040027           38 REGDINVITPNEAFCIFDYMLRMHPSPPPVSSFNILLASLAKNKHYDTRLNATGLFPNLYTYNILINCFCKIGRVSLGFI  117 (595)
Q Consensus        38 ~~~~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~  117 (595)
                      +..-++.|++++|.+.|+.+...+|.  ++.+                          ..+...++.++.+.+++++|+.
T Consensus        41 g~~~L~~gn~~~A~~~fe~l~~~~p~--s~~~--------------------------~qa~l~l~yA~Yk~~~y~~A~~   92 (254)
T COG4105          41 GLTELQKGNYEEAIKYFEALDSRHPF--SPYS--------------------------EQAQLDLAYAYYKNGEYDLALA   92 (254)
T ss_pred             HHHHHhcCCHHHHHHHHHHHHHcCCC--Cccc--------------------------HHHHHHHHHHHHhcccHHHHHH
Confidence            33446779999999999999998887  4332                          3444467888889999999999


Q ss_pred             HHHHHHhCCCCCCHHHHHHHHHHHH
Q 040027          118 AFGRILRSCFTPNAATFNSLIKGLH  142 (595)
Q Consensus       118 ~~~~~~~~~~~~~~~~~~~l~~~~~  142 (595)
                      ..++....-+......|...+.++.
T Consensus        93 ~~drFi~lyP~~~n~dY~~YlkgLs  117 (254)
T COG4105          93 YIDRFIRLYPTHPNADYAYYLKGLS  117 (254)
T ss_pred             HHHHHHHhCCCCCChhHHHHHHHHH
Confidence            9999988855444455655565554

>PF13281 DUF4071: Domain of unknown function (DUF4071)

Probab=97.08  E-value=0.25  Score=46.77  Aligned_cols=30  Identities=10%  Similarity=0.003  Sum_probs=21.4

Q ss_pred             HHHHHHHHHHHHHcCChhHHHHHHHHHHHC
Q 040027          522 VITFDMLIHGFIRINEPSKVNELLHKMKEK  551 (595)
Q Consensus       522 ~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~  551 (595)
                      .-.+..++.++.-.|++++|.+.+++|.+.
T Consensus       305 YWd~ATl~Ea~vL~~d~~ka~~a~e~~~~l  334 (374)
T PF13281_consen  305 YWDVATLLEASVLAGDYEKAIQAAEKAFKL  334 (374)
T ss_pred             HHHHHHHHHHHHHcCCHHHHHHHHHHHhhc
Confidence            334456677777778888888888888764

>PF06239 ECSIT: Evolutionarily conserved signalling intermediate in Toll pathway; InterPro: IPR010418 Activation of NF-kappaB as a consequence of signalling through the Toll and IL-1 receptors is a major element of innate immune responses

Probab=97.06  E-value=0.014  Score=49.49  Aligned_cols=123  Identities=25%  Similarity=0.318  Sum_probs=85.7

Q ss_pred             HHHHHHHHHCCCCCCHHHHHHHHHHHHh-----cCCHHHHHHHHHHHHHcCCCcCHHHHHHHHHHHHhcCChHHHHHHHH
Q 040027          402 LKLFDEMQRDGVAADTRTYTTFIDGLCK-----NGYIIEAVELFRTLRILKCELDIQAYNCLIDGLCKSGRLKFAWELFC  476 (595)
Q Consensus       402 ~~~~~~~~~~~~~~~~~~~~~l~~~~~~-----~g~~~~A~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~  476 (595)
                      ...|+....  -..+..++..+++.|.+     .|..+=....++.|.+.|+..|..+|+.|++++=+ |.+- -..+|+
T Consensus        34 ~~~f~~~~~--~~k~K~~F~~~V~~f~~~~~~RRGHVeFI~aAL~~M~efgv~kDL~~Y~~LLDvFPK-g~fv-p~n~fQ  109 (228)
T PF06239_consen   34 EELFERAPG--QAKDKATFLEAVDIFKQRDVRRRGHVEFIYAALKKMDEFGVEKDLEVYKALLDVFPK-GKFV-PRNFFQ  109 (228)
T ss_pred             HHHHHHHhh--ccccHHHHHHHHHHHHhcCCCCcChHHHHHHHHHHHHHcCCcccHHHHHHHHHhCCC-CCcc-cccHHH
Confidence            344444432  25688999999999875     47788888889999999999999999999998754 3322 111111


Q ss_pred             hcccCCCCCCHHHHHHHHHHHHhcCChhHHHHHHHHHHHcCCCCCHHHHHHHHHHHHHcCChhHHHHHHHHH
Q 040027          477 SLPHGVLVPNVVTYNIMIQGLCNDGQMDKARDLFLDMEENAAAPDVITFDMLIHGFIRINEPSKVNELLHKM  548 (595)
Q Consensus       477 ~~~~~~~~p~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~  548 (595)
                      .+               ..-  .-.+-+-|++++++|...|+-||..++..++..+.+   ...+.+-+.+|
T Consensus       110 ~~---------------F~h--yp~Qq~c~i~lL~qME~~gV~Pd~Et~~~ll~iFG~---~s~p~~K~~rm  161 (228)
T PF06239_consen  110 AE---------------FMH--YPRQQECAIDLLEQMENNGVMPDKETEQMLLNIFGR---KSHPMKKYRRM  161 (228)
T ss_pred             HH---------------hcc--CcHHHHHHHHHHHHHHHcCCCCcHHHHHHHHHHhcc---ccHHHHHHHHH
Confidence            11               111  123456789999999999999999999999999844   44444444444

ECSIT plays an important role in signalling to NF-kappaB, functioning as the intermediate in the signalling pathways between TRAF-6 and MEKK-1 [].

>PF07079 DUF1347: Protein of unknown function (DUF1347); InterPro: IPR010764 This family consists of several hypothetical bacterial proteins of around 610 residues in length

Probab=97.05  E-value=0.31  Score=46.34  Aligned_cols=448  Identities=11%  Similarity=0.089  Sum_probs=236.6

Q ss_pred             HHHhcCChhHHHHHHHHHHhCCCCCCHHH------HHHHHHHHHhcCCHhHHHHHHHHHHhcCCCCCHhhHHHHHHH--H
Q 040027          105 CFCKIGRVSLGFIAFGRILRSCFTPNAAT------FNSLIKGLHAESRIMEAAALFTKLKAFGCEPNVITYNTLING--L  176 (595)
Q Consensus       105 ~~~~~g~~~~A~~~~~~~~~~~~~~~~~~------~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~~l~~~--~  176 (595)
                      .+.+++++.+|..+|.++.+.. ..++..      .+.++++|.. .+.+.....+..+.+.  .| ...|..+..+  .
T Consensus        15 ~Lqkq~~~~esEkifskI~~e~-~~~~f~lkeEvl~grilnAffl-~nld~Me~~l~~l~~~--~~-~s~~l~LF~~L~~   89 (549)
T PF07079_consen   15 ILQKQKKFQESEKIFSKIYDEK-ESSPFLLKEEVLGGRILNAFFL-NNLDLMEKQLMELRQQ--FG-KSAYLPLFKALVA   89 (549)
T ss_pred             HHHHHhhhhHHHHHHHHHHHHh-hcchHHHHHHHHhhHHHHHHHH-hhHHHHHHHHHHHHHh--cC-CchHHHHHHHHHH
Confidence            3457899999999999998763 223222      2345566554 4555555555555554  22 3344444443  3


Q ss_pred             HhcCChhHHHHHHHHHHhcCCCCCcc-c-------cCcHHHHHHHHHHHHHcCCHhHHHHHHHHHhhC----CCCCCHhH
Q 040027          177 CRTGHTMIALNLFEEMANGNGEIGVV-C-------KPNTVTYSTIIDGLCKEGFVDKAKALFLQMKDE----NINPDVVT  244 (595)
Q Consensus       177 ~~~g~~~~A~~~~~~~~~~~~~~~~~-~-------~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~----~~~~~~~~  244 (595)
                      .+.+.+.+|++.+......-.....+ .       -++...-+..++++...|++.+++.+++++...    ....+..+
T Consensus        90 Y~~k~~~kal~~ls~w~~~~~~~~~~~Ld~ni~~l~~df~l~~i~a~sLIe~g~f~EgR~iLn~i~~~llkrE~~w~~d~  169 (549)
T PF07079_consen   90 YKQKEYRKALQALSVWKEQIKGTESPWLDTNIQQLFSDFFLDEIEAHSLIETGRFSEGRAILNRIIERLLKRECEWNSDM  169 (549)
T ss_pred             HHhhhHHHHHHHHHHHHhhhcccccchhhhhHHHHhhHHHHHHHHHHHHHhcCCcchHHHHHHHHHHHHhhhhhcccHHH
Confidence            47889999999988776541100000 0       001112244677888999999999998887764    33467888


Q ss_pred             HHHHHHHHHhcCCHHHHHHHHHHHHHC---CCCCCHhhHHHHHHHHHhcCChHHHHHHHHHHHHCCCCCCHHHHHHHHHH
Q 040027          245 YNSLIHGLCHANDWNEAKRLFIEMMDQ---GVQPSVVTFNVIMDELCKNRKMDEASRLLDLMVQRGVRPNACTYNTLMDG  321 (595)
Q Consensus       245 ~~~ll~~~~~~~~~~~A~~~~~~~~~~---~~~~~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~  321 (595)
                      |+.++-.+.+        ..|-++.+.   .+-|+  .|. ++-.|.+.=+.-+.. -|+     .+.|.......++..
T Consensus       170 yd~~vlmlsr--------SYfLEl~e~~s~dl~pd--yYe-milfY~kki~~~d~~-~Y~-----k~~peeeL~s~imqh  232 (549)
T PF07079_consen  170 YDRAVLMLSR--------SYFLELKESMSSDLYPD--YYE-MILFYLKKIHAFDQR-PYE-----KFIPEEELFSTIMQH  232 (549)
T ss_pred             HHHHHHHHhH--------HHHHHHHHhcccccChH--HHH-HHHHHHHHHHHHhhc-hHH-----hhCcHHHHHHHHHHH
Confidence            8876655543        233343322   12222  232 333332221111110 001     122333333333332


Q ss_pred             HHhc--CCHHHHHHHHHHHHhcCCCCCHH-HHHHHHHHHHhCCCHHHHHHHHHHHHHCCCCC----CHHHHHHHHHHHHc
Q 040027          322 FCLM--GKINRAEELFGSMESMGCKHDDV-SYNILINGYCKNKEVEEALSLYREMVSKGIKP----TVVTYNTLFLGLFE  394 (595)
Q Consensus       322 ~~~~--~~~~~a~~~~~~~~~~~~~~~~~-~~~~l~~~~~~~~~~~~A~~~~~~~~~~~~~~----~~~~~~~l~~~~~~  394 (595)
                      ..-.  ....--++++......-+.|+.. ....+..-+.+  +.+++..+.+.+....+.+    -..++..++....+
T Consensus       233 lfi~p~e~l~~~mq~l~~We~~yv~p~~~LVi~~L~~~f~~--~~e~~~~~ce~ia~~~i~~Lke~li~~F~~~Ls~~Vk  310 (549)
T PF07079_consen  233 LFIVPKERLPPLMQILENWENFYVHPNYDLVIEPLKQQFMS--DPEQVGHFCEAIASSKIEKLKEELIDRFGNLLSFKVK  310 (549)
T ss_pred             HHhCCHhhccHHHHHHHHHHhhccCCchhHHHHHHHHHHhc--ChHHHHHHHHHHHHHhHHHHHHHHHHHHHHHHHHHHH
Confidence            2211  12233344444444443444433 33344444443  4455555444443321111    23467777777888


Q ss_pred             cCCHHHHHHHHHHHHHCCCCCCHHHHHH-------HHHHHH----hcCCHHHHHHHHHHHHHcCCCcC--HHHHHHHHHH
Q 040027          395 IHQVEHALKLFDEMQRDGVAADTRTYTT-------FIDGLC----KNGYIIEAVELFRTLRILKCELD--IQAYNCLIDG  461 (595)
Q Consensus       395 ~~~~~~a~~~~~~~~~~~~~~~~~~~~~-------l~~~~~----~~g~~~~A~~~~~~~~~~~~~~~--~~~~~~l~~~  461 (595)
                      .++...|.+.+..+...  .|+...-..       +.+..+    ..-+..+=+.+|+.+...++...  +.....-+.-
T Consensus       311 ~~~T~~a~q~l~lL~~l--dp~~svs~Kllls~~~lq~Iv~~DD~~~Tklr~yL~lwe~~qs~DiDrqQLvh~L~~~Ak~  388 (549)
T PF07079_consen  311 QVQTEEAKQYLALLKIL--DPRISVSEKLLLSPKVLQDIVCEDDESYTKLRDYLNLWEEIQSYDIDRQQLVHYLVFGAKH  388 (549)
T ss_pred             HHhHHHHHHHHHHHHhc--CCcchhhhhhhcCHHHHHHHHhcchHHHHHHHHHHHHHHHHHhhcccHHHHHHHHHHHHHH
Confidence            88888888888877654  333221111       111112    11123334455555554432211  1112222334


Q ss_pred             HHhcCC-hHHHHHHHHhcccCCCCC-CHHHHHHHH----HHHHh---cCChhHHHHHHHHHHHcCCCCC----HHHHHHH
Q 040027          462 LCKSGR-LKFAWELFCSLPHGVLVP-NVVTYNIMI----QGLCN---DGQMDKARDLFLDMEENAAAPD----VITFDML  528 (595)
Q Consensus       462 ~~~~g~-~~~A~~~~~~~~~~~~~p-~~~~~~~l~----~~~~~---~g~~~~A~~~~~~~~~~~~~~~----~~~~~~l  528 (595)
                      +.+.|. -++|+++++.+..  +.| |...-|.+.    .+|.+   ...+.+-..+-+-..+.|++|-    ...-+.|
T Consensus       389 lW~~g~~dekalnLLk~il~--ft~yD~ec~n~v~~fvKq~Y~qaLs~~~~~rLlkLe~fi~e~gl~~i~i~e~eian~L  466 (549)
T PF07079_consen  389 LWEIGQCDEKALNLLKLILQ--FTNYDIECENIVFLFVKQAYKQALSMHAIPRLLKLEDFITEVGLTPITISEEEIANFL  466 (549)
T ss_pred             HHhcCCccHHHHHHHHHHHH--hccccHHHHHHHHHHHHHHHHHHHhhhhHHHHHHHHHHHHhcCCCcccccHHHHHHHH
Confidence            566666 8899999999987  444 333333322    22322   1223333333344445677664    2333444


Q ss_pred             HH--HHHHcCChhHHHHHHHHHHHCCCCCCHHHHHHHHHHHHhcCcccccchHHHH
Q 040027          529 IH--GFIRINEPSKVNELLHKMKEKKVMPDASIVSIVVDLLVKNEISLKSLPSFLV  582 (595)
Q Consensus       529 ~~--~~~~~g~~~~A~~~~~~~~~~~~~p~~~~~~~l~~~~~~~g~~~~~i~~~~~  582 (595)
                      .+  -+...|++.++.-+-.-+.+  +.|++.+|+.++-++....+++++.+-+..
T Consensus       467 aDAEyLysqgey~kc~~ys~WL~~--iaPS~~~~RLlGl~l~e~k~Y~eA~~~l~~  520 (549)
T PF07079_consen  467 ADAEYLYSQGEYHKCYLYSSWLTK--IAPSPQAYRLLGLCLMENKRYQEAWEYLQK  520 (549)
T ss_pred             HHHHHHHhcccHHHHHHHHHHHHH--hCCcHHHHHHHHHHHHHHhhHHHHHHHHHh
Confidence            33  45678999999988888876  779999999999999999999855554443

Members of this family are highly conserved and seem to be specific to Chlamydia species. The function of this family is unknown.

>PF03704 BTAD: Bacterial transcriptional activator domain; InterPro: IPR005158 Found in the DNRI/REDD/AFSR family of regulators, this region of AFSR (P25941 from SWISSPROT) along with the C-terminal region is capable of independently directing actinorhodin production

Probab=97.02  E-value=0.022  Score=46.84  Aligned_cols=69  Identities=19%  Similarity=0.260  Sum_probs=40.4

Q ss_pred             HHHHHHHHHhcCChhHHHHHHHHHHhcCCCCCccccCcHHHHHHHHHHHHHcCCHhHHHHHHHHHhh-----CCCCCCHh
Q 040027          169 YNTLINGLCRTGHTMIALNLFEEMANGNGEIGVVCKPNTVTYSTIIDGLCKEGFVDKAKALFLQMKD-----ENINPDVV  243 (595)
Q Consensus       169 ~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~-----~~~~~~~~  243 (595)
                      ...++..+...|++++|+...+.+...+       |.+...|..++.+|...|+...|.+.|+.+..     .|+.|+..
T Consensus        65 ~~~l~~~~~~~~~~~~a~~~~~~~l~~d-------P~~E~~~~~lm~~~~~~g~~~~A~~~Y~~~~~~l~~elg~~Ps~~  137 (146)
T PF03704_consen   65 LERLAEALLEAGDYEEALRLLQRALALD-------PYDEEAYRLLMRALAAQGRRAEALRVYERYRRRLREELGIEPSPE  137 (146)
T ss_dssp             HHHHHHHHHHTT-HHHHHHHHHHHHHHS-------TT-HHHHHHHHHHHHHTT-HHHHHHHHHHHHHHHHHHHS----HH
T ss_pred             HHHHHHHHHhccCHHHHHHHHHHHHhcC-------CCCHHHHHHHHHHHHHCcCHHHHHHHHHHHHHHHHHHhCcCcCHH
Confidence            4455566666777777777777777665       55666777777777777777777777766543     25555554


Q ss_pred             H
Q 040027          244 T  244 (595)
Q Consensus       244 ~  244 (595)
                      +
T Consensus       138 ~  138 (146)
T PF03704_consen  138 T  138 (146)
T ss_dssp             H
T ss_pred             H
Confidence            4

It is important for the formation of secondary metabolites.; PDB: 2FF4_B 2FEZ_A.

>PRK15331 chaperone protein SicA; Provisional

Probab=96.97  E-value=0.012  Score=47.73  Aligned_cols=104  Identities=12%  Similarity=-0.049  Sum_probs=84.2

Q ss_pred             CCCCCC-HHHHHHHHHHHHhcCChhHHHHHHHHHHhCCCCCCHHHHHHHHHHHHhcCCHhHHHHHHHHHHhcCCCCCHhh
Q 040027           90 TGLFPN-LYTYNILINCFCKIGRVSLGFIAFGRILRSCFTPNAATFNSLIKGLHAESRIMEAAALFTKLKAFGCEPNVIT  168 (595)
Q Consensus        90 ~~~~~~-~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~  168 (595)
                      .|++++ ....-.....+...|++++|..+|+-+...+ .-+..-|..|..++...+++++|+..|......+. -|+..
T Consensus        30 ~gis~~~le~iY~~Ay~~y~~Gk~~eA~~~F~~L~~~d-~~n~~Y~~GLaa~~Q~~k~y~~Ai~~Y~~A~~l~~-~dp~p  107 (165)
T PRK15331         30 HGIPQDMMDGLYAHAYEFYNQGRLDEAETFFRFLCIYD-FYNPDYTMGLAAVCQLKKQFQKACDLYAVAFTLLK-NDYRP  107 (165)
T ss_pred             hCCCHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHhC-cCcHHHHHHHHHHHHHHHHHHHHHHHHHHHHHccc-CCCCc
Confidence            344432 2334456666788999999999999999876 44677788888888999999999999999887764 37777


Q ss_pred             HHHHHHHHHhcCChhHHHHHHHHHHhc
Q 040027          169 YNTLINGLCRTGHTMIALNLFEEMANG  195 (595)
Q Consensus       169 ~~~l~~~~~~~g~~~~A~~~~~~~~~~  195 (595)
                      +......+...|+.+.|...|+.....
T Consensus       108 ~f~agqC~l~l~~~~~A~~~f~~a~~~  134 (165)
T PRK15331        108 VFFTGQCQLLMRKAAKARQCFELVNER  134 (165)
T ss_pred             cchHHHHHHHhCCHHHHHHHHHHHHhC
Confidence            788899999999999999999999874

>PF13371 TPR_9: Tetratricopeptide repeat

Probab=96.95  E-value=0.0063  Score=42.84  Aligned_cols=56  Identities=11%  Similarity=0.054  Sum_probs=40.0

Q ss_pred             HHHHhcCChhHHHHHHHHHHhCCCCCCHHHHHHHHHHHHhcCCHhHHHHHHHHHHhc
Q 040027          104 NCFCKIGRVSLGFIAFGRILRSCFTPNAATFNSLIKGLHAESRIMEAAALFTKLKAF  160 (595)
Q Consensus       104 ~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~  160 (595)
                      ..|.+.++++.|..++++++..+ |.++..|......+.+.|++++|.+.|+...+.
T Consensus         3 ~~~~~~~~~~~A~~~~~~~l~~~-p~~~~~~~~~a~~~~~~g~~~~A~~~l~~~l~~   58 (73)
T PF13371_consen    3 QIYLQQEDYEEALEVLERALELD-PDDPELWLQRARCLFQLGRYEEALEDLERALEL   58 (73)
T ss_pred             HHHHhCCCHHHHHHHHHHHHHhC-cccchhhHHHHHHHHHhccHHHHHHHHHHHHHH
Confidence            45667777777777777777764 446666667777777777777777777777765

>PRK15331 chaperone protein SicA; Provisional

Probab=96.93  E-value=0.068  Score=43.53  Aligned_cols=87  Identities=9%  Similarity=-0.036  Sum_probs=45.7

Q ss_pred             HHccCCHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCcCHHHHHHHHHHHHhcCChHHH
Q 040027          392 LFEIHQVEHALKLFDEMQRDGVAADTRTYTTFIDGLCKNGYIIEAVELFRTLRILKCELDIQAYNCLIDGLCKSGRLKFA  471 (595)
Q Consensus       392 ~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A  471 (595)
                      +...|++++|..+|.-+...+ +.+..-+..+..++...+++++|...|....... ..|+..+-....++...|+.+.|
T Consensus        47 ~y~~Gk~~eA~~~F~~L~~~d-~~n~~Y~~GLaa~~Q~~k~y~~Ai~~Y~~A~~l~-~~dp~p~f~agqC~l~l~~~~~A  124 (165)
T PRK15331         47 FYNQGRLDEAETFFRFLCIYD-FYNPDYTMGLAAVCQLKKQFQKACDLYAVAFTLL-KNDYRPVFFTGQCQLLMRKAAKA  124 (165)
T ss_pred             HHHCCCHHHHHHHHHHHHHhC-cCcHHHHHHHHHHHHHHHHHHHHHHHHHHHHHcc-cCCCCccchHHHHHHHhCCHHHH
Confidence            344556666666655555443 3334444555555555555666666555554433 23344444455555555555555


Q ss_pred             HHHHHhccc
Q 040027          472 WELFCSLPH  480 (595)
Q Consensus       472 ~~~~~~~~~  480 (595)
                      ...|....+
T Consensus       125 ~~~f~~a~~  133 (165)
T PRK15331        125 RQCFELVNE  133 (165)
T ss_pred             HHHHHHHHh
Confidence            555555554

>PF13424 TPR_12: Tetratricopeptide repeat; PDB: 3RO2_A 3Q15_A 3ASG_A 3ASD_A 3AS5_A 3AS4_A 3ASH_B 4A1S_B 3CEQ_B 3EDT_H

Probab=96.85  E-value=0.0023  Score=45.89  Aligned_cols=68  Identities=19%  Similarity=0.235  Sum_probs=48.5

Q ss_pred             hhHHHHHHHHHhcCChhHHHHHHHHHHhcCCCCCccccC-cHHHHHHHHHHHHHcCCHhHHHHHHHHHhh
Q 040027          167 ITYNTLINGLCRTGHTMIALNLFEEMANGNGEIGVVCKP-NTVTYSTIIDGLCKEGFVDKAKALFLQMKD  235 (595)
Q Consensus       167 ~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~-~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~  235 (595)
                      .++..+...|...|++++|++.|++..+.....+. ..+ ...++..+..++...|++++|.+.+++..+
T Consensus         6 ~~~~~la~~~~~~~~~~~A~~~~~~al~~~~~~~~-~~~~~a~~~~~lg~~~~~~g~~~~A~~~~~~al~   74 (78)
T PF13424_consen    6 NAYNNLARVYRELGRYDEALDYYEKALDIEEQLGD-DHPDTANTLNNLGECYYRLGDYEEALEYYQKALD   74 (78)
T ss_dssp             HHHHHHHHHHHHTT-HHHHHHHHHHHHHHHHHTTT-HHHHHHHHHHHHHHHHHHTTHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHHCC-CCHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHh
Confidence            45677888888888888888888887754211111 112 256788888999999999999999988654

...

>COG3118 Thioredoxin domain-containing protein [Posttranslational modification, protein turnover, chaperones]

Probab=96.83  E-value=0.28  Score=44.01  Aligned_cols=146  Identities=15%  Similarity=0.077  Sum_probs=85.3

Q ss_pred             HHHhcCCHHHHHHHHHHHHHcCCCcCHHHHHHHHHHHHhcCChHHHHHHHHhcccCCCCCCHHHHHHHHHHHHhcCChhH
Q 040027          426 GLCKNGYIIEAVELFRTLRILKCELDIQAYNCLIDGLCKSGRLKFAWELFCSLPHGVLVPNVVTYNIMIQGLCNDGQMDK  505 (595)
Q Consensus       426 ~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~p~~~~~~~l~~~~~~~g~~~~  505 (595)
                      .....|++.+|...|+.+.... +.+......++.+|...|+.+.|..++..+....-.........-+..+.+.....+
T Consensus       143 ~~~~~e~~~~a~~~~~~al~~~-~~~~~~~~~la~~~l~~g~~e~A~~iL~~lP~~~~~~~~~~l~a~i~ll~qaa~~~~  221 (304)
T COG3118         143 ELIEAEDFGEAAPLLKQALQAA-PENSEAKLLLAECLLAAGDVEAAQAILAALPLQAQDKAAHGLQAQIELLEQAAATPE  221 (304)
T ss_pred             hhhhccchhhHHHHHHHHHHhC-cccchHHHHHHHHHHHcCChHHHHHHHHhCcccchhhHHHHHHHHHHHHHHHhcCCC
Confidence            3456677777777777776654 444566666777777777777777777776543111112222223344444444444


Q ss_pred             HHHHHHHHHHcCCCCCHHHHHHHHHHHHHcCChhHHHHHHHHHHHCCCC-CCHHHHHHHHHHHHhcCccc
Q 040027          506 ARDLFLDMEENAAAPDVITFDMLIHGFIRINEPSKVNELLHKMKEKKVM-PDASIVSIVVDLLVKNEISL  574 (595)
Q Consensus       506 A~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~-p~~~~~~~l~~~~~~~g~~~  574 (595)
                      ...+-.+.-..  +.|...-..+...+...|+.++|.+.+=.++.++.. -|...-..+++.+.--|..+
T Consensus       222 ~~~l~~~~aad--Pdd~~aa~~lA~~~~~~g~~e~Ale~Ll~~l~~d~~~~d~~~Rk~lle~f~~~g~~D  289 (304)
T COG3118         222 IQDLQRRLAAD--PDDVEAALALADQLHLVGRNEAALEHLLALLRRDRGFEDGEARKTLLELFEAFGPAD  289 (304)
T ss_pred             HHHHHHHHHhC--CCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhcccccCcHHHHHHHHHHHhcCCCC
Confidence            44444444432  335556666777777777777777776666654322 25566666777776666555

>PF13281 DUF4071: Domain of unknown function (DUF4071)

Probab=96.82  E-value=0.47  Score=44.96  Aligned_cols=82  Identities=9%  Similarity=0.033  Sum_probs=52.8

Q ss_pred             HHHHHHHHHHHHHcCCHhHHHHHHHHHhhCC---CCCCHhHHHHHHHHHHh---cCCHHHHHHHHHHHHHCCCCCCHhhH
Q 040027          207 TVTYSTIIDGLCKEGFVDKAKALFLQMKDEN---INPDVVTYNSLIHGLCH---ANDWNEAKRLFIEMMDQGVQPSVVTF  280 (595)
Q Consensus       207 ~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~---~~~~~~~~~~ll~~~~~---~~~~~~A~~~~~~~~~~~~~~~~~~~  280 (595)
                      +.+...++-.|....+++..+++.+.+...-   +.-....-...+-++.+   .|+.++|++++..+......+++.++
T Consensus       141 ~div~~lllSyRdiqdydamI~Lve~l~~~p~~~~~~~~~i~~~yafALnRrn~~gdre~Al~il~~~l~~~~~~~~d~~  220 (374)
T PF13281_consen  141 PDIVINLLLSYRDIQDYDAMIKLVETLEALPTCDVANQHNIKFQYAFALNRRNKPGDREKALQILLPVLESDENPDPDTL  220 (374)
T ss_pred             hhHHHHHHHHhhhhhhHHHHHHHHHHhhccCccchhcchHHHHHHHHHHhhcccCCCHHHHHHHHHHHHhccCCCChHHH
Confidence            3444556666888888888888888887641   11122222233345555   78888888888886665566677778


Q ss_pred             HHHHHHHH
Q 040027          281 NVIMDELC  288 (595)
Q Consensus       281 ~~l~~~~~  288 (595)
                      ..+++.|-
T Consensus       221 gL~GRIyK  228 (374)
T PF13281_consen  221 GLLGRIYK  228 (374)
T ss_pred             HHHHHHHH
Confidence            77776654

>PF13424 TPR_12: Tetratricopeptide repeat; PDB: 3RO2_A 3Q15_A 3ASG_A 3ASD_A 3AS5_A 3AS4_A 3ASH_B 4A1S_B 3CEQ_B 3EDT_H

Probab=96.82  E-value=0.0037  Score=44.75  Aligned_cols=63  Identities=19%  Similarity=0.219  Sum_probs=42.3

Q ss_pred             HHHHHHHHHHHhcCChhHHHHHHHHHHHc--CCCCC----HHHHHHHHHHHHHcCChhHHHHHHHHHHH
Q 040027          488 VTYNIMIQGLCNDGQMDKARDLFLDMEEN--AAAPD----VITFDMLIHGFIRINEPSKVNELLHKMKE  550 (595)
Q Consensus       488 ~~~~~l~~~~~~~g~~~~A~~~~~~~~~~--~~~~~----~~~~~~l~~~~~~~g~~~~A~~~~~~~~~  550 (595)
                      .+++.+...|...|++++|++.|+++++.  ...++    ..++..++.+|...|++++|.+++++..+
T Consensus         6 ~~~~~la~~~~~~~~~~~A~~~~~~al~~~~~~~~~~~~~a~~~~~lg~~~~~~g~~~~A~~~~~~al~   74 (78)
T PF13424_consen    6 NAYNNLARVYRELGRYDEALDYYEKALDIEEQLGDDHPDTANTLNNLGECYYRLGDYEEALEYYQKALD   74 (78)
T ss_dssp             HHHHHHHHHHHHTT-HHHHHHHHHHHHHHHHHTTTHHHHHHHHHHHHHHHHHHTTHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHh
Confidence            46677777777777777777777777642  11111    34567777788888888888888877653

...

>KOG1538 consensus Uncharacterized conserved protein WDR10, contains WD40 repeats [General function prediction only]

Probab=96.80  E-value=0.33  Score=48.13  Aligned_cols=89  Identities=21%  Similarity=0.255  Sum_probs=43.3

Q ss_pred             HHHHHHHHHHhcCCHHHHHHHH---------HHHHHCCCCCCHhhHHHHHHHHHhcCCh--HHHHHHHHHHHHCCCCCCH
Q 040027          244 TYNSLIHGLCHANDWNEAKRLF---------IEMMDQGVQPSVVTFNVIMDELCKNRKM--DEASRLLDLMVQRGVRPNA  312 (595)
Q Consensus       244 ~~~~ll~~~~~~~~~~~A~~~~---------~~~~~~~~~~~~~~~~~l~~~~~~~g~~--~~a~~~~~~~~~~~~~~~~  312 (595)
                      .+.+=+..|...|.+.+|.++-         +.+...  ..+...++..=.+|.+..+.  -+..--++++.++|-.|+.
T Consensus       558 p~~~~m~q~Ieag~f~ea~~iaclgVv~~DW~~LA~~--ALeAL~f~~ARkAY~rVRdl~~L~li~EL~~~k~rge~P~~  635 (1081)
T KOG1538|consen  558 PQSAPMYQYIERGLFKEAYQIACLGVTDTDWRELAME--ALEALDFETARKAYIRVRDLRYLELISELEERKKRGETPND  635 (1081)
T ss_pred             cccccchhhhhccchhhhhcccccceecchHHHHHHH--HHhhhhhHHHHHHHHHHhccHHHHHHHHHHHHHhcCCCchH
Confidence            3444455677788887776542         111100  01122233333344443332  2233334555666665665


Q ss_pred             HHHHHHHHHHHhcCCHHHHHHHHHH
Q 040027          313 CTYNTLMDGFCLMGKINRAEELFGS  337 (595)
Q Consensus       313 ~~~~~l~~~~~~~~~~~~a~~~~~~  337 (595)
                      ..   +...++-.|++.+|.++|.+
T Consensus       636 iL---lA~~~Ay~gKF~EAAklFk~  657 (1081)
T KOG1538|consen  636 LL---LADVFAYQGKFHEAAKLFKR  657 (1081)
T ss_pred             HH---HHHHHHhhhhHHHHHHHHHH
Confidence            43   34455556777777776654

>PRK11906 transcriptional regulator; Provisional

Probab=96.78  E-value=0.1  Score=50.05  Aligned_cols=113  Identities=13%  Similarity=0.035  Sum_probs=85.3

Q ss_pred             CCHHHHHHHHHHHHHcCCCcCHHHHHHHHHHHHhcCChHHHHHHHHhcccCCCCCC-HHHHHHHHHHHHhcCChhHHHHH
Q 040027          431 GYIIEAVELFRTLRILKCELDIQAYNCLIDGLCKSGRLKFAWELFCSLPHGVLVPN-VVTYNIMIQGLCNDGQMDKARDL  509 (595)
Q Consensus       431 g~~~~A~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~p~-~~~~~~l~~~~~~~g~~~~A~~~  509 (595)
                      .+..+|.++.+++.+.+ +.|+.+...++.+....++++.|...|++...  +.|| ..+|......+...|+.++|.+.
T Consensus       318 ~~~~~a~~~A~rAveld-~~Da~a~~~~g~~~~~~~~~~~a~~~f~rA~~--L~Pn~A~~~~~~~~~~~~~G~~~~a~~~  394 (458)
T PRK11906        318 LAAQKALELLDYVSDIT-TVDGKILAIMGLITGLSGQAKVSHILFEQAKI--HSTDIASLYYYRALVHFHNEKIEEARIC  394 (458)
T ss_pred             HHHHHHHHHHHHHHhcC-CCCHHHHHHHHHHHHhhcchhhHHHHHHHHhh--cCCccHHHHHHHHHHHHHcCCHHHHHHH
Confidence            34567778888888877 77888888888888888889999999999888  6777 46777777778888999999999


Q ss_pred             HHHHHHcCCCCC---HHHHHHHHHHHHHcCChhHHHHHHHHHH
Q 040027          510 FLDMEENAAAPD---VITFDMLIHGFIRINEPSKVNELLHKMK  549 (595)
Q Consensus       510 ~~~~~~~~~~~~---~~~~~~l~~~~~~~g~~~~A~~~~~~~~  549 (595)
                      +++..+..  |.   .......++.|+..+ .++|.++|-+-.
T Consensus       395 i~~alrLs--P~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~~  434 (458)
T PRK11906        395 IDKSLQLE--PRRRKAVVIKECVDMYVPNP-LKNNIKLYYKET  434 (458)
T ss_pred             HHHHhccC--chhhHHHHHHHHHHHHcCCc-hhhhHHHHhhcc
Confidence            99987753  43   334445555676665 677777766544

>PLN03098 LPA1 LOW PSII ACCUMULATION1; Provisional

Probab=96.63  E-value=0.022  Score=54.37  Aligned_cols=66  Identities=15%  Similarity=-0.012  Sum_probs=39.9

Q ss_pred             CCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCcCH---HHHHHHHHHHHhcCChHHHHHHHHhccc
Q 040027          414 AADTRTYTTFIDGLCKNGYIIEAVELFRTLRILKCELDI---QAYNCLIDGLCKSGRLKFAWELFCSLPH  480 (595)
Q Consensus       414 ~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~~~---~~~~~l~~~~~~~g~~~~A~~~~~~~~~  480 (595)
                      +.+...+..+..+|...|++++|+..|++.++.+ +.+.   .+|..+..+|...|+.++|+..++++++
T Consensus        72 P~~a~a~~NLG~AL~~lGryeEAIa~f~rALeL~-Pd~aeA~~A~yNLAcaya~LGr~dEAla~LrrALe  140 (453)
T PLN03098         72 VKTAEDAVNLGLSLFSKGRVKDALAQFETALELN-PNPDEAQAAYYNKACCHAYREEGKKAADCLRTALR  140 (453)
T ss_pred             CCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHhhC-CCchHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHH
Confidence            3345556666666666666666666666666553 2222   2366666666666666666666666665

>KOG1585 consensus Protein required for fusion of vesicles in vesicular transport, gamma-SNAP [Intracellular trafficking, secretion, and vesicular transport]

Probab=96.63  E-value=0.33  Score=42.04  Aligned_cols=86  Identities=13%  Similarity=0.049  Sum_probs=40.0

Q ss_pred             HHHHHHHHHHhcCCHhHHHHHHHHHHhcCCCCCHhhHHHHHHHHHhcCChhHHHHHHHHHHhcCCCCCccccCcHHHHHH
Q 040027          133 TFNSLIKGLHAESRIMEAAALFTKLKAFGCEPNVITYNTLINGLCRTGHTMIALNLFEEMANGNGEIGVVCKPNTVTYST  212 (595)
Q Consensus       133 ~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~~~~~~~~  212 (595)
                      .|.....+|...+++++|...+.+..+. .+.+...|+       ....++.|.-+.+++....        .-...+..
T Consensus        33 ~yekAAvafRnAk~feKakdcLlkA~~~-yEnnrslfh-------AAKayEqaamLake~~kls--------Evvdl~eK   96 (308)
T KOG1585|consen   33 LYEKAAVAFRNAKKFEKAKDCLLKASKG-YENNRSLFH-------AAKAYEQAAMLAKELSKLS--------EVVDLYEK   96 (308)
T ss_pred             HHHHHHHHHHhhccHHHHHHHHHHHHHH-HHhcccHHH-------HHHHHHHHHHHHHHHHHhH--------HHHHHHHH
Confidence            3444445555566666666655555432 121221111       1222334444444444321        12334455


Q ss_pred             HHHHHHHcCCHhHHHHHHHHHh
Q 040027          213 IIDGLCKEGFVDKAKALFLQMK  234 (595)
Q Consensus       213 l~~~~~~~g~~~~A~~~~~~~~  234 (595)
                      ....|...|..+.|-..+++..
T Consensus        97 As~lY~E~GspdtAAmaleKAa  118 (308)
T KOG1585|consen   97 ASELYVECGSPDTAAMALEKAA  118 (308)
T ss_pred             HHHHHHHhCCcchHHHHHHHHH
Confidence            5556666666666666555543

>KOG2114 consensus Vacuolar assembly/sorting protein PEP5/VPS11 [Intracellular trafficking, secretion, and vesicular transport]

Probab=96.59  E-value=1.1  Score=46.21  Aligned_cols=148  Identities=15%  Similarity=0.121  Sum_probs=100.2

Q ss_pred             HHHHHHHHHHHhcCChhHHHHHHHHHHhCCCCCCHHHHHHHHHHHHhcCCHhHHHHHHHHHHhcCCCCCHhhHHHHHHHH
Q 040027           97 YTYNILINCFCKIGRVSLGFIAFGRILRSCFTPNAATFNSLIKGLHAESRIMEAAALFTKLKAFGCEPNVITYNTLINGL  176 (595)
Q Consensus        97 ~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~~l~~~~  176 (595)
                      ......+..+.+.|++++|...|-+.+..- .|     ..++.-+....+..+-...++.+.+.|.. +......|+.+|
T Consensus       369 ~i~~kYgd~Ly~Kgdf~~A~~qYI~tI~~l-e~-----s~Vi~kfLdaq~IknLt~YLe~L~~~gla-~~dhttlLLncY  441 (933)
T KOG2114|consen  369 EIHRKYGDYLYGKGDFDEATDQYIETIGFL-EP-----SEVIKKFLDAQRIKNLTSYLEALHKKGLA-NSDHTTLLLNCY  441 (933)
T ss_pred             HHHHHHHHHHHhcCCHHHHHHHHHHHcccC-Ch-----HHHHHHhcCHHHHHHHHHHHHHHHHcccc-cchhHHHHHHHH
Confidence            344555666778999999999999887652 22     23445556666667777888999998876 666678899999


Q ss_pred             HhcCChhHHHHHHHHHHhcCCCCCccccCcHHHHHHHHHHHHHcCCHhHHHHHHHHHhhCCCCCCHhHHHHHHHHHHhcC
Q 040027          177 CRTGHTMIALNLFEEMANGNGEIGVVCKPNTVTYSTIIDGLCKEGFVDKAKALFLQMKDENINPDVVTYNSLIHGLCHAN  256 (595)
Q Consensus       177 ~~~g~~~~A~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~~ll~~~~~~~  256 (595)
                      .+.++.++-.+.++... .+.     ...|   ....+..+.+.+-.++|.-+-.+...     +......   .+-..+
T Consensus       442 iKlkd~~kL~efI~~~~-~g~-----~~fd---~e~al~Ilr~snyl~~a~~LA~k~~~-----he~vl~i---lle~~~  504 (933)
T KOG2114|consen  442 IKLKDVEKLTEFISKCD-KGE-----WFFD---VETALEILRKSNYLDEAELLATKFKK-----HEWVLDI---LLEDLH  504 (933)
T ss_pred             HHhcchHHHHHHHhcCC-Ccc-----eeee---HHHHHHHHHHhChHHHHHHHHHHhcc-----CHHHHHH---HHHHhc
Confidence            99999988777766554 220     1112   34566777777777777766555433     2333333   345568


Q ss_pred             CHHHHHHHHHHH
Q 040027          257 DWNEAKRLFIEM  268 (595)
Q Consensus       257 ~~~~A~~~~~~~  268 (595)
                      ++++|++.+..+
T Consensus       505 ny~eAl~yi~sl  516 (933)
T KOG2114|consen  505 NYEEALRYISSL  516 (933)
T ss_pred             CHHHHHHHHhcC
Confidence            899999988765

>KOG1585 consensus Protein required for fusion of vesicles in vesicular transport, gamma-SNAP [Intracellular trafficking, secretion, and vesicular transport]

Probab=96.55  E-value=0.35  Score=41.91  Aligned_cols=210  Identities=14%  Similarity=0.115  Sum_probs=108.8

Q ss_pred             HHHHHHHHHHHHhcCChhHHHHHHHHHHhCCCCCCHHHHHHHHHHHHhcCCHhHHHHHHHHHHhcCCCCCHhhHHHHHHH
Q 040027           96 LYTYNILINCFCKIGRVSLGFIAFGRILRSCFTPNAATFNSLIKGLHAESRIMEAAALFTKLKAFGCEPNVITYNTLING  175 (595)
Q Consensus        96 ~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~~l~~~  175 (595)
                      ...|.....+|....++++|...+.++.+- .. +...|.....      -++.|..+.+++...  +--...+......
T Consensus        31 as~yekAAvafRnAk~feKakdcLlkA~~~-yE-nnrslfhAAK------ayEqaamLake~~kl--sEvvdl~eKAs~l  100 (308)
T KOG1585|consen   31 ASLYEKAAVAFRNAKKFEKAKDCLLKASKG-YE-NNRSLFHAAK------AYEQAAMLAKELSKL--SEVVDLYEKASEL  100 (308)
T ss_pred             HHHHHHHHHHHHhhccHHHHHHHHHHHHHH-HH-hcccHHHHHH------HHHHHHHHHHHHHHh--HHHHHHHHHHHHH
Confidence            456777888888889999999988888753 12 2222322332      335556666666554  2233455666777


Q ss_pred             HHhcCChhHHHHHHHHHHhcCCCCCccccCcH--HHHHHHHHHHHHcCCHhHHHHHHHHHhhCCCCCCHhHHHHHHHHHH
Q 040027          176 LCRTGHTMIALNLFEEMANGNGEIGVVCKPNT--VTYSTIIDGLCKEGFVDKAKALFLQMKDENINPDVVTYNSLIHGLC  253 (595)
Q Consensus       176 ~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~~~--~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~~ll~~~~  253 (595)
                      |...|..+.|-..+++.-+.-..    +.|+.  ..|..-+......++...|.++               +......+.
T Consensus       101 Y~E~GspdtAAmaleKAak~len----v~Pd~AlqlYqralavve~~dr~~ma~el---------------~gk~sr~lV  161 (308)
T KOG1585|consen  101 YVECGSPDTAAMALEKAAKALEN----VKPDDALQLYQRALAVVEEDDRDQMAFEL---------------YGKCSRVLV  161 (308)
T ss_pred             HHHhCCcchHHHHHHHHHHHhhc----CCHHHHHHHHHHHHHHHhccchHHHHHHH---------------HHHhhhHhh
Confidence            88888888887777766442100    12221  1222222222222333333332               333334555


Q ss_pred             hcCCHHHHHHHHHHHHHC----CCCCCH-hhHHHHHHHHHhcCChHHHHHHHHHHHHCC---CCCCHHHHHHHHHHHHhc
Q 040027          254 HANDWNEAKRLFIEMMDQ----GVQPSV-VTFNVIMDELCKNRKMDEASRLLDLMVQRG---VRPNACTYNTLMDGFCLM  325 (595)
Q Consensus       254 ~~~~~~~A~~~~~~~~~~----~~~~~~-~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~---~~~~~~~~~~l~~~~~~~  325 (595)
                      +...+.+|-..+.+-...    .--++. ..+...+-.+.-..++..|...++..-+.+   -.-+..+...|+.+| ..
T Consensus       162 rl~kf~Eaa~a~lKe~~~~~~~~~y~~~~k~~va~ilv~L~~~Dyv~aekc~r~~~qip~f~~sed~r~lenLL~ay-d~  240 (308)
T KOG1585|consen  162 RLEKFTEAATAFLKEGVAADKCDAYNSQCKAYVAAILVYLYAHDYVQAEKCYRDCSQIPAFLKSEDSRSLENLLTAY-DE  240 (308)
T ss_pred             hhHHhhHHHHHHHHhhhHHHHHhhcccHHHHHHHHHHHHhhHHHHHHHHHHhcchhcCccccChHHHHHHHHHHHHh-cc
Confidence            556666655444332111    001111 223444445556667777777777654432   122344555566555 45


Q ss_pred             CCHHHHHHHH
Q 040027          326 GKINRAEELF  335 (595)
Q Consensus       326 ~~~~~a~~~~  335 (595)
                      |+.+++..++
T Consensus       241 gD~E~~~kvl  250 (308)
T KOG1585|consen  241 GDIEEIKKVL  250 (308)
T ss_pred             CCHHHHHHHH
Confidence            6666555444

>PLN03098 LPA1 LOW PSII ACCUMULATION1; Provisional

Probab=96.54  E-value=0.032  Score=53.29  Aligned_cols=99  Identities=17%  Similarity=0.121  Sum_probs=67.2

Q ss_pred             CcCHHHHHHHHHHHHhcCChHHHHHHHHhcccCCCCCCH----HHHHHHHHHHHhcCChhHHHHHHHHHHHcCCCCCHHH
Q 040027          449 ELDIQAYNCLIDGLCKSGRLKFAWELFCSLPHGVLVPNV----VTYNIMIQGLCNDGQMDKARDLFLDMEENAAAPDVIT  524 (595)
Q Consensus       449 ~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~p~~----~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~  524 (595)
                      +.+...++.+..+|...|++++|+..|++.++  +.|+.    .+|..+..+|...|+.++|+..++++++.+ .+   .
T Consensus        72 P~~a~a~~NLG~AL~~lGryeEAIa~f~rALe--L~Pd~aeA~~A~yNLAcaya~LGr~dEAla~LrrALels-n~---~  145 (453)
T PLN03098         72 VKTAEDAVNLGLSLFSKGRVKDALAQFETALE--LNPNPDEAQAAYYNKACCHAYREEGKKAADCLRTALRDY-NL---K  145 (453)
T ss_pred             CCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHh--hCCCchHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhc-ch---h
Confidence            55677888888888888888888888888887  56764    358888888888888888888888888752 12   1


Q ss_pred             HHHHHH--HHHHcCChhHHHHHHHHHHHCCC
Q 040027          525 FDMLIH--GFIRINEPSKVNELLHKMKEKKV  553 (595)
Q Consensus       525 ~~~l~~--~~~~~g~~~~A~~~~~~~~~~~~  553 (595)
                      |..+..  .+....+..+..++++.+.+.|.
T Consensus       146 f~~i~~DpdL~plR~~pef~eLlee~rk~G~  176 (453)
T PLN03098        146 FSTILNDPDLAPFRASPEFKELQEEARKGGE  176 (453)
T ss_pred             HHHHHhCcchhhhcccHHHHHHHHHHHHhCC
Confidence            211110  11122233466666666666554

>PRK11906 transcriptional regulator; Provisional

Probab=96.52  E-value=0.12  Score=49.58  Aligned_cols=115  Identities=8%  Similarity=-0.051  Sum_probs=82.4

Q ss_pred             CChhHHHHHHHHHHhCCCCCCHHHHHHHHHHHHhcCCHhHHHHHHHHHHhcCCCCCHhhHHHHHHHHHhcCChhHHHHHH
Q 040027          110 GRVSLGFIAFGRILRSCFTPNAATFNSLIKGLHAESRIMEAAALFTKLKAFGCEPNVITYNTLINGLCRTGHTMIALNLF  189 (595)
Q Consensus       110 g~~~~A~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~  189 (595)
                      ....+|.+..+++++.+ +.|+.+...+..++.-.++++.|..+|++....+ +-...+|........-.|+.++|.+.+
T Consensus       318 ~~~~~a~~~A~rAveld-~~Da~a~~~~g~~~~~~~~~~~a~~~f~rA~~L~-Pn~A~~~~~~~~~~~~~G~~~~a~~~i  395 (458)
T PRK11906        318 LAAQKALELLDYVSDIT-TVDGKILAIMGLITGLSGQAKVSHILFEQAKIHS-TDIASLYYYRALVHFHNEKIEEARICI  395 (458)
T ss_pred             HHHHHHHHHHHHHHhcC-CCCHHHHHHHHHHHHhhcchhhHHHHHHHHhhcC-CccHHHHHHHHHHHHHcCCHHHHHHHH
Confidence            45567888888888886 6688888888888888888999999999999875 335667777777777899999999999


Q ss_pred             HHHHhcCCCCCccccCcHHHHHHHHHHHHHcCCHhHHHHHHHH
Q 040027          190 EEMANGNGEIGVVCKPNTVTYSTIIDGLCKEGFVDKAKALFLQ  232 (595)
Q Consensus       190 ~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~  232 (595)
                      ++..+.++     ...........+..|+.. ..+.|+++|-+
T Consensus       396 ~~alrLsP-----~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~  432 (458)
T PRK11906        396 DKSLQLEP-----RRRKAVVIKECVDMYVPN-PLKNNIKLYYK  432 (458)
T ss_pred             HHHhccCc-----hhhHHHHHHHHHHHHcCC-chhhhHHHHhh
Confidence            99887651     111223333344455544 46677776644

>COG3118 Thioredoxin domain-containing protein [Posttranslational modification, protein turnover, chaperones]

Probab=96.48  E-value=0.15  Score=45.60  Aligned_cols=31  Identities=19%  Similarity=0.155  Sum_probs=15.1

Q ss_pred             CHhhHHHHHHHHHhcCChhHHHHHHHHHHhc
Q 040027          165 NVITYNTLINGLCRTGHTMIALNLFEEMANG  195 (595)
Q Consensus       165 ~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~  195 (595)
                      |...-..+...+...|+.++|++.+-.+.+.
T Consensus       235 d~~aa~~lA~~~~~~g~~e~Ale~Ll~~l~~  265 (304)
T COG3118         235 DVEAALALADQLHLVGRNEAALEHLLALLRR  265 (304)
T ss_pred             CHHHHHHHHHHHHHcCCHHHHHHHHHHHHHh
Confidence            4444444455555555555555544444443

>PF04840 Vps16_C: Vps16, C-terminal region; InterPro: IPR006925 This protein forms part of the Class C vacuolar protein sorting (Vps) complex

Probab=96.48  E-value=0.77  Score=43.05  Aligned_cols=109  Identities=20%  Similarity=0.202  Sum_probs=75.5

Q ss_pred             HHHHHHHHHHccCCHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCcCHHHHHHHHHHHH
Q 040027          384 TYNTLFLGLFEIHQVEHALKLFDEMQRDGVAADTRTYTTFIDGLCKNGYIIEAVELFRTLRILKCELDIQAYNCLIDGLC  463 (595)
Q Consensus       384 ~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~~l~~~~~  463 (595)
                      +.+..+.-+...|+...|.++-.+..    .|+...|...+.+++..+++++-..+...      .-++.-|..++.+|.
T Consensus       179 Sl~~Ti~~li~~~~~k~A~kl~k~Fk----v~dkrfw~lki~aLa~~~~w~eL~~fa~s------kKsPIGyepFv~~~~  248 (319)
T PF04840_consen  179 SLNDTIRKLIEMGQEKQAEKLKKEFK----VPDKRFWWLKIKALAENKDWDELEKFAKS------KKSPIGYEPFVEACL  248 (319)
T ss_pred             CHHHHHHHHHHCCCHHHHHHHHHHcC----CcHHHHHHHHHHHHHhcCCHHHHHHHHhC------CCCCCChHHHHHHHH
Confidence            44455566667788777777765553    46778888888888888888877765432      224466777888888


Q ss_pred             hcCChHHHHHHHHhcccCCCCCCHHHHHHHHHHHHhcCChhHHHHHHHH
Q 040027          464 KSGRLKFAWELFCSLPHGVLVPNVVTYNIMIQGLCNDGQMDKARDLFLD  512 (595)
Q Consensus       464 ~~g~~~~A~~~~~~~~~~~~~p~~~~~~~l~~~~~~~g~~~~A~~~~~~  512 (595)
                      +.|+..+|..+..++.      +    ..-+..|.+.|++.+|.+...+
T Consensus       249 ~~~~~~eA~~yI~k~~------~----~~rv~~y~~~~~~~~A~~~A~~  287 (319)
T PF04840_consen  249 KYGNKKEASKYIPKIP------D----EERVEMYLKCGDYKEAAQEAFK  287 (319)
T ss_pred             HCCCHHHHHHHHHhCC------h----HHHHHHHHHCCCHHHHHHHHHH
Confidence            8888888888877732      1    3446677888888888765443

Vps16 is essential for vacuolar protein sorting, which is essential for viability in plants, but not yeast []. The Class C Vps complex is required for SNARE-mediated membrane fusion at the lysosome-like yeast vacuole. It is thought to play essential roles in membrane docking and fusion at the Golgi-to-endosome and endosome-to-vacuole stages of transport []. The role of VPS16 in this complex is not known.; GO: 0006886 intracellular protein transport, 0005737 cytoplasm

>PF10300 DUF3808: Protein of unknown function (DUF3808); InterPro: IPR019412 This entry represents a family of proteins conserved from fungi to humans

Probab=96.48  E-value=0.11  Score=51.75  Aligned_cols=167  Identities=14%  Similarity=0.146  Sum_probs=92.4

Q ss_pred             HHHHHHHHhcCChhHHHHHHHHHHhcCCCCCccccCcHHHHHHHHHHHHH----cCCHhHHHHHHHHHhhCCCCCCHhHH
Q 040027          170 NTLINGLCRTGHTMIALNLFEEMANGNGEIGVVCKPNTVTYSTIIDGLCK----EGFVDKAKALFLQMKDENINPDVVTY  245 (595)
Q Consensus       170 ~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~----~g~~~~A~~~~~~~~~~~~~~~~~~~  245 (595)
                      ..++....-.|+-+.+++.+.+..+.++-.++....-.-.|...+..++.    ..+.+.|.++++.+..+  -|+...|
T Consensus       192 ~kll~~vGF~gdR~~GL~~L~~~~~~~~i~~~la~L~LL~y~~~~~~~~~~~~~~~~~~~a~~lL~~~~~~--yP~s~lf  269 (468)
T PF10300_consen  192 LKLLSFVGFSGDRELGLRLLWEASKSENIRSPLAALVLLWYHLVVPSFLGIDGEDVPLEEAEELLEEMLKR--YPNSALF  269 (468)
T ss_pred             HHHHhhcCcCCcHHHHHHHHHHHhccCCcchHHHHHHHHHHHHHHHHHcCCcccCCCHHHHHHHHHHHHHh--CCCcHHH
Confidence            34455555678999999998887764421110000011223333333332    34567788888888776  3555555


Q ss_pred             HHH-HHHHHhcCCHHHHHHHHHHHHHCC---CCCCHhhHHHHHHHHHhcCChHHHHHHHHHHHHCCCCCCHHHHHHH-HH
Q 040027          246 NSL-IHGLCHANDWNEAKRLFIEMMDQG---VQPSVVTFNVIMDELCKNRKMDEASRLLDLMVQRGVRPNACTYNTL-MD  320 (595)
Q Consensus       246 ~~l-l~~~~~~~~~~~A~~~~~~~~~~~---~~~~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~l-~~  320 (595)
                      ... .+.+...|++++|++.|+......   .+.....+.-++..+.-..++++|...+..+.+..-. +...|..+ +.
T Consensus       270 l~~~gR~~~~~g~~~~Ai~~~~~a~~~q~~~~Ql~~l~~~El~w~~~~~~~w~~A~~~f~~L~~~s~W-Ska~Y~Y~~a~  348 (468)
T PF10300_consen  270 LFFEGRLERLKGNLEEAIESFERAIESQSEWKQLHHLCYFELAWCHMFQHDWEEAAEYFLRLLKESKW-SKAFYAYLAAA  348 (468)
T ss_pred             HHHHHHHHHHhcCHHHHHHHHHHhccchhhHHhHHHHHHHHHHHHHHHHchHHHHHHHHHHHHhcccc-HHHHHHHHHHH
Confidence            443 366777888888888888655321   0112233444556666777777777777777765322 23333322 23


Q ss_pred             HHHhcCCH-------HHHHHHHHHHH
Q 040027          321 GFCLMGKI-------NRAEELFGSME  339 (595)
Q Consensus       321 ~~~~~~~~-------~~a~~~~~~~~  339 (595)
                      ++...++.       ++|.++|.++.
T Consensus       349 c~~~l~~~~~~~~~~~~a~~l~~~vp  374 (468)
T PF10300_consen  349 CLLMLGREEEAKEHKKEAEELFRKVP  374 (468)
T ss_pred             HHHhhccchhhhhhHHHHHHHHHHHH
Confidence            34445555       55555555543

In humans this protein is expressed in primary breast carcinomas but not in normal breast tissue, and has a putative eukaryotic RNP-1 RNA binding region and a candidate anchoring transmembrane domain. The human protein is coordinately regulated with oestrogen receptor, but is not necessarily oestradiol-responsive []. Members of this family carry a tetratricopeptide repeat (IPR013105 from INTERPRO) at their C terminus.

>KOG0543 consensus FKBP-type peptidyl-prolyl cis-trans isomerase [Posttranslational modification, protein turnover, chaperones]

Probab=96.47  E-value=0.054  Score=50.59  Aligned_cols=125  Identities=18%  Similarity=0.109  Sum_probs=93.3

Q ss_pred             HHHHHhcCChhHHHHHHHHHHhCC-----CCC---------CHHHHHHHHHHHHhcCCHhHHHHHHHHHHhcCCCCCHhh
Q 040027          103 INCFCKIGRVSLGFIAFGRILRSC-----FTP---------NAATFNSLIKGLHAESRIMEAAALFTKLKAFGCEPNVIT  168 (595)
Q Consensus       103 ~~~~~~~g~~~~A~~~~~~~~~~~-----~~~---------~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~  168 (595)
                      ...+.+.|++..|..-|++++..-     .++         -..+++.+..++.+.+.+..|++.-++.+..+ +.|...
T Consensus       215 Gn~~fK~gk~~~A~~~Yerav~~l~~~~~~~~ee~~~~~~~k~~~~lNlA~c~lKl~~~~~Ai~~c~kvLe~~-~~N~KA  293 (397)
T KOG0543|consen  215 GNVLFKEGKFKLAKKRYERAVSFLEYRRSFDEEEQKKAEALKLACHLNLAACYLKLKEYKEAIESCNKVLELD-PNNVKA  293 (397)
T ss_pred             hhHHHhhchHHHHHHHHHHHHHHhhccccCCHHHHHHHHHHHHHHhhHHHHHHHhhhhHHHHHHHHHHHHhcC-CCchhH
Confidence            447888999999999999976531     111         23457778888899999999999999999886 558888


Q ss_pred             HHHHHHHHHhcCChhHHHHHHHHHHhcCCCCCccccCcHHHHHHHHHHHHHcCCHhH-HHHHHHHHhh
Q 040027          169 YNTLINGLCRTGHTMIALNLFEEMANGNGEIGVVCKPNTVTYSTIIDGLCKEGFVDK-AKALFLQMKD  235 (595)
Q Consensus       169 ~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~-A~~~~~~~~~  235 (595)
                      ...-..++...|+++.|+..|+++.+..       |.|..+-+.++.+--+.....+ ..++|..|..
T Consensus       294 LyRrG~A~l~~~e~~~A~~df~ka~k~~-------P~Nka~~~el~~l~~k~~~~~~kekk~y~~mF~  354 (397)
T KOG0543|consen  294 LYRRGQALLALGEYDLARDDFQKALKLE-------PSNKAARAELIKLKQKIREYEEKEKKMYANMFA  354 (397)
T ss_pred             HHHHHHHHHhhccHHHHHHHHHHHHHhC-------CCcHHHHHHHHHHHHHHHHHHHHHHHHHHHHhh
Confidence            8888899999999999999999999875       4555555566655555444433 3567777654

>KOG0543 consensus FKBP-type peptidyl-prolyl cis-trans isomerase [Posttranslational modification, protein turnover, chaperones]

Probab=96.43  E-value=0.069  Score=49.89  Aligned_cols=124  Identities=21%  Similarity=0.065  Sum_probs=68.1

Q ss_pred             HHHHhcCCHHHHHHHHHHHHHc-----CC---------CcCHHHHHHHHHHHHhcCChHHHHHHHHhcccCCCCCCHHHH
Q 040027          425 DGLCKNGYIIEAVELFRTLRIL-----KC---------ELDIQAYNCLIDGLCKSGRLKFAWELFCSLPHGVLVPNVVTY  490 (595)
Q Consensus       425 ~~~~~~g~~~~A~~~~~~~~~~-----~~---------~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~p~~~~~  490 (595)
                      ..|.+.|++..|...|+++...     ..         ..-..++..+..++.+.+++..|+..-++.+... ++|....
T Consensus       216 n~~fK~gk~~~A~~~Yerav~~l~~~~~~~~ee~~~~~~~k~~~~lNlA~c~lKl~~~~~Ai~~c~kvLe~~-~~N~KAL  294 (397)
T KOG0543|consen  216 NVLFKEGKFKLAKKRYERAVSFLEYRRSFDEEEQKKAEALKLACHLNLAACYLKLKEYKEAIESCNKVLELD-PNNVKAL  294 (397)
T ss_pred             hHHHhhchHHHHHHHHHHHHHHhhccccCCHHHHHHHHHHHHHHhhHHHHHHHhhhhHHHHHHHHHHHHhcC-CCchhHH
Confidence            3455555666555555554321     00         1123345666667777777777777777766631 2345566


Q ss_pred             HHHHHHHHhcCChhHHHHHHHHHHHcCCCCCHHHHHHHHHHHHHcCCh-hHHHHHHHHHHH
Q 040027          491 NIMIQGLCNDGQMDKARDLFLDMEENAAAPDVITFDMLIHGFIRINEP-SKVNELLHKMKE  550 (595)
Q Consensus       491 ~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~-~~A~~~~~~~~~  550 (595)
                      ..-..+|...|+++.|+..|+++++.. |.|..+-..++..-.+..++ +...++|..|..
T Consensus       295 yRrG~A~l~~~e~~~A~~df~ka~k~~-P~Nka~~~el~~l~~k~~~~~~kekk~y~~mF~  354 (397)
T KOG0543|consen  295 YRRGQALLALGEYDLARDDFQKALKLE-PSNKAARAELIKLKQKIREYEEKEKKMYANMFA  354 (397)
T ss_pred             HHHHHHHHhhccHHHHHHHHHHHHHhC-CCcHHHHHHHHHHHHHHHHHHHHHHHHHHHHhh
Confidence            666677777777777777777777743 22333333333333333333 334666666663

>PF10300 DUF3808: Protein of unknown function (DUF3808); InterPro: IPR019412 This entry represents a family of proteins conserved from fungi to humans

Probab=96.36  E-value=0.38  Score=48.12  Aligned_cols=117  Identities=15%  Similarity=0.061  Sum_probs=71.9

Q ss_pred             cCCHHHHHHHHHHHHHcCCCcCHHHH-HHHHHHHHhcCChHHHHHHHHhcccCC-CCC--CHHHHHHHHHHHHhcCChhH
Q 040027          430 NGYIIEAVELFRTLRILKCELDIQAY-NCLIDGLCKSGRLKFAWELFCSLPHGV-LVP--NVVTYNIMIQGLCNDGQMDK  505 (595)
Q Consensus       430 ~g~~~~A~~~~~~~~~~~~~~~~~~~-~~l~~~~~~~g~~~~A~~~~~~~~~~~-~~p--~~~~~~~l~~~~~~~g~~~~  505 (595)
                      ....+.|.++++.+.+.-  |+...| ..-.+.+...|++++|++.|++..... .-|  ....+--++.++....+|++
T Consensus       246 ~~~~~~a~~lL~~~~~~y--P~s~lfl~~~gR~~~~~g~~~~Ai~~~~~a~~~q~~~~Ql~~l~~~El~w~~~~~~~w~~  323 (468)
T PF10300_consen  246 DVPLEEAEELLEEMLKRY--PNSALFLFFEGRLERLKGNLEEAIESFERAIESQSEWKQLHHLCYFELAWCHMFQHDWEE  323 (468)
T ss_pred             CCCHHHHHHHHHHHHHhC--CCcHHHHHHHHHHHHHhcCHHHHHHHHHHhccchhhHHhHHHHHHHHHHHHHHHHchHHH
Confidence            345677777777777652  343333 333455667788888888887655411 011  23345566677778888888


Q ss_pred             HHHHHHHHHHcCCCCCHHHHHHH-HHHHHHcCCh-------hHHHHHHHHHH
Q 040027          506 ARDLFLDMEENAAAPDVITFDML-IHGFIRINEP-------SKVNELLHKMK  549 (595)
Q Consensus       506 A~~~~~~~~~~~~~~~~~~~~~l-~~~~~~~g~~-------~~A~~~~~~~~  549 (595)
                      |.+.|.++.+.. ..+..+|..+ +-++...|+.       ++|.+++++..
T Consensus       324 A~~~f~~L~~~s-~WSka~Y~Y~~a~c~~~l~~~~~~~~~~~~a~~l~~~vp  374 (468)
T PF10300_consen  324 AAEYFLRLLKES-KWSKAFYAYLAAACLLMLGREEEAKEHKKEAEELFRKVP  374 (468)
T ss_pred             HHHHHHHHHhcc-ccHHHHHHHHHHHHHHhhccchhhhhhHHHHHHHHHHHH
Confidence            888888888764 3344444333 3344456776       77777777775

In humans this protein is expressed in primary breast carcinomas but not in normal breast tissue, and has a putative eukaryotic RNP-1 RNA binding region and a candidate anchoring transmembrane domain. The human protein is coordinately regulated with oestrogen receptor, but is not necessarily oestradiol-responsive []. Members of this family carry a tetratricopeptide repeat (IPR013105 from INTERPRO) at their C terminus.

>COG1729 Uncharacterized protein conserved in bacteria [Function unknown]

Probab=96.25  E-value=0.06  Score=47.68  Aligned_cols=96  Identities=15%  Similarity=0.058  Sum_probs=58.3

Q ss_pred             ccccccCCCChHHHHHHHHHHHHhCCCCCCHhhHHHHHHHHHcCCCchhHHhhCCCCCCHHHHHHHHHHHHhcCChhHHH
Q 040027           37 TREGDINVITPNEAFCIFDYMLRMHPSPPPVSSFNILLASLAKNKHYDTRLNATGLFPNLYTYNILINCFCKIGRVSLGF  116 (595)
Q Consensus        37 ~~~~~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~  116 (595)
                      -+..+++.|++.+|...|...++.-|+  ++.                          .+..+-.|...+...|++++|.
T Consensus       147 ~A~~~~ksgdy~~A~~~F~~fi~~YP~--s~~--------------------------~~nA~yWLGe~~y~qg~y~~Aa  198 (262)
T COG1729         147 AALDLYKSGDYAEAEQAFQAFIKKYPN--STY--------------------------TPNAYYWLGESLYAQGDYEDAA  198 (262)
T ss_pred             HHHHHHHcCCHHHHHHHHHHHHHcCCC--Ccc--------------------------cchhHHHHHHHHHhcccchHHH
Confidence            344446667777777777777777766  211                          1222334666777777777777


Q ss_pred             HHHHHHHhCCC--CCCHHHHHHHHHHHHhcCCHhHHHHHHHHHHhc
Q 040027          117 IAFGRILRSCF--TPNAATFNSLIKGLHAESRIMEAAALFTKLKAF  160 (595)
Q Consensus       117 ~~~~~~~~~~~--~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~  160 (595)
                      .+|..+.+.-+  +.-+..+..+.....+.|+.++|..+|+++.+.
T Consensus       199 ~~f~~~~k~~P~s~KApdallKlg~~~~~l~~~d~A~atl~qv~k~  244 (262)
T COG1729         199 YIFARVVKDYPKSPKAPDALLKLGVSLGRLGNTDEACATLQQVIKR  244 (262)
T ss_pred             HHHHHHHHhCCCCCCChHHHHHHHHHHHHhcCHHHHHHHHHHHHHH
Confidence            77777766521  122445566666666667777777777776665

>PF08631 SPO22: Meiosis protein SPO22/ZIP4 like; InterPro: IPR013940 SPO22 is a meiosis-specific protein with similarity to phospholipase A2, involved in completion of nuclear divisions during meiosis; induced early in meiosis []

Probab=96.20  E-value=1  Score=41.63  Aligned_cols=123  Identities=14%  Similarity=0.110  Sum_probs=63.3

Q ss_pred             HhcCChhHHHHHHHHHHhCCCCCCHHHHH-------HHHHHHHhcC-CHhHHHHHHHHHHhc----C----CCCCH----
Q 040027          107 CKIGRVSLGFIAFGRILRSCFTPNAATFN-------SLIKGLHAES-RIMEAAALFTKLKAF----G----CEPNV----  166 (595)
Q Consensus       107 ~~~g~~~~A~~~~~~~~~~~~~~~~~~~~-------~l~~~~~~~g-~~~~A~~~~~~~~~~----~----~~~~~----  166 (595)
                      .+.|+.+.|..++.++.......++....       .+.....+.+ +++.|..++++..+.    +    ..++.    
T Consensus         4 ~~~~~~~~A~~~~~K~~~~~~~~~~~~~~~La~~~yn~G~~l~~~~~~~~~a~~wL~~a~~~l~~~~~~~~~~~~~~elr   83 (278)
T PF08631_consen    4 WKQGDLDLAEHMYSKAKDLLNSLDPDMAEELARVCYNIGKSLLSKKDKYEEAVKWLQRAYDILEKPGKMDKLSPDGSELR   83 (278)
T ss_pred             hhhCCHHHHHHHHHHhhhHHhcCCcHHHHHHHHHHHHHHHHHHHcCCChHHHHHHHHHHHHHHHhhhhccccCCcHHHHH
Confidence            45788888888888877643122222222       2223334455 777777777665443    1    11121    


Q ss_pred             -hhHHHHHHHHHhcCChh---HHHHHHHHHHhcCCCCCccccCcHHHHHHHHHHHHHcCCHhHHHHHHHHHhhC
Q 040027          167 -ITYNTLINGLCRTGHTM---IALNLFEEMANGNGEIGVVCKPNTVTYSTIIDGLCKEGFVDKAKALFLQMKDE  236 (595)
Q Consensus       167 -~~~~~l~~~~~~~g~~~---~A~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~  236 (595)
                       .+...++.+|...+..+   +|..+++.+....       +..+..+..-+..+.+.++.+.+.+.+.+|...
T Consensus        84 ~~iL~~La~~~l~~~~~~~~~ka~~~l~~l~~e~-------~~~~~~~~L~l~il~~~~~~~~~~~~L~~mi~~  150 (278)
T PF08631_consen   84 LSILRLLANAYLEWDTYESVEKALNALRLLESEY-------GNKPEVFLLKLEILLKSFDEEEYEEILMRMIRS  150 (278)
T ss_pred             HHHHHHHHHHHHcCCChHHHHHHHHHHHHHHHhC-------CCCcHHHHHHHHHHhccCChhHHHHHHHHHHHh
Confidence             23445555555555433   3344444443322       223444444555555566666666666666654

It is also involved in sporulation [].

>KOG2280 consensus Vacuolar assembly/sorting protein VPS16 [Intracellular trafficking, secretion, and vesicular transport]

Probab=96.17  E-value=1.8  Score=44.17  Aligned_cols=105  Identities=12%  Similarity=0.132  Sum_probs=53.6

Q ss_pred             HHHHHHHHhcCCHHHHHHHHHHHHHcCCCcCHHHHHHHHHHHHhcCChHHHHHHHHhcccCCCCCCHHHHHHHHHHHHhc
Q 040027          421 TTFIDGLCKNGYIIEAVELFRTLRILKCELDIQAYNCLIDGLCKSGRLKFAWELFCSLPHGVLVPNVVTYNIMIQGLCND  500 (595)
Q Consensus       421 ~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~p~~~~~~~l~~~~~~~  500 (595)
                      +.-+.-+...|...+|.++-.+.+    -||...|..-+.++...+++++-+++-+...      .+.-|.....+|.+.
T Consensus       688 ~dTv~~li~~g~~k~a~ql~~~Fk----ipdKr~~wLk~~aLa~~~kweeLekfAkskk------sPIGy~PFVe~c~~~  757 (829)
T KOG2280|consen  688 HDTVTTLILIGQNKRAEQLKSDFK----IPDKRLWWLKLTALADIKKWEELEKFAKSKK------SPIGYLPFVEACLKQ  757 (829)
T ss_pred             HHHHHHHHHccchHHHHHHHHhcC----CcchhhHHHHHHHHHhhhhHHHHHHHHhccC------CCCCchhHHHHHHhc
Confidence            333344445556666655555544    4555555555555666666655554444332      133344455556666


Q ss_pred             CChhHHHHHHHHHHHcCCCCCHHHHHHHHHHHHHcCChhHHHHH
Q 040027          501 GQMDKARDLFLDMEENAAAPDVITFDMLIHGFIRINEPSKVNEL  544 (595)
Q Consensus       501 g~~~~A~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~  544 (595)
                      |+.++|.+++.+...     ..    -...+|.+.|++.+|.+.
T Consensus       758 ~n~~EA~KYiprv~~-----l~----ekv~ay~~~~~~~eAad~  792 (829)
T KOG2280|consen  758 GNKDEAKKYIPRVGG-----LQ----EKVKAYLRVGDVKEAADL  792 (829)
T ss_pred             ccHHHHhhhhhccCC-----hH----HHHHHHHHhccHHHHHHH
Confidence            666666665554432     11    234445555555555544

>KOG2610 consensus Uncharacterized conserved protein [Function unknown]

Probab=96.17  E-value=0.17  Score=45.94  Aligned_cols=157  Identities=16%  Similarity=0.070  Sum_probs=84.2

Q ss_pred             HHhcCCHhHHHHHHHHHHhcCCCCCHhhHHHHHHHHHhcCChhHHHHHHHHHHhc-CCCCCccccCcHHHHHHHHHHHHH
Q 040027          141 LHAESRIMEAAALFTKLKAFGCEPNVITYNTLINGLCRTGHTMIALNLFEEMANG-NGEIGVVCKPNTVTYSTIIDGLCK  219 (595)
Q Consensus       141 ~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~-~~~~~~~~~~~~~~~~~l~~~~~~  219 (595)
                      +..+|++-+|...++++++. .+.|..++...=.++...|+...-...++++... +..    .|-.........-++..
T Consensus       113 ~~~~g~~h~a~~~wdklL~d-~PtDlla~kfsh~a~fy~G~~~~~k~ai~kIip~wn~d----lp~~sYv~GmyaFgL~E  187 (491)
T KOG2610|consen  113 LWGRGKHHEAAIEWDKLLDD-YPTDLLAVKFSHDAHFYNGNQIGKKNAIEKIIPKWNAD----LPCYSYVHGMYAFGLEE  187 (491)
T ss_pred             hhccccccHHHHHHHHHHHh-CchhhhhhhhhhhHHHhccchhhhhhHHHHhccccCCC----CcHHHHHHHHHHhhHHH
Confidence            34566666666666666654 3445555555556666666666666666666544 200    11112222233344455


Q ss_pred             cCCHhHHHHHHHHHhhCCCCCCHhHHHHHHHHHHhcCCHHHHHHHHHHHHHCCCC---CCHhhHHHHHHHHHhcCChHHH
Q 040027          220 EGFVDKAKALFLQMKDENINPDVVTYNSLIHGLCHANDWNEAKRLFIEMMDQGVQ---PSVVTFNVIMDELCKNRKMDEA  296 (595)
Q Consensus       220 ~g~~~~A~~~~~~~~~~~~~~~~~~~~~ll~~~~~~~~~~~A~~~~~~~~~~~~~---~~~~~~~~l~~~~~~~g~~~~a  296 (595)
                      .|-+++|++.-++..+.+ +-|...-.++...+-..+++.++.+...+-.+.--.   .-..-|-...-.+...+.++.|
T Consensus       188 ~g~y~dAEk~A~ralqiN-~~D~Wa~Ha~aHVlem~~r~Keg~eFM~~ted~Wr~s~mlasHNyWH~Al~~iE~aeye~a  266 (491)
T KOG2610|consen  188 CGIYDDAEKQADRALQIN-RFDCWASHAKAHVLEMNGRHKEGKEFMYKTEDDWRQSWMLASHNYWHTALFHIEGAEYEKA  266 (491)
T ss_pred             hccchhHHHHHHhhccCC-CcchHHHHHHHHHHHhcchhhhHHHHHHhcccchhhhhHHHhhhhHHHHHhhhcccchhHH
Confidence            666777777666666654 235555555666666666666666665443222101   1122233334455566777777


Q ss_pred             HHHHHHH
Q 040027          297 SRLLDLM  303 (595)
Q Consensus       297 ~~~~~~~  303 (595)
                      +.+|+.-
T Consensus       267 leIyD~e  273 (491)
T KOG2610|consen  267 LEIYDRE  273 (491)
T ss_pred             HHHHHHH
Confidence            7777643

>KOG2610 consensus Uncharacterized conserved protein [Function unknown]

Probab=96.14  E-value=0.18  Score=45.69  Aligned_cols=115  Identities=16%  Similarity=0.048  Sum_probs=49.3

Q ss_pred             cCCHHHHHHHHHHHHhcCCCCCHHHHHHHHHHHHhCCCHHHHHHHHHHHHHCCCCCCHH----HHHHHHHHHHccCCHHH
Q 040027          325 MGKINRAEELFGSMESMGCKHDDVSYNILINGYCKNKEVEEALSLYREMVSKGIKPTVV----TYNTLFLGLFEIHQVEH  400 (595)
Q Consensus       325 ~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~~~~~~~~~----~~~~l~~~~~~~~~~~~  400 (595)
                      .|++.+|-..++++++. .|.|..++...=.+|.-.|+.+.-...+++++.. ..++..    .-..+.-++...|-+++
T Consensus       116 ~g~~h~a~~~wdklL~d-~PtDlla~kfsh~a~fy~G~~~~~k~ai~kIip~-wn~dlp~~sYv~GmyaFgL~E~g~y~d  193 (491)
T KOG2610|consen  116 RGKHHEAAIEWDKLLDD-YPTDLLAVKFSHDAHFYNGNQIGKKNAIEKIIPK-WNADLPCYSYVHGMYAFGLEECGIYDD  193 (491)
T ss_pred             cccccHHHHHHHHHHHh-CchhhhhhhhhhhHHHhccchhhhhhHHHHhccc-cCCCCcHHHHHHHHHHhhHHHhccchh
Confidence            34444444444444433 2334444444444555555555555445444432 111221    11222223344555555


Q ss_pred             HHHHHHHHHHCCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHH
Q 040027          401 ALKLFDEMQRDGVAADTRTYTTFIDGLCKNGYIIEAVELFRT  442 (595)
Q Consensus       401 a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~  442 (595)
                      |++.-++..+.+ +.|.....+....+.-.|+..++.++..+
T Consensus       194 AEk~A~ralqiN-~~D~Wa~Ha~aHVlem~~r~Keg~eFM~~  234 (491)
T KOG2610|consen  194 AEKQADRALQIN-RFDCWASHAKAHVLEMNGRHKEGKEFMYK  234 (491)
T ss_pred             HHHHHHhhccCC-CcchHHHHHHHHHHHhcchhhhHHHHHHh
Confidence            555555444432 33333444444444445555555544443

>PF13512 TPR_18: Tetratricopeptide repeat

Probab=96.12  E-value=0.24  Score=39.39  Aligned_cols=84  Identities=10%  Similarity=-0.008  Sum_probs=61.4

Q ss_pred             CHHHHHHHHHHHHhcCChhHHHHHHHHHHhCCC--CCCHHHHHHHHHHHHhcCCHhHHHHHHHHHHhcCCCCCHhhHHHH
Q 040027           95 NLYTYNILINCFCKIGRVSLGFIAFGRILRSCF--TPNAATFNSLIKGLHAESRIMEAAALFTKLKAFGCEPNVITYNTL  172 (595)
Q Consensus        95 ~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~--~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~~l  172 (595)
                      ++..+-.-.....+.|++++|+..|+.+..+-+  +-...+...++.+|.+.+++++|+..+++.++..+.....-|...
T Consensus         9 ~~~~ly~~a~~~l~~~~Y~~A~~~le~L~~ryP~g~ya~qAqL~l~yayy~~~~y~~A~a~~~rFirLhP~hp~vdYa~Y   88 (142)
T PF13512_consen    9 SPQELYQEAQEALQKGNYEEAIKQLEALDTRYPFGEYAEQAQLDLAYAYYKQGDYEEAIAAYDRFIRLHPTHPNVDYAYY   88 (142)
T ss_pred             CHHHHHHHHHHHHHhCCHHHHHHHHHHHHhcCCCCcccHHHHHHHHHHHHHccCHHHHHHHHHHHHHhCCCCCCccHHHH
Confidence            444555566677788999999999999998732  223456678889999999999999999999998654333444444


Q ss_pred             HHHHHh
Q 040027          173 INGLCR  178 (595)
Q Consensus       173 ~~~~~~  178 (595)
                      +.+++.
T Consensus        89 ~~gL~~   94 (142)
T PF13512_consen   89 MRGLSY   94 (142)
T ss_pred             HHHHHH
Confidence            444443

>PF12921 ATP13: Mitochondrial ATPase expression; InterPro: IPR024319 ATPase expression protein 2 (also known as ATP13 in some species) is necessary for the expression of subunit 9 of mitochondrial ATPase

Probab=95.99  E-value=0.28  Score=38.65  Aligned_cols=97  Identities=12%  Similarity=0.110  Sum_probs=58.7

Q ss_pred             HHHHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCcCHHHHHHHHHHHHhcCChHHHHHHHHhcccCCCCCCHHHHHHHHHH
Q 040027          417 TRTYTTFIDGLCKNGYIIEAVELFRTLRILKCELDIQAYNCLIDGLCKSGRLKFAWELFCSLPHGVLVPNVVTYNIMIQG  496 (595)
Q Consensus       417 ~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~p~~~~~~~l~~~  496 (595)
                      ..++..++.++++.|+.+....+++..-.  +..+...         ..+.         --....+.|+..+..+++.+
T Consensus         2 e~~~~~ii~al~r~g~~~~i~~~i~~~Wg--I~~~~~~---------~~~~---------~~~~spl~Pt~~lL~AIv~s   61 (126)
T PF12921_consen    2 EELLCNIIYALGRSGQLDSIKSYIKSVWG--IDVNGKK---------KEGD---------YPPSSPLYPTSRLLIAIVHS   61 (126)
T ss_pred             hHHHHHHHHHHhhcCCHHHHHHHHHHhcC--CCCCCcc---------ccCc---------cCCCCCCCCCHHHHHHHHHH
Confidence            45566666666666766666666654432  1111100         0000         11223356788888888888


Q ss_pred             HHhcCChhHHHHHHHHHHHc-CCCCCHHHHHHHHHHHH
Q 040027          497 LCNDGQMDKARDLFLDMEEN-AAAPDVITFDMLIHGFI  533 (595)
Q Consensus       497 ~~~~g~~~~A~~~~~~~~~~-~~~~~~~~~~~l~~~~~  533 (595)
                      |+.+|++..|+++.+...+. +++.+..+|..|+.-..
T Consensus        62 f~~n~~i~~al~~vd~fs~~Y~I~i~~~~W~~Ll~W~~   99 (126)
T PF12921_consen   62 FGYNGDIFSALKLVDFFSRKYPIPIPKEFWRRLLEWAY   99 (126)
T ss_pred             HHhcccHHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHH
Confidence            88888888888888887764 56666777777765443

The protein has a basic amino terminal signal sequence that is cleaved upon import into mitochondria [].

>PF12921 ATP13: Mitochondrial ATPase expression; InterPro: IPR024319 ATPase expression protein 2 (also known as ATP13 in some species) is necessary for the expression of subunit 9 of mitochondrial ATPase

Probab=95.94  E-value=0.17  Score=39.86  Aligned_cols=87  Identities=13%  Similarity=0.023  Sum_probs=50.9

Q ss_pred             hhHHHHHHHHHhcCChhHHHHHHHHHHhcC---------CCCCccccCcHHHHHHHHHHHHHcCCHhHHHHHHHHHhhC-
Q 040027          167 ITYNTLINGLCRTGHTMIALNLFEEMANGN---------GEIGVVCKPNTVTYSTIIDGLCKEGFVDKAKALFLQMKDE-  236 (595)
Q Consensus       167 ~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~---------~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~-  236 (595)
                      .++..++.++++.|+.+....+++..=..+         ...+.+..|+..+..+++.+|+..|++..|.++.+...+. 
T Consensus         3 ~~~~~ii~al~r~g~~~~i~~~i~~~WgI~~~~~~~~~~~~~~spl~Pt~~lL~AIv~sf~~n~~i~~al~~vd~fs~~Y   82 (126)
T PF12921_consen    3 ELLCNIIYALGRSGQLDSIKSYIKSVWGIDVNGKKKEGDYPPSSPLYPTSRLLIAIVHSFGYNGDIFSALKLVDFFSRKY   82 (126)
T ss_pred             HHHHHHHHHHhhcCCHHHHHHHHHHhcCCCCCCccccCccCCCCCCCCCHHHHHHHHHHHHhcccHHHHHHHHHHHHHHc
Confidence            445555555555555555555554432211         0111224567777777777777777777777777776554 


Q ss_pred             CCCCCHhHHHHHHHHHH
Q 040027          237 NINPDVVTYNSLIHGLC  253 (595)
Q Consensus       237 ~~~~~~~~~~~ll~~~~  253 (595)
                      +++.+...|..|+.-..
T Consensus        83 ~I~i~~~~W~~Ll~W~~   99 (126)
T PF12921_consen   83 PIPIPKEFWRRLLEWAY   99 (126)
T ss_pred             CCCCCHHHHHHHHHHHH
Confidence            45555667777775433

The protein has a basic amino terminal signal sequence that is cleaved upon import into mitochondria [].

>PF13428 TPR_14: Tetratricopeptide repeat

Probab=95.93  E-value=0.028  Score=34.62  Aligned_cols=40  Identities=13%  Similarity=0.190  Sum_probs=24.9

Q ss_pred             HHHHHHHHHHHhcCChhHHHHHHHHHHhCCCCCCHHHHHHH
Q 040027           97 YTYNILINCFCKIGRVSLGFIAFGRILRSCFTPNAATFNSL  137 (595)
Q Consensus        97 ~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~~l  137 (595)
                      .+|..+...|.+.|++++|+.+|+++++.. +-|...|..+
T Consensus         2 ~~~~~la~~~~~~G~~~~A~~~~~~~l~~~-P~~~~a~~~L   41 (44)
T PF13428_consen    2 AAWLALARAYRRLGQPDEAERLLRRALALD-PDDPEAWRAL   41 (44)
T ss_pred             HHHHHHHHHHHHcCCHHHHHHHHHHHHHHC-cCCHHHHHHh
Confidence            355666667777777777777777777663 3345555444

>COG4105 ComL DNA uptake lipoprotein [General function prediction only]

Probab=95.93  E-value=1.1  Score=39.58  Aligned_cols=77  Identities=10%  Similarity=-0.069  Sum_probs=45.2

Q ss_pred             HHHHHHHhcCChhHHHHHHHHHHhCCC--CCCHHHHHHHHHHHHhcCCHhHHHHHHHHHHhcCCCCCHhhHHHHHHHHH
Q 040027          101 ILINCFCKIGRVSLGFIAFGRILRSCF--TPNAATFNSLIKGLHAESRIMEAAALFTKLKAFGCEPNVITYNTLINGLC  177 (595)
Q Consensus       101 ~l~~~~~~~g~~~~A~~~~~~~~~~~~--~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~~l~~~~~  177 (595)
                      .-+..-.+.|++++|...|+.+....+  +-...+...++-++.+.+++++|+...++..+.-.......|...+.+++
T Consensus        39 ~~g~~~L~~gn~~~A~~~fe~l~~~~p~s~~~~qa~l~l~yA~Yk~~~y~~A~~~~drFi~lyP~~~n~dY~~YlkgLs  117 (254)
T COG4105          39 NEGLTELQKGNYEEAIKYFEALDSRHPFSPYSEQAQLDLAYAYYKNGEYDLALAYIDRFIRLYPTHPNADYAYYLKGLS  117 (254)
T ss_pred             HHHHHHHhcCCHHHHHHHHHHHHHcCCCCcccHHHHHHHHHHHHhcccHHHHHHHHHHHHHhCCCCCChhHHHHHHHHH
Confidence            334445566788888888887776521  22334445556666777777777777777776643323333444444443

>PF04053 Coatomer_WDAD: Coatomer WD associated region ; InterPro: IPR006692 Proteins synthesised on the ribosome and processed in the endoplasmic reticulum are transported from the Golgi apparatus to the trans-Golgi network (TGN), and from there via small carrier vesicles to their final destination compartment

Probab=95.74  E-value=0.42  Score=47.08  Aligned_cols=155  Identities=15%  Similarity=0.110  Sum_probs=69.5

Q ss_pred             HhcCChhHHHHHHHHHHhCCCCCCHHHHHHHHHHHHhcCCHhHHHHHHHHHHhcCCCCCHhhHHHHHHHHHhcCChhHHH
Q 040027          107 CKIGRVSLGFIAFGRILRSCFTPNAATFNSLIKGLHAESRIMEAAALFTKLKAFGCEPNVITYNTLINGLCRTGHTMIAL  186 (595)
Q Consensus       107 ~~~g~~~~A~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~  186 (595)
                      .-.|+++.+.++.+.-.-. +.-+....+.++..+.+.|..+.|+++-..         +.+   -.....+.|+.+.|.
T Consensus       272 v~~~d~~~v~~~i~~~~ll-~~i~~~~~~~i~~fL~~~G~~e~AL~~~~D---------~~~---rFeLAl~lg~L~~A~  338 (443)
T PF04053_consen  272 VLRGDFEEVLRMIAASNLL-PNIPKDQGQSIARFLEKKGYPELALQFVTD---------PDH---RFELALQLGNLDIAL  338 (443)
T ss_dssp             HHTT-HHH-----HHHHTG-GG--HHHHHHHHHHHHHTT-HHHHHHHSS----------HHH---HHHHHHHCT-HHHHH
T ss_pred             HHcCChhhhhhhhhhhhhc-ccCChhHHHHHHHHHHHCCCHHHHHhhcCC---------hHH---HhHHHHhcCCHHHHH
Confidence            3456666655555411111 011233445566666666666666654322         211   123334566666665


Q ss_pred             HHHHHHHhcCCCCCccccCcHHHHHHHHHHHHHcCCHhHHHHHHHHHhhCCCCCCHhHHHHHHHHHHhcCCHHHHHHHHH
Q 040027          187 NLFEEMANGNGEIGVVCKPNTVTYSTIIDGLCKEGFVDKAKALFLQMKDENINPDVVTYNSLIHGLCHANDWNEAKRLFI  266 (595)
Q Consensus       187 ~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~~ll~~~~~~~~~~~A~~~~~  266 (595)
                      ++.++.            .+...|..|.....+.|+++-|++.|.+...         |..|+-.|.-.|+.+.-.++.+
T Consensus       339 ~~a~~~------------~~~~~W~~Lg~~AL~~g~~~lAe~c~~k~~d---------~~~L~lLy~~~g~~~~L~kl~~  397 (443)
T PF04053_consen  339 EIAKEL------------DDPEKWKQLGDEALRQGNIELAEECYQKAKD---------FSGLLLLYSSTGDREKLSKLAK  397 (443)
T ss_dssp             HHCCCC------------STHHHHHHHHHHHHHTTBHHHHHHHHHHCT----------HHHHHHHHHHCT-HHHHHHHHH
T ss_pred             HHHHhc------------CcHHHHHHHHHHHHHcCCHHHHHHHHHhhcC---------ccccHHHHHHhCCHHHHHHHHH
Confidence            543222            2355666666666666666666666655432         3445555555666555555554


Q ss_pred             HHHHCCCCCCHhhHHHHHHHHHhcCChHHHHHHHH
Q 040027          267 EMMDQGVQPSVVTFNVIMDELCKNRKMDEASRLLD  301 (595)
Q Consensus       267 ~~~~~~~~~~~~~~~~l~~~~~~~g~~~~a~~~~~  301 (595)
                      .....|      -++....++.-.|+.++..+++.
T Consensus       398 ~a~~~~------~~n~af~~~~~lgd~~~cv~lL~  426 (443)
T PF04053_consen  398 IAEERG------DINIAFQAALLLGDVEECVDLLI  426 (443)
T ss_dssp             HHHHTT-------HHHHHHHHHHHT-HHHHHHHHH
T ss_pred             HHHHcc------CHHHHHHHHHHcCCHHHHHHHHH
Confidence            444432      13334444445555555555544

This traffic is bidirectional, to ensure that proteins required to form vesicles are recycled. Vesicles have specific coat proteins (such as clathrin or coatomer) that are important for cargo selection and direction of transfer []. While clathrin mediates endocytic protein transport, and transport from ER to Golgi, coatomers primarily mediate intra-Golgi transport, as well as the reverse Golgi to ER transport of dilysine-tagged proteins []. For example, the coatomer COP1 (coat protein complex 1) is responsible for reverse transport of recycled proteins from Golgi and pre-Golgi compartments back to the ER, while COPII buds vesicles from the ER to the Golgi []. Coatomers reversibly associate with Golgi (non-clathrin-coated) vesicles to mediate protein transport and for budding from Golgi membranes []. Activated small guanine triphosphatases (GTPases) attract coat proteins to specific membrane export sites, thereby linking coatomers to export cargos. As coat proteins polymerise, vesicles are formed and budded from membrane-bound organelles. Coatomer complexes also influence Golgi structural integrity, as well as the processing, activity, and endocytic recycling of LDL receptors. In mammals, coatomer complexes can only be recruited by membranes associated to ADP-ribosylation factors (ARFs), which are small GTP-binding proteins. Coatomer complexes are hetero-oligomers composed of at least an alpha, beta, beta', gamma, delta, epsilon and zeta subunits. This entry represents the WD-associated region found in coatomer subunits alpha, beta and beta' subunits. The alpha-subunit (RET1P) of the coatomer complex in Saccharomyces cerevisiae (Baker's yeast), participates in membrane transport between the endoplasmic reticulum and Golgi apparatus. The protein contains six WD-40 repeat motifs in its N-terminal region []. More information about these proteins can be found at Protein of the Month: Clathrin [].; GO: 0005198 structural molecule activity, 0006886 intracellular protein transport, 0016192 vesicle-mediated transport, 0030117 membrane coat; PDB: 3MKQ_B.

>PF13428 TPR_14: Tetratricopeptide repeat

Probab=95.68  E-value=0.036  Score=34.18  Aligned_cols=27  Identities=19%  Similarity=0.134  Sum_probs=13.0

Q ss_pred             HHHHHHHHHhcCChhHHHHHHHHHHHc
Q 040027          490 YNIMIQGLCNDGQMDKARDLFLDMEEN  516 (595)
Q Consensus       490 ~~~l~~~~~~~g~~~~A~~~~~~~~~~  516 (595)
                      |..+..+|...|++++|+++|+++++.
T Consensus         4 ~~~la~~~~~~G~~~~A~~~~~~~l~~   30 (44)
T PF13428_consen    4 WLALARAYRRLGQPDEAERLLRRALAL   30 (44)
T ss_pred             HHHHHHHHHHcCCHHHHHHHHHHHHHH
Confidence            344444444555555555555554444

>PF04053 Coatomer_WDAD: Coatomer WD associated region ; InterPro: IPR006692 Proteins synthesised on the ribosome and processed in the endoplasmic reticulum are transported from the Golgi apparatus to the trans-Golgi network (TGN), and from there via small carrier vesicles to their final destination compartment

Probab=95.67  E-value=0.74  Score=45.38  Aligned_cols=156  Identities=16%  Similarity=0.158  Sum_probs=85.2

Q ss_pred             HHhCCCHHHHHHHHH--HHHHCCCCCCHHHHHHHHHHHHccCCHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHhcCCHH
Q 040027          357 YCKNKEVEEALSLYR--EMVSKGIKPTVVTYNTLFLGLFEIHQVEHALKLFDEMQRDGVAADTRTYTTFIDGLCKNGYII  434 (595)
Q Consensus       357 ~~~~~~~~~A~~~~~--~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~  434 (595)
                      ..-.++++++.+..+  ++... +  .......++.-+.+.|-++.|+.+..         |+.+   -.....+.|+++
T Consensus       271 av~~~d~~~v~~~i~~~~ll~~-i--~~~~~~~i~~fL~~~G~~e~AL~~~~---------D~~~---rFeLAl~lg~L~  335 (443)
T PF04053_consen  271 AVLRGDFEEVLRMIAASNLLPN-I--PKDQGQSIARFLEKKGYPELALQFVT---------DPDH---RFELALQLGNLD  335 (443)
T ss_dssp             HHHTT-HHH-----HHHHTGGG-----HHHHHHHHHHHHHTT-HHHHHHHSS----------HHH---HHHHHHHCT-HH
T ss_pred             HHHcCChhhhhhhhhhhhhccc-C--ChhHHHHHHHHHHHCCCHHHHHhhcC---------ChHH---HhHHHHhcCCHH
Confidence            344566666655554  11111 1  23345566666667777777766532         2221   123345677777


Q ss_pred             HHHHHHHHHHHcCCCcCHHHHHHHHHHHHhcCChHHHHHHHHhcccCCCCCCHHHHHHHHHHHHhcCChhHHHHHHHHHH
Q 040027          435 EAVELFRTLRILKCELDIQAYNCLIDGLCKSGRLKFAWELFCSLPHGVLVPNVVTYNIMIQGLCNDGQMDKARDLFLDME  514 (595)
Q Consensus       435 ~A~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~p~~~~~~~l~~~~~~~g~~~~A~~~~~~~~  514 (595)
                      .|.++.++      ..+...|..|......+|+++-|.+.|.+..+         |..|+-.|.-.|+.+.-.++.+...
T Consensus       336 ~A~~~a~~------~~~~~~W~~Lg~~AL~~g~~~lAe~c~~k~~d---------~~~L~lLy~~~g~~~~L~kl~~~a~  400 (443)
T PF04053_consen  336 IALEIAKE------LDDPEKWKQLGDEALRQGNIELAEECYQKAKD---------FSGLLLLYSSTGDREKLSKLAKIAE  400 (443)
T ss_dssp             HHHHHCCC------CSTHHHHHHHHHHHHHTTBHHHHHHHHHHCT----------HHHHHHHHHHCT-HHHHHHHHHHHH
T ss_pred             HHHHHHHh------cCcHHHHHHHHHHHHHcCCHHHHHHHHHhhcC---------ccccHHHHHHhCCHHHHHHHHHHHH
Confidence            77666543      23666788888888888888888888777664         4556666777777777777766666


Q ss_pred             HcCCCCCHHHHHHHHHHHHHcCChhHHHHHHHHH
Q 040027          515 ENAAAPDVITFDMLIHGFIRINEPSKVNELLHKM  548 (595)
Q Consensus       515 ~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~  548 (595)
                      ..| .     ++....++.-.|+.++..+++.+.
T Consensus       401 ~~~-~-----~n~af~~~~~lgd~~~cv~lL~~~  428 (443)
T PF04053_consen  401 ERG-D-----INIAFQAALLLGDVEECVDLLIET  428 (443)
T ss_dssp             HTT-------HHHHHHHHHHHT-HHHHHHHHHHT
T ss_pred             Hcc-C-----HHHHHHHHHHcCCHHHHHHHHHHc
Confidence            654 1     334444555667777666665443

This traffic is bidirectional, to ensure that proteins required to form vesicles are recycled. Vesicles have specific coat proteins (such as clathrin or coatomer) that are important for cargo selection and direction of transfer []. While clathrin mediates endocytic protein transport, and transport from ER to Golgi, coatomers primarily mediate intra-Golgi transport, as well as the reverse Golgi to ER transport of dilysine-tagged proteins []. For example, the coatomer COP1 (coat protein complex 1) is responsible for reverse transport of recycled proteins from Golgi and pre-Golgi compartments back to the ER, while COPII buds vesicles from the ER to the Golgi []. Coatomers reversibly associate with Golgi (non-clathrin-coated) vesicles to mediate protein transport and for budding from Golgi membranes []. Activated small guanine triphosphatases (GTPases) attract coat proteins to specific membrane export sites, thereby linking coatomers to export cargos. As coat proteins polymerise, vesicles are formed and budded from membrane-bound organelles. Coatomer complexes also influence Golgi structural integrity, as well as the processing, activity, and endocytic recycling of LDL receptors. In mammals, coatomer complexes can only be recruited by membranes associated to ADP-ribosylation factors (ARFs), which are small GTP-binding proteins. Coatomer complexes are hetero-oligomers composed of at least an alpha, beta, beta', gamma, delta, epsilon and zeta subunits. This entry represents the WD-associated region found in coatomer subunits alpha, beta and beta' subunits. The alpha-subunit (RET1P) of the coatomer complex in Saccharomyces cerevisiae (Baker's yeast), participates in membrane transport between the endoplasmic reticulum and Golgi apparatus. The protein contains six WD-40 repeat motifs in its N-terminal region []. More information about these proteins can be found at Protein of the Month: Clathrin [].; GO: 0005198 structural molecule activity, 0006886 intracellular protein transport, 0016192 vesicle-mediated transport, 0030117 membrane coat; PDB: 3MKQ_B.

>KOG4555 consensus TPR repeat-containing protein [Function unknown]

Probab=95.66  E-value=0.22  Score=38.41  Aligned_cols=89  Identities=18%  Similarity=0.056  Sum_probs=37.7

Q ss_pred             HhcCChHHHHHHHHhcccCCCCCCHHHHHHHHHHHHhcCChhHHHHHHHHHHHcCCCCCH---HHHHHHHHHHHHcCChh
Q 040027          463 CKSGRLKFAWELFCSLPHGVLVPNVVTYNIMIQGLCNDGQMDKARDLFLDMEENAAAPDV---ITFDMLIHGFIRINEPS  539 (595)
Q Consensus       463 ~~~g~~~~A~~~~~~~~~~~~~p~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~~~---~~~~~l~~~~~~~g~~~  539 (595)
                      ...|+.+.|++.|.+.+.. .+.+...||.-..++.-.|+.++|++-++++++..-+...   ..|..-...|...|+-+
T Consensus        54 aE~g~Ld~AlE~F~qal~l-~P~raSayNNRAQa~RLq~~~e~ALdDLn~AleLag~~trtacqa~vQRg~lyRl~g~dd  132 (175)
T KOG4555|consen   54 AEAGDLDGALELFGQALCL-APERASAYNNRAQALRLQGDDEEALDDLNKALELAGDQTRTACQAFVQRGLLYRLLGNDD  132 (175)
T ss_pred             HhccchHHHHHHHHHHHHh-cccchHhhccHHHHHHHcCChHHHHHHHHHHHHhcCccchHHHHHHHHHHHHHHHhCchH
Confidence            3444555555555444441 1123444455555555555555555555544443111111   11222233344445555


Q ss_pred             HHHHHHHHHHHCC
Q 040027          540 KVNELLHKMKEKK  552 (595)
Q Consensus       540 ~A~~~~~~~~~~~  552 (595)
                      .|..-|+.+.+.|
T Consensus       133 ~AR~DFe~AA~LG  145 (175)
T KOG4555|consen  133 AARADFEAAAQLG  145 (175)
T ss_pred             HHHHhHHHHHHhC
Confidence            5555555444443

>COG4649 Uncharacterized protein conserved in bacteria [Function unknown]

Probab=95.66  E-value=0.96  Score=37.05  Aligned_cols=52  Identities=15%  Similarity=0.207  Sum_probs=22.0

Q ss_pred             HcCCHhHHHHHHHHHhhCCCCCCHhHHHHHHHHHHhcCCHHHHHHHHHHHHH
Q 040027          219 KEGFVDKAKALFLQMKDENINPDVVTYNSLIHGLCHANDWNEAKRLFIEMMD  270 (595)
Q Consensus       219 ~~g~~~~A~~~~~~~~~~~~~~~~~~~~~ll~~~~~~~~~~~A~~~~~~~~~  270 (595)
                      ..|.+++.....+.+...+-+.-...-..|.-+-.+.|++..|.++|..+..
T Consensus       144 D~gsy~dV~srvepLa~d~n~mR~sArEALglAa~kagd~a~A~~~F~qia~  195 (221)
T COG4649         144 DNGSYDDVSSRVEPLAGDGNPMRHSAREALGLAAYKAGDFAKAKSWFVQIAN  195 (221)
T ss_pred             ccccHHHHHHHhhhccCCCChhHHHHHHHHhHHHHhccchHHHHHHHHHHHc
Confidence            3444444444444443333222233333344444444555555555544443

>COG0457 NrfG FOG: TPR repeat [General function prediction only]

Probab=95.58  E-value=1.6  Score=38.94  Aligned_cols=200  Identities=20%  Similarity=0.099  Sum_probs=90.1

Q ss_pred             HHHHHHHHHHHhcCCHHHHHHHHHHHHhc-CCCCCHHHHHHHHHHHHhCCCHHHHHHHHHHHHHCCCCCCHHHHHHHHH-
Q 040027          313 CTYNTLMDGFCLMGKINRAEELFGSMESM-GCKHDDVSYNILINGYCKNKEVEEALSLYREMVSKGIKPTVVTYNTLFL-  390 (595)
Q Consensus       313 ~~~~~l~~~~~~~~~~~~a~~~~~~~~~~-~~~~~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~~l~~-  390 (595)
                      .........+...+.+..+...+...... ........+......+...+++..+...+.........+ ......... 
T Consensus        60 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~  138 (291)
T COG0457          60 GLLLLLALALLKLGRLEEALELLEKALELELLPNLAEALLNLGLLLEALGKYEEALELLEKALALDPDP-DLAEALLALG  138 (291)
T ss_pred             HHHHHHHHHHHHcccHHHHHHHHHHHHhhhhccchHHHHHHHHHHHHHHhhHHHHHHHHHHHHcCCCCc-chHHHHHHHH
Confidence            34444445555555555555555554431 112333344444455555555555555555555432221 111111112 


Q ss_pred             HHHccCCHHHHHHHHHHHHHCCC--CCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCc-CHHHHHHHHHHHHhcCC
Q 040027          391 GLFEIHQVEHALKLFDEMQRDGV--AADTRTYTTFIDGLCKNGYIIEAVELFRTLRILKCEL-DIQAYNCLIDGLCKSGR  467 (595)
Q Consensus       391 ~~~~~~~~~~a~~~~~~~~~~~~--~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~-~~~~~~~l~~~~~~~g~  467 (595)
                      .+...|+++.+...+........  ......+......+...++.+.+...+....... +. ....+..+...+...++
T Consensus       139 ~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~a~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~  217 (291)
T COG0457         139 ALYELGDYEEALELYEKALELDPELNELAEALLALGALLEALGRYEEALELLEKALKLN-PDDDAEALLNLGLLYLKLGK  217 (291)
T ss_pred             HHHHcCCHHHHHHHHHHHHhcCCCccchHHHHHHhhhHHHHhcCHHHHHHHHHHHHhhC-cccchHHHHHhhHHHHHccc
Confidence            44555555555555555533210  0112222222223444555555655555555443 22 24445555555555555


Q ss_pred             hHHHHHHHHhcccCCCCCC-HHHHHHHHHHHHhcCChhHHHHHHHHHHHc
Q 040027          468 LKFAWELFCSLPHGVLVPN-VVTYNIMIQGLCNDGQMDKARDLFLDMEEN  516 (595)
Q Consensus       468 ~~~A~~~~~~~~~~~~~p~-~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~  516 (595)
                      ++.|...+.....  ..|+ ...+..+...+...+..+.+...+.+....
T Consensus       218 ~~~a~~~~~~~~~--~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  265 (291)
T COG0457         218 YEEALEYYEKALE--LDPDNAEALYNLALLLLELGRYEEALEALEKALEL  265 (291)
T ss_pred             HHHHHHHHHHHHh--hCcccHHHHhhHHHHHHHcCCHHHHHHHHHHHHHh
Confidence            5555555555554  2222 223333333333444455555555555543

>KOG1941 consensus Acetylcholine receptor-associated protein of the synapse (rapsyn) [Extracellular structures]

Probab=95.55  E-value=0.43  Score=43.95  Aligned_cols=228  Identities=12%  Similarity=0.121  Sum_probs=135.3

Q ss_pred             HHHcCCHhHHHHHHHHHhhCC--CCCCHhHHHHHHHHHHhcCCHHHHHHHHHHHHHC--CCCC---CHhhHHHHHHHHHh
Q 040027          217 LCKEGFVDKAKALFLQMKDEN--INPDVVTYNSLIHGLCHANDWNEAKRLFIEMMDQ--GVQP---SVVTFNVIMDELCK  289 (595)
Q Consensus       217 ~~~~g~~~~A~~~~~~~~~~~--~~~~~~~~~~ll~~~~~~~~~~~A~~~~~~~~~~--~~~~---~~~~~~~l~~~~~~  289 (595)
                      +....+.++|+..|.+...+-  ...-..++..+..+..+.|.+++++..--..++-  ....   --..|..+.+.+.+
T Consensus        16 Ly~s~~~~~al~~w~~~L~~l~~~~~Rf~~lG~l~~a~s~~g~y~~mL~~a~sqi~~a~~~~ds~~~~ea~lnlar~~e~   95 (518)
T KOG1941|consen   16 LYQSNQTEKALQVWTKVLEKLSDLMGRFRVLGCLVTAHSEMGRYKEMLKFAVSQIDTARELEDSDFLLEAYLNLARSNEK   95 (518)
T ss_pred             HhcCchHHHHHHHHHHHHHHHHHHHHHHHHhccchhhhhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            344567777777776655431  1112345566667778888877766543221110  0011   12345566666666


Q ss_pred             cCChHHHHHHHHHHHHC-CCCC---CHHHHHHHHHHHHhcCCHHHHHHHHHHHHhcCCC-----CCHHHHHHHHHHHHhC
Q 040027          290 NRKMDEASRLLDLMVQR-GVRP---NACTYNTLMDGFCLMGKINRAEELFGSMESMGCK-----HDDVSYNILINGYCKN  360 (595)
Q Consensus       290 ~g~~~~a~~~~~~~~~~-~~~~---~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~-----~~~~~~~~l~~~~~~~  360 (595)
                      .-++.+++.+-..-... |..+   .-.....+..++...+.++++.+.|+...+....     ....++..|...|.+.
T Consensus        96 l~~f~kt~~y~k~~l~lpgt~~~~~~gq~~l~~~~Ahlgls~fq~~Lesfe~A~~~A~~~~D~~LElqvcv~Lgslf~~l  175 (518)
T KOG1941|consen   96 LCEFHKTISYCKTCLGLPGTRAGQLGGQVSLSMGNAHLGLSVFQKALESFEKALRYAHNNDDAMLELQVCVSLGSLFAQL  175 (518)
T ss_pred             HHHhhhHHHHHHHHhcCCCCCcccccchhhhhHHHHhhhHHHHHHHHHHHHHHHHHhhccCCceeeeehhhhHHHHHHHH
Confidence            66777777766655543 2222   1233445777888888899999999887653211     1224678888999999


Q ss_pred             CCHHHHHHHHHHHHHC----CCCCCHHH-----HHHHHHHHHccCCHHHHHHHHHHHHH----CCCC-CCHHHHHHHHHH
Q 040027          361 KEVEEALSLYREMVSK----GIKPTVVT-----YNTLFLGLFEIHQVEHALKLFDEMQR----DGVA-ADTRTYTTFIDG  426 (595)
Q Consensus       361 ~~~~~A~~~~~~~~~~----~~~~~~~~-----~~~l~~~~~~~~~~~~a~~~~~~~~~----~~~~-~~~~~~~~l~~~  426 (595)
                      .++++|.-...+..+.    ++..-...     ...+.-++...|....|.+.-++..+    .|-. ........+.+.
T Consensus       176 ~D~~Kal~f~~kA~~lv~s~~l~d~~~kyr~~~lyhmaValR~~G~LgdA~e~C~Ea~klal~~Gdra~~arc~~~~aDI  255 (518)
T KOG1941|consen  176 KDYEKALFFPCKAAELVNSYGLKDWSLKYRAMSLYHMAVALRLLGRLGDAMECCEEAMKLALQHGDRALQARCLLCFADI  255 (518)
T ss_pred             HhhhHHhhhhHhHHHHHHhcCcCchhHHHHHHHHHHHHHHHHHhcccccHHHHHHHHHHHHHHhCChHHHHHHHHHHHHH
Confidence            9999988777665442    22211111     22333456667777777777666544    2322 122345566778


Q ss_pred             HHhcCCHHHHHHHHHHHH
Q 040027          427 LCKNGYIIEAVELFRTLR  444 (595)
Q Consensus       427 ~~~~g~~~~A~~~~~~~~  444 (595)
                      |...|+.+.|+.-|+++.
T Consensus       256 yR~~gd~e~af~rYe~Am  273 (518)
T KOG1941|consen  256 YRSRGDLERAFRRYEQAM  273 (518)
T ss_pred             HHhcccHhHHHHHHHHHH
Confidence            888899999888888765

>PF04184 ST7: ST7 protein; InterPro: IPR007311 The ST7 (for suppression of tumorigenicity 7) protein is thought to be a tumour suppressor gene

Probab=95.54  E-value=1.7  Score=42.29  Aligned_cols=64  Identities=17%  Similarity=0.101  Sum_probs=39.8

Q ss_pred             HHHHHHHHHHHHhcCCHHHHHHHHHHHHHcCCC-cCHHHHHHHHHHHHhcCChHHHHHHHHhccc
Q 040027          417 TRTYTTFIDGLCKNGYIIEAVELFRTLRILKCE-LDIQAYNCLIDGLCKSGRLKFAWELFCSLPH  480 (595)
Q Consensus       417 ~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~-~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~  480 (595)
                      ..+-..+..++.+.|+.++|++.++++.+.... ....+...|+.++...+.+.++..++.+..+
T Consensus       259 ~y~KrRLAmCarklGr~~EAIk~~rdLlke~p~~~~l~IrenLie~LLelq~Yad~q~lL~kYdD  323 (539)
T PF04184_consen  259 VYAKRRLAMCARKLGRLREAIKMFRDLLKEFPNLDNLNIRENLIEALLELQAYADVQALLAKYDD  323 (539)
T ss_pred             hhhHHHHHHHHHHhCChHHHHHHHHHHHhhCCccchhhHHHHHHHHHHhcCCHHHHHHHHHHhcc
Confidence            333344555566677777777777777654311 1334566677777777777777777777654

The molecular function of this protein is uncertain.

>KOG1941 consensus Acetylcholine receptor-associated protein of the synapse (rapsyn) [Extracellular structures]

Probab=95.53  E-value=0.36  Score=44.38  Aligned_cols=229  Identities=12%  Similarity=0.070  Sum_probs=140.7

Q ss_pred             HHhcCCHHHHHHHHHHHHHCC--CCCCHhhHHHHHHHHHhcCChHHHHHHHHHHHH----C-CCCCCHHHHHHHHHHHHh
Q 040027          252 LCHANDWNEAKRLFIEMMDQG--VQPSVVTFNVIMDELCKNRKMDEASRLLDLMVQ----R-GVRPNACTYNTLMDGFCL  324 (595)
Q Consensus       252 ~~~~~~~~~A~~~~~~~~~~~--~~~~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~----~-~~~~~~~~~~~l~~~~~~  324 (595)
                      +....+.++|+..|.+.+..-  ...-..++..+..+..+.|.+++++..--..++    . .-..--..|..+.+.+.+
T Consensus        16 Ly~s~~~~~al~~w~~~L~~l~~~~~Rf~~lG~l~~a~s~~g~y~~mL~~a~sqi~~a~~~~ds~~~~ea~lnlar~~e~   95 (518)
T KOG1941|consen   16 LYQSNQTEKALQVWTKVLEKLSDLMGRFRVLGCLVTAHSEMGRYKEMLKFAVSQIDTARELEDSDFLLEAYLNLARSNEK   95 (518)
T ss_pred             HhcCchHHHHHHHHHHHHHHHHHHHHHHHHhccchhhhhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            445677788887777665531  111233556667778888888877654322111    1 001112345556666666


Q ss_pred             cCCHHHHHHHHHHHHhc-CCCC---CHHHHHHHHHHHHhCCCHHHHHHHHHHHHHCC-----CCCCHHHHHHHHHHHHcc
Q 040027          325 MGKINRAEELFGSMESM-GCKH---DDVSYNILINGYCKNKEVEEALSLYREMVSKG-----IKPTVVTYNTLFLGLFEI  395 (595)
Q Consensus       325 ~~~~~~a~~~~~~~~~~-~~~~---~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~~~-----~~~~~~~~~~l~~~~~~~  395 (595)
                      ..++.+++.+-..-... |..+   .-.....+..++...+.++++++.|+...+.-     .......+..+...|...
T Consensus        96 l~~f~kt~~y~k~~l~lpgt~~~~~~gq~~l~~~~Ahlgls~fq~~Lesfe~A~~~A~~~~D~~LElqvcv~Lgslf~~l  175 (518)
T KOG1941|consen   96 LCEFHKTISYCKTCLGLPGTRAGQLGGQVSLSMGNAHLGLSVFQKALESFEKALRYAHNNDDAMLELQVCVSLGSLFAQL  175 (518)
T ss_pred             HHHhhhHHHHHHHHhcCCCCCcccccchhhhhHHHHhhhHHHHHHHHHHHHHHHHHhhccCCceeeeehhhhHHHHHHHH
Confidence            66777777666554432 1111   11234456778888889999999999877631     112335677788888999


Q ss_pred             CCHHHHHHHHHHHHH----CCCCCCHHHH-----HHHHHHHHhcCCHHHHHHHHHHHHHc----CC-CcCHHHHHHHHHH
Q 040027          396 HQVEHALKLFDEMQR----DGVAADTRTY-----TTFIDGLCKNGYIIEAVELFRTLRIL----KC-ELDIQAYNCLIDG  461 (595)
Q Consensus       396 ~~~~~a~~~~~~~~~----~~~~~~~~~~-----~~l~~~~~~~g~~~~A~~~~~~~~~~----~~-~~~~~~~~~l~~~  461 (595)
                      .|++++.-......+    .++..-..-|     ..+.-++...|++-.|.+.-++..+.    |- .........+.+.
T Consensus       176 ~D~~Kal~f~~kA~~lv~s~~l~d~~~kyr~~~lyhmaValR~~G~LgdA~e~C~Ea~klal~~Gdra~~arc~~~~aDI  255 (518)
T KOG1941|consen  176 KDYEKALFFPCKAAELVNSYGLKDWSLKYRAMSLYHMAVALRLLGRLGDAMECCEEAMKLALQHGDRALQARCLLCFADI  255 (518)
T ss_pred             HhhhHHhhhhHhHHHHHHhcCcCchhHHHHHHHHHHHHHHHHHhcccccHHHHHHHHHHHHHHhCChHHHHHHHHHHHHH
Confidence            999999877665543    2322222222     23344567788888888888877643    31 2234455677888


Q ss_pred             HHhcCChHHHHHHHHhccc
Q 040027          462 LCKSGRLKFAWELFCSLPH  480 (595)
Q Consensus       462 ~~~~g~~~~A~~~~~~~~~  480 (595)
                      |...|+.+.|+.-|+++..
T Consensus       256 yR~~gd~e~af~rYe~Am~  274 (518)
T KOG1941|consen  256 YRSRGDLERAFRRYEQAMG  274 (518)
T ss_pred             HHhcccHhHHHHHHHHHHH
Confidence            9999999999888887543

>COG1729 Uncharacterized protein conserved in bacteria [Function unknown]

Probab=95.43  E-value=0.34  Score=43.09  Aligned_cols=90  Identities=17%  Similarity=0.060  Sum_probs=43.3

Q ss_pred             hcCCHhHHHHHHHHHHhcCCC--CCHhhHHHHHHHHHhcCChhHHHHHHHHHHhcCCCCCccccCcHHHHHHHHHHHHHc
Q 040027          143 AESRIMEAAALFTKLKAFGCE--PNVITYNTLINGLCRTGHTMIALNLFEEMANGNGEIGVVCKPNTVTYSTIIDGLCKE  220 (595)
Q Consensus       143 ~~g~~~~A~~~~~~~~~~~~~--~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~  220 (595)
                      +.|++..|...|...++....  -...++.=|..++...|+++.|..+|..+.+..+.    .+.-+..+..|..+..+.
T Consensus       153 ksgdy~~A~~~F~~fi~~YP~s~~~~nA~yWLGe~~y~qg~y~~Aa~~f~~~~k~~P~----s~KApdallKlg~~~~~l  228 (262)
T COG1729         153 KSGDYAEAEQAFQAFIKKYPNSTYTPNAYYWLGESLYAQGDYEDAAYIFARVVKDYPK----SPKAPDALLKLGVSLGRL  228 (262)
T ss_pred             HcCCHHHHHHHHHHHHHcCCCCcccchhHHHHHHHHHhcccchHHHHHHHHHHHhCCC----CCCChHHHHHHHHHHHHh
Confidence            344455555555555544211  11223333455555555555555555555544321    122234455555555555


Q ss_pred             CCHhHHHHHHHHHhhC
Q 040027          221 GFVDKAKALFLQMKDE  236 (595)
Q Consensus       221 g~~~~A~~~~~~~~~~  236 (595)
                      |+.++|..+|+++.+.
T Consensus       229 ~~~d~A~atl~qv~k~  244 (262)
T COG1729         229 GNTDEACATLQQVIKR  244 (262)
T ss_pred             cCHHHHHHHHHHHHHH
Confidence            5555555555555554

>COG4649 Uncharacterized protein conserved in bacteria [Function unknown]

Probab=95.42  E-value=1.2  Score=36.50  Aligned_cols=137  Identities=14%  Similarity=0.085  Sum_probs=97.8

Q ss_pred             CCHHHHHHHHHHHHhcCChhHHHHHHHHHHhCCCCCCHHH-HHHHHHHHHhcCCHhHHHHHHHHHHhcCCCCCHh---hH
Q 040027           94 PNLYTYNILINCFCKIGRVSLGFIAFGRILRSCFTPNAAT-FNSLIKGLHAESRIMEAAALFTKLKAFGCEPNVI---TY  169 (595)
Q Consensus        94 ~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~-~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~~~~---~~  169 (595)
                      .+...|...+. +.+.|..++|+.-|..+.+.|...-+.. ...+.....+.|+...|+..|+++-.....|-..   ..
T Consensus        57 ~sgd~flaAL~-lA~~~k~d~Alaaf~~lektg~g~YpvLA~mr~at~~a~kgdta~AV~aFdeia~dt~~P~~~rd~AR  135 (221)
T COG4649          57 KSGDAFLAALK-LAQENKTDDALAAFTDLEKTGYGSYPVLARMRAATLLAQKGDTAAAVAAFDEIAADTSIPQIGRDLAR  135 (221)
T ss_pred             cchHHHHHHHH-HHHcCCchHHHHHHHHHHhcCCCcchHHHHHHHHHHHhhcccHHHHHHHHHHHhccCCCcchhhHHHH
Confidence            34556665554 5677899999999999999876543332 2344555778999999999999998753333222   11


Q ss_pred             HHHHHHHHhcCChhHHHHHHHHHHhcCCCCCccccCcHHHHHHHHHHHHHcCCHhHHHHHHHHHhhCC
Q 040027          170 NTLINGLCRTGHTMIALNLFEEMANGNGEIGVVCKPNTVTYSTIIDGLCKEGFVDKAKALFLQMKDEN  237 (595)
Q Consensus       170 ~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~  237 (595)
                      ..-.-.+...|.++......+-+...+      .+.....-..|.-+-.+.|++.+|.++|..+....
T Consensus       136 lraa~lLvD~gsy~dV~srvepLa~d~------n~mR~sArEALglAa~kagd~a~A~~~F~qia~Da  197 (221)
T COG4649         136 LRAAYLLVDNGSYDDVSSRVEPLAGDG------NPMRHSAREALGLAAYKAGDFAKAKSWFVQIANDA  197 (221)
T ss_pred             HHHHHHHhccccHHHHHHHhhhccCCC------ChhHHHHHHHHhHHHHhccchHHHHHHHHHHHccc
Confidence            222334567899998888888776554      34445666778888889999999999999988753

>PF09613 HrpB1_HrpK: Bacterial type III secretion protein (HrpB1_HrpK); InterPro: IPR013394 This family of proteins is encoded by genes found within type III secretion operons in a limited range of species including Xanthomonas, Ralstonia and Burkholderia

Probab=95.41  E-value=1  Score=36.76  Aligned_cols=104  Identities=19%  Similarity=0.137  Sum_probs=47.4

Q ss_pred             HhcCChHHHHHHHHhcccCCCCCCHHHH-HHHHHHHHhcCChhHHHHHHHHHHHcCCCCCHHHHHHHHHHHHHcCChhHH
Q 040027          463 CKSGRLKFAWELFCSLPHGVLVPNVVTY-NIMIQGLCNDGQMDKARDLFLDMEENAAAPDVITFDMLIHGFIRINEPSKV  541 (595)
Q Consensus       463 ~~~g~~~~A~~~~~~~~~~~~~p~~~~~-~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A  541 (595)
                      ...++.+++..+++.+.-  +.|..... ..-...+...|+|.+|+.+|+++.+..  |....-..|+..|.....-..-
T Consensus        21 l~~~~~~D~e~lL~ALrv--LRP~~~e~~~~~~~l~i~r~~w~dA~rlLr~l~~~~--~~~p~~kALlA~CL~~~~D~~W   96 (160)
T PF09613_consen   21 LRLGDPDDAEALLDALRV--LRPEFPELDLFDGWLHIVRGDWDDALRLLRELEERA--PGFPYAKALLALCLYALGDPSW   96 (160)
T ss_pred             HccCChHHHHHHHHHHHH--hCCCchHHHHHHHHHHHHhCCHHHHHHHHHHHhccC--CCChHHHHHHHHHHHHcCChHH
Confidence            345566666666666655  44543222 222344556666666666666655542  2222222333333322222233


Q ss_pred             HHHHHHHHHCCCCCCHHHHHHHHHHHHhcCc
Q 040027          542 NELLHKMKEKKVMPDASIVSIVVDLLVKNEI  572 (595)
Q Consensus       542 ~~~~~~~~~~~~~p~~~~~~~l~~~~~~~g~  572 (595)
                      ..+-+++.+.+  +|+.+...+-..+.+.+.
T Consensus        97 r~~A~evle~~--~d~~a~~Lv~~Ll~~~~~  125 (160)
T PF09613_consen   97 RRYADEVLESG--ADPDARALVRALLARADL  125 (160)
T ss_pred             HHHHHHHHhcC--CChHHHHHHHHHHHhccc
Confidence            33344444433  444444444444444443

>PF13512 TPR_18: Tetratricopeptide repeat

Probab=95.30  E-value=0.93  Score=36.17  Aligned_cols=75  Identities=17%  Similarity=0.173  Sum_probs=39.5

Q ss_pred             HHHHHHhcCCHHHHHHHHHHHHhcCC--CCCHHHHHHHHHHHHhCCCHHHHHHHHHHHHHCCCCCCHHHHHHHHHHH
Q 040027          318 LMDGFCLMGKINRAEELFGSMESMGC--KHDDVSYNILINGYCKNKEVEEALSLYREMVSKGIKPTVVTYNTLFLGL  392 (595)
Q Consensus       318 l~~~~~~~~~~~~a~~~~~~~~~~~~--~~~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~~l~~~~  392 (595)
                      -.....+.|++++|++.|+.+...-.  +....+-..++.+|.+.+++++|+..+++.++..+.....-|...+.++
T Consensus        16 ~a~~~l~~~~Y~~A~~~le~L~~ryP~g~ya~qAqL~l~yayy~~~~y~~A~a~~~rFirLhP~hp~vdYa~Y~~gL   92 (142)
T PF13512_consen   16 EAQEALQKGNYEEAIKQLEALDTRYPFGEYAEQAQLDLAYAYYKQGDYEEAIAAYDRFIRLHPTHPNVDYAYYMRGL   92 (142)
T ss_pred             HHHHHHHhCCHHHHHHHHHHHHhcCCCCcccHHHHHHHHHHHHHccCHHHHHHHHHHHHHhCCCCCCccHHHHHHHH
Confidence            34444556666666666666654410  1122344555666666666666666666666654433333344344333

>KOG2280 consensus Vacuolar assembly/sorting protein VPS16 [Intracellular trafficking, secretion, and vesicular transport]

Probab=95.30  E-value=4  Score=41.79  Aligned_cols=108  Identities=8%  Similarity=0.099  Sum_probs=74.4

Q ss_pred             HHHHHHHHHHHhcCChHHHHHHHHhcccCCCCCCHHHHHHHHHHHHhcCChhHHHHHHHHHHHcCCCCCHHHHHHHHHHH
Q 040027          453 QAYNCLIDGLCKSGRLKFAWELFCSLPHGVLVPNVVTYNIMIQGLCNDGQMDKARDLFLDMEENAAAPDVITFDMLIHGF  532 (595)
Q Consensus       453 ~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~p~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~~l~~~~  532 (595)
                      .+.+.-+..+...|+..+|.++-.+..    -||...|-.-+.+++..++|++-+++-+...      .+.-|.-.+.+|
T Consensus       685 lSl~dTv~~li~~g~~k~a~ql~~~Fk----ipdKr~~wLk~~aLa~~~kweeLekfAkskk------sPIGy~PFVe~c  754 (829)
T KOG2280|consen  685 LSLHDTVTTLILIGQNKRAEQLKSDFK----IPDKRLWWLKLTALADIKKWEELEKFAKSKK------SPIGYLPFVEAC  754 (829)
T ss_pred             CcHHHHHHHHHHccchHHHHHHHHhcC----CcchhhHHHHHHHHHhhhhHHHHHHHHhccC------CCCCchhHHHHH
Confidence            344555666777888888888877776    3677777777888888888887665544332      234566677888


Q ss_pred             HHcCChhHHHHHHHHHHHCCCCCCHHHHHHHHHHHHhcCcccccchH
Q 040027          533 IRINEPSKVNELLHKMKEKKVMPDASIVSIVVDLLVKNEISLKSLPS  579 (595)
Q Consensus       533 ~~~g~~~~A~~~~~~~~~~~~~p~~~~~~~l~~~~~~~g~~~~~i~~  579 (595)
                      .+.|+.++|.+++-+...  .+       -.+.+|.+.|.+.++++.
T Consensus       755 ~~~~n~~EA~KYiprv~~--l~-------ekv~ay~~~~~~~eAad~  792 (829)
T KOG2280|consen  755 LKQGNKDEAKKYIPRVGG--LQ-------EKVKAYLRVGDVKEAADL  792 (829)
T ss_pred             HhcccHHHHhhhhhccCC--hH-------HHHHHHHHhccHHHHHHH
Confidence            888888888888877642  11       456667777776655544

>COG0457 NrfG FOG: TPR repeat [General function prediction only]

Probab=95.27  E-value=2  Score=38.23  Aligned_cols=223  Identities=19%  Similarity=0.074  Sum_probs=157.2

Q ss_pred             cCCHHHHHHHHHHHHhcCCC-CCHHHHHHHHHHHHhCCCHHHHHHHHHHHHHC-CCCCCHHHHHHHHHHHHccCCHHHHH
Q 040027          325 MGKINRAEELFGSMESMGCK-HDDVSYNILINGYCKNKEVEEALSLYREMVSK-GIKPTVVTYNTLFLGLFEIHQVEHAL  402 (595)
Q Consensus       325 ~~~~~~a~~~~~~~~~~~~~-~~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~~-~~~~~~~~~~~l~~~~~~~~~~~~a~  402 (595)
                      .+....+...+......... ............+...+++..+...+...... ........+......+...+++..+.
T Consensus        36 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  115 (291)
T COG0457          36 LGELAEALELLEEALELLPNSDLAGLLLLLALALLKLGRLEEALELLEKALELELLPNLAEALLNLGLLLEALGKYEEAL  115 (291)
T ss_pred             HhhHHHHHHHHHHHHhcCccccchHHHHHHHHHHHHcccHHHHHHHHHHHHhhhhccchHHHHHHHHHHHHHHhhHHHHH
Confidence            34555566666665554211 12567777888888999999999988887752 22335566677777778888899999


Q ss_pred             HHHHHHHHCCCCCCHHHHHHHHH-HHHhcCCHHHHHHHHHHHHHcCC--CcCHHHHHHHHHHHHhcCChHHHHHHHHhcc
Q 040027          403 KLFDEMQRDGVAADTRTYTTFID-GLCKNGYIIEAVELFRTLRILKC--ELDIQAYNCLIDGLCKSGRLKFAWELFCSLP  479 (595)
Q Consensus       403 ~~~~~~~~~~~~~~~~~~~~l~~-~~~~~g~~~~A~~~~~~~~~~~~--~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~  479 (595)
                      ..+.........+ ......... .+...|+++.|...+.+......  ......+......+...++.+.+...+....
T Consensus       116 ~~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~a~~~~~~~~  194 (291)
T COG0457         116 ELLEKALALDPDP-DLAEALLALGALYELGDYEEALELYEKALELDPELNELAEALLALGALLEALGRYEEALELLEKAL  194 (291)
T ss_pred             HHHHHHHcCCCCc-chHHHHHHHHHHHHcCCHHHHHHHHHHHHhcCCCccchHHHHHHhhhHHHHhcCHHHHHHHHHHHH
Confidence            9999888753332 122222233 68899999999999999866321  1234444455555677899999999999988


Q ss_pred             cCCCCCC--HHHHHHHHHHHHhcCChhHHHHHHHHHHHcCCCCCHHHHHHHHHHHHHcCChhHHHHHHHHHHHC
Q 040027          480 HGVLVPN--VVTYNIMIQGLCNDGQMDKARDLFLDMEENAAAPDVITFDMLIHGFIRINEPSKVNELLHKMKEK  551 (595)
Q Consensus       480 ~~~~~p~--~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~  551 (595)
                      ..  .++  ...+..+...+...++++.|...+....... +.....+..+...+...+..+++...+++....
T Consensus       195 ~~--~~~~~~~~~~~~~~~~~~~~~~~~a~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  265 (291)
T COG0457         195 KL--NPDDDAEALLNLGLLYLKLGKYEEALEYYEKALELD-PDNAEALYNLALLLLELGRYEEALEALEKALEL  265 (291)
T ss_pred             hh--CcccchHHHHHhhHHHHHcccHHHHHHHHHHHHhhC-cccHHHHhhHHHHHHHcCCHHHHHHHHHHHHHh
Confidence            74  333  5778888888899999999999999998863 222455555666666777899999999988864

>COG4785 NlpI Lipoprotein NlpI, contains TPR repeats [General function prediction only]

Probab=95.21  E-value=1.7  Score=37.10  Aligned_cols=85  Identities=15%  Similarity=0.027  Sum_probs=48.2

Q ss_pred             CChhHHHHHHHHHHhCCCCCCHHHHHHHHHHHHhcCCHhHHHHHHHHHHhcCCCCCHhhHHHHHHHHHhcCChhHHHHHH
Q 040027          110 GRVSLGFIAFGRILRSCFTPNAATFNSLIKGLHAESRIMEAAALFTKLKAFGCEPNVITYNTLINGLCRTGHTMIALNLF  189 (595)
Q Consensus       110 g~~~~A~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~  189 (595)
                      |-+..|+.-|.+.+... |.-+.+||.+.-.+...|+++.|.+.|+...+.+.. ...++..-..++.--|++.-|.+-|
T Consensus        79 GL~~LAR~DftQaLai~-P~m~~vfNyLG~Yl~~a~~fdaa~eaFds~~ELDp~-y~Ya~lNRgi~~YY~gR~~LAq~d~  156 (297)
T COG4785          79 GLRALARNDFSQALAIR-PDMPEVFNYLGIYLTQAGNFDAAYEAFDSVLELDPT-YNYAHLNRGIALYYGGRYKLAQDDL  156 (297)
T ss_pred             hHHHHHhhhhhhhhhcC-CCcHHHHHHHHHHHHhcccchHHHHHhhhHhccCCc-chHHHhccceeeeecCchHhhHHHH
Confidence            44444445555555442 223556666666667777777777777777766422 2223333333334567777777766


Q ss_pred             HHHHhcC
Q 040027          190 EEMANGN  196 (595)
Q Consensus       190 ~~~~~~~  196 (595)
                      ...-+.+
T Consensus       157 ~~fYQ~D  163 (297)
T COG4785         157 LAFYQDD  163 (297)
T ss_pred             HHHHhcC
Confidence            6666554

>PF04184 ST7: ST7 protein; InterPro: IPR007311 The ST7 (for suppression of tumorigenicity 7) protein is thought to be a tumour suppressor gene

Probab=95.21  E-value=0.57  Score=45.37  Aligned_cols=66  Identities=17%  Similarity=0.053  Sum_probs=51.6

Q ss_pred             HHHHHHHHHHHHhcCCHhHHHHHHHHHHhcCCC-CCHhhHHHHHHHHHhcCChhHHHHHHHHHHhcC
Q 040027          131 AATFNSLIKGLHAESRIMEAAALFTKLKAFGCE-PNVITYNTLINGLCRTGHTMIALNLFEEMANGN  196 (595)
Q Consensus       131 ~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~-~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~  196 (595)
                      ..+-..+..++.+.|+.++|++.++++.+.... ....+...|+..+...+.+.++..++.+..+..
T Consensus       259 ~y~KrRLAmCarklGr~~EAIk~~rdLlke~p~~~~l~IrenLie~LLelq~Yad~q~lL~kYdDi~  325 (539)
T PF04184_consen  259 VYAKRRLAMCARKLGRLREAIKMFRDLLKEFPNLDNLNIRENLIEALLELQAYADVQALLAKYDDIS  325 (539)
T ss_pred             hhhHHHHHHHHHHhCChHHHHHHHHHHHhhCCccchhhHHHHHHHHHHhcCCHHHHHHHHHHhcccc
Confidence            334456777778899999999999999875322 234577889999999999999999999976543

The molecular function of this protein is uncertain.

>smart00299 CLH Clathrin heavy chain repeat homology

Probab=95.19  E-value=1.4  Score=35.76  Aligned_cols=123  Identities=15%  Similarity=0.078  Sum_probs=57.2

Q ss_pred             HHHHHHhcCCHHHHHHHHHHHHHcCCCcCHHHHHHHHHHHHhcCChHHHHHHHHhcccCCCCCCHHHHHHHHHHHHhcCC
Q 040027          423 FIDGLCKNGYIIEAVELFRTLRILKCELDIQAYNCLIDGLCKSGRLKFAWELFCSLPHGVLVPNVVTYNIMIQGLCNDGQ  502 (595)
Q Consensus       423 l~~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~p~~~~~~~l~~~~~~~g~  502 (595)
                      ++..+...+.+.....+++.+...+ ..+....+.++..|++.. ..+....+..      ..+......++..|.+.+-
T Consensus        13 vv~~~~~~~~~~~l~~yLe~~~~~~-~~~~~~~~~li~ly~~~~-~~~ll~~l~~------~~~~yd~~~~~~~c~~~~l   84 (140)
T smart00299       13 VVELFEKRNLLEELIPYLESALKLN-SENPALQTKLIELYAKYD-PQKEIERLDN------KSNHYDIEKVGKLCEKAKL   84 (140)
T ss_pred             HHHHHHhCCcHHHHHHHHHHHHccC-ccchhHHHHHHHHHHHHC-HHHHHHHHHh------ccccCCHHHHHHHHHHcCc
Confidence            3444444455555555555555544 344555555555555432 2333344332      0122223334555555555


Q ss_pred             hhHHHHHHHHHHHcCCCCCHHHHHHHHHHHHHc-CChhHHHHHHHHHHHCCCCCCHHHHHHHHHHHH
Q 040027          503 MDKARDLFLDMEENAAAPDVITFDMLIHGFIRI-NEPSKVNELLHKMKEKKVMPDASIVSIVVDLLV  568 (595)
Q Consensus       503 ~~~A~~~~~~~~~~~~~~~~~~~~~l~~~~~~~-g~~~~A~~~~~~~~~~~~~p~~~~~~~l~~~~~  568 (595)
                      ++++.-++.++-.         +...+..+... ++++.|.+++++-      .++..|..++..+.
T Consensus        85 ~~~~~~l~~k~~~---------~~~Al~~~l~~~~d~~~a~~~~~~~------~~~~lw~~~~~~~l  136 (140)
T smart00299       85 YEEAVELYKKDGN---------FKDAIVTLIEHLGNYEKAIEYFVKQ------NNPELWAEVLKALL  136 (140)
T ss_pred             HHHHHHHHHhhcC---------HHHHHHHHHHcccCHHHHHHHHHhC------CCHHHHHHHHHHHH
Confidence            6666555554421         11122222222 5566666655541      24556666655544

>COG3629 DnrI DNA-binding transcriptional activator of the SARP family [Signal transduction mechanisms]

Probab=95.12  E-value=0.3  Score=44.14  Aligned_cols=77  Identities=13%  Similarity=0.186  Sum_probs=49.4

Q ss_pred             HHHHHHHHHHhcCChhHHHHHHHHHHHcCCCCCHHHHHHHHHHHHHcCChhHHHHHHHHHH-----HCCCCCCHHHHHHH
Q 040027          489 TYNIMIQGLCNDGQMDKARDLFLDMEENAAAPDVITFDMLIHGFIRINEPSKVNELLHKMK-----EKKVMPDASIVSIV  563 (595)
Q Consensus       489 ~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~-----~~~~~p~~~~~~~l  563 (595)
                      ++..++..+...|+++.+.+.++++.... +-+...|..++.+|...|+...|+..|+++.     +.|+.|.+.+....
T Consensus       155 ~l~~lae~~~~~~~~~~~~~~l~~Li~~d-p~~E~~~~~lm~~y~~~g~~~~ai~~y~~l~~~~~edlgi~P~~~~~~~y  233 (280)
T COG3629         155 ALTKLAEALIACGRADAVIEHLERLIELD-PYDEPAYLRLMEAYLVNGRQSAAIRAYRQLKKTLAEELGIDPAPELRALY  233 (280)
T ss_pred             HHHHHHHHHHhcccHHHHHHHHHHHHhcC-ccchHHHHHHHHHHHHcCCchHHHHHHHHHHHHhhhhcCCCccHHHHHHH
Confidence            44555666666666666666666666654 4566666666667777776666666666665     34666666666666


Q ss_pred             HHH
Q 040027          564 VDL  566 (595)
Q Consensus       564 ~~~  566 (595)
                      .++
T Consensus       234 ~~~  236 (280)
T COG3629         234 EEI  236 (280)
T ss_pred             HHH
Confidence            555

>KOG4555 consensus TPR repeat-containing protein [Function unknown]

Probab=94.97  E-value=0.51  Score=36.47  Aligned_cols=91  Identities=20%  Similarity=0.037  Sum_probs=63.8

Q ss_pred             HHHhcCCHHHHHHHHHHHHHcCCCcCHHHHHHHHHHHHhcCChHHHHHHHHhcccCCCCCC---HHHHHHHHHHHHhcCC
Q 040027          426 GLCKNGYIIEAVELFRTLRILKCELDIQAYNCLIDGLCKSGRLKFAWELFCSLPHGVLVPN---VVTYNIMIQGLCNDGQ  502 (595)
Q Consensus       426 ~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~p~---~~~~~~l~~~~~~~g~  502 (595)
                      ++...|+++.|++.|.+.+..- +.....||.-..++.-+|+.++|+.-+++.++..-...   -..|..-...|...|+
T Consensus        52 alaE~g~Ld~AlE~F~qal~l~-P~raSayNNRAQa~RLq~~~e~ALdDLn~AleLag~~trtacqa~vQRg~lyRl~g~  130 (175)
T KOG4555|consen   52 ALAEAGDLDGALELFGQALCLA-PERASAYNNRAQALRLQGDDEEALDDLNKALELAGDQTRTACQAFVQRGLLYRLLGN  130 (175)
T ss_pred             HHHhccchHHHHHHHHHHHHhc-ccchHhhccHHHHHHHcCChHHHHHHHHHHHHhcCccchHHHHHHHHHHHHHHHhCc
Confidence            4566788888888888877654 56777888888888888888888888887776211111   1234444456677888


Q ss_pred             hhHHHHHHHHHHHcC
Q 040027          503 MDKARDLFLDMEENA  517 (595)
Q Consensus       503 ~~~A~~~~~~~~~~~  517 (595)
                      -+.|..-|+.+.+.|
T Consensus       131 dd~AR~DFe~AA~LG  145 (175)
T KOG4555|consen  131 DDAARADFEAAAQLG  145 (175)
T ss_pred             hHHHHHhHHHHHHhC
Confidence            888888888887766

>PF08631 SPO22: Meiosis protein SPO22/ZIP4 like; InterPro: IPR013940 SPO22 is a meiosis-specific protein with similarity to phospholipase A2, involved in completion of nuclear divisions during meiosis; induced early in meiosis []

Probab=94.89  E-value=3.2  Score=38.42  Aligned_cols=169  Identities=7%  Similarity=-0.042  Sum_probs=99.3

Q ss_pred             cCCCChHHHHHHHHHHHHhCCCCCCHhhHHHHHHHHHcCCCchhHHhhCCCCCCHHHHHHHHHHHHhcC-ChhHHHHHHH
Q 040027           42 INVITPNEAFCIFDYMLRMHPSPPPVSSFNILLASLAKNKHYDTRLNATGLFPNLYTYNILINCFCKIG-RVSLGFIAFG  120 (595)
Q Consensus        42 ~~~~~~~~A~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g-~~~~A~~~~~  120 (595)
                      .++|+.+.|...|.++-...+. .++.....+...|..-|                      ......+ +++.|...++
T Consensus         4 ~~~~~~~~A~~~~~K~~~~~~~-~~~~~~~~La~~~yn~G----------------------~~l~~~~~~~~~a~~wL~   60 (278)
T PF08631_consen    4 WKQGDLDLAEHMYSKAKDLLNS-LDPDMAEELARVCYNIG----------------------KSLLSKKDKYEEAVKWLQ   60 (278)
T ss_pred             hhhCCHHHHHHHHHHhhhHHhc-CCcHHHHHHHHHHHHHH----------------------HHHHHcCCChHHHHHHHH
Confidence            4679999999999999776632 35555544544333322                      2233344 7777777776


Q ss_pred             HHHhC----C----CCCCH-----HHHHHHHHHHHhcCCHh---HHHHHHHHHHhcCCCCCHhhHHHHHHHHHhcCChhH
Q 040027          121 RILRS----C----FTPNA-----ATFNSLIKGLHAESRIM---EAAALFTKLKAFGCEPNVITYNTLINGLCRTGHTMI  184 (595)
Q Consensus       121 ~~~~~----~----~~~~~-----~~~~~l~~~~~~~g~~~---~A~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~  184 (595)
                      ++.+.    +    ..++.     .++..++.+|...+..+   +|..+++.+.... +-.+.++..-+..+.+.++.++
T Consensus        61 ~a~~~l~~~~~~~~~~~~~~elr~~iL~~La~~~l~~~~~~~~~ka~~~l~~l~~e~-~~~~~~~~L~l~il~~~~~~~~  139 (278)
T PF08631_consen   61 RAYDILEKPGKMDKLSPDGSELRLSILRLLANAYLEWDTYESVEKALNALRLLESEY-GNKPEVFLLKLEILLKSFDEEE  139 (278)
T ss_pred             HHHHHHHhhhhccccCCcHHHHHHHHHHHHHHHHHcCCChHHHHHHHHHHHHHHHhC-CCCcHHHHHHHHHHhccCChhH
Confidence            65543    1    12222     35667778888777655   4555666665442 3235566566777777899999


Q ss_pred             HHHHHHHHHhcCCCCCccccCcHHHHHHHHHHH---HHcCCHhHHHHHHHHHhhCCCCCCH
Q 040027          185 ALNLFEEMANGNGEIGVVCKPNTVTYSTIIDGL---CKEGFVDKAKALFLQMKDENINPDV  242 (595)
Q Consensus       185 A~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~---~~~g~~~~A~~~~~~~~~~~~~~~~  242 (595)
                      +.+++.+|...-       ......+..++..+   ... ....+...++.+....+.|..
T Consensus       140 ~~~~L~~mi~~~-------~~~e~~~~~~l~~i~~l~~~-~~~~a~~~ld~~l~~r~~~~~  192 (278)
T PF08631_consen  140 YEEILMRMIRSV-------DHSESNFDSILHHIKQLAEK-SPELAAFCLDYLLLNRFKSSE  192 (278)
T ss_pred             HHHHHHHHHHhc-------ccccchHHHHHHHHHHHHhh-CcHHHHHHHHHHHHHHhCCCh
Confidence            999999998763       21233444444443   333 334555555555444344443

It is also involved in sporulation [].

>KOG1920 consensus IkappaB kinase complex, IKAP component [Transcription]

Probab=94.71  E-value=7.9  Score=42.12  Aligned_cols=134  Identities=16%  Similarity=0.168  Sum_probs=74.7

Q ss_pred             HHHHHHccCCHHHHHHHHHHHHHCCCCCCHH----HHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCcCHHHHHHHHHHHH
Q 040027          388 LFLGLFEIHQVEHALKLFDEMQRDGVAADTR----TYTTFIDGLCKNGYIIEAVELFRTLRILKCELDIQAYNCLIDGLC  463 (595)
Q Consensus       388 l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~----~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~~l~~~~~  463 (595)
                      .+...-++|.+.+|+.++        .|+..    +|.+....+...+.+++|.-+|+..-+.         ...+.+|.
T Consensus       914 ~~n~I~kh~Ly~~aL~ly--------~~~~e~~k~i~~~ya~hL~~~~~~~~Aal~Ye~~Gkl---------ekAl~a~~  976 (1265)
T KOG1920|consen  914 CKNYIKKHGLYDEALALY--------KPDSEKQKVIYEAYADHLREELMSDEAALMYERCGKL---------EKALKAYK  976 (1265)
T ss_pred             HHHHHHhcccchhhhhee--------ccCHHHHHHHHHHHHHHHHHhccccHHHHHHHHhccH---------HHHHHHHH
Confidence            333344555555555543        33443    3444444455566777776666654321         23356677


Q ss_pred             hcCChHHHHHHHHhcccCCCCCCHH--HHHHHHHHHHhcCChhHHHHHHHHHHHcCCCCCHHHHHHHHHHHHHcCChhHH
Q 040027          464 KSGRLKFAWELFCSLPHGVLVPNVV--TYNIMIQGLCNDGQMDKARDLFLDMEENAAAPDVITFDMLIHGFIRINEPSKV  541 (595)
Q Consensus       464 ~~g~~~~A~~~~~~~~~~~~~p~~~--~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A  541 (595)
                      .+|+|++|..+..++..   .-+..  +-..|+.-+...++.-+|-++..+....   |.     ..+..|++...|++|
T Consensus       977 ~~~dWr~~l~~a~ql~~---~~de~~~~a~~L~s~L~e~~kh~eAa~il~e~~sd---~~-----~av~ll~ka~~~~eA 1045 (1265)
T KOG1920|consen  977 ECGDWREALSLAAQLSE---GKDELVILAEELVSRLVEQRKHYEAAKILLEYLSD---PE-----EAVALLCKAKEWEEA 1045 (1265)
T ss_pred             HhccHHHHHHHHHhhcC---CHHHHHHHHHHHHHHHHHcccchhHHHHHHHHhcC---HH-----HHHHHHhhHhHHHHH
Confidence            77888888877777653   11221  2245666677777777777777766542   11     233345566667777


Q ss_pred             HHHHHHHH
Q 040027          542 NELLHKMK  549 (595)
Q Consensus       542 ~~~~~~~~  549 (595)
                      .++.....
T Consensus      1046 lrva~~~~ 1053 (1265)
T KOG1920|consen 1046 LRVASKAK 1053 (1265)
T ss_pred             HHHHHhcc
Confidence            66655443

>smart00299 CLH Clathrin heavy chain repeat homology

Probab=94.66  E-value=1.9  Score=34.87  Aligned_cols=126  Identities=14%  Similarity=0.118  Sum_probs=73.0

Q ss_pred             HHHHHHHHhcCChhHHHHHHHHHHhCCCCCCHHHHHHHHHHHHhcCCHhHHHHHHHHHHhcCCCCCHhhHHHHHHHHHhc
Q 040027          100 NILINCFCKIGRVSLGFIAFGRILRSCFTPNAATFNSLIKGLHAESRIMEAAALFTKLKAFGCEPNVITYNTLINGLCRT  179 (595)
Q Consensus       100 ~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~~l~~~~~~~  179 (595)
                      ..++..+.+.+........++.+...+ ..++...+.++..|++.+. ....+.++.      ..+......++..+.+.
T Consensus        11 ~~vv~~~~~~~~~~~l~~yLe~~~~~~-~~~~~~~~~li~ly~~~~~-~~ll~~l~~------~~~~yd~~~~~~~c~~~   82 (140)
T smart00299       11 SEVVELFEKRNLLEELIPYLESALKLN-SENPALQTKLIELYAKYDP-QKEIERLDN------KSNHYDIEKVGKLCEKA   82 (140)
T ss_pred             HHHHHHHHhCCcHHHHHHHHHHHHccC-ccchhHHHHHHHHHHHHCH-HHHHHHHHh------ccccCCHHHHHHHHHHc
Confidence            356667777778888888888887776 3566777788887776532 333333331      11233344566666667


Q ss_pred             CChhHHHHHHHHHHhcCCCCCccccCcHHHHHHHHHHHHHc-CCHhHHHHHHHHHhhCCCCCCHhHHHHHHHHHHh
Q 040027          180 GHTMIALNLFEEMANGNGEIGVVCKPNTVTYSTIIDGLCKE-GFVDKAKALFLQMKDENINPDVVTYNSLIHGLCH  254 (595)
Q Consensus       180 g~~~~A~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~-g~~~~A~~~~~~~~~~~~~~~~~~~~~ll~~~~~  254 (595)
                      +.++++.-++.++..               +...+..+... ++++.|.+.+.+.      .+...|..++..+..
T Consensus        83 ~l~~~~~~l~~k~~~---------------~~~Al~~~l~~~~d~~~a~~~~~~~------~~~~lw~~~~~~~l~  137 (140)
T smart00299       83 KLYEEAVELYKKDGN---------------FKDAIVTLIEHLGNYEKAIEYFVKQ------NNPELWAEVLKALLD  137 (140)
T ss_pred             CcHHHHHHHHHhhcC---------------HHHHHHHHHHcccCHHHHHHHHHhC------CCHHHHHHHHHHHHc
Confidence            777777766666522               12233333333 6666666666541      145566666655543

>COG4785 NlpI Lipoprotein NlpI, contains TPR repeats [General function prediction only]

Probab=94.61  E-value=2.6  Score=36.11  Aligned_cols=163  Identities=18%  Similarity=0.069  Sum_probs=95.8

Q ss_pred             CCC-CHHHHHHHHHHHHhcCChhHHHHHHHHHHhCCCCCCHHHHHHHHHHHHhcCCHhHHHHHHHHHHhcCC-CCCHhhH
Q 040027           92 LFP-NLYTYNILINCFCKIGRVSLGFIAFGRILRSCFTPNAATFNSLIKGLHAESRIMEAAALFTKLKAFGC-EPNVITY  169 (595)
Q Consensus        92 ~~~-~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~-~~~~~~~  169 (595)
                      +.| -+.+||.+.--+...|+++.|...|+...+..+.-+-...|.-|. +.--|++.-|.+-+...-+.+. +|-...|
T Consensus        94 i~P~m~~vfNyLG~Yl~~a~~fdaa~eaFds~~ELDp~y~Ya~lNRgi~-~YY~gR~~LAq~d~~~fYQ~D~~DPfR~LW  172 (297)
T COG4785          94 IRPDMPEVFNYLGIYLTQAGNFDAAYEAFDSVLELDPTYNYAHLNRGIA-LYYGGRYKLAQDDLLAFYQDDPNDPFRSLW  172 (297)
T ss_pred             cCCCcHHHHHHHHHHHHhcccchHHHHHhhhHhccCCcchHHHhcccee-eeecCchHhhHHHHHHHHhcCCCChHHHHH
Confidence            344 467888888889999999999999999999864433333343333 3345889999887777766532 2222333


Q ss_pred             HHHHHHHHhcCChhHHHHHHH-HHHhcCCCCCccccCcHHHHHHHHH-HHHHcCCHhHHHHHHHHHhhCCCC------CC
Q 040027          170 NTLINGLCRTGHTMIALNLFE-EMANGNGEIGVVCKPNTVTYSTIID-GLCKEGFVDKAKALFLQMKDENIN------PD  241 (595)
Q Consensus       170 ~~l~~~~~~~g~~~~A~~~~~-~~~~~~~~~~~~~~~~~~~~~~l~~-~~~~~g~~~~A~~~~~~~~~~~~~------~~  241 (595)
                      ..+..   +.-++.+|..-+. +....          +..-|...|. .|...=..+   .+++.+......      .-
T Consensus       173 LYl~E---~k~dP~~A~tnL~qR~~~~----------d~e~WG~~iV~~yLgkiS~e---~l~~~~~a~a~~n~~~Ae~L  236 (297)
T COG4785         173 LYLNE---QKLDPKQAKTNLKQRAEKS----------DKEQWGWNIVEFYLGKISEE---TLMERLKADATDNTSLAEHL  236 (297)
T ss_pred             HHHHH---hhCCHHHHHHHHHHHHHhc----------cHhhhhHHHHHHHHhhccHH---HHHHHHHhhccchHHHHHHH
Confidence            33322   4456667765443 33332          3344443332 232222222   233333321100      01


Q ss_pred             HhHHHHHHHHHHhcCCHHHHHHHHHHHHHC
Q 040027          242 VVTYNSLIHGLCHANDWNEAKRLFIEMMDQ  271 (595)
Q Consensus       242 ~~~~~~ll~~~~~~~~~~~A~~~~~~~~~~  271 (595)
                      +.||--|...+...|+.++|..+|+-.+..
T Consensus       237 TEtyFYL~K~~l~~G~~~~A~~LfKLaian  266 (297)
T COG4785         237 TETYFYLGKYYLSLGDLDEATALFKLAVAN  266 (297)
T ss_pred             HHHHHHHHHHHhccccHHHHHHHHHHHHHH
Confidence            456777788888888888888888877764

>PF13431 TPR_17: Tetratricopeptide repeat

Probab=94.50  E-value=0.072  Score=30.52  Aligned_cols=30  Identities=13%  Similarity=0.396  Sum_probs=24.0

Q ss_pred             HHHHHHhCCCCCCHhhHHHHHHHHHcCCCchh
Q 040027           54 FDYMLRMHPSPPPVSSFNILLASLAKNKHYDT   85 (595)
Q Consensus        54 ~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~   85 (595)
                      |+++++.+|+  ++.+|+.+...|...|++++
T Consensus         2 y~kAie~~P~--n~~a~~nla~~~~~~g~~~~   31 (34)
T PF13431_consen    2 YKKAIELNPN--NAEAYNNLANLYLNQGDYEE   31 (34)
T ss_pred             hHHHHHHCCC--CHHHHHHHHHHHHHCcCHHh
Confidence            7788999998  88888888888777777653

>COG3629 DnrI DNA-binding transcriptional activator of the SARP family [Signal transduction mechanisms]

Probab=94.48  E-value=0.51  Score=42.68  Aligned_cols=78  Identities=14%  Similarity=0.166  Sum_probs=59.5

Q ss_pred             HHHHHHHHHHHhcCChhHHHHHHHHHHhCCCCCCHHHHHHHHHHHHhcCCHhHHHHHHHHHHh-----cCCCCCHhhHHH
Q 040027           97 YTYNILINCFCKIGRVSLGFIAFGRILRSCFTPNAATFNSLIKGLHAESRIMEAAALFTKLKA-----FGCEPNVITYNT  171 (595)
Q Consensus        97 ~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~-----~~~~~~~~~~~~  171 (595)
                      .++..++..+...|+++.+...++++.... +-+...|..++.+|.+.|+...|+..|+.+.+     .|+.|...+...
T Consensus       154 ~~l~~lae~~~~~~~~~~~~~~l~~Li~~d-p~~E~~~~~lm~~y~~~g~~~~ai~~y~~l~~~~~edlgi~P~~~~~~~  232 (280)
T COG3629         154 KALTKLAEALIACGRADAVIEHLERLIELD-PYDEPAYLRLMEAYLVNGRQSAAIRAYRQLKKTLAEELGIDPAPELRAL  232 (280)
T ss_pred             HHHHHHHHHHHhcccHHHHHHHHHHHHhcC-ccchHHHHHHHHHHHHcCCchHHHHHHHHHHHHhhhhcCCCccHHHHHH
Confidence            345567777788888888888888888875 56788888888888888888888888888765     467777666655


Q ss_pred             HHHH
Q 040027          172 LING  175 (595)
Q Consensus       172 l~~~  175 (595)
                      ....
T Consensus       233 y~~~  236 (280)
T COG3629         233 YEEI  236 (280)
T ss_pred             HHHH
Confidence            5444

>PRK09687 putative lyase; Provisional

Probab=94.36  E-value=4.2  Score=37.50  Aligned_cols=203  Identities=11%  Similarity=0.047  Sum_probs=113.4

Q ss_pred             CHHHHHHHHHHHHhCCCH----HHHHHHHHHHHHCCCCCCHHHHHHHHHHHHccCCH-----HHHHHHHHHHHHCCCCCC
Q 040027          346 DDVSYNILINGYCKNKEV----EEALSLYREMVSKGIKPTVVTYNTLFLGLFEIHQV-----EHALKLFDEMQRDGVAAD  416 (595)
Q Consensus       346 ~~~~~~~l~~~~~~~~~~----~~A~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~-----~~a~~~~~~~~~~~~~~~  416 (595)
                      +...-...+.++.+.|+.    +++...+..+...  .++.......+.++...+..     ..+...+.....   .++
T Consensus        67 d~~vR~~A~~aLg~lg~~~~~~~~a~~~L~~l~~~--D~d~~VR~~A~~aLG~~~~~~~~~~~~a~~~l~~~~~---D~~  141 (280)
T PRK09687         67 NPIERDIGADILSQLGMAKRCQDNVFNILNNLALE--DKSACVRASAINATGHRCKKNPLYSPKIVEQSQITAF---DKS  141 (280)
T ss_pred             CHHHHHHHHHHHHhcCCCccchHHHHHHHHHHHhc--CCCHHHHHHHHHHHhcccccccccchHHHHHHHHHhh---CCC
Confidence            444444445555555542    3455555555332  23444444444444433211     122222222222   335


Q ss_pred             HHHHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCcCHHHHHHHHHHHHhcC-ChHHHHHHHHhcccCCCCCCHHHHHHHHH
Q 040027          417 TRTYTTFIDGLCKNGYIIEAVELFRTLRILKCELDIQAYNCLIDGLCKSG-RLKFAWELFCSLPHGVLVPNVVTYNIMIQ  495 (595)
Q Consensus       417 ~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g-~~~~A~~~~~~~~~~~~~p~~~~~~~l~~  495 (595)
                      ..+-...+.++.+.++ .++...+-.+.+   .++.......+.++...+ +...+...+..+..   .+|..+-...+.
T Consensus       142 ~~VR~~a~~aLg~~~~-~~ai~~L~~~L~---d~~~~VR~~A~~aLg~~~~~~~~~~~~L~~~L~---D~~~~VR~~A~~  214 (280)
T PRK09687        142 TNVRFAVAFALSVIND-EAAIPLLINLLK---DPNGDVRNWAAFALNSNKYDNPDIREAFVAMLQ---DKNEEIRIEAII  214 (280)
T ss_pred             HHHHHHHHHHHhccCC-HHHHHHHHHHhc---CCCHHHHHHHHHHHhcCCCCCHHHHHHHHHHhc---CCChHHHHHHHH
Confidence            5566666677776665 455666666554   445556666666666543 24456666666664   456666667777


Q ss_pred             HHHhcCChhHHHHHHHHHHHcCCCCCHHHHHHHHHHHHHcCChhHHHHHHHHHHHCCCCCCHHHHHHHHHHHHh
Q 040027          496 GLCNDGQMDKARDLFLDMEENAAAPDVITFDMLIHGFIRINEPSKVNELLHKMKEKKVMPDASIVSIVVDLLVK  569 (595)
Q Consensus       496 ~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~p~~~~~~~l~~~~~~  569 (595)
                      ++.+.|+ ..|+..+-+.++.+   +  .....+.++...|.. +|...+..+.+.  .||..+....++++.+
T Consensus       215 aLg~~~~-~~av~~Li~~L~~~---~--~~~~a~~ALg~ig~~-~a~p~L~~l~~~--~~d~~v~~~a~~a~~~  279 (280)
T PRK09687        215 GLALRKD-KRVLSVLIKELKKG---T--VGDLIIEAAGELGDK-TLLPVLDTLLYK--FDDNEIITKAIDKLKR  279 (280)
T ss_pred             HHHccCC-hhHHHHHHHHHcCC---c--hHHHHHHHHHhcCCH-hHHHHHHHHHhh--CCChhHHHHHHHHHhc
Confidence            7777777 46677666666643   2  234567777777774 688888888763  3577777777766653

>PRK15180 Vi polysaccharide biosynthesis protein TviD; Provisional

Probab=94.34  E-value=5.3  Score=38.60  Aligned_cols=90  Identities=11%  Similarity=0.088  Sum_probs=47.6

Q ss_pred             HHHhcCChhHHHHHHHHHHhCCCCCCHHHHHHHHHHHHhcCCHhHHHHHHHHHHhcCCCCCHhhHHHHHHHHHhcCChhH
Q 040027          105 CFCKIGRVSLGFIAFGRILRSCFTPNAATFNSLIKGLHAESRIMEAAALFTKLKAFGCEPNVITYNTLINGLCRTGHTMI  184 (595)
Q Consensus       105 ~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~  184 (595)
                      .+...|.++.+.+.+..+.+. ......+...+++...+.|++++|..+-+-|+...++ ++++........-+.|-+++
T Consensus       332 i~~~lg~ye~~~~~~s~~~~~-~~s~~~~~~~~~r~~~~l~r~~~a~s~a~~~l~~eie-~~ei~~iaa~sa~~l~~~d~  409 (831)
T PRK15180        332 IFSHLGYYEQAYQDISDVEKI-IGTTDSTLRCRLRSLHGLARWREALSTAEMMLSNEIE-DEEVLTVAAGSADALQLFDK  409 (831)
T ss_pred             HHHHhhhHHHHHHHhhchhhh-hcCCchHHHHHHHhhhchhhHHHHHHHHHHHhccccC-ChhheeeecccHHHHhHHHH
Confidence            344556666666666554443 1223444455666666666666666666666655444 33333322223334455566


Q ss_pred             HHHHHHHHHhcC
Q 040027          185 ALNLFEEMANGN  196 (595)
Q Consensus       185 A~~~~~~~~~~~  196 (595)
                      +.-.++++...+
T Consensus       410 ~~~~wk~~~~~~  421 (831)
T PRK15180        410 SYHYWKRVLLLN  421 (831)
T ss_pred             HHHHHHHHhccC
Confidence            666666655544

>KOG3941 consensus Intermediate in Toll signal transduction pathway (ECSIT) [Signal transduction mechanisms]

Probab=93.97  E-value=0.6  Score=41.46  Aligned_cols=106  Identities=13%  Similarity=0.219  Sum_probs=54.3

Q ss_pred             cCHHHHHHHHHHHHh-----cCChHHHHHHHHhcccCCCCCCHHHHHHHHHHHHhcCChhHHHHHHHHHHHcCCCCCHHH
Q 040027          450 LDIQAYNCLIDGLCK-----SGRLKFAWELFCSLPHGVLVPNVVTYNIMIQGLCNDGQMDKARDLFLDMEENAAAPDVIT  524 (595)
Q Consensus       450 ~~~~~~~~l~~~~~~-----~g~~~~A~~~~~~~~~~~~~p~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~  524 (595)
                      -|..+|...+..+..     .+.++-....++.|.+.|+..|..+|+.|+..+-+..-.                |. ..
T Consensus        65 RdK~sfl~~V~~F~E~sVr~R~HveFIy~ALk~m~eyGVerDl~vYk~LlnvfPKgkfi----------------P~-nv  127 (406)
T KOG3941|consen   65 RDKDSFLAAVATFKEKSVRGRTHVEFIYTALKYMKEYGVERDLDVYKGLLNVFPKGKFI----------------PQ-NV  127 (406)
T ss_pred             ccHHHHHHHHHHHHHhhhcccchHHHHHHHHHHHHHhcchhhHHHHHHHHHhCcccccc----------------cH-HH
Confidence            345555555555542     244555555556666666666666666666554322110                10 11


Q ss_pred             HHHHHHHHHHcCChhHHHHHHHHHHHCCCCCCHHHHHHHHHHHHhcCccc
Q 040027          525 FDMLIHGFIRINEPSKVNELLHKMKEKKVMPDASIVSIVVDLLVKNEISL  574 (595)
Q Consensus       525 ~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~p~~~~~~~l~~~~~~~g~~~  574 (595)
                      |....--|-+  .-+-+.+++++|..+|+-||.++-..++.++.+.|-.-
T Consensus       128 fQ~~F~HYP~--QQ~C~I~vLeqME~hGVmPdkE~e~~lvn~FGr~~~p~  175 (406)
T KOG3941|consen  128 FQKVFLHYPQ--QQNCAIKVLEQMEWHGVMPDKEIEDILVNAFGRWNFPT  175 (406)
T ss_pred             HHHHHhhCch--hhhHHHHHHHHHHHcCCCCchHHHHHHHHHhccccccH
Confidence            1111111111  12446677777777777777777777777776666544

>KOG1920 consensus IkappaB kinase complex, IKAP component [Transcription]

Probab=93.72  E-value=13  Score=40.69  Aligned_cols=125  Identities=10%  Similarity=0.077  Sum_probs=62.2

Q ss_pred             HHHHHHHhcCChhHHHHHHHHHHhC-C--CCCCHHHHHHHHHHHHhc-CCHhHHHHHHHHHHhcCCCCCHhhHH----HH
Q 040027          101 ILINCFCKIGRVSLGFIAFGRILRS-C--FTPNAATFNSLIKGLHAE-SRIMEAAALFTKLKAFGCEPNVITYN----TL  172 (595)
Q Consensus       101 ~l~~~~~~~g~~~~A~~~~~~~~~~-~--~~~~~~~~~~l~~~~~~~-g~~~~A~~~~~~~~~~~~~~~~~~~~----~l  172 (595)
                      .-++.+...+++.+|..+.++-.-. +  +.-++..+..-+.++.+. ++.+--..++..+...++.  ...|.    +-
T Consensus       682 a~vr~~l~~~~y~~AF~~~RkhRidlnii~d~~~~~Fl~nv~afl~~in~~~~l~lfl~~lk~eDvt--k~~y~~~~~s~  759 (1265)
T KOG1920|consen  682 AKVRTLLDRLRYKEAFEVMRKHRIDLNIIFDYDPKRFLKNVPAFLKQINRVNHLELFLTELKEEDVT--KTMYSSTSGSG  759 (1265)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHhccCccchhhcCHHHHHhhHHHHhccCCcHHHHHHHHhhcccchhh--hhhcccccccc
Confidence            4566677788888888887765422 1  122344555555555553 4444444444444432211  11111    11


Q ss_pred             HHHHHhc----CChhHHHHHHHHHHhcCCCCCccccCcHHHHHHHHHHHHHcC--CHhHHHHHHHHHhh
Q 040027          173 INGLCRT----GHTMIALNLFEEMANGNGEIGVVCKPNTVTYSTIIDGLCKEG--FVDKAKALFLQMKD  235 (595)
Q Consensus       173 ~~~~~~~----g~~~~A~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g--~~~~A~~~~~~~~~  235 (595)
                      ...|...    .+.+...+.+.....+.       .|+ .....++..|.+.+  .++.+.....+...
T Consensus       760 k~~~~~r~~~d~kv~~vc~~vr~~l~~~-------~~~-~~~~~ilTs~vk~~~~~ie~aL~kI~~l~~  820 (1265)
T KOG1920|consen  760 KQVYMSRDPYDNKVNSVCDAVRNALERR-------APD-KFNLFILTSYVKSNPPEIEEALQKIKELQL  820 (1265)
T ss_pred             ceeEEeccchhhHHHHHHHHHHHHHhhc-------Ccc-hhhHHHHHHHHhcCcHHHHHHHHHHHHHHh
Confidence            0111111    22333444444444443       344 44556777888876  56666666666553

>PF13431 TPR_17: Tetratricopeptide repeat

Probab=93.68  E-value=0.094  Score=30.03  Aligned_cols=32  Identities=6%  Similarity=0.107  Sum_probs=17.8

Q ss_pred             HHHHHHcCCCCCHHHHHHHHHHHHHcCChhHHH
Q 040027          510 FLDMEENAAAPDVITFDMLIHGFIRINEPSKVN  542 (595)
Q Consensus       510 ~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~  542 (595)
                      |+++++.. |.+...|..++..|...|++++|+
T Consensus         2 y~kAie~~-P~n~~a~~nla~~~~~~g~~~~A~   33 (34)
T PF13431_consen    2 YKKAIELN-PNNAEAYNNLANLYLNQGDYEEAI   33 (34)
T ss_pred             hHHHHHHC-CCCHHHHHHHHHHHHHCcCHHhhc
Confidence            34444443 445566666666666666666554

>PF10602 RPN7: 26S proteasome subunit RPN7; InterPro: IPR019585 This entry represents the regulatory subunit RPN7 (known as the non-ATPase regulatory subunit 6 in higher eukaryotes) of the 26S proteasome

Probab=93.49  E-value=1.8  Score=36.68  Aligned_cols=100  Identities=15%  Similarity=0.117  Sum_probs=71.9

Q ss_pred             HHHHHHHHHHHHhcCChhHHHHHHHHHHhCCCCCC--HHHHHHHHHHHHhcCCHhHHHHHHHHHHhcCCCC-CHhhHH--
Q 040027           96 LYTYNILINCFCKIGRVSLGFIAFGRILRSCFTPN--AATFNSLIKGLHAESRIMEAAALFTKLKAFGCEP-NVITYN--  170 (595)
Q Consensus        96 ~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~~--~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~-~~~~~~--  170 (595)
                      ...+..++..|.+.|+.+.|++.|.++......+.  ...+..+++.....+++..+.....++...-... |....+  
T Consensus        36 r~~~~~l~~~~~~~Gd~~~A~k~y~~~~~~~~~~~~~id~~l~~irv~i~~~d~~~v~~~i~ka~~~~~~~~d~~~~nrl  115 (177)
T PF10602_consen   36 RMALEDLADHYCKIGDLEEALKAYSRARDYCTSPGHKIDMCLNVIRVAIFFGDWSHVEKYIEKAESLIEKGGDWERRNRL  115 (177)
T ss_pred             HHHHHHHHHHHHHhhhHHHHHHHHHHHhhhcCCHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHhccchHHHHHHH
Confidence            35677899999999999999999999988754433  4467888999999999999998888776542121 222221  


Q ss_pred             HH--HHHHHhcCChhHHHHHHHHHHhc
Q 040027          171 TL--INGLCRTGHTMIALNLFEEMANG  195 (595)
Q Consensus       171 ~l--~~~~~~~g~~~~A~~~~~~~~~~  195 (595)
                      ..  ...+...+++..|-+.|-.....
T Consensus       116 k~~~gL~~l~~r~f~~AA~~fl~~~~t  142 (177)
T PF10602_consen  116 KVYEGLANLAQRDFKEAAELFLDSLST  142 (177)
T ss_pred             HHHHHHHHHHhchHHHHHHHHHccCcC
Confidence            11  22334578999999988777644

This entry also matches the evolutionarily related subunit 1 of the COP9 signalosome complex (CSN) from Arabidopsis []. The 26S proteasome plays a major role in ATP-dependent degradation of ubiquitinated proteins. Substrate specificity is conferred by the regulatory particle (RP), which can dissociate into stable lid and base subcomplexes. The regulatory subunit RPN7 is one of the lid subunits of the 26S proteasome and has been shown in Saccharomyces cerevisiae (Baker's yeast) to be required for structural integrity []. The COP9 signalosome is a conserved protein complex composed of eight subunits, where Individual subunits of the complex have been linked to various signal transduction pathways leading to gene expression and cell cycle control []. The overall organisation and the amino acid sequences of the COP9 signalosome subunits resemble the lid subcomplex of the 19 S regulatory particle for the 26 S proteasome []. COP9 subunit 1 (CSN1 or GPS1) of the COP9 complex is an essential subunit of the complex with regard to both structural integrity and functionality. The N-terminal region of subunit 1 (CSN1-N) can inhibit c-fos expression from either a transfected template or a chromosomal transgene (fos-lacZ), and may contain the activity domain that confers most of the repression functions of CSN1. The C-terminal region of subunit 1 (CSN1-C) allows integration of the protein into the COP9 signalosome.

>PF10602 RPN7: 26S proteasome subunit RPN7; InterPro: IPR019585 This entry represents the regulatory subunit RPN7 (known as the non-ATPase regulatory subunit 6 in higher eukaryotes) of the 26S proteasome

Probab=93.27  E-value=1.2  Score=37.78  Aligned_cols=97  Identities=15%  Similarity=0.069  Sum_probs=58.8

Q ss_pred             HHHHHHHHHHHhcCChHHHHHHHHhcccCCCCCC--HHHHHHHHHHHHhcCChhHHHHHHHHHHHcCCC-CCHHHHH--H
Q 040027          453 QAYNCLIDGLCKSGRLKFAWELFCSLPHGVLVPN--VVTYNIMIQGLCNDGQMDKARDLFLDMEENAAA-PDVITFD--M  527 (595)
Q Consensus       453 ~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~p~--~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~-~~~~~~~--~  527 (595)
                      ..+..++..|.+.|+.+.|.+.|.++.+....+.  ...+..+++.....+++..+...+.++...-.. .|...-+  .
T Consensus        37 ~~~~~l~~~~~~~Gd~~~A~k~y~~~~~~~~~~~~~id~~l~~irv~i~~~d~~~v~~~i~ka~~~~~~~~d~~~~nrlk  116 (177)
T PF10602_consen   37 MALEDLADHYCKIGDLEEALKAYSRARDYCTSPGHKIDMCLNVIRVAIFFGDWSHVEKYIEKAESLIEKGGDWERRNRLK  116 (177)
T ss_pred             HHHHHHHHHHHHhhhHHHHHHHHHHHhhhcCCHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHhccchHHHHHHHH
Confidence            3456677777777777777777777776544433  345566777777777887777777766543111 1111111  1


Q ss_pred             H--HHHHHHcCChhHHHHHHHHHH
Q 040027          528 L--IHGFIRINEPSKVNELLHKMK  549 (595)
Q Consensus       528 l--~~~~~~~g~~~~A~~~~~~~~  549 (595)
                      .  +-.+...+++.+|.+.|-...
T Consensus       117 ~~~gL~~l~~r~f~~AA~~fl~~~  140 (177)
T PF10602_consen  117 VYEGLANLAQRDFKEAAELFLDSL  140 (177)
T ss_pred             HHHHHHHHHhchHHHHHHHHHccC
Confidence            1  223356778888887776665

This entry also matches the evolutionarily related subunit 1 of the COP9 signalosome complex (CSN) from Arabidopsis []. The 26S proteasome plays a major role in ATP-dependent degradation of ubiquitinated proteins. Substrate specificity is conferred by the regulatory particle (RP), which can dissociate into stable lid and base subcomplexes. The regulatory subunit RPN7 is one of the lid subunits of the 26S proteasome and has been shown in Saccharomyces cerevisiae (Baker's yeast) to be required for structural integrity []. The COP9 signalosome is a conserved protein complex composed of eight subunits, where Individual subunits of the complex have been linked to various signal transduction pathways leading to gene expression and cell cycle control []. The overall organisation and the amino acid sequences of the COP9 signalosome subunits resemble the lid subcomplex of the 19 S regulatory particle for the 26 S proteasome []. COP9 subunit 1 (CSN1 or GPS1) of the COP9 complex is an essential subunit of the complex with regard to both structural integrity and functionality. The N-terminal region of subunit 1 (CSN1-N) can inhibit c-fos expression from either a transfected template or a chromosomal transgene (fos-lacZ), and may contain the activity domain that confers most of the repression functions of CSN1. The C-terminal region of subunit 1 (CSN1-C) allows integration of the protein into the COP9 signalosome.

>PF13176 TPR_7: Tetratricopeptide repeat; PDB: 3SF4_C 3RO3_A 3RO2_A

Probab=93.14  E-value=0.23  Score=28.88  Aligned_cols=26  Identities=12%  Similarity=0.052  Sum_probs=19.3

Q ss_pred             HHHHHHHHHHHcCChhHHHHHHHHHH
Q 040027          524 TFDMLIHGFIRINEPSKVNELLHKMK  549 (595)
Q Consensus       524 ~~~~l~~~~~~~g~~~~A~~~~~~~~  549 (595)
                      +|..++..|.+.|++++|.+++++.+
T Consensus         1 al~~Lg~~~~~~g~~~~Ai~~y~~aL   26 (36)
T PF13176_consen    1 ALNNLGRIYRQQGDYEKAIEYYEQAL   26 (36)
T ss_dssp             HHHHHHHHHHHCT-HHHHHHHHHHHH
T ss_pred             CHHHHHHHHHHcCCHHHHHHHHHHHH
Confidence            35677888888888888888888855

>KOG4648 consensus Uncharacterized conserved protein, contains LRR repeats [Function unknown]

Probab=93.11  E-value=0.33  Score=44.24  Aligned_cols=86  Identities=9%  Similarity=0.011  Sum_probs=35.8

Q ss_pred             HHhcCChHHHHHHHHhcccCCCCC-CHHHHHHHHHHHHhcCChhHHHHHHHHHHHcCCCCCHHHHHHHHHHHHHcCChhH
Q 040027          462 LCKSGRLKFAWELFCSLPHGVLVP-NVVTYNIMIQGLCNDGQMDKARDLFLDMEENAAAPDVITFDMLIHGFIRINEPSK  540 (595)
Q Consensus       462 ~~~~g~~~~A~~~~~~~~~~~~~p-~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~  540 (595)
                      |.++|.+++|+..|.....  ..| |+.++..-..+|.+...+..|..-...++..+ ..-...|..-+.+-...|+..+
T Consensus       107 yFKQgKy~EAIDCYs~~ia--~~P~NpV~~~NRA~AYlk~K~FA~AE~DC~~AiaLd-~~Y~KAYSRR~~AR~~Lg~~~E  183 (536)
T KOG4648|consen  107 YFKQGKYEEAIDCYSTAIA--VYPHNPVYHINRALAYLKQKSFAQAEEDCEAAIALD-KLYVKAYSRRMQARESLGNNME  183 (536)
T ss_pred             hhhccchhHHHHHhhhhhc--cCCCCccchhhHHHHHHHHHHHHHHHHhHHHHHHhh-HHHHHHHHHHHHHHHHHhhHHH
Confidence            4444555555555444443  233 44444444444444444444444444443321 1112223333333333444444


Q ss_pred             HHHHHHHHHH
Q 040027          541 VNELLHKMKE  550 (595)
Q Consensus       541 A~~~~~~~~~  550 (595)
                      |.+-++..++
T Consensus       184 AKkD~E~vL~  193 (536)
T KOG4648|consen  184 AKKDCETVLA  193 (536)
T ss_pred             HHHhHHHHHh
Confidence            4444444443

>PF09205 DUF1955: Domain of unknown function (DUF1955); InterPro: IPR015288 Members of this family are found in hypothetical proteins synthesised by the Archaeal organism Sulfolobus

Probab=93.05  E-value=3.5  Score=32.24  Aligned_cols=25  Identities=24%  Similarity=0.204  Sum_probs=8.8

Q ss_pred             HHHHHHHHHHhcCCHHHHHHHHHHH
Q 040027          419 TYTTFIDGLCKNGYIIEAVELFRTL  443 (595)
Q Consensus       419 ~~~~l~~~~~~~g~~~~A~~~~~~~  443 (595)
                      ....+..+|.+.|+..++.+++.++
T Consensus       122 ~L~kia~Ay~klg~~r~~~ell~~A  146 (161)
T PF09205_consen  122 FLVKIANAYKKLGNTREANELLKEA  146 (161)
T ss_dssp             HHHHHHHHHHHTT-HHHHHHHHHHH
T ss_pred             HHHHHHHHHHHhcchhhHHHHHHHH
Confidence            3333333333333333333333333

Their exact function has not, as yet, been determined. ; PDB: 1WY6_A.

>PF13176 TPR_7: Tetratricopeptide repeat; PDB: 3SF4_C 3RO3_A 3RO2_A

Probab=92.99  E-value=0.24  Score=28.77  Aligned_cols=27  Identities=15%  Similarity=0.149  Sum_probs=21.0

Q ss_pred             HHHHHHHHHHhcCChhHHHHHHHHHHH
Q 040027          489 TYNIMIQGLCNDGQMDKARDLFLDMEE  515 (595)
Q Consensus       489 ~~~~l~~~~~~~g~~~~A~~~~~~~~~  515 (595)
                      +|..|...|.+.|++++|++++++.+.
T Consensus         1 al~~Lg~~~~~~g~~~~Ai~~y~~aL~   27 (36)
T PF13176_consen    1 ALNNLGRIYRQQGDYEKAIEYYEQALA   27 (36)
T ss_dssp             HHHHHHHHHHHCT-HHHHHHHHHHHHH
T ss_pred             CHHHHHHHHHHcCCHHHHHHHHHHHHH
Confidence            467788888899999999999888553

>KOG1550 consensus Extracellular protein SEL-1 and related proteins [Cell wall/membrane/envelope biogenesis; Posttranslational modification, protein turnover, chaperones; Signal transduction mechanisms]

Probab=92.74  E-value=14  Score=38.27  Aligned_cols=177  Identities=12%  Similarity=0.009  Sum_probs=96.5

Q ss_pred             hhHHHHHHHHHHhCCCCCCHHHHHHHHHH-----HHhcCCHhHHHHHHHHHHh-------cCCCCCHhhHHHHHHHHHhc
Q 040027          112 VSLGFIAFGRILRSCFTPNAATFNSLIKG-----LHAESRIMEAAALFTKLKA-------FGCEPNVITYNTLINGLCRT  179 (595)
Q Consensus       112 ~~~A~~~~~~~~~~~~~~~~~~~~~l~~~-----~~~~g~~~~A~~~~~~~~~-------~~~~~~~~~~~~l~~~~~~~  179 (595)
                      ...|...++...+.|   +......+..+     +....+.+.|+..|..+..       .|   .......+..+|.+.
T Consensus       228 ~~~a~~~~~~~a~~g---~~~a~~~~g~~y~~G~~g~~~d~e~a~~~l~~aa~~~~~~a~~~---~~~a~~~lg~~Y~~g  301 (552)
T KOG1550|consen  228 LSEAFKYYREAAKLG---HSEAQYALGICYLAGTYGVTQDLESAIEYLKLAAESFKKAATKG---LPPAQYGLGRLYLQG  301 (552)
T ss_pred             hhHHHHHHHHHHhhc---chHHHHHHHHHHhhccccccccHHHHHHHHHHHHHHHHHHHhhc---CCccccHHHHHHhcC
Confidence            456778888877765   33332222222     3345678888888887766       44   334556666666653


Q ss_pred             C-----ChhHHHHHHHHHHhcCCCCCccccCcHHHHHHHHHHHHHc---CCHhHHHHHHHHHhhCCCCCCHhHHHHHHHH
Q 040027          180 G-----HTMIALNLFEEMANGNGEIGVVCKPNTVTYSTIIDGLCKE---GFVDKAKALFLQMKDENINPDVVTYNSLIHG  251 (595)
Q Consensus       180 g-----~~~~A~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~---g~~~~A~~~~~~~~~~~~~~~~~~~~~ll~~  251 (595)
                      .     +.+.|+.++.+....+       .|+..  ..+..++...   .+...|.++|....+.|.   ...+-.+..+
T Consensus       302 ~~~~~~d~~~A~~~~~~aA~~g-------~~~a~--~~lg~~~~~g~~~~d~~~A~~yy~~Aa~~G~---~~A~~~la~~  369 (552)
T KOG1550|consen  302 LGVEKIDYEKALKLYTKAAELG-------NPDAQ--YLLGVLYETGTKERDYRRAFEYYSLAAKAGH---ILAIYRLALC  369 (552)
T ss_pred             CCCccccHHHHHHHHHHHHhcC-------CchHH--HHHHHHHHcCCccccHHHHHHHHHHHHHcCC---hHHHHHHHHH
Confidence            3     5566777777777665       23332  2233333322   356778888888777763   2222223322


Q ss_pred             HHh----cCCHHHHHHHHHHHHHCCCCCCHhhHHHHHHHHHhcCChHHHHHHHHHHHHCCC
Q 040027          252 LCH----ANDWNEAKRLFIEMMDQGVQPSVVTFNVIMDELCKNRKMDEASRLLDLMVQRGV  308 (595)
Q Consensus       252 ~~~----~~~~~~A~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~~  308 (595)
                      |..    ..+...|..++.+..+.|. |........+..+.. +.++.+.-.+..+...|.
T Consensus       370 y~~G~gv~r~~~~A~~~~k~aA~~g~-~~A~~~~~~~~~~g~-~~~~~~~~~~~~~a~~g~  428 (552)
T KOG1550|consen  370 YELGLGVERNLELAFAYYKKAAEKGN-PSAAYLLGAFYEYGV-GRYDTALALYLYLAELGY  428 (552)
T ss_pred             HHhCCCcCCCHHHHHHHHHHHHHccC-hhhHHHHHHHHHHcc-ccccHHHHHHHHHHHhhh
Confidence            222    3367777777777777652 221111222223333 666666666665555543

>PF00515 TPR_1: Tetratricopeptide repeat; InterPro: IPR001440 The tetratrico peptide repeat (TPR) is a structural motif present in a wide range of proteins [, , ]

Probab=92.46  E-value=0.34  Score=27.59  Aligned_cols=27  Identities=11%  Similarity=0.238  Sum_probs=13.2

Q ss_pred             HHHHHHHHHHHcCChhHHHHHHHHHHH
Q 040027          524 TFDMLIHGFIRINEPSKVNELLHKMKE  550 (595)
Q Consensus       524 ~~~~l~~~~~~~g~~~~A~~~~~~~~~  550 (595)
                      +|..++.+|...|++++|...++++++
T Consensus         3 ~~~~~g~~~~~~~~~~~A~~~~~~al~   29 (34)
T PF00515_consen    3 AYYNLGNAYFQLGDYEEALEYYQRALE   29 (34)
T ss_dssp             HHHHHHHHHHHTT-HHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHhCCchHHHHHHHHHHH
Confidence            344445555555555555555555544

It mediates protein-protein interactions and the assembly of multiprotein complexes []. The TPR motif consists of 3-16 tandem-repeats of 34 amino acids residues, although individual TPR motifs can be dispersed in the protein sequence. Sequence alignment of the TPR domains reveals a consensus sequence defined by a pattern of small and large amino acids. TPR motifs have been identified in various different organisms, ranging from bacteria to humans. Proteins containing TPRs are involved in a variety of biological processes, such as cell cycle regulation, transcriptional control, mitochondrial and peroxisomal protein transport, neurogenesis and protein folding. The X-ray structure of a domain containing three TPRs from protein phosphatase 5 revealed that TPR adopts a helix-turn-helix arrangement, with adjacent TPR motifs packing in a parallel fashion, resulting in a spiral of repeating anti-parallel alpha-helices []. The two helices are denoted helix A and helix B. The packing angle between helix A and helix B is ~24 degrees; within a single TPR and generates a right-handed superhelical shape. Helix A interacts with helix B and with helix A' of the next TPR. Two protein surfaces are generated: the inner concave surface is contributed to mainly by residue on helices A, and the other surface presents residues from both helices A and B. ; GO: 0005515 protein binding; PDB: 3SF4_C 2LNI_A 1ELW_A 2C0M_A 1FCH_B 3R9A_B 2J9Q_A 2C0L_A 1KT1_A 3FWV_A ....

>PF13170 DUF4003: Protein of unknown function (DUF4003)

Probab=92.42  E-value=9.2  Score=35.55  Aligned_cols=129  Identities=16%  Similarity=0.250  Sum_probs=64.5

Q ss_pred             HHHHHHHHHHHHCCCCCCHhhHHHHHHHHHh--cC----ChHHHHHHHHHHHHCCCC---CCHHHHHHHHHHHHhcCC--
Q 040027          259 NEAKRLFIEMMDQGVQPSVVTFNVIMDELCK--NR----KMDEASRLLDLMVQRGVR---PNACTYNTLMDGFCLMGK--  327 (595)
Q Consensus       259 ~~A~~~~~~~~~~~~~~~~~~~~~l~~~~~~--~g----~~~~a~~~~~~~~~~~~~---~~~~~~~~l~~~~~~~~~--  327 (595)
                      ++.+.+++.+.+.|+.-+..++.........  ..    ....+..+|+.|.+...-   ++..++..++..  ..++  
T Consensus        79 ~~~~~~y~~L~~~gFk~~~y~~laA~~i~~~~~~~~~~~~~~ra~~iy~~mKk~H~fLTs~~D~~~a~lLA~--~~~~~e  156 (297)
T PF13170_consen   79 KEVLDIYEKLKEAGFKRSEYLYLAALIILEEEEKEDYDEIIQRAKEIYKEMKKKHPFLTSPEDYPFAALLAM--TSEDVE  156 (297)
T ss_pred             HHHHHHHHHHHHhccCccChHHHHHHHHHHhcccccHHHHHHHHHHHHHHHHHhCccccCccchhHHHHHhc--ccccHH
Confidence            4445666777777776665555443322222  11    245577777777775321   223333333222  2233  


Q ss_pred             --HHHHHHHHHHHHhcCCCCCHH--HHHHHHHHHHhCCC--HHHHHHHHHHHHHCCCCCCHHHHHHHH
Q 040027          328 --INRAEELFGSMESMGCKHDDV--SYNILINGYCKNKE--VEEALSLYREMVSKGIKPTVVTYNTLF  389 (595)
Q Consensus       328 --~~~a~~~~~~~~~~~~~~~~~--~~~~l~~~~~~~~~--~~~A~~~~~~~~~~~~~~~~~~~~~l~  389 (595)
                        .+.++.+|+.+.+.|+..+..  ....++........  ...+.++++.+.+.|+++....|..+.
T Consensus       157 ~l~~~~E~~Y~~L~~~~f~kgn~LQ~LS~iLaL~~~~~~~~v~r~~~l~~~l~~~~~kik~~~yp~lG  224 (297)
T PF13170_consen  157 ELAERMEQCYQKLADAGFKKGNDLQFLSHILALSEGDDQEKVARVIELYNALKKNGVKIKYMHYPTLG  224 (297)
T ss_pred             HHHHHHHHHHHHHHHhCCCCCcHHHHHHHHHHhccccchHHHHHHHHHHHHHHHcCCccccccccHHH
Confidence              345566666666656544333  22222322222111  346667777777777766655554443

>KOG1550 consensus Extracellular protein SEL-1 and related proteins [Cell wall/membrane/envelope biogenesis; Posttranslational modification, protein turnover, chaperones; Signal transduction mechanisms]

Probab=92.41  E-value=15  Score=37.96  Aligned_cols=176  Identities=15%  Similarity=0.090  Sum_probs=101.8

Q ss_pred             HhHHHHHHHHHhhCCCCCCHhHHHHHHHH-----HHhcCCHHHHHHHHHHHHH-------CCCCCCHhhHHHHHHHHHhc
Q 040027          223 VDKAKALFLQMKDENINPDVVTYNSLIHG-----LCHANDWNEAKRLFIEMMD-------QGVQPSVVTFNVIMDELCKN  290 (595)
Q Consensus       223 ~~~A~~~~~~~~~~~~~~~~~~~~~ll~~-----~~~~~~~~~A~~~~~~~~~-------~~~~~~~~~~~~l~~~~~~~  290 (595)
                      ...|.++++...+.|   +...-..+..+     +....+.+.|+.+|..+.+       .|   .......+..+|.+.
T Consensus       228 ~~~a~~~~~~~a~~g---~~~a~~~~g~~y~~G~~g~~~d~e~a~~~l~~aa~~~~~~a~~~---~~~a~~~lg~~Y~~g  301 (552)
T KOG1550|consen  228 LSEAFKYYREAAKLG---HSEAQYALGICYLAGTYGVTQDLESAIEYLKLAAESFKKAATKG---LPPAQYGLGRLYLQG  301 (552)
T ss_pred             hhHHHHHHHHHHhhc---chHHHHHHHHHHhhccccccccHHHHHHHHHHHHHHHHHHHhhc---CCccccHHHHHHhcC
Confidence            467888888888876   33333333333     3345689999999988876       43   333455666666664


Q ss_pred             C-----ChHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHhc---CCHHHHHHHHHHHHhcCCCCCHHHHHHHHHHHHh---
Q 040027          291 R-----KMDEASRLLDLMVQRGVRPNACTYNTLMDGFCLM---GKINRAEELFGSMESMGCKHDDVSYNILINGYCK---  359 (595)
Q Consensus       291 g-----~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~---~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~---  359 (595)
                      .     +.+.|..+|.+....|.+ +..  ..+..++...   .+...|.++|......|   ...++-.+..+|..   
T Consensus       302 ~~~~~~d~~~A~~~~~~aA~~g~~-~a~--~~lg~~~~~g~~~~d~~~A~~yy~~Aa~~G---~~~A~~~la~~y~~G~g  375 (552)
T KOG1550|consen  302 LGVEKIDYEKALKLYTKAAELGNP-DAQ--YLLGVLYETGTKERDYRRAFEYYSLAAKAG---HILAIYRLALCYELGLG  375 (552)
T ss_pred             CCCccccHHHHHHHHHHHHhcCCc-hHH--HHHHHHHHcCCccccHHHHHHHHHHHHHcC---ChHHHHHHHHHHHhCCC
Confidence            3     556688888888777533 332  2233333332   35678888888887776   23333344444432   


Q ss_pred             -CCCHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHccCCHHHHHHHHHHHHHCC
Q 040027          360 -NKEVEEALSLYREMVSKGIKPTVVTYNTLFLGLFEIHQVEHALKLFDEMQRDG  412 (595)
Q Consensus       360 -~~~~~~A~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~  412 (595)
                       ..+...|..++.+..+.|. |...-....+..+.. ++++.+.-.+..+...+
T Consensus       376 v~r~~~~A~~~~k~aA~~g~-~~A~~~~~~~~~~g~-~~~~~~~~~~~~~a~~g  427 (552)
T KOG1550|consen  376 VERNLELAFAYYKKAAEKGN-PSAAYLLGAFYEYGV-GRYDTALALYLYLAELG  427 (552)
T ss_pred             cCCCHHHHHHHHHHHHHccC-hhhHHHHHHHHHHcc-ccccHHHHHHHHHHHhh
Confidence             3467778888888777762 222212222222233 56666665555555543

>PF06552 TOM20_plant: Plant specific mitochondrial import receptor subunit TOM20; InterPro: IPR010547 This family consists of several plant specific mitochondrial import receptor subunit TOM20 (translocase of outer membrane 20 kDa subunit) proteins

Probab=92.17  E-value=2.8  Score=34.88  Aligned_cols=25  Identities=16%  Similarity=0.341  Sum_probs=10.1

Q ss_pred             hHHHHHHHHHHHcCCCCCHHHHHHHHH
Q 040027          504 DKARDLFLDMEENAAAPDVITFDMLIH  530 (595)
Q Consensus       504 ~~A~~~~~~~~~~~~~~~~~~~~~l~~  530 (595)
                      ++|.+.|+++.+.  .|+...|..-+.
T Consensus        97 ~kA~~~FqkAv~~--~P~ne~Y~ksLe  121 (186)
T PF06552_consen   97 EKATEYFQKAVDE--DPNNELYRKSLE  121 (186)
T ss_dssp             HHHHHHHHHHHHH---TT-HHHHHHHH
T ss_pred             HHHHHHHHHHHhc--CCCcHHHHHHHH
Confidence            3344444444442  355555544443

Most mitochondrial proteins are encoded by the nuclear genome, and are synthesised in the cytosol. TOM20 is a general import receptor that binds to mitochondrial pre-sequences in the early step of protein import into the mitochondria [].; GO: 0045040 protein import into mitochondrial outer membrane, 0005742 mitochondrial outer membrane translocase complex; PDB: 1ZU2_A.

>PF07719 TPR_2: Tetratricopeptide repeat; InterPro: IPR013105 The tetratrico peptide repeat (TPR) is a structural motif present in a wide range of proteins [, , ]

Probab=92.16  E-value=0.38  Score=27.28  Aligned_cols=27  Identities=15%  Similarity=0.224  Sum_probs=14.6

Q ss_pred             HHHHHHHHHHHcCChhHHHHHHHHHHH
Q 040027          524 TFDMLIHGFIRINEPSKVNELLHKMKE  550 (595)
Q Consensus       524 ~~~~l~~~~~~~g~~~~A~~~~~~~~~  550 (595)
                      .+..++.+|...|++++|.+.+++.++
T Consensus         3 ~~~~lg~~~~~~~~~~~A~~~~~~al~   29 (34)
T PF07719_consen    3 AWYYLGQAYYQLGNYEEAIEYFEKALE   29 (34)
T ss_dssp             HHHHHHHHHHHTT-HHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHhCCHHHHHHHHHHHHH
Confidence            344555555555666666655555554

It mediates protein-protein interactions and the assembly of multiprotein complexes []. The TPR motif consists of 3-16 tandem-repeats of 34 amino acids residues, although individual TPR motifs can be dispersed in the protein sequence. Sequence alignment of the TPR domains reveals a consensus sequence defined by a pattern of small and large amino acids. TPR motifs have been identified in various different organisms, ranging from bacteria to humans. Proteins containing TPRs are involved in a variety of biological processes, such as cell cycle regulation, transcriptional control, mitochondrial and peroxisomal protein transport, neurogenesis and protein folding. This repeat includes outlying Tetratricopeptide-like repeats (TPR) that are not matched by IPR001440 from INTERPRO.; PDB: 1XNF_B 3Q15_A 4ABN_A 1OUV_A 3U4T_A 3MA5_C 2KCV_A 2KCL_A 2XEV_A 3NF1_A ....

>KOG2396 consensus HAT (Half-A-TPR) repeat-containing protein [General function prediction only]

Probab=92.03  E-value=13  Score=36.44  Aligned_cols=80  Identities=15%  Similarity=0.040  Sum_probs=60.9

Q ss_pred             CCCCHHHHHHHHHHHHhcCChhHHHHHHHHHHhCCCCCCHHHHHHHHHHHHh-cCCHhHHHHHHHHHHhcCCCCCHhhHH
Q 040027           92 LFPNLYTYNILINCFCKIGRVSLGFIAFGRILRSCFTPNAATFNSLIKGLHA-ESRIMEAAALFTKLKAFGCEPNVITYN  170 (595)
Q Consensus        92 ~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~~l~~~~~~-~g~~~~A~~~~~~~~~~~~~~~~~~~~  170 (595)
                      ...|+..|...+..+.+.+.+.+...+|.+|+... +.++..|-........ +-+++.|..+|.+.++.+.. ++..|.
T Consensus       101 f~~D~~lW~~yi~f~kk~~~~~~v~ki~~~~l~~H-p~~~dLWI~aA~wefe~n~ni~saRalflrgLR~npd-sp~Lw~  178 (568)
T KOG2396|consen  101 FNGDVKLWLSYIAFCKKKKTYGEVKKIFAAMLAKH-PNNPDLWIYAAKWEFEINLNIESARALFLRGLRFNPD-SPKLWK  178 (568)
T ss_pred             cCCCHHHHHHHHHHHHHhcchhHHHHHHHHHHHhC-CCCchhHHhhhhhHHhhccchHHHHHHHHHHhhcCCC-ChHHHH
Confidence            44599999999999999999999999999999885 5677777666555444 44599999999999887422 455554


Q ss_pred             HHH
Q 040027          171 TLI  173 (595)
Q Consensus       171 ~l~  173 (595)
                      ..+
T Consensus       179 eyf  181 (568)
T KOG2396|consen  179 EYF  181 (568)
T ss_pred             HHH
Confidence            433

>PF09205 DUF1955: Domain of unknown function (DUF1955); InterPro: IPR015288 Members of this family are found in hypothetical proteins synthesised by the Archaeal organism Sulfolobus

Probab=91.93  E-value=5  Score=31.41  Aligned_cols=65  Identities=15%  Similarity=0.306  Sum_probs=34.5

Q ss_pred             HHHHHHHHHHHhcCChhHHHHHHHHHHHcCCCCCHHHHHHHHHHHHHcCChhHHHHHHHHHHHCCC
Q 040027          488 VTYNIMIQGLCNDGQMDKARDLFLDMEENAAAPDVITFDMLIHGFIRINEPSKVNELLHKMKEKKV  553 (595)
Q Consensus       488 ~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~  553 (595)
                      ..+...+......|+-++-.+++..+.+.+ .+++.....+..+|.+.|+..++.++++++-+.|+
T Consensus        87 e~vD~ALd~lv~~~kkDqLdki~~~l~kn~-~~~p~~L~kia~Ay~klg~~r~~~ell~~ACekG~  151 (161)
T PF09205_consen   87 EYVDLALDILVKQGKKDQLDKIYNELKKNE-EINPEFLVKIANAYKKLGNTREANELLKEACEKGL  151 (161)
T ss_dssp             HHHHHHHHHHHHTT-HHHHHHHHHHH------S-HHHHHHHHHHHHHTT-HHHHHHHHHHHHHTT-
T ss_pred             HHHHHHHHHHHHhccHHHHHHHHHHHhhcc-CCCHHHHHHHHHHHHHhcchhhHHHHHHHHHHhch
Confidence            334444555556666666666666655432 55666666666666666666666666666666653

Their exact function has not, as yet, been determined. ; PDB: 1WY6_A.

>KOG3941 consensus Intermediate in Toll signal transduction pathway (ECSIT) [Signal transduction mechanisms]

Probab=91.79  E-value=1.9  Score=38.47  Aligned_cols=35  Identities=17%  Similarity=0.219  Sum_probs=30.9

Q ss_pred             hHHHHHHHHHHhcCCCCCHhhHHHHHHHHHhcCCh
Q 040027          148 MEAAALFTKLKAFGCEPNVITYNTLINGLCRTGHT  182 (595)
Q Consensus       148 ~~A~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~  182 (595)
                      +-+++++++|...|+.||.++-..|+.++.+.+-.
T Consensus       140 ~C~I~vLeqME~hGVmPdkE~e~~lvn~FGr~~~p  174 (406)
T KOG3941|consen  140 NCAIKVLEQMEWHGVMPDKEIEDILVNAFGRWNFP  174 (406)
T ss_pred             hHHHHHHHHHHHcCCCCchHHHHHHHHHhcccccc
Confidence            45889999999999999999999999999877653

>KOG4234 consensus TPR repeat-containing protein [General function prediction only]

Probab=91.74  E-value=2.4  Score=35.77  Aligned_cols=55  Identities=11%  Similarity=0.021  Sum_probs=23.2

Q ss_pred             HHHHhcCChhHHHHHHHHHHHcCCCCCHHHHHHHHHHHHHcCChhHHHHHHHHHHH
Q 040027          495 QGLCNDGQMDKARDLFLDMEENAAAPDVITFDMLIHGFIRINEPSKVNELLHKMKE  550 (595)
Q Consensus       495 ~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~  550 (595)
                      .++.+.+.++.|++-..++++.+ +-....+..-..+|.+..++++|+.-|+++++
T Consensus       142 aa~iKl~k~e~aI~dcsKaiel~-pty~kAl~RRAeayek~ek~eealeDyKki~E  196 (271)
T KOG4234|consen  142 AALIKLRKWESAIEDCSKAIELN-PTYEKALERRAEAYEKMEKYEEALEDYKKILE  196 (271)
T ss_pred             HHHHHhhhHHHHHHHHHhhHhcC-chhHHHHHHHHHHHHhhhhHHHHHHHHHHHHH
Confidence            34444444444444444444432 11122222333344444444444444444444

>COG3947 Response regulator containing CheY-like receiver and SARP domains [Signal transduction mechanisms]

Probab=91.72  E-value=9.9  Score=34.39  Aligned_cols=72  Identities=11%  Similarity=0.049  Sum_probs=58.4

Q ss_pred             HHHHHHHHHHhcCChhHHHHHHHHHHHcCCCCCHHHHHHHHHHHHHcCChhHHHHHHHHHH-----HCCCCCCHHHHH
Q 040027          489 TYNIMIQGLCNDGQMDKARDLFLDMEENAAAPDVITFDMLIHGFIRINEPSKVNELLHKMK-----EKKVMPDASIVS  561 (595)
Q Consensus       489 ~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~-----~~~~~p~~~~~~  561 (595)
                      ++......|..+|.+.+|.++.++.+..+ +.+...+..++..+...|+--.+.+-++++.     +.|+..|..++.
T Consensus       281 llgkva~~yle~g~~neAi~l~qr~ltld-pL~e~~nk~lm~~la~~gD~is~~khyerya~vleaelgi~vddsiee  357 (361)
T COG3947         281 LLGKVARAYLEAGKPNEAIQLHQRALTLD-PLSEQDNKGLMASLATLGDEISAIKHYERYAEVLEAELGIDVDDSIEE  357 (361)
T ss_pred             HHHHHHHHHHHcCChHHHHHHHHHHhhcC-hhhhHHHHHHHHHHHHhccchhhhhHHHHHHHHHHHHhCCCcchhHHH
Confidence            34555678889999999999999999875 6778888999999999999888888888775     457777766554

>KOG4234 consensus TPR repeat-containing protein [General function prediction only]

Probab=91.19  E-value=5.3  Score=33.82  Aligned_cols=94  Identities=12%  Similarity=0.048  Sum_probs=72.6

Q ss_pred             HHHHHHhcCChhHHHHHHHHHHhCCCCCCH----HHHHHHHHHHHhcCCHhHHHHHHHHHHhcCCCCCHhhHHHHHHHHH
Q 040027          102 LINCFCKIGRVSLGFIAFGRILRSCFTPNA----ATFNSLIKGLHAESRIMEAAALFTKLKAFGCEPNVITYNTLINGLC  177 (595)
Q Consensus       102 l~~~~~~~g~~~~A~~~~~~~~~~~~~~~~----~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~~l~~~~~  177 (595)
                      =..-++..|++++|..-|.+++...++...    ..|..-..++.+.+.++.|+.-..+.++.+.. ...+...-..+|.
T Consensus       101 EGN~~F~ngdyeeA~skY~~Ale~cp~~~~e~rsIly~Nraaa~iKl~k~e~aI~dcsKaiel~pt-y~kAl~RRAeaye  179 (271)
T KOG4234|consen  101 EGNELFKNGDYEEANSKYQEALESCPSTSTEERSILYSNRAAALIKLRKWESAIEDCSKAIELNPT-YEKALERRAEAYE  179 (271)
T ss_pred             HHHHhhhcccHHHHHHHHHHHHHhCccccHHHHHHHHhhhHHHHHHhhhHHHHHHHHHhhHhcCch-hHHHHHHHHHHHH
Confidence            345678899999999999999998533222    23555567788999999999999999887633 4444455567888


Q ss_pred             hcCChhHHHHHHHHHHhcC
Q 040027          178 RTGHTMIALNLFEEMANGN  196 (595)
Q Consensus       178 ~~g~~~~A~~~~~~~~~~~  196 (595)
                      +...+++|++-|.++...+
T Consensus       180 k~ek~eealeDyKki~E~d  198 (271)
T KOG4234|consen  180 KMEKYEEALEDYKKILESD  198 (271)
T ss_pred             hhhhHHHHHHHHHHHHHhC
Confidence            8999999999999999865

>PF07719 TPR_2: Tetratricopeptide repeat; InterPro: IPR013105 The tetratrico peptide repeat (TPR) is a structural motif present in a wide range of proteins [, , ]

Probab=90.59  E-value=0.7  Score=26.12  Aligned_cols=28  Identities=14%  Similarity=0.268  Sum_probs=15.3

Q ss_pred             HHHHHHHHHHhcCChhHHHHHHHHHHhC
Q 040027           98 TYNILINCFCKIGRVSLGFIAFGRILRS  125 (595)
Q Consensus        98 ~~~~l~~~~~~~g~~~~A~~~~~~~~~~  125 (595)
                      .|..+...+...|++++|+..|+++++.
T Consensus         3 ~~~~lg~~~~~~~~~~~A~~~~~~al~l   30 (34)
T PF07719_consen    3 AWYYLGQAYYQLGNYEEAIEYFEKALEL   30 (34)
T ss_dssp             HHHHHHHHHHHTT-HHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHhCCHHHHHHHHHHHHHH
Confidence            4445555555566666666666655544

It mediates protein-protein interactions and the assembly of multiprotein complexes []. The TPR motif consists of 3-16 tandem-repeats of 34 amino acids residues, although individual TPR motifs can be dispersed in the protein sequence. Sequence alignment of the TPR domains reveals a consensus sequence defined by a pattern of small and large amino acids. TPR motifs have been identified in various different organisms, ranging from bacteria to humans. Proteins containing TPRs are involved in a variety of biological processes, such as cell cycle regulation, transcriptional control, mitochondrial and peroxisomal protein transport, neurogenesis and protein folding. This repeat includes outlying Tetratricopeptide-like repeats (TPR) that are not matched by IPR001440 from INTERPRO.; PDB: 1XNF_B 3Q15_A 4ABN_A 1OUV_A 3U4T_A 3MA5_C 2KCV_A 2KCL_A 2XEV_A 3NF1_A ....

>COG1747 Uncharacterized N-terminal domain of the transcription elongation factor GreA [Function unknown]

Probab=90.39  E-value=19  Score=35.42  Aligned_cols=217  Identities=12%  Similarity=0.114  Sum_probs=141.0

Q ss_pred             CCCChHHHHHHHHHHHHhCCCCCCHhhHHHHHHHHHcCCCchhHHhhCCCCCCHHHHHHHHHHHHhcCChhHHHHHHHHH
Q 040027           43 NVITPNEAFCIFDYMLRMHPSPPPVSSFNILLASLAKNKHYDTRLNATGLFPNLYTYNILINCFCKIGRVSLGFIAFGRI  122 (595)
Q Consensus        43 ~~~~~~~A~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~  122 (595)
                      +++-.+....+.++.+....+ .-...|-.-+..|.+.            ..|-....+++..+.+...+.-...+..++
T Consensus        26 ~~~~~~~~~~ic~~hl~~~k~-si~~lyisg~~~~s~~------------~l~d~~l~~~~~~f~~n~k~~~veh~c~~~   92 (711)
T COG1747          26 RQSILDVLKGICDEHLAHSKN-SIIALYISGIISLSKQ------------LLDDSCLVTLLTIFGDNHKNQIVEHLCTRV   92 (711)
T ss_pred             HhhHHHHHHHHHHHHHHHhhh-hhHHHHHHHHHHhhhc------------cccchHHHHHHHHhccchHHHHHHHHHHHH
Confidence            445555556666666655444 1223333333333333            235566778889999988999999999999


Q ss_pred             HhCCCCCCHHHHHHHHHHHHhcCCHhHHHHHHHHHHhcCCCCCHhhHHHHHHHHHhcCChhHHHHHHHHHHhcCCCCCcc
Q 040027          123 LRSCFTPNAATFNSLIKGLHAESRIMEAAALFTKLKAFGCEPNVITYNTLINGLCRTGHTMIALNLFEEMANGNGEIGVV  202 (595)
Q Consensus       123 ~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~~~~  202 (595)
                      +.-|  .+--.+..++..|..+ ..+.-..+|+++.+..+. |...-..|+..|.+ ++.+.+...|.++..+-      
T Consensus        93 l~~~--e~kmal~el~q~y~en-~n~~l~~lWer~ve~dfn-Dvv~~ReLa~~yEk-ik~sk~a~~f~Ka~yrf------  161 (711)
T COG1747          93 LEYG--ESKMALLELLQCYKEN-GNEQLYSLWERLVEYDFN-DVVIGRELADKYEK-IKKSKAAEFFGKALYRF------  161 (711)
T ss_pred             HHhc--chHHHHHHHHHHHHhc-CchhhHHHHHHHHHhcch-hHHHHHHHHHHHHH-hchhhHHHHHHHHHHHh------
Confidence            9874  4667788899999988 557888999999988654 55555666666655 88889999998887653      


Q ss_pred             ccC--c---HHHHHHHHHHHHHcCCHhHHHHHHHHHhhC-CCCCCHhHHHHHHHHHHhcCCHHHHHHHHHHHHHCCCCCC
Q 040027          203 CKP--N---TVTYSTIIDGLCKEGFVDKAKALFLQMKDE-NINPDVVTYNSLIHGLCHANDWNEAKRLFIEMMDQGVQPS  276 (595)
Q Consensus       203 ~~~--~---~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~-~~~~~~~~~~~ll~~~~~~~~~~~A~~~~~~~~~~~~~~~  276 (595)
                      ++.  +   ...|..+...-  ..+.+....+..++... |...-...+.-+-.-|....++.+|++++..+++..-+ |
T Consensus       162 I~~~q~~~i~evWeKL~~~i--~dD~D~fl~l~~kiqt~lg~~~~~Vl~qdv~~~Ys~~eN~~eai~Ilk~il~~d~k-~  238 (711)
T COG1747         162 IPRRQNAAIKEVWEKLPELI--GDDKDFFLRLQKKIQTKLGEGRGSVLMQDVYKKYSENENWTEAIRILKHILEHDEK-D  238 (711)
T ss_pred             cchhhhhhHHHHHHHHHHhc--cccHHHHHHHHHHHHHhhccchHHHHHHHHHHHhccccCHHHHHHHHHHHhhhcch-h
Confidence            221  1   23455554322  34667777777666553 22223444555556788889999999999988876432 4


Q ss_pred             HhhHHHHHHH
Q 040027          277 VVTFNVIMDE  286 (595)
Q Consensus       277 ~~~~~~l~~~  286 (595)
                      ..+-..++..
T Consensus       239 ~~ar~~~i~~  248 (711)
T COG1747         239 VWARKEIIEN  248 (711)
T ss_pred             hhHHHHHHHH
Confidence            4444444443

>PF13170 DUF4003: Protein of unknown function (DUF4003)

Probab=90.36  E-value=15  Score=34.15  Aligned_cols=135  Identities=13%  Similarity=0.159  Sum_probs=81.8

Q ss_pred             HhHHHHHHHHHhhCCCCCCHhHHHHHHHHHHh--cC----CHHHHHHHHHHHHHCCC---CCCHhhHHHHHHHHHhcCCh
Q 040027          223 VDKAKALFLQMKDENINPDVVTYNSLIHGLCH--AN----DWNEAKRLFIEMMDQGV---QPSVVTFNVIMDELCKNRKM  293 (595)
Q Consensus       223 ~~~A~~~~~~~~~~~~~~~~~~~~~ll~~~~~--~~----~~~~A~~~~~~~~~~~~---~~~~~~~~~l~~~~~~~g~~  293 (595)
                      +++...+++.+.+.|+.-+..+|.+.......  ..    ....+..+|+.|.+...   .++...+..++..  ..++.
T Consensus        78 ~~~~~~~y~~L~~~gFk~~~y~~laA~~i~~~~~~~~~~~~~~ra~~iy~~mKk~H~fLTs~~D~~~a~lLA~--~~~~~  155 (297)
T PF13170_consen   78 FKEVLDIYEKLKEAGFKRSEYLYLAALIILEEEEKEDYDEIIQRAKEIYKEMKKKHPFLTSPEDYPFAALLAM--TSEDV  155 (297)
T ss_pred             HHHHHHHHHHHHHhccCccChHHHHHHHHHHhcccccHHHHHHHHHHHHHHHHHhCccccCccchhHHHHHhc--ccccH
Confidence            34556788889999888777666553333332  22    35678999999988631   2344455555433  33333


Q ss_pred             ----HHHHHHHHHHHHCCCCCCHH--HHHHHHHHHHhcCC--HHHHHHHHHHHHhcCCCCCHHHHHHHHHHHHh
Q 040027          294 ----DEASRLLDLMVQRGVRPNAC--TYNTLMDGFCLMGK--INRAEELFGSMESMGCKHDDVSYNILINGYCK  359 (595)
Q Consensus       294 ----~~a~~~~~~~~~~~~~~~~~--~~~~l~~~~~~~~~--~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~  359 (595)
                          +.+..+|+.+.+.|...+-.  ....++........  ...+..+++.+.+.+++.....|..+.-...-
T Consensus       156 e~l~~~~E~~Y~~L~~~~f~kgn~LQ~LS~iLaL~~~~~~~~v~r~~~l~~~l~~~~~kik~~~yp~lGlLall  229 (297)
T PF13170_consen  156 EELAERMEQCYQKLADAGFKKGNDLQFLSHILALSEGDDQEKVARVIELYNALKKNGVKIKYMHYPTLGLLALL  229 (297)
T ss_pred             HHHHHHHHHHHHHHHHhCCCCCcHHHHHHHHHHhccccchHHHHHHHHHHHHHHHcCCccccccccHHHHHHhc
Confidence                56778888888877664432  22222222221111  45788889999999988877776665544333

>PF00515 TPR_1: Tetratricopeptide repeat; InterPro: IPR001440 The tetratrico peptide repeat (TPR) is a structural motif present in a wide range of proteins [, , ]

Probab=90.32  E-value=0.78  Score=26.03  Aligned_cols=29  Identities=21%  Similarity=0.282  Sum_probs=16.6

Q ss_pred             HHHHHHHHHHHhcCChhHHHHHHHHHHhC
Q 040027           97 YTYNILINCFCKIGRVSLGFIAFGRILRS  125 (595)
Q Consensus        97 ~~~~~l~~~~~~~g~~~~A~~~~~~~~~~  125 (595)
                      .+|..++..+...|++++|+..|+++++.
T Consensus         2 ~~~~~~g~~~~~~~~~~~A~~~~~~al~~   30 (34)
T PF00515_consen    2 EAYYNLGNAYFQLGDYEEALEYYQRALEL   30 (34)
T ss_dssp             HHHHHHHHHHHHTT-HHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHhCCchHHHHHHHHHHHH
Confidence            34555566666666666666666666554

It mediates protein-protein interactions and the assembly of multiprotein complexes []. The TPR motif consists of 3-16 tandem-repeats of 34 amino acids residues, although individual TPR motifs can be dispersed in the protein sequence. Sequence alignment of the TPR domains reveals a consensus sequence defined by a pattern of small and large amino acids. TPR motifs have been identified in various different organisms, ranging from bacteria to humans. Proteins containing TPRs are involved in a variety of biological processes, such as cell cycle regulation, transcriptional control, mitochondrial and peroxisomal protein transport, neurogenesis and protein folding. The X-ray structure of a domain containing three TPRs from protein phosphatase 5 revealed that TPR adopts a helix-turn-helix arrangement, with adjacent TPR motifs packing in a parallel fashion, resulting in a spiral of repeating anti-parallel alpha-helices []. The two helices are denoted helix A and helix B. The packing angle between helix A and helix B is ~24 degrees; within a single TPR and generates a right-handed superhelical shape. Helix A interacts with helix B and with helix A' of the next TPR. Two protein surfaces are generated: the inner concave surface is contributed to mainly by residue on helices A, and the other surface presents residues from both helices A and B. ; GO: 0005515 protein binding; PDB: 3SF4_C 2LNI_A 1ELW_A 2C0M_A 1FCH_B 3R9A_B 2J9Q_A 2C0L_A 1KT1_A 3FWV_A ....

>PF08424 NRDE-2: NRDE-2, necessary for RNA interference; InterPro: IPR013633 This is domain is found in eukaryotic proteins of unknown function

Probab=90.30  E-value=17  Score=34.52  Aligned_cols=121  Identities=7%  Similarity=-0.025  Sum_probs=78.6

Q ss_pred             HHHHHHHHhCCCCCCHhhHHHHHHHHHcCCCchhHHhhCCCCCCHHHHHHHHHHHHhcCChhHHHHHHHHHHhCCCCCCH
Q 040027           52 CIFDYMLRMHPSPPPVSSFNILLASLAKNKHYDTRLNATGLFPNLYTYNILINCFCKIGRVSLGFIAFGRILRSCFTPNA  131 (595)
Q Consensus        52 ~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~~~  131 (595)
                      .-|++.++.+|.  |+.+|-.++.---..-....         +.        .-....-.+.-+.+++++++.+ +.+.
T Consensus         6 ~el~~~v~~~P~--di~~Wl~li~~Qd~~~~~~~---------~~--------~~~~~a~~E~klsilerAL~~n-p~~~   65 (321)
T PF08424_consen    6 AELNRRVRENPH--DIEAWLELIEFQDELFRLQS---------SS--------KAERRALAERKLSILERALKHN-PDSE   65 (321)
T ss_pred             HHHHHHHHhCcc--cHHHHHHHHHHHHHhccccc---------cc--------hhhHHHHHHHHHHHHHHHHHhC-CCCH
Confidence            567888999998  99999888854322211110         00        1111223456678888888884 4677


Q ss_pred             HHHHHHHHHHHhcCCHhHHHHHHHHHHhcCCCCCHhhHHHHHHHHHh---cCChhHHHHHHHHHH
Q 040027          132 ATFNSLIKGLHAESRIMEAAALFTKLKAFGCEPNVITYNTLINGLCR---TGHTMIALNLFEEMA  193 (595)
Q Consensus       132 ~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~~l~~~~~~---~g~~~~A~~~~~~~~  193 (595)
                      ..+..++..+.+.-+.++..+.++++.... +-+...|...+.....   .-.++....+|.+..
T Consensus        66 ~L~l~~l~~~~~~~~~~~l~~~we~~l~~~-~~~~~LW~~yL~~~q~~~~~f~v~~~~~~y~~~l  129 (321)
T PF08424_consen   66 RLLLGYLEEGEKVWDSEKLAKKWEELLFKN-PGSPELWREYLDFRQSNFASFTVSDVRDVYEKCL  129 (321)
T ss_pred             HHHHHHHHHHHHhCCHHHHHHHHHHHHHHC-CCChHHHHHHHHHHHHHhccCcHHHHHHHHHHHH
Confidence            778888888888888888889999998873 3367777777665543   224555555555544

>TIGR02561 HrpB1_HrpK type III secretion protein HrpB1/HrpK

Probab=90.18  E-value=7.8  Score=31.21  Aligned_cols=50  Identities=16%  Similarity=-0.005  Sum_probs=20.9

Q ss_pred             cCCHHHHHHHHHHHHHcCCCcCHHHHHHHHHHHHhcCChHHHHHHHHhccc
Q 040027          430 NGYIIEAVELFRTLRILKCELDIQAYNCLIDGLCKSGRLKFAWELFCSLPH  480 (595)
Q Consensus       430 ~g~~~~A~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~  480 (595)
                      .++++++..++..+.-.. |.....-..-+..+...|++++|.++|+++.+
T Consensus        23 ~~d~~D~e~lLdALrvLr-P~~~e~d~~dg~l~i~rg~w~eA~rvlr~l~~   72 (153)
T TIGR02561        23 SADPYDAQAMLDALRVLR-PNLKELDMFDGWLLIARGNYDEAARILRELLS   72 (153)
T ss_pred             cCCHHHHHHHHHHHHHhC-CCccccchhHHHHHHHcCCHHHHHHHHHhhhc
Confidence            445555555555444332 11122222222333444555555555555444

This gene is found within type III secretion operons in a limited range of species including Xanthomonas, Ralstonia and Burkholderia.

>KOG2471 consensus TPR repeat-containing protein [General function prediction only]

Probab=90.15  E-value=20  Score=35.13  Aligned_cols=111  Identities=12%  Similarity=0.014  Sum_probs=75.7

Q ss_pred             HHHHhcCChHHHHHHHHhccc---CC--CCCC---HHHHHHHHHHHHhcCChhHHHHHHHHHHH-------cCCCCC---
Q 040027          460 DGLCKSGRLKFAWELFCSLPH---GV--LVPN---VVTYNIMIQGLCNDGQMDKARDLFLDMEE-------NAAAPD---  521 (595)
Q Consensus       460 ~~~~~~g~~~~A~~~~~~~~~---~~--~~p~---~~~~~~l~~~~~~~g~~~~A~~~~~~~~~-------~~~~~~---  521 (595)
                      ..+...|++.+|.+++...--   .|  +.|.   -..||.|...+.+.|.+.-+..+|.++++       .|+.|.   
T Consensus       248 q~eY~~gn~~kA~KlL~~sni~~~~g~~~T~q~~~cif~NNlGcIh~~~~~y~~~~~~F~kAL~N~c~qL~~g~~~~~~~  327 (696)
T KOG2471|consen  248 QLEYAHGNHPKAMKLLLVSNIHKEAGGTITPQLSSCIFNNNLGCIHYQLGCYQASSVLFLKALRNSCSQLRNGLKPAKTF  327 (696)
T ss_pred             HHHHHhcchHHHHHHHHhcccccccCccccchhhhheeecCcceEeeehhhHHHHHHHHHHHHHHHHHHHhccCCCCcce
Confidence            345567888888888765422   11  2221   23457777777778888888888877764       243332   


Q ss_pred             -------HHHHHHHHHHHHHcCChhHHHHHHHHHHHCCCCCCHHHHHHHHHHHHhcC
Q 040027          522 -------VITFDMLIHGFIRINEPSKVNELLHKMKEKKVMPDASIVSIVVDLLVKNE  571 (595)
Q Consensus       522 -------~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~p~~~~~~~l~~~~~~~g  571 (595)
                             ..+.....-.|...|++-.|.+.|.+.... +..++..|-.+..+|..+.
T Consensus       328 tls~nks~eilYNcG~~~Lh~grPl~AfqCf~~av~v-fh~nPrlWLRlAEcCima~  383 (696)
T KOG2471|consen  328 TLSQNKSMEILYNCGLLYLHSGRPLLAFQCFQKAVHV-FHRNPRLWLRLAECCIMAL  383 (696)
T ss_pred             ehhcccchhhHHhhhHHHHhcCCcHHHHHHHHHHHHH-HhcCcHHHHHHHHHHHHHh
Confidence                   223344566788999999999999998864 5678899999999887643

>PF07035 Mic1: Colon cancer-associated protein Mic1-like; InterPro: IPR009755 This entry represents the C terminus (approximately 160 residues) of a number of proteins that resemble colon cancer-associated protein Mic1

Probab=90.07  E-value=10  Score=31.59  Aligned_cols=35  Identities=23%  Similarity=0.214  Sum_probs=18.1

Q ss_pred             HHHHHhcCCCCCHhhHHHHHHHHHhcCChhHHHHH
Q 040027          154 FTKLKAFGCEPNVITYNTLINGLCRTGHTMIALNL  188 (595)
Q Consensus       154 ~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~  188 (595)
                      .+.+...+++++...+..++..+.+.|++.....+
T Consensus        17 irSl~~~~i~~~~~L~~lli~lLi~~~~~~~L~ql   51 (167)
T PF07035_consen   17 IRSLNQHNIPVQHELYELLIDLLIRNGQFSQLHQL   51 (167)
T ss_pred             HHHHHHcCCCCCHHHHHHHHHHHHHcCCHHHHHHH
Confidence            34444445555555555555555555554444333

>PRK11619 lytic murein transglycosylase; Provisional

Probab=89.90  E-value=28  Score=36.59  Aligned_cols=135  Identities=12%  Similarity=-0.029  Sum_probs=62.4

Q ss_pred             ccccCCCChHHHHHHHHHHHHhCCCCCCHhhHHHHHHHHHcCCCchh---HHhhC-CCCCCHHHHHHHHHHHHhcCChhH
Q 040027           39 EGDINVITPNEAFCIFDYMLRMHPSPPPVSSFNILLASLAKNKHYDT---RLNAT-GLFPNLYTYNILINCFCKIGRVSL  114 (595)
Q Consensus        39 ~~~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~---~~~~~-~~~~~~~~~~~l~~~~~~~g~~~~  114 (595)
                      ...++.|++..+..+-..+ +..|- ..-..|..+...+. ...+++   .+... +.+.....-...+..+.+.+++..
T Consensus        41 ~~a~~~g~~~~~~~~~~~l-~d~pL-~~yl~y~~L~~~l~-~~~~~ev~~Fl~~~~~~P~~~~Lr~~~l~~La~~~~w~~  117 (644)
T PRK11619         41 KQAWDNRQMDVVEQLMPTL-KDYPL-YPYLEYRQLTQDLM-NQPAVQVTNFIRANPTLPPARSLQSRFVNELARREDWRG  117 (644)
T ss_pred             HHHHHCCCHHHHHHHHHhc-cCCCc-HhHHHHHHHHhccc-cCCHHHHHHHHHHCCCCchHHHHHHHHHHHHHHccCHHH
Confidence            3346677777776655544 23332 22233433333222 222333   12221 222233333444445555566665


Q ss_pred             HHHHHHHHHhCCCCCCHHHHHHHHHHHHhcCCHhHHHHHHHHHHhcCCCCCHhhHHHHHHHHHhcCCh
Q 040027          115 GFIAFGRILRSCFTPNAATFNSLIKGLHAESRIMEAAALFTKLKAFGCEPNVITYNTLINGLCRTGHT  182 (595)
Q Consensus       115 A~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~  182 (595)
                      .+..+.    . .+.+.......+.+....|+.++|.+..+.+-..|.. .+.....++..+.+.|..
T Consensus       118 ~~~~~~----~-~p~~~~~~c~~~~A~~~~G~~~~A~~~a~~lW~~g~~-~p~~cd~l~~~~~~~g~l  179 (644)
T PRK11619        118 LLAFSP----E-KPKPVEARCNYYYAKWATGQQQEAWQGAKELWLTGKS-LPNACDKLFSVWQQSGKQ  179 (644)
T ss_pred             HHHhcC----C-CCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHhccCCC-CChHHHHHHHHHHHcCCC
Confidence            554221    1 1334444455566666667666666555555444422 344555555555544433

>PF07575 Nucleopor_Nup85: Nup85 Nucleoporin; InterPro: IPR011502 This is a family of nucleoporins conserved from yeast to human

Probab=89.61  E-value=28  Score=36.15  Aligned_cols=25  Identities=12%  Similarity=0.157  Sum_probs=14.4

Q ss_pred             HHHHHHHHHHHHhcCCHhHHHHHHHH
Q 040027          131 AATFNSLIKGLHAESRIMEAAALFTK  156 (595)
Q Consensus       131 ~~~~~~l~~~~~~~g~~~~A~~~~~~  156 (595)
                      +.-|+ .+..+.-+|.+++|.+++..
T Consensus       149 p~FW~-~v~~lvlrG~~~~a~~lL~~  173 (566)
T PF07575_consen  149 PDFWD-YVQRLVLRGLFDQARQLLRL  173 (566)
T ss_dssp             HHHHH-HHHHHHHTT-HHHHHHHH-T
T ss_pred             hhHHH-HHHHHHHcCCHHHHHHHHHh
Confidence            33443 56666677777777777643

Nup85 Nucleoporin is an essential component of the nuclear pore complex (NPC) that seems to be required for NPC assembly and maintenance. As part of the NPC Nup107-160 subcomplex plays a role in RNA export and in tethering NUP98/Nup98 and NUP153 to the nucleus. The Nup107-160 complex seems to be required for spindle assembly during mitosis. NUP85 is required for membrane clustering of CCL2-activated CCR2. Seems to be involved in CCR2-mediated chemotaxis of monocytes and may link activated CCR2 to the phosphatidyl-inositol-3-kinase-Rac-lammellipodium protrusion cascade [, , ]. ; PDB: 3F3F_D 3F3P_G 3F3G_G 3EWE_B.

>PF09613 HrpB1_HrpK: Bacterial type III secretion protein (HrpB1_HrpK); InterPro: IPR013394 This family of proteins is encoded by genes found within type III secretion operons in a limited range of species including Xanthomonas, Ralstonia and Burkholderia

Probab=89.46  E-value=11  Score=31.02  Aligned_cols=53  Identities=19%  Similarity=-0.031  Sum_probs=34.4

Q ss_pred             HhcCCHHHHHHHHHHHHHcCCCcCHHHHHHHHHHHHhcCChHHHHHHHHhcccC
Q 040027          428 CKNGYIIEAVELFRTLRILKCELDIQAYNCLIDGLCKSGRLKFAWELFCSLPHG  481 (595)
Q Consensus       428 ~~~g~~~~A~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~  481 (595)
                      .+.++.+++..++..+.-.. |.....-..-+..+...|++.+|+.+|+.+.+.
T Consensus        21 l~~~~~~D~e~lL~ALrvLR-P~~~e~~~~~~~l~i~r~~w~dA~rlLr~l~~~   73 (160)
T PF09613_consen   21 LRLGDPDDAEALLDALRVLR-PEFPELDLFDGWLHIVRGDWDDALRLLRELEER   73 (160)
T ss_pred             HccCChHHHHHHHHHHHHhC-CCchHHHHHHHHHHHHhCCHHHHHHHHHHHhcc
Confidence            45677777887777776553 323333333445566778888888888887663

>PF02259 FAT: FAT domain; InterPro: IPR003151 The FAT domain is a domain present in the PIK-related kinases

Probab=89.22  E-value=22  Score=34.26  Aligned_cols=53  Identities=13%  Similarity=0.322  Sum_probs=29.3

Q ss_pred             HHHHHhcCCHHHHHHHHHHHHHCCCCCCHhhHHHHHHHHHhcCChHHHHHHHHHHHH
Q 040027          249 IHGLCHANDWNEAKRLFIEMMDQGVQPSVVTFNVIMDELCKNRKMDEASRLLDLMVQ  305 (595)
Q Consensus       249 l~~~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~  305 (595)
                      ..+.-+.|+|+...+........  .++...+..+..  ...++++++....+.+..
T Consensus         5 ~eaaWrl~~Wd~l~~~~~~~~~~--~~~~~~~~al~~--l~~~~~~~~~~~i~~~r~   57 (352)
T PF02259_consen    5 AEAAWRLGDWDLLEEYLSQSNED--SPEYSFYRALLA--LRQGDYDEAKKYIEKARQ   57 (352)
T ss_pred             HHHHHhcCChhhHHHHHhhccCC--ChhHHHHHHHHH--HhCccHHHHHHHHHHHHH
Confidence            45667778888744444333221  123333333332  277888887777776655

Members of the family of PIK-related kinases may act as intracellular sensors that govern radial and horizontal pathways [].; GO: 0005515 protein binding

>PF02284 COX5A: Cytochrome c oxidase subunit Va; InterPro: IPR003204 Cytochrome c oxidase (1

Probab=89.19  E-value=6.9  Score=29.00  Aligned_cols=47  Identities=11%  Similarity=0.011  Sum_probs=23.8

Q ss_pred             HHHHHHHhcccCCCCCCHHHHHHHHHHHHhcCChhHHHHHHHHHHHc
Q 040027          470 FAWELFCSLPHGVLVPNVVTYNIMIQGLCNDGQMDKARDLFLDMEEN  516 (595)
Q Consensus       470 ~A~~~~~~~~~~~~~p~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~  516 (595)
                      +..+-++.+....+.|++.+..+.+.+|.+.+++..|+++|+-...+
T Consensus        28 e~rrglN~l~~~DlVP~P~ii~aALrAcRRvND~a~AVR~lE~iK~K   74 (108)
T PF02284_consen   28 ELRRGLNNLFGYDLVPEPKIIEAALRACRRVNDFALAVRILEGIKDK   74 (108)
T ss_dssp             HHHHHHHHHTTSSB---HHHHHHHHHHHHHTT-HHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHhccccCCChHHHHHHHHHHHHhhhHHHHHHHHHHHHHH
Confidence            34444455544455556655556666666666666666666555543

9.3.1 from EC) is an oligomeric enzymatic complex which is a component of the respiratory chain complex and is involved in the transfer of electrons from cytochrome c to oxygen []. In eukaryotes this enzyme complex is located in the mitochondrial inner membrane; in aerobic prokaryotes it is found in the plasma membrane. In eukaryotes, in addition to the three large subunits, I, II and III, that form the catalytic centre of the enzyme complex, there are a variable number of small polypeptidic subunits. One of these subunits is known as Va.; GO: 0004129 cytochrome-c oxidase activity; PDB: 2DYR_R 3AG1_E 3ABL_E 1V54_R 2EIJ_R 1OCR_E 2DYS_E 2EIM_E 2OCC_E 3ASN_R ....

>PF02284 COX5A: Cytochrome c oxidase subunit Va; InterPro: IPR003204 Cytochrome c oxidase (1

Probab=88.97  E-value=7.1  Score=28.95  Aligned_cols=62  Identities=15%  Similarity=0.194  Sum_probs=36.5

Q ss_pred             HHHHHHHHHHHcCCCCCHHHHHHHHHHHHHcCChhHHHHHHHHHHHCCCCCCHHHHHHHHHHH
Q 040027          505 KARDLFLDMEENAAAPDVITFDMLIHGFIRINEPSKVNELLHKMKEKKVMPDASIVSIVVDLL  567 (595)
Q Consensus       505 ~A~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~p~~~~~~~l~~~~  567 (595)
                      +..+-++.+...++-|++.+....+.+|.+.+++.-|.++++-...+ ..+...+|..+++-+
T Consensus        28 e~rrglN~l~~~DlVP~P~ii~aALrAcRRvND~a~AVR~lE~iK~K-~~~~~~~Y~~~lqEl   89 (108)
T PF02284_consen   28 ELRRGLNNLFGYDLVPEPKIIEAALRACRRVNDFALAVRILEGIKDK-CGNKKEIYPYILQEL   89 (108)
T ss_dssp             HHHHHHHHHTTSSB---HHHHHHHHHHHHHTT-HHHHHHHHHHHHHH-TTT-TTHHHHHHHHH
T ss_pred             HHHHHHHHHhccccCCChHHHHHHHHHHHHhhhHHHHHHHHHHHHHH-ccChHHHHHHHHHHH
Confidence            45555666666667777777777777777777777777777777643 122223666655543

9.3.1 from EC) is an oligomeric enzymatic complex which is a component of the respiratory chain complex and is involved in the transfer of electrons from cytochrome c to oxygen []. In eukaryotes this enzyme complex is located in the mitochondrial inner membrane; in aerobic prokaryotes it is found in the plasma membrane. In eukaryotes, in addition to the three large subunits, I, II and III, that form the catalytic centre of the enzyme complex, there are a variable number of small polypeptidic subunits. One of these subunits is known as Va.; GO: 0004129 cytochrome-c oxidase activity; PDB: 2DYR_R 3AG1_E 3ABL_E 1V54_R 2EIJ_R 1OCR_E 2DYS_E 2EIM_E 2OCC_E 3ASN_R ....

>COG2976 Uncharacterized protein conserved in bacteria [Function unknown]

Probab=88.90  E-value=13  Score=31.46  Aligned_cols=89  Identities=9%  Similarity=-0.019  Sum_probs=56.1

Q ss_pred             HHHHHhcCChHHHHHHHHhcccCCCCCCHHHH-----HHHHHHHHhcCChhHHHHHHHHHHHcCCCCCHHHHHHHHHHHH
Q 040027          459 IDGLCKSGRLKFAWELFCSLPHGVLVPNVVTY-----NIMIQGLCNDGQMDKARDLFLDMEENAAAPDVITFDMLIHGFI  533 (595)
Q Consensus       459 ~~~~~~~g~~~~A~~~~~~~~~~~~~p~~~~~-----~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~~l~~~~~  533 (595)
                      ...+...|++++|...++.....   |....+     ..|.+.....|.+++|+..++...+.+  ........-++++.
T Consensus        96 Ak~~ve~~~~d~A~aqL~~~l~~---t~De~lk~l~~lRLArvq~q~~k~D~AL~~L~t~~~~~--w~~~~~elrGDill  170 (207)
T COG2976          96 AKAEVEANNLDKAEAQLKQALAQ---TKDENLKALAALRLARVQLQQKKADAALKTLDTIKEES--WAAIVAELRGDILL  170 (207)
T ss_pred             HHHHHhhccHHHHHHHHHHHHcc---chhHHHHHHHHHHHHHHHHHhhhHHHHHHHHhcccccc--HHHHHHHHhhhHHH
Confidence            44566777777777777766642   222222     234456667777888877777665542  22333455567777


Q ss_pred             HcCChhHHHHHHHHHHHCC
Q 040027          534 RINEPSKVNELLHKMKEKK  552 (595)
Q Consensus       534 ~~g~~~~A~~~~~~~~~~~  552 (595)
                      ..|+-++|+.-|++.++.+
T Consensus       171 ~kg~k~~Ar~ay~kAl~~~  189 (207)
T COG2976         171 AKGDKQEARAAYEKALESD  189 (207)
T ss_pred             HcCchHHHHHHHHHHHHcc
Confidence            7888888888888887654

>PF00637 Clathrin: Region in Clathrin and VPS; InterPro: IPR000547 Proteins synthesized on the ribosome and processed in the endoplasmic reticulum are transported from the Golgi apparatus to the trans-Golgi network (TGN), and from there via small carrier vesicles to their final destination compartment

Probab=88.84  E-value=0.016  Score=47.38  Aligned_cols=83  Identities=13%  Similarity=0.062  Sum_probs=47.4

Q ss_pred             HHHHHHhcCCHHHHHHHHHHHHHcCCCcCHHHHHHHHHHHHhcCChHHHHHHHHhcccCCCCCCHHHHHHHHHHHHhcCC
Q 040027          423 FIDGLCKNGYIIEAVELFRTLRILKCELDIQAYNCLIDGLCKSGRLKFAWELFCSLPHGVLVPNVVTYNIMIQGLCNDGQ  502 (595)
Q Consensus       423 l~~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~p~~~~~~~l~~~~~~~g~  502 (595)
                      ++..+.+.+.+.....+++.+...+...+....+.++..|++.++.++..++++....  ..     ...++..|.+.|.
T Consensus        13 vi~~~~~~~~~~~l~~yLe~~~~~~~~~~~~~~~~L~~ly~~~~~~~~l~~~L~~~~~--yd-----~~~~~~~c~~~~l   85 (143)
T PF00637_consen   13 VISAFEERNQPEELIEYLEALVKENKENNPDLHTLLLELYIKYDPYEKLLEFLKTSNN--YD-----LDKALRLCEKHGL   85 (143)
T ss_dssp             CHHHCTTTT-GGGCTCCHHHHHHTSTC-SHHHHHHHHHHHHCTTTCCHHHHTTTSSSS--S------CTHHHHHHHTTTS
T ss_pred             HHHHHHhCCCHHHHHHHHHHHHhcccccCHHHHHHHHHHHHhcCCchHHHHHcccccc--cC-----HHHHHHHHHhcch
Confidence            3444555666666666777776555455567777777777777666776666663322  11     1234455555666


Q ss_pred             hhHHHHHHHH
Q 040027          503 MDKARDLFLD  512 (595)
Q Consensus       503 ~~~A~~~~~~  512 (595)
                      +++|.-++.+
T Consensus        86 ~~~a~~Ly~~   95 (143)
T PF00637_consen   86 YEEAVYLYSK   95 (143)
T ss_dssp             HHHHHHHHHC
T ss_pred             HHHHHHHHHH
Confidence            6666555554

These vesicles have specific coat proteins (such as clathrin or coatomer) that are important for cargo selection and direction of transport []. Clathrin coats contain both clathrin (acts as a scaffold) and adaptor complexes that link clathrin to receptors in coated vesicles. Clathrin-associated protein complexes are believed to interact with the cytoplasmic tails of membrane proteins, leading to their selection and concentration. The two major types of clathrin adaptor complexes are the heterotetrameric adaptor protein (AP) complexes, and the monomeric GGA (Golgi-localising, Gamma-adaptin ear domain homology, ARF-binding proteins) adaptors [, ]. Clathrin is a trimer composed of three heavy chains and three light chains, each monomer projecting outwards like a leg; this three-legged structure is known as a triskelion [, ]. The heavy chains form the legs, their N-terminal beta-propeller regions extending outwards, while their C-terminal alpha-alpha-superhelical regions form the central hub of the triskelion. Peptide motifs can bind between the beta-propeller blades. The light chains appear to have a regulatory role, and may help orient the assembly and disassembly of clathrin coats as they interact with hsc70 uncoating ATPase []. Clathrin triskelia self-polymerise into a curved lattice by twisting individual legs together. The clathrin lattice forms around a vesicle as it buds from the TGN, plasma membrane or endosomes, acting to stabilise the vesicle and facilitate the budding process []. The multiple blades created when the triskelia polymerise are involved in multiple protein interactions, enabling the recruitment of different cargo adaptors and membrane attachment proteins []. This entry represents the 7-fold alpha-alpha-superhelical ARM-type repeat found at the C-terminal of clathrin heavy chains and in VPS (vacuolar protein sorting-associated) proteins. In clathrin heavy chains, the C-terminal 7-fold ARM-type repeats interact to form the central hub of the triskelion. VPS proteins are required for vacuolar assembly and vacuolar traffick, and contain one clathrin-type repeat []. More information about these proteins can be found at Protein of the Month: Clathrin [].; GO: 0006886 intracellular protein transport, 0016192 vesicle-mediated transport; PDB: 3LVH_A 3LVG_C 1B89_A 3QIL_L.

>cd00923 Cyt_c_Oxidase_Va Cytochrome c oxidase subunit Va

Probab=88.75  E-value=3.4  Score=30.19  Aligned_cols=47  Identities=11%  Similarity=0.012  Sum_probs=28.5

Q ss_pred             HHHHHHHhcccCCCCCCHHHHHHHHHHHHhcCChhHHHHHHHHHHHc
Q 040027          470 FAWELFCSLPHGVLVPNVVTYNIMIQGLCNDGQMDKARDLFLDMEEN  516 (595)
Q Consensus       470 ~A~~~~~~~~~~~~~p~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~  516 (595)
                      ++.+-++.+....+.|++.+..+.+++|.+.+|+.-|+++|+-...+
T Consensus        25 e~rr~mN~l~~~DlVP~P~ii~aaLrAcRRvND~alAVR~lE~vK~K   71 (103)
T cd00923          25 ELRRGLNNLFGYDLVPEPKVIEAALRACRRVNDFALAVRILEAIKDK   71 (103)
T ss_pred             HHHHHHHHHhccccCCCcHHHHHHHHHHHHhhhHHHHHHHHHHHHHH
Confidence            34444555555556666666666666666666666666666655543

Cytochrome c oxidase (CcO), the terminal oxidase in the respiratory chains of eukaryotes and most bacteria, is a multi-chain transmembrane protein located in the inner membrane of mitochondria and the cell membrane of prokaryotes. It catalyzes the reduction of O2 and simultaneously pumps protons across the membrane. The number of subunits varies from three to five in bacteria and up to 13 in mammalian mitochondria. Subunits I, II, and III of mammalian CcO are encoded within the mitochondrial genome and the remaining 10 subunits are encoded within the nuclear genome. Found only in eukaryotes, subunit Va is one of three mammalian subunits that lacks a transmembrane region. Subunit Va is located on the matrix side of the membrane and binds thyroid hormone T2, releasing allosteric inhibition caused by the binding of ATP to subunit IV and allowing high turnover at elevated intramitochondrial ATP/ADP ratios.

>PF04097 Nic96: Nup93/Nic96; InterPro: IPR007231 Nup93/Nic96 is a component of the nuclear pore complex

Probab=88.66  E-value=34  Score=35.88  Aligned_cols=48  Identities=13%  Similarity=0.122  Sum_probs=29.4

Q ss_pred             CHHHHHHHHHHHHhcCChhHHHHHHHHHHhCCCCCCHHHHHHHHHHHHhc
Q 040027           95 NLYTYNILINCFCKIGRVSLGFIAFGRILRSCFTPNAATFNSLIKGLHAE  144 (595)
Q Consensus        95 ~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~~l~~~~~~~  144 (595)
                      +...| .++-.|.|+|.+++|.++....... .......+...+..|...
T Consensus       111 ~~p~W-a~Iyy~LR~G~~~~A~~~~~~~~~~-~~~~~~~f~~~l~~~~~s  158 (613)
T PF04097_consen  111 GDPIW-ALIYYCLRCGDYDEALEVANENRNQ-FQKIERSFPTYLKAYASS  158 (613)
T ss_dssp             TEEHH-HHHHHHHTTT-HHHHHHHHHHTGGG-S-TTTTHHHHHHHHCTTT
T ss_pred             CCccH-HHHHHHHhcCCHHHHHHHHHHhhhh-hcchhHHHHHHHHHHHhC
Confidence            44556 4666788889999998888444433 244445566666666553

It is required for the correct assembly of the nuclear pore complex []. In Saccharomyces cerevisiae, Nic96 has been shown to be involved in the distribution and cellular concentration of the GTPase Gsp1 []. The structure of Nic96 has revealed a mostly alpha helical structure [].; GO: 0006810 transport, 0005643 nuclear pore; PDB: 2QX5_B 2RFO_A.

>KOG2396 consensus HAT (Half-A-TPR) repeat-containing protein [General function prediction only]

Probab=88.63  E-value=26  Score=34.49  Aligned_cols=82  Identities=15%  Similarity=-0.008  Sum_probs=62.1

Q ss_pred             hHHHHHHHHHHhCCCCCCHHHHHHHHHHHHhcCCHhHHHHHHHHHHhcCCCCCHhhHHHHHHH-HHhcCChhHHHHHHHH
Q 040027          113 SLGFIAFGRILRSCFTPNAATFNSLIKGLHAESRIMEAAALFTKLKAFGCEPNVITYNTLING-LCRTGHTMIALNLFEE  191 (595)
Q Consensus       113 ~~A~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~~l~~~-~~~~g~~~~A~~~~~~  191 (595)
                      .....+|+.+..+ +..|+..|...+..+.+.+.+.+...+|.+|.... +.++..|-.-..- |...-+++.|..+|..
T Consensus        88 ~rIv~lyr~at~r-f~~D~~lW~~yi~f~kk~~~~~~v~ki~~~~l~~H-p~~~dLWI~aA~wefe~n~ni~saRalflr  165 (568)
T KOG2396|consen   88 NRIVFLYRRATNR-FNGDVKLWLSYIAFCKKKKTYGEVKKIFAAMLAKH-PNNPDLWIYAAKWEFEINLNIESARALFLR  165 (568)
T ss_pred             HHHHHHHHHHHHh-cCCCHHHHHHHHHHHHHhcchhHHHHHHHHHHHhC-CCCchhHHhhhhhHHhhccchHHHHHHHHH
Confidence            4556777777766 46699999999998888888999999999999874 3355555544333 3334459999999999


Q ss_pred             HHhcC
Q 040027          192 MANGN  196 (595)
Q Consensus       192 ~~~~~  196 (595)
                      .++.+
T Consensus       166 gLR~n  170 (568)
T KOG2396|consen  166 GLRFN  170 (568)
T ss_pred             HhhcC
Confidence            99876

>PRK09687 putative lyase; Provisional

Probab=88.59  E-value=20  Score=33.11  Aligned_cols=232  Identities=11%  Similarity=0.019  Sum_probs=100.6

Q ss_pred             CCHHHHHHHHHHHHhcCChhHHHHHHHHHHhCCCCCCHHHHHHHHHHHHhcCCH----hHHHHHHHHHHhcCCCCCHhhH
Q 040027           94 PNLYTYNILINCFCKIGRVSLGFIAFGRILRSCFTPNAATFNSLIKGLHAESRI----MEAAALFTKLKAFGCEPNVITY  169 (595)
Q Consensus        94 ~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~----~~A~~~~~~~~~~~~~~~~~~~  169 (595)
                      +|.......+..+...|. +++...+..+.+   .+|...-...+.++.+.|..    .++...+..+...  +++..+.
T Consensus        35 ~d~~vR~~A~~aL~~~~~-~~~~~~l~~ll~---~~d~~vR~~A~~aLg~lg~~~~~~~~a~~~L~~l~~~--D~d~~VR  108 (280)
T PRK09687         35 HNSLKRISSIRVLQLRGG-QDVFRLAIELCS---SKNPIERDIGADILSQLGMAKRCQDNVFNILNNLALE--DKSACVR  108 (280)
T ss_pred             CCHHHHHHHHHHHHhcCc-chHHHHHHHHHh---CCCHHHHHHHHHHHHhcCCCccchHHHHHHHHHHHhc--CCCHHHH
Confidence            444455555555555543 223333333332   22444444455555555542    3445555544322  3444555


Q ss_pred             HHHHHHHHhcCCh-----hHHHHHHHHHHhcCCCCCccccCcHHHHHHHHHHHHHcCCHhHHHHHHHHHhhCCCCCCHhH
Q 040027          170 NTLINGLCRTGHT-----MIALNLFEEMANGNGEIGVVCKPNTVTYSTIIDGLCKEGFVDKAKALFLQMKDENINPDVVT  244 (595)
Q Consensus       170 ~~l~~~~~~~g~~-----~~A~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~  244 (595)
                      ...+.++...+..     ..+...+.....         .++..+-...+.++.+.++ +.+...+-.+.+.   ++...
T Consensus       109 ~~A~~aLG~~~~~~~~~~~~a~~~l~~~~~---------D~~~~VR~~a~~aLg~~~~-~~ai~~L~~~L~d---~~~~V  175 (280)
T PRK09687        109 ASAINATGHRCKKNPLYSPKIVEQSQITAF---------DKSTNVRFAVAFALSVIND-EAAIPLLINLLKD---PNGDV  175 (280)
T ss_pred             HHHHHHHhcccccccccchHHHHHHHHHhh---------CCCHHHHHHHHHHHhccCC-HHHHHHHHHHhcC---CCHHH
Confidence            4444444443321     122232222222         1234444455555555554 3444444444432   23333


Q ss_pred             HHHHHHHHHhcC-CHHHHHHHHHHHHHCCCCCCHhhHHHHHHHHHhcCChHHHHHHHHHHHHCCCCCCHHHHHHHHHHHH
Q 040027          245 YNSLIHGLCHAN-DWNEAKRLFIEMMDQGVQPSVVTFNVIMDELCKNRKMDEASRLLDLMVQRGVRPNACTYNTLMDGFC  323 (595)
Q Consensus       245 ~~~ll~~~~~~~-~~~~A~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~  323 (595)
                      -...+.++.+.+ +...+...+..+...   ++..+-...+.++.+.|+. .+...+-...+.+   +  .....+.+..
T Consensus       176 R~~A~~aLg~~~~~~~~~~~~L~~~L~D---~~~~VR~~A~~aLg~~~~~-~av~~Li~~L~~~---~--~~~~a~~ALg  246 (280)
T PRK09687        176 RNWAAFALNSNKYDNPDIREAFVAMLQD---KNEEIRIEAIIGLALRKDK-RVLSVLIKELKKG---T--VGDLIIEAAG  246 (280)
T ss_pred             HHHHHHHHhcCCCCCHHHHHHHHHHhcC---CChHHHHHHHHHHHccCCh-hHHHHHHHHHcCC---c--hHHHHHHHHH
Confidence            333333444332 123444444444432   3444555555555565553 3444444444332   1  1233455555


Q ss_pred             hcCCHHHHHHHHHHHHhcCCCCCHHHHHHHHHH
Q 040027          324 LMGKINRAEELFGSMESMGCKHDDVSYNILING  356 (595)
Q Consensus       324 ~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~  356 (595)
                      ..|+. ++...+..+.+.  .+|...-...+.+
T Consensus       247 ~ig~~-~a~p~L~~l~~~--~~d~~v~~~a~~a  276 (280)
T PRK09687        247 ELGDK-TLLPVLDTLLYK--FDDNEIITKAIDK  276 (280)
T ss_pred             hcCCH-hHHHHHHHHHhh--CCChhHHHHHHHH
Confidence            55553 466666665543  2344444444433

>PF02259 FAT: FAT domain; InterPro: IPR003151 The FAT domain is a domain present in the PIK-related kinases

Probab=88.49  E-value=24  Score=33.91  Aligned_cols=54  Identities=13%  Similarity=0.155  Sum_probs=32.4

Q ss_pred             HHHHHHhcCChHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHh
Q 040027          283 IMDELCKNRKMDEASRLLDLMVQRGVRPNACTYNTLMDGFCLMGKINRAEELFGSMES  340 (595)
Q Consensus       283 l~~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~  340 (595)
                      ...+..+.|+++...++.......  .++...+..+...  ..++++++...++....
T Consensus         4 ~~eaaWrl~~Wd~l~~~~~~~~~~--~~~~~~~~al~~l--~~~~~~~~~~~i~~~r~   57 (352)
T PF02259_consen    4 AAEAAWRLGDWDLLEEYLSQSNED--SPEYSFYRALLAL--RQGDYDEAKKYIEKARQ   57 (352)
T ss_pred             HHHHHHhcCChhhHHHHHhhccCC--ChhHHHHHHHHHH--hCccHHHHHHHHHHHHH
Confidence            356777888888855555544322  1233344433332  77888888887777654

Members of the family of PIK-related kinases may act as intracellular sensors that govern radial and horizontal pathways [].; GO: 0005515 protein binding

>PF11207 DUF2989: Protein of unknown function (DUF2989); InterPro: IPR021372 Some members in this bacterial family of proteins are annotated as lipoproteins however this cannot be confirmed

Probab=88.40  E-value=8.4  Score=32.92  Aligned_cols=73  Identities=11%  Similarity=0.009  Sum_probs=39.8

Q ss_pred             HHHHHHHHhcccCCCCCCHHHHHHHHHHHHhcCChhHHHHHHHHHHHc---CCCCCHHHHHHHHHHHHHcCChhHHH
Q 040027          469 KFAWELFCSLPHGVLVPNVVTYNIMIQGLCNDGQMDKARDLFLDMEEN---AAAPDVITFDMLIHGFIRINEPSKVN  542 (595)
Q Consensus       469 ~~A~~~~~~~~~~~~~p~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~---~~~~~~~~~~~l~~~~~~~g~~~~A~  542 (595)
                      +.|.+.|-.+...+.--++.....|+..|. ..|.++++.++.++++.   +-.+|+..+..|+..|.+.|+++.|.
T Consensus       123 ~~A~~~fL~~E~~~~l~t~elq~aLAtyY~-krD~~Kt~~ll~~~L~l~~~~~~~n~eil~sLas~~~~~~~~e~AY  198 (203)
T PF11207_consen  123 QEALRRFLQLEGTPELETAELQYALATYYT-KRDPEKTIQLLLRALELSNPDDNFNPEILKSLASIYQKLKNYEQAY  198 (203)
T ss_pred             HHHHHHHHHHcCCCCCCCHHHHHHHHHHHH-ccCHHHHHHHHHHHHHhcCCCCCCCHHHHHHHHHHHHHhcchhhhh
Confidence            445555555544433334444444444443 45666666666666653   22455666666666666666666654

>KOG2471 consensus TPR repeat-containing protein [General function prediction only]

Probab=88.38  E-value=17  Score=35.49  Aligned_cols=37  Identities=11%  Similarity=0.007  Sum_probs=22.2

Q ss_pred             HHHhcCCHHHHHHHHHHHHHcCCCcCHHHHHHHHHHHH
Q 040027          426 GLCKNGYIIEAVELFRTLRILKCELDIQAYNCLIDGLC  463 (595)
Q Consensus       426 ~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~~l~~~~~  463 (595)
                      .|...|++-.|.+.|.+....- ..++..|..+..+|.
T Consensus       344 ~~Lh~grPl~AfqCf~~av~vf-h~nPrlWLRlAEcCi  380 (696)
T KOG2471|consen  344 LYLHSGRPLLAFQCFQKAVHVF-HRNPRLWLRLAECCI  380 (696)
T ss_pred             HHHhcCCcHHHHHHHHHHHHHH-hcCcHHHHHHHHHHH
Confidence            4555666666666666665432 445666666666664

>KOG0890 consensus Protein kinase of the PI-3 kinase family involved in mitotic growth, DNA repair and meiotic recombination [Signal transduction mechanisms; Chromatin structure and dynamics; Replication, recombination and repair; Cell cycle control, cell division, chromosome partitioning]

Probab=88.30  E-value=65  Score=38.64  Aligned_cols=152  Identities=10%  Similarity=0.027  Sum_probs=98.5

Q ss_pred             HHHHHHHhcCChhHHHHHHHHHHhCCC--CCCHHHHHHHHHHHHhcCCHhHHHHHHHHHHhcCCCCCHhhHHHHHHHHHh
Q 040027          101 ILINCFCKIGRVSLGFIAFGRILRSCF--TPNAATFNSLIKGLHAESRIMEAAALFTKLKAFGCEPNVITYNTLINGLCR  178 (595)
Q Consensus       101 ~l~~~~~~~g~~~~A~~~~~~~~~~~~--~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~~l~~~~~~  178 (595)
                      .+.++-.+++.+.+|...++.......  ......+..+...|..-+++|....+...-..   .|+   ....+.....
T Consensus      1388 tLa~aSfrc~~y~RalmylEs~~~~ek~~~~~e~l~fllq~lY~~i~dpDgV~Gv~~~r~a---~~s---l~~qil~~e~ 1461 (2382)
T KOG0890|consen 1388 TLARASFRCKAYARALMYLESHRSTEKEKETEEALYFLLQNLYGSIHDPDGVEGVSARRFA---DPS---LYQQILEHEA 1461 (2382)
T ss_pred             HHHHHHHhhHHHHHHHHHHHHhccccchhHHHHHHHHHHHHHHHhcCCcchhhhHHHHhhc---Ccc---HHHHHHHHHh
Confidence            677788899999999999998521110  11122334444588889999988877764211   222   3344556678


Q ss_pred             cCChhHHHHHHHHHHhcCCCCCccccCcHHHHHHHHHHHHHcCCHhHHHHHHHHHhhCCCCCCHhHHHHHH-HHHHhcCC
Q 040027          179 TGHTMIALNLFEEMANGNGEIGVVCKPNTVTYSTIIDGLCKEGFVDKAKALFLQMKDENINPDVVTYNSLI-HGLCHAND  257 (595)
Q Consensus       179 ~g~~~~A~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~~ll-~~~~~~~~  257 (595)
                      .|++..|...|+.+.+.+       ++....++.++......|.++...-..+-.... ..+....|+.+. .+--+.++
T Consensus      1462 ~g~~~da~~Cye~~~q~~-------p~~~~~~~g~l~sml~~~~l~t~i~~~dg~~~~-~se~~~~~~s~~~eaaW~l~q 1533 (2382)
T KOG0890|consen 1462 SGNWADAAACYERLIQKD-------PDKEKHHSGVLKSMLAIQHLSTEILHLDGLIIN-RSEEVDELNSLGVEAAWRLSQ 1533 (2382)
T ss_pred             hccHHHHHHHHHHhhcCC-------CccccchhhHHHhhhcccchhHHHhhhcchhhc-cCHHHHHHHHHHHHHHhhhcc
Confidence            899999999999999876       455667777777777778887777655554443 233344444433 44456667


Q ss_pred             HHHHHHHHH
Q 040027          258 WNEAKRLFI  266 (595)
Q Consensus       258 ~~~A~~~~~  266 (595)
                      |+.......
T Consensus      1534 wD~~e~~l~ 1542 (2382)
T KOG0890|consen 1534 WDLLESYLS 1542 (2382)
T ss_pred             hhhhhhhhh
Confidence            666655543

>COG2976 Uncharacterized protein conserved in bacteria [Function unknown]

Probab=88.28  E-value=15  Score=31.21  Aligned_cols=92  Identities=10%  Similarity=0.021  Sum_probs=40.6

Q ss_pred             HHHHhcCChhHHHHHHHHHHhcCCCCCccccCcHHHHHHHHHHHHHcCCHhHHHHHHHHHhhCCCCCCHhHHHHHHHHHH
Q 040027          174 NGLCRTGHTMIALNLFEEMANGNGEIGVVCKPNTVTYSTIIDGLCKEGFVDKAKALFLQMKDENINPDVVTYNSLIHGLC  253 (595)
Q Consensus       174 ~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~~ll~~~~  253 (595)
                      ..+...|++++|...++........    ......+-..|.+.....|.+|+|..+++.....+.  .......-.+.+.
T Consensus        97 k~~ve~~~~d~A~aqL~~~l~~t~D----e~lk~l~~lRLArvq~q~~k~D~AL~~L~t~~~~~w--~~~~~elrGDill  170 (207)
T COG2976          97 KAEVEANNLDKAEAQLKQALAQTKD----ENLKALAALRLARVQLQQKKADAALKTLDTIKEESW--AAIVAELRGDILL  170 (207)
T ss_pred             HHHHhhccHHHHHHHHHHHHccchh----HHHHHHHHHHHHHHHHHhhhHHHHHHHHhccccccH--HHHHHHHhhhHHH
Confidence            3444555555555555554432100    000011122233445555555555555555544321  1112222334555


Q ss_pred             hcCCHHHHHHHHHHHHHC
Q 040027          254 HANDWNEAKRLFIEMMDQ  271 (595)
Q Consensus       254 ~~~~~~~A~~~~~~~~~~  271 (595)
                      ..|+-++|..-|.+.+..
T Consensus       171 ~kg~k~~Ar~ay~kAl~~  188 (207)
T COG2976         171 AKGDKQEARAAYEKALES  188 (207)
T ss_pred             HcCchHHHHHHHHHHHHc
Confidence            555555555555555554

>KOG1464 consensus COP9 signalosome, subunit CSN2 [Posttranslational modification, protein turnover, chaperones; Signal transduction mechanisms]

Probab=88.27  E-value=18  Score=32.26  Aligned_cols=206  Identities=12%  Similarity=0.080  Sum_probs=126.8

Q ss_pred             CCCCCHhhHHHHHHH-HHhcCChHHHHHHHHHHHHCCCCCC---HHHHHHHHHHHHhcCCHHHHHHHHHHHHhc---C--
Q 040027          272 GVQPSVVTFNVIMDE-LCKNRKMDEASRLLDLMVQRGVRPN---ACTYNTLMDGFCLMGKINRAEELFGSMESM---G--  342 (595)
Q Consensus       272 ~~~~~~~~~~~l~~~-~~~~g~~~~a~~~~~~~~~~~~~~~---~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~---~--  342 (595)
                      +-.||+..-+..-.. -.+...+++|+.-|++.++......   -.....++..+.+.+++++....|.++...   .  
T Consensus        21 ~sEpdVDlENQYYnsK~l~e~~p~~Al~sF~kVlelEgEKgeWGFKALKQmiKI~f~l~~~~eMm~~Y~qlLTYIkSAVT  100 (440)
T KOG1464|consen   21 NSEPDVDLENQYYNSKGLKEDEPKEALSSFQKVLELEGEKGEWGFKALKQMIKINFRLGNYKEMMERYKQLLTYIKSAVT  100 (440)
T ss_pred             CCCCCcchHhhhhccccccccCHHHHHHHHHHHHhcccccchhHHHHHHHHHHHHhccccHHHHHHHHHHHHHHHHHHHh
Confidence            345665544432221 1234578899999999887532222   334556788889999999999988887532   1  


Q ss_pred             CCCCHHHHHHHHHHHHhCCCHHHHHHHHHHHHHC--CCC---CCHHHHHHHHHHHHccCCHHHHHHHHHHHHHCCC----
Q 040027          343 CKHDDVSYNILINGYCKNKEVEEALSLYREMVSK--GIK---PTVVTYNTLFLGLFEIHQVEHALKLFDEMQRDGV----  413 (595)
Q Consensus       343 ~~~~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~~--~~~---~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~----  413 (595)
                      -..+..+.+.++.......+.+--...|+.-+..  ..+   .-..|-..+...|...+.+.+..++++++...--    
T Consensus       101 rNySEKsIN~IlDyiStS~~m~LLQ~FYeTTL~ALkdAKNeRLWFKTNtKLgkl~fd~~e~~kl~KIlkqLh~SCq~edG  180 (440)
T KOG1464|consen  101 RNYSEKSINSILDYISTSKNMDLLQEFYETTLDALKDAKNERLWFKTNTKLGKLYFDRGEYTKLQKILKQLHQSCQTEDG  180 (440)
T ss_pred             ccccHHHHHHHHHHHhhhhhhHHHHHHHHHHHHHHHhhhcceeeeeccchHhhhheeHHHHHHHHHHHHHHHHHhccccC
Confidence            1234556777777777777777666666543321  011   1112335677778888888888888888876411    


Q ss_pred             CCC-------HHHHHHHHHHHHhcCCHHHHHHHHHHHHHcC-CCcCHHHHHHHH----HHHHhcCChHHHHHHHHh
Q 040027          414 AAD-------TRTYTTFIDGLCKNGYIIEAVELFRTLRILK-CELDIQAYNCLI----DGLCKSGRLKFAWELFCS  477 (595)
Q Consensus       414 ~~~-------~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~-~~~~~~~~~~l~----~~~~~~g~~~~A~~~~~~  477 (595)
                      ..|       ..+|..-|+.|..+.+-.+-..+|++.+... --|.+.+...+-    .+..+.|++++|-.-|-+
T Consensus       181 edD~kKGtQLLEiYAlEIQmYT~qKnNKkLK~lYeqalhiKSAIPHPlImGvIRECGGKMHlreg~fe~AhTDFFE  256 (440)
T KOG1464|consen  181 EDDQKKGTQLLEIYALEIQMYTEQKNNKKLKALYEQALHIKSAIPHPLIMGVIRECGGKMHLREGEFEKAHTDFFE  256 (440)
T ss_pred             chhhhccchhhhhHhhHhhhhhhhcccHHHHHHHHHHHHhhccCCchHHHhHHHHcCCccccccchHHHHHhHHHH
Confidence            111       2466667778888888888888888776422 134555444332    234567888877654433

>PF06552 TOM20_plant: Plant specific mitochondrial import receptor subunit TOM20; InterPro: IPR010547 This family consists of several plant specific mitochondrial import receptor subunit TOM20 (translocase of outer membrane 20 kDa subunit) proteins

Probab=88.19  E-value=3.8  Score=34.15  Aligned_cols=67  Identities=13%  Similarity=0.118  Sum_probs=41.1

Q ss_pred             hHHHHHHHHHHHcCCCCC-HHHHHHHHHHHHHcCC-----------hhHHHHHHHHHHHCCCCCCHHHHHHHHHHHHhcC
Q 040027          504 DKARDLFLDMEENAAAPD-VITFDMLIHGFIRINE-----------PSKVNELLHKMKEKKVMPDASIVSIVVDLLVKNE  571 (595)
Q Consensus       504 ~~A~~~~~~~~~~~~~~~-~~~~~~l~~~~~~~g~-----------~~~A~~~~~~~~~~~~~p~~~~~~~l~~~~~~~g  571 (595)
                      ++|+.-|++++..  .|+ ..++..++.+|...+.           +++|...|+++.+  ..|+...|..-++...++-
T Consensus        52 edAisK~eeAL~I--~P~~hdAlw~lGnA~ts~A~l~~d~~~A~~~F~kA~~~FqkAv~--~~P~ne~Y~ksLe~~~kap  127 (186)
T PF06552_consen   52 EDAISKFEEALKI--NPNKHDALWCLGNAYTSLAFLTPDTAEAEEYFEKATEYFQKAVD--EDPNNELYRKSLEMAAKAP  127 (186)
T ss_dssp             HHHHHHHHHHHHH---TT-HHHHHHHHHHHHHHHHH---HHHHHHHHHHHHHHHHHHHH--H-TT-HHHHHHHHHHHTHH
T ss_pred             HHHHHHHHHHHhc--CCchHHHHHHHHHHHHHHHhhcCChHHHHHHHHHHHHHHHHHHh--cCCCcHHHHHHHHHHHhhH
Confidence            3444455555553  344 4566666666654432           5677777777776  5699999999888887654


Q ss_pred             ccc
Q 040027          572 ISL  574 (595)
Q Consensus       572 ~~~  574 (595)
                      .+-
T Consensus       128 ~lh  130 (186)
T PF06552_consen  128 ELH  130 (186)
T ss_dssp             HHH
T ss_pred             HHH
Confidence            433

Most mitochondrial proteins are encoded by the nuclear genome, and are synthesised in the cytosol. TOM20 is a general import receptor that binds to mitochondrial pre-sequences in the early step of protein import into the mitochondria [].; GO: 0045040 protein import into mitochondrial outer membrane, 0005742 mitochondrial outer membrane translocase complex; PDB: 1ZU2_A.

>PF13374 TPR_10: Tetratricopeptide repeat; PDB: 3CEQ_B 3EDT_H 3NF1_A

Probab=87.23  E-value=1.6  Score=26.00  Aligned_cols=28  Identities=18%  Similarity=0.194  Sum_probs=21.2

Q ss_pred             HHHHHHHHHHHHcCChhHHHHHHHHHHH
Q 040027          523 ITFDMLIHGFIRINEPSKVNELLHKMKE  550 (595)
Q Consensus       523 ~~~~~l~~~~~~~g~~~~A~~~~~~~~~  550 (595)
                      .+++.+...|...|++++|..++++..+
T Consensus         3 ~~~~~la~~~~~~g~~~~A~~~~~~al~   30 (42)
T PF13374_consen    3 SALNNLANAYRAQGRYEEALELLEEALE   30 (42)
T ss_dssp             HHHHHHHHHHHHCT-HHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHhhhhcchhhHHHHHHHH
Confidence            4667788888888888888888888763

>PF11207 DUF2989: Protein of unknown function (DUF2989); InterPro: IPR021372 Some members in this bacterial family of proteins are annotated as lipoproteins however this cannot be confirmed

Probab=87.17  E-value=9.8  Score=32.55  Aligned_cols=82  Identities=11%  Similarity=-0.091  Sum_probs=57.9

Q ss_pred             HhcCCHhHHHHHHHHHHhcCCCCCHhhHHHHHHHHHhcCChhHHHHHHHHHHhcCCCCCccccCcHHHHHHHHHHHHHcC
Q 040027          142 HAESRIMEAAALFTKLKAFGCEPNVITYNTLINGLCRTGHTMIALNLFEEMANGNGEIGVVCKPNTVTYSTIIDGLCKEG  221 (595)
Q Consensus       142 ~~~g~~~~A~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g  221 (595)
                      +.+-.-++|.+.|-.+...+.--++.....|+..|. ..+.++++.++-...+...+.   -.+|+..+..|+..+.+.|
T Consensus       117 Wsr~~d~~A~~~fL~~E~~~~l~t~elq~aLAtyY~-krD~~Kt~~ll~~~L~l~~~~---~~~n~eil~sLas~~~~~~  192 (203)
T PF11207_consen  117 WSRFGDQEALRRFLQLEGTPELETAELQYALATYYT-KRDPEKTIQLLLRALELSNPD---DNFNPEILKSLASIYQKLK  192 (203)
T ss_pred             hhccCcHHHHHHHHHHcCCCCCCCHHHHHHHHHHHH-ccCHHHHHHHHHHHHHhcCCC---CCCCHHHHHHHHHHHHHhc
Confidence            334333778888888887765545666666655554 678889999888887754321   2567888888888888888


Q ss_pred             CHhHHH
Q 040027          222 FVDKAK  227 (595)
Q Consensus       222 ~~~~A~  227 (595)
                      +++.|.
T Consensus       193 ~~e~AY  198 (203)
T PF11207_consen  193 NYEQAY  198 (203)
T ss_pred             chhhhh
Confidence            888774

>KOG4642 consensus Chaperone-dependent E3 ubiquitin protein ligase (contains TPR repeats) [Posttranslational modification, protein turnover, chaperones]

Probab=87.01  E-value=5.9  Score=34.62  Aligned_cols=120  Identities=13%  Similarity=-0.055  Sum_probs=72.1

Q ss_pred             HHhcCCHHHHHHHHHHHHHcCCCcCHHHHHHHHHHHHhcCChHHHHHHHHhcccCCCCCCHH-HHHHHHHHHHhcCChhH
Q 040027          427 LCKNGYIIEAVELFRTLRILKCELDIQAYNCLIDGLCKSGRLKFAWELFCSLPHGVLVPNVV-TYNIMIQGLCNDGQMDK  505 (595)
Q Consensus       427 ~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~p~~~-~~~~l~~~~~~~g~~~~  505 (595)
                      |....++..|+..|.+.+..+ |..+.-|..=+.++.+..+++.+..--.+.++  +.||.. ...-+..+......+++
T Consensus        20 ~f~~k~y~~ai~~y~raI~~n-P~~~~Y~tnralchlk~~~~~~v~~dcrralq--l~~N~vk~h~flg~~~l~s~~~~e   96 (284)
T KOG4642|consen   20 CFIPKRYDDAIDCYSRAICIN-PTVASYYTNRALCHLKLKHWEPVEEDCRRALQ--LDPNLVKAHYFLGQWLLQSKGYDE   96 (284)
T ss_pred             ccchhhhchHHHHHHHHHhcC-CCcchhhhhHHHHHHHhhhhhhhhhhHHHHHh--cChHHHHHHHHHHHHHHhhccccH
Confidence            455567777888777777654 33335556666677777888877777777766  566643 33445556666777888


Q ss_pred             HHHHHHHHHHc----CCCCCHHHHHHHHHHHHHcCChhHHHHHHHHHH
Q 040027          506 ARDLFLDMEEN----AAAPDVITFDMLIHGFIRINEPSKVNELLHKMK  549 (595)
Q Consensus       506 A~~~~~~~~~~----~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~  549 (595)
                      |+..+.++.+.    .+++...+...|..+=-..=...+..++.++..
T Consensus        97 aI~~Lqra~sl~r~~~~~~~~di~~~L~~ak~~~w~v~e~~Ri~Q~~E  144 (284)
T KOG4642|consen   97 AIKVLQRAYSLLREQPFTFGDDIPKALRDAKKKRWEVSEEKRIRQELE  144 (284)
T ss_pred             HHHHHHHHHHHHhcCCCCCcchHHHHHHHHHhCccchhHHHHHHHHhh
Confidence            88887777442    334444555555544333333445555555443

>PF10345 Cohesin_load: Cohesin loading factor; InterPro: IPR019440 Cohesin loading factor is a conserved protein that has been characterised in fungi

Probab=86.98  E-value=44  Score=35.20  Aligned_cols=435  Identities=10%  Similarity=0.014  Sum_probs=207.8

Q ss_pred             CCCHHHHHHHHHHHHhcCCHhHHHHHHHHHH-hcCCCCC--HhhHHHHHHHHH-hcCChhHHHHHHHHHHhcCCCCCccc
Q 040027          128 TPNAATFNSLIKGLHAESRIMEAAALFTKLK-AFGCEPN--VITYNTLINGLC-RTGHTMIALNLFEEMANGNGEIGVVC  203 (595)
Q Consensus       128 ~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~-~~~~~~~--~~~~~~l~~~~~-~~g~~~~A~~~~~~~~~~~~~~~~~~  203 (595)
                      +.+...|..+|..         |++.++.+. ...++|.  ..++..++..+. ...+++.|...+++........+. .
T Consensus        27 ~~~l~~Y~kLI~~---------ai~CL~~~~~~~~l~p~~ea~~~l~la~iL~~eT~n~~~Ae~~L~k~~~l~~~~~~-~   96 (608)
T PF10345_consen   27 EEQLKQYYKLIAT---------AIKCLEAVLKQFKLSPRQEARVRLRLASILLEETENLDLAETYLEKAILLCERHRL-T   96 (608)
T ss_pred             hhhHHHHHHHHHH---------HHHHHHHHhccCCCCHHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhccccch-H
Confidence            3455566666643         566676666 3333332  344556666666 577888898888877654421000 0


Q ss_pred             cCcHHHHHHHHHHHHHcCCHhHHHHHHHHHhhCC----CCCCHhHHHHH-HHHHHhcCCHHHHHHHHHHHHHCCC-CCC-
Q 040027          204 KPNTVTYSTIIDGLCKEGFVDKAKALFLQMKDEN----INPDVVTYNSL-IHGLCHANDWNEAKRLFIEMMDQGV-QPS-  276 (595)
Q Consensus       204 ~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~----~~~~~~~~~~l-l~~~~~~~~~~~A~~~~~~~~~~~~-~~~-  276 (595)
                      .-.-..-..++..+.+.+... |...+++..+.-    ..+-...|..+ +..+...+++..|.+.++.+...-. ..| 
T Consensus        97 d~k~~~~~ll~~i~~~~~~~~-a~~~l~~~I~~~~~~~~~~w~~~frll~~~l~~~~~d~~~Al~~L~~~~~~a~~~~d~  175 (608)
T PF10345_consen   97 DLKFRCQFLLARIYFKTNPKA-ALKNLDKAIEDSETYGHSAWYYAFRLLKIQLALQHKDYNAALENLQSIAQLANQRGDP  175 (608)
T ss_pred             HHHHHHHHHHHHHHHhcCHHH-HHHHHHHHHHHHhccCchhHHHHHHHHHHHHHHhcccHHHHHHHHHHHHHHhhhcCCH
Confidence            001122334566666666655 888777765531    11112223333 2333334788888888887765421 122 


Q ss_pred             -HhhHHHHHHHH--HhcCChHHHHHHHHHHHHCC---------CCCCHHHHHHHHHHH--HhcCCHHHHHHHHHHHHhc-
Q 040027          277 -VVTFNVIMDEL--CKNRKMDEASRLLDLMVQRG---------VRPNACTYNTLMDGF--CLMGKINRAEELFGSMESM-  341 (595)
Q Consensus       277 -~~~~~~l~~~~--~~~g~~~~a~~~~~~~~~~~---------~~~~~~~~~~l~~~~--~~~~~~~~a~~~~~~~~~~-  341 (595)
                       ...+..++.+.  ...+..+++.+.++.+....         ..|...++..++..+  ...|+++.+...++.+.+. 
T Consensus       176 ~~~v~~~l~~~~l~l~~~~~~d~~~~l~~~~~~~~~~q~~~~~~~~qL~~~~lll~l~~~l~~~~~~~~~~~L~~lq~~~  255 (608)
T PF10345_consen  176 AVFVLASLSEALLHLRRGSPDDVLELLQRAIAQARSLQLDPSVHIPQLKALFLLLDLCCSLQQGDVKNSKQKLKQLQQFL  255 (608)
T ss_pred             HHHHHHHHHHHHHHhcCCCchhHHHHHHHHHHHHhhcccCCCCCcHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHH
Confidence             23333333333  34555667777776663321         123445555555544  4567766666665554321 


Q ss_pred             ----CCC-------------------------CCHH---------HHHHHHHH--HHhCCCHHHHHH-------HHHHHH
Q 040027          342 ----GCK-------------------------HDDV---------SYNILING--YCKNKEVEEALS-------LYREMV  374 (595)
Q Consensus       342 ----~~~-------------------------~~~~---------~~~~l~~~--~~~~~~~~~A~~-------~~~~~~  374 (595)
                          ..+                         +...         ....++.+  ....+..+.|.+       ..++..
T Consensus       256 ~~~~~~~~w~~~~~d~~i~l~~~~~~~~~~~~~~~f~wl~~~~l~~L~y~lS~l~~~~~~~~~ks~k~~~k~l~~i~~~~  335 (608)
T PF10345_consen  256 DEIKKSPSWPSWDEDGSIPLNIGEGSSNSGGTPLVFSWLPKEELYALVYFLSGLHNLYKGSMDKSEKFLEKALKQIEKLK  335 (608)
T ss_pred             HHhhcCccCCCcCCCeeEEeecccccccCCCceeEEeecCHHHHHHHHHHHHHHHHhhccCchHHHHHHHHHHHHHHHhh
Confidence                000                         0010         11111221  223344434444       444444


Q ss_pred             -HCCCCCCH--------HHHHHHHH---------HHHccCCHHHHHHHHHHHHHCCC-CCC-------HHHHHHHHHHHH
Q 040027          375 -SKGIKPTV--------VTYNTLFL---------GLFEIHQVEHALKLFDEMQRDGV-AAD-------TRTYTTFIDGLC  428 (595)
Q Consensus       375 -~~~~~~~~--------~~~~~l~~---------~~~~~~~~~~a~~~~~~~~~~~~-~~~-------~~~~~~l~~~~~  428 (595)
                       .....+..        ..|...+.         ...-.+++..+...+..+.+... .|+       +.++....-.+.
T Consensus       336 ~~~~~~~~~sl~~~~~~~~~~~~l~~~~~~y~~~~~~~~~~~~~a~~~l~~~~~~~~~~~~~~~~~~~~~~~yL~gl~~q  415 (608)
T PF10345_consen  336 IKSPSAPSESLSEASERIQWLRYLQCYLLFYQIWCNFIRGDWSKATQELEFMRQLCQRSPSKLYESLYPLLHYLLGLYYQ  415 (608)
T ss_pred             ccCCCCCCcCHHHHHHhHHHHHHHHHHHHHHHHHHHHHCcCHHHHHHHHHHHHHHHhcCccchhhhhhHHHHHHHHHHHH
Confidence             11111110        11211211         22457889999999998886411 111       222333333455


Q ss_pred             hcCCHHHHHHHHH--------HHHHcCCCcCHHHHHH--HHHHHHhcC--ChHH--HHHHHHhcccC-CCCC--CHHHHH
Q 040027          429 KNGYIIEAVELFR--------TLRILKCELDIQAYNC--LIDGLCKSG--RLKF--AWELFCSLPHG-VLVP--NVVTYN  491 (595)
Q Consensus       429 ~~g~~~~A~~~~~--------~~~~~~~~~~~~~~~~--l~~~~~~~g--~~~~--A~~~~~~~~~~-~~~p--~~~~~~  491 (595)
                      ..|+.+.|...|.        .....+...+..++..  ++..+...+  +.++  +..+++.+... .-.|  +..++.
T Consensus       416 ~~g~l~~A~~~y~~~~~~~~~~~~~~~~~~El~ila~LNl~~I~~~~~~~~~~~~~~~~l~~~i~p~~~~~~~~~~~~a~  495 (608)
T PF10345_consen  416 STGDLEAALYQYQKPRFLLCEAANRKSKFRELYILAALNLAIILQYESSRDDSESELNELLEQIEPLCSNSPNSYNRTAY  495 (608)
T ss_pred             HcCCHHHHHHHHhhhHHhhhhhhccCCcchHHHHHHHHHHHHHhHhhcccchhhhHHHHHHHhcCccccCCccHHHHHHH
Confidence            6799999999998        3333333333333332  222222222  2333  77777776552 1223  233444


Q ss_pred             HHH-HHHHhcC--ChhHHHHHHHHHHHc---CCCCCH---HHHHHHHHHHHHcCChhHHHHHHHHHHHCCCC-C--CHHH
Q 040027          492 IMI-QGLCNDG--QMDKARDLFLDMEEN---AAAPDV---ITFDMLIHGFIRINEPSKVNELLHKMKEKKVM-P--DASI  559 (595)
Q Consensus       492 ~l~-~~~~~~g--~~~~A~~~~~~~~~~---~~~~~~---~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~-p--~~~~  559 (595)
                      .++ .++....  ...++...+.+..+.   ....+.   .+++.+...+. .|+..+..+.........-+ |  ....
T Consensus       496 ~~~~~~~~~~~~~~~ne~k~~l~~~L~~~~~~~~n~~l~~~~L~lm~~~lf-~~~~~e~~~~s~~a~~~A~k~~d~~~~L  574 (608)
T PF10345_consen  496 CLVLATYNTFEPFSSNEAKRHLQEALKMANNKLGNSQLLAILLNLMGHRLF-EGDVGEQAKKSARAFQLAKKSSDYSDQL  574 (608)
T ss_pred             HHHHHHHhhCCccccHHHHHHHHHHHHHHHHhhccchHHHHHHHHHHHHHH-cCCHHHHHHHHHHHHHHHHhhhhhhhHH
Confidence            443 3333211  223555544443321   111221   22333333444 67877766555554422111 2  3455


Q ss_pred             HHH-----HHHHHHhcCccc
Q 040027          560 VSI-----VVDLLVKNEISL  574 (595)
Q Consensus       560 ~~~-----l~~~~~~~g~~~  574 (595)
                      |..     +.+.+...|..+
T Consensus       575 W~~v~~~~l~~~~~~~G~~~  594 (608)
T PF10345_consen  575 WHLVASGMLADSYEVQGDRD  594 (608)
T ss_pred             HHHHHHHHHHHHHHHcCcHH
Confidence            533     344466678777

It is associated with the cohesin complex and is required in G1 for cohesin binding to chromosomes, but is dispensable in G2 when cohesion has been established. It is often referred to as Ssl3 in Schizosaccharomyces pombe (Fission yeast), and Scc4 in Saccharomyces cerevisiae (Baker's yeast). It complexes with Mis4 [].

>PF13374 TPR_10: Tetratricopeptide repeat; PDB: 3CEQ_B 3EDT_H 3NF1_A

Probab=86.94  E-value=1.7  Score=25.96  Aligned_cols=28  Identities=18%  Similarity=0.274  Sum_probs=22.3

Q ss_pred             HHHHHHHHHHHhcCChhHHHHHHHHHHH
Q 040027          488 VTYNIMIQGLCNDGQMDKARDLFLDMEE  515 (595)
Q Consensus       488 ~~~~~l~~~~~~~g~~~~A~~~~~~~~~  515 (595)
                      .+++.+...|...|++++|..++++..+
T Consensus         3 ~~~~~la~~~~~~g~~~~A~~~~~~al~   30 (42)
T PF13374_consen    3 SALNNLANAYRAQGRYEEALELLEEALE   30 (42)
T ss_dssp             HHHHHHHHHHHHCT-HHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHhhhhcchhhHHHHHHHH
Confidence            4677888888888899988888888765

>KOG4648 consensus Uncharacterized conserved protein, contains LRR repeats [Function unknown]

Probab=86.70  E-value=4.7  Score=37.14  Aligned_cols=90  Identities=11%  Similarity=0.067  Sum_probs=49.2

Q ss_pred             HHHHHhcCCHHHHHHHHHHHHHCCCCC-CHhhHHHHHHHHHhcCChHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHhcCC
Q 040027          249 IHGLCHANDWNEAKRLFIEMMDQGVQP-SVVTFNVIMDELCKNRKMDEASRLLDLMVQRGVRPNACTYNTLMDGFCLMGK  327 (595)
Q Consensus       249 l~~~~~~~~~~~A~~~~~~~~~~~~~~-~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~  327 (595)
                      .+-|.++|.+++|+..|...+..  .| +++++..-..+|.+...+..|..-...++..+ ..-...|..-+.+-...|.
T Consensus       104 GN~yFKQgKy~EAIDCYs~~ia~--~P~NpV~~~NRA~AYlk~K~FA~AE~DC~~AiaLd-~~Y~KAYSRR~~AR~~Lg~  180 (536)
T KOG4648|consen  104 GNTYFKQGKYEEAIDCYSTAIAV--YPHNPVYHINRALAYLKQKSFAQAEEDCEAAIALD-KLYVKAYSRRMQARESLGN  180 (536)
T ss_pred             hhhhhhccchhHHHHHhhhhhcc--CCCCccchhhHHHHHHHHHHHHHHHHhHHHHHHhh-HHHHHHHHHHHHHHHHHhh
Confidence            44566677777777777665553  23 66666666667777777666666555555431 1112233333333334455


Q ss_pred             HHHHHHHHHHHHhc
Q 040027          328 INRAEELFGSMESM  341 (595)
Q Consensus       328 ~~~a~~~~~~~~~~  341 (595)
                      ..+|.+-++..+..
T Consensus       181 ~~EAKkD~E~vL~L  194 (536)
T KOG4648|consen  181 NMEAKKDCETVLAL  194 (536)
T ss_pred             HHHHHHhHHHHHhh
Confidence            55555555555544

>KOG4642 consensus Chaperone-dependent E3 ubiquitin protein ligase (contains TPR repeats) [Posttranslational modification, protein turnover, chaperones]

Probab=86.64  E-value=12  Score=32.89  Aligned_cols=100  Identities=15%  Similarity=0.073  Sum_probs=65.4

Q ss_pred             ccccCCCChHHHHHHHHHHHHhCCCCCCHhhHHHHHHHHHcCCCchh----HHhhCCCCCC-HHHHHHHHHHHHhcCChh
Q 040027           39 EGDINVITPNEAFCIFDYMLRMHPSPPPVSSFNILLASLAKNKHYDT----RLNATGLFPN-LYTYNILINCFCKIGRVS  113 (595)
Q Consensus        39 ~~~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~----~~~~~~~~~~-~~~~~~l~~~~~~~g~~~  113 (595)
                      ..+-...+++.|+..|-+++..+|.  .+..|+.-+.++.+..+++.    -.....+.|| +....-+...+.....++
T Consensus        18 nk~f~~k~y~~ai~~y~raI~~nP~--~~~Y~tnralchlk~~~~~~v~~dcrralql~~N~vk~h~flg~~~l~s~~~~   95 (284)
T KOG4642|consen   18 NKCFIPKRYDDAIDCYSRAICINPT--VASYYTNRALCHLKLKHWEPVEEDCRRALQLDPNLVKAHYFLGQWLLQSKGYD   95 (284)
T ss_pred             ccccchhhhchHHHHHHHHHhcCCC--cchhhhhHHHHHHHhhhhhhhhhhHHHHHhcChHHHHHHHHHHHHHHhhcccc
Confidence            3344557899999999999999997  77788888888888777776    2222333343 333444566667777788


Q ss_pred             HHHHHHHHHHhC----CCCCCHHHHHHHHHH
Q 040027          114 LGFIAFGRILRS----CFTPNAATFNSLIKG  140 (595)
Q Consensus       114 ~A~~~~~~~~~~----~~~~~~~~~~~l~~~  140 (595)
                      .|+..+.++...    .+++....+..|..+
T Consensus        96 eaI~~Lqra~sl~r~~~~~~~~di~~~L~~a  126 (284)
T KOG4642|consen   96 EAIKVLQRAYSLLREQPFTFGDDIPKALRDA  126 (284)
T ss_pred             HHHHHHHHHHHHHhcCCCCCcchHHHHHHHH
Confidence            888777777432    233444445544443

>PRK15180 Vi polysaccharide biosynthesis protein TviD; Provisional

Probab=86.62  E-value=34  Score=33.49  Aligned_cols=125  Identities=11%  Similarity=0.080  Sum_probs=81.5

Q ss_pred             HHHHhcCChhHHHHHHHHHHhcCCCCCccccCcHHHHHHHHHHHHHcCCHhHHHHHHHHHhhCCCCCCHhHHHHHHHHHH
Q 040027          174 NGLCRTGHTMIALNLFEEMANGNGEIGVVCKPNTVTYSTIIDGLCKEGFVDKAKALFLQMKDENINPDVVTYNSLIHGLC  253 (595)
Q Consensus       174 ~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~~ll~~~~  253 (595)
                      .--...|+.-.|-+-+.......       +.++.............|+++++.+.+...... +.....+...+++...
T Consensus       297 ~k~~~~gd~~aas~~~~~~lr~~-------~~~p~~i~l~~~i~~~lg~ye~~~~~~s~~~~~-~~s~~~~~~~~~r~~~  368 (831)
T PRK15180        297 TKQLADGDIIAASQQLFAALRNQ-------QQDPVLIQLRSVIFSHLGYYEQAYQDISDVEKI-IGTTDSTLRCRLRSLH  368 (831)
T ss_pred             HHHhhccCHHHHHHHHHHHHHhC-------CCCchhhHHHHHHHHHhhhHHHHHHHhhchhhh-hcCCchHHHHHHHhhh
Confidence            33345677666655555555443       334444445555667788888888887665543 2234566777888888


Q ss_pred             hcCCHHHHHHHHHHHHHCCCCCCHhhHHHHHHHHHhcCChHHHHHHHHHHHHCC
Q 040027          254 HANDWNEAKRLFIEMMDQGVQPSVVTFNVIMDELCKNRKMDEASRLLDLMVQRG  307 (595)
Q Consensus       254 ~~~~~~~A~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~  307 (595)
                      +.|++++|...-..|+...++ ++.......-.....|-++++.-.++++...+
T Consensus       369 ~l~r~~~a~s~a~~~l~~eie-~~ei~~iaa~sa~~l~~~d~~~~~wk~~~~~~  421 (831)
T PRK15180        369 GLARWREALSTAEMMLSNEIE-DEEVLTVAAGSADALQLFDKSYHYWKRVLLLN  421 (831)
T ss_pred             chhhHHHHHHHHHHHhccccC-ChhheeeecccHHHHhHHHHHHHHHHHHhccC
Confidence            888999998888888776555 44444444444556677888888888877653

>KOG1586 consensus Protein required for fusion of vesicles in vesicular transport, alpha-SNAP [Intracellular trafficking, secretion, and vesicular transport]

Probab=86.54  E-value=22  Score=31.23  Aligned_cols=30  Identities=10%  Similarity=0.104  Sum_probs=19.7

Q ss_pred             HHHHHHHHHHcCCHhHHHHHHHHHhhCCCC
Q 040027          210 YSTIIDGLCKEGFVDKAKALFLQMKDENIN  239 (595)
Q Consensus       210 ~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~  239 (595)
                      +..+.......+++.+|+++|+++....+.
T Consensus       157 ~lKvA~yaa~leqY~~Ai~iyeqva~~s~~  186 (288)
T KOG1586|consen  157 LLKVAQYAAQLEQYSKAIDIYEQVARSSLD  186 (288)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHhcc
Confidence            333444555677888888888887765433

>KOG2300 consensus Uncharacterized conserved protein [Function unknown]

Probab=86.40  E-value=35  Score=33.51  Aligned_cols=433  Identities=12%  Similarity=0.039  Sum_probs=223.5

Q ss_pred             HHHHHhcC--CHhHHHHHHHHHHhcCCCCC--HhhHHHHHHH-HHhcCChhHHHHHHHHHHhcCCCCCccccCcHHHHHH
Q 040027          138 IKGLHAES--RIMEAAALFTKLKAFGCEPN--VITYNTLING-LCRTGHTMIALNLFEEMANGNGEIGVVCKPNTVTYST  212 (595)
Q Consensus       138 ~~~~~~~g--~~~~A~~~~~~~~~~~~~~~--~~~~~~l~~~-~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~~~~~~~~  212 (595)
                      ...+...|  +...+++.++......++--  ..+...+... +....+++.|..-+++.-......+......-.++..
T Consensus        14 Ae~~rt~~PPkIkk~IkClqA~~~~~is~~veart~LqLg~lL~~yT~N~elAksHLekA~~i~~~ip~fydvKf~a~Sl   93 (629)
T KOG2300|consen   14 AEHFRTSGPPKIKKCIKCLQAIFQFQISFLVEARTHLQLGALLLRYTKNVELAKSHLEKAWLISKSIPSFYDVKFQAASL   93 (629)
T ss_pred             HHHHhhcCChhHHHHHHHHHHHhccCChHHHHHHHHHHHHHHHHHHhccHHHHHHHHHHHHHHHcccccHHhhhhHHHHH
Confidence            33344444  55566666666655432211  2222333333 3346778888887777654432222111223456777


Q ss_pred             HHHHHHHcC-CHhHHHHHHHHHhhCC--CC-CCHhHHHHHHHHHHhcCCHHHHHHHHHHHHHCCCCCCHhhHHHHHHH--
Q 040027          213 IIDGLCKEG-FVDKAKALFLQMKDEN--IN-PDVVTYNSLIHGLCHANDWNEAKRLFIEMMDQGVQPSVVTFNVIMDE--  286 (595)
Q Consensus       213 l~~~~~~~g-~~~~A~~~~~~~~~~~--~~-~~~~~~~~ll~~~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~~l~~~--  286 (595)
                      |...|.... .+..+..++++..+..  ++ .+-.....|+..+.-..++..|.+++.-=-.. -.+-...|..++..  
T Consensus        94 La~lh~~~~~s~~~~KalLrkaielsq~~p~wsckllfQLaql~~idkD~~sA~elLavga~s-Ad~~~~~ylr~~ftls  172 (629)
T KOG2300|consen   94 LAHLHHQLAQSFPPAKALLRKAIELSQSVPYWSCKLLFQLAQLHIIDKDFPSALELLAVGAES-ADHICFPYLRMLFTLS  172 (629)
T ss_pred             HHHHHHHhcCCCchHHHHHHHHHHHhcCCchhhHHHHHHHHHHHhhhccchhHHHHHhccccc-cchhhhHHHHHHHHHH
Confidence            888888776 7888999998877642  11 11122234567777788999998874321111 11112223222221  


Q ss_pred             ----HHhcC---ChHHHHHHHHHHHHCCCCCCHHH------HHH--HHHHHHhcCCHHHHHHHHHHHHhc---CC-----
Q 040027          287 ----LCKNR---KMDEASRLLDLMVQRGVRPNACT------YNT--LMDGFCLMGKINRAEELFGSMESM---GC-----  343 (595)
Q Consensus       287 ----~~~~g---~~~~a~~~~~~~~~~~~~~~~~~------~~~--l~~~~~~~~~~~~a~~~~~~~~~~---~~-----  343 (595)
                          .....   ++..+.....++.+. ..+|..-      |..  -+.-|...|+...+...++++...   +.     
T Consensus       173 ~~~ll~me~d~~dV~~ll~~~~qi~~n-~~sdk~~~E~LkvFyl~lql~yy~~~gq~rt~k~~lkQLQ~siqtist~~~~  251 (629)
T KOG2300|consen  173 MLMLLIMERDDYDVEKLLQRCGQIWQN-ISSDKTQKEMLKVFYLVLQLSYYLLPGQVRTVKPALKQLQDSIQTISTSSRG  251 (629)
T ss_pred             HHHHHHhCccHHHHHHHHHHHHHHHhc-cCCChHHHHHHHHHHHHHHHHHHhcccchhhhHHHHHHHHHHHhccCCCCCC
Confidence                12222   344455555566554 3444322      211  123345678877777777766432   11     


Q ss_pred             -------CCCHHHHHHHHH----H---------HHhCCCHHHHHHHHHHHHHC----CCCC-CHHHHHH--------HHH
Q 040027          344 -------KHDDVSYNILIN----G---------YCKNKEVEEALSLYREMVSK----GIKP-TVVTYNT--------LFL  390 (595)
Q Consensus       344 -------~~~~~~~~~l~~----~---------~~~~~~~~~A~~~~~~~~~~----~~~~-~~~~~~~--------l~~  390 (595)
                             .|++..+..+..    +         -...|-+++|.+.-++++..    ...+ ....++.        ++.
T Consensus       252 h~e~ilgsps~~l~~wlpkeqicaLV~l~tv~hsm~~gy~~~~~K~tDe~i~q~eklkq~d~~srilsm~km~~LE~iv~  331 (629)
T KOG2300|consen  252 HDEKILGSPSPILFEWLPKEQICALVYLVTVIHSMPAGYFKKAQKYTDEAIKQTEKLKQADLMSRILSMFKMILLEHIVM  331 (629)
T ss_pred             ccccccCCCChHHHhhccHhhhHhhhhhhHHhhhhhhHHHHHHHHHHHHHHHHHhhcccccchhHHHHHHHHHHHHHHHH
Confidence                   122222211111    0         11234455665555544432    1111 2222221        122


Q ss_pred             HHHccCCHHHHHHHHHHHHHCC-CCCCH--------HHHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCcCHHH--HHHHH
Q 040027          391 GLFEIHQVEHALKLFDEMQRDG-VAADT--------RTYTTFIDGLCKNGYIIEAVELFRTLRILKCELDIQA--YNCLI  459 (595)
Q Consensus       391 ~~~~~~~~~~a~~~~~~~~~~~-~~~~~--------~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~--~~~l~  459 (595)
                      .-.-.|++.+|++-..+|.+.- -.|.+        .+...+...++..+-++.|...|..+.+.--..|...  -..+.
T Consensus       332 c~lv~~~~~~al~~i~dm~~w~~r~p~~~Llr~~~~~ih~LlGlys~sv~~~enAe~hf~~a~k~t~~~dl~a~~nlnlA  411 (629)
T KOG2300|consen  332 CRLVRGDYVEALEEIVDMKNWCTRFPTPLLLRAHEAQIHMLLGLYSHSVNCYENAEFHFIEATKLTESIDLQAFCNLNLA  411 (629)
T ss_pred             HHHHhCCHHHHHHHHHHHHHHHHhCCchHHHHHhHHHHHHHHhhHhhhcchHHHHHHHHHHHHHhhhHHHHHHHHHHhHH
Confidence            2234799999999998887641 12331        1222333445567889999999988876533344333  34556


Q ss_pred             HHHHhcCChHHHHHHHHhcccCCCCC-CHH-----HHHHHHHHHHhcCChhHHHHHHHHHHHcCCCCC-----HHHHHHH
Q 040027          460 DGLCKSGRLKFAWELFCSLPHGVLVP-NVV-----TYNIMIQGLCNDGQMDKARDLFLDMEENAAAPD-----VITFDML  528 (595)
Q Consensus       460 ~~~~~~g~~~~A~~~~~~~~~~~~~p-~~~-----~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~~-----~~~~~~l  528 (595)
                      ..|.+.|+-+.-.++++.+-..+-.+ ...     .+....-.....+++.+|..++.+-++..-.-|     .-....|
T Consensus       412 i~YL~~~~~ed~y~~ld~i~p~nt~s~ssq~l~a~~~~v~glfaf~qn~lnEaK~~l~e~Lkmanaed~~rL~a~~LvLL  491 (629)
T KOG2300|consen  412 ISYLRIGDAEDLYKALDLIGPLNTNSLSSQRLEASILYVYGLFAFKQNDLNEAKRFLRETLKMANAEDLNRLTACSLVLL  491 (629)
T ss_pred             HHHHHhccHHHHHHHHHhcCCCCCCcchHHHHHHHHHHHHHHHHHHhccHHHHHHHHHHHHhhcchhhHHHHHHHHHHHH
Confidence            67888888888777777765321111 111     111111223378999999999998877421111     2223445


Q ss_pred             HHHHHHcCChhHHHHHHHHHHHC-CCCCCHHH--H--HHHHHHHHhcCc
Q 040027          529 IHGFIRINEPSKVNELLHKMKEK-KVMPDASI--V--SIVVDLLVKNEI  572 (595)
Q Consensus       529 ~~~~~~~g~~~~A~~~~~~~~~~-~~~p~~~~--~--~~l~~~~~~~g~  572 (595)
                      ...+...|+..++.+.+.-..+. .--||..+  |  ..+-+.+...|.
T Consensus       492 s~v~lslgn~~es~nmvrpamqlAkKi~Di~vqLws~si~~~L~~a~g~  540 (629)
T KOG2300|consen  492 SHVFLSLGNTVESRNMVRPAMQLAKKIPDIPVQLWSSSILTDLYQALGE  540 (629)
T ss_pred             HHHHHHhcchHHHHhccchHHHHHhcCCCchHHHHHHHHHHHHHHHhCc
Confidence            56677788888888777665532 22355322  2  233344555555

>KOG2066 consensus Vacuolar assembly/sorting protein VPS41 [Intracellular trafficking, secretion, and vesicular transport]

Probab=86.11  E-value=48  Score=34.76  Aligned_cols=102  Identities=13%  Similarity=0.097  Sum_probs=70.2

Q ss_pred             HHHHHhcCChhHHHHHHHHHHhCCCCC---CHHHHHHHHHHHHhcCCHhHHHHHHHHHHhcCCCCCHhhHHHHHHHHHhc
Q 040027          103 INCFCKIGRVSLGFIAFGRILRSCFTP---NAATFNSLIKGLHAESRIMEAAALFTKLKAFGCEPNVITYNTLINGLCRT  179 (595)
Q Consensus       103 ~~~~~~~g~~~~A~~~~~~~~~~~~~~---~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~~l~~~~~~~  179 (595)
                      +.-+.+.+.+++|+.+.+.....  .+   -...+..++..+...|++++|-...-.|...    +...|...+..+...
T Consensus       363 i~Wll~~k~yeeAl~~~k~~~~~--~~~~~i~kv~~~yI~HLl~~~~y~~Aas~~p~m~gn----~~~eWe~~V~~f~e~  436 (846)
T KOG2066|consen  363 IDWLLEKKKYEEALDAAKASIGN--EERFVIKKVGKTYIDHLLFEGKYDEAASLCPKMLGN----NAAEWELWVFKFAEL  436 (846)
T ss_pred             HHHHHHhhHHHHHHHHHHhccCC--ccccchHHHHHHHHHHHHhcchHHHHHhhhHHHhcc----hHHHHHHHHHHhccc
Confidence            44467788899998887776554  33   3456788888899999999999988888864    667777777777777


Q ss_pred             CChhHHHHHHHHHHhcCCCCCccccCcHHHHHHHHHHHHH
Q 040027          180 GHTMIALNLFEEMANGNGEIGVVCKPNTVTYSTIIDGLCK  219 (595)
Q Consensus       180 g~~~~A~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~  219 (595)
                      ++......   -+....      ...++..|..++..+..
T Consensus       437 ~~l~~Ia~---~lPt~~------~rL~p~vYemvLve~L~  467 (846)
T KOG2066|consen  437 DQLTDIAP---YLPTGP------PRLKPLVYEMVLVEFLA  467 (846)
T ss_pred             cccchhhc---cCCCCC------cccCchHHHHHHHHHHH
Confidence            66543322   222221      12356778888877776

>KOG0276 consensus Vesicle coat complex COPI, beta' subunit [Intracellular trafficking, secretion, and vesicular transport]

Probab=85.90  E-value=31  Score=34.89  Aligned_cols=150  Identities=16%  Similarity=0.085  Sum_probs=95.8

Q ss_pred             hcCChhHHHHHHHHHHhCCCCCCHHHHHHHHHHHHhcCCHhHHHHHHHHHHhcCCCCCHhhHHHHHHHHHhcCChhHHHH
Q 040027          108 KIGRVSLGFIAFGRILRSCFTPNAATFNSLIKGLHAESRIMEAAALFTKLKAFGCEPNVITYNTLINGLCRTGHTMIALN  187 (595)
Q Consensus       108 ~~g~~~~A~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~  187 (595)
                      -.|+++.|..++.++.       -...+.++..+.++|..++|+++         .+|+...   .....+.|+++.|.+
T Consensus       598 mrrd~~~a~~vLp~I~-------k~~rt~va~Fle~~g~~e~AL~~---------s~D~d~r---Felal~lgrl~iA~~  658 (794)
T KOG0276|consen  598 LRRDLEVADGVLPTIP-------KEIRTKVAHFLESQGMKEQALEL---------STDPDQR---FELALKLGRLDIAFD  658 (794)
T ss_pred             hhccccccccccccCc-------hhhhhhHHhHhhhccchHhhhhc---------CCChhhh---hhhhhhcCcHHHHHH
Confidence            3467777666544433       23345566666777777766653         2333322   233457788888887


Q ss_pred             HHHHHHhcCCCCCccccCcHHHHHHHHHHHHHcCCHhHHHHHHHHHhhCCCCCCHhHHHHHHHHHHhcCCHHHHHHHHHH
Q 040027          188 LFEEMANGNGEIGVVCKPNTVTYSTIIDGLCKEGFVDKAKALFLQMKDENINPDVVTYNSLIHGLCHANDWNEAKRLFIE  267 (595)
Q Consensus       188 ~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~~ll~~~~~~~~~~~A~~~~~~  267 (595)
                      +..+..            +..-|..|..+....+++..|.+.|.+...         |..|+-.+...|+-+....+-..
T Consensus       659 la~e~~------------s~~Kw~~Lg~~al~~~~l~lA~EC~~~a~d---------~~~LlLl~t~~g~~~~l~~la~~  717 (794)
T KOG0276|consen  659 LAVEAN------------SEVKWRQLGDAALSAGELPLASECFLRARD---------LGSLLLLYTSSGNAEGLAVLASL  717 (794)
T ss_pred             HHHhhc------------chHHHHHHHHHHhhcccchhHHHHHHhhcc---------hhhhhhhhhhcCChhHHHHHHHH
Confidence            765543            456688888888899999988888877654         44566667777777666666556


Q ss_pred             HHHCCCCCCHhhHHHHHHHHHhcCChHHHHHHHHHH
Q 040027          268 MMDQGVQPSVVTFNVIMDELCKNRKMDEASRLLDLM  303 (595)
Q Consensus       268 ~~~~~~~~~~~~~~~l~~~~~~~g~~~~a~~~~~~~  303 (595)
                      ..+.|.. |.     ...++...|+++++.+++..-
T Consensus       718 ~~~~g~~-N~-----AF~~~~l~g~~~~C~~lLi~t  747 (794)
T KOG0276|consen  718 AKKQGKN-NL-----AFLAYFLSGDYEECLELLIST  747 (794)
T ss_pred             HHhhccc-ch-----HHHHHHHcCCHHHHHHHHHhc
Confidence            6665533 22     233566788888888877654

>KOG0276 consensus Vesicle coat complex COPI, beta' subunit [Intracellular trafficking, secretion, and vesicular transport]

Probab=85.72  E-value=31  Score=34.87  Aligned_cols=150  Identities=16%  Similarity=0.089  Sum_probs=92.6

Q ss_pred             hCCCHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHccCCHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHhcCCHHHHHH
Q 040027          359 KNKEVEEALSLYREMVSKGIKPTVVTYNTLFLGLFEIHQVEHALKLFDEMQRDGVAADTRTYTTFIDGLCKNGYIIEAVE  438 (595)
Q Consensus       359 ~~~~~~~A~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~  438 (595)
                      ..++++.|..++..+.       ....+.+..-+.+.|-.++|+.+         .+|+..-   .....+.|+++.|.+
T Consensus       598 mrrd~~~a~~vLp~I~-------k~~rt~va~Fle~~g~~e~AL~~---------s~D~d~r---Felal~lgrl~iA~~  658 (794)
T KOG0276|consen  598 LRRDLEVADGVLPTIP-------KEIRTKVAHFLESQGMKEQALEL---------STDPDQR---FELALKLGRLDIAFD  658 (794)
T ss_pred             hhccccccccccccCc-------hhhhhhHHhHhhhccchHhhhhc---------CCChhhh---hhhhhhcCcHHHHHH
Confidence            3455555555433322       22334455555666666666543         2232221   123356788888887


Q ss_pred             HHHHHHHcCCCcCHHHHHHHHHHHHhcCChHHHHHHHHhcccCCCCCCHHHHHHHHHHHHhcCChhHHHHHHHHHHHcCC
Q 040027          439 LFRTLRILKCELDIQAYNCLIDGLCKSGRLKFAWELFCSLPHGVLVPNVVTYNIMIQGLCNDGQMDKARDLFLDMEENAA  518 (595)
Q Consensus       439 ~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~p~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~  518 (595)
                      +..+.      .+..-|..|.++....+++..|.+.|.+..+         |..|+..+...|+-+.-..+-....+.| 
T Consensus       659 la~e~------~s~~Kw~~Lg~~al~~~~l~lA~EC~~~a~d---------~~~LlLl~t~~g~~~~l~~la~~~~~~g-  722 (794)
T KOG0276|consen  659 LAVEA------NSEVKWRQLGDAALSAGELPLASECFLRARD---------LGSLLLLYTSSGNAEGLAVLASLAKKQG-  722 (794)
T ss_pred             HHHhh------cchHHHHHHHHHHhhcccchhHHHHHHhhcc---------hhhhhhhhhhcCChhHHHHHHHHHHhhc-
Confidence            76654      3567788888888888888888888887765         4456666777777776666666666655 


Q ss_pred             CCCHHHHHHHHHHHHHcCChhHHHHHHHHH
Q 040027          519 APDVITFDMLIHGFIRINEPSKVNELLHKM  548 (595)
Q Consensus       519 ~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~  548 (595)
                      ..|     ....+|...|+++++.+++..-
T Consensus       723 ~~N-----~AF~~~~l~g~~~~C~~lLi~t  747 (794)
T KOG0276|consen  723 KNN-----LAFLAYFLSGDYEECLELLIST  747 (794)
T ss_pred             ccc-----hHHHHHHHcCCHHHHHHHHHhc
Confidence            222     2334567788888888776654

>smart00386 HAT HAT (Half-A-TPR) repeats

Probab=85.64  E-value=2.1  Score=23.69  Aligned_cols=29  Identities=17%  Similarity=0.114  Sum_probs=24.8

Q ss_pred             CChHHHHHHHHHHHHhCCCCCCHhhHHHHHH
Q 040027           45 ITPNEAFCIFDYMLRMHPSPPPVSSFNILLA   75 (595)
Q Consensus        45 ~~~~~A~~~~~~~~~~~~~~~~~~~~~~l~~   75 (595)
                      |+.+.|..+|+++++..|.  ++..|...+.
T Consensus         1 ~~~~~~r~i~e~~l~~~~~--~~~~W~~y~~   29 (33)
T smart00386        1 GDIERARKIYERALEKFPK--SVELWLKYAE   29 (33)
T ss_pred             CcHHHHHHHHHHHHHHCCC--ChHHHHHHHH
Confidence            5789999999999999987  8888887664

Present in several RNA-binding proteins. Structurally and sequentially thought to be similar to TPRs.

>KOG4521 consensus Nuclear pore complex, Nup160 component [Nuclear structure; Intracellular trafficking, secretion, and vesicular transport]

Probab=85.35  E-value=49  Score=36.46  Aligned_cols=182  Identities=13%  Similarity=-0.001  Sum_probs=106.4

Q ss_pred             ccccccccccCCCChHHHHHHHHHHHHhCCCCCCHhhHHHHHHHHHcCCCchhHHhhCCCCCC-----HHHHHHHHHHHH
Q 040027           33 RDLTTREGDINVITPNEAFCIFDYMLRMHPSPPPVSSFNILLASLAKNKHYDTRLNATGLFPN-----LYTYNILINCFC  107 (595)
Q Consensus        33 ~~~~~~~~~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~-----~~~~~~l~~~~~  107 (595)
                      -+.-.+-+|+..|..-+|++.|.++...-..  .-.....+....-     ..--+..|-.|+     ...|..+++.+-
T Consensus       922 ~rfmlg~~yl~tge~~kAl~cF~~a~Sg~ge--~~aL~~lv~~~~p-----~~~sv~dG~t~s~e~t~lhYYlkv~rlle  994 (1480)
T KOG4521|consen  922 IRFMLGIAYLGTGEPVKALNCFQSALSGFGE--GNALRKLVYFLLP-----KRFSVADGKTPSEELTALHYYLKVVRLLE  994 (1480)
T ss_pred             HHHhhheeeecCCchHHHHHHHHHHhhcccc--HHHHHHHHHHhcC-----CCCchhcCCCCCchHHHHHHHHHHHHHHH
Confidence            3333445589999999999999999776554  2222222222111     111122333332     466899999999


Q ss_pred             hcCChhHHHHHHHHHHhCCCCCC---HHHHHHHHHHHHhcCCHhHHHHHHHHHHhcCCCCCHhhHHHHHHHHHhcCChhH
Q 040027          108 KIGRVSLGFIAFGRILRSCFTPN---AATFNSLIKGLHAESRIMEAAALFTKLKAFGCEPNVITYNTLINGLCRTGHTMI  184 (595)
Q Consensus       108 ~~g~~~~A~~~~~~~~~~~~~~~---~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~  184 (595)
                      +.|-.+.+.++...+++.-.+-+   ..+++.+.+.....|.+-+|.+.+-.-...  +........++..++..|+++.
T Consensus       995 ~hn~~E~vcQlA~~AIe~l~dd~ps~a~~~t~vFnhhldlgh~~qAy~ai~~npds--errrdcLRqlvivLfecg~l~~ 1072 (1480)
T KOG4521|consen  995 EHNHAEEVCQLAVKAIENLPDDNPSVALISTTVFNHHLDLGHWFQAYKAILRNPDS--ERRRDCLRQLVIVLFECGELEA 1072 (1480)
T ss_pred             HhccHHHHHHHHHHHHHhCCCcchhHHHHHHHHHHhhhchhhHHHHHHHHHcCCcH--HHHHHHHHHHHHHHHhccchHH
Confidence            99999999999999887632211   224566777777778777776554432211  1122345566777777776643


Q ss_pred             ------------HHH-HHHHHHhcCCCCCccccCcHHHHHHHHHHHHHcCCHhHHHHH
Q 040027          185 ------------ALN-LFEEMANGNGEIGVVCKPNTVTYSTIIDGLCKEGFVDKAKAL  229 (595)
Q Consensus       185 ------------A~~-~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~  229 (595)
                                  ... +++..-+..      .-.....|..|-..+...+++.+|-.+
T Consensus      1073 L~~fpfigl~~eve~~l~esaaRs~------~~mk~nyYelLYAfh~~RhN~Rkaatv 1124 (1480)
T KOG4521|consen 1073 LATFPFIGLEQEVEDFLRESAARSS------PSMKKNYYELLYAFHVARHNFRKAATV 1124 (1480)
T ss_pred             HhhCCccchHHHHHHHHHHHHhhcC------ccccccHHHHHHHHHHhhcchhHHHHH
Confidence                        222 233322222      112244566666667777777776544

>PF07035 Mic1: Colon cancer-associated protein Mic1-like; InterPro: IPR009755 This entry represents the C terminus (approximately 160 residues) of a number of proteins that resemble colon cancer-associated protein Mic1

Probab=85.22  E-value=21  Score=29.77  Aligned_cols=133  Identities=17%  Similarity=0.102  Sum_probs=68.1

Q ss_pred             HHHHHHHhCCCCCCHHHHHHHHHHHHhcCCHhHHHHHHHHHHhcCCCCCHhhHHHHHHHHHhcCChhHHHHHHHHHHhcC
Q 040027          117 IAFGRILRSCFTPNAATFNSLIKGLHAESRIMEAAALFTKLKAFGCEPNVITYNTLINGLCRTGHTMIALNLFEEMANGN  196 (595)
Q Consensus       117 ~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~  196 (595)
                      +.++.+.+.+.+++...+..++..+.+.|++....+    +...++-+|.......+..+.  +....+.++=-.|..+-
T Consensus        15 EYirSl~~~~i~~~~~L~~lli~lLi~~~~~~~L~q----llq~~Vi~DSk~lA~~LLs~~--~~~~~~~Ql~lDMLkRL   88 (167)
T PF07035_consen   15 EYIRSLNQHNIPVQHELYELLIDLLIRNGQFSQLHQ----LLQYHVIPDSKPLACQLLSLG--NQYPPAYQLGLDMLKRL   88 (167)
T ss_pred             HHHHHHHHcCCCCCHHHHHHHHHHHHHcCCHHHHHH----HHhhcccCCcHHHHHHHHHhH--ccChHHHHHHHHHHHHh
Confidence            344455566677777777777777777777554433    333444445444433332222  22233333333333221


Q ss_pred             CCCCccccCcHHHHHHHHHHHHHcCCHhHHHHHHHHHhhCCCCCCHhHHHHHHHHHHhcCCHHHHHHHHHHHH
Q 040027          197 GEIGVVCKPNTVTYSTIIDGLCKEGFVDKAKALFLQMKDENINPDVVTYNSLIHGLCHANDWNEAKRLFIEMM  269 (595)
Q Consensus       197 ~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~~ll~~~~~~~~~~~A~~~~~~~~  269 (595)
                                ...+..++..+...|++-+|..+.+.....    +......++.+..+.+|...-..+|+-..
T Consensus        89 ----------~~~~~~iievLL~~g~vl~ALr~ar~~~~~----~~~~~~~fLeAA~~~~D~~lf~~V~~ff~  147 (167)
T PF07035_consen   89 ----------GTAYEEIIEVLLSKGQVLEALRYARQYHKV----DSVPARKFLEAAANSNDDQLFYAVFRFFE  147 (167)
T ss_pred             ----------hhhHHHHHHHHHhCCCHHHHHHHHHHcCCc----ccCCHHHHHHHHHHcCCHHHHHHHHHHHH
Confidence                      123455666777777777777777665332    11222345555555565555444444443

>COG4455 ImpE Protein of avirulence locus involved in temperature-dependent protein secretion [General function prediction only]

Probab=84.76  E-value=7.5  Score=33.51  Aligned_cols=75  Identities=19%  Similarity=0.134  Sum_probs=50.9

Q ss_pred             HHHHHHHHHhcCChHHHHHHHHhcccCCCCC-CHHHHHHHHHHHHhcCChhHHHHHHHHHHHcC--CCCCHHHHHHHHHH
Q 040027          455 YNCLIDGLCKSGRLKFAWELFCSLPHGVLVP-NVVTYNIMIQGLCNDGQMDKARDLFLDMEENA--AAPDVITFDMLIHG  531 (595)
Q Consensus       455 ~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~p-~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~--~~~~~~~~~~l~~~  531 (595)
                      .+..+..+.+.+...+++...+.-++.  +| |...-..++..++-.|+|++|..-++-.-...  ..+....|..++.+
T Consensus         4 l~~t~seLL~~~sL~dai~~a~~qVka--kPtda~~RhflfqLlcvaGdw~kAl~Ql~l~a~l~p~~t~~a~lyr~lir~   81 (273)
T COG4455           4 LRDTISELLDDNSLQDAIGLARDQVKA--KPTDAGGRHFLFQLLCVAGDWEKALAQLNLAATLSPQDTVGASLYRHLIRC   81 (273)
T ss_pred             hHHHHHHHHHhccHHHHHHHHHHHHhc--CCccccchhHHHHHHhhcchHHHHHHHHHHHhhcCcccchHHHHHHHHHHH
Confidence            344556677888899999888877763  45 44555677788889999999988887776642  12234455555543

>COG4455 ImpE Protein of avirulence locus involved in temperature-dependent protein secretion [General function prediction only]

Probab=84.57  E-value=7.4  Score=33.55  Aligned_cols=53  Identities=21%  Similarity=0.200  Sum_probs=25.1

Q ss_pred             HHHHhcCCHHHHHHHHHHHHHcCCCcCHHHHHHHHHHHHhcCChHHHHHHHHhc
Q 040027          425 DGLCKNGYIIEAVELFRTLRILKCELDIQAYNCLIDGLCKSGRLKFAWELFCSL  478 (595)
Q Consensus       425 ~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~  478 (595)
                      +.+.+.+.+.+++...+.-.+.+ +.|......+++.++-.|++++|..-++-.
T Consensus         9 seLL~~~sL~dai~~a~~qVkak-Ptda~~RhflfqLlcvaGdw~kAl~Ql~l~   61 (273)
T COG4455           9 SELLDDNSLQDAIGLARDQVKAK-PTDAGGRHFLFQLLCVAGDWEKALAQLNLA   61 (273)
T ss_pred             HHHHHhccHHHHHHHHHHHHhcC-CccccchhHHHHHHhhcchHHHHHHHHHHH
Confidence            33444445555555544444433 334444444455555555555555444443

>KOG2066 consensus Vacuolar assembly/sorting protein VPS41 [Intracellular trafficking, secretion, and vesicular transport]

Probab=84.15  E-value=59  Score=34.14  Aligned_cols=151  Identities=15%  Similarity=0.182  Sum_probs=89.5

Q ss_pred             HHHHHHHcCCHhHHHHHHHHHhhCCCCC---CHhHHHHHHHHHHhcCCHHHHHHHHHHHHHCCCCCCHhhHHHHHHHHHh
Q 040027          213 IIDGLCKEGFVDKAKALFLQMKDENINP---DVVTYNSLIHGLCHANDWNEAKRLFIEMMDQGVQPSVVTFNVIMDELCK  289 (595)
Q Consensus       213 l~~~~~~~g~~~~A~~~~~~~~~~~~~~---~~~~~~~ll~~~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~~l~~~~~~  289 (595)
                      -+..+.+.+.+++|+++.+.....  .|   ....+...+..+...|++++|-...-.|...    +...|...+..+..
T Consensus       362 hi~Wll~~k~yeeAl~~~k~~~~~--~~~~~i~kv~~~yI~HLl~~~~y~~Aas~~p~m~gn----~~~eWe~~V~~f~e  435 (846)
T KOG2066|consen  362 HIDWLLEKKKYEEALDAAKASIGN--EERFVIKKVGKTYIDHLLFEGKYDEAASLCPKMLGN----NAAEWELWVFKFAE  435 (846)
T ss_pred             hHHHHHHhhHHHHHHHHHHhccCC--ccccchHHHHHHHHHHHHhcchHHHHHhhhHHHhcc----hHHHHHHHHHHhcc
Confidence            356677888899998887766543  23   3456777888888899999999888888764    56667777776666


Q ss_pred             cCChHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHH------------------HHhcCCCCCHHHHH
Q 040027          290 NRKMDEASRLLDLMVQRGVRPNACTYNTLMDGFCLMGKINRAEELFGS------------------MESMGCKHDDVSYN  351 (595)
Q Consensus       290 ~g~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~------------------~~~~~~~~~~~~~~  351 (595)
                      .++......++   .......++.+|..++..+.. .+...-.++...                  +.+.  ..+.....
T Consensus       436 ~~~l~~Ia~~l---Pt~~~rL~p~vYemvLve~L~-~~~~~F~e~i~~Wp~~Lys~l~iisa~~~q~~q~--Se~~~L~e  509 (846)
T KOG2066|consen  436 LDQLTDIAPYL---PTGPPRLKPLVYEMVLVEFLA-SDVKGFLELIKEWPGHLYSVLTIISATEPQIKQN--SESTALLE  509 (846)
T ss_pred             ccccchhhccC---CCCCcccCchHHHHHHHHHHH-HHHHHHHHHHHhCChhhhhhhHHHhhcchHHHhh--ccchhHHH
Confidence            66655443321   221122345556666555554 221111111111                  1111  11223344


Q ss_pred             HHHHHHHhCCCHHHHHHHHHHHHH
Q 040027          352 ILINGYCKNKEVEEALSLYREMVS  375 (595)
Q Consensus       352 ~l~~~~~~~~~~~~A~~~~~~~~~  375 (595)
                      .|+..|...+++..|+.++-.+..
T Consensus       510 ~La~LYl~d~~Y~~Al~~ylklk~  533 (846)
T KOG2066|consen  510 VLAHLYLYDNKYEKALPIYLKLQD  533 (846)
T ss_pred             HHHHHHHHccChHHHHHHHHhccC
Confidence            577778888888888887766543

>COG1747 Uncharacterized N-terminal domain of the transcription elongation factor GreA [Function unknown]

Probab=84.14  E-value=47  Score=32.97  Aligned_cols=60  Identities=12%  Similarity=0.186  Sum_probs=27.4

Q ss_pred             HHHHHHHHHHHhcCCHhHHHHHHHHHHhcCCCCCHhhHHHHHHHHHhcCChhHHHHHHHHHHh
Q 040027          132 ATFNSLIKGLHAESRIMEAAALFTKLKAFGCEPNVITYNTLINGLCRTGHTMIALNLFEEMAN  194 (595)
Q Consensus       132 ~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~  194 (595)
                      ....+++..+..+.+.+-...+..++...|  .+...+..++..|... ..+.-..+++++.+
T Consensus        67 ~~l~~~~~~f~~n~k~~~veh~c~~~l~~~--e~kmal~el~q~y~en-~n~~l~~lWer~ve  126 (711)
T COG1747          67 SCLVTLLTIFGDNHKNQIVEHLCTRVLEYG--ESKMALLELLQCYKEN-GNEQLYSLWERLVE  126 (711)
T ss_pred             hHHHHHHHHhccchHHHHHHHHHHHHHHhc--chHHHHHHHHHHHHhc-CchhhHHHHHHHHH
Confidence            333444444444444444444555554442  2444445555555444 33344444444444

>PF13181 TPR_8: Tetratricopeptide repeat; PDB: 3GW4_B 3MA5_C 2KCV_A 2KCL_A 3FP3_A 3LCA_A 3FP4_A 3FP2_A 1W3B_B 1ELW_A

Probab=83.99  E-value=3.2  Score=23.32  Aligned_cols=27  Identities=15%  Similarity=0.144  Sum_probs=20.5

Q ss_pred             HHHHHHHHHHHcCChhHHHHHHHHHHH
Q 040027          524 TFDMLIHGFIRINEPSKVNELLHKMKE  550 (595)
Q Consensus       524 ~~~~l~~~~~~~g~~~~A~~~~~~~~~  550 (595)
                      +|..+...|...|++++|.+.|++..+
T Consensus         3 ~~~~lg~~y~~~~~~~~A~~~~~~a~~   29 (34)
T PF13181_consen    3 AYYNLGKIYEQLGDYEEALEYFEKALE   29 (34)
T ss_dssp             HHHHHHHHHHHTTSHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHcCCHHHHHHHHHHHHh
Confidence            466677777788888888888887775

...

>PF04097 Nic96: Nup93/Nic96; InterPro: IPR007231 Nup93/Nic96 is a component of the nuclear pore complex

Probab=83.96  E-value=60  Score=34.12  Aligned_cols=47  Identities=11%  Similarity=0.041  Sum_probs=30.4

Q ss_pred             HHHHHHHHHHHHhcCCHhHHHHHHHHHHhcCCCCCHhhHHHHHHHHHhc
Q 040027          131 AATFNSLIKGLHAESRIMEAAALFTKLKAFGCEPNVITYNTLINGLCRT  179 (595)
Q Consensus       131 ~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~~l~~~~~~~  179 (595)
                      ..+| .++-.|.+.|.+++|.++....... .......+...+..|...
T Consensus       112 ~p~W-a~Iyy~LR~G~~~~A~~~~~~~~~~-~~~~~~~f~~~l~~~~~s  158 (613)
T PF04097_consen  112 DPIW-ALIYYCLRCGDYDEALEVANENRNQ-FQKIERSFPTYLKAYASS  158 (613)
T ss_dssp             EEHH-HHHHHHHTTT-HHHHHHHHHHTGGG-S-TTTTHHHHHHHHCTTT
T ss_pred             CccH-HHHHHHHhcCCHHHHHHHHHHhhhh-hcchhHHHHHHHHHHHhC
Confidence            3344 5677889999999999998555443 333445666677777654

It is required for the correct assembly of the nuclear pore complex []. In Saccharomyces cerevisiae, Nic96 has been shown to be involved in the distribution and cellular concentration of the GTPase Gsp1 []. The structure of Nic96 has revealed a mostly alpha helical structure [].; GO: 0006810 transport, 0005643 nuclear pore; PDB: 2QX5_B 2RFO_A.

>PF13181 TPR_8: Tetratricopeptide repeat; PDB: 3GW4_B 3MA5_C 2KCV_A 2KCL_A 3FP3_A 3LCA_A 3FP4_A 3FP2_A 1W3B_B 1ELW_A

Probab=83.84  E-value=3.2  Score=23.33  Aligned_cols=29  Identities=17%  Similarity=0.085  Sum_probs=23.5

Q ss_pred             HHHHHHHHHHHhcCChhHHHHHHHHHHHc
Q 040027          488 VTYNIMIQGLCNDGQMDKARDLFLDMEEN  516 (595)
Q Consensus       488 ~~~~~l~~~~~~~g~~~~A~~~~~~~~~~  516 (595)
                      .+|..+...|...|++++|...|++.++.
T Consensus         2 ~~~~~lg~~y~~~~~~~~A~~~~~~a~~~   30 (34)
T PF13181_consen    2 EAYYNLGKIYEQLGDYEEALEYFEKALEL   30 (34)
T ss_dssp             HHHHHHHHHHHHTTSHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHcCCHHHHHHHHHHHHhh
Confidence            35677788888889999999988888774

...

>COG2909 MalT ATP-dependent transcriptional regulator [Transcription]

Probab=83.46  E-value=68  Score=34.33  Aligned_cols=93  Identities=22%  Similarity=0.202  Sum_probs=49.2

Q ss_pred             HHhcCCHhHHHHHHHHHHhcCCCCCHh-------hHHHHH-HHHHhcCChhHHHHHHHHHHhcCCCCCccccCcHHHHHH
Q 040027          141 LHAESRIMEAAALFTKLKAFGCEPNVI-------TYNTLI-NGLCRTGHTMIALNLFEEMANGNGEIGVVCKPNTVTYST  212 (595)
Q Consensus       141 ~~~~g~~~~A~~~~~~~~~~~~~~~~~-------~~~~l~-~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~~~~~~~~  212 (595)
                      .....++++|..++.++...-..|+..       .+..+- ......|++++|.++.+.....-.+..  ..+....+..
T Consensus       425 ~~s~~r~~ea~~li~~l~~~l~~~~~~~~~~l~ae~~aL~a~val~~~~~e~a~~lar~al~~L~~~~--~~~r~~~~sv  502 (894)
T COG2909         425 LASQHRLAEAETLIARLEHFLKAPMHSRQGDLLAEFQALRAQVALNRGDPEEAEDLARLALVQLPEAA--YRSRIVALSV  502 (894)
T ss_pred             HHHccChHHHHHHHHHHHHHhCcCcccchhhHHHHHHHHHHHHHHhcCCHHHHHHHHHHHHHhccccc--chhhhhhhhh
Confidence            345677777777777765542222111       122221 122346777777777766655321100  1223445555


Q ss_pred             HHHHHHHcCCHhHHHHHHHHHhh
Q 040027          213 IIDGLCKEGFVDKAKALFLQMKD  235 (595)
Q Consensus       213 l~~~~~~~g~~~~A~~~~~~~~~  235 (595)
                      +..+..-.|++++|..+.....+
T Consensus       503 ~~~a~~~~G~~~~Al~~~~~a~~  525 (894)
T COG2909         503 LGEAAHIRGELTQALALMQQAEQ  525 (894)
T ss_pred             hhHHHHHhchHHHHHHHHHHHHH
Confidence            66666667777777776665544

>TIGR02561 HrpB1_HrpK type III secretion protein HrpB1/HrpK

Probab=83.35  E-value=22  Score=28.71  Aligned_cols=52  Identities=21%  Similarity=0.149  Sum_probs=31.8

Q ss_pred             hcCChHHHHHHHHhcccCCCCCCHHHH-HHHHHHHHhcCChhHHHHHHHHHHHcC
Q 040027          464 KSGRLKFAWELFCSLPHGVLVPNVVTY-NIMIQGLCNDGQMDKARDLFLDMEENA  517 (595)
Q Consensus       464 ~~g~~~~A~~~~~~~~~~~~~p~~~~~-~~l~~~~~~~g~~~~A~~~~~~~~~~~  517 (595)
                      ..++.+++..+++.+.-  +.|+..-. ..-.+.+...|+|++|+++|++..+.+
T Consensus        22 ~~~d~~D~e~lLdALrv--LrP~~~e~d~~dg~l~i~rg~w~eA~rvlr~l~~~~   74 (153)
T TIGR02561        22 RSADPYDAQAMLDALRV--LRPNLKELDMFDGWLLIARGNYDEAARILRELLSSA   74 (153)
T ss_pred             hcCCHHHHHHHHHHHHH--hCCCccccchhHHHHHHHcCCHHHHHHHHHhhhccC
Confidence            46777777777777665  45543211 222344567777777777777777653

This gene is found within type III secretion operons in a limited range of species including Xanthomonas, Ralstonia and Burkholderia.

>KOG4570 consensus Uncharacterized conserved protein [Function unknown]

Probab=82.96  E-value=26  Score=32.22  Aligned_cols=49  Identities=16%  Similarity=0.232  Sum_probs=28.1

Q ss_pred             CHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHccCCHHHHHHHHHHHHH
Q 040027          362 EVEEALSLYREMVSKGIKPTVVTYNTLFLGLFEIHQVEHALKLFDEMQR  410 (595)
Q Consensus       362 ~~~~A~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~  410 (595)
                      +.++++.++..=+..|+-||..+++.++..+.+.+++.+|..+.-.|..
T Consensus       115 ~pq~~i~~l~npIqYGiF~dqf~~c~l~D~flk~~n~~~aa~vvt~~~~  163 (418)
T KOG4570|consen  115 DPQKAIYTLVNPIQYGIFPDQFTFCLLMDSFLKKENYKDAASVVTEVMM  163 (418)
T ss_pred             ChHHHHHHHhCcchhccccchhhHHHHHHHHHhcccHHHHHHHHHHHHH
Confidence            4445555555555556666666666666666666666555555554443

>cd00923 Cyt_c_Oxidase_Va Cytochrome c oxidase subunit Va

Probab=82.92  E-value=16  Score=26.83  Aligned_cols=65  Identities=12%  Similarity=0.152  Sum_probs=51.6

Q ss_pred             ChhHHHHHHHHHHHcCCCCCHHHHHHHHHHHHHcCChhHHHHHHHHHHHCCCCCCHHHHHHHHHHH
Q 040027          502 QMDKARDLFLDMEENAAAPDVITFDMLIHGFIRINEPSKVNELLHKMKEKKVMPDASIVSIVVDLL  567 (595)
Q Consensus       502 ~~~~A~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~p~~~~~~~l~~~~  567 (595)
                      |.-++.+-++.+...++-|++.+....+++|.+.+++.-|.++++-.+.+ ...+..+|..+++-+
T Consensus        22 D~we~rr~mN~l~~~DlVP~P~ii~aaLrAcRRvND~alAVR~lE~vK~K-~~~~~~~y~~~lqei   86 (103)
T cd00923          22 DGWELRRGLNNLFGYDLVPEPKVIEAALRACRRVNDFALAVRILEAIKDK-CGAHKEIYPYILQEI   86 (103)
T ss_pred             cHHHHHHHHHHHhccccCCCcHHHHHHHHHHHHhhhHHHHHHHHHHHHHH-ccCchhhHHHHHHHH
Confidence            44467777888888888999999999999999999999999999988843 223556777766543

Cytochrome c oxidase (CcO), the terminal oxidase in the respiratory chains of eukaryotes and most bacteria, is a multi-chain transmembrane protein located in the inner membrane of mitochondria and the cell membrane of prokaryotes. It catalyzes the reduction of O2 and simultaneously pumps protons across the membrane. The number of subunits varies from three to five in bacteria and up to 13 in mammalian mitochondria. Subunits I, II, and III of mammalian CcO are encoded within the mitochondrial genome and the remaining 10 subunits are encoded within the nuclear genome. Found only in eukaryotes, subunit Va is one of three mammalian subunits that lacks a transmembrane region. Subunit Va is located on the matrix side of the membrane and binds thyroid hormone T2, releasing allosteric inhibition caused by the binding of ATP to subunit IV and allowing high turnover at elevated intramitochondrial ATP/ADP ratios.

>PF07721 TPR_4: Tetratricopeptide repeat; InterPro: IPR011717 This entry includes tetratricopeptide-like repeats not detected by the IPR001440 from INTERPRO, IPR013105 from INTERPRO and IPR011716 from INTERPRO models

Probab=82.70  E-value=2  Score=22.63  Aligned_cols=21  Identities=10%  Similarity=-0.083  Sum_probs=11.3

Q ss_pred             HHHHHHHHhcCChhHHHHHHH
Q 040027          100 NILINCFCKIGRVSLGFIAFG  120 (595)
Q Consensus       100 ~~l~~~~~~~g~~~~A~~~~~  120 (595)
                      ..+...+...|++++|..+++
T Consensus         5 ~~la~~~~~~G~~~eA~~~l~   25 (26)
T PF07721_consen    5 LALARALLAQGDPDEAERLLR   25 (26)
T ss_pred             HHHHHHHHHcCCHHHHHHHHh
Confidence            344555555555555555543

The tetratricopeptide repeat (TPR) motif is a protein-protein interaction module found in multiple copies in a number of functionally different proteins that facilitates specific interactions with a partner protein(s) [].; GO: 0042802 identical protein binding

>PF13174 TPR_6: Tetratricopeptide repeat; PDB: 3QKY_A 2XEV_A 3URZ_B 2Q7F_A

Probab=82.52  E-value=2.6  Score=23.39  Aligned_cols=27  Identities=7%  Similarity=0.277  Sum_probs=21.2

Q ss_pred             HHHHHHHHHHcCChhHHHHHHHHHHHC
Q 040027          525 FDMLIHGFIRINEPSKVNELLHKMKEK  551 (595)
Q Consensus       525 ~~~l~~~~~~~g~~~~A~~~~~~~~~~  551 (595)
                      +..++.++.+.|++++|.+.|+++++.
T Consensus         3 ~~~~a~~~~~~g~~~~A~~~~~~~~~~   29 (33)
T PF13174_consen    3 LYRLARCYYKLGDYDEAIEYFQRLIKR   29 (33)
T ss_dssp             HHHHHHHHHHHCHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHccCHHHHHHHHHHHHHH
Confidence            456777888888888888888888763

>PF08424 NRDE-2: NRDE-2, necessary for RNA interference; InterPro: IPR013633 This is domain is found in eukaryotic proteins of unknown function

Probab=82.30  E-value=46  Score=31.57  Aligned_cols=120  Identities=9%  Similarity=0.008  Sum_probs=73.0

Q ss_pred             HHHHHHHHHHHHcCCCcCHHHHHHHHHHHHhcCChHHHHHHHHhcccCCCCC-CHHHHHHHHHHHHh---cCChhHHHHH
Q 040027          434 IEAVELFRTLRILKCELDIQAYNCLIDGLCKSGRLKFAWELFCSLPHGVLVP-NVVTYNIMIQGLCN---DGQMDKARDL  509 (595)
Q Consensus       434 ~~A~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~p-~~~~~~~l~~~~~~---~g~~~~A~~~  509 (595)
                      +.-+.+++++++.+ +.+...+..++..+.+..+.++..+.|+++...  .| +...|...+.....   .-.++....+
T Consensus        48 E~klsilerAL~~n-p~~~~L~l~~l~~~~~~~~~~~l~~~we~~l~~--~~~~~~LW~~yL~~~q~~~~~f~v~~~~~~  124 (321)
T PF08424_consen   48 ERKLSILERALKHN-PDSERLLLGYLEEGEKVWDSEKLAKKWEELLFK--NPGSPELWREYLDFRQSNFASFTVSDVRDV  124 (321)
T ss_pred             HHHHHHHHHHHHhC-CCCHHHHHHHHHHHHHhCCHHHHHHHHHHHHHH--CCCChHHHHHHHHHHHHHhccCcHHHHHHH
Confidence            44556667766664 556666777777777777777777777777763  23 45666666654443   2345566665


Q ss_pred             HHHHHHc------CC------CCC-----HHHHHHHHHHHHHcCChhHHHHHHHHHHHCCC-CCC
Q 040027          510 FLDMEEN------AA------APD-----VITFDMLIHGFIRINEPSKVNELLHKMKEKKV-MPD  556 (595)
Q Consensus       510 ~~~~~~~------~~------~~~-----~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~-~p~  556 (595)
                      |.+.+..      +.      .++     ...+..+...+..+|..+.|..+++-+++.++ .|+
T Consensus       125 y~~~l~~L~~~~~~~~~~~~~~~~~e~~~l~v~~r~~~fl~~aG~~E~Ava~~Qa~lE~n~~~P~  189 (321)
T PF08424_consen  125 YEKCLRALSRRRSGRMTSHPDLPELEEFMLYVFLRLCRFLRQAGYTERAVALWQALLEFNFFRPE  189 (321)
T ss_pred             HHHHHHHHHHhhccccccccchhhHHHHHHHHHHHHHHHHHHCCchHHHHHHHHHHHHHHcCCcc
Confidence            5555431      11      011     12233344445678999999999999998876 343

>PF13174 TPR_6: Tetratricopeptide repeat; PDB: 3QKY_A 2XEV_A 3URZ_B 2Q7F_A

Probab=82.11  E-value=2.1  Score=23.85  Aligned_cols=24  Identities=25%  Similarity=0.610  Sum_probs=11.5

Q ss_pred             HHHHHHhcCChhHHHHHHHHHHhC
Q 040027          102 LINCFCKIGRVSLGFIAFGRILRS  125 (595)
Q Consensus       102 l~~~~~~~g~~~~A~~~~~~~~~~  125 (595)
                      ++.++.+.|++++|...|+++++.
T Consensus         6 ~a~~~~~~g~~~~A~~~~~~~~~~   29 (33)
T PF13174_consen    6 LARCYYKLGDYDEAIEYFQRLIKR   29 (33)
T ss_dssp             HHHHHHHHCHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHccCHHHHHHHHHHHHHH
Confidence            344444445555555555554443

>TIGR03504 FimV_Cterm FimV C-terminal domain

Probab=80.89  E-value=4  Score=24.98  Aligned_cols=23  Identities=26%  Similarity=0.478  Sum_probs=12.1

Q ss_pred             HHHHHHHcCChhHHHHHHHHHHH
Q 040027          528 LIHGFIRINEPSKVNELLHKMKE  550 (595)
Q Consensus       528 l~~~~~~~g~~~~A~~~~~~~~~  550 (595)
                      +..+|...|+.+.|.+++++...
T Consensus         5 LA~ayie~Gd~e~Ar~lL~evl~   27 (44)
T TIGR03504         5 LARAYIEMGDLEGARELLEEVIE   27 (44)
T ss_pred             HHHHHHHcCChHHHHHHHHHHHH
Confidence            44455555555555555555553

This protein is found at the extreme C-terminus of FimV from Pseudomonas aeruginosa, and of TspA of Neisseria meningitidis. Disruption of the former blocks twitching motility from type IV pili; Semmler, et al. suggest a role in peptidoglycan layer remodelling required by type IV fimbrial systems.

>COG2909 MalT ATP-dependent transcriptional regulator [Transcription]

Probab=80.39  E-value=88  Score=33.56  Aligned_cols=223  Identities=15%  Similarity=0.072  Sum_probs=120.5

Q ss_pred             HHHcCCHhHHHHHHHHHhhCCCCCC----H---hHHHHHH-HHHHhcCCHHHHHHHHHHHHHC----CCCCCHhhHHHHH
Q 040027          217 LCKEGFVDKAKALFLQMKDENINPD----V---VTYNSLI-HGLCHANDWNEAKRLFIEMMDQ----GVQPSVVTFNVIM  284 (595)
Q Consensus       217 ~~~~g~~~~A~~~~~~~~~~~~~~~----~---~~~~~ll-~~~~~~~~~~~A~~~~~~~~~~----~~~~~~~~~~~l~  284 (595)
                      .....++++|..++.++...-..|+    .   ..|+.|- ......|++++|.++-+.....    -..+....+..+.
T Consensus       425 ~~s~~r~~ea~~li~~l~~~l~~~~~~~~~~l~ae~~aL~a~val~~~~~e~a~~lar~al~~L~~~~~~~r~~~~sv~~  504 (894)
T COG2909         425 LASQHRLAEAETLIARLEHFLKAPMHSRQGDLLAEFQALRAQVALNRGDPEEAEDLARLALVQLPEAAYRSRIVALSVLG  504 (894)
T ss_pred             HHHccChHHHHHHHHHHHHHhCcCcccchhhHHHHHHHHHHHHHHhcCCHHHHHHHHHHHHHhcccccchhhhhhhhhhh
Confidence            3456889999988888765421222    1   1334333 3345678999999888877654    1223455667777


Q ss_pred             HHHHhcCChHHHHHHHHHHHHCCCCCCHHHHHH---H--HHHHHhcCC--HHHHHHHHHHHHhcC---CCC---CHHHHH
Q 040027          285 DELCKNRKMDEASRLLDLMVQRGVRPNACTYNT---L--MDGFCLMGK--INRAEELFGSMESMG---CKH---DDVSYN  351 (595)
Q Consensus       285 ~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~---l--~~~~~~~~~--~~~a~~~~~~~~~~~---~~~---~~~~~~  351 (595)
                      .+..-.|++++|..+..+..+..-..+...+..   +  ...+...|+  +.+....+..+....   .+.   -...+.
T Consensus       505 ~a~~~~G~~~~Al~~~~~a~~~a~~~~~~~l~~~~~~~~s~il~~qGq~~~a~~~~~~~~~~~q~l~q~~~~~f~~~~r~  584 (894)
T COG2909         505 EAAHIRGELTQALALMQQAEQMARQHDVYHLALWSLLQQSEILEAQGQVARAEQEKAFNLIREQHLEQKPRHEFLVRIRA  584 (894)
T ss_pred             HHHHHhchHHHHHHHHHHHHHHHHHcccHHHHHHHHHHHHHHHHHhhHHHHHHHHHHHHHHHHHHhhhcccchhHHHHHH
Confidence            888889999999988877766422223332222   2  233455663  233333333332211   011   122344


Q ss_pred             HHHHHHHhCCCHHHHHHHH----HHHHHCCCCCCHHHH--HHHHHHHHccCCHHHHHHHHHHHHHCCCCC----CHHHHH
Q 040027          352 ILINGYCKNKEVEEALSLY----REMVSKGIKPTVVTY--NTLFLGLFEIHQVEHALKLFDEMQRDGVAA----DTRTYT  421 (595)
Q Consensus       352 ~l~~~~~~~~~~~~A~~~~----~~~~~~~~~~~~~~~--~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~----~~~~~~  421 (595)
                      .+..++.+   .+.+..-.    .-.......|-....  ..++......|+.++|...++++......+    +.....
T Consensus       585 ~ll~~~~r---~~~~~~ear~~~~~~~~~~~~~~~~~~~~~~LA~l~~~~Gdl~~A~~~l~~~~~l~~~~~~~~~~~a~~  661 (894)
T COG2909         585 QLLRAWLR---LDLAEAEARLGIEVGSVYTPQPLLSRLALSMLAELEFLRGDLDKALAQLDELERLLLNGQYHVDYLAAA  661 (894)
T ss_pred             HHHHHHHH---HhhhhHHhhhcchhhhhcccchhHHHHHHHHHHHHHHhcCCHHHHHHHHHHHHHHhcCCCCCchHHHHH
Confidence            44445544   33333322    222222222222222  366777788999999999998887642222    222222


Q ss_pred             HHH--HHHHhcCCHHHHHHHHHH
Q 040027          422 TFI--DGLCKNGYIIEAVELFRT  442 (595)
Q Consensus       422 ~l~--~~~~~~g~~~~A~~~~~~  442 (595)
                      ..+  ......|+.+.+.....+
T Consensus       662 ~~v~~~lwl~qg~~~~a~~~l~~  684 (894)
T COG2909         662 YKVKLILWLAQGDKELAAEWLLK  684 (894)
T ss_pred             HHhhHHHhcccCCHHHHHHHHHh
Confidence            222  223457888887777665

>COG3947 Response regulator containing CheY-like receiver and SARP domains [Signal transduction mechanisms]

Probab=80.09  E-value=33  Score=31.27  Aligned_cols=60  Identities=10%  Similarity=0.081  Sum_probs=46.1

Q ss_pred             HHHHHHHHHhcCChhHHHHHHHHHHhcCCCCCccccCcHHHHHHHHHHHHHcCCHhHHHHHHHHHhh
Q 040027          169 YNTLINGLCRTGHTMIALNLFEEMANGNGEIGVVCKPNTVTYSTIIDGLCKEGFVDKAKALFLQMKD  235 (595)
Q Consensus       169 ~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~  235 (595)
                      +......|..+|.+.+|.++.+...+.+       +.+...+..++..++..||--.+.+-++++.+
T Consensus       282 lgkva~~yle~g~~neAi~l~qr~ltld-------pL~e~~nk~lm~~la~~gD~is~~khyerya~  341 (361)
T COG3947         282 LGKVARAYLEAGKPNEAIQLHQRALTLD-------PLSEQDNKGLMASLATLGDEISAIKHYERYAE  341 (361)
T ss_pred             HHHHHHHHHHcCChHHHHHHHHHHhhcC-------hhhhHHHHHHHHHHHHhccchhhhhHHHHHHH
Confidence            3455677788889999999888888876       56777888888888888887777766666543

>PF10345 Cohesin_load: Cohesin loading factor; InterPro: IPR019440 Cohesin loading factor is a conserved protein that has been characterised in fungi

Probab=80.03  E-value=84  Score=33.12  Aligned_cols=443  Identities=13%  Similarity=0.090  Sum_probs=203.7

Q ss_pred             CHHHHHHHHHHHHhcCChhHHHHHHHHHHh-CCCCCC--HHHHHHHHHHHH-hcCCHhHHHHHHHHHHhcCCCCCHh---
Q 040027           95 NLYTYNILINCFCKIGRVSLGFIAFGRILR-SCFTPN--AATFNSLIKGLH-AESRIMEAAALFTKLKAFGCEPNVI---  167 (595)
Q Consensus        95 ~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~-~~~~~~--~~~~~~l~~~~~-~~g~~~~A~~~~~~~~~~~~~~~~~---  167 (595)
                      +...|..+|..         |+..++.+.+ ..++|.  ..++..+...+. ...+++.|...+++.....-.++..   
T Consensus        29 ~l~~Y~kLI~~---------ai~CL~~~~~~~~l~p~~ea~~~l~la~iL~~eT~n~~~Ae~~L~k~~~l~~~~~~~d~k   99 (608)
T PF10345_consen   29 QLKQYYKLIAT---------AIKCLEAVLKQFKLSPRQEARVRLRLASILLEETENLDLAETYLEKAILLCERHRLTDLK   99 (608)
T ss_pred             hHHHHHHHHHH---------HHHHHHHHhccCCCCHHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhccccchHHHH
Confidence            44555555543         3445555553 222332  224455666665 4678888888887765443222211   


Q ss_pred             --hHHHHHHHHHhcCChhHHHHHHHHHHhcCCCCCccccCcHHHHHHH-HHHHHHcCCHhHHHHHHHHHhhCC---CCCC
Q 040027          168 --TYNTLINGLCRTGHTMIALNLFEEMANGNGEIGVVCKPNTVTYSTI-IDGLCKEGFVDKAKALFLQMKDEN---INPD  241 (595)
Q Consensus       168 --~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~~~~~~~~l-~~~~~~~g~~~~A~~~~~~~~~~~---~~~~  241 (595)
                        .-..++..+.+.+... |+..+++..+.-...+  ..+-...+..+ +..+...+++..|.+.++.+...-   ..|.
T Consensus       100 ~~~~~ll~~i~~~~~~~~-a~~~l~~~I~~~~~~~--~~~w~~~frll~~~l~~~~~d~~~Al~~L~~~~~~a~~~~d~~  176 (608)
T PF10345_consen  100 FRCQFLLARIYFKTNPKA-ALKNLDKAIEDSETYG--HSAWYYAFRLLKIQLALQHKDYNAALENLQSIAQLANQRGDPA  176 (608)
T ss_pred             HHHHHHHHHHHHhcCHHH-HHHHHHHHHHHHhccC--chhHHHHHHHHHHHHHHhcccHHHHHHHHHHHHHHhhhcCCHH
Confidence              1234456666666555 8877777665431100  00112222223 223333478888888887765531   2233


Q ss_pred             HhHHHHHHHHHH--hcCCHHHHHHHHHHHHHCC--C-------CCCHhhHHHHHHH--HHhcCChHHHHHHHHHHHH---
Q 040027          242 VVTYNSLIHGLC--HANDWNEAKRLFIEMMDQG--V-------QPSVVTFNVIMDE--LCKNRKMDEASRLLDLMVQ---  305 (595)
Q Consensus       242 ~~~~~~ll~~~~--~~~~~~~A~~~~~~~~~~~--~-------~~~~~~~~~l~~~--~~~~g~~~~a~~~~~~~~~---  305 (595)
                      ..++..++.+..  ..+..+++.+..+.+....  +       .|...+|..++..  +...|++..+...++++.+   
T Consensus       177 ~~v~~~l~~~~l~l~~~~~~d~~~~l~~~~~~~~~~q~~~~~~~~qL~~~~lll~l~~~l~~~~~~~~~~~L~~lq~~~~  256 (608)
T PF10345_consen  177 VFVLASLSEALLHLRRGSPDDVLELLQRAIAQARSLQLDPSVHIPQLKALFLLLDLCCSLQQGDVKNSKQKLKQLQQFLD  256 (608)
T ss_pred             HHHHHHHHHHHHHhcCCCchhHHHHHHHHHHHHhhcccCCCCCcHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHH
Confidence            334444444333  3455666666666553321  1       2234455555553  3456666666655554432   


Q ss_pred             ----CC-CC----------------------CCH---------HHHHHHHH--HHHhcCCHHHHHHHHHH-------HH-
Q 040027          306 ----RG-VR----------------------PNA---------CTYNTLMD--GFCLMGKINRAEELFGS-------ME-  339 (595)
Q Consensus       306 ----~~-~~----------------------~~~---------~~~~~l~~--~~~~~~~~~~a~~~~~~-------~~-  339 (595)
                          .. .+                      +..         ..+..++.  .....+..+++.+++++       .. 
T Consensus       257 ~~~~~~~w~~~~~d~~i~l~~~~~~~~~~~~~~~f~wl~~~~l~~L~y~lS~l~~~~~~~~~ks~k~~~k~l~~i~~~~~  336 (608)
T PF10345_consen  257 EIKKSPSWPSWDEDGSIPLNIGEGSSNSGGTPLVFSWLPKEELYALVYFLSGLHNLYKGSMDKSEKFLEKALKQIEKLKI  336 (608)
T ss_pred             HhhcCccCCCcCCCeeEEeecccccccCCCceeEEeecCHHHHHHHHHHHHHHHHhhccCchHHHHHHHHHHHHHHHhhc
Confidence                10 00                      000         01111111  22233444455555444       33 


Q ss_pred             hcCCCCC--H------HHHHHHHH---------HHHhCCCHHHHHHHHHHHHHCCC-CCC-------HHHHHHHHHHHHc
Q 040027          340 SMGCKHD--D------VSYNILIN---------GYCKNKEVEEALSLYREMVSKGI-KPT-------VVTYNTLFLGLFE  394 (595)
Q Consensus       340 ~~~~~~~--~------~~~~~l~~---------~~~~~~~~~~A~~~~~~~~~~~~-~~~-------~~~~~~l~~~~~~  394 (595)
                      .....++  .      ..|...+.         ...-.+++..|...+..+..... .|+       +..+....-.+-.
T Consensus       337 ~~~~~~~~sl~~~~~~~~~~~~l~~~~~~y~~~~~~~~~~~~~a~~~l~~~~~~~~~~~~~~~~~~~~~~~yL~gl~~q~  416 (608)
T PF10345_consen  337 KSPSAPSESLSEASERIQWLRYLQCYLLFYQIWCNFIRGDWSKATQELEFMRQLCQRSPSKLYESLYPLLHYLLGLYYQS  416 (608)
T ss_pred             cCCCCCCcCHHHHHHhHHHHHHHHHHHHHHHHHHHHHCcCHHHHHHHHHHHHHHHhcCccchhhhhhHHHHHHHHHHHHH
Confidence            1110111  0      11222222         22347889999999988876421 111       2222222333446


Q ss_pred             cCCHHHHHHHHH--------HHHHCCCCCCHHHHHHH--HHHHHhcC--CHHH--HHHHHHHHHHc-CCCc--CHHHHHH
Q 040027          395 IHQVEHALKLFD--------EMQRDGVAADTRTYTTF--IDGLCKNG--YIIE--AVELFRTLRIL-KCEL--DIQAYNC  457 (595)
Q Consensus       395 ~~~~~~a~~~~~--------~~~~~~~~~~~~~~~~l--~~~~~~~g--~~~~--A~~~~~~~~~~-~~~~--~~~~~~~  457 (595)
                      .|+.+.|...|.        .....+...+..++..+  +-.+...+  ...+  +..+++.+... .-.+  +..++..
T Consensus       417 ~g~l~~A~~~y~~~~~~~~~~~~~~~~~~El~ila~LNl~~I~~~~~~~~~~~~~~~~l~~~i~p~~~~~~~~~~~~a~~  496 (608)
T PF10345_consen  417 TGDLEAALYQYQKPRFLLCEAANRKSKFRELYILAALNLAIILQYESSRDDSESELNELLEQIEPLCSNSPNSYNRTAYC  496 (608)
T ss_pred             cCCHHHHHHHHhhhHHhhhhhhccCCcchHHHHHHHHHHHHHhHhhcccchhhhHHHHHHHhcCccccCCccHHHHHHHH
Confidence            799999999997        33344333333333221  11222222  2222  66666666532 1122  2233333


Q ss_pred             HH-HHHHhcCC--hHHHHHHHHhcccCC---CCCC---HHHHHHHHHHHHhcCChhHHHHHHHHHHHcCC-CC--CHHHH
Q 040027          458 LI-DGLCKSGR--LKFAWELFCSLPHGV---LVPN---VVTYNIMIQGLCNDGQMDKARDLFLDMEENAA-AP--DVITF  525 (595)
Q Consensus       458 l~-~~~~~~g~--~~~A~~~~~~~~~~~---~~p~---~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~-~~--~~~~~  525 (595)
                      ++ .++.....  ..++...+.+..+.-   ...+   ..+++.+...+. .|+..+..+.......... .|  ....|
T Consensus       497 ~~~~~~~~~~~~~~ne~k~~l~~~L~~~~~~~~n~~l~~~~L~lm~~~lf-~~~~~e~~~~s~~a~~~A~k~~d~~~~LW  575 (608)
T PF10345_consen  497 LVLATYNTFEPFSSNEAKRHLQEALKMANNKLGNSQLLAILLNLMGHRLF-EGDVGEQAKKSARAFQLAKKSSDYSDQLW  575 (608)
T ss_pred             HHHHHHhhCCccccHHHHHHHHHHHHHHHHhhccchHHHHHHHHHHHHHH-cCCHHHHHHHHHHHHHHHHhhhhhhhHHH
Confidence            33 22221111  123333333322210   1111   122333333333 7888876666555443211 12  23344


Q ss_pred             H-----HHHHHHHHcCChhHHHHHHHHHHH
Q 040027          526 D-----MLIHGFIRINEPSKVNELLHKMKE  550 (595)
Q Consensus       526 ~-----~l~~~~~~~g~~~~A~~~~~~~~~  550 (595)
                      .     .+...|-..|+.++|.....+...
T Consensus       576 ~~v~~~~l~~~~~~~G~~~ka~~~~~~~~~  605 (608)
T PF10345_consen  576 HLVASGMLADSYEVQGDRDKAEEARQQLDR  605 (608)
T ss_pred             HHHHHHHHHHHHHHcCcHHHHHHHHHHHHH
Confidence            2     334457778999999988887653

It is associated with the cohesin complex and is required in G1 for cohesin binding to chromosomes, but is dispensable in G2 when cohesion has been established. It is often referred to as Ssl3 in Schizosaccharomyces pombe (Fission yeast), and Scc4 in Saccharomyces cerevisiae (Baker's yeast). It complexes with Mis4 [].

---

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

No homologous structure with e-value below 0.005

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Length	Definition	E-value
Query	595
3spa_A	1134	Mtrpol, DNA-directed RNA polymerase, mitochondrial	7e-21
3spa_A	1134	Mtrpol, DNA-directed RNA polymerase, mitochondrial	2e-19
3spa_A	1134	Mtrpol, DNA-directed RNA polymerase, mitochondrial	3e-15
3spa_A	1134	Mtrpol, DNA-directed RNA polymerase, mitochondrial	8e-15
3spa_A	1134	Mtrpol, DNA-directed RNA polymerase, mitochondrial	5e-08
1vt4_I	1221	APAF-1 related killer DARK; drosophila apoptosome,	3e-12

>3spa_A Mtrpol, DNA-directed RNA polymerase, mitochondrial; single-subunit DNA-dependent RNA polymerase in mitochondria, transferase; 2.50A {Homo sapiens} Length = 1134

 Score = 96.4 bits (238), Expect = 7e-21
 Identities = 26/247 (10%), Positives = 78/247 (31%), Gaps = 5/247 (2%)

Query: 128 TPNAATFNSLIKGLHAESRIMEAAALFTKLKAFGCEPNVITYNTLINGLCRTGHTMIALN 187
           +P       L++    +  +    A   +                      T    +A +
Sbjct: 89  SPWEEQLARLLQEAPGKLSLDVEQAPSGQHSQAQLSGQQQRLLAFFKCCLLTDQLPLAHH 148

Query: 188 LFEEMANGNGEIGVVCKPNTVTYSTIIDGLCKEGFVDKAKALFLQMKDENINPDVVTYNS 247
           L         +  +        Y+ ++ G  ++G   +   +   +KD  + PD+++Y +
Sbjct: 149 LLVVHHGQRQKRKL---LTLDMYNAVMLGWARQGAFKELVYVLFMVKDAGLTPDLLSYAA 205

Query: 248 LIHGLCHANDWNEA-KRLFIEMMDQGVQPSVVTFNVIMDELCKNRKMDEASRLLDLMVQR 306
            +  +   +      +R   +M  +G++   +   V++ E  +   +    ++       
Sbjct: 206 ALQCMGRQDQDAGTIERCLEQMSQEGLKLQALFTAVLLSEEDRATVLKAVHKVKPTFSLP 265

Query: 307 GVRPNACTYNTLMDGFCLMGKINRAEELFGSMESMGCKHDDVSYNILINGYCKNKEVEEA 366
              P     + L+             +L   ++++ C  +    ++ +        VE+ 
Sbjct: 266 PQLPPPVNTSKLLRDVYAKDGRVSYPKLHLPLKTLQCLFEK-QLHMELASRVCVVSVEKP 324

Query: 367 LSLYREM 373
               +E+
Sbjct: 325 TLPSKEV 331

>3spa_A Mtrpol, DNA-directed RNA polymerase, mitochondrial; single-subunit DNA-dependent RNA polymerase in mitochondria, transferase; 2.50A {Homo sapiens} Length = 1134

 Score = 92.2 bits (227), Expect = 2e-19
 Identities = 27/232 (11%), Positives = 63/232 (27%), Gaps = 4/232 (1%)

Query: 226 AKALFLQMKDENINPDVVTYNSLIHGLCHANDWNEAKRLFIEMMDQGVQPSVVTFNVIMD 285
           A  L    +    +P       L+         +  +    +     +            
Sbjct: 76  AGCLEDCTRQAPESPWEEQLARLLQEAPGKLSLDVEQAPSGQHSQAQLSGQQQRLLAFFK 135

Query: 286 ELCKNRKMDEASRLLDL---MVQRGVRPNACTYNTLMDGFCLMGKINRAEELFGSMESMG 342
                 ++  A  LL +     Q+        YN +M G+   G       +   ++  G
Sbjct: 136 CCLLTDQLPLAHHLLVVHHGQRQKRKLLTLDMYNAVMLGWARQGAFKELVYVLFMVKDAG 195

Query: 343 CKHDDVSYNILINGYCKNKEVEEALSLY-REMVSKGIKPTVVTYNTLFLGLFEIHQVEHA 401
              D +SY   +    +  +    +     +M  +G+K   +    L         ++  
Sbjct: 196 LTPDLLSYAAALQCMGRQDQDAGTIERCLEQMSQEGLKLQALFTAVLLSEEDRATVLKAV 255

Query: 402 LKLFDEMQRDGVAADTRTYTTFIDGLCKNGYIIEAVELFRTLRILKCELDIQ 453
            K+                +  +  +      +   +L   L+ L+C  + Q
Sbjct: 256 HKVKPTFSLPPQLPPPVNTSKLLRDVYAKDGRVSYPKLHLPLKTLQCLFEKQ 307

>3spa_A Mtrpol, DNA-directed RNA polymerase, mitochondrial; single-subunit DNA-dependent RNA polymerase in mitochondria, transferase; 2.50A {Homo sapiens} Length = 1134

 Score = 78.7 bits (192), Expect = 3e-15
 Identities = 25/238 (10%), Positives = 68/238 (28%), Gaps = 15/238 (6%)

Query: 43  NVITPNEAFCIFDYMLRMHPSP-----PPVSSFNILLASLAKNKHYDTRLNATGLFPNLY 97
            +++   A C+ D   +   SP       +        SL   +    + +   L     
Sbjct: 69  RLLSKQMAGCLEDCTRQAPESPWEEQLARLLQEAPGKLSLDVEQAPSGQHSQAQLSGQQQ 128

Query: 98  TYNILINCFCKIGRVSLG---FIAFGRILRSCFTPNAATFNSLIKGLHAESRIMEAAALF 154
                  C     ++ L     +      +         +N+++ G   +    E   + 
Sbjct: 129 RLLAFFKCCLLTDQLPLAHHLLVVHHGQRQKRKLLTLDMYNAVMLGWARQGAFKELVYVL 188

Query: 155 TKLKAFGCEPNVITYNTLINGLCRTGHTMIALN-LFEEMANGNGEIGVVCKPNTVTYSTI 213
             +K  G  P++++Y   +  + R       +    E+M+          K   +  + +
Sbjct: 189 FMVKDAGLTPDLLSYAAALQCMGRQDQDAGTIERCLEQMSQEG------LKLQALFTAVL 242

Query: 214 IDGLCKEGFVDKAKALFLQMKDENINPDVVTYNSLIHGLCHANDWNEAKRLFIEMMDQ 271
           +    +   +     +          P  V  + L+  +   +      +L + +   
Sbjct: 243 LSEEDRATVLKAVHKVKPTFSLPPQLPPPVNTSKLLRDVYAKDGRVSYPKLHLPLKTL 300

>3spa_A Mtrpol, DNA-directed RNA polymerase, mitochondrial; single-subunit DNA-dependent RNA polymerase in mitochondria, transferase; 2.50A {Homo sapiens} Length = 1134

 Score = 77.2 bits (188), Expect = 8e-15
 Identities = 23/267 (8%), Positives = 58/267 (21%), Gaps = 39/267 (14%)

Query: 294 DEASRLLDLMVQRGVRPNACTYNTLMDGFCLMGKINRAEELFGSMESMGCKHDDVSYNIL 353
             A  L D   Q    P       L+        ++  +   G                 
Sbjct: 74  QMAGCLEDCTRQAPESPWEEQLARLLQEAPGKLSLDVEQAPSGQHSQAQLSGQQQRLLAF 133

Query: 354 INGYCKNKEVEEALSL---YREMVSKGIKPTVVTYNTLFLGLFEIHQVEHALKLFDEMQR 410
                   ++  A  L   +     K    T+  YN + LG       +  + +   ++ 
Sbjct: 134 FKCCLLTDQLPLAHHLLVVHHGQRQKRKLLTLDMYNAVMLGWARQGAFKELVYVLFMVKD 193

Query: 411 DGVAADTRTYTTFIDGLCKNGYIIEAVELFRTLRILKCELDIQAYNCLIDGLCKSGR-LK 469
            G+  D  +Y                                      +  + +  +   
Sbjct: 194 AGLTPDLLSY-----------------------------------AAALQCMGRQDQDAG 218

Query: 470 FAWELFCSLPHGVLVPNVVTYNIMIQGLCNDGQMDKARDLFLDMEENAAAPDVITFDMLI 529
                   +    L    +   +++        +     +          P  +    L+
Sbjct: 219 TIERCLEQMSQEGLKLQALFTAVLLSEEDRATVLKAVHKVKPTFSLPPQLPPPVNTSKLL 278

Query: 530 HGFIRINEPSKVNELLHKMKEKKVMPD 556
                 +      +L   +K  + + +
Sbjct: 279 RDVYAKDGRVSYPKLHLPLKTLQCLFE 305

>3spa_A Mtrpol, DNA-directed RNA polymerase, mitochondrial; single-subunit DNA-dependent RNA polymerase in mitochondria, transferase; 2.50A {Homo sapiens} Length = 1134

 Score = 55.2 bits (131), Expect = 5e-08
 Identities = 11/102 (10%), Positives = 34/102 (33%), Gaps = 3/102 (2%)

Query: 485 PNVVTYNIMIQGLCNDGQMDKARDLFL---DMEENAAAPDVITFDMLIHGFIRINEPSKV 541
                     +      Q+  A  L +      +      +  ++ ++ G+ R     ++
Sbjct: 125 GQQQRLLAFFKCCLLTDQLPLAHHLLVVHHGQRQKRKLLTLDMYNAVMLGWARQGAFKEL 184

Query: 542 NELLHKMKEKKVMPDASIVSIVVDLLVKNEISLKSLPSFLVQ 583
             +L  +K+  + PD    +  +  + + +    ++   L Q
Sbjct: 185 VYVLFMVKDAGLTPDLLSYAAALQCMGRQDQDAGTIERCLEQ 226

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

 Score = 69.1 bits (168), Expect = 3e-12
 Identities = 95/637 (14%), Positives = 195/637 (30%), Gaps = 163/637 (25%)

Query: 25  FSSLLVHFRDLTTREGDIN--------VITPNEAFCIFDYMLRMHPSPPPVSSFNILLAS 76
           +  +L  F D      D          +++  E     D+++    S   VS    L  +
Sbjct: 18  YKDILSVFEDAFVDNFDCKDVQDMPKSILSKEE----IDHIIM---SKDAVSGTLRLFWT 70

Query: 77  L-AKNKHYDTRLNATGLFPNLYTYNILINCFCKIGRVSLGFIAFGRILRSCFTPNAAT-- 133
           L +K +    +     L  N   Y  L++                 I      P+  T  
Sbjct: 71  LLSKQEEMVQKFVEEVLRIN---YKFLMS----------------PIKTEQRQPSMMTRM 111

Query: 134 FNSLIKGLHAE---------SRIMEAAALFTKLKAFGCEPNVITYNTLINGLCRTGHTMI 184
           +      L+ +         SR+     L   L       NV+     I+G+  +G T +
Sbjct: 112 YIEQRDRLYNDNQVFAKYNVSRLQPYLKLRQALLELRPAKNVL-----IDGVLGSGKTWV 166

Query: 185 ALNLFEEMANGNGEIGVVCK-PNTVTYSTIIDGLCKEGFVDKAKALFLQMKDENINPDVV 243
           AL++            V CK    + +  +          +  + +   ++         
Sbjct: 167 ALDVCLS-------YKVQCKMDFKIFWLNL-------KNCNSPETVLEMLQK-------- 204

Query: 244 TYNSLIHGLCHANDWNEAKRLFIEMMDQGVQPSVVTFNVIMDELCKNRKMDEASRLLDLM 303
                   L +  D N     +    D      +   + I  EL   R +        L+
Sbjct: 205 --------LLYQIDPN-----WTSRSDHSSNIKL-RIHSIQAEL--RRLLKSKPYENCLL 248

Query: 304 VQRGVRPNACTYNTLMDGFC--LMGKINRAEELFGSMESMGCKHDDVSYNILINGYCKNK 361
           V   V+ NA  +N   +  C  L+    R +++   + +    H  +S +          
Sbjct: 249 VLLNVQ-NAKAWNA-FNLSCKILL--TTRFKQVTDFLSAATTTH--ISLDHHSMTLTP-D 301

Query: 362 EVEEALSLYREMVSKGIKPTVVTYNTLFLGLF--EIHQVEHALKLFDEMQRDGVAADTRT 419
           EV+  L  Y +   + +   V+T N   L +    I         +  +  D +   T  
Sbjct: 302 EVKSLLLKYLDCRPQDLPREVLTTNPRRLSIIAESIRDGLATWDNWKHVNCDKL---TTI 358

Query: 420 YTTFIDGL----CKNGYIIEAVELFR--------TLRILKCELDIQAYNCLIDGLCKSGR 467
             + ++ L     +  +  + + +F          L ++  ++       +++ L K   
Sbjct: 359 IESSLNVLEPAEYRKMF--DRLSVFPPSAHIPTILLSLIWFDVIKSDVMVVVNKLHKYSL 416

Query: 468 LKFAW-ELFCSLP----------------HGVLVPNVVTYNIMIQGLCNDGQMDKARD-- 508
           ++    E   S+P                H  +V +   YNI  +   +D  +    D  
Sbjct: 417 VEKQPKESTISIPSIYLELKVKLENEYALHRSIVDH---YNI-PKTFDSDDLIPPYLDQY 472

Query: 509 --LFL-------DMEENAAAPDVITFDM------LIHGFIRINEPSKVNELLHKMKE-KK 552
               +       +  E      ++  D       + H     N    +   L ++K  K 
Sbjct: 473 FYSHIGHHLKNIEHPERMTLFRMVFLDFRFLEQKIRHDSTAWNASGSILNTLQQLKFYKP 532

Query: 553 VMPDAS-----IVSIVVDLLVK-NEISLKSLPSFLVQ 583
            + D       +V+ ++D L K  E  + S  + L++
Sbjct: 533 YICDNDPKYERLVNAILDFLPKIEENLICSKYTDLLR 569

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	595
2xpi_A	597	Anaphase-promoting complex subunit CUT9; cell cycl	100.0
2xpi_A	597	Anaphase-promoting complex subunit CUT9; cell cycl	100.0
1w3b_A	388	UDP-N-acetylglucosamine--peptide N-acetylglucosami	100.0
1w3b_A	388	UDP-N-acetylglucosamine--peptide N-acetylglucosami	100.0
2gw1_A	514	Mitochondrial precursor proteins import receptor;	99.96
4g26_A	501	Pentatricopeptide repeat-containing protein AT2G3	99.96
4g26_A	501	Pentatricopeptide repeat-containing protein AT2G3	99.95
2gw1_A	514	Mitochondrial precursor proteins import receptor;	99.95
3fp2_A	537	TPR repeat-containing protein YHR117W; TOM71, mito	99.95
2y4t_A	450	DNAJ homolog subfamily C member 3; chaperone, endo	99.94
2y4t_A	450	DNAJ homolog subfamily C member 3; chaperone, endo	99.94
3fp2_A	537	TPR repeat-containing protein YHR117W; TOM71, mito	99.93
2xm6_A	490	Protein corresponding to locus C5321 from CFT073 s	99.91
3ieg_A	359	DNAJ homolog subfamily C member 3; TPR motif, chap	99.91
3ieg_A	359	DNAJ homolog subfamily C member 3; TPR motif, chap	99.9
2xm6_A	490	Protein corresponding to locus C5321 from CFT073 s	99.9
2ooe_A	530	Cleavage stimulation factor 77 kDa subunit; HAT do	99.89
3hym_B	330	Cell division cycle protein 16 homolog; APC, anaph	99.88
2ooe_A	530	Cleavage stimulation factor 77 kDa subunit; HAT do	99.88
3hym_B	330	Cell division cycle protein 16 homolog; APC, anaph	99.87
1xi4_A	1630	Clathrin heavy chain; alpha-ZIG-ZAG, beta-propelle	99.87
1fch_A	368	Peroxisomal targeting signal 1 receptor; protein-p	99.84
1xi4_A	1630	Clathrin heavy chain; alpha-ZIG-ZAG, beta-propelle	99.84
1fch_A	368	Peroxisomal targeting signal 1 receptor; protein-p	99.84
4g1t_A	472	Interferon-induced protein with tetratricopeptide	99.83
4eqf_A	365	PEX5-related protein; accessory protein, tetratric	99.82
4g1t_A	472	Interferon-induced protein with tetratricopeptide	99.82
4eqf_A	365	PEX5-related protein; accessory protein, tetratric	99.81
1b89_A	449	Protein (clathrin heavy chain); triskelion, coated	99.81
3cv0_A	327	Peroxisome targeting signal 1 receptor PEX5; TPR m	99.8
3mkr_A	291	Coatomer subunit epsilon; tetratricopeptide repeat	99.79
1b89_A	449	Protein (clathrin heavy chain); triskelion, coated	99.79
3cv0_A	327	Peroxisome targeting signal 1 receptor PEX5; TPR m	99.79
3mkr_A	291	Coatomer subunit epsilon; tetratricopeptide repeat	99.79
3e4b_A	452	ALGK; tetratricopeptide repeat, superhelix, algina	99.75
3e4b_A	452	ALGK; tetratricopeptide repeat, superhelix, algina	99.73
2pl2_A	217	Hypothetical conserved protein TTC0263; TPR, prote	99.72
4e6h_A	679	MRNA 3'-END-processing protein RNA14; HAT domain,	99.72
2pl2_A	217	Hypothetical conserved protein TTC0263; TPR, prote	99.72
3uq3_A	258	Heat shock protein STI1; HSP90, peptide binding, c	99.71
3uq3_A	258	Heat shock protein STI1; HSP90, peptide binding, c	99.69
3u4t_A	272	TPR repeat-containing protein; structural genomics	99.69
4e6h_A	679	MRNA 3'-END-processing protein RNA14; HAT domain,	99.68
3u4t_A	272	TPR repeat-containing protein; structural genomics	99.68
2h6f_A	382	Protein farnesyltransferase/geranylgeranyltransfer	99.68
2h6f_A	382	Protein farnesyltransferase/geranylgeranyltransfer	99.68
1ouv_A	273	Conserved hypothetical secreted protein; TPR repea	99.67
1ouv_A	273	Conserved hypothetical secreted protein; TPR repea	99.67
1xnf_A	275	Lipoprotein NLPI; TPR, tetratricopeptide, structur	99.65
1xnf_A	275	Lipoprotein NLPI; TPR, tetratricopeptide, structur	99.64
2q7f_A	243	YRRB protein; TPR, protein binding; 2.49A {Bacillu	99.64
2ho1_A	252	Type 4 fimbrial biogenesis protein PILF; type IV p	99.62
2ho1_A	252	Type 4 fimbrial biogenesis protein PILF; type IV p	99.62
2q7f_A	243	YRRB protein; TPR, protein binding; 2.49A {Bacillu	99.62
3spa_A	1134	Mtrpol, DNA-directed RNA polymerase, mitochondrial	99.62
2vq2_A	225	PILW, putative fimbrial biogenesis and twitching m	99.61
2vq2_A	225	PILW, putative fimbrial biogenesis and twitching m	99.61
3sf4_A	406	G-protein-signaling modulator 2; tetratricopeptide	99.61
3spa_A	1134	Mtrpol, DNA-directed RNA polymerase, mitochondrial	99.6
4a1s_A	411	PINS, partner of inscuteable; cell cycle, LGN, mit	99.59
4a1s_A	411	PINS, partner of inscuteable; cell cycle, LGN, mit	99.58
3sf4_A	406	G-protein-signaling modulator 2; tetratricopeptide	99.58
2ond_A	308	Cleavage stimulation factor 77 kDa subunit; HAT do	99.57
3ro2_A	338	PINS homolog, G-protein-signaling modulator 2; TPR	99.55
2ond_A	308	Cleavage stimulation factor 77 kDa subunit; HAT do	99.55
3vtx_A	184	MAMA; tetratricopeptide repeats (TPR) containing p	99.54
3ro2_A	338	PINS homolog, G-protein-signaling modulator 2; TPR	99.54
4abn_A	474	Tetratricopeptide repeat protein 5; P53 cofactor,	99.53
3ulq_A	383	Response regulator aspartate phosphatase F; tetrat	99.53
3vtx_A	184	MAMA; tetratricopeptide repeats (TPR) containing p	99.53
3ulq_A	383	Response regulator aspartate phosphatase F; tetrat	99.52
4abn_A	474	Tetratricopeptide repeat protein 5; P53 cofactor,	99.47
3nf1_A	311	KLC 1, kinesin light chain 1; TPR, structural geno	99.47
3q15_A	378	PSP28, response regulator aspartate phosphatase H;	99.44
3nf1_A	311	KLC 1, kinesin light chain 1; TPR, structural geno	99.43
3q15_A	378	PSP28, response regulator aspartate phosphatase H;	99.42
1hz4_A	373	MALT regulatory protein; two-helix bundles, helix	99.42
1hz4_A	373	MALT regulatory protein; two-helix bundles, helix	99.41
4i17_A	228	Hypothetical protein; TPR repeats protein, structu	99.39
4gyw_A	723	UDP-N-acetylglucosamine--peptide N- acetylglucosam	99.38
4gyw_A	723	UDP-N-acetylglucosamine--peptide N- acetylglucosam	99.38
4i17_A	228	Hypothetical protein; TPR repeats protein, structu	99.37
3as5_A	186	MAMA; tetratricopeptide repeats (TPR) containing p	99.37
3as5_A	186	MAMA; tetratricopeptide repeats (TPR) containing p	99.37
2uy1_A	493	Cleavage stimulation factor 77; RNA-binding protei	99.28
2uy1_A	493	Cleavage stimulation factor 77; RNA-binding protei	99.25
3edt_B	283	KLC 2, kinesin light chain 2; superhelical, struct	99.25
3edt_B	283	KLC 2, kinesin light chain 2; superhelical, struct	99.25
3mv2_B	310	Coatomer subunit epsilon; vesicular membrane coat	99.23
1qqe_A	292	Vesicular transport protein SEC17; helix-turn-heli	99.2
3urz_A	208	Uncharacterized protein; tetratricopeptide repeats	99.2
3qky_A	261	Outer membrane assembly lipoprotein YFIO; membrane	99.19
3urz_A	208	Uncharacterized protein; tetratricopeptide repeats	99.19
4ga2_A	150	E3 SUMO-protein ligase ranbp2; TPR motif, nuclear	99.17
2pzi_A	681	Probable serine/threonine-protein kinase PKNG; ATP	99.17
1qqe_A	292	Vesicular transport protein SEC17; helix-turn-heli	99.17
3mv2_B	310	Coatomer subunit epsilon; vesicular membrane coat	99.17
3qky_A	261	Outer membrane assembly lipoprotein YFIO; membrane	99.16
4ga2_A	150	E3 SUMO-protein ligase ranbp2; TPR motif, nuclear	99.14
3rjv_A	212	Putative SEL1 repeat protein; alpha-alpha superhel	99.14
2fo7_A	136	Synthetic consensus TPR protein; tetratricopeptide	99.12
2fo7_A	136	Synthetic consensus TPR protein; tetratricopeptide	99.11
2r5s_A	176	Uncharacterized protein VP0806; APC090868.1, vibri	99.09
3rjv_A	212	Putative SEL1 repeat protein; alpha-alpha superhel	99.09
2yhc_A	225	BAMD, UPF0169 lipoprotein YFIO; essential BAM comp	99.09
2pzi_A	681	Probable serine/threonine-protein kinase PKNG; ATP	99.09
3dra_A	306	Protein farnesyltransferase/geranylgeranyltransfer	99.09
3dra_A	306	Protein farnesyltransferase/geranylgeranyltransfer	99.07
3qou_A	287	Protein YBBN; thioredoxin-like fold, tetratricopep	99.07
3qou_A	287	Protein YBBN; thioredoxin-like fold, tetratricopep	99.05
2r5s_A	176	Uncharacterized protein VP0806; APC090868.1, vibri	99.04
2vsy_A	568	XCC0866; transferase, glycosyl transferase, GT-B,	99.04
2yhc_A	225	BAMD, UPF0169 lipoprotein YFIO; essential BAM comp	99.02
4f3v_A	282	ESX-1 secretion system protein ECCA1; tetratricope	99.02
2vsy_A	568	XCC0866; transferase, glycosyl transferase, GT-B,	98.95
2ifu_A	307	Gamma-SNAP; membrane fusion, snare complex disasse	98.94
3gyz_A	151	Chaperone protein IPGC; asymmetric homodimer, tetr	98.88
4gco_A	126	Protein STI-1; structural genomics, PSI-biology, m	98.87
2ifu_A	307	Gamma-SNAP; membrane fusion, snare complex disasse	98.86
4f3v_A	282	ESX-1 secretion system protein ECCA1; tetratricope	98.86
4gco_A	126	Protein STI-1; structural genomics, PSI-biology, m	98.86
3u3w_A	293	Transcriptional activator PLCR protein; ternary co	98.84
1hh8_A	213	P67PHOX, NCF-2, neutrophil cytosol factor 2; cell	98.84
3q7a_A	349	Farnesyltransferase alpha subunit; protein prenylt	98.82
3q7a_A	349	Farnesyltransferase alpha subunit; protein prenylt	98.82
1hh8_A	213	P67PHOX, NCF-2, neutrophil cytosol factor 2; cell	98.82
3u3w_A	293	Transcriptional activator PLCR protein; ternary co	98.81
2e2e_A	177	Formate-dependent nitrite reductase complex NRFG;	98.81
1a17_A	166	Serine/threonine protein phosphatase 5; hydrolase,	98.81
1a17_A	166	Serine/threonine protein phosphatase 5; hydrolase,	98.8
2qfc_A	293	PLCR protein; TPR, HTH, transcription regulation;	98.77
2lni_A	133	Stress-induced-phosphoprotein 1; structural genomi	98.76
2vyi_A	131	SGTA protein; chaperone, TPR repeat, phosphoprotei	98.76
3gyz_A	151	Chaperone protein IPGC; asymmetric homodimer, tetr	98.76
2e2e_A	177	Formate-dependent nitrite reductase complex NRFG;	98.74
2vgx_A	148	Chaperone SYCD; alternative dimer assembly, tetrat	98.74
1na0_A	125	Designed protein CTPR3; de novo protein; HET: IPT;	98.73
2qfc_A	293	PLCR protein; TPR, HTH, transcription regulation;	98.73
2lni_A	133	Stress-induced-phosphoprotein 1; structural genomi	98.73
2vyi_A	131	SGTA protein; chaperone, TPR repeat, phosphoprotei	98.72
2c2l_A	281	CHIP, carboxy terminus of HSP70-interacting protei	98.72
2c2l_A	281	CHIP, carboxy terminus of HSP70-interacting protei	98.71
1na0_A	125	Designed protein CTPR3; de novo protein; HET: IPT;	98.71
2vgx_A	148	Chaperone SYCD; alternative dimer assembly, tetrat	98.68
3gw4_A	203	Uncharacterized protein; structural genomics, PSI-	98.67
1p5q_A	336	FKBP52, FK506-binding protein 4; isomerase; 2.80A	98.67
4gcn_A	127	Protein STI-1; structural genomics, PSI-biology, m	98.66
3dss_A	331	Geranylgeranyl transferase type-2 subunit alpha; p	98.65
1p5q_A	336	FKBP52, FK506-binding protein 4; isomerase; 2.80A	98.65
3gw4_A	203	Uncharacterized protein; structural genomics, PSI-	98.65
3dss_A	331	Geranylgeranyl transferase type-2 subunit alpha; p	98.65
3upv_A	126	Heat shock protein STI1; TPR-fold, adaptor protein	98.61
4gcn_A	127	Protein STI-1; structural genomics, PSI-biology, m	98.61
2xcb_A	142	PCRH, regulatory protein PCRH; protein transport,	98.6
2dba_A	148	Smooth muscle cell associated protein-1, isoform 2	98.6
3upv_A	126	Heat shock protein STI1; TPR-fold, adaptor protein	98.6
1elw_A	118	TPR1-domain of HOP; HOP, TPR-domain, peptide-compl	98.59
2xcb_A	142	PCRH, regulatory protein PCRH; protein transport,	98.59
1elw_A	118	TPR1-domain of HOP; HOP, TPR-domain, peptide-compl	98.58
1elr_A	131	TPR2A-domain of HOP; HOP, TPR-domain, peptide-comp	98.52
3q49_B	137	STIP1 homology and U box-containing protein 1; E3	98.51
3sz7_A	164	HSC70 cochaperone (SGT); TPR domain, GET4, GET5, G	98.5
1wao_1	477	Serine/threonine protein phosphatase 5; hydrolase,	98.5
3sz7_A	164	HSC70 cochaperone (SGT); TPR domain, GET4, GET5, G	98.5
2fbn_A	198	70 kDa peptidylprolyl isomerase, putative; sulfur	98.49
2fbn_A	198	70 kDa peptidylprolyl isomerase, putative; sulfur	98.49
2dba_A	148	Smooth muscle cell associated protein-1, isoform 2	98.47
3q49_B	137	STIP1 homology and U box-containing protein 1; E3	98.47
1elr_A	131	TPR2A-domain of HOP; HOP, TPR-domain, peptide-comp	98.44
1hxi_A	121	PEX5, peroxisome targeting signal 1 receptor PEX5;	98.42
2kck_A	112	TPR repeat; tetratricopeptide repeat, structural g	98.42
2kck_A	112	TPR repeat; tetratricopeptide repeat, structural g	98.4
1hxi_A	121	PEX5, peroxisome targeting signal 1 receptor PEX5;	98.39
2xev_A	129	YBGF; tetratricopeptide, alpha-helical, metal bind	98.36
4b4t_Q	434	26S proteasome regulatory subunit RPN6; hydrolase,	98.33
2xev_A	129	YBGF; tetratricopeptide, alpha-helical, metal bind	98.33
3ro3_A	164	PINS homolog, G-protein-signaling modulator 2; asy	98.32
3rkv_A	162	Putative peptidylprolyl isomerase; structural geno	98.31
2hr2_A	159	Hypothetical protein; alpha-alpha superhelix fold,	98.3
4b4t_Q	434	26S proteasome regulatory subunit RPN6; hydrolase,	98.29
3k9i_A	117	BH0479 protein; putative protein binding protein,	98.29
1ihg_A	370	Cyclophilin 40; ppiase immunophilin tetratricopept	98.26
3k9i_A	117	BH0479 protein; putative protein binding protein,	98.25
1kt0_A	457	FKBP51, 51 kDa FK506-binding protein; FKBP-like pp	98.25
1wao_1	477	Serine/threonine protein phosphatase 5; hydrolase,	98.25
3rkv_A	162	Putative peptidylprolyl isomerase; structural geno	98.25
3ro3_A	164	PINS homolog, G-protein-signaling modulator 2; asy	98.24
1ihg_A	370	Cyclophilin 40; ppiase immunophilin tetratricopept	98.22
1dce_A	567	Protein (RAB geranylgeranyltransferase alpha subun	98.21
1kt0_A	457	FKBP51, 51 kDa FK506-binding protein; FKBP-like pp	98.19
1dce_A	567	Protein (RAB geranylgeranyltransferase alpha subun	98.15
1klx_A	138	Cysteine rich protein B; structural genomics, heli	98.12
2hr2_A	159	Hypothetical protein; alpha-alpha superhelix fold,	98.12
2l6j_A	111	TPR repeat-containing protein associated with HSP;	98.12
2if4_A	338	ATFKBP42; FKBP-like, alpha-beta, TPR-like, alpha,	98.11
2if4_A	338	ATFKBP42; FKBP-like, alpha-beta, TPR-like, alpha,	98.0
1klx_A	138	Cysteine rich protein B; structural genomics, heli	97.99
3n71_A	490	Histone lysine methyltransferase SMYD1; heart deve	97.96
1zu2_A	158	Mitochondrial import receptor subunit TOM20-3; TPR	97.93
2l6j_A	111	TPR repeat-containing protein associated with HSP;	97.92
1na3_A	91	Designed protein CTPR2; de novo protein; HET: IPT;	97.91
1zu2_A	158	Mitochondrial import receptor subunit TOM20-3; TPR	97.9
2kat_A	115	Uncharacterized protein; NESG, structure, structur	97.85
3n71_A	490	Histone lysine methyltransferase SMYD1; heart deve	97.82
3ma5_A	100	Tetratricopeptide repeat domain protein; NESG, str	97.81
1na3_A	91	Designed protein CTPR2; de novo protein; HET: IPT;	97.79
2kat_A	115	Uncharacterized protein; NESG, structure, structur	97.78
3lvg_A	624	Clathrin heavy chain 1; SELF assembly, coated PIT,	97.6
3ma5_A	100	Tetratricopeptide repeat domain protein; NESG, str	97.52
3ly7_A	372	Transcriptional activator CADC; alpha/beta domain,	97.48
3ly7_A	372	Transcriptional activator CADC; alpha/beta domain,	97.44
3qww_A	433	SET and MYND domain-containing protein 2; methyltr	97.12
3u64_A	301	Protein TP_0956; tetratrico peptide repeat, protei	97.1
3bee_A	93	Putative YFRE protein; putaive YFRE protein, struc	97.07
3qwp_A	429	SET and MYND domain-containing protein 3; SMYD3,SE	97.03
3bee_A	93	Putative YFRE protein; putaive YFRE protein, struc	96.96
3qww_A	433	SET and MYND domain-containing protein 2; methyltr	96.93
2kc7_A	99	BFR218_protein; tetratricopeptide repeat, all-alph	96.92
3qwp_A	429	SET and MYND domain-containing protein 3; SMYD3,SE	96.92
1pc2_A	152	Mitochondria fission protein; unknown function; NM	96.83
3mkq_B	177	Coatomer subunit alpha; beta-propeller, alpha-sole	96.73
2kc7_A	99	BFR218_protein; tetratricopeptide repeat, all-alph	96.71
1pc2_A	152	Mitochondria fission protein; unknown function; NM	96.69
3mkq_A	814	Coatomer beta'-subunit; beta-propeller, alpha-sole	96.53
2v5f_A	104	Prolyl 4-hydroxylase subunit alpha-1; endoplasmic	96.51
3mkq_B	177	Coatomer subunit alpha; beta-propeller, alpha-sole	96.46
2v5f_A	104	Prolyl 4-hydroxylase subunit alpha-1; endoplasmic	96.39
4h7y_A	161	Dual specificity protein kinase TTK; mitotic check	96.34
3u64_A	301	Protein TP_0956; tetratrico peptide repeat, protei	96.29
3mkq_A	814	Coatomer beta'-subunit; beta-propeller, alpha-sole	96.07
4h7y_A	161	Dual specificity protein kinase TTK; mitotic check	95.93
4ady_A	963	RPN2, 26S proteasome regulatory subunit RPN2; prot	95.71
1nzn_A	126	CGI-135 protein, fission protein FIS1P; TPR, unkno	95.68
3lvg_A	624	Clathrin heavy chain 1; SELF assembly, coated PIT,	95.47
1nzn_A	126	CGI-135 protein, fission protein FIS1P; TPR, unkno	95.34
1wy6_A	172	Hypothetical protein ST1625; helical repeat protei	94.58
2ff4_A	388	Probable regulatory protein EMBR; winged-helix, te	94.48
1y8m_A	144	FIS1; mitochondria, unknown function; NMR {Sacchar	93.21
4ady_A	963	RPN2, 26S proteasome regulatory subunit RPN2; prot	93.18
3o48_A	134	Mitochondria fission 1 protein; tetratricopeptide	93.14
2ff4_A	388	Probable regulatory protein EMBR; winged-helix, te	92.96
3ffl_A	167	Anaphase-promoting complex subunit 7; tetratricope	92.43
4gns_B	754	Protein CSD3, chitin biosynthesis protein CHS6; FN	91.87
4b4t_P	445	26S proteasome regulatory subunit RPN5; hydrolase,	91.64
4gns_B	754	Protein CSD3, chitin biosynthesis protein CHS6; FN	91.56
1wy6_A	172	Hypothetical protein ST1625; helical repeat protei	91.46
2wpv_A	312	GET4, UPF0363 protein YOR164C; golgi-ER traffickin	91.06
4fhn_B	1139	Nucleoporin NUP120; protein complex,structural pro	90.64
3ffl_A	167	Anaphase-promoting complex subunit 7; tetratricope	89.87
1v54_E	109	Cytochrome C oxidase polypeptide VA; oxidoreductas	89.8
4fhn_B	1139	Nucleoporin NUP120; protein complex,structural pro	89.51
3lpz_A	336	GET4 (YOR164C homolog); protein targeting, tail-an	89.1
1v54_E	109	Cytochrome C oxidase polypeptide VA; oxidoreductas	88.99
3o48_A	134	Mitochondria fission 1 protein; tetratricopeptide	88.1
4b4t_P	445	26S proteasome regulatory subunit RPN5; hydrolase,	87.28
1zbp_A	273	Hypothetical protein VPA1032; alpha-beta protein,	86.2
2y69_E	152	Cytochrome C oxidase subunit 5A; electron transpor	85.81
2y69_E	152	Cytochrome C oxidase subunit 5A; electron transpor	85.8
1zbp_A	273	Hypothetical protein VPA1032; alpha-beta protein,	85.38
3lpz_A	336	GET4 (YOR164C homolog); protein targeting, tail-an	85.32
1y8m_A	144	FIS1; mitochondria, unknown function; NMR {Sacchar	84.86
3esl_A	202	Checkpoint serine/threonine-protein kinase BUB1; m	84.42
4b4t_R	429	RPN7, 26S proteasome regulatory subunit RPN7; hydr	83.05
3txn_A	394	26S proteasome regulatory complex subunit P42B; PC	82.6

>2xpi_A Anaphase-promoting complex subunit CUT9; cell cycle, TPR, ubiquitin ligase; 2.60A {Schizosaccharomyces pombe}

Probab=100.00  E-value=3.7e-41  Score=350.71  Aligned_cols=482  Identities=11%  Similarity=0.008  Sum_probs=356.3

Q ss_pred             CHhhHHHHHHHHHcCCCchh------HHhhCCCCCCHHHHHHHHHHHHhcCChhHHHHHHHHHHhCCCCCCHHHHHHHHH
Q 040027           66 PVSSFNILLASLAKNKHYDT------RLNATGLFPNLYTYNILINCFCKIGRVSLGFIAFGRILRSCFTPNAATFNSLIK  139 (595)
Q Consensus        66 ~~~~~~~l~~~~~~~~~~~~------~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~~l~~  139 (595)
                      ++..|+.++..+.+.|++++      .+.  +..|+..++..++.+|.+.|++++|+.+|+++...  +++..+++.++.
T Consensus        83 ~~~~~~~~~~~~~~~g~~~~A~~~~~~~~--~~~p~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~--~~~~~~~~~l~~  158 (597)
T 2xpi_A           83 REDYLRLWRHDALMQQQYKCAAFVGEKVL--DITGNPNDAFWLAQVYCCTGDYARAKCLLTKEDLY--NRSSACRYLAAF  158 (597)
T ss_dssp             HHHHHHHHHHHHHHTTCHHHHHHHHHHHH--HHHCCHHHHHHHHHHHHHTTCHHHHHHHHHHTCGG--GTCHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHccCchHHHHHHHHHH--hhCCCchHHHHHHHHHHHcCcHHHHHHHHHHHhcc--ccchhHHHHHHH
Confidence            44555555555555555554      111  22345555555555555555555555555555433  445555555555


Q ss_pred             HHHhcCCHhHHHHHHHHHHhc---------------CCCCCHhhHHHHHHHHHhcCChhHHHHHHHHHHhcCCCCCcccc
Q 040027          140 GLHAESRIMEAAALFTKLKAF---------------GCEPNVITYNTLINGLCRTGHTMIALNLFEEMANGNGEIGVVCK  204 (595)
Q Consensus       140 ~~~~~g~~~~A~~~~~~~~~~---------------~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~  204 (595)
                      +|.+.|++++|.++|+++...               +.+.+..+|..++.+|.+.|++++|++.|+++.+.+       +
T Consensus       159 ~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~-------p  231 (597)
T 2xpi_A          159 CLVKLYDWQGALNLLGETNPFRKDEKNANKLLMQDGGIKLEASMCYLRGQVYTNLSNFDRAKECYKEALMVD-------A  231 (597)
T ss_dssp             HHHHTTCHHHHHHHHCSSCTTC----------CCCSSCCHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-------T
T ss_pred             HHHHHhhHHHHHHHHhccCCccccccccccccccccccchhHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhC-------c
Confidence            555555555555555532111               111234555555555555555555555555555543       2


Q ss_pred             CcHHHHHHHHHHHHHcCCHhHHH--HH-HHHHhhCCCCCCHhHHHHHHHHHHhcCCHHHHHHHHHHHHHCCCCCCHhhHH
Q 040027          205 PNTVTYSTIIDGLCKEGFVDKAK--AL-FLQMKDENINPDVVTYNSLIHGLCHANDWNEAKRLFIEMMDQGVQPSVVTFN  281 (595)
Q Consensus       205 ~~~~~~~~l~~~~~~~g~~~~A~--~~-~~~~~~~~~~~~~~~~~~ll~~~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~  281 (595)
                      .+...+..+...+...+..+.+.  .+ +..+...+..+...+|+.++..|.+.|++++|.++|+++.+.  +++..+++
T Consensus       232 ~~~~~~~~l~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~~~A~~~~~~~~~~--~~~~~~~~  309 (597)
T 2xpi_A          232 KCYEAFDQLVSNHLLTADEEWDLVLKLNYSTYSKEDAAFLRSLYMLKLNKTSHEDELRRAEDYLSSINGL--EKSSDLLL  309 (597)
T ss_dssp             TCHHHHHHHHHTTCSCHHHHHHHHHHSCTHHHHGGGHHHHHHHHHTTSCTTTTHHHHHHHHHHHHTSTTG--GGCHHHHH
T ss_pred             hhhHHHHHHHHhhcccchhHHHHHHhcCCcccccchHHHHHHHHHHHHHHHcCcchHHHHHHHHHHhhcC--CchHHHHH
Confidence            23444444443332222111111  11 222222222223334555567777889999999999998765  57899999


Q ss_pred             HHHHHHHhcCChHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHhcCCCCCHHHHHHHHHHHHhCC
Q 040027          282 VIMDELCKNRKMDEASRLLDLMVQRGVRPNACTYNTLMDGFCLMGKINRAEELFGSMESMGCKHDDVSYNILINGYCKNK  361 (595)
Q Consensus       282 ~l~~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~  361 (595)
                      .++..+.+.|++++|..+|+++.+.+. .+..++..++.++...|++++|..+++++.+.. +.+..++..++.+|.+.|
T Consensus       310 ~l~~~~~~~g~~~~A~~~~~~~~~~~~-~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~-~~~~~~~~~l~~~~~~~g  387 (597)
T 2xpi_A          310 CKADTLFVRSRFIDVLAITTKILEIDP-YNLDVYPLHLASLHESGEKNKLYLISNDLVDRH-PEKAVTWLAVGIYYLCVN  387 (597)
T ss_dssp             HHHHHHHHTTCHHHHHHHHHHHHHHCT-TCCTTHHHHHHHHHHHTCHHHHHHHHHHHHHHC-TTSHHHHHHHHHHHHHTT
T ss_pred             HHHHHHHHhcCHHHHHHHHHHHHHcCc-ccHHHHHHHHHHHHHhCCHHHHHHHHHHHHhhC-cccHHHHHHHHHHHHHhc
Confidence            999999999999999999999998753 377789999999999999999999999998764 567889999999999999


Q ss_pred             CHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHccCCHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHhcCCHHHHHHHHH
Q 040027          362 EVEEALSLYREMVSKGIKPTVVTYNTLFLGLFEIHQVEHALKLFDEMQRDGVAADTRTYTTFIDGLCKNGYIIEAVELFR  441 (595)
Q Consensus       362 ~~~~A~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~  441 (595)
                      ++++|.++|+++.+.... +..+|..++..+.+.|++++|.++|+++.+.+ +.+..++..++.+|.+.|++++|.++|+
T Consensus       388 ~~~~A~~~~~~~~~~~~~-~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~-~~~~~~~~~l~~~~~~~g~~~~A~~~~~  465 (597)
T 2xpi_A          388 KISEARRYFSKSSTMDPQ-FGPAWIGFAHSFAIEGEHDQAISAYTTAARLF-QGTHLPYLFLGMQHMQLGNILLANEYLQ  465 (597)
T ss_dssp             CHHHHHHHHHHHHHHCTT-CHHHHHHHHHHHHHHTCHHHHHHHHHHHHHTT-TTCSHHHHHHHHHHHHHTCHHHHHHHHH
T ss_pred             cHHHHHHHHHHHHHhCCC-CHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhC-ccchHHHHHHHHHHHHcCCHHHHHHHHH
Confidence            999999999999886433 67899999999999999999999999999874 5678899999999999999999999999


Q ss_pred             HHHHcCCCcCHHHHHHHHHHHHhcCChHHHHHHHHhcccC----CCCCC--HHHHHHHHHHHHhcCChhHHHHHHHHHHH
Q 040027          442 TLRILKCELDIQAYNCLIDGLCKSGRLKFAWELFCSLPHG----VLVPN--VVTYNIMIQGLCNDGQMDKARDLFLDMEE  515 (595)
Q Consensus       442 ~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~----~~~p~--~~~~~~l~~~~~~~g~~~~A~~~~~~~~~  515 (595)
                      ++.+.. +.+..+|..++.+|.+.|++++|.++|+++.+.    +..|+  ..+|..++.+|.+.|++++|.+.|+++.+
T Consensus       466 ~~~~~~-~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~~~~p~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~  544 (597)
T 2xpi_A          466 SSYALF-QYDPLLLNELGVVAFNKSDMQTAINHFQNALLLVKKTQSNEKPWAATWANLGHAYRKLKMYDAAIDALNQGLL  544 (597)
T ss_dssp             HHHHHC-CCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHSCCCSGGGHHHHHHHHHHHHHTTCHHHHHHHHHHHHH
T ss_pred             HHHHhC-CCChHHHHHHHHHHHHhCCHHHHHHHHHHHHHhhhccccchhhHHHHHHHHHHHHHHhcCHHHHHHHHHHHHH
Confidence            999876 668999999999999999999999999999774    45777  78999999999999999999999999998


Q ss_pred             cCCCCCHHHHHHHHHHHHHcCChhHHHHHHHHHHHCCCCC-CHHHHHHHHHHHH
Q 040027          516 NAAAPDVITFDMLIHGFIRINEPSKVNELLHKMKEKKVMP-DASIVSIVVDLLV  568 (595)
Q Consensus       516 ~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~p-~~~~~~~l~~~~~  568 (595)
                      .+ +.+..+|..++.+|...|++++|.++++++.+.  .| +...+..+..+|.
T Consensus       545 ~~-p~~~~~~~~l~~~~~~~g~~~~A~~~~~~~l~~--~p~~~~~~~~l~~~~~  595 (597)
T 2xpi_A          545 LS-TNDANVHTAIALVYLHKKIPGLAITHLHESLAI--SPNEIMASDLLKRALE  595 (597)
T ss_dssp             HS-SCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH--CTTCHHHHHHHHHTTC
T ss_pred             hC-CCChHHHHHHHHHHHHhCCHHHHHHHHHHHHhc--CCCChHHHHHHHHHHh
Confidence            75 568899999999999999999999999999985  45 6778877777654

>2xpi_A Anaphase-promoting complex subunit CUT9; cell cycle, TPR, ubiquitin ligase; 2.60A {Schizosaccharomyces pombe}

Probab=100.00  E-value=3e-39  Score=336.36  Aligned_cols=479  Identities=11%  Similarity=0.030  Sum_probs=402.5

Q ss_pred             CCCCCCHHHHHHHHHHHHhcCChhHHHHHHHHHHhCCCCCCHHHHHHHHHHHHhcCCHhHHHHHHHHHHhcCCCCCHhhH
Q 040027           90 TGLFPNLYTYNILINCFCKIGRVSLGFIAFGRILRSCFTPNAATFNSLIKGLHAESRIMEAAALFTKLKAFGCEPNVITY  169 (595)
Q Consensus        90 ~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~  169 (595)
                      ....+++..|+.++..+.+.|++++|+.+|+++...  .|+..++..++.+|.+.|++++|..+|+++...  +++..++
T Consensus        78 ~~~~~~~~~~~~~~~~~~~~g~~~~A~~~~~~~~~~--~p~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~--~~~~~~~  153 (597)
T 2xpi_A           78 TDSLSREDYLRLWRHDALMQQQYKCAAFVGEKVLDI--TGNPNDAFWLAQVYCCTGDYARAKCLLTKEDLY--NRSSACR  153 (597)
T ss_dssp             ----CHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH--HCCHHHHHHHHHHHHHTTCHHHHHHHHHHTCGG--GTCHHHH
T ss_pred             cchHHHHHHHHHHHHHHHHccCchHHHHHHHHHHhh--CCCchHHHHHHHHHHHcCcHHHHHHHHHHHhcc--ccchhHH
Confidence            334468899999999999999999999999999965  568889999999999999999999999998654  6789999


Q ss_pred             HHHHHHHHhcCChhHHHHHHHHHHhcCC---------CCCccccCcHHHHHHHHHHHHHcCCHhHHHHHHHHHhhCCCCC
Q 040027          170 NTLINGLCRTGHTMIALNLFEEMANGNG---------EIGVVCKPNTVTYSTIIDGLCKEGFVDKAKALFLQMKDENINP  240 (595)
Q Consensus       170 ~~l~~~~~~~g~~~~A~~~~~~~~~~~~---------~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~  240 (595)
                      ..++.+|.+.|++++|+++|+++.....         ......+.+..+|+.++.+|.+.|++++|.++|+++.+.+ +.
T Consensus       154 ~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~-p~  232 (597)
T 2xpi_A          154 YLAAFCLVKLYDWQGALNLLGETNPFRKDEKNANKLLMQDGGIKLEASMCYLRGQVYTNLSNFDRAKECYKEALMVD-AK  232 (597)
T ss_dssp             HHHHHHHHHTTCHHHHHHHHCSSCTTC----------CCCSSCCHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TT
T ss_pred             HHHHHHHHHHhhHHHHHHHHhccCCccccccccccccccccccchhHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhC-ch
Confidence            9999999999999999999995332210         0000123468899999999999999999999999998864 22


Q ss_pred             CHhHHHHHHHHHHhcCCHHHHH--HH-HHHHHHCCCCCCHhhHHHHHHHHHhcCChHHHHHHHHHHHHCCCCCCHHHHHH
Q 040027          241 DVVTYNSLIHGLCHANDWNEAK--RL-FIEMMDQGVQPSVVTFNVIMDELCKNRKMDEASRLLDLMVQRGVRPNACTYNT  317 (595)
Q Consensus       241 ~~~~~~~ll~~~~~~~~~~~A~--~~-~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~  317 (595)
                      +...+..+...+...+..+.+.  .+ +..+...+..+...+|+.++..|.+.|++++|.++|+++.+.  +++..++..
T Consensus       233 ~~~~~~~l~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~~~A~~~~~~~~~~--~~~~~~~~~  310 (597)
T 2xpi_A          233 CYEAFDQLVSNHLLTADEEWDLVLKLNYSTYSKEDAAFLRSLYMLKLNKTSHEDELRRAEDYLSSINGL--EKSSDLLLC  310 (597)
T ss_dssp             CHHHHHHHHHTTCSCHHHHHHHHHHSCTHHHHGGGHHHHHHHHHTTSCTTTTHHHHHHHHHHHHTSTTG--GGCHHHHHH
T ss_pred             hhHHHHHHHHhhcccchhHHHHHHhcCCcccccchHHHHHHHHHHHHHHHcCcchHHHHHHHHHHhhcC--CchHHHHHH
Confidence            5666666665554443332222  11 444444433344556666788889999999999999998875  578999999


Q ss_pred             HHHHHHhcCCHHHHHHHHHHHHhcCCCCCHHHHHHHHHHHHhCCCHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHccCC
Q 040027          318 LMDGFCLMGKINRAEELFGSMESMGCKHDDVSYNILINGYCKNKEVEEALSLYREMVSKGIKPTVVTYNTLFLGLFEIHQ  397 (595)
Q Consensus       318 l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~  397 (595)
                      ++.+|.+.|++++|..+|+++.+.+ +.+..++..++.++.+.|++++|..+++++.+.. +.+..++..++..|.+.|+
T Consensus       311 l~~~~~~~g~~~~A~~~~~~~~~~~-~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~-~~~~~~~~~l~~~~~~~g~  388 (597)
T 2xpi_A          311 KADTLFVRSRFIDVLAITTKILEID-PYNLDVYPLHLASLHESGEKNKLYLISNDLVDRH-PEKAVTWLAVGIYYLCVNK  388 (597)
T ss_dssp             HHHHHHHTTCHHHHHHHHHHHHHHC-TTCCTTHHHHHHHHHHHTCHHHHHHHHHHHHHHC-TTSHHHHHHHHHHHHHTTC
T ss_pred             HHHHHHHhcCHHHHHHHHHHHHHcC-cccHHHHHHHHHHHHHhCCHHHHHHHHHHHHhhC-cccHHHHHHHHHHHHHhcc
Confidence            9999999999999999999999875 4577889999999999999999999999998764 3478899999999999999


Q ss_pred             HHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCcCHHHHHHHHHHHHhcCChHHHHHHHHh
Q 040027          398 VEHALKLFDEMQRDGVAADTRTYTTFIDGLCKNGYIIEAVELFRTLRILKCELDIQAYNCLIDGLCKSGRLKFAWELFCS  477 (595)
Q Consensus       398 ~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~  477 (595)
                      +++|.++|+++.+.. +.+..++..++..|.+.|++++|..+|+++.+.. +.+..++..++.+|.+.|++++|.++|++
T Consensus       389 ~~~A~~~~~~~~~~~-~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~-~~~~~~~~~l~~~~~~~g~~~~A~~~~~~  466 (597)
T 2xpi_A          389 ISEARRYFSKSSTMD-PQFGPAWIGFAHSFAIEGEHDQAISAYTTAARLF-QGTHLPYLFLGMQHMQLGNILLANEYLQS  466 (597)
T ss_dssp             HHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHHTCHHHHHHHHHHHHHTT-TTCSHHHHHHHHHHHHHTCHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHhC-CCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhC-ccchHHHHHHHHHHHHcCCHHHHHHHHHH
Confidence            999999999998863 5678899999999999999999999999999876 66889999999999999999999999999


Q ss_pred             cccCCCCCCHHHHHHHHHHHHhcCChhHHHHHHHHHHHc----CCCCC--HHHHHHHHHHHHHcCChhHHHHHHHHHHHC
Q 040027          478 LPHGVLVPNVVTYNIMIQGLCNDGQMDKARDLFLDMEEN----AAAPD--VITFDMLIHGFIRINEPSKVNELLHKMKEK  551 (595)
Q Consensus       478 ~~~~~~~p~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~----~~~~~--~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~  551 (595)
                      +.+.. +.+..+|+.++.+|.+.|++++|.++|+++.+.    +..|+  ..+|..++.+|.+.|++++|.++++++.+.
T Consensus       467 ~~~~~-~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~~~~p~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~  545 (597)
T 2xpi_A          467 SYALF-QYDPLLLNELGVVAFNKSDMQTAINHFQNALLLVKKTQSNEKPWAATWANLGHAYRKLKMYDAAIDALNQGLLL  545 (597)
T ss_dssp             HHHHC-CCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHSCCCSGGGHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH
T ss_pred             HHHhC-CCChHHHHHHHHHHHHhCCHHHHHHHHHHHHHhhhccccchhhHHHHHHHHHHHHHHhcCHHHHHHHHHHHHHh
Confidence            98742 336889999999999999999999999999886    55677  789999999999999999999999999986


Q ss_pred             CCCCCHHHHHHHHHHHHhcCcccccchHHH
Q 040027          552 KVMPDASIVSIVVDLLVKNEISLKSLPSFL  581 (595)
Q Consensus       552 ~~~p~~~~~~~l~~~~~~~g~~~~~i~~~~  581 (595)
                      + +.+..+|..++.+|.+.|+++++++.+.
T Consensus       546 ~-p~~~~~~~~l~~~~~~~g~~~~A~~~~~  574 (597)
T 2xpi_A          546 S-TNDANVHTAIALVYLHKKIPGLAITHLH  574 (597)
T ss_dssp             S-SCCHHHHHHHHHHHHHTTCHHHHHHHHH
T ss_pred             C-CCChHHHHHHHHHHHHhCCHHHHHHHHH
Confidence            4 4489999999999999999996655543

>1w3b_A UDP-N-acetylglucosamine--peptide N-acetylglucosaminyltransferase 110; OGT, glcnac, nucleoporin, O-linked glycosylation, TPR repeat, protein binding; 2.85A {Homo sapiens} SCOP: a.118.8.1

Probab=100.00  E-value=5.4e-29  Score=244.12  Aligned_cols=376  Identities=14%  Similarity=0.063  Sum_probs=167.4

Q ss_pred             HhcCCHhHHHHHHHHHHhcCCCCCHhhHHHHHHHHHhcCChhHHHHHHHHHHhcCCCCCccccCcHHHHHHHHHHHHHcC
Q 040027          142 HAESRIMEAAALFTKLKAFGCEPNVITYNTLINGLCRTGHTMIALNLFEEMANGNGEIGVVCKPNTVTYSTIIDGLCKEG  221 (595)
Q Consensus       142 ~~~g~~~~A~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g  221 (595)
                      .+.|++++|.+.++.+.+.. +.+...+..+...+...|++++|...++.....+       |.+..+|..+..++.+.|
T Consensus        10 ~~~g~~~~A~~~~~~~~~~~-p~~~~~~~~l~~~~~~~~~~~~a~~~~~~a~~~~-------p~~~~~~~~lg~~~~~~g   81 (388)
T 1w3b_A           10 YQAGDFEAAERHCMQLWRQE-PDNTGVLLLLSSIHFQCRRLDRSAHFSTLAIKQN-------PLLAEAYSNLGNVYKERG   81 (388)
T ss_dssp             HHHTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-------TTCHHHHHHHHHHHHHHT
T ss_pred             HHCCCHHHHHHHHHHHHHhC-CCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHhcC-------CCchHHHHHHHHHHHHCC
Confidence            33344444444444433332 1123333333333444444444444444443332       233344444444444444


Q ss_pred             CHhHHHHHHHHHhhCCCCCCHhHHHHHHHHHHhcCCHHHHHHHHHHHHHCCCCCCHhhHHHHHHHHHhcCChHHHHHHHH
Q 040027          222 FVDKAKALFLQMKDENINPDVVTYNSLIHGLCHANDWNEAKRLFIEMMDQGVQPSVVTFNVIMDELCKNRKMDEASRLLD  301 (595)
Q Consensus       222 ~~~~A~~~~~~~~~~~~~~~~~~~~~ll~~~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~a~~~~~  301 (595)
                      ++++|.+.|+++.... +.+...|..++.++...|++++|...|+++.+.. +.+...+..+...+...|++++|...|+
T Consensus        82 ~~~~A~~~~~~al~~~-p~~~~~~~~l~~~~~~~g~~~~A~~~~~~al~~~-p~~~~~~~~l~~~~~~~g~~~~A~~~~~  159 (388)
T 1w3b_A           82 QLQEAIEHYRHALRLK-PDFIDGYINLAAALVAAGDMEGAVQAYVSALQYN-PDLYCVRSDLGNLLKALGRLEEAKACYL  159 (388)
T ss_dssp             CHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHHSCSSHHHHHHHHHHHHC-TTCTHHHHHHHHHHHTTSCHHHHHHHHH
T ss_pred             CHHHHHHHHHHHHHcC-cchHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhC-CCcHHHHHHHHHHHHHccCHHHHHHHHH
Confidence            4444444444443321 1123334444444444444444444444443321 1122233333444444444444444444


Q ss_pred             HHHHCCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHhcCCCCCHHHHHHHHHHHHhCCCHHHHHHHHHHHHHCCCCCC
Q 040027          302 LMVQRGVRPNACTYNTLMDGFCLMGKINRAEELFGSMESMGCKHDDVSYNILINGYCKNKEVEEALSLYREMVSKGIKPT  381 (595)
Q Consensus       302 ~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~~~~~~~  381 (595)
                      ++.+.. +.+..++..++.++...|++++|...|+++.+.+ +.+...+..+...+...|++++|+..+++.....+. +
T Consensus       160 ~al~~~-p~~~~~~~~l~~~~~~~g~~~~A~~~~~~al~~~-p~~~~~~~~lg~~~~~~~~~~~A~~~~~~al~~~p~-~  236 (388)
T 1w3b_A          160 KAIETQ-PNFAVAWSNLGCVFNAQGEIWLAIHHFEKAVTLD-PNFLDAYINLGNVLKEARIFDRAVAAYLRALSLSPN-H  236 (388)
T ss_dssp             HHHHHC-TTCHHHHHHHHHHHHTTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHTTTCTTHHHHHHHHHHHHCTT-C
T ss_pred             HHHHhC-CCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHhcC-CCcHHHHHHHHHHHHHcCCHHHHHHHHHHHHhhCcC-C
Confidence            444331 1133444444444444444555554444444432 223344444455555555555555555544443221 3


Q ss_pred             HHHHHHHHHHHHccCCHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCcCHHHHHHHHHH
Q 040027          382 VVTYNTLFLGLFEIHQVEHALKLFDEMQRDGVAADTRTYTTFIDGLCKNGYIIEAVELFRTLRILKCELDIQAYNCLIDG  461 (595)
Q Consensus       382 ~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~~l~~~  461 (595)
                      ..++..+...+...|++++|...++++.+.+ +.+..++..+...+.+.|++++|...++++.+.. +.+..++..++..
T Consensus       237 ~~~~~~l~~~~~~~g~~~~A~~~~~~al~~~-p~~~~~~~~l~~~~~~~g~~~~A~~~~~~al~~~-p~~~~~~~~l~~~  314 (388)
T 1w3b_A          237 AVVHGNLACVYYEQGLIDLAIDTYRRAIELQ-PHFPDAYCNLANALKEKGSVAEAEDCYNTALRLC-PTHADSLNNLANI  314 (388)
T ss_dssp             HHHHHHHHHHHHHTTCHHHHHHHHHHHHHTC-SSCHHHHHHHHHHHHHHSCHHHHHHHHHHHHHHC-TTCHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHcCCHHHHHHHHHHHHhhC-CCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHhhC-cccHHHHHHHHHH
Confidence            3444444444555555555555555544432 2334445555555555555555555555555443 4445555555555


Q ss_pred             HHhcCChHHHHHHHHhcccCCCCC-CHHHHHHHHHHHHhcCChhHHHHHHHHHHHcCCCCCHHHHHHHHHHHHHc
Q 040027          462 LCKSGRLKFAWELFCSLPHGVLVP-NVVTYNIMIQGLCNDGQMDKARDLFLDMEENAAAPDVITFDMLIHGFIRI  535 (595)
Q Consensus       462 ~~~~g~~~~A~~~~~~~~~~~~~p-~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~~l~~~~~~~  535 (595)
                      +...|++++|...++++.+.  .| +..++..++.+|.+.|++++|+..|+++++.. +.+...+..+..++...
T Consensus       315 ~~~~g~~~~A~~~~~~al~~--~p~~~~~~~~l~~~~~~~g~~~~A~~~~~~a~~~~-p~~~~a~~~lg~~~~~~  386 (388)
T 1w3b_A          315 KREQGNIEEAVRLYRKALEV--FPEFAAAHSNLASVLQQQGKLQEALMHYKEAIRIS-PTFADAYSNMGNTLKEM  386 (388)
T ss_dssp             HHTTTCHHHHHHHHHHHTTS--CTTCHHHHHHHHHHHHTTTCCHHHHHHHHHHHTTC-TTCHHHHHHHHHHHHHT
T ss_pred             HHHcCCHHHHHHHHHHHHhc--CCCcHHHHHHHHHHHHHcCCHHHHHHHHHHHHhhC-CCCHHHHHhHHHHHHHc
Confidence            55555555555555555542  22 24455555555555555555555555555432 22344444444444433

>1w3b_A UDP-N-acetylglucosamine--peptide N-acetylglucosaminyltransferase 110; OGT, glcnac, nucleoporin, O-linked glycosylation, TPR repeat, protein binding; 2.85A {Homo sapiens} SCOP: a.118.8.1

Probab=100.00  E-value=3.5e-29  Score=245.42  Aligned_cols=383  Identities=13%  Similarity=0.036  Sum_probs=338.2

Q ss_pred             HHHHHHhcCChhHHHHHHHHHHhcCCCCCccccCcHHHHHHHHHHHHHcCCHhHHHHHHHHHhhCCCCCCHhHHHHHHHH
Q 040027          172 LINGLCRTGHTMIALNLFEEMANGNGEIGVVCKPNTVTYSTIIDGLCKEGFVDKAKALFLQMKDENINPDVVTYNSLIHG  251 (595)
Q Consensus       172 l~~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~~ll~~  251 (595)
                      +...+.+.|++++|++.++.+.+..       |.+...+..+...+...|++++|...++...+.. +.+..+|..++..
T Consensus         5 ~a~~~~~~g~~~~A~~~~~~~~~~~-------p~~~~~~~~l~~~~~~~~~~~~a~~~~~~a~~~~-p~~~~~~~~lg~~   76 (388)
T 1w3b_A            5 LAHREYQAGDFEAAERHCMQLWRQE-------PDNTGVLLLLSSIHFQCRRLDRSAHFSTLAIKQN-PLLAEAYSNLGNV   76 (388)
T ss_dssp             HHHHHHHHTCHHHHHHHHHHHHHHC-------TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHH
T ss_pred             HHHHHHHCCCHHHHHHHHHHHHHhC-------CCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHhcC-CCchHHHHHHHHH
Confidence            4567788999999999999998875       5667888889999999999999999999988764 4578899999999


Q ss_pred             HHhcCCHHHHHHHHHHHHHCCCCCCHhhHHHHHHHHHhcCChHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHhcCCHHHH
Q 040027          252 LCHANDWNEAKRLFIEMMDQGVQPSVVTFNVIMDELCKNRKMDEASRLLDLMVQRGVRPNACTYNTLMDGFCLMGKINRA  331 (595)
Q Consensus       252 ~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a  331 (595)
                      +.+.|++++|...|+++.+.. +.+...+..++.++...|++++|...|+++.+.+. .+...+..+...+...|++++|
T Consensus        77 ~~~~g~~~~A~~~~~~al~~~-p~~~~~~~~l~~~~~~~g~~~~A~~~~~~al~~~p-~~~~~~~~l~~~~~~~g~~~~A  154 (388)
T 1w3b_A           77 YKERGQLQEAIEHYRHALRLK-PDFIDGYINLAAALVAAGDMEGAVQAYVSALQYNP-DLYCVRSDLGNLLKALGRLEEA  154 (388)
T ss_dssp             HHHHTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHHSCSSHHHHHHHHHHHHCT-TCTHHHHHHHHHHHTTSCHHHH
T ss_pred             HHHCCCHHHHHHHHHHHHHcC-cchHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCC-CcHHHHHHHHHHHHHccCHHHH
Confidence            999999999999999998853 33566799999999999999999999999998743 3556778889999999999999


Q ss_pred             HHHHHHHHhcCCCCCHHHHHHHHHHHHhCCCHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHccCCHHHHHHHHHHHHHC
Q 040027          332 EELFGSMESMGCKHDDVSYNILINGYCKNKEVEEALSLYREMVSKGIKPTVVTYNTLFLGLFEIHQVEHALKLFDEMQRD  411 (595)
Q Consensus       332 ~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~  411 (595)
                      ...|+++.+.. +.+..+|..+..++...|++++|+..|+++.+.++. +...+..+...+...|++++|...+++..+.
T Consensus       155 ~~~~~~al~~~-p~~~~~~~~l~~~~~~~g~~~~A~~~~~~al~~~p~-~~~~~~~lg~~~~~~~~~~~A~~~~~~al~~  232 (388)
T 1w3b_A          155 KACYLKAIETQ-PNFAVAWSNLGCVFNAQGEIWLAIHHFEKAVTLDPN-FLDAYINLGNVLKEARIFDRAVAAYLRALSL  232 (388)
T ss_dssp             HHHHHHHHHHC-TTCHHHHHHHHHHHHTTTCHHHHHHHHHHHHHHCTT-CHHHHHHHHHHHHTTTCTTHHHHHHHHHHHH
T ss_pred             HHHHHHHHHhC-CCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHhcCCC-cHHHHHHHHHHHHHcCCHHHHHHHHHHHHhh
Confidence            99999998874 556789999999999999999999999999987544 6778899999999999999999999999886


Q ss_pred             CCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCcCHHHHHHHHHHHHhcCChHHHHHHHHhcccCCCCCCHHHHH
Q 040027          412 GVAADTRTYTTFIDGLCKNGYIIEAVELFRTLRILKCELDIQAYNCLIDGLCKSGRLKFAWELFCSLPHGVLVPNVVTYN  491 (595)
Q Consensus       412 ~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~p~~~~~~  491 (595)
                      . +.+..++..+..++...|++++|...++++.+.. +.+..++..++.++.+.|++++|...|+++.+. .+.+..++.
T Consensus       233 ~-p~~~~~~~~l~~~~~~~g~~~~A~~~~~~al~~~-p~~~~~~~~l~~~~~~~g~~~~A~~~~~~al~~-~p~~~~~~~  309 (388)
T 1w3b_A          233 S-PNHAVVHGNLACVYYEQGLIDLAIDTYRRAIELQ-PHFPDAYCNLANALKEKGSVAEAEDCYNTALRL-CPTHADSLN  309 (388)
T ss_dssp             C-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHTC-SSCHHHHHHHHHHHHHHSCHHHHHHHHHHHHHH-CTTCHHHHH
T ss_pred             C-cCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHhhC-CCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHhh-CcccHHHHH
Confidence            3 5568889999999999999999999999999876 667889999999999999999999999999884 244688999


Q ss_pred             HHHHHHHhcCChhHHHHHHHHHHHcCCCCCHHHHHHHHHHHHHcCChhHHHHHHHHHHHCCCCC-CHHHHHHHHHHHHhc
Q 040027          492 IMIQGLCNDGQMDKARDLFLDMEENAAAPDVITFDMLIHGFIRINEPSKVNELLHKMKEKKVMP-DASIVSIVVDLLVKN  570 (595)
Q Consensus       492 ~l~~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~p-~~~~~~~l~~~~~~~  570 (595)
                      .++..+...|++++|+..++++++.. +.+..++..++.+|.+.|++++|...++++.+.  .| +...+..++.++.+.
T Consensus       310 ~l~~~~~~~g~~~~A~~~~~~al~~~-p~~~~~~~~l~~~~~~~g~~~~A~~~~~~a~~~--~p~~~~a~~~lg~~~~~~  386 (388)
T 1w3b_A          310 NLANIKREQGNIEEAVRLYRKALEVF-PEFAAAHSNLASVLQQQGKLQEALMHYKEAIRI--SPTFADAYSNMGNTLKEM  386 (388)
T ss_dssp             HHHHHHHTTTCHHHHHHHHHHHTTSC-TTCHHHHHHHHHHHHTTTCCHHHHHHHHHHHTT--CTTCHHHHHHHHHHHHHT
T ss_pred             HHHHHHHHcCCHHHHHHHHHHHHhcC-CCcHHHHHHHHHHHHHcCCHHHHHHHHHHHHhh--CCCCHHHHHhHHHHHHHc
Confidence            99999999999999999999999864 556889999999999999999999999999974  45 678899999988877


Q ss_pred             Cc
Q 040027          571 EI  572 (595)
Q Consensus       571 g~  572 (595)
                      |+
T Consensus       387 ~~  388 (388)
T 1w3b_A          387 QD  388 (388)
T ss_dssp             CC
T ss_pred             cC
Confidence            64

>2gw1_A Mitochondrial precursor proteins import receptor; TPR, protein transport; 3.00A {Saccharomyces cerevisiae}

Probab=99.96  E-value=4.4e-26  Score=232.46  Aligned_cols=442  Identities=9%  Similarity=-0.050  Sum_probs=304.8

Q ss_pred             HHHHHHHHHHHHhcCChhHHHHHHHHHHhCCCCCCHHHHHHHHHHHHhcCCHhHHHHHHHHHHhcCCCCCHhhHHHHHHH
Q 040027           96 LYTYNILINCFCKIGRVSLGFIAFGRILRSCFTPNAATFNSLIKGLHAESRIMEAAALFTKLKAFGCEPNVITYNTLING  175 (595)
Q Consensus        96 ~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~~l~~~  175 (595)
                      ...+...+..+.+.|++++|+..|+++++..  |+..+|..+..++.+.|++++|++.++++.+.+ +.+..++..++.+
T Consensus         6 a~~~~~~g~~~~~~g~~~~A~~~~~~al~~~--p~~~~~~~la~~~~~~g~~~~A~~~~~~al~~~-p~~~~~~~~l~~~   82 (514)
T 2gw1_A            6 ALALKDKGNQFFRNKKYDDAIKYYNWALELK--EDPVFYSNLSACYVSVGDLKKVVEMSTKALELK-PDYSKVLLRRASA   82 (514)
T ss_dssp             HHHHHHHHHHHHHTSCHHHHHHHHHHHHHHC--CCHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHC-SCCHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHhccHHHHHHHHHHHHhcC--ccHHHHHhHHHHHHHHhhHHHHHHHHHHHhccC-hHHHHHHHHHHHH
Confidence            4567788889999999999999999999884  688999999999999999999999999999875 4467889999999


Q ss_pred             HHhcCChhHHHHHHHHHHhcCCCCCccccCcHHHHHHHHHHHHHcCCHhHHHHHHHHHhhCCCCCCHhHHHHHHHHHHhc
Q 040027          176 LCRTGHTMIALNLFEEMANGNGEIGVVCKPNTVTYSTIIDGLCKEGFVDKAKALFLQMKDENINPDVVTYNSLIHGLCHA  255 (595)
Q Consensus       176 ~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~~ll~~~~~~  255 (595)
                      +...|++++|+..|+++...+       +++......++..+........+.+.+..+...+..|+...+..........
T Consensus        83 ~~~~g~~~~A~~~~~~~~~~~-------~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~  155 (514)
T 2gw1_A           83 NEGLGKFADAMFDLSVLSLNG-------DFNDASIEPMLERNLNKQAMSKLKEKFGDIDTATATPTELSTQPAKERKDKQ  155 (514)
T ss_dssp             HHHTTCHHHHHHHHHHHHHSS-------SCCGGGTHHHHHHHHHHHHHHHHTTC--------------------------
T ss_pred             HHHHhhHHHHHHHHHHHHhcC-------CCccchHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhhccCChhhHHHhhc
Confidence            999999999999999998875       3344444444444444333333333332222211111111111000000000


Q ss_pred             CCHHHHHHHHHHHHHCCC---------CCCHhhHHHHHHHHHh---cCChHHHHHHHHHHHH-----CCC--------CC
Q 040027          256 NDWNEAKRLFIEMMDQGV---------QPSVVTFNVIMDELCK---NRKMDEASRLLDLMVQ-----RGV--------RP  310 (595)
Q Consensus       256 ~~~~~A~~~~~~~~~~~~---------~~~~~~~~~l~~~~~~---~g~~~~a~~~~~~~~~-----~~~--------~~  310 (595)
                      ........+...+.....         +.+...+......+..   .|++++|...++++.+     ...        +.
T Consensus       156 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~~~~~~~~  235 (514)
T 2gw1_A          156 ENLPSVTSMASFFGIFKPELTFANYDESNEADKELMNGLSNLYKRSPESYDKADESFTKAARLFEEQLDKNNEDEKLKEK  235 (514)
T ss_dssp             -CCCCHHHHHHHHTTSCCCCCCSSCCSSCHHHHHHHHHHHHHSSCCTTHHHHHHHHHHHHHHHHHHHTTTSTTCHHHHHH
T ss_pred             cCCchhHHHHHHHhhcCHHHHHHHhcCCcHHHHHHHHHHHHHHhhhhccHHHHHHHHHHHHHHhhhhhccCccccccChH
Confidence            011111111111111100         1123344444444444   7888888888888777     311        12


Q ss_pred             CHHHHHHHHHHHHhcCCHHHHHHHHHHHHhcCCCCCHHHHHHHHHHHHhCCCHHHHHHHHHHHHHCCCCCCHHHHHHHHH
Q 040027          311 NACTYNTLMDGFCLMGKINRAEELFGSMESMGCKHDDVSYNILINGYCKNKEVEEALSLYREMVSKGIKPTVVTYNTLFL  390 (595)
Q Consensus       311 ~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~~l~~  390 (595)
                      +..++..++..+...|++++|...++++.+..  |+...+..+..++...|++++|...++++...... +...+..+..
T Consensus       236 ~~~~~~~~~~~~~~~~~~~~A~~~~~~~l~~~--~~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~~~~~-~~~~~~~l~~  312 (514)
T 2gw1_A          236 LAISLEHTGIFKFLKNDPLGAHEDIKKAIELF--PRVNSYIYMALIMADRNDSTEYYNYFDKALKLDSN-NSSVYYHRGQ  312 (514)
T ss_dssp             HHHHHHHHHHHHHHSSCHHHHHHHHHHHHHHC--CCHHHHHHHHHHHHTSSCCTTGGGHHHHHHTTCTT-CTHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHCCCHHHHHHHHHHHHhhC--ccHHHHHHHHHHHHHCCCHHHHHHHHHHHhhcCcC-CHHHHHHHHH
Confidence            34566777788888888888888888887764  33677788888888888888888888888776433 5667778888


Q ss_pred             HHHccCCHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCcCHHHHHHHHHHHHhcCChHH
Q 040027          391 GLFEIHQVEHALKLFDEMQRDGVAADTRTYTTFIDGLCKNGYIIEAVELFRTLRILKCELDIQAYNCLIDGLCKSGRLKF  470 (595)
Q Consensus       391 ~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~  470 (595)
                      .+...|++++|...++++.+.. +.+...+..+...+...|++++|...++++.+.. +.+..++..++..+...|++++
T Consensus       313 ~~~~~~~~~~A~~~~~~~~~~~-~~~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~~~-~~~~~~~~~la~~~~~~~~~~~  390 (514)
T 2gw1_A          313 MNFILQNYDQAGKDFDKAKELD-PENIFPYIQLACLAYRENKFDDCETLFSEAKRKF-PEAPEVPNFFAEILTDKNDFDK  390 (514)
T ss_dssp             HHHHTTCTTHHHHHHHHHHHTC-SSCSHHHHHHHHHTTTTTCHHHHHHHHHHHHHHS-TTCSHHHHHHHHHHHHTTCHHH
T ss_pred             HHHHhCCHHHHHHHHHHHHHhC-hhhHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHc-ccCHHHHHHHHHHHHHCCCHHH
Confidence            8888888888888888888763 4456777778888888888888888888888765 5567788888888888888888


Q ss_pred             HHHHHHhcccCCCCCC-------HHHHHHHHHHHHh---cCChhHHHHHHHHHHHcCCCCCHHHHHHHHHHHHHcCChhH
Q 040027          471 AWELFCSLPHGVLVPN-------VVTYNIMIQGLCN---DGQMDKARDLFLDMEENAAAPDVITFDMLIHGFIRINEPSK  540 (595)
Q Consensus       471 A~~~~~~~~~~~~~p~-------~~~~~~l~~~~~~---~g~~~~A~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~  540 (595)
                      |...++++...  .|+       ...+..++.++..   .|++++|...++++.+.. +.+..++..++.+|...|++++
T Consensus       391 A~~~~~~a~~~--~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~A~~~~~~a~~~~-~~~~~~~~~la~~~~~~g~~~~  467 (514)
T 2gw1_A          391 ALKQYDLAIEL--ENKLDGIYVGIAPLVGKATLLTRNPTVENFIEATNLLEKASKLD-PRSEQAKIGLAQMKLQQEDIDE  467 (514)
T ss_dssp             HHHHHHHHHHH--HHTSSSCSSCSHHHHHHHHHHHTSCCTTHHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCHHH
T ss_pred             HHHHHHHHHHh--hhccchHHHHHHHHHHHHHHHhhhhhcCCHHHHHHHHHHHHHhC-cccHHHHHHHHHHHHHhcCHHH
Confidence            88888887662  222       2377888888888   888888888888888864 5567788888888888888888


Q ss_pred             HHHHHHHHHHCCCCCCH
Q 040027          541 VNELLHKMKEKKVMPDA  557 (595)
Q Consensus       541 A~~~~~~~~~~~~~p~~  557 (595)
                      |...++++.+.  .|+.
T Consensus       468 A~~~~~~a~~~--~~~~  482 (514)
T 2gw1_A          468 AITLFEESADL--ARTM  482 (514)
T ss_dssp             HHHHHHHHHHH--CSSH
T ss_pred             HHHHHHHHHHh--cccc
Confidence            88888888874  3543

>4g26_A Pentatricopeptide repeat-containing protein AT2G3 mitochondrial; metallonuclease, prorp, ribonuclease, PIN, tRNA processing, NYN domain; 1.75A {Arabidopsis thaliana} PDB: 4g23_A* 4g25_A 4g24_A

Probab=99.96  E-value=1.9e-27  Score=236.25  Aligned_cols=185  Identities=16%  Similarity=0.235  Sum_probs=107.2

Q ss_pred             HHHHHHHHHccCCHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHhcC---------CHHHHHHHHHHHHHcCCCcCHHHH
Q 040027          385 YNTLFLGLFEIHQVEHALKLFDEMQRDGVAADTRTYTTFIDGLCKNG---------YIIEAVELFRTLRILKCELDIQAY  455 (595)
Q Consensus       385 ~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g---------~~~~A~~~~~~~~~~~~~~~~~~~  455 (595)
                      ++.++.+|++.|++++|.++|++|.+.|+.||..+|+.+|.+|.+.+         .+++|.++|++|...|+.||..+|
T Consensus        29 l~~~id~c~k~G~~~~A~~lf~~M~~~Gv~pd~~tyn~Li~~c~~~~~~~~~~~~~~l~~A~~lf~~M~~~G~~Pd~~ty  108 (501)
T 4g26_A           29 LKQKLDMCSKKGDVLEALRLYDEARRNGVQLSQYHYNVLLYVCSLAEAATESSPNPGLSRGFDIFKQMIVDKVVPNEATF  108 (501)
T ss_dssp             HHHHHHHTTTSCCHHHHHHHHHHHHHHTCCCCHHHHHHHHHHHTTCCCCSSSSCCHHHHHHHHHHHHHHHTTCCCCHHHH
T ss_pred             HHHHHHHHHhCCCHHHHHHHHHHHHHcCCCCCHhHHHHHHHHHHhCCchhhhhhcchHHHHHHHHHHHHHhCCCCCHHHH
Confidence            34444445555555555555555554445555555555554444332         245556666666666666666666


Q ss_pred             HHHHHHHHhcCChHHHHHHHHhcccCCCCCCHHHHHHHHHHHHhcCChhHHHHHHHHHHHcCCCCCHHHHHHHHHHHHHc
Q 040027          456 NCLIDGLCKSGRLKFAWELFCSLPHGVLVPNVVTYNIMIQGLCNDGQMDKARDLFLDMEENAAAPDVITFDMLIHGFIRI  535 (595)
Q Consensus       456 ~~l~~~~~~~g~~~~A~~~~~~~~~~~~~p~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~~l~~~~~~~  535 (595)
                      +.++.+|++.|++++|.++|++|.+.|+.||..+|+.++.+|++.|++++|.++|++|.+.|+.||..+|+.++.+|++.
T Consensus       109 n~lI~~~~~~g~~~~A~~l~~~M~~~g~~Pd~~tyn~lI~~~~~~g~~~~A~~l~~~M~~~G~~Pd~~ty~~Li~~~~~~  188 (501)
T 4g26_A          109 TNGARLAVAKDDPEMAFDMVKQMKAFGIQPRLRSYGPALFGFCRKGDADKAYEVDAHMVESEVVPEEPELAALLKVSMDT  188 (501)
T ss_dssp             HHHHHHHHHHTCHHHHHHHHHHHHHTTCCCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHTTCCCCHHHHHHHHHHHHHT
T ss_pred             HHHHHHHHhcCCHHHHHHHHHHHHHcCCCCccceehHHHHHHHHCCCHHHHHHHHHHHHhcCCCCCHHHHHHHHHHHhhC
Confidence            66666666666666666666666665666666666666666666666666666666666666666666666666666666


Q ss_pred             CChhHHHHHHHHHHHCCCCCCHHHHHHHHHHHHh
Q 040027          536 NEPSKVNELLHKMKEKKVMPDASIVSIVVDLLVK  569 (595)
Q Consensus       536 g~~~~A~~~~~~~~~~~~~p~~~~~~~l~~~~~~  569 (595)
                      |++++|.+++++|.+.|..|+..||..+++.|..
T Consensus       189 g~~d~A~~ll~~Mr~~g~~ps~~T~~~l~~~F~s  222 (501)
T 4g26_A          189 KNADKVYKTLQRLRDLVRQVSKSTFDMIEEWFKS  222 (501)
T ss_dssp             TCHHHHHHHHHHHHHHTSSBCHHHHHHHHHHHHS
T ss_pred             CCHHHHHHHHHHHHHhCCCcCHHHHHHHHHHHhc
Confidence            6666666666666666666666666666655554

>4g26_A Pentatricopeptide repeat-containing protein AT2G3 mitochondrial; metallonuclease, prorp, ribonuclease, PIN, tRNA processing, NYN domain; 1.75A {Arabidopsis thaliana} PDB: 4g23_A* 4g25_A 4g24_A

Probab=99.95  E-value=1.1e-26  Score=230.72  Aligned_cols=185  Identities=18%  Similarity=0.263  Sum_probs=111.0

Q ss_pred             HHHHHHHHHhCCCHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHccCC---------HHHHHHHHHHHHHCCCCCCHHHH
Q 040027          350 YNILINGYCKNKEVEEALSLYREMVSKGIKPTVVTYNTLFLGLFEIHQ---------VEHALKLFDEMQRDGVAADTRTY  420 (595)
Q Consensus       350 ~~~l~~~~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~---------~~~a~~~~~~~~~~~~~~~~~~~  420 (595)
                      ++.+|.+|++.|++++|+++|++|.+.|+.||..+|+.++.+|.+.+.         .+.|.++|++|...|+.||..+|
T Consensus        29 l~~~id~c~k~G~~~~A~~lf~~M~~~Gv~pd~~tyn~Li~~c~~~~~~~~~~~~~~l~~A~~lf~~M~~~G~~Pd~~ty  108 (501)
T 4g26_A           29 LKQKLDMCSKKGDVLEALRLYDEARRNGVQLSQYHYNVLLYVCSLAEAATESSPNPGLSRGFDIFKQMIVDKVVPNEATF  108 (501)
T ss_dssp             HHHHHHHTTTSCCHHHHHHHHHHHHHHTCCCCHHHHHHHHHHHTTCCCCSSSSCCHHHHHHHHHHHHHHHTTCCCCHHHH
T ss_pred             HHHHHHHHHhCCCHHHHHHHHHHHHHcCCCCCHhHHHHHHHHHHhCCchhhhhhcchHHHHHHHHHHHHHhCCCCCHHHH
Confidence            444555555555555555555555555555555555555555544332         45566666666666666666666


Q ss_pred             HHHHHHHHhcCCHHHHHHHHHHHHHcCCCcCHHHHHHHHHHHHhcCChHHHHHHHHhcccCCCCCCHHHHHHHHHHHHhc
Q 040027          421 TTFIDGLCKNGYIIEAVELFRTLRILKCELDIQAYNCLIDGLCKSGRLKFAWELFCSLPHGVLVPNVVTYNIMIQGLCND  500 (595)
Q Consensus       421 ~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~p~~~~~~~l~~~~~~~  500 (595)
                      +.+|.+|++.|++++|.++|++|.+.|+.||..+|+.++.+|++.|++++|.++|++|.+.|+.||..+|+.|+.+|++.
T Consensus       109 n~lI~~~~~~g~~~~A~~l~~~M~~~g~~Pd~~tyn~lI~~~~~~g~~~~A~~l~~~M~~~G~~Pd~~ty~~Li~~~~~~  188 (501)
T 4g26_A          109 TNGARLAVAKDDPEMAFDMVKQMKAFGIQPRLRSYGPALFGFCRKGDADKAYEVDAHMVESEVVPEEPELAALLKVSMDT  188 (501)
T ss_dssp             HHHHHHHHHHTCHHHHHHHHHHHHHTTCCCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHTTCCCCHHHHHHHHHHHHHT
T ss_pred             HHHHHHHHhcCCHHHHHHHHHHHHHcCCCCccceehHHHHHHHHCCCHHHHHHHHHHHHhcCCCCCHHHHHHHHHHHhhC
Confidence            66666666666666666666666666666666666666666666666666666666666666666666666666666666


Q ss_pred             CChhHHHHHHHHHHHcCCCCCHHHHHHHHHHHHH
Q 040027          501 GQMDKARDLFLDMEENAAAPDVITFDMLIHGFIR  534 (595)
Q Consensus       501 g~~~~A~~~~~~~~~~~~~~~~~~~~~l~~~~~~  534 (595)
                      |++++|.+++++|.+.+..|+..||..++..|..
T Consensus       189 g~~d~A~~ll~~Mr~~g~~ps~~T~~~l~~~F~s  222 (501)
T 4g26_A          189 KNADKVYKTLQRLRDLVRQVSKSTFDMIEEWFKS  222 (501)
T ss_dssp             TCHHHHHHHHHHHHHHTSSBCHHHHHHHHHHHHS
T ss_pred             CCHHHHHHHHHHHHHhCCCcCHHHHHHHHHHHhc
Confidence            6666666666666666666666666665555543

>2gw1_A Mitochondrial precursor proteins import receptor; TPR, protein transport; 3.00A {Saccharomyces cerevisiae}

Probab=99.95  E-value=7.2e-25  Score=223.48  Aligned_cols=435  Identities=10%  Similarity=0.002  Sum_probs=324.7

Q ss_pred             HHHHHHHHHHHHhcCCHhHHHHHHHHHHhcCCCCCHhhHHHHHHHHHhcCChhHHHHHHHHHHhcCCCCCccccCcHHHH
Q 040027          131 AATFNSLIKGLHAESRIMEAAALFTKLKAFGCEPNVITYNTLINGLCRTGHTMIALNLFEEMANGNGEIGVVCKPNTVTY  210 (595)
Q Consensus       131 ~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~~~~~~  210 (595)
                      ...+......+.+.|++++|+..|+++....  |+..++..++.++...|++++|+..|+++.+.+       |.+..++
T Consensus         6 a~~~~~~g~~~~~~g~~~~A~~~~~~al~~~--p~~~~~~~la~~~~~~g~~~~A~~~~~~al~~~-------p~~~~~~   76 (514)
T 2gw1_A            6 ALALKDKGNQFFRNKKYDDAIKYYNWALELK--EDPVFYSNLSACYVSVGDLKKVVEMSTKALELK-------PDYSKVL   76 (514)
T ss_dssp             HHHHHHHHHHHHHTSCHHHHHHHHHHHHHHC--CCHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHC-------SCCHHHH
T ss_pred             HHHHHHHHHHHHHhccHHHHHHHHHHHHhcC--ccHHHHHhHHHHHHHHhhHHHHHHHHHHHhccC-------hHHHHHH
Confidence            4567778888999999999999999999874  689999999999999999999999999999875       5678899


Q ss_pred             HHHHHHHHHcCCHhHHHHHHHHHhhCCCCCCHhHHHHHHHHHHhcCCHHHHHHHHHHHHHCCCCCCHhhHHHHHHHHHhc
Q 040027          211 STIIDGLCKEGFVDKAKALFLQMKDENINPDVVTYNSLIHGLCHANDWNEAKRLFIEMMDQGVQPSVVTFNVIMDELCKN  290 (595)
Q Consensus       211 ~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~~ll~~~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~~l~~~~~~~  290 (595)
                      ..++.++...|++++|...|+++...+ +++......++..+........+.+.+..+...+..|+...+..........
T Consensus        77 ~~l~~~~~~~g~~~~A~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~  155 (514)
T 2gw1_A           77 LRRASANEGLGKFADAMFDLSVLSLNG-DFNDASIEPMLERNLNKQAMSKLKEKFGDIDTATATPTELSTQPAKERKDKQ  155 (514)
T ss_dssp             HHHHHHHHHTTCHHHHHHHHHHHHHSS-SCCGGGTHHHHHHHHHHHHHHHHTTC--------------------------
T ss_pred             HHHHHHHHHHhhHHHHHHHHHHHHhcC-CCccchHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhhccCChhhHHHhhc
Confidence            999999999999999999999998875 3344555555555544444444444333322221112111111111111111


Q ss_pred             CChHHHHHHHHHHHHCCC---------CCCHHHHHHHHHHHHh---cCCHHHHHHHHHHHHh-----cCC--------CC
Q 040027          291 RKMDEASRLLDLMVQRGV---------RPNACTYNTLMDGFCL---MGKINRAEELFGSMES-----MGC--------KH  345 (595)
Q Consensus       291 g~~~~a~~~~~~~~~~~~---------~~~~~~~~~l~~~~~~---~~~~~~a~~~~~~~~~-----~~~--------~~  345 (595)
                      ........+...+.....         +.+...+......+..   .|++++|...++++.+     ...        +.
T Consensus       156 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~~~~~~~~  235 (514)
T 2gw1_A          156 ENLPSVTSMASFFGIFKPELTFANYDESNEADKELMNGLSNLYKRSPESYDKADESFTKAARLFEEQLDKNNEDEKLKEK  235 (514)
T ss_dssp             -CCCCHHHHHHHHTTSCCCCCCSSCCSSCHHHHHHHHHHHHHSSCCTTHHHHHHHHHHHHHHHHHHHTTTSTTCHHHHHH
T ss_pred             cCCchhHHHHHHHhhcCHHHHHHHhcCCcHHHHHHHHHHHHHHhhhhccHHHHHHHHHHHHHHhhhhhccCccccccChH
Confidence            111111111111111111         1224555555555555   8999999999999987     311        22


Q ss_pred             CHHHHHHHHHHHHhCCCHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHccCCHHHHHHHHHHHHHCCCCCCHHHHHHHHH
Q 040027          346 DDVSYNILINGYCKNKEVEEALSLYREMVSKGIKPTVVTYNTLFLGLFEIHQVEHALKLFDEMQRDGVAADTRTYTTFID  425 (595)
Q Consensus       346 ~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~  425 (595)
                      +...+..+...+...|++++|...++++.+....  ...+..+...+...|++++|...++.+.+.. +.+...+..+..
T Consensus       236 ~~~~~~~~~~~~~~~~~~~~A~~~~~~~l~~~~~--~~~~~~l~~~~~~~~~~~~A~~~~~~~~~~~-~~~~~~~~~l~~  312 (514)
T 2gw1_A          236 LAISLEHTGIFKFLKNDPLGAHEDIKKAIELFPR--VNSYIYMALIMADRNDSTEYYNYFDKALKLD-SNNSSVYYHRGQ  312 (514)
T ss_dssp             HHHHHHHHHHHHHHSSCHHHHHHHHHHHHHHCCC--HHHHHHHHHHHHTSSCCTTGGGHHHHHHTTC-TTCTHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHCCCHHHHHHHHHHHHhhCcc--HHHHHHHHHHHHHCCCHHHHHHHHHHHhhcC-cCCHHHHHHHHH
Confidence            3457888899999999999999999999987544  7888899999999999999999999999874 557788999999


Q ss_pred             HHHhcCCHHHHHHHHHHHHHcCCCcCHHHHHHHHHHHHhcCChHHHHHHHHhcccCCCCCCHHHHHHHHHHHHhcCChhH
Q 040027          426 GLCKNGYIIEAVELFRTLRILKCELDIQAYNCLIDGLCKSGRLKFAWELFCSLPHGVLVPNVVTYNIMIQGLCNDGQMDK  505 (595)
Q Consensus       426 ~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~p~~~~~~~l~~~~~~~g~~~~  505 (595)
                      .+...|++++|...++++.+.. +.+...+..++..+...|++++|...++++.+. .+.+...+..++..+...|++++
T Consensus       313 ~~~~~~~~~~A~~~~~~~~~~~-~~~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~~-~~~~~~~~~~la~~~~~~~~~~~  390 (514)
T 2gw1_A          313 MNFILQNYDQAGKDFDKAKELD-PENIFPYIQLACLAYRENKFDDCETLFSEAKRK-FPEAPEVPNFFAEILTDKNDFDK  390 (514)
T ss_dssp             HHHHTTCTTHHHHHHHHHHHTC-SSCSHHHHHHHHHTTTTTCHHHHHHHHHHHHHH-STTCSHHHHHHHHHHHHTTCHHH
T ss_pred             HHHHhCCHHHHHHHHHHHHHhC-hhhHHHHHHHHHHHHHcCCHHHHHHHHHHHHHH-cccCHHHHHHHHHHHHHCCCHHH
Confidence            9999999999999999999876 567889999999999999999999999999874 12356788999999999999999


Q ss_pred             HHHHHHHHHHcCCC-CC----HHHHHHHHHHHHH---cCChhHHHHHHHHHHHCCCCCCHHHHHHHHHHHHhcCcccccc
Q 040027          506 ARDLFLDMEENAAA-PD----VITFDMLIHGFIR---INEPSKVNELLHKMKEKKVMPDASIVSIVVDLLVKNEISLKSL  577 (595)
Q Consensus       506 A~~~~~~~~~~~~~-~~----~~~~~~l~~~~~~---~g~~~~A~~~~~~~~~~~~~p~~~~~~~l~~~~~~~g~~~~~i  577 (595)
                      |...++++.+.... ++    ...+..++.+|..   .|++++|...++++.+.. +.+..++..++.+|.+.|++++++
T Consensus       391 A~~~~~~a~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~A~~~~~~a~~~~-~~~~~~~~~la~~~~~~g~~~~A~  469 (514)
T 2gw1_A          391 ALKQYDLAIELENKLDGIYVGIAPLVGKATLLTRNPTVENFIEATNLLEKASKLD-PRSEQAKIGLAQMKLQQEDIDEAI  469 (514)
T ss_dssp             HHHHHHHHHHHHHTSSSCSSCSHHHHHHHHHHHTSCCTTHHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCHHHHH
T ss_pred             HHHHHHHHHHhhhccchHHHHHHHHHHHHHHHhhhhhcCCHHHHHHHHHHHHHhC-cccHHHHHHHHHHHHHhcCHHHHH
Confidence            99999999875311 11    3388899999999   999999999999999853 346889999999999999999655


Q ss_pred             hHHH
Q 040027          578 PSFL  581 (595)
Q Consensus       578 ~~~~  581 (595)
                      ..+.
T Consensus       470 ~~~~  473 (514)
T 2gw1_A          470 TLFE  473 (514)
T ss_dssp             HHHH
T ss_pred             HHHH
Confidence            5543

>3fp2_A TPR repeat-containing protein YHR117W; TOM71, mitochondria translocation, allosteric REG phosphoprotein, TPR repeat, ATP-binding; 1.98A {Saccharomyces cerevisiae} PDB: 3fp3_A 3fp4_A 3lca_A

Probab=99.95  E-value=2.9e-24  Score=220.33  Aligned_cols=436  Identities=10%  Similarity=0.019  Sum_probs=324.6

Q ss_pred             CHHHHHHHHHHHHhcCChhHHHHHHHHHHhCCCCCCHHHHHHHHHHHHhcCCHhHHHHHHHHHHhcCCCCCHhhHHHHHH
Q 040027           95 NLYTYNILINCFCKIGRVSLGFIAFGRILRSCFTPNAATFNSLIKGLHAESRIMEAAALFTKLKAFGCEPNVITYNTLIN  174 (595)
Q Consensus        95 ~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~~l~~  174 (595)
                      ....|..++..+.+.|++++|+..|+++++.. +.++.+|..+..+|.+.|++++|++.|+++...+ +.+..++..++.
T Consensus        24 ~a~~~~~~g~~~~~~g~~~~A~~~~~~al~~~-p~~~~~~~~la~~~~~~g~~~~A~~~~~~al~~~-p~~~~~~~~la~  101 (537)
T 3fp2_A           24 YAVQLKNRGNHFFTAKNFNEAIKYYQYAIELD-PNEPVFYSNISACYISTGDLEKVIEFTTKALEIK-PDHSKALLRRAS  101 (537)
T ss_dssp             HHHHHHHHHHHHHHTTCCC-CHHHHHHHHHHC-TTCHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHC-TTCHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHhccHHHHHHHHHHHHhhC-CCCcHHHHHHHHHHHHcCCHHHHHHHHHHHHhcC-CchHHHHHHHHH
Confidence            35677888999999999999999999999885 5688899999999999999999999999999885 447888999999


Q ss_pred             HHHhcCChhHHHHHHHHHHhcCCCCCccccCcHHHHHHHHHHHHHcCCHhHHHHHHHHHhhCCC--CCCHhHHHHHHHHH
Q 040027          175 GLCRTGHTMIALNLFEEMANGNGEIGVVCKPNTVTYSTIIDGLCKEGFVDKAKALFLQMKDENI--NPDVVTYNSLIHGL  252 (595)
Q Consensus       175 ~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~--~~~~~~~~~ll~~~  252 (595)
                      ++...|++++|+..|+ .....        |+  .....+..+...+...+|...++++.....  .+........+..+
T Consensus       102 ~~~~~g~~~~A~~~~~-~~~~~--------~~--~~~~~~~~~~~~~~~~~a~~~~~~~l~~~~~~~~~~~~~~~~~~~~  170 (537)
T 3fp2_A          102 ANESLGNFTDAMFDLS-VLSLN--------GD--FDGASIEPMLERNLNKQAMKVLNENLSKDEGRGSQVLPSNTSLASF  170 (537)
T ss_dssp             HHHHHTCHHHHHHHHH-HHC---------------------CHHHHHHHHHHHHHHHHHCC-------CCCCCHHHHHHH
T ss_pred             HHHHcCCHHHHHHHHH-HHhcC--------CC--CChHHHHHHHHHHHHHHHHHHHHHHHHhCccccccccchHhHHHHH
Confidence            9999999999999996 44332        22  222234455566667889999988865410  00111112334445


Q ss_pred             HhcCCHHHHHHHHHHHHHCCCCCCHh-hHHHHHHHHH--------hcCChHHHHHHHHHHHHCCCCCC-------HHHHH
Q 040027          253 CHANDWNEAKRLFIEMMDQGVQPSVV-TFNVIMDELC--------KNRKMDEASRLLDLMVQRGVRPN-------ACTYN  316 (595)
Q Consensus       253 ~~~~~~~~A~~~~~~~~~~~~~~~~~-~~~~l~~~~~--------~~g~~~~a~~~~~~~~~~~~~~~-------~~~~~  316 (595)
                      ....+.+.+...+......  .+... ....+...+.        ..|++++|..+++++.+.... +       ..++.
T Consensus       171 ~~~~~~~~~~~~~~~~~~~--~~~~~~~~~~l~~~~~~~~~~~~~a~~~~~~A~~~~~~~l~~~p~-~~~~~~~~~~~~~  247 (537)
T 3fp2_A          171 FGIFDSHLEVSSVNTSSNY--DTAYALLSDALQRLYSATDEGYLVANDLLTKSTDMYHSLLSANTV-DDPLRENAALALC  247 (537)
T ss_dssp             HHTSCHHHHHHTSCCCCSS--CSSHHHHHHHHHHHHTCSHHHHHHHHHHHHHHHHHHHHHHC--CC-CHHHHHHHHHHHH
T ss_pred             HHhcChHHHHHHHhhcccc--ccHHHHHHHHHHHHHHhhhhhhHHHHHHHHHHHHHHHHHHHHCCC-cchhhHHHHHHHH
Confidence            5566666665554332221  11211 2222222222        224788899999988876422 2       23466


Q ss_pred             HHHHHHHhcCCHHHHHHHHHHHHhcCCCCCHHHHHHHHHHHHhCCCHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHccC
Q 040027          317 TLMDGFCLMGKINRAEELFGSMESMGCKHDDVSYNILINGYCKNKEVEEALSLYREMVSKGIKPTVVTYNTLFLGLFEIH  396 (595)
Q Consensus       317 ~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~  396 (595)
                      .+...+...|++++|...++++.+..  |+...+..+...+...|++++|+..++++.+..+. +..++..+...+...|
T Consensus       248 ~~g~~~~~~~~~~~A~~~~~~~~~~~--~~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~~~~~-~~~~~~~l~~~~~~~~  324 (537)
T 3fp2_A          248 YTGIFHFLKNNLLDAQVLLQESINLH--PTPNSYIFLALTLADKENSQEFFKFFQKAVDLNPE-YPPTYYHRGQMYFILQ  324 (537)
T ss_dssp             HHHHHHHHTTCHHHHHHHHHHHHHHC--CCHHHHHHHHHHTCCSSCCHHHHHHHHHHHHHCTT-CHHHHHHHHHHHHHTT
T ss_pred             HHHHHHHhcccHHHHHHHHHHHHhcC--CCchHHHHHHHHHHHhcCHHHHHHHHHHHhccCCC-CHHHHHHHHHHHHhcC
Confidence            67778888999999999999998873  55778888999999999999999999998886543 6778888999999999


Q ss_pred             CHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCcCHHHHHHHHHHHHhcCChHHHHHHHH
Q 040027          397 QVEHALKLFDEMQRDGVAADTRTYTTFIDGLCKNGYIIEAVELFRTLRILKCELDIQAYNCLIDGLCKSGRLKFAWELFC  476 (595)
Q Consensus       397 ~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~  476 (595)
                      ++++|...++++.+.. +.+...+..+..++...|++++|...++++.+.. +.+...+..++.++...|++++|...|+
T Consensus       325 ~~~~A~~~~~~a~~~~-~~~~~~~~~la~~~~~~g~~~~A~~~~~~~~~~~-~~~~~~~~~l~~~~~~~g~~~~A~~~~~  402 (537)
T 3fp2_A          325 DYKNAKEDFQKAQSLN-PENVYPYIQLACLLYKQGKFTESEAFFNETKLKF-PTLPEVPTFFAEILTDRGDFDTAIKQYD  402 (537)
T ss_dssp             CHHHHHHHHHHHHHHC-TTCSHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCTHHHHHHHHHHHHTTCHHHHHHHHH
T ss_pred             CHHHHHHHHHHHHHhC-CCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhC-CCChHHHHHHHHHHHHhCCHHHHHHHHH
Confidence            9999999999998864 4456788888999999999999999999998876 6677888999999999999999999999


Q ss_pred             hcccCC-----CCCCHHHHHHHHHHHHhc----------CChhHHHHHHHHHHHcCCCCCHHHHHHHHHHHHHcCChhHH
Q 040027          477 SLPHGV-----LVPNVVTYNIMIQGLCND----------GQMDKARDLFLDMEENAAAPDVITFDMLIHGFIRINEPSKV  541 (595)
Q Consensus       477 ~~~~~~-----~~p~~~~~~~l~~~~~~~----------g~~~~A~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A  541 (595)
                      ++.+..     .......+..+..++...          |++++|+..|+++.+.. +.+..++..++.+|...|++++|
T Consensus       403 ~a~~~~~~~~~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~A~~~~~~a~~~~-p~~~~~~~~l~~~~~~~g~~~~A  481 (537)
T 3fp2_A          403 IAKRLEEVQEKIHVGIGPLIGKATILARQSSQDPTQLDEEKFNAAIKLLTKACELD-PRSEQAKIGLAQLKLQMEKIDEA  481 (537)
T ss_dssp             HHHHHHHHCSSCSSTTHHHHHHHHHHHHHHTC----CCHHHHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCHHHH
T ss_pred             HHHHcCCcchhhHHHHHHHHHHHHHHHHHhhccchhhhHhHHHHHHHHHHHHHHhC-CCCHHHHHHHHHHHHHhccHHHH
Confidence            987621     111222344556677777          99999999999999874 55678889999999999999999


Q ss_pred             HHHHHHHHHCC
Q 040027          542 NELLHKMKEKK  552 (595)
Q Consensus       542 ~~~~~~~~~~~  552 (595)
                      .+.++++.+..
T Consensus       482 ~~~~~~al~~~  492 (537)
T 3fp2_A          482 IELFEDSAILA  492 (537)
T ss_dssp             HHHHHHHHHHC
T ss_pred             HHHHHHHHHhC
Confidence            99999999753

>2y4t_A DNAJ homolog subfamily C member 3; chaperone, endoplasmic reticulum, protein folding, tetratricopeptiderepeat, J domain, unfolded protein respons; 3.00A {Homo sapiens} PDB: 2y4u_A

Probab=99.94  E-value=4e-23  Score=206.73  Aligned_cols=316  Identities=12%  Similarity=0.066  Sum_probs=157.2

Q ss_pred             CCCHHHHHHHHHHHHhcCCHhHHHHHHHHHHhcCCCCCHhhHHHHHHHHHhcCChhHHHHHHHHHHhcCCCCCccccCcH
Q 040027          128 TPNAATFNSLIKGLHAESRIMEAAALFTKLKAFGCEPNVITYNTLINGLCRTGHTMIALNLFEEMANGNGEIGVVCKPNT  207 (595)
Q Consensus       128 ~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~~~  207 (595)
                      +.+...+..++..+.+.|++++|+.+|+++.... +.+..++..++.++...|++++|+..|+++.+.+       +.+.
T Consensus        23 p~~~~~~~~~~~~~~~~g~~~~A~~~~~~~l~~~-p~~~~~~~~l~~~~~~~g~~~~A~~~~~~al~~~-------p~~~   94 (450)
T 2y4t_A           23 MADVEKHLELGKKLLAAGQLADALSQFHAAVDGD-PDNYIAYYRRATVFLAMGKSKAALPDLTKVIQLK-------MDFT   94 (450)
T ss_dssp             CHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-------TTCH
T ss_pred             HHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHhC-CccHHHHHHHHHHHHHCCCHHHHHHHHHHHHhcC-------CCcH
Confidence            3445556666666666666666666666666543 3356666666666666666666666666666654       3445


Q ss_pred             HHHHHHHHHHHHcCCHhHHHHHHHHHhhCCCCCCH---hHHHHHHH------------HHHhcCCHHHHHHHHHHHHHCC
Q 040027          208 VTYSTIIDGLCKEGFVDKAKALFLQMKDENINPDV---VTYNSLIH------------GLCHANDWNEAKRLFIEMMDQG  272 (595)
Q Consensus       208 ~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~~~---~~~~~ll~------------~~~~~~~~~~A~~~~~~~~~~~  272 (595)
                      .++..++.+|...|++++|.+.|+++.... +.+.   ..+..++.            .+...|++++|+..|+++.+..
T Consensus        95 ~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~-~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~A~~~~~~~~~~~  173 (450)
T 2y4t_A           95 AARLQRGHLLLKQGKLDEAEDDFKKVLKSN-PSENEEKEAQSQLIKSDEMQRLRSQALNAFGSGDYTAAIAFLDKILEVC  173 (450)
T ss_dssp             HHHHHHHHHHHHTTCHHHHHHHHHHHHTSC-CCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHC
T ss_pred             HHHHHHHHHHHHcCCHHHHHHHHHHHHhcC-CCChhhHHHHHHHHHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhC
Confidence            666666666666666666666666666542 1122   33333332            3444455555555555544431


Q ss_pred             CCCCHhhHHHHHHHHHhcCChHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHhcCCCCCHHHHHH
Q 040027          273 VQPSVVTFNVIMDELCKNRKMDEASRLLDLMVQRGVRPNACTYNTLMDGFCLMGKINRAEELFGSMESMGCKHDDVSYNI  352 (595)
Q Consensus       273 ~~~~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~  352 (595)
                       +.+...+..++.++...|++++|...|+++.+.. +.+..++..++.+|...|++++|+..|+++.+.. +.+...+..
T Consensus       174 -~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~-~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~-p~~~~~~~~  250 (450)
T 2y4t_A          174 -VWDAELRELRAECFIKEGEPRKAISDLKAASKLK-NDNTEAFYKISTLYYQLGDHELSLSEVRECLKLD-QDHKRCFAH  250 (450)
T ss_dssp             -TTCHHHHHHHHHHHHHTTCGGGGHHHHHHHHHHH-CSCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHH
T ss_pred             -CCChHHHHHHHHHHHHCCCHHHHHHHHHHHHHhC-CCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhC-CChHHHHHH
Confidence             1233444444444444444444444444444331 1233444444444444444444444444444331 112222221


Q ss_pred             HHHHHHhCCCHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHccCCHHHHHHHHHHHHHCCCCCC----HHHHHHHHHHHH
Q 040027          353 LINGYCKNKEVEEALSLYREMVSKGIKPTVVTYNTLFLGLFEIHQVEHALKLFDEMQRDGVAAD----TRTYTTFIDGLC  428 (595)
Q Consensus       353 l~~~~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~----~~~~~~l~~~~~  428 (595)
                      +...              .         .......+...+...|++++|...++++.+.. +.+    ...+..+..++.
T Consensus       251 ~~~~--------------~---------~~~~~~~~~~~~~~~g~~~~A~~~~~~~l~~~-p~~~~~~~~~~~~l~~~~~  306 (450)
T 2y4t_A          251 YKQV--------------K---------KLNKLIESAEELIRDGRYTDATSKYESVMKTE-PSIAEYTVRSKERICHCFS  306 (450)
T ss_dssp             HHHH--------------H---------HHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHC-CSSHHHHHHHHHHHHHHHH
T ss_pred             HHHH--------------H---------HHHHHHHHHHHHHHcCCHHHHHHHHHHHHhcC-CcchHHHHHHHHHHHHHHH
Confidence            1000              0         00001112444555555555555555555431 111    224445555555


Q ss_pred             hcCCHHHHHHHHHHHHHcCCCcCHHHHHHHHHHHHhcCChHHHHHHHHhccc
Q 040027          429 KNGYIIEAVELFRTLRILKCELDIQAYNCLIDGLCKSGRLKFAWELFCSLPH  480 (595)
Q Consensus       429 ~~g~~~~A~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~  480 (595)
                      +.|++++|...++++.+.. +.+..++..++.+|...|++++|...++++.+
T Consensus       307 ~~g~~~~A~~~~~~a~~~~-p~~~~~~~~l~~~~~~~~~~~~A~~~~~~al~  357 (450)
T 2y4t_A          307 KDEKPVEAIRVCSEVLQME-PDNVNALKDRAEAYLIEEMYDEAIQDYETAQE  357 (450)
T ss_dssp             TTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHT
T ss_pred             HCCCHHHHHHHHHHHHHhC-cccHHHHHHHHHHHHHhcCHHHHHHHHHHHHH
Confidence            5555555555555555443 33455555555555555555555555555555

>2y4t_A DNAJ homolog subfamily C member 3; chaperone, endoplasmic reticulum, protein folding, tetratricopeptiderepeat, J domain, unfolded protein respons; 3.00A {Homo sapiens} PDB: 2y4u_A

Probab=99.94  E-value=1.2e-22  Score=203.21  Aligned_cols=371  Identities=11%  Similarity=0.047  Sum_probs=292.5

Q ss_pred             HHHHHHHHHhcCCCCCccccCcHHHHHHHHHHHHHcCCHhHHHHHHHHHhhCCCCCCHhHHHHHHHHHHhcCCHHHHHHH
Q 040027          185 ALNLFEEMANGNGEIGVVCKPNTVTYSTIIDGLCKEGFVDKAKALFLQMKDENINPDVVTYNSLIHGLCHANDWNEAKRL  264 (595)
Q Consensus       185 A~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~~ll~~~~~~~~~~~A~~~  264 (595)
                      +...+.++...+       |.+...+..++..+.+.|++++|..+|+++.... +.+...|..++.++...|++++|...
T Consensus        11 ~~~~~~~~~~~~-------p~~~~~~~~~~~~~~~~g~~~~A~~~~~~~l~~~-p~~~~~~~~l~~~~~~~g~~~~A~~~   82 (450)
T 2y4t_A           11 VDLGTENLYFQS-------MADVEKHLELGKKLLAAGQLADALSQFHAAVDGD-PDNYIAYYRRATVFLAMGKSKAALPD   82 (450)
T ss_dssp             -------------------CHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCHHHHHHH
T ss_pred             cccccccccccc-------HHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHhC-CccHHHHHHHHHHHHHCCCHHHHHHH
Confidence            344455555443       5678889999999999999999999999998763 44788999999999999999999999


Q ss_pred             HHHHHHCCCCCCHhhHHHHHHHHHhcCChHHHHHHHHHHHHCCCCCCH---HHHHHH------------HHHHHhcCCHH
Q 040027          265 FIEMMDQGVQPSVVTFNVIMDELCKNRKMDEASRLLDLMVQRGVRPNA---CTYNTL------------MDGFCLMGKIN  329 (595)
Q Consensus       265 ~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~~~~~~---~~~~~l------------~~~~~~~~~~~  329 (595)
                      |+++++.+ +.+...+..++.++...|++++|...|+++.+.... +.   ..+..+            +..+...|+++
T Consensus        83 ~~~al~~~-p~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~-~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~  160 (450)
T 2y4t_A           83 LTKVIQLK-MDFTAARLQRGHLLLKQGKLDEAEDDFKKVLKSNPS-ENEEKEAQSQLIKSDEMQRLRSQALNAFGSGDYT  160 (450)
T ss_dssp             HHHHHHHC-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHTSCCC-HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTCHH
T ss_pred             HHHHHhcC-CCcHHHHHHHHHHHHHcCCHHHHHHHHHHHHhcCCC-ChhhHHHHHHHHHHHHHHHHHHHHHHHHHcCCHH
Confidence            99999864 336778999999999999999999999999986422 33   444444            45588999999


Q ss_pred             HHHHHHHHHHhcCCCCCHHHHHHHHHHHHhCCCHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHccCCHHHHHHHHHHHH
Q 040027          330 RAEELFGSMESMGCKHDDVSYNILINGYCKNKEVEEALSLYREMVSKGIKPTVVTYNTLFLGLFEIHQVEHALKLFDEMQ  409 (595)
Q Consensus       330 ~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~  409 (595)
                      +|+..++++.+.. +.+...+..++.+|.+.|++++|+..|+++.+... .+..++..+...+...|++++|...++++.
T Consensus       161 ~A~~~~~~~~~~~-~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~-~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~  238 (450)
T 2y4t_A          161 AAIAFLDKILEVC-VWDAELRELRAECFIKEGEPRKAISDLKAASKLKN-DNTEAFYKISTLYYQLGDHELSLSEVRECL  238 (450)
T ss_dssp             HHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCGGGGHHHHHHHHHHHC-SCHHHHHHHHHHHHHTTCHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHhC-CCChHHHHHHHHHHHHCCCHHHHHHHHHHHHHhCC-CCHHHHHHHHHHHHHcCCHHHHHHHHHHHH
Confidence            9999999998874 56788899999999999999999999999987643 378899999999999999999999999998


Q ss_pred             HCCCCCCHHHHHHH------------HHHHHhcCCHHHHHHHHHHHHHcCCCcC----HHHHHHHHHHHHhcCChHHHHH
Q 040027          410 RDGVAADTRTYTTF------------IDGLCKNGYIIEAVELFRTLRILKCELD----IQAYNCLIDGLCKSGRLKFAWE  473 (595)
Q Consensus       410 ~~~~~~~~~~~~~l------------~~~~~~~g~~~~A~~~~~~~~~~~~~~~----~~~~~~l~~~~~~~g~~~~A~~  473 (595)
                      +.. +.+...+..+            +..+...|++++|...|+++.+.. +.+    ..++..++.++.+.|++++|+.
T Consensus       239 ~~~-p~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~~~A~~~~~~~l~~~-p~~~~~~~~~~~~l~~~~~~~g~~~~A~~  316 (450)
T 2y4t_A          239 KLD-QDHKRCFAHYKQVKKLNKLIESAEELIRDGRYTDATSKYESVMKTE-PSIAEYTVRSKERICHCFSKDEKPVEAIR  316 (450)
T ss_dssp             HHC-TTCHHHHHHHHHHHHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHC-CSSHHHHHHHHHHHHHHHHTTTCHHHHHH
T ss_pred             HhC-CChHHHHHHHHHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHhcC-CcchHHHHHHHHHHHHHHHHCCCHHHHHH
Confidence            763 4455555444            788999999999999999999864 333    4478889999999999999999


Q ss_pred             HHHhcccCCCCC-CHHHHHHHHHHHHhcCChhHHHHHHHHHHHcCCCCCHHHHHHHHHH------------HHHcC----
Q 040027          474 LFCSLPHGVLVP-NVVTYNIMIQGLCNDGQMDKARDLFLDMEENAAAPDVITFDMLIHG------------FIRIN----  536 (595)
Q Consensus       474 ~~~~~~~~~~~p-~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~~l~~~------------~~~~g----  536 (595)
                      .++++...  .| +...|..++.+|...|++++|...++++++.. +.+...+..+..+            |...|    
T Consensus       317 ~~~~a~~~--~p~~~~~~~~l~~~~~~~~~~~~A~~~~~~al~~~-p~~~~~~~~l~~~~~~~~~~~~~~~y~~lg~~~~  393 (450)
T 2y4t_A          317 VCSEVLQM--EPDNVNALKDRAEAYLIEEMYDEAIQDYETAQEHN-ENDQQIREGLEKAQRLLKQSQKRDYYKILGVKRN  393 (450)
T ss_dssp             HHHHHHHH--CTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHTTS-SSCHHHHHHHHHHHHHHHHHHSCCSGGGSCSSTT
T ss_pred             HHHHHHHh--CcccHHHHHHHHHHHHHhcCHHHHHHHHHHHHHhC-cchHHHHHHHHHHHHHhhcccchhHHHHhCCCcc
Confidence            99998873  45 57899999999999999999999999999864 4456677766633            33444    


Q ss_pred             -ChhHHHHHHHH-HHHCCCCCC----H-------HHHHHHHHHHHhcCccc
Q 040027          537 -EPSKVNELLHK-MKEKKVMPD----A-------SIVSIVVDLLVKNEISL  574 (595)
Q Consensus       537 -~~~~A~~~~~~-~~~~~~~p~----~-------~~~~~l~~~~~~~g~~~  574 (595)
                       +.+++.+.+++ ..+.  .||    .       ..+..+..+|..-|+.+
T Consensus       394 ~~~~~~~~~y~~~~l~~--~pd~~~~~~~~~~a~~~~~~i~~ay~~L~d~~  442 (450)
T 2y4t_A          394 AKKQEIIKAYRKLALQW--HPDNFQNEEEKKKAEKKFIDIAAAKEVLSDPE  442 (450)
T ss_dssp             CCTTHHHHHHHHHHHHS--CGGGCCSHHHHHHHHHHHHHHHHHHHHSSGGG
T ss_pred             CCHHHHHHHHHHHHHHh--CCCCCCCchHHHHHHHHHHHHHHHHHHhCCHH
Confidence             56778888887 4432  232    2       25666677776666654

>3fp2_A TPR repeat-containing protein YHR117W; TOM71, mitochondria translocation, allosteric REG phosphoprotein, TPR repeat, ATP-binding; 1.98A {Saccharomyces cerevisiae} PDB: 3fp3_A 3fp4_A 3lca_A

Probab=99.93  E-value=5e-23  Score=211.09  Aligned_cols=428  Identities=13%  Similarity=0.053  Sum_probs=324.0

Q ss_pred             HHHHHHHHHHHHhcCCHhHHHHHHHHHHhcCCCCCHhhHHHHHHHHHhcCChhHHHHHHHHHHhcCCCCCccccCcHHHH
Q 040027          131 AATFNSLIKGLHAESRIMEAAALFTKLKAFGCEPNVITYNTLINGLCRTGHTMIALNLFEEMANGNGEIGVVCKPNTVTY  210 (595)
Q Consensus       131 ~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~~~~~~  210 (595)
                      ...|..+...+.+.|++++|++.|+++.... +.+..++..++.+|...|++++|++.|+++...+       |.+..++
T Consensus        25 a~~~~~~g~~~~~~g~~~~A~~~~~~al~~~-p~~~~~~~~la~~~~~~g~~~~A~~~~~~al~~~-------p~~~~~~   96 (537)
T 3fp2_A           25 AVQLKNRGNHFFTAKNFNEAIKYYQYAIELD-PNEPVFYSNISACYISTGDLEKVIEFTTKALEIK-------PDHSKAL   96 (537)
T ss_dssp             HHHHHHHHHHHHHTTCCC-CHHHHHHHHHHC-TTCHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHC-------TTCHHHH
T ss_pred             HHHHHHHHHHHHHhccHHHHHHHHHHHHhhC-CCCcHHHHHHHHHHHHcCCHHHHHHHHHHHHhcC-------CchHHHH
Confidence            4567788889999999999999999999885 4478899999999999999999999999999876       5678899


Q ss_pred             HHHHHHHHHcCCHhHHHHHHHHHhhCCCCCCHhHHHHHHHHHHhcCCHHHHHHHHHHHHHCC--CCCCHhhHHHHHHHHH
Q 040027          211 STIIDGLCKEGFVDKAKALFLQMKDENINPDVVTYNSLIHGLCHANDWNEAKRLFIEMMDQG--VQPSVVTFNVIMDELC  288 (595)
Q Consensus       211 ~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~~ll~~~~~~~~~~~A~~~~~~~~~~~--~~~~~~~~~~l~~~~~  288 (595)
                      ..+..++...|++++|...|+.+ ..  .|+.  ....+..+...+....|...++.+....  ..+........+..+.
T Consensus        97 ~~la~~~~~~g~~~~A~~~~~~~-~~--~~~~--~~~~~~~~~~~~~~~~a~~~~~~~l~~~~~~~~~~~~~~~~~~~~~  171 (537)
T 3fp2_A           97 LRRASANESLGNFTDAMFDLSVL-SL--NGDF--DGASIEPMLERNLNKQAMKVLNENLSKDEGRGSQVLPSNTSLASFF  171 (537)
T ss_dssp             HHHHHHHHHHTCHHHHHHHHHHH-C---------------CHHHHHHHHHHHHHHHHHCC-------CCCCCHHHHHHHH
T ss_pred             HHHHHHHHHcCCHHHHHHHHHHH-hc--CCCC--ChHHHHHHHHHHHHHHHHHHHHHHHHhCccccccccchHhHHHHHH
Confidence            99999999999999999999744 32  1221  2223445556666788999998886531  0111111223344555


Q ss_pred             hcCChHHHHHHHHHHHHCCCCCCHH-HHHHHHHHHHh--------cCCHHHHHHHHHHHHhcCCCCCH-------HHHHH
Q 040027          289 KNRKMDEASRLLDLMVQRGVRPNAC-TYNTLMDGFCL--------MGKINRAEELFGSMESMGCKHDD-------VSYNI  352 (595)
Q Consensus       289 ~~g~~~~a~~~~~~~~~~~~~~~~~-~~~~l~~~~~~--------~~~~~~a~~~~~~~~~~~~~~~~-------~~~~~  352 (595)
                      ...+.+.+...+......  .+... ....+...+..        .|++++|..+++++.+.. +.+.       .++..
T Consensus       172 ~~~~~~~~~~~~~~~~~~--~~~~~~~~~~l~~~~~~~~~~~~~a~~~~~~A~~~~~~~l~~~-p~~~~~~~~~~~~~~~  248 (537)
T 3fp2_A          172 GIFDSHLEVSSVNTSSNY--DTAYALLSDALQRLYSATDEGYLVANDLLTKSTDMYHSLLSAN-TVDDPLRENAALALCY  248 (537)
T ss_dssp             HTSCHHHHHHTSCCCCSS--CSSHHHHHHHHHHHHTCSHHHHHHHHHHHHHHHHHHHHHHC---CCCHHHHHHHHHHHHH
T ss_pred             HhcChHHHHHHHhhcccc--ccHHHHHHHHHHHHHHhhhhhhHHHHHHHHHHHHHHHHHHHHC-CCcchhhHHHHHHHHH
Confidence            666666665554433222  22211 22233322222        257899999999998764 2332       24667


Q ss_pred             HHHHHHhCCCHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHccCCHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHhcCC
Q 040027          353 LINGYCKNKEVEEALSLYREMVSKGIKPTVVTYNTLFLGLFEIHQVEHALKLFDEMQRDGVAADTRTYTTFIDGLCKNGY  432 (595)
Q Consensus       353 l~~~~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~  432 (595)
                      +...+...|++++|...++++.+.  .|+...+..+...+...|++++|...++++.+.. +.+..++..+...+...|+
T Consensus       249 ~g~~~~~~~~~~~A~~~~~~~~~~--~~~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~~~-~~~~~~~~~l~~~~~~~~~  325 (537)
T 3fp2_A          249 TGIFHFLKNNLLDAQVLLQESINL--HPTPNSYIFLALTLADKENSQEFFKFFQKAVDLN-PEYPPTYYHRGQMYFILQD  325 (537)
T ss_dssp             HHHHHHHTTCHHHHHHHHHHHHHH--CCCHHHHHHHHHHTCCSSCCHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTC
T ss_pred             HHHHHHhcccHHHHHHHHHHHHhc--CCCchHHHHHHHHHHHhcCHHHHHHHHHHHhccC-CCCHHHHHHHHHHHHhcCC
Confidence            778889999999999999999986  4557888899999999999999999999999874 5678899999999999999


Q ss_pred             HHHHHHHHHHHHHcCCCcCHHHHHHHHHHHHhcCChHHHHHHHHhcccCCCCC-CHHHHHHHHHHHHhcCChhHHHHHHH
Q 040027          433 IIEAVELFRTLRILKCELDIQAYNCLIDGLCKSGRLKFAWELFCSLPHGVLVP-NVVTYNIMIQGLCNDGQMDKARDLFL  511 (595)
Q Consensus       433 ~~~A~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~p-~~~~~~~l~~~~~~~g~~~~A~~~~~  511 (595)
                      +++|...++++.+.. +.+...+..++.++...|++++|...++++.+.  .| +...+..++..+...|++++|+..|+
T Consensus       326 ~~~A~~~~~~a~~~~-~~~~~~~~~la~~~~~~g~~~~A~~~~~~~~~~--~~~~~~~~~~l~~~~~~~g~~~~A~~~~~  402 (537)
T 3fp2_A          326 YKNAKEDFQKAQSLN-PENVYPYIQLACLLYKQGKFTESEAFFNETKLK--FPTLPEVPTFFAEILTDRGDFDTAIKQYD  402 (537)
T ss_dssp             HHHHHHHHHHHHHHC-TTCSHHHHHHHHHHHHTTCHHHHHHHHHHHHHH--CTTCTHHHHHHHHHHHHTTCHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHhC-CCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHh--CCCChHHHHHHHHHHHHhCCHHHHHHHHH
Confidence            999999999999876 566788999999999999999999999999884  34 46788999999999999999999999


Q ss_pred             HHHHcC-----CCCCHHHHHHHHHHHHHc----------CChhHHHHHHHHHHHCCCCCCHHHHHHHHHHHHhcCccccc
Q 040027          512 DMEENA-----AAPDVITFDMLIHGFIRI----------NEPSKVNELLHKMKEKKVMPDASIVSIVVDLLVKNEISLKS  576 (595)
Q Consensus       512 ~~~~~~-----~~~~~~~~~~l~~~~~~~----------g~~~~A~~~~~~~~~~~~~p~~~~~~~l~~~~~~~g~~~~~  576 (595)
                      ++.+..     .......+.....++...          |++++|...++++.+.. +.+...+..++.+|.+.|+++++
T Consensus       403 ~a~~~~~~~~~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~A~~~~~~a~~~~-p~~~~~~~~l~~~~~~~g~~~~A  481 (537)
T 3fp2_A          403 IAKRLEEVQEKIHVGIGPLIGKATILARQSSQDPTQLDEEKFNAAIKLLTKACELD-PRSEQAKIGLAQLKLQMEKIDEA  481 (537)
T ss_dssp             HHHHHHHHCSSCSSTTHHHHHHHHHHHHHHTC----CCHHHHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCHHHH
T ss_pred             HHHHcCCcchhhHHHHHHHHHHHHHHHHHhhccchhhhHhHHHHHHHHHHHHHHhC-CCCHHHHHHHHHHHHHhccHHHH
Confidence            998742     111223355566778888          99999999999999853 34689999999999999999955


Q ss_pred             chHHH
Q 040027          577 LPSFL  581 (595)
Q Consensus       577 i~~~~  581 (595)
                      +..+.
T Consensus       482 ~~~~~  486 (537)
T 3fp2_A          482 IELFE  486 (537)
T ss_dssp             HHHHH
T ss_pred             HHHHH
Confidence            55443

>2xm6_A Protein corresponding to locus C5321 from CFT073 strain; unknown function, SEL1-like repeats; 1.68A {Escherichia coli}

Probab=99.91  E-value=4.3e-19  Score=178.95  Aligned_cols=364  Identities=14%  Similarity=0.043  Sum_probs=272.0

Q ss_pred             HHHHHHHHHhCCCCCCHHHHHHHHHHHHh----cCCHhHHHHHHHHHHhcCCCCCHhhHHHHHHHHHh----cCChhHHH
Q 040027          115 GFIAFGRILRSCFTPNAATFNSLIKGLHA----ESRIMEAAALFTKLKAFGCEPNVITYNTLINGLCR----TGHTMIAL  186 (595)
Q Consensus       115 A~~~~~~~~~~~~~~~~~~~~~l~~~~~~----~g~~~~A~~~~~~~~~~~~~~~~~~~~~l~~~~~~----~g~~~~A~  186 (595)
                      ++..+....+.|   ++.++..+...|..    .+++++|+.+|++..+.|   +...+..|...|..    .+++++|+
T Consensus        26 ~~~~~~~~a~~g---~~~a~~~lg~~y~~g~~~~~~~~~A~~~~~~a~~~~---~~~a~~~Lg~~y~~g~g~~~~~~~A~   99 (490)
T 2xm6_A           26 NLEQLKQKAESG---EAKAQLELGYRYFQGNETTKDLTQAMDWFRRAAEQG---YTPAEYVLGLRYMNGEGVPQDYAQAV   99 (490)
T ss_dssp             CHHHHHHHHHTT---CHHHHHHHHHHHHHTSSSCCCHHHHHHHHHHHHHTT---CHHHHHHHHHHHHHTSSSCCCHHHHH
T ss_pred             HHHHHHHHHHCC---CHHHHHHHHHHHHcCCCCCcCHHHHHHHHHHHHHCC---CHHHHHHHHHHHHcCCCCCCCHHHHH
Confidence            455566655543   67777777777777    788888888888887764   56777778888877    78888888


Q ss_pred             HHHHHHHhcCCCCCccccCcHHHHHHHHHHHHH----cCCHhHHHHHHHHHhhCCCCCCHhHHHHHHHHHHh----cCCH
Q 040027          187 NLFEEMANGNGEIGVVCKPNTVTYSTIIDGLCK----EGFVDKAKALFLQMKDENINPDVVTYNSLIHGLCH----ANDW  258 (595)
Q Consensus       187 ~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~----~g~~~~A~~~~~~~~~~~~~~~~~~~~~ll~~~~~----~~~~  258 (595)
                      +.|++....+         ++..+..|...|..    .+++++|..+|++..+.+   +...+..|...|..    .+++
T Consensus       100 ~~~~~a~~~~---------~~~a~~~Lg~~y~~g~g~~~~~~~A~~~~~~a~~~~---~~~a~~~Lg~~y~~g~g~~~d~  167 (490)
T 2xm6_A          100 IWYKKAALKG---------LPQAQQNLGVMYHEGNGVKVDKAESVKWFRLAAEQG---RDSGQQSMGDAYFEGDGVTRDY  167 (490)
T ss_dssp             HHHHHHHHTT---------CHHHHHHHHHHHHHTSSSCCCHHHHHHHHHHHHHTT---CHHHHHHHHHHHHHTSSSCCCH
T ss_pred             HHHHHHHHCC---------CHHHHHHHHHHHHcCCCCCCCHHHHHHHHHHHHHCC---CHHHHHHHHHHHHcCCCCCCCH
Confidence            8888887654         45667777777777    678888888888887765   56677777777776    6788


Q ss_pred             HHHHHHHHHHHHCCCCCCHhhHHHHHHHHHh----cCChHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHh----cCCHHH
Q 040027          259 NEAKRLFIEMMDQGVQPSVVTFNVIMDELCK----NRKMDEASRLLDLMVQRGVRPNACTYNTLMDGFCL----MGKINR  330 (595)
Q Consensus       259 ~~A~~~~~~~~~~~~~~~~~~~~~l~~~~~~----~g~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~----~~~~~~  330 (595)
                      ++|.++|++..+.+   +...+..+...|..    .+++++|..+|++..+.+   +...+..+...|..    .+++++
T Consensus       168 ~~A~~~~~~a~~~~---~~~a~~~Lg~~y~~g~g~~~~~~~A~~~~~~a~~~~---~~~a~~~lg~~y~~g~g~~~~~~~  241 (490)
T 2xm6_A          168 VMAREWYSKAAEQG---NVWSCNQLGYMYSRGLGVERNDAISAQWYRKSATSG---DELGQLHLADMYYFGIGVTQDYTQ  241 (490)
T ss_dssp             HHHHHHHHHHHHTT---CHHHHHHHHHHHHHTSSSCCCHHHHHHHHHHHHHTT---CHHHHHHHHHHHHHTSSSCCCHHH
T ss_pred             HHHHHHHHHHHHCC---CHHHHHHHHHHHhcCCCCCcCHHHHHHHHHHHHHCC---CHHHHHHHHHHHHcCCCCCCCHHH
Confidence            88888888887753   56677777777777    788888888888887764   45666777777775    678888


Q ss_pred             HHHHHHHHHhcCCCCCHHHHHHHHHHHHh----CCCHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHcc-----CCHHHH
Q 040027          331 AEELFGSMESMGCKHDDVSYNILINGYCK----NKEVEEALSLYREMVSKGIKPTVVTYNTLFLGLFEI-----HQVEHA  401 (595)
Q Consensus       331 a~~~~~~~~~~~~~~~~~~~~~l~~~~~~----~~~~~~A~~~~~~~~~~~~~~~~~~~~~l~~~~~~~-----~~~~~a  401 (595)
                      |...|++..+.+   +...+..+..+|..    .+++++|+..|++..+.+   +...+..+...+...     +++++|
T Consensus       242 A~~~~~~a~~~~---~~~a~~~lg~~y~~g~~~~~d~~~A~~~~~~a~~~~---~~~a~~~Lg~~y~~~~~g~~~~~~~A  315 (490)
T 2xm6_A          242 SRVLFSQSAEQG---NSIAQFRLGYILEQGLAGAKEPLKALEWYRKSAEQG---NSDGQYYLAHLYDKGAEGVAKNREQA  315 (490)
T ss_dssp             HHHHHHHHHTTT---CHHHHHHHHHHHHHTTTSSCCHHHHHHHHHHHHTTT---CHHHHHHHHHHHHHCBTTBCCCHHHH
T ss_pred             HHHHHHHHHHCC---CHHHHHHHHHHHHCCCCCCCCHHHHHHHHHHHHHcC---CHHHHHHHHHHHHcCCCCCcCCHHHH
Confidence            888888887653   45566677777777    788888888888887653   455666666666665     788888


Q ss_pred             HHHHHHHHHCCCCCCHHHHHHHHHHHHhcC---CHHHHHHHHHHHHHcCCCcCHHHHHHHHHHHHh----cCChHHHHHH
Q 040027          402 LKLFDEMQRDGVAADTRTYTTFIDGLCKNG---YIIEAVELFRTLRILKCELDIQAYNCLIDGLCK----SGRLKFAWEL  474 (595)
Q Consensus       402 ~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g---~~~~A~~~~~~~~~~~~~~~~~~~~~l~~~~~~----~g~~~~A~~~  474 (595)
                      ...+++..+.+   +...+..+...|...|   ++++|..+|++..+.+   ++..+..+...|..    .+++++|...
T Consensus       316 ~~~~~~a~~~~---~~~a~~~lg~~y~~~g~~~~~~~A~~~~~~a~~~~---~~~a~~~Lg~~y~~g~g~~~~~~~A~~~  389 (490)
T 2xm6_A          316 ISWYTKSAEQG---DATAQANLGAIYFRLGSEEEHKKAVEWFRKAAAKG---EKAAQFNLGNALLQGKGVKKDEQQAAIW  389 (490)
T ss_dssp             HHHHHHHHHTT---CHHHHHHHHHHHHHSCCHHHHHHHHHHHHHHHHTT---CHHHHHHHHHHHHHTSSSCCCHHHHHHH
T ss_pred             HHHHHHHHhcC---CHHHHHHHHHHHHhCCCcccHHHHHHHHHHHHHCC---CHHHHHHHHHHHHcCCCCCCCHHHHHHH
Confidence            88888887764   4456666677776655   6788888888888753   67777788888877    7888888888


Q ss_pred             HHhcccCCCCCCHHHHHHHHHHHHh----cCChhHHHHHHHHHHHcC
Q 040027          475 FCSLPHGVLVPNVVTYNIMIQGLCN----DGQMDKARDLFLDMEENA  517 (595)
Q Consensus       475 ~~~~~~~~~~p~~~~~~~l~~~~~~----~g~~~~A~~~~~~~~~~~  517 (595)
                      |++..+.+   +...+..+...|..    .+++++|...|+++.+.+
T Consensus       390 ~~~A~~~~---~~~a~~~Lg~~y~~g~g~~~d~~~A~~~~~~A~~~~  433 (490)
T 2xm6_A          390 MRKAAEQG---LSAAQVQLGEIYYYGLGVERDYVQAWAWFDTASTND  433 (490)
T ss_dssp             HHHHHHTT---CHHHHHHHHHHHHHTSSSCCCHHHHHHHHHHHHHHH
T ss_pred             HHHHHhCC---CHHHHHHHHHHHHcCCCCCCCHHHHHHHHHHHHHCC
Confidence            88887743   56677778888877    788888888888888765

>3ieg_A DNAJ homolog subfamily C member 3; TPR motif, chaperone, endoplasmic reticulum, TPR repeat, UNF protein response; 2.51A {Mus musculus}

Probab=99.91  E-value=2.1e-20  Score=180.72  Aligned_cols=331  Identities=10%  Similarity=0.010  Sum_probs=221.5

Q ss_pred             cHHHHHHHHHHHHHcCCHhHHHHHHHHHhhCCCCCCHhHHHHHHHHHHhcCCHHHHHHHHHHHHHCCCCCCHhhHHHHHH
Q 040027          206 NTVTYSTIIDGLCKEGFVDKAKALFLQMKDENINPDVVTYNSLIHGLCHANDWNEAKRLFIEMMDQGVQPSVVTFNVIMD  285 (595)
Q Consensus       206 ~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~~ll~~~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~~l~~  285 (595)
                      ++..+..+...+...|++++|...|+++.+.. +.+...+..+...+...|++++|...++++.+.. +.+...+..+..
T Consensus         2 ~~~~~~~~~~~~~~~g~~~~A~~~~~~~l~~~-p~~~~~~~~~a~~~~~~~~~~~A~~~~~~~~~~~-~~~~~~~~~l~~   79 (359)
T 3ieg_A            2 DVEKHLELGKKLLAAGQLADALSQFHAAVDGD-PDNYIAYYRRATVFLAMGKSKAALPDLTKVIALK-MDFTAARLQRGH   79 (359)
T ss_dssp             HHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHC-TTCHHHHHHHHH
T ss_pred             cHHHHHHHHHHHHHcCCHHHHHHHHHHHHhhC-cccHHHHHHHHHHHHHccCHHHHHHHHHHHHHhC-CCcchHHHHHHH
Confidence            45567777777888888888888888777653 3356677777777888888888888887777652 225566777777


Q ss_pred             HHHhcCChHHHHHHHHHHHHCCCC--CCHHHHHHHHHHHHhcCCHHHHHHHHHHHHhcCCCCCHHHHHHHHHHHHhCCCH
Q 040027          286 ELCKNRKMDEASRLLDLMVQRGVR--PNACTYNTLMDGFCLMGKINRAEELFGSMESMGCKHDDVSYNILINGYCKNKEV  363 (595)
Q Consensus       286 ~~~~~g~~~~a~~~~~~~~~~~~~--~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~  363 (595)
                      ++...|++++|...++++.+....  .+...+..+...+.                       ...+..+...+...|++
T Consensus        80 ~~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~~~~l~~~~~-----------------------~~~~~~~a~~~~~~~~~  136 (359)
T 3ieg_A           80 LLLKQGKLDEAEDDFKKVLKSNPSEQEEKEAESQLVKADE-----------------------MQRLRSQALDAFDGADY  136 (359)
T ss_dssp             HHHHHTCHHHHHHHHHHHHTSCCCHHHHHHHHHHHHHHHH-----------------------HHHHHHHHHHHHHTTCH
T ss_pred             HHHHcCChHHHHHHHHHHHhcCCcccChHHHHHHHHHHHH-----------------------HHHHHHHHHHHHHccCH
Confidence            777777777777777777765320  12333332211100                       01122234556666666


Q ss_pred             HHHHHHHHHHHHCCCCCCHHHHHHHHHHHHccCCHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHH
Q 040027          364 EEALSLYREMVSKGIKPTVVTYNTLFLGLFEIHQVEHALKLFDEMQRDGVAADTRTYTTFIDGLCKNGYIIEAVELFRTL  443 (595)
Q Consensus       364 ~~A~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~  443 (595)
                      ++|+..++++.+..+. +...+..+...+...|++++|...++.+.+.. +.+...+..+...+...|++++|...++++
T Consensus       137 ~~A~~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~A~~~~~~~~~~~-~~~~~~~~~la~~~~~~~~~~~A~~~~~~a  214 (359)
T 3ieg_A          137 TAAITFLDKILEVCVW-DAELRELRAECFIKEGEPRKAISDLKAASKLK-SDNTEAFYKISTLYYQLGDHELSLSEVREC  214 (359)
T ss_dssp             HHHHHHHHHHHHHCTT-CHHHHHHHHHHHHHTTCHHHHHHHHHHHHTTC-SCCHHHHHHHHHHHHHHTCHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHhCCC-chHHHHHHHHHHHHCCCHHHHHHHHHHHHHhC-CCCHHHHHHHHHHHHHcCCHHHHHHHHHHH
Confidence            6666666666655332 45566666666666667777776666666552 445666666666667777777777777766


Q ss_pred             HHcCCCcCHHHHH------------HHHHHHHhcCChHHHHHHHHhcccCCCCCC-H----HHHHHHHHHHHhcCChhHH
Q 040027          444 RILKCELDIQAYN------------CLIDGLCKSGRLKFAWELFCSLPHGVLVPN-V----VTYNIMIQGLCNDGQMDKA  506 (595)
Q Consensus       444 ~~~~~~~~~~~~~------------~l~~~~~~~g~~~~A~~~~~~~~~~~~~p~-~----~~~~~l~~~~~~~g~~~~A  506 (595)
                      .+.. +.+...+.            .++..+...|++++|...++++.+.  .|+ .    ..+..+..++...|++++|
T Consensus       215 ~~~~-~~~~~~~~~~~~~~~~~~~~~~a~~~~~~~~~~~A~~~~~~~~~~--~~~~~~~~~~~~~~la~~~~~~~~~~~A  291 (359)
T 3ieg_A          215 LKLD-QDHKRCFAHYKQVKKLNKLIESAEELIRDGRYTDATSKYESVMKT--EPSVAEYTVRSKERICHCFSKDEKPVEA  291 (359)
T ss_dssp             HHHC-TTCHHHHHHHHHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH--CCSSHHHHHHHHHHHHHHHHHTTCHHHH
T ss_pred             HhhC-ccchHHHHHHHHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHhc--CCCchHHHHHHHHHHHHHHHHccCHHHH
Confidence            6554 33333332            3366688889999999999888773  344 2    2345577888899999999


Q ss_pred             HHHHHHHHHcCCCCCHHHHHHHHHHHHHcCChhHHHHHHHHHHHCCCCC-CHHHHHHHHHHHHh
Q 040027          507 RDLFLDMEENAAAPDVITFDMLIHGFIRINEPSKVNELLHKMKEKKVMP-DASIVSIVVDLLVK  569 (595)
Q Consensus       507 ~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~p-~~~~~~~l~~~~~~  569 (595)
                      +..++++.+.. +.+..++..++.+|...|++++|...++++.+.  .| +...+..+..+...
T Consensus       292 ~~~~~~~~~~~-~~~~~~~~~~~~~~~~~g~~~~A~~~~~~a~~~--~p~~~~~~~~l~~~~~~  352 (359)
T 3ieg_A          292 IRICSEVLQME-PDNVNALKDRAEAYLIEEMYDEAIQDYEAAQEH--NENDQQIREGLEKAQRL  352 (359)
T ss_dssp             HHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHTT--CTTCHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHhC-cccHHHHHHHHHHHHHcCCHHHHHHHHHHHHhc--CCCChHHHHHHHHHHHH
Confidence            99999998864 557888888999999999999999999999874  35 46667766666544

>3ieg_A DNAJ homolog subfamily C member 3; TPR motif, chaperone, endoplasmic reticulum, TPR repeat, UNF protein response; 2.51A {Mus musculus}

Probab=99.90  E-value=6.9e-20  Score=177.12  Aligned_cols=331  Identities=9%  Similarity=-0.023  Sum_probs=210.5

Q ss_pred             CHHHHHHHHHHHHhcCChhHHHHHHHHHHhCCCCCCHHHHHHHHHHHHhcCCHhHHHHHHHHHHhcCCCCCHhhHHHHHH
Q 040027           95 NLYTYNILINCFCKIGRVSLGFIAFGRILRSCFTPNAATFNSLIKGLHAESRIMEAAALFTKLKAFGCEPNVITYNTLIN  174 (595)
Q Consensus        95 ~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~~l~~  174 (595)
                      |+..+..++..+...|++++|+..|+++++.. +.+..++..+...+...|++++|...|+++.+.. +.+..++..+..
T Consensus         2 ~~~~~~~~~~~~~~~g~~~~A~~~~~~~l~~~-p~~~~~~~~~a~~~~~~~~~~~A~~~~~~~~~~~-~~~~~~~~~l~~   79 (359)
T 3ieg_A            2 DVEKHLELGKKLLAAGQLADALSQFHAAVDGD-PDNYIAYYRRATVFLAMGKSKAALPDLTKVIALK-MDFTAARLQRGH   79 (359)
T ss_dssp             HHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHC-TTCHHHHHHHHH
T ss_pred             cHHHHHHHHHHHHHcCCHHHHHHHHHHHHhhC-cccHHHHHHHHHHHHHccCHHHHHHHHHHHHHhC-CCcchHHHHHHH
Confidence            56788899999999999999999999999875 5578899999999999999999999999999874 337788999999


Q ss_pred             HHHhcCChhHHHHHHHHHHhcCCCCCcccc---CcHHHHHHH------------HHHHHHcCCHhHHHHHHHHHhhCCCC
Q 040027          175 GLCRTGHTMIALNLFEEMANGNGEIGVVCK---PNTVTYSTI------------IDGLCKEGFVDKAKALFLQMKDENIN  239 (595)
Q Consensus       175 ~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~---~~~~~~~~l------------~~~~~~~g~~~~A~~~~~~~~~~~~~  239 (595)
                      .+...|++++|+..|+++....       +   .+...+..+            ...+...|++++|.+.++++.+.. +
T Consensus        80 ~~~~~~~~~~A~~~~~~~~~~~-------~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~A~~~~~~~~~~~-~  151 (359)
T 3ieg_A           80 LLLKQGKLDEAEDDFKKVLKSN-------PSEQEEKEAESQLVKADEMQRLRSQALDAFDGADYTAAITFLDKILEVC-V  151 (359)
T ss_dssp             HHHHHTCHHHHHHHHHHHHTSC-------CCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-T
T ss_pred             HHHHcCChHHHHHHHHHHHhcC-------CcccChHHHHHHHHHHHHHHHHHHHHHHHHHccCHHHHHHHHHHHHHhC-C
Confidence            9999999999999999999865       3   345555544            345555566666666655555442 2


Q ss_pred             CCHhHHHHHHHHHHhcCCHHHHHHHHHHHHHCCCCCCHhhHHHHHHHHHhcCChHHHHHHHHHHHHCCCCCCHHHHHHHH
Q 040027          240 PDVVTYNSLIHGLCHANDWNEAKRLFIEMMDQGVQPSVVTFNVIMDELCKNRKMDEASRLLDLMVQRGVRPNACTYNTLM  319 (595)
Q Consensus       240 ~~~~~~~~ll~~~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~l~  319 (595)
                      .+...+..+...+...|++++|...++++.+.. +.+...+..+...+...|++++|...++++.+.... +...+..+.
T Consensus       152 ~~~~~~~~~~~~~~~~~~~~~A~~~~~~~~~~~-~~~~~~~~~la~~~~~~~~~~~A~~~~~~a~~~~~~-~~~~~~~~~  229 (359)
T 3ieg_A          152 WDAELRELRAECFIKEGEPRKAISDLKAASKLK-SDNTEAFYKISTLYYQLGDHELSLSEVRECLKLDQD-HKRCFAHYK  229 (359)
T ss_dssp             TCHHHHHHHHHHHHHTTCHHHHHHHHHHHHTTC-SCCHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHCTT-CHHHHHHHH
T ss_pred             CchHHHHHHHHHHHHCCCHHHHHHHHHHHHHhC-CCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHhhCcc-chHHHHHHH
Confidence            244555555555555555555555555555432 224445555555555555555555555555543211 111111110


Q ss_pred             HHHHhcCCHHHHHHHHHHHHhcCCCCCHHHHHHHHHHHHhCCCHHHHHHHHHHHHHCCCCCCH----HHHHHHHHHHHcc
Q 040027          320 DGFCLMGKINRAEELFGSMESMGCKHDDVSYNILINGYCKNKEVEEALSLYREMVSKGIKPTV----VTYNTLFLGLFEI  395 (595)
Q Consensus       320 ~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~~~~~~~~----~~~~~l~~~~~~~  395 (595)
                      ..                 .      .......+...+...|++++|...++++.+.... +.    ..+..+...+...
T Consensus       230 ~~-----------------~------~~~~~~~~a~~~~~~~~~~~A~~~~~~~~~~~~~-~~~~~~~~~~~la~~~~~~  285 (359)
T 3ieg_A          230 QV-----------------K------KLNKLIESAEELIRDGRYTDATSKYESVMKTEPS-VAEYTVRSKERICHCFSKD  285 (359)
T ss_dssp             HH-----------------H------HHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCCS-SHHHHHHHHHHHHHHHHHT
T ss_pred             HH-----------------H------HHHHHHHHHHHHHHcCCHHHHHHHHHHHHhcCCC-chHHHHHHHHHHHHHHHHc
Confidence            00                 0      0001112244566666666666666666654322 22    1233455566666


Q ss_pred             CCHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCcCHHHHHHHHHHHH
Q 040027          396 HQVEHALKLFDEMQRDGVAADTRTYTTFIDGLCKNGYIIEAVELFRTLRILKCELDIQAYNCLIDGLC  463 (595)
Q Consensus       396 ~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~~l~~~~~  463 (595)
                      |++++|...++++.+.. +.+...+..+..++...|++++|...++++.+.. +.+...+..+..+..
T Consensus       286 ~~~~~A~~~~~~~~~~~-~~~~~~~~~~~~~~~~~g~~~~A~~~~~~a~~~~-p~~~~~~~~l~~~~~  351 (359)
T 3ieg_A          286 EKPVEAIRICSEVLQME-PDNVNALKDRAEAYLIEEMYDEAIQDYEAAQEHN-ENDQQIREGLEKAQR  351 (359)
T ss_dssp             TCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHTTC-TTCHHHHHHHHHHHH
T ss_pred             cCHHHHHHHHHHHHHhC-cccHHHHHHHHHHHHHcCCHHHHHHHHHHHHhcC-CCChHHHHHHHHHHH
Confidence            67777777766666642 4456666666666777777777777777766654 444555555555544

>2xm6_A Protein corresponding to locus C5321 from CFT073 strain; unknown function, SEL1-like repeats; 1.68A {Escherichia coli}

Probab=99.90  E-value=2e-18  Score=174.16  Aligned_cols=352  Identities=13%  Similarity=0.048  Sum_probs=303.2

Q ss_pred             CHHHHHHHHHHHHh----cCChhHHHHHHHHHHhCCCCCCHHHHHHHHHHHHh----cCCHhHHHHHHHHHHhcCCCCCH
Q 040027           95 NLYTYNILINCFCK----IGRVSLGFIAFGRILRSCFTPNAATFNSLIKGLHA----ESRIMEAAALFTKLKAFGCEPNV  166 (595)
Q Consensus        95 ~~~~~~~l~~~~~~----~g~~~~A~~~~~~~~~~~~~~~~~~~~~l~~~~~~----~g~~~~A~~~~~~~~~~~~~~~~  166 (595)
                      ++..+..+...|..    .+++++|+..|+++.+.|   ++.++..+...|..    .+++++|.++|++....|   +.
T Consensus        38 ~~~a~~~lg~~y~~g~~~~~~~~~A~~~~~~a~~~~---~~~a~~~Lg~~y~~g~g~~~~~~~A~~~~~~a~~~~---~~  111 (490)
T 2xm6_A           38 EAKAQLELGYRYFQGNETTKDLTQAMDWFRRAAEQG---YTPAEYVLGLRYMNGEGVPQDYAQAVIWYKKAALKG---LP  111 (490)
T ss_dssp             CHHHHHHHHHHHHHTSSSCCCHHHHHHHHHHHHHTT---CHHHHHHHHHHHHHTSSSCCCHHHHHHHHHHHHHTT---CH
T ss_pred             CHHHHHHHHHHHHcCCCCCcCHHHHHHHHHHHHHCC---CHHHHHHHHHHHHcCCCCCCCHHHHHHHHHHHHHCC---CH
Confidence            66677777777777    899999999999999875   67888889999998    899999999999999875   67


Q ss_pred             hhHHHHHHHHHh----cCChhHHHHHHHHHHhcCCCCCccccCcHHHHHHHHHHHHH----cCCHhHHHHHHHHHhhCCC
Q 040027          167 ITYNTLINGLCR----TGHTMIALNLFEEMANGNGEIGVVCKPNTVTYSTIIDGLCK----EGFVDKAKALFLQMKDENI  238 (595)
Q Consensus       167 ~~~~~l~~~~~~----~g~~~~A~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~----~g~~~~A~~~~~~~~~~~~  238 (595)
                      ..+..|...|..    .+++++|+..|++....+         ++.++..+...|..    .+++++|.++|++..+.+ 
T Consensus       112 ~a~~~Lg~~y~~g~g~~~~~~~A~~~~~~a~~~~---------~~~a~~~Lg~~y~~g~g~~~d~~~A~~~~~~a~~~~-  181 (490)
T 2xm6_A          112 QAQQNLGVMYHEGNGVKVDKAESVKWFRLAAEQG---------RDSGQQSMGDAYFEGDGVTRDYVMAREWYSKAAEQG-  181 (490)
T ss_dssp             HHHHHHHHHHHHTSSSCCCHHHHHHHHHHHHHTT---------CHHHHHHHHHHHHHTSSSCCCHHHHHHHHHHHHHTT-
T ss_pred             HHHHHHHHHHHcCCCCCCCHHHHHHHHHHHHHCC---------CHHHHHHHHHHHHcCCCCCCCHHHHHHHHHHHHHCC-
Confidence            788889999988    889999999999998764         57788888888887    789999999999998875 


Q ss_pred             CCCHhHHHHHHHHHHh----cCCHHHHHHHHHHHHHCCCCCCHhhHHHHHHHHHh----cCChHHHHHHHHHHHHCCCCC
Q 040027          239 NPDVVTYNSLIHGLCH----ANDWNEAKRLFIEMMDQGVQPSVVTFNVIMDELCK----NRKMDEASRLLDLMVQRGVRP  310 (595)
Q Consensus       239 ~~~~~~~~~ll~~~~~----~~~~~~A~~~~~~~~~~~~~~~~~~~~~l~~~~~~----~g~~~~a~~~~~~~~~~~~~~  310 (595)
                        +...+..|...|..    .+++++|..+|++..+.+   +...+..+...+..    .+++++|..+|++..+.+   
T Consensus       182 --~~~a~~~Lg~~y~~g~g~~~~~~~A~~~~~~a~~~~---~~~a~~~lg~~y~~g~g~~~~~~~A~~~~~~a~~~~---  253 (490)
T 2xm6_A          182 --NVWSCNQLGYMYSRGLGVERNDAISAQWYRKSATSG---DELGQLHLADMYYFGIGVTQDYTQSRVLFSQSAEQG---  253 (490)
T ss_dssp             --CHHHHHHHHHHHHHTSSSCCCHHHHHHHHHHHHHTT---CHHHHHHHHHHHHHTSSSCCCHHHHHHHHHHHHTTT---
T ss_pred             --CHHHHHHHHHHHhcCCCCCcCHHHHHHHHHHHHHCC---CHHHHHHHHHHHHcCCCCCCCHHHHHHHHHHHHHCC---
Confidence              78888889999988    899999999999998864   56677888888886    889999999999998864   


Q ss_pred             CHHHHHHHHHHHHh----cCCHHHHHHHHHHHHhcCCCCCHHHHHHHHHHHHhC-----CCHHHHHHHHHHHHHCCCCCC
Q 040027          311 NACTYNTLMDGFCL----MGKINRAEELFGSMESMGCKHDDVSYNILINGYCKN-----KEVEEALSLYREMVSKGIKPT  381 (595)
Q Consensus       311 ~~~~~~~l~~~~~~----~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~-----~~~~~A~~~~~~~~~~~~~~~  381 (595)
                      +...+..+..+|..    .++.++|+..|++..+.+   +...+..+...|...     +++++|+..|++..+.+   +
T Consensus       254 ~~~a~~~lg~~y~~g~~~~~d~~~A~~~~~~a~~~~---~~~a~~~Lg~~y~~~~~g~~~~~~~A~~~~~~a~~~~---~  327 (490)
T 2xm6_A          254 NSIAQFRLGYILEQGLAGAKEPLKALEWYRKSAEQG---NSDGQYYLAHLYDKGAEGVAKNREQAISWYTKSAEQG---D  327 (490)
T ss_dssp             CHHHHHHHHHHHHHTTTSSCCHHHHHHHHHHHHTTT---CHHHHHHHHHHHHHCBTTBCCCHHHHHHHHHHHHHTT---C
T ss_pred             CHHHHHHHHHHHHCCCCCCCCHHHHHHHHHHHHHcC---CHHHHHHHHHHHHcCCCCCcCCHHHHHHHHHHHHhcC---C
Confidence            56677778888888    899999999999998764   566788888888887     89999999999999874   4


Q ss_pred             HHHHHHHHHHHHccC---CHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHh----cCCHHHHHHHHHHHHHcCCCcCHHH
Q 040027          382 VVTYNTLFLGLFEIH---QVEHALKLFDEMQRDGVAADTRTYTTFIDGLCK----NGYIIEAVELFRTLRILKCELDIQA  454 (595)
Q Consensus       382 ~~~~~~l~~~~~~~~---~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~----~g~~~~A~~~~~~~~~~~~~~~~~~  454 (595)
                      ...+..+...+...|   ++++|.+.|++..+.+   +...+..+...|..    .+++++|..+|++..+.+   ++..
T Consensus       328 ~~a~~~lg~~y~~~g~~~~~~~A~~~~~~a~~~~---~~~a~~~Lg~~y~~g~g~~~~~~~A~~~~~~A~~~~---~~~a  401 (490)
T 2xm6_A          328 ATAQANLGAIYFRLGSEEEHKKAVEWFRKAAAKG---EKAAQFNLGNALLQGKGVKKDEQQAAIWMRKAAEQG---LSAA  401 (490)
T ss_dssp             HHHHHHHHHHHHHSCCHHHHHHHHHHHHHHHHTT---CHHHHHHHHHHHHHTSSSCCCHHHHHHHHHHHHHTT---CHHH
T ss_pred             HHHHHHHHHHHHhCCCcccHHHHHHHHHHHHHCC---CHHHHHHHHHHHHcCCCCCCCHHHHHHHHHHHHhCC---CHHH
Confidence            567777777777656   7899999999999864   67788888888988    899999999999999865   6788


Q ss_pred             HHHHHHHHHh----cCChHHHHHHHHhcccCC
Q 040027          455 YNCLIDGLCK----SGRLKFAWELFCSLPHGV  482 (595)
Q Consensus       455 ~~~l~~~~~~----~g~~~~A~~~~~~~~~~~  482 (595)
                      +..+..+|..    .+++++|...|++..+.+
T Consensus       402 ~~~Lg~~y~~g~g~~~d~~~A~~~~~~A~~~~  433 (490)
T 2xm6_A          402 QVQLGEIYYYGLGVERDYVQAWAWFDTASTND  433 (490)
T ss_dssp             HHHHHHHHHHTSSSCCCHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHcCCCCCCCHHHHHHHHHHHHHCC
Confidence            8899999998    899999999999999854

>2ooe_A Cleavage stimulation factor 77 kDa subunit; HAT domain, structural protein; 3.00A {Mus musculus} SCOP: a.118.8.7

Probab=99.89  E-value=7.2e-19  Score=179.22  Aligned_cols=421  Identities=11%  Similarity=0.042  Sum_probs=264.0

Q ss_pred             CHHHHHHHHHHHHhcCChhHHHHHHHHHHhCCCCCCHHHHHHHHHHHHhcCCHhHHHHHHHHHHhcCCCCCHhhHHHHHH
Q 040027           95 NLYTYNILINCFCKIGRVSLGFIAFGRILRSCFTPNAATFNSLIKGLHAESRIMEAAALFTKLKAFGCEPNVITYNTLIN  174 (595)
Q Consensus        95 ~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~~l~~  174 (595)
                      |...|..++. +.+.|++++|+.+|+++++.. |.+...|..++..+.+.|++++|.++|+++...  .|+...|..++.
T Consensus        12 ~~~~w~~l~~-~~~~~~~~~a~~~~e~al~~~-P~~~~~w~~~~~~~~~~~~~~~a~~~~~ral~~--~p~~~lw~~~~~   87 (530)
T 2ooe_A           12 DLDAWSILIR-EAQNQPIDKARKTYERLVAQF-PSSGRFWKLYIEAEIKAKNYDKVEKLFQRCLMK--VLHIDLWKCYLS   87 (530)
T ss_dssp             CHHHHHHHHH-HHHSSCHHHHHHHHHHHHTTC-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHTTT--CCCHHHHHHHHH
T ss_pred             CHHHHHHHHH-HHHhCCHHHHHHHHHHHHHHC-CCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHhc--CCChHHHHHHHH
Confidence            5566666666 367899999999999999874 667889999999999999999999999999987  457778877775


Q ss_pred             HH-HhcCChhHHHH----HHHHHHhcCCCCCccccCcHHHHHHHHHHHHH---------cCCHhHHHHHHHHHhhCCCCC
Q 040027          175 GL-CRTGHTMIALN----LFEEMANGNGEIGVVCKPNTVTYSTIIDGLCK---------EGFVDKAKALFLQMKDENINP  240 (595)
Q Consensus       175 ~~-~~~g~~~~A~~----~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~---------~g~~~~A~~~~~~~~~~~~~~  240 (595)
                      .. ...|+.+.|.+    +|+.....-+.    .+.+...|...+.....         .|++++|..+|++........
T Consensus        88 ~~~~~~~~~~~a~~~~~~~~~~al~~~g~----~~~~~~~w~~~~~~~~~~~~~~~~~~~~~~~~a~~~y~~al~~P~~~  163 (530)
T 2ooe_A           88 YVRETKGKLPSYKEKMAQAYDFALDKIGM----EIMSYQIWVDYINFLKGVEAVGSYAENQRITAVRRVYQRGCVNPMIN  163 (530)
T ss_dssp             HHHHHTTTSTTHHHHHHHHHHHHHHHTTT----STTCHHHHHHHHHHHHHSCCCSSTTHHHHHHHHHHHHHHHTTSCCTT
T ss_pred             HHHHHccchhhHHHHHHHHHHHHHHHCCC----CcccHHHHHHHHHHHhcCCCcccHHHHhHHHHHHHHHHHHHhchhhh
Confidence            33 45678777765    77777654210    13456788887776655         688999999999998731111


Q ss_pred             CHhHHHHHHHHHHhcCCHHHHHHHHHHHHHCCCCCCHhhHHHHHHHHHhcCChHHHHHHHHHH------HHCC---CCCC
Q 040027          241 DVVTYNSLIHGLCHANDWNEAKRLFIEMMDQGVQPSVVTFNVIMDELCKNRKMDEASRLLDLM------VQRG---VRPN  311 (595)
Q Consensus       241 ~~~~~~~ll~~~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~a~~~~~~~------~~~~---~~~~  311 (595)
                      ....|..........|. ..+..++    .                 ...+++..|..++..+      .+..   ++|+
T Consensus       164 ~~~~~~~~~~~e~~~~~-~~~~~~l----~-----------------~~~~~~~~A~~~~~~~~~~~~~l~~~~~~~~p~  221 (530)
T 2ooe_A          164 IEQLWRDYNKYEEGINI-HLAKKMI----E-----------------DRSRDYMNARRVAKEYETVMKGLDRNAPSVPPQ  221 (530)
T ss_dssp             HHHHHHHHHHHHHHHCH-HHHHHHH----H-----------------TTHHHHHHHHHHHHHHHHHHHHCCSSSCCCCCC
T ss_pred             HHHHHHHHHHHHHhhch-hHHHHHH----H-----------------HhhHHHHHHHHHHHHHHHHHHHhccccccCCCC
Confidence            12333322221111110 0000000    0                 0122334444444331      1111   1222


Q ss_pred             --------HHHHHHHHHHHHhc----CCH----HHHHHHHHHHHhcCCCCCHHHHHHHHHHHHh-------CCCHH----
Q 040027          312 --------ACTYNTLMDGFCLM----GKI----NRAEELFGSMESMGCKHDDVSYNILINGYCK-------NKEVE----  364 (595)
Q Consensus       312 --------~~~~~~l~~~~~~~----~~~----~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~-------~~~~~----  364 (595)
                              ...|...+......    ++.    +.+..+|++++... +.+...|..++..+.+       .|+++    
T Consensus       222 ~~~~~~~~~~~w~~~~~~e~~~~~~~~~~~~~~~~a~~~y~~al~~~-p~~~~~w~~~~~~~~~~~~~~~~~g~~~~a~~  300 (530)
T 2ooe_A          222 NTPQEAQQVDMWKKYIQWEKSNPLRTEDQTLITKRVMFAYEQCLLVL-GHHPDIWYEAAQYLEQSSKLLAEKGDMNNAKL  300 (530)
T ss_dssp             --CCHHHHHHHHHHHHHHHHHCSSCCSCSHHHHHHHHHHHHHHHHHH-TTCHHHHHHHHHHHHHHHHHHHTTTCCHHHHH
T ss_pred             CChhHHHHHHHHHHHHHHHHcCCccCCcchhHHHHHHHHHHHHHHhC-CCCHHHHHHHHHHHHHhchhhhhccchhhhhh
Confidence                    12333333222211    222    35666777766652 4556677777766664       57765    


Q ss_pred             ---HHHHHHHHHHHCCCCCCHHHHHHHHHHHHccCCHHHHHHHHHHHHHCCCCCCH-HHHHHHHHHHHhcCCHHHHHHHH
Q 040027          365 ---EALSLYREMVSKGIKPTVVTYNTLFLGLFEIHQVEHALKLFDEMQRDGVAADT-RTYTTFIDGLCKNGYIIEAVELF  440 (595)
Q Consensus       365 ---~A~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~-~~~~~l~~~~~~~g~~~~A~~~~  440 (595)
                         +|..+|++.++.-.+.+...|..++..+...|++++|..+|+++++.. +.+. ..|..++..+.+.|++++|..+|
T Consensus       301 ~~~~A~~~~~~Al~~~~p~~~~l~~~~~~~~~~~g~~~~A~~~~~~al~~~-p~~~~~~~~~~~~~~~~~~~~~~A~~~~  379 (530)
T 2ooe_A          301 FSDEAANIYERAISTLLKKNMLLYFAYADYEESRMKYEKVHSIYNRLLAIE-DIDPTLVYIQYMKFARRAEGIKSGRMIF  379 (530)
T ss_dssp             HHHHHHHHHHHHTTTTCSSCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHSS-SSCHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             hhHHHHHHHHHHHHHhCcccHHHHHHHHHHHHhcCCHHHHHHHHHHHhCcc-ccCchHHHHHHHHHHHHhcCHHHHHHHH
Confidence               777777777752123356677777777777788888888888777752 2232 46777777777778888888888


Q ss_pred             HHHHHcCCCcCHHHHHHHHHH-HHhcCChHHHHHHHHhcccCCCCC-CHHHHHHHHHHHHhcCChhHHHHHHHHHHHcC-
Q 040027          441 RTLRILKCELDIQAYNCLIDG-LCKSGRLKFAWELFCSLPHGVLVP-NVVTYNIMIQGLCNDGQMDKARDLFLDMEENA-  517 (595)
Q Consensus       441 ~~~~~~~~~~~~~~~~~l~~~-~~~~g~~~~A~~~~~~~~~~~~~p-~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~-  517 (595)
                      +++.+.. +.+...+...+.. +...|+.++|..+|++..+.  .| +...|..++..+.+.|+.++|..+|++++..+ 
T Consensus       380 ~~Al~~~-~~~~~~~~~~a~~~~~~~~~~~~A~~~~e~al~~--~p~~~~~~~~~~~~~~~~g~~~~Ar~~~~~al~~~~  456 (530)
T 2ooe_A          380 KKAREDA-RTRHHVYVTAALMEYYCSKDKSVAFKIFELGLKK--YGDIPEYVLAYIDYLSHLNEDNNTRVLFERVLTSGS  456 (530)
T ss_dssp             HHHHTCT-TCCTHHHHHHHHHHHHHTCCHHHHHHHHHHHHHH--HTTCHHHHHHHHHHHTTTTCHHHHHHHHHHHHHSCC
T ss_pred             HHHHhcc-CCchHHHHHHHHHHHHHcCChhHHHHHHHHHHHH--CCCCHHHHHHHHHHHHhCCCHhhHHHHHHHHHhccC
Confidence            8877653 2333333332222 33578888888888877763  34 46777777877778888888888888887753 


Q ss_pred             CCCC--HHHHHHHHHHHHHcCChhHHHHHHHHHHH
Q 040027          518 AAPD--VITFDMLIHGFIRINEPSKVNELLHKMKE  550 (595)
Q Consensus       518 ~~~~--~~~~~~l~~~~~~~g~~~~A~~~~~~~~~  550 (595)
                      ..|+  ...|...+......|+.+.+.++.+++.+
T Consensus       457 ~~~~~~~~lw~~~~~~e~~~G~~~~~~~~~~r~~~  491 (530)
T 2ooe_A          457 LPPEKSGEIWARFLAFESNIGDLASILKVEKRRFT  491 (530)
T ss_dssp             SCGGGCHHHHHHHHHHHHHSSCHHHHHHHHHHHHH
T ss_pred             CCHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHH
Confidence            1222  34666667777777888888888888775

>3hym_B Cell division cycle protein 16 homolog; APC, anaphase promoting complex, cell cycle, mitosis, cyclosome, TPR, ubiquitin, ubiquitin ligase, twinning; 2.80A {Homo sapiens}

Probab=99.88  E-value=8.7e-20  Score=174.21  Aligned_cols=292  Identities=9%  Similarity=-0.059  Sum_probs=186.1

Q ss_pred             CHhhHHHHHHHHHhcCChHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHhcCCCCCHHHHHHHHH
Q 040027          276 SVVTFNVIMDELCKNRKMDEASRLLDLMVQRGVRPNACTYNTLMDGFCLMGKINRAEELFGSMESMGCKHDDVSYNILIN  355 (595)
Q Consensus       276 ~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~  355 (595)
                      +...+..++..+...|++++|..+++++.+.. +.+...+..++.++...|++++|...++++.+.. +.+...+..+..
T Consensus        21 ~~~~~~~~a~~~~~~g~~~~A~~~~~~~l~~~-p~~~~~~~~~~~~~~~~~~~~~A~~~~~~~~~~~-~~~~~~~~~l~~   98 (330)
T 3hym_B           21 NLDVVVSLAERHYYNCDFKMCYKLTSVVMEKD-PFHASCLPVHIGTLVELNKANELFYLSHKLVDLY-PSNPVSWFAVGC   98 (330)
T ss_dssp             CCTTHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCTTTHHHHHHHHHHHTCHHHHHHHHHHHHHHC-TTSTHHHHHHHH
T ss_pred             hHHHHHHHHHHHHHcCCHHHHHHHHHHHHHcC-CCChhhHHHHHHHHHHhhhHHHHHHHHHHHHHhC-cCCHHHHHHHHH
Confidence            44445555555555566666666666655542 2233344445555556666666666666665543 334455566666


Q ss_pred             HHHhCC-CHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHccCCHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHhcCCHH
Q 040027          356 GYCKNK-EVEEALSLYREMVSKGIKPTVVTYNTLFLGLFEIHQVEHALKLFDEMQRDGVAADTRTYTTFIDGLCKNGYII  434 (595)
Q Consensus       356 ~~~~~~-~~~~A~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~  434 (595)
                      .+...| ++++|...++++.+.... +...+..+...+...|++++|...++++.+.. +.+...+..+...|...|+++
T Consensus        99 ~~~~~~~~~~~A~~~~~~a~~~~~~-~~~~~~~l~~~~~~~~~~~~A~~~~~~a~~~~-~~~~~~~~~l~~~~~~~~~~~  176 (330)
T 3hym_B           99 YYLMVGHKNEHARRYLSKATTLEKT-YGPAWIAYGHSFAVESEHDQAMAAYFTAAQLM-KGCHLPMLYIGLEYGLTNNSK  176 (330)
T ss_dssp             HHHHSCSCHHHHHHHHHHHHTTCTT-CTHHHHHHHHHHHHHTCHHHHHHHHHHHHHHT-TTCSHHHHHHHHHHHHTTCHH
T ss_pred             HHHHhhhhHHHHHHHHHHHHHhCCc-cHHHHHHHHHHHHHccCHHHHHHHHHHHHHhc-cccHHHHHHHHHHHHHHhhHH
Confidence            666666 666666666666654322 44556666666666666666666666666542 333455555666667777777


Q ss_pred             HHHHHHHHHHHcCCCcCHHHHHHHHHHHHhcCChHHHHHHHHhcccCC--------CCCCHHHHHHHHHHHHhcCChhHH
Q 040027          435 EAVELFRTLRILKCELDIQAYNCLIDGLCKSGRLKFAWELFCSLPHGV--------LVPNVVTYNIMIQGLCNDGQMDKA  506 (595)
Q Consensus       435 ~A~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~--------~~p~~~~~~~l~~~~~~~g~~~~A  506 (595)
                      +|...++++.+.. +.+...+..++..+...|++++|...++++.+..        .+.+..++..++.++...|++++|
T Consensus       177 ~A~~~~~~al~~~-~~~~~~~~~l~~~~~~~~~~~~A~~~~~~a~~~~~~~~~~~~~~~~~~~~~~la~~~~~~g~~~~A  255 (330)
T 3hym_B          177 LAERFFSQALSIA-PEDPFVMHEVGVVAFQNGEWKTAEKWFLDALEKIKAIGNEVTVDKWEPLLNNLGHVCRKLKKYAEA  255 (330)
T ss_dssp             HHHHHHHHHHTTC-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHTTTSCSCTTTTCCHHHHHHHHHHHHTTCHHHH
T ss_pred             HHHHHHHHHHHhC-CCChHHHHHHHHHHHHcccHHHHHHHHHHHHHHhhhccccccccHHHHHHHHHHHHHHHhcCHHHH
Confidence            7777777776654 4556677777777777777777777777665421        122356778888888888888888


Q ss_pred             HHHHHHHHHcCCCCCHHHHHHHHHHHHHcCChhHHHHHHHHHHHCCCCCCHHHHHHHHHHH-HhcCccc
Q 040027          507 RDLFLDMEENAAAPDVITFDMLIHGFIRINEPSKVNELLHKMKEKKVMPDASIVSIVVDLL-VKNEISL  574 (595)
Q Consensus       507 ~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~p~~~~~~~l~~~~-~~~g~~~  574 (595)
                      +..++++.+.. +.+...+..++.+|...|++++|.+.++++.+.. +.+...+..+..++ ...|+.+
T Consensus       256 ~~~~~~a~~~~-~~~~~~~~~la~~~~~~g~~~~A~~~~~~al~~~-p~~~~~~~~l~~~~~~~~g~~~  322 (330)
T 3hym_B          256 LDYHRQALVLI-PQNASTYSAIGYIHSLMGNFENAVDYFHTALGLR-RDDTFSVTMLGHCIEMYIGDSE  322 (330)
T ss_dssp             HHHHHHHHHHS-TTCSHHHHHHHHHHHHHTCHHHHHHHHHTTTTTC-SCCHHHHHHHHHHHHTTTTC--
T ss_pred             HHHHHHHHhhC-ccchHHHHHHHHHHHHhccHHHHHHHHHHHHccC-CCchHHHHHHHHHHHHHhCchh
Confidence            88888888764 4466778888888888888888888888887643 23677788888877 4566554

>2ooe_A Cleavage stimulation factor 77 kDa subunit; HAT domain, structural protein; 3.00A {Mus musculus} SCOP: a.118.8.7

Probab=99.88  E-value=2.1e-18  Score=175.74  Aligned_cols=428  Identities=9%  Similarity=0.004  Sum_probs=302.4

Q ss_pred             HHHHHhCCCCCCHHHHHHHHHHHHhcCCHhHHHHHHHHHHhcCCCCCHhhHHHHHHHHHhcCChhHHHHHHHHHHhcCCC
Q 040027          119 FGRILRSCFTPNAATFNSLIKGLHAESRIMEAAALFTKLKAFGCEPNVITYNTLINGLCRTGHTMIALNLFEEMANGNGE  198 (595)
Q Consensus       119 ~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~  198 (595)
                      +++.++.. |-+...|..++. +.+.|++++|..+|+++.+.. +.+...|..++..+.+.|++++|..+|++++...  
T Consensus         2 le~al~~~-P~~~~~w~~l~~-~~~~~~~~~a~~~~e~al~~~-P~~~~~w~~~~~~~~~~~~~~~a~~~~~ral~~~--   76 (530)
T 2ooe_A            2 AEKKLEEN-PYDLDAWSILIR-EAQNQPIDKARKTYERLVAQF-PSSGRFWKLYIEAEIKAKNYDKVEKLFQRCLMKV--   76 (530)
T ss_dssp             HHHHHHHC-TTCHHHHHHHHH-HHHSSCHHHHHHHHHHHHTTC-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHTTTC--
T ss_pred             hhhHhhhC-CCCHHHHHHHHH-HHHhCCHHHHHHHHHHHHHHC-CCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHhcC--
Confidence            45555553 558889999998 478899999999999999873 5578889999999999999999999999999864  


Q ss_pred             CCccccCcHHHHHHHHHHH-HHcCCHhHHHH----HHHHHhhC-CCC-CCHhHHHHHHHHHHh---------cCCHHHHH
Q 040027          199 IGVVCKPNTVTYSTIIDGL-CKEGFVDKAKA----LFLQMKDE-NIN-PDVVTYNSLIHGLCH---------ANDWNEAK  262 (595)
Q Consensus       199 ~~~~~~~~~~~~~~l~~~~-~~~g~~~~A~~----~~~~~~~~-~~~-~~~~~~~~ll~~~~~---------~~~~~~A~  262 (595)
                            |+...|...+... ...|+.+.|.+    +|++.... |.. ++...|...+.....         .|+++.|.
T Consensus        77 ------p~~~lw~~~~~~~~~~~~~~~~a~~~~~~~~~~al~~~g~~~~~~~~w~~~~~~~~~~~~~~~~~~~~~~~~a~  150 (530)
T 2ooe_A           77 ------LHIDLWKCYLSYVRETKGKLPSYKEKMAQAYDFALDKIGMEIMSYQIWVDYINFLKGVEAVGSYAENQRITAVR  150 (530)
T ss_dssp             ------CCHHHHHHHHHHHHHHTTTSTTHHHHHHHHHHHHHHHTTTSTTCHHHHHHHHHHHHHSCCCSSTTHHHHHHHHH
T ss_pred             ------CChHHHHHHHHHHHHHccchhhHHHHHHHHHHHHHHHCCCCcccHHHHHHHHHHHhcCCCcccHHHHhHHHHHH
Confidence                  5777787777533 45677777665    77766543 433 356677777776654         67889999


Q ss_pred             HHHHHHHHCCCCCCHhhHHHHHHHHHhcCChHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHH----
Q 040027          263 RLFIEMMDQGVQPSVVTFNVIMDELCKNRKMDEASRLLDLMVQRGVRPNACTYNTLMDGFCLMGKINRAEELFGSM----  338 (595)
Q Consensus       263 ~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~----  338 (595)
                      .+|++.++.........|..........|. ..+..                   ++.  ...++++.|..++..+    
T Consensus       151 ~~y~~al~~P~~~~~~~~~~~~~~e~~~~~-~~~~~-------------------~l~--~~~~~~~~A~~~~~~~~~~~  208 (530)
T 2ooe_A          151 RVYQRGCVNPMINIEQLWRDYNKYEEGINI-HLAKK-------------------MIE--DRSRDYMNARRVAKEYETVM  208 (530)
T ss_dssp             HHHHHHTTSCCTTHHHHHHHHHHHHHHHCH-HHHHH-------------------HHH--TTHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHhchhhhHHHHHHHHHHHHHhhch-hHHHH-------------------HHH--HhhHHHHHHHHHHHHHHHHH
Confidence            999988873111111222222211111110 00111                   110  1234566666666552    


Q ss_pred             --HhcC---CCCC--------HHHHHHHHHHHHhC----CCH----HHHHHHHHHHHHCCCCCCHHHHHHHHHHHHc---
Q 040027          339 --ESMG---CKHD--------DVSYNILINGYCKN----KEV----EEALSLYREMVSKGIKPTVVTYNTLFLGLFE---  394 (595)
Q Consensus       339 --~~~~---~~~~--------~~~~~~l~~~~~~~----~~~----~~A~~~~~~~~~~~~~~~~~~~~~l~~~~~~---  394 (595)
                        .+..   ++|+        ...|...+......    ++.    +.+..+|++++...+ .+...|..++..+..   
T Consensus       209 ~~l~~~~~~~~p~~~~~~~~~~~~w~~~~~~e~~~~~~~~~~~~~~~~a~~~y~~al~~~p-~~~~~w~~~~~~~~~~~~  287 (530)
T 2ooe_A          209 KGLDRNAPSVPPQNTPQEAQQVDMWKKYIQWEKSNPLRTEDQTLITKRVMFAYEQCLLVLG-HHPDIWYEAAQYLEQSSK  287 (530)
T ss_dssp             HHCCSSSCCCCCC--CCHHHHHHHHHHHHHHHHHCSSCCSCSHHHHHHHHHHHHHHHHHHT-TCHHHHHHHHHHHHHHHH
T ss_pred             HHhccccccCCCCCChhHHHHHHHHHHHHHHHHcCCccCCcchhHHHHHHHHHHHHHHhCC-CCHHHHHHHHHHHHHhch
Confidence              2211   2333        24566555443332    232    478889999988633 367888888887775   


Q ss_pred             ----cCCHH-------HHHHHHHHHHHCCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCcCH-HHHHHHHHHH
Q 040027          395 ----IHQVE-------HALKLFDEMQRDGVAADTRTYTTFIDGLCKNGYIIEAVELFRTLRILKCELDI-QAYNCLIDGL  462 (595)
Q Consensus       395 ----~~~~~-------~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~~~-~~~~~l~~~~  462 (595)
                          .|+++       +|..++++..+.-.+.+...+..++..+.+.|++++|..+|+++++.. +.+. ..|..++..+
T Consensus       288 ~~~~~g~~~~a~~~~~~A~~~~~~Al~~~~p~~~~l~~~~~~~~~~~g~~~~A~~~~~~al~~~-p~~~~~~~~~~~~~~  366 (530)
T 2ooe_A          288 LLAEKGDMNNAKLFSDEAANIYERAISTLLKKNMLLYFAYADYEESRMKYEKVHSIYNRLLAIE-DIDPTLVYIQYMKFA  366 (530)
T ss_dssp             HHHTTTCCHHHHHHHHHHHHHHHHHTTTTCSSCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHSS-SSCHHHHHHHHHHHH
T ss_pred             hhhhccchhhhhhhhHHHHHHHHHHHHHhCcccHHHHHHHHHHHHhcCCHHHHHHHHHHHhCcc-ccCchHHHHHHHHHH
Confidence                68876       999999999973235678899999999999999999999999999864 3343 5899999999


Q ss_pred             HhcCChHHHHHHHHhcccCCCCCC-HHHHHHHHHH-HHhcCChhHHHHHHHHHHHcCCCCCHHHHHHHHHHHHHcCChhH
Q 040027          463 CKSGRLKFAWELFCSLPHGVLVPN-VVTYNIMIQG-LCNDGQMDKARDLFLDMEENAAAPDVITFDMLIHGFIRINEPSK  540 (595)
Q Consensus       463 ~~~g~~~~A~~~~~~~~~~~~~p~-~~~~~~l~~~-~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~  540 (595)
                      .+.|++++|..+|+++.+.  .|+ ...|...+.. +...|++++|..+|+++++.. +.+...|..++..+.+.|+.++
T Consensus       367 ~~~~~~~~A~~~~~~Al~~--~~~~~~~~~~~a~~~~~~~~~~~~A~~~~e~al~~~-p~~~~~~~~~~~~~~~~g~~~~  443 (530)
T 2ooe_A          367 RRAEGIKSGRMIFKKARED--ARTRHHVYVTAALMEYYCSKDKSVAFKIFELGLKKY-GDIPEYVLAYIDYLSHLNEDNN  443 (530)
T ss_dssp             HHHHHHHHHHHHHHHHHTC--TTCCTHHHHHHHHHHHHHTCCHHHHHHHHHHHHHHH-TTCHHHHHHHHHHHTTTTCHHH
T ss_pred             HHhcCHHHHHHHHHHHHhc--cCCchHHHHHHHHHHHHHcCChhHHHHHHHHHHHHC-CCCHHHHHHHHHHHHhCCCHhh
Confidence            9999999999999999884  343 3344333322 346899999999999999874 5568899999999999999999


Q ss_pred             HHHHHHHHHHCC-CCCC--HHHHHHHHHHHHhcCccc-------ccchHHHHhh
Q 040027          541 VNELLHKMKEKK-VMPD--ASIVSIVVDLLVKNEISL-------KSLPSFLVQE  584 (595)
Q Consensus       541 A~~~~~~~~~~~-~~p~--~~~~~~l~~~~~~~g~~~-------~~i~~~~~~~  584 (595)
                      |..+|++++..+ ..|+  ...|..++....+.|+.+       ++++.+|.+.
T Consensus       444 Ar~~~~~al~~~~~~~~~~~~lw~~~~~~e~~~G~~~~~~~~~~r~~~~~p~~~  497 (530)
T 2ooe_A          444 TRVLFERVLTSGSLPPEKSGEIWARFLAFESNIGDLASILKVEKRRFTAFREEY  497 (530)
T ss_dssp             HHHHHHHHHHSCCSCGGGCHHHHHHHHHHHHHSSCHHHHHHHHHHHHHHTHHHH
T ss_pred             HHHHHHHHHhccCCCHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHCchhc
Confidence            999999999863 2332  458999999999999888       4445555443

>3hym_B Cell division cycle protein 16 homolog; APC, anaphase promoting complex, cell cycle, mitosis, cyclosome, TPR, ubiquitin, ubiquitin ligase, twinning; 2.80A {Homo sapiens}

Probab=99.87  E-value=3.3e-19  Score=170.13  Aligned_cols=298  Identities=12%  Similarity=0.002  Sum_probs=141.5

Q ss_pred             CHhhHHHHHHHHHhcCChhHHHHHHHHHHhcCCCCCccccCcHHHHHHHHHHHHHcCCHhHHHHHHHHHhhCCCCCCHhH
Q 040027          165 NVITYNTLINGLCRTGHTMIALNLFEEMANGNGEIGVVCKPNTVTYSTIIDGLCKEGFVDKAKALFLQMKDENINPDVVT  244 (595)
Q Consensus       165 ~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~  244 (595)
                      +...+..++..+...|++++|+++|+++....       +.+...+..++.++...|++++|..+++++.+.. +.+...
T Consensus        21 ~~~~~~~~a~~~~~~g~~~~A~~~~~~~l~~~-------p~~~~~~~~~~~~~~~~~~~~~A~~~~~~~~~~~-~~~~~~   92 (330)
T 3hym_B           21 NLDVVVSLAERHYYNCDFKMCYKLTSVVMEKD-------PFHASCLPVHIGTLVELNKANELFYLSHKLVDLY-PSNPVS   92 (330)
T ss_dssp             CCTTHHHHHHHHHHTTCHHHHHHHHHHHHHHC-------TTCTTTHHHHHHHHHHHTCHHHHHHHHHHHHHHC-TTSTHH
T ss_pred             hHHHHHHHHHHHHHcCCHHHHHHHHHHHHHcC-------CCChhhHHHHHHHHHHhhhHHHHHHHHHHHHHhC-cCCHHH
Confidence            33444444444555555555555555554443       2333344444444455555555555555544432 123444


Q ss_pred             HHHHHHHHHhcC-CHHHHHHHHHHHHHCCCCCCHhhHHHHHHHHHhcCChHHHHHHHHHHHHCCCCCCHHHHHHHHHHHH
Q 040027          245 YNSLIHGLCHAN-DWNEAKRLFIEMMDQGVQPSVVTFNVIMDELCKNRKMDEASRLLDLMVQRGVRPNACTYNTLMDGFC  323 (595)
Q Consensus       245 ~~~ll~~~~~~~-~~~~A~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~  323 (595)
                      |..+...+...| ++++|...|+++.+.. +.+...+..+...+...|++++|...++++.+.... +...+..+...+.
T Consensus        93 ~~~l~~~~~~~~~~~~~A~~~~~~a~~~~-~~~~~~~~~l~~~~~~~~~~~~A~~~~~~a~~~~~~-~~~~~~~l~~~~~  170 (330)
T 3hym_B           93 WFAVGCYYLMVGHKNEHARRYLSKATTLE-KTYGPAWIAYGHSFAVESEHDQAMAAYFTAAQLMKG-CHLPMLYIGLEYG  170 (330)
T ss_dssp             HHHHHHHHHHSCSCHHHHHHHHHHHHTTC-TTCTHHHHHHHHHHHHHTCHHHHHHHHHHHHHHTTT-CSHHHHHHHHHHH
T ss_pred             HHHHHHHHHHhhhhHHHHHHHHHHHHHhC-CccHHHHHHHHHHHHHccCHHHHHHHHHHHHHhccc-cHHHHHHHHHHHH
Confidence            444444455555 4555555555444432 112334444444444444444444444444443211 2233333444444


Q ss_pred             hcCCHHHHHHHHHHHHhcCCCCCHHHHHHHHHHHHhCCCHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHccCCHHHHHH
Q 040027          324 LMGKINRAEELFGSMESMGCKHDDVSYNILINGYCKNKEVEEALSLYREMVSKGIKPTVVTYNTLFLGLFEIHQVEHALK  403 (595)
Q Consensus       324 ~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~  403 (595)
                      ..|++++|...++++.+.. +.+...+..+...+...|++++|...++++.+......               +      
T Consensus       171 ~~~~~~~A~~~~~~al~~~-~~~~~~~~~l~~~~~~~~~~~~A~~~~~~a~~~~~~~~---------------~------  228 (330)
T 3hym_B          171 LTNNSKLAERFFSQALSIA-PEDPFVMHEVGVVAFQNGEWKTAEKWFLDALEKIKAIG---------------N------  228 (330)
T ss_dssp             HTTCHHHHHHHHHHHHTTC-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHTTTS---------------C------
T ss_pred             HHhhHHHHHHHHHHHHHhC-CCChHHHHHHHHHHHHcccHHHHHHHHHHHHHHhhhcc---------------c------
Confidence            4444444444444444432 22333444444444444444444444444433100000               0      


Q ss_pred             HHHHHHHCCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCcCHHHHHHHHHHHHhcCChHHHHHHHHhcccCCC
Q 040027          404 LFDEMQRDGVAADTRTYTTFIDGLCKNGYIIEAVELFRTLRILKCELDIQAYNCLIDGLCKSGRLKFAWELFCSLPHGVL  483 (595)
Q Consensus       404 ~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~  483 (595)
                            ....+....++..+..++...|++++|...++++.+.. +.+...+..+..++...|++++|...++++.+  +
T Consensus       229 ------~~~~~~~~~~~~~la~~~~~~g~~~~A~~~~~~a~~~~-~~~~~~~~~la~~~~~~g~~~~A~~~~~~al~--~  299 (330)
T 3hym_B          229 ------EVTVDKWEPLLNNLGHVCRKLKKYAEALDYHRQALVLI-PQNASTYSAIGYIHSLMGNFENAVDYFHTALG--L  299 (330)
T ss_dssp             ------SCTTTTCCHHHHHHHHHHHHTTCHHHHHHHHHHHHHHS-TTCSHHHHHHHHHHHHHTCHHHHHHHHHTTTT--T
T ss_pred             ------cccccHHHHHHHHHHHHHHHhcCHHHHHHHHHHHHhhC-ccchHHHHHHHHHHHHhccHHHHHHHHHHHHc--c
Confidence                  00012234555666666666666666666666666554 44556666666666677777777777776665  3


Q ss_pred             CC-CHHHHHHHHHHH-HhcCCh
Q 040027          484 VP-NVVTYNIMIQGL-CNDGQM  503 (595)
Q Consensus       484 ~p-~~~~~~~l~~~~-~~~g~~  503 (595)
                      .| +...+..+..++ ...|+.
T Consensus       300 ~p~~~~~~~~l~~~~~~~~g~~  321 (330)
T 3hym_B          300 RRDDTFSVTMLGHCIEMYIGDS  321 (330)
T ss_dssp             CSCCHHHHHHHHHHHHTTTTC-
T ss_pred             CCCchHHHHHHHHHHHHHhCch
Confidence            34 355555666555 344443

>1xi4_A Clathrin heavy chain; alpha-ZIG-ZAG, beta-propeller, endocytosis-exocyto complex; 7.90A {Bos taurus} SCOP: i.23.1.1 PDB: 1xi5_A 3iyv_A

Probab=99.87  E-value=1.3e-16  Score=168.01  Aligned_cols=465  Identities=11%  Similarity=0.062  Sum_probs=287.0

Q ss_pred             CCCChHHHHHHHHHHHHhCCCCCCHhhHHHHHHHHHcCCCchhHHhhCCCC------------CCHHH----------HH
Q 040027           43 NVITPNEAFCIFDYMLRMHPSPPPVSSFNILLASLAKNKHYDTRLNATGLF------------PNLYT----------YN  100 (595)
Q Consensus        43 ~~~~~~~A~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~------------~~~~~----------~~  100 (595)
                      ++++++--...++.-+..+-.  ++.++|+++..|...++-.++......-            .||..          -.
T Consensus       851 krnrLkll~p~LE~~~~~g~~--~~~~hnalakiyid~n~npe~fL~~n~~yd~~~vgkyce~rDp~la~iay~~g~~d~  928 (1630)
T 1xi4_A          851 KRNRLKLLLPWLEARIHEGCE--EPATHNALAKIYIDSNNNPERFLRENPYYDSRVVGKYCEKRDPHLACVAYERGQCDL  928 (1630)
T ss_pred             HHHHHHHHHHHHHHHHhCCCC--CHHHHHHHHHHHhccCCCHHHHhhccCcccHHHHHHHHHhcCcchHHHHhcccCCcH
Confidence            445566666667777777665  9999999999999988877632222111            12211          11


Q ss_pred             HHHHHHHhcCChhHHHHHHHHHHhCCCCCCHHHHH--------------------------------HHHHHHHhcCCHh
Q 040027          101 ILINCFCKIGRVSLGFIAFGRILRSCFTPNAATFN--------------------------------SLIKGLHAESRIM  148 (595)
Q Consensus       101 ~l~~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~--------------------------------~l~~~~~~~g~~~  148 (595)
                      .|++.+.+.|-+....+   .+++   ..|...|.                                ..+.+|...|.+.
T Consensus       929 eli~vt~~n~l~k~~ar---ylv~---r~d~~lW~~vl~~~n~~RR~Lidqv~a~aL~e~~~PeeVs~~vKaf~~aglp~ 1002 (1630)
T 1xi4_A          929 ELINVCNENSLFKSLSR---YLVR---RKDPELWGSVLLESNPYRRPLIDQVVQTALSETQDPEEVSVTVKAFMTADLPN 1002 (1630)
T ss_pred             HHHHHHhcchhHHHHHH---HHHH---hcCHHHHHHHhcCCcHHHHHHHHHHHHhhcccccCHHHhHHHHHHHHhCCCHH
Confidence            23333333333322111   1111   12333343                                3444555555555


Q ss_pred             HHHHHHHHHHhcCC--CCCHhhHHHHHHHHHhcCChhHHHHHHHHHHhcCCCCCccccCcHHHHHHHHHHHHHcCCHhHH
Q 040027          149 EAAALFTKLKAFGC--EPNVITYNTLINGLCRTGHTMIALNLFEEMANGNGEIGVVCKPNTVTYSTIIDGLCKEGFVDKA  226 (595)
Q Consensus       149 ~A~~~~~~~~~~~~--~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A  226 (595)
                      +|+++++++...+-  .-+...-+.++.+..+. +..+..+..++...-          +   ...+...+...|.+++|
T Consensus      1003 EaieLLEKivl~~s~fs~n~~LqnlLi~tAIka-D~~Rv~eyI~kLd~~----------d---~~eIA~Iai~lglyEEA 1068 (1630)
T 1xi4_A         1003 ELIELLEKIVLDNSVFSEHRNLQNLLILTAIKA-DRTRVMEYINRLDNY----------D---APDIANIAISNELFEEA 1068 (1630)
T ss_pred             HHHHHHHHHHcCCCcccccHHHHHHHHHHHHHh-ChhhHHHHHHHhhhc----------c---HHHHHHHHHhCCCHHHH
Confidence            55555555552210  01223333344443333 333333333333211          0   12245566667777777


Q ss_pred             HHHHHHHhhCCCCCCHhHHHHHHHHHHhcCCHHHHHHHHHHHHHCCCCCCHhhHHHHHHHHHhcCChHHHHHHHHHHHHC
Q 040027          227 KALFLQMKDENINPDVVTYNSLIHGLCHANDWNEAKRLFIEMMDQGVQPSVVTFNVIMDELCKNRKMDEASRLLDLMVQR  306 (595)
Q Consensus       227 ~~~~~~~~~~~~~~~~~~~~~ll~~~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~  306 (595)
                      ..+|++...     .....+.++   ...+++++|.++.++.      -+..+|..+..++...|++++|.+.|.+.   
T Consensus      1069 f~IYkKa~~-----~~~A~~VLi---e~i~nldrAiE~Aerv------n~p~vWsqLAKAql~~G~~kEAIdsYiKA--- 1131 (1630)
T 1xi4_A         1069 FAIFRKFDV-----NTSAVQVLI---EHIGNLDRAYEFAERC------NEPAVWSQLAKAQLQKGMVKEAIDSYIKA--- 1131 (1630)
T ss_pred             HHHHHHcCC-----HHHHHHHHH---HHHhhHHHHHHHHHhc------CCHHHHHHHHHHHHhCCCHHHHHHHHHhc---
Confidence            777776521     122222222   2556777777776644      24667778888888888888888887653   


Q ss_pred             CCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHhcCCCCCHHHHHHHHHHHHhCCCHHHHHHHHHHHHHCCCCCCHHHHH
Q 040027          307 GVRPNACTYNTLMDGFCLMGKINRAEELFGSMESMGCKHDDVSYNILINGYCKNKEVEEALSLYREMVSKGIKPTVVTYN  386 (595)
Q Consensus       307 ~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~  386 (595)
                         .|...|..++.++.+.|++++|.+.|....+..  +++...+.++.+|.+.+++++....    +.   .++...+.
T Consensus      1132 ---dD~say~eVa~~~~~lGkyEEAIeyL~mArk~~--~e~~Idt~LafaYAKl~rleele~f----I~---~~n~ad~~ 1199 (1630)
T 1xi4_A         1132 ---DDPSSYMEVVQAANTSGNWEELVKYLQMARKKA--RESYVETELIFALAKTNRLAELEEF----IN---GPNNAHIQ 1199 (1630)
T ss_pred             ---CChHHHHHHHHHHHHcCCHHHHHHHHHHHHhhc--ccccccHHHHHHHHhhcCHHHHHHH----Hh---CCCHHHHH
Confidence               266677777888888888888888887776653  3333344577778887777743322    22   23556666


Q ss_pred             HHHHHHHccCCHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCcCHHHHHHHHHHHHhcC
Q 040027          387 TLFLGLFEIHQVEHALKLFDEMQRDGVAADTRTYTTFIDGLCKNGYIIEAVELFRTLRILKCELDIQAYNCLIDGLCKSG  466 (595)
Q Consensus       387 ~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g  466 (595)
                      .+...|...|++++|...|..+         ..|..++.+|.+.|++++|.+.++++      .+..+|..+..+|...|
T Consensus      1200 ~iGd~le~eg~YeeA~~~Y~kA---------~ny~rLA~tLvkLge~q~AIEaarKA------~n~~aWkev~~acve~~ 1264 (1630)
T 1xi4_A         1200 QVGDRCYDEKMYDAAKLLYNNV---------SNFGRLASTLVHLGEYQAAVDGARKA------NSTRTWKEVCFACVDGK 1264 (1630)
T ss_pred             HHHHHHHhcCCHHHHHHHHHhh---------hHHHHHHHHHHHhCCHHHHHHHHHHh------CCHHHHHHHHHHHhhhh
Confidence            7778888888888888888774         36777788888888888888888776      25677888888888888


Q ss_pred             ChHHHHHHHHhcccCCCCCCHHHHHHHHHHHHhcCChhHHHHHHHHHHHcCCCCCHHHHHHHHHHHHHc--CChhHHHHH
Q 040027          467 RLKFAWELFCSLPHGVLVPNVVTYNIMIQGLCNDGQMDKARDLFLDMEENAAAPDVITFDMLIHGFIRI--NEPSKVNEL  544 (595)
Q Consensus       467 ~~~~A~~~~~~~~~~~~~p~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~~l~~~~~~~--g~~~~A~~~  544 (595)
                      ++..|......+.     .++..+..++..|.+.|.+++|+.+++..+... +-....|.-+...|.+.  ++..++.++
T Consensus      1265 Ef~LA~~cgl~Ii-----v~~deLeeli~yYe~~G~feEAI~LlE~aL~Le-raH~gmftELaiLyaKy~peklmEhlk~ 1338 (1630)
T 1xi4_A         1265 EFRLAQMCGLHIV-----VHADELEELINYYQDRGYFEELITMLEAALGLE-RAHMGMFTELAILYSKFKPQKMREHLEL 1338 (1630)
T ss_pred             HHHHHHHHHHhhh-----cCHHHHHHHHHHHHHcCCHHHHHHHHHHHhccC-hhHhHHHHHHHHHHHhCCHHHHHHHHHH
Confidence            8888877765433     356677788889999999999999998888764 44455666666666653  455566666


Q ss_pred             HHHHHHCCCCC------CHHHHHHHHHHHHhcCcccccchHHH
Q 040027          545 LHKMKEKKVMP------DASIVSIVVDLLVKNEISLKSLPSFL  581 (595)
Q Consensus       545 ~~~~~~~~~~p------~~~~~~~l~~~~~~~g~~~~~i~~~~  581 (595)
                      |..-.  +++|      +...|..++..|.+.|.+++++..|-
T Consensus      1339 f~~ri--ni~k~~r~~e~~~lW~elv~LY~~~~e~dnA~~tm~ 1379 (1630)
T 1xi4_A         1339 FWSRV--NIPKVLRAAEQAHLWAELVFLYDKYEEYDNAIITMM 1379 (1630)
T ss_pred             HHHhc--ccchHhHHHHHHHHHHHHHHHHHhcccHHHHHHHHH
Confidence            65443  3444      57889999999999999997775553

>1fch_A Peroxisomal targeting signal 1 receptor; protein-peptide complex, tetratricopeptide repeat, TPR, helical repeat, signaling protein; 2.20A {Homo sapiens} SCOP: a.118.8.1 PDB: 2j9q_A 3imz_B* 3r9a_B* 2c0m_A 2c0l_A

Probab=99.84  E-value=5.2e-19  Score=171.69  Aligned_cols=263  Identities=11%  Similarity=-0.002  Sum_probs=153.1

Q ss_pred             hhHHHHHHHHHhcCChHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHhcCCCCCHHHHHHHHHHH
Q 040027          278 VTFNVIMDELCKNRKMDEASRLLDLMVQRGVRPNACTYNTLMDGFCLMGKINRAEELFGSMESMGCKHDDVSYNILINGY  357 (595)
Q Consensus       278 ~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~  357 (595)
                      ..+..+...+...|++++|...|+++.+.. +.+..++..++.++...|++++|...++++.+.. +.+..++..+..+|
T Consensus        65 ~~~~~~~~~~~~~g~~~~A~~~~~~al~~~-p~~~~~~~~l~~~~~~~g~~~~A~~~~~~al~~~-~~~~~~~~~l~~~~  142 (368)
T 1fch_A           65 PQPFEEGLRRLQEGDLPNAVLLFEAAVQQD-PKHMEAWQYLGTTQAENEQELLAISALRRCLELK-PDNQTALMALAVSF  142 (368)
T ss_dssp             SSHHHHHHHHHHTTCHHHHHHHHHHHHHSC-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHCCCHHHHHHHHHHHHHhC-CCCHHHHHHHHHHHHHCcCHHHHHHHHHHHHhcC-CCCHHHHHHHHHHH
Confidence            345555555556666666666666655542 2244555555666666666666666666655543 33455566666666


Q ss_pred             HhCCCHHHHHHHHHHHHHCCCCCCHHHHHH---------------HHHHHHccCCHHHHHHHHHHHHHCCCCC--CHHHH
Q 040027          358 CKNKEVEEALSLYREMVSKGIKPTVVTYNT---------------LFLGLFEIHQVEHALKLFDEMQRDGVAA--DTRTY  420 (595)
Q Consensus       358 ~~~~~~~~A~~~~~~~~~~~~~~~~~~~~~---------------l~~~~~~~~~~~~a~~~~~~~~~~~~~~--~~~~~  420 (595)
                      ...|++++|+..++++....+. +...+..               .+..+...|++++|...++++.+.. +.  +..++
T Consensus       143 ~~~g~~~~A~~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~A~~~~~~a~~~~-p~~~~~~~~  220 (368)
T 1fch_A          143 TNESLQRQACEILRDWLRYTPA-YAHLVTPAEEGAGGAGLGPSKRILGSLLSDSLFLEVKELFLAAVRLD-PTSIDPDVQ  220 (368)
T ss_dssp             HHTTCHHHHHHHHHHHHHTSTT-TGGGCC---------------CTTHHHHHHHHHHHHHHHHHHHHHHS-TTSCCHHHH
T ss_pred             HHcCCHHHHHHHHHHHHHhCcC-cHHHHHHHHHHhhhhcccHHHHHHHHHhhcccHHHHHHHHHHHHHhC-cCcccHHHH
Confidence            6666666666666666554322 1111110               1222225666667777766666542 22  45666


Q ss_pred             HHHHHHHHhcCCHHHHHHHHHHHHHcCCCcCHHHHHHHHHHHHhcCChHHHHHHHHhcccCCCCC-CHHHHHHHHHHHHh
Q 040027          421 TTFIDGLCKNGYIIEAVELFRTLRILKCELDIQAYNCLIDGLCKSGRLKFAWELFCSLPHGVLVP-NVVTYNIMIQGLCN  499 (595)
Q Consensus       421 ~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~p-~~~~~~~l~~~~~~  499 (595)
                      ..+...+...|++++|...++++.... +.+..++..++.++...|++++|+..|+++.+.  .| +...+..++.+|..
T Consensus       221 ~~l~~~~~~~g~~~~A~~~~~~al~~~-~~~~~~~~~l~~~~~~~g~~~~A~~~~~~al~~--~~~~~~~~~~l~~~~~~  297 (368)
T 1fch_A          221 CGLGVLFNLSGEYDKAVDCFTAALSVR-PNDYLLWNKLGATLANGNQSEEAVAAYRRALEL--QPGYIRSRYNLGISCIN  297 (368)
T ss_dssp             HHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH--CTTCHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHcCCHHHHHHHHHHHHHhC-cCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHh--CCCcHHHHHHHHHHHHH
Confidence            666666666777777777777666654 445666666666666777777777777666652  33 35566666666667


Q ss_pred             cCChhHHHHHHHHHHHcCCCCC-----------HHHHHHHHHHHHHcCChhHHHHHHHHH
Q 040027          500 DGQMDKARDLFLDMEENAAAPD-----------VITFDMLIHGFIRINEPSKVNELLHKM  548 (595)
Q Consensus       500 ~g~~~~A~~~~~~~~~~~~~~~-----------~~~~~~l~~~~~~~g~~~~A~~~~~~~  548 (595)
                      .|++++|...|+++++.. +.+           ..+|..++.+|...|++++|..++++.
T Consensus       298 ~g~~~~A~~~~~~al~~~-~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~  356 (368)
T 1fch_A          298 LGAHREAVEHFLEALNMQ-RKSRGPRGEGGAMSENIWSTLRLALSMLGQSDAYGAADARD  356 (368)
T ss_dssp             HTCHHHHHHHHHHHHHHH-HTC------CCCCCHHHHHHHHHHHHHHTCGGGHHHHHTTC
T ss_pred             CCCHHHHHHHHHHHHHhC-CCCCCccccccchhhHHHHHHHHHHHHhCChHhHHHhHHHH
Confidence            777777777776666532 111           456666666666777776666665533

>1xi4_A Clathrin heavy chain; alpha-ZIG-ZAG, beta-propeller, endocytosis-exocyto complex; 7.90A {Bos taurus} SCOP: i.23.1.1 PDB: 1xi5_A 3iyv_A

Probab=99.84  E-value=2.2e-16  Score=166.22  Aligned_cols=397  Identities=14%  Similarity=0.114  Sum_probs=281.6

Q ss_pred             ccccCCCChHHHHHHHHHHHHhCCC--CCCHhhHHHHHHHHHcCCCch--hHHhhCCCCCCHHHHHHHHHHHHhcCChhH
Q 040027           39 EGDINVITPNEAFCIFDYMLRMHPS--PPPVSSFNILLASLAKNKHYD--TRLNATGLFPNLYTYNILINCFCKIGRVSL  114 (595)
Q Consensus        39 ~~~~~~~~~~~A~~~~~~~~~~~~~--~~~~~~~~~l~~~~~~~~~~~--~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~  114 (595)
                      -+|+.+|.+.+|+++|++++.. |+  .-+...-+.++....+.....  +......    ......++..+...|.+++
T Consensus       993 Kaf~~aglp~EaieLLEKivl~-~s~fs~n~~LqnlLi~tAIkaD~~Rv~eyI~kLd----~~d~~eIA~Iai~lglyEE 1067 (1630)
T 1xi4_A          993 KAFMTADLPNELIELLEKIVLD-NSVFSEHRNLQNLLILTAIKADRTRVMEYINRLD----NYDAPDIANIAISNELFEE 1067 (1630)
T ss_pred             HHHHhCCCHHHHHHHHHHHHcC-CCcccccHHHHHHHHHHHHHhChhhHHHHHHHhh----hccHHHHHHHHHhCCCHHH
Confidence            3456789999999999999833 33  124556666666666553211  1111111    1223447788888999999


Q ss_pred             HHHHHHHHHhCCCCCCHHHHHHHHHHHHhcCCHhHHHHHHHHHHhcCCCCCHhhHHHHHHHHHhcCChhHHHHHHHHHHh
Q 040027          115 GFIAFGRILRSCFTPNAATFNSLIKGLHAESRIMEAAALFTKLKAFGCEPNVITYNTLINGLCRTGHTMIALNLFEEMAN  194 (595)
Q Consensus       115 A~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~  194 (595)
                      |..+|++...     .....+.++   ...+++++|.++.++..      ++.+|..+..++...|++++|+..|.+.  
T Consensus      1068 Af~IYkKa~~-----~~~A~~VLi---e~i~nldrAiE~Aervn------~p~vWsqLAKAql~~G~~kEAIdsYiKA-- 1131 (1630)
T 1xi4_A         1068 AFAIFRKFDV-----NTSAVQVLI---EHIGNLDRAYEFAERCN------EPAVWSQLAKAQLQKGMVKEAIDSYIKA-- 1131 (1630)
T ss_pred             HHHHHHHcCC-----HHHHHHHHH---HHHhhHHHHHHHHHhcC------CHHHHHHHHHHHHhCCCHHHHHHHHHhc--
Confidence            9999998631     222223332   26788999999888652      5788999999999999999999998664  


Q ss_pred             cCCCCCccccCcHHHHHHHHHHHHHcCCHhHHHHHHHHHhhCCCCCCHhHHHHHHHHHHhcCCHHHHHHHHHHHHHCCCC
Q 040027          195 GNGEIGVVCKPNTVTYSTIIDGLCKEGFVDKAKALFLQMKDENINPDVVTYNSLIHGLCHANDWNEAKRLFIEMMDQGVQ  274 (595)
Q Consensus       195 ~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~~ll~~~~~~~~~~~A~~~~~~~~~~~~~  274 (595)
                                .+...|..++.++.+.|++++|.+.|...++..  +++...+.++.+|.+.+++++...+    ++   .
T Consensus      1132 ----------dD~say~eVa~~~~~lGkyEEAIeyL~mArk~~--~e~~Idt~LafaYAKl~rleele~f----I~---~ 1192 (1630)
T 1xi4_A         1132 ----------DDPSSYMEVVQAANTSGNWEELVKYLQMARKKA--RESYVETELIFALAKTNRLAELEEF----IN---G 1192 (1630)
T ss_pred             ----------CChHHHHHHHHHHHHcCCHHHHHHHHHHHHhhc--ccccccHHHHHHHHhhcCHHHHHHH----Hh---C
Confidence                      357788889999999999999999998877754  3333344588889998888853333    22   2


Q ss_pred             CCHhhHHHHHHHHHhcCChHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHhcCCCCCHHHHHHHH
Q 040027          275 PSVVTFNVIMDELCKNRKMDEASRLLDLMVQRGVRPNACTYNTLMDGFCLMGKINRAEELFGSMESMGCKHDDVSYNILI  354 (595)
Q Consensus       275 ~~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~  354 (595)
                      ++...+..+...|...|++++|..+|..+         ..|..++.++.+.|++++|.+.+++.      .+..+|..+.
T Consensus      1193 ~n~ad~~~iGd~le~eg~YeeA~~~Y~kA---------~ny~rLA~tLvkLge~q~AIEaarKA------~n~~aWkev~ 1257 (1630)
T 1xi4_A         1193 PNNAHIQQVGDRCYDEKMYDAAKLLYNNV---------SNFGRLASTLVHLGEYQAAVDGARKA------NSTRTWKEVC 1257 (1630)
T ss_pred             CCHHHHHHHHHHHHhcCCHHHHHHHHHhh---------hHHHHHHHHHHHhCCHHHHHHHHHHh------CCHHHHHHHH
Confidence            46667778899999999999999999885         36888899999999999999998876      3567888888


Q ss_pred             HHHHhCCCHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHccCCHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHhc--CC
Q 040027          355 NGYCKNKEVEEALSLYREMVSKGIKPTVVTYNTLFLGLFEIHQVEHALKLFDEMQRDGVAADTRTYTTFIDGLCKN--GY  432 (595)
Q Consensus       355 ~~~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~--g~  432 (595)
                      .+|...|++..|......+.     .+...+..++..|.+.|.+++|+.+++..+... +.....++.+...|.+.  ++
T Consensus      1258 ~acve~~Ef~LA~~cgl~Ii-----v~~deLeeli~yYe~~G~feEAI~LlE~aL~Le-raH~gmftELaiLyaKy~pek 1331 (1630)
T 1xi4_A         1258 FACVDGKEFRLAQMCGLHIV-----VHADELEELINYYQDRGYFEELITMLEAALGLE-RAHMGMFTELAILYSKFKPQK 1331 (1630)
T ss_pred             HHHhhhhHHHHHHHHHHhhh-----cCHHHHHHHHHHHHHcCCHHHHHHHHHHHhccC-hhHhHHHHHHHHHHHhCCHHH
Confidence            89999999988888766432     266677788888999999999999998887654 44455666666666653  34


Q ss_pred             HHHHHHHHHHHHHcCCC------cCHHHHHHHHHHHHhcCChHHHHHHHH-------------hcccCCCCCCHHHHHHH
Q 040027          433 IIEAVELFRTLRILKCE------LDIQAYNCLIDGLCKSGRLKFAWELFC-------------SLPHGVLVPNVVTYNIM  493 (595)
Q Consensus       433 ~~~A~~~~~~~~~~~~~------~~~~~~~~l~~~~~~~g~~~~A~~~~~-------------~~~~~~~~p~~~~~~~l  493 (595)
                      ..++.+.|..-.  +++      .+...|..++..|.+.|+++.|....-             ..+.  -..|+..|...
T Consensus      1332 lmEhlk~f~~ri--ni~k~~r~~e~~~lW~elv~LY~~~~e~dnA~~tm~~h~~~a~~~~~Fk~~i~--kv~n~elyyka 1407 (1630)
T 1xi4_A         1332 MREHLELFWSRV--NIPKVLRAAEQAHLWAELVFLYDKYEEYDNAIITMMNHPTDAWKEGQFKDIIT--KVANVELYYRA 1407 (1630)
T ss_pred             HHHHHHHHHHhc--ccchHhHHHHHHHHHHHHHHHHHhcccHHHHHHHHHhccHhhhhhHHHHHHhc--ccccHHHHHHH
Confidence            444455544332  222      256778889999999999998883322             2222  13467777777


Q ss_pred             HHHHHhc
Q 040027          494 IQGLCND  500 (595)
Q Consensus       494 ~~~~~~~  500 (595)
                      +..|...
T Consensus      1408 i~Fyl~~ 1414 (1630)
T 1xi4_A         1408 IQFYLEF 1414 (1630)
T ss_pred             HHHHHhh
Confidence            7777743

>1fch_A Peroxisomal targeting signal 1 receptor; protein-peptide complex, tetratricopeptide repeat, TPR, helical repeat, signaling protein; 2.20A {Homo sapiens} SCOP: a.118.8.1 PDB: 2j9q_A 3imz_B* 3r9a_B* 2c0m_A 2c0l_A

Probab=99.84  E-value=6.7e-19  Score=170.89  Aligned_cols=305  Identities=12%  Similarity=-0.035  Sum_probs=192.7

Q ss_pred             hcCCHhHHHH-HHHHHHhcCCC---CCHhhHHHHHHHHHhcCChhHHHHHHHHHHhcCCCCCccccCcHHHHHHHHHHHH
Q 040027          143 AESRIMEAAA-LFTKLKAFGCE---PNVITYNTLINGLCRTGHTMIALNLFEEMANGNGEIGVVCKPNTVTYSTIIDGLC  218 (595)
Q Consensus       143 ~~g~~~~A~~-~~~~~~~~~~~---~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~  218 (595)
                      ..|++++|++ .|++.......   .+...+..++..+...|++++|+..|+++.+..       +.+..++..+..++.
T Consensus        37 ~~~~~~~a~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~g~~~~A~~~~~~al~~~-------p~~~~~~~~l~~~~~  109 (368)
T 1fch_A           37 WLSDYDDLTSATYDKGYQFEEENPLRDHPQPFEEGLRRLQEGDLPNAVLLFEAAVQQD-------PKHMEAWQYLGTTQA  109 (368)
T ss_dssp             ---------CHHHHCCCCCCSSCTTTTCSSHHHHHHHHHHTTCHHHHHHHHHHHHHSC-------TTCHHHHHHHHHHHH
T ss_pred             HHHHHHHHHhhhhhHHHhcCCCCcccchHHHHHHHHHHHHCCCHHHHHHHHHHHHHhC-------CCCHHHHHHHHHHHH
Confidence            3467777777 77765544211   124557777778888888888888888887764       456777778888888


Q ss_pred             HcCCHhHHHHHHHHHhhCCCCCCHhHHHHHHHHHHhcCCHHHHHHHHHHHHHCCCCCCHhhHHHHHHHHHhcCChHHHHH
Q 040027          219 KEGFVDKAKALFLQMKDENINPDVVTYNSLIHGLCHANDWNEAKRLFIEMMDQGVQPSVVTFNVIMDELCKNRKMDEASR  298 (595)
Q Consensus       219 ~~g~~~~A~~~~~~~~~~~~~~~~~~~~~ll~~~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~a~~  298 (595)
                      ..|++++|.+.|+++.+.. +.+..++..++..+...|++++|...++++...... +...+..+...       ..   
T Consensus       110 ~~g~~~~A~~~~~~al~~~-~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~-~~~~~~~~~~~-------~~---  177 (368)
T 1fch_A          110 ENEQELLAISALRRCLELK-PDNQTALMALAVSFTNESLQRQACEILRDWLRYTPA-YAHLVTPAEEG-------AG---  177 (368)
T ss_dssp             HTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHTSTT-TGGGCC-----------------
T ss_pred             HCcCHHHHHHHHHHHHhcC-CCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCcC-cHHHHHHHHHH-------hh---
Confidence            8888888888888877654 336677777778888888888888888887775322 22222111000       00   


Q ss_pred             HHHHHHHCCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHhcCCCC--CHHHHHHHHHHHHhCCCHHHHHHHHHHHHHC
Q 040027          299 LLDLMVQRGVRPNACTYNTLMDGFCLMGKINRAEELFGSMESMGCKH--DDVSYNILINGYCKNKEVEEALSLYREMVSK  376 (595)
Q Consensus       299 ~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~--~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~~  376 (595)
                          .    ..+ ...+..+...+ ..|++++|...++++.+.. +.  +..++..+..+|...|++++|+..++++...
T Consensus       178 ----~----~~~-~~~~~~~~~~~-~~~~~~~A~~~~~~a~~~~-p~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~al~~  246 (368)
T 1fch_A          178 ----G----AGL-GPSKRILGSLL-SDSLFLEVKELFLAAVRLD-PTSIDPDVQCGLGVLFNLSGEYDKAVDCFTAALSV  246 (368)
T ss_dssp             -----------------CTTHHHH-HHHHHHHHHHHHHHHHHHS-TTSCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH
T ss_pred             ----h----hcc-cHHHHHHHHHh-hcccHHHHHHHHHHHHHhC-cCcccHHHHHHHHHHHHHcCCHHHHHHHHHHHHHh
Confidence                0    000 00111222223 6677777777777776653 22  3566777777777777777777777777665


Q ss_pred             CCCCCHHHHHHHHHHHHccCCHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCcC-----
Q 040027          377 GIKPTVVTYNTLFLGLFEIHQVEHALKLFDEMQRDGVAADTRTYTTFIDGLCKNGYIIEAVELFRTLRILKCELD-----  451 (595)
Q Consensus       377 ~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~~-----  451 (595)
                      .+. +...+..+...+...|++++|...++++.+.. +.+...+..+..+|.+.|++++|...++++.+.. +.+     
T Consensus       247 ~~~-~~~~~~~l~~~~~~~g~~~~A~~~~~~al~~~-~~~~~~~~~l~~~~~~~g~~~~A~~~~~~al~~~-~~~~~~~~  323 (368)
T 1fch_A          247 RPN-DYLLWNKLGATLANGNQSEEAVAAYRRALELQ-PGYIRSRYNLGISCINLGAHREAVEHFLEALNMQ-RKSRGPRG  323 (368)
T ss_dssp             CTT-CHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHH-HTC-----
T ss_pred             CcC-CHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhC-CCcHHHHHHHHHHHHHCCCHHHHHHHHHHHHHhC-CCCCCccc
Confidence            322 45667777777777777777777777777653 4556777777777888888888888887776543 222     


Q ss_pred             ------HHHHHHHHHHHHhcCChHHHHHHHHhccc
Q 040027          452 ------IQAYNCLIDGLCKSGRLKFAWELFCSLPH  480 (595)
Q Consensus       452 ------~~~~~~l~~~~~~~g~~~~A~~~~~~~~~  480 (595)
                            ..+|..+..++...|++++|..++.+..+
T Consensus       324 ~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~l~  358 (368)
T 1fch_A          324 EGGAMSENIWSTLRLALSMLGQSDAYGAADARDLS  358 (368)
T ss_dssp             -CCCCCHHHHHHHHHHHHHHTCGGGHHHHHTTCHH
T ss_pred             cccchhhHHHHHHHHHHHHhCChHhHHHhHHHHHH
Confidence                  67788888888888888888888776543

>4g1t_A Interferon-induced protein with tetratricopeptide 2; ISG, all alpha helix, antivirus, antiviral protein; 2.80A {Homo sapiens}

Probab=99.83  E-value=2.7e-17  Score=165.43  Aligned_cols=371  Identities=11%  Similarity=-0.069  Sum_probs=238.1

Q ss_pred             CHhhHHHHHHHHHhcCChhHHHHHHHHHHhcCCCCC--ccccCcHHHHHHHHHHHHHcCCHhHHHHHHHHHhhC-----C
Q 040027          165 NVITYNTLINGLCRTGHTMIALNLFEEMANGNGEIG--VVCKPNTVTYSTIIDGLCKEGFVDKAKALFLQMKDE-----N  237 (595)
Q Consensus       165 ~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~~--~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~-----~  237 (595)
                      ....|+.+...+...|++++|++.|++..+......  ...+....+|..+..+|...|++++|...++++...     +
T Consensus        50 ~a~~yn~Lg~~~~~~G~~~eAl~~~~kAl~~~~~~~~~~~~~~~~~~~~nla~~y~~~g~~~~A~~~~~ka~~i~~~~~~  129 (472)
T 4g1t_A           50 KATMCNLLAYLKHLKGQNEAALECLRKAEELIQQEHADQAEIRSLVTWGNYAWVYYHMGRLSDVQIYVDKVKHVCEKFSS  129 (472)
T ss_dssp             CCHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHHSGGGCTTTTHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHSCC
T ss_pred             HHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHhcCccccchHHHHHHHHHHHHHHHcCChHHHHHHHHHHHHHhHhccc
Confidence            355678888888888888888888887764210000  001334678999999999999999999999887642     1


Q ss_pred             --CCCCHhHHHHHHHHHHh--cCCHHHHHHHHHHHHHCCCCCCHhhHHHHHHH---HHhcCChHHHHHHHHHHHHCCCCC
Q 040027          238 --INPDVVTYNSLIHGLCH--ANDWNEAKRLFIEMMDQGVQPSVVTFNVIMDE---LCKNRKMDEASRLLDLMVQRGVRP  310 (595)
Q Consensus       238 --~~~~~~~~~~ll~~~~~--~~~~~~A~~~~~~~~~~~~~~~~~~~~~l~~~---~~~~g~~~~a~~~~~~~~~~~~~~  310 (595)
                        ......++..+..++..  .+++++|+..|++.++... .+...+..+..+   +...++.++|++.+++.++.+ +.
T Consensus       130 ~~~~~~~~~~~~~g~~~~~~~~~~y~~A~~~~~kal~~~p-~~~~~~~~~~~~~~~l~~~~~~~~al~~~~~al~l~-p~  207 (472)
T 4g1t_A          130 PYRIESPELDCEEGWTRLKCGGNQNERAKVCFEKALEKKP-KNPEFTSGLAIASYRLDNWPPSQNAIDPLRQAIRLN-PD  207 (472)
T ss_dssp             SSCCCCHHHHHHHHHHHHHHCTTHHHHHHHHHHHHHHHST-TCHHHHHHHHHHHHHHHHSCCCCCTHHHHHHHHHHC-SS
T ss_pred             ccchhhHHHHHHHHHHHHHHccccHHHHHHHHHHHHHhCC-CCHHHHHHHHHHHHHhcCchHHHHHHHHHHHHhhcC-Cc
Confidence              11234566666656555  4579999999999988532 244555554444   445678889999999988864 23


Q ss_pred             CHHHHHHHHHHHHh----cCCHHHHHHHHHHHHhcCCCCCHHHHHHHHHHHHhCCCHHHHHHHHHHHHHCCCCCCHHHHH
Q 040027          311 NACTYNTLMDGFCL----MGKINRAEELFGSMESMGCKHDDVSYNILINGYCKNKEVEEALSLYREMVSKGIKPTVVTYN  386 (595)
Q Consensus       311 ~~~~~~~l~~~~~~----~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~  386 (595)
                      +..++..+...+..    .+++++|...+++..... +.+..++..+...|...|++++|+..++++.+..+. +..++.
T Consensus       208 ~~~~~~~l~~~~~~~~~~~~~~~~a~~~~~~al~~~-~~~~~~~~~lg~~~~~~~~~~~A~~~~~~al~~~p~-~~~~~~  285 (472)
T 4g1t_A          208 NQYLKVLLALKLHKMREEGEEEGEGEKLVEEALEKA-PGVTDVLRSAAKFYRRKDEPDKAIELLKKALEYIPN-NAYLHC  285 (472)
T ss_dssp             CHHHHHHHHHHHHHCC------CHHHHHHHHHHHHC-SSCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHSTT-CHHHHH
T ss_pred             chHHHHHHHHHHHHHHhhhhHHHHHHHHHHHHHHhC-ccHHHHHHHHHHHHHHcCchHHHHHHHHHHHHhCCC-hHHHHH
Confidence            55566666555544    467889999999988775 567778999999999999999999999999987443 556666


Q ss_pred             HHHHHHHcc-------------------CCHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHHcC
Q 040027          387 TLFLGLFEI-------------------HQVEHALKLFDEMQRDGVAADTRTYTTFIDGLCKNGYIIEAVELFRTLRILK  447 (595)
Q Consensus       387 ~l~~~~~~~-------------------~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~  447 (595)
                      .+...|...                   +..+.|...++...+.+ +.+...+..+...|...|++++|...|+++++..
T Consensus       286 ~lg~~y~~~~~~~~~~~~~~~~~~~~~~~~~~~A~~~~~~a~~~~-~~~~~~~~~lg~~~~~~~~~~~A~~~~~kaL~~~  364 (472)
T 4g1t_A          286 QIGCCYRAKVFQVMNLRENGMYGKRKLLELIGHAVAHLKKADEAN-DNLFRVCSILASLHALADQYEEAEYYFQKEFSKE  364 (472)
T ss_dssp             HHHHHHHHHHHHHHHC------CHHHHHHHHHHHHHHHHHHHHHC-TTTCCCHHHHHHHHHHTTCHHHHHHHHHHHHHSC
T ss_pred             HHHHHHHHHHHHhhhHHHHHHHHHHHHHhhHHHHHHHHHHHhhcC-CchhhhhhhHHHHHHHhccHHHHHHHHHHHHhcC
Confidence            665554321                   23456666666666543 3444556677777888888888888888877654


Q ss_pred             CCcCH--HHHHHHHH-HHHhcCChHHHHHHHHhcccCCCCCCHHHHHHHHHHHHhcCChhHHHHHHHHHHHcCCCCCHHH
Q 040027          448 CELDI--QAYNCLID-GLCKSGRLKFAWELFCSLPHGVLVPNVVTYNIMIQGLCNDGQMDKARDLFLDMEENAAAPDVIT  524 (595)
Q Consensus       448 ~~~~~--~~~~~l~~-~~~~~g~~~~A~~~~~~~~~~~~~p~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~  524 (595)
                      ..+..  ..+..+.. .....|++++|+..|++.+.  +.|+.......         ...+.+++++.++.+ +.+..+
T Consensus       365 ~~~~~~~~~~~~~~~~~~~~~~~~~~Ai~~y~kal~--i~~~~~~~~~~---------~~~l~~~~~~~l~~~-p~~~~~  432 (472)
T 4g1t_A          365 LTPVAKQLLHLRYGNFQLYQMKCEDKAIHHFIEGVK--INQKSREKEKM---------KDKLQKIAKMRLSKN-GADSEA  432 (472)
T ss_dssp             CCHHHHHHHHHHHHHHHHHTSSCHHHHHHHHHHHHH--SCCCCHHHHHH---------HHHHHHHHHHHHHHC-C-CTTH
T ss_pred             CCChHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHh--cCcccHHHHHH---------HHHHHHHHHHHHHhC-CCCHHH
Confidence            22221  12223332 23456778888888888776  45554332222         233455566666654 556677


Q ss_pred             HHHHHHHHHHcCChhHHHHHHHHHHHCC
Q 040027          525 FDMLIHGFIRINEPSKVNELLHKMKEKK  552 (595)
Q Consensus       525 ~~~l~~~~~~~g~~~~A~~~~~~~~~~~  552 (595)
                      |..++.+|...|++++|.+.|+++++.+
T Consensus       433 ~~~LG~~~~~~g~~~~A~~~y~kALe~~  460 (472)
T 4g1t_A          433 LHVLAFLQELNEKMQQADEDSERGLESG  460 (472)
T ss_dssp             HHHHHHHHHHHHHCC-------------
T ss_pred             HHHHHHHHHHcCCHHHHHHHHHHHHhcC
Confidence            8888888888888888888888888754

>4eqf_A PEX5-related protein; accessory protein, tetratricopeptide repeat, TPR; 3.00A {Mus musculus}

Probab=99.82  E-value=5.5e-19  Score=171.29  Aligned_cols=265  Identities=12%  Similarity=0.008  Sum_probs=168.0

Q ss_pred             HhhHHHHHHHHHhcCChHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHhcCCCCCHHHHHHHHHH
Q 040027          277 VVTFNVIMDELCKNRKMDEASRLLDLMVQRGVRPNACTYNTLMDGFCLMGKINRAEELFGSMESMGCKHDDVSYNILING  356 (595)
Q Consensus       277 ~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~  356 (595)
                      ...+..++..+.+.|++++|..+|+++.+.. +.+..++..++.++...|++++|+..|+++.+.. +.+..++..+..+
T Consensus        65 ~~~~~~~~~~~~~~g~~~~A~~~~~~al~~~-p~~~~~~~~lg~~~~~~g~~~~A~~~~~~al~~~-p~~~~~~~~l~~~  142 (365)
T 4eqf_A           65 WPGAFEEGLKRLKEGDLPVTILFMEAAILQD-PGDAEAWQFLGITQAENENEQAAIVALQRCLELQ-PNNLKALMALAVS  142 (365)
T ss_dssp             CTTHHHHHHHHHHHTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHH
T ss_pred             hhHHHHHHHHHHHCCCHHHHHHHHHHHHHhC-cCCHHHHHHHHHHHHHCCCHHHHHHHHHHHHhcC-CCCHHHHHHHHHH
Confidence            3456777777777778888888877777753 3356677777777888888888888888777664 4456677777788


Q ss_pred             HHhCCCHHHHHHHHHHHHHCCCCC---------CHHHHHHHHHHHHccCCHHHHHHHHHHHHHCCCCC--CHHHHHHHHH
Q 040027          357 YCKNKEVEEALSLYREMVSKGIKP---------TVVTYNTLFLGLFEIHQVEHALKLFDEMQRDGVAA--DTRTYTTFID  425 (595)
Q Consensus       357 ~~~~~~~~~A~~~~~~~~~~~~~~---------~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~--~~~~~~~l~~  425 (595)
                      |...|++++|+..++++.+..+..         ....+..+...+...|++++|...++++.+.. +.  +..++..+..
T Consensus       143 ~~~~g~~~~A~~~~~~al~~~p~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~al~~~-p~~~~~~~~~~l~~  221 (365)
T 4eqf_A          143 YTNTSHQQDACEALKNWIKQNPKYKYLVKNKKGSPGLTRRMSKSPVDSSVLEGVKELYLEAAHQN-GDMIDPDLQTGLGV  221 (365)
T ss_dssp             HHHTTCHHHHHHHHHHHHHHCHHHHCC-------------------CCHHHHHHHHHHHHHHHHS-CSSCCHHHHHHHHH
T ss_pred             HHccccHHHHHHHHHHHHHhCccchHHHhhhccchHHHHHHHHHHhhhhhHHHHHHHHHHHHHhC-cCccCHHHHHHHHH
Confidence            888888888888887777642110         01122334556666777777777777766653 22  4666666677


Q ss_pred             HHHhcCCHHHHHHHHHHHHHcCCCcCHHHHHHHHHHHHhcCChHHHHHHHHhcccCCCCCC-HHHHHHHHHHHHhcCChh
Q 040027          426 GLCKNGYIIEAVELFRTLRILKCELDIQAYNCLIDGLCKSGRLKFAWELFCSLPHGVLVPN-VVTYNIMIQGLCNDGQMD  504 (595)
Q Consensus       426 ~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~p~-~~~~~~l~~~~~~~g~~~  504 (595)
                      .|...|++++|...++++.+.. +.+..++..++.+|...|++++|+..|+++.+.  .|+ ..++..++.+|...|+++
T Consensus       222 ~~~~~g~~~~A~~~~~~al~~~-p~~~~~~~~l~~~~~~~g~~~~A~~~~~~al~~--~p~~~~~~~~l~~~~~~~g~~~  298 (365)
T 4eqf_A          222 LFHLSGEFNRAIDAFNAALTVR-PEDYSLWNRLGATLANGDRSEEAVEAYTRALEI--QPGFIRSRYNLGISCINLGAYR  298 (365)
T ss_dssp             HHHHHTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH--CTTCHHHHHHHHHHHHHHTCCH
T ss_pred             HHHHCCCHHHHHHHHHHHHHhC-CCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHhc--CCCchHHHHHHHHHHHHCCCHH
Confidence            7777777777777777776654 455666777777777777777777777766652  333 566666667777777777


Q ss_pred             HHHHHHHHHHHcCCC-----------CCHHHHHHHHHHHHHcCChhHHHHHHHH
Q 040027          505 KARDLFLDMEENAAA-----------PDVITFDMLIHGFIRINEPSKVNELLHK  547 (595)
Q Consensus       505 ~A~~~~~~~~~~~~~-----------~~~~~~~~l~~~~~~~g~~~~A~~~~~~  547 (595)
                      +|...|+++++....           .+..+|..+..++...|+.+.+.++.++
T Consensus       299 ~A~~~~~~al~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~a~~~~~~  352 (365)
T 4eqf_A          299 EAVSNFLTALSLQRKSRNQQQVPHPAISGNIWAALRIALSLMDQPELFQAANLG  352 (365)
T ss_dssp             HHHHHHHHHHHHHHCC------------CHHHHHHHHHHHHHTCHHHHHHHHTT
T ss_pred             HHHHHHHHHHHhCcccCCCcccchhhhHHHHHHHHHHHHHHcCcHHHHHHHHHh
Confidence            777777766653100           0235566666666666766666655544

>4g1t_A Interferon-induced protein with tetratricopeptide 2; ISG, all alpha helix, antivirus, antiviral protein; 2.80A {Homo sapiens}

Probab=99.82  E-value=5.5e-17  Score=163.13  Aligned_cols=384  Identities=10%  Similarity=-0.081  Sum_probs=227.9

Q ss_pred             CHHHHHHHHHHHHhcCChhHHHHHHHHHHhC--------CCCCCHHHHHHHHHHHHhcCCHhHHHHHHHHHHhcC-----
Q 040027           95 NLYTYNILINCFCKIGRVSLGFIAFGRILRS--------CFTPNAATFNSLIKGLHAESRIMEAAALFTKLKAFG-----  161 (595)
Q Consensus        95 ~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~--------~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~-----  161 (595)
                      ....|+.+..++...|++++|+..|+++++.        ..+....+|+.+...|...|++++|...++++....     
T Consensus        50 ~a~~yn~Lg~~~~~~G~~~eAl~~~~kAl~~~~~~~~~~~~~~~~~~~~nla~~y~~~g~~~~A~~~~~ka~~i~~~~~~  129 (472)
T 4g1t_A           50 KATMCNLLAYLKHLKGQNEAALECLRKAEELIQQEHADQAEIRSLVTWGNYAWVYYHMGRLSDVQIYVDKVKHVCEKFSS  129 (472)
T ss_dssp             CCHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHHSGGGCTTTTHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHSCC
T ss_pred             HHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHhcCccccchHHHHHHHHHHHHHHHcCChHHHHHHHHHHHHHhHhccc
Confidence            4567888888899999999999999887653        113345678888899999999999999888876531     


Q ss_pred             --CCCCHhhHHHHHHHHHh--cCChhHHHHHHHHHHhcCCCCCccccCcHHHHHHHHHHH---HHcCCHhHHHHHHHHHh
Q 040027          162 --CEPNVITYNTLINGLCR--TGHTMIALNLFEEMANGNGEIGVVCKPNTVTYSTIIDGL---CKEGFVDKAKALFLQMK  234 (595)
Q Consensus       162 --~~~~~~~~~~l~~~~~~--~g~~~~A~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~---~~~g~~~~A~~~~~~~~  234 (595)
                        ......++.....++..  .+++++|++.|+++...+       |.++..+..+..++   ...++.++|++.+++..
T Consensus       130 ~~~~~~~~~~~~~g~~~~~~~~~~y~~A~~~~~kal~~~-------p~~~~~~~~~~~~~~~l~~~~~~~~al~~~~~al  202 (472)
T 4g1t_A          130 PYRIESPELDCEEGWTRLKCGGNQNERAKVCFEKALEKK-------PKNPEFTSGLAIASYRLDNWPPSQNAIDPLRQAI  202 (472)
T ss_dssp             SSCCCCHHHHHHHHHHHHHHCTTHHHHHHHHHHHHHHHS-------TTCHHHHHHHHHHHHHHHHSCCCCCTHHHHHHHH
T ss_pred             ccchhhHHHHHHHHHHHHHHccccHHHHHHHHHHHHHhC-------CCCHHHHHHHHHHHHHhcCchHHHHHHHHHHHHh
Confidence              01134556655555554  456889999999988875       44566666655553   34577788888888877


Q ss_pred             hCCCCCCHhHHHHHHHHHHh----cCCHHHHHHHHHHHHHCCCCCCHhhHHHHHHHHHhcCChHHHHHHHHHHHHCCCCC
Q 040027          235 DENINPDVVTYNSLIHGLCH----ANDWNEAKRLFIEMMDQGVQPSVVTFNVIMDELCKNRKMDEASRLLDLMVQRGVRP  310 (595)
Q Consensus       235 ~~~~~~~~~~~~~ll~~~~~----~~~~~~A~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~~~~  310 (595)
                      +.+ +.+...+..+...+..    .+++++|.+++++..... +.+...+..+...+...|++++|...++++.+.. +.
T Consensus       203 ~l~-p~~~~~~~~l~~~~~~~~~~~~~~~~a~~~~~~al~~~-~~~~~~~~~lg~~~~~~~~~~~A~~~~~~al~~~-p~  279 (472)
T 4g1t_A          203 RLN-PDNQYLKVLLALKLHKMREEGEEEGEGEKLVEEALEKA-PGVTDVLRSAAKFYRRKDEPDKAIELLKKALEYI-PN  279 (472)
T ss_dssp             HHC-SSCHHHHHHHHHHHHHCC------CHHHHHHHHHHHHC-SSCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHS-TT
T ss_pred             hcC-CcchHHHHHHHHHHHHHHhhhhHHHHHHHHHHHHHHhC-ccHHHHHHHHHHHHHHcCchHHHHHHHHHHHHhC-CC
Confidence            753 2355566655554443    467788888888887753 3356778888888999999999999999888763 33


Q ss_pred             CHHHHHHHHHHHHhcCCHHHHHHHHHHHHhcCCCCCHHHHHHHHHHHHhCCCHHHHHHHHHHHHHCCCCCCHHHHHHHHH
Q 040027          311 NACTYNTLMDGFCLMGKINRAEELFGSMESMGCKHDDVSYNILINGYCKNKEVEEALSLYREMVSKGIKPTVVTYNTLFL  390 (595)
Q Consensus       311 ~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~~l~~  390 (595)
                      +..++..+..+|...+....         ...       ...........+.++.|...+++..+..+. +...+..+..
T Consensus       280 ~~~~~~~lg~~y~~~~~~~~---------~~~-------~~~~~~~~~~~~~~~~A~~~~~~a~~~~~~-~~~~~~~lg~  342 (472)
T 4g1t_A          280 NAYLHCQIGCCYRAKVFQVM---------NLR-------ENGMYGKRKLLELIGHAVAHLKKADEANDN-LFRVCSILAS  342 (472)
T ss_dssp             CHHHHHHHHHHHHHHHHHHH---------HC-------------CHHHHHHHHHHHHHHHHHHHHHCTT-TCCCHHHHHH
T ss_pred             hHHHHHHHHHHHHHHHHHhh---------hHH-------HHHHHHHHHHHhhHHHHHHHHHHHhhcCCc-hhhhhhhHHH
Confidence            56666666666543211100         000       000000011122345667777766665332 4455666677


Q ss_pred             HHHccCCHHHHHHHHHHHHHCCCCCCHH--HHHHHHH-HHHhcCCHHHHHHHHHHHHHcCCCcCHHHHHHHHHHHHhcCC
Q 040027          391 GLFEIHQVEHALKLFDEMQRDGVAADTR--TYTTFID-GLCKNGYIIEAVELFRTLRILKCELDIQAYNCLIDGLCKSGR  467 (595)
Q Consensus       391 ~~~~~~~~~~a~~~~~~~~~~~~~~~~~--~~~~l~~-~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~  467 (595)
                      .+...|++++|...|++.++....+...  .+..+.. .+...|++++|+..|++.++..  |+.....         +.
T Consensus       343 ~~~~~~~~~~A~~~~~kaL~~~~~~~~~~~~~~~~~~~~~~~~~~~~~Ai~~y~kal~i~--~~~~~~~---------~~  411 (472)
T 4g1t_A          343 LHALADQYEEAEYYFQKEFSKELTPVAKQLLHLRYGNFQLYQMKCEDKAIHHFIEGVKIN--QKSREKE---------KM  411 (472)
T ss_dssp             HHHHTTCHHHHHHHHHHHHHSCCCHHHHHHHHHHHHHHHHHTSSCHHHHHHHHHHHHHSC--CCCHHHH---------HH
T ss_pred             HHHHhccHHHHHHHHHHHHhcCCCChHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHhcC--cccHHHH---------HH
Confidence            7777777777777777776653222111  1222222 2345677777777777777653  2222111         11


Q ss_pred             hHHHHHHHHhcccCCCCCCHHHHHHHHHHHHhcCChhHHHHHHHHHHHcC
Q 040027          468 LKFAWELFCSLPHGVLVPNVVTYNIMIQGLCNDGQMDKARDLFLDMEENA  517 (595)
Q Consensus       468 ~~~A~~~~~~~~~~~~~p~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~  517 (595)
                      ...+..++++.+.. -+.+..+|..++.+|...|++++|++.|+++++.+
T Consensus       412 ~~~l~~~~~~~l~~-~p~~~~~~~~LG~~~~~~g~~~~A~~~y~kALe~~  460 (472)
T 4g1t_A          412 KDKLQKIAKMRLSK-NGADSEALHVLAFLQELNEKMQQADEDSERGLESG  460 (472)
T ss_dssp             HHHHHHHHHHHHHH-CC-CTTHHHHHHHHHHHHHHCC-------------
T ss_pred             HHHHHHHHHHHHHh-CCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHhcC
Confidence            23334445544442 12346777888888888888888888888887754

>4eqf_A PEX5-related protein; accessory protein, tetratricopeptide repeat, TPR; 3.00A {Mus musculus}

Probab=99.81  E-value=4.8e-18  Score=164.64  Aligned_cols=267  Identities=12%  Similarity=0.007  Sum_probs=190.6

Q ss_pred             CCHHHHHHHHHHHHhcCChhHHHHHHHHHHhCCCCCCHHHHHHHHHHHHhcCCHhHHHHHHHHHHhcCCCCCHhhHHHHH
Q 040027           94 PNLYTYNILINCFCKIGRVSLGFIAFGRILRSCFTPNAATFNSLIKGLHAESRIMEAAALFTKLKAFGCEPNVITYNTLI  173 (595)
Q Consensus        94 ~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~~l~  173 (595)
                      .+...|..++..+.+.|++++|+..|+++++.. +.+..+|..+...+...|++++|++.|+++.... +.+..++..++
T Consensus        63 ~~~~~~~~~~~~~~~~g~~~~A~~~~~~al~~~-p~~~~~~~~lg~~~~~~g~~~~A~~~~~~al~~~-p~~~~~~~~l~  140 (365)
T 4eqf_A           63 KDWPGAFEEGLKRLKEGDLPVTILFMEAAILQD-PGDAEAWQFLGITQAENENEQAAIVALQRCLELQ-PNNLKALMALA  140 (365)
T ss_dssp             TTCTTHHHHHHHHHHHTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHH
T ss_pred             cchhHHHHHHHHHHHCCCHHHHHHHHHHHHHhC-cCCHHHHHHHHHHHHHCCCHHHHHHHHHHHHhcC-CCCHHHHHHHH
Confidence            355668899999999999999999999999885 5678899999999999999999999999999875 44688999999


Q ss_pred             HHHHhcCChhHHHHHHHHHHhcCCCCCccccCcHHHH----------HHHHHHHHHcCCHhHHHHHHHHHhhCCCC-CCH
Q 040027          174 NGLCRTGHTMIALNLFEEMANGNGEIGVVCKPNTVTY----------STIIDGLCKEGFVDKAKALFLQMKDENIN-PDV  242 (595)
Q Consensus       174 ~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~~~~~~----------~~l~~~~~~~g~~~~A~~~~~~~~~~~~~-~~~  242 (595)
                      ..|...|++++|+..|+++....       +.+...+          ..+...+...|++++|.+.|+++...... .+.
T Consensus       141 ~~~~~~g~~~~A~~~~~~al~~~-------p~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~al~~~p~~~~~  213 (365)
T 4eqf_A          141 VSYTNTSHQQDACEALKNWIKQN-------PKYKYLVKNKKGSPGLTRRMSKSPVDSSVLEGVKELYLEAAHQNGDMIDP  213 (365)
T ss_dssp             HHHHHTTCHHHHHHHHHHHHHHC-------HHHHCC-------------------CCHHHHHHHHHHHHHHHHSCSSCCH
T ss_pred             HHHHccccHHHHHHHHHHHHHhC-------ccchHHHhhhccchHHHHHHHHHHhhhhhHHHHHHHHHHHHHhCcCccCH
Confidence            99999999999999999998865       2223333          23466777778888888888877765321 146


Q ss_pred             hHHHHHHHHHHhcCCHHHHHHHHHHHHHCCCCCCHhhHHHHHHHHHhcCChHHHHHHHHHHHHCCCCCCHHHHHHHHHHH
Q 040027          243 VTYNSLIHGLCHANDWNEAKRLFIEMMDQGVQPSVVTFNVIMDELCKNRKMDEASRLLDLMVQRGVRPNACTYNTLMDGF  322 (595)
Q Consensus       243 ~~~~~ll~~~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~  322 (595)
                      .++..++..+...|++++|...|+++++.. +.+..++..++.++...|++++|...|+++.+.. +.+..++..++.+|
T Consensus       214 ~~~~~l~~~~~~~g~~~~A~~~~~~al~~~-p~~~~~~~~l~~~~~~~g~~~~A~~~~~~al~~~-p~~~~~~~~l~~~~  291 (365)
T 4eqf_A          214 DLQTGLGVLFHLSGEFNRAIDAFNAALTVR-PEDYSLWNRLGATLANGDRSEEAVEAYTRALEIQ-PGFIRSRYNLGISC  291 (365)
T ss_dssp             HHHHHHHHHHHHHTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHCCCHHHHHHHHHHHHHhC-CCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHhcC-CCchHHHHHHHHHH
Confidence            677777777777788888888777777652 2356667777777777777777777777776653 22466666777777


Q ss_pred             HhcCCHHHHHHHHHHHHhcCCC-----------CCHHHHHHHHHHHHhCCCHHHHHHHHH
Q 040027          323 CLMGKINRAEELFGSMESMGCK-----------HDDVSYNILINGYCKNKEVEEALSLYR  371 (595)
Q Consensus       323 ~~~~~~~~a~~~~~~~~~~~~~-----------~~~~~~~~l~~~~~~~~~~~~A~~~~~  371 (595)
                      ...|++++|...|+++.+....           .+...|..+..++...|+.+.+..+..
T Consensus       292 ~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~a~~~~~  351 (365)
T 4eqf_A          292 INLGAYREAVSNFLTALSLQRKSRNQQQVPHPAISGNIWAALRIALSLMDQPELFQAANL  351 (365)
T ss_dssp             HHHTCCHHHHHHHHHHHHHHHCC------------CHHHHHHHHHHHHHTCHHHHHHHHT
T ss_pred             HHCCCHHHHHHHHHHHHHhCcccCCCcccchhhhHHHHHHHHHHHHHHcCcHHHHHHHHH
Confidence            7777777777777776554200           013445555555555555555554443

>1b89_A Protein (clathrin heavy chain); triskelion, coated vesicles, endocytosis, SELF- assembly, alpha-alpha superhelix; 2.60A {Bos taurus} SCOP: a.118.1.3

Probab=99.81  E-value=3.5e-18  Score=161.47  Aligned_cols=284  Identities=11%  Similarity=0.094  Sum_probs=123.1

Q ss_pred             hcCChhHHHHHHHHHHhCCCCCCHHHHHHHHHHHHhcCCHhHHHHHHHHHHhcCCCCCHhhHHHHHHHHHhcCChhHHHH
Q 040027          108 KIGRVSLGFIAFGRILRSCFTPNAATFNSLIKGLHAESRIMEAAALFTKLKAFGCEPNVITYNTLINGLCRTGHTMIALN  187 (595)
Q Consensus       108 ~~g~~~~A~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~  187 (595)
                      +.|++++|...++++.      ++.+|..++.++.+.|++++|++.|.+.      +|...|..++..+...|++++|+.
T Consensus        15 ~~~~ld~A~~fae~~~------~~~vWs~La~A~l~~g~~~eAIdsfika------~D~~~y~~V~~~ae~~g~~EeAi~   82 (449)
T 1b89_A           15 HIGNLDRAYEFAERCN------EPAVWSQLAKAQLQKGMVKEAIDSYIKA------DDPSSYMEVVQAANTSGNWEELVK   82 (449)
T ss_dssp             --------------------------------------------------------------------------------
T ss_pred             HccCHHHHHHHHHhCC------ChHHHHHHHHHHHHcCCHHHHHHHHHcC------CCHHHHHHHHHHHHhCCCHHHHHH
Confidence            5678888888888872      3358888999999999999999888653      466788888888888999999998


Q ss_pred             HHHHHHhcCCCCCccccCcHHHHHHHHHHHHHcCCHhHHHHHHHHHhhCCCCCCHhHHHHHHHHHHhcCCHHHHHHHHHH
Q 040027          188 LFEEMANGNGEIGVVCKPNTVTYSTIIDGLCKEGFVDKAKALFLQMKDENINPDVVTYNSLIHGLCHANDWNEAKRLFIE  267 (595)
Q Consensus       188 ~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~~ll~~~~~~~~~~~A~~~~~~  267 (595)
                      .++...+..        +++.+.+.++.+|.+.|+++++.++++       .|+..+|..++..|...|.+++|...|..
T Consensus        83 yl~~ark~~--------~~~~i~~~Li~~Y~Klg~l~e~e~f~~-------~pn~~a~~~IGd~~~~~g~yeeA~~~Y~~  147 (449)
T 1b89_A           83 YLQMARKKA--------RESYVETELIFALAKTNRLAELEEFIN-------GPNNAHIQQVGDRCYDEKMYDAAKLLYNN  147 (449)
T ss_dssp             ----------------------------------CHHHHTTTTT-------CC----------------CTTTHHHHHHH
T ss_pred             HHHHHHHhC--------ccchhHHHHHHHHHHhCCHHHHHHHHc-------CCcHHHHHHHHHHHHHcCCHHHHHHHHHH
Confidence            777776632        446777888889999999888887774       25667888899999999999999999886


Q ss_pred             HHHCCCCCCHhhHHHHHHHHHhcCChHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHhcCCCCCH
Q 040027          268 MMDQGVQPSVVTFNVIMDELCKNRKMDEASRLLDLMVQRGVRPNACTYNTLMDGFCLMGKINRAEELFGSMESMGCKHDD  347 (595)
Q Consensus       268 ~~~~~~~~~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~  347 (595)
                      +         ..|..++.++.+.|++++|.+.+.++      .++.+|..++.+|...|+++.|......+.     ..+
T Consensus       148 a---------~n~~~LA~~L~~Lg~yq~AVea~~KA------~~~~~Wk~v~~aCv~~~ef~lA~~~~l~L~-----~~a  207 (449)
T 1b89_A          148 V---------SNFGRLASTLVHLGEYQAAVDGARKA------NSTRTWKEVCFACVDGKEFRLAQMCGLHIV-----VHA  207 (449)
T ss_dssp             T---------TCHHHHHHHHHTTTCHHHHHHHHHHH------TCHHHHHHHHHHHHHTTCHHHHHHTTTTTT-----TCH
T ss_pred             h---------hhHHHHHHHHHHhccHHHHHHHHHHc------CCchhHHHHHHHHHHcCcHHHHHHHHHHHH-----hCH
Confidence            5         36888888999999999999988887      267888888899999999998865554422     334


Q ss_pred             HHHHHHHHHHHhCCCHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHccCCHHHHHHHHHHHHHC-CCCC------CHHHH
Q 040027          348 VSYNILINGYCKNKEVEEALSLYREMVSKGIKPTVVTYNTLFLGLFEIHQVEHALKLFDEMQRD-GVAA------DTRTY  420 (595)
Q Consensus       348 ~~~~~l~~~~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~-~~~~------~~~~~  420 (595)
                      .....++..|.+.|++++|+.+++..+... +-....|+.+...+++- ++++..+.++..... +++|      +...|
T Consensus       208 d~l~~lv~~Yek~G~~eEai~lLe~aL~le-~ah~~~ftel~il~~ky-~p~k~~ehl~~~~~~ini~k~~~~~~~~~~w  285 (449)
T 1b89_A          208 DELEELINYYQDRGYFEELITMLEAALGLE-RAHMGMFTELAILYSKF-KPQKMREHLELFWSRVNIPKVLRAAEQAHLW  285 (449)
T ss_dssp             HHHHHHHHHHHHTTCHHHHHHHHHHHTTST-TCCHHHHHHHHHHHHTT-CHHHHHHHHHHHSTTSCHHHHHHHHHTTTCH
T ss_pred             hhHHHHHHHHHHCCCHHHHHHHHHHHhCCc-HHHHHHHHHHHHHHHhc-CHHHHHHHHHHHHHHhcCcHHHHHHHHHHHH
Confidence            445568888888999999999988887664 33556677766666553 344444444433322 2222      34567


Q ss_pred             HHHHHHHHhcCCHHHHHHHH
Q 040027          421 TTFIDGLCKNGYIIEAVELF  440 (595)
Q Consensus       421 ~~l~~~~~~~g~~~~A~~~~  440 (595)
                      ..+...|...++++.|....
T Consensus       286 ~e~~~ly~~~~e~d~A~~tm  305 (449)
T 1b89_A          286 AELVFLYDKYEEYDNAIITM  305 (449)
T ss_dssp             HHHHHHHHHTTCHHHHHHHH
T ss_pred             HHHHHHHHhhchHHHHHHHH
Confidence            77777888888888776643

>3cv0_A Peroxisome targeting signal 1 receptor PEX5; TPR motifs, TPR protein, peroxin 5, PEX5, PTS1 binding domain, protein-peptide complex, receptor; 2.00A {Trypanosoma brucei} PDB: 3cvl_A 3cvn_A 3cvp_A 3cvq_A

Probab=99.80  E-value=1.2e-17  Score=158.95  Aligned_cols=263  Identities=13%  Similarity=-0.024  Sum_probs=157.8

Q ss_pred             HHHHHHHHHhcCChHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHhcCCCCCHHHHHHHHHHHHh
Q 040027          280 FNVIMDELCKNRKMDEASRLLDLMVQRGVRPNACTYNTLMDGFCLMGKINRAEELFGSMESMGCKHDDVSYNILINGYCK  359 (595)
Q Consensus       280 ~~~l~~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~  359 (595)
                      +......+...|++++|..+++++.+.. +.+...+..++.++...|++++|...++++.+.. +.+...+..+...+..
T Consensus        24 ~~~~a~~~~~~~~~~~A~~~~~~~~~~~-~~~~~~~~~l~~~~~~~~~~~~A~~~~~~a~~~~-~~~~~~~~~la~~~~~  101 (327)
T 3cv0_A           24 PMEEGLSMLKLANLAEAALAFEAVCQAA-PEREEAWRSLGLTQAENEKDGLAIIALNHARMLD-PKDIAVHAALAVSHTN  101 (327)
T ss_dssp             HHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHhccHHHHHHHHHHHHHhC-CCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHhcC-cCCHHHHHHHHHHHHH
Confidence            3444444555555555555555554432 1234444455555555555555555555555442 3344455555555555


Q ss_pred             CCCHHHHHHHHHHHHHCCCCCCHHHHHHH--------------HH-HHHccCCHHHHHHHHHHHHHCCCCCCHHHHHHHH
Q 040027          360 NKEVEEALSLYREMVSKGIKPTVVTYNTL--------------FL-GLFEIHQVEHALKLFDEMQRDGVAADTRTYTTFI  424 (595)
Q Consensus       360 ~~~~~~A~~~~~~~~~~~~~~~~~~~~~l--------------~~-~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~  424 (595)
                      .|++++|...++++...... +...+..+              .. .+...|++++|...++++.+.. +.+...+..+.
T Consensus       102 ~~~~~~A~~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~A~~~~~~~~~~~-~~~~~~~~~la  179 (327)
T 3cv0_A          102 EHNANAALASLRAWLLSQPQ-YEQLGSVNLQADVDIDDLNVQSEDFFFAAPNEYRECRTLLHAALEMN-PNDAQLHASLG  179 (327)
T ss_dssp             TTCHHHHHHHHHHHHHTSTT-TTTC--------------------CCTTSHHHHHHHHHHHHHHHHHS-TTCHHHHHHHH
T ss_pred             cCCHHHHHHHHHHHHHhCCc-cHHHHHHHhHHHHHHHHHHHHHHhHHHHHcccHHHHHHHHHHHHhhC-CCCHHHHHHHH
Confidence            55555555555555544221 11111111              11 2566677777777777777653 44667777777


Q ss_pred             HHHHhcCCHHHHHHHHHHHHHcCCCcCHHHHHHHHHHHHhcCChHHHHHHHHhcccCCCCC-CHHHHHHHHHHHHhcCCh
Q 040027          425 DGLCKNGYIIEAVELFRTLRILKCELDIQAYNCLIDGLCKSGRLKFAWELFCSLPHGVLVP-NVVTYNIMIQGLCNDGQM  503 (595)
Q Consensus       425 ~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~p-~~~~~~~l~~~~~~~g~~  503 (595)
                      ..+...|++++|...++++.+.. +.+..++..++.++...|++++|...++++.+.  .| +...+..++.+|...|++
T Consensus       180 ~~~~~~~~~~~A~~~~~~~~~~~-~~~~~~~~~l~~~~~~~~~~~~A~~~~~~a~~~--~~~~~~~~~~l~~~~~~~g~~  256 (327)
T 3cv0_A          180 VLYNLSNNYDSAAANLRRAVELR-PDDAQLWNKLGATLANGNRPQEALDAYNRALDI--NPGYVRVMYNMAVSYSNMSQY  256 (327)
T ss_dssp             HHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH--CTTCHHHHHHHHHHHHHTTCH
T ss_pred             HHHHHhccHHHHHHHHHHHHHhC-CCcHHHHHHHHHHHHHcCCHHHHHHHHHHHHHc--CCCCHHHHHHHHHHHHHhccH
Confidence            77777777777777777777665 556677777777777777777777777777663  33 456777777777777777


Q ss_pred             hHHHHHHHHHHHcCCCC-----------CHHHHHHHHHHHHHcCChhHHHHHHHHHH
Q 040027          504 DKARDLFLDMEENAAAP-----------DVITFDMLIHGFIRINEPSKVNELLHKMK  549 (595)
Q Consensus       504 ~~A~~~~~~~~~~~~~~-----------~~~~~~~l~~~~~~~g~~~~A~~~~~~~~  549 (595)
                      ++|.+.++++.+.....           +...+..+..++...|++++|..++++..
T Consensus       257 ~~A~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~l  313 (327)
T 3cv0_A          257 DLAAKQLVRAIYMQVGGTTPTGEASREATRSMWDFFRMLLNVMNRPDLVELTYAQNV  313 (327)
T ss_dssp             HHHHHHHHHHHHHHTTSCC-----CCTHHHHHHHHHHHHHHHTTCHHHHHHHTTCCS
T ss_pred             HHHHHHHHHHHHhCCccccccccchhhcCHHHHHHHHHHHHhcCCHHHHHHHHHHHH
Confidence            77777777777653111           35667777777777777777777766543

>3mkr_A Coatomer subunit epsilon; tetratricopeptide repeats (TPR), beta-hairpin, alpha-solenoi transport protein; 2.60A {Bos taurus}

Probab=99.79  E-value=3.9e-17  Score=151.58  Aligned_cols=252  Identities=9%  Similarity=0.045  Sum_probs=145.6

Q ss_pred             HHHhcCChHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHhcCCCCCHHHHHHHHHHHHhCCCHHH
Q 040027          286 ELCKNRKMDEASRLLDLMVQRGVRPNACTYNTLMDGFCLMGKINRAEELFGSMESMGCKHDDVSYNILINGYCKNKEVEE  365 (595)
Q Consensus       286 ~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~  365 (595)
                      -....|++..|+..++.+..............+.++|...|+++.|+..++..    .+|+..++..+...+...++.++
T Consensus         8 ~~~~~g~y~~ai~~~~~~~~~~p~~~~e~~~~l~r~yi~~g~~~~al~~~~~~----~~~~~~a~~~la~~~~~~~~~~~   83 (291)
T 3mkr_A            8 NAFYIGSYQQCINEAQRVKPSSPERDVERDVFLYRAYLAQRKYGVVLDEIKPS----SAPELQAVRMFAEYLASHSRRDA   83 (291)
T ss_dssp             HHHHTTCHHHHHHHHHHSCCCSHHHHHHHHHHHHHHHHHTTCHHHHHHHSCTT----SCHHHHHHHHHHHHHHCSTTHHH
T ss_pred             HHHHHHHHHHHHHHHHhcccCCchhhHHHHHHHHHHHHHCCCHHHHHHHhccc----CChhHHHHHHHHHHHcCCCcHHH
Confidence            34455666666666655433211111223344556666666666666544331    23445556666666666666666


Q ss_pred             HHHHHHHHHHCCCCC-CHHHHHHHHHHHHccCCHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHH
Q 040027          366 ALSLYREMVSKGIKP-TVVTYNTLFLGLFEIHQVEHALKLFDEMQRDGVAADTRTYTTFIDGLCKNGYIIEAVELFRTLR  444 (595)
Q Consensus       366 A~~~~~~~~~~~~~~-~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~  444 (595)
                      |++.++++...+..| +...+..+...+...|++++|++.+++      +.+...+..++..+.+.|++++|...++++.
T Consensus        84 A~~~l~~ll~~~~~P~~~~~~~~la~~~~~~g~~~~Al~~l~~------~~~~~~~~~l~~~~~~~g~~~~A~~~l~~~~  157 (291)
T 3mkr_A           84 IVAELDREMSRSVDVTNTTFLLMAASIYFYDQNPDAALRTLHQ------GDSLECMAMTVQILLKLDRLDLARKELKKMQ  157 (291)
T ss_dssp             HHHHHHHHHHSCCCCSCHHHHHHHHHHHHHTTCHHHHHHHHTT------CCSHHHHHHHHHHHHHTTCHHHHHHHHHHHH
T ss_pred             HHHHHHHHHhcccCCCCHHHHHHHHHHHHHCCCHHHHHHHHhC------CCCHHHHHHHHHHHHHCCCHHHHHHHHHHHH
Confidence            666666666554323 344445555666666666666666655      3455666666666666777777777776666


Q ss_pred             HcCCCcCHHH--HHHHHHHHHhcCChHHHHHHHHhcccCCCCCCHHHHHHHHHHHHhcCChhHHHHHHHHHHHcCCCCCH
Q 040027          445 ILKCELDIQA--YNCLIDGLCKSGRLKFAWELFCSLPHGVLVPNVVTYNIMIQGLCNDGQMDKARDLFLDMEENAAAPDV  522 (595)
Q Consensus       445 ~~~~~~~~~~--~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~p~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~~~  522 (595)
                      +.. +.+...  ...++..+...|++++|..+|+++.+. .+.+...|+.++.++.+.|++++|+..|+++++.. +.+.
T Consensus       158 ~~~-p~~~~~~l~~a~~~l~~~~~~~~eA~~~~~~~l~~-~p~~~~~~~~la~~~~~~g~~~eA~~~l~~al~~~-p~~~  234 (291)
T 3mkr_A          158 DQD-EDATLTQLATAWVSLAAGGEKLQDAYYIFQEMADK-CSPTLLLLNGQAACHMAQGRWEAAEGVLQEALDKD-SGHP  234 (291)
T ss_dssp             HHC-TTCHHHHHHHHHHHHHHCTTHHHHHHHHHHHHHHH-SCCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCH
T ss_pred             hhC-cCcHHHHHHHHHHHHHhCchHHHHHHHHHHHHHHh-CCCcHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhC-CCCH
Confidence            553 222111  112223333446677777777776664 23356666667777777777777777777776654 4456


Q ss_pred             HHHHHHHHHHHHcCChhH-HHHHHHHHHH
Q 040027          523 ITFDMLIHGFIRINEPSK-VNELLHKMKE  550 (595)
Q Consensus       523 ~~~~~l~~~~~~~g~~~~-A~~~~~~~~~  550 (595)
                      .++..++.++...|+.++ +.++++++.+
T Consensus       235 ~~l~~l~~~~~~~g~~~eaa~~~~~~~~~  263 (291)
T 3mkr_A          235 ETLINLVVLSQHLGKPPEVTNRYLSQLKD  263 (291)
T ss_dssp             HHHHHHHHHHHHTTCCHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHcCCCHHHHHHHHHHHHH
Confidence            666666666777776654 4566666665

>1b89_A Protein (clathrin heavy chain); triskelion, coated vesicles, endocytosis, SELF- assembly, alpha-alpha superhelix; 2.60A {Bos taurus} SCOP: a.118.1.3

Probab=99.79  E-value=1.8e-18  Score=163.51  Aligned_cols=374  Identities=13%  Similarity=0.094  Sum_probs=187.5

Q ss_pred             HhcCCHhHHHHHHHHHHhcCCCCCHhhHHHHHHHHHhcCChhHHHHHHHHHHhcCCCCCccccCcHHHHHHHHHHHHHcC
Q 040027          142 HAESRIMEAAALFTKLKAFGCEPNVITYNTLINGLCRTGHTMIALNLFEEMANGNGEIGVVCKPNTVTYSTIIDGLCKEG  221 (595)
Q Consensus       142 ~~~g~~~~A~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g  221 (595)
                      .+.|++++|.+.++++.      ++.+|..++.++.+.|++++|++.|.+.            +|...|..++..+...|
T Consensus        14 ~~~~~ld~A~~fae~~~------~~~vWs~La~A~l~~g~~~eAIdsfika------------~D~~~y~~V~~~ae~~g   75 (449)
T 1b89_A           14 EHIGNLDRAYEFAERCN------EPAVWSQLAKAQLQKGMVKEAIDSYIKA------------DDPSSYMEVVQAANTSG   75 (449)
T ss_dssp             --------------------------------------------------------------------------------
T ss_pred             HHccCHHHHHHHHHhCC------ChHHHHHHHHHHHHcCCHHHHHHHHHcC------------CCHHHHHHHHHHHHhCC
Confidence            35688999999999983      3359999999999999999999999653            45678999999999999


Q ss_pred             CHhHHHHHHHHHhhCCCCCCHhHHHHHHHHHHhcCCHHHHHHHHHHHHHCCCCCCHhhHHHHHHHHHhcCChHHHHHHHH
Q 040027          222 FVDKAKALFLQMKDENINPDVVTYNSLIHGLCHANDWNEAKRLFIEMMDQGVQPSVVTFNVIMDELCKNRKMDEASRLLD  301 (595)
Q Consensus       222 ~~~~A~~~~~~~~~~~~~~~~~~~~~ll~~~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~a~~~~~  301 (595)
                      ++++|+.+++..++.  .+++.+.+.++.+|.+.|+++++.++++       .|+..+|..++..|...|.+++|..+|.
T Consensus        76 ~~EeAi~yl~~ark~--~~~~~i~~~Li~~Y~Klg~l~e~e~f~~-------~pn~~a~~~IGd~~~~~g~yeeA~~~Y~  146 (449)
T 1b89_A           76 NWEELVKYLQMARKK--ARESYVETELIFALAKTNRLAELEEFIN-------GPNNAHIQQVGDRCYDEKMYDAAKLLYN  146 (449)
T ss_dssp             -----------------------------------CHHHHTTTTT-------CC----------------CTTTHHHHHH
T ss_pred             CHHHHHHHHHHHHHh--CccchhHHHHHHHHHHhCCHHHHHHHHc-------CCcHHHHHHHHHHHHHcCCHHHHHHHHH
Confidence            999999988877764  4467888999999999999999988884       3677799999999999999999999999


Q ss_pred             HHHHCCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHhcCCCCCHHHHHHHHHHHHhCCCHHHHHHHHHHHHHCCCCCC
Q 040027          302 LMVQRGVRPNACTYNTLMDGFCLMGKINRAEELFGSMESMGCKHDDVSYNILINGYCKNKEVEEALSLYREMVSKGIKPT  381 (595)
Q Consensus       302 ~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~~~~~~~  381 (595)
                      .+         ..|..++.++.+.|++++|.+.+.++      .++.+|..++.+|...|+++.|......+.     ..
T Consensus       147 ~a---------~n~~~LA~~L~~Lg~yq~AVea~~KA------~~~~~Wk~v~~aCv~~~ef~lA~~~~l~L~-----~~  206 (449)
T 1b89_A          147 NV---------SNFGRLASTLVHLGEYQAAVDGARKA------NSTRTWKEVCFACVDGKEFRLAQMCGLHIV-----VH  206 (449)
T ss_dssp             HT---------TCHHHHHHHHHTTTCHHHHHHHHHHH------TCHHHHHHHHHHHHHTTCHHHHHHTTTTTT-----TC
T ss_pred             Hh---------hhHHHHHHHHHHhccHHHHHHHHHHc------CCchhHHHHHHHHHHcCcHHHHHHHHHHHH-----hC
Confidence            76         36889999999999999999999988      268899999999999999999966655432     24


Q ss_pred             HHHHHHHHHHHHccCCHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHH-cCCCc------CHHH
Q 040027          382 VVTYNTLFLGLFEIHQVEHALKLFDEMQRDGVAADTRTYTTFIDGLCKNGYIIEAVELFRTLRI-LKCEL------DIQA  454 (595)
Q Consensus       382 ~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~-~~~~~------~~~~  454 (595)
                      +.....++..|.+.|+++++..+++..+... +....+|+.+.-+|++- ++++..+.++...+ .++++      +...
T Consensus       207 ad~l~~lv~~Yek~G~~eEai~lLe~aL~le-~ah~~~ftel~il~~ky-~p~k~~ehl~~~~~~ini~k~~~~~~~~~~  284 (449)
T 1b89_A          207 ADELEELINYYQDRGYFEELITMLEAALGLE-RAHMGMFTELAILYSKF-KPQKMREHLELFWSRVNIPKVLRAAEQAHL  284 (449)
T ss_dssp             HHHHHHHHHHHHHTTCHHHHHHHHHHHTTST-TCCHHHHHHHHHHHHTT-CHHHHHHHHHHHSTTSCHHHHHHHHHTTTC
T ss_pred             HhhHHHHHHHHHHCCCHHHHHHHHHHHhCCc-HHHHHHHHHHHHHHHhc-CHHHHHHHHHHHHHHhcCcHHHHHHHHHHH
Confidence            4445678889999999999999999998775 66677888887777764 35555544443332 23333      4667


Q ss_pred             HHHHHHHHHhcCChHHHHHHHHhcccCC-----------CCCCHHHHHHHHHHHHhcCChhHHHHHHHHHHHcCCCCCHH
Q 040027          455 YNCLIDGLCKSGRLKFAWELFCSLPHGV-----------LVPNVVTYNIMIQGLCNDGQMDKARDLFLDMEENAAAPDVI  523 (595)
Q Consensus       455 ~~~l~~~~~~~g~~~~A~~~~~~~~~~~-----------~~p~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~~~~  523 (595)
                      |..++..|...++++.|....-+-....           -..|...|...+..|.  +....++.-+...+..  ..|. 
T Consensus       285 w~e~~~ly~~~~e~d~A~~tm~~h~~~a~~~~~f~~~~~kv~n~elyYkai~fyl--~~~p~~l~~ll~~l~~--~ld~-  359 (449)
T 1b89_A          285 WAELVFLYDKYEEYDNAIITMMNHPTDAWKEGQFKDIITKVANVELYYRAIQFYL--EFKPLLLNDLLMVLSP--RLDH-  359 (449)
T ss_dssp             HHHHHHHHHHTTCHHHHHHHHHHSTTTTCCHHHHHHHHHHCSSTHHHHHHHHHHH--HHCGGGHHHHHHHHGG--GCCH-
T ss_pred             HHHHHHHHHhhchHHHHHHHHHhCChhhhhhHHHHHHHhchhHHHHHHHHHHHHH--hcCHHHHHHHHHHHHh--ccCc-
Confidence            8899999999999998877544332110           1235666666666666  2223333333333322  1222 


Q ss_pred             HHHHHHHHHHHcCChhHHHHHHHHHHHCCCCCCHHHHHHHHHHHHhcCccc
Q 040027          524 TFDMLIHGFIRINEPSKVNELLHKMKEKKVMPDASIVSIVVDLLVKNEISL  574 (595)
Q Consensus       524 ~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~p~~~~~~~l~~~~~~~g~~~  574 (595)
                        ...+..+.+.|+..-+..+++.+...+   +..+-.++-+.|....+++
T Consensus       360 --~r~v~~~~~~~~l~l~~~yl~~v~~~n---~~~vnealn~l~ieeed~~  405 (449)
T 1b89_A          360 --TRAVNYFSKVKQLPLVKPYLRSVQNHN---NKSVNESLNNLFITEEDYQ  405 (449)
T ss_dssp             --HHHHHHHHHTTCTTTTHHHHHHHHTTC---CHHHHHHHHHHHHHTTCHH
T ss_pred             --HHHHHHHHHcCCcHHHHHHHHHHHHhh---HHHHHHHHHHHHHhhhhHH
Confidence              345556678888888888887777543   5677777777888777776

>3cv0_A Peroxisome targeting signal 1 receptor PEX5; TPR motifs, TPR protein, peroxin 5, PEX5, PTS1 binding domain, protein-peptide complex, receptor; 2.00A {Trypanosoma brucei} PDB: 3cvl_A 3cvn_A 3cvp_A 3cvq_A

Probab=99.79  E-value=2.5e-17  Score=156.85  Aligned_cols=278  Identities=8%  Similarity=-0.064  Sum_probs=174.9

Q ss_pred             HHHHHHHHHHHHHcCCHhHHHHHHHHHhhCCCCCCHhHHHHHHHHHHhcCCHHHHHHHHHHHHHCCCCCCHhhHHHHHHH
Q 040027          207 TVTYSTIIDGLCKEGFVDKAKALFLQMKDENINPDVVTYNSLIHGLCHANDWNEAKRLFIEMMDQGVQPSVVTFNVIMDE  286 (595)
Q Consensus       207 ~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~~ll~~~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~~l~~~  286 (595)
                      ...+..+...+...|++++|..+|+++.+.. +.+...+..++..+...|++++|...++++.+.. +.+...+..+...
T Consensus        21 ~~~~~~~a~~~~~~~~~~~A~~~~~~~~~~~-~~~~~~~~~l~~~~~~~~~~~~A~~~~~~a~~~~-~~~~~~~~~la~~   98 (327)
T 3cv0_A           21 HENPMEEGLSMLKLANLAEAALAFEAVCQAA-PEREEAWRSLGLTQAENEKDGLAIIALNHARMLD-PKDIAVHAALAVS   98 (327)
T ss_dssp             SSCHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHH
T ss_pred             hHHHHHHHHHHHHhccHHHHHHHHHHHHHhC-CCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHhcC-cCCHHHHHHHHHH
Confidence            3456667777777788888888887777653 2356677777777777777777777777777652 2355666677777


Q ss_pred             HHhcCChHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHhcCCCCCHHHHHHH-HH-HHHhCCCHH
Q 040027          287 LCKNRKMDEASRLLDLMVQRGVRPNACTYNTLMDGFCLMGKINRAEELFGSMESMGCKHDDVSYNIL-IN-GYCKNKEVE  364 (595)
Q Consensus       287 ~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l-~~-~~~~~~~~~  364 (595)
                      +...|++++|...++++.+.... +...+..+....                      ++......+ .. .+...|+++
T Consensus        99 ~~~~~~~~~A~~~~~~~~~~~~~-~~~~~~~~~~~~----------------------~~~~~~~~~~~~~~~~~~~~~~  155 (327)
T 3cv0_A           99 HTNEHNANAALASLRAWLLSQPQ-YEQLGSVNLQAD----------------------VDIDDLNVQSEDFFFAAPNEYR  155 (327)
T ss_dssp             HHHTTCHHHHHHHHHHHHHTSTT-TTTC------------------------------------------CCTTSHHHHH
T ss_pred             HHHcCCHHHHHHHHHHHHHhCCc-cHHHHHHHhHHH----------------------HHHHHHHHHHHhHHHHHcccHH
Confidence            77777777777777777765322 222222220000                      000001111 11 245556666


Q ss_pred             HHHHHHHHHHHCCCCCCHHHHHHHHHHHHccCCHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHH
Q 040027          365 EALSLYREMVSKGIKPTVVTYNTLFLGLFEIHQVEHALKLFDEMQRDGVAADTRTYTTFIDGLCKNGYIIEAVELFRTLR  444 (595)
Q Consensus       365 ~A~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~  444 (595)
                      +|...++++.+.... +...+..+...+...|++++|...++++.+.. +.+...+..+...+...|++++|...++++.
T Consensus       156 ~A~~~~~~~~~~~~~-~~~~~~~la~~~~~~~~~~~A~~~~~~~~~~~-~~~~~~~~~l~~~~~~~~~~~~A~~~~~~a~  233 (327)
T 3cv0_A          156 ECRTLLHAALEMNPN-DAQLHASLGVLYNLSNNYDSAAANLRRAVELR-PDDAQLWNKLGATLANGNRPQEALDAYNRAL  233 (327)
T ss_dssp             HHHHHHHHHHHHSTT-CHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHhhCCC-CHHHHHHHHHHHHHhccHHHHHHHHHHHHHhC-CCcHHHHHHHHHHHHHcCCHHHHHHHHHHHH
Confidence            676666666655332 55666666666677777777777777666552 4456667777777777777777777777777


Q ss_pred             HcCCCcCHHHHHHHHHHHHhcCChHHHHHHHHhcccCCCCCC-------------HHHHHHHHHHHHhcCChhHHHHHHH
Q 040027          445 ILKCELDIQAYNCLIDGLCKSGRLKFAWELFCSLPHGVLVPN-------------VVTYNIMIQGLCNDGQMDKARDLFL  511 (595)
Q Consensus       445 ~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~p~-------------~~~~~~l~~~~~~~g~~~~A~~~~~  511 (595)
                      +.. +.+...+..++.++...|++++|...++++...  .|+             ...|..+..++...|++++|..+++
T Consensus       234 ~~~-~~~~~~~~~l~~~~~~~g~~~~A~~~~~~a~~~--~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~  310 (327)
T 3cv0_A          234 DIN-PGYVRVMYNMAVSYSNMSQYDLAAKQLVRAIYM--QVGGTTPTGEASREATRSMWDFFRMLLNVMNRPDLVELTYA  310 (327)
T ss_dssp             HHC-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH--HTTSCC-----CCTHHHHHHHHHHHHHHHTTCHHHHHHHTT
T ss_pred             HcC-CCCHHHHHHHHHHHHHhccHHHHHHHHHHHHHh--CCccccccccchhhcCHHHHHHHHHHHHhcCCHHHHHHHHH
Confidence            654 456677777777777777777777777777652  233             5677777788888888888877776


Q ss_pred             HHH
Q 040027          512 DME  514 (595)
Q Consensus       512 ~~~  514 (595)
                      +.+
T Consensus       311 ~~l  313 (327)
T 3cv0_A          311 QNV  313 (327)
T ss_dssp             CCS
T ss_pred             HHH
Confidence            543

>3mkr_A Coatomer subunit epsilon; tetratricopeptide repeats (TPR), beta-hairpin, alpha-solenoi transport protein; 2.60A {Bos taurus}

Probab=99.79  E-value=9.3e-17  Score=149.04  Aligned_cols=247  Identities=11%  Similarity=0.016  Sum_probs=126.5

Q ss_pred             HHHcCCHhHHHHHHHHHhhCCCCCC--HhHHHHHHHHHHhcCCHHHHHHHHHHHHHCCCCCCHhhHHHHHHHHHhcCChH
Q 040027          217 LCKEGFVDKAKALFLQMKDENINPD--VVTYNSLIHGLCHANDWNEAKRLFIEMMDQGVQPSVVTFNVIMDELCKNRKMD  294 (595)
Q Consensus       217 ~~~~g~~~~A~~~~~~~~~~~~~~~--~~~~~~ll~~~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~  294 (595)
                      ....|++++|+..++.....  .|+  ......+..+|...|+++.|+..++.    .-+|+..++..+...+...++.+
T Consensus         9 ~~~~g~y~~ai~~~~~~~~~--~p~~~~e~~~~l~r~yi~~g~~~~al~~~~~----~~~~~~~a~~~la~~~~~~~~~~   82 (291)
T 3mkr_A            9 AFYIGSYQQCINEAQRVKPS--SPERDVERDVFLYRAYLAQRKYGVVLDEIKP----SSAPELQAVRMFAEYLASHSRRD   82 (291)
T ss_dssp             HHHTTCHHHHHHHHHHSCCC--SHHHHHHHHHHHHHHHHHTTCHHHHHHHSCT----TSCHHHHHHHHHHHHHHCSTTHH
T ss_pred             HHHHHHHHHHHHHHHhcccC--CchhhHHHHHHHHHHHHHCCCHHHHHHHhcc----cCChhHHHHHHHHHHHcCCCcHH
Confidence            44456666666666554432  122  22334455666666666666654433    12334455555566666666666


Q ss_pred             HHHHHHHHHHHCCC-CCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHhcCCCCCHHHHHHHHHHHHhCCCHHHHHHHHHHH
Q 040027          295 EASRLLDLMVQRGV-RPNACTYNTLMDGFCLMGKINRAEELFGSMESMGCKHDDVSYNILINGYCKNKEVEEALSLYREM  373 (595)
Q Consensus       295 ~a~~~~~~~~~~~~-~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~A~~~~~~~  373 (595)
                      +|++.++++...+. +.+...+..+..++...|++++|+..+++      +.+...+..++..+.+.|++++|.+.++++
T Consensus        83 ~A~~~l~~ll~~~~~P~~~~~~~~la~~~~~~g~~~~Al~~l~~------~~~~~~~~~l~~~~~~~g~~~~A~~~l~~~  156 (291)
T 3mkr_A           83 AIVAELDREMSRSVDVTNTTFLLMAASIYFYDQNPDAALRTLHQ------GDSLECMAMTVQILLKLDRLDLARKELKKM  156 (291)
T ss_dssp             HHHHHHHHHHHSCCCCSCHHHHHHHHHHHHHTTCHHHHHHHHTT------CCSHHHHHHHHHHHHHTTCHHHHHHHHHHH
T ss_pred             HHHHHHHHHHhcccCCCCHHHHHHHHHHHHHCCCHHHHHHHHhC------CCCHHHHHHHHHHHHHCCCHHHHHHHHHHH
Confidence            66666666655442 22344455555666666666666666654      344555556666666666666666666666


Q ss_pred             HHCCCCCCHHHHHHH----HHHHHccCCHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHHcCCC
Q 040027          374 VSKGIKPTVVTYNTL----FLGLFEIHQVEHALKLFDEMQRDGVAADTRTYTTFIDGLCKNGYIIEAVELFRTLRILKCE  449 (595)
Q Consensus       374 ~~~~~~~~~~~~~~l----~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~  449 (595)
                      .+..  |+.. ...+    +..+...|++++|..+|+++.+. .+.+...++.+..++.+.|++++|...++++++.. +
T Consensus       157 ~~~~--p~~~-~~~l~~a~~~l~~~~~~~~eA~~~~~~~l~~-~p~~~~~~~~la~~~~~~g~~~eA~~~l~~al~~~-p  231 (291)
T 3mkr_A          157 QDQD--EDAT-LTQLATAWVSLAAGGEKLQDAYYIFQEMADK-CSPTLLLLNGQAACHMAQGRWEAAEGVLQEALDKD-S  231 (291)
T ss_dssp             HHHC--TTCH-HHHHHHHHHHHHHCTTHHHHHHHHHHHHHHH-SCCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-T
T ss_pred             HhhC--cCcH-HHHHHHHHHHHHhCchHHHHHHHHHHHHHHh-CCCcHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhC-C
Confidence            5542  2221 1111    12222334555555555555544 23444455555555555555555555555555443 3


Q ss_pred             cCHHHHHHHHHHHHhcCChHH-HHHHHHhccc
Q 040027          450 LDIQAYNCLIDGLCKSGRLKF-AWELFCSLPH  480 (595)
Q Consensus       450 ~~~~~~~~l~~~~~~~g~~~~-A~~~~~~~~~  480 (595)
                      .++.++..++.++...|+.++ +.++++++.+
T Consensus       232 ~~~~~l~~l~~~~~~~g~~~eaa~~~~~~~~~  263 (291)
T 3mkr_A          232 GHPETLINLVVLSQHLGKPPEVTNRYLSQLKD  263 (291)
T ss_dssp             TCHHHHHHHHHHHHHTTCCHHHHHHHHHHHHH
T ss_pred             CCHHHHHHHHHHHHHcCCCHHHHHHHHHHHHH
Confidence            344455555555555555433 3444444444

>3e4b_A ALGK; tetratricopeptide repeat, superhelix, alginate biosynt pseudomonas, protein binding; 2.50A {Pseudomonas fluorescens}

Probab=99.75  E-value=2.4e-16  Score=156.19  Aligned_cols=188  Identities=11%  Similarity=-0.018  Sum_probs=97.1

Q ss_pred             HHHHHHHHHHhcC---CHHHHHHHHHHHHhcCCCCCHHHHHHHHHHHHhC----CCHHHHHHHHHHHHHCCCCCCHHHHH
Q 040027          314 TYNTLMDGFCLMG---KINRAEELFGSMESMGCKHDDVSYNILINGYCKN----KEVEEALSLYREMVSKGIKPTVVTYN  386 (595)
Q Consensus       314 ~~~~l~~~~~~~~---~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~----~~~~~A~~~~~~~~~~~~~~~~~~~~  386 (595)
                      .+..+..+|...|   +.++|+..|++..+.| +++...+..+..+|...    +++++|+..|++.. .   -+...+.
T Consensus       178 a~~~Lg~~~~~~g~~~~~~~A~~~~~~aa~~g-~~~a~~~~~Lg~~y~~g~~~~~d~~~A~~~~~~aa-~---g~~~a~~  252 (452)
T 3e4b_A          178 CYVELATVYQKKQQPEQQAELLKQMEAGVSRG-TVTAQRVDSVARVLGDATLGTPDEKTAQALLEKIA-P---GYPASWV  252 (452)
T ss_dssp             HHHHHHHHHHHTTCHHHHHHHHHHHHHHHHTT-CSCHHHHHHHHHHHTCGGGSSCCHHHHHHHHHHHG-G---GSTHHHH
T ss_pred             HHHHHHHHHHHcCCcccHHHHHHHHHHHHHCC-CHHHHHHHHHHHHHhCCCCCCCCHHHHHHHHHHHc-C---CCHHHHH
Confidence            4445555555555   5555555555555554 33333334444444333    45556666665554 2   1333444


Q ss_pred             HHHHH-H--HccCCHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHhcC-----CHHHHHHHHHHHHHcCCCcCHHHHHHH
Q 040027          387 TLFLG-L--FEIHQVEHALKLFDEMQRDGVAADTRTYTTFIDGLCKNG-----YIIEAVELFRTLRILKCELDIQAYNCL  458 (595)
Q Consensus       387 ~l~~~-~--~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g-----~~~~A~~~~~~~~~~~~~~~~~~~~~l  458 (595)
                      .+... +  ...+++++|...|++..+.|   +...+..+...|. .|     ++++|..+|++..    +.++.....+
T Consensus       253 ~Lg~~~~~~~~~~d~~~A~~~~~~Aa~~g---~~~A~~~Lg~~y~-~G~g~~~d~~~A~~~~~~Aa----~g~~~A~~~L  324 (452)
T 3e4b_A          253 SLAQLLYDFPELGDVEQMMKYLDNGRAAD---QPRAELLLGKLYY-EGKWVPADAKAAEAHFEKAV----GREVAADYYL  324 (452)
T ss_dssp             HHHHHHHHSGGGCCHHHHHHHHHHHHHTT---CHHHHHHHHHHHH-HCSSSCCCHHHHHHHHHTTT----TTCHHHHHHH
T ss_pred             HHHHHHHhCCCCCCHHHHHHHHHHHHHCC---CHHHHHHHHHHHH-cCCCCCCCHHHHHHHHHHHh----CCCHHHHHHH
Confidence            44443 2  34556666666666655543   4444444554444 33     6666666666655    2245555555


Q ss_pred             HHHHHh----cCChHHHHHHHHhcccCCCCCCHHHHHHHHHHHHh----cCChhHHHHHHHHHHHcC
Q 040027          459 IDGLCK----SGRLKFAWELFCSLPHGVLVPNVVTYNIMIQGLCN----DGQMDKARDLFLDMEENA  517 (595)
Q Consensus       459 ~~~~~~----~g~~~~A~~~~~~~~~~~~~p~~~~~~~l~~~~~~----~g~~~~A~~~~~~~~~~~  517 (595)
                      ..+|..    ..++++|...|++..+.|   +......|...|..    ..++.+|...|+...+.|
T Consensus       325 g~~y~~G~g~~~d~~~A~~~~~~Aa~~g---~~~A~~~Lg~~y~~G~g~~~d~~~A~~~~~~A~~~g  388 (452)
T 3e4b_A          325 GQIYRRGYLGKVYPQKALDHLLTAARNG---QNSADFAIAQLFSQGKGTKPDPLNAYVFSQLAKAQD  388 (452)
T ss_dssp             HHHHHTTTTSSCCHHHHHHHHHHHHTTT---CTTHHHHHHHHHHSCTTBCCCHHHHHHHHHHHHTTC
T ss_pred             HHHHHCCCCCCcCHHHHHHHHHHHHhhC---hHHHHHHHHHHHHhCCCCCCCHHHHHHHHHHHHHCC
Confidence            555554    236666666666665533   23344445555542    346666666666666654

>3e4b_A ALGK; tetratricopeptide repeat, superhelix, alginate biosynt pseudomonas, protein binding; 2.50A {Pseudomonas fluorescens}

Probab=99.73  E-value=5e-16  Score=153.96  Aligned_cols=379  Identities=10%  Similarity=-0.029  Sum_probs=255.8

Q ss_pred             HHHHHHHhcCChhHHHHHHHHHHhCCCCCCHHHHHHHHHHHHhcCCH---hHHHHHHHHHHhcCCCCCHhhHHHHHHHHH
Q 040027          101 ILINCFCKIGRVSLGFIAFGRILRSCFTPNAATFNSLIKGLHAESRI---MEAAALFTKLKAFGCEPNVITYNTLINGLC  177 (595)
Q Consensus       101 ~l~~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~---~~A~~~~~~~~~~~~~~~~~~~~~l~~~~~  177 (595)
                      .+...+.+.|++++|+.+|+++.+.|   ++.++..+...|...|+.   ++|.++|++..+.    ++..+..+...+.
T Consensus         8 ~la~~~~~~g~~~~A~~~~~~aa~~g---~~~A~~~Lg~~y~~~g~~~d~~~A~~~~~~A~~~----~~~A~~~Lg~~~~   80 (452)
T 3e4b_A            8 RLANEALKRGDTVTAQQNYQQLAELG---YSEAQVGLADIQVGTRDPAQIKQAEATYRAAADT----SPRAQARLGRLLA   80 (452)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHT---CCTGGGTCC--------------------------------CHHHHHHHHH
T ss_pred             HHHHHHHhCCCHHHHHHHHHHHHHCC---CHHHHHHHHHHHHccCCCCCHHHHHHHHHHHHhC----CHHHHHHHHHHHH
Confidence            36677888999999999999999875   455566677777778888   9999999999864    6667777887666


Q ss_pred             hcC-----ChhHHHHHHHHHHhcCCCCCccccCcHHHHHHHHHHHHHcCCHh---HHHHHHHHHhhCCCCCCHhHHHHHH
Q 040027          178 RTG-----HTMIALNLFEEMANGNGEIGVVCKPNTVTYSTIIDGLCKEGFVD---KAKALFLQMKDENINPDVVTYNSLI  249 (595)
Q Consensus       178 ~~g-----~~~~A~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~---~A~~~~~~~~~~~~~~~~~~~~~ll  249 (595)
                      ..|     ++++|+..|++....+         ++..+..|...|...+..+   ++.+.+......|   +...+..|.
T Consensus        81 ~~~~~~~~~~~~A~~~~~~Aa~~g---------~~~A~~~Lg~~y~~~~~~~~~~~a~~~~~~a~~~g---~~~a~~~Lg  148 (452)
T 3e4b_A           81 AKPGATEAEHHEAESLLKKAFANG---------EGNTLIPLAMLYLQYPHSFPNVNAQQQISQWQAAG---YPEAGLAQV  148 (452)
T ss_dssp             TC--CCHHHHHHHHHHHHHHHHTT---------CSSCHHHHHHHHHHCGGGCTTCCHHHHHHHHHHHT---CTTHHHHHH
T ss_pred             hCCCCCCcCHHHHHHHHHHHHHCC---------CHHHHHHHHHHHHhCCCCCCCHHHHHHHHHHHHCC---CHHHHHHHH
Confidence            655     7889999999999865         2346777888888766544   4555555555544   456777788


Q ss_pred             HHHHhcCCHHHHHHHHHHHHHCCCCCCHhhHHHHHHHHHhcC---ChHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHhc-
Q 040027          250 HGLCHANDWNEAKRLFIEMMDQGVQPSVVTFNVIMDELCKNR---KMDEASRLLDLMVQRGVRPNACTYNTLMDGFCLM-  325 (595)
Q Consensus       250 ~~~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g---~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~-  325 (595)
                      ..|...+.++++......+.+.-...++..+..+...|...|   +.++|...|++..+.|.. +...+..+..+|... 
T Consensus       149 ~~y~~~~~~~~~~~~a~~~~~~a~~~~~~a~~~Lg~~~~~~g~~~~~~~A~~~~~~aa~~g~~-~a~~~~~Lg~~y~~g~  227 (452)
T 3e4b_A          149 LLYRTQGTYDQHLDDVERICKAALNTTDICYVELATVYQKKQQPEQQAELLKQMEAGVSRGTV-TAQRVDSVARVLGDAT  227 (452)
T ss_dssp             HHHHHHTCGGGGHHHHHHHHHHHTTTCTTHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHTTCS-CHHHHHHHHHHHTCGG
T ss_pred             HHHHcCCCcccCHHHHHHHHHHHHcCCHHHHHHHHHHHHHcCCcccHHHHHHHHHHHHHCCCH-HHHHHHHHHHHHhCCC
Confidence            888888855554444333322212234448888999999999   999999999999998743 555556677777655 


Q ss_pred             ---CCHHHHHHHHHHHHhcCCCCCHHHHHHHHHH-H--HhCCCHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHccC---
Q 040027          326 ---GKINRAEELFGSMESMGCKHDDVSYNILING-Y--CKNKEVEEALSLYREMVSKGIKPTVVTYNTLFLGLFEIH---  396 (595)
Q Consensus       326 ---~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~-~--~~~~~~~~A~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~---  396 (595)
                         +++++|+..|++.. .   -+...+..+... +  ...+++++|+..|++..+.|   +...+..+...|. .|   
T Consensus       228 ~~~~d~~~A~~~~~~aa-~---g~~~a~~~Lg~~~~~~~~~~d~~~A~~~~~~Aa~~g---~~~A~~~Lg~~y~-~G~g~  299 (452)
T 3e4b_A          228 LGTPDEKTAQALLEKIA-P---GYPASWVSLAQLLYDFPELGDVEQMMKYLDNGRAAD---QPRAELLLGKLYY-EGKWV  299 (452)
T ss_dssp             GSSCCHHHHHHHHHHHG-G---GSTHHHHHHHHHHHHSGGGCCHHHHHHHHHHHHHTT---CHHHHHHHHHHHH-HCSSS
T ss_pred             CCCCCHHHHHHHHHHHc-C---CCHHHHHHHHHHHHhCCCCCCHHHHHHHHHHHHHCC---CHHHHHHHHHHHH-cCCCC
Confidence               78999999999988 3   356677777777 4  46899999999999999875   6677777777776 55   


Q ss_pred             --CHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHh----cCCHHHHHHHHHHHHHcCCCcCHHHHHHHHHHHHh----cC
Q 040027          397 --QVEHALKLFDEMQRDGVAADTRTYTTFIDGLCK----NGYIIEAVELFRTLRILKCELDIQAYNCLIDGLCK----SG  466 (595)
Q Consensus       397 --~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~----~g~~~~A~~~~~~~~~~~~~~~~~~~~~l~~~~~~----~g  466 (595)
                        ++++|...|++.. .   .+......+...|..    ..++++|..+|++..+.+   +......+..+|..    ..
T Consensus       300 ~~d~~~A~~~~~~Aa-~---g~~~A~~~Lg~~y~~G~g~~~d~~~A~~~~~~Aa~~g---~~~A~~~Lg~~y~~G~g~~~  372 (452)
T 3e4b_A          300 PADAKAAEAHFEKAV-G---REVAADYYLGQIYRRGYLGKVYPQKALDHLLTAARNG---QNSADFAIAQLFSQGKGTKP  372 (452)
T ss_dssp             CCCHHHHHHHHHTTT-T---TCHHHHHHHHHHHHTTTTSSCCHHHHHHHHHHHHTTT---CTTHHHHHHHHHHSCTTBCC
T ss_pred             CCCHHHHHHHHHHHh-C---CCHHHHHHHHHHHHCCCCCCcCHHHHHHHHHHHHhhC---hHHHHHHHHHHHHhCCCCCC
Confidence              9999999999887 3   466777777777766    349999999999999866   34556677777764    46


Q ss_pred             ChHHHHHHHHhcccCCCCCCHHHHHHHHHHHHhcCChhHHHHHHHHHHH
Q 040027          467 RLKFAWELFCSLPHGVLVPNVVTYNIMIQGLCNDGQMDKARDLFLDMEE  515 (595)
Q Consensus       467 ~~~~A~~~~~~~~~~~~~p~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~  515 (595)
                      +.++|...|+...+.|. ++.......+......++..+|..+.++...
T Consensus       373 d~~~A~~~~~~A~~~g~-~~a~~~l~~l~~~~~~~~~~~a~~~~~~~~~  420 (452)
T 3e4b_A          373 DPLNAYVFSQLAKAQDT-PEANDLATQLEAPLTPAQRAEGQRLVQQELA  420 (452)
T ss_dssp             CHHHHHHHHHHHHTTCC-HHHHHHHHHHHTTCCHHHHHHHHHHHHHHHH
T ss_pred             CHHHHHHHHHHHHHCCC-HHHHHHHHHHHHhCCHHHHHHHHHHHHHHHH
Confidence            89999999999988652 2222222222222233455666666666554

>2pl2_A Hypothetical conserved protein TTC0263; TPR, protein binding; 2.50A {Thermus thermophilus}

Probab=99.72  E-value=7.3e-16  Score=136.62  Aligned_cols=198  Identities=10%  Similarity=-0.025  Sum_probs=106.9

Q ss_pred             CHHHHHHHHHHHHhCCCHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHccCCHHHHHHHHHHHHHCCCCCCHHHHHHHHH
Q 040027          346 DDVSYNILINGYCKNKEVEEALSLYREMVSKGIKPTVVTYNTLFLGLFEIHQVEHALKLFDEMQRDGVAADTRTYTTFID  425 (595)
Q Consensus       346 ~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~  425 (595)
                      +...+..+...+.+.|++++|+..|+++++..+. +...+..+...+...|++++|+..+++..+.. |.+...+..+..
T Consensus         4 ~~~~~~~lg~~~~~~g~~~~A~~~~~~al~~~p~-~~~a~~~lg~~~~~~g~~~~A~~~~~~al~~~-P~~~~a~~~lg~   81 (217)
T 2pl2_A            4 AEQNPLRLGVQLYALGRYDAALTLFERALKENPQ-DPEALYWLARTQLKLGLVNPALENGKTLVART-PRYLGGYMVLSE   81 (217)
T ss_dssp             CCHHHHHHHHHHHHTTCHHHHHHHHHHHHTTSSS-CHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHH
T ss_pred             cHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCCC-CHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhC-CCcHHHHHHHHH
Confidence            3344444444445555555555555554443222 34444444444445555555555555444432 333444444444


Q ss_pred             HHHhc-----------CCHHHHHHHHHHHHHcCCCcCHHHHHHHHHHHHhcCChHHHHHHHHhcccCCCCCCHHHHHHHH
Q 040027          426 GLCKN-----------GYIIEAVELFRTLRILKCELDIQAYNCLIDGLCKSGRLKFAWELFCSLPHGVLVPNVVTYNIMI  494 (595)
Q Consensus       426 ~~~~~-----------g~~~~A~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~p~~~~~~~l~  494 (595)
                      ++...           |++++|...++++++.. |.+...+..+..++...|++++|+..|+++.+..  .+...+..+.
T Consensus        82 ~~~~~~~~~~~~~~~~g~~~~A~~~~~~al~~~-P~~~~~~~~lg~~~~~~g~~~~A~~~~~~al~~~--~~~~~~~~la  158 (217)
T 2pl2_A           82 AYVALYRQAEDRERGKGYLEQALSVLKDAERVN-PRYAPLHLQRGLVYALLGERDKAEASLKQALALE--DTPEIRSALA  158 (217)
T ss_dssp             HHHHHHHTCSSHHHHHHHHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC--CCHHHHHHHH
T ss_pred             HHHHhhhhhhhhcccccCHHHHHHHHHHHHHhC-cccHHHHHHHHHHHHHcCChHHHHHHHHHHHhcc--cchHHHHHHH
Confidence            44444           67777777777776654 4556666777777777777777777777766643  4566667777


Q ss_pred             HHHHhcCChhHHHHHHHHHHHcCCCCCHHHHHHHHHHHHHcCChhHHHHHHHHHH
Q 040027          495 QGLCNDGQMDKARDLFLDMEENAAAPDVITFDMLIHGFIRINEPSKVNELLHKMK  549 (595)
Q Consensus       495 ~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~  549 (595)
                      .+|...|++++|+..|+++++.. +.+...+..+..++...|++++|...+++..
T Consensus       159 ~~~~~~g~~~~A~~~~~~al~~~-P~~~~~~~~la~~~~~~g~~~~A~~~~~~~~  212 (217)
T 2pl2_A          159 ELYLSMGRLDEALAQYAKALEQA-PKDLDLRVRYASALLLKGKAEEAARAAALEH  212 (217)
T ss_dssp             HHHHHHTCHHHHHHHHHHHHHHS-TTCHHHHHHHHHHHTC---------------
T ss_pred             HHHHHcCCHHHHHHHHHHHHHhC-CCChHHHHHHHHHHHHccCHHHHHHHHHHHh
Confidence            77777777777777777777653 4456666667777777777777777766654

>4e6h_A MRNA 3'-END-processing protein RNA14; HAT domain, heat repeat, CLP1, PCF11, structural protein; 2.30A {Kluyveromyces lactis} PDB: 4e85_A 4eba_A

Probab=99.72  E-value=4.2e-13  Score=137.25  Aligned_cols=413  Identities=11%  Similarity=0.056  Sum_probs=256.5

Q ss_pred             CHHHHHHHHHHHHhcCChhHHHHHHHHHHhCCCCCCHHHHHHHHHHHHhcCC---HhHHHHHHHHHHhcCC-CCCHhhHH
Q 040027           95 NLYTYNILINCFCKIGRVSLGFIAFGRILRSCFTPNAATFNSLIKGLHAESR---IMEAAALFTKLKAFGC-EPNVITYN  170 (595)
Q Consensus        95 ~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~---~~~A~~~~~~~~~~~~-~~~~~~~~  170 (595)
                      |...|..++..+.+.+.++.+..+|++++.. ++.....|...+..-.+.++   ++.+.++|++...... +|+...|.
T Consensus        65 d~~~W~~yi~~~~~~~~~~~aR~vyEraL~~-fP~~~~lW~~Yi~~E~~~~~~~~~~~v~~lfeRal~~~~~~~sv~LW~  143 (679)
T 4e6h_A           65 DIFLYVKLLKHHVSLKQWKQVYETFDKLHDR-FPLMANIWCMRLSLEFDKMEELDAAVIEPVLARCLSKELGNNDLSLWL  143 (679)
T ss_dssp             CHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH-CTTCHHHHHHHHHHHHTC--CCCHHHHHHHHHHHTCSSSCCCCHHHHH
T ss_pred             CHHHHHHHHHHHHhcCcHHHHHHHHHHHHHH-CCCCHHHHHHHHHHHHhhCCcchHHHHHHHHHHHHHhcCCCCCHHHHH
Confidence            5666667777777778899999999999987 47788889988888888888   9999999999988631 37888888


Q ss_pred             HHHHHHHhcCCh--------hHHHHHHHHHHhcCCCCCccc--cCcHHHHHHHHHHHH---------HcCCHhHHHHHHH
Q 040027          171 TLINGLCRTGHT--------MIALNLFEEMANGNGEIGVVC--KPNTVTYSTIIDGLC---------KEGFVDKAKALFL  231 (595)
Q Consensus       171 ~l~~~~~~~g~~--------~~A~~~~~~~~~~~~~~~~~~--~~~~~~~~~l~~~~~---------~~g~~~~A~~~~~  231 (595)
                      ..+....+.++.        +...++|+.++..-+     .  +.+...|...+....         ..++++.+..+|+
T Consensus       144 ~Yl~f~~~~~~~~~~~~~~r~~vr~~FErAl~~vG-----~~d~~s~~iW~~Yi~f~~~~~~~~~~eeq~~~~~~R~iy~  218 (679)
T 4e6h_A          144 SYITYVRKKNDIITGGEEARNIVIQAFQVVVDKCA-----IFEPKSIQFWNEYLHFLEHWKPVNKFEEQQRVQYIRKLYK  218 (679)
T ss_dssp             HHHHHHHHHSCSTTTHHHHHHHHHHHHHHHHHHTT-----TTCSSCHHHHHHHHHHHHTCCCCSHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHhcccccccchhHHHHHHHHHHHHHHhC-----cccccchHHHHHHHHHHHhccccCcHHHHhHHHHHHHHHH
Confidence            877766555543        334578887775421     2  234567877776544         2345788999999


Q ss_pred             HHhhCCCCCCHhHHHHHHHHHHh-------------cCCHHHHHHHHHHHHHC--CC----C-----------C--C---
Q 040027          232 QMKDENINPDVVTYNSLIHGLCH-------------ANDWNEAKRLFIEMMDQ--GV----Q-----------P--S---  276 (595)
Q Consensus       232 ~~~~~~~~~~~~~~~~ll~~~~~-------------~~~~~~A~~~~~~~~~~--~~----~-----------~--~---  276 (595)
                      +++......-..+|......-..             ..+++.|...+.++...  ++    +           |  +   
T Consensus       219 raL~iP~~~~~~~w~~Y~~fe~~~~~~~a~~~~~e~~~~y~~Ar~~~~e~~~~~~~l~r~~p~~~~~~~~~~~p~~~~~~  298 (679)
T 4e6h_A          219 TLLCQPMDCLESMWQRYTQWEQDVNQLTARRHIGELSAQYMNARSLYQDWLNITKGLKRNLPITLNQATESNLPKPNEYD  298 (679)
T ss_dssp             HHTTSCCSSHHHHHHHHHHHHHHHCTTTHHHHHHHHHHHHHHHHHHHHHHHHHTTTCCCCCCSSSTTCCTTTSCCTTCCC
T ss_pred             HHHhCccHHHHHHHHHHHHHHHhcCcchHHHHHHHhhHHHHHHHHHHHHHHHHHHhHhhccccccccchhccCCCCchhH
Confidence            98863111112333222111111             11234445555443221  11    1           0  0   


Q ss_pred             ---HhhHHHHHHHHHhcC-------ChHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHhcCCHHHHH-HHHHHHHhcCCCC
Q 040027          277 ---VVTFNVIMDELCKNR-------KMDEASRLLDLMVQRGVRPNACTYNTLMDGFCLMGKINRAE-ELFGSMESMGCKH  345 (595)
Q Consensus       277 ---~~~~~~l~~~~~~~g-------~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~-~~~~~~~~~~~~~  345 (595)
                         ...|...+..-...+       ..+.+..+|++++.. .+.....|...+..+...|+.++|. .+|++.... +|.
T Consensus       299 ~~ql~lW~~yi~fEk~~~~~l~~~~~~~Rv~~~Ye~aL~~-~p~~~~lW~~ya~~~~~~~~~~~a~r~il~rAi~~-~P~  376 (679)
T 4e6h_A          299 VQQLLIWLEWIRWESDNKLELSDDLHKARMTYVYMQAAQH-VCFAPEIWFNMANYQGEKNTDSTVITKYLKLGQQC-IPN  376 (679)
T ss_dssp             HHHHHHHHHHHHHHHTCTTCCCHHHHHHHHHHHHHHHHHH-TTTCHHHHHHHHHHHHHHSCCTTHHHHHHHHHHHH-CTT
T ss_pred             HHHHHHHHHHHHHHHhCCccccchhhHHHHHHHHHHHHHH-cCCCHHHHHHHHHHHHhcCcHHHHHHHHHHHHHHh-CCC
Confidence               123334443322222       123345667777765 3446777777777777778777785 888887764 355


Q ss_pred             CHHHHHHHHHHHHhCCCHHHHHHHHHHHHHCCC---------CCC------------HHHHHHHHHHHHccCCHHHHHHH
Q 040027          346 DDVSYNILINGYCKNKEVEEALSLYREMVSKGI---------KPT------------VVTYNTLFLGLFEIHQVEHALKL  404 (595)
Q Consensus       346 ~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~~~~---------~~~------------~~~~~~l~~~~~~~~~~~~a~~~  404 (595)
                      +...|..++....+.|+++.|.++|++++....         .|+            ...|...+....+.|..+.|..+
T Consensus       377 s~~Lwl~~a~~ee~~~~~e~aR~iyek~l~~l~~~~~~~~~~~p~~~~~~~~~~~~~~~vWi~y~~~erR~~~l~~AR~v  456 (679)
T 4e6h_A          377 SAVLAFSLSEQYELNTKIPEIETTILSCIDRIHLDLAALMEDDPTNESAINQLKSKLTYVYCVYMNTMKRIQGLAASRKI  456 (679)
T ss_dssp             CHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHHHHHHHHHSTTCHHHHHHHHHHHHHHHHHHHHHHHHHHCHHHHHHH
T ss_pred             CHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHHhhhhhhccCcchhhhhhhccchHHHHHHHHHHHHHcCCHHHHHHH
Confidence            566677777777788888888888887765310         121            22466666666667777888888


Q ss_pred             HHHHHHCCCCCCHHHHHHHHHHHHhc-CCHHHHHHHHHHHHHcCCCcCHHHHHHHHHHHHhcCChHHHHHHHHhcccCCC
Q 040027          405 FDEMQRDGVAADTRTYTTFIDGLCKN-GYIIEAVELFRTLRILKCELDIQAYNCLIDGLCKSGRLKFAWELFCSLPHGVL  483 (595)
Q Consensus       405 ~~~~~~~~~~~~~~~~~~l~~~~~~~-g~~~~A~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~  483 (595)
                      |..+.+.........|...+..-.+. ++.+.|..+|+..++.- +.+...+...+......|+.+.|..+|++.+....
T Consensus       457 f~~A~~~~~~~~~~lyi~~A~lE~~~~~d~e~Ar~ife~~Lk~~-p~~~~~w~~y~~fe~~~~~~~~AR~lferal~~~~  535 (679)
T 4e6h_A          457 FGKCRRLKKLVTPDIYLENAYIEYHISKDTKTACKVLELGLKYF-ATDGEYINKYLDFLIYVNEESQVKSLFESSIDKIS  535 (679)
T ss_dssp             HHHHHHTGGGSCTHHHHHHHHHHHTTTSCCHHHHHHHHHHHHHH-TTCHHHHHHHHHHHHHHTCHHHHHHHHHHHTTTSS
T ss_pred             HHHHHHhcCCCChHHHHHHHHHHHHhCCCHHHHHHHHHHHHHHC-CCchHHHHHHHHHHHhCCCHHHHHHHHHHHHHhcC
Confidence            87777651112233343333332333 34778888888777652 55666667777777777888888888887776422


Q ss_pred             CC--CHHHHHHHHHHHHhcCChhHHHHHHHHHHHc
Q 040027          484 VP--NVVTYNIMIQGLCNDGQMDKARDLFLDMEEN  516 (595)
Q Consensus       484 ~p--~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~  516 (595)
                      .+  ....|...+..-...|+.+.+..+.+++.+.
T Consensus       536 ~~~~~~~lw~~~~~fE~~~G~~~~~~~v~~R~~~~  570 (679)
T 4e6h_A          536 DSHLLKMIFQKVIFFESKVGSLNSVRTLEKRFFEK  570 (679)
T ss_dssp             STTHHHHHHHHHHHHHHHTCCSHHHHHHHHHHHHH
T ss_pred             CHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHh
Confidence            11  2356777777777778888888888887776

>2pl2_A Hypothetical conserved protein TTC0263; TPR, protein binding; 2.50A {Thermus thermophilus}

Probab=99.72  E-value=9.6e-16  Score=135.86  Aligned_cols=200  Identities=16%  Similarity=0.017  Sum_probs=158.2

Q ss_pred             CCCHHHHHHHHHHHHhcCChhHHHHHHHHHHhCCCCCCHHHHHHHHHHHHhcCCHhHHHHHHHHHHhcCCCCCHhhHHHH
Q 040027           93 FPNLYTYNILINCFCKIGRVSLGFIAFGRILRSCFTPNAATFNSLIKGLHAESRIMEAAALFTKLKAFGCEPNVITYNTL  172 (595)
Q Consensus        93 ~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~~l  172 (595)
                      ++++..+..+...+.+.|++++|+..|+++++.. +.+...+..+...+.+.|++++|+..|++..+.. +.+...+..+
T Consensus         2 p~~~~~~~~lg~~~~~~g~~~~A~~~~~~al~~~-p~~~~a~~~lg~~~~~~g~~~~A~~~~~~al~~~-P~~~~a~~~l   79 (217)
T 2pl2_A            2 QTAEQNPLRLGVQLYALGRYDAALTLFERALKEN-PQDPEALYWLARTQLKLGLVNPALENGKTLVART-PRYLGGYMVL   79 (217)
T ss_dssp             --CCHHHHHHHHHHHHTTCHHHHHHHHHHHHTTS-SSCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHH
T ss_pred             CCcHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhC-CCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhC-CCcHHHHHHH
Confidence            5678889999999999999999999999999885 5688899999999999999999999999999985 3478889999


Q ss_pred             HHHHHhc-----------CChhHHHHHHHHHHhcCCCCCccccCcHHHHHHHHHHHHHcCCHhHHHHHHHHHhhCCCCCC
Q 040027          173 INGLCRT-----------GHTMIALNLFEEMANGNGEIGVVCKPNTVTYSTIIDGLCKEGFVDKAKALFLQMKDENINPD  241 (595)
Q Consensus       173 ~~~~~~~-----------g~~~~A~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~~  241 (595)
                      ..++...           |++++|+..|++..+.+       |.+...+..+..++...|++++|+..|++..+.+  .+
T Consensus        80 g~~~~~~~~~~~~~~~~~g~~~~A~~~~~~al~~~-------P~~~~~~~~lg~~~~~~g~~~~A~~~~~~al~~~--~~  150 (217)
T 2pl2_A           80 SEAYVALYRQAEDRERGKGYLEQALSVLKDAERVN-------PRYAPLHLQRGLVYALLGERDKAEASLKQALALE--DT  150 (217)
T ss_dssp             HHHHHHHHHTCSSHHHHHHHHHHHHHHHHHHHHHC-------TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC--CC
T ss_pred             HHHHHHhhhhhhhhcccccCHHHHHHHHHHHHHhC-------cccHHHHHHHHHHHHHcCChHHHHHHHHHHHhcc--cc
Confidence            9999999           99999999999988875       5567888888888999999999999998888776  57


Q ss_pred             HhHHHHHHHHHHhcCCHHHHHHHHHHHHHCCCCCCHhhHHHHHHHHHhcCChHHHHHHHHHHH
Q 040027          242 VVTYNSLIHGLCHANDWNEAKRLFIEMMDQGVQPSVVTFNVIMDELCKNRKMDEASRLLDLMV  304 (595)
Q Consensus       242 ~~~~~~ll~~~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~a~~~~~~~~  304 (595)
                      ...+..+..++...|++++|...|++.++.. +.+...+..+..++...|++++|...+++..
T Consensus       151 ~~~~~~la~~~~~~g~~~~A~~~~~~al~~~-P~~~~~~~~la~~~~~~g~~~~A~~~~~~~~  212 (217)
T 2pl2_A          151 PEIRSALAELYLSMGRLDEALAQYAKALEQA-PKDLDLRVRYASALLLKGKAEEAARAAALEH  212 (217)
T ss_dssp             HHHHHHHHHHHHHHTCHHHHHHHHHHHHHHS-TTCHHHHHHHHHHHTC---------------
T ss_pred             hHHHHHHHHHHHHcCCHHHHHHHHHHHHHhC-CCChHHHHHHHHHHHHccCHHHHHHHHHHHh
Confidence            8888888888888899999998888888753 2356677778888888888888888877654

>3uq3_A Heat shock protein STI1; HSP90, peptide binding, chaperone; 2.60A {Saccharomyces cerevisiae}

Probab=99.71  E-value=3.4e-15  Score=136.64  Aligned_cols=223  Identities=11%  Similarity=0.039  Sum_probs=141.5

Q ss_pred             HHHHHHHHHHhcCCHHHHHHHHHHHHhcCCCCCHHHHHHHHHHHHhCCCHHHHHHHHHHHHHCCCC--CC----HHHHHH
Q 040027          314 TYNTLMDGFCLMGKINRAEELFGSMESMGCKHDDVSYNILINGYCKNKEVEEALSLYREMVSKGIK--PT----VVTYNT  387 (595)
Q Consensus       314 ~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~~~~~--~~----~~~~~~  387 (595)
                      .+..++..+...|++++|+..++++.+..  .+...+..+..++...|++++|+..++++.+....  ++    ...+..
T Consensus         7 ~~~~~g~~~~~~~~~~~A~~~~~~a~~~~--~~~~~~~~~~~~~~~~~~~~~A~~~~~~a~~~~~~~~~~~~~~~~~~~~   84 (258)
T 3uq3_A            7 KEKAEGNKFYKARQFDEAIEHYNKAWELH--KDITYLNNRAAAEYEKGEYETAISTLNDAVEQGREMRADYKVISKSFAR   84 (258)
T ss_dssp             HHHHHHHHHHHTTCHHHHHHHHHHHHHHS--CCTHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCCHHHHHHHHHH
T ss_pred             HHHHHHHHHHHhccHHHHHHHHHHHHHhh--ccHHHHHHHHHHHHHcccHHHHHHHHHHHHHhCcccccchHHHHHHHHH
Confidence            34445555555555555555555555543  44455555555555555555555555555543111  01    345555


Q ss_pred             HHHHHHccCCHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCcCHHHHHHHHHHHHhcCC
Q 040027          388 LFLGLFEIHQVEHALKLFDEMQRDGVAADTRTYTTFIDGLCKNGYIIEAVELFRTLRILKCELDIQAYNCLIDGLCKSGR  467 (595)
Q Consensus       388 l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~  467 (595)
                      +...+...|++++|...++++.+.  .|+.       ..+...|++++|...++++.... +.+...+..++..+...|+
T Consensus        85 l~~~~~~~~~~~~A~~~~~~a~~~--~~~~-------~~~~~~~~~~~a~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~  154 (258)
T 3uq3_A           85 IGNAYHKLGDLKKTIEYYQKSLTE--HRTA-------DILTKLRNAEKELKKAEAEAYVN-PEKAEEARLEGKEYFTKSD  154 (258)
T ss_dssp             HHHHHHHTTCHHHHHHHHHHHHHH--CCCH-------HHHHHHHHHHHHHHHHHHHHHCC-HHHHHHHHHHHHHHHHTTC
T ss_pred             HHHHHHHcccHHHHHHHHHHHHhc--Cchh-------HHHHHHhHHHHHHHHHHHHHHcC-cchHHHHHHHHHHHHHhcC
Confidence            556666666666666666666653  2332       23455566777777777777654 4456677777777777788


Q ss_pred             hHHHHHHHHhcccCCCCCCHHHHHHHHHHHHhcCChhHHHHHHHHHHHcCCCCCHHHHHHHHHHHHHcCChhHHHHHHHH
Q 040027          468 LKFAWELFCSLPHGVLVPNVVTYNIMIQGLCNDGQMDKARDLFLDMEENAAAPDVITFDMLIHGFIRINEPSKVNELLHK  547 (595)
Q Consensus       468 ~~~A~~~~~~~~~~~~~p~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~  547 (595)
                      +++|...++++.... +.+...|..++.+|...|++++|+..++++++.. +.+...+..++.+|...|++++|...+++
T Consensus       155 ~~~A~~~~~~a~~~~-~~~~~~~~~l~~~~~~~~~~~~A~~~~~~al~~~-~~~~~~~~~l~~~~~~~g~~~~A~~~~~~  232 (258)
T 3uq3_A          155 WPNAVKAYTEMIKRA-PEDARGYSNRAAALAKLMSFPEAIADCNKAIEKD-PNFVRAYIRKATAQIAVKEYASALETLDA  232 (258)
T ss_dssp             HHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHhcC-cccHHHHHHHHHHHHHhCCHHHHHHHHHHHHHhC-HHHHHHHHHHHHHHHHHhhHHHHHHHHHH
Confidence            888888777777631 2246677777788888888888888888887764 45577777788888888888888888888


Q ss_pred             HHH
Q 040027          548 MKE  550 (595)
Q Consensus       548 ~~~  550 (595)
                      +.+
T Consensus       233 a~~  235 (258)
T 3uq3_A          233 ART  235 (258)
T ss_dssp             HHH
T ss_pred             HHH
Confidence            775

>3uq3_A Heat shock protein STI1; HSP90, peptide binding, chaperone; 2.60A {Saccharomyces cerevisiae}

Probab=99.69  E-value=9e-15  Score=133.76  Aligned_cols=117  Identities=12%  Similarity=-0.024  Sum_probs=61.3

Q ss_pred             cCCHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCcCHHHHHHHHHHHHhcCChHHHHHH
Q 040027          395 IHQVEHALKLFDEMQRDGVAADTRTYTTFIDGLCKNGYIIEAVELFRTLRILKCELDIQAYNCLIDGLCKSGRLKFAWEL  474 (595)
Q Consensus       395 ~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~  474 (595)
                      .|++++|...++.+.... +.+...+..+...+...|++++|...++++.+.. +.+..++..++.++...|++++|...
T Consensus       118 ~~~~~~a~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~A~~~~~~a~~~~-~~~~~~~~~l~~~~~~~~~~~~A~~~  195 (258)
T 3uq3_A          118 LRNAEKELKKAEAEAYVN-PEKAEEARLEGKEYFTKSDWPNAVKAYTEMIKRA-PEDARGYSNRAAALAKLMSFPEAIAD  195 (258)
T ss_dssp             HHHHHHHHHHHHHHHHCC-HHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCHHHHHHH
T ss_pred             HhHHHHHHHHHHHHHHcC-cchHHHHHHHHHHHHHhcCHHHHHHHHHHHHhcC-cccHHHHHHHHHHHHHhCCHHHHHHH
Confidence            344444454444444431 2233444445555555555555555555555543 33455555555555555555555555


Q ss_pred             HHhcccCCCCC-CHHHHHHHHHHHHhcCChhHHHHHHHHHHH
Q 040027          475 FCSLPHGVLVP-NVVTYNIMIQGLCNDGQMDKARDLFLDMEE  515 (595)
Q Consensus       475 ~~~~~~~~~~p-~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~  515 (595)
                      ++++.+.  .| +...|..+..++...|++++|...++++.+
T Consensus       196 ~~~al~~--~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~a~~  235 (258)
T 3uq3_A          196 CNKAIEK--DPNFVRAYIRKATAQIAVKEYASALETLDAART  235 (258)
T ss_dssp             HHHHHHH--CTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHH
T ss_pred             HHHHHHh--CHHHHHHHHHHHHHHHHHhhHHHHHHHHHHHHH
Confidence            5555542  22 245555555566666666666666655554

>3u4t_A TPR repeat-containing protein; structural genomics, PSI- protein structure initiative, northeast structural genomics consortium, NESG; 2.28A {Cytophaga hutchinsonii}

Probab=99.69  E-value=1e-14  Score=134.64  Aligned_cols=247  Identities=7%  Similarity=0.023  Sum_probs=170.9

Q ss_pred             HHHHHHHHHHHHhcCChhHHHHHHHHHHhCCCCCCHHHHHHHHHHHHhcCCHhHHHHHHHHHHhcCCCCC--HhhHHHHH
Q 040027           96 LYTYNILINCFCKIGRVSLGFIAFGRILRSCFTPNAATFNSLIKGLHAESRIMEAAALFTKLKAFGCEPN--VITYNTLI  173 (595)
Q Consensus        96 ~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~~--~~~~~~l~  173 (595)
                      +..+...+..+...|++++|+..|+++++.. +.+...+..+...+...|++++|++.++++......++  ..++..+.
T Consensus         3 ~~~~~~~a~~~~~~~~~~~A~~~~~~~l~~~-p~~~~~~~~l~~~~~~~~~~~~A~~~~~~a~~~~~~~~~~~~~~~~lg   81 (272)
T 3u4t_A            3 DDVEFRYADFLFKNNNYAEAIEVFNKLEAKK-YNSPYIYNRRAVCYYELAKYDLAQKDIETYFSKVNATKAKSADFEYYG   81 (272)
T ss_dssp             --CHHHHHHHHHTTTCHHHHHHHHHHHHHTT-CCCSTTHHHHHHHHHHTTCHHHHHHHHHHHHTTSCTTTCCHHHHHHHH
T ss_pred             HHHHHHHHHHHHHhcCHHHHHHHHHHHHHhC-CCcHHHHHHHHHHHHHHhhHHHHHHHHHHHHhccCchhHHHHHHHHHH
Confidence            4455667778888888888888888888874 34566788888888888888888888888887431111  22377888


Q ss_pred             HHHHhcCChhHHHHHHHHHHhcCCCCCccccCcHHHHHHHHHHHHHcCCHhHHHHHHHHHhhCCCCCCHhHHHHHHHHHH
Q 040027          174 NGLCRTGHTMIALNLFEEMANGNGEIGVVCKPNTVTYSTIIDGLCKEGFVDKAKALFLQMKDENINPDVVTYNSLIHGLC  253 (595)
Q Consensus       174 ~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~~ll~~~~  253 (595)
                      ..+...|++++|++.|+++.+..       +.+..++..+..++...|++++|.+.|++..+.. +.+...|..+...+.
T Consensus        82 ~~~~~~~~~~~A~~~~~~a~~~~-------~~~~~~~~~l~~~~~~~~~~~~A~~~~~~al~~~-~~~~~~~~~l~~~~~  153 (272)
T 3u4t_A           82 KILMKKGQDSLAIQQYQAAVDRD-------TTRLDMYGQIGSYFYNKGNFPLAIQYMEKQIRPT-TTDPKVFYELGQAYY  153 (272)
T ss_dssp             HHHHHTTCHHHHHHHHHHHHHHS-------TTCTHHHHHHHHHHHHTTCHHHHHHHHGGGCCSS-CCCHHHHHHHHHHHH
T ss_pred             HHHHHcccHHHHHHHHHHHHhcC-------cccHHHHHHHHHHHHHccCHHHHHHHHHHHhhcC-CCcHHHHHHHHHHHH
Confidence            88888888888888888888765       4556788888888888888888888888887763 335666766663444


Q ss_pred             hcCCHHHHHHHHHHHHHCCCCCCHhhHHHHHHHHHhcCC---hHHHHHHHHHHHHCC-CCCC------HHHHHHHHHHHH
Q 040027          254 HANDWNEAKRLFIEMMDQGVQPSVVTFNVIMDELCKNRK---MDEASRLLDLMVQRG-VRPN------ACTYNTLMDGFC  323 (595)
Q Consensus       254 ~~~~~~~A~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~---~~~a~~~~~~~~~~~-~~~~------~~~~~~l~~~~~  323 (595)
                      ..+++++|...|+++.+.. +.+...+..+..++...|+   +++|...++++.+.. ..|+      ..++..+...|.
T Consensus       154 ~~~~~~~A~~~~~~a~~~~-p~~~~~~~~~~~~~~~~~~~~~~~~A~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~  232 (272)
T 3u4t_A          154 YNKEYVKADSSFVKVLELK-PNIYIGYLWRARANAAQDPDTKQGLAKPYYEKLIEVCAPGGAKYKDELIEANEYIAYYYT  232 (272)
T ss_dssp             HTTCHHHHHHHHHHHHHHS-TTCHHHHHHHHHHHHHHSTTCSSCTTHHHHHHHHHHHGGGGGGGHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHhC-ccchHHHHHHHHHHHHcCcchhhHHHHHHHHHHHHHHhcccccchHHHHHHHHHHHHHHH
Confidence            4558888888888887752 2245666667777777776   677777777766531 1122      135556666777


Q ss_pred             hcCCHHHHHHHHHHHHhcCCCCCHHHHHHH
Q 040027          324 LMGKINRAEELFGSMESMGCKHDDVSYNIL  353 (595)
Q Consensus       324 ~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l  353 (595)
                      ..|++++|...++++.+.. |.+...+..+
T Consensus       233 ~~~~~~~A~~~~~~al~~~-p~~~~a~~~l  261 (272)
T 3u4t_A          233 INRDKVKADAAWKNILALD-PTNKKAIDGL  261 (272)
T ss_dssp             HTTCHHHHHHHHHHHHHHC-TTCHHHHHHH
T ss_pred             HcCCHHHHHHHHHHHHhcC-ccHHHHHHHh
Confidence            7777777777777776653 3344444433

>4e6h_A MRNA 3'-END-processing protein RNA14; HAT domain, heat repeat, CLP1, PCF11, structural protein; 2.30A {Kluyveromyces lactis} PDB: 4e85_A 4eba_A

Probab=99.68  E-value=1.2e-12  Score=134.00  Aligned_cols=445  Identities=10%  Similarity=0.012  Sum_probs=306.3

Q ss_pred             ChhHHHHHHHHHHhCCCCCCHHHHHHHHHHHHhcCCHhHHHHHHHHHHhcCCCCCHhhHHHHHHHHHhcCC---hhHHHH
Q 040027          111 RVSLGFIAFGRILRSCFTPNAATFNSLIKGLHAESRIMEAAALFTKLKAFGCEPNVITYNTLINGLCRTGH---TMIALN  187 (595)
Q Consensus       111 ~~~~A~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~---~~~A~~  187 (595)
                      ...+.+..|++.+..+ +-|...|..++..+.+.+.++.+..+|+++... ++.....|...+..-.+.|+   ++.+..
T Consensus        47 ~~~d~i~~lE~~l~~n-p~d~~~W~~yi~~~~~~~~~~~aR~vyEraL~~-fP~~~~lW~~Yi~~E~~~~~~~~~~~v~~  124 (679)
T 4e6h_A           47 DESDVIGKLNDMIEEQ-PTDIFLYVKLLKHHVSLKQWKQVYETFDKLHDR-FPLMANIWCMRLSLEFDKMEELDAAVIEP  124 (679)
T ss_dssp             CCSCHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH-CTTCHHHHHHHHHHHHTC--CCCHHHHHH
T ss_pred             CCHHHHHHHHHHHHHC-cCCHHHHHHHHHHHHhcCcHHHHHHHHHHHHHH-CCCCHHHHHHHHHHHHhhCCcchHHHHHH
Confidence            3455566677777665 679999999999999999999999999999987 56688889999998888898   999999


Q ss_pred             HHHHHHhcCCCCCccccCcHHHHHHHHHHHHHcCCH--------hHHHHHHHHHhh-CCC-CC-CHhHHHHHHHHHH---
Q 040027          188 LFEEMANGNGEIGVVCKPNTVTYSTIIDGLCKEGFV--------DKAKALFLQMKD-ENI-NP-DVVTYNSLIHGLC---  253 (595)
Q Consensus       188 ~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~--------~~A~~~~~~~~~-~~~-~~-~~~~~~~ll~~~~---  253 (595)
                      +|++.+....     .+|++..|...+....+.++.        +...++|+.... .|. .+ +...|...+....   
T Consensus       125 lfeRal~~~~-----~~~sv~LW~~Yl~f~~~~~~~~~~~~~~r~~vr~~FErAl~~vG~~d~~s~~iW~~Yi~f~~~~~  199 (679)
T 4e6h_A          125 VLARCLSKEL-----GNNDLSLWLSYITYVRKKNDIITGGEEARNIVIQAFQVVVDKCAIFEPKSIQFWNEYLHFLEHWK  199 (679)
T ss_dssp             HHHHHTCSSS-----CCCCHHHHHHHHHHHHHHSCSTTTHHHHHHHHHHHHHHHHHHTTTTCSSCHHHHHHHHHHHHTCC
T ss_pred             HHHHHHHhcC-----CCCCHHHHHHHHHHHHHhcccccccchhHHHHHHHHHHHHHHhCcccccchHHHHHHHHHHHhcc
Confidence            9999998631     137888898888776665553        344578887654 354 44 4567777776543   


Q ss_pred             ------hcCCHHHHHHHHHHHHHCCCCCCHhhHHHHHHHHHh-------------cCChHHHHHHHHHHHHC--CC----
Q 040027          254 ------HANDWNEAKRLFIEMMDQGVQPSVVTFNVIMDELCK-------------NRKMDEASRLLDLMVQR--GV----  308 (595)
Q Consensus       254 ------~~~~~~~A~~~~~~~~~~~~~~~~~~~~~l~~~~~~-------------~g~~~~a~~~~~~~~~~--~~----  308 (595)
                            .+++++.+..+|+.++......-..+|......-..             ..+++.|...+.++...  ++    
T Consensus       200 ~~~~~eeq~~~~~~R~iy~raL~iP~~~~~~~w~~Y~~fe~~~~~~~a~~~~~e~~~~y~~Ar~~~~e~~~~~~~l~r~~  279 (679)
T 4e6h_A          200 PVNKFEEQQRVQYIRKLYKTLLCQPMDCLESMWQRYTQWEQDVNQLTARRHIGELSAQYMNARSLYQDWLNITKGLKRNL  279 (679)
T ss_dssp             CCSHHHHHHHHHHHHHHHHHHTTSCCSSHHHHHHHHHHHHHHHCTTTHHHHHHHHHHHHHHHHHHHHHHHHHTTTCCCCC
T ss_pred             ccCcHHHHhHHHHHHHHHHHHHhCccHHHHHHHHHHHHHHHhcCcchHHHHHHHhhHHHHHHHHHHHHHHHHHHhHhhcc
Confidence                  234577889999998863211112233222211111             12234445555443221  11    


Q ss_pred             C-----------C-----C---HHHHHHHHHHHHhcC-------CHHHHHHHHHHHHhcCCCCCHHHHHHHHHHHHhCCC
Q 040027          309 R-----------P-----N---ACTYNTLMDGFCLMG-------KINRAEELFGSMESMGCKHDDVSYNILINGYCKNKE  362 (595)
Q Consensus       309 ~-----------~-----~---~~~~~~l~~~~~~~~-------~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~  362 (595)
                      +           |     +   ...|...+..-...+       ..+.+..+|++.+.. ++.....|...+..+...|+
T Consensus       280 p~~~~~~~~~~~p~~~~~~~~ql~lW~~yi~fEk~~~~~l~~~~~~~Rv~~~Ye~aL~~-~p~~~~lW~~ya~~~~~~~~  358 (679)
T 4e6h_A          280 PITLNQATESNLPKPNEYDVQQLLIWLEWIRWESDNKLELSDDLHKARMTYVYMQAAQH-VCFAPEIWFNMANYQGEKNT  358 (679)
T ss_dssp             CSSSTTCCTTTSCCTTCCCHHHHHHHHHHHHHHHTCTTCCCHHHHHHHHHHHHHHHHHH-TTTCHHHHHHHHHHHHHHSC
T ss_pred             ccccccchhccCCCCchhHHHHHHHHHHHHHHHHhCCccccchhhHHHHHHHHHHHHHH-cCCCHHHHHHHHHHHHhcCc
Confidence            1           1     0   123333333322222       123456778888766 36678889988998888999


Q ss_pred             HHHHH-HHHHHHHHCCCCCCHHHHHHHHHHHHccCCHHHHHHHHHHHHHCC---------CCCC------------HHHH
Q 040027          363 VEEAL-SLYREMVSKGIKPTVVTYNTLFLGLFEIHQVEHALKLFDEMQRDG---------VAAD------------TRTY  420 (595)
Q Consensus       363 ~~~A~-~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~---------~~~~------------~~~~  420 (595)
                      .++|. .+|++.... .+.+...|...+......|+++.|..+|+.++...         ..|+            ..+|
T Consensus       359 ~~~a~r~il~rAi~~-~P~s~~Lwl~~a~~ee~~~~~e~aR~iyek~l~~l~~~~~~~~~~~p~~~~~~~~~~~~~~~vW  437 (679)
T 4e6h_A          359 DSTVITKYLKLGQQC-IPNSAVLAFSLSEQYELNTKIPEIETTILSCIDRIHLDLAALMEDDPTNESAINQLKSKLTYVY  437 (679)
T ss_dssp             CTTHHHHHHHHHHHH-CTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHHHHHHHHHSTTCHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHh-CCCCHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHHhhhhhhccCcchhhhhhhccchHHHH
Confidence            99997 999999875 34466667778888889999999999999988631         0131            3467


Q ss_pred             HHHHHHHHhcCCHHHHHHHHHHHHHcCCCcCHHHHHHHHHHHHhc-CChHHHHHHHHhcccCCCCCCHHHHHHHHHHHHh
Q 040027          421 TTFIDGLCKNGYIIEAVELFRTLRILKCELDIQAYNCLIDGLCKS-GRLKFAWELFCSLPHGVLVPNVVTYNIMIQGLCN  499 (595)
Q Consensus       421 ~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~~l~~~~~~~-g~~~~A~~~~~~~~~~~~~p~~~~~~~l~~~~~~  499 (595)
                      ...+....+.|+.+.|..+|.++++.........|...+..-.+. ++.+.|..+|+..++. .+-+...|...+.....
T Consensus       438 i~y~~~erR~~~l~~AR~vf~~A~~~~~~~~~~lyi~~A~lE~~~~~d~e~Ar~ife~~Lk~-~p~~~~~w~~y~~fe~~  516 (679)
T 4e6h_A          438 CVYMNTMKRIQGLAASRKIFGKCRRLKKLVTPDIYLENAYIEYHISKDTKTACKVLELGLKY-FATDGEYINKYLDFLIY  516 (679)
T ss_dssp             HHHHHHHHHHHCHHHHHHHHHHHHHTGGGSCTHHHHHHHHHHHTTTSCCHHHHHHHHHHHHH-HTTCHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHcCCHHHHHHHHHHHHHhcCCCChHHHHHHHHHHHHhCCCHHHHHHHHHHHHHH-CCCchHHHHHHHHHHHh
Confidence            777777788899999999999998761133345555444444454 4589999999999885 33356777888888888


Q ss_pred             cCChhHHHHHHHHHHHcCCCC--CHHHHHHHHHHHHHcCChhHHHHHHHHHHHCCCCCCHHHHHHHHHHH
Q 040027          500 DGQMDKARDLFLDMEENAAAP--DVITFDMLIHGFIRINEPSKVNELLHKMKEKKVMPDASIVSIVVDLL  567 (595)
Q Consensus       500 ~g~~~~A~~~~~~~~~~~~~~--~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~p~~~~~~~l~~~~  567 (595)
                      .|+.+.|..+|++++....++  ....|..++..-...|+.+.+.++.+++.+.  .|+..-...+.+-|
T Consensus       517 ~~~~~~AR~lferal~~~~~~~~~~~lw~~~~~fE~~~G~~~~~~~v~~R~~~~--~P~~~~~~~f~~ry  584 (679)
T 4e6h_A          517 VNEESQVKSLFESSIDKISDSHLLKMIFQKVIFFESKVGSLNSVRTLEKRFFEK--FPEVNKLEEFTNKY  584 (679)
T ss_dssp             HTCHHHHHHHHHHHTTTSSSTTHHHHHHHHHHHHHHHTCCSHHHHHHHHHHHHH--STTCCHHHHHHHHT
T ss_pred             CCCHHHHHHHHHHHHHhcCCHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHh--CCCCcHHHHHHHHh
Confidence            999999999999999864222  3457777777778899999999999999985  35544555554433

>3u4t_A TPR repeat-containing protein; structural genomics, PSI- protein structure initiative, northeast structural genomics consortium, NESG; 2.28A {Cytophaga hutchinsonii}

Probab=99.68  E-value=1.2e-14  Score=134.27  Aligned_cols=251  Identities=12%  Similarity=0.039  Sum_probs=146.8

Q ss_pred             HHHHHHHHHHhcCCHHHHHHHHHHHHhcCCCCCHHHHHHHHHHHHhCCCHHHHHHHHHHHHHCCCCCC--HHHHHHHHHH
Q 040027          314 TYNTLMDGFCLMGKINRAEELFGSMESMGCKHDDVSYNILINGYCKNKEVEEALSLYREMVSKGIKPT--VVTYNTLFLG  391 (595)
Q Consensus       314 ~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~~~~~~~--~~~~~~l~~~  391 (595)
                      .+...+..+...|++++|+..++++.+.. +.+...+..+..+|...|++++|+..++++.+....++  ...+..+...
T Consensus         5 ~~~~~a~~~~~~~~~~~A~~~~~~~l~~~-p~~~~~~~~l~~~~~~~~~~~~A~~~~~~a~~~~~~~~~~~~~~~~lg~~   83 (272)
T 3u4t_A            5 VEFRYADFLFKNNNYAEAIEVFNKLEAKK-YNSPYIYNRRAVCYYELAKYDLAQKDIETYFSKVNATKAKSADFEYYGKI   83 (272)
T ss_dssp             CHHHHHHHHHTTTCHHHHHHHHHHHHHTT-CCCSTTHHHHHHHHHHTTCHHHHHHHHHHHHTTSCTTTCCHHHHHHHHHH
T ss_pred             HHHHHHHHHHHhcCHHHHHHHHHHHHHhC-CCcHHHHHHHHHHHHHHhhHHHHHHHHHHHHhccCchhHHHHHHHHHHHH
Confidence            34445555666666666666666665543 23344566666666666666666666666665321111  2235566666


Q ss_pred             HHccCCHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCcCHHHHHHHHHHHHhcCChHHH
Q 040027          392 LFEIHQVEHALKLFDEMQRDGVAADTRTYTTFIDGLCKNGYIIEAVELFRTLRILKCELDIQAYNCLIDGLCKSGRLKFA  471 (595)
Q Consensus       392 ~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A  471 (595)
                      +...|++++|...++++.+.. +.+...+..+...|...|++++|...++++.+.. +.+...+..+...+...+++++|
T Consensus        84 ~~~~~~~~~A~~~~~~a~~~~-~~~~~~~~~l~~~~~~~~~~~~A~~~~~~al~~~-~~~~~~~~~l~~~~~~~~~~~~A  161 (272)
T 3u4t_A           84 LMKKGQDSLAIQQYQAAVDRD-TTRLDMYGQIGSYFYNKGNFPLAIQYMEKQIRPT-TTDPKVFYELGQAYYYNKEYVKA  161 (272)
T ss_dssp             HHHTTCHHHHHHHHHHHHHHS-TTCTHHHHHHHHHHHHTTCHHHHHHHHGGGCCSS-CCCHHHHHHHHHHHHHTTCHHHH
T ss_pred             HHHcccHHHHHHHHHHHHhcC-cccHHHHHHHHHHHHHccCHHHHHHHHHHHhhcC-CCcHHHHHHHHHHHHHHHHHHHH
Confidence            666666666666666666542 3345566666667777777777777777666553 44566666666333334477777


Q ss_pred             HHHHHhcccCCCCCC-HHHHHHHHHHHHhcCC---hhHHHHHHHHHHHcC-CCCC------HHHHHHHHHHHHHcCChhH
Q 040027          472 WELFCSLPHGVLVPN-VVTYNIMIQGLCNDGQ---MDKARDLFLDMEENA-AAPD------VITFDMLIHGFIRINEPSK  540 (595)
Q Consensus       472 ~~~~~~~~~~~~~p~-~~~~~~l~~~~~~~g~---~~~A~~~~~~~~~~~-~~~~------~~~~~~l~~~~~~~g~~~~  540 (595)
                      ...|+++.+  ..|+ ...+..+..++...|+   +++|...++++.+.. -.|+      ..+|..++..|...|++++
T Consensus       162 ~~~~~~a~~--~~p~~~~~~~~~~~~~~~~~~~~~~~~A~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~  239 (272)
T 3u4t_A          162 DSSFVKVLE--LKPNIYIGYLWRARANAAQDPDTKQGLAKPYYEKLIEVCAPGGAKYKDELIEANEYIAYYYTINRDKVK  239 (272)
T ss_dssp             HHHHHHHHH--HSTTCHHHHHHHHHHHHHHSTTCSSCTTHHHHHHHHHHHGGGGGGGHHHHHHHHHHHHHHHHHTTCHHH
T ss_pred             HHHHHHHHH--hCccchHHHHHHHHHHHHcCcchhhHHHHHHHHHHHHHHhcccccchHHHHHHHHHHHHHHHHcCCHHH
Confidence            777777766  3343 5566666666666666   666777777766531 0122      2456667777777777777


Q ss_pred             HHHHHHHHHHCCCCCCHHHHHHHHHHHHhc
Q 040027          541 VNELLHKMKEKKVMPDASIVSIVVDLLVKN  570 (595)
Q Consensus       541 A~~~~~~~~~~~~~p~~~~~~~l~~~~~~~  570 (595)
                      |.++++++.+.. +-+...+..+.......
T Consensus       240 A~~~~~~al~~~-p~~~~a~~~l~~~~~~~  268 (272)
T 3u4t_A          240 ADAAWKNILALD-PTNKKAIDGLKMKLEHH  268 (272)
T ss_dssp             HHHHHHHHHHHC-TTCHHHHHHHC------
T ss_pred             HHHHHHHHHhcC-ccHHHHHHHhhhhhccc
Confidence            777777777643 22455555555544433

>2h6f_A Protein farnesyltransferase/geranylgeranyltransferase type I alpha subunit; ftase, farnesyltransferase, farnesyl transferase, prenyltransferase, CAAX, RAS, lipid modification, prenylation; HET: SUC FAR; 1.50A {Homo sapiens} SCOP: a.118.6.1 PDB: 1jcq_A* 1ld7_A* 1mzc_A* 1s63_A* 1sa4_A* 1tn6_A* 1ld8_A* 2h6g_A* 2h6h_A* 2h6i_A* 2iej_A* 3e37_A* 2f0y_A* 3ksl_A* 2zir_A* 2zis_A* 1o5m_A* 3ksq_A* 1o1t_A* 1o1s_A* ...

Probab=99.68  E-value=2.4e-14  Score=137.26  Aligned_cols=249  Identities=12%  Similarity=0.039  Sum_probs=198.6

Q ss_pred             CHHHHHHHHHHHHhcCChhHHHHHHHHHHhCCCCCCHHHHHHHHHHHHhcCC-HhHHHHHHHHHHhcCCCCCHhhHHHHH
Q 040027           95 NLYTYNILINCFCKIGRVSLGFIAFGRILRSCFTPNAATFNSLIKGLHAESR-IMEAAALFTKLKAFGCEPNVITYNTLI  173 (595)
Q Consensus        95 ~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~-~~~A~~~~~~~~~~~~~~~~~~~~~l~  173 (595)
                      +...|..+...+...|++++|+..++++++.. +.+..+|+.+...+...|+ +++|+..|++++... +-+..+|..+.
T Consensus        96 ~~~a~~~lg~~~~~~g~~~~Al~~~~~al~l~-P~~~~a~~~~g~~l~~~g~d~~eAl~~~~~al~l~-P~~~~a~~~~g  173 (382)
T 2h6f_A           96 FRDVYDYFRAVLQRDERSERAFKLTRDAIELN-AANYTVWHFRRVLLKSLQKDLHEEMNYITAIIEEQ-PKNYQVWHHRR  173 (382)
T ss_dssp             HHHHHHHHHHHHHHTCCCHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCCHHHHHHHHHHHHHHC-TTCHHHHHHHH
T ss_pred             hHHHHHHHHHHHHHCCChHHHHHHHHHHHHhC-ccCHHHHHHHHHHHHHcccCHHHHHHHHHHHHHHC-CCCHHHHHHHH
Confidence            45778888899999999999999999999885 5578899999999999997 999999999999885 33788999999


Q ss_pred             HHHHhcCChhHHHHHHHHHHhcCCCCCccccCcHHHHHHHHHHHHHcCCHhHHHHHHHHHhhCCCCCCHhHHHHHHHHHH
Q 040027          174 NGLCRTGHTMIALNLFEEMANGNGEIGVVCKPNTVTYSTIIDGLCKEGFVDKAKALFLQMKDENINPDVVTYNSLIHGLC  253 (595)
Q Consensus       174 ~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~~ll~~~~  253 (595)
                      .++...|++++|+..|++++..+       +.+..+|..+..++...|++++|+..|+++++.+. -+...|+.+..++.
T Consensus       174 ~~~~~~g~~~eAl~~~~kal~ld-------P~~~~a~~~lg~~~~~~g~~~eAl~~~~~al~l~P-~~~~a~~~lg~~l~  245 (382)
T 2h6f_A          174 VLVEWLRDPSQELEFIADILNQD-------AKNYHAWQHRQWVIQEFKLWDNELQYVDQLLKEDV-RNNSVWNQRYFVIS  245 (382)
T ss_dssp             HHHHHHTCCTTHHHHHHHHHHHC-------TTCHHHHHHHHHHHHHHTCCTTHHHHHHHHHHHCT-TCHHHHHHHHHHHH
T ss_pred             HHHHHccCHHHHHHHHHHHHHhC-------ccCHHHHHHHHHHHHHcCChHHHHHHHHHHHHhCC-CCHHHHHHHHHHHH
Confidence            99999999999999999999986       66789999999999999999999999999988753 37888999998888


Q ss_pred             h-cCCHHHH-----HHHHHHHHHCCCCCCHhhHHHHHHHHHhcC--ChHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHhc
Q 040027          254 H-ANDWNEA-----KRLFIEMMDQGVQPSVVTFNVIMDELCKNR--KMDEASRLLDLMVQRGVRPNACTYNTLMDGFCLM  325 (595)
Q Consensus       254 ~-~~~~~~A-----~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g--~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~  325 (595)
                      . .|..++|     +..|++.+... +-+...|..+..++...|  ++++|.+.+.++ +. .+.+...+..++.+|...
T Consensus       246 ~l~~~~~eA~~~~el~~~~~Al~l~-P~~~~a~~~l~~ll~~~g~~~~~~a~~~~~~~-~~-~p~~~~al~~La~~~~~~  322 (382)
T 2h6f_A          246 NTTGYNDRAVLEREVQYTLEMIKLV-PHNESAWNYLKGILQDRGLSKYPNLLNQLLDL-QP-SHSSPYLIAFLVDIYEDM  322 (382)
T ss_dssp             HTTCSCSHHHHHHHHHHHHHHHHHS-TTCHHHHHHHHHHHTTTCGGGCHHHHHHHHHH-TT-TCCCHHHHHHHHHHHHHH
T ss_pred             HhcCcchHHHHHHHHHHHHHHHHHC-CCCHHHHHHHHHHHHccCccchHHHHHHHHHh-cc-CCCCHHHHHHHHHHHHHH
Confidence            8 5665777     47788887753 225667888888888877  588888888887 33 344667777788888776


Q ss_pred             C---------CHHHHHHHHHHH-HhcCCCCCHHHHHHHHHHH
Q 040027          326 G---------KINRAEELFGSM-ESMGCKHDDVSYNILINGY  357 (595)
Q Consensus       326 ~---------~~~~a~~~~~~~-~~~~~~~~~~~~~~l~~~~  357 (595)
                      |         ..++|+.+++++ .+.+ +.....|..+...+
T Consensus       323 ~~~~~~~~~~~~~~A~~~~~~l~~~~D-P~r~~~w~~~~~~l  363 (382)
T 2h6f_A          323 LENQCDNKEDILNKALELCEILAKEKD-TIRKEYWRYIGRSL  363 (382)
T ss_dssp             HHTTCSSHHHHHHHHHHHHHHHHHTTC-GGGHHHHHHHHHHH
T ss_pred             hcccccchHHHHHHHHHHHHHHHHHhC-chhHHHHHHHHHHH
Confidence            3         257888888888 5553 23334555555444

>2h6f_A Protein farnesyltransferase/geranylgeranyltransferase type I alpha subunit; ftase, farnesyltransferase, farnesyl transferase, prenyltransferase, CAAX, RAS, lipid modification, prenylation; HET: SUC FAR; 1.50A {Homo sapiens} SCOP: a.118.6.1 PDB: 1jcq_A* 1ld7_A* 1mzc_A* 1s63_A* 1sa4_A* 1tn6_A* 1ld8_A* 2h6g_A* 2h6h_A* 2h6i_A* 2iej_A* 3e37_A* 2f0y_A* 3ksl_A* 2zir_A* 2zis_A* 1o5m_A* 3ksq_A* 1o1t_A* 1o1s_A* ...

Probab=99.68  E-value=1.3e-14  Score=139.05  Aligned_cols=248  Identities=11%  Similarity=0.059  Sum_probs=186.8

Q ss_pred             HHHHHHHHHHHHhcCCHHHHHHHHHHHHhcCCCCCHHHHHHHHHHHHhCCC-HHHHHHHHHHHHHCCCCCCHHHHHHHHH
Q 040027          312 ACTYNTLMDGFCLMGKINRAEELFGSMESMGCKHDDVSYNILINGYCKNKE-VEEALSLYREMVSKGIKPTVVTYNTLFL  390 (595)
Q Consensus       312 ~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~-~~~A~~~~~~~~~~~~~~~~~~~~~l~~  390 (595)
                      ...+..+..++...|++++|+..++++++.. +.+..+|..+..++...|+ +++|+..|+++++..+. +...|..+..
T Consensus        97 ~~a~~~lg~~~~~~g~~~~Al~~~~~al~l~-P~~~~a~~~~g~~l~~~g~d~~eAl~~~~~al~l~P~-~~~a~~~~g~  174 (382)
T 2h6f_A           97 RDVYDYFRAVLQRDERSERAFKLTRDAIELN-AANYTVWHFRRVLLKSLQKDLHEEMNYITAIIEEQPK-NYQVWHHRRV  174 (382)
T ss_dssp             HHHHHHHHHHHHHTCCCHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCCHHHHHHHHHHHHHHCTT-CHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHCCChHHHHHHHHHHHHhC-ccCHHHHHHHHHHHHHcccCHHHHHHHHHHHHHHCCC-CHHHHHHHHH
Confidence            3456666777777788888888888877764 4456677778888888885 88888888888776544 6677777888


Q ss_pred             HHHccCCHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCcCHHHHHHHHHHHHh-cCChH
Q 040027          391 GLFEIHQVEHALKLFDEMQRDGVAADTRTYTTFIDGLCKNGYIIEAVELFRTLRILKCELDIQAYNCLIDGLCK-SGRLK  469 (595)
Q Consensus       391 ~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~~l~~~~~~-~g~~~  469 (595)
                      ++...|++++|+..|+++++.+ +.+...|..+..++...|++++|+..++++++.. +.+...|+.+..++.. .|..+
T Consensus       175 ~~~~~g~~~eAl~~~~kal~ld-P~~~~a~~~lg~~~~~~g~~~eAl~~~~~al~l~-P~~~~a~~~lg~~l~~l~~~~~  252 (382)
T 2h6f_A          175 LVEWLRDPSQELEFIADILNQD-AKNYHAWQHRQWVIQEFKLWDNELQYVDQLLKED-VRNNSVWNQRYFVISNTTGYND  252 (382)
T ss_dssp             HHHHHTCCTTHHHHHHHHHHHC-TTCHHHHHHHHHHHHHHTCCTTHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCSCS
T ss_pred             HHHHccCHHHHHHHHHHHHHhC-ccCHHHHHHHHHHHHHcCChHHHHHHHHHHHHhC-CCCHHHHHHHHHHHHHhcCcch
Confidence            8888888888888888888764 5577788888888888888888888888888876 6678888888888888 55557


Q ss_pred             HH-----HHHHHhcccCCCCCC-HHHHHHHHHHHHhcC--ChhHHHHHHHHHHHcCCCCCHHHHHHHHHHHHHcC-----
Q 040027          470 FA-----WELFCSLPHGVLVPN-VVTYNIMIQGLCNDG--QMDKARDLFLDMEENAAAPDVITFDMLIHGFIRIN-----  536 (595)
Q Consensus       470 ~A-----~~~~~~~~~~~~~p~-~~~~~~l~~~~~~~g--~~~~A~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g-----  536 (595)
                      +|     +..+++++.  +.|+ ...|+.+..++...|  ++++|++.+.++ +. .+.+...+..++.+|.+.|     
T Consensus       253 eA~~~~el~~~~~Al~--l~P~~~~a~~~l~~ll~~~g~~~~~~a~~~~~~~-~~-~p~~~~al~~La~~~~~~~~~~~~  328 (382)
T 2h6f_A          253 RAVLEREVQYTLEMIK--LVPHNESAWNYLKGILQDRGLSKYPNLLNQLLDL-QP-SHSSPYLIAFLVDIYEDMLENQCD  328 (382)
T ss_dssp             HHHHHHHHHHHHHHHH--HSTTCHHHHHHHHHHHTTTCGGGCHHHHHHHHHH-TT-TCCCHHHHHHHHHHHHHHHHTTCS
T ss_pred             HHHHHHHHHHHHHHHH--HCCCCHHHHHHHHHHHHccCccchHHHHHHHHHh-cc-CCCCHHHHHHHHHHHHHHhccccc
Confidence            77     477888777  4554 678888888888877  688888888887 43 2556778888888888864     


Q ss_pred             ---C-hhHHHHHHHHH-HHCCCCC-CHHHHHHHHHHHHh
Q 040027          537 ---E-PSKVNELLHKM-KEKKVMP-DASIVSIVVDLLVK  569 (595)
Q Consensus       537 ---~-~~~A~~~~~~~-~~~~~~p-~~~~~~~l~~~~~~  569 (595)
                         + +++|.++++++ .+  +.| ....|..++..+..
T Consensus       329 ~~~~~~~~A~~~~~~l~~~--~DP~r~~~w~~~~~~l~~  365 (382)
T 2h6f_A          329 NKEDILNKALELCEILAKE--KDTIRKEYWRYIGRSLQS  365 (382)
T ss_dssp             SHHHHHHHHHHHHHHHHHT--TCGGGHHHHHHHHHHHHH
T ss_pred             chHHHHHHHHHHHHHHHHH--hCchhHHHHHHHHHHHHH
Confidence               2 58899999998 65  346 45677777776654

>1ouv_A Conserved hypothetical secreted protein; TPR repeat, HCP repeat, cysteine rich protein, loop-helix-TU repeat protein, hydrolase; 2.00A {Helicobacter pylori} SCOP: a.118.18.1

Probab=99.67  E-value=2.6e-13  Score=125.25  Aligned_cols=224  Identities=12%  Similarity=-0.042  Sum_probs=141.7

Q ss_pred             CHHHHHHHHHHHHhcCCHHHHHHHHHHHHhcCCCCCHHHHHHHHHHHHh----CCCHHHHHHHHHHHHHCCCCCCHHHHH
Q 040027          311 NACTYNTLMDGFCLMGKINRAEELFGSMESMGCKHDDVSYNILINGYCK----NKEVEEALSLYREMVSKGIKPTVVTYN  386 (595)
Q Consensus       311 ~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~----~~~~~~A~~~~~~~~~~~~~~~~~~~~  386 (595)
                      ++.++..+...+...|++++|+..|++..+.   .+...+..+...|..    .+++++|+..|++..+.+   +...+.
T Consensus         5 ~~~a~~~lg~~~~~~~~~~~A~~~~~~a~~~---~~~~a~~~lg~~~~~g~~~~~~~~~A~~~~~~a~~~~---~~~a~~   78 (273)
T 1ouv_A            5 DPKELVGLGAKSYKEKDFTQAKKYFEKACDL---KENSGCFNLGVLYYQGQGVEKNLKKAASFYAKACDLN---YSNGCH   78 (273)
T ss_dssp             CHHHHHHHHHHHHHTTCHHHHHHHHHHHHHT---TCHHHHHHHHHHHHHTSSSCCCHHHHHHHHHHHHHTT---CHHHHH
T ss_pred             ChHHHHHHHHHHHhCCCHHHHHHHHHHHHHC---CCHHHHHHHHHHHHcCCCcCCCHHHHHHHHHHHHHCC---CHHHHH
Confidence            3444555555566666666666666665552   234455555666666    666666666666666553   455555


Q ss_pred             HHHHHHHc----cCCHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHh----cCCHHHHHHHHHHHHHcCCCcCHHHHHHH
Q 040027          387 TLFLGLFE----IHQVEHALKLFDEMQRDGVAADTRTYTTFIDGLCK----NGYIIEAVELFRTLRILKCELDIQAYNCL  458 (595)
Q Consensus       387 ~l~~~~~~----~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~----~g~~~~A~~~~~~~~~~~~~~~~~~~~~l  458 (595)
                      .+...+..    .+++++|...|++..+.+   +...+..+...|..    .+++++|...++++.+.+   +...+..+
T Consensus        79 ~lg~~~~~g~~~~~~~~~A~~~~~~a~~~~---~~~a~~~lg~~~~~~~~~~~~~~~A~~~~~~a~~~~---~~~a~~~l  152 (273)
T 1ouv_A           79 LLGNLYYSGQGVSQNTNKALQYYSKACDLK---YAEGCASLGGIYHDGKVVTRDFKKAVEYFTKACDLN---DGDGCTIL  152 (273)
T ss_dssp             HHHHHHHHTSSSCCCHHHHHHHHHHHHHTT---CHHHHHHHHHHHHHCSSSCCCHHHHHHHHHHHHHTT---CHHHHHHH
T ss_pred             HHHHHHhCCCCcccCHHHHHHHHHHHHHcC---CccHHHHHHHHHHcCCCcccCHHHHHHHHHHHHhcC---cHHHHHHH
Confidence            56666666    666666666666666543   45566666666666    667777777777766644   45556666


Q ss_pred             HHHHHh----cCChHHHHHHHHhcccCCCCCCHHHHHHHHHHHHh----cCChhHHHHHHHHHHHcCCCCCHHHHHHHHH
Q 040027          459 IDGLCK----SGRLKFAWELFCSLPHGVLVPNVVTYNIMIQGLCN----DGQMDKARDLFLDMEENAAAPDVITFDMLIH  530 (595)
Q Consensus       459 ~~~~~~----~g~~~~A~~~~~~~~~~~~~p~~~~~~~l~~~~~~----~g~~~~A~~~~~~~~~~~~~~~~~~~~~l~~  530 (595)
                      ...|..    .+++++|+..|++..+.   .+...+..+...|..    .+++++|+..|+++.+.+   +...+..+..
T Consensus       153 g~~~~~~~~~~~~~~~A~~~~~~a~~~---~~~~a~~~lg~~~~~g~~~~~~~~~A~~~~~~a~~~~---~~~a~~~l~~  226 (273)
T 1ouv_A          153 GSLYDAGRGTPKDLKKALASYDKACDL---KDSPGCFNAGNMYHHGEGATKNFKEALARYSKACELE---NGGGCFNLGA  226 (273)
T ss_dssp             HHHHHHTSSSCCCHHHHHHHHHHHHHT---TCHHHHHHHHHHHHHTCSSCCCHHHHHHHHHHHHHTT---CHHHHHHHHH
T ss_pred             HHHHHcCCCCCCCHHHHHHHHHHHHHC---CCHHHHHHHHHHHHcCCCCCccHHHHHHHHHHHHhCC---CHHHHHHHHH
Confidence            666666    67777777777776663   245566667777777    777777777777777653   2556666777


Q ss_pred             HHHH----cCChhHHHHHHHHHHHCC
Q 040027          531 GFIR----INEPSKVNELLHKMKEKK  552 (595)
Q Consensus       531 ~~~~----~g~~~~A~~~~~~~~~~~  552 (595)
                      .|..    .+++++|.+++++..+.|
T Consensus       227 ~~~~g~~~~~~~~~A~~~~~~a~~~~  252 (273)
T 1ouv_A          227 MQYNGEGVTRNEKQAIENFKKGCKLG  252 (273)
T ss_dssp             HHHTTSSSSCCSTTHHHHHHHHHHHT
T ss_pred             HHHcCCCcccCHHHHHHHHHHHHHcC
Confidence            7776    777777777777777654

>1ouv_A Conserved hypothetical secreted protein; TPR repeat, HCP repeat, cysteine rich protein, loop-helix-TU repeat protein, hydrolase; 2.00A {Helicobacter pylori} SCOP: a.118.18.1

Probab=99.67  E-value=2.8e-13  Score=125.00  Aligned_cols=223  Identities=13%  Similarity=-0.048  Sum_probs=142.7

Q ss_pred             CHHHHHHHHHHHHhcCChhHHHHHHHHHHhCCCCCCHHHHHHHHHHHHh----cCCHhHHHHHHHHHHhcCCCCCHhhHH
Q 040027           95 NLYTYNILINCFCKIGRVSLGFIAFGRILRSCFTPNAATFNSLIKGLHA----ESRIMEAAALFTKLKAFGCEPNVITYN  170 (595)
Q Consensus        95 ~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~~l~~~~~~----~g~~~~A~~~~~~~~~~~~~~~~~~~~  170 (595)
                      ++..+..+...+...|++++|+..|+++.+.   .+..++..+...|..    .+++++|++.|++..+.+   +..++.
T Consensus         5 ~~~a~~~lg~~~~~~~~~~~A~~~~~~a~~~---~~~~a~~~lg~~~~~g~~~~~~~~~A~~~~~~a~~~~---~~~a~~   78 (273)
T 1ouv_A            5 DPKELVGLGAKSYKEKDFTQAKKYFEKACDL---KENSGCFNLGVLYYQGQGVEKNLKKAASFYAKACDLN---YSNGCH   78 (273)
T ss_dssp             CHHHHHHHHHHHHHTTCHHHHHHHHHHHHHT---TCHHHHHHHHHHHHHTSSSCCCHHHHHHHHHHHHHTT---CHHHHH
T ss_pred             ChHHHHHHHHHHHhCCCHHHHHHHHHHHHHC---CCHHHHHHHHHHHHcCCCcCCCHHHHHHHHHHHHHCC---CHHHHH
Confidence            5566666777777777777777777777763   245666666677777    777777777777776654   566666


Q ss_pred             HHHHHHHh----cCChhHHHHHHHHHHhcCCCCCccccCcHHHHHHHHHHHHH----cCCHhHHHHHHHHHhhCCCCCCH
Q 040027          171 TLINGLCR----TGHTMIALNLFEEMANGNGEIGVVCKPNTVTYSTIIDGLCK----EGFVDKAKALFLQMKDENINPDV  242 (595)
Q Consensus       171 ~l~~~~~~----~g~~~~A~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~----~g~~~~A~~~~~~~~~~~~~~~~  242 (595)
                      .+...|..    .+++++|+..|++....+         +..++..+...|..    .+++++|.+.|++..+.+   +.
T Consensus        79 ~lg~~~~~g~~~~~~~~~A~~~~~~a~~~~---------~~~a~~~lg~~~~~~~~~~~~~~~A~~~~~~a~~~~---~~  146 (273)
T 1ouv_A           79 LLGNLYYSGQGVSQNTNKALQYYSKACDLK---------YAEGCASLGGIYHDGKVVTRDFKKAVEYFTKACDLN---DG  146 (273)
T ss_dssp             HHHHHHHHTSSSCCCHHHHHHHHHHHHHTT---------CHHHHHHHHHHHHHCSSSCCCHHHHHHHHHHHHHTT---CH
T ss_pred             HHHHHHhCCCCcccCHHHHHHHHHHHHHcC---------CccHHHHHHHHHHcCCCcccCHHHHHHHHHHHHhcC---cH
Confidence            67777776    777777777777766543         45666666666666    677777777777666654   45


Q ss_pred             hHHHHHHHHHHh----cCCHHHHHHHHHHHHHCCCCCCHhhHHHHHHHHHh----cCChHHHHHHHHHHHHCCCCCCHHH
Q 040027          243 VTYNSLIHGLCH----ANDWNEAKRLFIEMMDQGVQPSVVTFNVIMDELCK----NRKMDEASRLLDLMVQRGVRPNACT  314 (595)
Q Consensus       243 ~~~~~ll~~~~~----~~~~~~A~~~~~~~~~~~~~~~~~~~~~l~~~~~~----~g~~~~a~~~~~~~~~~~~~~~~~~  314 (595)
                      ..+..+...|..    .+++++|..+|++..+.+   +...+..+...+..    .+++++|...|++..+.+   +...
T Consensus       147 ~a~~~lg~~~~~~~~~~~~~~~A~~~~~~a~~~~---~~~a~~~lg~~~~~g~~~~~~~~~A~~~~~~a~~~~---~~~a  220 (273)
T 1ouv_A          147 DGCTILGSLYDAGRGTPKDLKKALASYDKACDLK---DSPGCFNAGNMYHHGEGATKNFKEALARYSKACELE---NGGG  220 (273)
T ss_dssp             HHHHHHHHHHHHTSSSCCCHHHHHHHHHHHHHTT---CHHHHHHHHHHHHHTCSSCCCHHHHHHHHHHHHHTT---CHHH
T ss_pred             HHHHHHHHHHHcCCCCCCCHHHHHHHHHHHHHCC---CHHHHHHHHHHHHcCCCCCccHHHHHHHHHHHHhCC---CHHH
Confidence            555566666665    666666666666666542   34455555666666    666666666666666543   2444


Q ss_pred             HHHHHHHHHh----cCCHHHHHHHHHHHHhc
Q 040027          315 YNTLMDGFCL----MGKINRAEELFGSMESM  341 (595)
Q Consensus       315 ~~~l~~~~~~----~~~~~~a~~~~~~~~~~  341 (595)
                      +..+..+|..    .+++++|...|++..+.
T Consensus       221 ~~~l~~~~~~g~~~~~~~~~A~~~~~~a~~~  251 (273)
T 1ouv_A          221 CFNLGAMQYNGEGVTRNEKQAIENFKKGCKL  251 (273)
T ss_dssp             HHHHHHHHHTTSSSSCCSTTHHHHHHHHHHH
T ss_pred             HHHHHHHHHcCCCcccCHHHHHHHHHHHHHc
Confidence            5555555555    56666666666665554

>1xnf_A Lipoprotein NLPI; TPR, tetratricopeptide, structural genomi unknown function; 1.98A {Escherichia coli} SCOP: a.118.8.1

Probab=99.65  E-value=8.8e-15  Score=135.33  Aligned_cols=255  Identities=10%  Similarity=-0.015  Sum_probs=161.6

Q ss_pred             cccccCCCChHHHHHHHHHHHHhCCCCCCHhhHHHHHHHHHcCCCchhHHhhCCCCCCHHHHHHHHHHHHhcCChhHHHH
Q 040027           38 REGDINVITPNEAFCIFDYMLRMHPSPPPVSSFNILLASLAKNKHYDTRLNATGLFPNLYTYNILINCFCKIGRVSLGFI  117 (595)
Q Consensus        38 ~~~~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~  117 (595)
                      +..+...|++++|++.|+++++..+.  ++.                         .++..|..++..+...|++++|+.
T Consensus        12 ~~~~~~~~~~~~A~~~~~~~~~~~~~--~~~-------------------------~~~~~~~~l~~~~~~~~~~~~A~~   64 (275)
T 1xnf_A           12 AVPLQPTLQQEVILARMEQILASRAL--TDD-------------------------ERAQLLYERGVLYDSLGLRALARN   64 (275)
T ss_dssp             CCCCCCCHHHHHHHHHHHHHHTSSCC--CHH-------------------------HHHHHHHHHHHHHHHTTCHHHHHH
T ss_pred             eeccCccchHHHHHHHHHHHHhcccc--cCc-------------------------hhHHHHHHHHHHHHHcccHHHHHH
Confidence            33455668899999999998887543  110                         134556677788888888888888


Q ss_pred             HHHHHHhCCCCCCHHHHHHHHHHHHhcCCHhHHHHHHHHHHhcCCCCCHhhHHHHHHHHHhcCChhHHHHHHHHHHhcCC
Q 040027          118 AFGRILRSCFTPNAATFNSLIKGLHAESRIMEAAALFTKLKAFGCEPNVITYNTLINGLCRTGHTMIALNLFEEMANGNG  197 (595)
Q Consensus       118 ~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~  197 (595)
                      .|+++++.. +.+..+|..+...+...|++++|++.|+++.... +.+..++..++..+...|++++|+..|+++.... 
T Consensus        65 ~~~~al~~~-~~~~~~~~~la~~~~~~~~~~~A~~~~~~al~~~-~~~~~~~~~la~~~~~~g~~~~A~~~~~~a~~~~-  141 (275)
T 1xnf_A           65 DFSQALAIR-PDMPEVFNYLGIYLTQAGNFDAAYEAFDSVLELD-PTYNYAHLNRGIALYYGGRDKLAQDDLLAFYQDD-  141 (275)
T ss_dssp             HHHHHHHHC-CCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCTHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-
T ss_pred             HHHHHHHcC-CCcHHHHHHHHHHHHHccCHHHHHHHHHHHHhcC-ccccHHHHHHHHHHHHhccHHHHHHHHHHHHHhC-
Confidence            888888874 4467788888888888888888888888888764 3356777888888888888888888888887754 


Q ss_pred             CCCccccCcHHHHHHHHHHHHHcCCHhHHHHHHHHHhhCCCCCCHhHHHHHHHHHHhcCCHHHHHHHHHHHHHCCCCC--
Q 040027          198 EIGVVCKPNTVTYSTIIDGLCKEGFVDKAKALFLQMKDENINPDVVTYNSLIHGLCHANDWNEAKRLFIEMMDQGVQP--  275 (595)
Q Consensus       198 ~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~~ll~~~~~~~~~~~A~~~~~~~~~~~~~~--  275 (595)
                             |+.......+..+...|++++|...+++..... +++...+ .++..+...++.++|...+..........  
T Consensus       142 -------~~~~~~~~~~~~~~~~~~~~~A~~~~~~~~~~~-~~~~~~~-~~~~~~~~~~~~~~a~~~~~~~~~~~~~~~~  212 (275)
T 1xnf_A          142 -------PNDPFRSLWLYLAEQKLDEKQAKEVLKQHFEKS-DKEQWGW-NIVEFYLGNISEQTLMERLKADATDNTSLAE  212 (275)
T ss_dssp             -------TTCHHHHHHHHHHHHHHCHHHHHHHHHHHHHHS-CCCSTHH-HHHHHHTTSSCHHHHHHHHHHHCCSHHHHHH
T ss_pred             -------CCChHHHHHHHHHHHhcCHHHHHHHHHHHHhcC-CcchHHH-HHHHHHHHhcCHHHHHHHHHHHhcccccccc
Confidence                   222233334444456677888888777666542 2233333 35566666677777777776665431100  


Q ss_pred             -CHhhHHHHHHHHHhcCChHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHhcCCHHHHHHHH
Q 040027          276 -SVVTFNVIMDELCKNRKMDEASRLLDLMVQRGVRPNACTYNTLMDGFCLMGKINRAEELF  335 (595)
Q Consensus       276 -~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~  335 (595)
                       +...+..+..++...|++++|...|+++....  |+.  +.....++...|++++|++.+
T Consensus       213 ~~~~~~~~la~~~~~~g~~~~A~~~~~~al~~~--p~~--~~~~~~~~~~l~~~~~a~~~~  269 (275)
T 1xnf_A          213 HLSETNFYLGKYYLSLGDLDSATALFKLAVANN--VHN--FVEHRYALLELSLLGQDQDDL  269 (275)
T ss_dssp             HHHHHHHHHHHHHHHTTCHHHHHHHHHHHHTTC--CTT--CHHHHHHHHHHHHHHHC----
T ss_pred             cccHHHHHHHHHHHHcCCHHHHHHHHHHHHhCC--chh--HHHHHHHHHHHHHHHhhHHHH
Confidence             13445555666666666666666666665542  211  112233444455555554443

>1xnf_A Lipoprotein NLPI; TPR, tetratricopeptide, structural genomi unknown function; 1.98A {Escherichia coli} SCOP: a.118.8.1

Probab=99.64  E-value=2.8e-14  Score=131.95  Aligned_cols=243  Identities=9%  Similarity=-0.041  Sum_probs=121.1

Q ss_pred             CChHHHHHHHHHHHHCCC---CCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHhcCCCCCHHHHHHHHHHHHhCCCHHHHH
Q 040027          291 RKMDEASRLLDLMVQRGV---RPNACTYNTLMDGFCLMGKINRAEELFGSMESMGCKHDDVSYNILINGYCKNKEVEEAL  367 (595)
Q Consensus       291 g~~~~a~~~~~~~~~~~~---~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~A~  367 (595)
                      |++++|+..++++.+...   +.+..++..++.++...|++++|...|+++.+.. +.+...+..+..+|...|++++|+
T Consensus        19 ~~~~~A~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~A~~~~~~al~~~-~~~~~~~~~la~~~~~~~~~~~A~   97 (275)
T 1xnf_A           19 LQQEVILARMEQILASRALTDDERAQLLYERGVLYDSLGLRALARNDFSQALAIR-PDMPEVFNYLGIYLTQAGNFDAAY   97 (275)
T ss_dssp             HHHHHHHHHHHHHHTSSCCCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-CCCHHHHHHHHHHHHHTTCHHHHH
T ss_pred             chHHHHHHHHHHHHhcccccCchhHHHHHHHHHHHHHcccHHHHHHHHHHHHHcC-CCcHHHHHHHHHHHHHccCHHHHH
Confidence            445555555555554321   1123344455555555555555555555555443 334455555555555555555555


Q ss_pred             HHHHHHHHCCCCCCHHHHHHHHHHHHccCCHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHHcC
Q 040027          368 SLYREMVSKGIKPTVVTYNTLFLGLFEIHQVEHALKLFDEMQRDGVAADTRTYTTFIDGLCKNGYIIEAVELFRTLRILK  447 (595)
Q Consensus       368 ~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~  447 (595)
                      ..|+++++..+. +...+..+...+...|++++|...++++.+..  |+.......+..+...|++++|...+++.....
T Consensus        98 ~~~~~al~~~~~-~~~~~~~la~~~~~~g~~~~A~~~~~~a~~~~--~~~~~~~~~~~~~~~~~~~~~A~~~~~~~~~~~  174 (275)
T 1xnf_A           98 EAFDSVLELDPT-YNYAHLNRGIALYYGGRDKLAQDDLLAFYQDD--PNDPFRSLWLYLAEQKLDEKQAKEVLKQHFEKS  174 (275)
T ss_dssp             HHHHHHHHHCTT-CTHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC--TTCHHHHHHHHHHHHHHCHHHHHHHHHHHHHHS
T ss_pred             HHHHHHHhcCcc-ccHHHHHHHHHHHHhccHHHHHHHHHHHHHhC--CCChHHHHHHHHHHHhcCHHHHHHHHHHHHhcC
Confidence            555555554222 34455555555555555555555555555532  222222222333344566666666665555443


Q ss_pred             CCcCHHHHHHHHHHHHhcCChHHHHHHHHhcccCCCCCC-----HHHHHHHHHHHHhcCChhHHHHHHHHHHHcCCCCCH
Q 040027          448 CELDIQAYNCLIDGLCKSGRLKFAWELFCSLPHGVLVPN-----VVTYNIMIQGLCNDGQMDKARDLFLDMEENAAAPDV  522 (595)
Q Consensus       448 ~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~p~-----~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~~~  522 (595)
                       +++...+ .++..+...++.++|...++++...  .|+     ..++..++.+|...|++++|...|+++++.. +.+.
T Consensus       175 -~~~~~~~-~~~~~~~~~~~~~~a~~~~~~~~~~--~~~~~~~~~~~~~~la~~~~~~g~~~~A~~~~~~al~~~-p~~~  249 (275)
T 1xnf_A          175 -DKEQWGW-NIVEFYLGNISEQTLMERLKADATD--NTSLAEHLSETNFYLGKYYLSLGDLDSATALFKLAVANN-VHNF  249 (275)
T ss_dssp             -CCCSTHH-HHHHHHTTSSCHHHHHHHHHHHCCS--HHHHHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHTTC-CTTC
T ss_pred             -CcchHHH-HHHHHHHHhcCHHHHHHHHHHHhcc--cccccccccHHHHHHHHHHHHcCCHHHHHHHHHHHHhCC-chhH
Confidence             2332222 2444555555666666666665542  221     3455566666666666666666666666542 1121


Q ss_pred             HHHHHHHHHHHHcCChhHHHHHH
Q 040027          523 ITFDMLIHGFIRINEPSKVNELL  545 (595)
Q Consensus       523 ~~~~~l~~~~~~~g~~~~A~~~~  545 (595)
                      .   ....++...|++++|.+.+
T Consensus       250 ~---~~~~~~~~l~~~~~a~~~~  269 (275)
T 1xnf_A          250 V---EHRYALLELSLLGQDQDDL  269 (275)
T ss_dssp             H---HHHHHHHHHHHHHHC----
T ss_pred             H---HHHHHHHHHHHHHhhHHHH
Confidence            1   2233455556666655544

>2q7f_A YRRB protein; TPR, protein binding; 2.49A {Bacillus subtilis} SCOP: k.38.1.1

Probab=99.64  E-value=2.4e-14  Score=129.58  Aligned_cols=211  Identities=14%  Similarity=0.075  Sum_probs=127.8

Q ss_pred             HHHHHHHHHHHhCCCHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHccCCHHHHHHHHHHHHHCCCCCCHHHHHHHHHHH
Q 040027          348 VSYNILINGYCKNKEVEEALSLYREMVSKGIKPTVVTYNTLFLGLFEIHQVEHALKLFDEMQRDGVAADTRTYTTFIDGL  427 (595)
Q Consensus       348 ~~~~~l~~~~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~  427 (595)
                      ..+..+...+...|++++|...|+++.+.... +...+..+...+...|++++|...++++.+.. +.+...+..+...+
T Consensus        24 ~~~~~~a~~~~~~~~~~~A~~~~~~~l~~~~~-~~~~~~~la~~~~~~~~~~~A~~~~~~~~~~~-~~~~~~~~~la~~~  101 (243)
T 2q7f_A           24 MTGGQQMGRGSEFGDYEKAAEAFTKAIEENKE-DAIPYINFANLLSSVNELERALAFYDKALELD-SSAATAYYGAGNVY  101 (243)
T ss_dssp             ------------------CCTTHHHHHTTCTT-CHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHhhCHHHHHHHHHHHHHhCcc-cHHHHHHHHHHHHHcCCHHHHHHHHHHHHHcC-CcchHHHHHHHHHH
Confidence            34555555566666666666666666654322 45556666666666666666666666666542 34556666666777


Q ss_pred             HhcCCHHHHHHHHHHHHHcCCCcCHHHHHHHHHHHHhcCChHHHHHHHHhcccCCCCCCHHHHHHHHHHHHhcCChhHHH
Q 040027          428 CKNGYIIEAVELFRTLRILKCELDIQAYNCLIDGLCKSGRLKFAWELFCSLPHGVLVPNVVTYNIMIQGLCNDGQMDKAR  507 (595)
Q Consensus       428 ~~~g~~~~A~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~p~~~~~~~l~~~~~~~g~~~~A~  507 (595)
                      ...|++++|...++++.+.. +.+...+..++..+...|++++|...++++.+. .+.+...+..++..+...|++++|+
T Consensus       102 ~~~~~~~~A~~~~~~~~~~~-~~~~~~~~~~a~~~~~~~~~~~A~~~~~~~~~~-~~~~~~~~~~l~~~~~~~~~~~~A~  179 (243)
T 2q7f_A          102 VVKEMYKEAKDMFEKALRAG-MENGDLFYMLGTVLVKLEQPKLALPYLQRAVEL-NENDTEARFQFGMCLANEGMLDEAL  179 (243)
T ss_dssp             HHTTCHHHHHHHHHHHHHHT-CCSHHHHHHHHHHHHHTSCHHHHHHHHHHHHHH-CTTCHHHHHHHHHHHHHHTCCHHHH
T ss_pred             HHhccHHHHHHHHHHHHHhC-CCCHHHHHHHHHHHHHhccHHHHHHHHHHHHHh-CCccHHHHHHHHHHHHHcCCHHHHH
Confidence            77777777777777776654 456667777777777777777777777777663 1224666777777777778888888


Q ss_pred             HHHHHHHHcCCCCCHHHHHHHHHHHHHcCChhHHHHHHHHHHHCCCCCCHHHHHHHH
Q 040027          508 DLFLDMEENAAAPDVITFDMLIHGFIRINEPSKVNELLHKMKEKKVMPDASIVSIVV  564 (595)
Q Consensus       508 ~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~p~~~~~~~l~  564 (595)
                      ..++++.+.. +.+..++..++.+|...|++++|...++++.+.. +.+...+..+.
T Consensus       180 ~~~~~~~~~~-~~~~~~~~~la~~~~~~~~~~~A~~~~~~~~~~~-p~~~~~~~~~~  234 (243)
T 2q7f_A          180 SQFAAVTEQD-PGHADAFYNAGVTYAYKENREKALEMLDKAIDIQ-PDHMLALHAKK  234 (243)
T ss_dssp             HHHHHHHHHC-TTCHHHHHHHHHHHHHTTCTTHHHHHHHHHHHHC-TTCHHHHHHHT
T ss_pred             HHHHHHHHhC-cccHHHHHHHHHHHHHccCHHHHHHHHHHHHccC-cchHHHHHHHH
Confidence            8877777764 4456677777777778888888888888777642 22344444443

>2ho1_A Type 4 fimbrial biogenesis protein PILF; type IV pilus biogenesis, TPR, superhelix, protein binding; HET: MSE; 2.00A {Pseudomonas aeruginosa} PDB: 2fi7_A

Probab=99.62  E-value=3.8e-13  Score=122.46  Aligned_cols=202  Identities=12%  Similarity=-0.007  Sum_probs=130.9

Q ss_pred             HHHHHHHHHHHHhcCChhHHHHHHHHHHhCCCCCCHHHHHHHHHHHHhcCCHhHHHHHHHHHHhcCCCCCHhhHHHHHHH
Q 040027           96 LYTYNILINCFCKIGRVSLGFIAFGRILRSCFTPNAATFNSLIKGLHAESRIMEAAALFTKLKAFGCEPNVITYNTLING  175 (595)
Q Consensus        96 ~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~~l~~~  175 (595)
                      +..|..++..+...|++++|+..|+++.+.. +.+..++..+...+...|++++|.+.|+++.... +.+..++..++..
T Consensus        37 ~~~~~~~a~~~~~~~~~~~A~~~~~~al~~~-~~~~~~~~~la~~~~~~~~~~~A~~~~~~a~~~~-~~~~~~~~~la~~  114 (252)
T 2ho1_A           37 RDAYIQLGLGYLQRGNTEQAKVPLRKALEID-PSSADAHAALAVVFQTEMEPKLADEEYRKALASD-SRNARVLNNYGGF  114 (252)
T ss_dssp             HHHHHHHHHHHHHTTCTGGGHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHcCChHHHHHHHHHHHhcC-CChHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHC-cCcHHHHHHHHHH
Confidence            4556667777777777777777777777663 4456667777777777777777777777776653 2356666667777


Q ss_pred             HHhcCChhHHHHHHHHHHhcCCCCCccccCcHHHHHHHHHHHHHcCCHhHHHHHHHHHhhCCCCCCHhHHHHHHHHHHhc
Q 040027          176 LCRTGHTMIALNLFEEMANGNGEIGVVCKPNTVTYSTIIDGLCKEGFVDKAKALFLQMKDENINPDVVTYNSLIHGLCHA  255 (595)
Q Consensus       176 ~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~~ll~~~~~~  255 (595)
                      +...|++++|++.|+++...+.     .+.+...+..+..++...|++++|.+.|+++.... +.+...+..+...+...
T Consensus       115 ~~~~g~~~~A~~~~~~~~~~~~-----~~~~~~~~~~la~~~~~~g~~~~A~~~~~~~~~~~-~~~~~~~~~la~~~~~~  188 (252)
T 2ho1_A          115 LYEQKRYEEAYQRLLEASQDTL-----YPERSRVFENLGLVSLQMKKPAQAKEYFEKSLRLN-RNQPSVALEMADLLYKE  188 (252)
T ss_dssp             HHHTTCHHHHHHHHHHHTTCTT-----CTTHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-SCCHHHHHHHHHHHHHT
T ss_pred             HHHHhHHHHHHHHHHHHHhCcc-----CcccHHHHHHHHHHHHHcCCHHHHHHHHHHHHhcC-cccHHHHHHHHHHHHHc
Confidence            7777777777777777765110     13345566666677777777777777777666543 22455666666666667


Q ss_pred             CCHHHHHHHHHHHHHCCCCCCHhhHHHHHHHHHhcCChHHHHHHHHHHHHC
Q 040027          256 NDWNEAKRLFIEMMDQGVQPSVVTFNVIMDELCKNRKMDEASRLLDLMVQR  306 (595)
Q Consensus       256 ~~~~~A~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~  306 (595)
                      |++++|...++++.+.. +.+...+..+...+...|++++|.++++++.+.
T Consensus       189 g~~~~A~~~~~~~~~~~-~~~~~~~~~~~~~~~~~g~~~~A~~~~~~~~~~  238 (252)
T 2ho1_A          189 REYVPARQYYDLFAQGG-GQNARSLLLGIRLAKVFEDRDTAASYGLQLKRL  238 (252)
T ss_dssp             TCHHHHHHHHHHHHTTS-CCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH
T ss_pred             CCHHHHHHHHHHHHHhC-cCcHHHHHHHHHHHHHccCHHHHHHHHHHHHHH
Confidence            77777777766666542 234455555666666666666666666666654

>2ho1_A Type 4 fimbrial biogenesis protein PILF; type IV pilus biogenesis, TPR, superhelix, protein binding; HET: MSE; 2.00A {Pseudomonas aeruginosa} PDB: 2fi7_A

Probab=99.62  E-value=3.6e-13  Score=122.63  Aligned_cols=197  Identities=16%  Similarity=0.060  Sum_probs=78.9

Q ss_pred             HHHHHHHHHhcCCHHHHHHHHHHHHhcCCCCCHHHHHHHHHHHHhCCCHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHc
Q 040027          315 YNTLMDGFCLMGKINRAEELFGSMESMGCKHDDVSYNILINGYCKNKEVEEALSLYREMVSKGIKPTVVTYNTLFLGLFE  394 (595)
Q Consensus       315 ~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~~l~~~~~~  394 (595)
                      +..++..+...|++++|...++++.+.. +.+...+..+..++...|++++|.+.++++.+.... +...+..+...+..
T Consensus        40 ~~~~a~~~~~~~~~~~A~~~~~~al~~~-~~~~~~~~~la~~~~~~~~~~~A~~~~~~a~~~~~~-~~~~~~~la~~~~~  117 (252)
T 2ho1_A           40 YIQLGLGYLQRGNTEQAKVPLRKALEID-PSSADAHAALAVVFQTEMEPKLADEEYRKALASDSR-NARVLNNYGGFLYE  117 (252)
T ss_dssp             HHHHHHHHHHTTCTGGGHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTT-CHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHcCChHHHHHHHHHHHhcC-CChHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHCcC-cHHHHHHHHHHHHH
Confidence            3344444444444444444444444332 223334444444444444444444444444433211 33333344444444


Q ss_pred             cCCHHHHHHHHHHHHHCCCCC-CHHHHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCcCHHHHHHHHHHHHhcCChHHHHH
Q 040027          395 IHQVEHALKLFDEMQRDGVAA-DTRTYTTFIDGLCKNGYIIEAVELFRTLRILKCELDIQAYNCLIDGLCKSGRLKFAWE  473 (595)
Q Consensus       395 ~~~~~~a~~~~~~~~~~~~~~-~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~  473 (595)
                      .|++++|.+.++++.+.+..| +...+..+...+...|++++|...++++.+.. +.+...+..++.++...|++++|..
T Consensus       118 ~g~~~~A~~~~~~~~~~~~~~~~~~~~~~la~~~~~~g~~~~A~~~~~~~~~~~-~~~~~~~~~la~~~~~~g~~~~A~~  196 (252)
T 2ho1_A          118 QKRYEEAYQRLLEASQDTLYPERSRVFENLGLVSLQMKKPAQAKEYFEKSLRLN-RNQPSVALEMADLLYKEREYVPARQ  196 (252)
T ss_dssp             TTCHHHHHHHHHHHTTCTTCTTHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-SCCHHHHHHHHHHHHHTTCHHHHHH
T ss_pred             HhHHHHHHHHHHHHHhCccCcccHHHHHHHHHHHHHcCCHHHHHHHHHHHHhcC-cccHHHHHHHHHHHHHcCCHHHHHH
Confidence            444444444444443311111 22333333444444444444444444444332 2233334444444444444444444


Q ss_pred             HHHhcccCCCCCCHHHHHHHHHHHHhcCChhHHHHHHHHHHH
Q 040027          474 LFCSLPHGVLVPNVVTYNIMIQGLCNDGQMDKARDLFLDMEE  515 (595)
Q Consensus       474 ~~~~~~~~~~~p~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~  515 (595)
                      .++++.+. .+.+...+..+...+...|++++|.++++++.+
T Consensus       197 ~~~~~~~~-~~~~~~~~~~~~~~~~~~g~~~~A~~~~~~~~~  237 (252)
T 2ho1_A          197 YYDLFAQG-GGQNARSLLLGIRLAKVFEDRDTAASYGLQLKR  237 (252)
T ss_dssp             HHHHHHTT-SCCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHH
T ss_pred             HHHHHHHh-CcCcHHHHHHHHHHHHHccCHHHHHHHHHHHHH
Confidence            44443331 111233333333344444444444444444433

>2q7f_A YRRB protein; TPR, protein binding; 2.49A {Bacillus subtilis} SCOP: k.38.1.1

Probab=99.62  E-value=4.6e-14  Score=127.75  Aligned_cols=211  Identities=16%  Similarity=0.109  Sum_probs=133.8

Q ss_pred             HHHHHHHHHHHHhcCCHHHHHHHHHHHHhcCCCCCHHHHHHHHHHHHhCCCHHHHHHHHHHHHHCCCCCCHHHHHHHHHH
Q 040027          312 ACTYNTLMDGFCLMGKINRAEELFGSMESMGCKHDDVSYNILINGYCKNKEVEEALSLYREMVSKGIKPTVVTYNTLFLG  391 (595)
Q Consensus       312 ~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~~l~~~  391 (595)
                      ...+..++..+...|++++|...++++.+.. +.+...+..+...+...|++++|+..++++.+.... +...+..+...
T Consensus        23 ~~~~~~~a~~~~~~~~~~~A~~~~~~~l~~~-~~~~~~~~~la~~~~~~~~~~~A~~~~~~~~~~~~~-~~~~~~~la~~  100 (243)
T 2q7f_A           23 SMTGGQQMGRGSEFGDYEKAAEAFTKAIEEN-KEDAIPYINFANLLSSVNELERALAFYDKALELDSS-AATAYYGAGNV  100 (243)
T ss_dssp             -------------------CCTTHHHHHTTC-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTT-CHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHhhCHHHHHHHHHHHHHhC-cccHHHHHHHHHHHHHcCCHHHHHHHHHHHHHcCCc-chHHHHHHHHH
Confidence            3445555666666666777776666666543 345556666666777777777777777766665322 55666666677


Q ss_pred             HHccCCHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCcCHHHHHHHHHHHHhcCChHHH
Q 040027          392 LFEIHQVEHALKLFDEMQRDGVAADTRTYTTFIDGLCKNGYIIEAVELFRTLRILKCELDIQAYNCLIDGLCKSGRLKFA  471 (595)
Q Consensus       392 ~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A  471 (595)
                      +...|++++|...++++.+.. +.+...+..+...+...|++++|...++++.+.. +.+...+..++..+...|++++|
T Consensus       101 ~~~~~~~~~A~~~~~~~~~~~-~~~~~~~~~~a~~~~~~~~~~~A~~~~~~~~~~~-~~~~~~~~~l~~~~~~~~~~~~A  178 (243)
T 2q7f_A          101 YVVKEMYKEAKDMFEKALRAG-MENGDLFYMLGTVLVKLEQPKLALPYLQRAVELN-ENDTEARFQFGMCLANEGMLDEA  178 (243)
T ss_dssp             HHHTTCHHHHHHHHHHHHHHT-CCSHHHHHHHHHHHHHTSCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHHTCCHHH
T ss_pred             HHHhccHHHHHHHHHHHHHhC-CCCHHHHHHHHHHHHHhccHHHHHHHHHHHHHhC-CccHHHHHHHHHHHHHcCCHHHH
Confidence            777777777777777776653 4456667777777778888888888888877665 55677777888888888888888


Q ss_pred             HHHHHhcccCCCCCCHHHHHHHHHHHHhcCChhHHHHHHHHHHHcCCCCCHHHHHHH
Q 040027          472 WELFCSLPHGVLVPNVVTYNIMIQGLCNDGQMDKARDLFLDMEENAAAPDVITFDML  528 (595)
Q Consensus       472 ~~~~~~~~~~~~~p~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~~l  528 (595)
                      ...++++.... +.+..++..++.+|...|++++|...++++.+.. +.+...+..+
T Consensus       179 ~~~~~~~~~~~-~~~~~~~~~la~~~~~~~~~~~A~~~~~~~~~~~-p~~~~~~~~~  233 (243)
T 2q7f_A          179 LSQFAAVTEQD-PGHADAFYNAGVTYAYKENREKALEMLDKAIDIQ-PDHMLALHAK  233 (243)
T ss_dssp             HHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCTTHHHHHHHHHHHHC-TTCHHHHHHH
T ss_pred             HHHHHHHHHhC-cccHHHHHHHHHHHHHccCHHHHHHHHHHHHccC-cchHHHHHHH
Confidence            88888877631 2346677788888888888888888888888764 3344444443

>3spa_A Mtrpol, DNA-directed RNA polymerase, mitochondrial; single-subunit DNA-dependent RNA polymerase in mitochondria, transferase; 2.50A {Homo sapiens}

Probab=99.62  E-value=5.7e-16  Score=158.26  Aligned_cols=154  Identities=14%  Similarity=0.175  Sum_probs=127.1

Q ss_pred             CCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHH---cCCCcCHHHHHHHHHHHHhcCChHHHHHHHHhcccCCCCCCHHHH
Q 040027          414 AADTRTYTTFIDGLCKNGYIIEAVELFRTLRI---LKCELDIQAYNCLIDGLCKSGRLKFAWELFCSLPHGVLVPNVVTY  490 (595)
Q Consensus       414 ~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~---~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~p~~~~~  490 (595)
                      .....+|+++|.+|++.|++++|..+|++|.+   .|+.||..+||.|+.+|++.|++++|.++|++|.+.|+.||..||
T Consensus       124 ~~~~~TynaLIdglcK~G~leeA~~Lf~eM~~m~~kG~~PdvvTYNtLI~Glck~G~~~eA~~Lf~eM~~~G~~PDvvTY  203 (1134)
T 3spa_A          124 SGQQQRLLAFFKCCLLTDQLPLAHHLLVVHHGQRQKRKLLTLDMYNAVMLGWARQGAFKELVYVLFMVKDAGLTPDLLSY  203 (1134)
T ss_dssp             CHHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHSHHHHTTCCHHHHHHHHHHHHHHTCHHHHHHHHHHHHHTTCCCCHHHH
T ss_pred             HhHHHHHHHHHHHHHhCCCHHHHHHHHHHHHHHhhcCCCCCHhHHHHHHHHHHhCCCHHHHHHHHHHHHHcCCCCcHHHH
Confidence            34456899999999999999999999988763   477899999999999999999999999999999999999999999


Q ss_pred             HHHHHHHHhcCCh-hHHHHHHHHHHHcCCCCCHHHHHHHHHHHHHcCChhHHHHHHHHHHHCCCCCC------HHHHHHH
Q 040027          491 NIMIQGLCNDGQM-DKARDLFLDMEENAAAPDVITFDMLIHGFIRINEPSKVNELLHKMKEKKVMPD------ASIVSIV  563 (595)
Q Consensus       491 ~~l~~~~~~~g~~-~~A~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~p~------~~~~~~l  563 (595)
                      +++|.++++.|+. ++|.++|++|.+.|+.||..+|+.++..+.+.    ..++.++++ .-++.|+      ..+...|
T Consensus       204 ntLI~glcK~G~~~e~A~~Ll~EM~~kG~~PD~vtY~~ll~~~eR~----~vL~~Vrkv-~P~f~p~~~~~~~~~t~~LL  278 (1134)
T 3spa_A          204 AAALQCMGRQDQDAGTIERCLEQMSQEGLKLQALFTAVLLSEEDRA----TVLKAVHKV-KPTFSLPPQLPPPVNTSKLL  278 (1134)
T ss_dssp             HHHHHHHHHHTCCHHHHHHHHHHHHHHTCCSHHHHHHSCCCHHHHH----HHHHHHGGG-CCCCCCCCCCCCCCCCCTTT
T ss_pred             HHHHHHHHhCCCcHHHHHHHHHHHHHcCCCCChhhcccccChhhHH----HHHHHHHHh-CcccCCCCCCcccccchHHH
Confidence            9999999999985 78899999999999999999999887655443    455555555 3355554      4555667


Q ss_pred             HHHHHhcCc
Q 040027          564 VDLLVKNEI  572 (595)
Q Consensus       564 ~~~~~~~g~  572 (595)
                      .+.|.+.|.
T Consensus       279 ~dl~s~d~~  287 (1134)
T 3spa_A          279 RDVYAKDGR  287 (1134)
T ss_dssp             HHHHCCCSC
T ss_pred             HHHHccCCC
Confidence            788887774

>2vq2_A PILW, putative fimbrial biogenesis and twitching motility protein; secretin, TPR repeat, type IV pilus, bacterail virulence; 1.54A {Neisseria meningitidis}

Probab=99.61  E-value=2.6e-13  Score=121.04  Aligned_cols=199  Identities=10%  Similarity=-0.000  Sum_probs=119.5

Q ss_pred             HHHHHHHHHHHHhCCCHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHccCCHHHHHHHHHHHHHCCCCCCHHHHHHHHHH
Q 040027          347 DVSYNILINGYCKNKEVEEALSLYREMVSKGIKPTVVTYNTLFLGLFEIHQVEHALKLFDEMQRDGVAADTRTYTTFIDG  426 (595)
Q Consensus       347 ~~~~~~l~~~~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~  426 (595)
                      ...+..+...+...|++++|+..++++.+.... +...+..+...+...|++++|...++++.+.. +.+...+..+...
T Consensus         8 ~~~~~~~~~~~~~~~~~~~A~~~~~~~~~~~~~-~~~~~~~l~~~~~~~~~~~~A~~~~~~a~~~~-~~~~~~~~~l~~~   85 (225)
T 2vq2_A            8 SNIKTQLAMEYMRGQDYRQATASIEDALKSDPK-NELAWLVRAEIYQYLKVNDKAQESFRQALSIK-PDSAEINNNYGWF   85 (225)
T ss_dssp             HHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTT-CHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHhhHHHHHHHHHHHHHhCcc-chHHHHHHHHHHHHcCChHHHHHHHHHHHHhC-CCChHHHHHHHHH
Confidence            334555555555555555555555555554222 34455555555555666666666665555542 3345555566666


Q ss_pred             HHhc-CCHHHHHHHHHHHHHcCC-CcCHHHHHHHHHHHHhcCChHHHHHHHHhcccCCCCC-CHHHHHHHHHHHHhcCCh
Q 040027          427 LCKN-GYIIEAVELFRTLRILKC-ELDIQAYNCLIDGLCKSGRLKFAWELFCSLPHGVLVP-NVVTYNIMIQGLCNDGQM  503 (595)
Q Consensus       427 ~~~~-g~~~~A~~~~~~~~~~~~-~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~p-~~~~~~~l~~~~~~~g~~  503 (595)
                      +... |++++|...++++.+.+. +.+...+..++.++...|++++|...++++.+.  .| +...+..++.++...|++
T Consensus        86 ~~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~~--~~~~~~~~~~la~~~~~~~~~  163 (225)
T 2vq2_A           86 LCGRLNRPAESMAYFDKALADPTYPTPYIANLNKGICSAKQGQFGLAEAYLKRSLAA--QPQFPPAFKELARTKMLAGQL  163 (225)
T ss_dssp             HHTTTCCHHHHHHHHHHHHTSTTCSCHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH--STTCHHHHHHHHHHHHHHTCH
T ss_pred             HHHhcCcHHHHHHHHHHHHcCcCCcchHHHHHHHHHHHHHcCCHHHHHHHHHHHHHh--CCCCchHHHHHHHHHHHcCCH
Confidence            6666 666666666666665211 222456666666666777777777777666652  23 356666677777777777


Q ss_pred             hHHHHHHHHHHHcCCC-CCHHHHHHHHHHHHHcCChhHHHHHHHHHHH
Q 040027          504 DKARDLFLDMEENAAA-PDVITFDMLIHGFIRINEPSKVNELLHKMKE  550 (595)
Q Consensus       504 ~~A~~~~~~~~~~~~~-~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~  550 (595)
                      ++|...++++.+.. + .+...+..+...+...|+.++|..+++.+.+
T Consensus       164 ~~A~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~a~~~~~~~~~  210 (225)
T 2vq2_A          164 GDADYYFKKYQSRV-EVLQADDLLLGWKIAKALGNAQAAYEYEAQLQA  210 (225)
T ss_dssp             HHHHHHHHHHHHHH-CSCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHhC-CCCCHHHHHHHHHHHHhcCcHHHHHHHHHHHHH
Confidence            77777777776653 3 4556666666666777777777777777765

>2vq2_A PILW, putative fimbrial biogenesis and twitching motility protein; secretin, TPR repeat, type IV pilus, bacterail virulence; 1.54A {Neisseria meningitidis}

Probab=99.61  E-value=4.8e-13  Score=119.35  Aligned_cols=204  Identities=9%  Similarity=-0.054  Sum_probs=133.1

Q ss_pred             CHHHHHHHHHHHHhcCChhHHHHHHHHHHhCCCCCCHHHHHHHHHHHHhcCCHhHHHHHHHHHHhcCCCCCHhhHHHHHH
Q 040027           95 NLYTYNILINCFCKIGRVSLGFIAFGRILRSCFTPNAATFNSLIKGLHAESRIMEAAALFTKLKAFGCEPNVITYNTLIN  174 (595)
Q Consensus        95 ~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~~l~~  174 (595)
                      ++..|..++..+...|++++|+..|+++.+.. +.+...+..+...+...|++++|.+.++++.... +.+..++..++.
T Consensus         7 ~~~~~~~~~~~~~~~~~~~~A~~~~~~~~~~~-~~~~~~~~~l~~~~~~~~~~~~A~~~~~~a~~~~-~~~~~~~~~l~~   84 (225)
T 2vq2_A            7 VSNIKTQLAMEYMRGQDYRQATASIEDALKSD-PKNELAWLVRAEIYQYLKVNDKAQESFRQALSIK-PDSAEINNNYGW   84 (225)
T ss_dssp             HHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHH
T ss_pred             cHHHHHHHHHHHHHHhhHHHHHHHHHHHHHhC-ccchHHHHHHHHHHHHcCChHHHHHHHHHHHHhC-CCChHHHHHHHH
Confidence            45666777777777777777777777777663 3456667777777777777777777777777653 335666677777


Q ss_pred             HHHhc-CChhHHHHHHHHHHhcCCCCCccccCcHHHHHHHHHHHHHcCCHhHHHHHHHHHhhCCCCCCHhHHHHHHHHHH
Q 040027          175 GLCRT-GHTMIALNLFEEMANGNGEIGVVCKPNTVTYSTIIDGLCKEGFVDKAKALFLQMKDENINPDVVTYNSLIHGLC  253 (595)
Q Consensus       175 ~~~~~-g~~~~A~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~~ll~~~~  253 (595)
                      .+... |++++|+..++++.....     .+.+...+..+..++...|++++|...++++.+.. +.+...+..+...+.
T Consensus        85 ~~~~~~~~~~~A~~~~~~~~~~~~-----~~~~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~~~-~~~~~~~~~la~~~~  158 (225)
T 2vq2_A           85 FLCGRLNRPAESMAYFDKALADPT-----YPTPYIANLNKGICSAKQGQFGLAEAYLKRSLAAQ-PQFPPAFKELARTKM  158 (225)
T ss_dssp             HHHTTTCCHHHHHHHHHHHHTSTT-----CSCHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHS-TTCHHHHHHHHHHHH
T ss_pred             HHHHhcCcHHHHHHHHHHHHcCcC-----CcchHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhC-CCCchHHHHHHHHHH
Confidence            77777 777777777777766210     13335666667777777777777777777766543 224566666666777


Q ss_pred             hcCCHHHHHHHHHHHHHCCCCCCHhhHHHHHHHHHhcCChHHHHHHHHHHHHC
Q 040027          254 HANDWNEAKRLFIEMMDQGVQPSVVTFNVIMDELCKNRKMDEASRLLDLMVQR  306 (595)
Q Consensus       254 ~~~~~~~A~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~  306 (595)
                      ..|++++|...++++.+.....+...+..+...+...|+.+.+..+++.+.+.
T Consensus       159 ~~~~~~~A~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~a~~~~~~~~~~  211 (225)
T 2vq2_A          159 LAGQLGDADYYFKKYQSRVEVLQADDLLLGWKIAKALGNAQAAYEYEAQLQAN  211 (225)
T ss_dssp             HHTCHHHHHHHHHHHHHHHCSCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH
T ss_pred             HcCCHHHHHHHHHHHHHhCCCCCHHHHHHHHHHHHhcCcHHHHHHHHHHHHHh
Confidence            77777777777766665422134455555555666666666666666666543

>3sf4_A G-protein-signaling modulator 2; tetratricopeptide repeat, TPR, cell polarity, asymmetric CEL division, mitotic spindle orientation; 2.60A {Homo sapiens}

Probab=99.61  E-value=3.7e-14  Score=139.32  Aligned_cols=226  Identities=15%  Similarity=0.024  Sum_probs=142.5

Q ss_pred             HHHHHHHHHHhCCCHHHHHHHHHHHHHCCC-----CCCHHHHHHHHHHHHccCC--------------------HHHHHH
Q 040027          349 SYNILINGYCKNKEVEEALSLYREMVSKGI-----KPTVVTYNTLFLGLFEIHQ--------------------VEHALK  403 (595)
Q Consensus       349 ~~~~l~~~~~~~~~~~~A~~~~~~~~~~~~-----~~~~~~~~~l~~~~~~~~~--------------------~~~a~~  403 (595)
                      ++..+...|...|++++|+..++++.+...     .....++..+...+...|+                    +++|..
T Consensus        89 ~~~~la~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~~~~~~~~~~~~~~a~~~~~~A~~  168 (406)
T 3sf4_A           89 ASGNLGNTLKVLGNFDEAIVCCQRHLDISRELNDKVGEARALYNLGNVYHAKGKSFGCPGPQDVGEFPEEVRDALQAAVD  168 (406)
T ss_dssp             HHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHHHHHHTCC-------CCCCHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHcCCHHHHHHHHHHHHHHHHhcccccchHHHHHHHHHHHHHcCCcccccccchhhhhhhhHHHHHHHHHH
Confidence            344444455555555555555544443200     0012244555555556666                    666666


Q ss_pred             HHHHHHHC----CC-CCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHHcCC-CcC----HHHHHHHHHHHHhcCChHHHHH
Q 040027          404 LFDEMQRD----GV-AADTRTYTTFIDGLCKNGYIIEAVELFRTLRILKC-ELD----IQAYNCLIDGLCKSGRLKFAWE  473 (595)
Q Consensus       404 ~~~~~~~~----~~-~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~-~~~----~~~~~~l~~~~~~~g~~~~A~~  473 (595)
                      .+.+..+.    +. +....++..+...|...|++++|...++++.+... .++    ..++..++.++...|++++|..
T Consensus       169 ~~~~al~~~~~~~~~~~~~~~~~~la~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~la~~~~~~g~~~~A~~  248 (406)
T 3sf4_A          169 FYEENLSLVTALGDRAAQGRAFGNLGNTHYLLGNFRDAVIAHEQRLLIAKEFGDKAAERRAYSNLGNAYIFLGEFETASE  248 (406)
T ss_dssp             HHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHHTBHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCHHHHHH
T ss_pred             HHHHHHHHHHhccCcHHHHHHHHHHHHHHHHccCHHHHHHHHHHHHHHHHhcCCcHHHHHHHHHHHHHHHHcCChHHHHH
Confidence            66555432    10 11124566677778888888888888887764310 111    3367778888888899988888


Q ss_pred             HHHhcccCCC-CCC----HHHHHHHHHHHHhcCChhHHHHHHHHHHHcCC-CCC----HHHHHHHHHHHHHcCChhHHHH
Q 040027          474 LFCSLPHGVL-VPN----VVTYNIMIQGLCNDGQMDKARDLFLDMEENAA-APD----VITFDMLIHGFIRINEPSKVNE  543 (595)
Q Consensus       474 ~~~~~~~~~~-~p~----~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~-~~~----~~~~~~l~~~~~~~g~~~~A~~  543 (595)
                      .+++...... .++    ..++..++..|...|++++|...++++.+... ..+    ..++..+..+|...|++++|..
T Consensus       249 ~~~~al~~~~~~~~~~~~~~~~~~la~~~~~~g~~~~A~~~~~~a~~~~~~~~~~~~~~~~~~~la~~~~~~g~~~~A~~  328 (406)
T 3sf4_A          249 YYKKTLLLARQLKDRAVEAQSCYSLGNTYTLLQDYEKAIDYHLKHLAIAQELNDRIGEGRACWSLGNAYTALGNHDQAMH  328 (406)
T ss_dssp             HHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHHTCHHHHHH
T ss_pred             HHHHHHHHHHhCcCchHHHHHHHHHHHHHHHhCcHHHHHHHHHHHHHHHHhcCCcHHHHHHHHHHHHHHHHcCCHHHHHH
Confidence            8888765100 011    45677888888899999999999988876310 111    4567788888999999999999


Q ss_pred             HHHHHHHC----CCCC-CHHHHHHHHHHHHhcCccc
Q 040027          544 LLHKMKEK----KVMP-DASIVSIVVDLLVKNEISL  574 (595)
Q Consensus       544 ~~~~~~~~----~~~p-~~~~~~~l~~~~~~~g~~~  574 (595)
                      ++++..+.    +..+ ...++..+..++...|+..
T Consensus       329 ~~~~al~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~  364 (406)
T 3sf4_A          329 FAEKHLEISREVGDKSGELTARLNLSDLQMVLGLSY  364 (406)
T ss_dssp             HHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHHHTTS
T ss_pred             HHHHHHHHHHHhcCCcchhHHHHHHHHHHHHhhHhH
Confidence            99888742    2222 2567778888888888765

>3spa_A Mtrpol, DNA-directed RNA polymerase, mitochondrial; single-subunit DNA-dependent RNA polymerase in mitochondria, transferase; 2.50A {Homo sapiens}

Probab=99.60  E-value=1.6e-15  Score=155.12  Aligned_cols=126  Identities=11%  Similarity=0.189  Sum_probs=114.5

Q ss_pred             CcCHHHHHHHHHHHHhcCChHHHHHHHHhccc---CCCCCCHHHHHHHHHHHHhcCChhHHHHHHHHHHHcCCCCCHHHH
Q 040027          449 ELDIQAYNCLIDGLCKSGRLKFAWELFCSLPH---GVLVPNVVTYNIMIQGLCNDGQMDKARDLFLDMEENAAAPDVITF  525 (595)
Q Consensus       449 ~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~---~~~~p~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~  525 (595)
                      ..-..+|++++.+|++.|++++|..+|++|.+   .|+.||..|||+||.+|++.|++++|.++|++|.+.|+.||..||
T Consensus       124 ~~~~~TynaLIdglcK~G~leeA~~Lf~eM~~m~~kG~~PdvvTYNtLI~Glck~G~~~eA~~Lf~eM~~~G~~PDvvTY  203 (1134)
T 3spa_A          124 SGQQQRLLAFFKCCLLTDQLPLAHHLLVVHHGQRQKRKLLTLDMYNAVMLGWARQGAFKELVYVLFMVKDAGLTPDLLSY  203 (1134)
T ss_dssp             CHHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHSHHHHTTCCHHHHHHHHHHHHHHTCHHHHHHHHHHHHHTTCCCCHHHH
T ss_pred             HhHHHHHHHHHHHHHhCCCHHHHHHHHHHHHHHhhcCCCCCHhHHHHHHHHHHhCCCHHHHHHHHHHHHHcCCCCcHHHH
Confidence            44567899999999999999999999987653   578999999999999999999999999999999999999999999


Q ss_pred             HHHHHHHHHcCCh-hHHHHHHHHHHHCCCCCCHHHHHHHHHHHHhcCccc
Q 040027          526 DMLIHGFIRINEP-SKVNELLHKMKEKKVMPDASIVSIVVDLLVKNEISL  574 (595)
Q Consensus       526 ~~l~~~~~~~g~~-~~A~~~~~~~~~~~~~p~~~~~~~l~~~~~~~g~~~  574 (595)
                      +.++.++++.|+. ++|.++|++|.+.|+.||..+|+.++....+.+.++
T Consensus       204 ntLI~glcK~G~~~e~A~~Ll~EM~~kG~~PD~vtY~~ll~~~eR~~vL~  253 (1134)
T 3spa_A          204 AAALQCMGRQDQDAGTIERCLEQMSQEGLKLQALFTAVLLSEEDRATVLK  253 (1134)
T ss_dssp             HHHHHHHHHHTCCHHHHHHHHHHHHHHTCCSHHHHHHSCCCHHHHHHHHH
T ss_pred             HHHHHHHHhCCCcHHHHHHHHHHHHHcCCCCChhhcccccChhhHHHHHH
Confidence            9999999999985 789999999999999999999998777666665554

>4a1s_A PINS, partner of inscuteable; cell cycle, LGN, mitotic spindle orientation, asymmetric CEL divisions; 2.10A {Drosophila melanogaster}

Probab=99.59  E-value=8.4e-14  Score=137.06  Aligned_cols=278  Identities=12%  Similarity=0.037  Sum_probs=184.7

Q ss_pred             HHHHHHHHHHHHhcCChhHHHHHHHHHHhCCCCCCH----HHHHHHHHHHHhcCCHhHHHHHHHHHHhc----C-CCCCH
Q 040027           96 LYTYNILINCFCKIGRVSLGFIAFGRILRSCFTPNA----ATFNSLIKGLHAESRIMEAAALFTKLKAF----G-CEPNV  166 (595)
Q Consensus        96 ~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~~~----~~~~~l~~~~~~~g~~~~A~~~~~~~~~~----~-~~~~~  166 (595)
                      ...+..+...+...|++++|+..|+++++.. +.+.    .++..+...|...|++++|...++++...    + .+...
T Consensus        48 ~~~l~~~g~~~~~~g~~~~A~~~~~~al~~~-~~~~~~~~~~~~~lg~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~  126 (411)
T 4a1s_A           48 CLELALEGERLCNAGDCRAGVAFFQAAIQAG-TEDLRTLSAIYSQLGNAYFYLGDYNKAMQYHKHDLTLAKSMNDRLGEA  126 (411)
T ss_dssp             HHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-CSCHHHHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHHHTTCHHHHH
T ss_pred             HHHHHHHHHHHHHhCcHHHHHHHHHHHHHhc-ccChhHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHccCchHHH
Confidence            3445567788999999999999999999984 3343    47888889999999999999999988764    1 12245


Q ss_pred             hhHHHHHHHHHhcCChhHHHHHHHHHHhcCCCCCccccCcHHHHHHHHHHHHHcCC-----------------HhHHHHH
Q 040027          167 ITYNTLINGLCRTGHTMIALNLFEEMANGNGEIGVVCKPNTVTYSTIIDGLCKEGF-----------------VDKAKAL  229 (595)
Q Consensus       167 ~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~-----------------~~~A~~~  229 (595)
                      .++..+...|...|++++|+..++++.......+. .+....++..+..+|...|+                 +++|.+.
T Consensus       127 ~~~~~l~~~~~~~g~~~~A~~~~~~al~~~~~~~~-~~~~~~~~~~l~~~~~~~g~~~~~~~~~~~~~~a~~~~~~A~~~  205 (411)
T 4a1s_A          127 KSSGNLGNTLKVMGRFDEAAICCERHLTLARQLGD-RLSEGRALYNLGNVYHAKGKHLGQRNPGKFGDDVKEALTRAVEF  205 (411)
T ss_dssp             HHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHHTC-HHHHHHHHHHHHHHHHHHHHHHHHHSTTCCCHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHhhc-hHHHHHHHHHHHHHHHHcCcccccccchhhhhhhhHHHHHHHHH
Confidence            67788899999999999999999988764210000 12235578888899999999                 8888888


Q ss_pred             HHHHhhC----CC-CCCHhHHHHHHHHHHhcCCHHHHHHHHHHHHHCCCC-CC----HhhHHHHHHHHHhcCChHHHHHH
Q 040027          230 FLQMKDE----NI-NPDVVTYNSLIHGLCHANDWNEAKRLFIEMMDQGVQ-PS----VVTFNVIMDELCKNRKMDEASRL  299 (595)
Q Consensus       230 ~~~~~~~----~~-~~~~~~~~~ll~~~~~~~~~~~A~~~~~~~~~~~~~-~~----~~~~~~l~~~~~~~g~~~~a~~~  299 (595)
                      +++....    +. .....++..+...+...|++++|...+++..+.... .+    ...+..+..++...|++++|...
T Consensus       206 ~~~al~~~~~~~~~~~~~~~~~~la~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~la~~~~~~g~~~~A~~~  285 (411)
T 4a1s_A          206 YQENLKLMRDLGDRGAQGRACGNLGNTYYLLGDFQAAIEHHQERLRIAREFGDRAAERRANSNLGNSHIFLGQFEDAAEH  285 (411)
T ss_dssp             HHHHHHHHHHHTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHHTTTCHHHHHHH
T ss_pred             HHHHHHHHHHcCCHHHHHHHHHHHHHHHHHcCChHHHHHHHHHHHHHHHhcCCcHHHHHHHHHHHHHHHHCcCHHHHHHH
Confidence            8776542    11 112346677777888888888888888777653100 01    12566666777777777777777


Q ss_pred             HHHHHHCCCC-----CCHHHHHHHHHHHHhcCCHHHHHHHHHHHHhcCC-----CCCHHHHHHHHHHHHhCCCHHHHHHH
Q 040027          300 LDLMVQRGVR-----PNACTYNTLMDGFCLMGKINRAEELFGSMESMGC-----KHDDVSYNILINGYCKNKEVEEALSL  369 (595)
Q Consensus       300 ~~~~~~~~~~-----~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~-----~~~~~~~~~l~~~~~~~~~~~~A~~~  369 (595)
                      ++++......     ....++..+..++...|++++|...+++......     .....++..+..+|...|++++|...
T Consensus       286 ~~~al~~~~~~~~~~~~~~~~~~la~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~la~~~~~~g~~~~A~~~  365 (411)
T 4a1s_A          286 YKRTLALAVELGEREVEAQSCYSLGNTYTLLHEFNTAIEYHNRHLAIAQELGDRIGEARACWSLGNAHSAIGGHERALKY  365 (411)
T ss_dssp             HHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHHHTTCHHHHHHH
T ss_pred             HHHHHHHHHHcCCHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHCCChHHHHHHHHHHHHHHHHhccHHHHHHH
Confidence            7766543100     1134555566666666676666666666543210     00122455555566666666666666


Q ss_pred             HHHHHH
Q 040027          370 YREMVS  375 (595)
Q Consensus       370 ~~~~~~  375 (595)
                      +++..+
T Consensus       366 ~~~al~  371 (411)
T 4a1s_A          366 AEQHLQ  371 (411)
T ss_dssp             HHHHHH
T ss_pred             HHHHHH
Confidence            665554

>4a1s_A PINS, partner of inscuteable; cell cycle, LGN, mitotic spindle orientation, asymmetric CEL divisions; 2.10A {Drosophila melanogaster}

Probab=99.58  E-value=4.4e-14  Score=139.12  Aligned_cols=279  Identities=12%  Similarity=0.046  Sum_probs=164.3

Q ss_pred             HHHHHHHHHHhcCCHHHHHHHHHHHHHCCCCCCH----hhHHHHHHHHHhcCChHHHHHHHHHHHHC----C-CCCCHHH
Q 040027          244 TYNSLIHGLCHANDWNEAKRLFIEMMDQGVQPSV----VTFNVIMDELCKNRKMDEASRLLDLMVQR----G-VRPNACT  314 (595)
Q Consensus       244 ~~~~ll~~~~~~~~~~~A~~~~~~~~~~~~~~~~----~~~~~l~~~~~~~g~~~~a~~~~~~~~~~----~-~~~~~~~  314 (595)
                      .+..+...+...|++++|...|+++++.... +.    ..+..+...+...|++++|...++++.+.    + .+....+
T Consensus        50 ~l~~~g~~~~~~g~~~~A~~~~~~al~~~~~-~~~~~~~~~~~lg~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~  128 (411)
T 4a1s_A           50 ELALEGERLCNAGDCRAGVAFFQAAIQAGTE-DLRTLSAIYSQLGNAYFYLGDYNKAMQYHKHDLTLAKSMNDRLGEAKS  128 (411)
T ss_dssp             HHHHHHHHHHHTTCHHHHHHHHHHHHHHCCS-CHHHHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHHHTTCHHHHHHH
T ss_pred             HHHHHHHHHHHhCcHHHHHHHHHHHHHhccc-ChhHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHccCchHHHHH
Confidence            3444556667777777777777776664221 22    34556666666677777777766665542    1 0112334


Q ss_pred             HHHHHHHHHhcCCHHHHHHHHHHHHhcC-----CCCCHHHHHHHHHHHHhCCC----------HHHHHHHHHHHHHCCCC
Q 040027          315 YNTLMDGFCLMGKINRAEELFGSMESMG-----CKHDDVSYNILINGYCKNKE----------VEEALSLYREMVSKGIK  379 (595)
Q Consensus       315 ~~~l~~~~~~~~~~~~a~~~~~~~~~~~-----~~~~~~~~~~l~~~~~~~~~----------~~~A~~~~~~~~~~~~~  379 (595)
                      +..+...|...|++++|...++++.+..     .+....++..+...|...|+          +++|...          
T Consensus       129 ~~~l~~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~~~~~~~~~~~a~~~----------  198 (411)
T 4a1s_A          129 SGNLGNTLKVMGRFDEAAICCERHLTLARQLGDRLSEGRALYNLGNVYHAKGKHLGQRNPGKFGDDVKEA----------  198 (411)
T ss_dssp             HHHHHHHHHHTTCHHHHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHHHHHHHHHHHSTTCCCHHHHHH----------
T ss_pred             HHHHHHHHHHCCCHHHHHHHHHHHHHHHHHhhchHHHHHHHHHHHHHHHHcCcccccccchhhhhhhhHH----------
Confidence            5555555666666666666665554320     01112234444444444444          0000000          


Q ss_pred             CCHHHHHHHHHHHHccCCHHHHHHHHHHHHHC----C-CCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHHcCCC-cC--
Q 040027          380 PTVVTYNTLFLGLFEIHQVEHALKLFDEMQRD----G-VAADTRTYTTFIDGLCKNGYIIEAVELFRTLRILKCE-LD--  451 (595)
Q Consensus       380 ~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~----~-~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~-~~--  451 (595)
                                        +++|...+++..+.    + .+.....+..+...|...|++++|...++++.+.... .+  
T Consensus       199 ------------------~~~A~~~~~~al~~~~~~~~~~~~~~~~~~la~~~~~~g~~~~A~~~~~~al~~~~~~~~~~  260 (411)
T 4a1s_A          199 ------------------LTRAVEFYQENLKLMRDLGDRGAQGRACGNLGNTYYLLGDFQAAIEHHQERLRIAREFGDRA  260 (411)
T ss_dssp             ------------------HHHHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHHTCHH
T ss_pred             ------------------HHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHcCChHHHHHHHHHHHHHHHhcCCcH
Confidence                              44444444443321    1 0112235566667777778888887777777643200 11  


Q ss_pred             --HHHHHHHHHHHHhcCChHHHHHHHHhcccCC--CC---CCHHHHHHHHHHHHhcCChhHHHHHHHHHHHc----CC-C
Q 040027          452 --IQAYNCLIDGLCKSGRLKFAWELFCSLPHGV--LV---PNVVTYNIMIQGLCNDGQMDKARDLFLDMEEN----AA-A  519 (595)
Q Consensus       452 --~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~--~~---p~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~----~~-~  519 (595)
                        ..++..+..+|...|++++|...++++....  ..   ....++..+...|...|++++|...++++++.    +. .
T Consensus       261 ~~~~~~~~la~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~la~~~~~~g~~~~A~~~~~~al~~~~~~~~~~  340 (411)
T 4a1s_A          261 AERRANSNLGNSHIFLGQFEDAAEHYKRTLALAVELGEREVEAQSCYSLGNTYTLLHEFNTAIEYHNRHLAIAQELGDRI  340 (411)
T ss_dssp             HHHHHHHHHHHHHHTTTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHHTCHH
T ss_pred             HHHHHHHHHHHHHHHCcCHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHCCChH
Confidence              2367778888888888888888888776521  00   11456778888888999999999999888763    10 1


Q ss_pred             CCHHHHHHHHHHHHHcCChhHHHHHHHHHHHC
Q 040027          520 PDVITFDMLIHGFIRINEPSKVNELLHKMKEK  551 (595)
Q Consensus       520 ~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~  551 (595)
                      ....++..+..+|...|++++|.++++++.+.
T Consensus       341 ~~~~~~~~la~~~~~~g~~~~A~~~~~~al~~  372 (411)
T 4a1s_A          341 GEARACWSLGNAHSAIGGHERALKYAEQHLQL  372 (411)
T ss_dssp             HHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHhccHHHHHHHHHHHHHH
Confidence            11346778888999999999999999999864

>3sf4_A G-protein-signaling modulator 2; tetratricopeptide repeat, TPR, cell polarity, asymmetric CEL division, mitotic spindle orientation; 2.60A {Homo sapiens}

Probab=99.58  E-value=5.8e-14  Score=137.90  Aligned_cols=281  Identities=11%  Similarity=0.052  Sum_probs=187.2

Q ss_pred             CCCHHHHHHHHHHHHhcCChhHHHHHHHHHHhCCCCCC----HHHHHHHHHHHHhcCCHhHHHHHHHHHHhc----CCC-
Q 040027           93 FPNLYTYNILINCFCKIGRVSLGFIAFGRILRSCFTPN----AATFNSLIKGLHAESRIMEAAALFTKLKAF----GCE-  163 (595)
Q Consensus        93 ~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~~----~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~----~~~-  163 (595)
                      ......+......+...|++++|+..|+++++.. +.+    ..++..+...+...|++++|...++++...    +.. 
T Consensus         6 ~~~~~~l~~~g~~~~~~g~~~~A~~~~~~al~~~-~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~al~~~~~~~~~~   84 (406)
T 3sf4_A            6 EASCLELALEGERLCKSGDCRAGVSFFEAAVQVG-TEDLKTLSAIYSQLGNAYFYLHDYAKALEYHHHDLTLARTIGDQL   84 (406)
T ss_dssp             CCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-CSCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCHH
T ss_pred             HHHHHHHHHHHHHHHHhccHHHHHHHHHHHHhcC-cccHHHHHHHHHHHHHHHHHhcCHHHHHHHHHHHHHHHHhccccH
Confidence            3466777888899999999999999999999884 334    357888889999999999999999987653    111 


Q ss_pred             CCHhhHHHHHHHHHhcCChhHHHHHHHHHHhcCCCCCccccCcHHHHHHHHHHHHHcCC--------------------H
Q 040027          164 PNVITYNTLINGLCRTGHTMIALNLFEEMANGNGEIGVVCKPNTVTYSTIIDGLCKEGF--------------------V  223 (595)
Q Consensus       164 ~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~--------------------~  223 (595)
                      ....++..+...+...|++++|+..++++.......+. ......++..+...+...|+                    +
T Consensus        85 ~~~~~~~~la~~~~~~g~~~~A~~~~~~al~~~~~~~~-~~~~~~~~~~l~~~~~~~g~~~~~~~~~~~~~~~~~a~~~~  163 (406)
T 3sf4_A           85 GEAKASGNLGNTLKVLGNFDEAIVCCQRHLDISRELND-KVGEARALYNLGNVYHAKGKSFGCPGPQDVGEFPEEVRDAL  163 (406)
T ss_dssp             HHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHHTC-HHHHHHHHHHHHHHHHHHHHTCC-------CCCCHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHhccc-ccchHHHHHHHHHHHHHcCCcccccccchhhhhhhhHHHHH
Confidence            12456788889999999999999999988764310000 01124478888888999999                    8


Q ss_pred             hHHHHHHHHHhhC----CCC-CCHhHHHHHHHHHHhcCCHHHHHHHHHHHHHCCC-CCC----HhhHHHHHHHHHhcCCh
Q 040027          224 DKAKALFLQMKDE----NIN-PDVVTYNSLIHGLCHANDWNEAKRLFIEMMDQGV-QPS----VVTFNVIMDELCKNRKM  293 (595)
Q Consensus       224 ~~A~~~~~~~~~~----~~~-~~~~~~~~ll~~~~~~~~~~~A~~~~~~~~~~~~-~~~----~~~~~~l~~~~~~~g~~  293 (595)
                      ++|.+.+++....    +.. ....++..+...+...|++++|...+++..+... .++    ..++..+...+...|++
T Consensus       164 ~~A~~~~~~al~~~~~~~~~~~~~~~~~~la~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~la~~~~~~g~~  243 (406)
T 3sf4_A          164 QAAVDFYEENLSLVTALGDRAAQGRAFGNLGNTHYLLGNFRDAVIAHEQRLLIAKEFGDKAAERRAYSNLGNAYIFLGEF  243 (406)
T ss_dssp             HHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHHTBHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCH
T ss_pred             HHHHHHHHHHHHHHHhccCcHHHHHHHHHHHHHHHHccCHHHHHHHHHHHHHHHHhcCCcHHHHHHHHHHHHHHHHcCCh
Confidence            8888888776542    111 1234567777788888888888888877764310 011    22566667777777777


Q ss_pred             HHHHHHHHHHHHCCCC-CC----HHHHHHHHHHHHhcCCHHHHHHHHHHHHhcCCC-CC----HHHHHHHHHHHHhCCCH
Q 040027          294 DEASRLLDLMVQRGVR-PN----ACTYNTLMDGFCLMGKINRAEELFGSMESMGCK-HD----DVSYNILINGYCKNKEV  363 (595)
Q Consensus       294 ~~a~~~~~~~~~~~~~-~~----~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~-~~----~~~~~~l~~~~~~~~~~  363 (595)
                      ++|...+++....... .+    ..++..+..+|...|++++|...+++..+.... .+    ..++..+..+|...|++
T Consensus       244 ~~A~~~~~~al~~~~~~~~~~~~~~~~~~la~~~~~~g~~~~A~~~~~~a~~~~~~~~~~~~~~~~~~~la~~~~~~g~~  323 (406)
T 3sf4_A          244 ETASEYYKKTLLLARQLKDRAVEAQSCYSLGNTYTLLQDYEKAIDYHLKHLAIAQELNDRIGEGRACWSLGNAYTALGNH  323 (406)
T ss_dssp             HHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHHTCH
T ss_pred             HHHHHHHHHHHHHHHhCcCchHHHHHHHHHHHHHHHhCcHHHHHHHHHHHHHHHHhcCCcHHHHHHHHHHHHHHHHcCCH
Confidence            7777777766542100 01    345556666666777777777666665432100 01    23455556666666666


Q ss_pred             HHHHHHHHHHHH
Q 040027          364 EEALSLYREMVS  375 (595)
Q Consensus       364 ~~A~~~~~~~~~  375 (595)
                      ++|...+++..+
T Consensus       324 ~~A~~~~~~al~  335 (406)
T 3sf4_A          324 DQAMHFAEKHLE  335 (406)
T ss_dssp             HHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHH
Confidence            666666665543

>2ond_A Cleavage stimulation factor 77 kDa subunit; HAT domain, structural protein; 2.80A {Mus musculus} SCOP: a.118.8.7

Probab=99.57  E-value=1.2e-12  Score=122.99  Aligned_cols=225  Identities=11%  Similarity=0.068  Sum_probs=164.9

Q ss_pred             HHHHHHHHHHHHhCCCCCCHhhHHHHHHHHHcCCCchhHHhhCCCCCCHHHHHHHHHHHHhcCCh-------hHHHHHHH
Q 040027           48 NEAFCIFDYMLRMHPSPPPVSSFNILLASLAKNKHYDTRLNATGLFPNLYTYNILINCFCKIGRV-------SLGFIAFG  120 (595)
Q Consensus        48 ~~A~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~-------~~A~~~~~  120 (595)
                      ++|+..|+++++.+|.  ++..|..++..+...++                      .+.+.|++       ++|+.+|+
T Consensus        33 ~~a~~~~~~al~~~p~--~~~~w~~~~~~~~~~~~----------------------~l~~~g~~~~~~~~~~~A~~~~~   88 (308)
T 2ond_A           33 KRVMFAYEQCLLVLGH--HPDIWYEAAQYLEQSSK----------------------LLAEKGDMNNAKLFSDEAANIYE   88 (308)
T ss_dssp             HHHHHHHHHHHHHHTT--CHHHHHHHHHHHHHHHH----------------------HHHHTSCCHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHcCC--CHHHHHHHHHHHHHhch----------------------hhhhccchhhcccchHHHHHHHH
Confidence            7899999999999998  88888877766544322                      12345664       88999999


Q ss_pred             HHHhCCCCCCHHHHHHHHHHHHhcCCHhHHHHHHHHHHhcCCCCC-Hh-hHHHHHHHHHhcCChhHHHHHHHHHHhcCCC
Q 040027          121 RILRSCFTPNAATFNSLIKGLHAESRIMEAAALFTKLKAFGCEPN-VI-TYNTLINGLCRTGHTMIALNLFEEMANGNGE  198 (595)
Q Consensus       121 ~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~~-~~-~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~  198 (595)
                      ++++.-.+.+...|..++..+.+.|++++|.++|+++.+.  .|+ .. +|..++..+.+.|++++|..+|+++.+..  
T Consensus        89 rAl~~~~p~~~~~~~~~~~~~~~~~~~~~A~~~~~~al~~--~p~~~~~~~~~~~~~~~~~~~~~~A~~~~~~a~~~~--  164 (308)
T 2ond_A           89 RAISTLLKKNMLLYFAYADYEESRMKYEKVHSIYNRLLAI--EDIDPTLVYIQYMKFARRAEGIKSGRMIFKKAREDA--  164 (308)
T ss_dssp             HHHTTTTTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHTS--SSSCTHHHHHHHHHHHHHHHCHHHHHHHHHHHHTST--
T ss_pred             HHHHHhCcccHHHHHHHHHHHHhcCCHHHHHHHHHHHHhc--cccCccHHHHHHHHHHHHhcCHHHHHHHHHHHHhcC--
Confidence            9988322446778888888888899999999999998875  333 33 78888888888888899999988888764  


Q ss_pred             CCccccCcHHHHHHHHHHHH-HcCCHhHHHHHHHHHhhCCCCCCHhHHHHHHHHHHhcCCHHHHHHHHHHHHHCC-CCC-
Q 040027          199 IGVVCKPNTVTYSTIIDGLC-KEGFVDKAKALFLQMKDENINPDVVTYNSLIHGLCHANDWNEAKRLFIEMMDQG-VQP-  275 (595)
Q Consensus       199 ~~~~~~~~~~~~~~l~~~~~-~~g~~~~A~~~~~~~~~~~~~~~~~~~~~ll~~~~~~~~~~~A~~~~~~~~~~~-~~~-  275 (595)
                           +.+...|...+.... ..|++++|.++|++..+.. +.+...|..++..+.+.|++++|..+|++.+... .+| 
T Consensus       165 -----p~~~~~~~~~a~~~~~~~~~~~~A~~~~~~al~~~-p~~~~~~~~~~~~~~~~g~~~~A~~~~~~al~~~~l~p~  238 (308)
T 2ond_A          165 -----RTRHHVYVTAALMEYYCSKDKSVAFKIFELGLKKY-GDIPEYVLAYIDYLSHLNEDNNTRVLFERVLTSGSLPPE  238 (308)
T ss_dssp             -----TCCTHHHHHHHHHHHHTSCCHHHHHHHHHHHHHHH-TTCHHHHHHHHHHHHTTCCHHHHHHHHHHHHHSSSSCGG
T ss_pred             -----CCCHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhC-CCcHHHHHHHHHHHHHCCCHHHHHHHHHHHHhccCCCHH
Confidence                 344455544433322 2588888888888877653 2366777777888888888888888888887752 343 


Q ss_pred             -CHhhHHHHHHHHHhcCChHHHHHHHHHHHHC
Q 040027          276 -SVVTFNVIMDELCKNRKMDEASRLLDLMVQR  306 (595)
Q Consensus       276 -~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~  306 (595)
                       ....|..++......|+.+.|..+++++.+.
T Consensus       239 ~~~~l~~~~~~~~~~~g~~~~a~~~~~~a~~~  270 (308)
T 2ond_A          239 KSGEIWARFLAFESNIGDLASILKVEKRRFTA  270 (308)
T ss_dssp             GCHHHHHHHHHHHHHHSCHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHH
Confidence             3456777777777778888888888777765

>3ro2_A PINS homolog, G-protein-signaling modulator 2; TPR repeat, protein-protein interaction, protein-binding, PR binding; 2.30A {Mus musculus}

Probab=99.55  E-value=1.1e-13  Score=132.00  Aligned_cols=275  Identities=13%  Similarity=0.075  Sum_probs=158.2

Q ss_pred             HHHHHHHHHhcCCHHHHHHHHHHHHHCCCCCC----HhhHHHHHHHHHhcCChHHHHHHHHHHHHC----CCC-CCHHHH
Q 040027          245 YNSLIHGLCHANDWNEAKRLFIEMMDQGVQPS----VVTFNVIMDELCKNRKMDEASRLLDLMVQR----GVR-PNACTY  315 (595)
Q Consensus       245 ~~~ll~~~~~~~~~~~A~~~~~~~~~~~~~~~----~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~----~~~-~~~~~~  315 (595)
                      +......+...|++++|...|+++.+.... +    ...+..+...+...|++++|...++++...    +.. ....++
T Consensus         8 l~~~g~~~~~~g~~~~A~~~~~~al~~~~~-~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~   86 (338)
T 3ro2_A            8 LALEGERLCKSGDCRAGVSFFEAAVQVGTE-DLKTLSAIYSQLGNAYFYLHDYAKALEYHHHDLTLARTIGDQLGEAKAS   86 (338)
T ss_dssp             HHHHHHHHHHTTCHHHHHHHHHHHHHHCCS-CHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHHTCHHHHHHHH
T ss_pred             HHHHHHHHHHhccHHHHHHHHHHHHhhCcc-cHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHhhcccccHHHHHHH
Confidence            334445556666666666666666554211 2    234445555555666666666655554432    000 112334


Q ss_pred             HHHHHHHHhcCCHHHHHHHHHHHHhcCC-CCCHHHHHHHHHHHHhCCCHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHc
Q 040027          316 NTLMDGFCLMGKINRAEELFGSMESMGC-KHDDVSYNILINGYCKNKEVEEALSLYREMVSKGIKPTVVTYNTLFLGLFE  394 (595)
Q Consensus       316 ~~l~~~~~~~~~~~~a~~~~~~~~~~~~-~~~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~~l~~~~~~  394 (595)
                      ..+...+...|++++|...+++..+... ..+..                               ....++..+...+..
T Consensus        87 ~~l~~~~~~~g~~~~A~~~~~~al~~~~~~~~~~-------------------------------~~~~~~~~l~~~~~~  135 (338)
T 3ro2_A           87 GNLGNTLKVLGNFDEAIVCCQRHLDISRELNDKV-------------------------------GEARALYNLGNVYHA  135 (338)
T ss_dssp             HHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCHH-------------------------------HHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHccCHHHHHHHHHHHHHHHHHhcCch-------------------------------HHHHHHHHHHHHHHH
Confidence            4444444555555555555544432200 00000                               001233444444444


Q ss_pred             cCC--------------------HHHHHHHHHHHHHC----C-CCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHHcCC-
Q 040027          395 IHQ--------------------VEHALKLFDEMQRD----G-VAADTRTYTTFIDGLCKNGYIIEAVELFRTLRILKC-  448 (595)
Q Consensus       395 ~~~--------------------~~~a~~~~~~~~~~----~-~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~-  448 (595)
                      .|+                    +++|...+++....    + .+....++..+...+...|++++|...++++.+... 
T Consensus       136 ~~~~~~~~~~~~~~~~~~~a~~~~~~A~~~~~~a~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~A~~~~~~a~~~~~~  215 (338)
T 3ro2_A          136 KGKSFGCPGPQDTGEFPEDVRNALQAAVDLYEENLSLVTALGDRAAQGRAFGNLGNTHYLLGNFRDAVIAHEQRLLIAKE  215 (338)
T ss_dssp             HHHTSSSSSCC----CCHHHHHHHHHHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHHH
T ss_pred             cCcccccchhhhhhhhhhhHHHHHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHh
Confidence            455                    55555555444321    1 011123566667777788888888888887764310 


Q ss_pred             ----CcCHHHHHHHHHHHHhcCChHHHHHHHHhcccCCC-CCC----HHHHHHHHHHHHhcCChhHHHHHHHHHHHc---
Q 040027          449 ----ELDIQAYNCLIDGLCKSGRLKFAWELFCSLPHGVL-VPN----VVTYNIMIQGLCNDGQMDKARDLFLDMEEN---  516 (595)
Q Consensus       449 ----~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~-~p~----~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~---  516 (595)
                          .....++..++..+...|++++|...+++...... .++    ..++..+...|...|++++|...++++.+.   
T Consensus       216 ~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~la~~~~~~g~~~~A~~~~~~a~~~~~~  295 (338)
T 3ro2_A          216 FGDKAAERRAYSNLGNAYIFLGEFETASEYYKKTLLLARQLKDRAVEAQSCYSLGNTYTLLQDYEKAIDYHLKHLAIAQE  295 (338)
T ss_dssp             HTCHHHHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHH
T ss_pred             cCChHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHhhcchhHHHHHHHHHHHHHHHhcCHHHHHHHHHHHHHHHHh
Confidence                11133677788888888999999888888765100 011    456778888899999999999999988763   


Q ss_pred             -CCC-CCHHHHHHHHHHHHHcCChhHHHHHHHHHHHC
Q 040027          517 -AAA-PDVITFDMLIHGFIRINEPSKVNELLHKMKEK  551 (595)
Q Consensus       517 -~~~-~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~  551 (595)
                       +.. ....++..+..+|...|++++|..+++++.+.
T Consensus       296 ~~~~~~~~~~~~~la~~~~~~g~~~~A~~~~~~a~~~  332 (338)
T 3ro2_A          296 LKDRIGEGRACWSLGNAYTALGNHDQAMHFAEKHLEI  332 (338)
T ss_dssp             HTCHHHHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHC
T ss_pred             cCCcHHHHHHHHHHHHHHHHcCChHHHHHHHHHHHHH
Confidence             101 11446778889999999999999999999864

>2ond_A Cleavage stimulation factor 77 kDa subunit; HAT domain, structural protein; 2.80A {Mus musculus} SCOP: a.118.8.7

Probab=99.55  E-value=5e-12  Score=118.68  Aligned_cols=217  Identities=9%  Similarity=0.079  Sum_probs=109.9

Q ss_pred             hHHHHHHHHHHhCCCCCCHHHHHHHHHHHHh-------cCCH-------hHHHHHHHHHHh-cCCCCCHhhHHHHHHHHH
Q 040027          113 SLGFIAFGRILRSCFTPNAATFNSLIKGLHA-------ESRI-------MEAAALFTKLKA-FGCEPNVITYNTLINGLC  177 (595)
Q Consensus       113 ~~A~~~~~~~~~~~~~~~~~~~~~l~~~~~~-------~g~~-------~~A~~~~~~~~~-~~~~~~~~~~~~l~~~~~  177 (595)
                      ++|+.+|++++... +.++..|..++..+..       .|++       ++|..+|++..+ .. +.+...|..++..+.
T Consensus        33 ~~a~~~~~~al~~~-p~~~~~w~~~~~~~~~~~~~l~~~g~~~~~~~~~~~A~~~~~rAl~~~~-p~~~~~~~~~~~~~~  110 (308)
T 2ond_A           33 KRVMFAYEQCLLVL-GHHPDIWYEAAQYLEQSSKLLAEKGDMNNAKLFSDEAANIYERAISTLL-KKNMLLYFAYADYEE  110 (308)
T ss_dssp             HHHHHHHHHHHHHH-TTCHHHHHHHHHHHHHHHHHHHHTSCCHHHHHHHHHHHHHHHHHHTTTT-TTCHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHc-CCCHHHHHHHHHHHHHhchhhhhccchhhcccchHHHHHHHHHHHHHhC-cccHHHHHHHHHHHH
Confidence            56667777777653 4566677666666543       3554       566666666655 22 224445566666666


Q ss_pred             hcCChhHHHHHHHHHHhcCCCCCccccCcHH-HHHHHHHHHHHcCCHhHHHHHHHHHhhCCCCCCHhHHHHHHHHHH-hc
Q 040027          178 RTGHTMIALNLFEEMANGNGEIGVVCKPNTV-TYSTIIDGLCKEGFVDKAKALFLQMKDENINPDVVTYNSLIHGLC-HA  255 (595)
Q Consensus       178 ~~g~~~~A~~~~~~~~~~~~~~~~~~~~~~~-~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~~ll~~~~-~~  255 (595)
                      ..|++++|..+|+++.+..       +.+.. .|..++..+.+.|++++|..+|++..+.. +.+...|...+.... ..
T Consensus       111 ~~~~~~~A~~~~~~al~~~-------p~~~~~~~~~~~~~~~~~~~~~~A~~~~~~a~~~~-p~~~~~~~~~a~~~~~~~  182 (308)
T 2ond_A          111 SRMKYEKVHSIYNRLLAIE-------DIDPTLVYIQYMKFARRAEGIKSGRMIFKKAREDA-RTRHHVYVTAALMEYYCS  182 (308)
T ss_dssp             HTTCHHHHHHHHHHHHTSS-------SSCTHHHHHHHHHHHHHHHCHHHHHHHHHHHHTST-TCCTHHHHHHHHHHHHTS
T ss_pred             hcCCHHHHHHHHHHHHhcc-------ccCccHHHHHHHHHHHHhcCHHHHHHHHHHHHhcC-CCCHHHHHHHHHHHHHHc
Confidence            6666666666666666533       22232 55555555555666666666666655542 122333332222211 14


Q ss_pred             CCHHHHHHHHHHHHHCCCCCCHhhHHHHHHHHHhcCChHHHHHHHHHHHHCC-CCC--CHHHHHHHHHHHHhcCCHHHHH
Q 040027          256 NDWNEAKRLFIEMMDQGVQPSVVTFNVIMDELCKNRKMDEASRLLDLMVQRG-VRP--NACTYNTLMDGFCLMGKINRAE  332 (595)
Q Consensus       256 ~~~~~A~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~-~~~--~~~~~~~l~~~~~~~~~~~~a~  332 (595)
                      |++++|..+|+..++.. +.+...|..++..+.+.|++++|..+|+++.... .+|  ....|..++......|+.+.|.
T Consensus       183 ~~~~~A~~~~~~al~~~-p~~~~~~~~~~~~~~~~g~~~~A~~~~~~al~~~~l~p~~~~~l~~~~~~~~~~~g~~~~a~  261 (308)
T 2ond_A          183 KDKSVAFKIFELGLKKY-GDIPEYVLAYIDYLSHLNEDNNTRVLFERVLTSGSLPPEKSGEIWARFLAFESNIGDLASIL  261 (308)
T ss_dssp             CCHHHHHHHHHHHHHHH-TTCHHHHHHHHHHHHTTCCHHHHHHHHHHHHHSSSSCGGGCHHHHHHHHHHHHHHSCHHHHH
T ss_pred             CCHHHHHHHHHHHHHhC-CCcHHHHHHHHHHHHHCCCHHHHHHHHHHHHhccCCCHHHHHHHHHHHHHHHHHcCCHHHHH
Confidence            55555555555554431 1234444445555555555555555555555431 122  2334444444444455555555


Q ss_pred             HHHHHHHh
Q 040027          333 ELFGSMES  340 (595)
Q Consensus       333 ~~~~~~~~  340 (595)
                      .+++++.+
T Consensus       262 ~~~~~a~~  269 (308)
T 2ond_A          262 KVEKRRFT  269 (308)
T ss_dssp             HHHHHHHH
T ss_pred             HHHHHHHH
Confidence            55555444

>3vtx_A MAMA; tetratricopeptide repeats (TPR) containing protein, peptide protein, protein binding; 1.75A {Candidatus magnetobacterium bavaricum} PDB: 3vty_A

Probab=99.54  E-value=1.4e-12  Score=112.15  Aligned_cols=165  Identities=12%  Similarity=0.046  Sum_probs=110.5

Q ss_pred             CHHHHHHHHHHHHccCCHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCcCHHHHHHHHH
Q 040027          381 TVVTYNTLFLGLFEIHQVEHALKLFDEMQRDGVAADTRTYTTFIDGLCKNGYIIEAVELFRTLRILKCELDIQAYNCLID  460 (595)
Q Consensus       381 ~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~~l~~  460 (595)
                      +...|..+...+...|++++|++.|++.++.+ |.+...+..+..+|.+.|++++|...+..+.... +.+...+..+..
T Consensus         4 ~~~iy~~lG~~~~~~g~~~~A~~~~~~al~~~-p~~~~~~~~la~~~~~~~~~~~a~~~~~~~~~~~-~~~~~~~~~~~~   81 (184)
T 3vtx_A            4 TTTIYMDIGDKKRTKGDFDGAIRAYKKVLKAD-PNNVETLLKLGKTYMDIGLPNDAIESLKKFVVLD-TTSAEAYYILGS   81 (184)
T ss_dssp             CHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-CCCHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhC-CCCHHHHHHHHHHHHHCCCHHHHHHHHHHHHhcC-chhHHHHHHHHH
Confidence            44556666666666666666666666666553 4455666666666667777777777777666654 445666666666


Q ss_pred             HHHhcCChHHHHHHHHhcccCCCCC-CHHHHHHHHHHHHhcCChhHHHHHHHHHHHcCCCCCHHHHHHHHHHHHHcCChh
Q 040027          461 GLCKSGRLKFAWELFCSLPHGVLVP-NVVTYNIMIQGLCNDGQMDKARDLFLDMEENAAAPDVITFDMLIHGFIRINEPS  539 (595)
Q Consensus       461 ~~~~~g~~~~A~~~~~~~~~~~~~p-~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~  539 (595)
                      .+...++++.|...+.+....  .| +...+..+..+|...|++++|++.|+++++.. +.+..++..++.+|...|+++
T Consensus        82 ~~~~~~~~~~a~~~~~~a~~~--~~~~~~~~~~lg~~~~~~g~~~~A~~~~~~~l~~~-p~~~~~~~~lg~~~~~~g~~~  158 (184)
T 3vtx_A           82 ANFMIDEKQAAIDALQRAIAL--NTVYADAYYKLGLVYDSMGEHDKAIEAYEKTISIK-PGFIRAYQSIGLAYEGKGLRD  158 (184)
T ss_dssp             HHHHTTCHHHHHHHHHHHHHH--CTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCHH
T ss_pred             HHHHcCCHHHHHHHHHHHHHh--CccchHHHHHHHHHHHHhCCchhHHHHHHHHHHhc-chhhhHHHHHHHHHHHCCCHH
Confidence            677777777777777766652  33 35666677777777777777777777777654 445667777777777777777


Q ss_pred             HHHHHHHHHHH
Q 040027          540 KVNELLHKMKE  550 (595)
Q Consensus       540 ~A~~~~~~~~~  550 (595)
                      +|.+.|+++++
T Consensus       159 ~A~~~~~~al~  169 (184)
T 3vtx_A          159 EAVKYFKKALE  169 (184)
T ss_dssp             HHHHHHHHHHH
T ss_pred             HHHHHHHHHHh
Confidence            77777777776

>3ro2_A PINS homolog, G-protein-signaling modulator 2; TPR repeat, protein-protein interaction, protein-binding, PR binding; 2.30A {Mus musculus}

Probab=99.54  E-value=1.8e-13  Score=130.46  Aligned_cols=278  Identities=11%  Similarity=0.052  Sum_probs=172.6

Q ss_pred             HHHHHHHHHHHHhcCChhHHHHHHHHHHhCCCCCC----HHHHHHHHHHHHhcCCHhHHHHHHHHHHhc----CCC-CCH
Q 040027           96 LYTYNILINCFCKIGRVSLGFIAFGRILRSCFTPN----AATFNSLIKGLHAESRIMEAAALFTKLKAF----GCE-PNV  166 (595)
Q Consensus        96 ~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~~----~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~----~~~-~~~  166 (595)
                      ...+......+...|++++|+..|+++.+.. +.+    ...+..+...+...|++++|.+.+++....    +.. ...
T Consensus         5 ~~~l~~~g~~~~~~g~~~~A~~~~~~al~~~-~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~   83 (338)
T 3ro2_A            5 CLELALEGERLCKSGDCRAGVSFFEAAVQVG-TEDLKTLSAIYSQLGNAYFYLHDYAKALEYHHHDLTLARTIGDQLGEA   83 (338)
T ss_dssp             HHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-CSCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHHTCHHHHH
T ss_pred             HHHHHHHHHHHHHhccHHHHHHHHHHHHhhC-cccHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHhhcccccHHHH
Confidence            3455667788999999999999999999874 334    357788889999999999999999987653    111 135


Q ss_pred             hhHHHHHHHHHhcCChhHHHHHHHHHHhcCCCCCccccCcHHHHHHHHHHHHHcCC--------------------HhHH
Q 040027          167 ITYNTLINGLCRTGHTMIALNLFEEMANGNGEIGVVCKPNTVTYSTIIDGLCKEGF--------------------VDKA  226 (595)
Q Consensus       167 ~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~--------------------~~~A  226 (595)
                      .++..+...+...|++++|+..+++........+. ......++..+...+...|+                    +++|
T Consensus        84 ~~~~~l~~~~~~~g~~~~A~~~~~~al~~~~~~~~-~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~a~~~~~~A  162 (338)
T 3ro2_A           84 KASGNLGNTLKVLGNFDEAIVCCQRHLDISRELND-KVGEARALYNLGNVYHAKGKSFGCPGPQDTGEFPEDVRNALQAA  162 (338)
T ss_dssp             HHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTC-HHHHHHHHHHHHHHHHHHHHTSSSSSCC----CCHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHccCHHHHHHHHHHHHHHHHHhcC-chHHHHHHHHHHHHHHHcCcccccchhhhhhhhhhhHHHHHHHH
Confidence            57788899999999999999999998764211000 01114477888888989999                    8888


Q ss_pred             HHHHHHHhhC----CC-CCCHhHHHHHHHHHHhcCCHHHHHHHHHHHHHCCCC-CC----HhhHHHHHHHHHhcCChHHH
Q 040027          227 KALFLQMKDE----NI-NPDVVTYNSLIHGLCHANDWNEAKRLFIEMMDQGVQ-PS----VVTFNVIMDELCKNRKMDEA  296 (595)
Q Consensus       227 ~~~~~~~~~~----~~-~~~~~~~~~ll~~~~~~~~~~~A~~~~~~~~~~~~~-~~----~~~~~~l~~~~~~~g~~~~a  296 (595)
                      .+.+++....    +. ......+..+...+...|++++|...+++..+.... ++    ..++..+...+...|++++|
T Consensus       163 ~~~~~~a~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~A~~~~~~a~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A  242 (338)
T 3ro2_A          163 VDLYEENLSLVTALGDRAAQGRAFGNLGNTHYLLGNFRDAVIAHEQRLLIAKEFGDKAAERRAYSNLGNAYIFLGEFETA  242 (338)
T ss_dssp             HHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHHHHTCHHHH
T ss_pred             HHHHHHHHHHHHhcCCHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHhcCChHHHHHHHHHHHHHHHHcCCHHHH
Confidence            8888776432    10 112335666677777778888887777776542100 01    12455556666666666666


Q ss_pred             HHHHHHHHHCCCC-CC----HHHHHHHHHHHHhcCCHHHHHHHHHHHHhcC----C-CCCHHHHHHHHHHHHhCCCHHHH
Q 040027          297 SRLLDLMVQRGVR-PN----ACTYNTLMDGFCLMGKINRAEELFGSMESMG----C-KHDDVSYNILINGYCKNKEVEEA  366 (595)
Q Consensus       297 ~~~~~~~~~~~~~-~~----~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~----~-~~~~~~~~~l~~~~~~~~~~~~A  366 (595)
                      ...+++....... .+    ..++..+..++...|++++|...+++.....    . .....++..+...|...|++++|
T Consensus       243 ~~~~~~al~~~~~~~~~~~~~~~~~~la~~~~~~g~~~~A~~~~~~a~~~~~~~~~~~~~~~~~~~la~~~~~~g~~~~A  322 (338)
T 3ro2_A          243 SEYYKKTLLLARQLKDRAVEAQSCYSLGNTYTLLQDYEKAIDYHLKHLAIAQELKDRIGEGRACWSLGNAYTALGNHDQA  322 (338)
T ss_dssp             HHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHHHHTCHHHH
T ss_pred             HHHHHHHHHHHHhhcchhHHHHHHHHHHHHHHHhcCHHHHHHHHHHHHHHHHhcCCcHHHHHHHHHHHHHHHHcCChHHH
Confidence            6666655432100 01    2344445555555555555555555543321    0 00012344444455555555555


Q ss_pred             HHHHHHHHH
Q 040027          367 LSLYREMVS  375 (595)
Q Consensus       367 ~~~~~~~~~  375 (595)
                      ...+++..+
T Consensus       323 ~~~~~~a~~  331 (338)
T 3ro2_A          323 MHFAEKHLE  331 (338)
T ss_dssp             HHHHHHHHH
T ss_pred             HHHHHHHHH
Confidence            555554443

>4abn_A Tetratricopeptide repeat protein 5; P53 cofactor, stress-response, DNA repair, gene regulation; 2.05A {Mus musculus}

Probab=99.53  E-value=3.6e-13  Score=134.30  Aligned_cols=211  Identities=10%  Similarity=-0.037  Sum_probs=134.3

Q ss_pred             HHHHHHHHHHHhcCCCCCHHHHHHHHHHHHhCCCH-HHHHHHHHHHHHCCCCCCHHHHHHHHHHHHccCCHHHHHHHHHH
Q 040027          329 NRAEELFGSMESMGCKHDDVSYNILINGYCKNKEV-EEALSLYREMVSKGIKPTVVTYNTLFLGLFEIHQVEHALKLFDE  407 (595)
Q Consensus       329 ~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~-~~A~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~  407 (595)
                      +++...++...... +.+...+..+...+...|++ ++|++.|+++++..+. +...+..+...|...|++++|...|++
T Consensus        85 ~~al~~l~~~~~~~-~~~a~~~~~lg~~~~~~g~~~~~A~~~~~~al~~~p~-~~~a~~~lg~~~~~~g~~~~A~~~~~~  162 (474)
T 4abn_A           85 EKTLQQMEEVLGSA-QVEAQALMLKGKALNVTPDYSPEAEVLLSKAVKLEPE-LVEAWNQLGEVYWKKGDVTSAHTCFSG  162 (474)
T ss_dssp             HHHHHHHHHHHTTC-CCCHHHHHHHHHHHTSSSSCCHHHHHHHHHHHHHCTT-CHHHHHHHHHHHHHHTCHHHHHHHHHH
T ss_pred             HHHHHHHHHHhccC-chhHHHHHHHHHHHHhccccHHHHHHHHHHHHhhCCC-CHHHHHHHHHHHHHcCCHHHHHHHHHH
Confidence            34444444443331 23444555555555566666 6666666655554322 445555666666666666666666666


Q ss_pred             HHHCCCCCCHHHHHHHHHHHHhc---------CCHHHHHHHHHHHHHcCCCcCHHHHHHHHHHHHhc--------CChHH
Q 040027          408 MQRDGVAADTRTYTTFIDGLCKN---------GYIIEAVELFRTLRILKCELDIQAYNCLIDGLCKS--------GRLKF  470 (595)
Q Consensus       408 ~~~~~~~~~~~~~~~l~~~~~~~---------g~~~~A~~~~~~~~~~~~~~~~~~~~~l~~~~~~~--------g~~~~  470 (595)
                      +.+.  .|+...+..+..++...         |++++|...++++.+.. +.+...+..+..+|...        |++++
T Consensus       163 al~~--~p~~~~~~~lg~~~~~~~~~~~~~~~g~~~~A~~~~~~al~~~-p~~~~~~~~lg~~~~~~~~~~~~~~g~~~~  239 (474)
T 4abn_A          163 ALTH--CKNKVSLQNLSMVLRQLQTDSGDEHSRHVMDSVRQAKLAVQMD-VLDGRSWYILGNAYLSLYFNTGQNPKISQQ  239 (474)
T ss_dssp             HHTT--CCCHHHHHHHHHHHTTCCCSCHHHHHHHHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHHHHHTTCCHHHHHH
T ss_pred             HHhh--CCCHHHHHHHHHHHHHhccCChhhhhhhHHHHHHHHHHHHHhC-CCCHHHHHHHHHHHHHHHHhhccccchHHH
Confidence            6554  34455555566666666         77777777777777665 55667777777777776        77777


Q ss_pred             HHHHHHhcccCCCCC----CHHHHHHHHHHHHhcCChhHHHHHHHHHHHcCCCCCHHHHHHHHHHHHHcCChhHHHHHHH
Q 040027          471 AWELFCSLPHGVLVP----NVVTYNIMIQGLCNDGQMDKARDLFLDMEENAAAPDVITFDMLIHGFIRINEPSKVNELLH  546 (595)
Q Consensus       471 A~~~~~~~~~~~~~p----~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~  546 (595)
                      |+..|+++.+  +.|    +...|..+..+|...|++++|++.|+++++.. +.+...+..+..++...|++++|.+.++
T Consensus       240 A~~~~~~al~--~~p~~~~~~~~~~~lg~~~~~~g~~~~A~~~~~~al~l~-p~~~~a~~~l~~~~~~lg~~~eAi~~~~  316 (474)
T 4abn_A          240 ALSAYAQAEK--VDRKASSNPDLHLNRATLHKYEESYGEALEGFSQAAALD-PAWPEPQQREQQLLEFLSRLTSLLESKG  316 (474)
T ss_dssp             HHHHHHHHHH--HCGGGGGCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHHHHHHHHHHHTT
T ss_pred             HHHHHHHHHH--hCCCcccCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhC-CCCHHHHHHHHHHHHHHHHHHHHHHHhc
Confidence            7777777776  344    56777777788888888888888888887764 4456677777777777777777776543


Q ss_pred             H
Q 040027          547 K  547 (595)
Q Consensus       547 ~  547 (595)
                      +
T Consensus       317 ~  317 (474)
T 4abn_A          317 K  317 (474)
T ss_dssp             T
T ss_pred             c
Confidence            3

>3ulq_A Response regulator aspartate phosphatase F; tetratricopeptide repeat, response regulator helix-turn-HELX binding, 3-helix bundle; 2.30A {Bacillus subtilis}

Probab=99.53  E-value=2e-12  Score=125.75  Aligned_cols=226  Identities=14%  Similarity=0.056  Sum_probs=108.0

Q ss_pred             HHHcCCHhHHHHHHHHHhhC--CCCCC--HhHHHHHHHH--HHhcCCHHHHH-----------HHHHHHHHCCCCCCHh-
Q 040027          217 LCKEGFVDKAKALFLQMKDE--NINPD--VVTYNSLIHG--LCHANDWNEAK-----------RLFIEMMDQGVQPSVV-  278 (595)
Q Consensus       217 ~~~~g~~~~A~~~~~~~~~~--~~~~~--~~~~~~ll~~--~~~~~~~~~A~-----------~~~~~~~~~~~~~~~~-  278 (595)
                      +.+.+++++|..+++++.+.  ....+  ...|-.++..  ....++++.+.           +.++.+....  .+.. 
T Consensus        22 ~i~~~~~~~A~~l~~~i~~~~~~~~~~~~~~~y~~ll~~r~~~~~~~~~~~~~~~~e~~~~~~~~~~~i~~~~--~~~~~   99 (383)
T 3ulq_A           22 YIRRFSIPDAEYLRREIKQELDQMEEDQDLHLYYSLMEFRHNLMLEYLEPLEKMRIEEQPRLSDLLLEIDKKQ--ARLTG   99 (383)
T ss_dssp             HHHTTCHHHHHHHHHHHHHHHHTSCCCHHHHHHHHHHHHHHHHHHHHHGGGGGSCGGGSCCHHHHHHHHHHHT--HHHHH
T ss_pred             HHHHcCHHHHHHHHHHHHHHHHhhccchHHHHHHHHHHHHHHHHHhhcCcccccccccccchhhHHHHHHhcC--CCchh
Confidence            55689999999999988664  22223  3333333322  12223333333           4444443321  1111 


Q ss_pred             -----hHHHHHHHHHhcCChHHHHHHHHHHHHC----CCCC-CHHHHHHHHHHHHhcCCHHHHHHHHHHHHhcCCC-C--
Q 040027          279 -----TFNVIMDELCKNRKMDEASRLLDLMVQR----GVRP-NACTYNTLMDGFCLMGKINRAEELFGSMESMGCK-H--  345 (595)
Q Consensus       279 -----~~~~l~~~~~~~g~~~~a~~~~~~~~~~----~~~~-~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~-~--  345 (595)
                           .+......+...|++++|...++++.+.    +..+ ...++..++.+|...|+++.|...+.+..+.... +  
T Consensus       100 ~l~~~~~~~~g~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~a~~~~~lg~~~~~~~~~~~A~~~~~~al~~~~~~~~~  179 (383)
T 3ulq_A          100 LLEYYFNFFRGMYELDQREYLSAIKFFKKAESKLIFVKDRIEKAEFFFKMSESYYYMKQTYFSMDYARQAYEIYKEHEAY  179 (383)
T ss_dssp             HHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHTTGGGCCCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHTCSTT
T ss_pred             HHHHHHHHHHHHHHHHhcCHHHHHHHHHHHHHHHhhCCCHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHhCccc
Confidence                 1112445566667777777777766553    1111 2345556666666666666666666665432100 0  


Q ss_pred             ---CHHHHHHHHHHHHhCCCHHHHHHHHHHHHHCCCC-CC----HHHHHHHHHHHHccCCHHHHHHHHHHHHHC----CC
Q 040027          346 ---DDVSYNILINGYCKNKEVEEALSLYREMVSKGIK-PT----VVTYNTLFLGLFEIHQVEHALKLFDEMQRD----GV  413 (595)
Q Consensus       346 ---~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~~~~~-~~----~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~----~~  413 (595)
                         ...++..+..+|...|++++|+..+++..+.... ++    ..++..+...+...|++++|...+++..+.    +.
T Consensus       180 ~~~~~~~~~~lg~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~lg~~y~~~g~~~~A~~~~~~al~~~~~~~~  259 (383)
T 3ulq_A          180 NIRLLQCHSLFATNFLDLKQYEDAISHFQKAYSMAEAEKQPQLMGRTLYNIGLCKNSQSQYEDAIPYFKRAIAVFEESNI  259 (383)
T ss_dssp             HHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTC
T ss_pred             hHHHHHHHHHHHHHHHHhcCHHHHHHHHHHHHHHHHHcCChHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHhhcc
Confidence               1224555555666666666666666555432100 00    123444444444555555555554444431    11


Q ss_pred             -CCCHHHHHHHHHHHHhcCCHHHHHHHHHHHH
Q 040027          414 -AADTRTYTTFIDGLCKNGYIIEAVELFRTLR  444 (595)
Q Consensus       414 -~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~  444 (595)
                       +....++..+..+|.+.|++++|...+++..
T Consensus       260 ~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~al  291 (383)
T 3ulq_A          260 LPSLPQAYFLITQIHYKLGKIDKAHEYHSKGM  291 (383)
T ss_dssp             GGGHHHHHHHHHHHHHHTTCHHHHHHHHHHHH
T ss_pred             chhHHHHHHHHHHHHHHCCCHHHHHHHHHHHH
Confidence             2223334444444444444444444444443

>3vtx_A MAMA; tetratricopeptide repeats (TPR) containing protein, peptide protein, protein binding; 1.75A {Candidatus magnetobacterium bavaricum} PDB: 3vty_A

Probab=99.53  E-value=2.2e-12  Score=111.01  Aligned_cols=162  Identities=15%  Similarity=0.094  Sum_probs=68.3

Q ss_pred             HHHHHHHHHHhCCCHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHccCCHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHH
Q 040027          349 SYNILINGYCKNKEVEEALSLYREMVSKGIKPTVVTYNTLFLGLFEIHQVEHALKLFDEMQRDGVAADTRTYTTFIDGLC  428 (595)
Q Consensus       349 ~~~~l~~~~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~  428 (595)
                      .|..+...|...|++++|++.|++.++..+. +...+..+...+...|++++|...+..+.... +.+...+..+...+.
T Consensus         7 iy~~lG~~~~~~g~~~~A~~~~~~al~~~p~-~~~~~~~la~~~~~~~~~~~a~~~~~~~~~~~-~~~~~~~~~~~~~~~   84 (184)
T 3vtx_A            7 IYMDIGDKKRTKGDFDGAIRAYKKVLKADPN-NVETLLKLGKTYMDIGLPNDAIESLKKFVVLD-TTSAEAYYILGSANF   84 (184)
T ss_dssp             HHHHHHHHHHHHTCHHHHHHHHHHHHHHCTT-CHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-CCCHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHcCCHHHHHHHHHHHHHhCCC-CHHHHHHHHHHHHHCCCHHHHHHHHHHHHhcC-chhHHHHHHHHHHHH
Confidence            3333444444444444444444444333222 33333334444444444444444444433331 223333333344444


Q ss_pred             hcCCHHHHHHHHHHHHHcCCCcCHHHHHHHHHHHHhcCChHHHHHHHHhcccCCCCC-CHHHHHHHHHHHHhcCChhHHH
Q 040027          429 KNGYIIEAVELFRTLRILKCELDIQAYNCLIDGLCKSGRLKFAWELFCSLPHGVLVP-NVVTYNIMIQGLCNDGQMDKAR  507 (595)
Q Consensus       429 ~~g~~~~A~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~p-~~~~~~~l~~~~~~~g~~~~A~  507 (595)
                      ..++++.|...+.++.... +.+...+..++.++...|++++|+..|+++.+  +.| +..+|..++.+|...|++++|+
T Consensus        85 ~~~~~~~a~~~~~~a~~~~-~~~~~~~~~lg~~~~~~g~~~~A~~~~~~~l~--~~p~~~~~~~~lg~~~~~~g~~~~A~  161 (184)
T 3vtx_A           85 MIDEKQAAIDALQRAIALN-TVYADAYYKLGLVYDSMGEHDKAIEAYEKTIS--IKPGFIRAYQSIGLAYEGKGLRDEAV  161 (184)
T ss_dssp             HTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHH--HCTTCHHHHHHHHHHHHHTTCHHHHH
T ss_pred             HcCCHHHHHHHHHHHHHhC-ccchHHHHHHHHHHHHhCCchhHHHHHHHHHH--hcchhhhHHHHHHHHHHHCCCHHHHH
Confidence            4444444444444444433 33344444444444444444444444444444  122 2344444444444444455554


Q ss_pred             HHHHHHHH
Q 040027          508 DLFLDMEE  515 (595)
Q Consensus       508 ~~~~~~~~  515 (595)
                      +.|+++++
T Consensus       162 ~~~~~al~  169 (184)
T 3vtx_A          162 KYFKKALE  169 (184)
T ss_dssp             HHHHHHHH
T ss_pred             HHHHHHHh
Confidence            44444444

>3ulq_A Response regulator aspartate phosphatase F; tetratricopeptide repeat, response regulator helix-turn-HELX binding, 3-helix bundle; 2.30A {Bacillus subtilis}

Probab=99.52  E-value=1.3e-12  Score=127.09  Aligned_cols=297  Identities=11%  Similarity=-0.028  Sum_probs=206.5

Q ss_pred             HHHhcCCHHHHHHHHHHHHHC--CCCCCH--hhHHHHHH--HHHhcCChHHHH-----------HHHHHHHHCCCCCC--
Q 040027          251 GLCHANDWNEAKRLFIEMMDQ--GVQPSV--VTFNVIMD--ELCKNRKMDEAS-----------RLLDLMVQRGVRPN--  311 (595)
Q Consensus       251 ~~~~~~~~~~A~~~~~~~~~~--~~~~~~--~~~~~l~~--~~~~~g~~~~a~-----------~~~~~~~~~~~~~~--  311 (595)
                      .+.+.+++++|..+++++.+.  .+..+.  ..|..++.  .....+.++.+.           +.++.+.......+  
T Consensus        21 ~~i~~~~~~~A~~l~~~i~~~~~~~~~~~~~~~y~~ll~~r~~~~~~~~~~~~~~~~e~~~~~~~~~~~i~~~~~~~~~~  100 (383)
T 3ulq_A           21 MYIRRFSIPDAEYLRREIKQELDQMEEDQDLHLYYSLMEFRHNLMLEYLEPLEKMRIEEQPRLSDLLLEIDKKQARLTGL  100 (383)
T ss_dssp             HHHHTTCHHHHHHHHHHHHHHHHTSCCCHHHHHHHHHHHHHHHHHHHHHGGGGGSCGGGSCCHHHHHHHHHHHTHHHHHH
T ss_pred             HHHHHcCHHHHHHHHHHHHHHHHhhccchHHHHHHHHHHHHHHHHHhhcCcccccccccccchhhHHHHHHhcCCCchhH
Confidence            356789999999999998664  232333  23333332  222233344444           66666544211111  


Q ss_pred             --HHHHHHHHHHHHhcCCHHHHHHHHHHHHhc----CCCC-CHHHHHHHHHHHHhCCCHHHHHHHHHHHHHCCCC-C---
Q 040027          312 --ACTYNTLMDGFCLMGKINRAEELFGSMESM----GCKH-DDVSYNILINGYCKNKEVEEALSLYREMVSKGIK-P---  380 (595)
Q Consensus       312 --~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~----~~~~-~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~~~~~-~---  380 (595)
                        ...+...+..+...|++++|...+++..+.    +-++ ...++..+..+|...|++++|+..+.+..+.... +   
T Consensus       101 l~~~~~~~~g~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~a~~~~~lg~~~~~~~~~~~A~~~~~~al~~~~~~~~~~  180 (383)
T 3ulq_A          101 LEYYFNFFRGMYELDQREYLSAIKFFKKAESKLIFVKDRIEKAEFFFKMSESYYYMKQTYFSMDYARQAYEIYKEHEAYN  180 (383)
T ss_dssp             HHHHHHHHHHHHHHHTTCHHHHHHHHHHHHTTGGGCCCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHTCSTTH
T ss_pred             HHHHHHHHHHHHHHHhcCHHHHHHHHHHHHHHHhhCCCHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHhCccch
Confidence              112223667788899999999999998764    1111 2357888999999999999999999988763111 1   


Q ss_pred             --CHHHHHHHHHHHHccCCHHHHHHHHHHHHHCCC-CCC----HHHHHHHHHHHHhcCCHHHHHHHHHHHHHc----CC-
Q 040027          381 --TVVTYNTLFLGLFEIHQVEHALKLFDEMQRDGV-AAD----TRTYTTFIDGLCKNGYIIEAVELFRTLRIL----KC-  448 (595)
Q Consensus       381 --~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~-~~~----~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~----~~-  448 (595)
                        ...++..+...+...|++++|...+++..+... .++    ..++..+..+|...|++++|...++++.+.    +. 
T Consensus       181 ~~~~~~~~~lg~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~lg~~y~~~g~~~~A~~~~~~al~~~~~~~~~  260 (383)
T 3ulq_A          181 IRLLQCHSLFATNFLDLKQYEDAISHFQKAYSMAEAEKQPQLMGRTLYNIGLCKNSQSQYEDAIPYFKRAIAVFEESNIL  260 (383)
T ss_dssp             HHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCG
T ss_pred             HHHHHHHHHHHHHHHHhcCHHHHHHHHHHHHHHHHHcCChHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHhhccc
Confidence              234678888899999999999999988875310 112    246778888999999999999999998862    32 


Q ss_pred             CcCHHHHHHHHHHHHhcCChHHHHHHHHhcccCC---CCCC-HHHHHHHHHHHHhcCC---hhHHHHHHHHHHHcCCCC-
Q 040027          449 ELDIQAYNCLIDGLCKSGRLKFAWELFCSLPHGV---LVPN-VVTYNIMIQGLCNDGQ---MDKARDLFLDMEENAAAP-  520 (595)
Q Consensus       449 ~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~---~~p~-~~~~~~l~~~~~~~g~---~~~A~~~~~~~~~~~~~~-  520 (595)
                      +....++..++.++...|++++|...+++.....   -.|. ...+..+...|...|+   +++|+.++++.   +..+ 
T Consensus       261 ~~~~~~~~~l~~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~al~~~~~~---~~~~~  337 (383)
T 3ulq_A          261 PSLPQAYFLITQIHYKLGKIDKAHEYHSKGMAYSQKAGDVIYLSEFEFLKSLYLSGPDEEAIQGFFDFLESK---MLYAD  337 (383)
T ss_dssp             GGHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHTSSCCHHHHHHHHHHHHHT---TCHHH
T ss_pred             hhHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHhCCCcHHHHHHHHHHHHHC---cCHHH
Confidence            4446788899999999999999999999887621   0121 2335667788888888   77777777765   2222 


Q ss_pred             CHHHHHHHHHHHHHcCChhHHHHHHHHHHH
Q 040027          521 DVITFDMLIHGFIRINEPSKVNELLHKMKE  550 (595)
Q Consensus       521 ~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~  550 (595)
                      ....+..++..|...|++++|..+++++.+
T Consensus       338 ~~~~~~~la~~y~~~g~~~~A~~~~~~al~  367 (383)
T 3ulq_A          338 LEDFAIDVAKYYHERKNFQKASAYFLKVEQ  367 (383)
T ss_dssp             HHHHHHHHHHHHHHTTCHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHCCCHHHHHHHHHHHHH
Confidence            245677889999999999999999999874

>4abn_A Tetratricopeptide repeat protein 5; P53 cofactor, stress-response, DNA repair, gene regulation; 2.05A {Mus musculus}

Probab=99.47  E-value=4e-12  Score=126.76  Aligned_cols=192  Identities=15%  Similarity=0.034  Sum_probs=81.5

Q ss_pred             HhhHHHHHHHHHhcCCh-HHHHHHHHHHHHCCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHhcCCCCCHHHHHHHHH
Q 040027          277 VVTFNVIMDELCKNRKM-DEASRLLDLMVQRGVRPNACTYNTLMDGFCLMGKINRAEELFGSMESMGCKHDDVSYNILIN  355 (595)
Q Consensus       277 ~~~~~~l~~~~~~~g~~-~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~  355 (595)
                      ...+..+...+...|++ ++|...|+++.+.. +.+...+..+..+|...|++++|+..|+++.+.  .|+...+..+..
T Consensus       102 a~~~~~lg~~~~~~g~~~~~A~~~~~~al~~~-p~~~~a~~~lg~~~~~~g~~~~A~~~~~~al~~--~p~~~~~~~lg~  178 (474)
T 4abn_A          102 AQALMLKGKALNVTPDYSPEAEVLLSKAVKLE-PELVEAWNQLGEVYWKKGDVTSAHTCFSGALTH--CKNKVSLQNLSM  178 (474)
T ss_dssp             HHHHHHHHHHHTSSSSCCHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHHTCHHHHHHHHHHHHTT--CCCHHHHHHHHH
T ss_pred             HHHHHHHHHHHHhccccHHHHHHHHHHHHhhC-CCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHhh--CCCHHHHHHHHH
Confidence            33444444444444444 44444444444432 113334444444444444444444444444443  233344444444


Q ss_pred             HHHhC---------CCHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHcc--------CCHHHHHHHHHHHHHCCCC---C
Q 040027          356 GYCKN---------KEVEEALSLYREMVSKGIKPTVVTYNTLFLGLFEI--------HQVEHALKLFDEMQRDGVA---A  415 (595)
Q Consensus       356 ~~~~~---------~~~~~A~~~~~~~~~~~~~~~~~~~~~l~~~~~~~--------~~~~~a~~~~~~~~~~~~~---~  415 (595)
                      ++...         |++++|+..|+++++..+. +...+..+..++...        |++++|...|+++.+.. +   .
T Consensus       179 ~~~~~~~~~~~~~~g~~~~A~~~~~~al~~~p~-~~~~~~~lg~~~~~~~~~~~~~~g~~~~A~~~~~~al~~~-p~~~~  256 (474)
T 4abn_A          179 VLRQLQTDSGDEHSRHVMDSVRQAKLAVQMDVL-DGRSWYILGNAYLSLYFNTGQNPKISQQALSAYAQAEKVD-RKASS  256 (474)
T ss_dssp             HHTTCCCSCHHHHHHHHHHHHHHHHHHHHHCTT-CHHHHHHHHHHHHHHHHHTTCCHHHHHHHHHHHHHHHHHC-GGGGG
T ss_pred             HHHHhccCChhhhhhhHHHHHHHHHHHHHhCCC-CHHHHHHHHHHHHHHHHhhccccchHHHHHHHHHHHHHhC-CCccc
Confidence            44444         4444444444444443221 333444444444433        44444444444444331 1   2


Q ss_pred             CHHHHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCcCHHHHHHHHHHHHhcCChHHHHHH
Q 040027          416 DTRTYTTFIDGLCKNGYIIEAVELFRTLRILKCELDIQAYNCLIDGLCKSGRLKFAWEL  474 (595)
Q Consensus       416 ~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~  474 (595)
                      +...+..+..+|...|++++|...|+++.+.. +.+...+..+..++...|++++|+..
T Consensus       257 ~~~~~~~lg~~~~~~g~~~~A~~~~~~al~l~-p~~~~a~~~l~~~~~~lg~~~eAi~~  314 (474)
T 4abn_A          257 NPDLHLNRATLHKYEESYGEALEGFSQAAALD-PAWPEPQQREQQLLEFLSRLTSLLES  314 (474)
T ss_dssp             CHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             CHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhC-CCCHHHHHHHHHHHHHHHHHHHHHHH
Confidence            34444444444444444444444444444433 33334444444444444444444443

>3nf1_A KLC 1, kinesin light chain 1; TPR, structural genomics consortium (SGC), motor PR transport protein; 2.80A {Homo sapiens}

Probab=99.47  E-value=7.4e-13  Score=124.72  Aligned_cols=244  Identities=12%  Similarity=0.021  Sum_probs=112.7

Q ss_pred             hhHHHHHHHHHhcCChHHHHHHHHHHHHC-------CCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHhc------CC-
Q 040027          278 VTFNVIMDELCKNRKMDEASRLLDLMVQR-------GVRPNACTYNTLMDGFCLMGKINRAEELFGSMESM------GC-  343 (595)
Q Consensus       278 ~~~~~l~~~~~~~g~~~~a~~~~~~~~~~-------~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~------~~-  343 (595)
                      .++..+...+...|++++|..+++++.+.       ..+....++..+..+|...|++++|...++++...      +. 
T Consensus        28 ~~~~~l~~~~~~~g~~~~A~~~~~~a~~~~~~~~~~~~~~~~~~~~~la~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~  107 (311)
T 3nf1_A           28 RTLHNLVIQYASQGRYEVAVPLCKQALEDLEKTSGHDHPDVATMLNILALVYRDQNKYKDAANLLNDALAIREKTLGKDH  107 (311)
T ss_dssp             HHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHHHCSSSHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHHHCTTC
T ss_pred             HHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHHcCCCCHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHhCCCC
Confidence            34555555555666666666666555542       11222334445555555555555555555554432      10 


Q ss_pred             CCCHHHHHHHHHHHHhCCCHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHccCCHHHHHHHHHHHHHCCCCCCHHHHHHH
Q 040027          344 KHDDVSYNILINGYCKNKEVEEALSLYREMVSKGIKPTVVTYNTLFLGLFEIHQVEHALKLFDEMQRDGVAADTRTYTTF  423 (595)
Q Consensus       344 ~~~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l  423 (595)
                      +.....+..+...|...|++++|...++++.+...                            .......+.....+..+
T Consensus       108 ~~~~~~~~~l~~~~~~~g~~~~A~~~~~~a~~~~~----------------------------~~~~~~~~~~~~~~~~l  159 (311)
T 3nf1_A          108 PAVAATLNNLAVLYGKRGKYKEAEPLCKRALEIRE----------------------------KVLGKDHPDVAKQLNNL  159 (311)
T ss_dssp             HHHHHHHHHHHHHHHTTTCHHHHHHHHHHHHHHHH----------------------------HHHCTTCHHHHHHHHHH
T ss_pred             hHHHHHHHHHHHHHHHcCcHHHHHHHHHHHHHHHH----------------------------HhcCCCChHHHHHHHHH
Confidence            11223444444555555555555555544443200                            00000001122334445


Q ss_pred             HHHHHhcCCHHHHHHHHHHHHHc------C-CCcCHHHHHHHHHHHHhcCChHHHHHHHHhcccC-------CCCCC---
Q 040027          424 IDGLCKNGYIIEAVELFRTLRIL------K-CELDIQAYNCLIDGLCKSGRLKFAWELFCSLPHG-------VLVPN---  486 (595)
Q Consensus       424 ~~~~~~~g~~~~A~~~~~~~~~~------~-~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~-------~~~p~---  486 (595)
                      ...+...|++++|...++++...      + .+....++..++.+|...|++++|...++++.+.       ...+.   
T Consensus       160 a~~~~~~~~~~~A~~~~~~a~~~~~~~~~~~~~~~~~~~~~la~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~~  239 (311)
T 3nf1_A          160 ALLCQNQGKYEEVEYYYQRALEIYQTKLGPDDPNVAKTKNNLASCYLKQGKFKQAETLYKEILTRAHEREFGSVDDENKP  239 (311)
T ss_dssp             HHHHHTTTCHHHHHHHHHHHHHHHHHTSCTTCHHHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHHHHHHC------CC
T ss_pred             HHHHHHcCCHHHHHHHHHHHHHHHHHHhCCCCHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHhcCCCCCcchHH
Confidence            55555555555555555555443      1 1222344555566666666666666666655531       01111   


Q ss_pred             ----HHHHHHHHHHHHhcCChhHHHHHHHHHHHcCCCCCHHHHHHHHHHHHHcCChhHHHHHHHHHHH
Q 040027          487 ----VVTYNIMIQGLCNDGQMDKARDLFLDMEENAAAPDVITFDMLIHGFIRINEPSKVNELLHKMKE  550 (595)
Q Consensus       487 ----~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~  550 (595)
                          ...+..+...+...+.+.+|...+....... +....++..++.+|...|++++|.++++++.+
T Consensus       240 ~~~~~~~~~~~~~~~~~~~~~~~a~~~~~~~~~~~-~~~~~~~~~la~~~~~~g~~~~A~~~~~~al~  306 (311)
T 3nf1_A          240 IWMHAEEREECKGKQKDGTSFGEYGGWYKACKVDS-PTVTTTLKNLGALYRRQGKFEAAETLEEAAMR  306 (311)
T ss_dssp             HHHHHHHHHHC-------CCSCCCC---------C-HHHHHHHHHHHHHHHHHTCHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHhcCchhhHHHHHHHHHHHhhcCCCC-chHHHHHHHHHHHHHHCCCHHHHHHHHHHHHH
Confidence                1112222233344556666666666666542 33456777788888888888888888888775

>3q15_A PSP28, response regulator aspartate phosphatase H; tetratricopeptide repeat, 3-helix bundle, phosphorelay signa transduction, phosphatase; 2.19A {Bacillus subtilis}

Probab=99.44  E-value=2.1e-11  Score=118.25  Aligned_cols=312  Identities=11%  Similarity=-0.003  Sum_probs=140.9

Q ss_pred             cCcHHHHHHHHHHH--HHcCCHhHHHHHHHHHhhC--CCC--CCHhHHHHHHHHH--HhcCCHHHHH---------HHHH
Q 040027          204 KPNTVTYSTIIDGL--CKEGFVDKAKALFLQMKDE--NIN--PDVVTYNSLIHGL--CHANDWNEAK---------RLFI  266 (595)
Q Consensus       204 ~~~~~~~~~l~~~~--~~~g~~~~A~~~~~~~~~~--~~~--~~~~~~~~ll~~~--~~~~~~~~A~---------~~~~  266 (595)
                      .|+..+-..+-..|  ...+++++|..+++++.+.  ...  .+...|-.|+..-  .-.+.+..+.         ..++
T Consensus         7 ~~~~~v~~~l~~wy~~i~~~~~~~A~~l~~~i~~~~~~~~~~~~~~~yy~l~~~r~~~~~~~~~~~~~~~~~~~~~~~l~   86 (378)
T 3q15_A            7 IPSSRVGVKINEWYKMIRQFSVPDAEILKAEVEQDIQQMEEDQDLLIYYSLMCFRHQLMLDYLEPGKTYGNRPTVTELLE   86 (378)
T ss_dssp             BCHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHGGGBCCCHHHHHHHHHHHHHHHHHHHTCCC--------CHHHHHH
T ss_pred             ccHHHHHHHHHHHHHHHHHcCHHHHHHHHHHHHHHHHHhcccHHHHHHHHHHHHHHHHHHhhcCcccccccccchHHHHH
Confidence            34555555565565  7789999999999887653  111  2233333333221  1111111111         3333


Q ss_pred             HHHHCCCCCCH----hhHHHHHHHHHhcCChHHHHHHHHHHHHCCC-CC----CHHHHHHHHHHHHhcCCHHHHHHHHHH
Q 040027          267 EMMDQGVQPSV----VTFNVIMDELCKNRKMDEASRLLDLMVQRGV-RP----NACTYNTLMDGFCLMGKINRAEELFGS  337 (595)
Q Consensus       267 ~~~~~~~~~~~----~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~~-~~----~~~~~~~l~~~~~~~~~~~~a~~~~~~  337 (595)
                      .+.....+.+.    ..+......+...|++++|...|+++.+... .+    ...++..++.+|...|+++.|...+.+
T Consensus        87 ~i~~~~~~~~~~l~~~~~~~~g~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~a~~~~~lg~~y~~~~~~~~A~~~~~~  166 (378)
T 3q15_A           87 TIETPQKKLTGLLKYYSLFFRGMYEFDQKEYVEAIGYYREAEKELPFVSDDIEKAEFHFKVAEAYYHMKQTHVSMYHILQ  166 (378)
T ss_dssp             HHHGGGHHHHHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHTTGGGCCCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHH
T ss_pred             HHhccCCCCccHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHhhCCChHHHHHHHHHHHHHHHHcCCcHHHHHHHHH
Confidence            33221000000    0122233344555555555555555544210 01    123444455555555555555555555


Q ss_pred             HHhcCC--C----CCHHHHHHHHHHHHhCCCHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHccCCHHHHHHHHHHHHHC
Q 040027          338 MESMGC--K----HDDVSYNILINGYCKNKEVEEALSLYREMVSKGIKPTVVTYNTLFLGLFEIHQVEHALKLFDEMQRD  411 (595)
Q Consensus       338 ~~~~~~--~----~~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~  411 (595)
                      ..+...  .    ....++..+..+|...|++++|.+.+++..+..                               .+.
T Consensus       167 al~~~~~~~~~~~~~~~~~~~lg~~y~~~~~~~~A~~~~~~al~~~-------------------------------~~~  215 (378)
T 3q15_A          167 ALDIYQNHPLYSIRTIQSLFVIAGNYDDFKHYDKALPHLEAALELA-------------------------------MDI  215 (378)
T ss_dssp             HHHHHHTSTTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHH-------------------------------HHT
T ss_pred             HHHHHHhCCCchhhHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHH-------------------------------HHc
Confidence            432200  0    012234444444555555555555544443310                               000


Q ss_pred             CCC-CCHHHHHHHHHHHHhcCCHHHHHHHHHHHHH-----cCCCcCHHHHHHHHHHHHhcCChHHHHHHHHhcccCCC--
Q 040027          412 GVA-ADTRTYTTFIDGLCKNGYIIEAVELFRTLRI-----LKCELDIQAYNCLIDGLCKSGRLKFAWELFCSLPHGVL--  483 (595)
Q Consensus       412 ~~~-~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~-----~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~--  483 (595)
                      +.+ ....++..+..+|...|++++|...++++..     .. +....++..++.++.+.|++++|...+++..+...  
T Consensus       216 ~~~~~~~~~~~~lg~~y~~~~~~~~A~~~~~~al~~~~~~~~-~~~~~~~~~la~~~~~~g~~~~A~~~~~~al~~~~~~  294 (378)
T 3q15_A          216 QNDRFIAISLLNIANSYDRSGDDQMAVEHFQKAAKVSREKVP-DLLPKVLFGLSWTLCKAGQTQKAFQFIEEGLDHITAR  294 (378)
T ss_dssp             TCHHHHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHHHHCG-GGHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCCTT
T ss_pred             CCHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHhhCC-hhHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHc
Confidence            000 0122344455555555556655555555554     22 22345555566666666666666666665544110  


Q ss_pred             -CCC-HHHHHHHHHHHHhcCC---hhHHHHHHHHHHHcCCCC-CHHHHHHHHHHHHHcCChhHHHHHHHHHHH
Q 040027          484 -VPN-VVTYNIMIQGLCNDGQ---MDKARDLFLDMEENAAAP-DVITFDMLIHGFIRINEPSKVNELLHKMKE  550 (595)
Q Consensus       484 -~p~-~~~~~~l~~~~~~~g~---~~~A~~~~~~~~~~~~~~-~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~  550 (595)
                       .|. ...+..+...|...++   +.+|+..+++.   +..+ ....+..++..|...|++++|...++++.+
T Consensus       295 ~~~~~~~~~~~l~~ly~~~~~~~~~~~al~~~~~~---~~~~~~~~~~~~la~~y~~~g~~~~A~~~~~~al~  364 (378)
T 3q15_A          295 SHKFYKELFLFLQAVYKETVDERKIHDLLSYFEKK---NLHAYIEACARSAAAVFESSCHFEQAAAFYRKVLK  364 (378)
T ss_dssp             CCSCHHHHHHHHHHHHSSSCCHHHHHHHHHHHHHT---TCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHH
T ss_pred             CCHHHHHHHHHHHHHHhCCCcHHHHHHHHHHHHhC---CChhHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHH
Confidence             111 2233444444555555   55555555542   1112 223445566666666666666666666653

>3nf1_A KLC 1, kinesin light chain 1; TPR, structural genomics consortium (SGC), motor PR transport protein; 2.80A {Homo sapiens}

Probab=99.43  E-value=1.4e-12  Score=122.69  Aligned_cols=172  Identities=18%  Similarity=0.128  Sum_probs=128.7

Q ss_pred             cCcHHHHHHHHHHHHHcCCHhHHHHHHHHHhhC-------CCCCCHhHHHHHHHHHHhcCCHHHHHHHHHHHHHC-----
Q 040027          204 KPNTVTYSTIIDGLCKEGFVDKAKALFLQMKDE-------NINPDVVTYNSLIHGLCHANDWNEAKRLFIEMMDQ-----  271 (595)
Q Consensus       204 ~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~-------~~~~~~~~~~~ll~~~~~~~~~~~A~~~~~~~~~~-----  271 (595)
                      +....++..+...+...|++++|..+++++.+.       ..+.....+..+...+...|++++|...+++.+..     
T Consensus        24 ~~~~~~~~~l~~~~~~~g~~~~A~~~~~~a~~~~~~~~~~~~~~~~~~~~~la~~~~~~g~~~~A~~~~~~al~~~~~~~  103 (311)
T 3nf1_A           24 PARLRTLHNLVIQYASQGRYEVAVPLCKQALEDLEKTSGHDHPDVATMLNILALVYRDQNKYKDAANLLNDALAIREKTL  103 (311)
T ss_dssp             CHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHHHCSSSHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHHH
T ss_pred             hHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHHcCCCCHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHh
Confidence            445778888999999999999999999988763       22334567888889999999999999999888764     


Q ss_pred             -CC-CCCHhhHHHHHHHHHhcCChHHHHHHHHHHHHC------CC-CCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHhc-
Q 040027          272 -GV-QPSVVTFNVIMDELCKNRKMDEASRLLDLMVQR------GV-RPNACTYNTLMDGFCLMGKINRAEELFGSMESM-  341 (595)
Q Consensus       272 -~~-~~~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~------~~-~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~-  341 (595)
                       +. +.....+..+...+...|++++|...++++.+.      +. +.....+..+..++...|++++|+..++++.+. 
T Consensus       104 ~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~a~~~~~~~~~~~~~~~~~~~~~la~~~~~~~~~~~A~~~~~~a~~~~  183 (311)
T 3nf1_A          104 GKDHPAVAATLNNLAVLYGKRGKYKEAEPLCKRALEIREKVLGKDHPDVAKQLNNLALLCQNQGKYEEVEYYYQRALEIY  183 (311)
T ss_dssp             CTTCHHHHHHHHHHHHHHHTTTCHHHHHHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHHHTTTCHHHHHHHHHHHHHHH
T ss_pred             CCCChHHHHHHHHHHHHHHHcCcHHHHHHHHHHHHHHHHHhcCCCChHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHH
Confidence             11 223456777888888999999999998888764      11 223455677788888888888888888887654 


Q ss_pred             -----C-CCCCHHHHHHHHHHHHhCCCHHHHHHHHHHHHH
Q 040027          342 -----G-CKHDDVSYNILINGYCKNKEVEEALSLYREMVS  375 (595)
Q Consensus       342 -----~-~~~~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~  375 (595)
                           + .+....++..+..+|...|++++|...++++.+
T Consensus       184 ~~~~~~~~~~~~~~~~~la~~~~~~g~~~~A~~~~~~al~  223 (311)
T 3nf1_A          184 QTKLGPDDPNVAKTKNNLASCYLKQGKFKQAETLYKEILT  223 (311)
T ss_dssp             HHTSCTTCHHHHHHHHHHHHHHHHHTCHHHHHHHHHHHHH
T ss_pred             HHHhCCCCHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHH
Confidence                 1 122234677778888888888888888887775

>3q15_A PSP28, response regulator aspartate phosphatase H; tetratricopeptide repeat, 3-helix bundle, phosphorelay signa transduction, phosphatase; 2.19A {Bacillus subtilis}

Probab=99.42  E-value=3.6e-11  Score=116.53  Aligned_cols=226  Identities=11%  Similarity=-0.022  Sum_probs=158.8

Q ss_pred             HHHHHHHhCCCHHHHHHHHHHHHHCCC-CC----CHHHHHHHHHHHHccCCHHHHHHHHHHHHHC--CCC----CCHHHH
Q 040027          352 ILINGYCKNKEVEEALSLYREMVSKGI-KP----TVVTYNTLFLGLFEIHQVEHALKLFDEMQRD--GVA----ADTRTY  420 (595)
Q Consensus       352 ~l~~~~~~~~~~~~A~~~~~~~~~~~~-~~----~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~--~~~----~~~~~~  420 (595)
                      .....+...|++++|+..|+++..... .+    ...++..+...+...|+++.|...+.+..+.  ...    ....++
T Consensus       106 ~~g~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~a~~~~~lg~~y~~~~~~~~A~~~~~~al~~~~~~~~~~~~~~~~~  185 (378)
T 3q15_A          106 FRGMYEFDQKEYVEAIGYYREAEKELPFVSDDIEKAEFHFKVAEAYYHMKQTHVSMYHILQALDIYQNHPLYSIRTIQSL  185 (378)
T ss_dssp             HHHHHHHHTTCHHHHHHHHHHHHTTGGGCCCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHTSTTCHHHHHHHH
T ss_pred             HHHHHHHHHCCHHHHHHHHHHHHHHHhhCCChHHHHHHHHHHHHHHHHcCCcHHHHHHHHHHHHHHHhCCCchhhHHHHH
Confidence            344556667777777777777654311 01    2345666677777777777777777766542  111    123467


Q ss_pred             HHHHHHHHhcCCHHHHHHHHHHHHHc----CCC-cCHHHHHHHHHHHHhcCChHHHHHHHHhccc-----CCCCCCHHHH
Q 040027          421 TTFIDGLCKNGYIIEAVELFRTLRIL----KCE-LDIQAYNCLIDGLCKSGRLKFAWELFCSLPH-----GVLVPNVVTY  490 (595)
Q Consensus       421 ~~l~~~~~~~g~~~~A~~~~~~~~~~----~~~-~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~-----~~~~p~~~~~  490 (595)
                      ..+..+|...|++++|...++++.+.    +.+ ....++..++.+|...|++++|+..+++..+     .. +....++
T Consensus       186 ~~lg~~y~~~~~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~lg~~y~~~~~~~~A~~~~~~al~~~~~~~~-~~~~~~~  264 (378)
T 3q15_A          186 FVIAGNYDDFKHYDKALPHLEAALELAMDIQNDRFIAISLLNIANSYDRSGDDQMAVEHFQKAAKVSREKVP-DLLPKVL  264 (378)
T ss_dssp             HHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHHHHCG-GGHHHHH
T ss_pred             HHHHHHHHHhCCHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHhhCC-hhHHHHH
Confidence            77888888999999999988887753    111 1245788899999999999999999999876     32 2236788


Q ss_pred             HHHHHHHHhcCChhHHHHHHHHHHHcCC---CCC-HHHHHHHHHHHHHcCC---hhHHHHHHHHHHHCCCCC-CHHHHHH
Q 040027          491 NIMIQGLCNDGQMDKARDLFLDMEENAA---APD-VITFDMLIHGFIRINE---PSKVNELLHKMKEKKVMP-DASIVSI  562 (595)
Q Consensus       491 ~~l~~~~~~~g~~~~A~~~~~~~~~~~~---~~~-~~~~~~l~~~~~~~g~---~~~A~~~~~~~~~~~~~p-~~~~~~~  562 (595)
                      ..++.+|.+.|++++|...+++..+...   .+. ...+..+...|...|+   +.+|..++++.   +..| ....+..
T Consensus       265 ~~la~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~~l~~ly~~~~~~~~~~~al~~~~~~---~~~~~~~~~~~~  341 (378)
T 3q15_A          265 FGLSWTLCKAGQTQKAFQFIEEGLDHITARSHKFYKELFLFLQAVYKETVDERKIHDLLSYFEKK---NLHAYIEACARS  341 (378)
T ss_dssp             HHHHHHHHHTTCHHHHHHHHHHHHHHCCTTCCSCHHHHHHHHHHHHSSSCCHHHHHHHHHHHHHT---TCHHHHHHHHHH
T ss_pred             HHHHHHHHHCCCHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHhCCCcHHHHHHHHHHHHhC---CChhHHHHHHHH
Confidence            8999999999999999999999987421   222 3456666677777888   77777777763   3333 3567788


Q ss_pred             HHHHHHhcCcccccchHHH
Q 040027          563 VVDLLVKNEISLKSLPSFL  581 (595)
Q Consensus       563 l~~~~~~~g~~~~~i~~~~  581 (595)
                      ++..|.+.|++++++..+.
T Consensus       342 la~~y~~~g~~~~A~~~~~  360 (378)
T 3q15_A          342 AAAVFESSCHFEQAAAFYR  360 (378)
T ss_dssp             HHHHHHHTTCHHHHHHHHH
T ss_pred             HHHHHHHCCCHHHHHHHHH
Confidence            9999999999996655543

>1hz4_A MALT regulatory protein; two-helix bundles, helix repeats, protein superhelix, transc activator; 1.45A {Escherichia coli} SCOP: a.118.8.2

Probab=99.42  E-value=2e-10  Score=111.14  Aligned_cols=163  Identities=11%  Similarity=-0.002  Sum_probs=75.8

Q ss_pred             HHHHHHHccCCHHHHHHHHHHHHHCCC----CCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCc-C-HHHHH----
Q 040027          387 TLFLGLFEIHQVEHALKLFDEMQRDGV----AADTRTYTTFIDGLCKNGYIIEAVELFRTLRILKCEL-D-IQAYN----  456 (595)
Q Consensus       387 ~l~~~~~~~~~~~~a~~~~~~~~~~~~----~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~-~-~~~~~----  456 (595)
                      .+...+...|++++|...+++......    +.....+..+...+...|++++|...+++.......+ . .....    
T Consensus       140 ~la~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~~la~~~~~~g~~~~A~~~l~~a~~~~~~~~~~~~~~~~~~~  219 (373)
T 1hz4_A          140 IRAQLLWAWARLDEAEASARSGIEVLSSYQPQQQLQCLAMLIQCSLARGDLDNARSQLNRLENLLGNGKYHSDWISNANK  219 (373)
T ss_dssp             HHHHHHHHTTCHHHHHHHHHHHHHHTTTSCGGGGHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHTTSCCCHHHHHHHHH
T ss_pred             HHHHHHHHhcCHHHHHHHHHHHHHHhhccCcHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHhccCcchhHHHHHHH
Confidence            344444445555555555544443210    0012334444555555566666666555554321011 1 11111    


Q ss_pred             HHHHHHHhcCChHHHHHHHHhcccCCCCCC---HHHHHHHHHHHHhcCChhHHHHHHHHHHHc----CCCCCH-HHHHHH
Q 040027          457 CLIDGLCKSGRLKFAWELFCSLPHGVLVPN---VVTYNIMIQGLCNDGQMDKARDLFLDMEEN----AAAPDV-ITFDML  528 (595)
Q Consensus       457 ~l~~~~~~~g~~~~A~~~~~~~~~~~~~p~---~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~----~~~~~~-~~~~~l  528 (595)
                      ..+..+...|++++|...+++.......++   ...+..+...+...|++++|...++++...    +..++. ..+..+
T Consensus       220 ~~~~~~~~~g~~~~A~~~~~~a~~~~~~~~~~~~~~~~~la~~~~~~g~~~~A~~~l~~a~~~~~~~~~~~~~~~~~~~l  299 (373)
T 1hz4_A          220 VRVIYWQMTGDKAAAANWLRHTAKPEFANNHFLQGQWRNIARAQILLGEFEPAEIVLEELNENARSLRLMSDLNRNLLLL  299 (373)
T ss_dssp             HHHHHHHHTTCHHHHHHHHHHSCCCCCTTCGGGHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHH
T ss_pred             HHHHHHHHCCCHHHHHHHHHhCCCCCCCcchhhHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHhCcchhhHHHHHHHH
Confidence            122334556666666666666554211111   123445555666666666666666665432    111111 244455


Q ss_pred             HHHHHHcCChhHHHHHHHHHH
Q 040027          529 IHGFIRINEPSKVNELLHKMK  549 (595)
Q Consensus       529 ~~~~~~~g~~~~A~~~~~~~~  549 (595)
                      ..++...|++++|...+++..
T Consensus       300 a~~~~~~g~~~~A~~~l~~al  320 (373)
T 1hz4_A          300 NQLYWQAGRKSDAQRVLLDAL  320 (373)
T ss_dssp             HHHHHHHTCHHHHHHHHHHHH
T ss_pred             HHHHHHhCCHHHHHHHHHHHH
Confidence            556666666666666666655

>1hz4_A MALT regulatory protein; two-helix bundles, helix repeats, protein superhelix, transc activator; 1.45A {Escherichia coli} SCOP: a.118.8.2

Probab=99.41  E-value=1.4e-10  Score=112.36  Aligned_cols=277  Identities=11%  Similarity=-0.014  Sum_probs=179.7

Q ss_pred             HHHHHHHHHhcCChhHHHHHHHHHHhCCCCCCHH----HHHHHHHHHHhcCCHhHHHHHHHHHHhcCCC-CC----HhhH
Q 040027           99 YNILINCFCKIGRVSLGFIAFGRILRSCFTPNAA----TFNSLIKGLHAESRIMEAAALFTKLKAFGCE-PN----VITY  169 (595)
Q Consensus        99 ~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~~~~----~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~-~~----~~~~  169 (595)
                      +......+...|++++|...+++++......+..    +++.+...+...|++++|.+.+++....... .+    ..++
T Consensus        17 ~~~~a~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~   96 (373)
T 1hz4_A           17 NALRAQVAINDGNPDEAERLAKLALEELPPGWFYSRIVATSVLGEVLHCKGELTRSLALMQQTEQMARQHDVWHYALWSL   96 (373)
T ss_dssp             HHHHHHHHHHTTCHHHHHHHHHHHHHTCCTTCHHHHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHHHTTCHHHHHHHH
T ss_pred             HHHHHHHHHHCCCHHHHHHHHHHHHHcCCCCchhHHHHHHHHHHHHHHhcCcHHHHHHHHHHHHHHHHhcCcHHHHHHHH
Confidence            3445566778999999999999998875333332    4566677888999999999999988764211 12    2235


Q ss_pred             HHHHHHHHhcCChhHHHHHHHHHHhcCCCCCccc-cCcHHHHHHHHHHHHHcCCHhHHHHHHHHHhhCCCC----CCHhH
Q 040027          170 NTLINGLCRTGHTMIALNLFEEMANGNGEIGVVC-KPNTVTYSTIIDGLCKEGFVDKAKALFLQMKDENIN----PDVVT  244 (595)
Q Consensus       170 ~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~-~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~----~~~~~  244 (595)
                      ..+...+...|++++|...+++........+... +.....+..+...+...|++++|...+++.......    ....+
T Consensus        97 ~~la~~~~~~G~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~~~la~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~  176 (373)
T 1hz4_A           97 IQQSEILFAQGFLQTAWETQEKAFQLINEQHLEQLPMHEFLVRIRAQLLWAWARLDEAEASARSGIEVLSSYQPQQQLQC  176 (373)
T ss_dssp             HHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCTTSTHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHTTTSCGGGGHHH
T ss_pred             HHHHHHHHHCCCHHHHHHHHHHHHHHHHHhccccCcHHHHHHHHHHHHHHHhcCHHHHHHHHHHHHHHhhccCcHHHHHH
Confidence            6778889999999999999998876431111000 113456677888899999999999999987754211    12345


Q ss_pred             HHHHHHHHHhcCCHHHHHHHHHHHHHCCCCCCH-hhHH-----HHHHHHHhcCChHHHHHHHHHHHHCCCCC---CHHHH
Q 040027          245 YNSLIHGLCHANDWNEAKRLFIEMMDQGVQPSV-VTFN-----VIMDELCKNRKMDEASRLLDLMVQRGVRP---NACTY  315 (595)
Q Consensus       245 ~~~ll~~~~~~~~~~~A~~~~~~~~~~~~~~~~-~~~~-----~l~~~~~~~g~~~~a~~~~~~~~~~~~~~---~~~~~  315 (595)
                      +..+...+...|++++|...+++.......++. ..+.     ..+..+...|++++|...+++.......+   ....+
T Consensus       177 ~~~la~~~~~~g~~~~A~~~l~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~~~A~~~~~~a~~~~~~~~~~~~~~~  256 (373)
T 1hz4_A          177 LAMLIQCSLARGDLDNARSQLNRLENLLGNGKYHSDWISNANKVRVIYWQMTGDKAAAANWLRHTAKPEFANNHFLQGQW  256 (373)
T ss_dssp             HHHHHHHHHHHTCHHHHHHHHHHHHHHHTTSCCCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHSCCCCCTTCGGGHHHH
T ss_pred             HHHHHHHHHHcCCHHHHHHHHHHHHHHHhccCcchhHHHHHHHHHHHHHHHCCCHHHHHHHHHhCCCCCCCcchhhHHHH
Confidence            777788888899999999998887653111111 1111     22334667888888888887776543211   12234


Q ss_pred             HHHHHHHHhcCCHHHHHHHHHHHHhc----CCCCCH-HHHHHHHHHHHhCCCHHHHHHHHHHHHH
Q 040027          316 NTLMDGFCLMGKINRAEELFGSMESM----GCKHDD-VSYNILINGYCKNKEVEEALSLYREMVS  375 (595)
Q Consensus       316 ~~l~~~~~~~~~~~~a~~~~~~~~~~----~~~~~~-~~~~~l~~~~~~~~~~~~A~~~~~~~~~  375 (595)
                      ..+..++...|++++|...++.....    +.+++. ..+..+..++...|+.++|...+++...
T Consensus       257 ~~la~~~~~~g~~~~A~~~l~~a~~~~~~~~~~~~~~~~~~~la~~~~~~g~~~~A~~~l~~al~  321 (373)
T 1hz4_A          257 RNIARAQILLGEFEPAEIVLEELNENARSLRLMSDLNRNLLLLNQLYWQAGRKSDAQRVLLDALK  321 (373)
T ss_dssp             HHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHHTCHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHcCCHHHHHHHHHHHHHHHHhCcchhhHHHHHHHHHHHHHHhCCHHHHHHHHHHHHH
Confidence            55666777777777777777766432    111111 2444455556666666666666666554

>4i17_A Hypothetical protein; TPR repeats protein, structural genomics, joint center for S genomics, JCSG, protein structure initiative; HET: MSE; 1.83A {Bacteroides fragilis}

Probab=99.39  E-value=8.2e-11  Score=105.05  Aligned_cols=206  Identities=13%  Similarity=-0.010  Sum_probs=116.5

Q ss_pred             CHHHHHHHHHHHHhCCCHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHccCCHHHHHHHHHHHHHCCCCCCHHHHHHHHH
Q 040027          346 DDVSYNILINGYCKNKEVEEALSLYREMVSKGIKPTVVTYNTLFLGLFEIHQVEHALKLFDEMQRDGVAADTRTYTTFID  425 (595)
Q Consensus       346 ~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~  425 (595)
                      ++..+......+...|++++|+..|++.++....++...+..+..++...|++++|+..+++..+.. +.+...+..+..
T Consensus         6 ~~~~~~~~g~~~~~~~~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~~~~~~~~~A~~~~~~al~~~-p~~~~~~~~l~~   84 (228)
T 4i17_A            6 DPNQLKNEGNDALNAKNYAVAFEKYSEYLKLTNNQDSVTAYNCGVCADNIKKYKEAADYFDIAIKKN-YNLANAYIGKSA   84 (228)
T ss_dssp             CHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHTTTCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHTT-CSHHHHHHHHHH
T ss_pred             CHHHHHHHHHHHHHccCHHHHHHHHHHHHhccCCCCcHHHHHHHHHHHHhhcHHHHHHHHHHHHHhC-cchHHHHHHHHH
Confidence            3445555555555666666666666655554432445555555556666666666666666666542 334455566666


Q ss_pred             HHHhcCCHHHHHHHHHHHHHcCCCcCH-------HHHHHHHHHHHhcCChHHHHHHHHhcccCCCCCC---HHHHHHHHH
Q 040027          426 GLCKNGYIIEAVELFRTLRILKCELDI-------QAYNCLIDGLCKSGRLKFAWELFCSLPHGVLVPN---VVTYNIMIQ  495 (595)
Q Consensus       426 ~~~~~g~~~~A~~~~~~~~~~~~~~~~-------~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~p~---~~~~~~l~~  495 (595)
                      +|...|++++|...++++.+.. +.+.       ..+..+...+...|++++|+..|+++++  +.|+   ...|..+..
T Consensus        85 ~~~~~~~~~~A~~~~~~al~~~-p~~~~~~~~~~~~~~~~g~~~~~~~~~~~A~~~~~~al~--~~p~~~~~~~~~~l~~  161 (228)
T 4i17_A           85 AYRDMKNNQEYIATLTEGIKAV-PGNATIEKLYAIYYLKEGQKFQQAGNIEKAEENYKHATD--VTSKKWKTDALYSLGV  161 (228)
T ss_dssp             HHHHTTCHHHHHHHHHHHHHHS-TTCHHHHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHTT--SSCHHHHHHHHHHHHH
T ss_pred             HHHHcccHHHHHHHHHHHHHHC-CCcHHHHHHHHHHHHHHhHHHHHhccHHHHHHHHHHHHh--cCCCcccHHHHHHHHH
Confidence            6666666666666666666554 3334       3466666667777777777777777776  3454   345666666


Q ss_pred             HHHhcCChhHHHHHHHHHHHcCCCCCHHHHHHHHHHHHHcCChhHHHHHHHHHHHCCCCC-CHHHHHHHHH
Q 040027          496 GLCNDGQMDKARDLFLDMEENAAAPDVITFDMLIHGFIRINEPSKVNELLHKMKEKKVMP-DASIVSIVVD  565 (595)
Q Consensus       496 ~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~p-~~~~~~~l~~  565 (595)
                      +|...|     ...++++...+ ..+...+....  ....+.+++|...++++.+.  .| +..+...+..
T Consensus       162 ~~~~~~-----~~~~~~a~~~~-~~~~~~~~~~~--~~~~~~~~~A~~~~~~a~~l--~p~~~~~~~~l~~  222 (228)
T 4i17_A          162 LFYNNG-----ADVLRKATPLA-SSNKEKYASEK--AKADAAFKKAVDYLGEAVTL--SPNRTEIKQMQDQ  222 (228)
T ss_dssp             HHHHHH-----HHHHHHHGGGT-TTCHHHHHHHH--HHHHHHHHHHHHHHHHHHHH--CTTCHHHHHHHHH
T ss_pred             HHHHHH-----HHHHHHHHhcc-cCCHHHHHHHH--HHHHHHHHHHHHHHHHHhhc--CCCCHHHHHHHHH
Confidence            665433     33445554443 33334443332  23445677788888877764  35 3444444433

>4gyw_A UDP-N-acetylglucosamine--peptide N- acetylglucosaminyltransferase 110 kDa subunit...; GT-B, glycosyltransferase, glcnacylation, transferase-peptid; HET: UDP NAG; 1.70A {Homo sapiens} PDB: 3pe3_A* 3pe4_A* 4ay5_A* 4ay6_A* 3tax_A* 4gyy_A* 4gz3_A* 4gz5_A* 4gz6_A*

Probab=99.38  E-value=2.2e-11  Score=126.23  Aligned_cols=162  Identities=13%  Similarity=0.067  Sum_probs=87.6

Q ss_pred             HHHHHHHHHHHccCCHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCcCHHHHHHHHHHH
Q 040027          383 VTYNTLFLGLFEIHQVEHALKLFDEMQRDGVAADTRTYTTFIDGLCKNGYIIEAVELFRTLRILKCELDIQAYNCLIDGL  462 (595)
Q Consensus       383 ~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~~l~~~~  462 (595)
                      ..++.+...+...|++++|++.|++.++.. +-+...+..+..+|.+.|++++|+..|+++++.. +.+..++..++.+|
T Consensus        10 ~al~nLG~~~~~~G~~~eAi~~~~kAl~l~-P~~~~a~~nLg~~l~~~g~~~eA~~~~~~Al~l~-P~~~~a~~nLg~~l   87 (723)
T 4gyw_A           10 DSLNNLANIKREQGNIEEAVRLYRKALEVF-PEFAAAHSNLASVLQQQGKLQEALMHYKEAIRIS-PTFADAYSNMGNTL   87 (723)
T ss_dssp             HHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-SCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHcCCHHHHHHHHHHHHHhC-CCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhC-CCCHHHHHHHHHHH
Confidence            344445555555555555555555554432 3334455555555555555555555555555544 34455555555555


Q ss_pred             HhcCChHHHHHHHHhcccCCCCCC-HHHHHHHHHHHHhcCChhHHHHHHHHHHHcCCCCCHHHHHHHHHHHHHcCChhHH
Q 040027          463 CKSGRLKFAWELFCSLPHGVLVPN-VVTYNIMIQGLCNDGQMDKARDLFLDMEENAAAPDVITFDMLIHGFIRINEPSKV  541 (595)
Q Consensus       463 ~~~g~~~~A~~~~~~~~~~~~~p~-~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A  541 (595)
                      ...|++++|++.|+++++  +.|+ ...|+.+..+|...|++++|++.|+++++.. +.+...+..++.+|...|++++|
T Consensus        88 ~~~g~~~~A~~~~~kAl~--l~P~~~~a~~~Lg~~~~~~g~~~eAi~~~~~Al~l~-P~~~~a~~~L~~~l~~~g~~~~A  164 (723)
T 4gyw_A           88 KEMQDVQGALQCYTRAIQ--INPAFADAHSNLASIHKDSGNIPEAIASYRTALKLK-PDFPDAYCNLAHCLQIVCDWTDY  164 (723)
T ss_dssp             HHTTCHHHHHHHHHHHHH--HCTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-SCCHHHHHHHHHHHHHTTCCTTH
T ss_pred             HHcCCHHHHHHHHHHHHH--hCCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhC-CCChHHHhhhhhHHHhcccHHHH
Confidence            555555555555555555  3333 4555555566666666666666666665543 33455555566666666666666


Q ss_pred             HHHHHHHH
Q 040027          542 NELLHKMK  549 (595)
Q Consensus       542 ~~~~~~~~  549 (595)
                      .+.++++.
T Consensus       165 ~~~~~kal  172 (723)
T 4gyw_A          165 DERMKKLV  172 (723)
T ss_dssp             HHHHHHHH
T ss_pred             HHHHHHHH
Confidence            55555554

>4gyw_A UDP-N-acetylglucosamine--peptide N- acetylglucosaminyltransferase 110 kDa subunit...; GT-B, glycosyltransferase, glcnacylation, transferase-peptid; HET: UDP NAG; 1.70A {Homo sapiens} PDB: 3pe3_A* 3pe4_A* 4ay5_A* 4ay6_A* 3tax_A* 4gyy_A* 4gz3_A* 4gz5_A* 4gz6_A*

Probab=99.38  E-value=1.9e-11  Score=126.65  Aligned_cols=166  Identities=16%  Similarity=0.129  Sum_probs=149.2

Q ss_pred             CHHHHHHHHHHHHhcCChhHHHHHHHHHHhCCCCCCHHHHHHHHHHHHhcCCHhHHHHHHHHHHhcCCCCCHhhHHHHHH
Q 040027           95 NLYTYNILINCFCKIGRVSLGFIAFGRILRSCFTPNAATFNSLIKGLHAESRIMEAAALFTKLKAFGCEPNVITYNTLIN  174 (595)
Q Consensus        95 ~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~~l~~  174 (595)
                      ++..|+.+...+.+.|++++|+..|+++++.. +-+..+|..+...|.+.|++++|++.|++.++.. +-+..++..+..
T Consensus         8 ~a~al~nLG~~~~~~G~~~eAi~~~~kAl~l~-P~~~~a~~nLg~~l~~~g~~~eA~~~~~~Al~l~-P~~~~a~~nLg~   85 (723)
T 4gyw_A            8 HADSLNNLANIKREQGNIEEAVRLYRKALEVF-PEFAAAHSNLASVLQQQGKLQEALMHYKEAIRIS-PTFADAYSNMGN   85 (723)
T ss_dssp             HHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-SCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHH
T ss_pred             cHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhC-CCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhC-CCCHHHHHHHHH
Confidence            57889999999999999999999999999985 4578899999999999999999999999999885 337889999999


Q ss_pred             HHHhcCChhHHHHHHHHHHhcCCCCCccccCcHHHHHHHHHHHHHcCCHhHHHHHHHHHhhCCCCCCHhHHHHHHHHHHh
Q 040027          175 GLCRTGHTMIALNLFEEMANGNGEIGVVCKPNTVTYSTIIDGLCKEGFVDKAKALFLQMKDENINPDVVTYNSLIHGLCH  254 (595)
Q Consensus       175 ~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~~ll~~~~~  254 (595)
                      +|...|++++|++.|++..+.+       +.+..+|..+..+|...|++++|++.|++..+.. +-+...|..++.++..
T Consensus        86 ~l~~~g~~~~A~~~~~kAl~l~-------P~~~~a~~~Lg~~~~~~g~~~eAi~~~~~Al~l~-P~~~~a~~~L~~~l~~  157 (723)
T 4gyw_A           86 TLKEMQDVQGALQCYTRAIQIN-------PAFADAHSNLASIHKDSGNIPEAIASYRTALKLK-PDFPDAYCNLAHCLQI  157 (723)
T ss_dssp             HHHHTTCHHHHHHHHHHHHHHC-------TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-SCCHHHHHHHHHHHHH
T ss_pred             HHHHcCCHHHHHHHHHHHHHhC-------CCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhC-CCChHHHhhhhhHHHh
Confidence            9999999999999999999876       5678899999999999999999999999998864 3367889999999999


Q ss_pred             cCCHHHHHHHHHHHHH
Q 040027          255 ANDWNEAKRLFIEMMD  270 (595)
Q Consensus       255 ~~~~~~A~~~~~~~~~  270 (595)
                      .|++++|.+.++++++
T Consensus       158 ~g~~~~A~~~~~kal~  173 (723)
T 4gyw_A          158 VCDWTDYDERMKKLVS  173 (723)
T ss_dssp             TTCCTTHHHHHHHHHH
T ss_pred             cccHHHHHHHHHHHHH
Confidence            9999999998887764

>4i17_A Hypothetical protein; TPR repeats protein, structural genomics, joint center for S genomics, JCSG, protein structure initiative; HET: MSE; 1.83A {Bacteroides fragilis}

Probab=99.37  E-value=9.5e-11  Score=104.61  Aligned_cols=208  Identities=10%  Similarity=-0.017  Sum_probs=161.8

Q ss_pred             CCHHHHHHHHHHHHhcCChhHHHHHHHHHHhCCCCCCHHHHHHHHHHHHhcCCHhHHHHHHHHHHhcCCCCCHhhHHHHH
Q 040027           94 PNLYTYNILINCFCKIGRVSLGFIAFGRILRSCFTPNAATFNSLIKGLHAESRIMEAAALFTKLKAFGCEPNVITYNTLI  173 (595)
Q Consensus        94 ~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~~l~  173 (595)
                      .|+..+...+..+...|++++|+..|+++++...+++...+..+..++...|++++|++.|++..... +.+..++..+.
T Consensus         5 ~~~~~~~~~g~~~~~~~~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~~~~~~~~~A~~~~~~al~~~-p~~~~~~~~l~   83 (228)
T 4i17_A            5 TDPNQLKNEGNDALNAKNYAVAFEKYSEYLKLTNNQDSVTAYNCGVCADNIKKYKEAADYFDIAIKKN-YNLANAYIGKS   83 (228)
T ss_dssp             CCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHTTTCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHTT-CSHHHHHHHHH
T ss_pred             cCHHHHHHHHHHHHHccCHHHHHHHHHHHHhccCCCCcHHHHHHHHHHHHhhcHHHHHHHHHHHHHhC-cchHHHHHHHH
Confidence            46788999999999999999999999999998644788888889999999999999999999999875 33678899999


Q ss_pred             HHHHhcCChhHHHHHHHHHHhcCCCCCccccCcH-------HHHHHHHHHHHHcCCHhHHHHHHHHHhhCCCCCC---Hh
Q 040027          174 NGLCRTGHTMIALNLFEEMANGNGEIGVVCKPNT-------VTYSTIIDGLCKEGFVDKAKALFLQMKDENINPD---VV  243 (595)
Q Consensus       174 ~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~~~-------~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~~---~~  243 (595)
                      .++...|++++|+..|++..+..       |.+.       ..|..+...+...|++++|.+.|+++.+.  .|+   ..
T Consensus        84 ~~~~~~~~~~~A~~~~~~al~~~-------p~~~~~~~~~~~~~~~~g~~~~~~~~~~~A~~~~~~al~~--~p~~~~~~  154 (228)
T 4i17_A           84 AAYRDMKNNQEYIATLTEGIKAV-------PGNATIEKLYAIYYLKEGQKFQQAGNIEKAEENYKHATDV--TSKKWKTD  154 (228)
T ss_dssp             HHHHHTTCHHHHHHHHHHHHHHS-------TTCHHHHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHTTS--SCHHHHHH
T ss_pred             HHHHHcccHHHHHHHHHHHHHHC-------CCcHHHHHHHHHHHHHHhHHHHHhccHHHHHHHHHHHHhc--CCCcccHH
Confidence            99999999999999999999875       4445       56888889999999999999999999886  343   56


Q ss_pred             HHHHHHHHHHhcCCHHHHHHHHHHHHHCCCCCCHhhHHHHHHHHHhcCChHHHHHHHHHHHHCCCCCCHHHHHHHHH
Q 040027          244 TYNSLIHGLCHANDWNEAKRLFIEMMDQGVQPSVVTFNVIMDELCKNRKMDEASRLLDLMVQRGVRPNACTYNTLMD  320 (595)
Q Consensus       244 ~~~~ll~~~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~l~~  320 (595)
                      .|..+..+|...|+     .+++++...+. .+...+...  .....+.+++|...+++..+... .+..+...+..
T Consensus       155 ~~~~l~~~~~~~~~-----~~~~~a~~~~~-~~~~~~~~~--~~~~~~~~~~A~~~~~~a~~l~p-~~~~~~~~l~~  222 (228)
T 4i17_A          155 ALYSLGVLFYNNGA-----DVLRKATPLAS-SNKEKYASE--KAKADAAFKKAVDYLGEAVTLSP-NRTEIKQMQDQ  222 (228)
T ss_dssp             HHHHHHHHHHHHHH-----HHHHHHGGGTT-TCHHHHHHH--HHHHHHHHHHHHHHHHHHHHHCT-TCHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHH-----HHHHHHHhccc-CCHHHHHHH--HHHHHHHHHHHHHHHHHHhhcCC-CCHHHHHHHHH
Confidence            77778877765543     34455544321 233333333  23445678999999999998642 24444444433

>3as5_A MAMA; tetratricopeptide repeats (TPR) containing protein, TPR PROT protein-protein interactions, protein binding; 2.00A {Magnetospirillum magnetotacticum} PDB: 3as4_A 3asd_A 3asg_A 3ash_A 3as8_A 3asf_A

Probab=99.37  E-value=6.3e-11  Score=101.76  Aligned_cols=163  Identities=13%  Similarity=0.059  Sum_probs=111.2

Q ss_pred             HHHHHHHHHHccCCHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCcCHHHHHHHHHHHH
Q 040027          384 TYNTLFLGLFEIHQVEHALKLFDEMQRDGVAADTRTYTTFIDGLCKNGYIIEAVELFRTLRILKCELDIQAYNCLIDGLC  463 (595)
Q Consensus       384 ~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~~l~~~~~  463 (595)
                      .+..+...+...|++++|...++++.+.. +.+...+..+...+...|++++|...++++.+.. +.+...+..++..+.
T Consensus        10 ~~~~~~~~~~~~~~~~~A~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~A~~~~~~~~~~~-~~~~~~~~~~a~~~~   87 (186)
T 3as5_A           10 YYRDKGISHAKAGRYSQAVMLLEQVYDAD-AFDVDVALHLGIAYVKTGAVDRGTELLERSLADA-PDNVKVATVLGLTYV   87 (186)
T ss_dssp             HHHHHHHHHHHHTCHHHHHHHHTTTCCTT-SCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHhcCHHHHHHHHHHHHHhC-ccChHHHHHHHHHHHHcCCHHHHHHHHHHHHhcC-CCCHHHHHHHHHHHH
Confidence            34455555666666666666666665542 3455666666667777777777777777776654 455666777777777


Q ss_pred             hcCChHHHHHHHHhcccCCCCCCHHHHHHHHHHHHhcCChhHHHHHHHHHHHcCCCCCHHHHHHHHHHHHHcCChhHHHH
Q 040027          464 KSGRLKFAWELFCSLPHGVLVPNVVTYNIMIQGLCNDGQMDKARDLFLDMEENAAAPDVITFDMLIHGFIRINEPSKVNE  543 (595)
Q Consensus       464 ~~g~~~~A~~~~~~~~~~~~~p~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~  543 (595)
                      ..|++++|...++++... .+.+...+..++.++...|++++|...++++.+.. +.+...+..++.++...|++++|..
T Consensus        88 ~~~~~~~A~~~~~~~~~~-~~~~~~~~~~~a~~~~~~~~~~~A~~~~~~~~~~~-~~~~~~~~~la~~~~~~~~~~~A~~  165 (186)
T 3as5_A           88 QVQKYDLAVPLLIKVAEA-NPINFNVRFRLGVALDNLGRFDEAIDSFKIALGLR-PNEGKVHRAIAFSYEQMGRHEEALP  165 (186)
T ss_dssp             HHTCHHHHHHHHHHHHHH-CTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCHHHHHH
T ss_pred             HhcCHHHHHHHHHHHHhc-CcHhHHHHHHHHHHHHHcCcHHHHHHHHHHHHhcC-ccchHHHHHHHHHHHHcCCHHHHHH
Confidence            777777777777776653 12345667777777777777888877777777764 4456777777777777888888888


Q ss_pred             HHHHHHH
Q 040027          544 LLHKMKE  550 (595)
Q Consensus       544 ~~~~~~~  550 (595)
                      +++++.+
T Consensus       166 ~~~~~~~  172 (186)
T 3as5_A          166 HFKKANE  172 (186)
T ss_dssp             HHHHHHH
T ss_pred             HHHHHHH
Confidence            7777765

>3as5_A MAMA; tetratricopeptide repeats (TPR) containing protein, TPR PROT protein-protein interactions, protein binding; 2.00A {Magnetospirillum magnetotacticum} PDB: 3as4_A 3asd_A 3asg_A 3ash_A 3as8_A 3asf_A

Probab=99.37  E-value=7.8e-11  Score=101.15  Aligned_cols=164  Identities=15%  Similarity=0.024  Sum_probs=109.0

Q ss_pred             HHHHHHHHHHHhcCChhHHHHHHHHHHhCCCCCCHHHHHHHHHHHHhcCCHhHHHHHHHHHHhcCCCCCHhhHHHHHHHH
Q 040027           97 YTYNILINCFCKIGRVSLGFIAFGRILRSCFTPNAATFNSLIKGLHAESRIMEAAALFTKLKAFGCEPNVITYNTLINGL  176 (595)
Q Consensus        97 ~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~~l~~~~  176 (595)
                      ..+..++..+...|++++|...++++.+.. +.+..++..+...+...|++++|.+.++++.+.. +.+..++..++..+
T Consensus         9 ~~~~~~~~~~~~~~~~~~A~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~A~~~~~~~~~~~-~~~~~~~~~~a~~~   86 (186)
T 3as5_A            9 VYYRDKGISHAKAGRYSQAVMLLEQVYDAD-AFDVDVALHLGIAYVKTGAVDRGTELLERSLADA-PDNVKVATVLGLTY   86 (186)
T ss_dssp             HHHHHHHHHHHHHTCHHHHHHHHTTTCCTT-SCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHhcCHHHHHHHHHHHHHhC-ccChHHHHHHHHHHHHcCCHHHHHHHHHHHHhcC-CCCHHHHHHHHHHH
Confidence            445566667777777777777777776653 3456666677777777777777777777776653 33566666667777


Q ss_pred             HhcCChhHHHHHHHHHHhcCCCCCccccCcHHHHHHHHHHHHHcCCHhHHHHHHHHHhhCCCCCCHhHHHHHHHHHHhcC
Q 040027          177 CRTGHTMIALNLFEEMANGNGEIGVVCKPNTVTYSTIIDGLCKEGFVDKAKALFLQMKDENINPDVVTYNSLIHGLCHAN  256 (595)
Q Consensus       177 ~~~g~~~~A~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~~ll~~~~~~~  256 (595)
                      ...|++++|.+.++++....       +.+...+..+..++...|++++|.+.++++.... +.+...+..+...+...|
T Consensus        87 ~~~~~~~~A~~~~~~~~~~~-------~~~~~~~~~~a~~~~~~~~~~~A~~~~~~~~~~~-~~~~~~~~~la~~~~~~~  158 (186)
T 3as5_A           87 VQVQKYDLAVPLLIKVAEAN-------PINFNVRFRLGVALDNLGRFDEAIDSFKIALGLR-PNEGKVHRAIAFSYEQMG  158 (186)
T ss_dssp             HHHTCHHHHHHHHHHHHHHC-------TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTT
T ss_pred             HHhcCHHHHHHHHHHHHhcC-------cHhHHHHHHHHHHHHHcCcHHHHHHHHHHHHhcC-ccchHHHHHHHHHHHHcC
Confidence            77777777777777776654       3456666666677777777777777777666543 234566666666666777


Q ss_pred             CHHHHHHHHHHHHH
Q 040027          257 DWNEAKRLFIEMMD  270 (595)
Q Consensus       257 ~~~~A~~~~~~~~~  270 (595)
                      ++++|...++++.+
T Consensus       159 ~~~~A~~~~~~~~~  172 (186)
T 3as5_A          159 RHEEALPHFKKANE  172 (186)
T ss_dssp             CHHHHHHHHHHHHH
T ss_pred             CHHHHHHHHHHHHH
Confidence            77777776666654

>2uy1_A Cleavage stimulation factor 77; RNA-binding protein; 2.0A {Encephalitozoon cuniculi} PDB: 2uy1_B

Probab=99.28  E-value=1.1e-08  Score=101.67  Aligned_cols=385  Identities=10%  Similarity=-0.020  Sum_probs=196.6

Q ss_pred             hcC-ChhHHHHHHHHHHhCCCCCCHHHHHHHHHHHHhcCCHhHHHHHHHHHHhcCCCCCHhhHHHHHHHHHhcCC-hhHH
Q 040027          108 KIG-RVSLGFIAFGRILRSCFTPNAATFNSLIKGLHAESRIMEAAALFTKLKAFGCEPNVITYNTLINGLCRTGH-TMIA  185 (595)
Q Consensus       108 ~~g-~~~~A~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~-~~~A  185 (595)
                      +.| +.+.|+.+|++++..  -|.              |+++.+..+|++....  .|+...|...+....+.+. .+..
T Consensus         6 ~~~~~i~~aR~vyer~l~~--~P~--------------~~~e~~~~iferal~~--~ps~~LW~~Y~~f~~~~~~~~~~i   67 (493)
T 2uy1_A            6 KMGVELSSPSAIMEHARRL--YMS--------------KDYRSLESLFGRCLKK--SYNLDLWMLYIEYVRKVSQKKFKL   67 (493)
T ss_dssp             ------CCHHHHHHHHHHH--HHT--------------TCHHHHHHHHHHHSTT--CCCHHHHHHHHHHHHHHC----CT
T ss_pred             HcCcchHHHHHHHHHHHHH--CCC--------------CCHHHHHHHHHHHhcc--CCCHHHHHHHHHHHHHhCchHHHH
Confidence            346 488888888888765  222              7889999999998875  5688888888877766663 4567


Q ss_pred             HHHHHHHHhcCCCCCccccCcHHHHHHHHHHHH----HcCCHhHHHHHHHHHhhCCCCCCHhHHHHHHHHHHhcCCHHHH
Q 040027          186 LNLFEEMANGNGEIGVVCKPNTVTYSTIIDGLC----KEGFVDKAKALFLQMKDENINPDVVTYNSLIHGLCHANDWNEA  261 (595)
Q Consensus       186 ~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~----~~g~~~~A~~~~~~~~~~~~~~~~~~~~~ll~~~~~~~~~~~A  261 (595)
                      ..+|+.+...-+.    -+.+...|...+..+.    ..++.+.+.++|++.+......-...|...... ........+
T Consensus        68 ~~~fe~al~~vg~----d~~s~~iW~~Yi~f~~~~~~~~~~~~~vR~iy~rAL~~P~~~~~~lw~~Y~~f-E~~~~~~~~  142 (493)
T 2uy1_A           68 YEVYEFTLGQFEN----YWDSYGLYKEYIEEEGKIEDEQTRIEKIRNGYMRALQTPMGSLSELWKDFENF-ELELNKITG  142 (493)
T ss_dssp             HHHHHHHHHHSTT----CTTCHHHHHHHHHHTSSCSSHHHHHHHHHHHHHHHHTSCCTTHHHHHHHHHHH-HHHHCHHHH
T ss_pred             HHHHHHHHHHcCC----CcccHHHHHHHHHHHHhchhhhHHHHHHHHHHHHHHhChhhhHHHHHHHHHHH-HHHhccccH
Confidence            7788887764210    1345678887777654    346788899999999874211111122222111 111111122


Q ss_pred             HHHHHHHHHCCCCCCHhhHHHHHHHHHhcCChHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHhc--CC-----HHHHHHH
Q 040027          262 KRLFIEMMDQGVQPSVVTFNVIMDELCKNRKMDEASRLLDLMVQRGVRPNACTYNTLMDGFCLM--GK-----INRAEEL  334 (595)
Q Consensus       262 ~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~--~~-----~~~a~~~  334 (595)
                      ..++.+..                     +.+..|..+++.+...-...+...|...+..-...  +-     .+.+..+
T Consensus       143 ~~~~~~~~---------------------~~y~~ar~~y~~~~~~~~~~s~~~W~~y~~~E~~~~~~~~~~~~~~Rv~~~  201 (493)
T 2uy1_A          143 KKIVGDTL---------------------PIFQSSFQRYQQIQPLIRGWSVKNAARLIDLEMENGMKLGGRPHESRMHFI  201 (493)
T ss_dssp             HHHHHHHH---------------------HHHHHHHHHHHHHHHHHHTCSHHHHHHHHHHHHTCTTCCCHHHHHHHHHHH
T ss_pred             HHHHHHHh---------------------HHHHHHHHHHHHHHHHHhhccHHHHHHHHHHHhcCCccCcchhhHHHHHHH
Confidence            22211111                     11222222222222110001222333322221111  00     2334555


Q ss_pred             HHHHHhcCCCCCHHHHHHHHHHHHhCCCHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHccCCHHHHHHHHHHHHHC---
Q 040027          335 FGSMESMGCKHDDVSYNILINGYCKNKEVEEALSLYREMVSKGIKPTVVTYNTLFLGLFEIHQVEHALKLFDEMQRD---  411 (595)
Q Consensus       335 ~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~---  411 (595)
                      |++++... +.+...|...+..+.+.|+.+.|..+|++.+..  +.+...+..... +...++.  ...+.+.....   
T Consensus       202 ye~al~~~-p~~~~lW~~ya~~~~~~~~~~~ar~i~erAi~~--P~~~~l~~~y~~-~~e~~~~--~~~l~~~~~~~~~~  275 (493)
T 2uy1_A          202 HNYILDSF-YYAEEVYFFYSEYLIGIGQKEKAKKVVERGIEM--SDGMFLSLYYGL-VMDEEAV--YGDLKRKYSMGEAE  275 (493)
T ss_dssp             HHHHHHHT-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH--CCSSHHHHHHHH-HTTCTHH--HHHHHHHTC-----
T ss_pred             HHHHHHcC-CCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHhC--CCcHHHHHHHHh-hcchhHH--HHHHHHHHHhhccc
Confidence            66655532 444555666666666666666666666666655  212222211111 1111110  11111110000   


Q ss_pred             --CC---CCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCcCHHHHHHHHHHHHhcC-ChHHHHHHHHhcccCCCCC
Q 040027          412 --GV---AADTRTYTTFIDGLCKNGYIIEAVELFRTLRILKCELDIQAYNCLIDGLCKSG-RLKFAWELFCSLPHGVLVP  485 (595)
Q Consensus       412 --~~---~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g-~~~~A~~~~~~~~~~~~~p  485 (595)
                        +.   ......|...+....+.++.+.|..+|+++ ... ..+...|...+..-...+ +.+.|..+|+...+. .+-
T Consensus       276 ~~~~~~~~~~~~lw~~y~~~~~r~~~~~~AR~i~~~A-~~~-~~~~~v~i~~A~lE~~~~~d~~~ar~ife~al~~-~~~  352 (493)
T 2uy1_A          276 SAEKVFSKELDLLRINHLNYVLKKRGLELFRKLFIEL-GNE-GVGPHVFIYCAFIEYYATGSRATPYNIFSSGLLK-HPD  352 (493)
T ss_dssp             -----CHHHHHHHHHHHHHHHHHHHCHHHHHHHHHHH-TTS-CCCHHHHHHHHHHHHHHHCCSHHHHHHHHHHHHH-CTT
T ss_pred             hhhhhcccccHHHHHHHHHHHHHcCCHHHHHHHHHHh-hCC-CCChHHHHHHHHHHHHHCCChHHHHHHHHHHHHH-CCC
Confidence              00   011244555566666667788888888877 322 234444443333323333 588888888877763 222


Q ss_pred             CHHHHHHHHHHHHhcCChhHHHHHHHHHHHcCCCCCHHHHHHHHHHHHHcCChhHHHHHHHHHHH
Q 040027          486 NVVTYNIMIQGLCNDGQMDKARDLFLDMEENAAAPDVITFDMLIHGFIRINEPSKVNELLHKMKE  550 (595)
Q Consensus       486 ~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~  550 (595)
                      ++..|...+......|+.+.|..+|+++.     .....|...+..-...|+.+.+.++++++.+
T Consensus       353 ~~~~~~~yid~e~~~~~~~~aR~l~er~~-----k~~~lw~~~~~fE~~~G~~~~~r~v~~~~~~  412 (493)
T 2uy1_A          353 STLLKEEFFLFLLRIGDEENARALFKRLE-----KTSRMWDSMIEYEFMVGSMELFRELVDQKMD  412 (493)
T ss_dssp             CHHHHHHHHHHHHHHTCHHHHHHHHHHSC-----CBHHHHHHHHHHHHHHSCHHHHHHHHHHHHH
T ss_pred             CHHHHHHHHHHHHHcCCHHHHHHHHHHHH-----HHHHHHHHHHHHHHHCCCHHHHHHHHHHHHH
Confidence            34555666666677788888888888762     2566677766665667888888887777763

>2uy1_A Cleavage stimulation factor 77; RNA-binding protein; 2.0A {Encephalitozoon cuniculi} PDB: 2uy1_B

Probab=99.25  E-value=1.3e-08  Score=101.11  Aligned_cols=125  Identities=15%  Similarity=0.052  Sum_probs=90.3

Q ss_pred             HHHHHHHHHHHccCCHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHh-cCCHHHHHHHHHHHHHcCCCcCHHHHHHHHHH
Q 040027          383 VTYNTLFLGLFEIHQVEHALKLFDEMQRDGVAADTRTYTTFIDGLCK-NGYIIEAVELFRTLRILKCELDIQAYNCLIDG  461 (595)
Q Consensus       383 ~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~-~g~~~~A~~~~~~~~~~~~~~~~~~~~~l~~~  461 (595)
                      ..|...+....+.++.+.|..+|+.+ +. ...+...|......-.. .++.+.|..+|+...+.. +.++..+...++.
T Consensus       287 ~lw~~y~~~~~r~~~~~~AR~i~~~A-~~-~~~~~~v~i~~A~lE~~~~~d~~~ar~ife~al~~~-~~~~~~~~~yid~  363 (493)
T 2uy1_A          287 LLRINHLNYVLKKRGLELFRKLFIEL-GN-EGVGPHVFIYCAFIEYYATGSRATPYNIFSSGLLKH-PDSTLLKEEFFLF  363 (493)
T ss_dssp             HHHHHHHHHHHHHHCHHHHHHHHHHH-TT-SCCCHHHHHHHHHHHHHHHCCSHHHHHHHHHHHHHC-TTCHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHcCCHHHHHHHHHHh-hC-CCCChHHHHHHHHHHHHHCCChHHHHHHHHHHHHHC-CCCHHHHHHHHHH
Confidence            44566666666677889999999888 32 12344555433332222 336899999999988754 4456667777887


Q ss_pred             HHhcCChHHHHHHHHhcccCCCCCCHHHHHHHHHHHHhcCChhHHHHHHHHHHH
Q 040027          462 LCKSGRLKFAWELFCSLPHGVLVPNVVTYNIMIQGLCNDGQMDKARDLFLDMEE  515 (595)
Q Consensus       462 ~~~~g~~~~A~~~~~~~~~~~~~p~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~  515 (595)
                      ....|+.+.|..+|+++..     ....|...+..-...|+.+.+..+++++.+
T Consensus       364 e~~~~~~~~aR~l~er~~k-----~~~lw~~~~~fE~~~G~~~~~r~v~~~~~~  412 (493)
T 2uy1_A          364 LLRIGDEENARALFKRLEK-----TSRMWDSMIEYEFMVGSMELFRELVDQKMD  412 (493)
T ss_dssp             HHHHTCHHHHHHHHHHSCC-----BHHHHHHHHHHHHHHSCHHHHHHHHHHHHH
T ss_pred             HHHcCCHHHHHHHHHHHHH-----HHHHHHHHHHHHHHCCCHHHHHHHHHHHHH
Confidence            8888999999999999843     577888888877888999999998888875

>3edt_B KLC 2, kinesin light chain 2; superhelical, structural genomics, structural genomics conso SGC, microtubule, motor protein, phosphoprotein; 2.70A {Homo sapiens} PDB: 3ceq_A

Probab=99.25  E-value=9.7e-11  Score=108.32  Aligned_cols=227  Identities=12%  Similarity=-0.017  Sum_probs=154.9

Q ss_pred             HhcCCHHHHHHHHHHHHhc-------CCCCCHHHHHHHHHHHHhCCCHHHHHHHHHHHHHC------CC-CCCHHHHHHH
Q 040027          323 CLMGKINRAEELFGSMESM-------GCKHDDVSYNILINGYCKNKEVEEALSLYREMVSK------GI-KPTVVTYNTL  388 (595)
Q Consensus       323 ~~~~~~~~a~~~~~~~~~~-------~~~~~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~~------~~-~~~~~~~~~l  388 (595)
                      ...|++++|+..+++..+.       ..+....++..+...|...|++++|+..++++...      +- +....++..+
T Consensus        12 ~~~~~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~~~l   91 (283)
T 3edt_B           12 SGLVPRGSAVPLCKQALEDLEKTSGHDHPDVATMLNILALVYRDQNKYKEAAHLLNDALAIREKTLGKDHPAVAATLNNL   91 (283)
T ss_dssp             -CCSCSSSHHHHHHHHHHHHHHHHCSSSHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHHTCTTCHHHHHHHHHH
T ss_pred             CCCCCHHHHHHHHHHHHHHHHHhcCCCCHHHHHHHHHHHHHHHHcccHHHHHHHHHHHHHHHHHHcCCcchHHHHHHHHH
Confidence            3567777777777766542       21234557888999999999999999999998764      11 2234577888


Q ss_pred             HHHHHccCCHHHHHHHHHHHHHC------C-CCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHHc------C-CCcCHHH
Q 040027          389 FLGLFEIHQVEHALKLFDEMQRD------G-VAADTRTYTTFIDGLCKNGYIIEAVELFRTLRIL------K-CELDIQA  454 (595)
Q Consensus       389 ~~~~~~~~~~~~a~~~~~~~~~~------~-~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~------~-~~~~~~~  454 (595)
                      ...+...|++++|...+.++.+.      . .+.....+..+...|...|++++|...++++.+.      + .+....+
T Consensus        92 ~~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~~~la~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~~  171 (283)
T 3edt_B           92 AVLYGKRGKYKEAEPLCKRALEIREKVLGKFHPDVAKQLNNLALLCQNQGKAEEVEYYYRRALEIYATRLGPDDPNVAKT  171 (283)
T ss_dssp             HHHHHTTTCHHHHHHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHHHTTTCHHHHHHHHHHHHHHHHHHSCTTCHHHHHH
T ss_pred             HHHHHHhccHHHHHHHHHHHHHHHHHHcCCCChHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHhcCCCCHHHHHH
Confidence            88999999999999999988764      1 1233567778888899999999999999999865      1 1334567


Q ss_pred             HHHHHHHHHhcCChHHHHHHHHhcccC-------CCCCC-HHHHHHHHHHHHhcCChhHHHHHHHHHHH---c---CCCC
Q 040027          455 YNCLIDGLCKSGRLKFAWELFCSLPHG-------VLVPN-VVTYNIMIQGLCNDGQMDKARDLFLDMEE---N---AAAP  520 (595)
Q Consensus       455 ~~~l~~~~~~~g~~~~A~~~~~~~~~~-------~~~p~-~~~~~~l~~~~~~~g~~~~A~~~~~~~~~---~---~~~~  520 (595)
                      +..++.+|...|++++|...++++.+.       ...+. ...|..+...+...+....+.. +..+..   .   ..+.
T Consensus       172 ~~~la~~~~~~g~~~~A~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~  250 (283)
T 3edt_B          172 KNNLASCYLKQGKYQDAETLYKEILTRAHEKEFGSVNGDNKPIWMHAEEREESKDKRRDSAP-YGEYGSWYKACKVDSPT  250 (283)
T ss_dssp             HHHHHHHHHHHTCHHHHHHHHHHHHHHHHHHHSSSCCSSCCCHHHHHHHHHHTTCCCCC-------------CCCCCCHH
T ss_pred             HHHHHHHHHHcCCHHHHHHHHHHHHHHHHHhcCCCcchhHHHHHHHHHHHHhcCCchhHHHH-HHHHHHHHHhcCCCCHH
Confidence            888899999999999999999988752       11222 2334444444443333333222 222211   1   1122


Q ss_pred             CHHHHHHHHHHHHHcCChhHHHHHHHHHHH
Q 040027          521 DVITFDMLIHGFIRINEPSKVNELLHKMKE  550 (595)
Q Consensus       521 ~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~  550 (595)
                      ...++..++.+|...|++++|..+++++++
T Consensus       251 ~~~~~~~la~~~~~~g~~~~A~~~~~~al~  280 (283)
T 3edt_B          251 VNTTLRSLGALYRRQGKLEAAHTLEDCASR  280 (283)
T ss_dssp             HHHHHHHHHHHHHHTTCHHHHHHHHHHHHT
T ss_pred             HHHHHHHHHHHHHHcCCHHHHHHHHHHHHH
Confidence            245678889999999999999999999875

>3edt_B KLC 2, kinesin light chain 2; superhelical, structural genomics, structural genomics conso SGC, microtubule, motor protein, phosphoprotein; 2.70A {Homo sapiens} PDB: 3ceq_A

Probab=99.25  E-value=1.6e-10  Score=106.89  Aligned_cols=164  Identities=13%  Similarity=0.039  Sum_probs=123.4

Q ss_pred             HhcCChhHHHHHHHHHHhC-------CCCCCHHHHHHHHHHHHhcCCHhHHHHHHHHHHhc------CC-CCCHhhHHHH
Q 040027          107 CKIGRVSLGFIAFGRILRS-------CFTPNAATFNSLIKGLHAESRIMEAAALFTKLKAF------GC-EPNVITYNTL  172 (595)
Q Consensus       107 ~~~g~~~~A~~~~~~~~~~-------~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~------~~-~~~~~~~~~l  172 (595)
                      ...|++++|+..|+++++.       ..+....++..+...+...|++++|+..++++...      +. +....++..+
T Consensus        12 ~~~~~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~~~l   91 (283)
T 3edt_B           12 SGLVPRGSAVPLCKQALEDLEKTSGHDHPDVATMLNILALVYRDQNKYKEAAHLLNDALAIREKTLGKDHPAVAATLNNL   91 (283)
T ss_dssp             -CCSCSSSHHHHHHHHHHHHHHHHCSSSHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHHTCTTCHHHHHHHHHH
T ss_pred             CCCCCHHHHHHHHHHHHHHHHHhcCCCCHHHHHHHHHHHHHHHHcccHHHHHHHHHHHHHHHHHHcCCcchHHHHHHHHH
Confidence            3567888888888877763       22334667888999999999999999999998765      21 2245678889


Q ss_pred             HHHHHhcCChhHHHHHHHHHHhcCCCCCcc-ccCcHHHHHHHHHHHHHcCCHhHHHHHHHHHhhC------C-CCCCHhH
Q 040027          173 INGLCRTGHTMIALNLFEEMANGNGEIGVV-CKPNTVTYSTIIDGLCKEGFVDKAKALFLQMKDE------N-INPDVVT  244 (595)
Q Consensus       173 ~~~~~~~g~~~~A~~~~~~~~~~~~~~~~~-~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~------~-~~~~~~~  244 (595)
                      ...+...|++++|++.|+++.......... .+....++..+..++...|++++|...++++...      + .+....+
T Consensus        92 ~~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~~~la~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~~  171 (283)
T 3edt_B           92 AVLYGKRGKYKEAEPLCKRALEIREKVLGKFHPDVAKQLNNLALLCQNQGKAEEVEYYYRRALEIYATRLGPDDPNVAKT  171 (283)
T ss_dssp             HHHHHTTTCHHHHHHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHHHTTTCHHHHHHHHHHHHHHHHHHSCTTCHHHHHH
T ss_pred             HHHHHHhccHHHHHHHHHHHHHHHHHHcCCCChHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHhcCCCCHHHHHH
Confidence            999999999999999999988651000000 1334678888999999999999999999988764      1 1123556


Q ss_pred             HHHHHHHHHhcCCHHHHHHHHHHHHH
Q 040027          245 YNSLIHGLCHANDWNEAKRLFIEMMD  270 (595)
Q Consensus       245 ~~~ll~~~~~~~~~~~A~~~~~~~~~  270 (595)
                      +..+...+...|++++|...++++.+
T Consensus       172 ~~~la~~~~~~g~~~~A~~~~~~~l~  197 (283)
T 3edt_B          172 KNNLASCYLKQGKYQDAETLYKEILT  197 (283)
T ss_dssp             HHHHHHHHHHHTCHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHcCCHHHHHHHHHHHHH
Confidence            77888899999999999999988875

>3mv2_B Coatomer subunit epsilon; vesicular membrane coat COAT protein complex I, protein TRAN; 2.90A {Saccharomyces cerevisiae} PDB: 3mv3_B

Probab=99.23  E-value=7.2e-09  Score=93.96  Aligned_cols=178  Identities=9%  Similarity=0.016  Sum_probs=95.2

Q ss_pred             HHHHHHHHHHCCCCCCHHHHHHHHHHHHccCCHHHHHHHHHHHHHCCC-CCCHHHHHHHHHHHHhcCCHHHHHHHHHHHH
Q 040027          366 ALSLYREMVSKGIKPTVVTYNTLFLGLFEIHQVEHALKLFDEMQRDGV-AADTRTYTTFIDGLCKNGYIIEAVELFRTLR  444 (595)
Q Consensus       366 A~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~-~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~  444 (595)
                      |+..+++....+ .++..++..+..++...|++++|++++.+.+..+. .-+...+...+..+.+.|+.+.|.+.++++.
T Consensus        85 a~~~l~~l~~~~-~~~~~~~~~la~i~~~~g~~eeAL~~l~~~i~~~~~~~~lea~~l~vqi~L~~~r~d~A~k~l~~~~  163 (310)
T 3mv2_B           85 NIEELENLLKDK-QNSPYELYLLATAQAILGDLDKSLETCVEGIDNDEAEGTTELLLLAIEVALLNNNVSTASTIFDNYT  163 (310)
T ss_dssp             CCHHHHHTTTTS-CCCHHHHHHHHHHHHHHTCHHHHHHHHHHHHTSSCSTTHHHHHHHHHHHHHHTTCHHHHHHHHHHHH
T ss_pred             HHHHHHHHHhcC-CCCcHHHHHHHHHHHHcCCHHHHHHHHHHHhccCCCcCcHHHHHHHHHHHHHCCCHHHHHHHHHHHH
Confidence            455555555443 23444445555666666666666666666654431 1244555556666666666666666666665


Q ss_pred             HcCCCc-----CHHHHHHHHHH--HHhcC--ChHHHHHHHHhcccCCCCCCHHHHHHHHHHHHhcCChhHHHHHHHHHHH
Q 040027          445 ILKCEL-----DIQAYNCLIDG--LCKSG--RLKFAWELFCSLPHGVLVPNVVTYNIMIQGLCNDGQMDKARDLFLDMEE  515 (595)
Q Consensus       445 ~~~~~~-----~~~~~~~l~~~--~~~~g--~~~~A~~~~~~~~~~~~~p~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~  515 (595)
                      +.  .|     +..+...++.+  ....|  ++.+|..+|+++.+.  .|+..+...++.++.+.|++++|.+.++.+.+
T Consensus       164 ~~--~~d~~~~~d~~l~~Laea~v~l~~g~~~~q~A~~~f~El~~~--~p~~~~~~lLln~~~~~g~~~eAe~~L~~l~~  239 (310)
T 3mv2_B          164 NA--IEDTVSGDNEMILNLAESYIKFATNKETATSNFYYYEELSQT--FPTWKTQLGLLNLHLQQRNIAEAQGIVELLLS  239 (310)
T ss_dssp             HH--SCHHHHHHHHHHHHHHHHHHHHHHTCSTTTHHHHHHHHHHTT--SCSHHHHHHHHHHHHHHTCHHHHHHHHHHHHS
T ss_pred             hc--CccccccchHHHHHHHHHHHHHHhCCccHHHHHHHHHHHHHh--CCCcccHHHHHHHHHHcCCHHHHHHHHHHHHH
Confidence            54  23     23344444433  22223  666666666666552  34422222333356666666666666665543


Q ss_pred             c-----CC----CCCHHHHHHHHHHHHHcCChhHHHHHHHHHHH
Q 040027          516 N-----AA----APDVITFDMLIHGFIRINEPSKVNELLHKMKE  550 (595)
Q Consensus       516 ~-----~~----~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~  550 (595)
                      .     +.    +.++.++..++......|+  +|.++++++.+
T Consensus       240 ~~p~~~~k~~~~p~~~~~LaN~i~l~~~lgk--~a~~l~~qL~~  281 (310)
T 3mv2_B          240 DYYSVEQKENAVLYKPTFLANQITLALMQGL--DTEDLTNQLVK  281 (310)
T ss_dssp             HHHHTTTCHHHHSSHHHHHHHHHHHHHHTTC--TTHHHHHHHHH
T ss_pred             hcccccccccCCCCCHHHHHHHHHHHHHhCh--HHHHHHHHHHH
Confidence            2     00    2344555455555555665  66666666665

>1qqe_A Vesicular transport protein SEC17; helix-turn-helix TPR-like repeat, protein transport; 2.90A {Saccharomyces cerevisiae} SCOP: a.118.8.1

Probab=99.20  E-value=1.4e-09  Score=100.94  Aligned_cols=205  Identities=14%  Similarity=-0.018  Sum_probs=116.5

Q ss_pred             HHHHHHHHHHhCCCCCCHHHHHHHHHHHHhc--C-CHhHHHHHHHHHHhcCCCCCHhhHHHHHHHHHhcCChhHHHHHHH
Q 040027          114 LGFIAFGRILRSCFTPNAATFNSLIKGLHAE--S-RIMEAAALFTKLKAFGCEPNVITYNTLINGLCRTGHTMIALNLFE  190 (595)
Q Consensus       114 ~A~~~~~~~~~~~~~~~~~~~~~l~~~~~~~--g-~~~~A~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~  190 (595)
                      +|..++.++.+.- +++...| .+    .+.  + ++++|...|++.               +..|...|++++|+..|+
T Consensus         3 ~a~~~~~~a~k~~-~~~~~~~-~~----~~~~~~~~~~~A~~~~~~a---------------~~~~~~~g~~~~A~~~~~   61 (292)
T 1qqe_A            3 DPVELLKRAEKKG-VPSSGFM-KL----FSGSDSYKFEEAADLCVQA---------------ATIYRLRKELNLAGDSFL   61 (292)
T ss_dssp             CHHHHHHHHHHHS-SCCCTHH-HH----HSCCSHHHHHHHHHHHHHH---------------HHHHHHTTCTHHHHHHHH
T ss_pred             cHHHHHHHHHHHh-CcCCCcc-hh----cCCCCCccHHHHHHHHHHH---------------HHHHHHcCCHHHHHHHHH
Confidence            4666666666652 2222222 22    232  1 477777777776               345667888888888888


Q ss_pred             HHHhcCCCCCccccC-cHHHHHHHHHHHHHcCCHhHHHHHHHHHhhCCC---CC--CHhHHHHHHHHHHhc-CCHHHHHH
Q 040027          191 EMANGNGEIGVVCKP-NTVTYSTIIDGLCKEGFVDKAKALFLQMKDENI---NP--DVVTYNSLIHGLCHA-NDWNEAKR  263 (595)
Q Consensus       191 ~~~~~~~~~~~~~~~-~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~---~~--~~~~~~~ll~~~~~~-~~~~~A~~  263 (595)
                      +........+  .++ ...+|+.+..+|...|++++|+..|++......   .+  ...++..+...|... |++++|+.
T Consensus        62 ~al~~~~~~~--~~~~~a~~~~~lg~~~~~~g~~~~A~~~~~~Al~l~~~~g~~~~~a~~~~~lg~~~~~~lg~~~~A~~  139 (292)
T 1qqe_A           62 KAADYQKKAG--NEDEAGNTYVEAYKCFKSGGNSVNAVDSLENAIQIFTHRGQFRRGANFKFELGEILENDLHDYAKAID  139 (292)
T ss_dssp             HHHHHHHHTT--CHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCCHHHHHH
T ss_pred             HHHHHHHHhC--CHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHhhcCHHHHHH
Confidence            7765421000  011 245777888888888888888888877665310   00  123566666666664 77777777


Q ss_pred             HHHHHHHCCCCC-C----HhhHHHHHHHHHhcCChHHHHHHHHHHHHCCCCCCH------HHHHHHHHHHHhcCCHHHHH
Q 040027          264 LFIEMMDQGVQP-S----VVTFNVIMDELCKNRKMDEASRLLDLMVQRGVRPNA------CTYNTLMDGFCLMGKINRAE  332 (595)
Q Consensus       264 ~~~~~~~~~~~~-~----~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~~~~~~------~~~~~l~~~~~~~~~~~~a~  332 (595)
                      .|++.++..... +    ..++..+...+...|++++|+..|+++.........      ..+..++.++...|++++|+
T Consensus       140 ~~~~Al~~~~~~~~~~~~~~~~~~lg~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~~lg~~~~~~g~~~~A~  219 (292)
T 1qqe_A          140 CYELAGEWYAQDQSVALSNKCFIKCADLKALDGQYIEASDIYSKLIKSSMGNRLSQWSLKDYFLKKGLCQLAATDAVAAA  219 (292)
T ss_dssp             HHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHTTSSCTTTGGGHHHHHHHHHHHHHHTTCHHHHH
T ss_pred             HHHHHHHHHHhCCChHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHhcCCcccHHHHHHHHHHHHHHHHcCCHHHHH
Confidence            776665431000 0    234555666666666666666666666654322111      13444555566666666666


Q ss_pred             HHHHHHHhc
Q 040027          333 ELFGSMESM  341 (595)
Q Consensus       333 ~~~~~~~~~  341 (595)
                      ..+++..+.
T Consensus       220 ~~~~~al~l  228 (292)
T 1qqe_A          220 RTLQEGQSE  228 (292)
T ss_dssp             HHHHGGGCC
T ss_pred             HHHHHHHhh
Confidence            666665543

>3urz_A Uncharacterized protein; tetratricopeptide repeats (TPR) containing protein, structur genomics, joint center for structural genomics, JCSG; HET: PG4; 2.19A {Bacteroides ovatus}

Probab=99.20  E-value=7.1e-10  Score=97.09  Aligned_cols=191  Identities=10%  Similarity=0.038  Sum_probs=119.6

Q ss_pred             HHHHHHHHHHHhCCCHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHccCCHHHHHHHHHHHHHCCCCCCHHHHHHHHHHH
Q 040027          348 VSYNILINGYCKNKEVEEALSLYREMVSKGIKPTVVTYNTLFLGLFEIHQVEHALKLFDEMQRDGVAADTRTYTTFIDGL  427 (595)
Q Consensus       348 ~~~~~l~~~~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~  427 (595)
                      ..+......+...|++++|+..|+++++..+. +...+...     ....              ...........+..+|
T Consensus         5 ~~~~~~g~~~~~~g~~~~A~~~~~~al~~~p~-~~~~~~~~-----~~~~--------------~~~~~~~~~~~lg~~~   64 (208)
T 3urz_A            5 DEMLQKVSAAIEAGQNGQAVSYFRQTIALNID-RTEMYYWT-----NVDK--------------NSEISSKLATELALAY   64 (208)
T ss_dssp             HHHHHHHHHHHHTTCHHHHHHHHHHHHHHCHH-HHHHHHHH-----HSCT--------------TSHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHCCCHHHHHHHHHHHHHhCCC-ChHHHHHh-----hhcc--------------hhhhhHHHHHHHHHHH
Confidence            34444555666777777777777777765211 11222110     0000              0011112233467778


Q ss_pred             HhcCCHHHHHHHHHHHHHcCCCcCHHHHHHHHHHHHhcCChHHHHHHHHhcccCCCCCC-HHHHHHHHHHHHhcCC--hh
Q 040027          428 CKNGYIIEAVELFRTLRILKCELDIQAYNCLIDGLCKSGRLKFAWELFCSLPHGVLVPN-VVTYNIMIQGLCNDGQ--MD  504 (595)
Q Consensus       428 ~~~g~~~~A~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~p~-~~~~~~l~~~~~~~g~--~~  504 (595)
                      .+.|++++|...|+++++.. |.+...+..++.++...|++++|+..|+++++  +.|+ ...|..+..+|...|+  ..
T Consensus        65 ~~~g~~~~A~~~~~~al~~~-p~~~~~~~~lg~~~~~~g~~~~A~~~~~~al~--~~P~~~~a~~~lg~~~~~~~~~~~~  141 (208)
T 3urz_A           65 KKNRNYDKAYLFYKELLQKA-PNNVDCLEACAEMQVCRGQEKDALRMYEKILQ--LEADNLAANIFLGNYYYLTAEQEKK  141 (208)
T ss_dssp             HHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHHTCHHHHHHHHHHHHH--HCTTCHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHCCCHHHHHHHHHHHHHHC-CCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHH--cCCCCHHHHHHHHHHHHHHhHHHHH
Confidence            88888888888888888776 66788888888888888888888888888887  4554 6777777777765543  34


Q ss_pred             HHHHHHHHHHHcCCCCCHHHHHHHHHHHHHcCChhHHHHHHHHHHHCCCCCCHHHHHHHHH
Q 040027          505 KARDLFLDMEENAAAPDVITFDMLIHGFIRINEPSKVNELLHKMKEKKVMPDASIVSIVVD  565 (595)
Q Consensus       505 ~A~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~p~~~~~~~l~~  565 (595)
                      .+...++....  ..|....+.....++...|++++|...|+++++  +.|+......+.+
T Consensus       142 ~~~~~~~~~~~--~~~~~~a~~~~g~~~~~~~~~~~A~~~~~~al~--l~P~~~~~~~l~~  198 (208)
T 3urz_A          142 KLETDYKKLSS--PTKMQYARYRDGLSKLFTTRYEKARNSLQKVIL--RFPSTEAQKTLDK  198 (208)
T ss_dssp             HHHHHHC---C--CCHHHHHHHHHHHHHHHHHTHHHHHHHHHHHTT--TSCCHHHHHHHHH
T ss_pred             HHHHHHHHHhC--CCchhHHHHHHHHHHHHccCHHHHHHHHHHHHH--hCCCHHHHHHHHH
Confidence            45555555432  223333445566677778888888888888886  4577665555444

>3qky_A Outer membrane assembly lipoprotein YFIO; membrane protein; 2.15A {Rhodothermus marinus}

Probab=99.19  E-value=1.4e-09  Score=99.33  Aligned_cols=102  Identities=10%  Similarity=-0.020  Sum_probs=87.1

Q ss_pred             CCHHHHHHHHHHHHhcCChhHHHHHHHHHHhCCCCCC---HHHHHHHHHHHHhcCCHhHHHHHHHHHHhcCCC--CCHhh
Q 040027           94 PNLYTYNILINCFCKIGRVSLGFIAFGRILRSCFTPN---AATFNSLIKGLHAESRIMEAAALFTKLKAFGCE--PNVIT  168 (595)
Q Consensus        94 ~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~~---~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~--~~~~~  168 (595)
                      .++..+..++..+.+.|++++|+..|+++++.. +.+   ..++..+..++.+.|++++|+..|+++.+....  ....+
T Consensus        13 ~~~~~~~~~a~~~~~~g~~~~A~~~~~~~l~~~-p~~~~~~~a~~~lg~~~~~~~~~~~A~~~~~~~l~~~p~~~~~~~a   91 (261)
T 3qky_A           13 SSPQEAFERAMEFYNQGKYDRAIEYFKAVFTYG-RTHEWAADAQFYLARAYYQNKEYLLAASEYERFIQIYQIDPRVPQA   91 (261)
T ss_dssp             SSHHHHHHHHHHHHHTTCHHHHHHHHHHHGGGC-SCSTTHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTCTTHHHH
T ss_pred             CCHHHHHHHHHHHHHhCCHHHHHHHHHHHHHhC-CCCcchHHHHHHHHHHHHHhCcHHHHHHHHHHHHHHCCCCchhHHH
Confidence            467888889999999999999999999999874 333   678889999999999999999999999987421  12456


Q ss_pred             HHHHHHHHHh--------cCChhHHHHHHHHHHhcC
Q 040027          169 YNTLINGLCR--------TGHTMIALNLFEEMANGN  196 (595)
Q Consensus       169 ~~~l~~~~~~--------~g~~~~A~~~~~~~~~~~  196 (595)
                      +..+..++..        .|++++|+..|+++....
T Consensus        92 ~~~lg~~~~~~~~~~~~~~~~~~~A~~~~~~~l~~~  127 (261)
T 3qky_A           92 EYERAMCYYKLSPPYELDQTDTRKAIEAFQLFIDRY  127 (261)
T ss_dssp             HHHHHHHHHHHCCCTTSCCHHHHHHHHHHHHHHHHC
T ss_pred             HHHHHHHHHHhcccccccchhHHHHHHHHHHHHHHC
Confidence            7788888888        999999999999999875

>3urz_A Uncharacterized protein; tetratricopeptide repeats (TPR) containing protein, structur genomics, joint center for structural genomics, JCSG; HET: PG4; 2.19A {Bacteroides ovatus}

Probab=99.19  E-value=1.1e-09  Score=95.82  Aligned_cols=181  Identities=7%  Similarity=-0.038  Sum_probs=83.6

Q ss_pred             CHHHHHHHHHHHHhcCChhHHHHHHHHHHhCCCCCCHHHHHHHHHHHHhcCCHhHHHHHHHHHHhcCCCCCHhhHHHHHH
Q 040027           95 NLYTYNILINCFCKIGRVSLGFIAFGRILRSCFTPNAATFNSLIKGLHAESRIMEAAALFTKLKAFGCEPNVITYNTLIN  174 (595)
Q Consensus        95 ~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~~l~~  174 (595)
                      ++..+...+..+...|++++|+..|+++++.. +.+...|...     ...+.              ..........+..
T Consensus         3 ~~~~~~~~g~~~~~~g~~~~A~~~~~~al~~~-p~~~~~~~~~-----~~~~~--------------~~~~~~~~~~lg~   62 (208)
T 3urz_A            3 SVDEMLQKVSAAIEAGQNGQAVSYFRQTIALN-IDRTEMYYWT-----NVDKN--------------SEISSKLATELAL   62 (208)
T ss_dssp             CHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-HHHHHHHHHH-----HSCTT--------------SHHHHHHHHHHHH
T ss_pred             CHHHHHHHHHHHHHCCCHHHHHHHHHHHHHhC-CCChHHHHHh-----hhcch--------------hhhhHHHHHHHHH
Confidence            44555566677788888888888888888763 2233444440     00000              0001111222444


Q ss_pred             HHHhcCChhHHHHHHHHHHhcCCCCCccccCcHHHHHHHHHHHHHcCCHhHHHHHHHHHhhCCCCCCHhHHHHHHHHHHh
Q 040027          175 GLCRTGHTMIALNLFEEMANGNGEIGVVCKPNTVTYSTIIDGLCKEGFVDKAKALFLQMKDENINPDVVTYNSLIHGLCH  254 (595)
Q Consensus       175 ~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~~ll~~~~~  254 (595)
                      +|...|++++|+..|++..+.+       |.+...+..+..++...|++++|...|+++.+.. +.+..+|..+...|..
T Consensus        63 ~~~~~g~~~~A~~~~~~al~~~-------p~~~~~~~~lg~~~~~~g~~~~A~~~~~~al~~~-P~~~~a~~~lg~~~~~  134 (208)
T 3urz_A           63 AYKKNRNYDKAYLFYKELLQKA-------PNNVDCLEACAEMQVCRGQEKDALRMYEKILQLE-ADNLAANIFLGNYYYL  134 (208)
T ss_dssp             HHHHTTCHHHHHHHHHHHHHHC-------TTCHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHH
T ss_pred             HHHHCCCHHHHHHHHHHHHHHC-------CCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHcC-CCCHHHHHHHHHHHHH
Confidence            4555555555555555555443       3344455555555555555555555555554432 1234444444444433


Q ss_pred             cCC--HHHHHHHHHHHHHCCCCCCHhhHHHHHHHHHhcCChHHHHHHHHHHHH
Q 040027          255 AND--WNEAKRLFIEMMDQGVQPSVVTFNVIMDELCKNRKMDEASRLLDLMVQ  305 (595)
Q Consensus       255 ~~~--~~~A~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~  305 (595)
                      .|+  ...+...+.....  ..|....+.....++...|++++|...|+++++
T Consensus       135 ~~~~~~~~~~~~~~~~~~--~~~~~~a~~~~g~~~~~~~~~~~A~~~~~~al~  185 (208)
T 3urz_A          135 TAEQEKKKLETDYKKLSS--PTKMQYARYRDGLSKLFTTRYEKARNSLQKVIL  185 (208)
T ss_dssp             HHHHHHHHHHHHHC---C--CCHHHHHHHHHHHHHHHHHTHHHHHHHHHHHTT
T ss_pred             HhHHHHHHHHHHHHHHhC--CCchhHHHHHHHHHHHHccCHHHHHHHHHHHHH
Confidence            332  2223333333321  111112223333444445555555555555554

>4ga2_A E3 SUMO-protein ligase ranbp2; TPR motif, nuclear pore complex component nucleocytoplasmic transport, transport protein; 0.95A {Pan troglodytes} PDB: 4ga0_A 4ga1_A*

Probab=99.17  E-value=9.8e-11  Score=96.42  Aligned_cols=143  Identities=6%  Similarity=-0.047  Sum_probs=103.0

Q ss_pred             HHHHHhcCCHHHHHHHHHHHHHcCCCcCHHHHHHHHHHHHhcCChHHHHHHHHhcccCCCCC-CHHHHHHHHHHHHhcCC
Q 040027          424 IDGLCKNGYIIEAVELFRTLRILKCELDIQAYNCLIDGLCKSGRLKFAWELFCSLPHGVLVP-NVVTYNIMIQGLCNDGQ  502 (595)
Q Consensus       424 ~~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~p-~~~~~~~l~~~~~~~g~  502 (595)
                      ...+...|++++|+..++...... +.+...+..+...|.+.|++++|++.|+++++  +.| +..+|..+..+|...|+
T Consensus         4 G~~~~~~~~~e~ai~~~~~a~~~~-p~~~~~~~~la~~y~~~~~~~~A~~~~~~al~--~~p~~~~a~~~lg~~~~~~~~   80 (150)
T 4ga2_A            4 GSMRRSKADVERYIASVQGSTPSP-RQKSIKGFYFAKLYYEAKEYDLAKKYICTYIN--VQERDPKAHRFLGLLYELEEN   80 (150)
T ss_dssp             ---CCCHHHHHHHHHHHHHHSCSH-HHHHTTHHHHHHHHHHTTCHHHHHHHHHHHHH--HCTTCHHHHHHHHHHHHHTTC
T ss_pred             HHHHHHcChHHHHHHHHHHhcccC-cccHHHHHHHHHHHHHcCCHHHHHHHHHHHHH--hCCCCHHHHHHHHHHHHHcCc
Confidence            344555677788888887776542 33345566778888888888888888888877  445 46778888888888888


Q ss_pred             hhHHHHHHHHHHHcCCCCCHHHHHHHHHHHHHcCChhHHHHH-HHHHHHCCCCC-CHHHHHHHHHHHHhcCc
Q 040027          503 MDKARDLFLDMEENAAAPDVITFDMLIHGFIRINEPSKVNEL-LHKMKEKKVMP-DASIVSIVVDLLVKNEI  572 (595)
Q Consensus       503 ~~~A~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~-~~~~~~~~~~p-~~~~~~~l~~~~~~~g~  572 (595)
                      +++|+..|+++++.. +.+...+..++.+|.+.|++++|.+. ++++.+.  .| ++.+|.....++.+.|+
T Consensus        81 ~~~A~~~~~~al~~~-p~~~~~~~~la~~~~~~~~~~~aa~~~~~~al~l--~P~~~~~~~l~~~ll~~~G~  149 (150)
T 4ga2_A           81 TDKAVECYRRSVELN-PTQKDLVLKIAELLCKNDVTDGRAKYWVERAAKL--FPGSPAVYKLKEQLLDCEGE  149 (150)
T ss_dssp             HHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHHCSSSSHHHHHHHHHHHH--STTCHHHHHHHHHHHHTCCC
T ss_pred             hHHHHHHHHHHHHhC-CCCHHHHHHHHHHHHHcCChHHHHHHHHHHHHHh--CcCCHHHHHHHHHHHHHhCc
Confidence            888888888888864 44677788888888888888766554 5777763  35 56777777777777764

>2pzi_A Probable serine/threonine-protein kinase PKNG; ATP-recognition, kinase-INH complex, rubredoxin fold, TPR domain, transferase; HET: AXX; 2.40A {Mycobacterium tuberculosis}

Probab=99.17  E-value=4.2e-10  Score=117.42  Aligned_cols=152  Identities=9%  Similarity=-0.076  Sum_probs=126.9

Q ss_pred             CHHHHHHHHHHHHhcCChhHHHHHHHHHHhCCCCCCHHHHHHHHHHHHhcCCHhHHHHHHHHHHhcCCCCCHhhHHHHHH
Q 040027           95 NLYTYNILINCFCKIGRVSLGFIAFGRILRSCFTPNAATFNSLIKGLHAESRIMEAAALFTKLKAFGCEPNVITYNTLIN  174 (595)
Q Consensus        95 ~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~~l~~  174 (595)
                      +...+..+...+.+.|++++|+..|+++++.. +.+...|..+...+...|++++|++.|+++.+.. +.+...+..+..
T Consensus       432 ~~~~~~~~a~~~~~~g~~~~A~~~~~~al~~~-p~~~~a~~~lg~~~~~~g~~~~A~~~~~~al~l~-P~~~~~~~~lg~  509 (681)
T 2pzi_A          432 SVELPLMEVRALLDLGDVAKATRKLDDLAERV-GWRWRLVWYRAVAELLTGDYDSATKHFTEVLDTF-PGELAPKLALAA  509 (681)
T ss_dssp             CSHHHHHHHHHHHHHTCHHHHHHHHHHHHHHH-CCCHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHS-TTCSHHHHHHHH
T ss_pred             chhHHHHHHHHHHhcCCHHHHHHHHHHHhccC-cchHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhC-CCChHHHHHHHH
Confidence            66777788888999999999999999999875 5578899999999999999999999999999885 336788899999


Q ss_pred             HHHhcCChhHHHHHHHHHHhcCCCCCccccCcHHHHHHHHHHHHHcCCHhHHHHHHHHHhhCCCCCCHhHHHHHHHHHHh
Q 040027          175 GLCRTGHTMIALNLFEEMANGNGEIGVVCKPNTVTYSTIIDGLCKEGFVDKAKALFLQMKDENINPDVVTYNSLIHGLCH  254 (595)
Q Consensus       175 ~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~~ll~~~~~  254 (595)
                      ++...|++++ ++.|+++.+.+       +.+...|..+..++.+.|++++|.+.|+++.+.+ +.+...+..+..++..
T Consensus       510 ~~~~~g~~~~-~~~~~~al~~~-------P~~~~a~~~lg~~~~~~g~~~~A~~~~~~al~l~-P~~~~a~~~~~~~~~~  580 (681)
T 2pzi_A          510 TAELAGNTDE-HKFYQTVWSTN-------DGVISAAFGLARARSAEGDRVGAVRTLDEVPPTS-RHFTTARLTSAVTLLS  580 (681)
T ss_dssp             HHHHHTCCCT-TCHHHHHHHHC-------TTCHHHHHHHHHHHHHTTCHHHHHHHHHTSCTTS-TTHHHHHHHHHHHTC-
T ss_pred             HHHHcCChHH-HHHHHHHHHhC-------CchHHHHHHHHHHHHHcCCHHHHHHHHHhhcccC-cccHHHHHHHHHHHHc
Confidence            9999999999 99999999876       5678899999999999999999999999988763 2245677777777766


Q ss_pred             cCC
Q 040027          255 AND  257 (595)
Q Consensus       255 ~~~  257 (595)
                      .++
T Consensus       581 ~~~  583 (681)
T 2pzi_A          581 GRS  583 (681)
T ss_dssp             ---
T ss_pred             cCC
Confidence            554

>1qqe_A Vesicular transport protein SEC17; helix-turn-helix TPR-like repeat, protein transport; 2.90A {Saccharomyces cerevisiae} SCOP: a.118.8.1

Probab=99.17  E-value=1.9e-09  Score=100.05  Aligned_cols=205  Identities=10%  Similarity=0.020  Sum_probs=142.7

Q ss_pred             HHHHHHHHHHHhcCChhHHHHHHHHHHhC----CCCCC-HHHHHHHHHHHHhcCCHhHHHHHHHHHHhcCCCC-C----H
Q 040027           97 YTYNILINCFCKIGRVSLGFIAFGRILRS----CFTPN-AATFNSLIKGLHAESRIMEAAALFTKLKAFGCEP-N----V  166 (595)
Q Consensus        97 ~~~~~l~~~~~~~g~~~~A~~~~~~~~~~----~~~~~-~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~-~----~  166 (595)
                      ..|...+..|...|++++|...|+++...    +.+++ ..+|+.+...|...|++++|+..|++........ +    .
T Consensus        38 ~~~~~a~~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~a~~~~~lg~~~~~~g~~~~A~~~~~~Al~l~~~~g~~~~~a  117 (292)
T 1qqe_A           38 DLCVQAATIYRLRKELNLAGDSFLKAADYQKKAGNEDEAGNTYVEAYKCFKSGGNSVNAVDSLENAIQIFTHRGQFRRGA  117 (292)
T ss_dssp             HHHHHHHHHHHHTTCTHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCHHHHH
T ss_pred             HHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHcCCHHHHH
Confidence            35667788899999999999999998765    21111 4678899999999999999999999987642111 1    3


Q ss_pred             hhHHHHHHHHHhc-CChhHHHHHHHHHHhcCCCCCccccCcHHHHHHHHHHHHHcCCHhHHHHHHHHHhhCCCCCCH---
Q 040027          167 ITYNTLINGLCRT-GHTMIALNLFEEMANGNGEIGVVCKPNTVTYSTIIDGLCKEGFVDKAKALFLQMKDENINPDV---  242 (595)
Q Consensus       167 ~~~~~l~~~~~~~-g~~~~A~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~~~---  242 (595)
                      .++..+..+|... |++++|+..|++........+. ......++..+...+...|++++|...|++..........   
T Consensus       118 ~~~~~lg~~~~~~lg~~~~A~~~~~~Al~~~~~~~~-~~~~~~~~~~lg~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~  196 (292)
T 1qqe_A          118 NFKFELGEILENDLHDYAKAIDCYELAGEWYAQDQS-VALSNKCFIKCADLKALDGQYIEASDIYSKLIKSSMGNRLSQW  196 (292)
T ss_dssp             HHHHHHHHHHHHTTCCHHHHHHHHHHHHHHHHHTTC-HHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHTTSSCTTTGG
T ss_pred             HHHHHHHHHHHHhhcCHHHHHHHHHHHHHHHHhCCC-hHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHhcCCcccH
Confidence            5788899999996 9999999999999875310000 0001356788889999999999999999998875432221   


Q ss_pred             ---hHHHHHHHHHHhcCCHHHHHHHHHHHHHCCCCCCHh------hHHHHHHHHH--hcCChHHHHHHHHHHH
Q 040027          243 ---VTYNSLIHGLCHANDWNEAKRLFIEMMDQGVQPSVV------TFNVIMDELC--KNRKMDEASRLLDLMV  304 (595)
Q Consensus       243 ---~~~~~ll~~~~~~~~~~~A~~~~~~~~~~~~~~~~~------~~~~l~~~~~--~~g~~~~a~~~~~~~~  304 (595)
                         ..|..+..++...|++++|...|++.++.  .|+..      .+..++..+.  ..+++++|+..|+.+.
T Consensus       197 ~~~~~~~~lg~~~~~~g~~~~A~~~~~~al~l--~p~~~~~~~~~~l~~l~~~~~~~~~~~~~~A~~~~~~~~  267 (292)
T 1qqe_A          197 SLKDYFLKKGLCQLAATDAVAAARTLQEGQSE--DPNFADSRESNFLKSLIDAVNEGDSEQLSEHCKEFDNFM  267 (292)
T ss_dssp             GHHHHHHHHHHHHHHTTCHHHHHHHHHGGGCC-----------HHHHHHHHHHHHTTCTTTHHHHHHHHTTSS
T ss_pred             HHHHHHHHHHHHHHHcCCHHHHHHHHHHHHhh--CCCCCCcHHHHHHHHHHHHHHcCCHHHHHHHHHHhccCC
Confidence               14667778888889999999988887653  22211      2233444443  3455666666665544

>3mv2_B Coatomer subunit epsilon; vesicular membrane coat COAT protein complex I, protein TRAN; 2.90A {Saccharomyces cerevisiae} PDB: 3mv3_B

Probab=99.17  E-value=1.9e-08  Score=91.20  Aligned_cols=244  Identities=10%  Similarity=-0.025  Sum_probs=131.8

Q ss_pred             HHHHHhcCChhHHHHHHHHHHhCCCCCCHHHHHHHHHHHHhcCCHhHHHHHHHHHHhcCCCCCHhhHHHHHHHHHhcCCh
Q 040027          103 INCFCKIGRVSLGFIAFGRILRSCFTPNAATFNSLIKGLHAESRIMEAAALFTKLKAFGCEPNVITYNTLINGLCRTGHT  182 (595)
Q Consensus       103 ~~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~  182 (595)
                      ++...-.|++..++.-..   +.........-..+.++|...|+++..         ....|....+..+.. |...+  
T Consensus        20 ikn~fy~G~yq~~i~e~~---~~~~~~~~~~~~~~~Rs~iAlg~~~~~---------~~~~~~~~a~~~la~-~~~~~--   84 (310)
T 3mv2_B           20 IKQNYYTGNFVQCLQEIE---KFSKVTDNTLLFYKAKTLLALGQYQSQ---------DPTSKLGKVLDLYVQ-FLDTK--   84 (310)
T ss_dssp             HHHHHTTTCHHHHTHHHH---TSSCCCCHHHHHHHHHHHHHTTCCCCC---------CSSSTTHHHHHHHHH-HHTTT--
T ss_pred             HHHHHHhhHHHHHHHHHH---hcCccchHHHHHHHHHHHHHcCCCccC---------CCCCHHHHHHHHHHH-Hhccc--
Confidence            334455677777776332   222122223333445666666666531         111223223332222 22221  


Q ss_pred             hHHHHHHHHHHhcCCCCCccccCcHHHHHHHHHHHHHcCCHhHHHHHHHHHhhCCC-CCCHhHHHHHHHHHHhcCCHHHH
Q 040027          183 MIALNLFEEMANGNGEIGVVCKPNTVTYSTIIDGLCKEGFVDKAKALFLQMKDENI-NPDVVTYNSLIHGLCHANDWNEA  261 (595)
Q Consensus       183 ~~A~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~-~~~~~~~~~ll~~~~~~~~~~~A  261 (595)
                        |+..|++....+       +++..++..+..++...|++++|++++.+....+. .-+...+..++..+.+.|+.+.|
T Consensus        85 --a~~~l~~l~~~~-------~~~~~~~~~la~i~~~~g~~eeAL~~l~~~i~~~~~~~~lea~~l~vqi~L~~~r~d~A  155 (310)
T 3mv2_B           85 --NIEELENLLKDK-------QNSPYELYLLATAQAILGDLDKSLETCVEGIDNDEAEGTTELLLLAIEVALLNNNVSTA  155 (310)
T ss_dssp             --CCHHHHHTTTTS-------CCCHHHHHHHHHHHHHHTCHHHHHHHHHHHHTSSCSTTHHHHHHHHHHHHHHTTCHHHH
T ss_pred             --HHHHHHHHHhcC-------CCCcHHHHHHHHHHHHcCCHHHHHHHHHHHhccCCCcCcHHHHHHHHHHHHHCCCHHHH
Confidence              566666665542       23444455666777777777777777777655432 12455666667777777777777


Q ss_pred             HHHHHHHHHCCCCC-----CHhhHHHHHHH--HHhcC--ChHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHhcCCHHHHH
Q 040027          262 KRLFIEMMDQGVQP-----SVVTFNVIMDE--LCKNR--KMDEASRLLDLMVQRGVRPNACTYNTLMDGFCLMGKINRAE  332 (595)
Q Consensus       262 ~~~~~~~~~~~~~~-----~~~~~~~l~~~--~~~~g--~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~  332 (595)
                      .+.+++|.+.  .|     +..+...++.+  ....|  ++.+|..+|+++.+.  .|+..+...++.++.+.|++++|.
T Consensus       156 ~k~l~~~~~~--~~d~~~~~d~~l~~Laea~v~l~~g~~~~q~A~~~f~El~~~--~p~~~~~~lLln~~~~~g~~~eAe  231 (310)
T 3mv2_B          156 STIFDNYTNA--IEDTVSGDNEMILNLAESYIKFATNKETATSNFYYYEELSQT--FPTWKTQLGLLNLHLQQRNIAEAQ  231 (310)
T ss_dssp             HHHHHHHHHH--SCHHHHHHHHHHHHHHHHHHHHHHTCSTTTHHHHHHHHHHTT--SCSHHHHHHHHHHHHHHTCHHHHH
T ss_pred             HHHHHHHHhc--CccccccchHHHHHHHHHHHHHHhCCccHHHHHHHHHHHHHh--CCCcccHHHHHHHHHHcCCHHHHH
Confidence            7777777653  34     23444444444  22223  677777777776654  233222233334667777777777


Q ss_pred             HHHHHHHhcC---------CCCCHHHHHHHHHHHHhCCCHHHHHHHHHHHHHC
Q 040027          333 ELFGSMESMG---------CKHDDVSYNILINGYCKNKEVEEALSLYREMVSK  376 (595)
Q Consensus       333 ~~~~~~~~~~---------~~~~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~~  376 (595)
                      ..++.+.+..         -+.++.++..++......|+  +|.++++++.+.
T Consensus       232 ~~L~~l~~~~p~~~~k~~~~p~~~~~LaN~i~l~~~lgk--~a~~l~~qL~~~  282 (310)
T 3mv2_B          232 GIVELLLSDYYSVEQKENAVLYKPTFLANQITLALMQGL--DTEDLTNQLVKL  282 (310)
T ss_dssp             HHHHHHHSHHHHTTTCHHHHSSHHHHHHHHHHHHHHTTC--TTHHHHHHHHHT
T ss_pred             HHHHHHHHhcccccccccCCCCCHHHHHHHHHHHHHhCh--HHHHHHHHHHHh
Confidence            7777654320         03345555555555555565  666777777665

>3qky_A Outer membrane assembly lipoprotein YFIO; membrane protein; 2.15A {Rhodothermus marinus}

Probab=99.16  E-value=1.7e-09  Score=98.64  Aligned_cols=82  Identities=7%  Similarity=-0.015  Sum_probs=45.6

Q ss_pred             HHHHHHHHhcCChhHHHHHHHHHHHcCCCC--CHHHHHHHHHHHHHc----------CChhHHHHHHHHHHHCCCCCC--
Q 040027          491 NIMIQGLCNDGQMDKARDLFLDMEENAAAP--DVITFDMLIHGFIRI----------NEPSKVNELLHKMKEKKVMPD--  556 (595)
Q Consensus       491 ~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~--~~~~~~~l~~~~~~~----------g~~~~A~~~~~~~~~~~~~p~--  556 (595)
                      ..++..|...|++++|+..|+++++.....  ....+..++.+|...          |++++|...++++.+.  .|+  
T Consensus       152 ~~la~~~~~~g~~~~A~~~~~~~l~~~p~~~~~~~a~~~l~~~~~~~g~~~~~~~~~~~~~~A~~~~~~~~~~--~p~~~  229 (261)
T 3qky_A          152 YEAARLYERRELYEAAAVTYEAVFDAYPDTPWADDALVGAMRAYIAYAEQSVRARQPERYRRAVELYERLLQI--FPDSP  229 (261)
T ss_dssp             HHHHHHHHHTTCHHHHHHHHHHHHHHCTTSTTHHHHHHHHHHHHHHHHHTSCGGGHHHHHHHHHHHHHHHHHH--CTTCT
T ss_pred             HHHHHHHHHccCHHHHHHHHHHHHHHCCCCchHHHHHHHHHHHHHHhcccchhhcccchHHHHHHHHHHHHHH--CCCCh
Confidence            445566666666666666666666542110  234555566666554          6666677777666653  233  


Q ss_pred             --HHHHHHHHHHHHhcCccc
Q 040027          557 --ASIVSIVVDLLVKNEISL  574 (595)
Q Consensus       557 --~~~~~~l~~~~~~~g~~~  574 (595)
                        ......+..++.+.|+++
T Consensus       230 ~~~~a~~~l~~~~~~~~~~~  249 (261)
T 3qky_A          230 LLRTAEELYTRARQRLTELE  249 (261)
T ss_dssp             HHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHhh
Confidence              234445555555555555

>4ga2_A E3 SUMO-protein ligase ranbp2; TPR motif, nuclear pore complex component nucleocytoplasmic transport, transport protein; 0.95A {Pan troglodytes} PDB: 4ga0_A 4ga1_A*

Probab=99.14  E-value=3.6e-10  Score=93.02  Aligned_cols=145  Identities=9%  Similarity=-0.072  Sum_probs=117.4

Q ss_pred             cccccCCCChHHHHHHHHHHHHhCCCCCCHhhHHHHHHHHHcCCCchhHHhhCCCCCCHHHHHHHHHHHHhcCChhHHHH
Q 040027           38 REGDINVITPNEAFCIFDYMLRMHPSPPPVSSFNILLASLAKNKHYDTRLNATGLFPNLYTYNILINCFCKIGRVSLGFI  117 (595)
Q Consensus        38 ~~~~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~  117 (595)
                      +..+...|++++|++.|..++..+|.                               ++..+..+...|.+.|++++|+.
T Consensus         4 G~~~~~~~~~e~ai~~~~~a~~~~p~-------------------------------~~~~~~~la~~y~~~~~~~~A~~   52 (150)
T 4ga2_A            4 GSMRRSKADVERYIASVQGSTPSPRQ-------------------------------KSIKGFYFAKLYYEAKEYDLAKK   52 (150)
T ss_dssp             ---CCCHHHHHHHHHHHHHHSCSHHH-------------------------------HHTTHHHHHHHHHHTTCHHHHHH
T ss_pred             HHHHHHcChHHHHHHHHHHhcccCcc-------------------------------cHHHHHHHHHHHHHcCCHHHHHH
Confidence            34556779999999999999777665                               33345567788899999999999


Q ss_pred             HHHHHHhCCCCCCHHHHHHHHHHHHhcCCHhHHHHHHHHHHhcCCCCCHhhHHHHHHHHHhcCChhHHHHH-HHHHHhcC
Q 040027          118 AFGRILRSCFTPNAATFNSLIKGLHAESRIMEAAALFTKLKAFGCEPNVITYNTLINGLCRTGHTMIALNL-FEEMANGN  196 (595)
Q Consensus       118 ~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~-~~~~~~~~  196 (595)
                      .|+++++.. +.+..+|..+..+|...|++++|+..|++..+.. +-+..++..+...|...|++++|.+. ++++.+.+
T Consensus        53 ~~~~al~~~-p~~~~a~~~lg~~~~~~~~~~~A~~~~~~al~~~-p~~~~~~~~la~~~~~~~~~~~aa~~~~~~al~l~  130 (150)
T 4ga2_A           53 YICTYINVQ-ERDPKAHRFLGLLYELEENTDKAVECYRRSVELN-PTQKDLVLKIAELLCKNDVTDGRAKYWVERAAKLF  130 (150)
T ss_dssp             HHHHHHHHC-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHHCSSSSHHHHHHHHHHHHS
T ss_pred             HHHHHHHhC-CCCHHHHHHHHHHHHHcCchHHHHHHHHHHHHhC-CCCHHHHHHHHHHHHHcCChHHHHHHHHHHHHHhC
Confidence            999999885 5578899999999999999999999999999885 33788899999999999999877665 58888875


Q ss_pred             CCCCccccCcHHHHHHHHHHHHHcCC
Q 040027          197 GEIGVVCKPNTVTYSTIIDGLCKEGF  222 (595)
Q Consensus       197 ~~~~~~~~~~~~~~~~l~~~~~~~g~  222 (595)
                             |.++.+|......+...|+
T Consensus       131 -------P~~~~~~~l~~~ll~~~G~  149 (150)
T 4ga2_A          131 -------PGSPAVYKLKEQLLDCEGE  149 (150)
T ss_dssp             -------TTCHHHHHHHHHHHHTCCC
T ss_pred             -------cCCHHHHHHHHHHHHHhCc
Confidence                   5667888887777777764

>3rjv_A Putative SEL1 repeat protein; alpha-alpha superhelix, structural genomics, joint center FO structural genomics, JCSG; HET: MSE; 1.65A {Klebsiella pneumoniae subsp}

Probab=99.14  E-value=7.2e-09  Score=90.88  Aligned_cols=176  Identities=13%  Similarity=-0.032  Sum_probs=111.2

Q ss_pred             HHHHHHHHHHhCCCCCCHHHHHHHHHHHHhcCCHhHHHHHHHHHHhcCCCCCHhhHHHHHHHHHhcC----ChhHHHHHH
Q 040027          114 LGFIAFGRILRSCFTPNAATFNSLIKGLHAESRIMEAAALFTKLKAFGCEPNVITYNTLINGLCRTG----HTMIALNLF  189 (595)
Q Consensus       114 ~A~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g----~~~~A~~~~  189 (595)
                      +|+..|+++.+.|   ++.++..+...|...+++++|+++|++..+.|   +...+..+...|.. +    ++++|++.|
T Consensus         4 eA~~~~~~aa~~g---~~~a~~~lg~~~~~~~~~~~A~~~~~~a~~~g---~~~a~~~lg~~y~~-~g~~~~~~~A~~~~   76 (212)
T 3rjv_A            4 EPGSQYQQQAEAG---DRRAQYYLADTWVSSGDYQKAEYWAQKAAAQG---DGDALALLAQLKIR-NPQQADYPQARQLA   76 (212)
T ss_dssp             CTTHHHHHHHHTT---CHHHHHHHHHHHHHHTCHHHHHHHHHHHHHTT---CHHHHHHHHHHTTS-STTSCCHHHHHHHH
T ss_pred             hHHHHHHHHHHCC---CHHHHHHHHHHHhcCCCHHHHHHHHHHHHHcC---CHHHHHHHHHHHHc-CCCCCCHHHHHHHH
Confidence            4566677766653   56666777777777777777777777777654   55666666666666 5    677777777


Q ss_pred             HHHHhcCCCCCccccCcHHHHHHHHHHHHH----cCCHhHHHHHHHHHhhCCCC-CCHhHHHHHHHHHHh----cCCHHH
Q 040027          190 EEMANGNGEIGVVCKPNTVTYSTIIDGLCK----EGFVDKAKALFLQMKDENIN-PDVVTYNSLIHGLCH----ANDWNE  260 (595)
Q Consensus       190 ~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~----~g~~~~A~~~~~~~~~~~~~-~~~~~~~~ll~~~~~----~~~~~~  260 (595)
                      ++....+         ++.++..|...|..    .+++++|.++|++..+.+.. .+...+..|...|..    .+++++
T Consensus        77 ~~A~~~g---------~~~a~~~Lg~~y~~g~g~~~d~~~A~~~~~~A~~~~~~~~~~~a~~~Lg~~y~~g~g~~~d~~~  147 (212)
T 3rjv_A           77 EKAVEAG---------SKSGEIVLARVLVNRQAGATDVAHAITLLQDAARDSESDAAVDAQMLLGLIYASGVHGPEDDVK  147 (212)
T ss_dssp             HHHHHTT---------CHHHHHHHHHHHTCGGGSSCCHHHHHHHHHHHTSSTTSHHHHHHHHHHHHHHHHTSSSSCCHHH
T ss_pred             HHHHHCC---------CHHHHHHHHHHHHcCCCCccCHHHHHHHHHHHHHcCCCcchHHHHHHHHHHHHcCCCCCCCHHH
Confidence            7776543         45566666666665    66777777777777665421 015566666666666    666777


Q ss_pred             HHHHHHHHHHCCCCCCHhhHHHHHHHHHhc-C-----ChHHHHHHHHHHHHCC
Q 040027          261 AKRLFIEMMDQGVQPSVVTFNVIMDELCKN-R-----KMDEASRLLDLMVQRG  307 (595)
Q Consensus       261 A~~~~~~~~~~~~~~~~~~~~~l~~~~~~~-g-----~~~~a~~~~~~~~~~~  307 (595)
                      |..+|++..+.  ..+...+..+..+|... |     ++++|..+|+...+.|
T Consensus       148 A~~~~~~A~~~--~~~~~a~~~Lg~~y~~g~gg~~~~d~~~A~~~~~~A~~~g  198 (212)
T 3rjv_A          148 ASEYFKGSSSL--SRTGYAEYWAGMMFQQGEKGFIEPNKQKALHWLNVSCLEG  198 (212)
T ss_dssp             HHHHHHHHHHT--SCTTHHHHHHHHHHHHCBTTTBCCCHHHHHHHHHHHHHHT
T ss_pred             HHHHHHHHHHc--CCCHHHHHHHHHHHHcCCCCCCCCCHHHHHHHHHHHHHcC
Confidence            77777776664  12334455555555432 2     6666666666666654

>2fo7_A Synthetic consensus TPR protein; tetratricopeptide repeat, consensus protein, superhelix, de novo protein; 2.30A {Synthetic} SCOP: k.38.1.1 PDB: 2hyz_A

Probab=99.12  E-value=3.4e-09  Score=85.23  Aligned_cols=130  Identities=15%  Similarity=0.139  Sum_probs=92.9

Q ss_pred             HHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCcCHHHHHHHHHHHHhcCChHHHHHHHHhcccCCCCCCHHHHHHHHHHHH
Q 040027          419 TYTTFIDGLCKNGYIIEAVELFRTLRILKCELDIQAYNCLIDGLCKSGRLKFAWELFCSLPHGVLVPNVVTYNIMIQGLC  498 (595)
Q Consensus       419 ~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~p~~~~~~~l~~~~~  498 (595)
                      .+..+...+...|++++|..+++++.+.. +.+...+..++..+...|++++|...++++.... +.+...+..++..+.
T Consensus         3 ~~~~l~~~~~~~~~~~~A~~~~~~~~~~~-~~~~~~~~~~a~~~~~~~~~~~A~~~~~~~~~~~-~~~~~~~~~l~~~~~   80 (136)
T 2fo7_A            3 AWYNLGNAYYKQGDYDEAIEYYQKALELD-PRSAEAWYNLGNAYYKQGDYDEAIEYYQKALELD-PRSAEAWYNLGNAYY   80 (136)
T ss_dssp             HHHHHHHHHHHHTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHcCcHHHHHHHHHHHHHcC-CcchhHHHHHHHHHHHhcCHHHHHHHHHHHHHHC-CCchHHHHHHHHHHH
Confidence            34556666777777777777777777654 4466677777777777777777777777776631 224566777777777


Q ss_pred             hcCChhHHHHHHHHHHHcCCCCCHHHHHHHHHHHHHcCChhHHHHHHHHHHHC
Q 040027          499 NDGQMDKARDLFLDMEENAAAPDVITFDMLIHGFIRINEPSKVNELLHKMKEK  551 (595)
Q Consensus       499 ~~g~~~~A~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~  551 (595)
                      ..|++++|.+.++++.+.. +.+...+..++.++...|++++|...++++.+.
T Consensus        81 ~~~~~~~A~~~~~~~~~~~-~~~~~~~~~la~~~~~~~~~~~A~~~~~~~~~~  132 (136)
T 2fo7_A           81 KQGDYDEAIEYYQKALELD-PRSAEAWYNLGNAYYKQGDYDEAIEYYQKALEL  132 (136)
T ss_dssp             TTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHTTTCHHHHHHHHHHHHHH
T ss_pred             HhcCHHHHHHHHHHHHHhC-CCChHHHHHHHHHHHHHccHHHHHHHHHHHHcc
Confidence            8888888888888877764 445667777778888888888888888877753

>2fo7_A Synthetic consensus TPR protein; tetratricopeptide repeat, consensus protein, superhelix, de novo protein; 2.30A {Synthetic} SCOP: k.38.1.1 PDB: 2hyz_A

Probab=99.11  E-value=5.3e-09  Score=84.11  Aligned_cols=129  Identities=14%  Similarity=0.171  Sum_probs=78.0

Q ss_pred             HHHHHHHHHHhcCChhHHHHHHHHHHhCCCCCCHHHHHHHHHHHHhcCCHhHHHHHHHHHHhcCCCCCHhhHHHHHHHHH
Q 040027           98 TYNILINCFCKIGRVSLGFIAFGRILRSCFTPNAATFNSLIKGLHAESRIMEAAALFTKLKAFGCEPNVITYNTLINGLC  177 (595)
Q Consensus        98 ~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~~l~~~~~  177 (595)
                      .|..++..+...|++++|..+++++.+.. +.+...+..+...+...|++++|...++++...+ +.+...+..++..+.
T Consensus         3 ~~~~l~~~~~~~~~~~~A~~~~~~~~~~~-~~~~~~~~~~a~~~~~~~~~~~A~~~~~~~~~~~-~~~~~~~~~l~~~~~   80 (136)
T 2fo7_A            3 AWYNLGNAYYKQGDYDEAIEYYQKALELD-PRSAEAWYNLGNAYYKQGDYDEAIEYYQKALELD-PRSAEAWYNLGNAYY   80 (136)
T ss_dssp             HHHHHHHHHHHHTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHcCcHHHHHHHHHHHHHcC-CcchhHHHHHHHHHHHhcCHHHHHHHHHHHHHHC-CCchHHHHHHHHHHH
Confidence            45556666666667777777766666553 3345556666666666666666666666666553 224555566666666


Q ss_pred             hcCChhHHHHHHHHHHhcCCCCCccccCcHHHHHHHHHHHHHcCCHhHHHHHHHHHhh
Q 040027          178 RTGHTMIALNLFEEMANGNGEIGVVCKPNTVTYSTIIDGLCKEGFVDKAKALFLQMKD  235 (595)
Q Consensus       178 ~~g~~~~A~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~  235 (595)
                      ..|++++|.+.++++....       +.+...+..++.++...|++++|...++++..
T Consensus        81 ~~~~~~~A~~~~~~~~~~~-------~~~~~~~~~la~~~~~~~~~~~A~~~~~~~~~  131 (136)
T 2fo7_A           81 KQGDYDEAIEYYQKALELD-------PRSAEAWYNLGNAYYKQGDYDEAIEYYQKALE  131 (136)
T ss_dssp             TTTCHHHHHHHHHHHHHHC-------TTCHHHHHHHHHHHHTTTCHHHHHHHHHHHHH
T ss_pred             HhcCHHHHHHHHHHHHHhC-------CCChHHHHHHHHHHHHHccHHHHHHHHHHHHc
Confidence            6666666666666666543       33455555566666666666666666665554

>2r5s_A Uncharacterized protein VP0806; APC090868.1, vibrio parahaemolyticus RIMD 22 structural genomics, PSI-2, protein structure initiative; HET: MES; 2.14A {Vibrio parahaemolyticus}

Probab=99.09  E-value=1.2e-09  Score=92.83  Aligned_cols=162  Identities=10%  Similarity=0.014  Sum_probs=103.6

Q ss_pred             HHHHHHHHHHhcCChhHHHHHHHHHHhCCCCCCHHHHHHHHHHHHhcCCHhHHHHHHHHHHhcCCCCCHhhHHHHHHH-H
Q 040027           98 TYNILINCFCKIGRVSLGFIAFGRILRSCFTPNAATFNSLIKGLHAESRIMEAAALFTKLKAFGCEPNVITYNTLING-L  176 (595)
Q Consensus        98 ~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~~l~~~-~  176 (595)
                      .+......+.+.|++++|+..|+++++.. +.+...+..+...+...|++++|+..|+++....  |+...+..+... +
T Consensus         8 ~~~~~a~~~~~~g~~~~A~~~~~~al~~~-P~~~~a~~~la~~~~~~g~~~~A~~~~~~a~~~~--p~~~~~~~~~~~~~   84 (176)
T 2r5s_A            8 QLLKQVSELLQQGEHAQALNVIQTLSDEL-QSRGDVKLAKADCLLETKQFELAQELLATIPLEY--QDNSYKSLIAKLEL   84 (176)
T ss_dssp             THHHHHHHHHHTTCHHHHHHHHHTSCHHH-HTSHHHHHHHHHHHHHTTCHHHHHHHHTTCCGGG--CCHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHcCCHHHHHHHHHHHHHHC-CCcHHHHHHHHHHHHHCCCHHHHHHHHHHhhhcc--CChHHHHHHHHHHH
Confidence            34456667777788888888887777653 4456677777777777888888888777776653  243333222211 1


Q ss_pred             HhcCChhHHHHHHHHHHhcCCCCCccccCcHHHHHHHHHHHHHcCCHhHHHHHHHHHhhCCCCC-CHhHHHHHHHHHHhc
Q 040027          177 CRTGHTMIALNLFEEMANGNGEIGVVCKPNTVTYSTIIDGLCKEGFVDKAKALFLQMKDENINP-DVVTYNSLIHGLCHA  255 (595)
Q Consensus       177 ~~~g~~~~A~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~-~~~~~~~ll~~~~~~  255 (595)
                      ...+...+|+..|++....+       |.+...+..+..++...|++++|...|+++.+....+ +...+..+...+...
T Consensus        85 ~~~~~~~~a~~~~~~al~~~-------P~~~~~~~~la~~~~~~g~~~~A~~~~~~~l~~~p~~~~~~a~~~l~~~~~~~  157 (176)
T 2r5s_A           85 HQQAAESPELKRLEQELAAN-------PDNFELACELAVQYNQVGRDEEALELLWNILKVNLGAQDGEVKKTFMDILSAL  157 (176)
T ss_dssp             HHHHTSCHHHHHHHHHHHHS-------TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHTTCTTTTTTHHHHHHHHHHHHH
T ss_pred             HhhcccchHHHHHHHHHHhC-------CCCHHHHHHHHHHHHHcccHHHHHHHHHHHHHhCcccChHHHHHHHHHHHHHh
Confidence            22233344677777777654       4456777777777777777777777777776654222 244666677777777


Q ss_pred             CCHHHHHHHHHHHH
Q 040027          256 NDWNEAKRLFIEMM  269 (595)
Q Consensus       256 ~~~~~A~~~~~~~~  269 (595)
                      |+.++|...|++.+
T Consensus       158 g~~~~A~~~y~~al  171 (176)
T 2r5s_A          158 GQGNAIASKYRRQL  171 (176)
T ss_dssp             CSSCHHHHHHHHHH
T ss_pred             CCCCcHHHHHHHHH
Confidence            77777777776654

>3rjv_A Putative SEL1 repeat protein; alpha-alpha superhelix, structural genomics, joint center FO structural genomics, JCSG; HET: MSE; 1.65A {Klebsiella pneumoniae subsp}

Probab=99.09  E-value=1.5e-08  Score=88.79  Aligned_cols=173  Identities=12%  Similarity=-0.050  Sum_probs=108.6

Q ss_pred             HHHHHHHHHHCCCCCCHHHHHHHHHHHHccCCHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHhcC----CHHHHHHHHH
Q 040027          366 ALSLYREMVSKGIKPTVVTYNTLFLGLFEIHQVEHALKLFDEMQRDGVAADTRTYTTFIDGLCKNG----YIIEAVELFR  441 (595)
Q Consensus       366 A~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g----~~~~A~~~~~  441 (595)
                      |+..|++..+.|   +...+..+...+...+++++|...|++..+.+   +...+..+...|.. +    ++++|..+|+
T Consensus         5 A~~~~~~aa~~g---~~~a~~~lg~~~~~~~~~~~A~~~~~~a~~~g---~~~a~~~lg~~y~~-~g~~~~~~~A~~~~~   77 (212)
T 3rjv_A            5 PGSQYQQQAEAG---DRRAQYYLADTWVSSGDYQKAEYWAQKAAAQG---DGDALALLAQLKIR-NPQQADYPQARQLAE   77 (212)
T ss_dssp             TTHHHHHHHHTT---CHHHHHHHHHHHHHHTCHHHHHHHHHHHHHTT---CHHHHHHHHHHTTS-STTSCCHHHHHHHHH
T ss_pred             HHHHHHHHHHCC---CHHHHHHHHHHHhcCCCHHHHHHHHHHHHHcC---CHHHHHHHHHHHHc-CCCCCCHHHHHHHHH
Confidence            445555555542   44555555555656666666666666665543   34455555555555 4    6777777777


Q ss_pred             HHHHcCCCcCHHHHHHHHHHHHh----cCChHHHHHHHHhcccCCCCCC---HHHHHHHHHHHHh----cCChhHHHHHH
Q 040027          442 TLRILKCELDIQAYNCLIDGLCK----SGRLKFAWELFCSLPHGVLVPN---VVTYNIMIQGLCN----DGQMDKARDLF  510 (595)
Q Consensus       442 ~~~~~~~~~~~~~~~~l~~~~~~----~g~~~~A~~~~~~~~~~~~~p~---~~~~~~l~~~~~~----~g~~~~A~~~~  510 (595)
                      +..+.+   ++..+..+...|..    .+++++|+..|++..+.  .|+   ...+..|...|..    .+++++|+..|
T Consensus        78 ~A~~~g---~~~a~~~Lg~~y~~g~g~~~d~~~A~~~~~~A~~~--~~~~~~~~a~~~Lg~~y~~g~g~~~d~~~A~~~~  152 (212)
T 3rjv_A           78 KAVEAG---SKSGEIVLARVLVNRQAGATDVAHAITLLQDAARD--SESDAAVDAQMLLGLIYASGVHGPEDDVKASEYF  152 (212)
T ss_dssp             HHHHTT---CHHHHHHHHHHHTCGGGSSCCHHHHHHHHHHHTSS--TTSHHHHHHHHHHHHHHHHTSSSSCCHHHHHHHH
T ss_pred             HHHHCC---CHHHHHHHHHHHHcCCCCccCHHHHHHHHHHHHHc--CCCcchHHHHHHHHHHHHcCCCCCCCHHHHHHHH
Confidence            766543   55666666666665    66777777777777763  232   5666677777776    66777777777


Q ss_pred             HHHHHcCCCCCHHHHHHHHHHHHHc-C-----ChhHHHHHHHHHHHCC
Q 040027          511 LDMEENAAAPDVITFDMLIHGFIRI-N-----EPSKVNELLHKMKEKK  552 (595)
Q Consensus       511 ~~~~~~~~~~~~~~~~~l~~~~~~~-g-----~~~~A~~~~~~~~~~~  552 (595)
                      ++..+.  +.+...+..+...|... |     ++++|..++++..+.|
T Consensus       153 ~~A~~~--~~~~~a~~~Lg~~y~~g~gg~~~~d~~~A~~~~~~A~~~g  198 (212)
T 3rjv_A          153 KGSSSL--SRTGYAEYWAGMMFQQGEKGFIEPNKQKALHWLNVSCLEG  198 (212)
T ss_dssp             HHHHHT--SCTTHHHHHHHHHHHHCBTTTBCCCHHHHHHHHHHHHHHT
T ss_pred             HHHHHc--CCCHHHHHHHHHHHHcCCCCCCCCCHHHHHHHHHHHHHcC
Confidence            777775  23444566666666543 2     6777888877777765

>2yhc_A BAMD, UPF0169 lipoprotein YFIO; essential BAM component, membrane protein; 1.80A {Escherichia coli} PDB: 3tgo_A 3q5m_A

Probab=99.09  E-value=1.3e-08  Score=90.26  Aligned_cols=187  Identities=7%  Similarity=-0.030  Sum_probs=130.2

Q ss_pred             CHHHHHHHHHHHHhcCChhHHHHHHHHHHhCCCCC--CHHHHHHHHHHHHhcCCHhHHHHHHHHHHhcCCCCCH---hhH
Q 040027           95 NLYTYNILINCFCKIGRVSLGFIAFGRILRSCFTP--NAATFNSLIKGLHAESRIMEAAALFTKLKAFGCEPNV---ITY  169 (595)
Q Consensus        95 ~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~--~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~~~---~~~  169 (595)
                      ++..+..++..+.+.|++++|+..|+++++..+..  ...++..+..++.+.|++++|+..|+++.+.... +.   .++
T Consensus         3 ~~~~~~~~a~~~~~~g~~~~A~~~~~~~~~~~p~~~~~~~a~~~lg~~~~~~~~~~~A~~~~~~~l~~~P~-~~~~~~a~   81 (225)
T 2yhc_A            3 PPNEIYATAQQKLQDGNWRQAITQLEALDNRYPFGPYSQQVQLDLIYAYYKNADLPLAQAAIDRFIRLNPT-HPNIDYVM   81 (225)
T ss_dssp             CHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHCTTSTTHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTT-CTTHHHHH
T ss_pred             CHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCCCChHHHHHHHHHHHHHHhcCCHHHHHHHHHHHHHHCcC-CCcHHHHH
Confidence            45667778888999999999999999999874221  1357888899999999999999999999987432 22   245


Q ss_pred             HHHHHHHHh------------------cCChhHHHHHHHHHHhcCCCCCccccCcHHHHHHHHHHHHHcCCHhHHHHHHH
Q 040027          170 NTLINGLCR------------------TGHTMIALNLFEEMANGNGEIGVVCKPNTVTYSTIIDGLCKEGFVDKAKALFL  231 (595)
Q Consensus       170 ~~l~~~~~~------------------~g~~~~A~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~  231 (595)
                      ..+..++..                  .|++++|+..|+++.+..       |.+..++.......          .+..
T Consensus        82 ~~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~A~~~~~~~l~~~-------P~~~~a~~a~~~l~----------~~~~  144 (225)
T 2yhc_A           82 YMRGLTNMALDDSALQGFFGVDRSDRDPQQARAAFSDFSKLVRGY-------PNSQYTTDATKRLV----------FLKD  144 (225)
T ss_dssp             HHHHHHHHHHHC--------------CCHHHHHHHHHHHHHHTTC-------TTCTTHHHHHHHHH----------HHHH
T ss_pred             HHHHHHHHhhhhhhhhhhhccchhhcCcHHHHHHHHHHHHHHHHC-------cCChhHHHHHHHHH----------HHHH
Confidence            555555553                  678999999999999875       33333333221110          0111


Q ss_pred             HHhhCCCCCCHhHHHHHHHHHHhcCCHHHHHHHHHHHHHCCCCC--CHhhHHHHHHHHHhcCChHHHHHHHHHHHHCC
Q 040027          232 QMKDENINPDVVTYNSLIHGLCHANDWNEAKRLFIEMMDQGVQP--SVVTFNVIMDELCKNRKMDEASRLLDLMVQRG  307 (595)
Q Consensus       232 ~~~~~~~~~~~~~~~~ll~~~~~~~~~~~A~~~~~~~~~~~~~~--~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~  307 (595)
                      .+        ......+...|.+.|++++|+..|+++++.....  ....+..+..++.+.|++++|.+.++.+...+
T Consensus       145 ~~--------~~~~~~~a~~~~~~~~~~~A~~~~~~~l~~~p~~~~~~~a~~~l~~~~~~~g~~~~A~~~~~~l~~~~  214 (225)
T 2yhc_A          145 RL--------AKYEYSVAEYYTERGAWVAVVNRVEGMLRDYPDTQATRDALPLMENAYRQMQMNAQAEKVAKIIAANS  214 (225)
T ss_dssp             HH--------HHHHHHHHHHHHHHTCHHHHHHHHHHHHHHSTTSHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHCC
T ss_pred             HH--------HHHHHHHHHHHHHcCcHHHHHHHHHHHHHHCcCCCccHHHHHHHHHHHHHcCCcHHHHHHHHHHHhhC
Confidence            11        1112345677888888888888888887752111  12457778888888888888888888887764

>2pzi_A Probable serine/threonine-protein kinase PKNG; ATP-recognition, kinase-INH complex, rubredoxin fold, TPR domain, transferase; HET: AXX; 2.40A {Mycobacterium tuberculosis}

Probab=99.09  E-value=2.3e-09  Score=111.76  Aligned_cols=173  Identities=9%  Similarity=-0.060  Sum_probs=144.8

Q ss_pred             HhcCCHHHHHHHHHHHH--------hcCCCCCHHHHHHHHHHHHhCCCHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHc
Q 040027          323 CLMGKINRAEELFGSME--------SMGCKHDDVSYNILINGYCKNKEVEEALSLYREMVSKGIKPTVVTYNTLFLGLFE  394 (595)
Q Consensus       323 ~~~~~~~~a~~~~~~~~--------~~~~~~~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~~l~~~~~~  394 (595)
                      ...|++++|++.++++.        +.. +.+...+..+..++...|++++|+..|+++++.... +...+..+..++..
T Consensus       402 ~~~~~~~~A~~~~~~al~~~~~~~~~~~-p~~~~~~~~~a~~~~~~g~~~~A~~~~~~al~~~p~-~~~a~~~lg~~~~~  479 (681)
T 2pzi_A          402 TVLSQPVQTLDSLRAARHGALDADGVDF-SESVELPLMEVRALLDLGDVAKATRKLDDLAERVGW-RWRLVWYRAVAELL  479 (681)
T ss_dssp             TTTCCHHHHHHHHHHHHTC-------CC-TTCSHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHCC-CHHHHHHHHHHHHH
T ss_pred             ccccCHHHHHHHHHHhhhhccccccccc-ccchhHHHHHHHHHHhcCCHHHHHHHHHHHhccCcc-hHHHHHHHHHHHHH
Confidence            67899999999999988        442 456678888999999999999999999999886444 67788889999999


Q ss_pred             cCCHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCcCHHHHHHHHHHHHhcCChHHHHHH
Q 040027          395 IHQVEHALKLFDEMQRDGVAADTRTYTTFIDGLCKNGYIIEAVELFRTLRILKCELDIQAYNCLIDGLCKSGRLKFAWEL  474 (595)
Q Consensus       395 ~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~  474 (595)
                      .|++++|...|+++++.. +.+...+..+..++.+.|++++ ...|+++++.+ +.+...+..+..++...|++++|+..
T Consensus       480 ~g~~~~A~~~~~~al~l~-P~~~~~~~~lg~~~~~~g~~~~-~~~~~~al~~~-P~~~~a~~~lg~~~~~~g~~~~A~~~  556 (681)
T 2pzi_A          480 TGDYDSATKHFTEVLDTF-PGELAPKLALAATAELAGNTDE-HKFYQTVWSTN-DGVISAAFGLARARSAEGDRVGAVRT  556 (681)
T ss_dssp             HTCHHHHHHHHHHHHHHS-TTCSHHHHHHHHHHHHHTCCCT-TCHHHHHHHHC-TTCHHHHHHHHHHHHHTTCHHHHHHH
T ss_pred             cCCHHHHHHHHHHHHHhC-CCChHHHHHHHHHHHHcCChHH-HHHHHHHHHhC-CchHHHHHHHHHHHHHcCCHHHHHHH
Confidence            999999999999998874 5567888889999999999999 99999999876 66888999999999999999999999


Q ss_pred             HHhcccCCCCCC-HHHHHHHHHHHHhcCC
Q 040027          475 FCSLPHGVLVPN-VVTYNIMIQGLCNDGQ  502 (595)
Q Consensus       475 ~~~~~~~~~~p~-~~~~~~l~~~~~~~g~  502 (595)
                      |+++.+  +.|+ ...+..+..++...++
T Consensus       557 ~~~al~--l~P~~~~a~~~~~~~~~~~~~  583 (681)
T 2pzi_A          557 LDEVPP--TSRHFTTARLTSAVTLLSGRS  583 (681)
T ss_dssp             HHTSCT--TSTTHHHHHHHHHHHTC----
T ss_pred             HHhhcc--cCcccHHHHHHHHHHHHccCC
Confidence            999988  5676 5677778888766555

>3dra_A Protein farnesyltransferase/geranylgeranyltransferase type-1 subunit alpha; geranylgeranyltrasferase, ggtase, ggtase-I, PGGT, prenyltransferase, farnesyltransferase; HET: B3P GRG; 1.80A {Candida albicans}

Probab=99.09  E-value=1.6e-07  Score=86.25  Aligned_cols=225  Identities=9%  Similarity=0.017  Sum_probs=163.0

Q ss_pred             HHHhcCC-hhHHHHHHHHHHhCCCCCCHHHHHHHHHHHHhcC--CHhHHHHHHHHHHhcCCCCCHhhHHHHHHHH----H
Q 040027          105 CFCKIGR-VSLGFIAFGRILRSCFTPNAATFNSLIKGLHAES--RIMEAAALFTKLKAFGCEPNVITYNTLINGL----C  177 (595)
Q Consensus       105 ~~~~~g~-~~~A~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g--~~~~A~~~~~~~~~~~~~~~~~~~~~l~~~~----~  177 (595)
                      +..+.|. .++|+.+++.++..+ +-+..+|+.--..+...|  +++++++.++.++.... -+..+|+.-...+    .
T Consensus        41 a~~~~~e~s~~aL~~t~~~L~~n-P~~~taWn~R~~~L~~l~~~~~~eeL~~~~~~L~~nP-k~y~aW~~R~~iL~~~~~  118 (306)
T 3dra_A           41 ALMKAEEYSERALHITELGINEL-ASHYTIWIYRFNILKNLPNRNLYDELDWCEEIALDNE-KNYQIWNYRQLIIGQIME  118 (306)
T ss_dssp             HHHHTTCCSHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHTCTTSCHHHHHHHHHHHHHHCT-TCCHHHHHHHHHHHHHHH
T ss_pred             HHHHcCCCCHHHHHHHHHHHHHC-cHHHHHHHHHHHHHHHcccccHHHHHHHHHHHHHHCc-ccHHHHHHHHHHHHHHHH
Confidence            3344454 468999999999986 557788988888888888  99999999999998753 3667777655555    4


Q ss_pred             hc---CChhHHHHHHHHHHhcCCCCCccccCcHHHHHHHHHHHHHcCCHh--HHHHHHHHHhhCCCCCCHhHHHHHHHHH
Q 040027          178 RT---GHTMIALNLFEEMANGNGEIGVVCKPNTVTYSTIIDGLCKEGFVD--KAKALFLQMKDENINPDVVTYNSLIHGL  252 (595)
Q Consensus       178 ~~---g~~~~A~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~--~A~~~~~~~~~~~~~~~~~~~~~ll~~~  252 (595)
                      ..   +++++++..++++.+.+       +.+..+|+.-.-++.+.|.++  ++.+.++++.+.+.. |...|+.-....
T Consensus       119 ~l~~~~~~~~EL~~~~~~l~~~-------pkny~aW~~R~~vl~~l~~~~~~~EL~~~~~~i~~d~~-N~sAW~~R~~ll  190 (306)
T 3dra_A          119 LNNNDFDPYREFDILEAMLSSD-------PKNHHVWSYRKWLVDTFDLHNDAKELSFVDKVIDTDLK-NNSAWSHRFFLL  190 (306)
T ss_dssp             HTTTCCCTHHHHHHHHHHHHHC-------TTCHHHHHHHHHHHHHTTCTTCHHHHHHHHHHHHHCTT-CHHHHHHHHHHH
T ss_pred             hccccCCHHHHHHHHHHHHHhC-------CCCHHHHHHHHHHHHHhcccChHHHHHHHHHHHHhCCC-CHHHHHHHHHHH
Confidence            45   78999999999999886       678888988888888888888  899999998887543 777887776666


Q ss_pred             HhcCC------HHHHHHHHHHHHHCCCCCCHhhHHHHHHHHHhcCChHH-HHHHHHHHHHCC--CCCCHHHHHHHHHHHH
Q 040027          253 CHAND------WNEAKRLFIEMMDQGVQPSVVTFNVIMDELCKNRKMDE-ASRLLDLMVQRG--VRPNACTYNTLMDGFC  323 (595)
Q Consensus       253 ~~~~~------~~~A~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~-a~~~~~~~~~~~--~~~~~~~~~~l~~~~~  323 (595)
                      ...+.      ++++++.+++++...+ -|...|+.....+.+.|+... +..+..++...+  -..+...+..++.+|.
T Consensus       191 ~~l~~~~~~~~~~eEl~~~~~aI~~~p-~n~SaW~y~~~ll~~~~~~~~~~~~~~~~~~~~~~~~~~s~~al~~la~~~~  269 (306)
T 3dra_A          191 FSKKHLATDNTIDEELNYVKDKIVKCP-QNPSTWNYLLGIHERFDRSITQLEEFSLQFVDLEKDQVTSSFALETLAKIYT  269 (306)
T ss_dssp             HSSGGGCCHHHHHHHHHHHHHHHHHCS-SCHHHHHHHHHHHHHTTCCGGGGHHHHHTTEEGGGTEESCHHHHHHHHHHHH
T ss_pred             HhccccchhhhHHHHHHHHHHHHHhCC-CCccHHHHHHHHHHhcCCChHHHHHHHHHHHhccCCCCCCHHHHHHHHHHHH
Confidence            66665      7777777777776533 366677777767766666333 444555544332  1235556666666666


Q ss_pred             hcCCHHHHHHHHHHHHh
Q 040027          324 LMGKINRAEELFGSMES  340 (595)
Q Consensus       324 ~~~~~~~a~~~~~~~~~  340 (595)
                      +.|+.++|.++++.+.+
T Consensus       270 ~~~~~~~A~~~~~~l~~  286 (306)
T 3dra_A          270 QQKKYNESRTVYDLLKS  286 (306)
T ss_dssp             HTTCHHHHHHHHHHHHH
T ss_pred             ccCCHHHHHHHHHHHHh
Confidence            66677777777766654

>3dra_A Protein farnesyltransferase/geranylgeranyltransferase type-1 subunit alpha; geranylgeranyltrasferase, ggtase, ggtase-I, PGGT, prenyltransferase, farnesyltransferase; HET: B3P GRG; 1.80A {Candida albicans}

Probab=99.07  E-value=2.6e-07  Score=84.80  Aligned_cols=217  Identities=8%  Similarity=0.007  Sum_probs=112.8

Q ss_pred             HHHHHHHHHHHHCCCCCCHHHHHHHHHHHHhcC--CHHHHHHHHHHHHhcCCCCCHHHHHHHHHHH----HhC---CCHH
Q 040027          294 DEASRLLDLMVQRGVRPNACTYNTLMDGFCLMG--KINRAEELFGSMESMGCKHDDVSYNILINGY----CKN---KEVE  364 (595)
Q Consensus       294 ~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~--~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~----~~~---~~~~  364 (595)
                      ++|+..++.++..+.. +..+++.-..++...+  ++++++..++.+...+ +.+..+|+.-...+    ...   ++++
T Consensus        50 ~~aL~~t~~~L~~nP~-~~taWn~R~~~L~~l~~~~~~eeL~~~~~~L~~n-Pk~y~aW~~R~~iL~~~~~~l~~~~~~~  127 (306)
T 3dra_A           50 ERALHITELGINELAS-HYTIWIYRFNILKNLPNRNLYDELDWCEEIALDN-EKNYQIWNYRQLIIGQIMELNNNDFDPY  127 (306)
T ss_dssp             HHHHHHHHHHHHHCTT-CHHHHHHHHHHHHTCTTSCHHHHHHHHHHHHHHC-TTCCHHHHHHHHHHHHHHHHTTTCCCTH
T ss_pred             HHHHHHHHHHHHHCcH-HHHHHHHHHHHHHHcccccHHHHHHHHHHHHHHC-cccHHHHHHHHHHHHHHHHhccccCCHH
Confidence            3555555555554222 3334444444444445  5555555555555443 23334444333333    333   4555


Q ss_pred             HHHHHHHHHHHCCCCCCHHHHHHHHHHHHccCCHH--HHHHHHHHHHHCCCCCCHHHHHHHHHHHHhcCC------HHHH
Q 040027          365 EALSLYREMVSKGIKPTVVTYNTLFLGLFEIHQVE--HALKLFDEMQRDGVAADTRTYTTFIDGLCKNGY------IIEA  436 (595)
Q Consensus       365 ~A~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~--~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~------~~~A  436 (595)
                      +++.+++++.+..++ +..+|..-...+...+.++  ++++.++.+++.+ +-+...|+.....+...++      ++++
T Consensus       128 ~EL~~~~~~l~~~pk-ny~aW~~R~~vl~~l~~~~~~~EL~~~~~~i~~d-~~N~sAW~~R~~ll~~l~~~~~~~~~~eE  205 (306)
T 3dra_A          128 REFDILEAMLSSDPK-NHHVWSYRKWLVDTFDLHNDAKELSFVDKVIDTD-LKNNSAWSHRFFLLFSKKHLATDNTIDEE  205 (306)
T ss_dssp             HHHHHHHHHHHHCTT-CHHHHHHHHHHHHHTTCTTCHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHSSGGGCCHHHHHHH
T ss_pred             HHHHHHHHHHHhCCC-CHHHHHHHHHHHHHhcccChHHHHHHHHHHHHhC-CCCHHHHHHHHHHHHhccccchhhhHHHH
Confidence            555555555554333 4445544444444455444  5555555555543 3344444444444444443      6666


Q ss_pred             HHHHHHHHHcCCCcCHHHHHHHHHHHHhcCChH-HHHHHHHhcccCC--CCCCHHHHHHHHHHHHhcCChhHHHHHHHHH
Q 040027          437 VELFRTLRILKCELDIQAYNCLIDGLCKSGRLK-FAWELFCSLPHGV--LVPNVVTYNIMIQGLCNDGQMDKARDLFLDM  513 (595)
Q Consensus       437 ~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~-~A~~~~~~~~~~~--~~p~~~~~~~l~~~~~~~g~~~~A~~~~~~~  513 (595)
                      ++.+++++... +-|...|+.+...+.+.|+.. .+..+..++.+.+  -..+...+..++.+|.+.|+.++|+++++.+
T Consensus       206 l~~~~~aI~~~-p~n~SaW~y~~~ll~~~~~~~~~~~~~~~~~~~~~~~~~~s~~al~~la~~~~~~~~~~~A~~~~~~l  284 (306)
T 3dra_A          206 LNYVKDKIVKC-PQNPSTWNYLLGIHERFDRSITQLEEFSLQFVDLEKDQVTSSFALETLAKIYTQQKKYNESRTVYDLL  284 (306)
T ss_dssp             HHHHHHHHHHC-SSCHHHHHHHHHHHHHTTCCGGGGHHHHHTTEEGGGTEESCHHHHHHHHHHHHHTTCHHHHHHHHHHH
T ss_pred             HHHHHHHHHhC-CCCccHHHHHHHHHHhcCCChHHHHHHHHHHHhccCCCCCCHHHHHHHHHHHHccCCHHHHHHHHHHH
Confidence            66666666655 556666766666666666633 3445555555421  0224556666666666666666666666666


Q ss_pred             HH
Q 040027          514 EE  515 (595)
Q Consensus       514 ~~  515 (595)
                      .+
T Consensus       285 ~~  286 (306)
T 3dra_A          285 KS  286 (306)
T ss_dssp             HH
T ss_pred             Hh
Confidence            65

>3qou_A Protein YBBN; thioredoxin-like fold, tetratricopeptide repeat, lysine dimethylation, protein binding; HET: MLY; 1.80A {Escherichia coli} PDB: 3qdn_A*

Probab=99.07  E-value=7.5e-09  Score=95.60  Aligned_cols=162  Identities=10%  Similarity=0.016  Sum_probs=116.4

Q ss_pred             CCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCcCHHHHHHHHHHHHhcCChHHHHHHHHhcccCCCCCCHHHHH-H
Q 040027          414 AADTRTYTTFIDGLCKNGYIIEAVELFRTLRILKCELDIQAYNCLIDGLCKSGRLKFAWELFCSLPHGVLVPNVVTYN-I  492 (595)
Q Consensus       414 ~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~p~~~~~~-~  492 (595)
                      +.+...+..+...+...|++++|...|+++.... +.+...+..++.++...|++++|...++++..  ..|+..... .
T Consensus       114 p~~~~~~~~~a~~~~~~g~~~~A~~~~~~al~~~-P~~~~a~~~la~~~~~~g~~~~A~~~l~~~~~--~~p~~~~~~~~  190 (287)
T 3qou_A          114 PREEELXAQQAMQLMQESNYTDALPLLXDAWQLS-NQNGEIGLLLAETLIALNRSEDAEAVLXTIPL--QDQDTRYQGLV  190 (287)
T ss_dssp             CCHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHT-TSCHHHHHHHHHHHHHTTCHHHHHHHHTTSCG--GGCSHHHHHHH
T ss_pred             CCchhhHHHHHHHHHhCCCHHHHHHHHHHHHHhC-CcchhHHHHHHHHHHHCCCHHHHHHHHHhCch--hhcchHHHHHH
Confidence            4445566667777778888888888888887765 55677788888888888888888888888776  345543322 2


Q ss_pred             HHHHHHhcCChhHHHHHHHHHHHcCCCCCHHHHHHHHHHHHHcCChhHHHHHHHHHHHCCCCCC---HHHHHHHHHHHHh
Q 040027          493 MIQGLCNDGQMDKARDLFLDMEENAAAPDVITFDMLIHGFIRINEPSKVNELLHKMKEKKVMPD---ASIVSIVVDLLVK  569 (595)
Q Consensus       493 l~~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~p~---~~~~~~l~~~~~~  569 (595)
                      ....+...++.++|+..++++++.. +.+...+..+..+|...|++++|...++++++..  |+   ...+..++.+|..
T Consensus       191 ~~~~l~~~~~~~~a~~~l~~al~~~-P~~~~~~~~la~~l~~~g~~~~A~~~l~~~l~~~--p~~~~~~a~~~l~~~~~~  267 (287)
T 3qou_A          191 AQIELLXQAADTPEIQQLQQQVAEN-PEDAALATQLALQLHQVGRNEEALELLFGHLRXD--LTAADGQTRXTFQEILAA  267 (287)
T ss_dssp             HHHHHHHHHTSCHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC--TTGGGGHHHHHHHHHHHH
T ss_pred             HHHHHHhhcccCccHHHHHHHHhcC-CccHHHHHHHHHHHHHcccHHHHHHHHHHHHhcc--cccccchHHHHHHHHHHH
Confidence            2334556777777888888887764 5567777788888888888888888888888643  32   5677888888888


Q ss_pred             cCcccccchHHH
Q 040027          570 NEISLKSLPSFL  581 (595)
Q Consensus       570 ~g~~~~~i~~~~  581 (595)
                      .|+.++++..+.
T Consensus       268 ~g~~~~a~~~~r  279 (287)
T 3qou_A          268 LGTGDALASXYR  279 (287)
T ss_dssp             HCTTCHHHHHHH
T ss_pred             cCCCCcHHHHHH
Confidence            888776665543

>3qou_A Protein YBBN; thioredoxin-like fold, tetratricopeptide repeat, lysine dimethylation, protein binding; HET: MLY; 1.80A {Escherichia coli} PDB: 3qdn_A*

Probab=99.05  E-value=5.6e-09  Score=96.48  Aligned_cols=166  Identities=14%  Similarity=0.006  Sum_probs=96.6

Q ss_pred             CCHHHHHHHHHHHHhcCCHhHHHHHHHHHHhcCCCCCHhhHHHHHHHHHhcCChhHHHHHHHHHHhcCCCCCccccCcHH
Q 040027          129 PNAATFNSLIKGLHAESRIMEAAALFTKLKAFGCEPNVITYNTLINGLCRTGHTMIALNLFEEMANGNGEIGVVCKPNTV  208 (595)
Q Consensus       129 ~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~~~~  208 (595)
                      .+...+..+...+...|++++|...|+++.... +.+...+..+...+.+.|++++|+..++++....        |+..
T Consensus       115 ~~~~~~~~~a~~~~~~g~~~~A~~~~~~al~~~-P~~~~a~~~la~~~~~~g~~~~A~~~l~~~~~~~--------p~~~  185 (287)
T 3qou_A          115 REEELXAQQAMQLMQESNYTDALPLLXDAWQLS-NQNGEIGLLLAETLIALNRSEDAEAVLXTIPLQD--------QDTR  185 (287)
T ss_dssp             CHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHT-TSCHHHHHHHHHHHHHTTCHHHHHHHHTTSCGGG--------CSHH
T ss_pred             CchhhHHHHHHHHHhCCCHHHHHHHHHHHHHhC-CcchhHHHHHHHHHHHCCCHHHHHHHHHhCchhh--------cchH
Confidence            344455556666666666666666666666653 2255566666666666666666666666665543        2322


Q ss_pred             -HHHHHHHHHHHcCCHhHHHHHHHHHhhCCCCCCHhHHHHHHHHHHhcCCHHHHHHHHHHHHHCCCCC-CHhhHHHHHHH
Q 040027          209 -TYSTIIDGLCKEGFVDKAKALFLQMKDENINPDVVTYNSLIHGLCHANDWNEAKRLFIEMMDQGVQP-SVVTFNVIMDE  286 (595)
Q Consensus       209 -~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~~ll~~~~~~~~~~~A~~~~~~~~~~~~~~-~~~~~~~l~~~  286 (595)
                       ........+...++.++|.+.+++..... +.+...+..+...+...|++++|+..|.++++..... +...+..++..
T Consensus       186 ~~~~~~~~~l~~~~~~~~a~~~l~~al~~~-P~~~~~~~~la~~l~~~g~~~~A~~~l~~~l~~~p~~~~~~a~~~l~~~  264 (287)
T 3qou_A          186 YQGLVAQIELLXQAADTPEIQQLQQQVAEN-PEDAALATQLALQLHQVGRNEEALELLFGHLRXDLTAADGQTRXTFQEI  264 (287)
T ss_dssp             HHHHHHHHHHHHHHTSCHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTGGGGHHHHHHHHH
T ss_pred             HHHHHHHHHHHhhcccCccHHHHHHHHhcC-CccHHHHHHHHHHHHHcccHHHHHHHHHHHHhcccccccchHHHHHHHH
Confidence             22222233455566666666666665543 2355666666666666666666666666666642211 14456666666


Q ss_pred             HHhcCChHHHHHHHHHHH
Q 040027          287 LCKNRKMDEASRLLDLMV  304 (595)
Q Consensus       287 ~~~~g~~~~a~~~~~~~~  304 (595)
                      +...|+.++|...|++..
T Consensus       265 ~~~~g~~~~a~~~~r~al  282 (287)
T 3qou_A          265 LAALGTGDALASXYRRQL  282 (287)
T ss_dssp             HHHHCTTCHHHHHHHHHH
T ss_pred             HHHcCCCCcHHHHHHHHH
Confidence            666666666666666544

>2r5s_A Uncharacterized protein VP0806; APC090868.1, vibrio parahaemolyticus RIMD 22 structural genomics, PSI-2, protein structure initiative; HET: MES; 2.14A {Vibrio parahaemolyticus}

Probab=99.04  E-value=5.7e-09  Score=88.58  Aligned_cols=154  Identities=12%  Similarity=0.093  Sum_probs=77.3

Q ss_pred             HHHHHHhcCCHHHHHHHHHHHHHcCCCcCHHHHHHHHHHHHhcCChHHHHHHHHhcccCCCCCCHHHHHHHHHH-HHhcC
Q 040027          423 FIDGLCKNGYIIEAVELFRTLRILKCELDIQAYNCLIDGLCKSGRLKFAWELFCSLPHGVLVPNVVTYNIMIQG-LCNDG  501 (595)
Q Consensus       423 l~~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~p~~~~~~~l~~~-~~~~g  501 (595)
                      ....+...|++++|...++++.+.. +.+...+..+..++...|++++|+..++++..  ..|+...+..+... +...+
T Consensus        12 ~a~~~~~~g~~~~A~~~~~~al~~~-P~~~~a~~~la~~~~~~g~~~~A~~~~~~a~~--~~p~~~~~~~~~~~~~~~~~   88 (176)
T 2r5s_A           12 QVSELLQQGEHAQALNVIQTLSDEL-QSRGDVKLAKADCLLETKQFELAQELLATIPL--EYQDNSYKSLIAKLELHQQA   88 (176)
T ss_dssp             HHHHHHHTTCHHHHHHHHHTSCHHH-HTSHHHHHHHHHHHHHTTCHHHHHHHHTTCCG--GGCCHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHcCCHHHHHHHHHHHHHHC-CCcHHHHHHHHHHHHHCCCHHHHHHHHHHhhh--ccCChHHHHHHHHHHHHhhc
Confidence            3444555566666666665555443 34455555556666666666666666665554  22332222221111 11222


Q ss_pred             ChhHHHHHHHHHHHcCCCCCHHHHHHHHHHHHHcCChhHHHHHHHHHHHCCCCC-CHHHHHHHHHHHHhcCcccccchHH
Q 040027          502 QMDKARDLFLDMEENAAAPDVITFDMLIHGFIRINEPSKVNELLHKMKEKKVMP-DASIVSIVVDLLVKNEISLKSLPSF  580 (595)
Q Consensus       502 ~~~~A~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~p-~~~~~~~l~~~~~~~g~~~~~i~~~  580 (595)
                      +..+|+..++++++.. +.+...+..++.++...|++++|...++++++..-.+ +...+..++.++...|+.++++..+
T Consensus        89 ~~~~a~~~~~~al~~~-P~~~~~~~~la~~~~~~g~~~~A~~~~~~~l~~~p~~~~~~a~~~l~~~~~~~g~~~~A~~~y  167 (176)
T 2r5s_A           89 AESPELKRLEQELAAN-PDNFELACELAVQYNQVGRDEEALELLWNILKVNLGAQDGEVKKTFMDILSALGQGNAIASKY  167 (176)
T ss_dssp             TSCHHHHHHHHHHHHS-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHTTCTTTTTTHHHHHHHHHHHHHCSSCHHHHHH
T ss_pred             ccchHHHHHHHHHHhC-CCCHHHHHHHHHHHHHcccHHHHHHHHHHHHHhCcccChHHHHHHHHHHHHHhCCCCcHHHHH
Confidence            2334555555555543 3345555556666666666666666666665532111 2345555666666666665444443

>2vsy_A XCC0866; transferase, glycosyl transferase, GT-B, OGT, protein O-GLCN; HET: NHE; 2.10A {Xanthomonas campestris PV} PDB: 2jlb_A* 2xgm_A* 2xgo_A* 2xgs_A* 2vsn_A*

Probab=99.04  E-value=6.4e-09  Score=106.64  Aligned_cols=154  Identities=13%  Similarity=0.064  Sum_probs=106.8

Q ss_pred             CCChHHHHHHHHHHHHhCCCCCCHhhHHHHHHHHHcCCCchhHHhhCCCCCCHHHHHHHHHHHHhcCChhHHHHHHHHHH
Q 040027           44 VITPNEAFCIFDYMLRMHPSPPPVSSFNILLASLAKNKHYDTRLNATGLFPNLYTYNILINCFCKIGRVSLGFIAFGRIL  123 (595)
Q Consensus        44 ~~~~~~A~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~  123 (595)
                      .|++++|.+.|+++++.+|.                               +...|..+...+.+.|++++|+..|++++
T Consensus         2 ~g~~~~A~~~~~~al~~~p~-------------------------------~~~~~~~lg~~~~~~g~~~~A~~~~~~al   50 (568)
T 2vsy_A            2 TADGPRELLQLRAAVRHRPQ-------------------------------DFVAWLMLADAELGMGDTTAGEMAVQRGL   50 (568)
T ss_dssp             -------------------C-------------------------------CHHHHHHHHHHHHHHTCHHHHHHHHHHHH
T ss_pred             CccHHHHHHHHHHHHHhCCC-------------------------------CHHHHHHHHHHHHHcCCHHHHHHHHHHHH
Confidence            47899999999999998887                               34455566677777888888888888888


Q ss_pred             hCCCCCCHHHHHHHHHHHHhcCCHhHHHHHHHHHHhcCCCCCHhhHHHHHHHHHhcCChhHHHHHHHHHHhcCCCCCccc
Q 040027          124 RSCFTPNAATFNSLIKGLHAESRIMEAAALFTKLKAFGCEPNVITYNTLINGLCRTGHTMIALNLFEEMANGNGEIGVVC  203 (595)
Q Consensus       124 ~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~  203 (595)
                      +.. +.+...+..+...|...|++++|.+.|++..+.. +.+...+..+..++...|++++|++.|++..+.+       
T Consensus        51 ~~~-p~~~~~~~~lg~~~~~~g~~~~A~~~~~~al~~~-p~~~~~~~~la~~~~~~g~~~~A~~~~~~al~~~-------  121 (568)
T 2vsy_A           51 ALH-PGHPEAVARLGRVRWTQQRHAEAAVLLQQASDAA-PEHPGIALWLGHALEDAGQAEAAAAAYTRAHQLL-------  121 (568)
T ss_dssp             TTS-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-------
T ss_pred             HhC-CCCHHHHHHHHHHHHHCCCHHHHHHHHHHHHhcC-CCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhC-------
Confidence            874 4467788888888888888888888888888774 3367788888888888888888888888888765       


Q ss_pred             cCcHHHHHHHHHHHHHc---CCHhHHHHHHHHHhhCC
Q 040027          204 KPNTVTYSTIIDGLCKE---GFVDKAKALFLQMKDEN  237 (595)
Q Consensus       204 ~~~~~~~~~l~~~~~~~---g~~~~A~~~~~~~~~~~  237 (595)
                      +.+...+..+..++...   |+.++|.+.+++..+.+
T Consensus       122 p~~~~~~~~l~~~~~~~~~~g~~~~A~~~~~~al~~~  158 (568)
T 2vsy_A          122 PEEPYITAQLLNWRRRLCDWRALDVLSAQVRAAVAQG  158 (568)
T ss_dssp             TTCHHHHHHHHHHHHHTTCCTTHHHHHHHHHHHHHHT
T ss_pred             CCCHHHHHHHHHHHHHhhccccHHHHHHHHHHHHhcC
Confidence            45677788888888888   88888888888887764

>2yhc_A BAMD, UPF0169 lipoprotein YFIO; essential BAM component, membrane protein; 1.80A {Escherichia coli} PDB: 3tgo_A 3q5m_A

Probab=99.02  E-value=4.7e-08  Score=86.68  Aligned_cols=187  Identities=7%  Similarity=-0.079  Sum_probs=128.9

Q ss_pred             CHHHHHHHHHHHHhcCCHhHHHHHHHHHHhcCCCC--CHhhHHHHHHHHHhcCChhHHHHHHHHHHhcCCCCCccccCcH
Q 040027          130 NAATFNSLIKGLHAESRIMEAAALFTKLKAFGCEP--NVITYNTLINGLCRTGHTMIALNLFEEMANGNGEIGVVCKPNT  207 (595)
Q Consensus       130 ~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~--~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~~~  207 (595)
                      +...+..+...+.+.|++++|+..|+++.......  ....+..++.++...|++++|+..|+++.+..       |.+.
T Consensus         3 ~~~~~~~~a~~~~~~g~~~~A~~~~~~~~~~~p~~~~~~~a~~~lg~~~~~~~~~~~A~~~~~~~l~~~-------P~~~   75 (225)
T 2yhc_A            3 PPNEIYATAQQKLQDGNWRQAITQLEALDNRYPFGPYSQQVQLDLIYAYYKNADLPLAQAAIDRFIRLN-------PTHP   75 (225)
T ss_dssp             CHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHCTTSTTHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-------TTCT
T ss_pred             CHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCCCChHHHHHHHHHHHHHHhcCCHHHHHHHHHHHHHHC-------cCCC
Confidence            45566777788999999999999999999864321  13578889999999999999999999999875       2222


Q ss_pred             ---HHHHHHHHHHHH------------------cCCHhHHHHHHHHHhhCCCCCCHhHHHHHHHHHHhcCCHHHHHHHHH
Q 040027          208 ---VTYSTIIDGLCK------------------EGFVDKAKALFLQMKDENINPDVVTYNSLIHGLCHANDWNEAKRLFI  266 (595)
Q Consensus       208 ---~~~~~l~~~~~~------------------~g~~~~A~~~~~~~~~~~~~~~~~~~~~ll~~~~~~~~~~~A~~~~~  266 (595)
                         .++..+..++..                  .|++++|...|+++.+.. +-+...+.......          .+..
T Consensus        76 ~~~~a~~~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~A~~~~~~~l~~~-P~~~~a~~a~~~l~----------~~~~  144 (225)
T 2yhc_A           76 NIDYVMYMRGLTNMALDDSALQGFFGVDRSDRDPQQARAAFSDFSKLVRGY-PNSQYTTDATKRLV----------FLKD  144 (225)
T ss_dssp             THHHHHHHHHHHHHHHHC--------------CCHHHHHHHHHHHHHHTTC-TTCTTHHHHHHHHH----------HHHH
T ss_pred             cHHHHHHHHHHHHHhhhhhhhhhhhccchhhcCcHHHHHHHHHHHHHHHHC-cCChhHHHHHHHHH----------HHHH
Confidence               245555555554                  356666666666666542 11222222111100          0000


Q ss_pred             HHHHCCCCCCHhhHHHHHHHHHhcCChHHHHHHHHHHHHCCCCCC--HHHHHHHHHHHHhcCCHHHHHHHHHHHHhcC
Q 040027          267 EMMDQGVQPSVVTFNVIMDELCKNRKMDEASRLLDLMVQRGVRPN--ACTYNTLMDGFCLMGKINRAEELFGSMESMG  342 (595)
Q Consensus       267 ~~~~~~~~~~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~~~~~--~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~  342 (595)
                      .+        ......+...+.+.|++++|...|+++++......  ...+..+..++.+.|++++|.+.++.+...+
T Consensus       145 ~~--------~~~~~~~a~~~~~~~~~~~A~~~~~~~l~~~p~~~~~~~a~~~l~~~~~~~g~~~~A~~~~~~l~~~~  214 (225)
T 2yhc_A          145 RL--------AKYEYSVAEYYTERGAWVAVVNRVEGMLRDYPDTQATRDALPLMENAYRQMQMNAQAEKVAKIIAANS  214 (225)
T ss_dssp             HH--------HHHHHHHHHHHHHHTCHHHHHHHHHHHHHHSTTSHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHCC
T ss_pred             HH--------HHHHHHHHHHHHHcCcHHHHHHHHHHHHHHCcCCCccHHHHHHHHHHHHHcCCcHHHHHHHHHHHhhC
Confidence            00        01123567789999999999999999998632211  2567889999999999999999999988764

>4f3v_A ESX-1 secretion system protein ECCA1; tetratricopeptide repeat, TPR domain, ATPase, protein secret protein transport; 2.00A {Mycobacterium tuberculosis}

Probab=99.02  E-value=1.7e-08  Score=90.27  Aligned_cols=183  Identities=8%  Similarity=-0.082  Sum_probs=112.9

Q ss_pred             CCCChHHHHHHHHHHHHhCCCCCCHhhHHHH-------HHHHHcCCCchh----HHhhCCCCC-----------------
Q 040027           43 NVITPNEAFCIFDYMLRMHPSPPPVSSFNIL-------LASLAKNKHYDT----RLNATGLFP-----------------   94 (595)
Q Consensus        43 ~~~~~~~A~~~~~~~~~~~~~~~~~~~~~~l-------~~~~~~~~~~~~----~~~~~~~~~-----------------   94 (595)
                      ..+++..|.+.|.++++.+|.  .+..|..+       ...+.+.++..+    .....++.|                 
T Consensus        18 ~~~d~~~A~~~F~~a~~~dP~--~~Daw~g~~a~g~~~~~~L~~~~r~~~a~~~~~~~l~l~p~~l~a~~~~~g~y~~~~   95 (282)
T 4f3v_A           18 LPMSEARSLDLFTEITNYDES--ACDAWIGRIRCGDTDRVTLFRAWYSRRNFGQLSGSVQISMSTLNARIAIGGLYGDIT   95 (282)
T ss_dssp             TTTCHHHHHHHHHHHHHHCTT--CHHHHHHHHHTTCCCHHHHHHHHHTGGGTTHHHHTTTCCGGGGCCEEECCTTTCCCE
T ss_pred             cCCCHHHHHHHHHHHHHhChh--hhHHHHhHHHccCCcHHHHHHHHHHHHHHHHHHHHhcCChhhhhhhhccCCcccccc
Confidence            469999999999999999999  99999877       344444444333    111111111                 


Q ss_pred             -----CHHHHHHHHHHHHhcCChhHHHHHHHHHHhCCCCCCHHHHHHHHHHHHhcCCHhHHHHHHHHHHhcCCCCC--Hh
Q 040027           95 -----NLYTYNILINCFCKIGRVSLGFIAFGRILRSCFTPNAATFNSLIKGLHAESRIMEAAALFTKLKAFGCEPN--VI  167 (595)
Q Consensus        95 -----~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~~--~~  167 (595)
                           -...+..+...+...|++++|..+|+.+...+  |+......+...+.+.+++++|+..|+...... .|.  ..
T Consensus        96 ~~v~~r~dl~LayA~~L~~~g~y~eA~~~l~~~~~~~--p~~~~~~~~a~l~~~~~r~~dA~~~l~~a~~~~-d~~~~~~  172 (282)
T 4f3v_A           96 YPVTSPLAITMGFAACEAAQGNYADAMEALEAAPVAG--SEHLVAWMKAVVYGAAERWTDVIDQVKSAGKWP-DKFLAGA  172 (282)
T ss_dssp             EECSSHHHHHHHHHHHHHHHTCHHHHHHHHTSSCCTT--CHHHHHHHHHHHHHHTTCHHHHHHHHTTGGGCS-CHHHHHH
T ss_pred             cccCCHhHHHHHHHHHHHHCCCHHHHHHHHHHHHhcC--CchHHHHHHHHHHHHcCCHHHHHHHHHHhhccC-CcccHHH
Confidence                 12344556666777777777777777766543  222244445556667777777777776544321 111  23


Q ss_pred             hHHHHHHHHHhcCChhHHHHHHHHHHhcCCCCCccccC--cHHHHHHHHHHHHHcCCHhHHHHHHHHHhhC
Q 040027          168 TYNTLINGLCRTGHTMIALNLFEEMANGNGEIGVVCKP--NTVTYSTIIDGLCKEGFVDKAKALFLQMKDE  236 (595)
Q Consensus       168 ~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~--~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~  236 (595)
                      ++..+..++...|++++|+..|++.....      ..|  ..........++.+.|+.++|..+|+++...
T Consensus       173 a~~~LG~al~~LG~~~eAl~~l~~a~~g~------~~P~~~~da~~~~glaL~~lGr~deA~~~l~~a~a~  237 (282)
T 4f3v_A          173 AGVAHGVAAANLALFTEAERRLTEANDSP------AGEACARAIAWYLAMARRSQGNESAAVALLEWLQTT  237 (282)
T ss_dssp             HHHHHHHHHHHTTCHHHHHHHHHHHHTST------TTTTTHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHCCCHHHHHHHHHHHhcCC------CCccccHHHHHHHHHHHHHcCCHHHHHHHHHHHHhc
Confidence            56666677777777777777777766432      112  2345556666677777777777777777664

>2vsy_A XCC0866; transferase, glycosyl transferase, GT-B, OGT, protein O-GLCN; HET: NHE; 2.10A {Xanthomonas campestris PV} PDB: 2jlb_A* 2xgm_A* 2xgo_A* 2xgs_A* 2vsn_A*

Probab=98.95  E-value=1.7e-08  Score=103.54  Aligned_cols=163  Identities=10%  Similarity=-0.033  Sum_probs=118.4

Q ss_pred             CCCHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHccCCHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHhcCCHHHHHHH
Q 040027          360 NKEVEEALSLYREMVSKGIKPTVVTYNTLFLGLFEIHQVEHALKLFDEMQRDGVAADTRTYTTFIDGLCKNGYIIEAVEL  439 (595)
Q Consensus       360 ~~~~~~A~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~  439 (595)
                      .|++++|+..++++.+.... +...+..+...+...|++++|.+.+++..+.. +.+...+..+..+|...|++++|...
T Consensus         2 ~g~~~~A~~~~~~al~~~p~-~~~~~~~lg~~~~~~g~~~~A~~~~~~al~~~-p~~~~~~~~lg~~~~~~g~~~~A~~~   79 (568)
T 2vsy_A            2 TADGPRELLQLRAAVRHRPQ-DFVAWLMLADAELGMGDTTAGEMAVQRGLALH-PGHPEAVARLGRVRWTQQRHAEAAVL   79 (568)
T ss_dssp             -------------------C-CHHHHHHHHHHHHHHTCHHHHHHHHHHHHTTS-TTCHHHHHHHHHHHHHTTCHHHHHHH
T ss_pred             CccHHHHHHHHHHHHHhCCC-CHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhC-CCCHHHHHHHHHHHHHCCCHHHHHHH
Confidence            47888999999988876433 57788888889999999999999999998874 55678888888999999999999999


Q ss_pred             HHHHHHcCCCcCHHHHHHHHHHHHhcCChHHHHHHHHhcccCCCCC-CHHHHHHHHHHHHhc---CChhHHHHHHHHHHH
Q 040027          440 FRTLRILKCELDIQAYNCLIDGLCKSGRLKFAWELFCSLPHGVLVP-NVVTYNIMIQGLCND---GQMDKARDLFLDMEE  515 (595)
Q Consensus       440 ~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~p-~~~~~~~l~~~~~~~---g~~~~A~~~~~~~~~  515 (595)
                      ++++.+.. +.+...+..+..++...|++++|.+.++++.+.  .| +...+..+..++...   |++++|.+.++++++
T Consensus        80 ~~~al~~~-p~~~~~~~~la~~~~~~g~~~~A~~~~~~al~~--~p~~~~~~~~l~~~~~~~~~~g~~~~A~~~~~~al~  156 (568)
T 2vsy_A           80 LQQASDAA-PEHPGIALWLGHALEDAGQAEAAAAAYTRAHQL--LPEEPYITAQLLNWRRRLCDWRALDVLSAQVRAAVA  156 (568)
T ss_dssp             HHHHHHHC-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH--CTTCHHHHHHHHHHHHHTTCCTTHHHHHHHHHHHHH
T ss_pred             HHHHHhcC-CCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHh--CCCCHHHHHHHHHHHHHhhccccHHHHHHHHHHHHh
Confidence            99998876 667888999999999999999999999998873  44 467888888888888   999999999999988


Q ss_pred             cCCCCCHHHHHHH
Q 040027          516 NAAAPDVITFDML  528 (595)
Q Consensus       516 ~~~~~~~~~~~~l  528 (595)
                      .+ +.+...|..+
T Consensus       157 ~~-p~~~~~~~~l  168 (568)
T 2vsy_A          157 QG-VGAVEPFAFL  168 (568)
T ss_dssp             HT-CCCSCHHHHT
T ss_pred             cC-CcccChHHHh
Confidence            75 3333344433

>2ifu_A Gamma-SNAP; membrane fusion, snare complex disassembly, protein structure initiative, PSI, center for eukaryotic structural genomics, CESG; HET: MSE; 2.60A {Danio rerio}

Probab=98.94  E-value=2.4e-08  Score=93.34  Aligned_cols=204  Identities=14%  Similarity=0.058  Sum_probs=122.5

Q ss_pred             CCCChHHHHHHHHHHHHhCCCCCCHhhHHHHHHHHHc-CCCchhHHhhCCCCCCHHHHHHHHHHHHhcCChhHHHHHHHH
Q 040027           43 NVITPNEAFCIFDYMLRMHPSPPPVSSFNILLASLAK-NKHYDTRLNATGLFPNLYTYNILINCFCKIGRVSLGFIAFGR  121 (595)
Q Consensus        43 ~~~~~~~A~~~~~~~~~~~~~~~~~~~~~~l~~~~~~-~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~  121 (595)
                      ..|++++|.++++++.+..+.  .          +.+ .++++.         -...|..++..|...|++++|...|.+
T Consensus         3 ~~~~~~eA~~~~~~a~k~~~~--~----------~~~~~~~~~~---------A~~~~~~a~~~~~~~g~~~~A~~~~~~   61 (307)
T 2ifu_A            3 AAQKISEAHEHIAKAEKYLKT--S----------FMKWKPDYDS---------AASEYAKAAVAFKNAKQLEQAKDAYLQ   61 (307)
T ss_dssp             CHHHHHHHHHHHHHHHHHHCC--C----------SSSCSCCHHH---------HHHHHHHHHHHHHHTTCHHHHHHHHHH
T ss_pred             ccchHHHHHHHHHHHHHHccc--c----------ccCCCCCHHH---------HHHHHHHHHHHHHHcCCHHHHHHHHHH
Confidence            458899999999999887653  1          011 223222         123466667778888999999888888


Q ss_pred             HHhCCCC---C--CHHHHHHHHHHHHhcCCHhHHHHHHHHHHhcCC---CC--CHhhHHHHHHHHHhcCChhHHHHHHHH
Q 040027          122 ILRSCFT---P--NAATFNSLIKGLHAESRIMEAAALFTKLKAFGC---EP--NVITYNTLINGLCRTGHTMIALNLFEE  191 (595)
Q Consensus       122 ~~~~~~~---~--~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~---~~--~~~~~~~l~~~~~~~g~~~~A~~~~~~  191 (595)
                      +......   +  -..+|+.+...|...|++++|+..|++....-.   .+  ...++..+...|.. |++++|+..|++
T Consensus        62 al~~~~~~~~~~~~a~~~~~lg~~~~~~g~~~~A~~~~~~Al~l~~~~g~~~~~a~~~~~lg~~~~~-g~~~~A~~~~~~  140 (307)
T 2ifu_A           62 EAEAHANNRSLFHAAKAFEQAGMMLKDLQRMPEAVQYIEKASVMYVENGTPDTAAMALDRAGKLMEP-LDLSKAVHLYQQ  140 (307)
T ss_dssp             HHHHHHHTTCHHHHHHHHHHHHHHHHHTTCGGGGHHHHHHHHHHHHTTTCHHHHHHHHHHHHHHHTT-TCHHHHHHHHHH
T ss_pred             HHHHHHHcCCHHHHHHHHHHHHHHHHhCCCHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHc-CCHHHHHHHHHH
Confidence            7764210   0  133667777777888888888888877654311   11  13456666777766 777777777777


Q ss_pred             HHhcCCCCCccccCcHHHHHHHHHHHHHcCCHhHHHHHHHHHhhC----CCCCC-HhHHHHHHHHHHhcCCHHHHHHHHH
Q 040027          192 MANGNGEIGVVCKPNTVTYSTIIDGLCKEGFVDKAKALFLQMKDE----NINPD-VVTYNSLIHGLCHANDWNEAKRLFI  266 (595)
Q Consensus       192 ~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~----~~~~~-~~~~~~ll~~~~~~~~~~~A~~~~~  266 (595)
                      ........+. ......++..+..++...|++++|+..|++....    +..+. ...+..++.++...|++++|...|+
T Consensus       141 Al~~~~~~~~-~~~~~~~~~~lg~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~~g~~~~~~g~~~~A~~~~~  219 (307)
T 2ifu_A          141 AAAVFENEER-LRQAAELIGKASRLLVRQQKFDEAAASLQKEKSMYKEMENYPTCYKKCIAQVLVQLHRADYVAAQKCVR  219 (307)
T ss_dssp             HHHHHHHTTC-HHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHH
T ss_pred             HHHHHHhCCC-hhHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHcCChhHHHHHHHHHHHHHHHcCCHHHHHHHHH
Confidence            7653210000 0001345666677777777777777777766542    11011 1244445555556666666666666


Q ss_pred             HHH
Q 040027          267 EMM  269 (595)
Q Consensus       267 ~~~  269 (595)
                      +.+
T Consensus       220 ~al  222 (307)
T 2ifu_A          220 ESY  222 (307)
T ss_dssp             HHT
T ss_pred             HHh
Confidence            665

>3gyz_A Chaperone protein IPGC; asymmetric homodimer, tetratricopeptide repeat, TPR, chapero virulence; 2.15A {Shigella flexneri} PDB: 3gz1_A 3gz2_A 3ks2_A

Probab=98.88  E-value=6e-09  Score=85.11  Aligned_cols=103  Identities=17%  Similarity=0.044  Sum_probs=75.1

Q ss_pred             CHHHHHHHHHHHHhcCChHHHHHHHHhcccCCCCC-CHHHHHHHHHHHHhcCChhHHHHHHHHHHHcCCCCCHHHHHHHH
Q 040027          451 DIQAYNCLIDGLCKSGRLKFAWELFCSLPHGVLVP-NVVTYNIMIQGLCNDGQMDKARDLFLDMEENAAAPDVITFDMLI  529 (595)
Q Consensus       451 ~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~p-~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~~l~  529 (595)
                      +...+..+...+.+.|++++|+..|+++..  +.| +...|..+..+|...|++++|+..|+++++.. +.+...|..++
T Consensus        35 ~~~~~~~lg~~~~~~g~~~eA~~~~~~al~--~~P~~~~~~~~lg~~~~~~g~~~~Ai~~~~~al~l~-P~~~~~~~~lg  111 (151)
T 3gyz_A           35 MMDDIYSYAYDFYNKGRIEEAEVFFRFLCI--YDFYNVDYIMGLAAIYQIKEQFQQAADLYAVAFALG-KNDYTPVFHTG  111 (151)
T ss_dssp             HHHHHHHHHHHHHHTTCHHHHHHHHHHHHH--HCTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHS-SSCCHHHHHHH
T ss_pred             HHHHHHHHHHHHHHcCCHHHHHHHHHHHHH--hCCCCHHHHHHHHHHHHHHccHHHHHHHHHHHHhhC-CCCcHHHHHHH
Confidence            455666777777778888888888887776  344 46677777777888888888888888887764 44566777777


Q ss_pred             HHHHHcCChhHHHHHHHHHHHCCCCCCHH
Q 040027          530 HGFIRINEPSKVNELLHKMKEKKVMPDAS  558 (595)
Q Consensus       530 ~~~~~~g~~~~A~~~~~~~~~~~~~p~~~  558 (595)
                      .+|...|++++|...|+++++.  .|+..
T Consensus       112 ~~~~~lg~~~eA~~~~~~al~l--~~~~~  138 (151)
T 3gyz_A          112 QCQLRLKAPLKAKECFELVIQH--SNDEK  138 (151)
T ss_dssp             HHHHHTTCHHHHHHHHHHHHHH--CCCHH
T ss_pred             HHHHHcCCHHHHHHHHHHHHHh--CCCHH
Confidence            7888888888888888887764  35554

>4gco_A Protein STI-1; structural genomics, PSI-biology, midwest center for structu genomics, MCSG, tetratricopeptide repeat domain; 1.60A {Caenorhabditis elegans}

Probab=98.87  E-value=7.7e-08  Score=76.08  Aligned_cols=111  Identities=11%  Similarity=0.012  Sum_probs=97.3

Q ss_pred             HHHHHHHHHHHHhcCChhHHHHHHHHHHhCCCCCCHHHHHHHHHHHHhcCCHhHHHHHHHHHHhcCCCCCHhhHHHHHHH
Q 040027           96 LYTYNILINCFCKIGRVSLGFIAFGRILRSCFTPNAATFNSLIKGLHAESRIMEAAALFTKLKAFGCEPNVITYNTLING  175 (595)
Q Consensus        96 ~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~~l~~~  175 (595)
                      ...+...+..+.+.|++++|+..|+++++.. +.+..+|..+..++.+.|++++|++.|++.++.. +.+..+|..+..+
T Consensus        13 a~~~~~~G~~~~~~g~~~~A~~~~~~al~~~-p~~~~~~~~~~~~~~~~~~~~~A~~~~~~al~~~-p~~~~a~~~lg~~   90 (126)
T 4gco_A           13 AQEEKNKGNEYFKKGDYPTAMRHYNEAVKRD-PENAILYSNRAACLTKLMEFQRALDDCDTCIRLD-SKFIKGYIRKAAC   90 (126)
T ss_dssp             HHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHcCCHHHHHHHHHHHHHhC-CCCHHHHHHHhhHHHhhccHHHHHHHHHHHHHhh-hhhhHHHHHHHHH
Confidence            4567788999999999999999999999885 5688999999999999999999999999999985 4478899999999


Q ss_pred             HHhcCChhHHHHHHHHHHhcCCCCCccccCcHHHHHHHHH
Q 040027          176 LCRTGHTMIALNLFEEMANGNGEIGVVCKPNTVTYSTIID  215 (595)
Q Consensus       176 ~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~  215 (595)
                      +...|++++|++.|++..+.+       |.+..++..+..
T Consensus        91 ~~~~~~~~~A~~~~~~al~l~-------P~~~~a~~~l~~  123 (126)
T 4gco_A           91 LVAMREWSKAQRAYEDALQVD-------PSNEEAREGVRN  123 (126)
T ss_dssp             HHHTTCHHHHHHHHHHHHHHC-------TTCHHHHHHHHH
T ss_pred             HHHCCCHHHHHHHHHHHHHHC-------cCCHHHHHHHHH
Confidence            999999999999999999976       456666665544

>2ifu_A Gamma-SNAP; membrane fusion, snare complex disassembly, protein structure initiative, PSI, center for eukaryotic structural genomics, CESG; HET: MSE; 2.60A {Danio rerio}

Probab=98.86  E-value=5.8e-08  Score=90.71  Aligned_cols=159  Identities=10%  Similarity=0.000  Sum_probs=71.0

Q ss_pred             cCChhHHHHHHHHHHhCCC------CCCH----HHHHHHHHHHHhcCCHhHHHHHHHHHHhcCCCC-----CHhhHHHHH
Q 040027          109 IGRVSLGFIAFGRILRSCF------TPNA----ATFNSLIKGLHAESRIMEAAALFTKLKAFGCEP-----NVITYNTLI  173 (595)
Q Consensus       109 ~g~~~~A~~~~~~~~~~~~------~~~~----~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~-----~~~~~~~l~  173 (595)
                      .|++++|..+++++.+...      .++.    ..|......|...|++++|...|.+........     -..++..+.
T Consensus         4 ~~~~~eA~~~~~~a~k~~~~~~~~~~~~~~~A~~~~~~a~~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~a~~~~~lg   83 (307)
T 2ifu_A            4 AQKISEAHEHIAKAEKYLKTSFMKWKPDYDSAASEYAKAAVAFKNAKQLEQAKDAYLQEAEAHANNRSLFHAAKAFEQAG   83 (307)
T ss_dssp             HHHHHHHHHHHHHHHHHHCCCSSSCSCCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHH
T ss_pred             cchHHHHHHHHHHHHHHccccccCCCCCHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHH
Confidence            4667777777777665311      1111    123333444555566666666555554321000     123445555


Q ss_pred             HHHHhcCChhHHHHHHHHHHhcCCCCCccccCcHHHHHHHHHHHHHcCCHhHHHHHHHHHhhCCCC---C--CHhHHHHH
Q 040027          174 NGLCRTGHTMIALNLFEEMANGNGEIGVVCKPNTVTYSTIIDGLCKEGFVDKAKALFLQMKDENIN---P--DVVTYNSL  248 (595)
Q Consensus       174 ~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~---~--~~~~~~~l  248 (595)
                      ..|...|++++|+..|++........+. ......++..+..+|.. |++++|+..|++.......   +  ...++..+
T Consensus        84 ~~~~~~g~~~~A~~~~~~Al~l~~~~g~-~~~~a~~~~~lg~~~~~-g~~~~A~~~~~~Al~~~~~~~~~~~~~~~~~~l  161 (307)
T 2ifu_A           84 MMLKDLQRMPEAVQYIEKASVMYVENGT-PDTAAMALDRAGKLMEP-LDLSKAVHLYQQAAAVFENEERLRQAAELIGKA  161 (307)
T ss_dssp             HHHHHTTCGGGGHHHHHHHHHHHHTTTC-HHHHHHHHHHHHHHHTT-TCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHH
T ss_pred             HHHHhCCCHHHHHHHHHHHHHHHHHcCC-HHHHHHHHHHHHHHHHc-CCHHHHHHHHHHHHHHHHhCCChhHHHHHHHHH
Confidence            5555555666655555555432100000 00012344444455544 5555555555544332000   0  02234444


Q ss_pred             HHHHHhcCCHHHHHHHHHHHH
Q 040027          249 IHGLCHANDWNEAKRLFIEMM  269 (595)
Q Consensus       249 l~~~~~~~~~~~A~~~~~~~~  269 (595)
                      ...|...|++++|+..|++.+
T Consensus       162 g~~~~~~g~~~~A~~~~~~al  182 (307)
T 2ifu_A          162 SRLLVRQQKFDEAAASLQKEK  182 (307)
T ss_dssp             HHHHHHTTCHHHHHHHHHHHH
T ss_pred             HHHHHHcCCHHHHHHHHHHHH
Confidence            444444455555554444443

>4f3v_A ESX-1 secretion system protein ECCA1; tetratricopeptide repeat, TPR domain, ATPase, protein secret protein transport; 2.00A {Mycobacterium tuberculosis}

Probab=98.86  E-value=1.2e-07  Score=84.83  Aligned_cols=140  Identities=10%  Similarity=-0.051  Sum_probs=101.9

Q ss_pred             HHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCcCHHHHHHHHHHHHhcCChHHHHHHHHhcccCCCCCC--HHHHHHHHHH
Q 040027          419 TYTTFIDGLCKNGYIIEAVELFRTLRILKCELDIQAYNCLIDGLCKSGRLKFAWELFCSLPHGVLVPN--VVTYNIMIQG  496 (595)
Q Consensus       419 ~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~p~--~~~~~~l~~~  496 (595)
                      ....+...+...|++++|.++|+.+...+  |+......+...+.+.+++++|+..|+...... .|.  ...+..+..+
T Consensus       104 l~LayA~~L~~~g~y~eA~~~l~~~~~~~--p~~~~~~~~a~l~~~~~r~~dA~~~l~~a~~~~-d~~~~~~a~~~LG~a  180 (282)
T 4f3v_A          104 ITMGFAACEAAQGNYADAMEALEAAPVAG--SEHLVAWMKAVVYGAAERWTDVIDQVKSAGKWP-DKFLAGAAGVAHGVA  180 (282)
T ss_dssp             HHHHHHHHHHHHTCHHHHHHHHTSSCCTT--CHHHHHHHHHHHHHHTTCHHHHHHHHTTGGGCS-CHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHCCCHHHHHHHHHHHHhcC--CchHHHHHHHHHHHHcCCHHHHHHHHHHhhccC-CcccHHHHHHHHHHH
Confidence            44456667788888999988888877543  333266666678888999999999998776521 121  2467778888


Q ss_pred             HHhcCChhHHHHHHHHHHHcCCCCC--HHHHHHHHHHHHHcCChhHHHHHHHHHHHCCCCCCHHHHHHH
Q 040027          497 LCNDGQMDKARDLFLDMEENAAAPD--VITFDMLIHGFIRINEPSKVNELLHKMKEKKVMPDASIVSIV  563 (595)
Q Consensus       497 ~~~~g~~~~A~~~~~~~~~~~~~~~--~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~p~~~~~~~l  563 (595)
                      +...|++++|+..|++.......|.  .........++.+.|+.++|..+|+++...  .|+...+..|
T Consensus       181 l~~LG~~~eAl~~l~~a~~g~~~P~~~~da~~~~glaL~~lGr~deA~~~l~~a~a~--~P~~~~~~aL  247 (282)
T 4f3v_A          181 AANLALFTEAERRLTEANDSPAGEACARAIAWYLAMARRSQGNESAAVALLEWLQTT--HPEPKVAAAL  247 (282)
T ss_dssp             HHHTTCHHHHHHHHHHHHTSTTTTTTHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHH--SCCHHHHHHH
T ss_pred             HHHCCCHHHHHHHHHHHhcCCCCccccHHHHHHHHHHHHHcCCHHHHHHHHHHHHhc--CCcHHHHHHH
Confidence            9999999999999998885432143  346677888889999999999999999874  4665555444

>4gco_A Protein STI-1; structural genomics, PSI-biology, midwest center for structu genomics, MCSG, tetratricopeptide repeat domain; 1.60A {Caenorhabditis elegans}

Probab=98.86  E-value=7.8e-08  Score=76.06  Aligned_cols=109  Identities=14%  Similarity=0.017  Sum_probs=70.1

Q ss_pred             HHHHHHHHHHHhcCChHHHHHHHHhcccCCCCC-CHHHHHHHHHHHHhcCChhHHHHHHHHHHHcCCCCCHHHHHHHHHH
Q 040027          453 QAYNCLIDGLCKSGRLKFAWELFCSLPHGVLVP-NVVTYNIMIQGLCNDGQMDKARDLFLDMEENAAAPDVITFDMLIHG  531 (595)
Q Consensus       453 ~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~p-~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~~l~~~  531 (595)
                      ..+...+..|.+.|++++|+..|+++++  +.| +...|..+..+|...|++++|+..++++++.+ +.+...|..++.+
T Consensus        14 ~~~~~~G~~~~~~g~~~~A~~~~~~al~--~~p~~~~~~~~~~~~~~~~~~~~~A~~~~~~al~~~-p~~~~a~~~lg~~   90 (126)
T 4gco_A           14 QEEKNKGNEYFKKGDYPTAMRHYNEAVK--RDPENAILYSNRAACLTKLMEFQRALDDCDTCIRLD-SKFIKGYIRKAAC   90 (126)
T ss_dssp             HHHHHHHHHHHHTTCHHHHHHHHHHHHH--HCTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHcCCHHHHHHHHHHHHH--hCCCCHHHHHHHhhHHHhhccHHHHHHHHHHHHHhh-hhhhHHHHHHHHH
Confidence            4555666666677777777777776665  233 45666666777777777777777777776654 4456666777777


Q ss_pred             HHHcCChhHHHHHHHHHHHCCCCC-CHHHHHHHHHH
Q 040027          532 FIRINEPSKVNELLHKMKEKKVMP-DASIVSIVVDL  566 (595)
Q Consensus       532 ~~~~g~~~~A~~~~~~~~~~~~~p-~~~~~~~l~~~  566 (595)
                      |...|++++|.+.|+++++.  .| +...+..+..+
T Consensus        91 ~~~~~~~~~A~~~~~~al~l--~P~~~~a~~~l~~~  124 (126)
T 4gco_A           91 LVAMREWSKAQRAYEDALQV--DPSNEEAREGVRNC  124 (126)
T ss_dssp             HHHTTCHHHHHHHHHHHHHH--CTTCHHHHHHHHHH
T ss_pred             HHHCCCHHHHHHHHHHHHHH--CcCCHHHHHHHHHh
Confidence            77777777777777777763  34 45555555443

>3u3w_A Transcriptional activator PLCR protein; ternary complex, PLCR-PAPR7-DNA, HTH DNA-binding domain, QUO sensing; 2.40A {Bacillus thuringiensis} PDB: 2qfc_A

Probab=98.84  E-value=6.2e-07  Score=83.09  Aligned_cols=207  Identities=10%  Similarity=-0.018  Sum_probs=138.7

Q ss_pred             CCCCCCHhhHHHHHHHHHcCCCchhHHhhCCCCCCHHHH---HHHHHHHHhcCChhHHHHHHHHHHhCCC-CCCHH----
Q 040027           61 HPSPPPVSSFNILLASLAKNKHYDTRLNATGLFPNLYTY---NILINCFCKIGRVSLGFIAFGRILRSCF-TPNAA----  132 (595)
Q Consensus        61 ~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~---~~l~~~~~~~g~~~~A~~~~~~~~~~~~-~~~~~----  132 (595)
                      +...|+..+...+...+.-.-   ..+.......+...+   ...+..+...|++++|...++++.+... .++..    
T Consensus        40 g~~~~~~~~l~~i~~~l~~~~---~~~~~~~~~~~~~~~~~l~~~i~~~~~~~~y~~a~~~~~~~l~~~~~~~~~~~~~~  116 (293)
T 3u3w_A           40 GAVYPSMDILQGIAAKLQIPI---IHFYEVLIYSDIERKKQFKDQVIMLCKQKRYKEIYNKVWNELKKEEYHPEFQQFLQ  116 (293)
T ss_dssp             TSCCCCHHHHHHHHHHHTCCT---HHHHHTTTSSCHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHTTCCCCHHHHHHHH
T ss_pred             CCCCCCHHHHHHHHHHhCcCH---HHHhCCCCCCcchhHHHHHHHHHHHHHHhhHHHHHHHHHHHhccccCChHHHHHHH
Confidence            333366666666665554322   233333333333333   3346778999999999999999988532 12211    


Q ss_pred             HHHHHHHHHHhcCCHhHHHHHHHHHHhcCCCC-C----HhhHHHHHHHHHhcCChhHHHHHHHHHHhcCCCCCccccCcH
Q 040027          133 TFNSLIKGLHAESRIMEAAALFTKLKAFGCEP-N----VITYNTLINGLCRTGHTMIALNLFEEMANGNGEIGVVCKPNT  207 (595)
Q Consensus       133 ~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~-~----~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~~~  207 (595)
                      .+..+...+...|++++|+..|+++....... +    ..+++.++..|...|++++|+..|+++.+.-.......+...
T Consensus       117 ~~~~l~~~~~~~~~~~~Ai~~~~~al~~~~~~~~~~~~~~~~~~lg~~y~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~  196 (293)
T 3u3w_A          117 WQYYVAAYVLKKVDYEYCILELKKLLNQQLTGIDVYQNLYIENAIANIYAENGYLKKGIDLFEQILKQLEALHDNEEFDV  196 (293)
T ss_dssp             HHHHHHHHHTTSSCHHHHHHHHHHHHHTCCCCSCTTHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHSSCCHHHHH
T ss_pred             HHHHHHHHHHcccCHHHHHHHHHHHHHHhcccccHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHhcccchhHHH
Confidence            23346666777889999999999998853222 2    236889999999999999999999999842100000012234


Q ss_pred             HHHHHHHHHHHHcCCHhHHHHHHHHHhhC----CCCC-CHhHHHHHHHHHHhcC-CHHHHHHHHHHHHH
Q 040027          208 VTYSTIIDGLCKEGFVDKAKALFLQMKDE----NINP-DVVTYNSLIHGLCHAN-DWNEAKRLFIEMMD  270 (595)
Q Consensus       208 ~~~~~l~~~~~~~g~~~~A~~~~~~~~~~----~~~~-~~~~~~~ll~~~~~~~-~~~~A~~~~~~~~~  270 (595)
                      .++..+..+|...|++++|...+++..+.    +..+ -..+|..+..++.+.| ++++|...|++...
T Consensus       197 ~~~~nlg~~y~~~~~y~~A~~~~~~al~~~~~~~~~~~~~~~~~~lg~~~~~~g~~~~~A~~~~~~Al~  265 (293)
T 3u3w_A          197 KVRYNHAKALYLDSRYEESLYQVNKAIEISCRINSMALIGQLYYQRGECLRKLEYEEAEIEDAYKKASF  265 (293)
T ss_dssp             HHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTBCTTHHHHHHHHHHHHHHTTCCHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHhHHHHHHHHHHHHHHHHHHcCcHHHHHHHHHHHHHHHHHhCCcHHHHHHHHHHHHH
Confidence            57888999999999999999999887642    2111 2567788888888888 46888888877654

>1hh8_A P67PHOX, NCF-2, neutrophil cytosol factor 2; cell cycle, phagocyte oxidase factor, SH3 domain, repeat, TPR repeat cell cycle; HET: FLC; 1.8A {Homo sapiens} SCOP: a.118.8.1 PDB: 1wm5_A 1e96_B*

Probab=98.84  E-value=1.7e-07  Score=82.18  Aligned_cols=121  Identities=10%  Similarity=-0.101  Sum_probs=60.4

Q ss_pred             HHHHHhcCCHHHHHHHHHHHHHcCCCcCHHHHHHHHHHHHhcCChHHHHHHHHhcccCCCCCCHHHHHHHHHHHHhcCCh
Q 040027          424 IDGLCKNGYIIEAVELFRTLRILKCELDIQAYNCLIDGLCKSGRLKFAWELFCSLPHGVLVPNVVTYNIMIQGLCNDGQM  503 (595)
Q Consensus       424 ~~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~p~~~~~~~l~~~~~~~g~~  503 (595)
                      ...+...|++++|...++++.    +++...+..++.++...|++++|+..|++..... +.+...|..++.+|...|++
T Consensus        13 g~~~~~~~~~~~A~~~~~~a~----~~~~~~~~~lg~~~~~~g~~~~A~~~~~~al~~~-~~~~~~~~~lg~~~~~~~~~   87 (213)
T 1hh8_A           13 GVLAADKKDWKGALDAFSAVQ----DPHSRICFNIGCMYTILKNMTEAEKAFTRSINRD-KHLAVAYFQRGMLYYQTEKY   87 (213)
T ss_dssp             HHHHHHTTCHHHHHHHHHTSS----SCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCH
T ss_pred             HHHHHHhCCHHHHHHHHHHHc----CCChHHHHHHHHHHHHcCCHHHHHHHHHHHHHhC-ccchHHHHHHHHHHHHcccH
Confidence            334444555555555554442    3344555555555555555555555555554421 11344455555555555555


Q ss_pred             hHHHHHHHHHHHcCCCCC----------------HHHHHHHHHHHHHcCChhHHHHHHHHHHH
Q 040027          504 DKARDLFLDMEENAAAPD----------------VITFDMLIHGFIRINEPSKVNELLHKMKE  550 (595)
Q Consensus       504 ~~A~~~~~~~~~~~~~~~----------------~~~~~~l~~~~~~~g~~~~A~~~~~~~~~  550 (595)
                      ++|+..|+++.+.. +.+                ...+..++.+|...|++++|...++++.+
T Consensus        88 ~~A~~~~~~al~~~-~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~al~  149 (213)
T 1hh8_A           88 DLAIKDLKEALIQL-RGNQLIDYKILGLQFKLFACEVLYNIAFMYAKKEEWKKAEEQLALATS  149 (213)
T ss_dssp             HHHHHHHHHHHHTT-TTCSEEECGGGTBCCEEEHHHHHHHHHHHHHHTTCHHHHHHHHHHHHT
T ss_pred             HHHHHHHHHHHHhC-CCccHHHHHHhccccCccchHHHHHHHHHHHHccCHHHHHHHHHHHHH
Confidence            55555555555432 111                14455555555556666666666665554

>3q7a_A Farnesyltransferase alpha subunit; protein prenyltransferase, transferase-transferase inhibitor; HET: SUC 3FX FPP 778; 2.00A {Cryptococcus neoformans} PDB: 3q73_A* 3q78_A* 3q79_A* 3q75_A* 3q7f_A* 3sfx_A* 3sfy_A*

Probab=98.82  E-value=6.1e-06  Score=76.49  Aligned_cols=170  Identities=9%  Similarity=0.015  Sum_probs=82.5

Q ss_pred             hHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHhcC-CHHHHHHHHHHHHhcCCCCCHHHHHHHHHHHHhC-C-CHHHHHHH
Q 040027          293 MDEASRLLDLMVQRGVRPNACTYNTLMDGFCLMG-KINRAEELFGSMESMGCKHDDVSYNILINGYCKN-K-EVEEALSL  369 (595)
Q Consensus       293 ~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~-~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~-~-~~~~A~~~  369 (595)
                      .++|+++++.++..+.. +..+++.-..++...| .+++++..++.+.... +.+..+|+.-..++... + ++++++++
T Consensus        70 se~AL~lt~~~L~~nP~-~ytaWn~R~~iL~~l~~~l~eEL~~~~~~L~~n-PKny~aW~hR~wlL~~l~~~~~~~EL~~  147 (349)
T 3q7a_A           70 SERALELTEIIVRMNPA-HYTVWQYRFSLLTSLNKSLEDELRLMNEFAVQN-LKSYQVWHHRLLLLDRISPQDPVSEIEY  147 (349)
T ss_dssp             SHHHHHHHHHHHHHCTT-CHHHHHHHHHHHHHTTCCHHHHHHHHHHHHHTT-CCCHHHHHHHHHHHHHHCCSCCHHHHHH
T ss_pred             CHHHHHHHHHHHHhCch-hHHHHHHHHHHHHHhhhhHHHHHHHHHHHHHhC-CCcHHHHHHHHHHHHHhcCCChHHHHHH
Confidence            34555555555554322 3344444444444445 3555555555555543 33444555544444443 4 55555555


Q ss_pred             HHHHHHCCCCCCHHHHHHHHHHHHccCCHH--------HHHHHHHHHHHCCCCCCHHHHHHHHHHHHhcCC-------HH
Q 040027          370 YREMVSKGIKPTVVTYNTLFLGLFEIHQVE--------HALKLFDEMQRDGVAADTRTYTTFIDGLCKNGY-------II  434 (595)
Q Consensus       370 ~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~--------~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~-------~~  434 (595)
                      ++++++...+ +..+|+.-...+...+.++        ++++.++++++.+ +-+...|+.....+.+.++       ++
T Consensus       148 ~~k~L~~dpk-Ny~AW~~R~wvl~~l~~~~~~~~~~~~eELe~~~k~I~~d-p~N~SAW~~R~~lL~~l~~~~~~~~~~~  225 (349)
T 3q7a_A          148 IHGSLLPDPK-NYHTWAYLHWLYSHFSTLGRISEAQWGSELDWCNEMLRVD-GRNNSAWGWRWYLRVSRPGAETSSRSLQ  225 (349)
T ss_dssp             HHHHTSSCTT-CHHHHHHHHHHHHHHHHTTCCCHHHHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHTTSTTCCCCHHHHH
T ss_pred             HHHHHHhCCC-CHHHHHHHHHHHHHhccccccchhhHHHHHHHHHHHHHhC-CCCHHHHHHHHHHHHhccccccchHHHH
Confidence            5555554333 4444443333333332222        4555555555442 3344444444444444443       45


Q ss_pred             HHHHHHHHHHHcCCCcCHHHHHHHHHHHHhcCC
Q 040027          435 EAVELFRTLRILKCELDIQAYNCLIDGLCKSGR  467 (595)
Q Consensus       435 ~A~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~  467 (595)
                      ++++.+++++... +-|...|+.+-..+.+.|+
T Consensus       226 eELe~~~~aI~~~-P~n~SaW~Ylr~Ll~~~~~  257 (349)
T 3q7a_A          226 DELIYILKSIHLI-PHNVSAWNYLRGFLKHFSL  257 (349)
T ss_dssp             HHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTC
T ss_pred             HHHHHHHHHHHhC-CCCHHHHHHHHHHHHhcCC
Confidence            6666666666554 5556666555555554444

>3q7a_A Farnesyltransferase alpha subunit; protein prenyltransferase, transferase-transferase inhibitor; HET: SUC 3FX FPP 778; 2.00A {Cryptococcus neoformans} PDB: 3q73_A* 3q78_A* 3q79_A* 3q75_A* 3q7f_A* 3sfx_A* 3sfy_A*

Probab=98.82  E-value=3.7e-06  Score=77.90  Aligned_cols=184  Identities=7%  Similarity=-0.045  Sum_probs=137.6

Q ss_pred             HHHHHHHHHHhcCChhHHHHHHHHHHhCCCCCCHHHHHHHHHHHHhcC-CHhHHHHHHHHHHhcCCCCCHhhHHHHHHHH
Q 040027           98 TYNILINCFCKIGRVSLGFIAFGRILRSCFTPNAATFNSLIKGLHAES-RIMEAAALFTKLKAFGCEPNVITYNTLINGL  176 (595)
Q Consensus        98 ~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g-~~~~A~~~~~~~~~~~~~~~~~~~~~l~~~~  176 (595)
                      .++.+.......+..++|+.++++++..+ +-+..+|+.--..+...| .++++++.++.++... +-+..+|+.-...+
T Consensus        56 ~~~~~r~~~~~~e~se~AL~lt~~~L~~n-P~~ytaWn~R~~iL~~l~~~l~eEL~~~~~~L~~n-PKny~aW~hR~wlL  133 (349)
T 3q7a_A           56 AMDYFRAIAAKEEKSERALELTEIIVRMN-PAHYTVWQYRFSLLTSLNKSLEDELRLMNEFAVQN-LKSYQVWHHRLLLL  133 (349)
T ss_dssp             HHHHHHHHHHTTCCSHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCCHHHHHHHHHHHHHTT-CCCHHHHHHHHHHH
T ss_pred             HHHHHHHHHHhCCCCHHHHHHHHHHHHhC-chhHHHHHHHHHHHHHhhhhHHHHHHHHHHHHHhC-CCcHHHHHHHHHHH
Confidence            34444444455566679999999999986 557788888888888888 5999999999999875 34788888877777


Q ss_pred             Hhc-C-ChhHHHHHHHHHHhcCCCCCccccCcHHHHHHHHHHHHHcCCHh--------HHHHHHHHHhhCCCCCCHhHHH
Q 040027          177 CRT-G-HTMIALNLFEEMANGNGEIGVVCKPNTVTYSTIIDGLCKEGFVD--------KAKALFLQMKDENINPDVVTYN  246 (595)
Q Consensus       177 ~~~-g-~~~~A~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~--------~A~~~~~~~~~~~~~~~~~~~~  246 (595)
                      ... + +++++++.++++...+       +.+..+|+.-.-++.+.|.++        ++++.++++.+.++ -|...|+
T Consensus       134 ~~l~~~~~~~EL~~~~k~L~~d-------pkNy~AW~~R~wvl~~l~~~~~~~~~~~~eELe~~~k~I~~dp-~N~SAW~  205 (349)
T 3q7a_A          134 DRISPQDPVSEIEYIHGSLLPD-------PKNYHTWAYLHWLYSHFSTLGRISEAQWGSELDWCNEMLRVDG-RNNSAWG  205 (349)
T ss_dssp             HHHCCSCCHHHHHHHHHHTSSC-------TTCHHHHHHHHHHHHHHHHTTCCCHHHHHHHHHHHHHHHHHCT-TCHHHHH
T ss_pred             HHhcCCChHHHHHHHHHHHHhC-------CCCHHHHHHHHHHHHHhccccccchhhHHHHHHHHHHHHHhCC-CCHHHHH
Confidence            776 7 8999999999999876       677888887776666666666        88888888887653 3777888


Q ss_pred             HHHHHHHhcCC-------HHHHHHHHHHHHHCCCCCCHhhHHHHHHHHHhcCC
Q 040027          247 SLIHGLCHAND-------WNEAKRLFIEMMDQGVQPSVVTFNVIMDELCKNRK  292 (595)
Q Consensus       247 ~ll~~~~~~~~-------~~~A~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~  292 (595)
                      .....+.+.+.       ++++++.+++++... +-|...|+.+-..+.+.|.
T Consensus       206 ~R~~lL~~l~~~~~~~~~~~eELe~~~~aI~~~-P~n~SaW~Ylr~Ll~~~~~  257 (349)
T 3q7a_A          206 WRWYLRVSRPGAETSSRSLQDELIYILKSIHLI-PHNVSAWNYLRGFLKHFSL  257 (349)
T ss_dssp             HHHHHHTTSTTCCCCHHHHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTC
T ss_pred             HHHHHHHhccccccchHHHHHHHHHHHHHHHhC-CCCHHHHHHHHHHHHhcCC
Confidence            77777777665       677888887777653 2366667665555555554

>1hh8_A P67PHOX, NCF-2, neutrophil cytosol factor 2; cell cycle, phagocyte oxidase factor, SH3 domain, repeat, TPR repeat cell cycle; HET: FLC; 1.8A {Homo sapiens} SCOP: a.118.8.1 PDB: 1wm5_A 1e96_B*

Probab=98.82  E-value=3.8e-07  Score=79.92  Aligned_cols=136  Identities=11%  Similarity=-0.096  Sum_probs=112.7

Q ss_pred             HHHHHHHHHHHhcCChhHHHHHHHHHHhCCCCCCHHHHHHHHHHHHhcCCHhHHHHHHHHHHhcCCCCCHhhHHHHHHHH
Q 040027           97 YTYNILINCFCKIGRVSLGFIAFGRILRSCFTPNAATFNSLIKGLHAESRIMEAAALFTKLKAFGCEPNVITYNTLINGL  176 (595)
Q Consensus        97 ~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~~l~~~~  176 (595)
                      ..+..+...+...|++++|+..|+++.    .++..+|..+...+...|++++|++.|++..... +.+..++..+..++
T Consensus         7 ~~~~~~g~~~~~~~~~~~A~~~~~~a~----~~~~~~~~~lg~~~~~~g~~~~A~~~~~~al~~~-~~~~~~~~~lg~~~   81 (213)
T 1hh8_A            7 ISLWNEGVLAADKKDWKGALDAFSAVQ----DPHSRICFNIGCMYTILKNMTEAEKAFTRSINRD-KHLAVAYFQRGMLY   81 (213)
T ss_dssp             HHHHHHHHHHHHTTCHHHHHHHHHTSS----SCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHhCCHHHHHHHHHHHc----CCChHHHHHHHHHHHHcCCHHHHHHHHHHHHHhC-ccchHHHHHHHHHH
Confidence            345567788899999999999999885    5688899999999999999999999999999875 44788899999999


Q ss_pred             HhcCChhHHHHHHHHHHhcCCCCCc---------cccCcHHHHHHHHHHHHHcCCHhHHHHHHHHHhhCC
Q 040027          177 CRTGHTMIALNLFEEMANGNGEIGV---------VCKPNTVTYSTIIDGLCKEGFVDKAKALFLQMKDEN  237 (595)
Q Consensus       177 ~~~g~~~~A~~~~~~~~~~~~~~~~---------~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~  237 (595)
                      ...|++++|++.|+++.+.......         ..+.....+..+..++...|++++|.+.|++..+..
T Consensus        82 ~~~~~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~al~~~  151 (213)
T 1hh8_A           82 YQTEKYDLAIKDLKEALIQLRGNQLIDYKILGLQFKLFACEVLYNIAFMYAKKEEWKKAEEQLALATSMK  151 (213)
T ss_dssp             HHTTCHHHHHHHHHHHHHTTTTCSEEECGGGTBCCEEEHHHHHHHHHHHHHHTTCHHHHHHHHHHHHTTC
T ss_pred             HHcccHHHHHHHHHHHHHhCCCccHHHHHHhccccCccchHHHHHHHHHHHHccCHHHHHHHHHHHHHcC
Confidence            9999999999999999986521100         011234788889999999999999999999988864

>3u3w_A Transcriptional activator PLCR protein; ternary complex, PLCR-PAPR7-DNA, HTH DNA-binding domain, QUO sensing; 2.40A {Bacillus thuringiensis} PDB: 2qfc_A

Probab=98.81  E-value=9e-07  Score=81.98  Aligned_cols=163  Identities=9%  Similarity=-0.044  Sum_probs=115.7

Q ss_pred             HHHHHHccCCHHHHHHHHHHHHHCCC-CCCH----HHHHHHHHHHHhcCCHHHHHHHHHHHHHcCCC-cC----HHHHHH
Q 040027          388 LFLGLFEIHQVEHALKLFDEMQRDGV-AADT----RTYTTFIDGLCKNGYIIEAVELFRTLRILKCE-LD----IQAYNC  457 (595)
Q Consensus       388 l~~~~~~~~~~~~a~~~~~~~~~~~~-~~~~----~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~-~~----~~~~~~  457 (595)
                      .+..+...|++++|...+++..+... .++.    ..+..+...+...|++++|...++++...... .+    ..+++.
T Consensus        81 ~i~~~~~~~~y~~a~~~~~~~l~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~Ai~~~~~al~~~~~~~~~~~~~~~~~~  160 (293)
T 3u3w_A           81 QVIMLCKQKRYKEIYNKVWNELKKEEYHPEFQQFLQWQYYVAAYVLKKVDYEYCILELKKLLNQQLTGIDVYQNLYIENA  160 (293)
T ss_dssp             HHHHHHHTTCHHHHHHHHHHHHTTCCCCHHHHHHHHHHHHHHHHHTTSSCHHHHHHHHHHHHHTCCCCSCTTHHHHHHHH
T ss_pred             HHHHHHHHhhHHHHHHHHHHHhccccCChHHHHHHHHHHHHHHHHHcccCHHHHHHHHHHHHHHhcccccHHHHHHHHHH
Confidence            35566777888888888887776421 1221    12334555666777888888888888874222 22    336888


Q ss_pred             HHHHHHhcCChHHHHHHHHhccc----C-CCCCC-HHHHHHHHHHHHhcCChhHHHHHHHHHHHc----CCCCC-HHHHH
Q 040027          458 LIDGLCKSGRLKFAWELFCSLPH----G-VLVPN-VVTYNIMIQGLCNDGQMDKARDLFLDMEEN----AAAPD-VITFD  526 (595)
Q Consensus       458 l~~~~~~~g~~~~A~~~~~~~~~----~-~~~p~-~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~----~~~~~-~~~~~  526 (595)
                      ++.+|...|++++|+..|+++.+    . +..+. ..++..++.+|...|++++|+..++++++.    +..+. ..+|.
T Consensus       161 lg~~y~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~nlg~~y~~~~~y~~A~~~~~~al~~~~~~~~~~~~~~~~~  240 (293)
T 3u3w_A          161 IANIYAENGYLKKGIDLFEQILKQLEALHDNEEFDVKVRYNHAKALYLDSRYEESLYQVNKAIEISCRINSMALIGQLYY  240 (293)
T ss_dssp             HHHHHHHTTCHHHHHHHHHHHHHHHHHSSCCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTBCTTHHHHHH
T ss_pred             HHHHHHHcCCHHHHHHHHHHHHHHHHhcccchhHHHHHHHHHHHHHHHHhHHHHHHHHHHHHHHHHHHcCcHHHHHHHHH
Confidence            88889999999999998888773    1 11222 347788899999999999999999988763    21222 57888


Q ss_pred             HHHHHHHHcCC-hhHHHHHHHHHHH
Q 040027          527 MLIHGFIRINE-PSKVNELLHKMKE  550 (595)
Q Consensus       527 ~l~~~~~~~g~-~~~A~~~~~~~~~  550 (595)
                      .++.+|...|+ +++|.+.++++..
T Consensus       241 ~lg~~~~~~g~~~~~A~~~~~~Al~  265 (293)
T 3u3w_A          241 QRGECLRKLEYEEAEIEDAYKKASF  265 (293)
T ss_dssp             HHHHHHHHTTCCHHHHHHHHHHHHH
T ss_pred             HHHHHHHHhCCcHHHHHHHHHHHHH
Confidence            89999999995 6999999998874

>2e2e_A Formate-dependent nitrite reductase complex NRFG; TPR, cytochrome C biogenesis, O157:H7 EDL933, formate- nitrite reductase complex, lyase; 2.05A {Escherichia coli}

Probab=98.81  E-value=7.4e-08  Score=81.71  Aligned_cols=127  Identities=15%  Similarity=0.169  Sum_probs=100.6

Q ss_pred             ccccccCCCChHHHHHHHHHHHHhCCCCCCHhhHHHHHHHHHcCCCchhHHhhCCCCCCHHHHHHHHHHHHhcCChhHHH
Q 040027           37 TREGDINVITPNEAFCIFDYMLRMHPSPPPVSSFNILLASLAKNKHYDTRLNATGLFPNLYTYNILINCFCKIGRVSLGF  116 (595)
Q Consensus        37 ~~~~~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~  116 (595)
                      ....+...|++++|...|+++++.+|.                               ++..|..+...+...|++++|+
T Consensus        16 ~~~~~~~~~~~~~A~~~~~~al~~~p~-------------------------------~~~~~~~lg~~~~~~~~~~~A~   64 (177)
T 2e2e_A           16 PLHQFASQQNPEAQLQALQDKIRANPQ-------------------------------NSEQWALLGEYYLWQNDYSNSL   64 (177)
T ss_dssp             TTCCCC-----CCCCHHHHHHHHHCCS-------------------------------CHHHHHHHHHHHHHTTCHHHHH
T ss_pred             hhhhhhhccCHHHHHHHHHHHHHhCCC-------------------------------cHHHHHHHHHHHHHcCCHHHHH
Confidence            345578889999999999999999987                               3445556777778888999999


Q ss_pred             HHHHHHHhCCCCCCHHHHHHHHHH-HHhcCCH--hHHHHHHHHHHhcCCCCCHhhHHHHHHHHHhcCChhHHHHHHHHHH
Q 040027          117 IAFGRILRSCFTPNAATFNSLIKG-LHAESRI--MEAAALFTKLKAFGCEPNVITYNTLINGLCRTGHTMIALNLFEEMA  193 (595)
Q Consensus       117 ~~~~~~~~~~~~~~~~~~~~l~~~-~~~~g~~--~~A~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~  193 (595)
                      ..|+++.+.. +.+...+..+... +...|++  ++|+..|+++.... +.+...+..+...+...|++++|+..|+++.
T Consensus        65 ~~~~~al~~~-p~~~~~~~~la~~l~~~~~~~~~~~A~~~~~~al~~~-p~~~~~~~~la~~~~~~g~~~~A~~~~~~al  142 (177)
T 2e2e_A           65 LAYRQALQLR-GENAELYAALATVLYYQASQHMTAQTRAMIDKALALD-SNEITALMLLASDAFMQANYAQAIELWQKVM  142 (177)
T ss_dssp             HHHHHHHHHH-CSCHHHHHHHHHHHHHHTTTCCCHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHH
T ss_pred             HHHHHHHHcC-CCCHHHHHHHHHHHHHhcCCcchHHHHHHHHHHHHhC-CCcHHHHHHHHHHHHHcccHHHHHHHHHHHH
Confidence            9999988875 4567788888888 7788998  99999999998874 3367888889999999999999999999998


Q ss_pred             hcC
Q 040027          194 NGN  196 (595)
Q Consensus       194 ~~~  196 (595)
                      ...
T Consensus       143 ~~~  145 (177)
T 2e2e_A          143 DLN  145 (177)
T ss_dssp             HTC
T ss_pred             hhC
Confidence            865

>1a17_A Serine/threonine protein phosphatase 5; hydrolase, protein-protein interactions, TPR, S helix; 2.45A {Homo sapiens} SCOP: a.118.8.1 PDB: 2bug_A

Probab=98.81  E-value=2.1e-07  Score=77.77  Aligned_cols=130  Identities=11%  Similarity=-0.005  Sum_probs=101.0

Q ss_pred             HHHHHHHHHHHHhcCChhHHHHHHHHHHhCCCCCCHHHHHHHHHHHHhcCCHhHHHHHHHHHHhcCCCCCHhhHHHHHHH
Q 040027           96 LYTYNILINCFCKIGRVSLGFIAFGRILRSCFTPNAATFNSLIKGLHAESRIMEAAALFTKLKAFGCEPNVITYNTLING  175 (595)
Q Consensus        96 ~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~~l~~~  175 (595)
                      ...|..++..+...|++++|...|+++++.. +.+..++..+...+...|++++|++.+++..... +.+..++..+...
T Consensus        13 ~~~~~~~a~~~~~~~~~~~A~~~~~~al~~~-~~~~~~~~~~a~~~~~~~~~~~A~~~~~~a~~~~-~~~~~~~~~~a~~   90 (166)
T 1a17_A           13 AEELKTQANDYFKAKDYENAIKFYSQAIELN-PSNAIYYGNRSLAYLRTECYGYALGDATRAIELD-KKYIKGYYRRAAS   90 (166)
T ss_dssp             HHHHHHHHHHHHHTTCHHHHHHHHHHHHHHS-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHccCHHHHHHHHHHHHHhC-CCChHHHHHHHHHHHHcCCHHHHHHHHHHHHHhC-cccHHHHHHHHHH
Confidence            4567778888888999999999999988874 4567888888888888999999999999888874 3467788888888


Q ss_pred             HHhcCChhHHHHHHHHHHhcCCCCCccccCcHHHHHH--HHHHHHHcCCHhHHHHHHHHHh
Q 040027          176 LCRTGHTMIALNLFEEMANGNGEIGVVCKPNTVTYST--IIDGLCKEGFVDKAKALFLQMK  234 (595)
Q Consensus       176 ~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~~~~~~~~--l~~~~~~~g~~~~A~~~~~~~~  234 (595)
                      +...|++++|...|+++....       +.+...+..  .+..+...|++++|.+.++...
T Consensus        91 ~~~~~~~~~A~~~~~~a~~~~-------p~~~~~~~~~~~~~~~~~~~~~~~A~~~~~~~~  144 (166)
T 1a17_A           91 NMALGKFRAALRDYETVVKVK-------PHDKDAKMKYQECNKIVKQKAFERAIAGDEHKR  144 (166)
T ss_dssp             HHHTTCHHHHHHHHHHHHHHS-------TTCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHhccHHHHHHHHHHHHHhC-------CCCHHHHHHHHHHHHHHHHHHHHHHHHcccchH
Confidence            889999999999999888765       344555533  3344667788888888777654

>1a17_A Serine/threonine protein phosphatase 5; hydrolase, protein-protein interactions, TPR, S helix; 2.45A {Homo sapiens} SCOP: a.118.8.1 PDB: 2bug_A

Probab=98.80  E-value=2.2e-07  Score=77.69  Aligned_cols=128  Identities=8%  Similarity=-0.073  Sum_probs=92.6

Q ss_pred             HHHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCcCHHHHHHHHHHHHhcCChHHHHHHHHhcccCCCCC-CHHHHHHHHHH
Q 040027          418 RTYTTFIDGLCKNGYIIEAVELFRTLRILKCELDIQAYNCLIDGLCKSGRLKFAWELFCSLPHGVLVP-NVVTYNIMIQG  496 (595)
Q Consensus       418 ~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~p-~~~~~~~l~~~  496 (595)
                      ..+..+...+...|++++|...++++.... +.+..++..++.++...|++++|...+++....  .| +...|..++.+
T Consensus        14 ~~~~~~a~~~~~~~~~~~A~~~~~~al~~~-~~~~~~~~~~a~~~~~~~~~~~A~~~~~~a~~~--~~~~~~~~~~~a~~   90 (166)
T 1a17_A           14 EELKTQANDYFKAKDYENAIKFYSQAIELN-PSNAIYYGNRSLAYLRTECYGYALGDATRAIEL--DKKYIKGYYRRAAS   90 (166)
T ss_dssp             HHHHHHHHHHHHTTCHHHHHHHHHHHHHHS-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH--CTTCHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHccCHHHHHHHHHHHHHhC-CCChHHHHHHHHHHHHcCCHHHHHHHHHHHHHh--CcccHHHHHHHHHH
Confidence            345556667777888888888888877765 556777778888888888888888888887763  33 46677778888


Q ss_pred             HHhcCChhHHHHHHHHHHHcCCCCCHHHHHH--HHHHHHHcCChhHHHHHHHHHH
Q 040027          497 LCNDGQMDKARDLFLDMEENAAAPDVITFDM--LIHGFIRINEPSKVNELLHKMK  549 (595)
Q Consensus       497 ~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~~--l~~~~~~~g~~~~A~~~~~~~~  549 (595)
                      +...|++++|...++++.+.. +.+...+..  .+..+...|++++|...+++..
T Consensus        91 ~~~~~~~~~A~~~~~~a~~~~-p~~~~~~~~~~~~~~~~~~~~~~~A~~~~~~~~  144 (166)
T 1a17_A           91 NMALGKFRAALRDYETVVKVK-PHDKDAKMKYQECNKIVKQKAFERAIAGDEHKR  144 (166)
T ss_dssp             HHHTTCHHHHHHHHHHHHHHS-TTCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHhccHHHHHHHHHHHHHhC-CCCHHHHHHHHHHHHHHHHHHHHHHHHcccchH
Confidence            888888888888888888764 344555533  3334667788888888877665

>2qfc_A PLCR protein; TPR, HTH, transcription regulation; 2.60A {Bacillus thuringiensis serovar ISRAELE35646}

Probab=98.77  E-value=1.3e-06  Score=80.85  Aligned_cols=164  Identities=9%  Similarity=-0.039  Sum_probs=108.7

Q ss_pred             HHHHHHHHccCCHHHHHHHHHHHHHCCCCCCH------HHHHHHHHHHHhcCCHHHHHHHHHHHHHcCC---CcC--HHH
Q 040027          386 NTLFLGLFEIHQVEHALKLFDEMQRDGVAADT------RTYTTFIDGLCKNGYIIEAVELFRTLRILKC---ELD--IQA  454 (595)
Q Consensus       386 ~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~------~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~---~~~--~~~  454 (595)
                      ...+..+...|++++|.+.+.+..+... ...      ..+..+...+...|++++|...++++.....   .+.  ..+
T Consensus        79 ~~~~~~~~~~~~y~~A~~~~~~~l~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~A~~~~~~al~~~~~~~~~~~~~~~  157 (293)
T 2qfc_A           79 KDQVIMLCKQKRYKEIYNKVWNELKKEE-YHPEFQQFLQWQYYVAAYVLKKVDYEYCILELKKLLNQQLTGIDVYQNLYI  157 (293)
T ss_dssp             HHHHHHHHHTTCHHHHHHHHHHHHHTCC-CCHHHHHHHHHHHHHHHHHHTSSCHHHHHHHHHHHHTTCCCSSCTTHHHHH
T ss_pred             HHHHHHHHHhhhHHHHHHHHHHHhcccc-CChhHHHHHHHHHHHHHHHhcCCCHHHHHHHHHHHHHHHhcCCchHHHHHH
Confidence            3344455566666666666665555321 111      1223344556677788888888888765321   111  457


Q ss_pred             HHHHHHHHHhcCChHHHHHHHHhcccC-CCCCC-----HHHHHHHHHHHHhcCChhHHHHHHHHHHHcC----CCC-CHH
Q 040027          455 YNCLIDGLCKSGRLKFAWELFCSLPHG-VLVPN-----VVTYNIMIQGLCNDGQMDKARDLFLDMEENA----AAP-DVI  523 (595)
Q Consensus       455 ~~~l~~~~~~~g~~~~A~~~~~~~~~~-~~~p~-----~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~----~~~-~~~  523 (595)
                      ++.++..|...|++++|...++++.+. ...|+     ..++..++.+|...|++++|+..++++++..    ... -..
T Consensus       158 ~~~lg~~y~~~~~~~~A~~~~~kal~~~~~~~~~~~~~~~~~~nlg~~y~~~~~y~~Al~~~~kal~~~~~~~~~~~~~~  237 (293)
T 2qfc_A          158 ENAIANIYAENGYLKKGIDLFEQILKQLEALHDNEEFDVKVRYNHAKALYLDSRYEESLYQVNKAIEISCRINSMALIGQ  237 (293)
T ss_dssp             HHHHHHHHHHTTCHHHHHHHHHHHHHHHHHSCCCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTBCSSHHH
T ss_pred             HHHHHHHHHHcCCHHHHHHHHHHHHHHHHhcCccccchHHHHHhHHHHHHHHhhHHHHHHHHHHHHHHHHhcCcHHHHHH
Confidence            788888888888888888888887631 01122     2577888888999999999999998887531    111 156


Q ss_pred             HHHHHHHHHHHcCChhHH-HHHHHHHHH
Q 040027          524 TFDMLIHGFIRINEPSKV-NELLHKMKE  550 (595)
Q Consensus       524 ~~~~l~~~~~~~g~~~~A-~~~~~~~~~  550 (595)
                      +|..++.+|...|++++| ...++++..
T Consensus       238 ~~~~lg~~y~~~g~~~~Ai~~~~~~Al~  265 (293)
T 2qfc_A          238 LYYQRGECLRKLEYEEAEIEDAYKKASF  265 (293)
T ss_dssp             HHHHHHHHHHHTTCCHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHcCCcHHHHHHHHHHHHH
Confidence            788889999999999999 777887763

>2lni_A Stress-induced-phosphoprotein 1; structural genomics, northeast structural genomics consortiu PSI-biology, protein structure initiative, chaperone; NMR {Homo sapiens}

Probab=98.76  E-value=2.8e-07  Score=73.59  Aligned_cols=120  Identities=6%  Similarity=-0.050  Sum_probs=103.6

Q ss_pred             CCCHHHHHHHHHHHHhcCChhHHHHHHHHHHhCCCCCCHHHHHHHHHHHHhcCCHhHHHHHHHHHHhcCCCCCHhhHHHH
Q 040027           93 FPNLYTYNILINCFCKIGRVSLGFIAFGRILRSCFTPNAATFNSLIKGLHAESRIMEAAALFTKLKAFGCEPNVITYNTL  172 (595)
Q Consensus        93 ~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~~l  172 (595)
                      +.++..|..++..+...|++++|+..|+++.+.. +.+..++..+...+...|++++|++.++++.... +.+..++..+
T Consensus        13 ~~~~~~~~~~~~~~~~~~~~~~A~~~~~~al~~~-~~~~~~~~~la~~~~~~~~~~~A~~~~~~a~~~~-~~~~~~~~~l   90 (133)
T 2lni_A           13 PDLALMVKNKGNECFQKGDYPQAMKHYTEAIKRN-PKDAKLYSNRAACYTKLLEFQLALKDCEECIQLE-PTFIKGYTRK   90 (133)
T ss_dssp             SCHHHHHHHHHHHHHHTTCSHHHHHHHHHHHTTC-TTCHHHHHHHHHHHTTTTCHHHHHHHHHHHHHHC-TTCHHHHHHH
T ss_pred             cccHHHHHHHHHHHHHcCCHHHHHHHHHHHHHcC-CCcHHHHHHHHHHHHHhccHHHHHHHHHHHHHhC-CCchHHHHHH
Confidence            4567889999999999999999999999999874 4578889999999999999999999999999875 3478889999


Q ss_pred             HHHHHhcCChhHHHHHHHHHHhcCCCCCccccCcHHHHHHHHHHHHHcC
Q 040027          173 INGLCRTGHTMIALNLFEEMANGNGEIGVVCKPNTVTYSTIIDGLCKEG  221 (595)
Q Consensus       173 ~~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g  221 (595)
                      ..++...|++++|++.|++.....       +.+...+..+..++...|
T Consensus        91 a~~~~~~~~~~~A~~~~~~~~~~~-------p~~~~~~~~l~~~~~~~~  132 (133)
T 2lni_A           91 AAALEAMKDYTKAMDVYQKALDLD-------SSCKEAADGYQRCMMAQY  132 (133)
T ss_dssp             HHHHHHTTCHHHHHHHHHHHHHHC-------GGGTHHHHHHHHHHHHHT
T ss_pred             HHHHHHHhhHHHHHHHHHHHHHhC-------CCchHHHHHHHHHHHHhc
Confidence            999999999999999999999875       445667777777776655

>2vyi_A SGTA protein; chaperone, TPR repeat, phosphoprotein, tetratricopeptide repeat protein, HOST-virus interaction; 2.4A {Homo sapiens} SCOP: k.38.1.1

Probab=98.76  E-value=1.7e-07  Score=74.60  Aligned_cols=120  Identities=9%  Similarity=-0.067  Sum_probs=78.9

Q ss_pred             CHHHHHHHHHHHHhcCChHHHHHHHHhcccCCCCCCHHHHHHHHHHHHhcCChhHHHHHHHHHHHcCCCCCHHHHHHHHH
Q 040027          451 DIQAYNCLIDGLCKSGRLKFAWELFCSLPHGVLVPNVVTYNIMIQGLCNDGQMDKARDLFLDMEENAAAPDVITFDMLIH  530 (595)
Q Consensus       451 ~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~p~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~~l~~  530 (595)
                      +...+..++..+...|++++|...++++... .+.+...+..++.++...|++++|+..++++.+.. +.+...+..++.
T Consensus        11 ~~~~~~~~~~~~~~~~~~~~A~~~~~~~~~~-~~~~~~~~~~~a~~~~~~~~~~~A~~~~~~~~~~~-~~~~~~~~~~~~   88 (131)
T 2vyi_A           11 EAERLKTEGNEQMKVENFEAAVHFYGKAIEL-NPANAVYFCNRAAAYSKLGNYAGAVQDCERAICID-PAYSKAYGRMGL   88 (131)
T ss_dssp             HHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH-CTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHH
T ss_pred             hhHHHHHHHHHHHHccCHHHHHHHHHHHHHc-CCCCHHHHHHHHHHHHHhhchHHHHHHHHHHHhcC-ccCHHHHHHHHH
Confidence            3455566666666777777777777766652 12245666667777777777777777777777653 445666677777


Q ss_pred             HHHHcCChhHHHHHHHHHHHCCCCCCHHHHHHHHHHHHhcCcc
Q 040027          531 GFIRINEPSKVNELLHKMKEKKVMPDASIVSIVVDLLVKNEIS  573 (595)
Q Consensus       531 ~~~~~g~~~~A~~~~~~~~~~~~~p~~~~~~~l~~~~~~~g~~  573 (595)
                      +|...|++++|..+++++.+.. +.+...+..+..++.+.|++
T Consensus        89 ~~~~~~~~~~A~~~~~~~~~~~-p~~~~~~~~l~~~~~~~~~~  130 (131)
T 2vyi_A           89 ALSSLNKHVEAVAYYKKALELD-PDNETYKSNLKIAELKLREA  130 (131)
T ss_dssp             HHHHTTCHHHHHHHHHHHHHHS-TTCHHHHHHHHHHHHHHTTC
T ss_pred             HHHHhCCHHHHHHHHHHHHhcC-ccchHHHHHHHHHHHHHhcC
Confidence            7777777777777777777642 22566677777777766665

>3gyz_A Chaperone protein IPGC; asymmetric homodimer, tetratricopeptide repeat, TPR, chapero virulence; 2.15A {Shigella flexneri} PDB: 3gz1_A 3gz2_A 3ks2_A

Probab=98.76  E-value=2e-07  Score=75.99  Aligned_cols=121  Identities=12%  Similarity=0.055  Sum_probs=98.0

Q ss_pred             HHHHHHHHcCCCchhHHhhCCCCC-CHHHHHHHHHHHHhcCChhHHHHHHHHHHhCCCCCCHHHHHHHHHHHHhcCCHhH
Q 040027           71 NILLASLAKNKHYDTRLNATGLFP-NLYTYNILINCFCKIGRVSLGFIAFGRILRSCFTPNAATFNSLIKGLHAESRIME  149 (595)
Q Consensus        71 ~~l~~~~~~~~~~~~~~~~~~~~~-~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~  149 (595)
                      ..+...+...+.+...   ..+.| ++..+..+...+.+.|++++|+..|++++... |.+...|..+..+|...|++++
T Consensus        13 ~~l~~~~~~~~~l~~a---l~l~p~~~~~~~~lg~~~~~~g~~~eA~~~~~~al~~~-P~~~~~~~~lg~~~~~~g~~~~   88 (151)
T 3gyz_A           13 TAVIDAINSGATLKDI---NAIPDDMMDDIYSYAYDFYNKGRIEEAEVFFRFLCIYD-FYNVDYIMGLAAIYQIKEQFQQ   88 (151)
T ss_dssp             HHHHHHHHTSCCTGGG---CCSCHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCHHH
T ss_pred             HHHHHHHHCCCCHHHH---hCCCHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhC-CCCHHHHHHHHHHHHHHccHHH
Confidence            4444444444443321   22233 56778888999999999999999999999885 5678899999999999999999


Q ss_pred             HHHHHHHHHhcCCCCCHhhHHHHHHHHHhcCChhHHHHHHHHHHhcC
Q 040027          150 AAALFTKLKAFGCEPNVITYNTLINGLCRTGHTMIALNLFEEMANGN  196 (595)
Q Consensus       150 A~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~  196 (595)
                      |+..|+++.+.. +.+...+..+..+|...|++++|+..|+++.+..
T Consensus        89 Ai~~~~~al~l~-P~~~~~~~~lg~~~~~lg~~~eA~~~~~~al~l~  134 (151)
T 3gyz_A           89 AADLYAVAFALG-KNDYTPVFHTGQCQLRLKAPLKAKECFELVIQHS  134 (151)
T ss_dssp             HHHHHHHHHHHS-SSCCHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC
T ss_pred             HHHHHHHHHhhC-CCCcHHHHHHHHHHHHcCCHHHHHHHHHHHHHhC
Confidence            999999999885 3378889999999999999999999999999865

>2e2e_A Formate-dependent nitrite reductase complex NRFG; TPR, cytochrome C biogenesis, O157:H7 EDL933, formate- nitrite reductase complex, lyase; 2.05A {Escherichia coli}

Probab=98.74  E-value=8.5e-08  Score=81.34  Aligned_cols=119  Identities=8%  Similarity=-0.008  Sum_probs=75.0

Q ss_pred             hcCCHHHHHHHHHHHHHcCCCcCHHHHHHHHHHHHhcCChHHHHHHHHhcccCCCCC-CHHHHHHHHHH-HHhcCCh--h
Q 040027          429 KNGYIIEAVELFRTLRILKCELDIQAYNCLIDGLCKSGRLKFAWELFCSLPHGVLVP-NVVTYNIMIQG-LCNDGQM--D  504 (595)
Q Consensus       429 ~~g~~~~A~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~p-~~~~~~~l~~~-~~~~g~~--~  504 (595)
                      ..|++++|...+++..... +.+...+..++.+|...|++++|...|+++...  .| +...+..++.+ +...|++  +
T Consensus        22 ~~~~~~~A~~~~~~al~~~-p~~~~~~~~lg~~~~~~~~~~~A~~~~~~al~~--~p~~~~~~~~la~~l~~~~~~~~~~   98 (177)
T 2e2e_A           22 SQQNPEAQLQALQDKIRAN-PQNSEQWALLGEYYLWQNDYSNSLLAYRQALQL--RGENAELYAALATVLYYQASQHMTA   98 (177)
T ss_dssp             -----CCCCHHHHHHHHHC-CSCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH--HCSCHHHHHHHHHHHHHHTTTCCCH
T ss_pred             hccCHHHHHHHHHHHHHhC-CCcHHHHHHHHHHHHHcCCHHHHHHHHHHHHHc--CCCCHHHHHHHHHHHHHhcCCcchH
Confidence            3456666666666666554 455666666777777777777777777766652  23 45566666666 5566776  7


Q ss_pred             HHHHHHHHHHHcCCCCCHHHHHHHHHHHHHcCChhHHHHHHHHHHHC
Q 040027          505 KARDLFLDMEENAAAPDVITFDMLIHGFIRINEPSKVNELLHKMKEK  551 (595)
Q Consensus       505 ~A~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~  551 (595)
                      +|+..++++++.. +.+...+..++.+|...|++++|...++++.+.
T Consensus        99 ~A~~~~~~al~~~-p~~~~~~~~la~~~~~~g~~~~A~~~~~~al~~  144 (177)
T 2e2e_A           99 QTRAMIDKALALD-SNEITALMLLASDAFMQANYAQAIELWQKVMDL  144 (177)
T ss_dssp             HHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHT
T ss_pred             HHHHHHHHHHHhC-CCcHHHHHHHHHHHHHcccHHHHHHHHHHHHhh
Confidence            7777777777653 345566666777777777777777777777764

>2vgx_A Chaperone SYCD; alternative dimer assembly, tetratricopeptide repeat, type III secretion; HET: MLY; 1.95A {Yersinia enterocolitica} SCOP: k.38.1.1 PDB: 2vgx_B* 2vgy_A*

Probab=98.74  E-value=6.6e-08  Score=79.04  Aligned_cols=107  Identities=14%  Similarity=-0.009  Sum_probs=66.9

Q ss_pred             HHHHHHcCCCcCHHHHHHHHHHHHhcCChHHHHHHHHhcccCCCCC-CHHHHHHHHHHHHhcCChhHHHHHHHHHHHcCC
Q 040027          440 FRTLRILKCELDIQAYNCLIDGLCKSGRLKFAWELFCSLPHGVLVP-NVVTYNIMIQGLCNDGQMDKARDLFLDMEENAA  518 (595)
Q Consensus       440 ~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~p-~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~  518 (595)
                      ++++.... +.+...+..+...+...|++++|+..|+++..  ..| +...|..+..+|...|++++|+..|++++... 
T Consensus        10 ~~~al~~~-p~~~~~~~~~g~~~~~~g~~~~A~~~~~~al~--~~p~~~~~~~~lg~~~~~~g~~~~A~~~~~~al~l~-   85 (148)
T 2vgx_A           10 IAMLNEIS-SDTLEQLYSLAFNQYQSGXYEDAHXVFQALCV--LDHYDSRFFLGLGACRQAMGQYDLAIHSYSYGAVMD-   85 (148)
T ss_dssp             HHHHTTCC-HHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHH--HCTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHS-
T ss_pred             HHHHHcCC-HhhHHHHHHHHHHHHHcCChHHHHHHHHHHHH--cCcccHHHHHHHHHHHHHHhhHHHHHHHHHHHHhcC-
Confidence            34444332 33445556666666667777777777776665  233 45666666666777777777777777776653 


Q ss_pred             CCCHHHHHHHHHHHHHcCChhHHHHHHHHHHH
Q 040027          519 APDVITFDMLIHGFIRINEPSKVNELLHKMKE  550 (595)
Q Consensus       519 ~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~  550 (595)
                      +.+...+..++.+|...|++++|...|+++.+
T Consensus        86 p~~~~~~~~lg~~~~~~g~~~~A~~~~~~al~  117 (148)
T 2vgx_A           86 IXEPRFPFHAAECLLQXGELAEAESGLFLAQE  117 (148)
T ss_dssp             TTCTHHHHHHHHHHHHTTCHHHHHHHHHHHHH
T ss_pred             CCCchHHHHHHHHHHHcCCHHHHHHHHHHHHH
Confidence            34556666666777777777777777777665

>1na0_A Designed protein CTPR3; de novo protein; HET: IPT; 1.60A {Unidentified} SCOP: k.38.1.1 PDB: 2wqh_A 3kd7_A

Probab=98.73  E-value=4.6e-07  Score=71.27  Aligned_cols=116  Identities=16%  Similarity=0.146  Sum_probs=99.3

Q ss_pred             HHHHHHHHHHHHhcCChhHHHHHHHHHHhCCCCCCHHHHHHHHHHHHhcCCHhHHHHHHHHHHhcCCCCCHhhHHHHHHH
Q 040027           96 LYTYNILINCFCKIGRVSLGFIAFGRILRSCFTPNAATFNSLIKGLHAESRIMEAAALFTKLKAFGCEPNVITYNTLING  175 (595)
Q Consensus        96 ~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~~l~~~  175 (595)
                      ...|..++..+...|++++|+..++++.+.. +.+..++..+...+...|++++|...++++.... +.+..++..+...
T Consensus         9 ~~~~~~~~~~~~~~~~~~~A~~~~~~~~~~~-~~~~~~~~~la~~~~~~~~~~~A~~~~~~~~~~~-~~~~~~~~~la~~   86 (125)
T 1na0_A            9 AEAWYNLGNAYYKQGDYDEAIEYYQKALELD-PNNAEAWYNLGNAYYKQGDYDEAIEYYQKALELD-PNNAEAWYNLGNA   86 (125)
T ss_dssp             HHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHcCCHHHHHHHHHHHHHHC-cCcHHHHHHHHHHHHHhCCHHHHHHHHHHHHHhC-CccHHHHHHHHHH
Confidence            6778889999999999999999999999874 4578889999999999999999999999999875 4477888999999


Q ss_pred             HHhcCChhHHHHHHHHHHhcCCCCCccccCcHHHHHHHHHHHHHc
Q 040027          176 LCRTGHTMIALNLFEEMANGNGEIGVVCKPNTVTYSTIIDGLCKE  220 (595)
Q Consensus       176 ~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~  220 (595)
                      +...|++++|...|+++....       +.+...+..+..++...
T Consensus        87 ~~~~~~~~~A~~~~~~~~~~~-------~~~~~~~~~l~~~~~~~  124 (125)
T 1na0_A           87 YYKQGDYDEAIEYYQKALELD-------PNNAEAKQNLGNAKQKQ  124 (125)
T ss_dssp             HHHTTCHHHHHHHHHHHHHHC-------TTCHHHHHHHHHHHHHH
T ss_pred             HHHhcCHHHHHHHHHHHHHhC-------CCcHHHHHHHHHHHHhc
Confidence            999999999999999998875       45566666666665543

>2qfc_A PLCR protein; TPR, HTH, transcription regulation; 2.60A {Bacillus thuringiensis serovar ISRAELE35646}

Probab=98.73  E-value=1.6e-06  Score=80.32  Aligned_cols=167  Identities=10%  Similarity=0.008  Sum_probs=118.6

Q ss_pred             HHHHHHHHHHhCCCHHHHHHHHHHHHHCCCCCCH-----HHHHHHHHHHHccCCHHHHHHHHHHHHHCC---CCCC--HH
Q 040027          349 SYNILINGYCKNKEVEEALSLYREMVSKGIKPTV-----VTYNTLFLGLFEIHQVEHALKLFDEMQRDG---VAAD--TR  418 (595)
Q Consensus       349 ~~~~l~~~~~~~~~~~~A~~~~~~~~~~~~~~~~-----~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~---~~~~--~~  418 (595)
                      .+...+..+...|++++|.+.+.+..+.......     ..+..+...+...|++++|...+++..+..   ..+.  ..
T Consensus        77 ~l~~~~~~~~~~~~y~~A~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~A~~~~~~al~~~~~~~~~~~~~~  156 (293)
T 2qfc_A           77 QFKDQVIMLCKQKRYKEIYNKVWNELKKEEYHPEFQQFLQWQYYVAAYVLKKVDYEYCILELKKLLNQQLTGIDVYQNLY  156 (293)
T ss_dssp             HHHHHHHHHHHTTCHHHHHHHHHHHHHTCCCCHHHHHHHHHHHHHHHHHHTSSCHHHHHHHHHHHHTTCCCSSCTTHHHH
T ss_pred             HHHHHHHHHHHhhhHHHHHHHHHHHhccccCChhHHHHHHHHHHHHHHHhcCCCHHHHHHHHHHHHHHHhcCCchHHHHH
Confidence            4455666777888888888888877765322111     123334555677788999999888887531   1122  45


Q ss_pred             HHHHHHHHHHhcCCHHHHHHHHHHHHH---cC-CCc--CHHHHHHHHHHHHhcCChHHHHHHHHhcccC----CCCC-CH
Q 040027          419 TYTTFIDGLCKNGYIIEAVELFRTLRI---LK-CEL--DIQAYNCLIDGLCKSGRLKFAWELFCSLPHG----VLVP-NV  487 (595)
Q Consensus       419 ~~~~l~~~~~~~g~~~~A~~~~~~~~~---~~-~~~--~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~----~~~p-~~  487 (595)
                      +++.+...|...|++++|...++++.+   .. ..+  ...++..++.+|...|++++|+..+++..+.    +... -.
T Consensus       157 ~~~~lg~~y~~~~~~~~A~~~~~kal~~~~~~~~~~~~~~~~~~nlg~~y~~~~~y~~Al~~~~kal~~~~~~~~~~~~~  236 (293)
T 2qfc_A          157 IENAIANIYAENGYLKKGIDLFEQILKQLEALHDNEEFDVKVRYNHAKALYLDSRYEESLYQVNKAIEISCRINSMALIG  236 (293)
T ss_dssp             HHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHSCCCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTBCSSHH
T ss_pred             HHHHHHHHHHHcCCHHHHHHHHHHHHHHHHhcCccccchHHHHHhHHHHHHHHhhHHHHHHHHHHHHHHHHhcCcHHHHH
Confidence            778888889999999999999998873   21 111  1258888999999999999999999987652    1111 15


Q ss_pred             HHHHHHHHHHHhcCChhHH-HHHHHHHHH
Q 040027          488 VTYNIMIQGLCNDGQMDKA-RDLFLDMEE  515 (595)
Q Consensus       488 ~~~~~l~~~~~~~g~~~~A-~~~~~~~~~  515 (595)
                      .+|..+..+|...|++++| ...++++..
T Consensus       237 ~~~~~lg~~y~~~g~~~~Ai~~~~~~Al~  265 (293)
T 2qfc_A          237 QLYYQRGECLRKLEYEEAEIEDAYKKASF  265 (293)
T ss_dssp             HHHHHHHHHHHHTTCCHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHcCCcHHHHHHHHHHHHH
Confidence            6788899999999999999 777887764

>2lni_A Stress-induced-phosphoprotein 1; structural genomics, northeast structural genomics consortiu PSI-biology, protein structure initiative, chaperone; NMR {Homo sapiens}

Probab=98.73  E-value=2.3e-07  Score=74.18  Aligned_cols=119  Identities=6%  Similarity=-0.077  Sum_probs=86.3

Q ss_pred             CcCHHHHHHHHHHHHhcCChHHHHHHHHhcccCCCCC-CHHHHHHHHHHHHhcCChhHHHHHHHHHHHcCCCCCHHHHHH
Q 040027          449 ELDIQAYNCLIDGLCKSGRLKFAWELFCSLPHGVLVP-NVVTYNIMIQGLCNDGQMDKARDLFLDMEENAAAPDVITFDM  527 (595)
Q Consensus       449 ~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~p-~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~~  527 (595)
                      +.+...+..++..+...|++++|...|+++.+.  .| +...+..++.++...|++++|+..++++.+.. +.+...+..
T Consensus        13 ~~~~~~~~~~~~~~~~~~~~~~A~~~~~~al~~--~~~~~~~~~~la~~~~~~~~~~~A~~~~~~a~~~~-~~~~~~~~~   89 (133)
T 2lni_A           13 PDLALMVKNKGNECFQKGDYPQAMKHYTEAIKR--NPKDAKLYSNRAACYTKLLEFQLALKDCEECIQLE-PTFIKGYTR   89 (133)
T ss_dssp             SCHHHHHHHHHHHHHHTTCSHHHHHHHHHHHTT--CTTCHHHHHHHHHHHTTTTCHHHHHHHHHHHHHHC-TTCHHHHHH
T ss_pred             cccHHHHHHHHHHHHHcCCHHHHHHHHHHHHHc--CCCcHHHHHHHHHHHHHhccHHHHHHHHHHHHHhC-CCchHHHHH
Confidence            345666777777778888888888888887763  33 56777777788888888888888888887764 446677777


Q ss_pred             HHHHHHHcCChhHHHHHHHHHHHCCCCCCHHHHHHHHHHHHhcC
Q 040027          528 LIHGFIRINEPSKVNELLHKMKEKKVMPDASIVSIVVDLLVKNE  571 (595)
Q Consensus       528 l~~~~~~~g~~~~A~~~~~~~~~~~~~p~~~~~~~l~~~~~~~g  571 (595)
                      ++.+|...|++++|.+.++++.+.. +.+...+..+..++.+.|
T Consensus        90 la~~~~~~~~~~~A~~~~~~~~~~~-p~~~~~~~~l~~~~~~~~  132 (133)
T 2lni_A           90 KAAALEAMKDYTKAMDVYQKALDLD-SSCKEAADGYQRCMMAQY  132 (133)
T ss_dssp             HHHHHHHTTCHHHHHHHHHHHHHHC-GGGTHHHHHHHHHHHHHT
T ss_pred             HHHHHHHHhhHHHHHHHHHHHHHhC-CCchHHHHHHHHHHHHhc
Confidence            8888888888888888888887642 224566667777766655

>2vyi_A SGTA protein; chaperone, TPR repeat, phosphoprotein, tetratricopeptide repeat protein, HOST-virus interaction; 2.4A {Homo sapiens} SCOP: k.38.1.1

Probab=98.72  E-value=4.2e-07  Score=72.22  Aligned_cols=120  Identities=11%  Similarity=0.009  Sum_probs=104.6

Q ss_pred             CHHHHHHHHHHHHhcCChhHHHHHHHHHHhCCCCCCHHHHHHHHHHHHhcCCHhHHHHHHHHHHhcCCCCCHhhHHHHHH
Q 040027           95 NLYTYNILINCFCKIGRVSLGFIAFGRILRSCFTPNAATFNSLIKGLHAESRIMEAAALFTKLKAFGCEPNVITYNTLIN  174 (595)
Q Consensus        95 ~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~~l~~  174 (595)
                      +...+..++..+...|++++|...|+++.... +.+...+..+...+...|++++|++.+++..... +.+...+..+..
T Consensus        11 ~~~~~~~~~~~~~~~~~~~~A~~~~~~~~~~~-~~~~~~~~~~a~~~~~~~~~~~A~~~~~~~~~~~-~~~~~~~~~~~~   88 (131)
T 2vyi_A           11 EAERLKTEGNEQMKVENFEAAVHFYGKAIELN-PANAVYFCNRAAAYSKLGNYAGAVQDCERAICID-PAYSKAYGRMGL   88 (131)
T ss_dssp             HHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHH
T ss_pred             hhHHHHHHHHHHHHccCHHHHHHHHHHHHHcC-CCCHHHHHHHHHHHHHhhchHHHHHHHHHHHhcC-ccCHHHHHHHHH
Confidence            56778889999999999999999999999874 4578889999999999999999999999999874 346888999999


Q ss_pred             HHHhcCChhHHHHHHHHHHhcCCCCCccccCcHHHHHHHHHHHHHcCCH
Q 040027          175 GLCRTGHTMIALNLFEEMANGNGEIGVVCKPNTVTYSTIIDGLCKEGFV  223 (595)
Q Consensus       175 ~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~  223 (595)
                      .+...|++++|...|++.....       +.+...+..+..++...|++
T Consensus        89 ~~~~~~~~~~A~~~~~~~~~~~-------p~~~~~~~~l~~~~~~~~~~  130 (131)
T 2vyi_A           89 ALSSLNKHVEAVAYYKKALELD-------PDNETYKSNLKIAELKLREA  130 (131)
T ss_dssp             HHHHTTCHHHHHHHHHHHHHHS-------TTCHHHHHHHHHHHHHHTTC
T ss_pred             HHHHhCCHHHHHHHHHHHHhcC-------ccchHHHHHHHHHHHHHhcC
Confidence            9999999999999999999875       45677888888888887764

>2c2l_A CHIP, carboxy terminus of HSP70-interacting protein; chaperone, E3 ligase, ubiquitinylation, TPR, heat-shock protein complex; 3.3A {Mus musculus} SCOP: a.118.8.1 g.44.1.2

Probab=98.72  E-value=5.8e-08  Score=89.27  Aligned_cols=95  Identities=16%  Similarity=0.069  Sum_probs=44.8

Q ss_pred             HHHHHHHHHHHhcCCHHHHHHHHHHHHhcCCCCCHHHHHHHHHHHHhCCCHHHHHHHHHHHHHCCCCCCHHHHHHHHHHH
Q 040027          313 CTYNTLMDGFCLMGKINRAEELFGSMESMGCKHDDVSYNILINGYCKNKEVEEALSLYREMVSKGIKPTVVTYNTLFLGL  392 (595)
Q Consensus       313 ~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~~l~~~~  392 (595)
                      ..+..++..+...|++++|+..|+++.+.. +.+...+..+..+|.+.|++++|+..++++++..+. +...+..+..++
T Consensus         5 ~~~~~~g~~~~~~g~~~~A~~~~~~al~~~-p~~~~~~~~la~~~~~~~~~~~A~~~~~~al~~~p~-~~~~~~~lg~~~   82 (281)
T 2c2l_A            5 QELKEQGNRLFVGRKYPEAAACYGRAITRN-PLVAVYYTNRALCYLKMQQPEQALADCRRALELDGQ-SVKAHFFLGQCQ   82 (281)
T ss_dssp             HHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-SCCHHHHHHHHHHHHHTTCHHHHHHHHHHHTTSCTT-CHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHcCCHHHHHHHHHHHHHhC-CccHHHHHHHHHHHHHhcCHHHHHHHHHHHHHhCCC-CHHHHHHHHHHH
Confidence            344444455555555555555555554432 224444444555555555555555555554443221 334444444444


Q ss_pred             HccCCHHHHHHHHHHHH
Q 040027          393 FEIHQVEHALKLFDEMQ  409 (595)
Q Consensus       393 ~~~~~~~~a~~~~~~~~  409 (595)
                      ...|++++|...|++..
T Consensus        83 ~~~g~~~~A~~~~~~al   99 (281)
T 2c2l_A           83 LEMESYDEAIANLQRAY   99 (281)
T ss_dssp             HHTTCHHHHHHHHHHHH
T ss_pred             HHcCCHHHHHHHHHHHH
Confidence            44444444444444444

>2c2l_A CHIP, carboxy terminus of HSP70-interacting protein; chaperone, E3 ligase, ubiquitinylation, TPR, heat-shock protein complex; 3.3A {Mus musculus} SCOP: a.118.8.1 g.44.1.2

Probab=98.71  E-value=2.1e-07  Score=85.42  Aligned_cols=195  Identities=11%  Similarity=-0.005  Sum_probs=109.1

Q ss_pred             CHhhHHHHHHHHHhcCChHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHhcCCCCCHHHHHHHHH
Q 040027          276 SVVTFNVIMDELCKNRKMDEASRLLDLMVQRGVRPNACTYNTLMDGFCLMGKINRAEELFGSMESMGCKHDDVSYNILIN  355 (595)
Q Consensus       276 ~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~  355 (595)
                      +...+..+...+...|++++|...|+++.+.. +.+...+..+..+|...|++++|+..++++.+.. +.+...+..+..
T Consensus         3 ~a~~~~~~g~~~~~~g~~~~A~~~~~~al~~~-p~~~~~~~~la~~~~~~~~~~~A~~~~~~al~~~-p~~~~~~~~lg~   80 (281)
T 2c2l_A            3 SAQELKEQGNRLFVGRKYPEAAACYGRAITRN-PLVAVYYTNRALCYLKMQQPEQALADCRRALELD-GQSVKAHFFLGQ   80 (281)
T ss_dssp             CHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-SCCHHHHHHHHHHHHHTTCHHHHHHHHHHHTTSC-TTCHHHHHHHHH
T ss_pred             hHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhC-CccHHHHHHHHHHHHHhcCHHHHHHHHHHHHHhC-CCCHHHHHHHHH
Confidence            34455666666777777777777777766653 2256666677777777777777777777776653 445566777777


Q ss_pred             HHHhCCCHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHccCCHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHhcCCHHH
Q 040027          356 GYCKNKEVEEALSLYREMVSKGIKPTVVTYNTLFLGLFEIHQVEHALKLFDEMQRDGVAADTRTYTTFIDGLCKNGYIIE  435 (595)
Q Consensus       356 ~~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~  435 (595)
                      +|...|++++|+..|+++.+..+. +...+...+....+   ..... .+........+.+..+...+...  ..|+.++
T Consensus        81 ~~~~~g~~~~A~~~~~~al~l~p~-~~~~~~~~~~~~~~---~~~~~-~~~~~~~~~~~~~~~i~~~l~~l--~~~~~~~  153 (281)
T 2c2l_A           81 CQLEMESYDEAIANLQRAYSLAKE-QRLNFGDDIPSALR---IAKKK-RWNSIEERRIHQESELHSYLTRL--IAAERER  153 (281)
T ss_dssp             HHHHTTCHHHHHHHHHHHHHHHHH-TTCCCCSHHHHHHH---HHHHH-HHHHHHHTCCCCCCHHHHHHHHH--HHHHHHH
T ss_pred             HHHHcCCHHHHHHHHHHHHHhCcc-chhhHHHHHHHHHH---HHHHH-HHHHHHHHHHhhhHHHHHHHHHH--HHHHHHH
Confidence            777777777777777776654211 00001111111111   11111 12222223334444444333322  2577777


Q ss_pred             HHHHHHHHHHcCCCcCHHHHHHHHHHHHhc-CChHHHHHHHHhccc
Q 040027          436 AVELFRTLRILKCELDIQAYNCLIDGLCKS-GRLKFAWELFCSLPH  480 (595)
Q Consensus       436 A~~~~~~~~~~~~~~~~~~~~~l~~~~~~~-g~~~~A~~~~~~~~~  480 (595)
                      |.+.++++.+.. +.+......+...+.+. +.+++|.++|.++.+
T Consensus       154 A~~~~~~al~~~-p~~~~~~~~l~~~~~~~~~~~~~a~~~f~~a~~  198 (281)
T 2c2l_A          154 ELEECQRNHEGH-EDDGHIRAQQACIEAKHDKYMADMDELFSQVDE  198 (281)
T ss_dssp             HHTTTSGGGTTT-SCHHHHTHHHHHHHHHHHHHHHHHHHHHHHSSC
T ss_pred             HHHHHHhhhccc-cchhhhhhHHHHHHHHHHHHHHHHHHHHHhhhc
Confidence            877777776553 33344444444444444 567778888877665

>1na0_A Designed protein CTPR3; de novo protein; HET: IPT; 1.60A {Unidentified} SCOP: k.38.1.1 PDB: 2wqh_A 3kd7_A

Probab=98.71  E-value=6.9e-07  Score=70.25  Aligned_cols=116  Identities=15%  Similarity=0.097  Sum_probs=62.3

Q ss_pred             HHHHHHHHHHHHhcCChHHHHHHHHhcccCCCCCCHHHHHHHHHHHHhcCChhHHHHHHHHHHHcCCCCCHHHHHHHHHH
Q 040027          452 IQAYNCLIDGLCKSGRLKFAWELFCSLPHGVLVPNVVTYNIMIQGLCNDGQMDKARDLFLDMEENAAAPDVITFDMLIHG  531 (595)
Q Consensus       452 ~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~p~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~~l~~~  531 (595)
                      ...+..++..+...|++++|...++++.... +.+..++..++..+...|++++|+..++++.+.. +.+..++..++.+
T Consensus         9 ~~~~~~~~~~~~~~~~~~~A~~~~~~~~~~~-~~~~~~~~~la~~~~~~~~~~~A~~~~~~~~~~~-~~~~~~~~~la~~   86 (125)
T 1na0_A            9 AEAWYNLGNAYYKQGDYDEAIEYYQKALELD-PNNAEAWYNLGNAYYKQGDYDEAIEYYQKALELD-PNNAEAWYNLGNA   86 (125)
T ss_dssp             HHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHcCCHHHHHHHHHHHHHHC-cCcHHHHHHHHHHHHHhCCHHHHHHHHHHHHHhC-CccHHHHHHHHHH
Confidence            3444555555555555555555555555421 1234455555556666666666666666665543 3345555556666


Q ss_pred             HHHcCChhHHHHHHHHHHHCCCCCCHHHHHHHHHHHHhc
Q 040027          532 FIRINEPSKVNELLHKMKEKKVMPDASIVSIVVDLLVKN  570 (595)
Q Consensus       532 ~~~~g~~~~A~~~~~~~~~~~~~p~~~~~~~l~~~~~~~  570 (595)
                      |...|++++|..+++++.+.. +.+...+..+..++.+.
T Consensus        87 ~~~~~~~~~A~~~~~~~~~~~-~~~~~~~~~l~~~~~~~  124 (125)
T 1na0_A           87 YYKQGDYDEAIEYYQKALELD-PNNAEAKQNLGNAKQKQ  124 (125)
T ss_dssp             HHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHH
T ss_pred             HHHhcCHHHHHHHHHHHHHhC-CCcHHHHHHHHHHHHhc
Confidence            666666666666666665532 22445555555554443

>2vgx_A Chaperone SYCD; alternative dimer assembly, tetratricopeptide repeat, type III secretion; HET: MLY; 1.95A {Yersinia enterocolitica} SCOP: k.38.1.1 PDB: 2vgx_B* 2vgy_A*

Probab=98.68  E-value=1.1e-07  Score=77.77  Aligned_cols=97  Identities=12%  Similarity=0.037  Sum_probs=50.3

Q ss_pred             HHHHHHHHHHHHhcCCHhHHHHHHHHHHhcCCCCCHhhHHHHHHHHHhcCChhHHHHHHHHHHhcCCCCCccccCcHHHH
Q 040027          131 AATFNSLIKGLHAESRIMEAAALFTKLKAFGCEPNVITYNTLINGLCRTGHTMIALNLFEEMANGNGEIGVVCKPNTVTY  210 (595)
Q Consensus       131 ~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~~~~~~  210 (595)
                      ...+..+...+...|++++|+..|+++.... +.+...|..+..++...|++++|+..|+++...+       |.++..+
T Consensus        21 ~~~~~~~g~~~~~~g~~~~A~~~~~~al~~~-p~~~~~~~~lg~~~~~~g~~~~A~~~~~~al~l~-------p~~~~~~   92 (148)
T 2vgx_A           21 LEQLYSLAFNQYQSGXYEDAHXVFQALCVLD-HYDSRFFLGLGACRQAMGQYDLAIHSYSYGAVMD-------IXEPRFP   92 (148)
T ss_dssp             HHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHS-------TTCTHHH
T ss_pred             HHHHHHHHHHHHHcCChHHHHHHHHHHHHcC-cccHHHHHHHHHHHHHHhhHHHHHHHHHHHHhcC-------CCCchHH
Confidence            3344444455555555555555555555443 2244555555555555555555555555555543       3344455


Q ss_pred             HHHHHHHHHcCCHhHHHHHHHHHhh
Q 040027          211 STIIDGLCKEGFVDKAKALFLQMKD  235 (595)
Q Consensus       211 ~~l~~~~~~~g~~~~A~~~~~~~~~  235 (595)
                      ..+..++...|++++|.+.|++..+
T Consensus        93 ~~lg~~~~~~g~~~~A~~~~~~al~  117 (148)
T 2vgx_A           93 FHAAECLLQXGELAEAESGLFLAQE  117 (148)
T ss_dssp             HHHHHHHHHTTCHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHcCCHHHHHHHHHHHHH
Confidence            5555555555555555555555444

>3gw4_A Uncharacterized protein; structural genomics, PSI-2, protein structure initiative, no structural genomics consortium, NESG, DRR162B; 2.49A {Deinococcus radiodurans R1}

Probab=98.67  E-value=2e-07  Score=81.04  Aligned_cols=156  Identities=13%  Similarity=-0.031  Sum_probs=99.2

Q ss_pred             ccCCHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHHc----CC-CcCHHHHHHHHHHHHhcCCh
Q 040027          394 EIHQVEHALKLFDEMQRDGVAADTRTYTTFIDGLCKNGYIIEAVELFRTLRIL----KC-ELDIQAYNCLIDGLCKSGRL  468 (595)
Q Consensus       394 ~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~----~~-~~~~~~~~~l~~~~~~~g~~  468 (595)
                      ..|++++|.+.++.+... .......+..+...+...|++++|...+++....    +. +....++..+...+...|++
T Consensus         4 ~~g~~~~A~~~~~~~~~~-~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~l~~~~~~~g~~   82 (203)
T 3gw4_A            4 EAHDYALAERQAQALLAH-PATASGARFMLGYVYAFMDRFDEARASFQALQQQAQKSGDHTAEHRALHQVGMVERMAGNW   82 (203)
T ss_dssp             ---CHHHHHHHHHHHHTS-TTTHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHTTCCHHHHHHHHHHHHHHHHHTTCH
T ss_pred             ccccHHHHHHHHHHhcCC-hHHHHHHHHHHHHHHHHhCcHHHHHHHHHHHHHHHHHcCCcHHHHHHHHHHHHHHHHcCCH
Confidence            456666776644444331 1234456666667777777777777777776641    11 22345667777778888888


Q ss_pred             HHHHHHHHhcccC----CCCC--CHHHHHHHHHHHHhcCChhHHHHHHHHHHHcCC-CCC----HHHHHHHHHHHHHcCC
Q 040027          469 KFAWELFCSLPHG----VLVP--NVVTYNIMIQGLCNDGQMDKARDLFLDMEENAA-APD----VITFDMLIHGFIRINE  537 (595)
Q Consensus       469 ~~A~~~~~~~~~~----~~~p--~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~-~~~----~~~~~~l~~~~~~~g~  537 (595)
                      ++|...+++..+.    +..|  ....+..+...+...|++++|...+++..+... ..+    ..++..+..++...|+
T Consensus        83 ~~A~~~~~~al~~~~~~~~~~~~~~~~~~~lg~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~la~~~~~~g~  162 (203)
T 3gw4_A           83 DAARRCFLEERELLASLPEDPLAASANAYEVATVALHFGDLAGARQEYEKSLVYAQQADDQVAIACAFRGLGDLAQQEKN  162 (203)
T ss_dssp             HHHHHHHHHHHHHHHHSCCCHHHHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTC
T ss_pred             HHHHHHHHHHHHHHHHcCccHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHhccchHHHHHHHHHHHHHHHHCcC
Confidence            8888888776551    1011  134567777888888888888888888764210 112    2345677888888899


Q ss_pred             hhHHHHHHHHHHH
Q 040027          538 PSKVNELLHKMKE  550 (595)
Q Consensus       538 ~~~A~~~~~~~~~  550 (595)
                      +++|.+.+++..+
T Consensus       163 ~~~A~~~~~~al~  175 (203)
T 3gw4_A          163 LLEAQQHWLRARD  175 (203)
T ss_dssp             HHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHH
Confidence            9999888888874

>1p5q_A FKBP52, FK506-binding protein 4; isomerase; 2.80A {Homo sapiens} SCOP: a.118.8.1 d.26.1.1 PDB: 1qz2_A

Probab=98.67  E-value=5e-07  Score=85.32  Aligned_cols=132  Identities=11%  Similarity=-0.031  Sum_probs=105.9

Q ss_pred             CHHHHHHHHHHHHhcCChhHHHHHHHHHHhCCCCCC--------------HHHHHHHHHHHHhcCCHhHHHHHHHHHHhc
Q 040027           95 NLYTYNILINCFCKIGRVSLGFIAFGRILRSCFTPN--------------AATFNSLIKGLHAESRIMEAAALFTKLKAF  160 (595)
Q Consensus        95 ~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~~--------------~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~  160 (595)
                      +...|..+...+.+.|++++|+..|++++.......              ..+|..+..+|.+.|++++|+..|+++++.
T Consensus       146 ~a~~~~~~g~~~~~~g~~~~A~~~y~~Al~~~p~~~~~~~~~~~~~~~~~~~~~~nla~~~~~~g~~~~A~~~~~~al~~  225 (336)
T 1p5q_A          146 QSTIVKERGTVYFKEGKYKQALLQYKKIVSWLEYESSFSNEEAQKAQALRLASHLNLAMCHLKLQAFSAAIESCNKALEL  225 (336)
T ss_dssp             HHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHTTTCCCCCSHHHHHHHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHhhccccCChHHHHHHHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHh
Confidence            456778888889999999999999999988743221              478888888888999999999999988887


Q ss_pred             CCCCCHhhHHHHHHHHHhcCChhHHHHHHHHHHhcCCCCCccccCcHHHHHHHHHHHHHcCCHhHH-HHHHHHHh
Q 040027          161 GCEPNVITYNTLINGLCRTGHTMIALNLFEEMANGNGEIGVVCKPNTVTYSTIIDGLCKEGFVDKA-KALFLQMK  234 (595)
Q Consensus       161 ~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A-~~~~~~~~  234 (595)
                      . +.+..++..+..+|...|++++|+..|+++.+..       |.+..++..+..++...|+.++| ..+|+.|.
T Consensus       226 ~-p~~~~a~~~lg~~~~~~g~~~~A~~~~~~al~l~-------P~~~~a~~~l~~~~~~~~~~~~a~~~~~~~~~  292 (336)
T 1p5q_A          226 D-SNNEKGLSRRGEAHLAVNDFELARADFQKVLQLY-------PNNKAAKTQLAVCQQRIRRQLAREKKLYANMF  292 (336)
T ss_dssp             C-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-------SSCHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             C-CCcHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHC-------CCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            5 3477888888888889999999999999888875       55677888888888888888877 44555554

>4gcn_A Protein STI-1; structural genomics, PSI-biology, midwest center for structu genomics, MCSG, tetratricopeptide repeat domain; HET: PGE; 1.85A {Caenorhabditis elegans}

Probab=98.66  E-value=3.3e-07  Score=72.59  Aligned_cols=108  Identities=16%  Similarity=0.118  Sum_probs=71.6

Q ss_pred             HHHHHHHHHHHhcCChHHHHHHHHhcccCCCCCC-HHHHHHHHHHHHhcCChhHHHHHHHHHHHcC--CCCC----HHHH
Q 040027          453 QAYNCLIDGLCKSGRLKFAWELFCSLPHGVLVPN-VVTYNIMIQGLCNDGQMDKARDLFLDMEENA--AAPD----VITF  525 (595)
Q Consensus       453 ~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~p~-~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~--~~~~----~~~~  525 (595)
                      ..+..++..+.+.|++++|+..|+++++  +.|+ ...|..+..+|...|++++|++.++++++..  ..++    ..+|
T Consensus         9 ~a~~~lG~~~~~~~~~~~A~~~y~~Al~--~~p~~~~~~~nlg~~~~~~~~~~~A~~~~~~al~~~~~~~~~~~~~a~~~   86 (127)
T 4gcn_A            9 IAEKDLGNAAYKQKDFEKAHVHYDKAIE--LDPSNITFYNNKAAVYFEEKKFAECVQFCEKAVEVGRETRADYKLIAKAM   86 (127)
T ss_dssp             HHHHHHHHHHHHTTCHHHHHHHHHHHHH--HCTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCCHHHHHHHH
T ss_pred             HHHHHHHHHHHHcCCHHHHHHHHHHHHH--hCCCCHHHHHhHHHHHHHhhhHHHHHHHHHHHHHhCcccchhhHHHHHHH
Confidence            3455667777777777777777777766  3443 5667777777777777777777777776532  1111    2356


Q ss_pred             HHHHHHHHHcCChhHHHHHHHHHHHCCCCCCHHHHHHHH
Q 040027          526 DMLIHGFIRINEPSKVNELLHKMKEKKVMPDASIVSIVV  564 (595)
Q Consensus       526 ~~l~~~~~~~g~~~~A~~~~~~~~~~~~~p~~~~~~~l~  564 (595)
                      ..++.++...|++++|.+.|++.++  ..||+.+...+-
T Consensus        87 ~~lg~~~~~~~~~~~A~~~~~kal~--~~~~~~~~~~l~  123 (127)
T 4gcn_A           87 SRAGNAFQKQNDLSLAVQWFHRSLS--EFRDPELVKKVK  123 (127)
T ss_dssp             HHHHHHHHHTTCHHHHHHHHHHHHH--HSCCHHHHHHHH
T ss_pred             HHHHHHHHHcCCHHHHHHHHHHHHh--hCcCHHHHHHHH
Confidence            6677777788888888888888776  346766655443

>3dss_A Geranylgeranyl transferase type-2 subunit alpha; protein prenylation, metal-binding, prenyltransferase, zinc, phosphoprotein; 1.80A {Rattus norvegicus} PDB: 3dst_A* 3dsu_A* 3dsv_A* 3dsw_A* 3dsx_A* 3hxb_A* 3hxc_A* 3hxd_A* 3hxe_A* 3hxf_A* 3pz1_A* 3pz2_A* 3pz3_A* 3c72_A* 4gtv_A* 4gts_A* 4ehm_A* 4gtt_A*

Probab=98.65  E-value=3.5e-05  Score=71.10  Aligned_cols=194  Identities=11%  Similarity=0.012  Sum_probs=106.2

Q ss_pred             HHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHccC--CHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHhcCC-HHHHHHH
Q 040027          363 VEEALSLYREMVSKGIKPTVVTYNTLFLGLFEIH--QVEHALKLFDEMQRDGVAADTRTYTTFIDGLCKNGY-IIEAVEL  439 (595)
Q Consensus       363 ~~~A~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~--~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~-~~~A~~~  439 (595)
                      +++++.+++.+....++ +..+|+.-...+...+  ++++++.+++.+.+.+ +-+...|+.-..++...|. ++++++.
T Consensus        90 l~~EL~~~~~~L~~~PK-ny~aW~hR~wlL~~l~~~~~~~EL~~~~k~l~~d-prNy~AW~~R~~vl~~l~~~~~eel~~  167 (331)
T 3dss_A           90 VKAELGFLESCLRVNPK-SYGTWHHRCWLLSRLPEPNWARELELCARFLEAD-ERNFHCWDYRRFVAAQAAVAPAEELAF  167 (331)
T ss_dssp             HHHHHHHHHHHHHHCTT-CHHHHHHHHHHHHHCSSCCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCCHHHHHHH
T ss_pred             HHHHHHHHHHHHHhCCC-CHHHHHHHHHHHhccCcccHHHHHHHHHHHHHhC-CCCHHHHHHHHHHHHHhCcCHHHHHHH
Confidence            34555555555554333 4445544444444444  3556666666655543 4455555555555555555 4566666


Q ss_pred             HHHHHHcCCCcCHHHHHHHHHHHHhc--------------CChHHHHHHHHhcccCCCCC-CHHHHHHHHHHHHhc----
Q 040027          440 FRTLRILKCELDIQAYNCLIDGLCKS--------------GRLKFAWELFCSLPHGVLVP-NVVTYNIMIQGLCND----  500 (595)
Q Consensus       440 ~~~~~~~~~~~~~~~~~~l~~~~~~~--------------g~~~~A~~~~~~~~~~~~~p-~~~~~~~l~~~~~~~----  500 (595)
                      ++++++.+ +-|..+|+.....+...              +.++++++.+.+++.  ..| |...|+.+-..+.+.    
T Consensus       168 ~~~~I~~~-p~N~SAW~~R~~ll~~l~~~~~~~~~~~~~~~~~~eEle~~~~ai~--~~P~d~SaW~Y~r~ll~~~~~~~  244 (331)
T 3dss_A          168 TDSLITRN-FSNYSSWHYRSCLLPQLHPQPDSGPQGRLPENVLLKELELVQNAFF--TDPNDQSAWFYHRWLLGAGSGRC  244 (331)
T ss_dssp             HHHHHHHC-SCCHHHHHHHHHHHHHHSCCC------CCCHHHHHHHHHHHHHHHH--HSTTCHHHHHHHHHHHHSSSCGG
T ss_pred             HHHHHHHC-CCCHHHHHHHHHHHHHhhhccccccccccchHHHHHHHHHHHHHHH--hCCCCHHHHHHHHHHHHhccCcc
Confidence            66666554 44555555555544443              335666777776665  234 455666555444443    


Q ss_pred             -------CChhHHHHHHHHHHHcCCCCCHHHHHHHHH---HHHHcCChhHHHHHHHHHHHCCCCCC-HHHHHHHH
Q 040027          501 -------GQMDKARDLFLDMEENAAAPDVITFDMLIH---GFIRINEPSKVNELLHKMKEKKVMPD-ASIVSIVV  564 (595)
Q Consensus       501 -------g~~~~A~~~~~~~~~~~~~~~~~~~~~l~~---~~~~~g~~~~A~~~~~~~~~~~~~p~-~~~~~~l~  564 (595)
                             +.++++++.++++.+.. +.+.-++..++.   +....|..+++..++.++.+  +.|. ..-|..+.
T Consensus       245 ~~~~~~~~~l~~el~~~~elle~~-pd~~w~l~~~~~~~~~~~~~~~~~~~~~~l~~l~~--~Dp~r~~~y~d~~  316 (331)
T 3dss_A          245 ELSVEKSTVLQSELESCKELQELE-PENKWCLLTIILLMRALDPLLYEKETLQYFSTLKA--VDPMRAAYLDDLR  316 (331)
T ss_dssp             GCCHHHHHHHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHHCTTTTHHHHHHHHHHHHH--HCGGGHHHHHHHH
T ss_pred             ccchHHHHHHHHHHHHHHHHHhhC-cccchHHHHHHHHHHhhcccccHHHHHHHHHHHHH--hCcchhhHHHHHH
Confidence                   34678888888888863 223223222221   11235677888889998887  4463 34444443

>1p5q_A FKBP52, FK506-binding protein 4; isomerase; 2.80A {Homo sapiens} SCOP: a.118.8.1 d.26.1.1 PDB: 1qz2_A

Probab=98.65  E-value=6.4e-07  Score=84.58  Aligned_cols=129  Identities=13%  Similarity=-0.043  Sum_probs=93.7

Q ss_pred             HHHHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCcC---------------HHHHHHHHHHHHhcCChHHHHHHHHhcccC
Q 040027          417 TRTYTTFIDGLCKNGYIIEAVELFRTLRILKCELD---------------IQAYNCLIDGLCKSGRLKFAWELFCSLPHG  481 (595)
Q Consensus       417 ~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~~---------------~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~  481 (595)
                      ...+..+...|.+.|++++|...|++++... +.+               ..++..+..+|.+.|++++|+..++++++.
T Consensus       147 a~~~~~~g~~~~~~g~~~~A~~~y~~Al~~~-p~~~~~~~~~~~~~~~~~~~~~~nla~~~~~~g~~~~A~~~~~~al~~  225 (336)
T 1p5q_A          147 STIVKERGTVYFKEGKYKQALLQYKKIVSWL-EYESSFSNEEAQKAQALRLASHLNLAMCHLKLQAFSAAIESCNKALEL  225 (336)
T ss_dssp             HHHHHHHHHHHHHHTCHHHHHHHHHHHHHHT-TTCCCCCSHHHHHHHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHCCCHHHHHHHHHHHHHHh-hccccCChHHHHHHHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHh
Confidence            3445555666666666666666666666554 222               577788888888888888888888888773


Q ss_pred             CCCC-CHHHHHHHHHHHHhcCChhHHHHHHHHHHHcCCCCCHHHHHHHHHHHHHcCChhHH-HHHHHHHH
Q 040027          482 VLVP-NVVTYNIMIQGLCNDGQMDKARDLFLDMEENAAAPDVITFDMLIHGFIRINEPSKV-NELLHKMK  549 (595)
Q Consensus       482 ~~~p-~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A-~~~~~~~~  549 (595)
                        .| +...|..+..+|...|++++|+..|+++++.. +.+...+..+..++...|++++| ...+++|.
T Consensus       226 --~p~~~~a~~~lg~~~~~~g~~~~A~~~~~~al~l~-P~~~~a~~~l~~~~~~~~~~~~a~~~~~~~~~  292 (336)
T 1p5q_A          226 --DSNNEKGLSRRGEAHLAVNDFELARADFQKVLQLY-PNNKAAKTQLAVCQQRIRRQLAREKKLYANMF  292 (336)
T ss_dssp             --CTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-SSCHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             --CCCcHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHC-CCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence              44 46778888888888888888888888888864 45677778888888888888877 45666665

>3gw4_A Uncharacterized protein; structural genomics, PSI-2, protein structure initiative, no structural genomics consortium, NESG, DRR162B; 2.49A {Deinococcus radiodurans R1}

Probab=98.65  E-value=3.6e-07  Score=79.35  Aligned_cols=161  Identities=12%  Similarity=-0.009  Sum_probs=84.0

Q ss_pred             hcCCHhHHHHHHHHHHhcCCCCCHhhHHHHHHHHHhcCChhHHHHHHHHHHhcCCCCCccccCcHHHHHHHHHHHHHcCC
Q 040027          143 AESRIMEAAALFTKLKAFGCEPNVITYNTLINGLCRTGHTMIALNLFEEMANGNGEIGVVCKPNTVTYSTIIDGLCKEGF  222 (595)
Q Consensus       143 ~~g~~~~A~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~  222 (595)
                      ..|++++|.+.++.+... ......++..+...+...|++++|+..+++........+. .+....++..+...+...|+
T Consensus         4 ~~g~~~~A~~~~~~~~~~-~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~al~~~~~~~~-~~~~~~~~~~l~~~~~~~g~   81 (203)
T 3gw4_A            4 EAHDYALAERQAQALLAH-PATASGARFMLGYVYAFMDRFDEARASFQALQQQAQKSGD-HTAEHRALHQVGMVERMAGN   81 (203)
T ss_dssp             ---CHHHHHHHHHHHHTS-TTTHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHTTCC-HHHHHHHHHHHHHHHHHTTC
T ss_pred             ccccHHHHHHHHHHhcCC-hHHHHHHHHHHHHHHHHhCcHHHHHHHHHHHHHHHHHcCC-cHHHHHHHHHHHHHHHHcCC
Confidence            455666666644333321 1123455556666666666666666666665542110000 12234556666777777777


Q ss_pred             HhHHHHHHHHHhhC----CCCC--CHhHHHHHHHHHHhcCCHHHHHHHHHHHHHCCC-CCC----HhhHHHHHHHHHhcC
Q 040027          223 VDKAKALFLQMKDE----NINP--DVVTYNSLIHGLCHANDWNEAKRLFIEMMDQGV-QPS----VVTFNVIMDELCKNR  291 (595)
Q Consensus       223 ~~~A~~~~~~~~~~----~~~~--~~~~~~~ll~~~~~~~~~~~A~~~~~~~~~~~~-~~~----~~~~~~l~~~~~~~g  291 (595)
                      +++|.+.+++....    +..+  ....+..+...+...|++++|...+++...... ..+    ..++..+..++...|
T Consensus        82 ~~~A~~~~~~al~~~~~~~~~~~~~~~~~~~lg~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~la~~~~~~g  161 (203)
T 3gw4_A           82 WDAARRCFLEERELLASLPEDPLAASANAYEVATVALHFGDLAGARQEYEKSLVYAQQADDQVAIACAFRGLGDLAQQEK  161 (203)
T ss_dssp             HHHHHHHHHHHHHHHHHSCCCHHHHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTT
T ss_pred             HHHHHHHHHHHHHHHHHcCccHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHhccchHHHHHHHHHHHHHHHHCc
Confidence            77777777665442    1011  133455666667777777777777766653200 001    122445555666666


Q ss_pred             ChHHHHHHHHHHHH
Q 040027          292 KMDEASRLLDLMVQ  305 (595)
Q Consensus       292 ~~~~a~~~~~~~~~  305 (595)
                      ++++|...+++..+
T Consensus       162 ~~~~A~~~~~~al~  175 (203)
T 3gw4_A          162 NLLEAQQHWLRARD  175 (203)
T ss_dssp             CHHHHHHHHHHHHH
T ss_pred             CHHHHHHHHHHHHH
Confidence            66666666655543

>3dss_A Geranylgeranyl transferase type-2 subunit alpha; protein prenylation, metal-binding, prenyltransferase, zinc, phosphoprotein; 1.80A {Rattus norvegicus} PDB: 3dst_A* 3dsu_A* 3dsv_A* 3dsw_A* 3dsx_A* 3hxb_A* 3hxc_A* 3hxd_A* 3hxe_A* 3hxf_A* 3pz1_A* 3pz2_A* 3pz3_A* 3c72_A* 4gtv_A* 4gts_A* 4ehm_A* 4gtt_A*

Probab=98.65  E-value=2.8e-05  Score=71.70  Aligned_cols=246  Identities=11%  Similarity=0.061  Sum_probs=119.4

Q ss_pred             hcCCHH-HHHHHHHHHHHCCCCCCHhhHHHHHHHHHhcCC----------hHHHHHHHHHHHHCCCCCCHHHHHHHHHHH
Q 040027          254 HANDWN-EAKRLFIEMMDQGVQPSVVTFNVIMDELCKNRK----------MDEASRLLDLMVQRGVRPNACTYNTLMDGF  322 (595)
Q Consensus       254 ~~~~~~-~A~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~----------~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~  322 (595)
                      +.|.+. +|+.++..++..... +..+|+.--.++...+.          +++++.+++.+...+.+ +..+|+.-..++
T Consensus        41 ~~~e~s~eaL~~t~~~L~~nP~-~ytaWn~Rr~iL~~l~~~~~~~~~~~~l~~EL~~~~~~L~~~PK-ny~aW~hR~wlL  118 (331)
T 3dss_A           41 QAGELDESVLELTSQILGANPD-FATLWNCRREVLQHLETEKSPEESAALVKAELGFLESCLRVNPK-SYGTWHHRCWLL  118 (331)
T ss_dssp             HTTCCSHHHHHHHHHHHTTCTT-CHHHHHHHHHHHHHHHHHSCHHHHHHHHHHHHHHHHHHHHHCTT-CHHHHHHHHHHH
T ss_pred             HcCCCCHHHHHHHHHHHHHCch-hHHHHHHHHHHHHHhcccccchhhhHHHHHHHHHHHHHHHhCCC-CHHHHHHHHHHH
Confidence            344443 567777776664211 33344443333332222          34445555555444222 444444444444


Q ss_pred             HhcC--CHHHHHHHHHHHHhcCCCCCHHHHHHHHHHHHhCCC-HHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHccCCHH
Q 040027          323 CLMG--KINRAEELFGSMESMGCKHDDVSYNILINGYCKNKE-VEEALSLYREMVSKGIKPTVVTYNTLFLGLFEIHQVE  399 (595)
Q Consensus       323 ~~~~--~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~-~~~A~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~  399 (595)
                      ...+  .+++++.+++.+.+.. +.+..+|+.-..+....|. ++++++.+.++++..+. +...|+.....+...+...
T Consensus       119 ~~l~~~~~~~EL~~~~k~l~~d-prNy~AW~~R~~vl~~l~~~~~eel~~~~~~I~~~p~-N~SAW~~R~~ll~~l~~~~  196 (331)
T 3dss_A          119 SRLPEPNWARELELCARFLEAD-ERNFHCWDYRRFVAAQAAVAPAEELAFTDSLITRNFS-NYSSWHYRSCLLPQLHPQP  196 (331)
T ss_dssp             HHCSSCCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCCHHHHHHHHHHHHHHCSC-CHHHHHHHHHHHHHHSCCC
T ss_pred             hccCcccHHHHHHHHHHHHHhC-CCCHHHHHHHHHHHHHhCcCHHHHHHHHHHHHHHCCC-CHHHHHHHHHHHHHhhhcc
Confidence            4444  2445555555554443 3344444444444444444 34555555555444332 4444443333322221000


Q ss_pred             HHHHHHHHHHHCCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCcCHHHHHHHHHHHHhc-----------CCh
Q 040027          400 HALKLFDEMQRDGVAADTRTYTTFIDGLCKNGYIIEAVELFRTLRILKCELDIQAYNCLIDGLCKS-----------GRL  468 (595)
Q Consensus       400 ~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~~l~~~~~~~-----------g~~  468 (595)
                      .+       ...+ .             ...+.++++++.+.+++... |.|..+|+-+-..+.+.           +.+
T Consensus       197 ~~-------~~~~-~-------------~~~~~~~eEle~~~~ai~~~-P~d~SaW~Y~r~ll~~~~~~~~~~~~~~~~l  254 (331)
T 3dss_A          197 DS-------GPQG-R-------------LPENVLLKELELVQNAFFTD-PNDQSAWFYHRWLLGAGSGRCELSVEKSTVL  254 (331)
T ss_dssp             --------------C-------------CCHHHHHHHHHHHHHHHHHS-TTCHHHHHHHHHHHHSSSCGGGCCHHHHHHH
T ss_pred             cc-------cccc-c-------------cchHHHHHHHHHHHHHHHhC-CCCHHHHHHHHHHHHhccCccccchHHHHHH
Confidence            00       0000 0             00134667777777777665 66777776555555444           346


Q ss_pred             HHHHHHHHhcccCCCCCCHHHHHHHHHHH-----HhcCChhHHHHHHHHHHHcCCCCCHHHHHHHH
Q 040027          469 KFAWELFCSLPHGVLVPNVVTYNIMIQGL-----CNDGQMDKARDLFLDMEENAAAPDVITFDMLI  529 (595)
Q Consensus       469 ~~A~~~~~~~~~~~~~p~~~~~~~l~~~~-----~~~g~~~~A~~~~~~~~~~~~~~~~~~~~~l~  529 (595)
                      +++++.++++.+  +.||. .|..+..+.     ...|..+++...+.++.+.+ |....-|..+.
T Consensus       255 ~~el~~~~elle--~~pd~-~w~l~~~~~~~~~~~~~~~~~~~~~~l~~l~~~D-p~r~~~y~d~~  316 (331)
T 3dss_A          255 QSELESCKELQE--LEPEN-KWCLLTIILLMRALDPLLYEKETLQYFSTLKAVD-PMRAAYLDDLR  316 (331)
T ss_dssp             HHHHHHHHHHHH--HCTTC-HHHHHHHHHHHHHHCTTTTHHHHHHHHHHHHHHC-GGGHHHHHHHH
T ss_pred             HHHHHHHHHHHh--hCccc-chHHHHHHHHHHhhcccccHHHHHHHHHHHHHhC-cchhhHHHHHH
Confidence            788888888887  56664 343322222     23567778888888888754 33334444443

>3upv_A Heat shock protein STI1; TPR-fold, adaptor protein for HSP70 and HSP90, C-terminal PA HSP70, peptide binding protein; 1.60A {Saccharomyces cerevisiae}

Probab=98.61  E-value=8.3e-07  Score=70.18  Aligned_cols=96  Identities=11%  Similarity=-0.003  Sum_probs=62.5

Q ss_pred             HHHHHHHHHHHHhcCChHHHHHHHHhcccCCCCC-CHHHHHHHHHHHHhcCChhHHHHHHHHHHHcCCCCCHHHHHHHHH
Q 040027          452 IQAYNCLIDGLCKSGRLKFAWELFCSLPHGVLVP-NVVTYNIMIQGLCNDGQMDKARDLFLDMEENAAAPDVITFDMLIH  530 (595)
Q Consensus       452 ~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~p-~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~~l~~  530 (595)
                      ...+..++..+...|++++|+..|++.++.  .| +...|..+..+|...|++++|+..++++++.. +.+...+..++.
T Consensus         4 a~~~~~~g~~~~~~~~~~~A~~~~~~al~~--~p~~~~~~~~~a~~~~~~~~~~~A~~~~~~al~~~-p~~~~~~~~lg~   80 (126)
T 3upv_A            4 AEEARLEGKEYFTKSDWPNAVKAYTEMIKR--APEDARGYSNRAAALAKLMSFPEAIADCNKAIEKD-PNFVRAYIRKAT   80 (126)
T ss_dssp             HHHHHHHHHHHHHTTCHHHHHHHHHHHHHH--CTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHhcCHHHHHHHHHHHHHh--CCCChHHHHHHHHHHHHhcCHHHHHHHHHHHHHhC-CCcHHHHHHHHH
Confidence            344555566666666677776666666652  33 35666666677777777777777777776654 445666666777


Q ss_pred             HHHHcCChhHHHHHHHHHHH
Q 040027          531 GFIRINEPSKVNELLHKMKE  550 (595)
Q Consensus       531 ~~~~~g~~~~A~~~~~~~~~  550 (595)
                      ++...|++++|...++++.+
T Consensus        81 ~~~~~~~~~~A~~~~~~al~  100 (126)
T 3upv_A           81 AQIAVKEYASALETLDAART  100 (126)
T ss_dssp             HHHHTTCHHHHHHHHHHHHH
T ss_pred             HHHHHhCHHHHHHHHHHHHH
Confidence            77777777777777777665

>4gcn_A Protein STI-1; structural genomics, PSI-biology, midwest center for structu genomics, MCSG, tetratricopeptide repeat domain; HET: PGE; 1.85A {Caenorhabditis elegans}

Probab=98.61  E-value=5.7e-07  Score=71.16  Aligned_cols=105  Identities=9%  Similarity=-0.042  Sum_probs=77.6

Q ss_pred             HHHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCcCHHHHHHHHHHHHhcCChHHHHHHHHhcccCCCCCC--------HHH
Q 040027          418 RTYTTFIDGLCKNGYIIEAVELFRTLRILKCELDIQAYNCLIDGLCKSGRLKFAWELFCSLPHGVLVPN--------VVT  489 (595)
Q Consensus       418 ~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~p~--------~~~  489 (595)
                      ..+..+...+.+.|++++|+..|+++++.. |.+...|..+..+|...|++++|+..+++.++  +.|+        ..+
T Consensus         9 ~a~~~lG~~~~~~~~~~~A~~~y~~Al~~~-p~~~~~~~nlg~~~~~~~~~~~A~~~~~~al~--~~~~~~~~~~~~a~~   85 (127)
T 4gcn_A            9 IAEKDLGNAAYKQKDFEKAHVHYDKAIELD-PSNITFYNNKAAVYFEEKKFAECVQFCEKAVE--VGRETRADYKLIAKA   85 (127)
T ss_dssp             HHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHH--HHHHTTCCHHHHHHH
T ss_pred             HHHHHHHHHHHHcCCHHHHHHHHHHHHHhC-CCCHHHHHhHHHHHHHhhhHHHHHHHHHHHHH--hCcccchhhHHHHHH
Confidence            345567777888888888888888888766 56677888888888888888888888888765  2221        235


Q ss_pred             HHHHHHHHHhcCChhHHHHHHHHHHHcCCCCCHHHHHH
Q 040027          490 YNIMIQGLCNDGQMDKARDLFLDMEENAAAPDVITFDM  527 (595)
Q Consensus       490 ~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~~  527 (595)
                      |..+..++...|++++|++.|++.+..  .|++.....
T Consensus        86 ~~~lg~~~~~~~~~~~A~~~~~kal~~--~~~~~~~~~  121 (127)
T 4gcn_A           86 MSRAGNAFQKQNDLSLAVQWFHRSLSE--FRDPELVKK  121 (127)
T ss_dssp             HHHHHHHHHHTTCHHHHHHHHHHHHHH--SCCHHHHHH
T ss_pred             HHHHHHHHHHcCCHHHHHHHHHHHHhh--CcCHHHHHH
Confidence            667778888888899998888888874  466655443

>2xcb_A PCRH, regulatory protein PCRH; protein transport, bacterial toxin, type III secretion, protein binding; 1.85A {Pseudomonas aeruginosa} PDB: 2xcc_A

Probab=98.60  E-value=6.5e-07  Score=72.56  Aligned_cols=100  Identities=11%  Similarity=-0.150  Sum_probs=88.8

Q ss_pred             CHHHHHHHHHHHHhcCChhHHHHHHHHHHhCCCCCCHHHHHHHHHHHHhcCCHhHHHHHHHHHHhcCCCCCHhhHHHHHH
Q 040027           95 NLYTYNILINCFCKIGRVSLGFIAFGRILRSCFTPNAATFNSLIKGLHAESRIMEAAALFTKLKAFGCEPNVITYNTLIN  174 (595)
Q Consensus        95 ~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~~l~~  174 (595)
                      +...+..+...+.+.|++++|+..|++++... +.+...|..+..++...|++++|+..|++..... +.+...+..+..
T Consensus        17 ~~~~~~~~a~~~~~~g~~~~A~~~~~~al~~~-p~~~~~~~~lg~~~~~~g~~~~A~~~~~~al~~~-p~~~~~~~~lg~   94 (142)
T 2xcb_A           17 TLEQLYALGFNQYQAGKWDDAQKIFQALCMLD-HYDARYFLGLGACRQSLGLYEQALQSYSYGALMD-INEPRFPFHAAE   94 (142)
T ss_dssp             HHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCTHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHccHHHHHHHHHHHHHhC-CccHHHHHHHHHHHHHHhhHHHHHHHHHHHHhcC-CCCcHHHHHHHH
Confidence            44566778888999999999999999999885 5588899999999999999999999999999985 347788899999


Q ss_pred             HHHhcCChhHHHHHHHHHHhcC
Q 040027          175 GLCRTGHTMIALNLFEEMANGN  196 (595)
Q Consensus       175 ~~~~~g~~~~A~~~~~~~~~~~  196 (595)
                      ++...|++++|+..|++.....
T Consensus        95 ~~~~~g~~~~A~~~~~~al~~~  116 (142)
T 2xcb_A           95 CHLQLGDLDGAESGFYSARALA  116 (142)
T ss_dssp             HHHHTTCHHHHHHHHHHHHHHH
T ss_pred             HHHHcCCHHHHHHHHHHHHHhC
Confidence            9999999999999999998764

>2dba_A Smooth muscle cell associated protein-1, isoform 2; tetratricopeptide repeat, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=98.60  E-value=1.7e-06  Score=70.45  Aligned_cols=115  Identities=11%  Similarity=-0.021  Sum_probs=83.8

Q ss_pred             cCHHHHHHHHHHHHhcCChHHHHHHHHhcccCCCCCC----HHHHHHHHHHHHhcCChhHHHHHHHHHHHcCCCCCHHHH
Q 040027          450 LDIQAYNCLIDGLCKSGRLKFAWELFCSLPHGVLVPN----VVTYNIMIQGLCNDGQMDKARDLFLDMEENAAAPDVITF  525 (595)
Q Consensus       450 ~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~p~----~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~  525 (595)
                      .+...+..+...+...|++++|...|++..+  ..|+    ...|..+..+|...|++++|+..++++++.. +.+...+
T Consensus        26 ~~~~~~~~~a~~~~~~~~~~~A~~~~~~a~~--~~~~~~~~~~~~~~~a~~~~~~~~~~~A~~~~~~~~~~~-~~~~~~~  102 (148)
T 2dba_A           26 SSVEQLRKEGNELFKCGDYGGALAAYTQALG--LDATPQDQAVLHRNRAACHLKLEDYDKAETEASKAIEKD-GGDVKAL  102 (148)
T ss_dssp             CCHHHHHHHHHHHHTTTCHHHHHHHHHHHHT--SCCCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHT-SCCHHHH
T ss_pred             HHHHHHHHHHHHHHHhCCHHHHHHHHHHHHH--HcccchHHHHHHHHHHHHHHHHccHHHHHHHHHHHHhhC-ccCHHHH
Confidence            4566777777777888888888888888776  4555    5677777788888888888888888887764 4466777


Q ss_pred             HHHHHHHHHcCChhHHHHHHHHHHHCCCCCCHHHHHHHHHHHH
Q 040027          526 DMLIHGFIRINEPSKVNELLHKMKEKKVMPDASIVSIVVDLLV  568 (595)
Q Consensus       526 ~~l~~~~~~~g~~~~A~~~~~~~~~~~~~p~~~~~~~l~~~~~  568 (595)
                      ..+..+|...|++++|..++++..+.. +.+...+..+..+..
T Consensus       103 ~~~a~~~~~~~~~~~A~~~~~~al~~~-p~~~~~~~~l~~~~~  144 (148)
T 2dba_A          103 YRRSQALEKLGRLDQAVLDLQRCVSLE-PKNKVFQEALRNISG  144 (148)
T ss_dssp             HHHHHHHHHHTCHHHHHHHHHHHHHHC-SSCHHHHHHHHHHHC
T ss_pred             HHHHHHHHHcCCHHHHHHHHHHHHHcC-CCcHHHHHHHHHHHh
Confidence            788888888888888888888888643 224555555555443

>3upv_A Heat shock protein STI1; TPR-fold, adaptor protein for HSP70 and HSP90, C-terminal PA HSP70, peptide binding protein; 1.60A {Saccharomyces cerevisiae}

Probab=98.60  E-value=1.3e-06  Score=68.99  Aligned_cols=99  Identities=11%  Similarity=0.012  Sum_probs=89.3

Q ss_pred             CHHHHHHHHHHHHhcCChhHHHHHHHHHHhCCCCCCHHHHHHHHHHHHhcCCHhHHHHHHHHHHhcCCCCCHhhHHHHHH
Q 040027           95 NLYTYNILINCFCKIGRVSLGFIAFGRILRSCFTPNAATFNSLIKGLHAESRIMEAAALFTKLKAFGCEPNVITYNTLIN  174 (595)
Q Consensus        95 ~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~~l~~  174 (595)
                      +...|..+...+.+.|++++|+..|+++++.. +.+...|..+..++.+.|++++|+..|++..+.. +.+...+..+..
T Consensus         3 ~a~~~~~~g~~~~~~~~~~~A~~~~~~al~~~-p~~~~~~~~~a~~~~~~~~~~~A~~~~~~al~~~-p~~~~~~~~lg~   80 (126)
T 3upv_A            3 KAEEARLEGKEYFTKSDWPNAVKAYTEMIKRA-PEDARGYSNRAAALAKLMSFPEAIADCNKAIEKD-PNFVRAYIRKAT   80 (126)
T ss_dssp             HHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHH
T ss_pred             hHHHHHHHHHHHHHhcCHHHHHHHHHHHHHhC-CCChHHHHHHHHHHHHhcCHHHHHHHHHHHHHhC-CCcHHHHHHHHH
Confidence            35678888999999999999999999999885 5578899999999999999999999999999985 347889999999


Q ss_pred             HHHhcCChhHHHHHHHHHHhc
Q 040027          175 GLCRTGHTMIALNLFEEMANG  195 (595)
Q Consensus       175 ~~~~~g~~~~A~~~~~~~~~~  195 (595)
                      ++...|++++|+..|++....
T Consensus        81 ~~~~~~~~~~A~~~~~~al~~  101 (126)
T 3upv_A           81 AQIAVKEYASALETLDAARTK  101 (126)
T ss_dssp             HHHHTTCHHHHHHHHHHHHHH
T ss_pred             HHHHHhCHHHHHHHHHHHHHh
Confidence            999999999999999999875

>1elw_A TPR1-domain of HOP; HOP, TPR-domain, peptide-complex, helical repeat, HSP70, protein binding, chaperone; 1.60A {Homo sapiens} SCOP: a.118.8.1

Probab=98.59  E-value=1.8e-06  Score=67.00  Aligned_cols=111  Identities=9%  Similarity=0.014  Sum_probs=72.8

Q ss_pred             HHHHHHHHHHHHhcCChHHHHHHHHhcccCCCCC-CHHHHHHHHHHHHhcCChhHHHHHHHHHHHcCCCCCHHHHHHHHH
Q 040027          452 IQAYNCLIDGLCKSGRLKFAWELFCSLPHGVLVP-NVVTYNIMIQGLCNDGQMDKARDLFLDMEENAAAPDVITFDMLIH  530 (595)
Q Consensus       452 ~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~p-~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~~l~~  530 (595)
                      ...+..++..+...|++++|...+++....  .| +...+..++.++...|++++|...++++.+.. +.+...+..++.
T Consensus         4 ~~~~~~~~~~~~~~~~~~~A~~~~~~~~~~--~~~~~~~~~~~a~~~~~~~~~~~A~~~~~~~~~~~-~~~~~~~~~~a~   80 (118)
T 1elw_A            4 VNELKEKGNKALSVGNIDDALQCYSEAIKL--DPHNHVLYSNRSAAYAKKGDYQKAYEDGCKTVDLK-PDWGKGYSRKAA   80 (118)
T ss_dssp             HHHHHHHHHHHHHTTCHHHHHHHHHHHHHH--CTTCHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHC-TTCHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHcccHHHHHHHHHHHHHH--CCCcHHHHHHHHHHHHhhccHHHHHHHHHHHHHhC-cccHHHHHHHHH
Confidence            345556666667777777777777776653  33 45666677777777777777777777777653 445666777777


Q ss_pred             HHHHcCChhHHHHHHHHHHHCCCCCCHHHHHHHHHH
Q 040027          531 GFIRINEPSKVNELLHKMKEKKVMPDASIVSIVVDL  566 (595)
Q Consensus       531 ~~~~~g~~~~A~~~~~~~~~~~~~p~~~~~~~l~~~  566 (595)
                      ++...|++++|.+.+++..+.+ +.+...+..+..+
T Consensus        81 ~~~~~~~~~~A~~~~~~~~~~~-~~~~~~~~~l~~~  115 (118)
T 1elw_A           81 ALEFLNRFEEAKRTYEEGLKHE-ANNPQLKEGLQNM  115 (118)
T ss_dssp             HHHHTTCHHHHHHHHHHHHTTC-TTCHHHHHHHHHH
T ss_pred             HHHHHhhHHHHHHHHHHHHHcC-CCCHHHHHHHHHh
Confidence            7777777777777777777643 2244555444443

>2xcb_A PCRH, regulatory protein PCRH; protein transport, bacterial toxin, type III secretion, protein binding; 1.85A {Pseudomonas aeruginosa} PDB: 2xcc_A

Probab=98.59  E-value=1.6e-07  Score=76.23  Aligned_cols=96  Identities=7%  Similarity=-0.082  Sum_probs=55.7

Q ss_pred             HHHHHHHHHHHHhcCChHHHHHHHHhcccCCCCC-CHHHHHHHHHHHHhcCChhHHHHHHHHHHHcCCCCCHHHHHHHHH
Q 040027          452 IQAYNCLIDGLCKSGRLKFAWELFCSLPHGVLVP-NVVTYNIMIQGLCNDGQMDKARDLFLDMEENAAAPDVITFDMLIH  530 (595)
Q Consensus       452 ~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~p-~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~~l~~  530 (595)
                      ...+..+...+...|++++|+..|+++...  .| +...|..+..+|...|++++|+..|+++++.+ +.+...+..++.
T Consensus        18 ~~~~~~~a~~~~~~g~~~~A~~~~~~al~~--~p~~~~~~~~lg~~~~~~g~~~~A~~~~~~al~~~-p~~~~~~~~lg~   94 (142)
T 2xcb_A           18 LEQLYALGFNQYQAGKWDDAQKIFQALCML--DHYDARYFLGLGACRQSLGLYEQALQSYSYGALMD-INEPRFPFHAAE   94 (142)
T ss_dssp             HHHHHHHHHHHHHTTCHHHHHHHHHHHHHH--CTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCTHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHccHHHHHHHHHHHHHh--CCccHHHHHHHHHHHHHHhhHHHHHHHHHHHHhcC-CCCcHHHHHHHH
Confidence            344445555555666666666666665552  33 34555566666666666666666666666553 334455555666


Q ss_pred             HHHHcCChhHHHHHHHHHHH
Q 040027          531 GFIRINEPSKVNELLHKMKE  550 (595)
Q Consensus       531 ~~~~~g~~~~A~~~~~~~~~  550 (595)
                      +|...|++++|.+.|+++.+
T Consensus        95 ~~~~~g~~~~A~~~~~~al~  114 (142)
T 2xcb_A           95 CHLQLGDLDGAESGFYSARA  114 (142)
T ss_dssp             HHHHTTCHHHHHHHHHHHHH
T ss_pred             HHHHcCCHHHHHHHHHHHHH
Confidence            66666666666666666654

>1elw_A TPR1-domain of HOP; HOP, TPR-domain, peptide-complex, helical repeat, HSP70, protein binding, chaperone; 1.60A {Homo sapiens} SCOP: a.118.8.1

Probab=98.58  E-value=2.3e-06  Score=66.33  Aligned_cols=112  Identities=10%  Similarity=-0.019  Sum_probs=95.4

Q ss_pred             CHHHHHHHHHHHHhcCChhHHHHHHHHHHhCCCCCCHHHHHHHHHHHHhcCCHhHHHHHHHHHHhcCCCCCHhhHHHHHH
Q 040027           95 NLYTYNILINCFCKIGRVSLGFIAFGRILRSCFTPNAATFNSLIKGLHAESRIMEAAALFTKLKAFGCEPNVITYNTLIN  174 (595)
Q Consensus        95 ~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~~l~~  174 (595)
                      ++..+..++..+...|++++|...|+++.... +.+...+..+...+...|++++|...+++..... +.+...+..+..
T Consensus         3 ~~~~~~~~~~~~~~~~~~~~A~~~~~~~~~~~-~~~~~~~~~~a~~~~~~~~~~~A~~~~~~~~~~~-~~~~~~~~~~a~   80 (118)
T 1elw_A            3 QVNELKEKGNKALSVGNIDDALQCYSEAIKLD-PHNHVLYSNRSAAYAKKGDYQKAYEDGCKTVDLK-PDWGKGYSRKAA   80 (118)
T ss_dssp             HHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHC-TTCHHHHHHHHH
T ss_pred             hHHHHHHHHHHHHHcccHHHHHHHHHHHHHHC-CCcHHHHHHHHHHHHhhccHHHHHHHHHHHHHhC-cccHHHHHHHHH
Confidence            45678889999999999999999999999874 4578889999999999999999999999999875 336888999999


Q ss_pred             HHHhcCChhHHHHHHHHHHhcCCCCCccccCcHHHHHHHHH
Q 040027          175 GLCRTGHTMIALNLFEEMANGNGEIGVVCKPNTVTYSTIID  215 (595)
Q Consensus       175 ~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~  215 (595)
                      ++...|++++|.+.+++..+.+       +.+...+..+..
T Consensus        81 ~~~~~~~~~~A~~~~~~~~~~~-------~~~~~~~~~l~~  114 (118)
T 1elw_A           81 ALEFLNRFEEAKRTYEEGLKHE-------ANNPQLKEGLQN  114 (118)
T ss_dssp             HHHHTTCHHHHHHHHHHHHTTC-------TTCHHHHHHHHH
T ss_pred             HHHHHhhHHHHHHHHHHHHHcC-------CCCHHHHHHHHH
Confidence            9999999999999999999875       445555555443

>1elr_A TPR2A-domain of HOP; HOP, TPR-domain, peptide-complex, helical repeat, protein binding, chaperone; 1.90A {Homo sapiens} SCOP: a.118.8.1 PDB: 3esk_A 3fwv_A

Probab=98.52  E-value=8.1e-07  Score=70.56  Aligned_cols=114  Identities=10%  Similarity=0.029  Sum_probs=66.8

Q ss_pred             HHHHHHHHHHHhcCChHHHHHHHHhcccCCCCCCHHHHHHHHHHHHhcCChhHHHHHHHHHHHcCC--CCC----HHHHH
Q 040027          453 QAYNCLIDGLCKSGRLKFAWELFCSLPHGVLVPNVVTYNIMIQGLCNDGQMDKARDLFLDMEENAA--APD----VITFD  526 (595)
Q Consensus       453 ~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~p~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~--~~~----~~~~~  526 (595)
                      ..+..++..+...|++++|...|+++.... +.+...+..++.++...|++++|...++++.+...  .++    ..++.
T Consensus         5 ~~~~~l~~~~~~~~~~~~A~~~~~~a~~~~-~~~~~~~~~la~~~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~~~~~~~   83 (131)
T 1elr_A            5 LKEKELGNDAYKKKDFDTALKHYDKAKELD-PTNMTYITNQAAVYFEKGDYNKCRELCEKAIEVGRENREDYRQIAKAYA   83 (131)
T ss_dssp             HHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHHHSTTCHHHHHHHHH
T ss_pred             HHHHHHHHHHHHhcCHHHHHHHHHHHHhcC-CccHHHHHHHHHHHHHhccHHHHHHHHHHHHhhccccchhHHHHHHHHH
Confidence            345555566666666666666666665521 22455566666666666666666666666665421  111    55566


Q ss_pred             HHHHHHHHcCChhHHHHHHHHHHHCCCCCCHHHHHHHHHHHHh
Q 040027          527 MLIHGFIRINEPSKVNELLHKMKEKKVMPDASIVSIVVDLLVK  569 (595)
Q Consensus       527 ~l~~~~~~~g~~~~A~~~~~~~~~~~~~p~~~~~~~l~~~~~~  569 (595)
                      .++.+|...|++++|.+.++++.+.  .|+......+..+...
T Consensus        84 ~la~~~~~~~~~~~A~~~~~~~~~~--~~~~~~~~~l~~~~~~  124 (131)
T 1elr_A           84 RIGNSYFKEEKYKDAIHFYNKSLAE--HRTPDVLKKCQQAEKI  124 (131)
T ss_dssp             HHHHHHHHTTCHHHHHHHHHHHHHH--CCCHHHHHHHHHHHHH
T ss_pred             HHHHHHHHhccHHHHHHHHHHHHHh--CCCHHHHHHHHHHHHH
Confidence            6666777777777777777777663  3555555555554433

>3q49_B STIP1 homology and U box-containing protein 1; E3 ubiquitin ligase, ligase-chaperone complex; 1.54A {Mus musculus} PDB: 3q47_B 3q4a_B*

Probab=98.51  E-value=2.3e-06  Score=68.70  Aligned_cols=102  Identities=10%  Similarity=-0.083  Sum_probs=91.8

Q ss_pred             CCCHHHHHHHHHHHHhcCChhHHHHHHHHHHhCCCCCCHHHHHHHHHHHHhcCCHhHHHHHHHHHHhcCCCCCHhhHHHH
Q 040027           93 FPNLYTYNILINCFCKIGRVSLGFIAFGRILRSCFTPNAATFNSLIKGLHAESRIMEAAALFTKLKAFGCEPNVITYNTL  172 (595)
Q Consensus        93 ~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~~l  172 (595)
                      +.++..|..+...+...|++++|+..|++++... +.+...|..+...+...|++++|+..+++..... +.+...+..+
T Consensus         6 ~~~~~~~~~~g~~~~~~~~~~~A~~~~~~al~~~-~~~~~~~~~l~~~~~~~~~~~~A~~~~~~al~~~-p~~~~~~~~l   83 (137)
T 3q49_B            6 SPSAQELKEQGNRLFVGRKYPEAAACYGRAITRN-PLVAVYYTNRALCYLKMQQPEQALADCRRALELD-GQSVKAHFFL   83 (137)
T ss_dssp             CCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHH
T ss_pred             cccHHHHHHHHHHHHHhCcHHHHHHHHHHHHhhC-cCcHHHHHHHHHHHHHhcCHHHHHHHHHHHHHhC-chhHHHHHHH
Confidence            3578889999999999999999999999999885 5578899999999999999999999999999875 3478899999


Q ss_pred             HHHHHhcCChhHHHHHHHHHHhcC
Q 040027          173 INGLCRTGHTMIALNLFEEMANGN  196 (595)
Q Consensus       173 ~~~~~~~g~~~~A~~~~~~~~~~~  196 (595)
                      ..++...|++++|+..|+++....
T Consensus        84 ~~~~~~~~~~~~A~~~~~~a~~~~  107 (137)
T 3q49_B           84 GQCQLEMESYDEAIANLQRAYSLA  107 (137)
T ss_dssp             HHHHHHTTCHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHhhHHHHHHHHHHHHHHC
Confidence            999999999999999999998754

>3sz7_A HSC70 cochaperone (SGT); TPR domain, GET4, GET5, GET3, MDY2, SSA1, SSE1, chaperone regulator; 1.72A {Aspergillus fumigatus}

Probab=98.50  E-value=2.7e-06  Score=70.89  Aligned_cols=95  Identities=13%  Similarity=0.000  Sum_probs=46.5

Q ss_pred             HHHHHHHHHHHhcCChHHHHHHHHhcccCCCCC-CHHHHHHHHHHHHhcCChhHHHHHHHHHHHcCCCCCHHHHHHHHHH
Q 040027          453 QAYNCLIDGLCKSGRLKFAWELFCSLPHGVLVP-NVVTYNIMIQGLCNDGQMDKARDLFLDMEENAAAPDVITFDMLIHG  531 (595)
Q Consensus       453 ~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~p-~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~~l~~~  531 (595)
                      ..+..+...+...|++++|+..|++.++.  .| +...|..+..+|...|++++|+..|+++++.. +.+...|..+..+
T Consensus        12 ~~~~~~g~~~~~~g~~~~A~~~~~~al~~--~p~~~~~~~~l~~~~~~~g~~~~A~~~~~~al~~~-p~~~~~~~~lg~~   88 (164)
T 3sz7_A           12 DKLKSEGNAAMARKEYSKAIDLYTQALSI--APANPIYLSNRAAAYSASGQHEKAAEDAELATVVD-PKYSKAWSRLGLA   88 (164)
T ss_dssp             HHHHHHHHHHHHTTCHHHHHHHHHHHHHH--STTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHcCCHHHHHHHHHHHHHh--CCcCHHHHHHHHHHHHHccCHHHHHHHHHHHHHhC-CCCHHHHHHHHHH
Confidence            34444444445555555555555554442  22 34444455555555555555555555555443 3334445555555


Q ss_pred             HHHcCChhHHHHHHHHHHH
Q 040027          532 FIRINEPSKVNELLHKMKE  550 (595)
Q Consensus       532 ~~~~g~~~~A~~~~~~~~~  550 (595)
                      |...|++++|...|+++++
T Consensus        89 ~~~~g~~~~A~~~~~~al~  107 (164)
T 3sz7_A           89 RFDMADYKGAKEAYEKGIE  107 (164)
T ss_dssp             HHHTTCHHHHHHHHHHHHH
T ss_pred             HHHccCHHHHHHHHHHHHH
Confidence            5555555555555555554

>1wao_1 Serine/threonine protein phosphatase 5; hydrolase, protein-protein interactions, TPR, super-helix,; 2.9A {Homo sapiens} SCOP: a.118.8.1 d.159.1.3

Probab=98.50  E-value=2.2e-06  Score=85.07  Aligned_cols=122  Identities=9%  Similarity=-0.013  Sum_probs=97.8

Q ss_pred             cccccccCCCChHHHHHHHHHHHHhCCCCCCHhhHHHHHHHHHcCCCchhHHhhCCCCCCHHHHHHHHHHHHhcCChhHH
Q 040027           36 TTREGDINVITPNEAFCIFDYMLRMHPSPPPVSSFNILLASLAKNKHYDTRLNATGLFPNLYTYNILINCFCKIGRVSLG  115 (595)
Q Consensus        36 ~~~~~~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A  115 (595)
                      ..+..+.+.|++++|.+.|+++++.+|.                               +...|..+..++.+.|++++|
T Consensus        11 ~lg~~~~~~g~~~~A~~~~~~Al~~~p~-------------------------------~~~~~~~lg~~~~~~g~~~~A   59 (477)
T 1wao_1           11 TQANDYFKAKDYENAIKFYSQAIELNPS-------------------------------NAIYYGNRSLAYLRTECYGYA   59 (477)
T ss_dssp             SSSSSTTTTTCHHHHHHHHHHHHHHCTT-------------------------------CHHHHHHHHHHHHHTTCHHHH
T ss_pred             HHHHHHHHhCCHHHHHHHHHHHHHhCCc-------------------------------cHHHHHHHHHHHHHhcCHHHH
Confidence            4566778999999999999999999987                               345666777788889999999


Q ss_pred             HHHHHHHHhCCCCCCHHHHHHHHHHHHhcCCHhHHHHHHHHHHhcCCCCCHhhHHHHHHH--HHhcCChhHHHHHHH
Q 040027          116 FIAFGRILRSCFTPNAATFNSLIKGLHAESRIMEAAALFTKLKAFGCEPNVITYNTLING--LCRTGHTMIALNLFE  190 (595)
Q Consensus       116 ~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~~l~~~--~~~~g~~~~A~~~~~  190 (595)
                      +..++++++.. +.+..+|..+..+|...|++++|.+.|+++.+... .+...+..+..+  +...|++++|++.++
T Consensus        60 ~~~~~~al~l~-p~~~~~~~~lg~~~~~~g~~~eA~~~~~~al~~~p-~~~~~~~~l~~~~~~~~~g~~~~A~~~~~  134 (477)
T 1wao_1           60 LGDATRAIELD-KKYIKGYYRRAASNMALGKFRAALRDYETVVKVKP-HDKDAKMKYQECNKIVKQKAFERAIAGDE  134 (477)
T ss_dssp             HHHHHHHHHSC-TTCHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHST-TCTTHHHHHHHHHHHHHHHHHCCC-----
T ss_pred             HHHHHHHHHhC-CCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCC-CCHHHHHHHHHHHHHHHHHHHHHHhcccc
Confidence            99999999985 55788899999999999999999999999988742 245566666665  788899999999988

>3sz7_A HSC70 cochaperone (SGT); TPR domain, GET4, GET5, GET3, MDY2, SSA1, SSE1, chaperone regulator; 1.72A {Aspergillus fumigatus}

Probab=98.50  E-value=2.1e-06  Score=71.49  Aligned_cols=101  Identities=11%  Similarity=-0.033  Sum_probs=91.5

Q ss_pred             CCHHHHHHHHHHHHhcCChhHHHHHHHHHHhCCCCCCHHHHHHHHHHHHhcCCHhHHHHHHHHHHhcCCCCCHhhHHHHH
Q 040027           94 PNLYTYNILINCFCKIGRVSLGFIAFGRILRSCFTPNAATFNSLIKGLHAESRIMEAAALFTKLKAFGCEPNVITYNTLI  173 (595)
Q Consensus        94 ~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~~l~  173 (595)
                      .+...|..+...+.+.|++++|+..|+++++.. +.+...|..+..+|...|++++|+..|++..... +.+...+..+.
T Consensus         9 ~~a~~~~~~g~~~~~~g~~~~A~~~~~~al~~~-p~~~~~~~~l~~~~~~~g~~~~A~~~~~~al~~~-p~~~~~~~~lg   86 (164)
T 3sz7_A            9 PESDKLKSEGNAAMARKEYSKAIDLYTQALSIA-PANPIYLSNRAAAYSASGQHEKAAEDAELATVVD-PKYSKAWSRLG   86 (164)
T ss_dssp             HHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHS-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHH
T ss_pred             hhHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhC-CcCHHHHHHHHHHHHHccCHHHHHHHHHHHHHhC-CCCHHHHHHHH
Confidence            356788889999999999999999999999985 5578899999999999999999999999999985 34788999999


Q ss_pred             HHHHhcCChhHHHHHHHHHHhcC
Q 040027          174 NGLCRTGHTMIALNLFEEMANGN  196 (595)
Q Consensus       174 ~~~~~~g~~~~A~~~~~~~~~~~  196 (595)
                      .+|...|++++|+..|++..+..
T Consensus        87 ~~~~~~g~~~~A~~~~~~al~~~  109 (164)
T 3sz7_A           87 LARFDMADYKGAKEAYEKGIEAE  109 (164)
T ss_dssp             HHHHHTTCHHHHHHHHHHHHHHH
T ss_pred             HHHHHccCHHHHHHHHHHHHHhC
Confidence            99999999999999999999865

>2fbn_A 70 kDa peptidylprolyl isomerase, putative; sulfur SAD, PFL2275C, TPR-containing domain, structural genomics; 1.63A {Plasmodium falciparum} SCOP: a.118.8.1

Probab=98.49  E-value=2.3e-06  Score=73.89  Aligned_cols=123  Identities=14%  Similarity=-0.012  Sum_probs=76.9

Q ss_pred             HHHHHHHHHHHHhcCChhHHHHHHHHHHhCCCCCCH----------------HHHHHHHHHHHhcCCHhHHHHHHHHHHh
Q 040027           96 LYTYNILINCFCKIGRVSLGFIAFGRILRSCFTPNA----------------ATFNSLIKGLHAESRIMEAAALFTKLKA  159 (595)
Q Consensus        96 ~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~~~----------------~~~~~l~~~~~~~g~~~~A~~~~~~~~~  159 (595)
                      ...+..+...+...|++++|+..|++++..... +.                .+|..+..++...|++++|+..+++...
T Consensus        38 ~~~~~~~g~~~~~~~~~~~A~~~~~~al~~~~~-~~~~~~~~~~~~~~~~~~~~~~~la~~~~~~~~~~~A~~~~~~al~  116 (198)
T 2fbn_A           38 AFDIKEEGNEFFKKNEINEAIVKYKEALDFFIH-TEEWDDQILLDKKKNIEISCNLNLATCYNKNKDYPKAIDHASKVLK  116 (198)
T ss_dssp             HHHHHHHHHHHHHTTCHHHHHHHHHHHHHTTTT-CTTCCCHHHHHHHHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHhc-ccccchhhHHHHHHHHHHHHHHHHHHHHHHhcCHHHHHHHHHHHHH
Confidence            445666777788888888888888888876321 22                5566666666666666666666666666


Q ss_pred             cCCCCCHhhHHHHHHHHHhcCChhHHHHHHHHHHhcCCCCCccccCcHHHHHHHHHHHHHcCCHhHHH
Q 040027          160 FGCEPNVITYNTLINGLCRTGHTMIALNLFEEMANGNGEIGVVCKPNTVTYSTIIDGLCKEGFVDKAK  227 (595)
Q Consensus       160 ~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~  227 (595)
                      .. +.+..++..+..++...|++++|+..|++.....       +.+...+..+..++...++.+++.
T Consensus       117 ~~-p~~~~~~~~lg~~~~~~~~~~~A~~~~~~al~~~-------p~~~~~~~~l~~~~~~~~~~~~~~  176 (198)
T 2fbn_A          117 ID-KNNVKALYKLGVANMYFGFLEEAKENLYKAASLN-------PNNLDIRNSYELCVNKLKEARKKD  176 (198)
T ss_dssp             HS-TTCHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHS-------TTCHHHHHHHHHHHHHHHHHHC--
T ss_pred             hC-cccHHHHHHHHHHHHHcccHHHHHHHHHHHHHHC-------CCcHHHHHHHHHHHHHHHHHHHHH
Confidence            53 2355566666666666666666666666666553       334555555555555555444444

>2fbn_A 70 kDa peptidylprolyl isomerase, putative; sulfur SAD, PFL2275C, TPR-containing domain, structural genomics; 1.63A {Plasmodium falciparum} SCOP: a.118.8.1

Probab=98.49  E-value=2e-06  Score=74.33  Aligned_cols=119  Identities=12%  Similarity=-0.027  Sum_probs=58.2

Q ss_pred             HHHHHHHHHhcCCHHHHHHHHHHHHHcCCCcC----------------HHHHHHHHHHHHhcCChHHHHHHHHhcccCCC
Q 040027          420 YTTFIDGLCKNGYIIEAVELFRTLRILKCELD----------------IQAYNCLIDGLCKSGRLKFAWELFCSLPHGVL  483 (595)
Q Consensus       420 ~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~~----------------~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~  483 (595)
                      +..+...+...|++++|...|+++.... +.+                ..++..+..+|...|++++|+..++++...  
T Consensus        41 ~~~~g~~~~~~~~~~~A~~~~~~al~~~-~~~~~~~~~~~~~~~~~~~~~~~~~la~~~~~~~~~~~A~~~~~~al~~--  117 (198)
T 2fbn_A           41 IKEEGNEFFKKNEINEAIVKYKEALDFF-IHTEEWDDQILLDKKKNIEISCNLNLATCYNKNKDYPKAIDHASKVLKI--  117 (198)
T ss_dssp             HHHHHHHHHHTTCHHHHHHHHHHHHHTT-TTCTTCCCHHHHHHHHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH--
T ss_pred             HHHHHHHHHHcCCHHHHHHHHHHHHHHH-hcccccchhhHHHHHHHHHHHHHHHHHHHHHHhcCHHHHHHHHHHHHHh--
Confidence            3344444555555555555555555432 111                144555555555555555555555555542  


Q ss_pred             CC-CHHHHHHHHHHHHhcCChhHHHHHHHHHHHcCCCCCHHHHHHHHHHHHHcCChhHHH
Q 040027          484 VP-NVVTYNIMIQGLCNDGQMDKARDLFLDMEENAAAPDVITFDMLIHGFIRINEPSKVN  542 (595)
Q Consensus       484 ~p-~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~  542 (595)
                      .| +...+..+..+|...|++++|+..|+++++.. +.+...+..+..++...++.+++.
T Consensus       118 ~p~~~~~~~~lg~~~~~~~~~~~A~~~~~~al~~~-p~~~~~~~~l~~~~~~~~~~~~~~  176 (198)
T 2fbn_A          118 DKNNVKALYKLGVANMYFGFLEEAKENLYKAASLN-PNNLDIRNSYELCVNKLKEARKKD  176 (198)
T ss_dssp             STTCHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHS-TTCHHHHHHHHHHHHHHHHHHC--
T ss_pred             CcccHHHHHHHHHHHHHcccHHHHHHHHHHHHHHC-CCcHHHHHHHHHHHHHHHHHHHHH
Confidence            22 34455555555555555555555555555542 334444555555555554444443

>2dba_A Smooth muscle cell associated protein-1, isoform 2; tetratricopeptide repeat, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=98.47  E-value=5.7e-06  Score=67.29  Aligned_cols=113  Identities=12%  Similarity=-0.026  Sum_probs=95.4

Q ss_pred             CCHHHHHHHHHHHHhcCChhHHHHHHHHHHhCCCCCC----HHHHHHHHHHHHhcCCHhHHHHHHHHHHhcCCCCCHhhH
Q 040027           94 PNLYTYNILINCFCKIGRVSLGFIAFGRILRSCFTPN----AATFNSLIKGLHAESRIMEAAALFTKLKAFGCEPNVITY  169 (595)
Q Consensus        94 ~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~~----~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~  169 (595)
                      .+...+..+...+...|++++|+..|+++.+.  .|+    ...|..+...+...|++++|+..+++..... +.+...+
T Consensus        26 ~~~~~~~~~a~~~~~~~~~~~A~~~~~~a~~~--~~~~~~~~~~~~~~a~~~~~~~~~~~A~~~~~~~~~~~-~~~~~~~  102 (148)
T 2dba_A           26 SSVEQLRKEGNELFKCGDYGGALAAYTQALGL--DATPQDQAVLHRNRAACHLKLEDYDKAETEASKAIEKD-GGDVKAL  102 (148)
T ss_dssp             CCHHHHHHHHHHHHTTTCHHHHHHHHHHHHTS--CCCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHT-SCCHHHH
T ss_pred             HHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHH--cccchHHHHHHHHHHHHHHHHccHHHHHHHHHHHHhhC-ccCHHHH
Confidence            47788889999999999999999999999987  445    6788889999999999999999999998874 3367888


Q ss_pred             HHHHHHHHhcCChhHHHHHHHHHHhcCCCCCccccCcHHHHHHHHHH
Q 040027          170 NTLINGLCRTGHTMIALNLFEEMANGNGEIGVVCKPNTVTYSTIIDG  216 (595)
Q Consensus       170 ~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~  216 (595)
                      ..+..++...|++++|...|++.....       +.+...+..+...
T Consensus       103 ~~~a~~~~~~~~~~~A~~~~~~al~~~-------p~~~~~~~~l~~~  142 (148)
T 2dba_A          103 YRRSQALEKLGRLDQAVLDLQRCVSLE-------PKNKVFQEALRNI  142 (148)
T ss_dssp             HHHHHHHHHHTCHHHHHHHHHHHHHHC-------SSCHHHHHHHHHH
T ss_pred             HHHHHHHHHcCCHHHHHHHHHHHHHcC-------CCcHHHHHHHHHH
Confidence            999999999999999999999999875       4455555544443

>3q49_B STIP1 homology and U box-containing protein 1; E3 ubiquitin ligase, ligase-chaperone complex; 1.54A {Mus musculus} PDB: 3q47_B 3q4a_B*

Probab=98.47  E-value=7e-06  Score=65.78  Aligned_cols=98  Identities=12%  Similarity=-0.061  Sum_probs=58.8

Q ss_pred             cCHHHHHHHHHHHHhcCChHHHHHHHHhcccCCCCC-CHHHHHHHHHHHHhcCChhHHHHHHHHHHHcCCCCCHHHHHHH
Q 040027          450 LDIQAYNCLIDGLCKSGRLKFAWELFCSLPHGVLVP-NVVTYNIMIQGLCNDGQMDKARDLFLDMEENAAAPDVITFDML  528 (595)
Q Consensus       450 ~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~p-~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~~l  528 (595)
                      .+...+..++..+...|++++|...|+++...  .| +...|..+..++...|++++|+..++++++.. +.+...+..+
T Consensus         7 ~~~~~~~~~g~~~~~~~~~~~A~~~~~~al~~--~~~~~~~~~~l~~~~~~~~~~~~A~~~~~~al~~~-p~~~~~~~~l   83 (137)
T 3q49_B            7 PSAQELKEQGNRLFVGRKYPEAAACYGRAITR--NPLVAVYYTNRALCYLKMQQPEQALADCRRALELD-GQSVKAHFFL   83 (137)
T ss_dssp             CCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH--CTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHH
T ss_pred             ccHHHHHHHHHHHHHhCcHHHHHHHHHHHHhh--CcCcHHHHHHHHHHHHHhcCHHHHHHHHHHHHHhC-chhHHHHHHH
Confidence            34555556666666666666666666665552  23 34556666666666666666666666666653 3345566666


Q ss_pred             HHHHHHcCChhHHHHHHHHHHH
Q 040027          529 IHGFIRINEPSKVNELLHKMKE  550 (595)
Q Consensus       529 ~~~~~~~g~~~~A~~~~~~~~~  550 (595)
                      +.+|...|++++|...++++.+
T Consensus        84 ~~~~~~~~~~~~A~~~~~~a~~  105 (137)
T 3q49_B           84 GQCQLEMESYDEAIANLQRAYS  105 (137)
T ss_dssp             HHHHHHTTCHHHHHHHHHHHHH
T ss_pred             HHHHHHHhhHHHHHHHHHHHHH
Confidence            6666666666666666666654

>1elr_A TPR2A-domain of HOP; HOP, TPR-domain, peptide-complex, helical repeat, protein binding, chaperone; 1.90A {Homo sapiens} SCOP: a.118.8.1 PDB: 3esk_A 3fwv_A

Probab=98.44  E-value=2.3e-06  Score=67.82  Aligned_cols=112  Identities=7%  Similarity=-0.037  Sum_probs=77.6

Q ss_pred             HHHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCcCHHHHHHHHHHHHhcCChHHHHHHHHhcccCCC--CCC----HHHHH
Q 040027          418 RTYTTFIDGLCKNGYIIEAVELFRTLRILKCELDIQAYNCLIDGLCKSGRLKFAWELFCSLPHGVL--VPN----VVTYN  491 (595)
Q Consensus       418 ~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~--~p~----~~~~~  491 (595)
                      ..+..+...+...|++++|...++++.... +.+...+..++.++...|++++|...++++.....  .++    ..++.
T Consensus         5 ~~~~~l~~~~~~~~~~~~A~~~~~~a~~~~-~~~~~~~~~la~~~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~~~~~~~   83 (131)
T 1elr_A            5 LKEKELGNDAYKKKDFDTALKHYDKAKELD-PTNMTYITNQAAVYFEKGDYNKCRELCEKAIEVGRENREDYRQIAKAYA   83 (131)
T ss_dssp             HHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHHHSTTCHHHHHHHHH
T ss_pred             HHHHHHHHHHHHhcCHHHHHHHHHHHHhcC-CccHHHHHHHHHHHHHhccHHHHHHHHHHHHhhccccchhHHHHHHHHH
Confidence            445566667777777888888777777665 55677777777777788888888888777766210  111    56677


Q ss_pred             HHHHHHHhcCChhHHHHHHHHHHHcCCCCCHHHHHHHHHHH
Q 040027          492 IMIQGLCNDGQMDKARDLFLDMEENAAAPDVITFDMLIHGF  532 (595)
Q Consensus       492 ~l~~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~~l~~~~  532 (595)
                      .++.++...|++++|.+.|+++.+.  .|+......+..+.
T Consensus        84 ~la~~~~~~~~~~~A~~~~~~~~~~--~~~~~~~~~l~~~~  122 (131)
T 1elr_A           84 RIGNSYFKEEKYKDAIHFYNKSLAE--HRTPDVLKKCQQAE  122 (131)
T ss_dssp             HHHHHHHHTTCHHHHHHHHHHHHHH--CCCHHHHHHHHHHH
T ss_pred             HHHHHHHHhccHHHHHHHHHHHHHh--CCCHHHHHHHHHHH
Confidence            7788888888888888888888875  34655555554443

>1hxi_A PEX5, peroxisome targeting signal 1 receptor PEX5; alpha helical, transport protein; 1.60A {Trypanosoma brucei} SCOP: a.118.8.1

Probab=98.42  E-value=1.7e-06  Score=67.70  Aligned_cols=93  Identities=10%  Similarity=-0.108  Sum_probs=63.4

Q ss_pred             HHHHHHHHHhcCChHHHHHHHHhcccCCCCC-CHHHHHHHHHHHHhcCChhHHHHHHHHHHHcCCCCCHHHHHHHHHHHH
Q 040027          455 YNCLIDGLCKSGRLKFAWELFCSLPHGVLVP-NVVTYNIMIQGLCNDGQMDKARDLFLDMEENAAAPDVITFDMLIHGFI  533 (595)
Q Consensus       455 ~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~p-~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~~l~~~~~  533 (595)
                      +..++..+.+.|++++|+..|+++++  ..| +...|..+..++...|++++|+..|+++++.. +.+...+..++.+|.
T Consensus        20 ~~~~g~~~~~~g~~~~A~~~~~~al~--~~P~~~~a~~~lg~~~~~~g~~~~A~~~~~~al~l~-P~~~~~~~~la~~~~   96 (121)
T 1hxi_A           20 PMEEGLSMLKLANLAEAALAFEAVCQ--KEPEREEAWRSLGLTQAENEKDGLAIIALNHARMLD-PKDIAVHAALAVSHT   96 (121)
T ss_dssp             HHHHHHHHHHTTCHHHHHHHHHHHHH--HSTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHcCCHHHHHHHHHHHHH--HCCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhC-CCCHHHHHHHHHHHH
Confidence            34455566677777777777777766  334 45666677777777777777777777777754 445666677777777


Q ss_pred             HcCChhHHHHHHHHHHH
Q 040027          534 RINEPSKVNELLHKMKE  550 (595)
Q Consensus       534 ~~g~~~~A~~~~~~~~~  550 (595)
                      ..|++++|...++++++
T Consensus        97 ~~g~~~~A~~~~~~al~  113 (121)
T 1hxi_A           97 NEHNANAALASLRAWLL  113 (121)
T ss_dssp             HHHHHHHHHHHHHHHHC
T ss_pred             HcCCHHHHHHHHHHHHH
Confidence            77777777777777765

>2kck_A TPR repeat; tetratricopeptide repeat, structural genomics, unknown function, PSI-2, protein structure initiative; NMR {Methanococcus maripaludis}

Probab=98.42  E-value=2.7e-06  Score=65.23  Aligned_cols=95  Identities=14%  Similarity=0.005  Sum_probs=37.5

Q ss_pred             HHHHHHHHHHhcCChhHHHHHHHHHHhCCCCCCHHHHHHHHHHHHhcCCHhHHHHHHHHHHhcCCCC--CHhhHHHHHHH
Q 040027           98 TYNILINCFCKIGRVSLGFIAFGRILRSCFTPNAATFNSLIKGLHAESRIMEAAALFTKLKAFGCEP--NVITYNTLING  175 (595)
Q Consensus        98 ~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~--~~~~~~~l~~~  175 (595)
                      .|..++..+...|++++|+..|+++.+.. +.+...+..+...+...|++++|++.|++..+.. +.  +..++..+...
T Consensus         8 ~~~~~~~~~~~~~~~~~A~~~~~~a~~~~-~~~~~~~~~~a~~~~~~~~~~~A~~~~~~a~~~~-~~~~~~~~~~~l~~~   85 (112)
T 2kck_A            8 EYYLEGVLQYDAGNYTESIDLFEKAIQLD-PEESKYWLMKGKALYNLERYEEAVDCYNYVINVI-EDEYNKDVWAAKADA   85 (112)
T ss_dssp             GGGGHHHHHHSSCCHHHHHHHHHHHHHHC-CCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHTS-CCTTCHHHHHHHHHH
T ss_pred             HHHHHHHHHHHhhhHHHHHHHHHHHHHhC-cCCHHHHHHHHHHHHHccCHHHHHHHHHHHHHhC-cccchHHHHHHHHHH
Confidence            33334444444444444444444444332 2233333344444444444444444444443331 11  23333333444


Q ss_pred             HHhc-CChhHHHHHHHHHHh
Q 040027          176 LCRT-GHTMIALNLFEEMAN  194 (595)
Q Consensus       176 ~~~~-g~~~~A~~~~~~~~~  194 (595)
                      +... |++++|++.++.+..
T Consensus        86 ~~~~~~~~~~A~~~~~~~~~  105 (112)
T 2kck_A           86 LRYIEGKEVEAEIAEARAKL  105 (112)
T ss_dssp             HTTCSSCSHHHHHHHHHHGG
T ss_pred             HHHHhCCHHHHHHHHHHHhh
Confidence            4444 444444444444433

>2kck_A TPR repeat; tetratricopeptide repeat, structural genomics, unknown function, PSI-2, protein structure initiative; NMR {Methanococcus maripaludis}

Probab=98.40  E-value=2.8e-06  Score=65.19  Aligned_cols=94  Identities=7%  Similarity=-0.008  Sum_probs=80.6

Q ss_pred             CHhhHHHHHHHHHcCCCchh------HHhhCCCCCCHHHHHHHHHHHHhcCChhHHHHHHHHHHhCCCCC--CHHHHHHH
Q 040027           66 PVSSFNILLASLAKNKHYDT------RLNATGLFPNLYTYNILINCFCKIGRVSLGFIAFGRILRSCFTP--NAATFNSL  137 (595)
Q Consensus        66 ~~~~~~~l~~~~~~~~~~~~------~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~--~~~~~~~l  137 (595)
                      ++..|..+...+...|++++      ..... .+.+...|..+...+...|++++|+..++++.+.. +.  +...+..+
T Consensus         5 ~~~~~~~~~~~~~~~~~~~~A~~~~~~a~~~-~~~~~~~~~~~a~~~~~~~~~~~A~~~~~~a~~~~-~~~~~~~~~~~l   82 (112)
T 2kck_A            5 NPEEYYLEGVLQYDAGNYTESIDLFEKAIQL-DPEESKYWLMKGKALYNLERYEEAVDCYNYVINVI-EDEYNKDVWAAK   82 (112)
T ss_dssp             STTGGGGHHHHHHSSCCHHHHHHHHHHHHHH-CCCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHTS-CCTTCHHHHHHH
T ss_pred             cHHHHHHHHHHHHHhhhHHHHHHHHHHHHHh-CcCCHHHHHHHHHHHHHccCHHHHHHHHHHHHHhC-cccchHHHHHHH
Confidence            67788899999999999988      22222 24578889999999999999999999999999884 44  68889999


Q ss_pred             HHHHHhc-CCHhHHHHHHHHHHhcC
Q 040027          138 IKGLHAE-SRIMEAAALFTKLKAFG  161 (595)
Q Consensus       138 ~~~~~~~-g~~~~A~~~~~~~~~~~  161 (595)
                      ...+... |++++|.+.++++....
T Consensus        83 ~~~~~~~~~~~~~A~~~~~~~~~~~  107 (112)
T 2kck_A           83 ADALRYIEGKEVEAEIAEARAKLEH  107 (112)
T ss_dssp             HHHHTTCSSCSHHHHHHHHHHGGGC
T ss_pred             HHHHHHHhCCHHHHHHHHHHHhhcc
Confidence            9999999 99999999999999874

>1hxi_A PEX5, peroxisome targeting signal 1 receptor PEX5; alpha helical, transport protein; 1.60A {Trypanosoma brucei} SCOP: a.118.8.1

Probab=98.39  E-value=3.1e-06  Score=66.17  Aligned_cols=97  Identities=9%  Similarity=-0.002  Sum_probs=85.7

Q ss_pred             HHHHHHHHHHhcCChhHHHHHHHHHHhCCCCCCHHHHHHHHHHHHhcCCHhHHHHHHHHHHhcCCCCCHhhHHHHHHHHH
Q 040027           98 TYNILINCFCKIGRVSLGFIAFGRILRSCFTPNAATFNSLIKGLHAESRIMEAAALFTKLKAFGCEPNVITYNTLINGLC  177 (595)
Q Consensus        98 ~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~~l~~~~~  177 (595)
                      .+..+...+.+.|++++|+..|+++++.. +.+...|..+..++...|++++|+..|++..+.. +.+...+..+..++.
T Consensus        19 ~~~~~g~~~~~~g~~~~A~~~~~~al~~~-P~~~~a~~~lg~~~~~~g~~~~A~~~~~~al~l~-P~~~~~~~~la~~~~   96 (121)
T 1hxi_A           19 NPMEEGLSMLKLANLAEAALAFEAVCQKE-PEREEAWRSLGLTQAENEKDGLAIIALNHARMLD-PKDIAVHAALAVSHT   96 (121)
T ss_dssp             CHHHHHHHHHHTTCHHHHHHHHHHHHHHS-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHH
T ss_pred             hHHHHHHHHHHcCCHHHHHHHHHHHHHHC-CCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhC-CCCHHHHHHHHHHHH
Confidence            45667788999999999999999999985 5588899999999999999999999999999985 337889999999999


Q ss_pred             hcCChhHHHHHHHHHHhcC
Q 040027          178 RTGHTMIALNLFEEMANGN  196 (595)
Q Consensus       178 ~~g~~~~A~~~~~~~~~~~  196 (595)
                      ..|++++|+..|+++.+.+
T Consensus        97 ~~g~~~~A~~~~~~al~~~  115 (121)
T 1hxi_A           97 NEHNANAALASLRAWLLSQ  115 (121)
T ss_dssp             HHHHHHHHHHHHHHHHC--
T ss_pred             HcCCHHHHHHHHHHHHHhC
Confidence            9999999999999998764

>2xev_A YBGF; tetratricopeptide, alpha-helical, metal binding; 1.57A {Xanthomonas campestris}

Probab=98.36  E-value=9.6e-06  Score=64.14  Aligned_cols=92  Identities=15%  Similarity=0.092  Sum_probs=55.1

Q ss_pred             HHHHHHHhcCChHHHHHHHHhcccCCCCCC-H---HHHHHHHHHHHhcCChhHHHHHHHHHHHcCCCCC---HHHHHHHH
Q 040027          457 CLIDGLCKSGRLKFAWELFCSLPHGVLVPN-V---VTYNIMIQGLCNDGQMDKARDLFLDMEENAAAPD---VITFDMLI  529 (595)
Q Consensus       457 ~l~~~~~~~g~~~~A~~~~~~~~~~~~~p~-~---~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~~---~~~~~~l~  529 (595)
                      .++..+...|++++|...|+++.+.  .|+ .   ..+..++.++...|++++|+..|+++++.. +.+   ...+..++
T Consensus         7 ~~a~~~~~~~~~~~A~~~~~~~~~~--~p~~~~~~~~~~~lg~~~~~~~~~~~A~~~~~~~~~~~-p~~~~~~~~~~~la   83 (129)
T 2xev_A            7 NVAFDALKNGKYDDASQLFLSFLEL--YPNGVYTPNALYWLGESYYATRNFQLAEAQFRDLVSRY-PTHDKAAGGLLKLG   83 (129)
T ss_dssp             HHHHHHHHTTCHHHHHHHHHHHHHH--CSSSTTHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTSTTHHHHHHHHH
T ss_pred             HHHHHHHHhCCHHHHHHHHHHHHHH--CCCCcccHHHHHHHHHHHHHhccHHHHHHHHHHHHHHC-CCCcccHHHHHHHH
Confidence            3445555666666666666666552  232 2   355566666666666666666666666643 222   45566666


Q ss_pred             HHHHHcCChhHHHHHHHHHHHC
Q 040027          530 HGFIRINEPSKVNELLHKMKEK  551 (595)
Q Consensus       530 ~~~~~~g~~~~A~~~~~~~~~~  551 (595)
                      .++...|++++|...++++.+.
T Consensus        84 ~~~~~~g~~~~A~~~~~~~~~~  105 (129)
T 2xev_A           84 LSQYGEGKNTEAQQTLQQVATQ  105 (129)
T ss_dssp             HHHHHTTCHHHHHHHHHHHHHH
T ss_pred             HHHHHcCCHHHHHHHHHHHHHH
Confidence            6666677777777777766653

>4b4t_Q 26S proteasome regulatory subunit RPN6; hydrolase, AAA-atpases, protein degradation, ubiquitin-prote pathway; 7.40A {Saccharomyces cerevisiae}

Probab=98.33  E-value=2.1e-05  Score=77.44  Aligned_cols=203  Identities=5%  Similarity=-0.119  Sum_probs=119.8

Q ss_pred             HHHHHHHhcCChhHHHHHHHHHHhCCCCCC----------------HHHHHHHHHHHHhcCCHhHHHHHHHHHHhcCCC-
Q 040027          101 ILINCFCKIGRVSLGFIAFGRILRSCFTPN----------------AATFNSLIKGLHAESRIMEAAALFTKLKAFGCE-  163 (595)
Q Consensus       101 ~l~~~~~~~g~~~~A~~~~~~~~~~~~~~~----------------~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~-  163 (595)
                      .-.+.+...|++++|+..|..+++......                ..++..+...|...|++++|.+.+..+...-.. 
T Consensus         9 ~~a~~l~~~~~y~eA~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~al~~l~~~y~~~~~~~~a~~~~~~~~~~~~~~   88 (434)
T 4b4t_Q            9 EEARRLVNEKQYNEAEQVYLSLLDKDSSQSSAAAGASVDDKRRNEQETSILELGQLYVTMGAKDKLREFIPHSTEYMMQF   88 (434)
T ss_dssp             HHHHHHHHHTCHHHHHHHHHHHHHSCCCSSSBSSSSSBCSHHHHHHHHHHHHHHHHHHHHTCHHHHHHHHHHTHHHHHTS
T ss_pred             HHHHHHHHCCCHHHHHHHHHHHHhhCcccchhHHHHHHHHHHhhhHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHc
Confidence            345667888999999999999988642211                124667788888888888888888876653111 


Q ss_pred             CCH----hhHHHHHHHHHhcCChhHHHHHHHHHHhcCCCCCccccCcHHHHHHHHHHHHHcCCHhHHHHHHHHHhhC--C
Q 040027          164 PNV----ITYNTLINGLCRTGHTMIALNLFEEMANGNGEIGVVCKPNTVTYSTIIDGLCKEGFVDKAKALFLQMKDE--N  237 (595)
Q Consensus       164 ~~~----~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~--~  237 (595)
                      ++.    .+...+...+...|++++|..+++.........+. ......++..+...+...|++++|..+++++...  +
T Consensus        89 ~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~-~~~~~~~~~~la~~~~~~g~~~~A~~~l~~~~~~~~~  167 (434)
T 4b4t_Q           89 AKSKTVKVLKTLIEKFEQVPDSLDDQIFVCEKSIEFAKREKR-VFLKHSLSIKLATLHYQKKQYKDSLALINDLLREFKK  167 (434)
T ss_dssp             CHHHHHHHHHHHHHHHCSCCSCHHHHHHHHHHHHHHHHHSSC-CSSHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHTT
T ss_pred             cchHHHHHHHHHHHHHHhCCCCHHHHHHHHHHHHHHHHHhCc-cHHHHHHHHHHHHHHHHccChHHHHHHHHHHHHHHHh
Confidence            111    12223333444567788888877776543211000 1122456667777777778888887777766542  1


Q ss_pred             C---CCCHhHHHHHHHHHHhcCCHHHHHHHHHHHHHC--CCC-C-C--HhhHHHHHHHHHhcCChHHHHHHHHHHH
Q 040027          238 I---NPDVVTYNSLIHGLCHANDWNEAKRLFIEMMDQ--GVQ-P-S--VVTFNVIMDELCKNRKMDEASRLLDLMV  304 (595)
Q Consensus       238 ~---~~~~~~~~~ll~~~~~~~~~~~A~~~~~~~~~~--~~~-~-~--~~~~~~l~~~~~~~g~~~~a~~~~~~~~  304 (595)
                      .   +.....+..++..|...|++++|..++++....  ... | .  ...+..++..+...|++++|...|.+..
T Consensus       168 ~~~~~~~~~~~~~~~~~~~~~~~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~~~g~~~~~~~~y~~A~~~~~~a~  243 (434)
T 4b4t_Q          168 LDDKPSLVDVHLLESKVYHKLRNLAKSKASLTAARTAANSIYCPTQTVAELDLMSGILHCEDKDYKTAFSYFFESF  243 (434)
T ss_dssp             SSCSTHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHSCCCHHHHHHHHHHHHHHTTSSSCHHHHHHHHHHHH
T ss_pred             cccchhHHHHHHHHHHHHHHhCcHHHHHHHHHHHHHHhhcCCCchHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHH
Confidence            1   112345666667777777777777777665432  111 1 1  1234444555556666666666655554

>2xev_A YBGF; tetratricopeptide, alpha-helical, metal binding; 1.57A {Xanthomonas campestris}

Probab=98.33  E-value=1.6e-05  Score=62.89  Aligned_cols=96  Identities=15%  Similarity=-0.041  Sum_probs=81.7

Q ss_pred             HHHHHHHHHhcCChhHHHHHHHHHHhCCCCCCH---HHHHHHHHHHHhcCCHhHHHHHHHHHHhcCCCCC---HhhHHHH
Q 040027           99 YNILINCFCKIGRVSLGFIAFGRILRSCFTPNA---ATFNSLIKGLHAESRIMEAAALFTKLKAFGCEPN---VITYNTL  172 (595)
Q Consensus        99 ~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~~~---~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~~---~~~~~~l  172 (595)
                      +..++..+...|++++|+..|+++.+.. +.+.   ..+..+..++...|++++|+..|+++...... +   ..++..+
T Consensus         5 ~~~~a~~~~~~~~~~~A~~~~~~~~~~~-p~~~~~~~~~~~lg~~~~~~~~~~~A~~~~~~~~~~~p~-~~~~~~~~~~l   82 (129)
T 2xev_A            5 AYNVAFDALKNGKYDDASQLFLSFLELY-PNGVYTPNALYWLGESYYATRNFQLAEAQFRDLVSRYPT-HDKAAGGLLKL   82 (129)
T ss_dssp             HHHHHHHHHHTTCHHHHHHHHHHHHHHC-SSSTTHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTT-STTHHHHHHHH
T ss_pred             HHHHHHHHHHhCCHHHHHHHHHHHHHHC-CCCcccHHHHHHHHHHHHHhccHHHHHHHHHHHHHHCCC-CcccHHHHHHH
Confidence            4456778899999999999999999874 2233   57888889999999999999999999987432 3   6678889


Q ss_pred             HHHHHhcCChhHHHHHHHHHHhcC
Q 040027          173 INGLCRTGHTMIALNLFEEMANGN  196 (595)
Q Consensus       173 ~~~~~~~g~~~~A~~~~~~~~~~~  196 (595)
                      ..++...|++++|+..|+++....
T Consensus        83 a~~~~~~g~~~~A~~~~~~~~~~~  106 (129)
T 2xev_A           83 GLSQYGEGKNTEAQQTLQQVATQY  106 (129)
T ss_dssp             HHHHHHTTCHHHHHHHHHHHHHHS
T ss_pred             HHHHHHcCCHHHHHHHHHHHHHHC
Confidence            999999999999999999999865

>3ro3_A PINS homolog, G-protein-signaling modulator 2; asymmetric cell division, protein binding; 1.10A {Mus musculus}

Probab=98.32  E-value=3e-06  Score=70.14  Aligned_cols=132  Identities=14%  Similarity=-0.002  Sum_probs=88.4

Q ss_pred             HHHHHHHHHHhcCCHHHHHHHHHHHHHcCCC-cC----HHHHHHHHHHHHhcCChHHHHHHHHhcccC----CCCC-CHH
Q 040027          419 TYTTFIDGLCKNGYIIEAVELFRTLRILKCE-LD----IQAYNCLIDGLCKSGRLKFAWELFCSLPHG----VLVP-NVV  488 (595)
Q Consensus       419 ~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~-~~----~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~----~~~p-~~~  488 (595)
                      ++..+...+...|++++|...+++..+.... .+    ..++..+...+...|++++|...+++..+.    +..+ ...
T Consensus        11 ~~~~l~~~~~~~~~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~a~~~~~~~~~~~~~~~   90 (164)
T 3ro3_A           11 AFGNLGNTHYLLGNFRDAVIAHEQRLLIAKEFGDKAAERIAYSNLGNAYIFLGEFETASEYYKKTLLLARQLKDRAVEAQ   90 (164)
T ss_dssp             HHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCHHHHHH
T ss_pred             HHHHHHHHHHHhcCHHHHHHHHHHHHHHHHHhCCchHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHhCCcHHHHH
Confidence            4555666666777777777777766543100 11    235667777778888888888888776541    0001 134


Q ss_pred             HHHHHHHHHHhcCChhHHHHHHHHHHHc----CCCC-CHHHHHHHHHHHHHcCChhHHHHHHHHHHH
Q 040027          489 TYNIMIQGLCNDGQMDKARDLFLDMEEN----AAAP-DVITFDMLIHGFIRINEPSKVNELLHKMKE  550 (595)
Q Consensus       489 ~~~~l~~~~~~~g~~~~A~~~~~~~~~~----~~~~-~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~  550 (595)
                      .+..+...+...|++++|.+.+++..+.    +.++ ...++..+...|...|++++|.+.+++..+
T Consensus        91 ~~~~l~~~~~~~~~~~~A~~~~~~a~~~~~~~~~~~~~~~~~~~la~~~~~~g~~~~A~~~~~~a~~  157 (164)
T 3ro3_A           91 SCYSLGNTYTLLQDYEKAIDYHLKHLAIAQELKDRIGEGRACWSLGNAYTALGNHDQAMHFAEKHLE  157 (164)
T ss_dssp             HHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHHTCHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHhhHHHHHHHHHHHHHHHHHccchHhHHHHHHHHHHHHHHccCHHHHHHHHHHHHH
Confidence            6677778888889999998888887753    1111 134567788888899999999999988875

>3rkv_A Putative peptidylprolyl isomerase; structural genomics, APC102156, PSI-biology, midwest center structural genomics, MCSG; 2.41A {Caenorhabditis elegans}

Probab=98.31  E-value=7.1e-06  Score=68.08  Aligned_cols=67  Identities=15%  Similarity=0.106  Sum_probs=53.2

Q ss_pred             HHHHHHHHHHHHhcCChhHHHHHHHHHHHcCCCCCHHHHHHHHHHHHHcCChhHHHHHHHHHHHCCCCCC
Q 040027          487 VVTYNIMIQGLCNDGQMDKARDLFLDMEENAAAPDVITFDMLIHGFIRINEPSKVNELLHKMKEKKVMPD  556 (595)
Q Consensus       487 ~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~p~  556 (595)
                      ...|..+..+|.+.|++++|+..++++++.+ +.+...|..++.+|...|++++|...|++.++.  .|+
T Consensus        63 ~~~~~nla~~~~~~~~~~~A~~~~~~al~~~-p~~~~a~~~~g~~~~~~g~~~~A~~~~~~al~l--~p~  129 (162)
T 3rkv_A           63 IPLYANMSQCYLNIGDLHEAEETSSEVLKRE-ETNEKALFRRAKARIAAWKLDEAEEDLKLLLRN--HPA  129 (162)
T ss_dssp             HHHHHHHHHHHHHHTCHHHHHHHHHHHHHHS-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH--CGG
T ss_pred             HHHHHHHHHHHHhcCcHHHHHHHHHHHHhcC-CcchHHHHHHHHHHHHHhcHHHHHHHHHHHHhc--CCC
Confidence            4577778888888888888888888888864 556778888888888888888888888888874  454

>2hr2_A Hypothetical protein; alpha-alpha superhelix fold, structural genomics, joint CENT structural genomics, JCSG, protein structure initiative; 2.54A {Chlorobium tepidum} SCOP: a.118.8.8

Probab=98.30  E-value=6.3e-06  Score=66.34  Aligned_cols=92  Identities=8%  Similarity=-0.104  Sum_probs=64.1

Q ss_pred             HHHHHHHHhcCChHHHHHHHHhcccCCCCCC-------------HHHHHHHHHHHHhcCChhHHHHHHHHHHHc------
Q 040027          456 NCLIDGLCKSGRLKFAWELFCSLPHGVLVPN-------------VVTYNIMIQGLCNDGQMDKARDLFLDMEEN------  516 (595)
Q Consensus       456 ~~l~~~~~~~g~~~~A~~~~~~~~~~~~~p~-------------~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~------  516 (595)
                      ...+..+.+.|++++|+..|++.++  +.|+             ...|..+..++.+.|++++|+..++++++.      
T Consensus        15 ~~~G~~l~~~g~~eeAi~~Y~kAL~--l~p~~~~~~a~~~~~~~a~a~~n~g~al~~Lgr~~eAl~~~~kAL~l~n~~~e   92 (159)
T 2hr2_A           15 LSDAQRQLVAGEYDEAAANCRRAME--ISHTMPPEEAFDHAGFDAFCHAGLAEALAGLRSFDEALHSADKALHYFNRRGE   92 (159)
T ss_dssp             HHHHHHHHHHTCHHHHHHHHHHHHH--HHTTSCTTSCCCHHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHHCC
T ss_pred             HHHHHHHHHCCCHHHHHHHHHHHHh--hCCCCcchhhhhhccchHHHHHHHHHHHHHCCCHHHHHHHHHHHHHhhhcccc
Confidence            3344444455555555555555544  2222             237888888888888888888888888875      


Q ss_pred             -CCCCCHHHH----HHHHHHHHHcCChhHHHHHHHHHHH
Q 040027          517 -AAAPDVITF----DMLIHGFIRINEPSKVNELLHKMKE  550 (595)
Q Consensus       517 -~~~~~~~~~----~~l~~~~~~~g~~~~A~~~~~~~~~  550 (595)
                       + +.+...|    ...+.++...|++++|+..|++.++
T Consensus        93 ~~-pd~~~A~~~~~~~rG~aL~~lgr~eEAl~~y~kAle  130 (159)
T 2hr2_A           93 LN-QDEGKLWISAVYSRALALDGLGRGAEAMPEFKKVVE  130 (159)
T ss_dssp             TT-STHHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHH
T ss_pred             CC-CchHHHHHHHHHhHHHHHHHCCCHHHHHHHHHHHHh
Confidence             4 3345677    8888899999999999999999874

>4b4t_Q 26S proteasome regulatory subunit RPN6; hydrolase, AAA-atpases, protein degradation, ubiquitin-prote pathway; 7.40A {Saccharomyces cerevisiae}

Probab=98.29  E-value=4.8e-05  Score=74.77  Aligned_cols=198  Identities=10%  Similarity=0.050  Sum_probs=110.9

Q ss_pred             HHHHHHhcCChHHHHHHHHHHHHCCCCCC----------------HHHHHHHHHHHHhcCCHHHHHHHHHHHHhcCCCC-
Q 040027          283 IMDELCKNRKMDEASRLLDLMVQRGVRPN----------------ACTYNTLMDGFCLMGKINRAEELFGSMESMGCKH-  345 (595)
Q Consensus       283 l~~~~~~~g~~~~a~~~~~~~~~~~~~~~----------------~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~-  345 (595)
                      -.+.+.+.|++++|.+.|..+.+......                ...+..++..|...|++++|.+.+..+.+.-... 
T Consensus        10 ~a~~l~~~~~y~eA~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~al~~l~~~y~~~~~~~~a~~~~~~~~~~~~~~~   89 (434)
T 4b4t_Q           10 EARRLVNEKQYNEAEQVYLSLLDKDSSQSSAAAGASVDDKRRNEQETSILELGQLYVTMGAKDKLREFIPHSTEYMMQFA   89 (434)
T ss_dssp             HHHHHHHHTCHHHHHHHHHHHHHSCCCSSSBSSSSSBCSHHHHHHHHHHHHHHHHHHHHTCHHHHHHHHHHTHHHHHTSC
T ss_pred             HHHHHHHCCCHHHHHHHHHHHHhhCcccchhHHHHHHHHHHhhhHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHcc
Confidence            34566778888888888888877532211                1135566777777777777777777665421011 


Q ss_pred             CH----HHHHHHHHHHHhCCCHHHHHHHHHHHHHC----CCCCC-HHHHHHHHHHHHccCCHHHHHHHHHHHHHC--CC-
Q 040027          346 DD----VSYNILINGYCKNKEVEEALSLYREMVSK----GIKPT-VVTYNTLFLGLFEIHQVEHALKLFDEMQRD--GV-  413 (595)
Q Consensus       346 ~~----~~~~~l~~~~~~~~~~~~A~~~~~~~~~~----~~~~~-~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~--~~-  413 (595)
                      +.    .+.+.+...+...|+++.|..+++.....    +..+. ..++..+...+...|++++|..++.++...  +. 
T Consensus        90 ~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~la~~~~~~g~~~~A~~~l~~~~~~~~~~~  169 (434)
T 4b4t_Q           90 KSKTVKVLKTLIEKFEQVPDSLDDQIFVCEKSIEFAKREKRVFLKHSLSIKLATLHYQKKQYKDSLALINDLLREFKKLD  169 (434)
T ss_dssp             HHHHHHHHHHHHHHHCSCCSCHHHHHHHHHHHHHHHHHSSCCSSHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHTTSS
T ss_pred             chHHHHHHHHHHHHHHhCCCCHHHHHHHHHHHHHHHHHhCccHHHHHHHHHHHHHHHHccChHHHHHHHHHHHHHHHhcc
Confidence            11    12223333344556677777777665432    11111 335556666677777777777777665542  11 


Q ss_pred             --CCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHHc----CCCcC--HHHHHHHHHHHHhcCChHHHHHHHHhccc
Q 040027          414 --AADTRTYTTFIDGLCKNGYIIEAVELFRTLRIL----KCELD--IQAYNCLIDGLCKSGRLKFAWELFCSLPH  480 (595)
Q Consensus       414 --~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~----~~~~~--~~~~~~l~~~~~~~g~~~~A~~~~~~~~~  480 (595)
                        +....++..++..|...|++++|...+++....    +.++.  ...+..++..+...|++++|...|.+..+
T Consensus       170 ~~~~~~~~~~~~~~~~~~~~~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~~~g~~~~~~~~y~~A~~~~~~a~~  244 (434)
T 4b4t_Q          170 DKPSLVDVHLLESKVYHKLRNLAKSKASLTAARTAANSIYCPTQTVAELDLMSGILHCEDKDYKTAFSYFFESFE  244 (434)
T ss_dssp             CSTHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHSCCCHHHHHHHHHHHHHHTTSSSCHHHHHHHHHHHHH
T ss_pred             cchhHHHHHHHHHHHHHHhCcHHHHHHHHHHHHHHhhcCCCchHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHH
Confidence              111245566666667777777777777665532    11111  23444555555666667777666666654

>3k9i_A BH0479 protein; putative protein binding protein, structural genomics, joint for structural genomics, JCSG; 2.71A {Bacillus halodurans}

Probab=98.29  E-value=2.2e-06  Score=66.60  Aligned_cols=86  Identities=13%  Similarity=-0.033  Sum_probs=59.8

Q ss_pred             cCChHHHHHHHHhcccCCC-CC-CHHHHHHHHHHHHhcCChhHHHHHHHHHHHcCCCCCHHHHHHHHHHHHHcCChhHHH
Q 040027          465 SGRLKFAWELFCSLPHGVL-VP-NVVTYNIMIQGLCNDGQMDKARDLFLDMEENAAAPDVITFDMLIHGFIRINEPSKVN  542 (595)
Q Consensus       465 ~g~~~~A~~~~~~~~~~~~-~p-~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~  542 (595)
                      .|++++|+..|+++++.+. .| +...+..+..+|...|++++|+..|+++++.. +.+...+..++.++...|++++|.
T Consensus         3 ~g~~~~A~~~~~~al~~~~~~p~~~~~~~~lg~~~~~~~~~~~A~~~~~~al~~~-p~~~~~~~~l~~~~~~~g~~~~A~   81 (117)
T 3k9i_A            3 LGLEAQAVPYYEKAIASGLQGKDLAECYLGLGSTFRTLGEYRKAEAVLANGVKQF-PNHQALRVFYAMVLYNLGRYEQGV   81 (117)
T ss_dssp             ----CCCHHHHHHHHSSCCCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHHTCHHHHH
T ss_pred             CCcHHHHHHHHHHHHHcCCCCccHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhC-CCchHHHHHHHHHHHHcCCHHHHH
Confidence            5677777778877776321 13 34567777778888888888888888887764 445677777888888888888888


Q ss_pred             HHHHHHHHC
Q 040027          543 ELLHKMKEK  551 (595)
Q Consensus       543 ~~~~~~~~~  551 (595)
                      ..+++.++.
T Consensus        82 ~~~~~al~~   90 (117)
T 3k9i_A           82 ELLLKIIAE   90 (117)
T ss_dssp             HHHHHHHHH
T ss_pred             HHHHHHHHh
Confidence            888887764

>1ihg_A Cyclophilin 40; ppiase immunophilin tetratricopeptide, isomerase; 1.80A {Bos taurus} SCOP: a.118.8.1 b.62.1.1 PDB: 1iip_A

Probab=98.26  E-value=1.2e-05  Score=76.74  Aligned_cols=119  Identities=13%  Similarity=-0.008  Sum_probs=58.0

Q ss_pred             HHHHHHHHHhcCCHHHHHHHHHHHHHcC---------------CCcCHHHHHHHHHHHHhcCChHHHHHHHHhcccCCCC
Q 040027          420 YTTFIDGLCKNGYIIEAVELFRTLRILK---------------CELDIQAYNCLIDGLCKSGRLKFAWELFCSLPHGVLV  484 (595)
Q Consensus       420 ~~~l~~~~~~~g~~~~A~~~~~~~~~~~---------------~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~  484 (595)
                      +..+...+.+.|++++|...|+++++..               .+.+..++..+..+|.+.|++++|+..++++++  +.
T Consensus       226 ~~~~g~~~~~~g~~~~Ai~~y~kAl~~~~~~~~~~~~~~~~~~~~~~~~~~~nla~~~~~~g~~~~A~~~~~~al~--~~  303 (370)
T 1ihg_A          226 LKNIGNTFFKSQNWEMAIKKYTKVLRYVEGSRAAAEDADGAKLQPVALSCVLNIGACKLKMSDWQGAVDSCLEALE--ID  303 (370)
T ss_dssp             HHHHHHHHHHTTCHHHHHHHHHHHHHHHHHHHHHSCHHHHGGGHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHT--TC
T ss_pred             HHHHHHHHHHhcCHHHHHHHHHHHHHHhhcCccccChHHHHHHHHHHHHHHHHHHHHHHhccCHHHHHHHHHHHHH--hC
Confidence            4444555666666666666666665410               022334445555555555555555555555554  22


Q ss_pred             C-CHHHHHHHHHHHHhcCChhHHHHHHHHHHHcCCCCCHHHHHHHHHHHHHcCChhHH
Q 040027          485 P-NVVTYNIMIQGLCNDGQMDKARDLFLDMEENAAAPDVITFDMLIHGFIRINEPSKV  541 (595)
Q Consensus       485 p-~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A  541 (595)
                      | +...|..+..+|...|++++|+..|+++++.. +.+...+..+..++...++.+++
T Consensus       304 p~~~~a~~~lg~~~~~~g~~~eA~~~l~~Al~l~-P~~~~~~~~l~~~~~~~~~~~~a  360 (370)
T 1ihg_A          304 PSNTKALYRRAQGWQGLKEYDQALADLKKAQEIA-PEDKAIQAELLKVKQKIKAQKDK  360 (370)
T ss_dssp             TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHHHHHHHH
T ss_pred             chhHHHHHHHHHHHHHccCHHHHHHHHHHHHHhC-CCCHHHHHHHHHHHHHHHHHHHH
Confidence            3 23444455555555555555555555555442 22344444444444444444333

>3k9i_A BH0479 protein; putative protein binding protein, structural genomics, joint for structural genomics, JCSG; 2.71A {Bacillus halodurans}

Probab=98.25  E-value=2.6e-06  Score=66.25  Aligned_cols=88  Identities=10%  Similarity=-0.022  Sum_probs=72.9

Q ss_pred             hcCChhHHHHHHHHHHhCC--CCCCHHHHHHHHHHHHhcCCHhHHHHHHHHHHhcCCCCCHhhHHHHHHHHHhcCChhHH
Q 040027          108 KIGRVSLGFIAFGRILRSC--FTPNAATFNSLIKGLHAESRIMEAAALFTKLKAFGCEPNVITYNTLINGLCRTGHTMIA  185 (595)
Q Consensus       108 ~~g~~~~A~~~~~~~~~~~--~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A  185 (595)
                      ..|++++|+..|+++++.+  -+.+..++..+...|...|++++|++.|+++.+.. +-+..++..+..++...|++++|
T Consensus         2 ~~g~~~~A~~~~~~al~~~~~~p~~~~~~~~lg~~~~~~~~~~~A~~~~~~al~~~-p~~~~~~~~l~~~~~~~g~~~~A   80 (117)
T 3k9i_A            2 VLGLEAQAVPYYEKAIASGLQGKDLAECYLGLGSTFRTLGEYRKAEAVLANGVKQF-PNHQALRVFYAMVLYNLGRYEQG   80 (117)
T ss_dssp             -----CCCHHHHHHHHSSCCCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHHTCHHHH
T ss_pred             CCCcHHHHHHHHHHHHHcCCCCccHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhC-CCchHHHHHHHHHHHHcCCHHHH
Confidence            4689999999999999874  23456778899999999999999999999999885 33688899999999999999999


Q ss_pred             HHHHHHHHhcC
Q 040027          186 LNLFEEMANGN  196 (595)
Q Consensus       186 ~~~~~~~~~~~  196 (595)
                      +..|++.....
T Consensus        81 ~~~~~~al~~~   91 (117)
T 3k9i_A           81 VELLLKIIAET   91 (117)
T ss_dssp             HHHHHHHHHHH
T ss_pred             HHHHHHHHHhC
Confidence            99999998864

>1kt0_A FKBP51, 51 kDa FK506-binding protein; FKBP-like ppiase, TPR repeats, isomerase; 2.70A {Homo sapiens} SCOP: a.118.8.1 d.26.1.1 d.26.1.1 PDB: 1kt1_A 3o5d_A

Probab=98.25  E-value=1.3e-05  Score=79.08  Aligned_cols=133  Identities=14%  Similarity=0.015  Sum_probs=108.4

Q ss_pred             CHHHHHHHHHHHHhcCChhHHHHHHHHHHhCCCCCC--------------HHHHHHHHHHHHhcCCHhHHHHHHHHHHhc
Q 040027           95 NLYTYNILINCFCKIGRVSLGFIAFGRILRSCFTPN--------------AATFNSLIKGLHAESRIMEAAALFTKLKAF  160 (595)
Q Consensus        95 ~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~~--------------~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~  160 (595)
                      ....|..+...+.+.|++++|+..|+++++......              ..+|..+..+|.+.|++++|+..|++++..
T Consensus       267 ~a~~~~~~G~~~~~~g~~~~A~~~y~~Al~~~p~~~~~~~~~~~~~~~~~~~~~~nla~~~~~~g~~~~A~~~~~~al~~  346 (457)
T 1kt0_A          267 QAAIVKEKGTVYFKGGKYMQAVIQYGKIVSWLEMEYGLSEKESKASESFLLAAFLNLAMCYLKLREYTKAVECCDKALGL  346 (457)
T ss_dssp             HHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHTTCCSCCHHHHHHHHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHhCCCHHHHHHHHHHHHHHhcccccCChHHHHHHHHHHHHHHHHHHHHHHHhcCHHHHHHHHHHHHhc
Confidence            345678888999999999999999999998742221              578999999999999999999999999998


Q ss_pred             CCCCCHhhHHHHHHHHHhcCChhHHHHHHHHHHhcCCCCCccccCcHHHHHHHHHHHHHcCCHhHHHH-HHHHHhh
Q 040027          161 GCEPNVITYNTLINGLCRTGHTMIALNLFEEMANGNGEIGVVCKPNTVTYSTIIDGLCKEGFVDKAKA-LFLQMKD  235 (595)
Q Consensus       161 ~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~-~~~~~~~  235 (595)
                      . +.+..++..+..+|...|++++|+..|+++.+.+       +.+..++..+..++.+.++.+++.+ ++..|..
T Consensus       347 ~-p~~~~a~~~~g~a~~~~g~~~~A~~~~~~al~l~-------P~~~~a~~~l~~~~~~~~~~~~a~~~~~~~~f~  414 (457)
T 1kt0_A          347 D-SANEKGLYRRGEAQLLMNEFESAKGDFEKVLEVN-------PQNKAARLQISMCQKKAKEHNERDRRIYANMFK  414 (457)
T ss_dssp             S-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHTTC-----------CHHHHHHHHHHHHHHHHHHHHHHHHHC--
T ss_pred             C-CccHHHHHHHHHHHHHccCHHHHHHHHHHHHHhC-------CCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence            5 3478899999999999999999999999999876       5567888889999998888887763 4555543

>1wao_1 Serine/threonine protein phosphatase 5; hydrolase, protein-protein interactions, TPR, super-helix,; 2.9A {Homo sapiens} SCOP: a.118.8.1 d.159.1.3

Probab=98.25  E-value=2.8e-06  Score=84.32  Aligned_cols=145  Identities=7%  Similarity=-0.088  Sum_probs=100.1

Q ss_pred             HHHhcCCHHHHHHHHHHHHHcCCCcCHHHHHHHHHHHHhcCChHHHHHHHHhcccCCCCC-CHHHHHHHHHHHHhcCChh
Q 040027          426 GLCKNGYIIEAVELFRTLRILKCELDIQAYNCLIDGLCKSGRLKFAWELFCSLPHGVLVP-NVVTYNIMIQGLCNDGQMD  504 (595)
Q Consensus       426 ~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~p-~~~~~~~l~~~~~~~g~~~  504 (595)
                      .+.+.|++++|...++++++.. +.+..++..+..+|.+.|++++|+..++++.+.  .| +...|..+..+|...|+++
T Consensus        15 ~~~~~g~~~~A~~~~~~Al~~~-p~~~~~~~~lg~~~~~~g~~~~A~~~~~~al~l--~p~~~~~~~~lg~~~~~~g~~~   91 (477)
T 1wao_1           15 DYFKAKDYENAIKFYSQAIELN-PSNAIYYGNRSLAYLRTECYGYALGDATRAIEL--DKKYIKGYYRRAASNMALGKFR   91 (477)
T ss_dssp             STTTTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHS--CTTCHHHHHHHHHHHHHHTCHH
T ss_pred             HHHHhCCHHHHHHHHHHHHHhC-CccHHHHHHHHHHHHHhcCHHHHHHHHHHHHHh--CCCCHHHHHHHHHHHHHcCCHH
Confidence            4556788888888888888765 556788888888888888888888888888873  44 4677888888888888888


Q ss_pred             HHHHHHHHHHHcCCCCCHHHHHHHHHH--HHHcCChhHHHHHHH-----------HHHHCC---C-------CCCHHHHH
Q 040027          505 KARDLFLDMEENAAAPDVITFDMLIHG--FIRINEPSKVNELLH-----------KMKEKK---V-------MPDASIVS  561 (595)
Q Consensus       505 ~A~~~~~~~~~~~~~~~~~~~~~l~~~--~~~~g~~~~A~~~~~-----------~~~~~~---~-------~p~~~~~~  561 (595)
                      +|++.|+++++.. +.+...+..+..+  +.+.|++++|.+.++           +..+..   .       ..+...+.
T Consensus        92 eA~~~~~~al~~~-p~~~~~~~~l~~~~~~~~~g~~~~A~~~~~~~~~~~~~~~~~al~~~~~~~~~~~~~~~itl~~l~  170 (477)
T 1wao_1           92 AALRDYETVVKVK-PHDKDAKMKYQECNKIVKQKAFERAIAGDEHKRSVVDSLDIESMTIEDEYSGPKLEDGKVTISFMK  170 (477)
T ss_dssp             HHHHHHHHHHHHS-TTCTTHHHHHHHHHHHHHHHHHCCC------CCSTTTCCTTSSCCCCTTCCSCCCGGGSCCHHHHH
T ss_pred             HHHHHHHHHHHhC-CCCHHHHHHHHHHHHHHHHHHHHHHhccccccchhHhhhhhhhccccccccccccccccccHHHHH
Confidence            8888888888764 3344455555555  777888888888888           333210   0       12345566


Q ss_pred             HHHHHHHhcCccc
Q 040027          562 IVVDLLVKNEISL  574 (595)
Q Consensus       562 ~l~~~~~~~g~~~  574 (595)
                      .++..+.+.+.+.
T Consensus       171 ~lie~l~~~~~l~  183 (477)
T 1wao_1          171 ELMQWYKDQKKLH  183 (477)
T ss_dssp             HHHHHHHTCCCCC
T ss_pred             HHHHHHHcCCCCC
Confidence            6777777777666

>3rkv_A Putative peptidylprolyl isomerase; structural genomics, APC102156, PSI-biology, midwest center structural genomics, MCSG; 2.41A {Caenorhabditis elegans}

Probab=98.25  E-value=1e-05  Score=67.13  Aligned_cols=100  Identities=9%  Similarity=-0.084  Sum_probs=86.7

Q ss_pred             HHHHHHHHHHHHhcCChhHHHHHHHHHHhC--------C---------CCCCHHHHHHHHHHHHhcCCHhHHHHHHHHHH
Q 040027           96 LYTYNILINCFCKIGRVSLGFIAFGRILRS--------C---------FTPNAATFNSLIKGLHAESRIMEAAALFTKLK  158 (595)
Q Consensus        96 ~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~--------~---------~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~  158 (595)
                      ...+...+..+.+.|++++|+..|.+++..        .         .+.+..+|..+..+|.+.|++++|+..+++++
T Consensus        11 a~~~~~~G~~~~~~~~~~~A~~~y~~al~~~~~~~~~~~~~~~~~~~~~~~~~~~~~nla~~~~~~~~~~~A~~~~~~al   90 (162)
T 3rkv_A           11 VEALRQKGNELFVQKDYKEAIDAYRDALTRLDTLILREKPGEPEWVELDRKNIPLYANMSQCYLNIGDLHEAEETSSEVL   90 (162)
T ss_dssp             HHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHHHHTSCTTSHHHHHHHHTHHHHHHHHHHHHHHHTCHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHhcccCCCCHHHHHHHHHHHHHHHHHHHHHHHhcCcHHHHHHHHHHHH
Confidence            456778888999999999999999999875        1         02234678889999999999999999999999


Q ss_pred             hcCCCCCHhhHHHHHHHHHhcCChhHHHHHHHHHHhcC
Q 040027          159 AFGCEPNVITYNTLINGLCRTGHTMIALNLFEEMANGN  196 (595)
Q Consensus       159 ~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~  196 (595)
                      ... +.+..++..+..+|...|++++|+..|++....+
T Consensus        91 ~~~-p~~~~a~~~~g~~~~~~g~~~~A~~~~~~al~l~  127 (162)
T 3rkv_A           91 KRE-ETNEKALFRRAKARIAAWKLDEAEEDLKLLLRNH  127 (162)
T ss_dssp             HHS-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC
T ss_pred             hcC-CcchHHHHHHHHHHHHHhcHHHHHHHHHHHHhcC
Confidence            985 4478899999999999999999999999999875

>3ro3_A PINS homolog, G-protein-signaling modulator 2; asymmetric cell division, protein binding; 1.10A {Mus musculus}

Probab=98.24  E-value=7.1e-06  Score=67.85  Aligned_cols=139  Identities=12%  Similarity=0.001  Sum_probs=87.5

Q ss_pred             HHHHHHHHHHHHhcCChhHHHHHHHHHHhCCCC-CC----HHHHHHHHHHHHhcCCHhHHHHHHHHHHhcCCC-CC----
Q 040027           96 LYTYNILINCFCKIGRVSLGFIAFGRILRSCFT-PN----AATFNSLIKGLHAESRIMEAAALFTKLKAFGCE-PN----  165 (595)
Q Consensus        96 ~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~-~~----~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~-~~----  165 (595)
                      ..++..+...+...|++++|+..++++.+.... .+    ..++..+...+...|++++|.+.+++....... .+    
T Consensus         9 ~~~~~~l~~~~~~~~~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~a~~~~~~~~~~~~~   88 (164)
T 3ro3_A            9 GRAFGNLGNTHYLLGNFRDAVIAHEQRLLIAKEFGDKAAERIAYSNLGNAYIFLGEFETASEYYKKTLLLARQLKDRAVE   88 (164)
T ss_dssp             HHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCHHHH
T ss_pred             HHHHHHHHHHHHHhcCHHHHHHHHHHHHHHHHHhCCchHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHhCCcHHH
Confidence            345677888888889999999988888765211 11    135677777888888888888888876653111 11    


Q ss_pred             HhhHHHHHHHHHhcCChhHHHHHHHHHHhcCCCCCccccCcHHHHHHHHHHHHHcCCHhHHHHHHHHHhh
Q 040027          166 VITYNTLINGLCRTGHTMIALNLFEEMANGNGEIGVVCKPNTVTYSTIIDGLCKEGFVDKAKALFLQMKD  235 (595)
Q Consensus       166 ~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~  235 (595)
                      ..++..+...+...|++++|.+.+++........+. .......+..+...+...|++++|.+.+++..+
T Consensus        89 ~~~~~~l~~~~~~~~~~~~A~~~~~~a~~~~~~~~~-~~~~~~~~~~la~~~~~~g~~~~A~~~~~~a~~  157 (164)
T 3ro3_A           89 AQSCYSLGNTYTLLQDYEKAIDYHLKHLAIAQELKD-RIGEGRACWSLGNAYTALGNHDQAMHFAEKHLE  157 (164)
T ss_dssp             HHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTC-HHHHHHHHHHHHHHHHHHTCHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHhhHHHHHHHHHHHHHHHHHccc-hHhHHHHHHHHHHHHHHccCHHHHHHHHHHHHH
Confidence            345666777777788888888877776643200000 011134455566666666676666666666543

>1ihg_A Cyclophilin 40; ppiase immunophilin tetratricopeptide, isomerase; 1.80A {Bos taurus} SCOP: a.118.8.1 b.62.1.1 PDB: 1iip_A

Probab=98.22  E-value=1.3e-05  Score=76.45  Aligned_cols=124  Identities=10%  Similarity=-0.039  Sum_probs=103.9

Q ss_pred             HHHHHHHHHHHHhcCChhHHHHHHHHHHh----------------CCCCCCHHHHHHHHHHHHhcCCHhHHHHHHHHHHh
Q 040027           96 LYTYNILINCFCKIGRVSLGFIAFGRILR----------------SCFTPNAATFNSLIKGLHAESRIMEAAALFTKLKA  159 (595)
Q Consensus        96 ~~~~~~l~~~~~~~g~~~~A~~~~~~~~~----------------~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~  159 (595)
                      ...+..+...+.+.|++++|+..|+++++                .. +.+..+|..+..+|.+.|++++|++.++++++
T Consensus       223 a~~~~~~g~~~~~~g~~~~Ai~~y~kAl~~~~~~~~~~~~~~~~~~~-~~~~~~~~nla~~~~~~g~~~~A~~~~~~al~  301 (370)
T 1ihg_A          223 SEDLKNIGNTFFKSQNWEMAIKKYTKVLRYVEGSRAAAEDADGAKLQ-PVALSCVLNIGACKLKMSDWQGAVDSCLEALE  301 (370)
T ss_dssp             HHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHHHHHSCHHHHGGGH-HHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHT
T ss_pred             HHHHHHHHHHHHHhcCHHHHHHHHHHHHHHhhcCccccChHHHHHHH-HHHHHHHHHHHHHHHhccCHHHHHHHHHHHHH
Confidence            34577788899999999999999999987                21 33567888999999999999999999999998


Q ss_pred             cCCCCCHhhHHHHHHHHHhcCChhHHHHHHHHHHhcCCCCCccccCcHHHHHHHHHHHHHcCCHhHHHH
Q 040027          160 FGCEPNVITYNTLINGLCRTGHTMIALNLFEEMANGNGEIGVVCKPNTVTYSTIIDGLCKEGFVDKAKA  228 (595)
Q Consensus       160 ~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~  228 (595)
                      .. +.+..++..+..+|...|++++|+..|+++.+..       +.+...+..+..++...++.+++.+
T Consensus       302 ~~-p~~~~a~~~lg~~~~~~g~~~eA~~~l~~Al~l~-------P~~~~~~~~l~~~~~~~~~~~~a~k  362 (370)
T 1ihg_A          302 ID-PSNTKALYRRAQGWQGLKEYDQALADLKKAQEIA-------PEDKAIQAELLKVKQKIKAQKDKEK  362 (370)
T ss_dssp             TC-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-------TTCHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             hC-chhHHHHHHHHHHHHHccCHHHHHHHHHHHHHhC-------CCCHHHHHHHHHHHHHHHHHHHHHH
Confidence            75 3478899999999999999999999999999875       4567778888888877777766654

>1dce_A Protein (RAB geranylgeranyltransferase alpha subunit); 2.0 A resolution, N-formylmethionine, alpha subunit; HET: FME; 2.00A {Rattus norvegicus} SCOP: a.118.6.1 b.7.4.1 c.10.2.2 PDB: 1ltx_A*

Probab=98.21  E-value=0.00011  Score=74.11  Aligned_cols=132  Identities=13%  Similarity=0.014  Sum_probs=64.3

Q ss_pred             HHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHccCC----------HHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHhcC-
Q 040027          363 VEEALSLYREMVSKGIKPTVVTYNTLFLGLFEIHQ----------VEHALKLFDEMQRDGVAADTRTYTTFIDGLCKNG-  431 (595)
Q Consensus       363 ~~~A~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~----------~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g-  431 (595)
                      .++|++.+++++...+. +...|+.-...+...++          ++++++.++.+.+.+ +.+..+|..-..++.+.+ 
T Consensus        45 ~eeal~~~~~~l~~nP~-~~taW~~R~~~l~~l~~~~~~~~~~~~~~~eL~~~~~~l~~~-pK~y~aW~hR~w~l~~l~~  122 (567)
T 1dce_A           45 DESVLELTSQILGANPD-FATLWNCRREVLQHLETEKSPEESAALVKAELGFLESCLRVN-PKSYGTWHHRCWLLSRLPE  122 (567)
T ss_dssp             SHHHHHHHHHHHHHCTT-CHHHHHHHHHHHHHHHTTSCHHHHHHHHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHTCSS
T ss_pred             CHHHHHHHHHHHHHCch-hHHHHHHHHHHHHhcccccchhhhhhhHHHHHHHHHHHHHhC-CCCHHHHHHHHHHHHHccc
Confidence            34556666666654332 33444444333433333          455555555555442 344445554444455555 


Q ss_pred             -CHHHHHHHHHHHHHcCCCcCHHHHHHHHHHHHhcC-ChHHHHHHHHhcccCCCCCCHHHHHHHHHHHH
Q 040027          432 -YIIEAVELFRTLRILKCELDIQAYNCLIDGLCKSG-RLKFAWELFCSLPHGVLVPNVVTYNIMIQGLC  498 (595)
Q Consensus       432 -~~~~A~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g-~~~~A~~~~~~~~~~~~~p~~~~~~~l~~~~~  498 (595)
                       ++++++..++++.+.+ +.+..+|+.-..++.+.| .++++++.++++++.. .-|...|+.....+.
T Consensus       123 ~~~~~el~~~~k~l~~d-~~N~~aW~~R~~~l~~l~~~~~~el~~~~~~I~~~-p~n~saW~~r~~ll~  189 (567)
T 1dce_A          123 PNWARELELCARFLEAD-ERNFHCWDYRRFVAAQAAVAPAEELAFTDSLITRN-FSNYSSWHYRSCLLP  189 (567)
T ss_dssp             CCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTCCCHHHHHHHHHTTTTTT-CCCHHHHHHHHHHHH
T ss_pred             ccHHHHHHHHHHHHhhc-cccccHHHHHHHHHHHcCCChHHHHHHHHHHHHHC-CCCccHHHHHHHHHH
Confidence             4455555555555544 445555555555555555 4555555555555421 113445544444443

>1kt0_A FKBP51, 51 kDa FK506-binding protein; FKBP-like ppiase, TPR repeats, isomerase; 2.70A {Homo sapiens} SCOP: a.118.8.1 d.26.1.1 d.26.1.1 PDB: 1kt1_A 3o5d_A

Probab=98.19  E-value=1.7e-05  Score=78.39  Aligned_cols=127  Identities=13%  Similarity=-0.034  Sum_probs=80.5

Q ss_pred             HHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCcC---------------HHHHHHHHHHHHhcCChHHHHHHHHhcccCCC
Q 040027          419 TYTTFIDGLCKNGYIIEAVELFRTLRILKCELD---------------IQAYNCLIDGLCKSGRLKFAWELFCSLPHGVL  483 (595)
Q Consensus       419 ~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~~---------------~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~  483 (595)
                      .+..+...+.+.|++++|...|+++++.. +.+               ..+|..+..+|.+.|++++|+..++++++.  
T Consensus       270 ~~~~~G~~~~~~g~~~~A~~~y~~Al~~~-p~~~~~~~~~~~~~~~~~~~~~~nla~~~~~~g~~~~A~~~~~~al~~--  346 (457)
T 1kt0_A          270 IVKEKGTVYFKGGKYMQAVIQYGKIVSWL-EMEYGLSEKESKASESFLLAAFLNLAMCYLKLREYTKAVECCDKALGL--  346 (457)
T ss_dssp             HHHHHHHHHHHTTCHHHHHHHHHHHHHHH-TTCCSCCHHHHHHHHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH--
T ss_pred             HHHHHHHHHHhCCCHHHHHHHHHHHHHHh-cccccCChHHHHHHHHHHHHHHHHHHHHHHHhcCHHHHHHHHHHHHhc--
Confidence            34444455555555555555555555432 112               467777777788888888888888877763  


Q ss_pred             CC-CHHHHHHHHHHHHhcCChhHHHHHHHHHHHcCCCCCHHHHHHHHHHHHHcCChhHHH-HHHHHHH
Q 040027          484 VP-NVVTYNIMIQGLCNDGQMDKARDLFLDMEENAAAPDVITFDMLIHGFIRINEPSKVN-ELLHKMK  549 (595)
Q Consensus       484 ~p-~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~-~~~~~~~  549 (595)
                      .| +...|..+..+|...|++++|+..|+++++.. +.+...+..+..++...|+++++. ..+++|.
T Consensus       347 ~p~~~~a~~~~g~a~~~~g~~~~A~~~~~~al~l~-P~~~~a~~~l~~~~~~~~~~~~a~~~~~~~~f  413 (457)
T 1kt0_A          347 DSANEKGLYRRGEAQLLMNEFESAKGDFEKVLEVN-PQNKAARLQISMCQKKAKEHNERDRRIYANMF  413 (457)
T ss_dssp             STTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHTTC-----CHHHHHHHHHHHHHHHHHHHHHHHHHC-
T ss_pred             CCccHHHHHHHHHHHHHccCHHHHHHHHHHHHHhC-CCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            34 46677777788888888888888888887753 334556677777777777776664 3455554

>1dce_A Protein (RAB geranylgeranyltransferase alpha subunit); 2.0 A resolution, N-formylmethionine, alpha subunit; HET: FME; 2.00A {Rattus norvegicus} SCOP: a.118.6.1 b.7.4.1 c.10.2.2 PDB: 1ltx_A*

Probab=98.15  E-value=0.00011  Score=74.30  Aligned_cols=174  Identities=10%  Similarity=-0.049  Sum_probs=144.7

Q ss_pred             CCHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHhcCC----------HHHHHHHHHHHHHcCCCcCHHHHHHHHHHHHhc
Q 040027          396 HQVEHALKLFDEMQRDGVAADTRTYTTFIDGLCKNGY----------IIEAVELFRTLRILKCELDIQAYNCLIDGLCKS  465 (595)
Q Consensus       396 ~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~----------~~~A~~~~~~~~~~~~~~~~~~~~~l~~~~~~~  465 (595)
                      ...++|++.+++++..+ +.+..+|+.-..++...|+          +++++..++.+.+.. +.+..+|..-..++.+.
T Consensus        43 ~~~eeal~~~~~~l~~n-P~~~taW~~R~~~l~~l~~~~~~~~~~~~~~~eL~~~~~~l~~~-pK~y~aW~hR~w~l~~l  120 (567)
T 1dce_A           43 ELDESVLELTSQILGAN-PDFATLWNCRREVLQHLETEKSPEESAALVKAELGFLESCLRVN-PKSYGTWHHRCWLLSRL  120 (567)
T ss_dssp             CCSHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHHHTTSCHHHHHHHHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHTC
T ss_pred             CCCHHHHHHHHHHHHHC-chhHHHHHHHHHHHHhcccccchhhhhhhHHHHHHHHHHHHHhC-CCCHHHHHHHHHHHHHc
Confidence            34478899999999874 5566777777777777777          999999999999887 77899999999999999


Q ss_pred             C--ChHHHHHHHHhcccCCCCCCHHHHHHHHHHHHhcC-ChhHHHHHHHHHHHcCCCCCHHHHHHHHHHHHHc-------
Q 040027          466 G--RLKFAWELFCSLPHGVLVPNVVTYNIMIQGLCNDG-QMDKARDLFLDMEENAAAPDVITFDMLIHGFIRI-------  535 (595)
Q Consensus       466 g--~~~~A~~~~~~~~~~~~~p~~~~~~~l~~~~~~~g-~~~~A~~~~~~~~~~~~~~~~~~~~~l~~~~~~~-------  535 (595)
                      +  +++++++.++++.+.. +-|...|+.-..++.+.| .++++++.+.++++.+ +.|..+|.....++...       
T Consensus       121 ~~~~~~~el~~~~k~l~~d-~~N~~aW~~R~~~l~~l~~~~~~el~~~~~~I~~~-p~n~saW~~r~~ll~~l~~~~~~~  198 (567)
T 1dce_A          121 PEPNWARELELCARFLEAD-ERNFHCWDYRRFVAAQAAVAPAEELAFTDSLITRN-FSNYSSWHYRSCLLPQLHPQPDSG  198 (567)
T ss_dssp             SSCCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTCCCHHHHHHHHHTTTTTT-CCCHHHHHHHHHHHHHHSCCCCSS
T ss_pred             ccccHHHHHHHHHHHHhhc-cccccHHHHHHHHHHHcCCChHHHHHHHHHHHHHC-CCCccHHHHHHHHHHhhccccccc
Confidence            9  6799999999999842 236889999999999999 8999999999999876 56788898888877764       


Q ss_pred             -------CChhHHHHHHHHHHHCCCCC-CHHHHHHHHHHHHhcCcccc
Q 040027          536 -------NEPSKVNELLHKMKEKKVMP-DASIVSIVVDLLVKNEISLK  575 (595)
Q Consensus       536 -------g~~~~A~~~~~~~~~~~~~p-~~~~~~~l~~~~~~~g~~~~  575 (595)
                             +.++++.++++++...  .| |...|......+.+.|+.++
T Consensus       199 ~~~~~~~~~~~eel~~~~~ai~~--~P~~~saW~y~~~ll~~~~~~~~  244 (567)
T 1dce_A          199 PQGRLPENVLLKELELVQNAFFT--DPNDQSAWFYHRWLLGRAEPHDV  244 (567)
T ss_dssp             SCCSSCHHHHHHHHHHHHHHHHH--CSSCSHHHHHHHHHHSCCCCCSC
T ss_pred             ccccccHHHHHHHHHHHHHHHhh--CCCCccHHHHHHHHHhcCCCccc
Confidence                   5579999999999974  35 78999999999999988653

>1klx_A Cysteine rich protein B; structural genomics, helix-turn-helix, right handed super helix, modular structure', hydrolase; 1.95A {Helicobacter pylori} SCOP: a.118.18.1

Probab=98.12  E-value=7.4e-05  Score=59.73  Aligned_cols=111  Identities=9%  Similarity=-0.093  Sum_probs=76.7

Q ss_pred             CCHHHHHHHHHHHHHcCCCcCHHHHHHHHHHHHhcCChHHHHHHHHhcccCCCCCCHHHHHHHHHHHHh----cCChhHH
Q 040027          431 GYIIEAVELFRTLRILKCELDIQAYNCLIDGLCKSGRLKFAWELFCSLPHGVLVPNVVTYNIMIQGLCN----DGQMDKA  506 (595)
Q Consensus       431 g~~~~A~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~p~~~~~~~l~~~~~~----~g~~~~A  506 (595)
                      +++++|..+|++..+.+ .++..    +...|...+.+++|...|++..+.   -+...+..|...|..    .+++++|
T Consensus         9 ~d~~~A~~~~~~aa~~g-~~~a~----lg~~y~~g~~~~~A~~~~~~Aa~~---g~~~a~~~Lg~~y~~G~g~~~d~~~A   80 (138)
T 1klx_A            9 KDLKKAIQYYVKACELN-EMFGC----LSLVSNSQINKQKLFQYLSKACEL---NSGNGCRFLGDFYENGKYVKKDLRKA   80 (138)
T ss_dssp             HHHHHHHHHHHHHHHTT-CTTHH----HHHHTCTTSCHHHHHHHHHHHHHT---TCHHHHHHHHHHHHHCSSSCCCHHHH
T ss_pred             cCHHHHHHHHHHHHcCC-CHhhh----HHHHHHcCCCHHHHHHHHHHHHcC---CCHHHHHHHHHHHHcCCCCCccHHHH
Confidence            35667777777777665 33333    566666666677777777777764   256666677777776    6777788


Q ss_pred             HHHHHHHHHcCCCCCHHHHHHHHHHHHH----cCChhHHHHHHHHHHHCC
Q 040027          507 RDLFLDMEENAAAPDVITFDMLIHGFIR----INEPSKVNELLHKMKEKK  552 (595)
Q Consensus       507 ~~~~~~~~~~~~~~~~~~~~~l~~~~~~----~g~~~~A~~~~~~~~~~~  552 (595)
                      .++|++..+.|   +...+..+...|..    .+++++|.+++++..+.|
T Consensus        81 ~~~~~~Aa~~g---~~~a~~~Lg~~y~~G~g~~~d~~~A~~~~~~Aa~~g  127 (138)
T 1klx_A           81 AQYYSKACGLN---DQDGCLILGYKQYAGKGVVKNEKQAVKTFEKACRLG  127 (138)
T ss_dssp             HHHHHHHHHTT---CHHHHHHHHHHHHHTSSSCCCHHHHHHHHHHHHHTT
T ss_pred             HHHHHHHHcCC---CHHHHHHHHHHHHCCCCCCcCHHHHHHHHHHHHHCC
Confidence            88887777764   56667777777777    677788888888877765

>2hr2_A Hypothetical protein; alpha-alpha superhelix fold, structural genomics, joint CENT structural genomics, JCSG, protein structure initiative; 2.54A {Chlorobium tepidum} SCOP: a.118.8.8

Probab=98.12  E-value=5.2e-05  Score=61.01  Aligned_cols=95  Identities=15%  Similarity=-0.018  Sum_probs=67.5

Q ss_pred             HHHHHHHHhcCCHhHHHHHHHHHHhcCCCC------C-----HhhHHHHHHHHHhcCChhHHHHHHHHHHhc-------C
Q 040027          135 NSLIKGLHAESRIMEAAALFTKLKAFGCEP------N-----VITYNTLINGLCRTGHTMIALNLFEEMANG-------N  196 (595)
Q Consensus       135 ~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~------~-----~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~-------~  196 (595)
                      ......+.+.|++++|+..|++.++.....      +     ...|..+..++...|++++|+..+++.+..       +
T Consensus        15 ~~~G~~l~~~g~~eeAi~~Y~kAL~l~p~~~~~~a~~~~~~~a~a~~n~g~al~~Lgr~~eAl~~~~kAL~l~n~~~e~~   94 (159)
T 2hr2_A           15 LSDAQRQLVAGEYDEAAANCRRAMEISHTMPPEEAFDHAGFDAFCHAGLAEALAGLRSFDEALHSADKALHYFNRRGELN   94 (159)
T ss_dssp             HHHHHHHHHHTCHHHHHHHHHHHHHHHTTSCTTSCCCHHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHHCCTT
T ss_pred             HHHHHHHHHCCCHHHHHHHHHHHHhhCCCCcchhhhhhccchHHHHHHHHHHHHHCCCHHHHHHHHHHHHHhhhccccCC
Confidence            344444555555555555555555542110      1     237888888888888888888888888876       5


Q ss_pred             CCCCccccCcHHHH----HHHHHHHHHcCCHhHHHHHHHHHhhC
Q 040027          197 GEIGVVCKPNTVTY----STIIDGLCKEGFVDKAKALFLQMKDE  236 (595)
Q Consensus       197 ~~~~~~~~~~~~~~----~~l~~~~~~~g~~~~A~~~~~~~~~~  236 (595)
                             |.+...|    .....++...|++++|+..|++..+.
T Consensus        95 -------pd~~~A~~~~~~~rG~aL~~lgr~eEAl~~y~kAlel  131 (159)
T 2hr2_A           95 -------QDEGKLWISAVYSRALALDGLGRGAEAMPEFKKVVEM  131 (159)
T ss_dssp             -------STHHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH
T ss_pred             -------CchHHHHHHHHHhHHHHHHHCCCHHHHHHHHHHHHhc
Confidence                   4457788    89999999999999999999988763

>2l6j_A TPR repeat-containing protein associated with HSP; tetratricopeptide repeat (TPR), HSP90 CO-factor, protein BIN; NMR {Saccharomyces cerevisiae}

Probab=98.12  E-value=1.5e-05  Score=60.98  Aligned_cols=92  Identities=5%  Similarity=-0.018  Sum_probs=72.2

Q ss_pred             CHHHHHHHHHHHHhcCChhHHHHHHHHHHHcCCCCCHHHHHHHHHHHHHcCChhHHHHHHHHHHHCCCCCC-------HH
Q 040027          486 NVVTYNIMIQGLCNDGQMDKARDLFLDMEENAAAPDVITFDMLIHGFIRINEPSKVNELLHKMKEKKVMPD-------AS  558 (595)
Q Consensus       486 ~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~p~-------~~  558 (595)
                      +...|..+...+...|++++|++.|+++++.. +.+...+..++.+|...|++++|...++++++.  .|+       ..
T Consensus         3 ~~~~~~~~g~~~~~~~~~~~A~~~~~~al~~~-p~~~~~~~~lg~~~~~~g~~~~A~~~~~~al~~--~p~~~~~~~~~~   79 (111)
T 2l6j_A            3 QFEKQKEQGNSLFKQGLYREAVHCYDQLITAQ-PQNPVGYSNKAMALIKLGEYTQAIQMCQQGLRY--TSTAEHVAIRSK   79 (111)
T ss_dssp             HHHHHHHHHHHHHTTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHTS--CSSTTSHHHHHH
T ss_pred             hHHHHHHHHHHHHHcCCHHHHHHHHHHHHhcC-CCCHHHHHHHHHHHHHhcCHHHHHHHHHHHHHh--CCCccHHHHHHH
Confidence            45677788888888899999999998888864 556788888888888999999999999988874  354       66


Q ss_pred             HHHHHHHHHHhcCcccccchHH
Q 040027          559 IVSIVVDLLVKNEISLKSLPSF  580 (595)
Q Consensus       559 ~~~~l~~~~~~~g~~~~~i~~~  580 (595)
                      .+..+..++...|+.++++..+
T Consensus        80 ~~~~~~~~~~~~~~~~~a~~~~  101 (111)
T 2l6j_A           80 LQYRLELAQGAVGSVQIPVVEV  101 (111)
T ss_dssp             HHHHHHHHHHHHHCCCCCSSSS
T ss_pred             HHHHHHHHHHHHHhHhhhHhHH
Confidence            7777888888888877555443

>2if4_A ATFKBP42; FKBP-like, alpha-beta, TPR-like, alpha, signaling protein; 2.85A {Arabidopsis thaliana}

Probab=98.11  E-value=8.5e-06  Score=76.88  Aligned_cols=149  Identities=9%  Similarity=-0.003  Sum_probs=76.8

Q ss_pred             HHHHHHHHHHHHhcCChhHHHHHHHHHHhCCCCCCHHHHHHHHHHHHhcCCHhHHHHHHHHHHhcCCCCCHhhHHHHHHH
Q 040027           96 LYTYNILINCFCKIGRVSLGFIAFGRILRSCFTPNAATFNSLIKGLHAESRIMEAAALFTKLKAFGCEPNVITYNTLING  175 (595)
Q Consensus        96 ~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~~l~~~  175 (595)
                      ...+..+...+.+.|++++|+..|++++..  .|+...       +...++.+++...+          ...++..+..+
T Consensus       179 a~~~~~~g~~~~~~g~~~~A~~~y~~Al~~--~p~~~~-------~~~~~~~~~~~~~l----------~~~~~~nla~~  239 (338)
T 2if4_A          179 ADRRKMDGNSLFKEEKLEEAMQQYEMAIAY--MGDDFM-------FQLYGKYQDMALAV----------KNPCHLNIAAC  239 (338)
T ss_dssp             HHHHHHHHHHTCSSSCCHHHHHHHHHHHHH--SCHHHH-------HTCCHHHHHHHHHH----------HTHHHHHHHHH
T ss_pred             HHHHHHHHHHHHhcCCHHHHHHHHHHHHHH--hccchh-------hhhcccHHHHHHHH----------HHHHHHHHHHH
Confidence            345666777777888888888888888775  233221       11222333332211          11366777888


Q ss_pred             HHhcCChhHHHHHHHHHHhcCCCCCccccCcHHHHHHHHHHHHHcCCHhHHHHHHHHHhhCCCCCCHhHHHHHHHH-HHh
Q 040027          176 LCRTGHTMIALNLFEEMANGNGEIGVVCKPNTVTYSTIIDGLCKEGFVDKAKALFLQMKDENINPDVVTYNSLIHG-LCH  254 (595)
Q Consensus       176 ~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~~ll~~-~~~  254 (595)
                      |.+.|++++|+..+++++..+       +.+..+|..+..+|...|++++|...|+++.+.. +.+...+..+... ...
T Consensus       240 ~~~~g~~~~A~~~~~~al~~~-------p~~~~a~~~lg~a~~~~g~~~~A~~~l~~al~l~-p~~~~a~~~L~~l~~~~  311 (338)
T 2if4_A          240 LIKLKRYDEAIGHCNIVLTEE-------EKNPKALFRRGKAKAELGQMDSARDDFRKAQKYA-PDDKAIRRELRALAEQE  311 (338)
T ss_dssp             HHTTTCCHHHHHHHHHHHHHC-------TTCHHHHHHHHHHHHTTTCHHHHHHHHHHTTC--------------------
T ss_pred             HHHcCCHHHHHHHHHHHHHhC-------CCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHC-CCCHHHHHHHHHHHHHH
Confidence            888888888888888887765       4567778888888888888888888888877653 1234455555544 334


Q ss_pred             cCCHHHHHHHHHHHHHC
Q 040027          255 ANDWNEAKRLFIEMMDQ  271 (595)
Q Consensus       255 ~~~~~~A~~~~~~~~~~  271 (595)
                      .+..+++...|..+...
T Consensus       312 ~~~~~~a~~~~~~~l~~  328 (338)
T 2if4_A          312 KALYQKQKEMYKGIFKG  328 (338)
T ss_dssp             -----------------
T ss_pred             HHHHHHHHHHHHHhhCC
Confidence            45667777777777654

>2if4_A ATFKBP42; FKBP-like, alpha-beta, TPR-like, alpha, signaling protein; 2.85A {Arabidopsis thaliana}

Probab=98.00  E-value=2.2e-05  Score=74.05  Aligned_cols=149  Identities=10%  Similarity=-0.045  Sum_probs=86.3

Q ss_pred             HHHHHHHHHHHHhcCCHhHHHHHHHHHHhcCCCCCHhhHHHHHHHHHhcCChhHHHHHHHHHHhcCCCCCccccCcHHHH
Q 040027          131 AATFNSLIKGLHAESRIMEAAALFTKLKAFGCEPNVITYNTLINGLCRTGHTMIALNLFEEMANGNGEIGVVCKPNTVTY  210 (595)
Q Consensus       131 ~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~~~~~~  210 (595)
                      ...+..+...+.+.|++++|+..|++....  .|+...       +...|+..++...+                ...+|
T Consensus       179 a~~~~~~g~~~~~~g~~~~A~~~y~~Al~~--~p~~~~-------~~~~~~~~~~~~~l----------------~~~~~  233 (338)
T 2if4_A          179 ADRRKMDGNSLFKEEKLEEAMQQYEMAIAY--MGDDFM-------FQLYGKYQDMALAV----------------KNPCH  233 (338)
T ss_dssp             HHHHHHHHHHTCSSSCCHHHHHHHHHHHHH--SCHHHH-------HTCCHHHHHHHHHH----------------HTHHH
T ss_pred             HHHHHHHHHHHHhcCCHHHHHHHHHHHHHH--hccchh-------hhhcccHHHHHHHH----------------HHHHH
Confidence            345667777788899999999999998876  333221       22233333333221                12478


Q ss_pred             HHHHHHHHHcCCHhHHHHHHHHHhhCCCCCCHhHHHHHHHHHHhcCCHHHHHHHHHHHHHCCCCCCHhhHHHHHHH-HHh
Q 040027          211 STIIDGLCKEGFVDKAKALFLQMKDENINPDVVTYNSLIHGLCHANDWNEAKRLFIEMMDQGVQPSVVTFNVIMDE-LCK  289 (595)
Q Consensus       211 ~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~~ll~~~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~~l~~~-~~~  289 (595)
                      ..+..++.+.|++++|+..+++..... +.+...|..+..+|...|++++|...|++.++... .+...+..+... ...
T Consensus       234 ~nla~~~~~~g~~~~A~~~~~~al~~~-p~~~~a~~~lg~a~~~~g~~~~A~~~l~~al~l~p-~~~~a~~~L~~l~~~~  311 (338)
T 2if4_A          234 LNIAACLIKLKRYDEAIGHCNIVLTEE-EKNPKALFRRGKAKAELGQMDSARDDFRKAQKYAP-DDKAIRRELRALAEQE  311 (338)
T ss_dssp             HHHHHHHHTTTCCHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHTTTCHHHHHHHHHHTTC--------------------
T ss_pred             HHHHHHHHHcCCHHHHHHHHHHHHHhC-CCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHCC-CCHHHHHHHHHHHHHH
Confidence            889999999999999999999998864 34788999999999999999999999999876521 244455555554 344


Q ss_pred             cCChHHHHHHHHHHHHC
Q 040027          290 NRKMDEASRLLDLMVQR  306 (595)
Q Consensus       290 ~g~~~~a~~~~~~~~~~  306 (595)
                      .+..+.+...|..+...
T Consensus       312 ~~~~~~a~~~~~~~l~~  328 (338)
T 2if4_A          312 KALYQKQKEMYKGIFKG  328 (338)
T ss_dssp             -----------------
T ss_pred             HHHHHHHHHHHHHhhCC
Confidence            56778888899988765

>1klx_A Cysteine rich protein B; structural genomics, helix-turn-helix, right handed super helix, modular structure', hydrolase; 1.95A {Helicobacter pylori} SCOP: a.118.18.1

Probab=97.99  E-value=0.00016  Score=57.78  Aligned_cols=62  Identities=13%  Similarity=-0.077  Sum_probs=26.5

Q ss_pred             HHHHHHHHHHHHH----cCCHhHHHHHHHHHhhCCCCCCHhHHHHHHHHHHh----cCCHHHHHHHHHHHHHC
Q 040027          207 TVTYSTIIDGLCK----EGFVDKAKALFLQMKDENINPDVVTYNSLIHGLCH----ANDWNEAKRLFIEMMDQ  271 (595)
Q Consensus       207 ~~~~~~l~~~~~~----~g~~~~A~~~~~~~~~~~~~~~~~~~~~ll~~~~~----~~~~~~A~~~~~~~~~~  271 (595)
                      +..+..|...|..    .+++++|.++|++..+.|   +...+..|...|..    .+++++|..+|++..+.
T Consensus        57 ~~a~~~Lg~~y~~G~g~~~d~~~A~~~~~~Aa~~g---~~~a~~~Lg~~y~~G~g~~~d~~~A~~~~~~Aa~~  126 (138)
T 1klx_A           57 GNGCRFLGDFYENGKYVKKDLRKAAQYYSKACGLN---DQDGCLILGYKQYAGKGVVKNEKQAVKTFEKACRL  126 (138)
T ss_dssp             HHHHHHHHHHHHHCSSSCCCHHHHHHHHHHHHHTT---CHHHHHHHHHHHHHTSSSCCCHHHHHHHHHHHHHT
T ss_pred             HHHHHHHHHHHHcCCCCCccHHHHHHHHHHHHcCC---CHHHHHHHHHHHHCCCCCCcCHHHHHHHHHHHHHC
Confidence            3334444444444    344444444444444432   33334444444444    34444444444444443

>3n71_A Histone lysine methyltransferase SMYD1; heart development, transcription; HET: SFG MES; 2.30A {Mus musculus}

Probab=97.96  E-value=5.2e-05  Score=74.63  Aligned_cols=125  Identities=11%  Similarity=-0.026  Sum_probs=87.4

Q ss_pred             HHHhcCCHHHHHHHHHHHHHc-----C--CCcCHHHHHHHHHHHHhcCChHHHHHHHHhccc-----CC-CCCC-HHHHH
Q 040027          426 GLCKNGYIIEAVELFRTLRIL-----K--CELDIQAYNCLIDGLCKSGRLKFAWELFCSLPH-----GV-LVPN-VVTYN  491 (595)
Q Consensus       426 ~~~~~g~~~~A~~~~~~~~~~-----~--~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~-----~~-~~p~-~~~~~  491 (595)
                      .+...|++++|..++++.++.     |  .+....+++.|+.+|...|++++|+.++++.++     .| -.|+ ..+++
T Consensus       318 ~~~~qg~~~eA~~l~~~aL~~~~~~lg~~Hp~~a~~~~nLa~~y~~~g~~~eA~~~~~~aL~i~~~~lG~~Hp~~a~~l~  397 (490)
T 3n71_A          318 KARSEGLYHEVVKLCRECLEKQEPVFADTNLYVLRLLSIASEVLSYLQAYEEASHYARRMVDGYMKLYHHNNAQLGMAVM  397 (490)
T ss_dssp             HHHTTTCHHHHHHHHHHHHHHHTTTBCTTSHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHHSCTTCHHHHHHHH
T ss_pred             HHHhCCCHHHHHHHHHHHHHHHHHhcCCCCHHHHHHHHHHHHHHHHhcCHHHHHHHHHHHHHHHHHHcCCCCHHHHHHHH
Confidence            345678888888888777642     1  011245678888888888888888888887654     11 1233 35778


Q ss_pred             HHHHHHHhcCChhHHHHHHHHHHHc---CCCCC----HHHHHHHHHHHHHcCChhHHHHHHHHHHH
Q 040027          492 IMIQGLCNDGQMDKARDLFLDMEEN---AAAPD----VITFDMLIHGFIRINEPSKVNELLHKMKE  550 (595)
Q Consensus       492 ~l~~~~~~~g~~~~A~~~~~~~~~~---~~~~~----~~~~~~l~~~~~~~g~~~~A~~~~~~~~~  550 (595)
                      .|+..|...|++++|+.+++++++.   -+.|+    ..+...+..++...|.+++|..+++++.+
T Consensus       398 nLa~~~~~~G~~~eA~~~~~~Al~i~~~~lG~~Hp~~~~~~~~l~~~~~e~~~~~~ae~~~~~~~~  463 (490)
T 3n71_A          398 RAGLTNWHAGHIEVGHGMICKAYAILLVTHGPSHPITKDLEAMRMQTEMELRMFRQNEFMYHKMRE  463 (490)
T ss_dssp             HHHHHHHHTTCHHHHHHHHHHHHHHHHHHTCTTSHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHCCCHHHHHHHHHHHHHHHHHHhCCCChHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            8888888899999999888888652   11223    23446677777888888999988888875

>1zu2_A Mitochondrial import receptor subunit TOM20-3; TPR, tetratricopeptide repeat like, TPR-like, transport protein; NMR {Arabidopsis thaliana} SCOP: a.118.8.1

Probab=97.93  E-value=1.8e-05  Score=63.54  Aligned_cols=85  Identities=11%  Similarity=-0.049  Sum_probs=50.1

Q ss_pred             HhcCCHHHHHHHHHHHHHcCCCcCHHHHHHHHHHHHhcCChH----------HHHHHHHhcccCCCCCC-HHHHHHHHHH
Q 040027          428 CKNGYIIEAVELFRTLRILKCELDIQAYNCLIDGLCKSGRLK----------FAWELFCSLPHGVLVPN-VVTYNIMIQG  496 (595)
Q Consensus       428 ~~~g~~~~A~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~----------~A~~~~~~~~~~~~~p~-~~~~~~l~~~  496 (595)
                      .+.+.+++|...+++..+.. +.+...|..+..++...++++          +|+..|++.++  +.|+ ...|..+..+
T Consensus        13 ~r~~~feeA~~~~~~Ai~l~-P~~aea~~n~G~~l~~l~~~~~g~~al~~~~eAi~~le~AL~--ldP~~~~A~~~LG~a   89 (158)
T 1zu2_A           13 DRILLFEQIRQDAENTYKSN-PLDADNLTRWGGVLLELSQFHSISDAKQMIQEAITKFEEALL--IDPKKDEAVWCIGNA   89 (158)
T ss_dssp             HHHHHHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHHHHHSCHHHHHHHHHHHHHHHHHHHH--HCTTCHHHHHHHHHH
T ss_pred             HHHhHHHHHHHHHHHHHHHC-CCCHHHHHHHHHHHHHhcccchhhhhHhHHHHHHHHHHHHHH--hCcCcHHHHHHHHHH
Confidence            44556777777777777766 667777777777777666543          55555555555  3443 3455555555


Q ss_pred             HHhcC-----------ChhHHHHHHHHHHH
Q 040027          497 LCNDG-----------QMDKARDLFLDMEE  515 (595)
Q Consensus       497 ~~~~g-----------~~~~A~~~~~~~~~  515 (595)
                      |...|           ++++|++.|+++++
T Consensus        90 y~~lg~l~P~~~~a~g~~~eA~~~~~kAl~  119 (158)
T 1zu2_A           90 YTSFAFLTPDETEAKHNFDLATQFFQQAVD  119 (158)
T ss_dssp             HHHHHHHCCCHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHhcccCcchhhhhccHHHHHHHHHHHHH
Confidence            55442           44555555555544

>2l6j_A TPR repeat-containing protein associated with HSP; tetratricopeptide repeat (TPR), HSP90 CO-factor, protein BIN; NMR {Saccharomyces cerevisiae}

Probab=97.92  E-value=9e-06  Score=62.23  Aligned_cols=97  Identities=10%  Similarity=0.061  Sum_probs=78.8

Q ss_pred             CCHHHHHHHHHHHHhcCChhHHHHHHHHHHhCCCCCCHHHHHHHHHHHHhcCCHhHHHHHHHHHHhcCCCCC------Hh
Q 040027           94 PNLYTYNILINCFCKIGRVSLGFIAFGRILRSCFTPNAATFNSLIKGLHAESRIMEAAALFTKLKAFGCEPN------VI  167 (595)
Q Consensus        94 ~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~~------~~  167 (595)
                      ++...|..+...+...|++++|+..|+++++.. +.+...|..+..++...|++++|++.+++....... +      ..
T Consensus         2 ~~~~~~~~~g~~~~~~~~~~~A~~~~~~al~~~-p~~~~~~~~lg~~~~~~g~~~~A~~~~~~al~~~p~-~~~~~~~~~   79 (111)
T 2l6j_A            2 SQFEKQKEQGNSLFKQGLYREAVHCYDQLITAQ-PQNPVGYSNKAMALIKLGEYTQAIQMCQQGLRYTST-AEHVAIRSK   79 (111)
T ss_dssp             THHHHHHHHHHHHHTTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHTSCSS-TTSHHHHHH
T ss_pred             chHHHHHHHHHHHHHcCCHHHHHHHHHHHHhcC-CCCHHHHHHHHHHHHHhcCHHHHHHHHHHHHHhCCC-ccHHHHHHH
Confidence            356788889999999999999999999999885 557889999999999999999999999999987422 3      55


Q ss_pred             hHHHHHHHHHhcCChhHHHHHHHHH
Q 040027          168 TYNTLINGLCRTGHTMIALNLFEEM  192 (595)
Q Consensus       168 ~~~~l~~~~~~~g~~~~A~~~~~~~  192 (595)
                      .+..+..++...|+.+.|+..++++
T Consensus        80 ~~~~~~~~~~~~~~~~~a~~~~~~~  104 (111)
T 2l6j_A           80 LQYRLELAQGAVGSVQIPVVEVDEL  104 (111)
T ss_dssp             HHHHHHHHHHHHHCCCCCSSSSSSC
T ss_pred             HHHHHHHHHHHHHhHhhhHhHHHHh
Confidence            6667777777777777766655443

>1na3_A Designed protein CTPR2; de novo protein; HET: IPT; 1.55A {Unidentified} SCOP: k.38.1.1 PDB: 2avp_A

Probab=97.91  E-value=0.00013  Score=53.20  Aligned_cols=83  Identities=12%  Similarity=0.092  Sum_probs=55.1

Q ss_pred             HHHHHHHHHHHHhcCChhHHHHHHHHHHHcCCCCCHHHHHHHHHHHHHcCChhHHHHHHHHHHHCCCCCCHHHHHHHHHH
Q 040027          487 VVTYNIMIQGLCNDGQMDKARDLFLDMEENAAAPDVITFDMLIHGFIRINEPSKVNELLHKMKEKKVMPDASIVSIVVDL  566 (595)
Q Consensus       487 ~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~p~~~~~~~l~~~  566 (595)
                      ...+..+...+...|++++|+..++++++.. +.+...+..+..++...|++++|...++++.+.. +.+...+..+..+
T Consensus         9 ~~~~~~la~~~~~~~~~~~A~~~~~~a~~~~-~~~~~~~~~l~~~~~~~~~~~~A~~~~~~a~~~~-p~~~~~~~~l~~~   86 (91)
T 1na3_A            9 AEAWYNLGNAYYKQGDYDEAIEYYQKALELD-PNNAEAWYNLGNAYYKQGDYDEAIEYYQKALELD-PNNAEAKQNLGNA   86 (91)
T ss_dssp             HHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHccCHHHHHHHHHHHHhcC-CCCHHHHHHHHHHHHHHhhHHHHHHHHHHHHhcC-CCCHHHHHHHHHH
Confidence            4556666677777777777777777777653 4456667777777777777777777777777642 2246666666666


Q ss_pred             HHhcC
Q 040027          567 LVKNE  571 (595)
Q Consensus       567 ~~~~g  571 (595)
                      +.+.|
T Consensus        87 ~~~~g   91 (91)
T 1na3_A           87 KQKQG   91 (91)
T ss_dssp             HHHHC
T ss_pred             HHhcC
Confidence            65543

>1zu2_A Mitochondrial import receptor subunit TOM20-3; TPR, tetratricopeptide repeat like, TPR-like, transport protein; NMR {Arabidopsis thaliana} SCOP: a.118.8.1

Probab=97.90  E-value=2.2e-05  Score=63.02  Aligned_cols=99  Identities=7%  Similarity=-0.066  Sum_probs=51.3

Q ss_pred             cCChHHHHHHHHhcccCCCCC-CHHHHHHHHHHHHhcCCh----------hHHHHHHHHHHHcCCCCCHHHHHHHHHHHH
Q 040027          465 SGRLKFAWELFCSLPHGVLVP-NVVTYNIMIQGLCNDGQM----------DKARDLFLDMEENAAAPDVITFDMLIHGFI  533 (595)
Q Consensus       465 ~g~~~~A~~~~~~~~~~~~~p-~~~~~~~l~~~~~~~g~~----------~~A~~~~~~~~~~~~~~~~~~~~~l~~~~~  533 (595)
                      .+.+++|+..+++..+  +.| +...|..+..++...+++          ++|+..|+++++.+ +.+..+|..+..+|.
T Consensus        15 ~~~feeA~~~~~~Ai~--l~P~~aea~~n~G~~l~~l~~~~~g~~al~~~~eAi~~le~AL~ld-P~~~~A~~~LG~ay~   91 (158)
T 1zu2_A           15 ILLFEQIRQDAENTYK--SNPLDADNLTRWGGVLLELSQFHSISDAKQMIQEAITKFEEALLID-PKKDEAVWCIGNAYT   91 (158)
T ss_dssp             HHHHHHHHHHHHHHHH--HCTTCHHHHHHHHHHHHHHHHHSCHHHHHHHHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHH
T ss_pred             HhHHHHHHHHHHHHHH--HCCCCHHHHHHHHHHHHHhcccchhhhhHhHHHHHHHHHHHHHHhC-cCcHHHHHHHHHHHH
Confidence            3445555555555555  233 345555555555554443          35666666665543 334455555555555


Q ss_pred             HcC-----------ChhHHHHHHHHHHHCCCCCCHHHHHHHHHHHH
Q 040027          534 RIN-----------EPSKVNELLHKMKEKKVMPDASIVSIVVDLLV  568 (595)
Q Consensus       534 ~~g-----------~~~~A~~~~~~~~~~~~~p~~~~~~~l~~~~~  568 (595)
                      ..|           ++++|.+.|+++++  +.|+...|...+....
T Consensus        92 ~lg~l~P~~~~a~g~~~eA~~~~~kAl~--l~P~~~~y~~al~~~~  135 (158)
T 1zu2_A           92 SFAFLTPDETEAKHNFDLATQFFQQAVD--EQPDNTHYLKSLEMTA  135 (158)
T ss_dssp             HHHHHCCCHHHHHHHHHHHHHHHHHHHH--HCTTCHHHHHHHHHHH
T ss_pred             HhcccCcchhhhhccHHHHHHHHHHHHH--hCCCCHHHHHHHHHHH
Confidence            543           55666666666655  3455555544444433

>2kat_A Uncharacterized protein; NESG, structure, structural genomics, PSI-2, protein structure initiative; NMR {Bordetella parapertussis}

Probab=97.85  E-value=7.5e-05  Score=57.50  Aligned_cols=78  Identities=8%  Similarity=-0.045  Sum_probs=49.9

Q ss_pred             HHHHHHHhcccCCCCC-CHHHHHHHHHHHHhcCChhHHHHHHHHHHHcCCCCCHHHHHHHHHHHHHcCChhHHHHHHHHH
Q 040027          470 FAWELFCSLPHGVLVP-NVVTYNIMIQGLCNDGQMDKARDLFLDMEENAAAPDVITFDMLIHGFIRINEPSKVNELLHKM  548 (595)
Q Consensus       470 ~A~~~~~~~~~~~~~p-~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~  548 (595)
                      .|+..|+++.+.  .| +...+..+..+|...|++++|+..|+++++.. +.+...+..++.+|...|++++|...++++
T Consensus         3 ~a~~~~~~al~~--~p~~~~~~~~lg~~~~~~g~~~~A~~~~~~al~~~-p~~~~~~~~la~~~~~~g~~~~A~~~~~~a   79 (115)
T 2kat_A            3 AITERLEAMLAQ--GTDNMLLRFTLGKTYAEHEQFDAALPHLRAALDFD-PTYSVAWKWLGKTLQGQGDRAGARQAWESG   79 (115)
T ss_dssp             CHHHHHHHHHTT--TCCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHHTCHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHh--CCCcHHHHHHHHHHHHHccCHHHHHHHHHHHHHHC-CCcHHHHHHHHHHHHHcCCHHHHHHHHHHH
Confidence            355556655552  33 35566666667777777777777777776653 344566666777777777777777777776


Q ss_pred             HH
Q 040027          549 KE  550 (595)
Q Consensus       549 ~~  550 (595)
                      .+
T Consensus        80 l~   81 (115)
T 2kat_A           80 LA   81 (115)
T ss_dssp             HH
T ss_pred             HH
Confidence            64

>3n71_A Histone lysine methyltransferase SMYD1; heart development, transcription; HET: SFG MES; 2.30A {Mus musculus}

Probab=97.82  E-value=0.00012  Score=72.02  Aligned_cols=131  Identities=11%  Similarity=-0.049  Sum_probs=89.1

Q ss_pred             HHHhcCChhHHHHHHHHHHhcCCC-CCccccCcHHHHHHHHHHHHHcCCHhHHHHHHHHHhhC-----C--CCCCHhHHH
Q 040027          175 GLCRTGHTMIALNLFEEMANGNGE-IGVVCKPNTVTYSTIIDGLCKEGFVDKAKALFLQMKDE-----N--INPDVVTYN  246 (595)
Q Consensus       175 ~~~~~g~~~~A~~~~~~~~~~~~~-~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~-----~--~~~~~~~~~  246 (595)
                      .+...|++++|+.++++.+..... .|...+....+++.|..+|...|++++|..++++....     |  .+....+++
T Consensus       318 ~~~~qg~~~eA~~l~~~aL~~~~~~lg~~Hp~~a~~~~nLa~~y~~~g~~~eA~~~~~~aL~i~~~~lG~~Hp~~a~~l~  397 (490)
T 3n71_A          318 KARSEGLYHEVVKLCRECLEKQEPVFADTNLYVLRLLSIASEVLSYLQAYEEASHYARRMVDGYMKLYHHNNAQLGMAVM  397 (490)
T ss_dssp             HHHTTTCHHHHHHHHHHHHHHHTTTBCTTSHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHHSCTTCHHHHHHHH
T ss_pred             HHHhCCCHHHHHHHHHHHHHHHHHhcCCCCHHHHHHHHHHHHHHHHhcCHHHHHHHHHHHHHHHHHHcCCCCHHHHHHHH
Confidence            456789999999999988765332 22222334678899999999999999999998886642     2  111245677


Q ss_pred             HHHHHHHhcCCHHHHHHHHHHHHHC-----CCC-CC-HhhHHHHHHHHHhcCChHHHHHHHHHHHH
Q 040027          247 SLIHGLCHANDWNEAKRLFIEMMDQ-----GVQ-PS-VVTFNVIMDELCKNRKMDEASRLLDLMVQ  305 (595)
Q Consensus       247 ~ll~~~~~~~~~~~A~~~~~~~~~~-----~~~-~~-~~~~~~l~~~~~~~g~~~~a~~~~~~~~~  305 (595)
                      .|...|...|++++|..++++.++.     |.. |+ ..+...+..++...+.+++|..+|..+.+
T Consensus       398 nLa~~~~~~G~~~eA~~~~~~Al~i~~~~lG~~Hp~~~~~~~~l~~~~~e~~~~~~ae~~~~~~~~  463 (490)
T 3n71_A          398 RAGLTNWHAGHIEVGHGMICKAYAILLVTHGPSHPITKDLEAMRMQTEMELRMFRQNEFMYHKMRE  463 (490)
T ss_dssp             HHHHHHHHTTCHHHHHHHHHHHHHHHHHHTCTTSHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHCCCHHHHHHHHHHHHHHHHHHhCCCChHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            8888888888888888888776542     221 11 22344555566666677777777766654

>3ma5_A Tetratricopeptide repeat domain protein; NESG, structural genomics, PSI-2, protein structure initiative; 2.80A {Salinibacter ruber} PDB: 2kcl_A 2kcv_A

Probab=97.81  E-value=9e-05  Score=55.34  Aligned_cols=86  Identities=17%  Similarity=0.082  Sum_probs=52.8

Q ss_pred             CHHHHHHHHHHHHhcCChhHHHHHHHHHHHcCCCCCHHHHHHHHHHHHHcCChhHHHHHHHHHHHCC-CCCCHHHHHHHH
Q 040027          486 NVVTYNIMIQGLCNDGQMDKARDLFLDMEENAAAPDVITFDMLIHGFIRINEPSKVNELLHKMKEKK-VMPDASIVSIVV  564 (595)
Q Consensus       486 ~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~-~~p~~~~~~~l~  564 (595)
                      +...+..+..+|...|++++|+..|+++++.. +.+...|..++.+|...|++++|.+.+++.++.. -.++......+.
T Consensus         6 ~~~~~~~lg~~~~~~g~~~~A~~~~~~al~~~-p~~~~a~~~lg~~~~~~g~~~~A~~~~~~al~l~~~~~~~~~~~~l~   84 (100)
T 3ma5_A            6 DPFTRYALAQEHLKHDNASRALALFEELVETD-PDYVGTYYHLGKLYERLDRTDDAIDTYAQGIEVAREEGTQKDLSELQ   84 (100)
T ss_dssp             CHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHS-TTCTHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHHSCHHHHHHHH
T ss_pred             CHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhC-CCcHHHHHHHHHHHHHcCCHHHHHHHHHHHHhhhhcCCchhHHHHHH
Confidence            45566666677777777777777777776654 3345566667777777777777777777666431 123555555555


Q ss_pred             HHHHhcCc
Q 040027          565 DLLVKNEI  572 (595)
Q Consensus       565 ~~~~~~g~  572 (595)
                      ..+.+.+.
T Consensus        85 ~~l~~~~~   92 (100)
T 3ma5_A           85 DAKLKAEG   92 (100)
T ss_dssp             HHHHHHHT
T ss_pred             HHHHHccc
Confidence            55554443

>1na3_A Designed protein CTPR2; de novo protein; HET: IPT; 1.55A {Unidentified} SCOP: k.38.1.1 PDB: 2avp_A

Probab=97.79  E-value=0.00022  Score=51.91  Aligned_cols=83  Identities=17%  Similarity=0.127  Sum_probs=68.9

Q ss_pred             CHHHHHHHHHHHHhcCChhHHHHHHHHHHhCCCCCCHHHHHHHHHHHHhcCCHhHHHHHHHHHHhcCCCCCHhhHHHHHH
Q 040027           95 NLYTYNILINCFCKIGRVSLGFIAFGRILRSCFTPNAATFNSLIKGLHAESRIMEAAALFTKLKAFGCEPNVITYNTLIN  174 (595)
Q Consensus        95 ~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~~l~~  174 (595)
                      +...+..+...+...|++++|+..|+++++.. +.+...+..+...+...|++++|.+.|++..... +.+..++..+..
T Consensus         8 ~~~~~~~la~~~~~~~~~~~A~~~~~~a~~~~-~~~~~~~~~l~~~~~~~~~~~~A~~~~~~a~~~~-p~~~~~~~~l~~   85 (91)
T 1na3_A            8 SAEAWYNLGNAYYKQGDYDEAIEYYQKALELD-PNNAEAWYNLGNAYYKQGDYDEAIEYYQKALELD-PNNAEAKQNLGN   85 (91)
T ss_dssp             HHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHH
T ss_pred             cHHHHHHHHHHHHHccCHHHHHHHHHHHHhcC-CCCHHHHHHHHHHHHHHhhHHHHHHHHHHHHhcC-CCCHHHHHHHHH
Confidence            45678888899999999999999999999875 4577888999999999999999999999998874 336677777777


Q ss_pred             HHHhc
Q 040027          175 GLCRT  179 (595)
Q Consensus       175 ~~~~~  179 (595)
                      ++...
T Consensus        86 ~~~~~   90 (91)
T 1na3_A           86 AKQKQ   90 (91)
T ss_dssp             HHHHH
T ss_pred             HHHhc
Confidence            66554

>2kat_A Uncharacterized protein; NESG, structure, structural genomics, PSI-2, protein structure initiative; NMR {Bordetella parapertussis}

Probab=97.78  E-value=0.00015  Score=55.77  Aligned_cols=81  Identities=15%  Similarity=0.015  Sum_probs=67.7

Q ss_pred             hHHHHHHHHHHhCCCCCCHHHHHHHHHHHHhcCCHhHHHHHHHHHHhcCCCCCHhhHHHHHHHHHhcCChhHHHHHHHHH
Q 040027          113 SLGFIAFGRILRSCFTPNAATFNSLIKGLHAESRIMEAAALFTKLKAFGCEPNVITYNTLINGLCRTGHTMIALNLFEEM  192 (595)
Q Consensus       113 ~~A~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~  192 (595)
                      +.|+..|+++++.. +.+...+..+...+...|++++|+..|++..... +.+...+..+..++...|++++|...|++.
T Consensus         2 ~~a~~~~~~al~~~-p~~~~~~~~lg~~~~~~g~~~~A~~~~~~al~~~-p~~~~~~~~la~~~~~~g~~~~A~~~~~~a   79 (115)
T 2kat_A            2 QAITERLEAMLAQG-TDNMLLRFTLGKTYAEHEQFDAALPHLRAALDFD-PTYSVAWKWLGKTLQGQGDRAGARQAWESG   79 (115)
T ss_dssp             CCHHHHHHHHHTTT-CCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHHTCHHHHHHHHHHH
T ss_pred             hHHHHHHHHHHHhC-CCcHHHHHHHHHHHHHccCHHHHHHHHHHHHHHC-CCcHHHHHHHHHHHHHcCCHHHHHHHHHHH
Confidence            35778888888775 5578888889999999999999999999998875 336778888999999999999999999988


Q ss_pred             Hhc
Q 040027          193 ANG  195 (595)
Q Consensus       193 ~~~  195 (595)
                      ...
T Consensus        80 l~~   82 (115)
T 2kat_A           80 LAA   82 (115)
T ss_dssp             HHH
T ss_pred             HHh
Confidence            764

>3lvg_A Clathrin heavy chain 1; SELF assembly, coated PIT, cytoplasmic vesicle, membrane, Ca structural protein; 7.94A {Bos taurus} PDB: 3lvh_A

Probab=97.60  E-value=2e-07  Score=87.24  Aligned_cols=423  Identities=12%  Similarity=0.078  Sum_probs=239.8

Q ss_pred             CHhhHHHHHHHHHcCCCchhHHhhCCCCCCHHHHHHHHHHHHhcCChhHHHHHHHHHHhCCCCCCHHHHHHHHHHHHhcC
Q 040027           66 PVSSFNILLASLAKNKHYDTRLNATGLFPNLYTYNILINCFCKIGRVSLGFIAFGRILRSCFTPNAATFNSLIKGLHAES  145 (595)
Q Consensus        66 ~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g  145 (595)
                      .+..|..+..+..+.++..+....---..|+..|..++.+..+.|.+++-+..+.-+.+..  .++.+=+.|+-+|++.+
T Consensus        53 ~p~VWs~LgkAqL~~~~v~eAIdsyIkA~Dps~y~eVi~~A~~~~~~edLv~yL~MaRk~~--ke~~IDteLi~ayAk~~  130 (624)
T 3lvg_A           53 EPAVWSQLAKAQLQKGMVKEAIDSYIKADDPSSYMEVVQAANTSGNWEELVKYLQMARKKA--RESYVETELIFALAKTN  130 (624)
T ss_dssp             CCCCSSSHHHHTTTSSSCTTTTTSSCCCSCCCSSSHHHHHTTTSSCCTTHHHHHHTTSTTC--CSTTTTHHHHHHHHTSC
T ss_pred             CccHHHHHHHHHHccCchHHHHHHHHhCCChHHHHHHHHHHHhCCCHHHHHHHHHHHHHHh--cccccHHHHHHHHHhhC
Confidence            5678888888888888777633322223477778888999999999999998888777663  34444467888888888


Q ss_pred             CHhHHHHHHHHHHhcCCCCCHhhHHHHHHHHHhcCChhHHHHHHHHHHhcCCCCCccccCcHHHHHHHHHHHHHcCCHhH
Q 040027          146 RIMEAAALFTKLKAFGCEPNVITYNTLINGLCRTGHTMIALNLFEEMANGNGEIGVVCKPNTVTYSTIIDGLCKEGFVDK  225 (595)
Q Consensus       146 ~~~~A~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~  225 (595)
                      +..+-.+.+       ..|+..-...++.-|...|.++.|.-+|..+..               |..|..++.+.|+++.
T Consensus       131 rL~elEefl-------~~~N~A~iq~VGDrcf~e~lYeAAKilys~isN---------------~akLAstLV~L~~yq~  188 (624)
T 3lvg_A          131 RLAELEEFI-------NGPNNAHIQQVGDRCYDEKMYDAAKLLYNNVSN---------------FGRLASTLVHLGEYQA  188 (624)
T ss_dssp             SSSTTTSTT-------SCCSSSCTHHHHHHHHHSCCSTTSSTTGGGSCC---------------CTTTSSSSSSCSGGGS
T ss_pred             cHHHHHHHH-------cCCCcccHHHHHHHHHHccCHHHHHHHHHhCcc---------------HHHHHHHHHHHHHHHH
Confidence            865533322       135665667788888888888888777665533               3334555666777776


Q ss_pred             HHHHHHHHhhCCCCCCHhHHHHHHHHHHhcCCHHHHHHHHHHHHHCCCCCCHhhHHHHHHHHHhcCChHHHHHHHHHHHH
Q 040027          226 AKALFLQMKDENINPDVVTYNSLIHGLCHANDWNEAKRLFIEMMDQGVQPSVVTFNVIMDELCKNRKMDEASRLLDLMVQ  305 (595)
Q Consensus       226 A~~~~~~~~~~~~~~~~~~~~~ll~~~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~  305 (595)
                      |.+.-+   +.   .++.||..+..+|...+++.-|.-.--.++-.   +  .....++..|-..|.+++.+.+++....
T Consensus       189 AVdaAr---KA---ns~ktWKeV~~ACvd~~EfrLAqicGLniIvh---a--deL~elv~~YE~~G~f~ELIsLlEaglg  257 (624)
T 3lvg_A          189 AVDGAR---KA---NSTRTWKEVCFACVDGKEFRLAQMCGLHIVVH---A--DELEELINYYQDRGYFEELITMLEAALG  257 (624)
T ss_dssp             STTTTT---TC---CSSCSHHHHTHHHHHSCTTTTTTHHHHHHHCC---S--SCCSGGGSSSSTTCCCTTSTTTHHHHTT
T ss_pred             HHHHHH---hc---CChhHHHHHHHHHhCchHHHHHHHhcchhccc---H--HHHHHHHHHHHhCCCHHHHHHHHHHHhC
Confidence            654322   22   26777888888888888877776655555432   1  2233455667777888887777777664


Q ss_pred             CCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHh-cCCCC------CHHHHHHHHHHHHhCCCHHHHHHHH--------
Q 040027          306 RGVRPNACTYNTLMDGFCLMGKINRAEELFGSMES-MGCKH------DDVSYNILINGYCKNKEVEEALSLY--------  370 (595)
Q Consensus       306 ~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~-~~~~~------~~~~~~~l~~~~~~~~~~~~A~~~~--------  370 (595)
                      . -......|+-|.-.|++- +.++..+.++..-. .+++.      ....|.-++..|..-.+++.|....        
T Consensus       258 l-ErAHmGmFTELaILYsKY-~PeKlmEHlklf~sriNipKviracE~ahLW~ElvfLY~~ydE~DnA~ltMi~h~~~Aw  335 (624)
T 3lvg_A          258 L-ERAHMGMFTELAILYSKF-KPQKMREHLELFWSRVNIPKVLRAAEQAHLWAELVFLYDKYEEYDNAIITMMNHPTDAW  335 (624)
T ss_dssp             S-TTCCHHHHHHHHHHHHSS-CTTHHHHHHTTSSSSSCCTTTHHHHTTTTCHHHHHHHHHHHTCHHHHHHTTTSCHHHHC
T ss_pred             C-CchhHHHHHHHHHHHHhc-CHHHHHHHHHHHHHhccHHHHHHHHHHHhhHHHHHHHHhcchhHHHHHHHHHhCChhhc
Confidence            3 234556677666666654 34444444433211 11111      2234666666666666666554321        


Q ss_pred             -----HHHHHCCCCCCHHHH---------------HHHHHHHHccCCHHHHHHHHHHHHHC----------CCCCCHHHH
Q 040027          371 -----REMVSKGIKPTVVTY---------------NTLFLGLFEIHQVEHALKLFDEMQRD----------GVAADTRTY  420 (595)
Q Consensus       371 -----~~~~~~~~~~~~~~~---------------~~l~~~~~~~~~~~~a~~~~~~~~~~----------~~~~~~~~~  420 (595)
                           .+.+.+  ..+...|               +.++.++...=|..++.+++++.-..          .-.....+-
T Consensus       336 ~h~~Fkdii~K--VaN~EiyYKAi~FYL~e~P~lL~DLL~vL~prlDh~RvV~~~~k~~~LpLIkpYL~~Vq~~N~~aVN  413 (624)
T 3lvg_A          336 KEGQFKDIITK--VANVELYYRAIQFYLEFKPLLLNDLLMVLSPRLDHTRAVNYFSKVKQLPLVKPYLRSVQNHNNKSVN  413 (624)
T ss_dssp             CGGGGTTTGGG--CSCSHHHHHHHHHHTTSCCTTSHHHHHHHCTTCCSTTTHHHHHTTTCGGGGTGGGTSCCCSCCHHHH
T ss_pred             cHHHHHHHHHH--cchHHHHHHHHHHHHHhChHHHHHHHHhccccCChHHHHHHHHhcCCchhhHHHHHHHHHhhHHHHH
Confidence                 000000  1133333               33444444444444444444432110          012234444


Q ss_pred             HHHHHHHHhcCCHHHHHHH------------HHHHHHcCCCcCHHHHHHHHHHHHhcCChHHHHHHHHhcccCCCCCCHH
Q 040027          421 TTFIDGLCKNGYIIEAVEL------------FRTLRILKCELDIQAYNCLIDGLCKSGRLKFAWELFCSLPHGVLVPNVV  488 (595)
Q Consensus       421 ~~l~~~~~~~g~~~~A~~~------------~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~p~~~  488 (595)
                      .++-..|....+++.-...            -+++.+   .+-..........|.+.++|++++.+.++=.         
T Consensus       414 eAln~L~IEEEDy~~LR~SId~ydNFD~i~LA~rLEk---HeL~eFRrIAA~LYkkn~rw~qsi~l~KkDk---------  481 (624)
T 3lvg_A          414 ESLNNLFITEEDYQALRTSIDAYDNFDNISLAQRLEK---HELIEFRRIAAYLFKGNNRWKQSVELCKKDS---------  481 (624)
T ss_dssp             HHHHHHHHHTTCCHHHHHTTSSCCCSCTTHHHHHHHT---CSSHHHHHHHHHHHHTTCHHHHHSSCSSTTC---------
T ss_pred             HHHHHHHhhhhhHHHHHHHHHHhccccHHHHHHHHhh---CchHHHHHHHHHHHHhcccHHHHHHHHHhcc---------
Confidence            5555666666666544332            222222   2234444555666777888888776644321         


Q ss_pred             HHHHHHHHHHhcCChhHHHHHHHHHHHcCCCCCHHHHHHHHHHHHHcCChhHHH
Q 040027          489 TYNIMIQGLCNDGQMDKARDLFLDMEENAAAPDVITFDMLIHGFIRINEPSKVN  542 (595)
Q Consensus       489 ~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~  542 (595)
                      .|.-.+......|+.+-|.++++-.++.|   +...|...+-.|...=+++.++
T Consensus       482 lykDAietAa~S~~~elaeeLL~yFv~~g---~~EcF~a~LytCYdLlrpDvVl  532 (624)
T 3lvg_A          482 LYKDAMQYASESKDTELAEELLQWFLQEE---KRECFGACLFTCYDLLRPDVVL  532 (624)
T ss_dssp             CTTGGGTTTTTCCCTTHHHHHHHHHHHHC---STHHHHHHHHHTSSSSSCHHHH
T ss_pred             cHHHHHHHHHHcCCHHHHHHHHHHHHHcC---chHHHHHHHHHHhhccChHHHH
Confidence            11122333455666666667776666654   4445555555554444444443

>3ma5_A Tetratricopeptide repeat domain protein; NESG, structural genomics, PSI-2, protein structure initiative; 2.80A {Salinibacter ruber} PDB: 2kcl_A 2kcv_A

Probab=97.52  E-value=0.00048  Score=51.26  Aligned_cols=63  Identities=16%  Similarity=0.106  Sum_probs=31.3

Q ss_pred             CHHHHHHHHHHHHhcCChhHHHHHHHHHHhCCCCCCHHHHHHHHHHHHhcCCHhHHHHHHHHHH
Q 040027           95 NLYTYNILINCFCKIGRVSLGFIAFGRILRSCFTPNAATFNSLIKGLHAESRIMEAAALFTKLK  158 (595)
Q Consensus        95 ~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~  158 (595)
                      ++..|..+...+...|++++|+..|+++++.. +.+..+|..+..+|...|++++|++.|++..
T Consensus         6 ~~~~~~~lg~~~~~~g~~~~A~~~~~~al~~~-p~~~~a~~~lg~~~~~~g~~~~A~~~~~~al   68 (100)
T 3ma5_A            6 DPFTRYALAQEHLKHDNASRALALFEELVETD-PDYVGTYYHLGKLYERLDRTDDAIDTYAQGI   68 (100)
T ss_dssp             CHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHS-TTCTHHHHHHHHHHHHTTCHHHHHHHHHHHH
T ss_pred             CHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhC-CCcHHHHHHHHHHHHHcCCHHHHHHHHHHHH
Confidence            44445555555555555555555555555443 2234444455555555555555555555444

>3ly7_A Transcriptional activator CADC; alpha/beta domain, alpha domain, DNA-binding, transcription regulation, transmembrane; 1.80A {Escherichia coli} PDB: 3lya_A 3ly8_A 3ly9_A

Probab=97.48  E-value=0.0025  Score=59.02  Aligned_cols=75  Identities=9%  Similarity=0.015  Sum_probs=58.4

Q ss_pred             CCCHHHHHHHHHHHHhcCChhHHHHHHHHHHHcCCCCCHHHHHHHHHHHHHcCChhHHHHHHHHHHHCCCCCCHHHHHH
Q 040027          484 VPNVVTYNIMIQGLCNDGQMDKARDLFLDMEENAAAPDVITFDMLIHGFIRINEPSKVNELLHKMKEKKVMPDASIVSI  562 (595)
Q Consensus       484 ~p~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~p~~~~~~~  562 (595)
                      +.+..++..+...+...|++++|+..+++++..+  |+...|..+...+.-.|++++|.+.++++...  .|...+|..
T Consensus       274 ~~~a~~~~alal~~l~~gd~d~A~~~l~rAl~Ln--~s~~a~~llG~~~~~~G~~~eA~e~~~~AlrL--~P~~~t~~~  348 (372)
T 3ly7_A          274 NNLSIIYQIKAVSALVKGKTDESYQAINTGIDLE--MSWLNYVLLGKVYEMKGMNREAADAYLTAFNL--RPGANTLYW  348 (372)
T ss_dssp             TTCHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHC--CCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH--SCSHHHHHH
T ss_pred             CcCHHHHHHHHHHHHhCCCHHHHHHHHHHHHhcC--CCHHHHHHHHHHHHHCCCHHHHHHHHHHHHhc--CCCcChHHH
Confidence            3456777777777777788888888888888875  67777778888888888888888888888874  577766554

>3ly7_A Transcriptional activator CADC; alpha/beta domain, alpha domain, DNA-binding, transcription regulation, transmembrane; 1.80A {Escherichia coli} PDB: 3lya_A 3ly8_A 3ly9_A

Probab=97.44  E-value=0.0014  Score=60.64  Aligned_cols=32  Identities=9%  Similarity=-0.091  Sum_probs=25.8

Q ss_pred             CChHHHHHHHHHHHHhCCCCCCHhhHHHHHHHHH
Q 040027           45 ITPNEAFCIFDYMLRMHPSPPPVSSFNILLASLA   78 (595)
Q Consensus        45 ~~~~~A~~~~~~~~~~~~~~~~~~~~~~l~~~~~   78 (595)
                      .++.+|+.+|+++++.+|+  .+..|..+..++.
T Consensus       213 ~~~~~A~~l~e~Al~lDP~--~a~A~A~la~a~~  244 (372)
T 3ly7_A          213 KSLNRASELLGEIVQSSPE--FTYARAEKALVDI  244 (372)
T ss_dssp             HHHHHHHHHHHHHHHHCTT--CHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHhCCC--CHHHHHHHHHHHH
Confidence            4568999999999999998  7777776666554

>3qww_A SET and MYND domain-containing protein 2; methyltransferase, HSP90, transferase-transferase inhibitor; HET: SFG; 1.80A {Mus musculus} PDB: 3qwv_A* 3s7d_A* 3s7b_A* 3s7f_A* 3s7j_A* 3tg4_A* 3tg5_A* 3rib_A*

Probab=97.12  E-value=0.0018  Score=62.53  Aligned_cols=85  Identities=7%  Similarity=-0.088  Sum_probs=54.1

Q ss_pred             cCChHHHHHHHHhccc---CCCCCC----HHHHHHHHHHHHhcCChhHHHHHHHHHHHc-----C-CCCC-HHHHHHHHH
Q 040027          465 SGRLKFAWELFCSLPH---GVLVPN----VVTYNIMIQGLCNDGQMDKARDLFLDMEEN-----A-AAPD-VITFDMLIH  530 (595)
Q Consensus       465 ~g~~~~A~~~~~~~~~---~~~~p~----~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~-----~-~~~~-~~~~~~l~~  530 (595)
                      .|++++|+.++++.++   .-+.|+    ..+++.++.+|...|++++|+.+++++++.     | -.|+ ..+++.|+.
T Consensus       311 ~g~~~eA~~~~~~~L~i~~~~lg~~Hp~~a~~~~nLa~~y~~~g~~~eA~~~~~~aL~i~~~~lG~~Hp~~a~~l~nLa~  390 (433)
T 3qww_A          311 YKSPSELLEICELSQEKMSSVFEDSNVYMLHMMYQAMGVCLYMQDWEGALKYGQKIIKPYSKHYPVYSLNVASMWLKLGR  390 (433)
T ss_dssp             TSCHHHHHHHHHHHHHHHTTTBCTTSHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHHSCSSCHHHHHHHHHHHH
T ss_pred             ccCHHHHHHHHHHHHHHhhCccChhchHHHHHHHHHHHHHHhhcCHHHHHHHHHHHHHHHHHHcCCCChHHHHHHHHHHH
Confidence            4566666666665543   112222    356677777777777777777777777641     2 1122 345677778


Q ss_pred             HHHHcCChhHHHHHHHHHH
Q 040027          531 GFIRINEPSKVNELLHKMK  549 (595)
Q Consensus       531 ~~~~~g~~~~A~~~~~~~~  549 (595)
                      .|..+|++++|..++++++
T Consensus       391 ~~~~qg~~~eA~~~~~~Al  409 (433)
T 3qww_A          391 LYMGLENKAAGEKALKKAI  409 (433)
T ss_dssp             HHHHTTCHHHHHHHHHHHH
T ss_pred             HHHhccCHHHHHHHHHHHH
Confidence            8888888888888887776

>3u64_A Protein TP_0956; tetratrico peptide repeat, protein-prote interaction, syphilis, lipoprotein, transport protein; 2.30A {Treponema pallidum subsp} PDB: 4di3_A 4di4_A*

Probab=97.10  E-value=0.11  Score=46.15  Aligned_cols=93  Identities=12%  Similarity=0.096  Sum_probs=72.3

Q ss_pred             hhHHHHHHHHHHhcCCCCCccccC--cHHHHHHHHHHHHHc-----CCHhHHHHHHHHHhhCCCCCCHhHHHHHHHHHHh
Q 040027          182 TMIALNLFEEMANGNGEIGVVCKP--NTVTYSTIIDGLCKE-----GFVDKAKALFLQMKDENINPDVVTYNSLIHGLCH  254 (595)
Q Consensus       182 ~~~A~~~~~~~~~~~~~~~~~~~~--~~~~~~~l~~~~~~~-----g~~~~A~~~~~~~~~~~~~~~~~~~~~ll~~~~~  254 (595)
                      ...|...+++..+.+       +.  +...|..+...|.+.     |+.++|.+.|++....+..-+..++......++.
T Consensus       179 l~~A~a~lerAleLD-------P~~~~GsA~~~LG~lY~~vPp~~gGd~ekA~~~ferAL~LnP~~~id~~v~YA~~l~~  251 (301)
T 3u64_A          179 VHAAVMMLERACDLW-------PSYQEGAVWNVLTKFYAAAPESFGGGMEKAHTAFEHLTRYCSAHDPDHHITYADALCI  251 (301)
T ss_dssp             HHHHHHHHHHHHHHC-------TTHHHHHHHHHHHHHHHHSCTTTTCCHHHHHHHHHHHHHHCCTTCSHHHHHHHHHTTT
T ss_pred             HHHHHHHHHHHHHhC-------CCcccCHHHHHHHHHHHhCCCccCCCHHHHHHHHHHHHHhCCCCCchHHHHHHHHHHH
Confidence            467888889998876       22  367899999999994     9999999999999986532247778888888888


Q ss_pred             -cCCHHHHHHHHHHHHHCCCC--CCHhhHH
Q 040027          255 -ANDWNEAKRLFIEMMDQGVQ--PSVVTFN  281 (595)
Q Consensus       255 -~~~~~~A~~~~~~~~~~~~~--~~~~~~~  281 (595)
                       .|+.+++.+.+++.+.....  |+....+
T Consensus       252 ~~gd~~~a~~~L~kAL~a~p~~~P~~~lan  281 (301)
T 3u64_A          252 PLNNRAGFDEALDRALAIDPESVPHNKLLV  281 (301)
T ss_dssp             TTTCHHHHHHHHHHHHHCCGGGCSSCHHHH
T ss_pred             hcCCHHHHHHHHHHHHcCCCCCCCChhHHH
Confidence             49999999999999987554  4443333

>3bee_A Putative YFRE protein; putaive YFRE protein, structural GE PSI-2, protein structure initiative; 2.15A {Vibrio parahaemolyticus rimd 2210633}

Probab=97.07  E-value=0.0055  Score=44.48  Aligned_cols=67  Identities=4%  Similarity=-0.056  Sum_probs=49.5

Q ss_pred             CCCHHHHHHHHHHHHhcCC---hhHHHHHHHHHHHcCCCCCHHHHHHHHHHHHHcCChhHHHHHHHHHHHC
Q 040027          484 VPNVVTYNIMIQGLCNDGQ---MDKARDLFLDMEENAAAPDVITFDMLIHGFIRINEPSKVNELLHKMKEK  551 (595)
Q Consensus       484 ~p~~~~~~~l~~~~~~~g~---~~~A~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~  551 (595)
                      ++|+..+..+..++...++   .++|..+++++++.. +.+......++..+...|++++|...|+++.+.
T Consensus         3 p~~~~~~~~~a~al~~~~~~~~~~~A~~~l~~AL~~d-p~~~rA~~~lg~~~~~~g~y~~Ai~~w~~~l~~   72 (93)
T 3bee_A            3 AVTATQLAAKATTLYYLHKQAMTDEVSLLLEQALQLE-PYNEAALSLIANDHFISFRFQEAIDTWVLLLDS   72 (93)
T ss_dssp             CCCHHHHHHHHHHHHHTTTTCCCHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHTC
T ss_pred             CCCHHHHHHHHHHHHHhcCCCCCHHHHHHHHHHHHHC-cCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHhh
Confidence            3456677777777654443   678888888888865 556777777888888888888888888888864

>3qwp_A SET and MYND domain-containing protein 3; SMYD3,SET and MYND domain, zinc finger MYND domain-containin 1, structural genomics; HET: SAM; 1.53A {Homo sapiens} PDB: 3mek_A* 3oxg_A* 3oxf_A* 3pdn_A* 3oxl_A* 3ru0_A*

Probab=97.03  E-value=0.0061  Score=59.02  Aligned_cols=89  Identities=9%  Similarity=-0.071  Sum_probs=60.0

Q ss_pred             HHHhcCChHHHHHHHHhcccC---CCCCC----HHHHHHHHHHHHhcCChhHHHHHHHHHHHc-----C-CCCC-HHHHH
Q 040027          461 GLCKSGRLKFAWELFCSLPHG---VLVPN----VVTYNIMIQGLCNDGQMDKARDLFLDMEEN-----A-AAPD-VITFD  526 (595)
Q Consensus       461 ~~~~~g~~~~A~~~~~~~~~~---~~~p~----~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~-----~-~~~~-~~~~~  526 (595)
                      -+...|++++|+.++++.++.   -+.|+    ..+++.++.+|...|++++|+.+++++++.     | ..|+ ..+++
T Consensus       296 ~~~~~g~~~~a~~~~~~~L~~~~~~lg~~h~~~~~~~~~L~~~y~~~g~~~eA~~~~~~~L~i~~~~lg~~Hp~~a~~l~  375 (429)
T 3qwp_A          296 ELKAHWKWEQVLAMCQAIISSNSERLPDINIYQLKVLDCAMDACINLGLLEEALFYGTRTMEPYRIFFPGSHPVRGVQVM  375 (429)
T ss_dssp             HHHHTTCHHHHHHHHHHHHTCSSCCCCTTSHHHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHHHHSCSSCHHHHHHHH
T ss_pred             HHHhhccHHHHHHHHHHHHHhccCcCCccchHHHHHHHHHHHHHHhhccHHHHHHHHHHHHHhHHHHcCCCChHHHHHHH
Confidence            344667777777777776542   12232    346777778888888888888888877642     2 1122 34567


Q ss_pred             HHHHHHHHcCChhHHHHHHHHHH
Q 040027          527 MLIHGFIRINEPSKVNELLHKMK  549 (595)
Q Consensus       527 ~l~~~~~~~g~~~~A~~~~~~~~  549 (595)
                      .++..|...|++++|..+++++.
T Consensus       376 nLa~~~~~~g~~~eA~~~~~~Al  398 (429)
T 3qwp_A          376 KVGKLQLHQGMFPQAMKNLRLAF  398 (429)
T ss_dssp             HHHHHHHHTTCHHHHHHHHHHHH
T ss_pred             HHHHHHHhcCCHHHHHHHHHHHH
Confidence            78888888888888888888776

>3bee_A Putative YFRE protein; putaive YFRE protein, structural GE PSI-2, protein structure initiative; 2.15A {Vibrio parahaemolyticus rimd 2210633}

Probab=96.96  E-value=0.0074  Score=43.78  Aligned_cols=68  Identities=10%  Similarity=-0.000  Sum_probs=48.8

Q ss_pred             CCCHHHHHHHHHHHHhcCC---hhHHHHHHHHHHhCCCCCCHHHHHHHHHHHHhcCCHhHHHHHHHHHHhcC
Q 040027           93 FPNLYTYNILINCFCKIGR---VSLGFIAFGRILRSCFTPNAATFNSLIKGLHAESRIMEAAALFTKLKAFG  161 (595)
Q Consensus        93 ~~~~~~~~~l~~~~~~~g~---~~~A~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~  161 (595)
                      +.|+..+..+..++...++   .++|..+++++++.. +.++.+...+...+.+.|++++|+..|+++.+..
T Consensus         3 p~~~~~~~~~a~al~~~~~~~~~~~A~~~l~~AL~~d-p~~~rA~~~lg~~~~~~g~y~~Ai~~w~~~l~~~   73 (93)
T 3bee_A            3 AVTATQLAAKATTLYYLHKQAMTDEVSLLLEQALQLE-PYNEAALSLIANDHFISFRFQEAIDTWVLLLDSN   73 (93)
T ss_dssp             CCCHHHHHHHHHHHHHTTTTCCCHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHTCC
T ss_pred             CCCHHHHHHHHHHHHHhcCCCCCHHHHHHHHHHHHHC-cCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHhhC
Confidence            4567777777777654444   678888888888774 4466677777777778888888888888887763

>3qww_A SET and MYND domain-containing protein 2; methyltransferase, HSP90, transferase-transferase inhibitor; HET: SFG; 1.80A {Mus musculus} PDB: 3qwv_A* 3s7d_A* 3s7b_A* 3s7f_A* 3s7j_A* 3tg4_A* 3tg5_A* 3rib_A*

Probab=96.93  E-value=0.0025  Score=61.55  Aligned_cols=93  Identities=4%  Similarity=-0.166  Sum_probs=63.5

Q ss_pred             hcCChhHHHHHHHHHHhcCCC-CCccccCcHHHHHHHHHHHHHcCCHhHHHHHHHHHhhC-----CC-CC-CHhHHHHHH
Q 040027          178 RTGHTMIALNLFEEMANGNGE-IGVVCKPNTVTYSTIIDGLCKEGFVDKAKALFLQMKDE-----NI-NP-DVVTYNSLI  249 (595)
Q Consensus       178 ~~g~~~~A~~~~~~~~~~~~~-~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~-----~~-~~-~~~~~~~ll  249 (595)
                      ..|++++|+.++++.+..... +|...+....+++.|..+|...|++++|+.++++....     |. .| ...+++.|.
T Consensus       310 ~~g~~~eA~~~~~~~L~i~~~~lg~~Hp~~a~~~~nLa~~y~~~g~~~eA~~~~~~aL~i~~~~lG~~Hp~~a~~l~nLa  389 (433)
T 3qww_A          310 HYKSPSELLEICELSQEKMSSVFEDSNVYMLHMMYQAMGVCLYMQDWEGALKYGQKIIKPYSKHYPVYSLNVASMWLKLG  389 (433)
T ss_dssp             TTSCHHHHHHHHHHHHHHHTTTBCTTSHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHHSCSSCHHHHHHHHHHH
T ss_pred             hccCHHHHHHHHHHHHHHhhCccChhchHHHHHHHHHHHHHHhhcCHHHHHHHHHHHHHHHHHHcCCCChHHHHHHHHHH
Confidence            357888999988887764322 22222333567888888888899999988888876542     21 12 234577777


Q ss_pred             HHHHhcCCHHHHHHHHHHHHH
Q 040027          250 HGLCHANDWNEAKRLFIEMMD  270 (595)
Q Consensus       250 ~~~~~~~~~~~A~~~~~~~~~  270 (595)
                      ..|...|++++|..+|++.++
T Consensus       390 ~~~~~qg~~~eA~~~~~~Al~  410 (433)
T 3qww_A          390 RLYMGLENKAAGEKALKKAIA  410 (433)
T ss_dssp             HHHHHTTCHHHHHHHHHHHHH
T ss_pred             HHHHhccCHHHHHHHHHHHHH
Confidence            888888888888888777654

>2kc7_A BFR218_protein; tetratricopeptide repeat, all-alpha, GFT-structural genomics, PSI-2, protein structure initiative; NMR {Bacteroides fragilis}

Probab=96.92  E-value=0.0068  Score=44.59  Aligned_cols=56  Identities=13%  Similarity=0.205  Sum_probs=29.1

Q ss_pred             HHHHHhcCChhHHHHHHHHHHHcCCCCCHH-HHHHHHHHHHHcCChhHHHHHHHHHHH
Q 040027          494 IQGLCNDGQMDKARDLFLDMEENAAAPDVI-TFDMLIHGFIRINEPSKVNELLHKMKE  550 (595)
Q Consensus       494 ~~~~~~~g~~~~A~~~~~~~~~~~~~~~~~-~~~~l~~~~~~~g~~~~A~~~~~~~~~  550 (595)
                      +..+...|++++|+..++++++.. +.+.. .+..++.+|...|++++|.+.|+++++
T Consensus         7 a~~~~~~~~~~~A~~~~~~al~~~-p~~~~~~~~~lg~~~~~~~~~~~A~~~~~~al~   63 (99)
T 2kc7_A            7 IKELINQGDIENALQALEEFLQTE-PVGKDEAYYLMGNAYRKLGDWQKALNNYQSAIE   63 (99)
T ss_dssp             HHHHHHHTCHHHHHHHHHHHHHHC-SSTHHHHHHHHHHHHHHHTCHHHHHHHHHHHHH
T ss_pred             HHHHHHcCCHHHHHHHHHHHHHHC-CCcHHHHHHHHHHHHHHcCCHHHHHHHHHHHHh
Confidence            334445555555555555555542 23344 455555555555555555555555554

>3qwp_A SET and MYND domain-containing protein 3; SMYD3,SET and MYND domain, zinc finger MYND domain-containin 1, structural genomics; HET: SAM; 1.53A {Homo sapiens} PDB: 3mek_A* 3oxg_A* 3oxf_A* 3pdn_A* 3oxl_A* 3ru0_A*

Probab=96.92  E-value=0.0059  Score=59.11  Aligned_cols=99  Identities=12%  Similarity=0.015  Sum_probs=72.4

Q ss_pred             HHHHHHhcCChhHHHHHHHHHHhcCCC-CCccccCcHHHHHHHHHHHHHcCCHhHHHHHHHHHhhC-----C--CCCCHh
Q 040027          172 LINGLCRTGHTMIALNLFEEMANGNGE-IGVVCKPNTVTYSTIIDGLCKEGFVDKAKALFLQMKDE-----N--INPDVV  243 (595)
Q Consensus       172 l~~~~~~~g~~~~A~~~~~~~~~~~~~-~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~-----~--~~~~~~  243 (595)
                      .+..+...|++++|+.++++....... +|...+....+++.++.+|...|++++|+.+++++...     |  .+....
T Consensus       293 ~ie~~~~~g~~~~a~~~~~~~L~~~~~~lg~~h~~~~~~~~~L~~~y~~~g~~~eA~~~~~~~L~i~~~~lg~~Hp~~a~  372 (429)
T 3qwp_A          293 KIEELKAHWKWEQVLAMCQAIISSNSERLPDINIYQLKVLDCAMDACINLGLLEEALFYGTRTMEPYRIFFPGSHPVRGV  372 (429)
T ss_dssp             HHHHHHHTTCHHHHHHHHHHHHTCSSCCCCTTSHHHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHHHHSCSSCHHHHH
T ss_pred             HHHHHHhhccHHHHHHHHHHHHHhccCcCCccchHHHHHHHHHHHHHHhhccHHHHHHHHHHHHHhHHHHcCCCChHHHH
Confidence            345566789999999999999876432 23223334667889999999999999999999887642     2  111244


Q ss_pred             HHHHHHHHHHhcCCHHHHHHHHHHHHH
Q 040027          244 TYNSLIHGLCHANDWNEAKRLFIEMMD  270 (595)
Q Consensus       244 ~~~~ll~~~~~~~~~~~A~~~~~~~~~  270 (595)
                      +++.|...|...|++++|..++++.++
T Consensus       373 ~l~nLa~~~~~~g~~~eA~~~~~~Al~  399 (429)
T 3qwp_A          373 QVMKVGKLQLHQGMFPQAMKNLRLAFD  399 (429)
T ss_dssp             HHHHHHHHHHHTTCHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHhcCCHHHHHHHHHHHHH
Confidence            577788888888888888888877654

>1pc2_A Mitochondria fission protein; unknown function; NMR {Homo sapiens} SCOP: a.118.8.1

Probab=96.83  E-value=0.0087  Score=47.43  Aligned_cols=83  Identities=14%  Similarity=-0.004  Sum_probs=46.3

Q ss_pred             HHHHHHHhcccCCCCCCHHHHHHHHHHHHhcC---ChhHHHHHHHHHHHcCCCC--CHHHHHHHHHHHHHcCChhHHHHH
Q 040027          470 FAWELFCSLPHGVLVPNVVTYNIMIQGLCNDG---QMDKARDLFLDMEENAAAP--DVITFDMLIHGFIRINEPSKVNEL  544 (595)
Q Consensus       470 ~A~~~~~~~~~~~~~p~~~~~~~l~~~~~~~g---~~~~A~~~~~~~~~~~~~~--~~~~~~~l~~~~~~~g~~~~A~~~  544 (595)
                      .+.+.|.+....+. ++..+...+.+++++.+   +.++++.++++..+.+ .|  +...+..+.-+|.+.|++++|+++
T Consensus        16 ~~~~~y~~e~~~~~-~~~~~~F~ya~~Lv~S~~~~~~~~gI~lLe~ll~~~-~p~~~rd~lY~LAv~~~kl~~Y~~A~~y   93 (152)
T 1pc2_A           16 KFEKKFQSEKAAGS-VSKSTQFEYAWCLVRSKYNDDIRKGIVLLEELLPKG-SKEEQRDYVFYLAVGNYRLKEYEKALKY   93 (152)
T ss_dssp             HHHHHHHHHHHTTC-CCHHHHHHHHHHHHTCSSHHHHHHHHHHHHHHHHHS-CHHHHHHHHHHHHHHHHHTSCHHHHHHH
T ss_pred             HHHHHHHHHHccCC-CcHHHHHHHHHHHHcCCCHHHHHHHHHHHHHHHhcC-CccchHHHHHHHHHHHHHccCHHHHHHH
Confidence            34444444433322 45555566666666655   4446666666666643 23  244555566666666666666666


Q ss_pred             HHHHHHCCCCCC
Q 040027          545 LHKMKEKKVMPD  556 (595)
Q Consensus       545 ~~~~~~~~~~p~  556 (595)
                      ++.+++  +.|+
T Consensus        94 ~~~lL~--ieP~  103 (152)
T 1pc2_A           94 VRGLLQ--TEPQ  103 (152)
T ss_dssp             HHHHHH--HCTT
T ss_pred             HHHHHh--cCCC
Confidence            666665  3454

>3mkq_B Coatomer subunit alpha; beta-propeller, alpha-solenoid, transport protein; 2.50A {Saccharomyces cerevisiae}

Probab=96.73  E-value=0.18  Score=41.06  Aligned_cols=129  Identities=9%  Similarity=0.088  Sum_probs=80.4

Q ss_pred             HHHHhcCChhHHHHHHHHHHhCCCCCCHHHHHHHHHHHHhcCCHhHHHHHHHHHHhcCCCCCHhhHHHHHHHHHhcCChh
Q 040027          104 NCFCKIGRVSLGFIAFGRILRSCFTPNAATFNSLIKGLHAESRIMEAAALFTKLKAFGCEPNVITYNTLINGLCRTGHTM  183 (595)
Q Consensus       104 ~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~  183 (595)
                      ......|+++.|.++.+.+      .+...|..+.......|+++-|.+.|.+...         +..+.-.|...|+.+
T Consensus        13 ~LAL~lg~l~~A~e~a~~l------~~~~~Wk~Lg~~AL~~gn~~lAe~cy~~~~D---------~~~L~~Ly~~tg~~e   77 (177)
T 3mkq_B           13 DLALEYGNLDAALDEAKKL------NDSITWERLIQEALAQGNASLAEMIYQTQHS---------FDKLSFLYLVTGDVN   77 (177)
T ss_dssp             HHHHHTTCHHHHHHHHHHH------CCHHHHHHHHHHHHHTTCHHHHHHHHHHTTC---------HHHHHHHHHHHTCHH
T ss_pred             HHHHhcCCHHHHHHHHHHh------CCHHHHHHHHHHHHHcCChHHHHHHHHHhCC---------HHHHHHHHHHhCCHH
Confidence            3455678888888877665      2577888888888888888888888887653         345556666777776


Q ss_pred             HHHHHHHHHHhcCCCCCccccCcHHHHHHHHHHHHHcCCHhHHHHHHHHHhhCCCCCCHhHHHHHHHHHHhcCCHHHHHH
Q 040027          184 IALNLFEEMANGNGEIGVVCKPNTVTYSTIIDGLCKEGFVDKAKALFLQMKDENINPDVVTYNSLIHGLCHANDWNEAKR  263 (595)
Q Consensus       184 ~A~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~~ll~~~~~~~~~~~A~~  263 (595)
                      .-.++-+.....+            -++....++.-.|+++++.++|.+.-+.     ...    .......|..+.|.+
T Consensus        78 ~L~kla~iA~~~g------------~~n~af~~~l~lGdv~~~i~lL~~~~r~-----~eA----~~~A~t~g~~~~a~~  136 (177)
T 3mkq_B           78 KLSKMQNIAQTRE------------DFGSMLLNTFYNNSTKERSSIFAEGGSL-----PLA----YAVAKANGDEAAASA  136 (177)
T ss_dssp             HHHHHHHHHHHTT------------CHHHHHHHHHHHTCHHHHHHHHHHTTCH-----HHH----HHHHHHTTCHHHHHH
T ss_pred             HHHHHHHHHHHCc------------cHHHHHHHHHHcCCHHHHHHHHHHCCCh-----HHH----HHHHHHcCcHHHHHH
Confidence            6665555544433            1344455566678888888877554321     111    112223455666666


Q ss_pred             HHHHH
Q 040027          264 LFIEM  268 (595)
Q Consensus       264 ~~~~~  268 (595)
                      +...+
T Consensus       137 ~~~~~  141 (177)
T 3mkq_B          137 FLEQA  141 (177)
T ss_dssp             HHHHT
T ss_pred             HHHHh
Confidence            66554

>2kc7_A BFR218_protein; tetratricopeptide repeat, all-alpha, GFT-structural genomics, PSI-2, protein structure initiative; NMR {Bacteroides fragilis}

Probab=96.71  E-value=0.017  Score=42.39  Aligned_cols=84  Identities=10%  Similarity=0.065  Sum_probs=62.9

Q ss_pred             HHHHHHHhcCChhHHHHHHHHHHhCCCCCCHH-HHHHHHHHHHhcCCHhHHHHHHHHHHhcCCCCCHhhHHHHHHHHHhc
Q 040027          101 ILINCFCKIGRVSLGFIAFGRILRSCFTPNAA-TFNSLIKGLHAESRIMEAAALFTKLKAFGCEPNVITYNTLINGLCRT  179 (595)
Q Consensus       101 ~l~~~~~~~g~~~~A~~~~~~~~~~~~~~~~~-~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~~l~~~~~~~  179 (595)
                      ..+..+.+.|++++|+..|+++++.. +.+.. .+..+..++...|++++|++.|++..+.... +..++..        
T Consensus         5 ~~a~~~~~~~~~~~A~~~~~~al~~~-p~~~~~~~~~lg~~~~~~~~~~~A~~~~~~al~~~p~-~~~~~~~--------   74 (99)
T 2kc7_A            5 KTIKELINQGDIENALQALEEFLQTE-PVGKDEAYYLMGNAYRKLGDWQKALNNYQSAIELNPD-SPALQAR--------   74 (99)
T ss_dssp             HHHHHHHHHTCHHHHHHHHHHHHHHC-SSTHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHCTT-STHHHHH--------
T ss_pred             HHHHHHHHcCCHHHHHHHHHHHHHHC-CCcHHHHHHHHHHHHHHcCCHHHHHHHHHHHHhcCCC-cHHHHHH--------
Confidence            35667888999999999999999874 44677 8899999999999999999999999987432 3333321        


Q ss_pred             CChhHHHHHHHHHHh
Q 040027          180 GHTMIALNLFEEMAN  194 (595)
Q Consensus       180 g~~~~A~~~~~~~~~  194 (595)
                      +.+.++...|++...
T Consensus        75 ~~~~~a~~~~~~~~~   89 (99)
T 2kc7_A           75 KMVMDILNFYNKDMY   89 (99)
T ss_dssp             HHHHHHHHHHCCTTH
T ss_pred             HHHHHHHHHHHHHhc
Confidence            344555555554443

>1pc2_A Mitochondria fission protein; unknown function; NMR {Homo sapiens} SCOP: a.118.8.1

Probab=96.69  E-value=0.013  Score=46.43  Aligned_cols=84  Identities=14%  Similarity=-0.034  Sum_probs=69.2

Q ss_pred             ChhHHHHHHHHHHhCCCCCCHHHHHHHHHHHHhcC---CHhHHHHHHHHHHhcCCCC--CHhhHHHHHHHHHhcCChhHH
Q 040027          111 RVSLGFIAFGRILRSCFTPNAATFNSLIKGLHAES---RIMEAAALFTKLKAFGCEP--NVITYNTLINGLCRTGHTMIA  185 (595)
Q Consensus       111 ~~~~A~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g---~~~~A~~~~~~~~~~~~~~--~~~~~~~l~~~~~~~g~~~~A  185 (595)
                      ....+++.|.+..+.+ +++..+...+..++.+.+   ++++++.+++.+.+.+ .|  ....+..+..++.+.|++++|
T Consensus        13 ~l~~~~~~y~~e~~~~-~~~~~~~F~ya~~Lv~S~~~~~~~~gI~lLe~ll~~~-~p~~~rd~lY~LAv~~~kl~~Y~~A   90 (152)
T 1pc2_A           13 DLLKFEKKFQSEKAAG-SVSKSTQFEYAWCLVRSKYNDDIRKGIVLLEELLPKG-SKEEQRDYVFYLAVGNYRLKEYEKA   90 (152)
T ss_dssp             HHHHHHHHHHHHHHTT-CCCHHHHHHHHHHHHTCSSHHHHHHHHHHHHHHHHHS-CHHHHHHHHHHHHHHHHHTSCHHHH
T ss_pred             HHHHHHHHHHHHHccC-CCcHHHHHHHHHHHHcCCCHHHHHHHHHHHHHHHhcC-CccchHHHHHHHHHHHHHccCHHHH
Confidence            3455677777777766 478999999999999988   6679999999999875 23  467788888999999999999


Q ss_pred             HHHHHHHHhcC
Q 040027          186 LNLFEEMANGN  196 (595)
Q Consensus       186 ~~~~~~~~~~~  196 (595)
                      .+.++.+.+..
T Consensus        91 ~~y~~~lL~ie  101 (152)
T 1pc2_A           91 LKYVRGLLQTE  101 (152)
T ss_dssp             HHHHHHHHHHC
T ss_pred             HHHHHHHHhcC
Confidence            99999999975

>3mkq_A Coatomer beta'-subunit; beta-propeller, alpha-solenoid, transport protein; 2.50A {Saccharomyces cerevisiae} PDB: 2ynp_A

Probab=96.53  E-value=0.051  Score=57.98  Aligned_cols=41  Identities=17%  Similarity=-0.013  Sum_probs=23.7

Q ss_pred             HHHHHHHcCChhHHHHHHHHHHHCCCCCCH----HHHHHHHHHHHhcCcc
Q 040027          528 LIHGFIRINEPSKVNELLHKMKEKKVMPDA----SIVSIVVDLLVKNEIS  573 (595)
Q Consensus       528 l~~~~~~~g~~~~A~~~~~~~~~~~~~p~~----~~~~~l~~~~~~~g~~  573 (595)
                      .+..|.+.+++++|..+-++     ..|+.    .+...+...|...|+.
T Consensus       755 a~~~~~~~~~~~~A~~lA~~-----~~~~~~~i~~~~~~~~~~L~~~~~~  799 (814)
T 3mkq_A          755 AKDLLIKSQRFSEAAFLGST-----YGLGDNEVNDIVTKWKENLILNGKN  799 (814)
T ss_dssp             HHHHHHHTTCHHHHHHHHHH-----TTCCHHHHHHHHHHHHHHHHTTTCH
T ss_pred             HHHHHHHcCChHHHHHHHHH-----hCCChHHHHHHHHHHHHHHHhccch
Confidence            44445555666666655443     23555    6666666777777764

>2v5f_A Prolyl 4-hydroxylase subunit alpha-1; endoplasmic reticulum, metal-binding, oxidoreductase; 2.03A {Homo sapiens} PDB: 1tjc_A

Probab=96.51  E-value=0.027  Score=41.89  Aligned_cols=68  Identities=12%  Similarity=-0.027  Sum_probs=56.9

Q ss_pred             CCHHHHHHHHHHHHhcCChhHHHHHHHHHHhCC------CCCCHHHHHHHHHHHHhcCCHhHHHHHHHHHHhcC
Q 040027           94 PNLYTYNILINCFCKIGRVSLGFIAFGRILRSC------FTPNAATFNSLIKGLHAESRIMEAAALFTKLKAFG  161 (595)
Q Consensus        94 ~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~------~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~  161 (595)
                      .++.-+..++..+...|++..|...|+.+.+..      ..+...++..+..++.+.|+++.|+..++++.+..
T Consensus         3 Lsa~dc~~lG~~~~~~~~y~~A~~W~~~Al~~~~~~~~~~~~~~~i~~~L~~~~~~~g~~~~A~~~~~~al~l~   76 (104)
T 2v5f_A            3 LTAEDCFELGKVAYTEADYYHTELWMEQALRQLDEGEISTIDKVSVLDYLSYAVYQQGDLDKALLLTKKLLELD   76 (104)
T ss_dssp             CCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHTTCCCSSCHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC
T ss_pred             CCHHHHHHHHHHHHHccchHHHHHHHHHHHHhhhccCCCcccHHHHHHHHHHHHHHccCHHHHHHHHHHHHhcC
Confidence            466777889999999999999999999988752      13456778889999999999999999999998874

>3mkq_B Coatomer subunit alpha; beta-propeller, alpha-solenoid, transport protein; 2.50A {Saccharomyces cerevisiae}

Probab=96.46  E-value=0.15  Score=41.58  Aligned_cols=99  Identities=13%  Similarity=0.163  Sum_probs=55.0

Q ss_pred             HhcCCHHHHHHHHHHHHHcCCCcCHHHHHHHHHHHHhcCChHHHHHHHHhcccCCCCCCHHHHHHHHHHHHhcCChhHHH
Q 040027          428 CKNGYIIEAVELFRTLRILKCELDIQAYNCLIDGLCKSGRLKFAWELFCSLPHGVLVPNVVTYNIMIQGLCNDGQMDKAR  507 (595)
Q Consensus       428 ~~~g~~~~A~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~p~~~~~~~l~~~~~~~g~~~~A~  507 (595)
                      ...|+++.|.++.+.+      .+...|..|.......|+++-|.+.|.+..+         +..+.-.|...|+.+.-.
T Consensus        16 L~lg~l~~A~e~a~~l------~~~~~Wk~Lg~~AL~~gn~~lAe~cy~~~~D---------~~~L~~Ly~~tg~~e~L~   80 (177)
T 3mkq_B           16 LEYGNLDAALDEAKKL------NDSITWERLIQEALAQGNASLAEMIYQTQHS---------FDKLSFLYLVTGDVNKLS   80 (177)
T ss_dssp             HHTTCHHHHHHHHHHH------CCHHHHHHHHHHHHHTTCHHHHHHHHHHTTC---------HHHHHHHHHHHTCHHHHH
T ss_pred             HhcCCHHHHHHHHHHh------CCHHHHHHHHHHHHHcCChHHHHHHHHHhCC---------HHHHHHHHHHhCCHHHHH
Confidence            4566666666665544      2556666666666666777666666666654         233444455556665555


Q ss_pred             HHHHHHHHcCCCCCHHHHHHHHHHHHHcCChhHHHHHHHH
Q 040027          508 DLFLDMEENAAAPDVITFDMLIHGFIRINEPSKVNELLHK  547 (595)
Q Consensus       508 ~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~  547 (595)
                      ++-+.....|   +   ++....++...|+++++.+++.+
T Consensus        81 kla~iA~~~g---~---~n~af~~~l~lGdv~~~i~lL~~  114 (177)
T 3mkq_B           81 KMQNIAQTRE---D---FGSMLLNTFYNNSTKERSSIFAE  114 (177)
T ss_dssp             HHHHHHHHTT---C---HHHHHHHHHHHTCHHHHHHHHHH
T ss_pred             HHHHHHHHCc---c---HHHHHHHHHHcCCHHHHHHHHHH
Confidence            5544444433   1   23333344555666666655543

>2v5f_A Prolyl 4-hydroxylase subunit alpha-1; endoplasmic reticulum, metal-binding, oxidoreductase; 2.03A {Homo sapiens} PDB: 1tjc_A

Probab=96.39  E-value=0.037  Score=41.15  Aligned_cols=68  Identities=15%  Similarity=0.001  Sum_probs=57.8

Q ss_pred             CCHHHHHHHHHHHHhcCCHhHHHHHHHHHHhcC------CCCCHhhHHHHHHHHHhcCChhHHHHHHHHHHhcC
Q 040027          129 PNAATFNSLIKGLHAESRIMEAAALFTKLKAFG------CEPNVITYNTLINGLCRTGHTMIALNLFEEMANGN  196 (595)
Q Consensus       129 ~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~------~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~  196 (595)
                      .+..-+..+...+.+.|++..|+.+|+...+.-      ......++..+..++.+.|+++.|+..++++....
T Consensus         3 Lsa~dc~~lG~~~~~~~~y~~A~~W~~~Al~~~~~~~~~~~~~~~i~~~L~~~~~~~g~~~~A~~~~~~al~l~   76 (104)
T 2v5f_A            3 LTAEDCFELGKVAYTEADYYHTELWMEQALRQLDEGEISTIDKVSVLDYLSYAVYQQGDLDKALLLTKKLLELD   76 (104)
T ss_dssp             CCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHTTCCCSSCHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC
T ss_pred             CCHHHHHHHHHHHHHccchHHHHHHHHHHHHhhhccCCCcccHHHHHHHHHHHHHHccCHHHHHHHHHHHHhcC
Confidence            456777889999999999999999999987641      12356788999999999999999999999999865

>4h7y_A Dual specificity protein kinase TTK; mitotic checkpoint kinase, chromosome instability, cancer, tetratricopeptide repeat (TPR) motif; 1.80A {Homo sapiens} PDB: 4h7x_A

Probab=96.34  E-value=0.085  Score=41.17  Aligned_cols=101  Identities=12%  Similarity=0.040  Sum_probs=75.7

Q ss_pred             CCHHHHHHHHHHHHhcCCh------hHHHHHHHHHHhCCCCCCHH-HHHHHHHH------HHhcCCHhHHHHHHHHHHhc
Q 040027           94 PNLYTYNILINCFCKIGRV------SLGFIAFGRILRSCFTPNAA-TFNSLIKG------LHAESRIMEAAALFTKLKAF  160 (595)
Q Consensus        94 ~~~~~~~~l~~~~~~~g~~------~~A~~~~~~~~~~~~~~~~~-~~~~l~~~------~~~~g~~~~A~~~~~~~~~~  160 (595)
                      -|+.+|-..+...-+.|+.      ++.+.+|+++... ++|+.. .|...+..      +...++.++|.++|+.+...
T Consensus        11 ~~yd~W~~yl~llE~~g~p~~d~~l~rlrd~YerAia~-~Pp~k~~~wrrYI~LWIrYA~~~ei~D~d~aR~vy~~a~~~   89 (161)
T 4h7y_A           11 NNPEDWLSLLLKLEKNSVPLSDALLNKLIGRYSQAIEA-LPPDKYGQNESFARIQVRFAELKAIQEPDDARDYFQMARAN   89 (161)
T ss_dssp             CSHHHHHHHHHHHHHHTCSCCHHHHHHHHHHHHHHHHH-SCGGGGTTCHHHHHHHHHHHHHHHHHCGGGCHHHHHHHHHH
T ss_pred             CCHHHHHHHHHHHHHcCCCchhhHHHHHHHHHHHHHHc-CCccccccHHHHHHHHHHHHHHHHhcCHHHHHHHHHHHHHH
Confidence            4778888888888888888      8889999999876 355422 12221111      23458999999999999776


Q ss_pred             CCCCCHhhHHHHHHHHHhcCChhHHHHHHHHHHhcC
Q 040027          161 GCEPNVITYNTLINGLCRTGHTMIALNLFEEMANGN  196 (595)
Q Consensus       161 ~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~  196 (595)
                      + .--..+|......-.+.|+...|.+++......+
T Consensus        90 h-KkFAKiwi~~AqFEiRqgnl~kARkILg~AiG~~  124 (161)
T 4h7y_A           90 C-KKFAFVHISFAQFELSQGNVKKSKQLLQKAVERG  124 (161)
T ss_dssp             C-TTBHHHHHHHHHHHHHTTCHHHHHHHHHHHHHTT
T ss_pred             h-HHHHHHHHHHHHHHHHcccHHHHHHHHHHHhccC
Confidence            3 2237788888888889999999999999999876

>3u64_A Protein TP_0956; tetratrico peptide repeat, protein-prote interaction, syphilis, lipoprotein, transport protein; 2.30A {Treponema pallidum subsp} PDB: 4di3_A 4di4_A*

Probab=96.29  E-value=0.021  Score=50.55  Aligned_cols=80  Identities=14%  Similarity=0.038  Sum_probs=39.8

Q ss_pred             HHHHHHHHHHHHcCCCc--CHHHHHHHHHHHHhc-----CChHHHHHHHHhcccCCCCCC--HHHHHHHHHHHHhc-CCh
Q 040027          434 IEAVELFRTLRILKCEL--DIQAYNCLIDGLCKS-----GRLKFAWELFCSLPHGVLVPN--VVTYNIMIQGLCND-GQM  503 (595)
Q Consensus       434 ~~A~~~~~~~~~~~~~~--~~~~~~~l~~~~~~~-----g~~~~A~~~~~~~~~~~~~p~--~~~~~~l~~~~~~~-g~~  503 (595)
                      ..|...++++++.. +.  +...|..++..|...     |+.++|.+.|++.++  +.|+  ..++..+...++.. |+.
T Consensus       180 ~~A~a~lerAleLD-P~~~~GsA~~~LG~lY~~vPp~~gGd~ekA~~~ferAL~--LnP~~~id~~v~YA~~l~~~~gd~  256 (301)
T 3u64_A          180 HAAVMMLERACDLW-PSYQEGAVWNVLTKFYAAAPESFGGGMEKAHTAFEHLTR--YCSAHDPDHHITYADALCIPLNNR  256 (301)
T ss_dssp             HHHHHHHHHHHHHC-TTHHHHHHHHHHHHHHHHSCTTTTCCHHHHHHHHHHHHH--HCCTTCSHHHHHHHHHTTTTTTCH
T ss_pred             HHHHHHHHHHHHhC-CCcccCHHHHHHHHHHHhCCCccCCCHHHHHHHHHHHHH--hCCCCCchHHHHHHHHHHHhcCCH
Confidence            44555555555443 11  234555555555553     555555555555555  3442  44444445555442 555


Q ss_pred             hHHHHHHHHHHHc
Q 040027          504 DKARDLFLDMEEN  516 (595)
Q Consensus       504 ~~A~~~~~~~~~~  516 (595)
                      ++|.+.+++.+..
T Consensus       257 ~~a~~~L~kAL~a  269 (301)
T 3u64_A          257 AGFDEALDRALAI  269 (301)
T ss_dssp             HHHHHHHHHHHHC
T ss_pred             HHHHHHHHHHHcC
Confidence            5555555555554

>3mkq_A Coatomer beta'-subunit; beta-propeller, alpha-solenoid, transport protein; 2.50A {Saccharomyces cerevisiae} PDB: 2ynp_A

Probab=96.07  E-value=0.32  Score=51.77  Aligned_cols=27  Identities=11%  Similarity=0.146  Sum_probs=12.5

Q ss_pred             HHHHHHHHHHHHccCCHHHHHHHHHHH
Q 040027          382 VVTYNTLFLGLFEIHQVEHALKLFDEM  408 (595)
Q Consensus       382 ~~~~~~l~~~~~~~~~~~~a~~~~~~~  408 (595)
                      ...|..+...+.+.++++.|.+.|..+
T Consensus       681 ~~~W~~la~~al~~~~~~~A~~~y~~~  707 (814)
T 3mkq_A          681 EMKWRALGDASLQRFNFKLAIEAFTNA  707 (814)
T ss_dssp             HHHHHHHHHHHHHTTCHHHHHHHHHHH
T ss_pred             HhHHHHHHHHHHHcCCHHHHHHHHHHc
Confidence            344444444444444444444444433

>4h7y_A Dual specificity protein kinase TTK; mitotic checkpoint kinase, chromosome instability, cancer, tetratricopeptide repeat (TPR) motif; 1.80A {Homo sapiens} PDB: 4h7x_A

Probab=95.93  E-value=0.13  Score=40.11  Aligned_cols=104  Identities=14%  Similarity=0.065  Sum_probs=68.7

Q ss_pred             CCCHHHHHHHHHHHHhcCCH------hHHHHHHHHHHhcCCCCCHh-hHHHHHHH------HHhcCChhHHHHHHHHHHh
Q 040027          128 TPNAATFNSLIKGLHAESRI------MEAAALFTKLKAFGCEPNVI-TYNTLING------LCRTGHTMIALNLFEEMAN  194 (595)
Q Consensus       128 ~~~~~~~~~l~~~~~~~g~~------~~A~~~~~~~~~~~~~~~~~-~~~~l~~~------~~~~g~~~~A~~~~~~~~~  194 (595)
                      +.|..+|-..+...-+.|+.      ++.+++|++.... ++|+.. .|...+..      +...++.++|.++|+.+..
T Consensus        10 p~~yd~W~~yl~llE~~g~p~~d~~l~rlrd~YerAia~-~Pp~k~~~wrrYI~LWIrYA~~~ei~D~d~aR~vy~~a~~   88 (161)
T 4h7y_A           10 ANNPEDWLSLLLKLEKNSVPLSDALLNKLIGRYSQAIEA-LPPDKYGQNESFARIQVRFAELKAIQEPDDARDYFQMARA   88 (161)
T ss_dssp             CCSHHHHHHHHHHHHHHTCSCCHHHHHHHHHHHHHHHHH-SCGGGGTTCHHHHHHHHHHHHHHHHHCGGGCHHHHHHHHH
T ss_pred             CCCHHHHHHHHHHHHHcCCCchhhHHHHHHHHHHHHHHc-CCccccccHHHHHHHHHHHHHHHHhcCHHHHHHHHHHHHH
Confidence            56888888888888888888      8888999988875 455421 11111111      1234677777777777765


Q ss_pred             cCCCCCccccCcHHHHHHHHHHHHHcCCHhHHHHHHHHHhhCCCC
Q 040027          195 GNGEIGVVCKPNTVTYSTIIDGLCKEGFVDKAKALFLQMKDENIN  239 (595)
Q Consensus       195 ~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~  239 (595)
                      ..      -.. ...|......-.++|++..|.+++......+.+
T Consensus        89 ~h------KkF-AKiwi~~AqFEiRqgnl~kARkILg~AiG~~~k  126 (161)
T 4h7y_A           89 NC------KKF-AFVHISFAQFELSQGNVKKSKQLLQKAVERGAV  126 (161)
T ss_dssp             HC------TTB-HHHHHHHHHHHHHTTCHHHHHHHHHHHHHTTCB
T ss_pred             Hh------HHH-HHHHHHHHHHHHHcccHHHHHHHHHHHhccCCC
Confidence            43      122 666777777777777777777777777776544

>4ady_A RPN2, 26S proteasome regulatory subunit RPN2; protein binding, PC repeat; 2.70A {Saccharomyces cerevisiae} PDB: 4b4t_N

Probab=95.71  E-value=2.6  Score=44.47  Aligned_cols=314  Identities=10%  Similarity=-0.028  Sum_probs=170.1

Q ss_pred             HHHHhcCCHHHHHHHHHHHHHCCCCCCHh--hHHHHHHHHHhcCChHHHHHHHHHHHHCCC-------CCCHH--HHHHH
Q 040027          250 HGLCHANDWNEAKRLFIEMMDQGVQPSVV--TFNVIMDELCKNRKMDEASRLLDLMVQRGV-------RPNAC--TYNTL  318 (595)
Q Consensus       250 ~~~~~~~~~~~A~~~~~~~~~~~~~~~~~--~~~~l~~~~~~~g~~~~a~~~~~~~~~~~~-------~~~~~--~~~~l  318 (595)
                      -+....|+.++++.++...+..+...+..  .-..+.-.....|..+++..++...+...-       .+...  ....|
T Consensus       382 LGlIh~g~~~~gl~~L~~yL~~~~s~~~~ik~GAllaLGli~ag~~~~~~~lL~~~L~~~~~~~~~~~~~~ir~gAaLGL  461 (963)
T 4ady_A          382 LGVIHKGNLLEGKKVMAPYLPGSRASSRFIKGGSLYGLGLIYAGFGRDTTDYLKNIIVENSGTSGDEDVDVLLHGASLGI  461 (963)
T ss_dssp             HHHHTSSCTTTHHHHHTTTSTTSCCSCHHHHHHHHHHHHHHTTTTTHHHHHHHHHHHHHHSSCCSCHHHHHHHHHHHHHH
T ss_pred             hhhhccCchHHHHHHHHHhccccCCCcHHHHHHHHHHHHHhcCCCcHHHHHHHHHHHcCccccccccccHHHHHHHHHHH
Confidence            35667888888888877665421111222  222233345566666677777776665321       01111  12233


Q ss_pred             HHHHHhcCCHHHHHHHHHHHHhcCCCCCHH--HHHHHHHHHHhCCCHHHHHHHHHHHHHCCCCCCHHHHHH--HHHHHHc
Q 040027          319 MDGFCLMGKINRAEELFGSMESMGCKHDDV--SYNILINGYCKNKEVEEALSLYREMVSKGIKPTVVTYNT--LFLGLFE  394 (595)
Q Consensus       319 ~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~--~~~~l~~~~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~~--l~~~~~~  394 (595)
                      ..+|...++ +++.+.+..+.... .....  .-..+...+.-.|+.+....++..+.+..   +......  +.-++..
T Consensus       462 Gla~~GS~~-eev~e~L~~~L~dd-~~~~~~~AalALGli~vGTgn~~ai~~LL~~~~e~~---~e~vrR~aalgLGll~  536 (963)
T 4ady_A          462 GLAAMGSAN-IEVYEALKEVLYND-SATSGEAAALGMGLCMLGTGKPEAIHDMFTYSQETQ---HGNITRGLAVGLALIN  536 (963)
T ss_dssp             HHHSTTCCC-HHHHHHHHHHHHTC-CHHHHHHHHHHHHHHHTTCCCHHHHHHHHHHHHHCS---CHHHHHHHHHHHHHHT
T ss_pred             HHHhcCCCC-HHHHHHHHHHHhcC-CHHHHHHHHHHHhhhhcccCCHHHHHHHHHHHhccC---cHHHHHHHHHHHHhhh
Confidence            333344444 45556666655432 11111  12233444556788887778887777642   2233333  3334557


Q ss_pred             cCCHHHHHHHHHHHHHCCCCCCHHHH--HHHHHHHHhcCCHHHHHHHHHHHHHcCCCcCHHHHHHHHHHHHhcCChHHHH
Q 040027          395 IHQVEHALKLFDEMQRDGVAADTRTY--TTFIDGLCKNGYIIEAVELFRTLRILKCELDIQAYNCLIDGLCKSGRLKFAW  472 (595)
Q Consensus       395 ~~~~~~a~~~~~~~~~~~~~~~~~~~--~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~  472 (595)
                      .|+.+.+..+.+.+.... .|....-  ..+.-+|+..|+.....+++..+.... ..+..-...+.-++...|+.+.+.
T Consensus       537 ~g~~e~~~~li~~L~~~~-dp~vRygaa~alglAyaGTGn~~aIq~LL~~~~~d~-~d~VRraAViaLGlI~~g~~e~v~  614 (963)
T 4ady_A          537 YGRQELADDLITKMLASD-ESLLRYGGAFTIALAYAGTGNNSAVKRLLHVAVSDS-NDDVRRAAVIALGFVLLRDYTTVP  614 (963)
T ss_dssp             TTCGGGGHHHHHHHHHCS-CHHHHHHHHHHHHHHTTTSCCHHHHHHHHHHHHHCS-CHHHHHHHHHHHHHHTSSSCSSHH
T ss_pred             CCChHHHHHHHHHHHhCC-CHHHHHHHHHHHHHHhcCCCCHHHHHHHHHHhccCC-cHHHHHHHHHHHHhhccCCHHHHH
Confidence            889899988888887641 2222211  233446778899888888998888632 223333333334455578888888


Q ss_pred             HHHHhcccCCCCCCHHHHHHHHHHHHhcCCh-hHHHHHHHHHHHcCCCCCHHHHHHHHHHHHH--cCChh----HHHHHH
Q 040027          473 ELFCSLPHGVLVPNVVTYNIMIQGLCNDGQM-DKARDLFLDMEENAAAPDVITFDMLIHGFIR--INEPS----KVNELL  545 (595)
Q Consensus       473 ~~~~~~~~~~~~p~~~~~~~l~~~~~~~g~~-~~A~~~~~~~~~~~~~~~~~~~~~l~~~~~~--~g~~~----~A~~~~  545 (595)
                      ++++.+.+.+ .|....-..+..+....|.. .++++.+..+...   ++..+-...+.++..  .|..+    +..++.
T Consensus       615 rlv~~L~~~~-d~~VR~gAalALGli~aGn~~~~aid~L~~L~~D---~d~~Vrq~Ai~ALG~Ig~gtnna~~~rva~~l  690 (963)
T 4ady_A          615 RIVQLLSKSH-NAHVRCGTAFALGIACAGKGLQSAIDVLDPLTKD---PVDFVRQAAMIALSMILIQQTEKLNPQVADIN  690 (963)
T ss_dssp             HHTTTGGGCS-CHHHHHHHHHHHHHHTSSSCCHHHHHHHHHHHTC---SSHHHHHHHHHHHHHHSTTCCTTTCTTHHHHH
T ss_pred             HHHHHHHhcC-CHHHHHHHHHHHHHhccCCCcHHHHHHHHHHccC---CCHHHHHHHHHHHHHHhcCCccccchHHHHHH
Confidence            8888777642 44444444444555555554 5788888888753   454444333333333  33222    344444


Q ss_pred             HHHHHC----CCCCCHHHHHHHHHHHHhcCccc
Q 040027          546 HKMKEK----KVMPDASIVSIVVDLLVKNEISL  574 (595)
Q Consensus       546 ~~~~~~----~~~p~~~~~~~l~~~~~~~g~~~  574 (595)
                      +.+.+.    .-.++...-..+...+..+|.-.
T Consensus       691 ~~L~~~~~dk~~d~~~~fga~iAqGll~aG~~n  723 (963)
T 4ady_A          691 KNFLSVITNKHQEGLAKFGACVAQGIMNAGGRN  723 (963)
T ss_dssp             HHHHHHHHCSSSCHHHHHHHHHHHHHHTTGGGT
T ss_pred             HHHHHHHhcccccHHHHHHHHHHHHHHhcCCCc
Confidence            443321    22344566667777777777654

>1nzn_A CGI-135 protein, fission protein FIS1P; TPR, unknown function; 2.00A {Homo sapiens} SCOP: a.118.8.1 PDB: 1iyg_A

Probab=95.68  E-value=0.046  Score=41.55  Aligned_cols=65  Identities=14%  Similarity=-0.000  Sum_probs=29.5

Q ss_pred             CCHHHHHHHHHHHHhcCChhH---HHHHHHHHHHcCCCC--CHHHHHHHHHHHHHcCChhHHHHHHHHHHH
Q 040027          485 PNVVTYNIMIQGLCNDGQMDK---ARDLFLDMEENAAAP--DVITFDMLIHGFIRINEPSKVNELLHKMKE  550 (595)
Q Consensus       485 p~~~~~~~l~~~~~~~g~~~~---A~~~~~~~~~~~~~~--~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~  550 (595)
                      |+..+-..+++++.+..+...   ++.+++.....+ .|  .......+.-++.+.|+|++|.++++.+++
T Consensus        33 ~s~~~~F~yAw~Lv~S~~~~d~~~GI~lLe~l~~~~-~p~~~Rd~lY~LAvg~yklg~Y~~A~~~~~~lL~  102 (126)
T 1nzn_A           33 VSKSTQFEYAWCLVRTRYNDDIRKGIVLLEELLPKG-SKEEQRDYVFYLAVGNYRLKEYEKALKYVRGLLQ  102 (126)
T ss_dssp             CCHHHHHHHHHHHTTSSSHHHHHHHHHHHHHHTTTS-CHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHH
T ss_pred             CcHHHHHHHHHHHHcCCCHHHHHHHHHHHHHHHhcC-CcchHHHHHHHHHHHHHHhhhHHHHHHHHHHHHH
Confidence            344444444445544443333   444444444432 12  223334444455555555555555555554

>3lvg_A Clathrin heavy chain 1; SELF assembly, coated PIT, cytoplasmic vesicle, membrane, Ca structural protein; 7.94A {Bos taurus} PDB: 3lvh_A

Probab=95.47  E-value=0.0076  Score=57.16  Aligned_cols=386  Identities=10%  Similarity=0.043  Sum_probs=220.1

Q ss_pred             CCCChHHHHHHHHHHHHhCCCCCCHhhHHHHHHHHHcCCCchh-HHhhCCCCCCHHHHHHHHHHHHhcCChhHHHHHHHH
Q 040027           43 NVITPNEAFCIFDYMLRMHPSPPPVSSFNILLASLAKNKHYDT-RLNATGLFPNLYTYNILINCFCKIGRVSLGFIAFGR  121 (595)
Q Consensus        43 ~~~~~~~A~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~-~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~  121 (595)
                      +.|.+++-++++.-+.+. ..  ++..=+.|+-+|++.++..+ +-...|  ||..-...++.-|...|.++.|.-+|..
T Consensus        95 ~~~~~edLv~yL~MaRk~-~k--e~~IDteLi~ayAk~~rL~elEefl~~--~N~A~iq~VGDrcf~e~lYeAAKilys~  169 (624)
T 3lvg_A           95 TSGNWEELVKYLQMARKK-AR--ESYVETELIFALAKTNRLAELEEFING--PNNAHIQQVGDRCYDEKMYDAAKLLYNN  169 (624)
T ss_dssp             TSSCCTTHHHHHHTTSTT-CC--STTTTHHHHHHHHTSCSSSTTTSTTSC--CSSSCTHHHHHHHHHSCCSTTSSTTGGG
T ss_pred             hCCCHHHHHHHHHHHHHH-hc--ccccHHHHHHHHHhhCcHHHHHHHHcC--CCcccHHHHHHHHHHccCHHHHHHHHHh
Confidence            456777776666555443 22  56667788889999998876 222222  5555556677778888888877777665


Q ss_pred             HHhCC--------------------CCCCHHHHHHHHHHHHhcCCHhHHHHHHHHHHhcCCCCCHhhHHHHHHHHHhcCC
Q 040027          122 ILRSC--------------------FTPNAATFNSLIKGLHAESRIMEAAALFTKLKAFGCEPNVITYNTLINGLCRTGH  181 (595)
Q Consensus       122 ~~~~~--------------------~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~  181 (595)
                      +..-.                    -..++.+|..+-.+|...+.+.-|.-.--.++-.     +.-...++..|...|.
T Consensus       170 isN~akLAstLV~L~~yq~AVdaArKAns~ktWKeV~~ACvd~~EfrLAqicGLniIvh-----adeL~elv~~YE~~G~  244 (624)
T 3lvg_A          170 VSNFGRLASTLVHLGEYQAAVDGARKANSTRTWKEVCFACVDGKEFRLAQMCGLHIVVH-----ADELEELINYYQDRGY  244 (624)
T ss_dssp             SCCCTTTSSSSSSCSGGGSSTTTTTTCCSSCSHHHHTHHHHHSCTTTTTTHHHHHHHCC-----SSCCSGGGSSSSTTCC
T ss_pred             CccHHHHHHHHHHHHHHHHHHHHHHhcCChhHHHHHHHHHhCchHHHHHHHhcchhccc-----HHHHHHHHHHHHhCCC
Confidence            32210                    1346778999989999998888777655555432     2223456777888999


Q ss_pred             hhHHHHHHHHHHhcCCCCCccccCcHHHHHHHHHHHHHcCCHhHHHHHHHHHhhC-CCCC------CHhHHHHHHHHHHh
Q 040027          182 TMIALNLFEEMANGNGEIGVVCKPNTVTYSTIIDGLCKEGFVDKAKALFLQMKDE-NINP------DVVTYNSLIHGLCH  254 (595)
Q Consensus       182 ~~~A~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~-~~~~------~~~~~~~ll~~~~~  254 (595)
                      +++-+.+++......       ......|+-|.-.|++- ++++..+-++..-.+ +++-      ....|.-+.-.|.+
T Consensus       245 f~ELIsLlEaglglE-------rAHmGmFTELaILYsKY-~PeKlmEHlklf~sriNipKviracE~ahLW~ElvfLY~~  316 (624)
T 3lvg_A          245 FEELITMLEAALGLE-------RAHMGMFTELAILYSKF-KPQKMREHLELFWSRVNIPKVLRAAEQAHLWAELVFLYDK  316 (624)
T ss_dssp             CTTSTTTHHHHTTST-------TCCHHHHHHHHHHHHSS-CTTHHHHHHTTSSSSSCCTTTHHHHTTTTCHHHHHHHHHH
T ss_pred             HHHHHHHHHHHhCCC-------chhHHHHHHHHHHHHhc-CHHHHHHHHHHHHHhccHHHHHHHHHHHhhHHHHHHHHhc
Confidence            999999999988654       35677888888888776 455555544433222 2221      24457778888888


Q ss_pred             cCCHHHHHHHHH-------------HHHHCCCCCCHhhHHHHHHHHHhcCChHHHHHHHHHHHHCCCCCCHHHHHHHHHH
Q 040027          255 ANDWNEAKRLFI-------------EMMDQGVQPSVVTFNVIMDELCKNRKMDEASRLLDLMVQRGVRPNACTYNTLMDG  321 (595)
Q Consensus       255 ~~~~~~A~~~~~-------------~~~~~~~~~~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~  321 (595)
                      -.+++.|....-             +++.  -..+...|...+..|.... +...-+++.-+..+ +.++     ..++.
T Consensus       317 ydE~DnA~ltMi~h~~~Aw~h~~Fkdii~--KVaN~EiyYKAi~FYL~e~-P~lL~DLL~vL~pr-lDh~-----RvV~~  387 (624)
T 3lvg_A          317 YEEYDNAIITMMNHPTDAWKEGQFKDIIT--KVANVELYYRAIQFYLEFK-PLLLNDLLMVLSPR-LDHT-----RAVNY  387 (624)
T ss_dssp             HTCHHHHHHTTTSCHHHHCCGGGGTTTGG--GCSCSHHHHHHHHHHTTSC-CTTSHHHHHHHCTT-CCST-----TTHHH
T ss_pred             chhHHHHHHHHHhCChhhccHHHHHHHHH--HcchHHHHHHHHHHHHHhC-hHHHHHHHHhcccc-CChH-----HHHHH
Confidence            888887654321             1111  1234555555555554432 22222222222211 1111     12344


Q ss_pred             HHhcCCHHHHHHHHHHHHhcCCCCCHHHHHHHHHHHHhCCCHHHH------------HHHHHHHHHCCCCCCHHHHHH-H
Q 040027          322 FCLMGKINRAEELFGSMESMGCKHDDVSYNILINGYCKNKEVEEA------------LSLYREMVSKGIKPTVVTYNT-L  388 (595)
Q Consensus       322 ~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~A------------~~~~~~~~~~~~~~~~~~~~~-l  388 (595)
                      +.+.|++.-....+......   .+...-.++-..|....+++.-            +.+-+++.+.    ...-+.. .
T Consensus       388 ~~k~~~LpLIkpYL~~Vq~~---N~~aVNeAln~L~IEEEDy~~LR~SId~ydNFD~i~LA~rLEkH----eL~eFRrIA  460 (624)
T 3lvg_A          388 FSKVKQLPLVKPYLRSVQNH---NNKSVNESLNNLFITEEDYQALRTSIDAYDNFDNISLAQRLEKH----ELIEFRRIA  460 (624)
T ss_dssp             HHTTTCGGGGTGGGTSCCCS---CCHHHHHHHHHHHHHTTCCHHHHHTTSSCCCSCTTHHHHHHHTC----SSHHHHHHH
T ss_pred             HHhcCCchhhHHHHHHHHHh---hHHHHHHHHHHHHhhhhhHHHHHHHHHHhccccHHHHHHHHhhC----chHHHHHHH
Confidence            44555555444444333322   2333344444555555554432            2333444443    2233333 3


Q ss_pred             HHHHHccCCHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCcCHHHHHHHHHHHHhcCCh
Q 040027          389 FLGLFEIHQVEHALKLFDEMQRDGVAADTRTYTTFIDGLCKNGYIIEAVELFRTLRILKCELDIQAYNCLIDGLCKSGRL  468 (595)
Q Consensus       389 ~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~  468 (595)
                      ...|.+.++|++++.+.++         ...|...|......|+.+-|.++++-..+.|   +...|.+.+..|...=++
T Consensus       461 A~LYkkn~rw~qsi~l~Kk---------DklykDAietAa~S~~~elaeeLL~yFv~~g---~~EcF~a~LytCYdLlrp  528 (624)
T 3lvg_A          461 AYLFKGNNRWKQSVELCKK---------DSLYKDAMQYASESKDTELAEELLQWFLQEE---KRECFGACLFTCYDLLRP  528 (624)
T ss_dssp             HHHHHTTCHHHHHSSCSST---------TCCTTGGGTTTTTCCCTTHHHHHHHHHHHHC---STHHHHHHHHHTSSSSSC
T ss_pred             HHHHHhcccHHHHHHHHHh---------cccHHHHHHHHHHcCCHHHHHHHHHHHHHcC---chHHHHHHHHHHhhccCh
Confidence            3456667777777654321         1223334444556777777777777777655   455666666677666777


Q ss_pred             HHHHHH
Q 040027          469 KFAWEL  474 (595)
Q Consensus       469 ~~A~~~  474 (595)
                      +-++++
T Consensus       529 DvVlEl  534 (624)
T 3lvg_A          529 DVVLET  534 (624)
T ss_dssp             HHHHHH
T ss_pred             HHHHHH
Confidence            777666

>1nzn_A CGI-135 protein, fission protein FIS1P; TPR, unknown function; 2.00A {Homo sapiens} SCOP: a.118.8.1 PDB: 1iyg_A

Probab=95.34  E-value=0.14  Score=39.00  Aligned_cols=92  Identities=13%  Similarity=-0.039  Sum_probs=70.2

Q ss_pred             HHHHhcCChhHHHHHHHHHHhCCCCCCHHHHHHHHHHHHhcCCHhH---HHHHHHHHHhcCCC-CCHhhHHHHHHHHHhc
Q 040027          104 NCFCKIGRVSLGFIAFGRILRSCFTPNAATFNSLIKGLHAESRIME---AAALFTKLKAFGCE-PNVITYNTLINGLCRT  179 (595)
Q Consensus       104 ~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~---A~~~~~~~~~~~~~-~~~~~~~~l~~~~~~~  179 (595)
                      ..-........+...|.+....| .++..+-..+..++.+.++...   ++.+++.+...+.+ ........|..++.+.
T Consensus         9 ~~~~~~~~l~~~~~~y~~e~~~~-~~s~~~~F~yAw~Lv~S~~~~d~~~GI~lLe~l~~~~~p~~~Rd~lY~LAvg~ykl   87 (126)
T 1nzn_A            9 NELVSVEDLLKFEKKFQSEKAAG-SVSKSTQFEYAWCLVRTRYNDDIRKGIVLLEELLPKGSKEEQRDYVFYLAVGNYRL   87 (126)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHS-CCCHHHHHHHHHHHTTSSSHHHHHHHHHHHHHHTTTSCHHHHHHHHHHHHHHHHHT
T ss_pred             hccCCHHHHHHHHHHHHHHhccC-CCcHHHHHHHHHHHHcCCCHHHHHHHHHHHHHHHhcCCcchHHHHHHHHHHHHHHh
Confidence            33334445566677777776655 4788888889999998877766   89999998886411 2455667788899999


Q ss_pred             CChhHHHHHHHHHHhcC
Q 040027          180 GHTMIALNLFEEMANGN  196 (595)
Q Consensus       180 g~~~~A~~~~~~~~~~~  196 (595)
                      |++++|.+.++.+++..
T Consensus        88 g~Y~~A~~~~~~lL~~e  104 (126)
T 1nzn_A           88 KEYEKALKYVRGLLQTE  104 (126)
T ss_dssp             TCHHHHHHHHHHHHHHC
T ss_pred             hhHHHHHHHHHHHHHhC
Confidence            99999999999999975

>1wy6_A Hypothetical protein ST1625; helical repeat protein, structural genomics, unknown function; 2.20A {Sulfolobus tokodaii} SCOP: a.118.20.1

Probab=94.58  E-value=1.1  Score=34.15  Aligned_cols=63  Identities=16%  Similarity=0.191  Sum_probs=31.9

Q ss_pred             HHHHHHHHHHhcCChhHHHHHHHHHHHcCCCCCHHHHHHHHHHHHHcCChhHHHHHHHHHHHCC
Q 040027          489 TYNIMIQGLCNDGQMDKARDLFLDMEENAAAPDVITFDMLIHGFIRINEPSKVNELLHKMKEKK  552 (595)
Q Consensus       489 ~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~  552 (595)
                      .+...+......|+.++-.+++..++.. .+|++.....+..+|.+.|+..+|.++++++-+.|
T Consensus        93 ~vd~ALd~lv~~~KkDqLdki~~~~l~n-~~~~~~~l~kia~Ay~Klg~~r~a~eLl~~AC~kG  155 (172)
T 1wy6_A           93 HVNKALDILVIQGKRDKLEEIGREILKN-NEVSASILVAIANALRRVGDERDATTLLIEACKKG  155 (172)
T ss_dssp             HHHHHHHHHHHTTCHHHHHHHHHHHC---CCSCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHTT
T ss_pred             HHHHHHHHHHHhccHhHHHHHHHHHhcc-CCCChHHHHHHHHHHHHhcchhhHHHHHHHHHHhh
Confidence            3344444455555555555555554332 24455555555555555555555555555555555

>2ff4_A Probable regulatory protein EMBR; winged-helix, tetratricopeptide repeat, beta-sandwich, trans; HET: DNA TPO; 1.90A {Mycobacterium tuberculosis} SCOP: a.4.6.1 a.118.8.3 b.26.1.2 PDB: 2fez_A*

Probab=94.48  E-value=0.25  Score=47.02  Aligned_cols=79  Identities=9%  Similarity=0.071  Sum_probs=55.7

Q ss_pred             HHHHHHHHHhcCChhHHHHHHHHHHHcCCCCCHHHHHHHHHHHHHcCChhHHHHHHHHHH-----HCCCCCCHHHHHHHH
Q 040027          490 YNIMIQGLCNDGQMDKARDLFLDMEENAAAPDVITFDMLIHGFIRINEPSKVNELLHKMK-----EKKVMPDASIVSIVV  564 (595)
Q Consensus       490 ~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~-----~~~~~p~~~~~~~l~  564 (595)
                      ...++.++...|++++|+..+..+.... +-+...+..++.+|.+.|+..+|++.|+++.     +.|+.|++.+-...-
T Consensus       174 ~~~~~~~~l~~g~~~~a~~~l~~~~~~~-P~~E~~~~~lm~al~~~Gr~~~Al~~y~~~r~~L~~eLG~~P~~~l~~l~~  252 (388)
T 2ff4_A          174 HTAKAEAEIACGRASAVIAELEALTFEH-PYREPLWTQLITAYYLSDRQSDALGAYRRVKTTLADDLGIDPGPTLRALNE  252 (388)
T ss_dssp             HHHHHHHHHHTTCHHHHHHHHHHHHHHS-TTCHHHHHHHHHHHHTTTCHHHHHHHHHHHHHHHHHHHSCCCCHHHHHHHH
T ss_pred             HHHHHHHHHHCCCHHHHHHHHHHHHHhC-CCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHH
Confidence            3445566677788888877777777664 5567777778888888888888877777765     347778777766665


Q ss_pred             HHHHh
Q 040027          565 DLLVK  569 (595)
Q Consensus       565 ~~~~~  569 (595)
                      .++..
T Consensus       253 ~il~~  257 (388)
T 2ff4_A          253 RILRQ  257 (388)
T ss_dssp             HHHTT
T ss_pred             HHHcC
Confidence            55544

>1y8m_A FIS1; mitochondria, unknown function; NMR {Saccharomyces cerevisiae} SCOP: a.118.8.1

Probab=93.21  E-value=1.5  Score=33.92  Aligned_cols=71  Identities=13%  Similarity=0.120  Sum_probs=50.2

Q ss_pred             CCCHHHHHHHHHHHHhcCCh---hHHHHHHHHHHHcCCCCCHHHHHHHHHHHHHcCChhHHHHHHHHHHHCCCCCC
Q 040027          484 VPNVVTYNIMIQGLCNDGQM---DKARDLFLDMEENAAAPDVITFDMLIHGFIRINEPSKVNELLHKMKEKKVMPD  556 (595)
Q Consensus       484 ~p~~~~~~~l~~~~~~~g~~---~~A~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~p~  556 (595)
                      .|+..+-..+.+++.+..+.   .+++.+++.....+....-.....+.-++.+.|+|++|+++.+.+++  +.|+
T Consensus        36 ~vs~~t~F~YAw~Lv~S~~~~di~~GI~LLe~l~~~~~~~~RdcLYyLAvg~ykl~~Y~~Ar~y~d~lL~--~eP~  109 (144)
T 1y8m_A           36 TATIQSRFNYAWGLIKSTDVNDERLGVKILTDIYKEAESRRRECLYYLTIGCYKLGEYSMAKRYVDTLFE--HERN  109 (144)
T ss_dssp             TSCHHHHHHHHHHHHHSSSHHHHHHHHHHHHHHHHHCCSTHHHHHHHHHHHHHTTTCHHHHHHHHHHHHH--TCCC
T ss_pred             CCcHHHHHHHHHHHHcCCCHHHHHHHHHHHHHHHhcCccchhHHHHHHHHHHHHhhhHHHHHHHHHHHHh--cCCC
Confidence            46677767777777776544   46777888877754222345566677788888888888888888887  4575

>4ady_A RPN2, 26S proteasome regulatory subunit RPN2; protein binding, PC repeat; 2.70A {Saccharomyces cerevisiae} PDB: 4b4t_N

Probab=93.18  E-value=10  Score=40.17  Aligned_cols=274  Identities=9%  Similarity=-0.000  Sum_probs=146.7

Q ss_pred             HHHhcCChHHHHHHHHHHHHCCCCCCH--HHHHHHHHHHHhcCCHHHHHHHHHHHHhcCC-------CCCHHHHHHHHHH
Q 040027          286 ELCKNRKMDEASRLLDLMVQRGVRPNA--CTYNTLMDGFCLMGKINRAEELFGSMESMGC-------KHDDVSYNILING  356 (595)
Q Consensus       286 ~~~~~g~~~~a~~~~~~~~~~~~~~~~--~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~-------~~~~~~~~~l~~~  356 (595)
                      +....|+.++++.+++.....+...+.  ..-..+.-.....|..+++..++.......-       .+....-..+.-+
T Consensus       383 GlIh~g~~~~gl~~L~~yL~~~~s~~~~ik~GAllaLGli~ag~~~~~~~lL~~~L~~~~~~~~~~~~~~ir~gAaLGLG  462 (963)
T 4ady_A          383 GVIHKGNLLEGKKVMAPYLPGSRASSRFIKGGSLYGLGLIYAGFGRDTTDYLKNIIVENSGTSGDEDVDVLLHGASLGIG  462 (963)
T ss_dssp             HHHTSSCTTTHHHHHTTTSTTSCCSCHHHHHHHHHHHHHHTTTTTHHHHHHHHHHHHHHSSCCSCHHHHHHHHHHHHHHH
T ss_pred             hhhccCchHHHHHHHHHhccccCCCcHHHHHHHHHHHHHhcCCCcHHHHHHHHHHHcCccccccccccHHHHHHHHHHHH
Confidence            345667777777777665542101122  2222333344555655667777776654311       0111112222223


Q ss_pred             HHhCCC-HHHHHHHHHHHHHCCCCCCHH----HHHHHHHHHHccCCHHHHHHHHHHHHHCCCCCCHHHHHHHHHH--HHh
Q 040027          357 YCKNKE-VEEALSLYREMVSKGIKPTVV----TYNTLFLGLFEIHQVEHALKLFDEMQRDGVAADTRTYTTFIDG--LCK  429 (595)
Q Consensus       357 ~~~~~~-~~~A~~~~~~~~~~~~~~~~~----~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~--~~~  429 (595)
                      ..-.|. -+++.+.+..++...   +..    .-..+...+...|+.+....++..+.+.   .+..+...+..+  +..
T Consensus       463 la~~GS~~eev~e~L~~~L~dd---~~~~~~~AalALGli~vGTgn~~ai~~LL~~~~e~---~~e~vrR~aalgLGll~  536 (963)
T 4ady_A          463 LAAMGSANIEVYEALKEVLYND---SATSGEAAALGMGLCMLGTGKPEAIHDMFTYSQET---QHGNITRGLAVGLALIN  536 (963)
T ss_dssp             HHSTTCCCHHHHHHHHHHHHTC---CHHHHHHHHHHHHHHHTTCCCHHHHHHHHHHHHHC---SCHHHHHHHHHHHHHHT
T ss_pred             HHhcCCCCHHHHHHHHHHHhcC---CHHHHHHHHHHHhhhhcccCCHHHHHHHHHHHhcc---CcHHHHHHHHHHHHhhh
Confidence            333332 245666666666532   221    1122333455678888888888777654   233444444433  446


Q ss_pred             cCCHHHHHHHHHHHHHcCCCcCHHHH--HHHHHHHHhcCChHHHHHHHHhcccCCCCCCHHHHHHHHHHHHhcCChhHHH
Q 040027          430 NGYIIEAVELFRTLRILKCELDIQAY--NCLIDGLCKSGRLKFAWELFCSLPHGVLVPNVVTYNIMIQGLCNDGQMDKAR  507 (595)
Q Consensus       430 ~g~~~~A~~~~~~~~~~~~~~~~~~~--~~l~~~~~~~g~~~~A~~~~~~~~~~~~~p~~~~~~~l~~~~~~~g~~~~A~  507 (595)
                      .|+.+.+..+++.+.... .|....-  ..+.-+|+..|+.....+++..+... ...++.-...+..++...|+.+.+.
T Consensus       537 ~g~~e~~~~li~~L~~~~-dp~vRygaa~alglAyaGTGn~~aIq~LL~~~~~d-~~d~VRraAViaLGlI~~g~~e~v~  614 (963)
T 4ady_A          537 YGRQELADDLITKMLASD-ESLLRYGGAFTIALAYAGTGNNSAVKRLLHVAVSD-SNDDVRRAAVIALGFVLLRDYTTVP  614 (963)
T ss_dssp             TTCGGGGHHHHHHHHHCS-CHHHHHHHHHHHHHHTTTSCCHHHHHHHHHHHHHC-SCHHHHHHHHHHHHHHTSSSCSSHH
T ss_pred             CCChHHHHHHHHHHHhCC-CHHHHHHHHHHHHHHhcCCCCHHHHHHHHHHhccC-CcHHHHHHHHHHHHhhccCCHHHHH
Confidence            788888888888877632 2222222  23445667888888777788888763 1223333344445555677777777


Q ss_pred             HHHHHHHHcCCCCCHHHHHHHHHHHHHcCCh-hHHHHHHHHHHHCCCCCCHHHHHHHHHHHHhcC
Q 040027          508 DLFLDMEENAAAPDVITFDMLIHGFIRINEP-SKVNELLHKMKEKKVMPDASIVSIVVDLLVKNE  571 (595)
Q Consensus       508 ~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~-~~A~~~~~~~~~~~~~p~~~~~~~l~~~~~~~g  571 (595)
                      +++..+.+.+ .|....-..+.-+....|+. .++...+..+..   .+|..+-..-+.++..-|
T Consensus       615 rlv~~L~~~~-d~~VR~gAalALGli~aGn~~~~aid~L~~L~~---D~d~~Vrq~Ai~ALG~Ig  675 (963)
T 4ady_A          615 RIVQLLSKSH-NAHVRCGTAFALGIACAGKGLQSAIDVLDPLTK---DPVDFVRQAAMIALSMIL  675 (963)
T ss_dssp             HHTTTGGGCS-CHHHHHHHHHHHHHHTSSSCCHHHHHHHHHHHT---CSSHHHHHHHHHHHHHHS
T ss_pred             HHHHHHHhcC-CHHHHHHHHHHHHHhccCCCcHHHHHHHHHHcc---CCCHHHHHHHHHHHHHHh
Confidence            7777666543 33332223333333444544 678888888873   567766665555555533

>3o48_A Mitochondria fission 1 protein; tetratricopeptide repeat fold, TPR, scaffold, peroxisome, membrane fission, protein binding; 1.75A {Saccharomyces cerevisiae} PDB: 2pqr_A 2pqn_A 3uux_A

Probab=93.14  E-value=0.55  Score=35.83  Aligned_cols=71  Identities=13%  Similarity=0.120  Sum_probs=45.8

Q ss_pred             CCCHHHHHHHHHHHHhcCCh---hHHHHHHHHHHHcCCCCCHHHHHHHHHHHHHcCChhHHHHHHHHHHHCCCCCC
Q 040027          484 VPNVVTYNIMIQGLCNDGQM---DKARDLFLDMEENAAAPDVITFDMLIHGFIRINEPSKVNELLHKMKEKKVMPD  556 (595)
Q Consensus       484 ~p~~~~~~~l~~~~~~~g~~---~~A~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~p~  556 (595)
                      .|+..+--.+++++.+..+.   .+++.++++....+.......+..+.-++.+.|++++|+++.+.+++  +.|+
T Consensus        37 ~vs~qt~F~yAw~Lv~S~~~~d~~~GI~LLe~l~~~~~~~~Rd~LYyLAvg~yklgdY~~Ar~y~d~lL~--~eP~  110 (134)
T 3o48_A           37 TATIQSRFNYAWGLIKSTDVNDERLGVKILTDIYKEAESRRRECLYYLTIGCYKLGEYSMAKRYVDTLFE--HERN  110 (134)
T ss_dssp             GSCHHHHHHHHHHHHHSSCHHHHHHHHHHHHHHHHHCGGGHHHHHHHHHHHHHHHTCHHHHHHHHHHHHT--TCTT
T ss_pred             CCChhhHHHHHHHHHcCCCHHHHHHHHHHHHHHHhcCcchhHHHHHHHHHHHHHhhhHHHHHHHHHHHHh--hCCC
Confidence            45666666666777665543   45677777777654112345566677777788888888888887776  4564

>2ff4_A Probable regulatory protein EMBR; winged-helix, tetratricopeptide repeat, beta-sandwich, trans; HET: DNA TPO; 1.90A {Mycobacterium tuberculosis} SCOP: a.4.6.1 a.118.8.3 b.26.1.2 PDB: 2fez_A*

Probab=92.96  E-value=1.6  Score=41.47  Aligned_cols=73  Identities=14%  Similarity=0.151  Sum_probs=60.9

Q ss_pred             HHHHHHHHHHhcCChhHHHHHHHHHHhCCCCCCHHHHHHHHHHHHhcCCHhHHHHHHHHHHh-----cCCCCCHhhHHH
Q 040027           98 TYNILINCFCKIGRVSLGFIAFGRILRSCFTPNAATFNSLIKGLHAESRIMEAAALFTKLKA-----FGCEPNVITYNT  171 (595)
Q Consensus        98 ~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~-----~~~~~~~~~~~~  171 (595)
                      ....++..+...|++.+++..+..+.... +.+...|..++.++.+.|+..+|++.|+++.+     .|++|+..+-..
T Consensus       173 a~~~~~~~~l~~g~~~~a~~~l~~~~~~~-P~~E~~~~~lm~al~~~Gr~~~Al~~y~~~r~~L~~eLG~~P~~~l~~l  250 (388)
T 2ff4_A          173 AHTAKAEAEIACGRASAVIAELEALTFEH-PYREPLWTQLITAYYLSDRQSDALGAYRRVKTTLADDLGIDPGPTLRAL  250 (388)
T ss_dssp             HHHHHHHHHHHTTCHHHHHHHHHHHHHHS-TTCHHHHHHHHHHHHTTTCHHHHHHHHHHHHHHHHHHHSCCCCHHHHHH
T ss_pred             HHHHHHHHHHHCCCHHHHHHHHHHHHHhC-CCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHHhCCCCCHHHHHH
Confidence            34567778889999999999999998774 66888999999999999999999999998754     588888766443

>3ffl_A Anaphase-promoting complex subunit 7; tetratricopeptide repeat motif, helis-turn-helix, cell cycle division, mitosis, TPR repeat; 2.50A {Homo sapiens}

Probab=92.43  E-value=0.84  Score=36.46  Aligned_cols=98  Identities=9%  Similarity=-0.007  Sum_probs=65.0

Q ss_pred             HHHHHHHHHhcCChhHHHHHHHHHHhCC-CCCCH-------HHHHHHHHHHHhcCCHhHHHHHHHHHHhcC---------
Q 040027           99 YNILINCFCKIGRVSLGFIAFGRILRSC-FTPNA-------ATFNSLIKGLHAESRIMEAAALFTKLKAFG---------  161 (595)
Q Consensus        99 ~~~l~~~~~~~g~~~~A~~~~~~~~~~~-~~~~~-------~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~---------  161 (595)
                      +..=+..+...|.++.|+.+.+.++... ..++.       .++..+..++...|++.+|...|++.+...         
T Consensus        23 l~dqik~L~d~~LY~sA~~La~lLlSl~~~~~~~~sp~~~~~~l~~ladalf~~~eyrrA~~~y~qALq~~k~l~k~~s~  102 (167)
T 3ffl_A           23 VIDHVRDMAAAGLHSNVRLLSSLLLTLSNNNPELFSPPQKYQLLVYHADSLFHDKEYRNAVSKYTMALQQKKALSKTSKV  102 (167)
T ss_dssp             HHHHHHHHHHTTCHHHHHHHHHHHHHHHHHSTTSSCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHCC------
T ss_pred             HHHHHHHHHHhhhHHHHHHHHHHHHHhhcCCcccccHHHHHHHHHHHHHHHHcccHHHHHHHHHHHHHHHHHHHhcCCCc
Confidence            3344556777788888887777755431 12221       245556677788888888888887753210         


Q ss_pred             ---------------CCCCHhhHHHHHHHHHhcCChhHHHHHHHHHHhcC
Q 040027          162 ---------------CEPNVITYNTLINGLCRTGHTMIALNLFEEMANGN  196 (595)
Q Consensus       162 ---------------~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~  196 (595)
                                     ...+.+....+..+|...|++++|+.+++.+....
T Consensus       103 ~~~~~~~ss~p~s~~~~~e~Elkykia~C~~~l~~~~~Ai~~Le~Ip~k~  152 (167)
T 3ffl_A          103 RPSTGNSASTPQSQCLPSEIEVKYKLAECYTVLKQDKDAIAILDGIPSRQ  152 (167)
T ss_dssp             --------------CCCCHHHHHHHHHHHHHHTTCHHHHHHHHHTSCGGG
T ss_pred             cccccccCCCcccccccchHHHHHHHHHHHHHHCCHHHHHHHHhcCCchh
Confidence                           11123455678889999999999999999886543

>4gns_B Protein CSD3, chitin biosynthesis protein CHS6; FN3, BRCT, tetratricopeptide repeat, cargo adaptor, transpor; HET: EPE; 2.75A {Saccharomyces cerevisiae}

Probab=91.87  E-value=0.83  Score=47.09  Aligned_cols=127  Identities=12%  Similarity=0.044  Sum_probs=82.0

Q ss_pred             HHHHHHHHHhcCC-hhHHHHHHHHHHhCCCCCCHHHH--HHHHHHHHhcC-CHhHHHHHHHHHHhc------CCC-CCH-
Q 040027           99 YNILINCFCKIGR-VSLGFIAFGRILRSCFTPNAATF--NSLIKGLHAES-RIMEAAALFTKLKAF------GCE-PNV-  166 (595)
Q Consensus        99 ~~~l~~~~~~~g~-~~~A~~~~~~~~~~~~~~~~~~~--~~l~~~~~~~g-~~~~A~~~~~~~~~~------~~~-~~~-  166 (595)
                      -..++..+...|+ .+.|+.+|+++.+..  |...++  ..++..+.+.+ +--+|++++.+..+.      ..+ .+. 
T Consensus       251 ~~~Ll~~~~~t~~~~~~a~~~le~L~~~~--p~~~~~~~~~~i~~~~~~~~~Ev~av~ll~~~l~~~~~~~~~l~~~~~~  328 (754)
T 4gns_B          251 MYSLKSFIAITPSLVDFTIDYLKGLTKKD--PIHDIYYKTAMITILDHIETKELDMITILNETLDPLLSLLNDLPPRDAD  328 (754)
T ss_dssp             HHHHHHHHHTCGGGHHHHHHHHHHHHHHC--GGGHHHHHHHHHHHHTTCGGGHHHHHHHHHHHHHHHHHHHHTCSSCCHH
T ss_pred             HHHHHHHHcccccHHHHHHHHHHHHHhhC--CchhHHHHHHHHHHHHHhhhhhHHHHHHHHHHHHHhhhhhhhhcccccc
Confidence            3455666666666 578999999998873  433332  22333332222 223455555444321      111 111 


Q ss_pred             ---------hhHHHHHHHHHhcCChhHHHHHHHHHHhcCCCCCccccCcHHHHHHHHHHHHHcCCHhHHHHHHHHHh
Q 040027          167 ---------ITYNTLINGLCRTGHTMIALNLFEEMANGNGEIGVVCKPNTVTYSTIIDGLCKEGFVDKAKALFLQMK  234 (595)
Q Consensus       167 ---------~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~  234 (595)
                               .....-...+...|+++.|+++-++.....       |.+-.+|..|..+|...|+++.|+-.+..+.
T Consensus       329 ~~~~~~~~~~LL~~Qa~FLl~K~~~elAL~~Ak~AV~~a-------PseF~tW~~La~vYi~l~d~e~ALLtLNScP  398 (754)
T 4gns_B          329 SARLMNCMSDLLNIQTNFLLNRGDYELALGVSNTSTELA-------LDSFESWYNLARCHIKKEEYEKALFAINSMP  398 (754)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-------SSCHHHHHHHHHHHHHTTCHHHHHHHHHHSC
T ss_pred             cccccCcchHHHHHHHHHHhccCcHHHHHHHHHHHHhcC-------chhhHHHHHHHHHHHHhccHHHHHHHHhcCC
Confidence                     122233455667899999999999998864       5668999999999999999999999888875

>4b4t_P 26S proteasome regulatory subunit RPN5; hydrolase, AAA-atpases, protein degradation, ubiquitin-prote pathway; 7.40A {Saccharomyces cerevisiae}

Probab=91.64  E-value=10  Score=36.63  Aligned_cols=50  Identities=10%  Similarity=0.117  Sum_probs=30.9

Q ss_pred             CChHHHHHHHHHHHHC-----CCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHh
Q 040027          291 RKMDEASRLLDLMVQR-----GVRPNACTYNTLMDGFCLMGKINRAEELFGSMES  340 (595)
Q Consensus       291 g~~~~a~~~~~~~~~~-----~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~  340 (595)
                      |++++|++.+-.+.+.     +..........++..|...++++...+.+..+.+
T Consensus        30 ~~~~~a~e~ll~lEK~~r~~~d~~s~~r~l~~iv~l~~~~~~~~~l~e~i~~Lsk   84 (445)
T 4b4t_P           30 NDCNSALDQLLVLEKKTRQASDLASSKEVLAKIVDLLASRNKWDDLNEQLTLLSK   84 (445)
T ss_dssp             HHHHHHHHHHHHHHHHHSSSCSTTTCHHHHHHHHHHHHHHSCHHHHHHHHHHHHT
T ss_pred             CCHHHHHHHHHHHHHHhhhccchhhHHHHHHHHHHHHHHhccHHHHHHHHHHHHH
Confidence            5677777666555432     2333455666677777777777777666655543

>4gns_B Protein CSD3, chitin biosynthesis protein CHS6; FN3, BRCT, tetratricopeptide repeat, cargo adaptor, transpor; HET: EPE; 2.75A {Saccharomyces cerevisiae}

Probab=91.56  E-value=1.5  Score=45.26  Aligned_cols=52  Identities=8%  Similarity=-0.003  Sum_probs=43.9

Q ss_pred             CCCHHHHHHHHHHHHHcCChhHHHHHHHHHHHCCCCCCHHHHHHHHHHHHhcCc
Q 040027          519 APDVITFDMLIHGFIRINEPSKVNELLHKMKEKKVMPDASIVSIVVDLLVKNEI  572 (595)
Q Consensus       519 ~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~p~~~~~~~l~~~~~~~g~  572 (595)
                      +.+..-|..|+....+.+++++|.+.|+..+.  .+.++..+..|++.|.+.+.
T Consensus       610 kks~lEWEiLGlla~RL~h~~EA~~a~~~~l~--~RFs~ka~~kLLeiY~~~~~  661 (754)
T 4gns_B          610 KHSGLEWELLGLIMLRTWHWEDAVACLRTSIV--ARFDPVSCQQLLKIYLQPPK  661 (754)
T ss_dssp             CCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHS--SSCCHHHHHHHHHHHHSCCS
T ss_pred             ccCHHHHHHHHHHHHHhCCHHHHHHHHHHHHH--hccCHHHHHHHHHHHHhcCc
Confidence            34566688888888999999999999999996  46899999999999988763

>1wy6_A Hypothetical protein ST1625; helical repeat protein, structural genomics, unknown function; 2.20A {Sulfolobus tokodaii} SCOP: a.118.20.1

Probab=91.46  E-value=3.8  Score=31.38  Aligned_cols=141  Identities=15%  Similarity=0.126  Sum_probs=83.5

Q ss_pred             HHhcCChhHHHHHHHHHHhCCCCCCHHHHHHHHHHHHhcCCHhHHHHHHHHHHhcCCCCCHhhHHHHHHHHHhcCChhHH
Q 040027          106 FCKIGRVSLGFIAFGRILRSCFTPNAATFNSLIKGLHAESRIMEAAALFTKLKAFGCEPNVITYNTLINGLCRTGHTMIA  185 (595)
Q Consensus       106 ~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A  185 (595)
                      +.-.|..++..++..+....   .+..-+|.++--....-+-+-..++++.+-+. +  |.          ...|+....
T Consensus        17 ~ildG~v~qGveii~k~~~s---sni~E~NW~ICNiiD~a~C~y~v~vLd~IGki-F--Di----------s~C~NlKrV   80 (172)
T 1wy6_A           17 FLLDGYIDEGVKIVLEITKS---STKSEYNWFICNLLESIDCRYMFQVLDKIGSY-F--DL----------DKCQNLKSV   80 (172)
T ss_dssp             HHHTTCHHHHHHHHHHHHHH---SCHHHHTHHHHHHHHHCCHHHHHHHHHHHGGG-S--CG----------GGCSCTHHH
T ss_pred             HHHhhhHHHHHHHHHHHcCC---CCccccceeeeecchhhchhHHHHHHHHHhhh-c--Cc----------HhhhcHHHH
Confidence            34457777777777776664   24555666665555555555555555554332 1  11          124444444


Q ss_pred             HHHHHHHHhcCCCCCccccCcHHHHHHHHHHHHHcCCHhHHHHHHHHHhhCCCCCCHhHHHHHHHHHHhcCCHHHHHHHH
Q 040027          186 LNLFEEMANGNGEIGVVCKPNTVTYSTIIDGLCKEGFVDKAKALFLQMKDENINPDVVTYNSLIHGLCHANDWNEAKRLF  265 (595)
Q Consensus       186 ~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~~ll~~~~~~~~~~~A~~~~  265 (595)
                      ...+-.+-           .+....+..+..+...|.-++-.+++..+... .+|++.....+..+|.+.|+..++.+++
T Consensus        81 i~C~~~~n-----------~~se~vd~ALd~lv~~~KkDqLdki~~~~l~n-~~~~~~~l~kia~Ay~Klg~~r~a~eLl  148 (172)
T 1wy6_A           81 VECGVINN-----------TLNEHVNKALDILVIQGKRDKLEEIGREILKN-NEVSASILVAIANALRRVGDERDATTLL  148 (172)
T ss_dssp             HHHHHHTT-----------CCCHHHHHHHHHHHHTTCHHHHHHHHHHHC---CCSCHHHHHHHHHHHHHTTCHHHHHHHH
T ss_pred             HHHHHHhc-----------chHHHHHHHHHHHHHhccHhHHHHHHHHHhcc-CCCChHHHHHHHHHHHHhcchhhHHHHH
Confidence            44443322           23455566667777777777777777775442 3566777777777777777777777777


Q ss_pred             HHHHHCCCC
Q 040027          266 IEMMDQGVQ  274 (595)
Q Consensus       266 ~~~~~~~~~  274 (595)
                      .+.-+.|++
T Consensus       149 ~~AC~kG~k  157 (172)
T 1wy6_A          149 IEACKKGEK  157 (172)
T ss_dssp             HHHHHTTCH
T ss_pred             HHHHHhhhH
Confidence            777776654

>2wpv_A GET4, UPF0363 protein YOR164C; golgi-ER trafficking, tail-anchored protein, protein binding GET4; 1.99A {Saccharomyces cerevisiae} PDB: 3lku_A

Probab=91.06  E-value=8.6  Score=34.75  Aligned_cols=90  Identities=13%  Similarity=0.051  Sum_probs=48.1

Q ss_pred             HHhcCCHhHHHHH----HHHHHhcCCCCCHhhHHHHHHHHHhcCChh-HHHHHHHHHHhcCCCCCccccCcHHHHHHHHH
Q 040027          141 LHAESRIMEAAAL----FTKLKAFGCEPNVITYNTLINGLCRTGHTM-IALNLFEEMANGNGEIGVVCKPNTVTYSTIID  215 (595)
Q Consensus       141 ~~~~g~~~~A~~~----~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~-~A~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~  215 (595)
                      +.+.|+...|.++    .+.+.+.+.+++......++..+......+ .-.+.++.+.+...+.+....-++.....+..
T Consensus        63 ll~~~Q~~sa~DLa~llvev~~~~~~~~~~~~~~rl~~l~~~~p~~~~~r~~fi~~ai~WS~~~g~~~~Gdp~LH~~~a~  142 (312)
T 2wpv_A           63 FLKAKQGGSGTDLIFYLLEVYDLAEVKVDDISVARLVRLIAELDPSEPNLKDVITGMNNWSIKFSEYKFGDPYLHNTIGS  142 (312)
T ss_dssp             HHHTTCHHHHHHHHHHHHHHHHHTTCCCSHHHHHHHHHHHTTCCTTCTTHHHHHHHHHHHHHHTSSCTTCCHHHHHHHHH
T ss_pred             HHHCCCcchHHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHHCCCCCchHHHHHHHHHHHHhhcCCCCCCCHHHHHHHHH
Confidence            4555666555543    444455566777777676766665433211 22344444443221111101235666777777


Q ss_pred             HHHHcCCHhHHHHHH
Q 040027          216 GLCKEGFVDKAKALF  230 (595)
Q Consensus       216 ~~~~~g~~~~A~~~~  230 (595)
                      .|.+.|++.+|+.-|
T Consensus       143 ~~~~e~~~~~A~~H~  157 (312)
T 2wpv_A          143 KLLEGDFVYEAERYF  157 (312)
T ss_dssp             HHHHTTCHHHHHHHH
T ss_pred             HHhhcCCHHHHHHHH
Confidence            777777777776655

>4fhn_B Nucleoporin NUP120; protein complex,structural protein,nuclear pore complex,mRNA transport,protein transport, WD repeat; 6.99A {Schizosaccharomyces pombe 972h-}

Probab=90.64  E-value=4.6  Score=44.67  Aligned_cols=147  Identities=13%  Similarity=-0.044  Sum_probs=95.0

Q ss_pred             HHHHHHhcCCHHHHHHHHHHHHHcCCCcCHHHHHHHHHHHHhcCChHHHHHHHHhcccC----CC---------------
Q 040027          423 FIDGLCKNGYIIEAVELFRTLRILKCELDIQAYNCLIDGLCKSGRLKFAWELFCSLPHG----VL---------------  483 (595)
Q Consensus       423 l~~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~----~~---------------  483 (595)
                      ++..+...+..+.+.++..-.     +.++...-.++.++...|++++|...|.+....    ..               
T Consensus       818 l~~~l~~~~~~~~~~~l~~~~-----~~~~~~~yl~g~~~L~~ge~~~A~~~F~kaa~~~~~~~~l~~~~~~~~~~~~~~  892 (1139)
T 4fhn_B          818 LVEKLFLFKQYNACMQLIGWL-----NSDPIAVYLKALIYLKSKEAVKAVRCFKTTSLVLYSHTSQFAVLREFQEIAEKY  892 (1139)
T ss_dssp             HHHHHHHHSCTTHHHHHHHHS-----CCCHHHHHHHHHHHHHTTCHHHHHHHHHTCCCSCTTCCCSCSSHHHHHHHHHTT
T ss_pred             HHHHHHHhhhHHHHHHHhhhc-----cCCcHHHHHHHHHHHhcCCHHHHHHHHHHHhhhhcccchhhhhhcccccccccc
Confidence            444455556555554433211     334444445566677777777777777665321    00               


Q ss_pred             ---CCCHHHHHHHHHHHHhcCChhHHHHHHHHHHHcCCCCCH----HHHHHHHHHHHHcCChhHHHHHHHHHHHCCCCCC
Q 040027          484 ---VPNVVTYNIMIQGLCNDGQMDKARDLFLDMEENAAAPDV----ITFDMLIHGFIRINEPSKVNELLHKMKEKKVMPD  556 (595)
Q Consensus       484 ---~p~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~~~----~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~p~  556 (595)
                         ..-..-|..++..+.+.|.++.++++-+.+++...+.+.    ..|..+...+...|++++|...+-.+....  --
T Consensus       893 ~~~~~l~~YY~hv~~LFe~~~~~~~vi~fa~lAi~~~~~~~~~~~~~l~~~iFk~~L~l~~ye~Ay~aL~~~pd~~--~r  970 (1139)
T 4fhn_B          893 HHQNLLSCYYLHLSKKLFEESAYIDALEFSLLADASKETDDEDLSIAITHETLKTACAAGKFDAAHVALMVLSTTP--LK  970 (1139)
T ss_dssp             TSCCSSHHHHHHHHHHHHHTSCCHHHHHHHHHHHHHCCSCCHHHHHHHHHHHHHHHHHHCCSGGGGHHHHHHHHSS--SC
T ss_pred             cccccHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhccCCChhhHHHHHHHHHHHHHhhCCHHHHHHHHHhCCCHH--HH
Confidence               001234566777888889999999988888775322222    256778888899999999999998887643  34


Q ss_pred             HHHHHHHHHHHHhcCccccc
Q 040027          557 ASIVSIVVDLLVKNEISLKS  576 (595)
Q Consensus       557 ~~~~~~l~~~~~~~g~~~~~  576 (595)
                      ...+..++..++..|..+++
T Consensus       971 ~~cLr~LV~~lce~~~~~~L  990 (1139)
T 4fhn_B          971 KSCLLDFVNQLTKQGKINQL  990 (1139)
T ss_dssp             HHHHHHHHHHHHHHCCHHHH
T ss_pred             HHHHHHHHHHHHhCCChhhh
Confidence            67888888888888887733

>3ffl_A Anaphase-promoting complex subunit 7; tetratricopeptide repeat motif, helis-turn-helix, cell cycle division, mitosis, TPR repeat; 2.50A {Homo sapiens}

Probab=89.87  E-value=2  Score=34.37  Aligned_cols=62  Identities=10%  Similarity=0.045  Sum_probs=46.1

Q ss_pred             HHHHHHHHHhcCCHhHHHHHHHHHHhcC-CCCCH-------hhHHHHHHHHHhcCChhHHHHHHHHHHhc
Q 040027          134 FNSLIKGLHAESRIMEAAALFTKLKAFG-CEPNV-------ITYNTLINGLCRTGHTMIALNLFEEMANG  195 (595)
Q Consensus       134 ~~~l~~~~~~~g~~~~A~~~~~~~~~~~-~~~~~-------~~~~~l~~~~~~~g~~~~A~~~~~~~~~~  195 (595)
                      +..-+..+...|.++.|+-+.+.+.... ..++.       .++..+..++...|++..|...|++.++.
T Consensus        23 l~dqik~L~d~~LY~sA~~La~lLlSl~~~~~~~~sp~~~~~~l~~ladalf~~~eyrrA~~~y~qALq~   92 (167)
T 3ffl_A           23 VIDHVRDMAAAGLHSNVRLLSSLLLTLSNNNPELFSPPQKYQLLVYHADSLFHDKEYRNAVSKYTMALQQ   92 (167)
T ss_dssp             HHHHHHHHHHTTCHHHHHHHHHHHHHHHHHSTTSSCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHhhhHHHHHHHHHHHHHhhcCCcccccHHHHHHHHHHHHHHHHcccHHHHHHHHHHHHHHH
Confidence            4455677888999999998888766542 12331       25567788899999999999999997643

>1v54_E Cytochrome C oxidase polypeptide VA; oxidoreductase; HET: FME TPO HEA TGL PGV CHD CDL PEK PSC DMU; 1.80A {Bos taurus} SCOP: a.118.11.1 PDB: 1oco_E* 1occ_E* 1ocz_E* 1ocr_E* 1v55_E* 2dyr_E* 2dys_E* 2eij_E* 2eik_E* 2eil_E* 2eim_E* 2ein_E* 2occ_E* 2ybb_P* 2zxw_E* 3abk_E* 3abl_E* 3abm_E* 3ag1_E* 3ag2_E* ...

Probab=89.80  E-value=3.6  Score=29.52  Aligned_cols=48  Identities=10%  Similarity=-0.003  Sum_probs=31.0

Q ss_pred             HHHHHHHHhcccCCCCCCHHHHHHHHHHHHhcCChhHHHHHHHHHHHc
Q 040027          469 KFAWELFCSLPHGVLVPNVVTYNIMIQGLCNDGQMDKARDLFLDMEEN  516 (595)
Q Consensus       469 ~~A~~~~~~~~~~~~~p~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~  516 (595)
                      =+..+-++.+....+.|++.+..+.+.+|.+.+++.-|+++|+-...+
T Consensus        27 ~e~rrglN~l~~~DlVP~P~ii~aaLrAcRRvND~alAVR~lE~iK~K   74 (109)
T 1v54_E           27 WELRKGMNTLVGYDLVPEPKIIDAALRACRRLNDFASAVRILEVVKDK   74 (109)
T ss_dssp             HHHHHHHHHHTTSSBCCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHhccccCCCcHHHHHHHHHHHHhhhHHHHHHHHHHHHHH
Confidence            345555555555556667777777777777777777777777666654

>4fhn_B Nucleoporin NUP120; protein complex,structural protein,nuclear pore complex,mRNA transport,protein transport, WD repeat; 6.99A {Schizosaccharomyces pombe 972h-}

Probab=89.51  E-value=12  Score=41.31  Aligned_cols=51  Identities=8%  Similarity=0.105  Sum_probs=27.5

Q ss_pred             HHHHHHhcCChHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHH
Q 040027          283 IMDELCKNRKMDEASRLLDLMVQRGVRPNACTYNTLMDGFCLMGKINRAEELFGSM  338 (595)
Q Consensus       283 l~~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~  338 (595)
                      ++..+...+.++.+.++...+     +.++.....++.++...|++++|.+.|.+.
T Consensus       818 l~~~l~~~~~~~~~~~l~~~~-----~~~~~~~yl~g~~~L~~ge~~~A~~~F~ka  868 (1139)
T 4fhn_B          818 LVEKLFLFKQYNACMQLIGWL-----NSDPIAVYLKALIYLKSKEAVKAVRCFKTT  868 (1139)
T ss_dssp             HHHHHHHHSCTTHHHHHHHHS-----CCCHHHHHHHHHHHHHTTCHHHHHHHHHTC
T ss_pred             HHHHHHHhhhHHHHHHHhhhc-----cCCcHHHHHHHHHHHhcCCHHHHHHHHHHH
Confidence            344445555555554433221     223334445666777777777777777654

>3lpz_A GET4 (YOR164C homolog); protein targeting, tail-anchored protein biogenesis, GET PAT GET5 binding, protein transport; 1.98A {Chaetomium thermophilum}

Probab=89.10  E-value=13  Score=33.86  Aligned_cols=117  Identities=11%  Similarity=0.065  Sum_probs=56.9

Q ss_pred             HHHHHHHHHhcCChhHHHHHHHHHHhCCCCCCHHHHHHHHHHHHhcCCHhHHHHHH----HHHHhcCCCCCHhhHHHHHH
Q 040027           99 YNILINCFCKIGRVSLGFIAFGRILRSCFTPNAATFNSLIKGLHAESRIMEAAALF----TKLKAFGCEPNVITYNTLIN  174 (595)
Q Consensus        99 ~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~----~~~~~~~~~~~~~~~~~l~~  174 (595)
                      +.++..=|.+.+++++|+.++-.-.               ..+.+.|+...|.++-    +-+.+.++++|......++.
T Consensus        38 ~RTi~~Ry~~~k~y~eAidLL~~GA---------------~~ll~~~Q~~sg~DL~~llvevy~~~~~~~~~~~~~rL~~  102 (336)
T 3lpz_A           38 TRLVAARYSKQGNWAAAVDILASVS---------------QTLLRSGQGGSGGDLAVLLVDTFRQAGQRVDGASRGKLLG  102 (336)
T ss_dssp             HHHHHHHHHHTTCHHHHHHHHHHHH---------------HHHHHTTCHHHHHHHHHHHHHHHHHHTCCCCHHHHHHHHH
T ss_pred             HHHHHHHHHhhcCHHHHHHHHHHHH---------------HHHHHCCCcchHHHHHHHHHHHHHHcCCCCCHHHHHHHHH
Confidence            3344444555555555555443322               2344555555544433    44455566677666666666


Q ss_pred             HHHhcCChh-HHHHHHHHHHhcCCCCCccccCcHHHHHHHHHHHHHcCCHhHHHHHH
Q 040027          175 GLCRTGHTM-IALNLFEEMANGNGEIGVVCKPNTVTYSTIIDGLCKEGFVDKAKALF  230 (595)
Q Consensus       175 ~~~~~g~~~-~A~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~  230 (595)
                      .+......+ .-.++++++..+..+.+....-++.....+...|.+.+++.+|+.-|
T Consensus       103 L~~~~~~~~p~r~~fi~~ai~WS~~~g~~~~Gdp~LH~~ig~~~~~e~~~~~Ae~H~  159 (336)
T 3lpz_A          103 CLRLFQPGEPVRKRFVKEMIDWSKKFGDYPAGDPELHHVVGTLYVEEGEFEAAEKHL  159 (336)
T ss_dssp             HHTTSCTTCHHHHHHHHHHHHHHHHHSSCTTCCHHHHHHHHHHHHHTTCHHHHHHHH
T ss_pred             HHHhCCCCCcHHHHHHHHHHHHHhhcCCCCCCCHHHHHHHHHHHHccCCHHHHHHHH
Confidence            655443211 11223333332211111001224556666667777777777766655

>1v54_E Cytochrome C oxidase polypeptide VA; oxidoreductase; HET: FME TPO HEA TGL PGV CHD CDL PEK PSC DMU; 1.80A {Bos taurus} SCOP: a.118.11.1 PDB: 1oco_E* 1occ_E* 1ocz_E* 1ocr_E* 1v55_E* 2dyr_E* 2dys_E* 2eij_E* 2eik_E* 2eil_E* 2eim_E* 2ein_E* 2occ_E* 2ybb_P* 2zxw_E* 3abk_E* 3abl_E* 3abm_E* 3ag1_E* 3ag2_E* ...

Probab=88.99  E-value=4.9  Score=28.82  Aligned_cols=77  Identities=17%  Similarity=0.208  Sum_probs=57.5

Q ss_pred             HHHHHHHHHhc-C-ChhHHHHHHHHHHHcCCCCCHHHHHHHHHHHHHcCChhHHHHHHHHHHHCCCCCCHHHHHHHHHHH
Q 040027          490 YNIMIQGLCND-G-QMDKARDLFLDMEENAAAPDVITFDMLIHGFIRINEPSKVNELLHKMKEKKVMPDASIVSIVVDLL  567 (595)
Q Consensus       490 ~~~l~~~~~~~-g-~~~~A~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~p~~~~~~~l~~~~  567 (595)
                      |..--..|... . |.-+..+-++.+...++-|++.+....+.+|.+.+++.-|.++++-.+.+ ......+|..+++-+
T Consensus        11 F~aRy~~~F~~~~iD~~e~rrglN~l~~~DlVP~P~ii~aaLrAcRRvND~alAVR~lE~iK~K-~~~~~~iY~~~lqEl   89 (109)
T 1v54_E           11 FDARWVTYFNKPDIDAWELRKGMNTLVGYDLVPEPKIIDAALRACRRLNDFASAVRILEVVKDK-AGPHKEIYPYVIQEL   89 (109)
T ss_dssp             HHHHHHHHHTCTTCCHHHHHHHHHHHTTSSBCCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH-TTTCTTHHHHHHHHH
T ss_pred             HHHHHHHHcCCcCccHHHHHHHHHHHhccccCCCcHHHHHHHHHHHHhhhHHHHHHHHHHHHHH-hcCchhhHHHHHHHH
Confidence            33333444433 3 45567778888888889999999999999999999999999999999864 234456777776643

>3o48_A Mitochondria fission 1 protein; tetratricopeptide repeat fold, TPR, scaffold, peroxisome, membrane fission, protein binding; 1.75A {Saccharomyces cerevisiae} PDB: 2pqr_A 2pqn_A 3uux_A

Probab=88.10  E-value=7.3  Score=29.74  Aligned_cols=71  Identities=11%  Similarity=0.032  Sum_probs=55.6

Q ss_pred             CCCCCHHHHHHHHHHHHhcCCH---hHHHHHHHHHHhcCCCCCHhhHHHHHHHHHhcCChhHHHHHHHHHHhcC
Q 040027          126 CFTPNAATFNSLIKGLHAESRI---MEAAALFTKLKAFGCEPNVITYNTLINGLCRTGHTMIALNLFEEMANGN  196 (595)
Q Consensus       126 ~~~~~~~~~~~l~~~~~~~g~~---~~A~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~  196 (595)
                      +..|++.+-..+..++.+..+.   .+++.+++.+.+.+.......+..|..++.+.|++++|.+..+.+.+..
T Consensus        35 ~~~vs~qt~F~yAw~Lv~S~~~~d~~~GI~LLe~l~~~~~~~~Rd~LYyLAvg~yklgdY~~Ar~y~d~lL~~e  108 (134)
T 3o48_A           35 GPTATIQSRFNYAWGLIKSTDVNDERLGVKILTDIYKEAESRRRECLYYLTIGCYKLGEYSMAKRYVDTLFEHE  108 (134)
T ss_dssp             GGGSCHHHHHHHHHHHHHSSCHHHHHHHHHHHHHHHHHCGGGHHHHHHHHHHHHHHHTCHHHHHHHHHHHHTTC
T ss_pred             CCCCChhhHHHHHHHHHcCCCHHHHHHHHHHHHHHHhcCcchhHHHHHHHHHHHHHhhhHHHHHHHHHHHHhhC
Confidence            3467788877888888876654   4688899998887533346677788888999999999999999999865

>4b4t_P 26S proteasome regulatory subunit RPN5; hydrolase, AAA-atpases, protein degradation, ubiquitin-prote pathway; 7.40A {Saccharomyces cerevisiae}

Probab=87.28  E-value=22  Score=34.29  Aligned_cols=193  Identities=10%  Similarity=0.098  Sum_probs=109.0

Q ss_pred             CChhHHHHHHHHHHhC-----CCCCCHHHHHHHHHHHHhcCCHhHHHHHHHHHHhcCCCCCHhhHHHHHHHH----HhcC
Q 040027          110 GRVSLGFIAFGRILRS-----CFTPNAATFNSLIKGLHAESRIMEAAALFTKLKAFGCEPNVITYNTLINGL----CRTG  180 (595)
Q Consensus       110 g~~~~A~~~~~~~~~~-----~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~~l~~~~----~~~g  180 (595)
                      |+++.|+..+-.+.+.     ...........++..|...|+++...+.+..+....-. -......++..+    ....
T Consensus        30 ~~~~~a~e~ll~lEK~~r~~~d~~s~~r~l~~iv~l~~~~~~~~~l~e~i~~Lskkr~q-lk~ai~~~V~~~~~~l~~~~  108 (445)
T 4b4t_P           30 NDCNSALDQLLVLEKKTRQASDLASSKEVLAKIVDLLASRNKWDDLNEQLTLLSKKHGQ-LKLSIQYMIQKVMEYLKSSK  108 (445)
T ss_dssp             HHHHHHHHHHHHHHHHHSSSCSTTTCHHHHHHHHHHHHHHSCHHHHHHHHHHHHTTTTT-SHHHHHHHHHHHHHHHHHHC
T ss_pred             CCHHHHHHHHHHHHHHhhhccchhhHHHHHHHHHHHHHHhccHHHHHHHHHHHHHHhhh-hHHHHHHHHHHHHHHHhcCC
Confidence            5677777666555432     22344666778888888889988887777666544212 122223333322    2222


Q ss_pred             ChhH--HHHHHHHHHhcCCCCCcc-cc-CcHHHHHHHHHHHHHcCCHhHHHHHHHHHhhC--CCCCC---HhHHHHHHHH
Q 040027          181 HTMI--ALNLFEEMANGNGEIGVV-CK-PNTVTYSTIIDGLCKEGFVDKAKALFLQMKDE--NINPD---VVTYNSLIHG  251 (595)
Q Consensus       181 ~~~~--A~~~~~~~~~~~~~~~~~-~~-~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~--~~~~~---~~~~~~ll~~  251 (595)
                      ..+.  -..+.+......  .+.. +. ........|...+...|++.+|.+++..+...  +....   ...+...++.
T Consensus       109 ~~d~~~~~~~i~~l~~vt--e~kiflE~erarl~~~La~i~e~~g~~~eA~~iL~~l~~Et~~~~~~~~kve~~l~q~rl  186 (445)
T 4b4t_P          109 SLDLNTRISVIETIRVVT--ENKIFVEVERARVTKDLVEIKKEEGKIDEAADILCELQVETYGSMEMSEKIQFILEQMEL  186 (445)
T ss_dssp             TTHHHHHHHHHHCCSSSS--SCCCCCCHHHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHCSSSCHHHHHHHHHHHHHH
T ss_pred             chhHHHHHHHHHHHHHHh--ccchHHHHHHHHHHHHHHHHHHHccCHHHHHHHHHHHHHHHHhcccHHHHHHHHHHHHHH
Confidence            2221  122222211110  0000 00 02334466788888899999999998887643  21111   3456666788


Q ss_pred             HHhcCCHHHHHHHHHHHHH----CCCCCC--HhhHHHHHHHHHhcCChHHHHHHHHHHHH
Q 040027          252 LCHANDWNEAKRLFIEMMD----QGVQPS--VVTFNVIMDELCKNRKMDEASRLLDLMVQ  305 (595)
Q Consensus       252 ~~~~~~~~~A~~~~~~~~~----~~~~~~--~~~~~~l~~~~~~~g~~~~a~~~~~~~~~  305 (595)
                      |...+++..|..++.++..    ....|+  ...+...+..+...+++.+|-..|.++..
T Consensus       187 ~l~~~d~~~a~~~~~ki~~~~~~~~~~~~lk~~~~~~~~~~~~~e~~y~~a~~~y~e~~~  246 (445)
T 4b4t_P          187 SILKGDYSQATVLSRKILKKTFKNPKYESLKLEYYNLLVKISLHKREYLEVAQYLQEIYQ  246 (445)
T ss_dssp             HHHHTCHHHHHHHHHHHHHHHHHSSCCHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHH
T ss_pred             HHHCCCHHHHHHHHHHHHHhhcccCCcHHHHHHHHHHHHHHHHHhhhHHHHHHHHHHHHh
Confidence            8888999888888877642    111222  12445566677778888888777776654

>1zbp_A Hypothetical protein VPA1032; alpha-beta protein, structural genomics, PSI, protein struct initiative; 2.40A {Vibrio parahaemolyticus} SCOP: e.61.1.1

Probab=86.20  E-value=17  Score=31.85  Aligned_cols=54  Identities=11%  Similarity=0.101  Sum_probs=31.2

Q ss_pred             HHhcCChhHHHHHHHHHHhCCCCCCHHHHHHHHHHHHhcCCHhHHHHHHHHHHhc
Q 040027          106 FCKIGRVSLGFIAFGRILRSCFTPNAATFNSLIKGLHAESRIMEAAALFTKLKAF  160 (595)
Q Consensus       106 ~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~  160 (595)
                      ..+.|++++++......++.. |.|...-..++..++-.|++++|.+-++.+.+.
T Consensus         7 ll~~g~L~~al~~~~~~VR~~-P~da~~R~~LfqLLcv~G~w~RA~~QL~~~a~l   60 (273)
T 1zbp_A            7 ALSEGQLQQALELLIEAIKAS-PKDASLRSSFIELLCIDGDFERADEQLMQSIKL   60 (273)
T ss_dssp             HTTTTCHHHHHHHHHHHHHTC-TTCHHHHHHHHHHHHHHTCHHHHHHHHHHHHHH
T ss_pred             HHhCCCHHHHHHHHHHHHHhC-CcCHHHHHHHHHHHHhcCCHHHHHHHHHHHHHh
Confidence            445566666666666655553 445555555556666666666666655555554

>2y69_E Cytochrome C oxidase subunit 5A; electron transport, complex IV, proton pumps, membrane prote; HET: TPO HEA CHD PEK PGV DMU; 1.95A {Bos taurus}

Probab=85.81  E-value=8.2  Score=29.40  Aligned_cols=47  Identities=11%  Similarity=0.022  Sum_probs=25.6

Q ss_pred             HHHHHHHhcccCCCCCCHHHHHHHHHHHHhcCChhHHHHHHHHHHHc
Q 040027          470 FAWELFCSLPHGVLVPNVVTYNIMIQGLCNDGQMDKARDLFLDMEEN  516 (595)
Q Consensus       470 ~A~~~~~~~~~~~~~p~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~  516 (595)
                      +..+-++.+....+.|++.+....+.+|.+.+|+.-|+++|+-...+
T Consensus        71 ElrrglN~l~~~DlVPeP~Ii~AALrAcRRvNDfalAVR~lE~vK~K  117 (152)
T 2y69_E           71 ELRKGMNTLVGYDLVPEPKIIDAALRACRRLNDFASAVRILEVVKDK  117 (152)
T ss_dssp             HHHHHHHHHTTSSBCCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHhccccCCCcHHHHHHHHHHHHhhhHHHHHHHHHHHHHh
Confidence            34444444444445555555555555555555555555555555544

>2y69_E Cytochrome C oxidase subunit 5A; electron transport, complex IV, proton pumps, membrane prote; HET: TPO HEA CHD PEK PGV DMU; 1.95A {Bos taurus}

Probab=85.80  E-value=8.2  Score=29.40  Aligned_cols=62  Identities=19%  Similarity=0.262  Sum_probs=40.0

Q ss_pred             HHHHHHHHHHHcCCCCCHHHHHHHHHHHHHcCChhHHHHHHHHHHHCCCCCCHHHHHHHHHHH
Q 040027          505 KARDLFLDMEENAAAPDVITFDMLIHGFIRINEPSKVNELLHKMKEKKVMPDASIVSIVVDLL  567 (595)
Q Consensus       505 ~A~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~p~~~~~~~l~~~~  567 (595)
                      +..+-++.+...++-|++.+....+.+|.+.+++.-|.++++-.+.+ ..+...+|..+++-+
T Consensus        71 ElrrglN~l~~~DlVPeP~Ii~AALrAcRRvNDfalAVR~lE~vK~K-~~~~~~iY~y~lqEl  132 (152)
T 2y69_E           71 ELRKGMNTLVGYDLVPEPKIIDAALRACRRLNDFASAVRILEVVKDK-AGPHKEIYPYVIQEL  132 (152)
T ss_dssp             HHHHHHHHHTTSSBCCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH-TTTCTTHHHHHHHHH
T ss_pred             HHHHHHHHHhccccCCCcHHHHHHHHHHHHhhhHHHHHHHHHHHHHh-cCCchhhHHHHHHHH
Confidence            44555566666666777777777777777777777777777777643 234455566655543

>1zbp_A Hypothetical protein VPA1032; alpha-beta protein, structural genomics, PSI, protein struct initiative; 2.40A {Vibrio parahaemolyticus} SCOP: e.61.1.1

Probab=85.38  E-value=18  Score=31.59  Aligned_cols=112  Identities=19%  Similarity=0.204  Sum_probs=72.4

Q ss_pred             HHHhcCCHHHHHHHHHHHHHcCCCcCHHHHHHHHHHHHhcCChHHHHHHHHhcccCCCCCCHH----HHHHHHHHHHhcC
Q 040027          426 GLCKNGYIIEAVELFRTLRILKCELDIQAYNCLIDGLCKSGRLKFAWELFCSLPHGVLVPNVV----TYNIMIQGLCNDG  501 (595)
Q Consensus       426 ~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~p~~~----~~~~l~~~~~~~g  501 (595)
                      ...+.|++++|+.....-++.. |.|......+++.++-.|+++.|..-++.+.+  +.|+..    .|..+|.+     
T Consensus         6 ~ll~~g~L~~al~~~~~~VR~~-P~da~~R~~LfqLLcv~G~w~RA~~QL~~~a~--l~p~~~~~a~~yr~lI~a-----   77 (273)
T 1zbp_A            6 NALSEGQLQQALELLIEAIKAS-PKDASLRSSFIELLCIDGDFERADEQLMQSIK--LFPEYLPGASQLRHLVKA-----   77 (273)
T ss_dssp             HHTTTTCHHHHHHHHHHHHHTC-TTCHHHHHHHHHHHHHHTCHHHHHHHHHHHHH--HCGGGHHHHHHHHHHHHH-----
T ss_pred             HHHhCCCHHHHHHHHHHHHHhC-CcCHHHHHHHHHHHHhcCCHHHHHHHHHHHHH--hCchhhHHHHHHHHHHHH-----
Confidence            4567788888888888888776 77888888888999999999999888888877  455533    33333332     


Q ss_pred             ChhHHHHHHHHHHHcCCC-----CCHHHHHHHHHHHH--HcCChhHHHHHHHHHHH
Q 040027          502 QMDKARDLFLDMEENAAA-----PDVITFDMLIHGFI--RINEPSKVNELLHKMKE  550 (595)
Q Consensus       502 ~~~~A~~~~~~~~~~~~~-----~~~~~~~~l~~~~~--~~g~~~~A~~~~~~~~~  550 (595)
                           +..=.+...-+-.     ....-...++.+..  ..|+.++|..+-.++.+
T Consensus        78 -----E~~R~~vfaG~~~P~~~g~~~~w~~~ll~Al~~~~~G~~~~A~~lr~~A~e  128 (273)
T 1zbp_A           78 -----AQARKDFAQGAATAKVLGENEELTKSLVSFNLSMVSQDYEQVSELALQIEE  128 (273)
T ss_dssp             -----HHHHHHHTTSCCCEECCCSCHHHHHHHHHHHHHHHHTCHHHHHHHHHHHHH
T ss_pred             -----HHHHHHHHcCCCCCCCCCCCHHHHHHHHHHHHHhhcCCHHHHHHHHHHHHh
Confidence                 1111222221111     12233344444443  56899999988888875

>3lpz_A GET4 (YOR164C homolog); protein targeting, tail-anchored protein biogenesis, GET PAT GET5 binding, protein transport; 1.98A {Chaetomium thermophilum}

Probab=85.32  E-value=22  Score=32.42  Aligned_cols=81  Identities=6%  Similarity=-0.022  Sum_probs=48.5

Q ss_pred             CcCHHHHHHHHHHHHhcCChHHHHHHHHhcccCCCCCCHHHHHHHHHHHHhcCChhHHHHHHHHHHHcCCCCCHHHH-HH
Q 040027          449 ELDIQAYNCLIDGLCKSGRLKFAWELFCSLPHGVLVPNVVTYNIMIQGLCNDGQMDKARDLFLDMEENAAAPDVITF-DM  527 (595)
Q Consensus       449 ~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~p~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~-~~  527 (595)
                      .-|+.....+...|.+.+++.+|...|-  ..  -.+....+..++.-+...+...+                ...| ..
T Consensus       133 ~Gdp~LH~~ig~~~~~e~~~~~Ae~H~i--lg--~~~s~~~~a~mL~ew~~~~~~~e----------------~dlfiaR  192 (336)
T 3lpz_A          133 AGDPELHHVVGTLYVEEGEFEAAEKHLV--LG--TKESPEVLARMEYEWYKQDESHT----------------APLYCAR  192 (336)
T ss_dssp             TCCHHHHHHHHHHHHHTTCHHHHHHHHT--TS--CTTHHHHHHHHHHHHHHTSCGGG----------------HHHHHHH
T ss_pred             CCCHHHHHHHHHHHHccCCHHHHHHHHH--hc--CCchHHHHHHHHHHHHHhcCCcc----------------HHHHHHH
Confidence            3467788888899999999999888873  21  23334666555554444332221                1212 22


Q ss_pred             HHHHHHHcCChhHHHHHHHHHH
Q 040027          528 LIHGFIRINEPSKVNELLHKMK  549 (595)
Q Consensus       528 l~~~~~~~g~~~~A~~~~~~~~  549 (595)
                      .+--|.-.++...|..+++...
T Consensus       193 aVL~yL~l~n~~~A~~~~~~f~  214 (336)
T 3lpz_A          193 AVLPYLLVANVRAANTAYRIFT  214 (336)
T ss_dssp             HHHHHHHTTCHHHHHHHHHHHH
T ss_pred             HHHHHHHhCCHHHHHHHHHHHH
Confidence            3334566677777777666555

>1y8m_A FIS1; mitochondria, unknown function; NMR {Saccharomyces cerevisiae} SCOP: a.118.8.1

Probab=84.86  E-value=12  Score=29.01  Aligned_cols=69  Identities=12%  Similarity=0.061  Sum_probs=54.4

Q ss_pred             CCCHHHHHHHHHHHHhcCCH---hHHHHHHHHHHhcCCCCCHhhHHHHHHHHHhcCChhHHHHHHHHHHhcC
Q 040027          128 TPNAATFNSLIKGLHAESRI---MEAAALFTKLKAFGCEPNVITYNTLINGLCRTGHTMIALNLFEEMANGN  196 (595)
Q Consensus       128 ~~~~~~~~~l~~~~~~~g~~---~~A~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~  196 (595)
                      .++..+-..+..++.+..+.   .+++.+++.+...+..........|..++.+.|++++|.+..+.+++..
T Consensus        36 ~vs~~t~F~YAw~Lv~S~~~~di~~GI~LLe~l~~~~~~~~RdcLYyLAvg~ykl~~Y~~Ar~y~d~lL~~e  107 (144)
T 1y8m_A           36 TATIQSRFNYAWGLIKSTDVNDERLGVKILTDIYKEAESRRRECLYYLTIGCYKLGEYSMAKRYVDTLFEHE  107 (144)
T ss_dssp             TSCHHHHHHHHHHHHHSSSHHHHHHHHHHHHHHHHHCCSTHHHHHHHHHHHHHTTTCHHHHHHHHHHHHHTC
T ss_pred             CCcHHHHHHHHHHHHcCCCHHHHHHHHHHHHHHHhcCccchhHHHHHHHHHHHHhhhHHHHHHHHHHHHhcC
Confidence            57777777888888876654   4688889988886544456667778888999999999999999999865

>3esl_A Checkpoint serine/threonine-protein kinase BUB1; mitotic spindle checkpoint, TPR motif, all-alpha domain, MAD3-like domain; HET: NHE; 1.74A {Saccharomyces cerevisiae}

Probab=84.42  E-value=16  Score=30.24  Aligned_cols=63  Identities=10%  Similarity=0.091  Sum_probs=43.3

Q ss_pred             cCChhHHHHHHHHHHHcCCCCC-HHHHHHHHHHHHHcCChhHHHHHHHHHHHCCCCCCHHHHHH
Q 040027          500 DGQMDKARDLFLDMEENAAAPD-VITFDMLIHGFIRINEPSKVNELLHKMKEKKVMPDASIVSI  562 (595)
Q Consensus       500 ~g~~~~A~~~~~~~~~~~~~~~-~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~p~~~~~~~  562 (595)
                      .+...++.++|..|...|+.-. ...|...+..+...|++++|.++|+.-++.+-+|-...-..
T Consensus        92 ~~~~~~p~~if~~L~~~~IG~~~AlfYe~wA~~lE~~g~~~~A~~Vy~~GI~~~A~P~~rL~~~  155 (202)
T 3esl_A           92 SNNFHESENTFKYMFNKGIGTKLSLFYEEFSKLLENAQFFLEAKVLLELGAENNCRPYNRLLRS  155 (202)
T ss_dssp             TTCHHHHHHHHHHHHHHTSSTTBHHHHHHHHHHHHHTTCHHHHHHHHHHHHHTTCBSHHHHHHH
T ss_pred             ccccCCHHHHHHHHHHCCCcHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHcCCccHHHHHHH
Confidence            3346677788888877765544 45566777777778888888888888887777775444433

>4b4t_R RPN7, 26S proteasome regulatory subunit RPN7; hydrolase, AAA-atpases, protein degradation, ubiquitin-prote pathway; 7.40A {Saccharomyces cerevisiae}

Probab=83.05  E-value=8.6  Score=36.93  Aligned_cols=100  Identities=8%  Similarity=-0.062  Sum_probs=71.9

Q ss_pred             HHHHHHHHHHHhcCChhHHHHHHHHHHhCC--CCCCHHHHHHHHHHHHhcCCHhHHHHHHHHHHhcC-CCCCHhhHH---
Q 040027           97 YTYNILINCFCKIGRVSLGFIAFGRILRSC--FTPNAATFNSLIKGLHAESRIMEAAALFTKLKAFG-CEPNVITYN---  170 (595)
Q Consensus        97 ~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~--~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~-~~~~~~~~~---  170 (595)
                      .++..++..|.+.|+++.|.+.|.++....  ...-...+..+++.+...+++..+...+.++...- -.++....+   
T Consensus       132 ~~~~~la~~~~~~Gd~~~A~~~~~~~~~~~~~~~~kid~~l~~irl~l~~~d~~~~~~~~~ka~~~~~~~~d~~~~~~lk  211 (429)
T 4b4t_R          132 QAWINLGEYYAQIGDKDNAEKTLGKSLSKAISTGAKIDVMLTIARLGFFYNDQLYVKEKLEAVNSMIEKGGDWERRNRYK  211 (429)
T ss_dssp             SCCHHHHHHHHHHCCCTTHHHHHHHHHHHHTCCCSHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHTTCCCTHHHHHHH
T ss_pred             HHHHHHHHHHHHcCCHHHHHHHHHHHHHhcCChHHHHHHHHHHHHHHHHhccHHHHHHHHHHHHHhhhcCCCHHHHHHHH
Confidence            456789999999999999999999988753  23446678888999999999999999998876531 112222221   


Q ss_pred             -HHHHHHHhcCChhHHHHHHHHHHhcC
Q 040027          171 -TLINGLCRTGHTMIALNLFEEMANGN  196 (595)
Q Consensus       171 -~l~~~~~~~g~~~~A~~~~~~~~~~~  196 (595)
                       .-+..+...+++..|.+.|-++....
T Consensus       212 ~~~gl~~l~~r~f~~Aa~~f~e~~~t~  238 (429)
T 4b4t_R          212 TYYGIHCLAVRNFKEAAKLLVDSLATF  238 (429)
T ss_dssp             HHHHHGGGGTSCHHHHHHHHHHHHHHS
T ss_pred             HHHHHHHHHhChHHHHHHHHHHHhccC
Confidence             22333446789999988888776543

>3txn_A 26S proteasome regulatory complex subunit P42B; PCI domain, alpha solenoid, regulatory PART LID, hydrolase, protein binding; 2.50A {Drosophila melanogaster} PDB: 3txm_A

Probab=82.60  E-value=32  Score=32.29  Aligned_cols=25  Identities=12%  Similarity=0.045  Sum_probs=14.5

Q ss_pred             hHHHHHHHHHhcCChHHHHHHHHHH
Q 040027          279 TFNVIMDELCKNRKMDEASRLLDLM  303 (595)
Q Consensus       279 ~~~~l~~~~~~~g~~~~a~~~~~~~  303 (595)
                      ....+...|.+.|+.++..+++...
T Consensus        21 ~~~~l~~~~~~~~~~~~~~~~~~~~   45 (394)
T 3txn_A           21 GILQQGELYKQEGKAKELADLIKVT   45 (394)
T ss_dssp             HHHHHHHHHHHHTCHHHHHHHHHHT
T ss_pred             HHHHHHHHHHHcCCHHHHHHHHHHH
Confidence            4445556666666666666655544

---

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	595
d1w3ba_	388	a.118.8.1 (A:) O-GlcNAc transferase p110 subunit,	3e-07

>d1w3ba_ a.118.8.1 (A:) O-GlcNAc transferase p110 subunit, OGT {Human (Homo sapiens) [TaxId: 9606]} Length = 388

class: All alpha proteins
fold: alpha-alpha superhelix
superfamily: TPR-like
family: Tetratricopeptide repeat (TPR)
domain: O-GlcNAc transferase p110 subunit, OGT
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 50.4 bits (119), Expect = 3e-07
 Identities = 37/195 (18%), Positives = 77/195 (39%), Gaps = 9/195 (4%)

Query: 216 GLCKEGFVDKAKALFLQMKDENINPDVV-TYNSLIHGLCHANDWNEAKRLFIEMMDQGVQ 274
           G       +   A+    K   ++P+ +  Y +L + L  A  ++ A   ++  +     
Sbjct: 176 GCVFNAQGEIWLAIHHFEKAVTLDPNFLDAYINLGNVLKEARIFDRAVAAYLRALSLSPN 235

Query: 275 PSVVTFNVIMDELCKNRKMDEASRLLDLMVQRGVRPN-ACTYNTLMDGFCLMGKINRAEE 333
            +VV  N +     +   +D A       ++  ++P+    Y  L +     G +  AE+
Sbjct: 236 HAVVHGN-LACVYYEQGLIDLAIDTYRRAIE--LQPHFPDAYCNLANALKEKGSVAEAED 292

Query: 334 LFGSMESMGCKHDDVSYNILINGYCKNKEVEEALSLYREMVSKGIKPT-VVTYNTLFLGL 392
            + +     C     S N L N   +   +EEA+ LYR+ +   + P     ++ L   L
Sbjct: 293 CYNTA-LRLCPTHADSLNNLANIKREQGNIEEAVRLYRKALE--VFPEFAAAHSNLASVL 349

Query: 393 FEIHQVEHALKLFDE 407
            +  +++ AL  + E
Sbjct: 350 QQQGKLQEALMHYKE 364

Homologous Domains Detected by HHsearch

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

ID	Length	Definition	Probability
Query	595
d1w3ba_	388	O-GlcNAc transferase p110 subunit, OGT {Human (Hom	99.95
d1w3ba_	388	O-GlcNAc transferase p110 subunit, OGT {Human (Hom	99.95
d1fcha_	323	Peroxin pex5 (peroxisomal targeting signal 1 (PTS1	99.68
d1fcha_	323	Peroxin pex5 (peroxisomal targeting signal 1 (PTS1	99.68
d2h6fa1	315	Protein farnesyltransferase alpha-subunit {Human (	99.34
d2h6fa1	315	Protein farnesyltransferase alpha-subunit {Human (	99.33
d1dcea1	334	Rab geranylgeranyltransferase alpha-subunit, N-ter	99.3
d2onda1	308	Cleavage stimulation factor 77 kDa subunit CSTF3 {	99.29
d1hz4a_	366	Transcription factor MalT domain III {Escherichia	99.28
d1hz4a_	366	Transcription factor MalT domain III {Escherichia	99.28
d2onda1	308	Cleavage stimulation factor 77 kDa subunit CSTF3 {	99.25
d1dcea1	334	Rab geranylgeranyltransferase alpha-subunit, N-ter	99.19
d1xnfa_	259	Lipoprotein NlpI {Escherichia coli [TaxId: 562]}	99.19
d1xnfa_	259	Lipoprotein NlpI {Escherichia coli [TaxId: 562]}	99.17
d1hh8a_	192	Neutrophil cytosolic factor 2 (NCF-2, p67-phox) {H	98.84
d1ouva_	265	Cysteine rich protein C (HcpC) {Helicobacter pylor	98.82
d1ouva_	265	Cysteine rich protein C (HcpC) {Helicobacter pylor	98.81
d1hh8a_	192	Neutrophil cytosolic factor 2 (NCF-2, p67-phox) {H	98.78
d1elwa_	117	Hop {Human (Homo sapiens) [TaxId: 9606]}	98.75
d1elwa_	117	Hop {Human (Homo sapiens) [TaxId: 9606]}	98.71
d1a17a_	159	Protein phosphatase 5 {Human (Homo sapiens) [TaxId	98.67
d1qqea_	290	Vesicular transport protein sec17 {Baker's yeast (	98.66
d1a17a_	159	Protein phosphatase 5 {Human (Homo sapiens) [TaxId	98.66
d2c2la1	201	STIP1 homology and U box-containing protein 1, STU	98.64
d1qqea_	290	Vesicular transport protein sec17 {Baker's yeast (	98.62
d2c2la1	201	STIP1 homology and U box-containing protein 1, STU	98.57
d1hxia_	112	Peroxin pex5 (peroxisomal targeting signal 1 (PTS1	98.53
d1nzna_	122	Mitochondria fission protein Fis1 {Human (Homo sap	98.42
d1hxia_	112	Peroxin pex5 (peroxisomal targeting signal 1 (PTS1	98.4
d1nzna_	122	Mitochondria fission protein Fis1 {Human (Homo sap	98.39
d1p5qa1	170	FKBP52 (FKBP4), C-terminal domain {Human (Homo sap	98.39
d1p5qa1	170	FKBP52 (FKBP4), C-terminal domain {Human (Homo sap	98.3
d1ya0a1	497	SMG-7 {Human (Homo sapiens) [TaxId: 9606]}	98.27
d1ya0a1	497	SMG-7 {Human (Homo sapiens) [TaxId: 9606]}	98.25
d2ff4a2	179	Probable regulatory protein EmbR, middle domain {M	98.23
d1elra_	128	Hop {Human (Homo sapiens) [TaxId: 9606]}	98.22
d2fbna1	153	Putative 70 kda peptidylprolyl isomerase PFL2275c	98.19
d1b89a_	336	Clathrin heavy chain proximal leg segment {Cow (Bo	98.17
d1elra_	128	Hop {Human (Homo sapiens) [TaxId: 9606]}	98.15
d2fbna1	153	Putative 70 kda peptidylprolyl isomerase PFL2275c	98.13
d1kt1a1	168	FKBP51, C-terminal domain {Monkey (Saimiri bolivie	98.12
d1ihga1	169	Cyclophilin 40 {Cow (Bos taurus) [TaxId: 9913]}	98.11
d1kt1a1	168	FKBP51, C-terminal domain {Monkey (Saimiri bolivie	98.04
d1ihga1	169	Cyclophilin 40 {Cow (Bos taurus) [TaxId: 9913]}	98.02
d1b89a_	336	Clathrin heavy chain proximal leg segment {Cow (Bo	98.0
d1zu2a1	145	Mitochondrial import receptor subunit tom20-3 {Tha	97.99
d1zbpa1	264	Hypothetical protein VPA1032 {Vibrio parahaemolyti	97.95
d2ff4a2	179	Probable regulatory protein EmbR, middle domain {M	97.92
d1zu2a1	145	Mitochondrial import receptor subunit tom20-3 {Tha	97.89
d1zbpa1	264	Hypothetical protein VPA1032 {Vibrio parahaemolyti	97.78
d2hr2a1	156	Hypothetical protein CT2138 {Chlorobium tepidum [T	97.56
d2hr2a1	156	Hypothetical protein CT2138 {Chlorobium tepidum [T	97.55
d1tjca_	95	Prolyl 4-hydroxylase alpha-1 subunit, P4HA1 {Human	97.25
d1tjca_	95	Prolyl 4-hydroxylase alpha-1 subunit, P4HA1 {Human	97.18
d1klxa_	133	Cysteine rich protein B (HcpB) {Helicobacter pylor	96.99
d1klxa_	133	Cysteine rich protein B (HcpB) {Helicobacter pylor	96.96
d1qsaa1	450	70 KDa soluble lytic transglycosylase (SLT70), sup	96.48
d2pqrb1	124	Mitochondria fission protein Fis1 {Baker's yeast (	95.24
d2pqrb1	124	Mitochondria fission protein Fis1 {Baker's yeast (	94.59
d1wy6a1	161	Hypothetical protein ST1625 {Archaeon Sulfolobus t	94.37
d1qsaa1	450	70 KDa soluble lytic transglycosylase (SLT70), sup	92.25
d1v54e_	105	Cytochrome c oxidase subunit E {Cow (Bos taurus) [	90.11
d1v54e_	105	Cytochrome c oxidase subunit E {Cow (Bos taurus) [	89.93
d1wy6a1	161	Hypothetical protein ST1625 {Archaeon Sulfolobus t	88.4

>d1w3ba_ a.118.8.1 (A:) O-GlcNAc transferase p110 subunit, OGT {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: alpha-alpha superhelix
superfamily: TPR-like
family: Tetratricopeptide repeat (TPR)
domain: O-GlcNAc transferase p110 subunit, OGT
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.95  E-value=9.9e-24  Score=204.13  Aligned_cols=383  Identities=13%  Similarity=0.036  Sum_probs=313.9

Q ss_pred             HHHHHHhcCChhHHHHHHHHHHhcCCCCCccccCcHHHHHHHHHHHHHcCCHhHHHHHHHHHhhCCCCCCHhHHHHHHHH
Q 040027          172 LINGLCRTGHTMIALNLFEEMANGNGEIGVVCKPNTVTYSTIIDGLCKEGFVDKAKALFLQMKDENINPDVVTYNSLIHG  251 (595)
Q Consensus       172 l~~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~~ll~~  251 (595)
                      +...+.+.|++++|++.|+++.+..       |.++.++..+..++.+.|++++|...|+++.+.+ +-+..+|..++.+
T Consensus         5 la~~~~~~G~~~~A~~~~~~~l~~~-------p~~~~~~~~la~~~~~~~~~~~A~~~~~~al~~~-p~~~~a~~~l~~~   76 (388)
T d1w3ba_           5 LAHREYQAGDFEAAERHCMQLWRQE-------PDNTGVLLLLSSIHFQCRRLDRSAHFSTLAIKQN-PLLAEAYSNLGNV   76 (388)
T ss_dssp             HHHHHHHHTCHHHHHHHHHHHHHHC-------TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHH
T ss_pred             HHHHHHHcCCHHHHHHHHHHHHHhC-------CCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhC-CCCHHHHHHHHHH
Confidence            5566778899999999999998875       5568889999999999999999999999988764 3367788999999


Q ss_pred             HHhcCCHHHHHHHHHHHHHCCCCCCHhhHHHHHHHHHhcCChHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHhcCCHHHH
Q 040027          252 LCHANDWNEAKRLFIEMMDQGVQPSVVTFNVIMDELCKNRKMDEASRLLDLMVQRGVRPNACTYNTLMDGFCLMGKINRA  331 (595)
Q Consensus       252 ~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a  331 (595)
                      |...|++++|+..+......... +..............+....+............. ...............+....+
T Consensus        77 ~~~~g~~~~A~~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~  154 (388)
T d1w3ba_          77 YKERGQLQEAIEHYRHALRLKPD-FIDGYINLAAALVAAGDMEGAVQAYVSALQYNPD-LYCVRSDLGNLLKALGRLEEA  154 (388)
T ss_dssp             HHHHTCHHHHHHHHHHHHHHCTT-CHHHHHHHHHHHHHHSCSSHHHHHHHHHHHHCTT-CTHHHHHHHHHHHTTSCHHHH
T ss_pred             hhhhccccccccccccccccccc-cccccccccccccccccccccccccccccccccc-cccccccccccccccchhhhh
Confidence            99999999999999998876332 4455555555666666666666666665554333 444555566667778888888


Q ss_pred             HHHHHHHHhcCCCCCHHHHHHHHHHHHhCCCHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHccCCHHHHHHHHHHHHHC
Q 040027          332 EELFGSMESMGCKHDDVSYNILINGYCKNKEVEEALSLYREMVSKGIKPTVVTYNTLFLGLFEIHQVEHALKLFDEMQRD  411 (595)
Q Consensus       332 ~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~  411 (595)
                      ...+....... +.+...+..+...+...|++++|...+++.++..+. +...+..+...+...|++++|...++.....
T Consensus       155 ~~~~~~~~~~~-~~~~~~~~~l~~~~~~~~~~~~A~~~~~~al~~~p~-~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~~  232 (388)
T d1w3ba_         155 KACYLKAIETQ-PNFAVAWSNLGCVFNAQGEIWLAIHHFEKAVTLDPN-FLDAYINLGNVLKEARIFDRAVAAYLRALSL  232 (388)
T ss_dssp             HHHHHHHHHHC-TTCHHHHHHHHHHHHTTTCHHHHHHHHHHHHHHCTT-CHHHHHHHHHHHHTTTCTTHHHHHHHHHHHH
T ss_pred             HHHHHHhhccC-cchhHHHHhhcccccccCcHHHHHHHHHHHHHhCcc-cHHHHHHHhhhhhccccHHHHHHHHHHhHHH
Confidence            88888877663 456678888889999999999999999998886443 6678888899999999999999999998876


Q ss_pred             CCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCcCHHHHHHHHHHHHhcCChHHHHHHHHhcccCCCCCCHHHHH
Q 040027          412 GVAADTRTYTTFIDGLCKNGYIIEAVELFRTLRILKCELDIQAYNCLIDGLCKSGRLKFAWELFCSLPHGVLVPNVVTYN  491 (595)
Q Consensus       412 ~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~p~~~~~~  491 (595)
                      + +.+...+..+...+.+.|++++|...++++.+.. +.+..++..++.++...|++++|...++..... .+.+...+.
T Consensus       233 ~-~~~~~~~~~l~~~~~~~~~~~~A~~~~~~al~~~-p~~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~~-~~~~~~~~~  309 (388)
T d1w3ba_         233 S-PNHAVVHGNLACVYYEQGLIDLAIDTYRRAIELQ-PHFPDAYCNLANALKEKGSVAEAEDCYNTALRL-CPTHADSLN  309 (388)
T ss_dssp             C-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHTC-SSCHHHHHHHHHHHHHHSCHHHHHHHHHHHHHH-CTTCHHHHH
T ss_pred             h-hhHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHhC-CCCHHHHHHHHHHHHHcCCHHHHHHHHHhhhcc-CCccchhhh
Confidence            4 5667788888899999999999999999998876 667889999999999999999999999988774 244677888


Q ss_pred             HHHHHHHhcCChhHHHHHHHHHHHcCCCCCHHHHHHHHHHHHHcCChhHHHHHHHHHHHCCCCC-CHHHHHHHHHHHHhc
Q 040027          492 IMIQGLCNDGQMDKARDLFLDMEENAAAPDVITFDMLIHGFIRINEPSKVNELLHKMKEKKVMP-DASIVSIVVDLLVKN  570 (595)
Q Consensus       492 ~l~~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~p-~~~~~~~l~~~~~~~  570 (595)
                      .+...+...|++++|++.|+++++.. +.+..++..++.+|...|++++|...|+++++.  .| +...+..++.+|.+.
T Consensus       310 ~l~~~~~~~~~~~~A~~~~~~al~~~-p~~~~~~~~la~~~~~~g~~~~A~~~~~~al~l--~P~~~~a~~~lg~~~~~~  386 (388)
T d1w3ba_         310 NLANIKREQGNIEEAVRLYRKALEVF-PEFAAAHSNLASVLQQQGKLQEALMHYKEAIRI--SPTFADAYSNMGNTLKEM  386 (388)
T ss_dssp             HHHHHHHTTTCHHHHHHHHHHHTTSC-TTCHHHHHHHHHHHHTTTCCHHHHHHHHHHHTT--CTTCHHHHHHHHHHHHHT
T ss_pred             HHHHHHHHCCCHHHHHHHHHHHHHhC-CCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHh--CCCCHHHHHHHHHHHHHc
Confidence            89999999999999999999998864 456788899999999999999999999999974  56 578899999999887


Q ss_pred             Cc
Q 040027          571 EI  572 (595)
Q Consensus       571 g~  572 (595)
                      |+
T Consensus       387 ~D  388 (388)
T d1w3ba_         387 QD  388 (388)
T ss_dssp             CC
T ss_pred             CC
Confidence            74

>d1w3ba_ a.118.8.1 (A:) O-GlcNAc transferase p110 subunit, OGT {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: alpha-alpha superhelix
superfamily: TPR-like
family: Tetratricopeptide repeat (TPR)
domain: O-GlcNAc transferase p110 subunit, OGT
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.95  E-value=1.9e-23  Score=202.05  Aligned_cols=380  Identities=13%  Similarity=0.069  Sum_probs=227.6

Q ss_pred             HHHhcCCHhHHHHHHHHHHhcCCCCCHhhHHHHHHHHHhcCChhHHHHHHHHHHhcCCCCCccccCcHHHHHHHHHHHHH
Q 040027          140 GLHAESRIMEAAALFTKLKAFGCEPNVITYNTLINGLCRTGHTMIALNLFEEMANGNGEIGVVCKPNTVTYSTIIDGLCK  219 (595)
Q Consensus       140 ~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~  219 (595)
                      .+.+.|++++|++.|+++.+.. +-+..++..++.+|.+.|++++|+..|+++.+.+       |.+..++..+..++..
T Consensus         8 ~~~~~G~~~~A~~~~~~~l~~~-p~~~~~~~~la~~~~~~~~~~~A~~~~~~al~~~-------p~~~~a~~~l~~~~~~   79 (388)
T d1w3ba_           8 REYQAGDFEAAERHCMQLWRQE-PDNTGVLLLLSSIHFQCRRLDRSAHFSTLAIKQN-------PLLAEAYSNLGNVYKE   79 (388)
T ss_dssp             HHHHHTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-------TTCHHHHHHHHHHHHH
T ss_pred             HHHHcCCHHHHHHHHHHHHHhC-CCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhC-------CCCHHHHHHHHHHhhh
Confidence            3444455555555555544432 1234444445555555555555555555554443       2334455555555555


Q ss_pred             cCCHhHHHHHHHHHhhCCCCCCHhHHHHHHHHHHhcCCHHHHHHHHHHHHHCCCCCCHhhHHHHHHHHHhcCChHHHHHH
Q 040027          220 EGFVDKAKALFLQMKDENINPDVVTYNSLIHGLCHANDWNEAKRLFIEMMDQGVQPSVVTFNVIMDELCKNRKMDEASRL  299 (595)
Q Consensus       220 ~g~~~~A~~~~~~~~~~~~~~~~~~~~~ll~~~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~a~~~  299 (595)
                      .|++++|.+.+....... +.+...+..........+....+............ ................+....+...
T Consensus        80 ~g~~~~A~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~  157 (388)
T d1w3ba_          80 RGQLQEAIEHYRHALRLK-PDFIDGYINLAAALVAAGDMEGAVQAYVSALQYNP-DLYCVRSDLGNLLKALGRLEEAKAC  157 (388)
T ss_dssp             HTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHHSCSSHHHHHHHHHHHHCT-TCTHHHHHHHHHHHTTSCHHHHHHH
T ss_pred             hccccccccccccccccc-ccccccccccccccccccccccccccccccccccc-ccccccccccccccccchhhhhHHH
Confidence            555555555555554432 11233333333333333443343333333333211 1233333344444555555555555


Q ss_pred             HHHHHHCCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHhcCCCCCHHHHHHHHHHHHhCCCHHHHHHHHHHHHHCCCC
Q 040027          300 LDLMVQRGVRPNACTYNTLMDGFCLMGKINRAEELFGSMESMGCKHDDVSYNILINGYCKNKEVEEALSLYREMVSKGIK  379 (595)
Q Consensus       300 ~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~~~~~  379 (595)
                      +....... +.+...+..+...+...|++++|...+++..+.. +.+...+..+...+...|++++|+..+++.......
T Consensus       158 ~~~~~~~~-~~~~~~~~~l~~~~~~~~~~~~A~~~~~~al~~~-p~~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~~~~~  235 (388)
T d1w3ba_         158 YLKAIETQ-PNFAVAWSNLGCVFNAQGEIWLAIHHFEKAVTLD-PNFLDAYINLGNVLKEARIFDRAVAAYLRALSLSPN  235 (388)
T ss_dssp             HHHHHHHC-TTCHHHHHHHHHHHHTTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHTTTCTTHHHHHHHHHHHHCTT
T ss_pred             HHHhhccC-cchhHHHHhhcccccccCcHHHHHHHHHHHHHhC-cccHHHHHHHhhhhhccccHHHHHHHHHHhHHHhhh
Confidence            55555442 2244555556666666666666666666666543 334556666667777777777777777766665332


Q ss_pred             CCHHHHHHHHHHHHccCCHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCcCHHHHHHHH
Q 040027          380 PTVVTYNTLFLGLFEIHQVEHALKLFDEMQRDGVAADTRTYTTFIDGLCKNGYIIEAVELFRTLRILKCELDIQAYNCLI  459 (595)
Q Consensus       380 ~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~~l~  459 (595)
                       ....+..+...+...|++++|...|+++.+.. +.+..++..+..++...|++++|...++.+.... +.+...+..+.
T Consensus       236 -~~~~~~~l~~~~~~~~~~~~A~~~~~~al~~~-p~~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~~~-~~~~~~~~~l~  312 (388)
T d1w3ba_         236 -HAVVHGNLACVYYEQGLIDLAIDTYRRAIELQ-PHFPDAYCNLANALKEKGSVAEAEDCYNTALRLC-PTHADSLNNLA  312 (388)
T ss_dssp             -CHHHHHHHHHHHHHTTCHHHHHHHHHHHHHTC-SSCHHHHHHHHHHHHHHSCHHHHHHHHHHHHHHC-TTCHHHHHHHH
T ss_pred             -HHHHHHHHHHHHHHCCCHHHHHHHHHHHHHhC-CCCHHHHHHHHHHHHHcCCHHHHHHHHHhhhccC-CccchhhhHHH
Confidence             45556666677777777777777777776653 4456677777777888888888888888777665 66777788888


Q ss_pred             HHHHhcCChHHHHHHHHhcccCCCCCC-HHHHHHHHHHHHhcCChhHHHHHHHHHHHcCCCCCHHHHHHHHHHHHHcCC
Q 040027          460 DGLCKSGRLKFAWELFCSLPHGVLVPN-VVTYNIMIQGLCNDGQMDKARDLFLDMEENAAAPDVITFDMLIHGFIRINE  537 (595)
Q Consensus       460 ~~~~~~g~~~~A~~~~~~~~~~~~~p~-~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~  537 (595)
                      .++...|++++|+..|+++++  +.|+ ..++..++.+|...|++++|+..|+++++.. |.+..+|..++.+|.+.||
T Consensus       313 ~~~~~~~~~~~A~~~~~~al~--~~p~~~~~~~~la~~~~~~g~~~~A~~~~~~al~l~-P~~~~a~~~lg~~~~~~~D  388 (388)
T d1w3ba_         313 NIKREQGNIEEAVRLYRKALE--VFPEFAAAHSNLASVLQQQGKLQEALMHYKEAIRIS-PTFADAYSNMGNTLKEMQD  388 (388)
T ss_dssp             HHHHTTTCHHHHHHHHHHHTT--SCTTCHHHHHHHHHHHHTTTCCHHHHHHHHHHHTTC-TTCHHHHHHHHHHHHHTCC
T ss_pred             HHHHHCCCHHHHHHHHHHHHH--hCCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhC-CCCHHHHHHHHHHHHHcCC
Confidence            888888888888888888776  3454 5677788888888888888888888888753 3456778888888877765

>d1fcha_ a.118.8.1 (A:) Peroxin pex5 (peroxisomal targeting signal 1 (PTS1) receptor) {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: alpha-alpha superhelix
superfamily: TPR-like
family: Tetratricopeptide repeat (TPR)
domain: Peroxin pex5 (peroxisomal targeting signal 1 (PTS1) receptor)
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.68  E-value=2.5e-14  Score=133.45  Aligned_cols=269  Identities=14%  Similarity=0.013  Sum_probs=189.3

Q ss_pred             HHHHHHHHHhcCChHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHhcCCCCCHHHHHHHHHHHHh
Q 040027          280 FNVIMDELCKNRKMDEASRLLDLMVQRGVRPNACTYNTLMDGFCLMGKINRAEELFGSMESMGCKHDDVSYNILINGYCK  359 (595)
Q Consensus       280 ~~~l~~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~  359 (595)
                      ....+..+.+.|++++|...|+++++... .+..++..++.++...|++++|...+.++.+.. +.+...+..++.+|..
T Consensus        22 ~~~~g~~~~~~g~~~~A~~~~~~al~~~P-~~~~a~~~lg~~~~~~~~~~~A~~~~~~al~~~-p~~~~~~~~la~~~~~   99 (323)
T d1fcha_          22 PFEEGLRRLQEGDLPNAVLLFEAAVQQDP-KHMEAWQYLGTTQAENEQELLAISALRRCLELK-PDNQTALMALAVSFTN   99 (323)
T ss_dssp             HHHHHHHHHHTTCHHHHHHHHHHHHHSCT-TCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHcCCHHHHHHHHHHHHHhCC-CCHHHHHHHHHHHHHcCChHHHHHHHHhhhccc-cccccccccccccccc
Confidence            33456677888888888888888887643 356778888888888888888888888887764 4466777788888888


Q ss_pred             CCCHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHccCCHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHhcCCHHHHHHH
Q 040027          360 NKEVEEALSLYREMVSKGIKPTVVTYNTLFLGLFEIHQVEHALKLFDEMQRDGVAADTRTYTTFIDGLCKNGYIIEAVEL  439 (595)
Q Consensus       360 ~~~~~~A~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~  439 (595)
                      .|++++|.+.++++....  |+.............                   ..+.......+..+...+.+.+|...
T Consensus       100 ~~~~~~A~~~~~~~~~~~--~~~~~~~~~~~~~~~-------------------~~~~~~~~~~~~~~~~~~~~~~a~~~  158 (323)
T d1fcha_         100 ESLQRQACEILRDWLRYT--PAYAHLVTPAEEGAG-------------------GAGLGPSKRILGSLLSDSLFLEVKEL  158 (323)
T ss_dssp             TTCHHHHHHHHHHHHHTS--TTTGGGCC----------------------------------CTTHHHHHHHHHHHHHHH
T ss_pred             cccccccccchhhHHHhc--cchHHHHHhhhhhhh-------------------hcccccchhhHHHHHHhhHHHHHHHH
Confidence            888888888888877653  221111000000000                   00000111112233445667788888


Q ss_pred             HHHHHHcCC-CcCHHHHHHHHHHHHhcCChHHHHHHHHhcccCCCCC-CHHHHHHHHHHHHhcCChhHHHHHHHHHHHcC
Q 040027          440 FRTLRILKC-ELDIQAYNCLIDGLCKSGRLKFAWELFCSLPHGVLVP-NVVTYNIMIQGLCNDGQMDKARDLFLDMEENA  517 (595)
Q Consensus       440 ~~~~~~~~~-~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~p-~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~  517 (595)
                      +.++.+... ..+..++..+...+...|++++|+..|++....  .| +...|..++.+|...|++++|++.|+++++..
T Consensus       159 ~~~al~~~p~~~~~~~~~~l~~~~~~~~~~~~A~~~~~~al~~--~p~~~~~~~~lg~~~~~~g~~~~A~~~~~~al~~~  236 (323)
T d1fcha_         159 FLAAVRLDPTSIDPDVQCGLGVLFNLSGEYDKAVDCFTAALSV--RPNDYLLWNKLGATLANGNQSEEAVAAYRRALELQ  236 (323)
T ss_dssp             HHHHHHHSTTSCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH--CTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC
T ss_pred             HHHHHHHhhcccccccchhhHHHHHHHHHHhhhhccccccccc--ccccccchhhhhhcccccccchhHHHHHHHHHHHh
Confidence            888776532 345778888889999999999999999998873  44 47788889999999999999999999998864


Q ss_pred             CCCCHHHHHHHHHHHHHcCChhHHHHHHHHHHHCC----------CCCCHHHHHHHHHHHHhcCccc
Q 040027          518 AAPDVITFDMLIHGFIRINEPSKVNELLHKMKEKK----------VMPDASIVSIVVDLLVKNEISL  574 (595)
Q Consensus       518 ~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~----------~~p~~~~~~~l~~~~~~~g~~~  574 (595)
                       +.+..++..++.+|...|++++|...|+++++..          .......|..+..++...|+.+
T Consensus       237 -p~~~~a~~~lg~~~~~~g~~~~A~~~~~~al~l~p~~~~~~~~~~~~~~~~~~~l~~al~~~~~~d  302 (323)
T d1fcha_         237 -PGYIRSRYNLGISCINLGAHREAVEHFLEALNMQRKSRGPRGEGGAMSENIWSTLRLALSMLGQSD  302 (323)
T ss_dssp             -TTCHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHHTC------CCCCCHHHHHHHHHHHHHHTCGG
T ss_pred             -hccHHHHHHHHHHHHHCCCHHHHHHHHHHHHHhCCcChhhhhhhHHHHHHHHHHHHHHHHHcCCHH
Confidence             4567888899999999999999999999988521          1112345677777887778776

>d1fcha_ a.118.8.1 (A:) Peroxin pex5 (peroxisomal targeting signal 1 (PTS1) receptor) {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: alpha-alpha superhelix
superfamily: TPR-like
family: Tetratricopeptide repeat (TPR)
domain: Peroxin pex5 (peroxisomal targeting signal 1 (PTS1) receptor)
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.68  E-value=5.9e-14  Score=130.90  Aligned_cols=271  Identities=14%  Similarity=0.025  Sum_probs=196.6

Q ss_pred             HHHHHHHHHhcCCHHHHHHHHHHHHHCCCCCCHhhHHHHHHHHHhcCChHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHh
Q 040027          245 YNSLIHGLCHANDWNEAKRLFIEMMDQGVQPSVVTFNVIMDELCKNRKMDEASRLLDLMVQRGVRPNACTYNTLMDGFCL  324 (595)
Q Consensus       245 ~~~ll~~~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~  324 (595)
                      .-..+..+.+.|++++|+..|+++++.. +-+..+|..++.++...|++++|...+.++.+... -+...+..++.+|..
T Consensus        22 ~~~~g~~~~~~g~~~~A~~~~~~al~~~-P~~~~a~~~lg~~~~~~~~~~~A~~~~~~al~~~p-~~~~~~~~la~~~~~   99 (323)
T d1fcha_          22 PFEEGLRRLQEGDLPNAVLLFEAAVQQD-PKHMEAWQYLGTTQAENEQELLAISALRRCLELKP-DNQTALMALAVSFTN   99 (323)
T ss_dssp             HHHHHHHHHHTTCHHHHHHHHHHHHHSC-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCT-TCHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHcCCHHHHHHHHHHHHHhC-CCCHHHHHHHHHHHHHcCChHHHHHHHHhhhcccc-ccccccccccccccc
Confidence            3456778999999999999999999864 33678899999999999999999999999998643 367888889999999


Q ss_pred             cCCHHHHHHHHHHHHhcCCCCCHHH-HHHHHHHHHhCCCHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHccCCHHHHHH
Q 040027          325 MGKINRAEELFGSMESMGCKHDDVS-YNILINGYCKNKEVEEALSLYREMVSKGIKPTVVTYNTLFLGLFEIHQVEHALK  403 (595)
Q Consensus       325 ~~~~~~a~~~~~~~~~~~~~~~~~~-~~~l~~~~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~  403 (595)
                      .|++++|.+.++.+....  |+... +....... ..                   .+.......+..+...+.+.++..
T Consensus       100 ~~~~~~A~~~~~~~~~~~--~~~~~~~~~~~~~~-~~-------------------~~~~~~~~~~~~~~~~~~~~~a~~  157 (323)
T d1fcha_         100 ESLQRQACEILRDWLRYT--PAYAHLVTPAEEGA-GG-------------------AGLGPSKRILGSLLSDSLFLEVKE  157 (323)
T ss_dssp             TTCHHHHHHHHHHHHHTS--TTTGGGCC-----------------------------------CTTHHHHHHHHHHHHHH
T ss_pred             cccccccccchhhHHHhc--cchHHHHHhhhhhh-hh-------------------cccccchhhHHHHHHhhHHHHHHH
Confidence            999999999999998763  32211 11000000 00                   000011111122334455667777


Q ss_pred             HHHHHHHCC-CCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCcCHHHHHHHHHHHHhcCChHHHHHHHHhcccCC
Q 040027          404 LFDEMQRDG-VAADTRTYTTFIDGLCKNGYIIEAVELFRTLRILKCELDIQAYNCLIDGLCKSGRLKFAWELFCSLPHGV  482 (595)
Q Consensus       404 ~~~~~~~~~-~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~  482 (595)
                      .+.+..+.. ...+..++..+...+...|++++|...++++.... +.+..++..++.+|...|++++|...|+++++  
T Consensus       158 ~~~~al~~~p~~~~~~~~~~l~~~~~~~~~~~~A~~~~~~al~~~-p~~~~~~~~lg~~~~~~g~~~~A~~~~~~al~--  234 (323)
T d1fcha_         158 LFLAAVRLDPTSIDPDVQCGLGVLFNLSGEYDKAVDCFTAALSVR-PNDYLLWNKLGATLANGNQSEEAVAAYRRALE--  234 (323)
T ss_dssp             HHHHHHHHSTTSCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHH--
T ss_pred             HHHHHHHHhhcccccccchhhHHHHHHHHHHhhhhcccccccccc-cccccchhhhhhcccccccchhHHHHHHHHHH--
Confidence            777776542 23456777888888889999999999999988776 56788899999999999999999999999887  


Q ss_pred             CCCC-HHHHHHHHHHHHhcCChhHHHHHHHHHHHcC----------CCCCHHHHHHHHHHHHHcCChhHHH
Q 040027          483 LVPN-VVTYNIMIQGLCNDGQMDKARDLFLDMEENA----------AAPDVITFDMLIHGFIRINEPSKVN  542 (595)
Q Consensus       483 ~~p~-~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~----------~~~~~~~~~~l~~~~~~~g~~~~A~  542 (595)
                      +.|+ ..+|..++.+|.+.|++++|++.|+++++..          .......|..+..++...|+.+.+.
T Consensus       235 ~~p~~~~a~~~lg~~~~~~g~~~~A~~~~~~al~l~p~~~~~~~~~~~~~~~~~~~l~~al~~~~~~d~~~  305 (323)
T d1fcha_         235 LQPGYIRSRYNLGISCINLGAHREAVEHFLEALNMQRKSRGPRGEGGAMSENIWSTLRLALSMLGQSDAYG  305 (323)
T ss_dssp             HCTTCHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHHTC------CCCCCHHHHHHHHHHHHHHTCGGGHH
T ss_pred             HhhccHHHHHHHHHHHHHCCCHHHHHHHHHHHHHhCCcChhhhhhhHHHHHHHHHHHHHHHHHcCCHHHHH
Confidence            4554 6788889999999999999999999988731          1112334555666666667665544

>d2h6fa1 a.118.6.1 (A:55-369) Protein farnesyltransferase alpha-subunit {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: alpha-alpha superhelix
superfamily: Protein prenylyltransferase
family: Protein prenylyltransferase
domain: Protein farnesyltransferase alpha-subunit
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.34  E-value=2.6e-10  Score=104.50  Aligned_cols=213  Identities=9%  Similarity=0.052  Sum_probs=126.9

Q ss_pred             HHHHHHHHHHhcCCHHHHHHHHHHHHhcCCCCCHHHHHHHHHHHHhCC-CHHHHHHHHHHHHHCCCCCCHHHHHHHHHHH
Q 040027          314 TYNTLMDGFCLMGKINRAEELFGSMESMGCKHDDVSYNILINGYCKNK-EVEEALSLYREMVSKGIKPTVVTYNTLFLGL  392 (595)
Q Consensus       314 ~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~-~~~~A~~~~~~~~~~~~~~~~~~~~~l~~~~  392 (595)
                      .++.+..++.+.+.+++|+.+++++++.+ |.+..+|+....++...+ ++++|+..++.+++..+. +..+|......+
T Consensus        45 a~~~~~~~~~~~e~~~~Al~~~~~ai~ln-P~~~~a~~~r~~~l~~l~~~~~eal~~~~~al~~~p~-~~~a~~~~~~~~  122 (315)
T d2h6fa1          45 VYDYFRAVLQRDERSERAFKLTRDAIELN-AANYTVWHFRRVLLKSLQKDLHEEMNYITAIIEEQPK-NYQVWHHRRVLV  122 (315)
T ss_dssp             HHHHHHHHHHHTCCCHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCCHHHHHHHHHHHHHHCTT-CHHHHHHHHHHH
T ss_pred             HHHHHHHHHHhCCchHHHHHHHHHHHHHC-CCChHHHHHHHHHHHHhCcCHHHHHHHHHHHHHHHHh-hhhHHHHHhHHH
Confidence            34445555556666666666666666654 445556666666666554 366666666666665433 556666666666


Q ss_pred             HccCCHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCcCHHHHHHHHHHHHhcCC-----
Q 040027          393 FEIHQVEHALKLFDEMQRDGVAADTRTYTTFIDGLCKNGYIIEAVELFRTLRILKCELDIQAYNCLIDGLCKSGR-----  467 (595)
Q Consensus       393 ~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~-----  467 (595)
                      ...|++++|+..++.+++.. +.+...|..+...+...|++++|+..++++++.+ +.+...|+.+..++.+.+.     
T Consensus       123 ~~l~~~~eAl~~~~kal~~d-p~n~~a~~~~~~~~~~~~~~~~Al~~~~~al~~~-p~n~~a~~~r~~~l~~~~~~~~~~  200 (315)
T d2h6fa1         123 EWLRDPSQELEFIADILNQD-AKNYHAWQHRQWVIQEFKLWDNELQYVDQLLKED-VRNNSVWNQRYFVISNTTGYNDRA  200 (315)
T ss_dssp             HHHTCCTTHHHHHHHHHHHC-TTCHHHHHHHHHHHHHHTCCTTHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCSCSHH
T ss_pred             HhhccHHHHHHHHhhhhhhh-hcchHHHHHHHHHHHHHHhhHHHHHHHHHHHHHC-CccHHHHHHHHHHHHHccccchhh
Confidence            66666777777776666653 4456666666666667777777777777776665 4556666666665555444     


Q ss_pred             -hHHHHHHHHhcccCCCCC-CHHHHHHHHHHHHhcCChhHHHHHHHHHHHcCCC-CCHHHHHHHHHHHH
Q 040027          468 -LKFAWELFCSLPHGVLVP-NVVTYNIMIQGLCNDGQMDKARDLFLDMEENAAA-PDVITFDMLIHGFI  533 (595)
Q Consensus       468 -~~~A~~~~~~~~~~~~~p-~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~-~~~~~~~~l~~~~~  533 (595)
                       +++|+..+.++++  +.| +...|+.+...+.. ...+++.+.++...+.... .+...+..++..|.
T Consensus       201 ~~~~ai~~~~~al~--~~P~~~~~~~~l~~ll~~-~~~~~~~~~~~~~~~l~~~~~~~~~~~~l~~~y~  266 (315)
T d2h6fa1         201 VLEREVQYTLEMIK--LVPHNESAWNYLKGILQD-RGLSKYPNLLNQLLDLQPSHSSPYLIAFLVDIYE  266 (315)
T ss_dssp             HHHHHHHHHHHHHH--HSTTCHHHHHHHHHHHTT-TCGGGCHHHHHHHHHHTTTCCCHHHHHHHHHHHH
T ss_pred             hhHHhHHHHHHHHH--hCCCchHHHHHHHHHHHh-cChHHHHHHHHHHHHhCCCcCCHHHHHHHHHHHH
Confidence             4566666666665  334 35556655554433 3356666666666554222 23444555555554

>d2h6fa1 a.118.6.1 (A:55-369) Protein farnesyltransferase alpha-subunit {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: alpha-alpha superhelix
superfamily: Protein prenylyltransferase
family: Protein prenylyltransferase
domain: Protein farnesyltransferase alpha-subunit
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.33  E-value=9.8e-10  Score=100.57  Aligned_cols=216  Identities=11%  Similarity=0.065  Sum_probs=169.4

Q ss_pred             HHHHHHHHHHHHhcCChhHHHHHHHHHHhCCCCCCHHHHHHHHHHHHhcC-CHhHHHHHHHHHHhcCCCCCHhhHHHHHH
Q 040027           96 LYTYNILINCFCKIGRVSLGFIAFGRILRSCFTPNAATFNSLIKGLHAES-RIMEAAALFTKLKAFGCEPNVITYNTLIN  174 (595)
Q Consensus        96 ~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g-~~~~A~~~~~~~~~~~~~~~~~~~~~l~~  174 (595)
                      ...++.+...+.+.+.+++|+.+++++++.. |-+..+|+....++...| ++++|+..++++.+.. +-+..+|..+..
T Consensus        43 ~~a~~~~~~~~~~~e~~~~Al~~~~~ai~ln-P~~~~a~~~r~~~l~~l~~~~~eal~~~~~al~~~-p~~~~a~~~~~~  120 (315)
T d2h6fa1          43 RDVYDYFRAVLQRDERSERAFKLTRDAIELN-AANYTVWHFRRVLLKSLQKDLHEEMNYITAIIEEQ-PKNYQVWHHRRV  120 (315)
T ss_dssp             HHHHHHHHHHHHHTCCCHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCCHHHHHHHHHHHHHHC-TTCHHHHHHHHH
T ss_pred             HHHHHHHHHHHHhCCchHHHHHHHHHHHHHC-CCChHHHHHHHHHHHHhCcCHHHHHHHHHHHHHHH-HhhhhHHHHHhH
Confidence            4567777788889999999999999999986 557888999888888876 5899999999998885 347889999999


Q ss_pred             HHHhcCChhHHHHHHHHHHhcCCCCCccccCcHHHHHHHHHHHHHcCCHhHHHHHHHHHhhCCCCCCHhHHHHHHHHHHh
Q 040027          175 GLCRTGHTMIALNLFEEMANGNGEIGVVCKPNTVTYSTIIDGLCKEGFVDKAKALFLQMKDENINPDVVTYNSLIHGLCH  254 (595)
Q Consensus       175 ~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~~ll~~~~~  254 (595)
                      .+...|++++|+..++++.+.+       |.+..+|..+..++...|++++|.+.++++.+.+. .+...|+.+...+.+
T Consensus       121 ~~~~l~~~~eAl~~~~kal~~d-------p~n~~a~~~~~~~~~~~~~~~~Al~~~~~al~~~p-~n~~a~~~r~~~l~~  192 (315)
T d2h6fa1         121 LVEWLRDPSQELEFIADILNQD-------AKNYHAWQHRQWVIQEFKLWDNELQYVDQLLKEDV-RNNSVWNQRYFVISN  192 (315)
T ss_dssp             HHHHHTCCTTHHHHHHHHHHHC-------TTCHHHHHHHHHHHHHHTCCTTHHHHHHHHHHHCT-TCHHHHHHHHHHHHH
T ss_pred             HHHhhccHHHHHHHHhhhhhhh-------hcchHHHHHHHHHHHHHHhhHHHHHHHHHHHHHCC-ccHHHHHHHHHHHHH
Confidence            9999999999999999999986       67799999999999999999999999999998753 367788887777666


Q ss_pred             cCC------HHHHHHHHHHHHHCCCCCCHhhHHHHHHHHHhcCChHHHHHHHHHHHHCCCC-CCHHHHHHHHHHHH
Q 040027          255 AND------WNEAKRLFIEMMDQGVQPSVVTFNVIMDELCKNRKMDEASRLLDLMVQRGVR-PNACTYNTLMDGFC  323 (595)
Q Consensus       255 ~~~------~~~A~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~~~-~~~~~~~~l~~~~~  323 (595)
                      .+.      +++|+..+.+.++.. +.+...|..+...+.. ...+++...++...+.... .+...+..++..|.
T Consensus       193 ~~~~~~~~~~~~ai~~~~~al~~~-P~~~~~~~~l~~ll~~-~~~~~~~~~~~~~~~l~~~~~~~~~~~~l~~~y~  266 (315)
T d2h6fa1         193 TTGYNDRAVLEREVQYTLEMIKLV-PHNESAWNYLKGILQD-RGLSKYPNLLNQLLDLQPSHSSPYLIAFLVDIYE  266 (315)
T ss_dssp             TTCSCSHHHHHHHHHHHHHHHHHS-TTCHHHHHHHHHHHTT-TCGGGCHHHHHHHHHHTTTCCCHHHHHHHHHHHH
T ss_pred             ccccchhhhhHHhHHHHHHHHHhC-CCchHHHHHHHHHHHh-cChHHHHHHHHHHHHhCCCcCCHHHHHHHHHHHH
Confidence            554      678888888887753 2366667666655444 4457777777777664322 23444555555543

>d1dcea1 a.118.6.1 (A:1-241,A:351-443) Rab geranylgeranyltransferase alpha-subunit, N-terminal domain {Rat (Rattus norvegicus) [TaxId: 10116]}

class: All alpha proteins
fold: alpha-alpha superhelix
superfamily: Protein prenylyltransferase
family: Protein prenylyltransferase
domain: Rab geranylgeranyltransferase alpha-subunit, N-terminal domain
species: Rat (Rattus norvegicus) [TaxId: 10116]

Probab=99.30  E-value=5.4e-12  Score=117.77  Aligned_cols=275  Identities=9%  Similarity=-0.028  Sum_probs=189.1

Q ss_pred             CChHHHHHHHHHHHHhCCCCCCHhhHHHHHHHHHcCCCchhHHhhCCCCCCHHHHHHHHHHHHhcCChhHHHHHHHHHHh
Q 040027           45 ITPNEAFCIFDYMLRMHPSPPPVSSFNILLASLAKNKHYDTRLNATGLFPNLYTYNILINCFCKIGRVSLGFIAFGRILR  124 (595)
Q Consensus        45 ~~~~~A~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~  124 (595)
                      +..++|+++++++++.+|+  +...|+..-..+...+.                   ....+...|++++|+..++.+++
T Consensus        43 ~~~~~al~~~~~~l~~~P~--~~~a~~~r~~~l~~l~~-------------------~~~~~~~~~~~~~al~~~~~~l~  101 (334)
T d1dcea1          43 ELDESVLELTSQILGANPD--FATLWNCRREVLQHLET-------------------EKSPEESAALVKAELGFLESCLR  101 (334)
T ss_dssp             CCSHHHHHHHHHHHHHCTT--CHHHHHHHHHHHHHHHT-------------------TSCHHHHHHHHHHHHHHHHHHHH
T ss_pred             cccHHHHHHHHHHHHHCCC--cHHHHHHHHHHHHHHhh-------------------hcchHHHHHHHHHHHHHHHHHHH
Confidence            3458999999999999998  88888655443322211                   11124566778899999999988


Q ss_pred             CCCCCCHHHHHHHHHHHHhcC--CHhHHHHHHHHHHhcCCCCCHhhH-HHHHHHHHhcCChhHHHHHHHHHHhcCCCCCc
Q 040027          125 SCFTPNAATFNSLIKGLHAES--RIMEAAALFTKLKAFGCEPNVITY-NTLINGLCRTGHTMIALNLFEEMANGNGEIGV  201 (595)
Q Consensus       125 ~~~~~~~~~~~~l~~~~~~~g--~~~~A~~~~~~~~~~~~~~~~~~~-~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~~~  201 (595)
                      .. +.+...|..+...+...+  ++++|+..+.++.... +++...+ ......+...|.+++|+..++.+...+     
T Consensus       102 ~~-pk~~~~~~~~~~~~~~~~~~~~~~a~~~~~~al~~~-~~~~~~~~~~~~~~~~~~~~~~~Al~~~~~~i~~~-----  174 (334)
T d1dcea1         102 VN-PKSYGTWHHRCWLLSRLPEPNWARELELCARFLEAD-ERNFHCWDYRRFVAAQAAVAPAEELAFTDSLITRN-----  174 (334)
T ss_dssp             HC-TTCHHHHHHHHHHHHTCSSCCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTCCCHHHHHHHHHTTTTTT-----
T ss_pred             hC-CCcHHHHHHhhHHHHHhccccHHHHHHHHHHHHhhC-chhhhhhhhHHHHHHHhccccHHHHHHHHHHHHcC-----
Confidence            75 557778888777776655  5789999999998874 3355554 445577778899999999999998876     


Q ss_pred             cccCcHHHHHHHHHHHHHcCCHhHHHHHHHHHhhCCCCCCHhHHHHHHHHHHhcCCHHHHHHHHHHHHHCCCCCCHhhHH
Q 040027          202 VCKPNTVTYSTIIDGLCKEGFVDKAKALFLQMKDENINPDVVTYNSLIHGLCHANDWNEAKRLFIEMMDQGVQPSVVTFN  281 (595)
Q Consensus       202 ~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~~ll~~~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~  281 (595)
                        |.+..+|..+..++...|++++|...++......  |   ....+...+...+..+++...+....... +++...+.
T Consensus       175 --p~~~~a~~~l~~~~~~~~~~~~A~~~~~~~~~~~--~---~~~~~~~~~~~l~~~~~a~~~~~~~l~~~-~~~~~~~~  246 (334)
T d1dcea1         175 --FSNYSSWHYRSCLLPQLHPQPDSGPQGRLPENVL--L---KELELVQNAFFTDPNDQSAWFYHRWLLGR-AEPLFRCE  246 (334)
T ss_dssp             --CCCHHHHHHHHHHHHHHSCCCCSSSCCSSCHHHH--H---HHHHHHHHHHHHCSSCSHHHHHHHHHHSC-CCCSSSCC
T ss_pred             --CCCHHHHHHHHHHHHHhcCHHHHHHHHHHhHHhH--H---HHHHHHHHHHHhcchhHHHHHHHHHHHhC-cchhhHHH
Confidence              5678889999999999999888766655444321  1   11223334455566677777777776653 23444555


Q ss_pred             HHHHHHHhcCChHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHhcCCCCCHHHHHHHHHHH
Q 040027          282 VIMDELCKNRKMDEASRLLDLMVQRGVRPNACTYNTLMDGFCLMGKINRAEELFGSMESMGCKHDDVSYNILINGY  357 (595)
Q Consensus       282 ~l~~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~  357 (595)
                      .++..+...+++.+|...+.+....+ +.+..++..++.++...|++++|.+.++++.+.+ |.....|..+...+
T Consensus       247 ~l~~~~~~~~~~~~a~~~~~~~~~~~-p~~~~~~~~l~~~~~~~~~~~eA~~~~~~ai~ld-P~~~~y~~~L~~~~  320 (334)
T d1dcea1         247 LSVEKSTVLQSELESCKELQELEPEN-KWCLLTIILLMRALDPLLYEKETLQYFSTLKAVD-PMRAAYLDDLRSKF  320 (334)
T ss_dssp             CCHHHHHHHHHHHHHHHHHHHHCTTC-HHHHHHHHHHHHHHCTGGGHHHHHHHHHHHHHHC-GGGHHHHHHHHHHH
T ss_pred             HHHHHHHHHhhHHHHHHHHHHHHhhC-chHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHC-cccHHHHHHHHHHH
Confidence            66667777778888888887776653 2245566677777888888888888888887763 22333455454444

>d2onda1 a.118.8.7 (A:242-549) Cleavage stimulation factor 77 kDa subunit CSTF3 {Mouse (Mus musculus) [TaxId: 10090]}

class: All alpha proteins
fold: alpha-alpha superhelix
superfamily: TPR-like
family: HAT/Suf repeat
domain: Cleavage stimulation factor 77 kDa subunit CSTF3
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.29  E-value=7.2e-10  Score=101.51  Aligned_cols=235  Identities=10%  Similarity=0.024  Sum_probs=160.3

Q ss_pred             hHHHHHHHHHHHHhCCCCCCHhhHHHHHHHHHcCCCchhHHhhCCCCCCHHHHHHHHHHHHhcCChhHHHHHHHHHHhCC
Q 040027           47 PNEAFCIFDYMLRMHPSPPPVSSFNILLASLAKNKHYDTRLNATGLFPNLYTYNILINCFCKIGRVSLGFIAFGRILRSC  126 (595)
Q Consensus        47 ~~~A~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~  126 (595)
                      .+.+..+|++++...|.  ++..|..-+.-+...++..   ...+.            .....+..++|..+|+++++..
T Consensus        32 ~~Rv~~vyerAl~~~~~--~~~lW~~y~~~~~~~~~~~---~~~~~------------~~~~~~~~~~a~~i~~ral~~~   94 (308)
T d2onda1          32 TKRVMFAYEQCLLVLGH--HPDIWYEAAQYLEQSSKLL---AEKGD------------MNNAKLFSDEAANIYERAISTL   94 (308)
T ss_dssp             HHHHHHHHHHHHHHHTT--CHHHHHHHHHHHHHHHHHH---HHTSC------------CHHHHHHHHHHHHHHHHHHTTT
T ss_pred             HHHHHHHHHHHHHHCCC--CHHHHHHHHHHHHHcCchH---HHHHH------------HhhcccchHHHHHHHHHHHHHc
Confidence            45678899999999887  7788876655443322211   00110            1122345577888888888765


Q ss_pred             CCCCHHHHHHHHHHHHhcCCHhHHHHHHHHHHhcCCCCCHhhHHHHHHHHHhcCChhHHHHHHHHHHhcCCCCCccccCc
Q 040027          127 FTPNAATFNSLIKGLHAESRIMEAAALFTKLKAFGCEPNVITYNTLINGLCRTGHTMIALNLFEEMANGNGEIGVVCKPN  206 (595)
Q Consensus       127 ~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~~  206 (595)
                      .+.+...|...+..+...|++++|..+|+++..........+|...+..+.+.|+.+.|.++|+++....       +.+
T Consensus        95 ~p~~~~l~~~ya~~~~~~~~~~~a~~i~~~~l~~~~~~~~~~w~~~~~~~~~~~~~~~ar~i~~~al~~~-------~~~  167 (308)
T d2onda1          95 LKKNMLLYFAYADYEESRMKYEKVHSIYNRLLAIEDIDPTLVYIQYMKFARRAEGIKSGRMIFKKAREDA-------RTR  167 (308)
T ss_dssp             TTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHTSSSSCTHHHHHHHHHHHHHHHCHHHHHHHHHHHHTST-------TCC
T ss_pred             CCCCHHHHHHHHHHHHhcccHHHHHHHHHHHHHHhcCChHHHHHHHHHHHHHcCChHHHHHHHHHHHHhC-------CCc
Confidence            5666777888888888888888888888888876433334567888888888888888888888887764       344


Q ss_pred             HHHHHHHHHH-HHHcCCHhHHHHHHHHHhhCCCCCCHhHHHHHHHHHHhcCCHHHHHHHHHHHHHCC-CCCC--HhhHHH
Q 040027          207 TVTYSTIIDG-LCKEGFVDKAKALFLQMKDENINPDVVTYNSLIHGLCHANDWNEAKRLFIEMMDQG-VQPS--VVTFNV  282 (595)
Q Consensus       207 ~~~~~~l~~~-~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~~ll~~~~~~~~~~~A~~~~~~~~~~~-~~~~--~~~~~~  282 (595)
                      ...|...+.. +...|+.+.|..+|+.+.... +.+...|...+..+...|+++.|..+|++.+... ..|.  ...|..
T Consensus       168 ~~~~~~~a~~e~~~~~~~~~a~~i~e~~l~~~-p~~~~~w~~y~~~~~~~g~~~~aR~~fe~ai~~~~~~~~~~~~iw~~  246 (308)
T d2onda1         168 HHVYVTAALMEYYCSKDKSVAFKIFELGLKKY-GDIPEYVLAYIDYLSHLNEDNNTRVLFERVLTSGSLPPEKSGEIWAR  246 (308)
T ss_dssp             THHHHHHHHHHHHTSCCHHHHHHHHHHHHHHH-TTCHHHHHHHHHHHHTTCCHHHHHHHHHHHHHSSSSCGGGCHHHHHH
T ss_pred             HHHHHHHHHHHHHhccCHHHHHHHHHHHHHhh-hhhHHHHHHHHHHHHHcCChHHHHHHHHHHHHhCCCChHHHHHHHHH
Confidence            4455444443 234577888888888877752 3467778888888888888888888888877653 2222  235666


Q ss_pred             HHHHHHhcCChHHHHHHHHHHHHC
Q 040027          283 IMDELCKNRKMDEASRLLDLMVQR  306 (595)
Q Consensus       283 l~~~~~~~g~~~~a~~~~~~~~~~  306 (595)
                      .+..-...|+.+.+..+++++.+.
T Consensus       247 ~~~fE~~~G~~~~~~~~~~r~~~~  270 (308)
T d2onda1         247 FLAFESNIGDLASILKVEKRRFTA  270 (308)
T ss_dssp             HHHHHHHHSCHHHHHHHHHHHHHH
T ss_pred             HHHHHHHcCCHHHHHHHHHHHHHH
Confidence            666666778888888877776553

>d1hz4a_ a.118.8.2 (A:) Transcription factor MalT domain III {Escherichia coli [TaxId: 562]}

class: All alpha proteins
fold: alpha-alpha superhelix
superfamily: TPR-like
family: Transcription factor MalT domain III
domain: Transcription factor MalT domain III
species: Escherichia coli [TaxId: 562]

Probab=99.28  E-value=3.3e-09  Score=99.41  Aligned_cols=262  Identities=11%  Similarity=0.005  Sum_probs=147.1

Q ss_pred             HHHHHHHHHhcCCHHHHHHHHHHHHhcCC--C---CCHHHHHHHHHHHHhCCCHHHHHHHHHHHHHC----CCCCC---H
Q 040027          315 YNTLMDGFCLMGKINRAEELFGSMESMGC--K---HDDVSYNILINGYCKNKEVEEALSLYREMVSK----GIKPT---V  382 (595)
Q Consensus       315 ~~~l~~~~~~~~~~~~a~~~~~~~~~~~~--~---~~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~~----~~~~~---~  382 (595)
                      +..+..++...|++++|...+++..+...  .   .....+..+...+...|++..+...+......    +....   .
T Consensus        54 ~~~lg~~~~~~g~~~~A~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~a~~~~~~al~~~~~~~~~~~~~~~  133 (366)
T d1hz4a_          54 TSVLGEVLHCKGELTRSLALMQQTEQMARQHDVWHYALWSLIQQSEILFAQGFLQTAWETQEKAFQLINEQHLEQLPMHE  133 (366)
T ss_dssp             HHHHHHHHHHHTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCTTSTHHH
T ss_pred             HHHHHHHHHHCCCHHHHHHHHHHHHHHHHhhcchHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhHhcccchhhHHH
Confidence            33344444555555555555554432110  0   00123334444555556666665555544321    11111   1


Q ss_pred             HHHHHHHHHHHccCCHHHHHHHHHHHHHC----CCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHHcC--CCc----CH
Q 040027          383 VTYNTLFLGLFEIHQVEHALKLFDEMQRD----GVAADTRTYTTFIDGLCKNGYIIEAVELFRTLRILK--CEL----DI  452 (595)
Q Consensus       383 ~~~~~l~~~~~~~~~~~~a~~~~~~~~~~----~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~--~~~----~~  452 (595)
                      ..+..+...+...|+++.+...+......    +.......+......+...++...+...+.+.....  ...    ..
T Consensus       134 ~~~~~la~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~a~~~~~~a~~~~~~~~~~~~~~~  213 (366)
T d1hz4a_         134 FLVRIRAQLLWAWARLDEAEASARSGIEVLSSYQPQQQLQCLAMLIQCSLARGDLDNARSQLNRLENLLGNGKYHSDWIS  213 (366)
T ss_dssp             HHHHHHHHHHHHTTCHHHHHHHHHHHHHHTTTSCGGGGHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHTTSCCCHHHHH
T ss_pred             HHHHHHHHHHHHhcchhhhHHHHHHHHHHhhhhhhhhHHHHHHHHHHHHHhhhhHHHHHHHHHHHHHHHHHhcccCchHH
Confidence            23334445566666666666666665542    111223344445555666777777777766654321  011    12


Q ss_pred             HHHHHHHHHHHhcCChHHHHHHHHhcccCCCCCC---HHHHHHHHHHHHhcCChhHHHHHHHHHHHc----CCCCC-HHH
Q 040027          453 QAYNCLIDGLCKSGRLKFAWELFCSLPHGVLVPN---VVTYNIMIQGLCNDGQMDKARDLFLDMEEN----AAAPD-VIT  524 (595)
Q Consensus       453 ~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~p~---~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~----~~~~~-~~~  524 (595)
                      ..+..+...+...|++++|...+.+........+   ...+..+..++...|++++|...+++++..    +..|+ ..+
T Consensus       214 ~~~~~~~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~la~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~  293 (366)
T d1hz4a_         214 NANKVRVIYWQMTGDKAAAANWLRHTAKPEFANNHFLQGQWRNIARAQILLGEFEPAEIVLEELNENARSLRLMSDLNRN  293 (366)
T ss_dssp             HHHHHHHHHHHHTTCHHHHHHHHHHSCCCCCTTCGGGHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCHHHHHHH
T ss_pred             HHHHHHHHHHHhcccHHHHHHHHHHHHHhccccchHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHhhcccChHHHHH
Confidence            3455566677788888888888888776322211   345566778888889999999888887642    32333 356


Q ss_pred             HHHHHHHHHHcCChhHHHHHHHHHHHC----CCC----CCHHHHHHHHHHHHhcCccccc
Q 040027          525 FDMLIHGFIRINEPSKVNELLHKMKEK----KVM----PDASIVSIVVDLLVKNEISLKS  576 (595)
Q Consensus       525 ~~~l~~~~~~~g~~~~A~~~~~~~~~~----~~~----p~~~~~~~l~~~~~~~g~~~~~  576 (595)
                      +..+..+|...|++++|.+.+++.++.    |..    -....+..++..+...|+.+++
T Consensus       294 ~~~la~~~~~~g~~~~A~~~l~~Al~l~~~~~~~~~~~~~~~~~~~~~~~l~~~~~l~e~  353 (366)
T d1hz4a_         294 LLLLNQLYWQAGRKSDAQRVLLDALKLANRTGFISHFVIEGEAMAQQLRQLIQLNTLPEL  353 (366)
T ss_dssp             HHHHHHHHHHHTCHHHHHHHHHHHHHHHHHHCCCHHHHTTHHHHHHHHHHHHHTTCSCHH
T ss_pred             HHHHHHHHHHCCCHHHHHHHHHHHHHHhhhcCcHHHHHHHHHHHHHHHHHHHhcCCChHH
Confidence            777888888999999999988887642    221    1233455566667777776643

>d1hz4a_ a.118.8.2 (A:) Transcription factor MalT domain III {Escherichia coli [TaxId: 562]}

class: All alpha proteins
fold: alpha-alpha superhelix
superfamily: TPR-like
family: Transcription factor MalT domain III
domain: Transcription factor MalT domain III
species: Escherichia coli [TaxId: 562]

Probab=99.28  E-value=1.7e-09  Score=101.43  Aligned_cols=279  Identities=11%  Similarity=-0.015  Sum_probs=183.8

Q ss_pred             HHHHHHHHHHHhcCChhHHHHHHHHHHhCCCCCC----HHHHHHHHHHHHhcCCHhHHHHHHHHHHhcCCC-CC----Hh
Q 040027           97 YTYNILINCFCKIGRVSLGFIAFGRILRSCFTPN----AATFNSLIKGLHAESRIMEAAALFTKLKAFGCE-PN----VI  167 (595)
Q Consensus        97 ~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~~----~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~-~~----~~  167 (595)
                      .........+...|++++|+.++++++......+    ..++..+...+...|++++|++.|++....... ++    ..
T Consensus        13 e~~~lrA~~~~~~g~~~~A~~~~~~aL~~~~~~~~~~~~~a~~~lg~~~~~~g~~~~A~~~~~~a~~~~~~~~~~~~~~~   92 (366)
T d1hz4a_          13 EFNALRAQVAINDGNPDEAERLAKLALEELPPGWFYSRIVATSVLGEVLHCKGELTRSLALMQQTEQMARQHDVWHYALW   92 (366)
T ss_dssp             HHHHHHHHHHHHTTCHHHHHHHHHHHHHTCCTTCHHHHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHHHTTCHHHHHH
T ss_pred             HHHHHHHHHHHHCCCHHHHHHHHHHHHhhCcCCCcHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHhhcchHHHHH
Confidence            4444566778899999999999999998743222    235677788899999999999999988764211 11    23


Q ss_pred             hHHHHHHHHHhcCChhHHHHHHHHHHhcCCCCCccccC-cHHHHHHHHHHHHHcCCHhHHHHHHHHHhhCC----CCCCH
Q 040027          168 TYNTLINGLCRTGHTMIALNLFEEMANGNGEIGVVCKP-NTVTYSTIIDGLCKEGFVDKAKALFLQMKDEN----INPDV  242 (595)
Q Consensus       168 ~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~-~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~----~~~~~  242 (595)
                      .+..+...+...|++..+...+...............+ ....+..+...+...|+++.+...+.......    .....
T Consensus        93 ~~~~~~~~~~~~~~~~~a~~~~~~al~~~~~~~~~~~~~~~~~~~~la~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~  172 (366)
T d1hz4a_          93 SLIQQSEILFAQGFLQTAWETQEKAFQLINEQHLEQLPMHEFLVRIRAQLLWAWARLDEAEASARSGIEVLSSYQPQQQL  172 (366)
T ss_dssp             HHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCTTSTHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHTTTSCGGGGH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHhHhcccchhhHHHHHHHHHHHHHHHhcchhhhHHHHHHHHHHhhhhhhhhHH
Confidence            45667778889999999999998876432110000111 23456667788889999999999988876532    12233


Q ss_pred             hHHHHHHHHHHhcCCHHHHHHHHHHHHHCC--CCCC----HhhHHHHHHHHHhcCChHHHHHHHHHHHHCCCCC---CHH
Q 040027          243 VTYNSLIHGLCHANDWNEAKRLFIEMMDQG--VQPS----VVTFNVIMDELCKNRKMDEASRLLDLMVQRGVRP---NAC  313 (595)
Q Consensus       243 ~~~~~ll~~~~~~~~~~~A~~~~~~~~~~~--~~~~----~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~~~~---~~~  313 (595)
                      ..+..+...+...+++..+...+.+.....  ....    ...+......+...|+++.|...+..........   ...
T Consensus       173 ~~~~~~~~~~~~~~~~~~a~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~  252 (366)
T d1hz4a_         173 QCLAMLIQCSLARGDLDNARSQLNRLENLLGNGKYHSDWISNANKVRVIYWQMTGDKAAAANWLRHTAKPEFANNHFLQG  252 (366)
T ss_dssp             HHHHHHHHHHHHHTCHHHHHHHHHHHHHHHTTSCCCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHSCCCCCTTCGGGHH
T ss_pred             HHHHHHHHHHHhhhhHHHHHHHHHHHHHHHHHhcccCchHHHHHHHHHHHHHhcccHHHHHHHHHHHHHhccccchHHHH
Confidence            455566677788888888888877665421  1111    2234555667777888888888877766542221   233


Q ss_pred             HHHHHHHHHHhcCCHHHHHHHHHHHHhc----CCCC-CHHHHHHHHHHHHhCCCHHHHHHHHHHHHH
Q 040027          314 TYNTLMDGFCLMGKINRAEELFGSMESM----GCKH-DDVSYNILINGYCKNKEVEEALSLYREMVS  375 (595)
Q Consensus       314 ~~~~l~~~~~~~~~~~~a~~~~~~~~~~----~~~~-~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~  375 (595)
                      .+..+..++...|++++|...++.+...    +..| ....+..+..+|...|++++|.+.+++.++
T Consensus       253 ~~~~la~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~la~~~~~~g~~~~A~~~l~~Al~  319 (366)
T d1hz4a_         253 QWRNIARAQILLGEFEPAEIVLEELNENARSLRLMSDLNRNLLLLNQLYWQAGRKSDAQRVLLDALK  319 (366)
T ss_dssp             HHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHHTCHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHcCCHHHHHHHHHHHHHHHhhcccChHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHH
Confidence            4455677777788888888777776432    2222 223566666777777777777777776654

>d2onda1 a.118.8.7 (A:242-549) Cleavage stimulation factor 77 kDa subunit CSTF3 {Mouse (Mus musculus) [TaxId: 10090]}

class: All alpha proteins
fold: alpha-alpha superhelix
superfamily: TPR-like
family: HAT/Suf repeat
domain: Cleavage stimulation factor 77 kDa subunit CSTF3
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.25  E-value=1.8e-09  Score=98.83  Aligned_cols=187  Identities=12%  Similarity=0.007  Sum_probs=112.9

Q ss_pred             HHHHHHHHHHHHhcCCCCCHHHHHHHHHHHHhCCCHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHccCCHHHHHHHHHH
Q 040027          328 INRAEELFGSMESMGCKHDDVSYNILINGYCKNKEVEEALSLYREMVSKGIKPTVVTYNTLFLGLFEIHQVEHALKLFDE  407 (595)
Q Consensus       328 ~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~  407 (595)
                      .+++..+|++..+...+.+...|...+......|+++.|..+|++++..........|...+..+.+.|+.+.|.++|+.
T Consensus        80 ~~~a~~i~~ral~~~~p~~~~l~~~ya~~~~~~~~~~~a~~i~~~~l~~~~~~~~~~w~~~~~~~~~~~~~~~ar~i~~~  159 (308)
T d2onda1          80 SDEAANIYERAISTLLKKNMLLYFAYADYEESRMKYEKVHSIYNRLLAIEDIDPTLVYIQYMKFARRAEGIKSGRMIFKK  159 (308)
T ss_dssp             HHHHHHHHHHHHTTTTTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHTSSSSCTHHHHHHHHHHHHHHHCHHHHHHHHHH
T ss_pred             hHHHHHHHHHHHHHcCCCCHHHHHHHHHHHHhcccHHHHHHHHHHHHHHhcCChHHHHHHHHHHHHHcCChHHHHHHHHH
Confidence            45666677766654334455566666666777777777777777776653333334566666666667777777777777


Q ss_pred             HHHCCCCCCHHHHHHHHHH-HHhcCCHHHHHHHHHHHHHcCCCcCHHHHHHHHHHHHhcCChHHHHHHHHhcccCC-CCC
Q 040027          408 MQRDGVAADTRTYTTFIDG-LCKNGYIIEAVELFRTLRILKCELDIQAYNCLIDGLCKSGRLKFAWELFCSLPHGV-LVP  485 (595)
Q Consensus       408 ~~~~~~~~~~~~~~~l~~~-~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~-~~p  485 (595)
                      +.+.+ +.+...+...... +...|+.+.|..+|+.+.+.. +.+...|..++..+...|+++.|+.+|++..... ..|
T Consensus       160 al~~~-~~~~~~~~~~a~~e~~~~~~~~~a~~i~e~~l~~~-p~~~~~w~~y~~~~~~~g~~~~aR~~fe~ai~~~~~~~  237 (308)
T d2onda1         160 AREDA-RTRHHVYVTAALMEYYCSKDKSVAFKIFELGLKKY-GDIPEYVLAYIDYLSHLNEDNNTRVLFERVLTSGSLPP  237 (308)
T ss_dssp             HHTST-TCCTHHHHHHHHHHHHTSCCHHHHHHHHHHHHHHH-TTCHHHHHHHHHHHHTTCCHHHHHHHHHHHHHSSSSCG
T ss_pred             HHHhC-CCcHHHHHHHHHHHHHhccCHHHHHHHHHHHHHhh-hhhHHHHHHHHHHHHHcCChHHHHHHHHHHHHhCCCCh
Confidence            66653 3333333333322 233466777777777766653 4556666677777677777777777777665532 222


Q ss_pred             C--HHHHHHHHHHHHhcCChhHHHHHHHHHHHc
Q 040027          486 N--VVTYNIMIQGLCNDGQMDKARDLFLDMEEN  516 (595)
Q Consensus       486 ~--~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~  516 (595)
                      .  ...|...+..-...|+.+.+.++++++.+.
T Consensus       238 ~~~~~iw~~~~~fE~~~G~~~~~~~~~~r~~~~  270 (308)
T d2onda1         238 EKSGEIWARFLAFESNIGDLASILKVEKRRFTA  270 (308)
T ss_dssp             GGCHHHHHHHHHHHHHHSCHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHH
Confidence            2  235666666556667777777666666553

>d1dcea1 a.118.6.1 (A:1-241,A:351-443) Rab geranylgeranyltransferase alpha-subunit, N-terminal domain {Rat (Rattus norvegicus) [TaxId: 10116]}

class: All alpha proteins
fold: alpha-alpha superhelix
superfamily: Protein prenylyltransferase
family: Protein prenylyltransferase
domain: Rab geranylgeranyltransferase alpha-subunit, N-terminal domain
species: Rat (Rattus norvegicus) [TaxId: 10116]

Probab=99.19  E-value=1.5e-10  Score=107.70  Aligned_cols=265  Identities=10%  Similarity=0.037  Sum_probs=141.5

Q ss_pred             hcCChhHHHHHHHHHHhcCCCCCccccCcHHHHHHHHHHHH----------HcCCHhHHHHHHHHHhhCCCCCCHhHHHH
Q 040027          178 RTGHTMIALNLFEEMANGNGEIGVVCKPNTVTYSTIIDGLC----------KEGFVDKAKALFLQMKDENINPDVVTYNS  247 (595)
Q Consensus       178 ~~g~~~~A~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~----------~~g~~~~A~~~~~~~~~~~~~~~~~~~~~  247 (595)
                      ..+..++|+++++++...+       |.+...|+..-..+.          ..|++++|...++.+.+.+ +-+...|..
T Consensus        41 ~~~~~~~al~~~~~~l~~~-------P~~~~a~~~r~~~l~~l~~~~~~~~~~~~~~~al~~~~~~l~~~-pk~~~~~~~  112 (334)
T d1dcea1          41 AGELDESVLELTSQILGAN-------PDFATLWNCRREVLQHLETEKSPEESAALVKAELGFLESCLRVN-PKSYGTWHH  112 (334)
T ss_dssp             TTCCSHHHHHHHHHHHHHC-------TTCHHHHHHHHHHHHHHHTTSCHHHHHHHHHHHHHHHHHHHHHC-TTCHHHHHH
T ss_pred             cccccHHHHHHHHHHHHHC-------CCcHHHHHHHHHHHHHHhhhcchHHHHHHHHHHHHHHHHHHHhC-CCcHHHHHH
Confidence            3444588999999998876       445556654433322          2344667777777776653 235566666


Q ss_pred             HHHHHHhcC--CHHHHHHHHHHHHHCCCCCCHhhHH-HHHHHHHhcCChHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHh
Q 040027          248 LIHGLCHAN--DWNEAKRLFIEMMDQGVQPSVVTFN-VIMDELCKNRKMDEASRLLDLMVQRGVRPNACTYNTLMDGFCL  324 (595)
Q Consensus       248 ll~~~~~~~--~~~~A~~~~~~~~~~~~~~~~~~~~-~l~~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~  324 (595)
                      +..++...+  ++++|...+..+..... ++...+. .....+...+.++.|+..++.++..+. -+...+..+..++..
T Consensus       113 ~~~~~~~~~~~~~~~a~~~~~~al~~~~-~~~~~~~~~~~~~~~~~~~~~~Al~~~~~~i~~~p-~~~~a~~~l~~~~~~  190 (334)
T d1dcea1         113 RCWLLSRLPEPNWARELELCARFLEADE-RNFHCWDYRRFVAAQAAVAPAEELAFTDSLITRNF-SNYSSWHYRSCLLPQ  190 (334)
T ss_dssp             HHHHHHTCSSCCHHHHHHHHHHHHHHCT-TCHHHHHHHHHHHHHTCCCHHHHHHHHHTTTTTTC-CCHHHHHHHHHHHHH
T ss_pred             hhHHHHHhccccHHHHHHHHHHHHhhCc-hhhhhhhhHHHHHHHhccccHHHHHHHHHHHHcCC-CCHHHHHHHHHHHHH
Confidence            665555544  46777777777766422 2344433 344556666777777777777766643 256666667777777


Q ss_pred             cCCHHHHHHHHHHHHhcCCCCCHHHHHHHHHHHHhCCCHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHccCCHHHHHHH
Q 040027          325 MGKINRAEELFGSMESMGCKHDDVSYNILINGYCKNKEVEEALSLYREMVSKGIKPTVVTYNTLFLGLFEIHQVEHALKL  404 (595)
Q Consensus       325 ~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~  404 (595)
                      .|++++|...+....+.  .|.   .......+...+..+++...+......... +...+..+...+...++.+++...
T Consensus       191 ~~~~~~A~~~~~~~~~~--~~~---~~~~~~~~~~l~~~~~a~~~~~~~l~~~~~-~~~~~~~l~~~~~~~~~~~~a~~~  264 (334)
T d1dcea1         191 LHPQPDSGPQGRLPENV--LLK---ELELVQNAFFTDPNDQSAWFYHRWLLGRAE-PLFRCELSVEKSTVLQSELESCKE  264 (334)
T ss_dssp             HSCCCCSSSCCSSCHHH--HHH---HHHHHHHHHHHCSSCSHHHHHHHHHHSCCC-CSSSCCCCHHHHHHHHHHHHHHHH
T ss_pred             hcCHHHHHHHHHHhHHh--HHH---HHHHHHHHHHhcchhHHHHHHHHHHHhCcc-hhhHHHHHHHHHHHHhhHHHHHHH
Confidence            77766665444433322  011   111222233344455555555555544221 233333344444445555555555


Q ss_pred             HHHHHHCCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCcCHHHHHHHHH
Q 040027          405 FDEMQRDGVAADTRTYTTFIDGLCKNGYIIEAVELFRTLRILKCELDIQAYNCLID  460 (595)
Q Consensus       405 ~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~~l~~  460 (595)
                      +.+..+.+ +.+...+..+..++...|++++|...++++.+.+ |.+...|..+..
T Consensus       265 ~~~~~~~~-p~~~~~~~~l~~~~~~~~~~~eA~~~~~~ai~ld-P~~~~y~~~L~~  318 (334)
T d1dcea1         265 LQELEPEN-KWCLLTIILLMRALDPLLYEKETLQYFSTLKAVD-PMRAAYLDDLRS  318 (334)
T ss_dssp             HHHHCTTC-HHHHHHHHHHHHHHCTGGGHHHHHHHHHHHHHHC-GGGHHHHHHHHH
T ss_pred             HHHHHhhC-chHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHC-cccHHHHHHHHH
Confidence            55554432 2233444445555555555555555555555543 223334444433

>d1xnfa_ a.118.8.1 (A:) Lipoprotein NlpI {Escherichia coli [TaxId: 562]}

class: All alpha proteins
fold: alpha-alpha superhelix
superfamily: TPR-like
family: Tetratricopeptide repeat (TPR)
domain: Lipoprotein NlpI
species: Escherichia coli [TaxId: 562]

Probab=99.19  E-value=6.6e-10  Score=99.11  Aligned_cols=96  Identities=9%  Similarity=-0.059  Sum_probs=55.5

Q ss_pred             HHHHHHHHHHhcCCHHHHHHHHHHHHhcCCCCCHHHHHHHHHHHHhCCCHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHH
Q 040027          314 TYNTLMDGFCLMGKINRAEELFGSMESMGCKHDDVSYNILINGYCKNKEVEEALSLYREMVSKGIKPTVVTYNTLFLGLF  393 (595)
Q Consensus       314 ~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~~l~~~~~  393 (595)
                      ++..++.+|.+.|++++|+..|++.++.. |.+..+|..+..+|.+.|++++|+..|+++++..+. +..++..+...+.
T Consensus        39 ~~~~~G~~y~~~g~~~~A~~~~~~al~l~-p~~~~a~~~lg~~~~~~g~~~~A~~~~~~al~~~p~-~~~a~~~lg~~~~  116 (259)
T d1xnfa_          39 LLYERGVLYDSLGLRALARNDFSQALAIR-PDMPEVFNYLGIYLTQAGNFDAAYEAFDSVLELDPT-YNYAHLNRGIALY  116 (259)
T ss_dssp             HHHHHHHHHHHTTCHHHHHHHHHHHHHHC-CCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTT-CTHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHCCCHHHHHHHHHHhhccC-CCCHHHHhhhchHHHHHHHHHHhhhhhhHHHHHHhh-hhhhHHHHHHHHH
Confidence            44455556666666666666666665553 344555666666666666666666666666654332 3445555555566


Q ss_pred             ccCCHHHHHHHHHHHHHC
Q 040027          394 EIHQVEHALKLFDEMQRD  411 (595)
Q Consensus       394 ~~~~~~~a~~~~~~~~~~  411 (595)
                      ..|++++|...++...+.
T Consensus       117 ~~g~~~~A~~~~~~al~~  134 (259)
T d1xnfa_         117 YGGRDKLAQDDLLAFYQD  134 (259)
T ss_dssp             HTTCHHHHHHHHHHHHHH
T ss_pred             HHhhHHHHHHHHHHHHhh
Confidence            666666666666665554

>d1xnfa_ a.118.8.1 (A:) Lipoprotein NlpI {Escherichia coli [TaxId: 562]}

class: All alpha proteins
fold: alpha-alpha superhelix
superfamily: TPR-like
family: Tetratricopeptide repeat (TPR)
domain: Lipoprotein NlpI
species: Escherichia coli [TaxId: 562]

Probab=99.17  E-value=9.9e-10  Score=97.92  Aligned_cols=220  Identities=10%  Similarity=-0.108  Sum_probs=152.5

Q ss_pred             HHHHHHHHHHHHhcCCCC---CHHHHHHHHHHHHhCCCHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHccCCHHHHHHH
Q 040027          328 INRAEELFGSMESMGCKH---DDVSYNILINGYCKNKEVEEALSLYREMVSKGIKPTVVTYNTLFLGLFEIHQVEHALKL  404 (595)
Q Consensus       328 ~~~a~~~~~~~~~~~~~~---~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~  404 (595)
                      .+.++.-++++.......   ...++..+..+|.+.|++++|+..|++.++..+. +..++..+..++...|++++|+..
T Consensus        15 ~e~al~~~~e~l~~~~~~~~~~a~~~~~~G~~y~~~g~~~~A~~~~~~al~l~p~-~~~a~~~lg~~~~~~g~~~~A~~~   93 (259)
T d1xnfa_          15 QEVILARMEQILASRALTDDERAQLLYERGVLYDSLGLRALARNDFSQALAIRPD-MPEVFNYLGIYLTQAGNFDAAYEA   93 (259)
T ss_dssp             HHHHHHHHHHHHTSSCCCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCCC-CHHHHHHHHHHHHHTTCHHHHHHH
T ss_pred             HHHHHHHHHHHHHhhhcCCHHHHHHHHHHHHHHHHCCCHHHHHHHHHHhhccCCC-CHHHHhhhchHHHHHHHHHHhhhh
Confidence            445555566665432111   2236777889999999999999999999987544 778899999999999999999999


Q ss_pred             HHHHHHCCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCcCHHHHHHHHHHHHhcCChHHHHHHHHhcccCCCC
Q 040027          405 FDEMQRDGVAADTRTYTTFIDGLCKNGYIIEAVELFRTLRILKCELDIQAYNCLIDGLCKSGRLKFAWELFCSLPHGVLV  484 (595)
Q Consensus       405 ~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~  484 (595)
                      |+++++.. +.+..++..+..+|...|++++|...+++..+.. +.+......+...+.+.+..+.+..+.......  .
T Consensus        94 ~~~al~~~-p~~~~a~~~lg~~~~~~g~~~~A~~~~~~al~~~-p~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~--~  169 (259)
T d1xnfa_          94 FDSVLELD-PTYNYAHLNRGIALYYGGRDKLAQDDLLAFYQDD-PNDPFRSLWLYLAEQKLDEKQAKEVLKQHFEKS--D  169 (259)
T ss_dssp             HHHHHHHC-TTCTHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHHCHHHHHHHHHHHHHHS--C
T ss_pred             hhHHHHHH-hhhhhhHHHHHHHHHHHhhHHHHHHHHHHHHhhc-cccHHHHHHHHHHHHHhhhHHHHHHHHHHhhcc--c
Confidence            99999874 4567788889999999999999999999999876 556666555566666666666666655555442  2


Q ss_pred             CCHHHHHHHHHHHHhcCC----hhHHHHHHHHHHHcCCCCCHHHHHHHHHHHHHcCChhHHHHHHHHHHHCCCCCC
Q 040027          485 PNVVTYNIMIQGLCNDGQ----MDKARDLFLDMEENAAAPDVITFDMLIHGFIRINEPSKVNELLHKMKEKKVMPD  556 (595)
Q Consensus       485 p~~~~~~~l~~~~~~~g~----~~~A~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~p~  556 (595)
                      ++...+. ++..+.....    .+.+...+....... +....++..++..|...|++++|.+.|++++..  .|+
T Consensus       170 ~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~lg~~~~~~g~~~~A~~~~~~al~~--~p~  241 (259)
T d1xnfa_         170 KEQWGWN-IVEFYLGNISEQTLMERLKADATDNTSLA-EHLSETNFYLGKYYLSLGDLDSATALFKLAVAN--NVH  241 (259)
T ss_dssp             CCSTHHH-HHHHHTTSSCHHHHHHHHHHHCCSHHHHH-HHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHTT--CCT
T ss_pred             hhhhhhh-HHHHHHHHHHHHHHHHHHHHHHHHhhhcC-cccHHHHHHHHHHHHHCCCHHHHHHHHHHHHHc--CCC
Confidence            2222222 2222222211    222222222222211 112346777899999999999999999999974  465

>d1hh8a_ a.118.8.1 (A:) Neutrophil cytosolic factor 2 (NCF-2, p67-phox) {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: alpha-alpha superhelix
superfamily: TPR-like
family: Tetratricopeptide repeat (TPR)
domain: Neutrophil cytosolic factor 2 (NCF-2, p67-phox)
species: Human (Homo sapiens) [TaxId: 9606]

Probab=98.84  E-value=1e-07  Score=79.62  Aligned_cols=142  Identities=11%  Similarity=-0.039  Sum_probs=89.4

Q ss_pred             HHHhcCCHHHHHHHHHHHHHcCCCcCHHHHHHHHHHHHhcCChHHHHHHHHhcccCCCCCC-HHHHHHHHHHHHhcCChh
Q 040027          426 GLCKNGYIIEAVELFRTLRILKCELDIQAYNCLIDGLCKSGRLKFAWELFCSLPHGVLVPN-VVTYNIMIQGLCNDGQMD  504 (595)
Q Consensus       426 ~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~p~-~~~~~~l~~~~~~~g~~~  504 (595)
                      .+...|++++|++.|.++.    ++++.++..++.+|...|++++|+..|++.++  +.|+ ...|..+..+|.+.|+++
T Consensus        14 ~~~~~~d~~~Al~~~~~i~----~~~~~~~~nlG~~~~~~g~~~~A~~~~~kAl~--ldp~~~~a~~~~g~~~~~~g~~~   87 (192)
T d1hh8a_          14 LAADKKDWKGALDAFSAVQ----DPHSRICFNIGCMYTILKNMTEAEKAFTRSIN--RDKHLAVAYFQRGMLYYQTEKYD   87 (192)
T ss_dssp             HHHHTTCHHHHHHHHHTSS----SCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHH--HCTTCHHHHHHHHHHHHHTTCHH
T ss_pred             HHHHCCCHHHHHHHHHhcC----CCCHHHHHHHHHHHHHcCCchhHHHHHHHHHH--HhhhhhhhHHHHHHHHHhhccHH
Confidence            4456667777766666532    45666666677777777777777777777666  3443 556666777777777777


Q ss_pred             HHHHHHHHHHHcCC--------------CCC-HHHHHHHHHHHHHcCChhHHHHHHHHHHHCCCCCCHHHHHHHHHHHHh
Q 040027          505 KARDLFLDMEENAA--------------APD-VITFDMLIHGFIRINEPSKVNELLHKMKEKKVMPDASIVSIVVDLLVK  569 (595)
Q Consensus       505 ~A~~~~~~~~~~~~--------------~~~-~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~p~~~~~~~l~~~~~~  569 (595)
                      +|++.|++++....              ..+ ..++..+..++...|++++|.+.++++......++.......+..+.+
T Consensus        88 ~A~~~~~kAl~~~~~n~~~~~~~~~~~~~~~~~e~~~n~a~~~~~~~~~~~A~~~l~~A~~~~~~~~~~~~~~Al~~~~~  167 (192)
T d1hh8a_          88 LAIKDLKEALIQLRGNQLIDYKILGLQFKLFACEVLYNIAFMYAKKEEWKKAEEQLALATSMKSEPRHSKIDKAMECVWK  167 (192)
T ss_dssp             HHHHHHHHHHHTTTTCSEEECGGGTBCCEEEHHHHHHHHHHHHHHTTCHHHHHHHHHHHHTTCCSGGGGHHHHHHHHHHT
T ss_pred             HHHHHHHHHHHhCccCchHHHHHhhhhcccchHHHHHHHHHHHHHCCCHHHHHHHHHHHHhcCCCcchHHHHHHHHHHHh
Confidence            77777777664310              001 245566777888888888888888888875544444444444454444


Q ss_pred             cCcc
Q 040027          570 NEIS  573 (595)
Q Consensus       570 ~g~~  573 (595)
                      ...+
T Consensus       168 ~~~~  171 (192)
T d1hh8a_         168 QKLY  171 (192)
T ss_dssp             TCCC
T ss_pred             hhhC
Confidence            4333

>d1ouva_ a.118.18.1 (A:) Cysteine rich protein C (HcpC) {Helicobacter pylori [TaxId: 210]}

class: All alpha proteins
fold: alpha-alpha superhelix
superfamily: HCP-like
family: HCP-like
domain: Cysteine rich protein C (HcpC)
species: Helicobacter pylori [TaxId: 210]

Probab=98.82  E-value=7.3e-06  Score=72.32  Aligned_cols=94  Identities=14%  Similarity=-0.017  Sum_probs=46.1

Q ss_pred             CHHHHHHHHHHHHhcCChhHHHHHHHHHHhCCCCCCHHHHHHHHHHHHh----cCCHhHHHHHHHHHHhcCCCCCHhhHH
Q 040027           95 NLYTYNILINCFCKIGRVSLGFIAFGRILRSCFTPNAATFNSLIKGLHA----ESRIMEAAALFTKLKAFGCEPNVITYN  170 (595)
Q Consensus        95 ~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~~l~~~~~~----~g~~~~A~~~~~~~~~~~~~~~~~~~~  170 (595)
                      ||..+..|...+...|++++|+..|+++.+.|   +..++..|...|..    ..+...|...+......+   +.....
T Consensus         1 ~p~~~~~lG~~~~~~~d~~~A~~~~~kAa~~g---~~~A~~~Lg~~y~~G~~~~~d~~~a~~~~~~a~~~~---~~~a~~   74 (265)
T d1ouva_           1 DPKELVGLGAKSYKEKDFTQAKKYFEKACDLK---ENSGCFNLGVLYYQGQGVEKNLKKAASFYAKACDLN---YSNGCH   74 (265)
T ss_dssp             CHHHHHHHHHHHHHTTCHHHHHHHHHHHHHTT---CHHHHHHHHHHHHHTSSSCCCHHHHHHHHHHHHHTT---CHHHHH
T ss_pred             CHHHHHHHHHHHHHCCCHHHHHHHHHHHHHCC---CHHHHHHHHHHHHcCCCcchhHHHHHHhhccccccc---ccchhh
Confidence            34555555555556666666666666665554   44444445444443    345555555555555443   223333


Q ss_pred             HHHHHHHh----cCChhHHHHHHHHHHh
Q 040027          171 TLINGLCR----TGHTMIALNLFEEMAN  194 (595)
Q Consensus       171 ~l~~~~~~----~g~~~~A~~~~~~~~~  194 (595)
                      .+...+..    ..+.+.|...++....
T Consensus        75 ~l~~~~~~~~~~~~~~~~a~~~~~~a~~  102 (265)
T d1ouva_          75 LLGNLYYSGQGVSQNTNKALQYYSKACD  102 (265)
T ss_dssp             HHHHHHHHTSSSCCCHHHHHHHHHHHHH
T ss_pred             ccccccccccccchhhHHHHHHHhhhhh
Confidence            33333322    2344445555554444

>d1ouva_ a.118.18.1 (A:) Cysteine rich protein C (HcpC) {Helicobacter pylori [TaxId: 210]}

class: All alpha proteins
fold: alpha-alpha superhelix
superfamily: HCP-like
family: HCP-like
domain: Cysteine rich protein C (HcpC)
species: Helicobacter pylori [TaxId: 210]

Probab=98.81  E-value=9.1e-06  Score=71.67  Aligned_cols=226  Identities=11%  Similarity=0.007  Sum_probs=173.6

Q ss_pred             CHHHHHHHHHHHHhcCCHhHHHHHHHHHHhcCCCCCHhhHHHHHHHHHh----cCChhHHHHHHHHHHhcCCCCCccccC
Q 040027          130 NAATFNSLIKGLHAESRIMEAAALFTKLKAFGCEPNVITYNTLINGLCR----TGHTMIALNLFEEMANGNGEIGVVCKP  205 (595)
Q Consensus       130 ~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~~l~~~~~~----~g~~~~A~~~~~~~~~~~~~~~~~~~~  205 (595)
                      |+..+..+...+.+.+++++|++.|++..+.|   +..++..|...|..    ..+...|...++.....+         
T Consensus         1 ~p~~~~~lG~~~~~~~d~~~A~~~~~kAa~~g---~~~A~~~Lg~~y~~G~~~~~d~~~a~~~~~~a~~~~---------   68 (265)
T d1ouva_           1 DPKELVGLGAKSYKEKDFTQAKKYFEKACDLK---ENSGCFNLGVLYYQGQGVEKNLKKAASFYAKACDLN---------   68 (265)
T ss_dssp             CHHHHHHHHHHHHHTTCHHHHHHHHHHHHHTT---CHHHHHHHHHHHHHTSSSCCCHHHHHHHHHHHHHTT---------
T ss_pred             CHHHHHHHHHHHHHCCCHHHHHHHHHHHHHCC---CHHHHHHHHHHHHcCCCcchhHHHHHHhhccccccc---------
Confidence            46677888888889999999999999999876   67788888888876    668899999999988765         


Q ss_pred             cHHHHHHHHHHHHH----cCCHhHHHHHHHHHhhCCCCCCHhHHHHHHHHHHh----cCCHHHHHHHHHHHHHCCCCCCH
Q 040027          206 NTVTYSTIIDGLCK----EGFVDKAKALFLQMKDENINPDVVTYNSLIHGLCH----ANDWNEAKRLFIEMMDQGVQPSV  277 (595)
Q Consensus       206 ~~~~~~~l~~~~~~----~g~~~~A~~~~~~~~~~~~~~~~~~~~~ll~~~~~----~~~~~~A~~~~~~~~~~~~~~~~  277 (595)
                      ++.....+...+..    ..+.+.|...++.....|   .......+...+..    ......+...+......   .+.
T Consensus        69 ~~~a~~~l~~~~~~~~~~~~~~~~a~~~~~~a~~~g---~~~a~~~l~~~~~~~~~~~~~~~~a~~~~~~~~~~---~~~  142 (265)
T d1ouva_          69 YSNGCHLLGNLYYSGQGVSQNTNKALQYYSKACDLK---YAEGCASLGGIYHDGKVVTRDFKKAVEYFTKACDL---NDG  142 (265)
T ss_dssp             CHHHHHHHHHHHHHTSSSCCCHHHHHHHHHHHHHTT---CHHHHHHHHHHHHHCSSSCCCHHHHHHHHHHHHHT---TCH
T ss_pred             ccchhhccccccccccccchhhHHHHHHHhhhhhhh---hhhHHHhhcccccCCCcccchhHHHHHHhhhhhcc---ccc
Confidence            34555566655554    577889999999988876   33344444444443    45678888888887764   366


Q ss_pred             hhHHHHHHHHHh----cCChHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHh----cCCHHHHHHHHHHHHhcCCCCCHHH
Q 040027          278 VTFNVIMDELCK----NRKMDEASRLLDLMVQRGVRPNACTYNTLMDGFCL----MGKINRAEELFGSMESMGCKHDDVS  349 (595)
Q Consensus       278 ~~~~~l~~~~~~----~g~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~----~~~~~~a~~~~~~~~~~~~~~~~~~  349 (595)
                      ..+..+...+..    ..+...+..+++...+.|   +......+...|..    ..+++.|+..|.+..+.|   ++..
T Consensus       143 ~~~~~L~~~~~~~~~~~~~~~~~~~~~~~a~~~g---~~~A~~~lg~~y~~g~~~~~d~~~A~~~~~~aa~~g---~~~a  216 (265)
T d1ouva_         143 DGCTILGSLYDAGRGTPKDLKKALASYDKACDLK---DSPGCFNAGNMYHHGEGATKNFKEALARYSKACELE---NGGG  216 (265)
T ss_dssp             HHHHHHHHHHHHTSSSCCCHHHHHHHHHHHHHTT---CHHHHHHHHHHHHHTCSSCCCHHHHHHHHHHHHHTT---CHHH
T ss_pred             chhhhhhhhhccCCCcccccccchhhhhcccccc---ccccccchhhhcccCcccccchhhhhhhHhhhhccc---CHHH
Confidence            677777777775    457788888888888765   56677777777776    568999999999999876   5667


Q ss_pred             HHHHHHHHHh----CCCHHHHHHHHHHHHHCCCC
Q 040027          350 YNILINGYCK----NKEVEEALSLYREMVSKGIK  379 (595)
Q Consensus       350 ~~~l~~~~~~----~~~~~~A~~~~~~~~~~~~~  379 (595)
                      +..|..+|..    ..+.++|.+.|++....|..
T Consensus       217 ~~~LG~~y~~G~g~~~n~~~A~~~~~kAa~~g~~  250 (265)
T d1ouva_         217 CFNLGAMQYNGEGVTRNEKQAIENFKKGCKLGAK  250 (265)
T ss_dssp             HHHHHHHHHTTSSSSCCSTTHHHHHHHHHHHTCH
T ss_pred             HHHHHHHHHcCCCCccCHHHHHHHHHHHHHCcCH
Confidence            7788888876    44899999999999887654

>d1hh8a_ a.118.8.1 (A:) Neutrophil cytosolic factor 2 (NCF-2, p67-phox) {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: alpha-alpha superhelix
superfamily: TPR-like
family: Tetratricopeptide repeat (TPR)
domain: Neutrophil cytosolic factor 2 (NCF-2, p67-phox)
species: Human (Homo sapiens) [TaxId: 9606]

Probab=98.78  E-value=2.9e-07  Score=76.76  Aligned_cols=120  Identities=11%  Similarity=-0.004  Sum_probs=60.7

Q ss_pred             HHhcCCHhHHHHHHHHHHhcCCCCCHhhHHHHHHHHHhcCChhHHHHHHHHHHhcCCCCCccccCcHHHHHHHHHHHHHc
Q 040027          141 LHAESRIMEAAALFTKLKAFGCEPNVITYNTLINGLCRTGHTMIALNLFEEMANGNGEIGVVCKPNTVTYSTIIDGLCKE  220 (595)
Q Consensus       141 ~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~  220 (595)
                      +...|+++.|++.|+++.    +++..+|..+..+|...|++++|++.|++.++.+       |.++..|..+..++.+.
T Consensus        15 ~~~~~d~~~Al~~~~~i~----~~~~~~~~nlG~~~~~~g~~~~A~~~~~kAl~ld-------p~~~~a~~~~g~~~~~~   83 (192)
T d1hh8a_          15 AADKKDWKGALDAFSAVQ----DPHSRICFNIGCMYTILKNMTEAEKAFTRSINRD-------KHLAVAYFQRGMLYYQT   83 (192)
T ss_dssp             HHHTTCHHHHHHHHHTSS----SCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-------TTCHHHHHHHHHHHHHT
T ss_pred             HHHCCCHHHHHHHHHhcC----CCCHHHHHHHHHHHHHcCCchhHHHHHHHHHHHh-------hhhhhhHHHHHHHHHhh
Confidence            344555555555554421    3344455555555555555555555555555544       33455555555555555


Q ss_pred             CCHhHHHHHHHHHhhCCCC--------------C-CHhHHHHHHHHHHhcCCHHHHHHHHHHHHHC
Q 040027          221 GFVDKAKALFLQMKDENIN--------------P-DVVTYNSLIHGLCHANDWNEAKRLFIEMMDQ  271 (595)
Q Consensus       221 g~~~~A~~~~~~~~~~~~~--------------~-~~~~~~~ll~~~~~~~~~~~A~~~~~~~~~~  271 (595)
                      |++++|.+.|++.......              . ...++..+..++.+.|++++|.+.+......
T Consensus        84 g~~~~A~~~~~kAl~~~~~n~~~~~~~~~~~~~~~~~e~~~n~a~~~~~~~~~~~A~~~l~~A~~~  149 (192)
T d1hh8a_          84 EKYDLAIKDLKEALIQLRGNQLIDYKILGLQFKLFACEVLYNIAFMYAKKEEWKKAEEQLALATSM  149 (192)
T ss_dssp             TCHHHHHHHHHHHHHTTTTCSEEECGGGTBCCEEEHHHHHHHHHHHHHHTTCHHHHHHHHHHHHTT
T ss_pred             ccHHHHHHHHHHHHHhCccCchHHHHHhhhhcccchHHHHHHHHHHHHHCCCHHHHHHHHHHHHhc
Confidence            5555555555554332100              0 0133444555666666666666666665554

>d1elwa_ a.118.8.1 (A:) Hop {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: alpha-alpha superhelix
superfamily: TPR-like
family: Tetratricopeptide repeat (TPR)
domain: Hop
species: Human (Homo sapiens) [TaxId: 9606]

Probab=98.75  E-value=2.2e-07  Score=70.22  Aligned_cols=108  Identities=10%  Similarity=-0.023  Sum_probs=93.7

Q ss_pred             HHHHHHHHHhcCChhHHHHHHHHHHhCCCCCCHHHHHHHHHHHHhcCCHhHHHHHHHHHHhcCCCCCHhhHHHHHHHHHh
Q 040027           99 YNILINCFCKIGRVSLGFIAFGRILRSCFTPNAATFNSLIKGLHAESRIMEAAALFTKLKAFGCEPNVITYNTLINGLCR  178 (595)
Q Consensus        99 ~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~~l~~~~~~  178 (595)
                      +..-+..+...|++++|+..|+++++.. |.+...|..+..++...|++++|+..+++....+ +.+...|..+..++..
T Consensus         6 l~~~g~~~~~~g~~~eAi~~~~~al~~~-p~~~~~~~~~a~~~~~~~~~~~A~~~~~~al~~~-p~~~~~~~~~g~~~~~   83 (117)
T d1elwa_           6 LKEKGNKALSVGNIDDALQCYSEAIKLD-PHNHVLYSNRSAAYAKKGDYQKAYEDGCKTVDLK-PDWGKGYSRKAAALEF   83 (117)
T ss_dssp             HHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHcCCHHHHHHHHHHHHhcC-CcchhhhhcccccccccccccccchhhhhHHHhc-cchhhHHHHHHHHHHH
Confidence            3446778899999999999999999985 6688899999999999999999999999999986 4588999999999999


Q ss_pred             cCChhHHHHHHHHHHhcCCCCCccccCcHHHHHHHHH
Q 040027          179 TGHTMIALNLFEEMANGNGEIGVVCKPNTVTYSTIID  215 (595)
Q Consensus       179 ~g~~~~A~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~  215 (595)
                      .|++++|+..|++..+..       |.++..+..+..
T Consensus        84 ~~~~~~A~~~~~~a~~~~-------p~~~~~~~~l~~  113 (117)
T d1elwa_          84 LNRFEEAKRTYEEGLKHE-------ANNPQLKEGLQN  113 (117)
T ss_dssp             TTCHHHHHHHHHHHHTTC-------TTCHHHHHHHHH
T ss_pred             ccCHHHHHHHHHHHHHhC-------CCCHHHHHHHHH
Confidence            999999999999999876       455655555443

>d1elwa_ a.118.8.1 (A:) Hop {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: alpha-alpha superhelix
superfamily: TPR-like
family: Tetratricopeptide repeat (TPR)
domain: Hop
species: Human (Homo sapiens) [TaxId: 9606]

Probab=98.71  E-value=2.6e-07  Score=69.90  Aligned_cols=103  Identities=10%  Similarity=-0.004  Sum_probs=69.8

Q ss_pred             HHHHHHhcCChHHHHHHHHhcccCCCCC-CHHHHHHHHHHHHhcCChhHHHHHHHHHHHcCCCCCHHHHHHHHHHHHHcC
Q 040027          458 LIDGLCKSGRLKFAWELFCSLPHGVLVP-NVVTYNIMIQGLCNDGQMDKARDLFLDMEENAAAPDVITFDMLIHGFIRIN  536 (595)
Q Consensus       458 l~~~~~~~g~~~~A~~~~~~~~~~~~~p-~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g  536 (595)
                      -+..+.+.|++++|+..|+++++.  .| +...|..+..+|...|++++|+..+.++++.+ +.+...|..++.++...|
T Consensus         9 ~g~~~~~~g~~~eAi~~~~~al~~--~p~~~~~~~~~a~~~~~~~~~~~A~~~~~~al~~~-p~~~~~~~~~g~~~~~~~   85 (117)
T d1elwa_           9 KGNKALSVGNIDDALQCYSEAIKL--DPHNHVLYSNRSAAYAKKGDYQKAYEDGCKTVDLK-PDWGKGYSRKAAALEFLN   85 (117)
T ss_dssp             HHHHHHHTTCHHHHHHHHHHHHHH--CTTCHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTT
T ss_pred             HHHHHHHcCCHHHHHHHHHHHHhc--CCcchhhhhcccccccccccccccchhhhhHHHhc-cchhhHHHHHHHHHHHcc
Confidence            355566777777777777777663  34 45667777777777777777777777777764 556677777777777777


Q ss_pred             ChhHHHHHHHHHHHCCCCC-CHHHHHHHHH
Q 040027          537 EPSKVNELLHKMKEKKVMP-DASIVSIVVD  565 (595)
Q Consensus       537 ~~~~A~~~~~~~~~~~~~p-~~~~~~~l~~  565 (595)
                      ++++|...+++..+.  .| ++..+..+..
T Consensus        86 ~~~~A~~~~~~a~~~--~p~~~~~~~~l~~  113 (117)
T d1elwa_          86 RFEEAKRTYEEGLKH--EANNPQLKEGLQN  113 (117)
T ss_dssp             CHHHHHHHHHHHHTT--CTTCHHHHHHHHH
T ss_pred             CHHHHHHHHHHHHHh--CCCCHHHHHHHHH
Confidence            777777777777763  34 4444444443

>d1a17a_ a.118.8.1 (A:) Protein phosphatase 5 {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: alpha-alpha superhelix
superfamily: TPR-like
family: Tetratricopeptide repeat (TPR)
domain: Protein phosphatase 5
species: Human (Homo sapiens) [TaxId: 9606]

Probab=98.67  E-value=4.3e-07  Score=73.22  Aligned_cols=102  Identities=10%  Similarity=-0.042  Sum_probs=69.9

Q ss_pred             HHHHHHhcCCHHHHHHHHHHHHHcCCCcCHHHHHHHHHHHHhcCChHHHHHHHHhcccCCCCCC-HHHHHHHHHHHHhcC
Q 040027          423 FIDGLCKNGYIIEAVELFRTLRILKCELDIQAYNCLIDGLCKSGRLKFAWELFCSLPHGVLVPN-VVTYNIMIQGLCNDG  501 (595)
Q Consensus       423 l~~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~p~-~~~~~~l~~~~~~~g  501 (595)
                      ....|.+.|++++|+..|+++++.. +.+...|..++.+|...|++++|+..|+++++  +.|+ ...|..++.++...|
T Consensus        16 ~gn~~~~~~~y~~A~~~~~~al~~~-p~~~~~~~~lg~~~~~~~~~~~A~~~~~kal~--~~p~~~~a~~~~g~~~~~~g   92 (159)
T d1a17a_          16 QANDYFKAKDYENAIKFYSQAIELN-PSNAIYYGNRSLAYLRTECYGYALGDATRAIE--LDKKYIKGYYRRAASNMALG   92 (159)
T ss_dssp             HHHHHHHTTCHHHHHHHHHHHHHHS-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHH--HCTTCHHHHHHHHHHHHHTT
T ss_pred             HHHHHHHcCCHHHHHHHhhhccccc-hhhhhhhhhhHHHHHhccccchHHHHHHHHHH--HcccchHHHHHHHHHHHHcC
Confidence            3455667777777777777777766 56677777777777777777777777777776  3443 467777777777777


Q ss_pred             ChhHHHHHHHHHHHcCCCCCHHHHHHH
Q 040027          502 QMDKARDLFLDMEENAAAPDVITFDML  528 (595)
Q Consensus       502 ~~~~A~~~~~~~~~~~~~~~~~~~~~l  528 (595)
                      ++++|+..++++.... +.+...+..+
T Consensus        93 ~~~eA~~~~~~a~~~~-p~~~~~~~~l  118 (159)
T d1a17a_          93 KFRAALRDYETVVKVK-PHDKDAKMKY  118 (159)
T ss_dssp             CHHHHHHHHHHHHHHS-TTCHHHHHHH
T ss_pred             CHHHHHHHHHHHHHcC-CCCHHHHHHH
Confidence            7777777777777753 3344444433

>d1qqea_ a.118.8.1 (A:) Vesicular transport protein sec17 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: All alpha proteins
fold: alpha-alpha superhelix
superfamily: TPR-like
family: Tetratricopeptide repeat (TPR)
domain: Vesicular transport protein sec17
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=98.66  E-value=3.9e-07  Score=81.93  Aligned_cols=207  Identities=10%  Similarity=-0.005  Sum_probs=134.3

Q ss_pred             HHHHHHHHHHHhcCChhHHHHHHHHHHhCC----CC-CCHHHHHHHHHHHHhcCCHhHHHHHHHHHHhcCCC-----CCH
Q 040027           97 YTYNILINCFCKIGRVSLGFIAFGRILRSC----FT-PNAATFNSLIKGLHAESRIMEAAALFTKLKAFGCE-----PNV  166 (595)
Q Consensus        97 ~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~----~~-~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~-----~~~  166 (595)
                      ..|..++..|...|++++|...|.++....    -+ .-..+|..+..+|.+.|++++|++.+++.......     ...
T Consensus        38 ~~y~~aa~~y~~~~~~~~A~~~y~kA~~~~~~~~~~~~~a~~~~~~g~~y~~~~~~~~A~~~~~~a~~~~~~~~~~~~~~  117 (290)
T d1qqea_          38 DLCVQAATIYRLRKELNLAGDSFLKAADYQKKAGNEDEAGNTYVEAYKCFKSGGNSVNAVDSLENAIQIFTHRGQFRRGA  117 (290)
T ss_dssp             HHHHHHHHHHHHTTCTHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCHHHHH
T ss_pred             HHHHHHHHHHHHCcCHHHHHHHHHHHHHHHHHcCCCHHHHHHHHHHHHHHHHhCCcHHHHHHHHHhhHHhhhcccchhHH
Confidence            458888999999999999999999987641    11 12357888999999999999999999987653111     113


Q ss_pred             hhHHHHHHHHHh-cCChhHHHHHHHHHHhcCCCCCccccCcHHHHHHHHHHHHHcCCHhHHHHHHHHHhhCCCCCCH---
Q 040027          167 ITYNTLINGLCR-TGHTMIALNLFEEMANGNGEIGVVCKPNTVTYSTIIDGLCKEGFVDKAKALFLQMKDENINPDV---  242 (595)
Q Consensus       167 ~~~~~l~~~~~~-~g~~~~A~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~~~---  242 (595)
                      .++..+...|.. .|++++|++.+++........+. .+....++..+...+...|++++|.+.|+++.........   
T Consensus       118 ~~~~~l~~~~~~~~~~~~~A~~~~~~A~~l~~~~~~-~~~~~~~~~~la~~~~~~g~y~~A~~~~~~~~~~~~~~~~~~~  196 (290)
T d1qqea_         118 NFKFELGEILENDLHDYAKAIDCYELAGEWYAQDQS-VALSNKCFIKCADLKALDGQYIEASDIYSKLIKSSMGNRLSQW  196 (290)
T ss_dssp             HHHHHHHHHHHHTTCCHHHHHHHHHHHHHHHHHTTC-HHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHTTSSCTTTGG
T ss_pred             HHHHHHHHhHhhHHHHHHHHHHHHHHHHHHHHhcCc-hhhhhhHHHHHHHHHHHcChHHHHHHHHHHHHHhCccchhhhh
Confidence            455666666644 69999999999887653210000 0112455777888899999999999999987765321111   


Q ss_pred             ---hHHHHHHHHHHhcCCHHHHHHHHHHHHHCCCC-CC---HhhHHHHHHHHHh--cCChHHHHHHHHHHH
Q 040027          243 ---VTYNSLIHGLCHANDWNEAKRLFIEMMDQGVQ-PS---VVTFNVIMDELCK--NRKMDEASRLLDLMV  304 (595)
Q Consensus       243 ---~~~~~ll~~~~~~~~~~~A~~~~~~~~~~~~~-~~---~~~~~~l~~~~~~--~g~~~~a~~~~~~~~  304 (595)
                         ..+...+..+...|+++.|...++...+.... ++   ......++.++..  .+.+++|+..|+.+.
T Consensus       197 ~~~~~~~~~~~~~l~~~d~~~A~~~~~~~~~~~~~~~~sre~~~l~~l~~a~~~~d~e~~~eai~~y~~~~  267 (290)
T d1qqea_         197 SLKDYFLKKGLCQLAATDAVAAARTLQEGQSEDPNFADSRESNFLKSLIDAVNEGDSEQLSEHCKEFDNFM  267 (290)
T ss_dssp             GHHHHHHHHHHHHHHTTCHHHHHHHHHGGGCC---------HHHHHHHHHHHHTTCTTTHHHHHHHHTTSS
T ss_pred             hHHHHHHHHHHHHHHhccHHHHHHHHHHHHHhCCCccchHHHHHHHHHHHHHHhcCHHHHHHHHHHHHHHh
Confidence               12344455667788888888888877654211 11   1223444444443  234566666665443

>d1a17a_ a.118.8.1 (A:) Protein phosphatase 5 {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: alpha-alpha superhelix
superfamily: TPR-like
family: Tetratricopeptide repeat (TPR)
domain: Protein phosphatase 5
species: Human (Homo sapiens) [TaxId: 9606]

Probab=98.66  E-value=5.2e-07  Score=72.70  Aligned_cols=108  Identities=10%  Similarity=0.004  Sum_probs=91.3

Q ss_pred             HHHHHHHHHhcCChhHHHHHHHHHHhCCCCCCHHHHHHHHHHHHhcCCHhHHHHHHHHHHhcCCCCCHhhHHHHHHHHHh
Q 040027           99 YNILINCFCKIGRVSLGFIAFGRILRSCFTPNAATFNSLIKGLHAESRIMEAAALFTKLKAFGCEPNVITYNTLINGLCR  178 (595)
Q Consensus        99 ~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~~l~~~~~~  178 (595)
                      +...+..|.+.|++++|+..|+++++.. +.+...|..+..+|...|++++|++.|+++++.. +.+..+|..++.++..
T Consensus        13 l~~~gn~~~~~~~y~~A~~~~~~al~~~-p~~~~~~~~lg~~~~~~~~~~~A~~~~~kal~~~-p~~~~a~~~~g~~~~~   90 (159)
T d1a17a_          13 LKTQANDYFKAKDYENAIKFYSQAIELN-PSNAIYYGNRSLAYLRTECYGYALGDATRAIELD-KKYIKGYYRRAASNMA   90 (159)
T ss_dssp             HHHHHHHHHHTTCHHHHHHHHHHHHHHS-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHcCCHHHHHHHhhhccccc-hhhhhhhhhhHHHHHhccccchHHHHHHHHHHHc-ccchHHHHHHHHHHHH
Confidence            4456778899999999999999999986 5688899999999999999999999999999885 4477899999999999


Q ss_pred             cCChhHHHHHHHHHHhcCCCCCccccCcHHHHHHHHH
Q 040027          179 TGHTMIALNLFEEMANGNGEIGVVCKPNTVTYSTIID  215 (595)
Q Consensus       179 ~g~~~~A~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~  215 (595)
                      .|++++|+..++++....       |.+...+..+..
T Consensus        91 ~g~~~eA~~~~~~a~~~~-------p~~~~~~~~l~~  120 (159)
T d1a17a_          91 LGKFRAALRDYETVVKVK-------PHDKDAKMKYQE  120 (159)
T ss_dssp             TTCHHHHHHHHHHHHHHS-------TTCHHHHHHHHH
T ss_pred             cCCHHHHHHHHHHHHHcC-------CCCHHHHHHHHH
Confidence            999999999999999875       344555554433

>d2c2la1 a.118.8.1 (A:24-224) STIP1 homology and U box-containing protein 1, STUB1 {Mouse (Mus musculus) [TaxId: 10090]}

class: All alpha proteins
fold: alpha-alpha superhelix
superfamily: TPR-like
family: Tetratricopeptide repeat (TPR)
domain: STIP1 homology and U box-containing protein 1, STUB1
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=98.64  E-value=7e-08  Score=81.75  Aligned_cols=98  Identities=12%  Similarity=-0.106  Sum_probs=65.4

Q ss_pred             CCHHHHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCcCHHHHHHHHHHHHhcCChHHHHHHHHhcccCCCCCC-HHHHHHH
Q 040027          415 ADTRTYTTFIDGLCKNGYIIEAVELFRTLRILKCELDIQAYNCLIDGLCKSGRLKFAWELFCSLPHGVLVPN-VVTYNIM  493 (595)
Q Consensus       415 ~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~p~-~~~~~~l  493 (595)
                      |+...+...+..|.+.|++++|+..|++++... |.++.+|..++.+|.+.|++++|+..|+++++  +.|+ ..+|..+
T Consensus         2 ~~a~~l~~~Gn~~~~~g~~~~Ai~~~~kal~~~-p~~~~~~~~lg~~y~~~~~~~~Ai~~~~~al~--l~p~~~~a~~~l   78 (201)
T d2c2la1           2 PSAQELKEQGNRLFVGRKYPEAAACYGRAITRN-PLVAVYYTNRALCYLKMQQPEQALADCRRALE--LDGQSVKAHFFL   78 (201)
T ss_dssp             CCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-SCCHHHHHHHHHHHHHTTCHHHHHHHHHHHTT--SCTTCHHHHHHH
T ss_pred             hhHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhC-CCCHHHHHhHHHHHhhhhhhhhhhHHHHHHHH--hCCCcHHHHHHH
Confidence            445555556666667777777777777766655 55666677777777777777777777777766  4453 5566667


Q ss_pred             HHHHHhcCChhHHHHHHHHHHH
Q 040027          494 IQGLCNDGQMDKARDLFLDMEE  515 (595)
Q Consensus       494 ~~~~~~~g~~~~A~~~~~~~~~  515 (595)
                      +.+|...|++++|+..|+++++
T Consensus        79 g~~~~~l~~~~~A~~~~~~al~  100 (201)
T d2c2la1          79 GQCQLEMESYDEAIANLQRAYS  100 (201)
T ss_dssp             HHHHHHTTCHHHHHHHHHHHHH
T ss_pred             HHHHHHCCCHHHHHHHHHHHHH
Confidence            7777777777777777776655

>d1qqea_ a.118.8.1 (A:) Vesicular transport protein sec17 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: All alpha proteins
fold: alpha-alpha superhelix
superfamily: TPR-like
family: Tetratricopeptide repeat (TPR)
domain: Vesicular transport protein sec17
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=98.62  E-value=1.1e-06  Score=79.01  Aligned_cols=162  Identities=12%  Similarity=-0.002  Sum_probs=81.0

Q ss_pred             HHHHHhcCCHHHHHHHHHHHHhc----CCCC-CHHHHHHHHHHHHhCCCHHHHHHHHHHHHHCCCC-----CCHHHHHHH
Q 040027          319 MDGFCLMGKINRAEELFGSMESM----GCKH-DDVSYNILINGYCKNKEVEEALSLYREMVSKGIK-----PTVVTYNTL  388 (595)
Q Consensus       319 ~~~~~~~~~~~~a~~~~~~~~~~----~~~~-~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~~~~~-----~~~~~~~~l  388 (595)
                      +..|...+++++|...|.++.+.    +-++ -..+|..+..+|.+.|++++|++.+++..+....     ....++..+
T Consensus        44 a~~y~~~~~~~~A~~~y~kA~~~~~~~~~~~~~a~~~~~~g~~y~~~~~~~~A~~~~~~a~~~~~~~~~~~~~~~~~~~l  123 (290)
T d1qqea_          44 ATIYRLRKELNLAGDSFLKAADYQKKAGNEDEAGNTYVEAYKCFKSGGNSVNAVDSLENAIQIFTHRGQFRRGANFKFEL  123 (290)
T ss_dssp             HHHHHHTTCTHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHH
T ss_pred             HHHHHHCcCHHHHHHHHHHHHHHHHHcCCCHHHHHHHHHHHHHHHHhCCcHHHHHHHHHhhHHhhhcccchhHHHHHHHH
Confidence            45566777777777777766542    1111 1235666677777777777777777665542100     012233334


Q ss_pred             HHHHH-ccCCHHHHHHHHHHHHHC----CCCC-CHHHHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCcC------HHHHH
Q 040027          389 FLGLF-EIHQVEHALKLFDEMQRD----GVAA-DTRTYTTFIDGLCKNGYIIEAVELFRTLRILKCELD------IQAYN  456 (595)
Q Consensus       389 ~~~~~-~~~~~~~a~~~~~~~~~~----~~~~-~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~~------~~~~~  456 (595)
                      ...+. ..|++++|+..+.+..+.    +.++ ...++..+...+...|++++|...|+++........      ...+.
T Consensus       124 ~~~~~~~~~~~~~A~~~~~~A~~l~~~~~~~~~~~~~~~~la~~~~~~g~y~~A~~~~~~~~~~~~~~~~~~~~~~~~~~  203 (290)
T d1qqea_         124 GEILENDLHDYAKAIDCYELAGEWYAQDQSVALSNKCFIKCADLKALDGQYIEASDIYSKLIKSSMGNRLSQWSLKDYFL  203 (290)
T ss_dssp             HHHHHHTTCCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHTTSSCTTTGGGHHHHHH
T ss_pred             HHhHhhHHHHHHHHHHHHHHHHHHHHhcCchhhhhhHHHHHHHHHHHcChHHHHHHHHHHHHHhCccchhhhhhHHHHHH
Confidence            44442 246666666666555431    1011 122344455555666666666666665554321110      11223


Q ss_pred             HHHHHHHhcCChHHHHHHHHhccc
Q 040027          457 CLIDGLCKSGRLKFAWELFCSLPH  480 (595)
Q Consensus       457 ~l~~~~~~~g~~~~A~~~~~~~~~  480 (595)
                      ..+..+...|+++.|...+++..+
T Consensus       204 ~~~~~~l~~~d~~~A~~~~~~~~~  227 (290)
T d1qqea_         204 KKGLCQLAATDAVAAARTLQEGQS  227 (290)
T ss_dssp             HHHHHHHHTTCHHHHHHHHHGGGC
T ss_pred             HHHHHHHHhccHHHHHHHHHHHHH
Confidence            333444455566666666655554

>d2c2la1 a.118.8.1 (A:24-224) STIP1 homology and U box-containing protein 1, STUB1 {Mouse (Mus musculus) [TaxId: 10090]}

class: All alpha proteins
fold: alpha-alpha superhelix
superfamily: TPR-like
family: Tetratricopeptide repeat (TPR)
domain: STIP1 homology and U box-containing protein 1, STUB1
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=98.57  E-value=1.7e-07  Score=79.20  Aligned_cols=102  Identities=10%  Similarity=-0.083  Sum_probs=89.1

Q ss_pred             CCCHHHHHHHHHHHHhcCChhHHHHHHHHHHhCCCCCCHHHHHHHHHHHHhcCCHhHHHHHHHHHHhcCCCCCHhhHHHH
Q 040027           93 FPNLYTYNILINCFCKIGRVSLGFIAFGRILRSCFTPNAATFNSLIKGLHAESRIMEAAALFTKLKAFGCEPNVITYNTL  172 (595)
Q Consensus        93 ~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~~l  172 (595)
                      .|+...+...+..+.+.|++++|+..|+++++.. |.++..|..+..+|.+.|++++|+..|+++++.. +-+..+|..+
T Consensus         1 ~~~a~~l~~~Gn~~~~~g~~~~Ai~~~~kal~~~-p~~~~~~~~lg~~y~~~~~~~~Ai~~~~~al~l~-p~~~~a~~~l   78 (201)
T d2c2la1           1 SPSAQELKEQGNRLFVGRKYPEAAACYGRAITRN-PLVAVYYTNRALCYLKMQQPEQALADCRRALELD-GQSVKAHFFL   78 (201)
T ss_dssp             CCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-SCCHHHHHHHHHHHHHTTCHHHHHHHHHHHTTSC-TTCHHHHHHH
T ss_pred             ChhHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhC-CCCHHHHHhHHHHHhhhhhhhhhhHHHHHHHHhC-CCcHHHHHHH
Confidence            3777788888999999999999999999999885 5688889999999999999999999999998874 3367889999


Q ss_pred             HHHHHhcCChhHHHHHHHHHHhcC
Q 040027          173 INGLCRTGHTMIALNLFEEMANGN  196 (595)
Q Consensus       173 ~~~~~~~g~~~~A~~~~~~~~~~~  196 (595)
                      +.+|...|++++|+..|+++....
T Consensus        79 g~~~~~l~~~~~A~~~~~~al~l~  102 (201)
T d2c2la1          79 GQCQLEMESYDEAIANLQRAYSLA  102 (201)
T ss_dssp             HHHHHHTTCHHHHHHHHHHHHHHH
T ss_pred             HHHHHHCCCHHHHHHHHHHHHHhC
Confidence            999999999999999999887643

>d1hxia_ a.118.8.1 (A:) Peroxin pex5 (peroxisomal targeting signal 1 (PTS1) receptor) {Trypanosoma brucei [TaxId: 5691]}

class: All alpha proteins
fold: alpha-alpha superhelix
superfamily: TPR-like
family: Tetratricopeptide repeat (TPR)
domain: Peroxin pex5 (peroxisomal targeting signal 1 (PTS1) receptor)
species: Trypanosoma brucei [TaxId: 5691]

Probab=98.53  E-value=1.4e-07  Score=70.73  Aligned_cols=89  Identities=10%  Similarity=0.037  Sum_probs=47.7

Q ss_pred             HHHHHHhcCChhHHHHHHHHHHhCCCCCCHHHHHHHHHHHHhcCCHhHHHHHHHHHHhcCCCCCHhhHHHHHHHHHhcCC
Q 040027          102 LINCFCKIGRVSLGFIAFGRILRSCFTPNAATFNSLIKGLHAESRIMEAAALFTKLKAFGCEPNVITYNTLINGLCRTGH  181 (595)
Q Consensus       102 l~~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~  181 (595)
                      .+..+.+.|++++|+..|+++++.. +-++.+|..+..++.+.|++++|+..|++..+.. +.+..++..+...|...|+
T Consensus        22 ~g~~~~~~g~~~~A~~~~~~al~~~-p~~~~a~~~lg~~~~~~~~~~~A~~~~~~al~~~-p~~~~a~~~la~~y~~~g~   99 (112)
T d1hxia_          22 EGLSMLKLANLAEAALAFEAVCQKE-PEREEAWRSLGLTQAENEKDGLAIIALNHARMLD-PKDIAVHAALAVSHTNEHN   99 (112)
T ss_dssp             HHHHHHHTTCHHHHHHHHHHHHHHS-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHhhhHHHHHHHhhhcccc-cccchhhhhhhhhhhhhhhHHHhhcccccccccc-cccccchHHHHHHHHHCCC
Confidence            3444555555555555555555543 2345555555555555555555555555555543 2245555555555555555


Q ss_pred             hhHHHHHHHHH
Q 040027          182 TMIALNLFEEM  192 (595)
Q Consensus       182 ~~~A~~~~~~~  192 (595)
                      +++|++.|++.
T Consensus       100 ~~~A~~~l~~~  110 (112)
T d1hxia_         100 ANAALASLRAW  110 (112)
T ss_dssp             HHHHHHHHHHH
T ss_pred             HHHHHHHHHHH
Confidence            55555555543

>d1nzna_ a.118.8.1 (A:) Mitochondria fission protein Fis1 {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: alpha-alpha superhelix
superfamily: TPR-like
family: Tetratricopeptide repeat (TPR)
domain: Mitochondria fission protein Fis1
species: Human (Homo sapiens) [TaxId: 9606]

Probab=98.42  E-value=1.7e-06  Score=65.33  Aligned_cols=94  Identities=9%  Similarity=-0.023  Sum_probs=55.5

Q ss_pred             HHHHHHHhcCCHHHHHHHHHHHHHcCCCcCHHHHHHHHHHHHhcCC---hHHHHHHHHhcccCCCCCC-HHHHHHHHHHH
Q 040027          422 TFIDGLCKNGYIIEAVELFRTLRILKCELDIQAYNCLIDGLCKSGR---LKFAWELFCSLPHGVLVPN-VVTYNIMIQGL  497 (595)
Q Consensus       422 ~l~~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~---~~~A~~~~~~~~~~~~~p~-~~~~~~l~~~~  497 (595)
                      .++..+...+++++|.+.|++.+..+ +.++.++..++.++.+.++   +++|+.+++++...+..|+ ..+|..++.+|
T Consensus         4 ~l~n~~~~~~~l~~Ae~~Y~~aL~~~-p~~~~~~~n~a~~L~~s~~~~d~~~Ai~~l~~~l~~~~~~~~~~~~~~Lg~~y   82 (122)
T d1nzna_           4 AVLNELVSVEDLLKFEKKFQSEKAAG-SVSKSTQFEYAWCLVRTRYNDDIRKGIVLLEELLPKGSKEEQRDYVFYLAVGN   82 (122)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHS-CCCHHHHHHHHHHHTTSSSHHHHHHHHHHHHHHTTTSCHHHHHHHHHHHHHHH
T ss_pred             HHHHHhcCHHHHHHHHHHHHHHHhhC-CCCHHHHHHHHHHHHHhcchHHHHHHHHHHHHHHhccCCchHHHHHHHHHHHH
Confidence            34555556666666666666666655 5566666666666655433   3456666666665321122 12555666666


Q ss_pred             HhcCChhHHHHHHHHHHHc
Q 040027          498 CNDGQMDKARDLFLDMEEN  516 (595)
Q Consensus       498 ~~~g~~~~A~~~~~~~~~~  516 (595)
                      .+.|++++|++.|+++++.
T Consensus        83 ~~~g~~~~A~~~~~~aL~~  101 (122)
T d1nzna_          83 YRLKEYEKALKYVRGLLQT  101 (122)
T ss_dssp             HHTTCHHHHHHHHHHHHHH
T ss_pred             HHHhhhHHHHHHHHHHHHh
Confidence            6666666666666666664

>d1hxia_ a.118.8.1 (A:) Peroxin pex5 (peroxisomal targeting signal 1 (PTS1) receptor) {Trypanosoma brucei [TaxId: 5691]}

class: All alpha proteins
fold: alpha-alpha superhelix
superfamily: TPR-like
family: Tetratricopeptide repeat (TPR)
domain: Peroxin pex5 (peroxisomal targeting signal 1 (PTS1) receptor)
species: Trypanosoma brucei [TaxId: 5691]

Probab=98.40  E-value=1.6e-06  Score=64.77  Aligned_cols=92  Identities=10%  Similarity=-0.042  Sum_probs=78.7

Q ss_pred             HHHHHHHHhcCCHhHHHHHHHHHHhcCCCCCHhhHHHHHHHHHhcCChhHHHHHHHHHHhcCCCCCccccCcHHHHHHHH
Q 040027          135 NSLIKGLHAESRIMEAAALFTKLKAFGCEPNVITYNTLINGLCRTGHTMIALNLFEEMANGNGEIGVVCKPNTVTYSTII  214 (595)
Q Consensus       135 ~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~~~~~~~~l~  214 (595)
                      ..+...+.+.|++++|+..|++++... +-+..+|..+..++.+.|++++|+..|++..+.+       |.+..+|..+.
T Consensus        20 ~~~g~~~~~~g~~~~A~~~~~~al~~~-p~~~~a~~~lg~~~~~~~~~~~A~~~~~~al~~~-------p~~~~a~~~la   91 (112)
T d1hxia_          20 MEEGLSMLKLANLAEAALAFEAVCQKE-PEREEAWRSLGLTQAENEKDGLAIIALNHARMLD-------PKDIAVHAALA   91 (112)
T ss_dssp             HHHHHHHHHTTCHHHHHHHHHHHHHHS-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-------TTCHHHHHHHH
T ss_pred             HHHHHHHHHHhhhHHHHHHHhhhcccc-cccchhhhhhhhhhhhhhhHHHhhcccccccccc-------cccccchHHHH
Confidence            345667888999999999999998875 3378889999999999999999999999999876       56788899999


Q ss_pred             HHHHHcCCHhHHHHHHHHHh
Q 040027          215 DGLCKEGFVDKAKALFLQMK  234 (595)
Q Consensus       215 ~~~~~~g~~~~A~~~~~~~~  234 (595)
                      .+|...|++++|.+.+++.+
T Consensus        92 ~~y~~~g~~~~A~~~l~~~l  111 (112)
T d1hxia_          92 VSHTNEHNANAALASLRAWL  111 (112)
T ss_dssp             HHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHCCCHHHHHHHHHHHh
Confidence            99999999999999988753

>d1nzna_ a.118.8.1 (A:) Mitochondria fission protein Fis1 {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: alpha-alpha superhelix
superfamily: TPR-like
family: Tetratricopeptide repeat (TPR)
domain: Mitochondria fission protein Fis1
species: Human (Homo sapiens) [TaxId: 9606]

Probab=98.39  E-value=1.5e-06  Score=65.61  Aligned_cols=96  Identities=14%  Similarity=0.008  Sum_probs=81.5

Q ss_pred             HHHHHHHHhcCChhHHHHHHHHHHhCCCCCCHHHHHHHHHHHHhcC---CHhHHHHHHHHHHhcCCCCC-HhhHHHHHHH
Q 040027          100 NILINCFCKIGRVSLGFIAFGRILRSCFTPNAATFNSLIKGLHAES---RIMEAAALFTKLKAFGCEPN-VITYNTLING  175 (595)
Q Consensus       100 ~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g---~~~~A~~~~~~~~~~~~~~~-~~~~~~l~~~  175 (595)
                      ..++..+...+++++|.+.|++++..+ +.++.++..+..++.+.+   ++++|+.+|+++...+..|+ ..++..++.+
T Consensus         3 ~~l~n~~~~~~~l~~Ae~~Y~~aL~~~-p~~~~~~~n~a~~L~~s~~~~d~~~Ai~~l~~~l~~~~~~~~~~~~~~Lg~~   81 (122)
T d1nzna_           3 EAVLNELVSVEDLLKFEKKFQSEKAAG-SVSKSTQFEYAWCLVRTRYNDDIRKGIVLLEELLPKGSKEEQRDYVFYLAVG   81 (122)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHS-CCCHHHHHHHHHHHTTSSSHHHHHHHHHHHHHHTTTSCHHHHHHHHHHHHHH
T ss_pred             HHHHHHhcCHHHHHHHHHHHHHHHhhC-CCCHHHHHHHHHHHHHhcchHHHHHHHHHHHHHHhccCCchHHHHHHHHHHH
Confidence            457788889999999999999999986 668899999999998755   45579999999988653333 3478899999


Q ss_pred             HHhcCChhHHHHHHHHHHhcC
Q 040027          176 LCRTGHTMIALNLFEEMANGN  196 (595)
Q Consensus       176 ~~~~g~~~~A~~~~~~~~~~~  196 (595)
                      |.+.|++++|++.|+++++.+
T Consensus        82 y~~~g~~~~A~~~~~~aL~~~  102 (122)
T d1nzna_          82 NYRLKEYEKALKYVRGLLQTE  102 (122)
T ss_dssp             HHHTTCHHHHHHHHHHHHHHC
T ss_pred             HHHHhhhHHHHHHHHHHHHhC
Confidence            999999999999999999976

>d1p5qa1 a.118.8.1 (A:258-427) FKBP52 (FKBP4), C-terminal domain {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: alpha-alpha superhelix
superfamily: TPR-like
family: Tetratricopeptide repeat (TPR)
domain: FKBP52 (FKBP4), C-terminal domain
species: Human (Homo sapiens) [TaxId: 9606]

Probab=98.39  E-value=2.3e-06  Score=69.47  Aligned_cols=82  Identities=6%  Similarity=-0.076  Sum_probs=61.1

Q ss_pred             HHHHHHHHHHHhcCChhHHHHHHHHHHHcCCCCCHHHHHHHHHHHHHcCChhHHHHHHHHHHHCCCCC-CHHHHHHHHHH
Q 040027          488 VTYNIMIQGLCNDGQMDKARDLFLDMEENAAAPDVITFDMLIHGFIRINEPSKVNELLHKMKEKKVMP-DASIVSIVVDL  566 (595)
Q Consensus       488 ~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~p-~~~~~~~l~~~  566 (595)
                      .+|+.+..+|.+.|++++|+..++++++.+ |.+..++..++.+|...|++++|...|+++++.  .| +..+...+..+
T Consensus        63 ~~~~nla~~y~k~~~~~~A~~~~~~al~~~-p~~~~a~~~~g~~~~~~g~~~~A~~~~~~al~l--~P~n~~~~~~l~~~  139 (170)
T d1p5qa1          63 ASHLNLAMCHLKLQAFSAAIESCNKALELD-SNNEKGLSRRGEAHLAVNDFELARADFQKVLQL--YPNNKAAKTQLAVC  139 (170)
T ss_dssp             HHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH--CSSCHHHHHHHHHH
T ss_pred             HHHHHHHHHHHhhhhcccccchhhhhhhcc-ccchhhhHHHHHHHHHhhhHHHHHHHHHHHHHh--CCCCHHHHHHHHHH
Confidence            356677788888888888888888888875 557788888888888888888888888888874  35 56666666555


Q ss_pred             HHhcCc
Q 040027          567 LVKNEI  572 (595)
Q Consensus       567 ~~~~g~  572 (595)
                      ..+.+.
T Consensus       140 ~~~~~~  145 (170)
T d1p5qa1         140 QQRIRR  145 (170)
T ss_dssp             HHHHHH
T ss_pred             HHHHHH
Confidence            544333

>d1p5qa1 a.118.8.1 (A:258-427) FKBP52 (FKBP4), C-terminal domain {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: alpha-alpha superhelix
superfamily: TPR-like
family: Tetratricopeptide repeat (TPR)
domain: FKBP52 (FKBP4), C-terminal domain
species: Human (Homo sapiens) [TaxId: 9606]

Probab=98.30  E-value=1.6e-05  Score=64.35  Aligned_cols=114  Identities=10%  Similarity=-0.038  Sum_probs=81.6

Q ss_pred             HHHHHHHHHHHhcCChhHHHHHHHHHHhCCCCCC--------------HHHHHHHHHHHHhcCCHhHHHHHHHHHHhcCC
Q 040027           97 YTYNILINCFCKIGRVSLGFIAFGRILRSCFTPN--------------AATFNSLIKGLHAESRIMEAAALFTKLKAFGC  162 (595)
Q Consensus        97 ~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~~--------------~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~  162 (595)
                      ..+...+..+.+.|++++|+..|++++.......              ..+|+.+..+|.+.|++++|+..++..+... 
T Consensus        14 ~~l~~~G~~~~~~~~~~~Ai~~y~~al~~~~~~~~~~~~~~~~~~~~~~~~~~nla~~y~k~~~~~~A~~~~~~al~~~-   92 (170)
T d1p5qa1          14 TIVKERGTVYFKEGKYKQALLQYKKIVSWLEYESSFSNEEAQKAQALRLASHLNLAMCHLKLQAFSAAIESCNKALELD-   92 (170)
T ss_dssp             HHHHHHHHHHHHHTCHHHHHHHHHHHHHHTTTCCCCCSHHHHHHHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-
T ss_pred             HHHHHHHHHHHHcCCHHHHHHHHHHHHHHhhhccccchHHHhhhchhHHHHHHHHHHHHHhhhhcccccchhhhhhhcc-
Confidence            3445566788999999999999999887521111              2345667777888888888888888888774 


Q ss_pred             CCCHhhHHHHHHHHHhcCChhHHHHHHHHHHhcCCCCCccccCcHHHHHHHHHHHH
Q 040027          163 EPNVITYNTLINGLCRTGHTMIALNLFEEMANGNGEIGVVCKPNTVTYSTIIDGLC  218 (595)
Q Consensus       163 ~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~  218 (595)
                      +.++.++..++.+|...|++++|+..|+++.+.+       |.+..+...+..+..
T Consensus        93 p~~~~a~~~~g~~~~~~g~~~~A~~~~~~al~l~-------P~n~~~~~~l~~~~~  141 (170)
T d1p5qa1          93 SNNEKGLSRRGEAHLAVNDFELARADFQKVLQLY-------PNNKAAKTQLAVCQQ  141 (170)
T ss_dssp             TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-------SSCHHHHHHHHHHHH
T ss_pred             ccchhhhHHHHHHHHHhhhHHHHHHHHHHHHHhC-------CCCHHHHHHHHHHHH
Confidence            3377788888888888888888888888888765       345555555444433

>d1ya0a1 a.118.8.1 (A:1-497) SMG-7 {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: alpha-alpha superhelix
superfamily: TPR-like
family: Tetratricopeptide repeat (TPR)
domain: SMG-7
species: Human (Homo sapiens) [TaxId: 9606]

Probab=98.27  E-value=3.2e-07  Score=89.31  Aligned_cols=133  Identities=10%  Similarity=-0.103  Sum_probs=58.9

Q ss_pred             cCChhHHHHHHHHHHhcCCCCCccccCcHHHHHHHHHHHHHcCCHhHHHHHHHHHhhCCCCCCHhHHHHHHHHHHhcCCH
Q 040027          179 TGHTMIALNLFEEMANGNGEIGVVCKPNTVTYSTIIDGLCKEGFVDKAKALFLQMKDENINPDVVTYNSLIHGLCHANDW  258 (595)
Q Consensus       179 ~g~~~~A~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~~ll~~~~~~~~~  258 (595)
                      .+.++.++..++...+.+       +++...+..+...+.+.|+.+.|...+.......   ...++..++..+...|++
T Consensus        99 ~~~Y~~ai~~l~~~~~l~-------~~~~~~~~~lg~~~~~~~~~~~A~~~~~~al~~~---~~~~~~~LG~l~~~~~~~  168 (497)
T d1ya0a1          99 SGFYTQLLQELCTVFNVD-------LPCRVKSSQLGIISNKQTHTSAIVKPQSSSCSYI---CQHCLVHLGDIARYRNQT  168 (497)
T ss_dssp             HHHHHHHHHHHTC--------------------------------------CCHHHHHH---HHHHHHHHHHHHHHTTCH
T ss_pred             HHHHHHHHHHHHHHHCCC-------hhhHHHHHHhHHHHHhCCCHHHHHHHHHHHhCCC---HHHHHHHHHHHHHHcccH
Confidence            344444444444443332       3344555666666666666666666555544321   123455566666777777


Q ss_pred             HHHHHHHHHHHHCCCCCCHhhHHHHHHHHHhcCChHHHHHHHHHHHHCCCCCCHHHHHHHHHHHH
Q 040027          259 NEAKRLFIEMMDQGVQPSVVTFNVIMDELCKNRKMDEASRLLDLMVQRGVRPNACTYNTLMDGFC  323 (595)
Q Consensus       259 ~~A~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~  323 (595)
                      ++|...|.+..+.. +.+...|+.++..+...|+..+|...|.+.+... +|-..++..|...+.
T Consensus       169 ~~A~~~y~~A~~l~-P~~~~~~~~Lg~~~~~~~~~~~A~~~y~ral~~~-~~~~~a~~nL~~~~~  231 (497)
T d1ya0a1         169 SQAESYYRHAAQLV-PSNGQPYNQLAILASSKGDHLTTIFYYCRSIAVK-FPFPAASTNLQKALS  231 (497)
T ss_dssp             HHHHHHHHHHHHHC-TTBSHHHHHHHHHHHHTTCHHHHHHHHHHHHSSS-BCCHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHC-CCchHHHHHHHHHHHHcCCHHHHHHHHHHHHhCC-CCCHHHHHHHHHHHH
Confidence            77777777766642 2244566667777777777777777777766653 334555555555554

>d1ya0a1 a.118.8.1 (A:1-497) SMG-7 {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: alpha-alpha superhelix
superfamily: TPR-like
family: Tetratricopeptide repeat (TPR)
domain: SMG-7
species: Human (Homo sapiens) [TaxId: 9606]

Probab=98.25  E-value=5.7e-07  Score=87.56  Aligned_cols=227  Identities=8%  Similarity=-0.064  Sum_probs=123.5

Q ss_pred             HHHHHHHHHHHCCCCCC-HHHHHHHHHHHHhcCCHHHHHHHHHHHHhcCCCCCHH-HHHHHHHHHHhCCCHHHHHHHHHH
Q 040027          295 EASRLLDLMVQRGVRPN-ACTYNTLMDGFCLMGKINRAEELFGSMESMGCKHDDV-SYNILINGYCKNKEVEEALSLYRE  372 (595)
Q Consensus       295 ~a~~~~~~~~~~~~~~~-~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~-~~~~l~~~~~~~~~~~~A~~~~~~  372 (595)
                      +|.+.|+++.+.  +|+ ...+..+..++...+++++|   |++++..  .|+.. ..+.  ....-...+..+++.++.
T Consensus         4 eA~q~~~qA~~l--~p~~a~a~~~la~~~~~~~~l~ea---ye~~i~~--dp~~a~~~~~--e~~Lw~~~y~~~ie~~r~   74 (497)
T d1ya0a1           4 QSAQYLRQAEVL--KADMTDSKLGPAEVWTSRQALQDL---YQKMLVT--DLEYALDKKV--EQDLWNHAFKNQITTLQG   74 (497)
T ss_dssp             HHHHHHHHHHHH--HGGGTCSSSCSSSSHHHHHHHHHH---HHHHHHH--CHHHHHHHTH--HHHHHHHHTHHHHHHHHH
T ss_pred             HHHHHHHHHHHc--CCCCHHHHhhHHHHHHHHchHHHH---HHHHHHc--ChhhHHHHhH--HHHHHHHHHHHHHHHHHH
Confidence            677888888764  233 34455667777777777765   6666654  22211 1111  111111224566777777


Q ss_pred             HHHCCCCCCHHHHHHHHHHH--HccCCHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCc
Q 040027          373 MVSKGIKPTVVTYNTLFLGL--FEIHQVEHALKLFDEMQRDGVAADTRTYTTFIDGLCKNGYIIEAVELFRTLRILKCEL  450 (595)
Q Consensus       373 ~~~~~~~~~~~~~~~l~~~~--~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~  450 (595)
                      ..+....++..........+  ...+.++.++..+....+.. +++...+..+...+.+.|+.++|...++......   
T Consensus        75 ~~k~~~~~~~~~~~~~~~~~l~~a~~~Y~~ai~~l~~~~~l~-~~~~~~~~~lg~~~~~~~~~~~A~~~~~~al~~~---  150 (497)
T d1ya0a1          75 QAKNRANPNRSEVQANLSLFLEAASGFYTQLLQELCTVFNVD-LPCRVKSSQLGIISNKQTHTSAIVKPQSSSCSYI---  150 (497)
T ss_dssp             HHSCSSCTTTTHHHHHHHHHHHHHHHHHHHHHHHHTC--------------------------------CCHHHHHH---
T ss_pred             hcccccCccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCC-hhhHHHHHHhHHHHHhCCCHHHHHHHHHHHhCCC---
Confidence            66554333333222222222  22344555555444444332 3445566777777888888888888887776532   


Q ss_pred             CHHHHHHHHHHHHhcCChHHHHHHHHhcccCCCCCC-HHHHHHHHHHHHhcCChhHHHHHHHHHHHcCCCCCHHHHHHHH
Q 040027          451 DIQAYNCLIDGLCKSGRLKFAWELFCSLPHGVLVPN-VVTYNIMIQGLCNDGQMDKARDLFLDMEENAAAPDVITFDMLI  529 (595)
Q Consensus       451 ~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~p~-~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~~l~  529 (595)
                      ...++..++..+...|++++|+..|+++.+  +.|+ ...|+.++..+...|+..+|+..|.+.+... +|-..++..|.
T Consensus       151 ~~~~~~~LG~l~~~~~~~~~A~~~y~~A~~--l~P~~~~~~~~Lg~~~~~~~~~~~A~~~y~ral~~~-~~~~~a~~nL~  227 (497)
T d1ya0a1         151 CQHCLVHLGDIARYRNQTSQAESYYRHAAQ--LVPSNGQPYNQLAILASSKGDHLTTIFYYCRSIAVK-FPFPAASTNLQ  227 (497)
T ss_dssp             HHHHHHHHHHHHHHTTCHHHHHHHHHHHHH--HCTTBSHHHHHHHHHHHHTTCHHHHHHHHHHHHSSS-BCCHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHcccHHHHHHHHHHHHH--HCCCchHHHHHHHHHHHHcCCHHHHHHHHHHHHhCC-CCCHHHHHHHH
Confidence            235677788888889999999999999888  4565 5788889999999999999999999988875 66778888888


Q ss_pred             HHHHHcCC
Q 040027          530 HGFIRINE  537 (595)
Q Consensus       530 ~~~~~~g~  537 (595)
                      ..+.+..+
T Consensus       228 ~~~~~~~~  235 (497)
T d1ya0a1         228 KALSKALE  235 (497)
T ss_dssp             HHHHHHTT
T ss_pred             HHHHHhhh
Confidence            77765543

>d2ff4a2 a.118.8.3 (A:105-283) Probable regulatory protein EmbR, middle domain {Mycobacterium tuberculosis [TaxId: 1773]}

class: All alpha proteins
fold: alpha-alpha superhelix
superfamily: TPR-like
family: BTAD-like
domain: Probable regulatory protein EmbR, middle domain
species: Mycobacterium tuberculosis [TaxId: 1773]

Probab=98.23  E-value=1.9e-05  Score=64.11  Aligned_cols=134  Identities=10%  Similarity=0.021  Sum_probs=93.0

Q ss_pred             HHHHHHHhcCCHHHHHHHHHHHHHcCCCcCHHHHHHHHHHHHhcCChHHHHHHHHhcccCCCCCCHHHHHHHHHHHHhcC
Q 040027          422 TFIDGLCKNGYIIEAVELFRTLRILKCELDIQAYNCLIDGLCKSGRLKFAWELFCSLPHGVLVPNVVTYNIMIQGLCNDG  501 (595)
Q Consensus       422 ~l~~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~p~~~~~~~l~~~~~~~g  501 (595)
                      .........|++++|...|.+++... +-+..         ......+-+...-..+..    .....+..++.++...|
T Consensus        16 ~~g~~~~~~g~~e~A~~~~~~AL~l~-rG~~l---------~~~~~~~w~~~~r~~l~~----~~~~a~~~la~~~~~~g   81 (179)
T d2ff4a2          16 TAGVHAAAAGRFEQASRHLSAALREW-RGPVL---------DDLRDFQFVEPFATALVE----DKVLAHTAKAEAEIACG   81 (179)
T ss_dssp             HHHHHHHHTTCHHHHHHHHHHHHTTC-CSSTT---------GGGTTSTTHHHHHHHHHH----HHHHHHHHHHHHHHHTT
T ss_pred             HHHHHHHHCCCHHHHHHHHHHHHhhC-ccccc---------ccCcchHHHHHHHHHHHH----HHHHHHHHHHHHHHHCC
Confidence            34455677888888888888887653 11100         000111111111111111    12356778899999999


Q ss_pred             ChhHHHHHHHHHHHcCCCCCHHHHHHHHHHHHHcCChhHHHHHHHHHH-----HCCCCCCHHHHHHHHHHHHhc
Q 040027          502 QMDKARDLFLDMEENAAAPDVITFDMLIHGFIRINEPSKVNELLHKMK-----EKKVMPDASIVSIVVDLLVKN  570 (595)
Q Consensus       502 ~~~~A~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~-----~~~~~p~~~~~~~l~~~~~~~  570 (595)
                      ++++|+..++++++.. +-+...|..++.+|...|++++|++.|+++.     +.|+.|++.+....-.++...
T Consensus        82 ~~~~Al~~~~~al~~~-P~~e~~~~~l~~al~~~Gr~~eAl~~y~~~~~~L~~eLG~~P~~~l~~l~~~il~~~  154 (179)
T d2ff4a2          82 RASAVIAELEALTFEH-PYREPLWTQLITAYYLSDRQSDALGAYRRVKTTLADDLGIDPGPTLRALNERILRQQ  154 (179)
T ss_dssp             CHHHHHHHHHHHHHHS-TTCHHHHHHHHHHHHTTTCHHHHHHHHHHHHHHHHHHHSCCCCHHHHHHHHHHHTTC
T ss_pred             CchHHHHHHHHHHHhC-CccHHHHHHHHHHHHHhcCHHHHHHHHHHHHHHHHHHhCCCcCHHHHHHHHHHHhCC
Confidence            9999999999999985 6788999999999999999999999999985     469999988766666655443

>d1elra_ a.118.8.1 (A:) Hop {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: alpha-alpha superhelix
superfamily: TPR-like
family: Tetratricopeptide repeat (TPR)
domain: Hop
species: Human (Homo sapiens) [TaxId: 9606]

Probab=98.22  E-value=6.9e-06  Score=62.88  Aligned_cols=56  Identities=11%  Similarity=0.020  Sum_probs=26.1

Q ss_pred             HHHHHHhcCCHHHHHHHHHHHHHcCCCcCHHHHHHHHHHHHhcCChHHHHHHHHhcc
Q 040027          423 FIDGLCKNGYIIEAVELFRTLRILKCELDIQAYNCLIDGLCKSGRLKFAWELFCSLP  479 (595)
Q Consensus       423 l~~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~  479 (595)
                      +...+.+.|++++|+..|+++++.+ +.+...+..+..+|.+.|++++|+..+++++
T Consensus        10 ~G~~~~~~~~y~~Ai~~y~~al~~~-p~~~~~~~~~a~~~~~~~~~~~A~~~~~~al   65 (128)
T d1elra_          10 LGNDAYKKKDFDTALKHYDKAKELD-PTNMTYITNQAAVYFEKGDYNKCRELCEKAI   65 (128)
T ss_dssp             HHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHHTCHHHHHHHHHHHH
T ss_pred             HHHHHHHcCCHHHHHHHHHHHHHhC-cccHHHHHhHHHHHHHcCchHHHHHHHHHHH
Confidence            3344444444444444444444443 3344444444444444444444444444443

>d2fbna1 a.118.8.1 (A:22-174) Putative 70 kda peptidylprolyl isomerase PFL2275c {Plasmodium falciparum [TaxId: 5833]}

class: All alpha proteins
fold: alpha-alpha superhelix
superfamily: TPR-like
family: Tetratricopeptide repeat (TPR)
domain: Putative 70 kda peptidylprolyl isomerase PFL2275c
species: Plasmodium falciparum [TaxId: 5833]

Probab=98.19  E-value=2.2e-05  Score=62.14  Aligned_cols=77  Identities=13%  Similarity=-0.049  Sum_probs=63.7

Q ss_pred             HHHHHHHHHHHhcCChhHHHHHHHHHHHcCCCCCHHHHHHHHHHHHHcCChhHHHHHHHHHHHCCCCC-CHHHHHHHHHH
Q 040027          488 VTYNIMIQGLCNDGQMDKARDLFLDMEENAAAPDVITFDMLIHGFIRINEPSKVNELLHKMKEKKVMP-DASIVSIVVDL  566 (595)
Q Consensus       488 ~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~p-~~~~~~~l~~~  566 (595)
                      .+|..++.+|.+.|++++|++.++++++.+ |.+..+|..++.++...|++++|...|++.++.  .| +..+...+..+
T Consensus        68 ~~~~Nla~~~~~l~~~~~Al~~~~~al~~~-p~~~ka~~~~g~~~~~lg~~~~A~~~~~~al~l--~P~n~~~~~~l~~~  144 (153)
T d2fbna1          68 SCNLNLATCYNKNKDYPKAIDHASKVLKID-KNNVKALYKLGVANMYFGFLEEAKENLYKAASL--NPNNLDIRNSYELC  144 (153)
T ss_dssp             HHHHHHHHHHHHTTCHHHHHHHHHHHHHHS-TTCHHHHHHHHHHHHHHTCHHHHHHHHHHHHHH--STTCHHHHHHHHHH
T ss_pred             HHHhhHHHHHHHhcccchhhhhhhcccccc-chhhhhhHHhHHHHHHcCCHHHHHHHHHHHHHh--CCCCHHHHHHHHHH
Confidence            467788899999999999999999999875 667889999999999999999999999999984  46 45555555444


Q ss_pred             H
Q 040027          567 L  567 (595)
Q Consensus       567 ~  567 (595)
                      .
T Consensus       145 ~  145 (153)
T d2fbna1         145 V  145 (153)
T ss_dssp             H
T ss_pred             H
Confidence            3

>d1b89a_ a.118.1.3 (A:) Clathrin heavy chain proximal leg segment {Cow (Bos taurus) [TaxId: 9913]}

class: All alpha proteins
fold: alpha-alpha superhelix
superfamily: ARM repeat
family: Clathrin heavy chain proximal leg segment
domain: Clathrin heavy chain proximal leg segment
species: Cow (Bos taurus) [TaxId: 9913]

Probab=98.17  E-value=0.0014  Score=58.31  Aligned_cols=144  Identities=16%  Similarity=0.155  Sum_probs=91.0

Q ss_pred             CcHHHHHHHHHHHHHcCCHhHHHHHHHHHhhCCCCCCHhHHHHHHHHHHhcCCHHHHHHHHHHHHHCCCCCCHhhHHHHH
Q 040027          205 PNTVTYSTIIDGLCKEGFVDKAKALFLQMKDENINPDVVTYNSLIHGLCHANDWNEAKRLFIEMMDQGVQPSVVTFNVIM  284 (595)
Q Consensus       205 ~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~~ll~~~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~~l~  284 (595)
                      +|..-...++..|.+.|.++.|..+|..+..         |..++..+.+.++++.|.+...+.      -+..+|..+.
T Consensus        12 ~n~~d~~~i~~~c~~~~lye~A~~lY~~~~d---------~~rl~~~~v~l~~~~~avd~~~k~------~~~~~~k~~~   76 (336)
T d1b89a_          12 PNNAHIQQVGDRCYDEKMYDAAKLLYNNVSN---------FGRLASTLVHLGEYQAAVDGARKA------NSTRTWKEVC   76 (336)
T ss_dssp             C----------------CTTTHHHHHHHTTC---------HHHHHHHHHTTTCHHHHHHHHHHH------TCHHHHHHHH
T ss_pred             CCcCCHHHHHHHHHHCCCHHHHHHHHHhCCC---------HHHHHHHHHhhccHHHHHHHHHHc------CCHHHHHHHH
Confidence            4444455677778889999999999876543         566778888899999988887654      2566888888


Q ss_pred             HHHHhcCChHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHhcCCCCCHHHHHHHHHHHHhCCCHH
Q 040027          285 DELCKNRKMDEASRLLDLMVQRGVRPNACTYNTLMDGFCLMGKINRAEELFGSMESMGCKHDDVSYNILINGYCKNKEVE  364 (595)
Q Consensus       285 ~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~  364 (595)
                      ..+.+......+.     +.......++.....++..|-..|.+++...+++...... ..+...++.++..|++.+ .+
T Consensus        77 ~~l~~~~e~~la~-----i~~~~~~~~~d~l~~~v~~ye~~~~~e~Li~~Le~~~~~~-~~~~~~~~~L~~lyak~~-~~  149 (336)
T d1b89a_          77 FACVDGKEFRLAQ-----MCGLHIVVHADELEELINYYQDRGYFEELITMLEAALGLE-RAHMGMFTELAILYSKFK-PQ  149 (336)
T ss_dssp             HHHHHTTCHHHHH-----HTTTTTTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHTTST-TCCHHHHHHHHHHHHTTC-HH
T ss_pred             HHHHhCcHHHHHH-----HHHHHhhcCHHHHHHHHHHHHHcCChHHHHHHHHHHHcCC-ccchHHHHHHHHHHHHhC-hH
Confidence            8888777665432     2233334466666778888899999999999998876542 456778888888888754 33


Q ss_pred             HHHHHH
Q 040027          365 EALSLY  370 (595)
Q Consensus       365 ~A~~~~  370 (595)
                      +..+.+
T Consensus       150 kl~e~l  155 (336)
T d1b89a_         150 KMREHL  155 (336)
T ss_dssp             HHHHHH
T ss_pred             HHHHHH
Confidence            444433

>d1elra_ a.118.8.1 (A:) Hop {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: alpha-alpha superhelix
superfamily: TPR-like
family: Tetratricopeptide repeat (TPR)
domain: Hop
species: Human (Homo sapiens) [TaxId: 9606]

Probab=98.15  E-value=2.1e-05  Score=60.03  Aligned_cols=98  Identities=11%  Similarity=0.058  Sum_probs=81.3

Q ss_pred             HHHHHHHHHHhcCChhHHHHHHHHHHhCCCCCCHHHHHHHHHHHHhcCCHhHHHHHHHHHHhcCCC-CC-----HhhHHH
Q 040027           98 TYNILINCFCKIGRVSLGFIAFGRILRSCFTPNAATFNSLIKGLHAESRIMEAAALFTKLKAFGCE-PN-----VITYNT  171 (595)
Q Consensus        98 ~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~-~~-----~~~~~~  171 (595)
                      .+-.+...+.+.|++++|+..|+++++.+ +.+..++..+..+|.+.|++++|++.+++++..... +.     ..+|..
T Consensus         6 ~~k~~G~~~~~~~~y~~Ai~~y~~al~~~-p~~~~~~~~~a~~~~~~~~~~~A~~~~~~al~l~~~~~~~~~~~a~~~~~   84 (128)
T d1elra_           6 KEKELGNDAYKKKDFDTALKHYDKAKELD-PTNMTYITNQAAVYFEKGDYNKCRELCEKAIEVGRENREDYRQIAKAYAR   84 (128)
T ss_dssp             HHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHHHSTTCHHHHHHHHHH
T ss_pred             HHHHHHHHHHHcCCHHHHHHHHHHHHHhC-cccHHHHHhHHHHHHHcCchHHHHHHHHHHHHhCcccHHHHHHHHHHHHH
Confidence            34567888999999999999999999986 567889999999999999999999999998875311 11     235667


Q ss_pred             HHHHHHhcCChhHHHHHHHHHHhcC
Q 040027          172 LINGLCRTGHTMIALNLFEEMANGN  196 (595)
Q Consensus       172 l~~~~~~~g~~~~A~~~~~~~~~~~  196 (595)
                      +...+...+++++|++.|++.....
T Consensus        85 lg~~~~~~~~~~~A~~~~~kal~~~  109 (128)
T d1elra_          85 IGNSYFKEEKYKDAIHFYNKSLAEH  109 (128)
T ss_dssp             HHHHHHHTTCHHHHHHHHHHHHHHC
T ss_pred             HHHHHHHhCCHHHHHHHHHHHHhcC
Confidence            7778888999999999999988753

>d2fbna1 a.118.8.1 (A:22-174) Putative 70 kda peptidylprolyl isomerase PFL2275c {Plasmodium falciparum [TaxId: 5833]}

class: All alpha proteins
fold: alpha-alpha superhelix
superfamily: TPR-like
family: Tetratricopeptide repeat (TPR)
domain: Putative 70 kda peptidylprolyl isomerase PFL2275c
species: Plasmodium falciparum [TaxId: 5833]

Probab=98.13  E-value=3.5e-05  Score=60.94  Aligned_cols=111  Identities=14%  Similarity=0.001  Sum_probs=88.7

Q ss_pred             HHHHHHHHHHHhcCChhHHHHHHHHHHhCCCC----CC-----------HHHHHHHHHHHHhcCCHhHHHHHHHHHHhcC
Q 040027           97 YTYNILINCFCKIGRVSLGFIAFGRILRSCFT----PN-----------AATFNSLIKGLHAESRIMEAAALFTKLKAFG  161 (595)
Q Consensus        97 ~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~----~~-----------~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~  161 (595)
                      ..+..-+..+.+.|++.+|+..|.+++..-..    .+           ..+|..+..+|.+.|++++|++.+++++...
T Consensus        18 ~~~~~~G~~~f~~~~y~~A~~~Y~~al~~~~~~~~~~~~~~~~~~~~~~~~~~~Nla~~~~~l~~~~~Al~~~~~al~~~   97 (153)
T d2fbna1          18 FDIKEEGNEFFKKNEINEAIVKYKEALDFFIHTEEWDDQILLDKKKNIEISCNLNLATCYNKNKDYPKAIDHASKVLKID   97 (153)
T ss_dssp             HHHHHHHHHHHHTTCHHHHHHHHHHHHHTTTTCTTCCCHHHHHHHHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHS
T ss_pred             HHHHHHHHHHHHcCCHHHHHHHHHHHHhhCcchhhhhhHHHHHhhhhHHHHHHhhHHHHHHHhcccchhhhhhhcccccc
Confidence            34555677888999999999999998875211    11           2356778888999999999999999999885


Q ss_pred             CCCCHhhHHHHHHHHHhcCChhHHHHHHHHHHhcCCCCCccccCcHHHHHHHHH
Q 040027          162 CEPNVITYNTLINGLCRTGHTMIALNLFEEMANGNGEIGVVCKPNTVTYSTIID  215 (595)
Q Consensus       162 ~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~  215 (595)
                       +.+..+|..++.++...|++++|+..|++..+.+       |.+..+...+..
T Consensus        98 -p~~~ka~~~~g~~~~~lg~~~~A~~~~~~al~l~-------P~n~~~~~~l~~  143 (153)
T d2fbna1          98 -KNNVKALYKLGVANMYFGFLEEAKENLYKAASLN-------PNNLDIRNSYEL  143 (153)
T ss_dssp             -TTCHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHS-------TTCHHHHHHHHH
T ss_pred             -chhhhhhHHhHHHHHHcCCHHHHHHHHHHHHHhC-------CCCHHHHHHHHH
Confidence             4488999999999999999999999999999976       445555554433

>d1kt1a1 a.118.8.1 (A:254-421) FKBP51, C-terminal domain {Monkey (Saimiri boliviensis) [TaxId: 27679]}

class: All alpha proteins
fold: alpha-alpha superhelix
superfamily: TPR-like
family: Tetratricopeptide repeat (TPR)
domain: FKBP51, C-terminal domain
species: Monkey (Saimiri boliviensis) [TaxId: 27679]

Probab=98.12  E-value=6.6e-05  Score=60.43  Aligned_cols=81  Identities=9%  Similarity=-0.083  Sum_probs=54.8

Q ss_pred             HHHHHHHHHHhcCChhHHHHHHHHHHHcCCCCCHHHHHHHHHHHHHcCChhHHHHHHHHHHHCCCCCCHHHHHHHHHHHH
Q 040027          489 TYNIMIQGLCNDGQMDKARDLFLDMEENAAAPDVITFDMLIHGFIRINEPSKVNELLHKMKEKKVMPDASIVSIVVDLLV  568 (595)
Q Consensus       489 ~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~p~~~~~~~l~~~~~  568 (595)
                      +|..+..+|.+.|++++|+..++++++.+ +.+..+|..++.+|...|++++|...|+++++.. +.+..+...+..+..
T Consensus        66 ~~~Nla~~~~~l~~~~~Ai~~~~~al~l~-p~~~~a~~~~~~~~~~l~~~~~A~~~~~~al~l~-P~n~~~~~~l~~~~~  143 (168)
T d1kt1a1          66 AFLNLAMCYLKLREYTKAVECCDKALGLD-SANEKGLYRRGEAQLLMNEFESAKGDFEKVLEVN-PQNKAARLQIFMCQK  143 (168)
T ss_dssp             HHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHSC-TTCHHHHHHHHHHHH
T ss_pred             HHHhHHHHHHHhhhcccchhhhhhhhhcc-cchHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhC-CCCHHHHHHHHHHHH
Confidence            45566677777788888888887777764 5567777777777778888888888888777643 224555555555444


Q ss_pred             hcC
Q 040027          569 KNE  571 (595)
Q Consensus       569 ~~g  571 (595)
                      +.+
T Consensus       144 ~~~  146 (168)
T d1kt1a1         144 KAK  146 (168)
T ss_dssp             HHH
T ss_pred             HHH
Confidence            433

>d1ihga1 a.118.8.1 (A:197-365) Cyclophilin 40 {Cow (Bos taurus) [TaxId: 9913]}

class: All alpha proteins
fold: alpha-alpha superhelix
superfamily: TPR-like
family: Tetratricopeptide repeat (TPR)
domain: Cyclophilin 40
species: Cow (Bos taurus) [TaxId: 9913]

Probab=98.11  E-value=2.8e-05  Score=62.83  Aligned_cols=79  Identities=15%  Similarity=0.081  Sum_probs=47.2

Q ss_pred             HHHHHHHHHHHHhcCChhHHHHHHHHHHHcCCCCCHHHHHHHHHHHHHcCChhHHHHHHHHHHHCCCCC-CHHHHHHHHH
Q 040027          487 VVTYNIMIQGLCNDGQMDKARDLFLDMEENAAAPDVITFDMLIHGFIRINEPSKVNELLHKMKEKKVMP-DASIVSIVVD  565 (595)
Q Consensus       487 ~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~p-~~~~~~~l~~  565 (595)
                      ...|..+..++.+.|++++|+..+.++++.. +.+..+|..++.+|...|++++|...|+++++.  .| +..+...+..
T Consensus        77 ~~~~~nla~~~~~~~~~~~Ai~~~~~al~~~-p~~~~a~~~~g~~~~~l~~~~~A~~~~~~al~l--~p~n~~~~~~l~~  153 (169)
T d1ihga1          77 LSCVLNIGACKLKMSDWQGAVDSCLEALEID-PSNTKALYRRAQGWQGLKEYDQALADLKKAQEI--APEDKAIQAELLK  153 (169)
T ss_dssp             HHHHHHHHHHHHHTTCHHHHHHHHHHHHTTC-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH--CTTCHHHHHHHHH
T ss_pred             HHHHHHHHHHHHhhcccchhhhhhhhhhhhh-hhhhhHHHhHHHHHHHccCHHHHHHHHHHHHHh--CCCCHHHHHHHHH
Confidence            3455556666666666666666666666653 445566666666666666666666666666653  23 4445554444


Q ss_pred             HHH
Q 040027          566 LLV  568 (595)
Q Consensus       566 ~~~  568 (595)
                      +..
T Consensus       154 ~~~  156 (169)
T d1ihga1         154 VKQ  156 (169)
T ss_dssp             HHH
T ss_pred             HHH
Confidence            433

>d1kt1a1 a.118.8.1 (A:254-421) FKBP51, C-terminal domain {Monkey (Saimiri boliviensis) [TaxId: 27679]}

class: All alpha proteins
fold: alpha-alpha superhelix
superfamily: TPR-like
family: Tetratricopeptide repeat (TPR)
domain: FKBP51, C-terminal domain
species: Monkey (Saimiri boliviensis) [TaxId: 27679]

Probab=98.04  E-value=0.00011  Score=59.12  Aligned_cols=116  Identities=16%  Similarity=0.041  Sum_probs=80.3

Q ss_pred             HHHHHHHHHHHhcCChhHHHHHHHHHHhCC---CCCC-----------HHHHHHHHHHHHhcCCHhHHHHHHHHHHhcCC
Q 040027           97 YTYNILINCFCKIGRVSLGFIAFGRILRSC---FTPN-----------AATFNSLIKGLHAESRIMEAAALFTKLKAFGC  162 (595)
Q Consensus        97 ~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~---~~~~-----------~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~  162 (595)
                      ..+...+..+.+.|++.+|+..|++++..-   ...+           ..+|..+..+|.+.|++++|+..++..+... 
T Consensus        16 ~~~~e~G~~~~~~~~~~~A~~~Y~~al~~~~~~~~~~~~~~~~~~~~~~~~~~Nla~~~~~l~~~~~Ai~~~~~al~l~-   94 (168)
T d1kt1a1          16 AIVKEKGTVYFKGGKYVQAVIQYGKIVSWLEMEYGLSEKESKASESFLLAAFLNLAMCYLKLREYTKAVECCDKALGLD-   94 (168)
T ss_dssp             HHHHHHHHHHHHTTCHHHHHHHHHHHHHHHTTCCSCCHHHHHHHHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-
T ss_pred             HHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHhhccchhhhhhcchhHHHHHHhHHHHHHHhhhcccchhhhhhhhhcc-
Confidence            455667888899999999999998877531   1111           2235556667777888888888888887765 


Q ss_pred             CCCHhhHHHHHHHHHhcCChhHHHHHHHHHHhcCCCCCccccCcHHHHHHHHHHHHHc
Q 040027          163 EPNVITYNTLINGLCRTGHTMIALNLFEEMANGNGEIGVVCKPNTVTYSTIIDGLCKE  220 (595)
Q Consensus       163 ~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~  220 (595)
                      +.+..++..+..++...|++++|+..|+++...+       |.+..+...+..+....
T Consensus        95 p~~~~a~~~~~~~~~~l~~~~~A~~~~~~al~l~-------P~n~~~~~~l~~~~~~~  145 (168)
T d1kt1a1          95 SANEKGLYRRGEAQLLMNEFESAKGDFEKVLEVN-------PQNKAARLQIFMCQKKA  145 (168)
T ss_dssp             TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHSC-------TTCHHHHHHHHHHHHHH
T ss_pred             cchHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhC-------CCCHHHHHHHHHHHHHH
Confidence            4467777778888888888888888888887765       44555555554444333

>d1ihga1 a.118.8.1 (A:197-365) Cyclophilin 40 {Cow (Bos taurus) [TaxId: 9913]}

class: All alpha proteins
fold: alpha-alpha superhelix
superfamily: TPR-like
family: Tetratricopeptide repeat (TPR)
domain: Cyclophilin 40
species: Cow (Bos taurus) [TaxId: 9913]

Probab=98.02  E-value=5e-05  Score=61.30  Aligned_cols=111  Identities=10%  Similarity=-0.021  Sum_probs=85.9

Q ss_pred             HHHHHHHHhcCChhHHHHHHHHHHhCC---------------CCCCHHHHHHHHHHHHhcCCHhHHHHHHHHHHhcCCCC
Q 040027          100 NILINCFCKIGRVSLGFIAFGRILRSC---------------FTPNAATFNSLIKGLHAESRIMEAAALFTKLKAFGCEP  164 (595)
Q Consensus       100 ~~l~~~~~~~g~~~~A~~~~~~~~~~~---------------~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~  164 (595)
                      ......+...|++++|+..|.++++..               -+.....|..+..++.+.|++++|+..++++++.. +.
T Consensus        31 ~~~~~~~~~~~~y~~Ai~~y~~al~~~~~~~~~~~~~~~~~~~~~~~~~~~nla~~~~~~~~~~~Ai~~~~~al~~~-p~  109 (169)
T d1ihga1          31 KNIGNTFFKSQNWEMAIKKYTKVLRYVEGSRAAAEDADGAKLQPVALSCVLNIGACKLKMSDWQGAVDSCLEALEID-PS  109 (169)
T ss_dssp             HHHHHHHHHTTCHHHHHHHHHHHHHHHHHHHHHSCHHHHGGGHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHTTC-TT
T ss_pred             HHHHHHHHHcCCHHHHHHHHHHHHHhhhhhhhhhhhHHHHHhChhhHHHHHHHHHHHHhhcccchhhhhhhhhhhhh-hh
Confidence            345666778889999988888876421               02234466778888999999999999999999875 44


Q ss_pred             CHhhHHHHHHHHHhcCChhHHHHHHHHHHhcCCCCCccccCcHHHHHHHHHHHH
Q 040027          165 NVITYNTLINGLCRTGHTMIALNLFEEMANGNGEIGVVCKPNTVTYSTIIDGLC  218 (595)
Q Consensus       165 ~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~  218 (595)
                      +..+|..++.++...|++++|+..|+++.+.+       |.+..+...+..+..
T Consensus       110 ~~~a~~~~g~~~~~l~~~~~A~~~~~~al~l~-------p~n~~~~~~l~~~~~  156 (169)
T d1ihga1         110 NTKALYRRAQGWQGLKEYDQALADLKKAQEIA-------PEDKAIQAELLKVKQ  156 (169)
T ss_dssp             CHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-------TTCHHHHHHHHHHHH
T ss_pred             hhhHHHhHHHHHHHccCHHHHHHHHHHHHHhC-------CCCHHHHHHHHHHHH
Confidence            78899999999999999999999999999976       456666666555443

>d1b89a_ a.118.1.3 (A:) Clathrin heavy chain proximal leg segment {Cow (Bos taurus) [TaxId: 9913]}

class: All alpha proteins
fold: alpha-alpha superhelix
superfamily: ARM repeat
family: Clathrin heavy chain proximal leg segment
domain: Clathrin heavy chain proximal leg segment
species: Cow (Bos taurus) [TaxId: 9913]

Probab=98.00  E-value=0.0044  Score=55.05  Aligned_cols=43  Identities=5%  Similarity=-0.058  Sum_probs=21.3

Q ss_pred             cCCHHHHHHHHHHHHHcCCCcCHHHHHHHHHHHHhcCChHHHHHHH
Q 040027          430 NGYIIEAVELFRTLRILKCELDIQAYNCLIDGLCKSGRLKFAWELF  475 (595)
Q Consensus       430 ~g~~~~A~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~  475 (595)
                      .+++.-....++.....+   +....+++...|...++++.-....
T Consensus       261 ~~~l~li~p~Le~v~~~n---~~~vn~al~~lyie~~d~~~l~~~i  303 (336)
T d1b89a_         261 VKQLPLVKPYLRSVQNHN---NKSVNESLNNLFITEEDYQALRTSI  303 (336)
T ss_dssp             TTCTTTTHHHHHHHHTTC---CHHHHHHHHHHHHHTTCHHHHHHHH
T ss_pred             cCCcHHHHHHHHHHHHcC---hHHHHHHHHHHHhCcchhHHHHHHH
Confidence            333444444444444322   3345666666666666655444333

>d1zu2a1 a.118.8.1 (A:1-145) Mitochondrial import receptor subunit tom20-3 {Thale cress (Arabidopsis thaliana) [TaxId: 3702]}

class: All alpha proteins
fold: alpha-alpha superhelix
superfamily: TPR-like
family: Tetratricopeptide repeat (TPR)
domain: Mitochondrial import receptor subunit tom20-3
species: Thale cress (Arabidopsis thaliana) [TaxId: 3702]

Probab=97.99  E-value=8.6e-06  Score=63.82  Aligned_cols=128  Identities=9%  Similarity=-0.019  Sum_probs=90.5

Q ss_pred             cccccCCCChHHHHHHHHHHHHhCCCCCCHhhHHHHHHHHHcCCCchhHHhhCCCCCCHHHHHHHHHHHHhcCChhHHHH
Q 040027           38 REGDINVITPNEAFCIFDYMLRMHPSPPPVSSFNILLASLAKNKHYDTRLNATGLFPNLYTYNILINCFCKIGRVSLGFI  117 (595)
Q Consensus        38 ~~~~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~  117 (595)
                      ...|-+.+.+++|++.|+.+++.+|+  ++.++..+..++...+++....                   -..+.+++|+.
T Consensus         4 ~~~~~r~~~fe~A~~~~e~al~~~P~--~~~~~~~~g~~l~~~~~~~~~~-------------------e~~~~~~~Ai~   62 (145)
T d1zu2a1           4 ETEFDRILLFEQIRQDAENTYKSNPL--DADNLTRWGGVLLELSQFHSIS-------------------DAKQMIQEAIT   62 (145)
T ss_dssp             CCSHHHHHHHHHHHHHHHHHHHHCTT--CHHHHHHHHHHHHHHHHHSCHH-------------------HHHHHHHHHHH
T ss_pred             hHHHHHHccHHHHHHHHHHHHhhCCc--chHHHHHHHHHHHHhhhhhhhh-------------------HHHHHHHHHHH
Confidence            34455668899999999999999998  8888888888777665543211                   12356788999


Q ss_pred             HHHHHHhCCCCCCHHHHHHHHHHHHhcCC-----------HhHHHHHHHHHHhcCCCCCHhhHHHHHHHHHhcCChhHHH
Q 040027          118 AFGRILRSCFTPNAATFNSLIKGLHAESR-----------IMEAAALFTKLKAFGCEPNVITYNTLINGLCRTGHTMIAL  186 (595)
Q Consensus       118 ~~~~~~~~~~~~~~~~~~~l~~~~~~~g~-----------~~~A~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~  186 (595)
                      .|+++++.. |.+..+|..+..+|...|+           +++|.+.|++....  .|+...+...+..+      ..|.
T Consensus        63 ~~~kAl~l~-P~~~~a~~~lG~~y~~~g~~~~~~~~~~~~~~~A~~~~~kal~l--~P~~~~~~~~L~~~------~ka~  133 (145)
T d1zu2a1          63 KFEEALLID-PKKDEAVWCIGNAYTSFAFLTPDETEAKHNFDLATQFFQQAVDE--QPDNTHYLKSLEMT------AKAP  133 (145)
T ss_dssp             HHHHHHHHC-TTCHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHH--CTTCHHHHHHHHHH------HTHH
T ss_pred             HHHHHHHhc-chhhHHHhhHHHHHHHcccchhhHHHHHHhHHHhhhhhhccccc--CCCHHHHHHHHHHH------HHHH
Confidence            999999886 5678888888888876543           57788888888876  45554444333332      3556


Q ss_pred             HHHHHHHhc
Q 040027          187 NLFEEMANG  195 (595)
Q Consensus       187 ~~~~~~~~~  195 (595)
                      +++.++.+.
T Consensus       134 ~~~~e~~k~  142 (145)
T d1zu2a1         134 QLHAEAYKQ  142 (145)
T ss_dssp             HHHHHHHHS
T ss_pred             HHHHHHHHH
Confidence            666665543

>d1zbpa1 e.61.1.1 (A:2-265) Hypothetical protein VPA1032 {Vibrio parahaemolyticus [TaxId: 670]}

class: Multi-domain proteins (alpha and beta)
fold: ImpE-like
superfamily: ImpE-like
family: ImpE-like
domain: Hypothetical protein VPA1032
species: Vibrio parahaemolyticus [TaxId: 670]

Probab=97.95  E-value=6.7e-06  Score=71.60  Aligned_cols=125  Identities=10%  Similarity=-0.003  Sum_probs=86.7

Q ss_pred             cccCCCChHHHHHHHHHHHHhCCCCCCHhhHHHHHHHHHcCCCchhHHhhCCCCCCHHHHHHHHHHHHhcCChhHHHHHH
Q 040027           40 GDINVITPNEAFCIFDYMLRMHPSPPPVSSFNILLASLAKNKHYDTRLNATGLFPNLYTYNILINCFCKIGRVSLGFIAF  119 (595)
Q Consensus        40 ~~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~  119 (595)
                      ..++.|++++|+..|+++++.+|.                               |+..+..++..++..|++++|...+
T Consensus         5 ~aL~~G~l~eAl~~l~~al~~~P~-------------------------------d~~ar~~La~lL~~~G~~e~A~~~l   53 (264)
T d1zbpa1           5 NALSEGQLQQALELLIEAIKASPK-------------------------------DASLRSSFIELLCIDGDFERADEQL   53 (264)
T ss_dssp             HHTTTTCHHHHHHHHHHHHHTCTT-------------------------------CHHHHHHHHHHHHHHTCHHHHHHHH
T ss_pred             HHHHCCCHHHHHHHHHHHHHHCCC-------------------------------CHHHHHHHHHHHHHCCCHHHHHHHH
Confidence            346789999999999999999998                               6667778888899999999999999


Q ss_pred             HHHHhCCCCCCHHHHHHHHHHHHhcCCHhHHHHHHHHHHhcCCCCCHhhHHHHHHHHHhcCChhHHHHHHHHHHhcC
Q 040027          120 GRILRSCFTPNAATFNSLIKGLHAESRIMEAAALFTKLKAFGCEPNVITYNTLINGLCRTGHTMIALNLFEEMANGN  196 (595)
Q Consensus       120 ~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~  196 (595)
                      +.+.+.. +.+...+..+...+...+..+++...+......+.+++...+......+...|+.++|.+.++++.+..
T Consensus        54 ~~a~~l~-P~~~~~~~~l~~ll~a~~~~~~a~~~~~~~~~~~~p~~~~~~l~~a~~~~~~gd~~~A~~~~~~a~e~~  129 (264)
T d1zbpa1          54 MQSIKLF-PEYLPGASQLRHLVKAAQARKDFAQGAATAKVLGENEELTKSLVSFNLSMVSQDYEQVSELALQIEELR  129 (264)
T ss_dssp             HHHHHHC-GGGHHHHHHHHHHHHHHHHHHHHTTSCCCEECCCSCHHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHC
T ss_pred             HHHHHhC-CCcHHHHHHHHHHHHhccccHHHHHHhhhhhcccCchHHHHHHHHHHHHHhCCCHHHHHHHHHHHHhcC
Confidence            9999874 234445554544444333333332221111111212233444455667788999999999999988765

>d2ff4a2 a.118.8.3 (A:105-283) Probable regulatory protein EmbR, middle domain {Mycobacterium tuberculosis [TaxId: 1773]}

class: All alpha proteins
fold: alpha-alpha superhelix
superfamily: TPR-like
family: BTAD-like
domain: Probable regulatory protein EmbR, middle domain
species: Mycobacterium tuberculosis [TaxId: 1773]

Probab=97.92  E-value=0.00014  Score=58.85  Aligned_cols=122  Identities=11%  Similarity=0.064  Sum_probs=65.3

Q ss_pred             HHHHHHHhcCChhHHHHHHHHHHhCCCCCCHHHHHHHHHHHHhcCCHhHHHHHHHHHHhcCCCCCHhhHHHHHHHHHhcC
Q 040027          101 ILINCFCKIGRVSLGFIAFGRILRSCFTPNAATFNSLIKGLHAESRIMEAAALFTKLKAFGCEPNVITYNTLINGLCRTG  180 (595)
Q Consensus       101 ~l~~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g  180 (595)
                      .........|++++|...|.+++..-  +....        ......+.+...-..+...    ....+..++..+...|
T Consensus        16 ~~g~~~~~~g~~e~A~~~~~~AL~l~--rG~~l--------~~~~~~~w~~~~r~~l~~~----~~~a~~~la~~~~~~g   81 (179)
T d2ff4a2          16 TAGVHAAAAGRFEQASRHLSAALREW--RGPVL--------DDLRDFQFVEPFATALVED----KVLAHTAKAEAEIACG   81 (179)
T ss_dssp             HHHHHHHHTTCHHHHHHHHHHHHTTC--CSSTT--------GGGTTSTTHHHHHHHHHHH----HHHHHHHHHHHHHHTT
T ss_pred             HHHHHHHHCCCHHHHHHHHHHHHhhC--ccccc--------ccCcchHHHHHHHHHHHHH----HHHHHHHHHHHHHHCC
Confidence            34455666777777777777777651  11100        0001111111111222211    2344556666666677


Q ss_pred             ChhHHHHHHHHHHhcCCCCCccccCcHHHHHHHHHHHHHcCCHhHHHHHHHHHhh-----CCCCCCHh
Q 040027          181 HTMIALNLFEEMANGNGEIGVVCKPNTVTYSTIIDGLCKEGFVDKAKALFLQMKD-----ENINPDVV  243 (595)
Q Consensus       181 ~~~~A~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~-----~~~~~~~~  243 (595)
                      ++++|+..++++...+       |.+...|..++.++.+.|+..+|.+.|+++..     .|+.|+..
T Consensus        82 ~~~~Al~~~~~al~~~-------P~~e~~~~~l~~al~~~Gr~~eAl~~y~~~~~~L~~eLG~~P~~~  142 (179)
T d2ff4a2          82 RASAVIAELEALTFEH-------PYREPLWTQLITAYYLSDRQSDALGAYRRVKTTLADDLGIDPGPT  142 (179)
T ss_dssp             CHHHHHHHHHHHHHHS-------TTCHHHHHHHHHHHHTTTCHHHHHHHHHHHHHHHHHHHSCCCCHH
T ss_pred             CchHHHHHHHHHHHhC-------CccHHHHHHHHHHHHHhcCHHHHHHHHHHHHHHHHHHhCCCcCHH
Confidence            7777777777666654       45566666677777777777777666666533     25555543

>d1zu2a1 a.118.8.1 (A:1-145) Mitochondrial import receptor subunit tom20-3 {Thale cress (Arabidopsis thaliana) [TaxId: 3702]}

class: All alpha proteins
fold: alpha-alpha superhelix
superfamily: TPR-like
family: Tetratricopeptide repeat (TPR)
domain: Mitochondrial import receptor subunit tom20-3
species: Thale cress (Arabidopsis thaliana) [TaxId: 3702]

Probab=97.89  E-value=2.8e-05  Score=60.75  Aligned_cols=113  Identities=12%  Similarity=0.005  Sum_probs=59.9

Q ss_pred             hcCCHHHHHHHHHHHHHcCCCcCHHHHHHHHHHHHhc----------CChHHHHHHHHhcccCCCCCC-HHHHHHHHHHH
Q 040027          429 KNGYIIEAVELFRTLRILKCELDIQAYNCLIDGLCKS----------GRLKFAWELFCSLPHGVLVPN-VVTYNIMIQGL  497 (595)
Q Consensus       429 ~~g~~~~A~~~~~~~~~~~~~~~~~~~~~l~~~~~~~----------g~~~~A~~~~~~~~~~~~~p~-~~~~~~l~~~~  497 (595)
                      +.+.+++|...|+.+.+.. |.++.++..+..++...          +.+++|+..|+++++  +.|+ ..+|..++.+|
T Consensus         9 r~~~fe~A~~~~e~al~~~-P~~~~~~~~~g~~l~~~~~~~~~~e~~~~~~~Ai~~~~kAl~--l~P~~~~a~~~lG~~y   85 (145)
T d1zu2a1           9 RILLFEQIRQDAENTYKSN-PLDADNLTRWGGVLLELSQFHSISDAKQMIQEAITKFEEALL--IDPKKDEAVWCIGNAY   85 (145)
T ss_dssp             HHHHHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHHHHHSCHHHHHHHHHHHHHHHHHHHH--HCTTCHHHHHHHHHHH
T ss_pred             HHccHHHHHHHHHHHHhhC-CcchHHHHHHHHHHHHhhhhhhhhHHHHHHHHHHHHHHHHHH--hcchhhHHHhhHHHHH
Confidence            3445566666666666555 55555555555555432          233456666666555  3343 45555555555


Q ss_pred             HhcC-----------ChhHHHHHHHHHHHcCCCCCHHHHHHHHHHHHHcCChhHHHHHHHHHHHCC
Q 040027          498 CNDG-----------QMDKARDLFLDMEENAAAPDVITFDMLIHGFIRINEPSKVNELLHKMKEKK  552 (595)
Q Consensus       498 ~~~g-----------~~~~A~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~  552 (595)
                      ...|           .+++|.+.|+++++.  .|+...+...+..      ..+|.+++.+..+.|
T Consensus        86 ~~~g~~~~~~~~~~~~~~~A~~~~~kal~l--~P~~~~~~~~L~~------~~ka~~~~~e~~k~~  143 (145)
T d1zu2a1          86 TSFAFLTPDETEAKHNFDLATQFFQQAVDE--QPDNTHYLKSLEM------TAKAPQLHAEAYKQG  143 (145)
T ss_dssp             HHHHHHCCCHHHHHHHHHHHHHHHHHHHHH--CTTCHHHHHHHHH------HHTHHHHHHHHHHSS
T ss_pred             HHcccchhhHHHHHHhHHHhhhhhhccccc--CCCHHHHHHHHHH------HHHHHHHHHHHHHHh
Confidence            5433           356677777777764  3444433332222      245556666655554

>d1zbpa1 e.61.1.1 (A:2-265) Hypothetical protein VPA1032 {Vibrio parahaemolyticus [TaxId: 670]}

class: Multi-domain proteins (alpha and beta)
fold: ImpE-like
superfamily: ImpE-like
family: ImpE-like
domain: Hypothetical protein VPA1032
species: Vibrio parahaemolyticus [TaxId: 670]

Probab=97.78  E-value=7.4e-05  Score=64.81  Aligned_cols=122  Identities=16%  Similarity=0.054  Sum_probs=59.1

Q ss_pred             HccCCHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCcCHHHHHHHHHHHHhcCChHHHH
Q 040027          393 FEIHQVEHALKLFDEMQRDGVAADTRTYTTFIDGLCKNGYIIEAVELFRTLRILKCELDIQAYNCLIDGLCKSGRLKFAW  472 (595)
Q Consensus       393 ~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~  472 (595)
                      .+.|++++|+..+++.++.. |.+...+..+...++..|++++|...++.+.+.. +.+...+..+...+...+..+++.
T Consensus         7 L~~G~l~eAl~~l~~al~~~-P~d~~ar~~La~lL~~~G~~e~A~~~l~~a~~l~-P~~~~~~~~l~~ll~a~~~~~~a~   84 (264)
T d1zbpa1           7 LSEGQLQQALELLIEAIKAS-PKDASLRSSFIELLCIDGDFERADEQLMQSIKLF-PEYLPGASQLRHLVKAAQARKDFA   84 (264)
T ss_dssp             TTTTCHHHHHHHHHHHHHTC-TTCHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHC-GGGHHHHHHHHHHHHHHHHHHHHT
T ss_pred             HHCCCHHHHHHHHHHHHHHC-CCCHHHHHHHHHHHHHCCCHHHHHHHHHHHHHhC-CCcHHHHHHHHHHHHhccccHHHH
Confidence            34566666666666666553 4555666666666666666666666666666553 333444444444443333333322


Q ss_pred             HHHHhcccCCCCCCHHHHHHHHHHHHhcCChhHHHHHHHHHHHc
Q 040027          473 ELFCSLPHGVLVPNVVTYNIMIQGLCNDGQMDKARDLFLDMEEN  516 (595)
Q Consensus       473 ~~~~~~~~~~~~p~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~  516 (595)
                      .-.......+-+++...+...+..+...|+.++|.+.++++.+.
T Consensus        85 ~~~~~~~~~~~p~~~~~~l~~a~~~~~~gd~~~A~~~~~~a~e~  128 (264)
T d1zbpa1          85 QGAATAKVLGENEELTKSLVSFNLSMVSQDYEQVSELALQIEEL  128 (264)
T ss_dssp             TSCCCEECCCSCHHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHH
T ss_pred             HHhhhhhcccCchHHHHHHHHHHHHHhCCCHHHHHHHHHHHHhc
Confidence            22111111101111222233334455556666666666665553

>d2hr2a1 a.118.8.8 (A:2-157) Hypothetical protein CT2138 {Chlorobium tepidum [TaxId: 1097]}

class: All alpha proteins
fold: alpha-alpha superhelix
superfamily: TPR-like
family: CT2138-like
domain: Hypothetical protein CT2138
species: Chlorobium tepidum [TaxId: 1097]

Probab=97.56  E-value=0.00065  Score=53.55  Aligned_cols=99  Identities=16%  Similarity=0.076  Sum_probs=76.0

Q ss_pred             HHHHHH--HHHHHhcCChhHHHHHHHHHHhCCCC-C----------CHHHHHHHHHHHHhcCCHhHHHHHHHHHHhcC--
Q 040027           97 YTYNIL--INCFCKIGRVSLGFIAFGRILRSCFT-P----------NAATFNSLIKGLHAESRIMEAAALFTKLKAFG--  161 (595)
Q Consensus        97 ~~~~~l--~~~~~~~g~~~~A~~~~~~~~~~~~~-~----------~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~--  161 (595)
                      .+|..+  +..+.+.|++++|+..|++++..... |          ...+|+.+..+|.+.|++++|++.+++.+...  
T Consensus         8 ~a~~~l~~g~~~~~~g~y~~Ai~~y~~Al~i~~~~~~~~~~~~~~~~a~~~~nlg~~~~~lg~~~~A~~~~~~al~~~~~   87 (156)
T d2hr2a1           8 GAYLALSDAQRQLVAGEYDEAAANCRRAMEISHTMPPEEAFDHAGFDAFCHAGLAEALAGLRSFDEALHSADKALHYFNR   87 (156)
T ss_dssp             HHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHTTSCTTSCCCHHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhChhhhhhhhcccchhHHHHHHHHHHHHHHcCccchhhHhhhhhhhcccc
Confidence            345555  56677889999999999999875211 1          13578889999999999999999999887531  


Q ss_pred             ---CCCC-----HhhHHHHHHHHHhcCChhHHHHHHHHHHhc
Q 040027          162 ---CEPN-----VITYNTLINGLCRTGHTMIALNLFEEMANG  195 (595)
Q Consensus       162 ---~~~~-----~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~  195 (595)
                         ..++     ..++..+..+|...|++++|+..|++..+.
T Consensus        88 ~~~~~~~~~~~~~~a~~~~g~~~~~lg~~eeA~~~~~~Al~l  129 (156)
T d2hr2a1          88 RGELNQDEGKLWISAVYSRALALDGLGRGAEAMPEFKKVVEM  129 (156)
T ss_dssp             HCCTTSTHHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH
T ss_pred             cccccccccchhHHHHhhhHHHHHHHHHHHHHHHHHHHHHHh
Confidence               1111     235677889999999999999999998764

>d2hr2a1 a.118.8.8 (A:2-157) Hypothetical protein CT2138 {Chlorobium tepidum [TaxId: 1097]}

class: All alpha proteins
fold: alpha-alpha superhelix
superfamily: TPR-like
family: CT2138-like
domain: Hypothetical protein CT2138
species: Chlorobium tepidum [TaxId: 1097]

Probab=97.55  E-value=0.00048  Score=54.34  Aligned_cols=92  Identities=10%  Similarity=-0.043  Sum_probs=62.1

Q ss_pred             HHHHHhcCChHHHHHHHHhcccCC-CCC----------CHHHHHHHHHHHHhcCChhHHHHHHHHHHHc-----CCCCC-
Q 040027          459 IDGLCKSGRLKFAWELFCSLPHGV-LVP----------NVVTYNIMIQGLCNDGQMDKARDLFLDMEEN-----AAAPD-  521 (595)
Q Consensus       459 ~~~~~~~g~~~~A~~~~~~~~~~~-~~p----------~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~-----~~~~~-  521 (595)
                      +..+...|++++|+..|++.++.. -.|          ....|+.+..+|...|++++|+..+++.++.     ...++ 
T Consensus        16 g~~~~~~g~y~~Ai~~y~~Al~i~~~~~~~~~~~~~~~~a~~~~nlg~~~~~lg~~~~A~~~~~~al~~~~~~~~~~~~~   95 (156)
T d2hr2a1          16 AQRQLVAGEYDEAAANCRRAMEISHTMPPEEAFDHAGFDAFCHAGLAEALAGLRSFDEALHSADKALHYFNRRGELNQDE   95 (156)
T ss_dssp             HHHHHHHTCHHHHHHHHHHHHHHHTTSCTTSCCCHHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHHCCTTSTH
T ss_pred             HHHHHHcCCHHHHHHHHHHHHHhChhhhhhhhcccchhHHHHHHHHHHHHHHcCccchhhHhhhhhhhcccccccccccc
Confidence            344555667777777776665410 001          1346777888888888888888888887752     11222 


Q ss_pred             ----HHHHHHHHHHHHHcCChhHHHHHHHHHHH
Q 040027          522 ----VITFDMLIHGFIRINEPSKVNELLHKMKE  550 (595)
Q Consensus       522 ----~~~~~~l~~~~~~~g~~~~A~~~~~~~~~  550 (595)
                          ...+..++.+|...|++++|...|+++++
T Consensus        96 ~~~~~~a~~~~g~~~~~lg~~eeA~~~~~~Al~  128 (156)
T d2hr2a1          96 GKLWISAVYSRALALDGLGRGAEAMPEFKKVVE  128 (156)
T ss_dssp             HHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHH
T ss_pred             cchhHHHHhhhHHHHHHHHHHHHHHHHHHHHHH
Confidence                23567788899999999999999999874

>d1tjca_ a.118.8.1 (A:) Prolyl 4-hydroxylase alpha-1 subunit, P4HA1 {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: alpha-alpha superhelix
superfamily: TPR-like
family: Tetratricopeptide repeat (TPR)
domain: Prolyl 4-hydroxylase alpha-1 subunit, P4HA1
species: Human (Homo sapiens) [TaxId: 9606]

Probab=97.25  E-value=0.0013  Score=46.36  Aligned_cols=83  Identities=11%  Similarity=-0.030  Sum_probs=59.2

Q ss_pred             CHhhHHHHHHHHHhcCChhHHHHHHHHHHhcCCCCCccccCcHHHHHHHHHHHHHcCCHhHHHHHHHHHhhCCCCCCHhH
Q 040027          165 NVITYNTLINGLCRTGHTMIALNLFEEMANGNGEIGVVCKPNTVTYSTIIDGLCKEGFVDKAKALFLQMKDENINPDVVT  244 (595)
Q Consensus       165 ~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~  244 (595)
                      +...+..++..+.+.|++.+|+..|++..+..............++..+..++.+.|++++|++.++++.+..+ -+..+
T Consensus         4 saddc~~lG~~~~~~g~y~~A~~~~~~Al~~~~~~~~~~~~~~~~l~~Lg~~~~~~g~~~~A~~~y~~aL~l~P-~~~~a   82 (95)
T d1tjca_           4 TAEDSFELGKVAYTEADYYHTELWMEQALRQLDEGEISTIDKVSVLDYLSYAVYQQGDLDKALLLTKKLLELDP-EHQRA   82 (95)
T ss_dssp             CHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHTTCCCSSCHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCT-TCHHH
T ss_pred             cHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHhhhhccCccHHHHHHHHhhHHHhcCChHHHHHHHHHHHHhCc-CCHHH
Confidence            45556678888889999999999998887653211111122367788999999999999999999999988642 24445


Q ss_pred             HHHH
Q 040027          245 YNSL  248 (595)
Q Consensus       245 ~~~l  248 (595)
                      ++.+
T Consensus        83 ~~Nl   86 (95)
T d1tjca_          83 NGNL   86 (95)
T ss_dssp             HHHH
T ss_pred             HHHH
Confidence            5444

>d1tjca_ a.118.8.1 (A:) Prolyl 4-hydroxylase alpha-1 subunit, P4HA1 {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: alpha-alpha superhelix
superfamily: TPR-like
family: Tetratricopeptide repeat (TPR)
domain: Prolyl 4-hydroxylase alpha-1 subunit, P4HA1
species: Human (Homo sapiens) [TaxId: 9606]

Probab=97.18  E-value=0.0015  Score=46.17  Aligned_cols=77  Identities=13%  Similarity=-0.034  Sum_probs=60.1

Q ss_pred             CHHHHHHHHHHHHhcCChhHHHHHHHHHHhCCC-----CC-CHHHHHHHHHHHHhcCCHhHHHHHHHHHHhcCCCCCHhh
Q 040027           95 NLYTYNILINCFCKIGRVSLGFIAFGRILRSCF-----TP-NAATFNSLIKGLHAESRIMEAAALFTKLKAFGCEPNVIT  168 (595)
Q Consensus        95 ~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~-----~~-~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~  168 (595)
                      +...+..++..+.+.|+++.|+..|+++++...     .+ ...++..+..++.+.|++++|+..++++++..+ -+..+
T Consensus         4 saddc~~lG~~~~~~g~y~~A~~~~~~Al~~~~~~~~~~~~~~~~l~~Lg~~~~~~g~~~~A~~~y~~aL~l~P-~~~~a   82 (95)
T d1tjca_           4 TAEDSFELGKVAYTEADYYHTELWMEQALRQLDEGEISTIDKVSVLDYLSYAVYQQGDLDKALLLTKKLLELDP-EHQRA   82 (95)
T ss_dssp             CHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHTTCCCSSCHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCT-TCHHH
T ss_pred             cHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHhhhhccCccHHHHHHHHhhHHHhcCChHHHHHHHHHHHHhCc-CCHHH
Confidence            556667889999999999999999999887521     11 246788899999999999999999999998852 24555


Q ss_pred             HHHH
Q 040027          169 YNTL  172 (595)
Q Consensus       169 ~~~l  172 (595)
                      +..+
T Consensus        83 ~~Nl   86 (95)
T d1tjca_          83 NGNL   86 (95)
T ss_dssp             HHHH
T ss_pred             HHHH
Confidence            5554

>d1klxa_ a.118.18.1 (A:) Cysteine rich protein B (HcpB) {Helicobacter pylori [TaxId: 210]}

class: All alpha proteins
fold: alpha-alpha superhelix
superfamily: HCP-like
family: HCP-like
domain: Cysteine rich protein B (HcpB)
species: Helicobacter pylori [TaxId: 210]

Probab=96.99  E-value=0.013  Score=44.16  Aligned_cols=47  Identities=15%  Similarity=-0.021  Sum_probs=19.8

Q ss_pred             CHhHHHHHHHHHhhCCCCCCHhHHHHHHHHHHh----cCCHHHHHHHHHHHHHC
Q 040027          222 FVDKAKALFLQMKDENINPDVVTYNSLIHGLCH----ANDWNEAKRLFIEMMDQ  271 (595)
Q Consensus       222 ~~~~A~~~~~~~~~~~~~~~~~~~~~ll~~~~~----~~~~~~A~~~~~~~~~~  271 (595)
                      +.++|.++|++..+.|   ++.....|...|..    ..+.++|..+|++..+.
T Consensus        74 d~~~A~~~~~~aa~~g---~~~a~~~Lg~~y~~G~gv~~d~~~A~~~~~~Aa~~  124 (133)
T d1klxa_          74 DLRKAAQYYSKACGLN---DQDGCLILGYKQYAGKGVVKNEKQAVKTFEKACRL  124 (133)
T ss_dssp             CHHHHHHHHHHHHHTT---CHHHHHHHHHHHHHTSSSCCCHHHHHHHHHHHHHT
T ss_pred             hhHHHHHHHhhhhccC---cchHHHHHHHHHHcCCccCCCHHHHHHHHHHHHHC
Confidence            3444455554444433   23333333333333    23444444444444443

>d1klxa_ a.118.18.1 (A:) Cysteine rich protein B (HcpB) {Helicobacter pylori [TaxId: 210]}

class: All alpha proteins
fold: alpha-alpha superhelix
superfamily: HCP-like
family: HCP-like
domain: Cysteine rich protein B (HcpB)
species: Helicobacter pylori [TaxId: 210]

Probab=96.96  E-value=0.012  Score=44.40  Aligned_cols=111  Identities=7%  Similarity=-0.100  Sum_probs=85.6

Q ss_pred             CChhHHHHHHHHHHhCCCCCCHHHHHHHHHHHHhcCCHhHHHHHHHHHHhcCCCCCHhhHHHHHHHHHh----cCChhHH
Q 040027          110 GRVSLGFIAFGRILRSCFTPNAATFNSLIKGLHAESRIMEAAALFTKLKAFGCEPNVITYNTLINGLCR----TGHTMIA  185 (595)
Q Consensus       110 g~~~~A~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~~l~~~~~~----~g~~~~A  185 (595)
                      .++++|+.+|+++.+.|   ++..+..+..  ....+.++|++++++..+.|   ++.....|...|..    ..+.++|
T Consensus         7 kd~~~A~~~~~kaa~~g---~~~a~~~l~~--~~~~~~~~a~~~~~~aa~~g---~~~a~~~Lg~~y~~g~~~~~d~~~A   78 (133)
T d1klxa_           7 KDLKKAIQYYVKACELN---EMFGCLSLVS--NSQINKQKLFQYLSKACELN---SGNGCRFLGDFYENGKYVKKDLRKA   78 (133)
T ss_dssp             HHHHHHHHHHHHHHHTT---CTTHHHHHHT--CTTSCHHHHHHHHHHHHHTT---CHHHHHHHHHHHHHCSSSCCCHHHH
T ss_pred             cCHHHHHHHHHHHHHCC---Chhhhhhhcc--ccccCHHHHHHHHhhhhccc---chhhhhhHHHhhhhccccchhhHHH
Confidence            36789999999999886   3344444432  34578899999999998876   56677777777765    4578999


Q ss_pred             HHHHHHHHhcCCCCCccccCcHHHHHHHHHHHHH----cCCHhHHHHHHHHHhhCC
Q 040027          186 LNLFEEMANGNGEIGVVCKPNTVTYSTIIDGLCK----EGFVDKAKALFLQMKDEN  237 (595)
Q Consensus       186 ~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~----~g~~~~A~~~~~~~~~~~  237 (595)
                      ++.|++..+.+         ++.....|...|..    ..+.++|.++|++..+.|
T Consensus        79 ~~~~~~aa~~g---------~~~a~~~Lg~~y~~G~gv~~d~~~A~~~~~~Aa~~G  125 (133)
T d1klxa_          79 AQYYSKACGLN---------DQDGCLILGYKQYAGKGVVKNEKQAVKTFEKACRLG  125 (133)
T ss_dssp             HHHHHHHHHTT---------CHHHHHHHHHHHHHTSSSCCCHHHHHHHHHHHHHTT
T ss_pred             HHHHhhhhccC---------cchHHHHHHHHHHcCCccCCCHHHHHHHHHHHHHCC
Confidence            99999998866         46667777777776    468999999999998876

>d1qsaa1 a.118.5.1 (A:1-450) 70 KDa soluble lytic transglycosylase (SLT70), superhelical domain {Escherichia coli [TaxId: 562]}

class: All alpha proteins
fold: alpha-alpha superhelix
superfamily: Bacterial muramidases
family: Bacterial muramidases
domain: 70 KDa soluble lytic transglycosylase (SLT70), superhelical domain
species: Escherichia coli [TaxId: 562]

Probab=96.48  E-value=0.34  Score=45.00  Aligned_cols=202  Identities=9%  Similarity=-0.031  Sum_probs=88.5

Q ss_pred             CCHHHHHHHHHHHHhcCCCCCHHHHHHHHH----HHHhCCCHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHccCCHHHH
Q 040027          326 GKINRAEELFGSMESMGCKHDDVSYNILIN----GYCKNKEVEEALSLYREMVSKGIKPTVVTYNTLFLGLFEIHQVEHA  401 (595)
Q Consensus       326 ~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~----~~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a  401 (595)
                      .+.+.+...+....... ..+...+...-.    .....+..+.+...+......+.  +.......+......+++..+
T Consensus       228 ~d~~~a~~~l~~~~~~~-~~~~~~~~~~~~~~a~~~~~~~~~~~a~~~~~~~~~~~~--~~~~~~w~~~~al~~~~~~~~  304 (450)
T d1qsaa1         228 QDAENARLMIPSLAQAQ-QLNEDQIQELRDIVAWRLMGNDVTDEQAKWRDDAIMRSQ--STSLIERRVRMALGTGDRRGL  304 (450)
T ss_dssp             HCHHHHHHHHHHHHHHT-TCCHHHHHHHHHHHHHTSCSTTCCHHHHHHHHHHHHTCC--CHHHHHHHHHHHHHHTCHHHH
T ss_pred             cChhHHHHHHHhhhhcc-cccHHHHHHHHHHHHHHHHHcCchHHHHHHHHhhccccc--chHHHHHHHHHHHHcCChHHH
Confidence            35556666666554432 122222222211    12233445556555555554422  223223333334455666666


Q ss_pred             HHHHHHHHHCCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCcCHHHHHHHHHHHHhcCChHHHHHHHHhcccC
Q 040027          402 LKLFDEMQRDGVAADTRTYTTFIDGLCKNGYIIEAVELFRTLRILKCELDIQAYNCLIDGLCKSGRLKFAWELFCSLPHG  481 (595)
Q Consensus       402 ~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~  481 (595)
                      ...+..+... ......-.-=+..++...|+.+.|...|..+..   .++  -|.-+...  +.|..-.       +...
T Consensus       305 ~~~~~~l~~~-~~~~~r~~YW~gRa~~~~G~~~~A~~~~~~~a~---~~~--fYG~LAa~--~Lg~~~~-------~~~~  369 (450)
T d1qsaa1         305 NTWLARLPME-AKEKDEWRYWQADLLLERGREAEAKEILHQLMQ---QRG--FYPMVAAQ--RIGEEYE-------LKID  369 (450)
T ss_dssp             HHHHHHSCTT-GGGSHHHHHHHHHHHHHTTCHHHHHHHHHHHHT---SCS--HHHHHHHH--HTTCCCC-------CCCC
T ss_pred             HHHHHhcCcc-cccHHHHHHHHHHHHHHcCChhhHHHHHHHHhc---CCC--hHHHHHHH--HcCCCCC-------CCcC
Confidence            6666555332 111223333344556666666666666666653   222  22222111  1221100       0000


Q ss_pred             CC--CCCHH----HHHHHHHHHHhcCChhHHHHHHHHHHHcCCCCCHHHHHHHHHHHHHcCChhHHHHHHHHH
Q 040027          482 VL--VPNVV----TYNIMIQGLCNDGQMDKARDLFLDMEENAAAPDVITFDMLIHGFIRINEPSKVNELLHKM  548 (595)
Q Consensus       482 ~~--~p~~~----~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~  548 (595)
                      ..  .+...    .-...+..+...|+...|...|..+...   .+......+.....+.|.++.|+....+.
T Consensus       370 ~~~~~~~~~~~~~~~~~ra~~L~~~g~~~~A~~e~~~l~~~---~~~~~~~~la~lA~~~g~~~~aI~a~~~~  439 (450)
T d1qsaa1         370 KAPQNVDSALTQGPEMARVRELMYWNLDNTARSEWANLVKS---KSKTEQAQLARYAFNNQWWDLSVQATIAG  439 (450)
T ss_dssp             CCCSCCCCHHHHSHHHHHHHHHHHTTCHHHHHHHHHHHHTT---CCHHHHHHHHHHHHHTTCHHHHHHHHHHT
T ss_pred             CCCccHHHhhhcChHHHHHHHHHHcCCchHHHHHHHHHHhC---CCHHHHHHHHHHHHHCCChhHHHHHHHHH
Confidence            00  00000    0012234455666666666666666543   23444445555566666666666555544

>d2pqrb1 a.118.8.1 (B:5-128) Mitochondria fission protein Fis1 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: All alpha proteins
fold: alpha-alpha superhelix
superfamily: TPR-like
family: Tetratricopeptide repeat (TPR)
domain: Mitochondria fission protein Fis1
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=95.24  E-value=0.072  Score=38.52  Aligned_cols=69  Identities=13%  Similarity=0.107  Sum_probs=41.7

Q ss_pred             CCHHHHHHHHHHHHhcC---ChhHHHHHHHHHHHcCCCCCH-HHHHHHHHHHHHcCChhHHHHHHHHHHHCCCCCC
Q 040027          485 PNVVTYNIMIQGLCNDG---QMDKARDLFLDMEENAAAPDV-ITFDMLIHGFIRINEPSKVNELLHKMKEKKVMPD  556 (595)
Q Consensus       485 p~~~~~~~l~~~~~~~g---~~~~A~~~~~~~~~~~~~~~~-~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~p~  556 (595)
                      |...+-..+++++.+..   +.++++.++++....+ +.+. ..+..+.-+|.+.|++++|.++++++++  +.|+
T Consensus        33 ~s~qt~F~YAw~Lv~S~~~~d~~~gI~lLe~~~~~~-p~~~rd~lY~Lav~yyklgdy~~A~~~~~~~L~--ieP~  105 (124)
T d2pqrb1          33 ATIQSRFNYAWGLIKSTDVNDERLGVKILTDIYKEA-ESRRRECLYYLTIGCYKLGEYSMAKRYVDTLFE--HERN  105 (124)
T ss_dssp             SCHHHHHHHHHHHHHSSCHHHHHHHHHHHHHHHHHC-GGGHHHHHHHHHHHHHHHTCHHHHHHHHHHHHH--HCTT
T ss_pred             CCcchHHHHHHHHHcCCcHHHHHHHHHHHHHHHhcC-chhHHHHHHHHHHHHHHHhhHHHHHHHHHHHHc--cCCC
Confidence            34455555666666443   3456777777766543 2232 4556666677777777777777777776  3454

>d2pqrb1 a.118.8.1 (B:5-128) Mitochondria fission protein Fis1 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: All alpha proteins
fold: alpha-alpha superhelix
superfamily: TPR-like
family: Tetratricopeptide repeat (TPR)
domain: Mitochondria fission protein Fis1
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=94.59  E-value=0.25  Score=35.55  Aligned_cols=69  Identities=12%  Similarity=0.033  Sum_probs=52.3

Q ss_pred             CCCHHHHHHHHHHHHhcC---CHhHHHHHHHHHHhcCCCCCHhhHHHHHHHHHhcCChhHHHHHHHHHHhcC
Q 040027          128 TPNAATFNSLIKGLHAES---RIMEAAALFTKLKAFGCEPNVITYNTLINGLCRTGHTMIALNLFEEMANGN  196 (595)
Q Consensus       128 ~~~~~~~~~l~~~~~~~g---~~~~A~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~  196 (595)
                      .+++.+......++.+..   +.++++.+++++.+.+.......+..|..+|.+.|++++|.+.++.+++.+
T Consensus        32 ~~s~qt~F~YAw~Lv~S~~~~d~~~gI~lLe~~~~~~p~~~rd~lY~Lav~yyklgdy~~A~~~~~~~L~ie  103 (124)
T d2pqrb1          32 TATIQSRFNYAWGLIKSTDVNDERLGVKILTDIYKEAESRRRECLYYLTIGCYKLGEYSMAKRYVDTLFEHE  103 (124)
T ss_dssp             GSCHHHHHHHHHHHHHSSCHHHHHHHHHHHHHHHHHCGGGHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHC
T ss_pred             CCCcchHHHHHHHHHcCCcHHHHHHHHHHHHHHHhcCchhHHHHHHHHHHHHHHHhhHHHHHHHHHHHHccC
Confidence            456667777777777654   456888999998876422224677788888999999999999999999875

>d1wy6a1 a.118.20.1 (A:7-167) Hypothetical protein ST1625 {Archaeon Sulfolobus tokodaii [TaxId: 111955]}

class: All alpha proteins
fold: alpha-alpha superhelix
superfamily: Hypothetical protein ST1625
family: Hypothetical protein ST1625
domain: Hypothetical protein ST1625
species: Archaeon Sulfolobus tokodaii [TaxId: 111955]

Probab=94.37  E-value=0.55  Score=33.43  Aligned_cols=68  Identities=15%  Similarity=0.126  Sum_probs=55.5

Q ss_pred             CHHHHHHHHHHHHhcCChhHHHHHHHHHHHcCCCCCHHHHHHHHHHHHHcCChhHHHHHHHHHHHCCCC
Q 040027          486 NVVTYNIMIQGLCNDGQMDKARDLFLDMEENAAAPDVITFDMLIHGFIRINEPSKVNELLHKMKEKKVM  554 (595)
Q Consensus       486 ~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~  554 (595)
                      +...+...+.....+|+-++-.++++.+.+.+ .+++.....+..+|-+.|...++.+++.++-+.|+.
T Consensus        85 ~se~vdlALd~lv~~~kkd~Ld~i~~~l~kn~-~i~~~~llkia~A~kkig~~re~nell~~ACe~G~K  152 (161)
T d1wy6a1          85 LNEHVNKALDILVIQGKRDKLEEIGREILKNN-EVSASILVAIANALRRVGDERDATTLLIEACKKGEK  152 (161)
T ss_dssp             CCHHHHHHHHHHHHTTCHHHHHHHHHHHC--C-CSCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHTTCH
T ss_pred             hHHHHHHHHHHHHHhccHHHHHHHHHHHHhcC-CCCHHHHHHHHHHHHHhcchhhHHHHHHHHHHHhHH
Confidence            44555666778888899999889988877765 788888889999999999999999999999988854

>d1qsaa1 a.118.5.1 (A:1-450) 70 KDa soluble lytic transglycosylase (SLT70), superhelical domain {Escherichia coli [TaxId: 562]}

class: All alpha proteins
fold: alpha-alpha superhelix
superfamily: Bacterial muramidases
family: Bacterial muramidases
domain: 70 KDa soluble lytic transglycosylase (SLT70), superhelical domain
species: Escherichia coli [TaxId: 562]

Probab=92.25  E-value=4.1  Score=37.19  Aligned_cols=168  Identities=10%  Similarity=-0.032  Sum_probs=78.7

Q ss_pred             CCHHHHHHHHHHHHhcCCCCCHHHHHHHHHHHHhCCCHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHccCCHHHHHHHH
Q 040027          326 GKINRAEELFGSMESMGCKHDDVSYNILINGYCKNKEVEEALSLYREMVSKGIKPTVVTYNTLFLGLFEIHQVEHALKLF  405 (595)
Q Consensus       326 ~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~  405 (595)
                      +..+.+...+......+  .+.......+......+++..+...+..+... ......-..-+..++...|+.+.|...|
T Consensus       266 ~~~~~a~~~~~~~~~~~--~~~~~~~w~~~~al~~~~~~~~~~~~~~l~~~-~~~~~r~~YW~gRa~~~~G~~~~A~~~~  342 (450)
T d1qsaa1         266 DVTDEQAKWRDDAIMRS--QSTSLIERRVRMALGTGDRRGLNTWLARLPME-AKEKDEWRYWQADLLLERGREAEAKEIL  342 (450)
T ss_dssp             TCCHHHHHHHHHHHHTC--CCHHHHHHHHHHHHHHTCHHHHHHHHHHSCTT-GGGSHHHHHHHHHHHHHTTCHHHHHHHH
T ss_pred             CchHHHHHHHHhhcccc--cchHHHHHHHHHHHHcCChHHHHHHHHhcCcc-cccHHHHHHHHHHHHHHcCChhhHHHHH
Confidence            44455555555554432  23333333344444556666666666655332 1112233344455666666766666666


Q ss_pred             HHHHHCCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHHcCC--CcC-HH---HHHHHHHHHHhcCChHHHHHHHHhcc
Q 040027          406 DEMQRDGVAADTRTYTTFIDGLCKNGYIIEAVELFRTLRILKC--ELD-IQ---AYNCLIDGLCKSGRLKFAWELFCSLP  479 (595)
Q Consensus       406 ~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~--~~~-~~---~~~~l~~~~~~~g~~~~A~~~~~~~~  479 (595)
                      ..+...   ++  .|. .+.+ .+.|..-.       +.....  .+. ..   .-...+..+...|....|...|..+.
T Consensus       343 ~~~a~~---~~--fYG-~LAa-~~Lg~~~~-------~~~~~~~~~~~~~~~~~~~~~ra~~L~~~g~~~~A~~e~~~l~  408 (450)
T d1qsaa1         343 HQLMQQ---RG--FYP-MVAA-QRIGEEYE-------LKIDKAPQNVDSALTQGPEMARVRELMYWNLDNTARSEWANLV  408 (450)
T ss_dssp             HHHHTS---CS--HHH-HHHH-HHTTCCCC-------CCCCCCCSCCCCHHHHSHHHHHHHHHHHTTCHHHHHHHHHHHH
T ss_pred             HHHhcC---CC--hHH-HHHH-HHcCCCCC-------CCcCCCCccHHHhhhcChHHHHHHHHHHcCCchHHHHHHHHHH
Confidence            666532   22  122 2111 11111000       000000  000 00   01122344556777777777777666


Q ss_pred             cCCCCCCHHHHHHHHHHHHhcCChhHHHHHHHHH
Q 040027          480 HGVLVPNVVTYNIMIQGLCNDGQMDKARDLFLDM  513 (595)
Q Consensus       480 ~~~~~p~~~~~~~l~~~~~~~g~~~~A~~~~~~~  513 (595)
                      ..   .+......++....+.|.++.|+....+.
T Consensus       409 ~~---~~~~~~~~la~lA~~~g~~~~aI~a~~~~  439 (450)
T d1qsaa1         409 KS---KSKTEQAQLARYAFNNQWWDLSVQATIAG  439 (450)
T ss_dssp             TT---CCHHHHHHHHHHHHHTTCHHHHHHHHHHT
T ss_pred             hC---CCHHHHHHHHHHHHHCCChhHHHHHHHHH
Confidence            42   24445556666666777777777665554

>d1v54e_ a.118.11.1 (E:) Cytochrome c oxidase subunit E {Cow (Bos taurus) [TaxId: 9913]}

class: All alpha proteins
fold: alpha-alpha superhelix
superfamily: Cytochrome c oxidase subunit E
family: Cytochrome c oxidase subunit E
domain: Cytochrome c oxidase subunit E
species: Cow (Bos taurus) [TaxId: 9913]

Probab=90.11  E-value=1.8  Score=29.10  Aligned_cols=47  Identities=11%  Similarity=0.022  Sum_probs=29.8

Q ss_pred             HHHHHHHhcccCCCCCCHHHHHHHHHHHHhcCChhHHHHHHHHHHHc
Q 040027          470 FAWELFCSLPHGVLVPNVVTYNIMIQGLCNDGQMDKARDLFLDMEEN  516 (595)
Q Consensus       470 ~A~~~~~~~~~~~~~p~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~  516 (595)
                      ++.+-++.+....+.|++....+.+.+|.+.+|+.-|+++|+-...+
T Consensus        24 e~rrgmN~l~~~DlVPeP~Ii~aALrAcRRvND~alAVR~lE~vK~K   70 (105)
T d1v54e_          24 ELRKGMNTLVGYDLVPEPKIIDAALRACRRLNDFASAVRILEVVKDK   70 (105)
T ss_dssp             HHHHHHHHHTTSSBCCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHhccccCCCcHHHHHHHHHHHHhhhHHHHHHHHHHHHHH
Confidence            44555555555556666666666666666666777776666666554

>d1v54e_ a.118.11.1 (E:) Cytochrome c oxidase subunit E {Cow (Bos taurus) [TaxId: 9913]}

class: All alpha proteins
fold: alpha-alpha superhelix
superfamily: Cytochrome c oxidase subunit E
family: Cytochrome c oxidase subunit E
domain: Cytochrome c oxidase subunit E
species: Cow (Bos taurus) [TaxId: 9913]

Probab=89.93  E-value=1.8  Score=29.02  Aligned_cols=76  Identities=17%  Similarity=0.180  Sum_probs=56.9

Q ss_pred             HHHHHHHHhcC--ChhHHHHHHHHHHHcCCCCCHHHHHHHHHHHHHcCChhHHHHHHHHHHHCCCCCCHHHHHHHHHHH
Q 040027          491 NIMIQGLCNDG--QMDKARDLFLDMEENAAAPDVITFDMLIHGFIRINEPSKVNELLHKMKEKKVMPDASIVSIVVDLL  567 (595)
Q Consensus       491 ~~l~~~~~~~g--~~~~A~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~p~~~~~~~l~~~~  567 (595)
                      .+--..|...-  |.-++.+-++.+...++-|++.+....+++|.+.+++.-|.++++-...+ ..++..+|..+++-+
T Consensus         8 ~aRy~~~F~~~~iD~we~rrgmN~l~~~DlVPeP~Ii~aALrAcRRvND~alAVR~lE~vK~K-~~~~k~~y~yilqel   85 (105)
T d1v54e_           8 DARWVTYFNKPDIDAWELRKGMNTLVGYDLVPEPKIIDAALRACRRLNDFASAVRILEVVKDK-AGPHKEIYPYVIQEL   85 (105)
T ss_dssp             HHHHHHHHTCTTCCHHHHHHHHHHHTTSSBCCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH-TTTCTTHHHHHHHHH
T ss_pred             HHHHHHHhcCcCccHHHHHHHHHHHhccccCCCcHHHHHHHHHHHHhhhHHHHHHHHHHHHHH-hcCcHHHHHHHHHHH
Confidence            33333444433  44567777888887888999999999999999999999999999999854 234566777766543

>d1wy6a1 a.118.20.1 (A:7-167) Hypothetical protein ST1625 {Archaeon Sulfolobus tokodaii [TaxId: 111955]}

class: All alpha proteins
fold: alpha-alpha superhelix
superfamily: Hypothetical protein ST1625
family: Hypothetical protein ST1625
domain: Hypothetical protein ST1625
species: Archaeon Sulfolobus tokodaii [TaxId: 111955]

Probab=88.40  E-value=3.1  Score=29.55  Aligned_cols=141  Identities=15%  Similarity=0.118  Sum_probs=79.1

Q ss_pred             HHhcCChhHHHHHHHHHHhCCCCCCHHHHHHHHHHHHhcCCHhHHHHHHHHHHhcCCCCCHhhHHHHHHHHHhcCChhHH
Q 040027          106 FCKIGRVSLGFIAFGRILRSCFTPNAATFNSLIKGLHAESRIMEAAALFTKLKAFGCEPNVITYNTLINGLCRTGHTMIA  185 (595)
Q Consensus       106 ~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A  185 (595)
                      +.-.|..++..++..+....   .+..-||.++--....-+-+...++++.+-+. +..            ...++....
T Consensus        12 ~ildG~ve~Gveii~k~~~s---s~~~E~NW~ICNiidt~dC~~v~~~Ld~IG~~-FDl------------s~C~Nlk~v   75 (161)
T d1wy6a1          12 FLLDGYIDEGVKIVLEITKS---STKSEYNWFICNLLESIDCRYMFQVLDKIGSY-FDL------------DKCQNLKSV   75 (161)
T ss_dssp             HHHTTCHHHHHHHHHHHHHH---SCHHHHTHHHHHHHHHCCHHHHHHHHHHHGGG-SCG------------GGCSCTHHH
T ss_pred             HHHhhhHHhHHHHHHHHccc---CCccccceeeeecccccchHHHHHHHHHHhhh-cCc------------hhhhcHHHH
Confidence            34456666667766666654   24555565655555555555555555554332 111            122333333


Q ss_pred             HHHHHHHHhcCCCCCccccCcHHHHHHHHHHHHHcCCHhHHHHHHHHHhhCCCCCCHhHHHHHHHHHHhcCCHHHHHHHH
Q 040027          186 LNLFEEMANGNGEIGVVCKPNTVTYSTIIDGLCKEGFVDKAKALFLQMKDENINPDVVTYNSLIHGLCHANDWNEAKRLF  265 (595)
Q Consensus       186 ~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~~ll~~~~~~~~~~~A~~~~  265 (595)
                      ...+-.+-           .+...++..+..+..+|.-++-.++++.+.+. -.+++.....+..+|.+-|+..++-+++
T Consensus        76 v~C~~~~n-----------~~se~vdlALd~lv~~~kkd~Ld~i~~~l~kn-~~i~~~~llkia~A~kkig~~re~nell  143 (161)
T d1wy6a1          76 VECGVINN-----------TLNEHVNKALDILVIQGKRDKLEEIGREILKN-NEVSASILVAIANALRRVGDERDATTLL  143 (161)
T ss_dssp             HHHHHHTT-----------CCCHHHHHHHHHHHHTTCHHHHHHHHHHHC---CCSCHHHHHHHHHHHHHTTCHHHHHHHH
T ss_pred             HHHHHHhc-----------chHHHHHHHHHHHHHhccHHHHHHHHHHHHhc-CCCCHHHHHHHHHHHHHhcchhhHHHHH
Confidence            33332221           22344556666777777777777777776653 3556666777777777777777777777


Q ss_pred             HHHHHCCCC
Q 040027          266 IEMMDQGVQ  274 (595)
Q Consensus       266 ~~~~~~~~~  274 (595)
                      .+.-+.|++
T Consensus       144 ~~ACe~G~K  152 (161)
T d1wy6a1         144 IEACKKGEK  152 (161)
T ss_dssp             HHHHHTTCH
T ss_pred             HHHHHHhHH
Confidence            777766653